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Conserved domains on  [gi|1756851495|ref|XP_014163816|]
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LOW QUALITY PROTEIN: crooked neck-like protein 1 [Geospiza fortis]

Protein Classification

U3 small nucleolar RNA-associated family 6 protein; pre-mRNA-processing factor( domain architecture ID 1903493)

U3 small nucleolar RNA-associated family 6 protein such as Homo sapiens UTP6, which is part of the small subunit (SSU) processome, first precursor of the small eukaryotic ribosomal subunit; pre-mRNA-processing factor similar to Candida albicans mRNA 3'-end-processing protein RNA14, a component of the cleavage factor IA (CFIA) complex, which is involved in the endonucleolytic cleavage during polyadenylation-dependent pre-mRNA 3'-end formation

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
HAT super family cl03482
HAT (Half-A-TPR) repeat; The HAT (Half A TPR) repeat is found in several RNA processing ...
 201-232 1.06e-09

HAT (Half-A-TPR) repeat; The HAT (Half A TPR) repeat is found in several RNA processing proteins.


The actual alignment was detected with superfamily member pfam02184:

Pssm-ID: 111114 [Multi-domain]  Cd Length: 32  Bit Score: 54.11  E-value: 1.06e-09
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1756851495 201 KEVDRARSIYERFVLVHPSVKNWIKYACFEEK 232
Cdd:pfam02184   1 KEIDRARGIYERFVHVHPEVQNWIKWARFEEE 32
RNA14 super family cl34906
Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and ...
 323-527 1.55e-05

Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification];


The actual alignment was detected with superfamily member COG5107:

Pssm-ID: 227438 [Multi-domain]  Cd Length: 660  Bit Score: 48.09  E-value: 1.55e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756851495 323 QYEEEVKANPHNYDAWFDYLQLVESDMDAETVREVYERaIANVPPIQEkRHWKRYIylwinyalYEELEAKDAERTRQVY 402
Cdd:COG5107    30 RLRERIKDNPTNILSYFQLIQYLETQESMDAEREMYEQ-LSSPFPIME-HAWRLYM--------SGELARKDFRSVESLF 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756851495 403 QACLDllphEKFTLAkMWLLYARFeIRQENLLLARRAlgtsigkcpKNKLFKGYiELELQLREFD-RCRKLYEKFLEFaL 481
Cdd:COG5107   100 GRCLK----KSLNLD-LWMLYLEY-IRRVNNLITGQK---------RFKIYEAY-EFVLGCAIFEpQSENYWDEYGLF-L 162

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1756851495 482 EnctSWIKFAELETiLGDIDRARAIYEL*LDMP----EVLWKSYTDFEME 527
Cdd:COG5107   163 E---YIEELGKWEE-QQRIDKIRNGYMRALQTPmgnlEKLWKDYENFELE 208
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 98-292 8.79e-04

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


:

Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 41.64  E-value: 8.79e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756851495  98 ESLKEIQRARSIYERALDVD-YRNVT*LKYAEMEMKNHQVNHARNIWDRAITTLPRVNQFWYKCTYMEEMLGNVAGSRQV 176
Cdd:COG2956    53 RRRGEYDRAIRIHQKLLERDpDRAEALLELAQDYLKAGLLDRAEELLEKLLELDPDDAEALRLLAEIYEQEGDWEKAIEV 132

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756851495 177 FEWWMEWQPEE*AWHSYI-NFELRYKEVDRARSIYERFVLVHP-SVKNWIKYACFEEKHSYLAHARKVYERAVEffgEEH 254
Cdd:COG2956   133 LERLLKLGPENAHAYCELaELYLEQGDYDEAIEALEKALKLDPdCARALLLLAELYLEQGDYEEAIAALERALE---QDP 209

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1756851495 255 MDEHLYVAFAKFEENQKEFDRVRVIYKYALDRIPKQDA 292
Cdd:COG2956   210 DYLPALPRLAELYEKLGDPEEALELLRKALELDPSDDL 247
 
Name Accession Description Interval E-value
HAT pfam02184
HAT (Half-A-TPR) repeat; The HAT (Half A TPR) repeat is found in several RNA processing ...
 201-232 1.06e-09

HAT (Half-A-TPR) repeat; The HAT (Half A TPR) repeat is found in several RNA processing proteins.


Pssm-ID: 111114 [Multi-domain]  Cd Length: 32  Bit Score: 54.11  E-value: 1.06e-09
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1756851495 201 KEVDRARSIYERFVLVHPSVKNWIKYACFEEK 232
Cdd:pfam02184   1 KEIDRARGIYERFVHVHPEVQNWIKWARFEEE 32
RNA14 COG5107
Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and ...
 323-527 1.55e-05

Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification];


Pssm-ID: 227438 [Multi-domain]  Cd Length: 660  Bit Score: 48.09  E-value: 1.55e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756851495 323 QYEEEVKANPHNYDAWFDYLQLVESDMDAETVREVYERaIANVPPIQEkRHWKRYIylwinyalYEELEAKDAERTRQVY 402
Cdd:COG5107    30 RLRERIKDNPTNILSYFQLIQYLETQESMDAEREMYEQ-LSSPFPIME-HAWRLYM--------SGELARKDFRSVESLF 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756851495 403 QACLDllphEKFTLAkMWLLYARFeIRQENLLLARRAlgtsigkcpKNKLFKGYiELELQLREFD-RCRKLYEKFLEFaL 481
Cdd:COG5107   100 GRCLK----KSLNLD-LWMLYLEY-IRRVNNLITGQK---------RFKIYEAY-EFVLGCAIFEpQSENYWDEYGLF-L 162

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1756851495 482 EnctSWIKFAELETiLGDIDRARAIYEL*LDMP----EVLWKSYTDFEME 527
Cdd:COG5107   163 E---YIEELGKWEE-QQRIDKIRNGYMRALQTPmgnlEKLWKDYENFELE 208
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 98-292 8.79e-04

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 41.64  E-value: 8.79e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756851495  98 ESLKEIQRARSIYERALDVD-YRNVT*LKYAEMEMKNHQVNHARNIWDRAITTLPRVNQFWYKCTYMEEMLGNVAGSRQV 176
Cdd:COG2956    53 RRRGEYDRAIRIHQKLLERDpDRAEALLELAQDYLKAGLLDRAEELLEKLLELDPDDAEALRLLAEIYEQEGDWEKAIEV 132

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756851495 177 FEWWMEWQPEE*AWHSYI-NFELRYKEVDRARSIYERFVLVHP-SVKNWIKYACFEEKHSYLAHARKVYERAVEffgEEH 254
Cdd:COG2956   133 LERLLKLGPENAHAYCELaELYLEQGDYDEAIEALEKALKLDPdCARALLLLAELYLEQGDYEEAIAALERALE---QDP 209

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1756851495 255 MDEHLYVAFAKFEENQKEFDRVRVIYKYALDRIPKQDA 292
Cdd:COG2956   210 DYLPALPRLAELYEKLGDPEEALELLRKALELDPSDDL 247
HAT smart00386
HAT (Half-A-TPR) repeats; Present in several RNA-binding proteins. Structurally and ...
 201-232 7.55e-03

HAT (Half-A-TPR) repeats; Present in several RNA-binding proteins. Structurally and sequentially thought to be similar to TPRs.


Pssm-ID: 214642 [Multi-domain]  Cd Length: 33  Bit Score: 34.45  E-value: 7.55e-03
                           10        20        30
                   ....*....|....*....|....*....|...
gi 1756851495  201 KEVDRARSIYERFVLVHP-SVKNWIKYACFEEK 232
Cdd:smart00386   1 GDIERARKIYERALEKFPkSVELWLKYAEFEER 33
 
Name Accession Description Interval E-value
HAT pfam02184
HAT (Half-A-TPR) repeat; The HAT (Half A TPR) repeat is found in several RNA processing ...
 201-232 1.06e-09

HAT (Half-A-TPR) repeat; The HAT (Half A TPR) repeat is found in several RNA processing proteins.


Pssm-ID: 111114 [Multi-domain]  Cd Length: 32  Bit Score: 54.11  E-value: 1.06e-09
                          10        20        30
                  ....*....|....*....|....*....|..
gi 1756851495 201 KEVDRARSIYERFVLVHPSVKNWIKYACFEEK 232
Cdd:pfam02184   1 KEIDRARGIYERFVHVHPEVQNWIKWARFEEE 32
RNA14 COG5107
Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and ...
 323-527 1.55e-05

Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification];


Pssm-ID: 227438 [Multi-domain]  Cd Length: 660  Bit Score: 48.09  E-value: 1.55e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756851495 323 QYEEEVKANPHNYDAWFDYLQLVESDMDAETVREVYERaIANVPPIQEkRHWKRYIylwinyalYEELEAKDAERTRQVY 402
Cdd:COG5107    30 RLRERIKDNPTNILSYFQLIQYLETQESMDAEREMYEQ-LSSPFPIME-HAWRLYM--------SGELARKDFRSVESLF 99

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756851495 403 QACLDllphEKFTLAkMWLLYARFeIRQENLLLARRAlgtsigkcpKNKLFKGYiELELQLREFD-RCRKLYEKFLEFaL 481
Cdd:COG5107   100 GRCLK----KSLNLD-LWMLYLEY-IRRVNNLITGQK---------RFKIYEAY-EFVLGCAIFEpQSENYWDEYGLF-L 162

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 1756851495 482 EnctSWIKFAELETiLGDIDRARAIYEL*LDMP----EVLWKSYTDFEME 527
Cdd:COG5107   163 E---YIEELGKWEE-QQRIDKIRNGYMRALQTPmgnlEKLWKDYENFELE 208
LapB COG2956
Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal ...
 98-292 8.79e-04

Lipopolysaccharide biosynthesis regulator YciM/LapB, contains six TPR domains and a C-terminal metal-binding domain [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442196 [Multi-domain]  Cd Length: 275  Bit Score: 41.64  E-value: 8.79e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756851495  98 ESLKEIQRARSIYERALDVD-YRNVT*LKYAEMEMKNHQVNHARNIWDRAITTLPRVNQFWYKCTYMEEMLGNVAGSRQV 176
Cdd:COG2956    53 RRRGEYDRAIRIHQKLLERDpDRAEALLELAQDYLKAGLLDRAEELLEKLLELDPDDAEALRLLAEIYEQEGDWEKAIEV 132

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756851495 177 FEWWMEWQPEE*AWHSYI-NFELRYKEVDRARSIYERFVLVHP-SVKNWIKYACFEEKHSYLAHARKVYERAVEffgEEH 254
Cdd:COG2956   133 LERLLKLGPENAHAYCELaELYLEQGDYDEAIEALEKALKLDPdCARALLLLAELYLEQGDYEEAIAALERALE---QDP 209

                         170       180       190
                  ....*....|....*....|....*....|....*...
gi 1756851495 255 MDEHLYVAFAKFEENQKEFDRVRVIYKYALDRIPKQDA 292
Cdd:COG2956   210 DYLPALPRLAELYEKLGDPEEALELLRKALELDPSDDL 247
RNA14 COG5107
Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and ...
 78-525 4.25e-03

Pre-mRNA 3'-end processing (cleavage and polyadenylation) factor [RNA processing and modification];


Pssm-ID: 227438 [Multi-domain]  Cd Length: 660  Bit Score: 40.39  E-value: 4.25e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756851495  78 DNIRKNRTVISNWIKYAQWEESLKEIQRARSIYERALD-VDYRNVT*LKYAEMEMKNHQVNHARNIWDRAITTLPRVNQF 156
Cdd:COG5107    33 ERIKDNPTNILSYFQLIQYLETQESMDAEREMYEQLSSpFPIMEHAWRLYMSGELARKDFRSVESLFGRCLKKSLNLDLW 112

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756851495 157 WYKCTYMEEMLGNVAGSR-----QVFEWWMEWQPEE*A----WHSYINFELRYKE---------VDRARSIYERFVLV-- 216
Cdd:COG5107   113 MLYLEYIRRVNNLITGQKrfkiyEAYEFVLGCAIFEPQsenyWDEYGLFLEYIEElgkweeqqrIDKIRNGYMRALQTpm 192

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756851495 217 HPSVKNWIKYACFEEKHSYLAHARKVYERAVEFFGeehmdehlyvAFAKFEENQKEFDRVRV---IYKYALDRIPkQDAQ 293
Cdd:COG5107   193 GNLEKLWKDYENFELELNKITARKFVGETSPIYMS----------ARQRYQEIQNLTRGLSVknpINLRTANKAA-RTSD 261

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756851495 294 NLFKNYTIFEKKFGDRRGiEDIIVSKRRFQYEEEVKANPHNYDAWFDYLQLVESDMDAETVREVYERAIANVPPiqekrh 373
Cdd:COG5107   262 SNWLNWIKWEMENGLKLG-GRPHEQRIHYIHNQILDYFYYAEEVWFDYSEYLIGISDKQKALKTVERGIEMSPS------ 334

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756851495 374 wkryiyLWINYALYEELEaKDAERTRQVYQAC----------------------------LDLLPHEKFTLAkmWLLYAR 425
Cdd:COG5107   335 ------LTMFLSEYYELV-NDEEAVYGCFDKCtqdlkrkysmgesesaskvdnnfeyskeLLLKRINKLTFV--FCVHLN 405

                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756851495 426 FEIRQENLLLARralgTSIGKCPKNKLFKGYIELELQLREF--DRCRKLYEKFLEFAL---ENCTSWI-KFAELETILGD 499
Cdd:COG5107   406 YVLRKRGLEAAR----KLFIKLRKEGIVGHHVYIYCAFIEYyaTGDRATAYNIFELGLlkfPDSTLYKeKYLLFLIRIND 481

                         490       500       510
                  ....*....|....*....|....*....|.
gi 1756851495 500 IDRARAIYE-----L*LDMPEVLWKSYTDFE 525
Cdd:COG5107   482 EENARALFEtsverLEKTQLKRIYDKMIEYE 512
COG5191 COG5191
Uncharacterized conserved protein, contains HAT (Half-A-TPR) repeat [General function ...
 62-208 4.98e-03

Uncharacterized conserved protein, contains HAT (Half-A-TPR) repeat [General function prediction only];


Pssm-ID: 227518 [Multi-domain]  Cd Length: 435  Bit Score: 39.94  E-value: 4.98e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756851495  62 VEELNDYK-------------LRKRKTFEDNIRKNRTVISNWIKYAQWEESLKEIQRAR---------------SIYERA 113
Cdd:COG5191    13 IPELEDLKekgifspdelrriVKTRRKFELRLQRREKKLNDFMRYIKYECNLEKLRAKRvkrkkvgkkasfsdmSIPQKK 92

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1756851495 114 LDVDYRNVT*--------LKYAEMEMKNHQVNHARNIWDRAITTLPRVNQFW-YKCTYMEEMLGNVAGSRQVFEWWMEWQ 184
Cdd:COG5191    93 IFELYRSTNKffndpkiwSQYAAYVIKKKMYGEMKNIFAECLTKHPLNVDLWiYCCAFELFEIANIESSRAMFLKGLRMN 172

                         170       180
                  ....*....|....*....|....*
gi 1756851495 185 PE-E*AWHSYINFELRYKEVDRARS 208
Cdd:COG5191   173 SRsPRIWIEYFRMELMYITKLINRR 197
HAT smart00386
HAT (Half-A-TPR) repeats; Present in several RNA-binding proteins. Structurally and ...
 201-232 7.55e-03

HAT (Half-A-TPR) repeats; Present in several RNA-binding proteins. Structurally and sequentially thought to be similar to TPRs.


Pssm-ID: 214642 [Multi-domain]  Cd Length: 33  Bit Score: 34.45  E-value: 7.55e-03
                           10        20        30
                   ....*....|....*....|....*....|...
gi 1756851495  201 KEVDRARSIYERFVLVHP-SVKNWIKYACFEEK 232
Cdd:smart00386   1 GDIERARKIYERALEKFPkSVELWLKYAEFEER 33
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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