Query psy8635
Match_columns 177
No_of_seqs 125 out of 155
Neff 2.7
Searched_HMMs 46136
Date Fri Aug 16 23:48:55 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8635.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8635hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4086|consensus 100.0 1E-54 2.2E-59 342.8 11.1 126 2-127 2-127 (130)
2 PF05669 Med31: SOH1; InterPr 100.0 3.4E-55 7.4E-60 333.8 5.3 101 13-113 1-101 (101)
3 COG5088 SOH1 Rad5p-binding pro 100.0 2.3E-41 5E-46 261.9 10.4 100 12-111 12-111 (114)
4 KOG4086|consensus 59.7 10 0.00022 31.1 3.0 36 55-96 40-75 (130)
5 PF05669 Med31: SOH1; InterPr 53.3 5.4 0.00012 31.2 0.5 50 42-97 15-64 (101)
6 PF12672 DUF3793: Protein of u 38.5 52 0.0011 27.0 4.1 49 24-81 67-116 (176)
7 PHA03410 hypothetical protein; 27.9 36 0.00077 28.7 1.5 23 132-154 26-58 (170)
8 smart00727 STI1 Heat shock cha 24.9 1.3E+02 0.0028 18.4 3.3 22 75-96 5-30 (41)
9 cd01068 sensor_globin Globin d 24.8 2.9E+02 0.0063 20.4 6.0 44 79-122 44-96 (147)
10 PF05021 NPL4: NPL4 family; I 24.7 99 0.0021 27.8 3.8 36 20-55 247-282 (306)
11 cd07291 PX_SNX5 The phosphoino 23.7 50 0.0011 27.2 1.6 44 10-53 91-140 (141)
12 PF14307 Glyco_tran_WbsX: Glyc 22.1 72 0.0016 28.1 2.4 47 18-64 100-155 (345)
13 PF05783 DLIC: Dynein light in 22.1 2.2E+02 0.0049 27.0 5.7 66 88-163 136-206 (472)
14 PRK05321 nicotinate phosphorib 21.9 1.2E+02 0.0025 28.4 3.7 38 16-54 54-92 (400)
15 cd07292 PX_SNX6 The phosphoino 20.4 52 0.0011 27.2 1.1 44 10-53 91-140 (141)
No 1
>KOG4086|consensus
Probab=100.00 E-value=1e-54 Score=342.75 Aligned_cols=126 Identities=61% Similarity=1.044 Sum_probs=117.4
Q ss_pred CCCCCCCCchhhcchhHhhhhHHhhhcChHHHHHHHhhCCCCcHHHHHHHHHHhhhcCCCccccccccchHHHHHhhccH
Q psy8635 2 ANKGGPETEDQQRLRFQIELEFIQCLANPNYLNFLAQRGYLKDEAFVNYLKYLLYWKEPQYAKYLKYPMCLYFLDLLQYE 81 (177)
Q Consensus 2 ~~~~~~~~~~~~~~RFE~ELEFVQ~LANP~YL~~LAq~gyf~d~~FinYLkYL~YWk~PeYakyL~YP~cL~~LdLLQ~e 81 (177)
.++.+++++.+.+.|||+|||||||||||+||+||||+|||+|++|+||||||+|||+|+|+|||+||+|||||+|||++
T Consensus 2 ~~~a~~s~~~~~~~RFevELEFVQ~LaNp~YLnfLaQ~g~fk~e~F~nYLkYLeYWk~PeYak~l~YP~CL~mLelL~~~ 81 (130)
T KOG4086|consen 2 NGNAMESPESDKRSRFEVELEFVQCLANPNYLNFLAQRGYFKDEAFVNYLKYLEYWKEPEYAKFLKYPQCLHMLELLQSE 81 (130)
T ss_pred CCcccCCCCcccCcchhhhHHHHHHhcChHHHHHHHHcccccCHHHHHHHHHHHHhcCccHHHHHhhHhHHHHHHHhccH
Confidence 46677777777788999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhhChHHHHHHHHHHHHHHhhhhHHHHHHhHHHHhhccCCCC
Q psy8635 82 HFRREIVNSQCAKFIDDQQVLLWQHYTRKRTKLLNEAAQNNISGAP 127 (177)
Q Consensus 82 ~FR~~i~n~~~~~~i~~Qq~~~Wq~y~r~R~~~~~~~~e~~~~~~~ 127 (177)
.||..|++++++++|++||+++|+++.|+|.++.+...++.++..+
T Consensus 82 ~fr~~i~~~~~~k~ldeqq~~qW~~~~~kr~~~~~~l~q~qqe~~t 127 (130)
T KOG4086|consen 82 QFRDEISNAQLAKFLDEQQYLQWQNYMRKRWRLQQTLSQQQQEADT 127 (130)
T ss_pred HHHHHHhhhHHHHHhhHHHHHHHHHHHHHHHhhHHHHHhHHHhhcc
Confidence 9999999999999999999999999999999998866666655443
No 2
>PF05669 Med31: SOH1; InterPro: IPR008831 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This entry represents subunit Med31 of the Mediator complex. It contains the Saccharomyces cerevisiae SOH1 homologues. SOH1 is responsible for the repression of temperature sensitive growth of the HPR1 mutant [] and has been found to be a component of the RNA polymerase II transcription complex. SOH1 not only interacts with factors involved in DNA repair, but transcription as well. Thus, the SOH1 protein may serve to couple these two processes [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006355 regulation of transcription, DNA-dependent, 0016592 mediator complex; PDB: 3FBI_D 3FBN_D.
Probab=100.00 E-value=3.4e-55 Score=333.82 Aligned_cols=101 Identities=66% Similarity=1.215 Sum_probs=70.9
Q ss_pred hcchhHhhhhHHhhhcChHHHHHHHhhCCCCcHHHHHHHHHHhhhcCCCccccccccchHHHHHhhccHHHHHHhhChHH
Q psy8635 13 QRLRFQIELEFIQCLANPNYLNFLAQRGYLKDEAFVNYLKYLLYWKEPQYAKYLKYPMCLYFLDLLQYEHFRREIVNSQC 92 (177)
Q Consensus 13 ~~~RFE~ELEFVQ~LANP~YL~~LAq~gyf~d~~FinYLkYL~YWk~PeYakyL~YP~cL~~LdLLQ~e~FR~~i~n~~~ 92 (177)
+++|||+|||||||||||+||+|||++|||+||+|+||||||+|||+|+|+|||+||+||+||+|||+|+||++|+++++
T Consensus 1 ~~~RFe~ELEFVQ~LaNp~Yl~~La~~~y~~d~~F~nYLkYL~YW~~P~Yakyl~YP~cL~~L~LLq~~~FR~~i~~~~~ 80 (101)
T PF05669_consen 1 NPTRFELELEFVQCLANPQYLNYLAQQGYFEDPAFINYLKYLQYWKRPEYAKYLVYPHCLHFLELLQNEEFRQAIANPDF 80 (101)
T ss_dssp ---HHHHHHHHHHHTTSHHHHHHHH-SGGGTSTHHHHHHHHGGGGGSTTGGGG-SSTHHHHHHH-HHHHHHHH--B-TTS
T ss_pred CcchhHHHHHHHHHhcCHHHHHHHHhcCccCCHHHHHHHHHHHHhCCCchhhhhcChHHHHHHHHHCcHHHHHHHhCCcc
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhhhHHHHH
Q psy8635 93 AKFIDDQQVLLWQHYTRKRTK 113 (177)
Q Consensus 93 ~~~i~~Qq~~~Wq~y~r~R~~ 113 (177)
+++|++||+.||++++++|++
T Consensus 81 ~~~i~~q~~~~W~~~~~~r~~ 101 (101)
T PF05669_consen 81 AKFIMDQQFLHWQHYRRKRMR 101 (101)
T ss_dssp ---------------------
T ss_pred cchhcccchhhhhcccccccC
Confidence 999999999999999999985
No 3
>COG5088 SOH1 Rad5p-binding protein [General function prediction only]
Probab=100.00 E-value=2.3e-41 Score=261.88 Aligned_cols=100 Identities=38% Similarity=0.729 Sum_probs=95.4
Q ss_pred hhcchhHhhhhHHhhhcChHHHHHHHhhCCCCcHHHHHHHHHHhhhcCCCccccccccchHHHHHhhccHHHHHHhhChH
Q psy8635 12 QQRLRFQIELEFIQCLANPNYLNFLAQRGYLKDEAFVNYLKYLLYWKEPQYAKYLKYPMCLYFLDLLQYEHFRREIVNSQ 91 (177)
Q Consensus 12 ~~~~RFE~ELEFVQ~LANP~YL~~LAq~gyf~d~~FinYLkYL~YWk~PeYakyL~YP~cL~~LdLLQ~e~FR~~i~n~~ 91 (177)
.+.+|||+||||||+||||+||++|+|+|+|+|++|.+|||||+|||+|||+|||+||+||+||+||+++.|+..++.++
T Consensus 12 ~s~sRFE~ELEFvQ~L~Np~Yl~~Ltq~~~fese~F~~YL~YlEYWr~PeYs~fivYP~CL~iL~lLn~~~~~~~vs~~~ 91 (114)
T COG5088 12 SSDSRFEVELEFVQSLANPQYLTLLTQQQIFESENFKNYLKYLEYWRNPEYSQFIVYPNCLFILKLLNGFMESAIVSEDG 91 (114)
T ss_pred CCCchhHHHHHHHHHhcCHHHHHHHHHhhhhcCHHHHHHHHHHHHhhCCcccceeechhHHHHHHHhcchhHhhhhhhhH
Confidence 34699999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhhhHHH
Q psy8635 92 CAKFIDDQQVLLWQHYTRKR 111 (177)
Q Consensus 92 ~~~~i~~Qq~~~Wq~y~r~R 111 (177)
+.+-++++|+..|..-...|
T Consensus 92 l~~~l~e~qy~~Wlnk~~e~ 111 (114)
T COG5088 92 LLEGLDELQYPQWLNKMVER 111 (114)
T ss_pred HHHhhhHHHHHHHHHHHHHH
Confidence 99999999999998765543
No 4
>KOG4086|consensus
Probab=59.67 E-value=10 Score=31.05 Aligned_cols=36 Identities=25% Similarity=0.622 Sum_probs=19.5
Q ss_pred hhhcCCCccccccccchHHHHHhhccHHHHHHhhChHHHHHH
Q psy8635 55 LYWKEPQYAKYLKYPMCLYFLDLLQYEHFRREIVNSQCAKFI 96 (177)
Q Consensus 55 ~YWk~PeYakyL~YP~cL~~LdLLQ~e~FR~~i~n~~~~~~i 96 (177)
.||+++.+..||+| |+--.+|+.-+-|.-|+|-.++
T Consensus 40 g~fk~e~F~nYLkY------LeYWk~PeYak~l~YP~CL~mL 75 (130)
T KOG4086|consen 40 GYFKDEAFVNYLKY------LEYWKEPEYAKFLKYPQCLHML 75 (130)
T ss_pred ccccCHHHHHHHHH------HHHhcCccHHHHHhhHhHHHHH
Confidence 57777777776665 3333444444444444444333
No 5
>PF05669 Med31: SOH1; InterPro: IPR008831 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This entry represents subunit Med31 of the Mediator complex. It contains the Saccharomyces cerevisiae SOH1 homologues. SOH1 is responsible for the repression of temperature sensitive growth of the HPR1 mutant [] and has been found to be a component of the RNA polymerase II transcription complex. SOH1 not only interacts with factors involved in DNA repair, but transcription as well. Thus, the SOH1 protein may serve to couple these two processes [].; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006355 regulation of transcription, DNA-dependent, 0016592 mediator complex; PDB: 3FBI_D 3FBN_D.
Probab=53.31 E-value=5.4 Score=31.18 Aligned_cols=50 Identities=28% Similarity=0.721 Sum_probs=34.5
Q ss_pred CCcHHHHHHHHHHhhhcCCCccccccccchHHHHHhhccHHHHHHhhChHHHHHHH
Q psy8635 42 LKDEAFVNYLKYLLYWKEPQYAKYLKYPMCLYFLDLLQYEHFRREIVNSQCAKFID 97 (177)
Q Consensus 42 f~d~~FinYLkYL~YWk~PeYakyL~YP~cL~~LdLLQ~e~FR~~i~n~~~~~~i~ 97 (177)
+.+|..++||..=.||++|.+..||+| |+--..|+.-+-|.-|.|..+++
T Consensus 15 LaNp~Yl~~La~~~y~~d~~F~nYLkY------L~YW~~P~Yakyl~YP~cL~~L~ 64 (101)
T PF05669_consen 15 LANPQYLNYLAQQGYFEDPAFINYLKY------LQYWKRPEYAKYLVYPHCLHFLE 64 (101)
T ss_dssp TTSHHHHHHHH-SGGGTSTHHHHHHHH------GGGGGSTTGGGG-SSTHHHHHHH
T ss_pred hcCHHHHHHHHhcCccCCHHHHHHHHH------HHHhCCCchhhhhcChHHHHHHH
Confidence 446777777776679999988888775 44455677777777777776665
No 6
>PF12672 DUF3793: Protein of unknown function (DUF3793); InterPro: IPR024523 This family of bacterial proteins is functionally uncharacterised. The proteins in this family contain two conserved sequence motifs: PHE and LGYP.
Probab=38.55 E-value=52 Score=26.96 Aligned_cols=49 Identities=24% Similarity=0.484 Sum_probs=38.3
Q ss_pred HhhhcChHHHHHHHhhCCCCcHHHHHHHHHHh-hhcCCCccccccccchHHHHHhhccH
Q psy8635 24 IQCLANPNYLNFLAQRGYLKDEAFVNYLKYLL-YWKEPQYAKYLKYPMCLYFLDLLQYE 81 (177)
Q Consensus 24 VQ~LANP~YL~~LAq~gyf~d~~FinYLkYL~-YWk~PeYakyL~YP~cL~~LdLLQ~e 81 (177)
-..|++|.-..||++-|| .+..+.++|..|. =|+.-+ +||-+.+. |-.|
T Consensus 67 ~~~L~~~~~~~fL~~~GY-~~~~~~~~L~~L~~R~~~~~------FPHEIGiF--LGYP 116 (176)
T PF12672_consen 67 ERYLSDPEVRSFLKSYGY-PDSSLEDCLEHLKKRFESGE------FPHEIGIF--LGYP 116 (176)
T ss_pred HHHHCCHHHHHHHHHCCc-CCCCHHHHHHHHHHHhcCCC------CCchhHhc--cCCC
Confidence 367999999999999999 9999999999994 333332 88877763 5543
No 7
>PHA03410 hypothetical protein; Provisional
Probab=27.88 E-value=36 Score=28.68 Aligned_cols=23 Identities=52% Similarity=1.110 Sum_probs=17.5
Q ss_pred ccCCCCCCCCCCcch----------hheeeecC
Q psy8635 132 RSNLSPNDIQPRPEE----------VWTVLWGP 154 (177)
Q Consensus 132 r~~~~~~~~~~~~~~----------~~~~~~~~ 154 (177)
-|+.+|-.|.|.|.- +|||-|+|
T Consensus 26 y~gI~PPsIpp~Psys~~Qa~As~I~Wtvgw~p 58 (170)
T PHA03410 26 YSGITPPSIPPEPSYSFAQAIASSIVWTVGWGP 58 (170)
T ss_pred ccCCCCCCCCCCCcchHHHHhHhheEEecCCCc
Confidence 466777778877754 89999876
No 8
>smart00727 STI1 Heat shock chaperonin-binding motif.
Probab=24.88 E-value=1.3e+02 Score=18.42 Aligned_cols=22 Identities=14% Similarity=0.018 Sum_probs=13.5
Q ss_pred HHhhccHHHHHHhh----ChHHHHHH
Q psy8635 75 LDLLQYEHFRREIV----NSQCAKFI 96 (177)
Q Consensus 75 LdLLQ~e~FR~~i~----n~~~~~~i 96 (177)
..+|++|.|+..+. ||+.+..+
T Consensus 5 ~~~l~~P~~~~~l~~~~~nP~~~~~~ 30 (41)
T smart00727 5 ALRLQNPQVQSLLQDMQQNPDMLAQM 30 (41)
T ss_pred HHHHcCHHHHHHHHHHHHCHHHHHHH
Confidence 45556777777766 77655433
No 9
>cd01068 sensor_globin Globin domain present in Globin-Coupled-Sensors (GCS). These domains detect changes in intracellular concentrations of oxygen, carbon monoxyde, or nitrous oxide, which result in aerotaxis and/or gene regulation. One subgroup, the HemATs, are aerotactic heme sensors combining a globin with an MCP signaling domain, others function as gene regulators, by direct combination with DNA-binding domains, with domains modulating 2nd messengers, or with domains interacting with transcription factors or regulators.
Probab=24.79 E-value=2.9e+02 Score=20.39 Aligned_cols=44 Identities=11% Similarity=0.141 Sum_probs=21.8
Q ss_pred ccHHHHHHhhChHHHHHHHHHHHHHHh---------hhhHHHHHHhHHHHhhc
Q psy8635 79 QYEHFRREIVNSQCAKFIDDQQVLLWQ---------HYTRKRTKLLNEAAQNN 122 (177)
Q Consensus 79 Q~e~FR~~i~n~~~~~~i~~Qq~~~Wq---------~y~r~R~~~~~~~~e~~ 122 (177)
..|++++-+.++.....+...|..+|. .|..+|.++-..|+.-+
T Consensus 44 ~~p~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~d~~y~~~~~~iG~~H~~ig 96 (147)
T cd01068 44 RTPETAAFLGDESVVERLKSTQRRHWVELFSGVYDEAYIAQRVRIGEVHARIG 96 (147)
T ss_pred cChHHHHHhCCchHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHHHHcC
Confidence 344444444444444555555555553 34445555555555433
No 10
>PF05021 NPL4: NPL4 family; InterPro: IPR007717 The HRD4 gene is identical to NPL4, a gene previously implicated in nuclear transport. Using a diverse set of substrates and direct ubiquitination assays, analysis revealed that HRD4/NPL4 is required for a poorly characterised step in ER-associated degradation following ubiquitination of target proteins but preceding their recognition by the 26S proteasome []. Npl4p physically associates with Cdc48p via Ufd1p to form a Cdc48p-Ufd1p-Npl4p complex. The Cdc48-Ufd1-Npl4 complex functions in the recognition of several polyubiquitin-tagged proteins and facilitates their presentation to the 26S proteasome for processive degradation or even more specific processing [].
Probab=24.74 E-value=99 Score=27.84 Aligned_cols=36 Identities=22% Similarity=0.246 Sum_probs=31.0
Q ss_pred hhhHHhhhcChHHHHHHHhhCCCCcHHHHHHHHHHh
Q psy8635 20 ELEFIQCLANPNYLNFLAQRGYLKDEAFVNYLKYLL 55 (177)
Q Consensus 20 ELEFVQ~LANP~YL~~LAq~gyf~d~~FinYLkYL~ 55 (177)
.-.|+..|+|=+.|-||+..+.|.+..+..=++...
T Consensus 247 ~~~~~~~lsDFHLLlfL~~~~il~~~d~~~L~~av~ 282 (306)
T PF05021_consen 247 SQPFLERLSDFHLLLFLATMDILDKEDMPLLCEAVR 282 (306)
T ss_pred cchHhhhcccHHHHHHHHhCCCCCHHHHHHHHHHHH
Confidence 368999999999999999999999888877766654
No 11
>cd07291 PX_SNX5 The phosphoinositide binding Phox Homology domain of Sorting Nexin 5. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX5, abundantly expressed in macrophages, regulates macropinocytosis, a process that enables cells to internalize large amounts of external solutes. It may also be a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi, acting
Probab=23.75 E-value=50 Score=27.22 Aligned_cols=44 Identities=23% Similarity=0.491 Sum_probs=31.4
Q ss_pred chhhcchhHhhhhHHhhhcCh-----HHHHHHHhhC-CCCcHHHHHHHHH
Q psy8635 10 EDQQRLRFQIELEFIQCLANP-----NYLNFLAQRG-YLKDEAFVNYLKY 53 (177)
Q Consensus 10 ~~~~~~RFE~ELEFVQ~LANP-----~YL~~LAq~g-yf~d~~FinYLkY 53 (177)
++--..|.++|.|.+-+..-- .||+=||..- +-+|+.|..||.|
T Consensus 91 eef~~~r~~~~~~~~~~~kk~~a~lE~fL~Ria~HP~l~~d~~f~~FLe~ 140 (141)
T cd07291 91 EEFAKMKQELEAEYLAVFKKTVQVHEVFLQRLSSHPSLSKDRNFHIFLEY 140 (141)
T ss_pred HHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHhhCCeeccCcchhhhccC
Confidence 444577888888876544322 5888887764 5679999999875
No 12
>PF14307 Glyco_tran_WbsX: Glycosyltransferase WbsX
Probab=22.11 E-value=72 Score=28.10 Aligned_cols=47 Identities=30% Similarity=0.698 Sum_probs=32.1
Q ss_pred HhhhhHHhhhcChHHHH--------HHHhhCCCCcHHHHHHHHHH-hhhcCCCccc
Q psy8635 18 QIELEFIQCLANPNYLN--------FLAQRGYLKDEAFVNYLKYL-LYWKEPQYAK 64 (177)
Q Consensus 18 E~ELEFVQ~LANP~YL~--------~LAq~gyf~d~~FinYLkYL-~YWk~PeYak 64 (177)
+..+.|.=|=||-..-. -|..+.|-....+.++.+|| .|+++|-|.|
T Consensus 100 ~~d~pFcl~WAN~~w~~~w~g~~~~~l~~q~y~~~~d~~~~~~~l~~~F~D~rYik 155 (345)
T PF14307_consen 100 EPDFPFCLCWANENWTRRWDGRNNEILIEQKYSGEDDWKEHFRYLLPYFKDPRYIK 155 (345)
T ss_pred CCCCcEEEEECCChhhhccCCCCccccccccCCchhHHHHHHHHHHHHhCCCCcee
Confidence 34555655666665522 25566777666677777777 7999999987
No 13
>PF05783 DLIC: Dynein light intermediate chain (DLIC); InterPro: IPR022780 This entry consists of several eukaryotic dynein light intermediate chain proteins. The light intermediate chains (LICs) of cytoplasmic dynein consist of multiple isoforms, which undergo post-translational modification to produce a large number of species. DLIC1 is known to be involved in assembly, organisation, and function of centrosomes and mitotic spindles when bound to pericentrin [, ]. DLIC2 is a subunit of cytoplasmic dynein 2 that may play a role in maintaining Golgi organisation by binding cytoplasmic dynein 2 to its Golgi-associated cargo [].
Probab=22.09 E-value=2.2e+02 Score=27.00 Aligned_cols=66 Identities=24% Similarity=0.235 Sum_probs=41.9
Q ss_pred hChHHHHHHHHHHHHHHhhhhHHHHHHhHHHHhhccCCCCCcccccCCC-----CCCCCCCcchhheeeecCccceeeec
Q psy8635 88 VNSQCAKFIDDQQVLLWQHYTRKRTKLLNEAAQNNISGAPTMERRSNLS-----PNDIQPRPEEVWTVLWGPPINCLLTT 162 (177)
Q Consensus 88 ~n~~~~~~i~~Qq~~~Wq~y~r~R~~~~~~~~e~~~~~~~~~~~r~~~~-----~~~~~~~~~~~~~~~~~~~~~~~~~~ 162 (177)
.+++.++.+.+++..+||.|..--.... ..++.+|+..+ .++.-|-++.+||.--|-||-.+.|-
T Consensus 136 ~~~e~~~e~~~kl~~~~q~Y~ep~~~~~----------~~s~~~~~~~~~~~~~~~~~lpl~~g~l~~nlGipi~VV~tk 205 (472)
T PF05783_consen 136 SDPEEREELRQKLERQWQEYVEPGDSSD----------SGSPNRRSPSSSSSDDESVLLPLGEGVLTENLGIPIVVVCTK 205 (472)
T ss_pred ccHHHHHHHHHHHHHHHHHhhhcccccc----------ccCcccccccccccccccccCCCCCcccccccCcceEEEEec
Confidence 4566677888899999999976432221 12222332221 22455888999999999998666554
Q ss_pred C
Q psy8635 163 S 163 (177)
Q Consensus 163 ~ 163 (177)
+
T Consensus 206 s 206 (472)
T PF05783_consen 206 S 206 (472)
T ss_pred c
Confidence 4
No 14
>PRK05321 nicotinate phosphoribosyltransferase; Provisional
Probab=21.85 E-value=1.2e+02 Score=28.41 Aligned_cols=38 Identities=18% Similarity=0.475 Sum_probs=25.4
Q ss_pred hhHhhhhHHhhhc-ChHHHHHHHhhCCCCcHHHHHHHHHH
Q psy8635 16 RFQIELEFIQCLA-NPNYLNFLAQRGYLKDEAFVNYLKYL 54 (177)
Q Consensus 16 RFE~ELEFVQ~LA-NP~YL~~LAq~gyf~d~~FinYLkYL 54 (177)
-.+.+|+++..|. ...=+.||+..++|++ +|+.||+-.
T Consensus 54 gl~~~i~~l~~l~ft~eei~yL~~~~~~~~-~fl~~L~~f 92 (400)
T PRK05321 54 EIREQLDHLCTLRLTDDELDYLRGLPFFKP-DFLDWLRLF 92 (400)
T ss_pred HHHHHHHHHHhCCCCHHHHHHHHhCCCCCH-HHHHHHHhC
Confidence 4566777777765 5566788888788774 565555543
No 15
>cd07292 PX_SNX6 The phosphoinositide binding Phox Homology domain of Sorting Nexin 6. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. SNX6 forms a stable complex with SNX1 and may be a component of the retromer complex, a membrane coat multimeric complex required for endosomal retrieval of lysosomal hydrolase receptors to the Golgi, acting as a mammalian equivalent of yeast Vsp17p. It interacts with the receptor serine/threonine kinases from the transfo
Probab=20.44 E-value=52 Score=27.19 Aligned_cols=44 Identities=23% Similarity=0.428 Sum_probs=31.6
Q ss_pred chhhcchhHhhhhHHhhhc-----ChHHHHHHHhhCC-CCcHHHHHHHHH
Q psy8635 10 EDQQRLRFQIELEFIQCLA-----NPNYLNFLAQRGY-LKDEAFVNYLKY 53 (177)
Q Consensus 10 ~~~~~~RFE~ELEFVQ~LA-----NP~YL~~LAq~gy-f~d~~FinYLkY 53 (177)
++-...|.|+|.|.+-... ---||+=+|+.-. -+|+.|..||.|
T Consensus 91 ee~~~~~~~l~~~~~~~~kk~~a~~E~Fl~Ria~HP~l~~D~~f~~FLe~ 140 (141)
T cd07292 91 EEFTKMKQELEAEYLAIFKKTVAMHEVFLCRVAAHPILRKDLNFHVFLEY 140 (141)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccCcchhheecc
Confidence 4555678888888766552 2358888877654 579999999887
Done!