Query psy1281
Match_columns 144
No_of_seqs 111 out of 162
Neff 4.1
Searched_HMMs 46136
Date Fri Aug 16 20:20:41 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1281.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1281hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04054 Not1: CCR4-Not comple 100.0 3.3E-54 7.2E-59 374.0 11.3 112 1-112 264-379 (379)
2 KOG1831|consensus 100.0 3.6E-42 7.7E-47 330.6 12.1 114 1-114 1458-1571(1591)
3 COG5103 CDC39 Cell division co 100.0 8.7E-36 1.9E-40 285.4 10.9 112 3-114 1870-1985(2005)
4 KOG1831|consensus 96.8 0.00079 1.7E-08 67.8 3.0 90 35-133 1203-1294(1591)
5 PF04054 Not1: CCR4-Not comple 93.7 0.044 9.6E-07 48.5 2.3 74 51-132 18-92 (379)
6 cd03561 VHS VHS domain family; 82.6 18 0.00038 27.0 9.1 73 12-84 31-108 (133)
7 COG5099 RNA-binding protein of 78.9 12 0.00025 36.7 8.4 106 2-121 454-560 (777)
8 cd03568 VHS_STAM VHS domain fa 67.7 54 0.0012 25.2 8.7 84 12-101 31-117 (144)
9 PF00790 VHS: VHS domain; Int 67.6 49 0.0011 24.7 8.0 85 12-102 36-126 (140)
10 KOG1291|consensus 63.6 22 0.00049 33.3 6.3 84 4-97 76-161 (503)
11 smart00288 VHS Domain present 57.8 77 0.0017 23.7 8.5 74 12-85 31-108 (133)
12 PF14676 FANCI_S2: FANCI solen 57.8 15 0.00032 28.9 3.6 48 37-86 38-86 (158)
13 cd03569 VHS_Hrs_Vps27p VHS dom 52.6 61 0.0013 24.7 6.2 74 12-85 35-111 (142)
14 cd07920 Pumilio Pumilio-family 50.0 40 0.00086 27.6 5.1 45 4-49 205-249 (322)
15 PF09209 DUF1956: Domain of un 47.9 85 0.0018 21.9 5.9 30 55-84 6-35 (125)
16 PF02244 Propep_M14: Carboxype 47.8 15 0.00033 24.1 2.0 38 76-113 11-55 (74)
17 PF12717 Cnd1: non-SMC mitotic 45.1 1.4E+02 0.003 22.9 11.5 72 12-86 1-75 (178)
18 cd07920 Pumilio Pumilio-family 40.7 2E+02 0.0043 23.4 9.3 71 3-75 24-94 (322)
19 cd03562 CID CID (CTD-Interacti 38.8 1E+02 0.0022 21.8 5.2 55 5-61 43-103 (114)
20 PF12755 Vac14_Fab1_bd: Vacuol 35.2 1.4E+02 0.003 21.4 5.4 62 3-66 31-95 (97)
21 PF12726 SEN1_N: SEN1 N termin 34.2 36 0.00078 32.2 2.8 83 57-139 215-312 (727)
22 COG5057 LAG1 Phosphotyrosyl ph 31.6 37 0.00081 30.4 2.3 67 6-75 113-199 (353)
23 cd03567 VHS_GGA VHS domain fam 30.8 2.5E+02 0.0053 21.5 9.3 93 11-109 31-131 (139)
24 PF04818 CTD_bind: RNA polymer 29.8 49 0.0011 21.4 2.2 45 17-61 5-54 (64)
25 PF07875 Coat_F: Coat F domain 28.2 1.2E+02 0.0025 19.8 3.8 26 99-124 29-54 (64)
26 COG4458 SrfC Uncharacterized p 26.8 73 0.0016 31.4 3.5 64 3-68 495-561 (821)
27 PF11573 Med23: Mediator compl 26.2 3.1E+02 0.0067 29.0 7.9 82 5-86 540-635 (1341)
28 PF02985 HEAT: HEAT repeat; I 25.8 1E+02 0.0023 17.1 2.8 24 2-25 3-26 (31)
29 PF14514 TetR_C_9: Transcripti 25.7 2.6E+02 0.0057 20.9 5.8 99 15-121 8-120 (129)
30 COG5099 RNA-binding protein of 24.9 1.3E+02 0.0028 29.7 4.8 72 4-77 565-636 (777)
31 PF09324 DUF1981: Domain of un 24.8 93 0.002 21.7 3.0 46 41-86 22-70 (86)
32 KOG1763|consensus 24.3 1.2E+02 0.0026 27.2 4.2 41 57-97 140-181 (343)
33 PF12717 Cnd1: non-SMC mitotic 24.2 3.3E+02 0.0072 20.8 6.9 38 6-43 70-109 (178)
34 PF12243 CTK3: CTD kinase subu 22.6 3.7E+02 0.0081 20.8 6.3 56 17-75 39-104 (139)
35 PF11458 Mistic: Membrane-inte 21.0 2.5E+02 0.0053 20.5 4.5 45 76-123 22-71 (84)
36 COG5336 Uncharacterized protei 20.6 58 0.0012 25.1 1.3 20 59-80 63-82 (116)
37 TIGR01609 PF_unchar_267 Plasmo 20.3 3.1E+02 0.0068 21.9 5.4 59 59-121 5-70 (146)
No 1
>PF04054 Not1: CCR4-Not complex component, Not1; InterPro: IPR007196 The Ccr4-Not complex is a global regulator of gene expression that is conserved from yeast to human. It affects genes positively and negatively and is thought to regulate transcription factor IID function. In Saccharomyces cerevisiae, it exists in two prominent forms and consists of at least nine core subunits: the five Not proteins (Not1p to Not5p), Caf1p, Caf40p, Caf130p and Ccr4p []. The Ccr4-Not complex regulates many different cellular functions, including RNA degradation and transcription initiation. It may be a regulatory platform that senses nutrient levels and stress []. Caf1p and Ccr4p, are directly involved in mRNA deadenylation, and Caf1p is associated with Dhh1p, a putative RNA helicase thought to be a component of the decapping complex []. Pop2, a component of the Ccr4-Not complex, functions as a deadenylase []. The Ccr4-Not complex is a global regulator of transcription that affects genes positively and negatively and is thought to regulate transcription factor TFIID [].
Probab=100.00 E-value=3.3e-54 Score=374.05 Aligned_cols=112 Identities=71% Similarity=1.189 Sum_probs=108.0
Q ss_pred ChHHHHHHhccChHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHhh----hcChhHHHHHHHHHHHHHhhcCCCCchhHH
Q psy1281 1 MDIFLNFAVDLDTEGRYLFLNAIANQLRYPNSHTHYFSCLLLYLFA----EANTEAIQEQITRVLLERLIVNRPHPWGLL 76 (144)
Q Consensus 1 ~~i~~~L~~~ld~E~Ry~ll~aianqLRYPN~HT~~Fs~~ll~LF~----~~~~~~IqEqItRVLlERliv~rPHPWGll 76 (144)
|+++.+|++++|+||||++++||||||||||+|||||||+++++|+ +.++++|||||||||+||++|+||||||++
T Consensus 264 ~~ll~~Li~~ld~E~RY~ll~aiaNqLRYPN~HT~~Fs~~lL~lF~~~~~~~~~~~IqEqItRVLLERliv~rPHPWGll 343 (379)
T PF04054_consen 264 VTLLSKLIHELDPEGRYYLLSAIANQLRYPNSHTHFFSCVLLNLFSSDMNDPNDEDIQEQITRVLLERLIVNRPHPWGLL 343 (379)
T ss_pred HHHHHHHHHhCCHHHHHHHHHHHHHHcCCCchhHHHHHHHHHHHhcCCCCccchhhhHHHHHHHHHHHHhcCCCCCccHH
Confidence 5789999999999999999999999999999999999999999999 445689999999999999999999999999
Q ss_pred HHHHHHHhCCCccccccccccccHHHHHHHHhHHHH
Q psy1281 77 ITFIELIKNPVYKFWDHEFVHCAPEIEKLFESGWPL 112 (144)
Q Consensus 77 itfiELikn~~y~Fw~~pFv~~~PEi~~lf~~v~~~ 112 (144)
+||+||+||++|+||++||||++|||+++|+++++|
T Consensus 344 itfiELikN~~y~f~~~pFik~~pEI~~~f~~~~~~ 379 (379)
T PF04054_consen 344 ITFIELIKNPKYNFWELPFIKCAPEIEKLFESLARH 379 (379)
T ss_pred HHHHHHHhCccCCcccCcccccCHHHHHHHHHHhcC
Confidence 999999999999999999999999999999999875
No 2
>KOG1831|consensus
Probab=100.00 E-value=3.6e-42 Score=330.63 Aligned_cols=114 Identities=74% Similarity=1.243 Sum_probs=111.9
Q ss_pred ChHHHHHHhccChHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHhhhcChhHHHHHHHHHHHHHhhcCCCCchhHHHHHH
Q psy1281 1 MDIFLNFAVDLDTEGRYLFLNAIANQLRYPNSHTHYFSCLLLYLFAEANTEAIQEQITRVLLERLIVNRPHPWGLLITFI 80 (144)
Q Consensus 1 ~~i~~~L~~~ld~E~Ry~ll~aianqLRYPN~HT~~Fs~~ll~LF~~~~~~~IqEqItRVLlERliv~rPHPWGllitfi 80 (144)
|||+.+|+.+||.||||.+++||+|||||||+|||||||+++++|.+++...|||||||+++||++|+||||||+++||+
T Consensus 1458 ~~i~~nL~~nld~e~ry~~l~aianqlryp~~ht~~~s~~~l~lfk~~~~~pike~i~~~~lerii~nrPHpWGllitF~ 1537 (1591)
T KOG1831|consen 1458 MDIFQNLIVNLDTEGRYLLLNAIANQLRYPNSHTYYFSCVFLYLFKRAGNNPIKEQITRVLLERIIVNRPHPWGLLITFT 1537 (1591)
T ss_pred hhHHHHHHHhcchhhhHHHHHHHHHHhcCCchhhHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHhcCCCCCchhHHHHH
Confidence 79999999999999999999999999999999999999999999999987889999999999999999999999999999
Q ss_pred HHHhCCCccccccccccccHHHHHHHHhHHHHHH
Q psy1281 81 ELIKNPVYKFWDHEFVHCAPEIEKLFESGWPLYA 114 (144)
Q Consensus 81 ELikn~~y~Fw~~pFv~~~PEi~~lf~~v~~~~~ 114 (144)
||+|||.||||++|||+|+|||+++|++++++|.
T Consensus 1538 eLikN~~YNfw~~~fv~~~pEI~rlfqsl~~~~~ 1571 (1591)
T KOG1831|consen 1538 ELIKNPDYNFWDHPFVQCAPEIKRLFQSLAKYCK 1571 (1591)
T ss_pred HHHcCCCcccccCcccccCHHHHHHHHHHHHHhh
Confidence 9999999999999999999999999999999994
No 3
>COG5103 CDC39 Cell division control protein, negative regulator of transcription [Cell division and chromosome partitioning / Transcription]
Probab=100.00 E-value=8.7e-36 Score=285.44 Aligned_cols=112 Identities=46% Similarity=0.718 Sum_probs=106.2
Q ss_pred HHHHHHhccChHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHhhhcC----hhHHHHHHHHHHHHHhhcCCCCchhHHHH
Q psy1281 3 IFLNFAVDLDTEGRYLFLNAIANQLRYPNSHTHYFSCLLLYLFAEAN----TEAIQEQITRVLLERLIVNRPHPWGLLIT 78 (144)
Q Consensus 3 i~~~L~~~ld~E~Ry~ll~aianqLRYPN~HT~~Fs~~ll~LF~~~~----~~~IqEqItRVLlERliv~rPHPWGllit 78 (144)
++-.+..+++++.||.++.||++||||||+||+|||++++++|.++. .-.||||||||+|||+||+||||||+++|
T Consensus 1870 ~l~~~~r~g~~~~rY~ll~ai~~qlRYp~ihTy~fs~vfl~~fkS~~~N~QkL~ikE~m~t~lLeRII~NrPH~WGl~i~ 1949 (2005)
T COG5103 1870 MLWIRMRAGGPPKRYFLLTAILAQLRYPEIHTYDFSRVFLKSFKSHGYNPQKLLIKEQMTTVLLERIICNRPHPWGLLIT 1949 (2005)
T ss_pred HHHHHHhcCCCchhhHHHHHHHHHhcCCCcchhHHHHHHHHHHhhcCCChHHHHHHHHHHHHHHHHHHcCCCCcchhhee
Confidence 45678899999999999999999999999999999999999998873 36799999999999999999999999999
Q ss_pred HHHHHhCCCccccccccccccHHHHHHHHhHHHHHH
Q psy1281 79 FIELIKNPVYKFWDHEFVHCAPEIEKLFESGWPLYA 114 (144)
Q Consensus 79 fiELikn~~y~Fw~~pFv~~~PEi~~lf~~v~~~~~ 114 (144)
|+||+||.+||||++|||+.+|||.++|+++.+++.
T Consensus 1950 FTeLlkNeD~Nf~k~Pyikr~~EI~~lfdsL~e~v~ 1985 (2005)
T COG5103 1950 FTELLKNEDYNFWKHPYIKRNDEICRLFDSLHEHVM 1985 (2005)
T ss_pred HHHHhcccccchhcCcccccCHHHHHHHHHHHHHhh
Confidence 999999999999999999999999999999988874
No 4
>KOG1831|consensus
Probab=96.83 E-value=0.00079 Score=67.77 Aligned_cols=90 Identities=33% Similarity=0.552 Sum_probs=65.4
Q ss_pred HHHHHHHHHHhhhcC-hhHHHHHHHHHHHHHhhcCCCC-chhHHHHHHHHHhCCCccccccccccccHHHHHHHHhHHHH
Q psy1281 35 HYFSCLLLYLFAEAN-TEAIQEQITRVLLERLIVNRPH-PWGLLITFIELIKNPVYKFWDHEFVHCAPEIEKLFESGWPL 112 (144)
Q Consensus 35 ~~Fs~~ll~LF~~~~-~~~IqEqItRVLlERliv~rPH-PWGllitfiELikn~~y~Fw~~pFv~~~PEi~~lf~~v~~~ 112 (144)
..|+.++..+-+... .+.+-=.|..+..+-.+.-+|| =.|....+++|+..+ .+.-.-.... =+++|..
T Consensus 1203 Rlf~~ll~E~~~~~~~le~~~~~i~SaF~~tfhalqp~~~Pgf~fawL~lishr--~li~~~L~~~-------~~k~~~~ 1273 (1591)
T KOG1831|consen 1203 RLFSMLLPELMTADSVLEPISLDILSAFKNTFHALQPRRFPGFAFAWLELISHR--GLIPRMLAET-------NQKGWPL 1273 (1591)
T ss_pred HHHHHHHHHhccccchhhhHHHHHHHHHHHHHHHhCcccCcccceeeeecccch--hHHHHHHHhc-------cccccHH
Confidence 355555555444331 2445556788888888999999 668999999999887 3333322222 2778999
Q ss_pred HHHHHHhHHhhhcccchhHHH
Q psy1281 113 YAQLLIDIFKFLAPFLPQQQQ 133 (144)
Q Consensus 113 ~~q~l~~~~~~~~~~l~~~~~ 133 (144)
++|+++|+||||+|||||-+-
T Consensus 1274 ~~~llislfkfL~~ylrn~~~ 1294 (1591)
T KOG1831|consen 1274 YAQLLISLFKFLAPYLRNYEL 1294 (1591)
T ss_pred HHHHHHHHHHHHHHHHhhhhh
Confidence 999999999999999999753
No 5
>PF04054 Not1: CCR4-Not complex component, Not1; InterPro: IPR007196 The Ccr4-Not complex is a global regulator of gene expression that is conserved from yeast to human. It affects genes positively and negatively and is thought to regulate transcription factor IID function. In Saccharomyces cerevisiae, it exists in two prominent forms and consists of at least nine core subunits: the five Not proteins (Not1p to Not5p), Caf1p, Caf40p, Caf130p and Ccr4p []. The Ccr4-Not complex regulates many different cellular functions, including RNA degradation and transcription initiation. It may be a regulatory platform that senses nutrient levels and stress []. Caf1p and Ccr4p, are directly involved in mRNA deadenylation, and Caf1p is associated with Dhh1p, a putative RNA helicase thought to be a component of the decapping complex []. Pop2, a component of the Ccr4-Not complex, functions as a deadenylase []. The Ccr4-Not complex is a global regulator of transcription that affects genes positively and negatively and is thought to regulate transcription factor TFIID [].
Probab=93.65 E-value=0.044 Score=48.53 Aligned_cols=74 Identities=31% Similarity=0.663 Sum_probs=59.1
Q ss_pred hHHHHHHHHHHHHHhhcCCCC-chhHHHHHHHHHhCCCccccccccccccHHHHHHHHhHHHHHHHHHHhHHhhhcccch
Q psy1281 51 EAIQEQITRVLLERLIVNRPH-PWGLLITFIELIKNPVYKFWDHEFVHCAPEIEKLFESGWPLYAQLLIDIFKFLAPFLP 129 (144)
Q Consensus 51 ~~IqEqItRVLlERliv~rPH-PWGllitfiELikn~~y~Fw~~pFv~~~PEi~~lf~~v~~~~~q~l~~~~~~~~~~l~ 129 (144)
+....++...+.+++..-+|- =.|....|+||+.++. |.- ...+..|+ ++.|..++++|+|++||+.|+|+
T Consensus 18 ~~~~~~~~~~fa~~l~~lqP~~~PgF~faWl~LisHR~--Flp-~lL~~~~~-----~~gW~~~~~Ll~~ll~Fl~~~l~ 89 (379)
T PF04054_consen 18 EELDRQFLLAFASFLHSLQPLYFPGFAFAWLELISHRM--FLP-KLLRNSPD-----QKGWPAYTRLLIDLLKFLGPYLK 89 (379)
T ss_pred hhhHHHHHHHHHHHHHhcCCccCcchHHHHHHHHHHHH--HHH-HHHhcCCC-----CCChHHHHHHHHHHHHHHHHhcc
Confidence 345568999999999999998 7899999999999883 322 11221333 58999999999999999999999
Q ss_pred hHH
Q psy1281 130 QQQ 132 (144)
Q Consensus 130 ~~~ 132 (144)
+.+
T Consensus 90 ~~~ 92 (379)
T PF04054_consen 90 NEE 92 (379)
T ss_pred ccc
Confidence 875
No 6
>cd03561 VHS VHS domain family; The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It has a superhelical structure similar to that of the ARM (Armadillo) repeats and is present at the N-termini of proteins involved in intracellular membrane trafficking. There are four general groups of VHS domain containing proteins based on their association with other domains. The first group consists of proteins of the STAM/EAST/Hbp family which has the domain composition VHS-SH3-ITAM. The second consists of proteins with a FYVE domain C-terminal to VHS. The third consists of GGA proteins with a domain composition VHS-GAT (GGA and TOM)-GAE (gamma-adaptin ear) domain. The fourth consists of proteins with a VHS domain alone or with domains other than those mentioned above. In GGA proteins, VHS domains are involved in cargo recognition in trans-Golgi, thereby having a general me
Probab=82.62 E-value=18 Score=26.97 Aligned_cols=73 Identities=21% Similarity=0.230 Sum_probs=48.8
Q ss_pred ChHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHhhhcChhHHHHHHHH-HHHHH---hhcCC-CCchhHHHHHHHHHh
Q psy1281 12 DTEGRYLFLNAIANQLRYPNSHTHYFSCLLLYLFAEANTEAIQEQITR-VLLER---LIVNR-PHPWGLLITFIELIK 84 (144)
Q Consensus 12 d~E~Ry~ll~aianqLRYPN~HT~~Fs~~ll~LF~~~~~~~IqEqItR-VLlER---liv~r-PHPWGllitfiELik 84 (144)
++++-.-.+.++-..|.|+|.|+-+.+-.++......-+..+..+|.. -.+++ ++..+ ..+=-+.--.+|++.
T Consensus 31 ~~~~~k~a~raL~krl~~~n~~vql~AL~lLd~~vkNcg~~f~~~i~s~~fl~~l~~l~~~~~~~~~~Vk~kil~ll~ 108 (133)
T cd03561 31 KPNGPKEAARAIRKKIKYGNPHVQLLALTLLELLVKNCGKPFHLQVADKEFLLELVKIAKNSPKYDPKVREKALELIL 108 (133)
T ss_pred CCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCChHHHHHHhhHHHHHHHHHHhCCCCCCCHHHHHHHHHHHH
Confidence 356777789999999999999999999999998877655556555544 44443 33332 123344444555554
No 7
>COG5099 RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal structure and biogenesis]
Probab=78.95 E-value=12 Score=36.66 Aligned_cols=106 Identities=20% Similarity=0.204 Sum_probs=78.3
Q ss_pred hHHHHHHhccChHHHHHHHHHHHHhhcCCCchHHHHHH-HHHHHhhhcChhHHHHHHHHHHHHHhhcCCCCchhHHHHHH
Q psy1281 2 DIFLNFAVDLDTEGRYLFLNAIANQLRYPNSHTHYFSC-LLLYLFAEANTEAIQEQITRVLLERLIVNRPHPWGLLITFI 80 (144)
Q Consensus 2 ~i~~~L~~~ld~E~Ry~ll~aianqLRYPN~HT~~Fs~-~ll~LF~~~~~~~IqEqItRVLlERliv~rPHPWGllitfi 80 (144)
..++.++...+.+..-.+..+|.+++ +-.++.||+- ++-.+|+.+. +.++...++.+..++.-..=||.|..+. -
T Consensus 454 r~LQk~Lds~s~~~~~~~~~e~~d~~--~eLs~d~fGNyliQK~fe~~s-~~q~~~ml~~~~~~~~~ls~~~~Gtrv~-Q 529 (777)
T COG5099 454 RFLQKLLDSNSSPEIEVIFNEILDQL--VELSSDYFGNYLIQKLFEYGS-EIQKSIMLSKSSKHLVSLSVHKYGTRVL-Q 529 (777)
T ss_pred HHHHHHhcccchHHHHHHHHHHhhhh--HHHHHhhhcchhhHHHHHhcc-HHHHHHHHHHhhhhHHHhhccccccHHH-H
Confidence 35677888888888888999999887 7889999998 6677777775 6889999999999999999999998764 3
Q ss_pred HHHhCCCccccccccccccHHHHHHHHhHHHHHHHHHHhHH
Q psy1281 81 ELIKNPVYKFWDHEFVHCAPEIEKLFESGWPLYAQLLIDIF 121 (144)
Q Consensus 81 ELikn~~y~Fw~~pFv~~~PEi~~lf~~v~~~~~q~l~~~~ 121 (144)
++++.. ...-++..+++.+...+-++..|.+
T Consensus 530 K~id~~----------~t~~qi~~lv~~l~~~~~~li~dqn 560 (777)
T COG5099 530 KAIDIV----------STDIQISLLVEELRPYCLQLIKDQN 560 (777)
T ss_pred HHHhcc----------CchhhHHHHHHHhhhhhHHHHHhcc
Confidence 444322 1122344566666666666555544
No 8
>cd03568 VHS_STAM VHS domain family, STAM subfamily; members include STAM (Signal Transducing Adaptor Molecule), EAST (EGFR-associated protein with SH3 and TAM domains) and Hbp (Hrs-binding protein). Collectively, they are referred to as STAM. All STAMs have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a SH3 (Src homology 3) domain, a well-established protein-protein interaction domain. At the C-termini of most vertebrate STAMS, an ITAM (Immunoreceptor Tyrosine-based Activation) motif is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries.
Probab=67.65 E-value=54 Score=25.18 Aligned_cols=84 Identities=25% Similarity=0.314 Sum_probs=61.2
Q ss_pred ChHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHhhhc-ChhHHHHHHHHHHHHHh--hcCCCCchhHHHHHHHHHhCCCc
Q psy1281 12 DTEGRYLFLNAIANQLRYPNSHTHYFSCLLLYLFAEA-NTEAIQEQITRVLLERL--IVNRPHPWGLLITFIELIKNPVY 88 (144)
Q Consensus 12 d~E~Ry~ll~aianqLRYPN~HT~~Fs~~ll~LF~~~-~~~~IqEqItRVLlERl--iv~rPHPWGllitfiELikn~~y 88 (144)
+..|-...+.||.--|.++|.|+-.++-.++..-... +..--+|...|.+++.+ ++.++.+-.+.--..+|++.
T Consensus 31 ~~~~~k~a~ral~KRl~~~n~~v~l~AL~LLe~~vkNCG~~fh~evask~Fl~eL~kl~~~~~~~~Vk~kil~li~~--- 107 (144)
T cd03568 31 DENGAKDCLKAIMKRLNHKDPNVQLRALTLLDACAENCGKRFHQEVASRDFTQELKKLINDRVHPTVKEKLREVVKQ--- 107 (144)
T ss_pred CCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCCHHHHHHHhhHHHHHHHHHHhcccCCHHHHHHHHHHHHH---
Confidence 3566677889999999999999999998888776554 43444566677777775 24444556888888888876
Q ss_pred cccccccccccHH
Q psy1281 89 KFWDHEFVHCAPE 101 (144)
Q Consensus 89 ~Fw~~pFv~~~PE 101 (144)
|...|-. .|+
T Consensus 108 --W~~~f~~-~~~ 117 (144)
T cd03568 108 --WADEFKN-DPS 117 (144)
T ss_pred --HHHHhCC-Ccc
Confidence 7766653 454
No 9
>PF00790 VHS: VHS domain; InterPro: IPR002014 The VHS domain is a ~140 residues long domain, whose name is derived from its occurrence in VPS-27, Hrs and STAM. Based on regions surrounding the domain, VHS-proteins can be divided into 4 groups []: STAM/EAST/Hbp which all share the domain composition VHS-SH3-ITAM and carry one or two ubiquitin-interacting motifs Proteins with a FYVE domain (IPR000306 from INTERPRO) C-terminal to VHS which also carry one or two ubiquitin-interacting motifs GGA proteins with a domain composition VHS-GAT (GGA and Tom1) homology domain VHS domain alone or in combination with domains other than those listed above The VHS domain is always found at the N- terminus of proteins suggesting that such topology is important for function. The domain is considered to have a general membrane targeting/cargo recognition role in vesicular trafficking []. Resolution of the crystal structure of the VHS domain of Drosophila Hrs and human Tom1 revealed that it consists of eight helices arranged in a double-layer superhelix []. The existence of conserved patches of residues on the domain surface suggests that VHS domains may be involved in protein-protein recognition and docking. Overall, sequence similarity is low (approx 25%) amongst domain family members.; GO: 0006886 intracellular protein transport; PDB: 1X5B_A 2L0T_B 1DVP_A 3LDZ_C 3ZYQ_A 4AVX_A 3G2U_A 3G2W_A 1UJJ_A 3G2V_A ....
Probab=67.59 E-value=49 Score=24.70 Aligned_cols=85 Identities=18% Similarity=0.360 Sum_probs=60.6
Q ss_pred ChHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHhhhcChhHHHHHH-HHHHHHHh---hcCCCCchh--HHHHHHHHHhC
Q psy1281 12 DTEGRYLFLNAIANQLRYPNSHTHYFSCLLLYLFAEANTEAIQEQI-TRVLLERL---IVNRPHPWG--LLITFIELIKN 85 (144)
Q Consensus 12 d~E~Ry~ll~aianqLRYPN~HT~~Fs~~ll~LF~~~~~~~IqEqI-tRVLlERl---iv~rPHPWG--llitfiELikn 85 (144)
++++-.-.+.+|...|.++|.|+-+.+-.++.......+..++.++ .+-+++++ +..++.+=. +.--.++++..
T Consensus 36 ~~~~~kea~~~l~krl~~~~~~vq~~aL~lld~lvkNcg~~f~~ev~~~~fl~~l~~l~~~~~~~~~~~Vk~k~l~ll~~ 115 (140)
T PF00790_consen 36 SPDGAKEAARALRKRLKHGNPNVQLLALTLLDALVKNCGPRFHREVASKEFLDELVKLIKSKKTDPETPVKEKILELLQE 115 (140)
T ss_dssp STTHHHHHHHHHHHHHTTSSHHHHHHHHHHHHHHHHHSHHHHHHHHTSHHHHHHHHHHHHHTTTHHHSHHHHHHHHHHHH
T ss_pred CCccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHcCCHHHHHHHhHHHHHHHHHHHHccCCCCchhHHHHHHHHHHHH
Confidence 3778888999999999999999999998888888776555666665 44455543 333444332 77788888864
Q ss_pred CCccccccccccccHHH
Q psy1281 86 PVYKFWDHEFVHCAPEI 102 (144)
Q Consensus 86 ~~y~Fw~~pFv~~~PEi 102 (144)
|...| +..|+.
T Consensus 116 -----W~~~f-~~~~~~ 126 (140)
T PF00790_consen 116 -----WAEAF-KSDPEL 126 (140)
T ss_dssp -----HHHHT-TTSTTG
T ss_pred -----HHHHH-CCCCCc
Confidence 77777 555654
No 10
>KOG1291|consensus
Probab=63.63 E-value=22 Score=33.27 Aligned_cols=84 Identities=23% Similarity=0.317 Sum_probs=57.3
Q ss_pred HHHHHhccChHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHhhhcC--hhHHHHHHHHHHHHHhhcCCCCchhHHHHHHH
Q psy1281 4 FLNFAVDLDTEGRYLFLNAIANQLRYPNSHTHYFSCLLLYLFAEAN--TEAIQEQITRVLLERLIVNRPHPWGLLITFIE 81 (144)
Q Consensus 4 ~~~L~~~ld~E~Ry~ll~aianqLRYPN~HT~~Fs~~ll~LF~~~~--~~~IqEqItRVLlERliv~rPHPWGllitfiE 81 (144)
+++|+..+..-+-+++...+-++ || -.-+.+|+++.|.. ..|+||-|-+.+-=-++.+-|-.||+++|...
T Consensus 76 lQ~LaARLGvVTG~hLAe~Cr~~--Yp-----k~~~~~Lwi~aEiAiI~sDiqEVIGTAiAlniL~~IPL~~GVliTilD 148 (503)
T KOG1291|consen 76 LQRLAARLGVVTGKHLAEICREE--YP-----KWPRMVLWIMAEIAIIASDIQEVIGTAIALNILSNIPLWAGVLITILD 148 (503)
T ss_pred HHHHHHHHcccccHHHHHHHHHH--cc-----ccHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHhCCcHHHHHHHHHHH
Confidence 46666666665556665555444 33 23357788888753 37899999777766777779999999999877
Q ss_pred HHhCCCcccccccccc
Q psy1281 82 LIKNPVYKFWDHEFVH 97 (144)
Q Consensus 82 Likn~~y~Fw~~pFv~ 97 (144)
-+-- -|.+++.++
T Consensus 149 ~f~f---L~l~kyGiR 161 (503)
T KOG1291|consen 149 TFLF---LFLDKYGIR 161 (503)
T ss_pred HHHH---HHHhccchH
Confidence 6543 255656554
No 11
>smart00288 VHS Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.
Probab=57.79 E-value=77 Score=23.65 Aligned_cols=74 Identities=16% Similarity=0.162 Sum_probs=53.6
Q ss_pred ChHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHhhhcChhHH-HHHHHHHHHHHhh---cCCCCchhHHHHHHHHHhC
Q psy1281 12 DTEGRYLFLNAIANQLRYPNSHTHYFSCLLLYLFAEANTEAI-QEQITRVLLERLI---VNRPHPWGLLITFIELIKN 85 (144)
Q Consensus 12 d~E~Ry~ll~aianqLRYPN~HT~~Fs~~ll~LF~~~~~~~I-qEqItRVLlERli---v~rPHPWGllitfiELikn 85 (144)
++++-.-.+.++...|.|+|.|+-.++-.++......-+..+ +|.-.+-+++++. ..+++.-++.--.++++.+
T Consensus 31 ~~~~~k~a~r~l~krl~~~n~~v~l~AL~lLe~~vkNcg~~f~~ev~s~~fl~~L~~l~~~~~~~~~Vk~kil~li~~ 108 (133)
T smart00288 31 TPDGPKDAVRLLKKRLNNKNPHVALLALTLLDACVKNCGSKFHLEVASKEFLNELVKLIKPKYPLPLVKKRILELIQE 108 (133)
T ss_pred CCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHhHHHHHHHHHHHcCCCCcHHHHHHHHHHHHH
Confidence 467778889999999999999999999999998876533444 4444666666644 3344433477777888765
No 12
>PF14676 FANCI_S2: FANCI solenoid 2; PDB: 3S51_A 3S4Z_A 3S4W_A.
Probab=57.76 E-value=15 Score=28.91 Aligned_cols=48 Identities=27% Similarity=0.380 Sum_probs=31.6
Q ss_pred HHHHHHHHhhhcChhHHHHHHHHHHHHHhhcCCCCc-hhHHHHHHHHHhCC
Q psy1281 37 FSCLLLYLFAEANTEAIQEQITRVLLERLIVNRPHP-WGLLITFIELIKNP 86 (144)
Q Consensus 37 Fs~~ll~LF~~~~~~~IqEqItRVLlERliv~rPHP-WGllitfiELikn~ 86 (144)
=+.+++.+|... +.++..|..-+++|+++..+.| =...-++.++++.-
T Consensus 38 G~~IL~~~fk~h--~~~r~~Ile~l~~rI~~~s~~~~~~~idlL~~lv~~~ 86 (158)
T PF14676_consen 38 GIQILLELFKVH--EMIRSEILEQLLNRIVTKSSSPSSQYIDLLSELVRKA 86 (158)
T ss_dssp HHHHHHHHHHH---GGGHHHHHHHHHHHHHH--SS--HHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHHh--HHHHHHHHHHHHHHHHhcCccchhHHHHHHHHHHHHC
Confidence 356788999876 5688889999999999888872 12255666666654
No 13
>cd03569 VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p subfamily; composed of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and its yeast homolog Vps27p (vacuolar protein sorting). The VHS domain, an essential part of Hrs/Vps27p, has a superhelical structure similar to the structure of ARM (Armadillo) repeats and is present at the N-termini of proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain C-terminal to VHS, as well as two coiled-coil domains. Hrs has been proposed to play a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane.
Probab=52.61 E-value=61 Score=24.73 Aligned_cols=74 Identities=18% Similarity=0.193 Sum_probs=52.6
Q ss_pred ChHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHhhhc-ChhHHHHHHHHHHHHHhhc--CCCCchhHHHHHHHHHhC
Q psy1281 12 DTEGRYLFLNAIANQLRYPNSHTHYFSCLLLYLFAEA-NTEAIQEQITRVLLERLIV--NRPHPWGLLITFIELIKN 85 (144)
Q Consensus 12 d~E~Ry~ll~aianqLRYPN~HT~~Fs~~ll~LF~~~-~~~~IqEqItRVLlERliv--~rPHPWGllitfiELikn 85 (144)
+..+-.-.+.|+-..|.|+|.|+-.++-.+|...... +..--+|..++-+++++.. .+..|--+.--.++|+.+
T Consensus 35 ~~~~~k~a~ral~krl~~~n~~vql~AL~LLe~~vkNCG~~fh~evas~~fl~~l~~l~~~~~~~~Vk~kil~li~~ 111 (142)
T cd03569 35 KDVQPKYAMRALKKRLLSKNPNVQLYALLLLESCVKNCGTHFHDEVASREFMDELKDLIKTTKNEEVRQKILELIQA 111 (142)
T ss_pred CCCCHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHCCHHHHHHHhhHHHHHHHHHHHcccCCHHHHHHHHHHHHH
Confidence 4567778899999999999999999999999998765 4444566667888777542 112234455555566554
No 14
>cd07920 Pumilio Pumilio-family RNA binding domain. Puf repeats (also labelled PUM-HD or Pumilio homology domain) mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio. These proteins function as translational repressors in early embryonic development by binding to sequences in the 3' UTR of target mRNAs, such as the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA. Other proteins that contain Puf domains are also plausible RNA binding proteins. Yeast PUF1 (JSN1), for instance, appears to contain a single RNA-recognition motif (RRM) domain. Puf repeat proteins have been observed to function asymmetrically and may be responsible for creating protein gradients involved in the specification of cell fate and differentiation. Puf domains usually occur as a tandem repeat of 8 domains. This model encompasses all 8 tandem repeats. Some proteins may have fewer (canon
Probab=50.00 E-value=40 Score=27.55 Aligned_cols=45 Identities=9% Similarity=0.032 Sum_probs=23.5
Q ss_pred HHHHHhccChHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHhhhcC
Q psy1281 4 FLNFAVDLDTEGRYLFLNAIANQLRYPNSHTHYFSCLLLYLFAEAN 49 (144)
Q Consensus 4 ~~~L~~~ld~E~Ry~ll~aianqLRYPN~HT~~Fs~~ll~LF~~~~ 49 (144)
++.++...+++.+-.++..+..++ .+-+++.|-|.++-..+...+
T Consensus 205 vq~~l~~~~~~~~~~i~~~l~~~~-~~l~~~k~Gs~Vve~~l~~~~ 249 (322)
T cd07920 205 VQHVLELGDPDDTSRIIEKLLGNI-VQLSCHKFASNVVEKCLKHAS 249 (322)
T ss_pred HHHHHhcCCHHHHHHHHHHHHHHH-HHHHcCcchHHHHHHHHHHCC
Confidence 444555555555555555555433 222555566666666665554
No 15
>PF09209 DUF1956: Domain of unknown function (DUF1956); InterPro: IPR015292 This entry represents the C-terminal domain found in the hypothetical transcriptional regulator YbiH from bacteria such as Salmonella typhimurium and Escherichia coli. YbiH is a member of the TetR (tetracycline resistance) transcriptional regulator family of proteins. The C-terminal domains of YbiH and TetR share a multi-helical, interlocking structure.; PDB: 1T33_A.
Probab=47.89 E-value=85 Score=21.90 Aligned_cols=30 Identities=27% Similarity=0.484 Sum_probs=21.6
Q ss_pred HHHHHHHHHHhhcCCCCchhHHHHHHHHHh
Q psy1281 55 EQITRVLLERLIVNRPHPWGLLITFIELIK 84 (144)
Q Consensus 55 EqItRVLlERliv~rPHPWGllitfiELik 84 (144)
+.+.+.+++++......+|...+..-|+..
T Consensus 6 ~~~i~~~~~~l~~~~~~~~~~~l~~RE~~~ 35 (125)
T PF09209_consen 6 RAFIRALLRRLLSDPESRWWLRLIAREMLN 35 (125)
T ss_dssp HHHHHHHHHHTTSG-GGHHHHHHHHHHHHS
T ss_pred HHHHHHHHHHHHcccchhHHHHHHHHHhcC
Confidence 455677788887776668888888888743
No 16
>PF02244 Propep_M14: Carboxypeptidase activation peptide; InterPro: IPR003146 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. The peptidases are synthesised as inactive molecules, zymogens, with propeptides that must be removed by proteolytic cleavage to activate the enzyme. Structural studies of carboxypeptidases A and B reveal the propeptide to exist as a globular domain, followed by an extended alpha-helix; this shields the catalytic site, without specifically binding to it, while the substrate-binding site is blocked by making specific contacts [, ]. Members of this propeptide family are found in the metallocarboxypeptidases: A1, A2 [], A3, A4, A5, A6, U, insect gut carboxypeptidase and B [], and and are associated with peptidases belonging to MEROPS peptidase family M14A. Carboxypeptidases are found in abundance in pancreatic secretions. The pro-segment moiety (activation peptide) accounts for up to a quarter of the total length of the peptidase.; GO: 0004180 carboxypeptidase activity, 0006508 proteolysis; PDB: 3D68_C 3D67_B 3D66_A 1PBA_A 3GLJ_A 1NSA_A 1KWM_A 2BOA_B 1PYT_A 1JQG_A ....
Probab=47.81 E-value=15 Score=24.11 Aligned_cols=38 Identities=26% Similarity=0.274 Sum_probs=26.2
Q ss_pred HHHHHHHHhCCCcccccccc-------ccccHHHHHHHHhHHHHH
Q psy1281 76 LITFIELIKNPVYKFWDHEF-------VHCAPEIEKLFESGWPLY 113 (144)
Q Consensus 76 litfiELikn~~y~Fw~~pF-------v~~~PEi~~lf~~v~~~~ 113 (144)
+-++-+|-++..|+||+.|- |.-+|+-..-|+...+..
T Consensus 11 ~~~L~~L~~~~~~dfW~~~~~~~~~~dv~V~p~~~~~f~~~L~~~ 55 (74)
T PF02244_consen 11 LELLQELEQSNELDFWKEPSSVGRPVDVMVPPEKLEEFEELLKEH 55 (74)
T ss_dssp HHHHHHHHHHSTEEEEESSSSTTSEEEEEEEGGGHHHHHHHHHHT
T ss_pred HHHHHHHhcccceeeecCCCCCCCeEEEEECHHHHHHHHHHHHHC
Confidence 44566777899999999998 333566666666665543
No 17
>PF12717 Cnd1: non-SMC mitotic condensation complex subunit 1
Probab=45.06 E-value=1.4e+02 Score=22.92 Aligned_cols=72 Identities=25% Similarity=0.308 Sum_probs=47.8
Q ss_pred ChHHHHHHHHHHHHh-hcCCCchHHHHHHHHHHHhhhcChhHHHHHHHHHHHHHhhcCCCC-chhHH-HHHHHHHhCC
Q psy1281 12 DTEGRYLFLNAIANQ-LRYPNSHTHYFSCLLLYLFAEANTEAIQEQITRVLLERLIVNRPH-PWGLL-ITFIELIKNP 86 (144)
Q Consensus 12 d~E~Ry~ll~aianq-LRYPN~HT~~Fs~~ll~LF~~~~~~~IqEqItRVLlERliv~rPH-PWGll-itfiELikn~ 86 (144)
|+..|-..+-+|.+- .||||.--.|-..+...|-.+ +..||++-..+|.. ++..-.- +.|-+ .-+..++.++
T Consensus 1 ~~~vR~n~i~~l~DL~~r~~~~ve~~~~~l~~~L~D~--~~~VR~~al~~Ls~-Li~~d~ik~k~~l~~~~l~~l~D~ 75 (178)
T PF12717_consen 1 DPSVRNNAIIALGDLCIRYPNLVEPYLPNLYKCLRDE--DPLVRKTALLVLSH-LILEDMIKVKGQLFSRILKLLVDE 75 (178)
T ss_pred CHHHHHHHHHHHHHHHHhCcHHHHhHHHHHHHHHCCC--CHHHHHHHHHHHHH-HHHcCceeehhhhhHHHHHHHcCC
Confidence 567888888888874 699987766655555544443 36899987666554 4444333 56666 6677777665
No 18
>cd07920 Pumilio Pumilio-family RNA binding domain. Puf repeats (also labelled PUM-HD or Pumilio homology domain) mediate sequence specific RNA binding in fly Pumilio, worm FBF-1 and FBF-2, and many other proteins such as vertebrate Pumilio. These proteins function as translational repressors in early embryonic development by binding to sequences in the 3' UTR of target mRNAs, such as the nanos response element (NRE) in fly Hunchback mRNA, or the point mutation element (PME) in worm fem-3 mRNA. Other proteins that contain Puf domains are also plausible RNA binding proteins. Yeast PUF1 (JSN1), for instance, appears to contain a single RNA-recognition motif (RRM) domain. Puf repeat proteins have been observed to function asymmetrically and may be responsible for creating protein gradients involved in the specification of cell fate and differentiation. Puf domains usually occur as a tandem repeat of 8 domains. This model encompasses all 8 tandem repeats. Some proteins may have fewer (canon
Probab=40.69 E-value=2e+02 Score=23.43 Aligned_cols=71 Identities=13% Similarity=0.149 Sum_probs=42.0
Q ss_pred HHHHHHhccChHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHhhhcChhHHHHHHHHHHHHHhhcCCCCchhH
Q psy1281 3 IFLNFAVDLDTEGRYLFLNAIANQLRYPNSHTHYFSCLLLYLFAEANTEAIQEQITRVLLERLIVNRPHPWGL 75 (144)
Q Consensus 3 i~~~L~~~ld~E~Ry~ll~aianqLRYPN~HT~~Fs~~ll~LF~~~~~~~IqEqItRVLlERliv~rPHPWGl 75 (144)
+++.++...++|.|-.+++++...+.--..| .|=+.++-.++..++ .+-++.|...+..++..--=||-|-
T Consensus 24 ~lQ~~l~~~~~~~~~~i~~~l~~~~~~l~~~-~~g~~vvq~~l~~~~-~~~~~~i~~~~~~~~~~l~~~~~g~ 94 (322)
T cd07920 24 FLQQKLEEATPEEKELIFDEILPHVVELMVD-PFGNYVIQKLFEHGT-EEQRLQLLEKILGHVVRLSLDMYGC 94 (322)
T ss_pred HHHHHhccCCHHHHHHHHHHHHHhHHHHhcC-ccccHHHHHHHHhCC-HHHHHHHHHHHHHHHHHHcccchhH
Confidence 5677777888888888888877666433333 245556666666654 3445555555555544444444443
No 19
>cd03562 CID CID (CTD-Interacting Domain) domain family; CID is present in several RNA-processing factors such as Pcf11 and Nrd1. Pcf11 is a conserved and essential subunit of the yeast cleavage factor IA, which is required for polyadenylation-dependent 3'-RNA processing and transcription termination. Nrd1 is implicated in polyadenylation-independent 3'-RNA processing. CID binds tightly to the carboxy-terminal domain (CTD) of RNA polymerase (Pol) II. During transcription, Pol II synthesizes eukaryotic messenger RNA. Transcription is coupled to RNA processing through the CTD, which consists of up to 52 repeats of the sequence Tyr 1-Ser 2-Pro 3-Thr 4-Ser 5-Pro 6-Ser 7. CID contains eight alpha-helices in a right-handed superhelical arrangement, which closely resembles that of the VHS domains and ARM (Armadillo) repeat proteins, except for its two amino-terminal helices.
Probab=38.77 E-value=1e+02 Score=21.80 Aligned_cols=55 Identities=22% Similarity=0.366 Sum_probs=35.5
Q ss_pred HHHHhccChHHH---HHHHHHHHHhhcCCCchHHHHHHHHHHHhhhc---ChhHHHHHHHHHH
Q psy1281 5 LNFAVDLDTEGR---YLFLNAIANQLRYPNSHTHYFSCLLLYLFAEA---NTEAIQEQITRVL 61 (144)
Q Consensus 5 ~~L~~~ld~E~R---y~ll~aianqLRYPN~HT~~Fs~~ll~LF~~~---~~~~IqEqItRVL 61 (144)
..-+...+++-| -|++++|+-+-+.|+. .+|...+..+|... .++.+++-|.|++
T Consensus 43 ~~~i~~~~~~~KL~~LYL~dsIvkn~~~~~~--~~~~~~~~~~f~~~~~~~~~~~r~kl~rl~ 103 (114)
T cd03562 43 EKHIKKCPPEQKLPLLYLLDSIVKNVGRKYK--EFFSEFLVPLFLDAYEKVDEKTRKKLERLL 103 (114)
T ss_pred HHHHHhCCcccchHHHHHHHHHHHHcccchH--HHHHHHHHHHHHHHHHhCCHHHHHHHHHHH
Confidence 334455555443 4789999999988854 35666666777543 2467777776654
No 20
>PF12755 Vac14_Fab1_bd: Vacuolar 14 Fab1-binding region
Probab=35.18 E-value=1.4e+02 Score=21.45 Aligned_cols=62 Identities=24% Similarity=0.283 Sum_probs=41.4
Q ss_pred HHHHHHhccChHHHHHHHHHHHHhhcC-CCchHHHHHHHHHHHhhhcC--hhHHHHHHHHHHHHHhh
Q psy1281 3 IFLNFAVDLDTEGRYLFLNAIANQLRY-PNSHTHYFSCLLLYLFAEAN--TEAIQEQITRVLLERLI 66 (144)
Q Consensus 3 i~~~L~~~ld~E~Ry~ll~aianqLRY-PN~HT~~Fs~~ll~LF~~~~--~~~IqEqItRVLlERli 66 (144)
.+...+.+-|...||+-..|+.|=.+- .+..=.+|..++-.|+.... ++.||. .-.+|.|++
T Consensus 31 pVL~~~~D~d~rVRy~AcEaL~ni~k~~~~~~l~~f~~IF~~L~kl~~D~d~~Vr~--~a~~Ld~ll 95 (97)
T PF12755_consen 31 PVLKCFDDQDSRVRYYACEALYNISKVARGEILPYFNEIFDALCKLSADPDENVRS--AAELLDRLL 95 (97)
T ss_pred HHHHHcCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCchhHHH--HHHHHHHHh
Confidence 345667788899999999999887654 33444478888877776543 344554 345666664
No 21
>PF12726 SEN1_N: SEN1 N terminal; InterPro: IPR024481 The yeast helicase Sen1 is an RNA polymerase II termination factor for noncoding RNA genes []. The C-terminal domain of Sen1 is essential for cell growth, while the N-terminal domain appears to be dispensible []. This entry represents the N-terminal domain.
Probab=34.19 E-value=36 Score=32.16 Aligned_cols=83 Identities=28% Similarity=0.371 Sum_probs=55.3
Q ss_pred HHHHHHHHhhcC-CCCchhHHHHHHHHHhCCCcccccc--cc--------ccccHHHHHHHHhHHHHHH----HHHHhHH
Q psy1281 57 ITRVLLERLIVN-RPHPWGLLITFIELIKNPVYKFWDH--EF--------VHCAPEIEKLFESGWPLYA----QLLIDIF 121 (144)
Q Consensus 57 ItRVLlERliv~-rPHPWGllitfiELikn~~y~Fw~~--pF--------v~~~PEi~~lf~~v~~~~~----q~l~~~~ 121 (144)
|.|.+++-+..+ .|+=+-++-++.-|++--.-+||+. |+ |..+|...+.+.+....-. .-+.|++
T Consensus 215 i~~L~~~hL~~~~~~~l~~lL~~l~~lL~k~~~~FW~~~~~~~p~~ild~If~np~f~~~L~~~~~~~~~~~~~~~~~~~ 294 (727)
T PF12726_consen 215 IYRLLLNHLSSNLSPPLPILLRCLSILLEKLGSDFWDAMGPISPQVILDQIFDNPAFKKLLLQSQEDEISESDDDLPDLL 294 (727)
T ss_pred HHHHHHHHhhcccchhHHHHHHHHHHHHHhCHHHHhcccCCCCHHHHHHHHhCChHHHHHHHhhccCCccccchhhHHHH
Confidence 788999999888 8888888889999999888999993 21 1222332222222221110 1278999
Q ss_pred hhhcccchhHHHHHHhhc
Q psy1281 122 KFLAPFLPQQQQQQQQSA 139 (144)
Q Consensus 122 ~~~~~~l~~~~~~~~~~~ 139 (144)
.++.||++--...++++|
T Consensus 295 sWi~pf~~SL~~~~~~~~ 312 (727)
T PF12726_consen 295 SWISPFLRSLSPSQRSQA 312 (727)
T ss_pred HHHHHHHHHhcccchhhH
Confidence 999999988754444444
No 22
>COG5057 LAG1 Phosphotyrosyl phosphatase activator [Cell division and chromosome partitioning / Signal transduction mechanisms]
Probab=31.62 E-value=37 Score=30.38 Aligned_cols=67 Identities=30% Similarity=0.486 Sum_probs=50.1
Q ss_pred HHHhccChHHHHHHHHHHHHhhc--CCCchHHHHHHHHHHHhhhc-----C------------hhHHHHHHHHHHHHHhh
Q psy1281 6 NFAVDLDTEGRYLFLNAIANQLR--YPNSHTHYFSCLLLYLFAEA-----N------------TEAIQEQITRVLLERLI 66 (144)
Q Consensus 6 ~L~~~ld~E~Ry~ll~aianqLR--YPN~HT~~Fs~~ll~LF~~~-----~------------~~~IqEqItRVLlERli 66 (144)
.+.++--+|..|++.+|--|+-| |-.-|-..|.|.+.-|..-+ . -+.+|+.|+.--||=+
T Consensus 113 ~~~~ea~~el~~Yl~~SfGN~~RiDYGtGHELnFm~~l~~L~~lGif~~~d~~a~V~~ifvkY~eimR~Li~~Y~LEPA- 191 (353)
T COG5057 113 SEYHEAVPELQYYLRNSFGNSIRIDYGTGHELNFMCYLYALYCLGIFGIADYGALVFTIFVKYLEIMRLLITKYTLEPA- 191 (353)
T ss_pred chhhHHHHHHHHHHHhccCceeeeccCCccchhHHHHHHHHHHccCCCcccccceehhhHHHHHHHHHHHHHheecccC-
Confidence 44566678999999999999977 88999999999987765432 1 0566777777666644
Q ss_pred cCCCC-chhH
Q psy1281 67 VNRPH-PWGL 75 (144)
Q Consensus 67 v~rPH-PWGl 75 (144)
..| -|||
T Consensus 192 --GSHGVWGL 199 (353)
T COG5057 192 --GSHGVWGL 199 (353)
T ss_pred --ccCCcccc
Confidence 556 8997
No 23
>cd03567 VHS_GGA VHS domain family, GGA subfamily; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprise a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (gamma-adaptin ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the trans-Golgi network and the endosomal system.
Probab=30.81 E-value=2.5e+02 Score=21.54 Aligned_cols=93 Identities=17% Similarity=0.299 Sum_probs=60.1
Q ss_pred cChHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHhhhcChhHHHHHHH-HHHHH---HhhcCC----CCchhHHHHHHHH
Q psy1281 11 LDTEGRYLFLNAIANQLRYPNSHTHYFSCLLLYLFAEANTEAIQEQIT-RVLLE---RLIVNR----PHPWGLLITFIEL 82 (144)
Q Consensus 11 ld~E~Ry~ll~aianqLRYPN~HT~~Fs~~ll~LF~~~~~~~IqEqIt-RVLlE---Rliv~r----PHPWGllitfiEL 82 (144)
.+++|--.-+.||...|.++|.|.-.++-.+|..-...-+..++.+|. +-.+. |++..+ ..|--+.--.++|
T Consensus 31 ~~~~~~k~a~rai~krl~~~n~~v~l~AL~LLe~~vkNCG~~fh~evas~~Fl~el~kl~~~k~~~~~~~~~Vk~kil~l 110 (139)
T cd03567 31 KEPEGPQLAVRLLAHKIQSPQEKEALQALTVLEACMKNCGERFHSEVGKFRFLNELIKLVSPKYLGSRTSEKVKTKIIEL 110 (139)
T ss_pred cCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCHHHHHHHHhHHHHHHHHHHhccccCCCCCCHHHHHHHHHH
Confidence 356677778999999999999999988888887765543355655554 44443 333321 1355677777777
Q ss_pred HhCCCccccccccccccHHHHHHHHhH
Q psy1281 83 IKNPVYKFWDHEFVHCAPEIEKLFESG 109 (144)
Q Consensus 83 ikn~~y~Fw~~pFv~~~PEi~~lf~~v 109 (144)
+.. |...|- ..|.+...++.+
T Consensus 111 i~~-----W~~~f~-~~p~~~~~Y~~L 131 (139)
T cd03567 111 LYS-----WTLELP-HEPKIKEAYDML 131 (139)
T ss_pred HHH-----HHHHhc-ccchHHHHHHHH
Confidence 764 666664 346665555544
No 24
>PF04818 CTD_bind: RNA polymerase II-binding domain.; InterPro: IPR006903 This entry represents a conserved region found in a number of uncharacterised eukaryotic proteins.; PDB: 2L0I_A 2KM4_A 3D9I_B 3D9N_B 3D9O_A 3D9P_B 3D9K_A 3D9M_A 3D9J_A 3D9L_A ....
Probab=29.84 E-value=49 Score=21.39 Aligned_cols=45 Identities=24% Similarity=0.332 Sum_probs=31.2
Q ss_pred HHHHHHHHHhhcCCCchH--HHHHHHHHHHhhhcC---hhHHHHHHHHHH
Q psy1281 17 YLFLNAIANQLRYPNSHT--HYFSCLLLYLFAEAN---TEAIQEQITRVL 61 (144)
Q Consensus 17 y~ll~aianqLRYPN~HT--~~Fs~~ll~LF~~~~---~~~IqEqItRVL 61 (144)
.|++++++-+-|-.+.++ .-|+..+-.+|.... +++.++.+.|++
T Consensus 5 lYl~ndI~q~sk~k~~~~f~~~F~~~l~~~~~~~~~~~~~~~~~kv~rll 54 (64)
T PF04818_consen 5 LYLANDILQNSKRKNPDEFAPAFSPVLPDAFAHAYKNVDPEVRKKVQRLL 54 (64)
T ss_dssp HHHHHHHHHHHHHHTTHCHHHHHHCCHHHHHHHHCCCS-HHHHHHHHHHH
T ss_pred eehHHHHHHHhhhcChHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHH
Confidence 467778887777655544 477888888886643 577888888775
No 25
>PF07875 Coat_F: Coat F domain; InterPro: IPR012851 The Coat F proteins contribute to the Bacillales spore coat. They occur multiple times in the genomes in which they are found. Bacillus subtilis endospore protein coats protect them and may play a role in their germination []. Spore coat protein F, on the outer surface of the endospore, is one of a suite of proteins that could be used to differentiate between members of the Bacillus genus [].
Probab=28.21 E-value=1.2e+02 Score=19.76 Aligned_cols=26 Identities=15% Similarity=0.476 Sum_probs=22.4
Q ss_pred cHHHHHHHHhHHHHHHHHHHhHHhhh
Q psy1281 99 APEIEKLFESGWPLYAQLLIDIFKFL 124 (144)
Q Consensus 99 ~PEi~~lf~~v~~~~~q~l~~~~~~~ 124 (144)
+|++++.|.++.....+.=-++|.++
T Consensus 29 np~lR~~l~~~~~~~~~~~~~l~~~m 54 (64)
T PF07875_consen 29 NPELRQILQQILNECQQMQYELFNYM 54 (64)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 69999999999999988777888775
No 26
>COG4458 SrfC Uncharacterized protein conserved in bacteria, putative virulence factor [Function unknown]
Probab=26.75 E-value=73 Score=31.35 Aligned_cols=64 Identities=19% Similarity=0.134 Sum_probs=51.1
Q ss_pred HHHHHHhccChHHHHHHHHHHHHhhc---CCCchHHHHHHHHHHHhhhcChhHHHHHHHHHHHHHhhcC
Q psy1281 3 IFLNFAVDLDTEGRYLFLNAIANQLR---YPNSHTHYFSCLLLYLFAEANTEAIQEQITRVLLERLIVN 68 (144)
Q Consensus 3 i~~~L~~~ld~E~Ry~ll~aianqLR---YPN~HT~~Fs~~ll~LF~~~~~~~IqEqItRVLlERliv~ 68 (144)
+..+|.....+|.||.=+..-.++|+ --|.-|+|+..=+...+.+. ..+-|++.++|-+|.-|+
T Consensus 495 l~eyLs~i~lpeiK~~rLqeql~el~he~~~nlf~~wyqsd~~~e~a~k--r~~ve~llk~Lq~q~gvh 561 (821)
T COG4458 495 LAEYLSAICLPEIKYGRLQEQLGELAHEIRRNLFPYWYQSDINKEIAEK--REVVEQLLKCLQEQFGVH 561 (821)
T ss_pred HHHHHHHHhcchhhHHHHHHHHHHHHHHHHhhcccccccccccHHHHHH--HHHHHHHHHHHHHHhhHH
Confidence 56778888999999999999999888 45666778877777777664 578899999999986553
No 27
>PF11573 Med23: Mediator complex subunit 23; InterPro: IPR021629 Med23 is one of the subunits of the Tail portion of the Mediator complex that regulates RNA polymerase II activity. Med23 is required for heat-shock-specific gene expression, and has been shown to mediate transcriptional activation of E1A in mice.
Probab=26.25 E-value=3.1e+02 Score=28.95 Aligned_cols=82 Identities=20% Similarity=0.307 Sum_probs=45.9
Q ss_pred HHHHhccChHHHHHHHHHHHHhhcC------CCchHHHHHHHHHHHhhhcC-hhHHHHHHHHHHHHHh-------hcCCC
Q psy1281 5 LNFAVDLDTEGRYLFLNAIANQLRY------PNSHTHYFSCLLLYLFAEAN-TEAIQEQITRVLLERL-------IVNRP 70 (144)
Q Consensus 5 ~~L~~~ld~E~Ry~ll~aianqLRY------PN~HT~~Fs~~ll~LF~~~~-~~~IqEqItRVLlERl-------iv~rP 70 (144)
..|+..|+.-+|-.++.+|+++++= |-.-+.==+-.+..-.+.-- -.++.-...|-+.--+ .+.++
T Consensus 540 m~lLd~LT~h~k~sL~~~i~~~l~~~a~~k~~~P~~~~~s~alvETY~rlL~~~eiesL~~r~l~s~~~~~~~~~~~~k~ 619 (1341)
T PF11573_consen 540 MSLLDSLTVHSKMSLIHSIVTHLFKFAQSKQPVPAVFETSPALVETYSRLLVYKEIESLGIRSLASQLVPDRSPNTVQKS 619 (1341)
T ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHhcccCCCCCchhhhHHHHHHHHHHHHHHHHHHHHHHhHhHHhhcccccccccccc
Confidence 3578889999999999999988772 11101101111111111100 0112112233333222 35788
Q ss_pred CchhHHHHHHHHHhCC
Q psy1281 71 HPWGLLITFIELIKNP 86 (144)
Q Consensus 71 HPWGllitfiELikn~ 86 (144)
+-||++.++.|++..+
T Consensus 620 ~a~~~l~~LlEilsYR 635 (1341)
T PF11573_consen 620 QAWGQLHTLLEILSYR 635 (1341)
T ss_pred cchHHHHHHHHHHHhc
Confidence 9999999999999876
No 28
>PF02985 HEAT: HEAT repeat; InterPro: IPR000357 The HEAT repeat is a tandemly repeated, 37-47 amino acid long module occurring in a number of cytoplasmic proteins, including the four name-giving proteins huntingtin, elongation factor 3 (EF3), the 65 Kd alpha regulatory subunit of protein phosphatase 2A (PP2A) and the yeast PI3-kinase TOR1 []. Arrays of HEAT repeats consists of 3 to 36 units forming a rod-like helical structure and appear to function as protein-protein interaction surfaces. It has been noted that many HEAT repeat-containing proteins are involved in intracellular transport processes. In the crystal structure of PP2A PR65/A [], the HEAT repeats consist of pairs of antiparallel alpha helices [].; GO: 0005515 protein binding; PDB: 3FGA_A 2PF4_C 2IAE_A 2BKU_D 3EA5_B 3ND2_A 2BPT_A 2NYL_A 2NPP_D 2PKG_B ....
Probab=25.85 E-value=1e+02 Score=17.11 Aligned_cols=24 Identities=21% Similarity=0.205 Sum_probs=16.9
Q ss_pred hHHHHHHhccChHHHHHHHHHHHH
Q psy1281 2 DIFLNFAVDLDTEGRYLFLNAIAN 25 (144)
Q Consensus 2 ~i~~~L~~~ld~E~Ry~ll~aian 25 (144)
..+..++.+-+++.|+.-+.++.+
T Consensus 3 p~l~~~l~D~~~~VR~~a~~~l~~ 26 (31)
T PF02985_consen 3 PILLQLLNDPSPEVRQAAAECLGA 26 (31)
T ss_dssp HHHHHHHT-SSHHHHHHHHHHHHH
T ss_pred HHHHHHcCCCCHHHHHHHHHHHHH
Confidence 456778888888888877776654
No 29
>PF14514 TetR_C_9: Transcriptional regulator, TetR, C-terminal; PDB: 2QTQ_D 2RHA_A.
Probab=25.70 E-value=2.6e+02 Score=20.92 Aligned_cols=99 Identities=26% Similarity=0.333 Sum_probs=45.5
Q ss_pred HHHHHHHHHHHhhcCCCchHHHHHHHHHHHhhhcCh---hHHHHHH-------HHHHHHHhh---cCCCC-chhHHHHHH
Q psy1281 15 GRYLFLNAIANQLRYPNSHTHYFSCLLLYLFAEANT---EAIQEQI-------TRVLLERLI---VNRPH-PWGLLITFI 80 (144)
Q Consensus 15 ~Ry~ll~aianqLRYPN~HT~~Fs~~ll~LF~~~~~---~~IqEqI-------tRVLlERli---v~rPH-PWGllitfi 80 (144)
.|.++-..+=...+|| |+..++..+-.+.+. ..+-++. .+-++||-+ +-||. |.=+-++.+
T Consensus 8 lR~~i~~~i~~y~~~P-----~~~rL~~~~l~~~~~~~~~~~~~~~~~P~~~~l~~il~~GvaaG~fR~vDP~~~y~si~ 82 (129)
T PF14514_consen 8 LRRHIAGVIRYYFDFP-----YLNRLLNRLLHEAEHERARRLIEQFISPLVDALRRILEEGVAAGVFRPVDPRLFYISII 82 (129)
T ss_dssp HHHHHHHHHHHHHH-T-----THHHHHHHHHHHS-HHHHHHHHHHHTHHHHHHHHHHHHHHHHTTSB-S--HHHHHHHHH
T ss_pred HHHHHHHHHHHHHhCC-----cHHHHHHHHHhcccHHHHHHHHHHHHhhHHHHHHHHHHHHHHcCCCcCCCHHHHHHHHH
Confidence 3555555566677888 666666553332221 1222221 234456655 56788 555556666
Q ss_pred HHHhCCCccccccccccccHHHHHHHHhHHHHHHHHHHhHH
Q psy1281 81 ELIKNPVYKFWDHEFVHCAPEIEKLFESGWPLYAQLLIDIF 121 (144)
Q Consensus 81 ELikn~~y~Fw~~pFv~~~PEi~~lf~~v~~~~~q~l~~~~ 121 (144)
-++-.- |-+++-++....++.+=+.+.+.+.+|.+|+.
T Consensus 83 gl~~~~---fs~r~~l~~~~g~d~~s~~~~~~~~~h~~~li 120 (129)
T PF14514_consen 83 GLCYFY---FSNRHTLSAVFGVDLLSDEVRERYAEHVVDLI 120 (129)
T ss_dssp HHHHHH---HHHHHHHHHHH--SSSSHHHHHHHHHHHHHHH
T ss_pred HHHHHH---HhhHHHHHHHcCCCCCCHHHHHHHHHHHHHHH
Confidence 566432 22322222221122222345566777777764
No 30
>COG5099 RNA-binding protein of the Puf family, translational repressor [Translation, ribosomal structure and biogenesis]
Probab=24.87 E-value=1.3e+02 Score=29.70 Aligned_cols=72 Identities=13% Similarity=0.181 Sum_probs=50.2
Q ss_pred HHHHHhccChHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHhhhcChhHHHHHHHHHHHHHhhcCCCCchhHHH
Q psy1281 4 FLNFAVDLDTEGRYLFLNAIANQLRYPNSHTHYFSCLLLYLFAEANTEAIQEQITRVLLERLIVNRPHPWGLLI 77 (144)
Q Consensus 4 ~~~L~~~ld~E~Ry~ll~aianqLRYPN~HT~~Fs~~ll~LF~~~~~~~IqEqItRVLlERliv~rPHPWGlli 77 (144)
.+..+..+..|-.-.++.++.++++ -=+++.|.++++-.+|+.++. +.+|.|+-.++-=....-+-+||..+
T Consensus 565 iqKci~~~~~~~~~fif~~~~~~~~-~is~~r~Gs~vvq~~le~~~~-~~~~~~~~~Ii~~~~~L~~dq~GNyv 636 (777)
T COG5099 565 IQKCIEKFNKEKNQFIFDSINENLY-DLSTHRYGSRVVQRCLENCNS-EDKENLVEEIISNSKYLSQDQYGNYV 636 (777)
T ss_pred HHHHHHhcCccccchHHHHHHhhhH-hhhccccccHHHHHHHHhccH-hHHHHHHHHHHHHHHhhccCCcchhh
Confidence 4455666677777777888888776 446777999999999999863 44455555555444455567999755
No 31
>PF09324 DUF1981: Domain of unknown function (DUF1981); InterPro: IPR015403 This domain is functionally uncharacterised and found in various plant and yeast protein transport proteins. It is noramlly associated with and C-termianl to the SEC7 domain. The SEC7 domain was named after the first protein found to contain such a region []. It has been shown to be linked with guanine nucleotide exchange function [, ].
Probab=24.77 E-value=93 Score=21.70 Aligned_cols=46 Identities=13% Similarity=0.340 Sum_probs=29.1
Q ss_pred HHHHhhhcChhHHHHHHHHHHHHHhhcCCC---CchhHHHHHHHHHhCC
Q psy1281 41 LLYLFAEANTEAIQEQITRVLLERLIVNRP---HPWGLLITFIELIKNP 86 (144)
Q Consensus 41 ll~LF~~~~~~~IqEqItRVLlERliv~rP---HPWGllitfiELikn~ 86 (144)
+..++....+.+|||.|.+++.+=+-.... +=|-.+.-.+....+.
T Consensus 22 f~~i~~~~~~~~vre~il~ci~qil~~~~~~i~SGW~~if~il~~aa~~ 70 (86)
T PF09324_consen 22 FEYIMSNNPSIDVRELILECILQILQSRGENIKSGWKVIFSILRAAAKD 70 (86)
T ss_pred HHHHHhccCcHHHHHHHHHHHHHHHHHhHHHHHhccHHHHHHHHHHHhC
Confidence 344445555689999999998765543222 2577776666666553
No 32
>KOG1763|consensus
Probab=24.33 E-value=1.2e+02 Score=27.16 Aligned_cols=41 Identities=22% Similarity=0.340 Sum_probs=28.2
Q ss_pred HHHHHHHHhhcCCCCchhHHHHHHHHHhCCCcc-cccccccc
Q psy1281 57 ITRVLLERLIVNRPHPWGLLITFIELIKNPVYK-FWDHEFVH 97 (144)
Q Consensus 57 ItRVLlERliv~rPHPWGllitfiELikn~~y~-Fw~~pFv~ 97 (144)
...|.++.-=-++|..--+.=.|+|-+.|.+|+ ||++|+-.
T Consensus 140 l~~vv~~K~~k~k~~tdiVCKfFLeAvE~~kYGWfW~CPnGg 181 (343)
T KOG1763|consen 140 LEEVVLKKHGKPKPTTDIVCKFFLEAVENGKYGWFWECPNGG 181 (343)
T ss_pred HHHHHHhhccCCCCchhHHHHHHHHHHhcCCccceeECCCCC
Confidence 444444443333333444889999999999997 89999843
No 33
>PF12717 Cnd1: non-SMC mitotic condensation complex subunit 1
Probab=24.16 E-value=3.3e+02 Score=20.83 Aligned_cols=38 Identities=26% Similarity=0.251 Sum_probs=17.4
Q ss_pred HHHhccChHHHHHHHHHHHHhhc--CCCchHHHHHHHHHH
Q psy1281 6 NFAVDLDTEGRYLFLNAIANQLR--YPNSHTHYFSCLLLY 43 (144)
Q Consensus 6 ~L~~~ld~E~Ry~ll~aianqLR--YPN~HT~~Fs~~ll~ 43 (144)
.++.+-|++.|-.-...+.+-++ +||.-.+-|..++-.
T Consensus 70 ~~l~D~~~~Ir~~A~~~~~e~~~~~~~~~i~~~~~e~i~~ 109 (178)
T PF12717_consen 70 KLLVDENPEIRSLARSFFSELLKKRNPNIIYNNFPELISS 109 (178)
T ss_pred HHHcCCCHHHHHHHHHHHHHHHHhccchHHHHHHHHHHHH
Confidence 34455555555444433333322 355555555554443
No 34
>PF12243 CTK3: CTD kinase subunit gamma CTK3
Probab=22.57 E-value=3.7e+02 Score=20.84 Aligned_cols=56 Identities=23% Similarity=0.249 Sum_probs=39.8
Q ss_pred HHHHHHHHHhhcCCCchHH----HHHHHHHHHhhhcC--h----hHHHHHHHHHHHHHhhcCCCCchhH
Q psy1281 17 YLFLNAIANQLRYPNSHTH----YFSCLLLYLFAEAN--T----EAIQEQITRVLLERLIVNRPHPWGL 75 (144)
Q Consensus 17 y~ll~aianqLRYPN~HT~----~Fs~~ll~LF~~~~--~----~~IqEqItRVLlERliv~rPHPWGl 75 (144)
-.+.++|.++|+=+|.+|. ||...+...+...+ . ..++.-|-|++ -.|.+|-.||.
T Consensus 39 edL~~cIle~le~~~lN~R~nI~~fID~l~e~~~~~~~~~~~Yv~~l~~dL~~Iv---~~V~P~~~~g~ 104 (139)
T PF12243_consen 39 EDLWSCILEQLEKENLNTRINIFYFIDSLCESSQKSKKYNYPYVSMLQRDLPRIV---DAVAPPDNSGA 104 (139)
T ss_pred HHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHHhcccccchhHHHHHHHHHHHH---HHhCCCCCccc
Confidence 3578999999999999987 77777777776554 2 44555555555 23667778975
No 35
>PF11458 Mistic: Membrane-integrating protein Mistic; InterPro: IPR021078 Mistic is an integral membrane protein that folds autonomously into the membrane []. It is conserved in the Bacilli bacteria. The protein forms a helical bundle with a polar lipid-facing surface. Mistic can be used for high-level production of other membrane proteins in their native conformations [].
Probab=21.02 E-value=2.5e+02 Score=20.49 Aligned_cols=45 Identities=29% Similarity=0.350 Sum_probs=36.0
Q ss_pred HHHHHHHHhCCCccccccccccccHHHHHHHHhHHHHHHH-----HHHhHHhh
Q psy1281 76 LITFIELIKNPVYKFWDHEFVHCAPEIEKLFESGWPLYAQ-----LLIDIFKF 123 (144)
Q Consensus 76 litfiELikn~~y~Fw~~pFv~~~PEi~~lf~~v~~~~~q-----~l~~~~~~ 123 (144)
+=||++|..+..- |.|.+.-..|-+++......+++| +|+-++|=
T Consensus 22 LD~fI~lYNeSe~---DepLiql~detael~~~A~~~yG~e~~n~klN~iIkq 71 (84)
T PF11458_consen 22 LDTFIQLYNESEK---DEPLIQLEDETAELIRQAREKYGQEKLNEKLNAIIKQ 71 (84)
T ss_pred HHHHHHHHccccc---ccchhhcchhHHHHHHHHHHHHhHHHHHHHHHHHHHH
Confidence 4589999988643 689999999999999998888865 77777764
No 36
>COG5336 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.56 E-value=58 Score=25.12 Aligned_cols=20 Identities=30% Similarity=0.846 Sum_probs=12.3
Q ss_pred HHHHHHhhcCCCCchhHHHHHH
Q psy1281 59 RVLLERLIVNRPHPWGLLITFI 80 (144)
Q Consensus 59 RVLlERliv~rPHPWGllitfi 80 (144)
-.|+.|.. .-.|||+++..+
T Consensus 63 G~llD~~a--gTsPwglIv~ll 82 (116)
T COG5336 63 GWLLDKFA--GTSPWGLIVFLL 82 (116)
T ss_pred HHHHHHhc--CCCcHHHHHHHH
Confidence 34455553 345899998654
No 37
>TIGR01609 PF_unchar_267 Plasmodium falciparum uncharacterized protein TIGR01609. This model represents a family of at least four proteins in Plasmodium falciparum. An interesting feature is five perfectly conserved Trp residues.
Probab=20.34 E-value=3.1e+02 Score=21.87 Aligned_cols=59 Identities=20% Similarity=0.314 Sum_probs=40.0
Q ss_pred HHHHHHhhcCCCCchh--HHHHHH-HHHhCCCccccccccccccHH----HHHHHHhHHHHHHHHHHhHH
Q psy1281 59 RVLLERLIVNRPHPWG--LLITFI-ELIKNPVYKFWDHEFVHCAPE----IEKLFESGWPLYAQLLIDIF 121 (144)
Q Consensus 59 RVLlERliv~rPHPWG--llitfi-ELikn~~y~Fw~~pFv~~~PE----i~~lf~~v~~~~~q~l~~~~ 121 (144)
|++.|+. ..-+||- ..++.- +-++|+.++ +.|..++.|| +..|+.++.+....-+.|+.
T Consensus 5 ri~~e~~--~~~~~wk~~f~~~~n~~~~~~~~~~--~~~~~~~~~e~i~~l~eL~~k~s~~Wk~~i~~M~ 70 (146)
T TIGR01609 5 RILSEQH--DQKNDWRNEFSLVINEEELKNIPEE--DQLGEQQEPEYIYKLNELCKNASKYWKNAIKDME 70 (146)
T ss_pred HHHHHHh--hcccchhhhhhhhccHHhccCcccc--cCCCcccCchhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5666665 3467885 444443 456677788 9999998765 66778777777777776664
Done!