Query 046621
Match_columns 213
No_of_seqs 167 out of 416
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 02:44:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046621.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046621hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2669 Regulator of nuclear m 100.0 2.6E-42 5.6E-47 306.6 15.7 205 4-209 2-208 (325)
2 smart00582 RPR domain present 100.0 2E-29 4.3E-34 195.5 10.9 118 10-127 1-120 (121)
3 cd03562 CID CID (CTD-Interacti 99.9 1.7E-26 3.7E-31 177.7 12.4 114 5-121 1-114 (114)
4 PF04818 CTD_bind: RNA polymer 99.8 8.3E-21 1.8E-25 132.5 5.9 63 58-120 1-64 (64)
5 KOG0151 Predicted splicing reg 99.7 2E-17 4.3E-22 158.0 11.4 129 8-136 433-575 (877)
6 PF12243 CTK3: CTD kinase subu 99.7 6E-16 1.3E-20 123.9 12.1 126 4-129 2-134 (139)
7 KOG4368 Predicted RNA binding 99.5 7.3E-14 1.6E-18 131.5 9.9 183 5-210 100-291 (757)
8 KOG0132 RNA polymerase II C-te 98.6 7E-08 1.5E-12 94.1 7.9 125 9-134 5-139 (894)
9 KOG2071 mRNA cleavage and poly 98.1 8.2E-06 1.8E-10 78.1 7.8 103 9-114 7-110 (579)
10 cd00197 VHS_ENTH_ANTH VHS, ENT 96.7 0.037 7.9E-07 42.2 10.6 92 21-115 17-115 (115)
11 PF00790 VHS: VHS domain; Int 95.4 0.22 4.9E-06 39.4 9.9 91 23-116 24-119 (140)
12 cd03561 VHS VHS domain family; 94.5 0.71 1.5E-05 36.3 10.6 95 22-121 18-116 (133)
13 smart00288 VHS Domain present 93.8 1.2 2.6E-05 35.1 10.5 90 23-115 19-111 (133)
14 cd03569 VHS_Hrs_Vps27p VHS dom 93.3 1.6 3.5E-05 34.9 10.7 106 11-121 5-118 (142)
15 cd03568 VHS_STAM VHS domain fa 91.8 3.3 7.1E-05 33.2 10.6 90 23-115 19-110 (144)
16 cd03567 VHS_GGA VHS domain fam 91.2 4.5 9.8E-05 32.3 10.8 91 25-120 22-119 (139)
17 KOG1087 Cytosolic sorting prot 82.9 9.3 0.0002 36.7 9.3 83 30-115 27-112 (470)
18 cd03565 VHS_Tom1 VHS domain fa 71.9 48 0.001 26.3 10.3 94 23-121 20-119 (141)
19 PF01417 ENTH: ENTH domain; I 64.4 34 0.00074 26.2 6.8 90 21-114 20-120 (125)
20 PF01603 B56: Protein phosphat 63.0 27 0.00059 32.5 7.0 92 22-119 236-327 (409)
21 PF03392 OS-D: Insect pheromon 47.2 29 0.00062 26.0 3.6 39 77-115 34-72 (95)
22 KOG2085 Serine/threonine prote 36.3 1.2E+02 0.0025 29.0 6.5 76 36-117 294-369 (457)
23 KOG4353 RNA export factor NXT1 34.1 24 0.00053 28.2 1.4 63 27-91 4-68 (139)
24 KOG2199 Signal transducing ada 31.9 4.6E+02 0.0099 25.1 9.5 106 8-122 6-123 (462)
25 PF11357 Spy1: Cell cycle regu 31.7 86 0.0019 25.0 4.2 50 23-72 13-69 (131)
26 PF14733 ACDC: AP2-coincident 29.8 2.2E+02 0.0047 20.6 7.6 66 57-122 8-78 (91)
27 PF12652 CotJB: CotJB protein; 29.7 1.2E+02 0.0026 21.9 4.4 35 174-208 16-50 (78)
28 PF07261 DnaB_2: Replication i 26.0 1.7E+02 0.0037 19.8 4.6 40 82-122 29-69 (77)
29 PF12348 CLASP_N: CLASP N term 25.8 3.7E+02 0.0081 22.0 9.7 99 21-123 24-131 (228)
30 TIGR02753 sodN superoxide dism 21.0 4.6E+02 0.0099 21.3 8.4 64 10-73 43-114 (145)
31 PF08926 DUF1908: Domain of un 20.0 4.8E+02 0.01 23.5 7.1 51 62-112 169-225 (282)
No 1
>KOG2669 consensus Regulator of nuclear mRNA [RNA processing and modification]
Probab=100.00 E-value=2.6e-42 Score=306.57 Aligned_cols=205 Identities=36% Similarity=0.590 Sum_probs=177.9
Q ss_pred CCCCHHHHHHHHhhccCcHHHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhcChhHHHHH
Q 046621 4 EAFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNEF 83 (213)
Q Consensus 4 ~~F~~~~~~~kL~~L~~Sq~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk~~~f~~~F 83 (213)
.+|+++.|..||++|++||+|||++|.|||+|+++|+.||++|+++|++++.++||.||||||||+|||+|++++|+++|
T Consensus 2 ~~fsee~l~~kL~~L~~TQeSIqtlS~Wli~hkk~a~~IV~~Wl~~~~~~~~~~Kl~llYLaNDVvQnskrk~~ef~~ef 81 (325)
T KOG2669|consen 2 SAFSEEALEKKLAELSNTQESIQTLSLWLIHHKKHARLIVDVWLKELKKSSVNHKLTLLYLANDVVQNSKRKGPEFVDEF 81 (325)
T ss_pred CcccHHHHHHHHHhccchHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhccCCCceeeehhhhHHHHHHhhhcCchhHHHH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhcCChHHHHhHHHHHHHhhhCcccCCCccchhhhhhCCC-CCCCCCCCCCCCCcccccccccchhhhh
Q 046621 84 WKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSRGQGLKDEMLGKN-PPPVPASNGRSSNPIKIVKRDANSVRIK 162 (213)
Q Consensus 84 ~~vLp~~~~~v~~~~d~~~~~kv~rll~IWeeR~Vf~~~~~~L~~~~lg~~-p~~~~~~~~~~~~~~k~~~~~~~s~~~~ 162 (213)
+++++.+|.+++..++..++.++.|||+||++|+||+++......++++.. |||.....+ ..+..+..+++.....+.
T Consensus 82 ~~v~~~a~~~i~~~~~~~~k~~l~Rl~nIw~eR~Vf~~~~~~~l~~~l~~e~p~~~d~~~~-~~~~~~~~k~~~~~~~~~ 160 (325)
T KOG2669|consen 82 WPVVLKAFAHIVEETDVKCKKKLGRLINIWEERNVFSPESLVDLEESLGAEKPPPLDEAKK-LPRGSKQIKLDEKGSKPG 160 (325)
T ss_pred HHHHHHHHHHHHHhcchhhhHHHHHHHHHHHHhccCCHHHHHHHHHHhcccCCcchhhhhc-cccchHhhhhhhhccCCC
Confidence 999999999999998888899999999999999999999866666777644 444333332 223445666665554444
Q ss_pred -cccCCChHHHHHHHHHHHhhCCChHHHHHHhHHHHHHHhhhhhhhhc
Q 046621 163 -LAVGALPEKILTAFQSVLDEHPNEEVALNNCNAAVHHAGKVSEDVEN 209 (213)
Q Consensus 163 -~~~~~~~eki~~~~~~~~~~~~~e~~~~~k~~~~~~~~~~~~~~~~~ 209 (213)
...|+++++|.+.++.+-+....+++.+..|+.+..++++|.+++..
T Consensus 161 ~~~~~~v~~~~~~~~~l~~a~~s~~~~~~k~~~~~~~~i~~~~~e~~e 208 (325)
T KOG2669|consen 161 LSSLGEVHEKIDSSVELVRALQSLENAASKLDAVLEERIARLPQEVEE 208 (325)
T ss_pred CCCccccchhHHhHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence 45689999999999888888888999999999999999999888763
No 2
>smart00582 RPR domain present in proteins, which are involved in regulation of nuclear pre-mRNA.
Probab=99.96 E-value=2e-29 Score=195.46 Aligned_cols=118 Identities=42% Similarity=0.734 Sum_probs=111.6
Q ss_pred HHHHHHhhccCcHHHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhc-ChhHHHHHHHHHH
Q 046621 10 ILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRK-GSEFVNEFWKVLP 88 (213)
Q Consensus 10 ~~~~kL~~L~~Sq~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk-~~~f~~~F~~vLp 88 (213)
.|.++|++|++|+++|++++.||++|.+++..||++|.+++.++++++||++|||+|||+|||+++ ++.|..+|.++++
T Consensus 1 ~f~~~L~~L~~s~~~I~~lt~~~~~~~~~a~~Iv~~i~~~~~~~~~~~kL~~LYlindIl~n~~~~~~~~f~~~~~~~~~ 80 (121)
T smart00582 1 AFEQKLESLNNSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPPPRKLPLLYLLDSIVQNSKRKYGSEFGDELGPVFQ 80 (121)
T ss_pred ChHHHHHhccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccceehhHHhHHHHHHHHhhccHHHHHHHHHHHHH
Confidence 488999999999999999999999999999999999999999999999999999999999999988 5789999999999
Q ss_pred HHHHHHhhcCChHHHHhHHHHHHHhhhCcccCCCc-cchh
Q 046621 89 AALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSRG-QGLK 127 (213)
Q Consensus 89 ~~~~~v~~~~d~~~~~kv~rll~IWeeR~Vf~~~~-~~L~ 127 (213)
.++.+++..+++..++++.+||+||++|+||++++ .+|+
T Consensus 81 ~~~~~~~~~~~~~~~~ki~kll~iW~~~~iF~~~~i~~L~ 120 (121)
T smart00582 81 DALRDVLGAANDETKKKIRRLLNIWEERGIFPPSVLRPLR 120 (121)
T ss_pred HHHHHHHHhCCHHHHHHHHHHHHHHhcCCCCCHHHHHHhh
Confidence 99999998878899999999999999999999986 5554
No 3
>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=99.94 E-value=1.7e-26 Score=177.71 Aligned_cols=114 Identities=43% Similarity=0.640 Sum_probs=104.6
Q ss_pred CCCHHHHHHHHhhccCcHHHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhcChhHHHHHH
Q 046621 5 AFDGQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNEFW 84 (213)
Q Consensus 5 ~F~~~~~~~kL~~L~~Sq~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk~~~f~~~F~ 84 (213)
.|+.+.+.++|..+++|+++|++++.||++|.++++.||++|.+++.++++.+||++|||+|||+||+++++..+ |.
T Consensus 1 ~~~~~~~l~~L~~~~~S~~~I~~lt~~a~~~~~~a~~iv~~i~~~i~~~~~~~KL~~LYL~dsIvkn~~~~~~~~---~~ 77 (114)
T cd03562 1 VFDYNALLEKLTFNKNSQPSIQTLTKLAIENRKHAKEIVEIIEKHIKKCPPEQKLPLLYLLDSIVKNVGRKYKEF---FS 77 (114)
T ss_pred CccHHHHHHHHHcCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccchHHHHHHHHHHHHcccchHHH---HH
Confidence 367788899999999999999999999999999999999999999999999999999999999999999886543 55
Q ss_pred HHHHHHHHHHhhcCChHHHHhHHHHHHHhhhCcccCC
Q 046621 85 KVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGS 121 (213)
Q Consensus 85 ~vLp~~~~~v~~~~d~~~~~kv~rll~IWeeR~Vf~~ 121 (213)
..++++|.+++..+|+.+++++.||++||++|++|++
T Consensus 78 ~~~~~~f~~~~~~~~~~~r~kl~rl~~iW~~~~~f~~ 114 (114)
T cd03562 78 EFLVPLFLDAYEKVDEKTRKKLERLLNIWEERFVFGS 114 (114)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHHccCCCCCCC
Confidence 5568899999988999999999999999999999984
No 4
>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=99.83 E-value=8.3e-21 Score=132.53 Aligned_cols=63 Identities=54% Similarity=0.899 Sum_probs=59.1
Q ss_pred hhHHHHHhHHHHHHhhhcCh-hHHHHHHHHHHHHHHHHhhcCChHHHHhHHHHHHHhhhCcccC
Q 046621 58 RVSFLYLANDILQNSRRKGS-EFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFG 120 (213)
Q Consensus 58 KL~lLYLaNDIlqnskrk~~-~f~~~F~~vLp~~~~~v~~~~d~~~~~kv~rll~IWeeR~Vf~ 120 (213)
||++|||+|||+|||++++. +|.++|+++||++|.+++..++++.++++.||++||++|+||+
T Consensus 1 KL~~lYl~ndI~q~sk~k~~~~f~~~F~~~l~~~~~~~~~~~~~~~~~kv~rll~iW~~r~if~ 64 (64)
T PF04818_consen 1 KLALLYLANDILQNSKRKNPDEFAPAFSPVLPDAFAHAYKNVDPEVRKKVQRLLNIWEERNIFS 64 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHTTHCHHHHHHCCHHHHHHHHCCCS-HHHHHHHHHHHHHHHHCTSS-
T ss_pred CcceeehHHHHHHHhhhcChHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHhhCCCCCC
Confidence 79999999999999999885 9999999999999999999889999999999999999999996
No 5
>KOG0151 consensus Predicted splicing regulator, contains RRM, SWAP and RPR domains [General function prediction only]
Probab=99.73 E-value=2e-17 Score=158.03 Aligned_cols=129 Identities=25% Similarity=0.403 Sum_probs=115.6
Q ss_pred HHHHHHHHhhccCcHHHHHHHHHHHHhchhchHHHHHHHHHHhc--cCcccchhHHHHHhHHHHHHhhhc--C-hhHHHH
Q 046621 8 GQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFN--SSQKEQRVSFLYLANDILQNSRRK--G-SEFVNE 82 (213)
Q Consensus 8 ~~~~~~kL~~L~~Sq~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~--~a~~~~KL~lLYLaNDIlqnskrk--~-~~f~~~ 82 (213)
++.|+.+|+.||.-+.+|..++.||+.|...|.+||+|+.+.|. ..+..+||+.|||+|||||||..+ + +-|+..
T Consensus 433 RdklE~liR~LTpEk~sIg~aM~FalenA~aa~EI~eci~eSlt~~~t~~~kKiarLyLvsDIL~N~sarv~nas~YR~~ 512 (877)
T KOG0151|consen 433 RDKLEDLIRGLTPEKSSIGDAMVFALENADAAGEIVECITESLTNKETPLPKKIARLYLVSDILHNSSARVANASAYRKS 512 (877)
T ss_pred HHHHHHHHHhcCcccchHHHHHHHHHhhhhhHHHHHHHHHHHHhccCCcchhHHHHHHHHHHHHhhhhhhhhHHHHHHHH
Confidence 57899999999999999999999999999999999999999886 467899999999999999999965 3 689999
Q ss_pred HHHHHHHHHHHHhh---c-----CChHHHHhHHHHHHHhhhCcccCCCc-cchhhhhhCCCCC
Q 046621 83 FWKVLPAALKHVYD---N-----GDEYGKKAVTRLVDIWEERKVFGSRG-QGLKDEMLGKNPP 136 (213)
Q Consensus 83 F~~vLp~~~~~v~~---~-----~d~~~~~kv~rll~IWeeR~Vf~~~~-~~L~~~~lg~~p~ 136 (213)
|++.|+.+|..++. . ..+..+++|++||.+|+++-+|+.++ ..|...++|..+.
T Consensus 513 FEa~L~~Ifd~l~~~yr~I~gRIkaE~fkqRV~kVirvWedW~ifpe~~l~~l~~~Flg~~~~ 575 (877)
T KOG0151|consen 513 FEATLEDIFDDLNDLYRSIGGRIKAEAFKQRVMKVIRVWEDWAIFPEDFLIGLQNTFLGLNNI 575 (877)
T ss_pred HHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHHHHHhCcHHHHHHHHHHHhcCCCC
Confidence 99999999987753 2 24577999999999999999999996 8899999996543
No 6
>PF12243 CTK3: CTD kinase subunit gamma CTK3
Probab=99.68 E-value=6e-16 Score=123.90 Aligned_cols=126 Identities=17% Similarity=0.385 Sum_probs=113.8
Q ss_pred CCCC-HHHHHHHHhhccCcHHHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhcC---hhH
Q 046621 4 EAFD-GQILSEKLSKLNNSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKG---SEF 79 (213)
Q Consensus 4 ~~F~-~~~~~~kL~~L~~Sq~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk~---~~f 79 (213)
|+|. +.+|.+.|++||.|++||+.+.+|++.|+..++.+.+|+++++.+.+.+.|+++||++..+++-|...+ ..|
T Consensus 2 DpFE~r~~F~~~L~~L~aS~qSi~kaa~fAlk~~~~~edL~~cIle~le~~~lN~R~nI~~fID~l~e~~~~~~~~~~~Y 81 (139)
T PF12243_consen 2 DPFEVRMQFTQLLRRLNASQQSIQKAAQFALKNRDMEEDLWSCILEQLEKENLNTRINIFYFIDSLCESSQKSKKYNYPY 81 (139)
T ss_pred ChHHHHHHHHHHHHHcchhHHHHHHHHHHHHHccccHHHHHHHHHHHHhccchhhHHHHHHHHHHHHHHHHhcccccchh
Confidence 7888 589999999999999999999999999999999999999999999999999999999999999988754 689
Q ss_pred HHHHHHHHHHHHHHHhhcCCh--HHHHhHHHHHHHhhhCcccCCCc-cchhhh
Q 046621 80 VNEFWKVLPAALKHVYDNGDE--YGKKAVTRLVDIWEERKVFGSRG-QGLKDE 129 (213)
Q Consensus 80 ~~~F~~vLp~~~~~v~~~~d~--~~~~kv~rll~IWeeR~Vf~~~~-~~L~~~ 129 (213)
+...++.||.++..|.+.+.. .....+.++|+.|.+|++++... .++...
T Consensus 82 v~~l~~dL~~Iv~~V~P~~~~g~~N~~~~~kvL~~~~~k~~l~~~~~~~~~~~ 134 (139)
T PF12243_consen 82 VSMLQRDLPRIVDAVAPPDNSGAANLKSVRKVLKNWSKKKILDPEEYEEIEAS 134 (139)
T ss_pred HHHHHHHHHHHHHHhCCCCCccchHHHHHHHHHHHHHHcCCCCHHHHHHHHHH
Confidence 999999999999999976433 67899999999999999999874 444433
No 7
>KOG4368 consensus Predicted RNA binding protein, contains SWAP, RPR and G-patch domains [General function prediction only]
Probab=99.50 E-value=7.3e-14 Score=131.53 Aligned_cols=183 Identities=17% Similarity=0.310 Sum_probs=135.7
Q ss_pred CCCHHHHHHHHhhc--cCcHHHHHHHHHHHHhchh---chHHHHHHHHHHhcc--CcccchhHHHHHhHHHHHHhhhcC-
Q 046621 5 AFDGQILSEKLSKL--NNSQQSIESLSRWCITHRK---KAKQIVETWDKSFNS--SQKEQRVSFLYLANDILQNSRRKG- 76 (213)
Q Consensus 5 ~F~~~~~~~kL~~L--~~Sq~SIqs~s~W~l~h~~---~a~~Iv~~w~~~l~~--a~~~~KL~lLYLaNDIlqnskrk~- 76 (213)
..+...|...|+.+ ++|.+.|...+.||+.+++ +++.|+..+...++. +..+-||+||||+||+++||.||.
T Consensus 100 ~l~~~~~~~~l~~~~~~c~kd~is~~k~w~f~~~~s~~~~e~~~~~l~n~~~~~~~~~~lrlh~~ylind~~~hcqrk~~ 179 (757)
T KOG4368|consen 100 QLDMNEFDNLLQPIIDTCTKDAISAGKNWMFSNAKSPPHCELMAGHLRNRITADGAHFELRLHLIYLINDVLHHCQRKQA 179 (757)
T ss_pred cCCHHHHHHHHHHHHHHHhHHHHHHhhhhhhhcCCCchHHHHHHHHHHhhhcccccchhhhhhhHHHHHHHHHHHHHHHH
Confidence 45566777777766 5899999999999999988 567888888888875 568899999999999999999986
Q ss_pred hhHHHHHHHHHHHHHHHHhhcCChHHHHhHHHHHHHhhhCcccCCCc-cchhhhhhCCCCCCCCCCCCCCCCcccccccc
Q 046621 77 SEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSRG-QGLKDEMLGKNPPPVPASNGRSSNPIKIVKRD 155 (213)
Q Consensus 77 ~~f~~~F~~vLp~~~~~v~~~~d~~~~~kv~rll~IWeeR~Vf~~~~-~~L~~~~lg~~p~~~~~~~~~~~~~~k~~~~~ 155 (213)
.+...++++++..+.+..+....+.-.+++.|||..|+.|++|...+ ++|+..++|.....
T Consensus 180 ~~~~~~l~~~v~~~yc~~~~~~~e~~~~~~~~ll~~we~~~yf~ds~~~ql~~~~~~~~~~~------------------ 241 (757)
T KOG4368|consen 180 RELLAALQKVVVPIYCTSFLAVEEDKQQKIARLLQLWEKNGYFDDSIIQQLQSPALGLGQYQ------------------ 241 (757)
T ss_pred HHHHHHHHHHhHHHHHhhhhhhHhHHHHHHHHHHHHHhhcCchhHHHHHHhhhhhhhhhhHH------------------
Confidence 68999999998888887776666777899999999999999999885 99998887754210
Q ss_pred cchhhhhcccCCChHHHHHHHHHHHhhCCChHHHHHHhHHHHHHHhhhhhhhhcC
Q 046621 156 ANSVRIKLAVGALPEKILTAFQSVLDEHPNEEVALNNCNAAVHHAGKVSEDVENT 210 (213)
Q Consensus 156 ~~s~~~~~~~~~~~eki~~~~~~~~~~~~~e~~~~~k~~~~~~~~~~~~~~~~~~ 210 (213)
...+.+-+.+.+-|-.+|+.-++..-.--. +-...--+-+..||.+|+.+
T Consensus 242 ---~~~~~~y~~~~~~~~~~~~~~~~~~~~qh~--~~~q~~q~q~~~~e~~~~~~ 291 (757)
T KOG4368|consen 242 ---ATLINEYSSVVQPVQLAFQQQIQTLKTQHE--EFVQQQQQQMPQMEAEVKAT 291 (757)
T ss_pred ---HHHHhhhhHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHhhHHHHHhhhcc
Confidence 012233345667777788666553211111 11122334566777777754
No 8
>KOG0132 consensus RNA polymerase II C-terminal domain-binding protein RA4, contains RPR and RRM domains [RNA processing and modification; Transcription]
Probab=98.64 E-value=7e-08 Score=94.12 Aligned_cols=125 Identities=23% Similarity=0.390 Sum_probs=107.9
Q ss_pred HHHHHHHhhccC-----cHHHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhc----ChhH
Q 046621 9 QILSEKLSKLNN-----SQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRK----GSEF 79 (213)
Q Consensus 9 ~~~~~kL~~L~~-----Sq~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk----~~~f 79 (213)
..|...|.+|.. |..-|..+....|.|.+.+++||....+++.++..++||.-||+++.|+..++.. ...|
T Consensus 5 ~~Fn~eL~SL~DsK~~IS~sKi~~ITkaAikaIk~ykhVVqsVeKfi~kCkpe~Kl~gLYVIDSIVRqsrhq~~~~kd~F 84 (894)
T KOG0132|consen 5 KEFNGELDSLEDSKPGISGSKILKITKAAIKAIKLYKHVVQSVEKFIKKCKPEYKLPGLYVIDSIVRQSRHQFGKEKDVF 84 (894)
T ss_pred HHHHHHHHHhhccCCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcccccCeeEEehHHHHHHHHhhccccccc
Confidence 568888888875 6678999999999999999999999999999999999999999999999999953 2568
Q ss_pred HHHHHHHHHHHHHHHhhcCChHHHHhHHHHHHHhhhCcccCCCc-cchhhhhhCCC
Q 046621 80 VNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSRG-QGLKDEMLGKN 134 (213)
Q Consensus 80 ~~~F~~vLp~~~~~v~~~~d~~~~~kv~rll~IWeeR~Vf~~~~-~~L~~~~lg~~ 134 (213)
...|..-+-..|..+|.+. .+.+.++.|++++|..++||-.++ +-|.+-..|..
T Consensus 85 ~prf~~n~~~tf~~L~~c~-~edks~iIrvlNlwqkn~VfK~e~IqpLlDm~~~s~ 139 (894)
T KOG0132|consen 85 GPRFSKNFTGTFQNLYECP-QEDKSDIIRVLNLWQKNNVFKSEIIQPLLDMADGSG 139 (894)
T ss_pred CCccchhHHHHHHHHHhcC-HHHHHHHHHhhhhhhcccchhHHHHHHHHHHHhccC
Confidence 8889888999999999874 456888999999999999999996 55666555543
No 9
>KOG2071 consensus mRNA cleavage and polyadenylation factor I/II complex, subunit Pcf11 [RNA processing and modification]
Probab=98.11 E-value=8.2e-06 Score=78.15 Aligned_cols=103 Identities=23% Similarity=0.378 Sum_probs=96.4
Q ss_pred HHHHHHHhhcc-CcHHHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhcChhHHHHHHHHH
Q 046621 9 QILSEKLSKLN-NSQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNEFWKVL 87 (213)
Q Consensus 9 ~~~~~kL~~L~-~Sq~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk~~~f~~~F~~vL 87 (213)
..+...|..|+ ++..-|.++..-.-+|...|..||..+..++.++++.+||..+|++..|+.| -|.+|...|...|
T Consensus 7 ~dy~s~ledltfnskp~i~~lt~la~En~~~a~~iv~~iE~hi~kcpp~~kL~~~y~~dsi~kn---vg~py~~~fs~~l 83 (579)
T KOG2071|consen 7 RDYQSSLEDLTFNSKPIINTLTILAEENLPFAKSIVSAIEAHIAKCPPSQKLPVMYLLDSIVKN---VGSPYTTAFSRNL 83 (579)
T ss_pred HHHHHHHHHHhcCCcchhHHhhHhhhhcccccHHHHHHHHHHHhhCCcccccchhhhhHHHHhh---cCCcchhhhhhhH
Confidence 45667788886 8999999999999999999999999999999999999999999999999988 6778999999999
Q ss_pred HHHHHHHhhcCChHHHHhHHHHHHHhh
Q 046621 88 PAALKHVYDNGDEYGKKAVTRLVDIWE 114 (213)
Q Consensus 88 p~~~~~v~~~~d~~~~~kv~rll~IWe 114 (213)
-..|..+|..+|+..+.++.+++..|.
T Consensus 84 ~a~f~~~~~~vd~r~r~~l~~~~~tw~ 110 (579)
T KOG2071|consen 84 VATFICAFTKVDERTRTSLFKLRATWD 110 (579)
T ss_pred HHHHHHHHhhccccccchhHhhHHhhc
Confidence 999999999999999999999999999
No 10
>cd00197 VHS_ENTH_ANTH VHS, ENTH and ANTH domain superfamily; composed of proteins containing a VHS, ENTH or ANTH domain. 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 is located at the N-termini of proteins involved in intracellular membrane trafficking. The epsin N-terminal homology (ENTH) domain is an evolutionarily conserved protein module found primarily in proteins that participate in clathrin-mediated endocytosis. A set of proteins previously designated as harboring an ENTH domain in fact contains a highly similar, yet unique module referred to as an AP180 N-terminal homology (ANTH) domain. VHS, ENTH and ANTH domains are structurally similar and are composed of a superhelix of eight alpha helices. ENTH adnd ANTH (E/ANTH) domains bind both inositol phospholipids and proteins and contribute to the nucleation and formation of clathrin coats on membra
Probab=96.66 E-value=0.037 Score=42.17 Aligned_cols=92 Identities=16% Similarity=0.164 Sum_probs=68.6
Q ss_pred cHHHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhcChhHHHHHHH--HHHHHHHHHhh--
Q 046621 21 SQQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNEFWK--VLPAALKHVYD-- 96 (213)
Q Consensus 21 Sq~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk~~~f~~~F~~--vLp~~~~~v~~-- 96 (213)
+...|..+..-+-.....+..++..+.+.+...+....+.-|||+.-+++||- ..|..+|.. ++..++...+.
T Consensus 17 ~~~~i~~i~d~~~~~~~~~~~~~~~l~kRl~~~~~~~~lkaL~lLe~lvkN~g---~~f~~~i~~~~~~~~l~~~~~~~~ 93 (115)
T cd00197 17 DWPLIMEICDLINETNVGPKEAVDAIKKRINNKNPHVVLKALTLLEYCVKNCG---ERFHQEVASNDFAVELLKFDKSKL 93 (115)
T ss_pred CHHHHHHHHHHHHCCCccHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHcc---HHHHHHHHHhHHHHHHHHhhcccc
Confidence 56667777777765656789999999999998888889999999999999954 455555544 44444433221
Q ss_pred ---cCChHHHHhHHHHHHHhhh
Q 046621 97 ---NGDEYGKKAVTRLVDIWEE 115 (213)
Q Consensus 97 ---~~d~~~~~kv~rll~IWee 115 (213)
..+..+++++..++..|.+
T Consensus 94 ~~~~~~~~Vr~k~~~l~~~w~~ 115 (115)
T cd00197 94 LGDDVSTNVREKAIELVQLWAS 115 (115)
T ss_pred ccCCCChHHHHHHHHHHHHHhC
Confidence 2357889999999999964
No 11
>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=95.36 E-value=0.22 Score=39.41 Aligned_cols=91 Identities=16% Similarity=0.223 Sum_probs=63.8
Q ss_pred HHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhcChhHHHHH--HHHHHHHHHHHhhcCCh
Q 046621 23 QSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNEF--WKVLPAALKHVYDNGDE 100 (213)
Q Consensus 23 ~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk~~~f~~~F--~~vLp~~~~~v~~~~d~ 100 (213)
+.|-.+..-+-.....+++.+..+.+.|...++...+.-|.|++-++.||-. .|..++ ..++-.+...+......
T Consensus 24 ~~~l~icD~i~~~~~~~kea~~~l~krl~~~~~~vq~~aL~lld~lvkNcg~---~f~~ev~~~~fl~~l~~l~~~~~~~ 100 (140)
T PF00790_consen 24 SLILEICDLINSSPDGAKEAARALRKRLKHGNPNVQLLALTLLDALVKNCGP---RFHREVASKEFLDELVKLIKSKKTD 100 (140)
T ss_dssp HHHHHHHHHHHTSTTHHHHHHHHHHHHHTTSSHHHHHHHHHHHHHHHHHSHH---HHHHHHTSHHHHHHHHHHHHHTTTH
T ss_pred HHHHHHHHHHHcCCccHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHcCCH---HHHHHHhHHHHHHHHHHHHccCCCC
Confidence 4566666666666678899999999999998888888889999999999743 333332 11333333333332232
Q ss_pred H---HHHhHHHHHHHhhhC
Q 046621 101 Y---GKKAVTRLVDIWEER 116 (213)
Q Consensus 101 ~---~~~kv~rll~IWeeR 116 (213)
. +++++..+|.-|.+.
T Consensus 101 ~~~~Vk~k~l~ll~~W~~~ 119 (140)
T PF00790_consen 101 PETPVKEKILELLQEWAEA 119 (140)
T ss_dssp HHSHHHHHHHHHHHHHHHH
T ss_pred chhHHHHHHHHHHHHHHHH
Confidence 2 899999999999954
No 12
>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=94.51 E-value=0.71 Score=36.25 Aligned_cols=95 Identities=16% Similarity=0.147 Sum_probs=67.0
Q ss_pred HHHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhcChhHHHHHH--HHHHHHHHHHhh--c
Q 046621 22 QQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNEFW--KVLPAALKHVYD--N 97 (213)
Q Consensus 22 q~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk~~~f~~~F~--~vLp~~~~~v~~--~ 97 (213)
-+.|-.+..-+-.....++..+..+.+.|...++...+.-|+|+.-++.||-.. |..++. .+|-+++..+.. .
T Consensus 18 ~~~il~icd~I~~~~~~~k~a~raL~krl~~~n~~vql~AL~lLd~~vkNcg~~---f~~~i~s~~fl~~l~~l~~~~~~ 94 (133)
T cd03561 18 WALNLELCDLINLKPNGPKEAARAIRKKIKYGNPHVQLLALTLLELLVKNCGKP---FHLQVADKEFLLELVKIAKNSPK 94 (133)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCChH---HHHHHhhHHHHHHHHHHhCCCCC
Confidence 344555555555555688999999999999888888888899999999997543 333222 234443333333 3
Q ss_pred CChHHHHhHHHHHHHhhhCcccCC
Q 046621 98 GDEYGKKAVTRLVDIWEERKVFGS 121 (213)
Q Consensus 98 ~d~~~~~kv~rll~IWeeR~Vf~~ 121 (213)
.++.+++++..++.-|.+ .|+.
T Consensus 95 ~~~~Vk~kil~ll~~W~~--~f~~ 116 (133)
T cd03561 95 YDPKVREKALELILAWSE--SFGG 116 (133)
T ss_pred CCHHHHHHHHHHHHHHHH--HhcC
Confidence 578999999999999995 5554
No 13
>smart00288 VHS Domain present in VPS-27, Hrs and STAM. Unpublished observations. Domain of unknown function.
Probab=93.77 E-value=1.2 Score=35.10 Aligned_cols=90 Identities=19% Similarity=0.208 Sum_probs=60.5
Q ss_pred HHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhcChhHHHHHHH--HHHHHHHHHhhcCC-
Q 046621 23 QSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNEFWK--VLPAALKHVYDNGD- 99 (213)
Q Consensus 23 ~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk~~~f~~~F~~--vLp~~~~~v~~~~d- 99 (213)
+.|-.+..-+-.....++..+..+.+.|...++...+.-|-|+..++.||- ..|..++.. ++..+...+....+
T Consensus 19 ~~~l~icD~i~~~~~~~k~a~r~l~krl~~~n~~v~l~AL~lLe~~vkNcg---~~f~~ev~s~~fl~~L~~l~~~~~~~ 95 (133)
T smart00288 19 ELILEICDLINSTPDGPKDAVRLLKKRLNNKNPHVALLALTLLDACVKNCG---SKFHLEVASKEFLNELVKLIKPKYPL 95 (133)
T ss_pred HHHHHHHHHHhCCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCC---HHHHHHHHhHHHHHHHHHHHcCCCCc
Confidence 444555555545555689999999999998777778888999999999974 333333321 23333333222222
Q ss_pred hHHHHhHHHHHHHhhh
Q 046621 100 EYGKKAVTRLVDIWEE 115 (213)
Q Consensus 100 ~~~~~kv~rll~IWee 115 (213)
+.+++++..++.-|.+
T Consensus 96 ~~Vk~kil~li~~W~~ 111 (133)
T smart00288 96 PLVKKRILELIQEWAD 111 (133)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3489999999999995
No 14
>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=93.35 E-value=1.6 Score=34.92 Aligned_cols=106 Identities=18% Similarity=0.267 Sum_probs=68.3
Q ss_pred HHHHHhhccC---cH---HHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhc-ChhH-HHH
Q 046621 11 LSEKLSKLNN---SQ---QSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRK-GSEF-VNE 82 (213)
Q Consensus 11 ~~~kL~~L~~---Sq---~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk-~~~f-~~~ 82 (213)
|.+.+.+.++ +. +.|-.+..-+-.....+++.+..+.+.|...++...+.-|-|+.-++.||-.+ ..++ ...
T Consensus 5 ~~~~I~kATs~~l~~~dw~~ileicD~In~~~~~~k~a~ral~krl~~~n~~vql~AL~LLe~~vkNCG~~fh~evas~~ 84 (142)
T cd03569 5 FDELIEKATSELLGEPDLASILEICDMIRSKDVQPKYAMRALKKRLLSKNPNVQLYALLLLESCVKNCGTHFHDEVASRE 84 (142)
T ss_pred HHHHHHHHcCcccCccCHHHHHHHHHHHhCCCCCHHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHHCCHHHHHHHhhHH
Confidence 4455555543 22 33344555554555678999999999998877777777799999999998543 1111 112
Q ss_pred HHHHHHHHHHHHhhcCChHHHHhHHHHHHHhhhCcccCC
Q 046621 83 FWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGS 121 (213)
Q Consensus 83 F~~vLp~~~~~v~~~~d~~~~~kv~rll~IWeeR~Vf~~ 121 (213)
|-..|..++.. ..++.+++++..++.-|.+ .|..
T Consensus 85 fl~~l~~l~~~---~~~~~Vk~kil~li~~W~~--~f~~ 118 (142)
T cd03569 85 FMDELKDLIKT---TKNEEVRQKILELIQAWAL--AFRN 118 (142)
T ss_pred HHHHHHHHHcc---cCCHHHHHHHHHHHHHHHH--HhCC
Confidence 22222222222 4578999999999999994 5654
No 15
>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=91.81 E-value=3.3 Score=33.25 Aligned_cols=90 Identities=17% Similarity=0.195 Sum_probs=61.6
Q ss_pred HHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhcChhHHHHHH--HHHHHHHHHHhhcCCh
Q 046621 23 QSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNEFW--KVLPAALKHVYDNGDE 100 (213)
Q Consensus 23 ~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk~~~f~~~F~--~vLp~~~~~v~~~~d~ 100 (213)
+.|-.+..-+-.....++..+.++.+.+....+...+.-|-|+..+++||-.. |..++. .++..+...+....++
T Consensus 19 ~~il~icD~I~~~~~~~k~a~ral~KRl~~~n~~v~l~AL~LLe~~vkNCG~~---fh~evask~Fl~eL~kl~~~~~~~ 95 (144)
T cd03568 19 GLILDVCDKVKSDENGAKDCLKAIMKRLNHKDPNVQLRALTLLDACAENCGKR---FHQEVASRDFTQELKKLINDRVHP 95 (144)
T ss_pred HHHHHHHHHHhcCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCCHH---HHHHHhhHHHHHHHHHHhcccCCH
Confidence 34445555555566678999999999998777777777788999999997643 222221 1333333333222578
Q ss_pred HHHHhHHHHHHHhhh
Q 046621 101 YGKKAVTRLVDIWEE 115 (213)
Q Consensus 101 ~~~~kv~rll~IWee 115 (213)
.++.++..++.-|.+
T Consensus 96 ~Vk~kil~li~~W~~ 110 (144)
T cd03568 96 TVKEKLREVVKQWAD 110 (144)
T ss_pred HHHHHHHHHHHHHHH
Confidence 999999999999983
No 16
>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=91.17 E-value=4.5 Score=32.32 Aligned_cols=91 Identities=18% Similarity=0.211 Sum_probs=59.8
Q ss_pred HHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhcChhHHHHHHH--HHHHHHHHHhh-----c
Q 046621 25 IESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNEFWK--VLPAALKHVYD-----N 97 (213)
Q Consensus 25 Iqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk~~~f~~~F~~--vLp~~~~~v~~-----~ 97 (213)
|-.+..-+-.....+...+..+.+.+..-++...|.-|-|+.-+++||-.. |..++.. +|.++++.+.. .
T Consensus 22 ileicD~In~~~~~~k~a~rai~krl~~~n~~v~l~AL~LLe~~vkNCG~~---fh~evas~~Fl~el~kl~~~k~~~~~ 98 (139)
T cd03567 22 IQAFCEQINKEPEGPQLAVRLLAHKIQSPQEKEALQALTVLEACMKNCGER---FHSEVGKFRFLNELIKLVSPKYLGSR 98 (139)
T ss_pred HHHHHHHHHcCCccHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCHH---HHHHHHhHHHHHHHHHHhccccCCCC
Confidence 334444444444566888999999998766666777789999999997543 3222221 33333333321 2
Q ss_pred CChHHHHhHHHHHHHhhhCcccC
Q 046621 98 GDEYGKKAVTRLVDIWEERKVFG 120 (213)
Q Consensus 98 ~d~~~~~kv~rll~IWeeR~Vf~ 120 (213)
.++.+++++..++.-|.+ -|+
T Consensus 99 ~~~~Vk~kil~li~~W~~--~f~ 119 (139)
T cd03567 99 TSEKVKTKIIELLYSWTL--ELP 119 (139)
T ss_pred CCHHHHHHHHHHHHHHHH--Hhc
Confidence 468999999999999994 454
No 17
>KOG1087 consensus Cytosolic sorting protein GGA2/TOM1 [Intracellular trafficking, secretion, and vesicular transport]
Probab=82.89 E-value=9.3 Score=36.65 Aligned_cols=83 Identities=18% Similarity=0.249 Sum_probs=58.9
Q ss_pred HHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhcChhHHHHH--HHHHHHHHHHHhhc-CChHHHHhH
Q 046621 30 RWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNEF--WKVLPAALKHVYDN-GDEYGKKAV 106 (213)
Q Consensus 30 ~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk~~~f~~~F--~~vLp~~~~~v~~~-~d~~~~~kv 106 (213)
..|=.-...++++|..+.+.+......-.+--|+|+.-++.||-. .|-..+ ..+|.+++..+... .+..++++|
T Consensus 27 D~IN~~~~~~~eAvralkKRi~~k~s~vq~lALtlLE~cvkNCG~---~fh~~Va~k~fL~emVk~~k~~~~~~~Vr~ki 103 (470)
T KOG1087|consen 27 DLINSTEGGPKEAVRALKKRLNSKNSKVQLLALTLLETCVKNCGY---SFHLQVASKEFLNEMVKRPKNKPRDLKVREKI 103 (470)
T ss_pred HHHhcCccCcHHHHHHHHHHhccCCcHHHHHHHHHHHHHHHhhhH---HHHHHHHHHHHHHHHHhccccCCcchhHHHHH
Confidence 333334456789999999999865554445556777777777643 333333 34788888888776 688999999
Q ss_pred HHHHHHhhh
Q 046621 107 TRLVDIWEE 115 (213)
Q Consensus 107 ~rll~IWee 115 (213)
.-+|+-|.+
T Consensus 104 L~LI~~W~~ 112 (470)
T KOG1087|consen 104 LELIDTWQQ 112 (470)
T ss_pred HHHHHHHHH
Confidence 999999994
No 18
>cd03565 VHS_Tom1 VHS domain family, Tom1 subfamily; The VHS domain is an essential part of Tom1 (Target of myb1 - retroviral oncogene) protein. The VHS domain has a superhelical structure similar to the structure of the ARM repeats and is present at the very N-termini of proteins. It is a right-handed superhelix of eight alpha helices. The VHS domain has been found in a number of proteins, some of which have been implicated in intracellular trafficking and sorting. The VHS domain of the Tom1 protein is essential for the negative regulation of Interleukin-1 and Tumor Necrosis Factor-induced signaling pathways.
Probab=71.94 E-value=48 Score=26.31 Aligned_cols=94 Identities=13% Similarity=0.175 Sum_probs=58.4
Q ss_pred HHHHHHHHHHHhchhchHHHHHHHHHHhccC-cccchhHHHHHhHHHHHHhhhcChhHHHHHH--HHHHH-HHHHHhhc-
Q 046621 23 QSIESLSRWCITHRKKAKQIVETWDKSFNSS-QKEQRVSFLYLANDILQNSRRKGSEFVNEFW--KVLPA-ALKHVYDN- 97 (213)
Q Consensus 23 ~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a-~~~~KL~lLYLaNDIlqnskrk~~~f~~~F~--~vLp~-~~~~v~~~- 97 (213)
+.|-.+..-+-.....++..+.++.+.+... ++...+.-|-|+.-+++||-.. |..++. .++.+ ++..+...
T Consensus 20 ~~ileicD~In~~~~~~k~a~ralkkRl~~~~n~~v~l~aL~LLe~~vkNCG~~---fh~eiask~Fl~e~L~~~i~~~~ 96 (141)
T cd03565 20 GLNMEICDIINETEDGPKDAVRALKKRLNGNKNHKEVMLTLTVLETCVKNCGHR---FHVLVAKKDFIKDVLVKLINPKN 96 (141)
T ss_pred HHHHHHHHHHhCCCCcHHHHHHHHHHHHccCCCHHHHHHHHHHHHHHHHHccHH---HHHHHHHHHhhhHHHHHHHcccC
Confidence 4555566656555567899999999999642 3334454588999999997533 322221 13333 22222211
Q ss_pred -CChHHHHhHHHHHHHhhhCcccCC
Q 046621 98 -GDEYGKKAVTRLVDIWEERKVFGS 121 (213)
Q Consensus 98 -~d~~~~~kv~rll~IWeeR~Vf~~ 121 (213)
.+..+++++..++.-|.+ -|..
T Consensus 97 ~~~~~Vk~kil~li~~W~~--~f~~ 119 (141)
T cd03565 97 NPPTIVQEKVLALIQAWAD--AFRG 119 (141)
T ss_pred CCcHHHHHHHHHHHHHHHH--HhCC
Confidence 245889999999999994 4543
No 19
>PF01417 ENTH: ENTH domain; InterPro: IPR001026 The ENTH (Epsin N-terminal homology) domain is approximately 150 amino acids in length and is always found located at the N-termini of proteins. The domain forms a compact globular structure, composed of 9 alpha-helices connected by loops of varying length. The general topology is determined by three helical hairpins that are stacked consecutively with a right hand twist []. An N-terminal helix folds back, forming a deep basic groove that forms the binding pocket for the Ins(1,4,5)P3 ligand []. The ligand is coordinated by residues from surrounding alpha-helices and all three phosphates are multiply coordinated. The coordination of Ins(1,4,5)P3 suggests that ENTH is specific for particular head groups. Proteins containing this domain have been found to bind PtdIns(4,5)P2 and PtdIns(1,4,5)P3 suggesting that the domain may be a membrane interacting module. The main function of proteins containing this domain appears to be to act as accessory clathrin adaptors in endocytosis, Epsin is able to recruit and promote clathrin polymerisation on a lipid monolayer, but may have additional roles in signalling and actin regulation []. Epsin causes a strong degree of membrane curvature and tubulation, even fragmentation of membranes with a high PtdIns(4,5)P2 content. Epsin binding to membranes facilitates their deformation by insertion of the N-terminal helix into the outer leaflet of the bilayer, pushing the head groups apart. This would reduce the energy needed to curve the membrane into a vesicle, making it easier for the clathrin cage to fix and stabilise the curved membrane. This points to a pioneering role for epsin in vesicle budding as it provides both a driving force and a link between membrane invagination and clathrin polymerisation. ; PDB: 1H0A_A 1EYH_A 1EDU_A 2QY7_B 1XGW_A 2V8S_E 1VDY_A 2DCP_A 1INZ_A 3ONL_B ....
Probab=64.38 E-value=34 Score=26.18 Aligned_cols=90 Identities=12% Similarity=0.242 Sum_probs=58.2
Q ss_pred cHHHHHHHHHHHHhchhchHHHHHHHHHHh---ccCcccchhHHHHHhHHHHHHhhhcChhHHHHHHHHHHHHH--HHHh
Q 046621 21 SQQSIESLSRWCITHRKKAKQIVETWDKSF---NSSQKEQRVSFLYLANDILQNSRRKGSEFVNEFWKVLPAAL--KHVY 95 (213)
Q Consensus 21 Sq~SIqs~s~W~l~h~~~a~~Iv~~w~~~l---~~a~~~~KL~lLYLaNDIlqnskrk~~~f~~~F~~vLp~~~--~~v~ 95 (213)
+..-...++.+..+. ..+..|++++.+.| ......+++--|.|+..+++| ..+.|+..|...+..+- ..+.
T Consensus 20 ~~~~l~eIa~~t~~~-~~~~~I~~~l~kRL~~~~~k~wr~~~KaL~ll~yLl~n---G~~~~~~~~~~~~~~I~~l~~f~ 95 (125)
T PF01417_consen 20 PGKLLAEIAQLTYNS-KDCQEIMDVLWKRLSKSDGKNWRHVYKALTLLEYLLKN---GSERFVDELRDHIDIIRELQDFQ 95 (125)
T ss_dssp -HHHHHHHHHHTTSC-HHHHHHHHHHHHHHHSSTSSGHHHHHHHHHHHHHHHHH---S-HHHHHHHHHTHHHHHGGGG--
T ss_pred CHHHHHHHHHHHhcc-ccHHHHHHHHHHHHHhcCCcchhHHHHHHHHHHHHHHH---CCHHHHHHHHHHHHHHhhcceee
Confidence 455566777777655 88899999999999 344556777788999999988 33578888876544322 1111
Q ss_pred ---hcCCh---HHHHhHHHHHHHhh
Q 046621 96 ---DNGDE---YGKKAVTRLVDIWE 114 (213)
Q Consensus 96 ---~~~d~---~~~~kv~rll~IWe 114 (213)
..|+. .+|++...|+++=.
T Consensus 96 ~~d~~g~d~~~~VR~~A~~i~~lL~ 120 (125)
T PF01417_consen 96 YVDPKGKDQGQNVREKAKEILELLN 120 (125)
T ss_dssp -BBTTSTBHHHHHHHHHHHHHHHHT
T ss_pred ccCCCCccHHHHHHHHHHHHHHHhC
Confidence 11222 35777777777644
No 20
>PF01603 B56: Protein phosphatase 2A regulatory B subunit (B56 family); InterPro: IPR002554 Protein phosphatase 2A (PP2A) is a major intracellular protein phosphatase that regulates multiple aspects of cell growth and metabolism. The ability of this widely distributed heterotrimeric enzyme to act on a diverse array of substrates is largely controlled by the nature of its regulatory B subunit. There are multiple families of B subunits, this family is called the B56 family [].; GO: 0008601 protein phosphatase type 2A regulator activity, 0007165 signal transduction, 0000159 protein phosphatase type 2A complex; PDB: 2NYM_B 2NYL_B 2IAE_E 2NPP_B 3FGA_B 2JAK_A.
Probab=63.00 E-value=27 Score=32.54 Aligned_cols=92 Identities=16% Similarity=0.209 Sum_probs=68.7
Q ss_pred HHHHHHHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhcChhHHHHHHHHHHHHHHHHhhcCChH
Q 046621 22 QQSIESLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEY 101 (213)
Q Consensus 22 q~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk~~~f~~~F~~vLp~~~~~v~~~~d~~ 101 (213)
++=+.-+..++-....-+..++..+.++--.+...+.+.+|..+.+|+...- -..|.++++.+|..+..+.+..
T Consensus 236 ~~L~~~~~~f~~kdp~l~~~~i~~llk~WP~t~s~Kev~FL~el~~il~~~~------~~~f~~i~~~lf~~la~ci~S~ 309 (409)
T PF01603_consen 236 QQLSYCVVQFLEKDPSLAEPVIKGLLKHWPKTNSQKEVLFLNELEEILEVLP------PEEFQKIMVPLFKRLAKCISSP 309 (409)
T ss_dssp HHHHHHHHHHHHH-GGGHHHHHHHHHHHS-SS-HHHHHHHHHHHHHHHTT--------HHHHHHHHHHHHHHHHHHHTSS
T ss_pred HHHHHHHHHHHHhCchhHHHHHHHHHHhCCCCCchhHHHHHHHHHHHHHhcC------HHHHHHHHHHHHHHHHHHhCCC
Confidence 4444455666666677778888888888878888899999999999997522 2568888999998888776667
Q ss_pred HHHhHHHHHHHhhhCccc
Q 046621 102 GKKAVTRLVDIWEERKVF 119 (213)
Q Consensus 102 ~~~kv~rll~IWeeR~Vf 119 (213)
.-+...|.+.+|....+.
T Consensus 310 h~qVAErAl~~w~n~~~~ 327 (409)
T PF01603_consen 310 HFQVAERALYFWNNEYFL 327 (409)
T ss_dssp SHHHHHHHHGGGGSHHHH
T ss_pred CHHHHHHHHHHHCCHHHH
Confidence 788999999999976554
No 21
>PF03392 OS-D: Insect pheromone-binding family, A10/OS-D; InterPro: IPR005055 A class of small (14-20 Kd) water-soluble proteins, called odorant binding proteins (OBPs), first discovered in the insect sensillar lymph but also in the mucus of vertebrates, is postulated to mediate the solubilisation of hydrophobic odorant molecules, and thereby to facilitate their transport to the receptor neurons. The product of a gene expressed in the olfactory system of Drosophila melanogaster (Fruit fly), OS-D, shares features common to vertebrate odorant-binding proteins, but has a primary structure unlike odorant-binding proteins []. OS-D derivatives have subsequently been found in chemosensory organs of phylogenetically distinct insects, including cockroaches, phasmids and moths, suggesting that OS-D-like proteins seem to be conserved in the insect phylum.; PDB: 1KX9_A 1N8U_A 1KX8_A 1K19_A 1N8V_A 2GVS_A 2JNT_A.
Probab=47.20 E-value=29 Score=25.97 Aligned_cols=39 Identities=21% Similarity=0.258 Sum_probs=32.6
Q ss_pred hhHHHHHHHHHHHHHHHHhhcCChHHHHhHHHHHHHhhh
Q 046621 77 SEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEE 115 (213)
Q Consensus 77 ~~f~~~F~~vLp~~~~~v~~~~d~~~~~kv~rll~IWee 115 (213)
+.-...|..+||++|...+..+.+..+..+.+++..-.+
T Consensus 34 t~~~~~lK~~ipeal~t~C~KCt~kQK~~~~kv~~~l~~ 72 (95)
T PF03392_consen 34 TPEGKELKKVIPEALKTNCAKCTPKQKENARKVIKFLKK 72 (95)
T ss_dssp HHHHHHHHHHHHHHHHCTTTTS-HHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHccccCCCHHHHHHHHHHHHHHHH
Confidence 456788999999999999998899999999999876553
No 22
>KOG2085 consensus Serine/threonine protein phosphatase 2A, regulatory subunit [Signal transduction mechanisms]
Probab=36.32 E-value=1.2e+02 Score=29.02 Aligned_cols=76 Identities=16% Similarity=0.247 Sum_probs=63.1
Q ss_pred hhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhcChhHHHHHHHHHHHHHHHHhhcCChHHHHhHHHHHHHhhh
Q 046621 36 RKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRKGSEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEE 115 (213)
Q Consensus 36 ~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk~~~f~~~F~~vLp~~~~~v~~~~d~~~~~kv~rll~IWee 115 (213)
.+-++.++..++++.-.....+.+.+|-.+-+||.- -. -.+|++...++|..+..+.+..+-+...|.+-.|.-
T Consensus 294 ~kl~~~VIrglLK~WP~tnS~KEVmFL~ElEEILe~---ie---p~eFqk~~~PLf~qia~c~sS~HFQVAEraL~~wnN 367 (457)
T KOG2085|consen 294 PKLTETVIRGLLKYWPKTNSSKEVMFLNELEEILEV---IE---PSEFQKIMVPLFRQIARCVSSPHFQVAERALYLWNN 367 (457)
T ss_pred ccccHHHHHHHHHhcCCCCCcceeeeHhhHHHHHHh---cC---HHHHHHHhHHHHHHHHHHcCChhHHHHHHHHHHHhh
Confidence 334677888888888777888999999999999976 22 368899999999999998888889999999999985
Q ss_pred Cc
Q 046621 116 RK 117 (213)
Q Consensus 116 R~ 117 (213)
..
T Consensus 368 e~ 369 (457)
T KOG2085|consen 368 EY 369 (457)
T ss_pred HH
Confidence 43
No 23
>KOG4353 consensus RNA export factor NXT1 [RNA processing and modification]
Probab=34.08 E-value=24 Score=28.18 Aligned_cols=63 Identities=24% Similarity=0.479 Sum_probs=46.7
Q ss_pred HHHHHHHhchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHH-Hhhh-cChhHHHHHHHHHHHHH
Q 046621 27 SLSRWCITHRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQ-NSRR-KGSEFVNEFWKVLPAAL 91 (213)
Q Consensus 27 s~s~W~l~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlq-nskr-k~~~f~~~F~~vLp~~~ 91 (213)
.++.++-+-++.|++.++.....+.+ .+++|..||+-|..|- |... .|.++..+|...||..=
T Consensus 4 d~k~~ves~cr~A~eFv~~YY~smD~--rR~~i~rlY~~~atlvWNGn~v~g~esls~ff~~LPsS~ 68 (139)
T KOG4353|consen 4 DFKTYVESACRAAEEFVNVYYSSMDK--RRRGIGRLYLDNATLVWNGNPVSGTESLSEFFNMLPSSE 68 (139)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHhHHHhhccceEEEcCCcchhHHHHHHHHHhCCCcc
Confidence 45667777788899999988887765 5678999999886553 3332 24689999999898543
No 24
>KOG2199 consensus Signal transducing adaptor protein STAM/STAM2 [Signal transduction mechanisms]
Probab=31.85 E-value=4.6e+02 Score=25.05 Aligned_cols=106 Identities=15% Similarity=0.257 Sum_probs=76.8
Q ss_pred HHHHHHHHhhcc---CcHHHHHHHHHHHH---hchhchHHHHHHHHHHhccCcccchhHHHHHhHHHHHHhhhc---C--
Q 046621 8 GQILSEKLSKLN---NSQQSIESLSRWCI---THRKKAKQIVETWDKSFNSSQKEQRVSFLYLANDILQNSRRK---G-- 76 (213)
Q Consensus 8 ~~~~~~kL~~L~---~Sq~SIqs~s~W~l---~h~~~a~~Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnskrk---~-- 76 (213)
.-.|+.-|-+.+ +|.+.=+-+...|- ....-++..+..+++++....++--|--|-|+..++-||... .
T Consensus 6 ~n~~e~~v~KAT~e~nT~enW~~IlDvCD~v~~~~~~~kd~lk~i~KRln~~dphV~L~AlTLlda~~~NCg~~~r~EVs 85 (462)
T KOG2199|consen 6 ANPFEQDVEKATDEKNTSENWSLILDVCDKVGSDPDGGKDCLKAIMKRLNHKDPHVVLQALTLLDACVANCGKRFRLEVS 85 (462)
T ss_pred cchHHHHHHHhcCcccccccHHHHHHHHHhhcCCCcccHHHHHHHHHHhcCCCcchHHHHHHHHHHHHHhcchHHHHHHh
Confidence 334555555444 56666666666664 344577899999999999888887888899999999999854 1
Q ss_pred -hhHHHHHHHHHHHHHHHHhhcCChHHHHhHHHHHHHhhhCcccCCC
Q 046621 77 -SEFVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSR 122 (213)
Q Consensus 77 -~~f~~~F~~vLp~~~~~v~~~~d~~~~~kv~rll~IWeeR~Vf~~~ 122 (213)
.+|..+|..++-. .+.+.++.++.-++.=|-+ .|-.+
T Consensus 86 Sr~F~~el~al~~~-------~~h~kV~~k~~~lv~eWse--e~K~D 123 (462)
T KOG2199|consen 86 SRDFTTELRALIES-------KAHPKVCEKMRDLVKEWSE--EFKKD 123 (462)
T ss_pred hhhHHHHHHHHHhh-------cccHHHHHHHHHHHHHHHH--HhccC
Confidence 3677666654432 3467899999999999998 77765
No 25
>PF11357 Spy1: Cell cycle regulatory protein; InterPro: IPR020984 Speedy (Spy1) is a cell cycle regulatory protein which activates CDK2, the major kinase that allows progression through G1/S phase and further replication events. Spy1 expression overcomes a p27-induced cell cycle arrest to allow for DNA synthesis, so cell cycle progression occurs due to an interaction between Spy1 and p27 []. Spy1 is also known as Ringo protein A.
Probab=31.67 E-value=86 Score=25.02 Aligned_cols=50 Identities=28% Similarity=0.432 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHhchhchHHHHHHHHHHhccCc----ccchhHH---HHHhHHHHHHh
Q 046621 23 QSIESLSRWCITHRKKAKQIVETWDKSFNSSQ----KEQRVSF---LYLANDILQNS 72 (213)
Q Consensus 23 ~SIqs~s~W~l~h~~~a~~Iv~~w~~~l~~a~----~~~KL~l---LYLaNDIlqns 72 (213)
.-|+..=.|=..++-.-+-+......+|..+. ..+++++ ||||||+=...
T Consensus 13 p~I~~FL~~D~~~~~sDKYLLAmV~~YF~Ragl~~~~Y~ri~FFlALYLAndmEED~ 69 (131)
T PF11357_consen 13 PVIQKFLAWDKCLRVSDKYLLAMVIAYFSRAGLFSWQYQRIHFFLALYLANDMEEDD 69 (131)
T ss_pred HHHHHHHHhCcchhhhhHHHHHHHHHHHHhcccchhhcchHHHHHHHHHhhHHHhcc
Confidence 55666655544444455556666667777654 2567765 89999996653
No 26
>PF14733 ACDC: AP2-coincident C-terminal
Probab=29.83 E-value=2.2e+02 Score=20.61 Aligned_cols=66 Identities=12% Similarity=0.097 Sum_probs=41.1
Q ss_pred chhHHHHHhHHHHHHhhhcC-hh----HHHHHHHHHHHHHHHHhhcCChHHHHhHHHHHHHhhhCcccCCC
Q 046621 57 QRVSFLYLANDILQNSRRKG-SE----FVNEFWKVLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSR 122 (213)
Q Consensus 57 ~KL~lLYLaNDIlqnskrk~-~~----f~~~F~~vLp~~~~~v~~~~d~~~~~kv~rll~IWeeR~Vf~~~ 122 (213)
.|.++.|+++|+..+|.-.. +. .++....++-.-+..+....+...-.....|+.--=..++-|++
T Consensus 8 ~K~Ai~~iL~DL~~~c~~~~~~~~~~~~~~~~~~~i~~H~~~V~~a~~~~~L~pyl~lF~~cI~~~~LPS~ 78 (91)
T PF14733_consen 8 CKEAILLILSDLKDNCLPNLFSKLLNASRKIYKRVIDYHIRYVNSAKNIEELQPYLALFSNCIKNNILPSQ 78 (91)
T ss_pred HHHHHHHHHHHHHHhhchhhhhhhhhhhHHHHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHcCCCCCc
Confidence 57889999999999999653 22 33345555665566665443444445555555555566666665
No 27
>PF12652 CotJB: CotJB protein; InterPro: IPR024207 The cotJ operon proteins affect spore coat composition, and is controlled by sigma E. The genes, which include CotJB, are either required for the normal formation of the inner layers of the coat or are themselves structural components of the coat []. CotJB has been identified as a spore coat protein [].
Probab=29.71 E-value=1.2e+02 Score=21.90 Aligned_cols=35 Identities=23% Similarity=0.401 Sum_probs=31.0
Q ss_pred HHHHHHHhhCCChHHHHHHhHHHHHHHhhhhhhhh
Q 046621 174 TAFQSVLDEHPNEEVALNNCNAAVHHAGKVSEDVE 208 (213)
Q Consensus 174 ~~~~~~~~~~~~e~~~~~k~~~~~~~~~~~~~~~~ 208 (213)
-....-+|.|.++..+++-.+.......++.++++
T Consensus 16 ~dl~LyLDTHP~d~~Al~~y~~~~~~~~~l~~~Ye 50 (78)
T PF12652_consen 16 VDLNLYLDTHPDDQEALEYYNEYSKQRKQLKKEYE 50 (78)
T ss_pred HHHHHHhcCCCCcHHHHHHHHHHHHHHHHHHHHHH
Confidence 34467789999999999999999999999999876
No 28
>PF07261 DnaB_2: Replication initiation and membrane attachment; InterPro: IPR006343 This entry represents a domain found in several bacterial replication initiation and membrane attachment proteins, DnaB and DnaD. The DnaD protein is a component of the PriA primosome. The PriA primosome functions to recruit the replication fork helicase onto the DNA []. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria []. The DnaB protein is essential for both replication initiation and membrane attachment of the origin region of the chromosome and Plasmid pUB110 in Bacillus subtilis. It is known that there are two different classes (DnaBI and DnaBII) in the DnaB mutants; DnaBI is essential for both chromosome and pUB110 replication, whereas DnaBII is necessary only for chromosome replication []. This domain tends to be found towards the C terminus of DnaB and DnaD proteins and is alpha helical in nature.; PDB: 2I5U_A 2ZC2_A.
Probab=25.99 E-value=1.7e+02 Score=19.76 Aligned_cols=40 Identities=13% Similarity=0.330 Sum_probs=25.7
Q ss_pred HHHH-HHHHHHHHHhhcCChHHHHhHHHHHHHhhhCcccCCC
Q 046621 82 EFWK-VLPAALKHVYDNGDEYGKKAVTRLVDIWEERKVFGSR 122 (213)
Q Consensus 82 ~F~~-vLp~~~~~v~~~~d~~~~~kv~rll~IWeeR~Vf~~~ 122 (213)
.|.+ ++-.++..+...+ .....=+.+|++=|.+++|.+.+
T Consensus 29 ~~~~~~v~~ai~~~~~~~-~~~~~Yi~~Il~~W~~~gi~t~e 69 (77)
T PF07261_consen 29 GFSPEVVNEAIEYALENN-KRSFNYIEKILNNWKQKGIKTVE 69 (77)
T ss_dssp HHHHHHHHHHHHHHHHCT---SHHHHHHHHHHHHHCT--SCC
T ss_pred CCCHHHHHHHHHHHHHcC-CCCHHHHHHHHHHHHHcCCCCHH
Confidence 3443 5555666666432 23378889999999999999976
No 29
>PF12348 CLASP_N: CLASP N terminal; InterPro: IPR024395 This domain is found in the N-terminal region of CLIP-associated proteins (CLASPs), which are widely conserved microtubule plus-end-tracking proteins that regulate the stability of dynamic microtubules [, ]. The domain is also found in other proteins involved in microtubule binding, including STU1, MOR1 and spindle pole body component Alp14.; PDB: 2QK2_A.
Probab=25.76 E-value=3.7e+02 Score=21.97 Aligned_cols=99 Identities=16% Similarity=0.170 Sum_probs=51.0
Q ss_pred cHHHHHHHHHHHHhc--hhchHHHHHHHH---HHhccCc--ccchh--HHHHHhHHHHHHhhhcChhHHHHHHHHHHHHH
Q 046621 21 SQQSIESLSRWCITH--RKKAKQIVETWD---KSFNSSQ--KEQRV--SFLYLANDILQNSRRKGSEFVNEFWKVLPAAL 91 (213)
Q Consensus 21 Sq~SIqs~s~W~l~h--~~~a~~Iv~~w~---~~l~~a~--~~~KL--~lLYLaNDIlqnskrk~~~f~~~F~~vLp~~~ 91 (213)
-.+.++.+...+..| ....+.++.++. ..+...- .+.+| .-+.++.++..+.+ ..|...+..++|.++
T Consensus 24 r~~al~~L~~l~~~~~~~~~~~~~~~~l~~~~~~i~~~l~d~Rs~v~~~A~~~l~~l~~~l~---~~~~~~~~~~l~~Ll 100 (228)
T PF12348_consen 24 RVEALQKLRSLIKGNAPEDFPPDFVECLRQLLDAIIKQLSDLRSKVSKTACQLLSDLARQLG---SHFEPYADILLPPLL 100 (228)
T ss_dssp HHHHHHHHHHHHHH-B-----HHHHHHHH---HHHHH-S-HH---HHHHHHHHHHHHHHHHG---GGGHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCccccHHHHHHHHHHhHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHh---HhHHHHHHHHHHHHH
Confidence 367899999999998 445566666665 2332221 22222 22445555555533 346666777888888
Q ss_pred HHHhhcCChHHHHhHHHHHHHhhhCcccCCCc
Q 046621 92 KHVYDNGDEYGKKAVTRLVDIWEERKVFGSRG 123 (213)
Q Consensus 92 ~~v~~~~d~~~~~kv~rll~IWeeR~Vf~~~~ 123 (213)
..+... ...++.....++..+-+.--|++.+
T Consensus 101 ~~~~~~-~~~i~~~a~~~L~~i~~~~~~~~~~ 131 (228)
T PF12348_consen 101 KKLGDS-KKFIREAANNALDAIIESCSYSPKI 131 (228)
T ss_dssp HGGG----HHHHHHHHHHHHHHHTTS-H--HH
T ss_pred HHHccc-cHHHHHHHHHHHHHHHHHCCcHHHH
Confidence 777543 3456777777655554433344554
No 30
>TIGR02753 sodN superoxide dismutase, Ni. This superoxide dismutase uses nickel, rather than iron, manganese, copper, or zinc. Its gene is always accompanied by a gene for a required protease.
Probab=21.01 E-value=4.6e+02 Score=21.30 Aligned_cols=64 Identities=19% Similarity=0.266 Sum_probs=43.3
Q ss_pred HHHHHHhhcc----CcHHHHHHHHHHHHhchhchHH----HHHHHHHHhccCcccchhHHHHHhHHHHHHhh
Q 046621 10 ILSEKLSKLN----NSQQSIESLSRWCITHRKKAKQ----IVETWDKSFNSSQKEQRVSFLYLANDILQNSR 73 (213)
Q Consensus 10 ~~~~kL~~L~----~Sq~SIqs~s~W~l~h~~~a~~----Iv~~w~~~l~~a~~~~KL~lLYLaNDIlqnsk 73 (213)
...+++..|. ++-++-...+.|++.-..++.. |.-.|-++|+...+++--.+.=+.+.++..+.
T Consensus 43 ~~~~ki~~l~~~~~~~~~~~n~~~R~i~~KE~~A~~vk~~i~vlWtDYFKp~h~e~yP~lh~l~h~~~~~a~ 114 (145)
T TIGR02753 43 AMTKKLNALKPPSSLDADYQNTFSRFVAVKEEQAIETKKEISVLWTDYFKPPHLEQFPELHELVWKAAKACS 114 (145)
T ss_pred HHHHHHHhccCCcccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccHhhchHHHHHHHHHHHHHH
Confidence 4556666665 2456778899999987777755 66678899976555543444556666666543
No 31
>PF08926 DUF1908: Domain of unknown function (DUF1908); InterPro: IPR015022 This domain is found in microtubule-associated serine/threonine-protein kinases. ; GO: 0000287 magnesium ion binding, 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1V9V_A.
Probab=20.02 E-value=4.8e+02 Score=23.47 Aligned_cols=51 Identities=27% Similarity=0.344 Sum_probs=36.1
Q ss_pred HHHhHHHHHHhhhcC--hhHHHHHHHHHHHHHHHHhhcCCh----HHHHhHHHHHHH
Q 046621 62 LYLANDILQNSRRKG--SEFVNEFWKVLPAALKHVYDNGDE----YGKKAVTRLVDI 112 (213)
Q Consensus 62 LYLaNDIlqnskrk~--~~f~~~F~~vLp~~~~~v~~~~d~----~~~~kv~rll~I 112 (213)
+=+|.|.|+.|+..- ..|.-++...|..++..++....+ .+.+-|++++-|
T Consensus 169 vElARDCL~KS~~~lITs~YF~ElsEnLekLl~ea~erS~~~~~~~~~~lvrklL~I 225 (282)
T PF08926_consen 169 VELARDCLQKSREGLITSRYFYELSENLEKLLQEAHERSESEEVAFVTQLVRKLLII 225 (282)
T ss_dssp HHHHHHHHHHHHTT---HHHHHHHHHHHHHHHHHHHHTS-HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhccCchHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHHHHHHHH
Confidence 569999999998763 578888888899999888876423 334555555544
Done!