Query psy12936
Match_columns 187
No_of_seqs 181 out of 369
Neff 4.3
Searched_HMMs 46136
Date Fri Aug 16 23:31:56 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12936.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12936hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1763|consensus 100.0 4E-61 8.7E-66 424.1 8.8 156 1-170 158-314 (343)
2 COG5252 Uncharacterized conser 100.0 6.1E-44 1.3E-48 308.7 5.0 134 1-141 143-278 (299)
3 KOG4018|consensus 98.9 4.9E-10 1.1E-14 96.1 3.0 71 49-128 125-195 (215)
4 PF01396 zf-C4_Topoisom: Topoi 95.7 0.0065 1.4E-07 39.1 1.8 26 9-34 13-38 (39)
5 smart00356 ZnF_C3H1 zinc finge 94.8 0.014 2.9E-07 33.4 1.0 14 19-32 14-27 (27)
6 PF00642 zf-CCCH: Zinc finger 94.8 0.01 2.3E-07 35.1 0.5 22 1-31 5-26 (27)
7 PF14608 zf-CCCH_2: Zinc finge 93.2 0.052 1.1E-06 30.1 1.3 13 19-31 7-19 (19)
8 KOG1763|consensus 72.8 1.4 3.1E-05 40.5 0.6 53 1-66 94-153 (343)
9 COG0551 TopA Zn-finger domain 69.6 2.6 5.6E-05 33.1 1.4 18 11-28 31-48 (140)
10 KOG1039|consensus 63.6 4.1 8.9E-05 37.6 1.6 27 2-36 252-278 (344)
11 KOG2185|consensus 60.7 4.2 9.1E-05 39.0 1.1 22 1-32 142-163 (486)
12 COG5175 MOT2 Transcriptional r 55.0 10 0.00022 35.9 2.6 16 18-34 212-227 (480)
13 KOG1039|consensus 53.8 4.3 9.3E-05 37.5 -0.0 24 1-34 10-33 (344)
14 KOG1040|consensus 53.1 6 0.00013 36.3 0.8 15 19-33 116-130 (325)
15 PF13295 DUF4077: Domain of un 52.7 4.6 0.0001 33.2 0.0 22 1-22 27-56 (175)
16 PF08432 Vfa1: AAA-ATPase Vps4 49.9 15 0.00032 30.6 2.6 11 12-22 31-41 (182)
17 KOG2494|consensus 49.7 6.7 0.00015 36.3 0.6 21 1-31 39-60 (331)
18 PF15086 UPF0542: Uncharacteri 45.9 40 0.00087 25.1 4.0 33 70-102 30-63 (74)
19 smart00661 RPOL9 RNA polymeras 45.5 9.5 0.00021 24.7 0.7 25 16-43 19-43 (52)
20 KOG0878|consensus 43.8 11 0.00024 30.4 0.9 14 23-36 60-73 (124)
21 PRK07561 DNA topoisomerase I s 42.9 12 0.00025 38.2 1.1 26 9-34 599-627 (859)
22 KOG2295|consensus 40.4 9.2 0.0002 37.9 -0.0 47 4-52 496-543 (648)
23 PF06839 zf-GRF: GRF zinc fing 40.3 19 0.00041 23.3 1.5 20 11-30 19-40 (45)
24 KOG1040|consensus 40.1 12 0.00027 34.3 0.8 17 19-35 144-160 (325)
25 PF00706 Toxin_4: Anenome neur 39.8 9.7 0.00021 25.6 0.0 14 16-29 21-35 (43)
26 PRK06319 DNA topoisomerase I/S 39.6 17 0.00037 37.1 1.7 24 10-33 658-681 (860)
27 KOG4791|consensus 39.4 15 0.00032 36.2 1.2 18 17-34 66-86 (667)
28 PRK07220 DNA topoisomerase I; 37.1 28 0.00061 34.9 2.7 68 11-84 651-738 (740)
29 COG5222 Uncharacterized conser 37.1 41 0.00088 31.5 3.6 58 7-74 300-358 (427)
30 PRK07219 DNA topoisomerase I; 35.9 17 0.00038 36.7 1.1 24 11-34 616-640 (822)
31 PF02662 FlpD: Methyl-viologen 34.4 31 0.00067 27.0 2.1 28 3-31 43-71 (124)
32 PF05416 Peptidase_C37: Southa 34.0 13 0.00028 36.1 -0.1 20 15-35 381-401 (535)
33 COG5084 YTH1 Cleavage and poly 33.7 17 0.00038 32.9 0.6 18 20-37 146-163 (285)
34 PF03194 LUC7: LUC7 N_terminus 32.0 15 0.00031 32.4 -0.1 22 1-32 32-62 (254)
35 cd01121 Sms Sms (bacterial rad 31.1 19 0.00042 33.1 0.5 9 14-22 11-19 (372)
36 KOG4312|consensus 30.6 26 0.00057 33.2 1.3 17 19-35 368-384 (449)
37 PF07141 Phage_term_sma: Putat 30.4 57 0.0012 27.2 3.1 47 71-121 41-91 (174)
38 KOG0378|consensus 30.2 24 0.00052 31.7 0.9 34 11-44 21-54 (263)
39 PRK06319 DNA topoisomerase I/S 29.8 29 0.00064 35.4 1.6 26 9-34 605-630 (860)
40 TIGR00416 sms DNA repair prote 29.7 20 0.00043 33.8 0.4 9 14-22 18-26 (454)
41 COG1781 PyrI Aspartate carbamo 28.9 30 0.00064 28.9 1.2 26 17-43 106-133 (153)
42 KOG1677|consensus 28.1 29 0.00062 30.5 1.1 15 19-33 188-202 (332)
43 PF14753 DUF4475: Domain of un 27.9 24 0.00052 30.5 0.5 22 6-28 28-49 (196)
44 PRK11823 DNA repair protein Ra 27.8 23 0.0005 33.2 0.4 9 14-22 18-26 (446)
45 KOG4791|consensus 27.2 22 0.00047 35.1 0.1 8 24-31 46-53 (667)
46 PF07936 Defensin_4: Potassium 27.1 16 0.00035 23.4 -0.5 13 16-28 13-31 (34)
47 PRK06599 DNA topoisomerase I; 26.5 40 0.00086 33.4 1.8 25 10-34 599-623 (675)
48 PF10587 EF-1_beta_acid: Eukar 25.5 30 0.00065 21.3 0.5 7 124-130 1-7 (28)
49 PF02748 PyrI_C: Aspartate car 25.4 33 0.00072 23.4 0.8 21 18-39 7-29 (52)
50 PRK11548 outer membrane biogen 23.8 64 0.0014 24.7 2.2 49 20-78 20-68 (113)
51 PRK14973 DNA topoisomerase I; 23.4 32 0.0007 35.7 0.6 71 8-84 648-723 (936)
52 PF10050 DUF2284: Predicted me 22.9 23 0.00049 28.8 -0.5 11 12-22 25-35 (166)
53 PF00111 Fer2: 2Fe-2S iron-sul 22.5 74 0.0016 21.7 2.1 32 5-37 19-52 (78)
54 PRK07561 DNA topoisomerase I s 20.7 47 0.001 34.0 1.0 24 10-33 716-740 (859)
55 PRK14973 DNA topoisomerase I; 20.1 52 0.0011 34.3 1.2 24 10-33 601-624 (936)
No 1
>KOG1763|consensus
Probab=100.00 E-value=4e-61 Score=424.09 Aligned_cols=156 Identities=50% Similarity=0.950 Sum_probs=138.3
Q ss_pred CchhHHHHHHcCCCCccccCCC-CCCccccccCCCccccccchhhHhhhcccChHHHHHHHHHHhccCCCcccccHHHHH
Q psy12936 1 ICKYFIEAVENSKYGWFWSCPN-GPTCIYKHALPPGFVLKKDKKKEEKKDQISLEDLIERERAALAASSKFTKVTLDSFL 79 (187)
Q Consensus 1 vCk~fl~Ave~~kYGwfW~CPn-G~~C~YrH~LPpG~Vlk~~~k~ee~~~eisLEE~iE~ER~kL~~~~~gTpVT~EsFl 79 (187)
||||||+|||+|+|||||+||| |+.|+||||||+|||||+++|+++++++||||++||.||++|++| +||||+|||+
T Consensus 158 VCKfFLeAvE~~kYGWfW~CPnGg~~C~YrHaLP~GyVLk~dkkk~ek~~eISlEe~IE~ER~~L~~n--lT~~T~e~F~ 235 (343)
T KOG1763|consen 158 VCKFFLEAVENGKYGWFWECPNGGDKCIYRHALPEGYVLKRDKKKLEKQDEISLEELIEKERAALGPN--LTPLTEETFK 235 (343)
T ss_pred HHHHHHHHHhcCCccceeECCCCCCeeeeeecCCcchhhhhhhhhhcccccccHHHHHHHHHHhcCCC--CccccHHHHH
Confidence 8999999999999999999999 589999999999999999999999999999999999999999999 9999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhhhccccCcccccccccCCCCccCCCCcCcccccccccCCCCCCccccccchhhhh
Q psy12936 80 AWKKRKLKEKSEAMTKAEEKKRSDFKAGRQVGLSGRDMFSFNPDLAKDDMDEGDEAFDSYTRDEEEDPESNYRELDLDML 159 (187)
Q Consensus 80 ~WKkkk~~Ek~~~~~~~~e~kk~~~kaGk~~~LSGRELFe~dp~L~~DD~d~~dea~d~~~~~~~~~~~~~~~~idl~~~ 159 (187)
+||+++++++++++++.+++++ +.|++. |||||||+++++||+||+++ .++++...+.+++|+.+.+++||+..|
T Consensus 236 ~WKk~k~~er~~k~~~~~~~~k---~~gk~~-~sGRElF~~~~dl~~dd~~e-~~d~e~~~~~ee~d~~~k~~e~d~~~~ 310 (343)
T KOG1763|consen 236 AWKKRKIRERKEKLAAEKAERK---KVGKSN-MSGRELFESNADLVNDDDEE-AGDLEYTEYSEETDEEAKVKEADAPIF 310 (343)
T ss_pred HHHHhhHHHHHHHHHHHHHHhh---hhccCC-CchHHHHhhchhhccCchhh-ccchhhhhhccchhhhhhhhhcccccc
Confidence 9999999999999888776665 678866 99999999999999996322 222333334678889999999999888
Q ss_pred hhhccccccCC
Q psy12936 160 LNEAAELDETN 170 (187)
Q Consensus 160 ~~~~~~vd~tg 170 (187)
|++|
T Consensus 311 -------d~~~ 314 (343)
T KOG1763|consen 311 -------DGSG 314 (343)
T ss_pred -------cccC
Confidence 6777
No 2
>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=6.1e-44 Score=308.74 Aligned_cols=134 Identities=40% Similarity=0.757 Sum_probs=110.0
Q ss_pred CchhHHHHHHcCCCCccccCCCC-CCccccccCCCccccccchhhHhhhcccChHHHHHHHHHHhccCCCcccccHHHHH
Q psy12936 1 ICKYFIEAVENSKYGWFWSCPNG-PTCIYKHALPPGFVLKKDKKKEEKKDQISLEDLIERERAALAASSKFTKVTLDSFL 79 (187)
Q Consensus 1 vCk~fl~Ave~~kYGwfW~CPnG-~~C~YrH~LPpG~Vlk~~~k~ee~~~eisLEE~iE~ER~kL~~~~~gTpVT~EsFl 79 (187)
||||||+|+|+|+|||||.|||| +.|+|+|+||.||||++++++.+.+.+||||++||.||+.|+++ +||||.|+|.
T Consensus 143 VCkffieA~e~GkYgw~W~CPng~~~C~y~H~Lp~GyVLsrdk~Kd~tq~eislEefIE~eR~~L~~~--LTP~TeenFk 220 (299)
T COG5252 143 VCKFFIEAMESGKYGWGWTCPNGNMRCSYIHKLPDGYVLSRDKIKDSTQVEISLEEFIELERQSLPEK--LTPLTEENFK 220 (299)
T ss_pred HHHHHHHHHhcCCccceeeCCCCCceeeeeeccCccceeccccccccccccccHHHHHHHHhccCCCc--CCcccHHHHH
Confidence 79999999999999999999995 89999999999999999999999999999999999999999999 9999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhhhccccCcccc-cccccCCCCccCCCCcCccccccccc
Q psy12936 80 AWKKRKLKEKSEAMTKAEEKKRSDFKAGRQVGLSGR-DMFSFNPDLAKDDMDEGDEAFDSYTR 141 (187)
Q Consensus 80 ~WKkkk~~Ek~~~~~~~~e~kk~~~kaGk~~~LSGR-ELFe~dp~L~~DD~d~~dea~d~~~~ 141 (187)
+||.-++-.....+++....|+ -.|+.+ +||+ ++|+.+..++-||.. +.++||..++
T Consensus 221 ~Wkd~~~~r~lkq~ee~~s~Rk---~~gr~~-~~k~~e~FEt~~d~~~ddv~-~ge~wD~te~ 278 (299)
T COG5252 221 EWKDGRRLRILKQKEEKESARK---VKGRAT-GTKGVELFETRRDLFKDDVE-AGEEWDYTER 278 (299)
T ss_pred HhccchHHHHHHHHHHHHhccc---chhhhh-hccchhhhhccccccccccc-ccccccHHHH
Confidence 9998777554333332222222 235644 4555 999999999999754 3345665544
No 3
>KOG4018|consensus
Probab=98.93 E-value=4.9e-10 Score=96.08 Aligned_cols=71 Identities=28% Similarity=0.400 Sum_probs=52.5
Q ss_pred cccChHHHHHHHHHHhccCCCcccccHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhccccCcccccccccCCCCccCC
Q psy12936 49 DQISLEDLIERERAALAASSKFTKVTLDSFLAWKKRKLKEKSEAMTKAEEKKRSDFKAGRQVGLSGRDMFSFNPDLAKDD 128 (187)
Q Consensus 49 ~eisLEE~iE~ER~kL~~~~~gTpVT~EsFl~WKkkk~~Ek~~~~~~~~e~kk~~~kaGk~~~LSGRELFe~dp~L~~DD 128 (187)
-++..++..|.||++++ |||||++||++||.+|.++......+.+. + .++ ..+++|||++|+.++.+-.+|
T Consensus 125 ~e~~~~~~ee~e~~kfh----gt~VT~esfl~Wk~~fe~el~~~~~k~~~-~---~~~-~~~k~tgRQ~f~~d~~~~~~~ 195 (215)
T KOG4018|consen 125 REQEAREAEEEERKKFH----GTPVTLESFLEWKLKFEEELLQIKAKVKK-R---LQA-LAKKLTGRQLFETDHKGDRSD 195 (215)
T ss_pred HHHHHHHHHHHhhcccc----CCceehhhhHHHHHhhhhhhhhhhhhhhh-H---HHH-HhhhHHHHHHHHhcccCChhh
Confidence 34566777778888877 99999999999999999998433333222 2 122 235699999999998887764
No 4
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=95.72 E-value=0.0065 Score=39.13 Aligned_cols=26 Identities=38% Similarity=0.795 Sum_probs=23.3
Q ss_pred HHcCCCCccccCCCCCCccccccCCC
Q psy12936 9 VENSKYGWFWSCPNGPTCIYKHALPP 34 (187)
Q Consensus 9 ve~~kYGwfW~CPnG~~C~YrH~LPp 34 (187)
+..+++|.||.|.|-..|.|...||+
T Consensus 13 ~r~~k~g~F~~Cs~yP~C~~~~~~~~ 38 (39)
T PF01396_consen 13 LRRGKKGKFLGCSNYPECKYTEPLPK 38 (39)
T ss_pred EEECCCCCEEECCCCCCcCCeEeCCC
Confidence 35789999999999999999999985
No 5
>smart00356 ZnF_C3H1 zinc finger.
Probab=94.83 E-value=0.014 Score=33.41 Aligned_cols=14 Identities=43% Similarity=1.092 Sum_probs=12.6
Q ss_pred cCCCCCCccccccC
Q psy12936 19 SCPNGPTCIYKHAL 32 (187)
Q Consensus 19 ~CPnG~~C~YrH~L 32 (187)
.|+.|+.|.|.|.+
T Consensus 14 ~C~~g~~C~~~H~~ 27 (27)
T smart00356 14 YCPYGDRCKFAHPL 27 (27)
T ss_pred CCCCCCCcCCCCcC
Confidence 79999999999964
No 6
>PF00642 zf-CCCH: Zinc finger C-x8-C-x5-C-x3-H type (and similar); InterPro: IPR000571 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents C-x8-C-x5-C-x3-H (CCCH) type Zinc finger (Znf) domains. Proteins containing CCCH Znf domains include Znf proteins from eukaryotes involved in cell cycle or growth phase-related regulation, e.g. human TIS11B (butyrate response factor 1), a probable regulatory protein involved in regulating the response to growth factors, and the mouse TTP growth factor-inducible nuclear protein, which has the same function. The mouse TTP protein is induced by growth factors. Another protein containing this domain is the human splicing factor U2AF 35kDa subunit, which plays a critical role in both constitutive and enhancer-dependent splicing by mediating essential protein-protein interactions and protein-RNA interactions required for 3' splice site selection. It has been shown that different CCCH-type Znf proteins interact with the 3'-untranslated region of various mRNA [, ]. This type of Znf is very often present in two copies. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding; PDB: 1M9O_A 1RGO_A 2CQE_A 2FC6_A 2D9M_A 2E5S_A 2RHK_C 2D9N_A 3D2S_A 3D2Q_C ....
Probab=94.78 E-value=0.01 Score=35.14 Aligned_cols=22 Identities=36% Similarity=1.256 Sum_probs=16.0
Q ss_pred CchhHHHHHHcCCCCccccCCCCCCcccccc
Q psy12936 1 ICKYFIEAVENSKYGWFWSCPNGPTCIYKHA 31 (187)
Q Consensus 1 vCk~fl~Ave~~kYGwfW~CPnG~~C~YrH~ 31 (187)
+|++|+.. | .||.|+.|.|.|.
T Consensus 5 ~C~~f~~~------g---~C~~G~~C~f~H~ 26 (27)
T PF00642_consen 5 LCRFFMRT------G---TCPFGDKCRFAHG 26 (27)
T ss_dssp B-HHHHHT------S-----TTGGGSSSBSS
T ss_pred cChhhccC------C---ccCCCCCcCccCC
Confidence 58999874 2 5999999999994
No 7
>PF14608 zf-CCCH_2: Zinc finger C-x8-C-x5-C-x3-H type
Probab=93.24 E-value=0.052 Score=30.06 Aligned_cols=13 Identities=38% Similarity=1.104 Sum_probs=11.5
Q ss_pred cCCCCCCcccccc
Q psy12936 19 SCPNGPTCIYKHA 31 (187)
Q Consensus 19 ~CPnG~~C~YrH~ 31 (187)
.|+||++|.|+|.
T Consensus 7 ~C~~~~~C~f~HP 19 (19)
T PF14608_consen 7 NCTNGDNCPFSHP 19 (19)
T ss_pred CCCCCCcCccCCc
Confidence 3999999999994
No 8
>KOG1763|consensus
Probab=72.80 E-value=1.4 Score=40.45 Aligned_cols=53 Identities=25% Similarity=0.600 Sum_probs=36.0
Q ss_pred CchhHHHHHHcCCCCccccCCCCCCccccccCCCccccccchhh-------HhhhcccChHHHHHHHHHHhcc
Q psy12936 1 ICKYFIEAVENSKYGWFWSCPNGPTCIYKHALPPGFVLKKDKKK-------EEKKDQISLEDLIERERAALAA 66 (187)
Q Consensus 1 vCk~fl~Ave~~kYGwfW~CPnG~~C~YrH~LPpG~Vlk~~~k~-------ee~~~eisLEE~iE~ER~kL~~ 66 (187)
||=||.+++ |--|+.|++.|-|-.+ ++..|. .+-.++-.|+++++.-+.+..+
T Consensus 94 vCafFk~g~----------C~KG~kCKFsHdl~~~---~k~eK~dly~d~rdemWD~~kl~~vv~~K~~k~k~ 153 (343)
T KOG1763|consen 94 VCAFFKQGT----------CTKGDKCKFSHDLAVE---RKKEKIDLYPDTRDEMWDEEKLEEVVLKKHGKPKP 153 (343)
T ss_pred HHHHHhccC----------CCCCCcccccchHHHh---hhccchhccccchhhhhhHHHHHHHHHhhccCCCC
Confidence 688888874 8889999999999842 221221 1125667888888877654444
No 9
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=69.63 E-value=2.6 Score=33.09 Aligned_cols=18 Identities=50% Similarity=1.012 Sum_probs=16.7
Q ss_pred cCCCCccccCCCCCCccc
Q psy12936 11 NSKYGWFWSCPNGPTCIY 28 (187)
Q Consensus 11 ~~kYGwfW~CPnG~~C~Y 28 (187)
.++||||+.|-|..+|.|
T Consensus 31 ~~~~g~f~gCs~yP~C~~ 48 (140)
T COG0551 31 FGKYGIFLGCSNYPKCDY 48 (140)
T ss_pred EccCCeEEEeCCCCCCCC
Confidence 578999999999999999
No 10
>KOG1039|consensus
Probab=63.61 E-value=4.1 Score=37.65 Aligned_cols=27 Identities=56% Similarity=1.148 Sum_probs=21.0
Q ss_pred chhHHHHHHcCCCCccccCCCCCCccccccCCCcc
Q psy12936 2 CKYFIEAVENSKYGWFWSCPNGPTCIYKHALPPGF 36 (187)
Q Consensus 2 Ck~fl~Ave~~kYGwfW~CPnG~~C~YrH~LPpG~ 36 (187)
|+||- ++ -=.||.|.+|-|+|.+|-|=
T Consensus 252 c~yf~------~~--~g~cPf~s~~~y~h~~~~~~ 278 (344)
T KOG1039|consen 252 CKYFS------QG--LGSCPFGSKCFYKHLLPSGA 278 (344)
T ss_pred hhhhc------CC--CCCCCCCCcccccccccccc
Confidence 77776 11 24699999999999999764
No 11
>KOG2185|consensus
Probab=60.72 E-value=4.2 Score=38.96 Aligned_cols=22 Identities=41% Similarity=1.056 Sum_probs=19.3
Q ss_pred CchhHHHHHHcCCCCccccCCCCCCccccccC
Q psy12936 1 ICKYFIEAVENSKYGWFWSCPNGPTCIYKHAL 32 (187)
Q Consensus 1 vCk~fl~Ave~~kYGwfW~CPnG~~C~YrH~L 32 (187)
.|+|||+- .|-.|.+|.+.|-+
T Consensus 142 pC~ffLeg----------~CRF~enCRfSHG~ 163 (486)
T KOG2185|consen 142 PCKFFLEG----------RCRFGENCRFSHGL 163 (486)
T ss_pred cchHhhcc----------ccccCcccccccCc
Confidence 59999986 69999999999954
No 12
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=54.99 E-value=10 Score=35.94 Aligned_cols=16 Identities=50% Similarity=1.151 Sum_probs=13.1
Q ss_pred ccCCCCCCccccccCCC
Q psy12936 18 WSCPNGPTCIYKHALPP 34 (187)
Q Consensus 18 W~CPnG~~C~YrH~LPp 34 (187)
=+||| .+|||.|-.-|
T Consensus 212 ~~CpN-p~CMyLHEpg~ 227 (480)
T COG5175 212 AVCPN-PDCMYLHEPGP 227 (480)
T ss_pred CCCCC-CCeeeecCCCc
Confidence 47999 88999997553
No 13
>KOG1039|consensus
Probab=53.81 E-value=4.3 Score=37.55 Aligned_cols=24 Identities=42% Similarity=0.955 Sum_probs=20.7
Q ss_pred CchhHHHHHHcCCCCccccCCCCCCccccccCCC
Q psy12936 1 ICKYFIEAVENSKYGWFWSCPNGPTCIYKHALPP 34 (187)
Q Consensus 1 vCk~fl~Ave~~kYGwfW~CPnG~~C~YrH~LPp 34 (187)
|||||+.-+ |-.|+.|.|-|.+|.
T Consensus 10 ic~~~~~g~----------c~~g~~cr~~h~~~~ 33 (344)
T KOG1039|consen 10 ICKYYQKGN----------CKFGDLCRLSHSLPD 33 (344)
T ss_pred hhhhccccc----------ccccceeeeeccCch
Confidence 799988764 778899999999994
No 14
>KOG1040|consensus
Probab=53.14 E-value=6 Score=36.32 Aligned_cols=15 Identities=47% Similarity=1.028 Sum_probs=12.2
Q ss_pred cCCCCCCccccccCC
Q psy12936 19 SCPNGPTCIYKHALP 33 (187)
Q Consensus 19 ~CPnG~~C~YrH~LP 33 (187)
.|-||.+|-|.|-=|
T Consensus 116 ~c~~~~~c~y~h~dp 130 (325)
T KOG1040|consen 116 ECTNGKDCPYLHGDP 130 (325)
T ss_pred ccccccCCcccCCCh
Confidence 488888888888877
No 15
>PF13295 DUF4077: Domain of unknown function (DUF4077)
Probab=52.67 E-value=4.6 Score=33.16 Aligned_cols=22 Identities=36% Similarity=1.109 Sum_probs=19.9
Q ss_pred CchhHHHHHHcCCCCc--------cccCCC
Q psy12936 1 ICKYFIEAVENSKYGW--------FWSCPN 22 (187)
Q Consensus 1 vCk~fl~Ave~~kYGw--------fW~CPn 22 (187)
+|.|||--|--|-||. ||+|.-
T Consensus 27 icsfflgiiaigyygyifteraiafwvcgi 56 (175)
T PF13295_consen 27 ICSFFLGIIAIGYYGYIFTERAIAFWVCGI 56 (175)
T ss_pred HHHHHHHHHHHhhhheeehhHHHHHHhhch
Confidence 6999999999999997 899974
No 16
>PF08432 Vfa1: AAA-ATPase Vps4-associated protein 1; InterPro: IPR013640 This is a family of fungal proteins of unknown function.
Probab=49.92 E-value=15 Score=30.61 Aligned_cols=11 Identities=27% Similarity=0.999 Sum_probs=8.8
Q ss_pred CCCCccccCCC
Q psy12936 12 SKYGWFWSCPN 22 (187)
Q Consensus 12 ~kYGwfW~CPn 22 (187)
+.=-||.+||.
T Consensus 31 ~~~DfFY~C~~ 41 (182)
T PF08432_consen 31 DNKDFFYVCPS 41 (182)
T ss_pred CCCCeEEeCcc
Confidence 34479999998
No 17
>KOG2494|consensus
Probab=49.68 E-value=6.7 Score=36.28 Aligned_cols=21 Identities=29% Similarity=0.996 Sum_probs=13.7
Q ss_pred CchhHHHHHHcCCCCccccCCCCCC-cccccc
Q psy12936 1 ICKYFIEAVENSKYGWFWSCPNGPT-CIYKHA 31 (187)
Q Consensus 1 vCk~fl~Ave~~kYGwfW~CPnG~~-C~YrH~ 31 (187)
||+-||--+ |--|+. |+|+|-
T Consensus 39 VCReF~rn~----------C~R~d~~CkfaHP 60 (331)
T KOG2494|consen 39 VCREFLRNT----------CSRGDRECKFAHP 60 (331)
T ss_pred HHHHHHhcc----------ccCCCccccccCC
Confidence 677777653 666665 777774
No 18
>PF15086 UPF0542: Uncharacterised protein family UPF0542
Probab=45.92 E-value=40 Score=25.05 Aligned_cols=33 Identities=30% Similarity=0.489 Sum_probs=22.1
Q ss_pred ccccc-HHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q psy12936 70 FTKVT-LDSFLAWKKRKLKEKSEAMTKAEEKKRS 102 (187)
Q Consensus 70 gTpVT-~EsFl~WKkkk~~Ek~~~~~~~~e~kk~ 102 (187)
+||.= +--|+.||-.+.-+++++.++.+.+|.+
T Consensus 30 LtPlfiisa~lSwkLaK~ie~~ere~K~k~Kr~~ 63 (74)
T PF15086_consen 30 LTPLFIISAVLSWKLAKAIEKEEREKKKKAKRQA 63 (74)
T ss_pred HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56654 3459999999988877766654444443
No 19
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=45.53 E-value=9.5 Score=24.65 Aligned_cols=25 Identities=24% Similarity=0.553 Sum_probs=19.5
Q ss_pred ccccCCCCCCccccccCCCccccccchh
Q psy12936 16 WFWSCPNGPTCIYKHALPPGFVLKKDKK 43 (187)
Q Consensus 16 wfW~CPnG~~C~YrH~LPpG~Vlk~~~k 43 (187)
..|+||. |-|.|.++|-.|++....
T Consensus 19 ~~~vC~~---Cg~~~~~~~~~~~~~~~~ 43 (52)
T smart00661 19 RRFVCRK---CGYEEPIEQKYVYKEKLK 43 (52)
T ss_pred CEEECCc---CCCeEECCCcEEEEEEec
Confidence 4899995 889999998867765543
No 20
>KOG0878|consensus
Probab=43.78 E-value=11 Score=30.37 Aligned_cols=14 Identities=43% Similarity=0.786 Sum_probs=11.4
Q ss_pred CCCccccccCCCcc
Q psy12936 23 GPTCIYKHALPPGF 36 (187)
Q Consensus 23 G~~C~YrH~LPpG~ 36 (187)
|.+=+.||.||+||
T Consensus 60 gsnKkTrh~lP~G~ 73 (124)
T KOG0878|consen 60 GSNKKTRHMLPNGF 73 (124)
T ss_pred CCCccceecCChhh
Confidence 45667899999996
No 21
>PRK07561 DNA topoisomerase I subunit omega; Validated
Probab=42.87 E-value=12 Score=38.19 Aligned_cols=26 Identities=27% Similarity=0.560 Sum_probs=21.6
Q ss_pred HHcCCCCccccCCCC---CCccccccCCC
Q psy12936 9 VENSKYGWFWSCPNG---PTCIYKHALPP 34 (187)
Q Consensus 9 ve~~kYGwfW~CPnG---~~C~YrH~LPp 34 (187)
+..|+||.||.|.|. ..|.|..-++|
T Consensus 599 ~r~gr~G~Fl~Cs~y~~~p~C~~~~~l~~ 627 (859)
T PRK07561 599 IRTGKTGVFLGCSGYALKERCKTTRNLTP 627 (859)
T ss_pred EEecCCCCeeeccCCcCCCCCCCCCCCCc
Confidence 345899999999986 79999887775
No 22
>KOG2295|consensus
Probab=40.45 E-value=9.2 Score=37.94 Aligned_cols=47 Identities=23% Similarity=0.282 Sum_probs=30.2
Q ss_pred hHHHHHHcCCCCccccCCCCCCccccccCCCccccccchhh-HhhhcccC
Q psy12936 4 YFIEAVENSKYGWFWSCPNGPTCIYKHALPPGFVLKKDKKK-EEKKDQIS 52 (187)
Q Consensus 4 ~fl~Ave~~kYGwfW~CPnG~~C~YrH~LPpG~Vlk~~~k~-ee~~~eis 52 (187)
-||+-+--.+|+|.|-||-+.--+--| -|.||-|.=.+| .++-++|+
T Consensus 496 ~~v~s~t~e~~kdKy~C~lsgc~KlF~--gpEFvrKHi~~KH~d~leeir 543 (648)
T KOG2295|consen 496 NFVDSNTMELDKDKYLCPLSGCAKLFK--GPEFVRKHINKKHKDKLEEIR 543 (648)
T ss_pred HHHHHHHHHhhcccccCCCcchHhhcc--CHHHHHHHHHHHHHHHHHHHH
Confidence 377777788999999999832212223 367888876655 44433443
No 23
>PF06839 zf-GRF: GRF zinc finger; InterPro: IPR010666 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This presumed zinc-binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to IPR000380 from INTERPRO. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=40.29 E-value=19 Score=23.31 Aligned_cols=20 Identities=25% Similarity=0.549 Sum_probs=14.8
Q ss_pred cCCCCccccCCCCC--Cccccc
Q psy12936 11 NSKYGWFWSCPNGP--TCIYKH 30 (187)
Q Consensus 11 ~~kYGwfW~CPnG~--~C~YrH 30 (187)
.|.--.||.||+.. .|.|-.
T Consensus 19 ~N~GR~Fy~C~~~~~~~C~fF~ 40 (45)
T PF06839_consen 19 PNPGRRFYKCPNYKDKGCNFFQ 40 (45)
T ss_pred CCCCCcceECCCCCCCCcCCEE
Confidence 45667899999954 688743
No 24
>KOG1040|consensus
Probab=40.10 E-value=12 Score=34.30 Aligned_cols=17 Identities=29% Similarity=0.606 Sum_probs=14.5
Q ss_pred cCCCCCCccccccCCCc
Q psy12936 19 SCPNGPTCIYKHALPPG 35 (187)
Q Consensus 19 ~CPnG~~C~YrH~LPpG 35 (187)
.|++|.+|+|||.++++
T Consensus 144 ~c~~g~~c~~~h~~~~~ 160 (325)
T KOG1040|consen 144 FCRGGPSCKKRHERKVL 160 (325)
T ss_pred cCCCcchhhhhhhcccC
Confidence 49999999999988754
No 25
>PF00706 Toxin_4: Anenome neurotoxin; InterPro: IPR000693 Sea anemones produce many different neurotoxins with related structure and function. Proteins belonging to this family include the neurotoxins, of which there are several, including calitoxin and anthopleurin. The neurotoxins bind specifically to the sodium channel, thereby delaying its inactivation during signal transduction, resulting in strong stimulation of mammalian cardiac muscle contraction. Calitoxin 1 has been found in neuromuscular prearations of crustaceans, where it increases transmitter release, causing firing of the axons. Three disulphide bonds are present in this protein [, , ].; GO: 0009966 regulation of signal transduction, 0005576 extracellular region; PDB: 2H9X_A 1AHL_A 1APF_A 1SHI_A 1SH1_A 2SH1_A 1ATX_A.
Probab=39.84 E-value=9.7 Score=25.59 Aligned_cols=14 Identities=36% Similarity=1.270 Sum_probs=11.0
Q ss_pred ccccCCCC-CCcccc
Q psy12936 16 WFWSCPNG-PTCIYK 29 (187)
Q Consensus 16 wfW~CPnG-~~C~Yr 29 (187)
|+|.||.| .+|.-.
T Consensus 21 w~~~CpsGWh~C~~~ 35 (43)
T PF00706_consen 21 WLFGCPSGWHKCKSS 35 (43)
T ss_dssp ETSSS-TTEEECCSC
T ss_pred eecCCCchhhhhhcc
Confidence 99999999 899753
No 26
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=39.62 E-value=17 Score=37.12 Aligned_cols=24 Identities=25% Similarity=0.558 Sum_probs=20.1
Q ss_pred HcCCCCccccCCCCCCccccccCC
Q psy12936 10 ENSKYGWFWSCPNGPTCIYKHALP 33 (187)
Q Consensus 10 e~~kYGwfW~CPnG~~C~YrH~LP 33 (187)
.+|+||-||.|.|...|+|.-.+|
T Consensus 658 K~gr~G~Fl~Cs~yP~Ck~~~~l~ 681 (860)
T PRK06319 658 RHGRFGTFLGCENYPECRGIINIH 681 (860)
T ss_pred ecCCCCceeeCCCCccccccccCC
Confidence 468999999999889999875554
No 27
>KOG4791|consensus
Probab=39.42 E-value=15 Score=36.23 Aligned_cols=18 Identities=33% Similarity=0.818 Sum_probs=14.1
Q ss_pred cccCCCC---CCccccccCCC
Q psy12936 17 FWSCPNG---PTCIYKHALPP 34 (187)
Q Consensus 17 fW~CPnG---~~C~YrH~LPp 34 (187)
.|-=||| ++|-|||+-||
T Consensus 66 we~~p~gC~k~~CgfRH~~pP 86 (667)
T KOG4791|consen 66 WENQPTGCQKLNCGFRHNRPP 86 (667)
T ss_pred eecCCCccCCCccccccCCCc
Confidence 3556775 89999999876
No 28
>PRK07220 DNA topoisomerase I; Validated
Probab=37.08 E-value=28 Score=34.93 Aligned_cols=68 Identities=22% Similarity=0.396 Sum_probs=0.0
Q ss_pred cCCCCccccCCCCCCccccccCCCc---------------cccccchhh-----HhhhcccChHHHHHHHHHHhccCCCc
Q psy12936 11 NSKYGWFWSCPNGPTCIYKHALPPG---------------FVLKKDKKK-----EEKKDQISLEDLIERERAALAASSKF 70 (187)
Q Consensus 11 ~~kYGwfW~CPnG~~C~YrH~LPpG---------------~Vlk~~~k~-----ee~~~eisLEE~iE~ER~kL~~~~~g 70 (187)
.|+.+|||.||+ |.|.....|. .--++...+ ......-+++++....+..+...
T Consensus 651 ~g~~~~~~~Cp~---C~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~kt~~Kl~~~~i~t~~~l~~a~~~~~a~~--- 724 (740)
T PRK07220 651 GGKRPWDLGCPQ---CNFIEWQKKQKEEKAQQPKKEKPKSIKDIKGIGKKTAEKLEEAGITTVEALAEADPVELSKT--- 724 (740)
T ss_pred cCCccceeeCCC---CCCccccCCcccccccccccccchhhhcccccchhhhhhhhhcCccchhhhccCCHHHhhhh---
Q ss_pred ccccHHHHHHHHHH
Q psy12936 71 TKVTLDSFLAWKKR 84 (187)
Q Consensus 71 TpVT~EsFl~WKkk 84 (187)
|-|....-..|++.
T Consensus 725 ~~is~~~~~~~~~~ 738 (740)
T PRK07220 725 TKISVKKIKSWQES 738 (740)
T ss_pred cCCchhhhhhhhhh
No 29
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=37.08 E-value=41 Score=31.52 Aligned_cols=58 Identities=28% Similarity=0.461 Sum_probs=42.9
Q ss_pred HHHHcCCCCccccCCCCCCccccccCCCccccccchhhHhhhcccChHHHHHHHHHHhccCC-Cccccc
Q psy12936 7 EAVENSKYGWFWSCPNGPTCIYKHALPPGFVLKKDKKKEEKKDQISLEDLIERERAALAASS-KFTKVT 74 (187)
Q Consensus 7 ~Ave~~kYGwfW~CPnG~~C~YrH~LPpG~Vlk~~~k~ee~~~eisLEE~iE~ER~kL~~~~-~gTpVT 74 (187)
++|++...---.+||| |.-|..|=.|++---++++| +|-+++.+|.+.++.- .-||.|
T Consensus 300 eci~~al~dsDf~Cpn---C~rkdvlld~l~pD~dk~~E-------vE~~lkkq~~~~gts~d~n~p~s 358 (427)
T COG5222 300 ECIGTALLDSDFKCPN---CSRKDVLLDGLTPDIDKKLE-------VEKALKKQRKKVGTSDDNNTPMS 358 (427)
T ss_pred HHHhhhhhhccccCCC---cccccchhhccCccHHHHHH-------HHHHHHHHHHhcCCCCCCCCchh
Confidence 6777777777889998 88888888888876666544 6677888998887431 146655
No 30
>PRK07219 DNA topoisomerase I; Validated
Probab=35.94 E-value=17 Score=36.72 Aligned_cols=24 Identities=29% Similarity=0.638 Sum_probs=19.8
Q ss_pred cCCCC-ccccCCCCCCccccccCCC
Q psy12936 11 NSKYG-WFWSCPNGPTCIYKHALPP 34 (187)
Q Consensus 11 ~~kYG-wfW~CPnG~~C~YrH~LPp 34 (187)
+++.| +||.|.|...|.|...||.
T Consensus 616 ~~~~g~~F~gCs~yp~C~~t~~lp~ 640 (822)
T PRK07219 616 RTDKGSRFVGCSGYPDCRNTFPLPS 640 (822)
T ss_pred eccCCceeeecCCCcCCCCeeecCC
Confidence 34556 9999999788999988885
No 31
>PF02662 FlpD: Methyl-viologen-reducing hydrogenase, delta subunit; InterPro: IPR003813 Methyl-viologen-reducing hydrogenase (MVH) is one of the enzymes involved in methanogenesis and coded in the mth-flp-mvh-mrt cluster of methane genes in Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum) []. No specific functions have been assigned to the delta subunit.; GO: 0015948 methanogenesis, 0055114 oxidation-reduction process
Probab=34.40 E-value=31 Score=26.97 Aligned_cols=28 Identities=25% Similarity=0.657 Sum_probs=21.6
Q ss_pred hhHHHHHHcCCCCccc-cCCCCCCcccccc
Q psy12936 3 KYFIEAVENSKYGWFW-SCPNGPTCIYKHA 31 (187)
Q Consensus 3 k~fl~Ave~~kYGwfW-~CPnG~~C~YrH~ 31 (187)
.|.|.|+++|-=|=+= -||.| +|+|++.
T Consensus 43 ~~il~Af~~GADGV~V~gC~~g-~Ch~~~G 71 (124)
T PF02662_consen 43 EFILRAFEKGADGVLVAGCHPG-DCHYREG 71 (124)
T ss_pred HHHHHHHHcCCCEEEEeCCCCC-CCCcchh
Confidence 4789999999877544 79984 5999854
No 32
>PF05416 Peptidase_C37: Southampton virus-type processing peptidase; InterPro: IPR001665 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C37, (clan PA(C)). The type example is calicivirin from Southampton virus, an endopeptidase that cleaves the polyprotein at sites N-terminal to itself, liberating the polyprotein helicase. Southampton virus is a positive-stranded ssRNA virus belonging to the Caliciviruses, which are viruses that cause gastroenteritis. The calicivirus genome contains two open reading frames, ORF1 and ORF2. ORF1 encodes a non-structural polypeptide, which has RNA helicase, cysteine protease and RNA polymerase activity []. The regions of the polyprotein in which these activities lie are similar to proteins produced by the picornaviruses []. ORF2 encodes a structural, capsid protein. Two different families of caliciviruses can be distinguished on the basis of sequence similarity, namely the Norwalk-like viruses or small round structured viruses (SRSVs), and those classed as non-SRSVs.; GO: 0004197 cysteine-type endopeptidase activity, 0006508 proteolysis; PDB: 2FYQ_A 2FYR_A 1WQS_D 4ASH_A 2IPH_B.
Probab=34.03 E-value=13 Score=36.07 Aligned_cols=20 Identities=45% Similarity=1.197 Sum_probs=13.1
Q ss_pred Cc-cccCCCCCCccccccCCCc
Q psy12936 15 GW-FWSCPNGPTCIYKHALPPG 35 (187)
Q Consensus 15 Gw-fW~CPnG~~C~YrH~LPpG 35 (187)
|| |||-|+ -----.|.+|+|
T Consensus 381 GWGfWVS~~-lfITttHViP~g 401 (535)
T PF05416_consen 381 GWGFWVSPT-LFITTTHVIPPG 401 (535)
T ss_dssp EEEEESSSS-EEEEEGGGS-ST
T ss_pred ceeeeecce-EEEEeeeecCCc
Confidence 56 899998 111246999988
No 33
>COG5084 YTH1 Cleavage and polyadenylation specificity factor (CPSF) Clipper subunit and related makorin family Zn-finger proteins [General function prediction only]
Probab=33.75 E-value=17 Score=32.89 Aligned_cols=18 Identities=44% Similarity=1.091 Sum_probs=11.5
Q ss_pred CCCCCCccccccCCCccc
Q psy12936 20 CPNGPTCIYKHALPPGFV 37 (187)
Q Consensus 20 CPnG~~C~YrH~LPpG~V 37 (187)
|-+|..|-|.|-+|-++.
T Consensus 146 cs~g~~c~~~h~dp~~~~ 163 (285)
T COG5084 146 CSSGPSCGYSHIDPDSFA 163 (285)
T ss_pred eccCCCCCccccCccccc
Confidence 666777777777764443
No 34
>PF03194 LUC7: LUC7 N_terminus; InterPro: IPR004882 This family consists of several LUC7 protein homologues that are restricted to eukaryotes. LUC7 has been shown to be a U1 snRNA associated protein [] with a role in splice site recognition []. The entry contains human and mouse LUC7 like (LUC7L) proteins [] and human cisplatin resistance-associated overexpressed protein (CROP) [].
Probab=31.98 E-value=15 Score=32.37 Aligned_cols=22 Identities=36% Similarity=0.922 Sum_probs=16.9
Q ss_pred CchhHHHHHHcCCCCccccCCC----C-----CCccccccC
Q psy12936 1 ICKYFIEAVENSKYGWFWSCPN----G-----PTCIYKHAL 32 (187)
Q Consensus 1 vCk~fl~Ave~~kYGwfW~CPn----G-----~~C~YrH~L 32 (187)
||||||=.+ ||+ + ..|...|..
T Consensus 32 VCk~~L~g~----------CPhdLF~nTK~DLG~C~kiHd~ 62 (254)
T PF03194_consen 32 VCKYFLVGF----------CPHDLFVNTKSDLGPCPKIHDE 62 (254)
T ss_pred cCHHHHhCC----------CcHHHHhhcccccchhhhhcCH
Confidence 899999775 897 2 378888853
No 35
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=31.15 E-value=19 Score=33.13 Aligned_cols=9 Identities=33% Similarity=1.040 Sum_probs=7.8
Q ss_pred CCccccCCC
Q psy12936 14 YGWFWSCPN 22 (187)
Q Consensus 14 YGwfW~CPn 22 (187)
.-|+|.||+
T Consensus 11 ~~~~g~cp~ 19 (372)
T cd01121 11 PKWLGKCPE 19 (372)
T ss_pred CCccEECcC
Confidence 459999998
No 36
>KOG4312|consensus
Probab=30.62 E-value=26 Score=33.23 Aligned_cols=17 Identities=29% Similarity=0.712 Sum_probs=14.8
Q ss_pred cCCCCCCccccccCCCc
Q psy12936 19 SCPNGPTCIYKHALPPG 35 (187)
Q Consensus 19 ~CPnG~~C~YrH~LPpG 35 (187)
-||.-..|+|||++--|
T Consensus 368 ~CP~~~~C~h~H~~~~g 384 (449)
T KOG4312|consen 368 ACPVRLSCKHRHSNKTG 384 (449)
T ss_pred cCCCCcccccccCCccc
Confidence 49988999999998855
No 37
>PF07141 Phage_term_sma: Putative bacteriophage terminase small subunit; InterPro: IPR010789 This entry is represented by Bacteriophage 712, Gp1; it is a family of uncharacterised viral proteins. This family consists of several putative Lactococcus bacteriophage terminase small subunit proteins. The exact function of this family is unknown.
Probab=30.37 E-value=57 Score=27.24 Aligned_cols=47 Identities=15% Similarity=0.339 Sum_probs=26.5
Q ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHhhhhh----hhhccccCcccccccccC
Q psy12936 71 TKVTLDSFLAWKKRKLKEKSEAMTKAEEKKRSD----FKAGRQVGLSGRDMFSFN 121 (187)
Q Consensus 71 TpVT~EsFl~WKkkk~~Ek~~~~~~~~e~kk~~----~kaGk~~~LSGRELFe~d 121 (187)
-.++.-||.+||..+++.-.... ..+... ..+.-..+|+||-|=+..
T Consensus 41 L~isrKtFyeWrdtk~eA~eeA~----~~rdd~LlmLArssLk~KLegyTLtET~ 91 (174)
T PF07141_consen 41 LHISRKTFYEWRDTKIEAYEEAK----GIRDDNLLMLARSSLKSKLEGYTLTETE 91 (174)
T ss_pred HhccHHHHHHHHhhhHHHHHHHH----hhccchHHHHHHHHHHhhcceeeeccce
Confidence 45778999999998853322211 111000 011112579999988776
No 38
>KOG0378|consensus
Probab=30.16 E-value=24 Score=31.74 Aligned_cols=34 Identities=21% Similarity=0.216 Sum_probs=28.1
Q ss_pred cCCCCccccCCCCCCccccccCCCccccccchhh
Q psy12936 11 NSKYGWFWSCPNGPTCIYKHALPPGFVLKKDKKK 44 (187)
Q Consensus 11 ~~kYGwfW~CPnG~~C~YrH~LPpG~Vlk~~~k~ 44 (187)
.++=|=||.+|+-.-=+||-|||-+|+|...-|.
T Consensus 21 dk~~G~fa~~ps~gphk~reclpl~~~~~~~Lky 54 (263)
T KOG0378|consen 21 DKLGGVFAPMPSSGPHKLRECLPLIVFLRNRLKY 54 (263)
T ss_pred cccCcEEecCCCCCCcccccceeEEEEeehhhhh
Confidence 4667899999994467899999999999876665
No 39
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=29.76 E-value=29 Score=35.45 Aligned_cols=26 Identities=27% Similarity=0.533 Sum_probs=21.4
Q ss_pred HHcCCCCccccCCCCCCccccccCCC
Q psy12936 9 VENSKYGWFWSCPNGPTCIYKHALPP 34 (187)
Q Consensus 9 ve~~kYGwfW~CPnG~~C~YrH~LPp 34 (187)
+..++||-||.|.|...|.|.-.|++
T Consensus 605 ~k~gr~G~Fl~Cs~yP~C~~t~~~~~ 630 (860)
T PRK06319 605 KIWAKNRYFYGCSEYPECDYKTSEEE 630 (860)
T ss_pred EEecCCCceeeccCCccccccCCccc
Confidence 34689999999999889998776663
No 40
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=29.72 E-value=20 Score=33.82 Aligned_cols=9 Identities=33% Similarity=0.826 Sum_probs=7.9
Q ss_pred CCccccCCC
Q psy12936 14 YGWFWSCPN 22 (187)
Q Consensus 14 YGwfW~CPn 22 (187)
.-|+|.||+
T Consensus 18 ~~~~g~Cp~ 26 (454)
T TIGR00416 18 PKWQGKCPA 26 (454)
T ss_pred ccccEECcC
Confidence 459999998
No 41
>COG1781 PyrI Aspartate carbamoyltransferase, regulatory subunit [Nucleotide transport and metabolism]
Probab=28.92 E-value=30 Score=28.91 Aligned_cols=26 Identities=27% Similarity=0.662 Sum_probs=20.1
Q ss_pred cccCCCCCCcccccc--CCCccccccchh
Q psy12936 17 FWSCPNGPTCIYKHA--LPPGFVLKKDKK 43 (187)
Q Consensus 17 fW~CPnG~~C~YrH~--LPpG~Vlk~~~k 43 (187)
+-.||| .+|+-.+. .++.|++.++..
T Consensus 106 vlkCpN-~nCITn~e~pv~s~F~~~~~~~ 133 (153)
T COG1781 106 VLRCPN-PNCITNAEEPVESKFYVVSKEP 133 (153)
T ss_pred EEEcCC-CCcccCCCccCCccEEEEecCC
Confidence 367999 99996655 778898887554
No 42
>KOG1677|consensus
Probab=28.14 E-value=29 Score=30.53 Aligned_cols=15 Identities=33% Similarity=0.835 Sum_probs=13.9
Q ss_pred cCCCCCCccccccCC
Q psy12936 19 SCPNGPTCIYKHALP 33 (187)
Q Consensus 19 ~CPnG~~C~YrH~LP 33 (187)
.||.|..|+|.|-.+
T Consensus 188 ~C~yG~rC~F~H~~~ 202 (332)
T KOG1677|consen 188 LCKYGSRCRFIHGEP 202 (332)
T ss_pred CCCCCCcCeecCCCc
Confidence 599999999999987
No 43
>PF14753 DUF4475: Domain of unknown function (DUF4475)
Probab=27.88 E-value=24 Score=30.47 Aligned_cols=22 Identities=27% Similarity=0.502 Sum_probs=18.1
Q ss_pred HHHHHcCCCCccccCCCCCCccc
Q psy12936 6 IEAVENSKYGWFWSCPNGPTCIY 28 (187)
Q Consensus 6 l~Ave~~kYGwfW~CPnG~~C~Y 28 (187)
..||.|+.|-+ |.||+|-+|+-
T Consensus 28 p~~~knrlyv~-Wr~~~~~DC~~ 49 (196)
T PF14753_consen 28 PLRIKNRLYVS-WRNPTGMDCKR 49 (196)
T ss_pred HhhhcCceEEE-EeCCCCcceeE
Confidence 34899999997 99999877763
No 44
>PRK11823 DNA repair protein RadA; Provisional
Probab=27.76 E-value=23 Score=33.22 Aligned_cols=9 Identities=33% Similarity=1.028 Sum_probs=7.9
Q ss_pred CCccccCCC
Q psy12936 14 YGWFWSCPN 22 (187)
Q Consensus 14 YGwfW~CPn 22 (187)
.-|+|.||+
T Consensus 18 ~~~~g~Cp~ 26 (446)
T PRK11823 18 PKWLGRCPE 26 (446)
T ss_pred cccCeeCcC
Confidence 459999999
No 45
>KOG4791|consensus
Probab=27.18 E-value=22 Score=35.10 Aligned_cols=8 Identities=38% Similarity=1.086 Sum_probs=6.7
Q ss_pred CCcccccc
Q psy12936 24 PTCIYKHA 31 (187)
Q Consensus 24 ~~C~YrH~ 31 (187)
+.|.|||.
T Consensus 46 k~C~YRHS 53 (667)
T KOG4791|consen 46 KVCRYRHS 53 (667)
T ss_pred ccccchhh
Confidence 68999996
No 46
>PF07936 Defensin_4: Potassium-channel blocking toxin; InterPro: IPR012414 This family features the antihypertensive and antiviral proteins BDS-I (P11494 from SWISSPROT) and BDS-II (P59084 from SWISSPROT) expressed by Anemonia sulcata. BDS-I is organised into a triple-stranded antiparallel beta-sheet, with an additional small antiparallel beta-sheet at the N terminus []. Both peptides are known to specifically block the Kv3.4 potassium channel, and thus bring about a decrease in blood pressure []. Moreover, they inhibit the cytopathic effects of mouse hepatitis virus strain MHV-A59 on mouse liver cells, by an unknown mechanism []. ; GO: 0008200 ion channel inhibitor activity, 0009405 pathogenesis, 0042151 nematocyst; PDB: 2BDS_A 1BDS_A 1WXN_A 1WQK_A.
Probab=27.12 E-value=16 Score=23.41 Aligned_cols=13 Identities=62% Similarity=1.551 Sum_probs=7.5
Q ss_pred ccc--cCCCC----CCccc
Q psy12936 16 WFW--SCPNG----PTCIY 28 (187)
Q Consensus 16 wfW--~CPnG----~~C~Y 28 (187)
||| .||+| ..|-|
T Consensus 13 W~~~~~CP~g~GYTg~C~y 31 (34)
T PF07936_consen 13 WFARGSCPGGYGYTGSCGY 31 (34)
T ss_dssp EESTSS--TTST--EEEEE
T ss_pred EEEecCCCCCCccccEeee
Confidence 888 79995 36655
No 47
>PRK06599 DNA topoisomerase I; Validated
Probab=26.46 E-value=40 Score=33.39 Aligned_cols=25 Identities=28% Similarity=0.609 Sum_probs=20.6
Q ss_pred HcCCCCccccCCCCCCccccccCCC
Q psy12936 10 ENSKYGWFWSCPNGPTCIYKHALPP 34 (187)
Q Consensus 10 e~~kYGwfW~CPnG~~C~YrH~LPp 34 (187)
.+++||=||.|.|-+.|.+...+|.
T Consensus 599 k~~k~g~F~~Cs~~p~C~~~~~~~~ 623 (675)
T PRK06599 599 KLGKNGKFLGCSGYPECKYTKNITR 623 (675)
T ss_pred EecCCCceeeCCCCCccCCCCCCcc
Confidence 3578999999998788998887773
No 48
>PF10587 EF-1_beta_acid: Eukaryotic elongation factor 1 beta central acidic region; InterPro: IPR018940 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) []. This region is found in the centre of the beta subunits of Elongation factor-1. More information about these proteins can be found at Protein of the Month: Elongation Factors [].
Probab=25.48 E-value=30 Score=21.31 Aligned_cols=7 Identities=29% Similarity=0.264 Sum_probs=4.5
Q ss_pred CccCCCC
Q psy12936 124 LAKDDMD 130 (187)
Q Consensus 124 L~~DD~d 130 (187)
||++|++
T Consensus 1 LFGSddE 7 (28)
T PF10587_consen 1 LFGSDDE 7 (28)
T ss_pred CCCCccc
Confidence 6787544
No 49
>PF02748 PyrI_C: Aspartate carbamoyltransferase regulatory chain, metal binding domain; InterPro: IPR020542 Aspartate carbamoyltransferase (aspartate transcarbamylase, ATCase) 2.1.3.2 from EC is an allosteric enzyme that plays a central role in the regulation of the pyrimidine pathway in bacteria. The holoenzyme is a dodecamer composed of six catalytic chains, each with an active site, and six regulatory chains lacking catalytic activity []. The catalytic subunits exist as a dimer of catalytic trimers, (c3)2, while the regulatory subunits exist as a trimer of regulatory dimers, (r2)3, therefore the complete holoenzyme can be represented as (c3)2(r2)3. The association of the catalytic subunits c3 with the regulatory subunits r2 is responsible for the establishment of positive co-operativity between catalytic sites for the binding of aspartate and it dictates the pattern of allosteric response toward nucleotide effectors. ATCase from Escherichia coli is the most extensively studied allosteric enzyme []. The crystal structure of the T-state, the T-state with CTP bound, the R-state with N-phosphonacetyl-L-aspartate (PALA) bound, and the R-state with phosphonoacetamide plus malonate bound have been used in interpreting kinetic and mutational studies. A high-resolution structure of E. coli ATCase in the presence of PALA (a bisubstrate analog) allows a detailed description of the binding at the active site of the enzyme and allows a detailed model of the tetrahedral intermediate to be constructed. The entire regulatory chain has been traced showing that the N-terminal regions of the regulatory chains R1 and R6 are located in close proximity to each other and to the regulatory site. This portion of the molecule may be involved in the observed asymmetry between the regulatory binding sites as well as in the heterotropic response of the enzyme []. The C-terminal domain of the regulatory chains have a rubredoxin-like zinc-bound fold. ATCase from Enterobacter agglomerans (Erwinia herbicola) (Pantoea agglomerans) differs from the other investigated enterobacterial ATCases by its absence of homotropic co-operativity toward the substrate aspartate and its lack of response to ATP which is an allosteric effector (activator) of this family of enzymes. Nevertheless, the E. herbicola ATCase has the same quaternary structure, two trimers of catalytic chains with three dimers of regulatory chains, (c3)2(r2)3, as other enterobacterial ATCases and shows extensive primary structure conservation []. This entry represents the C-terminal domain.; PDB: 2YWW_B 1SKU_D 1Q95_L 8ATC_B 3AT1_D 1RAI_D 4E2F_D 1NBE_B 6AT1_B 2FZC_D ....
Probab=25.40 E-value=33 Score=23.39 Aligned_cols=21 Identities=33% Similarity=0.822 Sum_probs=14.5
Q ss_pred ccCCCCCCcccc--ccCCCccccc
Q psy12936 18 WSCPNGPTCIYK--HALPPGFVLK 39 (187)
Q Consensus 18 W~CPnG~~C~Yr--H~LPpG~Vlk 39 (187)
-.||| .+|+-. ..+++-|.+.
T Consensus 7 l~C~N-p~CITn~~E~v~~~F~v~ 29 (52)
T PF02748_consen 7 LKCPN-PNCITNSNEPVESRFYVI 29 (52)
T ss_dssp SE-SS-TTBTTT-TSSS--EEEEE
T ss_pred EEcCC-CCcccCCCCCCCceEEEE
Confidence 47999 999987 7788899773
No 50
>PRK11548 outer membrane biogenesis protein BamE; Provisional
Probab=23.75 E-value=64 Score=24.67 Aligned_cols=49 Identities=16% Similarity=0.286 Sum_probs=29.6
Q ss_pred CCCCCCccccccCCCccccccchhhHhhhcccChHHHHHHHHHHhccCCCcccccHHHH
Q psy12936 20 CPNGPTCIYKHALPPGFVLKKDKKKEEKKDQISLEDLIERERAALAASSKFTKVTLDSF 78 (187)
Q Consensus 20 CPnG~~C~YrH~LPpG~Vlk~~~k~ee~~~eisLEE~iE~ER~kL~~~~~gTpVT~EsF 78 (187)
|-..+.+.|++..|.|+++..+.-..-+.- .|-++.. ..| |||.+.+.|
T Consensus 20 Cs~~~~~~y~~~v~qG~~~~~~~l~~l~~G-mTk~qV~----~lL-----GtP~~~~~f 68 (113)
T PRK11548 20 CSTLERVVYRPDINQGNYLTPNDVAKIHVG-MTQQQVA----YTL-----GTPMMQDPF 68 (113)
T ss_pred cCCCCcccccccCCccccCCHHHHHHhcCC-CCHHHHH----HHc-----CCCccccCC
Confidence 544456779999999999975443222222 3544443 333 588777665
No 51
>PRK14973 DNA topoisomerase I; Provisional
Probab=23.42 E-value=32 Score=35.70 Aligned_cols=71 Identities=17% Similarity=0.248 Sum_probs=35.2
Q ss_pred HHHcCCCCccccCCCCCCccccccCCCccccccchhh--Hh---hhcccChHHHHHHHHHHhccCCCcccccHHHHHHHH
Q psy12936 8 AVENSKYGWFWSCPNGPTCIYKHALPPGFVLKKDKKK--EE---KKDQISLEDLIERERAALAASSKFTKVTLDSFLAWK 82 (187)
Q Consensus 8 Ave~~kYGwfW~CPnG~~C~YrH~LPpG~Vlk~~~k~--ee---~~~eisLEE~iE~ER~kL~~~~~gTpVT~EsFl~WK 82 (187)
.+.+|.||||.-| +.|+|.-..-+..-......+ .+ ..---++.++...+...+... +-|...+=-.|+
T Consensus 648 ~~r~Gr~g~fl~C---P~C~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~ 721 (936)
T PRK14973 648 LIRKGARPWDIGC---PLCSHIESNTESLLLMPSMTEELLQKLNAVHIYTVSELASREPEALAKS---LGLSKKEAEKLI 721 (936)
T ss_pred EeecCCCcccccC---ccccchhhcccchhhccccchhhhhhhhhccCCchhhhccCCHhHhhhh---cCcchHHHHHHH
Confidence 3478899999999 468775442221111111111 01 111224445544444444433 226666666777
Q ss_pred HH
Q psy12936 83 KR 84 (187)
Q Consensus 83 kk 84 (187)
+.
T Consensus 722 ~~ 723 (936)
T PRK14973 722 RE 723 (936)
T ss_pred HH
Confidence 65
No 52
>PF10050 DUF2284: Predicted metal-binding protein (DUF2284); InterPro: IPR019271 This entry represents a family of predicted metal-binding bacterial and archaeal proteins with no known function.
Probab=22.93 E-value=23 Score=28.77 Aligned_cols=11 Identities=55% Similarity=1.319 Sum_probs=9.6
Q ss_pred CCCCccccCCC
Q psy12936 12 SKYGWFWSCPN 22 (187)
Q Consensus 12 ~kYGwfW~CPn 22 (187)
+.||=.|.||.
T Consensus 25 ~~Yg~~~~CPP 35 (166)
T PF10050_consen 25 PNYGKNWSCPP 35 (166)
T ss_pred hhcCCCCCCcc
Confidence 67999999997
No 53
>PF00111 Fer2: 2Fe-2S iron-sulfur cluster binding domain; InterPro: IPR001041 The ferredoxin protein family are electron carrier proteins with an iron-sulphur cofactor that act in a wide variety of metabolic reactions. Ferredoxins can be divided into several subgroups depending upon the physiological nature of the iron-sulphur cluster(s) and according to sequence similarities. This entry represents members of the 2Fe-2S ferredoxin family that have a general core structure consisting of beta(2)-alpha-beta(2), which includes putidaredoxin and terpredoxin, and adrenodoxin [, , , ]. They are proteins of around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated. This conserved region is also found as a domain in various metabolic enzymes and in multidomain proteins, such as aldehyde oxidoreductase (N-terminal), xanthine oxidase (N-terminal), phthalate dioxygenase reductase (C-terminal), succinate dehydrogenase iron-sulphur protein (N-terminal), and methane monooxygenase reductase (N-terminal).; GO: 0009055 electron carrier activity, 0051536 iron-sulfur cluster binding; PDB: 3M9S_C 2FUG_L 3IAS_L 2YBB_3 3IAM_3 3I9V_3 1JQ4_A 1DOX_A 1DOY_A 2KAJ_A ....
Probab=22.47 E-value=74 Score=21.69 Aligned_cols=32 Identities=28% Similarity=0.476 Sum_probs=22.5
Q ss_pred HHHHHHcC-CCCccccCCCCCCcccccc-CCCccc
Q psy12936 5 FIEAVENS-KYGWFWSCPNGPTCIYKHA-LPPGFV 37 (187)
Q Consensus 5 fl~Ave~~-kYGwfW~CPnG~~C~YrH~-LPpG~V 37 (187)
.|+|++.. .+++.+.|-+|- |--=|+ +-.|-|
T Consensus 19 ll~~~~~~~gi~i~~~C~~g~-Cg~C~v~v~~G~~ 52 (78)
T PF00111_consen 19 LLDALERAGGIGIPYSCGGGG-CGTCRVRVLEGEV 52 (78)
T ss_dssp HHHHHHHTTTTTSTTSSSSSS-SSTTEEEEEESEE
T ss_pred HHHHHHHcCCCCcccCCCCCc-cCCcEEEEeeCcc
Confidence 68999987 999999999975 543332 234444
No 54
>PRK07561 DNA topoisomerase I subunit omega; Validated
Probab=20.68 E-value=47 Score=33.97 Aligned_cols=24 Identities=8% Similarity=0.193 Sum_probs=17.7
Q ss_pred HcCCCCccccCC-CCCCccccccCC
Q psy12936 10 ENSKYGWFWSCP-NGPTCIYKHALP 33 (187)
Q Consensus 10 e~~kYGwfW~CP-nG~~C~YrH~LP 33 (187)
.+|+||-||.|. +...|.|...+.
T Consensus 716 k~gr~G~yl~c~~~~~sc~~~~~~~ 740 (859)
T PRK07561 716 KIGRFGPYVKCGGTYASLKNTRKVL 740 (859)
T ss_pred ecCCCCCeEEeCCCcCCCCCCCccc
Confidence 589999999994 457887754433
No 55
>PRK14973 DNA topoisomerase I; Provisional
Probab=20.08 E-value=52 Score=34.26 Aligned_cols=24 Identities=25% Similarity=0.605 Sum_probs=19.6
Q ss_pred HcCCCCccccCCCCCCccccccCC
Q psy12936 10 ENSKYGWFWSCPNGPTCIYKHALP 33 (187)
Q Consensus 10 e~~kYGwfW~CPnG~~C~YrH~LP 33 (187)
.++++|-||.|.|-..|.|...||
T Consensus 601 k~~k~gkFigCS~Yp~Ck~t~~L~ 624 (936)
T PRK14973 601 KHIGSSQFIGCSGYPDCTFNIGLP 624 (936)
T ss_pred ecccCceeEECCCCCCCCccccCC
Confidence 346889999999878899887765
Done!