Query 029682
Match_columns 189
No_of_seqs 125 out of 181
Neff 3.3
Searched_HMMs 46136
Date Fri Mar 29 16:49:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029682.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029682hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04690 YABBY: YABBY protein; 100.0 1.7E-80 3.7E-85 511.8 12.3 156 7-162 4-170 (170)
2 PF09011 HMG_box_2: HMG-box do 98.2 2.5E-06 5.4E-11 60.0 4.6 46 111-156 1-47 (73)
3 cd01390 HMGB-UBF_HMG-box HMGB- 97.7 9.3E-05 2E-09 49.5 4.9 41 116-156 3-43 (66)
4 cd01388 SOX-TCF_HMG-box SOX-TC 97.6 0.00013 2.8E-09 51.1 4.9 41 116-156 4-44 (72)
5 PF00505 HMG_box: HMG (high mo 97.6 0.00013 2.8E-09 49.4 4.5 41 116-156 3-43 (69)
6 cd00084 HMG-box High Mobility 97.6 0.00018 4E-09 47.5 5.0 42 116-157 3-44 (66)
7 smart00398 HMG high mobility g 97.5 0.00032 6.9E-09 46.8 5.2 41 116-156 4-44 (70)
8 cd01389 MATA_HMG-box MATA_HMG- 97.4 0.00045 9.7E-09 48.9 5.3 43 115-157 3-45 (77)
9 PTZ00199 high mobility group p 97.3 0.00054 1.2E-08 51.1 5.7 48 109-156 18-67 (94)
10 KOG0381 HMG box-containing pro 96.2 0.012 2.6E-07 42.5 5.0 44 113-156 22-65 (96)
11 PF06244 DUF1014: Protein of u 95.7 0.016 3.6E-07 46.4 4.3 51 108-160 69-119 (122)
12 PF11331 DUF3133: Protein of u 93.4 0.042 9.1E-07 37.7 1.4 38 15-54 6-46 (46)
13 KOG3223 Uncharacterized conser 93.1 0.05 1.1E-06 47.6 1.6 52 108-161 161-212 (221)
14 KOG4684 Uncharacterized conser 83.5 1.2 2.6E-05 40.0 3.3 17 36-52 167-183 (275)
15 TIGR02098 MJ0042_CXXC MJ0042 f 82.7 1.4 3.1E-05 27.4 2.6 34 16-51 3-37 (38)
16 PF13719 zinc_ribbon_5: zinc-r 80.6 1.4 2.9E-05 28.2 1.9 34 16-51 3-37 (37)
17 PRK14892 putative transcriptio 77.3 2.9 6.2E-05 32.5 3.2 44 14-60 20-63 (99)
18 PF05129 Elf1: Transcription e 75.5 1.6 3.5E-05 32.4 1.4 42 15-56 22-63 (81)
19 TIGR01562 FdhE formate dehydro 74.4 1.8 4E-05 39.3 1.7 27 11-47 206-232 (305)
20 PRK03954 ribonuclease P protei 72.0 2.2 4.7E-05 34.3 1.4 32 18-49 67-103 (121)
21 PF04032 Rpr2: RNAse P Rpr2/Rp 71.9 1.8 3.8E-05 30.7 0.8 32 16-47 47-85 (85)
22 PF13717 zinc_ribbon_4: zinc-r 69.1 6.2 0.00013 25.1 2.8 30 16-49 3-35 (36)
23 PF10122 Mu-like_Com: Mu-like 67.4 3.1 6.6E-05 29.4 1.2 32 16-51 5-36 (51)
24 PRK03564 formate dehydrogenase 66.9 3.5 7.5E-05 37.7 1.8 27 11-47 208-234 (309)
25 PF09788 Tmemb_55A: Transmembr 62.8 6.1 0.00013 35.6 2.5 39 11-53 153-191 (256)
26 COG3058 FdhE Uncharacterized p 61.5 1.2 2.5E-05 41.0 -2.2 34 10-53 206-239 (308)
27 KOG4684 Uncharacterized conser 60.4 3.8 8.2E-05 36.9 0.8 33 13-53 168-203 (275)
28 PF04216 FdhE: Protein involve 55.5 4.1 8.9E-05 35.5 0.2 32 13-54 195-226 (290)
29 PF11331 DUF3133: Protein of u 52.7 9.8 0.00021 26.1 1.6 19 12-30 28-46 (46)
30 PF06382 DUF1074: Protein of u 41.3 37 0.00081 29.4 3.7 35 119-157 84-118 (183)
31 PF03811 Zn_Tnp_IS1: InsA N-te 40.9 19 0.00042 23.2 1.5 17 35-51 1-17 (36)
32 TIGR01053 LSD1 zinc finger dom 39.8 27 0.00058 22.0 2.0 25 16-46 2-26 (31)
33 PF08073 CHDNT: CHDNT (NUC034) 39.5 51 0.0011 23.5 3.6 33 120-155 18-50 (55)
34 COG4416 Com Mu-like prophage p 37.5 7.9 0.00017 28.1 -0.7 13 37-49 2-14 (60)
35 COG5648 NHP6B Chromatin-associ 36.3 62 0.0013 28.6 4.4 40 116-155 73-112 (211)
36 PF05047 L51_S25_CI-B8: Mitoch 35.9 29 0.00063 22.7 1.8 19 122-140 2-20 (52)
37 COG4888 Uncharacterized Zn rib 35.4 32 0.00069 27.5 2.2 46 15-60 22-67 (104)
38 PF14599 zinc_ribbon_6: Zinc-r 34.5 30 0.00066 24.8 1.9 30 12-47 27-56 (61)
39 COG3712 FecR Fe2+-dicitrate se 32.5 39 0.00084 31.2 2.7 31 124-156 32-62 (322)
40 PF12876 Cellulase-like: Sugar 32.4 65 0.0014 23.1 3.4 31 110-140 29-59 (88)
41 PF00527 E7: E7 protein, Early 31.6 24 0.00051 26.8 1.0 30 16-45 53-91 (92)
42 PF02892 zf-BED: BED zinc fing 31.4 24 0.00052 22.2 0.9 17 12-28 13-29 (45)
43 PF01020 Ribosomal_L40e: Ribos 30.8 19 0.00041 25.6 0.3 9 41-49 38-46 (52)
44 PF05180 zf-DNL: DNL zinc fing 29.0 31 0.00067 25.2 1.2 32 17-48 6-38 (66)
45 TIGR02147 Fsuc_second hypothet 28.0 55 0.0012 29.1 2.8 24 120-143 9-32 (271)
46 PF04420 CHD5: CHD5-like prote 27.3 43 0.00094 27.3 1.9 36 116-151 36-71 (161)
47 KOG4520 Predicted coiled-coil 26.2 78 0.0017 28.3 3.3 35 122-156 62-112 (238)
48 KOG3404 G10 protein/predicted 26.0 51 0.0011 27.6 2.0 37 10-47 97-139 (145)
49 PF13408 Zn_ribbon_recom: Reco 26.0 32 0.0007 22.2 0.7 13 39-51 5-17 (58)
50 smart00614 ZnF_BED BED zinc fi 25.7 44 0.00096 22.0 1.4 14 14-27 17-30 (50)
51 PRK12336 translation initiatio 25.5 87 0.0019 26.6 3.4 36 15-56 98-136 (201)
52 COG5509 Uncharacterized small 25.1 72 0.0016 23.6 2.5 13 124-136 36-48 (65)
53 PF05164 ZapA: Cell division p 25.0 1.1E+02 0.0023 21.5 3.4 32 123-154 28-59 (89)
54 PF02723 NS3_envE: Non-structu 24.1 15 0.00032 28.0 -1.3 16 11-26 37-52 (82)
55 PF14722 KRAP_IP3R_bind: Ki-ra 24.0 83 0.0018 26.8 3.0 28 121-148 71-98 (160)
56 PRK09774 fec operon regulator 22.9 62 0.0013 28.7 2.2 29 126-156 33-61 (319)
57 TIGR00311 aIF-2beta translatio 22.6 1E+02 0.0022 25.0 3.1 33 14-52 96-131 (133)
58 PF04690 YABBY: YABBY protein; 22.4 47 0.001 28.2 1.3 19 15-33 36-54 (170)
59 COG4357 Zinc finger domain con 21.7 25 0.00055 28.0 -0.4 39 15-53 26-76 (105)
60 PF01667 Ribosomal_S27e: Ribos 20.7 62 0.0013 22.9 1.4 12 16-27 27-38 (55)
No 1
>PF04690 YABBY: YABBY protein; InterPro: IPR006780 YABBY proteins are a group of plant-specific transcription factors involved in the specification of abaxial polarity in lateral organs such as leaves and floral organs [, ].
Probab=100.00 E-value=1.7e-80 Score=511.85 Aligned_cols=156 Identities=61% Similarity=0.960 Sum_probs=118.0
Q ss_pred CCCCCceeeeeCCCcceeeEecccCCCccceeeeecCCCCCcccccccccccCCCchhhc-cc-CCC---CC--CCCccc
Q 029682 7 DVAPEQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSLSWQDVH-HH-QAP---SY--ASPECR 79 (189)
Q Consensus 7 ~~~~E~lCYV~CnfCnTiLaVsVPcssL~~~VTVRCGHCtnLlSVNm~~llqs~~~q~~~-~~-~~~---~~--~~~~~~ 79 (189)
+.++|||||||||||||||||||||+|||+|||||||||+|||||||++++++++.+++. .. ..+ .. ..+...
T Consensus 4 ~~~sE~lCYVhCnFC~TiLaVsVP~ssL~~~VTVRCGHCtNLLSVNm~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~ 83 (170)
T PF04690_consen 4 FSPSEQLCYVHCNFCNTILAVSVPCSSLLKTVTVRCGHCTNLLSVNMRALLQPLPSQDHLQHSLLPPQSQELQFQPENFG 83 (170)
T ss_pred cCCCCcEEEEEcCCcCeEEEEecchhhhhhhhceeccCccceeeeeccccccCCCcccchhccccccccccccccccccc
Confidence 336899999999999999999999999999999999999999999999999888766541 11 000 00 011111
Q ss_pred ccCCCCCcCcc-ccc-ccCCCCCCccCCCC--CCCCccCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccC
Q 029682 80 IDLGSSSKCNN-KIS-AMRTPTNKATEERV--VNPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHF 155 (189)
Q Consensus 80 ~~~~sss~~~~-~~~-~~~~~~~~e~p~~~--~KPPEKRQRvpsayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~ 155 (189)
....++++.+. ... .+....+++.|+.+ +||||||||+|||||+||||||||||++||||+|||||++|||||||+
T Consensus 84 ~~~~~~~~~~~~~~~~~~~~~~~~~~pr~~~v~kPPEKRqR~psaYn~f~k~ei~rik~~~p~ishkeaFs~aAknW~h~ 163 (170)
T PF04690_consen 84 SNSSSSSSSSSSSSSSSMSFSEEEEIPRAPPVNKPPEKRQRVPSAYNRFMKEEIQRIKAENPDISHKEAFSAAAKNWAHF 163 (170)
T ss_pred cccccCCCccccccccccCccccccccccccccCCccccCCCchhHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhC
Confidence 11111111111 000 11123344566544 999999999999999999999999999999999999999999999999
Q ss_pred Ccccccc
Q 029682 156 PHIHFGL 162 (189)
Q Consensus 156 phihfGl 162 (189)
|||||||
T Consensus 164 phihfgl 170 (170)
T PF04690_consen 164 PHIHFGL 170 (170)
T ss_pred cccccCC
Confidence 9999997
No 2
>PF09011 HMG_box_2: HMG-box domain; InterPro: IPR015101 This domain is predominantly found in Maelstrom homologue proteins. It has no known function. ; GO: 0005634 nucleus; PDB: 2EQZ_A 1V64_A 2CTO_A 1H5P_A 3TQ6_A 3FGH_A 3TMM_A 1J3X_A 2YRQ_A 1AAB_A ....
Probab=98.19 E-value=2.5e-06 Score=59.96 Aligned_cols=46 Identities=35% Similarity=0.634 Sum_probs=38.4
Q ss_pred CccCCCCchhhhHHHHHHHHHHHhh-CCCCCHHHHHHHHHHhhccCC
Q 029682 111 PEKRQRVPSAYNQFIKEEIQRIKAN-NPDISHREAFSTAAKNWAHFP 156 (189)
Q Consensus 111 PEKRQRvpsayN~fmK~ei~riK~~-~P~i~HkEaFs~aAknW~~~p 156 (189)
|.|-.|.+|||+.||++.+.+++.. .+.++++|++..++..|+..+
T Consensus 1 p~kpK~~~say~lF~~~~~~~~k~~G~~~~~~~e~~k~~~~~Wk~Ls 47 (73)
T PF09011_consen 1 PKKPKRPPSAYNLFMKEMRKEVKEEGGQKQSFREVMKEISERWKSLS 47 (73)
T ss_dssp SSS--SSSSHHHHHHHHHHHHHHHHT-T-SSHHHHHHHHHHHHHHS-
T ss_pred CcCCCCCCCHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHhcC
Confidence 5666799999999999999999999 888999999999999999754
No 3
>cd01390 HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.
Probab=97.67 E-value=9.3e-05 Score=49.48 Aligned_cols=41 Identities=32% Similarity=0.498 Sum_probs=38.7
Q ss_pred CCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029682 116 RVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP 156 (189)
Q Consensus 116 RvpsayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~p 156 (189)
|-+|||..|+++....+++.+|+++..|....++..|+..+
T Consensus 3 rp~saf~~f~~~~r~~~~~~~p~~~~~~i~~~~~~~W~~ls 43 (66)
T cd01390 3 RPLSAYFLFSQEQRPKLKKENPDASVTEVTKILGEKWKELS 43 (66)
T ss_pred CCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCC
Confidence 66899999999999999999999999999999999999754
No 4
>cd01388 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and transcription factor-like proteins, TCF-1, -3, -4, and LEF-1. They appear to bind the minor groove of the A/T C A A A G/C-motif.
Probab=97.60 E-value=0.00013 Score=51.12 Aligned_cols=41 Identities=17% Similarity=0.289 Sum_probs=38.6
Q ss_pred CCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029682 116 RVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP 156 (189)
Q Consensus 116 RvpsayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~p 156 (189)
|-|+||..|+++.-.++++++|+++..|.-+.++..|+..+
T Consensus 4 rP~naf~~F~~~~r~~~~~~~p~~~~~eisk~l~~~Wk~ls 44 (72)
T cd01388 4 RPMNAFMLFSKRHRRKVLQEYPLKENRAISKILGDRWKALS 44 (72)
T ss_pred CCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCC
Confidence 67899999999999999999999999999999999999754
No 5
>PF00505 HMG_box: HMG (high mobility group) box; InterPro: IPR000910 High mobility group (HMG or HMGB) proteins are a family of relatively low molecular weight non-histone components in chromatin. HMG1 (also called HMG-T in fish) and HMG2 are two highly related proteins that bind single-stranded DNA preferentially and unwind double-stranded DNA. Although they have no sequence specificity, they have a high affinity for bent or distorted DNA, and bend linear DNA. HMG1 and HMG2 contain two DNA-binding HMG-box domains (A and B) that show structural and functional differences, and have a long acidic C-terminal domain rich in aspartic and glutamic acid residues. The acidic tail modulates the affinity of the tandem HMG boxes in HMG1 and 2 for a variety of DNA targets. HMG1 and 2 appear to play important architectural roles in the assembly of nucleoprotein complexes in a variety of biological processes, for example V(D)J recombination, the initiation of transcription, and DNA repair []. The profile in this entry describing the HMG-domains is much more general than the signature. In addition to the HMG1 and HMG2 proteins, HMG-domains occur in single or multiple copies in the following protein classes; the SOX family of transcription factors; SRY sex determining region Y protein and related proteins []; LEF1 lymphoid enhancer binding factor 1 []; SSRP recombination signal recognition protein; MTF1 mitochondrial transcription factor 1; UBF1/2 nucleolar transcription factors; Abf2 yeast ARS-binding factor []; and Saccharomyces cerevisiae transcription factors Ixr1, Rox1, Nhp6a, Nhp6b and Spp41.; GO: 0003677 DNA binding; PDB: 1I11_A 1J3C_A 1J3D_A 1WZ6_A 1WGF_A 2D7L_A 1GT0_D 3U2B_C 2CRJ_A 2CS1_A ....
Probab=97.57 E-value=0.00013 Score=49.36 Aligned_cols=41 Identities=34% Similarity=0.638 Sum_probs=36.9
Q ss_pred CCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029682 116 RVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP 156 (189)
Q Consensus 116 RvpsayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~p 156 (189)
|-++||..|+++....||+++|+++..|.-+.+++.|+..+
T Consensus 3 rP~~af~lf~~~~~~~~k~~~p~~~~~~i~~~~~~~W~~l~ 43 (69)
T PF00505_consen 3 RPPNAFMLFCKEKRAKLKEENPDLSNKEISKILAQMWKNLS 43 (69)
T ss_dssp SS--HHHHHHHHHHHHHHHHSTTSTHHHHHHHHHHHHHCSH
T ss_pred CCCCHHHHHHHHHHHHHHHHhcccccccchhhHHHHHhcCC
Confidence 77899999999999999999999999999999999999753
No 6
>cd00084 HMG-box High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III member
Probab=97.56 E-value=0.00018 Score=47.49 Aligned_cols=42 Identities=31% Similarity=0.430 Sum_probs=39.0
Q ss_pred CCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 029682 116 RVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH 157 (189)
Q Consensus 116 RvpsayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~ph 157 (189)
|-++||..|++++...+++.+|+++..|....+++.|+..+.
T Consensus 3 rp~~af~~f~~~~~~~~~~~~~~~~~~~i~~~~~~~W~~l~~ 44 (66)
T cd00084 3 RPLSAYFLFSQEHRAEVKAENPGLSVGEISKILGEMWKSLSE 44 (66)
T ss_pred CCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCH
Confidence 668999999999999999999999999999999999997653
No 7
>smart00398 HMG high mobility group.
Probab=97.46 E-value=0.00032 Score=46.83 Aligned_cols=41 Identities=34% Similarity=0.531 Sum_probs=38.7
Q ss_pred CCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029682 116 RVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP 156 (189)
Q Consensus 116 RvpsayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~p 156 (189)
|-+|+|..|+++....+++.+|+++..|..+.++..|+..+
T Consensus 4 rp~~~y~~f~~~~r~~~~~~~~~~~~~~i~~~~~~~W~~l~ 44 (70)
T smart00398 4 RPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLS 44 (70)
T ss_pred CCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHcCC
Confidence 67899999999999999999999999999999999999754
No 8
>cd01389 MATA_HMG-box MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include the fungal mating type gene products MC, MATA1 and Ste11.
Probab=97.37 E-value=0.00045 Score=48.87 Aligned_cols=43 Identities=16% Similarity=0.358 Sum_probs=39.9
Q ss_pred CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 029682 115 QRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH 157 (189)
Q Consensus 115 QRvpsayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~ph 157 (189)
.|-++||-.|+++....|+++||++++.|.-+.++..|+..+.
T Consensus 3 kRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~~g~~Wk~ls~ 45 (77)
T cd01389 3 PRPRNAFILYRQDKHAQLKTENPGLTNNEISRIIGRMWRSESP 45 (77)
T ss_pred CCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCCH
Confidence 3789999999999999999999999999999999999998653
No 9
>PTZ00199 high mobility group protein; Provisional
Probab=97.34 E-value=0.00054 Score=51.10 Aligned_cols=48 Identities=27% Similarity=0.448 Sum_probs=41.0
Q ss_pred CCCccCCCCchhhhHHHHHHHHHHHhhCCCCC--HHHHHHHHHHhhccCC
Q 029682 109 NPPEKRQRVPSAYNQFIKEEIQRIKANNPDIS--HREAFSTAAKNWAHFP 156 (189)
Q Consensus 109 KPPEKRQRvpsayN~fmK~ei~riK~~~P~i~--HkEaFs~aAknW~~~p 156 (189)
+.|.+-.|-+|||..|+++.-..|+++||+++ -.|.-+.++..|+..+
T Consensus 18 kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls 67 (94)
T PTZ00199 18 KDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLS 67 (94)
T ss_pred CCCCCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCC
Confidence 44555568899999999999999999999986 5677888999999865
No 10
>KOG0381 consensus HMG box-containing protein [General function prediction only]
Probab=96.17 E-value=0.012 Score=42.49 Aligned_cols=44 Identities=30% Similarity=0.445 Sum_probs=39.4
Q ss_pred cCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029682 113 KRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFP 156 (189)
Q Consensus 113 KRQRvpsayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~p 156 (189)
.-+|-+|||..|+.+.-.+||++||+++..|.=+.+..+|....
T Consensus 22 ~pkrp~sa~~~f~~~~~~~~k~~~p~~~~~~v~k~~g~~W~~l~ 65 (96)
T KOG0381|consen 22 APKRPLSAFFLFSSEQRSKIKAENPGLSVGEVAKALGEMWKNLA 65 (96)
T ss_pred CCCCCCcHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCC
Confidence 34577889999999999999999999999999999999998754
No 11
>PF06244 DUF1014: Protein of unknown function (DUF1014); InterPro: IPR010422 This family consists of several hypothetical eukaryotic proteins of unknown function.
Probab=95.67 E-value=0.016 Score=46.42 Aligned_cols=51 Identities=25% Similarity=0.468 Sum_probs=45.2
Q ss_pred CCCCccCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCcccc
Q 029682 108 VNPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHF 160 (189)
Q Consensus 108 ~KPPEKRQRvpsayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~phihf 160 (189)
-|.||||- --||..|--.+|.+||++||++.+-+-=-..=|.|...|.=.|
T Consensus 69 drHPErR~--KAAy~afeE~~Lp~lK~E~PgLrlsQ~kq~l~K~w~KSPeNP~ 119 (122)
T PF06244_consen 69 DRHPERRM--KAAYKAFEERRLPELKEENPGLRLSQYKQMLWKEWQKSPENPF 119 (122)
T ss_pred CCCcchhH--HHHHHHHHHHHhHHHHhhCCCchHHHHHHHHHHHHhcCCCCCc
Confidence 68899976 5699999999999999999999999988889999999986544
No 12
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=93.41 E-value=0.042 Score=37.66 Aligned_cols=38 Identities=29% Similarity=0.697 Sum_probs=29.3
Q ss_pred eeeCCCcceeeEecccCCCccc---eeeeecCCCCCccccccc
Q 029682 15 YIPCNFCNIVLAVSVPCSSLLD---IVTVRCGHCSNLWSVNMA 54 (189)
Q Consensus 15 YV~CnfCnTiLaVsVPcssL~~---~VTVRCGHCtnLlSVNm~ 54 (189)
||-|+.|...|- +|-+.++. .-.+|||.|+.++++.++
T Consensus 6 Fv~C~~C~~lLq--lP~~~~~~~k~~~klrCGaCs~vl~~s~~ 46 (46)
T PF11331_consen 6 FVVCSSCFELLQ--LPAKFSLSKKNQQKLRCGACSEVLSFSLP 46 (46)
T ss_pred EeECccHHHHHc--CCCccCCCccceeEEeCCCCceeEEEecC
Confidence 788999977765 47775443 568999999999987653
No 13
>KOG3223 consensus Uncharacterized conserved protein [Function unknown]
Probab=93.07 E-value=0.05 Score=47.60 Aligned_cols=52 Identities=29% Similarity=0.519 Sum_probs=46.3
Q ss_pred CCCCccCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCccccc
Q 029682 108 VNPPEKRQRVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPHIHFG 161 (189)
Q Consensus 108 ~KPPEKRQRvpsayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~phihfG 161 (189)
-|-||||-| -||--|=..+|.|||.+||+++|-+-=-..-|.|...|.=.|.
T Consensus 161 drHPEkRmr--AA~~afEe~~LPrLK~e~P~lrlsQ~Kqll~Kew~KsPDNP~N 212 (221)
T KOG3223|consen 161 DRHPEKRMR--AAFKAFEEARLPRLKKENPGLRLSQYKQLLKKEWQKSPDNPFN 212 (221)
T ss_pred ccChHHHHH--HHHHHHHHhhchhhhhcCCCccHHHHHHHHHHHHhhCCCChhh
Confidence 388999877 5999999999999999999999998877888999999987775
No 14
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=83.47 E-value=1.2 Score=40.01 Aligned_cols=17 Identities=35% Similarity=0.841 Sum_probs=12.6
Q ss_pred ceeeeecCCCCCccccc
Q 029682 36 DIVTVRCGHCSNLWSVN 52 (189)
Q Consensus 36 ~~VTVRCGHCtnLlSVN 52 (189)
..+-|+||||++..--|
T Consensus 167 ~gcRV~CgHC~~tFLfn 183 (275)
T KOG4684|consen 167 TGCRVKCGHCNETFLFN 183 (275)
T ss_pred cceEEEecCccceeehh
Confidence 34889999999875433
No 15
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=82.73 E-value=1.4 Score=27.41 Aligned_cols=34 Identities=35% Similarity=0.721 Sum_probs=24.2
Q ss_pred eeCCCcceeeEecccCCCcc-ceeeeecCCCCCcccc
Q 029682 16 IPCNFCNIVLAVSVPCSSLL-DIVTVRCGHCSNLWSV 51 (189)
Q Consensus 16 V~CnfCnTiLaVsVPcssL~-~~VTVRCGHCtnLlSV 51 (189)
+.|..|.+..-|.. +.+- +...|+|++|.+.+.+
T Consensus 3 ~~CP~C~~~~~v~~--~~~~~~~~~v~C~~C~~~~~~ 37 (38)
T TIGR02098 3 IQCPNCKTSFRVVD--SQLGANGGKVRCGKCGHVWYA 37 (38)
T ss_pred EECCCCCCEEEeCH--HHcCCCCCEEECCCCCCEEEe
Confidence 68999999877653 2221 3347999999987754
No 16
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=80.63 E-value=1.4 Score=28.16 Aligned_cols=34 Identities=32% Similarity=0.665 Sum_probs=25.4
Q ss_pred eeCCCcceeeEecccCCCc-cceeeeecCCCCCcccc
Q 029682 16 IPCNFCNIVLAVSVPCSSL-LDIVTVRCGHCSNLWSV 51 (189)
Q Consensus 16 V~CnfCnTiLaVsVPcssL-~~~VTVRCGHCtnLlSV 51 (189)
++|.-|.|.+.| |-+.| -....|||++|.+...|
T Consensus 3 i~CP~C~~~f~v--~~~~l~~~~~~vrC~~C~~~f~v 37 (37)
T PF13719_consen 3 ITCPNCQTRFRV--PDDKLPAGGRKVRCPKCGHVFRV 37 (37)
T ss_pred EECCCCCceEEc--CHHHcccCCcEEECCCCCcEeeC
Confidence 789999998865 44443 34679999999987653
No 17
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=77.29 E-value=2.9 Score=32.51 Aligned_cols=44 Identities=18% Similarity=0.530 Sum_probs=35.3
Q ss_pred eeeeCCCcceeeEecccCCCccceeeeecCCCCCcccccccccccCC
Q 029682 14 CYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSL 60 (189)
Q Consensus 14 CYV~CnfCnTiLaVsVPcssL~~~VTVRCGHCtnLlSVNm~~llqs~ 60 (189)
=++.|.||+. ..|+||... .+..+.|..|.---.-.+.+|.++.
T Consensus 20 t~f~CP~Cge-~~v~v~~~k--~~~h~~C~~CG~y~~~~V~~l~epI 63 (99)
T PRK14892 20 KIFECPRCGK-VSISVKIKK--NIAIITCGNCGLYTEFEVPSVYDEV 63 (99)
T ss_pred cEeECCCCCC-eEeeeecCC--CcceEECCCCCCccCEECCccccch
Confidence 3789999995 688888888 7999999999887666666665554
No 18
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=75.50 E-value=1.6 Score=32.38 Aligned_cols=42 Identities=24% Similarity=0.453 Sum_probs=26.3
Q ss_pred eeeCCCcceeeEecccCCCccceeeeecCCCCCccccccccc
Q 029682 15 YIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAA 56 (189)
Q Consensus 15 YV~CnfCnTiLaVsVPcssL~~~VTVRCGHCtnLlSVNm~~l 56 (189)
+-.|-||+.--+|+|=.+.-..+-++.||-|.---..++..|
T Consensus 22 ~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~i~~L 63 (81)
T PF05129_consen 22 VFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTKINPL 63 (81)
T ss_dssp ----TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE--SS
T ss_pred eEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEccCcc
Confidence 457999999999999999999999999999954444444444
No 19
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=74.39 E-value=1.8 Score=39.27 Aligned_cols=27 Identities=33% Similarity=0.897 Sum_probs=23.1
Q ss_pred CceeeeeCCCcceeeEecccCCCccceeeeecCCCCC
Q 029682 11 EQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSN 47 (189)
Q Consensus 11 E~lCYV~CnfCnTiLaVsVPcssL~~~VTVRCGHCtn 47 (189)
+..=|.||++|.| -...|-++|.+|.|
T Consensus 206 ~G~RyL~CslC~t----------eW~~~R~~C~~Cg~ 232 (305)
T TIGR01562 206 TGLRYLSCSLCAT----------EWHYVRVKCSHCEE 232 (305)
T ss_pred CCceEEEcCCCCC----------cccccCccCCCCCC
Confidence 4566999999977 57889999999998
No 20
>PRK03954 ribonuclease P protein component 4; Validated
Probab=72.00 E-value=2.2 Score=34.28 Aligned_cols=32 Identities=25% Similarity=0.561 Sum_probs=24.7
Q ss_pred CCCcceeeEecccCCC-ccc----eeeeecCCCCCcc
Q 029682 18 CNFCNIVLAVSVPCSS-LLD----IVTVRCGHCSNLW 49 (189)
Q Consensus 18 CnfCnTiLaVsVPcss-L~~----~VTVRCGHCtnLl 49 (189)
|-.|+|.|.-||-|.- +-+ -|.|+|..|...-
T Consensus 67 CK~C~t~LiPG~n~~vRi~~~~~~~vvitCl~CG~~k 103 (121)
T PRK03954 67 CKRCHSFLVPGVNARVRLRQKRMPHVVITCLECGHIM 103 (121)
T ss_pred hhcCCCeeecCCceEEEEecCCcceEEEECccCCCEE
Confidence 8899999998887652 222 4899999998764
No 21
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=71.95 E-value=1.8 Score=30.66 Aligned_cols=32 Identities=25% Similarity=0.580 Sum_probs=20.1
Q ss_pred eeCCCcceeeEecccCCC-------ccceeeeecCCCCC
Q 029682 16 IPCNFCNIVLAVSVPCSS-------LLDIVTVRCGHCSN 47 (189)
Q Consensus 16 V~CnfCnTiLaVsVPcss-------L~~~VTVRCGHCtn 47 (189)
.-|.-|.++|.-|+-|+- .-+.|.++|..|.+
T Consensus 47 ~~Ck~C~~~liPG~~~~vri~~~~~~~~~l~~~C~~C~~ 85 (85)
T PF04032_consen 47 TICKKCGSLLIPGVNCSVRIRKKKKKKNFLVYTCLNCGH 85 (85)
T ss_dssp TB-TTT--B--CTTTEEEEEE---SSS-EEEEEETTTTE
T ss_pred ccccCCCCEEeCCCccEEEEEecCCCCCEEEEEccccCC
Confidence 358999999999988863 24688999999963
No 22
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=69.07 E-value=6.2 Score=25.14 Aligned_cols=30 Identities=27% Similarity=0.739 Sum_probs=23.4
Q ss_pred eeCCCcceeeEec---ccCCCccceeeeecCCCCCcc
Q 029682 16 IPCNFCNIVLAVS---VPCSSLLDIVTVRCGHCSNLW 49 (189)
Q Consensus 16 V~CnfCnTiLaVs---VPcssL~~~VTVRCGHCtnLl 49 (189)
+.|.-|.+...|. || =+.+.|||+.|.+.+
T Consensus 3 i~Cp~C~~~y~i~d~~ip----~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIP----PKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHHCC----CCCcEEECCCCCCEe
Confidence 6899999988765 34 345799999998865
No 23
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=67.44 E-value=3.1 Score=29.36 Aligned_cols=32 Identities=28% Similarity=0.598 Sum_probs=23.1
Q ss_pred eeCCCcceeeEecccCCCccceeeeecCCCCCcccc
Q 029682 16 IPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSV 51 (189)
Q Consensus 16 V~CnfCnTiLaVsVPcssL~~~VTVRCGHCtnLlSV 51 (189)
+||..||..||-+- -+..+.++|..|..+-.|
T Consensus 5 iRC~~CnklLa~~g----~~~~leIKCpRC~tiN~~ 36 (51)
T PF10122_consen 5 IRCGHCNKLLAKAG----EVIELEIKCPRCKTINHV 36 (51)
T ss_pred eeccchhHHHhhhc----CccEEEEECCCCCccceE
Confidence 68888888888642 244778888888776554
No 24
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=66.92 E-value=3.5 Score=37.68 Aligned_cols=27 Identities=33% Similarity=0.922 Sum_probs=23.0
Q ss_pred CceeeeeCCCcceeeEecccCCCccceeeeecCCCCC
Q 029682 11 EQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSN 47 (189)
Q Consensus 11 E~lCYV~CnfCnTiLaVsVPcssL~~~VTVRCGHCtn 47 (189)
+-.=|.||++|.| ....|-++|.+|.|
T Consensus 208 ~G~RyL~CslC~t----------eW~~~R~~C~~Cg~ 234 (309)
T PRK03564 208 QGLRYLHCNLCES----------EWHVVRVKCSNCEQ 234 (309)
T ss_pred CCceEEEcCCCCC----------cccccCccCCCCCC
Confidence 5567999999977 57889999999997
No 25
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=62.80 E-value=6.1 Score=35.64 Aligned_cols=39 Identities=26% Similarity=0.534 Sum_probs=27.6
Q ss_pred CceeeeeCCCcceeeEecccCCCccceeeeecCCCCCcccccc
Q 029682 11 EQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNM 53 (189)
Q Consensus 11 E~lCYV~CnfCnTiLaVsVPcssL~~~VTVRCGHCtnLlSVNm 53 (189)
..-|=|.|+.|+...+...+-++- -.||-||-.++||..
T Consensus 153 p~~~rv~CghC~~~Fl~~~~~~~t----lARCPHCrKvSSVG~ 191 (256)
T PF09788_consen 153 PGSCRVICGHCSNTFLFNTLTSNT----LARCPHCRKVSSVGP 191 (256)
T ss_pred CCceeEECCCCCCcEeccCCCCCc----cccCCCCceeccccc
Confidence 356778888888777766555332 268888888888864
No 26
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=61.52 E-value=1.2 Score=41.00 Aligned_cols=34 Identities=24% Similarity=0.647 Sum_probs=27.0
Q ss_pred CCceeeeeCCCcceeeEecccCCCccceeeeecCCCCCcccccc
Q 029682 10 PEQLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNM 53 (189)
Q Consensus 10 ~E~lCYV~CnfCnTiLaVsVPcssL~~~VTVRCGHCtnLlSVNm 53 (189)
.+-+=|.|||.|.| ....|-|+|-+|.+---+++
T Consensus 206 ~~GlRYL~CslC~t----------eW~~VR~KC~nC~~t~~l~y 239 (308)
T COG3058 206 EQGLRYLHCSLCET----------EWHYVRVKCSNCEQSKKLHY 239 (308)
T ss_pred cccchhhhhhhHHH----------HHHHHHHHhccccccCCccc
Confidence 46788999999977 57789999999998544433
No 27
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=60.43 E-value=3.8 Score=36.92 Aligned_cols=33 Identities=33% Similarity=0.775 Sum_probs=26.7
Q ss_pred eeeeeCCCcceeeEecccCCCccceee---eecCCCCCcccccc
Q 029682 13 LCYIPCNFCNIVLAVSVPCSSLLDIVT---VRCGHCSNLWSVNM 53 (189)
Q Consensus 13 lCYV~CnfCnTiLaVsVPcssL~~~VT---VRCGHCtnLlSVNm 53 (189)
-|-|-|+.|+.+.+ |++.| -||-||-..+||--
T Consensus 168 gcRV~CgHC~~tFL--------fnt~tnaLArCPHCrKvSsvGs 203 (275)
T KOG4684|consen 168 GCRVKCGHCNETFL--------FNTLTNALARCPHCRKVSSVGS 203 (275)
T ss_pred ceEEEecCccceee--------hhhHHHHHhcCCcccchhhhhh
Confidence 49999999998874 55554 69999999999843
No 28
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=55.55 E-value=4.1 Score=35.55 Aligned_cols=32 Identities=22% Similarity=0.588 Sum_probs=17.2
Q ss_pred eeeeeCCCcceeeEecccCCCccceeeeecCCCCCccccccc
Q 029682 13 LCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMA 54 (189)
Q Consensus 13 lCYV~CnfCnTiLaVsVPcssL~~~VTVRCGHCtnLlSVNm~ 54 (189)
.=|-+|.+|.|- ...+-++|.+|.|--...+.
T Consensus 195 ~R~L~Cs~C~t~----------W~~~R~~Cp~Cg~~~~~~l~ 226 (290)
T PF04216_consen 195 KRYLHCSLCGTE----------WRFVRIKCPYCGNTDHEKLE 226 (290)
T ss_dssp EEEEEETTT--E----------EE--TTS-TTT---SS-EEE
T ss_pred cEEEEcCCCCCe----------eeecCCCCcCCCCCCCccee
Confidence 468899999884 56778899999996554443
No 29
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=52.74 E-value=9.8 Score=26.11 Aligned_cols=19 Identities=32% Similarity=0.632 Sum_probs=16.4
Q ss_pred ceeeeeCCCcceeeEeccc
Q 029682 12 QLCYIPCNFCNIVLAVSVP 30 (189)
Q Consensus 12 ~lCYV~CnfCnTiLaVsVP 30 (189)
..-=+||+-|..||-+++|
T Consensus 28 ~~~klrCGaCs~vl~~s~~ 46 (46)
T PF11331_consen 28 NQQKLRCGACSEVLSFSLP 46 (46)
T ss_pred ceeEEeCCCCceeEEEecC
Confidence 3556899999999999987
No 30
>PF06382 DUF1074: Protein of unknown function (DUF1074); InterPro: IPR024460 This family consists of several proteins which appear to be specific to Insecta. The function of this family is unknown.
Probab=41.25 E-value=37 Score=29.42 Aligned_cols=35 Identities=23% Similarity=0.574 Sum_probs=30.2
Q ss_pred hhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 029682 119 SAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHFPH 157 (189)
Q Consensus 119 sayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~ph 157 (189)
++|=.||.+ .+..|.++.-+|.-..||+-|...+.
T Consensus 84 naYLNFLRe----FRrkh~~L~p~dlI~~AAraW~rLSe 118 (183)
T PF06382_consen 84 NAYLNFLRE----FRRKHCGLSPQDLIQRAARAWCRLSE 118 (183)
T ss_pred hHHHHHHHH----HHHHccCCCHHHHHHHHHHHHHhCCH
Confidence 688888765 77789999999999999999987654
No 31
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=40.90 E-value=19 Score=23.25 Aligned_cols=17 Identities=24% Similarity=0.565 Sum_probs=13.8
Q ss_pred cceeeeecCCCCCcccc
Q 029682 35 LDIVTVRCGHCSNLWSV 51 (189)
Q Consensus 35 ~~~VTVRCGHCtnLlSV 51 (189)
|.+|+|.|-+|.+-.+|
T Consensus 1 Ma~i~v~CP~C~s~~~v 17 (36)
T PF03811_consen 1 MAKIDVHCPRCQSTEGV 17 (36)
T ss_pred CCcEeeeCCCCCCCCcc
Confidence 46899999999887654
No 32
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=39.83 E-value=27 Score=21.97 Aligned_cols=25 Identities=28% Similarity=0.681 Sum_probs=12.9
Q ss_pred eeCCCcceeeEecccCCCccceeeeecCCCC
Q 029682 16 IPCNFCNIVLAVSVPCSSLLDIVTVRCGHCS 46 (189)
Q Consensus 16 V~CnfCnTiLaVsVPcssL~~~VTVRCGHCt 46 (189)
|.|+-|.|+|+.- ...-.|||--|.
T Consensus 2 ~~C~~C~t~L~yP------~gA~~vrCs~C~ 26 (31)
T TIGR01053 2 VVCGGCRTLLMYP------RGASSVRCALCQ 26 (31)
T ss_pred cCcCCCCcEeecC------CCCCeEECCCCC
Confidence 3466666666542 223355665554
No 33
>PF08073 CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958 The CHD N-terminal domain is found in PHD/RING fingers and chromo domain-associated helicases [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0008270 zinc ion binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=39.49 E-value=51 Score=23.47 Aligned_cols=33 Identities=18% Similarity=0.446 Sum_probs=26.2
Q ss_pred hhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccC
Q 029682 120 AYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHF 155 (189)
Q Consensus 120 ayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~ 155 (189)
+|..+|+-- |-+.||++.+-.-+...+.-|+.|
T Consensus 18 ~Fsq~vRP~---l~~~NPk~~~sKl~~l~~AKwrEF 50 (55)
T PF08073_consen 18 AFSQHVRPL---LAKANPKAPMSKLMMLLQAKWREF 50 (55)
T ss_pred HHHHHHHHH---HHHHCCCCcHHHHHHHHHHHHHHH
Confidence 455556544 457899999999999999999986
No 34
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=37.47 E-value=7.9 Score=28.08 Aligned_cols=13 Identities=38% Similarity=1.035 Sum_probs=11.0
Q ss_pred eeeeecCCCCCcc
Q 029682 37 IVTVRCGHCSNLW 49 (189)
Q Consensus 37 ~VTVRCGHCtnLl 49 (189)
+-|.||.||+-||
T Consensus 2 ~~tiRC~~CnKlL 14 (60)
T COG4416 2 MQTIRCAKCNKLL 14 (60)
T ss_pred ceeeehHHHhHHH
Confidence 4589999999887
No 35
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
Probab=36.34 E-value=62 Score=28.60 Aligned_cols=40 Identities=25% Similarity=0.437 Sum_probs=36.9
Q ss_pred CCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccC
Q 029682 116 RVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKNWAHF 155 (189)
Q Consensus 116 RvpsayN~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~ 155 (189)
|--|||-.|..+.=.+|...+|+++--|-=+.+.+.|+.+
T Consensus 73 Rp~sayf~y~~~~R~ei~~~~p~l~~~e~~k~~~e~WK~L 112 (211)
T COG5648 73 RPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKEL 112 (211)
T ss_pred CchhHHHHHHHHHHHHHHHhCCCCChHHHHHHHHHHHHhc
Confidence 6789999999999999999999999999999999999974
No 36
>PF05047 L51_S25_CI-B8: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain ; InterPro: IPR007741 Proteins containing this domain are located in the mitochondrion and include ribosomal protein L51, and S25. This domain is also found in mitochondrial NADH-ubiquinone oxidoreductase B8 subunit (CI-B8) 1.6.5.3 from EC. It is not known whether all members of this family form part of the NADH-ubiquinone oxidoreductase and whether they are also all ribosomal proteins.; PDB: 1S3A_A.
Probab=35.86 E-value=29 Score=22.73 Aligned_cols=19 Identities=26% Similarity=0.684 Sum_probs=15.6
Q ss_pred hHHHHHHHHHHHhhCCCCC
Q 029682 122 NQFIKEEIQRIKANNPDIS 140 (189)
Q Consensus 122 N~fmK~ei~riK~~~P~i~ 140 (189)
..|+++-+..||..||++.
T Consensus 2 R~F~~~~lp~l~~~NP~v~ 20 (52)
T PF05047_consen 2 RDFLKNNLPTLKYHNPQVQ 20 (52)
T ss_dssp HHHHHHTHHHHHHHSTT--
T ss_pred HhHHHHhHHHHHHHCCCcE
Confidence 3699999999999999964
No 37
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=35.35 E-value=32 Score=27.49 Aligned_cols=46 Identities=17% Similarity=0.367 Sum_probs=34.3
Q ss_pred eeeCCCcceeeEecccCCCccceeeeecCCCCCcccccccccccCC
Q 029682 15 YIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAAFQSL 60 (189)
Q Consensus 15 YV~CnfCnTiLaVsVPcssL~~~VTVRCGHCtnLlSVNm~~llqs~ 60 (189)
|--|-||+-...|+--.+--.++-|+-||-|.----+-..+++++.
T Consensus 22 ~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e~ev~~l~~~v 67 (104)
T COG4888 22 TFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFECEVPELSEPV 67 (104)
T ss_pred eEecCccCCeeeeEEEEEecCceeEEEcccCcceEEEeccccccch
Confidence 6789999999998877777788889999999744434444454443
No 38
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=34.50 E-value=30 Score=24.76 Aligned_cols=30 Identities=30% Similarity=0.703 Sum_probs=16.0
Q ss_pred ceeeeeCCCcceeeEecccCCCccceeeeecCCCCC
Q 029682 12 QLCYIPCNFCNIVLAVSVPCSSLLDIVTVRCGHCSN 47 (189)
Q Consensus 12 ~lCYV~CnfCnTiLaVsVPcssL~~~VTVRCGHCtn 47 (189)
..+.+-||=|+.-=- | -|-++-.||+||.+
T Consensus 27 ~~v~IlCNDC~~~s~--v----~fH~lg~KC~~C~S 56 (61)
T PF14599_consen 27 KKVWILCNDCNAKSE--V----PFHFLGHKCSHCGS 56 (61)
T ss_dssp -EEEEEESSS--EEE--E----E--TT----TTTS-
T ss_pred CEEEEECCCCCCccc--e----eeeHhhhcCCCCCC
Confidence 579999999987543 3 37788899999975
No 39
>COG3712 FecR Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]
Probab=32.46 E-value=39 Score=31.24 Aligned_cols=31 Identities=23% Similarity=0.492 Sum_probs=28.0
Q ss_pred HHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029682 124 FIKEEIQRIKANNPDISHREAFSTAAKNWAHFP 156 (189)
Q Consensus 124 fmK~ei~riK~~~P~i~HkEaFs~aAknW~~~p 156 (189)
-..+|.++|++..|+ |.+||..+..-|..+.
T Consensus 32 ~~r~af~~W~~~~p~--H~~A~~~~e~lw~~l~ 62 (322)
T COG3712 32 ADRAAFERWRAASPE--HARAWERAERLWQALG 62 (322)
T ss_pred HHHHHHHHHHhcCHH--HHHHHHHHHHHHhhhc
Confidence 357899999999997 9999999999999865
No 40
>PF12876 Cellulase-like: Sugar-binding cellulase-like; InterPro: IPR024778 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. This entry represents a family of putative cellulase enzymes.; PDB: 3GYC_B.
Probab=32.39 E-value=65 Score=23.15 Aligned_cols=31 Identities=29% Similarity=0.509 Sum_probs=22.8
Q ss_pred CCccCCCCchhhhHHHHHHHHHHHhhCCCCC
Q 029682 110 PPEKRQRVPSAYNQFIKEEIQRIKANNPDIS 140 (189)
Q Consensus 110 PPEKRQRvpsayN~fmK~ei~riK~~~P~i~ 140 (189)
|.+..+....+|-.++++=++.||+.+|+.+
T Consensus 29 ~~~~~~~~~~~~~~~l~~~~~~iR~~dP~~p 59 (88)
T PF12876_consen 29 PAEWGDPKAEAYAEWLKEAFRWIRAVDPSQP 59 (88)
T ss_dssp TT-TT-TTSHHHHHHHHHHHHHHHTT-TTS-
T ss_pred cccccchhHHHHHHHHHHHHHHHHHhCCCCc
Confidence 3344555788999999999999999999854
No 41
>PF00527 E7: E7 protein, Early protein; InterPro: IPR000148 This family includes the E7 oncoprotein from various papillomaviruses []. Along with E5 and E6 their activities seem to be especially important for viral oncogenesis. E5 is located at the cell surface and reduces cell gap-gap junction communication. In cervical cancer E5 is expressed in earlier stages of neoplastic transformation of the cervical epithelium during viral infection. The role of E7 is less well understood but it has been shown to impede growth arrest signals in both NIH 3T3 cells and HFKs and that this correlates with elevated cdc25A gene expression. This deregulation of cdc25A is linked to disruption of cell cycle arrest [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2F8B_A 2EWL_A 2B9D_A.
Probab=31.56 E-value=24 Score=26.76 Aligned_cols=30 Identities=30% Similarity=0.543 Sum_probs=13.6
Q ss_pred eeCCCcceeeEecccCCC---------ccceeeeecCCC
Q 029682 16 IPCNFCNIVLAVSVPCSS---------LLDIVTVRCGHC 45 (189)
Q Consensus 16 V~CnfCnTiLaVsVPcss---------L~~~VTVRCGHC 45 (189)
+.|.+|+..|-+.|=++. |+..+..-|..|
T Consensus 53 t~C~~C~~~lrl~V~as~~~Ir~lq~LLl~~L~lvCp~C 91 (92)
T PF00527_consen 53 TCCGRCGKRLRLVVVASHEGIRTLQQLLLGDLSLVCPPC 91 (92)
T ss_dssp EEBTTT--EEEEEEEC-HHHHHHHHHHHHCT-EE--CCC
T ss_pred eECCCCCCEEEEEEEeChhhHHHHHHHhhcCceEeCCCC
Confidence 456666666666655552 445555555555
No 42
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 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 predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=31.37 E-value=24 Score=22.22 Aligned_cols=17 Identities=24% Similarity=0.522 Sum_probs=10.2
Q ss_pred ceeeeeCCCcceeeEec
Q 029682 12 QLCYIPCNFCNIVLAVS 28 (189)
Q Consensus 12 ~lCYV~CnfCnTiLaVs 28 (189)
..-++.|.+|..++..+
T Consensus 13 ~~~~a~C~~C~~~~~~~ 29 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYS 29 (45)
T ss_dssp CSS-EEETTTTEE----
T ss_pred CcCeEEeCCCCeEEeeC
Confidence 45689999999988765
No 43
>PF01020 Ribosomal_L40e: Ribosomal L40e family; InterPro: IPR001975 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family contains the L40 ribosomal protein from both archaea and eukaryotes. Bovine ribosomal protein L40 has been identified as a secondary RNA binding protein []. L40 is fused to a ubiquitin protein [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3IZS_p 3IZR_p 2AYJ_A 4A1B_K 4A19_K 4A18_K 4A1D_K.
Probab=30.81 E-value=19 Score=25.58 Aligned_cols=9 Identities=56% Similarity=1.258 Sum_probs=5.5
Q ss_pred ecCCCCCcc
Q 029682 41 RCGHCSNLW 49 (189)
Q Consensus 41 RCGHCtnLl 49 (189)
+|||++||-
T Consensus 38 kCGhsn~LR 46 (52)
T PF01020_consen 38 KCGHSNNLR 46 (52)
T ss_dssp SCTS-S-EE
T ss_pred cCCCCcccC
Confidence 499999884
No 44
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 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. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=28.95 E-value=31 Score=25.24 Aligned_cols=32 Identities=28% Similarity=0.482 Sum_probs=17.1
Q ss_pred eCCCcceeeEecccCCC-ccceeeeecCCCCCc
Q 029682 17 PCNFCNIVLAVSVPCSS-LLDIVTVRCGHCSNL 48 (189)
Q Consensus 17 ~CnfCnTiLaVsVPcss-L~~~VTVRCGHCtnL 48 (189)
-|+-|+|-=+-.+-=.+ =--+|-|||+.|.|.
T Consensus 6 TC~~C~~Rs~~~~sk~aY~~GvViv~C~gC~~~ 38 (66)
T PF05180_consen 6 TCNKCGTRSAKMFSKQAYHKGVVIVQCPGCKNR 38 (66)
T ss_dssp EETTTTEEEEEEEEHHHHHTSEEEEE-TTS--E
T ss_pred EcCCCCCccceeeCHHHHhCCeEEEECCCCcce
Confidence 46777766553321111 134799999999985
No 45
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=28.02 E-value=55 Score=29.14 Aligned_cols=24 Identities=21% Similarity=0.486 Sum_probs=23.0
Q ss_pred hhhHHHHHHHHHHHhhCCCCCHHH
Q 029682 120 AYNQFIKEEIQRIKANNPDISHRE 143 (189)
Q Consensus 120 ayN~fmK~ei~riK~~~P~i~HkE 143 (189)
-|..||++...+-|+.+|.+|.|+
T Consensus 9 dYR~fl~d~ye~rk~~~p~fS~R~ 32 (271)
T TIGR02147 9 DYRKYLRDYYEERKKTDPAFSWRF 32 (271)
T ss_pred hHHHHHHHHHHHHhccCcCcCHHH
Confidence 599999999999999999999998
No 46
>PF04420 CHD5: CHD5-like protein; InterPro: IPR007514 Members of this family are probably coiled-coil proteins that are similar to the CHD5 (Congenital heart disease 5) protein. The exact molecular function of these eukaryotic proteins is unknown.; PDB: 3SJA_H 3SJC_D 3SJB_D 3ZS8_D 3VLC_E.
Probab=27.32 E-value=43 Score=27.28 Aligned_cols=36 Identities=25% Similarity=0.282 Sum_probs=30.4
Q ss_pred CCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHh
Q 029682 116 RVPSAYNQFIKEEIQRIKANNPDISHREAFSTAAKN 151 (189)
Q Consensus 116 RvpsayN~fmK~ei~riK~~~P~i~HkEaFs~aAkn 151 (189)
..++.-.+=++.||+.+|++.-.|+..+-|-..||+
T Consensus 36 ~~~~~~~~~l~~Ei~~l~~E~~~iS~qDeFAkwaKl 71 (161)
T PF04420_consen 36 SKSSKEQRQLRKEILQLKRELNAISAQDEFAKWAKL 71 (161)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHTTS-TTTSHHHHHHH
T ss_pred ccccHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHH
Confidence 346667788999999999999999999999998886
No 47
>KOG4520 consensus Predicted coiled-coil protein [General function prediction only]
Probab=26.22 E-value=78 Score=28.25 Aligned_cols=35 Identities=31% Similarity=0.293 Sum_probs=24.2
Q ss_pred hHHHHHHHHHHHhhC----------------CCCCHHHHHHHHHHhhccCC
Q 029682 122 NQFIKEEIQRIKANN----------------PDISHREAFSTAAKNWAHFP 156 (189)
Q Consensus 122 N~fmK~ei~riK~~~----------------P~i~HkEaFs~aAknW~~~p 156 (189)
---|||||++||+.. |.---|+-|+.++|.=-..|
T Consensus 62 ~~~~keEi~~vkE~E~~al~eALGl~k~stqP~gL~k~~fse~~kR~g~~~ 112 (238)
T KOG4520|consen 62 KEKYKEEILEVKEREQRALAEALGLPKSSTQPSGLLKLTFSEAAKRSGTNT 112 (238)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhCCCccccCCcchhHHHHHHHHhhcCCCH
Confidence 345899999999864 43336778888887644333
No 48
>KOG3404 consensus G10 protein/predicted nuclear transcription regulator [Transcription]
Probab=26.00 E-value=51 Score=27.58 Aligned_cols=37 Identities=38% Similarity=0.597 Sum_probs=29.3
Q ss_pred CCceeeeeC------CCcceeeEecccCCCccceeeeecCCCCC
Q 029682 10 PEQLCYIPC------NFCNIVLAVSVPCSSLLDIVTVRCGHCSN 47 (189)
Q Consensus 10 ~E~lCYV~C------nfCnTiLaVsVPcssL~~~VTVRCGHCtn 47 (189)
-|.||.++| ||=+| -.--||-+.|=.--.|+|-||.-
T Consensus 97 YE~LCClRCIq~~dsn~Gt~-CICRVPk~~ld~~~~~~C~hCGC 139 (145)
T KOG3404|consen 97 YENLCCLRCIQTRDSNFGTT-CICRVPKSKLDVERIVECVHCGC 139 (145)
T ss_pred ccceeeeeeccccccCCCce-EEEeCChhhcChhheeeeeccCc
Confidence 389999999 56444 34579999998888999999963
No 49
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=25.97 E-value=32 Score=22.22 Aligned_cols=13 Identities=38% Similarity=0.986 Sum_probs=10.7
Q ss_pred eeecCCCCCcccc
Q 029682 39 TVRCGHCSNLWSV 51 (189)
Q Consensus 39 TVRCGHCtnLlSV 51 (189)
.++||+|.+-+..
T Consensus 5 ~l~C~~CG~~m~~ 17 (58)
T PF13408_consen 5 LLRCGHCGSKMTR 17 (58)
T ss_pred cEEcccCCcEeEE
Confidence 4799999988765
No 50
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=25.72 E-value=44 Score=21.96 Aligned_cols=14 Identities=21% Similarity=0.548 Sum_probs=11.7
Q ss_pred eeeeCCCcceeeEe
Q 029682 14 CYIPCNFCNIVLAV 27 (189)
Q Consensus 14 CYV~CnfCnTiLaV 27 (189)
-++.|++|..+|..
T Consensus 17 ~~a~C~~C~~~l~~ 30 (50)
T smart00614 17 QRAKCKYCGKKLSR 30 (50)
T ss_pred eEEEecCCCCEeee
Confidence 58999999998863
No 51
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=25.47 E-value=87 Score=26.58 Aligned_cols=36 Identities=25% Similarity=0.602 Sum_probs=28.1
Q ss_pred eeeCCCc---ceeeEecccCCCccceeeeecCCCCCccccccccc
Q 029682 15 YIPCNFC---NIVLAVSVPCSSLLDIVTVRCGHCSNLWSVNMAAA 56 (189)
Q Consensus 15 YV~CnfC---nTiLaVsVPcssL~~~VTVRCGHCtnLlSVNm~~l 56 (189)
||.|.-| +|.|.+. . .+...+|.-|..-.+|.-...
T Consensus 98 yV~C~~C~~pdT~l~k~---~---~~~~l~C~aCGa~~~v~~~~~ 136 (201)
T PRK12336 98 YVICSECGLPDTRLVKE---D---RVLMLRCDACGAHRPVKKRKA 136 (201)
T ss_pred eEECCCCCCCCcEEEEc---C---CeEEEEcccCCCCcccccccc
Confidence 9999999 4777764 2 566789999999998865544
No 52
>COG5509 Uncharacterized small protein containing a coiled-coil domain [Function unknown]
Probab=25.05 E-value=72 Score=23.56 Aligned_cols=13 Identities=38% Similarity=0.682 Sum_probs=11.0
Q ss_pred HHHHHHHHHHhhC
Q 029682 124 FIKEEIQRIKANN 136 (189)
Q Consensus 124 fmK~ei~riK~~~ 136 (189)
...+||.|+|++-
T Consensus 36 lLq~EIeRlkAe~ 48 (65)
T COG5509 36 LLQAEIERLKAEL 48 (65)
T ss_pred HHHHHHHHHHHHH
Confidence 5789999999874
No 53
>PF05164 ZapA: Cell division protein ZapA; InterPro: IPR007838 This entry a structural domain found in the cell division protein ZapA, as well as in related proteins. This domain has a core structure consisting of two layers alpha/beta, and has a long C-terminal helix that forms dimeric parallel and tetrameric antiparallel coiled coils []. ZapA interacts with FtsZ, where FtsZ is part of a mid-cell cytokinetic structure termed the Z-ring that recruits a hierarchy of fission related proteins early in the bacterial cell cycle. ZapA drives the polymerisation and filament bundling of FtsZ, thereby contributing to the spatio-temporal tuning of the Z-ring.; PDB: 1T3U_B 1W2E_B 3HNW_A.
Probab=25.02 E-value=1.1e+02 Score=21.45 Aligned_cols=32 Identities=34% Similarity=0.420 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHhhCCCCCHHHHHHHHHHhhcc
Q 029682 123 QFIKEEIQRIKANNPDISHREAFSTAAKNWAH 154 (189)
Q Consensus 123 ~fmK~ei~riK~~~P~i~HkEaFs~aAknW~~ 154 (189)
.++.+.|..++..+|.++-..+...||-|-++
T Consensus 28 ~~i~~~i~~~~~~~~~~~~~~~~vlaaLnla~ 59 (89)
T PF05164_consen 28 ELINEKINEIKKKYPKLSPERLAVLAALNLAD 59 (89)
T ss_dssp HHHHHHHHHHCTTCCTSSHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHH
Confidence 57889999999999999999999999987654
No 54
>PF02723 NS3_envE: Non-structural protein NS3/Small envelope protein E; InterPro: IPR003873 This is a family of small nonstructural proteins, well conserved among Coronavirus strains. This protein is also found in Murine hepatitis virus as small envelope protein E.; GO: 0016020 membrane
Probab=24.08 E-value=15 Score=28.04 Aligned_cols=16 Identities=38% Similarity=0.910 Sum_probs=13.2
Q ss_pred CceeeeeCCCcceeeE
Q 029682 11 EQLCYIPCNFCNIVLA 26 (189)
Q Consensus 11 E~lCYV~CnfCnTiLa 26 (189)
=|+|..=|++|||++.
T Consensus 37 IqLC~~cc~~~n~~v~ 52 (82)
T PF02723_consen 37 IQLCFQCCRLCNTTVY 52 (82)
T ss_pred HHHHHHHhhhhcceEe
Confidence 4788899999998875
No 55
>PF14722 KRAP_IP3R_bind: Ki-ras-induced actin-interacting protein-IP3R-interacting domain
Probab=23.97 E-value=83 Score=26.80 Aligned_cols=28 Identities=21% Similarity=0.470 Sum_probs=22.4
Q ss_pred hhHHHHHHHHHHHhhCCCCCHHHHHHHH
Q 029682 121 YNQFIKEEIQRIKANNPDISHREAFSTA 148 (189)
Q Consensus 121 yN~fmK~ei~riK~~~P~i~HkEaFs~a 148 (189)
...|++.++|||..+||...---+|.+.
T Consensus 71 ~~~FL~aQ~qrm~~E~p~~~l~~RFRQ~ 98 (160)
T PF14722_consen 71 IRVFLEAQKQRMDIENPNLALASRFRQL 98 (160)
T ss_pred HHHHHHHHHHHHHhhCccHHHHHHHHHH
Confidence 4679999999999999996655556543
No 56
>PRK09774 fec operon regulator FecR; Reviewed
Probab=22.93 E-value=62 Score=28.68 Aligned_cols=29 Identities=10% Similarity=0.109 Sum_probs=25.2
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029682 126 KEEIQRIKANNPDISHREAFSTAAKNWAHFP 156 (189)
Q Consensus 126 K~ei~riK~~~P~i~HkEaFs~aAknW~~~p 156 (189)
.++.++|.+++|+ |++||..+..-|....
T Consensus 33 ~~~f~~Wl~a~p~--H~~A~~~~~~lw~~~~ 61 (319)
T PRK09774 33 EARWQQWYEQDQD--NQWAWQQVENLRNQMG 61 (319)
T ss_pred HHHHHHHHhCCHH--HHHHHHHHHHHHHHhh
Confidence 4678999999997 9999999999997754
No 57
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=22.63 E-value=1e+02 Score=25.00 Aligned_cols=33 Identities=15% Similarity=0.494 Sum_probs=24.4
Q ss_pred eeeeCCCc---ceeeEecccCCCccceeeeecCCCCCccccc
Q 029682 14 CYIPCNFC---NIVLAVSVPCSSLLDIVTVRCGHCSNLWSVN 52 (189)
Q Consensus 14 CYV~CnfC---nTiLaVsVPcssL~~~VTVRCGHCtnLlSVN 52 (189)
=||-|.-| +|.|... ++ +-..+|.-|..-.+|.
T Consensus 96 ~yVlC~~C~sPdT~l~k~---~r---~~~l~C~ACGa~~~v~ 131 (133)
T TIGR00311 96 KYVICRECNRPDTRIIKE---GR---VSLLKCEACGAKAPLR 131 (133)
T ss_pred heEECCCCCCCCcEEEEe---CC---eEEEecccCCCCCccC
Confidence 49999999 4777763 33 3367999999887773
No 58
>PF04690 YABBY: YABBY protein; InterPro: IPR006780 YABBY proteins are a group of plant-specific transcription factors involved in the specification of abaxial polarity in lateral organs such as leaves and floral organs [, ].
Probab=22.36 E-value=47 Score=28.22 Aligned_cols=19 Identities=21% Similarity=0.518 Sum_probs=16.0
Q ss_pred eeeCCCcceeeEecccCCC
Q 029682 15 YIPCNFCNIVLAVSVPCSS 33 (189)
Q Consensus 15 YV~CnfCnTiLaVsVPcss 33 (189)
=|+|+-|+.+|-|.+.-..
T Consensus 36 TVRCGHCtNLLSVNm~~~~ 54 (170)
T PF04690_consen 36 TVRCGHCTNLLSVNMRALL 54 (170)
T ss_pred ceeccCccceeeeeccccc
Confidence 4999999999999986544
No 59
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=21.74 E-value=25 Score=28.02 Aligned_cols=39 Identities=21% Similarity=0.477 Sum_probs=27.4
Q ss_pred eeeCCCcceeeEe--------cccCC----CccceeeeecCCCCCcccccc
Q 029682 15 YIPCNFCNIVLAV--------SVPCS----SLLDIVTVRCGHCSNLWSVNM 53 (189)
Q Consensus 15 YV~CnfCnTiLaV--------sVPcs----sL~~~VTVRCGHCtnLlSVNm 53 (189)
=.+|.-|++--|- .-|.. ..++.-.|-||+|-++|+++-
T Consensus 26 alkc~~C~kyYaCy~CHdel~~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~E 76 (105)
T COG4357 26 ALKCKCCQKYYACYHCHDELEDHPFEPWGLQEFNPKAIICGVCRKLLTRAE 76 (105)
T ss_pred eeeechhhhhhhHHHHHhHHhcCCCccCChhhcCCccEEhhhhhhhhhHHH
Confidence 3577777776652 22322 577788899999999998763
No 60
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=20.74 E-value=62 Score=22.95 Aligned_cols=12 Identities=42% Similarity=0.874 Sum_probs=9.3
Q ss_pred eeCCCcceeeEe
Q 029682 16 IPCNFCNIVLAV 27 (189)
Q Consensus 16 V~CnfCnTiLaV 27 (189)
|.|..|.|+|+=
T Consensus 27 V~C~~Cg~~L~~ 38 (55)
T PF01667_consen 27 VKCVVCGTVLAQ 38 (55)
T ss_dssp EE-SSSTSEEEE
T ss_pred EEcccCCCEecC
Confidence 889999999973
Done!