Query 027215
Match_columns 226
No_of_seqs 130 out of 184
Neff 3.0
Searched_HMMs 46136
Date Fri Mar 29 06:40:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027215.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027215hhsearch_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 4.7E-82 1E-86 532.3 11.5 167 11-187 1-170 (170)
2 PF09011 HMG_box_2: HMG-box do 98.1 3.7E-06 8.1E-11 60.4 4.5 46 136-181 1-47 (73)
3 cd01390 HMGB-UBF_HMG-box HMGB- 97.7 8.3E-05 1.8E-09 50.8 4.8 41 141-181 3-43 (66)
4 cd01388 SOX-TCF_HMG-box SOX-TC 97.6 0.00012 2.5E-09 52.5 4.8 41 141-181 4-44 (72)
5 PF00505 HMG_box: HMG (high mo 97.6 0.00011 2.4E-09 50.7 4.5 41 140-180 2-42 (69)
6 cd00084 HMG-box High Mobility 97.6 0.00015 3.2E-09 49.0 4.9 41 141-181 3-43 (66)
7 smart00398 HMG high mobility g 97.4 0.00031 6.7E-09 47.9 5.1 42 140-181 3-44 (70)
8 cd01389 MATA_HMG-box MATA_HMG- 97.4 0.00037 8E-09 50.4 5.1 42 140-181 3-44 (77)
9 PTZ00199 high mobility group p 97.3 0.00068 1.5E-08 51.7 5.6 48 134-181 18-67 (94)
10 KOG0381 HMG box-containing pro 96.0 0.014 3.1E-07 43.1 4.9 43 138-180 22-64 (96)
11 PF06244 DUF1014: Protein of u 96.0 0.011 2.4E-07 48.6 4.4 50 131-182 67-116 (122)
12 PF11331 DUF3133: Protein of u 93.9 0.057 1.2E-06 38.0 2.7 39 22-69 6-46 (46)
13 KOG3223 Uncharacterized conser 92.8 0.063 1.4E-06 48.1 1.9 49 133-183 161-209 (221)
14 PF13719 zinc_ribbon_5: zinc-r 85.4 0.33 7.2E-06 31.8 0.5 34 23-66 3-37 (37)
15 PF14599 zinc_ribbon_6: Zinc-r 80.4 0.66 1.4E-05 34.1 0.5 31 18-62 26-56 (61)
16 PF05129 Elf1: Transcription e 76.8 1.7 3.6E-05 33.2 1.8 42 22-71 22-63 (81)
17 PF10122 Mu-like_Com: Mu-like 74.1 3 6.5E-05 30.2 2.4 32 23-66 5-36 (51)
18 TIGR02098 MJ0042_CXXC MJ0042 f 72.2 1.6 3.5E-05 27.8 0.6 34 23-66 3-37 (38)
19 PRK14892 putative transcriptio 70.9 4.4 9.5E-05 32.3 2.9 42 22-74 21-62 (99)
20 COG3058 FdhE Uncharacterized p 52.2 3.6 7.7E-05 38.9 -0.8 44 7-68 195-239 (308)
21 TIGR01562 FdhE formate dehydro 51.7 7.3 0.00016 36.4 1.1 28 17-62 205-232 (305)
22 PF13717 zinc_ribbon_4: zinc-r 50.7 7.2 0.00016 25.5 0.7 32 23-64 3-35 (36)
23 PRK03954 ribonuclease P protei 50.6 5.5 0.00012 32.8 0.2 37 25-64 67-103 (121)
24 PF08073 CHDNT: CHDNT (NUC034) 49.6 28 0.00061 25.5 3.6 33 145-180 18-50 (55)
25 KOG4684 Uncharacterized conser 49.0 5.5 0.00012 36.8 -0.1 33 20-68 168-203 (275)
26 TIGR01053 LSD1 zinc finger dom 48.9 9.3 0.0002 24.7 1.0 26 23-62 2-27 (31)
27 COG4416 Com Mu-like prophage p 47.7 6.6 0.00014 29.3 0.1 30 23-64 5-34 (60)
28 PRK03564 formate dehydrogenase 40.7 18 0.00039 34.0 1.9 28 17-62 207-234 (309)
29 COG5648 NHP6B Chromatin-associ 38.5 54 0.0012 29.8 4.4 41 141-181 73-113 (211)
30 PF06382 DUF1074: Protein of u 38.2 43 0.00093 29.8 3.7 34 144-181 84-117 (183)
31 PF04032 Rpr2: RNAse P Rpr2/Rp 38.1 9.1 0.0002 27.7 -0.3 37 24-62 48-85 (85)
32 PF09788 Tmemb_55A: Transmembr 36.5 20 0.00043 33.3 1.4 39 18-68 153-191 (256)
33 PF04420 CHD5: CHD5-like prote 36.3 18 0.00039 30.2 1.1 36 141-176 36-71 (161)
34 KOG4684 Uncharacterized conser 35.5 18 0.00039 33.6 1.0 18 51-68 167-184 (275)
35 PF12876 Cellulase-like: Sugar 34.9 55 0.0012 24.2 3.4 31 135-165 29-59 (88)
36 PF03811 Zn_Tnp_IS1: InsA N-te 31.2 33 0.00072 22.8 1.5 18 50-67 1-18 (36)
37 PF05047 L51_S25_CI-B8: Mitoch 30.7 36 0.00078 22.9 1.7 19 147-165 2-20 (52)
38 COG3712 FecR Fe2+-dicitrate se 29.2 48 0.001 31.4 2.7 30 150-181 33-62 (322)
39 PF04216 FdhE: Protein involve 29.1 17 0.00036 32.6 -0.2 32 20-69 195-226 (290)
40 COG5629 Predicted metal-bindin 26.9 27 0.00059 33.2 0.7 31 22-61 169-203 (321)
41 PF05180 zf-DNL: DNL zinc fing 26.0 37 0.00079 25.5 1.1 14 51-64 26-39 (66)
42 PF02723 NS3_envE: Non-structu 24.5 11 0.00023 29.6 -2.0 18 18-35 37-54 (82)
43 TIGR02147 Fsuc_second hypothet 24.5 71 0.0015 29.2 2.9 24 145-168 9-32 (271)
44 KOG3404 G10 protein/predicted 24.1 34 0.00074 29.3 0.7 36 17-61 97-138 (145)
45 PF01020 Ribosomal_L40e: Ribos 23.8 29 0.00063 25.3 0.2 9 56-64 38-46 (52)
46 KOG0493 Transcription factor E 23.5 37 0.0008 32.4 0.9 32 137-173 246-280 (342)
47 KOG4520 Predicted coiled-coil 23.5 85 0.0018 28.8 3.1 15 147-161 62-76 (238)
48 PF13408 Zn_ribbon_recom: Reco 23.4 38 0.00083 22.4 0.8 14 54-67 5-18 (58)
49 PF05164 ZapA: Cell division p 22.9 1.3E+02 0.0028 21.6 3.5 32 148-179 28-59 (89)
50 PF04769 MAT_Alpha1: Mating-ty 22.3 2.1E+02 0.0045 25.3 5.3 47 133-183 38-84 (201)
51 PRK09774 fec operon regulator 21.8 69 0.0015 29.1 2.3 29 151-181 33-61 (319)
52 PF14722 KRAP_IP3R_bind: Ki-ra 21.4 93 0.002 27.2 2.9 27 146-172 71-97 (160)
53 KOG4715 SWI/SNF-related matrix 21.4 1.2E+02 0.0026 29.7 3.8 45 134-181 63-107 (410)
54 PF02892 zf-BED: BED zinc fing 20.8 31 0.00068 22.3 -0.1 16 18-33 12-27 (45)
55 COG4357 Zinc finger domain con 20.7 28 0.0006 28.6 -0.4 50 18-68 22-76 (105)
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=4.7e-82 Score=532.33 Aligned_cols=167 Identities=66% Similarity=1.100 Sum_probs=130.9
Q ss_pred CCCCCCCCceeeeeCCchhhhhcCCCcccceeeecCCCCcceeeeecCCcCCcccccccccCCccccccccCCCCCCCch
Q 027215 11 PDHLSSSEQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTNLLSVNMRGLLLPAANQLHLGHPFFTPQN 90 (226)
Q Consensus 11 ~d~l~~~EqlCYV~CnFCnTILa~~~~~~~~VsVPcssL~~~VTVRCGHCtnLlSVNmr~ll~p~~~q~~~~~~~~~~~~ 90 (226)
||++.++|||||||||||||||| |||||+|||+|||||||||+|||||||++++++.+.|+++++.++.+..
T Consensus 1 ~~~~~~sE~lCYVhCnFC~TiLa--------VsVP~ssL~~~VTVRCGHCtNLLSVNm~~~~~~~~~~~~l~~~~~~~~~ 72 (170)
T PF04690_consen 1 MDLFSPSEQLCYVHCNFCNTILA--------VSVPCSSLLKTVTVRCGHCTNLLSVNMRALLQPLPSQDHLQHSLLPPQS 72 (170)
T ss_pred CCccCCCCcEEEEEcCCcCeEEE--------EecchhhhhhhhceeccCccceeeeeccccccCCCcccchhcccccccc
Confidence 57778899999999999999999 9999999999999999999999999999999888888776666543321
Q ss_pred hHHhhhcCccc--c-ccCCCCCCCCCCCCCccccCCCCCCCCCCCCCCCccCCCCchhhhHHHHHHHHHHHhcCCCCCHH
Q 027215 91 LLEEIRNVPAN--M-LMINPPNPADQSVMPVRVVDHQEIPKSPVVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHR 167 (226)
Q Consensus 91 ~~~e~~~~~~~--~-~~~~~s~~~~ss~~~~~~~~~~~~p~~p~v~kPPEKRQRvPSaYN~FmK~ei~riK~~nP~i~Hk 167 (226)
++....... . ..+..+..+..+.......++++.|+.++|+||||||||+|||||+||||||||||++||||+||
T Consensus 73 --~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pr~~~v~kPPEKRqR~psaYn~f~k~ei~rik~~~p~ishk 150 (170)
T PF04690_consen 73 --QELQFQPENFGSNSSSSSSSSSSSSSSSMSFSEEEEIPRAPPVNKPPEKRQRVPSAYNRFMKEEIQRIKAENPDISHK 150 (170)
T ss_pred --ccccccccccccccccCCCccccccccccCccccccccccccccCCccccCCCchhHHHHHHHHHHHHHhcCCCCCHH
Confidence 111111011 0 01111101111011112233568899988999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhccCCcccccc
Q 027215 168 EAFSAAAKNWAHFPHIHFGL 187 (226)
Q Consensus 168 EaFs~aAknWa~~PhIhfGL 187 (226)
|||++|||||||+|||||||
T Consensus 151 eaFs~aAknW~h~phihfgl 170 (170)
T PF04690_consen 151 EAFSAAAKNWAHFPHIHFGL 170 (170)
T ss_pred HHHHHHHHhhhhCcccccCC
Confidence 99999999999999999998
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=98.13 E-value=3.7e-06 Score=60.39 Aligned_cols=46 Identities=33% Similarity=0.611 Sum_probs=38.2
Q ss_pred CccCCCCchhhhHHHHHHHHHHHhc-CCCCCHHHHHHHHHHhhccCC
Q 027215 136 PEKRQRVPSAYNRFIKDEIQRIKAG-NPDISHREAFSAAAKNWAHFP 181 (226)
Q Consensus 136 PEKRQRvPSaYN~FmK~ei~riK~~-nP~i~HkEaFs~aAknWa~~P 181 (226)
|.|-.|.+|||+.||++.+.++|+. .+.++.+|++..++..|+..+
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 5566899999999999999999999 888999999999999999753
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=97.68 E-value=8.3e-05 Score=50.81 Aligned_cols=41 Identities=29% Similarity=0.470 Sum_probs=38.4
Q ss_pred CCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215 141 RVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP 181 (226)
Q Consensus 141 RvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P 181 (226)
|-+|||..|+++....+++++|+++..|....++..|+..+
T Consensus 3 rp~saf~~f~~~~r~~~~~~~p~~~~~~i~~~~~~~W~~ls 43 (66)
T cd01390 3 RPLSAYFLFSQEQRPKLKKENPDASVTEVTKILGEKWKELS 43 (66)
T ss_pred CCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCC
Confidence 56899999999999999999999999999999999999754
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=0.00012 Score=52.55 Aligned_cols=41 Identities=17% Similarity=0.263 Sum_probs=38.3
Q ss_pred CCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215 141 RVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP 181 (226)
Q Consensus 141 RvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P 181 (226)
|-++||..|+++.-.++++++|+++..|.-+.++..|+..+
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 56899999999999999999999999999999999998754
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=97.59 E-value=0.00011 Score=50.71 Aligned_cols=41 Identities=32% Similarity=0.619 Sum_probs=36.8
Q ss_pred CCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 027215 140 QRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF 180 (226)
Q Consensus 140 QRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~ 180 (226)
.|-++||..|+++....||+++|+++..|.-+.+++.|+..
T Consensus 2 krP~~af~lf~~~~~~~~k~~~p~~~~~~i~~~~~~~W~~l 42 (69)
T PF00505_consen 2 KRPPNAFMLFCKEKRAKLKEENPDLSNKEISKILAQMWKNL 42 (69)
T ss_dssp SSS--HHHHHHHHHHHHHHHHSTTSTHHHHHHHHHHHHHCS
T ss_pred cCCCCHHHHHHHHHHHHHHHHhcccccccchhhHHHHHhcC
Confidence 36789999999999999999999999999999999999974
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=97.58 E-value=0.00015 Score=48.99 Aligned_cols=41 Identities=29% Similarity=0.410 Sum_probs=38.5
Q ss_pred CCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215 141 RVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP 181 (226)
Q Consensus 141 RvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P 181 (226)
|-++||..|++++...+++++|+++..|....+++.|+..+
T Consensus 3 rp~~af~~f~~~~~~~~~~~~~~~~~~~i~~~~~~~W~~l~ 43 (66)
T cd00084 3 RPLSAYFLFSQEHRAEVKAENPGLSVGEISKILGEMWKSLS 43 (66)
T ss_pred CCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCC
Confidence 56899999999999999999999999999999999999754
No 7
>smart00398 HMG high mobility group.
Probab=97.44 E-value=0.00031 Score=47.91 Aligned_cols=42 Identities=31% Similarity=0.501 Sum_probs=38.8
Q ss_pred CCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215 140 QRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP 181 (226)
Q Consensus 140 QRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P 181 (226)
.|-+|+|..|+++....+++++|+++..|.-+.++..|+..+
T Consensus 3 krp~~~y~~f~~~~r~~~~~~~~~~~~~~i~~~~~~~W~~l~ 44 (70)
T smart00398 3 KRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLS 44 (70)
T ss_pred CCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHcCC
Confidence 457899999999999999999999999999999999999754
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=97.38 E-value=0.00037 Score=50.39 Aligned_cols=42 Identities=19% Similarity=0.371 Sum_probs=39.4
Q ss_pred CCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215 140 QRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP 181 (226)
Q Consensus 140 QRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P 181 (226)
.|-++||-.|+++....|+++||++++.|.-+.++..|+..+
T Consensus 3 kRP~naf~lf~~~~r~~~~~~~p~~~~~eisk~~g~~Wk~ls 44 (77)
T cd01389 3 PRPRNAFILYRQDKHAQLKTENPGLTNNEISRIIGRMWRSES 44 (77)
T ss_pred CCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHhhCC
Confidence 477899999999999999999999999999999999999754
No 9
>PTZ00199 high mobility group protein; Provisional
Probab=97.26 E-value=0.00068 Score=51.73 Aligned_cols=48 Identities=25% Similarity=0.438 Sum_probs=41.3
Q ss_pred CCCccCCCCchhhhHHHHHHHHHHHhcCCCCC--HHHHHHHHHHhhccCC
Q 027215 134 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDIS--HREAFSAAAKNWAHFP 181 (226)
Q Consensus 134 kPPEKRQRvPSaYN~FmK~ei~riK~~nP~i~--HkEaFs~aAknWa~~P 181 (226)
+.|.+-.|-+|||..|+++.-..|+++||+++ -.|.-+.++..|+..+
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 45556668899999999999999999999986 5788889999999865
No 10
>KOG0381 consensus HMG box-containing protein [General function prediction only]
Probab=96.02 E-value=0.014 Score=43.05 Aligned_cols=43 Identities=30% Similarity=0.442 Sum_probs=38.9
Q ss_pred cCCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 027215 138 KRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF 180 (226)
Q Consensus 138 KRQRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~ 180 (226)
.-+|-+|||..|+.+.-.+||++||+++..|.=+.+..+|...
T Consensus 22 ~pkrp~sa~~~f~~~~~~~~k~~~p~~~~~~v~k~~g~~W~~l 64 (96)
T KOG0381|consen 22 APKRPLSAFFLFSSEQRSKIKAENPGLSVGEVAKALGEMWKNL 64 (96)
T ss_pred CCCCCCcHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcC
Confidence 4467788999999999999999999999999999999999864
No 11
>PF06244 DUF1014: Protein of unknown function (DUF1014); InterPro: IPR010422 This family consists of several hypothetical eukaryotic proteins of unknown function.
Probab=95.95 E-value=0.011 Score=48.60 Aligned_cols=50 Identities=26% Similarity=0.531 Sum_probs=44.8
Q ss_pred CCCCCCccCCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCCc
Q 027215 131 VVNRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPH 182 (226)
Q Consensus 131 ~v~kPPEKRQRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~Ph 182 (226)
.+-|.||||-+ -||..|--.+|.+||++||++.+-+-=-..=|.|..+|.
T Consensus 67 ~~drHPErR~K--AAy~afeE~~Lp~lK~E~PgLrlsQ~kq~l~K~w~KSPe 116 (122)
T PF06244_consen 67 PIDRHPERRMK--AAYKAFEERRLPELKEENPGLRLSQYKQMLWKEWQKSPE 116 (122)
T ss_pred CCCCCcchhHH--HHHHHHHHHHhHHHHhhCCCchHHHHHHHHHHHHhcCCC
Confidence 35689999865 699999999999999999999999988888999999884
No 12
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=93.87 E-value=0.057 Score=37.98 Aligned_cols=39 Identities=38% Similarity=0.835 Sum_probs=29.3
Q ss_pred eeeCCchhhhhcCCCcccceeeecCCCCcc--eeeeecCCcCCccccccc
Q 027215 22 YVHCTFCDTVLAVPYHFIFSVSVPCTSLFK--TVTVRCGHCTNLLSVNMR 69 (226)
Q Consensus 22 YV~CnFCnTILa~~~~~~~~VsVPcssL~~--~VTVRCGHCtnLlSVNmr 69 (226)
||-|.-|..+|=+|-.+ .+.+ .-.+|||.|..++++.++
T Consensus 6 Fv~C~~C~~lLqlP~~~---------~~~~k~~~klrCGaCs~vl~~s~~ 46 (46)
T PF11331_consen 6 FVVCSSCFELLQLPAKF---------SLSKKNQQKLRCGACSEVLSFSLP 46 (46)
T ss_pred EeECccHHHHHcCCCcc---------CCCccceeEEeCCCCceeEEEecC
Confidence 78999999998854432 1222 578999999999998753
No 13
>KOG3223 consensus Uncharacterized conserved protein [Function unknown]
Probab=92.79 E-value=0.063 Score=48.09 Aligned_cols=49 Identities=31% Similarity=0.550 Sum_probs=43.3
Q ss_pred CCCCccCCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCCcc
Q 027215 133 NRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHI 183 (226)
Q Consensus 133 ~kPPEKRQRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~PhI 183 (226)
-|-||||-|. ||--|=..++-|||.++|+++|-+-=-..-|.|...|-=
T Consensus 161 drHPEkRmrA--A~~afEe~~LPrLK~e~P~lrlsQ~Kqll~Kew~KsPDN 209 (221)
T KOG3223|consen 161 DRHPEKRMRA--AFKAFEEARLPRLKKENPGLRLSQYKQLLKKEWQKSPDN 209 (221)
T ss_pred ccChHHHHHH--HHHHHHHhhchhhhhcCCCccHHHHHHHHHHHHhhCCCC
Confidence 4899999775 999999999999999999999998777788899988753
No 14
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=85.40 E-value=0.33 Score=31.80 Aligned_cols=34 Identities=32% Similarity=0.670 Sum_probs=25.4
Q ss_pred eeCCchhhhhcCCCcccceeeecCCCC-cceeeeecCCcCCcccc
Q 027215 23 VHCTFCDTVLAVPYHFIFSVSVPCTSL-FKTVTVRCGHCTNLLSV 66 (226)
Q Consensus 23 V~CnFCnTILa~~~~~~~~VsVPcssL-~~~VTVRCGHCtnLlSV 66 (226)
++|.-|.|..- ||-+.| -....|||++|.+.+.|
T Consensus 3 i~CP~C~~~f~----------v~~~~l~~~~~~vrC~~C~~~f~v 37 (37)
T PF13719_consen 3 ITCPNCQTRFR----------VPDDKLPAGGRKVRCPKCGHVFRV 37 (37)
T ss_pred EECCCCCceEE----------cCHHHcccCCcEEECCCCCcEeeC
Confidence 68899988877 455544 34679999999987654
No 15
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=80.41 E-value=0.66 Score=34.14 Aligned_cols=31 Identities=29% Similarity=0.862 Sum_probs=18.1
Q ss_pred CceeeeeCCchhhhhcCCCcccceeeecCCCCcceeeeecCCcCC
Q 027215 18 EQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTN 62 (226)
Q Consensus 18 EqlCYV~CnFCnTILa~~~~~~~~VsVPcssL~~~VTVRCGHCtn 62 (226)
...+.+.||=|..-=-|+|||+. .+|+||.+
T Consensus 26 ~~~v~IlCNDC~~~s~v~fH~lg--------------~KC~~C~S 56 (61)
T PF14599_consen 26 NKKVWILCNDCNAKSEVPFHFLG--------------HKCSHCGS 56 (61)
T ss_dssp --EEEEEESSS--EEEEE--TT------------------TTTS-
T ss_pred CCEEEEECCCCCCccceeeeHhh--------------hcCCCCCC
Confidence 46799999999998888899865 58999975
No 16
>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=76.84 E-value=1.7 Score=33.18 Aligned_cols=42 Identities=21% Similarity=0.412 Sum_probs=26.3
Q ss_pred eeeCCchhhhhcCCCcccceeeecCCCCcceeeeecCCcCCccccccccc
Q 027215 22 YVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTNLLSVNMRGL 71 (226)
Q Consensus 22 YV~CnFCnTILa~~~~~~~~VsVPcssL~~~VTVRCGHCtnLlSVNmr~l 71 (226)
+-.|-||+.--+ |+|=.+.--.+-++.||-|.---..++..|
T Consensus 22 ~F~CPfC~~~~s--------V~v~idkk~~~~~~~C~~Cg~~~~~~i~~L 63 (81)
T PF05129_consen 22 VFDCPFCNHEKS--------VSVKIDKKEGIGILSCRVCGESFQTKINPL 63 (81)
T ss_dssp ----TTT--SS---------EEEEEETTTTEEEEEESSS--EEEEE--SS
T ss_pred eEcCCcCCCCCe--------EEEEEEccCCEEEEEecCCCCeEEEccCcc
Confidence 347999999999 999999999999999999955444444433
No 17
>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=74.14 E-value=3 Score=30.21 Aligned_cols=32 Identities=22% Similarity=0.667 Sum_probs=25.1
Q ss_pred eeCCchhhhhcCCCcccceeeecCCCCcceeeeecCCcCCcccc
Q 027215 23 VHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTNLLSV 66 (226)
Q Consensus 23 V~CnFCnTILa~~~~~~~~VsVPcssL~~~VTVRCGHCtnLlSV 66 (226)
+||..|+..|| -+ --+..+.++|..|..+-.|
T Consensus 5 iRC~~CnklLa--------~~----g~~~~leIKCpRC~tiN~~ 36 (51)
T PF10122_consen 5 IRCGHCNKLLA--------KA----GEVIELEIKCPRCKTINHV 36 (51)
T ss_pred eeccchhHHHh--------hh----cCccEEEEECCCCCccceE
Confidence 79999999999 21 1355789999999887665
No 18
>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=72.20 E-value=1.6 Score=27.84 Aligned_cols=34 Identities=29% Similarity=0.597 Sum_probs=22.9
Q ss_pred eeCCchhhhhcCCCcccceeeecCCCCc-ceeeeecCCcCCcccc
Q 027215 23 VHCTFCDTVLAVPYHFIFSVSVPCTSLF-KTVTVRCGHCTNLLSV 66 (226)
Q Consensus 23 V~CnFCnTILa~~~~~~~~VsVPcssL~-~~VTVRCGHCtnLlSV 66 (226)
+.|..|.+..- |+-+.+- +...|+|++|.+.+.+
T Consensus 3 ~~CP~C~~~~~----------v~~~~~~~~~~~v~C~~C~~~~~~ 37 (38)
T TIGR02098 3 IQCPNCKTSFR----------VVDSQLGANGGKVRCGKCGHVWYA 37 (38)
T ss_pred EECCCCCCEEE----------eCHHHcCCCCCEEECCCCCCEEEe
Confidence 67888888766 3333332 3457999999987754
No 19
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=70.86 E-value=4.4 Score=32.31 Aligned_cols=42 Identities=17% Similarity=0.458 Sum_probs=33.4
Q ss_pred eeeCCchhhhhcCCCcccceeeecCCCCcceeeeecCCcCCcccccccccCCc
Q 027215 22 YVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTNLLSVNMRGLLLP 74 (226)
Q Consensus 22 YV~CnFCnTILa~~~~~~~~VsVPcssL~~~VTVRCGHCtnLlSVNmr~ll~p 74 (226)
++.|.||+. .. |+||... .+..+.|..|.---.-.+..|..|
T Consensus 21 ~f~CP~Cge-~~--------v~v~~~k--~~~h~~C~~CG~y~~~~V~~l~ep 62 (99)
T PRK14892 21 IFECPRCGK-VS--------ISVKIKK--NIAIITCGNCGLYTEFEVPSVYDE 62 (99)
T ss_pred EeECCCCCC-eE--------eeeecCC--CcceEECCCCCCccCEECCccccc
Confidence 689999995 56 8888888 799999999987766666655544
No 20
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=52.24 E-value=3.6 Score=38.88 Aligned_cols=44 Identities=25% Similarity=0.606 Sum_probs=31.5
Q ss_pred CccCCCCCC-CCCceeeeeCCchhhhhcCCCcccceeeecCCCCcceeeeecCCcCCcccccc
Q 027215 7 AALSPDHLS-SSEQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTNLLSVNM 68 (226)
Q Consensus 7 ~~~~~d~l~-~~EqlCYV~CnFCnTILa~~~~~~~~VsVPcssL~~~VTVRCGHCtnLlSVNm 68 (226)
+.-||=+.. ..|-+=|.||+-|-|--- .|-|+|-+|.+---+++
T Consensus 195 PvaSmV~~g~~~~GlRYL~CslC~teW~------------------~VR~KC~nC~~t~~l~y 239 (308)
T COG3058 195 PVASMVQIGETEQGLRYLHCSLCETEWH------------------YVRVKCSNCEQSKKLHY 239 (308)
T ss_pred CcceeeeecCccccchhhhhhhHHHHHH------------------HHHHHhccccccCCccc
Confidence 344444455 457889999999987544 68999999997555444
No 21
>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=51.73 E-value=7.3 Score=36.35 Aligned_cols=28 Identities=36% Similarity=0.939 Sum_probs=22.3
Q ss_pred CCceeeeeCCchhhhhcCCCcccceeeecCCCCcceeeeecCCcCC
Q 027215 17 SEQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTN 62 (226)
Q Consensus 17 ~EqlCYV~CnFCnTILa~~~~~~~~VsVPcssL~~~VTVRCGHCtn 62 (226)
.+-.=|.||++|.|- ...|-++|.+|.|
T Consensus 205 ~~G~RyL~CslC~te------------------W~~~R~~C~~Cg~ 232 (305)
T TIGR01562 205 ETGLRYLSCSLCATE------------------WHYVRVKCSHCEE 232 (305)
T ss_pred CCCceEEEcCCCCCc------------------ccccCccCCCCCC
Confidence 356779999999774 4568899999997
No 22
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=50.75 E-value=7.2 Score=25.52 Aligned_cols=32 Identities=22% Similarity=0.594 Sum_probs=21.7
Q ss_pred eeCCchhhhhcCCCcccceeeecCCCC-cceeeeecCCcCCcc
Q 027215 23 VHCTFCDTVLAVPYHFIFSVSVPCTSL-FKTVTVRCGHCTNLL 64 (226)
Q Consensus 23 V~CnFCnTILa~~~~~~~~VsVPcssL-~~~VTVRCGHCtnLl 64 (226)
+.|.-|.+... ||=+.+ =+.+.|||+.|.+.+
T Consensus 3 i~Cp~C~~~y~----------i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYE----------IDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEe----------CCHHHCCCCCcEEECCCCCCEe
Confidence 67888888766 222222 245789999998865
No 23
>PRK03954 ribonuclease P protein component 4; Validated
Probab=50.65 E-value=5.5 Score=32.83 Aligned_cols=37 Identities=22% Similarity=0.502 Sum_probs=21.9
Q ss_pred CCchhhhhcCCCcccceeeecCCCCcceeeeecCCcCCcc
Q 027215 25 CTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTNLL 64 (226)
Q Consensus 25 CnFCnTILa~~~~~~~~VsVPcssL~~~VTVRCGHCtnLl 64 (226)
|-.|+|.|. |.. ...|-+--.. +.-|.++|..|...-
T Consensus 67 CK~C~t~Li-PG~-n~~vRi~~~~-~~~vvitCl~CG~~k 103 (121)
T PRK03954 67 CKRCHSFLV-PGV-NARVRLRQKR-MPHVVITCLECGHIM 103 (121)
T ss_pred hhcCCCeee-cCC-ceEEEEecCC-cceEEEECccCCCEE
Confidence 889999997 221 1112221111 235899999998754
No 24
>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=49.63 E-value=28 Score=25.49 Aligned_cols=33 Identities=15% Similarity=0.441 Sum_probs=26.5
Q ss_pred hhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccC
Q 027215 145 AYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHF 180 (226)
Q Consensus 145 aYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~ 180 (226)
+|..+|+-- |-+.||++.+-.-+...+..|+.|
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 455555544 457899999999999999999986
No 25
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=49.02 E-value=5.5 Score=36.81 Aligned_cols=33 Identities=39% Similarity=0.865 Sum_probs=22.4
Q ss_pred eeeeeCCchhhhhcCCCcccceeeecCCCCcceee---eecCCcCCcccccc
Q 027215 20 LCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVT---VRCGHCTNLLSVNM 68 (226)
Q Consensus 20 lCYV~CnFCnTILa~~~~~~~~VsVPcssL~~~VT---VRCGHCtnLlSVNm 68 (226)
-|-|-|+-|+.+.. |++.| -||-||...+||--
T Consensus 168 gcRV~CgHC~~tFL----------------fnt~tnaLArCPHCrKvSsvGs 203 (275)
T KOG4684|consen 168 GCRVKCGHCNETFL----------------FNTLTNALARCPHCRKVSSVGS 203 (275)
T ss_pred ceEEEecCccceee----------------hhhHHHHHhcCCcccchhhhhh
Confidence 48888888876654 33333 58888888887743
No 26
>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=48.92 E-value=9.3 Score=24.72 Aligned_cols=26 Identities=38% Similarity=0.773 Sum_probs=16.9
Q ss_pred eeCCchhhhhcCCCcccceeeecCCCCcceeeeecCCcCC
Q 027215 23 VHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTN 62 (226)
Q Consensus 23 V~CnFCnTILa~~~~~~~~VsVPcssL~~~VTVRCGHCtn 62 (226)
|.|.-|.|+|+.|. ..-.|||--|.-
T Consensus 2 ~~C~~C~t~L~yP~--------------gA~~vrCs~C~~ 27 (31)
T TIGR01053 2 VVCGGCRTLLMYPR--------------GASSVRCALCQT 27 (31)
T ss_pred cCcCCCCcEeecCC--------------CCCeEECCCCCe
Confidence 46888888888442 334677777754
No 27
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=47.70 E-value=6.6 Score=29.28 Aligned_cols=30 Identities=20% Similarity=0.558 Sum_probs=20.4
Q ss_pred eeCCchhhhhcCCCcccceeeecCCCCcceeeeecCCcCCcc
Q 027215 23 VHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTNLL 64 (226)
Q Consensus 23 V~CnFCnTILa~~~~~~~~VsVPcssL~~~VTVRCGHCtnLl 64 (226)
++|.+||.+|| .++ ----.-++|..|--+-
T Consensus 5 iRC~~CnKlLa-------~a~-----~~~yle~KCPrCK~vN 34 (60)
T COG4416 5 IRCAKCNKLLA-------EAE-----GQAYLEKKCPRCKEVN 34 (60)
T ss_pred eehHHHhHHHH-------hcc-----cceeeeecCCccceee
Confidence 68999999999 111 1123567899987543
No 28
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=40.69 E-value=18 Score=33.97 Aligned_cols=28 Identities=32% Similarity=1.024 Sum_probs=22.4
Q ss_pred CCceeeeeCCchhhhhcCCCcccceeeecCCCCcceeeeecCCcCC
Q 027215 17 SEQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTN 62 (226)
Q Consensus 17 ~EqlCYV~CnFCnTILa~~~~~~~~VsVPcssL~~~VTVRCGHCtn 62 (226)
.+-.=|.||++|.|- ...|-++|.+|.|
T Consensus 207 ~~G~RyL~CslC~te------------------W~~~R~~C~~Cg~ 234 (309)
T PRK03564 207 TQGLRYLHCNLCESE------------------WHVVRVKCSNCEQ 234 (309)
T ss_pred CCCceEEEcCCCCCc------------------ccccCccCCCCCC
Confidence 466789999999774 4568899999997
No 29
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
Probab=38.53 E-value=54 Score=29.75 Aligned_cols=41 Identities=22% Similarity=0.402 Sum_probs=37.4
Q ss_pred CCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215 141 RVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP 181 (226)
Q Consensus 141 RvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P 181 (226)
|--|||-.|..+.=.+|+..+|+++--|.=+.+.+.|+.+-
T Consensus 73 Rp~sayf~y~~~~R~ei~~~~p~l~~~e~~k~~~e~WK~Lt 113 (211)
T COG5648 73 RPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELT 113 (211)
T ss_pred CchhHHHHHHHHHHHHHHHhCCCCChHHHHHHHHHHHHhcc
Confidence 56799999999999999999999999999999999999853
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=38.25 E-value=43 Score=29.83 Aligned_cols=34 Identities=21% Similarity=0.552 Sum_probs=29.2
Q ss_pred hhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215 144 SAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP 181 (226)
Q Consensus 144 SaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P 181 (226)
++|=.||.+ .+..|.++..+|.-..||+-|...+
T Consensus 84 naYLNFLRe----FRrkh~~L~p~dlI~~AAraW~rLS 117 (183)
T PF06382_consen 84 NAYLNFLRE----FRRKHCGLSPQDLIQRAARAWCRLS 117 (183)
T ss_pred hHHHHHHHH----HHHHccCCCHHHHHHHHHHHHHhCC
Confidence 678888764 7778999999999999999998754
No 31
>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=38.07 E-value=9.1 Score=27.67 Aligned_cols=37 Identities=22% Similarity=0.388 Sum_probs=16.8
Q ss_pred eCCchhhhhcCCCcccceeeec-CCCCcceeeeecCCcCC
Q 027215 24 HCTFCDTVLAVPYHFIFSVSVP-CTSLFKTVTVRCGHCTN 62 (226)
Q Consensus 24 ~CnFCnTILa~~~~~~~~VsVP-cssL~~~VTVRCGHCtn 62 (226)
-|.-|.++|. |- +.-+|-|- =+..-+.|.++|..|.+
T Consensus 48 ~Ck~C~~~li-PG-~~~~vri~~~~~~~~~l~~~C~~C~~ 85 (85)
T PF04032_consen 48 ICKKCGSLLI-PG-VNCSVRIRKKKKKKNFLVYTCLNCGH 85 (85)
T ss_dssp B-TTT--B---CT-TTEEEEEE---SSS-EEEEEETTTTE
T ss_pred cccCCCCEEe-CC-CccEEEEEecCCCCCEEEEEccccCC
Confidence 5899999998 11 11112111 12346788999999963
No 32
>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=36.52 E-value=20 Score=33.29 Aligned_cols=39 Identities=26% Similarity=0.564 Sum_probs=27.6
Q ss_pred CceeeeeCCchhhhhcCCCcccceeeecCCCCcceeeeecCCcCCcccccc
Q 027215 18 EQLCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTNLLSVNM 68 (226)
Q Consensus 18 EqlCYV~CnFCnTILa~~~~~~~~VsVPcssL~~~VTVRCGHCtnLlSVNm 68 (226)
..-|=|.|+.|+.... ...+-+ .--.||-||-.++||.-
T Consensus 153 p~~~rv~CghC~~~Fl--------~~~~~~----~tlARCPHCrKvSSVG~ 191 (256)
T PF09788_consen 153 PGSCRVICGHCSNTFL--------FNTLTS----NTLARCPHCRKVSSVGP 191 (256)
T ss_pred CCceeEECCCCCCcEe--------ccCCCC----CccccCCCCceeccccc
Confidence 4678899999987766 222221 12379999999999964
No 33
>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=36.32 E-value=18 Score=30.21 Aligned_cols=36 Identities=28% Similarity=0.285 Sum_probs=30.5
Q ss_pred CCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHh
Q 027215 141 RVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKN 176 (226)
Q Consensus 141 RvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAkn 176 (226)
...+.-.+=++.||+++|+|.-.|+.+|-|...||+
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 345666778999999999999999999999999996
No 34
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=35.54 E-value=18 Score=33.56 Aligned_cols=18 Identities=33% Similarity=0.811 Sum_probs=13.6
Q ss_pred ceeeeecCCcCCcccccc
Q 027215 51 KTVTVRCGHCTNLLSVNM 68 (226)
Q Consensus 51 ~~VTVRCGHCtnLlSVNm 68 (226)
..+-|+||||.+..--|.
T Consensus 167 ~gcRV~CgHC~~tFLfnt 184 (275)
T KOG4684|consen 167 TGCRVKCGHCNETFLFNT 184 (275)
T ss_pred cceEEEecCccceeehhh
Confidence 348899999998765553
No 35
>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=34.85 E-value=55 Score=24.16 Aligned_cols=31 Identities=26% Similarity=0.473 Sum_probs=22.9
Q ss_pred CCccCCCCchhhhHHHHHHHHHHHhcCCCCC
Q 027215 135 PPEKRQRVPSAYNRFIKDEIQRIKAGNPDIS 165 (226)
Q Consensus 135 PPEKRQRvPSaYN~FmK~ei~riK~~nP~i~ 165 (226)
|.+..+....+|-.++++-++.||+.+|+.+
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 3455555788999999999999999999743
No 36
>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=31.21 E-value=33 Score=22.76 Aligned_cols=18 Identities=22% Similarity=0.589 Sum_probs=14.5
Q ss_pred cceeeeecCCcCCccccc
Q 027215 50 FKTVTVRCGHCTNLLSVN 67 (226)
Q Consensus 50 ~~~VTVRCGHCtnLlSVN 67 (226)
+.+|+|.|-+|.+-.+|.
T Consensus 1 Ma~i~v~CP~C~s~~~v~ 18 (36)
T PF03811_consen 1 MAKIDVHCPRCQSTEGVK 18 (36)
T ss_pred CCcEeeeCCCCCCCCcce
Confidence 458999999999877663
No 37
>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=30.72 E-value=36 Score=22.87 Aligned_cols=19 Identities=26% Similarity=0.641 Sum_probs=15.3
Q ss_pred hHHHHHHHHHHHhcCCCCC
Q 027215 147 NRFIKDEIQRIKAGNPDIS 165 (226)
Q Consensus 147 N~FmK~ei~riK~~nP~i~ 165 (226)
..|+++-+..||..||++.
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 3699999999999999863
No 38
>COG3712 FecR Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]
Probab=29.21 E-value=48 Score=31.44 Aligned_cols=30 Identities=23% Similarity=0.535 Sum_probs=27.6
Q ss_pred HHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215 150 IKDEIQRIKAGNPDISHREAFSAAAKNWAHFP 181 (226)
Q Consensus 150 mK~ei~riK~~nP~i~HkEaFs~aAknWa~~P 181 (226)
.++|.+||++..|+ |.+||..+..-|+...
T Consensus 33 ~r~af~~W~~~~p~--H~~A~~~~e~lw~~l~ 62 (322)
T COG3712 33 DRAAFERWRAASPE--HARAWERAERLWQALG 62 (322)
T ss_pred HHHHHHHHHhcCHH--HHHHHHHHHHHHhhhc
Confidence 57899999999997 9999999999999865
No 39
>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=29.09 E-value=17 Score=32.56 Aligned_cols=32 Identities=28% Similarity=0.730 Sum_probs=16.6
Q ss_pred eeeeeCCchhhhhcCCCcccceeeecCCCCcceeeeecCCcCCccccccc
Q 027215 20 LCYVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCTNLLSVNMR 69 (226)
Q Consensus 20 lCYV~CnFCnTILa~~~~~~~~VsVPcssL~~~VTVRCGHCtnLlSVNmr 69 (226)
.=|-+|.+|.|- ...+-++|.+|.|--...+.
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 468889999774 34567889999986655544
No 40
>COG5629 Predicted metal-binding protein [Function unknown]
Probab=26.91 E-value=27 Score=33.21 Aligned_cols=31 Identities=35% Similarity=0.687 Sum_probs=21.1
Q ss_pred eeeCCchhhhhcCCCcccceeeecCCCCccee----eeecCCcC
Q 027215 22 YVHCTFCDTVLAVPYHFIFSVSVPCTSLFKTV----TVRCGHCT 61 (226)
Q Consensus 22 YV~CnFCnTILa~~~~~~~~VsVPcssL~~~V----TVRCGHCt 61 (226)
-+||.|||.+|.+| --+|+.+-+ .+-|--||
T Consensus 169 klhCsfCnA~lGlp---------n~~s~~kl~r~~k~~I~~g~t 203 (321)
T COG5629 169 KLHCSFCNARLGLP---------NDSSIRKLFRYNKEVIPNGCT 203 (321)
T ss_pred ceeeehhhhhhCCC---------CchhhhhhhhcchheecCCCc
Confidence 37999999999842 234555555 56666666
No 41
>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=26.03 E-value=37 Score=25.55 Aligned_cols=14 Identities=36% Similarity=0.629 Sum_probs=8.9
Q ss_pred ceeeeecCCcCCcc
Q 027215 51 KTVTVRCGHCTNLL 64 (226)
Q Consensus 51 ~~VTVRCGHCtnLl 64 (226)
-+|-|||+.|.|.-
T Consensus 26 GvViv~C~gC~~~H 39 (66)
T PF05180_consen 26 GVVIVQCPGCKNRH 39 (66)
T ss_dssp SEEEEE-TTS--EE
T ss_pred CeEEEECCCCccee
Confidence 47999999999853
No 42
>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=24.52 E-value=11 Score=29.57 Aligned_cols=18 Identities=39% Similarity=0.977 Sum_probs=14.9
Q ss_pred CceeeeeCCchhhhhcCC
Q 027215 18 EQLCYVHCTFCDTVLAVP 35 (226)
Q Consensus 18 EqlCYV~CnFCnTILa~~ 35 (226)
=|||..=|++|||++-.|
T Consensus 37 IqLC~~cc~~~n~~v~~P 54 (82)
T PF02723_consen 37 IQLCFQCCRLCNTTVYKP 54 (82)
T ss_pred HHHHHHHhhhhcceEecc
Confidence 378999999999988844
No 43
>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=24.48 E-value=71 Score=29.20 Aligned_cols=24 Identities=25% Similarity=0.508 Sum_probs=23.0
Q ss_pred hhhHHHHHHHHHHHhcCCCCCHHH
Q 027215 145 AYNRFIKDEIQRIKAGNPDISHRE 168 (226)
Q Consensus 145 aYN~FmK~ei~riK~~nP~i~HkE 168 (226)
-|..||++...+-|+.+|.+|.|+
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 44
>KOG3404 consensus G10 protein/predicted nuclear transcription regulator [Transcription]
Probab=24.09 E-value=34 Score=29.32 Aligned_cols=36 Identities=36% Similarity=0.701 Sum_probs=28.6
Q ss_pred CCceeeeeC------CchhhhhcCCCcccceeeecCCCCcceeeeecCCcC
Q 027215 17 SEQLCYVHC------TFCDTVLAVPYHFIFSVSVPCTSLFKTVTVRCGHCT 61 (226)
Q Consensus 17 ~EqlCYV~C------nFCnTILa~~~~~~~~VsVPcssL~~~VTVRCGHCt 61 (226)
-|.||.++| ||=+|-+. -||-+.|=.--.|+|-||.
T Consensus 97 YE~LCClRCIq~~dsn~Gt~CIC---------RVPk~~ld~~~~~~C~hCG 138 (145)
T KOG3404|consen 97 YENLCCLRCIQTRDSNFGTTCIC---------RVPKSKLDVERIVECVHCG 138 (145)
T ss_pred ccceeeeeeccccccCCCceEEE---------eCChhhcChhheeeeeccC
Confidence 489999999 55544443 6899988888889999996
No 45
>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=23.77 E-value=29 Score=25.32 Aligned_cols=9 Identities=56% Similarity=1.220 Sum_probs=5.4
Q ss_pred ecCCcCCcc
Q 027215 56 RCGHCTNLL 64 (226)
Q Consensus 56 RCGHCtnLl 64 (226)
+|||++||-
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 399999874
No 46
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=23.53 E-value=37 Score=32.36 Aligned_cols=32 Identities=31% Similarity=0.442 Sum_probs=22.0
Q ss_pred ccCCCCchhhhHHHHHHHHHHHhcCC---CCCHHHHHHHH
Q 027215 137 EKRQRVPSAYNRFIKDEIQRIKAGNP---DISHREAFSAA 173 (226)
Q Consensus 137 EKRQRvPSaYN~FmK~ei~riK~~nP---~i~HkEaFs~a 173 (226)
|||.|+ -|--|+|||||+|.- -|+-+-+=.+|
T Consensus 246 eKRPRT-----AFtaeQL~RLK~EF~enRYlTEqRRQ~La 280 (342)
T KOG0493|consen 246 EKRPRT-----AFTAEQLQRLKAEFQENRYLTEQRRQELA 280 (342)
T ss_pred hcCccc-----cccHHHHHHHHHHHhhhhhHHHHHHHHHH
Confidence 677775 477899999999865 34545444444
No 47
>KOG4520 consensus Predicted coiled-coil protein [General function prediction only]
Probab=23.46 E-value=85 Score=28.77 Aligned_cols=15 Identities=27% Similarity=0.350 Sum_probs=12.0
Q ss_pred hHHHHHHHHHHHhcC
Q 027215 147 NRFIKDEIQRIKAGN 161 (226)
Q Consensus 147 N~FmK~ei~riK~~n 161 (226)
---|||||++||+..
T Consensus 62 ~~~~keEi~~vkE~E 76 (238)
T KOG4520|consen 62 KEKYKEEILEVKERE 76 (238)
T ss_pred hHHHHHHHHHHHHHH
Confidence 345899999999864
No 48
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=23.44 E-value=38 Score=22.43 Aligned_cols=14 Identities=36% Similarity=0.978 Sum_probs=11.2
Q ss_pred eeecCCcCCccccc
Q 027215 54 TVRCGHCTNLLSVN 67 (226)
Q Consensus 54 TVRCGHCtnLlSVN 67 (226)
.++||+|..-+...
T Consensus 5 ~l~C~~CG~~m~~~ 18 (58)
T PF13408_consen 5 LLRCGHCGSKMTRR 18 (58)
T ss_pred cEEcccCCcEeEEE
Confidence 47999999887763
No 49
>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=22.88 E-value=1.3e+02 Score=21.56 Aligned_cols=32 Identities=31% Similarity=0.378 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHHHhhcc
Q 027215 148 RFIKDEIQRIKAGNPDISHREAFSAAAKNWAH 179 (226)
Q Consensus 148 ~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~ 179 (226)
.++.+.|++++..+|.++-..+...||-|-++
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 50
>PF04769 MAT_Alpha1: Mating-type protein MAT alpha 1; InterPro: IPR006856 This family includes Saccharomyces cerevisiae (Baker's yeast) mating type protein alpha 1 (P01365 from SWISSPROT). MAT alpha 1 is a transcription activator that activates mating-type alpha-specific genes with the help of the MADS-box containing MCM1 transcription factor, which together bind cooperatively to PQ elements upstream of alpha-specific genes. The MCM1-MATalpha1 complex is required for the proper DNA-bending that is needed for transcriptional activation []. Alpha 1 interacts in vivo with STE12, linking expression of alpha-specific genes to the alpha-pheromone (IPR006742 from INTERPRO) response pathway [].; GO: 0000772 mating pheromone activity, 0003677 DNA binding, 0045895 positive regulation of transcription, mating-type specific, 0005634 nucleus
Probab=22.30 E-value=2.1e+02 Score=25.35 Aligned_cols=47 Identities=23% Similarity=0.328 Sum_probs=38.7
Q ss_pred CCCCccCCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCCcc
Q 027215 133 NRPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFPHI 183 (226)
Q Consensus 133 ~kPPEKRQRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~PhI 183 (226)
.+.++|+-|.-.+|+.|+-== +...|+++.|++=...++-|...|+-
T Consensus 38 ~~~~~~~kr~lN~Fm~FRsyy----~~~~~~~~Qk~~S~~l~~lW~~dp~k 84 (201)
T PF04769_consen 38 KRSPEKAKRPLNGFMAFRSYY----SPIFPPLPQKELSGILTKLWEKDPFK 84 (201)
T ss_pred cccccccccchhHHHHHHHHH----HhhcCCcCHHHHHHHHHHHHhCCccH
Confidence 456788889999999987643 36678899999999999999998874
No 51
>PRK09774 fec operon regulator FecR; Reviewed
Probab=21.76 E-value=69 Score=29.07 Aligned_cols=29 Identities=10% Similarity=0.084 Sum_probs=25.2
Q ss_pred HHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215 151 KDEIQRIKAGNPDISHREAFSAAAKNWAHFP 181 (226)
Q Consensus 151 K~ei~riK~~nP~i~HkEaFs~aAknWa~~P 181 (226)
+++.++|.+++|+ |++||..+..-|....
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 3678999999997 9999999999997754
No 52
>PF14722 KRAP_IP3R_bind: Ki-ras-induced actin-interacting protein-IP3R-interacting domain
Probab=21.40 E-value=93 Score=27.20 Aligned_cols=27 Identities=22% Similarity=0.469 Sum_probs=21.9
Q ss_pred hhHHHHHHHHHHHhcCCCCCHHHHHHH
Q 027215 146 YNRFIKDEIQRIKAGNPDISHREAFSA 172 (226)
Q Consensus 146 YN~FmK~ei~riK~~nP~i~HkEaFs~ 172 (226)
...|++.++|||..|||+..---+|.+
T Consensus 71 ~~~FL~aQ~qrm~~E~p~~~l~~RFRQ 97 (160)
T PF14722_consen 71 IRVFLEAQKQRMDIENPNLALASRFRQ 97 (160)
T ss_pred HHHHHHHHHHHHHhhCccHHHHHHHHH
Confidence 467999999999999999665555554
No 53
>KOG4715 consensus SWI/SNF-related matrix-associated actin-dependent regulator of chromatin [Chromatin structure and dynamics]
Probab=21.35 E-value=1.2e+02 Score=29.75 Aligned_cols=45 Identities=29% Similarity=0.555 Sum_probs=39.7
Q ss_pred CCCccCCCCchhhhHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhccCC
Q 027215 134 RPPEKRQRVPSAYNRFIKDEIQRIKAGNPDISHREAFSAAAKNWAHFP 181 (226)
Q Consensus 134 kPPEKRQRvPSaYN~FmK~ei~riK~~nP~i~HkEaFs~aAknWa~~P 181 (226)
|||||- .-.|=||-+.=-..+||.||++---|.=+.+.+.|.+.|
T Consensus 63 kppekp---l~pymrySrkvWd~VkA~nPe~kLWeiGK~Ig~mW~dLp 107 (410)
T KOG4715|consen 63 KPPEKP---LMPYMRYSRKVWDQVKASNPELKLWEIGKIIGGMWLDLP 107 (410)
T ss_pred CCCCcc---cchhhHHhhhhhhhhhccCcchHHHHHHHHHHHHHhhCc
Confidence 788874 457999999999999999999999999999999999876
No 54
>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=20.83 E-value=31 Score=22.27 Aligned_cols=16 Identities=19% Similarity=0.584 Sum_probs=10.7
Q ss_pred CceeeeeCCchhhhhc
Q 027215 18 EQLCYVHCTFCDTVLA 33 (226)
Q Consensus 18 EqlCYV~CnFCnTILa 33 (226)
+..-++.|.+|+.++.
T Consensus 12 ~~~~~a~C~~C~~~~~ 27 (45)
T PF02892_consen 12 GDKKKAKCKYCGKVIK 27 (45)
T ss_dssp GCSS-EEETTTTEE--
T ss_pred CCcCeEEeCCCCeEEe
Confidence 3567899999998887
No 55
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=20.71 E-value=28 Score=28.58 Aligned_cols=50 Identities=24% Similarity=0.482 Sum_probs=30.8
Q ss_pred CceeeeeCCchhhhhcCCCccccee-e---ecCC-CCcceeeeecCCcCCcccccc
Q 027215 18 EQLCYVHCTFCDTVLAVPYHFIFSV-S---VPCT-SLFKTVTVRCGHCTNLLSVNM 68 (226)
Q Consensus 18 EqlCYV~CnFCnTILa~~~~~~~~V-s---VPcs-sL~~~VTVRCGHCtnLlSVNm 68 (226)
+-+==.+|.-|++--| =||---+. . +|-. ..++.-.|-||+|-++|+++=
T Consensus 22 ~Diialkc~~C~kyYa-Cy~CHdel~~Hpf~p~~~~~~~~~~iiCGvC~~~LT~~E 76 (105)
T COG4357 22 LDIIALKCKCCQKYYA-CYHCHDELEDHPFEPWGLQEFNPKAIICGVCRKLLTRAE 76 (105)
T ss_pred cceEeeeechhhhhhh-HHHHHhHHhcCCCccCChhhcCCccEEhhhhhhhhhHHH
Confidence 3344468888888776 11110000 1 1221 578888899999999999864
Done!