Query 029974
Match_columns 184
No_of_seqs 117 out of 183
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 06:33:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029974.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029974hhsearch_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 1.2E-78 2.7E-83 499.4 12.1 157 1-157 1-170 (170)
2 PF09011 HMG_box_2: HMG-box do 98.1 7.1E-06 1.5E-10 57.6 4.6 45 107-151 2-47 (73)
3 cd01390 HMGB-UBF_HMG-box HMGB- 97.8 5.7E-05 1.2E-09 50.4 5.0 42 110-151 2-43 (66)
4 cd01388 SOX-TCF_HMG-box SOX-TC 97.7 7.4E-05 1.6E-09 52.3 5.0 42 110-151 3-44 (72)
5 PF00505 HMG_box: HMG (high mo 97.7 7.5E-05 1.6E-09 50.4 4.6 41 110-150 2-42 (69)
6 cd00084 HMG-box High Mobility 97.7 9.8E-05 2.1E-09 48.7 5.0 43 110-152 2-44 (66)
7 smart00398 HMG high mobility g 97.6 0.00015 3.2E-09 48.4 5.3 44 109-152 2-45 (70)
8 cd01389 MATA_HMG-box MATA_HMG- 97.6 0.00018 3.9E-09 50.8 5.3 43 110-152 3-45 (77)
9 PTZ00199 high mobility group p 97.2 0.00092 2E-08 49.7 5.3 45 108-152 22-68 (94)
10 KOG0381 HMG box-containing pro 96.3 0.0095 2.1E-07 43.0 5.3 45 108-152 22-66 (96)
11 PF06244 DUF1014: Protein of u 95.3 0.023 5.1E-07 45.4 4.0 47 107-155 73-119 (122)
12 PF11331 DUF3133: Protein of u 94.2 0.027 5.9E-07 38.4 1.5 38 12-51 6-46 (46)
13 KOG3223 Uncharacterized conser 86.7 0.56 1.2E-05 41.0 2.7 49 107-157 165-213 (221)
14 TIGR02098 MJ0042_CXXC MJ0042 f 80.8 1.5 3.2E-05 27.2 2.1 34 13-48 3-37 (38)
15 PF13719 zinc_ribbon_5: zinc-r 80.2 1.2 2.7E-05 28.2 1.7 34 13-48 3-37 (37)
16 PF05129 Elf1: Transcription e 76.2 1.5 3.3E-05 32.4 1.4 41 12-52 22-62 (81)
17 PRK14892 putative transcriptio 75.7 3 6.5E-05 32.3 2.9 43 11-56 20-62 (99)
18 TIGR01562 FdhE formate dehydro 72.3 2.1 4.5E-05 38.8 1.5 27 8-44 206-232 (305)
19 PF04032 Rpr2: RNAse P Rpr2/Rp 71.6 1.9 4E-05 30.5 0.8 32 13-44 47-85 (85)
20 PRK03954 ribonuclease P protei 70.8 2.3 5.1E-05 34.0 1.3 32 15-46 67-103 (121)
21 PF10122 Mu-like_Com: Mu-like 68.0 3.2 7E-05 29.1 1.4 32 13-48 5-36 (51)
22 PF13717 zinc_ribbon_4: zinc-r 67.6 6.2 0.00014 25.0 2.6 30 13-46 3-35 (36)
23 PRK03564 formate dehydrogenase 64.4 3.9 8.5E-05 37.2 1.6 27 8-44 208-234 (309)
24 COG3058 FdhE Uncharacterized p 60.6 1.3 2.8E-05 40.5 -2.1 34 7-50 206-239 (308)
25 PF09788 Tmemb_55A: Transmembr 59.8 7 0.00015 35.1 2.3 39 8-50 153-191 (256)
26 KOG4684 Uncharacterized conser 59.3 3.8 8.2E-05 36.7 0.6 12 35-46 169-180 (275)
27 PF08073 CHDNT: CHDNT (NUC034) 54.9 22 0.00048 25.2 3.7 33 115-150 18-50 (55)
28 PF04216 FdhE: Protein involve 53.1 4.7 0.0001 35.1 0.1 32 10-51 195-226 (290)
29 PF11331 DUF3133: Protein of u 52.6 8.4 0.00018 26.3 1.3 19 9-27 28-46 (46)
30 KOG4684 Uncharacterized conser 43.6 11 0.00024 33.9 0.9 33 10-50 168-203 (275)
31 PF06382 DUF1074: Protein of u 43.0 35 0.00076 29.5 3.8 36 113-152 83-118 (183)
32 COG5648 NHP6B Chromatin-associ 41.3 48 0.001 29.2 4.5 42 110-151 72-113 (211)
33 PF03811 Zn_Tnp_IS1: InsA N-te 40.9 18 0.0004 23.2 1.4 17 32-48 1-17 (36)
34 PF04420 CHD5: CHD5-like prote 40.3 17 0.00037 29.5 1.5 35 112-146 37-71 (161)
35 COG4416 Com Mu-like prophage p 40.2 6.9 0.00015 28.2 -0.7 13 34-46 2-14 (60)
36 TIGR01053 LSD1 zinc finger dom 39.9 25 0.00054 22.0 1.9 25 13-43 2-26 (31)
37 PF05047 L51_S25_CI-B8: Mitoch 37.3 27 0.00057 22.8 1.8 19 117-135 2-20 (52)
38 KOG0493 Transcription factor E 30.6 43 0.00093 31.0 2.6 50 107-170 246-304 (342)
39 PF01020 Ribosomal_L40e: Ribos 30.2 19 0.00041 25.4 0.2 9 38-46 38-46 (52)
40 COG4888 Uncharacterized Zn rib 30.0 38 0.00082 26.9 1.9 45 12-56 22-66 (104)
41 PF14599 zinc_ribbon_6: Zinc-r 29.5 33 0.00072 24.5 1.4 30 9-44 27-56 (61)
42 PF05180 zf-DNL: DNL zinc fing 29.4 29 0.00063 25.2 1.1 32 14-45 6-38 (66)
43 COG3712 FecR Fe2+-dicitrate se 28.6 50 0.0011 30.4 2.7 31 119-151 32-62 (322)
44 PF02892 zf-BED: BED zinc fing 28.0 28 0.0006 21.9 0.7 17 9-25 13-29 (45)
45 PF00527 E7: E7 protein, Early 27.2 25 0.00055 26.5 0.5 30 13-42 53-91 (92)
46 KOG4520 Predicted coiled-coil 27.1 74 0.0016 28.3 3.3 35 117-151 62-112 (238)
47 TIGR02147 Fsuc_second hypothet 27.0 60 0.0013 28.8 2.8 24 115-138 9-32 (271)
48 PF13408 Zn_ribbon_recom: Reco 26.4 31 0.00067 22.2 0.7 13 36-48 5-17 (58)
49 PF14722 KRAP_IP3R_bind: Ki-ra 25.2 76 0.0017 26.9 3.0 28 116-143 71-98 (160)
50 PF05164 ZapA: Cell division p 25.1 1.1E+02 0.0024 21.3 3.4 32 118-149 28-59 (89)
51 COG4357 Zinc finger domain con 24.7 20 0.00044 28.4 -0.5 39 12-50 26-76 (105)
52 PRK12336 translation initiatio 24.6 79 0.0017 26.7 3.0 36 12-53 98-136 (201)
53 PF02723 NS3_envE: Non-structu 24.5 14 0.0003 28.0 -1.3 16 8-23 37-52 (82)
54 PF12876 Cellulase-like: Sugar 24.1 1E+02 0.0022 22.1 3.1 27 109-135 33-59 (88)
55 smart00614 ZnF_BED BED zinc fi 23.0 49 0.0011 21.7 1.2 14 11-24 17-30 (50)
56 TIGR00311 aIF-2beta translatio 21.3 94 0.002 25.0 2.7 33 11-49 96-131 (133)
57 KOG1522 RNA polymerase II, sub 21.1 51 0.0011 30.1 1.3 26 5-30 82-107 (285)
58 PF06943 zf-LSD1: LSD1 zinc fi 20.6 48 0.001 20.1 0.7 10 12-21 16-25 (25)
59 PF01667 Ribosomal_S27e: Ribos 20.3 57 0.0012 23.0 1.1 11 13-23 27-37 (55)
60 PF04690 YABBY: YABBY protein; 20.2 51 0.0011 27.9 1.0 19 12-30 36-54 (170)
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=1.2e-78 Score=499.41 Aligned_cols=157 Identities=64% Similarity=0.999 Sum_probs=120.4
Q ss_pred CCCCCCCCceeeeeCCccceeeeccccCCCccceeeeecccCCCcccccccccccCCCCCCchhhhhc-------CCCcc
Q 029974 1 MSLDLASERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQDPQLQKQH-------INLED 73 (184)
Q Consensus 1 ms~~~~~E~lCYV~CnfC~TiLaVsVPcssL~~~VTVRCGHCtnLlSVNm~~ll~s~~~q~~~~~~~~-------~~~~~ 73 (184)
|+.+.++|||||||||||||||||||||+|||+|||||||||+|||||||++++++++.|++..+... ....+
T Consensus 1 ~~~~~~sE~lCYVhCnFC~TiLaVsVP~ssL~~~VTVRCGHCtNLLSVNm~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~ 80 (170)
T PF04690_consen 1 MDLFSPSEQLCYVHCNFCNTILAVSVPCSSLLKTVTVRCGHCTNLLSVNMRALLQPLPSQDHLQHSLLPPQSQELQFQPE 80 (170)
T ss_pred CCccCCCCcEEEEEcCCcCeEEEEecchhhhhhhhceeccCccceeeeeccccccCCCcccchhcccccccccccccccc
Confidence 67777899999999999999999999999999999999999999999999999999887765211110 00011
Q ss_pred cccccCC---CCCcCCCCCCcccCCCCCCCCCCC-CC--ccCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhh
Q 029974 74 SITKDCG---SSSKCNKFSSAFETAEHETPRMPP-IR--QKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNW 147 (184)
Q Consensus 74 ~~~~~~~---sss~~~~~~~~~~~~~~e~p~~~~-~r--EKRQRvpsayN~fmK~ei~riK~~~P~i~hkEaF~~aA~nW 147 (184)
....... +++.+........+.+++.|+.++ +| |||||+|||||+||||||||||++||||+|||||++|||||
T Consensus 81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~pr~~~v~kPPEKRqR~psaYn~f~k~ei~rik~~~p~ishkeaFs~aAknW 160 (170)
T PF04690_consen 81 NFGSNSSSSSSSSSSSSSSSMSFSEEEEIPRAPPVNKPPEKRQRVPSAYNRFMKEEIQRIKAENPDISHKEAFSAAAKNW 160 (170)
T ss_pred ccccccccCCCccccccccccCccccccccccccccCCccccCCCchhHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhh
Confidence 1111111 111111100112233456677655 34 99999999999999999999999999999999999999999
Q ss_pred ccCCcccccc
Q 029974 148 AHFPHIHFGL 157 (184)
Q Consensus 148 ~~~phihfGl 157 (184)
||+|||||||
T Consensus 161 ~h~phihfgl 170 (170)
T PF04690_consen 161 AHFPHIHFGL 170 (170)
T ss_pred hhCcccccCC
Confidence 9999999997
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=98.05 E-value=7.1e-06 Score=57.55 Aligned_cols=45 Identities=33% Similarity=0.584 Sum_probs=37.4
Q ss_pred ccCCCCchhhhHHHHHHHHHHHhh-CCCCCHHHHHHHHHHhhccCC
Q 029974 107 QKRQRVPSAYNRFIKEEIQRIKAS-NPDISHREAFSTAAKNWAHFP 151 (184)
Q Consensus 107 EKRQRvpsayN~fmK~ei~riK~~-~P~i~hkEaF~~aA~nW~~~p 151 (184)
.|..|.+|||+.||++.+.+++.. .+.++.+|++..++..|+..+
T Consensus 2 ~kpK~~~say~lF~~~~~~~~k~~G~~~~~~~e~~k~~~~~Wk~Ls 47 (73)
T PF09011_consen 2 KKPKRPPSAYNLFMKEMRKEVKEEGGQKQSFREVMKEISERWKSLS 47 (73)
T ss_dssp SS--SSSSHHHHHHHHHHHHHHHHT-T-SSHHHHHHHHHHHHHHS-
T ss_pred cCCCCCCCHHHHHHHHHHHHHHHhcccCCCHHHHHHHHHHHHHhcC
Confidence 345789999999999999999999 889999999999999999754
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=97.77 E-value=5.7e-05 Score=50.45 Aligned_cols=42 Identities=31% Similarity=0.487 Sum_probs=39.2
Q ss_pred CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029974 110 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP 151 (184)
Q Consensus 110 QRvpsayN~fmK~ei~riK~~~P~i~hkEaF~~aA~nW~~~p 151 (184)
.|-+|||..|+++....+++.+|+++..|....++..|+..+
T Consensus 2 krp~saf~~f~~~~r~~~~~~~p~~~~~~i~~~~~~~W~~ls 43 (66)
T cd01390 2 KRPLSAYFLFSQEQRPKLKKENPDASVTEVTKILGEKWKELS 43 (66)
T ss_pred CCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCC
Confidence 367899999999999999999999999999999999999754
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=97.71 E-value=7.4e-05 Score=52.26 Aligned_cols=42 Identities=17% Similarity=0.284 Sum_probs=39.2
Q ss_pred CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029974 110 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP 151 (184)
Q Consensus 110 QRvpsayN~fmK~ei~riK~~~P~i~hkEaF~~aA~nW~~~p 151 (184)
.|-|+||..|+++.-.+|++++|+++..|.-+.++..|+..+
T Consensus 3 KrP~naf~~F~~~~r~~~~~~~p~~~~~eisk~l~~~Wk~ls 44 (72)
T cd01388 3 KRPMNAFMLFSKRHRRKVLQEYPLKENRAISKILGDRWKALS 44 (72)
T ss_pred CCCCcHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCC
Confidence 478999999999999999999999999999999999998754
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=97.68 E-value=7.5e-05 Score=50.43 Aligned_cols=41 Identities=34% Similarity=0.636 Sum_probs=37.0
Q ss_pred CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccC
Q 029974 110 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHF 150 (184)
Q Consensus 110 QRvpsayN~fmK~ei~riK~~~P~i~hkEaF~~aA~nW~~~ 150 (184)
.|-++||..|+++....||+++|+++..|.-+.+++.|+..
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 47899999999999999999999999999999999999875
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=97.68 E-value=9.8e-05 Score=48.74 Aligned_cols=43 Identities=30% Similarity=0.422 Sum_probs=39.7
Q ss_pred CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 029974 110 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH 152 (184)
Q Consensus 110 QRvpsayN~fmK~ei~riK~~~P~i~hkEaF~~aA~nW~~~ph 152 (184)
.|-+|+|..|++++...+++.+|+++..|....+++.|+..+.
T Consensus 2 krp~~af~~f~~~~~~~~~~~~~~~~~~~i~~~~~~~W~~l~~ 44 (66)
T cd00084 2 KRPLSAYFLFSQEHRAEVKAENPGLSVGEISKILGEMWKSLSE 44 (66)
T ss_pred CCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCH
Confidence 4678999999999999999999999999999999999997654
No 7
>smart00398 HMG high mobility group.
Probab=97.62 E-value=0.00015 Score=48.38 Aligned_cols=44 Identities=32% Similarity=0.493 Sum_probs=40.2
Q ss_pred CCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 029974 109 RQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH 152 (184)
Q Consensus 109 RQRvpsayN~fmK~ei~riK~~~P~i~hkEaF~~aA~nW~~~ph 152 (184)
..|-+|+|..|+++....+++.+|+++..|....++..|+..+.
T Consensus 2 pkrp~~~y~~f~~~~r~~~~~~~~~~~~~~i~~~~~~~W~~l~~ 45 (70)
T smart00398 2 PKRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSE 45 (70)
T ss_pred cCCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHcCCH
Confidence 35688999999999999999999999999999999999997553
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=97.57 E-value=0.00018 Score=50.80 Aligned_cols=43 Identities=16% Similarity=0.348 Sum_probs=40.3
Q ss_pred CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 029974 110 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH 152 (184)
Q Consensus 110 QRvpsayN~fmK~ei~riK~~~P~i~hkEaF~~aA~nW~~~ph 152 (184)
.|-|+||-.|+++....|+++||++++.|.-+.++..|+..+.
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 5789999999999999999999999999999999999998654
No 9
>PTZ00199 high mobility group protein; Provisional
Probab=97.16 E-value=0.00092 Score=49.72 Aligned_cols=45 Identities=27% Similarity=0.407 Sum_probs=39.1
Q ss_pred cCCCCchhhhHHHHHHHHHHHhhCCCCC--HHHHHHHHHHhhccCCc
Q 029974 108 KRQRVPSAYNRFIKEEIQRIKASNPDIS--HREAFSTAAKNWAHFPH 152 (184)
Q Consensus 108 KRQRvpsayN~fmK~ei~riK~~~P~i~--hkEaF~~aA~nW~~~ph 152 (184)
+..|-+|||..|+++.-..|+++||+++ -.|.-+.++..|+..+.
T Consensus 22 ~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls~ 68 (94)
T PTZ00199 22 APKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSE 68 (94)
T ss_pred CCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCCH
Confidence 4457899999999999999999999986 57888889999998663
No 10
>KOG0381 consensus HMG box-containing protein [General function prediction only]
Probab=96.34 E-value=0.0095 Score=42.97 Aligned_cols=45 Identities=29% Similarity=0.429 Sum_probs=40.2
Q ss_pred cCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 029974 108 KRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH 152 (184)
Q Consensus 108 KRQRvpsayN~fmK~ei~riK~~~P~i~hkEaF~~aA~nW~~~ph 152 (184)
..+|-+|||..|+.+.-.+||++||+++..|.=+.+..+|.....
T Consensus 22 ~pkrp~sa~~~f~~~~~~~~k~~~p~~~~~~v~k~~g~~W~~l~~ 66 (96)
T KOG0381|consen 22 APKRPLSAFFLFSSEQRSKIKAENPGLSVGEVAKALGEMWKNLAE 66 (96)
T ss_pred CCCCCCcHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHhcCCH
Confidence 456788999999999999999999999999999999999987543
No 11
>PF06244 DUF1014: Protein of unknown function (DUF1014); InterPro: IPR010422 This family consists of several hypothetical eukaryotic proteins of unknown function.
Probab=95.31 E-value=0.023 Score=45.39 Aligned_cols=47 Identities=23% Similarity=0.458 Sum_probs=42.5
Q ss_pred ccCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCcccc
Q 029974 107 QKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHF 155 (184)
Q Consensus 107 EKRQRvpsayN~fmK~ei~riK~~~P~i~hkEaF~~aA~nW~~~phihf 155 (184)
|||- --||..|--.+|.+||++||++.+-+-=-..=|.|..+|...|
T Consensus 73 ErR~--KAAy~afeE~~Lp~lK~E~PgLrlsQ~kq~l~K~w~KSPeNP~ 119 (122)
T PF06244_consen 73 ERRM--KAAYKAFEERRLPELKEENPGLRLSQYKQMLWKEWQKSPENPF 119 (122)
T ss_pred chhH--HHHHHHHHHHHhHHHHhhCCCchHHHHHHHHHHHHhcCCCCCc
Confidence 6654 5699999999999999999999999988889999999998876
No 12
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=94.19 E-value=0.027 Score=38.37 Aligned_cols=38 Identities=26% Similarity=0.725 Sum_probs=29.5
Q ss_pred eeeCCccceeeeccccCCCccc---eeeeecccCCCccccccc
Q 029974 12 YVHCNYCNTILAVSVPCSSLFN---IVTVRCGHCANLLNVNMV 51 (184)
Q Consensus 12 YV~CnfC~TiLaVsVPcssL~~---~VTVRCGHCtnLlSVNm~ 51 (184)
||-|+-|..+|- +|-+.++. .-.+|||.|+.++++.++
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 788999977665 47775443 568999999999988653
No 13
>KOG3223 consensus Uncharacterized conserved protein [Function unknown]
Probab=86.69 E-value=0.56 Score=41.01 Aligned_cols=49 Identities=27% Similarity=0.493 Sum_probs=43.4
Q ss_pred ccCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCcccccc
Q 029974 107 QKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGL 157 (184)
Q Consensus 107 EKRQRvpsayN~fmK~ei~riK~~~P~i~hkEaF~~aA~nW~~~phihfGl 157 (184)
|||-| -||--|=..+|.|||.++|+++|-+-=-..-|.|...|...|.-
T Consensus 165 EkRmr--AA~~afEe~~LPrLK~e~P~lrlsQ~Kqll~Kew~KsPDNP~Nq 213 (221)
T KOG3223|consen 165 EKRMR--AAFKAFEEARLPRLKKENPGLRLSQYKQLLKKEWQKSPDNPFNQ 213 (221)
T ss_pred HHHHH--HHHHHHHHhhchhhhhcCCCccHHHHHHHHHHHHhhCCCChhhH
Confidence 77766 59999999999999999999999987778889999999988753
No 14
>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=80.77 E-value=1.5 Score=27.20 Aligned_cols=34 Identities=35% Similarity=0.633 Sum_probs=24.1
Q ss_pred eeCCccceeeeccccCCCcc-ceeeeecccCCCcccc
Q 029974 13 VHCNYCNTILAVSVPCSSLF-NIVTVRCGHCANLLNV 48 (184)
Q Consensus 13 V~CnfC~TiLaVsVPcssL~-~~VTVRCGHCtnLlSV 48 (184)
+.|..|.+..-|.. +.|- +...|+|++|.+.+.+
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 15
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=80.18 E-value=1.2 Score=28.20 Aligned_cols=34 Identities=32% Similarity=0.678 Sum_probs=25.4
Q ss_pred eeCCccceeeeccccCCCc-cceeeeecccCCCcccc
Q 029974 13 VHCNYCNTILAVSVPCSSL-FNIVTVRCGHCANLLNV 48 (184)
Q Consensus 13 V~CnfC~TiLaVsVPcssL-~~~VTVRCGHCtnLlSV 48 (184)
++|.-|.|.+.| |=+.| -....|||++|.+.+.|
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 689999998865 44443 34679999999987654
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=76.23 E-value=1.5 Score=32.43 Aligned_cols=41 Identities=22% Similarity=0.439 Sum_probs=25.7
Q ss_pred eeeCCccceeeeccccCCCccceeeeecccCCCcccccccc
Q 029974 12 YVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVS 52 (184)
Q Consensus 12 YV~CnfC~TiLaVsVPcssL~~~VTVRCGHCtnLlSVNm~~ 52 (184)
+-.|-||+.--+|+|=.+.-..+-++.||-|.--...++..
T Consensus 22 ~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~i~~ 62 (81)
T PF05129_consen 22 VFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTKINP 62 (81)
T ss_dssp ----TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE--S
T ss_pred eEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEccCc
Confidence 45799999999999999999999999999995444444433
No 17
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=75.75 E-value=3 Score=32.27 Aligned_cols=43 Identities=23% Similarity=0.543 Sum_probs=33.9
Q ss_pred eeeeCCccceeeeccccCCCccceeeeecccCCCcccccccccccC
Q 029974 11 CYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQA 56 (184)
Q Consensus 11 CYV~CnfC~TiLaVsVPcssL~~~VTVRCGHCtnLlSVNm~~ll~s 56 (184)
=++.|.||+. ..|+||... .+..+.|..|.---.-.+..|.++
T Consensus 20 t~f~CP~Cge-~~v~v~~~k--~~~h~~C~~CG~y~~~~V~~l~ep 62 (99)
T PRK14892 20 KIFECPRCGK-VSISVKIKK--NIAIITCGNCGLYTEFEVPSVYDE 62 (99)
T ss_pred cEeECCCCCC-eEeeeecCC--CcceEECCCCCCccCEECCccccc
Confidence 3789999995 688888888 799999999987765555555444
No 18
>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=72.33 E-value=2.1 Score=38.79 Aligned_cols=27 Identities=33% Similarity=0.924 Sum_probs=22.9
Q ss_pred CceeeeeCCccceeeeccccCCCccceeeeecccCCC
Q 029974 8 ERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCAN 44 (184)
Q Consensus 8 E~lCYV~CnfC~TiLaVsVPcssL~~~VTVRCGHCtn 44 (184)
+..=|.||++|.| -...|-++|.+|.|
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 19
>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=71.61 E-value=1.9 Score=30.48 Aligned_cols=32 Identities=28% Similarity=0.703 Sum_probs=20.1
Q ss_pred eeCCccceeeeccccCCC-c------cceeeeecccCCC
Q 029974 13 VHCNYCNTILAVSVPCSS-L------FNIVTVRCGHCAN 44 (184)
Q Consensus 13 V~CnfC~TiLaVsVPcss-L------~~~VTVRCGHCtn 44 (184)
.-|.-|.++|.-|+-|+- + -+.|.++|..|.+
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 358999999999998863 2 4688999999963
No 20
>PRK03954 ribonuclease P protein component 4; Validated
Probab=70.81 E-value=2.3 Score=33.97 Aligned_cols=32 Identities=25% Similarity=0.647 Sum_probs=24.8
Q ss_pred CCccceeeeccccCCC-ccc----eeeeecccCCCcc
Q 029974 15 CNYCNTILAVSVPCSS-LFN----IVTVRCGHCANLL 46 (184)
Q Consensus 15 CnfC~TiLaVsVPcss-L~~----~VTVRCGHCtnLl 46 (184)
|-.|+|.|.-||-|.- +-+ -|.++|..|...-
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 8899999998887662 222 4899999998764
No 21
>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=68.00 E-value=3.2 Score=29.07 Aligned_cols=32 Identities=25% Similarity=0.624 Sum_probs=23.4
Q ss_pred eeCCccceeeeccccCCCccceeeeecccCCCcccc
Q 029974 13 VHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNV 48 (184)
Q Consensus 13 V~CnfC~TiLaVsVPcssL~~~VTVRCGHCtnLlSV 48 (184)
+||..||..||-+- -+..+.++|..|..+-.|
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 244778888888876654
No 22
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=67.64 E-value=6.2 Score=24.99 Aligned_cols=30 Identities=23% Similarity=0.724 Sum_probs=23.2
Q ss_pred eeCCccceeeecc---ccCCCccceeeeecccCCCcc
Q 029974 13 VHCNYCNTILAVS---VPCSSLFNIVTVRCGHCANLL 46 (184)
Q Consensus 13 V~CnfC~TiLaVs---VPcssL~~~VTVRCGHCtnLl 46 (184)
+.|.-|.+...|. || =+.+.|||+.|.+.+
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
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=64.43 E-value=3.9 Score=37.21 Aligned_cols=27 Identities=33% Similarity=1.046 Sum_probs=22.8
Q ss_pred CceeeeeCCccceeeeccccCCCccceeeeecccCCC
Q 029974 8 ERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCAN 44 (184)
Q Consensus 8 E~lCYV~CnfC~TiLaVsVPcssL~~~VTVRCGHCtn 44 (184)
+-.=|.||++|.| ....|-++|.+|.|
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 5567899999876 57889999999997
No 24
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=60.64 E-value=1.3 Score=40.53 Aligned_cols=34 Identities=26% Similarity=0.771 Sum_probs=27.0
Q ss_pred CCceeeeeCCccceeeeccccCCCccceeeeecccCCCcccccc
Q 029974 7 SERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNM 50 (184)
Q Consensus 7 ~E~lCYV~CnfC~TiLaVsVPcssL~~~VTVRCGHCtnLlSVNm 50 (184)
.+-+=|.|||.|-| ....|-|+|-+|.+---+++
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 56789999999998654444
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=59.78 E-value=7 Score=35.13 Aligned_cols=39 Identities=26% Similarity=0.550 Sum_probs=27.7
Q ss_pred CceeeeeCCccceeeeccccCCCccceeeeecccCCCcccccc
Q 029974 8 ERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNM 50 (184)
Q Consensus 8 E~lCYV~CnfC~TiLaVsVPcssL~~~VTVRCGHCtnLlSVNm 50 (184)
..-|=|.|+.|+...+...+-++- -.||-||-.++||..
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 456778888888777766555332 268888888888864
No 26
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=59.34 E-value=3.8 Score=36.72 Aligned_cols=12 Identities=42% Similarity=1.187 Sum_probs=7.4
Q ss_pred eeeecccCCCcc
Q 029974 35 VTVRCGHCANLL 46 (184)
Q Consensus 35 VTVRCGHCtnLl 46 (184)
+-|+||||++..
T Consensus 169 cRV~CgHC~~tF 180 (275)
T KOG4684|consen 169 CRVKCGHCNETF 180 (275)
T ss_pred eEEEecCcccee
Confidence 666666666654
No 27
>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=54.89 E-value=22 Score=25.16 Aligned_cols=33 Identities=15% Similarity=0.448 Sum_probs=26.3
Q ss_pred hhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccC
Q 029974 115 AYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHF 150 (184)
Q Consensus 115 ayN~fmK~ei~riK~~~P~i~hkEaF~~aA~nW~~~ 150 (184)
+|..+|+-- |-+.||++++-.-+...+..|+.|
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 557899999999999999999986
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=53.13 E-value=4.7 Score=35.14 Aligned_cols=32 Identities=28% Similarity=0.718 Sum_probs=17.2
Q ss_pred eeeeeCCccceeeeccccCCCccceeeeecccCCCccccccc
Q 029974 10 VCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMV 51 (184)
Q Consensus 10 lCYV~CnfC~TiLaVsVPcssL~~~VTVRCGHCtnLlSVNm~ 51 (184)
.=|-+|.+|.|- ...+-++|.+|.|--...+.
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 458899999874 56788899999996554443
No 29
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=52.59 E-value=8.4 Score=26.29 Aligned_cols=19 Identities=26% Similarity=0.677 Sum_probs=16.4
Q ss_pred ceeeeeCCccceeeecccc
Q 029974 9 RVCYVHCNYCNTILAVSVP 27 (184)
Q Consensus 9 ~lCYV~CnfC~TiLaVsVP 27 (184)
..-=+||+-|..||-+++|
T Consensus 28 ~~~klrCGaCs~vl~~s~~ 46 (46)
T PF11331_consen 28 NQQKLRCGACSEVLSFSLP 46 (46)
T ss_pred ceeEEeCCCCceeEEEecC
Confidence 3556899999999999987
No 30
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=43.60 E-value=11 Score=33.90 Aligned_cols=33 Identities=42% Similarity=0.914 Sum_probs=28.5
Q ss_pred eeeeeCCccceeeeccccCCCccceee---eecccCCCcccccc
Q 029974 10 VCYVHCNYCNTILAVSVPCSSLFNIVT---VRCGHCANLLNVNM 50 (184)
Q Consensus 10 lCYV~CnfC~TiLaVsVPcssL~~~VT---VRCGHCtnLlSVNm 50 (184)
-|-|-|+.|+.+. ||+|.| -||-||-..+||--
T Consensus 168 gcRV~CgHC~~tF--------Lfnt~tnaLArCPHCrKvSsvGs 203 (275)
T KOG4684|consen 168 GCRVKCGHCNETF--------LFNTLTNALARCPHCRKVSSVGS 203 (275)
T ss_pred ceEEEecCcccee--------ehhhHHHHHhcCCcccchhhhhh
Confidence 4899999998876 789998 59999999999844
No 31
>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=43.02 E-value=35 Score=29.45 Aligned_cols=36 Identities=22% Similarity=0.540 Sum_probs=30.5
Q ss_pred chhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 029974 113 PSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH 152 (184)
Q Consensus 113 psayN~fmK~ei~riK~~~P~i~hkEaF~~aA~nW~~~ph 152 (184)
-++|=.||.+ .+..|.++..+|.-..||+-|...+.
T Consensus 83 nnaYLNFLRe----FRrkh~~L~p~dlI~~AAraW~rLSe 118 (183)
T PF06382_consen 83 NNAYLNFLRE----FRRKHCGLSPQDLIQRAARAWCRLSE 118 (183)
T ss_pred chHHHHHHHH----HHHHccCCCHHHHHHHHHHHHHhCCH
Confidence 3688888764 77789999999999999999987654
No 32
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
Probab=41.27 E-value=48 Score=29.15 Aligned_cols=42 Identities=24% Similarity=0.419 Sum_probs=37.7
Q ss_pred CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029974 110 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP 151 (184)
Q Consensus 110 QRvpsayN~fmK~ei~riK~~~P~i~hkEaF~~aA~nW~~~p 151 (184)
.|--|||-.|..+-=.+|...+|+++--|.=..+.+.|+..-
T Consensus 72 KRp~sayf~y~~~~R~ei~~~~p~l~~~e~~k~~~e~WK~Lt 113 (211)
T COG5648 72 KRPLSAYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELT 113 (211)
T ss_pred CCchhHHHHHHHHHHHHHHHhCCCCChHHHHHHHHHHHHhcc
Confidence 456799999999999999999999999999999999999753
No 33
>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=40.94 E-value=18 Score=23.20 Aligned_cols=17 Identities=24% Similarity=0.563 Sum_probs=14.0
Q ss_pred cceeeeecccCCCcccc
Q 029974 32 FNIVTVRCGHCANLLNV 48 (184)
Q Consensus 32 ~~~VTVRCGHCtnLlSV 48 (184)
|.+|+|.|-+|.+-.+|
T Consensus 1 Ma~i~v~CP~C~s~~~v 17 (36)
T PF03811_consen 1 MAKIDVHCPRCQSTEGV 17 (36)
T ss_pred CCcEeeeCCCCCCCCcc
Confidence 46899999999987755
No 34
>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=40.34 E-value=17 Score=29.51 Aligned_cols=35 Identities=29% Similarity=0.316 Sum_probs=30.1
Q ss_pred CchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHh
Q 029974 112 VPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKN 146 (184)
Q Consensus 112 vpsayN~fmK~ei~riK~~~P~i~hkEaF~~aA~n 146 (184)
.++.-.+=++.||+++|+|.-.|+..+-|...||+
T Consensus 37 ~~~~~~~~l~~Ei~~l~~E~~~iS~qDeFAkwaKl 71 (161)
T PF04420_consen 37 KSSKEQRQLRKEILQLKRELNAISAQDEFAKWAKL 71 (161)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTTS-TTTSHHHHHHH
T ss_pred cccHHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHH
Confidence 45666777999999999999999999999999985
No 35
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=40.19 E-value=6.9 Score=28.19 Aligned_cols=13 Identities=46% Similarity=1.124 Sum_probs=11.1
Q ss_pred eeeeecccCCCcc
Q 029974 34 IVTVRCGHCANLL 46 (184)
Q Consensus 34 ~VTVRCGHCtnLl 46 (184)
+-|.||-||+-||
T Consensus 2 ~~tiRC~~CnKlL 14 (60)
T COG4416 2 MQTIRCAKCNKLL 14 (60)
T ss_pred ceeeehHHHhHHH
Confidence 4589999999987
No 36
>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=39.88 E-value=25 Score=21.99 Aligned_cols=25 Identities=36% Similarity=0.739 Sum_probs=14.0
Q ss_pred eeCCccceeeeccccCCCccceeeeecccCC
Q 029974 13 VHCNYCNTILAVSVPCSSLFNIVTVRCGHCA 43 (184)
Q Consensus 13 V~CnfC~TiLaVsVPcssL~~~VTVRCGHCt 43 (184)
|.|+-|.|+|+.- ...-.|||--|.
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 4566677666643 233456666664
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=37.31 E-value=27 Score=22.81 Aligned_cols=19 Identities=26% Similarity=0.639 Sum_probs=15.6
Q ss_pred hHHHHHHHHHHHhhCCCCC
Q 029974 117 NRFIKEEIQRIKASNPDIS 135 (184)
Q Consensus 117 N~fmK~ei~riK~~~P~i~ 135 (184)
..|+++-+..||..||++.
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 38
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=30.58 E-value=43 Score=31.00 Aligned_cols=50 Identities=34% Similarity=0.501 Sum_probs=32.7
Q ss_pred ccCCCCchhhhHHHHHHHHHHHhhCC---CCCHHHHHHHHHHhhccCCccccccccC------CccchhhhHH
Q 029974 107 QKRQRVPSAYNRFIKEEIQRIKASNP---DISHREAFSTAAKNWAHFPHIHFGLKLD------GNKQAKLDKA 170 (184)
Q Consensus 107 EKRQRvpsayN~fmK~ei~riK~~~P---~i~hkEaF~~aA~nW~~~phihfGl~~~------~~~~~~~d~~ 170 (184)
|||.|+ -|--|+|+|||+|.- -|+-+-+=.+|-. +||... +||++|+...
T Consensus 246 eKRPRT-----AFtaeQL~RLK~EF~enRYlTEqRRQ~La~E---------LgLNEsQIKIWFQNKRAKiKKs 304 (342)
T KOG0493|consen 246 EKRPRT-----AFTAEQLQRLKAEFQENRYLTEQRRQELAQE---------LGLNESQIKIWFQNKRAKIKKS 304 (342)
T ss_pred hcCccc-----cccHHHHHHHHHHHhhhhhHHHHHHHHHHHH---------hCcCHHHhhHHhhhhhhhhhhc
Confidence 888886 478899999999863 3555555555433 444422 3777777664
No 39
>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=30.21 E-value=19 Score=25.38 Aligned_cols=9 Identities=56% Similarity=1.191 Sum_probs=5.6
Q ss_pred ecccCCCcc
Q 029974 38 RCGHCANLL 46 (184)
Q Consensus 38 RCGHCtnLl 46 (184)
+|||++||-
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 399999985
No 40
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=29.98 E-value=38 Score=26.91 Aligned_cols=45 Identities=20% Similarity=0.355 Sum_probs=32.5
Q ss_pred eeeCCccceeeeccccCCCccceeeeecccCCCcccccccccccC
Q 029974 12 YVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQA 56 (184)
Q Consensus 12 YV~CnfC~TiLaVsVPcssL~~~VTVRCGHCtnLlSVNm~~ll~s 56 (184)
|--|-||+-...|+---+--.++-|+-||-|.--.-+-.++++++
T Consensus 22 ~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e~ev~~l~~~ 66 (104)
T COG4888 22 TFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFECEVPELSEP 66 (104)
T ss_pred eEecCccCCeeeeEEEEEecCceeEEEcccCcceEEEeccccccc
Confidence 567999999998887777777888999999974333434444333
No 41
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=29.53 E-value=33 Score=24.45 Aligned_cols=30 Identities=30% Similarity=0.811 Sum_probs=15.9
Q ss_pred ceeeeeCCccceeeeccccCCCccceeeeecccCCC
Q 029974 9 RVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCAN 44 (184)
Q Consensus 9 ~lCYV~CnfC~TiLaVsVPcssL~~~VTVRCGHCtn 44 (184)
..+.+.||=|+.-=- | -|-++-.+|+||.+
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 37788899999986
No 42
>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=29.35 E-value=29 Score=25.24 Aligned_cols=32 Identities=31% Similarity=0.504 Sum_probs=16.4
Q ss_pred eCCccceeeeccccCCC-ccceeeeecccCCCc
Q 029974 14 HCNYCNTILAVSVPCSS-LFNIVTVRCGHCANL 45 (184)
Q Consensus 14 ~CnfC~TiLaVsVPcss-L~~~VTVRCGHCtnL 45 (184)
-|+-|+|--+-.+-=.+ =--+|-|||+.|.|.
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 36667665442221111 134799999999985
No 43
>COG3712 FecR Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]
Probab=28.61 E-value=50 Score=30.43 Aligned_cols=31 Identities=23% Similarity=0.507 Sum_probs=28.0
Q ss_pred HHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029974 119 FIKEEIQRIKASNPDISHREAFSTAAKNWAHFP 151 (184)
Q Consensus 119 fmK~ei~riK~~~P~i~hkEaF~~aA~nW~~~p 151 (184)
-..+|.++|++..|+ |.+||..+..-|....
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 9999999999999866
No 44
>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=28.04 E-value=28 Score=21.86 Aligned_cols=17 Identities=24% Similarity=0.638 Sum_probs=10.0
Q ss_pred ceeeeeCCccceeeecc
Q 029974 9 RVCYVHCNYCNTILAVS 25 (184)
Q Consensus 9 ~lCYV~CnfC~TiLaVs 25 (184)
..-++.|.+|..++..+
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 45688999999888765
No 45
>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=27.24 E-value=25 Score=26.48 Aligned_cols=30 Identities=27% Similarity=0.586 Sum_probs=12.3
Q ss_pred eeCCccceeeeccccCCC---------ccceeeeecccC
Q 029974 13 VHCNYCNTILAVSVPCSS---------LFNIVTVRCGHC 42 (184)
Q Consensus 13 V~CnfC~TiLaVsVPcss---------L~~~VTVRCGHC 42 (184)
+.|.+|+..|-+.|=++. |+..+..-|..|
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 356666666555554442 344555555555
No 46
>KOG4520 consensus Predicted coiled-coil protein [General function prediction only]
Probab=27.11 E-value=74 Score=28.25 Aligned_cols=35 Identities=31% Similarity=0.276 Sum_probs=24.1
Q ss_pred hHHHHHHHHHHHhhC----------------CCCCHHHHHHHHHHhhccCC
Q 029974 117 NRFIKEEIQRIKASN----------------PDISHREAFSTAAKNWAHFP 151 (184)
Q Consensus 117 N~fmK~ei~riK~~~----------------P~i~hkEaF~~aA~nW~~~p 151 (184)
---|||||++||+.. |.---|+-|+.+++.=-..|
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 456899999999864 33336777888887643333
No 47
>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=26.95 E-value=60 Score=28.82 Aligned_cols=24 Identities=21% Similarity=0.516 Sum_probs=23.0
Q ss_pred hhhHHHHHHHHHHHhhCCCCCHHH
Q 029974 115 AYNRFIKEEIQRIKASNPDISHRE 138 (184)
Q Consensus 115 ayN~fmK~ei~riK~~~P~i~hkE 138 (184)
-|..||++...+-|+.+|.+|.|+
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 48
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=26.39 E-value=31 Score=22.23 Aligned_cols=13 Identities=38% Similarity=1.060 Sum_probs=10.7
Q ss_pred eeecccCCCcccc
Q 029974 36 TVRCGHCANLLNV 48 (184)
Q Consensus 36 TVRCGHCtnLlSV 48 (184)
.++||+|.+-+..
T Consensus 5 ~l~C~~CG~~m~~ 17 (58)
T PF13408_consen 5 LLRCGHCGSKMTR 17 (58)
T ss_pred cEEcccCCcEeEE
Confidence 4799999988765
No 49
>PF14722 KRAP_IP3R_bind: Ki-ras-induced actin-interacting protein-IP3R-interacting domain
Probab=25.17 E-value=76 Score=26.88 Aligned_cols=28 Identities=21% Similarity=0.456 Sum_probs=22.4
Q ss_pred hhHHHHHHHHHHHhhCCCCCHHHHHHHH
Q 029974 116 YNRFIKEEIQRIKASNPDISHREAFSTA 143 (184)
Q Consensus 116 yN~fmK~ei~riK~~~P~i~hkEaF~~a 143 (184)
...|++.++|||..|||.+.---+|.+.
T Consensus 71 ~~~FL~aQ~qrm~~E~p~~~l~~RFRQ~ 98 (160)
T PF14722_consen 71 IRVFLEAQKQRMDIENPNLALASRFRQL 98 (160)
T ss_pred HHHHHHHHHHHHHhhCccHHHHHHHHHH
Confidence 4689999999999999996655555543
No 50
>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=25.10 E-value=1.1e+02 Score=21.34 Aligned_cols=32 Identities=34% Similarity=0.399 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHhhCCCCCHHHHHHHHHHhhcc
Q 029974 118 RFIKEEIQRIKASNPDISHREAFSTAAKNWAH 149 (184)
Q Consensus 118 ~fmK~ei~riK~~~P~i~hkEaF~~aA~nW~~ 149 (184)
.++.+.|..++..+|.++-..+...||-|-++
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 51
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=24.65 E-value=20 Score=28.42 Aligned_cols=39 Identities=28% Similarity=0.588 Sum_probs=26.9
Q ss_pred eeeCCccceeeec--------cccCC----CccceeeeecccCCCcccccc
Q 029974 12 YVHCNYCNTILAV--------SVPCS----SLFNIVTVRCGHCANLLNVNM 50 (184)
Q Consensus 12 YV~CnfC~TiLaV--------sVPcs----sL~~~VTVRCGHCtnLlSVNm 50 (184)
=.+|.-|++--|- .-|.. +.++.-.|.||+|-+||+++-
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 3567777766552 22222 577888899999999998863
No 52
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=24.62 E-value=79 Score=26.75 Aligned_cols=36 Identities=31% Similarity=0.625 Sum_probs=28.0
Q ss_pred eeeCCcc---ceeeeccccCCCccceeeeecccCCCccccccccc
Q 029974 12 YVHCNYC---NTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSA 53 (184)
Q Consensus 12 YV~CnfC---~TiLaVsVPcssL~~~VTVRCGHCtnLlSVNm~~l 53 (184)
||.|.-| +|.|.+. + .+...+|.-|..-.+|.-...
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 4777664 2 566789999999998865544
No 53
>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=24.55 E-value=14 Score=28.03 Aligned_cols=16 Identities=31% Similarity=0.895 Sum_probs=12.7
Q ss_pred CceeeeeCCccceeee
Q 029974 8 ERVCYVHCNYCNTILA 23 (184)
Q Consensus 8 E~lCYV~CnfC~TiLa 23 (184)
=|||..=|++|||++.
T Consensus 37 IqLC~~cc~~~n~~v~ 52 (82)
T PF02723_consen 37 IQLCFQCCRLCNTTVY 52 (82)
T ss_pred HHHHHHHhhhhcceEe
Confidence 3788888999988765
No 54
>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=24.13 E-value=1e+02 Score=22.07 Aligned_cols=27 Identities=26% Similarity=0.484 Sum_probs=21.2
Q ss_pred CCCCchhhhHHHHHHHHHHHhhCCCCC
Q 029974 109 RQRVPSAYNRFIKEEIQRIKASNPDIS 135 (184)
Q Consensus 109 RQRvpsayN~fmK~ei~riK~~~P~i~ 135 (184)
......+|-.++++-++.||+.+|+.+
T Consensus 33 ~~~~~~~~~~~l~~~~~~iR~~dP~~p 59 (88)
T PF12876_consen 33 GDPKAEAYAEWLKEAFRWIRAVDPSQP 59 (88)
T ss_dssp T-TTSHHHHHHHHHHHHHHHTT-TTS-
T ss_pred cchhHHHHHHHHHHHHHHHHHhCCCCc
Confidence 344678999999999999999999854
No 55
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=23.01 E-value=49 Score=21.67 Aligned_cols=14 Identities=29% Similarity=0.705 Sum_probs=11.3
Q ss_pred eeeeCCccceeeec
Q 029974 11 CYVHCNYCNTILAV 24 (184)
Q Consensus 11 CYV~CnfC~TiLaV 24 (184)
-++.|++|..+|..
T Consensus 17 ~~a~C~~C~~~l~~ 30 (50)
T smart00614 17 QRAKCKYCGKKLSR 30 (50)
T ss_pred eEEEecCCCCEeee
Confidence 48899999988853
No 56
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=21.32 E-value=94 Score=25.03 Aligned_cols=33 Identities=21% Similarity=0.552 Sum_probs=24.1
Q ss_pred eeeeCCcc---ceeeeccccCCCccceeeeecccCCCccccc
Q 029974 11 CYVHCNYC---NTILAVSVPCSSLFNIVTVRCGHCANLLNVN 49 (184)
Q Consensus 11 CYV~CnfC---~TiLaVsVPcssL~~~VTVRCGHCtnLlSVN 49 (184)
=||.|.-| +|.|... ++ +-..+|--|..-.+|.
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 39999999 4777663 33 3367999999887773
No 57
>KOG1522 consensus RNA polymerase II, subunit POLR2C/RPB3 [Transcription]
Probab=21.14 E-value=51 Score=30.09 Aligned_cols=26 Identities=19% Similarity=0.571 Sum_probs=21.7
Q ss_pred CCCCceeeeeCCccceeeeccccCCC
Q 029974 5 LASERVCYVHCNYCNTILAVSVPCSS 30 (184)
Q Consensus 5 ~~~E~lCYV~CnfC~TiLaVsVPcss 30 (184)
...+--|--+|.+|...+-.+|=|..
T Consensus 82 ytrdC~C~~~C~eCSVef~L~~kc~~ 107 (285)
T KOG1522|consen 82 YTRDCECDEFCPECSVEFTLDVKCTD 107 (285)
T ss_pred hcccCchhccCCcceEEEEEeeeecc
Confidence 33566799999999999999998873
No 58
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 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 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 []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=20.60 E-value=48 Score=20.07 Aligned_cols=10 Identities=40% Similarity=1.036 Sum_probs=8.3
Q ss_pred eeeCCcccee
Q 029974 12 YVHCNYCNTI 21 (184)
Q Consensus 12 YV~CnfC~Ti 21 (184)
.|+|.-|+||
T Consensus 16 sVrCa~C~~V 25 (25)
T PF06943_consen 16 SVRCACCHTV 25 (25)
T ss_pred CeECCccCcC
Confidence 5899999886
No 59
>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=20.27 E-value=57 Score=22.98 Aligned_cols=11 Identities=55% Similarity=1.093 Sum_probs=8.8
Q ss_pred eeCCccceeee
Q 029974 13 VHCNYCNTILA 23 (184)
Q Consensus 13 V~CnfC~TiLa 23 (184)
|.|..|.|+|+
T Consensus 27 V~C~~Cg~~L~ 37 (55)
T PF01667_consen 27 VKCVVCGTVLA 37 (55)
T ss_dssp EE-SSSTSEEE
T ss_pred EEcccCCCEec
Confidence 78999999987
No 60
>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=20.21 E-value=51 Score=27.92 Aligned_cols=19 Identities=26% Similarity=0.588 Sum_probs=15.8
Q ss_pred eeeCCccceeeeccccCCC
Q 029974 12 YVHCNYCNTILAVSVPCSS 30 (184)
Q Consensus 12 YV~CnfC~TiLaVsVPcss 30 (184)
=|+|+-|+.+|-|.+.-..
T Consensus 36 TVRCGHCtNLLSVNm~~~~ 54 (170)
T PF04690_consen 36 TVRCGHCTNLLSVNMRALL 54 (170)
T ss_pred ceeccCccceeeeeccccc
Confidence 3999999999999886544
Done!