Query 029862
Match_columns 186
No_of_seqs 119 out of 186
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 04:50:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029862.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029862hhsearch_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 2.1E-81 4.6E-86 516.4 12.7 159 1-159 1-170 (170)
2 PF09011 HMG_box_2: HMG-box do 98.2 2E-06 4.4E-11 60.4 4.8 46 108-153 1-47 (73)
3 cd01390 HMGB-UBF_HMG-box HMGB- 97.8 5.7E-05 1.2E-09 50.5 5.1 42 112-153 2-43 (66)
4 cd01388 SOX-TCF_HMG-box SOX-TC 97.7 7.6E-05 1.6E-09 52.3 5.0 42 112-153 3-44 (72)
5 cd00084 HMG-box High Mobility 97.7 8.9E-05 1.9E-09 49.0 5.1 43 112-154 2-44 (66)
6 PF00505 HMG_box: HMG (high mo 97.7 7.1E-05 1.5E-09 50.6 4.5 41 112-152 2-42 (69)
7 smart00398 HMG high mobility g 97.6 0.00016 3.5E-09 48.3 5.1 43 112-154 3-45 (70)
8 cd01389 MATA_HMG-box MATA_HMG- 97.5 0.00018 4E-09 50.8 5.1 43 112-154 3-45 (77)
9 PTZ00199 high mobility group p 97.5 0.0003 6.6E-09 52.4 5.6 49 106-154 18-68 (94)
10 PF06244 DUF1014: Protein of u 96.7 0.0027 5.8E-08 50.8 4.8 54 103-158 67-120 (122)
11 KOG0381 HMG box-containing pro 96.3 0.0087 1.9E-07 43.2 5.1 45 110-154 22-66 (96)
12 KOG3223 Uncharacterized conser 95.2 0.0097 2.1E-07 51.8 1.7 53 105-159 161-213 (221)
13 PF11331 DUF3133: Protein of u 94.3 0.022 4.8E-07 38.9 1.4 38 12-51 6-46 (46)
14 KOG4684 Uncharacterized conser 84.4 1 2.2E-05 40.4 3.2 17 33-49 167-183 (275)
15 TIGR02098 MJ0042_CXXC MJ0042 f 82.5 1.5 3.1E-05 27.3 2.5 35 12-48 2-37 (38)
16 PF13719 zinc_ribbon_5: zinc-r 80.8 1.3 2.8E-05 28.2 1.9 34 13-48 3-37 (37)
17 PRK14892 putative transcriptio 79.4 2.4 5.2E-05 32.9 3.3 43 11-56 20-62 (99)
18 PF05129 Elf1: Transcription e 77.2 1.4 3E-05 32.7 1.4 42 12-53 22-63 (81)
19 TIGR01562 FdhE formate dehydro 74.4 1.8 4E-05 39.2 1.7 27 8-44 206-232 (305)
20 PRK03954 ribonuclease P protei 69.9 2.6 5.6E-05 33.8 1.4 32 15-46 67-103 (121)
21 PF04032 Rpr2: RNAse P Rpr2/Rp 69.7 2.2 4.7E-05 30.2 0.8 31 14-44 48-85 (85)
22 PF13717 zinc_ribbon_4: zinc-r 68.3 6.3 0.00014 25.0 2.7 30 13-46 3-35 (36)
23 PF10122 Mu-like_Com: Mu-like 67.8 2.9 6.3E-05 29.4 1.1 32 13-48 5-36 (51)
24 PRK03564 formate dehydrogenase 66.8 3.5 7.5E-05 37.6 1.7 27 8-44 208-234 (309)
25 COG3058 FdhE Uncharacterized p 63.6 1 2.2E-05 41.3 -2.3 35 7-51 206-240 (308)
26 PF09788 Tmemb_55A: Transmembr 61.6 6.7 0.00014 35.3 2.5 39 8-50 153-191 (256)
27 KOG4684 Uncharacterized conser 61.3 3.6 7.9E-05 36.9 0.8 33 10-50 168-203 (275)
28 PF04216 FdhE: Protein involve 55.6 4.4 9.5E-05 35.3 0.3 32 10-51 195-226 (290)
29 PF08073 CHDNT: CHDNT (NUC034) 55.3 22 0.00048 25.2 3.8 33 117-152 18-50 (55)
30 PF11331 DUF3133: Protein of u 54.2 9.1 0.0002 26.2 1.6 19 9-27 28-46 (46)
31 PF06382 DUF1074: Protein of u 43.9 31 0.00067 29.8 3.6 35 116-154 84-118 (183)
32 COG5648 NHP6B Chromatin-associ 42.8 45 0.00097 29.4 4.5 42 112-153 72-113 (211)
33 TIGR01053 LSD1 zinc finger dom 40.8 23 0.00051 22.2 1.8 26 13-44 2-27 (31)
34 PF03811 Zn_Tnp_IS1: InsA N-te 38.6 21 0.00046 23.0 1.4 17 32-48 1-17 (36)
35 PF12876 Cellulase-like: Sugar 36.3 53 0.0011 23.6 3.4 31 107-137 29-59 (88)
36 PF05047 L51_S25_CI-B8: Mitoch 35.7 31 0.00067 22.5 1.9 19 119-137 2-20 (52)
37 COG4888 Uncharacterized Zn rib 35.3 32 0.0007 27.4 2.3 45 12-56 22-66 (104)
38 PF14599 zinc_ribbon_6: Zinc-r 35.0 30 0.00065 24.7 1.9 30 9-44 27-56 (61)
39 PF04420 CHD5: CHD5-like prote 33.7 30 0.00066 28.1 2.0 36 113-148 36-71 (161)
40 COG4416 Com Mu-like prophage p 33.5 11 0.00024 27.2 -0.5 13 34-46 2-14 (60)
41 PF02892 zf-BED: BED zinc fing 31.1 26 0.00056 22.0 1.0 17 9-25 13-29 (45)
42 PF00527 E7: E7 protein, Early 30.6 26 0.00056 26.5 1.0 30 13-42 53-91 (92)
43 PF05180 zf-DNL: DNL zinc fing 29.9 28 0.00061 25.4 1.1 32 14-45 6-38 (66)
44 PF01020 Ribosomal_L40e: Ribos 29.9 19 0.00042 25.4 0.2 9 38-46 38-46 (52)
45 COG3712 FecR Fe2+-dicitrate se 29.5 47 0.001 30.6 2.7 31 121-153 32-62 (322)
46 TIGR02147 Fsuc_second hypothet 28.0 56 0.0012 29.1 2.8 25 116-140 8-32 (271)
47 PRK12336 translation initiatio 26.7 80 0.0017 26.7 3.4 36 12-53 98-136 (201)
48 smart00614 ZnF_BED BED zinc fi 26.5 43 0.00094 22.0 1.5 14 11-24 17-30 (50)
49 KOG4520 Predicted coiled-coil 26.3 78 0.0017 28.2 3.3 36 119-154 62-113 (238)
50 PF13408 Zn_ribbon_recom: Reco 25.7 32 0.0007 22.2 0.7 13 36-48 5-17 (58)
51 KOG4715 SWI/SNF-related matrix 25.2 93 0.002 29.6 3.8 48 104-154 61-108 (410)
52 COG5509 Uncharacterized small 25.1 72 0.0016 23.5 2.5 13 121-133 36-48 (65)
53 COG4357 Zinc finger domain con 24.9 20 0.00042 28.6 -0.5 39 12-50 26-76 (105)
54 PF05164 ZapA: Cell division p 24.8 1.1E+02 0.0025 21.3 3.4 32 120-151 28-59 (89)
55 PF02723 NS3_envE: Non-structu 23.9 13 0.00027 28.3 -1.7 16 8-23 37-52 (82)
56 TIGR00311 aIF-2beta translatio 23.4 98 0.0021 25.0 3.2 33 11-49 96-131 (133)
57 PF14722 KRAP_IP3R_bind: Ki-ra 23.4 86 0.0019 26.6 3.0 28 118-145 71-98 (160)
58 PF04769 MAT_Alpha1: Mating-ty 22.8 2.3E+02 0.0049 24.4 5.5 46 105-154 38-83 (201)
59 PF01667 Ribosomal_S27e: Ribos 22.6 56 0.0012 23.1 1.5 12 13-24 27-38 (55)
60 KOG0493 Transcription factor E 22.2 45 0.00097 31.0 1.1 50 109-172 246-304 (342)
61 PF09788 Tmemb_55A: Transmembr 22.1 76 0.0017 28.7 2.6 17 33-49 154-170 (256)
62 KOG4253 Tryptophan-rich basic 21.1 1.2E+02 0.0026 26.1 3.4 34 117-150 44-77 (175)
63 KOG1522 RNA polymerase II, sub 20.7 58 0.0013 29.8 1.5 26 5-30 82-107 (285)
64 PF06943 zf-LSD1: LSD1 zinc fi 20.6 50 0.0011 20.0 0.8 10 12-21 16-25 (25)
65 PF04690 YABBY: YABBY protein; 20.5 55 0.0012 27.7 1.3 19 12-30 36-54 (170)
66 KOG3404 G10 protein/predicted 20.5 80 0.0017 26.3 2.2 37 7-44 97-139 (145)
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=2.1e-81 Score=516.44 Aligned_cols=159 Identities=64% Similarity=1.002 Sum_probs=123.2
Q ss_pred CCcccCCCceeEEeCCCcceeeEecccCCCccceeeeecccCCCcccccccccccCCCCCCchhhhhc-------CCCcc
Q 029862 1 MSLDLASERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQAVPLQDPQLQKQH-------INLED 73 (186)
Q Consensus 1 ms~~~~~E~lCYV~CnfCnTiLaVsVPcssL~~~VTVRCGHCtnLlSVNm~~llqs~~~q~~~~~~~~-------~~~~~ 73 (186)
|+.+.++|||||||||||||||||||||+|||+|||||||||+|||||||++++++++.|++..+... ....+
T Consensus 1 ~~~~~~sE~lCYVhCnFC~TiLaVsVP~ssL~~~VTVRCGHCtNLLSVNm~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~ 80 (170)
T PF04690_consen 1 MDLFSPSEQLCYVHCNFCNTILAVSVPCSSLLKTVTVRCGHCTNLLSVNMRALLQPLPSQDHLQHSLLPPQSQELQFQPE 80 (170)
T ss_pred CCccCCCCcEEEEEcCCcCeEEEEecchhhhhhhhceeccCccceeeeeccccccCCCcccchhcccccccccccccccc
Confidence 66777899999999999999999999999999999999999999999999999999887665211110 00011
Q ss_pred cccccCC---CCCcCCCCCCccccCCCCCCCCC-CCCCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhh
Q 029862 74 SITKDCG---SSSKCNKFSSAFETAEHETPRMP-PIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNW 149 (186)
Q Consensus 74 ~~~~~~~---sss~~~~~~~~~~~~~~e~p~~~-~~KPPEKRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW 149 (186)
....... +++.+.....+....+++.|+++ ++||||||||+|||||+||||||||||++||||+|||||++|||||
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 11111110011233445566654 6899999999999999999999999999999999999999999999
Q ss_pred ccCCcccccc
Q 029862 150 AHFPHIHFGL 159 (186)
Q Consensus 150 ~~~P~ihfGl 159 (186)
||+|||||||
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=98.23 E-value=2e-06 Score=60.37 Aligned_cols=46 Identities=35% Similarity=0.624 Sum_probs=38.5
Q ss_pred CCCCCCCchhhhHHHHHHHHHHHhh-CCCCCHHHHHHHHHHhhccCC
Q 029862 108 PEKRQRVPSAYNRFIKEEIQRIKAS-NPDISHREAFSTAAKNWAHFP 153 (186)
Q Consensus 108 PEKRQR~psayN~fmK~ei~riK~~-~P~i~hkEaF~~aAknW~~~P 153 (186)
|.|-.|.+|||+.||++.+.+++.. .+.++++|++..++..|+..+
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 5677899999999999999999999 889999999999999999753
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=50.49 Aligned_cols=42 Identities=31% Similarity=0.487 Sum_probs=39.1
Q ss_pred CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862 112 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP 153 (186)
Q Consensus 112 QR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P 153 (186)
.|-+|||..|+++....+++.+|+++..|....++..|+..+
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=97.70 E-value=7.6e-05 Score=52.26 Aligned_cols=42 Identities=17% Similarity=0.284 Sum_probs=39.1
Q ss_pred CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862 112 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP 153 (186)
Q Consensus 112 QR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P 153 (186)
.|-|+||..|+++.-.+|++++|+++..|.-+.++..|+..+
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 467899999999999999999999999999999999999754
No 5
>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=97.70 E-value=8.9e-05 Score=48.98 Aligned_cols=43 Identities=30% Similarity=0.422 Sum_probs=39.6
Q ss_pred CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 029862 112 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH 154 (186)
Q Consensus 112 QR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P~ 154 (186)
.|-+|+|..|++++...+++.+|+++..|....+++.|+..+.
T Consensus 2 krp~~af~~f~~~~~~~~~~~~~~~~~~~i~~~~~~~W~~l~~ 44 (66)
T cd00084 2 KRPLSAYFLFSQEHRAEVKAENPGLSVGEISKILGEMWKSLSE 44 (66)
T ss_pred CCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCH
Confidence 4678999999999999999999999999999999999997654
No 6
>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=97.69 E-value=7.1e-05 Score=50.58 Aligned_cols=41 Identities=34% Similarity=0.636 Sum_probs=36.9
Q ss_pred CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccC
Q 029862 112 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHF 152 (186)
Q Consensus 112 QR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~ 152 (186)
.|-++||..|+++....||+++|+++..|.-+.+++.|+..
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 47899999999999999999999999999999999999974
No 7
>smart00398 HMG high mobility group.
Probab=97.59 E-value=0.00016 Score=48.27 Aligned_cols=43 Identities=33% Similarity=0.511 Sum_probs=39.5
Q ss_pred CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 029862 112 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH 154 (186)
Q Consensus 112 QR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P~ 154 (186)
.|-+|+|..|+++....+++.+|+++..|....++..|+..+.
T Consensus 3 krp~~~y~~f~~~~r~~~~~~~~~~~~~~i~~~~~~~W~~l~~ 45 (70)
T smart00398 3 KRPMSAFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSE 45 (70)
T ss_pred CCCCcHHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHcCCH
Confidence 4678999999999999999999999999999999999997543
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=97.54 E-value=0.00018 Score=50.77 Aligned_cols=43 Identities=16% Similarity=0.348 Sum_probs=40.1
Q ss_pred CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 029862 112 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH 154 (186)
Q Consensus 112 QR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P~ 154 (186)
.|-++||-.|+++....|+++||++++.|.-+.++..|+..+.
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 5789999999999999999999999999999999999997654
No 9
>PTZ00199 high mobility group protein; Provisional
Probab=97.46 E-value=0.0003 Score=52.36 Aligned_cols=49 Identities=27% Similarity=0.445 Sum_probs=42.5
Q ss_pred CCCCCCCCCchhhhHHHHHHHHHHHhhCCCCC--HHHHHHHHHHhhccCCc
Q 029862 106 RPPEKRQRVPSAYNRFIKEEIQRIKASNPDIS--HREAFSTAAKNWAHFPH 154 (186)
Q Consensus 106 KPPEKRQR~psayN~fmK~ei~riK~~~P~i~--hkEaF~~aAknW~~~P~ 154 (186)
+.|.+-.|-+|||..|+++.-..|+++||+++ -.|.-+.++..|+..+.
T Consensus 18 kdp~~PKrP~sAY~~F~~~~R~~i~~~~P~~~~~~~evsk~ige~Wk~ls~ 68 (94)
T PTZ00199 18 KDPNAPKRALSAYMFFAKEKRAEIIAENPELAKDVAAVGKMVGEAWNKLSE 68 (94)
T ss_pred CCCCCCCCCCcHHHHHHHHHHHHHHHHCcCCcccHHHHHHHHHHHHHcCCH
Confidence 55667778999999999999999999999986 57888889999998653
No 10
>PF06244 DUF1014: Protein of unknown function (DUF1014); InterPro: IPR010422 This family consists of several hypothetical eukaryotic proteins of unknown function.
Probab=96.72 E-value=0.0027 Score=50.78 Aligned_cols=54 Identities=28% Similarity=0.510 Sum_probs=48.3
Q ss_pred CCCCCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCccccc
Q 029862 103 PPIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFG 158 (186)
Q Consensus 103 ~~~KPPEKRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P~ihfG 158 (186)
.+-|.||||-+ -||..|--.+|.+||++||++.+-+-=-..=|.|..+|...|-
T Consensus 67 ~~drHPErR~K--AAy~afeE~~Lp~lK~E~PgLrlsQ~kq~l~K~w~KSPeNP~N 120 (122)
T PF06244_consen 67 PIDRHPERRMK--AAYKAFEERRLPELKEENPGLRLSQYKQMLWKEWQKSPENPFN 120 (122)
T ss_pred CCCCCcchhHH--HHHHHHHHHHhHHHHhhCCCchHHHHHHHHHHHHhcCCCCCcc
Confidence 45589999874 6999999999999999999999999888999999999998763
No 11
>KOG0381 consensus HMG box-containing protein [General function prediction only]
Probab=96.34 E-value=0.0087 Score=43.19 Aligned_cols=45 Identities=29% Similarity=0.429 Sum_probs=40.4
Q ss_pred CCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 029862 110 KRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH 154 (186)
Q Consensus 110 KRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P~ 154 (186)
.-+|-+|||..|+.+.-.+||++||+++..|.=+.+..+|.....
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 457788899999999999999999999999999999999987544
No 12
>KOG3223 consensus Uncharacterized conserved protein [Function unknown]
Probab=95.22 E-value=0.0097 Score=51.76 Aligned_cols=53 Identities=30% Similarity=0.508 Sum_probs=47.6
Q ss_pred CCCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCcccccc
Q 029862 105 IRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPHIHFGL 159 (186)
Q Consensus 105 ~KPPEKRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P~ihfGl 159 (186)
-|-||||-|. ||--|=..+|-|||.+||+++|-+-=-..-|.|...|...|.-
T Consensus 161 drHPEkRmrA--A~~afEe~~LPrLK~e~P~lrlsQ~Kqll~Kew~KsPDNP~Nq 213 (221)
T KOG3223|consen 161 DRHPEKRMRA--AFKAFEEARLPRLKKENPGLRLSQYKQLLKKEWQKSPDNPFNQ 213 (221)
T ss_pred ccChHHHHHH--HHHHHHHhhchhhhhcCCCccHHHHHHHHHHHHhhCCCChhhH
Confidence 3899999875 8999999999999999999999988788889999999988753
No 13
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=94.33 E-value=0.022 Score=38.88 Aligned_cols=38 Identities=26% Similarity=0.725 Sum_probs=29.6
Q ss_pred EEeCCCcceeeEecccCCCccc---eeeeecccCCCccccccc
Q 029862 12 YVHCNYCNTILAVSVPCSSLFN---IVTVRCGHCANLLNVNMV 51 (186)
Q Consensus 12 YV~CnfCnTiLaVsVPcssL~~---~VTVRCGHCtnLlSVNm~ 51 (186)
||-|+-|..+|- +|-+.++. .-.+|||.|+.++++.++
T Consensus 6 Fv~C~~C~~lLq--lP~~~~~~~k~~~klrCGaCs~vl~~s~~ 46 (46)
T PF11331_consen 6 FVVCSSCFELLQ--LPAKFSLSKKNQQKLRCGACSEVLSFSLP 46 (46)
T ss_pred EeECccHHHHHc--CCCccCCCccceeEEeCCCCceeEEEecC
Confidence 788999977765 47775443 568999999999988653
No 14
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=84.45 E-value=1 Score=40.38 Aligned_cols=17 Identities=35% Similarity=0.778 Sum_probs=12.6
Q ss_pred ceeeeecccCCCccccc
Q 029862 33 NIVTVRCGHCANLLNVN 49 (186)
Q Consensus 33 ~~VTVRCGHCtnLlSVN 49 (186)
..+-|+||||++..--|
T Consensus 167 ~gcRV~CgHC~~tFLfn 183 (275)
T KOG4684|consen 167 TGCRVKCGHCNETFLFN 183 (275)
T ss_pred cceEEEecCccceeehh
Confidence 34889999999875433
No 15
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=82.51 E-value=1.5 Score=27.30 Aligned_cols=35 Identities=34% Similarity=0.598 Sum_probs=24.6
Q ss_pred EEeCCCcceeeEecccCCCcc-ceeeeecccCCCcccc
Q 029862 12 YVHCNYCNTILAVSVPCSSLF-NIVTVRCGHCANLLNV 48 (186)
Q Consensus 12 YV~CnfCnTiLaVsVPcssL~-~~VTVRCGHCtnLlSV 48 (186)
.+.|..|.+..-|.. +.+. +...|+|++|.+.+.+
T Consensus 2 ~~~CP~C~~~~~v~~--~~~~~~~~~v~C~~C~~~~~~ 37 (38)
T TIGR02098 2 RIQCPNCKTSFRVVD--SQLGANGGKVRCGKCGHVWYA 37 (38)
T ss_pred EEECCCCCCEEEeCH--HHcCCCCCEEECCCCCCEEEe
Confidence 378999999877653 2221 3347999999987754
No 16
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=80.75 E-value=1.3 Score=28.15 Aligned_cols=34 Identities=32% Similarity=0.678 Sum_probs=25.5
Q ss_pred EeCCCcceeeEecccCCCc-cceeeeecccCCCcccc
Q 029862 13 VHCNYCNTILAVSVPCSSL-FNIVTVRCGHCANLLNV 48 (186)
Q Consensus 13 V~CnfCnTiLaVsVPcssL-~~~VTVRCGHCtnLlSV 48 (186)
++|--|.|.+.| |-+.| -....|||++|.+.+.|
T Consensus 3 i~CP~C~~~f~v--~~~~l~~~~~~vrC~~C~~~f~v 37 (37)
T PF13719_consen 3 ITCPNCQTRFRV--PDDKLPAGGRKVRCPKCGHVFRV 37 (37)
T ss_pred EECCCCCceEEc--CHHHcccCCcEEECCCCCcEeeC
Confidence 789999998865 44443 34679999999987654
No 17
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=79.40 E-value=2.4 Score=32.87 Aligned_cols=43 Identities=23% Similarity=0.543 Sum_probs=34.3
Q ss_pred eEEeCCCcceeeEecccCCCccceeeeecccCCCcccccccccccC
Q 029862 11 CYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQA 56 (186)
Q Consensus 11 CYV~CnfCnTiLaVsVPcssL~~~VTVRCGHCtnLlSVNm~~llqs 56 (186)
=++.|.||+. ..|+||... .+..+.|..|.---.-.+.+|.++
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 688999988 799999999987766555555444
No 18
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=77.20 E-value=1.4 Score=32.67 Aligned_cols=42 Identities=21% Similarity=0.419 Sum_probs=26.2
Q ss_pred EEeCCCcceeeEecccCCCccceeeeecccCCCccccccccc
Q 029862 12 YVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSA 53 (186)
Q Consensus 12 YV~CnfCnTiLaVsVPcssL~~~VTVRCGHCtnLlSVNm~~l 53 (186)
+-.|-||+.--+|+|=.+.-..+-++.||-|.--...++..|
T Consensus 22 ~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~i~~L 63 (81)
T PF05129_consen 22 VFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTKINPL 63 (81)
T ss_dssp ----TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE--SS
T ss_pred eEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEccCcc
Confidence 457999999999999999999999999999954444444433
No 19
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=74.38 E-value=1.8 Score=39.20 Aligned_cols=27 Identities=33% Similarity=0.924 Sum_probs=23.1
Q ss_pred CceeEEeCCCcceeeEecccCCCccceeeeecccCCC
Q 029862 8 ERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCAN 44 (186)
Q Consensus 8 E~lCYV~CnfCnTiLaVsVPcssL~~~VTVRCGHCtn 44 (186)
+..=|-||++|.| -...|-++|.+|.|
T Consensus 206 ~G~RyL~CslC~t----------eW~~~R~~C~~Cg~ 232 (305)
T TIGR01562 206 TGLRYLSCSLCAT----------EWHYVRVKCSHCEE 232 (305)
T ss_pred CCceEEEcCCCCC----------cccccCccCCCCCC
Confidence 4566999999977 57889999999998
No 20
>PRK03954 ribonuclease P protein component 4; Validated
Probab=69.86 E-value=2.6 Score=33.77 Aligned_cols=32 Identities=25% Similarity=0.647 Sum_probs=24.5
Q ss_pred CCCcceeeEecccCCC-ccc----eeeeecccCCCcc
Q 029862 15 CNYCNTILAVSVPCSS-LFN----IVTVRCGHCANLL 46 (186)
Q Consensus 15 CnfCnTiLaVsVPcss-L~~----~VTVRCGHCtnLl 46 (186)
|-.|+|.|.-||-|.- +-+ -|.++|..|...-
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 8899999998876652 222 4899999998764
No 21
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=69.70 E-value=2.2 Score=30.18 Aligned_cols=31 Identities=29% Similarity=0.726 Sum_probs=19.5
Q ss_pred eCCCcceeeEecccCCC-c------cceeeeecccCCC
Q 029862 14 HCNYCNTILAVSVPCSS-L------FNIVTVRCGHCAN 44 (186)
Q Consensus 14 ~CnfCnTiLaVsVPcss-L------~~~VTVRCGHCtn 44 (186)
-|.-|.++|.-|+-|+- + -+.|.++|..|.+
T Consensus 48 ~Ck~C~~~liPG~~~~vri~~~~~~~~~l~~~C~~C~~ 85 (85)
T PF04032_consen 48 ICKKCGSLLIPGVNCSVRIRKKKKKKNFLVYTCLNCGH 85 (85)
T ss_dssp B-TTT--B--CTTTEEEEEE---SSS-EEEEEETTTTE
T ss_pred cccCCCCEEeCCCccEEEEEecCCCCCEEEEEccccCC
Confidence 58999999998888763 2 4688999999963
No 22
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=68.29 E-value=6.3 Score=25.02 Aligned_cols=30 Identities=23% Similarity=0.724 Sum_probs=23.3
Q ss_pred EeCCCcceeeEec---ccCCCccceeeeecccCCCcc
Q 029862 13 VHCNYCNTILAVS---VPCSSLFNIVTVRCGHCANLL 46 (186)
Q Consensus 13 V~CnfCnTiLaVs---VPcssL~~~VTVRCGHCtnLl 46 (186)
+.|.-|.+...|. || =+.+.|||+.|.+.+
T Consensus 3 i~Cp~C~~~y~i~d~~ip----~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIP----PKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHHCC----CCCcEEECCCCCCEe
Confidence 6899999988765 34 345799999998865
No 23
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=67.85 E-value=2.9 Score=29.36 Aligned_cols=32 Identities=25% Similarity=0.624 Sum_probs=23.4
Q ss_pred EeCCCcceeeEecccCCCccceeeeecccCCCcccc
Q 029862 13 VHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNV 48 (186)
Q Consensus 13 V~CnfCnTiLaVsVPcssL~~~VTVRCGHCtnLlSV 48 (186)
+||..||..||-+- -+..+.++|..|..+-.|
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 24
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=66.84 E-value=3.5 Score=37.59 Aligned_cols=27 Identities=33% Similarity=1.046 Sum_probs=23.0
Q ss_pred CceeEEeCCCcceeeEecccCCCccceeeeecccCCC
Q 029862 8 ERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCAN 44 (186)
Q Consensus 8 E~lCYV~CnfCnTiLaVsVPcssL~~~VTVRCGHCtn 44 (186)
+-.=|-||++|.| ....|-++|.+|.|
T Consensus 208 ~G~RyL~CslC~t----------eW~~~R~~C~~Cg~ 234 (309)
T PRK03564 208 QGLRYLHCNLCES----------EWHVVRVKCSNCEQ 234 (309)
T ss_pred CCceEEEcCCCCC----------cccccCccCCCCCC
Confidence 5567999999977 57889999999997
No 25
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=63.63 E-value=1 Score=41.30 Aligned_cols=35 Identities=26% Similarity=0.725 Sum_probs=27.7
Q ss_pred CCceeEEeCCCcceeeEecccCCCccceeeeecccCCCccccccc
Q 029862 7 SERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMV 51 (186)
Q Consensus 7 ~E~lCYV~CnfCnTiLaVsVPcssL~~~VTVRCGHCtnLlSVNm~ 51 (186)
.+-+=|.|||.|.| ..+.|-|+|-+|.+---+++-
T Consensus 206 ~~GlRYL~CslC~t----------eW~~VR~KC~nC~~t~~l~y~ 240 (308)
T COG3058 206 EQGLRYLHCSLCET----------EWHYVRVKCSNCEQSKKLHYW 240 (308)
T ss_pred cccchhhhhhhHHH----------HHHHHHHHhccccccCCccce
Confidence 46788999999977 578899999999986544443
No 26
>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=61.58 E-value=6.7 Score=35.31 Aligned_cols=39 Identities=26% Similarity=0.550 Sum_probs=26.9
Q ss_pred CceeEEeCCCcceeeEecccCCCccceeeeecccCCCcccccc
Q 029862 8 ERVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNM 50 (186)
Q Consensus 8 E~lCYV~CnfCnTiLaVsVPcssL~~~VTVRCGHCtnLlSVNm 50 (186)
..-|=|.|+.|+...+...+-++- -.||-||-.++||.-
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 356778888888777666555321 268888888888853
No 27
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=61.31 E-value=3.6 Score=36.91 Aligned_cols=33 Identities=39% Similarity=0.862 Sum_probs=26.7
Q ss_pred eeEEeCCCcceeeEecccCCCccceee---eecccCCCcccccc
Q 029862 10 VCYVHCNYCNTILAVSVPCSSLFNIVT---VRCGHCANLLNVNM 50 (186)
Q Consensus 10 lCYV~CnfCnTiLaVsVPcssL~~~VT---VRCGHCtnLlSVNm 50 (186)
-|-|-|+.|+.+.+ |+|.| -||-||-..+||--
T Consensus 168 gcRV~CgHC~~tFL--------fnt~tnaLArCPHCrKvSsvGs 203 (275)
T KOG4684|consen 168 GCRVKCGHCNETFL--------FNTLTNALARCPHCRKVSSVGS 203 (275)
T ss_pred ceEEEecCccceee--------hhhHHHHHhcCCcccchhhhhh
Confidence 49999999998874 55554 69999999999843
No 28
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=55.55 E-value=4.4 Score=35.35 Aligned_cols=32 Identities=28% Similarity=0.718 Sum_probs=17.4
Q ss_pred eeEEeCCCcceeeEecccCCCccceeeeecccCCCccccccc
Q 029862 10 VCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMV 51 (186)
Q Consensus 10 lCYV~CnfCnTiLaVsVPcssL~~~VTVRCGHCtnLlSVNm~ 51 (186)
.=|-+|.+|.|- ...+-++|.+|.|--...+.
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 468999999884 56788899999997655444
No 29
>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=55.33 E-value=22 Score=25.23 Aligned_cols=33 Identities=15% Similarity=0.448 Sum_probs=26.2
Q ss_pred hhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccC
Q 029862 117 AYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHF 152 (186)
Q Consensus 117 ayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~ 152 (186)
+|..+|+=- |-+.||++.+-.-+...+..|+.|
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 445555544 557899999999999999999986
No 30
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=54.21 E-value=9.1 Score=26.17 Aligned_cols=19 Identities=26% Similarity=0.677 Sum_probs=16.4
Q ss_pred ceeEEeCCCcceeeEeccc
Q 029862 9 RVCYVHCNYCNTILAVSVP 27 (186)
Q Consensus 9 ~lCYV~CnfCnTiLaVsVP 27 (186)
..-=+||+-|..||-+++|
T Consensus 28 ~~~klrCGaCs~vl~~s~~ 46 (46)
T PF11331_consen 28 NQQKLRCGACSEVLSFSLP 46 (46)
T ss_pred ceeEEeCCCCceeEEEecC
Confidence 3556899999999999987
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=43.95 E-value=31 Score=29.82 Aligned_cols=35 Identities=23% Similarity=0.563 Sum_probs=30.2
Q ss_pred hhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 029862 116 SAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH 154 (186)
Q Consensus 116 sayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P~ 154 (186)
++|=.||.+ .+..|.++..+|.-..||+-|...+.
T Consensus 84 naYLNFLRe----FRrkh~~L~p~dlI~~AAraW~rLSe 118 (183)
T PF06382_consen 84 NAYLNFLRE----FRRKHCGLSPQDLIQRAARAWCRLSE 118 (183)
T ss_pred hHHHHHHHH----HHHHccCCCHHHHHHHHHHHHHhCCH
Confidence 688888764 77789999999999999999998654
No 32
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
Probab=42.82 E-value=45 Score=29.40 Aligned_cols=42 Identities=24% Similarity=0.419 Sum_probs=37.9
Q ss_pred CCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862 112 QRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFP 153 (186)
Q Consensus 112 QR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P 153 (186)
.|--|||-.|..+-=.+|...+|+++--|.=..+.+.|+..-
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 467899999999999999999999999999999999999753
No 33
>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=40.81 E-value=23 Score=22.16 Aligned_cols=26 Identities=35% Similarity=0.717 Sum_probs=14.3
Q ss_pred EeCCCcceeeEecccCCCccceeeeecccCCC
Q 029862 13 VHCNYCNTILAVSVPCSSLFNIVTVRCGHCAN 44 (186)
Q Consensus 13 V~CnfCnTiLaVsVPcssL~~~VTVRCGHCtn 44 (186)
|.|+-|.|+|+.- ...-.|||--|.-
T Consensus 2 ~~C~~C~t~L~yP------~gA~~vrCs~C~~ 27 (31)
T TIGR01053 2 VVCGGCRTLLMYP------RGASSVRCALCQT 27 (31)
T ss_pred cCcCCCCcEeecC------CCCCeEECCCCCe
Confidence 4566666666642 2334566666643
No 34
>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=38.61 E-value=21 Score=22.98 Aligned_cols=17 Identities=24% Similarity=0.563 Sum_probs=13.9
Q ss_pred cceeeeecccCCCcccc
Q 029862 32 FNIVTVRCGHCANLLNV 48 (186)
Q Consensus 32 ~~~VTVRCGHCtnLlSV 48 (186)
|.+|+|.|-+|.+-.+|
T Consensus 1 Ma~i~v~CP~C~s~~~v 17 (36)
T PF03811_consen 1 MAKIDVHCPRCQSTEGV 17 (36)
T ss_pred CCcEeeeCCCCCCCCcc
Confidence 45799999999987755
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=36.32 E-value=53 Score=23.59 Aligned_cols=31 Identities=29% Similarity=0.507 Sum_probs=23.0
Q ss_pred CCCCCCCCchhhhHHHHHHHHHHHhhCCCCC
Q 029862 107 PPEKRQRVPSAYNRFIKEEIQRIKASNPDIS 137 (186)
Q Consensus 107 PPEKRQR~psayN~fmK~ei~riK~~~P~i~ 137 (186)
|.+.......+|-.++++-++.||+.+|+.+
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 3345555788999999999999999999854
No 36
>PF05047 L51_S25_CI-B8: Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain ; InterPro: IPR007741 Proteins containing this domain are located in the mitochondrion and include ribosomal protein L51, and S25. This domain is also found in mitochondrial NADH-ubiquinone oxidoreductase B8 subunit (CI-B8) 1.6.5.3 from EC. It is not known whether all members of this family form part of the NADH-ubiquinone oxidoreductase and whether they are also all ribosomal proteins.; PDB: 1S3A_A.
Probab=35.67 E-value=31 Score=22.54 Aligned_cols=19 Identities=26% Similarity=0.639 Sum_probs=15.6
Q ss_pred hHHHHHHHHHHHhhCCCCC
Q 029862 119 NRFIKEEIQRIKASNPDIS 137 (186)
Q Consensus 119 N~fmK~ei~riK~~~P~i~ 137 (186)
..|+++-+..||..||++.
T Consensus 2 R~F~~~~lp~l~~~NP~v~ 20 (52)
T PF05047_consen 2 RDFLKNNLPTLKYHNPQVQ 20 (52)
T ss_dssp HHHHHHTHHHHHHHSTT--
T ss_pred HhHHHHhHHHHHHHCCCcE
Confidence 3699999999999999964
No 37
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=35.30 E-value=32 Score=27.36 Aligned_cols=45 Identities=20% Similarity=0.355 Sum_probs=33.3
Q ss_pred EEeCCCcceeeEecccCCCccceeeeecccCCCcccccccccccC
Q 029862 12 YVHCNYCNTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSALQA 56 (186)
Q Consensus 12 YV~CnfCnTiLaVsVPcssL~~~VTVRCGHCtnLlSVNm~~llqs 56 (186)
|--|-||+-...|+--.+--.++-|+-||-|.--.-+-.++++++
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 667999999999887777778888999999974433444444443
No 38
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=34.96 E-value=30 Score=24.73 Aligned_cols=30 Identities=30% Similarity=0.811 Sum_probs=16.0
Q ss_pred ceeEEeCCCcceeeEecccCCCccceeeeecccCCC
Q 029862 9 RVCYVHCNYCNTILAVSVPCSSLFNIVTVRCGHCAN 44 (186)
Q Consensus 9 ~lCYV~CnfCnTiLaVsVPcssL~~~VTVRCGHCtn 44 (186)
..+.+.||=|+.-=- | -|-++-.+|+||.+
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 39
>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=33.69 E-value=30 Score=28.13 Aligned_cols=36 Identities=28% Similarity=0.305 Sum_probs=30.9
Q ss_pred CCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHh
Q 029862 113 RVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKN 148 (186)
Q Consensus 113 R~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAkn 148 (186)
...+.-.+=++.||+++|++.-.|+..+-|...||+
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 456777788999999999999999999999999985
No 40
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=33.55 E-value=11 Score=27.25 Aligned_cols=13 Identities=46% Similarity=1.124 Sum_probs=11.0
Q ss_pred eeeeecccCCCcc
Q 029862 34 IVTVRCGHCANLL 46 (186)
Q Consensus 34 ~VTVRCGHCtnLl 46 (186)
+-|.||-||+-||
T Consensus 2 ~~tiRC~~CnKlL 14 (60)
T COG4416 2 MQTIRCAKCNKLL 14 (60)
T ss_pred ceeeehHHHhHHH
Confidence 4589999999887
No 41
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=31.13 E-value=26 Score=22.02 Aligned_cols=17 Identities=24% Similarity=0.638 Sum_probs=10.1
Q ss_pred ceeEEeCCCcceeeEec
Q 029862 9 RVCYVHCNYCNTILAVS 25 (186)
Q Consensus 9 ~lCYV~CnfCnTiLaVs 25 (186)
..-++.|++|..++..+
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 45689999999888765
No 42
>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=30.59 E-value=26 Score=26.48 Aligned_cols=30 Identities=27% Similarity=0.586 Sum_probs=13.3
Q ss_pred EeCCCcceeeEecccCCC---------ccceeeeecccC
Q 029862 13 VHCNYCNTILAVSVPCSS---------LFNIVTVRCGHC 42 (186)
Q Consensus 13 V~CnfCnTiLaVsVPcss---------L~~~VTVRCGHC 42 (186)
+.|.+|+..|-+.|=++. |+..+..-|..|
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 456666666666555542 444555555555
No 43
>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=29.93 E-value=28 Score=25.36 Aligned_cols=32 Identities=31% Similarity=0.504 Sum_probs=17.5
Q ss_pred eCCCcceeeEecccCCC-ccceeeeecccCCCc
Q 029862 14 HCNYCNTILAVSVPCSS-LFNIVTVRCGHCANL 45 (186)
Q Consensus 14 ~CnfCnTiLaVsVPcss-L~~~VTVRCGHCtnL 45 (186)
-|+-|+|--+-.+-=.+ =--+|-|||+.|.|.
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 47777776553321111 134799999999995
No 44
>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=29.91 E-value=19 Score=25.43 Aligned_cols=9 Identities=56% Similarity=1.191 Sum_probs=5.5
Q ss_pred ecccCCCcc
Q 029862 38 RCGHCANLL 46 (186)
Q Consensus 38 RCGHCtnLl 46 (186)
+|||++||-
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 399999884
No 45
>COG3712 FecR Fe2+-dicitrate sensor, membrane component [Inorganic ion transport and metabolism / Signal transduction mechanisms]
Probab=29.53 E-value=47 Score=30.63 Aligned_cols=31 Identities=23% Similarity=0.507 Sum_probs=27.9
Q ss_pred HHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCC
Q 029862 121 FIKEEIQRIKASNPDISHREAFSTAAKNWAHFP 153 (186)
Q Consensus 121 fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P 153 (186)
-..+|.++|++..|+ |.+||..+..-|....
T Consensus 32 ~~r~af~~W~~~~p~--H~~A~~~~e~lw~~l~ 62 (322)
T COG3712 32 ADRAAFERWRAASPE--HARAWERAERLWQALG 62 (322)
T ss_pred HHHHHHHHHHhcCHH--HHHHHHHHHHHHhhhc
Confidence 357899999999997 9999999999999865
No 46
>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=27.99 E-value=56 Score=29.05 Aligned_cols=25 Identities=20% Similarity=0.515 Sum_probs=23.4
Q ss_pred hhhhHHHHHHHHHHHhhCCCCCHHH
Q 029862 116 SAYNRFIKEEIQRIKASNPDISHRE 140 (186)
Q Consensus 116 sayN~fmK~ei~riK~~~P~i~hkE 140 (186)
..|..||++...+-|+.+|.+|.|+
T Consensus 8 ~dYR~fl~d~ye~rk~~~p~fS~R~ 32 (271)
T TIGR02147 8 TDYRKYLRDYYEERKKTDPAFSWRF 32 (271)
T ss_pred hhHHHHHHHHHHHHhccCcCcCHHH
Confidence 3599999999999999999999998
No 47
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=26.69 E-value=80 Score=26.74 Aligned_cols=36 Identities=31% Similarity=0.625 Sum_probs=28.1
Q ss_pred EEeCCCc---ceeeEecccCCCccceeeeecccCCCccccccccc
Q 029862 12 YVHCNYC---NTILAVSVPCSSLFNIVTVRCGHCANLLNVNMVSA 53 (186)
Q Consensus 12 YV~CnfC---nTiLaVsVPcssL~~~VTVRCGHCtnLlSVNm~~l 53 (186)
||.|.-| +|.|.+. + .+...+|.-|..-.+|.-...
T Consensus 98 yV~C~~C~~pdT~l~k~---~---~~~~l~C~aCGa~~~v~~~~~ 136 (201)
T PRK12336 98 YVICSECGLPDTRLVKE---D---RVLMLRCDACGAHRPVKKRKA 136 (201)
T ss_pred eEECCCCCCCCcEEEEc---C---CeEEEEcccCCCCcccccccc
Confidence 9999999 4777764 2 566789999999998865543
No 48
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=26.52 E-value=43 Score=21.95 Aligned_cols=14 Identities=29% Similarity=0.705 Sum_probs=11.6
Q ss_pred eEEeCCCcceeeEe
Q 029862 11 CYVHCNYCNTILAV 24 (186)
Q Consensus 11 CYV~CnfCnTiLaV 24 (186)
-++.|++|..+|..
T Consensus 17 ~~a~C~~C~~~l~~ 30 (50)
T smart00614 17 QRAKCKYCGKKLSR 30 (50)
T ss_pred eEEEecCCCCEeee
Confidence 58999999998863
No 49
>KOG4520 consensus Predicted coiled-coil protein [General function prediction only]
Probab=26.26 E-value=78 Score=28.16 Aligned_cols=36 Identities=31% Similarity=0.272 Sum_probs=24.8
Q ss_pred hHHHHHHHHHHHhhC----------------CCCCHHHHHHHHHHhhccCCc
Q 029862 119 NRFIKEEIQRIKASN----------------PDISHREAFSTAAKNWAHFPH 154 (186)
Q Consensus 119 N~fmK~ei~riK~~~----------------P~i~hkEaF~~aAknW~~~P~ 154 (186)
---|||||++||+.. |.---|+-|+.++|.=-..|+
T Consensus 62 ~~~~keEi~~vkE~E~~al~eALGl~k~stqP~gL~k~~fse~~kR~g~~~E 113 (238)
T KOG4520|consen 62 KEKYKEEILEVKEREQRALAEALGLPKSSTQPSGLLKLTFSEAAKRSGTNTE 113 (238)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhCCCccccCCcchhHHHHHHHHhhcCCCHH
Confidence 345899999999864 333367788888877444443
No 50
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=25.73 E-value=32 Score=22.17 Aligned_cols=13 Identities=38% Similarity=1.060 Sum_probs=10.7
Q ss_pred eeecccCCCcccc
Q 029862 36 TVRCGHCANLLNV 48 (186)
Q Consensus 36 TVRCGHCtnLlSV 48 (186)
.++||+|.+-+..
T Consensus 5 ~l~C~~CG~~m~~ 17 (58)
T PF13408_consen 5 LLRCGHCGSKMTR 17 (58)
T ss_pred cEEcccCCcEeEE
Confidence 4799999988765
No 51
>KOG4715 consensus SWI/SNF-related matrix-associated actin-dependent regulator of chromatin [Chromatin structure and dynamics]
Probab=25.18 E-value=93 Score=29.59 Aligned_cols=48 Identities=31% Similarity=0.576 Sum_probs=41.5
Q ss_pred CCCCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 029862 104 PIRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH 154 (186)
Q Consensus 104 ~~KPPEKRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P~ 154 (186)
+-|||||- .-.|=||-+.=-..+|+.||++---|.=+.+.+.|.+.|.
T Consensus 61 pPkppekp---l~pymrySrkvWd~VkA~nPe~kLWeiGK~Ig~mW~dLpd 108 (410)
T KOG4715|consen 61 PPKPPEKP---LMPYMRYSRKVWDQVKASNPELKLWEIGKIIGGMWLDLPD 108 (410)
T ss_pred CCCCCCcc---cchhhHHhhhhhhhhhccCcchHHHHHHHHHHHHHhhCcc
Confidence 45788874 4579999999999999999999999999999999998774
No 52
>COG5509 Uncharacterized small protein containing a coiled-coil domain [Function unknown]
Probab=25.09 E-value=72 Score=23.47 Aligned_cols=13 Identities=38% Similarity=0.664 Sum_probs=10.9
Q ss_pred HHHHHHHHHHhhC
Q 029862 121 FIKEEIQRIKASN 133 (186)
Q Consensus 121 fmK~ei~riK~~~ 133 (186)
...+||.|+|++-
T Consensus 36 lLq~EIeRlkAe~ 48 (65)
T COG5509 36 LLQAEIERLKAEL 48 (65)
T ss_pred HHHHHHHHHHHHH
Confidence 5789999999874
No 53
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=24.95 E-value=20 Score=28.56 Aligned_cols=39 Identities=28% Similarity=0.588 Sum_probs=27.2
Q ss_pred EEeCCCcceeeEe--------cccCC----CccceeeeecccCCCcccccc
Q 029862 12 YVHCNYCNTILAV--------SVPCS----SLFNIVTVRCGHCANLLNVNM 50 (186)
Q Consensus 12 YV~CnfCnTiLaV--------sVPcs----sL~~~VTVRCGHCtnLlSVNm 50 (186)
=.+|.-|++--|- .-|.. +.++.-.|-||+|-+||+++=
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 3567777776652 22332 577888899999999998863
No 54
>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=24.79 E-value=1.1e+02 Score=21.30 Aligned_cols=32 Identities=34% Similarity=0.399 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHhhCCCCCHHHHHHHHHHhhcc
Q 029862 120 RFIKEEIQRIKASNPDISHREAFSTAAKNWAH 151 (186)
Q Consensus 120 ~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~ 151 (186)
.++.+.|..++..+|.++-..+...||-|-++
T Consensus 28 ~~i~~~i~~~~~~~~~~~~~~~~vlaaLnla~ 59 (89)
T PF05164_consen 28 ELINEKINEIKKKYPKLSPERLAVLAALNLAD 59 (89)
T ss_dssp HHHHHHHHHHCTTCCTSSHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHH
Confidence 57889999999999999999999999988664
No 55
>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=23.90 E-value=13 Score=28.30 Aligned_cols=16 Identities=31% Similarity=0.895 Sum_probs=12.7
Q ss_pred CceeEEeCCCcceeeE
Q 029862 8 ERVCYVHCNYCNTILA 23 (186)
Q Consensus 8 E~lCYV~CnfCnTiLa 23 (186)
=|+|..=|++|||++.
T Consensus 37 IqLC~~cc~~~n~~v~ 52 (82)
T PF02723_consen 37 IQLCFQCCRLCNTTVY 52 (82)
T ss_pred HHHHHHHhhhhcceEe
Confidence 3788888899988765
No 56
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=23.40 E-value=98 Score=25.00 Aligned_cols=33 Identities=21% Similarity=0.552 Sum_probs=24.4
Q ss_pred eEEeCCCc---ceeeEecccCCCccceeeeecccCCCccccc
Q 029862 11 CYVHCNYC---NTILAVSVPCSSLFNIVTVRCGHCANLLNVN 49 (186)
Q Consensus 11 CYV~CnfC---nTiLaVsVPcssL~~~VTVRCGHCtnLlSVN 49 (186)
=||.|.-| +|.|... ++ +-..+|--|..-.+|.
T Consensus 96 ~yVlC~~C~sPdT~l~k~---~r---~~~l~C~ACGa~~~v~ 131 (133)
T TIGR00311 96 KYVICRECNRPDTRIIKE---GR---VSLLKCEACGAKAPLR 131 (133)
T ss_pred heEECCCCCCCCcEEEEe---CC---eEEEecccCCCCCccC
Confidence 49999999 4777763 33 3367999999887773
No 57
>PF14722 KRAP_IP3R_bind: Ki-ras-induced actin-interacting protein-IP3R-interacting domain
Probab=23.37 E-value=86 Score=26.62 Aligned_cols=28 Identities=21% Similarity=0.456 Sum_probs=22.4
Q ss_pred hhHHHHHHHHHHHhhCCCCCHHHHHHHH
Q 029862 118 YNRFIKEEIQRIKASNPDISHREAFSTA 145 (186)
Q Consensus 118 yN~fmK~ei~riK~~~P~i~hkEaF~~a 145 (186)
...|++.++|||..+||...---+|.+.
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 58
>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=22.76 E-value=2.3e+02 Score=24.43 Aligned_cols=46 Identities=24% Similarity=0.365 Sum_probs=37.9
Q ss_pred CCCCCCCCCCchhhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccCCc
Q 029862 105 IRPPEKRQRVPSAYNRFIKEEIQRIKASNPDISHREAFSTAAKNWAHFPH 154 (186)
Q Consensus 105 ~KPPEKRQR~psayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~~~P~ 154 (186)
.+.++++.|.-.+|+.|+-= .+...|+++.|+.=...++-|...|+
T Consensus 38 ~~~~~~~kr~lN~Fm~FRsy----y~~~~~~~~Qk~~S~~l~~lW~~dp~ 83 (201)
T PF04769_consen 38 KRSPEKAKRPLNGFMAFRSY----YSPIFPPLPQKELSGILTKLWEKDPF 83 (201)
T ss_pred cccccccccchhHHHHHHHH----HHhhcCCcCHHHHHHHHHHHHhCCcc
Confidence 35678888888899998764 33667889999999999999998886
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=22.63 E-value=56 Score=23.09 Aligned_cols=12 Identities=50% Similarity=0.960 Sum_probs=9.4
Q ss_pred EeCCCcceeeEe
Q 029862 13 VHCNYCNTILAV 24 (186)
Q Consensus 13 V~CnfCnTiLaV 24 (186)
|.|..|.|+|+=
T Consensus 27 V~C~~Cg~~L~~ 38 (55)
T PF01667_consen 27 VKCVVCGTVLAQ 38 (55)
T ss_dssp EE-SSSTSEEEE
T ss_pred EEcccCCCEecC
Confidence 889999999973
No 60
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=22.21 E-value=45 Score=30.96 Aligned_cols=50 Identities=36% Similarity=0.514 Sum_probs=30.9
Q ss_pred CCCCCCchhhhHHHHHHHHHHHhhCC---CCCHHHHHHHHHHhhccCCccccccccC------CccchhhhHH
Q 029862 109 EKRQRVPSAYNRFIKEEIQRIKASNP---DISHREAFSTAAKNWAHFPHIHFGLKLD------GNKQAKLDKA 172 (186)
Q Consensus 109 EKRQR~psayN~fmK~ei~riK~~~P---~i~hkEaF~~aAknW~~~P~ihfGl~~~------~~~~~~~d~~ 172 (186)
|||.|+ -|--|+|+|||++.- -|+-+-+=.+|-. +||... +||.+|+...
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 566664 477899999999863 3455555444433 344422 3677777654
No 61
>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=22.08 E-value=76 Score=28.71 Aligned_cols=17 Identities=41% Similarity=0.813 Sum_probs=13.1
Q ss_pred ceeeeecccCCCccccc
Q 029862 33 NIVTVRCGHCANLLNVN 49 (186)
Q Consensus 33 ~~VTVRCGHCtnLlSVN 49 (186)
...-|+||||.+-..-|
T Consensus 154 ~~~rv~CghC~~~Fl~~ 170 (256)
T PF09788_consen 154 GSCRVICGHCSNTFLFN 170 (256)
T ss_pred CceeEECCCCCCcEecc
Confidence 45779999999976544
No 62
>KOG4253 consensus Tryptophan-rich basic nuclear protein [General function prediction only]
Probab=21.11 E-value=1.2e+02 Score=26.10 Aligned_cols=34 Identities=21% Similarity=0.136 Sum_probs=28.8
Q ss_pred hhhHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhc
Q 029862 117 AYNRFIKEEIQRIKASNPDISHREAFSTAAKNWA 150 (186)
Q Consensus 117 ayN~fmK~ei~riK~~~P~i~hkEaF~~aAknW~ 150 (186)
-=|.=|++||+.+|+++-.++-.+-|..-|++=+
T Consensus 44 kk~~q~~~ei~dmKqelnavs~qD~fAkwaRlnR 77 (175)
T KOG4253|consen 44 KKESQKVAEIQDMKQELNAVSMQDNFAKWARLNR 77 (175)
T ss_pred HHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHHH
Confidence 3466799999999999999999999988777644
No 63
>KOG1522 consensus RNA polymerase II, subunit POLR2C/RPB3 [Transcription]
Probab=20.66 E-value=58 Score=29.80 Aligned_cols=26 Identities=19% Similarity=0.571 Sum_probs=21.7
Q ss_pred cCCCceeEEeCCCcceeeEecccCCC
Q 029862 5 LASERVCYVHCNYCNTILAVSVPCSS 30 (186)
Q Consensus 5 ~~~E~lCYV~CnfCnTiLaVsVPcss 30 (186)
...+--|--+|.+|...+-.+|=|..
T Consensus 82 ytrdC~C~~~C~eCSVef~L~~kc~~ 107 (285)
T KOG1522|consen 82 YTRDCECDEFCPECSVEFTLDVKCTD 107 (285)
T ss_pred hcccCchhccCCcceEEEEEeeeecc
Confidence 34566799999999999999998873
No 64
>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=20.57 E-value=50 Score=20.03 Aligned_cols=10 Identities=40% Similarity=1.036 Sum_probs=8.4
Q ss_pred EEeCCCccee
Q 029862 12 YVHCNYCNTI 21 (186)
Q Consensus 12 YV~CnfCnTi 21 (186)
.|+|.-|+||
T Consensus 16 sVrCa~C~~V 25 (25)
T PF06943_consen 16 SVRCACCHTV 25 (25)
T ss_pred CeECCccCcC
Confidence 5899999886
No 65
>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=20.51 E-value=55 Score=27.74 Aligned_cols=19 Identities=26% Similarity=0.588 Sum_probs=15.9
Q ss_pred EEeCCCcceeeEecccCCC
Q 029862 12 YVHCNYCNTILAVSVPCSS 30 (186)
Q Consensus 12 YV~CnfCnTiLaVsVPcss 30 (186)
=|+|+-|+.+|-|.+.-..
T Consensus 36 TVRCGHCtNLLSVNm~~~~ 54 (170)
T PF04690_consen 36 TVRCGHCTNLLSVNMRALL 54 (170)
T ss_pred ceeccCccceeeeeccccc
Confidence 3999999999999886544
No 66
>KOG3404 consensus G10 protein/predicted nuclear transcription regulator [Transcription]
Probab=20.48 E-value=80 Score=26.34 Aligned_cols=37 Identities=35% Similarity=0.602 Sum_probs=29.4
Q ss_pred CCceeEEeC------CCcceeeEecccCCCccceeeeecccCCC
Q 029862 7 SERVCYVHC------NYCNTILAVSVPCSSLFNIVTVRCGHCAN 44 (186)
Q Consensus 7 ~E~lCYV~C------nfCnTiLaVsVPcssL~~~VTVRCGHCtn 44 (186)
-|.||.++| ||=+| -.--||-+.|=.--.|+|-||..
T Consensus 97 YE~LCClRCIq~~dsn~Gt~-CICRVPk~~ld~~~~~~C~hCGC 139 (145)
T KOG3404|consen 97 YENLCCLRCIQTRDSNFGTT-CICRVPKSKLDVERIVECVHCGC 139 (145)
T ss_pred ccceeeeeeccccccCCCce-EEEeCChhhcChhheeeeeccCc
Confidence 489999999 55444 34579999998888999999963
Done!