Query 030347
Match_columns 179
No_of_seqs 134 out of 148
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 12:21:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030347.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030347hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2612 Predicted integral mem 100.0 9.9E-30 2.2E-34 191.7 4.4 99 9-122 5-103 (103)
2 PF08209 Sgf11: Sgf11 (transcr 99.8 1.2E-20 2.5E-25 118.6 1.4 32 91-122 2-33 (33)
3 PF13913 zf-C2HC_2: zinc-finge 96.4 0.00093 2E-08 39.2 0.2 23 93-115 2-24 (25)
4 smart00734 ZnF_Rad18 Rad18-lik 95.5 0.0049 1.1E-07 36.6 0.6 25 93-117 1-25 (26)
5 KOG3623 Homeobox transcription 86.1 0.38 8.3E-06 48.5 1.6 66 91-156 307-376 (1007)
6 PF12230 PRP21_like_P: Pre-mRN 77.6 0.73 1.6E-05 38.8 0.0 26 91-116 166-191 (229)
7 TIGR00599 rad18 DNA repair pro 73.7 1.2 2.6E-05 41.5 0.4 30 91-120 179-209 (397)
8 PF07754 DUF1610: Domain of un 71.9 2.5 5.5E-05 25.0 1.3 11 90-100 13-23 (24)
9 PF05605 zf-Di19: Drought indu 71.5 1.6 3.5E-05 29.0 0.5 23 93-115 2-24 (54)
10 COG5432 RAD18 RING-finger-cont 68.4 3.1 6.8E-05 38.3 1.8 29 90-118 157-185 (391)
11 PF12647 RNHCP: RNHCP domain; 61.9 3.1 6.8E-05 31.8 0.5 27 91-117 2-32 (92)
12 PLN03086 PRLI-interacting fact 58.0 5 0.00011 39.2 1.2 27 91-117 405-431 (567)
13 PF12269 zf-CpG_bind_C: CpG bi 53.5 55 0.0012 28.9 6.8 29 90-118 81-109 (236)
14 COG4481 Uncharacterized protei 52.9 6.2 0.00013 28.0 0.7 18 91-108 32-49 (60)
15 PF12209 SAC3: Leucine permeas 52.5 26 0.00056 25.7 3.9 27 12-38 39-65 (79)
16 COG1110 Reverse gyrase [DNA re 51.9 5.1 0.00011 42.0 0.2 28 94-121 9-38 (1187)
17 PRK14701 reverse gyrase; Provi 51.4 5.6 0.00012 43.2 0.4 25 93-117 6-32 (1638)
18 PF02591 DUF164: Putative zinc 51.1 9.3 0.0002 25.6 1.3 12 91-102 44-55 (56)
19 PF02892 zf-BED: BED zinc fing 48.9 7.3 0.00016 24.4 0.5 24 90-113 13-41 (45)
20 PF13248 zf-ribbon_3: zinc-rib 47.4 9.5 0.00021 22.1 0.8 17 94-110 3-20 (26)
21 PF03884 DUF329: Domain of unk 46.9 9.6 0.00021 26.7 0.9 23 93-115 2-28 (57)
22 PF13240 zinc_ribbon_2: zinc-r 46.5 9.7 0.00021 21.8 0.7 11 95-105 1-11 (23)
23 PF11023 DUF2614: Protein of u 45.0 11 0.00024 29.9 1.1 24 91-118 67-91 (114)
24 COG2888 Predicted Zn-ribbon RN 44.8 14 0.00031 26.4 1.5 17 87-103 21-37 (61)
25 PF00096 zf-C2H2: Zinc finger, 43.2 12 0.00025 20.2 0.7 11 94-104 1-11 (23)
26 PF02176 zf-TRAF: TRAF-type zi 41.9 12 0.00026 24.5 0.7 26 92-117 8-36 (60)
27 PF10571 UPF0547: Uncharacteri 41.1 12 0.00026 22.2 0.5 17 95-111 2-19 (26)
28 PF05253 zf-U11-48K: U11-48K-l 39.9 22 0.00047 20.9 1.6 24 93-116 2-26 (27)
29 PRK00398 rpoP DNA-directed RNA 38.8 12 0.00026 24.1 0.3 12 93-104 21-32 (46)
30 PF06107 DUF951: Bacterial pro 38.3 16 0.00035 25.7 0.9 16 93-108 31-46 (57)
31 PRK14890 putative Zn-ribbon RN 37.4 22 0.00048 25.2 1.5 13 90-102 22-34 (59)
32 PF07295 DUF1451: Protein of u 37.4 12 0.00027 30.3 0.3 29 93-122 112-140 (146)
33 TIGR01054 rgy reverse gyrase. 36.1 12 0.00025 39.3 -0.0 25 93-117 7-33 (1171)
34 PRK09401 reverse gyrase; Revie 35.7 13 0.00028 39.1 0.2 25 93-117 7-33 (1176)
35 PF04423 Rad50_zn_hook: Rad50 35.2 15 0.00033 24.3 0.4 14 95-108 22-35 (54)
36 PRK06266 transcription initiat 33.9 22 0.00048 29.4 1.2 17 89-105 113-129 (178)
37 PF14353 CpXC: CpXC protein 32.7 23 0.00051 26.9 1.1 13 93-105 38-50 (128)
38 smart00531 TFIIE Transcription 32.3 25 0.00055 27.8 1.3 17 90-106 96-112 (147)
39 PF10601 zf-LITAF-like: LITAF- 31.3 29 0.00063 24.2 1.3 17 91-107 56-72 (73)
40 PF12677 DUF3797: Domain of un 30.7 20 0.00042 24.7 0.3 16 90-105 10-25 (49)
41 TIGR00373 conserved hypothetic 30.5 28 0.0006 28.2 1.2 16 89-104 105-120 (158)
42 KOG2186 Cell growth-regulating 30.4 22 0.00048 32.0 0.7 27 90-117 26-52 (276)
43 TIGR02098 MJ0042_CXXC MJ0042 f 30.0 36 0.00078 20.7 1.5 14 92-105 24-37 (38)
44 KOG3940 Uncharacterized conser 29.6 25 0.00053 32.6 0.9 33 87-119 316-348 (351)
45 PRK02935 hypothetical protein; 28.7 30 0.00066 27.3 1.1 13 91-103 68-80 (110)
46 PF09889 DUF2116: Uncharacteri 28.1 26 0.00057 24.6 0.7 13 94-106 4-16 (59)
47 PRK00418 DNA gyrase inhibitor; 28.1 30 0.00066 24.7 1.0 25 92-116 5-33 (62)
48 TIGR01206 lysW lysine biosynth 26.9 26 0.00057 24.1 0.5 14 93-106 2-15 (54)
49 PF12773 DZR: Double zinc ribb 26.6 35 0.00077 21.8 1.0 12 93-104 12-23 (50)
50 PF11113 Phage_head_chap: Head 26.5 27 0.00059 24.6 0.5 12 107-118 43-54 (56)
51 PF14577 SEO_C: Sieve element 26.3 33 0.00072 30.2 1.1 13 92-104 213-225 (235)
52 PRK01343 zinc-binding protein; 25.9 49 0.0011 23.3 1.7 19 91-110 7-25 (57)
53 TIGR03826 YvyF flagellar opero 25.8 34 0.00075 27.6 1.0 26 90-118 78-103 (137)
54 PF13465 zf-H2C2_2: Zinc-finge 25.7 32 0.00069 19.7 0.6 11 93-103 14-24 (26)
55 PF10609 ParA: ParA/MinD ATPas 24.6 34 0.00073 25.4 0.7 24 78-104 53-76 (81)
56 PRK14892 putative transcriptio 24.5 37 0.00081 26.0 1.0 11 91-101 19-29 (99)
57 cd02341 ZZ_ZZZ3 Zinc finger, Z 23.9 33 0.00072 22.9 0.5 15 94-108 1-16 (48)
58 KOG2593 Transcription initiati 23.0 65 0.0014 30.9 2.4 13 92-104 152-164 (436)
59 PF05304 DUF728: Protein of un 22.7 46 0.001 25.9 1.2 26 93-118 39-75 (103)
60 PF13894 zf-C2H2_4: C2H2-type 22.7 44 0.00096 17.2 0.8 20 94-113 1-21 (24)
61 cd02340 ZZ_NBR1_like Zinc fing 22.1 40 0.00086 21.8 0.6 14 95-108 2-15 (43)
62 COG1579 Zn-ribbon protein, pos 22.0 36 0.00077 29.9 0.5 14 90-103 218-231 (239)
63 PF08790 zf-LYAR: LYAR-type C2 21.9 53 0.0012 20.1 1.1 23 94-117 1-23 (28)
64 PF10013 DUF2256: Uncharacteri 21.8 41 0.00089 22.4 0.6 12 93-104 8-19 (42)
65 COG2051 RPS27A Ribosomal prote 21.6 57 0.0012 23.7 1.4 14 91-104 36-49 (67)
66 PF08271 TF_Zn_Ribbon: TFIIB z 21.6 45 0.00098 21.1 0.8 10 94-103 1-10 (43)
67 PF03847 TFIID_20kDa: Transcri 21.4 2.1E+02 0.0045 20.3 4.2 34 7-40 13-46 (68)
68 PF11687 DUF3284: Domain of un 20.9 96 0.0021 23.8 2.6 23 16-38 11-33 (120)
69 smart00714 LITAF Possible memb 20.4 58 0.0012 22.3 1.2 16 91-106 50-65 (67)
70 COG5248 TAF19 Transcription in 20.0 1.8E+02 0.004 23.3 4.0 33 7-40 24-56 (126)
No 1
>KOG2612 consensus Predicted integral membrane protein [Function unknown]
Probab=99.96 E-value=9.9e-30 Score=191.69 Aligned_cols=99 Identities=31% Similarity=0.494 Sum_probs=85.1
Q ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhccCccchhhHHHHHHHHHhhhhhcCCCCCCCCCCCcccceeCccCCC
Q 030347 9 MSAHSQLSSHFFEDLLDSIIVDVASECHRVARLGLDRNFEEEEEELRLSAQARARVADSSNNGETNSKYVVDIFGQTHPA 88 (179)
Q Consensus 9 ~s~l~~LA~~Iy~dLLddiIlDIv~EvHR~~KlGl~~~l~~~~~el~~~~~a~~~~~Dps~~~~~~~~~~~DIfG~~~~~ 88 (179)
...++++++.||++|||+.|+||+.|.|+.+|+|-...++...|. ..+++ +|. +.+||||..+++
T Consensus 5 ~iniDe~aNgilnnLL~~~iqdI~a~e~~~qkl~k~~~~D~rped------ssY~f-~~~--------gnLDI~Giqkqa 69 (103)
T KOG2612|consen 5 PINIDEAANGILNNLLDDAIQDIFAEEHHLQKLGKLAALDGRPED------SSYRF-CEM--------GNLDIFGIQKQA 69 (103)
T ss_pred cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCccc------cceee-cCC--------CCcchhhhhhhc
Confidence 456899999999999999999999999999999988887754332 22333 333 579999999999
Q ss_pred CCCceeeeCCCCCcccccccchhHHHhhcCCccc
Q 030347 89 VANEIFECMNCGRSIVAGRFAPHLEKCMGKGRKA 122 (179)
Q Consensus 89 ~~~~~~~C~nC~R~v~a~RfA~HLekCmg~gr~s 122 (179)
+...+++|+||+|.|+|+|||||||||||||++|
T Consensus 70 ek~~~~hCeNC~RdVaAaR~AaHLekCl~~Ga~r 103 (103)
T KOG2612|consen 70 EKPMDCHCENCDRDVAAARFAAHLEKCLGMGAIR 103 (103)
T ss_pred cCCccccCCCCccHHHHHHHHHHHHHHHhccccC
Confidence 9999999999999999999999999999999864
No 2
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=99.80 E-value=1.2e-20 Score=118.59 Aligned_cols=32 Identities=63% Similarity=1.274 Sum_probs=25.5
Q ss_pred CceeeeCCCCCcccccccchhHHHhhcCCccc
Q 030347 91 NEIFECMNCGRSIVAGRFAPHLEKCMGKGRKA 122 (179)
Q Consensus 91 ~~~~~C~nC~R~v~a~RfA~HLekCmg~gr~s 122 (179)
+++|+|+||+|+|+++|||||||||||+||+|
T Consensus 2 ~~~~~C~nC~R~v~a~RfA~HLekCmg~g~~~ 33 (33)
T PF08209_consen 2 SPYVECPNCGRPVAASRFAPHLEKCMGRGRRR 33 (33)
T ss_dssp S-EEE-TTTSSEEEGGGHHHHHHHHTCH----
T ss_pred CCeEECCCCcCCcchhhhHHHHHHHHccCCCC
Confidence 67999999999999999999999999999864
No 3
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=96.41 E-value=0.00093 Score=39.18 Aligned_cols=23 Identities=30% Similarity=0.735 Sum_probs=21.6
Q ss_pred eeeeCCCCCcccccccchhHHHh
Q 030347 93 IFECMNCGRSIVAGRFAPHLEKC 115 (179)
Q Consensus 93 ~~~C~nC~R~v~a~RfA~HLekC 115 (179)
.+.|+.|+|.+...|+.-|+..|
T Consensus 2 l~~C~~CgR~F~~~~l~~H~~~C 24 (25)
T PF13913_consen 2 LVPCPICGRKFNPDRLEKHEKIC 24 (25)
T ss_pred CCcCCCCCCEECHHHHHHHHHhc
Confidence 57899999999999999999988
No 4
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=95.53 E-value=0.0049 Score=36.56 Aligned_cols=25 Identities=24% Similarity=0.662 Sum_probs=22.6
Q ss_pred eeeeCCCCCcccccccchhHHHhhc
Q 030347 93 IFECMNCGRSIVAGRFAPHLEKCMG 117 (179)
Q Consensus 93 ~~~C~nC~R~v~a~RfA~HLekCmg 117 (179)
++.||.|++.|....+-.||+.|+.
T Consensus 1 ~v~CPiC~~~v~~~~in~HLD~CL~ 25 (26)
T smart00734 1 LVQCPVCFREVPENLINSHLDSCLX 25 (26)
T ss_pred CCcCCCCcCcccHHHHHHHHHHhcc
Confidence 3689999999999999999999975
No 5
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=86.08 E-value=0.38 Score=48.54 Aligned_cols=66 Identities=23% Similarity=0.324 Sum_probs=44.1
Q ss_pred CceeeeCCCCCccc-ccccchhHH--HhhcCCcccchhhhhhhh-hhhcccCCCCCCCCCCCCCCCCCCC
Q 030347 91 NEIFECMNCGRSIV-AGRFAPHLE--KCMGKGRKARLKVTRSAT-AAQNRYTRGSPGSSYSSYSNSTGMN 156 (179)
Q Consensus 91 ~~~~~C~nC~R~v~-a~RfA~HLe--kCmg~gr~sr~~a~rs~~-a~~~~~~~~~~~~s~spy~~~~~~n 156 (179)
-+-|+|+||++-++ .+-|--|+. ||.+|+-.-.|..+---| -+...+.+.+|+++++||.----+|
T Consensus 307 EKPfeCpnCkKRFSHSGSySSHmSSKKCIsli~vngr~R~~lKt~~~Sp~saSsSp~~s~~pq~r~klen 376 (1007)
T KOG3623|consen 307 EKPFECPNCKKRFSHSGSYSSHMSSKKCISLILVNGRNRALLKTLEKSPGSASSSPRRSPSPQGRGKLEN 376 (1007)
T ss_pred CCCcCCcccccccccCCcccccccccchhhhhcccCcchhhhhhcccCCcccCCCCCCCCChhHhhhccC
Confidence 45699999998775 568999995 799886554432211111 1223445677899999988766666
No 6
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=77.58 E-value=0.73 Score=38.80 Aligned_cols=26 Identities=19% Similarity=0.349 Sum_probs=0.0
Q ss_pred CceeeeCCCCCcccccccchhHHHhh
Q 030347 91 NEIFECMNCGRSIVAGRFAPHLEKCM 116 (179)
Q Consensus 91 ~~~~~C~nC~R~v~a~RfA~HLekCm 116 (179)
..+..||.||..|.++.|.-||.-=|
T Consensus 166 ~~~~~cPitGe~IP~~e~~eHmRi~L 191 (229)
T PF12230_consen 166 EKMIICPITGEMIPADEMDEHMRIEL 191 (229)
T ss_dssp --------------------------
T ss_pred cccccccccccccccccccccccccc
Confidence 46789999999999999999996543
No 7
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=73.74 E-value=1.2 Score=41.54 Aligned_cols=30 Identities=20% Similarity=0.589 Sum_probs=26.9
Q ss_pred CceeeeCCCCCcccccccchhHHH-hhcCCc
Q 030347 91 NEIFECMNCGRSIVAGRFAPHLEK-CMGKGR 120 (179)
Q Consensus 91 ~~~~~C~nC~R~v~a~RfA~HLek-Cmg~gr 120 (179)
..++.||.|++.|.....-.||.. |+|.+.
T Consensus 179 d~~v~CPiC~~~~~~~~i~~Hld~~Cl~~~~ 209 (397)
T TIGR00599 179 EGLVQCPICQQRMPEKAVERHLDSECLGSPS 209 (397)
T ss_pred CCcccCCCcccccCHHHHHHHHhccCCCCCC
Confidence 457999999999999999999999 999754
No 8
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=71.90 E-value=2.5 Score=24.96 Aligned_cols=11 Identities=45% Similarity=0.984 Sum_probs=9.2
Q ss_pred CCceeeeCCCC
Q 030347 90 ANEIFECMNCG 100 (179)
Q Consensus 90 ~~~~~~C~nC~ 100 (179)
....|.|||||
T Consensus 13 ~~v~f~CPnCG 23 (24)
T PF07754_consen 13 QAVPFPCPNCG 23 (24)
T ss_pred cCceEeCCCCC
Confidence 35689999998
No 9
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=71.50 E-value=1.6 Score=29.03 Aligned_cols=23 Identities=26% Similarity=0.600 Sum_probs=20.3
Q ss_pred eeeeCCCCCcccccccchhHHHh
Q 030347 93 IFECMNCGRSIVAGRFAPHLEKC 115 (179)
Q Consensus 93 ~~~C~nC~R~v~a~RfA~HLekC 115 (179)
.|.||-|++.+....+..|++.-
T Consensus 2 ~f~CP~C~~~~~~~~L~~H~~~~ 24 (54)
T PF05605_consen 2 SFTCPYCGKGFSESSLVEHCEDE 24 (54)
T ss_pred CcCCCCCCCccCHHHHHHHHHhH
Confidence 58999999999999999998773
No 10
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=68.39 E-value=3.1 Score=38.32 Aligned_cols=29 Identities=17% Similarity=0.641 Sum_probs=26.0
Q ss_pred CCceeeeCCCCCcccccccchhHHHhhcC
Q 030347 90 ANEIFECMNCGRSIVAGRFAPHLEKCMGK 118 (179)
Q Consensus 90 ~~~~~~C~nC~R~v~a~RfA~HLekCmg~ 118 (179)
.-+.++||.|..-|..+-.-+||+.||..
T Consensus 157 ~E~l~~CP~C~~~~P~~~i~~HLD~CL~~ 185 (391)
T COG5432 157 REDLVHCPACSNLVPHNQINQHLDSCLNS 185 (391)
T ss_pred HHhhhcCchhhccCchHHHHHHHHHHhcC
Confidence 35688999999999999999999999985
No 11
>PF12647 RNHCP: RNHCP domain; InterPro: IPR024439 This domain is found in uncharacterised bacterial proteins. It is typically between 94 and 143 amino acids in length and has a conserved RNHCP sequence motif.
Probab=61.95 E-value=3.1 Score=31.80 Aligned_cols=27 Identities=30% Similarity=0.801 Sum_probs=22.8
Q ss_pred CceeeeCCCCCcc----cccccchhHHHhhc
Q 030347 91 NEIFECMNCGRSI----VAGRFAPHLEKCMG 117 (179)
Q Consensus 91 ~~~~~C~nC~R~v----~a~RfA~HLekCmg 117 (179)
+..|.|.+|++.| ..+.+--|=..||-
T Consensus 2 ~~~F~C~~CG~~V~p~~~g~~~RNHCP~CL~ 32 (92)
T PF12647_consen 2 NESFTCVHCGLTVSPLAAGSAHRNHCPSCLS 32 (92)
T ss_pred CcccCccccCCCcccCCCCCCccCcCccccc
Confidence 3579999999999 66778889888986
No 12
>PLN03086 PRLI-interacting factor K; Provisional
Probab=57.95 E-value=5 Score=39.20 Aligned_cols=27 Identities=30% Similarity=0.491 Sum_probs=24.2
Q ss_pred CceeeeCCCCCcccccccchhHHHhhc
Q 030347 91 NEIFECMNCGRSIVAGRFAPHLEKCMG 117 (179)
Q Consensus 91 ~~~~~C~nC~R~v~a~RfA~HLekCmg 117 (179)
...+.|+||++.|...-|.-|+..|+=
T Consensus 405 ~~~V~C~NC~~~i~l~~l~lHe~~C~r 431 (567)
T PLN03086 405 VDTVECRNCKHYIPSRSIALHEAYCSR 431 (567)
T ss_pred CCeEECCCCCCccchhHHHHHHhhCCC
Confidence 346799999999999999999999973
No 13
>PF12269 zf-CpG_bind_C: CpG binding protein zinc finger C terminal domain; InterPro: IPR022056 This domain family is found in eukaryotes, and is approximately 240 amino acids in length. This domain is the zinc finger domain of a CpG binding DNA methyltransferase protein. It contains a CxxC motif which forms the zinc finger and binds to DNA.
Probab=53.51 E-value=55 Score=28.85 Aligned_cols=29 Identities=31% Similarity=0.705 Sum_probs=26.0
Q ss_pred CCceeeeCCCCCcccccccchhHHHhhcC
Q 030347 90 ANEIFECMNCGRSIVAGRFAPHLEKCMGK 118 (179)
Q Consensus 90 ~~~~~~C~nC~R~v~a~RfA~HLekCmg~ 118 (179)
......|..||-+|.+--+--|+|||..+
T Consensus 81 ~~~~~~Cv~Cg~~i~~~~a~kHmEkCf~K 109 (236)
T PF12269_consen 81 DDLSIYCVTCGHEIPSKKALKHMEKCFAK 109 (236)
T ss_pred cceeeeeeeCCCcCCHHHHHHHHHHHHHH
Confidence 45578999999999999999999999874
No 14
>COG4481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=52.87 E-value=6.2 Score=27.99 Aligned_cols=18 Identities=33% Similarity=0.851 Sum_probs=15.4
Q ss_pred CceeeeCCCCCccccccc
Q 030347 91 NEIFECMNCGRSIVAGRF 108 (179)
Q Consensus 91 ~~~~~C~nC~R~v~a~Rf 108 (179)
..-..|.||++.|...||
T Consensus 32 DIkikC~nC~h~vm~pR~ 49 (60)
T COG4481 32 DIKIKCENCGHSVMMPRY 49 (60)
T ss_pred cEEEEecCCCcEEEecHH
Confidence 346899999999999886
No 15
>PF12209 SAC3: Leucine permease transcriptional regulator helical domain; InterPro: IPR024293 This domain is found in fungal proteins, including the nuclear mRNA export protein SAC3. It has been suggested this domain provides a scaffold within the yeast Sac3:Cdc31:Sus1:Thp1 (TREX-2) complex to integrate interactions between protein complexes to facilitate the coupling of transcription and mRNA export during gene expression [].; PDB: 3FWC_N 3FWB_B.
Probab=52.46 E-value=26 Score=25.69 Aligned_cols=27 Identities=11% Similarity=0.255 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 030347 12 HSQLSSHFFEDLLDSIIVDVASECHRV 38 (179)
Q Consensus 12 l~~LA~~Iy~dLLddiIlDIv~EvHR~ 38 (179)
++.|++++|+.+|.+++-.+++|+.-.
T Consensus 39 I~sLs~ELy~AFi~E~~Y~~~leskAd 65 (79)
T PF12209_consen 39 IDSLSEELYDAFIHEQLYQIYLESKAD 65 (79)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 678999999999999999999886654
No 16
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=51.85 E-value=5.1 Score=42.05 Aligned_cols=28 Identities=32% Similarity=0.729 Sum_probs=24.9
Q ss_pred eeeCCCCCcccccccchhH--HHhhcCCcc
Q 030347 94 FECMNCGRSIVAGRFAPHL--EKCMGKGRK 121 (179)
Q Consensus 94 ~~C~nC~R~v~a~RfA~HL--ekCmg~gr~ 121 (179)
-.|||||-.|..-|.+-+| |+||-....
T Consensus 9 ~~CpNCGG~isseRL~~glpCe~CLp~~~~ 38 (1187)
T COG1110 9 SSCPNCGGDISSERLEKGLPCERCLPEDTE 38 (1187)
T ss_pred ccCCCCCCcCcHHHHhcCCCchhccCCccc
Confidence 4799999999999999999 899987653
No 17
>PRK14701 reverse gyrase; Provisional
Probab=51.42 E-value=5.6 Score=43.16 Aligned_cols=25 Identities=40% Similarity=0.670 Sum_probs=23.0
Q ss_pred eeeeCCCCCcccccccchhH--HHhhc
Q 030347 93 IFECMNCGRSIVAGRFAPHL--EKCMG 117 (179)
Q Consensus 93 ~~~C~nC~R~v~a~RfA~HL--ekCmg 117 (179)
...||||+-.|..-|.+-.| ++||-
T Consensus 6 ~~~cpnc~g~~~~~rl~~g~~c~~cl~ 32 (1638)
T PRK14701 6 KEMCPNCGGDITDERLAEKGVCEKCLK 32 (1638)
T ss_pred cccCCCCCCccchhHHhcCCCchhhcc
Confidence 45799999999999999999 99996
No 18
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=51.07 E-value=9.3 Score=25.56 Aligned_cols=12 Identities=58% Similarity=1.107 Sum_probs=10.3
Q ss_pred CceeeeCCCCCc
Q 030347 91 NEIFECMNCGRS 102 (179)
Q Consensus 91 ~~~~~C~nC~R~ 102 (179)
...+.||+|+|-
T Consensus 44 ~~i~~Cp~CgRi 55 (56)
T PF02591_consen 44 DEIVFCPNCGRI 55 (56)
T ss_pred CCeEECcCCCcc
Confidence 568999999995
No 19
>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=48.90 E-value=7.3 Score=24.42 Aligned_cols=24 Identities=25% Similarity=0.552 Sum_probs=15.7
Q ss_pred CCceeeeCCCCCccccc-----ccchhHH
Q 030347 90 ANEIFECMNCGRSIVAG-----RFAPHLE 113 (179)
Q Consensus 90 ~~~~~~C~nC~R~v~a~-----RfA~HLe 113 (179)
......|.-|+..+... ++-.||.
T Consensus 13 ~~~~a~C~~C~~~~~~~~~~ts~l~~HL~ 41 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYSSGGTSNLKRHLK 41 (45)
T ss_dssp CSS-EEETTTTEE-----SSTHHHHHHHH
T ss_pred CcCeEEeCCCCeEEeeCCCcHHHHHHhhh
Confidence 45679999999999885 7888883
No 20
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=47.39 E-value=9.5 Score=22.11 Aligned_cols=17 Identities=41% Similarity=0.940 Sum_probs=9.1
Q ss_pred eeeCCCCCcccc-cccch
Q 030347 94 FECMNCGRSIVA-GRFAP 110 (179)
Q Consensus 94 ~~C~nC~R~v~a-~RfA~ 110 (179)
..||+|+..|.. .||-|
T Consensus 3 ~~Cp~Cg~~~~~~~~fC~ 20 (26)
T PF13248_consen 3 MFCPNCGAEIDPDAKFCP 20 (26)
T ss_pred CCCcccCCcCCcccccCh
Confidence 357777776432 34444
No 21
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=46.91 E-value=9.6 Score=26.67 Aligned_cols=23 Identities=30% Similarity=0.804 Sum_probs=11.5
Q ss_pred eeeeCCCCCcccc---cccchhH-HHh
Q 030347 93 IFECMNCGRSIVA---GRFAPHL-EKC 115 (179)
Q Consensus 93 ~~~C~nC~R~v~a---~RfA~HL-ekC 115 (179)
.+.||.|++++.. +.|.|-= +||
T Consensus 2 ~v~CP~C~k~~~~~~~n~~rPFCS~RC 28 (57)
T PF03884_consen 2 TVKCPICGKPVEWSPENPFRPFCSERC 28 (57)
T ss_dssp EEE-TTT--EEE-SSSSS--SSSSHHH
T ss_pred cccCCCCCCeecccCCCCcCCcccHhh
Confidence 4789999999887 5665542 345
No 22
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=46.51 E-value=9.7 Score=21.82 Aligned_cols=11 Identities=45% Similarity=0.899 Sum_probs=9.0
Q ss_pred eeCCCCCcccc
Q 030347 95 ECMNCGRSIVA 105 (179)
Q Consensus 95 ~C~nC~R~v~a 105 (179)
.||+|+.+|..
T Consensus 1 ~Cp~CG~~~~~ 11 (23)
T PF13240_consen 1 YCPNCGAEIED 11 (23)
T ss_pred CCcccCCCCCC
Confidence 49999999864
No 23
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=44.98 E-value=11 Score=29.92 Aligned_cols=24 Identities=38% Similarity=0.768 Sum_probs=15.9
Q ss_pred CceeeeCCCCCccc-ccccchhHHHhhcC
Q 030347 91 NEIFECMNCGRSIV-AGRFAPHLEKCMGK 118 (179)
Q Consensus 91 ~~~~~C~nC~R~v~-a~RfA~HLekCmg~ 118 (179)
...++||||+++-- .+|- +.||-=
T Consensus 67 av~V~CP~C~K~TKmLGr~----D~CM~C 91 (114)
T PF11023_consen 67 AVQVECPNCGKQTKMLGRV----DACMHC 91 (114)
T ss_pred ceeeECCCCCChHhhhchh----hccCcC
Confidence 45789999999752 2332 567754
No 24
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=44.83 E-value=14 Score=26.39 Aligned_cols=17 Identities=35% Similarity=0.720 Sum_probs=12.7
Q ss_pred CCCCCceeeeCCCCCcc
Q 030347 87 PAVANEIFECMNCGRSI 103 (179)
Q Consensus 87 ~~~~~~~~~C~nC~R~v 103 (179)
+.+....|.|||||..+
T Consensus 21 p~e~~v~F~CPnCGe~~ 37 (61)
T COG2888 21 PGETAVKFPCPNCGEVE 37 (61)
T ss_pred cCCceeEeeCCCCCcee
Confidence 44567789999999544
No 25
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 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 C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=43.24 E-value=12 Score=20.17 Aligned_cols=11 Identities=36% Similarity=1.077 Sum_probs=9.1
Q ss_pred eeeCCCCCccc
Q 030347 94 FECMNCGRSIV 104 (179)
Q Consensus 94 ~~C~nC~R~v~ 104 (179)
|.|+.|++...
T Consensus 1 y~C~~C~~~f~ 11 (23)
T PF00096_consen 1 YKCPICGKSFS 11 (23)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCccC
Confidence 68999998764
No 26
>PF02176 zf-TRAF: TRAF-type zinc finger; PDB: 2EOD_A 2YUC_A 3HCU_A 3HCS_B 3HCT_A.
Probab=41.90 E-value=12 Score=24.50 Aligned_cols=26 Identities=31% Similarity=0.589 Sum_probs=20.8
Q ss_pred ceeeeCC--CCCcccccccchhHH-Hhhc
Q 030347 92 EIFECMN--CGRSIVAGRFAPHLE-KCMG 117 (179)
Q Consensus 92 ~~~~C~n--C~R~v~a~RfA~HLe-kCmg 117 (179)
..+.||+ |...|.-..+..|++ .|.-
T Consensus 8 ~~v~C~~~cc~~~i~r~~l~~H~~~~C~~ 36 (60)
T PF02176_consen 8 RPVPCPNGCCNEMIPRKELDDHLENECPK 36 (60)
T ss_dssp SEEE-TT--S-BEEECCCHHHHHHTTSTT
T ss_pred CEeeCCCCCcccceeHHHHHHHHHccCCC
Confidence 3689999 888899999999999 7865
No 27
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=41.06 E-value=12 Score=22.17 Aligned_cols=17 Identities=35% Similarity=1.042 Sum_probs=11.5
Q ss_pred eeCCCCCcccc-cccchh
Q 030347 95 ECMNCGRSIVA-GRFAPH 111 (179)
Q Consensus 95 ~C~nC~R~v~a-~RfA~H 111 (179)
+||+|+..|.. .++-||
T Consensus 2 ~CP~C~~~V~~~~~~Cp~ 19 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPH 19 (26)
T ss_pred cCCCCcCCchhhcCcCCC
Confidence 59999998864 344443
No 28
>PF05253 zf-U11-48K: U11-48K-like CHHC zinc finger; InterPro: IPR022776 This zinc binding domain [] has four conserved zinc chelating residues in a CHHC pattern. This domain is predicted to have an RNA-binding function []. ; PDB: 2VY5_A 2VY4_A.
Probab=39.91 E-value=22 Score=20.88 Aligned_cols=24 Identities=21% Similarity=0.510 Sum_probs=16.9
Q ss_pred eeeeCC-CCCcccccccchhHHHhh
Q 030347 93 IFECMN-CGRSIVAGRFAPHLEKCM 116 (179)
Q Consensus 93 ~~~C~n-C~R~v~a~RfA~HLekCm 116 (179)
++.||. -.=.|...++.-||.+|-
T Consensus 2 ~v~CPyn~~H~v~~~~l~~Hi~~C~ 26 (27)
T PF05253_consen 2 LVRCPYNPSHRVPASELQKHIKKCP 26 (27)
T ss_dssp EEE-TTTSS-EEEGGGHHHHHHHHH
T ss_pred ceeCCCCCCcCcCHHHHHHHHHHcC
Confidence 356663 344788999999999994
No 29
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=38.83 E-value=12 Score=24.09 Aligned_cols=12 Identities=33% Similarity=0.711 Sum_probs=7.6
Q ss_pred eeeeCCCCCccc
Q 030347 93 IFECMNCGRSIV 104 (179)
Q Consensus 93 ~~~C~nC~R~v~ 104 (179)
.+.||+||-.+.
T Consensus 21 ~~~Cp~CG~~~~ 32 (46)
T PRK00398 21 GVRCPYCGYRIL 32 (46)
T ss_pred ceECCCCCCeEE
Confidence 567777776543
No 30
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=38.33 E-value=16 Score=25.74 Aligned_cols=16 Identities=38% Similarity=0.885 Sum_probs=14.0
Q ss_pred eeeeCCCCCccccccc
Q 030347 93 IFECMNCGRSIVAGRF 108 (179)
Q Consensus 93 ~~~C~nC~R~v~a~Rf 108 (179)
-+.|..|+|.|-..|.
T Consensus 31 kikC~gCg~~imlpR~ 46 (57)
T PF06107_consen 31 KIKCLGCGRQIMLPRS 46 (57)
T ss_pred EEEECCCCCEEEEeHH
Confidence 5789999999998874
No 31
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=37.43 E-value=22 Score=25.22 Aligned_cols=13 Identities=38% Similarity=0.766 Sum_probs=10.8
Q ss_pred CCceeeeCCCCCc
Q 030347 90 ANEIFECMNCGRS 102 (179)
Q Consensus 90 ~~~~~~C~nC~R~ 102 (179)
....|.|||||..
T Consensus 22 ~~~~F~CPnCG~~ 34 (59)
T PRK14890 22 KAVKFLCPNCGEV 34 (59)
T ss_pred ccCEeeCCCCCCe
Confidence 3568999999986
No 32
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=37.41 E-value=12 Score=30.34 Aligned_cols=29 Identities=24% Similarity=0.541 Sum_probs=24.1
Q ss_pred eeeeCCCCCcccccccchhHHHhhcCCccc
Q 030347 93 IFECMNCGRSIVAGRFAPHLEKCMGKGRKA 122 (179)
Q Consensus 93 ~~~C~nC~R~v~a~RfA~HLekCmg~gr~s 122 (179)
.+.|.+|+..+.... +.+|..|-.=|...
T Consensus 112 ~l~C~~Cg~~~~~~~-~~~l~~Cp~C~~~~ 140 (146)
T PF07295_consen 112 TLVCENCGHEVELTH-PERLPPCPKCGHTE 140 (146)
T ss_pred eEecccCCCEEEecC-CCcCCCCCCCCCCe
Confidence 699999999999985 88999987766543
No 33
>TIGR01054 rgy reverse gyrase. Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.
Probab=36.11 E-value=12 Score=39.33 Aligned_cols=25 Identities=32% Similarity=0.666 Sum_probs=22.8
Q ss_pred eeeeCCCCCcccccccchhH--HHhhc
Q 030347 93 IFECMNCGRSIVAGRFAPHL--EKCMG 117 (179)
Q Consensus 93 ~~~C~nC~R~v~a~RfA~HL--ekCmg 117 (179)
...|||||-.|..-|..-.| +|||.
T Consensus 7 ~~~CPnCgg~i~~~rl~~~~~c~~Clp 33 (1171)
T TIGR01054 7 SNLCPNCGGEISSERLEKGLPCARCLP 33 (1171)
T ss_pred cCCCCCCCCccchhHhhcCCCccccCc
Confidence 45799999999999999988 89997
No 34
>PRK09401 reverse gyrase; Reviewed
Probab=35.70 E-value=13 Score=39.05 Aligned_cols=25 Identities=40% Similarity=0.741 Sum_probs=21.3
Q ss_pred eeeeCCCCCcccccccchhH--HHhhc
Q 030347 93 IFECMNCGRSIVAGRFAPHL--EKCMG 117 (179)
Q Consensus 93 ~~~C~nC~R~v~a~RfA~HL--ekCmg 117 (179)
...|||||..|..-|..--| ++||-
T Consensus 7 ~~~cpnc~g~i~~~rl~~g~~c~~cl~ 33 (1176)
T PRK09401 7 KNSCPNCGGDISDERLEKGLPCEKCLP 33 (1176)
T ss_pred cccCCCCCCcCcHhHHhcCCcChhhCC
Confidence 45799999999999988765 77997
No 35
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=35.22 E-value=15 Score=24.30 Aligned_cols=14 Identities=29% Similarity=0.543 Sum_probs=7.9
Q ss_pred eeCCCCCccccccc
Q 030347 95 ECMNCGRSIVAGRF 108 (179)
Q Consensus 95 ~C~nC~R~v~a~Rf 108 (179)
.||.|+|.+.-...
T Consensus 22 ~CPlC~r~l~~e~~ 35 (54)
T PF04423_consen 22 CCPLCGRPLDEEHR 35 (54)
T ss_dssp E-TTT--EE-HHHH
T ss_pred cCCCCCCCCCHHHH
Confidence 89999999876554
No 36
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=33.88 E-value=22 Score=29.42 Aligned_cols=17 Identities=29% Similarity=0.448 Sum_probs=12.9
Q ss_pred CCCceeeeCCCCCcccc
Q 030347 89 VANEIFECMNCGRSIVA 105 (179)
Q Consensus 89 ~~~~~~~C~nC~R~v~a 105 (179)
..+++|.||+|++.+..
T Consensus 113 ~~~~~Y~Cp~C~~rytf 129 (178)
T PRK06266 113 ENNMFFFCPNCHIRFTF 129 (178)
T ss_pred cCCCEEECCCCCcEEeH
Confidence 45678999999976643
No 37
>PF14353 CpXC: CpXC protein
Probab=32.74 E-value=23 Score=26.93 Aligned_cols=13 Identities=31% Similarity=0.812 Sum_probs=11.1
Q ss_pred eeeeCCCCCcccc
Q 030347 93 IFECMNCGRSIVA 105 (179)
Q Consensus 93 ~~~C~nC~R~v~a 105 (179)
.++||+||..+..
T Consensus 38 ~~~CP~Cg~~~~~ 50 (128)
T PF14353_consen 38 SFTCPSCGHKFRL 50 (128)
T ss_pred EEECCCCCCceec
Confidence 6899999998754
No 38
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=32.30 E-value=25 Score=27.78 Aligned_cols=17 Identities=24% Similarity=0.491 Sum_probs=12.9
Q ss_pred CCceeeeCCCCCccccc
Q 030347 90 ANEIFECMNCGRSIVAG 106 (179)
Q Consensus 90 ~~~~~~C~nC~R~v~a~ 106 (179)
.+..+.||+|+..+.+.
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ 112 (147)
T smart00531 96 NNAYYKCPNCQSKYTFL 112 (147)
T ss_pred CCcEEECcCCCCEeeHH
Confidence 46688899998877753
No 39
>PF10601 zf-LITAF-like: LITAF-like zinc ribbon domain; InterPro: IPR006629 Members of this family display a conserved zinc ribbon structure [] with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure [].
Probab=31.34 E-value=29 Score=24.19 Aligned_cols=17 Identities=24% Similarity=0.456 Sum_probs=13.9
Q ss_pred CceeeeCCCCCcccccc
Q 030347 91 NEIFECMNCGRSIVAGR 107 (179)
Q Consensus 91 ~~~~~C~nC~R~v~a~R 107 (179)
..+..||+|++.|+.-+
T Consensus 56 d~~H~Cp~C~~~lg~~~ 72 (73)
T PF10601_consen 56 DVYHYCPNCGAFLGTYK 72 (73)
T ss_pred CceEECCCCCCEeEEEe
Confidence 56799999999987654
No 40
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=30.73 E-value=20 Score=24.69 Aligned_cols=16 Identities=31% Similarity=0.758 Sum_probs=12.4
Q ss_pred CCceeeeCCCCCcccc
Q 030347 90 ANEIFECMNCGRSIVA 105 (179)
Q Consensus 90 ~~~~~~C~nC~R~v~a 105 (179)
...|..||+|+-+...
T Consensus 10 ~~kY~~Cp~CGN~~vG 25 (49)
T PF12677_consen 10 SNKYCKCPKCGNDKVG 25 (49)
T ss_pred hhhhccCcccCCcEee
Confidence 3569999999987644
No 41
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=30.46 E-value=28 Score=28.18 Aligned_cols=16 Identities=25% Similarity=0.326 Sum_probs=11.8
Q ss_pred CCCceeeeCCCCCccc
Q 030347 89 VANEIFECMNCGRSIV 104 (179)
Q Consensus 89 ~~~~~~~C~nC~R~v~ 104 (179)
..++++.||+|++.+.
T Consensus 105 ~~~~~Y~Cp~c~~r~t 120 (158)
T TIGR00373 105 TNNMFFICPNMCVRFT 120 (158)
T ss_pred cCCCeEECCCCCcEee
Confidence 3567888999987653
No 42
>KOG2186 consensus Cell growth-regulating nucleolar protein [Cell cycle control, cell division, chromosome partitioning]
Probab=30.38 E-value=22 Score=32.02 Aligned_cols=27 Identities=30% Similarity=0.837 Sum_probs=22.7
Q ss_pred CCceeeeCCCCCcccccccchhHHHhhc
Q 030347 90 ANEIFECMNCGRSIVAGRFAPHLEKCMG 117 (179)
Q Consensus 90 ~~~~~~C~nC~R~v~a~RfA~HLekCmg 117 (179)
.+.+|.|+-|+..+--.-|--|. +||.
T Consensus 26 rn~~fSCIDC~k~F~~~sYknH~-kCIT 52 (276)
T KOG2186|consen 26 RNAYFSCIDCGKTFERVSYKNHT-KCIT 52 (276)
T ss_pred cCCeeEEeecccccccchhhhhh-hhcc
Confidence 46899999999999888888886 6875
No 43
>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=29.95 E-value=36 Score=20.69 Aligned_cols=14 Identities=29% Similarity=0.562 Sum_probs=10.9
Q ss_pred ceeeeCCCCCcccc
Q 030347 92 EIFECMNCGRSIVA 105 (179)
Q Consensus 92 ~~~~C~nC~R~v~a 105 (179)
..+.|++|+..+-+
T Consensus 24 ~~v~C~~C~~~~~~ 37 (38)
T TIGR02098 24 GKVRCGKCGHVWYA 37 (38)
T ss_pred CEEECCCCCCEEEe
Confidence 36999999987643
No 44
>KOG3940 consensus Uncharacterized conserved protein [Function unknown]
Probab=29.56 E-value=25 Score=32.61 Aligned_cols=33 Identities=24% Similarity=0.523 Sum_probs=25.5
Q ss_pred CCCCCceeeeCCCCCcccccccchhHHHhhcCC
Q 030347 87 PAVANEIFECMNCGRSIVAGRFAPHLEKCMGKG 119 (179)
Q Consensus 87 ~~~~~~~~~C~nC~R~v~a~RfA~HLekCmg~g 119 (179)
+.+...|..||.|+|...---.|-|+-||-.|.
T Consensus 316 gse~~s~~~Cp~cg~r~~~~~~ak~~~~c~~r~ 348 (351)
T KOG3940|consen 316 GSENPSYVQCPHCGRRFNEQAAAKHIPKCVNRV 348 (351)
T ss_pred CCCCCCcccCccccccchHHHHHhhcccccccc
Confidence 345666899999999877666678889997763
No 45
>PRK02935 hypothetical protein; Provisional
Probab=28.74 E-value=30 Score=27.34 Aligned_cols=13 Identities=15% Similarity=0.424 Sum_probs=10.1
Q ss_pred CceeeeCCCCCcc
Q 030347 91 NEIFECMNCGRSI 103 (179)
Q Consensus 91 ~~~~~C~nC~R~v 103 (179)
...++||+|+++.
T Consensus 68 avqV~CP~C~K~T 80 (110)
T PRK02935 68 AVQVICPSCEKPT 80 (110)
T ss_pred ceeeECCCCCchh
Confidence 3468999999864
No 46
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=28.14 E-value=26 Score=24.60 Aligned_cols=13 Identities=31% Similarity=0.713 Sum_probs=11.1
Q ss_pred eeeCCCCCccccc
Q 030347 94 FECMNCGRSIVAG 106 (179)
Q Consensus 94 ~~C~nC~R~v~a~ 106 (179)
-.|++||.+|...
T Consensus 4 kHC~~CG~~Ip~~ 16 (59)
T PF09889_consen 4 KHCPVCGKPIPPD 16 (59)
T ss_pred CcCCcCCCcCCcc
Confidence 4799999999865
No 47
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=28.09 E-value=30 Score=24.66 Aligned_cols=25 Identities=24% Similarity=0.736 Sum_probs=17.3
Q ss_pred ceeeeCCCCCccc---ccccchhH-HHhh
Q 030347 92 EIFECMNCGRSIV---AGRFAPHL-EKCM 116 (179)
Q Consensus 92 ~~~~C~nC~R~v~---a~RfA~HL-ekCm 116 (179)
..+.||.|+++|. .+.|-|-= +||-
T Consensus 5 ~~v~CP~C~k~~~w~~~~~~rPFCS~RCk 33 (62)
T PRK00418 5 ITVNCPTCGKPVEWGEISPFRPFCSKRCQ 33 (62)
T ss_pred ccccCCCCCCcccccCCCCcCCcccHHHH
Confidence 3578999999985 46676653 3353
No 48
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=26.91 E-value=26 Score=24.14 Aligned_cols=14 Identities=43% Similarity=0.899 Sum_probs=11.0
Q ss_pred eeeeCCCCCccccc
Q 030347 93 IFECMNCGRSIVAG 106 (179)
Q Consensus 93 ~~~C~nC~R~v~a~ 106 (179)
.|+||.|+..|...
T Consensus 2 ~~~CP~CG~~iev~ 15 (54)
T TIGR01206 2 QFECPDCGAEIELE 15 (54)
T ss_pred ccCCCCCCCEEecC
Confidence 47899999988654
No 49
>PF12773 DZR: Double zinc ribbon
Probab=26.64 E-value=35 Score=21.77 Aligned_cols=12 Identities=25% Similarity=0.600 Sum_probs=8.6
Q ss_pred eeeeCCCCCccc
Q 030347 93 IFECMNCGRSIV 104 (179)
Q Consensus 93 ~~~C~nC~R~v~ 104 (179)
.-.|++|+.++.
T Consensus 12 ~~fC~~CG~~l~ 23 (50)
T PF12773_consen 12 AKFCPHCGTPLP 23 (50)
T ss_pred ccCChhhcCChh
Confidence 356888887776
No 50
>PF11113 Phage_head_chap: Head assembly gene product; InterPro: IPR021049 This head assembly protein is also refereed to as gene product 40 (Gp40). A specific gp20-gp40 membrane insertion structure constitutes the T4 prohead assembly initiation complex [].
Probab=26.53 E-value=27 Score=24.57 Aligned_cols=12 Identities=50% Similarity=1.099 Sum_probs=9.8
Q ss_pred ccchhHHHhhcC
Q 030347 107 RFAPHLEKCMGK 118 (179)
Q Consensus 107 RfA~HLekCmg~ 118 (179)
-.|||.++|+-+
T Consensus 43 el~phVe~ci~~ 54 (56)
T PF11113_consen 43 ELAPHVEKCIQA 54 (56)
T ss_pred HHHHHHHHHHhh
Confidence 368999999864
No 51
>PF14577 SEO_C: Sieve element occlusion C-terminus
Probab=26.31 E-value=33 Score=30.19 Aligned_cols=13 Identities=38% Similarity=0.920 Sum_probs=11.3
Q ss_pred ceeeeCCCCCccc
Q 030347 92 EIFECMNCGRSIV 104 (179)
Q Consensus 92 ~~~~C~nC~R~v~ 104 (179)
..+.||+|+|++-
T Consensus 213 e~i~CpeC~R~ME 225 (235)
T PF14577_consen 213 ETIVCPECGRPME 225 (235)
T ss_pred ceeECCCCCCchh
Confidence 4689999999986
No 52
>PRK01343 zinc-binding protein; Provisional
Probab=25.93 E-value=49 Score=23.26 Aligned_cols=19 Identities=21% Similarity=0.481 Sum_probs=13.6
Q ss_pred CceeeeCCCCCcccccccch
Q 030347 91 NEIFECMNCGRSIVAGRFAP 110 (179)
Q Consensus 91 ~~~~~C~nC~R~v~a~RfA~ 110 (179)
.....||.|++++. ..|-|
T Consensus 7 ~p~~~CP~C~k~~~-~~~rP 25 (57)
T PRK01343 7 RPTRPCPECGKPST-REAYP 25 (57)
T ss_pred CCCCcCCCCCCcCc-CCCCc
Confidence 45689999999976 33444
No 53
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=25.84 E-value=34 Score=27.58 Aligned_cols=26 Identities=38% Similarity=0.834 Sum_probs=21.8
Q ss_pred CCceeeeCCCCCcccccccchhHHHhhcC
Q 030347 90 ANEIFECMNCGRSIVAGRFAPHLEKCMGK 118 (179)
Q Consensus 90 ~~~~~~C~nC~R~v~a~RfA~HLekCmg~ 118 (179)
.+....|..||.+|-.+||.+ +|...
T Consensus 78 ~nl~~~CE~CG~~I~~Gr~C~---~C~~~ 103 (137)
T TIGR03826 78 PNLGYPCERCGTSIREGRLCD---SCAGE 103 (137)
T ss_pred CCCcCcccccCCcCCCCCccH---HHHHH
Confidence 467899999999999999985 67653
No 54
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=25.75 E-value=32 Score=19.65 Aligned_cols=11 Identities=36% Similarity=1.071 Sum_probs=9.2
Q ss_pred eeeeCCCCCcc
Q 030347 93 IFECMNCGRSI 103 (179)
Q Consensus 93 ~~~C~nC~R~v 103 (179)
.|.|+.|++..
T Consensus 14 ~~~C~~C~k~F 24 (26)
T PF13465_consen 14 PYKCPYCGKSF 24 (26)
T ss_dssp SEEESSSSEEE
T ss_pred CCCCCCCcCee
Confidence 49999999864
No 55
>PF10609 ParA: ParA/MinD ATPase like; InterPro: IPR019591 This entry represents ATPases involved in plasmid partitioning []. It also contains cytosolic Fe-S cluster assembling factors, NBP35 and CFD1 which are required for biogenesis and export of both ribosomal subunits probably through assembling the ISCs in RLI1, a protein which performs rRNA processing and ribosome export [, , ].; PDB: 2PH1_A 3KB1_B.
Probab=24.61 E-value=34 Score=25.35 Aligned_cols=24 Identities=33% Similarity=0.602 Sum_probs=12.9
Q ss_pred ccceeCccCCCCCCceeeeCCCCCccc
Q 030347 78 VVDIFGQTHPAVANEIFECMNCGRSIV 104 (179)
Q Consensus 78 ~~DIfG~~~~~~~~~~~~C~nC~R~v~ 104 (179)
++.|-|-. +.-.+|.||.|+..+.
T Consensus 53 ~vpilGvV---ENMs~~~Cp~Cg~~~~ 76 (81)
T PF10609_consen 53 NVPILGVV---ENMSYFVCPHCGERIY 76 (81)
T ss_dssp T-EEEEEE---ECT-EEE-TTT--EEE
T ss_pred CCCcEEEE---ECCCccCCCCCCCeec
Confidence 45566654 3456999999998653
No 56
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=24.53 E-value=37 Score=26.01 Aligned_cols=11 Identities=55% Similarity=1.364 Sum_probs=9.1
Q ss_pred CceeeeCCCCC
Q 030347 91 NEIFECMNCGR 101 (179)
Q Consensus 91 ~~~~~C~nC~R 101 (179)
..+|.||+|+-
T Consensus 19 pt~f~CP~Cge 29 (99)
T PRK14892 19 PKIFECPRCGK 29 (99)
T ss_pred CcEeECCCCCC
Confidence 35899999994
No 57
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=23.91 E-value=33 Score=22.90 Aligned_cols=15 Identities=40% Similarity=1.001 Sum_probs=10.0
Q ss_pred eeeCCCCC-ccccccc
Q 030347 94 FECMNCGR-SIVAGRF 108 (179)
Q Consensus 94 ~~C~nC~R-~v~a~Rf 108 (179)
+.|.+|++ +|...||
T Consensus 1 y~Cd~C~~~pI~G~R~ 16 (48)
T cd02341 1 FKCDSCGIEPIPGTRY 16 (48)
T ss_pred CCCCCCCCCccccceE
Confidence 35777776 6766666
No 58
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=23.03 E-value=65 Score=30.87 Aligned_cols=13 Identities=46% Similarity=1.043 Sum_probs=10.4
Q ss_pred ceeeeCCCCCccc
Q 030347 92 EIFECMNCGRSIV 104 (179)
Q Consensus 92 ~~~~C~nC~R~v~ 104 (179)
..|.|.+|+-.|-
T Consensus 152 ~~F~C~~C~gelv 164 (436)
T KOG2593|consen 152 GEFHCENCGGELV 164 (436)
T ss_pred ceEEEecCCCchh
Confidence 4799999987764
No 59
>PF05304 DUF728: Protein of unknown function (DUF728); InterPro: IPR007968 This entry is represented by the Tobacco rattle virus, 16kDa protein; it is a family of uncharacterised viral proteins.
Probab=22.74 E-value=46 Score=25.86 Aligned_cols=26 Identities=42% Similarity=0.621 Sum_probs=18.2
Q ss_pred eeeeCCCCCccccccc-----------chhHHHhhcC
Q 030347 93 IFECMNCGRSIVAGRF-----------APHLEKCMGK 118 (179)
Q Consensus 93 ~~~C~nC~R~v~a~Rf-----------A~HLekCmg~ 118 (179)
-++|.|||--+++.-- -.|||||-..
T Consensus 39 kC~~~NCGWf~~i~v~~~~~eVY~CCg~~HL~Kc~s~ 75 (103)
T PF05304_consen 39 KCECNNCGWFPAISVNDDTFEVYFCCGMKHLEKCRSK 75 (103)
T ss_pred hhhccCCCceEEEEEeccEEeeeeecCHHHHHHHhcC
Confidence 4788888876655432 2699999854
No 60
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=22.67 E-value=44 Score=17.18 Aligned_cols=20 Identities=30% Similarity=0.796 Sum_probs=10.8
Q ss_pred eeeCCCCCccc-ccccchhHH
Q 030347 94 FECMNCGRSIV-AGRFAPHLE 113 (179)
Q Consensus 94 ~~C~nC~R~v~-a~RfA~HLe 113 (179)
|.|+.|+.... ...+..|+.
T Consensus 1 ~~C~~C~~~~~~~~~l~~H~~ 21 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELRQHMR 21 (24)
T ss_dssp EE-SSTS-EESSHHHHHHHHH
T ss_pred CCCcCCCCcCCcHHHHHHHHH
Confidence 67999998654 334445544
No 61
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=22.06 E-value=40 Score=21.79 Aligned_cols=14 Identities=36% Similarity=0.726 Sum_probs=7.5
Q ss_pred eeCCCCCccccccc
Q 030347 95 ECMNCGRSIVAGRF 108 (179)
Q Consensus 95 ~C~nC~R~v~a~Rf 108 (179)
.|..|+++|...||
T Consensus 2 ~Cd~C~~~i~G~ry 15 (43)
T cd02340 2 ICDGCQGPIVGVRY 15 (43)
T ss_pred CCCCCCCcCcCCeE
Confidence 35555555555554
No 62
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=22.01 E-value=36 Score=29.95 Aligned_cols=14 Identities=43% Similarity=0.883 Sum_probs=11.5
Q ss_pred CCceeeeCCCCCcc
Q 030347 90 ANEIFECMNCGRSI 103 (179)
Q Consensus 90 ~~~~~~C~nC~R~v 103 (179)
....+.||.|||-+
T Consensus 218 ~d~iv~CP~CgRIL 231 (239)
T COG1579 218 KDEIVFCPYCGRIL 231 (239)
T ss_pred CCCCccCCccchHH
Confidence 56789999999954
No 63
>PF08790 zf-LYAR: LYAR-type C2HC zinc finger ; InterPro: IPR014898 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 C2HC zinc finger domain is found in LYAR proteins such as Q08288 from SWISSPROT, which are involved in cell growth regulation. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1WJV_A.
Probab=21.93 E-value=53 Score=20.06 Aligned_cols=23 Identities=22% Similarity=0.866 Sum_probs=16.1
Q ss_pred eeeCCCCCcccccccchhHHHhhc
Q 030347 94 FECMNCGRSIVAGRFAPHLEKCMG 117 (179)
Q Consensus 94 ~~C~nC~R~v~a~RfA~HLekCmg 117 (179)
|.|..|+..+...-|..|- +|+.
T Consensus 1 ~sCiDC~~~F~~~~y~~Ht-~CIt 23 (28)
T PF08790_consen 1 FSCIDCSKDFDGDSYKSHT-SCIT 23 (28)
T ss_dssp EEETTTTEEEEGGGTTT------S
T ss_pred CeeecCCCCcCcCCcCCCC-cccC
Confidence 6899999999999999995 4553
No 64
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=21.76 E-value=41 Score=22.42 Aligned_cols=12 Identities=33% Similarity=0.647 Sum_probs=10.0
Q ss_pred eeeeCCCCCccc
Q 030347 93 IFECMNCGRSIV 104 (179)
Q Consensus 93 ~~~C~nC~R~v~ 104 (179)
.-.|+.|+|++.
T Consensus 8 ~K~C~~C~rpf~ 19 (42)
T PF10013_consen 8 SKICPVCGRPFT 19 (42)
T ss_pred CCcCcccCCcch
Confidence 457999999985
No 65
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=21.59 E-value=57 Score=23.73 Aligned_cols=14 Identities=21% Similarity=0.897 Sum_probs=10.2
Q ss_pred CceeeeCCCCCccc
Q 030347 91 NEIFECMNCGRSIV 104 (179)
Q Consensus 91 ~~~~~C~nC~R~v~ 104 (179)
+..+.|+.|++-++
T Consensus 36 st~V~C~~CG~~l~ 49 (67)
T COG2051 36 STVVTCLICGTTLA 49 (67)
T ss_pred ceEEEecccccEEE
Confidence 45678888888765
No 66
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 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 a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=21.58 E-value=45 Score=21.08 Aligned_cols=10 Identities=40% Similarity=1.032 Sum_probs=6.5
Q ss_pred eeeCCCCCcc
Q 030347 94 FECMNCGRSI 103 (179)
Q Consensus 94 ~~C~nC~R~v 103 (179)
+.||+|+..-
T Consensus 1 m~Cp~Cg~~~ 10 (43)
T PF08271_consen 1 MKCPNCGSKE 10 (43)
T ss_dssp ESBTTTSSSE
T ss_pred CCCcCCcCCc
Confidence 4677777653
No 67
>PF03847 TFIID_20kDa: Transcription initiation factor TFIID subunit A; InterPro: IPR003228 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription [].; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_B.
Probab=21.42 E-value=2.1e+02 Score=20.30 Aligned_cols=34 Identities=24% Similarity=0.255 Sum_probs=19.5
Q ss_pred CCcchHHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 030347 7 DNMSAHSQLSSHFFEDLLDSIIVDVASECHRVAR 40 (179)
Q Consensus 7 d~~s~l~~LA~~Iy~dLLddiIlDIv~EvHR~~K 40 (179)
|....++.-+++++-+|.|+.|-+++-..=+.+|
T Consensus 13 Dp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAK 46 (68)
T PF03847_consen 13 DPNEKLDPDVEELLLELADDFVDDVVSFACRLAK 46 (68)
T ss_dssp -SS----HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4555666667777777777777777665555555
No 68
>PF11687 DUF3284: Domain of unknown function (DUF3284); InterPro: IPR021701 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=20.86 E-value=96 Score=23.76 Aligned_cols=23 Identities=26% Similarity=0.587 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhh
Q 030347 16 SSHFFEDLLDSIIVDVASECHRV 38 (179)
Q Consensus 16 A~~Iy~dLLddiIlDIv~EvHR~ 38 (179)
|.+||+-|+++++.||-..+.+.
T Consensus 11 a~~ff~~l~~s~~~DI~~~tgk~ 33 (120)
T PF11687_consen 11 AEEFFDYLIDSLLYDIKQATGKK 33 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHcCCC
Confidence 68999999999999998877764
No 69
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=20.42 E-value=58 Score=22.34 Aligned_cols=16 Identities=25% Similarity=0.384 Sum_probs=12.9
Q ss_pred CceeeeCCCCCccccc
Q 030347 91 NEIFECMNCGRSIVAG 106 (179)
Q Consensus 91 ~~~~~C~nC~R~v~a~ 106 (179)
..+..||+|++.|+.-
T Consensus 50 d~~H~Cp~C~~~lg~~ 65 (67)
T smart00714 50 DVNHYCPNCGAFLGTY 65 (67)
T ss_pred CccEECCCCCCEeEEe
Confidence 5579999999988753
No 70
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=20.04 E-value=1.8e+02 Score=23.33 Aligned_cols=33 Identities=9% Similarity=0.236 Sum_probs=24.6
Q ss_pred CCcchHHHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 030347 7 DNMSAHSQLSSHFFEDLLDSIIVDVASECHRVAR 40 (179)
Q Consensus 7 d~~s~l~~LA~~Iy~dLLddiIlDIv~EvHR~~K 40 (179)
|.+.++-. +-+.+++++-+.+.++|.+.|+.+.
T Consensus 24 Dvv~P~~d-t~~~L~e~V~dY~~~~ctna~~~Aq 56 (126)
T COG5248 24 DVVAPRYD-TAEALHEYVLDYMSILCTNAHNMAQ 56 (126)
T ss_pred CCCCcchh-HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444444 4567888888999999999999764
Done!