Query 034621
Match_columns 89
No_of_seqs 102 out of 277
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 04:45:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/034621.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/034621hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF04968 CHORD: CHORD ; Inter 99.8 2.7E-20 5.9E-25 113.5 1.7 55 13-84 2-64 (64)
2 KOG1667 Zn2+-binding protein M 99.6 1.9E-16 4.1E-21 118.7 2.6 57 13-86 2-66 (320)
3 KOG1667 Zn2+-binding protein M 99.5 2E-14 4.4E-19 107.9 2.7 60 9-85 139-206 (320)
4 PF00779 BTK: BTK motif; Inte 98.0 3.3E-06 7.2E-11 45.1 1.2 18 63-80 11-28 (32)
5 smart00107 BTK Bruton's tyrosi 97.9 8.7E-06 1.9E-10 44.5 2.2 18 63-80 16-33 (36)
6 PF11822 DUF3342: Domain of un 95.8 0.0062 1.3E-07 47.1 2.4 50 12-71 261-312 (317)
7 KOG2059 Ras GTPase-activating 82.8 0.82 1.8E-05 39.2 1.9 50 10-80 642-699 (800)
8 PF13717 zinc_ribbon_4: zinc-r 78.4 1 2.3E-05 24.0 0.8 20 3-22 16-35 (36)
9 PF09538 FYDLN_acid: Protein o 71.4 2.2 4.8E-05 28.2 1.1 33 7-39 4-36 (108)
10 PF13719 zinc_ribbon_5: zinc-r 67.9 3 6.5E-05 22.2 1.0 17 6-22 19-35 (37)
11 PF13913 zf-C2HC_2: zinc-finge 67.4 2.3 4.9E-05 20.9 0.4 14 12-25 2-15 (25)
12 TIGR02300 FYDLN_acid conserved 66.1 3.6 7.8E-05 28.3 1.3 32 8-39 5-36 (129)
13 PF13912 zf-C2H2_6: C2H2-type 59.8 4 8.6E-05 19.5 0.5 13 13-25 2-14 (27)
14 PF03604 DNA_RNApol_7kD: DNA d 59.1 6.9 0.00015 20.5 1.4 23 14-36 2-24 (32)
15 smart00659 RPOLCX RNA polymera 55.9 5.8 0.00013 22.1 0.8 26 12-38 2-27 (44)
16 PRK00398 rpoP DNA-directed RNA 55.6 5.7 0.00012 21.8 0.7 27 12-38 3-30 (46)
17 PF00096 zf-C2H2: Zinc finger, 51.6 6.2 0.00013 18.0 0.4 12 14-25 2-13 (23)
18 PF13465 zf-H2C2_2: Zinc-finge 47.0 9.5 0.00021 18.5 0.6 14 10-23 12-25 (26)
19 TIGR02098 MJ0042_CXXC MJ0042 f 46.7 9.8 0.00021 19.8 0.7 13 13-25 3-15 (38)
20 PF10080 DUF2318: Predicted me 41.6 15 0.00032 24.1 1.1 31 8-38 48-80 (102)
21 COG1996 RPC10 DNA-directed RNA 40.7 11 0.00025 21.7 0.4 29 10-38 4-33 (49)
22 PF05191 ADK_lid: Adenylate ki 40.1 15 0.00033 19.5 0.8 16 13-28 2-17 (36)
23 PF08790 zf-LYAR: LYAR-type C2 38.4 19 0.00041 18.5 1.0 19 14-32 2-21 (28)
24 PF13894 zf-C2H2_4: C2H2-type 36.3 16 0.00034 16.1 0.4 11 14-24 2-12 (24)
25 PF05766 NinG: Bacteriophage L 35.4 18 0.0004 26.2 0.9 30 9-38 3-32 (189)
26 PF10571 UPF0547: Uncharacteri 33.9 18 0.00038 18.0 0.4 15 9-23 11-25 (26)
27 PRK00564 hypA hydrogenase nick 33.5 19 0.00041 23.7 0.7 27 6-32 65-91 (117)
28 COG4888 Uncharacterized Zn rib 33.4 20 0.00043 23.8 0.7 23 5-27 39-61 (104)
29 PF13878 zf-C2H2_3: zinc-finge 32.3 27 0.00058 18.9 1.0 15 12-26 13-27 (41)
30 PF06170 DUF983: Protein of un 32.2 24 0.00052 22.3 0.9 17 12-28 8-24 (86)
31 PRK03681 hypA hydrogenase nick 31.9 24 0.00053 23.1 1.0 27 7-33 65-91 (114)
32 TIGR03831 YgiT_finger YgiT-typ 31.3 24 0.00052 18.5 0.7 16 10-25 30-45 (46)
33 PHA02768 hypothetical protein; 30.2 16 0.00035 21.5 -0.1 25 12-36 5-29 (55)
34 PF04032 Rpr2: RNAse P Rpr2/Rp 29.7 30 0.00065 20.7 1.0 19 10-28 44-62 (85)
35 PF01155 HypA: Hydrogenase exp 29.6 16 0.00035 23.8 -0.2 22 7-28 65-86 (113)
36 PF04997 RNA_pol_Rpb1_1: RNA p 29.5 15 0.00033 26.4 -0.3 28 13-52 55-82 (337)
37 PF13451 zf-trcl: Probable zin 29.2 26 0.00056 20.2 0.6 13 11-23 3-15 (49)
38 TIGR02605 CxxC_CxxC_SSSS putat 29.1 26 0.00056 19.3 0.6 14 12-25 5-18 (52)
39 PF10013 DUF2256: Uncharacteri 29.0 26 0.00056 19.6 0.6 17 7-23 3-19 (42)
40 PF03966 Trm112p: Trm112p-like 28.6 26 0.00056 20.7 0.6 17 8-24 49-65 (68)
41 PF10853 DUF2650: Protein of u 27.1 40 0.00088 18.4 1.1 9 63-71 8-16 (38)
42 PF08792 A2L_zn_ribbon: A2L zi 26.7 33 0.00071 17.9 0.7 16 8-23 17-32 (33)
43 PF01286 XPA_N: XPA protein N- 26.5 30 0.00065 18.4 0.6 14 12-25 3-16 (34)
44 PF10892 DUF2688: Protein of u 26.4 21 0.00046 21.3 -0.0 15 9-23 7-21 (60)
45 TIGR03829 YokU_near_AblA uncha 26.4 22 0.00049 22.8 0.0 20 7-26 30-49 (89)
46 cd00350 rubredoxin_like Rubred 26.0 48 0.001 16.9 1.3 14 13-26 2-15 (33)
47 TIGR00100 hypA hydrogenase nic 26.0 31 0.00067 22.6 0.7 22 6-27 64-85 (115)
48 PF09723 Zn-ribbon_8: Zinc rib 26.0 31 0.00067 18.6 0.6 15 12-26 5-19 (42)
49 smart00614 ZnF_BED BED zinc fi 25.0 38 0.00083 18.7 0.9 16 11-26 17-32 (50)
50 PHA00616 hypothetical protein 24.5 20 0.00044 20.1 -0.4 26 13-38 2-27 (44)
51 cd00729 rubredoxin_SM Rubredox 24.3 57 0.0012 16.9 1.4 19 13-32 3-21 (34)
52 PF03668 ATP_bind_2: P-loop AT 24.0 22 0.00047 27.3 -0.4 12 75-86 246-257 (284)
53 PRK12380 hydrogenase nickel in 23.9 41 0.0009 22.0 1.0 22 6-27 64-85 (113)
54 PF05129 Elf1: Transcription e 23.4 33 0.00072 21.3 0.4 21 7-27 41-61 (81)
55 PHA00689 hypothetical protein 23.0 31 0.00067 20.3 0.2 12 10-21 15-26 (62)
56 COG4049 Uncharacterized protei 22.9 25 0.00054 21.2 -0.2 16 10-25 15-30 (65)
57 COG1660 Predicted P-loop-conta 22.8 25 0.00055 27.1 -0.3 12 75-86 247-258 (286)
58 TIGR03826 YvyF flagellar opero 22.8 35 0.00076 23.4 0.5 14 11-24 2-15 (137)
59 COG3357 Predicted transcriptio 22.2 48 0.001 21.7 1.0 24 12-35 58-82 (97)
60 PF14446 Prok-RING_1: Prokaryo 22.1 38 0.00082 19.9 0.5 28 7-34 16-44 (54)
61 PHA00626 hypothetical protein 22.0 42 0.00091 20.1 0.6 20 7-26 18-37 (59)
62 smart00834 CxxC_CXXC_SSSS Puta 21.4 46 0.001 17.1 0.7 15 12-26 5-19 (41)
63 smart00132 LIM Zinc-binding do 21.0 42 0.00091 16.4 0.4 26 14-39 1-28 (39)
64 COG1773 Rubredoxin [Energy pro 21.0 59 0.0013 19.1 1.1 26 12-38 3-28 (55)
65 smart00355 ZnF_C2H2 zinc finge 20.2 41 0.00089 14.7 0.3 11 14-24 2-12 (26)
66 PF05810 NinF: NinF protein; 20.1 26 0.00056 20.9 -0.5 15 14-28 19-33 (58)
No 1
>PF04968 CHORD: CHORD ; InterPro: IPR007051 Cysteine- and histidine-rich domains (CHORDs) are 60-amino acid modules that bind two zinc ions. They are usually arranged in tandem and are found in all tested eukaryotes, with the exception of yeast, where they are involved in processes ranging from pressure sensing in the heart to maintenance of diploidy in fungi, and exhibit distinct protein-protein interaction specificity. Six cysteine and two histidine residues are invariant within the CHORD domain. Three other residues are also invariant and some positions are confined to positive, negative, or aromatic amino acids [, ]. Silencing of the Caenorhabditis elegansCHORD-containing gene results in semisterility and embryo lethality, suggesting an essential function of the wild-type gene in nematode development. The CHORD domain is sometimes found N-terminal to the CS domain, IPR007052 from INTERPRO, in metazoan proteins, but occurs separately from the CS domain in plants. This association is thought to be indicative of an functional interaction between CS and CHORD domains []. ; PDB: 2XCM_E 2YRT_A.
Probab=99.79 E-value=2.7e-20 Score=113.51 Aligned_cols=55 Identities=29% Similarity=0.702 Sum_probs=36.4
Q ss_pred ccccc--ccceeeccCCCCCCceeCCCCcccccCCCCcceeecCCCCCCCCCceeecCCCCC------CCCCCCCccccc
Q 034621 13 KVCKR--CKQTYTASSNSSSSCRFHPSFFVCRRHDDQKRYYELGPDDPPYAAKFYDCCGAED------ADASGCITGFHV 84 (89)
Q Consensus 13 ~~C~~--C~~~F~~~~N~~~sC~yHpG~~~~~~~~d~~~~f~~~~~d~~~~~k~WsCCg~~~------~~~~GC~~g~H~ 84 (89)
.+|+| |++.|.+++|.+++|+||||. |+| |+++|+||||.++. ..+|||++|+|.
T Consensus 2 ~~C~n~GC~~~y~~~~n~~~~C~yHpG~----------PvF-------Heg~K~WsCC~~k~~dF~~Fl~i~GC~~G~H~ 64 (64)
T PF04968_consen 2 TKCKNKGCGKEYDEEENDDGACHYHPGP----------PVF-------HEGMKGWSCCKKKVSDFDEFLKIPGCTTGKHS 64 (64)
T ss_dssp EE--SCTT--EE-TTT--TTTEEEBSS-----------EEE-------ETTEEEETTTTEEESSHHHHTT---SCEE---
T ss_pred CceECCCCCCEECCCCCCCCceEecCCC----------cee-------cCCceEEecCCCEeeCHHHHhcCCCCcccCCC
Confidence 57877 999999999999999999998 688 69999999999953 269999999994
No 2
>KOG1667 consensus Zn2+-binding protein Melusin/RAR1, contains CHORD domain [General function prediction only]
Probab=99.61 E-value=1.9e-16 Score=118.73 Aligned_cols=57 Identities=30% Similarity=0.741 Sum_probs=50.1
Q ss_pred ccc--ccccceeeccCCCCCCceeCCCCcccccCCCCcceeecCCCCCCCCCceeecCCCCCC------CCCCCCccccc
Q 034621 13 KVC--KRCKQTYTASSNSSSSCRFHPSFFVCRRHDDQKRYYELGPDDPPYAAKFYDCCGAEDA------DASGCITGFHV 84 (89)
Q Consensus 13 ~~C--~~C~~~F~~~~N~~~sC~yHpG~~~~~~~~d~~~~f~~~~~d~~~~~k~WsCCg~~~~------~~~GC~~g~H~ 84 (89)
+.| +.|||.|++.+|.+.||+||||. |+| |+++|.||||.++.- ++.|||.|+|.
T Consensus 2 l~CynkGCGq~FDP~tN~deaC~~HPG~----------P~F-------HDA~KgWsCC~kkstDFseflnikGCT~gkHs 64 (320)
T KOG1667|consen 2 LQCYNKGCGQLFDPKTNDDEACTYHPGV----------PYF-------HDAYKGWSCCDKKSTDFSEFLNIKGCTRGKHS 64 (320)
T ss_pred ceeeccCcccccCCCCCCccccccCCCC----------cch-------hhhhccccccccccccHHHhhccccccccccc
Confidence 467 45999999999999999999998 688 799999999999632 69999999998
Q ss_pred cc
Q 034621 85 SY 86 (89)
Q Consensus 85 ~~ 86 (89)
+.
T Consensus 65 ne 66 (320)
T KOG1667|consen 65 NE 66 (320)
T ss_pred cC
Confidence 64
No 3
>KOG1667 consensus Zn2+-binding protein Melusin/RAR1, contains CHORD domain [General function prediction only]
Probab=99.47 E-value=2e-14 Score=107.88 Aligned_cols=60 Identities=23% Similarity=0.666 Sum_probs=52.2
Q ss_pred ccccccccc--ccceeeccCCCCCCceeCCCCcccccCCCCcceeecCCCCCCCCCceeecCCCCCC------CCCCCCc
Q 034621 9 KEKEKVCKR--CKQTYTASSNSSSSCRFHPSFFVCRRHDDQKRYYELGPDDPPYAAKFYDCCGAEDA------DASGCIT 80 (89)
Q Consensus 9 ~~~~~~C~~--C~~~F~~~~N~~~sC~yHpG~~~~~~~~d~~~~f~~~~~d~~~~~k~WsCCg~~~~------~~~GC~~ 80 (89)
-+....|+| |...|+...+..+.|.||||. |+| |++|||||||++... .++||+.
T Consensus 139 I~iGtsCkN~GCs~~fqG~esd~~~CtyHpGa----------piF-------HEGMKyWSCC~kkTsdF~aFlaQ~GCt~ 201 (320)
T KOG1667|consen 139 IQIGTSCKNNGCSTEFQGSESDKENCTYHPGA----------PIF-------HEGMKYWSCCNKKTSDFGAFLAQVGCTS 201 (320)
T ss_pred ceeCCcccCCCcceeeeccccccccceeCCCC----------hhh-------hccchhhhhcccccccHHHHhhhcCccc
Confidence 345678997 999999999999999999998 688 799999999999642 5999999
Q ss_pred ccccc
Q 034621 81 GFHVS 85 (89)
Q Consensus 81 g~H~~ 85 (89)
|.|.-
T Consensus 202 GeH~w 206 (320)
T KOG1667|consen 202 GEHKW 206 (320)
T ss_pred cchhh
Confidence 99953
No 4
>PF00779 BTK: BTK motif; InterPro: IPR001562 The Btk-type zinc finger or Btk motif (BM) is a conserved zinc-binding motif containing conserved cysteines and a histidine that is present in certain eukaryotic signalling proteins. The motif is named after Bruton's tyrosine kinase (Btk), an enzyme which is essential for B cell maturation in humans and mice [, ]. Btk is a member of the Tec family of protein tyrosine kinases (PTK). These kinases contain a conserved Tec homology (TH) domain between the N-terminal pleckstrin homology (PH) domain (IPR001849 from INTERPRO) and the Src homology 3 (SH3) domain (IPR001452 from INTERPRO). The N-terminal of the TH domain is highly conserved and known as the Btf motif, while the C-terminal region of the TH domain contains a proline-rich region (PRR). The Btk motif contains a conserved His and three Cys residues that form a zinc finger (although these differ from known zinc finger topologies), while PRRs are commonly involved in protein-protein interactions, including interactions with G proteins [, ]. The TH domain may be of functional importance in various signalling pathways in different species []. A complete TH domain, containing both the Btk and PRR regions, has not been found outside the Tec family; however, the Btk motif on its own does occur in other proteins, usually C-terminal to a PH domain (note that although a Btk motif always occurs C-terminal to a PH domain, not all PH domains are followed by a Btk motif). The crystal structures of Btk show that the Btk-type zinc finger has a globular core, formed by a long loop which is held together by a zinc ion, and that the Btk motif is packed against the PH domain []. The zinc-binding residues are a histidine and three cysteines, which are fully conserved in the Btk motif []. Proteins known to contain a Btk-type zinc finger include: Mammalian Bruton's tyrosine kinase (Btk), a protein tyrosine kinase involved in modulation of diverse cellular processes. Mutations affecting Btk are the cause of X-linked agammaglobulinemia (XLA) in humans and X-linked immunodeficiency in mice. Mammalian Tec, Bmx, and Itk proteins, which are tyrosine protein kinases of the Tec subfamily. Drosophila tyrosine-protein kinase Btk29A, which is required for the development of proper ring canals and of male genitalia and required for adult survival. Mammalian Ras GTPase-activating proteins (RasGAP), which regulate the activation of inactive GDP-bound Ras by converting GDP to GTP. ; GO: 0035556 intracellular signal transduction; PDB: 2E6I_A 2YS2_A 2Z0P_A 1B55_A 1BTK_B 1BWN_A.
Probab=97.96 E-value=3.3e-06 Score=45.08 Aligned_cols=18 Identities=33% Similarity=0.763 Sum_probs=13.2
Q ss_pred ceeecCCCCCCCCCCCCc
Q 034621 63 KFYDCCGAEDADASGCIT 80 (89)
Q Consensus 63 k~WsCCg~~~~~~~GC~~ 80 (89)
..|+||++.+..++||+.
T Consensus 11 g~W~CC~q~~k~a~GC~~ 28 (32)
T PF00779_consen 11 GKWLCCKQTDKSAPGCQP 28 (32)
T ss_dssp TCESSSS-SSTTS--SEE
T ss_pred CcCcCCCCcCcCCCCCcc
Confidence 489999999889999985
No 5
>smart00107 BTK Bruton's tyrosine kinase Cys-rich motif. Zinc-binding motif containing conserved cysteines and a histidine. Always found C-terminal to PH domains (but not all PH domains are followed by BTK motifs). The crystal structure shows this motif packs against the PH domain. The PH+Btk module pair has been called the Tec homology (TH) region.
Probab=97.90 E-value=8.7e-06 Score=44.49 Aligned_cols=18 Identities=28% Similarity=0.789 Sum_probs=15.9
Q ss_pred ceeecCCCCCCCCCCCCc
Q 034621 63 KFYDCCGAEDADASGCIT 80 (89)
Q Consensus 63 k~WsCCg~~~~~~~GC~~ 80 (89)
..|+||++.+..++||+.
T Consensus 16 G~W~CC~q~~k~a~GC~~ 33 (36)
T smart00107 16 GKWLCCQQSEKNAPGCTP 33 (36)
T ss_pred CeEccCCCcCcCCCCCcc
Confidence 379999999889999985
No 6
>PF11822 DUF3342: Domain of unknown function (DUF3342); InterPro: IPR021777 This family of proteins are functionally uncharacterised. This family is found in bacteria. This presumed domain is typically between 170 to 303 amino acids in length. The N-terminal half of this family is a BTB-like domain.
Probab=95.83 E-value=0.0062 Score=47.14 Aligned_cols=50 Identities=32% Similarity=0.737 Sum_probs=36.1
Q ss_pred ccccccccceeeccCCCCCCceeCCCCcccccCCCCcceeecCC--CCCCCCCceeecCCCC
Q 034621 12 EKVCKRCKQTYTASSNSSSSCRFHPSFFVCRRHDDQKRYYELGP--DDPPYAAKFYDCCGAE 71 (89)
Q Consensus 12 ~~~C~~C~~~F~~~~N~~~sC~yHpG~~~~~~~~d~~~~f~~~~--~d~~~~~k~WsCCg~~ 71 (89)
...|.+|++.|...+-+-..|.|||..+ .|.... .+.+.....|.||++.
T Consensus 261 ~l~CsrC~q~F~~~el~~~~C~yHp~~~----------~~~~~~~~~~~~~~~G~YpCC~q~ 312 (317)
T PF11822_consen 261 FLYCSRCNQVFPCSELSTHHCRYHPESP----------VFPDNASSEDSPGLLGWYPCCGQK 312 (317)
T ss_pred EEECccCCcEeeHHHcccccccCCCCCc----------ccCCcccccCcccceeeecccCCc
Confidence 4589999999998886666899999984 343211 1233456799999874
No 7
>KOG2059 consensus Ras GTPase-activating protein [Signal transduction mechanisms]
Probab=82.83 E-value=0.82 Score=39.21 Aligned_cols=50 Identities=20% Similarity=0.529 Sum_probs=33.6
Q ss_pred ccccccccccceee--------ccCCCCCCceeCCCCcccccCCCCcceeecCCCCCCCCCceeecCCCCCCCCCCCCc
Q 034621 10 EKEKVCKRCKQTYT--------ASSNSSSSCRFHPSFFVCRRHDDQKRYYELGPDDPPYAAKFYDCCGAEDADASGCIT 80 (89)
Q Consensus 10 ~~~~~C~~C~~~F~--------~~~N~~~sC~yHpG~~~~~~~~d~~~~f~~~~~d~~~~~k~WsCCg~~~~~~~GC~~ 80 (89)
.....|++|.+.=+ ...|....=.||||.|+ .-.|+||.+....++||+.
T Consensus 642 tly~Q~~n~vEandWldaL~kvs~~N~~rLas~HPgaF~---------------------s~~wsCC~q~~~~s~GC~~ 699 (800)
T KOG2059|consen 642 TLYVQAKNCVEANDWLDALRKVSCCNQNRLASYHPGAFR---------------------SDSWSCCPQPEENSPGCKK 699 (800)
T ss_pred ceeEecCCchHHHHHHHHHHHHhccCcchhhhcCCcccc---------------------cCcccccCCCCCCCCCCCc
Confidence 33445777765421 13455556679999852 2289999998888999984
No 8
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=78.38 E-value=1 Score=24.00 Aligned_cols=20 Identities=30% Similarity=0.718 Sum_probs=15.6
Q ss_pred chhhhcccccccccccccee
Q 034621 3 TEKIKDKEKEKVCKRCKQTY 22 (89)
Q Consensus 3 ~~~~~~~~~~~~C~~C~~~F 22 (89)
.+|+........|.+|+..|
T Consensus 16 d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 16 DEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred HHHCCCCCcEEECCCCCCEe
Confidence 46677777778888888887
No 9
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=71.43 E-value=2.2 Score=28.16 Aligned_cols=33 Identities=12% Similarity=0.343 Sum_probs=25.8
Q ss_pred hccccccccccccceeeccCCCCCCceeCCCCc
Q 034621 7 KDKEKEKVCKRCKQTYTASSNSSSSCRFHPSFF 39 (89)
Q Consensus 7 ~~~~~~~~C~~C~~~F~~~~N~~~sC~yHpG~~ 39 (89)
......++|..||.+|..-...|..|-|=--.+
T Consensus 4 pelGtKR~Cp~CG~kFYDLnk~PivCP~CG~~~ 36 (108)
T PF09538_consen 4 PELGTKRTCPSCGAKFYDLNKDPIVCPKCGTEF 36 (108)
T ss_pred cccCCcccCCCCcchhccCCCCCccCCCCCCcc
Confidence 345677899999999987777888887765554
No 10
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=67.88 E-value=3 Score=22.19 Aligned_cols=17 Identities=12% Similarity=0.599 Sum_probs=8.1
Q ss_pred hhcccccccccccccee
Q 034621 6 IKDKEKEKVCKRCKQTY 22 (89)
Q Consensus 6 ~~~~~~~~~C~~C~~~F 22 (89)
+.+......|.+|+..|
T Consensus 19 l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 19 LPAGGRKVRCPKCGHVF 35 (37)
T ss_pred cccCCcEEECCCCCcEe
Confidence 33444444555555554
No 11
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=67.43 E-value=2.3 Score=20.89 Aligned_cols=14 Identities=14% Similarity=0.491 Sum_probs=11.5
Q ss_pred ccccccccceeecc
Q 034621 12 EKVCKRCKQTYTAS 25 (89)
Q Consensus 12 ~~~C~~C~~~F~~~ 25 (89)
+..|..|+..|.++
T Consensus 2 l~~C~~CgR~F~~~ 15 (25)
T PF13913_consen 2 LVPCPICGRKFNPD 15 (25)
T ss_pred CCcCCCCCCEECHH
Confidence 56899999999654
No 12
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=66.14 E-value=3.6 Score=28.27 Aligned_cols=32 Identities=9% Similarity=0.294 Sum_probs=25.9
Q ss_pred ccccccccccccceeeccCCCCCCceeCCCCc
Q 034621 8 DKEKEKVCKRCKQTYTASSNSSSSCRFHPSFF 39 (89)
Q Consensus 8 ~~~~~~~C~~C~~~F~~~~N~~~sC~yHpG~~ 39 (89)
.....++|..|+++|..-...+..|-|=--.+
T Consensus 5 elGtKr~Cp~cg~kFYDLnk~p~vcP~cg~~~ 36 (129)
T TIGR02300 5 DLGTKRICPNTGSKFYDLNRRPAVSPYTGEQF 36 (129)
T ss_pred hhCccccCCCcCccccccCCCCccCCCcCCcc
Confidence 45677899999999998888899998765543
No 13
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=59.84 E-value=4 Score=19.50 Aligned_cols=13 Identities=23% Similarity=0.697 Sum_probs=10.7
Q ss_pred cccccccceeecc
Q 034621 13 KVCKRCKQTYTAS 25 (89)
Q Consensus 13 ~~C~~C~~~F~~~ 25 (89)
..|..|++.|...
T Consensus 2 ~~C~~C~~~F~~~ 14 (27)
T PF13912_consen 2 FECDECGKTFSSL 14 (27)
T ss_dssp EEETTTTEEESSH
T ss_pred CCCCccCCccCCh
Confidence 5799999999754
No 14
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=59.14 E-value=6.9 Score=20.49 Aligned_cols=23 Identities=13% Similarity=0.367 Sum_probs=16.8
Q ss_pred ccccccceeeccCCCCCCceeCC
Q 034621 14 VCKRCKQTYTASSNSSSSCRFHP 36 (89)
Q Consensus 14 ~C~~C~~~F~~~~N~~~sC~yHp 36 (89)
+|-.|+..+.-+.+.+..|.+=-
T Consensus 2 ~C~~Cg~~~~~~~~~~irC~~CG 24 (32)
T PF03604_consen 2 ICGECGAEVELKPGDPIRCPECG 24 (32)
T ss_dssp BESSSSSSE-BSTSSTSSBSSSS
T ss_pred CCCcCCCeeEcCCCCcEECCcCC
Confidence 68889999987777777777543
No 15
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=55.95 E-value=5.8 Score=22.11 Aligned_cols=26 Identities=19% Similarity=0.501 Sum_probs=20.9
Q ss_pred ccccccccceeeccCCCCCCceeCCCC
Q 034621 12 EKVCKRCKQTYTASSNSSSSCRFHPSF 38 (89)
Q Consensus 12 ~~~C~~C~~~F~~~~N~~~sC~yHpG~ 38 (89)
..+|..||..|......+..|. +-|.
T Consensus 2 ~Y~C~~Cg~~~~~~~~~~irC~-~CG~ 27 (44)
T smart00659 2 IYICGECGRENEIKSKDVVRCR-ECGY 27 (44)
T ss_pred EEECCCCCCEeecCCCCceECC-CCCc
Confidence 3689999999998877788888 5554
No 16
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=55.61 E-value=5.7 Score=21.81 Aligned_cols=27 Identities=19% Similarity=0.391 Sum_probs=17.8
Q ss_pred ccccccccceeeccCCC-CCCceeCCCC
Q 034621 12 EKVCKRCKQTYTASSNS-SSSCRFHPSF 38 (89)
Q Consensus 12 ~~~C~~C~~~F~~~~N~-~~sC~yHpG~ 38 (89)
...|.+||..|.-..+. ...|.|=-+.
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~ 30 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYR 30 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCe
Confidence 46789999988765554 5666655443
No 17
>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=51.62 E-value=6.2 Score=18.02 Aligned_cols=12 Identities=17% Similarity=0.778 Sum_probs=9.9
Q ss_pred ccccccceeecc
Q 034621 14 VCKRCKQTYTAS 25 (89)
Q Consensus 14 ~C~~C~~~F~~~ 25 (89)
.|..|++.|...
T Consensus 2 ~C~~C~~~f~~~ 13 (23)
T PF00096_consen 2 KCPICGKSFSSK 13 (23)
T ss_dssp EETTTTEEESSH
T ss_pred CCCCCCCccCCH
Confidence 689999999754
No 18
>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=46.98 E-value=9.5 Score=18.49 Aligned_cols=14 Identities=29% Similarity=0.752 Sum_probs=11.4
Q ss_pred ccccccccccceee
Q 034621 10 EKEKVCKRCKQTYT 23 (89)
Q Consensus 10 ~~~~~C~~C~~~F~ 23 (89)
+....|..|++.|.
T Consensus 12 ~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 12 EKPYKCPYCGKSFS 25 (26)
T ss_dssp SSSEEESSSSEEES
T ss_pred CCCCCCCCCcCeeC
Confidence 45578999999995
No 19
>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=46.68 E-value=9.8 Score=19.77 Aligned_cols=13 Identities=23% Similarity=0.713 Sum_probs=7.7
Q ss_pred cccccccceeecc
Q 034621 13 KVCKRCKQTYTAS 25 (89)
Q Consensus 13 ~~C~~C~~~F~~~ 25 (89)
..|.+|++.|...
T Consensus 3 ~~CP~C~~~~~v~ 15 (38)
T TIGR02098 3 IQCPNCKTSFRVV 15 (38)
T ss_pred EECCCCCCEEEeC
Confidence 3566666666543
No 20
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=41.63 E-value=15 Score=24.06 Aligned_cols=31 Identities=23% Similarity=0.459 Sum_probs=22.8
Q ss_pred ccccccccccccceeeccCC--CCCCceeCCCC
Q 034621 8 DKEKEKVCKRCKQTYTASSN--SSSSCRFHPSF 38 (89)
Q Consensus 8 ~~~~~~~C~~C~~~F~~~~N--~~~sC~yHpG~ 38 (89)
+.....+|++|+.+|..++. .++-|+=.|=.
T Consensus 48 q~g~~lvC~~C~~~~~~~~ig~~~GGCNP~P~~ 80 (102)
T PF10080_consen 48 QEGDQLVCKNCGVRFNLPTIGGKSGGCNPIPLP 80 (102)
T ss_pred EECCEEEEecCCCEEehhhcccccCCCCccCCc
Confidence 45677899999999986544 46788766643
No 21
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=40.70 E-value=11 Score=21.66 Aligned_cols=29 Identities=21% Similarity=0.378 Sum_probs=21.2
Q ss_pred ccccccccccceeecc-CCCCCCceeCCCC
Q 034621 10 EKEKVCKRCKQTYTAS-SNSSSSCRFHPSF 38 (89)
Q Consensus 10 ~~~~~C~~C~~~F~~~-~N~~~sC~yHpG~ 38 (89)
....+|-+|++.|+.. .-....|.|=...
T Consensus 4 ~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 4 MMEYKCARCGREVELDQETRGIRCPYCGSR 33 (49)
T ss_pred eEEEEhhhcCCeeehhhccCceeCCCCCcE
Confidence 3567899999999743 4455778876665
No 22
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=40.08 E-value=15 Score=19.52 Aligned_cols=16 Identities=25% Similarity=0.812 Sum_probs=12.3
Q ss_pred cccccccceeeccCCC
Q 034621 13 KVCKRCKQTYTASSNS 28 (89)
Q Consensus 13 ~~C~~C~~~F~~~~N~ 28 (89)
.+|..||..|...-|.
T Consensus 2 r~C~~Cg~~Yh~~~~p 17 (36)
T PF05191_consen 2 RICPKCGRIYHIEFNP 17 (36)
T ss_dssp EEETTTTEEEETTTB-
T ss_pred cCcCCCCCccccccCC
Confidence 5799999999876654
No 23
>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=38.43 E-value=19 Score=18.47 Aligned_cols=19 Identities=32% Similarity=0.795 Sum_probs=10.9
Q ss_pred ccccccceeeccCC-CCCCc
Q 034621 14 VCKRCKQTYTASSN-SSSSC 32 (89)
Q Consensus 14 ~C~~C~~~F~~~~N-~~~sC 32 (89)
.|.-|++.|...+- .-++|
T Consensus 2 sCiDC~~~F~~~~y~~Ht~C 21 (28)
T PF08790_consen 2 SCIDCSKDFDGDSYKSHTSC 21 (28)
T ss_dssp EETTTTEEEEGGGTTT----
T ss_pred eeecCCCCcCcCCcCCCCcc
Confidence 68899999975432 22444
No 24
>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=36.28 E-value=16 Score=16.11 Aligned_cols=11 Identities=18% Similarity=0.800 Sum_probs=7.1
Q ss_pred ccccccceeec
Q 034621 14 VCKRCKQTYTA 24 (89)
Q Consensus 14 ~C~~C~~~F~~ 24 (89)
.|..|+..|..
T Consensus 2 ~C~~C~~~~~~ 12 (24)
T PF13894_consen 2 QCPICGKSFRS 12 (24)
T ss_dssp E-SSTS-EESS
T ss_pred CCcCCCCcCCc
Confidence 58889999864
No 25
>PF05766 NinG: Bacteriophage Lambda NinG protein; InterPro: IPR008713 The ninR region of phage lambda contains two recombination genes, ninB (also known as orf) and ninG (also known as rap). These genes are involved in the RecF and RecBCD recombination pathways of Escherichia coli that operate on phage lambda [, ]. NinB and NinG participate in Red recombination, the primary pathway operating when wild-type lambda grows lytically in rec+ cells [].
Probab=35.44 E-value=18 Score=26.16 Aligned_cols=30 Identities=20% Similarity=0.478 Sum_probs=23.5
Q ss_pred cccccccccccceeeccCCCCCCceeCCCC
Q 034621 9 KEKEKVCKRCKQTYTASSNSSSSCRFHPSF 38 (89)
Q Consensus 9 ~~~~~~C~~C~~~F~~~~N~~~sC~yHpG~ 38 (89)
+.....|+.|+..|.|....-.-|..--|.
T Consensus 3 ~~k~rKCKvCg~~F~P~~s~q~vCSpeCa~ 32 (189)
T PF05766_consen 3 KPKRRKCKVCGEWFVPARSNQKVCSPECAI 32 (189)
T ss_pred CCCCCcCcccCCccccCCCceeeeCHHHHh
Confidence 345678999999999987777888866663
No 26
>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=33.90 E-value=18 Score=18.00 Aligned_cols=15 Identities=27% Similarity=0.702 Sum_probs=9.9
Q ss_pred cccccccccccceee
Q 034621 9 KEKEKVCKRCKQTYT 23 (89)
Q Consensus 9 ~~~~~~C~~C~~~F~ 23 (89)
+...+.|.+||-.|.
T Consensus 11 ~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 11 PESAKFCPHCGYDFE 25 (26)
T ss_pred hhhcCcCCCCCCCCc
Confidence 445567777777764
No 27
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=33.54 E-value=19 Score=23.72 Aligned_cols=27 Identities=26% Similarity=0.599 Sum_probs=18.5
Q ss_pred hhccccccccccccceeeccCCCCCCc
Q 034621 6 IKDKEKEKVCKRCKQTYTASSNSSSSC 32 (89)
Q Consensus 6 ~~~~~~~~~C~~C~~~F~~~~N~~~sC 32 (89)
|........|..|++.|....+....|
T Consensus 65 Ie~vp~~~~C~~Cg~~~~~~~~~~~~C 91 (117)
T PRK00564 65 IVDEKVELECKDCSHVFKPNALDYGVC 91 (117)
T ss_pred EEecCCEEEhhhCCCccccCCccCCcC
Confidence 344456678999999998876544334
No 28
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=33.41 E-value=20 Score=23.77 Aligned_cols=23 Identities=17% Similarity=0.335 Sum_probs=16.9
Q ss_pred hhhccccccccccccceeeccCC
Q 034621 5 KIKDKEKEKVCKRCKQTYTASSN 27 (89)
Q Consensus 5 ~~~~~~~~~~C~~C~~~F~~~~N 27 (89)
|.+......+|.+||+.|.-+-|
T Consensus 39 kk~~~~g~~~Cg~CGls~e~ev~ 61 (104)
T COG4888 39 KKTVNIGTAVCGNCGLSFECEVP 61 (104)
T ss_pred EecCceeEEEcccCcceEEEecc
Confidence 45566667788899999876655
No 29
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=32.25 E-value=27 Score=18.94 Aligned_cols=15 Identities=27% Similarity=0.691 Sum_probs=12.3
Q ss_pred ccccccccceeeccC
Q 034621 12 EKVCKRCKQTYTASS 26 (89)
Q Consensus 12 ~~~C~~C~~~F~~~~ 26 (89)
..+|..||..|.+..
T Consensus 13 ~~~C~~CgM~Y~~~~ 27 (41)
T PF13878_consen 13 ATTCPTCGMLYSPGS 27 (41)
T ss_pred CcCCCCCCCEECCCC
Confidence 569999999998653
No 30
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=32.20 E-value=24 Score=22.26 Aligned_cols=17 Identities=18% Similarity=0.536 Sum_probs=13.2
Q ss_pred ccccccccceeeccCCC
Q 034621 12 EKVCKRCKQTYTASSNS 28 (89)
Q Consensus 12 ~~~C~~C~~~F~~~~N~ 28 (89)
...|.+||+.|...+..
T Consensus 8 ~~~C~~CG~d~~~~~ad 24 (86)
T PF06170_consen 8 APRCPHCGLDYSHARAD 24 (86)
T ss_pred CCcccccCCccccCCcC
Confidence 35799999999876643
No 31
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=31.92 E-value=24 Score=23.11 Aligned_cols=27 Identities=26% Similarity=0.524 Sum_probs=18.1
Q ss_pred hccccccccccccceeeccCCCCCCce
Q 034621 7 KDKEKEKVCKRCKQTYTASSNSSSSCR 33 (89)
Q Consensus 7 ~~~~~~~~C~~C~~~F~~~~N~~~sC~ 33 (89)
........|..|++.|....+....|-
T Consensus 65 ~~~p~~~~C~~Cg~~~~~~~~~~~~CP 91 (114)
T PRK03681 65 EEQEAECWCETCQQYVTLLTQRVRRCP 91 (114)
T ss_pred EeeCcEEEcccCCCeeecCCccCCcCc
Confidence 344556789999999877665434454
No 32
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=31.32 E-value=24 Score=18.49 Aligned_cols=16 Identities=25% Similarity=0.636 Sum_probs=11.7
Q ss_pred ccccccccccceeecc
Q 034621 10 EKEKVCKRCKQTYTAS 25 (89)
Q Consensus 10 ~~~~~C~~C~~~F~~~ 25 (89)
.....|.+||..|...
T Consensus 30 vp~~~C~~CGE~~~~~ 45 (46)
T TIGR03831 30 VPALVCPQCGEEYLDA 45 (46)
T ss_pred CCccccccCCCEeeCC
Confidence 3456799999998643
No 33
>PHA02768 hypothetical protein; Provisional
Probab=30.19 E-value=16 Score=21.50 Aligned_cols=25 Identities=20% Similarity=0.347 Sum_probs=16.9
Q ss_pred ccccccccceeeccCCCCCCceeCC
Q 034621 12 EKVCKRCKQTYTASSNSSSSCRFHP 36 (89)
Q Consensus 12 ~~~C~~C~~~F~~~~N~~~sC~yHp 36 (89)
...|..||+.|...++...-=+-|.
T Consensus 5 ~y~C~~CGK~Fs~~~~L~~H~r~H~ 29 (55)
T PHA02768 5 GYECPICGEIYIKRKSMITHLRKHN 29 (55)
T ss_pred ccCcchhCCeeccHHHHHHHHHhcC
Confidence 4689999999998776433333344
No 34
>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=29.67 E-value=30 Score=20.70 Aligned_cols=19 Identities=26% Similarity=0.593 Sum_probs=10.8
Q ss_pred ccccccccccceeeccCCC
Q 034621 10 EKEKVCKRCKQTYTASSNS 28 (89)
Q Consensus 10 ~~~~~C~~C~~~F~~~~N~ 28 (89)
....+|++|+..|.|..|.
T Consensus 44 ~kr~~Ck~C~~~liPG~~~ 62 (85)
T PF04032_consen 44 IKRTICKKCGSLLIPGVNC 62 (85)
T ss_dssp CCCTB-TTT--B--CTTTE
T ss_pred HhcccccCCCCEEeCCCcc
Confidence 4567899999999988774
No 35
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=29.60 E-value=16 Score=23.80 Aligned_cols=22 Identities=9% Similarity=0.427 Sum_probs=14.9
Q ss_pred hccccccccccccceeeccCCC
Q 034621 7 KDKEKEKVCKRCKQTYTASSNS 28 (89)
Q Consensus 7 ~~~~~~~~C~~C~~~F~~~~N~ 28 (89)
........|..|+..|....+.
T Consensus 65 e~~p~~~~C~~Cg~~~~~~~~~ 86 (113)
T PF01155_consen 65 EEVPARARCRDCGHEFEPDEFD 86 (113)
T ss_dssp EEE--EEEETTTS-EEECHHCC
T ss_pred EecCCcEECCCCCCEEecCCCC
Confidence 3445567899999999987765
No 36
>PF04997 RNA_pol_Rpb1_1: RNA polymerase Rpb1, domain 1; InterPro: IPR007080 RNA polymerases catalyse the DNA-dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 1, represents the clamp domain, which is a mobile domain involved in positioning the DNA, maintenance of the transcription bubble and positioning of the nascent RNA strand [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2Y0S_W 3QQC_A 1YNJ_D 1HQM_D 1YNN_D 1I6V_D 2GHO_D 2AUJ_D 1ZYR_D 1SMY_D ....
Probab=29.52 E-value=15 Score=26.39 Aligned_cols=28 Identities=25% Similarity=0.530 Sum_probs=20.9
Q ss_pred cccccccceeeccCCCCCCceeCCCCcccccCCCCcceee
Q 034621 13 KVCKRCKQTYTASSNSSSSCRFHPSFFVCRRHDDQKRYYE 52 (89)
Q Consensus 13 ~~C~~C~~~F~~~~N~~~sC~yHpG~~~~~~~~d~~~~f~ 52 (89)
..|..|++.+.. |..|.|...+-. |+|+
T Consensus 55 ~~C~tC~~~~~~-------CpGHfGhI~L~~-----PV~h 82 (337)
T PF04997_consen 55 QICSTCGLNYTE-------CPGHFGHIELAL-----PVYH 82 (337)
T ss_dssp STSSSSSSSSSS-------CCCSEEEEEEEE-----EEET
T ss_pred cccccccccccc-------cCCceeEEEeCH-----HHHh
Confidence 589999988655 999999864432 6664
No 37
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=29.24 E-value=26 Score=20.16 Aligned_cols=13 Identities=31% Similarity=0.784 Sum_probs=10.7
Q ss_pred cccccccccceee
Q 034621 11 KEKVCKRCKQTYT 23 (89)
Q Consensus 11 ~~~~C~~C~~~F~ 23 (89)
..++|+.||..|.
T Consensus 3 k~l~C~dCg~~Fv 15 (49)
T PF13451_consen 3 KTLTCKDCGAEFV 15 (49)
T ss_pred eeEEcccCCCeEE
Confidence 4578999999985
No 38
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=29.10 E-value=26 Score=19.27 Aligned_cols=14 Identities=21% Similarity=0.593 Sum_probs=11.4
Q ss_pred ccccccccceeecc
Q 034621 12 EKVCKRCKQTYTAS 25 (89)
Q Consensus 12 ~~~C~~C~~~F~~~ 25 (89)
...|..|+..|...
T Consensus 5 ey~C~~Cg~~fe~~ 18 (52)
T TIGR02605 5 EYRCTACGHRFEVL 18 (52)
T ss_pred EEEeCCCCCEeEEE
Confidence 46899999999864
No 39
>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=28.97 E-value=26 Score=19.62 Aligned_cols=17 Identities=29% Similarity=0.708 Sum_probs=13.1
Q ss_pred hccccccccccccceee
Q 034621 7 KDKEKEKVCKRCKQTYT 23 (89)
Q Consensus 7 ~~~~~~~~C~~C~~~F~ 23 (89)
+......+|..|+..|.
T Consensus 3 K~~lp~K~C~~C~rpf~ 19 (42)
T PF10013_consen 3 KSNLPSKICPVCGRPFT 19 (42)
T ss_pred cccCCCCcCcccCCcch
Confidence 34556788999999986
No 40
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=28.56 E-value=26 Score=20.67 Aligned_cols=17 Identities=29% Similarity=0.624 Sum_probs=13.3
Q ss_pred ccccccccccccceeec
Q 034621 8 DKEKEKVCKRCKQTYTA 24 (89)
Q Consensus 8 ~~~~~~~C~~C~~~F~~ 24 (89)
..+...+|.+|+..|--
T Consensus 49 i~eg~L~Cp~c~r~YPI 65 (68)
T PF03966_consen 49 IVEGELICPECGREYPI 65 (68)
T ss_dssp TTTTEEEETTTTEEEEE
T ss_pred ccCCEEEcCCCCCEEeC
Confidence 44577899999999953
No 41
>PF10853 DUF2650: Protein of unknown function (DUF2650); InterPro: IPR022559 This region is found in proteins with unknown function in metazoa.
Probab=27.05 E-value=40 Score=18.35 Aligned_cols=9 Identities=44% Similarity=1.497 Sum_probs=7.4
Q ss_pred ceeecCCCC
Q 034621 63 KFYDCCGAE 71 (89)
Q Consensus 63 k~WsCCg~~ 71 (89)
.||+|||..
T Consensus 8 ~yy~CCg~~ 16 (38)
T PF10853_consen 8 HYYKCCGDL 16 (38)
T ss_pred EEEECCCCC
Confidence 499999974
No 42
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=26.68 E-value=33 Score=17.91 Aligned_cols=16 Identities=19% Similarity=0.632 Sum_probs=12.6
Q ss_pred ccccccccccccceee
Q 034621 8 DKEKEKVCKRCKQTYT 23 (89)
Q Consensus 8 ~~~~~~~C~~C~~~F~ 23 (89)
......+|..|+..|.
T Consensus 17 ~~~~~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 17 KEDDYEVCIFCGSSFP 32 (33)
T ss_pred ecCCeEEcccCCcEee
Confidence 5667788999998874
No 43
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=26.52 E-value=30 Score=18.40 Aligned_cols=14 Identities=21% Similarity=0.615 Sum_probs=7.2
Q ss_pred ccccccccceeecc
Q 034621 12 EKVCKRCKQTYTAS 25 (89)
Q Consensus 12 ~~~C~~C~~~F~~~ 25 (89)
..+|..|++.|..+
T Consensus 3 ~~~C~eC~~~f~dS 16 (34)
T PF01286_consen 3 YPKCDECGKPFMDS 16 (34)
T ss_dssp -EE-TTT--EES-S
T ss_pred CchHhHhCCHHHHH
Confidence 45788999999765
No 44
>PF10892 DUF2688: Protein of unknown function (DUF2688); InterPro: IPR024392 Members of this protein family are annotated as KleB, and may play a role in the regulation of transcription in plasmids.
Probab=26.43 E-value=21 Score=21.33 Aligned_cols=15 Identities=27% Similarity=0.669 Sum_probs=11.2
Q ss_pred cccccccccccceee
Q 034621 9 KEKEKVCKRCKQTYT 23 (89)
Q Consensus 9 ~~~~~~C~~C~~~F~ 23 (89)
......|+|||+.-.
T Consensus 7 eIV~t~CrRCGk~i~ 21 (60)
T PF10892_consen 7 EIVETPCRRCGKSIR 21 (60)
T ss_pred EeeeehhhhhCccHH
Confidence 356677999999754
No 45
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=26.36 E-value=22 Score=22.83 Aligned_cols=20 Identities=15% Similarity=0.451 Sum_probs=14.9
Q ss_pred hccccccccccccceeeccC
Q 034621 7 KDKEKEKVCKRCKQTYTASS 26 (89)
Q Consensus 7 ~~~~~~~~C~~C~~~F~~~~ 26 (89)
.....-.+|.+||..|..++
T Consensus 30 IknVPa~~C~~CGe~y~~de 49 (89)
T TIGR03829 30 IKETPSISCSHCGMEYQDDT 49 (89)
T ss_pred EecCCcccccCCCcEeecHH
Confidence 34556678999999997643
No 46
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=26.03 E-value=48 Score=16.89 Aligned_cols=14 Identities=29% Similarity=0.643 Sum_probs=10.8
Q ss_pred cccccccceeeccC
Q 034621 13 KVCKRCKQTYTASS 26 (89)
Q Consensus 13 ~~C~~C~~~F~~~~ 26 (89)
.+|..||-.|+++.
T Consensus 2 ~~C~~CGy~y~~~~ 15 (33)
T cd00350 2 YVCPVCGYIYDGEE 15 (33)
T ss_pred EECCCCCCEECCCc
Confidence 46888998887654
No 47
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=25.97 E-value=31 Score=22.61 Aligned_cols=22 Identities=23% Similarity=0.527 Sum_probs=16.5
Q ss_pred hhccccccccccccceeeccCC
Q 034621 6 IKDKEKEKVCKRCKQTYTASSN 27 (89)
Q Consensus 6 ~~~~~~~~~C~~C~~~F~~~~N 27 (89)
|........|.+|++.|....+
T Consensus 64 I~~~p~~~~C~~Cg~~~~~~~~ 85 (115)
T TIGR00100 64 IEDEPVECECEDCSEEVSPEID 85 (115)
T ss_pred EEeeCcEEEcccCCCEEecCCc
Confidence 3445566789999999987765
No 48
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=25.96 E-value=31 Score=18.60 Aligned_cols=15 Identities=20% Similarity=0.607 Sum_probs=11.6
Q ss_pred ccccccccceeeccC
Q 034621 12 EKVCKRCKQTYTASS 26 (89)
Q Consensus 12 ~~~C~~C~~~F~~~~ 26 (89)
...|..||..|....
T Consensus 5 ey~C~~Cg~~fe~~~ 19 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQ 19 (42)
T ss_pred EEEeCCCCCEEEEEE
Confidence 357999999997643
No 49
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=25.01 E-value=38 Score=18.65 Aligned_cols=16 Identities=31% Similarity=0.625 Sum_probs=13.0
Q ss_pred cccccccccceeeccC
Q 034621 11 KEKVCKRCKQTYTASS 26 (89)
Q Consensus 11 ~~~~C~~C~~~F~~~~ 26 (89)
....|+.|++.|....
T Consensus 17 ~~a~C~~C~~~l~~~~ 32 (50)
T smart00614 17 QRAKCKYCGKKLSRSS 32 (50)
T ss_pred eEEEecCCCCEeeeCC
Confidence 4678999999997654
No 50
>PHA00616 hypothetical protein
Probab=24.50 E-value=20 Score=20.12 Aligned_cols=26 Identities=12% Similarity=0.130 Sum_probs=18.7
Q ss_pred cccccccceeeccCCCCCCceeCCCC
Q 034621 13 KVCKRCKQTYTASSNSSSSCRFHPSF 38 (89)
Q Consensus 13 ~~C~~C~~~F~~~~N~~~sC~yHpG~ 38 (89)
..|.+||+.|.-..+-..-.+=|-|.
T Consensus 2 YqC~~CG~~F~~~s~l~~H~r~~hg~ 27 (44)
T PHA00616 2 YQCLRCGGIFRKKKEVIEHLLSVHKQ 27 (44)
T ss_pred CccchhhHHHhhHHHHHHHHHHhcCC
Confidence 46999999998766655555666665
No 51
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=24.27 E-value=57 Score=16.90 Aligned_cols=19 Identities=21% Similarity=0.506 Sum_probs=12.7
Q ss_pred cccccccceeeccCCCCCCc
Q 034621 13 KVCKRCKQTYTASSNSSSSC 32 (89)
Q Consensus 13 ~~C~~C~~~F~~~~N~~~sC 32 (89)
.+|..||-.|+... .+..|
T Consensus 3 ~~C~~CG~i~~g~~-~p~~C 21 (34)
T cd00729 3 WVCPVCGYIHEGEE-APEKC 21 (34)
T ss_pred EECCCCCCEeECCc-CCCcC
Confidence 57999998887543 34444
No 52
>PF03668 ATP_bind_2: P-loop ATPase protein family; InterPro: IPR005337 This entry represents UPF0042 nucleotide-binding proteins. This is a family of putative P-loop ATPases [], as they contain an ATP-binding site and display ATPase and GTPase activities.; GO: 0005524 ATP binding
Probab=23.98 E-value=22 Score=27.31 Aligned_cols=12 Identities=50% Similarity=0.725 Sum_probs=10.4
Q ss_pred CCCCCccccccc
Q 034621 75 ASGCITGFHVSY 86 (89)
Q Consensus 75 ~~GC~~g~H~~~ 86 (89)
+.|||-|+|.|.
T Consensus 246 aiGCTGG~HRSV 257 (284)
T PF03668_consen 246 AIGCTGGQHRSV 257 (284)
T ss_pred EEEcCCCcCcHH
Confidence 789999999873
No 53
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=23.93 E-value=41 Score=21.96 Aligned_cols=22 Identities=23% Similarity=0.330 Sum_probs=16.0
Q ss_pred hhccccccccccccceeeccCC
Q 034621 6 IKDKEKEKVCKRCKQTYTASSN 27 (89)
Q Consensus 6 ~~~~~~~~~C~~C~~~F~~~~N 27 (89)
+........|..|++.|....+
T Consensus 64 I~~vp~~~~C~~Cg~~~~~~~~ 85 (113)
T PRK12380 64 IVYKPAQAWCWDCSQVVEIHQH 85 (113)
T ss_pred EEeeCcEEEcccCCCEEecCCc
Confidence 3444556789999999987654
No 54
>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=23.44 E-value=33 Score=21.33 Aligned_cols=21 Identities=19% Similarity=0.458 Sum_probs=12.3
Q ss_pred hccccccccccccceeeccCC
Q 034621 7 KDKEKEKVCKRCKQTYTASSN 27 (89)
Q Consensus 7 ~~~~~~~~C~~C~~~F~~~~N 27 (89)
+.......|..|++.|+-.-|
T Consensus 41 k~~~~~~~C~~Cg~~~~~~i~ 61 (81)
T PF05129_consen 41 KEGIGILSCRVCGESFQTKIN 61 (81)
T ss_dssp TTTEEEEEESSS--EEEEE--
T ss_pred cCCEEEEEecCCCCeEEEccC
Confidence 345667789999999975543
No 55
>PHA00689 hypothetical protein
Probab=23.03 E-value=31 Score=20.28 Aligned_cols=12 Identities=42% Similarity=0.952 Sum_probs=9.1
Q ss_pred ccccccccccce
Q 034621 10 EKEKVCKRCKQT 21 (89)
Q Consensus 10 ~~~~~C~~C~~~ 21 (89)
..-.+|+||++.
T Consensus 15 pravtckrcgkt 26 (62)
T PHA00689 15 PRAVTCKRCGKT 26 (62)
T ss_pred cceeehhhcccc
Confidence 345689999986
No 56
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=22.85 E-value=25 Score=21.18 Aligned_cols=16 Identities=25% Similarity=0.540 Sum_probs=12.9
Q ss_pred ccccccccccceeecc
Q 034621 10 EKEKVCKRCKQTYTAS 25 (89)
Q Consensus 10 ~~~~~C~~C~~~F~~~ 25 (89)
+....|.+|+..|...
T Consensus 15 E~~lrCPRC~~~FR~~ 30 (65)
T COG4049 15 EEFLRCPRCGMVFRRR 30 (65)
T ss_pred ceeeeCCchhHHHHHh
Confidence 4567899999999754
No 57
>COG1660 Predicted P-loop-containing kinase [General function prediction only]
Probab=22.80 E-value=25 Score=27.12 Aligned_cols=12 Identities=50% Similarity=0.725 Sum_probs=10.4
Q ss_pred CCCCCccccccc
Q 034621 75 ASGCITGFHVSY 86 (89)
Q Consensus 75 ~~GC~~g~H~~~ 86 (89)
+.|||-|+|.|.
T Consensus 247 aIGCTGGqHRSV 258 (286)
T COG1660 247 AIGCTGGQHRSV 258 (286)
T ss_pred EEccCCCccchH
Confidence 789999999873
No 58
>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=22.75 E-value=35 Score=23.42 Aligned_cols=14 Identities=14% Similarity=0.589 Sum_probs=11.8
Q ss_pred cccccccccceeec
Q 034621 11 KEKVCKRCKQTYTA 24 (89)
Q Consensus 11 ~~~~C~~C~~~F~~ 24 (89)
.+..|++||+.|..
T Consensus 2 ~l~nC~~CgklF~~ 15 (137)
T TIGR03826 2 ELANCPKCGRLFVK 15 (137)
T ss_pred CCccccccchhhhh
Confidence 36789999999986
No 59
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=22.21 E-value=48 Score=21.66 Aligned_cols=24 Identities=21% Similarity=0.479 Sum_probs=17.3
Q ss_pred ccccccccceeec-cCCCCCCceeC
Q 034621 12 EKVCKRCKQTYTA-SSNSSSSCRFH 35 (89)
Q Consensus 12 ~~~C~~C~~~F~~-~~N~~~sC~yH 35 (89)
...|+.||-.|.. .-|.++.|--=
T Consensus 58 Pa~CkkCGfef~~~~ik~pSRCP~C 82 (97)
T COG3357 58 PARCKKCGFEFRDDKIKKPSRCPKC 82 (97)
T ss_pred ChhhcccCccccccccCCcccCCcc
Confidence 3479999999987 45557777433
No 60
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=22.14 E-value=38 Score=19.86 Aligned_cols=28 Identities=25% Similarity=0.520 Sum_probs=13.8
Q ss_pred hccccccccccccceeecc-CCCCCCcee
Q 034621 7 KDKEKEKVCKRCKQTYTAS-SNSSSSCRF 34 (89)
Q Consensus 7 ~~~~~~~~C~~C~~~F~~~-~N~~~sC~y 34 (89)
+...++.+|..|+..|-.+ -...+.|.+
T Consensus 16 ~~~dDiVvCp~CgapyHR~C~~~~g~C~~ 44 (54)
T PF14446_consen 16 KDGDDIVVCPECGAPYHRDCWEKAGGCIN 44 (54)
T ss_pred cCCCCEEECCCCCCcccHHHHhhCCceEe
Confidence 3345555555555555322 223455666
No 61
>PHA00626 hypothetical protein
Probab=22.04 E-value=42 Score=20.06 Aligned_cols=20 Identities=15% Similarity=0.360 Sum_probs=15.5
Q ss_pred hccccccccccccceeeccC
Q 034621 7 KDKEKEKVCKRCKQTYTASS 26 (89)
Q Consensus 7 ~~~~~~~~C~~C~~~F~~~~ 26 (89)
..+.+..+|+.||-.|+.+.
T Consensus 18 r~~snrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 18 RGWSDDYVCCDCGYNDSKDA 37 (59)
T ss_pred cccCcceEcCCCCCeechhh
Confidence 34578889999999997543
No 62
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=21.44 E-value=46 Score=17.06 Aligned_cols=15 Identities=27% Similarity=0.649 Sum_probs=11.4
Q ss_pred ccccccccceeeccC
Q 034621 12 EKVCKRCKQTYTASS 26 (89)
Q Consensus 12 ~~~C~~C~~~F~~~~ 26 (89)
...|..|++.|....
T Consensus 5 ~y~C~~Cg~~fe~~~ 19 (41)
T smart00834 5 EYRCEDCGHTFEVLQ 19 (41)
T ss_pred EEEcCCCCCEEEEEE
Confidence 457999999997543
No 63
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=21.02 E-value=42 Score=16.41 Aligned_cols=26 Identities=19% Similarity=0.442 Sum_probs=14.6
Q ss_pred ccccccceeecc--CCCCCCceeCCCCc
Q 034621 14 VCKRCKQTYTAS--SNSSSSCRFHPSFF 39 (89)
Q Consensus 14 ~C~~C~~~F~~~--~N~~~sC~yHpG~~ 39 (89)
.|.+|++...+. ......=.||+.-+
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf 28 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECF 28 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCC
Confidence 477888876653 11223346666654
No 64
>COG1773 Rubredoxin [Energy production and conversion]
Probab=21.02 E-value=59 Score=19.13 Aligned_cols=26 Identities=19% Similarity=0.503 Sum_probs=20.1
Q ss_pred ccccccccceeeccCCCCCCceeCCCC
Q 034621 12 EKVCKRCKQTYTASSNSSSSCRFHPSF 38 (89)
Q Consensus 12 ~~~C~~C~~~F~~~~N~~~sC~yHpG~ 38 (89)
...|+.||-.|+++.- +..+-.=||.
T Consensus 3 ~~~C~~CG~vYd~e~G-dp~~gi~pgT 28 (55)
T COG1773 3 RWRCSVCGYVYDPEKG-DPRCGIAPGT 28 (55)
T ss_pred ceEecCCceEeccccC-CccCCCCCCC
Confidence 4579999999998774 5566777776
No 65
>smart00355 ZnF_C2H2 zinc finger.
Probab=20.18 E-value=41 Score=14.65 Aligned_cols=11 Identities=18% Similarity=0.833 Sum_probs=8.2
Q ss_pred ccccccceeec
Q 034621 14 VCKRCKQTYTA 24 (89)
Q Consensus 14 ~C~~C~~~F~~ 24 (89)
.|..|++.|..
T Consensus 2 ~C~~C~~~f~~ 12 (26)
T smart00355 2 RCPECGKVFKS 12 (26)
T ss_pred CCCCCcchhCC
Confidence 57788888864
No 66
>PF05810 NinF: NinF protein; InterPro: IPR008712 This family consists of several bacteriophage NinF proteins as well as related sequences from Escherichia coli.
Probab=20.13 E-value=26 Score=20.89 Aligned_cols=15 Identities=20% Similarity=0.609 Sum_probs=11.8
Q ss_pred ccccccceeeccCCC
Q 034621 14 VCKRCKQTYTASSNS 28 (89)
Q Consensus 14 ~C~~C~~~F~~~~N~ 28 (89)
.|.+|+|...+.+.+
T Consensus 19 lCa~C~~~L~~~E~h 33 (58)
T PF05810_consen 19 LCANCGQKLHPDETH 33 (58)
T ss_pred HHhccCcccccchhh
Confidence 499999998876643
Done!