Query 031507
Match_columns 158
No_of_seqs 119 out of 918
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 15:06:13 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031507.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031507hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0229 Conserved domain frequ 100.0 3.1E-43 6.6E-48 275.7 7.9 101 12-151 27-131 (140)
2 TIGR00357 methionine-R-sulfoxi 100.0 2.4E-42 5.1E-47 269.5 8.1 101 12-151 25-128 (134)
3 PRK00222 methionine sulfoxide 100.0 1.1E-41 2.3E-46 268.0 8.1 102 11-151 27-131 (142)
4 PF01641 SelR: SelR domain; I 100.0 8.4E-41 1.8E-45 257.8 7.1 100 11-148 21-123 (124)
5 PRK05508 methionine sulfoxide 100.0 5.1E-40 1.1E-44 252.2 8.0 98 11-149 17-117 (119)
6 KOG0856 Predicted pilin-like t 100.0 1.7E-37 3.7E-42 244.1 8.0 101 14-152 41-145 (146)
7 PRK14018 trifunctional thiored 100.0 6.8E-36 1.5E-40 272.7 9.3 103 11-151 402-507 (521)
8 PRK05550 bifunctional methioni 100.0 1E-34 2.2E-39 248.9 6.5 98 12-151 21-122 (283)
9 PF03226 Yippee-Mis18: Yippee 93.4 0.11 2.4E-06 37.4 3.7 38 94-145 56-93 (96)
10 PF04828 GFA: Glutathione-depe 71.1 4.7 0.0001 27.2 2.8 20 92-111 45-64 (92)
11 PF09855 DUF2082: Nucleic-acid 67.9 6.3 0.00014 27.5 2.8 20 26-46 1-20 (64)
12 PF08271 TF_Zn_Ribbon: TFIIB z 65.9 3.7 8E-05 25.7 1.3 23 21-46 15-37 (43)
13 COG1645 Uncharacterized Zn-fin 57.6 4.4 9.6E-05 32.1 0.6 24 25-48 28-51 (131)
14 PF06170 DUF983: Protein of un 56.2 5.2 0.00011 29.2 0.8 22 27-53 10-31 (86)
15 PF13248 zf-ribbon_3: zinc-rib 55.6 6.4 0.00014 22.4 0.9 20 27-48 4-23 (26)
16 PRK13796 GTPase YqeH; Provisio 49.1 7.8 0.00017 34.2 0.9 19 27-47 2-20 (365)
17 TIGR01384 TFS_arch transcripti 47.4 38 0.00082 24.4 4.1 20 91-110 58-77 (104)
18 PF15288 zf-CCHC_6: Zinc knuck 44.9 7.4 0.00016 25.1 0.1 16 95-111 1-16 (40)
19 COG3791 Uncharacterized conser 43.5 28 0.00062 26.6 3.1 16 97-112 71-86 (133)
20 KOG3507 DNA-directed RNA polym 42.7 19 0.00041 25.3 1.8 23 21-43 16-38 (62)
21 PF03811 Zn_Tnp_IS1: InsA N-te 41.8 35 0.00075 21.2 2.7 22 91-113 1-22 (36)
22 PF13240 zinc_ribbon_2: zinc-r 40.2 16 0.00034 20.5 0.9 19 28-48 2-20 (23)
23 TIGR03597 GTPase_YqeH ribosome 40.0 12 0.00025 33.0 0.5 18 28-47 1-18 (360)
24 PF11781 RRN7: RNA polymerase 39.8 15 0.00032 22.8 0.8 15 20-34 20-34 (36)
25 PRK00398 rpoP DNA-directed RNA 39.4 56 0.0012 20.4 3.5 13 25-37 3-15 (46)
26 PRK00420 hypothetical protein; 39.0 17 0.00037 27.9 1.3 23 26-48 24-47 (112)
27 cd05720 Ig_CD8_alpha Immunoglo 36.1 21 0.00045 25.5 1.3 12 20-31 78-89 (104)
28 COG2126 RPL37A Ribosomal prote 30.3 23 0.0005 24.9 0.6 19 92-110 13-31 (61)
29 PF10601 zf-LITAF-like: LITAF- 29.5 35 0.00075 23.3 1.4 66 23-107 5-70 (73)
30 smart00659 RPOLCX RNA polymera 27.7 69 0.0015 20.6 2.5 13 25-37 2-14 (44)
31 PF07295 DUF1451: Protein of u 27.4 41 0.0009 26.7 1.7 21 20-40 107-127 (146)
32 TIGR02098 MJ0042_CXXC MJ0042 f 27.2 40 0.00087 20.1 1.3 12 94-105 24-35 (38)
33 PF13842 Tnp_zf-ribbon_2: DDE_ 26.1 49 0.0011 19.8 1.5 14 92-105 13-26 (32)
34 PF10058 DUF2296: Predicted in 26.1 43 0.00092 22.4 1.4 21 92-112 19-39 (54)
35 PF13790 DUF4182: Domain of un 24.8 48 0.001 21.2 1.3 17 95-111 3-19 (38)
36 COG1996 RPC10 DNA-directed RNA 23.6 40 0.00087 22.6 0.9 13 23-35 4-16 (49)
37 PRK00423 tfb transcription ini 23.5 50 0.0011 28.6 1.7 32 20-64 25-56 (310)
38 smart00709 Zpr1 Duplicated dom 23.0 1.3E+02 0.0028 24.1 3.9 34 94-143 28-61 (160)
39 COG5349 Uncharacterized protei 23.0 36 0.00077 27.0 0.6 24 25-53 40-63 (126)
40 PF06677 Auto_anti-p27: Sjogre 22.9 35 0.00077 21.8 0.5 10 27-36 19-28 (41)
41 PF03604 DNA_RNApol_7kD: DNA d 22.8 56 0.0012 19.8 1.3 12 26-37 1-12 (32)
42 COG1644 RPB10 DNA-directed RNA 22.8 22 0.00048 25.1 -0.5 17 94-110 3-19 (63)
43 PF01020 Ribosomal_L40e: Ribos 22.3 39 0.00085 23.0 0.6 12 94-105 16-27 (52)
44 PF00047 ig: Immunoglobulin do 21.1 55 0.0012 20.2 1.1 17 14-30 48-64 (64)
45 PF10955 DUF2757: Protein of u 20.8 60 0.0013 23.5 1.4 13 23-35 2-14 (76)
46 COG0358 DnaG DNA primase (bact 20.6 66 0.0014 30.2 1.9 15 20-34 50-64 (568)
No 1
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=3.1e-43 Score=275.68 Aligned_cols=101 Identities=25% Similarity=0.401 Sum_probs=84.1
Q ss_pred cccCCCCc--cccCeEEEccccCcccccCCCCccCCCCCCCCCCcCCCCceeEEc-ccCccceeecccccccccccCCCC
Q 031507 12 HHSFSSSI--SQRHVSYSCGSCGYELNLSSCNRNISSIGLKYGKSMKRGIIAFVD-IDESRFTQVDELQCIPHFSKNSWG 88 (158)
Q Consensus 12 ~~~~~~s~--~~~~G~Y~C~~Cg~~Lf~sS~~KfdSg~Gpsf~~~~~~G~~sF~~-id~~~~~~~~e~~~~p~f~~~s~g 88 (158)
-++|++.+ .+++|+|+|++||+||| +|++||||||| ||||++ |++..|++.+ |.|+|
T Consensus 27 E~pft~~y~~~~~~GiY~c~~cg~pLF-~S~~KfdSgcG----------WPSF~~pi~~~~I~~~~---------D~S~g 86 (140)
T COG0229 27 ERPFTGEYLDNKEKGIYVCIVCGEPLF-SSEDKFDSGCG----------WPSFTKPISPDAITYKE---------DRSHG 86 (140)
T ss_pred CCCCCChhhcccCCceEEeecCCCccc-cccccccCCCC----------CccccccCCcccceEee---------ccCCC
Confidence 46777777 88999999999999997 89999999995 555554 3344444443 46666
Q ss_pred CceeeeEEecCccCCCeeeecCCCCCCCCCCCCCCCCCCCCCCCCC-ceeeeeeceeeecCCCC
Q 031507 89 ILRHRTKLLCRKCGNPIGIAYTDKTSAYSPKSNGSDSPSVPGASGR-RKYDVRIRALQPSSSEE 151 (158)
Q Consensus 89 ~~m~RTEv~C~~Cg~HLGHVF~DGP~~~~~~~~~~~~~~~~~~ptg-~RYcIns~AL~~~~~~~ 151 (158)
|.||||+|++|++||||||+|||+ |+| +||||||+||+|++.++
T Consensus 87 --M~RtEVrc~~c~sHLGHVF~DGP~-----------------~tgglRYCINSasL~Fip~~~ 131 (140)
T COG0229 87 --MVRTEVRCANCDSHLGHVFPDGPP-----------------PTGGLRYCINSASLRFIPKEE 131 (140)
T ss_pred --cEEEEEEecCCCCccccccCCCCC-----------------CCCCeeEeecchheeecchhh
Confidence 899999999999999999999998 777 99999999999999743
No 2
>TIGR00357 methionine-R-sulfoxide reductase. This model describes a domain found in PilB, a protein important for pilin expression, N-terminal to a domain coextensive to with the known peptide methionine sulfoxide reductase (MsrA), a protein repair enzyme, of E. coli. Among the early completed genomes, this module is found if and only if MsrA is also found, whether N-terminal to MsrA (as for Helicobacter pylori), C-terminal (as for Treponema pallidum), or in a separate polypeptide. Although the function of this region is not clear, an auxiliary function to MsrA is suggested.
Probab=100.00 E-value=2.4e-42 Score=269.52 Aligned_cols=101 Identities=26% Similarity=0.351 Sum_probs=83.5
Q ss_pred cccCCCCc--cccCeEEEccccCcccccCCCCccCCCCCCCCCCcCCCCceeEEc-ccCccceeecccccccccccCCCC
Q 031507 12 HHSFSSSI--SQRHVSYSCGSCGYELNLSSCNRNISSIGLKYGKSMKRGIIAFVD-IDESRFTQVDELQCIPHFSKNSWG 88 (158)
Q Consensus 12 ~~~~~~s~--~~~~G~Y~C~~Cg~~Lf~sS~~KfdSg~Gpsf~~~~~~G~~sF~~-id~~~~~~~~e~~~~p~f~~~s~g 88 (158)
-++|++.+ .+++|+|+|++||+||| +|++||+|||| ||||++ +++.+|++.. |.++|
T Consensus 25 E~pftg~y~~~~~~G~Y~C~~Cg~pLF-~S~~KfdSg~G----------WPSF~~~i~~~~V~~~~---------D~s~g 84 (134)
T TIGR00357 25 EPPFTNEYWDNKEEGIYVDITCGEPLF-SSEDKFDSGCG----------WPSFYKPISEEVVAYER---------DESHG 84 (134)
T ss_pred CCCCCCCCCCCCCCeEEEccCCCCccc-cccchhcCCCC----------CcCcCcccCCCceEEee---------cCCCC
Confidence 35677776 78999999999999997 89999999995 555554 3344444443 35555
Q ss_pred CceeeeEEecCccCCCeeeecCCCCCCCCCCCCCCCCCCCCCCCCCceeeeeeceeeecCCCC
Q 031507 89 ILRHRTKLLCRKCGNPIGIAYTDKTSAYSPKSNGSDSPSVPGASGRRKYDVRIRALQPSSSEE 151 (158)
Q Consensus 89 ~~m~RTEv~C~~Cg~HLGHVF~DGP~~~~~~~~~~~~~~~~~~ptg~RYcIns~AL~~~~~~~ 151 (158)
|+||||+|++||+||||||+|||+ |||+||||||+||.|++.++
T Consensus 85 --m~RtEv~C~~Cg~HLGHVF~DGP~-----------------ptg~RyCINs~sL~F~p~~~ 128 (134)
T TIGR00357 85 --MIRTEVRCRNCDAHLGHVFDDGPE-----------------PTGLRYCINSAALKFIPLEE 128 (134)
T ss_pred --cEEEEEEecCCCCccCcccCCCCC-----------------CCCceEeecceeEecccchh
Confidence 899999999999999999999997 99999999999999998643
No 3
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=100.00 E-value=1.1e-41 Score=268.01 Aligned_cols=102 Identities=24% Similarity=0.402 Sum_probs=84.3
Q ss_pred ccccCCCCc--cccCeEEEccccCcccccCCCCccCCCCCCCCCCcCCCCceeEEc-ccCccceeecccccccccccCCC
Q 031507 11 HHHSFSSSI--SQRHVSYSCGSCGYELNLSSCNRNISSIGLKYGKSMKRGIIAFVD-IDESRFTQVDELQCIPHFSKNSW 87 (158)
Q Consensus 11 ~~~~~~~s~--~~~~G~Y~C~~Cg~~Lf~sS~~KfdSg~Gpsf~~~~~~G~~sF~~-id~~~~~~~~e~~~~p~f~~~s~ 87 (158)
--++|++.+ .+++|+|+|++||+||| +|.+||+|||| ||||++ +++++|++.. |.++
T Consensus 27 TE~pftg~~~~~~~~G~Y~C~~Cg~pLF-~S~~Kf~Sg~G----------WPSF~~~i~~~~V~~~~---------D~s~ 86 (142)
T PRK00222 27 TERPFTGEYLDNKEKGIYVCIVCGEPLF-SSDTKFDSGCG----------WPSFTKPIDEEAIRELR---------DTSH 86 (142)
T ss_pred CCCCCCCCCCCCCCCeEEEecCCCchhc-CCcccccCCCC----------CcCcCcccCCCceEEee---------ccCC
Confidence 346677776 78999999999999997 99999999995 555554 3344455443 3455
Q ss_pred CCceeeeEEecCccCCCeeeecCCCCCCCCCCCCCCCCCCCCCCCCCceeeeeeceeeecCCCC
Q 031507 88 GILRHRTKLLCRKCGNPIGIAYTDKTSAYSPKSNGSDSPSVPGASGRRKYDVRIRALQPSSSEE 151 (158)
Q Consensus 88 g~~m~RTEv~C~~Cg~HLGHVF~DGP~~~~~~~~~~~~~~~~~~ptg~RYcIns~AL~~~~~~~ 151 (158)
| |.||||+|++||+||||||+|||+ |||+||||||+||+|++.++
T Consensus 87 g--m~RtEv~C~~Cg~HLGHVF~DGP~-----------------ptg~RyCINs~sL~F~p~~~ 131 (142)
T PRK00222 87 G--MVRTEVRCANCDSHLGHVFPDGPK-----------------PTGLRYCINSASLKFIPKDG 131 (142)
T ss_pred C--ceEEEEEeCCCCCccCcccCCCCC-----------------CCCCEeeeceeeEEeeccch
Confidence 5 899999999999999999999997 99999999999999999753
No 4
>PF01641 SelR: SelR domain; InterPro: IPR002579 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine []. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [, ]. The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represents MsrB, the crystal structure of which has been determined to 1.8A []. The overall structure shows no resemblance to the structures of MsrA (IPR002569 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. Unlike the MsrA domain, the MsrB domain activates the cysteine or selenocysteine nucleophile through a unique Cys-Arg-Asp/Glu catalytic triad. The collapse of the reaction intermediate most likely results in the formation of a sulphenic or selenenic acid moiety. Regeneration of the active site occurs through a series of thiol-disulphide exchange steps involving another active site Cys residue and thioredoxin. In a number of pathogenic bacteria, including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis, a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0008113 peptide-methionine-(S)-S-oxide reductase activity, 0055114 oxidation-reduction process; PDB: 1L1D_A 3E0O_D 2KZN_A 3HCG_B 3HCH_A 2L1U_A 3MAO_A 2K8D_A 3HCJ_A 3HCI_A ....
Probab=100.00 E-value=8.4e-41 Score=257.79 Aligned_cols=100 Identities=24% Similarity=0.395 Sum_probs=81.1
Q ss_pred ccccCCCCc--cccCeEEEccccCcccccCCCCccCCCCCCCCCCcCCCCceeEEc-ccCccceeecccccccccccCCC
Q 031507 11 HHHSFSSSI--SQRHVSYSCGSCGYELNLSSCNRNISSIGLKYGKSMKRGIIAFVD-IDESRFTQVDELQCIPHFSKNSW 87 (158)
Q Consensus 11 ~~~~~~~s~--~~~~G~Y~C~~Cg~~Lf~sS~~KfdSg~Gpsf~~~~~~G~~sF~~-id~~~~~~~~e~~~~p~f~~~s~ 87 (158)
--++|++.+ .+++|+|+|++||+||| +|++||+||| |||||++ +++.+|+... |.++
T Consensus 21 TE~pfsg~y~~~~~~G~Y~C~~Cg~pLF-~S~~Kf~Sg~----------GWPSF~~~i~~~~v~~~~---------D~s~ 80 (124)
T PF01641_consen 21 TERPFSGEYWDHKEEGIYVCAVCGTPLF-SSDTKFDSGC----------GWPSFWQPIPGDAVKERE---------DFSH 80 (124)
T ss_dssp SSSTTSSGGCCTTSSEEEEETTTS-EEE-EGGGEETSSS----------SSSEESSCSSTTSEEEEE---------EECT
T ss_pred CCCCCccCCcCCCCCEEEEcCCCCCccc-cCcccccCCc----------CCccccCcCChHHEEEec---------cccC
Confidence 345677776 78999999999999997 8999999999 6666666 4554555543 3455
Q ss_pred CCceeeeEEecCccCCCeeeecCCCCCCCCCCCCCCCCCCCCCCCCCceeeeeeceeeecC
Q 031507 88 GILRHRTKLLCRKCGNPIGIAYTDKTSAYSPKSNGSDSPSVPGASGRRKYDVRIRALQPSS 148 (158)
Q Consensus 88 g~~m~RTEv~C~~Cg~HLGHVF~DGP~~~~~~~~~~~~~~~~~~ptg~RYcIns~AL~~~~ 148 (158)
| |+||||+|++||+||||||+|||+ .+||+||||||+||.|.+
T Consensus 81 g--~~R~Ev~C~~Cg~HLGHVF~DGp~----------------~~tg~RyCINS~sL~F~p 123 (124)
T PF01641_consen 81 G--MVRTEVRCARCGSHLGHVFDDGPP----------------PPTGLRYCINSASLKFIP 123 (124)
T ss_dssp S--SEEEEEEETTTCCEEEEEESTSST----------------TCTSCEEEE-GGGEEEEE
T ss_pred C--ceEEEEEecCCCCccccEeCCCCC----------------CCCCcEEEeeeeeEEEec
Confidence 5 899999999999999999999997 157999999999999975
No 5
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=100.00 E-value=5.1e-40 Score=252.19 Aligned_cols=98 Identities=20% Similarity=0.351 Sum_probs=77.3
Q ss_pred ccccCCCCc--cccCeEEEccccCcccccCCCCccCCCCCCCCCCcCCCCceeEEcccCccceeecccccccccccCCCC
Q 031507 11 HHHSFSSSI--SQRHVSYSCGSCGYELNLSSCNRNISSIGLKYGKSMKRGIIAFVDIDESRFTQVDELQCIPHFSKNSWG 88 (158)
Q Consensus 11 ~~~~~~~s~--~~~~G~Y~C~~Cg~~Lf~sS~~KfdSg~Gpsf~~~~~~G~~sF~~id~~~~~~~~e~~~~p~f~~~s~g 88 (158)
--++|++.+ .+++|+|+|++||+||| +|++||||||| ||||++..+.+|+.+. |.+
T Consensus 17 TE~pftg~y~~~~~~G~Y~C~~Cg~pLF-~S~~KfdSg~G----------WPSF~~~i~~~v~~~~---------D~~-- 74 (119)
T PRK05508 17 TEPPFSGEYNDFFEKGTYVCKQCGAPLY-RSEDKFKSGCG----------WPSFDDEIKGAVKRIP---------DAD-- 74 (119)
T ss_pred CCCCCCCCCcCcCCCeEEEecCCCCccc-cccccccCCCC----------CcccCcccccceEEEe---------cCC--
Confidence 345677766 78999999999999997 99999999995 5555542123333332 233
Q ss_pred CceeeeEEecCccCCCeeeecCCC-CCCCCCCCCCCCCCCCCCCCCCceeeeeeceeeecCC
Q 031507 89 ILRHRTKLLCRKCGNPIGIAYTDK-TSAYSPKSNGSDSPSVPGASGRRKYDVRIRALQPSSS 149 (158)
Q Consensus 89 ~~m~RTEv~C~~Cg~HLGHVF~DG-P~~~~~~~~~~~~~~~~~~ptg~RYcIns~AL~~~~~ 149 (158)
|+||||+|++||+||||||+|+ |+ |||+||||||+||+|.+.
T Consensus 75 --~~RtEv~C~~C~~HLGHVF~d~gp~-----------------ptg~RyCINS~sL~F~p~ 117 (119)
T PRK05508 75 --GRRTEIVCANCGGHLGHVFEGEGFT-----------------PKNTRHCVNSISLKFVPD 117 (119)
T ss_pred --CcEEEEEeCCCCCccCcccCCCCCC-----------------CCCCEEeecceeEEeecC
Confidence 3699999999999999999954 54 899999999999999874
No 6
>KOG0856 consensus Predicted pilin-like transcription factor [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.7e-37 Score=244.13 Aligned_cols=101 Identities=22% Similarity=0.379 Sum_probs=83.1
Q ss_pred cCCCCc--cccCeEEEccccCcccccCCCCccCCCCC-CCCCCcCCCCceeEEcccCccceeecccccccccccCCCCCc
Q 031507 14 SFSSSI--SQRHVSYSCGSCGYELNLSSCNRNISSIG-LKYGKSMKRGIIAFVDIDESRFTQVDELQCIPHFSKNSWGIL 90 (158)
Q Consensus 14 ~~~~s~--~~~~G~Y~C~~Cg~~Lf~sS~~KfdSg~G-psf~~~~~~G~~sF~~id~~~~~~~~e~~~~p~f~~~s~g~~ 90 (158)
.+...+ .+++|+|+|++|++||| +|++||||||| |+|+++|..|.| ++.+ |++++
T Consensus 41 p~tGey~~~~e~GvY~C~~C~~pLy-kS~tKfdsgcGWPAF~e~i~~gaI----------~r~~---------d~s~~-- 98 (146)
T KOG0856|consen 41 PGTGEYTKHFEEGVYVCAGCGTPLY-KSTTKFDSGCGWPAFFEAIGPGAI----------TRTP---------DNSRG-- 98 (146)
T ss_pred CCCcccccccCCceEEEeecCCccc-cccccccCCCCCchhhhccCCCce----------eecc---------ccCCC--
Confidence 344444 67999999999999997 99999999996 666666655554 3333 35555
Q ss_pred eeeeEEecCccCCCeeeecC-CCCCCCCCCCCCCCCCCCCCCCCCceeeeeeceeeecCCCCC
Q 031507 91 RHRTKLLCRKCGNPIGIAYT-DKTSAYSPKSNGSDSPSVPGASGRRKYDVRIRALQPSSSEES 152 (158)
Q Consensus 91 m~RTEv~C~~Cg~HLGHVF~-DGP~~~~~~~~~~~~~~~~~~ptg~RYcIns~AL~~~~~~~~ 152 (158)
|.||||.|++||+||||||+ |||. .||++||||||+||.|.+++.+
T Consensus 99 ~~R~Ev~Ca~C~~HLGHVF~~eG~~----------------~Pt~~R~CiNS~sL~F~~~~~s 145 (146)
T KOG0856|consen 99 GRRTEVSCATCGGHLGHVFKGEGPK----------------TPTDERHCINSVSLKFVPADSS 145 (146)
T ss_pred CcceEEEEeecCCceeeeecCCCCC----------------CCCCceeEeeeeeeeeccCCCC
Confidence 68999999999999999998 9997 5999999999999999998764
No 7
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=100.00 E-value=6.8e-36 Score=272.74 Aligned_cols=103 Identities=23% Similarity=0.264 Sum_probs=84.3
Q ss_pred ccccCCCCc--cccCeEEEccccCcccccCCCCccCCCCCCCCCCcCCCCceeEEc-ccCccceeecccccccccccCCC
Q 031507 11 HHHSFSSSI--SQRHVSYSCGSCGYELNLSSCNRNISSIGLKYGKSMKRGIIAFVD-IDESRFTQVDELQCIPHFSKNSW 87 (158)
Q Consensus 11 ~~~~~~~s~--~~~~G~Y~C~~Cg~~Lf~sS~~KfdSg~Gpsf~~~~~~G~~sF~~-id~~~~~~~~e~~~~p~f~~~s~ 87 (158)
--++|++.+ .+++|+|+|++||+||| +|.+||+|||| ||||++ ++++.+++.. |.++
T Consensus 402 tE~~f~~~~~~~~~~G~y~c~~c~~pLf-~s~~Kf~sg~G----------WPsF~~~i~~~~v~~~~---------d~s~ 461 (521)
T PRK14018 402 TERAFSHEYDHLFKPGIYVDVVSGEPLF-SSADKYDSGCG----------WPSFTRPIDAKVVTEHD---------DFSY 461 (521)
T ss_pred CCCCCCCCCcCCCCCEEEEecCCCCccc-cCcccccCCCC----------CcccCcccCcCceEEee---------ccCC
Confidence 346777776 88999999999999997 99999999995 555554 3444444433 4566
Q ss_pred CCceeeeEEecCccCCCeeeecCCCCCCCCCCCCCCCCCCCCCCCCCceeeeeeceeeecCCCC
Q 031507 88 GILRHRTKLLCRKCGNPIGIAYTDKTSAYSPKSNGSDSPSVPGASGRRKYDVRIRALQPSSSEE 151 (158)
Q Consensus 88 g~~m~RTEv~C~~Cg~HLGHVF~DGP~~~~~~~~~~~~~~~~~~ptg~RYcIns~AL~~~~~~~ 151 (158)
| |.||||+|++||+||||||+|||+ .|||+||||||+||+|.+.++
T Consensus 462 g--~~R~Ev~c~~c~~HLGHvf~dgp~----------------~~~g~RyCiNs~~l~f~~~~~ 507 (521)
T PRK14018 462 N--MRRTEVRSRAADSHLGHVFPDGPR----------------DKGGLRYCINGASLKFIPLEQ 507 (521)
T ss_pred C--ceEEEEEECCCCCcCCcccCCCCC----------------CCCCCEeeeceeEEEeecchh
Confidence 5 899999999999999999999996 279999999999999998753
No 8
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=100.00 E-value=1e-34 Score=248.90 Aligned_cols=98 Identities=22% Similarity=0.438 Sum_probs=78.2
Q ss_pred cccCCCCc--cccCeEEEccccCcccccCCCCccCCCCC-CCCCCcCCCCceeEEcccCccceeecccccccccccCCCC
Q 031507 12 HHSFSSSI--SQRHVSYSCGSCGYELNLSSCNRNISSIG-LKYGKSMKRGIIAFVDIDESRFTQVDELQCIPHFSKNSWG 88 (158)
Q Consensus 12 ~~~~~~s~--~~~~G~Y~C~~Cg~~Lf~sS~~KfdSg~G-psf~~~~~~G~~sF~~id~~~~~~~~e~~~~p~f~~~s~g 88 (158)
-++|++.+ .+++|+|+|++||+||| +|++||+|||| |||+++|+. .++... |.+ |
T Consensus 21 E~pf~g~~~~~~~~G~y~c~~c~~~LF-~s~~Kf~sg~GWPsF~~~~~~-----------~~~~~~---------d~~-~ 78 (283)
T PRK05550 21 ERPFSGEYYDHDEKGVYLCRRCGAPLF-RSEDKFNSGCGWPSFDDEIPG-----------AVKRLP---------DAD-G 78 (283)
T ss_pred CCCCCCcCcCCCCCcEEEcCCCCchhc-CChhhccCCCCCcCcCcccCC-----------ccEEEE---------cCC-C
Confidence 45677766 78999999999999997 99999999995 444444432 222222 222 3
Q ss_pred CceeeeEEecCccCCCeeeecC-CCCCCCCCCCCCCCCCCCCCCCCCceeeeeeceeeecCCCC
Q 031507 89 ILRHRTKLLCRKCGNPIGIAYT-DKTSAYSPKSNGSDSPSVPGASGRRKYDVRIRALQPSSSEE 151 (158)
Q Consensus 89 ~~m~RTEv~C~~Cg~HLGHVF~-DGP~~~~~~~~~~~~~~~~~~ptg~RYcIns~AL~~~~~~~ 151 (158)
| ||||+|++||+||||||+ |||+ |||+||||||+||+|.+.+.
T Consensus 79 --~-R~Ev~c~~c~~HLGHvF~ddgp~-----------------ptg~RyCiNs~sL~f~p~~~ 122 (283)
T PRK05550 79 --R-RTEIVCANCGAHLGHVFEGEGLT-----------------PKNTRHCVNSASLDFVPAEE 122 (283)
T ss_pred --c-eEEEEecCCCCccCcccCCCCCC-----------------CCCccccccccccccCcccc
Confidence 4 999999999999999998 7776 89999999999999999755
No 9
>PF03226 Yippee-Mis18: Yippee zinc-binding/DNA-binding /Mis18, centromere assembly; InterPro: IPR004910 This entry represents the Yippee-like (YPEL) family of putative zinc-binding proteins which is highly conserved among eukaryotes. The first protein in this family to be characterised, the Yippee protein from Drosophila, was identified by yeast interaction trap screen as a protein that physically interacts with moth hemolin []. It was subsequently found to be a member of a highly conserved family of proteins found in diverse eukaryotes including plants, animals and fungi []. Mammals contain five members of this family, YPEL1 to YPEL5, while other organisms tend to contain only two or three members. The mammalian proteins all appear to localise in the nucleus. YPEL1-4 are located in an unknown structure located on or close to the mitotic apparatus in the mitotic phase, whereas in the interphase they are located in the nuclei and nucleoli. In contrast, YPEL5 is localised to the centrosome and nucleus during interphase and at the mitotic spindle during mitosis, suggesting a function distinct from that of YPEL1-4. The localisation of the YPEL proteins suggests a novel, thopugh still unknown, function involved in cell division.
Probab=93.44 E-value=0.11 Score=37.36 Aligned_cols=38 Identities=16% Similarity=0.393 Sum_probs=28.3
Q ss_pred eEEecCccCCCeeeecCCCCCCCCCCCCCCCCCCCCCCCCCceeeeeeceee
Q 031507 94 TKLLCRKCGNPIGIAYTDKTSAYSPKSNGSDSPSVPGASGRRKYDVRIRALQ 145 (158)
Q Consensus 94 TEv~C~~Cg~HLGHVF~DGP~~~~~~~~~~~~~~~~~~ptg~RYcIns~AL~ 145 (158)
..|.|++|+.+||=.|..-|++ .....-+|++...+|.
T Consensus 56 ~~l~C~~C~~~lGwkY~~a~~~--------------~~~k~g~file~~~i~ 93 (96)
T PF03226_consen 56 RDLFCSGCNTILGWKYESAPEE--------------QKYKEGKFILEKASIS 93 (96)
T ss_pred EEeEcccCChhHCcEEEEcCHh--------------HhhhCCEEEEEhhHEE
Confidence 6799999999999999766541 1244558888877765
No 10
>PF04828 GFA: Glutathione-dependent formaldehyde-activating enzyme; InterPro: IPR006913 The GFA family consists mainly of glutathione-dependent formaldehyde-activating enzymes, but also includes centromere protein V and a fission yeast protein described as uncharacterised lyase. Glutathione-dependent formaldehyde-activating enzyme catalyse the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione. All known members of this family contain 5 strongly conserved cysteine residues.; GO: 0016846 carbon-sulfur lyase activity, 0008152 metabolic process; PDB: 3FAC_B 1XA8_A 1X6M_B.
Probab=71.08 E-value=4.7 Score=27.22 Aligned_cols=20 Identities=20% Similarity=0.519 Sum_probs=13.5
Q ss_pred eeeEEecCccCCCeeeecCC
Q 031507 92 HRTKLLCRKCGNPIGIAYTD 111 (158)
Q Consensus 92 ~RTEv~C~~Cg~HLGHVF~D 111 (158)
..+...|++||.+|....+.
T Consensus 45 ~~~r~FC~~CGs~l~~~~~~ 64 (92)
T PF04828_consen 45 GVERYFCPTCGSPLFSEDER 64 (92)
T ss_dssp SCEEEEETTT--EEEEEESS
T ss_pred cCcCcccCCCCCeeecccCC
Confidence 45669999999999876433
No 11
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=67.91 E-value=6.3 Score=27.51 Aligned_cols=20 Identities=30% Similarity=0.579 Sum_probs=14.3
Q ss_pred EEccccCcccccCCCCccCCC
Q 031507 26 YSCGSCGYELNLSSCNRNISS 46 (158)
Q Consensus 26 Y~C~~Cg~~Lf~sS~~KfdSg 46 (158)
|.|.-||..-+ .+...-.+|
T Consensus 1 y~C~KCg~~~~-e~~~v~~tg 20 (64)
T PF09855_consen 1 YKCPKCGNEEY-ESGEVRATG 20 (64)
T ss_pred CCCCCCCCcce-ecceEEccC
Confidence 78999999876 455555555
No 12
>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=65.89 E-value=3.7 Score=25.68 Aligned_cols=23 Identities=22% Similarity=0.306 Sum_probs=14.8
Q ss_pred ccCeEEEccccCcccccCCCCccCCC
Q 031507 21 QRHVSYSCGSCGYELNLSSCNRNISS 46 (158)
Q Consensus 21 ~~~G~Y~C~~Cg~~Lf~sS~~KfdSg 46 (158)
...|.+.|..||.-|- +...+++
T Consensus 15 ~~~g~~vC~~CG~Vl~---e~~i~~~ 37 (43)
T PF08271_consen 15 PERGELVCPNCGLVLE---ENIIDEG 37 (43)
T ss_dssp TTTTEEEETTT-BBEE----TTBSCC
T ss_pred CCCCeEECCCCCCEee---cccccCC
Confidence 4568999999999883 3444444
No 13
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=57.61 E-value=4.4 Score=32.11 Aligned_cols=24 Identities=21% Similarity=0.299 Sum_probs=17.8
Q ss_pred EEEccccCcccccCCCCccCCCCC
Q 031507 25 SYSCGSCGYELNLSSCNRNISSIG 48 (158)
Q Consensus 25 ~Y~C~~Cg~~Lf~sS~~KfdSg~G 48 (158)
.++|..||.|||-.-..-|-+-||
T Consensus 28 ~~hCp~Cg~PLF~KdG~v~CPvC~ 51 (131)
T COG1645 28 AKHCPKCGTPLFRKDGEVFCPVCG 51 (131)
T ss_pred HhhCcccCCcceeeCCeEECCCCC
Confidence 489999999998555555666663
No 14
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=56.19 E-value=5.2 Score=29.20 Aligned_cols=22 Identities=23% Similarity=0.481 Sum_probs=16.9
Q ss_pred EccccCcccccCCCCccCCCCCCCCCC
Q 031507 27 SCGSCGYELNLSSCNRNISSIGLKYGK 53 (158)
Q Consensus 27 ~C~~Cg~~Lf~sS~~KfdSg~Gpsf~~ 53 (158)
.|..||+++. ..+++=||+|+-
T Consensus 10 ~C~~CG~d~~-----~~~adDgPA~fv 31 (86)
T PF06170_consen 10 RCPHCGLDYS-----HARADDGPAYFV 31 (86)
T ss_pred cccccCCccc-----cCCcCccchhHH
Confidence 6999999995 566776777763
No 15
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=55.56 E-value=6.4 Score=22.42 Aligned_cols=20 Identities=25% Similarity=0.551 Sum_probs=17.3
Q ss_pred EccccCcccccCCCCccCCCCC
Q 031507 27 SCGSCGYELNLSSCNRNISSIG 48 (158)
Q Consensus 27 ~C~~Cg~~Lf~sS~~KfdSg~G 48 (158)
.|..||+++ ..++||=+.||
T Consensus 4 ~Cp~Cg~~~--~~~~~fC~~CG 23 (26)
T PF13248_consen 4 FCPNCGAEI--DPDAKFCPNCG 23 (26)
T ss_pred CCcccCCcC--CcccccChhhC
Confidence 589999976 68999999886
No 16
>PRK13796 GTPase YqeH; Provisional
Probab=49.14 E-value=7.8 Score=34.23 Aligned_cols=19 Identities=21% Similarity=0.550 Sum_probs=15.3
Q ss_pred EccccCcccccCCCCccCCCC
Q 031507 27 SCGSCGYELNLSSCNRNISSI 47 (158)
Q Consensus 27 ~C~~Cg~~Lf~sS~~KfdSg~ 47 (158)
.|.+||..| -++++-..|-
T Consensus 2 ~C~GCG~~l--q~~~~~~~Gy 20 (365)
T PRK13796 2 RCIGCGAAI--QTEDKNKPGY 20 (365)
T ss_pred cccCCCcee--EcCCCCCCCC
Confidence 599999999 4788877774
No 17
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=47.40 E-value=38 Score=24.39 Aligned_cols=20 Identities=25% Similarity=0.516 Sum_probs=15.4
Q ss_pred eeeeEEecCccCCCeeeecC
Q 031507 91 RHRTKLLCRKCGNPIGIAYT 110 (158)
Q Consensus 91 m~RTEv~C~~Cg~HLGHVF~ 110 (158)
..||++.|.+||+.-...|.
T Consensus 58 ~~~~~~~Cp~Cg~~~a~f~~ 77 (104)
T TIGR01384 58 LPTTRVECPKCGHKEAYYWL 77 (104)
T ss_pred CCcccCCCCCCCCCeeEEEE
Confidence 46899999999877666554
No 18
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=44.94 E-value=7.4 Score=25.13 Aligned_cols=16 Identities=38% Similarity=0.902 Sum_probs=11.9
Q ss_pred EEecCccCCCeeeecCC
Q 031507 95 KLLCRKCGNPIGIAYTD 111 (158)
Q Consensus 95 Ev~C~~Cg~HLGHVF~D 111 (158)
++.|.+||+ +||.=.+
T Consensus 1 k~kC~~CG~-~GH~~t~ 16 (40)
T PF15288_consen 1 KVKCKNCGA-FGHMRTN 16 (40)
T ss_pred Ccccccccc-ccccccC
Confidence 368999976 7896543
No 19
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=43.54 E-value=28 Score=26.60 Aligned_cols=16 Identities=31% Similarity=0.760 Sum_probs=12.6
Q ss_pred ecCccCCCeeeecCCC
Q 031507 97 LCRKCGNPIGIAYTDK 112 (158)
Q Consensus 97 ~C~~Cg~HLGHVF~DG 112 (158)
-|++||.||-.-..++
T Consensus 71 FC~~CGs~l~~~~~~~ 86 (133)
T COG3791 71 FCPTCGSPLFWRGPDE 86 (133)
T ss_pred ecccCCCceEEecCCC
Confidence 9999999997655443
No 20
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=42.74 E-value=19 Score=25.33 Aligned_cols=23 Identities=30% Similarity=0.585 Sum_probs=17.5
Q ss_pred ccCeEEEccccCcccccCCCCcc
Q 031507 21 QRHVSYSCGSCGYELNLSSCNRN 43 (158)
Q Consensus 21 ~~~G~Y~C~~Cg~~Lf~sS~~Kf 43 (158)
....+|.|+-||+++-+++.+-+
T Consensus 16 ~~~miYiCgdC~~en~lk~~D~i 38 (62)
T KOG3507|consen 16 TATMIYICGDCGQENTLKRGDVI 38 (62)
T ss_pred cccEEEEeccccccccccCCCcE
Confidence 35689999999999976555443
No 21
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=41.77 E-value=35 Score=21.21 Aligned_cols=22 Identities=14% Similarity=0.425 Sum_probs=15.6
Q ss_pred eeeeEEecCccCCCeeeecCCCC
Q 031507 91 RHRTKLLCRKCGNPIGIAYTDKT 113 (158)
Q Consensus 91 m~RTEv~C~~Cg~HLGHVF~DGP 113 (158)
|.-++|.|..|++..+ |..-|.
T Consensus 1 Ma~i~v~CP~C~s~~~-v~k~G~ 22 (36)
T PF03811_consen 1 MAKIDVHCPRCQSTEG-VKKNGK 22 (36)
T ss_pred CCcEeeeCCCCCCCCc-ceeCCC
Confidence 4568999999998863 344343
No 22
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=40.19 E-value=16 Score=20.54 Aligned_cols=19 Identities=26% Similarity=0.625 Sum_probs=15.2
Q ss_pred ccccCcccccCCCCccCCCCC
Q 031507 28 CGSCGYELNLSSCNRNISSIG 48 (158)
Q Consensus 28 C~~Cg~~Lf~sS~~KfdSg~G 48 (158)
|..||++| .-.++|=+.||
T Consensus 2 Cp~CG~~~--~~~~~fC~~CG 20 (23)
T PF13240_consen 2 CPNCGAEI--EDDAKFCPNCG 20 (23)
T ss_pred CcccCCCC--CCcCcchhhhC
Confidence 77899998 47788888776
No 23
>TIGR03597 GTPase_YqeH ribosome biogenesis GTPase YqeH. This family describes YqeH, a member of a larger family of GTPases involved in ribosome biogenesis. Like YqlF, it shows a cyclical permutation relative to GTPases EngA (in which the GTPase domain is duplicated), Era, and others. Members of this protein family are found in a relatively small number of bacterial species, including Bacillus subtilis but not Escherichia coli.
Probab=39.97 E-value=12 Score=33.03 Aligned_cols=18 Identities=17% Similarity=0.508 Sum_probs=13.8
Q ss_pred ccccCcccccCCCCccCCCC
Q 031507 28 CGSCGYELNLSSCNRNISSI 47 (158)
Q Consensus 28 C~~Cg~~Lf~sS~~KfdSg~ 47 (158)
|.+||..| -|++.-..|-
T Consensus 1 C~GCG~~l--q~~d~~~~Gy 18 (360)
T TIGR03597 1 CIGCGAAI--QTTDPKKPGY 18 (360)
T ss_pred CCCCCcee--EcCCCCCCCC
Confidence 89999988 4777777663
No 24
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=39.85 E-value=15 Score=22.80 Aligned_cols=15 Identities=27% Similarity=0.605 Sum_probs=12.9
Q ss_pred cccCeEEEccccCcc
Q 031507 20 SQRHVSYSCGSCGYE 34 (158)
Q Consensus 20 ~~~~G~Y~C~~Cg~~ 34 (158)
..++|.|.|..||..
T Consensus 20 ~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 20 YSDDGFYYCDRCGHQ 34 (36)
T ss_pred EccCCEEEhhhCceE
Confidence 567899999999975
No 25
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=39.41 E-value=56 Score=20.45 Aligned_cols=13 Identities=46% Similarity=1.191 Sum_probs=10.9
Q ss_pred EEEccccCccccc
Q 031507 25 SYSCGSCGYELNL 37 (158)
Q Consensus 25 ~Y~C~~Cg~~Lf~ 37 (158)
.|.|..||+.+-+
T Consensus 3 ~y~C~~CG~~~~~ 15 (46)
T PRK00398 3 EYKCARCGREVEL 15 (46)
T ss_pred EEECCCCCCEEEE
Confidence 6999999998853
No 26
>PRK00420 hypothetical protein; Validated
Probab=39.03 E-value=17 Score=27.94 Aligned_cols=23 Identities=22% Similarity=0.296 Sum_probs=15.7
Q ss_pred EEccccCccccc-CCCCccCCCCC
Q 031507 26 YSCGSCGYELNL-SSCNRNISSIG 48 (158)
Q Consensus 26 Y~C~~Cg~~Lf~-sS~~KfdSg~G 48 (158)
-+|..||.|||- .....|-..||
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg 47 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHG 47 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCC
Confidence 468888888863 35666666664
No 27
>cd05720 Ig_CD8_alpha Immunoglobulin (Ig) like domain of CD8 alpha chain. Ig_CD8_alpha: immunoglobulin (Ig)-like domain in CD8 alpha. The CD8 glycoprotein plays an essential role in the control of T-cell selection, maturation and the T-cell receptor (TCR)-mediated response to peptide antigen. CD8 is comprised of alpha and beta subunits and is expressed as either an alphaalpha or alphabeta dimer. Both dimeric isoforms can serve as a coreceptor for T cell activation and differentiation, however they have distinct physiological roles, different cellular distributions, unique binding partners etc. Each CD8 subunit is comprised of an extracellular domain containing a v-type Ig-like domain, a single pass transmembrane portion and a short intracellular domain. The Ig domain of CD8 alpha binds to antibodies.
Probab=36.11 E-value=21 Score=25.50 Aligned_cols=12 Identities=17% Similarity=0.382 Sum_probs=9.9
Q ss_pred cccCeEEEcccc
Q 031507 20 SQRHVSYSCGSC 31 (158)
Q Consensus 20 ~~~~G~Y~C~~C 31 (158)
..+.|+|.|+..
T Consensus 78 ~sDsgtY~Ca~~ 89 (104)
T cd05720 78 KENEGYYFCSVA 89 (104)
T ss_pred HHHCEEEEEEEc
Confidence 567799999976
No 28
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=30.27 E-value=23 Score=24.87 Aligned_cols=19 Identities=26% Similarity=0.593 Sum_probs=16.0
Q ss_pred eeeEEecCccCCCeeeecC
Q 031507 92 HRTKLLCRKCGNPIGIAYT 110 (158)
Q Consensus 92 ~RTEv~C~~Cg~HLGHVF~ 110 (158)
.+|-++|++||-|-=||=.
T Consensus 13 k~tH~~CRRCGr~syhv~k 31 (61)
T COG2126 13 KKTHIRCRRCGRRSYHVRK 31 (61)
T ss_pred Ccceehhhhccchheeecc
Confidence 4899999999998877754
No 29
>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=29.52 E-value=35 Score=23.30 Aligned_cols=66 Identities=20% Similarity=0.285 Sum_probs=36.8
Q ss_pred CeEEEccccCcccccCCCCccCCCCCCCCCCcCCCCceeEEcccCccceeecccccccccccCCCCCceeeeEEecCccC
Q 031507 23 HVSYSCGSCGYELNLSSCNRNISSIGLKYGKSMKRGIIAFVDIDESRFTQVDELQCIPHFSKNSWGILRHRTKLLCRKCG 102 (158)
Q Consensus 23 ~G~Y~C~~Cg~~Lf~sS~~KfdSg~Gpsf~~~~~~G~~sF~~id~~~~~~~~e~~~~p~f~~~s~g~~m~RTEv~C~~Cg 102 (158)
...-.|..|++..- +.-++.+|.+ -|+...-. --+.- --.-++|++.+. -+-++-.|.+|+
T Consensus 5 p~~~~CP~C~~~~~--T~v~~~~g~~---------t~~~~~~l--~~~~~-~~~~~iP~~~~~-----~kd~~H~Cp~C~ 65 (73)
T PF10601_consen 5 PVRIYCPYCQQQVQ--TRVEYKSGTM---------TYICAALL--CLFGC-WPCCCIPFCCDS-----CKDVYHYCPNCG 65 (73)
T ss_pred ceeeECCCCCCEEE--EEEEEEeChH---------HHHHHHHH--HHHHH-HHHhhHhhcccc-----ccCceEECCCCC
Confidence 34567999999883 7778888753 12110000 00000 001234553222 246899999999
Q ss_pred CCeee
Q 031507 103 NPIGI 107 (158)
Q Consensus 103 ~HLGH 107 (158)
+.||.
T Consensus 66 ~~lg~ 70 (73)
T PF10601_consen 66 AFLGT 70 (73)
T ss_pred CEeEE
Confidence 99996
No 30
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=27.72 E-value=69 Score=20.56 Aligned_cols=13 Identities=46% Similarity=1.104 Sum_probs=11.4
Q ss_pred EEEccccCccccc
Q 031507 25 SYSCGSCGYELNL 37 (158)
Q Consensus 25 ~Y~C~~Cg~~Lf~ 37 (158)
+|.|+.||.+..+
T Consensus 2 ~Y~C~~Cg~~~~~ 14 (44)
T smart00659 2 IYICGECGRENEI 14 (44)
T ss_pred EEECCCCCCEeec
Confidence 7999999999864
No 31
>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=27.37 E-value=41 Score=26.74 Aligned_cols=21 Identities=24% Similarity=0.455 Sum_probs=16.7
Q ss_pred cccCeEEEccccCcccccCCC
Q 031507 20 SQRHVSYSCGSCGYELNLSSC 40 (158)
Q Consensus 20 ~~~~G~Y~C~~Cg~~Lf~sS~ 40 (158)
--..|+|+|..||..+-+...
T Consensus 107 ~~g~G~l~C~~Cg~~~~~~~~ 127 (146)
T PF07295_consen 107 VVGPGTLVCENCGHEVELTHP 127 (146)
T ss_pred EecCceEecccCCCEEEecCC
Confidence 445799999999999977443
No 32
>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=27.23 E-value=40 Score=20.06 Aligned_cols=12 Identities=42% Similarity=0.863 Sum_probs=9.8
Q ss_pred eEEecCccCCCe
Q 031507 94 TKLLCRKCGNPI 105 (158)
Q Consensus 94 TEv~C~~Cg~HL 105 (158)
.++.|.+|+..+
T Consensus 24 ~~v~C~~C~~~~ 35 (38)
T TIGR02098 24 GKVRCGKCGHVW 35 (38)
T ss_pred CEEECCCCCCEE
Confidence 489999998755
No 33
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=26.13 E-value=49 Score=19.84 Aligned_cols=14 Identities=36% Similarity=1.013 Sum_probs=11.5
Q ss_pred eeeEEecCccCCCe
Q 031507 92 HRTKLLCRKCGNPI 105 (158)
Q Consensus 92 ~RTEv~C~~Cg~HL 105 (158)
+.|...|++|+-+|
T Consensus 13 k~T~~~C~~C~v~l 26 (32)
T PF13842_consen 13 KDTRYMCSKCDVPL 26 (32)
T ss_pred ceeEEEccCCCCcc
Confidence 34999999998665
No 34
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=26.07 E-value=43 Score=22.45 Aligned_cols=21 Identities=33% Similarity=0.649 Sum_probs=17.8
Q ss_pred eeeEEecCccCCCeeeecCCC
Q 031507 92 HRTKLLCRKCGNPIGIAYTDK 112 (158)
Q Consensus 92 ~RTEv~C~~Cg~HLGHVF~DG 112 (158)
.|.-++|++|..|=|-+....
T Consensus 19 ~r~aLIC~~C~~hNGla~~~~ 39 (54)
T PF10058_consen 19 NRYALICSKCFSHNGLAPKEE 39 (54)
T ss_pred CceeEECcccchhhccccccc
Confidence 589999999999999887443
No 35
>PF13790 DUF4182: Domain of unknown function (DUF4182)
Probab=24.75 E-value=48 Score=21.22 Aligned_cols=17 Identities=24% Similarity=0.653 Sum_probs=13.9
Q ss_pred EEecCccCCCeeeecCC
Q 031507 95 KLLCRKCGNPIGIAYTD 111 (158)
Q Consensus 95 Ev~C~~Cg~HLGHVF~D 111 (158)
-|+|..|+.-+.|+=++
T Consensus 3 tIvCq~C~~~Id~~e~e 19 (38)
T PF13790_consen 3 TIVCQHCNETIDHFETE 19 (38)
T ss_pred EEEeccccceeeeecCC
Confidence 48999999999996433
No 36
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=23.56 E-value=40 Score=22.57 Aligned_cols=13 Identities=38% Similarity=1.073 Sum_probs=11.0
Q ss_pred CeEEEccccCccc
Q 031507 23 HVSYSCGSCGYEL 35 (158)
Q Consensus 23 ~G~Y~C~~Cg~~L 35 (158)
.-.|.|+.||..+
T Consensus 4 ~~~Y~C~~Cg~~~ 16 (49)
T COG1996 4 MMEYKCARCGREV 16 (49)
T ss_pred eEEEEhhhcCCee
Confidence 4579999999988
No 37
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=23.51 E-value=50 Score=28.61 Aligned_cols=32 Identities=19% Similarity=0.182 Sum_probs=25.1
Q ss_pred cccCeEEEccccCcccccCCCCccCCCCCCCCCCcCCCCceeEEc
Q 031507 20 SQRHVSYSCGSCGYELNLSSCNRNISSIGLKYGKSMKRGIIAFVD 64 (158)
Q Consensus 20 ~~~~G~Y~C~~Cg~~Lf~sS~~KfdSg~Gpsf~~~~~~G~~sF~~ 64 (158)
..+.|.+.|..||.-| .+.--|.|. .|-.|..
T Consensus 25 d~~~Ge~vC~~CG~Vl---~e~~iD~g~----------EWR~f~~ 56 (310)
T PRK00423 25 DYERGEIVCADCGLVI---EENIIDQGP----------EWRAFDP 56 (310)
T ss_pred ECCCCeEeecccCCcc---cccccccCC----------CccCCCc
Confidence 3567999999999988 566777775 6888863
No 38
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=23.04 E-value=1.3e+02 Score=24.10 Aligned_cols=34 Identities=9% Similarity=0.280 Sum_probs=23.3
Q ss_pred eEEecCccCCCeeeecCCCCCCCCCCCCCCCCCCCCCCCCCceeeeeece
Q 031507 94 TKLLCRKCGNPIGIAYTDKTSAYSPKSNGSDSPSVPGASGRRKYDVRIRA 143 (158)
Q Consensus 94 TEv~C~~Cg~HLGHVF~DGP~~~~~~~~~~~~~~~~~~ptg~RYcIns~A 143 (158)
+-..|..||-+---|-..|.. .|.|.||-++...
T Consensus 28 ~sf~C~~CGyk~~ev~~~~~~----------------~p~G~r~~l~V~~ 61 (160)
T smart00709 28 MSFECEHCGYRNNEVKSGGAI----------------EPKGTRITLKVES 61 (160)
T ss_pred EEEECCCCCCccceEEECccc----------------CCCceEEEEEECC
Confidence 456899998776555444432 3889999887654
No 39
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.04 E-value=36 Score=27.02 Aligned_cols=24 Identities=21% Similarity=0.353 Sum_probs=17.9
Q ss_pred EEEccccCcccccCCCCccCCCCCCCCCC
Q 031507 25 SYSCGSCGYELNLSSCNRNISSIGLKYGK 53 (158)
Q Consensus 25 ~Y~C~~Cg~~Lf~sS~~KfdSg~Gpsf~~ 53 (158)
.=.|.+||.++- ..|++=||+||-
T Consensus 40 ~p~C~aCG~dyg-----~~~a~DgPa~fv 63 (126)
T COG5349 40 VPACEACGLDYG-----FADADDGPAYFV 63 (126)
T ss_pred Cchhhhcccccc-----CCcccCCCcEEE
Confidence 346889998884 678887777764
No 40
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=22.89 E-value=35 Score=21.79 Aligned_cols=10 Identities=40% Similarity=0.923 Sum_probs=8.6
Q ss_pred EccccCcccc
Q 031507 27 SCGSCGYELN 36 (158)
Q Consensus 27 ~C~~Cg~~Lf 36 (158)
+|..||.||+
T Consensus 19 ~Cp~C~~PL~ 28 (41)
T PF06677_consen 19 HCPDCGTPLM 28 (41)
T ss_pred ccCCCCCeeE
Confidence 6888999997
No 41
>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=22.78 E-value=56 Score=19.85 Aligned_cols=12 Identities=58% Similarity=1.401 Sum_probs=9.1
Q ss_pred EEccccCccccc
Q 031507 26 YSCGSCGYELNL 37 (158)
Q Consensus 26 Y~C~~Cg~~Lf~ 37 (158)
|.|+.||.+.-+
T Consensus 1 Y~C~~Cg~~~~~ 12 (32)
T PF03604_consen 1 YICGECGAEVEL 12 (32)
T ss_dssp EBESSSSSSE-B
T ss_pred CCCCcCCCeeEc
Confidence 889999988753
No 42
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=22.76 E-value=22 Score=25.11 Aligned_cols=17 Identities=29% Similarity=0.704 Sum_probs=14.9
Q ss_pred eEEecCccCCCeeeecC
Q 031507 94 TKLLCRKCGNPIGIAYT 110 (158)
Q Consensus 94 TEv~C~~Cg~HLGHVF~ 110 (158)
.-|+|=.||.-+||.|+
T Consensus 3 iPiRCFsCGkvi~~~w~ 19 (63)
T COG1644 3 IPVRCFSCGKVIGHKWE 19 (63)
T ss_pred CceEeecCCCCHHHHHH
Confidence 35899999999999986
No 43
>PF01020 Ribosomal_L40e: Ribosomal L40e family; InterPro: IPR001975 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family contains the L40 ribosomal protein from both archaea and eukaryotes. Bovine ribosomal protein L40 has been identified as a secondary RNA binding protein []. L40 is fused to a ubiquitin protein [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3IZS_p 3IZR_p 2AYJ_A 4A1B_K 4A19_K 4A18_K 4A1D_K.
Probab=22.33 E-value=39 Score=23.04 Aligned_cols=12 Identities=42% Similarity=1.035 Sum_probs=7.8
Q ss_pred eEEecCccCCCe
Q 031507 94 TKLLCRKCGNPI 105 (158)
Q Consensus 94 TEv~C~~Cg~HL 105 (158)
.+.+|++|.+||
T Consensus 16 ~k~ICrkCyarl 27 (52)
T PF01020_consen 16 DKMICRKCYARL 27 (52)
T ss_dssp S-EEETTT--EE
T ss_pred cceecccccCcC
Confidence 367899999999
No 44
>PF00047 ig: Immunoglobulin domain The Prosite family only concerns antibodies and MHCs.; InterPro: IPR013151 Members of the immunoglobulin superfamily are found in hundreds of proteins of different functions. Examples include antibodies, the giant muscle kinase titin and receptor tyrosine kinases. Immunoglobulin-like domains may be involved in protein-protein and protein-ligand interactions. The Pfam alignments do not include the first and last strand of the immunoglobulin-like domain.; PDB: 1B6U_A 3O4O_C 3VH8_H 1BIH_A 2C9A_A 2V5Y_A 1BQH_K 2ATP_A 3B9K_A 1NEZ_H ....
Probab=21.13 E-value=55 Score=20.24 Aligned_cols=17 Identities=18% Similarity=0.399 Sum_probs=11.3
Q ss_pred cCCCCccccCeEEEccc
Q 031507 14 SFSSSISQRHVSYSCGS 30 (158)
Q Consensus 14 ~~~~s~~~~~G~Y~C~~ 30 (158)
.+..-.....|+|.|.+
T Consensus 48 ~i~~v~~~d~G~Y~C~v 64 (64)
T PF00047_consen 48 TISNVTPEDSGTYTCVV 64 (64)
T ss_dssp EESSCTGGGTEEEEEEE
T ss_pred EEccCCHHHCEEEEEEC
Confidence 33444356889999964
No 45
>PF10955 DUF2757: Protein of unknown function (DUF2757); InterPro: IPR020115 This entry contains proteins with no known function.
Probab=20.81 E-value=60 Score=23.52 Aligned_cols=13 Identities=31% Similarity=0.986 Sum_probs=11.5
Q ss_pred CeEEEccccCccc
Q 031507 23 HVSYSCGSCGYEL 35 (158)
Q Consensus 23 ~G~Y~C~~Cg~~L 35 (158)
...|.|+-||..+
T Consensus 2 ai~Y~CRHCg~~I 14 (76)
T PF10955_consen 2 AIHYYCRHCGTKI 14 (76)
T ss_pred ceEEEecCCCCEE
Confidence 3689999999998
No 46
>COG0358 DnaG DNA primase (bacterial type) [DNA replication, recombination, and repair]
Probab=20.58 E-value=66 Score=30.18 Aligned_cols=15 Identities=33% Similarity=0.585 Sum_probs=13.9
Q ss_pred cccCeEEEccccCcc
Q 031507 20 SQRHVSYSCGSCGYE 34 (158)
Q Consensus 20 ~~~~G~Y~C~~Cg~~ 34 (158)
+..+|.|+|-+||.-
T Consensus 50 ~~~k~~yhCFGCg~~ 64 (568)
T COG0358 50 SPEKGFYHCFGCGAG 64 (568)
T ss_pred eCCCCeEecCCCCCC
Confidence 789999999999987
Done!