Query 028857
Match_columns 202
No_of_seqs 231 out of 2314
Neff 4.5
Searched_HMMs 46136
Date Fri Mar 29 03:38:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028857.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028857hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK14018 trifunctional thiored 100.0 4.1E-48 8.8E-53 366.8 13.8 149 47-200 286-456 (521)
2 COG0229 Conserved domain frequ 100.0 7.5E-38 1.6E-42 252.7 7.6 79 123-201 2-81 (140)
3 KOG0856 Predicted pilin-like t 100.0 1.5E-37 3.3E-42 251.5 6.9 85 117-201 8-93 (146)
4 TIGR00357 methionine-R-sulfoxi 100.0 1.7E-36 3.7E-41 244.5 8.1 76 125-200 2-78 (134)
5 PRK00222 methionine sulfoxide 100.0 1.8E-36 3.9E-41 246.4 8.3 78 123-200 3-81 (142)
6 PF01641 SelR: SelR domain; I 100.0 1.3E-36 2.8E-41 242.5 5.0 74 127-200 1-75 (124)
7 PRK05508 methionine sulfoxide 100.0 3.8E-35 8.2E-40 232.5 7.0 69 132-200 2-70 (119)
8 PRK05550 bifunctional methioni 100.0 1.5E-31 3.2E-36 238.0 6.6 72 129-200 2-73 (283)
9 COG0225 MsrA Peptide methionin 99.6 1.9E-16 4E-21 133.0 6.1 63 48-113 96-161 (174)
10 PRK14054 methionine sulfoxide 99.6 1.7E-15 3.6E-20 126.9 4.3 71 46-119 91-164 (172)
11 PRK13014 methionine sulfoxide 99.5 7.6E-15 1.7E-19 124.4 6.3 72 46-120 96-170 (186)
12 TIGR00401 msrA methionine-S-su 99.5 2.6E-14 5.6E-19 117.2 5.3 59 46-107 88-149 (149)
13 PF01625 PMSR: Peptide methion 99.5 2.5E-14 5.3E-19 117.9 4.8 65 45-113 87-154 (155)
14 PRK05528 methionine sulfoxide 99.5 7.1E-14 1.5E-18 115.6 5.6 60 47-113 85-147 (156)
15 PRK00058 methionine sulfoxide 99.4 2.5E-13 5.4E-18 117.4 4.6 65 46-113 133-202 (213)
16 PRK05550 bifunctional methioni 99.3 2.1E-12 4.6E-17 115.6 5.6 59 46-110 215-276 (283)
17 KOG1635 Peptide methionine sul 99.2 5.6E-12 1.2E-16 106.5 4.6 56 48-108 114-172 (191)
18 COG1645 Uncharacterized Zn-fin 76.3 0.84 1.8E-05 37.4 0.0 23 164-186 29-52 (131)
19 PRK00420 hypothetical protein; 68.2 2.5 5.4E-05 33.7 1.0 22 165-186 25-48 (112)
20 PF06677 Auto_anti-p27: Sjogre 59.3 3.8 8.3E-05 27.1 0.4 14 165-178 19-32 (41)
21 PF11781 RRN7: RNA polymerase 58.9 4.6 0.0001 25.8 0.8 21 152-172 14-34 (36)
22 PRK12495 hypothetical protein; 56.5 4.7 0.0001 35.8 0.7 14 161-174 40-53 (226)
23 PHA02540 61 DNA primase; Provi 48.7 8.8 0.00019 35.7 1.2 10 162-171 54-63 (337)
24 PF08271 TF_Zn_Ribbon: TFIIB z 48.2 15 0.00033 23.7 1.9 29 159-189 15-43 (43)
25 smart00778 Prim_Zn_Ribbon Zinc 42.7 21 0.00046 23.1 1.9 16 155-170 17-32 (37)
26 PRK00423 tfb transcription ini 41.9 23 0.0005 32.0 2.8 31 159-191 26-56 (310)
27 cd04983 IgV_TCR_alpha_like Imm 41.3 17 0.00036 26.4 1.5 15 157-171 78-92 (109)
28 COG3791 Uncharacterized conser 36.5 15 0.00032 29.3 0.6 22 156-177 62-83 (133)
29 PF07295 DUF1451: Protein of u 36.3 18 0.00039 29.9 1.1 39 125-173 84-122 (146)
30 cd04984 IgV_L_lambda Immunoglo 35.2 20 0.00043 25.9 1.1 13 157-169 71-83 (98)
31 COG0358 DnaG DNA primase (bact 35.1 29 0.00062 33.9 2.4 45 128-172 8-64 (568)
32 PRK00398 rpoP DNA-directed RNA 33.6 38 0.00082 22.0 2.1 36 163-198 3-41 (46)
33 cd05720 Ig_CD8_alpha Immunoglo 33.1 24 0.00053 26.2 1.3 27 157-189 77-103 (104)
34 TIGR03655 anti_R_Lar restricti 32.2 33 0.00072 23.1 1.7 18 155-172 18-35 (53)
35 PRK08624 hypothetical protein; 32.0 33 0.00072 32.6 2.2 14 158-171 54-68 (373)
36 cd04980 IgV_L_kappa Immunoglob 31.8 21 0.00045 26.2 0.7 13 157-169 79-91 (106)
37 PRK04179 rpl37e 50S ribosomal 30.7 26 0.00057 25.4 1.0 27 162-188 16-43 (62)
38 PF04828 GFA: Glutathione-depe 29.7 22 0.00048 24.9 0.5 19 158-176 43-61 (92)
39 COG1885 Uncharacterized protei 29.3 21 0.00046 28.6 0.4 14 160-173 46-59 (115)
40 PF13248 zf-ribbon_3: zinc-rib 29.2 27 0.00057 20.4 0.7 21 165-186 4-24 (26)
41 smart00531 TFIIE Transcription 28.8 25 0.00054 28.4 0.7 18 161-178 121-138 (147)
42 PTZ00073 60S ribosomal protein 28.6 31 0.00067 26.8 1.2 28 161-188 14-41 (91)
43 PF08273 Prim_Zn_Ribbon: Zinc- 28.5 28 0.0006 22.9 0.8 16 155-170 18-33 (40)
44 cd05895 Ig_Pro_neuregulin-1 Im 26.9 38 0.00083 23.1 1.3 15 157-171 52-66 (76)
45 smart00408 IGc2 Immunoglobulin 25.9 45 0.00097 20.2 1.4 11 158-168 48-58 (63)
46 cd05861 Ig1_PDGFR-alphabeta Fr 25.7 44 0.00094 23.8 1.5 14 157-170 54-67 (84)
47 cd05765 Ig_3 Subgroup of the i 25.7 43 0.00094 22.7 1.4 14 157-170 55-68 (81)
48 cd04974 Ig3_FGFR Third immunog 25.7 43 0.00093 23.9 1.4 13 158-170 64-76 (90)
49 cd04977 Ig1_NCAM-1_like First 25.1 44 0.00095 24.1 1.4 15 157-171 65-79 (92)
50 PF09889 DUF2116: Uncharacteri 25.0 30 0.00064 24.6 0.5 10 165-174 5-14 (59)
51 cd05734 Ig7_DSCAM Seventh immu 24.4 48 0.001 22.8 1.5 13 158-170 53-65 (79)
52 cd05726 Ig4_Robo Fhird immunog 24.4 40 0.00087 23.9 1.1 13 158-170 56-68 (90)
53 cd05763 Ig_1 Subgroup of the i 24.3 49 0.0011 22.4 1.5 13 158-170 49-61 (75)
54 PF10367 Vps39_2: Vacuolar sor 24.2 37 0.0008 24.7 0.9 12 165-176 80-91 (109)
55 PRK00432 30S ribosomal protein 23.9 45 0.00097 22.7 1.2 14 162-175 36-49 (50)
56 cd05862 Ig1_VEGFR First immuno 23.8 42 0.00092 24.1 1.1 21 157-177 58-79 (86)
57 cd05899 IgV_TCR_beta Immunoglo 23.5 47 0.001 24.5 1.3 13 158-170 81-93 (110)
58 cd02181 GH16_fungal_Lam16A_glu 23.4 24 0.00052 32.4 -0.3 19 173-191 82-102 (293)
59 cd05725 Ig3_Robo Third immunog 23.2 42 0.00091 22.4 0.9 13 158-170 44-56 (69)
60 cd07693 Ig1_Robo First immunog 23.2 55 0.0012 22.6 1.6 14 157-170 72-85 (100)
61 PF00047 ig: Immunoglobulin do 23.1 42 0.00091 21.7 0.9 10 159-168 55-64 (64)
62 COG1734 DksA DnaK suppressor p 22.9 28 0.0006 27.9 -0.0 14 160-173 76-90 (120)
63 PF13240 zinc_ribbon_2: zinc-r 22.9 52 0.0011 18.9 1.1 20 166-186 2-21 (23)
64 smart00406 IGv Immunoglobulin 22.8 40 0.00087 22.4 0.8 10 159-168 72-81 (81)
65 cd05738 Ig2_RPTP_IIa_LAR_like 22.8 46 0.001 22.8 1.1 14 157-170 46-59 (74)
66 PF06397 Desulfoferrod_N: Desu 22.6 55 0.0012 21.2 1.3 13 160-172 3-15 (36)
67 PF01907 Ribosomal_L37e: Ribos 22.4 38 0.00082 24.0 0.6 27 162-188 14-40 (55)
68 PRK12496 hypothetical protein; 22.2 49 0.0011 27.5 1.3 50 139-191 102-156 (164)
69 cd07700 IgV_CD8_beta Immunoglo 22.0 45 0.00097 24.7 1.0 14 156-169 79-92 (107)
70 cd05742 Ig1_VEGFR_like First i 21.6 47 0.001 23.1 1.0 13 158-170 58-70 (84)
71 PRK13945 formamidopyrimidine-D 21.4 1.6E+02 0.0035 26.2 4.5 71 89-173 177-264 (282)
72 COG1996 RPC10 DNA-directed RNA 21.1 47 0.001 22.9 0.8 36 162-198 5-44 (49)
73 PRK10445 endonuclease VIII; Pr 20.4 1.2E+02 0.0025 26.9 3.4 73 89-173 164-245 (263)
74 COG2126 RPL37A Ribosomal prote 20.3 49 0.0011 23.9 0.8 27 161-187 14-40 (61)
75 cd04981 IgV_H Immunoglobulin ( 20.3 38 0.00082 25.8 0.2 13 158-170 85-97 (117)
76 cd05723 Ig4_Neogenin Fourth im 20.2 62 0.0013 21.9 1.3 14 157-170 45-58 (71)
77 KOG4397 Uncharacterized conser 20.0 28 0.00061 30.5 -0.5 13 163-175 88-100 (213)
No 1
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=100.00 E-value=4.1e-48 Score=366.84 Aligned_cols=149 Identities=25% Similarity=0.395 Sum_probs=133.6
Q ss_pred ccccceEEEeCCHHHHHHHHHHHHHHccCCCCCCCeeeeccceeeccCceechhhhc---cccCcCCcceeeccCCC---
Q 028857 47 SSVLSNLNFIHSPTTTRLFTNRLNSLAPSLLKLKPLTVTGTGCISSSGFYRSLRFEQ---NKRSFRGGVVLAVASGP--- 120 (202)
Q Consensus 47 s~~~~~aIFy~de~Qk~~A~~~i~~l~~~~~~~kpI~vTe~~I~p~~~Fy~AEeYHQ---~KNP~Ry~vVlAaap~~--- 120 (202)
-.||.++|||+|++|+++|+++++.++. .+.++| +|| |.|+.+||+||+||| .|||.+|+.+..+.-..
T Consensus 286 G~qYrs~I~~~~~eq~~~a~~~~~~~~~--~~~~~i-~te--i~~~~~Fy~AE~yHQ~Yl~k~p~~yc~~~~~~~~~~~~ 360 (521)
T PRK14018 286 GTQYRSGVYYTDPADKAVIAAALKREQQ--KYQLPL-VVE--NEPLKNFYDAEEYHQDYLIKNPNGYCHIDLRKADEPLP 360 (521)
T ss_pred CCCceEEEEeCCHHHHHHHHHHHHHHHH--HcCCCe-EEE--EecCCCeeecHHHHHHHHHhCCCceeEeeccccccccc
Confidence 4799999999999999999999999986 468899 999 999999999999999 89999888776552110
Q ss_pred ---------------CCCCCCHHHHHhcCCHHHHHHHHhcCCCCCCCCCCCCCCCCeEEEeccCCCCCCCCCCCCCCCCC
Q 028857 121 ---------------ASVNKSEEEWRAILSPEQFRILRQKATEYPGTGEYDKHFEEGIYNCSACGTPLYKSTTKFNSGCG 185 (202)
Q Consensus 121 ---------------~~~~~sd~ewr~~Lt~~qy~Vlr~~gTE~pfsg~y~~~~~~G~Y~C~~C~~pLF~S~~KFdSg~G 185 (202)
....+++++||+.|||+||+|||++|||+||||+||+++++|+|+|++||+|||+|.+|||||||
T Consensus 361 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~Lt~~~y~v~~~~gtE~~f~~~~~~~~~~G~y~c~~c~~pLf~s~~Kf~sg~G 440 (521)
T PRK14018 361 GKTKTAPQGKGFDAATYKKPSDAELKRTLTEEQYQITQNAATERAFSHEYDHLFKPGIYVDVVSGEPLFSSADKYDSGCG 440 (521)
T ss_pred ccccccccccccchhhccCCChHHHhccCCHHHHHHHHhcCCCCCCCCCCcCCCCCEEEEecCCCCccccCcccccCCCC
Confidence 12346899999999999999999999999999999999999999999999999999999999999
Q ss_pred CccCCccc-cCCccee
Q 028857 186 WPAFYEGL-PGAINCS 200 (202)
Q Consensus 186 WPSF~~~i-~~aV~~~ 200 (202)
||||++|| +++|.++
T Consensus 441 WPsF~~~i~~~~v~~~ 456 (521)
T PRK14018 441 WPSFTRPIDAKVVTEH 456 (521)
T ss_pred CcccCcccCcCceEEe
Confidence 99999999 4677654
No 2
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=7.5e-38 Score=252.72 Aligned_cols=79 Identities=47% Similarity=0.931 Sum_probs=75.0
Q ss_pred CCCCHHHHHhcCCHHHHHHHHhcCCCCCCCCCCCCCCCCeEEEeccCCCCCCCCCCCCCCCCCCccCCccc-cCCcceee
Q 028857 123 VNKSEEEWRAILSPEQFRILRQKATEYPGTGEYDKHFEEGIYNCSACGTPLYKSTTKFNSGCGWPAFYEGL-PGAINCSM 201 (202)
Q Consensus 123 ~~~sd~ewr~~Lt~~qy~Vlr~~gTE~pfsg~y~~~~~~G~Y~C~~C~~pLF~S~~KFdSg~GWPSF~~~i-~~aV~~~~ 201 (202)
..+++++||++|||+||+|||++|||+||+|+||+++++|+|+|++||+|||+|++|||||||||||++|| +++|.++.
T Consensus 2 ~~~sd~e~~~~Lt~~qy~Vtq~~gTE~pft~~y~~~~~~GiY~c~~cg~pLF~S~~KfdSgcGWPSF~~pi~~~~I~~~~ 81 (140)
T COG0229 2 IKPSDEELKEKLTPEQYRVTQNHGTERPFTGEYLDNKEKGIYVCIVCGEPLFSSEDKFDSGCGWPSFTKPISPDAITYKE 81 (140)
T ss_pred CccchHHHHHhcCHHHHHHHHhcCCCCCCCChhhcccCCceEEeecCCCccccccccccCCCCCccccccCCcccceEee
Confidence 35789999999999999999999999999999999999999999999999999999999999999999999 77997753
No 3
>KOG0856 consensus Predicted pilin-like transcription factor [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.5e-37 Score=251.53 Aligned_cols=85 Identities=69% Similarity=1.311 Sum_probs=81.4
Q ss_pred cCCCCCCCCCHHHHHhcCCHHHHHHHHhcCCCCCCCCCCCCCCCCeEEEeccCCCCCCCCCCCCCCCCCCccCCccc-cC
Q 028857 117 ASGPASVNKSEEEWRAILSPEQFRILRQKATEYPGTGEYDKHFEEGIYNCSACGTPLYKSTTKFNSGCGWPAFYEGL-PG 195 (202)
Q Consensus 117 ap~~~~~~~sd~ewr~~Lt~~qy~Vlr~~gTE~pfsg~y~~~~~~G~Y~C~~C~~pLF~S~~KFdSg~GWPSF~~~i-~~ 195 (202)
+|+...++++++|||+.|||+||+|||++|||+||+|+|++++++|+|+|++|+.|||+|.+|||||||||||+++| ||
T Consensus 8 ~~~~~~v~k~~~EWr~~LsPeQ~~v~RekgTE~p~tGey~~~~e~GvY~C~~C~~pLykS~tKfdsgcGWPAF~e~i~~g 87 (146)
T KOG0856|consen 8 APKTGSVQKNDEEWRKVLSPEQFRVLREKGTERPGTGEYTKHFEEGVYVCAGCGTPLYKSTTKFDSGCGWPAFFEAIGPG 87 (146)
T ss_pred cCCCcccccCHHHHHhhcCHHHhhhhHhhcccCCCCcccccccCCceEEEeecCCccccccccccCCCCCchhhhccCCC
Confidence 46778899999999999999999999999999999999999999999999999999999999999999999999999 99
Q ss_pred Ccceee
Q 028857 196 AINCSM 201 (202)
Q Consensus 196 aV~~~~ 201 (202)
||.++.
T Consensus 88 aI~r~~ 93 (146)
T KOG0856|consen 88 AITRTP 93 (146)
T ss_pred ceeecc
Confidence 998763
No 4
>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=1.7e-36 Score=244.51 Aligned_cols=76 Identities=42% Similarity=0.803 Sum_probs=73.7
Q ss_pred CCHHHHHhcCCHHHHHHHHhcCCCCCCCCCCCCCCCCeEEEeccCCCCCCCCCCCCCCCCCCccCCccc-cCCccee
Q 028857 125 KSEEEWRAILSPEQFRILRQKATEYPGTGEYDKHFEEGIYNCSACGTPLYKSTTKFNSGCGWPAFYEGL-PGAINCS 200 (202)
Q Consensus 125 ~sd~ewr~~Lt~~qy~Vlr~~gTE~pfsg~y~~~~~~G~Y~C~~C~~pLF~S~~KFdSg~GWPSF~~~i-~~aV~~~ 200 (202)
+++++||+.|||+||+|||++|||+||||+||+++++|+|+|++||+|||+|++|||||||||||+++| +++|.++
T Consensus 2 ~~~~ewr~~Lt~~qy~V~r~~gTE~pftg~y~~~~~~G~Y~C~~Cg~pLF~S~~KfdSg~GWPSF~~~i~~~~V~~~ 78 (134)
T TIGR00357 2 PSDEELKKKLTPLQYEVTQNAGTEPPFTNEYWDNKEEGIYVDITCGEPLFSSEDKFDSGCGWPSFYKPISEEVVAYE 78 (134)
T ss_pred CCHHHHHHhCCHHHHHHHHHhCCCCCCCCCCCCCCCCeEEEccCCCCccccccchhcCCCCCcCcCcccCCCceEEe
Confidence 578999999999999999999999999999999999999999999999999999999999999999999 8899775
No 5
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=100.00 E-value=1.8e-36 Score=246.35 Aligned_cols=78 Identities=50% Similarity=0.980 Sum_probs=74.9
Q ss_pred CCCCHHHHHhcCCHHHHHHHHhcCCCCCCCCCCCCCCCCeEEEeccCCCCCCCCCCCCCCCCCCccCCccc-cCCccee
Q 028857 123 VNKSEEEWRAILSPEQFRILRQKATEYPGTGEYDKHFEEGIYNCSACGTPLYKSTTKFNSGCGWPAFYEGL-PGAINCS 200 (202)
Q Consensus 123 ~~~sd~ewr~~Lt~~qy~Vlr~~gTE~pfsg~y~~~~~~G~Y~C~~C~~pLF~S~~KFdSg~GWPSF~~~i-~~aV~~~ 200 (202)
+.+++++||+.|||+||+|||++|||+||||+||+++++|+|+|++||+|||+|++|||||||||||+++| +++|+++
T Consensus 3 ~~~~~~ew~~~Lt~~qy~V~r~~gTE~pftg~~~~~~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~i~~~~V~~~ 81 (142)
T PRK00222 3 IEKSKEEWKKQLTPEQYRVTQEHGTERPFTGEYLDNKEKGIYVCIVCGEPLFSSDTKFDSGCGWPSFTKPIDEEAIREL 81 (142)
T ss_pred ccCCHHHHHhhCCHHHHHHHHhcCCCCCCCCCCCCCCCCeEEEecCCCchhcCCcccccCCCCCcCcCcccCCCceEEe
Confidence 45799999999999999999999999999999999999999999999999999999999999999999999 6888765
No 6
>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=1.3e-36 Score=242.54 Aligned_cols=74 Identities=59% Similarity=1.207 Sum_probs=69.8
Q ss_pred HHHHHhcCCHHHHHHHHhcCCCCCCCCCCCCCCCCeEEEeccCCCCCCCCCCCCCCCCCCccCCccccC-Cccee
Q 028857 127 EEEWRAILSPEQFRILRQKATEYPGTGEYDKHFEEGIYNCSACGTPLYKSTTKFNSGCGWPAFYEGLPG-AINCS 200 (202)
Q Consensus 127 d~ewr~~Lt~~qy~Vlr~~gTE~pfsg~y~~~~~~G~Y~C~~C~~pLF~S~~KFdSg~GWPSF~~~i~~-aV~~~ 200 (202)
|+|||++|||+||+|||++|||+||||+|++++++|+|+|++||+|||+|++|||||||||||+++|++ +|.++
T Consensus 1 d~ew~~~Lt~~qy~V~r~~gTE~pfsg~y~~~~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~i~~~~v~~~ 75 (124)
T PF01641_consen 1 DEEWRKRLTPEQYRVLREKGTERPFSGEYWDHKEEGIYVCAVCGTPLFSSDTKFDSGCGWPSFWQPIPGDAVKER 75 (124)
T ss_dssp -HHHHHHSCHHHHHHHHHTTSSSTTSSGGCCTTSSEEEEETTTS-EEEEGGGEETSSSSSSEESSCSSTTSEEEE
T ss_pred CHHHHhhCCHHHHHHHHhcCCCCCCccCCcCCCCCEEEEcCCCCCccccCcccccCCcCCccccCcCChHHEEEe
Confidence 689999999999999999999999999999999999999999999999999999999999999999966 88765
No 7
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=100.00 E-value=3.8e-35 Score=232.54 Aligned_cols=69 Identities=46% Similarity=0.980 Sum_probs=66.9
Q ss_pred hcCCHHHHHHHHhcCCCCCCCCCCCCCCCCeEEEeccCCCCCCCCCCCCCCCCCCccCCccccCCccee
Q 028857 132 AILSPEQFRILRQKATEYPGTGEYDKHFEEGIYNCSACGTPLYKSTTKFNSGCGWPAFYEGLPGAINCS 200 (202)
Q Consensus 132 ~~Lt~~qy~Vlr~~gTE~pfsg~y~~~~~~G~Y~C~~C~~pLF~S~~KFdSg~GWPSF~~~i~~aV~~~ 200 (202)
+.|||+||+|||++||||||+|+||+++++|+|+|++||+|||+|++|||||||||||++||+++|.++
T Consensus 2 ~~Lt~~qy~V~r~~gTE~pftg~y~~~~~~G~Y~C~~Cg~pLF~S~~KfdSg~GWPSF~~~i~~~v~~~ 70 (119)
T PRK05508 2 NELTPEEEAVILRKGTEPPFSGEYNDFFEKGTYVCKQCGAPLYRSEDKFKSGCGWPSFDDEIKGAVKRI 70 (119)
T ss_pred CcCCHHHHHHHHhcCCCCCCCCCCcCcCCCeEEEecCCCCccccccccccCCCCCcccCcccccceEEE
Confidence 579999999999999999999999999999999999999999999999999999999999999999765
No 8
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=99.97 E-value=1.5e-31 Score=238.04 Aligned_cols=72 Identities=46% Similarity=0.978 Sum_probs=69.9
Q ss_pred HHHhcCCHHHHHHHHhcCCCCCCCCCCCCCCCCeEEEeccCCCCCCCCCCCCCCCCCCccCCccccCCccee
Q 028857 129 EWRAILSPEQFRILRQKATEYPGTGEYDKHFEEGIYNCSACGTPLYKSTTKFNSGCGWPAFYEGLPGAINCS 200 (202)
Q Consensus 129 ewr~~Lt~~qy~Vlr~~gTE~pfsg~y~~~~~~G~Y~C~~C~~pLF~S~~KFdSg~GWPSF~~~i~~aV~~~ 200 (202)
.||++|||+||+|||++||||||+|+||+++++|+|+|++||+|||+|++|||||||||||+++|+++|.++
T Consensus 2 ~~~~~Lt~~~y~v~r~~gTE~pf~g~~~~~~~~G~y~c~~c~~~LF~s~~Kf~sg~GWPsF~~~~~~~~~~~ 73 (283)
T PRK05550 2 DKMKSLTPFEYRVIEDKGTERPFSGEYYDHDEKGVYLCRRCGAPLFRSEDKFNSGCGWPSFDDEIPGAVKRL 73 (283)
T ss_pred hhhhhCCHHHHHHHHhcCCCCCCCCcCcCCCCCcEEEcCCCCchhcCChhhccCCCCCcCcCcccCCccEEE
Confidence 599999999999999999999999999999999999999999999999999999999999999999988765
No 9
>COG0225 MsrA Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=99.64 E-value=1.9e-16 Score=132.96 Aligned_cols=63 Identities=16% Similarity=0.183 Sum_probs=60.1
Q ss_pred cccceEEEeCCHHHHHHHHHHHHHHccCCCCCCCeeeeccceeeccCceechhhhc---cccCcCCcce
Q 028857 48 SVLSNLNFIHSPTTTRLFTNRLNSLAPSLLKLKPLTVTGTGCISSSGFYRSLRFEQ---NKRSFRGGVV 113 (202)
Q Consensus 48 ~~~~~aIFy~de~Qk~~A~~~i~~l~~~~~~~kpI~vTe~~I~p~~~Fy~AEeYHQ---~KNP~Ry~vV 113 (202)
.||-++|||+|++|+++|+++++++++++.+.+|| ||| |+|+++||+|||||| +|||.+|+.+
T Consensus 96 tqYRs~Iy~~~~~q~~~a~~~~~~~q~~~~~~~~I-vte--I~p~~~Fy~AEeYHQ~Yl~KNP~gY~~~ 161 (174)
T COG0225 96 TQYRSAIYYTNEEQKAIAEASIEELQASGYFKKPI-VTE--IEPAKNFYPAEEYHQDYLKKNPNGYCHI 161 (174)
T ss_pred ccceeEEEEcCHHHHHHHHHHHHHHHHhccCCCCe-EEE--eeccccCcccHHHHHHHHHhCCCCceee
Confidence 58999999999999999999999999877788899 999 999999999999999 9999999987
No 10
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=99.57 E-value=1.7e-15 Score=126.93 Aligned_cols=71 Identities=18% Similarity=0.232 Sum_probs=64.1
Q ss_pred cccccceEEEeCCHHHHHHHHHHHHHHccCCCCCCCeeeeccceeeccCceechhhhc---cccCcCCcceeeccCC
Q 028857 46 FSSVLSNLNFIHSPTTTRLFTNRLNSLAPSLLKLKPLTVTGTGCISSSGFYRSLRFEQ---NKRSFRGGVVLAVASG 119 (202)
Q Consensus 46 ~s~~~~~aIFy~de~Qk~~A~~~i~~l~~~~~~~kpI~vTe~~I~p~~~Fy~AEeYHQ---~KNP~Ry~vVlAaap~ 119 (202)
-..||.|+|||+|++|+++|++++++++..+.+.++| +|+ |+|+.+||+||+||| .|||.+++.+..+.|+
T Consensus 91 ~G~qYRS~If~~~~~q~~~a~~~~~~~~~~~~~~~~i-~Te--i~~~~~Fy~AEeyHQ~Yl~k~p~~~~~~~~~~~~ 164 (172)
T PRK14054 91 RGTQYRSAIFYHDEEQKEIAEASIAELQASGLFDKPI-VTE--VEPAETFYEAEEYHQDYLEKNPNGYCCIFVIPPK 164 (172)
T ss_pred CCcCceeEEEeCCHHHHHHHHHHHHHHHHhcccCCCc-EEE--EecCCCceECHHHHHHHHHhCCCCcceeeccCHH
Confidence 3579999999999999999999999998754478899 999 999999999999999 8999999988887654
No 11
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=99.54 E-value=7.6e-15 Score=124.39 Aligned_cols=72 Identities=17% Similarity=0.169 Sum_probs=62.8
Q ss_pred cccccceEEEeCCHHHHHHHHHHHHHHccCCCCCCCeeeeccceeeccCceechhhhc---cccCcCCcceeeccCCC
Q 028857 46 FSSVLSNLNFIHSPTTTRLFTNRLNSLAPSLLKLKPLTVTGTGCISSSGFYRSLRFEQ---NKRSFRGGVVLAVASGP 120 (202)
Q Consensus 46 ~s~~~~~aIFy~de~Qk~~A~~~i~~l~~~~~~~kpI~vTe~~I~p~~~Fy~AEeYHQ---~KNP~Ry~vVlAaap~~ 120 (202)
-..||.++|||+|++|+++|++++++++.++.+.++| +|+ |+|+.+||+||+||| .|||.++++.....|+.
T Consensus 96 ~G~QYRS~If~~~~eQ~~~a~~~~~~~~~~~~~~~~i-~Te--i~p~~~Fy~AEeyHQ~Yl~k~p~~~yc~~~~~~~~ 170 (186)
T PRK13014 96 RGEQYRSAIFYHDEEQKKVAEAYIAQLDEAGIFKKPI-VTP--IKPYKNFYPAEDYHQDYLKKNPTHPYIVYNDLPKG 170 (186)
T ss_pred CCCCceEEEEeCCHHHHHHHHHHHHHHHhccccCCCc-EEE--EecCCCeeeCHHHHHHHHHhCCCCCccEEEeChhh
Confidence 3579999999999999999999999998765578899 999 999999999999999 89999877656655543
No 12
>TIGR00401 msrA methionine-S-sulfoxide reductase. This model describes peptide methionine sulfoxide reductase (MsrA), a repair enzyme for proteins that have been inactivated by oxidation. The enzyme from E. coli is coextensive with this model and has enzymatic activity. However, in all completed genomes in which this module is present, a second protein module, described in TIGR00357, is also found, and in several cases as part of the same polypeptide chain: N-terminal to this module in Helicobacter pylori and Haemophilus influenzae (as in PilB of Neisseria gonorrhoeae) but C-terminal to it in Treponema pallidum. PilB, containing both domains, has been shown to be important for the expression of adhesins in certain pathogens.
Probab=99.49 E-value=2.6e-14 Score=117.25 Aligned_cols=59 Identities=17% Similarity=0.211 Sum_probs=54.0
Q ss_pred cccccceEEEeCCHHHHHHHHHHHHHHccCCCCCCCeeeeccceeeccCceechhhhc---cccC
Q 028857 46 FSSVLSNLNFIHSPTTTRLFTNRLNSLAPSLLKLKPLTVTGTGCISSSGFYRSLRFEQ---NKRS 107 (202)
Q Consensus 46 ~s~~~~~aIFy~de~Qk~~A~~~i~~l~~~~~~~kpI~vTe~~I~p~~~Fy~AEeYHQ---~KNP 107 (202)
-..||.|+||++|++|+++|++++++++++..+.+|| +|+ |+|+++||+||+||| +|||
T Consensus 88 ~G~qYRs~If~~~~~q~~~a~~~~~~~~~~~~~~~~i-~te--i~~~~~Fy~AE~yHQ~Yl~k~p 149 (149)
T TIGR00401 88 IGTQYRSGIYYHSDEQEKAARASKERLQAAANYGDPI-VTE--IEPAENFYYAEEYHQQYLKKNP 149 (149)
T ss_pred CCCCceEEEEeCCHHHHHHHHHHHHHHHHhcccCCCe-EEE--EecCCCeeecHHHHHHHHhhCc
Confidence 3579999999999999999999999998765578899 999 999999999999999 7887
No 13
>PF01625 PMSR: Peptide methionine sulfoxide reductase; InterPro: IPR002569 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 represent MsrA, the crystal structure of which has been determined in a number of organisms. In Mycobacterium tuberculosis, the MsrA structure has been determined to 1.5 Angstrom resolution []. In contrast to the three catalytic cysteine residues found in previously characterised MsrA structures, M. tuberculosis MsrA represents a class containing only two functional cysteine residues. The overall structure shows no resemblance to the structures of MsrB (IPR002579 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. 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: 0016671 oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor, 0019538 protein metabolic process, 0055114 oxidation-reduction process; PDB: 2GT3_A 1FF3_B 2IEM_A 3E0M_D 2J89_A 3PIN_B 3PIM_B 3PIL_B 2L90_A 3BQF_A ....
Probab=99.49 E-value=2.5e-14 Score=117.90 Aligned_cols=65 Identities=15% Similarity=0.163 Sum_probs=57.5
Q ss_pred ccccccceEEEeCCHHHHHHHHHHHHHHccCCCCCCCeeeeccceeeccCceechhhhc---cccCcCCcce
Q 028857 45 TFSSVLSNLNFIHSPTTTRLFTNRLNSLAPSLLKLKPLTVTGTGCISSSGFYRSLRFEQ---NKRSFRGGVV 113 (202)
Q Consensus 45 ~~s~~~~~aIFy~de~Qk~~A~~~i~~l~~~~~~~kpI~vTe~~I~p~~~Fy~AEeYHQ---~KNP~Ry~vV 113 (202)
....||.++||++|++|+++|++++++++.. .+.++| +|+ |+|+..||+||+||| .|||.+|+.+
T Consensus 87 d~G~qYrs~If~~~~~q~~~a~~~~~~~~~~-~~~~~i-~te--i~p~~~Fy~AE~yHQ~Yl~k~p~~yc~~ 154 (155)
T PF01625_consen 87 DRGTQYRSAIFYHDEEQKKIAEASIAELQAK-RFGRPI-VTE--IEPLKNFYPAEEYHQKYLEKNPNGYCHY 154 (155)
T ss_dssp EESGGG-EEEEESSHHHHHHHHHHHHHHHHH-TTSSSB-S-E--EEECEEEEEHHGGGTTHHHHSTTSTTSS
T ss_pred cccccceeEEecCCHHHHHHHHHHHHHHHHh-cCCCCe-EEE--EecCCcEEECHHHHHHHHHhCCcccEec
Confidence 4568999999999999999999999999885 478899 999 999999999999999 8999997764
No 14
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=99.46 E-value=7.1e-14 Score=115.59 Aligned_cols=60 Identities=5% Similarity=-0.074 Sum_probs=54.3
Q ss_pred ccccceEEEeCCHHHHHHHHHHHHHHccCCCCCCCeeeeccceeeccCceechhhhc---cccCcCCcce
Q 028857 47 SSVLSNLNFIHSPTTTRLFTNRLNSLAPSLLKLKPLTVTGTGCISSSGFYRSLRFEQ---NKRSFRGGVV 113 (202)
Q Consensus 47 s~~~~~aIFy~de~Qk~~A~~~i~~l~~~~~~~kpI~vTe~~I~p~~~Fy~AEeYHQ---~KNP~Ry~vV 113 (202)
-.||.|+|||+|++|+++|++++++++. .++| +|+ |.|+.+||+||+||| .|||.+|+.+
T Consensus 85 G~QYRS~If~~d~eQ~~~a~~~~~~~~~----~~~i-~Te--i~~~~~Fy~AE~yHQ~Yl~k~p~~yc~~ 147 (156)
T PRK05528 85 GEKYRTGIYSEVDDHLIEARQFIERRED----ADKI-AVE--VLPLTNYVKSAEEHQDRLEKFPEDYCHI 147 (156)
T ss_pred CCCceEEEEeCCHHHHHHHHHHHHHHhc----CCCe-EEE--EecCCCeeecHHHHHHHHHhCCCCCccc
Confidence 4699999999999999999999988865 3589 999 999999999999999 8999988764
No 15
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=99.39 E-value=2.5e-13 Score=117.37 Aligned_cols=65 Identities=12% Similarity=0.117 Sum_probs=55.4
Q ss_pred cccccceEEEeCCHHHHHHHHHHHHHHccCCCC--CCCeeeeccceeeccCceechhhhc---cccCcCCcce
Q 028857 46 FSSVLSNLNFIHSPTTTRLFTNRLNSLAPSLLK--LKPLTVTGTGCISSSGFYRSLRFEQ---NKRSFRGGVV 113 (202)
Q Consensus 46 ~s~~~~~aIFy~de~Qk~~A~~~i~~l~~~~~~--~kpI~vTe~~I~p~~~Fy~AEeYHQ---~KNP~Ry~vV 113 (202)
-..||.++|||+|++|+++|+++++.++..... .++| +|+ |+|+.+||+||+||| .|||.+|+.+
T Consensus 133 ~G~QYRS~Ify~~~eQ~~~a~~~~~~~~~~~~~~~~~~i-~Te--I~~~~~Fy~AEeyHQ~Yl~k~p~~yc~~ 202 (213)
T PRK00058 133 VGTQYRSAIYTLTPEQLAAAEASREAYQQALAAAGDGPI-TTE--IAPAPPFYYAEDYHQQYLAKNPNGYCGL 202 (213)
T ss_pred CCcCceEEEEeCCHHHHHHHHHHHHHHHHHhhhccCCCe-EEE--EecCCCcccCHHHHHHHHHhCCCCcccc
Confidence 347999999999999999999999988763211 3589 999 999999999999999 8999977653
No 16
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=99.31 E-value=2.1e-12 Score=115.63 Aligned_cols=59 Identities=17% Similarity=0.259 Sum_probs=53.5
Q ss_pred cccccceEEEeCCHHHHHHHHHHHHHHccCCCCCCCeeeeccceeeccCceechhhhc---cccCcCC
Q 028857 46 FSSVLSNLNFIHSPTTTRLFTNRLNSLAPSLLKLKPLTVTGTGCISSSGFYRSLRFEQ---NKRSFRG 110 (202)
Q Consensus 46 ~s~~~~~aIFy~de~Qk~~A~~~i~~l~~~~~~~kpI~vTe~~I~p~~~Fy~AEeYHQ---~KNP~Ry 110 (202)
-..||.++|||+|++|+++|+++++++++.+ ++| +|+ |+|+.+||+||+||| .|||.++
T Consensus 215 ~G~QYRS~If~~d~eq~~~A~~~~~~~~~~~---~~i-~Te--I~~l~~Fy~AEeyHQ~Yl~k~p~~~ 276 (283)
T PRK05550 215 IGTQYRSAIFYHDDEQKQIAEKLIAELTKKG---YPV-VTE--VEAAGPFYPAEDYHQDYYEKHGKQP 276 (283)
T ss_pred CCcCceEEEEeCCHHHHHHHHHHHHHHHhcC---Cce-EEE--EeeCCCeeECHHHHHHHHHhCCCCC
Confidence 3579999999999999999999999998743 389 999 999999999999999 8999984
No 17
>KOG1635 consensus Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=99.25 E-value=5.6e-12 Score=106.46 Aligned_cols=56 Identities=18% Similarity=0.212 Sum_probs=51.8
Q ss_pred cccceEEEeCCHHHHHHHHHHHHHHccCCCCCCCeeeeccceeeccCceechhhhc---cccCc
Q 028857 48 SVLSNLNFIHSPTTTRLFTNRLNSLAPSLLKLKPLTVTGTGCISSSGFYRSLRFEQ---NKRSF 108 (202)
Q Consensus 48 ~~~~~aIFy~de~Qk~~A~~~i~~l~~~~~~~kpI~vTe~~I~p~~~Fy~AEeYHQ---~KNP~ 108 (202)
.||-|+||+++++|+++|+.++++.+.. ..++| +|+ |+|++.||.||+||| .|||-
T Consensus 114 tQYRS~I~~~s~eq~k~A~~s~e~~Q~k--~~~kI-~T~--I~p~~kFY~AE~yHQqYl~K~~~ 172 (191)
T KOG1635|consen 114 TQYRSGIYTYSPEQEKLARESKEREQKK--WNGKI-VTE--ILPAKKFYRAEEYHQQYLSKNPR 172 (191)
T ss_pred ceeeeeeeeCCHHHHHHHHHHHHHHHhc--cCCcc-eEE--EeeccchhhchHHHHHHHhhCCC
Confidence 5899999999999999999999998873 67899 999 999999999999999 78883
No 18
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=76.30 E-value=0.84 Score=37.35 Aligned_cols=23 Identities=39% Similarity=1.090 Sum_probs=16.7
Q ss_pred EEeccCCCCCCCCCCC-CCCCCCC
Q 028857 164 YNCSACGTPLYKSTTK-FNSGCGW 186 (202)
Q Consensus 164 Y~C~~C~~pLF~S~~K-FdSg~GW 186 (202)
+||..||.|||.=+-+ |=+-||-
T Consensus 29 ~hCp~Cg~PLF~KdG~v~CPvC~~ 52 (131)
T COG1645 29 KHCPKCGTPLFRKDGEVFCPVCGY 52 (131)
T ss_pred hhCcccCCcceeeCCeEECCCCCc
Confidence 6899999999993322 5555664
No 19
>PRK00420 hypothetical protein; Validated
Probab=68.17 E-value=2.5 Score=33.66 Aligned_cols=22 Identities=27% Similarity=0.647 Sum_probs=11.8
Q ss_pred EeccCCCCCCC--CCCCCCCCCCC
Q 028857 165 NCSACGTPLYK--STTKFNSGCGW 186 (202)
Q Consensus 165 ~C~~C~~pLF~--S~~KFdSg~GW 186 (202)
+|..||.|||. ...-|=+.||=
T Consensus 25 ~CP~Cg~pLf~lk~g~~~Cp~Cg~ 48 (112)
T PRK00420 25 HCPVCGLPLFELKDGEVVCPVHGK 48 (112)
T ss_pred CCCCCCCcceecCCCceECCCCCC
Confidence 56666666664 44445555553
No 20
>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=59.26 E-value=3.8 Score=27.10 Aligned_cols=14 Identities=43% Similarity=1.144 Sum_probs=11.7
Q ss_pred EeccCCCCCCCCCC
Q 028857 165 NCSACGTPLYKSTT 178 (202)
Q Consensus 165 ~C~~C~~pLF~S~~ 178 (202)
+|..||.|||.+.+
T Consensus 19 ~Cp~C~~PL~~~k~ 32 (41)
T PF06677_consen 19 HCPDCGTPLMRDKD 32 (41)
T ss_pred ccCCCCCeeEEecC
Confidence 68899999998544
No 21
>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=58.94 E-value=4.6 Score=25.85 Aligned_cols=21 Identities=29% Similarity=0.626 Sum_probs=16.6
Q ss_pred CCCCCCCCCCeEEEeccCCCC
Q 028857 152 TGEYDKHFEEGIYNCSACGTP 172 (202)
Q Consensus 152 sg~y~~~~~~G~Y~C~~C~~p 172 (202)
.|..+...++|.|.|..||.-
T Consensus 14 C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 14 CGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CCCeEeEccCCEEEhhhCceE
Confidence 556677788999999999863
No 22
>PRK12495 hypothetical protein; Provisional
Probab=56.53 E-value=4.7 Score=35.82 Aligned_cols=14 Identities=29% Similarity=0.921 Sum_probs=10.8
Q ss_pred CeEEEeccCCCCCC
Q 028857 161 EGIYNCSACGTPLY 174 (202)
Q Consensus 161 ~G~Y~C~~C~~pLF 174 (202)
.+-++|..||.|||
T Consensus 40 msa~hC~~CG~PIp 53 (226)
T PRK12495 40 MTNAHCDECGDPIF 53 (226)
T ss_pred cchhhcccccCccc
Confidence 45678888888888
No 23
>PHA02540 61 DNA primase; Provisional
Probab=48.73 E-value=8.8 Score=35.72 Aligned_cols=10 Identities=40% Similarity=1.424 Sum_probs=8.9
Q ss_pred eEEEeccCCC
Q 028857 162 GIYNCSACGT 171 (202)
Q Consensus 162 G~Y~C~~C~~ 171 (202)
++|+|-+||.
T Consensus 54 ~~yhCFgCGa 63 (337)
T PHA02540 54 GVFKCHNCGY 63 (337)
T ss_pred eEEEecCCCC
Confidence 4999999996
No 24
>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=48.15 E-value=15 Score=23.68 Aligned_cols=29 Identities=31% Similarity=0.660 Sum_probs=18.4
Q ss_pred CCCeEEEeccCCCCCCCCCCCCCCCCCCccC
Q 028857 159 FEEGIYNCSACGTPLYKSTTKFNSGCGWPAF 189 (202)
Q Consensus 159 ~~~G~Y~C~~C~~pLF~S~~KFdSg~GWPSF 189 (202)
...|.++|..||.-| .+...+++--|-+|
T Consensus 15 ~~~g~~vC~~CG~Vl--~e~~i~~~~e~r~f 43 (43)
T PF08271_consen 15 PERGELVCPNCGLVL--EENIIDEGPEWREF 43 (43)
T ss_dssp TTTTEEEETTT-BBE--E-TTBSCCCSCCHC
T ss_pred CCCCeEECCCCCCEe--ecccccCCcccccC
Confidence 678999999999876 33444555555443
No 25
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=42.73 E-value=21 Score=23.11 Aligned_cols=16 Identities=38% Similarity=0.935 Sum_probs=13.9
Q ss_pred CCCCCCCeEEEeccCC
Q 028857 155 YDKHFEEGIYNCSACG 170 (202)
Q Consensus 155 y~~~~~~G~Y~C~~C~ 170 (202)
|.|....|.++|..|+
T Consensus 17 ~~d~~g~G~~~C~~Cg 32 (37)
T smart00778 17 FDDKDGRGTWFCSVCG 32 (37)
T ss_pred cccCCCCcCEEeCCCC
Confidence 6777788999999996
No 26
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=41.87 E-value=23 Score=31.95 Aligned_cols=31 Identities=29% Similarity=0.690 Sum_probs=26.6
Q ss_pred CCCeEEEeccCCCCCCCCCCCCCCCCCCccCCc
Q 028857 159 FEEGIYNCSACGTPLYKSTTKFNSGCGWPAFYE 191 (202)
Q Consensus 159 ~~~G~Y~C~~C~~pLF~S~~KFdSg~GWPSF~~ 191 (202)
...|-++|..||.-| .+.-.|.|.-|.+|..
T Consensus 26 ~~~Ge~vC~~CG~Vl--~e~~iD~g~EWR~f~~ 56 (310)
T PRK00423 26 YERGEIVCADCGLVI--EENIIDQGPEWRAFDP 56 (310)
T ss_pred CCCCeEeecccCCcc--cccccccCCCccCCCc
Confidence 579999999999877 5667889999999975
No 27
>cd04983 IgV_TCR_alpha_like Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) alpha chain and similar proteins. IgV_TCR_alpha: immunoglobulin (Ig) variable domain of the alpha chain of alpha/beta T-cell antigen receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are composed of alpha and beta, or gamma and delta, polypeptide chains with variable (V) and constant (C) regions. This group represents the variable domain of the alpha chain of TCRs and also includes the variable domain of delta chains of TCRs. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. The variable domain of TCRs is responsible for antigen recognition, and is located at the N-terminus of the receptor. Gamma/delta TCRs recognize intact protein antigens; they recognize proteins antigens directly and without antigen processing, and MHC independently of the bound peptide.
Probab=41.33 E-value=17 Score=26.39 Aligned_cols=15 Identities=13% Similarity=0.450 Sum_probs=11.4
Q ss_pred CCCCCeEEEeccCCC
Q 028857 157 KHFEEGIYNCSACGT 171 (202)
Q Consensus 157 ~~~~~G~Y~C~~C~~ 171 (202)
...+.|+|.|++...
T Consensus 78 ~~~DsG~Y~C~~~~~ 92 (109)
T cd04983 78 QLSDSAVYFCALSES 92 (109)
T ss_pred CHHHCEEEEEEEecC
Confidence 345899999998754
No 28
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=36.45 E-value=15 Score=29.27 Aligned_cols=22 Identities=27% Similarity=0.478 Sum_probs=16.9
Q ss_pred CCCCCCeEEEeccCCCCCCCCC
Q 028857 156 DKHFEEGIYNCSACGTPLYKST 177 (202)
Q Consensus 156 ~~~~~~G~Y~C~~C~~pLF~S~ 177 (202)
......+.+.|..||.+||...
T Consensus 62 ~~s~~~~r~FC~~CGs~l~~~~ 83 (133)
T COG3791 62 FSSGSAGRGFCPTCGSPLFWRG 83 (133)
T ss_pred eecCCCCCeecccCCCceEEec
Confidence 3445667779999999999763
No 29
>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=36.32 E-value=18 Score=29.87 Aligned_cols=39 Identities=26% Similarity=0.563 Sum_probs=24.5
Q ss_pred CCHHHHHhcCCHHHHHHHHhcCCCCCCCCCCCCCCCCeEEEeccCCCCC
Q 028857 125 KSEEEWRAILSPEQFRILRQKATEYPGTGEYDKHFEEGIYNCSACGTPL 173 (202)
Q Consensus 125 ~sd~ewr~~Lt~~qy~Vlr~~gTE~pfsg~y~~~~~~G~Y~C~~C~~pL 173 (202)
++.-||.+.. .=++.+| .--+|+. -..|+|+|..||..+
T Consensus 84 kTqvEw~el~-----~d~~h~g--~Y~sGE~---~g~G~l~C~~Cg~~~ 122 (146)
T PF07295_consen 84 KTQVEWAELA-----QDLEHHG--VYHSGEV---VGPGTLVCENCGHEV 122 (146)
T ss_pred hhHHHHHHHH-----HHHHhcC--CeecCcE---ecCceEecccCCCEE
Confidence 5566675433 2344555 3345553 379999999999865
No 30
>cd04984 IgV_L_lambda Immunoglobulin (Ig) lambda light chain variable (V) domain. IgV_L_lambda: Immunoglobulin (Ig) light chain, lambda type, variable (V) domain. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determine the type of immunoglobulin: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which seem to be functionally identical, and can associate with any of the heavy chains.
Probab=35.18 E-value=20 Score=25.91 Aligned_cols=13 Identities=23% Similarity=0.450 Sum_probs=10.3
Q ss_pred CCCCCeEEEeccC
Q 028857 157 KHFEEGIYNCSAC 169 (202)
Q Consensus 157 ~~~~~G~Y~C~~C 169 (202)
...+.|+|.|++-
T Consensus 71 ~~~Dsg~Y~C~~~ 83 (98)
T cd04984 71 QTEDEADYYCQVW 83 (98)
T ss_pred ChhhCEEEEEEEc
Confidence 3468999999874
No 31
>COG0358 DnaG DNA primase (bacterial type) [DNA replication, recombination, and repair]
Probab=35.10 E-value=29 Score=33.92 Aligned_cols=45 Identities=24% Similarity=0.489 Sum_probs=26.1
Q ss_pred HHHHhcCCHHH----HHHHHhcCCC----CCCCCCCC----CCCCCeEEEeccCCCC
Q 028857 128 EEWRAILSPEQ----FRILRQKATE----YPGTGEYD----KHFEEGIYNCSACGTP 172 (202)
Q Consensus 128 ~ewr~~Lt~~q----y~Vlr~~gTE----~pfsg~y~----~~~~~G~Y~C~~C~~p 172 (202)
++.|++++..+ |--|+..|-. =||-++-. -..+.|+|||-+||.-
T Consensus 8 ~~l~~~~dIvdvI~~~v~Lkk~G~~y~~lCPFH~EktPSf~V~~~k~~yhCFGCg~~ 64 (568)
T COG0358 8 DELRERIDIVDVIGEYVKLKKQGANYTGLCPFHAEKTPSFTVSPEKGFYHCFGCGAG 64 (568)
T ss_pred HHHHHcCCHHHHHhhheEeeecCCCceeECcCCCCCCCCceEeCCCCeEecCCCCCC
Confidence 45666665433 3344555533 34444322 2358999999999974
No 32
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=33.62 E-value=38 Score=22.03 Aligned_cols=36 Identities=19% Similarity=0.611 Sum_probs=18.1
Q ss_pred EEEeccCCCCC-CCCCC-CCCC-CCCCccCCccccCCcc
Q 028857 163 IYNCSACGTPL-YKSTT-KFNS-GCGWPAFYEGLPGAIN 198 (202)
Q Consensus 163 ~Y~C~~C~~pL-F~S~~-KFdS-g~GWPSF~~~i~~aV~ 198 (202)
.|.|..||..+ |.... .+.. -||=|-+...-+..|+
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~~~~~~v~ 41 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYRILFKERPPVVK 41 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCeEEEccCCCcce
Confidence 47777777754 22222 2333 2666665554444443
No 33
>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=33.07 E-value=24 Score=26.20 Aligned_cols=27 Identities=26% Similarity=0.415 Sum_probs=17.3
Q ss_pred CCCCCeEEEeccCCCCCCCCCCCCCCCCCCccC
Q 028857 157 KHFEEGIYNCSACGTPLYKSTTKFNSGCGWPAF 189 (202)
Q Consensus 157 ~~~~~G~Y~C~~C~~pLF~S~~KFdSg~GWPSF 189 (202)
...+.|+|.|+.... ....=|.|=|.|
T Consensus 77 ~~sDsgtY~Ca~~~~------~~~~Fg~~~~~~ 103 (104)
T cd05720 77 QKENEGYYFCSVASN------SVLYFSSFVPVF 103 (104)
T ss_pred CHHHCEEEEEEEccC------CceEEcCceecc
Confidence 345899999987632 233334566666
No 34
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=32.21 E-value=33 Score=23.09 Aligned_cols=18 Identities=28% Similarity=0.695 Sum_probs=13.7
Q ss_pred CCCCCCCeEEEeccCCCC
Q 028857 155 YDKHFEEGIYNCSACGTP 172 (202)
Q Consensus 155 y~~~~~~G~Y~C~~C~~p 172 (202)
+.+....|+|.|..||.-
T Consensus 18 ~~~~~~~~~~~C~~Cga~ 35 (53)
T TIGR03655 18 FDPLDLSHYFECSTCGAS 35 (53)
T ss_pred cCCCCCEEEEECCCCCCC
Confidence 345567889999999864
No 35
>PRK08624 hypothetical protein; Provisional
Probab=32.04 E-value=33 Score=32.58 Aligned_cols=14 Identities=29% Similarity=0.809 Sum_probs=11.8
Q ss_pred CCCCeEEEec-cCCC
Q 028857 158 HFEEGIYNCS-ACGT 171 (202)
Q Consensus 158 ~~~~G~Y~C~-~C~~ 171 (202)
..+.++|+|- +||.
T Consensus 54 ~pekq~yhCF~GCGa 68 (373)
T PRK08624 54 YIENDNFHCYTRCGD 68 (373)
T ss_pred cCCCCEEEEeCCCCC
Confidence 3478999999 9997
No 36
>cd04980 IgV_L_kappa Immunoglobulin (Ig) light chain, kappa type, variable (V) domain. IgV_L_kappa: Immunoglobulin (Ig) light chain, kappa type, variable (V) domain. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determine the type of immunoglobulin: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which seem to be functionally identical, and can associate with any of the heavy chains.
Probab=31.82 E-value=21 Score=26.18 Aligned_cols=13 Identities=15% Similarity=0.511 Sum_probs=10.1
Q ss_pred CCCCCeEEEeccC
Q 028857 157 KHFEEGIYNCSAC 169 (202)
Q Consensus 157 ~~~~~G~Y~C~~C 169 (202)
...+.|+|.|+.-
T Consensus 79 ~~~Dsg~Y~Ca~~ 91 (106)
T cd04980 79 EPEDAAVYYCQQY 91 (106)
T ss_pred ChHHCEEEEEEEe
Confidence 3458999999873
No 37
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=30.74 E-value=26 Score=25.38 Aligned_cols=27 Identities=26% Similarity=0.731 Sum_probs=24.4
Q ss_pred eEEEeccCCCCCCCCCCCCCCCCCC-cc
Q 028857 162 GIYNCSACGTPLYKSTTKFNSGCGW-PA 188 (202)
Q Consensus 162 G~Y~C~~C~~pLF~S~~KFdSg~GW-PS 188 (202)
=.-.|..||.--|....+.=+.||+ ||
T Consensus 16 tHt~CrRCG~~syh~qK~~CasCGygps 43 (62)
T PRK04179 16 THIRCRRCGRHSYNVRKKYCAACGFGRS 43 (62)
T ss_pred ccchhcccCcccccccccchhhcCCCcc
Confidence 4568999999999999999999999 76
No 38
>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=29.69 E-value=22 Score=24.94 Aligned_cols=19 Identities=32% Similarity=0.758 Sum_probs=13.2
Q ss_pred CCCCeEEEeccCCCCCCCC
Q 028857 158 HFEEGIYNCSACGTPLYKS 176 (202)
Q Consensus 158 ~~~~G~Y~C~~C~~pLF~S 176 (202)
....=.+.|..||.+||.-
T Consensus 43 ~~~~~r~FC~~CGs~l~~~ 61 (92)
T PF04828_consen 43 GKGVERYFCPTCGSPLFSE 61 (92)
T ss_dssp TSSCEEEEETTT--EEEEE
T ss_pred CCcCcCcccCCCCCeeecc
Confidence 4455569999999999965
No 39
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=29.30 E-value=21 Score=28.58 Aligned_cols=14 Identities=43% Similarity=1.061 Sum_probs=12.9
Q ss_pred CCeEEEeccCCCCC
Q 028857 160 EEGIYNCSACGTPL 173 (202)
Q Consensus 160 ~~G~Y~C~~C~~pL 173 (202)
+-|.+.|..||+++
T Consensus 46 e~G~t~CP~Cg~~~ 59 (115)
T COG1885 46 EVGSTSCPKCGEPF 59 (115)
T ss_pred ecccccCCCCCCcc
Confidence 78999999999986
No 40
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=29.25 E-value=27 Score=20.44 Aligned_cols=21 Identities=33% Similarity=0.868 Sum_probs=14.8
Q ss_pred EeccCCCCCCCCCCCCCCCCCC
Q 028857 165 NCSACGTPLYKSTTKFNSGCGW 186 (202)
Q Consensus 165 ~C~~C~~pLF~S~~KFdSg~GW 186 (202)
.|..||.++ ..+++|=+.||=
T Consensus 4 ~Cp~Cg~~~-~~~~~fC~~CG~ 24 (26)
T PF13248_consen 4 FCPNCGAEI-DPDAKFCPNCGA 24 (26)
T ss_pred CCcccCCcC-CcccccChhhCC
Confidence 577788853 777777777773
No 41
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=28.82 E-value=25 Score=28.37 Aligned_cols=18 Identities=28% Similarity=0.863 Sum_probs=14.8
Q ss_pred CeEEEeccCCCCCCCCCC
Q 028857 161 EGIYNCSACGTPLYKSTT 178 (202)
Q Consensus 161 ~G~Y~C~~C~~pLF~S~~ 178 (202)
.|.|.|..||.+|..-+.
T Consensus 121 ~~~f~Cp~Cg~~l~~~dn 138 (147)
T smart00531 121 DGTFTCPRCGEELEEDDN 138 (147)
T ss_pred CCcEECCCCCCEEEEcCc
Confidence 688999999999976443
No 42
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=28.55 E-value=31 Score=26.75 Aligned_cols=28 Identities=25% Similarity=0.647 Sum_probs=25.2
Q ss_pred CeEEEeccCCCCCCCCCCCCCCCCCCcc
Q 028857 161 EGIYNCSACGTPLYKSTTKFNSGCGWPA 188 (202)
Q Consensus 161 ~G~Y~C~~C~~pLF~S~~KFdSg~GWPS 188 (202)
.=.-.|..||.--|.-..+.=+.||+||
T Consensus 14 ktHtlCrRCG~~syH~qK~~CasCGyps 41 (91)
T PTZ00073 14 KTHTLCRRCGKRSFHVQKKRCASCGYPS 41 (91)
T ss_pred cCcchhcccCccccccccccchhcCCch
Confidence 4456899999999999999999999997
No 43
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=28.47 E-value=28 Score=22.91 Aligned_cols=16 Identities=31% Similarity=0.885 Sum_probs=8.7
Q ss_pred CCCCCCCeEEEeccCC
Q 028857 155 YDKHFEEGIYNCSACG 170 (202)
Q Consensus 155 y~~~~~~G~Y~C~~C~ 170 (202)
|.|....|.|+|..|+
T Consensus 18 ~~d~~~~G~~~C~~C~ 33 (40)
T PF08273_consen 18 FDDKDGRGTWICRQCG 33 (40)
T ss_dssp ETT----S-EEETTTT
T ss_pred CcCcccCCCEECCCCC
Confidence 3455667999999994
No 44
>cd05895 Ig_Pro_neuregulin-1 Immunoglobulin (Ig)-like domain found in neuregulin (NRG)-1. Ig_Pro_neuregulin-1: immunoglobulin (Ig)-like domain found in neuregulin (NRG)-1. There are many NRG-1 isoforms which arise from the alternative splicing of mRNA. NRG-1 belongs to the neuregulin gene family, which is comprised of four genes. This group represents NRG-1. NRGs are signaling molecules, which participate in cell-cell interactions in the nervous system, breast, and heart, and other organ systems, and are implicated in the pathology of diseases including schizophrenia, multiple sclerosis, and breast cancer. The NRG-1 protein binds to and activates the tyrosine kinases receptors ErbB3 and ErbB4, initiating signaling cascades. NRG-1 has multiple functions; for example, in the brain it regulates various processes such as radial glia formation and neuronal migration, dendritic development, and expression of neurotransmitters receptors; in the peripheral nervous system NRG-1 regulates process
Probab=26.95 E-value=38 Score=23.06 Aligned_cols=15 Identities=20% Similarity=0.508 Sum_probs=11.3
Q ss_pred CCCCCeEEEeccCCC
Q 028857 157 KHFEEGIYNCSACGT 171 (202)
Q Consensus 157 ~~~~~G~Y~C~~C~~ 171 (202)
...+.|.|.|.+.+.
T Consensus 52 ~~~DsG~Y~C~a~N~ 66 (76)
T cd05895 52 SLADNGEYKCMVSSK 66 (76)
T ss_pred CcccCEEEEEEEEeC
Confidence 346899999987643
No 45
>smart00408 IGc2 Immunoglobulin C-2 Type.
Probab=25.88 E-value=45 Score=20.24 Aligned_cols=11 Identities=36% Similarity=0.673 Sum_probs=8.9
Q ss_pred CCCCeEEEecc
Q 028857 158 HFEEGIYNCSA 168 (202)
Q Consensus 158 ~~~~G~Y~C~~ 168 (202)
..+.|.|.|.+
T Consensus 48 ~~d~G~Y~C~~ 58 (63)
T smart00408 48 LEDSGEYTCVA 58 (63)
T ss_pred cccCEEEEEEE
Confidence 45789999976
No 46
>cd05861 Ig1_PDGFR-alphabeta Frst immunoglobulin (Ig)-like domain of platelet-derived growth factor (PDGF) receptors (R), alpha (CD140a), and beta (CD140b). Ig1_PDGFR-alphabeta: The first immunoglobulin (Ig)-like domain of platelet-derived growth factor (PDGF) receptors (R), alpha (CD140a), and beta (CD140b). PDGF is a potent mitogen for connective tissue cells. PDGF-stimulated processes are mediated by three different PDGFs (PDGF-A,-B, and C). PDGFRalpha binds to all three PDGFs, whereas the PDGFRbeta binds only to PDGF-B. PDGFRs alpha and beta have similar organization: an extracellular component with five Ig-like domains, a transmembrane segment, and a cytoplasmic portion having protein tyrosine kinase activity. In mice, PDGFRalpha and PDGFRbeta are essential for normal development.
Probab=25.74 E-value=44 Score=23.76 Aligned_cols=14 Identities=29% Similarity=0.589 Sum_probs=10.9
Q ss_pred CCCCCeEEEeccCC
Q 028857 157 KHFEEGIYNCSACG 170 (202)
Q Consensus 157 ~~~~~G~Y~C~~C~ 170 (202)
...+.|+|.|.+-+
T Consensus 54 ~~~DsG~Y~C~a~n 67 (84)
T cd05861 54 TVEDSGTYECAAHE 67 (84)
T ss_pred CcCCCEEEEEEEEE
Confidence 35689999998743
No 47
>cd05765 Ig_3 Subgroup of the immunoglobulin (Ig) superfamily. Ig_3: subgroup of the immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of the Ig superfamily are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond.
Probab=25.74 E-value=43 Score=22.66 Aligned_cols=14 Identities=29% Similarity=0.757 Sum_probs=11.1
Q ss_pred CCCCCeEEEeccCC
Q 028857 157 KHFEEGIYNCSACG 170 (202)
Q Consensus 157 ~~~~~G~Y~C~~C~ 170 (202)
...+.|+|.|.+.+
T Consensus 55 ~~~D~G~Y~C~a~N 68 (81)
T cd05765 55 QPQDAGLYTCTARN 68 (81)
T ss_pred CcccCEEEEEEEec
Confidence 44689999998765
No 48
>cd04974 Ig3_FGFR Third immunoglobulin (Ig)-like domain of fibroblast growth factor receptor (FGFR). Ig3_FGFR: third immunoglobulin (Ig)-like domain of fibroblast growth factor receptor (FGFR). Fibroblast growth factors (FGFs) participate in morphogenesis, development, angiogenesis, and wound healing. These FGF-stimulated processes are mediated by four FGFR tyrosine kinases (FGRF1-4). FGFRs are comprised of an extracellular portion consisting of three Ig-like domains, a transmembrane helix, and a cytoplasmic portion having protein tyrosine kinase activity. The highly conserved Ig-like domains 2 and 3, and the linker region between D2 and D3 define a general binding site for FGFs.
Probab=25.68 E-value=43 Score=23.94 Aligned_cols=13 Identities=31% Similarity=0.526 Sum_probs=10.7
Q ss_pred CCCCeEEEeccCC
Q 028857 158 HFEEGIYNCSACG 170 (202)
Q Consensus 158 ~~~~G~Y~C~~C~ 170 (202)
..+.|.|.|.+.+
T Consensus 64 ~~D~G~Y~C~A~N 76 (90)
T cd04974 64 FDDAGEYTCLAGN 76 (90)
T ss_pred cccCcEEEEEeec
Confidence 4699999998765
No 49
>cd04977 Ig1_NCAM-1_like First immunoglobulin (Ig)-like domain of neural cell adhesion molecule NCAM-1 and similar proteins. Ig1_NCAM-1 like: first immunoglobulin (Ig)-like domain of neural cell adhesion molecule NCAM-1. NCAM-1 plays important roles in the development and regeneration of the central nervous system, in synaptogenesis and neural migration. NCAM mediates cell-cell and cell-substratum recognition and adhesion via homophilic (NCAM-NCAM), and heterophilic (NCAM-nonNCAM), interactions. NCAM is expressed as three major isoforms having different intracellular extensions. The extracellular portion of NCAM has five N-terminal Ig-like domains and two fibronectin type III domains. The double zipper adhesion complex model for NCAM homophilic binding involves the Ig1, Ig2, and Ig3 domains. By this model, Ig1 and Ig2 mediate dimerization of NCAM molecules situated on the same cell surface (cis interactions), and Ig3 domains mediate interactions between NCAM molecules expressed on the s
Probab=25.06 E-value=44 Score=24.10 Aligned_cols=15 Identities=33% Similarity=0.660 Sum_probs=11.9
Q ss_pred CCCCCeEEEeccCCC
Q 028857 157 KHFEEGIYNCSACGT 171 (202)
Q Consensus 157 ~~~~~G~Y~C~~C~~ 171 (202)
...+.|+|.|.+.+.
T Consensus 65 ~~~D~G~Y~C~A~N~ 79 (92)
T cd04977 65 NIEDAGIYKCVATDA 79 (92)
T ss_pred CcccCEEEEEEEEcC
Confidence 446899999988764
No 50
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=25.02 E-value=30 Score=24.64 Aligned_cols=10 Identities=40% Similarity=1.288 Sum_probs=8.7
Q ss_pred EeccCCCCCC
Q 028857 165 NCSACGTPLY 174 (202)
Q Consensus 165 ~C~~C~~pLF 174 (202)
||..||.|+=
T Consensus 5 HC~~CG~~Ip 14 (59)
T PF09889_consen 5 HCPVCGKPIP 14 (59)
T ss_pred cCCcCCCcCC
Confidence 7999999974
No 51
>cd05734 Ig7_DSCAM Seventh immunoglobulin (Ig)-like domain of Down Syndrome Cell Adhesion molecule (DSCAM). Ig7_DSCAM: the seventh immunoglobulin (Ig)-like domain of Down Syndrome Cell Adhesion molecule (DSCAM). DSCAM is a cell adhesion molecule expressed largely in the developing nervous system. The gene encoding DSCAM is located at human chromosome 21q22, the locus associated with the mental retardation phenotype of Down Syndrome. DSCAM is predicted to be the largest member of the IG superfamily. It has been demonstrated that DSCAM can mediate cation-independent homophilic intercellular adhesion.
Probab=24.44 E-value=48 Score=22.80 Aligned_cols=13 Identities=23% Similarity=0.572 Sum_probs=10.6
Q ss_pred CCCCeEEEeccCC
Q 028857 158 HFEEGIYNCSACG 170 (202)
Q Consensus 158 ~~~~G~Y~C~~C~ 170 (202)
..+.|+|.|.+.+
T Consensus 53 ~~D~G~Y~C~a~N 65 (79)
T cd05734 53 EEDSGYYLCKVSN 65 (79)
T ss_pred cccCEEEEEEEEe
Confidence 3689999998865
No 52
>cd05726 Ig4_Robo Fhird immunoglobulin (Ig)-like domain in Robo (roundabout) receptors. Ig4_Robo: domain similar to the fhird immunoglobulin (Ig)-like domain in Robo (roundabout) receptors. Robo receptors play a role in the development of the central nervous system (CNS), and are receptors of Slit protein. Slit is a repellant secreted by the neural cells in the midline. Slit acts through Robo to prevent most neurons from crossing the midline from either side. Three mammalian Robo homologs (robo1, -2, and -3), and three mammalian Slit homologs (Slit-1,-2, -3), have been identified. Commissural axons, which cross the midline, express low levels of Robo; longitudinal axons, which avoid the midline, express high levels of Robo. robo1, -2, and -3 are expressed by commissural neurons in the vertebrate spinal cord and Slits 1, -2, -3 are expressed at the ventral midline. Robo-3 is a divergent member of the Robo family which instead of being a positive regulator of slit responsiveness, antagoni
Probab=24.36 E-value=40 Score=23.90 Aligned_cols=13 Identities=23% Similarity=0.531 Sum_probs=10.6
Q ss_pred CCCCeEEEeccCC
Q 028857 158 HFEEGIYNCSACG 170 (202)
Q Consensus 158 ~~~~G~Y~C~~C~ 170 (202)
..+.|+|.|.+.+
T Consensus 56 ~~D~G~Y~C~a~N 68 (90)
T cd05726 56 RSDVGYYICQTLN 68 (90)
T ss_pred hhhCEEEEEEEEc
Confidence 4588999998865
No 53
>cd05763 Ig_1 Subgroup of the immunoglobulin (Ig) superfamily. Ig_1: subgroup of the immunoglobulin (Ig) domain found in the Ig superfamily. The Ig superfamily is a heterogenous group of proteins, built on a common fold comprised of a sandwich of two beta sheets. Members of the Ig superfamily are components of immunoglobulin, neuroglia, cell surface glycoproteins, such as T-cell receptors, CD2, CD4, CD8, and membrane glycoproteins, such as butyrophilin and chondroitin sulfate proteoglycan core protein. A predominant feature of most Ig domains is a disulfide bridge connecting the two beta-sheets with a tryptophan residue packed against the disulfide bond.
Probab=24.30 E-value=49 Score=22.44 Aligned_cols=13 Identities=31% Similarity=0.726 Sum_probs=10.6
Q ss_pred CCCCeEEEeccCC
Q 028857 158 HFEEGIYNCSACG 170 (202)
Q Consensus 158 ~~~~G~Y~C~~C~ 170 (202)
..+.|.|.|.+.+
T Consensus 49 ~~D~G~Y~C~A~N 61 (75)
T cd05763 49 IEDTGVYSCTAQN 61 (75)
T ss_pred cccCEEEEEEEEc
Confidence 4589999998854
No 54
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=24.24 E-value=37 Score=24.69 Aligned_cols=12 Identities=58% Similarity=1.204 Sum_probs=10.2
Q ss_pred EeccCCCCCCCC
Q 028857 165 NCSACGTPLYKS 176 (202)
Q Consensus 165 ~C~~C~~pLF~S 176 (202)
.|..|+.+|+.+
T Consensus 80 ~C~vC~k~l~~~ 91 (109)
T PF10367_consen 80 KCSVCGKPLGNS 91 (109)
T ss_pred CccCcCCcCCCc
Confidence 399999999874
No 55
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=23.89 E-value=45 Score=22.71 Aligned_cols=14 Identities=29% Similarity=0.864 Sum_probs=10.9
Q ss_pred eEEEeccCCCCCCC
Q 028857 162 GIYNCSACGTPLYK 175 (202)
Q Consensus 162 G~Y~C~~C~~pLF~ 175 (202)
+.++|..||...|.
T Consensus 36 ~r~~C~~Cgyt~~~ 49 (50)
T PRK00432 36 DRWHCGKCGYTEFK 49 (50)
T ss_pred CcEECCCcCCEEec
Confidence 78888888887663
No 56
>cd05862 Ig1_VEGFR First immunoglobulin (Ig)-like domain of vascular endothelial growth factor (VEGF) receptor(R). IG1_VEGFR: first immunoglobulin (Ig)-like domain of vascular endothelial growth factor (VEGF) receptor(R). The VEGFRs have an extracellular component with seven Ig-like domains, a transmembrane segment, and an intracellular tyrosine kinase domain interrupted by a kinase-insert domain. The VEGFR family consists of three members, VEGFR-1 (Flt-1), VEGFR-2 (KDR/Flk-1) and VEGFR-3 (Flt-4). VEGF_A interacts with both VEGFR-1 and VEGFR-2. VEGFR-1 binds strongest to VEGF, VEGF-2 binds more weakly. VEGFR-3 appears not to bind VEGF, but binds other members of the VEGF family (VEGF-C and -D). VEGFRs bind VEGFs with high affinity with the IG-like domains. VEGF-A is important to the growth and maintenance of vascular endothelial cells and to the development of new blood- and lymphatic-vessels in physiological and pathological states. VEGFR-2 is a major mediator of the mitogenic, angioge
Probab=23.77 E-value=42 Score=24.06 Aligned_cols=21 Identities=24% Similarity=0.437 Sum_probs=13.1
Q ss_pred CCCCCeEEEeccCC-CCCCCCC
Q 028857 157 KHFEEGIYNCSACG-TPLYKST 177 (202)
Q Consensus 157 ~~~~~G~Y~C~~C~-~pLF~S~ 177 (202)
...+.|.|.|.+-+ .-.+.+.
T Consensus 58 ~~~DsG~Y~C~a~n~~~~~~~~ 79 (86)
T cd05862 58 TLSDLGRYTCTASSGQMIAKNS 79 (86)
T ss_pred CcccCEEEEEEEeecceEeccc
Confidence 35689999996543 3334433
No 57
>cd05899 IgV_TCR_beta Immunoglobulin (Ig) variable (V) domain of T-cell receptor (TCR) bet a chain. IgV_TCR_beta: immunoglobulin (Ig) variable domain of the beta chain of alpha/beta T-cell antigen receptors (TCRs). TCRs mediate antigen recognition by T lymphocytes, and are composed of alpha and beta, or gamma and delta, polypeptide chains with variable (V) and constant (C) regions. This group includes the variable domain of the alpha chain of alpha/beta TCRs. Alpha/beta TCRs recognize antigen as peptide fragments presented by major histocompatibility complex (MHC) molecules. The variable domain of TCRs is responsible for antigen recognition, and is located at the N-terminus of the receptor. Gamma/delta TCRs recognize intact protein antigens; they recognize proteins antigens directly and without antigen processing, and MHC independently of the bound peptide.
Probab=23.48 E-value=47 Score=24.45 Aligned_cols=13 Identities=15% Similarity=0.404 Sum_probs=10.1
Q ss_pred CCCCeEEEeccCC
Q 028857 158 HFEEGIYNCSACG 170 (202)
Q Consensus 158 ~~~~G~Y~C~~C~ 170 (202)
..+.|+|.|+.-.
T Consensus 81 ~~Dsg~Y~Ca~~~ 93 (110)
T cd05899 81 PEDSAVYLCASSL 93 (110)
T ss_pred hhhCEEEEEEeeC
Confidence 4589999998653
No 58
>cd02181 GH16_fungal_Lam16A_glucanase fungal 1,3(4)-beta-D-glucanases, similar to Phanerochaete chrysosporium laminarinase 16A. Group of fungal 1,3(4)-beta-D-glucanases, similar to Phanerochaete chrysosporium laminarinase 16A. Lam16A belongs to the 'nonspecific' 1,3(4)-beta-glucanase subfamily, although beta-1,6 branching and beta-1,4 bonds specifically define where Lam16A hydrolyzes its substrates, like curdlan (beta-1,3-glucan), lichenin (beta-1,3-1,4-mixed linkage glucan), and laminarin (beta-1,6-branched-1,3-glucan).
Probab=23.36 E-value=24 Score=32.38 Aligned_cols=19 Identities=42% Similarity=1.232 Sum_probs=14.2
Q ss_pred CCCCC-CCCCCCCC-CccCCc
Q 028857 173 LYKST-TKFNSGCG-WPAFYE 191 (202)
Q Consensus 173 LF~S~-~KFdSg~G-WPSF~~ 191 (202)
||..+ .|+-.||| ||+||.
T Consensus 82 ~~~~~~~~~P~g~G~WPAfW~ 102 (293)
T cd02181 82 LFIADIAHMPGGCGTWPAFWT 102 (293)
T ss_pred eEEEEhhhCCCCCCccchhhh
Confidence 45554 37777999 999996
No 59
>cd05725 Ig3_Robo Third immunoglobulin (Ig)-like domain in Robo (roundabout) receptors. Ig3_Robo: domain similar to the third immunoglobulin (Ig)-like domain in Robo (roundabout) receptors. Robo receptors play a role in the development of the central nervous system (CNS), and are receptors of Slit protein. Slit is a repellant secreted by the neural cells in the midline. Slit acts through Robo to prevent most neurons from crossing the midline from either side. Three mammalian Robo homologs (robo1, -2, and -3), and three mammalian Slit homologs (Slit-1,-2, -3), have been identified. Commissural axons, which cross the midline, express low levels of Robo; longitudinal axons, which avoid the midline, express high levels of Robo. robo1, -2, and -3 are expressed by commissural neurons in the vertebrate spinal cord and Slits 1, -2, -3 are expressed at the ventral midline. Robo-3 is a divergent member of the Robo family which instead of being a positive regulator of slit responsiveness, antagoni
Probab=23.21 E-value=42 Score=22.41 Aligned_cols=13 Identities=38% Similarity=0.639 Sum_probs=10.2
Q ss_pred CCCCeEEEeccCC
Q 028857 158 HFEEGIYNCSACG 170 (202)
Q Consensus 158 ~~~~G~Y~C~~C~ 170 (202)
..+.|.|.|.+.+
T Consensus 44 ~~D~G~Y~C~a~N 56 (69)
T cd05725 44 AGDEGSYTCEAEN 56 (69)
T ss_pred hhHCEEEEEEEEc
Confidence 3588999998754
No 60
>cd07693 Ig1_Robo First immunoglobulin (Ig)-like domain in Robo (roundabout) receptors and similar proteins. Ig1_Robo: domain similar to the first immunoglobulin (Ig)-like domain in Robo (roundabout) receptors. Robo receptors play a role in the development of the central nervous system (CNS), and are receptors of Slit protein. Slit is a repellant secreted by the neural cells in the midline. Slit acts through Robo to prevent most neurons from crossing the midline from either side. Three mammalian Robo homologs (robo1, -2, and -3), and three mammalian Slit homologs (Slit-1,-2, -3), have been identified. Commissural axons, which cross the midline, express low levels of Robo; longitudinal axons, which avoid the midline, express high levels of Robo. robo1, -2, and -3 are expressed by commissural neurons in the vertebrate spinal cord and Slits 1, -2, -3 are expressed at the ventral midline. Robo-3 is a divergent member of the Robo family which instead of being a positive regulator of slit res
Probab=23.20 E-value=55 Score=22.65 Aligned_cols=14 Identities=36% Similarity=0.722 Sum_probs=11.0
Q ss_pred CCCCCeEEEeccCC
Q 028857 157 KHFEEGIYNCSACG 170 (202)
Q Consensus 157 ~~~~~G~Y~C~~C~ 170 (202)
...+.|.|.|.+.+
T Consensus 72 ~~~D~G~Y~C~a~N 85 (100)
T cd07693 72 GRSDEGVYVCVAHN 85 (100)
T ss_pred CcCcCEEEEEEEEc
Confidence 35689999998754
No 61
>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=23.11 E-value=42 Score=21.69 Aligned_cols=10 Identities=30% Similarity=0.796 Sum_probs=7.0
Q ss_pred CCCeEEEecc
Q 028857 159 FEEGIYNCSA 168 (202)
Q Consensus 159 ~~~G~Y~C~~ 168 (202)
.+.|+|.|.+
T Consensus 55 ~d~G~Y~C~v 64 (64)
T PF00047_consen 55 EDSGTYTCVV 64 (64)
T ss_dssp GGTEEEEEEE
T ss_pred HHCEEEEEEC
Confidence 3678888853
No 62
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=22.94 E-value=28 Score=27.94 Aligned_cols=14 Identities=57% Similarity=1.386 Sum_probs=11.1
Q ss_pred CCeEE-EeccCCCCC
Q 028857 160 EEGIY-NCSACGTPL 173 (202)
Q Consensus 160 ~~G~Y-~C~~C~~pL 173 (202)
+.|+| +|..||.|+
T Consensus 76 e~gtYG~Ce~cG~~I 90 (120)
T COG1734 76 EEGTYGICEECGEPI 90 (120)
T ss_pred HcCCccchhccCCcC
Confidence 56676 799999985
No 63
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=22.92 E-value=52 Score=18.95 Aligned_cols=20 Identities=35% Similarity=0.978 Sum_probs=12.2
Q ss_pred eccCCCCCCCCCCCCCCCCCC
Q 028857 166 CSACGTPLYKSTTKFNSGCGW 186 (202)
Q Consensus 166 C~~C~~pLF~S~~KFdSg~GW 186 (202)
|..||.+| .-+++|=+.||=
T Consensus 2 Cp~CG~~~-~~~~~fC~~CG~ 21 (23)
T PF13240_consen 2 CPNCGAEI-EDDAKFCPNCGT 21 (23)
T ss_pred CcccCCCC-CCcCcchhhhCC
Confidence 56666666 456666666653
No 64
>smart00406 IGv Immunoglobulin V-Type.
Probab=22.85 E-value=40 Score=22.38 Aligned_cols=10 Identities=30% Similarity=0.793 Sum_probs=7.7
Q ss_pred CCCeEEEecc
Q 028857 159 FEEGIYNCSA 168 (202)
Q Consensus 159 ~~~G~Y~C~~ 168 (202)
.+.|+|.|..
T Consensus 72 ~D~G~Y~C~v 81 (81)
T smart00406 72 EDTGTYYCAV 81 (81)
T ss_pred HHCEEEEEcC
Confidence 4789999963
No 65
>cd05738 Ig2_RPTP_IIa_LAR_like Second immunoglobulin (Ig)-like domain of the receptor protein tyrosine phosphatase (RPTP)-F, also known as LAR. Ig2_RPTP_IIa_LAR_like: domain similar to the second immunoglobulin (Ig)-like domain found in the receptor protein tyrosine phosphatase (RPTP)-F, also known as LAR. LAR belongs to the RPTP type IIa subfamily. Members of this subfamily are cell adhesion molecule-like proteins involved in central nervous system (CNS) development. They have large extracellular portions, comprised of multiple Ig-like domains and two to nine fibronectin type III (FNIII) domains, and a cytoplasmic portion having two tandem phosphatase domains.
Probab=22.77 E-value=46 Score=22.79 Aligned_cols=14 Identities=29% Similarity=0.695 Sum_probs=11.1
Q ss_pred CCCCCeEEEeccCC
Q 028857 157 KHFEEGIYNCSACG 170 (202)
Q Consensus 157 ~~~~~G~Y~C~~C~ 170 (202)
...+.|.|.|.+.+
T Consensus 46 ~~~D~G~Y~C~a~N 59 (74)
T cd05738 46 EESDQGKYECVATN 59 (74)
T ss_pred ChhhCEEEEEEEEC
Confidence 34689999998873
No 66
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=22.59 E-value=55 Score=21.16 Aligned_cols=13 Identities=31% Similarity=0.925 Sum_probs=7.9
Q ss_pred CCeEEEeccCCCC
Q 028857 160 EEGIYNCSACGTP 172 (202)
Q Consensus 160 ~~G~Y~C~~C~~p 172 (202)
.-.+|.|..||+-
T Consensus 3 ~~~~YkC~~CGni 15 (36)
T PF06397_consen 3 KGEFYKCEHCGNI 15 (36)
T ss_dssp TTEEEE-TTT--E
T ss_pred cccEEEccCCCCE
Confidence 4578999999974
No 67
>PF01907 Ribosomal_L37e: Ribosomal protein L37e; InterPro: IPR001569 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of proteins of 56 to 96 amino-acid residues that share a highly conserved region located in the N-terminal part.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A19_A 4A1D_A 4A18_A 4A1B_A 1S1I_Y 3O5H_d 3IZS_l 3O58_d 2ZKR_2 3IZR_l ....
Probab=22.38 E-value=38 Score=24.00 Aligned_cols=27 Identities=33% Similarity=0.704 Sum_probs=23.0
Q ss_pred eEEEeccCCCCCCCCCCCCCCCCCCcc
Q 028857 162 GIYNCSACGTPLYKSTTKFNSGCGWPA 188 (202)
Q Consensus 162 G~Y~C~~C~~pLF~S~~KFdSg~GWPS 188 (202)
-.-.|..||.--|.-..|-=+.||+|+
T Consensus 14 tH~~CrRCG~~syH~qK~~CasCGyp~ 40 (55)
T PF01907_consen 14 THTLCRRCGRRSYHIQKKTCASCGYPA 40 (55)
T ss_dssp SEEE-TTTSSEEEETTTTEETTTBTTT
T ss_pred cEeeecccCCeeeecCCCcccccCCCc
Confidence 455799999999999999999999996
No 68
>PRK12496 hypothetical protein; Provisional
Probab=22.17 E-value=49 Score=27.47 Aligned_cols=50 Identities=14% Similarity=0.144 Sum_probs=25.6
Q ss_pred HHHHHhcCCCCCCCCCCCCCC---CCeEEEeccCCCCCCCCCC--CCCCCCCCccCCc
Q 028857 139 FRILRQKATEYPGTGEYDKHF---EEGIYNCSACGTPLYKSTT--KFNSGCGWPAFYE 191 (202)
Q Consensus 139 y~Vlr~~gTE~pfsg~y~~~~---~~G~Y~C~~C~~pLF~S~~--KFdSg~GWPSF~~ 191 (202)
..|.+..|-. +.|-....- ..=.|.|.+|| ..|..+. .|=+-||=|-...
T Consensus 102 ~~vA~~lgi~--v~~~~~~~i~~~~~w~~~C~gC~-~~~~~~~~~~~C~~CG~~~~r~ 156 (164)
T PRK12496 102 QNVAKKLNIK--FENIKTKGIKKVIKWRKVCKGCK-KKYPEDYPDDVCEICGSPVKRK 156 (164)
T ss_pred HHHHHHcCCe--EeccccccchhheeeeEECCCCC-ccccCCCCCCcCCCCCChhhhc
Confidence 3566666654 333321111 12248888888 4565432 4456677664433
No 69
>cd07700 IgV_CD8_beta Immunoglobulin (Ig) like domain of CD8 beta chain. IgV_CD8_beta: immunoglobulin (Ig)-like domain in CD8 beta. 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 alpha/alpha or alpha/beta 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.
Probab=22.03 E-value=45 Score=24.70 Aligned_cols=14 Identities=29% Similarity=0.468 Sum_probs=10.9
Q ss_pred CCCCCCeEEEeccC
Q 028857 156 DKHFEEGIYNCSAC 169 (202)
Q Consensus 156 ~~~~~~G~Y~C~~C 169 (202)
....+.|+|.|+..
T Consensus 79 ~~~~Dsg~YyCa~~ 92 (107)
T cd07700 79 VKPEDSGTYFCMTV 92 (107)
T ss_pred CCHHHCEEEEEeEc
Confidence 34568999999864
No 70
>cd05742 Ig1_VEGFR_like First immunoglobulin (Ig)-like domain of vascular endothelial growth factor (VEGF) receptor (R) and similar proteins. Ig1_VEGFR_like: first immunoglobulin (Ig)-like domain of vascular endothelial growth factor (VEGF) receptor(R) related proteins. The VEGFRs have an extracellular component with seven Ig-like domains, a transmembrane segment, and an intracellular tyrosine kinase domain interrupted by a kinase-insert domain. The VEGFR family consists of three members, VEGFR-1 (Flt-1), VEGFR-2 (KDR/Flk-1) and VEGFR-3 (Flt-4). VEGF-A interacts with both VEGFR-1 and VEGFR-2. VEGFR-1 binds strongest to VEGF, VEGF-2 binds more weakly. VEGFR-3 appears not to bind VEGF, but binds other members of the VEGF family (VEGF-C and -D). VEGFRs bind VEGFs with high affinity with the IG-like domains. VEGF-A is important to the growth and maintenance of vascular endothelial cells and to the development of new blood- and lymphatic-vessels in physiological and pathological states. VEGF
Probab=21.55 E-value=47 Score=23.13 Aligned_cols=13 Identities=31% Similarity=0.705 Sum_probs=10.4
Q ss_pred CCCCeEEEeccCC
Q 028857 158 HFEEGIYNCSACG 170 (202)
Q Consensus 158 ~~~~G~Y~C~~C~ 170 (202)
..+.|+|.|.+-+
T Consensus 58 ~~DsG~Y~C~a~n 70 (84)
T cd05742 58 LKDSGTYTCAASS 70 (84)
T ss_pred hhhCEEEEEEEcc
Confidence 4689999998754
No 71
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=21.37 E-value=1.6e+02 Score=26.21 Aligned_cols=71 Identities=15% Similarity=0.299 Sum_probs=38.4
Q ss_pred eeeccCceechhhhc-cccCcCCcceeeccCCCCCCCCCHHHHHhcCCHHHHHHHHh----cCCC-CCCC------CCCC
Q 028857 89 CISSSGFYRSLRFEQ-NKRSFRGGVVLAVASGPASVNKSEEEWRAILSPEQFRILRQ----KATE-YPGT------GEYD 156 (202)
Q Consensus 89 I~p~~~Fy~AEeYHQ-~KNP~Ry~vVlAaap~~~~~~~sd~ewr~~Lt~~qy~Vlr~----~gTE-~pfs------g~y~ 156 (202)
|.-+.|.|.+|-=++ .=||.+. ...+++++|+....... +|++. +||. ..|. |.|-
T Consensus 177 vaGIGNiya~EiLf~A~IhP~~~-----------~~~Ls~~~~~~L~~~i~-~vl~~ai~~gg~~~~~~~~~~g~~g~~~ 244 (282)
T PRK13945 177 VAGIGNIYADESLFKAGIHPTTP-----------AGQLKKKQLERLREAII-EVLKTSIGAGGTTFSDFRDLEGVNGNYG 244 (282)
T ss_pred EeccchhHHHHHHHHcCCCccCc-----------cccCCHHHHHHHHHHHH-HHHHHHHHcCCCccccccccCCCCCccc
Confidence 444677787777777 5556532 23478888776544333 34444 4543 2232 1111
Q ss_pred CCCCCeEE-----EeccCCCCC
Q 028857 157 KHFEEGIY-----NCSACGTPL 173 (202)
Q Consensus 157 ~~~~~G~Y-----~C~~C~~pL 173 (202)
+ .--+| .|..||.++
T Consensus 245 ~--~~~Vy~R~g~pC~~Cg~~I 264 (282)
T PRK13945 245 G--QAWVYRRTGKPCRKCGTPI 264 (282)
T ss_pred c--eEEEeCCCcCCCCcCCCee
Confidence 0 11245 799999886
No 72
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=21.14 E-value=47 Score=22.92 Aligned_cols=36 Identities=19% Similarity=0.421 Sum_probs=21.2
Q ss_pred eEEEeccCCCCCCCCCCCCC----CCCCCccCCccccCCcc
Q 028857 162 GIYNCSACGTPLYKSTTKFN----SGCGWPAFYEGLPGAIN 198 (202)
Q Consensus 162 G~Y~C~~C~~pLF~S~~KFd----Sg~GWPSF~~~i~~aV~ 198 (202)
=.|.|+.||..+ ....+.+ +-||---+.++-+..++
T Consensus 5 ~~Y~C~~Cg~~~-~~~~~~~~irCp~Cg~rIl~K~R~~~~k 44 (49)
T COG1996 5 MEYKCARCGREV-ELDQETRGIRCPYCGSRILVKERPKVPK 44 (49)
T ss_pred EEEEhhhcCCee-ehhhccCceeCCCCCcEEEEeccCCccE
Confidence 479999999988 3232322 23665555555544443
No 73
>PRK10445 endonuclease VIII; Provisional
Probab=20.35 E-value=1.2e+02 Score=26.90 Aligned_cols=73 Identities=16% Similarity=0.166 Sum_probs=39.3
Q ss_pred eeeccCceechhhhc-cccCcCCcceeeccCCCCCCCCCHHHHHhcCCHHHHHHHHh----cCCCCCC--CCCCC--CCC
Q 028857 89 CISSSGFYRSLRFEQ-NKRSFRGGVVLAVASGPASVNKSEEEWRAILSPEQFRILRQ----KATEYPG--TGEYD--KHF 159 (202)
Q Consensus 89 I~p~~~Fy~AEeYHQ-~KNP~Ry~vVlAaap~~~~~~~sd~ewr~~Lt~~qy~Vlr~----~gTE~pf--sg~y~--~~~ 159 (202)
|.-+.|.|.+|-=+| .=||.+ ....+++++|+....... +|++. +||..+. .|.+. .-+
T Consensus 164 vaGIGNiyadEiLf~A~I~P~~-----------~~~~Ls~~~~~~L~~~i~-~vl~~ai~~gg~~~~~~~~g~~~~~~Vy 231 (263)
T PRK10445 164 LAGLGNYLRVEILWQAGLTPQH-----------KAKDLNEAQLDALAHALL-DIPRLSYATRGQVDENKHHGALFRFKVF 231 (263)
T ss_pred cccccHHHHHHHHHHcCCCcCC-----------CcccCCHHHHHHHHHHHH-HHHHHHHHcCCCCCCCCCCCCcceEEEe
Confidence 444667777777777 556664 123478888886655443 45555 4554322 23221 001
Q ss_pred CCeEEEeccCCCCC
Q 028857 160 EEGIYNCSACGTPL 173 (202)
Q Consensus 160 ~~G~Y~C~~C~~pL 173 (202)
...--.|..||.++
T Consensus 232 ~r~g~~Cp~Cg~~I 245 (263)
T PRK10445 232 HRDGEACERCGGII 245 (263)
T ss_pred CCCCCCCCCCCCEe
Confidence 11122588888776
No 74
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=20.33 E-value=49 Score=23.88 Aligned_cols=27 Identities=26% Similarity=0.724 Sum_probs=24.5
Q ss_pred CeEEEeccCCCCCCCCCCCCCCCCCCc
Q 028857 161 EGIYNCSACGTPLYKSTTKFNSGCGWP 187 (202)
Q Consensus 161 ~G~Y~C~~C~~pLF~S~~KFdSg~GWP 187 (202)
.-.=.|..||.--|.-..|+=+.||.|
T Consensus 14 ~tH~~CRRCGr~syhv~k~~CaaCGfg 40 (61)
T COG2126 14 KTHIRCRRCGRRSYHVRKKYCAACGFG 40 (61)
T ss_pred cceehhhhccchheeeccceecccCCC
Confidence 445679999999999999999999999
No 75
>cd04981 IgV_H Immunoglobulin (Ig) heavy chain (H), variable (V) domain. IgV_H: Immunoglobulin (Ig) heavy chain (H), variable (V) domain. The basic structure of Ig molecules is a tetramer of two light chains and two heavy chains linked by disulfide bonds. In Ig, each chain is composed of one variable domain (IgV) and one or more constant domains (IgC); these names reflect the fact that the variability in sequences is higher in the variable domain than in the constant domain. There are five types of heavy chains (alpha, gamma, delta, epsilon, and mu), which determine the type of immunoglobulin: IgA, IgG, IgD, IgE, and IgM, respectively. In higher vertebrates, there are two types of light chain, designated kappa and lambda, which can associate with any of the heavy chains. This family includes alpha, gamma, delta, epsilon, and mu heavy chains.
Probab=20.25 E-value=38 Score=25.82 Aligned_cols=13 Identities=15% Similarity=0.340 Sum_probs=10.1
Q ss_pred CCCCeEEEeccCC
Q 028857 158 HFEEGIYNCSACG 170 (202)
Q Consensus 158 ~~~~G~Y~C~~C~ 170 (202)
..+.|+|.|+...
T Consensus 85 ~~Dsa~YyCa~~~ 97 (117)
T cd04981 85 PEDTAVYYCARGL 97 (117)
T ss_pred HHHCEEEEEEEEc
Confidence 3589999998743
No 76
>cd05723 Ig4_Neogenin Fourth immunoglobulin (Ig)-like domain in neogenin and similar proteins. Ig4_Neogenin: fourth immunoglobulin (Ig)-like domain in neogenin and related proteins. Neogenin is a cell surface protein which is expressed in the developing nervous system of vertebrate embryos in the growing nerve cells. It is also expressed in other embryonic tissues, and may play a general role in developmental processes such as cell migration, cell-cell recognition, and tissue growth regulation. Included in this group is the tumor suppressor protein DCC, which is deleted in colorectal carcinoma . DCC and neogenin each have four Ig-like domains followed by six fibronectin type III domains, a transmembrane domain, and an intracellular domain.
Probab=20.20 E-value=62 Score=21.94 Aligned_cols=14 Identities=36% Similarity=0.667 Sum_probs=10.7
Q ss_pred CCCCCeEEEeccCC
Q 028857 157 KHFEEGIYNCSACG 170 (202)
Q Consensus 157 ~~~~~G~Y~C~~C~ 170 (202)
...+.|.|.|.+.+
T Consensus 45 ~~~D~G~Y~C~A~N 58 (71)
T cd05723 45 VKSDEGFYQCIAEN 58 (71)
T ss_pred CcccCEEEEEEEEc
Confidence 34578999998764
No 77
>KOG4397 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.01 E-value=28 Score=30.49 Aligned_cols=13 Identities=31% Similarity=0.789 Sum_probs=11.3
Q ss_pred EEEeccCCCCCCC
Q 028857 163 IYNCSACGTPLYK 175 (202)
Q Consensus 163 ~Y~C~~C~~pLF~ 175 (202)
.|.|+.|+.|||-
T Consensus 88 R~~C~~C~Lpl~Y 100 (213)
T KOG4397|consen 88 RKKCIKCSLPLFY 100 (213)
T ss_pred HHhhhcCCceeEE
Confidence 3789999999984
Done!