Query 033176
Match_columns 125
No_of_seqs 289 out of 1369
Neff 8.1
Searched_HMMs 46136
Date Fri Mar 29 10:45:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033176.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033176hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00403 HMA: Heavy-metal-asso 99.4 2.5E-12 5.3E-17 76.2 7.7 53 1-53 7-62 (62)
2 KOG1603 Copper chaperone [Inor 99.4 4.5E-12 9.8E-17 77.9 7.2 59 1-59 13-72 (73)
3 COG2608 CopZ Copper chaperone 99.2 7E-11 1.5E-15 72.2 8.0 57 1-57 11-70 (71)
4 KOG4656 Copper chaperone for s 99.0 1.7E-09 3.7E-14 77.9 7.1 63 1-63 15-77 (247)
5 PLN02957 copper, zinc superoxi 98.4 3.2E-06 7E-11 62.7 8.9 63 1-63 14-76 (238)
6 PRK10671 copA copper exporting 98.0 1.3E-05 2.7E-10 68.8 6.7 55 1-57 12-66 (834)
7 COG2217 ZntA Cation transport 97.8 7.5E-05 1.6E-09 63.1 6.8 55 1-56 11-69 (713)
8 TIGR00003 copper ion binding p 97.4 0.0018 4E-08 35.6 7.3 54 1-54 11-67 (68)
9 KOG0207 Cation transport ATPas 97.2 0.001 2.2E-08 57.2 6.3 61 1-61 3-65 (951)
10 KOG0207 Cation transport ATPas 97.1 0.0015 3.3E-08 56.2 6.3 61 1-61 155-218 (951)
11 PRK10671 copA copper exporting 97.0 0.0029 6.3E-08 54.5 7.1 58 1-58 108-165 (834)
12 PRK11033 zntA zinc/cadmium/mer 96.4 0.0098 2.1E-07 50.8 6.7 57 1-57 62-119 (741)
13 TIGR02052 MerP mercuric transp 92.0 1.6 3.5E-05 25.9 7.8 56 1-56 32-90 (92)
14 COG1888 Uncharacterized protei 91.4 0.91 2E-05 28.9 5.4 50 10-59 24-81 (97)
15 PF02680 DUF211: Uncharacteriz 90.5 0.85 1.8E-05 29.2 4.7 50 9-58 21-78 (95)
16 PRK13748 putative mercuric red 86.5 5 0.00011 32.9 8.0 60 1-60 9-70 (561)
17 cd00371 HMA Heavy-metal-associ 85.2 3 6.6E-05 20.2 7.3 52 1-52 7-60 (63)
18 PRK10553 assembly protein for 78.8 14 0.00029 23.3 6.1 43 7-49 19-62 (87)
19 PF13732 DUF4162: Domain of un 71.3 16 0.00035 21.9 5.0 44 13-58 25-70 (84)
20 PRK14054 methionine sulfoxide 70.4 12 0.00026 26.5 4.7 46 4-49 10-77 (172)
21 PF03927 NapD: NapD protein; 68.0 25 0.00054 21.5 6.3 43 7-50 17-60 (79)
22 PF01206 TusA: Sulfurtransfera 60.5 27 0.00059 20.2 4.4 48 1-57 8-57 (70)
23 PF01883 DUF59: Domain of unkn 60.5 13 0.00028 21.8 2.9 19 7-25 54-72 (72)
24 PRK00058 methionine sulfoxide 55.6 29 0.00062 25.5 4.5 45 4-48 52-118 (213)
25 PRK13014 methionine sulfoxide 53.1 25 0.00055 25.3 3.8 45 4-48 15-81 (186)
26 PF09580 Spore_YhcN_YlaJ: Spor 48.3 71 0.0015 22.1 5.5 29 7-35 77-105 (177)
27 PHA01634 hypothetical protein 46.2 6.3 0.00014 27.1 -0.1 13 1-13 98-110 (156)
28 KOG3411 40S ribosomal protein 46.1 22 0.00047 24.3 2.4 44 4-50 97-141 (143)
29 PRK05528 methionine sulfoxide 46.1 18 0.00039 25.2 2.1 46 4-49 8-70 (156)
30 cd04888 ACT_PheB-BS C-terminal 42.6 35 0.00075 19.7 2.8 19 7-25 56-74 (76)
31 TIGR00489 aEF-1_beta translati 42.3 31 0.00067 21.7 2.6 21 6-26 63-83 (88)
32 PF04972 BON: BON domain; Int 41.2 15 0.00033 20.8 1.0 30 8-38 2-34 (64)
33 PF14492 EFG_II: Elongation Fa 39.8 79 0.0017 18.8 4.1 50 7-56 18-73 (75)
34 PRK11023 outer membrane lipopr 37.9 1.3E+02 0.0028 21.4 5.6 37 7-43 129-167 (191)
35 PRK11023 outer membrane lipopr 37.0 90 0.002 22.2 4.7 42 7-48 51-95 (191)
36 TIGR02945 SUF_assoc FeS assemb 36.0 33 0.00072 21.4 2.1 23 7-29 57-79 (99)
37 cd02410 archeal_CPSF_KH The ar 36.0 1.5E+02 0.0032 20.5 5.9 54 8-61 56-116 (145)
38 TIGR00401 msrA methionine-S-su 35.9 31 0.00066 23.9 2.0 27 4-30 7-33 (149)
39 PRK09577 multidrug efflux prot 35.2 1.4E+02 0.0031 27.0 6.4 46 7-52 158-211 (1032)
40 PF09158 MotCF: Bacteriophage 35.2 1.3E+02 0.0028 19.6 4.7 40 17-57 40-79 (103)
41 PF01625 PMSR: Peptide methion 34.7 43 0.00094 23.2 2.6 27 4-30 7-33 (155)
42 COG4004 Uncharacterized protei 34.3 98 0.0021 19.8 3.9 21 16-36 38-58 (96)
43 PRK05550 bifunctional methioni 34.2 94 0.002 23.9 4.5 27 4-30 134-160 (283)
44 COG2092 EFB1 Translation elong 33.5 42 0.00092 21.2 2.2 21 6-26 63-83 (88)
45 PRK00435 ef1B elongation facto 32.4 53 0.0012 20.6 2.5 21 6-26 63-83 (88)
46 PRK10555 aminoglycoside/multid 32.3 1.6E+02 0.0034 26.7 6.2 44 7-50 159-210 (1037)
47 COG3062 NapD Uncharacterized p 30.9 1.5E+02 0.0032 19.0 5.3 43 7-50 20-63 (94)
48 TIGR01676 GLDHase galactonolac 30.6 1.1E+02 0.0024 25.8 4.7 39 14-54 110-148 (541)
49 TIGR02830 spore_III_AG stage I 30.6 50 0.0011 23.8 2.4 29 6-34 62-92 (186)
50 KOG4730 D-arabinono-1, 4-lacto 30.2 75 0.0016 26.3 3.6 33 23-55 105-137 (518)
51 COG2151 PaaD Predicted metal-s 29.8 60 0.0013 21.4 2.5 21 7-27 69-89 (111)
52 PF01514 YscJ_FliF: Secretory 29.2 69 0.0015 23.2 3.0 21 7-27 117-137 (206)
53 COG2331 Uncharacterized protei 27.6 33 0.00072 21.2 0.9 16 2-17 35-50 (82)
54 PF05046 Img2: Mitochondrial l 27.5 1.6E+02 0.0034 18.2 5.7 45 7-52 42-87 (87)
55 PF03434 DUF276: DUF276 ; Int 27.2 1.1E+02 0.0023 23.3 3.7 29 7-35 89-117 (291)
56 COG5561 Predicted metal-bindin 27.0 81 0.0018 20.1 2.6 9 3-11 7-15 (101)
57 PF01849 NAC: NAC domain; Int 26.7 76 0.0016 18.0 2.4 21 15-35 14-34 (58)
58 PF00352 TBP: Transcription fa 25.7 1E+02 0.0022 18.8 3.0 22 27-48 55-76 (86)
59 COG0277 GlcD FAD/FMN-containin 25.7 85 0.0018 24.8 3.2 38 16-55 83-120 (459)
60 COG1094 Predicted RNA-binding 25.5 2.3E+02 0.0049 20.6 5.0 37 8-45 27-66 (194)
61 PRK11198 LysM domain/BON super 25.5 1.7E+02 0.0037 19.8 4.3 42 7-48 28-70 (147)
62 PRK09019 translation initiatio 25.5 89 0.0019 20.5 2.7 34 15-48 27-68 (108)
63 TIGR02571 ComEB ComE operon pr 25.4 2.3E+02 0.005 19.4 5.1 44 2-58 96-139 (151)
64 PRK11018 hypothetical protein; 25.3 1.6E+02 0.0035 17.6 5.5 47 2-57 17-65 (78)
65 cd08032 LARP_7 La RNA-binding 25.1 23 0.0005 22.0 -0.1 6 113-118 16-21 (82)
66 PRK15127 multidrug efflux syst 24.8 2.5E+02 0.0054 25.5 6.2 43 8-50 160-210 (1049)
67 cd06167 LabA_like LabA_like pr 24.6 1.3E+02 0.0029 19.7 3.6 29 32-60 104-132 (149)
68 PF13216 DUF4024: Protein of u 24.4 25 0.00053 17.8 -0.0 11 111-121 9-19 (35)
69 TIGR00915 2A0602 The (Largely 24.1 2.6E+02 0.0056 25.4 6.1 43 8-50 160-210 (1044)
70 cd03421 SirA_like_N SirA_like_ 23.6 1.5E+02 0.0033 16.8 5.4 47 1-57 7-55 (67)
71 PF04805 Pox_E10: E10-like pro 23.5 69 0.0015 19.3 1.7 22 1-22 16-37 (70)
72 PF11150 DUF2927: Protein of u 23.4 48 0.001 24.3 1.3 22 100-121 158-179 (213)
73 PRK07451 translation initiatio 23.4 99 0.0022 20.5 2.7 10 39-48 66-75 (115)
74 PRK06824 translation initiatio 23.2 1.2E+02 0.0026 20.2 3.0 10 39-48 69-78 (118)
75 COG0225 MsrA Peptide methionin 23.2 56 0.0012 23.3 1.5 28 4-31 13-40 (174)
76 TIGR03406 FeS_long_SufT probab 23.1 96 0.0021 22.0 2.8 21 7-27 133-153 (174)
77 TIGR02544 III_secr_YscJ type I 22.7 91 0.002 22.4 2.6 21 7-27 109-129 (193)
78 PF13193 AMP-binding_C: AMP-bi 22.7 1.1E+02 0.0024 17.5 2.7 18 9-26 1-18 (73)
79 PRK11282 glcE glycolate oxidas 22.7 1.7E+02 0.0037 23.1 4.3 37 15-53 44-80 (352)
80 cd00292 EF1B Elongation factor 22.5 1.1E+02 0.0023 19.2 2.6 20 7-26 64-83 (88)
81 PRK11200 grxA glutaredoxin 1; 22.4 1.6E+02 0.0035 17.4 3.4 26 2-28 10-39 (85)
82 COG4669 EscJ Type III secretor 22.1 1.1E+02 0.0024 23.0 3.0 20 7-26 111-130 (246)
83 PF08712 Nfu_N: Scaffold prote 21.8 2.1E+02 0.0045 17.7 5.1 39 9-49 38-78 (87)
84 PRK07334 threonine dehydratase 21.5 3.1E+02 0.0066 21.8 5.6 51 7-57 340-402 (403)
85 cd08623 PI-PLCc_beta1 Catalyti 21.3 1.8E+02 0.0039 22.1 4.0 47 7-55 32-89 (258)
86 PRK10568 periplasmic protein; 20.7 2.4E+02 0.0051 20.3 4.5 34 6-39 61-96 (203)
87 PF08002 DUF1697: Protein of u 20.6 2.8E+02 0.006 18.6 6.0 47 9-56 23-74 (137)
88 COG3643 Glutamate formiminotra 20.6 2.9E+02 0.0062 21.2 4.9 41 7-47 20-62 (302)
89 PF08821 CGGC: CGGC domain; I 20.6 1.4E+02 0.003 19.4 2.9 18 39-56 86-104 (107)
90 cd04877 ACT_TyrR N-terminal AC 20.5 1.2E+02 0.0025 17.6 2.4 17 8-24 52-68 (74)
91 PF00736 EF1_GNE: EF-1 guanine 20.4 1.6E+02 0.0034 18.4 3.1 21 6-26 63-84 (89)
No 1
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=99.39 E-value=2.5e-12 Score=76.18 Aligned_cols=53 Identities=40% Similarity=0.659 Sum_probs=49.5
Q ss_pred CCcHhHHHHHHHHHhCCCCeeEEEEeCCCCEEEEEeC---CCHHHHHHHHHHcCCc
Q 033176 1 MCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVGY---VDRNKVLKAVRRAGKR 53 (125)
Q Consensus 1 m~C~~C~~~V~~~L~~~~GV~~v~vd~~~~kvtV~g~---~~~~~i~~~i~~~G~~ 53 (125)
|+|++|+.+|+++|.+++||.++.+|+.+++++|.+. +++++|.++|+++||+
T Consensus 7 m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~~~~~~~i~~~i~~~Gy~ 62 (62)
T PF00403_consen 7 MTCEGCAKKVEKALSKLPGVKSVKVDLETKTVTVTYDPDKTSIEKIIEAIEKAGYE 62 (62)
T ss_dssp TTSHHHHHHHHHHHHTSTTEEEEEEETTTTEEEEEESTTTSCHHHHHHHHHHTTSE
T ss_pred cccHHHHHHHHHHHhcCCCCcEEEEECCCCEEEEEEecCCCCHHHHHHHHHHhCcC
Confidence 8999999999999999999999999999999999965 4679999999999984
No 2
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.35 E-value=4.5e-12 Score=77.86 Aligned_cols=59 Identities=47% Similarity=0.882 Sum_probs=55.7
Q ss_pred CCcHhHHHHHHHHHhCCCCeeEEEEeCCCCEEEEEeCCCHHHHHHHHHHcC-CceeecCC
Q 033176 1 MCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVGYVDRNKVLKAVRRAG-KRAEFWPY 59 (125)
Q Consensus 1 m~C~~C~~~V~~~L~~~~GV~~v~vd~~~~kvtV~g~~~~~~i~~~i~~~G-~~a~~~~~ 59 (125)
|+|++|..+|++.|+.++||.++.+|...++++|.|.+++..|++.|++.| .++++|..
T Consensus 13 ~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~k~~~k~~~~~~~ 72 (73)
T KOG1603|consen 13 MHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLKKTGGKRAELWKV 72 (73)
T ss_pred cccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHHhcCCCceEEecC
Confidence 799999999999999999999999999999999999999999999999888 78888854
No 3
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.24 E-value=7e-11 Score=72.20 Aligned_cols=57 Identities=33% Similarity=0.539 Sum_probs=51.6
Q ss_pred CCcHhHHHHHHHHHhCCCCeeEEEEeCCCCEEEEE--e-CCCHHHHHHHHHHcCCceeec
Q 033176 1 MCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAV--G-YVDRNKVLKAVRRAGKRAEFW 57 (125)
Q Consensus 1 m~C~~C~~~V~~~L~~~~GV~~v~vd~~~~kvtV~--g-~~~~~~i~~~i~~~G~~a~~~ 57 (125)
|+|++|+.+|+++|.+++||.++++++..+.++|+ + .++.++|.++|+++||.+..+
T Consensus 11 MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~~aGy~~~~~ 70 (71)
T COG2608 11 MTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIEDAGYKVEEI 70 (71)
T ss_pred cCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHHHcCCCeeec
Confidence 89999999999999999999999999999777665 4 479999999999999988764
No 4
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=98.99 E-value=1.7e-09 Score=77.86 Aligned_cols=63 Identities=27% Similarity=0.472 Sum_probs=59.6
Q ss_pred CCcHhHHHHHHHHHhCCCCeeEEEEeCCCCEEEEEeCCCHHHHHHHHHHcCCceeecCCCCCC
Q 033176 1 MCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVGYVDRNKVLKAVRRAGKRAEFWPYPNPP 63 (125)
Q Consensus 1 m~C~~C~~~V~~~L~~~~GV~~v~vd~~~~kvtV~g~~~~~~i~~~i~~~G~~a~~~~~~~~~ 63 (125)
|+|++|+..|++.|..++||.+|++|+.+|.|.|.+.+.+++|..+|+.+|.++.+.....+.
T Consensus 15 M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~ts~p~s~i~~~le~tGr~Avl~G~G~ps 77 (247)
T KOG4656|consen 15 MTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVETSVPPSEIQNTLENTGRDAVLRGAGKPS 77 (247)
T ss_pred chhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEccCChHHHHHHHHhhChheEEecCCchh
Confidence 899999999999999999999999999999999999999999999999999999998876543
No 5
>PLN02957 copper, zinc superoxide dismutase
Probab=98.37 E-value=3.2e-06 Score=62.69 Aligned_cols=63 Identities=32% Similarity=0.538 Sum_probs=57.1
Q ss_pred CCcHhHHHHHHHHHhCCCCeeEEEEeCCCCEEEEEeCCCHHHHHHHHHHcCCceeecCCCCCC
Q 033176 1 MCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVGYVDRNKVLKAVRRAGKRAEFWPYPNPP 63 (125)
Q Consensus 1 m~C~~C~~~V~~~L~~~~GV~~v~vd~~~~kvtV~g~~~~~~i~~~i~~~G~~a~~~~~~~~~ 63 (125)
|.|+.|+.+|++.|.+++||..+.+++..++++|........+++.|++.||.++++......
T Consensus 14 MsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~~~~~~I~~aIe~~Gy~a~~~~~~~~~ 76 (238)
T PLN02957 14 MKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGSSPVKAMTAALEQTGRKARLIGQGDPE 76 (238)
T ss_pred ccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEecCCHHHHHHHHHHcCCcEEEecCCCcc
Confidence 789999999999999999999999999999999987778889999999999999988775543
No 6
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.03 E-value=1.3e-05 Score=68.78 Aligned_cols=55 Identities=18% Similarity=0.430 Sum_probs=49.4
Q ss_pred CCcHhHHHHHHHHHhCCCCeeEEEEeCCCCEEEEEeCCCHHHHHHHHHHcCCceeec
Q 033176 1 MCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVGYVDRNKVLKAVRRAGKRAEFW 57 (125)
Q Consensus 1 m~C~~C~~~V~~~L~~~~GV~~v~vd~~~~kvtV~g~~~~~~i~~~i~~~G~~a~~~ 57 (125)
|+|++|+.+|+++|++++||..+++++. +.+|++..+.+.+.+.+++.||+++..
T Consensus 12 mtC~~C~~~i~~al~~~~gv~~v~v~~~--~~~v~~~~~~~~i~~~i~~~Gy~~~~~ 66 (834)
T PRK10671 12 LSCGHCVKRVKESLEQRPDVEQADVSIT--EAHVTGTASAEALIETIKQAGYDASVS 66 (834)
T ss_pred cccHHHHHHHHHHHhcCCCcceEEEeee--EEEEEecCCHHHHHHHHHhcCCccccc
Confidence 8999999999999999999999999994 556666678999999999999998875
No 7
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.77 E-value=7.5e-05 Score=63.14 Aligned_cols=55 Identities=36% Similarity=0.597 Sum_probs=49.8
Q ss_pred CCcHhHHHHHHHHHhCCCCeeEEEEeCCCCEEEEEeC---CC-HHHHHHHHHHcCCceee
Q 033176 1 MCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVGY---VD-RNKVLKAVRRAGKRAEF 56 (125)
Q Consensus 1 m~C~~C~~~V~~~L~~~~GV~~v~vd~~~~kvtV~g~---~~-~~~i~~~i~~~G~~a~~ 56 (125)
|+|..|+++|+ +|++++||.++.+|+.++++.|..+ .+ .+.+...+++.||.+..
T Consensus 11 m~Ca~C~~~ie-~l~~~~gV~~~~vn~~t~~~~v~~~~~~~~~~~~~~~~v~~~gy~~~~ 69 (713)
T COG2217 11 MTCAACASRIE-ALNKLPGVEEARVNLATERATVVYDPEEVDLPADIVAAVEKAGYSARL 69 (713)
T ss_pred cCcHHHHHHHH-HHhcCCCeeEEEeecccceEEEEecccccccHHHHHHHHHhcCccccc
Confidence 89999999999 9999999999999999999998743 45 78899999999998765
No 8
>TIGR00003 copper ion binding protein. This model describes an apparently copper-specific subfamily of the metal-binding domain HMA (Pfam family pfam00403). Closely related sequences outside this model include mercury resistance proteins and repeated domains of eukaryotic eukaryotic copper transport proteins. Members of this family are strictly prokaryotic. The model identifies both small proteins consisting of just this domain and N-terminal regions of cation (probably copper) transporting ATPases.
Probab=97.40 E-value=0.0018 Score=35.63 Aligned_cols=54 Identities=26% Similarity=0.360 Sum_probs=44.3
Q ss_pred CCcHhHHHHHHHHHhCCCCeeEEEEeCCCCEEEEEe---CCCHHHHHHHHHHcCCce
Q 033176 1 MCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVG---YVDRNKVLKAVRRAGKRA 54 (125)
Q Consensus 1 m~C~~C~~~V~~~L~~~~GV~~v~vd~~~~kvtV~g---~~~~~~i~~~i~~~G~~a 54 (125)
|.|..|...+++.+..+.++....+++...++.+.. ..+...+...+...|+.+
T Consensus 11 ~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~ 67 (68)
T TIGR00003 11 MTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAILDAGYEV 67 (68)
T ss_pred eEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHHHcCCCc
Confidence 469999999999999999999999999999888763 246677777777777653
No 9
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.18 E-value=0.001 Score=57.16 Aligned_cols=61 Identities=21% Similarity=0.416 Sum_probs=55.6
Q ss_pred CCcHhHHHHHHHHHhCCCCeeEEEEeCCCCEEEEEe--CCCHHHHHHHHHHcCCceeecCCCC
Q 033176 1 MCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVG--YVDRNKVLKAVRRAGKRAEFWPYPN 61 (125)
Q Consensus 1 m~C~~C~~~V~~~L~~~~GV~~v~vd~~~~kvtV~g--~~~~~~i~~~i~~~G~~a~~~~~~~ 61 (125)
|+|..|.+.|++++...+||.++.+++.++..+|.. ..+++.+.++|++.|+.+++.....
T Consensus 3 mtc~ac~~si~~~~~~~~g~~~i~vsl~~~~~~v~~~~~~~~~~i~~~ied~gf~~~~~~~~~ 65 (951)
T KOG0207|consen 3 MTCSACSNSIEKAISRKPGVQKIEVSLAQKRANVSYDNIVSPESIKETIEDMGFEASLLSDSE 65 (951)
T ss_pred ccHHHHhhhHHHHHhcCCCceeEEEEeccccceEEEeeccCHHHHHHHhhcccceeeecccCc
Confidence 899999999999999999999999999999998874 3789999999999999999886544
No 10
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.07 E-value=0.0015 Score=56.15 Aligned_cols=61 Identities=28% Similarity=0.531 Sum_probs=54.9
Q ss_pred CCcHhHHHHHHHHHhCCCCeeEEEEeCCCCEEEEEe---CCCHHHHHHHHHHcCCceeecCCCC
Q 033176 1 MCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVG---YVDRNKVLKAVRRAGKRAEFWPYPN 61 (125)
Q Consensus 1 m~C~~C~~~V~~~L~~~~GV~~v~vd~~~~kvtV~g---~~~~~~i~~~i~~~G~~a~~~~~~~ 61 (125)
|.|.+|+.+|++.|.+++||.++++++.++++.|.. .+.+.++++.|+.+|+.+.+.++..
T Consensus 155 ~~c~s~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~~~~~pr~i~k~ie~~~~~~~~~~~~~ 218 (951)
T KOG0207|consen 155 MTCASCVSKIESILERLRGVKSFSVSLATDTAIVVYDPEITGPRDIIKAIEETGFEASVRPYGD 218 (951)
T ss_pred ccccchhhhhHHHHhhccCeeEEEEeccCCceEEEecccccChHHHHHHHHhhcccceeeeccc
Confidence 789999999999999999999999999999999873 3789999999999999988776543
No 11
>PRK10671 copA copper exporting ATPase; Provisional
Probab=96.95 E-value=0.0029 Score=54.50 Aligned_cols=58 Identities=29% Similarity=0.470 Sum_probs=51.0
Q ss_pred CCcHhHHHHHHHHHhCCCCeeEEEEeCCCCEEEEEeCCCHHHHHHHHHHcCCceeecC
Q 033176 1 MCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVGYVDRNKVLKAVRRAGKRAEFWP 58 (125)
Q Consensus 1 m~C~~C~~~V~~~L~~~~GV~~v~vd~~~~kvtV~g~~~~~~i~~~i~~~G~~a~~~~ 58 (125)
|+|..|..+|++.+.+++||.++.+++..+++.+.+..+.+++.+.+++.|+.+.++.
T Consensus 108 m~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~~~s~~~I~~~I~~~Gy~a~~~~ 165 (834)
T PRK10671 108 MSCASCVSRVQNALQSVPGVTQARVNLAERTALVMGSASPQDLVQAVEKAGYGAEAIE 165 (834)
T ss_pred cCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEccCCHHHHHHHHHhcCCCccccc
Confidence 7899999999999999999999999999998888755678888888999999876543
No 12
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=96.44 E-value=0.0098 Score=50.79 Aligned_cols=57 Identities=35% Similarity=0.426 Sum_probs=47.0
Q ss_pred CCcHhHHHHHHHHHhCCCCeeEEEEeCCCCEEEEEeC-CCHHHHHHHHHHcCCceeec
Q 033176 1 MCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVGY-VDRNKVLKAVRRAGKRAEFW 57 (125)
Q Consensus 1 m~C~~C~~~V~~~L~~~~GV~~v~vd~~~~kvtV~g~-~~~~~i~~~i~~~G~~a~~~ 57 (125)
|+|..|..++++.+.+++||.++.+++..+++.+... ...+++...+++.|+.+..+
T Consensus 62 m~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~~~~I~~aI~~~Gy~a~~~ 119 (741)
T PRK11033 62 MDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDIRAQVESAVQKAGFSLRDE 119 (741)
T ss_pred CCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccchHHHHHHHHhcccccccc
Confidence 7899999999999999999999999999999877632 12266777888899987654
No 13
>TIGR02052 MerP mercuric transport protein periplasmic component. This model represents the periplasmic mercury (II) binding protein of the bacterial mercury detoxification system which passes mercuric ion to the MerT transporter for subsequent reduction to Hg(0) by the mercuric reductase MerA. MerP contains a distinctive GMTCXXC motif associated with metal binding. MerP is related to a larger family of metal binding proteins (pfam00403).
Probab=92.01 E-value=1.6 Score=25.87 Aligned_cols=56 Identities=23% Similarity=0.374 Sum_probs=41.4
Q ss_pred CCcHhHHHHHHHHHhCCCCeeEEEEeCCCCEEEEEe---CCCHHHHHHHHHHcCCceee
Q 033176 1 MCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVG---YVDRNKVLKAVRRAGKRAEF 56 (125)
Q Consensus 1 m~C~~C~~~V~~~L~~~~GV~~v~vd~~~~kvtV~g---~~~~~~i~~~i~~~G~~a~~ 56 (125)
+.|..|...++..+....++....++.......+.. ......+...+.+.|+.+++
T Consensus 32 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~ 90 (92)
T TIGR02052 32 MTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATTDAGYPSSL 90 (92)
T ss_pred eEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHHhcCCCeEe
Confidence 469999999999999999988888888877765542 23555555666777776544
No 14
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=91.43 E-value=0.91 Score=28.90 Aligned_cols=50 Identities=22% Similarity=0.312 Sum_probs=35.9
Q ss_pred HHHHHhCCCCeeEEEEeC-----C--CCEEEEEeC-CCHHHHHHHHHHcCCceeecCC
Q 033176 10 VKNAIYKLRGVDSVEVEL-----E--LEKVTAVGY-VDRNKVLKAVRRAGKRAEFWPY 59 (125)
Q Consensus 10 V~~~L~~~~GV~~v~vd~-----~--~~kvtV~g~-~~~~~i~~~i~~~G~~a~~~~~ 59 (125)
+-+.|.+++||..|++.. . .-+++|.|. ++-++|.+.|++.|-....+..
T Consensus 24 ~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE~~Gg~IHSiDe 81 (97)
T COG1888 24 LALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIEELGGAIHSIDE 81 (97)
T ss_pred HHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHHHcCCeeeehhh
Confidence 456678888887766543 3 335566664 8999999999999987766544
No 15
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=90.45 E-value=0.85 Score=29.25 Aligned_cols=50 Identities=26% Similarity=0.401 Sum_probs=35.1
Q ss_pred HHHHHHhCCCCeeEEEEeC-----CCCE--EEEEeC-CCHHHHHHHHHHcCCceeecC
Q 033176 9 VVKNAIYKLRGVDSVEVEL-----ELEK--VTAVGY-VDRNKVLKAVRRAGKRAEFWP 58 (125)
Q Consensus 9 ~V~~~L~~~~GV~~v~vd~-----~~~k--vtV~g~-~~~~~i~~~i~~~G~~a~~~~ 58 (125)
.+-+.|.+++||..+++.. .+.. ++|.|. ++.++|.++|++.|-....+.
T Consensus 21 e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie~~Gg~IHSID 78 (95)
T PF02680_consen 21 ELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIEELGGVIHSID 78 (95)
T ss_dssp HHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHHTT-EEEEEE
T ss_pred HHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHHHcCCeEEeee
Confidence 3567889999998776543 4443 455575 999999999999998765543
No 16
>PRK13748 putative mercuric reductase; Provisional
Probab=86.49 E-value=5 Score=32.94 Aligned_cols=60 Identities=28% Similarity=0.367 Sum_probs=46.8
Q ss_pred CCcHhHHHHHHHHHhCCCCeeEEEEeCCCCEEEEEe--CCCHHHHHHHHHHcCCceeecCCC
Q 033176 1 MCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVG--YVDRNKVLKAVRRAGKRAEFWPYP 60 (125)
Q Consensus 1 m~C~~C~~~V~~~L~~~~GV~~v~vd~~~~kvtV~g--~~~~~~i~~~i~~~G~~a~~~~~~ 60 (125)
|.|..|..+++..+..++++....+++......+.. ......+...+.+.|+..+.+...
T Consensus 9 ~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~~~~~~~i~~~i~~~g~~~~~~~~~ 70 (561)
T PRK13748 9 MTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVGTSPDALTAAVAGLGYRATLADAP 70 (561)
T ss_pred eecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECCCCCHHHHHHHHHHcCCeeeccCcc
Confidence 579999999999999999999889998888866653 245566666677888877666553
No 17
>cd00371 HMA Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions.
Probab=85.17 E-value=3 Score=20.17 Aligned_cols=52 Identities=42% Similarity=0.638 Sum_probs=34.6
Q ss_pred CCcHhHHHHHHHHHhCCCCeeEEEEeCCCCEEEEEeC--CCHHHHHHHHHHcCC
Q 033176 1 MCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVGY--VDRNKVLKAVRRAGK 52 (125)
Q Consensus 1 m~C~~C~~~V~~~L~~~~GV~~v~vd~~~~kvtV~g~--~~~~~i~~~i~~~G~ 52 (125)
+.|..|...++..+....++.....++....+.+... .....+...++..++
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 60 (63)
T cd00371 7 MTCAGCVSKIEKALEKLPGVESVEVDLETGKATVEYDPEVSPEELLEAIEDAGY 60 (63)
T ss_pred eEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEEECCCCCHHHHHHHHHHcCC
Confidence 4588999999988888888877777777666555432 244444444444443
No 18
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=78.81 E-value=14 Score=23.28 Aligned_cols=43 Identities=9% Similarity=0.149 Sum_probs=30.2
Q ss_pred HHHHHHHHhCCCCeeEEEEeCCCCEEEEEe-CCCHHHHHHHHHH
Q 033176 7 ERVVKNAIYKLRGVDSVEVELELEKVTAVG-YVDRNKVLKAVRR 49 (125)
Q Consensus 7 ~~~V~~~L~~~~GV~~v~vd~~~~kvtV~g-~~~~~~i~~~i~~ 49 (125)
...|.+.|..++|++-...|...+|+.|+- ..+...+++.|..
T Consensus 19 ~~~V~~~l~~ipg~Evh~~d~~~GKiVVtiE~~~~~~~~~~i~~ 62 (87)
T PRK10553 19 ISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLLQTIES 62 (87)
T ss_pred HHHHHHHHHcCCCcEEEeecCCCCeEEEEEEeCChHHHHHHHHH
Confidence 567889999999998776777788887762 2345555554443
No 19
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=71.35 E-value=16 Score=21.87 Aligned_cols=44 Identities=23% Similarity=0.237 Sum_probs=31.4
Q ss_pred HHhCCCCeeEEEEeCCCCEEE--EEeCCCHHHHHHHHHHcCCceeecC
Q 033176 13 AIYKLRGVDSVEVELELEKVT--AVGYVDRNKVLKAVRRAGKRAEFWP 58 (125)
Q Consensus 13 ~L~~~~GV~~v~vd~~~~kvt--V~g~~~~~~i~~~i~~~G~~a~~~~ 58 (125)
.|..++||.++...- .+.+. +.......+|+..|...|. +.-+.
T Consensus 25 ~l~~~~~v~~v~~~~-~~~~~i~l~~~~~~~~ll~~l~~~g~-I~~f~ 70 (84)
T PF13732_consen 25 ELEELPGVESVEQDG-DGKLRIKLEDEETANELLQELIEKGI-IRSFE 70 (84)
T ss_pred HHhhCCCeEEEEEeC-CcEEEEEECCcccHHHHHHHHHhCCC-eeEEE
Confidence 377889999887653 44344 4455678999999999998 65443
No 20
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=70.38 E-value=12 Score=26.54 Aligned_cols=46 Identities=17% Similarity=0.205 Sum_probs=35.4
Q ss_pred HhHHHHHHHHHhCCCCeeEEEEeCCCCE-------------------EEEEe---CCCHHHHHHHHHH
Q 033176 4 TGCERVVKNAIYKLRGVDSVEVELELEK-------------------VTAVG---YVDRNKVLKAVRR 49 (125)
Q Consensus 4 ~~C~~~V~~~L~~~~GV~~v~vd~~~~k-------------------vtV~g---~~~~~~i~~~i~~ 49 (125)
.||-+-++..+.+++||.++.+-...+. |.|+- .++.++|++..-+
T Consensus 10 gGCFWg~E~~f~~~~GV~~t~vGYagG~~~~PtY~~Vcsg~tgh~E~V~V~yDp~~isy~~Ll~~f~~ 77 (172)
T PRK14054 10 GGCFWGMEAPFDRVKGVISTRVGYTGGHVENPTYEQVCSGTTGHAEAVEITYDPAVISYRELLELFFQ 77 (172)
T ss_pred cCChhhhHHHHccCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCCcCCHHHHHHHHHH
Confidence 5799999999999999999999877654 44442 3778888876543
No 21
>PF03927 NapD: NapD protein; InterPro: IPR005623 This entry represents NapD, the twin-arginine signal-peptide-binding chaperone for NapA, functioning as an assembly protein for the periplasmic nitrate reductase NapABC. The periplasmic NapABC enzyme likely functions during growth in nitrate-limited environments [].; PDB: 2JSX_A 2PQ4_A.
Probab=67.96 E-value=25 Score=21.46 Aligned_cols=43 Identities=14% Similarity=0.156 Sum_probs=30.4
Q ss_pred HHHHHHHHhCCCCeeEEEEeCCCCEEEEEe-CCCHHHHHHHHHHc
Q 033176 7 ERVVKNAIYKLRGVDSVEVELELEKVTAVG-YVDRNKVLKAVRRA 50 (125)
Q Consensus 7 ~~~V~~~L~~~~GV~~v~vd~~~~kvtV~g-~~~~~~i~~~i~~~ 50 (125)
...|.++|..++|++-...+.. +|+.|+- ..+...+.+.+...
T Consensus 17 ~~~v~~~l~~~~gvEVh~~~~~-GKiVVtiE~~~~~~~~~~~~~i 60 (79)
T PF03927_consen 17 LEEVAEALAAIPGVEVHAVDED-GKIVVTIEAESSEEEVDLIDAI 60 (79)
T ss_dssp HHHHHHHHCCSTTEEEEEEETT-TEEEEEEEESSHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCcEEEeeCCC-CeEEEEEEeCChHHHHHHHHHH
Confidence 4578899999999976667665 7777662 34666666666544
No 22
>PF01206 TusA: Sulfurtransferase TusA; InterPro: IPR001455 SirA functions as a response regulator as part of a two-component system, where BarA is the sensor kinase. This system increases the expression of virulence genes and decreases the expression of motility genes []. BarA phosphorylates SirA, thereby activating the protein. Phosphorylated SirA directly activates virulence expression by interacting with hilA and hilC promoters, while repressing the flagellar regulon indirectly by binding to the csrB promoter, which in turn affects flagellar gene expression. Orthologues of SirA from Salmonella spp. can be found throughout proteobacteria, such as GacA in Psuedomonas spp., VarA in Vibrio cholerae, ExpA in Erwinia carotovora, LetA in Legionella pneumophila, and UvrY in Escherichia coli []. A sensor kinase for SirA is present in each of these organisms as well; the sensor kinase is known as BarA in E. coli and Salmonella spp., but has different names in other genera. In different species, SirA/BarA orthologues are required for virulence gene expression, exoenzyme and antibiotic production, motility, and biofilm formation. The structure of SirA consists of an alpha/beta sandwich with a beta-alpha-beta-alpha-beta(2) fold, comprising a mixed four-stranded beta-sheet stacked against two alpha-helices, both of which are nearly parallel to the strands of the beta-sheet []. Several uncharacterised bacterial proteins (73 to 81 amino-acid residues in length) that contain a well-conserved region in their N-terminal region show structural similarity to the SirA protein, including the E. coli protein YedF (P0AA31 from SWISSPROT), and other members of the UPF0033 family.; GO: 0016783 sulfurtransferase activity, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 3LVJ_D 3LVK_B 1DCJ_A 3HZ7_A 1JDQ_A 1JE3_A 1PAV_A.
Probab=60.51 E-value=27 Score=20.22 Aligned_cols=48 Identities=13% Similarity=0.024 Sum_probs=34.0
Q ss_pred CCcHhHHHHHHHHHhCCCCeeEEEEeCCCCEEEEEe--CCCHHHHHHHHHHcCCceeec
Q 033176 1 MCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVG--YVDRNKVLKAVRRAGKRAEFW 57 (125)
Q Consensus 1 m~C~~C~~~V~~~L~~~~GV~~v~vd~~~~kvtV~g--~~~~~~i~~~i~~~G~~a~~~ 57 (125)
+.|+...-+++++|.+++.- +.+.|.. ......|...++..|+....+
T Consensus 8 ~~CP~Pll~~~~~l~~l~~G---------~~l~v~~d~~~~~~di~~~~~~~g~~~~~~ 57 (70)
T PF01206_consen 8 LSCPMPLLKAKKALKELPPG---------EVLEVLVDDPAAVEDIPRWCEENGYEVVEV 57 (70)
T ss_dssp -STTHHHHHHHHHHHTSGTT----------EEEEEESSTTHHHHHHHHHHHHTEEEEEE
T ss_pred CCCCHHHHHHHHHHHhcCCC---------CEEEEEECCccHHHHHHHHHHHCCCEEEEE
Confidence 36999999999999998432 3344443 245677888999999986555
No 23
>PF01883 DUF59: Domain of unknown function DUF59; InterPro: IPR002744 This family includes prokaryotic proteins of unknown function. The family also includes PhaH (O84984 from SWISSPROT) from Pseudomonas putida. PhaH forms a complex with PhaF (O84982 from SWISSPROT), PhaG (O84983 from SWISSPROT) and PhaI (O84985 from SWISSPROT), which hydroxylates phenylacetic acid to 2-hydroxyphenylacetic acid []. So members of this family may all be components of ring hydroxylating complexes.; PDB: 3LNO_C 3CQ3_A 3CQ2_D 2CU6_B 3CQ1_A 3UX3_B 3UX2_A 1WCJ_A 1UWD_A.
Probab=60.48 E-value=13 Score=21.83 Aligned_cols=19 Identities=37% Similarity=0.564 Sum_probs=15.4
Q ss_pred HHHHHHHHhCCCCeeEEEE
Q 033176 7 ERVVKNAIYKLRGVDSVEV 25 (125)
Q Consensus 7 ~~~V~~~L~~~~GV~~v~v 25 (125)
...|+++|..++||.+++|
T Consensus 54 ~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 54 REEIREALKALPGVKSVKV 72 (72)
T ss_dssp HHHHHHHHHTSTT-SEEEE
T ss_pred HHHHHHHHHhCCCCceEeC
Confidence 5678999999999998875
No 24
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=55.57 E-value=29 Score=25.54 Aligned_cols=45 Identities=22% Similarity=0.262 Sum_probs=34.6
Q ss_pred HhHHHHHHHHHhCCCCeeEEEEeCCCCE-------------------EEEEe---CCCHHHHHHHHH
Q 033176 4 TGCERVVKNAIYKLRGVDSVEVELELEK-------------------VTAVG---YVDRNKVLKAVR 48 (125)
Q Consensus 4 ~~C~~~V~~~L~~~~GV~~v~vd~~~~k-------------------vtV~g---~~~~~~i~~~i~ 48 (125)
.||-+-++..+.+++||.++.+-...+. |.|+- .++.++|++..-
T Consensus 52 gGCFWg~E~~F~~l~GV~~t~vGYagG~~~~PtY~~VcsG~tgH~EaV~V~YDp~~ISy~~LL~~Ff 118 (213)
T PRK00058 52 MGCFWGAERLFWQLPGVYSTAVGYAGGYTPNPTYREVCSGRTGHAEVVRVVYDPAVISYEQLLQVFW 118 (213)
T ss_pred ccCcchhHHHHhcCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCccCCHHHHHHHHH
Confidence 5799999999999999999999887442 34442 377888887664
No 25
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=53.06 E-value=25 Score=25.27 Aligned_cols=45 Identities=22% Similarity=0.171 Sum_probs=34.3
Q ss_pred HhHHHHHHHHHhCCCCeeEEEEeCCCCE-------------------EEEEe---CCCHHHHHHHHH
Q 033176 4 TGCERVVKNAIYKLRGVDSVEVELELEK-------------------VTAVG---YVDRNKVLKAVR 48 (125)
Q Consensus 4 ~~C~~~V~~~L~~~~GV~~v~vd~~~~k-------------------vtV~g---~~~~~~i~~~i~ 48 (125)
.||-+-++..+.+++||.++.+-...+. |.|+- .++.++|++..-
T Consensus 15 gGCFWg~E~~f~~l~GV~~t~vGYagG~~~nPtY~~Vcsg~tgH~E~V~V~yDp~~iSy~~LL~~Ff 81 (186)
T PRK13014 15 GGCFWGVEGVFQHVPGVVSVVSGYSGGHVDNPTYEQVCTGTTGHAEAVQITYDPKQVSYENLLQIFF 81 (186)
T ss_pred cCCceeeHHHHccCCCEEEEEeeecCCCCCCCChhhhcCCCCCceEEEEEEECCCcCCHHHHHHHHH
Confidence 4788999999999999999999877653 34442 267788877653
No 26
>PF09580 Spore_YhcN_YlaJ: Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ); InterPro: IPR019076 This entry contains YhcN and YlaJ, which are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic, 40-residue C-terminal domain.
Probab=48.27 E-value=71 Score=22.05 Aligned_cols=29 Identities=17% Similarity=0.266 Sum_probs=24.2
Q ss_pred HHHHHHHHhCCCCeeEEEEeCCCCEEEEE
Q 033176 7 ERVVKNAIYKLRGVDSVEVELELEKVTAV 35 (125)
Q Consensus 7 ~~~V~~~L~~~~GV~~v~vd~~~~kvtV~ 35 (125)
+.+|.+.+.+++||.++.+-.....+.|.
T Consensus 77 a~~i~~~v~~~~~V~~A~vvv~~~~a~Va 105 (177)
T PF09580_consen 77 ADRIANRVKKVPGVEDATVVVTDDNAYVA 105 (177)
T ss_pred HHHHHHHHhcCCCceEEEEEEECCEEEEE
Confidence 56889999999999999988877777654
No 27
>PHA01634 hypothetical protein
Probab=46.21 E-value=6.3 Score=27.09 Aligned_cols=13 Identities=38% Similarity=0.882 Sum_probs=10.6
Q ss_pred CCcHhHHHHHHHH
Q 033176 1 MCCTGCERVVKNA 13 (125)
Q Consensus 1 m~C~~C~~~V~~~ 13 (125)
|+|++|+.+|.-.
T Consensus 98 iDCeGCE~~l~v~ 110 (156)
T PHA01634 98 MDCEGCEEKLNVS 110 (156)
T ss_pred EEccchHHhcCHH
Confidence 7899999988544
No 28
>KOG3411 consensus 40S ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=46.13 E-value=22 Score=24.29 Aligned_cols=44 Identities=25% Similarity=0.306 Sum_probs=28.2
Q ss_pred HhHHHHHHHHHhCCCCeeEEEEeCCCC-EEEEEeCCCHHHHHHHHHHc
Q 033176 4 TGCERVVKNAIYKLRGVDSVEVELELE-KVTAVGYVDRNKVLKAVRRA 50 (125)
Q Consensus 4 ~~C~~~V~~~L~~~~GV~~v~vd~~~~-kvtV~g~~~~~~i~~~i~~~ 50 (125)
++|.++|-++|+++ .-|+.+...+ +++-.|..+.++|...|...
T Consensus 97 ~~i~rkvlQ~Le~~---~~ve~hp~gGR~lt~~GqrdldrIa~~i~~~ 141 (143)
T KOG3411|consen 97 GGIARKVLQALEKM---GIVEKHPKGGRRLTEQGQRDLDRIAGQIREE 141 (143)
T ss_pred cHHHHHHHHHHHhC---CceeeCCCCcceeCcccchhHHHHHHHHHhc
Confidence 45666665555554 4566666665 44555778888888877643
No 29
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=46.11 E-value=18 Score=25.24 Aligned_cols=46 Identities=20% Similarity=0.138 Sum_probs=34.1
Q ss_pred HhHHHHHHHHHhCCCCeeEEEEeCCCCE--------------EEEEe---CCCHHHHHHHHHH
Q 033176 4 TGCERVVKNAIYKLRGVDSVEVELELEK--------------VTAVG---YVDRNKVLKAVRR 49 (125)
Q Consensus 4 ~~C~~~V~~~L~~~~GV~~v~vd~~~~k--------------vtV~g---~~~~~~i~~~i~~ 49 (125)
.||-+-++..+.+++||.++.+-...+. |.|+- .++.++|++..-+
T Consensus 8 gGCFWg~E~~f~~l~GV~~t~vGYagG~~~~p~~~~tgH~E~V~V~yDp~~isy~~LL~~f~~ 70 (156)
T PRK05528 8 GGCLWGVQAFFKTLPGVIHTEAGRANGRTSTLDGPYDGYAECVKTHFDPRMVSITDLMGYLFE 70 (156)
T ss_pred cCCchhhHHHHhcCCCEEEEEEEcCCCCCCCCCCCCCCcEEEEEEEECCCcCCHHHHHHHHHH
Confidence 5799999999999999999998776543 33332 2677788776543
No 30
>cd04888 ACT_PheB-BS C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and related domains. This CD includes the C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and other related ACT domains. In B. subtilis, the upstream gene of pheB, pheA encodes prephenate dehydratase (PDT). The presumed product of the pheB gene is chorismate mutase (CM). The deduced product of the B. subtilis pheB gene, however, has no significant homology to the CM portion of the bifunctional CM-PDT of Escherichia coli. The presence of an ACT domain lends support to the prediction that these proteins function as a phenylalanine-binding regulatory protein. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=42.60 E-value=35 Score=19.65 Aligned_cols=19 Identities=21% Similarity=0.387 Sum_probs=15.6
Q ss_pred HHHHHHHHhCCCCeeEEEE
Q 033176 7 ERVVKNAIYKLRGVDSVEV 25 (125)
Q Consensus 7 ~~~V~~~L~~~~GV~~v~v 25 (125)
..++-+.|++++||.+|.+
T Consensus 56 l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 56 IDELLEELREIDGVEKVEL 74 (76)
T ss_pred HHHHHHHHhcCCCeEEEEE
Confidence 4577888999999998875
No 31
>TIGR00489 aEF-1_beta translation elongation factor aEF-1 beta. This model describes the archaeal translation elongation factor aEF-1 beta. The member from Sulfolobus solfataricus was demonstrated experimentally. It is a dimer that catalyzes the exchange of GDP for GTP on aEF-1 alpha.
Probab=42.33 E-value=31 Score=21.72 Aligned_cols=21 Identities=29% Similarity=0.476 Sum_probs=18.0
Q ss_pred HHHHHHHHHhCCCCeeEEEEe
Q 033176 6 CERVVKNAIYKLRGVDSVEVE 26 (125)
Q Consensus 6 C~~~V~~~L~~~~GV~~v~vd 26 (125)
-...|+.+|++++||+++++-
T Consensus 63 ~td~lee~i~~ve~V~svev~ 83 (88)
T TIGR00489 63 GTEAAEESLSGIEGVESVEVT 83 (88)
T ss_pred ChHHHHHHHhcCCCccEEEEE
Confidence 356789999999999999875
No 32
>PF04972 BON: BON domain; InterPro: IPR007055 The BON domain is typically ~60 residues long and has an alpha/beta predicted fold. There is a conserved glycine residue and several hydrophobic regions. This pattern of conservation is more suggestive of a binding or structural function rather than a catalytic function. Most proteobacteria seem to possess one or two BON-containing proteins, typically of the OsmY-type proteins; outside of this group the distribution is more disparate. The OsmY protein is an Escherichia coli 20 kDa outer membrane or periplasmic protein that is expressed in response to a variety of stress conditions, in particular, helping to provide protection against osmotic shock. One hypothesis is that OsmY prevents shrinkage of the cytoplasmic compartment by contacting the phospholipid interfaces surrounding the periplasmic space. The domain architecture of two BON domains alone suggests that these domains contact the surfaces of phospholipids, with each domain contacting a membrane [].; PDB: 2L26_A 2KGS_A 2KSM_A.
Probab=41.17 E-value=15 Score=20.82 Aligned_cols=30 Identities=27% Similarity=0.222 Sum_probs=14.7
Q ss_pred HHHHHHHhCC---CCeeEEEEeCCCCEEEEEeCC
Q 033176 8 RVVKNAIYKL---RGVDSVEVELELEKVTAVGYV 38 (125)
Q Consensus 8 ~~V~~~L~~~---~GV~~v~vd~~~~kvtV~g~~ 38 (125)
.+|+.+|... ++. .+.+....+.++++|.+
T Consensus 2 ~~v~~~L~~~~~~~~~-~i~v~v~~g~v~L~G~v 34 (64)
T PF04972_consen 2 TKVRAALRADPWLPDS-NISVSVENGVVTLSGEV 34 (64)
T ss_dssp -----------CTT-T-TEEEEEECTEEEEEEEE
T ss_pred cccccccccccccCCC-eEEEEEECCEEEEEeeC
Confidence 3566777663 333 57777889999999875
No 33
>PF14492 EFG_II: Elongation Factor G, domain II; PDB: 1WDT_A 2DY1_A 2XEX_A 1ELO_A 2XSY_Y 2WRK_Y 1DAR_A 2WRI_Y 2XUY_Y 3J0E_H ....
Probab=39.81 E-value=79 Score=18.80 Aligned_cols=50 Identities=26% Similarity=0.311 Sum_probs=32.3
Q ss_pred HHHHHHHHhCC---CCeeEEEEeCCCCEEEEE--eCCCHHHHHHHHH-HcCCceee
Q 033176 7 ERVVKNAIYKL---RGVDSVEVELELEKVTAV--GYVDRNKVLKAVR-RAGKRAEF 56 (125)
Q Consensus 7 ~~~V~~~L~~~---~GV~~v~vd~~~~kvtV~--g~~~~~~i~~~i~-~~G~~a~~ 56 (125)
..++..+|.++ +-.-.+..|..++.+.|. |.+..+-+++.|+ +.|..+++
T Consensus 18 ~~kl~~aL~~l~~eDP~l~~~~d~et~e~~l~g~Gelhlev~~~~L~~~~~v~v~~ 73 (75)
T PF14492_consen 18 EPKLSEALQKLSEEDPSLRVERDEETGELILSGMGELHLEVLLERLKRRFGVEVEF 73 (75)
T ss_dssp HHHHHHHHHHHHHH-TTSEEEEETTTSEEEEEESSHHHHHHHHHHHHHTTCEBEEE
T ss_pred HHHHHHHHHHHHhcCCeEEEEEcchhceEEEEECCHHHHHHHHHHHHHHHCCeeEe
Confidence 34555555554 223368889888888887 5577788888886 44655543
No 34
>PRK11023 outer membrane lipoprotein; Provisional
Probab=37.88 E-value=1.3e+02 Score=21.39 Aligned_cols=37 Identities=22% Similarity=0.299 Sum_probs=25.4
Q ss_pred HHHHHHHHhCCCCee--EEEEeCCCCEEEEEeCCCHHHH
Q 033176 7 ERVVKNAIYKLRGVD--SVEVELELEKVTAVGYVDRNKV 43 (125)
Q Consensus 7 ~~~V~~~L~~~~GV~--~v~vd~~~~kvtV~g~~~~~~i 43 (125)
..+|+.+|...+++. .++|....+.|++.|.++.++.
T Consensus 129 t~kik~~L~~~~~v~~~~I~V~t~~G~V~L~G~v~~~e~ 167 (191)
T PRK11023 129 TTKVRSQLLTSDSVKSSNVKVTTENGEVFLLGLVTQREA 167 (191)
T ss_pred HHHHHHHHhcCCCCCcceEEEEEECcEEEEEEEeCHHHH
Confidence 457788887777665 4555556888888887765544
No 35
>PRK11023 outer membrane lipoprotein; Provisional
Probab=36.96 E-value=90 Score=22.20 Aligned_cols=42 Identities=21% Similarity=0.203 Sum_probs=29.6
Q ss_pred HHHHHHHHhCCCCee---EEEEeCCCCEEEEEeCCCHHHHHHHHH
Q 033176 7 ERVVKNAIYKLRGVD---SVEVELELEKVTAVGYVDRNKVLKAVR 48 (125)
Q Consensus 7 ~~~V~~~L~~~~GV~---~v~vd~~~~kvtV~g~~~~~~i~~~i~ 48 (125)
..+|+.+|...+.+. ++++.-..+.|+++|.++.......+.
T Consensus 51 ~~~V~~aL~~~~~l~~~~~I~V~v~~G~V~L~G~V~~~~~k~~A~ 95 (191)
T PRK11023 51 ELRVNNALSKDEQIKKEARINVTAYQGKVLLTGQSPNAELSERAK 95 (191)
T ss_pred HHHHHHHHhhCcccCcCceEEEEEECCEEEEEEEeCCHHHHHHHH
Confidence 567888887766663 577777899999999865544443333
No 36
>TIGR02945 SUF_assoc FeS assembly SUF system protein. Members of this family belong to the broader Pfam family pfam01883, or Domain of Unknown Function DUF59. Many members of DUF59 are candidate ring hydroxylating complex subunits. However, members of the narrower family defined here all are found in genomes that carry the FeS assembly SUF system. For 70 % of these species, the member of this protein family is found as part of the SUF locus, usually immediately downstream of the sufS gene.
Probab=36.04 E-value=33 Score=21.40 Aligned_cols=23 Identities=43% Similarity=0.482 Sum_probs=18.0
Q ss_pred HHHHHHHHhCCCCeeEEEEeCCC
Q 033176 7 ERVVKNAIYKLRGVDSVEVELEL 29 (125)
Q Consensus 7 ~~~V~~~L~~~~GV~~v~vd~~~ 29 (125)
...++.+|..++|+.++++++..
T Consensus 57 ~~~i~~al~~l~gv~~v~v~i~~ 79 (99)
T TIGR02945 57 PGEVENAVRAVPGVGSVTVELVW 79 (99)
T ss_pred HHHHHHHHHhCCCCceEEEEEEe
Confidence 35678889999999988887643
No 37
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=35.95 E-value=1.5e+02 Score=20.54 Aligned_cols=54 Identities=9% Similarity=0.146 Sum_probs=37.3
Q ss_pred HHHHHHHhCCCCeeEEEEeCCCCEEEEEeC-------CCHHHHHHHHHHcCCceeecCCCC
Q 033176 8 RVVKNAIYKLRGVDSVEVELELEKVTAVGY-------VDRNKVLKAVRRAGKRAEFWPYPN 61 (125)
Q Consensus 8 ~~V~~~L~~~~GV~~v~vd~~~~kvtV~g~-------~~~~~i~~~i~~~G~~a~~~~~~~ 61 (125)
..|++.+-.-.||.++.+|..++.|.|... ....-+.+...++|........++
T Consensus 56 ~~I~~ivP~ea~i~di~Fd~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtpP 116 (145)
T cd02410 56 KIILEIVPEEAGITDIYFDDDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTPP 116 (145)
T ss_pred HHHHHhCCCccCceeeEecCCCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecCC
Confidence 345555555579999999999999988621 222333455569999988887666
No 38
>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=35.87 E-value=31 Score=23.86 Aligned_cols=27 Identities=26% Similarity=0.286 Sum_probs=23.4
Q ss_pred HhHHHHHHHHHhCCCCeeEEEEeCCCC
Q 033176 4 TGCERVVKNAIYKLRGVDSVEVELELE 30 (125)
Q Consensus 4 ~~C~~~V~~~L~~~~GV~~v~vd~~~~ 30 (125)
.||-+-++..+.+++||.++.+-...+
T Consensus 7 gGCFWg~E~~f~~~~GV~~t~~GYagG 33 (149)
T TIGR00401 7 GGCFWGVEKYFWLIPGVYSTAVGYTGG 33 (149)
T ss_pred cCCchhhHHHHhcCCCEEEEEEeeCCC
Confidence 579999999999999999999877654
No 39
>PRK09577 multidrug efflux protein; Reviewed
Probab=35.22 E-value=1.4e+02 Score=26.96 Aligned_cols=46 Identities=17% Similarity=0.088 Sum_probs=34.8
Q ss_pred HHHHHHHHhCCCCeeEEEEeCCCCEEEEE--------eCCCHHHHHHHHHHcCC
Q 033176 7 ERVVKNAIYKLRGVDSVEVELELEKVTAV--------GYVDRNKVLKAVRRAGK 52 (125)
Q Consensus 7 ~~~V~~~L~~~~GV~~v~vd~~~~kvtV~--------g~~~~~~i~~~i~~~G~ 52 (125)
..+++..|++++||.+|++.-....+.|. -.++..+|.++|+..+.
T Consensus 158 ~~~l~~~L~~v~GV~~V~~~G~e~~v~V~vD~~kl~~~Gls~~~V~~~l~~~n~ 211 (1032)
T PRK09577 158 SANVLQALRRVEGVGKVQFWGAEYAMRIWPDPVKLAALGLTASDIASAVRAHNA 211 (1032)
T ss_pred HHHHHHHHhcCCCcEEEEecCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHhCC
Confidence 35789999999999999998755555553 12678888888886543
No 40
>PF09158 MotCF: Bacteriophage T4 MotA, C-terminal; InterPro: IPR015241 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the C-terminal domain of MotA factors, which adopts a compact alpha/beta structure comprising three alpha-helices and six beta-strands in the order: alpha1-beta1-beta2-beta3-beta4-alpha2-beta5-beta6-alpha3. In this architecture, the domain's hydrophobic core is at the sheet-helix interface, and the second surface of the beta-sheet is completely exposed. It contains a DNA-binding motif, with a consensus sequence containing nine base pairs (5'-TTTGCTTTA-3'), that appears to bind to various mot boxes, allowing access to the minor groove towards the 5'-end of this sequence and the major groove towards the 3'-end [].; PDB: 1KAF_B.
Probab=35.19 E-value=1.3e+02 Score=19.61 Aligned_cols=40 Identities=15% Similarity=0.303 Sum_probs=27.5
Q ss_pred CCCeeEEEEeCCCCEEEEEeCCCHHHHHHHHHHcCCceeec
Q 033176 17 LRGVDSVEVELELEKVTAVGYVDRNKVLKAVRRAGKRAEFW 57 (125)
Q Consensus 17 ~~GV~~v~vd~~~~kvtV~g~~~~~~i~~~i~~~G~~a~~~ 57 (125)
..|+...++. ..+...|.|+--.+++++.+.+.|..+...
T Consensus 40 t~GirqfEi~-n~G~~RI~gYk~se~~~~~f~slG~~~K~~ 79 (103)
T PF09158_consen 40 TKGIRQFEIR-NKGEFRIFGYKMSEEIIKKFTSLGMEVKQK 79 (103)
T ss_dssp ETTEEEEEEE-TTSEEEEEEES--HHHHHHHHHTT-EEEE-
T ss_pred cCceeEEEEe-cCCcEEEEEEcCCHHHHHHHHhcCcEEEEc
Confidence 3566666664 456677778878889999999999887763
No 41
>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=34.68 E-value=43 Score=23.23 Aligned_cols=27 Identities=33% Similarity=0.324 Sum_probs=23.7
Q ss_pred HhHHHHHHHHHhCCCCeeEEEEeCCCC
Q 033176 4 TGCERVVKNAIYKLRGVDSVEVELELE 30 (125)
Q Consensus 4 ~~C~~~V~~~L~~~~GV~~v~vd~~~~ 30 (125)
.||-+.++..+.+++||.++.+-...+
T Consensus 7 ~GCFW~~e~~f~~~~GV~~t~vGYagG 33 (155)
T PF01625_consen 7 GGCFWGVEAAFRRLPGVISTRVGYAGG 33 (155)
T ss_dssp ESSHHHHHHHHHTSTTEEEEEEEEESS
T ss_pred cCCCeEhHHHHhhCCCEEEEEecccCC
Confidence 479999999999999999999877654
No 42
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=34.34 E-value=98 Score=19.78 Aligned_cols=21 Identities=19% Similarity=0.289 Sum_probs=18.3
Q ss_pred CCCCeeEEEEeCCCCEEEEEe
Q 033176 16 KLRGVDSVEVELELEKVTAVG 36 (125)
Q Consensus 16 ~~~GV~~v~vd~~~~kvtV~g 36 (125)
..+|++.+++.+.++++.|++
T Consensus 38 s~pgis~ieik~E~kkL~v~t 58 (96)
T COG4004 38 SSPGISRIEIKPENKKLLVNT 58 (96)
T ss_pred ecCCceEEEEecccceEEEec
Confidence 457899999999999999875
No 43
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=34.17 E-value=94 Score=23.90 Aligned_cols=27 Identities=37% Similarity=0.279 Sum_probs=23.7
Q ss_pred HhHHHHHHHHHhCCCCeeEEEEeCCCC
Q 033176 4 TGCERVVKNAIYKLRGVDSVEVELELE 30 (125)
Q Consensus 4 ~~C~~~V~~~L~~~~GV~~v~vd~~~~ 30 (125)
.+|-+-++..+.+++||.++.+-...+
T Consensus 134 gGCFWg~E~~F~~~~GV~~t~vGYagG 160 (283)
T PRK05550 134 GGCFWGVEYYFKKLPGVLSVESGYTGG 160 (283)
T ss_pred cCCchhhhhhHhhCcCEEEEEEeeCCC
Confidence 579999999999999999999877654
No 44
>COG2092 EFB1 Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis]
Probab=33.53 E-value=42 Score=21.20 Aligned_cols=21 Identities=38% Similarity=0.578 Sum_probs=17.8
Q ss_pred HHHHHHHHHhCCCCeeEEEEe
Q 033176 6 CERVVKNAIYKLRGVDSVEVE 26 (125)
Q Consensus 6 C~~~V~~~L~~~~GV~~v~vd 26 (125)
-...++.+|+.+.||+++++-
T Consensus 63 ~td~~ee~l~~vegV~sveve 83 (88)
T COG2092 63 GTDALEEALEEVEGVESVEVE 83 (88)
T ss_pred CcHHHHHHHhhccCcceEEEE
Confidence 356789999999999998874
No 45
>PRK00435 ef1B elongation factor 1-beta; Validated
Probab=32.38 E-value=53 Score=20.65 Aligned_cols=21 Identities=43% Similarity=0.558 Sum_probs=17.6
Q ss_pred HHHHHHHHHhCCCCeeEEEEe
Q 033176 6 CERVVKNAIYKLRGVDSVEVE 26 (125)
Q Consensus 6 C~~~V~~~L~~~~GV~~v~vd 26 (125)
-...++.++++++||+++++-
T Consensus 63 ~td~lee~i~~~e~Vqsvei~ 83 (88)
T PRK00435 63 GTEPVEEAFANVEGVESVEVE 83 (88)
T ss_pred CcHHHHHHHhccCCCcEEEEE
Confidence 346788999999999999875
No 46
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=32.29 E-value=1.6e+02 Score=26.71 Aligned_cols=44 Identities=9% Similarity=0.142 Sum_probs=33.4
Q ss_pred HHHHHHHHhCCCCeeEEEEeCCCCEEEEEe--------CCCHHHHHHHHHHc
Q 033176 7 ERVVKNAIYKLRGVDSVEVELELEKVTAVG--------YVDRNKVLKAVRRA 50 (125)
Q Consensus 7 ~~~V~~~L~~~~GV~~v~vd~~~~kvtV~g--------~~~~~~i~~~i~~~ 50 (125)
+..++..|++++||.+|++.-....+.|.- .++..+|..+|+..
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~~v~~al~~~ 210 (1037)
T PRK10555 159 ASNIQDPLSRVNGVGDIDAYGSQYSMRIWLDPAKLNSFQMTTKDVTDAIESQ 210 (1037)
T ss_pred HHHHHHHhhcCCCeEEEEEcCCceEEEEEECHHHHHHcCCCHHHHHHHHHHh
Confidence 467899999999999999986544455541 26788888888753
No 47
>COG3062 NapD Uncharacterized protein involved in formation of periplasmic nitrate reductase [Inorganic ion transport and metabolism]
Probab=30.93 E-value=1.5e+02 Score=18.99 Aligned_cols=43 Identities=21% Similarity=0.303 Sum_probs=29.5
Q ss_pred HHHHHHHHhCCCCeeEEEEeCCCCEEEEE-eCCCHHHHHHHHHHc
Q 033176 7 ERVVKNAIYKLRGVDSVEVELELEKVTAV-GYVDRNKVLKAVRRA 50 (125)
Q Consensus 7 ~~~V~~~L~~~~GV~~v~vd~~~~kvtV~-g~~~~~~i~~~i~~~ 50 (125)
...|..+|..++|++--.-+.. +|+.|. ...+...+++.++..
T Consensus 20 l~av~~~L~~ip~~EV~~~d~~-GKlVVVie~~~~~~l~~tie~i 63 (94)
T COG3062 20 LSAVKTALLAIPGCEVYGEDAE-GKLVVVIEAEDSETLLETIESI 63 (94)
T ss_pred HHHHHHHHhcCCCcEeeccCCC-ceEEEEEEcCchHHHHHHHHHH
Confidence 4578899999999986666655 666654 334666677766543
No 48
>TIGR01676 GLDHase galactonolactone dehydrogenase. This model represents L-Galactono-gamma-lactone dehydrogenase (EC 1.3.2.3). This enzyme catalyzes the final step in ascorbic acid biosynthesis in higher plants. This protein is homologous to ascorbic acid biosynthesis enzymes of other species: L-gulono-gamma-lactone oxidase in rat and L-galactono-gamma-lactone oxidase in yeast. All three covalently bind the cofactor FAD.
Probab=30.65 E-value=1.1e+02 Score=25.77 Aligned_cols=39 Identities=18% Similarity=0.278 Sum_probs=30.7
Q ss_pred HhCCCCeeEEEEeCCCCEEEEEeCCCHHHHHHHHHHcCCce
Q 033176 14 IYKLRGVDSVEVELELEKVTAVGYVDRNKVLKAVRRAGKRA 54 (125)
Q Consensus 14 L~~~~GV~~v~vd~~~~kvtV~g~~~~~~i~~~i~~~G~~a 54 (125)
|..+.+| +++|...+.|+|.+.+...+|.+.|...|+..
T Consensus 110 L~~ln~V--l~vD~~~~tVtV~AG~~l~~L~~~L~~~Glal 148 (541)
T TIGR01676 110 LALMDKV--LEVDEEKKRVRVQAGIRVQQLVDAIKEYGITL 148 (541)
T ss_pred hhhCCCC--EEEcCCCCEEEEcCCCCHHHHHHHHHHcCCEe
Confidence 4455555 35777888999998889999999999999754
No 49
>TIGR02830 spore_III_AG stage III sporulation protein AG. CC A comparative genome analysis of all sequenced genomes of shows a number of proteins conserved strictly among the endospore-forming subset of the Firmicutes. This protein, a member of this panel, is found in a spore formation operon and is designated stage III sporulation protein AG.
Probab=30.57 E-value=50 Score=23.75 Aligned_cols=29 Identities=28% Similarity=0.410 Sum_probs=20.3
Q ss_pred HHHHHHHHHhCCCCeeEEEE--eCCCCEEEE
Q 033176 6 CERVVKNAIYKLRGVDSVEV--ELELEKVTA 34 (125)
Q Consensus 6 C~~~V~~~L~~~~GV~~v~v--d~~~~kvtV 34 (125)
-+.+++..|+++.||.+|+| .+..+.-.|
T Consensus 62 lE~~L~~iL~~I~GvG~V~VmItl~s~~e~v 92 (186)
T TIGR02830 62 YENELKEILEKIEGVGDVTVMVNLDSSEEKV 92 (186)
T ss_pred HHHHHHHHHHhccCcceeEEEEEECCCceEE
Confidence 36788999999999987664 455444333
No 50
>KOG4730 consensus D-arabinono-1, 4-lactone oxidase [Defense mechanisms]
Probab=30.17 E-value=75 Score=26.32 Aligned_cols=33 Identities=21% Similarity=0.314 Sum_probs=27.7
Q ss_pred EEEeCCCCEEEEEeCCCHHHHHHHHHHcCCcee
Q 033176 23 VEVELELEKVTAVGYVDRNKVLKAVRRAGKRAE 55 (125)
Q Consensus 23 v~vd~~~~kvtV~g~~~~~~i~~~i~~~G~~a~ 55 (125)
+++|.+..+|||+..+...+|++.+++.|+...
T Consensus 105 v~~dpe~~tvTV~aGirlrQLie~~~~~GlsL~ 137 (518)
T KOG4730|consen 105 VEFDPELKTVTVQAGIRLRQLIEELAKLGLSLP 137 (518)
T ss_pred eeeCchhceEEeccCcCHHHHHHHHHhcCcccc
Confidence 456778888899888899999999999998644
No 51
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=29.83 E-value=60 Score=21.35 Aligned_cols=21 Identities=43% Similarity=0.624 Sum_probs=17.8
Q ss_pred HHHHHHHHhCCCCeeEEEEeC
Q 033176 7 ERVVKNAIYKLRGVDSVEVEL 27 (125)
Q Consensus 7 ~~~V~~~L~~~~GV~~v~vd~ 27 (125)
...|+.+|..++||.+++|++
T Consensus 69 ~~~v~~al~~~~~v~~v~V~l 89 (111)
T COG2151 69 ADQVEAALEEIPGVEDVEVEL 89 (111)
T ss_pred HHHHHHHHHhcCCcceEEEEE
Confidence 567899999999999888763
No 52
>PF01514 YscJ_FliF: Secretory protein of YscJ/FliF family; InterPro: IPR006182 This domain is found in proteins that are related to the YscJ lipoprotein, where it covers most of the sequence, and the flagellar M-ring protein FliF, where it covers the N-terminal region. The members of the YscJ family are thought to be involved in secretion of several proteins. The FliF protein ring is thought to be part of the export apparatus for flagellar proteins, based on the similarity to YscJ proteins [].; PDB: 1YJ7_A 2Y9J_d.
Probab=29.23 E-value=69 Score=23.16 Aligned_cols=21 Identities=33% Similarity=0.504 Sum_probs=18.0
Q ss_pred HHHHHHHHhCCCCeeEEEEeC
Q 033176 7 ERVVKNAIYKLRGVDSVEVEL 27 (125)
Q Consensus 7 ~~~V~~~L~~~~GV~~v~vd~ 27 (125)
+..+++.|+.++||.++.|.+
T Consensus 117 e~eL~~tI~~i~gV~~A~V~l 137 (206)
T PF01514_consen 117 EGELERTIESIDGVESARVHL 137 (206)
T ss_dssp HHHHHHHHTTSTTEEEEEEEE
T ss_pred HHHHHHHHHcCCCeeEEEEEE
Confidence 467889999999999988874
No 53
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.61 E-value=33 Score=21.16 Aligned_cols=16 Identities=19% Similarity=0.534 Sum_probs=13.7
Q ss_pred CcHhHHHHHHHHHhCC
Q 033176 2 CCTGCERVVKNAIYKL 17 (125)
Q Consensus 2 ~C~~C~~~V~~~L~~~ 17 (125)
.|+.|..++++.|...
T Consensus 35 ~ce~c~a~~kk~l~~v 50 (82)
T COG2331 35 TCEECGARLKKLLNAV 50 (82)
T ss_pred cChhhChHHHHhhccc
Confidence 5999999999998754
No 54
>PF05046 Img2: Mitochondrial large subunit ribosomal protein (Img2); InterPro: IPR007740 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 of proteins has been identified as part of the mitochondrial large ribosomal subunit in Saccharomyces cerevisiae [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome
Probab=27.47 E-value=1.6e+02 Score=18.24 Aligned_cols=45 Identities=13% Similarity=0.036 Sum_probs=29.4
Q ss_pred HHHHHHHHhCCCC-eeEEEEeCCCCEEEEEeCCCHHHHHHHHHHcCC
Q 033176 7 ERVVKNAIYKLRG-VDSVEVELELEKVTAVGYVDRNKVLKAVRRAGK 52 (125)
Q Consensus 7 ~~~V~~~L~~~~G-V~~v~vd~~~~kvtV~g~~~~~~i~~~i~~~G~ 52 (125)
...+.+.|....+ -..+.|+..++.+.|.|. ...+|.+-|.+.||
T Consensus 42 ~~dL~~~l~~~~~~~~~~~V~~~~g~i~IkG~-~~~~Vk~wL~~~GF 87 (87)
T PF05046_consen 42 KKDLRKFLGEKPKKKIDVRVNELTGHIEIKGD-HVEEVKKWLLEKGF 87 (87)
T ss_pred HHHHHHHhhhhcCCCcceEEeecCCEEEEcCc-cHHHHHHHHHHCcC
Confidence 3344444433322 236788889999999987 36777777777775
No 55
>PF03434 DUF276: DUF276 ; InterPro: IPR005096 This family is specific to Borrelia burgdorferi (Lyme disease spirochete). The protein is encoded on extrachromosomal DNA and is of unknown function.
Probab=27.19 E-value=1.1e+02 Score=23.30 Aligned_cols=29 Identities=21% Similarity=0.361 Sum_probs=24.8
Q ss_pred HHHHHHHHhCCCCeeEEEEeCCCCEEEEE
Q 033176 7 ERVVKNAIYKLRGVDSVEVELELEKVTAV 35 (125)
Q Consensus 7 ~~~V~~~L~~~~GV~~v~vd~~~~kvtV~ 35 (125)
-..|+++|..++||..+++--..+++.+-
T Consensus 89 y~Avk~aLL~~~gv~haNI~SsaGtiniY 117 (291)
T PF03434_consen 89 YEAVKSALLNLNGVEHANIKSSAGTINIY 117 (291)
T ss_pred HHHHHHHhcCCCCceeeeeecCCCeeEEE
Confidence 35789999999999999998888887653
No 56
>COG5561 Predicted metal-binding protein [Function unknown]
Probab=26.98 E-value=81 Score=20.15 Aligned_cols=9 Identities=44% Similarity=0.789 Sum_probs=4.1
Q ss_pred cHhHHHHHH
Q 033176 3 CTGCERVVK 11 (125)
Q Consensus 3 C~~C~~~V~ 11 (125)
|++|++=.+
T Consensus 7 CPG~v~CfK 15 (101)
T COG5561 7 CPGEVRCFK 15 (101)
T ss_pred CCchHHHHH
Confidence 555444433
No 57
>PF01849 NAC: NAC domain; InterPro: IPR002715 Nascent polypeptide-associated complex (NAC) is among the first ribosome-associated entities to bind the nascent polypeptide after peptide bond formation. The nascent polypeptide-associated complex (NAC) of yeast functions in the targeting process of ribosomes to the ER membrane []. NAC may prevent binding of ribosome nascent chains (RNCs) without a signal sequence to yeast membranes.; PDB: 3MCE_D 3MCB_A 3LKX_B 1TR8_B.
Probab=26.71 E-value=76 Score=17.96 Aligned_cols=21 Identities=14% Similarity=0.283 Sum_probs=15.1
Q ss_pred hCCCCeeEEEEeCCCCEEEEE
Q 033176 15 YKLRGVDSVEVELELEKVTAV 35 (125)
Q Consensus 15 ~~~~GV~~v~vd~~~~kvtV~ 35 (125)
..++||..|.+-...+++.+-
T Consensus 14 ~~i~~i~eV~i~~~dg~~~~~ 34 (58)
T PF01849_consen 14 KEIPGIEEVTIRKDDGTVFVF 34 (58)
T ss_dssp EEETTEEEEEEEETTTEEEEE
T ss_pred cccCCcEEEEEEECCceEEEE
Confidence 344788889888888766543
No 58
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=25.73 E-value=1e+02 Score=18.78 Aligned_cols=22 Identities=18% Similarity=0.268 Sum_probs=15.8
Q ss_pred CCCCEEEEEeCCCHHHHHHHHH
Q 033176 27 LELEKVTAVGYVDRNKVLKAVR 48 (125)
Q Consensus 27 ~~~~kvtV~g~~~~~~i~~~i~ 48 (125)
+.+++++++|..+.+++..+++
T Consensus 55 F~sGki~itGaks~~~~~~a~~ 76 (86)
T PF00352_consen 55 FSSGKIVITGAKSEEEAKKAIE 76 (86)
T ss_dssp ETTSEEEEEEESSHHHHHHHHH
T ss_pred EcCCEEEEEecCCHHHHHHHHH
Confidence 5688999998767766655554
No 59
>COG0277 GlcD FAD/FMN-containing dehydrogenases [Energy production and conversion]
Probab=25.70 E-value=85 Score=24.81 Aligned_cols=38 Identities=21% Similarity=0.135 Sum_probs=29.3
Q ss_pred CCCCeeEEEEeCCCCEEEEEeCCCHHHHHHHHHHcCCcee
Q 033176 16 KLRGVDSVEVELELEKVTAVGYVDRNKVLKAVRRAGKRAE 55 (125)
Q Consensus 16 ~~~GV~~v~vd~~~~kvtV~g~~~~~~i~~~i~~~G~~a~ 55 (125)
++.+|. ++|...+.++|..-+...+|.+.++..|+..-
T Consensus 83 ~mn~i~--~id~~~~~~~v~aGv~l~~l~~~l~~~G~~~p 120 (459)
T COG0277 83 RLNRIL--EIDPEDGTATVQAGVTLEDLEKALAPHGLFLP 120 (459)
T ss_pred hhcchh--ccCcCCCEEEEcCCccHHHHHHHHHHcCCccC
Confidence 344443 67888999999977889999999998887543
No 60
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=25.54 E-value=2.3e+02 Score=20.64 Aligned_cols=37 Identities=30% Similarity=0.275 Sum_probs=27.0
Q ss_pred HHHHHHHhCCCCeeEEEEeCCCCEEEEEeC---CCHHHHHH
Q 033176 8 RVVKNAIYKLRGVDSVEVELELEKVTAVGY---VDRNKVLK 45 (125)
Q Consensus 8 ~~V~~~L~~~~GV~~v~vd~~~~kvtV~g~---~~~~~i~~ 45 (125)
..+.+.|....|+. +.+|..++.|+|... .+|-.+++
T Consensus 27 g~v~k~ie~~~~~~-~~iD~~~~~V~i~~~~~t~Dp~~~~k 66 (194)
T COG1094 27 GEVKKAIEEKTGVK-LRIDSKTGSVTIRTTRKTEDPLALLK 66 (194)
T ss_pred ccchHHHHhhcCeE-EEEECCCCeEEEEecCCCCChHHHHH
Confidence 35677788777775 999999999999743 46655544
No 61
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=25.54 E-value=1.7e+02 Score=19.83 Aligned_cols=42 Identities=24% Similarity=0.241 Sum_probs=25.5
Q ss_pred HHHHHHHHhCC-CCeeEEEEeCCCCEEEEEeCCCHHHHHHHHH
Q 033176 7 ERVVKNAIYKL-RGVDSVEVELELEKVTAVGYVDRNKVLKAVR 48 (125)
Q Consensus 7 ~~~V~~~L~~~-~GV~~v~vd~~~~kvtV~g~~~~~~i~~~i~ 48 (125)
..+|.++|.+. -+...++|....+.|++.|.+.......++.
T Consensus 28 ~~~i~~~i~~~~~~~~~i~V~v~~G~v~l~G~v~s~~~~~~~~ 70 (147)
T PRK11198 28 ADALKEHISKQGLGDADVNVQVEDGKATVSGDAASQEAKEKIL 70 (147)
T ss_pred HHHHHHHHHhcCCCcCCceEEEeCCEEEEEEEeCCHHHHHHHH
Confidence 35566666553 2334456666799999998765444444443
No 62
>PRK09019 translation initiation factor Sui1; Validated
Probab=25.53 E-value=89 Score=20.48 Aligned_cols=34 Identities=15% Similarity=0.216 Sum_probs=16.1
Q ss_pred hCCCCeeEEEEeCC---CCEEEEE-eC----CCHHHHHHHHH
Q 033176 15 YKLRGVDSVEVELE---LEKVTAV-GY----VDRNKVLKAVR 48 (125)
Q Consensus 15 ~~~~GV~~v~vd~~---~~kvtV~-g~----~~~~~i~~~i~ 48 (125)
..-.++..+..... ...|||. |. .+..+|++.|+
T Consensus 27 ~~~~~~vri~~~r~gRkGK~VTiI~Gl~~~~~dlk~l~K~lK 68 (108)
T PRK09019 27 PKGDGIVRIQRQTSGRKGKGVCLITGLDLDDAELKKLAAELK 68 (108)
T ss_pred CCcCceEEEEEecCCCCCCeEEEEeCCcCCHHHHHHHHHHHH
Confidence 33455555554433 2356654 32 24455566665
No 63
>TIGR02571 ComEB ComE operon protein 2. This protein is found in the ComE operon for "late competence" as characterized in B. subtilis. Proteins in this family contain homology to a cytidine/deoxycytidine deaminase domain family (pfam00383), and may carry out this activity.
Probab=25.37 E-value=2.3e+02 Score=19.43 Aligned_cols=44 Identities=18% Similarity=0.391 Sum_probs=26.0
Q ss_pred CcHhHHHHHHHHHhCCCCeeEEEEeCCCCEEEEEeCCCHHHHHHHHHHcCCceeecC
Q 033176 2 CCTGCERVVKNAIYKLRGVDSVEVELELEKVTAVGYVDRNKVLKAVRRAGKRAEFWP 58 (125)
Q Consensus 2 ~C~~C~~~V~~~L~~~~GV~~v~vd~~~~kvtV~g~~~~~~i~~~i~~~G~~a~~~~ 58 (125)
-|..|...|..+ ||..|-+. ....+...-.+.+++.|..++.++
T Consensus 96 PC~~Ca~ai~~a-----gI~~Vvy~--------~~~~~~~~~~~~l~~~gi~v~~~~ 139 (151)
T TIGR02571 96 PCLQCTKSIIQA-----GIKKIYYA--------QDYHNHPYAIELFEQAGVELKKVP 139 (151)
T ss_pred CcHHHHHHHHHh-----CCCEEEEc--------cCCCCcHHHHHHHHHCCCEEEEeC
Confidence 377888777654 55554332 111222345667888888877664
No 64
>PRK11018 hypothetical protein; Provisional
Probab=25.31 E-value=1.6e+02 Score=17.62 Aligned_cols=47 Identities=17% Similarity=0.038 Sum_probs=32.7
Q ss_pred CcHhHHHHHHHHHhCCCCeeEEEEeCCCCEEEEE--eCCCHHHHHHHHHHcCCceeec
Q 033176 2 CCTGCERVVKNAIYKLRGVDSVEVELELEKVTAV--GYVDRNKVLKAVRRAGKRAEFW 57 (125)
Q Consensus 2 ~C~~C~~~V~~~L~~~~GV~~v~vd~~~~kvtV~--g~~~~~~i~~~i~~~G~~a~~~ 57 (125)
.|+.=.-+.+++|.+++.- +.+.|. .......|...+++.|+.+...
T Consensus 17 ~CP~Pvl~~kk~l~~l~~G---------~~L~V~~d~~~a~~di~~~~~~~G~~v~~~ 65 (78)
T PRK11018 17 PCPYPAVATLEALPQLKKG---------EILEVVSDCPQSINNIPLDARNHGYTVLDI 65 (78)
T ss_pred cCCHHHHHHHHHHHhCCCC---------CEEEEEeCCccHHHHHHHHHHHcCCEEEEE
Confidence 5888888999999988532 233333 2345677888889999987543
No 65
>cd08032 LARP_7 La RNA-binding domain of La-related protein 7. LARP7 is a component of the 7SK snRNP, a key factor in the regulation of RNA polymerase II transcription. 7SK functionality is dependent on the presence of LARP7, which is thought to stabilize the 7SK RNA by interacting with its 3' end. The release of 7SK RNA from P-TEFb/HEXIM/7SK complexes activates the cyclin-dependent kinase P-TEFb, which in turn phosphorylates the C-terminal domain of RNA pol II and mediates a transition into productive transcription elongation.
Probab=25.12 E-value=23 Score=22.01 Aligned_cols=6 Identities=50% Similarity=0.667 Sum_probs=4.8
Q ss_pred CCCCCC
Q 033176 113 MFNDDN 118 (125)
Q Consensus 113 ~fsd~n 118 (125)
+|||+|
T Consensus 16 YFSd~N 21 (82)
T cd08032 16 WFGDVN 21 (82)
T ss_pred hcchhh
Confidence 688887
No 66
>PRK15127 multidrug efflux system protein AcrB; Provisional
Probab=24.83 E-value=2.5e+02 Score=25.49 Aligned_cols=43 Identities=16% Similarity=0.149 Sum_probs=32.7
Q ss_pred HHHHHHHhCCCCeeEEEEeCCCCEEEEEe--------CCCHHHHHHHHHHc
Q 033176 8 RVVKNAIYKLRGVDSVEVELELEKVTAVG--------YVDRNKVLKAVRRA 50 (125)
Q Consensus 8 ~~V~~~L~~~~GV~~v~vd~~~~kvtV~g--------~~~~~~i~~~i~~~ 50 (125)
..++..|++++||.++++.-....+.|.- .++...|..+|+..
T Consensus 160 ~~l~~~L~~v~GV~~V~~~G~~~ei~V~vDp~kl~~~gls~~~V~~~l~~~ 210 (1049)
T PRK15127 160 ANMKDPISRTSGVGDVQLFGSQYAMRIWMNPNELNKFQLTPVDVINAIKAQ 210 (1049)
T ss_pred HHHHHHHhcCCCceEEEEcCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHh
Confidence 56899999999999999876554466651 26778888888744
No 67
>cd06167 LabA_like LabA_like proteins. A well conserved group of bacterial proteins with no defined function. LabA, a member from Synechococcus elongatus PCC 7942, has been shown to play a role in cyanobacterial circadian timing. It is required for negative feedback regulation of the autokinase/autophosphatase KaiC, a central component of the circadian clock system. In particular, LabA seems necessary for KaiC-dependent repression of gene expression.
Probab=24.63 E-value=1.3e+02 Score=19.70 Aligned_cols=29 Identities=24% Similarity=0.289 Sum_probs=23.8
Q ss_pred EEEEeCCCHHHHHHHHHHcCCceeecCCC
Q 033176 32 VTAVGYVDRNKVLKAVRRAGKRAEFWPYP 60 (125)
Q Consensus 32 vtV~g~~~~~~i~~~i~~~G~~a~~~~~~ 60 (125)
+.|+|+.+-..+++.+++.|.++.++...
T Consensus 104 vLvSgD~Df~~~i~~lr~~G~~V~v~~~~ 132 (149)
T cd06167 104 VLVSGDSDFVPLVERLRELGKRVIVVGFE 132 (149)
T ss_pred EEEECCccHHHHHHHHHHcCCEEEEEccC
Confidence 34567788888999999999999988665
No 68
>PF13216 DUF4024: Protein of unknown function (DUF4024)
Probab=24.35 E-value=25 Score=17.76 Aligned_cols=11 Identities=36% Similarity=0.676 Sum_probs=9.0
Q ss_pred CCCCCCCCCCc
Q 033176 111 SNMFNDDNVNA 121 (125)
Q Consensus 111 ~~~fsd~npna 121 (125)
..+|-|||.|-
T Consensus 9 lhlfrde~vnf 19 (35)
T PF13216_consen 9 LHLFRDEKVNF 19 (35)
T ss_pred EEEeecCCccE
Confidence 46899999984
No 69
>TIGR00915 2A0602 The (Largely Gram-negative Bacterial) Hydrophobe/Amphiphile Efflux-1 (HAE1) Family. This family is one of several subfamilies within the scope of pfam model pfam00873.
Probab=24.07 E-value=2.6e+02 Score=25.40 Aligned_cols=43 Identities=16% Similarity=0.152 Sum_probs=33.3
Q ss_pred HHHHHHHhCCCCeeEEEEeCCCCEEEEEe--------CCCHHHHHHHHHHc
Q 033176 8 RVVKNAIYKLRGVDSVEVELELEKVTAVG--------YVDRNKVLKAVRRA 50 (125)
Q Consensus 8 ~~V~~~L~~~~GV~~v~vd~~~~kvtV~g--------~~~~~~i~~~i~~~ 50 (125)
..++..|++++||.+|++.-....+.|.- .++..+|..+|+..
T Consensus 160 ~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~dV~~~i~~~ 210 (1044)
T TIGR00915 160 SNMVDPISRLEGVGDVQLFGSQYAMRIWLDPAKLNSYQLTPADVISAIQAQ 210 (1044)
T ss_pred HHHHHHHhCCCCceEEEecCCceEEEEEECHHHHHHcCCCHHHHHHHHHHh
Confidence 56899999999999999987744566651 27788888888763
No 70
>cd03421 SirA_like_N SirA_like_N, a protein of unknown function with an N-terminal SirA-like domain. The SirA, YedF, YeeD protein family is present in bacteria as well as archaea. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=23.61 E-value=1.5e+02 Score=16.80 Aligned_cols=47 Identities=15% Similarity=0.205 Sum_probs=31.1
Q ss_pred CCcHhHHHHHHHHHhCCCCeeEEEEeCCCCEEEEE--eCCCHHHHHHHHHHcCCceeec
Q 033176 1 MCCTGCERVVKNAIYKLRGVDSVEVELELEKVTAV--GYVDRNKVLKAVRRAGKRAEFW 57 (125)
Q Consensus 1 m~C~~C~~~V~~~L~~~~GV~~v~vd~~~~kvtV~--g~~~~~~i~~~i~~~G~~a~~~ 57 (125)
+.|+.=.-+++++| ++.. .+.+.|. .......|...+++.|+.....
T Consensus 7 ~~CP~P~l~~k~al-~~~~---------g~~l~v~~d~~~s~~~i~~~~~~~G~~~~~~ 55 (67)
T cd03421 7 LACPQPVIKTKKAL-ELEA---------GGEIEVLVDNEVAKENVSRFAESRGYEVSVE 55 (67)
T ss_pred CCCCHHHHHHHHHH-hcCC---------CCEEEEEEcChhHHHHHHHHHHHcCCEEEEE
Confidence 35888888889998 5532 2233333 2244567888889999988543
No 71
>PF04805 Pox_E10: E10-like protein conserved region; InterPro: IPR006890 This entry represents a family of probable FAD-linked sulphydryl oxidases found in poxviruses.; GO: 0016972 thiol oxidase activity, 0055114 oxidation-reduction process
Probab=23.46 E-value=69 Score=19.26 Aligned_cols=22 Identities=32% Similarity=0.413 Sum_probs=16.2
Q ss_pred CCcHhHHHHHHHHHhCCCCeeE
Q 033176 1 MCCTGCERVVKNAIYKLRGVDS 22 (125)
Q Consensus 1 m~C~~C~~~V~~~L~~~~GV~~ 22 (125)
|-|+.|.....+++++-.=.++
T Consensus 16 LPC~~Cr~HA~~ai~kNNiMSs 37 (70)
T PF04805_consen 16 LPCPECRIHAKEAIQKNNIMSS 37 (70)
T ss_pred CCCHHHHHHHHHHHHhcCcccc
Confidence 4699999999998886543333
No 72
>PF11150 DUF2927: Protein of unknown function (DUF2927); InterPro: IPR021323 This family is conserved in Proteobacteria. Several members are described as being putative lipoproteins, but otherwise the function is not known.
Probab=23.42 E-value=48 Score=24.28 Aligned_cols=22 Identities=32% Similarity=0.416 Sum_probs=15.1
Q ss_pred CCcCCCCCCCCCCCCCCCCCCc
Q 033176 100 LPVTHRGDDKVSNMFNDDNVNA 121 (125)
Q Consensus 100 ~~~~~~~~~~~~~~fsd~npna 121 (125)
+.-++....-..++|+|||+++
T Consensus 158 LGl~NDs~~~~pSIFNDd~~~~ 179 (213)
T PF11150_consen 158 LGLPNDSPRARPSIFNDDNEFA 179 (213)
T ss_pred cCCccCCCcCCCceeeCCCccc
Confidence 3334444555779999999875
No 73
>PRK07451 translation initiation factor Sui1; Validated
Probab=23.36 E-value=99 Score=20.49 Aligned_cols=10 Identities=30% Similarity=0.468 Sum_probs=5.3
Q ss_pred CHHHHHHHHH
Q 033176 39 DRNKVLKAVR 48 (125)
Q Consensus 39 ~~~~i~~~i~ 48 (125)
+..+|++.|+
T Consensus 66 dlk~LaK~LK 75 (115)
T PRK07451 66 TLAKLLKQLK 75 (115)
T ss_pred HHHHHHHHHH
Confidence 3455555554
No 74
>PRK06824 translation initiation factor Sui1; Validated
Probab=23.24 E-value=1.2e+02 Score=20.21 Aligned_cols=10 Identities=10% Similarity=0.262 Sum_probs=5.1
Q ss_pred CHHHHHHHHH
Q 033176 39 DRNKVLKAVR 48 (125)
Q Consensus 39 ~~~~i~~~i~ 48 (125)
+..+|++.|+
T Consensus 69 dlk~l~K~LK 78 (118)
T PRK06824 69 ALKELAKELK 78 (118)
T ss_pred HHHHHHHHHH
Confidence 3445555554
No 75
>COG0225 MsrA Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=23.20 E-value=56 Score=23.32 Aligned_cols=28 Identities=21% Similarity=0.144 Sum_probs=23.5
Q ss_pred HhHHHHHHHHHhCCCCeeEEEEeCCCCE
Q 033176 4 TGCERVVKNAIYKLRGVDSVEVELELEK 31 (125)
Q Consensus 4 ~~C~~~V~~~L~~~~GV~~v~vd~~~~k 31 (125)
.||-+-+++.+.+++||.++.+-...+.
T Consensus 13 gGCFWg~E~~f~~i~GV~~t~~GYagG~ 40 (174)
T COG0225 13 GGCFWGVEAYFEQIPGVLSTVSGYAGGH 40 (174)
T ss_pred ccCccchHHHHhhCCCeEEEeeeEcCCC
Confidence 5788999999999999999988766543
No 76
>TIGR03406 FeS_long_SufT probable FeS assembly SUF system protein SufT. The function is unknown for this protein family, but members are found almost always in operons for the the SUF system of iron-sulfur cluster biosynthesis. The SUF system is present elsewhere on the chromosome for those few species where SUF genes are not adjacent. This family shares this property of association with the SUF system with a related family, TIGR02945. TIGR02945 consists largely of a DUF59 domain (see Pfam family pfam01883), while this protein is about double the length, with a unique N-terminal domain and DUF59 C-terminal domain. A location immediately downstream of the cysteine desulfurase gene sufS in many contexts suggests the gene symbol sufT. Note that some other homologs of this family and of TIGR02945, but no actual members of this family, are found in operons associated with phenylacetic acid (or other ring-hydroxylating) degradation pathways.
Probab=23.12 E-value=96 Score=21.98 Aligned_cols=21 Identities=38% Similarity=0.514 Sum_probs=17.1
Q ss_pred HHHHHHHHhCCCCeeEEEEeC
Q 033176 7 ERVVKNAIYKLRGVDSVEVEL 27 (125)
Q Consensus 7 ~~~V~~~L~~~~GV~~v~vd~ 27 (125)
...|+.+|..++||.+++|++
T Consensus 133 ~~dV~~aL~~l~gV~~V~V~l 153 (174)
T TIGR03406 133 VEDVEDKVLAVPNVDEVEVEL 153 (174)
T ss_pred HHHHHHHHHhCCCceeEEEEE
Confidence 356889999999999888764
No 77
>TIGR02544 III_secr_YscJ type III secretion apparatus lipoprotein, YscJ/HrcJ family. All members of this protein family are predicted lipoproteins with a conserved Cys near the N-terminus for cleavage and modification, and are part of known or predicted type III secretion systems. Members are found in both plant and animal pathogens, including the obligately intracellular chlamydial species and (non-pathogenic) root nodule bacteria. The most closely related proteins outside this family are examples of the flagellar M-ring protein FliF.
Probab=22.74 E-value=91 Score=22.36 Aligned_cols=21 Identities=24% Similarity=0.427 Sum_probs=17.4
Q ss_pred HHHHHHHHhCCCCeeEEEEeC
Q 033176 7 ERVVKNAIYKLRGVDSVEVEL 27 (125)
Q Consensus 7 ~~~V~~~L~~~~GV~~v~vd~ 27 (125)
+..+.+.|+.++||.++.|.+
T Consensus 109 e~EL~rtI~~i~~V~~ArVhl 129 (193)
T TIGR02544 109 EQRLEQTLSQIDGVISARVHV 129 (193)
T ss_pred HHHHHHHHHhcCCeeeeEEEE
Confidence 467889999999999877765
No 78
>PF13193 AMP-binding_C: AMP-binding enzyme C-terminal domain; PDB: 3L8C_B 2VSQ_A 3R44_A 3RG2_B 3A9U_A 3A9V_A 3NI2_A 1V26_B 1ULT_B 1V25_B ....
Probab=22.68 E-value=1.1e+02 Score=17.53 Aligned_cols=18 Identities=17% Similarity=0.272 Sum_probs=14.3
Q ss_pred HHHHHHhCCCCeeEEEEe
Q 033176 9 VVKNAIYKLRGVDSVEVE 26 (125)
Q Consensus 9 ~V~~~L~~~~GV~~v~vd 26 (125)
.|+.+|.+.+||.++-+-
T Consensus 1 EIE~~l~~~~~V~~~~V~ 18 (73)
T PF13193_consen 1 EIESVLRQHPGVAEAAVV 18 (73)
T ss_dssp HHHHHHHTSTTEEEEEEE
T ss_pred CHHHHHhcCCCccEEEEE
Confidence 378999999999876543
No 79
>PRK11282 glcE glycolate oxidase FAD binding subunit; Provisional
Probab=22.68 E-value=1.7e+02 Score=23.06 Aligned_cols=37 Identities=19% Similarity=0.105 Sum_probs=28.7
Q ss_pred hCCCCeeEEEEeCCCCEEEEEeCCCHHHHHHHHHHcCCc
Q 033176 15 YKLRGVDSVEVELELEKVTAVGYVDRNKVLKAVRRAGKR 53 (125)
Q Consensus 15 ~~~~GV~~v~vd~~~~kvtV~g~~~~~~i~~~i~~~G~~ 53 (125)
.++.+|. ++|.....++|..-+...+|.+.+.+.|..
T Consensus 44 ~~ln~Il--e~d~~~~~vtV~AG~~l~el~~~L~~~G~~ 80 (352)
T PRK11282 44 RAHRGIV--SYDPTELVITARAGTPLAELEAALAEAGQM 80 (352)
T ss_pred ccCCCcE--EEcCCCCEEEECCCCCHHHHHHHHHHcCCe
Confidence 4455553 577778888998778999999999998864
No 80
>cd00292 EF1B Elongation factor 1 beta (EF1B) guanine nucleotide exchange domain. EF1B catalyzes the exchange of GDP bound to the G-protein, EF1A, for GTP, an important step in the elongation cycle of the protein biosynthesis. EF1A binds to and delivers the aminoacyl tRNA to the ribosome. The guanine nucleotide exchange domain of EF1B, which is the alpha subunit in yeast, is responsible for the catalysis of this exchange reaction.
Probab=22.50 E-value=1.1e+02 Score=19.20 Aligned_cols=20 Identities=40% Similarity=0.508 Sum_probs=16.9
Q ss_pred HHHHHHHHhCCCCeeEEEEe
Q 033176 7 ERVVKNAIYKLRGVDSVEVE 26 (125)
Q Consensus 7 ~~~V~~~L~~~~GV~~v~vd 26 (125)
...++.++++.+||+++++.
T Consensus 64 td~lee~i~~~d~VqsveI~ 83 (88)
T cd00292 64 TDELEEAISEEDGVQSVDVE 83 (88)
T ss_pred cHHHHHHHhccCCceEEEEE
Confidence 45788889999999999875
No 81
>PRK11200 grxA glutaredoxin 1; Provisional
Probab=22.40 E-value=1.6e+02 Score=17.41 Aligned_cols=26 Identities=31% Similarity=0.436 Sum_probs=15.5
Q ss_pred CcHhHHHHHHHHHhCC----CCeeEEEEeCC
Q 033176 2 CCTGCERVVKNAIYKL----RGVDSVEVELE 28 (125)
Q Consensus 2 ~C~~C~~~V~~~L~~~----~GV~~v~vd~~ 28 (125)
.|+.|.+ +++.|..+ .|+.-..+|..
T Consensus 10 ~C~~C~~-a~~~L~~l~~~~~~i~~~~idi~ 39 (85)
T PRK11200 10 GCPYCVR-AKELAEKLSEERDDFDYRYVDIH 39 (85)
T ss_pred CChhHHH-HHHHHHhhcccccCCcEEEEECC
Confidence 5899974 45556664 46655555543
No 82
>COG4669 EscJ Type III secretory pathway, lipoprotein EscJ [Intracellular trafficking and secretion]
Probab=22.06 E-value=1.1e+02 Score=23.03 Aligned_cols=20 Identities=30% Similarity=0.454 Sum_probs=16.1
Q ss_pred HHHHHHHHhCCCCeeEEEEe
Q 033176 7 ERVVKNAIYKLRGVDSVEVE 26 (125)
Q Consensus 7 ~~~V~~~L~~~~GV~~v~vd 26 (125)
+..+++.|++++||.++.|.
T Consensus 111 eQ~le~tLs~mDGVi~ArV~ 130 (246)
T COG4669 111 EQQLEQTLSKMDGVISARVH 130 (246)
T ss_pred HHHHHHHHHhcCceEEEEEE
Confidence 57889999999999865543
No 83
>PF08712 Nfu_N: Scaffold protein Nfu/NifU N terminal; InterPro: IPR014824 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This domain is found at the N terminus of NifU (from NIF system) and NifU related proteins, and in the human Nfu protein. Both of these proteins are thought to be involved in the assembly of iron-sulphur clusters, functioning as scaffolds [, ]. ; GO: 0005506 iron ion binding; PDB: 2FFM_A 1PQX_A 2K1H_A.
Probab=21.85 E-value=2.1e+02 Score=17.66 Aligned_cols=39 Identities=21% Similarity=0.302 Sum_probs=26.9
Q ss_pred HHHHHHhCCCCeeEEEEeCCCCEEEEE--eCCCHHHHHHHHHH
Q 033176 9 VVKNAIYKLRGVDSVEVELELEKVTAV--GYVDRNKVLKAVRR 49 (125)
Q Consensus 9 ~V~~~L~~~~GV~~v~vd~~~~kvtV~--g~~~~~~i~~~i~~ 49 (125)
-+-+.|-.++||.+|-+. ..=++|+ ..++-+.|...|..
T Consensus 38 pLA~~Lf~i~gV~~Vf~~--~dfItVtK~~~~~W~~l~~~I~~ 78 (87)
T PF08712_consen 38 PLAQALFAIPGVKSVFIG--DDFITVTKNPDADWEDLKPEIRE 78 (87)
T ss_dssp HHHHHHHTSTTEEEEEEE--TTEEEEEE-TTS-HHHHHHHHHH
T ss_pred HHHHHhcCCCCEeEEEEE--CCEEEEeeCCCCCHHHHHHHHHH
Confidence 344566689999987775 5567776 45788888777654
No 84
>PRK07334 threonine dehydratase; Provisional
Probab=21.51 E-value=3.1e+02 Score=21.77 Aligned_cols=51 Identities=18% Similarity=0.038 Sum_probs=30.7
Q ss_pred HHHHHHHHhCCC-CeeEEEEeCC-----CCEEEEE--e----CCCHHHHHHHHHHcCCceeec
Q 033176 7 ERVVKNAIYKLR-GVDSVEVELE-----LEKVTAV--G----YVDRNKVLKAVRRAGKRAEFW 57 (125)
Q Consensus 7 ~~~V~~~L~~~~-GV~~v~vd~~-----~~kvtV~--g----~~~~~~i~~~i~~~G~~a~~~ 57 (125)
...|-+.|+..+ .|.+++.... .+...+. - ....+.|++.|++.|+.++++
T Consensus 340 L~dI~~~is~~~~nI~~v~~~~~~~~~~~~~~~i~l~i~V~d~~~L~~vi~~Lr~~g~~~~~~ 402 (403)
T PRK07334 340 LARVTALIGEAGANIIEVSHQRLFTDLPAKGAELELVIETRDAAHLQEVIAALRAAGFEARLV 402 (403)
T ss_pred HHHHHHHHhhCCCceEEEEEEecccCCCCCeEEEEEEEEeCCHHHHHHHHHHHHHcCCeeEeC
Confidence 355666776552 2455555432 3443332 1 134568899999999998875
No 85
>cd08623 PI-PLCc_beta1 Catalytic domain of metazoan phosphoinositide-specific phospholipase C-beta1. This subfamily corresponds to the catalytic domain present in metazoan phosphoinositide-specific phospholipase C (PI-PLC, EC 3.1.4.11)-beta isozyme 1. PI-PLC is a signaling enzyme that hydrolyzes the membrane phospholipids phosphatidylinositol-4,5-bisphosphate (PIP2) to generate two important second messengers in eukaryotic signal transduction cascades, Inositol 1,4,5-trisphosphate (InsP3) and diacylglycerol (DAG). InsP3 triggers inflow of calcium from intracellular stores, while DAG, together with calcium, activates protein kinase C, which goes on to phosphorylate other molecules, leading to altered cellular activity. Calcium is required for the catalysis. PLC-beta represents a class of mammalian PI-PLC that has an N-terminal pleckstrin homology (PH) domain, an array of EF hands, a PLC catalytic core domain, a C2 domain, and a unique C-terminal coiled-coil (CT) domain necessary for ho
Probab=21.33 E-value=1.8e+02 Score=22.06 Aligned_cols=47 Identities=11% Similarity=0.193 Sum_probs=32.8
Q ss_pred HHHHHHHHhCCCCeeEEEEeCCCCE-----EEE------EeCCCHHHHHHHHHHcCCcee
Q 033176 7 ERVVKNAIYKLRGVDSVEVELELEK-----VTA------VGYVDRNKVLKAVRRAGKRAE 55 (125)
Q Consensus 7 ~~~V~~~L~~~~GV~~v~vd~~~~k-----vtV------~g~~~~~~i~~~i~~~G~~a~ 55 (125)
+....++|. .|+.-+++|.-.+. -.| +..+..++++++|++..|.+.
T Consensus 32 ~e~y~~aL~--~GcRcvElD~wdG~~~~~ePiV~HG~tlts~i~f~dv~~~I~~~AF~~S 89 (258)
T cd08623 32 VEMYRQVLL--SGCRCVELDCWKGRTAEEEPVITHGFTMTTEISFKEVIEAIAECAFKTS 89 (258)
T ss_pred HHHHHHHHH--cCCCEEEEEeeCCCCCCCCCEEeeCCCcccCcCHHHHHHHHHHHhccCC
Confidence 345566774 68888999876553 223 345888999999999887643
No 86
>PRK10568 periplasmic protein; Provisional
Probab=20.69 E-value=2.4e+02 Score=20.25 Aligned_cols=34 Identities=24% Similarity=0.355 Sum_probs=25.4
Q ss_pred HHHHHHHHHhCCCCee--EEEEeCCCCEEEEEeCCC
Q 033176 6 CERVVKNAIYKLRGVD--SVEVELELEKVTAVGYVD 39 (125)
Q Consensus 6 C~~~V~~~L~~~~GV~--~v~vd~~~~kvtV~g~~~ 39 (125)
=..+|+.+|...+++. .+++....+.|++.|.+.
T Consensus 61 I~~~v~~~L~~~~~i~~~~I~V~v~~G~V~L~G~V~ 96 (203)
T PRK10568 61 ITAKVKAALVDHDNIKSTDISVKTHQKVVTLSGFVE 96 (203)
T ss_pred HHHHHHHHHHhCCCCCCCceEEEEECCEEEEEEEeC
Confidence 3567888887766664 567777899999998754
No 87
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=20.65 E-value=2.8e+02 Score=18.60 Aligned_cols=47 Identities=17% Similarity=0.211 Sum_probs=29.9
Q ss_pred HHHHHHhCCCCeeEEEEeCCCCEEEEEeCCCHHHHHHHHH-----HcCCceee
Q 033176 9 VVKNAIYKLRGVDSVEVELELEKVTAVGYVDRNKVLKAVR-----RAGKRAEF 56 (125)
Q Consensus 9 ~V~~~L~~~~GV~~v~vd~~~~kvtV~g~~~~~~i~~~i~-----~~G~~a~~ 56 (125)
.++..|.++ |-..|+.-+.++-|.++...+...+...|+ ..|+.+..
T Consensus 23 eLr~~l~~~-Gf~~V~Tyi~SGNvvf~~~~~~~~l~~~ie~~l~~~fG~~v~v 74 (137)
T PF08002_consen 23 ELREALEDL-GFTNVRTYIQSGNVVFESDRDPAELAAKIEKALEERFGFDVPV 74 (137)
T ss_dssp HHHHHHHHC-T-EEEEEETTTTEEEEEESS-HHHHHHHHHHHHHHH-TT---E
T ss_pred HHHHHHHHc-CCCCceEEEeeCCEEEecCCChHHHHHHHHHHHHHhcCCCeEE
Confidence 345666665 889999999999999987677776665543 56776543
No 88
>COG3643 Glutamate formiminotransferase [Amino acid transport and metabolism]
Probab=20.62 E-value=2.9e+02 Score=21.15 Aligned_cols=41 Identities=17% Similarity=0.144 Sum_probs=25.5
Q ss_pred HHHHHHHHhCCCCeeEEEE--eCCCCEEEEEeCCCHHHHHHHH
Q 033176 7 ERVVKNAIYKLRGVDSVEV--ELELEKVTAVGYVDRNKVLKAV 47 (125)
Q Consensus 7 ~~~V~~~L~~~~GV~~v~v--d~~~~kvtV~g~~~~~~i~~~i 47 (125)
..+|..+..+.++|.-+++ |....+-.++..-+++++++++
T Consensus 20 ie~i~a~~~~~~~v~ildve~danhNRsViT~vgdp~~~~~A~ 62 (302)
T COG3643 20 IEKIVAAAKSIPTVKILDVEMDANHNRSVITLVGDPSKVVNAA 62 (302)
T ss_pred HHHHHHHHhcCCceEEEEeccCCCCCceEEEEecChHHHHHHH
Confidence 4567777888888875444 4455555555444666666544
No 89
>PF08821 CGGC: CGGC domain; InterPro: IPR014925 Proteins in this entry are a quite highly conserved sequence of CGGC in its central region. The region has many conserved cysteines and histidines suggestive of a zinc binding function.
Probab=20.60 E-value=1.4e+02 Score=19.36 Aligned_cols=18 Identities=11% Similarity=0.141 Sum_probs=11.4
Q ss_pred CHHHHHHHHHHc-CCceee
Q 033176 39 DRNKVLKAVRRA-GKRAEF 56 (125)
Q Consensus 39 ~~~~i~~~i~~~-G~~a~~ 56 (125)
..+++.+.|++. |.++..
T Consensus 86 ~~~~~~~~I~~~~gi~VV~ 104 (107)
T PF08821_consen 86 HIDEIKKIIEEKFGIEVVE 104 (107)
T ss_pred CHHHHHHHHHHHhCCCEee
Confidence 467777777755 765543
No 90
>cd04877 ACT_TyrR N-terminal ACT domain of the TyrR protein. ACT_TyrR: N-terminal ACT domain of the TyrR protein. The TyrR protein of Escherichia coli controls the expression of a group of transcription units (TyrR regulon) whose gene products are involved in the biosynthesis or transport of the aromatic amino acids. Binding to specific DNA sequences known as TyrR boxes, the TyrR protein can either activate or repress transcription at different sigma70 promoters. Its regulatory activity occurs in response to intracellular levels of tyrosine, phenylalanine and tryptophan. The TyrR protein consists of an N-terminal region important for transcription activation with an ATP-independent aromatic amino acid binding site (contained within the ACT domain) and is involved in dimerization; a central region with an ATP binding site, an ATP-dependent aromatic amino acid binding site and is involved in hexamerization; and a helix turn helix DNA binding C-terminal region. In solution, in the absence
Probab=20.49 E-value=1.2e+02 Score=17.61 Aligned_cols=17 Identities=24% Similarity=0.514 Sum_probs=13.5
Q ss_pred HHHHHHHhCCCCeeEEE
Q 033176 8 RVVKNAIYKLRGVDSVE 24 (125)
Q Consensus 8 ~~V~~~L~~~~GV~~v~ 24 (125)
..+-+.|++++||.+|.
T Consensus 52 ~~li~~L~~i~gV~~V~ 68 (74)
T cd04877 52 QTLMPEIRRIDGVEDVK 68 (74)
T ss_pred HHHHHHHhCCCCceEEE
Confidence 46677889999998775
No 91
>PF00736 EF1_GNE: EF-1 guanine nucleotide exchange domain; InterPro: IPR014038 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) []. This entry represents the guanine nucleotide exchange domain of the beta (EF-1beta, also known as EF1B-alpha) and delta (EF-1delta, also known as EF1B-beta) chains of EF1B proteins from eukaryotes and archaea. The beta and delta chains have exchange activity, which mainly resides in their homologous guanine nucleotide exchange domains, found in the C-terminal region of the peptides. Their N-terminal regions may be involved in interactions with the gamma chain (EF-1gamma). More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0003746 translation elongation factor activity, 0006414 translational elongation, 0005853 eukaryotic translation elongation factor 1 complex; PDB: 2YY3_B 1GH8_A 1B64_A 1IJE_B 1IJF_B 1F60_B 1G7C_B 2B7B_B 2B7C_B.
Probab=20.40 E-value=1.6e+02 Score=18.43 Aligned_cols=21 Identities=38% Similarity=0.419 Sum_probs=17.3
Q ss_pred HHHHHHHHH-hCCCCeeEEEEe
Q 033176 6 CERVVKNAI-YKLRGVDSVEVE 26 (125)
Q Consensus 6 C~~~V~~~L-~~~~GV~~v~vd 26 (125)
-...|+.+| ...+||+++++.
T Consensus 63 ~~d~lee~i~~~~e~Vqsvei~ 84 (89)
T PF00736_consen 63 STDDLEEAIESFEEGVQSVEIE 84 (89)
T ss_dssp GHHHHHHHHTTCTTTEEEEEEE
T ss_pred ChHHHHHHHHhcCCCccEEEEE
Confidence 356788888 899999999875
Done!