Query 031710
Match_columns 154
No_of_seqs 278 out of 1395
Neff 7.8
Searched_HMMs 46136
Date Fri Mar 29 04:17:31 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031710.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031710hhsearch_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 99.5 5.4E-14 1.2E-18 87.7 8.3 58 30-88 1-62 (62)
2 COG2608 CopZ Copper chaperone 99.4 7.7E-13 1.7E-17 85.2 8.6 66 26-92 1-70 (71)
3 KOG1603 Copper chaperone [Inor 99.4 7.8E-13 1.7E-17 85.5 8.5 68 25-93 3-71 (73)
4 KOG4656 Copper chaperone for s 99.1 6.8E-10 1.5E-14 84.0 8.2 69 27-96 7-75 (247)
5 PLN02957 copper, zinc superoxi 98.6 5.7E-07 1.2E-11 70.4 10.3 72 26-98 5-76 (238)
6 PRK10671 copA copper exporting 98.5 3.4E-07 7.4E-12 83.0 8.2 64 27-93 3-67 (834)
7 COG2217 ZntA Cation transport 98.3 2.5E-06 5.3E-11 76.0 7.8 63 27-91 2-69 (713)
8 TIGR00003 copper ion binding p 98.1 3.7E-05 8E-10 45.1 8.4 62 27-89 2-67 (68)
9 KOG0207 Cation transport ATPas 97.7 0.00012 2.6E-09 66.1 7.2 67 27-94 146-216 (951)
10 PRK10671 copA copper exporting 97.6 0.0003 6.6E-09 64.0 8.2 64 28-92 100-164 (834)
11 KOG0207 Cation transport ATPas 97.4 0.00055 1.2E-08 62.0 7.0 68 26-94 68-139 (951)
12 PRK11033 zntA zinc/cadmium/mer 97.3 0.00099 2.1E-08 60.0 7.8 66 26-92 52-119 (741)
13 TIGR02052 MerP mercuric transp 95.4 0.32 7E-06 30.6 9.2 64 27-91 23-90 (92)
14 COG1888 Uncharacterized protei 93.0 1.1 2.4E-05 30.0 7.6 68 26-94 5-81 (97)
15 PF02680 DUF211: Uncharacteriz 91.0 1.7 3.6E-05 29.4 6.7 66 26-93 4-78 (95)
16 PRK13748 putative mercuric red 90.6 1.8 3.9E-05 37.5 8.6 64 30-94 3-69 (561)
17 cd00371 HMA Heavy-metal-associ 90.3 1.5 3.3E-05 22.6 7.3 55 31-86 2-59 (63)
18 PF01206 TusA: Sulfurtransfera 89.7 1.4 3.1E-05 27.3 5.4 54 30-93 2-58 (70)
19 PF01883 DUF59: Domain of unkn 82.9 2.8 6E-05 26.1 4.0 33 27-59 34-72 (72)
20 PRK11018 hypothetical protein; 81.3 8.1 0.00018 24.7 5.9 55 29-91 9-64 (78)
21 cd03421 SirA_like_N SirA_like_ 80.6 5.9 0.00013 24.3 4.9 51 31-92 2-55 (67)
22 PRK10553 assembly protein for 78.0 13 0.00028 24.6 6.1 43 40-82 18-61 (87)
23 PRK11152 ilvM acetolactate syn 73.7 6.6 0.00014 25.3 3.7 56 2-59 15-75 (76)
24 cd03420 SirA_RHOD_Pry_redox Si 71.7 16 0.00034 22.7 5.1 53 31-93 2-57 (69)
25 PRK14054 methionine sulfoxide 71.2 16 0.00034 27.4 5.7 45 38-82 10-76 (172)
26 PF03927 NapD: NapD protein; 71.1 25 0.00054 22.6 6.4 41 41-82 17-58 (79)
27 PF14437 MafB19-deam: MafB19-l 68.9 15 0.00033 26.7 5.1 40 27-67 100-141 (146)
28 PRK11198 LysM domain/BON super 68.6 15 0.00032 26.5 5.0 48 39-86 26-74 (147)
29 cd03423 SirA SirA (also known 68.3 25 0.00055 21.7 5.5 53 31-93 2-57 (69)
30 cd03422 YedF YedF is a bacteri 67.0 23 0.00049 22.0 5.1 54 31-92 2-56 (69)
31 cd00291 SirA_YedF_YeeD SirA, Y 66.7 26 0.00056 21.2 5.4 53 31-93 2-57 (69)
32 PRK00299 sulfur transfer prote 65.1 34 0.00074 22.0 5.9 54 28-91 9-65 (81)
33 TIGR02945 SUF_assoc FeS assemb 62.4 11 0.00023 25.0 3.1 35 28-62 40-78 (99)
34 COG2151 PaaD Predicted metal-s 60.6 16 0.00035 25.3 3.8 32 30-61 52-89 (111)
35 cd02410 archeal_CPSF_KH The ar 59.4 37 0.00081 24.7 5.6 59 38-96 52-116 (145)
36 TIGR03406 FeS_long_SufT probab 57.1 16 0.00034 27.4 3.5 33 29-61 115-153 (174)
37 PF08821 CGGC: CGGC domain; I 56.7 17 0.00037 24.9 3.4 66 22-91 26-104 (107)
38 COG2177 FtsX Cell division pro 56.6 52 0.0011 26.7 6.6 47 29-88 63-109 (297)
39 PF13732 DUF4162: Domain of un 55.8 49 0.0011 20.8 5.7 43 48-92 26-69 (84)
40 PF14492 EFG_II: Elongation Fa 55.1 51 0.0011 20.7 6.1 54 38-91 15-73 (75)
41 PRK13014 methionine sulfoxide 53.3 36 0.00079 25.8 4.9 36 25-65 7-42 (186)
42 PRK00058 methionine sulfoxide 52.3 57 0.0012 25.3 5.9 34 26-64 45-78 (213)
43 COG0425 SirA Predicted redox p 50.6 65 0.0014 20.6 5.7 49 28-86 5-56 (78)
44 PRK06418 transcription elongat 50.1 1E+02 0.0023 22.9 7.1 69 26-94 5-98 (166)
45 PRK05528 methionine sulfoxide 49.6 22 0.00047 26.2 3.1 45 38-82 8-69 (156)
46 PF05046 Img2: Mitochondrial l 49.5 72 0.0016 20.9 6.7 60 26-87 27-87 (87)
47 TIGR03527 selenium_YedF seleni 48.8 49 0.0011 25.1 5.1 51 34-92 5-55 (194)
48 PF04972 BON: BON domain; Int 48.6 15 0.00032 22.0 1.9 30 42-72 2-34 (64)
49 PF09580 Spore_YhcN_YlaJ: Spor 46.8 72 0.0016 23.2 5.7 45 38-82 74-123 (177)
50 COG4492 PheB ACT domain-contai 44.8 39 0.00085 24.4 3.7 22 38-59 125-146 (150)
51 cd04888 ACT_PheB-BS C-terminal 44.7 70 0.0015 19.3 5.1 34 26-59 40-74 (76)
52 PRK11023 outer membrane lipopr 41.7 98 0.0021 23.2 5.8 43 38-80 126-170 (191)
53 PF08712 Nfu_N: Scaffold prote 41.2 1E+02 0.0022 20.1 5.2 39 42-82 37-77 (87)
54 TIGR00489 aEF-1_beta translati 38.7 61 0.0013 21.5 3.7 23 38-60 61-83 (88)
55 PRK13562 acetolactate synthase 38.6 1.1E+02 0.0025 20.0 5.0 61 2-62 14-80 (84)
56 PF09158 MotCF: Bacteriophage 38.5 81 0.0018 21.6 4.3 40 50-91 39-78 (103)
57 PHA01634 hypothetical protein 38.1 11 0.00023 27.3 -0.0 16 31-46 93-109 (156)
58 COG4004 Uncharacterized protei 36.8 73 0.0016 21.4 3.8 22 49-70 37-58 (96)
59 COG2092 EFB1 Translation elong 36.7 67 0.0014 21.4 3.6 34 27-60 49-83 (88)
60 PRK11023 outer membrane lipopr 36.4 95 0.0021 23.3 5.0 47 36-82 46-95 (191)
61 PRK08178 acetolactate synthase 36.0 1.1E+02 0.0023 20.7 4.6 57 1-59 19-80 (96)
62 COG3062 NapD Uncharacterized p 35.0 1.4E+02 0.0031 20.0 5.4 43 39-82 18-61 (94)
63 COG1084 Predicted GTPase [Gene 34.9 1.1E+02 0.0023 25.6 5.3 49 41-98 151-201 (346)
64 PRK09577 multidrug efflux prot 34.9 1.2E+02 0.0026 28.9 6.4 45 41-86 158-210 (1032)
65 PF13291 ACT_4: ACT domain; PD 33.5 1.2E+02 0.0026 18.7 4.7 35 24-58 45-79 (80)
66 COG3643 Glutamate formiminotra 33.0 71 0.0015 25.5 3.8 49 41-89 20-70 (302)
67 PRK04435 hypothetical protein; 32.9 1E+02 0.0022 22.1 4.5 33 27-59 110-143 (147)
68 PF01625 PMSR: Peptide methion 32.8 73 0.0016 23.3 3.7 27 38-64 7-33 (155)
69 PRK10555 aminoglycoside/multid 32.7 1.2E+02 0.0026 28.9 6.0 44 41-85 159-210 (1037)
70 PRK05550 bifunctional methioni 32.2 1.4E+02 0.003 24.2 5.5 27 38-64 134-160 (283)
71 COG2761 FrnE Predicted dithiol 32.0 1.2E+02 0.0025 23.8 4.9 39 26-64 3-46 (225)
72 PRK07334 threonine dehydratase 31.1 2.7E+02 0.0058 23.3 7.3 64 28-92 326-402 (403)
73 PF00352 TBP: Transcription fa 31.0 80 0.0017 20.3 3.4 22 61-82 55-76 (86)
74 PF13740 ACT_6: ACT domain; PD 30.8 1.4E+02 0.0029 18.5 5.4 55 28-82 2-63 (76)
75 COG0225 MsrA Peptide methionin 30.5 63 0.0014 24.2 3.1 35 25-64 5-39 (174)
76 cd04902 ACT_3PGDH-xct C-termin 30.1 92 0.002 18.5 3.4 31 25-59 39-70 (73)
77 PRK00435 ef1B elongation facto 29.8 59 0.0013 21.5 2.5 23 38-60 61-83 (88)
78 PF13192 Thioredoxin_3: Thiore 29.5 75 0.0016 19.7 2.9 10 33-42 6-15 (76)
79 PF08002 DUF1697: Protein of u 29.1 2.1E+02 0.0046 20.2 6.0 49 42-91 22-74 (137)
80 PF13383 Methyltransf_22: Meth 28.7 1.1E+02 0.0024 24.0 4.3 56 30-96 167-229 (242)
81 KOG3411 40S ribosomal protein 27.3 55 0.0012 23.5 2.1 42 38-82 97-139 (143)
82 PF03434 DUF276: DUF276 ; Int 27.1 94 0.002 24.7 3.6 30 40-69 88-117 (291)
83 cd04877 ACT_TyrR N-terminal AC 27.0 1.3E+02 0.0028 18.4 3.7 16 42-57 52-67 (74)
84 TIGR00401 msrA methionine-S-su 26.7 49 0.0011 24.1 1.9 27 38-64 7-33 (149)
85 PF13216 DUF4024: Protein of u 26.0 23 0.00049 18.8 0.0 11 140-150 9-19 (35)
86 PF01514 YscJ_FliF: Secretory 25.7 76 0.0017 24.2 2.9 21 41-61 117-137 (206)
87 TIGR01676 GLDHase galactonolac 25.7 1.2E+02 0.0027 26.8 4.5 39 48-89 110-148 (541)
88 TIGR02830 spore_III_AG stage I 25.4 66 0.0014 24.4 2.4 29 40-68 62-92 (186)
89 PRK15127 multidrug efflux syst 25.2 2E+02 0.0043 27.5 6.0 44 41-85 159-210 (1049)
90 PF13193 AMP-binding_C: AMP-bi 25.1 80 0.0017 19.2 2.5 40 43-82 1-45 (73)
91 PF08777 RRM_3: RNA binding mo 24.9 2.2E+02 0.0048 19.1 6.1 55 30-85 3-60 (105)
92 TIGR00915 2A0602 The (Largely 24.9 2E+02 0.0043 27.5 6.0 43 41-84 159-209 (1044)
93 cd04887 ACT_MalLac-Enz ACT_Mal 24.7 1.6E+02 0.0036 17.5 4.1 35 25-59 38-72 (74)
94 COG4669 EscJ Type III secretor 24.2 78 0.0017 25.1 2.7 21 39-59 109-129 (246)
95 PF01849 NAC: NAC domain; Int 24.0 92 0.002 18.5 2.5 21 49-69 14-34 (58)
96 PRK15078 polysaccharide export 23.8 1.9E+02 0.0041 24.2 5.1 56 30-86 133-202 (379)
97 PF12685 SpoIIIAH: SpoIIIAH-li 23.7 2E+02 0.0044 21.5 4.9 48 41-89 137-190 (196)
98 TIGR03675 arCOG00543 arCOG0054 23.0 2.1E+02 0.0047 25.7 5.5 62 36-97 67-134 (630)
99 COG0178 UvrA Excinuclease ATPa 22.9 36 0.00079 31.7 0.7 37 2-42 699-738 (935)
100 TIGR02159 PA_CoA_Oxy4 phenylac 22.8 1.1E+02 0.0025 22.0 3.2 56 29-87 27-88 (146)
101 PF04805 Pox_E10: E10-like pro 22.2 77 0.0017 20.0 1.9 23 34-56 15-37 (70)
102 TIGR00914 2A0601 heavy metal e 22.1 1.4E+02 0.003 28.5 4.3 55 28-82 683-751 (1051)
103 cd06167 LabA_like LabA_like pr 21.9 1.3E+02 0.0029 20.8 3.4 29 66-95 104-132 (149)
104 TIGR02898 spore_YhcN_YlaJ spor 21.8 3.3E+02 0.0072 20.0 5.9 31 39-69 54-84 (158)
105 KOG4730 D-arabinono-1, 4-lacto 21.7 1.1E+02 0.0025 26.6 3.4 61 23-89 73-136 (518)
106 PF07837 FTCD_N: Formiminotran 21.0 3.1E+02 0.0067 20.6 5.2 42 40-81 17-60 (178)
107 COG1094 Predicted RNA-binding 21.0 2.6E+02 0.0057 21.4 4.9 35 42-77 27-64 (194)
108 TIGR03143 AhpF_homolog putativ 20.7 4.1E+02 0.0088 23.2 6.8 27 29-55 478-509 (555)
109 PF13710 ACT_5: ACT domain; PD 20.6 92 0.002 18.9 2.0 56 1-57 3-63 (63)
110 PF00873 ACR_tran: AcrB/AcrD/A 20.6 2.1E+02 0.0045 27.1 5.2 42 42-84 63-108 (1021)
111 PRK10568 periplasmic protein; 20.4 2.5E+02 0.0055 21.2 4.9 40 34-73 55-96 (203)
112 PRK11670 antiporter inner memb 20.2 4.5E+02 0.0098 21.8 6.7 56 41-97 67-147 (369)
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=99.54 E-value=5.4e-14 Score=87.72 Aligned_cols=58 Identities=34% Similarity=0.611 Sum_probs=54.0
Q ss_pred EEEE-cCCCHhHHHHHHHHHhCCCCceEEEEeCCCcEEEEEec---CCHHHHHHHHHHhhCCc
Q 031710 30 EVKV-RIDCEGCERKVKRAVEGMKGVKQVDVERKANKVTVVGY---VEPSKVVSRIAHRTGKK 88 (154)
Q Consensus 30 ~l~V-gm~C~~C~~kI~kal~~~~GV~~v~vd~~~~~v~V~g~---~~~~~v~~~i~~~~G~~ 88 (154)
+|+| ||+|++|+.+|+++|.+++||.++.+|+.+++++|.+. +++++|.++|+ ++||+
T Consensus 1 t~~v~~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~~~~~~~i~~~i~-~~Gy~ 62 (62)
T PF00403_consen 1 TFKVPGMTCEGCAKKVEKALSKLPGVKSVKVDLETKTVTVTYDPDKTSIEKIIEAIE-KAGYE 62 (62)
T ss_dssp EEEEESTTSHHHHHHHHHHHHTSTTEEEEEEETTTTEEEEEESTTTSCHHHHHHHHH-HTTSE
T ss_pred CEEECCcccHHHHHHHHHHHhcCCCCcEEEEECCCCEEEEEEecCCCCHHHHHHHHH-HhCcC
Confidence 5889 99999999999999999999999999999999999965 46799999999 99984
No 2
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.45 E-value=7.7e-13 Score=85.15 Aligned_cols=66 Identities=29% Similarity=0.493 Sum_probs=58.9
Q ss_pred ceEEEEEE-cCCCHhHHHHHHHHHhCCCCceEEEEeCCCcEEEEE--e-cCCHHHHHHHHHHhhCCceEec
Q 031710 26 LQTVEVKV-RIDCEGCERKVKRAVEGMKGVKQVDVERKANKVTVV--G-YVEPSKVVSRIAHRTGKKAEIW 92 (154)
Q Consensus 26 ~~~~~l~V-gm~C~~C~~kI~kal~~~~GV~~v~vd~~~~~v~V~--g-~~~~~~v~~~i~~~~G~~a~~~ 92 (154)
|++..|+| +|+|.+|+.+|+++|.+++||.++++|+..++++|+ + .++.++|.++|+ ++||.+..+
T Consensus 1 ~~~~~l~v~~MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~-~aGy~~~~~ 70 (71)
T COG2608 1 MMKTTLKVEGMTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIE-DAGYKVEEI 70 (71)
T ss_pred CceEEEEECCcCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHH-HcCCCeeec
Confidence 45678999 999999999999999999999999999999776665 4 479999999999 999988764
No 3
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.44 E-value=7.8e-13 Score=85.53 Aligned_cols=68 Identities=49% Similarity=0.920 Sum_probs=62.7
Q ss_pred CceEEEEEEcCCCHhHHHHHHHHHhCCCCceEEEEeCCCcEEEEEecCCHHHHHHHHHHhhC-CceEecc
Q 031710 25 QLQTVEVKVRIDCEGCERKVKRAVEGMKGVKQVDVERKANKVTVVGYVEPSKVVSRIAHRTG-KKAEIWP 93 (154)
Q Consensus 25 ~~~~~~l~Vgm~C~~C~~kI~kal~~~~GV~~v~vd~~~~~v~V~g~~~~~~v~~~i~~~~G-~~a~~~~ 93 (154)
.+++.++++.|+|.+|+.+|++.|+.++||.++.+|...++++|.|.+++..|++.|+ +.| +++++|.
T Consensus 3 ~~~~~v~kv~~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~-k~~~k~~~~~~ 71 (73)
T KOG1603|consen 3 PIKTVVLKVNMHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLK-KTGGKRAELWK 71 (73)
T ss_pred CccEEEEEECcccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHH-hcCCCceEEec
Confidence 4567788899999999999999999999999999999999999999999999999999 677 8888775
No 4
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=99.07 E-value=6.8e-10 Score=84.05 Aligned_cols=69 Identities=28% Similarity=0.486 Sum_probs=64.4
Q ss_pred eEEEEEEcCCCHhHHHHHHHHHhCCCCceEEEEeCCCcEEEEEecCCHHHHHHHHHHhhCCceEecccCC
Q 031710 27 QTVEVKVRIDCEGCERKVKRAVEGMKGVKQVDVERKANKVTVVGYVEPSKVVSRIAHRTGKKAEIWPYVP 96 (154)
Q Consensus 27 ~~~~l~Vgm~C~~C~~kI~kal~~~~GV~~v~vd~~~~~v~V~g~~~~~~v~~~i~~~~G~~a~~~~~~p 96 (154)
-+.+|.|.|+|++|+..|++.|..++||.+|+||++++.|.|.+...+.+|...|+ .+|.+|.+....-
T Consensus 7 ~~~efaV~M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~ts~p~s~i~~~le-~tGr~Avl~G~G~ 75 (247)
T KOG4656|consen 7 YEAEFAVQMTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVETSVPPSEIQNTLE-NTGRDAVLRGAGK 75 (247)
T ss_pred eeEEEEEechhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEccCChHHHHHHHH-hhChheEEecCCc
Confidence 45689999999999999999999999999999999999999999999999999999 9999999877643
No 5
>PLN02957 copper, zinc superoxide dismutase
Probab=98.59 E-value=5.7e-07 Score=70.43 Aligned_cols=72 Identities=29% Similarity=0.448 Sum_probs=63.4
Q ss_pred ceEEEEEEcCCCHhHHHHHHHHHhCCCCceEEEEeCCCcEEEEEecCCHHHHHHHHHHhhCCceEecccCCCC
Q 031710 26 LQTVEVKVRIDCEGCERKVKRAVEGMKGVKQVDVERKANKVTVVGYVEPSKVVSRIAHRTGKKAEIWPYVPYD 98 (154)
Q Consensus 26 ~~~~~l~Vgm~C~~C~~kI~kal~~~~GV~~v~vd~~~~~v~V~g~~~~~~v~~~i~~~~G~~a~~~~~~p~~ 98 (154)
.++++|.++|+|+.|+.+|+++|.+++||..+.+|+..++++|........+.+.|+ ++||.++++...+.+
T Consensus 5 ~~~~~~~VgMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~~~~~~I~~aIe-~~Gy~a~~~~~~~~~ 76 (238)
T PLN02957 5 ELLTEFMVDMKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGSSPVKAMTAALE-QTGRKARLIGQGDPE 76 (238)
T ss_pred cEEEEEEECccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEecCCHHHHHHHHH-HcCCcEEEecCCCcc
Confidence 345678889999999999999999999999999999999999987778899999999 999999888764433
No 6
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.52 E-value=3.4e-07 Score=82.96 Aligned_cols=64 Identities=25% Similarity=0.477 Sum_probs=57.2
Q ss_pred eEEEEEE-cCCCHhHHHHHHHHHhCCCCceEEEEeCCCcEEEEEecCCHHHHHHHHHHhhCCceEecc
Q 031710 27 QTVEVKV-RIDCEGCERKVKRAVEGMKGVKQVDVERKANKVTVVGYVEPSKVVSRIAHRTGKKAEIWP 93 (154)
Q Consensus 27 ~~~~l~V-gm~C~~C~~kI~kal~~~~GV~~v~vd~~~~~v~V~g~~~~~~v~~~i~~~~G~~a~~~~ 93 (154)
++++|.| ||+|.+|+.+|+++|++++||..+.+|+. +.+|.+..+.+.+.+.|+ +.||.++...
T Consensus 3 ~~~~l~V~gmtC~~C~~~i~~al~~~~gv~~v~v~~~--~~~v~~~~~~~~i~~~i~-~~Gy~~~~~~ 67 (834)
T PRK10671 3 QTIDLTLDGLSCGHCVKRVKESLEQRPDVEQADVSIT--EAHVTGTASAEALIETIK-QAGYDASVSH 67 (834)
T ss_pred eEEEEEECCcccHHHHHHHHHHHhcCCCcceEEEeee--EEEEEecCCHHHHHHHHH-hcCCcccccc
Confidence 5688999 99999999999999999999999999995 455666679999999999 9999998754
No 7
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.29 E-value=2.5e-06 Score=76.04 Aligned_cols=63 Identities=24% Similarity=0.556 Sum_probs=56.6
Q ss_pred eEEEEEE-cCCCHhHHHHHHHHHhCCCCceEEEEeCCCcEEEEEec---CC-HHHHHHHHHHhhCCceEe
Q 031710 27 QTVEVKV-RIDCEGCERKVKRAVEGMKGVKQVDVERKANKVTVVGY---VE-PSKVVSRIAHRTGKKAEI 91 (154)
Q Consensus 27 ~~~~l~V-gm~C~~C~~kI~kal~~~~GV~~v~vd~~~~~v~V~g~---~~-~~~v~~~i~~~~G~~a~~ 91 (154)
.+.+|.| ||+|..|+.+|| +|++++||.++.+|+.++++.|..+ .+ .+++.+.++ +.||.+..
T Consensus 2 ~~~~l~v~Gm~Ca~C~~~ie-~l~~~~gV~~~~vn~~t~~~~v~~~~~~~~~~~~~~~~v~-~~gy~~~~ 69 (713)
T COG2217 2 RETSLSVEGMTCAACASRIE-ALNKLPGVEEARVNLATERATVVYDPEEVDLPADIVAAVE-KAGYSARL 69 (713)
T ss_pred ceeEEeecCcCcHHHHHHHH-HHhcCCCeeEEEeecccceEEEEecccccccHHHHHHHHH-hcCccccc
Confidence 4568999 999999999999 9999999999999999999999843 45 789999999 99998765
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=98.13 E-value=3.7e-05 Score=45.12 Aligned_cols=62 Identities=24% Similarity=0.387 Sum_probs=51.7
Q ss_pred eEEEEEE-cCCCHhHHHHHHHHHhCCCCceEEEEeCCCcEEEEEe---cCCHHHHHHHHHHhhCCce
Q 031710 27 QTVEVKV-RIDCEGCERKVKRAVEGMKGVKQVDVERKANKVTVVG---YVEPSKVVSRIAHRTGKKA 89 (154)
Q Consensus 27 ~~~~l~V-gm~C~~C~~kI~kal~~~~GV~~v~vd~~~~~v~V~g---~~~~~~v~~~i~~~~G~~a 89 (154)
++..+.| +++|..|...+++.+...+++..+.+++...++.+.. ..+...+...+. ..|+.+
T Consensus 2 ~~~~~~v~~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~g~~~ 67 (68)
T TIGR00003 2 QKFTVQVMSMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAIL-DAGYEV 67 (68)
T ss_pred cEEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHH-HcCCCc
Confidence 4567999 9999999999999999999999999999999888873 246777777777 777653
No 9
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.69 E-value=0.00012 Score=66.09 Aligned_cols=67 Identities=28% Similarity=0.554 Sum_probs=61.1
Q ss_pred eEEEEEE-cCCCHhHHHHHHHHHhCCCCceEEEEeCCCcEEEEEe---cCCHHHHHHHHHHhhCCceEeccc
Q 031710 27 QTVEVKV-RIDCEGCERKVKRAVEGMKGVKQVDVERKANKVTVVG---YVEPSKVVSRIAHRTGKKAEIWPY 94 (154)
Q Consensus 27 ~~~~l~V-gm~C~~C~~kI~kal~~~~GV~~v~vd~~~~~v~V~g---~~~~~~v~~~i~~~~G~~a~~~~~ 94 (154)
+++.|.| ||.|.+|..+|++.|.+++||.++++++.++++.|.. .+.+.++.+.|+ .+|+.+.+...
T Consensus 146 ~~i~L~v~g~~c~s~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~~~~~pr~i~k~ie-~~~~~~~~~~~ 216 (951)
T KOG0207|consen 146 QKIYLDVLGMTCASCVSKIESILERLRGVKSFSVSLATDTAIVVYDPEITGPRDIIKAIE-ETGFEASVRPY 216 (951)
T ss_pred CcEEEEeecccccchhhhhHHHHhhccCeeEEEEeccCCceEEEecccccChHHHHHHHH-hhcccceeeec
Confidence 6789999 9999999999999999999999999999999999874 378999999999 99998777654
No 10
>PRK10671 copA copper exporting ATPase; Provisional
Probab=97.57 E-value=0.0003 Score=64.00 Aligned_cols=64 Identities=23% Similarity=0.478 Sum_probs=57.0
Q ss_pred EEEEEE-cCCCHhHHHHHHHHHhCCCCceEEEEeCCCcEEEEEecCCHHHHHHHHHHhhCCceEec
Q 031710 28 TVEVKV-RIDCEGCERKVKRAVEGMKGVKQVDVERKANKVTVVGYVEPSKVVSRIAHRTGKKAEIW 92 (154)
Q Consensus 28 ~~~l~V-gm~C~~C~~kI~kal~~~~GV~~v~vd~~~~~v~V~g~~~~~~v~~~i~~~~G~~a~~~ 92 (154)
++.+.+ ||+|.+|...|++.+.+++||.++.+++.++++.+.+..+++++.+.++ +.||.+.++
T Consensus 100 ~~~l~V~Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~~~s~~~I~~~I~-~~Gy~a~~~ 164 (834)
T PRK10671 100 SQQLLLSGMSCASCVSRVQNALQSVPGVTQARVNLAERTALVMGSASPQDLVQAVE-KAGYGAEAI 164 (834)
T ss_pred eEEEEeCCcCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEccCCHHHHHHHHH-hcCCCcccc
Confidence 567889 9999999999999999999999999999999988876668888888998 999987644
No 11
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.37 E-value=0.00055 Score=62.00 Aligned_cols=68 Identities=22% Similarity=0.381 Sum_probs=61.2
Q ss_pred ceEEEEEE-cCCCHhHHHHHHHHHhCCCCceEEEEeCCCcEEEEEe---cCCHHHHHHHHHHhhCCceEeccc
Q 031710 26 LQTVEVKV-RIDCEGCERKVKRAVEGMKGVKQVDVERKANKVTVVG---YVEPSKVVSRIAHRTGKKAEIWPY 94 (154)
Q Consensus 26 ~~~~~l~V-gm~C~~C~~kI~kal~~~~GV~~v~vd~~~~~v~V~g---~~~~~~v~~~i~~~~G~~a~~~~~ 94 (154)
..+..|.+ ||+|..|...|++.|++++||.++.+.+...+..+.. .+.++.+.+.++ +.|+.+++...
T Consensus 68 ~~~~~l~v~GmtC~scv~~i~~~l~~~~gv~~~~val~~~~~~v~~dp~v~s~~~~~e~ie-~~gf~a~~i~~ 139 (951)
T KOG0207|consen 68 ASKCYLSVNGMTCASCVATIERNLRKIEGVESAVVALSASKAEVIYDPAVTSPDSIAESIE-DLGFSAELIES 139 (951)
T ss_pred cceeEEEecCceeHHHHHHHHHHhhccCCcceEEEEeeccceeEEECCcccCchhHHHHHH-hcCccceehhc
Confidence 34678999 9999999999999999999999999999999999873 378999999999 99999988765
No 12
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=97.29 E-value=0.00099 Score=60.04 Aligned_cols=66 Identities=30% Similarity=0.342 Sum_probs=54.2
Q ss_pred ceEEEEEE-cCCCHhHHHHHHHHHhCCCCceEEEEeCCCcEEEEEec-CCHHHHHHHHHHhhCCceEec
Q 031710 26 LQTVEVKV-RIDCEGCERKVKRAVEGMKGVKQVDVERKANKVTVVGY-VEPSKVVSRIAHRTGKKAEIW 92 (154)
Q Consensus 26 ~~~~~l~V-gm~C~~C~~kI~kal~~~~GV~~v~vd~~~~~v~V~g~-~~~~~v~~~i~~~~G~~a~~~ 92 (154)
-.++.+.+ +|+|.+|..++++++.+++||..+.+++.++++.+... ...+++.+.++ +.||.+..+
T Consensus 52 ~~r~~l~V~Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~~~~I~~aI~-~~Gy~a~~~ 119 (741)
T PRK11033 52 GTRYSWKVSGMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDIRAQVESAVQ-KAGFSLRDE 119 (741)
T ss_pred CceEEEEECCCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccchHHHHHHHH-hcccccccc
Confidence 45678899 99999999999999999999999999999998887632 12267778888 889876544
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=95.42 E-value=0.32 Score=30.63 Aligned_cols=64 Identities=22% Similarity=0.357 Sum_probs=48.5
Q ss_pred eEEEEEE-cCCCHhHHHHHHHHHhCCCCceEEEEeCCCcEEEEEe---cCCHHHHHHHHHHhhCCceEe
Q 031710 27 QTVEVKV-RIDCEGCERKVKRAVEGMKGVKQVDVERKANKVTVVG---YVEPSKVVSRIAHRTGKKAEI 91 (154)
Q Consensus 27 ~~~~l~V-gm~C~~C~~kI~kal~~~~GV~~v~vd~~~~~v~V~g---~~~~~~v~~~i~~~~G~~a~~ 91 (154)
.++.+.+ ++.|..|...++..+...+++....++.....+.+.. ..+...+...+. ..|+.+++
T Consensus 23 ~~~~~~~~~~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~g~~~~~ 90 (92)
T TIGR02052 23 QTVTLEVPGMTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATT-DAGYPSSL 90 (92)
T ss_pred eEEEEEECCeEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHH-hcCCCeEe
Confidence 3556888 9999999999999999999988888888777765541 245666656666 77776554
No 14
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=93.04 E-value=1.1 Score=29.99 Aligned_cols=68 Identities=13% Similarity=0.204 Sum_probs=44.3
Q ss_pred ceEEEEEE-cCCCHhHHHHHHHHHhCCCCceEEEE-----eCC--CcEEEEEec-CCHHHHHHHHHHhhCCceEeccc
Q 031710 26 LQTVEVKV-RIDCEGCERKVKRAVEGMKGVKQVDV-----ERK--ANKVTVVGY-VEPSKVVSRIAHRTGKKAEIWPY 94 (154)
Q Consensus 26 ~~~~~l~V-gm~C~~C~~kI~kal~~~~GV~~v~v-----d~~--~~~v~V~g~-~~~~~v~~~i~~~~G~~a~~~~~ 94 (154)
..++.|.| .-+-.--.--+-+.|++++||+.|.+ |.. +-+++|.|. ++-++|.+.|+ +.|-.++.+..
T Consensus 5 iRRlVLDvlKP~~~p~ive~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE-~~Gg~IHSiDe 81 (97)
T COG1888 5 IRRLVLDVLKPHRGPTIVELALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIE-ELGGAIHSIDE 81 (97)
T ss_pred ceeeeeeecCCcCCCcHHHHHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHH-HcCCeeeehhh
Confidence 44556666 33322234455677888888876654 333 345666664 89999999999 99977665543
No 15
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=90.95 E-value=1.7 Score=29.35 Aligned_cols=66 Identities=12% Similarity=0.262 Sum_probs=43.7
Q ss_pred ceEEEEEE-cCCCHhHHHHHHHHHhCCCCceEEEE-----eCCCcEEE--EEec-CCHHHHHHHHHHhhCCceEecc
Q 031710 26 LQTVEVKV-RIDCEGCERKVKRAVEGMKGVKQVDV-----ERKANKVT--VVGY-VEPSKVVSRIAHRTGKKAEIWP 93 (154)
Q Consensus 26 ~~~~~l~V-gm~C~~C~~kI~kal~~~~GV~~v~v-----d~~~~~v~--V~g~-~~~~~v~~~i~~~~G~~a~~~~ 93 (154)
++++.|.| .-+-+. .-.+-++|.+++||..|.+ |..+..+. |.|. ++.++|.++|+ +.|-.+.-+.
T Consensus 4 irRlVLDVlKP~~p~-i~e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie-~~Gg~IHSID 78 (95)
T PF02680_consen 4 IRRLVLDVLKPHEPS-IVELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIE-ELGGVIHSID 78 (95)
T ss_dssp EEEEEEEEEEESSS--HHHHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHH-HTT-EEEEEE
T ss_pred eeEEEEEeecCCCCC-HHHHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHH-HcCCeEEeee
Confidence 45667777 444333 4567788999999987754 44555444 4575 89999999999 9997665543
No 16
>PRK13748 putative mercuric reductase; Provisional
Probab=90.63 E-value=1.8 Score=37.54 Aligned_cols=64 Identities=23% Similarity=0.418 Sum_probs=50.5
Q ss_pred EEEE-cCCCHhHHHHHHHHHhCCCCceEEEEeCCCcEEEEEe--cCCHHHHHHHHHHhhCCceEeccc
Q 031710 30 EVKV-RIDCEGCERKVKRAVEGMKGVKQVDVERKANKVTVVG--YVEPSKVVSRIAHRTGKKAEIWPY 94 (154)
Q Consensus 30 ~l~V-gm~C~~C~~kI~kal~~~~GV~~v~vd~~~~~v~V~g--~~~~~~v~~~i~~~~G~~a~~~~~ 94 (154)
.+.+ ++.|..|..+++..+...+++....++.....+.+.. ..+...+...+. ..|+..++...
T Consensus 3 ~i~i~g~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~~~~~~~i~~~i~-~~g~~~~~~~~ 69 (561)
T PRK13748 3 TLKITGMTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVGTSPDALTAAVA-GLGYRATLADA 69 (561)
T ss_pred EEEECCeecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECCCCCHHHHHHHHH-HcCCeeeccCc
Confidence 3668 9999999999999999999999888998888766652 245666666777 78887666554
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=90.34 E-value=1.5 Score=22.59 Aligned_cols=55 Identities=33% Similarity=0.632 Sum_probs=37.2
Q ss_pred EEE-cCCCHhHHHHHHHHHhCCCCceEEEEeCCCcEEEEEec--CCHHHHHHHHHHhhC
Q 031710 31 VKV-RIDCEGCERKVKRAVEGMKGVKQVDVERKANKVTVVGY--VEPSKVVSRIAHRTG 86 (154)
Q Consensus 31 l~V-gm~C~~C~~kI~kal~~~~GV~~v~vd~~~~~v~V~g~--~~~~~v~~~i~~~~G 86 (154)
+.+ ++.|..|...++..+....++.....+.......+... .+...+...+. ..+
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~ 59 (63)
T cd00371 2 LSVEGMTCAGCVSKIEKALEKLPGVESVEVDLETGKATVEYDPEVSPEELLEAIE-DAG 59 (63)
T ss_pred eeECCeEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEEECCCCCHHHHHHHHH-HcC
Confidence 345 78899999999999988899877777776666555432 24444444444 444
No 18
>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=89.72 E-value=1.4 Score=27.29 Aligned_cols=54 Identities=11% Similarity=0.105 Sum_probs=38.9
Q ss_pred EEEE-cCCCHhHHHHHHHHHhCCCCceEEEEeCCCcEEEEE--ecCCHHHHHHHHHHhhCCceEecc
Q 031710 30 EVKV-RIDCEGCERKVKRAVEGMKGVKQVDVERKANKVTVV--GYVEPSKVVSRIAHRTGKKAEIWP 93 (154)
Q Consensus 30 ~l~V-gm~C~~C~~kI~kal~~~~GV~~v~vd~~~~~v~V~--g~~~~~~v~~~i~~~~G~~a~~~~ 93 (154)
++.+ |+.|+....+++++|.+++.-+ .+.|. .......|...++ +.|+....+.
T Consensus 2 ~lD~rg~~CP~Pll~~~~~l~~l~~G~---------~l~v~~d~~~~~~di~~~~~-~~g~~~~~~~ 58 (70)
T PF01206_consen 2 TLDLRGLSCPMPLLKAKKALKELPPGE---------VLEVLVDDPAAVEDIPRWCE-ENGYEVVEVE 58 (70)
T ss_dssp EEECSS-STTHHHHHHHHHHHTSGTT----------EEEEEESSTTHHHHHHHHHH-HHTEEEEEEE
T ss_pred EEeCCCCCCCHHHHHHHHHHHhcCCCC---------EEEEEECCccHHHHHHHHHH-HCCCEEEEEE
Confidence 5788 9999999999999999984322 23333 2345688999998 9999755543
No 19
>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=82.89 E-value=2.8 Score=26.14 Aligned_cols=33 Identities=27% Similarity=0.591 Sum_probs=21.9
Q ss_pred eEEEEEEcCCCHhH------HHHHHHHHhCCCCceEEEE
Q 031710 27 QTVEVKVRIDCEGC------ERKVKRAVEGMKGVKQVDV 59 (154)
Q Consensus 27 ~~~~l~Vgm~C~~C------~~kI~kal~~~~GV~~v~v 59 (154)
.++.+.+.+..++| ...|+++|..++||.+|+|
T Consensus 34 ~~V~v~l~l~~~~~~~~~~l~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 34 GKVSVSLELPTPACPAAEPLREEIREALKALPGVKSVKV 72 (72)
T ss_dssp CEEEEEE--SSTTHTTHHHHHHHHHHHHHTSTT-SEEEE
T ss_pred CEEEEEEEECCCCchHHHHHHHHHHHHHHhCCCCceEeC
Confidence 44555565555555 5778999999999998875
No 20
>PRK11018 hypothetical protein; Provisional
Probab=81.34 E-value=8.1 Score=24.74 Aligned_cols=55 Identities=9% Similarity=-0.031 Sum_probs=39.7
Q ss_pred EEEEE-cCCCHhHHHHHHHHHhCCCCceEEEEeCCCcEEEEEecCCHHHHHHHHHHhhCCceEe
Q 031710 29 VEVKV-RIDCEGCERKVKRAVEGMKGVKQVDVERKANKVTVVGYVEPSKVVSRIAHRTGKKAEI 91 (154)
Q Consensus 29 ~~l~V-gm~C~~C~~kI~kal~~~~GV~~v~vd~~~~~v~V~g~~~~~~v~~~i~~~~G~~a~~ 91 (154)
.++.+ |+.|+.-.-+.+++|.+++.-+.+.| .+........|...++ +.|+.+..
T Consensus 9 ~~lD~rG~~CP~Pvl~~kk~l~~l~~G~~L~V-------~~d~~~a~~di~~~~~-~~G~~v~~ 64 (78)
T PRK11018 9 YRLDMVGEPCPYPAVATLEALPQLKKGEILEV-------VSDCPQSINNIPLDAR-NHGYTVLD 64 (78)
T ss_pred eeEECCCCcCCHHHHHHHHHHHhCCCCCEEEE-------EeCCccHHHHHHHHHH-HcCCEEEE
Confidence 57889 99999999999999999853222221 1222346678888888 99998753
No 21
>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=80.58 E-value=5.9 Score=24.30 Aligned_cols=51 Identities=16% Similarity=0.223 Sum_probs=36.1
Q ss_pred EEE-cCCCHhHHHHHHHHHhCCCCceEEEEeCCCcEEEEE--ecCCHHHHHHHHHHhhCCceEec
Q 031710 31 VKV-RIDCEGCERKVKRAVEGMKGVKQVDVERKANKVTVV--GYVEPSKVVSRIAHRTGKKAEIW 92 (154)
Q Consensus 31 l~V-gm~C~~C~~kI~kal~~~~GV~~v~vd~~~~~v~V~--g~~~~~~v~~~i~~~~G~~a~~~ 92 (154)
+.+ |+.|+.-..+++++| ++..-+ .+.|. .......|...++ +.|+..+..
T Consensus 2 lD~rG~~CP~P~l~~k~al-~~~~g~---------~l~v~~d~~~s~~~i~~~~~-~~G~~~~~~ 55 (67)
T cd03421 2 IDARGLACPQPVIKTKKAL-ELEAGG---------EIEVLVDNEVAKENVSRFAE-SRGYEVSVE 55 (67)
T ss_pred cccCCCCCCHHHHHHHHHH-hcCCCC---------EEEEEEcChhHHHHHHHHHH-HcCCEEEEE
Confidence 567 999999999999999 653222 23332 2345678888998 999988543
No 22
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=78.03 E-value=13 Score=24.58 Aligned_cols=43 Identities=9% Similarity=0.184 Sum_probs=31.9
Q ss_pred HHHHHHHHHhCCCCceEEEEeCCCcEEEEE-ecCCHHHHHHHHH
Q 031710 40 CERKVKRAVEGMKGVKQVDVERKANKVTVV-GYVEPSKVVSRIA 82 (154)
Q Consensus 40 C~~kI~kal~~~~GV~~v~vd~~~~~v~V~-g~~~~~~v~~~i~ 82 (154)
=...+.++|..++|++-...|...+|+.|+ ...+...+.+.|.
T Consensus 18 ~~~~V~~~l~~ipg~Evh~~d~~~GKiVVtiE~~~~~~~~~~i~ 61 (87)
T PRK10553 18 RISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLLQTIE 61 (87)
T ss_pred HHHHHHHHHHcCCCcEEEeecCCCCeEEEEEEeCChHHHHHHHH
Confidence 367899999999999876677788888887 2345666666555
No 23
>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional
Probab=73.74 E-value=6.6 Score=25.30 Aligned_cols=56 Identities=13% Similarity=0.157 Sum_probs=38.9
Q ss_pred ccccchhhcccC-CCCCcchh----hcCCceEEEEEEcCCCHhHHHHHHHHHhCCCCceEEEE
Q 031710 2 GVVDHFSDYFDC-SHGSSKLK----KRRQLQTVEVKVRIDCEGCERKVKRAVEGMKGVKQVDV 59 (154)
Q Consensus 2 ~~~~~~~~~~~~-~~~~~~~~----~~~~~~~~~l~Vgm~C~~C~~kI~kal~~~~GV~~v~v 59 (154)
|+|..++.++.. |..+.... ......++++-|+ -+.....|.+.|.++.+|..|++
T Consensus 15 GVL~Ri~~lf~rRGfnI~sl~v~~t~~~~~sriti~v~--~~~~i~ql~kQL~KL~dV~~V~~ 75 (76)
T PRK11152 15 EVLERVLRVVRHRGFQVCSMNMTQNTDAQNINIELTVA--SERPIDLLSSQLNKLVDVAHVEI 75 (76)
T ss_pred cHHHHHHHHHhcCCeeeeeEEeeecCCCCEEEEEEEEC--CCchHHHHHHHHhcCcCeEEEEE
Confidence 778888887743 32222222 1344566777774 58889999999999999988876
No 24
>cd03420 SirA_RHOD_Pry_redox SirA_RHOD_Pry_redox. SirA-like domain located within a multidomain protein of unknown function. Other domains include RHOD (rhodanese homology domain), and Pry_redox (pyridine nucleotide-disulphide oxidoreductase) as well as a C-terminal domain that corresponds to COG2210. This fold is referred to as a two-layered alpha/beta sandwich, structurally similar to that of translation initiation factor 3.
Probab=71.71 E-value=16 Score=22.69 Aligned_cols=53 Identities=15% Similarity=0.184 Sum_probs=38.4
Q ss_pred EEE-cCCCHhHHHHHHHHHhCCCCceEEEEeCCCcEEEEE--ecCCHHHHHHHHHHhhCCceEecc
Q 031710 31 VKV-RIDCEGCERKVKRAVEGMKGVKQVDVERKANKVTVV--GYVEPSKVVSRIAHRTGKKAEIWP 93 (154)
Q Consensus 31 l~V-gm~C~~C~~kI~kal~~~~GV~~v~vd~~~~~v~V~--g~~~~~~v~~~i~~~~G~~a~~~~ 93 (154)
+.+ |+.|+.=.-+++++|.+++.-+ .+.|. .......|....+ +.|+......
T Consensus 2 lD~rG~~CP~Pvl~~kkal~~l~~G~---------~l~V~~d~~~a~~di~~~~~-~~G~~~~~~~ 57 (69)
T cd03420 2 VDACGLQCPGPILKLKKEIDKLQDGE---------QLEVKASDPGFARDAQAWCK-STGNTLISLE 57 (69)
T ss_pred cccCCCcCCHHHHHHHHHHHcCCCCC---------EEEEEECCccHHHHHHHHHH-HcCCEEEEEE
Confidence 567 8999999999999999885322 23333 2346788888998 9999876433
No 25
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=71.20 E-value=16 Score=27.37 Aligned_cols=45 Identities=16% Similarity=0.245 Sum_probs=34.1
Q ss_pred HhHHHHHHHHHhCCCCceEEEEeCCCcE-------------------EEEEe---cCCHHHHHHHHH
Q 031710 38 EGCERKVKRAVEGMKGVKQVDVERKANK-------------------VTVVG---YVEPSKVVSRIA 82 (154)
Q Consensus 38 ~~C~~kI~kal~~~~GV~~v~vd~~~~~-------------------v~V~g---~~~~~~v~~~i~ 82 (154)
.+|-.-++..+.+++||.++.+-...+. |.|.- .++.++|++..-
T Consensus 10 gGCFWg~E~~f~~~~GV~~t~vGYagG~~~~PtY~~Vcsg~tgh~E~V~V~yDp~~isy~~Ll~~f~ 76 (172)
T PRK14054 10 GGCFWGMEAPFDRVKGVISTRVGYTGGHVENPTYEQVCSGTTGHAEAVEITYDPAVISYRELLELFF 76 (172)
T ss_pred cCChhhhHHHHccCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCCcCCHHHHHHHHH
Confidence 7888899999999999999999876664 44542 367777776654
No 26
>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=71.08 E-value=25 Score=22.63 Aligned_cols=41 Identities=22% Similarity=0.277 Sum_probs=30.3
Q ss_pred HHHHHHHHhCCCCceEEEEeCCCcEEEEE-ecCCHHHHHHHHH
Q 031710 41 ERKVKRAVEGMKGVKQVDVERKANKVTVV-GYVEPSKVVSRIA 82 (154)
Q Consensus 41 ~~kI~kal~~~~GV~~v~vd~~~~~v~V~-g~~~~~~v~~~i~ 82 (154)
...+.++|..++|++-...+.. +|+.|+ ...+..++.+.+.
T Consensus 17 ~~~v~~~l~~~~gvEVh~~~~~-GKiVVtiE~~~~~~~~~~~~ 58 (79)
T PF03927_consen 17 LEEVAEALAAIPGVEVHAVDED-GKIVVTIEAESSEEEVDLID 58 (79)
T ss_dssp HHHHHHHHCCSTTEEEEEEETT-TEEEEEEEESSHHHHHHHHH
T ss_pred HHHHHHHHHcCCCcEEEeeCCC-CeEEEEEEeCChHHHHHHHH
Confidence 5688999999999965556665 777776 3356677777776
No 27
>PF14437 MafB19-deam: MafB19-like deaminase
Probab=68.88 E-value=15 Score=26.74 Aligned_cols=40 Identities=23% Similarity=0.438 Sum_probs=31.7
Q ss_pred eEEEEEE-cCCCHhHHHHHHHHHhCCCCceEEEEeCC-CcEEE
Q 031710 27 QTVEVKV-RIDCEGCERKVKRAVEGMKGVKQVDVERK-ANKVT 67 (154)
Q Consensus 27 ~~~~l~V-gm~C~~C~~kI~kal~~~~GV~~v~vd~~-~~~v~ 67 (154)
..+++.| .-.|..|..-|.....++ |+.++.|... ++++.
T Consensus 100 ~~~tm~Vdr~vC~~C~~~i~~~a~~l-Gl~~L~I~~~~sG~~~ 141 (146)
T PF14437_consen 100 RSMTMYVDRDVCGYCGGDIPSMAEKL-GLKSLTIHEPDSGKVY 141 (146)
T ss_pred CeEEEEECcccchHHHHHHHHHHHHc-CCCeEEEEecCCCcEE
Confidence 4578889 888999998888887766 8888888766 66554
No 28
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=68.58 E-value=15 Score=26.53 Aligned_cols=48 Identities=21% Similarity=0.279 Sum_probs=30.2
Q ss_pred hHHHHHHHHHhCC-CCceEEEEeCCCcEEEEEecCCHHHHHHHHHHhhC
Q 031710 39 GCERKVKRAVEGM-KGVKQVDVERKANKVTVVGYVEPSKVVSRIAHRTG 86 (154)
Q Consensus 39 ~C~~kI~kal~~~-~GV~~v~vd~~~~~v~V~g~~~~~~v~~~i~~~~G 86 (154)
.=...|.++|.+. -+...+.|....+.|++.|.+.......++...++
T Consensus 26 ~~~~~i~~~i~~~~~~~~~i~V~v~~G~v~l~G~v~s~~~~~~~~~aa~ 74 (147)
T PRK11198 26 DAADALKEHISKQGLGDADVNVQVEDGKATVSGDAASQEAKEKILLAVG 74 (147)
T ss_pred HHHHHHHHHHHhcCCCcCCceEEEeCCEEEEEEEeCCHHHHHHHHHHhc
Confidence 3456777777654 23445667777999999998655444555541444
No 29
>cd03423 SirA SirA (also known as UvrY, and YhhP) belongs to a family of 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 thought 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=68.33 E-value=25 Score=21.67 Aligned_cols=53 Identities=11% Similarity=0.078 Sum_probs=38.1
Q ss_pred EEE-cCCCHhHHHHHHHHHhCCCCceEEEEeCCCcEEEEE--ecCCHHHHHHHHHHhhCCceEecc
Q 031710 31 VKV-RIDCEGCERKVKRAVEGMKGVKQVDVERKANKVTVV--GYVEPSKVVSRIAHRTGKKAEIWP 93 (154)
Q Consensus 31 l~V-gm~C~~C~~kI~kal~~~~GV~~v~vd~~~~~v~V~--g~~~~~~v~~~i~~~~G~~a~~~~ 93 (154)
+.+ |+.|+.=.-+++++|.+++--+ .+.|. .......|...++ +.|+.+....
T Consensus 2 lD~~G~~CP~P~i~~k~~l~~l~~G~---------~l~V~~dd~~s~~di~~~~~-~~g~~~~~~~ 57 (69)
T cd03423 2 LDTRGLRCPEPVMMLHKKVRKMKPGD---------TLLVLATDPSTTRDIPKFCT-FLGHELLAQE 57 (69)
T ss_pred ccccCCcCCHHHHHHHHHHHcCCCCC---------EEEEEeCCCchHHHHHHHHH-HcCCEEEEEE
Confidence 456 8899999999999999885211 22332 3356788999998 9999876443
No 30
>cd03422 YedF YedF is a bacterial SirA-like protein of unknown function. 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=67.05 E-value=23 Score=21.96 Aligned_cols=54 Identities=11% Similarity=0.002 Sum_probs=37.8
Q ss_pred EEE-cCCCHhHHHHHHHHHhCCCCceEEEEeCCCcEEEEEecCCHHHHHHHHHHhhCCceEec
Q 031710 31 VKV-RIDCEGCERKVKRAVEGMKGVKQVDVERKANKVTVVGYVEPSKVVSRIAHRTGKKAEIW 92 (154)
Q Consensus 31 l~V-gm~C~~C~~kI~kal~~~~GV~~v~vd~~~~~v~V~g~~~~~~v~~~i~~~~G~~a~~~ 92 (154)
+.+ |+.|+.=.-+.+++|++++.-+.+.| .++.......|...++ ..|+.+...
T Consensus 2 lD~rG~~CP~Pvi~~kkal~~l~~G~~l~V-------~~d~~~s~~ni~~~~~-~~g~~v~~~ 56 (69)
T cd03422 2 LDLRGEPCPYPAIATLEALPSLKPGEILEV-------ISDCPQSINNIPIDAR-NHGYKVLAI 56 (69)
T ss_pred cccCCCcCCHHHHHHHHHHHcCCCCCEEEE-------EecCchHHHHHHHHHH-HcCCEEEEE
Confidence 456 88999999999999999853222221 2223356788888888 999987543
No 31
>cd00291 SirA_YedF_YeeD SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial 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=66.68 E-value=26 Score=21.17 Aligned_cols=53 Identities=17% Similarity=0.130 Sum_probs=37.8
Q ss_pred EEE-cCCCHhHHHHHHHHHhCCCCceEEEEeCCCcEEEEEe--cCCHHHHHHHHHHhhCCceEecc
Q 031710 31 VKV-RIDCEGCERKVKRAVEGMKGVKQVDVERKANKVTVVG--YVEPSKVVSRIAHRTGKKAEIWP 93 (154)
Q Consensus 31 l~V-gm~C~~C~~kI~kal~~~~GV~~v~vd~~~~~v~V~g--~~~~~~v~~~i~~~~G~~a~~~~ 93 (154)
+.+ |+.|+.=..++.++|.+++.-+ .+.|.. ......|.+.++ ..|+....+.
T Consensus 2 lD~rg~~CP~Pl~~~~~~l~~l~~g~---------~l~v~~d~~~~~~~i~~~~~-~~g~~~~~~~ 57 (69)
T cd00291 2 LDLRGLPCPLPVLKTKKALEKLKSGE---------VLEVLLDDPGAVEDIPAWAK-ETGHEVLEVE 57 (69)
T ss_pred ccccCCcCCHHHHHHHHHHhcCCCCC---------EEEEEecCCcHHHHHHHHHH-HcCCEEEEEE
Confidence 456 8999999999999999875322 233332 245788889998 9999865443
No 32
>PRK00299 sulfur transfer protein SirA; Reviewed
Probab=65.11 E-value=34 Score=21.96 Aligned_cols=54 Identities=9% Similarity=0.099 Sum_probs=39.3
Q ss_pred EEEEEE-cCCCHhHHHHHHHHHhCCCCceEEEEeCCCcEEEEE--ecCCHHHHHHHHHHhhCCceEe
Q 031710 28 TVEVKV-RIDCEGCERKVKRAVEGMKGVKQVDVERKANKVTVV--GYVEPSKVVSRIAHRTGKKAEI 91 (154)
Q Consensus 28 ~~~l~V-gm~C~~C~~kI~kal~~~~GV~~v~vd~~~~~v~V~--g~~~~~~v~~~i~~~~G~~a~~ 91 (154)
..++.+ |+.|+.=.-+++++|.+++.-+ .+.|. .....+.|....+ ..|++...
T Consensus 9 ~~~lD~~Gl~CP~Pll~~kk~l~~l~~G~---------~l~V~~dd~~~~~di~~~~~-~~G~~~~~ 65 (81)
T PRK00299 9 DHTLDALGLRCPEPVMMVRKTVRNMQPGE---------TLLIIADDPATTRDIPSFCR-FMDHELLA 65 (81)
T ss_pred CeEEecCCCCCCHHHHHHHHHHHcCCCCC---------EEEEEeCCccHHHHHHHHHH-HcCCEEEE
Confidence 356888 9999999999999999885222 22332 2346778888888 99987754
No 33
>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=62.41 E-value=11 Score=25.05 Aligned_cols=35 Identities=26% Similarity=0.414 Sum_probs=22.7
Q ss_pred EEEEEE-cCCCHhH---HHHHHHHHhCCCCceEEEEeCC
Q 031710 28 TVEVKV-RIDCEGC---ERKVKRAVEGMKGVKQVDVERK 62 (154)
Q Consensus 28 ~~~l~V-gm~C~~C---~~kI~kal~~~~GV~~v~vd~~ 62 (154)
.+.+.+ .-.|... ...++.+|..++|+.++++++.
T Consensus 40 ~i~l~l~~p~~~~~~~l~~~i~~al~~l~gv~~v~v~i~ 78 (99)
T TIGR02945 40 DIQMTLTAPNCPVAGSMPGEVENAVRAVPGVGSVTVELV 78 (99)
T ss_pred EEEEEECCCCCChHHHHHHHHHHHHHhCCCCceEEEEEE
Confidence 344444 3334433 3457888999999998888754
No 34
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=60.61 E-value=16 Score=25.34 Aligned_cols=32 Identities=38% Similarity=0.696 Sum_probs=23.1
Q ss_pred EEEEcCCCHhH------HHHHHHHHhCCCCceEEEEeC
Q 031710 30 EVKVRIDCEGC------ERKVKRAVEGMKGVKQVDVER 61 (154)
Q Consensus 30 ~l~Vgm~C~~C------~~kI~kal~~~~GV~~v~vd~ 61 (154)
.+++.++-.+| ...++.+|..++||.+++|++
T Consensus 52 ~v~mtlT~~gCP~~~~i~~~v~~al~~~~~v~~v~V~l 89 (111)
T COG2151 52 KVKMTLTSPGCPLAEVIADQVEAALEEIPGVEDVEVEL 89 (111)
T ss_pred EEEEecCCCCCCccHHHHHHHHHHHHhcCCcceEEEEE
Confidence 33444444555 678899999999999888754
No 35
>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=59.39 E-value=37 Score=24.70 Aligned_cols=59 Identities=14% Similarity=0.231 Sum_probs=42.3
Q ss_pred HhHHHHHHHHHhCCCCceEEEEeCCCcEEEEEec-----C-CHHHHHHHHHHhhCCceEecccCC
Q 031710 38 EGCERKVKRAVEGMKGVKQVDVERKANKVTVVGY-----V-EPSKVVSRIAHRTGKKAEIWPYVP 96 (154)
Q Consensus 38 ~~C~~kI~kal~~~~GV~~v~vd~~~~~v~V~g~-----~-~~~~v~~~i~~~~G~~a~~~~~~p 96 (154)
+.-...|++.+-.-.||.++.+|..++.|.|... + -....+..|..++|....++...|
T Consensus 52 e~A~~~I~~ivP~ea~i~di~Fd~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtpP 116 (145)
T cd02410 52 EEAIKIILEIVPEEAGITDIYFDDDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTPP 116 (145)
T ss_pred HHHHHHHHHhCCCccCceeeEecCCCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecCC
Confidence 4445566666666679999999999999999722 1 334555666658999888877655
No 36
>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=57.09 E-value=16 Score=27.39 Aligned_cols=33 Identities=27% Similarity=0.552 Sum_probs=22.6
Q ss_pred EEEEEcCCCHhH------HHHHHHHHhCCCCceEEEEeC
Q 031710 29 VEVKVRIDCEGC------ERKVKRAVEGMKGVKQVDVER 61 (154)
Q Consensus 29 ~~l~Vgm~C~~C------~~kI~kal~~~~GV~~v~vd~ 61 (154)
+.+.+-+..++| ...|+.+|.+++||.+++|++
T Consensus 115 V~I~mtLt~p~c~~~~~L~~dV~~aL~~l~gV~~V~V~l 153 (174)
T TIGR03406 115 VDIEMTLTAPGCGMGPVLVEDVEDKVLAVPNVDEVEVEL 153 (174)
T ss_pred EEEEEEeCCCCCcHHHHHHHHHHHHHHhCCCceeEEEEE
Confidence 445554444444 345889999999999888754
No 37
>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=56.67 E-value=17 Score=24.93 Aligned_cols=66 Identities=18% Similarity=0.379 Sum_probs=34.7
Q ss_pred hcCCceEE---EEEE-cC-CCHhHH-HHHHHHHhC--CCCceEEEEeCCCcEEEEEe----c-CCHHHHHHHHHHhhCCc
Q 031710 22 KRRQLQTV---EVKV-RI-DCEGCE-RKVKRAVEG--MKGVKQVDVERKANKVTVVG----Y-VEPSKVVSRIAHRTGKK 88 (154)
Q Consensus 22 ~~~~~~~~---~l~V-gm-~C~~C~-~kI~kal~~--~~GV~~v~vd~~~~~v~V~g----~-~~~~~v~~~i~~~~G~~ 88 (154)
+...+... .+.+ +| +|.+|- .++...+.. ..|++.|-+. += .+.+ . -..+++.+.|++++|.+
T Consensus 26 r~g~F~~y~~~~~elvgf~~CgGCpg~~~~~~~~~l~~~~~d~IHls--sC--~~~~~~~~~CP~~~~~~~~I~~~~gi~ 101 (107)
T PF08821_consen 26 RKGAFARYDDEDVELVGFFTCGGCPGRKLVRRIKKLKKNGADVIHLS--SC--MVKGNPHGPCPHIDEIKKIIEEKFGIE 101 (107)
T ss_pred ccCccccCCCCCeEEEEEeeCCCCChhHHHHHHHHHHHCCCCEEEEc--CC--EecCCCCCCCCCHHHHHHHHHHHhCCC
Confidence 34445444 2677 87 899883 233333222 3566533221 11 1111 1 35799999999555876
Q ss_pred eEe
Q 031710 89 AEI 91 (154)
Q Consensus 89 a~~ 91 (154)
+..
T Consensus 102 VV~ 104 (107)
T PF08821_consen 102 VVE 104 (107)
T ss_pred Eee
Confidence 543
No 38
>COG2177 FtsX Cell division protein [Cell division and chromosome partitioning]
Probab=56.62 E-value=52 Score=26.75 Aligned_cols=47 Identities=21% Similarity=0.367 Sum_probs=35.8
Q ss_pred EEEEEcCCCHhHHHHHHHHHhCCCCceEEEEeCCCcEEEEEecCCHHHHHHHHHHhhCCc
Q 031710 29 VEVKVRIDCEGCERKVKRAVEGMKGVKQVDVERKANKVTVVGYVEPSKVVSRIAHRTGKK 88 (154)
Q Consensus 29 ~~l~Vgm~C~~C~~kI~kal~~~~GV~~v~vd~~~~~v~V~g~~~~~~v~~~i~~~~G~~ 88 (154)
+.++++.+ ..|...+++.+.+++||.++++ .+.++-.+.+++..|+.
T Consensus 63 vyL~~~~~-~~~~~~v~~~i~~~~gV~~v~~------------~sre~~l~~L~~~lg~~ 109 (297)
T COG2177 63 VYLQIDAD-QDDAALVREKIEGIPGVKSVRF------------ISREEALKELQPWLGFG 109 (297)
T ss_pred EEEecCCC-hHHHHHHHHHHhcCCCcceEEE------------eCHHHHHHHHHHHcCch
Confidence 34444555 8999999999999999998765 35667777777678864
No 39
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=55.84 E-value=49 Score=20.75 Aligned_cols=43 Identities=12% Similarity=0.302 Sum_probs=30.7
Q ss_pred HhCCCCceEEEEeCCC-cEEEEEecCCHHHHHHHHHHhhCCceEec
Q 031710 48 VEGMKGVKQVDVERKA-NKVTVVGYVEPSKVVSRIAHRTGKKAEIW 92 (154)
Q Consensus 48 l~~~~GV~~v~vd~~~-~~v~V~g~~~~~~v~~~i~~~~G~~a~~~ 92 (154)
|..++||..+..+-.. -.+.+....+..+|++.+. ..|. +.-.
T Consensus 26 l~~~~~v~~v~~~~~~~~~i~l~~~~~~~~ll~~l~-~~g~-I~~f 69 (84)
T PF13732_consen 26 LEELPGVESVEQDGDGKLRIKLEDEETANELLQELI-EKGI-IRSF 69 (84)
T ss_pred HhhCCCeEEEEEeCCcEEEEEECCcccHHHHHHHHH-hCCC-eeEE
Confidence 7888999998764433 3444445568899999998 8887 5543
No 40
>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=55.13 E-value=51 Score=20.73 Aligned_cols=54 Identities=17% Similarity=0.310 Sum_probs=39.5
Q ss_pred HhHHHHHHHHHhCC---CCceEEEEeCCCcEEEEE--ecCCHHHHHHHHHHhhCCceEe
Q 031710 38 EGCERKVKRAVEGM---KGVKQVDVERKANKVTVV--GYVEPSKVVSRIAHRTGKKAEI 91 (154)
Q Consensus 38 ~~C~~kI~kal~~~---~GV~~v~vd~~~~~v~V~--g~~~~~~v~~~i~~~~G~~a~~ 91 (154)
..-..++..+|.++ +---.+..|..++.+.|. |.+..+-++++|+++.|-.+++
T Consensus 15 ~~d~~kl~~aL~~l~~eDP~l~~~~d~et~e~~l~g~Gelhlev~~~~L~~~~~v~v~~ 73 (75)
T PF14492_consen 15 KEDEPKLSEALQKLSEEDPSLRVERDEETGELILSGMGELHLEVLLERLKRRFGVEVEF 73 (75)
T ss_dssp HHHHHHHHHHHHHHHHH-TTSEEEEETTTSEEEEEESSHHHHHHHHHHHHHTTCEBEEE
T ss_pred HhHHHHHHHHHHHHHhcCCeEEEEEcchhceEEEEECCHHHHHHHHHHHHHHHCCeeEe
Confidence 55567777777766 223378889999998887 5678888999998666766554
No 41
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=53.31 E-value=36 Score=25.76 Aligned_cols=36 Identities=19% Similarity=0.266 Sum_probs=27.7
Q ss_pred CceEEEEEEcCCCHhHHHHHHHHHhCCCCceEEEEeCCCcE
Q 031710 25 QLQTVEVKVRIDCEGCERKVKRAVEGMKGVKQVDVERKANK 65 (154)
Q Consensus 25 ~~~~~~l~Vgm~C~~C~~kI~kal~~~~GV~~v~vd~~~~~ 65 (154)
.++++.|. .+|-.-++..+.+++||.++.+-...+.
T Consensus 7 ~~~~a~~a-----gGCFWg~E~~f~~l~GV~~t~vGYagG~ 42 (186)
T PRK13014 7 GMETATFA-----GGCFWGVEGVFQHVPGVVSVVSGYSGGH 42 (186)
T ss_pred CccEEEEe-----cCCceeeHHHHccCCCEEEEEeeecCCC
Confidence 34555554 6788888899999999999999876663
No 42
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=52.32 E-value=57 Score=25.29 Aligned_cols=34 Identities=18% Similarity=0.211 Sum_probs=27.2
Q ss_pred ceEEEEEEcCCCHhHHHHHHHHHhCCCCceEEEEeCCCc
Q 031710 26 LQTVEVKVRIDCEGCERKVKRAVEGMKGVKQVDVERKAN 64 (154)
Q Consensus 26 ~~~~~l~Vgm~C~~C~~kI~kal~~~~GV~~v~vd~~~~ 64 (154)
++++.|. .+|-.-++..+.+++||.++.+-...+
T Consensus 45 ~~~a~fa-----gGCFWg~E~~F~~l~GV~~t~vGYagG 78 (213)
T PRK00058 45 MEQAIFG-----MGCFWGAERLFWQLPGVYSTAVGYAGG 78 (213)
T ss_pred ccEEEEE-----ccCcchhHHHHhcCCCEEEEEeeecCC
Confidence 4555554 788888999999999999999987744
No 43
>COG0425 SirA Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]
Probab=50.56 E-value=65 Score=20.63 Aligned_cols=49 Identities=14% Similarity=0.255 Sum_probs=35.1
Q ss_pred EEEEEE-cCCCHhHHHHHHHHHhCCCCceEEEEeCCCcEEEEEe--cCCHHHHHHHHHHhhC
Q 031710 28 TVEVKV-RIDCEGCERKVKRAVEGMKGVKQVDVERKANKVTVVG--YVEPSKVVSRIAHRTG 86 (154)
Q Consensus 28 ~~~l~V-gm~C~~C~~kI~kal~~~~GV~~v~vd~~~~~v~V~g--~~~~~~v~~~i~~~~G 86 (154)
..+|.+ |+.|+.=...++++|.+++-- ..+.|.. ......|...++ +.|
T Consensus 5 ~~~LD~rG~~CP~Pv~~~kk~l~~m~~G---------e~LeV~~ddp~~~~dIp~~~~-~~~ 56 (78)
T COG0425 5 DKVLDLRGLRCPGPVVETKKALAKLKPG---------EILEVIADDPAAKEDIPAWAK-KEG 56 (78)
T ss_pred ceEEeccCCcCCccHHHHHHHHHcCCCC---------CEEEEEecCcchHHHHHHHHH-HcC
Confidence 457899 999999999999999998532 2333332 245577888887 555
No 44
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=50.07 E-value=1e+02 Score=22.86 Aligned_cols=69 Identities=20% Similarity=0.342 Sum_probs=40.9
Q ss_pred ceEEEEEEcCCCHhHHHHHH------------HHHhCC------CCceEEEEeCCCcEEEE-E--ec---C-CHHHHHHH
Q 031710 26 LQTVEVKVRIDCEGCERKVK------------RAVEGM------KGVKQVDVERKANKVTV-V--GY---V-EPSKVVSR 80 (154)
Q Consensus 26 ~~~~~l~Vgm~C~~C~~kI~------------kal~~~------~GV~~v~vd~~~~~v~V-~--g~---~-~~~~v~~~ 80 (154)
+-.+-++-|+-|+.|..+++ ++|.++ .++.-...-....++.+ . |+ + .--+.+++
T Consensus 5 ~~~~c~kt~ilC~~c~~~~~~G~v~~~dv~i~~~l~~l~~~~~l~~~~~~k~~~~ddrvIfvV~~gdg~aIGk~G~~ik~ 84 (166)
T PRK06418 5 ICEVCVKTGLLCPRCQSLLDSGEVTELDVEVSKVLLKLEEDKELKDVEYKKAYEVDDLVILLVTSGPRIPIGKGGKIAKA 84 (166)
T ss_pred eeeEEeccCccChhHHhHhhcCceEEeehHHHHHHHHhhccccccCceEEEEEEeCCEEEEEEeCCCcccccccchHHHH
Confidence 33445555899999998875 455554 23332221122344443 2 32 1 22456788
Q ss_pred HHHhhCCceEeccc
Q 031710 81 IAHRTGKKAEIWPY 94 (154)
Q Consensus 81 i~~~~G~~a~~~~~ 94 (154)
+++.+|++++++.+
T Consensus 85 l~~~lgk~VevVE~ 98 (166)
T PRK06418 85 LSRKLGKKVRVVEK 98 (166)
T ss_pred HHHHhCCcEEEEEc
Confidence 87789999999886
No 45
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=49.61 E-value=22 Score=26.16 Aligned_cols=45 Identities=18% Similarity=0.268 Sum_probs=32.6
Q ss_pred HhHHHHHHHHHhCCCCceEEEEeCCCcE--------------EEEEe---cCCHHHHHHHHH
Q 031710 38 EGCERKVKRAVEGMKGVKQVDVERKANK--------------VTVVG---YVEPSKVVSRIA 82 (154)
Q Consensus 38 ~~C~~kI~kal~~~~GV~~v~vd~~~~~--------------v~V~g---~~~~~~v~~~i~ 82 (154)
.+|-.-++..+.+++||.++.+-...+. |.|+- .++.++|++..-
T Consensus 8 gGCFWg~E~~f~~l~GV~~t~vGYagG~~~~p~~~~tgH~E~V~V~yDp~~isy~~LL~~f~ 69 (156)
T PRK05528 8 GGCLWGVQAFFKTLPGVIHTEAGRANGRTSTLDGPYDGYAECVKTHFDPRMVSITDLMGYLF 69 (156)
T ss_pred cCCchhhHHHHhcCCCEEEEEEEcCCCCCCCCCCCCCCcEEEEEEEECCCcCCHHHHHHHHH
Confidence 6788889999999999999998765543 33332 256677776654
No 46
>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=49.47 E-value=72 Score=20.85 Aligned_cols=60 Identities=15% Similarity=0.126 Sum_probs=41.9
Q ss_pred ceEEEEEEcCCCHhHHHHHHHHHhCCCC-ceEEEEeCCCcEEEEEecCCHHHHHHHHHHhhCC
Q 031710 26 LQTVEVKVRIDCEGCERKVKRAVEGMKG-VKQVDVERKANKVTVVGYVEPSKVVSRIAHRTGK 87 (154)
Q Consensus 26 ~~~~~l~Vgm~C~~C~~kI~kal~~~~G-V~~v~vd~~~~~v~V~g~~~~~~v~~~i~~~~G~ 87 (154)
..|+.=+|.=+=..+...+.+.|....+ -..+.|+..++.+.|.|. -..+|.+.|. ..||
T Consensus 27 ~~T~IrkI~GD~~aL~~dL~~~l~~~~~~~~~~~V~~~~g~i~IkG~-~~~~Vk~wL~-~~GF 87 (87)
T PF05046_consen 27 KITVIRKIEGDIWALKKDLRKFLGEKPKKKIDVRVNELTGHIEIKGD-HVEEVKKWLL-EKGF 87 (87)
T ss_pred eEEEEEeecCCHHHHHHHHHHHhhhhcCCCcceEEeecCCEEEEcCc-cHHHHHHHHH-HCcC
Confidence 3444445633446667777777765543 236789999999999997 4778888887 7775
No 47
>TIGR03527 selenium_YedF selenium metabolism protein YedF. Members of this protein family are about 200 amino acids in size, and include the uncharacterized YedF protein of Escherichia coli. This family shares an N-terminal domain, modeled by pfam01206, with the sulfurtransferase TusA (also called SirA). The C-terminal domain includes a typical redox-active disulfide motif, CGXC. This protein family found only among those genomes that also carry the selenium donor protein SelD, and its connection to selenium metabolism is indicated by the method of partial phylogenetic profiling vs. SelD. Its gene typically is found next to selD. Members of this family are found even when selenocysteine and selenouridine biosynthesis pathways are, except for SelD, completely absent, as in Enterococcus faecalis. Its role in selenium metabolism is unclear, but may include either detoxification or a role in labile selenoprotein biosynthesis.
Probab=48.84 E-value=49 Score=25.09 Aligned_cols=51 Identities=16% Similarity=0.130 Sum_probs=36.3
Q ss_pred cCCCHhHHHHHHHHHhCCCCceEEEEeCCCcEEEEEecCCHHHHHHHHHHhhCCceEec
Q 031710 34 RIDCEGCERKVKRAVEGMKGVKQVDVERKANKVTVVGYVEPSKVVSRIAHRTGKKAEIW 92 (154)
Q Consensus 34 gm~C~~C~~kI~kal~~~~GV~~v~vd~~~~~v~V~g~~~~~~v~~~i~~~~G~~a~~~ 92 (154)
|+.|+.-.-+.+++|.+++.-..+. |.+......+.|.+.++ ..|+++...
T Consensus 5 Gl~CP~Pvi~tKkal~~l~~g~~L~-------VlvD~~~a~~nV~~~~~-~~G~~v~~~ 55 (194)
T TIGR03527 5 GLACPQPVILTKKALDELGEEGVLT-------VIVDNEAAKENVSKFAT-SLGYEVEVE 55 (194)
T ss_pred CCCCCHHHHHHHHHHHcCCCCCEEE-------EEECCccHHHHHHHHHH-HcCCEEEEE
Confidence 8899999999999999985211121 12223356778888888 999988643
No 48
>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=48.64 E-value=15 Score=21.96 Aligned_cols=30 Identities=27% Similarity=0.384 Sum_probs=14.7
Q ss_pred HHHHHHHhC---CCCceEEEEeCCCcEEEEEecC
Q 031710 42 RKVKRAVEG---MKGVKQVDVERKANKVTVVGYV 72 (154)
Q Consensus 42 ~kI~kal~~---~~GV~~v~vd~~~~~v~V~g~~ 72 (154)
.+|+.+|.. +++- .+.+....+.|++.|.+
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 356666665 3343 56777788889998875
No 49
>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=46.84 E-value=72 Score=23.24 Aligned_cols=45 Identities=13% Similarity=0.226 Sum_probs=32.5
Q ss_pred HhHHHHHHHHHhCCCCceEEEEeCCCcEEEEEec-----CCHHHHHHHHH
Q 031710 38 EGCERKVKRAVEGMKGVKQVDVERKANKVTVVGY-----VEPSKVVSRIA 82 (154)
Q Consensus 38 ~~C~~kI~kal~~~~GV~~v~vd~~~~~v~V~g~-----~~~~~v~~~i~ 82 (154)
..=+.+|.+.+.+++||.++.|=.....+.|.-. ...++|.+.|+
T Consensus 74 ~~~a~~i~~~v~~~~~V~~A~vvv~~~~a~Vav~~~~~~~~~~~i~~~V~ 123 (177)
T PF09580_consen 74 QQLADRIANRVKKVPGVEDATVVVTDDNAYVAVDLDFNRFNTKKIKKKVE 123 (177)
T ss_pred HHHHHHHHHHHhcCCCceEEEEEEECCEEEEEEEecccccchhHHHHHHH
Confidence 4558899999999999999998877777776422 33445555544
No 50
>COG4492 PheB ACT domain-containing protein [General function prediction only]
Probab=44.75 E-value=39 Score=24.39 Aligned_cols=22 Identities=23% Similarity=0.412 Sum_probs=14.6
Q ss_pred HhHHHHHHHHHhCCCCceEEEE
Q 031710 38 EGCERKVKRAVEGMKGVKQVDV 59 (154)
Q Consensus 38 ~~C~~kI~kal~~~~GV~~v~v 59 (154)
+.-..+|-.+|.+++||..|++
T Consensus 125 ~~~V~~ii~kl~k~e~V~kVei 146 (150)
T COG4492 125 EKDVDKIIEKLRKVEGVEKVEI 146 (150)
T ss_pred hhhHHHHHHHHhcccceeEEEE
Confidence 3445566666777788877765
No 51
>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=44.74 E-value=70 Score=19.31 Aligned_cols=34 Identities=12% Similarity=0.250 Sum_probs=24.3
Q ss_pred ceEEEEEEcCCCHh-HHHHHHHHHhCCCCceEEEE
Q 031710 26 LQTVEVKVRIDCEG-CERKVKRAVEGMKGVKQVDV 59 (154)
Q Consensus 26 ~~~~~l~Vgm~C~~-C~~kI~kal~~~~GV~~v~v 59 (154)
...+.|.+...-.. --..+-++|++++||.+|.+
T Consensus 40 ~~~i~~~v~v~~~~~~l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 40 RANVTISIDTSTMNGDIDELLEELREIDGVEKVEL 74 (76)
T ss_pred eEEEEEEEEcCchHHHHHHHHHHHhcCCCeEEEEE
Confidence 34455555444444 77889999999999998875
No 52
>PRK11023 outer membrane lipoprotein; Provisional
Probab=41.71 E-value=98 Score=23.21 Aligned_cols=43 Identities=21% Similarity=0.250 Sum_probs=30.4
Q ss_pred HhHHHHHHHHHhCCCCce--EEEEeCCCcEEEEEecCCHHHHHHH
Q 031710 38 EGCERKVKRAVEGMKGVK--QVDVERKANKVTVVGYVEPSKVVSR 80 (154)
Q Consensus 38 ~~C~~kI~kal~~~~GV~--~v~vd~~~~~v~V~g~~~~~~v~~~ 80 (154)
..=..+|+.+|..-+.+. .++|...++.|++.|.++.++..++
T Consensus 126 ~~It~kik~~L~~~~~v~~~~I~V~t~~G~V~L~G~v~~~e~~~a 170 (191)
T PRK11023 126 TWITTKVRSQLLTSDSVKSSNVKVTTENGEVFLLGLVTQREAKAA 170 (191)
T ss_pred HHHHHHHHHHHhcCCCCCcceEEEEEECcEEEEEEEeCHHHHHHH
Confidence 335678888888777766 4556667899999988776555333
No 53
>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=41.23 E-value=1e+02 Score=20.14 Aligned_cols=39 Identities=21% Similarity=0.219 Sum_probs=27.6
Q ss_pred HHHHHHHhCCCCceEEEEeCCCcEEEEE--ecCCHHHHHHHHH
Q 031710 42 RKVKRAVEGMKGVKQVDVERKANKVTVV--GYVEPSKVVSRIA 82 (154)
Q Consensus 42 ~kI~kal~~~~GV~~v~vd~~~~~v~V~--g~~~~~~v~~~i~ 82 (154)
.-+-++|-.++||.+|-+. ..=|+|+ ..++.+.|...|.
T Consensus 37 spLA~~Lf~i~gV~~Vf~~--~dfItVtK~~~~~W~~l~~~I~ 77 (87)
T PF08712_consen 37 SPLAQALFAIPGVKSVFIG--DDFITVTKNPDADWEDLKPEIR 77 (87)
T ss_dssp -HHHHHHHTSTTEEEEEEE--TTEEEEEE-TTS-HHHHHHHHH
T ss_pred CHHHHHhcCCCCEeEEEEE--CCEEEEeeCCCCCHHHHHHHHH
Confidence 4566667799999988754 4456776 4578899888887
No 54
>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=38.66 E-value=61 Score=21.46 Aligned_cols=23 Identities=30% Similarity=0.638 Sum_probs=19.7
Q ss_pred HhHHHHHHHHHhCCCCceEEEEe
Q 031710 38 EGCERKVKRAVEGMKGVKQVDVE 60 (154)
Q Consensus 38 ~~C~~kI~kal~~~~GV~~v~vd 60 (154)
.+-...++.++++++||+++++-
T Consensus 61 ~g~td~lee~i~~ve~V~svev~ 83 (88)
T TIGR00489 61 EGGTEAAEESLSGIEGVESVEVT 83 (88)
T ss_pred CcChHHHHHHHhcCCCccEEEEE
Confidence 35568999999999999999874
No 55
>PRK13562 acetolactate synthase 1 regulatory subunit; Provisional
Probab=38.63 E-value=1.1e+02 Score=20.03 Aligned_cols=61 Identities=11% Similarity=0.178 Sum_probs=39.6
Q ss_pred ccccchhhcccC-CCCCcchh----hcCCceEEEEEEcCCCHhHHHHHHHHHhCCCCceEEE-EeCC
Q 031710 2 GVVDHFSDYFDC-SHGSSKLK----KRRQLQTVEVKVRIDCEGCERKVKRAVEGMKGVKQVD-VERK 62 (154)
Q Consensus 2 ~~~~~~~~~~~~-~~~~~~~~----~~~~~~~~~l~Vgm~C~~C~~kI~kal~~~~GV~~v~-vd~~ 62 (154)
|+|-.++.+|+. +..+...- -.+...++++-+.-..+.-..+|.+.|+++..|..|. +|+.
T Consensus 14 GVL~Rit~lFsRRg~NI~SLtvg~Te~~~iSRmtivv~~~d~~~ieqI~kQL~KlidVikV~~~~~~ 80 (84)
T PRK13562 14 STLNRITSAFVRLQYNIDTLHVTHSEQPGISNMEIQVDIQDDTSLHILIKKLKQQINVLTVECYDLV 80 (84)
T ss_pred CHHHHHHHHHhccCcCeeeEEecccCCCCceEEEEEEeCCCHHHHHHHHHHHhCCccEEEEEEeecc
Confidence 788888888754 33332221 2344566666664456777788899999998887765 4443
No 56
>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=38.46 E-value=81 Score=21.59 Aligned_cols=40 Identities=18% Similarity=0.499 Sum_probs=30.6
Q ss_pred CCCCceEEEEeCCCcEEEEEecCCHHHHHHHHHHhhCCceEe
Q 031710 50 GMKGVKQVDVERKANKVTVVGYVEPSKVVSRIAHRTGKKAEI 91 (154)
Q Consensus 50 ~~~GV~~v~vd~~~~~v~V~g~~~~~~v~~~i~~~~G~~a~~ 91 (154)
+..|+...++ ...+.++|.|+--.+++++.++ ++|..+..
T Consensus 39 Rt~GirqfEi-~n~G~~RI~gYk~se~~~~~f~-slG~~~K~ 78 (103)
T PF09158_consen 39 RTKGIRQFEI-RNKGEFRIFGYKMSEEIIKKFT-SLGMEVKQ 78 (103)
T ss_dssp EETTEEEEEE-ETTSEEEEEEES--HHHHHHHH-HTT-EEEE
T ss_pred ccCceeEEEE-ecCCcEEEEEEcCCHHHHHHHH-hcCcEEEE
Confidence 4578888888 5667889999878899999999 99987766
No 57
>PHA01634 hypothetical protein
Probab=38.14 E-value=11 Score=27.31 Aligned_cols=16 Identities=50% Similarity=1.107 Sum_probs=13.0
Q ss_pred EEE-cCCCHhHHHHHHH
Q 031710 31 VKV-RIDCEGCERKVKR 46 (154)
Q Consensus 31 l~V-gm~C~~C~~kI~k 46 (154)
+.| -|+|++|+++|.-
T Consensus 93 ~Di~~iDCeGCE~~l~v 109 (156)
T PHA01634 93 VDIFVMDCEGCEEKLNV 109 (156)
T ss_pred cceEEEEccchHHhcCH
Confidence 557 7999999998853
No 58
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=36.77 E-value=73 Score=21.39 Aligned_cols=22 Identities=14% Similarity=0.371 Sum_probs=19.5
Q ss_pred hCCCCceEEEEeCCCcEEEEEe
Q 031710 49 EGMKGVKQVDVERKANKVTVVG 70 (154)
Q Consensus 49 ~~~~GV~~v~vd~~~~~v~V~g 70 (154)
...+|++.++++.+++++.|.+
T Consensus 37 as~pgis~ieik~E~kkL~v~t 58 (96)
T COG4004 37 ASSPGISRIEIKPENKKLLVNT 58 (96)
T ss_pred EecCCceEEEEecccceEEEec
Confidence 4578999999999999999985
No 59
>COG2092 EFB1 Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis]
Probab=36.74 E-value=67 Score=21.37 Aligned_cols=34 Identities=32% Similarity=0.496 Sum_probs=24.8
Q ss_pred eEEEEEE-cCCCHhHHHHHHHHHhCCCCceEEEEe
Q 031710 27 QTVEVKV-RIDCEGCERKVKRAVEGMKGVKQVDVE 60 (154)
Q Consensus 27 ~~~~l~V-gm~C~~C~~kI~kal~~~~GV~~v~vd 60 (154)
+.+.+.| --+-.+--..++++|+.++||.++++-
T Consensus 49 kal~l~vvv~D~Eg~td~~ee~l~~vegV~sveve 83 (88)
T COG2092 49 KALKLYVVVEDKEGGTDALEEALEEVEGVESVEVE 83 (88)
T ss_pred eeEEEEEEEcccccCcHHHHHHHhhccCcceEEEE
Confidence 3444555 334466688999999999999998863
No 60
>PRK11023 outer membrane lipoprotein; Provisional
Probab=36.44 E-value=95 Score=23.28 Aligned_cols=47 Identities=21% Similarity=0.268 Sum_probs=35.0
Q ss_pred CCHhHHHHHHHHHhCCCCce---EEEEeCCCcEEEEEecCCHHHHHHHHH
Q 031710 36 DCEGCERKVKRAVEGMKGVK---QVDVERKANKVTVVGYVEPSKVVSRIA 82 (154)
Q Consensus 36 ~C~~C~~kI~kal~~~~GV~---~v~vd~~~~~v~V~g~~~~~~v~~~i~ 82 (154)
+...=..+|+.+|..-+.+. .+.|....+.|+++|.++.++......
T Consensus 46 dD~~i~~~V~~aL~~~~~l~~~~~I~V~v~~G~V~L~G~V~~~~~k~~A~ 95 (191)
T PRK11023 46 DDGTLELRVNNALSKDEQIKKEARINVTAYQGKVLLTGQSPNAELSERAK 95 (191)
T ss_pred hhHHHHHHHHHHHhhCcccCcCceEEEEEECCEEEEEEEeCCHHHHHHHH
Confidence 45666889999998877664 588888999999999876554444444
No 61
>PRK08178 acetolactate synthase 1 regulatory subunit; Reviewed
Probab=35.99 E-value=1.1e+02 Score=20.73 Aligned_cols=57 Identities=16% Similarity=0.223 Sum_probs=36.7
Q ss_pred CccccchhhcccC-CCCCcchh----hcCCceEEEEEEcCCCHhHHHHHHHHHhCCCCceEEEE
Q 031710 1 MGVVDHFSDYFDC-SHGSSKLK----KRRQLQTVEVKVRIDCEGCERKVKRAVEGMKGVKQVDV 59 (154)
Q Consensus 1 ~~~~~~~~~~~~~-~~~~~~~~----~~~~~~~~~l~Vgm~C~~C~~kI~kal~~~~GV~~v~v 59 (154)
.|+|-+++.+|+. +..+...- ..+.+.++++-+. + +.-..+|.+.|+++..|..|..
T Consensus 19 pGVL~RIaglFsRRgyNIeSLtvg~te~~~iSRmtivv~-~-~~~i~Qi~kQL~KLidVikV~~ 80 (96)
T PRK08178 19 PGVMSHVCGLFARRAFNVEGILCLPIQDGDKSRIWLLVN-D-DQRLEQMISQIEKLEDVLKVRR 80 (96)
T ss_pred cCHHHHHHHHHhcCCcCeeeEEEeecCCCCceEEEEEEc-C-chHHHHHHHHHhCCcCEEEEEE
Confidence 3888889998864 33332221 2345566777664 2 5677888888888888876643
No 62
>COG3062 NapD Uncharacterized protein involved in formation of periplasmic nitrate reductase [Inorganic ion transport and metabolism]
Probab=35.00 E-value=1.4e+02 Score=20.05 Aligned_cols=43 Identities=19% Similarity=0.225 Sum_probs=30.4
Q ss_pred hHHHHHHHHHhCCCCceEEEEeCCCcEEEEE-ecCCHHHHHHHHH
Q 031710 39 GCERKVKRAVEGMKGVKQVDVERKANKVTVV-GYVEPSKVVSRIA 82 (154)
Q Consensus 39 ~C~~kI~kal~~~~GV~~v~vd~~~~~v~V~-g~~~~~~v~~~i~ 82 (154)
.=...|..+|..++|++--.-|.. +|+.|. ...+...+++.|+
T Consensus 18 e~l~av~~~L~~ip~~EV~~~d~~-GKlVVVie~~~~~~l~~tie 61 (94)
T COG3062 18 ERLSAVKTALLAIPGCEVYGEDAE-GKLVVVIEAEDSETLLETIE 61 (94)
T ss_pred HHHHHHHHHHhcCCCcEeeccCCC-ceEEEEEEcCchHHHHHHHH
Confidence 345788999999999975555555 666654 3347777777776
No 63
>COG1084 Predicted GTPase [General function prediction only]
Probab=34.92 E-value=1.1e+02 Score=25.59 Aligned_cols=49 Identities=27% Similarity=0.560 Sum_probs=34.9
Q ss_pred HHHHHHHHhCCCCceEEEEeCCCcEEEEEec--CCHHHHHHHHHHhhCCceEecccCCCC
Q 031710 41 ERKVKRAVEGMKGVKQVDVERKANKVTVVGY--VEPSKVVSRIAHRTGKKAEIWPYVPYD 98 (154)
Q Consensus 41 ~~kI~kal~~~~GV~~v~vd~~~~~v~V~g~--~~~~~v~~~i~~~~G~~a~~~~~~p~~ 98 (154)
..+++..|.++|.|+ ...-++.|.|. +--..++.+|. +-+.++.+| ||.
T Consensus 151 L~~~r~~l~~LP~Id-----p~~pTivVaG~PNVGKSSlv~~lT---~AkpEvA~Y-PFT 201 (346)
T COG1084 151 LRKARDHLKKLPAID-----PDLPTIVVAGYPNVGKSSLVRKLT---TAKPEVAPY-PFT 201 (346)
T ss_pred HHHHHHHHhcCCCCC-----CCCCeEEEecCCCCcHHHHHHHHh---cCCCccCCC-Ccc
Confidence 345566688888764 77788899886 67788999987 445566655 554
No 64
>PRK09577 multidrug efflux protein; Reviewed
Probab=34.91 E-value=1.2e+02 Score=28.86 Aligned_cols=45 Identities=16% Similarity=0.164 Sum_probs=35.3
Q ss_pred HHHHHHHHhCCCCceEEEEeCCCcEEEEE--------ecCCHHHHHHHHHHhhC
Q 031710 41 ERKVKRAVEGMKGVKQVDVERKANKVTVV--------GYVEPSKVVSRIAHRTG 86 (154)
Q Consensus 41 ~~kI~kal~~~~GV~~v~vd~~~~~v~V~--------g~~~~~~v~~~i~~~~G 86 (154)
+..++..|++++||.+|+++-....+.|. ..++..+|.++|+ ..+
T Consensus 158 ~~~l~~~L~~v~GV~~V~~~G~e~~v~V~vD~~kl~~~Gls~~~V~~~l~-~~n 210 (1032)
T PRK09577 158 SANVLQALRRVEGVGKVQFWGAEYAMRIWPDPVKLAALGLTASDIASAVR-AHN 210 (1032)
T ss_pred HHHHHHHHhcCCCcEEEEecCCceEEEEEeCHHHHHHcCCCHHHHHHHHH-HhC
Confidence 46789999999999999998765666664 2378888999998 654
No 65
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=33.51 E-value=1.2e+02 Score=18.72 Aligned_cols=35 Identities=14% Similarity=0.219 Sum_probs=25.7
Q ss_pred CCceEEEEEEcCCCHhHHHHHHHHHhCCCCceEEE
Q 031710 24 RQLQTVEVKVRIDCEGCERKVKRAVEGMKGVKQVD 58 (154)
Q Consensus 24 ~~~~~~~l~Vgm~C~~C~~kI~kal~~~~GV~~v~ 58 (154)
.....+.|.|...-..=-..|-+.|++++||.+|.
T Consensus 45 ~~~~~~~l~v~V~d~~~L~~ii~~L~~i~~V~~V~ 79 (80)
T PF13291_consen 45 DGTARITLTVEVKDLEHLNQIIRKLRQIPGVISVE 79 (80)
T ss_dssp TTEEEEEEEEEESSHHHHHHHHHHHCTSTTEEEEE
T ss_pred CCEEEEEEEEEECCHHHHHHHHHHHHCCCCeeEEE
Confidence 44555666665566666778888999999998774
No 66
>COG3643 Glutamate formiminotransferase [Amino acid transport and metabolism]
Probab=33.03 E-value=71 Score=25.54 Aligned_cols=49 Identities=27% Similarity=0.284 Sum_probs=29.7
Q ss_pred HHHHHHHHhCCCCceEEE--EeCCCcEEEEEecCCHHHHHHHHHHhhCCce
Q 031710 41 ERKVKRAVEGMKGVKQVD--VERKANKVTVVGYVEPSKVVSRIAHRTGKKA 89 (154)
Q Consensus 41 ~~kI~kal~~~~GV~~v~--vd~~~~~v~V~g~~~~~~v~~~i~~~~G~~a 89 (154)
..+|..+..++++|.-++ .|....+-.++-.-++++++++.-.-+++.+
T Consensus 20 ie~i~a~~~~~~~v~ildve~danhNRsViT~vgdp~~~~~A~f~~ik~Aa 70 (302)
T COG3643 20 IEKIVAAAKSIPTVKILDVEMDANHNRSVITLVGDPSKVVNAAFALIKKAA 70 (302)
T ss_pred HHHHHHHHhcCCceEEEEeccCCCCCceEEEEecChHHHHHHHHHHHHHHH
Confidence 456777788889987444 4455555555544577777776642344333
No 67
>PRK04435 hypothetical protein; Provisional
Probab=32.95 E-value=1e+02 Score=22.12 Aligned_cols=33 Identities=18% Similarity=0.405 Sum_probs=23.0
Q ss_pred eEEEEEEcC-CCHhHHHHHHHHHhCCCCceEEEE
Q 031710 27 QTVEVKVRI-DCEGCERKVKRAVEGMKGVKQVDV 59 (154)
Q Consensus 27 ~~~~l~Vgm-~C~~C~~kI~kal~~~~GV~~v~v 59 (154)
..+.|.|.. +-......+-..|++++||.+|++
T Consensus 110 a~vs~tVevs~~~~~L~~Li~~L~~i~gV~~V~i 143 (147)
T PRK04435 110 ANVTISIDTSSMEGDIDELLEKLRNLDGVEKVEL 143 (147)
T ss_pred EEEEEEEEeCChHHHHHHHHHHHHcCCCcEEEEE
Confidence 445555522 234468888899999999998875
No 68
>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=32.75 E-value=73 Score=23.27 Aligned_cols=27 Identities=26% Similarity=0.346 Sum_probs=23.0
Q ss_pred HhHHHHHHHHHhCCCCceEEEEeCCCc
Q 031710 38 EGCERKVKRAVEGMKGVKQVDVERKAN 64 (154)
Q Consensus 38 ~~C~~kI~kal~~~~GV~~v~vd~~~~ 64 (154)
.+|-..++..+.+++||.++.+-...+
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 578888999999999999999876554
No 69
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=32.67 E-value=1.2e+02 Score=28.88 Aligned_cols=44 Identities=11% Similarity=0.195 Sum_probs=34.1
Q ss_pred HHHHHHHHhCCCCceEEEEeCCCcEEEEE--------ecCCHHHHHHHHHHhh
Q 031710 41 ERKVKRAVEGMKGVKQVDVERKANKVTVV--------GYVEPSKVVSRIAHRT 85 (154)
Q Consensus 41 ~~kI~kal~~~~GV~~v~vd~~~~~v~V~--------g~~~~~~v~~~i~~~~ 85 (154)
+..++..|++++||.+|++.-....+.|. ..++..+|..+|+ ..
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~~v~~al~-~~ 210 (1037)
T PRK10555 159 ASNIQDPLSRVNGVGDIDAYGSQYSMRIWLDPAKLNSFQMTTKDVTDAIE-SQ 210 (1037)
T ss_pred HHHHHHHhhcCCCeEEEEEcCCceEEEEEECHHHHHHcCCCHHHHHHHHH-Hh
Confidence 46788999999999999998655556664 1378888999997 53
No 70
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=32.22 E-value=1.4e+02 Score=24.19 Aligned_cols=27 Identities=22% Similarity=0.314 Sum_probs=23.1
Q ss_pred HhHHHHHHHHHhCCCCceEEEEeCCCc
Q 031710 38 EGCERKVKRAVEGMKGVKQVDVERKAN 64 (154)
Q Consensus 38 ~~C~~kI~kal~~~~GV~~v~vd~~~~ 64 (154)
.+|-..++..+.+++||.++.+-...+
T Consensus 134 gGCFWg~E~~F~~~~GV~~t~vGYagG 160 (283)
T PRK05550 134 GGCFWGVEYYFKKLPGVLSVESGYTGG 160 (283)
T ss_pred cCCchhhhhhHhhCcCEEEEEEeeCCC
Confidence 778888999999999999999876655
No 71
>COG2761 FrnE Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=31.96 E-value=1.2e+02 Score=23.78 Aligned_cols=39 Identities=18% Similarity=0.434 Sum_probs=29.6
Q ss_pred ceEEEEEE--cCCCHhH---HHHHHHHHhCCCCceEEEEeCCCc
Q 031710 26 LQTVEVKV--RIDCEGC---ERKVKRAVEGMKGVKQVDVERKAN 64 (154)
Q Consensus 26 ~~~~~l~V--gm~C~~C---~~kI~kal~~~~GV~~v~vd~~~~ 64 (154)
+.++++.| +.-|+-| .+++++++...++=..+++....-
T Consensus 3 ~~~i~I~v~sD~vCPwC~ig~~rL~ka~~~~~~~~~v~i~w~pf 46 (225)
T COG2761 3 PMKIEIDVFSDVVCPWCYIGKRRLEKALAEYPQEVRVEIRWRPF 46 (225)
T ss_pred CceEEEEEEeCCcCchhhcCHHHHHHHHHhcCcceeEEEEeccc
Confidence 45566776 8999999 789999999988655677665444
No 72
>PRK07334 threonine dehydratase; Provisional
Probab=31.14 E-value=2.7e+02 Score=23.32 Aligned_cols=64 Identities=16% Similarity=0.171 Sum_probs=43.0
Q ss_pred EEEEEE-cCCCHhHHHHHHHHHhCCC-CceEEEEeCC-----CcEEEEE--ec----CCHHHHHHHHHHhhCCceEec
Q 031710 28 TVEVKV-RIDCEGCERKVKRAVEGMK-GVKQVDVERK-----ANKVTVV--GY----VEPSKVVSRIAHRTGKKAEIW 92 (154)
Q Consensus 28 ~~~l~V-gm~C~~C~~kI~kal~~~~-GV~~v~vd~~-----~~~v~V~--g~----~~~~~v~~~i~~~~G~~a~~~ 92 (154)
.+.|.| ..+=.+=-..|-+.|+... .|.++..... .+.+.+. -. ...+.|+++|+ +.||.++++
T Consensus 326 ~v~l~I~~~dr~GlL~dI~~~is~~~~nI~~v~~~~~~~~~~~~~~~i~l~i~V~d~~~L~~vi~~Lr-~~g~~~~~~ 402 (403)
T PRK07334 326 LARLRVDIRDRPGALARVTALIGEAGANIIEVSHQRLFTDLPAKGAELELVIETRDAAHLQEVIAALR-AAGFEARLV 402 (403)
T ss_pred EEEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEEecccCCCCCeEEEEEEEEeCCHHHHHHHHHHHH-HcCCeeEeC
Confidence 367888 6677777888989887663 3555555432 3444333 11 24568899999 999999876
No 73
>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=31.03 E-value=80 Score=20.30 Aligned_cols=22 Identities=14% Similarity=0.206 Sum_probs=18.1
Q ss_pred CCCcEEEEEecCCHHHHHHHHH
Q 031710 61 RKANKVTVVGYVEPSKVVSRIA 82 (154)
Q Consensus 61 ~~~~~v~V~g~~~~~~v~~~i~ 82 (154)
+.+|+++|+|..+.+++.++++
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 6889999999878888777765
No 74
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=30.77 E-value=1.4e+02 Score=18.54 Aligned_cols=55 Identities=11% Similarity=0.067 Sum_probs=35.6
Q ss_pred EEEEEE-cCCCHhHHHHHHHHHhCCCC-ceEEEEeCCCcEEEEE----ec-CCHHHHHHHHH
Q 031710 28 TVEVKV-RIDCEGCERKVKRAVEGMKG-VKQVDVERKANKVTVV----GY-VEPSKVVSRIA 82 (154)
Q Consensus 28 ~~~l~V-gm~C~~C~~kI~kal~~~~G-V~~v~vd~~~~~v~V~----g~-~~~~~v~~~i~ 82 (154)
.+.+.| |.+.++-...|-+.|....+ |.+++...-.+..+.. +. .+.+++.+.++
T Consensus 2 ~~vItv~G~DrpGiv~~v~~~l~~~g~ni~d~~~~~~~~~f~~~~~v~~~~~~~~~l~~~L~ 63 (76)
T PF13740_consen 2 QLVITVVGPDRPGIVAAVTGVLAEHGCNIEDSRQAVLGGRFTLIMLVSIPEDSLERLESALE 63 (76)
T ss_dssp EEEEEEEEE--TTHHHHHHHHHHCTT-EEEEEEEEEETTEEEEEEEEEESHHHHHHHHHHHH
T ss_pred EEEEEEEecCCCcHHHHHHHHHHHCCCcEEEEEEEEEcCeEEEEEEEEeCcccHHHHHHHHH
Confidence 567888 99999999999999999866 5566666555555433 22 24455555555
No 75
>COG0225 MsrA Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=30.52 E-value=63 Score=24.24 Aligned_cols=35 Identities=17% Similarity=0.191 Sum_probs=26.9
Q ss_pred CceEEEEEEcCCCHhHHHHHHHHHhCCCCceEEEEeCCCc
Q 031710 25 QLQTVEVKVRIDCEGCERKVKRAVEGMKGVKQVDVERKAN 64 (154)
Q Consensus 25 ~~~~~~l~Vgm~C~~C~~kI~kal~~~~GV~~v~vd~~~~ 64 (154)
.|+++.|. .+|-.-+++.+.+++||.++.+-...+
T Consensus 5 ~~~~a~fa-----gGCFWg~E~~f~~i~GV~~t~~GYagG 39 (174)
T COG0225 5 GMEKAYFA-----GGCFWGVEAYFEQIPGVLSTVSGYAGG 39 (174)
T ss_pred CcEEEEEe-----ccCccchHHHHhhCCCeEEEeeeEcCC
Confidence 34555554 678888899999999999998876555
No 76
>cd04902 ACT_3PGDH-xct C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH). The C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with an extended C-terminal (xct) region from bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback-controlled by the end product L-serine in an allosteric manner. Some 3PGDH enzymes have an additional domain formed by an extended C-terminal region. This additional domain introduces significant asymmetry to the homotetramer. Adjacent ACT (regulatory) domains interact, creating two serine-binding sites, however, this asymmetric arrangement results in the formation of two different and distinct domain interfaces between iden
Probab=30.08 E-value=92 Score=18.46 Aligned_cols=31 Identities=13% Similarity=0.146 Sum_probs=21.2
Q ss_pred CceEEEEEE-cCCCHhHHHHHHHHHhCCCCceEEEE
Q 031710 25 QLQTVEVKV-RIDCEGCERKVKRAVEGMKGVKQVDV 59 (154)
Q Consensus 25 ~~~~~~l~V-gm~C~~C~~kI~kal~~~~GV~~v~v 59 (154)
....+.+.+ +.. ...+.+.|++++||..+.+
T Consensus 39 ~~~~~~i~v~~~~----~~~~~~~l~~~~~v~~v~~ 70 (73)
T cd04902 39 GEALMVLSVDEPV----PDEVLEELRALPGILSAKV 70 (73)
T ss_pred CEEEEEEEeCCCC----CHHHHHHHHcCCCccEEEE
Confidence 344566777 532 3478888999999987764
No 77
>PRK00435 ef1B elongation factor 1-beta; Validated
Probab=29.81 E-value=59 Score=21.54 Aligned_cols=23 Identities=39% Similarity=0.625 Sum_probs=20.2
Q ss_pred HhHHHHHHHHHhCCCCceEEEEe
Q 031710 38 EGCERKVKRAVEGMKGVKQVDVE 60 (154)
Q Consensus 38 ~~C~~kI~kal~~~~GV~~v~vd 60 (154)
.+-...++.++++++||+++++-
T Consensus 61 ~~~td~lee~i~~~e~Vqsvei~ 83 (88)
T PRK00435 61 EGGTEPVEEAFANVEGVESVEVE 83 (88)
T ss_pred CcCcHHHHHHHhccCCCcEEEEE
Confidence 57778999999999999999874
No 78
>PF13192 Thioredoxin_3: Thioredoxin domain; PDB: 1ZYP_B 1ZYN_A 1HYU_A 1ILO_A 1J08_F 2YWM_B 2AYT_B 2HLS_B 1A8L_A 2K8S_B ....
Probab=29.51 E-value=75 Score=19.70 Aligned_cols=10 Identities=20% Similarity=0.527 Sum_probs=8.0
Q ss_pred EcCCCHhHHH
Q 031710 33 VRIDCEGCER 42 (154)
Q Consensus 33 Vgm~C~~C~~ 42 (154)
++..|+.|..
T Consensus 6 ~~~~C~~C~~ 15 (76)
T PF13192_consen 6 FSPGCPYCPE 15 (76)
T ss_dssp ECSSCTTHHH
T ss_pred eCCCCCCcHH
Confidence 4888999983
No 79
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=29.08 E-value=2.1e+02 Score=20.21 Aligned_cols=49 Identities=18% Similarity=0.371 Sum_probs=31.6
Q ss_pred HHHHHHHhCCCCceEEEEeCCCcEEEEEecCCHHHHHHHH----HHhhCCceEe
Q 031710 42 RKVKRAVEGMKGVKQVDVERKANKVTVVGYVEPSKVVSRI----AHRTGKKAEI 91 (154)
Q Consensus 42 ~kI~kal~~~~GV~~v~vd~~~~~v~V~g~~~~~~v~~~i----~~~~G~~a~~ 91 (154)
..++..|.++ |-..|+.-+.++.|......+++++..+| ++..|+.+..
T Consensus 22 aeLr~~l~~~-Gf~~V~Tyi~SGNvvf~~~~~~~~l~~~ie~~l~~~fG~~v~v 74 (137)
T PF08002_consen 22 AELREALEDL-GFTNVRTYIQSGNVVFESDRDPAELAAKIEKALEERFGFDVPV 74 (137)
T ss_dssp HHHHHHHHHC-T-EEEEEETTTTEEEEEESS-HHHHHHHHHHHHHHH-TT---E
T ss_pred HHHHHHHHHc-CCCCceEEEeeCCEEEecCCChHHHHHHHHHHHHHhcCCCeEE
Confidence 4556667666 88999999999999999666776665554 4456877543
No 80
>PF13383 Methyltransf_22: Methyltransferase domain
Probab=28.74 E-value=1.1e+02 Score=24.03 Aligned_cols=56 Identities=25% Similarity=0.375 Sum_probs=36.4
Q ss_pred EEEE-cCCCHhHHHHHHHHHhCCCCceEEEEeCCCcEEEEE--ecC----CHHHHHHHHHHhhCCceEecccCC
Q 031710 30 EVKV-RIDCEGCERKVKRAVEGMKGVKQVDVERKANKVTVV--GYV----EPSKVVSRIAHRTGKKAEIWPYVP 96 (154)
Q Consensus 30 ~l~V-gm~C~~C~~kI~kal~~~~GV~~v~vd~~~~~v~V~--g~~----~~~~v~~~i~~~~G~~a~~~~~~p 96 (154)
.+.| .|+|++|+..+-..+.. .|+ ..+.|+ +.. ...++++.|+ +.||..--..+.|
T Consensus 167 ~idiLKiDIEG~Ew~~L~~~l~-~~~---------~Qi~iEiH~~~~~~~~~~~~l~~l~-~~gfr~F~~e~N~ 229 (242)
T PF13383_consen 167 EIDILKIDIEGAEWTVLEPLLE-SGV---------CQILIEIHGWPSEHREWYKLLQELE-KAGFRLFNVEPNP 229 (242)
T ss_pred cccEEEEEcCccHHHHHHHHHh-cCC---------cEEEEEEEeCccchhHHHHHHHHHH-HCCcEEEEecCCh
Confidence 4666 89999999999777643 344 233333 321 2346899999 9998755555444
No 81
>KOG3411 consensus 40S ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=27.28 E-value=55 Score=23.50 Aligned_cols=42 Identities=29% Similarity=0.398 Sum_probs=28.4
Q ss_pred HhHHHHHHHHHhCCCCceEEEEeCCCc-EEEEEecCCHHHHHHHHH
Q 031710 38 EGCERKVKRAVEGMKGVKQVDVERKAN-KVTVVGYVEPSKVVSRIA 82 (154)
Q Consensus 38 ~~C~~kI~kal~~~~GV~~v~vd~~~~-~v~V~g~~~~~~v~~~i~ 82 (154)
.+|.+++-++|+++. -|+-+...+ +++-.|..+.+.|...|.
T Consensus 97 ~~i~rkvlQ~Le~~~---~ve~hp~gGR~lt~~GqrdldrIa~~i~ 139 (143)
T KOG3411|consen 97 GGIARKVLQALEKMG---IVEKHPKGGRRLTEQGQRDLDRIAGQIR 139 (143)
T ss_pred cHHHHHHHHHHHhCC---ceeeCCCCcceeCcccchhHHHHHHHHH
Confidence 667777777766654 345555544 455568889999988886
No 82
>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=27.11 E-value=94 Score=24.73 Aligned_cols=30 Identities=20% Similarity=0.401 Sum_probs=26.1
Q ss_pred HHHHHHHHHhCCCCceEEEEeCCCcEEEEE
Q 031710 40 CERKVKRAVEGMKGVKQVDVERKANKVTVV 69 (154)
Q Consensus 40 C~~kI~kal~~~~GV~~v~vd~~~~~v~V~ 69 (154)
-...|+++|..++||..+.+-...+++.+-
T Consensus 88 Ty~Avk~aLL~~~gv~haNI~SsaGtiniY 117 (291)
T PF03434_consen 88 TYEAVKSALLNLNGVEHANIKSSAGTINIY 117 (291)
T ss_pred hHHHHHHHhcCCCCceeeeeecCCCeeEEE
Confidence 367899999999999999998888888763
No 83
>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=27.04 E-value=1.3e+02 Score=18.40 Aligned_cols=16 Identities=19% Similarity=0.461 Sum_probs=8.5
Q ss_pred HHHHHHHhCCCCceEE
Q 031710 42 RKVKRAVEGMKGVKQV 57 (154)
Q Consensus 42 ~kI~kal~~~~GV~~v 57 (154)
..+-+.|++++||.+|
T Consensus 52 ~~li~~L~~i~gV~~V 67 (74)
T cd04877 52 QTLMPEIRRIDGVEDV 67 (74)
T ss_pred HHHHHHHhCCCCceEE
Confidence 4445555555555544
No 84
>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=26.68 E-value=49 Score=24.05 Aligned_cols=27 Identities=22% Similarity=0.233 Sum_probs=22.7
Q ss_pred HhHHHHHHHHHhCCCCceEEEEeCCCc
Q 031710 38 EGCERKVKRAVEGMKGVKQVDVERKAN 64 (154)
Q Consensus 38 ~~C~~kI~kal~~~~GV~~v~vd~~~~ 64 (154)
.+|-.-++..+.+++||.++.+-...+
T Consensus 7 gGCFWg~E~~f~~~~GV~~t~~GYagG 33 (149)
T TIGR00401 7 GGCFWGVEKYFWLIPGVYSTAVGYTGG 33 (149)
T ss_pred cCCchhhHHHHhcCCCEEEEEEeeCCC
Confidence 678888899999999999998876554
No 85
>PF13216 DUF4024: Protein of unknown function (DUF4024)
Probab=26.00 E-value=23 Score=18.78 Aligned_cols=11 Identities=27% Similarity=0.350 Sum_probs=8.8
Q ss_pred CCCCCCCCCCC
Q 031710 140 TTAFSDENTQA 150 (154)
Q Consensus 140 ~~~FsDdNpna 150 (154)
.++|.|||.|-
T Consensus 9 lhlfrde~vnf 19 (35)
T PF13216_consen 9 LHLFRDEKVNF 19 (35)
T ss_pred EEEeecCCccE
Confidence 46899999883
No 86
>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=25.73 E-value=76 Score=24.16 Aligned_cols=21 Identities=29% Similarity=0.556 Sum_probs=18.2
Q ss_pred HHHHHHHHhCCCCceEEEEeC
Q 031710 41 ERKVKRAVEGMKGVKQVDVER 61 (154)
Q Consensus 41 ~~kI~kal~~~~GV~~v~vd~ 61 (154)
+..+++.|+.++||.++.|.+
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 578899999999999888873
No 87
>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=25.67 E-value=1.2e+02 Score=26.78 Aligned_cols=39 Identities=21% Similarity=0.304 Sum_probs=30.8
Q ss_pred HhCCCCceEEEEeCCCcEEEEEecCCHHHHHHHHHHhhCCce
Q 031710 48 VEGMKGVKQVDVERKANKVTVVGYVEPSKVVSRIAHRTGKKA 89 (154)
Q Consensus 48 l~~~~GV~~v~vd~~~~~v~V~g~~~~~~v~~~i~~~~G~~a 89 (154)
|..+.+| +++|..+++|+|.+.+...+|.+.+. +.|+..
T Consensus 110 L~~ln~V--l~vD~~~~tVtV~AG~~l~~L~~~L~-~~Glal 148 (541)
T TIGR01676 110 LALMDKV--LEVDEEKKRVRVQAGIRVQQLVDAIK-EYGITL 148 (541)
T ss_pred hhhCCCC--EEEcCCCCEEEEcCCCCHHHHHHHHH-HcCCEe
Confidence 3445555 46788899999998889999999999 888654
No 88
>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=25.44 E-value=66 Score=24.37 Aligned_cols=29 Identities=28% Similarity=0.436 Sum_probs=20.9
Q ss_pred HHHHHHHHHhCCCCceEEEE--eCCCcEEEE
Q 031710 40 CERKVKRAVEGMKGVKQVDV--ERKANKVTV 68 (154)
Q Consensus 40 C~~kI~kal~~~~GV~~v~v--d~~~~~v~V 68 (154)
-+.+++..|+++.||.+|+| .+..+.-.|
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 57788999999999987654 555544444
No 89
>PRK15127 multidrug efflux system protein AcrB; Provisional
Probab=25.23 E-value=2e+02 Score=27.52 Aligned_cols=44 Identities=16% Similarity=0.225 Sum_probs=33.7
Q ss_pred HHHHHHHHhCCCCceEEEEeCCCcEEEEE--------ecCCHHHHHHHHHHhh
Q 031710 41 ERKVKRAVEGMKGVKQVDVERKANKVTVV--------GYVEPSKVVSRIAHRT 85 (154)
Q Consensus 41 ~~kI~kal~~~~GV~~v~vd~~~~~v~V~--------g~~~~~~v~~~i~~~~ 85 (154)
+..++..|++++||.+|++.-....+.|. ..+++.+|..+|+ ..
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vDp~kl~~~gls~~~V~~~l~-~~ 210 (1049)
T PRK15127 159 AANMKDPISRTSGVGDVQLFGSQYAMRIWMNPNELNKFQLTPVDVINAIK-AQ 210 (1049)
T ss_pred HHHHHHHHhcCCCceEEEEcCCceEEEEEeCHHHHHHcCCCHHHHHHHHH-Hh
Confidence 35688999999999999987655556665 1368888888887 54
No 90
>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=25.11 E-value=80 Score=19.18 Aligned_cols=40 Identities=10% Similarity=0.172 Sum_probs=24.1
Q ss_pred HHHHHHhCCCCceEEEEeC----CCcEEEEE-ecCCHHHHHHHHH
Q 031710 43 KVKRAVEGMKGVKQVDVER----KANKVTVV-GYVEPSKVVSRIA 82 (154)
Q Consensus 43 kI~kal~~~~GV~~v~vd~----~~~~v~V~-g~~~~~~v~~~i~ 82 (154)
.||.+|.+.+||.++.|-. ..+...+- -..+.++|.+.++
T Consensus 1 EIE~~l~~~~~V~~~~V~~~~d~~~g~~l~a~vv~~~~~i~~~~~ 45 (73)
T PF13193_consen 1 EIESVLRQHPGVAEAAVVGVPDEDWGERLVAFVVLDEEEIRDHLR 45 (73)
T ss_dssp HHHHHHHTSTTEEEEEEEEEEETTTEEEEEEEEEEHHHHHHHHHH
T ss_pred CHHHHHhcCCCccEEEEEEEEcccccccceeEEEeeecccccchh
Confidence 3789999999998776532 12221111 1114577777777
No 91
>PF08777 RRM_3: RNA binding motif; InterPro: IPR014886 This domain is found in protein La which functions as an RNA chaperone during RNA polymerase III transcription, and can also stimulate translation initiation. It contains a five stranded beta sheet which forms an atypical RNA recognition motif []. ; PDB: 1OWX_A.
Probab=24.93 E-value=2.2e+02 Score=19.12 Aligned_cols=55 Identities=16% Similarity=0.159 Sum_probs=31.4
Q ss_pred EEEE-cCCCHhHHHHHHHHHhCCCCceEEEEeCCCcEEEEE--ecCCHHHHHHHHHHhh
Q 031710 30 EVKV-RIDCEGCERKVKRAVEGMKGVKQVDVERKANKVTVV--GYVEPSKVVSRIAHRT 85 (154)
Q Consensus 30 ~l~V-gm~C~~C~~kI~kal~~~~GV~~v~vd~~~~~v~V~--g~~~~~~v~~~i~~~~ 85 (154)
.+++ |+.-+-+...|+..|+....|.-|++........|. ..-....+++++. ..
T Consensus 3 il~~~g~~~~~~re~iK~~f~~~g~V~yVD~~~G~~~g~VRf~~~~~A~~a~~~~~-~~ 60 (105)
T PF08777_consen 3 ILKFSGLGEPTSREDIKEAFSQFGEVAYVDFSRGDTEGYVRFKTPEAAQKALEKLK-EA 60 (105)
T ss_dssp EEEEEE--SS--HHHHHHHT-SS--EEEEE--TT-SEEEEEESS---HHHHHHHHH-HT
T ss_pred EEEEecCCCCcCHHHHHHHHHhcCCcceEEecCCCCEEEEEECCcchHHHHHHHHH-hc
Confidence 4666 666666688999999999888888877766666665 3345777888887 54
No 92
>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=24.87 E-value=2e+02 Score=27.50 Aligned_cols=43 Identities=16% Similarity=0.268 Sum_probs=34.1
Q ss_pred HHHHHHHHhCCCCceEEEEeCCCcEEEEE--------ecCCHHHHHHHHHHh
Q 031710 41 ERKVKRAVEGMKGVKQVDVERKANKVTVV--------GYVEPSKVVSRIAHR 84 (154)
Q Consensus 41 ~~kI~kal~~~~GV~~v~vd~~~~~v~V~--------g~~~~~~v~~~i~~~ 84 (154)
...++..|++++||.+|++.-....+.|. ..+++.+|..+|+ .
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~dV~~~i~-~ 209 (1044)
T TIGR00915 159 ASNMVDPISRLEGVGDVQLFGSQYAMRIWLDPAKLNSYQLTPADVISAIQ-A 209 (1044)
T ss_pred HHHHHHHHhCCCCceEEEecCCceEEEEEECHHHHHHcCCCHHHHHHHHH-H
Confidence 35689999999999999998665556665 1378899999998 5
No 93
>cd04887 ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI and related domains. The ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI, a malolactic enzyme (MalLac-Enz) which converts malate to lactate, and other related ACT domains. The yqkJ product is predicted to convert malate directly to lactate, as opposed to related malic enzymes that convert malate to pyruvate. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=24.73 E-value=1.6e+02 Score=17.52 Aligned_cols=35 Identities=20% Similarity=0.270 Sum_probs=22.3
Q ss_pred CceEEEEEEcCCCHhHHHHHHHHHhCCCCceEEEE
Q 031710 25 QLQTVEVKVRIDCEGCERKVKRAVEGMKGVKQVDV 59 (154)
Q Consensus 25 ~~~~~~l~Vgm~C~~C~~kI~kal~~~~GV~~v~v 59 (154)
....+.|.+...-..=...|.+.|++++||...++
T Consensus 38 ~~~~~~~~vev~~~~~l~~i~~~L~~i~gV~~~~~ 72 (74)
T cd04887 38 DYTVRDITVDAPSEEHAETIVAAVRALPEVKVLSV 72 (74)
T ss_pred CEEEEEEEEEcCCHHHHHHHHHHHhcCCCeEEEEe
Confidence 34444555544445556678888999999875544
No 94
>COG4669 EscJ Type III secretory pathway, lipoprotein EscJ [Intracellular trafficking and secretion]
Probab=24.15 E-value=78 Score=25.05 Aligned_cols=21 Identities=24% Similarity=0.420 Sum_probs=17.0
Q ss_pred hHHHHHHHHHhCCCCceEEEE
Q 031710 39 GCERKVKRAVEGMKGVKQVDV 59 (154)
Q Consensus 39 ~C~~kI~kal~~~~GV~~v~v 59 (154)
+=+..+++.|++|+||.++.|
T Consensus 109 ~~eQ~le~tLs~mDGVi~ArV 129 (246)
T COG4669 109 AKEQQLEQTLSKMDGVISARV 129 (246)
T ss_pred HHHHHHHHHHHhcCceEEEEE
Confidence 447789999999999976554
No 95
>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=23.98 E-value=92 Score=18.53 Aligned_cols=21 Identities=19% Similarity=0.476 Sum_probs=15.3
Q ss_pred hCCCCceEEEEeCCCcEEEEE
Q 031710 49 EGMKGVKQVDVERKANKVTVV 69 (154)
Q Consensus 49 ~~~~GV~~v~vd~~~~~v~V~ 69 (154)
..++||..|.+-...+++.+.
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 345789999888888666653
No 96
>PRK15078 polysaccharide export protein Wza; Provisional
Probab=23.82 E-value=1.9e+02 Score=24.24 Aligned_cols=56 Identities=21% Similarity=0.309 Sum_probs=39.2
Q ss_pred EEEE-cCCCHhHHHHHHHHHhCCCCceEEEEe---CCCcEEEEEec--------C-C-HHHHHHHHHHhhC
Q 031710 30 EVKV-RIDCEGCERKVKRAVEGMKGVKQVDVE---RKANKVTVVGY--------V-E-PSKVVSRIAHRTG 86 (154)
Q Consensus 30 ~l~V-gm~C~~C~~kI~kal~~~~GV~~v~vd---~~~~~v~V~g~--------~-~-~~~v~~~i~~~~G 86 (154)
.++| |++-+.=...|++.|.+.----.|.|. ....+|+|.|. + + +..|+++|. .+|
T Consensus 133 ~V~vaG~T~~e~~~~I~~~L~~~~~~PqV~V~v~~~~s~~V~V~GeV~~PG~~~l~~~~~tlldaIa-~AG 202 (379)
T PRK15078 133 KVHVAGKTVTEIRSDITGRLAKYIESPQVDVNIAAFRSQKAYVTGEVNKSGQQAITNVPLTILDAIN-AAG 202 (379)
T ss_pred eEEECCCCHHHHHHHHHHHHHHhccCCeEEEEEccCCceEEEEEceecCCeEEEecCCCccHHHHHH-Hcc
Confidence 6889 999999999999999865111133333 45668998753 2 2 467899998 665
No 97
>PF12685 SpoIIIAH: SpoIIIAH-like protein; InterPro: IPR024232 Stage III sporulation protein AH (SpoIIIAH) is a protein that is involved in forespore engulfment. It forms a channel with SpoIIIAH that is open on the forespore end and closed (or gated) on the mother cell end. This allows sigma-E-directed gene expression in the mother-cell compartment of the sporangium to trigger the activation of sigma-G forespore-specific gene expression by a pathway of intercellular signaling. This family of proteins is found in bacteria, archaea and eukaryotes and so must have a wider function than in sporulation. Proteins in this family are typically between 174 and 223 amino acids in length.; PDB: 3UZ0_A 3TUF_A.
Probab=23.70 E-value=2e+02 Score=21.54 Aligned_cols=48 Identities=21% Similarity=0.328 Sum_probs=31.9
Q ss_pred HHHHHHHHhCCCCceEEEEeCCCcEEEEE--e-c---CCHHHHHHHHHHhhCCce
Q 031710 41 ERKVKRAVEGMKGVKQVDVERKANKVTVV--G-Y---VEPSKVVSRIAHRTGKKA 89 (154)
Q Consensus 41 ~~kI~kal~~~~GV~~v~vd~~~~~v~V~--g-~---~~~~~v~~~i~~~~G~~a 89 (154)
+..||..|+.- |-.++-|.+...++.|. . . .+..+|...+.+.+|..+
T Consensus 137 E~~iE~llkak-Gf~davv~~~~~~v~VvV~~~~L~~~~~~~I~diV~~~~~v~~ 190 (196)
T PF12685_consen 137 EMEIENLLKAK-GFEDAVVFIEDDSVDVVVKADKLSDAEAAQIIDIVMRETGVPA 190 (196)
T ss_dssp HHHHHHHHHTT-S-SEEEEE-SSSEEEEEEE-S---HHHHHHHHHHHHHHHC-ST
T ss_pred HHHHHHHHHhC-CCCceEEEeeCCEEEEEEeCCCCCHHHHHHHHHHHHHHhCCCc
Confidence 56777777754 99999999998888876 2 2 345667777776777554
No 98
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=22.97 E-value=2.1e+02 Score=25.73 Aligned_cols=62 Identities=18% Similarity=0.225 Sum_probs=44.1
Q ss_pred CCHhHHHHHHHHHhCCCCceEEEEeCCCcEEEEEec----C--CHHHHHHHHHHhhCCceEecccCCC
Q 031710 36 DCEGCERKVKRAVEGMKGVKQVDVERKANKVTVVGY----V--EPSKVVSRIAHRTGKKAEIWPYVPY 97 (154)
Q Consensus 36 ~C~~C~~kI~kal~~~~GV~~v~vd~~~~~v~V~g~----~--~~~~v~~~i~~~~G~~a~~~~~~p~ 97 (154)
.-+.-..+|++.+-.-.||.++.+|..++.|.|... + .....+..|.+++|....++...|-
T Consensus 67 ~~~~~~~~i~~~~~~~~~~~~~~f~~~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~~~ 134 (630)
T TIGR03675 67 PPEEAIEKIKEIVPEEAGITDIYFDDVTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTPPI 134 (630)
T ss_pred CHHHHHHHHHHhCCCcCCceeEEecCCCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecCCC
Confidence 345556677777777789999999999999999732 1 2344455555589998888776553
No 99
>COG0178 UvrA Excinuclease ATPase subunit [DNA replication, recombination, and repair]
Probab=22.93 E-value=36 Score=31.75 Aligned_cols=37 Identities=27% Similarity=0.456 Sum_probs=25.6
Q ss_pred ccccchhhcccCCCCCcchhhcCC--ceEEEEEE-cCCCHhHHH
Q 031710 2 GVVDHFSDYFDCSHGSSKLKKRRQ--LQTVEVKV-RIDCEGCER 42 (154)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~l~V-gm~C~~C~~ 42 (154)
|++|.|++||... ...|... --++.|.| |=.|+.|..
T Consensus 699 g~Fd~IR~lFA~t----peAK~rGyk~grFSFNvkGGRCe~C~G 738 (935)
T COG0178 699 GVFDDIRELFAGT----PEAKARGYKPGRFSFNVKGGRCEACQG 738 (935)
T ss_pred cchHHHHHHHhcC----hHHHHcCCCcccccccCCCcCCccccC
Confidence 8999999999763 3322222 23466788 888999964
No 100
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=22.76 E-value=1.1e+02 Score=22.04 Aligned_cols=56 Identities=21% Similarity=0.414 Sum_probs=28.5
Q ss_pred EEEEEcCCCHhH------HHHHHHHHhCCCCceEEEEeCCCcEEEEEecCCHHHHHHHHHHhhCC
Q 031710 29 VEVKVRIDCEGC------ERKVKRAVEGMKGVKQVDVERKANKVTVVGYVEPSKVVSRIAHRTGK 87 (154)
Q Consensus 29 ~~l~Vgm~C~~C------~~kI~kal~~~~GV~~v~vd~~~~~v~V~g~~~~~~v~~~i~~~~G~ 87 (154)
+.+.|-+.-.+| ...|+.+|..+ |+.+|+|++.-.-..-+..+ .++-.++|+ ..|.
T Consensus 27 V~VtIt~Ty~gcpa~e~L~~~I~~aL~~~-Gv~~V~V~i~~~p~Wt~d~i-t~~gr~~l~-~~gi 88 (146)
T TIGR02159 27 VVVKFTPTYSGCPALEVIRQDIRDAVRAL-GVEVVEVSTSLDPPWTTDWI-TEDAREKLR-EYGI 88 (146)
T ss_pred EEEEEEeCCCCCchHHHHHHHHHHHHHhc-CCCeEEEeEeeCCCCChHHC-CHHHHHHHH-hcCc
Confidence 444444444444 34578888886 88877775422211111112 234456666 5563
No 101
>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=22.19 E-value=77 Score=20.02 Aligned_cols=23 Identities=17% Similarity=0.407 Sum_probs=17.9
Q ss_pred cCCCHhHHHHHHHHHhCCCCceE
Q 031710 34 RIDCEGCERKVKRAVEGMKGVKQ 56 (154)
Q Consensus 34 gm~C~~C~~kI~kal~~~~GV~~ 56 (154)
-|-|+.|.....+++++-.=..+
T Consensus 15 tLPC~~Cr~HA~~ai~kNNiMSs 37 (70)
T PF04805_consen 15 TLPCPECRIHAKEAIQKNNIMSS 37 (70)
T ss_pred cCCCHHHHHHHHHHHHhcCcccc
Confidence 57899999999999987644433
No 102
>TIGR00914 2A0601 heavy metal efflux pump (cobalt-zinc-cadmium). This model represents a family of H+/heavy metal cation antiporters. This family is one of several subfamilies within the scope of pfam model pfam00873.
Probab=22.12 E-value=1.4e+02 Score=28.53 Aligned_cols=55 Identities=27% Similarity=0.335 Sum_probs=39.2
Q ss_pred EEEEEE-cCCCH---hHHHHHHHHHhCCCCceEEEEeCCC--cEEEEE--------ecCCHHHHHHHHH
Q 031710 28 TVEVKV-RIDCE---GCERKVKRAVEGMKGVKQVDVERKA--NKVTVV--------GYVEPSKVVSRIA 82 (154)
Q Consensus 28 ~~~l~V-gm~C~---~C~~kI~kal~~~~GV~~v~vd~~~--~~v~V~--------g~~~~~~v~~~i~ 82 (154)
.+++.+ |-+=+ .-+.+|+..|.+++||.+++.|... ..+.|. ..+++++|.+.++
T Consensus 683 ~i~i~l~G~d~~~L~~~a~~v~~~l~~~pgv~~v~~~~~~~~~e~~i~id~~~~~~~Glt~~~v~~~l~ 751 (1051)
T TIGR00914 683 DVAVKVFGDDLDDLDATAEKISAVLKGVPGAADVKVEQTTGLPYLTVEIDREKAARYGLTVGDVQDTVA 751 (1051)
T ss_pred CeEEEEECCCHHHHHHHHHHHHHHHhcCCCceeeeccccCCCceEEEEECHHHHHHcCCCHHHHHHHHH
Confidence 477888 74422 3366789999999999999988654 344443 1268888888887
No 103
>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=21.93 E-value=1.3e+02 Score=20.82 Aligned_cols=29 Identities=24% Similarity=0.323 Sum_probs=24.1
Q ss_pred EEEEecCCHHHHHHHHHHhhCCceEecccC
Q 031710 66 VTVVGYVEPSKVVSRIAHRTGKKAEIWPYV 95 (154)
Q Consensus 66 v~V~g~~~~~~v~~~i~~~~G~~a~~~~~~ 95 (154)
+.|+|+.|-..+++.++ +.|+++.++...
T Consensus 104 vLvSgD~Df~~~i~~lr-~~G~~V~v~~~~ 132 (149)
T cd06167 104 VLVSGDSDFVPLVERLR-ELGKRVIVVGFE 132 (149)
T ss_pred EEEECCccHHHHHHHHH-HcCCEEEEEccC
Confidence 34568889999999999 889999998863
No 104
>TIGR02898 spore_YhcN_YlaJ sporulation lipoprotein, YhcN/YlaJ family. YhcN and YlaJ 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 that is not included in the seed alignment for this model. A portion of the low-complexity region between the lipoprotein signal sequence and the main conserved region of the protein family was also excised from the seed alignment.
Probab=21.84 E-value=3.3e+02 Score=19.97 Aligned_cols=31 Identities=23% Similarity=0.230 Sum_probs=25.7
Q ss_pred hHHHHHHHHHhCCCCceEEEEeCCCcEEEEE
Q 031710 39 GCERKVKRAVEGMKGVKQVDVERKANKVTVV 69 (154)
Q Consensus 39 ~C~~kI~kal~~~~GV~~v~vd~~~~~v~V~ 69 (154)
.=+.+|.+.+.+++||.++.+=.....+.|-
T Consensus 54 ~~A~~Ia~~v~~v~~V~dA~vvVtg~~A~Vg 84 (158)
T TIGR02898 54 DVADEIASEAAKVKGVKDATVVITGNYAYVG 84 (158)
T ss_pred HHHHHHHHHHhcCCCCceEEEEEECCEEEEE
Confidence 5678899999999999999887777777664
No 105
>KOG4730 consensus D-arabinono-1, 4-lactone oxidase [Defense mechanisms]
Probab=21.65 E-value=1.1e+02 Score=26.59 Aligned_cols=61 Identities=15% Similarity=0.321 Sum_probs=40.3
Q ss_pred cCCceEEEE--EE-cCCCHhHHHHHHHHHhCCCCceEEEEeCCCcEEEEEecCCHHHHHHHHHHhhCCce
Q 031710 23 RRQLQTVEV--KV-RIDCEGCERKVKRAVEGMKGVKQVDVERKANKVTVVGYVEPSKVVSRIAHRTGKKA 89 (154)
Q Consensus 23 ~~~~~~~~l--~V-gm~C~~C~~kI~kal~~~~GV~~v~vd~~~~~v~V~g~~~~~~v~~~i~~~~G~~a 89 (154)
+.++..+.. .+ +|.|..- .--.+..++-| +++|.+..+|||...+...+|++.+. +.|+..
T Consensus 73 ~~kirvVg~gHSp~~l~ctdg---~lisl~~lnkV--v~~dpe~~tvTV~aGirlrQLie~~~-~~GlsL 136 (518)
T KOG4730|consen 73 GKKIRVVGSGHSPSKLVCTDG---LLISLDKLNKV--VEFDPELKTVTVQAGIRLRQLIEELA-KLGLSL 136 (518)
T ss_pred CceEEEecccCCCCcceeccc---cEEEhhhhccc--eeeCchhceEEeccCcCHHHHHHHHH-hcCccc
Confidence 344444443 24 6677655 11122333444 56688889999998889999999999 999864
No 106
>PF07837 FTCD_N: Formiminotransferase domain, N-terminal subdomain; InterPro: IPR012886 The formiminotransferase (FT) domain of formiminotransferase-cyclodeaminase (FTCD) forms a homodimer, with each protomer being comprised of two subdomains. The formiminotransferase domain has an N-terminal subdomain that is made up of a six-stranded mixed beta-pleated sheet and five alpha helices, which are arranged on the external surface of the beta sheet. This, in turn, faces the beta-sheet of the C-terminal subdomain to form a double beta-sheet layer. The two subdomains are separated by a short linker sequence, which is not thought to be any more flexible than the remainder of the molecule. The substrate is predicted to form a number of contacts with residues found in both the N-terminal and C-terminal subdomains []. This entry represents the N-terminal subdomain of the formiminotransferase domain.; GO: 0005542 folic acid binding, 0016740 transferase activity, 0008152 metabolic process; PDB: 2PFD_C 1QD1_B.
Probab=21.04 E-value=3.1e+02 Score=20.64 Aligned_cols=42 Identities=21% Similarity=0.260 Sum_probs=26.9
Q ss_pred HHHHHHHHHhCCCCce--EEEEeCCCcEEEEEecCCHHHHHHHH
Q 031710 40 CERKVKRAVEGMKGVK--QVDVERKANKVTVVGYVEPSKVVSRI 81 (154)
Q Consensus 40 C~~kI~kal~~~~GV~--~v~vd~~~~~v~V~g~~~~~~v~~~i 81 (154)
=..+|.+++...+||. ++..|....+..++-.-+++.|.+++
T Consensus 17 ~ie~I~~a~~~~~gv~ll~~~~D~~~NRsv~T~vG~p~~v~~a~ 60 (178)
T PF07837_consen 17 VIEAIAKAARNVPGVKLLDVFSDADYNRSVITLVGEPEAVAEAA 60 (178)
T ss_dssp HHHHHHHHCCTSTTEEEEEEEEETTTTEEEEEEEE-HHHHHHHH
T ss_pred HHHHHHHHHHcCCCCEEEecCCCCCCCCCeEEEeeChHHHHHHH
Confidence 3568888888899976 55556666776666322455555544
No 107
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=20.97 E-value=2.6e+02 Score=21.36 Aligned_cols=35 Identities=29% Similarity=0.488 Sum_probs=26.0
Q ss_pred HHHHHHHhCCCCceEEEEeCCCcEEEEEec---CCHHHH
Q 031710 42 RKVKRAVEGMKGVKQVDVERKANKVTVVGY---VEPSKV 77 (154)
Q Consensus 42 ~kI~kal~~~~GV~~v~vd~~~~~v~V~g~---~~~~~v 77 (154)
..+.+.|....|+ .+.+|..++.|+|... .||-.+
T Consensus 27 g~v~k~ie~~~~~-~~~iD~~~~~V~i~~~~~t~Dp~~~ 64 (194)
T COG1094 27 GEVKKAIEEKTGV-KLRIDSKTGSVTIRTTRKTEDPLAL 64 (194)
T ss_pred ccchHHHHhhcCe-EEEEECCCCeEEEEecCCCCChHHH
Confidence 4677777777777 6999999999999732 455444
No 108
>TIGR03143 AhpF_homolog putative alkyl hydroperoxide reductase F subunit. This family of thioredoxin reductase homologs is found adjacent to alkylhydroperoxide reductase C subunit predominantly in cases where there is only one C subunit in the genome and that genome is lacking the F subunit partner (also a thioredcxin reductase homolog) that is usually found (TIGR03140).
Probab=20.71 E-value=4.1e+02 Score=23.24 Aligned_cols=27 Identities=26% Similarity=0.491 Sum_probs=15.9
Q ss_pred EEEEE--cCCCHhHHHHH---HHHHhCCCCce
Q 031710 29 VEVKV--RIDCEGCERKV---KRAVEGMKGVK 55 (154)
Q Consensus 29 ~~l~V--gm~C~~C~~kI---~kal~~~~GV~ 55 (154)
+.++| +.+|+.|-..+ ++.....++|.
T Consensus 478 ~~i~v~~~~~C~~Cp~~~~~~~~~~~~~~~i~ 509 (555)
T TIGR03143 478 VNIKIGVSLSCTLCPDVVLAAQRIASLNPNVE 509 (555)
T ss_pred eEEEEEECCCCCCcHHHHHHHHHHHHhCCCce
Confidence 44555 99999997533 23333335554
No 109
>PF13710 ACT_5: ACT domain; PDB: 2FGC_A 2PC6_A 2F1F_B.
Probab=20.64 E-value=92 Score=18.86 Aligned_cols=56 Identities=16% Similarity=0.259 Sum_probs=29.0
Q ss_pred CccccchhhcccC-CCCCcchh----hcCCceEEEEEEcCCCHhHHHHHHHHHhCCCCceEE
Q 031710 1 MGVVDHFSDYFDC-SHGSSKLK----KRRQLQTVEVKVRIDCEGCERKVKRAVEGMKGVKQV 57 (154)
Q Consensus 1 ~~~~~~~~~~~~~-~~~~~~~~----~~~~~~~~~l~Vgm~C~~C~~kI~kal~~~~GV~~v 57 (154)
.|+|..+..++.- +..+.... ......++++.|.-+ +.....+.+.|+++..|.+|
T Consensus 3 ~GvL~Ri~~vf~rRg~nI~sl~v~~~~~~~~~riti~v~~~-~~~i~~l~~Ql~KlidV~~V 63 (63)
T PF13710_consen 3 PGVLNRITGVFRRRGFNIESLSVGPTEDPGISRITIVVSGD-DREIEQLVKQLEKLIDVVKV 63 (63)
T ss_dssp TTHHHHHHHHHHTTT-EECEEEEEE-SSTTEEEEEEEEES--CCHHHHHHHHHHCSTTEEEE
T ss_pred cHHHHHHHHHHhcCCeEEeeEEeeecCCCCEEEEEEEEeeC-chhHHHHHHHHhccCCeEeC
Confidence 3677777776642 21111111 223345555555211 45566777778887777553
No 110
>PF00873 ACR_tran: AcrB/AcrD/AcrF family; InterPro: IPR001036 The Escherichia coli acrA and acrB genes encode a multi-drug efflux system that is believed to protect the bacterium against hydrophobic inhibitors []. The E. coli AcrB protein is a transporter that is energized by proton-motive force and that shows the widest substrate specificity among all known multidrug pumps, ranging from most of the currently used antibiotics, disinfectants, dyes, and detergents to simple solvents. The structure of ligand-free AcrB shows that it is a homotrimer of 110kDa per subunit. Each subunit contains 12 transmembrane helices and two large periplasmic domains (each exceeding 300 residues) between helices 1 and 2, and helices 7 and 8. X-ray analysis of the overexpressed AcrB protein demonstrated that the three periplasmic domains form, in the centre, a funnel-like structure and a connected narrow (or closed) pore. The pore is opened to the periplasm through three vestibules located at subunit interfaces. These vestibules were proposed to allow direct access of drugs from the periplasm as well as the outer leaflet of the cytoplasmic membrane. The three transmembrane domains of AcrB protomers form a large, 30A-wide central cavity that spans the cytoplasmic membrane and extends to the cytoplasm X-ray crystallographic structures of the trimeric AcrB pump from E. coli with four structurally diverse ligands demonstrated that three molecules of ligand bind simultaneously to the extremely large central cavity of 5000 cubic angstroms, primarily by hydrophobic, aromatic stacking and van der Waals interactions. Each ligand uses a slightly different subset of AcrB residues for binding. The bound ligand molecules often interact with each other, stabilising the binding. ; GO: 0005215 transporter activity, 0006810 transport, 0016020 membrane; PDB: 2V50_B 1T9U_A 2HRT_B 3NOC_A 3NOG_A 4DX7_A 1OYD_A 3AOB_A 1T9V_A 4DX6_B ....
Probab=20.58 E-value=2.1e+02 Score=27.09 Aligned_cols=42 Identities=10% Similarity=0.316 Sum_probs=0.0
Q ss_pred HHHHHHHhCCCCceEEEEeCCCcEEEEE----ecCCHHHHHHHHHHh
Q 031710 42 RKVKRAVEGMKGVKQVDVERKANKVTVV----GYVEPSKVVSRIAHR 84 (154)
Q Consensus 42 ~kI~kal~~~~GV~~v~vd~~~~~v~V~----g~~~~~~v~~~i~~~ 84 (154)
..+|++|..++||+.++-....+...|+ ...|.++....++ +
T Consensus 63 ~plE~~l~~v~gv~~i~S~s~~g~s~i~v~f~~~~d~~~a~~~v~-~ 108 (1021)
T PF00873_consen 63 KPLEEALSSVEGVKEIRSTSREGSSSITVEFDDGTDIDEALQEVR-E 108 (1021)
T ss_dssp HHHHHTHCSSTTEEEEEEEETTSEEEEEEEESTTS-HHHHHHHHH-H
T ss_pred HHHHHHHcCCCCeEEEEEEecCCcEEEEEEeccccCHHHHHHHHH-H
No 111
>PRK10568 periplasmic protein; Provisional
Probab=20.43 E-value=2.5e+02 Score=21.16 Aligned_cols=40 Identities=30% Similarity=0.426 Sum_probs=31.2
Q ss_pred cCCCHhHHHHHHHHHhCCCCce--EEEEeCCCcEEEEEecCC
Q 031710 34 RIDCEGCERKVKRAVEGMKGVK--QVDVERKANKVTVVGYVE 73 (154)
Q Consensus 34 gm~C~~C~~kI~kal~~~~GV~--~v~vd~~~~~v~V~g~~~ 73 (154)
.++...=..+|+.+|..-+++. .+.|....+.|++.|.+.
T Consensus 55 ~~~D~~I~~~v~~~L~~~~~i~~~~I~V~v~~G~V~L~G~V~ 96 (203)
T PRK10568 55 FMDDSAITAKVKAALVDHDNIKSTDISVKTHQKVVTLSGFVE 96 (203)
T ss_pred CccHHHHHHHHHHHHHhCCCCCCCceEEEEECCEEEEEEEeC
Confidence 4556677889999988777664 677778899999999864
No 112
>PRK11670 antiporter inner membrane protein; Provisional
Probab=20.19 E-value=4.5e+02 Score=21.81 Aligned_cols=56 Identities=20% Similarity=0.257 Sum_probs=36.0
Q ss_pred HHHHHHHHhCCCCceEEEEeCCC------------------cEEEEE------ec-CCHHHHHHHHHHhhCCceEecccC
Q 031710 41 ERKVKRAVEGMKGVKQVDVERKA------------------NKVTVV------GY-VEPSKVVSRIAHRTGKKAEIWPYV 95 (154)
Q Consensus 41 ~~kI~kal~~~~GV~~v~vd~~~------------------~~v~V~------g~-~~~~~v~~~i~~~~G~~a~~~~~~ 95 (154)
...++.+|+.++||.++.+.+.. ..+.|. |+ +...-+...+. +.|+++-++..=
T Consensus 67 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vIaV~S~KGGVGKTT~avNLA~aLA-~~G~rVlLID~D 145 (369)
T PRK11670 67 KEQCSAELLRITGAKAIDWKLSHNIATLKRVNNQPGVNGVKNIIAVSSGKGGVGKSSTAVNLALALA-AEGAKVGILDAD 145 (369)
T ss_pred HHHHHHHHHhcCCCceEEEEEeeehhhhccccccccCCCCCEEEEEeCCCCCCCHHHHHHHHHHHHH-HCCCcEEEEeCC
Confidence 45689999999999877654322 223343 22 23455666777 889999887653
Q ss_pred CC
Q 031710 96 PY 97 (154)
Q Consensus 96 p~ 97 (154)
++
T Consensus 146 ~q 147 (369)
T PRK11670 146 IY 147 (369)
T ss_pred CC
Confidence 33
Done!