Query 036595
Match_columns 120
No_of_seqs 245 out of 1162
Neff 8.3
Searched_HMMs 46136
Date Fri Mar 29 03:36:51 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036595.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036595hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00403 HMA: Heavy-metal-asso 99.4 6E-13 1.3E-17 77.5 7.1 53 1-54 7-62 (62)
2 KOG1603 Copper chaperone [Inor 99.4 2.2E-12 4.7E-17 77.9 7.2 58 1-59 13-71 (73)
3 COG2608 CopZ Copper chaperone 99.3 2E-11 4.4E-16 73.3 6.8 57 1-58 11-70 (71)
4 KOG4656 Copper chaperone for s 99.0 2.2E-09 4.9E-14 75.8 6.8 60 1-61 15-74 (247)
5 PLN02957 copper, zinc superoxi 98.4 2.5E-06 5.4E-11 62.2 8.6 63 1-64 14-76 (238)
6 PRK10671 copA copper exporting 98.2 5.2E-06 1.1E-10 69.9 6.6 56 1-59 12-67 (834)
7 COG2217 ZntA Cation transport 97.9 3.3E-05 7.2E-10 64.1 6.4 55 1-57 11-69 (713)
8 TIGR00003 copper ion binding p 97.3 0.0019 4.2E-08 35.0 6.7 53 1-54 11-66 (68)
9 KOG0207 Cation transport ATPas 97.3 0.00071 1.5E-08 57.1 6.4 63 1-64 3-67 (951)
10 PRK10671 copA copper exporting 97.1 0.0015 3.3E-08 55.2 6.7 57 1-58 108-164 (834)
11 KOG0207 Cation transport ATPas 97.0 0.0024 5.3E-08 54.0 6.4 61 1-62 155-218 (951)
12 PRK11033 zntA zinc/cadmium/mer 96.6 0.0061 1.3E-07 51.1 6.2 57 1-58 62-119 (741)
13 COG1888 Uncharacterized protei 92.1 0.81 1.8E-05 28.6 5.6 48 10-58 24-79 (97)
14 TIGR02052 MerP mercuric transp 91.9 1.6 3.4E-05 25.5 7.6 56 1-57 32-90 (92)
15 PF02680 DUF211: Uncharacteriz 90.7 0.89 1.9E-05 28.6 4.8 49 9-58 21-77 (95)
16 PRK13748 putative mercuric red 87.0 4.1 8.8E-05 32.9 7.6 59 1-60 9-69 (561)
17 cd00371 HMA Heavy-metal-associ 83.9 3.4 7.3E-05 19.7 6.6 52 1-53 7-60 (63)
18 PRK10553 assembly protein for 73.4 19 0.00041 22.2 5.8 41 7-47 19-60 (87)
19 PRK14054 methionine sulfoxide 71.8 9.3 0.0002 26.6 4.3 28 4-31 10-37 (172)
20 PF01883 DUF59: Domain of unkn 70.6 6.1 0.00013 22.9 2.8 19 7-25 54-72 (72)
21 PF14492 EFG_II: Elongation Fa 69.2 21 0.00045 21.0 5.5 49 8-57 19-73 (75)
22 PF04972 BON: BON domain; Int 64.5 5.4 0.00012 22.4 1.7 31 8-39 2-35 (64)
23 cd02410 archeal_CPSF_KH The ar 64.5 39 0.00084 23.0 6.0 55 8-62 56-116 (145)
24 PF03927 NapD: NapD protein; 62.5 31 0.00068 20.7 6.0 40 8-48 18-58 (79)
25 PF13732 DUF4162: Domain of un 62.4 30 0.00064 20.3 5.2 43 14-58 26-69 (84)
26 PF09580 Spore_YhcN_YlaJ: Spor 58.6 37 0.00079 23.1 5.3 29 7-35 77-105 (177)
27 PRK05528 methionine sulfoxide 57.0 8.8 0.00019 26.4 1.9 28 4-31 8-35 (156)
28 PRK11023 outer membrane lipopr 56.0 55 0.0012 22.9 5.9 38 7-44 129-168 (191)
29 PF08712 Nfu_N: Scaffold prote 55.4 39 0.00085 20.6 4.5 38 9-48 38-77 (87)
30 PRK13014 methionine sulfoxide 54.1 20 0.00044 25.3 3.4 28 4-31 15-42 (186)
31 PRK11023 outer membrane lipopr 53.9 38 0.00082 23.8 4.8 38 7-44 51-91 (191)
32 COG4004 Uncharacterized protei 52.1 26 0.00056 22.0 3.2 22 15-36 37-58 (96)
33 TIGR00489 aEF-1_beta translati 51.2 17 0.00038 22.5 2.4 20 7-26 64-83 (88)
34 PHA01634 hypothetical protein 48.8 5.6 0.00012 26.9 -0.1 13 1-13 98-110 (156)
35 PF01206 TusA: Sulfurtransfera 47.1 53 0.0011 18.6 4.6 49 1-59 8-58 (70)
36 cd04888 ACT_PheB-BS C-terminal 46.9 25 0.00053 20.0 2.6 18 8-25 57-74 (76)
37 TIGR00401 msrA methionine-S-su 46.1 16 0.00034 24.9 1.8 28 4-31 7-34 (149)
38 COG3643 Glutamate formiminotra 45.7 39 0.00084 25.3 3.8 52 8-59 21-74 (302)
39 TIGR02945 SUF_assoc FeS assemb 45.6 23 0.0005 21.8 2.4 21 8-28 58-78 (99)
40 PRK11198 LysM domain/BON super 45.5 63 0.0014 21.6 4.7 45 8-52 29-74 (147)
41 PF01625 PMSR: Peptide methion 45.2 19 0.00042 24.6 2.2 27 4-30 7-33 (155)
42 PRK06418 transcription elongat 44.3 1.1E+02 0.0023 21.3 6.2 23 42-64 80-102 (166)
43 PRK00058 methionine sulfoxide 44.0 18 0.00039 26.2 1.9 27 4-30 52-78 (213)
44 PF04468 PSP1: PSP1 C-terminal 44.0 74 0.0016 19.4 5.2 53 5-58 30-86 (88)
45 PRK00435 ef1B elongation facto 42.1 29 0.00062 21.5 2.4 21 7-27 64-84 (88)
46 COG2092 EFB1 Translation elong 41.9 27 0.00058 21.7 2.2 20 7-26 64-83 (88)
47 KOG3411 40S ribosomal protein 40.4 28 0.00061 23.3 2.3 42 4-48 97-139 (143)
48 COG2151 PaaD Predicted metal-s 39.8 36 0.00077 22.0 2.6 21 7-27 69-89 (111)
49 PF12685 SpoIIIAH: SpoIIIAH-li 39.3 75 0.0016 22.3 4.5 48 7-55 137-190 (196)
50 PRK10555 aminoglycoside/multid 39.0 97 0.0021 27.5 5.9 42 7-48 159-208 (1037)
51 TIGR02830 spore_III_AG stage I 38.9 31 0.00068 24.4 2.5 29 6-34 62-92 (186)
52 PRK09577 multidrug efflux prot 38.7 1.1E+02 0.0024 27.2 6.2 45 7-52 158-210 (1032)
53 cd06167 LabA_like LabA_like pr 38.5 61 0.0013 21.1 3.8 29 32-61 104-132 (149)
54 PF01849 NAC: NAC domain; Int 37.5 46 0.001 18.6 2.6 27 8-34 2-33 (58)
55 PF08002 DUF1697: Protein of u 35.9 1.3E+02 0.0028 19.9 5.8 49 9-58 23-75 (137)
56 COG2177 FtsX Cell division pro 35.8 1.4E+02 0.003 22.6 5.7 39 4-54 71-109 (297)
57 COG3062 NapD Uncharacterized p 35.5 1.2E+02 0.0025 19.1 5.1 40 8-48 21-61 (94)
58 PF01514 YscJ_FliF: Secretory 34.9 46 0.00099 23.7 2.8 21 7-27 117-137 (206)
59 PRK10568 periplasmic protein; 33.9 1.1E+02 0.0024 21.6 4.7 33 7-39 62-96 (203)
60 TIGR02571 ComEB ComE operon pr 33.0 1.6E+02 0.0034 19.9 5.1 44 2-59 96-139 (151)
61 TIGR01676 GLDHase galactonolac 33.0 90 0.002 25.8 4.5 39 14-55 110-148 (541)
62 PF00352 TBP: Transcription fa 32.7 76 0.0016 19.0 3.2 22 27-48 55-76 (86)
63 PRK00741 prfC peptide chain re 32.2 1.2E+02 0.0027 24.8 5.2 54 6-59 405-462 (526)
64 COG0225 MsrA Peptide methionin 32.1 29 0.00063 24.3 1.4 28 4-31 13-40 (174)
65 PRK11200 grxA glutaredoxin 1; 32.1 85 0.0018 18.4 3.4 26 2-28 10-39 (85)
66 PF11150 DUF2927: Protein of u 31.3 31 0.00066 24.9 1.5 19 98-116 161-179 (213)
67 PRK15127 multidrug efflux syst 31.1 1.6E+02 0.0035 26.3 6.0 41 8-48 160-208 (1049)
68 TIGR00503 prfC peptide chain r 30.9 1.3E+02 0.0028 24.7 5.1 54 6-59 406-463 (527)
69 TIGR03406 FeS_long_SufT probab 30.9 60 0.0013 22.6 2.8 20 8-27 134-153 (174)
70 COG1094 Predicted RNA-binding 30.8 1.6E+02 0.0034 21.1 4.9 34 9-43 28-64 (194)
71 PF02672 CP12: CP12 domain; I 30.7 8 0.00017 23.0 -1.4 15 105-119 52-68 (71)
72 PF13383 Methyltransf_22: Meth 30.7 97 0.0021 22.7 4.0 44 1-55 173-222 (242)
73 TIGR00288 conserved hypothetic 30.3 95 0.0021 21.4 3.7 29 32-61 110-138 (160)
74 PF13193 AMP-binding_C: AMP-bi 30.1 56 0.0012 18.5 2.3 37 10-48 2-45 (73)
75 cd08032 LARP_7 La RNA-binding 29.4 17 0.00038 22.2 -0.1 7 107-113 15-21 (82)
76 cd00292 EF1B Elongation factor 29.4 61 0.0013 20.0 2.4 20 8-27 65-84 (88)
77 PF05046 Img2: Mitochondrial l 29.1 1.4E+02 0.003 18.2 5.6 46 6-53 41-87 (87)
78 KOG3782 Predicted membrane pro 29.1 1.5E+02 0.0034 20.7 4.5 35 1-35 25-67 (189)
79 TIGR00915 2A0602 The (Largely 28.8 1.8E+02 0.004 25.9 6.0 41 8-48 160-208 (1044)
80 PF09158 MotCF: Bacteriophage 28.7 1.6E+02 0.0035 18.8 4.9 39 17-57 40-78 (103)
81 PF04805 Pox_E10: E10-like pro 28.6 51 0.0011 19.5 1.8 26 1-26 16-41 (70)
82 PF07837 FTCD_N: Formiminotran 28.3 2.1E+02 0.0046 20.1 5.2 38 8-45 19-58 (178)
83 KOG1796 Vacuolar protein sorti 27.9 20 0.00043 29.4 0.0 16 104-119 92-108 (609)
84 COG4669 EscJ Type III secretor 27.7 63 0.0014 23.9 2.5 20 7-26 111-130 (246)
85 TIGR02544 III_secr_YscJ type I 27.5 69 0.0015 22.6 2.7 21 7-27 109-129 (193)
86 PF03434 DUF276: DUF276 ; Int 27.5 1E+02 0.0022 23.0 3.5 28 7-34 89-116 (291)
87 TIGR03675 arCOG00543 arCOG0054 27.4 2.2E+02 0.0047 24.0 6.0 58 7-64 72-135 (630)
88 TIGR00914 2A0601 heavy metal e 26.8 1.1E+02 0.0024 27.2 4.3 42 7-48 700-751 (1051)
89 PRK05550 bifunctional methioni 26.1 40 0.00088 25.4 1.4 28 4-31 134-161 (283)
90 KOG3476 Microtubule-associated 25.8 33 0.00072 21.3 0.7 14 1-14 1-14 (100)
91 TIGR02898 spore_YhcN_YlaJ spor 25.3 1.4E+02 0.0031 20.5 3.8 29 7-35 56-84 (158)
92 PF13216 DUF4024: Protein of u 24.5 22 0.00048 17.6 -0.2 11 106-116 9-19 (35)
93 KOG4730 D-arabinono-1, 4-lacto 24.1 97 0.0021 25.3 3.2 34 23-57 105-138 (518)
94 PF01936 NYN: NYN domain; Int 24.1 72 0.0016 20.4 2.2 29 31-60 99-127 (146)
95 PRK15348 type III secretion sy 23.9 88 0.0019 23.2 2.8 21 7-27 109-129 (249)
96 PF00736 EF1_GNE: EF-1 guanine 23.8 90 0.0019 19.2 2.4 20 7-26 64-84 (89)
97 cd04877 ACT_TyrR N-terminal AC 23.6 91 0.002 17.8 2.4 17 8-24 52-68 (74)
98 COG2331 Uncharacterized protei 22.6 47 0.001 20.2 0.9 16 2-17 35-50 (82)
99 PF08478 POTRA_1: POTRA domain 22.6 72 0.0016 17.8 1.8 27 8-34 37-64 (69)
100 PF00873 ACR_tran: AcrB/AcrD/A 22.5 1.8E+02 0.004 25.6 4.9 42 7-48 689-740 (1021)
101 cd06482 ACD_HspB10 Alpha cryst 22.0 83 0.0018 19.2 2.0 23 16-38 15-39 (87)
102 PF15643 Tox-PL-2: Papain fold 22.0 65 0.0014 20.5 1.5 18 2-20 20-37 (100)
103 cd03421 SirA_like_N SirA_like_ 21.6 1.6E+02 0.0036 16.4 6.0 47 1-58 7-55 (67)
104 KOG0364 Chaperonin complex com 21.6 29 0.00062 28.1 -0.2 20 101-120 351-371 (527)
105 PRK11282 glcE glycolate oxidas 21.2 1.9E+02 0.004 22.5 4.2 37 15-54 44-80 (352)
106 PRK09019 translation initiatio 20.9 1.4E+02 0.003 19.2 2.9 41 14-54 26-74 (108)
107 cd04879 ACT_3PGDH-like ACT_3PG 20.6 1.3E+02 0.0028 16.0 2.5 16 9-24 54-69 (71)
108 TIGR02194 GlrX_NrdH Glutaredox 20.4 1.8E+02 0.0039 16.3 3.3 25 2-28 8-32 (72)
109 PF11491 DUF3213: Protein of u 20.3 1.9E+02 0.0042 17.8 3.3 44 10-54 16-62 (88)
110 KOG1635 Peptide methionine sul 20.2 97 0.0021 21.9 2.2 28 4-31 31-58 (191)
111 PRK07334 threonine dehydratase 20.2 2.7E+02 0.0058 21.8 5.0 50 8-58 341-402 (403)
112 PRK10509 bacterioferritin-asso 20.2 67 0.0015 18.4 1.3 16 2-17 38-53 (64)
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=99.44 E-value=6e-13 Score=77.54 Aligned_cols=53 Identities=30% Similarity=0.601 Sum_probs=49.3
Q ss_pred CcchhHHHHHHHHHhcCCCccEEEEecCCCEEEEEec---CCHHHHHHHHHHhcCCc
Q 036595 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVTGR---IDPQKVLKKLKKKTGKK 54 (120)
Q Consensus 1 m~C~~C~~~I~~~l~~~~GV~~v~v~~~~~~v~V~g~---~~~~~v~~~i~~~~G~~ 54 (120)
|+|++|+++|+++|.+++||.++.+|+.+++++|.+. ++.++|.++|+ ++||+
T Consensus 7 m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~~~~~~~i~~~i~-~~Gy~ 62 (62)
T PF00403_consen 7 MTCEGCAKKVEKALSKLPGVKSVKVDLETKTVTVTYDPDKTSIEKIIEAIE-KAGYE 62 (62)
T ss_dssp TTSHHHHHHHHHHHHTSTTEEEEEEETTTTEEEEEESTTTSCHHHHHHHHH-HTTSE
T ss_pred cccHHHHHHHHHHHhcCCCCcEEEEECCCCEEEEEEecCCCCHHHHHHHHH-HhCcC
Confidence 8999999999999999999999999999999999875 45699999998 99984
No 2
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.39 E-value=2.2e-12 Score=77.92 Aligned_cols=58 Identities=50% Similarity=0.871 Sum_probs=54.4
Q ss_pred CcchhHHHHHHHHHhcCCCccEEEEecCCCEEEEEecCCHHHHHHHHHHhcC-CceEEec
Q 036595 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVTGRIDPQKVLKKLKKKTG-KKVEIVD 59 (120)
Q Consensus 1 m~C~~C~~~I~~~l~~~~GV~~v~v~~~~~~v~V~g~~~~~~v~~~i~~~~G-~~~~~~~ 59 (120)
|+|.+|+.+|++.|..++||.++.+|..+++++|.|.+++..|++.|+ +.| +++.+|.
T Consensus 13 ~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~-k~~~k~~~~~~ 71 (73)
T KOG1603|consen 13 MHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLK-KTGGKRAELWK 71 (73)
T ss_pred cccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHH-hcCCCceEEec
Confidence 799999999999999999999999999999999999999999999998 666 8887774
No 3
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.28 E-value=2e-11 Score=73.33 Aligned_cols=57 Identities=30% Similarity=0.610 Sum_probs=51.1
Q ss_pred CcchhHHHHHHHHHhcCCCccEEEEecCCCEEEEE--e-cCCHHHHHHHHHHhcCCceEEe
Q 036595 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVT--G-RIDPQKVLKKLKKKTGKKVEIV 58 (120)
Q Consensus 1 m~C~~C~~~I~~~l~~~~GV~~v~v~~~~~~v~V~--g-~~~~~~v~~~i~~~~G~~~~~~ 58 (120)
|+|++|+.+|+++|.+++||.++++++..+++.|+ + .++.++|.++|+ .+||.+..+
T Consensus 11 MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~-~aGy~~~~~ 70 (71)
T COG2608 11 MTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIE-DAGYKVEEI 70 (71)
T ss_pred cCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHH-HcCCCeeec
Confidence 89999999999999999999999999999666664 4 589999999998 999988654
No 4
>KOG4656 consensus Copper chaperone for superoxide dismutase [Inorganic ion transport and metabolism]
Probab=98.96 E-value=2.2e-09 Score=75.84 Aligned_cols=60 Identities=20% Similarity=0.477 Sum_probs=57.0
Q ss_pred CcchhHHHHHHHHHhcCCCccEEEEecCCCEEEEEecCCHHHHHHHHHHhcCCceEEecCC
Q 036595 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVTGRIDPQKVLKKLKKKTGKKVEIVDNN 61 (120)
Q Consensus 1 m~C~~C~~~I~~~l~~~~GV~~v~v~~~~~~v~V~g~~~~~~v~~~i~~~~G~~~~~~~~~ 61 (120)
|+|++|+..|++.|..++||.+|+||+.++.|.|.+...+.+|...|+ .+|.+|.+....
T Consensus 15 M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~ts~p~s~i~~~le-~tGr~Avl~G~G 74 (247)
T KOG4656|consen 15 MTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVETSVPPSEIQNTLE-NTGRDAVLRGAG 74 (247)
T ss_pred chhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEEccCChHHHHHHHH-hhChheEEecCC
Confidence 899999999999999999999999999999999999999999999998 999999887643
No 5
>PLN02957 copper, zinc superoxide dismutase
Probab=98.40 E-value=2.5e-06 Score=62.19 Aligned_cols=63 Identities=22% Similarity=0.481 Sum_probs=56.6
Q ss_pred CcchhHHHHHHHHHhcCCCccEEEEecCCCEEEEEecCCHHHHHHHHHHhcCCceEEecCCCCC
Q 036595 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVTGRIDPQKVLKKLKKKTGKKVEIVDNNNNN 64 (120)
Q Consensus 1 m~C~~C~~~I~~~l~~~~GV~~v~v~~~~~~v~V~g~~~~~~v~~~i~~~~G~~~~~~~~~~~~ 64 (120)
|+|..|+.+|++.|.+++||..+.+++..++++|........+...|+ ++||.++++.....+
T Consensus 14 MsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~~~~~~I~~aIe-~~Gy~a~~~~~~~~~ 76 (238)
T PLN02957 14 MKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGSSPVKAMTAALE-QTGRKARLIGQGDPE 76 (238)
T ss_pred ccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEecCCHHHHHHHHH-HcCCcEEEecCCCcc
Confidence 789999999999999999999999999999999987778888999998 999999888764433
No 6
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.16 E-value=5.2e-06 Score=69.87 Aligned_cols=56 Identities=18% Similarity=0.436 Sum_probs=50.1
Q ss_pred CcchhHHHHHHHHHhcCCCccEEEEecCCCEEEEEecCCHHHHHHHHHHhcCCceEEec
Q 036595 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVTGRIDPQKVLKKLKKKTGKKVEIVD 59 (120)
Q Consensus 1 m~C~~C~~~I~~~l~~~~GV~~v~v~~~~~~v~V~g~~~~~~v~~~i~~~~G~~~~~~~ 59 (120)
|+|++|+.+|+++|.+++||..+++++. +.+|.+..+.+.+.++++ ++||+++...
T Consensus 12 mtC~~C~~~i~~al~~~~gv~~v~v~~~--~~~v~~~~~~~~i~~~i~-~~Gy~~~~~~ 67 (834)
T PRK10671 12 LSCGHCVKRVKESLEQRPDVEQADVSIT--EAHVTGTASAEALIETIK-QAGYDASVSH 67 (834)
T ss_pred cccHHHHHHHHHHHhcCCCcceEEEeee--EEEEEecCCHHHHHHHHH-hcCCcccccc
Confidence 8999999999999999999999999994 556666778999999998 9999998754
No 7
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.89 E-value=3.3e-05 Score=64.08 Aligned_cols=55 Identities=27% Similarity=0.587 Sum_probs=49.7
Q ss_pred CcchhHHHHHHHHHhcCCCccEEEEecCCCEEEEEec---CC-HHHHHHHHHHhcCCceEE
Q 036595 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVTGR---ID-PQKVLKKLKKKTGKKVEI 57 (120)
Q Consensus 1 m~C~~C~~~I~~~l~~~~GV~~v~v~~~~~~v~V~g~---~~-~~~v~~~i~~~~G~~~~~ 57 (120)
|+|..|+++|| +|++++||..+.+|+.++++.|... .+ .+.+..+++ +.||.+..
T Consensus 11 m~Ca~C~~~ie-~l~~~~gV~~~~vn~~t~~~~v~~~~~~~~~~~~~~~~v~-~~gy~~~~ 69 (713)
T COG2217 11 MTCAACASRIE-ALNKLPGVEEARVNLATERATVVYDPEEVDLPADIVAAVE-KAGYSARL 69 (713)
T ss_pred cCcHHHHHHHH-HHhcCCCeeEEEeecccceEEEEecccccccHHHHHHHHH-hcCccccc
Confidence 89999999999 9999999999999999999998742 45 789999997 99998766
No 8
>TIGR00003 copper ion binding protein. This model describes an apparently copper-specific subfamily of the metal-binding domain HMA (Pfam family pfam00403). Closely related sequences outside this model include mercury resistance proteins and repeated domains of eukaryotic eukaryotic copper transport proteins. Members of this family are strictly prokaryotic. The model identifies both small proteins consisting of just this domain and N-terminal regions of cation (probably copper) transporting ATPases.
Probab=97.33 E-value=0.0019 Score=35.01 Aligned_cols=53 Identities=19% Similarity=0.379 Sum_probs=43.9
Q ss_pred CcchhHHHHHHHHHhcCCCccEEEEecCCCEEEEEe---cCCHHHHHHHHHHhcCCc
Q 036595 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVTG---RIDPQKVLKKLKKKTGKK 54 (120)
Q Consensus 1 m~C~~C~~~I~~~l~~~~GV~~v~v~~~~~~v~V~g---~~~~~~v~~~i~~~~G~~ 54 (120)
+.|..|...+++.+..++++..+.+++....+.+.. ..+...+...+. ..|+.
T Consensus 11 ~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~g~~ 66 (68)
T TIGR00003 11 MTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAIL-DAGYE 66 (68)
T ss_pred eEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHH-HcCCC
Confidence 469999999999999999999999999999988863 246667777776 77764
No 9
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=97.30 E-value=0.00071 Score=57.11 Aligned_cols=63 Identities=22% Similarity=0.512 Sum_probs=56.3
Q ss_pred CcchhHHHHHHHHHhcCCCccEEEEecCCCEEEEEe--cCCHHHHHHHHHHhcCCceEEecCCCCC
Q 036595 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVTG--RIDPQKVLKKLKKKTGKKVEIVDNNNNN 64 (120)
Q Consensus 1 m~C~~C~~~I~~~l~~~~GV~~v~v~~~~~~v~V~g--~~~~~~v~~~i~~~~G~~~~~~~~~~~~ 64 (120)
|+|..|.+.|++++...+||.+..|++.++..+|.- .++++.+.+.|+ ..|+++++.......
T Consensus 3 mtc~ac~~si~~~~~~~~g~~~i~vsl~~~~~~v~~~~~~~~~~i~~~ie-d~gf~~~~~~~~~~~ 67 (951)
T KOG0207|consen 3 MTCSACSNSIEKAISRKPGVQKIEVSLAQKRANVSYDNIVSPESIKETIE-DMGFEASLLSDSEIT 67 (951)
T ss_pred ccHHHHhhhHHHHHhcCCCceeEEEEeccccceEEEeeccCHHHHHHHhh-cccceeeecccCccc
Confidence 899999999999999999999999999999998863 478999999998 999999988765543
No 10
>PRK10671 copA copper exporting ATPase; Provisional
Probab=97.11 E-value=0.0015 Score=55.18 Aligned_cols=57 Identities=25% Similarity=0.528 Sum_probs=50.8
Q ss_pred CcchhHHHHHHHHHhcCCCccEEEEecCCCEEEEEecCCHHHHHHHHHHhcCCceEEe
Q 036595 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVTGRIDPQKVLKKLKKKTGKKVEIV 58 (120)
Q Consensus 1 m~C~~C~~~I~~~l~~~~GV~~v~v~~~~~~v~V~g~~~~~~v~~~i~~~~G~~~~~~ 58 (120)
|+|.+|...|++.+.+++||.++.+++..+++.+.+..+..++.+.++ +.|+.+.++
T Consensus 108 m~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~~~s~~~I~~~I~-~~Gy~a~~~ 164 (834)
T PRK10671 108 MSCASCVSRVQNALQSVPGVTQARVNLAERTALVMGSASPQDLVQAVE-KAGYGAEAI 164 (834)
T ss_pred cCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEccCCHHHHHHHHH-hcCCCcccc
Confidence 789999999999999999999999999999988876667888888997 999987654
No 11
>KOG0207 consensus Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=96.96 E-value=0.0024 Score=54.01 Aligned_cols=61 Identities=18% Similarity=0.503 Sum_probs=54.0
Q ss_pred CcchhHHHHHHHHHhcCCCccEEEEecCCCEEEEEe---cCCHHHHHHHHHHhcCCceEEecCCC
Q 036595 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVTG---RIDPQKVLKKLKKKTGKKVEIVDNNN 62 (120)
Q Consensus 1 m~C~~C~~~I~~~l~~~~GV~~v~v~~~~~~v~V~g---~~~~~~v~~~i~~~~G~~~~~~~~~~ 62 (120)
|.|.+|..+|++.|.+++||.++.+++.++++.|.. ...+.++++.|+ .+|+.+.+.+...
T Consensus 155 ~~c~s~~~~ie~~l~~l~gV~~~sv~~~t~~~~V~~~~~~~~pr~i~k~ie-~~~~~~~~~~~~~ 218 (951)
T KOG0207|consen 155 MTCASCVSKIESILERLRGVKSFSVSLATDTAIVVYDPEITGPRDIIKAIE-ETGFEASVRPYGD 218 (951)
T ss_pred ccccchhhhhHHHHhhccCeeEEEEeccCCceEEEecccccChHHHHHHHH-hhcccceeeeccc
Confidence 689999999999999999999999999999999863 368899999998 9999887766433
No 12
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=96.59 E-value=0.0061 Score=51.14 Aligned_cols=57 Identities=23% Similarity=0.373 Sum_probs=46.9
Q ss_pred CcchhHHHHHHHHHhcCCCccEEEEecCCCEEEEEec-CCHHHHHHHHHHhcCCceEEe
Q 036595 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVTGR-IDPQKVLKKLKKKTGKKVEIV 58 (120)
Q Consensus 1 m~C~~C~~~I~~~l~~~~GV~~v~v~~~~~~v~V~g~-~~~~~v~~~i~~~~G~~~~~~ 58 (120)
|+|.+|..+|++.+.+++||..+.+++..+++.+... ...+++...++ ..||.+..+
T Consensus 62 m~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~~~~~I~~aI~-~~Gy~a~~~ 119 (741)
T PRK11033 62 MDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADNDIRAQVESAVQ-KAGFSLRDE 119 (741)
T ss_pred CCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEecccchHHHHHHHH-hcccccccc
Confidence 7899999999999999999999999999999887632 12267778887 899987544
No 13
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=92.05 E-value=0.81 Score=28.62 Aligned_cols=48 Identities=19% Similarity=0.439 Sum_probs=34.6
Q ss_pred HHHHHhcCCCccEEEEe-----cC--CCEEEEEe-cCCHHHHHHHHHHhcCCceEEe
Q 036595 10 VARAISKFKGVEKFTTD-----MN--KHRVVVTG-RIDPQKVLKKLKKKTGKKVEIV 58 (120)
Q Consensus 10 I~~~l~~~~GV~~v~v~-----~~--~~~v~V~g-~~~~~~v~~~i~~~~G~~~~~~ 58 (120)
+.+.|.+++||..|.+. .. +-+++|.| .++.++|.+.|+ ..|-.++-+
T Consensus 24 ~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE-~~Gg~IHSi 79 (97)
T COG1888 24 LALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIE-ELGGAIHSI 79 (97)
T ss_pred HHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHH-HcCCeeeeh
Confidence 45678888998866543 33 44556667 489999999998 999766543
No 14
>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=91.87 E-value=1.6 Score=25.49 Aligned_cols=56 Identities=27% Similarity=0.385 Sum_probs=41.7
Q ss_pred CcchhHHHHHHHHHhcCCCccEEEEecCCCEEEEEe---cCCHHHHHHHHHHhcCCceEE
Q 036595 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVTG---RIDPQKVLKKLKKKTGKKVEI 57 (120)
Q Consensus 1 m~C~~C~~~I~~~l~~~~GV~~v~v~~~~~~v~V~g---~~~~~~v~~~i~~~~G~~~~~ 57 (120)
+.|..|...++..+....|+....++.......+.. ..+...+...+. ..|+.+++
T Consensus 32 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~g~~~~~ 90 (92)
T TIGR02052 32 MTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATT-DAGYPSSL 90 (92)
T ss_pred eEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHH-hcCCCeEe
Confidence 469999999999999999988888888777765541 245556666666 77776544
No 15
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=90.68 E-value=0.89 Score=28.64 Aligned_cols=49 Identities=18% Similarity=0.458 Sum_probs=34.0
Q ss_pred HHHHHHhcCCCccEEEEe-----cCCCE--EEEEec-CCHHHHHHHHHHhcCCceEEe
Q 036595 9 TVARAISKFKGVEKFTTD-----MNKHR--VVVTGR-IDPQKVLKKLKKKTGKKVEIV 58 (120)
Q Consensus 9 ~I~~~l~~~~GV~~v~v~-----~~~~~--v~V~g~-~~~~~v~~~i~~~~G~~~~~~ 58 (120)
.+.+.|.+++||..|.+. ..+.. ++|+|. ++.++|.++|+ +.|-.++-+
T Consensus 21 e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie-~~Gg~IHSI 77 (95)
T PF02680_consen 21 ELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIE-ELGGVIHSI 77 (95)
T ss_dssp HHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHH-HTT-EEEEE
T ss_pred HHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHH-HcCCeEEee
Confidence 356788999998877654 34444 445675 89999999998 999665543
No 16
>PRK13748 putative mercuric reductase; Provisional
Probab=86.96 E-value=4.1 Score=32.91 Aligned_cols=59 Identities=20% Similarity=0.373 Sum_probs=46.5
Q ss_pred CcchhHHHHHHHHHhcCCCccEEEEecCCCEEEEEe--cCCHHHHHHHHHHhcCCceEEecC
Q 036595 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVTG--RIDPQKVLKKLKKKTGKKVEIVDN 60 (120)
Q Consensus 1 m~C~~C~~~I~~~l~~~~GV~~v~v~~~~~~v~V~g--~~~~~~v~~~i~~~~G~~~~~~~~ 60 (120)
|.|.+|..+++..+..++++....+++....+.+.. ..+...+...+. ..|+..+....
T Consensus 9 ~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~~~~~~~i~~~i~-~~g~~~~~~~~ 69 (561)
T PRK13748 9 MTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVGTSPDALTAAVA-GLGYRATLADA 69 (561)
T ss_pred eecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECCCCCHHHHHHHHH-HcCCeeeccCc
Confidence 579999999999999999999899999888877653 245566667776 88887766554
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=83.92 E-value=3.4 Score=19.68 Aligned_cols=52 Identities=25% Similarity=0.592 Sum_probs=34.5
Q ss_pred CcchhHHHHHHHHHhcCCCccEEEEecCCCEEEEEec--CCHHHHHHHHHHhcCC
Q 036595 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVTGR--IDPQKVLKKLKKKTGK 53 (120)
Q Consensus 1 m~C~~C~~~I~~~l~~~~GV~~v~v~~~~~~v~V~g~--~~~~~v~~~i~~~~G~ 53 (120)
+.|..|...++..+....|+....+++......+... .+...+...+. ..|+
T Consensus 7 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~ 60 (63)
T cd00371 7 MTCAGCVSKIEKALEKLPGVESVEVDLETGKATVEYDPEVSPEELLEAIE-DAGY 60 (63)
T ss_pred eEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEEECCCCCHHHHHHHHH-HcCC
Confidence 4588999999988888889877777777666555422 24444444444 4443
No 18
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=73.39 E-value=19 Score=22.24 Aligned_cols=41 Identities=17% Similarity=0.330 Sum_probs=27.4
Q ss_pred HHHHHHHHhcCCCccEEEEecCCCEEEEEe-cCCHHHHHHHH
Q 036595 7 ERTVARAISKFKGVEKFTTDMNKHRVVVTG-RIDPQKVLKKL 47 (120)
Q Consensus 7 ~~~I~~~l~~~~GV~~v~v~~~~~~v~V~g-~~~~~~v~~~i 47 (120)
...+.+.|..++|++-...|...+|+.|+- ..+...+++.|
T Consensus 19 ~~~V~~~l~~ipg~Evh~~d~~~GKiVVtiE~~~~~~~~~~i 60 (87)
T PRK10553 19 ISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAEDSETLLQTI 60 (87)
T ss_pred HHHHHHHHHcCCCcEEEeecCCCCeEEEEEEeCChHHHHHHH
Confidence 457889999999997666777778877752 23344444433
No 19
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=71.77 E-value=9.3 Score=26.65 Aligned_cols=28 Identities=14% Similarity=0.217 Sum_probs=24.9
Q ss_pred hhHHHHHHHHHhcCCCccEEEEecCCCE
Q 036595 4 NACERTVARAISKFKGVEKFTTDMNKHR 31 (120)
Q Consensus 4 ~~C~~~I~~~l~~~~GV~~v~v~~~~~~ 31 (120)
.||=+.++..+.+++||.++.+-...+.
T Consensus 10 gGCFWg~E~~f~~~~GV~~t~vGYagG~ 37 (172)
T PRK14054 10 GGCFWGMEAPFDRVKGVISTRVGYTGGH 37 (172)
T ss_pred cCChhhhHHHHccCCCEEEEEeeecCCC
Confidence 5899999999999999999999877664
No 20
>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=70.57 E-value=6.1 Score=22.87 Aligned_cols=19 Identities=16% Similarity=0.377 Sum_probs=15.2
Q ss_pred HHHHHHHHhcCCCccEEEE
Q 036595 7 ERTVARAISKFKGVEKFTT 25 (120)
Q Consensus 7 ~~~I~~~l~~~~GV~~v~v 25 (120)
...|+++|..++||.+|+|
T Consensus 54 ~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 54 REEIREALKALPGVKSVKV 72 (72)
T ss_dssp HHHHHHHHHTSTT-SEEEE
T ss_pred HHHHHHHHHhCCCCceEeC
Confidence 4678899999999998875
No 21
>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=69.22 E-value=21 Score=21.03 Aligned_cols=49 Identities=20% Similarity=0.478 Sum_probs=35.8
Q ss_pred HHHHHHHhcC----CCccEEEEecCCCEEEEE--ecCCHHHHHHHHHHhcCCceEE
Q 036595 8 RTVARAISKF----KGVEKFTTDMNKHRVVVT--GRIDPQKVLKKLKKKTGKKVEI 57 (120)
Q Consensus 8 ~~I~~~l~~~----~GV~~v~v~~~~~~v~V~--g~~~~~~v~~~i~~~~G~~~~~ 57 (120)
.++..+|.++ ++. .+..|-.++.+.|. |.+..+-++..|+++.|..+++
T Consensus 19 ~kl~~aL~~l~~eDP~l-~~~~d~et~e~~l~g~Gelhlev~~~~L~~~~~v~v~~ 73 (75)
T PF14492_consen 19 PKLSEALQKLSEEDPSL-RVERDEETGELILSGMGELHLEVLLERLKRRFGVEVEF 73 (75)
T ss_dssp HHHHHHHHHHHHH-TTS-EEEEETTTSEEEEEESSHHHHHHHHHHHHHTTCEBEEE
T ss_pred HHHHHHHHHHHhcCCeE-EEEEcchhceEEEEECCHHHHHHHHHHHHHHHCCeeEe
Confidence 3444555444 555 78889899998887 5688888999998777776654
No 22
>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=64.54 E-value=5.4 Score=22.37 Aligned_cols=31 Identities=13% Similarity=0.292 Sum_probs=16.5
Q ss_pred HHHHHHHhc---CCCccEEEEecCCCEEEEEecCC
Q 036595 8 RTVARAISK---FKGVEKFTTDMNKHRVVVTGRID 39 (120)
Q Consensus 8 ~~I~~~l~~---~~GV~~v~v~~~~~~v~V~g~~~ 39 (120)
.+|+..|.. +++. .+.+....+.|+++|.+.
T Consensus 2 ~~v~~~L~~~~~~~~~-~i~v~v~~g~v~L~G~v~ 35 (64)
T PF04972_consen 2 TKVRAALRADPWLPDS-NISVSVENGVVTLSGEVP 35 (64)
T ss_dssp -----------CTT-T-TEEEEEECTEEEEEEEES
T ss_pred cccccccccccccCCC-eEEEEEECCEEEEEeeCc
Confidence 356677766 3444 678888899999999763
No 23
>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=64.51 E-value=39 Score=22.99 Aligned_cols=55 Identities=13% Similarity=0.287 Sum_probs=38.6
Q ss_pred HHHHHHHhcCCCccEEEEecCCCEEEEEe----cC--CHHHHHHHHHHhcCCceEEecCCC
Q 036595 8 RTVARAISKFKGVEKFTTDMNKHRVVVTG----RI--DPQKVLKKLKKKTGKKVEIVDNNN 62 (120)
Q Consensus 8 ~~I~~~l~~~~GV~~v~v~~~~~~v~V~g----~~--~~~~v~~~i~~~~G~~~~~~~~~~ 62 (120)
..|++.+-.-.||.++.++..++.|.+.. -+ -....+..|.+++|+...++..++
T Consensus 56 ~~I~~ivP~ea~i~di~Fd~~tGEV~IeaeKPG~ViGk~g~~~reI~~~tgW~p~vvRtpP 116 (145)
T cd02410 56 KIILEIVPEEAGITDIYFDDDTGEVIIEAEKPGLVIGKGGSTLREITRETGWAPKVVRTPP 116 (145)
T ss_pred HHHHHhCCCccCceeeEecCCCcEEEEEEcCCeEEEecCchhHHHHHHHhCCeeEEEecCC
Confidence 35556565557999999999999999962 21 223444555569999988876555
No 24
>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=62.48 E-value=31 Score=20.66 Aligned_cols=40 Identities=25% Similarity=0.377 Sum_probs=27.0
Q ss_pred HHHHHHHhcCCCccEEEEecCCCEEEEE-ecCCHHHHHHHHH
Q 036595 8 RTVARAISKFKGVEKFTTDMNKHRVVVT-GRIDPQKVLKKLK 48 (120)
Q Consensus 8 ~~I~~~l~~~~GV~~v~v~~~~~~v~V~-g~~~~~~v~~~i~ 48 (120)
..+.++|..++|++=...+-. +|+.|+ -..+...+.+.+.
T Consensus 18 ~~v~~~l~~~~gvEVh~~~~~-GKiVVtiE~~~~~~~~~~~~ 58 (79)
T PF03927_consen 18 EEVAEALAAIPGVEVHAVDED-GKIVVTIEAESSEEEVDLID 58 (79)
T ss_dssp HHHHHHHCCSTTEEEEEEETT-TEEEEEEEESSHHHHHHHHH
T ss_pred HHHHHHHHcCCCcEEEeeCCC-CeEEEEEEeCChHHHHHHHH
Confidence 568899999999965556655 777765 2345555555554
No 25
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=62.38 E-value=30 Score=20.32 Aligned_cols=43 Identities=19% Similarity=0.354 Sum_probs=30.4
Q ss_pred HhcCCCccEEEEecCC-CEEEEEecCCHHHHHHHHHHhcCCceEEe
Q 036595 14 ISKFKGVEKFTTDMNK-HRVVVTGRIDPQKVLKKLKKKTGKKVEIV 58 (120)
Q Consensus 14 l~~~~GV~~v~v~~~~-~~v~V~g~~~~~~v~~~i~~~~G~~~~~~ 58 (120)
|..++||..+...-.. -.+.+.......+|+..|. ..|. +.-+
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 7788999988765333 3444555567889999997 8887 5543
No 26
>PF09580 Spore_YhcN_YlaJ: Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ); InterPro: IPR019076 This entry contains YhcN and YlaJ, which are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic, 40-residue C-terminal domain.
Probab=58.62 E-value=37 Score=23.14 Aligned_cols=29 Identities=24% Similarity=0.327 Sum_probs=25.0
Q ss_pred HHHHHHHHhcCCCccEEEEecCCCEEEEE
Q 036595 7 ERTVARAISKFKGVEKFTTDMNKHRVVVT 35 (120)
Q Consensus 7 ~~~I~~~l~~~~GV~~v~v~~~~~~v~V~ 35 (120)
+..|.+.+.+++||..+.+=.....+.|.
T Consensus 77 a~~i~~~v~~~~~V~~A~vvv~~~~a~Va 105 (177)
T PF09580_consen 77 ADRIANRVKKVPGVEDATVVVTDDNAYVA 105 (177)
T ss_pred HHHHHHHHhcCCCceEEEEEEECCEEEEE
Confidence 56789999999999999988888887773
No 27
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=56.96 E-value=8.8 Score=26.35 Aligned_cols=28 Identities=18% Similarity=0.219 Sum_probs=24.3
Q ss_pred hhHHHHHHHHHhcCCCccEEEEecCCCE
Q 036595 4 NACERTVARAISKFKGVEKFTTDMNKHR 31 (120)
Q Consensus 4 ~~C~~~I~~~l~~~~GV~~v~v~~~~~~ 31 (120)
+||=+-++..+.+++||.++++-...+.
T Consensus 8 gGCFWg~E~~f~~l~GV~~t~vGYagG~ 35 (156)
T PRK05528 8 GGCLWGVQAFFKTLPGVIHTEAGRANGR 35 (156)
T ss_pred cCCchhhHHHHhcCCCEEEEEEEcCCCC
Confidence 5899999999999999999998876543
No 28
>PRK11023 outer membrane lipoprotein; Provisional
Probab=55.99 E-value=55 Score=22.95 Aligned_cols=38 Identities=11% Similarity=0.167 Sum_probs=26.9
Q ss_pred HHHHHHHHhcCCCcc--EEEEecCCCEEEEEecCCHHHHH
Q 036595 7 ERTVARAISKFKGVE--KFTTDMNKHRVVVTGRIDPQKVL 44 (120)
Q Consensus 7 ~~~I~~~l~~~~GV~--~v~v~~~~~~v~V~g~~~~~~v~ 44 (120)
..+|+.+|...+++. .++|...++.|++.|.++.++..
T Consensus 129 t~kik~~L~~~~~v~~~~I~V~t~~G~V~L~G~v~~~e~~ 168 (191)
T PRK11023 129 TTKVRSQLLTSDSVKSSNVKVTTENGEVFLLGLVTQREAK 168 (191)
T ss_pred HHHHHHHHhcCCCCCcceEEEEEECcEEEEEEEeCHHHHH
Confidence 457888887777766 45555568889999987665543
No 29
>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=55.42 E-value=39 Score=20.63 Aligned_cols=38 Identities=18% Similarity=0.253 Sum_probs=27.9
Q ss_pred HHHHHHhcCCCccEEEEecCCCEEEEE--ecCCHHHHHHHHH
Q 036595 9 TVARAISKFKGVEKFTTDMNKHRVVVT--GRIDPQKVLKKLK 48 (120)
Q Consensus 9 ~I~~~l~~~~GV~~v~v~~~~~~v~V~--g~~~~~~v~~~i~ 48 (120)
-+-+.|-.++||.+|-+. .+=|+|+ ..++.+.|...|.
T Consensus 38 pLA~~Lf~i~gV~~Vf~~--~dfItVtK~~~~~W~~l~~~I~ 77 (87)
T PF08712_consen 38 PLAQALFAIPGVKSVFIG--DDFITVTKNPDADWEDLKPEIR 77 (87)
T ss_dssp HHHHHHHTSTTEEEEEEE--TTEEEEEE-TTS-HHHHHHHHH
T ss_pred HHHHHhcCCCCEeEEEEE--CCEEEEeeCCCCCHHHHHHHHH
Confidence 345667799999988776 5567776 5689999888775
No 30
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=54.15 E-value=20 Score=25.31 Aligned_cols=28 Identities=14% Similarity=0.220 Sum_probs=24.6
Q ss_pred hhHHHHHHHHHhcCCCccEEEEecCCCE
Q 036595 4 NACERTVARAISKFKGVEKFTTDMNKHR 31 (120)
Q Consensus 4 ~~C~~~I~~~l~~~~GV~~v~v~~~~~~ 31 (120)
.||-+-++..+.+++||.++++-...+.
T Consensus 15 gGCFWg~E~~f~~l~GV~~t~vGYagG~ 42 (186)
T PRK13014 15 GGCFWGVEGVFQHVPGVVSVVSGYSGGH 42 (186)
T ss_pred cCCceeeHHHHccCCCEEEEEeeecCCC
Confidence 5899999999999999999999877664
No 31
>PRK11023 outer membrane lipoprotein; Provisional
Probab=53.85 E-value=38 Score=23.75 Aligned_cols=38 Identities=21% Similarity=0.309 Sum_probs=28.6
Q ss_pred HHHHHHHHhcCCCcc---EEEEecCCCEEEEEecCCHHHHH
Q 036595 7 ERTVARAISKFKGVE---KFTTDMNKHRVVVTGRIDPQKVL 44 (120)
Q Consensus 7 ~~~I~~~l~~~~GV~---~v~v~~~~~~v~V~g~~~~~~v~ 44 (120)
+.+|+.+|...+++. .+.|....+.|+++|.++.+...
T Consensus 51 ~~~V~~aL~~~~~l~~~~~I~V~v~~G~V~L~G~V~~~~~k 91 (191)
T PRK11023 51 ELRVNNALSKDEQIKKEARINVTAYQGKVLLTGQSPNAELS 91 (191)
T ss_pred HHHHHHHHhhCcccCcCceEEEEEECCEEEEEEEeCCHHHH
Confidence 567888887776664 57788889999999987655443
No 32
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=52.05 E-value=26 Score=21.99 Aligned_cols=22 Identities=9% Similarity=0.308 Sum_probs=19.4
Q ss_pred hcCCCccEEEEecCCCEEEEEe
Q 036595 15 SKFKGVEKFTTDMNKHRVVVTG 36 (120)
Q Consensus 15 ~~~~GV~~v~v~~~~~~v~V~g 36 (120)
...+|++.+++..+++++.|++
T Consensus 37 as~pgis~ieik~E~kkL~v~t 58 (96)
T COG4004 37 ASSPGISRIEIKPENKKLLVNT 58 (96)
T ss_pred EecCCceEEEEecccceEEEec
Confidence 4568899999999999999975
No 33
>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=51.18 E-value=17 Score=22.47 Aligned_cols=20 Identities=20% Similarity=0.373 Sum_probs=17.4
Q ss_pred HHHHHHHHhcCCCccEEEEe
Q 036595 7 ERTVARAISKFKGVEKFTTD 26 (120)
Q Consensus 7 ~~~I~~~l~~~~GV~~v~v~ 26 (120)
...|+.+|++++||+++++-
T Consensus 64 td~lee~i~~ve~V~svev~ 83 (88)
T TIGR00489 64 TEAAEESLSGIEGVESVEVT 83 (88)
T ss_pred hHHHHHHHhcCCCccEEEEE
Confidence 45789999999999999875
No 34
>PHA01634 hypothetical protein
Probab=48.77 E-value=5.6 Score=26.86 Aligned_cols=13 Identities=31% Similarity=0.784 Sum_probs=10.5
Q ss_pred CcchhHHHHHHHH
Q 036595 1 MYCNACERTVARA 13 (120)
Q Consensus 1 m~C~~C~~~I~~~ 13 (120)
|+|+||+++|.-.
T Consensus 98 iDCeGCE~~l~v~ 110 (156)
T PHA01634 98 MDCEGCEEKLNVS 110 (156)
T ss_pred EEccchHHhcCHH
Confidence 6899999998543
No 35
>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=47.10 E-value=53 Score=18.60 Aligned_cols=49 Identities=12% Similarity=0.109 Sum_probs=33.7
Q ss_pred CcchhHHHHHHHHHhcCCCccEEEEecCCCEEEEEe--cCCHHHHHHHHHHhcCCceEEec
Q 036595 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVTG--RIDPQKVLKKLKKKTGKKVEIVD 59 (120)
Q Consensus 1 m~C~~C~~~I~~~l~~~~GV~~v~v~~~~~~v~V~g--~~~~~~v~~~i~~~~G~~~~~~~ 59 (120)
+.|+....+++++|.+++.= +.+.|.. ......|...++ ..|++...+.
T Consensus 8 ~~CP~Pll~~~~~l~~l~~G---------~~l~v~~d~~~~~~di~~~~~-~~g~~~~~~~ 58 (70)
T PF01206_consen 8 LSCPMPLLKAKKALKELPPG---------EVLEVLVDDPAAVEDIPRWCE-ENGYEVVEVE 58 (70)
T ss_dssp -STTHHHHHHHHHHHTSGTT----------EEEEEESSTTHHHHHHHHHH-HHTEEEEEEE
T ss_pred CCCCHHHHHHHHHHHhcCCC---------CEEEEEECCccHHHHHHHHHH-HCCCEEEEEE
Confidence 36999999999999998432 3344432 345577888887 9999755543
No 36
>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=46.86 E-value=25 Score=19.98 Aligned_cols=18 Identities=22% Similarity=0.398 Sum_probs=14.7
Q ss_pred HHHHHHHhcCCCccEEEE
Q 036595 8 RTVARAISKFKGVEKFTT 25 (120)
Q Consensus 8 ~~I~~~l~~~~GV~~v~v 25 (120)
..|-+.|++++||.+|.+
T Consensus 57 ~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 57 DELLEELREIDGVEKVEL 74 (76)
T ss_pred HHHHHHHhcCCCeEEEEE
Confidence 567788899999998865
No 37
>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=46.05 E-value=16 Score=24.85 Aligned_cols=28 Identities=14% Similarity=0.093 Sum_probs=24.0
Q ss_pred hhHHHHHHHHHhcCCCccEEEEecCCCE
Q 036595 4 NACERTVARAISKFKGVEKFTTDMNKHR 31 (120)
Q Consensus 4 ~~C~~~I~~~l~~~~GV~~v~v~~~~~~ 31 (120)
.||=+-++..+.+++||.++.+-...+.
T Consensus 7 gGCFWg~E~~f~~~~GV~~t~~GYagG~ 34 (149)
T TIGR00401 7 GGCFWGVEKYFWLIPGVYSTAVGYTGGY 34 (149)
T ss_pred cCCchhhHHHHhcCCCEEEEEEeeCCCC
Confidence 5899999999999999999988766553
No 38
>COG3643 Glutamate formiminotransferase [Amino acid transport and metabolism]
Probab=45.65 E-value=39 Score=25.26 Aligned_cols=52 Identities=25% Similarity=0.308 Sum_probs=30.9
Q ss_pred HHHHHHHhcCCCccEEEEe--cCCCEEEEEecCCHHHHHHHHHHhcCCceEEec
Q 036595 8 RTVARAISKFKGVEKFTTD--MNKHRVVVTGRIDPQKVLKKLKKKTGKKVEIVD 59 (120)
Q Consensus 8 ~~I~~~l~~~~GV~~v~v~--~~~~~v~V~g~~~~~~v~~~i~~~~G~~~~~~~ 59 (120)
.+|..++.+.++|.-++++ ..-++-.++---++++++.+....+++.++++.
T Consensus 21 e~i~a~~~~~~~v~ildve~danhNRsViT~vgdp~~~~~A~f~~ik~AaelID 74 (302)
T COG3643 21 EKIVAAAKSIPTVKILDVEMDANHNRSVITLVGDPSKVVNAAFALIKKAAELID 74 (302)
T ss_pred HHHHHHHhcCCceEEEEeccCCCCCceEEEEecChHHHHHHHHHHHHHHHHhhc
Confidence 4667778888998855554 444554445444677776655435555555544
No 39
>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=45.56 E-value=23 Score=21.78 Aligned_cols=21 Identities=24% Similarity=0.354 Sum_probs=17.1
Q ss_pred HHHHHHHhcCCCccEEEEecC
Q 036595 8 RTVARAISKFKGVEKFTTDMN 28 (120)
Q Consensus 8 ~~I~~~l~~~~GV~~v~v~~~ 28 (120)
..|+.+|..++|+.++++++.
T Consensus 58 ~~i~~al~~l~gv~~v~v~i~ 78 (99)
T TIGR02945 58 GEVENAVRAVPGVGSVTVELV 78 (99)
T ss_pred HHHHHHHHhCCCCceEEEEEE
Confidence 457888999999998888854
No 40
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=45.51 E-value=63 Score=21.62 Aligned_cols=45 Identities=20% Similarity=0.281 Sum_probs=27.9
Q ss_pred HHHHHHHhcC-CCccEEEEecCCCEEEEEecCCHHHHHHHHHHhcC
Q 036595 8 RTVARAISKF-KGVEKFTTDMNKHRVVVTGRIDPQKVLKKLKKKTG 52 (120)
Q Consensus 8 ~~I~~~l~~~-~GV~~v~v~~~~~~v~V~g~~~~~~v~~~i~~~~G 52 (120)
..|.++|.+. -+...+.|....+.|++.|.+.......++...+|
T Consensus 29 ~~i~~~i~~~~~~~~~i~V~v~~G~v~l~G~v~s~~~~~~~~~aa~ 74 (147)
T PRK11198 29 DALKEHISKQGLGDADVNVQVEDGKATVSGDAASQEAKEKILLAVG 74 (147)
T ss_pred HHHHHHHHhcCCCcCCceEEEeCCEEEEEEEeCCHHHHHHHHHHhc
Confidence 4566666553 23445667777999999998755554444432444
No 41
>PF01625 PMSR: Peptide methionine sulfoxide reductase; InterPro: IPR002569 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine []. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [, ]. The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represent MsrA, the crystal structure of which has been determined in a number of organisms. In Mycobacterium tuberculosis, the MsrA structure has been determined to 1.5 Angstrom resolution []. In contrast to the three catalytic cysteine residues found in previously characterised MsrA structures, M. tuberculosis MsrA represents a class containing only two functional cysteine residues. The overall structure shows no resemblance to the structures of MsrB (IPR002579 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. In a number of pathogenic bacteria including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0016671 oxidoreductase activity, acting on a sulfur group of donors, disulfide as acceptor, 0019538 protein metabolic process, 0055114 oxidation-reduction process; PDB: 2GT3_A 1FF3_B 2IEM_A 3E0M_D 2J89_A 3PIN_B 3PIM_B 3PIL_B 2L90_A 3BQF_A ....
Probab=45.25 E-value=19 Score=24.55 Aligned_cols=27 Identities=19% Similarity=0.224 Sum_probs=23.7
Q ss_pred hhHHHHHHHHHhcCCCccEEEEecCCC
Q 036595 4 NACERTVARAISKFKGVEKFTTDMNKH 30 (120)
Q Consensus 4 ~~C~~~I~~~l~~~~GV~~v~v~~~~~ 30 (120)
.||=+.++..+.+++||.++.+-...+
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 589999999999999999999876555
No 42
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=44.32 E-value=1.1e+02 Score=21.31 Aligned_cols=23 Identities=43% Similarity=0.683 Sum_probs=18.3
Q ss_pred HHHHHHHHhcCCceEEecCCCCC
Q 036595 42 KVLKKLKKKTGKKVEIVDNNNNN 64 (120)
Q Consensus 42 ~v~~~i~~~~G~~~~~~~~~~~~ 64 (120)
+.++++++..|++++++++.+..
T Consensus 80 ~~ik~l~~~lgk~VevVE~s~d~ 102 (166)
T PRK06418 80 KIAKALSRKLGKKVRVVEKTNDI 102 (166)
T ss_pred hHHHHHHHHhCCcEEEEEcCCCH
Confidence 56788888999999999876643
No 43
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=44.05 E-value=18 Score=26.17 Aligned_cols=27 Identities=15% Similarity=0.129 Sum_probs=24.1
Q ss_pred hhHHHHHHHHHhcCCCccEEEEecCCC
Q 036595 4 NACERTVARAISKFKGVEKFTTDMNKH 30 (120)
Q Consensus 4 ~~C~~~I~~~l~~~~GV~~v~v~~~~~ 30 (120)
.||-+.++..+.+++||.++.+-+..+
T Consensus 52 gGCFWg~E~~F~~l~GV~~t~vGYagG 78 (213)
T PRK00058 52 MGCFWGAERLFWQLPGVYSTAVGYAGG 78 (213)
T ss_pred ccCcchhHHHHhcCCCEEEEEeeecCC
Confidence 589999999999999999999987744
No 44
>PF04468 PSP1: PSP1 C-terminal conserved region; InterPro: IPR007557 The yeast polymerase suppressor 1 (PSP1) protein partially suppresses mutations in DNA polymerases alpha and delta []. The C-terminal half of PSP1 contains a domain, which is also found in several hypothetical proteins from both eukaryotic and prokaryotic sources: Crithidia fasciculata RBP45 and RBP33, subunits of the cycling sequence binding protein (CSBP) II. RBP45 and RBP33 proteins bind specifically to the cycling sequences present in several mRNAs that accumulate periodically during the cell cycle. RBP45 and RBP33 are phosphoproteins, which are phosphorylated differentially during progression through the cell cycle. Hypothetical proteins with high sequence similarity have been identified in other kinetoplastid organisms []. Bacillus subtilis yaaT protein, which plays a significant role in phosphorelay during initiation of sporulation. It is possible that the yaaT protein is also related to DNA replication. The sequence of the yaaT protein is widely conserved in prokaryotes (bacteria and archaea), but the functions of the protein are unknown []. The actual biological significance of the PSP1 C-terminal domain has not yet been clearly established.
Probab=44.03 E-value=74 Score=19.39 Aligned_cols=53 Identities=11% Similarity=0.263 Sum_probs=35.9
Q ss_pred hHHHHHHHHHhcCCCccEEEEecCCCEEEEE----ecCCHHHHHHHHHHhcCCceEEe
Q 036595 5 ACERTVARAISKFKGVEKFTTDMNKHRVVVT----GRIDPQKVLKKLKKKTGKKVEIV 58 (120)
Q Consensus 5 ~C~~~I~~~l~~~~GV~~v~v~~~~~~v~V~----g~~~~~~v~~~i~~~~G~~~~~~ 58 (120)
-|...++..-..| -+.+++..+..+++++- +.+|...+++.|.+..+-++++.
T Consensus 30 ~c~~~~~~~~L~m-~lvd~e~~~D~~k~~fyy~a~~rvDFR~Lvr~L~~~f~~RIem~ 86 (88)
T PF04468_consen 30 FCRELVKELGLPM-KLVDVEYQFDGSKLTFYYTAESRVDFRELVRDLAREFKTRIEMR 86 (88)
T ss_pred HHHHHHHHcCCCe-EEEEEEEEcCCCEEEEEEEeCCcCcHHHHHHHHHHHhCceEEEE
Confidence 3555554432222 24478888999999984 45899999999986776666553
No 45
>PRK00435 ef1B elongation factor 1-beta; Validated
Probab=42.06 E-value=29 Score=21.48 Aligned_cols=21 Identities=24% Similarity=0.401 Sum_probs=17.4
Q ss_pred HHHHHHHHhcCCCccEEEEec
Q 036595 7 ERTVARAISKFKGVEKFTTDM 27 (120)
Q Consensus 7 ~~~I~~~l~~~~GV~~v~v~~ 27 (120)
...++.+|++++||++++|-.
T Consensus 64 td~lee~i~~~e~Vqsvei~~ 84 (88)
T PRK00435 64 TEPVEEAFANVEGVESVEVEE 84 (88)
T ss_pred cHHHHHHHhccCCCcEEEEEE
Confidence 356888999999999998753
No 46
>COG2092 EFB1 Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis]
Probab=41.88 E-value=27 Score=21.73 Aligned_cols=20 Identities=20% Similarity=0.446 Sum_probs=17.2
Q ss_pred HHHHHHHHhcCCCccEEEEe
Q 036595 7 ERTVARAISKFKGVEKFTTD 26 (120)
Q Consensus 7 ~~~I~~~l~~~~GV~~v~v~ 26 (120)
...++.+|.+++||.++++-
T Consensus 64 td~~ee~l~~vegV~sveve 83 (88)
T COG2092 64 TDALEEALEEVEGVESVEVE 83 (88)
T ss_pred cHHHHHHHhhccCcceEEEE
Confidence 45789999999999998875
No 47
>KOG3411 consensus 40S ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=40.45 E-value=28 Score=23.34 Aligned_cols=42 Identities=17% Similarity=0.288 Sum_probs=27.1
Q ss_pred hhHHHHHHHHHhcCCCccEEEEecCCC-EEEEEecCCHHHHHHHHH
Q 036595 4 NACERTVARAISKFKGVEKFTTDMNKH-RVVVTGRIDPQKVLKKLK 48 (120)
Q Consensus 4 ~~C~~~I~~~l~~~~GV~~v~v~~~~~-~v~V~g~~~~~~v~~~i~ 48 (120)
++|.+++-++|++ +.-|+.+...+ +++-.|..+.++|...|.
T Consensus 97 ~~i~rkvlQ~Le~---~~~ve~hp~gGR~lt~~GqrdldrIa~~i~ 139 (143)
T KOG3411|consen 97 GGIARKVLQALEK---MGIVEKHPKGGRRLTEQGQRDLDRIAGQIR 139 (143)
T ss_pred cHHHHHHHHHHHh---CCceeeCCCCcceeCcccchhHHHHHHHHH
Confidence 3555555555544 44566666654 455568889999988875
No 48
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=39.81 E-value=36 Score=22.04 Aligned_cols=21 Identities=24% Similarity=0.463 Sum_probs=17.6
Q ss_pred HHHHHHHHhcCCCccEEEEec
Q 036595 7 ERTVARAISKFKGVEKFTTDM 27 (120)
Q Consensus 7 ~~~I~~~l~~~~GV~~v~v~~ 27 (120)
...++.+|..++||..++|++
T Consensus 69 ~~~v~~al~~~~~v~~v~V~l 89 (111)
T COG2151 69 ADQVEAALEEIPGVEDVEVEL 89 (111)
T ss_pred HHHHHHHHHhcCCcceEEEEE
Confidence 457899999999999888774
No 49
>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=39.30 E-value=75 Score=22.29 Aligned_cols=48 Identities=17% Similarity=0.329 Sum_probs=31.2
Q ss_pred HHHHHHHHhcCCCccEEEEecCCCEEEEE---ecC---CHHHHHHHHHHhcCCce
Q 036595 7 ERTVARAISKFKGVEKFTTDMNKHRVVVT---GRI---DPQKVLKKLKKKTGKKV 55 (120)
Q Consensus 7 ~~~I~~~l~~~~GV~~v~v~~~~~~v~V~---g~~---~~~~v~~~i~~~~G~~~ 55 (120)
+..|+..|.. +|-..+-|....+++.|. ..+ +..+|...+.+.+|..+
T Consensus 137 E~~iE~llka-kGf~davv~~~~~~v~VvV~~~~L~~~~~~~I~diV~~~~~v~~ 190 (196)
T PF12685_consen 137 EMEIENLLKA-KGFEDAVVFIEDDSVDVVVKADKLSDAEAAQIIDIVMRETGVPA 190 (196)
T ss_dssp HHHHHHHHHT-TS-SEEEEE-SSSEEEEEEE-S---HHHHHHHHHHHHHHHC-ST
T ss_pred HHHHHHHHHh-CCCCceEEEeeCCEEEEEEeCCCCCHHHHHHHHHHHHHHhCCCc
Confidence 3466776655 599999999999998874 223 45567778877888543
No 50
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=38.97 E-value=97 Score=27.52 Aligned_cols=42 Identities=10% Similarity=0.192 Sum_probs=32.9
Q ss_pred HHHHHHHHhcCCCccEEEEecCCCEEEEEe--------cCCHHHHHHHHH
Q 036595 7 ERTVARAISKFKGVEKFTTDMNKHRVVVTG--------RIDPQKVLKKLK 48 (120)
Q Consensus 7 ~~~I~~~l~~~~GV~~v~v~~~~~~v~V~g--------~~~~~~v~~~i~ 48 (120)
+..++..|++++||.+|++.-....+.|.- .++..+|..+|+
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~~v~~al~ 208 (1037)
T PRK10555 159 ASNIQDPLSRVNGVGDIDAYGSQYSMRIWLDPAKLNSFQMTTKDVTDAIE 208 (1037)
T ss_pred HHHHHHHhhcCCCeEEEEEcCCceEEEEEECHHHHHHcCCCHHHHHHHHH
Confidence 467889999999999999987655566641 267888888886
No 51
>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=38.85 E-value=31 Score=24.37 Aligned_cols=29 Identities=21% Similarity=0.373 Sum_probs=20.2
Q ss_pred HHHHHHHHHhcCCCccEEEE--ecCCCEEEE
Q 036595 6 CERTVARAISKFKGVEKFTT--DMNKHRVVV 34 (120)
Q Consensus 6 C~~~I~~~l~~~~GV~~v~v--~~~~~~v~V 34 (120)
=+.+++..|.++.||..|+| .+....-.|
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 35788999999999986654 455444433
No 52
>PRK09577 multidrug efflux protein; Reviewed
Probab=38.69 E-value=1.1e+02 Score=27.19 Aligned_cols=45 Identities=11% Similarity=0.120 Sum_probs=34.5
Q ss_pred HHHHHHHHhcCCCccEEEEecCCCEEEEE--------ecCCHHHHHHHHHHhcC
Q 036595 7 ERTVARAISKFKGVEKFTTDMNKHRVVVT--------GRIDPQKVLKKLKKKTG 52 (120)
Q Consensus 7 ~~~I~~~l~~~~GV~~v~v~~~~~~v~V~--------g~~~~~~v~~~i~~~~G 52 (120)
+..|+..|.+++||.+|++.-....+.|. -.++..+|.++|+ ..+
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 35789999999999999998766566663 1267888889997 544
No 53
>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=38.54 E-value=61 Score=21.06 Aligned_cols=29 Identities=31% Similarity=0.519 Sum_probs=24.5
Q ss_pred EEEEecCCHHHHHHHHHHhcCCceEEecCC
Q 036595 32 VVVTGRIDPQKVLKKLKKKTGKKVEIVDNN 61 (120)
Q Consensus 32 v~V~g~~~~~~v~~~i~~~~G~~~~~~~~~ 61 (120)
+.|+|+.+...+++.++ ..|+++.++...
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 44578889999999997 889999998776
No 54
>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=37.48 E-value=46 Score=18.56 Aligned_cols=27 Identities=22% Similarity=0.442 Sum_probs=15.6
Q ss_pred HHHHHHHhc-----CCCccEEEEecCCCEEEE
Q 036595 8 RTVARAISK-----FKGVEKFTTDMNKHRVVV 34 (120)
Q Consensus 8 ~~I~~~l~~-----~~GV~~v~v~~~~~~v~V 34 (120)
+++++.|.+ ++||..|.+-...+++.+
T Consensus 2 kk~~~~l~klgl~~i~~i~eV~i~~~dg~~~~ 33 (58)
T PF01849_consen 2 KKLQKMLKKLGLKEIPGIEEVTIRKDDGTVFV 33 (58)
T ss_dssp ------GHHCT-EEETTEEEEEEEETTTEEEE
T ss_pred HHHHHHHHHcCCcccCCcEEEEEEECCceEEE
Confidence 345555544 478888888888877665
No 55
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=35.90 E-value=1.3e+02 Score=19.88 Aligned_cols=49 Identities=22% Similarity=0.396 Sum_probs=32.3
Q ss_pred HHHHHHhcCCCccEEEEecCCCEEEEEecCCHHHH----HHHHHHhcCCceEEe
Q 036595 9 TVARAISKFKGVEKFTTDMNKHRVVVTGRIDPQKV----LKKLKKKTGKKVEIV 58 (120)
Q Consensus 9 ~I~~~l~~~~GV~~v~v~~~~~~v~V~g~~~~~~v----~~~i~~~~G~~~~~~ 58 (120)
.++..|.++ |...|+.=+.++.|.++...+.+.| .+.|++..|+.+.++
T Consensus 23 eLr~~l~~~-Gf~~V~Tyi~SGNvvf~~~~~~~~l~~~ie~~l~~~fG~~v~v~ 75 (137)
T PF08002_consen 23 ELREALEDL-GFTNVRTYIQSGNVVFESDRDPAELAAKIEKALEERFGFDVPVI 75 (137)
T ss_dssp HHHHHHHHC-T-EEEEEETTTTEEEEEESS-HHHHHHHHHHHHHHH-TT---EE
T ss_pred HHHHHHHHc-CCCCceEEEeeCCEEEecCCChHHHHHHHHHHHHHhcCCCeEEE
Confidence 456667776 8899999999999999976666655 455556888876543
No 56
>COG2177 FtsX Cell division protein [Cell division and chromosome partitioning]
Probab=35.79 E-value=1.4e+02 Score=22.64 Aligned_cols=39 Identities=21% Similarity=0.174 Sum_probs=30.5
Q ss_pred hhHHHHHHHHHhcCCCccEEEEecCCCEEEEEecCCHHHHHHHHHHhcCCc
Q 036595 4 NACERTVARAISKFKGVEKFTTDMNKHRVVVTGRIDPQKVLKKLKKKTGKK 54 (120)
Q Consensus 4 ~~C~~~I~~~l~~~~GV~~v~v~~~~~~v~V~g~~~~~~v~~~i~~~~G~~ 54 (120)
..|...++..+..++||+++++- +.++-.+.+++..|+.
T Consensus 71 ~~~~~~v~~~i~~~~gV~~v~~~------------sre~~l~~L~~~lg~~ 109 (297)
T COG2177 71 QDDAALVREKIEGIPGVKSVRFI------------SREEALKELQPWLGFG 109 (297)
T ss_pred hHHHHHHHHHHhcCCCcceEEEe------------CHHHHHHHHHHHcCch
Confidence 45778899999999999887665 6777777777678865
No 57
>COG3062 NapD Uncharacterized protein involved in formation of periplasmic nitrate reductase [Inorganic ion transport and metabolism]
Probab=35.46 E-value=1.2e+02 Score=19.14 Aligned_cols=40 Identities=23% Similarity=0.391 Sum_probs=26.5
Q ss_pred HHHHHHHhcCCCccEEEEecCCCEEEE-EecCCHHHHHHHHH
Q 036595 8 RTVARAISKFKGVEKFTTDMNKHRVVV-TGRIDPQKVLKKLK 48 (120)
Q Consensus 8 ~~I~~~l~~~~GV~~v~v~~~~~~v~V-~g~~~~~~v~~~i~ 48 (120)
..|+++|..++|++-..-+.. +|+.| .-..+...+++.++
T Consensus 21 ~av~~~L~~ip~~EV~~~d~~-GKlVVVie~~~~~~l~~tie 61 (94)
T COG3062 21 SAVKTALLAIPGCEVYGEDAE-GKLVVVIEAEDSETLLETIE 61 (94)
T ss_pred HHHHHHHhcCCCcEeeccCCC-ceEEEEEEcCchHHHHHHHH
Confidence 568899999999964444544 66555 33445666666665
No 58
>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=34.87 E-value=46 Score=23.69 Aligned_cols=21 Identities=29% Similarity=0.474 Sum_probs=17.8
Q ss_pred HHHHHHHHhcCCCccEEEEec
Q 036595 7 ERTVARAISKFKGVEKFTTDM 27 (120)
Q Consensus 7 ~~~I~~~l~~~~GV~~v~v~~ 27 (120)
+..+++.|..++||.++.|.+
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 457889999999999888874
No 59
>PRK10568 periplasmic protein; Provisional
Probab=33.86 E-value=1.1e+02 Score=21.56 Aligned_cols=33 Identities=12% Similarity=0.322 Sum_probs=25.3
Q ss_pred HHHHHHHHhcCCCcc--EEEEecCCCEEEEEecCC
Q 036595 7 ERTVARAISKFKGVE--KFTTDMNKHRVVVTGRID 39 (120)
Q Consensus 7 ~~~I~~~l~~~~GV~--~v~v~~~~~~v~V~g~~~ 39 (120)
..+|+.+|...+++. .+.|....+.|++.|.+.
T Consensus 62 ~~~v~~~L~~~~~i~~~~I~V~v~~G~V~L~G~V~ 96 (203)
T PRK10568 62 TAKVKAALVDHDNIKSTDISVKTHQKVVTLSGFVE 96 (203)
T ss_pred HHHHHHHHHhCCCCCCCceEEEEECCEEEEEEEeC
Confidence 467888887766664 567777899999999865
No 60
>TIGR02571 ComEB ComE operon protein 2. This protein is found in the ComE operon for "late competence" as characterized in B. subtilis. Proteins in this family contain homology to a cytidine/deoxycytidine deaminase domain family (pfam00383), and may carry out this activity.
Probab=32.99 E-value=1.6e+02 Score=19.94 Aligned_cols=44 Identities=16% Similarity=0.379 Sum_probs=27.9
Q ss_pred cchhHHHHHHHHHhcCCCccEEEEecCCCEEEEEecCCHHHHHHHHHHhcCCceEEec
Q 036595 2 YCNACERTVARAISKFKGVEKFTTDMNKHRVVVTGRIDPQKVLKKLKKKTGKKVEIVD 59 (120)
Q Consensus 2 ~C~~C~~~I~~~l~~~~GV~~v~v~~~~~~v~V~g~~~~~~v~~~i~~~~G~~~~~~~ 59 (120)
-|..|+..|.++ ||..|-+. ..+.+...-.+.++ ++|..++-++
T Consensus 96 PC~~Ca~ai~~a-----gI~~Vvy~--------~~~~~~~~~~~~l~-~~gi~v~~~~ 139 (151)
T TIGR02571 96 PCLQCTKSIIQA-----GIKKIYYA--------QDYHNHPYAIELFE-QAGVELKKVP 139 (151)
T ss_pred CcHHHHHHHHHh-----CCCEEEEc--------cCCCCcHHHHHHHH-HCCCEEEEeC
Confidence 388888888765 77665432 11222234567786 9998887764
No 61
>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=32.96 E-value=90 Score=25.80 Aligned_cols=39 Identities=26% Similarity=0.394 Sum_probs=31.2
Q ss_pred HhcCCCccEEEEecCCCEEEEEecCCHHHHHHHHHHhcCCce
Q 036595 14 ISKFKGVEKFTTDMNKHRVVVTGRIDPQKVLKKLKKKTGKKV 55 (120)
Q Consensus 14 l~~~~GV~~v~v~~~~~~v~V~g~~~~~~v~~~i~~~~G~~~ 55 (120)
|..+.+| +++|..+++|+|.+-+...+|.+.|. ..|+..
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 3455665 47788899999998889999999997 888754
No 62
>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=32.71 E-value=76 Score=19.05 Aligned_cols=22 Identities=18% Similarity=0.419 Sum_probs=16.8
Q ss_pred cCCCEEEEEecCCHHHHHHHHH
Q 036595 27 MNKHRVVVTGRIDPQKVLKKLK 48 (120)
Q Consensus 27 ~~~~~v~V~g~~~~~~v~~~i~ 48 (120)
+.+++++++|..+.+++..+++
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 5789999999877777666554
No 63
>PRK00741 prfC peptide chain release factor 3; Provisional
Probab=32.20 E-value=1.2e+02 Score=24.76 Aligned_cols=54 Identities=9% Similarity=0.269 Sum_probs=39.8
Q ss_pred HHHHHHHHHhcC--CCccEEEEecCCCEEEEE--ecCCHHHHHHHHHHhcCCceEEec
Q 036595 6 CERTVARAISKF--KGVEKFTTDMNKHRVVVT--GRIDPQKVLKKLKKKTGKKVEIVD 59 (120)
Q Consensus 6 C~~~I~~~l~~~--~GV~~v~v~~~~~~v~V~--g~~~~~~v~~~i~~~~G~~~~~~~ 59 (120)
-..++.++|.++ +|.-.+..+..++...|. |.+..+-++.+|+++.|-.+++-+
T Consensus 405 d~~kl~~aL~~L~eED~l~~~~~~~t~e~il~g~G~lhleV~~~RL~~ey~v~v~~~~ 462 (526)
T PRK00741 405 KQKQLQKGLVQLSEEGAVQVFRPLDNNDLILGAVGQLQFEVVAHRLKNEYNVEAIYEP 462 (526)
T ss_pred hHHHHHHHHHHHhhcCCeEEEECCCCCCEEEEEEeHHHHHHHHHHHHHHhCCEEEEec
Confidence 356788888776 565566667677766664 778999999999878888777643
No 64
>COG0225 MsrA Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=32.10 E-value=29 Score=24.30 Aligned_cols=28 Identities=14% Similarity=0.166 Sum_probs=24.0
Q ss_pred hhHHHHHHHHHhcCCCccEEEEecCCCE
Q 036595 4 NACERTVARAISKFKGVEKFTTDMNKHR 31 (120)
Q Consensus 4 ~~C~~~I~~~l~~~~GV~~v~v~~~~~~ 31 (120)
+||=+-+++.+.+++||.++.+-...+.
T Consensus 13 gGCFWg~E~~f~~i~GV~~t~~GYagG~ 40 (174)
T COG0225 13 GGCFWGVEAYFEQIPGVLSTVSGYAGGH 40 (174)
T ss_pred ccCccchHHHHhhCCCeEEEeeeEcCCC
Confidence 5899999999999999999988766554
No 65
>PRK11200 grxA glutaredoxin 1; Provisional
Probab=32.05 E-value=85 Score=18.37 Aligned_cols=26 Identities=15% Similarity=0.282 Sum_probs=17.4
Q ss_pred cchhHHHHHHHHHhcC----CCccEEEEecC
Q 036595 2 YCNACERTVARAISKF----KGVEKFTTDMN 28 (120)
Q Consensus 2 ~C~~C~~~I~~~l~~~----~GV~~v~v~~~ 28 (120)
.|..|. ++++.|..+ .||.-..+|..
T Consensus 10 ~C~~C~-~a~~~L~~l~~~~~~i~~~~idi~ 39 (85)
T PRK11200 10 GCPYCV-RAKELAEKLSEERDDFDYRYVDIH 39 (85)
T ss_pred CChhHH-HHHHHHHhhcccccCCcEEEEECC
Confidence 599998 556666665 57766666654
No 66
>PF11150 DUF2927: Protein of unknown function (DUF2927); InterPro: IPR021323 This family is conserved in Proteobacteria. Several members are described as being putative lipoproteins, but otherwise the function is not known.
Probab=31.31 E-value=31 Score=24.87 Aligned_cols=19 Identities=21% Similarity=0.128 Sum_probs=14.2
Q ss_pred CCCCCCccCCCCCCCCCCc
Q 036595 98 CCKYNDEVLMMFSDENPNA 116 (120)
Q Consensus 98 ~~~~~~~~~~~FsDeNp~a 116 (120)
++....-..++|+|+|+++
T Consensus 161 ~NDs~~~~pSIFNDd~~~~ 179 (213)
T PF11150_consen 161 PNDSPRARPSIFNDDNEFA 179 (213)
T ss_pred ccCCCcCCCceeeCCCccc
Confidence 3455556779999999875
No 67
>PRK15127 multidrug efflux system protein AcrB; Provisional
Probab=31.09 E-value=1.6e+02 Score=26.27 Aligned_cols=41 Identities=17% Similarity=0.223 Sum_probs=32.2
Q ss_pred HHHHHHHhcCCCccEEEEecCCCEEEEEe--------cCCHHHHHHHHH
Q 036595 8 RTVARAISKFKGVEKFTTDMNKHRVVVTG--------RIDPQKVLKKLK 48 (120)
Q Consensus 8 ~~I~~~l~~~~GV~~v~v~~~~~~v~V~g--------~~~~~~v~~~i~ 48 (120)
..|+..|.+++||.+|++.-....+.|.- .++..+|..+|+
T Consensus 160 ~~l~~~L~~v~GV~~V~~~G~~~ei~V~vDp~kl~~~gls~~~V~~~l~ 208 (1049)
T PRK15127 160 ANMKDPISRTSGVGDVQLFGSQYAMRIWMNPNELNKFQLTPVDVINAIK 208 (1049)
T ss_pred HHHHHHHhcCCCceEEEEcCCceEEEEEeCHHHHHHcCCCHHHHHHHHH
Confidence 56889999999999999987655566641 267788888886
No 68
>TIGR00503 prfC peptide chain release factor 3. This translation releasing factor, RF-3 (prfC) was originally described as stop codon-independent, in contrast to peptide chain release factor 1 (RF-1, prfA) and RF-2 (prfB). RF-1 and RF-2 are closely related to each other, while RF-3 is similar to elongation factors EF-Tu and EF-G; RF-1 is active at UAA and UAG and RF-2 is active at UAA and UGA. More recently, RF-3 was shown to be active primarily at UGA stop codons in E. coli. All bacteria and organelles have RF-1. The Mycoplasmas and organelles, which translate UGA as Trp rather than as a stop codon, lack RF-2. RF-3, in contrast, seems to be rare among bacteria and is found so far only in Escherichia coli and some other gamma subdivision Proteobacteria, in Synechocystis PCC6803, and in Staphylococcus aureus.
Probab=30.92 E-value=1.3e+02 Score=24.68 Aligned_cols=54 Identities=11% Similarity=0.270 Sum_probs=39.5
Q ss_pred HHHHHHHHHhcC--CCccEEEEecCCCEEEEE--ecCCHHHHHHHHHHhcCCceEEec
Q 036595 6 CERTVARAISKF--KGVEKFTTDMNKHRVVVT--GRIDPQKVLKKLKKKTGKKVEIVD 59 (120)
Q Consensus 6 C~~~I~~~l~~~--~GV~~v~v~~~~~~v~V~--g~~~~~~v~~~i~~~~G~~~~~~~ 59 (120)
-..++.++|.++ +|.-.+..+..++...|. |.+..+-++.+|+++.|-.+++-+
T Consensus 406 d~~kl~~aL~~L~eED~l~v~~~~~t~e~il~g~GelhleV~~~RL~~ey~v~v~~~~ 463 (527)
T TIGR00503 406 KQKQLLKGLVQLSEEGAVQVFRPLDNNDLIVGAVGVLQFDVVVYRLKEEYNVEARYEP 463 (527)
T ss_pred hHHHHHHHHHHHHhhCCeEEEEcCCCCCEEEEEEeHHHHHHHHHHHHHHhCCeEEEeC
Confidence 356778888776 565566666667766664 778999999999878887776643
No 69
>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=30.86 E-value=60 Score=22.62 Aligned_cols=20 Identities=10% Similarity=0.275 Sum_probs=16.7
Q ss_pred HHHHHHHhcCCCccEEEEec
Q 036595 8 RTVARAISKFKGVEKFTTDM 27 (120)
Q Consensus 8 ~~I~~~l~~~~GV~~v~v~~ 27 (120)
..|+.+|..++||.+|+|++
T Consensus 134 ~dV~~aL~~l~gV~~V~V~l 153 (174)
T TIGR03406 134 EDVEDKVLAVPNVDEVEVEL 153 (174)
T ss_pred HHHHHHHHhCCCceeEEEEE
Confidence 45888999999999888774
No 70
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=30.84 E-value=1.6e+02 Score=21.06 Aligned_cols=34 Identities=29% Similarity=0.409 Sum_probs=25.5
Q ss_pred HHHHHHhcCCCccEEEEecCCCEEEEEec---CCHHHH
Q 036595 9 TVARAISKFKGVEKFTTDMNKHRVVVTGR---IDPQKV 43 (120)
Q Consensus 9 ~I~~~l~~~~GV~~v~v~~~~~~v~V~g~---~~~~~v 43 (120)
.+.+.|....|+ .+.+|..++.|+|... .|+-.+
T Consensus 28 ~v~k~ie~~~~~-~~~iD~~~~~V~i~~~~~t~Dp~~~ 64 (194)
T COG1094 28 EVKKAIEEKTGV-KLRIDSKTGSVTIRTTRKTEDPLAL 64 (194)
T ss_pred cchHHHHhhcCe-EEEEECCCCeEEEEecCCCCChHHH
Confidence 456777777777 6999999999999743 455544
No 71
>PF02672 CP12: CP12 domain; InterPro: IPR003823 This entry represents an uncharacterised domain in proteins of unknown function. This domain is found associated with CBS domains in some proteins IPR000644 from INTERPRO.; PDB: 3B1K_I 3B1J_D 3RVD_N 3QV1_I 2LJ9_A.
Probab=30.66 E-value=8 Score=22.98 Aligned_cols=15 Identities=47% Similarity=1.012 Sum_probs=11.3
Q ss_pred cCCCCCCCCCCc--ccc
Q 036595 105 VLMMFSDENPNA--CSI 119 (120)
Q Consensus 105 ~~~~FsDeNp~a--CsI 119 (120)
.+-.|.|+||.| |.|
T Consensus 52 ~lE~yC~~nPea~Ecrv 68 (71)
T PF02672_consen 52 PLELYCDENPEADECRV 68 (71)
T ss_dssp CHHHHHHHSTTSTTTTT
T ss_pred HHHHHHHHCCCcHHhhh
Confidence 345788999998 865
No 72
>PF13383 Methyltransf_22: Methyltransferase domain
Probab=30.65 E-value=97 Score=22.68 Aligned_cols=44 Identities=25% Similarity=0.416 Sum_probs=28.2
Q ss_pred CcchhHHHHHHHHHhcCCCccEEEEecCCCEEEEE--ec--C--CHHHHHHHHHHhcCCce
Q 036595 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVT--GR--I--DPQKVLKKLKKKTGKKV 55 (120)
Q Consensus 1 m~C~~C~~~I~~~l~~~~GV~~v~v~~~~~~v~V~--g~--~--~~~~v~~~i~~~~G~~~ 55 (120)
|+|++|+..+-..+.. .|+ .++.|+ +. . ...++++.|+ +.|++.
T Consensus 173 iDIEG~Ew~~L~~~l~-~~~---------~Qi~iEiH~~~~~~~~~~~~l~~l~-~~gfr~ 222 (242)
T PF13383_consen 173 IDIEGAEWTVLEPLLE-SGV---------CQILIEIHGWPSEHREWYKLLQELE-KAGFRL 222 (242)
T ss_pred EEcCccHHHHHHHHHh-cCC---------cEEEEEEEeCccchhHHHHHHHHHH-HCCcEE
Confidence 6799999988666543 254 333333 32 1 2346899998 999864
No 73
>TIGR00288 conserved hypothetical protein TIGR00288. This family of orthologs is restricted to but universal among the completed archaeal genomes so far. Eubacterial proteins showing at least local homology include slr1870 from Synechocystis PCC6803 and two proteins from Aquifex aeolicusr, none of which is characterized.
Probab=30.27 E-value=95 Score=21.40 Aligned_cols=29 Identities=28% Similarity=0.386 Sum_probs=24.3
Q ss_pred EEEEecCCHHHHHHHHHHhcCCceEEecCC
Q 036595 32 VVVTGRIDPQKVLKKLKKKTGKKVEIVDNN 61 (120)
Q Consensus 32 v~V~g~~~~~~v~~~i~~~~G~~~~~~~~~ 61 (120)
+.|+|+-|...|+.+|+ ..|.++..++.+
T Consensus 110 vLvSgD~DF~~Lv~~lr-e~G~~V~v~g~~ 138 (160)
T TIGR00288 110 ALVTRDADFLPVINKAK-ENGKETIVIGAE 138 (160)
T ss_pred EEEeccHhHHHHHHHHH-HCCCEEEEEeCC
Confidence 45678889999999997 889999988753
No 74
>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=30.13 E-value=56 Score=18.55 Aligned_cols=37 Identities=19% Similarity=0.246 Sum_probs=22.8
Q ss_pred HHHHHhcCCCccEEEEecC----CC-EEE--EEecCCHHHHHHHHH
Q 036595 10 VARAISKFKGVEKFTTDMN----KH-RVV--VTGRIDPQKVLKKLK 48 (120)
Q Consensus 10 I~~~l~~~~GV~~v~v~~~----~~-~v~--V~g~~~~~~v~~~i~ 48 (120)
|+.+|.+.+||.++-|=.. .+ .+. |.. +.++|.+.++
T Consensus 2 IE~~l~~~~~V~~~~V~~~~d~~~g~~l~a~vv~--~~~~i~~~~~ 45 (73)
T PF13193_consen 2 IESVLRQHPGVAEAAVVGVPDEDWGERLVAFVVL--DEEEIRDHLR 45 (73)
T ss_dssp HHHHHHTSTTEEEEEEEEEEETTTEEEEEEEEEE--HHHHHHHHHH
T ss_pred HHHHHhcCCCccEEEEEEEEcccccccceeEEEe--eecccccchh
Confidence 7899999999987654321 12 221 123 4467777776
No 75
>cd08032 LARP_7 La RNA-binding domain of La-related protein 7. LARP7 is a component of the 7SK snRNP, a key factor in the regulation of RNA polymerase II transcription. 7SK functionality is dependent on the presence of LARP7, which is thought to stabilize the 7SK RNA by interacting with its 3' end. The release of 7SK RNA from P-TEFb/HEXIM/7SK complexes activates the cyclin-dependent kinase P-TEFb, which in turn phosphorylates the C-terminal domain of RNA pol II and mediates a transition into productive transcription elongation.
Probab=29.42 E-value=17 Score=22.17 Aligned_cols=7 Identities=43% Similarity=0.696 Sum_probs=5.5
Q ss_pred CCCCCCC
Q 036595 107 MMFSDEN 113 (120)
Q Consensus 107 ~~FsDeN 113 (120)
-+|||+|
T Consensus 15 fYFSd~N 21 (82)
T cd08032 15 FWFGDVN 21 (82)
T ss_pred hhcchhh
Confidence 3788888
No 76
>cd00292 EF1B Elongation factor 1 beta (EF1B) guanine nucleotide exchange domain. EF1B catalyzes the exchange of GDP bound to the G-protein, EF1A, for GTP, an important step in the elongation cycle of the protein biosynthesis. EF1A binds to and delivers the aminoacyl tRNA to the ribosome. The guanine nucleotide exchange domain of EF1B, which is the alpha subunit in yeast, is responsible for the catalysis of this exchange reaction.
Probab=29.40 E-value=61 Score=19.96 Aligned_cols=20 Identities=25% Similarity=0.370 Sum_probs=16.6
Q ss_pred HHHHHHHhcCCCccEEEEec
Q 036595 8 RTVARAISKFKGVEKFTTDM 27 (120)
Q Consensus 8 ~~I~~~l~~~~GV~~v~v~~ 27 (120)
..++.+|++.+||+++++..
T Consensus 65 d~lee~i~~~d~VqsveI~~ 84 (88)
T cd00292 65 DELEEAISEEDGVQSVDVEA 84 (88)
T ss_pred HHHHHHHhccCCceEEEEEE
Confidence 56788899999999998763
No 77
>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=29.10 E-value=1.4e+02 Score=18.16 Aligned_cols=46 Identities=11% Similarity=0.096 Sum_probs=30.7
Q ss_pred HHHHHHHHHhcCCC-ccEEEEecCCCEEEEEecCCHHHHHHHHHHhcCC
Q 036595 6 CERTVARAISKFKG-VEKFTTDMNKHRVVVTGRIDPQKVLKKLKKKTGK 53 (120)
Q Consensus 6 C~~~I~~~l~~~~G-V~~v~v~~~~~~v~V~g~~~~~~v~~~i~~~~G~ 53 (120)
+...+.+.|....+ -..+.|+..++.+.|.|.. ..+|.+.|. ..||
T Consensus 41 L~~dL~~~l~~~~~~~~~~~V~~~~g~i~IkG~~-~~~Vk~wL~-~~GF 87 (87)
T PF05046_consen 41 LKKDLRKFLGEKPKKKIDVRVNELTGHIEIKGDH-VEEVKKWLL-EKGF 87 (87)
T ss_pred HHHHHHHHhhhhcCCCcceEEeecCCEEEEcCcc-HHHHHHHHH-HCcC
Confidence 34445555544332 2367889999999999874 667777776 6665
No 78
>KOG3782 consensus Predicted membrane protein, contains type II SA sequence [General function prediction only]
Probab=29.10 E-value=1.5e+02 Score=20.73 Aligned_cols=35 Identities=29% Similarity=0.482 Sum_probs=24.0
Q ss_pred CcchhHHHHH---HHHHhcC-----CCccEEEEecCCCEEEEE
Q 036595 1 MYCNACERTV---ARAISKF-----KGVEKFTTDMNKHRVVVT 35 (120)
Q Consensus 1 m~C~~C~~~I---~~~l~~~-----~GV~~v~v~~~~~~v~V~ 35 (120)
+.|+.|...| +.+|.+. -.|.++++|.......+.
T Consensus 25 ~~CgaC~alVtelE~~IA~vDPkK~i~vgsFR~~p~G~q~~~k 67 (189)
T KOG3782|consen 25 VKCGACKALVTELEEAIAKVDPKKMIDVGSFRLDPQGNQISKK 67 (189)
T ss_pred cccchHHHHHHHHHHHHHhcCchheeeecceEECCCCCeeeee
Confidence 3699998776 4445443 357789999877776654
No 79
>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=28.84 E-value=1.8e+02 Score=25.88 Aligned_cols=41 Identities=15% Similarity=0.257 Sum_probs=32.8
Q ss_pred HHHHHHHhcCCCccEEEEecCCCEEEEEe--------cCCHHHHHHHHH
Q 036595 8 RTVARAISKFKGVEKFTTDMNKHRVVVTG--------RIDPQKVLKKLK 48 (120)
Q Consensus 8 ~~I~~~l~~~~GV~~v~v~~~~~~v~V~g--------~~~~~~v~~~i~ 48 (120)
..|+..|.+++||.+|++.-....+.|.- .++..+|..+|+
T Consensus 160 ~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~dV~~~i~ 208 (1044)
T TIGR00915 160 SNMVDPISRLEGVGDVQLFGSQYAMRIWLDPAKLNSYQLTPADVISAIQ 208 (1044)
T ss_pred HHHHHHHhCCCCceEEEecCCceEEEEEECHHHHHHcCCCHHHHHHHHH
Confidence 56889999999999999987755566651 268888888987
No 80
>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=28.70 E-value=1.6e+02 Score=18.80 Aligned_cols=39 Identities=26% Similarity=0.419 Sum_probs=27.8
Q ss_pred CCCccEEEEecCCCEEEEEecCCHHHHHHHHHHhcCCceEE
Q 036595 17 FKGVEKFTTDMNKHRVVVTGRIDPQKVLKKLKKKTGKKVEI 57 (120)
Q Consensus 17 ~~GV~~v~v~~~~~~v~V~g~~~~~~v~~~i~~~~G~~~~~ 57 (120)
..|+.+.++. ..+...|-|+--.+++++.+. ++|..+..
T Consensus 40 t~GirqfEi~-n~G~~RI~gYk~se~~~~~f~-slG~~~K~ 78 (103)
T PF09158_consen 40 TKGIRQFEIR-NKGEFRIFGYKMSEEIIKKFT-SLGMEVKQ 78 (103)
T ss_dssp ETTEEEEEEE-TTSEEEEEEES--HHHHHHHH-HTT-EEEE
T ss_pred cCceeEEEEe-cCCcEEEEEEcCCHHHHHHHH-hcCcEEEE
Confidence 4677777765 356778888888899999998 99987765
No 81
>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=28.57 E-value=51 Score=19.46 Aligned_cols=26 Identities=19% Similarity=0.296 Sum_probs=18.4
Q ss_pred CcchhHHHHHHHHHhcCCCccEEEEe
Q 036595 1 MYCNACERTVARAISKFKGVEKFTTD 26 (120)
Q Consensus 1 m~C~~C~~~I~~~l~~~~GV~~v~v~ 26 (120)
|-|..|....++++++-.=.++-++|
T Consensus 16 LPC~~Cr~HA~~ai~kNNiMSs~DiN 41 (70)
T PF04805_consen 16 LPCPECRIHAKEAIQKNNIMSSNDIN 41 (70)
T ss_pred CCCHHHHHHHHHHHHhcCccccCCcc
Confidence 46999999999998876544444333
No 82
>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=28.30 E-value=2.1e+02 Score=20.11 Aligned_cols=38 Identities=26% Similarity=0.388 Sum_probs=24.0
Q ss_pred HHHHHHHhcCCCcc--EEEEecCCCEEEEEecCCHHHHHH
Q 036595 8 RTVARAISKFKGVE--KFTTDMNKHRVVVTGRIDPQKVLK 45 (120)
Q Consensus 8 ~~I~~~l~~~~GV~--~v~v~~~~~~v~V~g~~~~~~v~~ 45 (120)
.+|.+++.+.+||. ++..|..-++..++-.-+++.|.+
T Consensus 19 e~I~~a~~~~~gv~ll~~~~D~~~NRsv~T~vG~p~~v~~ 58 (178)
T PF07837_consen 19 EAIAKAARNVPGVKLLDVFSDADYNRSVITLVGEPEAVAE 58 (178)
T ss_dssp HHHHHHCCTSTTEEEEEEEEETTTTEEEEEEEE-HHHHHH
T ss_pred HHHHHHHHcCCCCEEEecCCCCCCCCCeEEEeeChHHHHH
Confidence 56788888888977 555666777766653224455543
No 83
>KOG1796 consensus Vacuolar protein sorting-associated protein [Intracellular trafficking, secretion, and vesicular transport]
Probab=27.87 E-value=20 Score=29.41 Aligned_cols=16 Identities=44% Similarity=0.933 Sum_probs=13.1
Q ss_pred ccCCCCCCCC-CCcccc
Q 036595 104 EVLMMFSDEN-PNACSI 119 (120)
Q Consensus 104 ~~~~~FsDeN-p~aCsI 119 (120)
.++..|+|+| |++|+.
T Consensus 92 plmf~fad~~qP~~c~~ 108 (609)
T KOG1796|consen 92 PLMFSFADENQPKACRS 108 (609)
T ss_pred ceeeeeecccCcchhhh
Confidence 5678999999 788973
No 84
>COG4669 EscJ Type III secretory pathway, lipoprotein EscJ [Intracellular trafficking and secretion]
Probab=27.66 E-value=63 Score=23.91 Aligned_cols=20 Identities=25% Similarity=0.411 Sum_probs=16.0
Q ss_pred HHHHHHHHhcCCCccEEEEe
Q 036595 7 ERTVARAISKFKGVEKFTTD 26 (120)
Q Consensus 7 ~~~I~~~l~~~~GV~~v~v~ 26 (120)
+..+++.|++|+||-++.|.
T Consensus 111 eQ~le~tLs~mDGVi~ArV~ 130 (246)
T COG4669 111 EQQLEQTLSKMDGVISARVH 130 (246)
T ss_pred HHHHHHHHHhcCceEEEEEE
Confidence 56899999999998855544
No 85
>TIGR02544 III_secr_YscJ type III secretion apparatus lipoprotein, YscJ/HrcJ family. All members of this protein family are predicted lipoproteins with a conserved Cys near the N-terminus for cleavage and modification, and are part of known or predicted type III secretion systems. Members are found in both plant and animal pathogens, including the obligately intracellular chlamydial species and (non-pathogenic) root nodule bacteria. The most closely related proteins outside this family are examples of the flagellar M-ring protein FliF.
Probab=27.55 E-value=69 Score=22.59 Aligned_cols=21 Identities=19% Similarity=0.377 Sum_probs=17.2
Q ss_pred HHHHHHHHhcCCCccEEEEec
Q 036595 7 ERTVARAISKFKGVEKFTTDM 27 (120)
Q Consensus 7 ~~~I~~~l~~~~GV~~v~v~~ 27 (120)
+..+++.|..++||.++.|.+
T Consensus 109 e~EL~rtI~~i~~V~~ArVhl 129 (193)
T TIGR02544 109 EQRLEQTLSQIDGVISARVHV 129 (193)
T ss_pred HHHHHHHHHhcCCeeeeEEEE
Confidence 456888999999999887764
No 86
>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=27.46 E-value=1e+02 Score=22.99 Aligned_cols=28 Identities=18% Similarity=0.259 Sum_probs=24.6
Q ss_pred HHHHHHHHhcCCCccEEEEecCCCEEEE
Q 036595 7 ERTVARAISKFKGVEKFTTDMNKHRVVV 34 (120)
Q Consensus 7 ~~~I~~~l~~~~GV~~v~v~~~~~~v~V 34 (120)
...|+++|..++||..+.+--..+++.+
T Consensus 89 y~Avk~aLL~~~gv~haNI~SsaGtini 116 (291)
T PF03434_consen 89 YEAVKSALLNLNGVEHANIKSSAGTINI 116 (291)
T ss_pred HHHHHHHhcCCCCceeeeeecCCCeeEE
Confidence 3578999999999999999988888776
No 87
>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=27.42 E-value=2.2e+02 Score=23.99 Aligned_cols=58 Identities=12% Similarity=0.201 Sum_probs=40.1
Q ss_pred HHHHHHHHhcCCCccEEEEecCCCEEEEEe----cC--CHHHHHHHHHHhcCCceEEecCCCCC
Q 036595 7 ERTVARAISKFKGVEKFTTDMNKHRVVVTG----RI--DPQKVLKKLKKKTGKKVEIVDNNNNN 64 (120)
Q Consensus 7 ~~~I~~~l~~~~GV~~v~v~~~~~~v~V~g----~~--~~~~v~~~i~~~~G~~~~~~~~~~~~ 64 (120)
...|++.+-.-.||.++.++..++.|.|+. -+ -....+..|.+++|++.+++..++.+
T Consensus 72 ~~~i~~~~~~~~~~~~~~f~~~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~~w~~~~~~~~~~~ 135 (630)
T TIGR03675 72 IEKIKEIVPEEAGITDIYFDDVTGEVIIEAEKPGLVIGKGGSTLREITAETGWTPKVVRTPPIE 135 (630)
T ss_pred HHHHHHhCCCcCCceeEEecCCCceEEEEEcCCeEEEecCcchHHHHHHHhCCeeeEEecCCCC
Confidence 345666666668999999999999999963 22 12233444445999999887665543
No 88
>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=26.84 E-value=1.1e+02 Score=27.22 Aligned_cols=42 Identities=7% Similarity=0.131 Sum_probs=31.2
Q ss_pred HHHHHHHHhcCCCccEEEEecCC--CEEEEEe--------cCCHHHHHHHHH
Q 036595 7 ERTVARAISKFKGVEKFTTDMNK--HRVVVTG--------RIDPQKVLKKLK 48 (120)
Q Consensus 7 ~~~I~~~l~~~~GV~~v~v~~~~--~~v~V~g--------~~~~~~v~~~i~ 48 (120)
+.+|++.|.+++||.+++.+... ..+.|.- .+++++|.+.++
T Consensus 700 a~~v~~~l~~~pgv~~v~~~~~~~~~e~~i~id~~~~~~~Glt~~~v~~~l~ 751 (1051)
T TIGR00914 700 AEKISAVLKGVPGAADVKVEQTTGLPYLTVEIDREKAARYGLTVGDVQDTVA 751 (1051)
T ss_pred HHHHHHHHhcCCCceeeeccccCCCceEEEEECHHHHHHcCCCHHHHHHHHH
Confidence 46789999999999999998654 3444431 267788888885
No 89
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=26.09 E-value=40 Score=25.43 Aligned_cols=28 Identities=18% Similarity=0.208 Sum_probs=24.3
Q ss_pred hhHHHHHHHHHhcCCCccEEEEecCCCE
Q 036595 4 NACERTVARAISKFKGVEKFTTDMNKHR 31 (120)
Q Consensus 4 ~~C~~~I~~~l~~~~GV~~v~v~~~~~~ 31 (120)
.||=+.++..+.+++||.++.+-+..+.
T Consensus 134 gGCFWg~E~~F~~~~GV~~t~vGYagG~ 161 (283)
T PRK05550 134 GGCFWGVEYYFKKLPGVLSVESGYTGGD 161 (283)
T ss_pred cCCchhhhhhHhhCcCEEEEEEeeCCCC
Confidence 5899999999999999999998776553
No 90
>KOG3476 consensus Microtubule-associated protein CRIPT [Cytoskeleton]
Probab=25.76 E-value=33 Score=21.32 Aligned_cols=14 Identities=36% Similarity=1.018 Sum_probs=11.4
Q ss_pred CcchhHHHHHHHHH
Q 036595 1 MYCNACERTVARAI 14 (120)
Q Consensus 1 m~C~~C~~~I~~~l 14 (120)
|-|+.|+.++.+++
T Consensus 1 MVC~kCEkKLskvi 14 (100)
T KOG3476|consen 1 MVCEKCEKKLSKVI 14 (100)
T ss_pred CchhHHHHHhcccc
Confidence 77999998887765
No 91
>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=25.34 E-value=1.4e+02 Score=20.46 Aligned_cols=29 Identities=24% Similarity=0.269 Sum_probs=24.3
Q ss_pred HHHHHHHHhcCCCccEEEEecCCCEEEEE
Q 036595 7 ERTVARAISKFKGVEKFTTDMNKHRVVVT 35 (120)
Q Consensus 7 ~~~I~~~l~~~~GV~~v~v~~~~~~v~V~ 35 (120)
+.+|.+.+.+++||.++.+=.....+.|-
T Consensus 56 A~~Ia~~v~~v~~V~dA~vvVtg~~A~Vg 84 (158)
T TIGR02898 56 ADEIASEAAKVKGVKDATVVITGNYAYVG 84 (158)
T ss_pred HHHHHHHHhcCCCCceEEEEEECCEEEEE
Confidence 56788889999999999988888887763
No 92
>PF13216 DUF4024: Protein of unknown function (DUF4024)
Probab=24.51 E-value=22 Score=17.59 Aligned_cols=11 Identities=45% Similarity=0.640 Sum_probs=9.2
Q ss_pred CCCCCCCCCCc
Q 036595 106 LMMFSDENPNA 116 (120)
Q Consensus 106 ~~~FsDeNp~a 116 (120)
.+.|-|||+|-
T Consensus 9 lhlfrde~vnf 19 (35)
T PF13216_consen 9 LHLFRDEKVNF 19 (35)
T ss_pred EEEeecCCccE
Confidence 47899999985
No 93
>KOG4730 consensus D-arabinono-1, 4-lactone oxidase [Defense mechanisms]
Probab=24.13 E-value=97 Score=25.30 Aligned_cols=34 Identities=21% Similarity=0.253 Sum_probs=28.7
Q ss_pred EEEecCCCEEEEEecCCHHHHHHHHHHhcCCceEE
Q 036595 23 FTTDMNKHRVVVTGRIDPQKVLKKLKKKTGKKVEI 57 (120)
Q Consensus 23 v~v~~~~~~v~V~g~~~~~~v~~~i~~~~G~~~~~ 57 (120)
+++|.+..+|||..-+...+|++.++ +.|+...-
T Consensus 105 v~~dpe~~tvTV~aGirlrQLie~~~-~~GlsL~~ 138 (518)
T KOG4730|consen 105 VEFDPELKTVTVQAGIRLRQLIEELA-KLGLSLPN 138 (518)
T ss_pred eeeCchhceEEeccCcCHHHHHHHHH-hcCccccC
Confidence 56688889999998899999999998 99987543
No 94
>PF01936 NYN: NYN domain; InterPro: IPR021139 This highly conserved domain has no known function. However it contains many conserved aspartates, suggesting an enzymatic function such as an endonuclease or glycosyl hydrolase.; PDB: 2QIP_A.
Probab=24.05 E-value=72 Score=20.37 Aligned_cols=29 Identities=34% Similarity=0.564 Sum_probs=19.2
Q ss_pred EEEEEecCCHHHHHHHHHHhcCCceEEecC
Q 036595 31 RVVVTGRIDPQKVLKKLKKKTGKKVEIVDN 60 (120)
Q Consensus 31 ~v~V~g~~~~~~v~~~i~~~~G~~~~~~~~ 60 (120)
-+.|+|+.+...+++.++ ..|+++.++..
T Consensus 99 ivLvSgD~Df~~~v~~l~-~~g~~V~v~~~ 127 (146)
T PF01936_consen 99 IVLVSGDSDFAPLVRKLR-ERGKRVIVVGA 127 (146)
T ss_dssp EEEE---GGGHHHHHHHH-HH--EEEEEE-
T ss_pred EEEEECcHHHHHHHHHHH-HcCCEEEEEEe
Confidence 345678889999999997 99999998873
No 95
>PRK15348 type III secretion system lipoprotein SsaJ; Provisional
Probab=23.92 E-value=88 Score=23.16 Aligned_cols=21 Identities=19% Similarity=0.382 Sum_probs=17.4
Q ss_pred HHHHHHHHhcCCCccEEEEec
Q 036595 7 ERTVARAISKFKGVEKFTTDM 27 (120)
Q Consensus 7 ~~~I~~~l~~~~GV~~v~v~~ 27 (120)
+..+++.|..++||.++.|.+
T Consensus 109 egELarTI~~idgV~~ArVhL 129 (249)
T PRK15348 109 EQRIEGMLSQMEGVINAKVTI 129 (249)
T ss_pred HHHHHHHHHhCCCeeEeEEEE
Confidence 356889999999999888864
No 96
>PF00736 EF1_GNE: EF-1 guanine nucleotide exchange domain; InterPro: IPR014038 Translation elongation factors are responsible for two main processes during protein synthesis on the ribosome [, , ]. EF1A (or EF-Tu) is responsible for the selection and binding of the cognate aminoacyl-tRNA to the A-site (acceptor site) of the ribosome. EF2 (or EF-G) is responsible for the translocation of the peptidyl-tRNA from the A-site to the P-site (peptidyl-tRNA site) of the ribosome, thereby freeing the A-site for the next aminoacyl-tRNA to bind. Elongation factors are responsible for achieving accuracy of translation and both EF1A and EF2 are remarkably conserved throughout evolution. Elongation factor EF1B (also known as EF-Ts or EF-1beta/gamma/delta) is a nucleotide exchange factor that is required to regenerate EF1A from its inactive form (EF1A-GDP) to its active form (EF1A-GTP). EF1A is then ready to interact with a new aminoacyl-tRNA to begin the cycle again. EF1B is more complex in eukaryotes than in bacteria, and can consist of three subunits: EF1B-alpha (or EF-1beta), EF1B-gamma (or EF-1gamma) and EF1B-beta (or EF-1delta) []. This entry represents the guanine nucleotide exchange domain of the beta (EF-1beta, also known as EF1B-alpha) and delta (EF-1delta, also known as EF1B-beta) chains of EF1B proteins from eukaryotes and archaea. The beta and delta chains have exchange activity, which mainly resides in their homologous guanine nucleotide exchange domains, found in the C-terminal region of the peptides. Their N-terminal regions may be involved in interactions with the gamma chain (EF-1gamma). More information about these proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0003746 translation elongation factor activity, 0006414 translational elongation, 0005853 eukaryotic translation elongation factor 1 complex; PDB: 2YY3_B 1GH8_A 1B64_A 1IJE_B 1IJF_B 1F60_B 1G7C_B 2B7B_B 2B7C_B.
Probab=23.78 E-value=90 Score=19.21 Aligned_cols=20 Identities=25% Similarity=0.307 Sum_probs=16.5
Q ss_pred HHHHHHHH-hcCCCccEEEEe
Q 036595 7 ERTVARAI-SKFKGVEKFTTD 26 (120)
Q Consensus 7 ~~~I~~~l-~~~~GV~~v~v~ 26 (120)
...|+.+| ...+||+++++.
T Consensus 64 ~d~lee~i~~~~e~Vqsvei~ 84 (89)
T PF00736_consen 64 TDDLEEAIESFEEGVQSVEIE 84 (89)
T ss_dssp HHHHHHHHTTCTTTEEEEEEE
T ss_pred hHHHHHHHHhcCCCccEEEEE
Confidence 45678888 889999999875
No 97
>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=23.56 E-value=91 Score=17.80 Aligned_cols=17 Identities=29% Similarity=0.520 Sum_probs=13.0
Q ss_pred HHHHHHHhcCCCccEEE
Q 036595 8 RTVARAISKFKGVEKFT 24 (120)
Q Consensus 8 ~~I~~~l~~~~GV~~v~ 24 (120)
..+-+.|++++||.+|.
T Consensus 52 ~~li~~L~~i~gV~~V~ 68 (74)
T cd04877 52 QTLMPEIRRIDGVEDVK 68 (74)
T ss_pred HHHHHHHhCCCCceEEE
Confidence 45667788899998775
No 98
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.60 E-value=47 Score=20.17 Aligned_cols=16 Identities=13% Similarity=0.557 Sum_probs=13.5
Q ss_pred cchhHHHHHHHHHhcC
Q 036595 2 YCNACERTVARAISKF 17 (120)
Q Consensus 2 ~C~~C~~~I~~~l~~~ 17 (120)
.|+.|..++++.|+..
T Consensus 35 ~ce~c~a~~kk~l~~v 50 (82)
T COG2331 35 TCEECGARLKKLLNAV 50 (82)
T ss_pred cChhhChHHHHhhccc
Confidence 5999999999988664
No 99
>PF08478 POTRA_1: POTRA domain, FtsQ-type; InterPro: IPR013685 FtsQ/DivIB bacterial division proteins (IPR005548 from INTERPRO) contain an N-terminal POTRA domain (for polypeptide-transport-associated domain). This is found in different types of proteins, usually associated with a transmembrane beta-barrel. FtsQ/DivIB may have chaperone-like roles, which has also been postulated for the POTRA domain in other contexts []. ; PDB: 2ALJ_A 2VH1_B 3J00_Z 2VH2_B.
Probab=22.56 E-value=72 Score=17.76 Aligned_cols=27 Identities=7% Similarity=0.197 Sum_probs=20.4
Q ss_pred HHHHHHHhcCCCccEEEEec-CCCEEEE
Q 036595 8 RTVARAISKFKGVEKFTTDM-NKHRVVV 34 (120)
Q Consensus 8 ~~I~~~l~~~~GV~~v~v~~-~~~~v~V 34 (120)
..+++.|.+++.|++|.|.. -.+++.|
T Consensus 37 ~~~~~~l~~~p~V~~v~V~r~~P~~l~I 64 (69)
T PF08478_consen 37 KKIEQRLEKLPWVKSVSVSRRFPNTLEI 64 (69)
T ss_dssp HHHHHCCCCTTTEEEEEEEEETTTEEEE
T ss_pred HHHHHHHHcCCCEEEEEEEEeCCCEEEE
Confidence 46788888999999999984 3455554
No 100
>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=22.51 E-value=1.8e+02 Score=25.63 Aligned_cols=42 Identities=17% Similarity=0.315 Sum_probs=32.4
Q ss_pred HHHHHHHHhcCCCccEEEEecCCCEEEEEec----------CCHHHHHHHHH
Q 036595 7 ERTVARAISKFKGVEKFTTDMNKHRVVVTGR----------IDPQKVLKKLK 48 (120)
Q Consensus 7 ~~~I~~~l~~~~GV~~v~v~~~~~~v~V~g~----------~~~~~v~~~i~ 48 (120)
+.+|++.|++.+|+.++..+....+-.+.-. ++.++|...|+
T Consensus 689 a~~v~~~l~~~pgv~dv~~~~~~~~~el~i~~dreka~~~Gls~~~va~~l~ 740 (1021)
T PF00873_consen 689 AEKVKAKLAEIPGVTDVRDDWEDGQPELRIDPDREKAARLGLSPADVARTLR 740 (1021)
T ss_dssp HHHHHHHHHHSTTEEEEEESSSSBEEEEEEEE-HHHHHHTTB-HHHHHHHHH
T ss_pred HHHHHHHHHhCCCcccccccccccCcceEEEecHHHHHHcCCCHHHHHHHHH
Confidence 5688999999999999999998877665421 56677777775
No 101
>cd06482 ACD_HspB10 Alpha crystallin domain (ACD) found in mammalian small heat shock protein (sHsp) HspB10, also known as sperm outer dense fiber protein (ODFP), and similar proteins. sHsps are molecular chaperones that suppress protein aggregation and protect against cell stress, and are generally active as large oligomers consisting of multiple subunits. Human (h) HspB10 occurs exclusively in the axoneme of sperm cells and may have a cytoskeletal role.
Probab=22.03 E-value=83 Score=19.19 Aligned_cols=23 Identities=17% Similarity=0.289 Sum_probs=17.3
Q ss_pred cCCCcc--EEEEecCCCEEEEEecC
Q 036595 16 KFKGVE--KFTTDMNKHRVVVTGRI 38 (120)
Q Consensus 16 ~~~GV~--~v~v~~~~~~v~V~g~~ 38 (120)
.++|+. .++|.+..+.++|.|..
T Consensus 15 dlPG~~kedI~V~v~~~~L~I~ger 39 (87)
T cd06482 15 DVCGFEPDQVKVKVKDGKVQVSAER 39 (87)
T ss_pred ECCCCCHHHeEEEEECCEEEEEEEE
Confidence 357766 67777888999998863
No 102
>PF15643 Tox-PL-2: Papain fold toxin 2
Probab=22.01 E-value=65 Score=20.50 Aligned_cols=18 Identities=17% Similarity=0.591 Sum_probs=14.9
Q ss_pred cchhHHHHHHHHHhcCCCc
Q 036595 2 YCNACERTVARAISKFKGV 20 (120)
Q Consensus 2 ~C~~C~~~I~~~l~~~~GV 20 (120)
.|..|+..|++.|.+. ||
T Consensus 20 qC~~cA~Al~~~L~~~-gI 37 (100)
T PF15643_consen 20 QCVECASALKQFLKQA-GI 37 (100)
T ss_pred ehHHHHHHHHHHHHHC-CC
Confidence 6999999999998764 54
No 103
>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=21.61 E-value=1.6e+02 Score=16.39 Aligned_cols=47 Identities=13% Similarity=0.227 Sum_probs=30.9
Q ss_pred CcchhHHHHHHHHHhcCCCccEEEEecCCCEEEEE--ecCCHHHHHHHHHHhcCCceEEe
Q 036595 1 MYCNACERTVARAISKFKGVEKFTTDMNKHRVVVT--GRIDPQKVLKKLKKKTGKKVEIV 58 (120)
Q Consensus 1 m~C~~C~~~I~~~l~~~~GV~~v~v~~~~~~v~V~--g~~~~~~v~~~i~~~~G~~~~~~ 58 (120)
+.|+.-.-+++++| ++..- +.+.|. .......|...++ +.|+..+..
T Consensus 7 ~~CP~P~l~~k~al-~~~~g---------~~l~v~~d~~~s~~~i~~~~~-~~G~~~~~~ 55 (67)
T cd03421 7 LACPQPVIKTKKAL-ELEAG---------GEIEVLVDNEVAKENVSRFAE-SRGYEVSVE 55 (67)
T ss_pred CCCCHHHHHHHHHH-hcCCC---------CEEEEEEcChhHHHHHHHHHH-HcCCEEEEE
Confidence 35888888889998 65332 233333 3344567888886 999988543
No 104
>KOG0364 consensus Chaperonin complex component, TCP-1 gamma subunit (CCT3) [Posttranslational modification, protein turnover, chaperones]
Probab=21.60 E-value=29 Score=28.06 Aligned_cols=20 Identities=40% Similarity=0.929 Sum_probs=15.9
Q ss_pred CCCccCCCCCC-CCCCccccC
Q 036595 101 YNDEVLMMFSD-ENPNACSIM 120 (120)
Q Consensus 101 ~~~~~~~~FsD-eNp~aCsIM 120 (120)
..+.|+++|++ -+|.||+|+
T Consensus 351 ~gdeyf~f~~~Ck~pkaCtil 371 (527)
T KOG0364|consen 351 IGDEYFTFFTDCKEPKACTIL 371 (527)
T ss_pred cCchhhhhhhhcCCCcceEEE
Confidence 45678888888 569999985
No 105
>PRK11282 glcE glycolate oxidase FAD binding subunit; Provisional
Probab=21.20 E-value=1.9e+02 Score=22.48 Aligned_cols=37 Identities=11% Similarity=0.197 Sum_probs=28.8
Q ss_pred hcCCCccEEEEecCCCEEEEEecCCHHHHHHHHHHhcCCc
Q 036595 15 SKFKGVEKFTTDMNKHRVVVTGRIDPQKVLKKLKKKTGKK 54 (120)
Q Consensus 15 ~~~~GV~~v~v~~~~~~v~V~g~~~~~~v~~~i~~~~G~~ 54 (120)
.++.+| +++|.....++|..-+...+|.+.+. +.|..
T Consensus 44 ~~ln~I--le~d~~~~~vtV~AG~~l~el~~~L~-~~G~~ 80 (352)
T PRK11282 44 RAHRGI--VSYDPTELVITARAGTPLAELEAALA-EAGQM 80 (352)
T ss_pred ccCCCc--EEEcCCCCEEEECCCCCHHHHHHHHH-HcCCe
Confidence 445555 36788888999988888999999997 88864
No 106
>PRK09019 translation initiation factor Sui1; Validated
Probab=20.92 E-value=1.4e+02 Score=19.23 Aligned_cols=41 Identities=24% Similarity=0.310 Sum_probs=21.9
Q ss_pred HhcCCCccEEEEecC---CCEEEEE-ec----CCHHHHHHHHHHhcCCc
Q 036595 14 ISKFKGVEKFTTDMN---KHRVVVT-GR----IDPQKVLKKLKKKTGKK 54 (120)
Q Consensus 14 l~~~~GV~~v~v~~~---~~~v~V~-g~----~~~~~v~~~i~~~~G~~ 54 (120)
+..-.++..+..... .+.|||. |- .+..+|++.|+++.|-.
T Consensus 26 ~~~~~~~vri~~~r~gRkGK~VTiI~Gl~~~~~dlk~l~K~lKkk~gcG 74 (108)
T PRK09019 26 RPKGDGIVRIQRQTSGRKGKGVCLITGLDLDDAELKKLAAELKKKCGCG 74 (108)
T ss_pred CCCcCceEEEEEecCCCCCCeEEEEeCCcCCHHHHHHHHHHHHHHhcCC
Confidence 334455545554432 3357753 32 35566777777666654
No 107
>cd04879 ACT_3PGDH-like ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH). ACT_3PGDH-like: The ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with or without an extended C-terminal (xct) region found in various 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. In the Escherichia coli homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active
Probab=20.56 E-value=1.3e+02 Score=16.04 Aligned_cols=16 Identities=13% Similarity=0.335 Sum_probs=12.1
Q ss_pred HHHHHHhcCCCccEEE
Q 036595 9 TVARAISKFKGVEKFT 24 (120)
Q Consensus 9 ~I~~~l~~~~GV~~v~ 24 (120)
.+.+.|++++||.+|.
T Consensus 54 ~l~~~l~~~~~V~~v~ 69 (71)
T cd04879 54 EVLEELKALPGIIRVR 69 (71)
T ss_pred HHHHHHHcCCCeEEEE
Confidence 5667788888887765
No 108
>TIGR02194 GlrX_NrdH Glutaredoxin-like protein NrdH. NrdH-redoxin is a representative of a class of small redox proteins that contain a conserved CXXC motif and are characterized by a glutaredoxin-like amino acid sequence and thioredoxin-like activity profile. Unlike other the glutaredoxins to which it is most closely related, NrdH aparrently does not interact with glutathione/glutathione reductase, but rather with thioredoxin reductase to catalyze the reduction of ribonucleotide reductase.
Probab=20.37 E-value=1.8e+02 Score=16.33 Aligned_cols=25 Identities=16% Similarity=0.498 Sum_probs=15.9
Q ss_pred cchhHHHHHHHHHhcCCCccEEEEecC
Q 036595 2 YCNACERTVARAISKFKGVEKFTTDMN 28 (120)
Q Consensus 2 ~C~~C~~~I~~~l~~~~GV~~v~v~~~ 28 (120)
.|..|. ++++.|.+. ||.-..+|..
T Consensus 8 ~Cp~C~-~ak~~L~~~-~i~~~~~di~ 32 (72)
T TIGR02194 8 NCVQCK-MTKKALEEH-GIAFEEINID 32 (72)
T ss_pred CCHHHH-HHHHHHHHC-CCceEEEECC
Confidence 589997 566777653 6655444443
No 109
>PF11491 DUF3213: Protein of unknown function (DUF3213) ; InterPro: IPR021583 The backbone structure of this family of proteins has been determined however the function remains unknown. The protein has an alpha and beta structure with a ferredoxin-like fold []. ; PDB: 2F40_A.
Probab=20.30 E-value=1.9e+02 Score=17.81 Aligned_cols=44 Identities=14% Similarity=0.147 Sum_probs=21.5
Q ss_pred HHHHHhcCCCccEEEEecCCCEEEEE---ecCCHHHHHHHHHHhcCCc
Q 036595 10 VARAISKFKGVEKFTTDMNKHRVVVT---GRIDPQKVLKKLKKKTGKK 54 (120)
Q Consensus 10 I~~~l~~~~GV~~v~v~~~~~~v~V~---g~~~~~~v~~~i~~~~G~~ 54 (120)
+.=.|++.++|-.|-+|.-.+...|. ..+..++|++.++ ..+..
T Consensus 16 ~QYeLsk~~~vyRvFiNgYar~g~VifDe~kl~~e~lL~~le-~~kpE 62 (88)
T PF11491_consen 16 KQYELSKNEAVYRVFINGYARNGFVIFDESKLSKEELLEMLE-EFKPE 62 (88)
T ss_dssp HHHTTTTTTTB------TTSS--EEE--B-S-SHHHH---HH-HTTT-
T ss_pred HHHHhhcccceeeeeecccccceEEEECcccCCHHHHHHHHH-hcChh
Confidence 34457888999999999766665553 3478999999998 77643
No 110
>KOG1635 consensus Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=20.25 E-value=97 Score=21.90 Aligned_cols=28 Identities=18% Similarity=0.186 Sum_probs=24.2
Q ss_pred hhHHHHHHHHHhcCCCccEEEEecCCCE
Q 036595 4 NACERTVARAISKFKGVEKFTTDMNKHR 31 (120)
Q Consensus 4 ~~C~~~I~~~l~~~~GV~~v~v~~~~~~ 31 (120)
.+|-+.++.+..+++||...+|-+..++
T Consensus 31 ~GCFWg~E~a~~~l~gV~~T~vGYagG~ 58 (191)
T KOG1635|consen 31 AGCFWGVELAYQRLPGVVRTEVGYAGGI 58 (191)
T ss_pred ccchhhHHHHHhhcCCeEEEeecccCCc
Confidence 4799999999999999999888877664
No 111
>PRK07334 threonine dehydratase; Provisional
Probab=20.23 E-value=2.7e+02 Score=21.76 Aligned_cols=50 Identities=14% Similarity=0.147 Sum_probs=29.7
Q ss_pred HHHHHHHhcCC-CccEEEEecC-----CCEEEEE--e----cCCHHHHHHHHHHhcCCceEEe
Q 036595 8 RTVARAISKFK-GVEKFTTDMN-----KHRVVVT--G----RIDPQKVLKKLKKKTGKKVEIV 58 (120)
Q Consensus 8 ~~I~~~l~~~~-GV~~v~v~~~-----~~~v~V~--g----~~~~~~v~~~i~~~~G~~~~~~ 58 (120)
..|-+.|++.+ .|.++.+... .+...+. - ..+.+.|+..|+ +.||.++++
T Consensus 341 ~dI~~~is~~~~nI~~v~~~~~~~~~~~~~~~i~l~i~V~d~~~L~~vi~~Lr-~~g~~~~~~ 402 (403)
T PRK07334 341 ARVTALIGEAGANIIEVSHQRLFTDLPAKGAELELVIETRDAAHLQEVIAALR-AAGFEARLV 402 (403)
T ss_pred HHHHHHHhhCCCceEEEEEEecccCCCCCeEEEEEEEEeCCHHHHHHHHHHHH-HcCCeeEeC
Confidence 45666776552 2445554422 3443332 1 234568899997 999999875
No 112
>PRK10509 bacterioferritin-associated ferredoxin; Provisional
Probab=20.22 E-value=67 Score=18.43 Aligned_cols=16 Identities=19% Similarity=0.484 Sum_probs=12.7
Q ss_pred cchhHHHHHHHHHhcC
Q 036595 2 YCNACERTVARAISKF 17 (120)
Q Consensus 2 ~C~~C~~~I~~~l~~~ 17 (120)
.|+.|...|++.|...
T Consensus 38 ~CG~C~~~i~~il~~~ 53 (64)
T PRK10509 38 QCGKCIRAAREVMQDE 53 (64)
T ss_pred CccchHHHHHHHHHHH
Confidence 5899999998887553
Done!