Query psy13022
Match_columns 93
No_of_seqs 170 out of 1275
Neff 7.6
Searched_HMMs 46136
Date Fri Aug 16 17:22:14 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy13022.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/13022hhsearch_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 99.6 4.7E-15 1E-19 83.9 8.5 60 3-62 2-62 (62)
2 COG2608 CopZ Copper chaperone 99.5 2.8E-13 6.1E-18 79.3 8.1 61 5-65 9-69 (71)
3 KOG4656|consensus 99.0 1.4E-09 3.1E-14 75.2 7.3 66 2-70 10-75 (247)
4 PLN02957 copper, zinc superoxi 98.6 6.3E-07 1.4E-11 63.1 9.1 66 3-71 10-75 (238)
5 KOG1603|consensus 98.5 6.3E-07 1.4E-11 52.4 7.0 59 3-64 9-68 (73)
6 COG2217 ZntA Cation transport 98.5 2.6E-07 5.7E-12 73.7 6.9 59 6-65 10-69 (713)
7 KOG0207|consensus 98.4 5.3E-07 1.2E-11 72.9 6.4 68 6-74 2-69 (951)
8 KOG0207|consensus 98.3 2.4E-06 5.1E-11 69.3 6.5 67 6-72 77-143 (951)
9 TIGR00003 copper ion binding p 98.2 1.6E-05 3.6E-10 41.9 7.5 58 6-63 10-67 (68)
10 PRK10671 copA copper exporting 98.1 8.6E-06 1.9E-10 65.8 6.6 56 6-66 11-66 (834)
11 PRK11033 zntA zinc/cadmium/mer 97.5 0.00035 7.5E-09 56.2 6.5 59 6-66 61-119 (741)
12 PRK10671 copA copper exporting 97.0 0.003 6.6E-08 51.3 7.1 58 6-66 107-164 (834)
13 PRK14054 methionine sulfoxide 96.6 0.0059 1.3E-07 41.4 5.0 57 1-57 1-76 (172)
14 TIGR02052 MerP mercuric transp 96.0 0.13 2.8E-06 29.2 8.1 58 7-64 32-89 (92)
15 PRK05528 methionine sulfoxide 95.8 0.033 7.2E-07 37.2 5.3 48 10-57 8-69 (156)
16 PRK00058 methionine sulfoxide 95.5 0.035 7.6E-07 38.8 4.8 47 10-56 52-117 (213)
17 PRK13014 methionine sulfoxide 95.4 0.03 6.5E-07 38.4 4.2 49 10-58 15-82 (186)
18 PF01625 PMSR: Peptide methion 95.1 0.097 2.1E-06 34.8 5.8 49 10-58 7-74 (155)
19 TIGR00401 msrA methionine-S-su 94.1 0.15 3.2E-06 33.8 4.8 48 10-57 7-73 (149)
20 COG0225 MsrA Peptide methionin 94.0 0.15 3.2E-06 34.7 4.8 50 9-58 12-80 (174)
21 PRK13748 putative mercuric red 93.9 0.49 1.1E-05 36.6 8.1 63 6-69 8-70 (561)
22 PRK05550 bifunctional methioni 93.9 0.14 3.1E-06 37.3 4.8 47 10-56 134-199 (283)
23 COG1888 Uncharacterized protei 93.3 0.51 1.1E-05 28.9 5.8 52 15-66 23-79 (97)
24 PF01206 TusA: Sulfurtransfera 93.3 0.33 7.2E-06 27.4 4.8 56 6-71 7-62 (70)
25 PF02680 DUF211: Uncharacteriz 92.1 0.65 1.4E-05 28.6 5.2 52 15-66 21-77 (95)
26 cd00371 HMA Heavy-metal-associ 90.9 0.92 2E-05 21.0 7.3 56 6-62 6-61 (63)
27 PRK11018 hypothetical protein; 90.0 2.5 5.4E-05 24.7 6.2 53 6-68 15-67 (78)
28 PRK14018 trifunctional thiored 90.0 0.72 1.6E-05 36.3 4.9 48 10-57 205-270 (521)
29 PF11491 DUF3213: Protein of u 88.8 0.92 2E-05 27.4 3.7 55 11-65 11-65 (88)
30 cd03422 YedF YedF is a bacteri 87.2 3.8 8.2E-05 23.2 6.1 53 7-69 7-59 (69)
31 PF09580 Spore_YhcN_YlaJ: Spor 87.0 3 6.4E-05 27.6 5.8 46 12-57 76-123 (177)
32 cd03423 SirA SirA (also known 86.7 4 8.7E-05 23.0 6.3 53 7-69 7-59 (69)
33 cd00291 SirA_YedF_YeeD SirA, Y 86.6 3.8 8.3E-05 22.6 6.2 54 6-69 6-59 (69)
34 cd03420 SirA_RHOD_Pry_redox Si 85.9 4.6 9.9E-05 22.8 6.2 53 7-69 7-59 (69)
35 PF01883 DUF59: Domain of unkn 85.8 1.1 2.5E-05 25.3 2.9 29 3-31 38-72 (72)
36 KOG1635|consensus 82.8 3.9 8.4E-05 28.1 4.8 48 10-57 31-97 (191)
37 cd03421 SirA_like_N SirA_like_ 82.4 6.5 0.00014 21.8 6.0 50 7-67 7-56 (67)
38 PF04805 Pox_E10: E10-like pro 82.2 1 2.3E-05 26.0 1.6 27 6-32 15-41 (70)
39 TIGR03527 selenium_YedF seleni 80.0 11 0.00023 25.9 6.3 53 7-69 6-58 (194)
40 COG4669 EscJ Type III secretor 77.4 10 0.00023 27.1 5.7 39 13-52 111-163 (246)
41 PHA03005 sulfhydryl oxidase; P 76.2 2 4.4E-05 26.4 1.7 27 6-32 40-66 (96)
42 cd04906 ACT_ThrD-I_1 First of 74.9 14 0.00031 21.5 7.0 64 3-67 4-73 (85)
43 TIGR02898 spore_YhcN_YlaJ spor 72.9 17 0.00037 24.3 5.6 34 12-45 55-88 (158)
44 PRK00299 sulfur transfer prote 71.0 18 0.0004 21.1 6.3 52 7-68 17-68 (81)
45 cd04888 ACT_PheB-BS C-terminal 70.7 9.9 0.00021 21.0 3.7 29 3-31 45-74 (76)
46 PF02682 AHS1: Allophanate hyd 68.3 16 0.00035 25.1 4.9 48 10-59 24-73 (202)
47 TIGR03406 FeS_long_SufT probab 67.9 5.9 0.00013 26.8 2.6 44 3-54 117-166 (174)
48 TIGR02945 SUF_assoc FeS assemb 63.1 6.9 0.00015 23.4 2.1 32 3-34 41-78 (99)
49 TIGR00268 conserved hypothetic 61.7 26 0.00056 24.6 5.0 53 13-66 187-244 (252)
50 TIGR02024 FtcD glutamate formi 59.3 52 0.0011 24.3 6.3 57 2-58 184-250 (298)
51 PF03698 UPF0180: Uncharacteri 58.5 20 0.00043 21.3 3.4 24 47-70 8-31 (80)
52 PRK09577 multidrug efflux prot 56.6 44 0.00095 28.5 6.2 50 13-62 158-212 (1032)
53 PRK10555 aminoglycoside/multid 55.9 41 0.00089 28.6 6.0 47 13-59 159-210 (1037)
54 PRK15348 type III secretion sy 52.7 68 0.0015 23.0 5.9 38 13-51 109-159 (249)
55 PRK03094 hypothetical protein; 51.8 50 0.0011 19.7 4.7 22 47-68 8-29 (80)
56 cd04908 ACT_Bt0572_1 N-termina 51.7 39 0.00084 18.3 5.9 53 10-64 12-65 (66)
57 smart00796 AHS1 Allophanate hy 50.5 74 0.0016 21.8 5.7 46 12-59 26-73 (201)
58 COG2151 PaaD Predicted metal-s 50.4 21 0.00045 22.5 2.7 21 13-33 69-89 (111)
59 COG4004 Uncharacterized protei 49.9 14 0.00031 22.6 1.9 25 18-42 34-58 (96)
60 cd04883 ACT_AcuB C-terminal AC 49.9 41 0.00089 18.2 6.6 60 3-64 4-69 (72)
61 PF05922 Inhibitor_I9: Peptida 49.8 18 0.00039 20.3 2.2 27 2-33 51-77 (82)
62 TIGR00915 2A0602 The (Largely 49.6 59 0.0013 27.7 6.0 46 14-59 160-210 (1044)
63 PF13732 DUF4162: Domain of un 49.5 47 0.001 18.8 6.0 43 20-65 26-68 (84)
64 PF13291 ACT_4: ACT domain; PD 48.3 34 0.00073 19.2 3.3 28 3-30 52-79 (80)
65 COG2049 DUR1 Allophanate hydro 47.8 82 0.0018 22.3 5.6 46 12-59 24-71 (223)
66 PRK15127 multidrug efflux syst 47.2 68 0.0015 27.4 6.0 46 14-59 160-210 (1049)
67 PF14437 MafB19-deam: MafB19-l 44.8 44 0.00095 22.2 3.7 30 7-37 109-139 (146)
68 PF01514 YscJ_FliF: Secretory 43.3 29 0.00063 23.9 2.8 21 13-33 117-137 (206)
69 TIGR02571 ComEB ComE operon pr 42.7 96 0.0021 20.3 5.9 51 3-69 91-141 (151)
70 COG0425 SirA Predicted redox p 41.5 72 0.0016 18.5 6.2 54 7-70 13-67 (78)
71 PF14424 Toxin-deaminase: The 41.5 42 0.00091 21.6 3.2 25 3-27 102-126 (133)
72 KOG3355|consensus 40.6 21 0.00045 24.4 1.7 22 3-24 107-128 (177)
73 cd04877 ACT_TyrR N-terminal AC 40.4 55 0.0012 18.2 3.3 27 4-30 42-68 (74)
74 COG4827 Predicted transporter 39.9 19 0.00041 25.5 1.4 15 3-17 108-122 (239)
75 COG5054 ERV1 Mitochondrial sul 39.0 22 0.00048 24.2 1.6 22 3-24 116-137 (181)
76 PRK10503 multidrug efflux syst 37.7 1.1E+02 0.0024 26.1 5.9 46 14-59 169-220 (1040)
77 PRK10553 assembly protein for 37.5 92 0.002 18.6 5.9 47 10-58 16-62 (87)
78 COG1834 N-Dimethylarginine dim 35.7 41 0.00088 24.5 2.7 53 35-88 128-182 (267)
79 TIGR02544 III_secr_YscJ type I 35.5 42 0.00091 22.9 2.6 21 13-33 109-129 (193)
80 TIGR00302 phosphoribosylformyl 34.5 95 0.0021 17.9 3.9 26 37-62 4-31 (80)
81 PF14026 DUF4242: Protein of u 33.7 99 0.0021 17.9 6.7 50 15-66 23-74 (77)
82 PRK04435 hypothetical protein; 33.6 81 0.0018 20.5 3.6 28 4-31 115-143 (147)
83 PF11287 DUF3088: Protein of u 33.4 83 0.0018 19.9 3.5 43 7-58 22-64 (112)
84 PHA02119 hypothetical protein 32.7 45 0.00097 19.6 2.0 39 37-75 41-82 (87)
85 PF11080 DUF2622: Protein of u 32.4 97 0.0021 19.1 3.6 42 37-78 10-52 (96)
86 COG0277 GlcD FAD/FMN-containin 32.4 79 0.0017 23.6 3.9 53 30-85 89-141 (459)
87 COG4545 Glutaredoxin-related p 32.1 27 0.00058 20.9 1.1 14 6-19 9-22 (85)
88 TIGR00489 aEF-1_beta translati 31.7 58 0.0012 19.6 2.5 21 13-33 64-84 (88)
89 PF13193 AMP-binding_C: AMP-bi 31.6 55 0.0012 18.0 2.3 41 16-58 2-46 (73)
90 PF00873 ACR_tran: AcrB/AcrD/A 31.4 2.1E+02 0.0046 24.2 6.5 39 13-52 62-102 (1021)
91 TIGR00370 conserved hypothetic 31.4 1.5E+02 0.0033 20.4 4.9 45 11-58 20-64 (202)
92 cd04909 ACT_PDH-BS C-terminal 30.7 93 0.002 16.6 4.8 51 12-63 14-69 (69)
93 PRK06423 phosphoribosylformylg 30.6 1.1E+02 0.0023 17.4 3.8 26 37-62 4-31 (73)
94 cd04887 ACT_MalLac-Enz ACT_Mal 29.8 1E+02 0.0022 16.7 3.6 27 4-30 45-71 (74)
95 PF14814 UB2H: Bifunctional tr 29.6 63 0.0014 18.9 2.4 49 43-91 3-52 (85)
96 COG1400 SEC65 Signal recogniti 29.0 67 0.0015 19.7 2.5 19 46-64 31-49 (93)
97 KOG2836|consensus 29.0 1.7E+02 0.0038 19.5 4.5 38 28-65 9-46 (173)
98 PRK10614 multidrug efflux syst 28.2 2.1E+02 0.0045 24.5 6.0 46 14-59 160-211 (1025)
99 PRK11200 grxA glutaredoxin 1; 27.8 1.1E+02 0.0024 17.3 3.3 27 6-33 8-38 (85)
100 PF14408 Actino_peptide: Ribos 27.8 23 0.00051 19.9 0.3 31 56-87 18-48 (59)
101 PRK05974 phosphoribosylformylg 27.8 1.3E+02 0.0028 17.3 3.9 26 37-62 4-31 (80)
102 cd04882 ACT_Bt0572_2 C-termina 27.6 1E+02 0.0022 16.0 6.1 15 49-63 50-64 (65)
103 PRK02935 hypothetical protein; 27.6 15 0.00032 23.2 -0.6 20 4-24 68-87 (110)
104 KOG1352|consensus 27.4 30 0.00065 27.2 0.9 25 1-26 342-366 (618)
105 PF03927 NapD: NapD protein; 27.2 1.3E+02 0.0029 17.4 5.7 44 12-58 16-59 (79)
106 PF00356 LacI: Bacterial regul 27.1 37 0.0008 17.8 1.0 16 48-63 30-45 (46)
107 TIGR01709 typeII_sec_gspL gene 27.0 1.8E+02 0.004 21.5 5.0 57 15-72 314-373 (384)
108 PF02005 TRM: N2,N2-dimethylgu 26.7 94 0.002 23.5 3.4 32 46-77 336-367 (377)
109 COG2177 FtsX Cell division pro 26.6 2.6E+02 0.0057 20.5 6.0 23 9-31 70-92 (297)
110 COG0841 AcrB Cation/multidrug 26.3 2.7E+02 0.0059 24.1 6.3 50 13-62 157-212 (1009)
111 PRK04338 N(2),N(2)-dimethylgua 26.2 91 0.002 23.5 3.3 32 46-77 337-368 (382)
112 KOG2792|consensus 26.2 63 0.0014 23.6 2.3 51 8-59 150-201 (280)
113 COG1999 Uncharacterized protei 26.0 1.1E+02 0.0024 21.0 3.4 26 37-63 107-132 (207)
114 TIGR00308 TRM1 tRNA(guanine-26 25.4 1E+02 0.0022 23.3 3.4 31 46-76 328-358 (374)
115 PF12404 DUF3663: Peptidase ; 25.3 55 0.0012 19.4 1.5 49 28-77 17-66 (77)
116 PRK15324 type III secretion sy 25.2 76 0.0016 22.8 2.6 23 13-35 110-132 (252)
117 COG0027 PurT Formate-dependent 25.1 85 0.0018 23.9 2.8 37 47-83 136-172 (394)
118 PF02700 PurS: Phosphoribosylf 24.8 1.6E+02 0.0034 17.3 3.7 26 37-62 4-31 (80)
119 PF12960 DUF3849: Protein of u 24.7 77 0.0017 20.6 2.3 35 10-62 27-61 (133)
120 PRK10503 multidrug efflux syst 24.4 3.1E+02 0.0067 23.6 6.3 45 13-58 73-123 (1040)
121 PRK10555 aminoglycoside/multid 24.2 2.6E+02 0.0057 24.0 5.9 45 13-58 62-113 (1037)
122 PF11468 PTase_Orf2: Aromatic 24.1 2.3E+02 0.0049 21.0 4.9 60 23-82 147-211 (292)
123 PRK11670 antiporter inner memb 24.1 3.1E+02 0.0068 20.5 7.4 74 2-75 50-151 (369)
124 PRK09579 multidrug efflux prot 24.0 3.1E+02 0.0066 23.5 6.2 45 13-58 64-114 (1017)
125 COG2092 EFB1 Translation elong 23.6 79 0.0017 19.2 2.1 20 13-32 64-83 (88)
126 PF08478 POTRA_1: POTRA domain 23.6 93 0.002 16.7 2.3 21 13-33 36-56 (69)
127 PRK15127 multidrug efflux syst 23.5 2.8E+02 0.0061 23.9 5.9 46 13-59 62-114 (1049)
128 PF09902 DUF2129: Uncharacteri 23.4 1.5E+02 0.0031 17.2 3.1 25 9-33 38-62 (71)
129 TIGR02764 spore_ybaN_pdaB poly 23.1 2.1E+02 0.0045 18.7 4.3 32 34-65 4-37 (191)
130 PRK00435 ef1B elongation facto 23.1 98 0.0021 18.6 2.4 22 12-33 63-84 (88)
131 PLN02495 oxidoreductase, actin 22.7 2.7E+02 0.0058 21.2 5.2 31 36-66 183-213 (385)
132 cd01286 deoxycytidylate_deamin 22.5 1.3E+02 0.0027 19.1 3.0 24 3-31 92-115 (131)
133 cd04885 ACT_ThrD-I Tandem C-te 22.2 1.5E+02 0.0032 16.1 6.5 60 4-63 2-66 (68)
134 PF10955 DUF2757: Protein of u 22.2 66 0.0014 19.0 1.5 16 3-18 49-64 (76)
135 COG1828 PurS Phosphoribosylfor 22.1 1.9E+02 0.0041 17.3 3.5 26 37-62 5-32 (83)
136 COG0841 AcrB Cation/multidrug 22.0 3.2E+02 0.0068 23.7 5.9 47 13-60 63-115 (1009)
137 COG0217 Uncharacterized conser 22.0 1.6E+02 0.0034 21.2 3.6 43 16-64 153-195 (241)
138 PF14056 DUF4250: Domain of un 21.9 99 0.0022 17.0 2.1 18 47-64 32-49 (55)
139 PF11360 DUF3110: Protein of u 21.8 1.3E+02 0.0029 17.9 2.8 23 47-69 55-77 (86)
140 PF07530 PRE_C2HC: Associated 21.7 1.1E+02 0.0024 17.3 2.4 19 50-68 2-20 (68)
141 PRK10614 multidrug efflux syst 21.6 3.8E+02 0.0083 23.0 6.3 45 13-58 64-114 (1025)
142 PF07194 P2: P2 response regul 21.2 95 0.0021 18.0 2.1 30 3-32 52-81 (84)
143 PRK09579 multidrug efflux prot 20.7 3.3E+02 0.0072 23.4 5.8 46 14-59 159-210 (1017)
144 COG3062 NapD Uncharacterized p 20.4 2.2E+02 0.0048 17.5 4.8 47 10-59 17-63 (94)
145 PF07862 Nif11: Nitrogen fixat 20.3 1.1E+02 0.0023 15.8 2.0 18 47-64 27-44 (49)
146 CHL00193 ycf35 Ycf35; Provisio 20.3 1.4E+02 0.0031 19.1 2.9 31 47-77 12-42 (128)
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=99.62 E-value=4.7e-15 Score=83.94 Aligned_cols=60 Identities=27% Similarity=0.423 Sum_probs=57.0
Q ss_pred cee-cCCChhhHHHHHHhhhcCCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHhCCCc
Q psy13022 3 YEV-FLPLLDKSSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFD 62 (93)
Q Consensus 3 ~~v-~m~c~~C~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~Gy~ 62 (93)
|.| .|.|.+|+.+|+++|.+++||.++.+|+.++++.|.|++...++++|.++|+++||+
T Consensus 2 ~~v~~m~C~~C~~~v~~~l~~~~GV~~v~vd~~~~~v~v~~~~~~~~~~~i~~~i~~~Gy~ 62 (62)
T PF00403_consen 2 FKVPGMTCEGCAKKVEKALSKLPGVKSVKVDLETKTVTVTYDPDKTSIEKIIEAIEKAGYE 62 (62)
T ss_dssp EEEESTTSHHHHHHHHHHHHTSTTEEEEEEETTTTEEEEEESTTTSCHHHHHHHHHHTTSE
T ss_pred EEECCcccHHHHHHHHHHHhcCCCCcEEEEECCCCEEEEEEecCCCCHHHHHHHHHHhCcC
Confidence 567 799999999999999999999999999999999999998878899999999999995
No 2
>COG2608 CopZ Copper chaperone [Inorganic ion transport and metabolism]
Probab=99.49 E-value=2.8e-13 Score=79.30 Aligned_cols=61 Identities=21% Similarity=0.270 Sum_probs=57.6
Q ss_pred ecCCChhhHHHHHHhhhcCCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHhCCCceee
Q psy13022 5 VFLPLLDKSSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFDTKV 65 (93)
Q Consensus 5 v~m~c~~C~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~Gy~~~~ 65 (93)
-.|+|.+|+..|+++|.+++||.++++++..+.+.+.|++...+.++|.++|+++||.+..
T Consensus 9 ~~MtC~~C~~~V~~al~~v~gv~~v~v~l~~~~~~V~~d~~~~~~~~i~~ai~~aGy~~~~ 69 (71)
T COG2608 9 EGMTCGHCVKTVEKALEEVDGVASVDVDLEKGTATVTFDSNKVDIEAIIEAIEDAGYKVEE 69 (71)
T ss_pred CCcCcHHHHHHHHHHHhcCCCeeEEEEEcccCeEEEEEcCCcCCHHHHHHHHHHcCCCeee
Confidence 3699999999999999999999999999999999999998779999999999999999764
No 3
>KOG4656|consensus
Probab=99.02 E-value=1.4e-09 Score=75.19 Aligned_cols=66 Identities=17% Similarity=0.293 Sum_probs=60.3
Q ss_pred CceecCCChhhHHHHHHhhhcCCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHhCCCceeeecCCC
Q psy13022 2 GYEVFLPLLDKSSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFDTKVTQVDG 70 (93)
Q Consensus 2 ~~~v~m~c~~C~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~Gy~~~~~~~~~ 70 (93)
-|+|+|+|.+|++.|.+.|..++||.++++++..+.+.|. ....+.+|...|+..|-++.+.....
T Consensus 10 efaV~M~cescvnavk~~L~~V~Gi~~vevdle~q~v~v~---ts~p~s~i~~~le~tGr~Avl~G~G~ 75 (247)
T KOG4656|consen 10 EFAVQMTCESCVNAVKACLKGVPGINSVEVDLEQQIVSVE---TSVPPSEIQNTLENTGRDAVLRGAGK 75 (247)
T ss_pred EEEEechhHHHHHHHHHHhccCCCcceEEEEhhhcEEEEE---ccCChHHHHHHHHhhChheEEecCCc
Confidence 3999999999999999999999999999999999999998 55788999999999999988876543
No 4
>PLN02957 copper, zinc superoxide dismutase
Probab=98.58 E-value=6.3e-07 Score=63.09 Aligned_cols=66 Identities=12% Similarity=0.171 Sum_probs=58.4
Q ss_pred ceecCCChhhHHHHHHhhhcCCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHhCCCceeeecCCCC
Q psy13022 3 YEVFLPLLDKSSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFDTKVTQVDGK 71 (93)
Q Consensus 3 ~~v~m~c~~C~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~Gy~~~~~~~~~~ 71 (93)
|.|.|.|.+|+..+++.|.+++||..+.+++..+.+.|.++ ...+.|.+.|++.||.+.+......
T Consensus 10 ~~VgMsC~~Ca~~Iek~L~~~~GV~~v~vn~~~~~v~V~~~---~~~~~I~~aIe~~Gy~a~~~~~~~~ 75 (238)
T PLN02957 10 FMVDMKCEGCVAAVKNKLETLEGVKAVEVDLSNQVVRVLGS---SPVKAMTAALEQTGRKARLIGQGDP 75 (238)
T ss_pred EEECccCHHHHHHHHHHHhcCCCeEEEEEEcCCCEEEEEec---CCHHHHHHHHHHcCCcEEEecCCCc
Confidence 66789999999999999999999999999999999999883 4788899999999999877655443
No 5
>KOG1603|consensus
Probab=98.54 E-value=6.3e-07 Score=52.43 Aligned_cols=59 Identities=15% Similarity=0.263 Sum_probs=52.3
Q ss_pred ceecCCChhhHHHHHHhhhcCCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHhCC-Ccee
Q psy13022 3 YEVFLPLLDKSSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMG-FDTK 64 (93)
Q Consensus 3 ~~v~m~c~~C~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~G-y~~~ 64 (93)
+-|.|+|.+|...|.+.|+.+.||.++.++...+.+++.-+ .++..+++.+++.| .+..
T Consensus 9 ~kv~~~C~gc~~kV~~~l~~~~GV~~v~id~~~~kvtV~g~---~~p~~vl~~l~k~~~k~~~ 68 (73)
T KOG1603|consen 9 LKVNMHCEGCARKVKRVLQKLKGVESVDIDIKKQKVTVKGN---VDPVKLLKKLKKTGGKRAE 68 (73)
T ss_pred EEECcccccHHHHHHHHhhccCCeEEEEecCCCCEEEEEEe---cCHHHHHHHHHhcCCCceE
Confidence 45799999999999999999999999999999999999843 78999999999877 5443
No 6
>COG2217 ZntA Cation transport ATPase [Inorganic ion transport and metabolism]
Probab=98.53 E-value=2.6e-07 Score=73.66 Aligned_cols=59 Identities=22% Similarity=0.430 Sum_probs=54.6
Q ss_pred cCCChhhHHHHHHhhhcCCCceEEEEecCCcEEEEEECCCCCC-HHHHHHHHHhCCCceee
Q psy13022 6 FLPLLDKSSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVS-PKELSEAIYDMGFDTKV 65 (93)
Q Consensus 6 ~m~c~~C~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~-~~~I~~~I~~~Gy~~~~ 65 (93)
-|+|..|+++|| +|++++||.++++|+.++++.+.|++...+ .+++...++..||....
T Consensus 10 Gm~Ca~C~~~ie-~l~~~~gV~~~~vn~~t~~~~v~~~~~~~~~~~~~~~~v~~~gy~~~~ 69 (713)
T COG2217 10 GMTCAACASRIE-ALNKLPGVEEARVNLATERATVVYDPEEVDLPADIVAAVEKAGYSARL 69 (713)
T ss_pred CcCcHHHHHHHH-HHhcCCCeeEEEeecccceEEEEecccccccHHHHHHHHHhcCccccc
Confidence 499999999999 999999999999999999999999976566 79999999999998764
No 7
>KOG0207|consensus
Probab=98.43 E-value=5.3e-07 Score=72.91 Aligned_cols=68 Identities=32% Similarity=0.454 Sum_probs=61.4
Q ss_pred cCCChhhHHHHHHhhhcCCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHhCCCceeeecCCCCCcc
Q psy13022 6 FLPLLDKSSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFDTKVTQVDGKPYV 74 (93)
Q Consensus 6 ~m~c~~C~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~Gy~~~~~~~~~~~~~ 74 (93)
-|+|..|++.+++++...+|+.++.|++.++.+.|.|+ ...+++.|.++|+++||++..........+
T Consensus 2 gmtc~ac~~si~~~~~~~~g~~~i~vsl~~~~~~v~~~-~~~~~~~i~~~ied~gf~~~~~~~~~~~~~ 69 (951)
T KOG0207|consen 2 GMTCSACSNSIEKAISRKPGVQKIEVSLAQKRANVSYD-NIVSPESIKETIEDMGFEASLLSDSEITAS 69 (951)
T ss_pred CccHHHHhhhHHHHHhcCCCceeEEEEeccccceEEEe-eccCHHHHHHHhhcccceeeecccCccccc
Confidence 49999999999999999999999999999999999999 779999999999999999987665444333
No 8
>KOG0207|consensus
Probab=98.27 E-value=2.4e-06 Score=69.28 Aligned_cols=67 Identities=22% Similarity=0.380 Sum_probs=62.1
Q ss_pred cCCChhhHHHHHHhhhcCCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHhCCCceeeecCCCCC
Q psy13022 6 FLPLLDKSSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFDTKVTQVDGKP 72 (93)
Q Consensus 6 ~m~c~~C~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~Gy~~~~~~~~~~~ 72 (93)
-|+|.+|+..+++.|++.+|+.++.+.+..+.+.+.|||..++++.+.+.+++.||.+.........
T Consensus 77 GmtC~scv~~i~~~l~~~~gv~~~~val~~~~~~v~~dp~v~s~~~~~e~ie~~gf~a~~i~~~~~~ 143 (951)
T KOG0207|consen 77 GMTCASCVATIERNLRKIEGVESAVVALSASKAEVIYDPAVTSPDSIAESIEDLGFSAELIESVNGN 143 (951)
T ss_pred CceeHHHHHHHHHHhhccCCcceEEEEeeccceeEEECCcccCchhHHHHHHhcCccceehhcccCC
Confidence 4999999999999999999999999999999999999999999999999999999999877654433
No 9
>TIGR00003 copper ion binding protein. This model describes an apparently copper-specific subfamily of the metal-binding domain HMA (Pfam family pfam00403). Closely related sequences outside this model include mercury resistance proteins and repeated domains of eukaryotic eukaryotic copper transport proteins. Members of this family are strictly prokaryotic. The model identifies both small proteins consisting of just this domain and N-terminal regions of cation (probably copper) transporting ATPases.
Probab=98.23 E-value=1.6e-05 Score=41.87 Aligned_cols=58 Identities=17% Similarity=0.347 Sum_probs=50.7
Q ss_pred cCCChhhHHHHHHhhhcCCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHhCCCce
Q psy13022 6 FLPLLDKSSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFDT 63 (93)
Q Consensus 6 ~m~c~~C~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~Gy~~ 63 (93)
.|.|..|...+++.+...+++....+++....+.+.|++.......+...+...||.+
T Consensus 10 ~~~~~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~ 67 (68)
T TIGR00003 10 SMTCQHCVDKIEKFVGELEGVSKVQVKLEKASVKVEFDAPQATEICIAEAILDAGYEV 67 (68)
T ss_pred CeEcHHHHHHHHHHHhcCCCEEEEEEEcCCCEEEEEeCCCCCCHHHHHHHHHHcCCCc
Confidence 3679999999999999999999999999999999999866567788888888888864
No 10
>PRK10671 copA copper exporting ATPase; Provisional
Probab=98.10 E-value=8.6e-06 Score=65.82 Aligned_cols=56 Identities=27% Similarity=0.283 Sum_probs=48.4
Q ss_pred cCCChhhHHHHHHhhhcCCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHhCCCceeee
Q psy13022 6 FLPLLDKSSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFDTKVT 66 (93)
Q Consensus 6 ~m~c~~C~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~Gy~~~~~ 66 (93)
.|+|.+|+.+|+++|++++||..+.+++. +..+.. ..+.+.+.++++++||++...
T Consensus 11 gmtC~~C~~~i~~al~~~~gv~~v~v~~~--~~~v~~---~~~~~~i~~~i~~~Gy~~~~~ 66 (834)
T PRK10671 11 GLSCGHCVKRVKESLEQRPDVEQADVSIT--EAHVTG---TASAEALIETIKQAGYDASVS 66 (834)
T ss_pred CcccHHHHHHHHHHHhcCCCcceEEEeee--EEEEEe---cCCHHHHHHHHHhcCCccccc
Confidence 49999999999999999999999999994 445543 258899999999999998764
No 11
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=97.49 E-value=0.00035 Score=56.20 Aligned_cols=59 Identities=14% Similarity=0.244 Sum_probs=51.7
Q ss_pred cCCChhhHHHHHHhhhcCCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHhCCCceeee
Q psy13022 6 FLPLLDKSSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFDTKVT 66 (93)
Q Consensus 6 ~m~c~~C~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~Gy~~~~~ 66 (93)
.|.|++|...+++.+.+++||..+.+++.+++..+.|++. .. +.+.+.+++.||++...
T Consensus 61 Gm~C~sCa~~Ie~aL~~~~GV~~v~Vn~at~k~~V~~d~~-~~-~~I~~aI~~~Gy~a~~~ 119 (741)
T PRK11033 61 GMDCPSCARKVENAVRQLAGVNQVQVLFATEKLVVDADND-IR-AQVESAVQKAGFSLRDE 119 (741)
T ss_pred CCCcHHHHHHHHHHHhcCCCeeeEEEEcCCCeEEEEeccc-ch-HHHHHHHHhcccccccc
Confidence 4899999999999999999999999999999999999865 33 77888899999987543
No 12
>PRK10671 copA copper exporting ATPase; Provisional
Probab=97.00 E-value=0.003 Score=51.32 Aligned_cols=58 Identities=21% Similarity=0.328 Sum_probs=50.4
Q ss_pred cCCChhhHHHHHHhhhcCCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHhCCCceeee
Q psy13022 6 FLPLLDKSSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFDTKVT 66 (93)
Q Consensus 6 ~m~c~~C~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~Gy~~~~~ 66 (93)
.|.|..|+..+++.+.+++||..+.+++.+++..+.. ..+.+.+.+.+++.||.+.+.
T Consensus 107 Gm~Ca~Ca~~Ie~~L~~~~GV~~a~vnl~t~~~~V~~---~~s~~~I~~~I~~~Gy~a~~~ 164 (834)
T PRK10671 107 GMSCASCVSRVQNALQSVPGVTQARVNLAERTALVMG---SASPQDLVQAVEKAGYGAEAI 164 (834)
T ss_pred CcCcHHHHHHHHHHHhcCCCceeeeeecCCCeEEEEc---cCCHHHHHHHHHhcCCCcccc
Confidence 5899999999999999999999999999999988863 256788888999999987543
No 13
>PRK14054 methionine sulfoxide reductase A; Provisional
Probab=96.57 E-value=0.0059 Score=41.36 Aligned_cols=57 Identities=25% Similarity=0.244 Sum_probs=47.1
Q ss_pred CCceecCCChhhHHHHHHhhhcCCCceEEEEecCCcE-------------------EEEEECCCCCCHHHHHHHHH
Q psy13022 1 MGYEVFLPLLDKSSSKSSMIGARTGVDSIKVSLADKE-------------------AVITYNPTLVSPKELSEAIY 57 (93)
Q Consensus 1 ~~~~v~m~c~~C~~~Iek~L~~l~GV~~v~v~l~~~~-------------------v~V~~d~~~~~~~~I~~~I~ 57 (93)
|+...-.--.+|-+.+|..+.+++||.++.+-+..+. +.|.|||..++.++|++..=
T Consensus 1 ~~~~~a~fagGCFWg~E~~f~~~~GV~~t~vGYagG~~~~PtY~~Vcsg~tgh~E~V~V~yDp~~isy~~Ll~~f~ 76 (172)
T PRK14054 1 MMMETAVLAGGCFWGMEAPFDRVKGVISTRVGYTGGHVENPTYEQVCSGTTGHAEAVEITYDPAVISYRELLELFF 76 (172)
T ss_pred CCceEEEEEcCChhhhHHHHccCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCCcCCHHHHHHHHH
Confidence 3444444456899999999999999999999888875 78999999999999988653
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=95.95 E-value=0.13 Score=29.16 Aligned_cols=58 Identities=22% Similarity=0.349 Sum_probs=45.6
Q ss_pred CCChhhHHHHHHhhhcCCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHhCCCcee
Q psy13022 7 LPLLDKSSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFDTK 64 (93)
Q Consensus 7 m~c~~C~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~Gy~~~ 64 (93)
+.|..|...++..+...+++....++.......+.++........+...+...||...
T Consensus 32 ~~c~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~ 89 (92)
T TIGR02052 32 MTCVACPITVETALQKVDGVSKAEVTFKTKLAVVTFDDEKTNVKALTEATTDAGYPSS 89 (92)
T ss_pred eEcHHHHHHHHHHHhcCCCEEEEEEEecCCEEEEEECCCCCCHHHHHHHHHhcCCCeE
Confidence 4589999999999999999988999998888777765443466666666778888753
No 15
>PRK05528 methionine sulfoxide reductase A; Provisional
Probab=95.76 E-value=0.033 Score=37.17 Aligned_cols=48 Identities=15% Similarity=0.149 Sum_probs=41.5
Q ss_pred hhhHHHHHHhhhcCCCceEEEEecCCc--------------EEEEEECCCCCCHHHHHHHHH
Q psy13022 10 LDKSSSKSSMIGARTGVDSIKVSLADK--------------EAVITYNPTLVSPKELSEAIY 57 (93)
Q Consensus 10 ~~C~~~Iek~L~~l~GV~~v~v~l~~~--------------~v~V~~d~~~~~~~~I~~~I~ 57 (93)
.+|-+.+|..+.+++||.++++-+..+ .+.|.|||..++.++|++..=
T Consensus 8 gGCFWg~E~~f~~l~GV~~t~vGYagG~~~~p~~~~tgH~E~V~V~yDp~~isy~~LL~~f~ 69 (156)
T PRK05528 8 GGCLWGVQAFFKTLPGVIHTEAGRANGRTSTLDGPYDGYAECVKTHFDPRMVSITDLMGYLF 69 (156)
T ss_pred cCCchhhHHHHhcCCCEEEEEEEcCCCCCCCCCCCCCCcEEEEEEEECCCcCCHHHHHHHHH
Confidence 579999999999999999999887764 277899999999999988653
No 16
>PRK00058 methionine sulfoxide reductase A; Provisional
Probab=95.48 E-value=0.035 Score=38.83 Aligned_cols=47 Identities=19% Similarity=0.244 Sum_probs=41.6
Q ss_pred hhhHHHHHHhhhcCCCceEEEEecCCc-------------------EEEEEECCCCCCHHHHHHHH
Q psy13022 10 LDKSSSKSSMIGARTGVDSIKVSLADK-------------------EAVITYNPTLVSPKELSEAI 56 (93)
Q Consensus 10 ~~C~~~Iek~L~~l~GV~~v~v~l~~~-------------------~v~V~~d~~~~~~~~I~~~I 56 (93)
.+|-+.+|..+.+++||.++.+-+..+ .+.|.|||..++.++|++..
T Consensus 52 gGCFWg~E~~F~~l~GV~~t~vGYagG~~~~PtY~~VcsG~tgH~EaV~V~YDp~~ISy~~LL~~F 117 (213)
T PRK00058 52 MGCFWGAERLFWQLPGVYSTAVGYAGGYTPNPTYREVCSGRTGHAEVVRVVYDPAVISYEQLLQVF 117 (213)
T ss_pred ccCcchhHHHHhcCCCEEEEEeeecCCCCCCCChhhcccCCCCCeEEEEEEECCccCCHHHHHHHH
Confidence 479999999999999999999998844 37899999999999998865
No 17
>PRK13014 methionine sulfoxide reductase A; Provisional
Probab=95.40 E-value=0.03 Score=38.42 Aligned_cols=49 Identities=20% Similarity=0.211 Sum_probs=42.9
Q ss_pred hhhHHHHHHhhhcCCCceEEEEecCCcE-------------------EEEEECCCCCCHHHHHHHHHh
Q psy13022 10 LDKSSSKSSMIGARTGVDSIKVSLADKE-------------------AVITYNPTLVSPKELSEAIYD 58 (93)
Q Consensus 10 ~~C~~~Iek~L~~l~GV~~v~v~l~~~~-------------------v~V~~d~~~~~~~~I~~~I~~ 58 (93)
.+|-+.+|..+.+++||.++++-+..+. +.|.|||..++.++|++..-+
T Consensus 15 gGCFWg~E~~f~~l~GV~~t~vGYagG~~~nPtY~~Vcsg~tgH~E~V~V~yDp~~iSy~~LL~~Ff~ 82 (186)
T PRK13014 15 GGCFWGVEGVFQHVPGVVSVVSGYSGGHVDNPTYEQVCTGTTGHAEAVQITYDPKQVSYENLLQIFFS 82 (186)
T ss_pred cCCceeeHHHHccCCCEEEEEeeecCCCCCCCChhhhcCCCCCceEEEEEEECCCcCCHHHHHHHHHH
Confidence 5789999999999999999999888774 789999999999999886533
No 18
>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=95.08 E-value=0.097 Score=34.82 Aligned_cols=49 Identities=22% Similarity=0.282 Sum_probs=41.6
Q ss_pred hhhHHHHHHhhhcCCCceEEEEecCCc-------------------EEEEEECCCCCCHHHHHHHHHh
Q psy13022 10 LDKSSSKSSMIGARTGVDSIKVSLADK-------------------EAVITYNPTLVSPKELSEAIYD 58 (93)
Q Consensus 10 ~~C~~~Iek~L~~l~GV~~v~v~l~~~-------------------~v~V~~d~~~~~~~~I~~~I~~ 58 (93)
.+|-+.+|..+.+++||.++.+-+..+ .+.|.|||..++.++|++..-+
T Consensus 7 ~GCFW~~e~~f~~~~GV~~t~vGYagG~~~~PtY~~v~~g~tgh~E~V~V~yD~~~is~~~Ll~~f~~ 74 (155)
T PF01625_consen 7 GGCFWGVEAAFRRLPGVISTRVGYAGGTTPNPTYRQVCSGRTGHAEAVRVTYDPSVISYEELLDVFFR 74 (155)
T ss_dssp ESSHHHHHHHHHTSTTEEEEEEEEESSSSSS--HHHHHTTTTT-EEEEEEEEETTTS-HHHHHHHHHH
T ss_pred cCCCeEhHHHHhhCCCEEEEEecccCCCCCCCcceeeecCCCCCeEEEEEEECCCcccHHHHHHHHHH
Confidence 479999999999999999999988776 4678999999999999887643
No 19
>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=94.09 E-value=0.15 Score=33.77 Aligned_cols=48 Identities=21% Similarity=0.220 Sum_probs=40.6
Q ss_pred hhhHHHHHHhhhcCCCceEEEEecCCc-------------------EEEEEECCCCCCHHHHHHHHH
Q psy13022 10 LDKSSSKSSMIGARTGVDSIKVSLADK-------------------EAVITYNPTLVSPKELSEAIY 57 (93)
Q Consensus 10 ~~C~~~Iek~L~~l~GV~~v~v~l~~~-------------------~v~V~~d~~~~~~~~I~~~I~ 57 (93)
.+|-+.+|..+.+++||.++.+-+..+ .+.|.|||..++.++|++..-
T Consensus 7 gGCFWg~E~~f~~~~GV~~t~~GYagG~~~~PtY~~Vc~g~tgh~E~V~V~yDp~~is~~~Ll~~f~ 73 (149)
T TIGR00401 7 GGCFWGVEKYFWLIPGVYSTAVGYTGGYTPNPTYEEVCSGDTGHAEAVQVTYDPKVISYEELLDVFW 73 (149)
T ss_pred cCCchhhHHHHhcCCCEEEEEEeeCCCCCCCCChhhcccCCCCceEEEEEEECCCcCcHHHHHHHHH
Confidence 478999999999999999999876654 367899999999999988653
No 20
>COG0225 MsrA Peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=93.99 E-value=0.15 Score=34.66 Aligned_cols=50 Identities=22% Similarity=0.234 Sum_probs=42.9
Q ss_pred ChhhHHHHHHhhhcCCCceEEEEecCCcE-------------------EEEEECCCCCCHHHHHHHHHh
Q psy13022 9 LLDKSSSKSSMIGARTGVDSIKVSLADKE-------------------AVITYNPTLVSPKELSEAIYD 58 (93)
Q Consensus 9 c~~C~~~Iek~L~~l~GV~~v~v~l~~~~-------------------v~V~~d~~~~~~~~I~~~I~~ 58 (93)
-.+|-+-+|+.+.+++||.++.+-+..+. |.|.|||..++.++|++..=+
T Consensus 12 agGCFWg~E~~f~~i~GV~~t~~GYagG~~~nptY~~Vcsg~TgHaE~V~V~yDp~~isy~~LL~~ff~ 80 (174)
T COG0225 12 AGGCFWGVEAYFEQIPGVLSTVSGYAGGHTPNPTYEEVCSGTTGHAEAVEVTYDPKVISYEELLEVFFE 80 (174)
T ss_pred eccCccchHHHHhhCCCeEEEeeeEcCCCCCCCChhhccCCCCCceEEEEEEeCCccccHHHHHHHHhe
Confidence 35799999999999999999998777663 678999999999999987644
No 21
>PRK13748 putative mercuric reductase; Provisional
Probab=93.92 E-value=0.49 Score=36.59 Aligned_cols=63 Identities=17% Similarity=0.248 Sum_probs=51.4
Q ss_pred cCCChhhHHHHHHhhhcCCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHhCCCceeeecCC
Q psy13022 6 FLPLLDKSSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFDTKVTQVD 69 (93)
Q Consensus 6 ~m~c~~C~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~Gy~~~~~~~~ 69 (93)
.|.|.+|..+++..+...+++....+++..+...+.+++. .....+...++..||.......+
T Consensus 8 g~~C~~c~~~ie~~l~~~~gv~~a~~~~~~~~~~v~~~~~-~~~~~i~~~i~~~g~~~~~~~~~ 70 (561)
T PRK13748 8 GMTCDSCAAHVKDALEKVPGVQSADVSYPKGSAQLAIEVG-TSPDALTAAVAGLGYRATLADAP 70 (561)
T ss_pred CeecHHHHHHHHHHHhcCCCeeEEEEEcCCCEEEEEECCC-CCHHHHHHHHHHcCCeeeccCcc
Confidence 4779999999999999999999999999999988887643 46667777788899987665553
No 22
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=93.89 E-value=0.14 Score=37.26 Aligned_cols=47 Identities=13% Similarity=0.124 Sum_probs=41.3
Q ss_pred hhhHHHHHHhhhcCCCceEEEEecCCcE-------------------EEEEECCCCCCHHHHHHHH
Q psy13022 10 LDKSSSKSSMIGARTGVDSIKVSLADKE-------------------AVITYNPTLVSPKELSEAI 56 (93)
Q Consensus 10 ~~C~~~Iek~L~~l~GV~~v~v~l~~~~-------------------v~V~~d~~~~~~~~I~~~I 56 (93)
.+|-+.+|..+.+++||.++++-+..+. |.|.|||..++.++|++..
T Consensus 134 gGCFWg~E~~F~~~~GV~~t~vGYagG~~~nPtY~~VcsG~tgH~EaV~V~yDp~~isy~~LL~~F 199 (283)
T PRK05550 134 GGCFWGVEYYFKKLPGVLSVESGYTGGDTKNPTYEQVCSGTTGHAEAVRVEFDPAKISYETLLKVF 199 (283)
T ss_pred cCCchhhhhhHhhCcCEEEEEEeeCCCCCCCCChhhcccCCCCCeEEEEEEECCccCCHHHHHHHH
Confidence 5799999999999999999998877653 7799999999999998865
No 23
>COG1888 Uncharacterized protein conserved in archaea [Function unknown]
Probab=93.31 E-value=0.51 Score=28.95 Aligned_cols=52 Identities=17% Similarity=0.246 Sum_probs=40.8
Q ss_pred HHHHhhhcCCCceEEEE-----ecCCcEEEEEECCCCCCHHHHHHHHHhCCCceeee
Q psy13022 15 SKSSMIGARTGVDSIKV-----SLADKEAVITYNPTLVSPKELSEAIYDMGFDTKVT 66 (93)
Q Consensus 15 ~Iek~L~~l~GV~~v~v-----~l~~~~v~V~~d~~~~~~~~I~~~I~~~Gy~~~~~ 66 (93)
.+.+.|.+++||..+++ +..+..+.++.....++-++|.+.|++.|..++..
T Consensus 23 e~A~~lskl~gVegVNItv~eiD~et~~~~itIeG~~ldydei~~~iE~~Gg~IHSi 79 (97)
T COG1888 23 ELALELSKLEGVEGVNITVTEIDVETENLKITIEGTNLDYDEIEEVIEELGGAIHSI 79 (97)
T ss_pred HHHHHHhhcCCcceEEEEEEEeeehhcceEEEEEcCCCCHHHHHHHHHHcCCeeeeh
Confidence 45677899999888774 45566677777767789999999999999877654
No 24
>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=93.29 E-value=0.33 Score=27.38 Aligned_cols=56 Identities=5% Similarity=0.016 Sum_probs=41.6
Q ss_pred cCCChhhHHHHHHhhhcCCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHhCCCceeeecCCCC
Q psy13022 6 FLPLLDKSSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFDTKVTQVDGK 71 (93)
Q Consensus 6 ~m~c~~C~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~Gy~~~~~~~~~~ 71 (93)
.+.||.....+.++|.+++. .+.+.|..+.. .....|...+++.||..........
T Consensus 7 g~~CP~Pll~~~~~l~~l~~---------G~~l~v~~d~~-~~~~di~~~~~~~g~~~~~~~~~~~ 62 (70)
T PF01206_consen 7 GLSCPMPLLKAKKALKELPP---------GEVLEVLVDDP-AAVEDIPRWCEENGYEVVEVEEEGG 62 (70)
T ss_dssp S-STTHHHHHHHHHHHTSGT---------T-EEEEEESST-THHHHHHHHHHHHTEEEEEEEESSS
T ss_pred CCCCCHHHHHHHHHHHhcCC---------CCEEEEEECCc-cHHHHHHHHHHHCCCEEEEEEEeCC
Confidence 36899999999999998753 34556666644 6789999999999999766654443
No 25
>PF02680 DUF211: Uncharacterized ArCR, COG1888; InterPro: IPR003831 This entry describes proteins of unknown function.; PDB: 3BPD_I 2RAQ_F 2X3D_E.
Probab=92.14 E-value=0.65 Score=28.63 Aligned_cols=52 Identities=19% Similarity=0.263 Sum_probs=39.3
Q ss_pred HHHHhhhcCCCceEEEE-----ecCCcEEEEEECCCCCCHHHHHHHHHhCCCceeee
Q psy13022 15 SKSSMIGARTGVDSIKV-----SLADKEAVITYNPTLVSPKELSEAIYDMGFDTKVT 66 (93)
Q Consensus 15 ~Iek~L~~l~GV~~v~v-----~l~~~~v~V~~d~~~~~~~~I~~~I~~~Gy~~~~~ 66 (93)
.+.+.|.+++||..+++ +..+..+.|......++.+.|.++|++.|-.++.+
T Consensus 21 e~A~~l~~~~gV~gVnitv~EvD~ete~lkitiEG~~id~d~i~~~Ie~~Gg~IHSI 77 (95)
T PF02680_consen 21 ELAKALSELEGVDGVNITVVEVDVETENLKITIEGDDIDFDEIKEAIEELGGVIHSI 77 (95)
T ss_dssp HHHHHHHTSTTEEEEEEEEEEE-SSEEEEEEEEEESSE-HHHHHHHHHHTT-EEEEE
T ss_pred HHHHHHHhCCCcceEEEEEEEeeccccEEEEEEEeCCCCHHHHHHHHHHcCCeEEee
Confidence 46788999999988874 45666777777766789999999999999876543
No 26
>cd00371 HMA Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions.
Probab=90.88 E-value=0.92 Score=20.96 Aligned_cols=56 Identities=34% Similarity=0.501 Sum_probs=39.2
Q ss_pred cCCChhhHHHHHHhhhcCCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHhCCCc
Q psy13022 6 FLPLLDKSSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFD 62 (93)
Q Consensus 6 ~m~c~~C~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~Gy~ 62 (93)
.+.|..|...++..+...+++.....++......+.++.. .....+...+...|+.
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~ 61 (63)
T cd00371 6 GMTCAGCVSKIEKALEKLPGVESVEVDLETGKATVEYDPE-VSPEELLEAIEDAGYK 61 (63)
T ss_pred CeEcHHHHHHHHHHHhcCCCEeEEEEEccCCEEEEEECCC-CCHHHHHHHHHHcCCC
Confidence 4668999999998888888988888888877777776543 3444444444555543
No 27
>PRK11018 hypothetical protein; Provisional
Probab=90.00 E-value=2.5 Score=24.65 Aligned_cols=53 Identities=8% Similarity=-0.073 Sum_probs=39.7
Q ss_pred cCCChhhHHHHHHhhhcCCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHhCCCceeeecC
Q psy13022 6 FLPLLDKSSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFDTKVTQV 68 (93)
Q Consensus 6 ~m~c~~C~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~Gy~~~~~~~ 68 (93)
-..||.-.-...++|++++. .+.+.|..|. ..+...|...+++.||++.....
T Consensus 15 G~~CP~Pvl~~kk~l~~l~~---------G~~L~V~~d~-~~a~~di~~~~~~~G~~v~~~~~ 67 (78)
T PRK11018 15 GEPCPYPAVATLEALPQLKK---------GEILEVVSDC-PQSINNIPLDARNHGYTVLDIQQ 67 (78)
T ss_pred CCcCCHHHHHHHHHHHhCCC---------CCEEEEEeCC-ccHHHHHHHHHHHcCCEEEEEEe
Confidence 35788888899999988752 3345566564 36888999999999999865544
No 28
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=89.98 E-value=0.72 Score=36.26 Aligned_cols=48 Identities=13% Similarity=0.072 Sum_probs=41.8
Q ss_pred hhhHHHHHHhhhcCCCceEEEEecCCc------------------EEEEEECCCCCCHHHHHHHHH
Q psy13022 10 LDKSSSKSSMIGARTGVDSIKVSLADK------------------EAVITYNPTLVSPKELSEAIY 57 (93)
Q Consensus 10 ~~C~~~Iek~L~~l~GV~~v~v~l~~~------------------~v~V~~d~~~~~~~~I~~~I~ 57 (93)
.+|-+.+|..+.+++||.++++-+..+ .+.|.|||..++.++|++..=
T Consensus 205 gGCFWg~e~~f~~~~GV~~t~~GYagG~~~~PtY~~Vc~gtgH~E~V~V~yDp~~is~~~Ll~~f~ 270 (521)
T PRK14018 205 GGCFWGLEAYFQRIDGVVDAVSGYANGNTKNPSYEDVYRHSGHAETVKVTYDADKLSLDTILQYYF 270 (521)
T ss_pred cCCchhhHHHHccCCCEEEEEEeeCCCCCCCCChhhccCCCCcEEEEEEEECCCcCcHHHHHHHHH
Confidence 579999999999999999999988766 267899999999999988653
No 29
>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=88.81 E-value=0.92 Score=27.36 Aligned_cols=55 Identities=11% Similarity=0.166 Sum_probs=32.5
Q ss_pred hhHHHHHHhhhcCCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHhCCCceee
Q psy13022 11 DKSSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFDTKV 65 (93)
Q Consensus 11 ~C~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~Gy~~~~ 65 (93)
.-+..++=.|...++|-.+-+|-=.+...|.||+...+.+.|.+.+++..+++..
T Consensus 11 eeA~~~QYeLsk~~~vyRvFiNgYar~g~VifDe~kl~~e~lL~~le~~kpEVi~ 65 (88)
T PF11491_consen 11 EEAMVKQYELSKNEAVYRVFINGYARNGFVIFDESKLSKEELLEMLEEFKPEVIE 65 (88)
T ss_dssp TTTHHHHHTTTTTTTB------TTSS--EEE--B-S-SHHHH---HHHTTT-SS-
T ss_pred HHHHHHHHHhhcccceeeeeecccccceEEEECcccCCHHHHHHHHHhcChhhee
Confidence 3455677789999999999999999999999999999999999999999887643
No 30
>cd03422 YedF YedF is a bacterial SirA-like protein of unknown function. SirA (also known as UvrY, and YhhP) belongs to a family of a two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=87.21 E-value=3.8 Score=23.19 Aligned_cols=53 Identities=6% Similarity=-0.013 Sum_probs=39.8
Q ss_pred CCChhhHHHHHHhhhcCCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHhCCCceeeecCC
Q psy13022 7 LPLLDKSSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFDTKVTQVD 69 (93)
Q Consensus 7 m~c~~C~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~Gy~~~~~~~~ 69 (93)
..||.=.-...++|++++ ..+.+.|..|. ..+...|....++.||++......
T Consensus 7 ~~CP~Pvi~~kkal~~l~---------~G~~l~V~~d~-~~s~~ni~~~~~~~g~~v~~~~~~ 59 (69)
T cd03422 7 EPCPYPAIATLEALPSLK---------PGEILEVISDC-PQSINNIPIDARNHGYKVLAIEQS 59 (69)
T ss_pred CcCCHHHHHHHHHHHcCC---------CCCEEEEEecC-chHHHHHHHHHHHcCCEEEEEEec
Confidence 568888888999998875 23445566664 478899999999999998765443
No 31
>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=86.97 E-value=3 Score=27.60 Aligned_cols=46 Identities=13% Similarity=0.232 Sum_probs=36.1
Q ss_pred hHHHHHHhhhcCCCceEEEEecCCcEEEEEECCC--CCCHHHHHHHHH
Q psy13022 12 KSSSKSSMIGARTGVDSIKVSLADKEAVITYNPT--LVSPKELSEAIY 57 (93)
Q Consensus 12 C~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~--~~~~~~I~~~I~ 57 (93)
=+..|.+.+.+++||..+.+-.....+.|.++.. ....++|...|+
T Consensus 76 ~a~~i~~~v~~~~~V~~A~vvv~~~~a~Vav~~~~~~~~~~~i~~~V~ 123 (177)
T PF09580_consen 76 LADRIANRVKKVPGVEDATVVVTDDNAYVAVDLDFNRFNTKKIKKKVE 123 (177)
T ss_pred HHHHHHHHHhcCCCceEEEEEEECCEEEEEEEecccccchhHHHHHHH
Confidence 4678999999999999999999999999887655 345555554443
No 32
>cd03423 SirA SirA (also known as UvrY, and YhhP) belongs to a family of two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is thought to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=86.74 E-value=4 Score=23.01 Aligned_cols=53 Identities=4% Similarity=0.057 Sum_probs=39.4
Q ss_pred CCChhhHHHHHHhhhcCCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHhCCCceeeecCC
Q psy13022 7 LPLLDKSSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFDTKVTQVD 69 (93)
Q Consensus 7 m~c~~C~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~Gy~~~~~~~~ 69 (93)
..||.=.-...++|.+++ ..+.+.|..+.. .+.+.|...+++.||++......
T Consensus 7 ~~CP~P~i~~k~~l~~l~---------~G~~l~V~~dd~-~s~~di~~~~~~~g~~~~~~~~~ 59 (69)
T cd03423 7 LRCPEPVMMLHKKVRKMK---------PGDTLLVLATDP-STTRDIPKFCTFLGHELLAQETE 59 (69)
T ss_pred CcCCHHHHHHHHHHHcCC---------CCCEEEEEeCCC-chHHHHHHHHHHcCCEEEEEEEc
Confidence 568888888899998875 233456666643 68899999999999998765443
No 33
>cd00291 SirA_YedF_YeeD SirA, YedF, and YeeD. Two-layered alpha/beta sandwich domain. SirA (also known as UvrY, and YhhP) belongs to a family of bacterial two-component response regulators that controls secondary metabolism and virulence. The other member of this two-component system is a sensor kinase called BarA which phosphorylates SirA. A variety of microorganisms have similar proteins, all of which contain a common CPxP sequence motif in the N-terminal region. YhhP is suggested to be important for normal cell division and growth in rich nutrient medium. Moreover, despite a low primary sequence similarity, the YccP structure closely resembles the non-homologous C-terminal RNA-binding domain of E. coli translation initiation factor IF3. The signature CPxP motif serves to stabilize the N-terminal helix as part of the N-capping box and might be important in mRNA-binding.
Probab=86.63 E-value=3.8 Score=22.63 Aligned_cols=54 Identities=6% Similarity=0.011 Sum_probs=39.5
Q ss_pred cCCChhhHHHHHHhhhcCCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHhCCCceeeecCC
Q psy13022 6 FLPLLDKSSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFDTKVTQVD 69 (93)
Q Consensus 6 ~m~c~~C~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~Gy~~~~~~~~ 69 (93)
.+.||.=...+.++|++++ ....+.|..+.. .....|...+++.||........
T Consensus 6 g~~CP~Pl~~~~~~l~~l~---------~g~~l~v~~d~~-~~~~~i~~~~~~~g~~~~~~~~~ 59 (69)
T cd00291 6 GLPCPLPVLKTKKALEKLK---------SGEVLEVLLDDP-GAVEDIPAWAKETGHEVLEVEEE 59 (69)
T ss_pred CCcCCHHHHHHHHHHhcCC---------CCCEEEEEecCC-cHHHHHHHHHHHcCCEEEEEEEe
Confidence 3678888888888888765 334456666643 57899999999999997654443
No 34
>cd03420 SirA_RHOD_Pry_redox SirA_RHOD_Pry_redox. SirA-like domain located within a multidomain protein of unknown function. Other domains include RHOD (rhodanese homology domain), and Pry_redox (pyridine nucleotide-disulphide oxidoreductase) as well as a C-terminal domain that corresponds to COG2210. This fold is referred to as a two-layered alpha/beta sandwich, structurally similar to that of translation initiation factor 3.
Probab=85.86 E-value=4.6 Score=22.81 Aligned_cols=53 Identities=6% Similarity=-0.087 Sum_probs=40.2
Q ss_pred CCChhhHHHHHHhhhcCCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHhCCCceeeecCC
Q psy13022 7 LPLLDKSSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFDTKVTQVD 69 (93)
Q Consensus 7 m~c~~C~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~Gy~~~~~~~~ 69 (93)
+.||.=.....++|++++ ..+.+.|..+. ..+...|....++.||+.......
T Consensus 7 ~~CP~Pvl~~kkal~~l~---------~G~~l~V~~d~-~~a~~di~~~~~~~G~~~~~~~~~ 59 (69)
T cd03420 7 LQCPGPILKLKKEIDKLQ---------DGEQLEVKASD-PGFARDAQAWCKSTGNTLISLETE 59 (69)
T ss_pred CcCCHHHHHHHHHHHcCC---------CCCEEEEEECC-ccHHHHHHHHHHHcCCEEEEEEec
Confidence 678888889999998875 23445566663 368899999999999998755443
No 35
>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=85.83 E-value=1.1 Score=25.28 Aligned_cols=29 Identities=28% Similarity=0.281 Sum_probs=20.3
Q ss_pred ceecCCChhhH------HHHHHhhhcCCCceEEEE
Q psy13022 3 YEVFLPLLDKS------SSKSSMIGARTGVDSIKV 31 (93)
Q Consensus 3 ~~v~m~c~~C~------~~Iek~L~~l~GV~~v~v 31 (93)
|.+.++.++|. ..++++|..++||.+++|
T Consensus 38 v~l~l~~~~~~~~~~l~~~i~~~l~~l~gv~~V~V 72 (72)
T PF01883_consen 38 VSLELPTPACPAAEPLREEIREALKALPGVKSVKV 72 (72)
T ss_dssp EEE--SSTTHTTHHHHHHHHHHHHHTSTT-SEEEE
T ss_pred EEEEECCCCchHHHHHHHHHHHHHHhCCCCceEeC
Confidence 45667777774 668899999999998875
No 36
>KOG1635|consensus
Probab=82.81 E-value=3.9 Score=28.06 Aligned_cols=48 Identities=19% Similarity=0.193 Sum_probs=40.9
Q ss_pred hhhHHHHHHhhhcCCCceEEEEecCCc-------------------EEEEEECCCCCCHHHHHHHHH
Q psy13022 10 LDKSSSKSSMIGARTGVDSIKVSLADK-------------------EAVITYNPTLVSPKELSEAIY 57 (93)
Q Consensus 10 ~~C~~~Iek~L~~l~GV~~v~v~l~~~-------------------~v~V~~d~~~~~~~~I~~~I~ 57 (93)
.+|-+.+|.+...++||...+|-++.+ .+.|.|||..++.++|.+..=
T Consensus 31 ~GCFWg~E~a~~~l~gV~~T~vGYagG~~~nPtYk~vc~~tT~HaEvvrV~ydpk~~sy~~Lld~Fw 97 (191)
T KOG1635|consen 31 AGCFWGVELAYQRLPGVVRTEVGYAGGITDNPTYKDVCSGTTNHAEVVRVQYDPKVISYEELLDFFW 97 (191)
T ss_pred ccchhhHHHHHhhcCCeEEEeecccCCccCCcchhhhccCCCCcceEEEEEeCcccccHHHHHHHHH
Confidence 579999999999999999999887654 467899999999999988653
No 37
>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=82.38 E-value=6.5 Score=21.81 Aligned_cols=50 Identities=14% Similarity=0.153 Sum_probs=35.7
Q ss_pred CCChhhHHHHHHhhhcCCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHhCCCceeeec
Q psy13022 7 LPLLDKSSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFDTKVTQ 67 (93)
Q Consensus 7 m~c~~C~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~Gy~~~~~~ 67 (93)
+.||.-.....++| ++. ..+.+.|..+. ..+...|...+++.||......
T Consensus 7 ~~CP~P~l~~k~al-~~~---------~g~~l~v~~d~-~~s~~~i~~~~~~~G~~~~~~~ 56 (67)
T cd03421 7 LACPQPVIKTKKAL-ELE---------AGGEIEVLVDN-EVAKENVSRFAESRGYEVSVEE 56 (67)
T ss_pred CCCCHHHHHHHHHH-hcC---------CCCEEEEEEcC-hhHHHHHHHHHHHcCCEEEEEe
Confidence 57888888889988 543 22345555553 3677899999999999985443
No 38
>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=82.21 E-value=1 Score=26.04 Aligned_cols=27 Identities=15% Similarity=0.094 Sum_probs=20.8
Q ss_pred cCCChhhHHHHHHhhhcCCCceEEEEe
Q psy13022 6 FLPLLDKSSSKSSMIGARTGVDSIKVS 32 (93)
Q Consensus 6 ~m~c~~C~~~Iek~L~~l~GV~~v~v~ 32 (93)
-|||+.|..+..+++++..=.++-++|
T Consensus 15 tLPC~~Cr~HA~~ai~kNNiMSs~DiN 41 (70)
T PF04805_consen 15 TLPCPECRIHAKEAIQKNNIMSSNDIN 41 (70)
T ss_pred cCCCHHHHHHHHHHHHhcCccccCCcc
Confidence 389999999999999877655554444
No 39
>TIGR03527 selenium_YedF selenium metabolism protein YedF. Members of this protein family are about 200 amino acids in size, and include the uncharacterized YedF protein of Escherichia coli. This family shares an N-terminal domain, modeled by pfam01206, with the sulfurtransferase TusA (also called SirA). The C-terminal domain includes a typical redox-active disulfide motif, CGXC. This protein family found only among those genomes that also carry the selenium donor protein SelD, and its connection to selenium metabolism is indicated by the method of partial phylogenetic profiling vs. SelD. Its gene typically is found next to selD. Members of this family are found even when selenocysteine and selenouridine biosynthesis pathways are, except for SelD, completely absent, as in Enterococcus faecalis. Its role in selenium metabolism is unclear, but may include either detoxification or a role in labile selenoprotein biosynthesis.
Probab=79.96 E-value=11 Score=25.94 Aligned_cols=53 Identities=8% Similarity=0.131 Sum_probs=39.7
Q ss_pred CCChhhHHHHHHhhhcCCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHhCCCceeeecCC
Q psy13022 7 LPLLDKSSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFDTKVTQVD 69 (93)
Q Consensus 7 m~c~~C~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~Gy~~~~~~~~ 69 (93)
+.||.-.....++|.+++. .+.+.|..|. ..+.+.|.+..+..||++.....+
T Consensus 6 l~CP~Pvi~tKkal~~l~~---------g~~L~VlvD~-~~a~~nV~~~~~~~G~~v~~~e~~ 58 (194)
T TIGR03527 6 LACPQPVILTKKALDELGE---------EGVLTVIVDN-EAAKENVSKFATSLGYEVEVEEKE 58 (194)
T ss_pred CCCCHHHHHHHHHHHcCCC---------CCEEEEEECC-ccHHHHHHHHHHHcCCEEEEEEec
Confidence 6899999999999998862 2344555553 368889999999999998654443
No 40
>COG4669 EscJ Type III secretory pathway, lipoprotein EscJ [Intracellular trafficking and secretion]
Probab=77.42 E-value=10 Score=27.14 Aligned_cols=39 Identities=21% Similarity=0.319 Sum_probs=27.2
Q ss_pred HHHHHHhhhcCCCceEEEEecC--------------CcEEEEEECCCCCCHHHH
Q psy13022 13 SSSKSSMIGARTGVDSIKVSLA--------------DKEAVITYNPTLVSPKEL 52 (93)
Q Consensus 13 ~~~Iek~L~~l~GV~~v~v~l~--------------~~~v~V~~d~~~~~~~~I 52 (93)
...+++.|+.++||..++|... +-++.|.|.+. .+++..
T Consensus 111 eQ~le~tLs~mDGVi~ArV~I~lp~~~~~g~~~~P~saSVfIky~~~-~nl~~~ 163 (246)
T COG4669 111 EQQLEQTLSKMDGVISARVHISLPEDDDEGKNALPSSASVFIKYSPD-VNLSIY 163 (246)
T ss_pred HHHHHHHHHhcCceEEEEEEEEcCCCCccCCCCCCceeEEEEEecCC-CChhHh
Confidence 4678999999999877766544 22466788865 555543
No 41
>PHA03005 sulfhydryl oxidase; Provisional
Probab=76.21 E-value=2 Score=26.38 Aligned_cols=27 Identities=15% Similarity=0.063 Sum_probs=20.7
Q ss_pred cCCChhhHHHHHHhhhcCCCceEEEEe
Q psy13022 6 FLPLLDKSSSKSSMIGARTGVDSIKVS 32 (93)
Q Consensus 6 ~m~c~~C~~~Iek~L~~l~GV~~v~v~ 32 (93)
-+||+.|..+..+++.+..=+++-++|
T Consensus 40 tLPC~~Cr~HA~~ai~knnimSs~diN 66 (96)
T PHA03005 40 TLPCPACRRHAKEAIEKNNIMSSNDLN 66 (96)
T ss_pred cCCCHHHHHHHHHHHhhcCccccCCcc
Confidence 489999999999999876555554444
No 42
>cd04906 ACT_ThrD-I_1 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes the first of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=74.88 E-value=14 Score=21.49 Aligned_cols=64 Identities=14% Similarity=0.180 Sum_probs=37.6
Q ss_pred ceecCCC-hhhHHHHHHhhhcCCCceEEEEec---CCcEEEEEECCC--CCCHHHHHHHHHhCCCceeeec
Q psy13022 3 YEVFLPL-LDKSSSKSSMIGARTGVDSIKVSL---ADKEAVITYNPT--LVSPKELSEAIYDMGFDTKVTQ 67 (93)
Q Consensus 3 ~~v~m~c-~~C~~~Iek~L~~l~GV~~v~v~l---~~~~v~V~~d~~--~~~~~~I~~~I~~~Gy~~~~~~ 67 (93)
|.|.++. |+--.++-+.|. -..|..+.... ....+.+..+.. ....+.+.+.+++.||......
T Consensus 4 l~v~ipD~PG~L~~ll~~l~-~anI~~~~y~~~~~~~~~v~i~ie~~~~~~~~~~i~~~L~~~G~~~~~~~ 73 (85)
T cd04906 4 LAVTIPERPGSFKKFCELIG-PRNITEFNYRYADEKDAHIFVGVSVANGAEELAELLEDLKSAGYEVVDLS 73 (85)
T ss_pred EEEecCCCCcHHHHHHHHhC-CCceeEEEEEccCCCeeEEEEEEEeCCcHHHHHHHHHHHHHCCCCeEECC
Confidence 4556655 444555556665 33455555544 233444444321 2457889999999999986543
No 43
>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=72.94 E-value=17 Score=24.27 Aligned_cols=34 Identities=18% Similarity=0.155 Sum_probs=30.1
Q ss_pred hHHHHHHhhhcCCCceEEEEecCCcEEEEEECCC
Q psy13022 12 KSSSKSSMIGARTGVDSIKVSLADKEAVITYNPT 45 (93)
Q Consensus 12 C~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~ 45 (93)
=+.+|.+.+.++++|.++.+-.....+.|-++..
T Consensus 55 ~A~~Ia~~v~~v~~V~dA~vvVtg~~A~Vgv~~~ 88 (158)
T TIGR02898 55 VADEIASEAAKVKGVKDATVVITGNYAYVGVDLT 88 (158)
T ss_pred HHHHHHHHHhcCCCCceEEEEEECCEEEEEEEcC
Confidence 4678899999999999999999999999988754
No 44
>PRK00299 sulfur transfer protein SirA; Reviewed
Probab=70.99 E-value=18 Score=21.07 Aligned_cols=52 Identities=6% Similarity=0.028 Sum_probs=38.2
Q ss_pred CCChhhHHHHHHhhhcCCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHhCCCceeeecC
Q psy13022 7 LPLLDKSSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFDTKVTQV 68 (93)
Q Consensus 7 m~c~~C~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~Gy~~~~~~~ 68 (93)
+.||.=.-.+.++|++++ ..+.+.|..+. ....+.|....+..|++......
T Consensus 17 l~CP~Pll~~kk~l~~l~---------~G~~l~V~~dd-~~~~~di~~~~~~~G~~~~~~~~ 68 (81)
T PRK00299 17 LRCPEPVMMVRKTVRNMQ---------PGETLLIIADD-PATTRDIPSFCRFMDHELLAQET 68 (81)
T ss_pred CCCCHHHHHHHHHHHcCC---------CCCEEEEEeCC-ccHHHHHHHHHHHcCCEEEEEEe
Confidence 568888888899998875 23345555553 36888999999999999865443
No 45
>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=70.67 E-value=9.9 Score=20.99 Aligned_cols=29 Identities=7% Similarity=0.147 Sum_probs=20.9
Q ss_pred ceecCCChh-hHHHHHHhhhcCCCceEEEE
Q psy13022 3 YEVFLPLLD-KSSSKSSMIGARTGVDSIKV 31 (93)
Q Consensus 3 ~~v~m~c~~-C~~~Iek~L~~l~GV~~v~v 31 (93)
|.|...... --..+-+.|++++||.++.+
T Consensus 45 ~~v~v~~~~~~l~~l~~~L~~i~~V~~v~~ 74 (76)
T cd04888 45 ISIDTSTMNGDIDELLEELREIDGVEKVEL 74 (76)
T ss_pred EEEEcCchHHHHHHHHHHHhcCCCeEEEEE
Confidence 445555555 66778888899999988764
No 46
>PF02682 AHS1: Allophanate hydrolase subunit 1; InterPro: IPR003833 Allophanate hydrolase catalyses the second reaction in an ATP-dependent, two-step degradation of urea to ammonia and C02. This follows the action of the biotin-containing urea carboxylase. Saccharomyces cerevisiae can use urea as a sole nitrogen source via this degradation pathway []. In yeast, the fusion of allophanate hydrolase to urea carboxylase is called urea amidolyase. In bacteria, the second step in the urea degradation pathway is also the ATP-dependent allophanate hydrolase. The gene encoding this enzyme is found adjacent to the urea carboxylase gene []. Allophanate hydrolase has strict substrate specificity, as analogues of allophanate are not hydrolysed by it []. This domain represents subunit 1 of allophanate hydrolase (AHS1), which is found in urea carboxylase.; PDB: 3VA7_A 3MML_H 3OEP_A 3OPF_C 3ORE_A 2ZP2_A 2KWA_A 2PHC_B.
Probab=68.26 E-value=16 Score=25.10 Aligned_cols=48 Identities=10% Similarity=0.240 Sum_probs=35.6
Q ss_pred hhhHHHHHHhhhc--CCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHhC
Q psy13022 10 LDKSSSKSSMIGA--RTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDM 59 (93)
Q Consensus 10 ~~C~~~Iek~L~~--l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~ 59 (93)
......+.+.|++ .+||.++.-. -.++.|.||+..++...+.+.|.+.
T Consensus 24 ~~~v~al~~~l~~~~~~gi~e~vp~--~~sllV~fdp~~~~~~~l~~~l~~~ 73 (202)
T PF02682_consen 24 NARVLALARALRAAPLPGIVEVVPA--YRSLLVHFDPLRIDRAALRAALEEL 73 (202)
T ss_dssp HHHHHHHHHHHHHHT-TTEEEEEEE--SSEEEEEESTTTSHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhcCCCCCeEEeecc--ccEEEEEEcCCcCCHHHHHHHHHHh
Confidence 3455677788887 7888766554 4589999999878888888888764
No 47
>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=67.89 E-value=5.9 Score=26.83 Aligned_cols=44 Identities=25% Similarity=0.294 Sum_probs=30.7
Q ss_pred ceecCCChhhHH------HHHHhhhcCCCceEEEEecCCcEEEEEECCCCCCHHHHHH
Q psy13022 3 YEVFLPLLDKSS------SKSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSE 54 (93)
Q Consensus 3 ~~v~m~c~~C~~------~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~ 54 (93)
+.+.++.+.|.. .++.+|.+++||.+++|++ .++|. .+.+.|-+
T Consensus 117 I~mtLt~p~c~~~~~L~~dV~~aL~~l~gV~~V~V~l-------~~dp~-W~~~~~s~ 166 (174)
T TIGR03406 117 IEMTLTAPGCGMGPVLVEDVEDKVLAVPNVDEVEVEL-------VFDPP-WSREMMSE 166 (174)
T ss_pred EEEEeCCCCCcHHHHHHHHHHHHHHhCCCceeEEEEE-------EecCC-CChHHCCH
Confidence 456677777754 4889999999999888764 55653 55555544
No 48
>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=63.09 E-value=6.9 Score=23.42 Aligned_cols=32 Identities=22% Similarity=0.271 Sum_probs=22.7
Q ss_pred ceecCCChhhH------HHHHHhhhcCCCceEEEEecC
Q psy13022 3 YEVFLPLLDKS------SSKSSMIGARTGVDSIKVSLA 34 (93)
Q Consensus 3 ~~v~m~c~~C~------~~Iek~L~~l~GV~~v~v~l~ 34 (93)
+.+.++.+.|. ..++.+|..++|+.++++++.
T Consensus 41 i~l~l~~p~~~~~~~l~~~i~~al~~l~gv~~v~v~i~ 78 (99)
T TIGR02945 41 IQMTLTAPNCPVAGSMPGEVENAVRAVPGVGSVTVELV 78 (99)
T ss_pred EEEEECCCCCChHHHHHHHHHHHHHhCCCCceEEEEEE
Confidence 34555555553 347888999999998888764
No 49
>TIGR00268 conserved hypothetical protein TIGR00268. The N-terminal region of the model shows similarity to Argininosuccinate synthase proteins using PSI-blast and using the recognize protein identification server.
Probab=61.67 E-value=26 Score=24.60 Aligned_cols=53 Identities=23% Similarity=0.350 Sum_probs=40.1
Q ss_pred HHHHHHhhhcCCCceEEEEecCCcEEEEEECCCCCC-----HHHHHHHHHhCCCceeee
Q psy13022 13 SSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVS-----PKELSEAIYDMGFDTKVT 66 (93)
Q Consensus 13 ~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~-----~~~I~~~I~~~Gy~~~~~ 66 (93)
....|+.|..+ |...++|-.....+.|+.++.... .+.|...++++||.-..+
T Consensus 187 v~~~E~~l~~~-g~~~~rvr~~~~~a~ie~~~~~~~~~~~~~~~i~~~~~~~gf~~v~l 244 (252)
T TIGR00268 187 VDEAEEVLRNA-GVGQVRVRNYDNLAVIEVPEDELSKLLNEAEEVRDKFKDIGFRKVLI 244 (252)
T ss_pred HHHHHHHHHHc-CCCeEEEEecCCeEEEEECHHHHHHHHhhHHHHHHHHHHcCCCeEEE
Confidence 44567788884 888999999999999988654221 367788999999986544
No 50
>TIGR02024 FtcD glutamate formiminotransferase. This model covers enzymes from metazoa as well as gram-positive bacteria and archaea. In humans, deficiency of this enzyme results in a disease phenotype. The crystal structure of the enzyme has been studied in the context of the catalytic mechanism.
Probab=59.32 E-value=52 Score=24.32 Aligned_cols=57 Identities=16% Similarity=0.061 Sum_probs=43.1
Q ss_pred CceecCCChhh--HHHHHHhhh----cCCCceEEEEecC-CcEEEEEE---CCCCCCHHHHHHHHHh
Q psy13022 2 GYEVFLPLLDK--SSSKSSMIG----ARTGVDSIKVSLA-DKEAVITY---NPTLVSPKELSEAIYD 58 (93)
Q Consensus 2 ~~~v~m~c~~C--~~~Iek~L~----~l~GV~~v~v~l~-~~~v~V~~---d~~~~~~~~I~~~I~~ 58 (93)
.|||.+.+... +.+|-+.++ .+++|+..-+.+. .+.+.|.. |...+++..+.+.|+.
T Consensus 184 ayNV~L~t~d~~~a~~IAk~vR~~gGGL~~VqAmgl~~~~~~~vqVsmNl~d~~~t~~~~v~e~v~~ 250 (298)
T TIGR02024 184 AFNVNLGTSNLEIAKKIAKAIRFQGGGLRFVKAIGLYLEEKNLVQVSMNLTNYEKTPLYRVFELIKM 250 (298)
T ss_pred EEEEeecCCCHHHHHHHHHHhhhcCCCccceEEeeEeecCCCeEEEEeeccCCccCCHHHHHHHHHH
Confidence 59999966664 677888888 7778998888886 46677764 4566788888777764
No 51
>PF03698 UPF0180: Uncharacterised protein family (UPF0180); InterPro: IPR005370 The members of this family are small uncharacterised proteins.
Probab=58.52 E-value=20 Score=21.31 Aligned_cols=24 Identities=13% Similarity=0.239 Sum_probs=19.9
Q ss_pred CCHHHHHHHHHhCCCceeeecCCC
Q psy13022 47 VSPKELSEAIYDMGFDTKVTQVDG 70 (93)
Q Consensus 47 ~~~~~I~~~I~~~Gy~~~~~~~~~ 70 (93)
-++..|.+.|++.||++..+....
T Consensus 8 ~~Ls~v~~~L~~~GyeVv~l~~~~ 31 (80)
T PF03698_consen 8 EGLSNVKEALREKGYEVVDLENEQ 31 (80)
T ss_pred CCchHHHHHHHHCCCEEEecCCcc
Confidence 478899999999999998776543
No 52
>PRK09577 multidrug efflux protein; Reviewed
Probab=56.58 E-value=44 Score=28.46 Aligned_cols=50 Identities=14% Similarity=0.133 Sum_probs=38.4
Q ss_pred HHHHHHhhhcCCCceEEEEecCCcEEEEEECCC-----CCCHHHHHHHHHhCCCc
Q psy13022 13 SSSKSSMIGARTGVDSIKVSLADKEAVITYNPT-----LVSPKELSEAIYDMGFD 62 (93)
Q Consensus 13 ~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~-----~~~~~~I~~~I~~~Gy~ 62 (93)
...++..|++++||.+++++-....+.|..|+. .++..+|.++|+..+..
T Consensus 158 ~~~l~~~L~~v~GV~~V~~~G~e~~v~V~vD~~kl~~~Gls~~~V~~~l~~~n~~ 212 (1032)
T PRK09577 158 SANVLQALRRVEGVGKVQFWGAEYAMRIWPDPVKLAALGLTASDIASAVRAHNAR 212 (1032)
T ss_pred HHHHHHHHhcCCCcEEEEecCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHhCCc
Confidence 356889999999999999987655566666652 36788899999886544
No 53
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=55.94 E-value=41 Score=28.63 Aligned_cols=47 Identities=19% Similarity=0.253 Sum_probs=37.8
Q ss_pred HHHHHHhhhcCCCceEEEEecCCcEEEEEECCC-----CCCHHHHHHHHHhC
Q psy13022 13 SSSKSSMIGARTGVDSIKVSLADKEAVITYNPT-----LVSPKELSEAIYDM 59 (93)
Q Consensus 13 ~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~-----~~~~~~I~~~I~~~ 59 (93)
...++..|++++||.++++.-....+.|.+|+. .+++.+|.++|...
T Consensus 159 ~~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~~v~~al~~~ 210 (1037)
T PRK10555 159 ASNIQDPLSRVNGVGDIDAYGSQYSMRIWLDPAKLNSFQMTTKDVTDAIESQ 210 (1037)
T ss_pred HHHHHHHhhcCCCeEEEEEcCCceEEEEEECHHHHHHcCCCHHHHHHHHHHh
Confidence 356889999999999999986666678888762 36778899999864
No 54
>PRK15348 type III secretion system lipoprotein SsaJ; Provisional
Probab=52.73 E-value=68 Score=23.00 Aligned_cols=38 Identities=26% Similarity=0.407 Sum_probs=26.7
Q ss_pred HHHHHHhhhcCCCceEEEEecC-------------CcEEEEEECCCCCCHHH
Q psy13022 13 SSSKSSMIGARTGVDSIKVSLA-------------DKEAVITYNPTLVSPKE 51 (93)
Q Consensus 13 ~~~Iek~L~~l~GV~~v~v~l~-------------~~~v~V~~d~~~~~~~~ 51 (93)
...+++.|..++||..++|.+. +-.+.+.+.+. .+++.
T Consensus 109 egELarTI~~idgV~~ArVhL~lP~~~~~~~~~~asASV~I~~~~~-~~~~~ 159 (249)
T PRK15348 109 EQRIEGMLSQMEGVINAKVTIALPTYDEGSNASPSSVAVFIKYSPQ-VNMEA 159 (249)
T ss_pred HHHHHHHHHhCCCeeEeEEEEECCCCCcccCCCCccEEEEEEeCCC-CChHH
Confidence 3568999999999999998765 22455667664 44443
No 55
>PRK03094 hypothetical protein; Provisional
Probab=51.80 E-value=50 Score=19.66 Aligned_cols=22 Identities=14% Similarity=0.273 Sum_probs=18.8
Q ss_pred CCHHHHHHHHHhCCCceeeecC
Q psy13022 47 VSPKELSEAIYDMGFDTKVTQV 68 (93)
Q Consensus 47 ~~~~~I~~~I~~~Gy~~~~~~~ 68 (93)
.++..|.+.|++.||++..+..
T Consensus 8 ~~Ls~i~~~L~~~GYeVv~l~~ 29 (80)
T PRK03094 8 QSLTDVQQALKQKGYEVVQLRS 29 (80)
T ss_pred cCcHHHHHHHHHCCCEEEecCc
Confidence 4788999999999999987654
No 56
>cd04908 ACT_Bt0572_1 N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains. Included in this CD is the N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains as seen in the uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related ACT domains. These tandem ACT domain proteins belong to the superfamily of ACT regulatory domains.
Probab=51.65 E-value=39 Score=18.33 Aligned_cols=53 Identities=11% Similarity=0.253 Sum_probs=29.0
Q ss_pred hhhHHHHHHhhhcCCC-ceEEEEecCCcEEEEEECCCCCCHHHHHHHHHhCCCcee
Q psy13022 10 LDKSSSKSSMIGARTG-VDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFDTK 64 (93)
Q Consensus 10 ~~C~~~Iek~L~~l~G-V~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~Gy~~~ 64 (93)
|+--..+-+.|.+... |..+-+....+...+.++. .+.+.+.+.+++.||++.
T Consensus 12 pG~La~v~~~l~~~~inI~~i~~~~~~~~~~~rl~~--~~~~~~~~~L~~~G~~v~ 65 (66)
T cd04908 12 PGRLAAVTEILSEAGINIRALSIADTSEFGILRLIV--SDPDKAKEALKEAGFAVK 65 (66)
T ss_pred CChHHHHHHHHHHCCCCEEEEEEEecCCCCEEEEEE--CCHHHHHHHHHHCCCEEE
Confidence 3344455555544432 3344433333344444432 356788888999998864
No 57
>smart00796 AHS1 Allophanate hydrolase subunit 1. This domain represents subunit 1 of allophanate hydrolase (AHS1).
Probab=50.48 E-value=74 Score=21.81 Aligned_cols=46 Identities=13% Similarity=0.311 Sum_probs=33.0
Q ss_pred hHHHHHHhhhc--CCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHhC
Q psy13022 12 KSSSKSSMIGA--RTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDM 59 (93)
Q Consensus 12 C~~~Iek~L~~--l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~ 59 (93)
....+.+.|++ .+||. ++-..-.++.|.||+..++...+.+.|++.
T Consensus 26 ~v~~l~~~l~~~~~~gi~--e~vp~~~sllv~fdp~~~~~~~l~~~l~~~ 73 (201)
T smart00796 26 RVLALARALRAAPLPGVV--ELVPGYRSLLVHFDPLVIDPAALLARLRAL 73 (201)
T ss_pred HHHHHHHHHHhcCCCCeE--EccccceEEEEEEcCCCCCHHHHHHHHHHH
Confidence 34566666664 45664 555677788999999888888888887654
No 58
>COG2151 PaaD Predicted metal-sulfur cluster biosynthetic enzyme [General function prediction only]
Probab=50.44 E-value=21 Score=22.50 Aligned_cols=21 Identities=19% Similarity=0.406 Sum_probs=17.8
Q ss_pred HHHHHHhhhcCCCceEEEEec
Q psy13022 13 SSSKSSMIGARTGVDSIKVSL 33 (93)
Q Consensus 13 ~~~Iek~L~~l~GV~~v~v~l 33 (93)
...+++++..++||..++|++
T Consensus 69 ~~~v~~al~~~~~v~~v~V~l 89 (111)
T COG2151 69 ADQVEAALEEIPGVEDVEVEL 89 (111)
T ss_pred HHHHHHHHHhcCCcceEEEEE
Confidence 567899999999998888764
No 59
>COG4004 Uncharacterized protein conserved in archaea [Function unknown]
Probab=49.93 E-value=14 Score=22.63 Aligned_cols=25 Identities=12% Similarity=0.426 Sum_probs=20.9
Q ss_pred HhhhcCCCceEEEEecCCcEEEEEE
Q psy13022 18 SMIGARTGVDSIKVSLADKEAVITY 42 (93)
Q Consensus 18 k~L~~l~GV~~v~v~l~~~~v~V~~ 42 (93)
..+...||++.++++..++++.|.-
T Consensus 34 ~ivas~pgis~ieik~E~kkL~v~t 58 (96)
T COG4004 34 RIVASSPGISRIEIKPENKKLLVNT 58 (96)
T ss_pred EEEEecCCceEEEEecccceEEEec
Confidence 3456789999999999999998863
No 60
>cd04883 ACT_AcuB C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. This CD includes the C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. AcuB is putatively involved in the anaerobic catabolism of acetoin, and related proteins. Studies report the induction of AcuB by nitrate respiration and also by fermentation. Since acetoin can be secreted and later serve as a source of carbon, it has been proposed that, during anaerobic growth when other carbon sources are exhausted, the induction of the AcuB protein results in acetoin catabolism. AcuB-like proteins have two N-terminal tandem CBS domains and a single C-terminal ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=49.91 E-value=41 Score=18.17 Aligned_cols=60 Identities=17% Similarity=0.296 Sum_probs=34.3
Q ss_pred ceecCCCh-hhHHHHHHhhhcCC-CceEEEEecC--CcE--EEEEECCCCCCHHHHHHHHHhCCCcee
Q psy13022 3 YEVFLPLL-DKSSSKSSMIGART-GVDSIKVSLA--DKE--AVITYNPTLVSPKELSEAIYDMGFDTK 64 (93)
Q Consensus 3 ~~v~m~c~-~C~~~Iek~L~~l~-GV~~v~v~l~--~~~--v~V~~d~~~~~~~~I~~~I~~~Gy~~~ 64 (93)
+.|.|+.. +.-..+.+.|.+.. .+.++..... .+. +.+..+. .+.+++.+.|++.||.+.
T Consensus 4 ~~v~~~d~pG~l~~i~~~l~~~~inI~~i~~~~~~~~~~~~v~i~v~~--~~~~~~~~~L~~~G~~v~ 69 (72)
T cd04883 4 IEVRVPDRPGQLADIAAIFKDRGVNIVSVLVYPSKEEDNKILVFRVQT--MNPRPIIEDLRRAGYEVL 69 (72)
T ss_pred EEEEECCCCCHHHHHHHHHHHcCCCEEEEEEeccCCCCeEEEEEEEec--CCHHHHHHHHHHCCCeee
Confidence 34445444 35556666665543 3444443332 123 3444443 466799999999999865
No 61
>PF05922 Inhibitor_I9: Peptidase inhibitor I9; InterPro: IPR010259 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. Limited proteolysis of most large protein precursors is carried out in vivo by the subtilisin-like pro-protein convertases. Many important biological processes such as peptide hormone synthesis, viral protein processing and receptor maturation involve proteolytic processing by these enzymes []. The subtilisin-serine protease (SRSP) family hormone and pro-protein convertases (furin, PC1/3, PC2, PC4, PACE4, PC5/6, and PC7/7/LPC) act within the secretory pathway to cleave polypeptide precursors at specific basic sites, generating their biologically active forms. Serum proteins, pro-hormones, receptors, zymogens, viral surface glycoproteins, bacterial toxins, amongst others, are activated by this route []. The SRSPs share the same domain structure, including a signal peptide, the pro-peptide, the catalytic domain, the P/middle or homo B domain, and the C terminus. Proteinase propeptide inhibitors (sometimes refered to as activation peptides) are responsible for the modulation of folding and activity of the pro-enzyme or zymogen. The pro-segment docks into the enzyme moiety shielding the substrate binding site, thereby promoting inhibition of the enzyme. Several such propeptides share a similar topology [], despite often low sequence identities []. The propeptide region has an open-sandwich antiparallel-alpha/antiparallel-beta fold, with two alpha-helices and four beta-strands with a (beta/alpha/beta)x2 topology. This group of sequences contain the propeptide domain at the N terminus of peptidases belonging to MEROPS family S8A, subtilisins. A number of the members of this group of sequences belong to MEROPS inhibitor family I9, clan I-. The propeptide is removed by proteolytic cleavage; removal activating the enzyme.; GO: 0004252 serine-type endopeptidase activity, 0042802 identical protein binding, 0043086 negative regulation of catalytic activity; PDB: 3CNQ_P 1SPB_P 3CO0_P 1ITP_A 1V5I_B 1SCJ_B 3P5B_P 2XTJ_P 2W2M_P 2P4E_P ....
Probab=49.84 E-value=18 Score=20.27 Aligned_cols=27 Identities=19% Similarity=0.298 Sum_probs=19.5
Q ss_pred CceecCCChhhHHHHHHhhhcCCCceEEEEec
Q psy13022 2 GYEVFLPLLDKSSSKSSMIGARTGVDSIKVSL 33 (93)
Q Consensus 2 ~~~v~m~c~~C~~~Iek~L~~l~GV~~v~v~l 33 (93)
||.+.|+. ..-+.|++.|+|..+.-|.
T Consensus 51 Gfs~~l~~-----~~i~~L~~~p~V~~Ve~D~ 77 (82)
T PF05922_consen 51 GFSAKLSE-----EEIEKLRKDPGVKSVEPDQ 77 (82)
T ss_dssp EEEEEE-H-----HHHHHHHTSTTEEEEEEEC
T ss_pred EEEEEeCH-----HHHHHHHcCCCeEEEEeCc
Confidence 78888874 3347788999999887653
No 62
>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=49.58 E-value=59 Score=27.74 Aligned_cols=46 Identities=20% Similarity=0.244 Sum_probs=37.8
Q ss_pred HHHHHhhhcCCCceEEEEecCCcEEEEEECCC-----CCCHHHHHHHHHhC
Q psy13022 14 SSKSSMIGARTGVDSIKVSLADKEAVITYNPT-----LVSPKELSEAIYDM 59 (93)
Q Consensus 14 ~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~-----~~~~~~I~~~I~~~ 59 (93)
..++..|++++||.++++.-....+.|.+|+. .+++.++.++|+..
T Consensus 160 ~~l~~~L~~v~GV~~V~~~G~~~ei~V~vD~~kl~~~gls~~dV~~~i~~~ 210 (1044)
T TIGR00915 160 SNMVDPISRLEGVGDVQLFGSQYAMRIWLDPAKLNSYQLTPADVISAIQAQ 210 (1044)
T ss_pred HHHHHHHhCCCCceEEEecCCceEEEEEECHHHHHHcCCCHHHHHHHHHHh
Confidence 46889999999999999988866688888762 46778899999874
No 63
>PF13732 DUF4162: Domain of unknown function (DUF4162)
Probab=49.52 E-value=47 Score=18.75 Aligned_cols=43 Identities=19% Similarity=0.346 Sum_probs=33.4
Q ss_pred hhcCCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHhCCCceee
Q psy13022 20 IGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFDTKV 65 (93)
Q Consensus 20 L~~l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~Gy~~~~ 65 (93)
|..++||..+... ..+.+.+..+.. ....+|...+.+.|+ +..
T Consensus 26 l~~~~~v~~v~~~-~~~~~~i~l~~~-~~~~~ll~~l~~~g~-I~~ 68 (84)
T PF13732_consen 26 LEELPGVESVEQD-GDGKLRIKLEDE-ETANELLQELIEKGI-IRS 68 (84)
T ss_pred HhhCCCeEEEEEe-CCcEEEEEECCc-ccHHHHHHHHHhCCC-eeE
Confidence 7888999988754 455577887765 678999999999998 543
No 64
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=48.27 E-value=34 Score=19.24 Aligned_cols=28 Identities=18% Similarity=0.114 Sum_probs=20.0
Q ss_pred ceecCCChhhHHHHHHhhhcCCCceEEE
Q psy13022 3 YEVFLPLLDKSSSKSSMIGARTGVDSIK 30 (93)
Q Consensus 3 ~~v~m~c~~C~~~Iek~L~~l~GV~~v~ 30 (93)
|.|......--..+-+.|++++||.+|.
T Consensus 52 l~v~V~d~~~L~~ii~~L~~i~~V~~V~ 79 (80)
T PF13291_consen 52 LTVEVKDLEHLNQIIRKLRQIPGVISVE 79 (80)
T ss_dssp EEEEESSHHHHHHHHHHHCTSTTEEEEE
T ss_pred EEEEECCHHHHHHHHHHHHCCCCeeEEE
Confidence 4455566666677788888899988764
No 65
>COG2049 DUR1 Allophanate hydrolase subunit 1 [Amino acid transport and metabolism]
Probab=47.77 E-value=82 Score=22.31 Aligned_cols=46 Identities=20% Similarity=0.417 Sum_probs=33.9
Q ss_pred hHHHHHHhhhcCC--CceEEEEecCCcEEEEEECCCCCCHHHHHHHHHhC
Q psy13022 12 KSSSKSSMIGART--GVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDM 59 (93)
Q Consensus 12 C~~~Iek~L~~l~--GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~ 59 (93)
-.+.+.+.|++.+ || +++-..-.++.|.||+..++...+.+.+...
T Consensus 24 ~i~al~~~l~~~~~~gv--ve~vP~~~sllv~~d~~~~~~~~l~~~L~~~ 71 (223)
T COG2049 24 RIWALARALEAAPLPGV--VEIVPGYRSLLVIYDPPRLDPQELLERLRAL 71 (223)
T ss_pred HHHHHHHHHHhcCCCCe--EEecccceeEEEEecccccCHHHHHHHHHHH
Confidence 3455677787777 66 4566677889999998888988887766543
No 66
>PRK15127 multidrug efflux system protein AcrB; Provisional
Probab=47.19 E-value=68 Score=27.42 Aligned_cols=46 Identities=20% Similarity=0.272 Sum_probs=37.2
Q ss_pred HHHHHhhhcCCCceEEEEecCCcEEEEEECCC-----CCCHHHHHHHHHhC
Q psy13022 14 SSKSSMIGARTGVDSIKVSLADKEAVITYNPT-----LVSPKELSEAIYDM 59 (93)
Q Consensus 14 ~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~-----~~~~~~I~~~I~~~ 59 (93)
..++..|++++||.++++.-..+.+.|..|+. .+++.+|..+|...
T Consensus 160 ~~l~~~L~~v~GV~~V~~~G~~~ei~V~vDp~kl~~~gls~~~V~~~l~~~ 210 (1049)
T PRK15127 160 ANMKDPISRTSGVGDVQLFGSQYAMRIWMNPNELNKFQLTPVDVINAIKAQ 210 (1049)
T ss_pred HHHHHHHhcCCCceEEEEcCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHh
Confidence 45889999999999999886666688888762 46778889998855
No 67
>PF14437 MafB19-deam: MafB19-like deaminase
Probab=44.77 E-value=44 Score=22.15 Aligned_cols=30 Identities=13% Similarity=-0.002 Sum_probs=23.2
Q ss_pred CCChhhHHHHHHhhhcCCCceEEEEecC-CcE
Q psy13022 7 LPLLDKSSSKSSMIGARTGVDSIKVSLA-DKE 37 (93)
Q Consensus 7 m~c~~C~~~Iek~L~~l~GV~~v~v~l~-~~~ 37 (93)
-.|..|...|.+..+++ |+.++.|.-. +++
T Consensus 109 ~vC~~C~~~i~~~a~~l-Gl~~L~I~~~~sG~ 139 (146)
T PF14437_consen 109 DVCGYCGGDIPSMAEKL-GLKSLTIHEPDSGK 139 (146)
T ss_pred ccchHHHHHHHHHHHHc-CCCeEEEEecCCCc
Confidence 47999998888877765 8888888777 553
No 68
>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=43.26 E-value=29 Score=23.89 Aligned_cols=21 Identities=29% Similarity=0.382 Sum_probs=18.0
Q ss_pred HHHHHHhhhcCCCceEEEEec
Q psy13022 13 SSSKSSMIGARTGVDSIKVSL 33 (93)
Q Consensus 13 ~~~Iek~L~~l~GV~~v~v~l 33 (93)
...+++.|+.++||..++|.+
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 356899999999999999884
No 69
>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=42.70 E-value=96 Score=20.33 Aligned_cols=51 Identities=22% Similarity=0.285 Sum_probs=33.0
Q ss_pred ceecCCChhhHHHHHHhhhcCCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHhCCCceeeecCC
Q psy13022 3 YEVFLPLLDKSSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFDTKVTQVD 69 (93)
Q Consensus 3 ~~v~m~c~~C~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~Gy~~~~~~~~ 69 (93)
|.=..||+.|+..|-.+ ||..|-+. ..|. ....-.+.+++.|-++..++.+
T Consensus 91 YvT~ePC~~Ca~ai~~a-----gI~~Vvy~-------~~~~----~~~~~~~~l~~~gi~v~~~~~~ 141 (151)
T TIGR02571 91 YVTHFPCLQCTKSIIQA-----GIKKIYYA-------QDYH----NHPYAIELFEQAGVELKKVPFD 141 (151)
T ss_pred EEeCCCcHHHHHHHHHh-----CCCEEEEc-------cCCC----CcHHHHHHHHHCCCEEEEeCcc
Confidence 34467999999888764 77765432 1121 2234567899999998877543
No 70
>COG0425 SirA Predicted redox protein, regulator of disulfide bond formation [Posttranslational modification, protein turnover, chaperones]
Probab=41.45 E-value=72 Score=18.53 Aligned_cols=54 Identities=6% Similarity=0.053 Sum_probs=38.6
Q ss_pred CCChhhHHHHHHhhhcCCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHhCC-CceeeecCCC
Q psy13022 7 LPLLDKSSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMG-FDTKVTQVDG 70 (93)
Q Consensus 7 m~c~~C~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~G-y~~~~~~~~~ 70 (93)
+.||.=...+.++|++++ ..+.+.|..+.. .+.++|....+..| |.........
T Consensus 13 ~~CP~Pv~~~kk~l~~m~---------~Ge~LeV~~ddp-~~~~dIp~~~~~~~~~~ll~~e~~~ 67 (78)
T COG0425 13 LRCPGPVVETKKALAKLK---------PGEILEVIADDP-AAKEDIPAWAKKEGGHELLEVEQEG 67 (78)
T ss_pred CcCCccHHHHHHHHHcCC---------CCCEEEEEecCc-chHHHHHHHHHHcCCcEEEEEEecC
Confidence 578888999999999886 344556666543 57789999999555 7766554433
No 71
>PF14424 Toxin-deaminase: The BURPS668_1122 family of deaminases
Probab=41.45 E-value=42 Score=21.64 Aligned_cols=25 Identities=8% Similarity=0.045 Sum_probs=21.1
Q ss_pred ceecCCChhhHHHHHHhhhcCCCce
Q psy13022 3 YEVFLPLLDKSSSKSSMIGARTGVD 27 (93)
Q Consensus 3 ~~v~m~c~~C~~~Iek~L~~l~GV~ 27 (93)
|.-.-+|++|...|++-....|.|.
T Consensus 102 ~te~~pC~SC~~vi~qF~~~~pni~ 126 (133)
T PF14424_consen 102 FTELPPCESCSNVIEQFKKDFPNIK 126 (133)
T ss_pred EecCCcChhHHHHHHHHHHHCCCcE
Confidence 4556799999999999999888875
No 72
>KOG3355|consensus
Probab=40.63 E-value=21 Score=24.40 Aligned_cols=22 Identities=9% Similarity=0.244 Sum_probs=19.0
Q ss_pred ceecCCChhhHHHHHHhhhcCC
Q psy13022 3 YEVFLPLLDKSSSKSSMIGART 24 (93)
Q Consensus 3 ~~v~m~c~~C~~~Iek~L~~l~ 24 (93)
|...+||..|+...++.|...|
T Consensus 107 ~s~~yPC~eCa~dl~K~l~~np 128 (177)
T KOG3355|consen 107 FSKFYPCGECAKDLRKILRKNP 128 (177)
T ss_pred hhhhcchHHHHHHHHHHHHhCC
Confidence 5667999999999999998754
No 73
>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=40.39 E-value=55 Score=18.17 Aligned_cols=27 Identities=19% Similarity=0.155 Sum_probs=18.2
Q ss_pred eecCCChhhHHHHHHhhhcCCCceEEE
Q psy13022 4 EVFLPLLDKSSSKSSMIGARTGVDSIK 30 (93)
Q Consensus 4 ~v~m~c~~C~~~Iek~L~~l~GV~~v~ 30 (93)
.+......--..+-+.|++++||.++.
T Consensus 42 ~i~v~~~~~L~~li~~L~~i~gV~~V~ 68 (74)
T cd04877 42 NFPTIEFEKLQTLMPEIRRIDGVEDVK 68 (74)
T ss_pred EeEecCHHHHHHHHHHHhCCCCceEEE
Confidence 344444455567778888888887765
No 74
>COG4827 Predicted transporter [General function prediction only]
Probab=39.89 E-value=19 Score=25.51 Aligned_cols=15 Identities=7% Similarity=0.002 Sum_probs=12.2
Q ss_pred ceecCCChhhHHHHH
Q psy13022 3 YEVFLPLLDKSSSKS 17 (93)
Q Consensus 3 ~~v~m~c~~C~~~Ie 17 (93)
+.|+||||-|-..+-
T Consensus 108 ~ais~PCPvCl~ava 122 (239)
T COG4827 108 LAISMPCPVCLGAVA 122 (239)
T ss_pred EEEecCCcHHHHHHH
Confidence 689999999976654
No 75
>COG5054 ERV1 Mitochondrial sulfhydryl oxidase involved in the biogenesis of cytosolic Fe/S proteins [Posttranslational modification, protein turnover, chaperones]
Probab=39.01 E-value=22 Score=24.25 Aligned_cols=22 Identities=9% Similarity=0.169 Sum_probs=18.8
Q ss_pred ceecCCChhhHHHHHHhhhcCC
Q psy13022 3 YEVFLPLLDKSSSKSSMIGART 24 (93)
Q Consensus 3 ~~v~m~c~~C~~~Iek~L~~l~ 24 (93)
|..-+||..|+.+.++.|...|
T Consensus 116 ~s~~yPCgeCs~~f~K~l~~~p 137 (181)
T COG5054 116 FSITYPCGECSKHFQKLLDVYP 137 (181)
T ss_pred hhheeecHHHHHHHHHHHhhCC
Confidence 6778999999999999998543
No 76
>PRK10503 multidrug efflux system subunit MdtB; Provisional
Probab=37.73 E-value=1.1e+02 Score=26.12 Aligned_cols=46 Identities=15% Similarity=0.182 Sum_probs=35.5
Q ss_pred HHHHHhhhcCCCceEEEEecC-CcEEEEEECCC-----CCCHHHHHHHHHhC
Q psy13022 14 SSKSSMIGARTGVDSIKVSLA-DKEAVITYNPT-----LVSPKELSEAIYDM 59 (93)
Q Consensus 14 ~~Iek~L~~l~GV~~v~v~l~-~~~v~V~~d~~-----~~~~~~I~~~I~~~ 59 (93)
..++..|+++|||.++++.=. ...+.|.+|+. .+++.++..+|...
T Consensus 169 ~~l~~~L~~i~gV~~V~~~G~~~~ei~V~vd~~kl~~~gls~~~v~~ai~~~ 220 (1040)
T PRK10503 169 TRVAQKISQVSGVGLVTLSGGQRPAVRVKLNAQAIAALGLTSETVRTAITGA 220 (1040)
T ss_pred HHHHHHhcCCCCceEEEecCCCceEEEEEECHHHHHHcCCCHHHHHHHHHHh
Confidence 468899999999999887743 35677888762 36777888888754
No 77
>PRK10553 assembly protein for periplasmic nitrate reductase; Provisional
Probab=37.47 E-value=92 Score=18.63 Aligned_cols=47 Identities=13% Similarity=0.185 Sum_probs=32.6
Q ss_pred hhhHHHHHHhhhcCCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHh
Q psy13022 10 LDKSSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYD 58 (93)
Q Consensus 10 ~~C~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~ 58 (93)
|.=...+.+.|..+||+.-.-.+-..+++.|+.... +.+.+.+.+..
T Consensus 16 Pe~~~~V~~~l~~ipg~Evh~~d~~~GKiVVtiE~~--~~~~~~~~i~~ 62 (87)
T PRK10553 16 SERISDISTQLNAFPGCEVAVSDAPSGQLIVVVEAE--DSETLLQTIES 62 (87)
T ss_pred hHHHHHHHHHHHcCCCcEEEeecCCCCeEEEEEEeC--ChHHHHHHHHH
Confidence 334667899999999987666666778888887643 55555554443
No 78
>COG1834 N-Dimethylarginine dimethylaminohydrolase [Amino acid transport and metabolism]
Probab=35.72 E-value=41 Score=24.47 Aligned_cols=53 Identities=23% Similarity=0.360 Sum_probs=39.2
Q ss_pred CcEEEEEEC--CCCCCHHHHHHHHHhCCCceeeecCCCCCccccceeeeccchhhh
Q psy13022 35 DKEAVITYN--PTLVSPKELSEAIYDMGFDTKVTQVDGKPYVPETNVNTSADGLAF 88 (93)
Q Consensus 35 ~~~v~V~~d--~~~~~~~~I~~~I~~~Gy~~~~~~~~~~~~~~~~~~~~~~~~~~~ 88 (93)
.+.+.+-+. ......++|...+. .||.+.....+..=+-++|.||.-+++++.
T Consensus 128 ~~~v~iG~s~RTn~egi~~l~~~L~-~~~~v~~~~~~~~~lHLdt~~~~l~e~~al 182 (267)
T COG1834 128 GDTVYIGYSFRTNLEGIEQLQAWLE-EGYEVSLVRLDERYLHLDTVFNPLAEGLAL 182 (267)
T ss_pred CcEEEEEeccccchHHHHHHHHHhc-cCcEEEEEecCCceeehhheeeeccCccee
Confidence 445555433 22334556777788 899999888888889999999999999874
No 79
>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=35.45 E-value=42 Score=22.93 Aligned_cols=21 Identities=19% Similarity=0.221 Sum_probs=17.5
Q ss_pred HHHHHHhhhcCCCceEEEEec
Q psy13022 13 SSSKSSMIGARTGVDSIKVSL 33 (93)
Q Consensus 13 ~~~Iek~L~~l~GV~~v~v~l 33 (93)
...+++.|..++||..++|.+
T Consensus 109 e~EL~rtI~~i~~V~~ArVhl 129 (193)
T TIGR02544 109 EQRLEQTLSQIDGVISARVHV 129 (193)
T ss_pred HHHHHHHHHhcCCeeeeEEEE
Confidence 346889999999999888865
No 80
>TIGR00302 phosphoribosylformylglycinamidine synthase, purS protein. In species such as Bacillus subtilis in which FGAM synthetase is split into two ORFs purL and purQ, this small protein, previously called yexA, is required for FGAM synthetase activity. Although the article does not make it clear whether this is a subunit or an accessory protein, it is encoded as part of the operon, which suggests stochiometric amounts, = subunit.
Probab=34.53 E-value=95 Score=17.93 Aligned_cols=26 Identities=19% Similarity=0.461 Sum_probs=20.6
Q ss_pred EEEEEECCCCCCH--HHHHHHHHhCCCc
Q psy13022 37 EAVITYNPTLVSP--KELSEAIYDMGFD 62 (93)
Q Consensus 37 ~v~V~~d~~~~~~--~~I~~~I~~~Gy~ 62 (93)
++.|.+.|+..++ +.+..+|.+.||.
T Consensus 4 ~I~V~~k~gV~Dp~G~ti~~~l~~lg~~ 31 (80)
T TIGR00302 4 EVYIRLKKGVLDPEGAAIQRALALLGYN 31 (80)
T ss_pred EEEEEECCCCcChHHHHHHHHHHHcCCC
Confidence 4567777776777 7889999999997
No 81
>PF14026 DUF4242: Protein of unknown function (DUF4242)
Probab=33.72 E-value=99 Score=17.86 Aligned_cols=50 Identities=12% Similarity=0.205 Sum_probs=37.6
Q ss_pred HHHHhhhcCCCceEEEEecC--CcEEEEEECCCCCCHHHHHHHHHhCCCceeee
Q psy13022 15 SKSSMIGARTGVDSIKVSLA--DKEAVITYNPTLVSPKELSEAIYDMGFDTKVT 66 (93)
Q Consensus 15 ~Iek~L~~l~GV~~v~v~l~--~~~v~V~~d~~~~~~~~I~~~I~~~Gy~~~~~ 66 (93)
+-...+.+++||..++.-+. .+++.=.|+. .+.+.|.+.-++.|+.+..+
T Consensus 23 ~~~~~~~~~~~V~w~~s~v~~d~~k~~Cly~A--p~~eaV~~~~~~aG~p~d~I 74 (77)
T PF14026_consen 23 KSCAVQAEMPGVQWLRSYVSEDDGKIFCLYEA--PDEEAVREHARRAGLPADRI 74 (77)
T ss_pred HhHHHHhhcCCeEEEEEEEecCCCeEEEEEEC--CCHHHHHHHHHHcCCCcceE
Confidence 34455666789999997777 6776656764 58999999999999987543
No 82
>PRK04435 hypothetical protein; Provisional
Probab=33.63 E-value=81 Score=20.45 Aligned_cols=28 Identities=7% Similarity=0.163 Sum_probs=18.1
Q ss_pred eecCCChh-hHHHHHHhhhcCCCceEEEE
Q psy13022 4 EVFLPLLD-KSSSKSSMIGARTGVDSIKV 31 (93)
Q Consensus 4 ~v~m~c~~-C~~~Iek~L~~l~GV~~v~v 31 (93)
.|...... ....+-..|++++||.++++
T Consensus 115 tVevs~~~~~L~~Li~~L~~i~gV~~V~i 143 (147)
T PRK04435 115 SIDTSSMEGDIDELLEKLRNLDGVEKVEL 143 (147)
T ss_pred EEEeCChHHHHHHHHHHHHcCCCcEEEEE
Confidence 34444443 56677777888888877764
No 83
>PF11287 DUF3088: Protein of unknown function (DUF3088); InterPro: IPR021439 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=33.43 E-value=83 Score=19.93 Aligned_cols=43 Identities=0% Similarity=-0.078 Sum_probs=28.3
Q ss_pred CCChhhHHHHHHhhhcCCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHh
Q psy13022 7 LPLLDKSSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYD 58 (93)
Q Consensus 7 m~c~~C~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~ 58 (93)
--|++|. .||..|..-|... ..+.|.|-+-.-....+++.+-+
T Consensus 22 f~Cp~c~-~iEGlLa~~P~l~--------~~ldV~rV~f~RPR~~vi~llGE 64 (112)
T PF11287_consen 22 FYCPHCA-AIEGLLASFPDLR--------ERLDVRRVDFPRPRQAVIALLGE 64 (112)
T ss_pred EECCchH-HHHhHHhhChhhh--------hcccEEEeCCCCchHHHHHHhCh
Confidence 3599997 7899999888743 33444443333455677777755
No 84
>PHA02119 hypothetical protein
Probab=32.71 E-value=45 Score=19.56 Aligned_cols=39 Identities=15% Similarity=0.443 Sum_probs=27.3
Q ss_pred EEEEEECCC---CCCHHHHHHHHHhCCCceeeecCCCCCccc
Q psy13022 37 EAVITYNPT---LVSPKELSEAIYDMGFDTKVTQVDGKPYVP 75 (93)
Q Consensus 37 ~v~V~~d~~---~~~~~~I~~~I~~~Gy~~~~~~~~~~~~~~ 75 (93)
..+|.|+.. .+-+.+|.+-+...||++...+...+.+-.
T Consensus 41 ~f~isf~~~kfp~i~~~divdylr~lgy~~~~~s~rnes~i~ 82 (87)
T PHA02119 41 SFKISFDVAKFPAIMPKDIVDYLRSLGYDAKSDSFRNESVIT 82 (87)
T ss_pred eeEEEeccccCCccccHHHHHHHHHccchhccccccCceEEE
Confidence 344555432 256789999999999998877766666543
No 85
>PF11080 DUF2622: Protein of unknown function (DUF2622); InterPro: IPR022597 This family is conserved in the Enterobacteriaceae family. The function is not known.
Probab=32.38 E-value=97 Score=19.07 Aligned_cols=42 Identities=31% Similarity=0.459 Sum_probs=30.7
Q ss_pred EEEEEECCC-CCCHHHHHHHHHhCCCceeeecCCCCCccccce
Q psy13022 37 EAVITYNPT-LVSPKELSEAIYDMGFDTKVTQVDGKPYVPETN 78 (93)
Q Consensus 37 ~v~V~~d~~-~~~~~~I~~~I~~~Gy~~~~~~~~~~~~~~~~~ 78 (93)
.++|.|.+. .....++...+...||...+...+....-+-|+
T Consensus 10 VVt~~~~e~~l~d~~~L~~~lt~~GF~~tl~D~~G~~HeLgtn 52 (96)
T PF11080_consen 10 VVTFEYQEAGLTDINELNNHLTRAGFSTTLTDEDGNPHELGTN 52 (96)
T ss_pred EEEEEeccCChHHHHHHHHHHHhcCceeEEecCCCCEeecCCC
Confidence 356666543 355677888999999999888888777766654
No 86
>COG0277 GlcD FAD/FMN-containing dehydrogenases [Energy production and conversion]
Probab=32.36 E-value=79 Score=23.56 Aligned_cols=53 Identities=21% Similarity=0.255 Sum_probs=33.6
Q ss_pred EEecCCcEEEEEECCCCCCHHHHHHHHHhCCCceeeecCCCCCccccceeeeccch
Q psy13022 30 KVSLADKEAVITYNPTLVSPKELSEAIYDMGFDTKVTQVDGKPYVPETNVNTSADG 85 (93)
Q Consensus 30 ~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~Gy~~~~~~~~~~~~~~~~~~~~~~~~ 85 (93)
+++..+..+++. +. ....++.+.+...|+.....+.....-+---...|.+.|
T Consensus 89 ~id~~~~~~~v~--aG-v~l~~l~~~l~~~G~~~p~~p~s~~~~tIGG~ia~~~~G 141 (459)
T COG0277 89 EIDPEDGTATVQ--AG-VTLEDLEKALAPHGLFLPVDPSSSGTATIGGNIATNAGG 141 (459)
T ss_pred ccCcCCCEEEEc--CC-ccHHHHHHHHHHcCCccCCCccccccceEccchhcCCCC
Confidence 566677777776 34 789999999999998865444433233333334444444
No 87
>COG4545 Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones]
Probab=32.09 E-value=27 Score=20.85 Aligned_cols=14 Identities=7% Similarity=-0.187 Sum_probs=11.6
Q ss_pred cCCChhhHHHHHHh
Q psy13022 6 FLPLLDKSSSKSSM 19 (93)
Q Consensus 6 ~m~c~~C~~~Iek~ 19 (93)
++.||.|+..++-.
T Consensus 9 sn~Cpdca~a~eyl 22 (85)
T COG4545 9 SNLCPDCAPAVEYL 22 (85)
T ss_pred cccCcchHHHHHHH
Confidence 68999999888764
No 88
>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=31.69 E-value=58 Score=19.62 Aligned_cols=21 Identities=19% Similarity=0.362 Sum_probs=18.2
Q ss_pred HHHHHHhhhcCCCceEEEEec
Q psy13022 13 SSSKSSMIGARTGVDSIKVSL 33 (93)
Q Consensus 13 ~~~Iek~L~~l~GV~~v~v~l 33 (93)
...++.++++++||+++++.-
T Consensus 64 td~lee~i~~ve~V~svev~~ 84 (88)
T TIGR00489 64 TEAAEESLSGIEGVESVEVTD 84 (88)
T ss_pred hHHHHHHHhcCCCccEEEEEE
Confidence 578999999999999988753
No 89
>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=31.61 E-value=55 Score=17.99 Aligned_cols=41 Identities=17% Similarity=0.266 Sum_probs=24.2
Q ss_pred HHHhhhcCCCceEEEEecCC----cEEEEEECCCCCCHHHHHHHHHh
Q psy13022 16 KSSMIGARTGVDSIKVSLAD----KEAVITYNPTLVSPKELSEAIYD 58 (93)
Q Consensus 16 Iek~L~~l~GV~~v~v~l~~----~~v~V~~d~~~~~~~~I~~~I~~ 58 (93)
||+.|.+.+||.++-|-... +...+.|-.. ..++|.+.+.+
T Consensus 2 IE~~l~~~~~V~~~~V~~~~d~~~g~~l~a~vv~--~~~~i~~~~~~ 46 (73)
T PF13193_consen 2 IESVLRQHPGVAEAAVVGVPDEDWGERLVAFVVL--DEEEIRDHLRD 46 (73)
T ss_dssp HHHHHHTSTTEEEEEEEEEEETTTEEEEEEEEEE--HHHHHHHHHHH
T ss_pred HHHHHhcCCCccEEEEEEEEcccccccceeEEEe--eecccccchhh
Confidence 78999999999887653322 2222222111 34677777765
No 90
>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=31.42 E-value=2.1e+02 Score=24.22 Aligned_cols=39 Identities=10% Similarity=0.243 Sum_probs=29.4
Q ss_pred HHHHHHhhhcCCCceEEEEecCCcEEE--EEECCCCCCHHHH
Q psy13022 13 SSSKSSMIGARTGVDSIKVSLADKEAV--ITYNPTLVSPKEL 52 (93)
Q Consensus 13 ~~~Iek~L~~l~GV~~v~v~l~~~~v~--V~~d~~~~~~~~I 52 (93)
...+|++|+.++|+.+++..-..+... +.|+.+ .+.+..
T Consensus 62 t~plE~~l~~v~gv~~i~S~s~~g~s~i~v~f~~~-~d~~~a 102 (1021)
T PF00873_consen 62 TKPLEEALSSVEGVKEIRSTSREGSSSITVEFDDG-TDIDEA 102 (1021)
T ss_dssp HHHHHHTHCSSTTEEEEEEEETTSEEEEEEEESTT-S-HHHH
T ss_pred HHHHHHHHcCCCCeEEEEEEecCCcEEEEEEeccc-cCHHHH
Confidence 457899999999999999888888665 567765 455543
No 91
>TIGR00370 conserved hypothetical protein TIGR00370.
Probab=31.38 E-value=1.5e+02 Score=20.38 Aligned_cols=45 Identities=11% Similarity=0.102 Sum_probs=30.1
Q ss_pred hhHHHHHHhhhcCCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHh
Q psy13022 11 DKSSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYD 58 (93)
Q Consensus 11 ~C~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~ 58 (93)
.....+.+.|++.+||. ++-..-.++.|.||+... ...+.+.|++
T Consensus 20 ~~v~~l~~~l~~~~gi~--e~vP~~~sllv~fdp~~~-~~~l~~~l~~ 64 (202)
T TIGR00370 20 GIVWAAAAYLEEQPGFV--ECIPGMNNLTVFYDMYEV-YKHLPQRLSS 64 (202)
T ss_pred HHHHHHHHHHhcCCCcE--EeecccEEEEEEECchhh-HHHHHHHHHH
Confidence 34566777777667765 455666788899998754 5556666654
No 92
>cd04909 ACT_PDH-BS C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH). The C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate, found in Bacillus subtilis (BS) and other Firmicutes, Deinococci, and Bacteroidetes. PDH is the first enzyme in the aromatic amino acid pathway specific for the biosynthesis of tyrosine. This enzyme is feedback-inhibited by tyrosine in B. subtilis and other microorganisms. Both phenylalanine and tryptophan have been shown to be inhibitors of this activity in B. subtilis. Bifunctional chorismate mutase-PDH (TyrA) enzymes such as those seen in Escherichia coli do not contain an ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=30.73 E-value=93 Score=16.65 Aligned_cols=51 Identities=10% Similarity=0.249 Sum_probs=29.4
Q ss_pred hHHHHHHhhhcCC-CceEEEEecC----CcEEEEEECCCCCCHHHHHHHHHhCCCce
Q psy13022 12 KSSSKSSMIGART-GVDSIKVSLA----DKEAVITYNPTLVSPKELSEAIYDMGFDT 63 (93)
Q Consensus 12 C~~~Iek~L~~l~-GV~~v~v~l~----~~~v~V~~d~~~~~~~~I~~~I~~~Gy~~ 63 (93)
.-..+.+.|.+.. .+..+..... ...+.+..+.. ...+.+.+.+++.||.+
T Consensus 14 ~L~~l~~~l~~~~i~i~~~~~~~~~~~~~~~~~i~v~~~-~~~~~~~~~L~~~G~~v 69 (69)
T cd04909 14 VIAEVTQILGDAGISIKNIEILEIREGIGGILRISFKTQ-EDRERAKEILKEAGYEV 69 (69)
T ss_pred HHHHHHHHHHHcCCCceeeEeEEeecCCcEEEEEEECCH-HHHHHHHHHHHHcCCcC
Confidence 4556666665543 2444433332 23344555422 36789999999999963
No 93
>PRK06423 phosphoribosylformylglycinamidine synthase; Provisional
Probab=30.56 E-value=1.1e+02 Score=17.35 Aligned_cols=26 Identities=19% Similarity=0.537 Sum_probs=20.4
Q ss_pred EEEEEECCCCCCH--HHHHHHHHhCCCc
Q psy13022 37 EAVITYNPTLVSP--KELSEAIYDMGFD 62 (93)
Q Consensus 37 ~v~V~~d~~~~~~--~~I~~~I~~~Gy~ 62 (93)
.+.|.+.|+..++ +.+.+++...||.
T Consensus 4 ~v~V~~k~gv~Dp~G~ti~~~l~~lg~~ 31 (73)
T PRK06423 4 KVEVTYKPGVEDPEALTILKNLNILGYN 31 (73)
T ss_pred EEEEEECCCCcChHHHHHHHHHHHcCCC
Confidence 4567777776677 6889999999987
No 94
>cd04887 ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI and related domains. The ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI, a malolactic enzyme (MalLac-Enz) which converts malate to lactate, and other related ACT domains. The yqkJ product is predicted to convert malate directly to lactate, as opposed to related malic enzymes that convert malate to pyruvate. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=29.82 E-value=1e+02 Score=16.70 Aligned_cols=27 Identities=15% Similarity=0.139 Sum_probs=16.4
Q ss_pred eecCCChhhHHHHHHhhhcCCCceEEE
Q psy13022 4 EVFLPLLDKSSSKSSMIGARTGVDSIK 30 (93)
Q Consensus 4 ~v~m~c~~C~~~Iek~L~~l~GV~~v~ 30 (93)
.|......-...+-+.|++++||.-.+
T Consensus 45 ~vev~~~~~l~~i~~~L~~i~gV~~~~ 71 (74)
T cd04887 45 TVDAPSEEHAETIVAAVRALPEVKVLS 71 (74)
T ss_pred EEEcCCHHHHHHHHHHHhcCCCeEEEE
Confidence 344455555566777777777765544
No 95
>PF14814 UB2H: Bifunctional transglycosylase second domain; PDB: 3FWL_A 3VMA_A.
Probab=29.61 E-value=63 Score=18.90 Aligned_cols=49 Identities=16% Similarity=0.315 Sum_probs=25.3
Q ss_pred CCCCCCHHHHHHHHHhCCCceeeecCCCCCccc-cceeeeccchhhhhcc
Q psy13022 43 NPTLVSPKELSEAIYDMGFDTKVTQVDGKPYVP-ETNVNTSADGLAFKQG 91 (93)
Q Consensus 43 d~~~~~~~~I~~~I~~~Gy~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~ 91 (93)
....++.+++...++.+||.-......+-+|.. ...+....-|+.|..|
T Consensus 3 ~G~~ls~~~l~~eL~~LgYR~v~~~~~pG~y~~~g~~i~i~~R~F~F~Dg 52 (85)
T PF14814_consen 3 PGAPLSPAQLEQELELLGYRKVSNPDRPGEYSRSGNRIEIYTRGFDFPDG 52 (85)
T ss_dssp TT-S--HHHHHHHHHHTT-EE-SS--STTEEEEETTEEEEEE--EEETTC
T ss_pred CCcccCHHHHHHHHHHcCCCcCCCCCCCeEEEEECCEEEEEECCCCCCCC
Confidence 344688999999999999997754444444433 3444444445555443
No 96
>COG1400 SEC65 Signal recognition particle 19 kDa protein [Intracellular trafficking and secretion]
Probab=29.01 E-value=67 Score=19.66 Aligned_cols=19 Identities=32% Similarity=0.504 Sum_probs=17.0
Q ss_pred CCCHHHHHHHHHhCCCcee
Q psy13022 46 LVSPKELSEAIYDMGFDTK 64 (93)
Q Consensus 46 ~~~~~~I~~~I~~~Gy~~~ 64 (93)
...+++|.++++++||.+.
T Consensus 31 ~P~~~ei~~a~~~LGl~~~ 49 (93)
T COG1400 31 NPSLEEIAEALRELGLKPK 49 (93)
T ss_pred CCCHHHHHHHHHHcCCCee
Confidence 3688999999999999986
No 97
>KOG2836|consensus
Probab=28.97 E-value=1.7e+02 Score=19.50 Aligned_cols=38 Identities=26% Similarity=0.374 Sum_probs=32.7
Q ss_pred EEEEecCCcEEEEEECCCCCCHHHHHHHHHhCCCceee
Q psy13022 28 SIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFDTKV 65 (93)
Q Consensus 28 ~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~Gy~~~~ 65 (93)
-+.+++...+..|+.+|...++....+-+++.|-....
T Consensus 9 PveIsy~~MrFLIThnPtnaTln~fieELkKygvttvV 46 (173)
T KOG2836|consen 9 PVEISYKNMRFLITHNPTNATLNKFIEELKKYGVTTVV 46 (173)
T ss_pred CeeeeccceEEEEecCCCchhHHHHHHHHHhcCCeEEE
Confidence 46788999999999999888999999999999987643
No 98
>PRK10614 multidrug efflux system subunit MdtC; Provisional
Probab=28.16 E-value=2.1e+02 Score=24.49 Aligned_cols=46 Identities=22% Similarity=0.289 Sum_probs=35.5
Q ss_pred HHHHHhhhcCCCceEEEEecCC-cEEEEEECCC-----CCCHHHHHHHHHhC
Q psy13022 14 SSKSSMIGARTGVDSIKVSLAD-KEAVITYNPT-----LVSPKELSEAIYDM 59 (93)
Q Consensus 14 ~~Iek~L~~l~GV~~v~v~l~~-~~v~V~~d~~-----~~~~~~I~~~I~~~ 59 (93)
..++..|++++||.++++.-.. ..+.|.+|+. .++++++..+|...
T Consensus 160 ~~l~~~L~~i~GV~~V~~~G~~~~ei~V~vd~~kl~~~gls~~dV~~al~~~ 211 (1025)
T PRK10614 160 TQLAQTISQIDGVGDVDVGGSSLPAVRVGLNPQALFNQGVSLDDVRQAISNA 211 (1025)
T ss_pred HHHHHHhcCCCCceEEEecCCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHh
Confidence 5689999999999999987543 3567777763 36778899988765
No 99
>PRK11200 grxA glutaredoxin 1; Provisional
Probab=27.83 E-value=1.1e+02 Score=17.27 Aligned_cols=27 Identities=7% Similarity=-0.170 Sum_probs=16.0
Q ss_pred cCCChhhHHHHHHhhhcC----CCceEEEEec
Q psy13022 6 FLPLLDKSSSKSSMIGAR----TGVDSIKVSL 33 (93)
Q Consensus 6 ~m~c~~C~~~Iek~L~~l----~GV~~v~v~l 33 (93)
.-.|+.|. ++.+.|.++ .|+.-..+|+
T Consensus 8 ~~~C~~C~-~a~~~L~~l~~~~~~i~~~~idi 38 (85)
T PRK11200 8 RPGCPYCV-RAKELAEKLSEERDDFDYRYVDI 38 (85)
T ss_pred CCCChhHH-HHHHHHHhhcccccCCcEEEEEC
Confidence 34799997 455566654 4555444443
No 100
>PF14408 Actino_peptide: Ribosomally synthesized peptide in actinomycetes
Probab=27.81 E-value=23 Score=19.87 Aligned_cols=31 Identities=26% Similarity=0.220 Sum_probs=21.1
Q ss_pred HHhCCCceeeecCCCCCccccceeeeccchhh
Q psy13022 56 IYDMGFDTKVTQVDGKPYVPETNVNTSADGLA 87 (93)
Q Consensus 56 I~~~Gy~~~~~~~~~~~~~~~~~~~~~~~~~~ 87 (93)
+...| .+..+.........+|.=+|+.||-.
T Consensus 18 ~D~~G-~~vemgkHgTst~~~t~T~Ts~DG~~ 48 (59)
T PF14408_consen 18 VDRDG-PVVEMGKHGTSTGTETSTTTSPDGQN 48 (59)
T ss_pred EcCCC-CceeccccccccccccccccCCCCCC
Confidence 34456 44445556777788888888888865
No 101
>PRK05974 phosphoribosylformylglycinamidine synthase subunit PurS; Reviewed
Probab=27.78 E-value=1.3e+02 Score=17.35 Aligned_cols=26 Identities=19% Similarity=0.543 Sum_probs=20.1
Q ss_pred EEEEEECCCCCCH--HHHHHHHHhCCCc
Q psy13022 37 EAVITYNPTLVSP--KELSEAIYDMGFD 62 (93)
Q Consensus 37 ~v~V~~d~~~~~~--~~I~~~I~~~Gy~ 62 (93)
++.|.+.|+..++ +.+.+++...||.
T Consensus 4 ~V~V~~k~gv~Dp~G~ai~~~l~~lg~~ 31 (80)
T PRK05974 4 KVTVTLKEGVLDPQGQAIKGALGSLGYD 31 (80)
T ss_pred EEEEEECCCCcChHHHHHHHHHHHcCCC
Confidence 3556677776666 6889999999997
No 102
>cd04882 ACT_Bt0572_2 C-terminal ACT domain of a novel protein composed of just two ACT domains. Included in this CD is the C-terminal ACT domain of a novel protein composed of just two ACT domains, as seen in the yet uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related proteins. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=27.58 E-value=1e+02 Score=16.01 Aligned_cols=15 Identities=13% Similarity=0.240 Sum_probs=13.2
Q ss_pred HHHHHHHHHhCCCce
Q psy13022 49 PKELSEAIYDMGFDT 63 (93)
Q Consensus 49 ~~~I~~~I~~~Gy~~ 63 (93)
.+.+.+.+++.||.+
T Consensus 50 ~~~~~~~L~~~G~~v 64 (65)
T cd04882 50 IEKAIEVLQERGVEL 64 (65)
T ss_pred HHHHHHHHHHCCceE
Confidence 889999999999964
No 103
>PRK02935 hypothetical protein; Provisional
Probab=27.58 E-value=15 Score=23.15 Aligned_cols=20 Identities=15% Similarity=0.107 Sum_probs=14.2
Q ss_pred eecCCChhhHHHHHHhhhcCC
Q psy13022 4 EVFLPLLDKSSSKSSMIGART 24 (93)
Q Consensus 4 ~v~m~c~~C~~~Iek~L~~l~ 24 (93)
+|+..||+|. +..|.|.+.+
T Consensus 68 avqV~CP~C~-K~TKmLGrvD 87 (110)
T PRK02935 68 AVQVICPSCE-KPTKMLGRVD 87 (110)
T ss_pred ceeeECCCCC-chhhhcccee
Confidence 5788999996 5566665443
No 104
>KOG1352|consensus
Probab=27.45 E-value=30 Score=27.17 Aligned_cols=25 Identities=24% Similarity=0.276 Sum_probs=18.7
Q ss_pred CCceecCCChhhHHHHHHhhhcCCCc
Q psy13022 1 MGYEVFLPLLDKSSSKSSMIGARTGV 26 (93)
Q Consensus 1 ~~~~v~m~c~~C~~~Iek~L~~l~GV 26 (93)
|||+|+|.-.+-. +...+|+.+.|-
T Consensus 342 mG~nVsMmADStS-RWAEALREISGR 366 (618)
T KOG1352|consen 342 MGYNVSMMADSTS-RWAEALREISGR 366 (618)
T ss_pred cCcceeeeecchh-HHHHHHHHhhhh
Confidence 8999999877654 566777777663
No 105
>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=27.21 E-value=1.3e+02 Score=17.35 Aligned_cols=44 Identities=20% Similarity=0.200 Sum_probs=30.7
Q ss_pred hHHHHHHhhhcCCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHh
Q psy13022 12 KSSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYD 58 (93)
Q Consensus 12 C~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~ 58 (93)
=...+.+.|..+||+.---.+-. +++.|.... .+..++.+.+..
T Consensus 16 ~~~~v~~~l~~~~gvEVh~~~~~-GKiVVtiE~--~~~~~~~~~~~~ 59 (79)
T PF03927_consen 16 RLEEVAEALAAIPGVEVHAVDED-GKIVVTIEA--ESSEEEVDLIDA 59 (79)
T ss_dssp CHHHHHHHHCCSTTEEEEEEETT-TEEEEEEEE--SSHHHHHHHHHH
T ss_pred hHHHHHHHHHcCCCcEEEeeCCC-CeEEEEEEe--CChHHHHHHHHH
Confidence 45678999999999955455544 888777754 366666666654
No 106
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=27.06 E-value=37 Score=17.78 Aligned_cols=16 Identities=19% Similarity=0.468 Sum_probs=12.4
Q ss_pred CHHHHHHHHHhCCCce
Q psy13022 48 SPKELSEAIYDMGFDT 63 (93)
Q Consensus 48 ~~~~I~~~I~~~Gy~~ 63 (93)
..+.|.+++++.||.+
T Consensus 30 tr~rI~~~a~~lgY~p 45 (46)
T PF00356_consen 30 TRERILEAAEELGYRP 45 (46)
T ss_dssp HHHHHHHHHHHHTB-S
T ss_pred HHHHHHHHHHHHCCCC
Confidence 5568899999999974
No 107
>TIGR01709 typeII_sec_gspL general secretion pathway protein L. This model represents GspL, protein L of the main terminal branch of the general secretion pathway, also called type II secretion. It transports folded proteins across the bacterial outer membrane and is widely distributed in Gram-negative pathogens.
Probab=27.04 E-value=1.8e+02 Score=21.52 Aligned_cols=57 Identities=14% Similarity=0.274 Sum_probs=36.6
Q ss_pred HHHHhhhcCCCceEEEEecC--CcEEEEEEC-CCCCCHHHHHHHHHhCCCceeeecCCCCC
Q psy13022 15 SKSSMIGARTGVDSIKVSLA--DKEAVITYN-PTLVSPKELSEAIYDMGFDTKVTQVDGKP 72 (93)
Q Consensus 15 ~Iek~L~~l~GV~~v~v~l~--~~~v~V~~d-~~~~~~~~I~~~I~~~Gy~~~~~~~~~~~ 72 (93)
.+..++...+++.--.+++. .+.+.+... +.....+.+...++ .||.+..-....+.
T Consensus 314 ~l~~al~~~~~~~l~sL~y~~~~~~L~l~l~a~~~~~le~l~~~l~-~g~~v~~~~~~~~~ 373 (384)
T TIGR01709 314 ALATALGQLPGLQLQSLDFDGARGELRLKLEAPSDADLEQLRSRLA-RGFQVALGQAGAEG 373 (384)
T ss_pred HHHHHhccCCCCceeEEeEcCCCCEEEEEEecCChHHHHHHHHHHh-hhceecccccccCC
Confidence 45566666777655555565 455555543 23356677788899 99998876665554
No 108
>PF02005 TRM: N2,N2-dimethylguanosine tRNA methyltransferase; InterPro: IPR002905 This enzyme 2.1.1.32 from EC uses S-adenosyl-L-methionine to methylate tRNA: S-AdoMet + tRNA = S-adenosyl-L-homocysteine + tRNA containing N2-methylguanine The TRM1 gene of Saccharomyces cerevisiae is necessary for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNAs []. The enzyme is found in both eukaryotes and archaea [].; GO: 0003723 RNA binding, 0004809 tRNA (guanine-N2-)-methyltransferase activity, 0008033 tRNA processing; PDB: 2YTZ_B 2DUL_A 2EJU_A 2EJT_A 3AXT_A 3AXS_A.
Probab=26.72 E-value=94 Score=23.50 Aligned_cols=32 Identities=13% Similarity=0.200 Sum_probs=24.5
Q ss_pred CCCHHHHHHHHHhCCCceeeecCCCCCccccc
Q psy13022 46 LVSPKELSEAIYDMGFDTKVTQVDGKPYVPET 77 (93)
Q Consensus 46 ~~~~~~I~~~I~~~Gy~~~~~~~~~~~~~~~~ 77 (93)
....+.++++|.+.||.+....-++...+++-
T Consensus 336 ~P~~~~ii~aL~~~Gy~aSrTH~~p~giKTdA 367 (377)
T PF02005_consen 336 PPPLDKIISALRNAGYRASRTHFDPNGIKTDA 367 (377)
T ss_dssp C--HHHHHHHHHHTTTTEEEETTCCCEEEESS
T ss_pred CCCHHHHHHHHhhcceEEEecccCCCcEecCC
Confidence 35678999999999999988877777666553
No 109
>COG2177 FtsX Cell division protein [Cell division and chromosome partitioning]
Probab=26.62 E-value=2.6e+02 Score=20.49 Aligned_cols=23 Identities=22% Similarity=0.242 Sum_probs=19.7
Q ss_pred ChhhHHHHHHhhhcCCCceEEEE
Q psy13022 9 LLDKSSSKSSMIGARTGVDSIKV 31 (93)
Q Consensus 9 c~~C~~~Iek~L~~l~GV~~v~v 31 (93)
...|...+++.+...+||.+++.
T Consensus 70 ~~~~~~~v~~~i~~~~gV~~v~~ 92 (297)
T COG2177 70 DQDDAALVREKIEGIPGVKSVRF 92 (297)
T ss_pred ChHHHHHHHHHHhcCCCcceEEE
Confidence 47789999999999999987664
No 110
>COG0841 AcrB Cation/multidrug efflux pump [Defense mechanisms]
Probab=26.33 E-value=2.7e+02 Score=24.06 Aligned_cols=50 Identities=20% Similarity=0.271 Sum_probs=38.7
Q ss_pred HHHHHHhhhcCCCceEEEEecC-CcEEEEEECCC-----CCCHHHHHHHHHhCCCc
Q psy13022 13 SSSKSSMIGARTGVDSIKVSLA-DKEAVITYNPT-----LVSPKELSEAIYDMGFD 62 (93)
Q Consensus 13 ~~~Iek~L~~l~GV~~v~v~l~-~~~v~V~~d~~-----~~~~~~I~~~I~~~Gy~ 62 (93)
...+...|..++||.++.+.=. ...+.|..||. .+++.++..+|+.....
T Consensus 157 ~~~l~~~L~~v~GV~~V~~~G~~~~~~rI~ldp~kLa~~gLt~~dV~~ai~~qN~~ 212 (1009)
T COG0841 157 ASNVRDELSRVPGVGSVQLFGAQEYAMRIWLDPAKLAAYGLTPSDVQSAIRAQNVQ 212 (1009)
T ss_pred HHHHHHHHhcCCCceEEEEcCCCceeEEEEeCHHHHHHcCCCHHHHHHHHHHhCcc
Confidence 4568999999999999998765 44567877763 36788999999876554
No 111
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=26.22 E-value=91 Score=23.54 Aligned_cols=32 Identities=19% Similarity=0.333 Sum_probs=25.5
Q ss_pred CCCHHHHHHHHHhCCCceeeecCCCCCccccc
Q psy13022 46 LVSPKELSEAIYDMGFDTKVTQVDGKPYVPET 77 (93)
Q Consensus 46 ~~~~~~I~~~I~~~Gy~~~~~~~~~~~~~~~~ 77 (93)
....+.++++|.+.||.+....-++...+++-
T Consensus 337 ~p~~~~~~~~L~~~Gy~as~tH~~p~~iKTdA 368 (382)
T PRK04338 337 APPMDEILEALREAGFEASRTHFSPTGFKTDA 368 (382)
T ss_pred CCCHHHHHHHHHHCCCeEEeeEECCCcEecCC
Confidence 46889999999999999987776666666543
No 112
>KOG2792|consensus
Probab=26.17 E-value=63 Score=23.63 Aligned_cols=51 Identities=16% Similarity=0.160 Sum_probs=28.5
Q ss_pred CChh-hHHHHHHhhhcCCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHhC
Q psy13022 8 PLLD-KSSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDM 59 (93)
Q Consensus 8 ~c~~-C~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~ 59 (93)
.||. |-..+++....++-|.. ...+.-..+-|..||+.-+++.+.+-+++-
T Consensus 150 hCPDICPdELeKm~~~Vd~i~~-~~~~~~~PlFIsvDPeRD~~~~~~eY~~eF 201 (280)
T KOG2792|consen 150 HCPDICPDELEKMSAVVDEIEA-KPGLPPVPLFISVDPERDSVEVVAEYVSEF 201 (280)
T ss_pred CCCCcChHHHHHHHHHHHHHhc-cCCCCccceEEEeCcccCCHHHHHHHHHhc
Confidence 4554 55555544333322211 111222367888999888888888777653
No 113
>COG1999 Uncharacterized protein SCO1/SenC/PrrC, involved in biogenesis of respiratory and photosynthetic systems [General function prediction only]
Probab=26.04 E-value=1.1e+02 Score=20.97 Aligned_cols=26 Identities=27% Similarity=0.402 Sum_probs=18.4
Q ss_pred EEEEEECCCCCCHHHHHHHHHhCCCce
Q psy13022 37 EAVITYNPTLVSPKELSEAIYDMGFDT 63 (93)
Q Consensus 37 ~v~V~~d~~~~~~~~I~~~I~~~Gy~~ 63 (93)
-+.|++||+.-.++.+.+-.+ .++..
T Consensus 107 vv~itvDPerDtp~~lk~Y~~-~~~~~ 132 (207)
T COG1999 107 VVFITVDPERDTPEVLKKYAE-LNFDP 132 (207)
T ss_pred EEEEEECCCCCCHHHHHHHhc-ccCCC
Confidence 466888998777787777777 44443
No 114
>TIGR00308 TRM1 tRNA(guanine-26,N2-N2) methyltransferase. This enzyme is responsible for two methylations of a characteristic guanine of most tRNA molecules. The activity has been demonstrated for eukaryotic and archaeal proteins, which are active when expressed in E. coli, a species that lacks this enzyme. At least one Eubacterium, Aquifex aeolicus, has an ortholog, as do all completed archaeal genomes.
Probab=25.43 E-value=1e+02 Score=23.32 Aligned_cols=31 Identities=13% Similarity=0.272 Sum_probs=25.0
Q ss_pred CCCHHHHHHHHHhCCCceeeecCCCCCcccc
Q psy13022 46 LVSPKELSEAIYDMGFDTKVTQVDGKPYVPE 76 (93)
Q Consensus 46 ~~~~~~I~~~I~~~Gy~~~~~~~~~~~~~~~ 76 (93)
....+.++++|.+.||.+....-++...+++
T Consensus 328 ~p~~~~~~~~L~~~Gy~as~tH~~p~~iKTd 358 (374)
T TIGR00308 328 VPPLKDVVAGLKSLGFEASRTHYQPSGIKTD 358 (374)
T ss_pred CCCHHHHHHHHHHCCCeEEeeeeCCCcEecC
Confidence 4678899999999999998877666666654
No 115
>PF12404 DUF3663: Peptidase ; InterPro: IPR008330 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This family represents the peptidase B group of leucyl aminopeptidases, which are restricted to the gammaproteobacteria. They contain a C-terminal aminopeptidase catalytic domain and an N-terminal domain of unknown function. They are zinc-dependent exopeptidases (3.4.11.1 from EC) and belong to MEROPS peptidase family M17 (leucyl aminopeptidase family, clan MF). They selectively release N-terminal amino acid residues from polypeptides and proteins and are involved in the processing, catabolism and degradation of intracellular proteins [, , ]. Leucyl aminopeptidase forms a homohexamer containing two trimers stacked on top of one another []. Each monomer binds two zinc ions. The zinc-binding and catalytic sites are located within the C-terminal catalytic domain []. The same catalytic aminopeptidase domain is found in the other M17 peptidases IPR011356 from INTERPRO. These two groups of aminopeptidases differ by their N-terminal domains. The N-terminal domain in members of IPR011356 from INTERPRO has been implicated in DNA binding [, ] and it is not associated with members of this family which have a different N-terminal domain and therefore are not expected to bind DNA or be involved in transcriptional regulation. In addition, there are related proteins with the same catalytic domain and unique N-terminal sequences unrelated to any of the two N-terminal domains discussed above. For additional information please see [, , , ]. ; GO: 0004177 aminopeptidase activity, 0008235 metalloexopeptidase activity, 0030145 manganese ion binding, 0005737 cytoplasm
Probab=25.29 E-value=55 Score=19.38 Aligned_cols=49 Identities=16% Similarity=0.221 Sum_probs=29.0
Q ss_pred EEEEecCCcEEEEEECCCCCCHHHHHHHHHhC-CCceeeecCCCCCccccc
Q psy13022 28 SIKVSLADKEAVITYNPTLVSPKELSEAIYDM-GFDTKVTQVDGKPYVPET 77 (93)
Q Consensus 28 ~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~-Gy~~~~~~~~~~~~~~~~ 77 (93)
++.+++....++|..... ..+..|.++-+++ |-.+..+.-..+.+.+|.
T Consensus 17 ~AllSf~~~ga~IHl~~~-~~l~~IQrAaRkLd~qGI~~V~L~G~~W~lE~ 66 (77)
T PF12404_consen 17 KALLSFNEQGATIHLSEG-DDLRAIQRAARKLDGQGIKNVALAGEGWDLES 66 (77)
T ss_pred CcEEEEcCCCEEEEECCC-cchHHHHHHHHHHhhCCCceEEEecCCcCHHH
Confidence 567888888888887543 5677776654433 222333444455555554
No 116
>PRK15324 type III secretion system lipoprotein PrgK; Provisional
Probab=25.20 E-value=76 Score=22.77 Aligned_cols=23 Identities=17% Similarity=0.177 Sum_probs=18.2
Q ss_pred HHHHHHhhhcCCCceEEEEecCC
Q psy13022 13 SSSKSSMIGARTGVDSIKVSLAD 35 (93)
Q Consensus 13 ~~~Iek~L~~l~GV~~v~v~l~~ 35 (93)
...+++.|..++||..++|.+.-
T Consensus 110 e~ELarTI~~IdgV~~ARVHl~l 132 (252)
T PRK15324 110 EQRLEQSLQTMEGVLSARVHISY 132 (252)
T ss_pred HHHHHHHHHhcCCcceEEEEEEC
Confidence 35678999999999988876544
No 117
>COG0027 PurT Formate-dependent phosphoribosylglycinamide formyltransferase (GAR transformylase) [Nucleotide transport and metabolism]
Probab=25.11 E-value=85 Score=23.88 Aligned_cols=37 Identities=24% Similarity=0.236 Sum_probs=29.1
Q ss_pred CCHHHHHHHHHhCCCceeeecCCCCCccccceeeecc
Q psy13022 47 VSPKELSEAIYDMGFDTKVTQVDGKPYVPETNVNTSA 83 (93)
Q Consensus 47 ~~~~~I~~~I~~~Gy~~~~~~~~~~~~~~~~~~~~~~ 83 (93)
.+.+++.++.+++||++...+.++..=+-...++...
T Consensus 136 ~s~~e~~~a~~~iGfPcvvKPvMSSSGkGqsvv~~~e 172 (394)
T COG0027 136 DSLEELRAAVEKIGFPCVVKPVMSSSGKGQSVVRSPE 172 (394)
T ss_pred ccHHHHHHHHHHcCCCeecccccccCCCCceeecCHH
Confidence 4789999999999999998888777666655555443
No 118
>PF02700 PurS: Phosphoribosylformylglycinamidine (FGAM) synthase; InterPro: IPR003850 Phosphoribosylformylglycinamidine(FGAM) synthetase, 6.3.5.3 from EC, catalyses the fourth step in the de novo purine biosynthetic pathway []. 5-phosphoribosylformylglycinamide (FGAR) + glutamine + ATP = FGAM + glutamate + ADP + Pi In eukaryotes and many bacterial systems (including Escherichia coli and Salmonella typhimurium), the FGAM synthetase is encoded by the large form of PurL (lgPurL), which contains an N-terminal ATPase domain and a C-terminal glutamine-binding domain. In archaeal and other bacterial systems, however, FGAM synthetase is encoded by separate genes, making it a multisubunit (rather than multidomain) enzyme. The protein is composed of the small form of PurL (smPurL), which is homologus to the ATPase domain of lgPurL, PurQ which is homologous to the glutamine-binding domain of of lgPurL, and PurS, whose function is not known. This entry represents the PurS subunit of the multisubunit FGAM synthetase. Recent studies showed that disruption of the purS gene in Bacillus subtilis resulted in a purine auxotrophic phenotype, due to defective FGAM synthetase activity. Therefore, the PurS protein appears to be required for the function of the PurL and PurQ subunits of the FGAM synthetase, but the molecular mechanism for the functional role of PurS is currently not known. For additional information please see [, ].; GO: 0016879 ligase activity, forming carbon-nitrogen bonds; PDB: 2ZW2_B 3D54_B 1VQ3_B 1GTD_A 2YX5_A 2CUW_A 1TWJ_B 1T4A_B 2DGB_B.
Probab=24.75 E-value=1.6e+02 Score=17.25 Aligned_cols=26 Identities=23% Similarity=0.636 Sum_probs=17.1
Q ss_pred EEEEEECCCCCCH--HHHHHHHHhCCCc
Q psy13022 37 EAVITYNPTLVSP--KELSEAIYDMGFD 62 (93)
Q Consensus 37 ~v~V~~d~~~~~~--~~I~~~I~~~Gy~ 62 (93)
.+.|.+.++..++ +.|..++...||.
T Consensus 4 ~V~V~~K~gvlDPqG~ai~~al~~lG~~ 31 (80)
T PF02700_consen 4 RVEVTLKPGVLDPQGEAIKRALHRLGYD 31 (80)
T ss_dssp EEEEEE-TTS--HHHHHHHHHHHHTT-T
T ss_pred EEEEEECCCCcCcHHHHHHHHHHHcCCc
Confidence 3566777776677 4789999999998
No 119
>PF12960 DUF3849: Protein of unknown function (DUF3849); InterPro: IPR024383 This domain is found in a family of uncharacterised proteins found by clustering human gut metagenomic sequences [].
Probab=24.75 E-value=77 Score=20.64 Aligned_cols=35 Identities=14% Similarity=0.375 Sum_probs=25.9
Q ss_pred hhhHHHHHHhhhcCCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHhCCCc
Q psy13022 10 LDKSSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFD 62 (93)
Q Consensus 10 ~~C~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~Gy~ 62 (93)
..|...|+++++. .|+.-.++.+.+.+.|++-||+
T Consensus 27 ~~Ck~aIE~aI~~------------------~~~~~~L~~~a~~~vie~fG~e 61 (133)
T PF12960_consen 27 IACKEAIEQAIRE------------------HFDGNRLDPDAVKEVIEKFGYE 61 (133)
T ss_pred HHHHHHHHHHHHH------------------HcCCCcCCHHHHHHHHHHHHHH
Confidence 4689999999875 3454456677788888888875
No 120
>PRK10503 multidrug efflux system subunit MdtB; Provisional
Probab=24.39 E-value=3.1e+02 Score=23.57 Aligned_cols=45 Identities=13% Similarity=0.280 Sum_probs=31.3
Q ss_pred HHHHHHhhhcCCCceEEEEecCCcEE--EEEECCCCCCH----HHHHHHHHh
Q psy13022 13 SSSKSSMIGARTGVDSIKVSLADKEA--VITYNPTLVSP----KELSEAIYD 58 (93)
Q Consensus 13 ~~~Iek~L~~l~GV~~v~v~l~~~~v--~V~~d~~~~~~----~~I~~~I~~ 58 (93)
...+|++|+.++||..++..-..+.. .+.|+.+ .+. .++.+.|..
T Consensus 73 t~piE~~l~~v~gv~~i~S~S~~G~s~i~v~f~~g-~d~~~a~~ev~~~i~~ 123 (1040)
T PRK10503 73 TAPLERQFGQMSGLKQMSSQSSGGASVITLQFQLT-LPLDVAEQEVQAAINA 123 (1040)
T ss_pred HHHHHHHhcCCCCccEEEEEecCCeEEEEEEEECC-CChHHHHHHHHHHHHH
Confidence 45789999999999999986666654 4567655 344 445555554
No 121
>PRK10555 aminoglycoside/multidrug efflux system; Provisional
Probab=24.19 E-value=2.6e+02 Score=23.97 Aligned_cols=45 Identities=2% Similarity=0.139 Sum_probs=30.7
Q ss_pred HHHHHHhhhcCCCceEEEEecC-C--cEEEEEECCCCCCHH----HHHHHHHh
Q psy13022 13 SSSKSSMIGARTGVDSIKVSLA-D--KEAVITYNPTLVSPK----ELSEAIYD 58 (93)
Q Consensus 13 ~~~Iek~L~~l~GV~~v~v~l~-~--~~v~V~~d~~~~~~~----~I~~~I~~ 58 (93)
...+|++|+.++||..++..-. . ..+.+.|+.. .+.+ ++.+.|..
T Consensus 62 t~plE~~l~~v~gv~~i~S~S~~~G~s~i~v~f~~g-~d~~~a~~~V~~~v~~ 113 (1037)
T PRK10555 62 TQVIEQNMTGLDNLMYMSSQSSGTGQASVTLSFKAG-TDPDEAVQQVQNQLQS 113 (1037)
T ss_pred hHHHHHHhcCCCCceEEEEEecCCCeEEEEEEEECC-CCHHHHHHHHHHHHHH
Confidence 4568999999999999987432 3 4466778766 4554 44555543
No 122
>PF11468 PTase_Orf2: Aromatic prenyltransferase Orf2; InterPro: IPR020965 This entry represents an aromatic prenyltransferase encoded by Orf2 from Streptomyces sp. strain CL190 []. In vivo Orf2 attaches a geranyl group to a 1,3,6,8-tetrahydroxynaphthalene-derived polyketide during naphterpin biosynthesis []. In vitro, Orf2 catalyses carbon-carbon based and carbon-oxygen based prenylation of hydroxyl-containing aromatic acceptors of synthetic, microbial and plant origin []. ; PDB: 1ZDY_A 1ZB6_A 1ZDW_A 1ZCW_A 2XM5_A 2XLQ_A 2XM7_A 2XLY_A.
Probab=24.10 E-value=2.3e+02 Score=20.97 Aligned_cols=60 Identities=8% Similarity=0.198 Sum_probs=41.0
Q ss_pred CCCceEEEEecCCcEEEEEE--CCCCCCHHHHHHHHHhCCCcee---eecCCCCCccccceeeec
Q psy13022 23 RTGVDSIKVSLADKEAVITY--NPTLVSPKELSEAIYDMGFDTK---VTQVDGKPYVPETNVNTS 82 (93)
Q Consensus 23 l~GV~~v~v~l~~~~v~V~~--d~~~~~~~~I~~~I~~~Gy~~~---~~~~~~~~~~~~~~~~~~ 82 (93)
++-|.-+-|++..+++-+-| .++..+.+.+...+.+.|...- .+.-..+.+.--+++|..
T Consensus 147 Ld~V~~vavDy~~rT~NlYF~~~~g~~~~~~v~a~~~e~G~~~Ps~e~l~~~~~af~iy~Tl~wd 211 (292)
T PF11468_consen 147 LDRVRFVAVDYRHRTMNLYFVRSPGPLEAETVAAMLRELGLPPPSEEMLAFCRRAFCIYTTLSWD 211 (292)
T ss_dssp --EEEEEEEETTTTEEEEEESEETTTTSHHHHHHHHHCCT-----HHHHHCCHCSCEEEEEEETT
T ss_pred ccceeEEEeeccCcceEEEEecCCCCcCHHHHHHHHHhcCCCCCCHHHHHHhhcceEEEEEEecC
Confidence 35688999999999999876 4667899999999999998742 223344455555666543
No 123
>PRK11670 antiporter inner membrane protein; Provisional
Probab=24.06 E-value=3.1e+02 Score=20.50 Aligned_cols=74 Identities=18% Similarity=0.119 Sum_probs=45.3
Q ss_pred CceecCCChhhH------HHHHHhhhcCCCceEEEEecCCc------------------EEEEEECCCCCCHH----HHH
Q psy13022 2 GYEVFLPLLDKS------SSKSSMIGARTGVDSIKVSLADK------------------EAVITYNPTLVSPK----ELS 53 (93)
Q Consensus 2 ~~~v~m~c~~C~------~~Iek~L~~l~GV~~v~v~l~~~------------------~v~V~~d~~~~~~~----~I~ 53 (93)
+|.|.++-+.|. ..++.+|+.++|+..+.+.+... .+.|.-.-+..... -+.
T Consensus 50 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vIaV~S~KGGVGKTT~avNLA 129 (369)
T PRK11670 50 HIELVMPFVWNSAFEELKEQCSAELLRITGAKAIDWKLSHNIATLKRVNNQPGVNGVKNIIAVSSGKGGVGKSSTAVNLA 129 (369)
T ss_pred EEEEEECCCCchHHHHHHHHHHHHHHhcCCCceEEEEEeeehhhhccccccccCCCCCEEEEEeCCCCCCCHHHHHHHHH
Confidence 366777777774 35899999999998887655432 11122111112222 345
Q ss_pred HHHHhCCCceeeecCCCCCccc
Q psy13022 54 EAIYDMGFDTKVTQVDGKPYVP 75 (93)
Q Consensus 54 ~~I~~~Gy~~~~~~~~~~~~~~ 75 (93)
.++.+.|+.+.++..+.+....
T Consensus 130 ~aLA~~G~rVlLID~D~qgps~ 151 (369)
T PRK11670 130 LALAAEGAKVGILDADIYGPSI 151 (369)
T ss_pred HHHHHCCCcEEEEeCCCCCCCc
Confidence 6778889998888776665443
No 124
>PRK09579 multidrug efflux protein; Reviewed
Probab=24.03 E-value=3.1e+02 Score=23.54 Aligned_cols=45 Identities=11% Similarity=0.141 Sum_probs=31.5
Q ss_pred HHHHHHhhhcCCCceEEEEecCCcEEE--EEECCCCCCHH----HHHHHHHh
Q psy13022 13 SSSKSSMIGARTGVDSIKVSLADKEAV--ITYNPTLVSPK----ELSEAIYD 58 (93)
Q Consensus 13 ~~~Iek~L~~l~GV~~v~v~l~~~~v~--V~~d~~~~~~~----~I~~~I~~ 58 (93)
...+|++|+.++||.+++..-..+... +.|+.. .+.+ ++.+++.+
T Consensus 64 t~plE~~L~~v~gi~~i~S~S~~G~s~I~v~f~~g-~d~~~a~~~v~~~v~~ 114 (1017)
T PRK09579 64 TQPLQQSLASAEGIDYMTSVSRQNFSIISIYARIG-ADSDRLFTELLAKANE 114 (1017)
T ss_pred HHHHHHHhcCCCCceEEEEEecCCeEEEEEEEECC-CCHHHHHHHHHHHHHH
Confidence 456899999999999999877776554 467655 4554 44555543
No 125
>COG2092 EFB1 Translation elongation factor EF-1beta [Translation, ribosomal structure and biogenesis]
Probab=23.65 E-value=79 Score=19.18 Aligned_cols=20 Identities=20% Similarity=0.391 Sum_probs=17.5
Q ss_pred HHHHHHhhhcCCCceEEEEe
Q psy13022 13 SSSKSSMIGARTGVDSIKVS 32 (93)
Q Consensus 13 ~~~Iek~L~~l~GV~~v~v~ 32 (93)
...++.+|+.++||.++++-
T Consensus 64 td~~ee~l~~vegV~sveve 83 (88)
T COG2092 64 TDALEEALEEVEGVESVEVE 83 (88)
T ss_pred cHHHHHHHhhccCcceEEEE
Confidence 56899999999999988874
No 126
>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=23.63 E-value=93 Score=16.72 Aligned_cols=21 Identities=19% Similarity=0.048 Sum_probs=17.5
Q ss_pred HHHHHHhhhcCCCceEEEEec
Q psy13022 13 SSSKSSMIGARTGVDSIKVSL 33 (93)
Q Consensus 13 ~~~Iek~L~~l~GV~~v~v~l 33 (93)
...+++.|.++|.|.++.+..
T Consensus 36 ~~~~~~~l~~~p~V~~v~V~r 56 (69)
T PF08478_consen 36 LKKIEQRLEKLPWVKSVSVSR 56 (69)
T ss_dssp HHHHHHCCCCTTTEEEEEEEE
T ss_pred HHHHHHHHHcCCCEEEEEEEE
Confidence 456788899999999998874
No 127
>PRK15127 multidrug efflux system protein AcrB; Provisional
Probab=23.47 E-value=2.8e+02 Score=23.86 Aligned_cols=46 Identities=2% Similarity=0.052 Sum_probs=31.8
Q ss_pred HHHHHHhhhcCCCceEEEEecC-C--cEEEEEECCCCCCHH----HHHHHHHhC
Q psy13022 13 SSSKSSMIGARTGVDSIKVSLA-D--KEAVITYNPTLVSPK----ELSEAIYDM 59 (93)
Q Consensus 13 ~~~Iek~L~~l~GV~~v~v~l~-~--~~v~V~~d~~~~~~~----~I~~~I~~~ 59 (93)
...+|+.|..++|+..++..-. . ..+.+.|+.. .+.+ ++.+.|...
T Consensus 62 t~piE~~l~~v~gi~~i~S~S~~~G~s~I~v~f~~g-~d~~~a~~~V~~~i~~~ 114 (1049)
T PRK15127 62 TQVIEQNMNGIDNLMYMSSNSDSTGTVQITLTFESG-TDADIAQVQVQNKLQLA 114 (1049)
T ss_pred hHHHHHHhcCCCCceEEEEEecCCceEEEEEEEECC-CChHHHHHHHHHHHHHH
Confidence 3568999999999999997542 3 3566778765 4554 555666543
No 128
>PF09902 DUF2129: Uncharacterized protein conserved in bacteria (DUF2129); InterPro: IPR016979 This is a group of uncharacterised conserved proteins.
Probab=23.43 E-value=1.5e+02 Score=17.18 Aligned_cols=25 Identities=8% Similarity=-0.102 Sum_probs=14.0
Q ss_pred ChhhHHHHHHhhhcCCCceEEEEec
Q psy13022 9 LLDKSSSKSSMIGARTGVDSIKVSL 33 (93)
Q Consensus 9 c~~C~~~Iek~L~~l~GV~~v~v~l 33 (93)
...-+..+.+.|.+++.|..|+.+.
T Consensus 38 n~~~~e~~~~kl~~l~fVk~Ve~S~ 62 (71)
T PF09902_consen 38 NEEDVEEIIEKLKKLKFVKKVEPSP 62 (71)
T ss_pred CHHHHHHHHHHHhcCCCeeEEeccC
Confidence 3344455555666666666665543
No 129
>TIGR02764 spore_ybaN_pdaB polysaccharide deacetylase family sporulation protein PdaB. This model describes the YbaN protein family, also called PdaB and SpoVIE, of Gram-positive bacteria. Although ybaN null mutants have only a mild sporulation defect, ybaN/ytrI double mutants show drastically reducted sporulation efficiencies. This synthetic defect suggests the role of this sigmaE-controlled gene in sporulation had been masked by functional redundancy. Members of this family are homologous to a characterized polysaccharide deacetylase; the exact function this protein family is unknown.
Probab=23.13 E-value=2.1e+02 Score=18.73 Aligned_cols=32 Identities=9% Similarity=0.287 Sum_probs=19.0
Q ss_pred CCcEEEEEECCCCCC--HHHHHHHHHhCCCceee
Q psy13022 34 ADKEAVITYNPTLVS--PKELSEAIYDMGFDTKV 65 (93)
Q Consensus 34 ~~~~v~V~~d~~~~~--~~~I~~~I~~~Gy~~~~ 65 (93)
..+.+.++||..... ...+.+.+++.|..+..
T Consensus 4 ~~k~V~LTFDDgp~~~~t~~~l~~L~~~~ikaTf 37 (191)
T TIGR02764 4 SDKKIALTFDISWGNDYTEPILDTLKEYDVKATF 37 (191)
T ss_pred CCCEEEEEEECCCCcccHHHHHHHHHHcCCCEEE
Confidence 445666777765432 34566777777666554
No 130
>PRK00435 ef1B elongation factor 1-beta; Validated
Probab=23.12 E-value=98 Score=18.59 Aligned_cols=22 Identities=18% Similarity=0.276 Sum_probs=18.2
Q ss_pred hHHHHHHhhhcCCCceEEEEec
Q psy13022 12 KSSSKSSMIGARTGVDSIKVSL 33 (93)
Q Consensus 12 C~~~Iek~L~~l~GV~~v~v~l 33 (93)
-...++.++++++||+++++.-
T Consensus 63 ~td~lee~i~~~e~Vqsvei~~ 84 (88)
T PRK00435 63 GTEPVEEAFANVEGVESVEVEE 84 (88)
T ss_pred CcHHHHHHHhccCCCcEEEEEE
Confidence 4567899999999999988753
No 131
>PLN02495 oxidoreductase, acting on the CH-CH group of donors
Probab=22.73 E-value=2.7e+02 Score=21.23 Aligned_cols=31 Identities=6% Similarity=0.104 Sum_probs=23.2
Q ss_pred cEEEEEECCCCCCHHHHHHHHHhCCCceeee
Q psy13022 36 KEAVITYNPTLVSPKELSEAIYDMGFDTKVT 66 (93)
Q Consensus 36 ~~v~V~~d~~~~~~~~I~~~I~~~Gy~~~~~ 66 (93)
..+.++..|...++..+.+++.+.|-+....
T Consensus 183 iPv~vKLsPn~t~i~~ia~aa~~~Gadgi~l 213 (385)
T PLN02495 183 VPVWAKMTPNITDITQPARVALKSGCEGVAA 213 (385)
T ss_pred CceEEEeCCChhhHHHHHHHHHHhCCCEEEE
Confidence 4677777776667888999999999876543
No 132
>cd01286 deoxycytidylate_deaminase Deoxycytidylate deaminase domain. Deoxycytidylate deaminase catalyzes the deamination of dCMP to dUMP, providing the nucleotide substrate for thymidylate synthase. The enzyme binds Zn++, which is required for catalytic activity. The activity of the enzyme is allosterically regulated by the ratio of dCTP to dTTP not only in eukaryotic cells but also in T-even phage-infected Escherichia coli, with dCTP acting as an activator and dTTP as an inhibitor.
Probab=22.53 E-value=1.3e+02 Score=19.08 Aligned_cols=24 Identities=13% Similarity=0.335 Sum_probs=16.2
Q ss_pred ceecCCChhhHHHHHHhhhcCCCceEEEE
Q psy13022 3 YEVFLPLLDKSSSKSSMIGARTGVDSIKV 31 (93)
Q Consensus 3 ~~v~m~c~~C~~~Iek~L~~l~GV~~v~v 31 (93)
|.-..||+.|...|-.+ ||..|-+
T Consensus 92 yvT~ePC~~C~~ai~~~-----gI~~Vvy 115 (131)
T cd01286 92 YVTLFPCIECAKLIIQA-----GIKKVVY 115 (131)
T ss_pred EEecCcHHHHHHHHHHh-----CCCEEEE
Confidence 44467899998887553 6665544
No 133
>cd04885 ACT_ThrD-I Tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes each of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=22.19 E-value=1.5e+02 Score=16.10 Aligned_cols=60 Identities=12% Similarity=0.179 Sum_probs=31.3
Q ss_pred eecCC-ChhhHHHHHHhhhcCCCceEEEEec---CCcEEEEEECC-CCCCHHHHHHHHHhCCCce
Q psy13022 4 EVFLP-LLDKSSSKSSMIGARTGVDSIKVSL---ADKEAVITYNP-TLVSPKELSEAIYDMGFDT 63 (93)
Q Consensus 4 ~v~m~-c~~C~~~Iek~L~~l~GV~~v~v~l---~~~~v~V~~d~-~~~~~~~I~~~I~~~Gy~~ 63 (93)
.|.++ .|+--.++-+.|..-.-|..+.-+. ....+.+..+. .....++|.+.+++.||..
T Consensus 2 ~v~ipdkPG~l~~~~~~i~~~~nI~~~~~~~~~~~~~~v~v~ie~~~~~~~~~i~~~L~~~G~~~ 66 (68)
T cd04885 2 AVTFPERPGALKKFLELLGPPRNITEFHYRNQGGDEARVLVGIQVPDREDLAELKERLEALGYPY 66 (68)
T ss_pred EEECCCCCCHHHHHHHHhCCCCcEEEEEEEcCCCCceEEEEEEEeCCHHHHHHHHHHHHHcCCCc
Confidence 44554 3333445555555411244443332 22334444332 2246678899999999975
No 134
>PF10955 DUF2757: Protein of unknown function (DUF2757); InterPro: IPR020115 This entry contains proteins with no known function.
Probab=22.15 E-value=66 Score=18.95 Aligned_cols=16 Identities=13% Similarity=-0.081 Sum_probs=12.5
Q ss_pred ceecCCChhhHHHHHH
Q psy13022 3 YEVFLPLLDKSSSKSS 18 (93)
Q Consensus 3 ~~v~m~c~~C~~~Iek 18 (93)
..|+..|..|...+++
T Consensus 49 i~V~~iCe~C~eaL~~ 64 (76)
T PF10955_consen 49 IHVKVICEDCQEALER 64 (76)
T ss_pred EEEEEecHHHHHHHHh
Confidence 5689999999766654
No 135
>COG1828 PurS Phosphoribosylformylglycinamidine (FGAM) synthase, PurS component [Nucleotide transport and metabolism]
Probab=22.06 E-value=1.9e+02 Score=17.29 Aligned_cols=26 Identities=19% Similarity=0.625 Sum_probs=19.3
Q ss_pred EEEEEECCCCCCH--HHHHHHHHhCCCc
Q psy13022 37 EAVITYNPTLVSP--KELSEAIYDMGFD 62 (93)
Q Consensus 37 ~v~V~~d~~~~~~--~~I~~~I~~~Gy~ 62 (93)
++.|.+.++..+| ..|..++...||.
T Consensus 5 ~V~V~lK~~VlDPqG~ti~~aL~~lg~~ 32 (83)
T COG1828 5 RVYVTLKPGVLDPEGETIEKALHRLGYN 32 (83)
T ss_pred EEEEEeCCcccCchhHHHHHHHHHcCCc
Confidence 3556666665565 4789999999997
No 136
>COG0841 AcrB Cation/multidrug efflux pump [Defense mechanisms]
Probab=22.04 E-value=3.2e+02 Score=23.69 Aligned_cols=47 Identities=11% Similarity=0.255 Sum_probs=32.7
Q ss_pred HHHHHHhhhcCCCceEEEEecCCc--EEEEEECCCCCCHH----HHHHHHHhCC
Q psy13022 13 SSSKSSMIGARTGVDSIKVSLADK--EAVITYNPTLVSPK----ELSEAIYDMG 60 (93)
Q Consensus 13 ~~~Iek~L~~l~GV~~v~v~l~~~--~v~V~~d~~~~~~~----~I~~~I~~~G 60 (93)
...||++++.++|+..++..-..+ .++++|+.+ .+++ ++.++|.++-
T Consensus 63 t~piE~~l~~i~gi~~i~S~S~~G~s~itv~F~~~-~d~d~A~~~V~~kv~~~~ 115 (1009)
T COG0841 63 TQPIEQQLNGLDGLDYMSSTSSSGSSSITVTFELG-TDPDTAAVQVQNKIQQAE 115 (1009)
T ss_pred hHHHHHHHhcCCCccEEEEEEcCCcEEEEEEEeCC-CChHHHHHHHHHHHHHHH
Confidence 457899999999988776554444 456678765 4655 6677776543
No 137
>COG0217 Uncharacterized conserved protein [Function unknown]
Probab=22.00 E-value=1.6e+02 Score=21.22 Aligned_cols=43 Identities=16% Similarity=0.332 Sum_probs=24.2
Q ss_pred HHHhhhcCCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHhCCCcee
Q psy13022 16 KSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDMGFDTK 64 (93)
Q Consensus 16 Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~Gy~~~ 64 (93)
++.+|.. |..++..+ .+...|...| .+...+.++|++.||+..
T Consensus 153 ~e~~iea--gaeDv~~~--~~~~~V~t~p--~~~~~V~~~L~~~g~~~~ 195 (241)
T COG0217 153 LEAAIEA--GAEDVEED--EGSIEVYTEP--EDFNKVKEALEAAGYEIE 195 (241)
T ss_pred HHHHHHC--CchhhhcC--CCeEEEEECh--HHHHHHHHHHHHcCCcee
Confidence 3444443 55555555 4445555443 366677777777776543
No 138
>PF14056 DUF4250: Domain of unknown function (DUF4250)
Probab=21.86 E-value=99 Score=17.01 Aligned_cols=18 Identities=22% Similarity=0.589 Sum_probs=15.5
Q ss_pred CCHHHHHHHHHhCCCcee
Q psy13022 47 VSPKELSEAIYDMGFDTK 64 (93)
Q Consensus 47 ~~~~~I~~~I~~~Gy~~~ 64 (93)
++.++|.+.+..+||...
T Consensus 32 id~~~l~~kL~~~Gy~Y~ 49 (55)
T PF14056_consen 32 IDKEELEEKLASIGYEYD 49 (55)
T ss_pred CCHHHHHHHHHHcCCeEc
Confidence 678899999999999854
No 139
>PF11360 DUF3110: Protein of unknown function (DUF3110); InterPro: IPR021503 This family of proteins has no known function.
Probab=21.77 E-value=1.3e+02 Score=17.91 Aligned_cols=23 Identities=17% Similarity=0.466 Sum_probs=19.0
Q ss_pred CCHHHHHHHHHhCCCceeeecCC
Q psy13022 47 VSPKELSEAIYDMGFDTKVTQVD 69 (93)
Q Consensus 47 ~~~~~I~~~I~~~Gy~~~~~~~~ 69 (93)
++.++|.....+.||.+..++++
T Consensus 55 id~~~i~~fC~~~gy~~~iv~~g 77 (86)
T PF11360_consen 55 IDPEEIEEFCRSAGYEYEIVPPG 77 (86)
T ss_pred ECHHHHHHHHHHCCceEEEECCC
Confidence 56778888889999998888776
No 140
>PF07530 PRE_C2HC: Associated with zinc fingers; InterPro: IPR006579 This domain is present in proteins found exclusively in the arthropods, including a number of Drosophila species, the silk moth and the gypsy moth. These proteins are possibly involved in RNA binding or single strand DNA binding.
Probab=21.67 E-value=1.1e+02 Score=17.27 Aligned_cols=19 Identities=21% Similarity=0.359 Sum_probs=15.3
Q ss_pred HHHHHHHHhCCCceeeecC
Q psy13022 50 KELSEAIYDMGFDTKVTQV 68 (93)
Q Consensus 50 ~~I~~~I~~~Gy~~~~~~~ 68 (93)
++|.+.+++.||.+..+..
T Consensus 2 ~~I~~~L~~~G~~v~~i~~ 20 (68)
T PF07530_consen 2 EEIKEELKDQGHPVRNIHN 20 (68)
T ss_pred HHHHHHHHHcCCceEEEEc
Confidence 5789999999999875533
No 141
>PRK10614 multidrug efflux system subunit MdtC; Provisional
Probab=21.57 E-value=3.8e+02 Score=22.97 Aligned_cols=45 Identities=13% Similarity=0.249 Sum_probs=30.2
Q ss_pred HHHHHHhhhcCCCceEEEEecCCcE--EEEEECCCCCCH----HHHHHHHHh
Q psy13022 13 SSSKSSMIGARTGVDSIKVSLADKE--AVITYNPTLVSP----KELSEAIYD 58 (93)
Q Consensus 13 ~~~Iek~L~~l~GV~~v~v~l~~~~--v~V~~d~~~~~~----~~I~~~I~~ 58 (93)
...+|++|+.++||.+++.....+. +.+.|+.. .+. .++.+.+.+
T Consensus 64 t~piE~~l~~i~gv~~i~S~s~~G~s~i~l~f~~~-~d~~~a~~~v~~~v~~ 114 (1025)
T PRK10614 64 ATPLERSLGRIAGVNEMTSSSSLGSTRIILQFDFD-RDINGAARDVQAAINA 114 (1025)
T ss_pred HHHHHHHhcCCCCceEEEEEecCCeEEEEEEEECC-CChHHHHHHHHHHHHH
Confidence 3578999999999999986555554 44566655 343 345555544
No 142
>PF07194 P2: P2 response regulator binding domain; InterPro: IPR010808 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. The response regulators for CheA bind to the P2 domain, which is found between IPR008207 from INTERPRO and IPR004105 from INTERPRO as either one or two copies. Highly flexible linkers connect P2 to the rest of CheA and impart remarkable mobility to the P2 domain. This feature is thought to enhance the inter CheA dimer phosphotransfer reactions within the signalling complex, thereby amplifying the phosphorylation signal [].; GO: 0000155 two-component sensor activity, 0004673 protein histidine kinase activity, 0000160 two-component signal transduction system (phosphorelay), 0006928 cellular component movement; PDB: 1U0S_A.
Probab=21.25 E-value=95 Score=17.96 Aligned_cols=30 Identities=13% Similarity=0.348 Sum_probs=15.8
Q ss_pred ceecCCChhhHHHHHHhhhcCCCceEEEEe
Q psy13022 3 YEVFLPLLDKSSSKSSMIGARTGVDSIKVS 32 (93)
Q Consensus 3 ~~v~m~c~~C~~~Iek~L~~l~GV~~v~v~ 32 (93)
|.+......-...|++.|.+++.|.+++|.
T Consensus 52 f~~~~~s~~~~e~i~~~l~~~~~V~~v~V~ 81 (84)
T PF07194_consen 52 FDVLFESDEDEEEIEEVLASISEVESVEVE 81 (84)
T ss_dssp EEEEEEESS-HHHHHHHHHTSSS-SEEEEE
T ss_pred EEEEEEeCCCHHHHHHHHhCCCcEEEEEEE
Confidence 333333334455666767777777666653
No 143
>PRK09579 multidrug efflux protein; Reviewed
Probab=20.72 E-value=3.3e+02 Score=23.35 Aligned_cols=46 Identities=9% Similarity=0.115 Sum_probs=34.1
Q ss_pred HHHHHhhhcCCCceEEEEecCCc-EEEEEECC-----CCCCHHHHHHHHHhC
Q psy13022 14 SSKSSMIGARTGVDSIKVSLADK-EAVITYNP-----TLVSPKELSEAIYDM 59 (93)
Q Consensus 14 ~~Iek~L~~l~GV~~v~v~l~~~-~v~V~~d~-----~~~~~~~I~~~I~~~ 59 (93)
..++..|++++||.++++.=... .+.|..|+ -.+++.+|.++|+..
T Consensus 159 ~~i~~~L~~i~GV~~V~~~G~~~~ei~V~vd~~kl~~~gls~~dV~~al~~~ 210 (1017)
T PRK09579 159 RVIQPKLATLPGMAEAEILGNQVFAMRLWLDPVKLAGFGLSAGDVTQAVRRY 210 (1017)
T ss_pred HHHHHHhhcCCCceEEEecCCCceEEEEEeCHHHHHHcCCCHHHHHHHHHHh
Confidence 56889999999999998653332 45666665 236888999999775
No 144
>COG3062 NapD Uncharacterized protein involved in formation of periplasmic nitrate reductase [Inorganic ion transport and metabolism]
Probab=20.40 E-value=2.2e+02 Score=17.45 Aligned_cols=47 Identities=15% Similarity=0.160 Sum_probs=31.6
Q ss_pred hhhHHHHHHhhhcCCCceEEEEecCCcEEEEEECCCCCCHHHHHHHHHhC
Q psy13022 10 LDKSSSKSSMIGARTGVDSIKVSLADKEAVITYNPTLVSPKELSEAIYDM 59 (93)
Q Consensus 10 ~~C~~~Iek~L~~l~GV~~v~v~l~~~~v~V~~d~~~~~~~~I~~~I~~~ 59 (93)
|.=-..|...|..+||+.--.-+.. +++.|..+. .+.+.+.+.++..
T Consensus 17 pe~l~av~~~L~~ip~~EV~~~d~~-GKlVVVie~--~~~~~l~~tie~i 63 (94)
T COG3062 17 PERLSAVKTALLAIPGCEVYGEDAE-GKLVVVIEA--EDSETLLETIESI 63 (94)
T ss_pred HHHHHHHHHHHhcCCCcEeeccCCC-ceEEEEEEc--CchHHHHHHHHHH
Confidence 3345678899999999865555555 677776654 3666777766543
No 145
>PF07862 Nif11: Nitrogen fixation protein of unknown function; InterPro: IPR012903 This domain is found in the cyanobacteria, and the nitrogen-fixing proteobacterium Azotobacter vinelandii and may be involved in nitrogen fixation, but no role has been assigned [].
Probab=20.35 E-value=1.1e+02 Score=15.75 Aligned_cols=18 Identities=22% Similarity=0.466 Sum_probs=15.1
Q ss_pred CCHHHHHHHHHhCCCcee
Q psy13022 47 VSPKELSEAIYDMGFDTK 64 (93)
Q Consensus 47 ~~~~~I~~~I~~~Gy~~~ 64 (93)
.++++++....+.||...
T Consensus 27 ~~~~e~~~lA~~~Gy~ft 44 (49)
T PF07862_consen 27 QNPEEVVALAREAGYDFT 44 (49)
T ss_pred CCHHHHHHHHHHcCCCCC
Confidence 378899999999999864
No 146
>CHL00193 ycf35 Ycf35; Provisional
Probab=20.27 E-value=1.4e+02 Score=19.12 Aligned_cols=31 Identities=23% Similarity=0.167 Sum_probs=22.3
Q ss_pred CCHHHHHHHHHhCCCceeeecCCCCCccccc
Q psy13022 47 VSPKELSEAIYDMGFDTKVTQVDGKPYVPET 77 (93)
Q Consensus 47 ~~~~~I~~~I~~~Gy~~~~~~~~~~~~~~~~ 77 (93)
.+++.|..++.+.||.+......-+.|.-+|
T Consensus 12 ~d~~~L~~AL~dLg~~~~~~~~~vrgy~gq~ 42 (128)
T CHL00193 12 QNLNLLKKALNDLNIEWKKENQVIKGYNGQT 42 (128)
T ss_pred cCHHHHHHHHHHcCCCceeCCceeeccCCCe
Confidence 5788999999999999866444444444443
Done!