Query 033498
Match_columns 118
No_of_seqs 192 out of 1534
Neff 7.8
Searched_HMMs 46136
Date Fri Mar 29 02:58:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033498.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033498hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1575 Voltage-gated shaker-l 99.7 4.1E-17 9E-22 124.8 10.2 82 17-98 254-335 (336)
2 COG0667 Tas Predicted oxidored 99.7 3.3E-16 7E-21 119.6 10.1 81 9-89 230-310 (316)
3 PRK10625 tas putative aldo-ket 99.6 3.1E-15 6.6E-20 115.0 9.8 72 17-88 268-339 (346)
4 TIGR01293 Kv_beta voltage-depe 99.6 5.6E-15 1.2E-19 112.3 9.1 69 18-86 246-316 (317)
5 PRK09912 L-glyceraldehyde 3-ph 99.6 1.8E-14 3.9E-19 110.9 9.3 73 17-89 261-334 (346)
6 PRK11565 dkgA 2,5-diketo-D-glu 99.5 2.6E-13 5.6E-18 101.6 9.3 63 24-88 200-262 (275)
7 COG0656 ARA1 Aldo/keto reducta 99.5 2.8E-13 6E-18 101.8 8.8 66 23-90 201-266 (280)
8 PRK10376 putative oxidoreducta 99.5 2.8E-13 6E-18 102.0 8.4 66 23-88 223-288 (290)
9 PLN02587 L-galactose dehydroge 99.5 4E-13 8.6E-18 102.0 9.2 72 17-88 225-300 (314)
10 PF00248 Aldo_ket_red: Aldo/ke 99.4 2.1E-13 4.4E-18 101.4 6.5 69 19-87 214-282 (283)
11 PRK11172 dkgB 2,5-diketo-D-glu 99.4 1.6E-12 3.4E-17 96.9 8.1 63 24-88 190-252 (267)
12 KOG1577 Aldo/keto reductase fa 99.4 2.5E-12 5.4E-17 97.2 7.6 66 22-89 221-286 (300)
13 COG4989 Predicted oxidoreducta 99.3 1.7E-11 3.6E-16 90.8 9.4 86 1-88 206-293 (298)
14 cd06660 Aldo_ket_red Aldo-keto 99.3 2E-11 4.4E-16 90.7 8.4 64 22-85 221-284 (285)
15 PRK14863 bifunctional regulato 99.2 1.4E-11 3.1E-16 93.0 6.5 68 18-85 212-279 (292)
16 COG1453 Predicted oxidoreducta 98.6 2.1E-07 4.5E-12 72.2 6.9 64 24-87 216-284 (391)
17 KOG1576 Predicted oxidoreducta 98.2 2.4E-05 5.1E-10 59.1 10.1 69 8-77 242-310 (342)
18 PF10668 Phage_terminase: Phag 86.0 2.2 4.8E-05 25.0 4.2 29 13-41 6-40 (60)
19 PF00356 LacI: Bacterial regul 84.3 2.6 5.7E-05 23.2 3.8 42 26-73 2-43 (46)
20 PF01402 RHH_1: Ribbon-helix-h 77.7 5.1 0.00011 20.6 3.4 23 21-43 9-31 (39)
21 PF11242 DUF2774: Protein of u 74.2 5.6 0.00012 23.5 3.1 21 26-46 16-36 (63)
22 PF01527 HTH_Tnp_1: Transposas 70.8 6.3 0.00014 23.1 3.0 41 7-48 3-47 (76)
23 PF14502 HTH_41: Helix-turn-he 67.3 5.6 0.00012 22.3 2.0 31 22-52 5-37 (48)
24 PF06603 UpxZ: UpxZ family of 67.2 30 0.00064 22.6 5.6 66 2-69 14-82 (106)
25 PF12651 RHH_3: Ribbon-helix-h 64.5 14 0.00031 19.9 3.3 22 20-41 11-32 (44)
26 PF11020 DUF2610: Domain of un 62.1 25 0.00054 21.8 4.3 29 17-45 48-76 (82)
27 PF13518 HTH_28: Helix-turn-he 57.1 17 0.00037 19.4 2.9 22 25-47 14-35 (52)
28 PF13700 DUF4158: Domain of un 55.8 15 0.00032 25.3 3.0 44 21-67 119-164 (166)
29 TIGR03070 couple_hipB transcri 55.2 21 0.00047 19.2 3.1 20 24-43 5-24 (58)
30 PRK09413 IS2 repressor TnpA; R 54.4 32 0.0007 22.4 4.3 46 2-48 4-53 (121)
31 COG1026 Predicted Zn-dependent 52.1 57 0.0012 29.2 6.4 79 10-88 407-493 (978)
32 PF08418 Pol_alpha_B_N: DNA po 50.7 18 0.00039 26.5 2.9 50 19-69 8-60 (253)
33 PRK11675 LexA regulated protei 48.1 28 0.00061 22.1 3.1 24 20-43 59-82 (90)
34 PF01476 LysM: LysM domain; I 47.8 22 0.00048 18.3 2.3 19 24-42 7-25 (44)
35 PF07027 DUF1318: Protein of u 46.8 53 0.0012 20.9 4.2 29 17-45 44-72 (95)
36 PF10723 RepB-RCR_reg: Replica 45.1 42 0.00091 20.8 3.5 26 21-46 51-76 (84)
37 COG0497 RecN ATPase involved i 43.5 37 0.00081 28.4 3.9 60 11-70 294-353 (557)
38 COG5484 Uncharacterized conser 43.2 20 0.00043 27.2 2.1 24 25-49 21-44 (279)
39 PRK08561 rps15p 30S ribosomal 42.9 1.1E+02 0.0024 21.2 6.7 72 12-87 22-96 (151)
40 PF13467 RHH_4: Ribbon-helix-h 40.5 36 0.00077 20.3 2.5 26 22-47 22-47 (67)
41 COG2307 Uncharacterized protei 39.6 25 0.00054 27.3 2.2 70 18-89 46-115 (313)
42 COG1564 THI80 Thiamine pyropho 39.3 73 0.0016 23.3 4.5 40 32-71 74-115 (212)
43 PF14096 DUF4274: Domain of un 38.2 37 0.0008 20.3 2.4 28 24-51 5-32 (77)
44 TIGR02899 spore_safA spore coa 37.6 43 0.00094 16.7 2.4 17 25-41 6-22 (44)
45 PF02796 HTH_7: Helix-turn-hel 37.2 37 0.0008 18.1 2.1 15 25-39 23-37 (45)
46 PHA01623 hypothetical protein 36.9 64 0.0014 18.3 3.2 21 20-40 22-42 (56)
47 PRK10558 alpha-dehydro-beta-de 35.7 1.6E+02 0.0035 21.9 6.0 51 23-73 58-115 (256)
48 cd01068 sensor_globin Globin d 35.3 93 0.002 20.3 4.3 74 17-90 14-92 (147)
49 COG0350 Ada Methylated DNA-pro 35.0 64 0.0014 22.5 3.6 34 26-59 108-141 (168)
50 PF12551 PHBC_N: Poly-beta-hyd 34.6 37 0.0008 18.7 1.8 13 33-45 22-34 (46)
51 PF12244 DUF3606: Protein of u 34.6 49 0.0011 18.9 2.4 20 24-43 21-40 (57)
52 PHA01748 hypothetical protein 34.0 78 0.0017 18.2 3.3 23 20-42 11-33 (60)
53 PF00816 Histone_HNS: H-NS his 33.9 42 0.00091 20.7 2.3 23 18-40 21-43 (93)
54 PF12162 STAT1_TAZ2bind: STAT1 33.8 24 0.00052 16.6 0.8 15 73-87 8-22 (23)
55 PF07862 Nif11: Nitrogen fixat 33.6 71 0.0015 17.2 2.9 23 58-80 26-48 (49)
56 PHA01976 helix-turn-helix prot 33.3 36 0.00079 19.2 1.8 11 28-38 20-30 (67)
57 smart00657 RPOL4c DNA-directed 32.9 1.4E+02 0.0031 19.4 6.3 59 21-89 55-113 (118)
58 PRK09726 antitoxin HipB; Provi 32.6 79 0.0017 19.2 3.4 26 22-47 13-38 (88)
59 PF12668 DUF3791: Protein of u 32.5 98 0.0021 17.7 3.6 23 23-45 5-27 (62)
60 PF11563 Protoglobin: Protoglo 32.5 49 0.0011 21.9 2.6 74 17-90 16-94 (158)
61 PF06971 Put_DNA-bind_N: Putat 32.1 48 0.001 18.5 2.1 13 28-40 33-45 (50)
62 TIGR01378 thi_PPkinase thiamin 31.5 86 0.0019 22.4 3.8 40 32-71 69-110 (203)
63 KOG0693 Myo-inositol-1-phospha 31.2 76 0.0016 25.6 3.7 74 17-92 204-278 (512)
64 PF04967 HTH_10: HTH DNA bindi 31.1 63 0.0014 18.2 2.5 16 26-41 26-41 (53)
65 PF02570 CbiC: Precorrin-8X me 31.0 1.2E+02 0.0025 22.0 4.4 35 25-59 94-128 (198)
66 PF13443 HTH_26: Cro/C1-type H 30.8 20 0.00044 20.1 0.4 13 27-39 14-26 (63)
67 PRK10945 gene expression modul 30.7 1.2E+02 0.0025 18.4 3.7 31 57-87 17-47 (72)
68 TIGR02384 RelB_DinJ addiction 30.6 1.2E+02 0.0027 18.5 4.0 30 21-50 12-44 (83)
69 COG0761 lytB 4-Hydroxy-3-methy 30.5 79 0.0017 24.4 3.6 44 24-68 228-277 (294)
70 cd00086 homeodomain Homeodomai 30.2 96 0.0021 16.6 3.2 25 23-47 27-51 (59)
71 PLN02438 inositol-3-phosphate 30.1 1.2E+02 0.0027 25.1 4.9 73 16-90 203-276 (510)
72 PRK00901 methylated-DNA--prote 29.9 80 0.0017 21.8 3.3 35 25-59 92-126 (155)
73 PF13404 HTH_AsnC-type: AsnC-t 29.7 94 0.002 16.4 2.9 19 26-44 20-38 (42)
74 PF10771 DUF2582: Protein of u 29.7 61 0.0013 19.2 2.3 26 26-51 25-52 (65)
75 PF07836 DmpG_comm: DmpG-like 29.6 88 0.0019 18.6 3.0 25 23-47 22-46 (66)
76 COG2963 Transposase and inacti 29.5 1.3E+02 0.0029 19.0 4.2 38 8-46 5-47 (116)
77 COG0673 MviM Predicted dehydro 29.1 1.6E+02 0.0035 22.0 5.1 66 25-90 42-117 (342)
78 TIGR02530 flg_new flagellar op 29.0 72 0.0016 20.4 2.7 29 61-89 18-46 (96)
79 PRK10328 DNA binding protein, 28.9 1E+02 0.0023 20.8 3.7 23 18-40 53-75 (134)
80 smart00354 HTH_LACI helix_turn 28.8 1.2E+02 0.0027 17.5 4.5 45 26-76 3-47 (70)
81 PF13936 HTH_38: Helix-turn-he 28.6 65 0.0014 17.1 2.2 16 25-40 22-37 (44)
82 PRK09943 DNA-binding transcrip 28.4 64 0.0014 22.4 2.7 56 19-74 5-62 (185)
83 PRK10869 recombination and rep 28.4 86 0.0019 26.1 3.8 36 10-46 292-327 (553)
84 PRK10128 2-keto-3-deoxy-L-rham 28.1 2.6E+02 0.0056 21.1 6.0 35 39-73 80-114 (267)
85 PRK10014 DNA-binding transcrip 28.0 1.1E+02 0.0025 22.6 4.2 44 25-74 8-51 (342)
86 PF07498 Rho_N: Rho terminatio 27.8 40 0.00086 18.0 1.2 14 23-36 7-20 (43)
87 smart00342 HTH_ARAC helix_turn 27.7 1.2E+02 0.0026 17.0 3.9 22 26-47 4-25 (84)
88 PF00046 Homeobox: Homeobox do 27.5 1.1E+02 0.0024 16.5 3.6 25 22-46 26-50 (57)
89 PF04221 RelB: RelB antitoxin; 27.4 1.4E+02 0.003 18.1 3.8 30 21-50 11-43 (83)
90 TIGR03239 GarL 2-dehydro-3-deo 27.3 2.6E+02 0.0056 20.7 5.9 48 26-73 54-108 (249)
91 PRK13702 replication protein; 27.1 1.4E+02 0.0031 18.7 3.7 26 22-47 52-77 (85)
92 PRK08286 cbiC cobalt-precorrin 27.0 74 0.0016 23.4 2.8 45 26-70 108-154 (214)
93 TIGR03798 ocin_TIGR03798 bacte 26.7 1.3E+02 0.0028 17.3 3.4 27 57-83 23-49 (64)
94 PF13833 EF-hand_8: EF-hand do 26.7 1.1E+02 0.0024 16.2 3.3 30 59-88 5-35 (54)
95 PRK06424 transcription factor; 26.5 1.6E+02 0.0036 20.0 4.3 25 20-44 83-107 (144)
96 PRK14981 DNA-directed RNA poly 26.3 1.3E+02 0.0028 19.5 3.7 33 56-88 76-108 (112)
97 PF04760 IF2_N: Translation in 26.2 44 0.00095 18.4 1.3 18 26-43 6-23 (54)
98 PRK09526 lacI lac repressor; R 25.9 1.4E+02 0.003 22.2 4.3 43 25-73 7-49 (342)
99 PF03869 Arc: Arc-like DNA bin 25.8 1.3E+02 0.0027 16.6 3.5 20 21-40 14-33 (50)
100 smart00389 HOX Homeodomain. DN 25.6 1.2E+02 0.0026 16.2 3.3 25 23-47 27-51 (56)
101 PF05119 Terminase_4: Phage te 25.4 1.3E+02 0.0028 18.3 3.5 25 15-39 62-86 (100)
102 PF13744 HTH_37: Helix-turn-he 25.3 23 0.00051 21.3 -0.0 57 17-73 14-73 (80)
103 PRK09492 treR trehalose repres 24.9 1.3E+02 0.0027 22.1 3.9 43 25-73 6-48 (315)
104 PF04218 CENP-B_N: CENP-B N-te 24.8 37 0.0008 18.9 0.8 12 34-45 22-33 (53)
105 PF13384 HTH_23: Homeodomain-l 24.5 85 0.0018 16.5 2.2 22 25-47 19-40 (50)
106 PF05534 HicB: HicB family; I 24.4 1.4E+02 0.003 16.5 3.6 22 21-42 27-48 (51)
107 PRK10727 DNA-binding transcrip 24.4 1.8E+02 0.004 21.6 4.7 43 26-74 4-46 (343)
108 PRK01045 ispH 4-hydroxy-3-meth 24.3 1.4E+02 0.0031 22.9 4.1 43 25-68 227-275 (298)
109 TIGR01481 ccpA catabolite cont 24.2 1.9E+02 0.0042 21.2 4.8 43 26-74 4-46 (329)
110 PF04545 Sigma70_r4: Sigma-70, 24.1 95 0.0021 16.5 2.4 15 26-40 23-37 (50)
111 PF05673 DUF815: Protein of un 23.9 98 0.0021 23.3 3.0 42 22-68 199-245 (249)
112 PF00984 UDPG_MGDP_dh: UDP-glu 23.8 2E+02 0.0042 18.1 5.1 40 17-57 16-57 (96)
113 PF00165 HTH_AraC: Bacterial r 23.4 1.2E+02 0.0026 15.5 2.9 23 25-47 10-32 (42)
114 PRK10423 transcriptional repre 23.2 1.4E+02 0.003 22.0 3.8 16 27-42 2-17 (327)
115 PRK06552 keto-hydroxyglutarate 23.2 1.2E+02 0.0025 22.1 3.3 48 39-88 99-154 (213)
116 TIGR01761 thiaz-red thiazoliny 23.0 2.9E+02 0.0064 21.5 5.7 66 24-90 39-114 (343)
117 cd01392 HTH_LacI Helix-turn-he 22.7 1.3E+02 0.0029 15.8 3.5 42 28-75 2-43 (52)
118 PF02401 LYTB: LytB protein; 22.6 1E+02 0.0022 23.5 3.0 44 24-68 225-274 (281)
119 cd00118 LysM Lysin domain, fou 22.5 1.1E+02 0.0023 14.5 2.5 17 25-41 10-26 (46)
120 smart00760 Bac_DnaA_C Bacteria 22.4 1.1E+02 0.0025 17.1 2.6 17 24-40 4-20 (60)
121 PHA00617 ribbon-helix-helix do 22.4 1.6E+02 0.0034 18.2 3.2 23 20-42 48-70 (80)
122 cd07995 TPK Thiamine pyrophosp 22.3 1.5E+02 0.0033 21.0 3.7 39 33-71 74-114 (208)
123 TIGR02311 HpaI 2,4-dihydroxyhe 22.3 1.6E+02 0.0034 21.8 3.9 34 40-73 75-108 (249)
124 PRK11235 bifunctional antitoxi 22.2 2E+02 0.0044 17.6 4.0 29 22-50 12-43 (80)
125 PRK12360 4-hydroxy-3-methylbut 22.1 1.3E+02 0.0029 22.9 3.5 43 25-68 226-274 (281)
126 PHA00675 hypothetical protein 22.1 2E+02 0.0044 17.7 3.9 11 28-38 44-54 (78)
127 COG0182 Predicted translation 21.9 51 0.0011 25.9 1.2 29 33-61 208-239 (346)
128 PF13167 GTP-bdg_N: GTP-bindin 21.8 88 0.0019 19.9 2.1 66 21-88 8-80 (95)
129 TIGR02405 trehalos_R_Ecol treh 21.4 2E+02 0.0042 21.2 4.3 42 26-73 4-45 (311)
130 PF08840 BAAT_C: BAAT / Acyl-C 21.3 83 0.0018 22.4 2.2 33 39-71 7-42 (213)
131 PF11116 DUF2624: Protein of u 21.2 2.2E+02 0.0048 17.8 4.1 29 60-88 16-44 (85)
132 PF08765 Mor: Mor transcriptio 21.2 89 0.0019 19.9 2.1 15 34-48 72-86 (108)
133 COG1609 PurR Transcriptional r 21.1 1.9E+02 0.004 22.1 4.2 43 26-74 3-45 (333)
134 PF01371 Trp_repressor: Trp re 21.1 1E+02 0.0023 19.2 2.4 15 27-41 53-67 (87)
135 PRK10703 DNA-binding transcrip 20.8 1.8E+02 0.0039 21.6 4.0 42 26-73 4-45 (341)
136 TIGR00277 HDIG uncharacterized 20.7 1.7E+02 0.0038 16.3 4.8 35 14-48 4-38 (80)
137 PRK00819 RNA 2'-phosphotransfe 20.6 2E+02 0.0043 20.4 4.0 48 41-88 12-63 (179)
138 COG4321 Uncharacterized protei 20.6 1.1E+02 0.0024 19.8 2.4 21 22-42 35-55 (102)
139 TIGR00216 ispH_lytB (E)-4-hydr 20.5 1.4E+02 0.0031 22.7 3.4 44 24-68 224-273 (280)
140 TIGR00789 flhB_rel flhB C-term 20.5 1.3E+02 0.0027 18.6 2.6 28 21-48 27-55 (82)
141 COG3784 Uncharacterized protei 20.3 1.9E+02 0.004 18.8 3.4 23 19-41 60-82 (109)
142 KOG1461 Translation initiation 20.3 1.6E+02 0.0035 25.3 3.8 44 34-77 54-97 (673)
143 PF03861 ANTAR: ANTAR domain; 20.2 1.7E+02 0.0037 16.2 3.0 18 24-41 35-52 (56)
144 PF11017 DUF2855: Protein of u 20.1 38 0.00083 26.3 0.2 50 36-85 146-197 (314)
145 TIGR00190 thiC thiamine biosyn 20.0 97 0.0021 25.1 2.5 42 21-69 203-244 (423)
No 1
>KOG1575 consensus Voltage-gated shaker-like K+ channel, subunit beta/KCNAB [Energy production and conversion]
Probab=99.72 E-value=4.1e-17 Score=124.77 Aligned_cols=82 Identities=51% Similarity=0.728 Sum_probs=77.1
Q ss_pred HhhHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhhcCCCCCHHHHHHHHhhhcCCCcCCCC
Q 033498 17 EHNKKLFERVNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKALSVKLTPEEIAELESIASADAVRGHR 96 (118)
Q Consensus 17 ~~~~~~~~~l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~~~~Ls~e~~~~l~~~~~~~~~~~~~ 96 (118)
..++.+++.+.++|+++|+|++|+||+|+++++.+++||||+++++||+||++|+.+.|+++++..|+++.+.....+.+
T Consensus 254 ~~~~~~~~~~~~iA~k~g~T~~qlALawv~~~~~v~~pIpG~s~ve~l~eni~Al~~~Lt~e~~~~l~~~~~~~~~~~~~ 333 (336)
T KOG1575|consen 254 DKQKPILEALSKIAEKHGCTVPQLALAWVLSNGKVSSPIPGASKIEQLKENIGALSVKLTPEEIKELEEIIDKILGFGPR 333 (336)
T ss_pred hhHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhCCCEEecCCCCcHHHHHHHHhhhhccCCHHHHHHHHHhhccccCcCCC
Confidence 66888999999999999999999999999999999999999999999999999999999999999999999987777776
Q ss_pred CC
Q 033498 97 YG 98 (118)
Q Consensus 97 ~~ 98 (118)
+.
T Consensus 334 ~~ 335 (336)
T KOG1575|consen 334 SI 335 (336)
T ss_pred CC
Confidence 63
No 2
>COG0667 Tas Predicted oxidoreductases (related to aryl-alcohol dehydrogenases) [Energy production and conversion]
Probab=99.68 E-value=3.3e-16 Score=119.58 Aligned_cols=81 Identities=42% Similarity=0.639 Sum_probs=76.4
Q ss_pred CCCCccchHhhHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhhcCCCCCHHHHHHHHhhhc
Q 033498 9 PRFQPENLEHNKKLFERVNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKALSVKLTPEEIAELESIAS 88 (118)
Q Consensus 9 ~~~~~~~~~~~~~~~~~l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~~~~Ls~e~~~~l~~~~~ 88 (118)
++|..+.++++..+++.++++|+++|+|++|+||+|++++|.+++||+|+++++||++|+++.++.|++++++.|++...
T Consensus 230 ~~~~~~~~~~~~~~~~~l~~~a~~~g~t~aq~ALawvl~~~~v~~~I~Ga~~~~qL~en~~A~~~~L~~~~~~~l~~~~~ 309 (316)
T COG0667 230 PRFQRELTERGLAILRALEELAKELGATPAQVALAWVLAQPGVTSPIVGASKAEQLEENLAALDIKLSEEELAALDEISA 309 (316)
T ss_pred ccchhhhhHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHhCCCCceEeecCCCHHHHHHHHHHhcCCCCHHHHHHHHHHhh
Confidence 56777788999999999999999999999999999999999999999999999999999999999999999999998876
Q ss_pred C
Q 033498 89 A 89 (118)
Q Consensus 89 ~ 89 (118)
.
T Consensus 310 ~ 310 (316)
T COG0667 310 E 310 (316)
T ss_pred h
Confidence 4
No 3
>PRK10625 tas putative aldo-keto reductase; Provisional
Probab=99.62 E-value=3.1e-15 Score=114.98 Aligned_cols=72 Identities=31% Similarity=0.462 Sum_probs=68.2
Q ss_pred HhhHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhhcCCCCCHHHHHHHHhhhc
Q 033498 17 EHNKKLFERVNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKALSVKLTPEEIAELESIAS 88 (118)
Q Consensus 17 ~~~~~~~~~l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~~~~Ls~e~~~~l~~~~~ 88 (118)
+.+++.++.++++|+++|+|++|+||+|++++|.++++|+|+++++||++|+++.+++|++++++.|+++.+
T Consensus 268 ~~~~~~~~~l~~la~~~g~t~aqval~w~l~~~~v~~~I~G~~~~~~l~en~~a~~~~L~~~~~~~l~~~~~ 339 (346)
T PRK10625 268 EQTQKAVAAYVDIAKRHGLDPAQMALAFVRRQPFVASTLLGATTMEQLKTNIESLHLTLSEEVLAEIEAVHQ 339 (346)
T ss_pred hhHHHHHHHHHHHHHHhCCCHHHHHHHHHHhCCCCeeEEeCCCCHHHHHHHHhhccCCCCHHHHHHHHHHHh
Confidence 556778899999999999999999999999999999999999999999999999999999999999999875
No 4
>TIGR01293 Kv_beta voltage-dependent potassium channel beta subunit, animal. Plant beta subunits and their closely related bacterial homologs (in Deinococcus radiudurans, Xylella fastidiosa, etc.) appear more closely related to each other than to animal forms. However, the bacterial species lack convincing counterparts the Kv alpha subunit and the Kv beta homolog may serve as an enzyme. Cutoffs are set for this model such that yeast and plant forms and bacterial close homologs score between trusted and noise cutoffs.
Probab=99.59 E-value=5.6e-15 Score=112.33 Aligned_cols=69 Identities=30% Similarity=0.511 Sum_probs=64.6
Q ss_pred hhHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhhcCC--CCCHHHHHHHHhh
Q 033498 18 HNKKLFERVNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKALSV--KLTPEEIAELESI 86 (118)
Q Consensus 18 ~~~~~~~~l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~~~--~Ls~e~~~~l~~~ 86 (118)
...+.++.|+++|+++|+|++|+||+|++++|.++++|||+++++|+++|+++.++ +|+++++++|+++
T Consensus 246 ~~~~~~~~l~~ia~~~g~s~aqlal~w~l~~~~v~~~i~G~~~~~ql~en~~a~~~~~~Ls~e~~~~l~~~ 316 (317)
T TIGR01293 246 RQQARLKDLQAIAERLGCTLPQLAIAWCLRNEGVSSVLLGASSAEQLMENLGSLQVLPKLSSSIIHEIDSI 316 (317)
T ss_pred HHHHHHHHHHHHHHHHCcCHHHHHHHHHhcCCCCeEEEeCCCCHHHHHHHHHHhhccCCCCHHHHHHHHhh
Confidence 45677889999999999999999999999999999999999999999999999987 9999999999875
No 5
>PRK09912 L-glyceraldehyde 3-phosphate reductase; Provisional
Probab=99.56 E-value=1.8e-14 Score=110.88 Aligned_cols=73 Identities=26% Similarity=0.499 Sum_probs=67.8
Q ss_pred HhhHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhhc-CCCCCHHHHHHHHhhhcC
Q 033498 17 EHNKKLFERVNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKAL-SVKLTPEEIAELESIASA 89 (118)
Q Consensus 17 ~~~~~~~~~l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~-~~~Ls~e~~~~l~~~~~~ 89 (118)
+++++.++.++++|+++|+|++|+||+|++++|.+++||||+++++||++|+++. +++|++++++.|++++..
T Consensus 261 ~~~~~~~~~l~~~a~~~g~t~aq~AL~w~l~~~~v~~~i~G~~~~~ql~en~~a~~~~~L~~e~~~~l~~~~~~ 334 (346)
T PRK09912 261 EANLNSLRLLNEMAQQRGQSMAQMALSWLLKDERVTSVLIGASRAEQLEENVQALNNLTFSTEELAQIDQHIAD 334 (346)
T ss_pred HHHHHHHHHHHHHHHHhCCCHHHHHHHHHHhCCCCeEEEeCCCCHHHHHHHHhhhcCCCCCHHHHHHHHHhhCc
Confidence 4567788999999999999999999999999999999999999999999999998 589999999999998754
No 6
>PRK11565 dkgA 2,5-diketo-D-gluconate reductase A; Provisional
Probab=99.48 E-value=2.6e-13 Score=101.58 Aligned_cols=63 Identities=22% Similarity=0.471 Sum_probs=59.0
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhhcCCCCCHHHHHHHHhhhc
Q 033498 24 ERVNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKALSVKLTPEEIAELESIAS 88 (118)
Q Consensus 24 ~~l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~~~~Ls~e~~~~l~~~~~ 88 (118)
+.|+++|+++|+|++|+||+|+++++ .+||||+++++|+++|+++.++.|++++++.|+.+..
T Consensus 200 ~~l~~ia~~~g~s~aq~aL~w~l~~~--~~~I~g~~~~~~i~~n~~a~~~~Ls~~~~~~i~~~~~ 262 (275)
T PRK11565 200 KVIRDLADKYGKTPAQIVIRWHLDSG--LVVIPKSVTPSRIAENFDVFDFRLDKDELGEIAKLDQ 262 (275)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHcCC--CEeeCCCCCHHHHHHHHhccCCCcCHHHHHHHHhhcc
Confidence 56889999999999999999999997 5699999999999999999999999999999999864
No 7
>COG0656 ARA1 Aldo/keto reductases, related to diketogulonate reductase [General function prediction only]
Probab=99.47 E-value=2.8e-13 Score=101.82 Aligned_cols=66 Identities=30% Similarity=0.489 Sum_probs=62.1
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhhcCCCCCHHHHHHHHhhhcCC
Q 033498 23 FERVNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKALSVKLTPEEIAELESIASAD 90 (118)
Q Consensus 23 ~~~l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~~~~Ls~e~~~~l~~~~~~~ 90 (118)
-..++.||++||.|++|++|+|+++++ ++|||.+++++|++||++++++.||++|++.|+++....
T Consensus 201 ~~~l~~Ia~k~g~t~AQv~L~W~i~~g--v~~Ipks~~~~ri~eN~~~~~f~Ls~ed~~~i~~l~~~~ 266 (280)
T COG0656 201 NPVLAEIAKKYGKTPAQVALRWHIQRG--VIVIPKSTTPERIRENLAAFDFELSEEDMAAIDALDRGY 266 (280)
T ss_pred ChHHHHHHHHhCCCHHHHHHHHHHhCC--cEEecCCCCHHHHHHHHhhhcCCCCHHHHHHHHhhcccc
Confidence 357899999999999999999999999 899999999999999999999999999999999998754
No 8
>PRK10376 putative oxidoreductase; Provisional
Probab=99.46 E-value=2.8e-13 Score=101.98 Aligned_cols=66 Identities=33% Similarity=0.569 Sum_probs=61.4
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhhcCCCCCHHHHHHHHhhhc
Q 033498 23 FERVNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKALSVKLTPEEIAELESIAS 88 (118)
Q Consensus 23 ~~~l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~~~~Ls~e~~~~l~~~~~ 88 (118)
.+.++++|+++|+|++|+||+|+++++.++++|+|+++++|+++|+++.++.|++++++.|+++.+
T Consensus 223 ~~~l~~ia~~~~~t~aq~al~w~l~~~~~~~~i~G~~~~~~l~en~~a~~~~L~~e~~~~l~~~~~ 288 (290)
T PRK10376 223 SSTLSDVAASLGATPMQVALAWLLQRSPNILLIPGTSSVAHLRENLAAAELVLSEEVLAELDGIAR 288 (290)
T ss_pred hHHHHHHHHHhCCCHHHHHHHHHHhCCCCeeEeeCCCCHHHHHHHHhhccCCCCHHHHHHHHHHHh
Confidence 467889999999999999999999987777899999999999999999999999999999998764
No 9
>PLN02587 L-galactose dehydrogenase
Probab=99.46 E-value=4e-13 Score=102.02 Aligned_cols=72 Identities=21% Similarity=0.280 Sum_probs=65.9
Q ss_pred HhhHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhhcC----CCCCHHHHHHHHhhhc
Q 033498 17 EHNKKLFERVNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKALS----VKLTPEEIAELESIAS 88 (118)
Q Consensus 17 ~~~~~~~~~l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~~----~~Ls~e~~~~l~~~~~ 88 (118)
+...+.++.++++|+++|+|++|+||+|++++|.|++||+|+++++|+++|+++.+ .+|+++++++|++++.
T Consensus 225 ~~~~~~~~~l~~~a~~~~~s~aq~al~~~l~~~~v~~~i~G~~~~~~l~~nl~a~~~~~~~~l~~~~~~~l~~~~~ 300 (314)
T PLN02587 225 PELKSACAAAATHCKEKGKNISKLALQYSLSNKDISTTLVGMNSVQQVEENVAAATELETSGIDEELLSEVEAILA 300 (314)
T ss_pred HHHHHHHHHHHHHHHHhCCCHHHHHHHHHHhCCCCeeEEecCCCHHHHHHHHHHHhhcccCCCCHHHHHHHHHhhc
Confidence 45567788899999999999999999999999999999999999999999999975 3799999999999885
No 10
>PF00248 Aldo_ket_red: Aldo/keto reductase family; InterPro: IPR023210 The aldo-keto reductase family includes a number of related monomeric NADPH-dependent oxidoreductases, such as aldehyde reductase, aldose reductase, prostaglandin F synthase, xylose reductase, rho crystallin, and many others []. All possess a similar structure, with a beta-alpha-beta fold characteristic of nucleotide binding proteins []. The fold comprises a parallel beta-8/alpha-8-barrel, which contains a novel NADP-binding motif. The binding site is located in a large, deep, elliptical pocket in the C-terminal end of the beta sheet, the substrate being bound in an extended conformation. The hydrophobic nature of the pocket favours aromatic and apolar substrates over highly polar ones []. Binding of the NADPH coenzyme causes a massive conformational change, reorienting a loop, effectively locking the coenzyme in place. This binding is more similar to FAD- than to NAD(P)-binding oxidoreductases []. Some proteins of this entry contain a K+ ion channel beta chain regulatory domain; these are reported to have oxidoreductase activity []. This entry represents the NADP-dependent oxidoreductase domain found in these proteins.; PDB: 1C9W_A 4F40_B 1VBJ_A 1XGD_A 1X97_A 2ACS_A 1EF3_A 2ACU_A 1PWM_A 2NVD_A ....
Probab=99.44 E-value=2.1e-13 Score=101.37 Aligned_cols=69 Identities=36% Similarity=0.545 Sum_probs=62.1
Q ss_pred hHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhhcCCCCCHHHHHHHHhhh
Q 033498 19 NKKLFERVNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKALSVKLTPEEIAELESIA 87 (118)
Q Consensus 19 ~~~~~~~l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~~~~Ls~e~~~~l~~~~ 87 (118)
.....+.+.++++++|+|++|+||+|+++++.+++||+|+++++|+++|+++.+++|++++++.|+++.
T Consensus 214 ~~~~~~~l~~~a~~~g~s~~q~al~~~l~~~~~~~~i~g~~~~~~l~en~~a~~~~L~~~~~~~i~~~~ 282 (283)
T PF00248_consen 214 AQELADALRELAEEHGVSPAQLALRWVLSHPGVASVIVGASSPEHLEENLAALDFPLTEEELAEIDQIL 282 (283)
T ss_dssp HGGGHHHHHHHHHHHTSSHHHHHHHHHHTSHTTEEEEEB-SSHHHHHHHHGGSSSG--HHHHHHHHTTH
T ss_pred hhhhhhhhhhhhhhcccccchhhhhhhhhccccccccCCCCCHHHHHHHHHHhCCCCCHHHHHHHHhhh
Confidence 446788899999999999999999999999999999999999999999999999999999999999875
No 11
>PRK11172 dkgB 2,5-diketo-D-gluconate reductase B; Provisional
Probab=99.39 E-value=1.6e-12 Score=96.86 Aligned_cols=63 Identities=32% Similarity=0.524 Sum_probs=58.8
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhhcCCCCCHHHHHHHHhhhc
Q 033498 24 ERVNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKALSVKLTPEEIAELESIAS 88 (118)
Q Consensus 24 ~~l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~~~~Ls~e~~~~l~~~~~ 88 (118)
..++++|+++|+|++|+||+|+++++ ++||||+++++|+++|+++.+++|+++++++|+++..
T Consensus 190 ~~l~~~a~~~~~s~aqval~w~l~~~--~~~i~g~~~~~~l~~n~~~~~~~L~~~~~~~i~~~~~ 252 (267)
T PRK11172 190 PVIARIAAKHNATPAQVILAWAMQLG--YSVIPSSTKRENLASNLLAQDLQLDAEDMAAIAALDR 252 (267)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHhCC--CEeecCCCCHHHHHHHHhhcCCCcCHHHHHHHhhhcc
Confidence 45889999999999999999999997 5799999999999999999999999999999999864
No 12
>KOG1577 consensus Aldo/keto reductase family proteins [General function prediction only]
Probab=99.36 E-value=2.5e-12 Score=97.23 Aligned_cols=66 Identities=30% Similarity=0.476 Sum_probs=61.2
Q ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhhcCCCCCHHHHHHHHhhhcC
Q 033498 22 LFERVNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKALSVKLTPEEIAELESIASA 89 (118)
Q Consensus 22 ~~~~l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~~~~Ls~e~~~~l~~~~~~ 89 (118)
.-+.+++||++||.|++|++|+|.++++ ++|||.++|++||+||++.+++.|+++|++.|+.....
T Consensus 221 ~~~~l~~iA~K~~kt~aQIlLrw~~q~g--~~vipKS~~~~Ri~eN~~vfdf~Lt~ed~~~i~~~~~~ 286 (300)
T KOG1577|consen 221 EDPVLKEIAKKYNKTPAQILLRWALQRG--VSVIPKSSNPERIKENFKVFDFELTEEDMKKLDSLNSN 286 (300)
T ss_pred cCHHHHHHHHHhCCCHHHHHHHHHHhCC--cEEEeccCCHHHHHHHHhhccccCCHHHHHHHhhcccc
Confidence 4467899999999999999999999998 89999999999999999999999999999999977653
No 13
>COG4989 Predicted oxidoreductase [General function prediction only]
Probab=99.31 E-value=1.7e-11 Score=90.79 Aligned_cols=86 Identities=26% Similarity=0.311 Sum_probs=74.1
Q ss_pred CcccCCCCCC-CCccchHhhHHHHHHHHHHHHHhC-CCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhhcCCCCCHH
Q 033498 1 MILDMSLLPR-FQPENLEHNKKLFERVNELAVKKG-CTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKALSVKLTPE 78 (118)
Q Consensus 1 ~~~~~~~~~~-~~~~~~~~~~~~~~~l~~ia~~~g-~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~~~~Ls~e 78 (118)
|.||+-.... |.. .++...+.+.|..+|+++| +|..++|++|++.||.-..||+|+.+++++++.+++.++.|+.+
T Consensus 206 maWSpl~gG~~F~g--~~~~q~l~~~l~~ia~e~ga~s~~~VaiAWllR~Pa~~~PiiGt~~~eRi~~a~~Al~~~LtRq 283 (298)
T COG4989 206 MAWSPLGGGGLFLG--DDKFQRLRKVLDRIAEEYGAVSITAVAIAWLLRHPAKPQPIIGTGNLERIRAAIKALSLTLTRQ 283 (298)
T ss_pred ccccccCCCccccC--CcchHHHHHHHHHHHHHhCcccHHHHHHHHHHhCcCcccceecCCCHHHHHHHHHHhhccccHH
Confidence 5677766543 442 4555667788999999999 79999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhhc
Q 033498 79 EIAELESIAS 88 (118)
Q Consensus 79 ~~~~l~~~~~ 88 (118)
+|-+|.....
T Consensus 284 qWf~Iy~Aa~ 293 (298)
T COG4989 284 QWFEIYTAAI 293 (298)
T ss_pred HHHHHHHHhc
Confidence 9999987764
No 14
>cd06660 Aldo_ket_red Aldo-keto reductases (AKRs) are a superfamily of soluble NAD(P)(H) oxidoreductases whose chief purpose is to reduce aldehydes and ketones to primary and secondary alcohols. AKRs are present in all phyla and are of importance to both health and industrial applications. Members have very distinct functions and include the prokaryotic 2,5-diketo-D-gluconic acid reductases and beta-keto ester reductases, the eukaryotic aldose reductases, aldehyde reductases, hydroxysteroid dehydrogenases, steroid 5beta-reductases, potassium channel beta-subunits and aflatoxin aldehyde reductases, among others.
Probab=99.28 E-value=2e-11 Score=90.73 Aligned_cols=64 Identities=38% Similarity=0.629 Sum_probs=60.7
Q ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhhcCCCCCHHHHHHHHh
Q 033498 22 LFERVNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKALSVKLTPEEIAELES 85 (118)
Q Consensus 22 ~~~~l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~~~~Ls~e~~~~l~~ 85 (118)
....+..+++++|++++|+||+|++++|.++++|+|+++++|+++|+++..++|++++++.|++
T Consensus 221 ~~~~~~~~~~~~~~s~~q~al~~~l~~p~~~~~i~g~~~~~~l~~n~~~~~~~L~~~~~~~l~~ 284 (285)
T cd06660 221 LLEALKEIAEKHGVTPAQVALRWLLQQPGVTSVIPGASSPERLEENLAALDFELSDEDLAALDA 284 (285)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHHhcCCCCeEEEeCCCCHHHHHHHHhhccCCCCHHHHHHHhh
Confidence 4577889999999999999999999999999999999999999999999999999999999975
No 15
>PRK14863 bifunctional regulator KidO; Provisional
Probab=99.25 E-value=1.4e-11 Score=93.00 Aligned_cols=68 Identities=13% Similarity=0.143 Sum_probs=60.0
Q ss_pred hhHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhhcCCCCCHHHHHHHHh
Q 033498 18 HNKKLFERVNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKALSVKLTPEEIAELES 85 (118)
Q Consensus 18 ~~~~~~~~l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~~~~Ls~e~~~~l~~ 85 (118)
+....+..+.++++++|+|++|+||+|++++|.|+++|+|+++++|+++|+++.+..+++..+++|..
T Consensus 212 ~~~~~~~~~~~~~~~~~~s~aqlalaw~l~~p~v~~~I~G~~~~~ql~~n~~a~~~~~~~~~~~~l~~ 279 (292)
T PRK14863 212 GASGRLSRVRRMIAEGRSDPLQAALGFALSRPEGSAVLVGVNSAAELSAVVAAASSPPPDLDWDDMAI 279 (292)
T ss_pred hhhHHHHHHHHHHHHcCCCHHHHHHHHHHhCCCCCeEEEecCCHHHHHHHHHHHhcCCCccchhhccC
Confidence 33456677888898999999999999999999999999999999999999999998999988776653
No 16
>COG1453 Predicted oxidoreductases of the aldo/keto reductase family [General function prediction only]
Probab=98.56 E-value=2.1e-07 Score=72.23 Aligned_cols=64 Identities=27% Similarity=0.376 Sum_probs=55.1
Q ss_pred HHHHHHHHHhC--CCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhhcCC---CCCHHHHHHHHhhh
Q 033498 24 ERVNELAVKKG--CTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKALSV---KLTPEEIAELESIA 87 (118)
Q Consensus 24 ~~l~~ia~~~g--~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~~~---~Ls~e~~~~l~~~~ 87 (118)
+++++++++++ .||+..|++|+++||.|++++.|+++++|++||++..+- +||+++...|.++-
T Consensus 216 ~~~~~l~~~~~~~~sP~~wa~R~~~shp~V~~vlsGm~~~~~l~enLk~~~~~~p~lte~e~~il~~v~ 284 (391)
T COG1453 216 EKLEELCRPASPKRSPAEWALRYLLSHPEVTTVLSGMNTPEQLEENLKIASELEPSLTEEELQILEKVE 284 (391)
T ss_pred HHHHHHHHhcCCCCCcHHHHHHHHhcCCCeEEEecCCCCHHHHHHHHHHHhhcCCccCHHHHHHHHHHH
Confidence 56777888764 789999999999999999999999999999999997753 39998887777664
No 17
>KOG1576 consensus Predicted oxidoreductase [Energy production and conversion]
Probab=98.20 E-value=2.4e-05 Score=59.07 Aligned_cols=69 Identities=16% Similarity=0.187 Sum_probs=59.4
Q ss_pred CCCCCccchHhhHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhhcCCCCCH
Q 033498 8 LPRFQPENLEHNKKLFERVNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKALSVKLTP 77 (118)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~~~~Ls~ 77 (118)
-+.|.| --++..+...+-.++|++.|+.++.+|+.|.++.+++.++++|+++.++++.|+.+..-.||+
T Consensus 242 p~~wHP-aS~Elk~~a~~aa~~Cq~rnv~l~kLA~~Yam~~~~~~~~lvGm~s~~~l~~nLdan~~~ls~ 310 (342)
T KOG1576|consen 242 PPPWHP-ASDELKEAAKAAAEYCQSRNVELGKLAMYYAMSLPGVSTVLVGMSSRQLLRINLDANFDRLSS 310 (342)
T ss_pred CCCCCC-CCHHHHHHHHHHHHHHHHcCccHHHHHHHHHHccCCcceEEecCchHHHHHHHHHhhhccccc
Confidence 344554 346677778888899999999999999999999999999999999999999999987667766
No 18
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=85.96 E-value=2.2 Score=25.00 Aligned_cols=29 Identities=17% Similarity=0.424 Sum_probs=22.0
Q ss_pred ccchHhhHHHHH------HHHHHHHHhCCCHHHHH
Q 033498 13 PENLEHNKKLFE------RVNELAVKKGCTRSQLA 41 (118)
Q Consensus 13 ~~~~~~~~~~~~------~l~~ia~~~g~s~aqlA 41 (118)
..+.++..++.. .+++||+++|++..+|.
T Consensus 6 sp~rdkA~e~y~~~~g~i~lkdIA~~Lgvs~~tIr 40 (60)
T PF10668_consen 6 SPNRDKAFEIYKESNGKIKLKDIAEKLGVSESTIR 40 (60)
T ss_pred CcCHHHHHHHHHHhCCCccHHHHHHHHCCCHHHHH
Confidence 335566666655 68999999999999875
No 19
>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=84.32 E-value=2.6 Score=23.17 Aligned_cols=42 Identities=14% Similarity=0.249 Sum_probs=30.0
Q ss_pred HHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhhcCC
Q 033498 26 VNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKALSV 73 (118)
Q Consensus 26 l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~~~ 73 (118)
|++||+..|+|.+.+... ++.+ .-+...+.+++.+.++..++
T Consensus 2 i~dIA~~agvS~~TVSr~--ln~~----~~vs~~tr~rI~~~a~~lgY 43 (46)
T PF00356_consen 2 IKDIAREAGVSKSTVSRV--LNGP----PRVSEETRERILEAAEELGY 43 (46)
T ss_dssp HHHHHHHHTSSHHHHHHH--HTTC----SSSTHHHHHHHHHHHHHHTB
T ss_pred HHHHHHHHCcCHHHHHHH--HhCC----CCCCHHHHHHHHHHHHHHCC
Confidence 689999999999966554 5554 34566677777777766554
No 20
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=77.66 E-value=5.1 Score=20.60 Aligned_cols=23 Identities=43% Similarity=0.660 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHHhCCCHHHHHHH
Q 033498 21 KLFERVNELAVKKGCTRSQLALA 43 (118)
Q Consensus 21 ~~~~~l~~ia~~~g~s~aqlAL~ 43 (118)
+..+.|+++|++.|.|.+++.-.
T Consensus 9 ~~~~~l~~~a~~~g~s~s~~ir~ 31 (39)
T PF01402_consen 9 ELYERLDELAKELGRSRSELIRE 31 (39)
T ss_dssp HHHHHHHHHHHHHTSSHHHHHHH
T ss_pred HHHHHHHHHHHHHCcCHHHHHHH
Confidence 46788999999999999876543
No 21
>PF11242 DUF2774: Protein of unknown function (DUF2774); InterPro: IPR021404 This entry is represented by Bacteriophage T4, Gp24.3; it is a family of uncharacterised viral proteins.
Probab=74.22 E-value=5.6 Score=23.46 Aligned_cols=21 Identities=38% Similarity=0.544 Sum_probs=18.8
Q ss_pred HHHHHHHhCCCHHHHHHHHHH
Q 033498 26 VNELAVKKGCTRSQLALAWVH 46 (118)
Q Consensus 26 l~~ia~~~g~s~aqlAL~w~l 46 (118)
+.+||+++|.++.++|..|+.
T Consensus 16 FveIAr~~~i~a~e~a~~w~~ 36 (63)
T PF11242_consen 16 FVEIARKIGITAKEVAKAWAE 36 (63)
T ss_pred HHHHHHHhCCCHHHHHHHHHH
Confidence 468999999999999999975
No 22
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=70.81 E-value=6.3 Score=23.08 Aligned_cols=41 Identities=24% Similarity=0.264 Sum_probs=23.1
Q ss_pred CCCCCCccchHhhHHH----HHHHHHHHHHhCCCHHHHHHHHHHcC
Q 033498 7 LLPRFQPENLEHNKKL----FERVNELAVKKGCTRSQLALAWVHHQ 48 (118)
Q Consensus 7 ~~~~~~~~~~~~~~~~----~~~l~~ia~~~g~s~aqlAL~w~l~~ 48 (118)
...+|+++.-...+.. -..+.++|.+||++++ ....|+-..
T Consensus 3 ~r~~ys~e~K~~~v~~~~~~g~sv~~va~~~gi~~~-~l~~W~~~~ 47 (76)
T PF01527_consen 3 KRRRYSPEFKLQAVREYLESGESVSEVAREYGISPS-TLYNWRKQY 47 (76)
T ss_dssp SS----HHHHHHHHHHHHHHHCHHHHHHHHHTS-HH-HHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHCCCceEeeecccccccc-cccHHHHHH
Confidence 3345555443333333 2457899999999666 557888776
No 23
>PF14502 HTH_41: Helix-turn-helix domain
Probab=67.34 E-value=5.6 Score=22.28 Aligned_cols=31 Identities=26% Similarity=0.315 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHhCCCH--HHHHHHHHHcCCCCc
Q 033498 22 LFERVNELAVKKGCTR--SQLALAWVHHQGDDV 52 (118)
Q Consensus 22 ~~~~l~~ia~~~g~s~--aqlAL~w~l~~~~v~ 52 (118)
++..+.+++++++++. .|-||.++-..+.|.
T Consensus 5 Ri~tI~e~~~~~~vs~GtiQ~Alk~Le~~gaI~ 37 (48)
T PF14502_consen 5 RIPTISEYSEKFGVSRGTIQNALKFLEENGAIK 37 (48)
T ss_pred ccCCHHHHHHHhCcchhHHHHHHHHHHHCCcEE
Confidence 4556788999998887 599999999887543
No 24
>PF06603 UpxZ: UpxZ family of transcription anti-terminator antagonists; InterPro: IPR010570 This family consists of several hypothetical proteins of unknown function and seems to be specific to Bacteroides species.
Probab=67.18 E-value=30 Score=22.58 Aligned_cols=66 Identities=23% Similarity=0.281 Sum_probs=49.1
Q ss_pred cccCCCCCCCCccchHhhHHHHHHHHHHHHHhCCCH---HHHHHHHHHcCCCCceecCCCCcHHHHHHHHh
Q 033498 2 ILDMSLLPRFQPENLEHNKKLFERVNELAVKKGCTR---SQLALAWVHHQGDDVCPIPGTTKIENLNQNIK 69 (118)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~l~~ia~~~g~s~---aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~ 69 (118)
-+.+...|.|......-+.++.+...++-..+|.|+ |.++|+-++.-. ++..-...+.+++.+.+.
T Consensus 14 ~lG~dg~piYsD~~~rLN~ev~~~~~~Ly~~~G~t~EeeA~lCLaLLmGYn--at~yd~geke~~~Q~vL~ 82 (106)
T PF06603_consen 14 YLGMDGSPIYSDDFSRLNKEVYEQSNDLYSQHGSTPEEEANLCLALLMGYN--ATIYDNGEKEEKKQEVLD 82 (106)
T ss_pred hcCCCCCeeehHHHHHHhHHHHHHHHHHHhccCCCHHHHHHHHHHHHHhcc--chhhhCccHHHHHHHHHH
Confidence 467788888888777888889998998888899998 678899888765 444445555555555443
No 25
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=64.53 E-value=14 Score=19.94 Aligned_cols=22 Identities=36% Similarity=0.687 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHHHhCCCHHHHH
Q 033498 20 KKLFERVNELAVKKGCTRSQLA 41 (118)
Q Consensus 20 ~~~~~~l~~ia~~~g~s~aqlA 41 (118)
.++.+.|+.++++.|++.+.+.
T Consensus 11 ~el~~~L~~ls~~t~i~~S~Ll 32 (44)
T PF12651_consen 11 KELYEKLKELSEETGIPKSKLL 32 (44)
T ss_pred HHHHHHHHHHHHHHCCCHHHHH
Confidence 4578889999999999998663
No 26
>PF11020 DUF2610: Domain of unknown function (DUF2610); InterPro: IPR021277 This family is conserved in Proteobacteria. One member is annotated as being elongation factor P but this could not be confirmed.
Probab=62.09 E-value=25 Score=21.84 Aligned_cols=29 Identities=14% Similarity=0.175 Sum_probs=24.6
Q ss_pred HhhHHHHHHHHHHHHHhCCCHHHHHHHHH
Q 033498 17 EHNKKLFERVNELAVKKGCTRSQLALAWV 45 (118)
Q Consensus 17 ~~~~~~~~~l~~ia~~~g~s~aqlAL~w~ 45 (118)
++..+.+.+|.++|++.|++..+++.-.+
T Consensus 48 ~~V~~sl~kL~~La~~N~v~feeLc~YAL 76 (82)
T PF11020_consen 48 EKVMDSLSKLYKLAKENNVSFEELCVYAL 76 (82)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 56788999999999999999999876443
No 27
>PF13518 HTH_28: Helix-turn-helix domain
Probab=57.13 E-value=17 Score=19.40 Aligned_cols=22 Identities=32% Similarity=0.634 Sum_probs=15.3
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHc
Q 033498 25 RVNELAVKKGCTRSQLALAWVHH 47 (118)
Q Consensus 25 ~l~~ia~~~g~s~aqlAL~w~l~ 47 (118)
.+.++|.++|+|..++ ..|+..
T Consensus 14 s~~~~a~~~gis~~tv-~~w~~~ 35 (52)
T PF13518_consen 14 SVREIAREFGISRSTV-YRWIKR 35 (52)
T ss_pred CHHHHHHHHCCCHhHH-HHHHHH
Confidence 4567888888877665 677653
No 28
>PF13700 DUF4158: Domain of unknown function (DUF4158)
Probab=55.84 E-value=15 Score=25.26 Aligned_cols=44 Identities=20% Similarity=0.320 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHh--CCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHH
Q 033498 21 KLFERVNELAVKK--GCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQN 67 (118)
Q Consensus 21 ~~~~~l~~ia~~~--g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en 67 (118)
.+.+.+...|... +..+...++.|+..+. +.+||.++.+++-..
T Consensus 119 ~L~~~l~~~a~~~~~~~~l~~~~~~~L~~~r---I~lP~~~~L~rli~~ 164 (166)
T PF13700_consen 119 ELEEWLREAARTTDDPDDLFNALIEWLRQRR---IELPGYSTLERLISS 164 (166)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHHHCC---eeCCCHHHHHHHHHH
Confidence 3445555555553 4446799999999986 789999999887643
No 29
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=55.21 E-value=21 Score=19.17 Aligned_cols=20 Identities=25% Similarity=0.082 Sum_probs=11.8
Q ss_pred HHHHHHHHHhCCCHHHHHHH
Q 033498 24 ERVNELAVKKGCTRSQLALA 43 (118)
Q Consensus 24 ~~l~~ia~~~g~s~aqlAL~ 43 (118)
+.++.+.++.|++..++|-.
T Consensus 5 ~~l~~~r~~~gltq~~lA~~ 24 (58)
T TIGR03070 5 MLVRARRKALGLTQADLADL 24 (58)
T ss_pred HHHHHHHHHcCCCHHHHHHH
Confidence 34555555666666666644
No 30
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=54.35 E-value=32 Score=22.40 Aligned_cols=46 Identities=15% Similarity=0.101 Sum_probs=29.5
Q ss_pred cccCCCCCCCCccchHhhHHHH----HHHHHHHHHhCCCHHHHHHHHHHcC
Q 033498 2 ILDMSLLPRFQPENLEHNKKLF----ERVNELAVKKGCTRSQLALAWVHHQ 48 (118)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~----~~l~~ia~~~g~s~aqlAL~w~l~~ 48 (118)
|+.+....+|+.+........+ ..+.++|.+||++.+ ...+|+...
T Consensus 4 ~~~~~~rr~ys~EfK~~aV~~~~~~g~sv~evA~e~gIs~~-tl~~W~r~y 53 (121)
T PRK09413 4 VLGPEKRRRRTTQEKIAIVQQSFEPGMTVSLVARQHGVAAS-QLFLWRKQY 53 (121)
T ss_pred cCCCCCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHHCcCHH-HHHHHHHHH
Confidence 4555555667665444333322 257799999999765 567898864
No 31
>COG1026 Predicted Zn-dependent peptidases, insulinase-like [General function prediction only]
Probab=52.08 E-value=57 Score=29.24 Aligned_cols=79 Identities=15% Similarity=0.186 Sum_probs=53.8
Q ss_pred CCCccchHhhHHHHHHHHHHHHHhCCC--HHHHHHHHHHcCCC--CceecCCCCcHHHHHH----HHhhcCCCCCHHHHH
Q 033498 10 RFQPENLEHNKKLFERVNELAVKKGCT--RSQLALAWVHHQGD--DVCPIPGTTKIENLNQ----NIKALSVKLTPEEIA 81 (118)
Q Consensus 10 ~~~~~~~~~~~~~~~~l~~ia~~~g~s--~aqlAL~w~l~~~~--v~~~I~G~~~~~ql~e----n~~a~~~~Ls~e~~~ 81 (118)
+.........+.....++.+-+..... -..+.-.|++.+|. +.+++|...-.+++++ -++.....|++++++
T Consensus 407 w~~G~dp~~~Lr~~~~~~~Lr~~le~~~~fe~LI~ky~l~N~h~~~v~~~Ps~~~~~~~ekee~e~L~~~~~~l~de~~~ 486 (978)
T COG1026 407 WLNGGDPEDSLRFLDYLQNLREKLEKGPYFEKLIRKYFLDNPHYVTVIVLPSPELEEKLEKEERELLQKRSSELTDEDLE 486 (978)
T ss_pred cccCCChhhhhhhHHHHHHHHHhhhcChHHHHHHHHHhhcCCccEEEEEecChHHHHHHHHHHHHHHHHHHhhcCHHHHH
Confidence 334445566666666666666655445 57899999999983 3456677666666664 455556689999999
Q ss_pred HHHhhhc
Q 033498 82 ELESIAS 88 (118)
Q Consensus 82 ~l~~~~~ 88 (118)
.|.+-.+
T Consensus 487 ki~~~~~ 493 (978)
T COG1026 487 KIIKDSK 493 (978)
T ss_pred HHHHHHH
Confidence 9876654
No 32
>PF08418 Pol_alpha_B_N: DNA polymerase alpha subunit B N-terminal; InterPro: IPR013627 This is the eukaryotic DNA polymerase alpha subunit B N-terminal domain which is involved in complex formation []. ; PDB: 4E2I_9 2KEB_A 3FLO_G.
Probab=50.73 E-value=18 Score=26.54 Aligned_cols=50 Identities=12% Similarity=0.210 Sum_probs=30.8
Q ss_pred hHHHHHHHHHHHHHhCCCHHHHHHHHH---HcCCCCceecCCCCcHHHHHHHHh
Q 033498 19 NKKLFERVNELAVKKGCTRSQLALAWV---HHQGDDVCPIPGTTKIENLNQNIK 69 (118)
Q Consensus 19 ~~~~~~~l~~ia~~~g~s~aqlAL~w~---l~~~~v~~~I~G~~~~~ql~en~~ 69 (118)
..+++.++..||.-|++++-+++..|. +++..- ..-+...+++++++.+.
T Consensus 8 ~~~vl~kl~slc~~~~ls~edL~~kWeaf~~~~~~~-~~~l~~~~L~~F~~~lq 60 (253)
T PF08418_consen 8 DPDVLEKLQSLCRLYNLSAEDLFYKWEAFSLNMQLD-DTKLTLDNLDQFKQYLQ 60 (253)
T ss_dssp -HHHHHHHHTHHHHST--HHHHHHHHTTHHHHTT-S-C----TTTTTGGGTTTS
T ss_pred CHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhhcCCC-cCcCCHHHHHHHHHHHH
Confidence 567899999999999999999999984 333321 22355566666655544
No 33
>PRK11675 LexA regulated protein; Provisional
Probab=48.14 E-value=28 Score=22.05 Aligned_cols=24 Identities=33% Similarity=0.447 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHHHhCCCHHHHHHH
Q 033498 20 KKLFERVNELAVKKGCTRSQLALA 43 (118)
Q Consensus 20 ~~~~~~l~~ia~~~g~s~aqlAL~ 43 (118)
.+.++.|.++|++.|+|.+++.-.
T Consensus 59 edl~ekL~eyAe~~nitRSElIr~ 82 (90)
T PRK11675 59 ADLVDALNELAEARNISRSELIEE 82 (90)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHH
Confidence 467889999999999999987654
No 34
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=47.84 E-value=22 Score=18.30 Aligned_cols=19 Identities=16% Similarity=0.225 Sum_probs=12.5
Q ss_pred HHHHHHHHHhCCCHHHHHH
Q 033498 24 ERVNELAVKKGCTRSQLAL 42 (118)
Q Consensus 24 ~~l~~ia~~~g~s~aqlAL 42 (118)
+.+..||+++|++..++.-
T Consensus 7 Dtl~~IA~~~~~~~~~l~~ 25 (44)
T PF01476_consen 7 DTLWSIAKRYGISVDELME 25 (44)
T ss_dssp --HHHHHHHTTS-HHHHHH
T ss_pred CcHHHHHhhhhhhHhHHHH
Confidence 3567889999988887653
No 35
>PF07027 DUF1318: Protein of unknown function (DUF1318); InterPro: IPR008309 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=46.85 E-value=53 Score=20.88 Aligned_cols=29 Identities=28% Similarity=0.161 Sum_probs=23.6
Q ss_pred HhhHHHHHHHHHHHHHhCCCHHHHHHHHH
Q 033498 17 EHNKKLFERVNELAVKKGCTRSQLALAWV 45 (118)
Q Consensus 17 ~~~~~~~~~l~~ia~~~g~s~aqlAL~w~ 45 (118)
..|.++.....+||++.|+|+.++.-.+.
T Consensus 44 ~~N~~R~~~Y~~iA~~ng~t~~~V~~~~a 72 (95)
T PF07027_consen 44 AINADRRALYQEIAKKNGITVEQVAATAA 72 (95)
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 56777888899999999999988765543
No 36
>PF10723 RepB-RCR_reg: Replication regulatory protein RepB; InterPro: IPR019661 This family of proteins regulates the replication of rolling circle replication (RCR) plasmids that have a double-strand replication origin (dso). Regulation of the replication of the RCR plasmids occurs mainly at the initiation of leading strand synthesis at the dso, such that concentration of Rep protein controls plasmid replication []. ; PDB: 2KEL_B.
Probab=45.14 E-value=42 Score=20.83 Aligned_cols=26 Identities=27% Similarity=0.456 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHHhCCCHHHHHHHHHH
Q 033498 21 KLFERVNELAVKKGCTRSQLALAWVH 46 (118)
Q Consensus 21 ~~~~~l~~ia~~~g~s~aqlAL~w~l 46 (118)
++.+.|..+|+..|+|.+++.=.++.
T Consensus 51 ~~K~~L~~lc~~~GlTQae~IE~LI~ 76 (84)
T PF10723_consen 51 ELKERLEELCKEQGLTQAEMIERLIK 76 (84)
T ss_dssp HHHHHHHHHHHHS---HHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCcHHHHHHHHHH
Confidence 46678999999999999998766553
No 37
>COG0497 RecN ATPase involved in DNA repair [DNA replication, recombination, and repair]
Probab=43.47 E-value=37 Score=28.44 Aligned_cols=60 Identities=22% Similarity=0.216 Sum_probs=39.9
Q ss_pred CCccchHhhHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhh
Q 033498 11 FQPENLEHNKKLFERVNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKA 70 (118)
Q Consensus 11 ~~~~~~~~~~~~~~~l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a 70 (118)
|.|....+...++..|+.+++|||+++..+.-..---+......--+..+.++|+..+..
T Consensus 294 ~Dp~~L~~ve~Rl~~L~~l~RKY~~~~~~l~~~~~~~~~el~~L~~~~~~~~~Le~~~~~ 353 (557)
T COG0497 294 FDPNRLEEVEERLFALKSLARKYGVTIEDLLEYLDKIKEELAQLDNSEESLEALEKEVKK 353 (557)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHH
Confidence 677788999999999999999999999876433222222222333344556666655543
No 38
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=43.24 E-value=20 Score=27.17 Aligned_cols=24 Identities=21% Similarity=0.605 Sum_probs=19.3
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHcCC
Q 033498 25 RVNELAVKKGCTRSQLALAWVHHQG 49 (118)
Q Consensus 25 ~l~~ia~~~g~s~aqlAL~w~l~~~ 49 (118)
.+++||+++||++.++ -+|-..++
T Consensus 21 k~~dIAeklGvspnti-ksWKrr~g 44 (279)
T COG5484 21 KLKDIAEKLGVSPNTI-KSWKRRDG 44 (279)
T ss_pred cHHHHHHHhCCChHHH-HHHHHhcC
Confidence 3679999999999976 57877765
No 39
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=42.92 E-value=1.1e+02 Score=21.21 Aligned_cols=72 Identities=15% Similarity=0.204 Sum_probs=39.3
Q ss_pred CccchHhh-HHHHHHHHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhhcCC--CCCHHHHHHHHhhh
Q 033498 12 QPENLEHN-KKLFERVNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKALSV--KLTPEEIAELESIA 87 (118)
Q Consensus 12 ~~~~~~~~-~~~~~~l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~~~--~Ls~e~~~~l~~~~ 87 (118)
.+.|..-. .++.+.+.++|+ .|.+++|+-+--==+++ +|.+..-+-.-|.+.++.-++ .++++.+..+..+.
T Consensus 22 ~P~W~~~~~eeve~~I~~lak-kG~~pSqIG~~LRD~~g---ip~Vk~vtG~ki~~iLk~~gl~p~iPEDL~~L~~ri~ 96 (151)
T PRK08561 22 PPEWVDYSPEEIEELVVELAK-QGYSPSMIGIILRDQYG---IPDVKLITGKKITEILEENGLAPEIPEDLRNLIKKAV 96 (151)
T ss_pred CCccccCCHHHHHHHHHHHHH-CCCCHHHhhhhHhhccC---CCceeeeccchHHHHHHHcCCCCCCcHHHHHHHHHHH
Confidence 44454333 334455566664 69999998776333443 333333333444455554443 67777766665543
No 40
>PF13467 RHH_4: Ribbon-helix-helix domain; PDB: 3KK4_C.
Probab=40.48 E-value=36 Score=20.31 Aligned_cols=26 Identities=15% Similarity=0.327 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHc
Q 033498 22 LFERVNELAVKKGCTRSQLALAWVHH 47 (118)
Q Consensus 22 ~~~~l~~ia~~~g~s~aqlAL~w~l~ 47 (118)
..+.|++||+..|+|.+++.-..-..
T Consensus 22 FW~~L~eiA~~~g~s~~~li~~id~~ 47 (67)
T PF13467_consen 22 FWDALEEIAAREGLSLNALIAEIDAR 47 (67)
T ss_dssp HHHHHHHHHHHTT--HHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHc
Confidence 45678999999999999887766433
No 41
>COG2307 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.59 E-value=25 Score=27.29 Aligned_cols=70 Identities=16% Similarity=0.246 Sum_probs=53.0
Q ss_pred hhHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhhcCCCCCHHHHHHHHhhhcC
Q 033498 18 HNKKLFERVNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKALSVKLTPEEIAELESIASA 89 (118)
Q Consensus 18 ~~~~~~~~l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~~~~Ls~e~~~~l~~~~~~ 89 (118)
..+..+..+..+-++||.-.+.=++.|++.-+.....| +++++...+|.+++.-.||.|-|+.|++.+..
T Consensus 46 ~~l~~~g~~~~~~~~~g~~t~~~~~~~l~~D~~~P~Sl--~ssl~~ar~nAr~VR~~ls~etWe~LN~~~~~ 115 (313)
T COG2307 46 PLLPLLGGIEDYLAGYGVLTAADVLDFLTRDRDNPSSL--VSSLEAARENARAVRDRLSSETWEALNELYLA 115 (313)
T ss_pred hhhhhhcccccccccccccchhHHHHHHHhCCCCcHHH--HHHHHHHHHHHHHHHhccCHHHHHHHHHHHHH
Confidence 33555666666666788777777888888766333333 46788999999999889999999999998753
No 42
>COG1564 THI80 Thiamine pyrophosphokinase [Coenzyme metabolism]
Probab=39.29 E-value=73 Score=23.31 Aligned_cols=40 Identities=28% Similarity=0.312 Sum_probs=31.8
Q ss_pred HhCCCHHHHHHHHHHcCCCCceecCCCC--cHHHHHHHHhhc
Q 033498 32 KKGCTRSQLALAWVHHQGDDVCPIPGTT--KIENLNQNIKAL 71 (118)
Q Consensus 32 ~~g~s~aqlAL~w~l~~~~v~~~I~G~~--~~~ql~en~~a~ 71 (118)
+...|=.++|+.|++.+.....+|.|+. +.+|+-.|+.-.
T Consensus 74 eKd~TD~elAl~~a~e~g~d~i~i~Ga~GGR~DH~l~nl~ll 115 (212)
T COG1564 74 EKDSTDLELALDEALERGADEIVILGALGGRLDHALANLFLL 115 (212)
T ss_pred hhccchHHHHHHHHHHcCCCEEEEEecCCChHHHHHHHHHHH
Confidence 4567888999999999998677777554 889988887643
No 43
>PF14096 DUF4274: Domain of unknown function (DUF4274)
Probab=38.23 E-value=37 Score=20.34 Aligned_cols=28 Identities=14% Similarity=0.162 Sum_probs=19.8
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHHcCCCC
Q 033498 24 ERVNELAVKKGCTRSQLALAWVHHQGDD 51 (118)
Q Consensus 24 ~~l~~ia~~~g~s~aqlAL~w~l~~~~v 51 (118)
+.+..++.+++-+-..-.+.|++.||..
T Consensus 5 ~~lh~~~~~~NwD~~~~v~~~il~~p~C 32 (77)
T PF14096_consen 5 EELHALADNYNWDDGFEVPKWILEHPKC 32 (77)
T ss_pred HHHHHHHHHcCCCCCcHHHHHHHcCCcc
Confidence 4566777777777667777888887754
No 44
>TIGR02899 spore_safA spore coat assembly protein SafA. in which one of which is found in most examples of endospore-forming bacteria. Lysin motifs are repeated in many proteins.
Probab=37.56 E-value=43 Score=16.72 Aligned_cols=17 Identities=24% Similarity=0.249 Sum_probs=13.1
Q ss_pred HHHHHHHHhCCCHHHHH
Q 033498 25 RVNELAVKKGCTRSQLA 41 (118)
Q Consensus 25 ~l~~ia~~~g~s~aqlA 41 (118)
.+..||++||++..+++
T Consensus 6 tl~~IA~~~~~~~~~l~ 22 (44)
T TIGR02899 6 TLWKIAKKYGVDFDELI 22 (44)
T ss_pred CHHHHHHHHCcCHHHHH
Confidence 46678999999887664
No 45
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=37.24 E-value=37 Score=18.07 Aligned_cols=15 Identities=33% Similarity=0.510 Sum_probs=9.3
Q ss_pred HHHHHHHHhCCCHHH
Q 033498 25 RVNELAVKKGCTRSQ 39 (118)
Q Consensus 25 ~l~~ia~~~g~s~aq 39 (118)
.+.+||+.+|+|.+.
T Consensus 23 si~~IA~~~gvsr~T 37 (45)
T PF02796_consen 23 SIAEIAKQFGVSRST 37 (45)
T ss_dssp -HHHHHHHTTS-HHH
T ss_pred CHHHHHHHHCcCHHH
Confidence 356777777877764
No 46
>PHA01623 hypothetical protein
Probab=36.90 E-value=64 Score=18.34 Aligned_cols=21 Identities=24% Similarity=0.224 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHhCCCHHHH
Q 033498 20 KKLFERVNELAVKKGCTRSQL 40 (118)
Q Consensus 20 ~~~~~~l~~ia~~~g~s~aql 40 (118)
-++.+.|..+|.++|++.+++
T Consensus 22 eel~~~Ld~y~~~~g~~rSe~ 42 (56)
T PHA01623 22 KDLKTRLKVYCAKNNLQLTQA 42 (56)
T ss_pred HHHHHHHHHHHHHcCCCHHHH
Confidence 357788999999999997754
No 47
>PRK10558 alpha-dehydro-beta-deoxy-D-glucarate aldolase; Provisional
Probab=35.69 E-value=1.6e+02 Score=21.92 Aligned_cols=51 Identities=10% Similarity=-0.011 Sum_probs=38.0
Q ss_pred HHHHHHHHHHhCCCH-------HHHHHHHHHcCCCCceecCCCCcHHHHHHHHhhcCC
Q 033498 23 FERVNELAVKKGCTR-------SQLALAWVHHQGDDVCPIPGTTKIENLNQNIKALSV 73 (118)
Q Consensus 23 ~~~l~~ia~~~g~s~-------aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~~~ 73 (118)
+..+-..++.+|+++ ....+..++..+...+++|-..|.+|.++.++++.+
T Consensus 58 ~~~~i~a~~~~g~~~lVRvp~~~~~~i~r~LD~Ga~giivP~v~tae~a~~~v~a~ky 115 (256)
T PRK10558 58 FIPQLMALKGSASAPVVRVPTNEPVIIKRLLDIGFYNFLIPFVETAEEARRAVASTRY 115 (256)
T ss_pred HHHHHHHHhhcCCCcEEECCCCCHHHHHHHhCCCCCeeeecCcCCHHHHHHHHHHcCC
Confidence 333444455566653 345778899998888999999999999999887766
No 48
>cd01068 sensor_globin Globin domain present in Globin-Coupled-Sensors (GCS). These domains detect changes in intracellular concentrations of oxygen, carbon monoxyde, or nitrous oxide, which result in aerotaxis and/or gene regulation. One subgroup, the HemATs, are aerotactic heme sensors combining a globin with an MCP signaling domain, others function as gene regulators, by direct combination with DNA-binding domains, with domains modulating 2nd messengers, or with domains interacting with transcription factors or regulators.
Probab=35.27 E-value=93 Score=20.35 Aligned_cols=74 Identities=11% Similarity=0.096 Sum_probs=55.2
Q ss_pred HhhHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhh-----cCCCCCHHHHHHHHhhhcCC
Q 033498 17 EHNKKLFERVNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKA-----LSVKLTPEEIAELESIASAD 90 (118)
Q Consensus 17 ~~~~~~~~~l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a-----~~~~Ls~e~~~~l~~~~~~~ 90 (118)
+...+.++.+..+.+++.-..+.-...++.++|.....+-...+.++++..... ++-.++++-++....+...|
T Consensus 14 ~~d~~~l~~~~~~~~~~~~~i~~~FY~~l~~~p~~~~~~~~~~~~~~l~~~~~~~~~~l~~~~~d~~y~~~~~~iG~~H 92 (147)
T cd01068 14 EDDLSLLKALRPVIEANADELVDRFYDHLRRTPETAAFLGDESVVERLKSTQRRHWVELFSGVYDEAYIAQRVRIGEVH 92 (147)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHhcChHHHHHhCCchHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHHHHH
Confidence 567788888899998888788899999999999876666667777887765432 34467777777776666543
No 49
>COG0350 Ada Methylated DNA-protein cysteine methyltransferase [DNA replication, recombination, and repair]
Probab=35.02 E-value=64 Score=22.52 Aligned_cols=34 Identities=18% Similarity=0.086 Sum_probs=27.1
Q ss_pred HHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCC
Q 033498 26 VNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTT 59 (118)
Q Consensus 26 l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~ 59 (118)
..++|++.|.+.+.-|.+..+....+..+||.-|
T Consensus 108 Y~eiA~~ig~p~a~rAVG~A~~~NPl~IiIPCHR 141 (168)
T COG0350 108 YGEIARRLGRPTAVRAVGNANGANPLPIIIPCHR 141 (168)
T ss_pred HHHHHHHhCCCcHHHHHHHHhccCCceEEecCeE
Confidence 4789999999777778888888887888888543
No 50
>PF12551 PHBC_N: Poly-beta-hydroxybutyrate polymerase N terminal; InterPro: IPR022211 This domain family is found in bacteria and eukaryotes, and is approximately 50 amino acids in length. The family is found in association with PF07167 from PFAM, PF00561 from PFAM. There is a single completely conserved residue W that may be functionally important. PHBC is the third enzyme of the poly-beta-hydroxybutyrate biosynthetic pathway.
Probab=34.62 E-value=37 Score=18.75 Aligned_cols=13 Identities=38% Similarity=0.621 Sum_probs=11.4
Q ss_pred hCCCHHHHHHHHH
Q 033498 33 KGCTRSQLALAWV 45 (118)
Q Consensus 33 ~g~s~aqlAL~w~ 45 (118)
.|+||+.++++|+
T Consensus 22 ~GlSPaal~lA~~ 34 (46)
T PF12551_consen 22 GGLSPAALALAYL 34 (46)
T ss_pred cCcCHHHHHHHHH
Confidence 5999999999985
No 51
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=34.58 E-value=49 Score=18.87 Aligned_cols=20 Identities=35% Similarity=0.227 Sum_probs=15.9
Q ss_pred HHHHHHHHHhCCCHHHHHHH
Q 033498 24 ERVNELAVKKGCTRSQLALA 43 (118)
Q Consensus 24 ~~l~~ia~~~g~s~aqlAL~ 43 (118)
.+++-+|+++|+|..||.-+
T Consensus 21 ~ev~ywa~~~gvt~~~L~~A 40 (57)
T PF12244_consen 21 YEVRYWAKRFGVTEEQLREA 40 (57)
T ss_pred HHHHHHHHHHCcCHHHHHHH
Confidence 45678999999999887654
No 52
>PHA01748 hypothetical protein
Probab=34.00 E-value=78 Score=18.18 Aligned_cols=23 Identities=30% Similarity=0.476 Sum_probs=17.8
Q ss_pred HHHHHHHHHHHHHhCCCHHHHHH
Q 033498 20 KKLFERVNELAVKKGCTRSQLAL 42 (118)
Q Consensus 20 ~~~~~~l~~ia~~~g~s~aqlAL 42 (118)
.+.++.+..+|+++|++-+++.-
T Consensus 11 ~el~~eld~~a~~~g~~RSE~Ir 33 (60)
T PHA01748 11 EDLLELLDRYAIKHGLNRSEAIR 33 (60)
T ss_pred HHHHHHHHHHHHHhCCCHHHHHH
Confidence 35678899999999998776543
No 53
>PF00816 Histone_HNS: H-NS histone family Partial NMR structure.; InterPro: IPR001801 The histone-like nucleoid-structuring (H-NS) protein belongs to a family of bacterial proteins that play a role in the formation of nucleoid structure and affect gene expression under certain conditions [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2LEV_A 1HNS_A 1LR1_B 1HNR_A 1NI8_A 1OV9_A 2JR1_A 3NR7_A 2L93_A 2L92_A.
Probab=33.93 E-value=42 Score=20.74 Aligned_cols=23 Identities=17% Similarity=0.361 Sum_probs=16.9
Q ss_pred hhHHHHHHHHHHHHHhCCCHHHH
Q 033498 18 HNKKLFERVNELAVKKGCTRSQL 40 (118)
Q Consensus 18 ~~~~~~~~l~~ia~~~g~s~aql 40 (118)
+..+.+..+++++..||+|+.+|
T Consensus 21 e~~~~~~~i~~~~~~~Gis~~el 43 (93)
T PF00816_consen 21 EREEAIAEIRELMAEYGISPEEL 43 (93)
T ss_dssp CCHHHHHHHHHHHHHTT--HHHC
T ss_pred HHHHHHHHHHHHHHHhCCCHHHh
Confidence 34567788888999999999888
No 54
>PF12162 STAT1_TAZ2bind: STAT1 TAZ2 binding domain; InterPro: IPR022752 This entry represents the C-terminal domain of STAT1, which selectively binds the TAZ2 domain of CRB (CREB-binding protein) []. This group of eukaryotic proteins is approximately 20 amino acids in length, and is found in association with PF02865 from PFAM, PF00017 from PFAM, PF01017 from PFAM, PF02864 from PFAM. By binding to CRB, it becomes a transcriptional activator and can initiate transcription of certain genes. ; GO: 0003700 sequence-specific DNA binding transcription factor activity; PDB: 2KA6_B.
Probab=33.83 E-value=24 Score=16.61 Aligned_cols=15 Identities=27% Similarity=0.687 Sum_probs=9.7
Q ss_pred CCCCHHHHHHHHhhh
Q 033498 73 VKLTPEEIAELESIA 87 (118)
Q Consensus 73 ~~Ls~e~~~~l~~~~ 87 (118)
.+++.+++.++....
T Consensus 8 mPMSPddy~~l~~~V 22 (23)
T PF12162_consen 8 MPMSPDDYDELERMV 22 (23)
T ss_dssp --S-HHHHHHHHHHH
T ss_pred cCCCHHHHHHHHHhh
Confidence 488999999887653
No 55
>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=33.57 E-value=71 Score=17.19 Aligned_cols=23 Identities=17% Similarity=0.192 Sum_probs=16.8
Q ss_pred CCcHHHHHHHHhhcCCCCCHHHH
Q 033498 58 TTKIENLNQNIKALSVKLTPEEI 80 (118)
Q Consensus 58 ~~~~~ql~en~~a~~~~Ls~e~~ 80 (118)
+.+.+.+....+..++.+|.+++
T Consensus 26 ~~~~~e~~~lA~~~Gy~ft~~el 48 (49)
T PF07862_consen 26 CQNPEEVVALAREAGYDFTEEEL 48 (49)
T ss_pred cCCHHHHHHHHHHcCCCCCHHHh
Confidence 55777777777777777777765
No 56
>PHA01976 helix-turn-helix protein
Probab=33.30 E-value=36 Score=19.23 Aligned_cols=11 Identities=36% Similarity=0.552 Sum_probs=5.2
Q ss_pred HHHHHhCCCHH
Q 033498 28 ELAVKKGCTRS 38 (118)
Q Consensus 28 ~ia~~~g~s~a 38 (118)
++|+..|++..
T Consensus 20 ~lA~~~gvs~~ 30 (67)
T PHA01976 20 ELSRRAGVRHS 30 (67)
T ss_pred HHHHHhCCCHH
Confidence 44444554444
No 57
>smart00657 RPOL4c DNA-directed RNA-polymerase II subunit.
Probab=32.87 E-value=1.4e+02 Score=19.38 Aligned_cols=59 Identities=20% Similarity=0.168 Sum_probs=38.6
Q ss_pred HHHHHHHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhhcCCCCCHHHHHHHHhhhcC
Q 033498 21 KLFERVNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKALSVKLTPEEIAELESIASA 89 (118)
Q Consensus 21 ~~~~~l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~~~~Ls~e~~~~l~~~~~~ 89 (118)
+.+..+....++++.+..++|.- +=..+++.+.+...+..++-.++++++..|-.....
T Consensus 55 e~i~~~~~~L~~~~L~k~E~~~i----------~Nl~P~s~~E~~~lI~sl~~r~~ee~l~~iL~~i~~ 113 (118)
T smart00657 55 EIVRAVRTLLKSKKLHKFEIAQL----------GNLRPETAEEAQLLIPSLEERIDEEELEELLDDLSS 113 (118)
T ss_pred HHHHHHHHHHHhcCCCHHHHHHH----------hCCCCCCHHHHHHHhhhhhccCCHHHHHHHHHHHHH
Confidence 34444455555677777666532 223456788888888877767888888887776553
No 58
>PRK09726 antitoxin HipB; Provisional
Probab=32.65 E-value=79 Score=19.21 Aligned_cols=26 Identities=23% Similarity=0.185 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHc
Q 033498 22 LFERVNELAVKKGCTRSQLALAWVHH 47 (118)
Q Consensus 22 ~~~~l~~ia~~~g~s~aqlAL~w~l~ 47 (118)
+.+.|+.+.++.|+|..++|-.--.+
T Consensus 13 l~~~lk~~R~~~gltq~elA~~~gvs 38 (88)
T PRK09726 13 LANAMKLVRQQNGWTQSELAKKIGIK 38 (88)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCcC
Confidence 33455556666677777666654333
No 59
>PF12668 DUF3791: Protein of unknown function (DUF3791); InterPro: IPR024269 This entry represents proteins of unknown function.
Probab=32.51 E-value=98 Score=17.67 Aligned_cols=23 Identities=13% Similarity=0.008 Sum_probs=18.5
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHH
Q 033498 23 FERVNELAVKKGCTRSQLALAWV 45 (118)
Q Consensus 23 ~~~l~~ia~~~g~s~aqlAL~w~ 45 (118)
+-.+..+|+++|+|+.++.-.|-
T Consensus 5 v~~Ie~~A~~~~~s~~ea~~~~~ 27 (62)
T PF12668_consen 5 VFCIEEFAKKLNISGEEAYNYFK 27 (62)
T ss_pred HHHHHHHHHHHCcCHHHHHHHHH
Confidence 44678999999999998766654
No 60
>PF11563 Protoglobin: Protoglobin; PDB: 2VEE_G 3QZZ_A 3R0G_A 3QZX_A 2VEB_A 1OR6_A 1OR4_B 2W31_B.
Probab=32.45 E-value=49 Score=21.93 Aligned_cols=74 Identities=11% Similarity=0.093 Sum_probs=56.2
Q ss_pred HhhHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhh-----cCCCCCHHHHHHHHhhhcCC
Q 033498 17 EHNKKLFERVNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKA-----LSVKLTPEEIAELESIASAD 90 (118)
Q Consensus 17 ~~~~~~~~~l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a-----~~~~Ls~e~~~~l~~~~~~~ 90 (118)
++..+.+..+..+..++.-....-...++.++|.....+-.....++++..... ++-.++++-++....+...|
T Consensus 16 ~~d~~~L~~~~~~~~~~~~~iv~~FY~~l~~~pe~~~~~~~~~~~~~lk~~q~~~~~~l~s~~~d~~y~~~~~~iG~~H 94 (158)
T PF11563_consen 16 EEDLELLRSLAPIIEPHAPEIVDDFYDHLLRFPETARIFDSESTIERLKATQRRHWRELFSGDFDEEYVERRRRIGQVH 94 (158)
T ss_dssp HHHHHHHHHHHHHHHCTHHHHHHHHHHHHHTSHHHHGGGCCHCCHHHHHHHHHHHHHHCTSS-CSHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHhCChHHHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHHH
Confidence 567778888888888776677888999999999876666666899999987664 34478888888877776543
No 61
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=32.07 E-value=48 Score=18.51 Aligned_cols=13 Identities=46% Similarity=0.470 Sum_probs=8.9
Q ss_pred HHHHHhCCCHHHH
Q 033498 28 ELAVKKGCTRSQL 40 (118)
Q Consensus 28 ~ia~~~g~s~aql 40 (118)
++|+..|++++|+
T Consensus 33 ~La~~~gi~~~qV 45 (50)
T PF06971_consen 33 ELAEALGITPAQV 45 (50)
T ss_dssp HHHHHHTS-HHHH
T ss_pred HHHHHHCCCHHHh
Confidence 4777788888776
No 62
>TIGR01378 thi_PPkinase thiamine pyrophosphokinase. This model has been revised. Originally, it described strictly eukaryotic thiamine pyrophosphokinase. However, it is now expanded to include also homologous enzymes, apparently functionally equivalent, from species that rely on thiamine pyrophosphokinase rather than thiamine-monophosphate kinase (TIGR01379) to produce the active TPP cofactor. This includes the thiamine pyrophosphokinase from Bacillus subtilis, previously designated YloS.
Probab=31.46 E-value=86 Score=22.36 Aligned_cols=40 Identities=30% Similarity=0.456 Sum_probs=31.0
Q ss_pred HhCCCHHHHHHHHHHcCCCCceecCCCC--cHHHHHHHHhhc
Q 033498 32 KKGCTRSQLALAWVHHQGDDVCPIPGTT--KIENLNQNIKAL 71 (118)
Q Consensus 32 ~~g~s~aqlAL~w~l~~~~v~~~I~G~~--~~~ql~en~~a~ 71 (118)
+...|=.++||+|+..++.-.+.|.|+. +.+|.-.|+...
T Consensus 69 eKD~TD~e~Al~~~~~~~~~~i~i~Ga~GgR~DH~lani~~L 110 (203)
T TIGR01378 69 EKDTTDLELALKYALERGADEITILGATGGRLDHTLANLNLL 110 (203)
T ss_pred CCCCCHHHHHHHHHHHCCCCEEEEEcCCCCcHHHHHHHHHHH
Confidence 3466778999999998876567777765 788888888754
No 63
>KOG0693 consensus Myo-inositol-1-phosphate synthase [Lipid transport and metabolism]
Probab=31.23 E-value=76 Score=25.56 Aligned_cols=74 Identities=19% Similarity=0.305 Sum_probs=57.9
Q ss_pred HhhHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCC-cHHHHHHHHhhcCCCCCHHHHHHHHhhhcCCCc
Q 033498 17 EHNKKLFERVNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTT-KIENLNQNIKALSVKLTPEEIAELESIASADAV 92 (118)
Q Consensus 17 ~~~~~~~~~l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~-~~~ql~en~~a~~~~Ls~e~~~~l~~~~~~~~~ 92 (118)
++...+.+.++++-++.++. .+..-|..+....+-|+||.. +.+.|-+.++.-+.++++..+-++..+...+++
T Consensus 204 eqle~Ir~Dir~Fke~~~ld--kViVLWTANTERy~~V~~GlNdT~enl~~si~~~~~EisPStifA~AsilEg~~y 278 (512)
T KOG0693|consen 204 EQLEQIRKDIREFKEENKLD--KVIVLWTANTERYSNVIPGLNDTAENLLESIEKDESEISPSTIFAIASILEGCPY 278 (512)
T ss_pred HHHHHHHHHHHHHHHhcCCc--eEEEEEecCcceeeccccccchHHHHHHHHHhcCccccChHHHHHHHHHHcCCCc
Confidence 44445566777777777766 456678888888888999987 677888888887789999999999999876654
No 64
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=31.07 E-value=63 Score=18.24 Aligned_cols=16 Identities=31% Similarity=0.515 Sum_probs=13.2
Q ss_pred HHHHHHHhCCCHHHHH
Q 033498 26 VNELAVKKGCTRSQLA 41 (118)
Q Consensus 26 l~~ia~~~g~s~aqlA 41 (118)
+.++|++.|+|.+.+.
T Consensus 26 l~elA~~lgis~st~~ 41 (53)
T PF04967_consen 26 LEELAEELGISKSTVS 41 (53)
T ss_pred HHHHHHHhCCCHHHHH
Confidence 6789999999988654
No 65
>PF02570 CbiC: Precorrin-8X methylmutase; InterPro: IPR003722 Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase []. In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase []. There are at least two distinct cobalamin biosynthetic pathways in bacteria []: Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway []; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis []; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii subsp. shermanii. Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) []. There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans. This entry represents CbiC and CobH precorrin-8X methylmutase (also known as precorrin isomerase, 5.4.1.2 from EC), both as stand-alone enzymes and when CobJ forms part of a bifunctional enzyme. CobH and CbiC from the aerobic and anaerobic pathways, respectively, catalyse a methyl rearrangement in precorrin-8 that moves the methyl group from C-11 to C-12 to produce hydrogenobyrinic acid []. Hydrogenobyrinic acid now contains all the major framework alterations associated with corrin synthesis []. CobH and CbiC can sometimes be fused to other enzymes in the cobalamin pathway to make bifunctional enzymes: e.g., with CobJ/CibH (precorrin-3B C17-methylase/precorrin isomerase, IPR014422 from INTERPRO) and with CbiX (precorrin isomerase, IPR012067 from INTERPRO).; GO: 0016993 precorrin-8X methylmutase activity, 0009236 cobalamin biosynthetic process; PDB: 1V9C_B 1I1H_A 1F2V_A 1OU0_B 2AFV_A 2AFR_A 3E7D_D.
Probab=31.00 E-value=1.2e+02 Score=22.03 Aligned_cols=35 Identities=29% Similarity=0.295 Sum_probs=26.6
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCC
Q 033498 25 RVNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTT 59 (118)
Q Consensus 25 ~l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~ 59 (118)
...++|++.|.|-+..+++....+.....+.+|-.
T Consensus 94 ~v~~~A~~~g~TRs~aa~~~a~~~~~~~I~vIGNA 128 (198)
T PF02570_consen 94 EVAELAKEEGITRSAAAMRKAAKELPGAIVVIGNA 128 (198)
T ss_dssp HHHHHHHHHTS-HHHHHHHHHHCTTTTCEEEESS-
T ss_pred chHHHHhhcCCcHHHHHHHHHHHHcCCcEEEEeCc
Confidence 45678999999999999999998766566677754
No 66
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=30.81 E-value=20 Score=20.05 Aligned_cols=13 Identities=46% Similarity=0.644 Sum_probs=5.8
Q ss_pred HHHHHHhCCCHHH
Q 033498 27 NELAVKKGCTRSQ 39 (118)
Q Consensus 27 ~~ia~~~g~s~aq 39 (118)
.++|++.|++.++
T Consensus 14 ~~La~~~gis~~t 26 (63)
T PF13443_consen 14 KDLARKTGISRST 26 (63)
T ss_dssp HHHHHHHT--HHH
T ss_pred HHHHHHHCcCHHH
Confidence 4555555655543
No 67
>PRK10945 gene expression modulator; Provisional
Probab=30.70 E-value=1.2e+02 Score=18.44 Aligned_cols=31 Identities=26% Similarity=0.319 Sum_probs=25.8
Q ss_pred CCCcHHHHHHHHhhcCCCCCHHHHHHHHhhh
Q 033498 57 GTTKIENLNQNIKALSVKLTPEEIAELESIA 87 (118)
Q Consensus 57 G~~~~~ql~en~~a~~~~Ls~e~~~~l~~~~ 87 (118)
.|++.+-|+..+.-....|++.++..+....
T Consensus 17 rcss~eTLEkvie~~~~~L~~~E~~~f~~Aa 47 (72)
T PRK10945 17 RCQTIDTLERVIEKNKYELSDDELAVFYSAA 47 (72)
T ss_pred hcCcHHHHHHHHHHhhccCCHHHHHHHHHHH
Confidence 5788899999998888899999888777654
No 68
>TIGR02384 RelB_DinJ addiction module antitoxin, RelB/DinJ family. Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the seed for this alignment all were found adjacent to toxin genes. The resulting model appears to describe a narrower set of proteins than Pfam model pfam04221, although many in the scope of this model are not obviously paired with toxin proteins. Several toxin/antitoxin pairs may occur in a single species.
Probab=30.58 E-value=1.2e+02 Score=18.50 Aligned_cols=30 Identities=20% Similarity=0.133 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHHhCCCHHH---HHHHHHHcCCC
Q 033498 21 KLFERVNELAVKKGCTRSQ---LALAWVHHQGD 50 (118)
Q Consensus 21 ~~~~~l~~ia~~~g~s~aq---lAL~w~l~~~~ 50 (118)
++-+....+++++|+++++ +.++++..+.+
T Consensus 12 ~lK~~a~~i~~~lGl~~s~ai~~fl~qvv~~~~ 44 (83)
T TIGR02384 12 ELKKEAYAVFEELGLTPSTAIRMFLKQVIREQG 44 (83)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 3556677889999999975 45666676664
No 69
>COG0761 lytB 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]
Probab=30.47 E-value=79 Score=24.36 Aligned_cols=44 Identities=20% Similarity=0.369 Sum_probs=35.0
Q ss_pred HHHHHHHHHhCC------CHHHHHHHHHHcCCCCceecCCCCcHHHHHHHH
Q 033498 24 ERVNELAVKKGC------TRSQLALAWVHHQGDDVCPIPGTTKIENLNQNI 68 (118)
Q Consensus 24 ~~l~~ia~~~g~------s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~ 68 (118)
.+|.++|++.|. ++.++=..|+.... .+.+-.|+++++-|-+++
T Consensus 228 ~rL~eiA~~~g~~aylId~~~ei~~~w~~~~~-~VGvTAGAStPd~lV~~V 277 (294)
T COG0761 228 NRLAEIAKRHGKPAYLIDDAEEIDPEWLKGVK-TVGVTAGASTPDWLVQEV 277 (294)
T ss_pred HHHHHHHHHhCCCeEEeCChHhCCHHHhcCcc-EEEEecCCCCCHHHHHHH
Confidence 356788888887 55788899988844 467889999999998876
No 70
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=30.25 E-value=96 Score=16.65 Aligned_cols=25 Identities=28% Similarity=0.296 Sum_probs=19.7
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHc
Q 033498 23 FERVNELAVKKGCTRSQLALAWVHH 47 (118)
Q Consensus 23 ~~~l~~ia~~~g~s~aqlAL~w~l~ 47 (118)
.+.+..||...|++..+|---|...
T Consensus 27 ~~~~~~la~~~~l~~~qV~~WF~nr 51 (59)
T cd00086 27 REEREELAKELGLTERQVKIWFQNR 51 (59)
T ss_pred HHHHHHHHHHHCcCHHHHHHHHHHH
Confidence 4567889999999999988766544
No 71
>PLN02438 inositol-3-phosphate synthase
Probab=30.07 E-value=1.2e+02 Score=25.14 Aligned_cols=73 Identities=16% Similarity=0.284 Sum_probs=55.9
Q ss_pred hHhhHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCCCceecCCC-CcHHHHHHHHhhcCCCCCHHHHHHHHhhhcCC
Q 033498 16 LEHNKKLFERVNELAVKKGCTRSQLALAWVHHQGDDVCPIPGT-TKIENLNQNIKALSVKLTPEEIAELESIASAD 90 (118)
Q Consensus 16 ~~~~~~~~~~l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~-~~~~ql~en~~a~~~~Ls~e~~~~l~~~~~~~ 90 (118)
.+....+.+.++++.+++|++. +..-|+.+.....-+++|. .+.+.++..++.-+-.+++..+-....+...+
T Consensus 203 ~e~ve~ir~DIr~Fk~~n~ld~--vVVlwtAsTEr~~~~~~~~~~t~~~l~~ai~~~~~eispS~~YA~AAl~eG~ 276 (510)
T PLN02438 203 KEQMDQIRKDIREFKEKNKVDK--VVVLWTANTERYSNVVVGLNDTMENLLASIEKDEAEISPSTLYALACILEGV 276 (510)
T ss_pred HHHHHHHHHHHHHHHHHhCCCe--EEEEECCCCCCCCcCCCcccCCHHHHHHHHhcCCCcCChHHHHHHHHHHcCC
Confidence 3444556677888999999884 6777888887655546565 69999999999877789999988888776543
No 72
>PRK00901 methylated-DNA--protein-cysteine methyltransferase; Provisional
Probab=29.93 E-value=80 Score=21.81 Aligned_cols=35 Identities=20% Similarity=0.200 Sum_probs=26.6
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCC
Q 033498 25 RVNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTT 59 (118)
Q Consensus 25 ~l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~ 59 (118)
...++|+..|.+.+.-|.+..+.+..+..+||.-|
T Consensus 92 tY~~lA~~~g~p~a~RAVg~A~~~NP~~iiIPCHR 126 (155)
T PRK00901 92 SYKEIAVNIGNPKACRAVGLANNKNPIPIFIPCHR 126 (155)
T ss_pred CHHHHHHHHCCCchHHHHHHHHHhCCCCCccCCce
Confidence 34678888898888888888888777777777543
No 73
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=29.69 E-value=94 Score=16.41 Aligned_cols=19 Identities=26% Similarity=0.205 Sum_probs=14.0
Q ss_pred HHHHHHHhCCCHHHHHHHH
Q 033498 26 VNELAVKKGCTRSQLALAW 44 (118)
Q Consensus 26 l~~ia~~~g~s~aqlAL~w 44 (118)
+.++|+..|+|.+++.=++
T Consensus 20 ~~~la~~lglS~~~v~~Ri 38 (42)
T PF13404_consen 20 YAELAEELGLSESTVRRRI 38 (42)
T ss_dssp HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 5688999999998876553
No 74
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea. The function is not known. ; PDB: 2L02_B 2L01_A.
Probab=29.66 E-value=61 Score=19.15 Aligned_cols=26 Identities=27% Similarity=0.480 Sum_probs=17.8
Q ss_pred HHHHHHHhCCCH--HHHHHHHHHcCCCC
Q 033498 26 VNELAVKKGCTR--SQLALAWVHHQGDD 51 (118)
Q Consensus 26 l~~ia~~~g~s~--aqlAL~w~l~~~~v 51 (118)
+.++++..|.+. ..+||.|+.+...+
T Consensus 25 ~~el~k~~~l~~~~~~~AiGWLarE~KI 52 (65)
T PF10771_consen 25 VSELKKATGLSDKEVYLAIGWLARENKI 52 (65)
T ss_dssp HHHHHHHCT-SCHHHHHHHHHHHCTTSE
T ss_pred HHHHHHHhCcCHHHHHHHHHHHhccCce
Confidence 455666665554 68899999987754
No 75
>PF07836 DmpG_comm: DmpG-like communication domain; InterPro: IPR012425 This domain is found towards the C-terminal region of various aldolase enzymes. It consists of five alpha-helices, four of which form an antiparallel helical bundle that plugs the C terminus of the N-terminal TIM barrel domain []. The communication domain is thought to play an important role in the heterodimerisation of the enzyme []. Members of this entry heterodimerise with members of IPR003361 from INTERPRO to form a bifunctional aldolase-dehydrogenase [].; GO: 0016833 oxo-acid-lyase activity, 0019439 aromatic compound catabolic process; PDB: 1NVM_E.
Probab=29.62 E-value=88 Score=18.64 Aligned_cols=25 Identities=8% Similarity=0.110 Sum_probs=17.8
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHc
Q 033498 23 FERVNELAVKKGCTRSQLALAWVHH 47 (118)
Q Consensus 23 ~~~l~~ia~~~g~s~aqlAL~w~l~ 47 (118)
+...+..|++||+++.++.+.--..
T Consensus 22 l~ha~raa~~ygVd~r~il~elgrR 46 (66)
T PF07836_consen 22 LLHAERAAERYGVDPRDILVELGRR 46 (66)
T ss_dssp HHHHHHHHHHHT--HHHHHHHHHHC
T ss_pred HHHHHHHHHHhCcCHHHHHHHHhcc
Confidence 4456788999999999998886544
No 76
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=29.54 E-value=1.3e+02 Score=18.97 Aligned_cols=38 Identities=29% Similarity=0.436 Sum_probs=23.3
Q ss_pred CCCCCccchHhhHHHHHH----HHHHHHHhCC-CHHHHHHHHHH
Q 033498 8 LPRFQPENLEHNKKLFER----VNELAVKKGC-TRSQLALAWVH 46 (118)
Q Consensus 8 ~~~~~~~~~~~~~~~~~~----l~~ia~~~g~-s~aqlAL~w~l 46 (118)
..+|+++.-.+....... +..+|.++|+ +..++ ..|..
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~sv~~vAr~~gv~~~~~l-~~W~~ 47 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGDTVSEVAREFGIVSATQL-YKWRI 47 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCccHHHHHHHhCCCChHHH-HHHHH
Confidence 345655544455554443 8899999996 66654 44554
No 77
>COG0673 MviM Predicted dehydrogenases and related proteins [General function prediction only]
Probab=29.06 E-value=1.6e+02 Score=21.95 Aligned_cols=66 Identities=23% Similarity=0.160 Sum_probs=44.6
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhhcC--------C--CCCHHHHHHHHhhhcCC
Q 033498 25 RVNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKALS--------V--KLTPEEIAELESIASAD 90 (118)
Q Consensus 25 ~l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~~--------~--~Ls~e~~~~l~~~~~~~ 90 (118)
..+++++++|....---+.=+++.+.+..|++.+.+..|.+-.++++. . .+|.+|.++|.++.+..
T Consensus 42 ~a~~~a~~~~~~~~~~~~~~ll~~~~iD~V~Iatp~~~H~e~~~~AL~aGkhVl~EKPla~t~~ea~~l~~~a~~~ 117 (342)
T COG0673 42 RAEAFAEEFGIAKAYTDLEELLADPDIDAVYIATPNALHAELALAALEAGKHVLCEKPLALTLEEAEELVELARKA 117 (342)
T ss_pred HHHHHHHHcCCCcccCCHHHHhcCCCCCEEEEcCCChhhHHHHHHHHhcCCEEEEcCCCCCCHHHHHHHHHHHHHc
Confidence 367889999987222225556777777777777777766665555532 2 46889999888877654
No 78
>TIGR02530 flg_new flagellar operon protein. Members of this family are found in a subset of bacterial flagellar operons, generally between genes designated flgD and flgE, in species as diverse as Bacillus halodurans and various other Firmicutes, Geobacter sulfurreducens, and Bdellovibrio bacteriovorus. The specific molecular function is unknown.
Probab=28.97 E-value=72 Score=20.45 Aligned_cols=29 Identities=7% Similarity=0.251 Sum_probs=23.6
Q ss_pred HHHHHHHHhhcCCCCCHHHHHHHHhhhcC
Q 033498 61 IENLNQNIKALSVKLTPEEIAELESIASA 89 (118)
Q Consensus 61 ~~ql~en~~a~~~~Ls~e~~~~l~~~~~~ 89 (118)
-.|..+-+..-++.|+++++..|++....
T Consensus 18 SkHA~~RL~~R~I~l~~~~~~~i~~av~~ 46 (96)
T TIGR02530 18 SKHALERMRERNISINPDDWKKLLEAVEE 46 (96)
T ss_pred cHHHHHHHHHcCCCCCHHHHHHHHHHHHH
Confidence 45777777777889999999999987653
No 79
>PRK10328 DNA binding protein, nucleoid-associated; Provisional
Probab=28.86 E-value=1e+02 Score=20.82 Aligned_cols=23 Identities=17% Similarity=0.201 Sum_probs=18.1
Q ss_pred hhHHHHHHHHHHHHHhCCCHHHH
Q 033498 18 HNKKLFERVNELAVKKGCTRSQL 40 (118)
Q Consensus 18 ~~~~~~~~l~~ia~~~g~s~aql 40 (118)
+....+..+++++..+|+|+.++
T Consensus 53 er~~~l~~i~~~~~~~Git~eeL 75 (134)
T PRK10328 53 ERQEKINTWLELMKADGINPEEL 75 (134)
T ss_pred HHHHHHHHHHHHHHHhCCCHHHH
Confidence 34467778888888899999888
No 80
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=28.84 E-value=1.2e+02 Score=17.47 Aligned_cols=45 Identities=11% Similarity=0.155 Sum_probs=31.6
Q ss_pred HHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhhcCCCCC
Q 033498 26 VNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKALSVKLT 76 (118)
Q Consensus 26 l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~~~~Ls 76 (118)
++++|+..|+|.+.+.. +++... -+...+.+++.+.++..+...+
T Consensus 3 ~~~iA~~~gvS~~TVSr--~ln~~~----~v~~~t~~~i~~~~~~~gy~~~ 47 (70)
T smart00354 3 IKDVARLAGVSKATVSR--VLNGNG----RVSEETREKVLAAMEELGYIPN 47 (70)
T ss_pred HHHHHHHHCCCHHHHHH--HHCCCC----CCCHHHHHHHHHHHHHhCCCCC
Confidence 56899999999997765 344331 1256678888888888877543
No 81
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=28.61 E-value=65 Score=17.05 Aligned_cols=16 Identities=31% Similarity=0.532 Sum_probs=9.3
Q ss_pred HHHHHHHHhCCCHHHH
Q 033498 25 RVNELAVKKGCTRSQL 40 (118)
Q Consensus 25 ~l~~ia~~~g~s~aql 40 (118)
.+.+||+..|++.+.|
T Consensus 22 s~~~IA~~lg~s~sTV 37 (44)
T PF13936_consen 22 SIREIAKRLGRSRSTV 37 (44)
T ss_dssp -HHHHHHHTT--HHHH
T ss_pred CHHHHHHHHCcCcHHH
Confidence 4567888888877654
No 82
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=28.44 E-value=64 Score=22.38 Aligned_cols=56 Identities=13% Similarity=0.066 Sum_probs=30.0
Q ss_pred hHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCC--cHHHHHHHHhhcCCC
Q 033498 19 NKKLFERVNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTT--KIENLNQNIKALSVK 74 (118)
Q Consensus 19 ~~~~~~~l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~--~~~ql~en~~a~~~~ 74 (118)
...+-+.|+++.++.|+|..++|=..-+++..+.-..-|-+ +.+.+...++++++.
T Consensus 5 ~~~~g~~l~~~R~~~glt~~elA~~~gis~~~is~~E~g~~~p~~~~l~~ia~~l~v~ 62 (185)
T PRK09943 5 GLAPGKRLSEIRQQQGLSQRRAAELSGLTHSAISTIEQDKVSPAISTLQKLLKVYGLS 62 (185)
T ss_pred hhHHHHHHHHHHHHcCCCHHHHHHHHCCCHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Confidence 34455667777777777777777665444443322222322 345555555555544
No 83
>PRK10869 recombination and repair protein; Provisional
Probab=28.43 E-value=86 Score=26.07 Aligned_cols=36 Identities=17% Similarity=0.218 Sum_probs=29.7
Q ss_pred CCCccchHhhHHHHHHHHHHHHHhCCCHHHHHHHHHH
Q 033498 10 RFQPENLEHNKKLFERVNELAVKKGCTRSQLALAWVH 46 (118)
Q Consensus 10 ~~~~~~~~~~~~~~~~l~~ia~~~g~s~aqlAL~w~l 46 (118)
.|.+..++...+++..+..+.++||.|+.++ +.|.-
T Consensus 292 ~~dp~~l~~ie~Rl~~l~~L~rKyg~~~~~~-~~~~~ 327 (553)
T PRK10869 292 DLDPNRLAELEQRLSKQISLARKHHVSPEEL-PQHHQ 327 (553)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHhCCCHHHH-HHHHH
Confidence 4667788999999999999999999998776 55543
No 84
>PRK10128 2-keto-3-deoxy-L-rhamnonate aldolase; Provisional
Probab=28.14 E-value=2.6e+02 Score=21.06 Aligned_cols=35 Identities=20% Similarity=0.149 Sum_probs=30.5
Q ss_pred HHHHHHHHcCCCCceecCCCCcHHHHHHHHhhcCC
Q 033498 39 QLALAWVHHQGDDVCPIPGTTKIENLNQNIKALSV 73 (118)
Q Consensus 39 qlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~~~ 73 (118)
...+..+|..+.-.+++|-..|.+|.++.++++.+
T Consensus 80 ~~~i~r~LD~GA~GIivP~V~saeeA~~~V~a~rY 114 (267)
T PRK10128 80 KPLIKQVLDIGAQTLLIPMVDTAEQARQVVSATRY 114 (267)
T ss_pred HHHHHHHhCCCCCeeEecCcCCHHHHHHHHHhcCC
Confidence 45678899999888999999999999999998876
No 85
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=28.00 E-value=1.1e+02 Score=22.62 Aligned_cols=44 Identities=23% Similarity=0.283 Sum_probs=30.1
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhhcCCC
Q 033498 25 RVNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKALSVK 74 (118)
Q Consensus 25 ~l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~~~~ 74 (118)
.+++||++.|+|.+.+.-. +++.. -++..+.+++.+.++..+..
T Consensus 8 Ti~dIA~~agVS~~TVSr~--Ln~~~----~vs~~tr~~V~~~a~elgY~ 51 (342)
T PRK10014 8 TIHDVALAAGVSVSTVSLV--LSGKG----RISTATGERVNQAIEELGFV 51 (342)
T ss_pred cHHHHHHHhCCCHHHHHHH--HCCCC----CCCHHHHHHHHHHHHHhCCC
Confidence 4788999999998876655 44432 35666777777776666553
No 86
>PF07498 Rho_N: Rho termination factor, N-terminal domain; InterPro: IPR011112 The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It is thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers []. This domain is found to the N terminus of the RNA binding domain (IPR011113 from INTERPRO).; GO: 0006353 transcription termination, DNA-dependent; PDB: 1A8V_B 1PVO_A 1PV4_D 3ICE_A 1XPU_C 1XPO_D 1XPR_F 2A8V_B 2HT1_B 1A63_A ....
Probab=27.78 E-value=40 Score=17.99 Aligned_cols=14 Identities=21% Similarity=0.389 Sum_probs=9.9
Q ss_pred HHHHHHHHHHhCCC
Q 033498 23 FERVNELAVKKGCT 36 (118)
Q Consensus 23 ~~~l~~ia~~~g~s 36 (118)
+.+|+++|+++|++
T Consensus 7 ~~eL~~iAk~lgI~ 20 (43)
T PF07498_consen 7 LSELREIAKELGIE 20 (43)
T ss_dssp HHHHHHHHHCTT-T
T ss_pred HHHHHHHHHHcCCC
Confidence 56788888888764
No 87
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=27.72 E-value=1.2e+02 Score=17.01 Aligned_cols=22 Identities=18% Similarity=0.274 Sum_probs=15.3
Q ss_pred HHHHHHHhCCCHHHHHHHHHHc
Q 033498 26 VNELAVKKGCTRSQLALAWVHH 47 (118)
Q Consensus 26 l~~ia~~~g~s~aqlAL~w~l~ 47 (118)
+.++|+..|++...+.-.+...
T Consensus 4 ~~~la~~~~~s~~~l~~~f~~~ 25 (84)
T smart00342 4 LEDLAEALGMSPRHLQRLFKKE 25 (84)
T ss_pred HHHHHHHhCCCHHHHHHHHHHH
Confidence 5678888888887766655443
No 88
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=27.51 E-value=1.1e+02 Score=16.53 Aligned_cols=25 Identities=28% Similarity=0.182 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHhCCCHHHHHHHHHH
Q 033498 22 LFERVNELAVKKGCTRSQLALAWVH 46 (118)
Q Consensus 22 ~~~~l~~ia~~~g~s~aqlAL~w~l 46 (118)
-.+....||...|++..+|-.-|..
T Consensus 26 ~~~~~~~la~~l~l~~~~V~~WF~n 50 (57)
T PF00046_consen 26 SKEEREELAKELGLTERQVKNWFQN 50 (57)
T ss_dssp HHHHHHHHHHHHTSSHHHHHHHHHH
T ss_pred cccccccccccccccccccccCHHH
Confidence 3456788999999999998766543
No 89
>PF04221 RelB: RelB antitoxin; InterPro: IPR007337 Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the seed for this alignment all were found adjacent to toxin genes. Several toxin/antitoxin pairs may occur in a single species. RelE and RelB form a toxin-antitoxin system; RelE represses translation, probably through binding ribosomes [, ]. RelB stably binds RelE, presumably deactivating it.; PDB: 2KC8_B 2K29_A.
Probab=27.43 E-value=1.4e+02 Score=18.09 Aligned_cols=30 Identities=23% Similarity=0.243 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHHhCCCHHHH---HHHHHHcCCC
Q 033498 21 KLFERVNELAVKKGCTRSQL---ALAWVHHQGD 50 (118)
Q Consensus 21 ~~~~~l~~ia~~~g~s~aql---AL~w~l~~~~ 50 (118)
++.++..++++++|+++++. .+..+..+.+
T Consensus 11 ~lK~~a~~il~~~Glt~s~ai~~fl~qiv~~~~ 43 (83)
T PF04221_consen 11 ELKEEAEAILEELGLTLSDAINMFLKQIVREGG 43 (83)
T ss_dssp HHHHHHHHHHHHTT--HHHHHHHHHHHHHHHSS
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhCC
Confidence 45567788999999999754 4555555553
No 90
>TIGR03239 GarL 2-dehydro-3-deoxyglucarate aldolase. In E. coli this enzyme (GarL, ) 2-dehydro-3-deoxyglucarate aldolase acts in the catabolism of several sugars including D-galactarate, D-glucarate and L-idarate. In fact, 5-dehydro-4-deoxy-D-glucarate aldolase is a synonym for this enzyme as it is unclear in the literature whether the enzyme acts on only one of these or, as seems likely, has no preference. (Despite the apparent large difference in substrate stucture indicated by their names, 2-DH-3DO- and 5-DH-4DO-glucarate differ only by the chirality of most central hydroxyl-bearing carbon and is alternately named 2-DH-3DO-galactarate.) The reported product of D-galactarate dehydratase (4.2.1.42) is the 5DH-4DO-glucarate isomer and this enzyme is found proximal to the aldolase in many genomes (GenProp0714) where no epimerase is known. Similarly, the product of D-glucarate dehydratase (4.2.1.40) is again the 5-DH-4DO isomer, so the provenance of the 2-DH-3DO-glucarate isomer for which
Probab=27.28 E-value=2.6e+02 Score=20.68 Aligned_cols=48 Identities=10% Similarity=-0.022 Sum_probs=36.0
Q ss_pred HHHHHHHhCCCH-------HHHHHHHHHcCCCCceecCCCCcHHHHHHHHhhcCC
Q 033498 26 VNELAVKKGCTR-------SQLALAWVHHQGDDVCPIPGTTKIENLNQNIKALSV 73 (118)
Q Consensus 26 l~~ia~~~g~s~-------aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~~~ 73 (118)
+-..++..|+++ ....+..+|..+...+++|-..|.+|.++.++++.+
T Consensus 54 ~~~a~~~~g~~~~VRvp~~~~~~i~r~LD~Ga~gIivP~v~taeea~~~v~a~ky 108 (249)
T TIGR03239 54 QLMALKGSASAPVVRPPWNEPVIIKRLLDIGFYNFLIPFVESAEEAERAVAATRY 108 (249)
T ss_pred HHHHHhhcCCCcEEECCCCCHHHHHHHhcCCCCEEEecCcCCHHHHHHHHHHcCC
Confidence 333455566553 245678889988888999999999999999887765
No 91
>PRK13702 replication protein; Provisional
Probab=27.07 E-value=1.4e+02 Score=18.65 Aligned_cols=26 Identities=19% Similarity=0.363 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHc
Q 033498 22 LFERVNELAVKKGCTRSQLALAWVHH 47 (118)
Q Consensus 22 ~~~~l~~ia~~~g~s~aqlAL~w~l~ 47 (118)
+-+.|.++|++.|+|-+++.=.++..
T Consensus 52 lK~~L~elc~~~glTQAe~IE~LIe~ 77 (85)
T PRK13702 52 LKDKLMELCEEEGLTQAEMIERLIER 77 (85)
T ss_pred HHHHHHHHHHHcCCcHHHHHHHHHHH
Confidence 45678899999999999998777654
No 92
>PRK08286 cbiC cobalt-precorrin-8X methylmutase; Validated
Probab=27.03 E-value=74 Score=23.35 Aligned_cols=45 Identities=27% Similarity=0.228 Sum_probs=31.1
Q ss_pred HHHHHHHhCCCHHHHHHHHHHcCCCCceecCCC--CcHHHHHHHHhh
Q 033498 26 VNELAVKKGCTRSQLALAWVHHQGDDVCPIPGT--TKIENLNQNIKA 70 (118)
Q Consensus 26 l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~--~~~~ql~en~~a 70 (118)
..++|++.|.|-+..+++....++...++++|- +-+-.|.+.++.
T Consensus 108 v~e~A~~~g~TRsaaam~~a~~~~~~~IvvIGNAPTAL~~l~~li~~ 154 (214)
T PRK08286 108 VVELAKEQGITRSMAAVDIAAAEEGPKLFVFGNAPTALFRLLEMVEH 154 (214)
T ss_pred hHHHHHhcCCcHHHHHHHHHHhccCCcEEEEeCcHHHHHHHHHHHHc
Confidence 456799999999999999888765544566663 344455555543
No 93
>TIGR03798 ocin_TIGR03798 bacteriocin propeptide, TIGR03798 family. This model describes a conserved, fairly long (about 65 residue) propeptide region for a family of putative microcins, that is, bacteriocins of small size. Members of the seed alignment tend to have the Gly-Gly motif as the last two residues of the matched region. This is a cleavage site for a combination processing/export ABC transporter with a peptidase domain.
Probab=26.73 E-value=1.3e+02 Score=17.26 Aligned_cols=27 Identities=19% Similarity=0.177 Sum_probs=19.1
Q ss_pred CCCcHHHHHHHHhhcCCCCCHHHHHHH
Q 033498 57 GTTKIENLNQNIKALSVKLTPEEIAEL 83 (118)
Q Consensus 57 G~~~~~ql~en~~a~~~~Ls~e~~~~l 83 (118)
.+.+++.+....+..++.+|.+++...
T Consensus 23 ~~~~~e~~~~lA~~~Gf~ft~~el~~~ 49 (64)
T TIGR03798 23 AAEDPEDRVAIAKEAGFEFTGEDLKEA 49 (64)
T ss_pred HcCCHHHHHHHHHHcCCCCCHHHHHHH
Confidence 356677777777777778888777653
No 94
>PF13833 EF-hand_8: EF-hand domain pair; PDB: 3KF9_A 1TTX_A 1WLZ_A 1ALV_A 1NX3_A 1ALW_A 1NX2_A 1NX1_A 1NX0_A 1DF0_A ....
Probab=26.69 E-value=1.1e+02 Score=16.23 Aligned_cols=30 Identities=23% Similarity=0.325 Sum_probs=23.8
Q ss_pred CcHHHHHHHHhhcCCC-CCHHHHHHHHhhhc
Q 033498 59 TKIENLNQNIKALSVK-LTPEEIAELESIAS 88 (118)
Q Consensus 59 ~~~~ql~en~~a~~~~-Ls~e~~~~l~~~~~ 88 (118)
-+.+.+...+...+.. ++++++..|-..+.
T Consensus 5 i~~~~~~~~l~~~g~~~~s~~e~~~l~~~~D 35 (54)
T PF13833_consen 5 ITREEFRRALSKLGIKDLSEEEVDRLFREFD 35 (54)
T ss_dssp EEHHHHHHHHHHTTSSSSCHHHHHHHHHHHT
T ss_pred ECHHHHHHHHHHhCCCCCCHHHHHHHHHhcc
Confidence 3677888888777888 99999888877764
No 95
>PRK06424 transcription factor; Provisional
Probab=26.50 E-value=1.6e+02 Score=20.04 Aligned_cols=25 Identities=16% Similarity=0.139 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHHHhCCCHHHHHHHH
Q 033498 20 KKLFERVNELAVKKGCTRSQLALAW 44 (118)
Q Consensus 20 ~~~~~~l~~ia~~~g~s~aqlAL~w 44 (118)
...-+.|+.+-++.|+|..+||-.-
T Consensus 83 ~~~g~~Ir~lRe~~GLSQ~eLA~~i 107 (144)
T PRK06424 83 EDYAELVKNARERLSMSQADLAAKI 107 (144)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHh
Confidence 3455667777778899999888664
No 96
>PRK14981 DNA-directed RNA polymerase subunit F; Provisional
Probab=26.26 E-value=1.3e+02 Score=19.54 Aligned_cols=33 Identities=21% Similarity=0.233 Sum_probs=26.1
Q ss_pred CCCCcHHHHHHHHhhcCCCCCHHHHHHHHhhhc
Q 033498 56 PGTTKIENLNQNIKALSVKLTPEEIAELESIAS 88 (118)
Q Consensus 56 ~G~~~~~ql~en~~a~~~~Ls~e~~~~l~~~~~ 88 (118)
..+.+.+.++..+...+..+++++++.|-....
T Consensus 76 L~P~~~dElrai~~~~~~~~~~e~l~~ILd~l~ 108 (112)
T PRK14981 76 ILPETRDELRAIFAKERYTLSPEELDEILDIVK 108 (112)
T ss_pred cCCCCHHHHHHHHHHhccCCCHHHHHHHHHHHH
Confidence 356778888888888888899999888876654
No 97
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=26.19 E-value=44 Score=18.39 Aligned_cols=18 Identities=28% Similarity=0.362 Sum_probs=14.1
Q ss_pred HHHHHHHhCCCHHHHHHH
Q 033498 26 VNELAVKKGCTRSQLALA 43 (118)
Q Consensus 26 l~~ia~~~g~s~aqlAL~ 43 (118)
+.++|++.|+++.++.-.
T Consensus 6 V~elAk~l~v~~~~ii~~ 23 (54)
T PF04760_consen 6 VSELAKELGVPSKEIIKK 23 (54)
T ss_dssp TTHHHHHHSSSHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHH
Confidence 568999999999876544
No 98
>PRK09526 lacI lac repressor; Reviewed
Probab=25.91 E-value=1.4e+02 Score=22.15 Aligned_cols=43 Identities=12% Similarity=0.159 Sum_probs=25.4
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhhcCC
Q 033498 25 RVNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKALSV 73 (118)
Q Consensus 25 ~l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~~~ 73 (118)
.+++||++.|+|.+.+.-. +++.. -++..+.+++.+.++..+.
T Consensus 7 ti~dIA~~aGVS~~TVSrv--Ln~~~----~vs~~tr~rV~~~a~elgY 49 (342)
T PRK09526 7 TLYDVARYAGVSYQTVSRV--LNQAS----HVSAKTREKVEAAMAELNY 49 (342)
T ss_pred cHHHHHHHhCCCHHHHHHH--hcCCC----CCCHHHHHHHHHHHHHHCC
Confidence 4677888888887766544 33331 2445566666666555443
No 99
>PF03869 Arc: Arc-like DNA binding domain; InterPro: IPR005569 Arc repressor act by the cooperative binding of two Arc repressor dimers to a 21-base-pair operator site. Each Arc dimer uses an antiparallel beta-sheet to recognise bases in the major groove [].; GO: 0003677 DNA binding; PDB: 3QOQ_D 1MNT_B 1QTG_B 1BDV_A 1PAR_C 1BDT_C 1ARR_B 1MYL_F 1MYK_A 1NLA_B ....
Probab=25.84 E-value=1.3e+02 Score=16.60 Aligned_cols=20 Identities=25% Similarity=0.288 Sum_probs=15.2
Q ss_pred HHHHHHHHHHHHhCCCHHHH
Q 033498 21 KLFERVNELAVKKGCTRSQL 40 (118)
Q Consensus 21 ~~~~~l~~ia~~~g~s~aql 40 (118)
++.+.|+..|+..|.|+..-
T Consensus 14 ~l~~~lk~~A~~~gRS~NsE 33 (50)
T PF03869_consen 14 ELKEKLKERAEENGRSMNSE 33 (50)
T ss_dssp HHHHHHHHHHHHTTS-HHHH
T ss_pred HHHHHHHHHHHHhCCChHHH
Confidence 56778899999999998643
No 100
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=25.56 E-value=1.2e+02 Score=16.18 Aligned_cols=25 Identities=28% Similarity=0.320 Sum_probs=19.5
Q ss_pred HHHHHHHHHHhCCCHHHHHHHHHHc
Q 033498 23 FERVNELAVKKGCTRSQLALAWVHH 47 (118)
Q Consensus 23 ~~~l~~ia~~~g~s~aqlAL~w~l~ 47 (118)
.+.+..+|+..|++..+|-.-|...
T Consensus 27 ~~~~~~la~~~~l~~~qV~~WF~nr 51 (56)
T smart00389 27 REEREELAAKLGLSERQVKVWFQNR 51 (56)
T ss_pred HHHHHHHHHHHCcCHHHHHHhHHHH
Confidence 4567889999999999888766554
No 101
>PF05119 Terminase_4: Phage terminase, small subunit; InterPro: IPR006448 This entry is represented by Streptococcus phage 7201, Orf21. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This group of sequences describe the distinct family of phage (and integrated prophage) putative terminase small subunit sequnces. Members tend to be encoded by the gene adjacent to the phage terminase large subunit gene.
Probab=25.39 E-value=1.3e+02 Score=18.33 Aligned_cols=25 Identities=20% Similarity=0.244 Sum_probs=20.1
Q ss_pred chHhhHHHHHHHHHHHHHhCCCHHH
Q 033498 15 NLEHNKKLFERVNELAVKKGCTRSQ 39 (118)
Q Consensus 15 ~~~~~~~~~~~l~~ia~~~g~s~aq 39 (118)
......+..+.+..++.++|+||+.
T Consensus 62 ~~~~~~~~~~~~~~l~~~lGLtP~s 86 (100)
T PF05119_consen 62 AVSILNKAMKQMRSLASELGLTPAS 86 (100)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCHHH
Confidence 3455667888999999999999974
No 102
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=25.31 E-value=23 Score=21.31 Aligned_cols=57 Identities=23% Similarity=0.227 Sum_probs=35.0
Q ss_pred HhhHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCCCceecCC---CCcHHHHHHHHhhcCC
Q 033498 17 EHNKKLFERVNELAVKKGCTRSQLALAWVHHQGDDVCPIPG---TTKIENLNQNIKALSV 73 (118)
Q Consensus 17 ~~~~~~~~~l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G---~~~~~ql~en~~a~~~ 73 (118)
.....++..+.++-++.|.|..++|=.--.++|.|+-..-| --+.+.|...+.+++.
T Consensus 14 ~~k~~l~~~i~~~~~~~~ltQ~e~A~~lgisq~~vS~l~~g~~~~~sl~~L~~~l~aLG~ 73 (80)
T PF13744_consen 14 EAKAQLMAAIRELREERGLTQAELAERLGISQPRVSRLENGKIDDFSLDTLLRYLEALGG 73 (80)
T ss_dssp HHHHHHHHHHHHHHHCCT--HHHHHHHHTS-HHHHHHHHTT-GCC--HHHHHHHHHHTTE
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHCCChhHHHHHHcCcccCCCHHHHHHHHHHcCC
Confidence 33445666777888888999999988877777765544432 3456677776666554
No 103
>PRK09492 treR trehalose repressor; Provisional
Probab=24.92 E-value=1.3e+02 Score=22.07 Aligned_cols=43 Identities=12% Similarity=0.138 Sum_probs=27.1
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhhcCC
Q 033498 25 RVNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKALSV 73 (118)
Q Consensus 25 ~l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~~~ 73 (118)
.++++|+..|+|.+.+.-. ++++. -+...+.+++.+.++..++
T Consensus 6 ti~dIA~~agVS~~TVSrv--Ln~~~----~vs~~tr~rV~~~a~elgY 48 (315)
T PRK09492 6 TIKDIARLSGVGKSTVSRV--LNNES----GVSEETRERVEAVINQHGF 48 (315)
T ss_pred cHHHHHHHhCCCHHHHhHH--hCCCC----CCCHHHHHHHHHHHHHHCC
Confidence 3678888888888766544 44431 2455667777766666655
No 104
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=24.83 E-value=37 Score=18.92 Aligned_cols=12 Identities=17% Similarity=0.329 Sum_probs=5.0
Q ss_pred CCCHHHHHHHHH
Q 033498 34 GCTRSQLALAWV 45 (118)
Q Consensus 34 g~s~aqlAL~w~ 45 (118)
|.+..++|-.|-
T Consensus 22 g~s~~~ia~~fg 33 (53)
T PF04218_consen 22 GESKRDIAREFG 33 (53)
T ss_dssp TT-HHHHHHHHT
T ss_pred CCCHHHHHHHhC
Confidence 444444444443
No 105
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=24.55 E-value=85 Score=16.54 Aligned_cols=22 Identities=27% Similarity=0.665 Sum_probs=12.8
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHc
Q 033498 25 RVNELAVKKGCTRSQLALAWVHH 47 (118)
Q Consensus 25 ~l~~ia~~~g~s~aqlAL~w~l~ 47 (118)
..+++|+.+|+|... +-+|+..
T Consensus 19 s~~~ia~~lgvs~~T-v~~w~kr 40 (50)
T PF13384_consen 19 SIREIAKRLGVSRST-VYRWIKR 40 (50)
T ss_dssp -HHHHHHHHTS-HHH-HHHHHT-
T ss_pred CHHHHHHHHCcCHHH-HHHHHHH
Confidence 456788888888764 3455544
No 106
>PF05534 HicB: HicB family; InterPro: IPR008651 This family consists of several bacterial HicB related proteins. The function of HicB is unknown although it is thought to be involved in pilus formation. It has been speculated that HicB performs a function antagonistic to that of pili and yet is necessary for invasion of certain niches [].
Probab=24.40 E-value=1.4e+02 Score=16.53 Aligned_cols=22 Identities=23% Similarity=0.264 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHHhCCCHHHHHH
Q 033498 21 KLFERVNELAVKKGCTRSQLAL 42 (118)
Q Consensus 21 ~~~~~l~~ia~~~g~s~aqlAL 42 (118)
++-+.+...|+..|+|+-++..
T Consensus 27 ~Lh~~l~~~A~~~gvSlN~~I~ 48 (51)
T PF05534_consen 27 ELHRALAEAAAAEGVSLNQWIE 48 (51)
T ss_pred HHHHHHHHHHHHhCCCHHHHHH
Confidence 4667788899999999988764
No 107
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=24.38 E-value=1.8e+02 Score=21.63 Aligned_cols=43 Identities=9% Similarity=0.163 Sum_probs=25.9
Q ss_pred HHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhhcCCC
Q 033498 26 VNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKALSVK 74 (118)
Q Consensus 26 l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~~~~ 74 (118)
+++||+.-|+|.+.+... +++.. -+...+.+++.+.++..+..
T Consensus 4 i~dIA~~aGVS~~TVSrv--Ln~~~----~Vs~~tr~rV~~~a~elgY~ 46 (343)
T PRK10727 4 IKDVARLAGVSVATVSRV--INNSP----KASEASRLAVHSAMESLSYH 46 (343)
T ss_pred HHHHHHHhCCCHHHHHHH--hCCCC----CCCHHHHHHHHHHHHHHCCC
Confidence 667777778777765443 44331 24556666776666665553
No 108
>PRK01045 ispH 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed
Probab=24.30 E-value=1.4e+02 Score=22.92 Aligned_cols=43 Identities=26% Similarity=0.349 Sum_probs=31.7
Q ss_pred HHHHHHHHhC------CCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHH
Q 033498 25 RVNELAVKKG------CTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNI 68 (118)
Q Consensus 25 ~l~~ia~~~g------~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~ 68 (118)
.|.++|+++| -+..++-..|+.... .+.+..|+++++.+-+.+
T Consensus 227 kL~~i~~~~~~~t~~Ie~~~el~~~~l~~~~-~VGitaGASTP~~li~eV 275 (298)
T PRK01045 227 RLREVAEEAGAPAYLIDDASEIDPEWFKGVK-TVGVTAGASAPEWLVQEV 275 (298)
T ss_pred HHHHHHHHHCCCEEEECChHHCcHHHhcCCC-EEEEEecCCCCHHHHHHH
Confidence 4566777766 356788889986554 467889999999887655
No 109
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=24.15 E-value=1.9e+02 Score=21.23 Aligned_cols=43 Identities=12% Similarity=0.152 Sum_probs=25.1
Q ss_pred HHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhhcCCC
Q 033498 26 VNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKALSVK 74 (118)
Q Consensus 26 l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~~~~ 74 (118)
++++|+.-|+|.+.+... ++++. -+...+.+++.+.++..+..
T Consensus 4 i~dIA~~agvS~~TVSrv--Ln~~~----~vs~~tr~rV~~~a~~lgY~ 46 (329)
T TIGR01481 4 IYDVAREAGVSMATVSRV--VNGNP----NVKPATRKKVLEVIKRLDYR 46 (329)
T ss_pred HHHHHHHhCCCHHHHHHH--hCCCC----CCCHHHHHHHHHHHHHHCCC
Confidence 567777777777755543 34331 24455666666666655543
No 110
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=24.07 E-value=95 Score=16.48 Aligned_cols=15 Identities=33% Similarity=0.576 Sum_probs=11.2
Q ss_pred HHHHHHHhCCCHHHH
Q 033498 26 VNELAVKKGCTRSQL 40 (118)
Q Consensus 26 l~~ia~~~g~s~aql 40 (118)
+.++|+.+|+|...+
T Consensus 23 ~~eIa~~lg~s~~~V 37 (50)
T PF04545_consen 23 LEEIAERLGISRSTV 37 (50)
T ss_dssp HHHHHHHHTSCHHHH
T ss_pred HHHHHHHHCCcHHHH
Confidence 567888888887654
No 111
>PF05673 DUF815: Protein of unknown function (DUF815); InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function.
Probab=23.86 E-value=98 Score=23.28 Aligned_cols=42 Identities=19% Similarity=0.317 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHhCCCHH-----HHHHHHHHcCCCCceecCCCCcHHHHHHHH
Q 033498 22 LFERVNELAVKKGCTRS-----QLALAWVHHQGDDVCPIPGTTKIENLNQNI 68 (118)
Q Consensus 22 ~~~~l~~ia~~~g~s~a-----qlAL~w~l~~~~v~~~I~G~~~~~ql~en~ 68 (118)
.++.++.+++++|+... +-|++|.+.+++- ..|+..|.-+.+
T Consensus 199 YL~IV~~~~~~~g~~~~~e~l~~~Al~wa~~rg~R-----SGRtA~QF~~~l 245 (249)
T PF05673_consen 199 YLAIVRHYAERYGLELDEEELRQEALQWALRRGGR-----SGRTARQFIDDL 245 (249)
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHcCCC-----CHHHHHHHHHHH
Confidence 45556778888987775 7899999998743 235555555443
No 112
>PF00984 UDPG_MGDP_dh: UDP-glucose/GDP-mannose dehydrogenase family, central domain; InterPro: IPR014026 The UDP-glucose/GDP-mannose dehydrogenases are a small group of enzymes which possesses the ability to catalyse the NAD-dependent 2-fold oxidation of an alcohol to an acid without the release of an aldehyde intermediate [, ]. The enzymes have a wide range of functions. In plants UDP-glucose dehydrogenase, 1.1.1.22 from EC, is an important enzyme in the synthesis of hemicellulose and pectin [], which are the components of newly formed cell walls; while in zebrafish UDP-glucose dehydrogenase is required for cardiac valve formation []. In Xanthomonas campestris, a plant pathogen, UDP-glucose dehydrogenase is required for virulence []. GDP-mannose dehydrogenase, 1.1.1.132 from EC, catalyses the formation of GDP-mannuronic acid, which is the monomeric unit from which the exopolysaccharide alginate is formed. Alginate is secreted by a number of bacteria, which include Pseudomonas aeruginosa and Azotobacter vinelandii. In P. aeruginosa, alginate is believed to play an important role in the bacteria's resistance to antibiotics and the host immune response [], while in A. vinelandii it is essential for the encystment process []. This entry represents an alpha helical region that serves as the dimerisation interface for these enzymes [, ].; GO: 0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 2O3J_A 3OJO_A 3OJL_A 3PLR_A 3PJG_A 3PID_A 3PLN_A 3PHL_A 3TDK_B 2Q3E_A ....
Probab=23.75 E-value=2e+02 Score=18.05 Aligned_cols=40 Identities=15% Similarity=0.026 Sum_probs=29.6
Q ss_pred HhhHHHHHHHHHHHHHhCCCHHHHHHHHHHcCCCCc--eecCC
Q 033498 17 EHNKKLFERVNELAVKKGCTRSQLALAWVHHQGDDV--CPIPG 57 (118)
Q Consensus 17 ~~~~~~~~~l~~ia~~~g~s~aqlAL~w~l~~~~v~--~~I~G 57 (118)
.-.+....+|..+|+++|++..++.-..... +.+. ..-||
T Consensus 16 a~~iaf~Nel~~lce~~giD~~~V~~~~~~d-~ri~~~~~~pg 57 (96)
T PF00984_consen 16 ATKIAFANELARLCEKLGIDVYEVIEAANTD-PRIGPHYLRPG 57 (96)
T ss_dssp HHHHHHHHHHHHHHHHHTSBHHHHHHHHHTS-TTTTSSS-S-S
T ss_pred HHHHHHHHHHHHHHHHcCCCHHHHHHHHccC-cccccccCCCC
Confidence 4456678999999999999999998887665 5554 44554
No 113
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=23.36 E-value=1.2e+02 Score=15.45 Aligned_cols=23 Identities=13% Similarity=0.278 Sum_probs=14.6
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHc
Q 033498 25 RVNELAVKKGCTRSQLALAWVHH 47 (118)
Q Consensus 25 ~l~~ia~~~g~s~aqlAL~w~l~ 47 (118)
.|.++|...|+|+..+.-.|-..
T Consensus 10 ~l~~iA~~~g~S~~~f~r~Fk~~ 32 (42)
T PF00165_consen 10 TLEDIAEQAGFSPSYFSRLFKKE 32 (42)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHHHHH
Confidence 35778888888877776665443
No 114
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=23.22 E-value=1.4e+02 Score=21.97 Aligned_cols=16 Identities=19% Similarity=0.300 Sum_probs=7.9
Q ss_pred HHHHHHhCCCHHHHHH
Q 033498 27 NELAVKKGCTRSQLAL 42 (118)
Q Consensus 27 ~~ia~~~g~s~aqlAL 42 (118)
++||+.-|+|.+.+.-
T Consensus 2 ~dIA~~agVS~~TVSr 17 (327)
T PRK10423 2 KDVARLAGVSTSTVSH 17 (327)
T ss_pred hhHHHHhCCcHHHHHH
Confidence 3455555555554433
No 115
>PRK06552 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=23.18 E-value=1.2e+02 Score=22.05 Aligned_cols=48 Identities=13% Similarity=0.185 Sum_probs=31.8
Q ss_pred HHHHHHHHcCCCCceecCCCCcHHHHHHHHhhc-CC-------CCCHHHHHHHHhhhc
Q 033498 39 QLALAWVHHQGDDVCPIPGTTKIENLNQNIKAL-SV-------KLTPEEIAELESIAS 88 (118)
Q Consensus 39 qlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~-~~-------~Ls~e~~~~l~~~~~ 88 (118)
.-.+.++..++ ...|||+.|++++.+..+.- ++ .+..+.++.+...+.
T Consensus 99 ~~v~~~~~~~~--i~~iPG~~T~~E~~~A~~~Gad~vklFPa~~~G~~~ik~l~~~~p 154 (213)
T PRK06552 99 RETAKICNLYQ--IPYLPGCMTVTEIVTALEAGSEIVKLFPGSTLGPSFIKAIKGPLP 154 (213)
T ss_pred HHHHHHHHHcC--CCEECCcCCHHHHHHHHHcCCCEEEECCcccCCHHHHHHHhhhCC
Confidence 33567777776 67899999999999887532 22 234555666655543
No 116
>TIGR01761 thiaz-red thiazolinyl imide reductase. This reductase is found associated with gene clusters for the biosynthesis of various non-ribosomal peptide derived natural products in which cysteine is cyclized to a thiazoline ring containing an imide double bond. Examples include yersiniabactin (irp3/YbtU) and pyochelin (PchG).
Probab=23.01 E-value=2.9e+02 Score=21.53 Aligned_cols=66 Identities=18% Similarity=0.187 Sum_probs=39.8
Q ss_pred HHHHHHHHHhCCCHHHHHHHHHHcCCCCceecCCC-----CcHHHHHHHHhh-----cCCCCCHHHHHHHHhhhcCC
Q 033498 24 ERVNELAVKKGCTRSQLALAWVHHQGDDVCPIPGT-----TKIENLNQNIKA-----LSVKLTPEEIAELESIASAD 90 (118)
Q Consensus 24 ~~l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~-----~~~~ql~en~~a-----~~~~Ls~e~~~~l~~~~~~~ 90 (118)
+..+++|+++|+... -.+.=++..+.+++|.+.+ ...+...+.+++ ++.+|..++.++|.+..+..
T Consensus 39 erA~~~A~~~gi~~y-~~~eell~d~Di~~V~ipt~~P~~~H~e~a~~aL~aGkHVL~EKPla~~Ea~el~~~A~~~ 114 (343)
T TIGR01761 39 ERSRALAHRLGVPLY-CEVEELPDDIDIACVVVRSAIVGGQGSALARALLARGIHVLQEHPLHPRDIQDLLRLAERQ 114 (343)
T ss_pred HHHHHHHHHhCCCcc-CCHHHHhcCCCEEEEEeCCCCCCccHHHHHHHHHhCCCeEEEcCCCCHHHHHHHHHHHHHc
Confidence 345677888886421 1122223455555555433 556777777776 25588888888887776643
No 117
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=22.71 E-value=1.3e+02 Score=15.75 Aligned_cols=42 Identities=10% Similarity=0.097 Sum_probs=26.9
Q ss_pred HHHHHhCCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhhcCCCC
Q 033498 28 ELAVKKGCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKALSVKL 75 (118)
Q Consensus 28 ~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~~~~L 75 (118)
++|+..|++.+.+.. |+...+ -+...+...+.+.+..++...
T Consensus 2 ~lA~~~gvs~~tvs~-~l~g~~-----~vs~~~~~~i~~~~~~l~~~~ 43 (52)
T cd01392 2 DIARAAGVSVATVSR-VLNGKP-----RVSEETRERVLAAAEELGYRP 43 (52)
T ss_pred cHHHHHCcCHHHHHH-HHcCCC-----CCCHHHHHHHHHHHHHhCCCC
Confidence 578889999887654 333322 244456777777777766543
No 118
>PF02401 LYTB: LytB protein; InterPro: IPR003451 Terpenes are among the largest groups of natural products and include compounds such as vitamins, cholesterol and carotenoids. The biosynthesis of all terpenoids begins with one or both of the two C5 precursors of the pathway: isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP). In animals, fungi, and certain bacteria, the synthesis of IPP and DMAPP occurs via the well-known mevalonate pathway, however, a second, nonmevalonate terpenoid pathway has been identified in many eubacteria, algae and the chloroplasts of higher plants []. LytB(IspH) catalyses the conversion of 1-hydroy-2-methyl-2-(E)-butenyl 4-diphosphate into IPP and DMAPP in this second pathway The enzyme appears to be responsible for a branch-step in the nonmevalonate pathway, in that IPP and DMAPP are produced in parallel from a single precursor although the exact mechanism of this is not currently fully understood []. Escherichia coli LytB protein had been found to regulate the activity of RelA (guanosine 3',5'-bispyrophosphate synthetase I), which in turn controls the level of a regulatory metabolite. It is involved in penicillin tolerance and the stringent response [].; GO: 0019288 isopentenyl diphosphate biosynthetic process, mevalonate-independent pathway, 0055114 oxidation-reduction process; PDB: 3DNF_B 3SZL_B 3KE8_B 3KEF_B 3SZU_A 3KEL_A 3F7T_B 3KE9_B 3KEM_B 3T0G_A ....
Probab=22.57 E-value=1e+02 Score=23.46 Aligned_cols=44 Identities=18% Similarity=0.345 Sum_probs=30.1
Q ss_pred HHHHHHHHHhCC------CHHHHHHHHHHcCCCCceecCCCCcHHHHHHHH
Q 033498 24 ERVNELAVKKGC------TRSQLALAWVHHQGDDVCPIPGTTKIENLNQNI 68 (118)
Q Consensus 24 ~~l~~ia~~~g~------s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~ 68 (118)
..|.++|+++|. +..++-..|+.... .+.+..|+++++.+-+.+
T Consensus 225 ~kL~eia~~~~~~t~~Ie~~~el~~~~l~~~~-~VGItaGASTP~~ii~eV 274 (281)
T PF02401_consen 225 RKLAEIAKEHGKPTYHIETADELDPEWLKGVK-KVGITAGASTPDWIIEEV 274 (281)
T ss_dssp HHHHHHHHHCTTCEEEESSGGG--HHHHTT-S-EEEEEE-TTS-HHHHHHH
T ss_pred HHHHHHHHHhCCCEEEeCCccccCHhHhCCCC-EEEEEccCCCCHHHHHHH
Confidence 456778888774 56799999988765 467899999999988765
No 119
>cd00118 LysM Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function.
Probab=22.52 E-value=1.1e+02 Score=14.54 Aligned_cols=17 Identities=18% Similarity=0.329 Sum_probs=12.2
Q ss_pred HHHHHHHHhCCCHHHHH
Q 033498 25 RVNELAVKKGCTRSQLA 41 (118)
Q Consensus 25 ~l~~ia~~~g~s~aqlA 41 (118)
.+..+++++|++..+++
T Consensus 10 t~~~ia~~~~~~~~~~~ 26 (46)
T cd00118 10 TLSSIAQRYGISVEELL 26 (46)
T ss_pred CHHHHHHHHCcCHHHHH
Confidence 35678888888887654
No 120
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=22.37 E-value=1.1e+02 Score=17.08 Aligned_cols=17 Identities=24% Similarity=0.257 Sum_probs=13.3
Q ss_pred HHHHHHHHHhCCCHHHH
Q 033498 24 ERVNELAVKKGCTRSQL 40 (118)
Q Consensus 24 ~~l~~ia~~~g~s~aql 40 (118)
+.++.+|+.+|+++.++
T Consensus 4 ~I~~~Va~~~~i~~~~i 20 (60)
T smart00760 4 EIIEAVAEYFGVKPEDL 20 (60)
T ss_pred HHHHHHHHHhCCCHHHH
Confidence 34667889999998875
No 121
>PHA00617 ribbon-helix-helix domain containing protein
Probab=22.36 E-value=1.6e+02 Score=18.23 Aligned_cols=23 Identities=17% Similarity=0.316 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHHHhCCCHHHHHH
Q 033498 20 KKLFERVNELAVKKGCTRSQLAL 42 (118)
Q Consensus 20 ~~~~~~l~~ia~~~g~s~aqlAL 42 (118)
.++.+.|..+|+..|.+.+.+.-
T Consensus 48 ~eL~erLD~LA~~~GrsRSelIr 70 (80)
T PHA00617 48 PELNAKLEQVAIKMKKSKSEIIR 70 (80)
T ss_pred HHHHHHHHHHHHHhCcCHHHHHH
Confidence 45788899999999999876643
No 122
>cd07995 TPK Thiamine pyrophosphokinase. Thiamine pyrophosphokinase (TPK, EC:2.7.6.2, also spelled thiamin pyrophosphokinase) catalyzes the transfer of a pyrophosphate group from ATP to vitamin B1 (thiamine) to form the coenzyme thiamine pyrophosphate (TPP). TPP is required for central metabolic functions, and thiamine deficiency is associated with potentially fatal human diseases. The structure of thiamine pyrophosphokinase suggests that the enzyme may operate by a mechanism of pyrophosphoryl transfer similar to those described for pyrophosphokinases functioning in nucleotide biosynthesis.
Probab=22.31 E-value=1.5e+02 Score=21.03 Aligned_cols=39 Identities=28% Similarity=0.340 Sum_probs=31.6
Q ss_pred hCCCHHHHHHHHHHcCCCCceecCCCC--cHHHHHHHHhhc
Q 033498 33 KGCTRSQLALAWVHHQGDDVCPIPGTT--KIENLNQNIKAL 71 (118)
Q Consensus 33 ~g~s~aqlAL~w~l~~~~v~~~I~G~~--~~~ql~en~~a~ 71 (118)
...|=.++||.++..+....+.|.|+. +.+|.-.|+...
T Consensus 74 KD~TD~e~Al~~~~~~~~~~i~i~Ga~GgR~DH~lani~~l 114 (208)
T cd07995 74 KDFTDFEKALKLALERGADEIVILGATGGRLDHTLANLNLL 114 (208)
T ss_pred CCCCHHHHHHHHHHHcCCCEEEEEccCCCcHHHHHHHHHHH
Confidence 567788999999999977677787765 888888888753
No 123
>TIGR02311 HpaI 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase. This model represents the aldolase which performs the final step unique to the 4-hydroxyphenylacetic acid catabolism pathway in which 2,4-dihydroxyhept-2-ene-1,7-dioic acid is split into pyruvate and succinate-semialdehyde. The gene for enzyme is generally found adjacent to other genes for this pathway organized into an operon.
Probab=22.30 E-value=1.6e+02 Score=21.77 Aligned_cols=34 Identities=12% Similarity=0.138 Sum_probs=28.3
Q ss_pred HHHHHHHcCCCCceecCCCCcHHHHHHHHhhcCC
Q 033498 40 LALAWVHHQGDDVCPIPGTTKIENLNQNIKALSV 73 (118)
Q Consensus 40 lAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~~~ 73 (118)
.-+..++..+.-.+++|-..+.+|+++.++++.+
T Consensus 75 ~~i~~~Ld~Ga~gIivP~v~s~e~a~~~v~~~~y 108 (249)
T TIGR02311 75 VLIKQLLDIGAQTLLVPMIETAEQAEAAVAATRY 108 (249)
T ss_pred HHHHHHhCCCCCEEEecCcCCHHHHHHHHHHcCC
Confidence 3678888888878899999999999988887664
No 124
>PRK11235 bifunctional antitoxin/transcriptional repressor RelB; Provisional
Probab=22.17 E-value=2e+02 Score=17.64 Aligned_cols=29 Identities=34% Similarity=0.423 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHhCCCHHH---HHHHHHHcCCC
Q 033498 22 LFERVNELAVKKGCTRSQ---LALAWVHHQGD 50 (118)
Q Consensus 22 ~~~~l~~ia~~~g~s~aq---lAL~w~l~~~~ 50 (118)
.-+...++++++|+|+++ +.+.++..+..
T Consensus 12 lK~~A~~vl~~lGls~S~Ai~~fl~qi~~~~~ 43 (80)
T PRK11235 12 LKARAYAVLEKLGVTPSEALRLLLQYVAENGR 43 (80)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 455677899999999985 45566666653
No 125
>PRK12360 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Provisional
Probab=22.11 E-value=1.3e+02 Score=22.88 Aligned_cols=43 Identities=12% Similarity=0.157 Sum_probs=31.8
Q ss_pred HHHHHHHHhCC------CHHHHHHHHHHcCCCCceecCCCCcHHHHHHHH
Q 033498 25 RVNELAVKKGC------TRSQLALAWVHHQGDDVCPIPGTTKIENLNQNI 68 (118)
Q Consensus 25 ~l~~ia~~~g~------s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~ 68 (118)
.|.++|.++|. +..++-..|+.... .+.+..|+++++.+-+.+
T Consensus 226 rL~eia~~~~~~t~~Ie~~~el~~~~~~~~~-~VGitaGASTP~~li~eV 274 (281)
T PRK12360 226 KLVKICEKNCPNTFHIETADELDLEMLKDYK-IIGITAGASTPDWIIEEV 274 (281)
T ss_pred HHHHHHHHHCCCEEEECChHHCCHHHhCCCC-EEEEEccCCCCHHHHHHH
Confidence 45667777663 56788888987654 467889999999887654
No 126
>PHA00675 hypothetical protein
Probab=22.09 E-value=2e+02 Score=17.67 Aligned_cols=11 Identities=27% Similarity=0.120 Sum_probs=8.2
Q ss_pred HHHHHhCCCHH
Q 033498 28 ELAVKKGCTRS 38 (118)
Q Consensus 28 ~ia~~~g~s~a 38 (118)
+||+++|++.+
T Consensus 44 ~IA~~fGVsrs 54 (78)
T PHA00675 44 VLAEKFEQSKG 54 (78)
T ss_pred HHHHHhCCCHH
Confidence 67777787766
No 127
>COG0182 Predicted translation initiation factor 2B subunit, eIF-2B alpha/beta/delta family [Translation, ribosomal structure and biogenesis]
Probab=21.92 E-value=51 Score=25.92 Aligned_cols=29 Identities=24% Similarity=0.237 Sum_probs=23.4
Q ss_pred hCCCH---HHHHHHHHHcCCCCceecCCCCcH
Q 033498 33 KGCTR---SQLALAWVHHQGDDVCPIPGTTKI 61 (118)
Q Consensus 33 ~g~s~---aqlAL~w~l~~~~v~~~I~G~~~~ 61 (118)
.|++. +.-+.+|+++++.|..+|+|+.+.
T Consensus 208 ~GIpvtLItD~aag~~M~~g~Id~viVGADRI 239 (346)
T COG0182 208 DGIPVTLITDNAAGHLMQQGMIDAVIVGADRI 239 (346)
T ss_pred cCCceEEEeccHHHHHHHhCCCcEEEEcccee
Confidence 35444 467889999999999999999764
No 128
>PF13167 GTP-bdg_N: GTP-binding GTPase N-terminal
Probab=21.84 E-value=88 Score=19.86 Aligned_cols=66 Identities=23% Similarity=0.318 Sum_probs=46.8
Q ss_pred HHHHHHHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhhc-------CCCCCHHHHHHHHhhhc
Q 033498 21 KLFERVNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKAL-------SVKLTPEEIAELESIAS 88 (118)
Q Consensus 21 ~~~~~l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~-------~~~Ls~e~~~~l~~~~~ 88 (118)
+.+++++.+++-.|..+..-... .+.+| -....+|.-+.+.|.+.+... +-.||+.+..-|.+.+.
T Consensus 8 ~~l~El~~L~~t~g~~vv~~~~q-~~~~~-~p~~~iG~GK~eei~~~~~~~~~d~vvfd~~Lsp~Q~rNLe~~~~ 80 (95)
T PF13167_consen 8 ESLEELEELAETAGYEVVGTVVQ-KRRKP-DPKTYIGSGKVEEIKELIEELDADLVVFDNELSPSQQRNLEKALG 80 (95)
T ss_pred HHHHHHHHHHHHCCCeEEEEEEe-cCCCC-CcceeechhHHHHHHHHHhhcCCCEEEECCCCCHHHHHHHHHHHC
Confidence 45777888888888776532222 12233 245689999999999988754 33799999999988874
No 129
>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial. This family consists of repressors of the LacI family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis
Probab=21.43 E-value=2e+02 Score=21.17 Aligned_cols=42 Identities=14% Similarity=0.171 Sum_probs=23.5
Q ss_pred HHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhhcCC
Q 033498 26 VNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKALSV 73 (118)
Q Consensus 26 l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~~~ 73 (118)
+++||+..|+|.+.+.-. ++... -++..+.+++.+.++..+.
T Consensus 4 i~dIA~~agVS~sTVSr~--Ln~~~----~vs~~tr~rV~~~a~~lgY 45 (311)
T TIGR02405 4 IKDIARLAGVGKSTVSRV--LNNEP----KVSIETRERVEQVIQQSGF 45 (311)
T ss_pred HHHHHHHhCCCHHHHHHH--hCCCC----CCCHHHHHHHHHHHHHHCC
Confidence 567777777777755544 33321 2445556666555554443
No 130
>PF08840 BAAT_C: BAAT / Acyl-CoA thioester hydrolase C terminal; InterPro: IPR014940 Acyl-CoA thioesterases are a group of enzymes that catalyse the hydrolysis of acyl-CoAs to the free fatty acid and coenzyme A (CoASH), providing the potential to regulate intracellular levels of acyl-CoAs, free fatty acids and CoASH. Bile acid-CoA:amino acid N-acetyltransferase (BAAT) is involved in bile acid metabolism and may also act as an acyl-CoA thioesterase that regulates intracellular levels of free fatty acids []. This entry represents a catalytic domain is found at the C terminus of acyl-CoA thioester hydrolases and bile acid-CoA:amino acid N-acetyltransferases. ; PDB: 3K2I_B 3HLK_B.
Probab=21.35 E-value=83 Score=22.43 Aligned_cols=33 Identities=18% Similarity=0.233 Sum_probs=25.6
Q ss_pred HHHHHHHHcCCCCc---eecCCCCcHHHHHHHHhhc
Q 033498 39 QLALAWVHHQGDDV---CPIPGTTKIENLNQNIKAL 71 (118)
Q Consensus 39 qlAL~w~l~~~~v~---~~I~G~~~~~ql~en~~a~ 71 (118)
+-|+.|+.++|.|. +.|.|.+.-..+.-.+++.
T Consensus 7 e~Ai~~L~~~p~v~~~~Igi~G~SkGaelALllAs~ 42 (213)
T PF08840_consen 7 EEAIDWLKSHPEVDPDKIGIIGISKGAELALLLASR 42 (213)
T ss_dssp HHHHHHHHCSTTB--SSEEEEEETHHHHHHHHHHHH
T ss_pred HHHHHHHHhCCCCCCCCEEEEEECHHHHHHHHHHhc
Confidence 55888999998875 7888888888887777654
No 131
>PF11116 DUF2624: Protein of unknown function (DUF2624); InterPro: IPR020277 This entry contains proteins with no known function.
Probab=21.22 E-value=2.2e+02 Score=17.77 Aligned_cols=29 Identities=14% Similarity=0.261 Sum_probs=14.9
Q ss_pred cHHHHHHHHhhcCCCCCHHHHHHHHhhhc
Q 033498 60 KIENLNQNIKALSVKLTPEEIAELESIAS 88 (118)
Q Consensus 60 ~~~ql~en~~a~~~~Ls~e~~~~l~~~~~ 88 (118)
+.+.|.......++++++++.+.|-.+.+
T Consensus 16 T~~eLlkyskqy~i~it~~QA~~I~~~lr 44 (85)
T PF11116_consen 16 TAKELLKYSKQYNISITKKQAEQIANILR 44 (85)
T ss_pred CHHHHHHHHHHhCCCCCHHHHHHHHHHHh
Confidence 34444445555555555555555555544
No 132
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=21.18 E-value=89 Score=19.91 Aligned_cols=15 Identities=20% Similarity=0.222 Sum_probs=8.8
Q ss_pred CCCHHHHHHHHHHcC
Q 033498 34 GCTRSQLALAWVHHQ 48 (118)
Q Consensus 34 g~s~aqlAL~w~l~~ 48 (118)
|.+..++|-.|-++.
T Consensus 72 G~n~~eLA~kyglS~ 86 (108)
T PF08765_consen 72 GMNVRELARKYGLSE 86 (108)
T ss_dssp SS-HHHHHHHHT--H
T ss_pred CCCHHHHHHHHCcCH
Confidence 777778887776553
No 133
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=21.14 E-value=1.9e+02 Score=22.11 Aligned_cols=43 Identities=14% Similarity=0.224 Sum_probs=24.6
Q ss_pred HHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhhcCCC
Q 033498 26 VNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKALSVK 74 (118)
Q Consensus 26 l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~~~~ 74 (118)
++++|+.-|+|.+.+.-. ++.+. -+...+.+++.+.++..+..
T Consensus 3 ikDVA~~AGVS~sTVSrv--ln~~~----~Vs~eTr~kV~~a~~elgY~ 45 (333)
T COG1609 3 IKDVAKLAGVSKATVSRV--LNGSP----YVSEETREKVLAAIKELGYR 45 (333)
T ss_pred HHHHHHHhCCCHHHHHHH--HcCCC----CCCHHHHHHHHHHHHHHCCC
Confidence 566677677776655544 33331 44555666666666665554
No 134
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=21.10 E-value=1e+02 Score=19.21 Aligned_cols=15 Identities=20% Similarity=0.417 Sum_probs=11.0
Q ss_pred HHHHHHhCCCHHHHH
Q 033498 27 NELAVKKGCTRSQLA 41 (118)
Q Consensus 27 ~~ia~~~g~s~aqlA 41 (118)
++|++++|+|.+.+.
T Consensus 53 reIa~~tgvS~aTIt 67 (87)
T PF01371_consen 53 REIAEETGVSIATIT 67 (87)
T ss_dssp HHHHHHHTSTHHHHH
T ss_pred HHHHHHhCCCHHHHH
Confidence 577888888887654
No 135
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=20.84 E-value=1.8e+02 Score=21.58 Aligned_cols=42 Identities=12% Similarity=0.210 Sum_probs=21.3
Q ss_pred HHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhhcCC
Q 033498 26 VNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKALSV 73 (118)
Q Consensus 26 l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~~~ 73 (118)
+++||+..|+|.+.+.... ++. .-++..+.+++.+.++..+.
T Consensus 4 i~dIA~~agVS~~TVSrvL--n~~----~~vs~~tr~~V~~~a~elgY 45 (341)
T PRK10703 4 IKDVAKRAGVSTTTVSHVI--NKT----RFVAEETRNAVWAAIKELHY 45 (341)
T ss_pred HHHHHHHhCCCHHHHHHHH--cCC----CCCCHHHHHHHHHHHHHHCC
Confidence 4566666666666554442 222 12344555555555555444
No 136
>TIGR00277 HDIG uncharacterized domain HDIG. This domain is found in a few known nucleotidyltransferes and in a large number of uncharacterized proteins. It contains four widely separated His residues, the second of which is part of an invariant dipeptide His-Asp in a region matched approximately by the motif HDIG.
Probab=20.71 E-value=1.7e+02 Score=16.31 Aligned_cols=35 Identities=17% Similarity=0.143 Sum_probs=27.0
Q ss_pred cchHhhHHHHHHHHHHHHHhCCCHHHHHHHHHHcC
Q 033498 14 ENLEHNKKLFERVNELAVKKGCTRSQLALAWVHHQ 48 (118)
Q Consensus 14 ~~~~~~~~~~~~l~~ia~~~g~s~aqlAL~w~l~~ 48 (118)
..+............+|+..|.+...+.++-+++.
T Consensus 4 ~~~~H~~~v~~~a~~la~~~~~~~~~l~~AalLHD 38 (80)
T TIGR00277 4 NVLQHSLEVAKLAEALARELGLDVELARRGALLHD 38 (80)
T ss_pred hHHHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHc
Confidence 34566777788888899999998887887777764
No 137
>PRK00819 RNA 2'-phosphotransferase; Reviewed
Probab=20.65 E-value=2e+02 Score=20.37 Aligned_cols=48 Identities=15% Similarity=0.071 Sum_probs=32.3
Q ss_pred HHHHHHcCCCCce----ecCCCCcHHHHHHHHhhcCCCCCHHHHHHHHhhhc
Q 033498 41 ALAWVHHQGDDVC----PIPGTTKIENLNQNIKALSVKLTPEEIAELESIAS 88 (118)
Q Consensus 41 AL~w~l~~~~v~~----~I~G~~~~~ql~en~~a~~~~Ls~e~~~~l~~~~~ 88 (118)
.|+|+|.|.+... =-=|-..++.|-..++.....++.+++.++-+-..
T Consensus 12 ~LS~lLRH~p~~~GL~ld~~G~v~v~~Ll~~~~~~~~~~t~~~l~~vV~~d~ 63 (179)
T PRK00819 12 FLSGVLRHKPEAIGLTLDEEGWVDIDALIEALAKAYKWVTRELLEAVVESDD 63 (179)
T ss_pred HHHHHHCCCHHHcCCccCCCCCEEHHHHHHHHHHccCCCCHHHHHHHHHcCC
Confidence 6889998865322 12277788888887764444689998777765443
No 138
>COG4321 Uncharacterized protein related to arylsulfate sulfotransferase involved in siderophore biosynthesis [General function prediction only]
Probab=20.56 E-value=1.1e+02 Score=19.81 Aligned_cols=21 Identities=19% Similarity=0.344 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHhCCCHHHHHH
Q 033498 22 LFERVNELAVKKGCTRSQLAL 42 (118)
Q Consensus 22 ~~~~l~~ia~~~g~s~aqlAL 42 (118)
....|++||+..++|.+++.-
T Consensus 35 FW~~L~eIA~~r~lt~a~LIa 55 (102)
T COG4321 35 FWDILKEIAERRKLTVAALIA 55 (102)
T ss_pred HHHHHHHHHHhcCCcHHHHHH
Confidence 346688899999999887743
No 139
>TIGR00216 ispH_lytB (E)-4-hydroxy-3-methyl-but-2-enyl pyrophosphate reductase (IPP and DMAPP forming). Escherichia coli LytB protein had been found to regulate the activity of RelA (guanosine 3',5'-bispyrophosphate synthetase I), which in turn controls the level of a regulatory metabolite. It is involved in penicillin tolerance and the stringent response.
Probab=20.47 E-value=1.4e+02 Score=22.69 Aligned_cols=44 Identities=20% Similarity=0.318 Sum_probs=33.0
Q ss_pred HHHHHHHHHhC------CCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHH
Q 033498 24 ERVNELAVKKG------CTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNI 68 (118)
Q Consensus 24 ~~l~~ia~~~g------~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~ 68 (118)
..|.++|+++| -+..++-..|+.... .+.+..|+++++.+-+.+
T Consensus 224 ~rL~ei~~~~~~~t~~Ie~~~el~~~~l~~~~-~VGiTAGASTP~~li~eV 273 (280)
T TIGR00216 224 TRLYEIAEEHGPPSYLIETAEELPEEWLKGVK-VVGITAGASTPDWIIEEV 273 (280)
T ss_pred HHHHHHHHHhCCCEEEECChHHCCHHHhCCCC-EEEEEecCCCCHHHHHHH
Confidence 34667777776 356788899987654 467889999999887654
No 140
>TIGR00789 flhB_rel flhB C-terminus-related protein. This model describes a short protein (80-93 residues) homologous to the C-terminus of the flagellar biosynthetic protein FlhB. It is found so far only in species that also have FlhB. In a phylogenetic tree based on alignment of both this family and the homologous region of FlhB and its homologs, the members of this family form a monophyletic set.
Probab=20.46 E-value=1.3e+02 Score=18.57 Aligned_cols=28 Identities=29% Similarity=0.248 Sum_probs=18.9
Q ss_pred HHHHHHHHHHHHhCCCHH-HHHHHHHHcC
Q 033498 21 KLFERVNELAVKKGCTRS-QLALAWVHHQ 48 (118)
Q Consensus 21 ~~~~~l~~ia~~~g~s~a-qlAL~w~l~~ 48 (118)
.....+.++|+++|++.- ...|+-.|.+
T Consensus 27 ~~A~~I~~~A~e~~VPi~~~~~LAr~L~~ 55 (82)
T TIGR00789 27 EVAERIIEIAKKHGIPIVEDPDLVDVLLK 55 (82)
T ss_pred HHHHHHHHHHHHcCCCEEeCHHHHHHHHh
Confidence 466778899999998763 4445544443
No 141
>COG3784 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.33 E-value=1.9e+02 Score=18.84 Aligned_cols=23 Identities=26% Similarity=0.332 Sum_probs=17.3
Q ss_pred hHHHHHHHHHHHHHhCCCHHHHH
Q 033498 19 NKKLFERVNELAVKKGCTRSQLA 41 (118)
Q Consensus 19 ~~~~~~~l~~ia~~~g~s~aqlA 41 (118)
|..+....+++|++.|.|+.+++
T Consensus 60 N~aR~a~Yq~lA~~n~~s~~~va 82 (109)
T COG3784 60 NAARAASYQQLAKKNGASTEEVA 82 (109)
T ss_pred HHHHHHHHHHHHHhcCCCHHHHH
Confidence 44566778889999999987655
No 142
>KOG1461 consensus Translation initiation factor 2B, epsilon subunit (eIF-2Bepsilon/GCD6) [Translation, ribosomal structure and biogenesis]
Probab=20.27 E-value=1.6e+02 Score=25.32 Aligned_cols=44 Identities=11% Similarity=0.154 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHhhcCCCCCH
Q 033498 34 GCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIKALSVKLTP 77 (118)
Q Consensus 34 g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~a~~~~Ls~ 77 (118)
++++..-+|.|+.+.+---+.+.++....|+.|.++...+.+..
T Consensus 54 NVpmIdYtL~~L~~agV~eVfvfc~~~~~qi~e~i~~sew~~~~ 97 (673)
T KOG1461|consen 54 NVPMIDYTLEWLERAGVEEVFVFCSAHAAQIIEYIEKSEWYLPM 97 (673)
T ss_pred CchHHHHHHHHHHhcCceEEEEEecccHHHHHHHHhhccccccc
Confidence 68899999999999886557788999999999999987764443
No 143
>PF03861 ANTAR: ANTAR domain; InterPro: IPR005561 ANTAR (AmiR and NasR transcription antitermination regulators) is an RNA-binding domain found in bacterial transcription antitermination regulatory proteins []. This domain has been detected in various response regulators of two-component systems, which are structured around two proteins, a histidine kinase and a response regulator. This domain is also found in one-component sensory regulators from a variety of bacteria. Most response regulators interact with DNA, however ANTAR-containing regulators interact with RNA. The majority of the domain consists of a coiled-coil.; PDB: 4AKK_A 1SD5_A 1S8N_A 1QO0_E.
Probab=20.23 E-value=1.7e+02 Score=16.16 Aligned_cols=18 Identities=11% Similarity=0.202 Sum_probs=7.6
Q ss_pred HHHHHHHHHhCCCHHHHH
Q 033498 24 ERVNELAVKKGCTRSQLA 41 (118)
Q Consensus 24 ~~l~~ia~~~g~s~aqlA 41 (118)
+.|+..|...|+++.++|
T Consensus 35 ~~Lr~~Am~~~~~l~~vA 52 (56)
T PF03861_consen 35 RLLRRQAMRRRRSLADVA 52 (56)
T ss_dssp HHHHHHHHHCTS-HHHHH
T ss_pred HHHHHHHHHcCCCHHHHH
Confidence 334444444444444444
No 144
>PF11017 DUF2855: Protein of unknown function (DUF2855); InterPro: IPR021276 This family of proteins has no known function.
Probab=20.14 E-value=38 Score=26.28 Aligned_cols=50 Identities=18% Similarity=0.329 Sum_probs=31.0
Q ss_pred CHHHHHHHHHHcCCCCceecCCCCcHHHHH--HHHhhcCCCCCHHHHHHHHh
Q 033498 36 TRSQLALAWVHHQGDDVCPIPGTTKIENLN--QNIKALSVKLTPEEIAELES 85 (118)
Q Consensus 36 s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~--en~~a~~~~Ls~e~~~~l~~ 85 (118)
|-+.++++|+|++..-..-++|.++..... +.++..+-.++=+++..|+.
T Consensus 146 SKTA~glA~~L~~~~~~~~~vglTS~~N~~Fve~lg~Yd~V~~Yd~i~~l~~ 197 (314)
T PF11017_consen 146 SKTAIGLAYCLKKQRGPPKVVGLTSARNVAFVESLGCYDEVLTYDDIDSLDA 197 (314)
T ss_pred hHHHHHHHHHhhccCCCceEEEEecCcchhhhhccCCceEEeehhhhhhccC
Confidence 447899999999433345566666555443 45555555666666666643
No 145
>TIGR00190 thiC thiamine biosynthesis protein ThiC. The thiC ortholog is designated thiA in Bacillus subtilis.
Probab=20.02 E-value=97 Score=25.10 Aligned_cols=42 Identities=24% Similarity=0.142 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHhCCCHHHHHHHHHHcCCCCceecCCCCcHHHHHHHHh
Q 033498 21 KLFERVNELAVKKGCTRSQLALAWVHHQGDDVCPIPGTTKIENLNQNIK 69 (118)
Q Consensus 21 ~~~~~l~~ia~~~g~s~aqlAL~w~l~~~~v~~~I~G~~~~~ql~en~~ 69 (118)
+..+.|-+|+++|++|++ |.=-++ ...|.-++...|+.|.+-
T Consensus 203 e~fD~lLeI~~~yDVtlS---LGDglR----PG~i~DA~D~aQi~El~~ 244 (423)
T TIGR00190 203 KNFDYILEIAKEYDVTLS---LGDGLR----PGCIADATDRAQISELIT 244 (423)
T ss_pred HHHHHHHHHHHHhCeeee---ccCCcC----CCccccCCcHHHHHHHHH
Confidence 345667788999998854 332222 335667778888887553
Done!