Query 031854
Match_columns 152
No_of_seqs 123 out of 247
Neff 3.4
Searched_HMMs 46136
Date Fri Mar 29 06:17:14 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031854.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031854hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00072 40S ribosomal protein 100.0 1E-75 2.2E-80 461.5 13.0 133 4-136 1-133 (148)
2 PRK08561 rps15p 30S ribosomal 100.0 4.9E-72 1.1E-76 442.0 14.1 136 1-136 1-136 (151)
3 KOG0400 40S ribosomal protein 100.0 1.2E-71 2.7E-76 436.7 9.6 137 1-137 1-137 (151)
4 PF08069 Ribosomal_S13_N: Ribo 100.0 4.4E-37 9.5E-42 211.8 3.3 60 1-60 1-60 (60)
5 COG0184 RpsO Ribosomal protein 99.9 1.2E-24 2.6E-29 159.5 6.3 76 44-135 1-76 (89)
6 PF00312 Ribosomal_S15: Riboso 99.5 1.1E-14 2.3E-19 104.1 4.6 68 66-133 2-69 (83)
7 cd00353 Ribosomal_S15p_S13e Ri 99.5 6.8E-14 1.5E-18 99.5 6.8 63 71-133 2-68 (80)
8 cd00677 S15_NS1_EPRS_RNA-bind 99.1 1.3E-10 2.8E-15 74.5 5.0 46 85-130 1-46 (46)
9 TIGR00952 S15_bact ribosomal p 97.3 0.00045 9.8E-09 50.6 4.9 46 88-133 26-71 (86)
10 CHL00027 rps15 ribosomal prote 97.2 0.00086 1.9E-08 49.8 5.1 47 88-134 26-72 (90)
11 PRK05626 rpsO 30S ribosomal pr 97.1 0.00078 1.7E-08 49.6 4.3 45 89-133 30-74 (89)
12 PTZ00119 40S ribosomal protein 96.6 0.003 6.5E-08 55.5 4.5 64 70-133 109-176 (302)
13 COG2257 Uncharacterized homolo 95.3 0.12 2.7E-06 38.8 7.6 70 20-106 20-89 (92)
14 PF13565 HTH_32: Homeodomain-l 91.5 0.38 8.2E-06 32.1 4.1 44 30-75 32-77 (77)
15 PF13276 HTH_21: HTH-like doma 88.4 1.2 2.6E-05 29.0 4.4 51 31-85 4-57 (60)
16 TIGR00789 flhB_rel flhB C-term 86.9 2.4 5.3E-05 30.6 5.7 60 21-97 16-75 (82)
17 COG3328 Transposase and inacti 86.2 0.76 1.6E-05 41.4 3.4 48 9-60 69-116 (379)
18 PF07750 GcrA: GcrA cell cycle 82.0 1.2 2.6E-05 35.6 2.5 25 31-55 5-29 (162)
19 PF00292 PAX: 'Paired box' dom 81.7 0.84 1.8E-05 35.7 1.5 31 29-59 18-48 (125)
20 PF00356 LacI: Bacterial regul 79.2 1.3 2.9E-05 28.6 1.6 41 39-82 4-45 (46)
21 PF13361 UvrD_C: UvrD-like hel 77.8 2 4.4E-05 34.1 2.6 43 31-81 61-103 (351)
22 PHA02591 hypothetical protein; 77.6 2 4.2E-05 31.9 2.2 28 27-54 42-69 (83)
23 PHA02517 putative transposase 75.9 4.6 0.0001 32.8 4.2 48 30-82 28-78 (277)
24 PRK15364 pathogenicity island 75.1 9.8 0.00021 32.1 6.0 81 29-117 77-162 (196)
25 PF00872 Transposase_mut: Tran 74.1 2.6 5.7E-05 37.0 2.6 39 22-61 93-132 (381)
26 PF13551 HTH_29: Winged helix- 73.9 6.3 0.00014 27.2 3.9 53 21-79 52-112 (112)
27 COG1202 Superfamily II helicas 73.3 2.2 4.8E-05 41.9 2.0 45 33-98 755-799 (830)
28 KOG1802 RNA helicase nonsense 73.2 1.9 4.2E-05 42.8 1.6 51 29-92 708-760 (935)
29 PRK01322 6-carboxyhexanoate--C 72.5 3.5 7.5E-05 35.6 2.8 74 3-95 6-108 (242)
30 cd01106 HTH_TipAL-Mta Helix-Tu 71.6 12 0.00026 26.7 5.1 40 17-56 28-69 (103)
31 PF11740 KfrA_N: Plasmid repli 71.5 6.2 0.00014 28.4 3.6 59 28-93 1-68 (120)
32 TIGR00328 flhB flagellar biosy 71.1 16 0.00035 32.5 6.7 62 21-99 278-340 (347)
33 PF15652 Tox-SHH: HNH/Endo VII 70.1 3.9 8.5E-05 31.2 2.3 34 25-58 63-96 (100)
34 PRK13902 alaS alanyl-tRNA synt 70.0 11 0.00024 37.5 6.0 55 36-96 419-474 (900)
35 smart00354 HTH_LACI helix_turn 68.7 5.3 0.00011 26.9 2.6 39 43-84 10-48 (70)
36 COG1964 Predicted Fe-S oxidore 67.7 16 0.00034 34.5 6.2 76 9-109 72-149 (475)
37 PF10593 Z1: Z1 domain; Inter 67.5 1.5 3.2E-05 36.7 -0.4 58 1-58 172-233 (239)
38 PF02899 Phage_int_SAM_1: Phag 67.2 6.7 0.00015 25.7 2.8 33 21-53 37-69 (84)
39 smart00845 GatB_Yqey GatB doma 66.4 25 0.00055 26.8 6.2 64 27-97 38-102 (147)
40 PF02885 Glycos_trans_3N: Glyc 66.3 6.1 0.00013 26.5 2.5 29 27-55 14-42 (66)
41 PF06983 3-dmu-9_3-mt: 3-demet 65.5 3 6.6E-05 30.9 0.9 32 29-61 81-112 (116)
42 COG3028 Uncharacterized protei 65.5 6.7 0.00014 32.9 3.0 62 44-119 26-87 (187)
43 PF13936 HTH_38: Helix-turn-he 65.3 3.6 7.7E-05 25.9 1.1 26 28-54 5-30 (44)
44 PF02637 GatB_Yqey: GatB domai 64.5 17 0.00036 27.6 4.8 65 26-97 38-103 (148)
45 PRK05702 flhB flagellar biosyn 64.4 22 0.00049 31.7 6.3 67 21-104 285-352 (359)
46 PRK06298 type III secretion sy 64.1 31 0.00067 30.9 7.1 71 21-108 279-351 (356)
47 COG3415 Transposase and inacti 62.7 21 0.00046 28.1 5.2 65 15-85 53-117 (138)
48 KOG3862 Transcription factor P 62.1 15 0.00032 33.1 4.7 51 29-85 26-76 (327)
49 PF13592 HTH_33: Winged helix- 61.6 7 0.00015 25.8 2.0 37 46-86 6-42 (60)
50 TIGR01204 bioW 6-carboxyhexano 58.3 7.9 0.00017 33.3 2.3 62 29-99 15-104 (232)
51 TIGR03859 PQQ_PqqD coenzyme PQ 57.4 10 0.00022 26.6 2.3 34 28-61 27-60 (81)
52 KOG3517 Transcription factor P 57.1 7.7 0.00017 34.6 2.1 31 30-60 22-52 (334)
53 cd08045 TAF4 TATA Binding Prot 56.7 18 0.00039 29.4 4.0 33 65-98 48-80 (212)
54 PF00196 GerE: Bacterial regul 56.2 12 0.00026 23.9 2.4 25 28-54 4-28 (58)
55 PF07508 Recombinase: Recombin 55.8 24 0.00052 24.2 4.1 49 30-79 3-53 (102)
56 cd01104 HTH_MlrA-CarA Helix-Tu 54.5 27 0.00059 22.4 3.9 32 23-54 34-67 (68)
57 TIGR03683 A-tRNA_syn_arch alan 54.3 26 0.00057 35.0 5.4 56 36-97 423-479 (902)
58 COG2445 Uncharacterized conser 54.2 45 0.00098 26.2 5.8 79 49-132 50-128 (138)
59 PF06056 Terminase_5: Putative 54.0 11 0.00023 25.5 2.0 26 32-61 1-26 (58)
60 smart00422 HTH_MERR helix_turn 53.8 33 0.00071 22.0 4.2 36 20-55 31-68 (70)
61 PF12990 DUF3874: Domain of un 53.6 11 0.00024 26.9 2.1 35 45-80 26-60 (73)
62 smart00550 Zalpha Z-DNA-bindin 52.6 26 0.00055 23.7 3.7 49 28-83 2-54 (68)
63 smart00733 Mterf Mitochondrial 51.3 21 0.00045 18.8 2.6 27 20-46 5-31 (31)
64 cd04766 HTH_HspR Helix-Turn-He 51.3 75 0.0016 22.2 6.0 39 16-55 28-69 (91)
65 PRK13413 mpi multiple promoter 50.8 28 0.00061 27.4 4.2 53 16-81 147-199 (200)
66 cd01392 HTH_LacI Helix-turn-he 50.6 12 0.00026 22.9 1.7 39 43-84 7-45 (52)
67 cd00592 HTH_MerR-like Helix-Tu 50.5 33 0.00071 24.0 4.1 41 17-57 27-69 (100)
68 PF13411 MerR_1: MerR HTH fami 50.1 18 0.00039 23.3 2.5 37 20-56 30-68 (69)
69 PF04947 Pox_VLTF3: Poxvirus L 48.0 64 0.0014 26.1 5.9 36 28-79 31-66 (171)
70 PF11338 DUF3140: Protein of u 47.0 43 0.00094 25.1 4.4 38 65-104 37-75 (92)
71 PF02796 HTH_7: Helix-turn-hel 44.9 12 0.00025 23.4 0.9 26 28-54 6-31 (45)
72 PF01411 tRNA-synt_2c: tRNA sy 44.4 15 0.00034 34.3 2.1 55 31-91 367-421 (552)
73 smart00421 HTH_LUXR helix_turn 43.7 29 0.00063 20.5 2.6 25 28-54 4-28 (58)
74 TIGR01293 Kv_beta voltage-depe 43.4 50 0.0011 27.7 4.8 60 34-95 251-316 (317)
75 COG5352 Uncharacterized protei 43.2 20 0.00044 29.5 2.3 24 31-54 5-28 (169)
76 PF03918 CcmH: Cytochrome C bi 42.2 19 0.00041 28.5 2.0 35 29-64 58-92 (148)
77 cd04788 HTH_NolA-AlbR Helix-Tu 41.8 45 0.00097 23.7 3.7 40 17-56 28-69 (96)
78 PF13495 Phage_int_SAM_4: Phag 41.7 27 0.00059 23.0 2.5 30 26-55 39-69 (85)
79 PF01244 Peptidase_M19: Membra 41.6 35 0.00075 29.6 3.7 41 23-77 280-320 (320)
80 PF11181 YflT: Heat induced st 41.5 17 0.00037 26.2 1.5 32 29-60 8-39 (103)
81 cd04786 HTH_MerR-like_sg7 Heli 41.4 1.4E+02 0.0031 22.6 6.7 40 17-56 28-69 (131)
82 PF10929 DUF2811: Protein of u 41.1 24 0.00052 24.5 2.1 22 80-107 2-23 (57)
83 cd05116 PTKc_Syk Catalytic dom 41.0 80 0.0017 24.2 5.3 67 51-129 185-256 (257)
84 PF00690 Cation_ATPase_N: Cati 40.9 14 0.00031 24.4 1.0 53 25-78 1-53 (69)
85 PRK10014 DNA-binding transcrip 40.9 23 0.0005 28.7 2.3 37 43-82 16-52 (342)
86 PRK01584 alanyl-tRNA synthetas 40.2 76 0.0016 30.6 6.0 57 33-96 375-431 (594)
87 PRK14810 formamidopyrimidine-D 39.3 1.1E+02 0.0025 25.9 6.3 72 18-101 131-211 (272)
88 PLN02389 biotin synthase 39.3 39 0.00084 30.2 3.7 37 22-58 110-146 (379)
89 PRK12721 secretion system appa 39.1 92 0.002 27.8 6.0 62 20-98 277-339 (349)
90 TIGR00180 parB_part ParB-like 38.8 1.1E+02 0.0024 24.1 5.8 55 36-94 94-156 (187)
91 PF14361 RsbRD_N: RsbT co-anta 38.8 33 0.00071 24.7 2.6 36 18-54 56-91 (105)
92 PF10752 DUF2533: Protein of u 38.6 28 0.00062 25.9 2.3 21 29-49 49-69 (84)
93 cd03527 RuBisCO_small Ribulose 38.5 29 0.00062 26.1 2.3 21 28-48 12-32 (99)
94 COG2771 CsgD DNA-binding HTH d 38.4 29 0.00063 21.5 2.1 24 34-57 9-32 (65)
95 PRK05477 gatB aspartyl/glutamy 37.8 97 0.0021 29.0 6.1 64 27-97 365-429 (474)
96 TIGR00344 alaS alanine--tRNA l 37.7 79 0.0017 31.4 5.8 56 34-97 372-427 (851)
97 cd01105 HTH_GlnR-like Helix-Tu 37.5 65 0.0014 22.6 4.0 34 24-57 36-71 (88)
98 TIGR00593 pola DNA polymerase 37.3 89 0.0019 31.2 6.1 48 30-77 523-578 (887)
99 PRK02228 V-type ATP synthase s 37.1 35 0.00075 24.9 2.6 62 28-98 27-96 (100)
100 cd04768 HTH_BmrR-like Helix-Tu 37.1 52 0.0011 23.4 3.5 42 16-57 27-70 (96)
101 smart00753 PAM PCI/PINT associ 36.5 33 0.00071 23.2 2.2 37 26-66 34-70 (88)
102 smart00088 PINT motif in prote 36.5 33 0.00071 23.2 2.2 37 26-66 34-70 (88)
103 cd04782 HTH_BltR Helix-Turn-He 36.2 65 0.0014 22.9 3.8 41 16-56 27-69 (97)
104 PF05931 AgrD: Staphylococcal 36.0 21 0.00044 23.7 1.1 12 81-92 33-44 (45)
105 PRK09108 type III secretion sy 35.8 1.4E+02 0.003 26.7 6.6 66 21-103 280-345 (353)
106 TIGR02051 MerR Hg(II)-responsi 35.4 1E+02 0.0022 22.9 4.9 40 17-56 27-68 (124)
107 PRK10401 DNA-binding transcrip 35.1 33 0.00072 28.1 2.4 37 43-82 11-47 (346)
108 PF05698 Trigger_C: Bacterial 35.0 11 0.00025 27.7 -0.3 35 26-60 109-144 (162)
109 PF14475 Mso1_Sec1_bdg: Sec1-b 34.9 28 0.0006 22.8 1.5 14 119-132 19-33 (41)
110 PRK09912 L-glyceraldehyde 3-ph 34.8 1.3E+02 0.0028 25.8 6.0 63 32-96 265-332 (346)
111 TIGR03147 cyt_nit_nrfF cytochr 34.7 44 0.00096 26.2 3.0 31 30-60 59-89 (126)
112 PF00476 DNA_pol_A: DNA polyme 34.5 1E+02 0.0023 27.0 5.6 48 31-78 18-75 (383)
113 PF12188 STAT2_C: Signal trans 34.2 12 0.00025 26.1 -0.3 11 81-91 6-16 (56)
114 PF09682 Holin_LLH: Phage holi 34.1 71 0.0015 23.5 3.9 28 70-98 76-103 (108)
115 PF14420 Clr5: Clr5 domain 34.1 49 0.0011 21.7 2.7 32 31-62 6-38 (54)
116 COG0749 PolA DNA polymerase I 33.6 74 0.0016 30.8 4.8 59 30-88 227-292 (593)
117 PF12025 Phage_C: Phage protei 33.5 13 0.00029 26.6 -0.1 31 49-80 36-67 (68)
118 PF15051 FAM198: FAM198 protei 33.5 37 0.00079 30.8 2.6 24 13-38 1-24 (326)
119 TIGR00676 fadh2 5,10-methylene 33.3 1.8E+02 0.0039 24.4 6.6 71 61-144 190-261 (272)
120 PRK12772 bifunctional flagella 33.2 1.2E+02 0.0025 29.0 6.0 60 21-97 541-601 (609)
121 cd00569 HTH_Hin_like Helix-tur 33.1 56 0.0012 16.4 2.4 23 32-54 9-31 (42)
122 COG3530 Uncharacterized protei 33.1 40 0.00086 24.4 2.3 22 34-55 29-50 (71)
123 PLN02751 glutamyl-tRNA(Gln) am 33.1 1.3E+02 0.0028 28.8 6.3 63 27-97 432-496 (544)
124 TIGR01404 FlhB_rel_III type II 32.3 1.4E+02 0.003 26.6 5.9 59 21-96 277-336 (342)
125 KOG4279 Serine/threonine prote 32.3 44 0.00095 34.3 3.1 43 56-98 1003-1048(1226)
126 KOG3089 Predicted DEAD-box-con 32.0 59 0.0013 28.7 3.6 33 67-99 63-95 (271)
127 PF10078 DUF2316: Uncharacteri 32.0 1.4E+02 0.003 22.2 5.0 51 36-96 15-65 (89)
128 PF12832 MFS_1_like: MFS_1 lik 31.9 23 0.0005 24.5 0.9 15 40-54 27-41 (77)
129 PRK14703 glutaminyl-tRNA synth 31.7 1.3E+02 0.0029 29.8 6.3 66 25-97 659-725 (771)
130 PF03433 EspA: EspA-like secre 31.6 16 0.00034 30.7 0.0 62 29-96 77-143 (188)
131 cd00056 ENDO3c endonuclease II 31.5 1.1E+02 0.0024 22.7 4.6 49 29-81 77-125 (158)
132 PRK04028 glutamyl-tRNA(Gln) am 30.8 1.4E+02 0.0031 29.0 6.2 63 28-96 519-581 (630)
133 COG1141 Fer Ferredoxin [Energy 30.4 29 0.00063 24.5 1.2 23 75-97 35-57 (68)
134 PF01402 RHH_1: Ribbon-helix-h 30.4 39 0.00085 19.9 1.6 25 30-54 7-32 (39)
135 PF11829 DUF3349: Protein of u 30.3 59 0.0013 24.4 2.9 27 27-53 35-64 (96)
136 PRK12773 flhB flagellar biosyn 30.2 1.7E+02 0.0037 28.8 6.6 61 20-97 576-637 (646)
137 TIGR00677 fadh2_euk methylenet 30.1 3.3E+02 0.0071 23.3 7.7 91 28-144 171-265 (281)
138 PF04926 PAP_RNA-bind: Poly(A) 30.0 23 0.00051 27.0 0.7 20 115-134 26-45 (157)
139 cd01109 HTH_YyaN Helix-Turn-He 30.0 2.1E+02 0.0046 20.6 9.2 40 17-56 28-69 (113)
140 PF09012 FeoC: FeoC like trans 29.9 49 0.0011 22.1 2.2 20 26-45 24-43 (69)
141 PTZ00081 enolase; Provisional 29.7 64 0.0014 29.6 3.6 72 79-150 219-311 (439)
142 cd08642 DNA_pol_A_pol_I_A Poly 29.5 84 0.0018 28.5 4.2 33 30-62 13-47 (378)
143 PRK03002 prsA peptidylprolyl i 29.5 2.6E+02 0.0056 23.6 6.9 47 69-131 89-135 (285)
144 PF09494 Slx4: Slx4 endonuclea 29.4 84 0.0018 21.1 3.3 40 27-81 21-60 (64)
145 PRK10144 formate-dependent nit 29.3 62 0.0013 25.4 3.0 31 30-60 59-89 (126)
146 PF12759 HTH_Tnp_IS1: InsA C-t 29.3 50 0.0011 22.1 2.1 20 31-50 8-27 (46)
147 PF06348 DUF1059: Protein of u 29.1 58 0.0013 21.7 2.5 18 78-96 37-54 (57)
148 cd08637 DNA_pol_A_pol_I_C Poly 29.0 1E+02 0.0022 27.3 4.7 35 30-64 16-53 (377)
149 PRK08156 type III secretion sy 29.0 1.7E+02 0.0037 26.4 6.1 66 20-102 272-338 (361)
150 cd04784 HTH_CadR-PbrR Helix-Tu 29.0 1E+02 0.0022 22.8 4.0 40 17-56 28-69 (127)
151 PF08542 Rep_fac_C: Replicatio 28.9 38 0.00082 23.0 1.6 29 27-55 17-45 (89)
152 PRK14987 gluconate operon tran 28.8 47 0.001 27.0 2.3 35 44-81 16-50 (331)
153 PRK10625 tas putative aldo-ket 28.2 1.9E+02 0.0041 24.6 6.0 61 34-96 274-338 (346)
154 PF13812 PPR_3: Pentatricopept 28.2 73 0.0016 17.1 2.4 19 29-47 16-34 (34)
155 TIGR02417 fruct_sucro_rep D-fr 28.1 58 0.0013 26.3 2.7 39 44-82 10-48 (327)
156 PRK05755 DNA polymerase I; Pro 28.0 1.9E+02 0.0041 28.5 6.6 48 30-77 516-571 (880)
157 PLN02641 anthranilate phosphor 28.0 55 0.0012 29.0 2.8 28 27-55 16-43 (343)
158 PRK13109 flhB flagellar biosyn 27.5 2.4E+02 0.0053 25.3 6.8 65 21-102 287-352 (358)
159 COG2082 CobH Precorrin isomera 27.3 1E+02 0.0022 26.2 4.1 69 10-83 82-156 (210)
160 PF05402 PqqD: Coenzyme PQQ sy 27.3 52 0.0011 21.3 1.9 35 28-62 13-47 (68)
161 PRK13870 transcriptional regul 27.0 47 0.001 27.3 2.1 28 27-56 173-200 (234)
162 PF13910 DUF4209: Domain of un 26.8 27 0.00059 25.3 0.6 45 52-96 6-55 (93)
163 PRK09526 lacI lac repressor; R 26.6 56 0.0012 26.5 2.4 35 44-81 16-50 (342)
164 TIGR01795 CM_mono_cladeE monof 26.6 89 0.0019 22.8 3.2 72 30-103 12-88 (94)
165 PRK12468 flhB flagellar biosyn 26.5 2E+02 0.0043 26.2 6.1 62 21-99 285-347 (386)
166 PF01325 Fe_dep_repress: Iron 26.2 55 0.0012 21.8 1.9 22 24-45 30-51 (60)
167 KOG2815 Mitochondrial/cholorop 26.2 98 0.0021 27.1 3.9 82 57-138 133-240 (256)
168 TIGR01481 ccpA catabolite cont 26.1 59 0.0013 26.2 2.4 37 43-82 11-47 (329)
169 smart00530 HTH_XRE Helix-turn- 26.0 1.2E+02 0.0027 16.6 3.9 33 44-82 21-53 (56)
170 TIGR00133 gatB glutamyl-tRNA(G 26.0 2E+02 0.0044 26.9 6.1 64 27-97 368-432 (478)
171 KOG4115 Dynein-associated prot 26.0 35 0.00077 26.0 1.0 60 30-103 2-62 (97)
172 cd04773 HTH_TioE_rpt2 Second H 25.9 1.4E+02 0.0031 21.6 4.2 40 17-56 28-69 (108)
173 PF13384 HTH_23: Homeodomain-l 25.6 39 0.00085 20.6 1.1 24 31-54 4-27 (50)
174 COG1609 PurR Transcriptional r 25.6 56 0.0012 27.8 2.3 38 43-83 10-47 (333)
175 cd01301 rDP_like renal dipepti 25.3 1.1E+02 0.0024 26.5 4.1 34 22-56 271-304 (309)
176 PLN03196 MOC1-like protein; Pr 25.3 1.6E+02 0.0034 27.3 5.3 57 28-94 87-147 (487)
177 TIGR02773 addB_Gpos ATP-depend 25.1 42 0.0009 33.7 1.6 34 31-64 319-366 (1158)
178 PF08212 Lipocalin_2: Lipocali 25.0 67 0.0015 24.0 2.4 23 28-50 116-138 (143)
179 TIGR00756 PPR pentatricopeptid 24.9 1E+02 0.0022 16.1 2.6 20 29-48 15-34 (35)
180 KOG1575 Voltage-gated shaker-l 24.9 1.7E+02 0.0037 26.4 5.3 47 31-79 257-305 (336)
181 PRK02998 prsA peptidylprolyl i 24.7 3.3E+02 0.0072 22.9 6.7 32 69-102 87-118 (283)
182 PF01934 DUF86: Protein of unk 24.5 2.6E+02 0.0057 19.8 5.3 76 43-125 37-112 (119)
183 PF14907 NTP_transf_5: Unchara 24.4 1.5E+02 0.0032 23.4 4.3 55 31-85 58-123 (249)
184 smart00352 POU Found in Pit-Oc 24.4 1.4E+02 0.003 21.6 3.9 50 28-82 4-57 (75)
185 PRK10376 putative oxidoreducta 24.4 2E+02 0.0044 23.8 5.4 59 36-95 225-286 (290)
186 PF01399 PCI: PCI domain; Int 24.3 72 0.0016 21.4 2.3 25 26-50 70-94 (105)
187 cd04783 HTH_MerR1 Helix-Turn-H 24.2 1.1E+02 0.0023 22.7 3.3 40 18-57 29-70 (126)
188 PRK10974 glycerol-3-phosphate 24.2 80 0.0017 27.2 3.0 45 56-100 136-182 (438)
189 PF00101 RuBisCO_small: Ribulo 24.1 57 0.0012 24.4 1.9 21 28-48 11-31 (99)
190 PRK00726 murG undecaprenyldiph 23.9 1.5E+02 0.0032 24.4 4.4 64 57-120 270-349 (357)
191 PF03744 BioW: 6-carboxyhexano 23.8 61 0.0013 28.0 2.2 58 29-95 22-106 (239)
192 cd04770 HTH_HMRTR Helix-Turn-H 23.7 1.8E+02 0.004 21.1 4.5 39 17-55 28-68 (123)
193 PRK09071 hypothetical protein; 23.6 78 0.0017 27.8 2.9 28 27-54 20-47 (323)
194 PF13643 DUF4145: Domain of un 23.5 1.5E+02 0.0033 19.8 3.7 50 68-118 37-86 (87)
195 PF10044 Ret_tiss: Retinal tis 23.4 43 0.00092 25.2 1.0 60 13-75 28-94 (95)
196 PRK01103 formamidopyrimidine/5 23.3 1.8E+02 0.004 24.4 5.0 62 28-98 142-209 (274)
197 cd01528 RHOD_2 Member of the R 23.3 1.5E+02 0.0032 20.3 3.7 46 23-69 35-92 (101)
198 PF07905 PucR: Purine cataboli 23.3 1.7E+02 0.0036 21.5 4.2 24 29-52 57-80 (123)
199 smart00794 AgrD Staphylococcal 23.0 49 0.0011 22.0 1.2 12 81-92 33-44 (45)
200 cd01107 HTH_BmrR Helix-Turn-He 22.8 3E+02 0.0065 19.8 7.6 36 23-58 35-72 (108)
201 PRK00252 alaS alanyl-tRNA synt 22.7 1.8E+02 0.004 28.9 5.5 47 45-98 376-422 (865)
202 cd04764 HTH_MlrA-like_sg1 Heli 22.6 1.8E+02 0.0038 18.8 3.8 34 21-54 31-66 (67)
203 COG1393 ArsC Arsenate reductas 22.5 49 0.0011 25.0 1.2 37 57-95 5-50 (117)
204 PF11919 DUF3437: Domain of un 22.5 66 0.0014 23.5 1.9 33 15-56 19-51 (90)
205 PRK09492 treR trehalose repres 22.4 77 0.0017 25.3 2.4 36 44-82 15-50 (315)
206 PRK10727 DNA-binding transcrip 22.2 72 0.0016 26.1 2.3 34 44-80 12-45 (343)
207 PRK09875 putative hydrolase; P 22.2 79 0.0017 27.3 2.6 63 21-83 88-180 (292)
208 PLN02900 alanyl-tRNA synthetas 22.2 2.1E+02 0.0045 29.1 5.8 59 33-98 396-456 (936)
209 cd04763 HTH_MlrA-like Helix-Tu 22.1 2E+02 0.0044 18.6 4.0 35 20-54 31-67 (68)
210 PF11463 R-HINP1I: R.HinP1I re 22.0 66 0.0014 27.4 2.0 51 82-135 66-119 (205)
211 TIGR01075 uvrD DNA helicase II 21.9 53 0.0011 31.1 1.6 35 30-64 325-371 (715)
212 cd04780 HTH_MerR-like_sg5 Heli 21.8 3.1E+02 0.0067 19.6 6.0 41 16-56 27-70 (95)
213 PRK01490 tig trigger factor; P 21.8 61 0.0013 28.6 1.9 52 26-77 366-419 (435)
214 PF14230 DUF4333: Domain of un 21.8 1.1E+02 0.0024 21.4 2.9 25 27-64 19-43 (80)
215 cd04769 HTH_MerR2 Helix-Turn-H 21.7 1.5E+02 0.0033 21.6 3.7 39 17-56 28-68 (116)
216 cd01108 HTH_CueR Helix-Turn-He 21.7 1.6E+02 0.0035 21.9 3.9 39 17-55 28-68 (127)
217 PF14842 FliG_N: FliG N-termin 21.7 89 0.0019 22.8 2.5 32 27-58 29-61 (108)
218 TIGR02329 propionate_PrpR prop 21.5 2E+02 0.0043 26.9 5.2 49 28-76 129-180 (526)
219 PF05504 Spore_GerAC: Spore ge 21.5 90 0.002 23.4 2.5 28 31-58 108-136 (171)
220 PRK13752 putative transcriptio 21.5 1.4E+02 0.003 23.1 3.6 40 17-56 35-76 (144)
221 KOG2598 Phosphomethylpyrimidin 21.4 2.3E+02 0.005 27.3 5.6 91 28-126 75-194 (523)
222 PRK10339 DNA-binding transcrip 21.4 81 0.0018 25.6 2.4 20 31-50 32-52 (327)
223 PF03825 Nuc_H_symport: Nucleo 21.4 46 0.001 29.3 1.1 16 39-54 28-43 (400)
224 PF04695 Pex14_N: Peroxisomal 21.3 79 0.0017 24.2 2.2 29 33-61 23-51 (136)
225 PRK11880 pyrroline-5-carboxyla 21.1 1.2E+02 0.0027 24.3 3.4 65 28-99 193-265 (267)
226 cd00423 Pterin_binding Pterin 20.9 81 0.0018 26.1 2.3 44 4-50 126-169 (258)
227 PF13783 DUF4177: Domain of un 20.5 99 0.0021 20.2 2.3 20 28-47 17-36 (61)
228 PRK14702 insertion element IS2 20.4 2.2E+02 0.0047 23.8 4.8 52 27-81 7-63 (262)
229 PRK13317 pantothenate kinase; 20.4 1.9E+02 0.0041 24.7 4.5 57 35-97 144-207 (277)
230 PF04233 Phage_Mu_F: Phage Mu 20.3 95 0.0021 21.6 2.3 30 31-60 1-30 (112)
231 cd04765 HTH_MlrA-like_sg2 Heli 20.2 2.1E+02 0.0046 20.6 4.2 39 20-58 31-72 (99)
232 TIGR00134 gatE_arch glutamyl-t 20.1 3E+02 0.0066 26.7 6.2 63 28-97 513-575 (620)
233 cd08643 DNA_pol_A_pol_I_B Poly 20.1 1.4E+02 0.0029 27.5 3.8 53 46-104 69-124 (429)
No 1
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=100.00 E-value=1e-75 Score=461.55 Aligned_cols=133 Identities=77% Similarity=1.151 Sum_probs=131.1
Q ss_pred CCCCCCCCCCcCCCCCCCCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCC
Q 031854 4 MHSRGKGISASALPYKRTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPE 83 (152)
Q Consensus 4 Mh~~~kG~S~S~~P~~~~~P~Wl~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlape 83 (152)
||++|||+|+|++||++++|+|+++++||||++||+|||+|+||||||++||||||||+||.|||+||++|||+||+||+
T Consensus 1 Mhs~gkG~S~S~~P~~r~~P~w~~~~~eeVe~~I~klaKkG~~pSqIG~iLRD~~gi~~vk~vtG~kI~rILk~~Glap~ 80 (148)
T PTZ00072 1 MYGKGKGISSSALPYRRKPPSWLKLSSSEVEDQICKLAKKGLTPSQIGVILRDSMGIPQVKNVTGSKILRILKKNGLAPE 80 (148)
T ss_pred CCCCCCCCCCCCCCCCCCCCchhcCCHHHHHHHHHHHHHCCCCHhHhhhhhhhccCccceeeccchHHHHHHHhcCCCCC
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ChhhHHHHHHHHHHHHHHHhHcCCccccchhhhhhHHHHHHHHHhhhhhceee
Q 031854 84 IPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHDWLATTRRQRSFH 136 (152)
Q Consensus 84 IPEDL~~LIkKAv~iRKHLe~n~KD~~sK~~L~LiESkI~RL~kYYk~~~~~~ 136 (152)
||||||+||||||+||||||+|+||+||||+|||||||||||+||||+++++-
T Consensus 81 iPeDly~LikKAv~iRkHLe~n~kD~~sK~~LiLiESkI~RL~rYYk~~~~lP 133 (148)
T PTZ00072 81 IPEDLYFLIKKAVSIRKHLEKNRKDKDSKFRLILVESRIHRLARYYKRTKQLP 133 (148)
T ss_pred CchHHHHHHHHHHHHHHHHHHcccchhhhHHHHHHHHHHHHHHHHHhhccCCC
Confidence 99999999999999999999999999999999999999999999999997754
No 2
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=100.00 E-value=4.9e-72 Score=441.98 Aligned_cols=136 Identities=49% Similarity=0.781 Sum_probs=134.4
Q ss_pred CCCCCCCCCCCCCcCCCCCCCCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCC
Q 031854 1 MGRMHSRGKGISASALPYKRTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGL 80 (152)
Q Consensus 1 M~RMh~~~kG~S~S~~P~~~~~P~Wl~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGl 80 (152)
|||||++|||+|+|++||++++|+|+++++||||++||+|||+|+||||||++||||||||+||.|||+||++|||+||+
T Consensus 1 M~rmh~~~kG~S~S~~P~~~~~P~W~~~~~eeve~~I~~lakkG~~pSqIG~~LRD~~gip~Vk~vtG~ki~~iLk~~gl 80 (151)
T PRK08561 1 MARMHTRRRGKSGSTRPARTEPPEWVDYSPEEIEELVVELAKQGYSPSMIGIILRDQYGIPDVKLITGKKITEILEENGL 80 (151)
T ss_pred CCCcCCCCCCCCCCCCCCCCCCCccccCCHHHHHHHHHHHHHCCCCHHHhhhhHhhccCCCceeeeccchHHHHHHHcCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCChhhHHHHHHHHHHHHHHHhHcCCccccchhhhhhHHHHHHHHHhhhhhceee
Q 031854 81 APEIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHDWLATTRRQRSFH 136 (152)
Q Consensus 81 apeIPEDL~~LIkKAv~iRKHLe~n~KD~~sK~~L~LiESkI~RL~kYYk~~~~~~ 136 (152)
+|+|||||||||+||++|++||+.|+||+||||+|+++|||+|||++||+++.++-
T Consensus 81 ~p~iPEDL~~L~~ri~~L~~HL~~nkKD~~skRgL~~~~skrrRLl~Yyk~~~~LP 136 (151)
T PRK08561 81 APEIPEDLRNLIKKAVNLRKHLEENPKDLHNKRGLQLIESKIRRLVKYYKRTGVLP 136 (151)
T ss_pred CCCCcHHHHHHHHHHHHHHHHHHhCCCcchhHHHHHHHHHHHHHHHHHHHhcCCCC
Confidence 99999999999999999999999999999999999999999999999999998764
No 3
>KOG0400 consensus 40S ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.2e-71 Score=436.69 Aligned_cols=137 Identities=74% Similarity=1.112 Sum_probs=135.1
Q ss_pred CCCCCCCCCCCCCcCCCCCCCCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCC
Q 031854 1 MGRMHSRGKGISASALPYKRTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGL 80 (152)
Q Consensus 1 M~RMh~~~kG~S~S~~P~~~~~P~Wl~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGl 80 (152)
|||||++|||+|+|++||++.+|+|+++++|||.++|++|||||+||||||++|||+|||++|+.|||+||+|||+.||+
T Consensus 1 MgrMHs~GKGis~SAlPY~r~~PtWlK~~~ddvkeqI~K~akKGltpsqIGviLRDshGi~q~r~v~G~kI~Rilk~~Gl 80 (151)
T KOG0400|consen 1 MGRMHSPGKGISGSALPYRRSVPTWLKLTADDVKEQIYKLAKKGLTPSQIGVILRDSHGIGQVRFVTGNKILRILKSNGL 80 (151)
T ss_pred CCcccCCCcccccCccccccCCcHHHhcCHHHHHHHHHHHHHcCCChhHceeeeecccCcchhheechhHHHHHHHHcCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCChhhHHHHHHHHHHHHHHHhHcCCccccchhhhhhHHHHHHHHHhhhhhceeee
Q 031854 81 APEIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHDWLATTRRQRSFHL 137 (152)
Q Consensus 81 apeIPEDL~~LIkKAv~iRKHLe~n~KD~~sK~~L~LiESkI~RL~kYYk~~~~~~~ 137 (152)
+||||||||+||+|||++|||||+|+||+|+||||||||||||||+||||+++++-|
T Consensus 81 ~PeiPeDLy~likkAv~iRkHLer~RKD~d~K~RLILveSRihRlARYYk~~~~lPp 137 (151)
T KOG0400|consen 81 APEIPEDLYHLIKKAVAIRKHLERNRKDKDAKFRLILVESRIHRLARYYKTKMVLPP 137 (151)
T ss_pred CCCCcHHHHHHHHHHHHHHHHHHHhccccccceEEEeehHHHHHHHHHHHhcccCCC
Confidence 999999999999999999999999999999999999999999999999999988754
No 4
>PF08069 Ribosomal_S13_N: Ribosomal S13/S15 N-terminal domain; InterPro: IPR012606 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This domain is found at the N terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 2XZN_O 2XZM_O 3IZ6_O.
Probab=100.00 E-value=4.4e-37 Score=211.77 Aligned_cols=60 Identities=75% Similarity=1.200 Sum_probs=41.8
Q ss_pred CCCCCCCCCCCCCcCCCCCCCCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCC
Q 031854 1 MGRMHSRGKGISASALPYKRTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGI 60 (152)
Q Consensus 1 M~RMh~~~kG~S~S~~P~~~~~P~Wl~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GI 60 (152)
|||||+++||+|+|++||++++|+|+++++||||++||+|||+|+||||||++|||||||
T Consensus 1 M~RMh~~~kG~S~S~~P~~~~~P~W~~~~~~eVe~~I~klakkG~tpSqIG~iLRD~~GI 60 (60)
T PF08069_consen 1 MGRMHSRGKGISGSTRPYRRSPPSWLKYSPEEVEELIVKLAKKGLTPSQIGVILRDQYGI 60 (60)
T ss_dssp ---TTSSS---------S-SS--TT--S-HHHHHHHHHHHCCTTHCHHHHHHHHHHSCTC
T ss_pred CCCccCCCCCccCCCCCCCCCCCCCcCCCHHHHHHHHHHHHHcCCCHHHhhhhhhhccCC
Confidence 999999999999999999999999999999999999999999999999999999999998
No 5
>COG0184 RpsO Ribosomal protein S15P/S13E [Translation, ribosomal structure and biogenesis]
Probab=99.91 E-value=1.2e-24 Score=159.47 Aligned_cols=76 Identities=28% Similarity=0.370 Sum_probs=73.5
Q ss_pred CCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHhHcCCccccchhhhhhHHHHH
Q 031854 44 GLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIH 123 (152)
Q Consensus 44 G~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv~iRKHLe~n~KD~~sK~~L~LiESkI~ 123 (152)
|..||+||..|||+||+|.++..+| |||+.+|+++|++|++|++.|+||.||||+|++++||++
T Consensus 1 m~~~~~~k~~l~~eyg~~~~dtgs~----------------evq~a~Lt~ri~~L~~Hlk~hkKD~~srRGL~~~vskrr 64 (89)
T COG0184 1 MSLTSEIKQELRDEYGIPEVDTGSG----------------EVQLALLTERINNLTEHLKEHKKDHHSRRGLLLLVSKRR 64 (89)
T ss_pred CCchHHHHHHHHHHhCCCCCCCCCc----------------HHHHHHHHHHHHHHHHHHHHCCcchhHHHHHHHHHHHHH
Confidence 6789999999999999999999988 999999999999999999999999999999999999999
Q ss_pred HHHHhhhhhcee
Q 031854 124 DWLATTRRQRSF 135 (152)
Q Consensus 124 RL~kYYk~~~~~ 135 (152)
||++|||++.+.
T Consensus 65 rLl~Ylk~~~~~ 76 (89)
T COG0184 65 RLLKYLKRKDVL 76 (89)
T ss_pred HHHHHHHhcCcc
Confidence 999999998764
No 6
>PF00312 Ribosomal_S15: Ribosomal protein S15; InterPro: IPR000589 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S15 is one of the proteins from the small ribosomal subunit. In Escherichia coli, this protein binds to 16S ribosomal RNA and functions at early steps in ribosome assembly. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ,], groups bacterial and plant chloroplast S15; archaeal Haloarcula marismortui HmaS15 (HS11); yeast mitochondrial S28; and mammalian, yeast, Brugia pahangi and Wuchereria bancrofti S13. S15 is a protein of 80 to 250 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1YSH_E 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 1S1H_O 3MR8_O 3D5C_O 3MS0_O ....
Probab=99.52 E-value=1.1e-14 Score=104.07 Aligned_cols=68 Identities=22% Similarity=0.259 Sum_probs=65.9
Q ss_pred ecchhHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHhHcCCccccchhhhhhHHHHHHHHHhhhhhc
Q 031854 66 VTGSKILRILKAHGLAPEIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHDWLATTRRQR 133 (152)
Q Consensus 66 vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv~iRKHLe~n~KD~~sK~~L~LiESkI~RL~kYYk~~~ 133 (152)
++++.|.++++++|-.+.+|+|+..|..|+.+|++|++.|+||++|+++|..++||.+||.+||+++.
T Consensus 2 ~k~~~i~~~~~~~~dtgs~evqia~LT~rI~~L~~Hl~~~kkD~~skr~L~~lv~kRrrlL~YLrr~~ 69 (83)
T PF00312_consen 2 RKQKSIKKFQRHPNDTGSPEVQIAILTERIRNLQEHLKKNKKDKHSKRGLLKLVSKRRRLLKYLRRKD 69 (83)
T ss_dssp HHHHHHHHHSSSTTSSSSHHHHHHHHHHHHHHHHHHHHHTTTSHHHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred hHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHHHHHHHHhccccccceehhHHHHHHHHHHHHHHhCC
Confidence 46889999999999999999999999999999999999999999999999999999999999999876
No 7
>cd00353 Ribosomal_S15p_S13e Ribosomal protein S15 (prokaryotic)_S13 (eukaryotic) binds the central domain of 16S rRNA and is required for assembly of the small ribosomal subunit and for intersubunit association, thus representing a key element in the assembly of the whole ribosome. S15 also plays an important autoregulatory role by binding and preventing its own mRNA from being translated. S15 has a predominantly alpha-helical fold that is highly structured except for the N-terminal alpha helix.
Probab=99.49 E-value=6.8e-14 Score=99.51 Aligned_cols=63 Identities=37% Similarity=0.455 Sum_probs=60.3
Q ss_pred HHHHHHHcCCC----CCChhhHHHHHHHHHHHHHHHhHcCCccccchhhhhhHHHHHHHHHhhhhhc
Q 031854 71 ILRILKAHGLA----PEIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHDWLATTRRQR 133 (152)
Q Consensus 71 I~~ILk~nGla----peIPEDL~~LIkKAv~iRKHLe~n~KD~~sK~~L~LiESkI~RL~kYYk~~~ 133 (152)
+.+|+++.|.. +.+|+++..|..|+.+|++||+.|+||++|+++|+.++||++||.+||+++.
T Consensus 2 ~~~i~~~~~~~~~DtGs~evQia~LT~rI~~L~~Hl~~~~KD~~~krgL~~lv~kRrrLL~YLk~~~ 68 (80)
T cd00353 2 KQEILKEFGLAEGDTGSPEVQLALLTERIVNLTEHLEKNKKDKHSKRGLLLLVSKRRRLLKYLKRKD 68 (80)
T ss_pred HHHHHHHhCCCCCCCCChHHHHHHHHHHHHHHHHHHHHccccchHHHhHHHHHHHHHHHHHHHHHcC
Confidence 56899999988 8999999999999999999999999999999999999999999999999884
No 8
>cd00677 S15_NS1_EPRS_RNA-bind S15/NS1/EPRS_RNA-binding domain. This short domain consists of a helix-turn-helix structure, which can bind to several types of RNA. It is found in the ribosomal protein S15, the influenza A viral nonstructural protein (NSA) and in several eukaryotic aminoacyl tRNA synthetases (aaRSs), where it occurs as a single or a repeated unit. It is involved in both protein-RNA interactions by binding tRNA and protein-protein interactions in the formation of tRNA-synthetases into multienzyme complexes. While this domain lacks significant sequence similarity between the subgroups in which it is found, they share similar electrostatic surface potentials and thus are likely to bind to RNA via the same mechanism.
Probab=99.11 E-value=1.3e-10 Score=74.55 Aligned_cols=46 Identities=28% Similarity=0.341 Sum_probs=44.6
Q ss_pred hhhHHHHHHHHHHHHHHHhHcCCccccchhhhhhHHHHHHHHHhhh
Q 031854 85 PEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHDWLATTR 130 (152)
Q Consensus 85 PEDL~~LIkKAv~iRKHLe~n~KD~~sK~~L~LiESkI~RL~kYYk 130 (152)
|+++..|..++.++..|++.|+||++++++|..++++++||.+||+
T Consensus 1 ~vqia~lt~~i~~L~~hl~~~~kD~~~kr~L~~~v~kr~rLl~ylk 46 (46)
T cd00677 1 EVQIALLTERIRNLKEHLAKNKKDKHSKRGLDLLVSKRLRLLKYLK 46 (46)
T ss_pred CHHHHHHHHHHHHHHHHHHHCCCCcchHHHHHHHHHHHHHHHHHhC
Confidence 6789999999999999999999999999999999999999999996
No 9
>TIGR00952 S15_bact ribosomal protein S15, bacterial/organelle. This model is built to recognize specifically bacterial, chloroplast, and mitochondrial ribosomal protein S15. The homologous proteins of Archaea and Eukarya are designated S13.
Probab=97.32 E-value=0.00045 Score=50.57 Aligned_cols=46 Identities=24% Similarity=0.347 Sum_probs=41.4
Q ss_pred HHHHHHHHHHHHHHHhHcCCccccchhhhhhHHHHHHHHHhhhhhc
Q 031854 88 LYHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHDWLATTRRQR 133 (152)
Q Consensus 88 L~~LIkKAv~iRKHLe~n~KD~~sK~~L~LiESkI~RL~kYYk~~~ 133 (152)
...|=.+-.+|..|++.|+||.+|+++|.-.-+|=+||.+|-+++.
T Consensus 26 iA~LT~rI~~L~~Hl~~h~KD~~srrgL~~lv~kRkrlL~YL~~~d 71 (86)
T TIGR00952 26 IALLTERINQLTEHLKANKKDHHSRRGLLKLVGRRRRLLKYLKRTD 71 (86)
T ss_pred HHHHHHHHHHHHHHHHHCCCchHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 3556678889999999999999999999999999999999998764
No 10
>CHL00027 rps15 ribosomal protein S15
Probab=97.16 E-value=0.00086 Score=49.76 Aligned_cols=47 Identities=21% Similarity=0.289 Sum_probs=41.9
Q ss_pred HHHHHHHHHHHHHHHhHcCCccccchhhhhhHHHHHHHHHhhhhhce
Q 031854 88 LYHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHDWLATTRRQRS 134 (152)
Q Consensus 88 L~~LIkKAv~iRKHLe~n~KD~~sK~~L~LiESkI~RL~kYYk~~~~ 134 (152)
..-|=.+-..+..||+.|+||.+++++|.-.-++=+||.+|.+++..
T Consensus 26 iA~LT~rI~~Lt~Hlk~hkKD~~s~RgL~~lv~kRkrLL~YL~r~d~ 72 (90)
T CHL00027 26 VFSFTNKIRRLTSHLELHKKDYSSQRGLRKILGKRQRLLAYLSKKNR 72 (90)
T ss_pred HHHHHHHHHHHHHHHHHCCCcchhHHHHHHHHHHHHHHHHHHHhCCH
Confidence 45566788899999999999999999999999999999999988753
No 11
>PRK05626 rpsO 30S ribosomal protein S15; Reviewed
Probab=97.11 E-value=0.00078 Score=49.61 Aligned_cols=45 Identities=18% Similarity=0.296 Sum_probs=40.4
Q ss_pred HHHHHHHHHHHHHHhHcCCccccchhhhhhHHHHHHHHHhhhhhc
Q 031854 89 YHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHDWLATTRRQR 133 (152)
Q Consensus 89 ~~LIkKAv~iRKHLe~n~KD~~sK~~L~LiESkI~RL~kYYk~~~ 133 (152)
.-|=.+-.++..|++.|+||.+|+++|...=++=+||.+|-+++.
T Consensus 30 A~LT~rI~~L~~Hlk~~~KD~~srrgL~~lv~kRkrlL~YL~~~d 74 (89)
T PRK05626 30 ALLTERINHLTEHLKEHKKDHHSRRGLLKMVGQRRKLLDYLKKKD 74 (89)
T ss_pred HHHHHHHHHHHHHHHHcccchhhHHHHHHHHHhHHHHHHHHHhcC
Confidence 445568889999999999999999999999999999999998764
No 12
>PTZ00119 40S ribosomal protein S15; Provisional
Probab=96.57 E-value=0.003 Score=55.52 Aligned_cols=64 Identities=22% Similarity=0.224 Sum_probs=50.1
Q ss_pred hHHHHHHHcCCCCC----ChhhHHHHHHHHHHHHHHHhHcCCccccchhhhhhHHHHHHHHHhhhhhc
Q 031854 70 KILRILKAHGLAPE----IPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHDWLATTRRQR 133 (152)
Q Consensus 70 kI~~ILk~nGlape----IPEDL~~LIkKAv~iRKHLe~n~KD~~sK~~L~LiESkI~RL~kYYk~~~ 133 (152)
+..+|.++-+..+. ..--..-|=.|-.+|..||+.|+||.+|+++|...-+|=+||.+|.+++.
T Consensus 109 rK~eIIkkfqr~~~DTGS~EVQIAiLTeRI~~LTeHLk~hkKD~~SrRGLlkLV~KRRKLLkYLKrkD 176 (302)
T PTZ00119 109 KKLCIRRCLQRRPFDTGSAPVQIGCLTEKILNLRAHLILRCKDHPKKRTMSILLARRQKLMKYLYKTD 176 (302)
T ss_pred HHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhCCCccHhHHHHHHHHHHHHHHHHHHHhcC
Confidence 34455555554332 22234667788899999999999999999999999999999999999875
No 13
>COG2257 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]
Probab=95.33 E-value=0.12 Score=38.83 Aligned_cols=70 Identities=23% Similarity=0.424 Sum_probs=61.0
Q ss_pred CCCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHHHHH
Q 031854 20 RTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVAIR 99 (152)
Q Consensus 20 ~~~P~Wl~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv~iR 99 (152)
..+|.=+-.-.-||-+.|++.||+ ||||.+.. ..+.+.|-.-.+..+|||.||.-|-.-...-
T Consensus 20 ~~AP~vvA~G~G~iAe~II~~Ake--------------~~Vpi~ed---p~Lv~~L~~lelg~~IPeelY~vVAEifafi 82 (92)
T COG2257 20 DKAPKVVASGKGEIAEKIIEKAKE--------------HGVPIQED---PLLVELLLKLELGDEIPEELYEVVAEIFAFI 82 (92)
T ss_pred CCCCEEEeecchHHHHHHHHHHHH--------------cCCCcccC---HHHHHHHHhccccccCCHHHHHHHHHHHHHH
Confidence 468888888899999999999985 89998765 5699999999999999999999999888888
Q ss_pred HHHhHcC
Q 031854 100 KHLERNR 106 (152)
Q Consensus 100 KHLe~n~ 106 (152)
.+++.|-
T Consensus 83 ~~~~~~~ 89 (92)
T COG2257 83 YEVDNNV 89 (92)
T ss_pred HHHHccC
Confidence 8887763
No 14
>PF13565 HTH_32: Homeodomain-like domain
Probab=91.49 E-value=0.38 Score=32.05 Aligned_cols=44 Identities=27% Similarity=0.468 Sum_probs=34.7
Q ss_pred hHHHHHHHHHHHhcC--CCcchhhhHhhhccCCCceeeecchhHHHHH
Q 031854 30 SQDVEDNICKFAKKG--LTPSQIGVILRDSHGIAQVKSVTGSKILRIL 75 (152)
Q Consensus 30 ~eEVe~~IvklaKkG--~tpSqIG~iLRD~~GIp~VK~vtGkkI~~IL 75 (152)
++|+++.|+++.... .|+.+|-..|.++|||.. .+.-..|.++|
T Consensus 32 ~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~--~~S~~tv~R~L 77 (77)
T PF13565_consen 32 DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISV--RVSRSTVYRIL 77 (77)
T ss_pred cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCC--CccHhHHHHhC
Confidence 677878899988765 899999999999999865 44555566554
No 15
>PF13276 HTH_21: HTH-like domain
Probab=88.37 E-value=1.2 Score=29.02 Aligned_cols=51 Identities=22% Similarity=0.321 Sum_probs=39.5
Q ss_pred HHHHHHHHHHHhcC---CCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCCh
Q 031854 31 QDVEDNICKFAKKG---LTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIP 85 (152)
Q Consensus 31 eEVe~~IvklaKkG---~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIP 85 (152)
+++.+.|.++.... +-.-.|-..|++++|+ .|.-++|.++++++||...++
T Consensus 4 ~~l~~~I~~i~~~~~~~yG~rri~~~L~~~~~~----~v~~krV~RlM~~~gL~~~~r 57 (60)
T PF13276_consen 4 EALRELIKEIFKESKPTYGYRRIWAELRREGGI----RVSRKRVRRLMREMGLRSKRR 57 (60)
T ss_pred HHHHHHHHHHHHHcCCCeehhHHHHHHhccCcc----cccHHHHHHHHHHcCCcccCC
Confidence 55666677766643 4556888999999987 578889999999999987653
No 16
>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=86.90 E-value=2.4 Score=30.59 Aligned_cols=60 Identities=32% Similarity=0.549 Sum_probs=46.9
Q ss_pred CCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHHH
Q 031854 21 TPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVA 97 (152)
Q Consensus 21 ~~P~Wl~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv~ 97 (152)
.+|-=+-.-.+++-+.|.++|++ +|||.+.. ..+.+.|-.-++.-+||||||.-+-....
T Consensus 16 ~aP~VvAKG~g~~A~~I~~~A~e--------------~~VPi~~~---~~LAr~L~~~~ig~~IP~~ly~aVAeil~ 75 (82)
T TIGR00789 16 KAPKVVASGVGEVAERIIEIAKK--------------HGIPIVED---PDLVDVLLKLDLDDEIPEELYEVVAEIFA 75 (82)
T ss_pred CCCEEEEEeCCHHHHHHHHHHHH--------------cCCCEEeC---HHHHHHHHhCCCCCccCHHHHHHHHHHHH
Confidence 45555555678888889988874 79999876 45888888889999999999977665543
No 17
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=86.24 E-value=0.76 Score=41.39 Aligned_cols=48 Identities=17% Similarity=0.203 Sum_probs=43.7
Q ss_pred CCCCCcCCCCCCCCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCC
Q 031854 9 KGISASALPYKRTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGI 60 (152)
Q Consensus 9 kG~S~S~~P~~~~~P~Wl~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GI 60 (152)
|+..+|-.| .++|.+.....+++.|..|.++|+|+.+|...++..|+.
T Consensus 69 r~r~g~f~p----l~~~~~r~~~~~~~~v~~~y~~gv~Tr~i~~~~~~~~~~ 116 (379)
T COG3328 69 RDRKGSFEP----LIERYQRRERALDLPVLSMYAKGVTTREIEALLEELYGH 116 (379)
T ss_pred cccccCccc----cchhhHhhhhhHHHHHHHHHHcCCcHHHHHHHHHHhhCc
Confidence 566777666 689999999999999999999999999999999999998
No 18
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=81.99 E-value=1.2 Score=35.56 Aligned_cols=25 Identities=28% Similarity=0.356 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHhcCCCcchhhhHhh
Q 031854 31 QDVEDNICKFAKKGLTPSQIGVILR 55 (152)
Q Consensus 31 eEVe~~IvklaKkG~tpSqIG~iLR 55 (152)
||-.+.+.+|+++|+|-|||+..|=
T Consensus 5 de~~~~L~~lw~~G~SasqIA~~lg 29 (162)
T PF07750_consen 5 DERVERLRKLWAEGLSASQIARQLG 29 (162)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHhC
Confidence 4445589999999999999998874
No 19
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]. Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.
Probab=81.72 E-value=0.84 Score=35.66 Aligned_cols=31 Identities=35% Similarity=0.613 Sum_probs=23.9
Q ss_pred ChHHHHHHHHHHHhcCCCcchhhhHhhhccC
Q 031854 29 SSQDVEDNICKFAKKGLTPSQIGVILRDSHG 59 (152)
Q Consensus 29 ~~eEVe~~IvklaKkG~tpSqIG~iLRD~~G 59 (152)
-++|+-+.|++||+.|+.|.+|--.|+=+||
T Consensus 18 Lp~~~R~rIvela~~G~rp~~Isr~l~Vs~g 48 (125)
T PF00292_consen 18 LPNELRQRIVELAKEGVRPCDISRQLRVSHG 48 (125)
T ss_dssp S-HHHHHHHHHHHHTT--HHHHHHHHT--HH
T ss_pred CcHHHHHHHHHHhhhcCCHHHHHHHHccchh
Confidence 3689999999999999999999999988875
No 20
>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=79.24 E-value=1.3 Score=28.65 Aligned_cols=41 Identities=24% Similarity=0.443 Sum_probs=34.6
Q ss_pred HHHh-cCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCC
Q 031854 39 KFAK-KGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAP 82 (152)
Q Consensus 39 klaK-kG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlap 82 (152)
++|+ -|+|+|-+-.+|.+. +.|..-|-.+|.++.++.|-.|
T Consensus 4 dIA~~agvS~~TVSr~ln~~---~~vs~~tr~rI~~~a~~lgY~p 45 (46)
T PF00356_consen 4 DIAREAGVSKSTVSRVLNGP---PRVSEETRERILEAAEELGYRP 45 (46)
T ss_dssp HHHHHHTSSHHHHHHHHTTC---SSSTHHHHHHHHHHHHHHTB-S
T ss_pred HHHHHHCcCHHHHHHHHhCC---CCCCHHHHHHHHHHHHHHCCCC
Confidence 3444 599999999999998 7888899999999999998776
No 21
>PF13361 UvrD_C: UvrD-like helicase C-terminal domain; PDB: 1UAA_B 3U4Q_A 3U44_A 1W36_B 3K70_B 2IS6_B 3LFU_A 2IS2_B 2IS1_B 2IS4_A ....
Probab=77.83 E-value=2 Score=34.10 Aligned_cols=43 Identities=26% Similarity=0.495 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCC
Q 031854 31 QDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLA 81 (152)
Q Consensus 31 eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGla 81 (152)
+.|.+.|.++...|++++.|++..|+.. ....|.+.|+++|+.
T Consensus 61 ~~i~~~I~~l~~~~~~~~diAVL~R~~~--------~~~~i~~~L~~~gIp 103 (351)
T PF13361_consen 61 EYIAEEIKELIRNGIPPSDIAVLVRTNS--------QIKEIEDALKEAGIP 103 (351)
T ss_dssp HHHHHHHHHHHHTTS-GGGEEEEESSGG--------HHHHHHHHHHHTTS-
T ss_pred HHHHHHHHHHhhcCCCcccEEEEEECch--------hHHHHHHHHhhhcce
Confidence 4477888888888999999999999842 233466777777765
No 22
>PHA02591 hypothetical protein; Provisional
Probab=77.61 E-value=2 Score=31.94 Aligned_cols=28 Identities=29% Similarity=0.381 Sum_probs=25.1
Q ss_pred cCChHHHHHHHHHHHhcCCCcchhhhHh
Q 031854 27 KISSQDVEDNICKFAKKGLTPSQIGVIL 54 (152)
Q Consensus 27 ~~~~eEVe~~IvklaKkG~tpSqIG~iL 54 (152)
--+.|++..+.-+|++.|+|.+||...|
T Consensus 42 i~~~dd~~~vA~eL~eqGlSqeqIA~~L 69 (83)
T PHA02591 42 VESEDDLISVTHELARKGFTVEKIASLL 69 (83)
T ss_pred EeccchHHHHHHHHHHcCCCHHHHHHHh
Confidence 3478899999999999999999999877
No 23
>PHA02517 putative transposase OrfB; Reviewed
Probab=75.86 E-value=4.6 Score=32.83 Aligned_cols=48 Identities=21% Similarity=0.246 Sum_probs=39.6
Q ss_pred hHHHHHHHHHHHhc---CCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCC
Q 031854 30 SQDVEDNICKFAKK---GLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAP 82 (152)
Q Consensus 30 ~eEVe~~IvklaKk---G~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlap 82 (152)
.+|+.+.|.++..+ .+...+|-..|+++ |+ .+.-++|.++|+++|+..
T Consensus 28 ~~~l~~~I~~i~~~~~~~~G~r~I~~~L~~~-g~----~vs~~tV~Rim~~~gl~~ 78 (277)
T PHA02517 28 DDWLKSEILRVYDENHQVYGVRKVWRQLNRE-GI----RVARCTVGRLMKELGLAG 78 (277)
T ss_pred hHHHHHHHHHHHHHhCCCCCHHHHHHHHHhc-Cc----ccCHHHHHHHHHHcCCce
Confidence 46889999999643 47889999999987 76 368889999999999965
No 24
>PRK15364 pathogenicity island 2 effector protein SseB; Provisional
Probab=75.10 E-value=9.8 Score=32.13 Aligned_cols=81 Identities=22% Similarity=0.279 Sum_probs=58.8
Q ss_pred ChHHHHHHHHHHHhcCC-----CcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHh
Q 031854 29 SSQDVEDNICKFAKKGL-----TPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVAIRKHLE 103 (152)
Q Consensus 29 ~~eEVe~~IvklaKkG~-----tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv~iRKHLe 103 (152)
.+.+|.+.|.+++|.|= -|-.+=..+|| +||- |+|++|-..|+++|..+++-.-=...||-|+.--.
T Consensus 77 mAN~VDevIA~v~k~ddK~k~~LPddVI~Ymrd-NgI~----VdG~sid~Yl~k~~~~~~LdkG~LqAVKAALd~~s--- 148 (196)
T PRK15364 77 KSNEMDEVIAKAAKGDAKTKEEVPEDVIKYMRD-NGIL----IDGMTIDDYMAKYGDHGKLDKGGLQAIKAALDNDA--- 148 (196)
T ss_pred HHHHHHHHHHHHhcCCCcccccCCHHHHHHHHH-cCce----ecccchHHHHhccCCccCCChhhHHHHHHHHHhhc---
Confidence 35689999999987443 25566678999 8884 79999999999999999998877778888864321
Q ss_pred HcCCccccchhhhh
Q 031854 104 RNRKDKDSKFRLIL 117 (152)
Q Consensus 104 ~n~KD~~sK~~L~L 117 (152)
.+--|.-+..+|++
T Consensus 149 nr~TD~vsQsQLqi 162 (196)
T PRK15364 149 NRNTDLMSQGQITI 162 (196)
T ss_pred cccchhhhHHHHHH
Confidence 22345555555543
No 25
>PF00872 Transposase_mut: Transposase, Mutator family; InterPro: IPR001207 Autonomous mobile genetic elements such as transposon or insertion sequences (IS) encode an enzyme, transposase, that is required for excising and inserting the mobile element. Transposases have been grouped into various families [, , ]. The mutator family of transposases consists of a number of elements that include, mutator from maize, IsT2 from Thiobacillus ferrooxidans, Is256 from Staphylococcus aureus, Is1201 from Lactobacillus helveticus, Is1081 from Mycobacterium bovis, IsRm3 from Rhizobium meliloti and others. 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
Probab=74.12 E-value=2.6 Score=37.01 Aligned_cols=39 Identities=23% Similarity=0.404 Sum_probs=34.5
Q ss_pred CCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccC-CC
Q 031854 22 PPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHG-IA 61 (152)
Q Consensus 22 ~P~Wl~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~G-Ip 61 (152)
.|.|-. ..+++++.|..|.-+|+|+.+|+.+|.+-|| .+
T Consensus 93 l~~y~r-~~~~l~~~i~~ly~~G~Str~i~~~l~~l~g~~~ 132 (381)
T PF00872_consen 93 LPKYQR-REDSLEELIISLYLKGVSTRDIEEALEELYGEVA 132 (381)
T ss_pred cchhhh-hhhhhhhhhhhhhccccccccccchhhhhhcccc
Confidence 455554 4689999999999999999999999999999 87
No 26
>PF13551 HTH_29: Winged helix-turn helix
Probab=73.87 E-value=6.3 Score=27.16 Aligned_cols=53 Identities=28% Similarity=0.423 Sum_probs=35.3
Q ss_pred CCCCCccCChHHHHHHHHHHHhc----C---CCcchhhhHh-hhccCCCceeeecchhHHHHHHHcC
Q 031854 21 TPPSWLKISSQDVEDNICKFAKK----G---LTPSQIGVIL-RDSHGIAQVKSVTGSKILRILKAHG 79 (152)
Q Consensus 21 ~~P~Wl~~~~eEVe~~IvklaKk----G---~tpSqIG~iL-RD~~GIp~VK~vtGkkI~~ILk~nG 79 (152)
..|.+. +++++. +.|+++..+ | .|+.+|-..| .+++|+. +.-..|.++|++.|
T Consensus 52 g~~~~~-l~~~~~-~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~----~s~~ti~r~L~~~G 112 (112)
T PF13551_consen 52 GRPRKR-LSEEQR-AQLIELLRENPPEGRSRWTLEELAEWLIEEEFGID----VSPSTIRRILKRAG 112 (112)
T ss_pred CCCCCC-CCHHHH-HHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCcc----CCHHHHHHHHHHCc
Confidence 344443 455444 456666654 3 5778888766 8888886 45578999999887
No 27
>COG1202 Superfamily II helicase, archaea-specific [General function prediction only]
Probab=73.34 E-value=2.2 Score=41.87 Aligned_cols=45 Identities=29% Similarity=0.533 Sum_probs=36.9
Q ss_pred HHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHHHH
Q 031854 33 VEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVAI 98 (152)
Q Consensus 33 Ve~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv~i 98 (152)
.-+.|++|.-.|.+|+||-.+|++.|||- ..|-|.++-...+|+.
T Consensus 755 lse~ii~lR~~gk~p~~Isr~l~~~Ygi~---------------------aYpgDif~wLd~~vr~ 799 (830)
T COG1202 755 LSEKIIELRIEGKDPSQISRILEKRYGIQ---------------------AYPGDIFTWLDTLVRL 799 (830)
T ss_pred HHHHHHHHHhcCCCHHHHHHHHHHhhCee---------------------ecChhHHHHHHHHHHH
Confidence 44789999999999999999999999984 3567777776666654
No 28
>KOG1802 consensus RNA helicase nonsense mRNA reducing factor (pNORF1) [RNA processing and modification]
Probab=73.21 E-value=1.9 Score=42.81 Aligned_cols=51 Identities=35% Similarity=0.625 Sum_probs=38.9
Q ss_pred ChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecch--hHHHHHHHcCCCCCChhhHHHHH
Q 031854 29 SSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGS--KILRILKAHGLAPEIPEDLYHLI 92 (152)
Q Consensus 29 ~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGk--kI~~ILk~nGlapeIPEDL~~LI 92 (152)
.+-++|++|-+|-+.|+.|||||+|- +..|. .|..+|..+| .++-|||.-|
T Consensus 708 Ea~~~ekii~~l~~~gv~~~qIGVIT----------pYegQr~~i~~ym~~~g---sl~~~ly~~v 760 (935)
T KOG1802|consen 708 EAANCEKIITKLLKSGVKPSQIGVIT----------PYEGQRSYIVNYMQTNG---SLHKDLYKEV 760 (935)
T ss_pred HHHHHHHHHHHHHHcCCCHHHeeeec----------ccchhHHHHHHHHHhcC---ccccchhhee
Confidence 35678999999999999999999863 33343 4788886666 5677888655
No 29
>PRK01322 6-carboxyhexanoate--CoA ligase; Provisional
Probab=72.46 E-value=3.5 Score=35.56 Aligned_cols=74 Identities=22% Similarity=0.351 Sum_probs=53.1
Q ss_pred CCCCCC--CCCCCcCCCCCCCCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchh----------
Q 031854 3 RMHSRG--KGISASALPYKRTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSK---------- 70 (152)
Q Consensus 3 RMh~~~--kG~S~S~~P~~~~~P~Wl~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkk---------- 70 (152)
||.+.. +=+||--+=. +.++|++.+.+|.+++++- +.|.|+-=+++=.+
T Consensus 6 kMRAs~~g~HISGAErIv----------~~~~i~~~~~~L~~Ral~H---------~~G~pDfinIkve~i~~~I~~i~~ 66 (242)
T PRK01322 6 KMRASKNGKHISGAERIV----------EFEKIEETVSELLKRALFH---------ENGKPDFINIKIEKIEEPIQYIKA 66 (242)
T ss_pred EeEccCCCCccccccccC----------CHHHHHHHHHHHHHhhhhc---------cCCCCCeeEEEEEEccCcceeccC
Confidence 565544 5566654432 6899999999999998765 46666653333222
Q ss_pred -----------------HHHHHHHcCCCCCChhhHHHHHHHH
Q 031854 71 -----------------ILRILKAHGLAPEIPEDLYHLIKKA 95 (152)
Q Consensus 71 -----------------I~~ILk~nGlapeIPEDL~~LIkKA 95 (152)
+..+|++.|+.++++|..+.+|.+-
T Consensus 67 LpV~t~~~~~~eea~~~a~~lL~~~gv~~~~~~~~~~~l~~~ 108 (242)
T PRK01322 67 LPIKTIDVKSVEEARALARELLQEEGVSEEAIEKAFELIKEG 108 (242)
T ss_pred cceeEEecCCHHHHHHHHHHHHHhcCCCHHHHHHHHHHHhcC
Confidence 2455999999999999999999885
No 30
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=71.57 E-value=12 Score=26.74 Aligned_cols=40 Identities=25% Similarity=0.406 Sum_probs=32.4
Q ss_pred CCCCCCCCCccCChHHHHHH--HHHHHhcCCCcchhhhHhhh
Q 031854 17 PYKRTPPSWLKISSQDVEDN--ICKFAKKGLTPSQIGVILRD 56 (152)
Q Consensus 17 P~~~~~P~Wl~~~~eEVe~~--IvklaKkG~tpSqIG~iLRD 56 (152)
|.++...-+-.++.++|..+ |+.|..-|+|.++|..++..
T Consensus 28 ~~~~~~~g~R~y~~~di~~l~~i~~lr~~g~~l~~i~~~~~~ 69 (103)
T cd01106 28 PSRRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELLKD 69 (103)
T ss_pred CCccCCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 44555556778999999875 88899999999999999854
No 31
>PF11740 KfrA_N: Plasmid replication region DNA-binding N-term; InterPro: IPR021104 The KfrA family of protiens are encoded on plasmids, generally in or near gene clusters invloved in stable inheritance functions. These proteins are thought to form an all-helical structure, consisting of an N-terminal helix-turn-helix DNA binding domain and an extended coiled-coil tail. The best-characterised KfrA protein, encoded on the broad host-range Plasmid RK2, is a site-specific DNA-binding protein whose operator overlaps its own promoter. The DNA-binding domain is essential for function, while the coiled-coil domain is probably responsible for formation of multimers, and may provide an example of a bridge to host structures required for plasmid partitioning []. This entry represents the N-terminal DNA-binding domain.
Probab=71.54 E-value=6.2 Score=28.45 Aligned_cols=59 Identities=27% Similarity=0.399 Sum_probs=38.7
Q ss_pred CChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHc------C---CCCCChhhHHHHHH
Q 031854 28 ISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAH------G---LAPEIPEDLYHLIK 93 (152)
Q Consensus 28 ~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~n------G---lapeIPEDL~~LIk 93 (152)
+|.++|.+....|...|-.||- ..+|..-|-++- ..|.+.|++- . ..|++|++|...+.
T Consensus 1 IT~e~V~~Aa~~L~~~G~~pT~--~~Vr~~lG~GS~-----~ti~~~l~~w~~~~~~~~~~~~~~lP~~l~~~~~ 68 (120)
T PF11740_consen 1 ITYEDVIEAADELLAAGKKPTV--RAVRERLGGGSM-----STISKHLKEWREEREAQVSEAAPDLPEALQDALA 68 (120)
T ss_pred CcHHHHHHHHHHHHHcCCCCCH--HHHHHHHCCCCH-----HHHHHHHHHHHHhhhccccccccCCChhHHHHHH
Confidence 4789999999999999999974 345555552211 3355555542 1 36788988844333
No 32
>TIGR00328 flhB flagellar biosynthetic protein FlhB. FlhB and its functionally equivalent orthologs, from among a larger superfamily of proteins involved in type III protein export systems, are specifically involved in flagellar protein export. The seed members are restricted and the trusted cutoff is set high such that the proteins gathered by this model play roles specifically related to flagellar structures. Full-length homologs scoring below the trusted cutoff are involved in peptide export but not necessarily in the creation of flagella.
Probab=71.10 E-value=16 Score=32.48 Aligned_cols=62 Identities=19% Similarity=0.377 Sum_probs=49.2
Q ss_pred CCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHH-HHcCCCCCChhhHHHHHHHHHHHH
Q 031854 21 TPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRIL-KAHGLAPEIPEDLYHLIKKAVAIR 99 (152)
Q Consensus 21 ~~P~Wl~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~IL-k~nGlapeIPEDL~~LIkKAv~iR 99 (152)
.+|-=+-.-.+++-..|.++|++ ||||-|.. ..+.|-| +.-.+..+|||+||.-|-.....-
T Consensus 278 ~aP~vvakG~~~~A~~I~~~A~~--------------~~vPi~~~---~~LAr~Ly~~~~~g~~IP~~ly~aVA~il~~v 340 (347)
T TIGR00328 278 PAPVVVAKGVDELALKIKEIARE--------------NNVPIVEN---PPLARALYRQVEIGQEIPPELYKAVAEVLAYV 340 (347)
T ss_pred CCCEEEEeeCcHHHHHHHHHHHH--------------cCCCEEeC---HHHHHHHHHcCCCCCcCCHHHHHHHHHHHHHH
Confidence 45655666788999999999986 89999876 4588888 667888999999998887765543
No 33
>PF15652 Tox-SHH: HNH/Endo VII superfamily toxin with a SHH signature
Probab=70.10 E-value=3.9 Score=31.23 Aligned_cols=34 Identities=9% Similarity=0.212 Sum_probs=33.0
Q ss_pred CccCChHHHHHHHHHHHhcCCCcchhhhHhhhcc
Q 031854 25 WLKISSQDVEDNICKFAKKGLTPSQIGVILRDSH 58 (152)
Q Consensus 25 Wl~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~ 58 (152)
|-....+|+....-+|-+.|++++++=..|+|+|
T Consensus 63 w~t~~~~Ef~~~~~eM~dAGV~~~~~~~~l~~~Y 96 (100)
T PF15652_consen 63 WSTTLQEEFNNSYREMFDAGVSKECRKKALKAQY 96 (100)
T ss_pred ccchHHHHHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 9999999999999999999999999999999988
No 34
>PRK13902 alaS alanyl-tRNA synthetase; Provisional
Probab=69.97 E-value=11 Score=37.53 Aligned_cols=55 Identities=31% Similarity=0.457 Sum_probs=41.9
Q ss_pred HHHHHHhc-CCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHH
Q 031854 36 NICKFAKK-GLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAV 96 (152)
Q Consensus 36 ~IvklaKk-G~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv 96 (152)
++-+++++ +.=|-+.-..|-|.||+|.= =+..|.+++|+.-++|++.+.+|.+.-
T Consensus 419 ~~~~~~~~~~~l~g~~~f~LYDt~G~P~d------l~~eia~e~g~~vd~p~~F~~~~~~~~ 474 (900)
T PRK13902 419 IVERLAKKKEEIPLDDLIELYDSHGIPPE------IVKEIAKKKGVEVEVPDNFYSLVAERH 474 (900)
T ss_pred HHHHHHHhcCCCCHHHHhhhhhcCCCCHH------HHHHHHHHcCCccCchhhHHHHHHHHH
Confidence 33444443 55577888999999999952 145789999999999999999886653
No 35
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=68.70 E-value=5.3 Score=26.90 Aligned_cols=39 Identities=21% Similarity=0.377 Sum_probs=33.4
Q ss_pred cCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCC
Q 031854 43 KGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEI 84 (152)
Q Consensus 43 kG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeI 84 (152)
-|+|.+.|-.+|.|.-+ |..-|-.+|.+++++.|..|..
T Consensus 10 ~gvS~~TVSr~ln~~~~---v~~~t~~~i~~~~~~~gy~~~~ 48 (70)
T smart00354 10 AGVSKATVSRVLNGNGR---VSEETREKVLAAMEELGYIPNR 48 (70)
T ss_pred HCCCHHHHHHHHCCCCC---CCHHHHHHHHHHHHHhCCCCCH
Confidence 49999999999988755 4678889999999999997764
No 36
>COG1964 Predicted Fe-S oxidoreductases [General function prediction only]
Probab=67.74 E-value=16 Score=34.53 Aligned_cols=76 Identities=20% Similarity=0.303 Sum_probs=57.2
Q ss_pred CCCCCcCCCCCCCCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhcc-CCCceeeecchhHHHHHHHcCCCCCChhh
Q 031854 9 KGISASALPYKRTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSH-GIAQVKSVTGSKILRILKAHGLAPEIPED 87 (152)
Q Consensus 9 kG~S~S~~P~~~~~P~Wl~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~-GIp~VK~vtGkkI~~ILk~nGlapeIPED 87 (152)
.|.+-.+-+|...++-=+.-|-|+|++++-.|.++ + +.+.+-++||- .|.|++|
T Consensus 72 ~g~~~~CFa~A~~ag~vYEpt~eqi~~Ml~~lk~e--------------~p~~~~aIq~tGG-----------EPTvr~D 126 (475)
T COG1964 72 FGVNNECFAYAEEAGYIYEPTLEQIREMLRNLKKE--------------HPVGANAVQFTGG-----------EPTLRDD 126 (475)
T ss_pred cCCCCcCcCchhhcCcccCCCHHHHHHHHHHHHhc--------------CCCCCceeEecCC-----------Cccchhh
Confidence 67777788888888887888999999999886654 3 34566677764 6999999
Q ss_pred HHHHHHHHHHH-HHHHhHcCCcc
Q 031854 88 LYHLIKKAVAI-RKHLERNRKDK 109 (152)
Q Consensus 88 L~~LIkKAv~i-RKHLe~n~KD~ 109 (152)
|+.||+-|-.. =+|...|..-.
T Consensus 127 L~eiv~~a~e~g~~hVqinTnGi 149 (475)
T COG1964 127 LIEIIKIAREEGYDHVQLNTNGI 149 (475)
T ss_pred HHHHHHHHhhcCccEEEEccCce
Confidence 99999988654 23666555444
No 37
>PF10593 Z1: Z1 domain; InterPro: IPR018310 This entry represents the Z1 domain of unknown function that is found in a group of putative endonucleases. This domain is found associated with a helicase domain of superfamily type II [].
Probab=67.49 E-value=1.5 Score=36.66 Aligned_cols=58 Identities=24% Similarity=0.472 Sum_probs=43.9
Q ss_pred CCCCCCCCCCCCCcCCCCCC-CCCCCccC---ChHHHHHHHHHHHhcCCCcchhhhHhhhcc
Q 031854 1 MGRMHSRGKGISASALPYKR-TPPSWLKI---SSQDVEDNICKFAKKGLTPSQIGVILRDSH 58 (152)
Q Consensus 1 M~RMh~~~kG~S~S~~P~~~-~~P~Wl~~---~~eEVe~~IvklaKkG~tpSqIG~iLRD~~ 58 (152)
||||.+=++|--.-+|=|.. ..=+|+.. ..||+.+.|.+++..|+||.++|..+|..-
T Consensus 172 mgRwFGYR~gY~dl~Ri~~~~~l~~~f~~i~~~~e~lr~~i~~~~~~~~tp~~~~~~vr~~~ 233 (239)
T PF10593_consen 172 MGRWFGYRPGYEDLCRIYMPEELYDWFRHIAEAEEELREEIKEMANNGLTPKDFGLRVRSHP 233 (239)
T ss_pred HhhcccCCcccccceEEecCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHhcccccCCC
Confidence 78888888886666665532 22334432 578899999999999999999999998754
No 38
>PF02899 Phage_int_SAM_1: Phage integrase, N-terminal SAM-like domain; InterPro: IPR004107 Proteins containing this domain cleave DNA substrates by a series of staggered cuts, during which the protein becomes covalently linked to the DNA through a catalytic tyrosine residue at the carboxy end of the alignment [, ]. The phage integrase N-terminal SAM-like domain is almost always found with the signature that defines the phage integrase family (see IPR002104 from INTERPRO).; GO: 0003677 DNA binding, 0015074 DNA integration; PDB: 1Z1G_B 1Z19_A 1Z1B_A 2OXO_A 1P7D_B 3NRW_A 1A0P_A.
Probab=67.21 E-value=6.7 Score=25.70 Aligned_cols=33 Identities=36% Similarity=0.526 Sum_probs=24.5
Q ss_pred CCCCCccCChHHHHHHHHHHHhcCCCcchhhhH
Q 031854 21 TPPSWLKISSQDVEDNICKFAKKGLTPSQIGVI 53 (152)
Q Consensus 21 ~~P~Wl~~~~eEVe~~IvklaKkG~tpSqIG~i 53 (152)
....|.+++.++|++-+..+.++|++|+-|-..
T Consensus 37 ~~~~~~~i~~~~v~~f~~~~~~~~~s~~T~~~~ 69 (84)
T PF02899_consen 37 GIIDWEDITEEDVRDFLEYLAKEGLSPSTINRR 69 (84)
T ss_dssp TS-CGGG--HHHHHHHHHHHHCTT--HHHHHHH
T ss_pred hhhhhhhhhhHHHHHHHHHHHccCCCHHHHHHH
Confidence 457899999999999999999999999877654
No 39
>smart00845 GatB_Yqey GatB domain. This domain is found in GatB and proteins related to bacterial Yqey. It is about 140 amino acid residues long. This domain is found at the C terminus of GatB which transamidates Glu-tRNA to Gln-tRNA. The function of this domain is uncertain. It does however suggest that Yqey and its relatives have a role in tRNA metabolism.
Probab=66.44 E-value=25 Score=26.84 Aligned_cols=64 Identities=14% Similarity=0.227 Sum_probs=49.3
Q ss_pred cCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChh-hHHHHHHHHHH
Q 031854 27 KISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPE-DLYHLIKKAVA 97 (152)
Q Consensus 27 ~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIPE-DL~~LIkKAv~ 97 (152)
.++++.+.++|.-++..-+|.+++=.+|+.-. -.|+.+.++++++|+.+--.| +|-.+|+++++
T Consensus 38 ~i~~~~l~~li~lv~~g~It~~~ak~vl~~~~-------~~~~~~~~ii~~~~l~~isd~~el~~~v~~vi~ 102 (147)
T smart00845 38 PITPEHLAELLKLIEDGTISGKIAKEVLEELL-------ESGKSPEEIVEEKGLKQISDEGELEAIVDEVIA 102 (147)
T ss_pred CCCHHHHHHHHHHHHcCCCcHHHHHHHHHHHH-------HcCCCHHHHHHHcCCccCCCHHHHHHHHHHHHH
Confidence 46889999998888888888888777776432 126679999999999875444 79999999864
No 40
>PF02885 Glycos_trans_3N: Glycosyl transferase family, helical bundle domain Prosite entry for Thymidine and pyrimidine-nucleoside phosphorylases; InterPro: IPR017459 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. The glycosyl transferase family includes anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase (2.4.2.2 from EC) catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism. This N-terminal domain is found in various family 3 glycosyl transferases, including anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism.; PDB: 2DSJ_B 2ELC_B 2BPQ_A 1ZVW_B 3QR9_B 1V8G_B 2WK5_C 2J0F_C 2WK6_B 1UOU_A ....
Probab=66.27 E-value=6.1 Score=26.49 Aligned_cols=29 Identities=14% Similarity=0.237 Sum_probs=22.8
Q ss_pred cCChHHHHHHHHHHHhcCCCcchhhhHhh
Q 031854 27 KISSQDVEDNICKFAKKGLTPSQIGVILR 55 (152)
Q Consensus 27 ~~~~eEVe~~IvklaKkG~tpSqIG~iLR 55 (152)
.+|.+|+.+.+..+...-++|.|||-.|-
T Consensus 14 ~Ls~~e~~~~~~~i~~g~~s~~qiaAfL~ 42 (66)
T PF02885_consen 14 DLSREEAKAAFDAILDGEVSDAQIAAFLM 42 (66)
T ss_dssp ---HHHHHHHHHHHHTTSS-HHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHHH
Confidence 56899999999999999999999998763
No 41
>PF06983 3-dmu-9_3-mt: 3-demethylubiquinone-9 3-methyltransferase; PDB: 1U7I_A 1TSJ_A 1U69_D 3L20_B 3OMS_A.
Probab=65.51 E-value=3 Score=30.91 Aligned_cols=32 Identities=19% Similarity=0.362 Sum_probs=26.1
Q ss_pred ChHHHHHHHHHHHhcCCCcchhhhHhhhccCCC
Q 031854 29 SSQDVEDNICKFAKKGLTPSQIGVILRDSHGIA 61 (152)
Q Consensus 29 ~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp 61 (152)
+.||++..=.+|+..|-.-|.-| .|.|+|||.
T Consensus 81 ~~ee~~~~f~~Ls~gG~~~~~~G-~v~DkFGv~ 112 (116)
T PF06983_consen 81 DEEEIDRIFDKLSEGGQWFSRYG-WVTDKFGVS 112 (116)
T ss_dssp SHHHHHHHHHHHHTTTETCCEEE-EEE-TTS-E
T ss_pred CHHHHHHHHHHHHcCCCccceeE-EEEeCCCCE
Confidence 78999999999999997556777 799999985
No 42
>COG3028 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=65.46 E-value=6.7 Score=32.90 Aligned_cols=62 Identities=26% Similarity=0.342 Sum_probs=44.5
Q ss_pred CCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHhHcCCccccchhhhhhH
Q 031854 44 GLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVE 119 (152)
Q Consensus 44 G~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv~iRKHLe~n~KD~~sK~~L~LiE 119 (152)
+.|-|||- ||-.++ ...|.+|+..=+..=-.-.+||||+.-|.-|-++.+|..+ ||.||.|-
T Consensus 26 wvSKSqiK---Rd~~aL----q~LGe~L~~L~~~~L~KiPL~E~L~~Ai~~aqri~~~~ar-------rRQlQyIG 87 (187)
T COG3028 26 WVSKSQIK---RDAEAL----QDLGEELVDLTKAALAKIPLDEDLLEAIELAQRIKSEIAR-------RRQLQYIG 87 (187)
T ss_pred cccHHHHH---HHHHHH----HHHHHHHHhcCHHHHhhCCCChHHHHHHHHHHHHHHHHHH-------HHHHHHHH
Confidence 56777764 444432 2466666665555555678999999999999999999877 67777764
No 43
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=65.31 E-value=3.6 Score=25.87 Aligned_cols=26 Identities=15% Similarity=0.350 Sum_probs=13.6
Q ss_pred CChHHHHHHHHHHHhcCCCcchhhhHh
Q 031854 28 ISSQDVEDNICKFAKKGLTPSQIGVIL 54 (152)
Q Consensus 28 ~~~eEVe~~IvklaKkG~tpSqIG~iL 54 (152)
+|.+|... |..|.++|+|.++|+..|
T Consensus 5 Lt~~eR~~-I~~l~~~G~s~~~IA~~l 30 (44)
T PF13936_consen 5 LTPEERNQ-IEALLEQGMSIREIAKRL 30 (44)
T ss_dssp -------H-HHHHHCS---HHHHHHHT
T ss_pred hhhhHHHH-HHHHHHcCCCHHHHHHHH
Confidence 45666554 778899999999999776
No 44
>PF02637 GatB_Yqey: GatB domain; InterPro: IPR018027 The GatB domain, the function of which is uncertain, is associated with aspartyl/glutamyl amidotransferase subunit B and glutamyl amidotransferase subunit E. These are involved in the formation of correctly charged Asn-tRNA(Asn) or Gln-tRNA(Gln) through the transamidation of misacylated Asp-tRNA(Asn) or Glu-tRNA(Gln) in organisms which lack either or both of asparaginyl-tRNA or glutaminyl-tRNA synthetases. The reaction takes place in the presence of glutamine and ATP through an activated phospho-Asp-tRNA(Asn) or phospho-Glu-tRNA(Gln). ; GO: 0016884 carbon-nitrogen ligase activity, with glutamine as amido-N-donor; PDB: 2D6F_D 3H0M_H 3H0R_K 3H0L_K 3KFU_F 3AL0_B 3IP4_B 2DF4_B 2G5I_B 2F2A_B ....
Probab=64.53 E-value=17 Score=27.60 Aligned_cols=65 Identities=20% Similarity=0.266 Sum_probs=49.6
Q ss_pred ccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCC-hhhHHHHHHHHHH
Q 031854 26 LKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEI-PEDLYHLIKKAVA 97 (152)
Q Consensus 26 l~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeI-PEDL~~LIkKAv~ 97 (152)
+.++++++.++|.-+...-+|.++.-.+|+.-. -+|..+.++.+++|+..-- ++.|..++..+++
T Consensus 38 ~~i~~~~l~~li~l~~~~~Is~~~ak~ll~~~~-------~~~~~~~~ii~~~~l~~i~d~~el~~~v~~vi~ 103 (148)
T PF02637_consen 38 SPISPEHLAELINLLEDGKISKKSAKELLRELL-------ENGKSPEEIIEENGLWQISDEEELEALVEEVIA 103 (148)
T ss_dssp SSSTHHHHHHHHHHHHTTSSGHHHHHHHHHHHH-------HHTS-HHHHHHHTT---B--CCHHHHHHHHHHH
T ss_pred cCCCHHHHHHHHHHHHcCCCCHHHHHHHHHHHH-------HcCCCHHHHHHHcCCCcCCCHHHHHHHHHHHHH
Confidence 357999999999888888888888888887654 3388899999999997654 5789999999854
No 45
>PRK05702 flhB flagellar biosynthesis protein FlhB; Reviewed
Probab=64.35 E-value=22 Score=31.73 Aligned_cols=67 Identities=25% Similarity=0.426 Sum_probs=51.4
Q ss_pred CCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHH-HcCCCCCChhhHHHHHHHHHHHH
Q 031854 21 TPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILK-AHGLAPEIPEDLYHLIKKAVAIR 99 (152)
Q Consensus 21 ~~P~Wl~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk-~nGlapeIPEDL~~LIkKAv~iR 99 (152)
.+|-=+-.-.+++-..|.++|+ +||||-+.. ..+.|-|= .-.+..+|||+||.-+-..+..-
T Consensus 285 ~aP~vvakg~~~~A~~i~~~A~--------------~~~vpi~~~---~~LAr~Ly~~~~~g~~Ip~~~~~aVA~il~~v 347 (359)
T PRK05702 285 AAPVVVAKGVDEVALKIREIAR--------------EHNVPIVEN---PPLARALYATVEIGQEIPEELYKAVAEVLAYV 347 (359)
T ss_pred CCCEEEEeeCcHHHHHHHHHHH--------------HcCCCEEeC---HHHHHHHHHcCCCCCccCHHHHHHHHHHHHHH
Confidence 4565555677888889999887 689999876 45888885 66788899999998888776665
Q ss_pred HHHhH
Q 031854 100 KHLER 104 (152)
Q Consensus 100 KHLe~ 104 (152)
.-++.
T Consensus 348 ~~~~~ 352 (359)
T PRK05702 348 YQLKR 352 (359)
T ss_pred HHHHh
Confidence 55543
No 46
>PRK06298 type III secretion system protein; Validated
Probab=64.07 E-value=31 Score=30.85 Aligned_cols=71 Identities=17% Similarity=0.199 Sum_probs=51.2
Q ss_pred CCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHH-HHcCCCCCChhhHHHHHHHHHHHH
Q 031854 21 TPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRIL-KAHGLAPEIPEDLYHLIKKAVAIR 99 (152)
Q Consensus 21 ~~P~Wl~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~IL-k~nGlapeIPEDL~~LIkKAv~iR 99 (152)
.+|-=+-.-.+++-..|.++|+ +||||-|.. ..+.|-| +.--+.-+|||+||.-+-..+.-=
T Consensus 279 ~AP~VvAKG~d~~A~~Ir~iA~--------------e~~VPiven---~pLARaLy~~~evg~~IP~ely~AVA~IL~~v 341 (356)
T PRK06298 279 KAPWIIAMGINLRAKRIIAEAE--------------KYGVPIMRN---VPLAHQLLDEGKELKFIPESTYEAIGEILLYI 341 (356)
T ss_pred CCCEEEEeeCcHHHHHHHHHHH--------------HcCCCEEeC---HHHHHHHHHcCCCCCcCCHHHHHHHHHHHHHH
Confidence 4555555567888888888887 489999876 4688888 456688899999997777666554
Q ss_pred HHHh-HcCCc
Q 031854 100 KHLE-RNRKD 108 (152)
Q Consensus 100 KHLe-~n~KD 108 (152)
-.++ +|+.+
T Consensus 342 ~~l~~~~~~~ 351 (356)
T PRK06298 342 TSLNAQNPNN 351 (356)
T ss_pred HHHhCcCcCC
Confidence 4444 44443
No 47
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=62.70 E-value=21 Score=28.15 Aligned_cols=65 Identities=22% Similarity=0.223 Sum_probs=53.0
Q ss_pred CCCCCCCCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCCh
Q 031854 15 ALPYKRTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIP 85 (152)
Q Consensus 15 ~~P~~~~~P~Wl~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIP 85 (152)
...++...|+++ +.++++.+...+..+-.|...+=.+|--.+||..... .+.++|++-|+...=|
T Consensus 53 ~~~~~~GrP~kl--~~~q~~~l~e~~~~k~wTl~~~~~~l~~e~gv~y~~~----~v~~~l~~~GlsykK~ 117 (138)
T COG3415 53 PPKPRKGRPRKL--SEEQLEILLERLREKDWTLKELVEELGLEFGVWYHAS----AVRRLLHELGLSYKKP 117 (138)
T ss_pred cCccCCCCCccc--CHHHHHHHHHHHhcccchHHHHHHHHhhhcCeEEeHH----HHHHHHHHcCCCcCCC
Confidence 334678889777 7888888888888888999999999989999976543 6999999999987654
No 48
>KOG3862 consensus Transcription factor PAX2/5/8, contains PAX domain [Transcription]
Probab=62.11 E-value=15 Score=33.05 Aligned_cols=51 Identities=25% Similarity=0.400 Sum_probs=42.3
Q ss_pred ChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCCh
Q 031854 29 SSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIP 85 (152)
Q Consensus 29 ~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIP 85 (152)
-++-|-..|++||..|.-|+.|-..||-+||-+. +.+++.++.--.+|-.|
T Consensus 26 lpd~Vr~rIv~La~~gvrpcdisrQl~vShGcvS------kil~r~yEtgS~~pg~i 76 (327)
T KOG3862|consen 26 LPDVVRQRIVELAQNGVRPCDISRQLRVSHGCVS------KILGRYYETGSIRPGVI 76 (327)
T ss_pred CchHHHHHHHHHHHcCCcchhHHHHHhhccCCch------hHHHHHHHhcCcccCCC
Confidence 3678999999999999999999999999999875 45677787766666544
No 49
>PF13592 HTH_33: Winged helix-turn helix
Probab=61.61 E-value=7 Score=25.82 Aligned_cols=37 Identities=24% Similarity=0.457 Sum_probs=30.2
Q ss_pred CcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChh
Q 031854 46 TPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPE 86 (152)
Q Consensus 46 tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIPE 86 (152)
|..+|...+..+|||- ++-..|.++|+..|+...-|-
T Consensus 6 t~~~i~~~I~~~fgv~----ys~~~v~~lL~r~G~s~~kp~ 42 (60)
T PF13592_consen 6 TLKEIAAYIEEEFGVK----YSPSGVYRLLKRLGFSYQKPR 42 (60)
T ss_pred cHHHHHHHHHHHHCCE----EcHHHHHHHHHHcCCccccCC
Confidence 5667888888999985 477789999999999887763
No 50
>TIGR01204 bioW 6-carboxyhexanoate--CoA ligase. Alternate name: pimeloyl-CoA synthase.
Probab=58.30 E-value=7.9 Score=33.26 Aligned_cols=62 Identities=16% Similarity=0.294 Sum_probs=44.9
Q ss_pred ChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchh----------------------------HHHHHHHcCC
Q 031854 29 SSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSK----------------------------ILRILKAHGL 80 (152)
Q Consensus 29 ~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkk----------------------------I~~ILk~nGl 80 (152)
+.++|++.+.+|.+++++. +.|.|+-=+++=.+ +..+|++.|+
T Consensus 15 ~~~~ie~~~~~L~~Ral~H---------~~G~pDfinIkve~v~~~~i~~i~~LpV~t~~~~~~ee~~~~a~~lL~~~gv 85 (232)
T TIGR01204 15 KKEELETAVKELLNKPKSH---------SRGEFDFMQIKVEKVKDFEIVKFNPLKISTYSFSSPEEARKFARKKLTQEGV 85 (232)
T ss_pred CHHHHHHHHHHHHHhhhhc---------cCCCCCeeEEEEEEccCccceeecccceEEEecCCHHHHHHHHHHHHHhCCC
Confidence 6899999999999999876 34555432222222 3445999999
Q ss_pred CCCChhhHHHHHHHHHHHH
Q 031854 81 APEIPEDLYHLIKKAVAIR 99 (152)
Q Consensus 81 apeIPEDL~~LIkKAv~iR 99 (152)
.++++|..+.+|.+--+||
T Consensus 86 ~~~~~~~~~~~l~~~~~MR 104 (232)
T TIGR01204 86 SEEVAKKAVEILSKGANMR 104 (232)
T ss_pred CHHHHHHHHHHHhcCCCCc
Confidence 9999999999988844443
No 51
>TIGR03859 PQQ_PqqD coenzyme PQQ biosynthesis protein PqqD. This model identifies PqqD, a protein involved in the final steps of the biosynthesis of pyrroloquinoline quinone, coenzyme PQQ.
Probab=57.36 E-value=10 Score=26.63 Aligned_cols=34 Identities=15% Similarity=0.101 Sum_probs=29.7
Q ss_pred CChHHHHHHHHHHHhcCCCcchhhhHhhhccCCC
Q 031854 28 ISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIA 61 (152)
Q Consensus 28 ~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp 61 (152)
+.-+|+-..|.++-...-|.++|...|-+.|+++
T Consensus 27 ~~Ln~~g~~Iw~lldg~~tv~eI~~~L~~~Y~~~ 60 (81)
T TIGR03859 27 VKLNDSAGEILELCDGKRSLAEIIQELAQRFPAA 60 (81)
T ss_pred eeeChHHHHHHHHccCCCcHHHHHHHHHHHcCCh
Confidence 3567888899999998999999999999999883
No 52
>KOG3517 consensus Transcription factor PAX1/9 [Transcription]
Probab=57.09 E-value=7.7 Score=34.61 Aligned_cols=31 Identities=32% Similarity=0.523 Sum_probs=28.8
Q ss_pred hHHHHHHHHHHHhcCCCcchhhhHhhhccCC
Q 031854 30 SQDVEDNICKFAKKGLTPSQIGVILRDSHGI 60 (152)
Q Consensus 30 ~eEVe~~IvklaKkG~tpSqIG~iLRD~~GI 60 (152)
+.++.-.||+||+.|..|..|-..||-+||.
T Consensus 22 Pna~RlrIVELarlGiRPCDISRQLrvSHGC 52 (334)
T KOG3517|consen 22 PNAIRLRIVELARLGIRPCDISRQLRVSHGC 52 (334)
T ss_pred cchhhhhHHHHHHcCCCccchhhhhhhccch
Confidence 5678889999999999999999999999986
No 53
>cd08045 TAF4 TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryote. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are
Probab=56.73 E-value=18 Score=29.43 Aligned_cols=33 Identities=42% Similarity=0.538 Sum_probs=27.8
Q ss_pred eecchhHHHHHHHcCCCCCChhhHHHHHHHHHHH
Q 031854 65 SVTGSKILRILKAHGLAPEIPEDLYHLIKKAVAI 98 (152)
Q Consensus 65 ~vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv~i 98 (152)
....++|.+|++++|+. ++.||+.+||--|+..
T Consensus 48 ~~l~~~~~~i~~~~g~~-~~~~d~~~lis~a~e~ 80 (212)
T cd08045 48 SPLAKKIRKIAKKHGLK-EVDEDVLDLISLALEE 80 (212)
T ss_pred HHHHHHHHHHHHHcCCC-CCCHHHHHHHHHHHHH
Confidence 45678899999999999 9999999888777654
No 54
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=56.18 E-value=12 Score=23.95 Aligned_cols=25 Identities=12% Similarity=0.445 Sum_probs=18.9
Q ss_pred CChHHHHHHHHHHHhcCCCcchhhhHh
Q 031854 28 ISSQDVEDNICKFAKKGLTPSQIGVIL 54 (152)
Q Consensus 28 ~~~eEVe~~IvklaKkG~tpSqIG~iL 54 (152)
+|+.|+ .|+.+.-.|+++.+|+..|
T Consensus 4 LT~~E~--~vl~~l~~G~~~~eIA~~l 28 (58)
T PF00196_consen 4 LTEREL--EVLRLLAQGMSNKEIAEEL 28 (58)
T ss_dssp S-HHHH--HHHHHHHTTS-HHHHHHHH
T ss_pred cCHHHH--HHHHHHHhcCCcchhHHhc
Confidence 345554 5999999999999999887
No 55
>PF07508 Recombinase: Recombinase; InterPro: IPR011109 This domain is usually found associated with IPR006119 from INTERPRO in putative integrases/recombinases of mobile genetic elements of diverse bacteria and phages.
Probab=55.75 E-value=24 Score=24.18 Aligned_cols=49 Identities=27% Similarity=0.350 Sum_probs=37.5
Q ss_pred hHHHHHHHHHHHhcCCCcchhhhHhhhccCC--CceeeecchhHHHHHHHcC
Q 031854 30 SQDVEDNICKFAKKGLTPSQIGVILRDSHGI--AQVKSVTGSKILRILKAHG 79 (152)
Q Consensus 30 ~eEVe~~IvklaKkG~tpSqIG~iLRD~~GI--p~VK~vtGkkI~~ILk~nG 79 (152)
..+|...|.++.-.|++..+|...|-+. || |.-+..+...|.+||+.--
T Consensus 3 ea~vVr~if~~~~~g~s~~~I~~~ln~~-gi~~~~~~~W~~~~v~~iL~np~ 53 (102)
T PF07508_consen 3 EAEVVREIFELYLEGYSLRQIARELNEK-GIPTPRGKKWSKSTVRRILRNPA 53 (102)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHhc-CCccccCCcccHHHHHHHHhhhh
Confidence 3467777888877999999999999655 55 4455677888999997643
No 56
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=54.49 E-value=27 Score=22.43 Aligned_cols=32 Identities=22% Similarity=0.213 Sum_probs=24.9
Q ss_pred CCCccCChHHHHH--HHHHHHhcCCCcchhhhHh
Q 031854 23 PSWLKISSQDVED--NICKFAKKGLTPSQIGVIL 54 (152)
Q Consensus 23 P~Wl~~~~eEVe~--~IvklaKkG~tpSqIG~iL 54 (152)
...-.++.+||.. .|..|.+.|+|..+|...|
T Consensus 34 ~~~r~yt~~~v~~l~~i~~l~~~g~~l~~i~~~~ 67 (68)
T cd01104 34 GGHRLYSEADVARLRLIRRLTSEGVRISQAAALA 67 (68)
T ss_pred CCCeecCHHHHHHHHHHHHHHHCCCCHHHHHHHh
Confidence 3555678888865 4788888999999998765
No 57
>TIGR03683 A-tRNA_syn_arch alanyl-tRNA synthetase. This family of alanyl-tRNA synthetases is limited to the archaea, and is a subset of those sequences identified by the model pfam07973 covering the second additional domain (SAD) of alanyl and threonyl tRNA synthetases.
Probab=54.31 E-value=26 Score=34.98 Aligned_cols=56 Identities=25% Similarity=0.354 Sum_probs=41.5
Q ss_pred HHHHHHhc-CCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHHH
Q 031854 36 NICKFAKK-GLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVA 97 (152)
Q Consensus 36 ~IvklaKk-G~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv~ 97 (152)
++-+++++ +.=|-+.-..|-|.||+|.= =+..|.+++|+.-++|++.+.+|.+.-.
T Consensus 423 ~~~~~~~~~~~i~g~~~f~LyDTyGfP~d------l~~eia~e~g~~vd~~~~F~~~~~~~~~ 479 (902)
T TIGR03683 423 IVERLLKTKKEIPLDDLIELYDSHGIPPE------IVKEIAAELGAEVEIPDNFYSIVAERHE 479 (902)
T ss_pred HHHHHHhcCCcCCHHHHHHHHHccCCCHH------HHHHHHHHcCCcccCCccHHHHHHHHHH
Confidence 34445533 23366778899999999952 1457899999999999999998876543
No 58
>COG2445 Uncharacterized conserved protein [Function unknown]
Probab=54.19 E-value=45 Score=26.16 Aligned_cols=79 Identities=23% Similarity=0.261 Sum_probs=54.0
Q ss_pred hhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHhHcCCccccchhhhhhHHHHHHHHHh
Q 031854 49 QIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHDWLAT 128 (152)
Q Consensus 49 qIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv~iRKHLe~n~KD~~sK~~L~LiESkI~RL~kY 128 (152)
-||..+-+..|.-. +-|...+.++|.++|+ |||+....+++++++|+=|=.-=-+.|...=...++.-+.-+-.+
T Consensus 50 Di~~~li~~~~~~~--p~~y~d~~~~L~~~gv---i~~e~~e~L~~~~gfRN~lVH~Y~~vD~~~v~~~l~~~~~~~~~f 124 (138)
T COG2445 50 DIGNMLISKFGLRD--PGTYDDCIDILVEEGV---IPEEEAEELKKMVGFRNILVHRYWAVDPEKVYRSLKELLEDYENF 124 (138)
T ss_pred HHHHHHHHHhCCCC--CCCHHHHHHHHHHcCC---CCHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHH
Confidence 46777777776422 2477889999999998 789999999999999998766555555554444444434434444
Q ss_pred hhhh
Q 031854 129 TRRQ 132 (152)
Q Consensus 129 Yk~~ 132 (152)
.+..
T Consensus 125 ~e~i 128 (138)
T COG2445 125 LEEI 128 (138)
T ss_pred HHHH
Confidence 4333
No 59
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=54.00 E-value=11 Score=25.45 Aligned_cols=26 Identities=19% Similarity=0.354 Sum_probs=22.1
Q ss_pred HHHHHHHHHHhcCCCcchhhhHhhhccCCC
Q 031854 32 DVEDNICKFAKKGLTPSQIGVILRDSHGIA 61 (152)
Q Consensus 32 EVe~~IvklaKkG~tpSqIG~iLRD~~GIp 61 (152)
|+.+....|.-+|+++++|...| |||
T Consensus 1 e~k~~A~~LY~~G~~~~eIA~~L----g~~ 26 (58)
T PF06056_consen 1 EVKEQARSLYLQGWSIKEIAEEL----GVP 26 (58)
T ss_pred CHHHHHHHHHHcCCCHHHHHHHH----CCC
Confidence 67888899999999999998765 666
No 60
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=53.76 E-value=33 Score=22.01 Aligned_cols=36 Identities=25% Similarity=0.355 Sum_probs=27.4
Q ss_pred CCCCCCccCChHHHHH--HHHHHHhcCCCcchhhhHhh
Q 031854 20 RTPPSWLKISSQDVED--NICKFAKKGLTPSQIGVILR 55 (152)
Q Consensus 20 ~~~P~Wl~~~~eEVe~--~IvklaKkG~tpSqIG~iLR 55 (152)
+....--.++.+||.. .|..|...|+++++|..+|.
T Consensus 31 ~~~~g~r~y~~~dl~~l~~i~~lr~~g~~~~~i~~~l~ 68 (70)
T smart00422 31 RTEGGYRLYSDEDLERLRFIKRLKELGFSLEEIKELLE 68 (70)
T ss_pred cCCCCCEecCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence 3344445678888865 58999999999999988763
No 61
>PF12990 DUF3874: Domain of unknonw function from B. Theta Gene description (DUF3874); InterPro: IPR024450 This domain of unknown function if found in uncharacterised proteins from Bacteroides thetaiotaomicron and other Bacteroidetes.
Probab=53.62 E-value=11 Score=26.86 Aligned_cols=35 Identities=23% Similarity=0.299 Sum_probs=21.1
Q ss_pred CCcchhhhHhhhccCCCceeeecchhHHHHHHHcCC
Q 031854 45 LTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGL 80 (152)
Q Consensus 45 ~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGl 80 (152)
+|+++|=..|.-++++. .+..+=..+.|||+.+|+
T Consensus 26 lsa~~If~~L~k~~~~~-l~~~~~~~FGriL~~~gi 60 (73)
T PF12990_consen 26 LSAAEIFERLQKKSPAA-LRGSNPNHFGRILQKLGI 60 (73)
T ss_pred ecHHHHHHHHHHhCccc-cccCCHHHHHHHHHHcCC
Confidence 55666666666666664 444555556666666665
No 62
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=52.58 E-value=26 Score=23.71 Aligned_cols=49 Identities=18% Similarity=0.314 Sum_probs=36.3
Q ss_pred CChHHHHHHHHHHHhc--C--CCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCC
Q 031854 28 ISSQDVEDNICKFAKK--G--LTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPE 83 (152)
Q Consensus 28 ~~~eEVe~~IvklaKk--G--~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlape 83 (152)
.+++++++.|+++-+. | ++.++|... -||+-. +..+++.-|++.|+.-.
T Consensus 2 ~~~~~~~~~IL~~L~~~g~~~~ta~eLa~~----lgl~~~---~v~r~L~~L~~~G~V~~ 54 (68)
T smart00550 2 LTQDSLEEKILEFLENSGDETSTALQLAKN----LGLPKK---EVNRVLYSLEKKGKVCK 54 (68)
T ss_pred CCchHHHHHHHHHHHHCCCCCcCHHHHHHH----HCCCHH---HHHHHHHHHHHCCCEEe
Confidence 4778899999988775 3 777777654 477653 77888888899987543
No 63
>smart00733 Mterf Mitochondrial termination factor repeats. Human mitochondrial termination factor is a DNA-binding protein that acts as a transcription termination factor. Six repeats occur in human mTERF, that also are present in numerous plant proteins.
Probab=51.32 E-value=21 Score=18.77 Aligned_cols=27 Identities=15% Similarity=0.277 Sum_probs=21.8
Q ss_pred CCCCCCccCChHHHHHHHHHHHhcCCC
Q 031854 20 RTPPSWLKISSQDVEDNICKFAKKGLT 46 (152)
Q Consensus 20 ~~~P~Wl~~~~eEVe~~IvklaKkG~t 46 (152)
...|.++.++.+.++..+--|...|++
T Consensus 5 ~~~P~il~~~~~~l~~~~~~l~~~g~~ 31 (31)
T smart00733 5 KKFPQILGYSEKKLKPKVEFLKELGFS 31 (31)
T ss_pred hhCcCcccccHHHhhHHHHHHHHcCCC
Confidence 356999999988999888888777764
No 64
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=51.30 E-value=75 Score=22.16 Aligned_cols=39 Identities=26% Similarity=0.359 Sum_probs=29.7
Q ss_pred CCCCCCCCCCccCChHHHHH--HHHHHHh-cCCCcchhhhHhh
Q 031854 16 LPYKRTPPSWLKISSQDVED--NICKFAK-KGLTPSQIGVILR 55 (152)
Q Consensus 16 ~P~~~~~P~Wl~~~~eEVe~--~IvklaK-kG~tpSqIG~iLR 55 (152)
.|. ++....-.+++++|.. .|..|.. .|++.+.|-.+|.
T Consensus 28 ~p~-r~~~g~R~y~~~dv~~l~~i~~L~~d~g~~l~~i~~~l~ 69 (91)
T cd04766 28 SPS-RTDGGTRRYSERDIERLRRIQRLTQELGVNLAGVKRILE 69 (91)
T ss_pred CCC-cCCCCCeeECHHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 354 3445656689999875 5788888 9999999988886
No 65
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=50.77 E-value=28 Score=27.39 Aligned_cols=53 Identities=32% Similarity=0.517 Sum_probs=37.0
Q ss_pred CCCCCCCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCC
Q 031854 16 LPYKRTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLA 81 (152)
Q Consensus 16 ~P~~~~~P~Wl~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGla 81 (152)
+|+ ...|.+.... +.++.|.++..+|+|.++|-..| || .-..+-+++++.||.
T Consensus 147 rp~-g~~~~~~~~~--~~~~~i~~~~~~g~s~~~iak~l----gi------s~~Tv~r~~k~~~~~ 199 (200)
T PRK13413 147 RPK-GSTPKKYKLT--GKEEKIKKLLDKGTSKSEIARKL----GV------SRTTLARFLKTRGLR 199 (200)
T ss_pred CCC-CCcchhhhcc--hhHHHHHHHHHCCCCHHHHHHHH----CC------CHHHHHHHHHhcccC
Confidence 365 3445554442 33467889999999999999888 43 445688888888763
No 66
>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=50.61 E-value=12 Score=22.91 Aligned_cols=39 Identities=18% Similarity=0.360 Sum_probs=32.6
Q ss_pred cCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCC
Q 031854 43 KGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEI 84 (152)
Q Consensus 43 kG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeI 84 (152)
-|++++.|-.+|++.. .|..-|-.+|.+++++-|..|+-
T Consensus 7 ~gvs~~tvs~~l~g~~---~vs~~~~~~i~~~~~~l~~~~~~ 45 (52)
T cd01392 7 AGVSVATVSRVLNGKP---RVSEETRERVLAAAEELGYRPNA 45 (52)
T ss_pred HCcCHHHHHHHHcCCC---CCCHHHHHHHHHHHHHhCCCCCH
Confidence 5999999999998765 57778889999999999987653
No 67
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=50.46 E-value=33 Score=23.96 Aligned_cols=41 Identities=24% Similarity=0.364 Sum_probs=32.1
Q ss_pred CCCCCCCCCccCChHHHHH--HHHHHHhcCCCcchhhhHhhhc
Q 031854 17 PYKRTPPSWLKISSQDVED--NICKFAKKGLTPSQIGVILRDS 57 (152)
Q Consensus 17 P~~~~~P~Wl~~~~eEVe~--~IvklaKkG~tpSqIG~iLRD~ 57 (152)
|..+..+.+-.++.+||.. .|..|.+.|++.++|-.++...
T Consensus 27 ~~~~~~~g~r~y~~~dv~~l~~i~~l~~~g~~~~~i~~~l~~~ 69 (100)
T cd00592 27 PPERSENGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLDAR 69 (100)
T ss_pred CCCcCCCCCcccCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcc
Confidence 3445666788899999984 5788888999999999888543
No 68
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=50.06 E-value=18 Score=23.34 Aligned_cols=37 Identities=27% Similarity=0.450 Sum_probs=28.0
Q ss_pred CCCCCCccCChHHHHH--HHHHHHhcCCCcchhhhHhhh
Q 031854 20 RTPPSWLKISSQDVED--NICKFAKKGLTPSQIGVILRD 56 (152)
Q Consensus 20 ~~~P~Wl~~~~eEVe~--~IvklaKkG~tpSqIG~iLRD 56 (152)
+..-.+-.++.++|+. .|..|.+.|+|..+|-..|..
T Consensus 30 ~~~~g~r~y~~~dv~~l~~i~~l~~~G~sl~~I~~~l~~ 68 (69)
T PF13411_consen 30 RDENGYRYYSEEDVERLREIKELRKQGMSLEEIKKLLKQ 68 (69)
T ss_dssp ESTTSSEEE-HHHHHHHHHHHHHHHTTTHHHHHHHHH--
T ss_pred cccCceeeccHHHHHHHHHHHHHHHCcCCHHHHHHHHcc
Confidence 3555667889998875 688999999999999888764
No 69
>PF04947 Pox_VLTF3: Poxvirus Late Transcription Factor VLTF3 like ; InterPro: IPR007031 Members of this family are approximately 26 kDa, and are involved in trans-activation of late transcription [].; GO: 0046782 regulation of viral transcription
Probab=48.02 E-value=64 Score=26.10 Aligned_cols=36 Identities=19% Similarity=0.291 Sum_probs=28.3
Q ss_pred CChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcC
Q 031854 28 ISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHG 79 (152)
Q Consensus 28 ~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nG 79 (152)
.+.|=++++..+|++.+++ ...||-..|..+||++|
T Consensus 31 i~~~V~~~l~~~l~k~~i~----------------~~~it~~~V~~~LK~l~ 66 (171)
T PF04947_consen 31 IPDEVYEELRKELKKYNID----------------ISDITKNHVREFLKKLG 66 (171)
T ss_pred CCHHHHHHHHHHHHHcCCC----------------HHHcCHHHHHHHHHHcC
Confidence 4555567777788889988 45688888999999998
No 70
>PF11338 DUF3140: Protein of unknown function (DUF3140); InterPro: IPR021487 Some members in this family of proteins are annotated as DNA binding proteins. No function is currently known.
Probab=47.03 E-value=43 Score=25.13 Aligned_cols=38 Identities=26% Similarity=0.641 Sum_probs=32.5
Q ss_pred eecchhHHHHHHHcCCCCCChhhHHHHHHHHHH-HHHHHhH
Q 031854 65 SVTGSKILRILKAHGLAPEIPEDLYHLIKKAVA-IRKHLER 104 (152)
Q Consensus 65 ~vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv~-iRKHLe~ 104 (152)
.-+|.+|++||..+ ..++-+|=+.-|+|.|. ++.|+..
T Consensus 37 h~sGRrIv~IL~K~--k~dltddD~~hMrkVV~yv~rhlaq 75 (92)
T PF11338_consen 37 HESGRRIVEILRKR--KTDLTDDDYEHMRKVVGYVKRHLAQ 75 (92)
T ss_pred cchhhHHHHHHhcC--cccCCHHHHHHHHHHHHHHHHHHhc
Confidence 57899999999965 46778888999999995 7999988
No 71
>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=44.86 E-value=12 Score=23.43 Aligned_cols=26 Identities=15% Similarity=0.330 Sum_probs=17.6
Q ss_pred CChHHHHHHHHHHHhcCCCcchhhhHh
Q 031854 28 ISSQDVEDNICKFAKKGLTPSQIGVIL 54 (152)
Q Consensus 28 ~~~eEVe~~IvklaKkG~tpSqIG~iL 54 (152)
+++++ .+.|++|...|+|.++|-..+
T Consensus 6 ~~~~~-~~~i~~l~~~G~si~~IA~~~ 31 (45)
T PF02796_consen 6 LSKEQ-IEEIKELYAEGMSIAEIAKQF 31 (45)
T ss_dssp SSHCC-HHHHHHHHHTT--HHHHHHHT
T ss_pred CCHHH-HHHHHHHHHCCCCHHHHHHHH
Confidence 34443 567888999999999997643
No 72
>PF01411 tRNA-synt_2c: tRNA synthetases class II (A); InterPro: IPR018164 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Alanyl-tRNA synthetase (6.1.1.7 from EC) is an alpha4 tetramer that belongs to class IIc. ; GO: 0000166 nucleotide binding, 0004813 alanine-tRNA ligase activity, 0005524 ATP binding, 0006419 alanyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 3HY1_A 3HXZ_C 3HXY_A 3HXU_A 3HY0_B 3HXV_A 3HXX_A 3HXW_A 2E1B_A 2ZZG_B ....
Probab=44.35 E-value=15 Score=34.30 Aligned_cols=55 Identities=22% Similarity=0.174 Sum_probs=37.8
Q ss_pred HHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHH
Q 031854 31 QDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHL 91 (152)
Q Consensus 31 eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIPEDL~~L 91 (152)
+-+++.|-++.+++.=|...-..|-|.||+|. --+..|++++|+.-++|+.-+.+
T Consensus 367 ~~l~~~i~~~~~~~~lsge~aF~LYDTyGfP~------Dlt~eia~e~gl~vD~~~f~~~m 421 (552)
T PF01411_consen 367 KLLEKLIKKLKKKKELSGEDAFKLYDTYGFPL------DLTEEIAEEKGLSVDEEGFEYAM 421 (552)
T ss_dssp HHHHHHHHHHHCCSEE-HHHHHHHHHHH---H------HHHHHHHHTTT-EE-HHCCHHHH
T ss_pred HHHHHHHhhhccccCCChHHheeehhccCCCH------HHHHHHHHHhceeecHHHHHHHH
Confidence 34666667766667778899999999999997 34677999999999998876633
No 73
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=43.67 E-value=29 Score=20.47 Aligned_cols=25 Identities=24% Similarity=0.462 Sum_probs=18.9
Q ss_pred CChHHHHHHHHHHHhcCCCcchhhhHh
Q 031854 28 ISSQDVEDNICKFAKKGLTPSQIGVIL 54 (152)
Q Consensus 28 ~~~eEVe~~IvklaKkG~tpSqIG~iL 54 (152)
++++|.+ |+.+...|++..+|+..|
T Consensus 4 l~~~e~~--i~~~~~~g~s~~eia~~l 28 (58)
T smart00421 4 LTPRERE--VLRLLAEGLTNKEIAERL 28 (58)
T ss_pred CCHHHHH--HHHHHHcCCCHHHHHHHH
Confidence 4666665 667778999999999765
No 74
>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=43.40 E-value=50 Score=27.71 Aligned_cols=60 Identities=17% Similarity=0.247 Sum_probs=34.0
Q ss_pred HHHHHHHHh-cCCCcchhhhHhhhcc-CCCceeeecchhHHHHHHH----cCCCCCChhhHHHHHHHH
Q 031854 34 EDNICKFAK-KGLTPSQIGVILRDSH-GIAQVKSVTGSKILRILKA----HGLAPEIPEDLYHLIKKA 95 (152)
Q Consensus 34 e~~IvklaK-kG~tpSqIG~iLRD~~-GIp~VK~vtGkkI~~ILk~----nGlapeIPEDL~~LIkKA 95 (152)
.+.+.++|+ .|.||+||-+.=-=++ || +-.+.|.+=.+-|++ -.+..+++++-+.-|.++
T Consensus 251 ~~~l~~ia~~~g~s~aqlal~w~l~~~~v--~~~i~G~~~~~ql~en~~a~~~~~~Ls~e~~~~l~~~ 316 (317)
T TIGR01293 251 LKDLQAIAERLGCTLPQLAIAWCLRNEGV--SSVLLGASSAEQLMENLGSLQVLPKLSSSIIHEIDSI 316 (317)
T ss_pred HHHHHHHHHHHCcCHHHHHHHHHhcCCCC--eEEEeCCCCHHHHHHHHHHhhccCCCCHHHHHHHHhh
Confidence 345666665 6999999877322233 33 133444443333444 333347888888777653
No 75
>COG5352 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.19 E-value=20 Score=29.49 Aligned_cols=24 Identities=29% Similarity=0.415 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHhcCCCcchhhhHh
Q 031854 31 QDVEDNICKFAKKGLTPSQIGVIL 54 (152)
Q Consensus 31 eEVe~~IvklaKkG~tpSqIG~iL 54 (152)
||=.+...||.-+|+|.|||...|
T Consensus 5 dERve~LkKLWseGLSASQIAaQL 28 (169)
T COG5352 5 DERVETLKKLWSEGLSASQIAAQL 28 (169)
T ss_pred HHHHHHHHHHHHcccCHHHHHHHh
Confidence 566678899999999999998766
No 76
>PF03918 CcmH: Cytochrome C biogenesis protein; InterPro: IPR005616 Members of this family include NrfF, CcmH, CycL, Ccl2.; PDB: 2KW0_A 2HL7_A.
Probab=42.20 E-value=19 Score=28.46 Aligned_cols=35 Identities=17% Similarity=0.202 Sum_probs=28.2
Q ss_pred ChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCcee
Q 031854 29 SSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVK 64 (152)
Q Consensus 29 ~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK 64 (152)
.+.|..+.|.++-.+|.|..||=..+.+.|| ..|-
T Consensus 58 ~A~dmR~~I~~~l~~G~s~~eI~~~~v~rYG-~~Vl 92 (148)
T PF03918_consen 58 IARDMRREIREMLAEGKSDEEIIDYFVERYG-EFVL 92 (148)
T ss_dssp HHHHHHHHHHHHHHHT--HHHHHHHHHHHHT-TT-E
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHhcC-ccee
Confidence 3678899999999999999999999999999 4443
No 77
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=41.82 E-value=45 Score=23.73 Aligned_cols=40 Identities=23% Similarity=0.349 Sum_probs=31.3
Q ss_pred CCCCCCCCCccCChHHHH--HHHHHHHhcCCCcchhhhHhhh
Q 031854 17 PYKRTPPSWLKISSQDVE--DNICKFAKKGLTPSQIGVILRD 56 (152)
Q Consensus 17 P~~~~~P~Wl~~~~eEVe--~~IvklaKkG~tpSqIG~iLRD 56 (152)
|..++.--+=.++.++|+ ..|..|.+-|+|.++|..+|..
T Consensus 28 p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~~l~eI~~~l~~ 69 (96)
T cd04788 28 PSQRTEGGHRLYDRADIRRLHQIIALRRLGFSLREIGRALDG 69 (96)
T ss_pred CCccCCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHhC
Confidence 434455566678999887 5688999999999999998854
No 78
>PF13495 Phage_int_SAM_4: Phage integrase, N-terminal SAM-like domain; PDB: 2A3V_A.
Probab=41.68 E-value=27 Score=23.03 Aligned_cols=30 Identities=30% Similarity=0.536 Sum_probs=21.1
Q ss_pred ccCChHHHHHHHHHHH-hcCCCcchhhhHhh
Q 031854 26 LKISSQDVEDNICKFA-KKGLTPSQIGVILR 55 (152)
Q Consensus 26 l~~~~eEVe~~Ivkla-KkG~tpSqIG~iLR 55 (152)
-++++++|++-+..|. .+|++|+-|-..++
T Consensus 39 ~~it~~~i~~y~~~l~~~~~~s~~T~~~~~~ 69 (85)
T PF13495_consen 39 DEITPEDIEQYLNYLQNERGLSPSTINQYLS 69 (85)
T ss_dssp GG--HHHHHHHHHHHHTTT---HHHHHHHHH
T ss_pred chhHHHHHHHHHHHHHHhcCCCHHHHHHHHH
Confidence 4678999999999999 89999998876654
No 79
>PF01244 Peptidase_M19: Membrane dipeptidase (Peptidase family M19); InterPro: IPR008257 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of peptidases belong to the MEROPS peptidase family M19 (membrane dipeptidase family, clan MJ). The protein fold of the peptidase domain for members of this family resembles that of Klebsiella urease, the type example for clan MJ. Renal dipeptidase (rDP) (3.4.13.19 from EC), also known as microsomal dipeptidase, is a zinc-dependent metalloenzyme that hydrolyzes a wide range of dipeptides. It is involved in renal metabolism of glutathione and its conjugates. It is a homodimeric disulphide-linked glycoprotein attached to the renal brush border microvilli membrane by a GPI-anchor. A glutamate residue has recently been shown [,] to be important for the catalytic activity of rDP. rDP seems to be evolutionary related to hypothetical proteins in the PQQ biosynthesis operons of Acinetobacter calcoaceticus and Klebsiella pneumoniae.; GO: 0008235 metalloexopeptidase activity, 0008239 dipeptidyl-peptidase activity, 0016805 dipeptidase activity, 0006508 proteolysis; PDB: 3NEH_B 2RAG_D 3LU2_A 3B40_A 3LY0_A 3FDG_B 2I5G_B 3S2J_A 3S2N_A 3S2L_A ....
Probab=41.57 E-value=35 Score=29.61 Aligned_cols=41 Identities=29% Similarity=0.530 Sum_probs=30.8
Q ss_pred CCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHH
Q 031854 23 PSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKA 77 (152)
Q Consensus 23 P~Wl~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~ 77 (152)
|.++. ++.++..++..|.+.||+.++|-.++ |.+..|+|+|
T Consensus 280 ~~gl~-~~~~~~~l~~~L~~rG~s~~~i~kI~-------------g~N~lRv~~e 320 (320)
T PF01244_consen 280 PEGLE-DPSDLPNLTEELLKRGYSEEDIEKIL-------------GGNFLRVLRE 320 (320)
T ss_dssp BBTBS-SGGGHHHHHHHHHHTTS-HHHHHHHH-------------THHHHHHHH-
T ss_pred CCccC-CHHHHHHHHHHHHHCCCCHHHHHHHH-------------hHhHHHHhcC
Confidence 55555 57899999999999999999886554 6677777765
No 80
>PF11181 YflT: Heat induced stress protein YflT
Probab=41.55 E-value=17 Score=26.25 Aligned_cols=32 Identities=16% Similarity=0.298 Sum_probs=28.4
Q ss_pred ChHHHHHHHHHHHhcCCCcchhhhHhhhccCC
Q 031854 29 SSQDVEDNICKFAKKGLTPSQIGVILRDSHGI 60 (152)
Q Consensus 29 ~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GI 60 (152)
+.+|+.+.|-+|..+||....|-++-.|..-+
T Consensus 8 ~~~E~~~~I~~L~~~Gy~~ddI~Vva~d~~~~ 39 (103)
T PF11181_consen 8 NEEEALSAIEELKAQGYSEDDIYVVAKDKDRT 39 (103)
T ss_pred CHHHHHHHHHHHHHcCCCcccEEEEEcCchHH
Confidence 78999999999999999999999888776544
No 81
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic su
Probab=41.43 E-value=1.4e+02 Score=22.63 Aligned_cols=40 Identities=15% Similarity=0.248 Sum_probs=32.5
Q ss_pred CCCCCCCCCccCChHHHH--HHHHHHHhcCCCcchhhhHhhh
Q 031854 17 PYKRTPPSWLKISSQDVE--DNICKFAKKGLTPSQIGVILRD 56 (152)
Q Consensus 17 P~~~~~P~Wl~~~~eEVe--~~IvklaKkG~tpSqIG~iLRD 56 (152)
|.+++...+=.|+.++|+ ..|..|.+-|+|-++|..+|-.
T Consensus 28 p~~r~~~gyR~Y~~~~v~~l~~I~~lr~~GfsL~eI~~ll~~ 69 (131)
T cd04786 28 SVERSANGYRDYPPETVWVLEIISSAQQAGFSLDEIRQLLPA 69 (131)
T ss_pred CCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 555666677778988887 5688899999999999999864
No 82
>PF10929 DUF2811: Protein of unknown function (DUF2811); InterPro: IPR021231 This is a bacterial family of uncharacterised proteins.
Probab=41.12 E-value=24 Score=24.51 Aligned_cols=22 Identities=32% Similarity=0.614 Sum_probs=15.7
Q ss_pred CCCCChhhHHHHHHHHHHHHHHHhHcCC
Q 031854 80 LAPEIPEDLYHLIKKAVAIRKHLERNRK 107 (152)
Q Consensus 80 lapeIPEDL~~LIkKAv~iRKHLe~n~K 107 (152)
+.-||||+|+.=| +.-+|.||.
T Consensus 2 ~~aeiPe~L~~~m------~~fie~hP~ 23 (57)
T PF10929_consen 2 FEAEIPEDLHQAM------KDFIETHPN 23 (57)
T ss_pred ccccccHHHHHHH------HHHHHcCCC
Confidence 3568999999754 455777764
No 83
>cd05116 PTKc_Syk Catalytic domain of the Protein Tyrosine Kinase, Spleen tyrosine kinase. Protein Tyrosine Kinase (PTK) family; Spleen tyrosine kinase (Syk); catalytic (c) domain. The PTKc family is part of a larger superfamily that includes the catalytic domains of other kinases such as protein serine/threonine kinases, RIO kinases, and phosphoinositide 3-kinase (PI3K). PTKs catalyze the transfer of the gamma-phosphoryl group from ATP to tyrosine (tyr) residues in protein substrates. Syk, together with Zap-70, form the Syk subfamily of kinases which are cytoplasmic (or nonreceptor) tyr kinases containing two Src homology 2 (SH2) domains N-terminal to the catalytic tyr kinase domain. Syk was first cloned from the spleen, and its function in hematopoietic cells is well-established. Syk is involved in the signaling downstream of activated receptors (including B-cell and Fc receptors) that contain ITAMs (immunoreceptor tyr activation motifs), leading to processes such as cell proliferatio
Probab=41.04 E-value=80 Score=24.20 Aligned_cols=67 Identities=16% Similarity=0.299 Sum_probs=39.8
Q ss_pred hhHhhhc--cCCCceeeecchhHHHHHHHcC---CCCCChhhHHHHHHHHHHHHHHHhHcCCccccchhhhhhHHHHHHH
Q 031854 51 GVILRDS--HGIAQVKSVTGSKILRILKAHG---LAPEIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHDW 125 (152)
Q Consensus 51 G~iLRD~--~GIp~VK~vtGkkI~~ILk~nG---lapeIPEDL~~LIkKAv~iRKHLe~n~KD~~sK~~L~LiESkI~RL 125 (152)
|++|-.- +|-+--....+..+.+.+++.. ..+.+|+++.+||.+..+ .|-+.+-....| +.+|
T Consensus 185 G~~l~el~t~g~~p~~~~~~~~~~~~i~~~~~~~~~~~~~~~l~~li~~~~~---------~~p~~Rp~~~~i---~~~l 252 (257)
T cd05116 185 GVLMWEAFSYGQKPYKGMKGNEVTQMIESGERMECPQRCPPEMYDLMKLCWT---------YGVDERPGFAVV---ELRL 252 (257)
T ss_pred HHHHHHHHhCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHhc---------cCchhCcCHHHH---HHHH
Confidence 5555443 3544444455666666665432 223467899999988843 334444555555 7788
Q ss_pred HHhh
Q 031854 126 LATT 129 (152)
Q Consensus 126 ~kYY 129 (152)
..||
T Consensus 253 ~~~~ 256 (257)
T cd05116 253 RNYY 256 (257)
T ss_pred hccc
Confidence 8887
No 84
>PF00690 Cation_ATPase_N: Cation transporter/ATPase, N-terminus; InterPro: IPR004014 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles []. P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H+, Na+, K+, Mg2+, Ca2+, Ag+ and Ag2+, Zn2+, Co2+, Pb2+, Ni2+, Cd2+, Cu+ and Cu2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2. This entry represents the conserved N-terminal region found in several classes of cation-transporting P-type ATPases, including those that transport H+ (3.6.3.6 from EC), Na+ (3.6.3.7 from EC), Ca2+ (3.6.3.8 from EC), Na+/K+ (3.6.3.9 from EC), and H+/K+ (3.6.3.10 from EC). In the H+/K+- and Na+/K+-exchange P-ATPases, this domain is found in the catalytic alpha chain. In gastric H+/K+-ATPases, this domain undergoes reversible sequential phosphorylation inducing conformational changes that may be important for regulating the function of these ATPases [, ]. More information about this protein can be found at Protein of the Month: ATP Synthases [].; PDB: 3KDP_C 3N2F_A 3B8E_A 3N23_A 2XZB_A 1MHS_B 3A3Y_A 2ZXE_A 3B8C_A 3B9B_A ....
Probab=40.94 E-value=14 Score=24.43 Aligned_cols=53 Identities=17% Similarity=0.354 Sum_probs=38.8
Q ss_pred CccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHc
Q 031854 25 WLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAH 78 (152)
Q Consensus 25 Wl~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~n 78 (152)
|...+.|||.+..--=...|+|..|+-. .|.+||--.+.....+++.+++-+.
T Consensus 1 w~~~~~~~v~~~l~t~~~~GLs~~ev~~-r~~~~G~N~l~~~~~~s~~~~~~~~ 53 (69)
T PF00690_consen 1 WHQLSVEEVLKRLNTSSSQGLSSEEVEE-RRKKYGPNELPEPKKKSLWRIFLKQ 53 (69)
T ss_dssp -TTSSHHHHHHHHTTBTSSBBTHHHHHH-HHHHHSSSSTTTTTSSSHHHHHHHH
T ss_pred CCCCCHHHHHHHHCcCCCCCCCHHHHHH-HHHhcccccccccccCcHHHHHHHH
Confidence 7778888888877544589999988865 4578998777777777777766543
No 85
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=40.90 E-value=23 Score=28.72 Aligned_cols=37 Identities=16% Similarity=0.468 Sum_probs=31.1
Q ss_pred cCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCC
Q 031854 43 KGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAP 82 (152)
Q Consensus 43 kG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlap 82 (152)
-|+|+|-+-..|... |.|..-|..+|.++.++-|..|
T Consensus 16 agVS~~TVSr~Ln~~---~~vs~~tr~~V~~~a~elgY~p 52 (342)
T PRK10014 16 AGVSVSTVSLVLSGK---GRISTATGERVNQAIEELGFVR 52 (342)
T ss_pred hCCCHHHHHHHHCCC---CCCCHHHHHHHHHHHHHhCCCc
Confidence 499999999999754 6788999999999999988665
No 86
>PRK01584 alanyl-tRNA synthetase; Provisional
Probab=40.24 E-value=76 Score=30.59 Aligned_cols=57 Identities=16% Similarity=0.189 Sum_probs=41.9
Q ss_pred HHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHH
Q 031854 33 VEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAV 96 (152)
Q Consensus 33 Ve~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv 96 (152)
+++.|-++.+.+.=|.+.--.|-|.||+|.= + +..|.+|+|+.-++| ....+|+++-
T Consensus 375 l~~~i~~~~~~~~~~g~~af~LydTyGfP~d--l----t~~~a~e~g~~vd~~-~f~~~~~~~~ 431 (594)
T PRK01584 375 FIKLIPNLGSSKIIPGDIAFKLYDTYGFPYE--I----TEELASEYGFTVDRE-GFDEHFKKHQ 431 (594)
T ss_pred HHHHHHHhccCCccCHHHHHhhhccCCCCHH--H----HHHHHHHcCCeecHH-HHHHHHHHHH
Confidence 3445555544456688999999999999952 1 457899999999998 7777775553
No 87
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=39.33 E-value=1.1e+02 Score=25.85 Aligned_cols=72 Identities=21% Similarity=0.259 Sum_probs=50.7
Q ss_pred CCCCCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhc---cCCCceeeecchhHHHHHHHcCCCCCCh------hhH
Q 031854 18 YKRTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDS---HGIAQVKSVTGSKILRILKAHGLAPEIP------EDL 88 (152)
Q Consensus 18 ~~~~~P~Wl~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~---~GIp~VK~vtGkkI~~ILk~nGlapeIP------EDL 88 (152)
+..--|+=+..+.+++.+.+. + +-..|+..|-|| -||+++= -.+||=..|+.|.-| +|+
T Consensus 131 ~~~LGpdpl~~~~~~~~~~~~---~---~~~~ik~~Lldq~viaGiGNiy------a~EiLf~a~i~P~~~~~~l~~~~~ 198 (272)
T PRK14810 131 FARPGPEPLEISFEDFAALFR---G---RKTRIKSALLNQTLLRGVGNIY------ADEALFRAGIRPQRLASSLSRERL 198 (272)
T ss_pred hhhCCCCCCCCCHHHHHHHHh---c---CCccHHHHhhcCceeccccHhH------HHHHHHHcCCCCCCCcccCCHHHH
Confidence 344556656677777766653 2 235699999999 7887764 468999999999887 788
Q ss_pred HHHHHHHHHHHHH
Q 031854 89 YHLIKKAVAIRKH 101 (152)
Q Consensus 89 ~~LIkKAv~iRKH 101 (152)
..|...+..+=..
T Consensus 199 ~~l~~a~~~vl~~ 211 (272)
T PRK14810 199 RKLHDAIGEVLRE 211 (272)
T ss_pred HHHHHHHHHHHHH
Confidence 7776655555333
No 88
>PLN02389 biotin synthase
Probab=39.26 E-value=39 Score=30.21 Aligned_cols=37 Identities=22% Similarity=0.181 Sum_probs=26.5
Q ss_pred CCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhcc
Q 031854 22 PPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSH 58 (152)
Q Consensus 22 ~P~Wl~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~ 58 (152)
.|.|-.+++|||.+.+.++++.|.+---||.-.|+.+
T Consensus 110 ~~~~~~Ls~EeIl~~a~~~~~~G~~~~~ivts~rg~~ 146 (379)
T PLN02389 110 VKAQKLMSKDDVLEAAKRAKEAGSTRFCMGAAWRDTV 146 (379)
T ss_pred CcccccCCHHHHHHHHHHHHHcCCCEEEEEecccCCC
Confidence 4568788999999999999988886543433333333
No 89
>PRK12721 secretion system apparatus protein SsaU; Reviewed
Probab=39.13 E-value=92 Score=27.80 Aligned_cols=62 Identities=24% Similarity=0.347 Sum_probs=45.9
Q ss_pred CCCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHH-HHcCCCCCChhhHHHHHHHHHHH
Q 031854 20 RTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRIL-KAHGLAPEIPEDLYHLIKKAVAI 98 (152)
Q Consensus 20 ~~~P~Wl~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~IL-k~nGlapeIPEDL~~LIkKAv~i 98 (152)
..+|-=+---.+++-..|.++|++ ||||-|.+ ..+.|-| +.-.+..+||||||.-|-...+-
T Consensus 277 ~~aP~VvAKG~d~~A~~Ir~iA~e--------------~~VPiven---~pLARaLY~~~~vg~~IP~ely~aVA~ILa~ 339 (349)
T PRK12721 277 TPLPRVLEKGKDAQALHIVKLAER--------------NGIPVVEN---IPLARALFKEVECGDYIPETLFEPVAALLRM 339 (349)
T ss_pred CCCCEEEEEeCcHHHHHHHHHHHH--------------cCCCEEeC---HHHHHHHHHhCCCCCcCCHHHHHHHHHHHHH
Confidence 345655555678888888888864 79999876 4577777 56678899999999777665544
No 90
>TIGR00180 parB_part ParB-like partition proteins. This model represents the most well-conserved core of a set of chromosomal and plasmid partition proteins related to ParB, including Spo0J, RepB, and SopB. Spo0J has been shown to bind a specific DNA sequence that, when introduced into a plasmid, can serve as partition site. Study of RepB, which has nicking-closing activity, suggests that it forms a transient protein-DNA covalent intermediate during the strand transfer reaction.
Probab=38.85 E-value=1.1e+02 Score=24.09 Aligned_cols=55 Identities=15% Similarity=0.328 Sum_probs=30.1
Q ss_pred HHHHHHhcCCCcchhhhHhh---hccCCCc--eee---ecchhHHHHHHHcCCCCCChhhHHHHHHH
Q 031854 36 NICKFAKKGLTPSQIGVILR---DSHGIAQ--VKS---VTGSKILRILKAHGLAPEIPEDLYHLIKK 94 (152)
Q Consensus 36 ~IvklaKkG~tpSqIG~iLR---D~~GIp~--VK~---vtGkkI~~ILk~nGlapeIPEDL~~LIkK 94 (152)
.+.+..+..+||.+.+.... +.+|.-. +-. ++-..|.+.|.-. ++|+++..++..
T Consensus 94 l~eN~~r~~lt~~e~a~~~~~l~~~~g~s~~~iA~~lg~s~~~V~r~l~l~----~lp~~v~~~~~~ 156 (187)
T TIGR00180 94 LIENIQREDLSPIEEAQAYKRLLEKFSMTQEDLAKKIGKSRAHITNLLRLL----KLPSEIQSAIPE 156 (187)
T ss_pred HHHHhCccCCCHHHHHHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHHHH----cCCHHHHHHHHh
Confidence 34445556777776665442 2344221 111 2333455555542 499999999987
No 91
>PF14361 RsbRD_N: RsbT co-antagonist protein rsbRD N-terminal domain
Probab=38.79 E-value=33 Score=24.72 Aligned_cols=36 Identities=22% Similarity=0.382 Sum_probs=24.5
Q ss_pred CCCCCCCCccCChHHHHHHHHHHHhcCCCcchhhhHh
Q 031854 18 YKRTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVIL 54 (152)
Q Consensus 18 ~~~~~P~Wl~~~~eEVe~~IvklaKkG~tpSqIG~iL 54 (152)
+....+.| .-=.+.+++++..-|.+|+|||+....+
T Consensus 56 ~d~~~~~~-~~l~~~L~~lsr~RA~Qgftpseta~fv 91 (105)
T PF14361_consen 56 LDLAAPEW-EELREALEELSRIRAVQGFTPSETASFV 91 (105)
T ss_pred hhccccch-HHHHHHHHHHHHHHHhCCCCHHHHHHHH
Confidence 44556777 2234556667777788999999987644
No 92
>PF10752 DUF2533: Protein of unknown function (DUF2533) ; InterPro: IPR019688 This entry represents proteins with unknown function, and appear to be restricted to Bacillus spp.
Probab=38.64 E-value=28 Score=25.94 Aligned_cols=21 Identities=24% Similarity=0.594 Sum_probs=16.9
Q ss_pred ChHHHHHHHHHHHhcCCCcch
Q 031854 29 SSQDVEDNICKFAKKGLTPSQ 49 (152)
Q Consensus 29 ~~eEVe~~IvklaKkG~tpSq 49 (152)
.-.||.+.|-+|||+|+.|..
T Consensus 49 ~IN~vT~~mN~LAk~givP~R 69 (84)
T PF10752_consen 49 KINEVTKEMNELAKQGIVPTR 69 (84)
T ss_pred HHHHHHHHHHHHHHcCCCCcc
Confidence 346788899999999988763
No 93
>cd03527 RuBisCO_small Ribulose bisphosphate carboxylase/oxygenase (Rubisco), small subunit. Rubisco is a bifunctional enzyme catalyzes the initial steps of two opposing metabolic pathways: photosynthetic carbon fixation and the competing process of photorespiration. Rubisco Form I, present in plants and green algae, is composed of eight large and eight small subunits. The nearly identical small subunits are encoded by a family of nuclear genes. After translation, the small subunits are translocated across the chloroplast membrane, where an N-terminal signal peptide is cleaved off. While the large subunits contain the catalytic activities, it has been shown that the small subunits are important for catalysis by enhancing the catalytic rate through inducing conformational changes in the large subunits.
Probab=38.52 E-value=29 Score=26.15 Aligned_cols=21 Identities=14% Similarity=0.409 Sum_probs=19.2
Q ss_pred CChHHHHHHHHHHHhcCCCcc
Q 031854 28 ISSQDVEDNICKFAKKGLTPS 48 (152)
Q Consensus 28 ~~~eEVe~~IvklaKkG~tpS 48 (152)
+|.+||.++|.-+..+|..|+
T Consensus 12 lt~~~i~~QI~yll~qG~~~~ 32 (99)
T cd03527 12 LTDEQIAKQIDYIISNGWAPC 32 (99)
T ss_pred CCHHHHHHHHHHHHhCCCEEE
Confidence 589999999999999999875
No 94
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=38.44 E-value=29 Score=21.54 Aligned_cols=24 Identities=29% Similarity=0.382 Sum_probs=18.8
Q ss_pred HHHHHHHHhcCCCcchhhhHhhhc
Q 031854 34 EDNICKFAKKGLTPSQIGVILRDS 57 (152)
Q Consensus 34 e~~IvklaKkG~tpSqIG~iLRD~ 57 (152)
|..|..+...|.++.+|+..|--+
T Consensus 9 E~~v~~l~~~G~s~~eia~~l~is 32 (65)
T COG2771 9 EREILRLVAQGKSNKEIARILGIS 32 (65)
T ss_pred HHHHHHHHHCCCCHHHHHHHHCCC
Confidence 345677888899999999988543
No 95
>PRK05477 gatB aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated
Probab=37.83 E-value=97 Score=28.98 Aligned_cols=64 Identities=14% Similarity=0.185 Sum_probs=47.6
Q ss_pred cCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCCh-hhHHHHHHHHHH
Q 031854 27 KISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIP-EDLYHLIKKAVA 97 (152)
Q Consensus 27 ~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIP-EDL~~LIkKAv~ 97 (152)
.++++.+.++|.-+...-+|..++-.+|..-. -+|+.+.++.+++|+..--- ++|..+|+++++
T Consensus 365 ~i~~~~l~~Li~lv~~g~Is~~~ak~vl~~~~-------~~~~~~~~ii~~~gl~~isd~~~l~~iv~evi~ 429 (474)
T PRK05477 365 PITPEQLAELIKLIDDGTISGKIAKEVFEEML-------ETGGDPDEIVEEKGLKQISDEGALEAIVDEVLA 429 (474)
T ss_pred CCCHHHHHHHHHHHHcCCccHHHHHHHHHHHH-------hcCCCHHHHHHHcCCcccCCHHHHHHHHHHHHH
Confidence 46899999997666666677777766666543 23788999999999975333 369999999864
No 96
>TIGR00344 alaS alanine--tRNA ligase. The model describes alanine--tRNA ligase. This enzyme catalyzes the reaction (tRNAala + L-alanine + ATP = L-alanyl-tRNAala + pyrophosphate + AMP).
Probab=37.74 E-value=79 Score=31.43 Aligned_cols=56 Identities=21% Similarity=0.252 Sum_probs=41.9
Q ss_pred HHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHHH
Q 031854 34 EDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVA 97 (152)
Q Consensus 34 e~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv~ 97 (152)
++.|-++ +++.=|.+.-..|-|.||+|.= + +..|.+|+|+.-++| ..+.+|.++-.
T Consensus 372 ~~~~~~~-~~~~i~g~~af~LydTyGfP~d--l----t~~~a~e~g~~vd~~-~F~~~~~~~~~ 427 (851)
T TIGR00344 372 EKLLKKL-GKKELDGEDAFKLYDTYGFPVE--L----TKEIAEERGLTVDIP-GFETLMAEQRE 427 (851)
T ss_pred HHHHHHh-cCCccCHHHHHHHHHccCCCHH--H----HHHHHHHcCCccCHH-HHHHHHHHHHH
Confidence 3444444 3455678888999999999952 1 457899999999999 89988876643
No 97
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=37.51 E-value=65 Score=22.58 Aligned_cols=34 Identities=26% Similarity=0.171 Sum_probs=28.5
Q ss_pred CCccCChHHHH--HHHHHHHhcCCCcchhhhHhhhc
Q 031854 24 SWLKISSQDVE--DNICKFAKKGLTPSQIGVILRDS 57 (152)
Q Consensus 24 ~Wl~~~~eEVe--~~IvklaKkG~tpSqIG~iLRD~ 57 (152)
-.-.|+.++|+ ..|..|...|+|..+|-..|...
T Consensus 36 g~R~Ys~~dv~~l~~I~~Lr~~G~sl~~i~~~l~~~ 71 (88)
T cd01105 36 GQRKYSLADVDRLLVIKELLDEGFTLAAAVEKLRRR 71 (88)
T ss_pred CceecCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHc
Confidence 45568999998 56999999999999999998743
No 98
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=37.28 E-value=89 Score=31.25 Aligned_cols=48 Identities=27% Similarity=0.451 Sum_probs=35.5
Q ss_pred hHHHHHHHHHHHhcC---CCcchhhhHhhhccCCCceee-----ecchhHHHHHHH
Q 031854 30 SQDVEDNICKFAKKG---LTPSQIGVILRDSHGIAQVKS-----VTGSKILRILKA 77 (152)
Q Consensus 30 ~eEVe~~IvklaKkG---~tpSqIG~iLRD~~GIp~VK~-----vtGkkI~~ILk~ 77 (152)
-+++++.|.+++..- -||-|+|.+|-+..|+|.+|. -|...+++-|.+
T Consensus 523 l~~le~~i~~~~g~~fN~~SpkQl~~~Lf~~lgl~~~kktktg~ST~~~vL~~L~~ 578 (887)
T TIGR00593 523 IADLEEEIYELAGEEFNINSPKQLGEVLFEKLGLPVGKKTKTGYSTDADVLEKLRE 578 (887)
T ss_pred HHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCCCCCCCCCCCCChHHHHHHhhh
Confidence 467888888887643 378899999999999997652 355666666654
No 99
>PRK02228 V-type ATP synthase subunit F; Provisional
Probab=37.09 E-value=35 Score=24.92 Aligned_cols=62 Identities=13% Similarity=0.407 Sum_probs=35.1
Q ss_pred CChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCC---CCh-----hhHHHHHHHHHHH
Q 031854 28 ISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAP---EIP-----EDLYHLIKKAVAI 98 (152)
Q Consensus 28 ~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlap---eIP-----EDL~~LIkKAv~i 98 (152)
.+++|+++.+.+|.+.. .+|+++-.+.=...+. ..|.++++ +...| +|| +.+..+++||+.+
T Consensus 27 ~~~ee~~~~l~~l~~~~----d~gII~Ite~~~~~i~----e~i~~~~~-~~~~P~ii~IP~~~~~~~i~~~v~raIG~ 96 (100)
T PRK02228 27 PDDEKLDEAVEEVLEDD----DVGILVMHDDDLEKLP----RRLRRTLE-ESVEPTVVTLGGGGGSGGLREKIKRAIGV 96 (100)
T ss_pred CCHHHHHHHHHHHhhCC----CEEEEEEehhHhHhhH----HHHHHHHh-cCCCCEEEEECCCccchHHHHHHHHHhCc
Confidence 46689999999985544 5777766555222221 12222222 22221 222 5688999999864
No 100
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=37.08 E-value=52 Score=23.38 Aligned_cols=42 Identities=17% Similarity=0.150 Sum_probs=33.4
Q ss_pred CCCCCCCCCCccCChHHHHH--HHHHHHhcCCCcchhhhHhhhc
Q 031854 16 LPYKRTPPSWLKISSQDVED--NICKFAKKGLTPSQIGVILRDS 57 (152)
Q Consensus 16 ~P~~~~~P~Wl~~~~eEVe~--~IvklaKkG~tpSqIG~iLRD~ 57 (152)
.|.++....+=.++.++|+. .|..|..-|+|-++|-.+|...
T Consensus 27 ~p~~~~~~gyR~Y~~~~l~~l~~I~~lr~~G~~l~~I~~~l~~~ 70 (96)
T cd04768 27 KPAKIAENGYRYYSYAQLYQLQFILFLRELGFSLAEIKELLDTE 70 (96)
T ss_pred CCCccCCCCeeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcC
Confidence 35555666778889999875 5888999999999999988753
No 101
>smart00753 PAM PCI/PINT associated module.
Probab=36.47 E-value=33 Score=23.17 Aligned_cols=37 Identities=27% Similarity=0.440 Sum_probs=25.6
Q ss_pred ccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeee
Q 031854 26 LKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSV 66 (152)
Q Consensus 26 l~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~v 66 (152)
+.++.+|||+.|+++...|.=.+.| -..-|+-.+...
T Consensus 34 ~~l~~~~vE~~i~~~i~~~~l~~~I----D~~~~~v~~~~~ 70 (88)
T smart00753 34 LGLSVPEVEKLVSKAIRDGEISAKI----DQVNGIVEFEEV 70 (88)
T ss_pred hCcCHHHHHHHHHHHHHCCCeEEEE----cCcCCEEEECCC
Confidence 4678899999999999999655544 333454444433
No 102
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=36.47 E-value=33 Score=23.17 Aligned_cols=37 Identities=27% Similarity=0.440 Sum_probs=25.6
Q ss_pred ccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeee
Q 031854 26 LKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSV 66 (152)
Q Consensus 26 l~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~v 66 (152)
+.++.+|||+.|+++...|.=.+.| -..-|+-.+...
T Consensus 34 ~~l~~~~vE~~i~~~i~~~~l~~~I----D~~~~~v~~~~~ 70 (88)
T smart00088 34 LGLSVPEVEKLVSKAIRDGEISAKI----DQVNGIVEFEEV 70 (88)
T ss_pred hCcCHHHHHHHHHHHHHCCCeEEEE----cCcCCEEEECCC
Confidence 4678899999999999999655544 333454444433
No 103
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=36.19 E-value=65 Score=22.94 Aligned_cols=41 Identities=15% Similarity=0.143 Sum_probs=31.3
Q ss_pred CCCCCCCCCCccCChHHHHH--HHHHHHhcCCCcchhhhHhhh
Q 031854 16 LPYKRTPPSWLKISSQDVED--NICKFAKKGLTPSQIGVILRD 56 (152)
Q Consensus 16 ~P~~~~~P~Wl~~~~eEVe~--~IvklaKkG~tpSqIG~iLRD 56 (152)
.|.++...-+=.++.++|+. .|..|..-|+|-++|-.+|..
T Consensus 27 ~p~~~~~~gyR~Y~~~~~~~l~~I~~lr~~G~~l~eI~~~l~~ 69 (97)
T cd04782 27 KPEIVKENGYRYYTLEQFEQLDIILLLKELGISLKEIKDYLDN 69 (97)
T ss_pred CCCccCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 35545555566788888775 588899999999999988864
No 104
>PF05931 AgrD: Staphylococcal AgrD protein; InterPro: IPR009229 This family consists of several AgrD proteins from many Staphylococcus species. The agr locus was initially described in Staphylococcus aureus as an element controlling the production of exoproteins implicated in virulence. Its pattern of action has been shown to be complex, upregulating certain extracellular toxins and enzymes expressed post-exponentially and repressing some exponential-phase surface components. AgrD encodes the precursor of the autoinducing peptide (AIP).The AIP derived from AgrD by the action of AgrB interacts with AgrC in the membrane to activate AgrA, which upregulates transcription both from promoter P2, amplifying the response, and from P3, initiating the production of a novel effector: RNAIII. In S. aureus, delta-hemolysin is the only translation product of RNA III and is not involved in the regulatory functions of the transcript, which is therefore the primary agent for modulating the expression of other operons controlled by agr [].
Probab=36.00 E-value=21 Score=23.70 Aligned_cols=12 Identities=42% Similarity=0.883 Sum_probs=10.2
Q ss_pred CCCChhhHHHHH
Q 031854 81 APEIPEDLYHLI 92 (152)
Q Consensus 81 apeIPEDL~~LI 92 (152)
.|||||.|.+|-
T Consensus 33 EpEVP~ELt~l~ 44 (45)
T PF05931_consen 33 EPEVPKELTKLY 44 (45)
T ss_pred CCcCcHHHHhhc
Confidence 699999998773
No 105
>PRK09108 type III secretion system protein HrcU; Validated
Probab=35.76 E-value=1.4e+02 Score=26.71 Aligned_cols=66 Identities=21% Similarity=0.266 Sum_probs=49.2
Q ss_pred CCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHHHHHH
Q 031854 21 TPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVAIRK 100 (152)
Q Consensus 21 ~~P~Wl~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv~iRK 100 (152)
.+|-=+---.+++-..|.+.|++ ||||-|.. ..+.|-|=.-.+.-+|||+||.-+-..++-=-
T Consensus 280 ~AP~VvAKG~d~~A~~Ir~~A~e--------------~~VPvven---~pLARaLy~~~vg~~IP~ely~aVA~iL~~v~ 342 (353)
T PRK09108 280 PLPRVIAKGVDDGALALRRHAHA--------------LGIPIVGN---PPVARALYRVELDEPIPEELFETVAAILRWVD 342 (353)
T ss_pred CCCEEEEEeCcHHHHHHHHHHHH--------------cCCCEEeC---HHHHHHHhcCCCCCcCCHHHHHHHHHHHHHHH
Confidence 45555555678888889888874 89998876 45888887556888999999988777665544
Q ss_pred HHh
Q 031854 101 HLE 103 (152)
Q Consensus 101 HLe 103 (152)
.++
T Consensus 343 ~l~ 345 (353)
T PRK09108 343 ELG 345 (353)
T ss_pred HHh
Confidence 443
No 106
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=35.44 E-value=1e+02 Score=22.92 Aligned_cols=40 Identities=18% Similarity=0.224 Sum_probs=31.6
Q ss_pred CCCCCCCCCccCChHHHHH--HHHHHHhcCCCcchhhhHhhh
Q 031854 17 PYKRTPPSWLKISSQDVED--NICKFAKKGLTPSQIGVILRD 56 (152)
Q Consensus 17 P~~~~~P~Wl~~~~eEVe~--~IvklaKkG~tpSqIG~iLRD 56 (152)
|..++...+-.|+.++|+. .|..|..-|+|.++|..+|..
T Consensus 27 ~~~r~~~g~R~Y~~~~l~~l~~I~~l~~~G~sl~eI~~~l~~ 68 (124)
T TIGR02051 27 EPDRPEGGYRRYPEETVKRLRFIKRAQELGFSLEEIGGLLGL 68 (124)
T ss_pred CCccCCCCCEeECHHHHHHHHHHHHHHHCCCCHHHHHHHHhc
Confidence 3445566777788888875 688899999999999998854
No 107
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=35.06 E-value=33 Score=28.07 Aligned_cols=37 Identities=22% Similarity=0.427 Sum_probs=29.0
Q ss_pred cCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCC
Q 031854 43 KGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAP 82 (152)
Q Consensus 43 kG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlap 82 (152)
-|+|.|-+-.+|.+. |.|+.-|-++|.++.++.|-.|
T Consensus 11 aGVS~~TVSrvLn~~---~~Vs~~tr~kV~~~a~elgY~p 47 (346)
T PRK10401 11 AGVSVATVSRVLNNS---ALVSADTREAVMKAVSELGYRP 47 (346)
T ss_pred hCCCHHHHHHHHCCC---CCCCHHHHHHHHHHHHHHCCCC
Confidence 388888888888765 4688888888888888888654
No 108
>PF05698 Trigger_C: Bacterial trigger factor protein (TF) C-terminus; InterPro: IPR008880 In the Escherichia coli cytosol, a fraction of the newly synthesised proteins requires the activity of molecular chaperones for folding to the native state. The major chaperones implicated in this folding process are the ribosome-associated Trigger Factor (TF), and the DnaK and GroEL chaperones with their respective co-chaperones. Trigger Factor is an ATP-independent chaperone and displays chaperone and peptidyl-prolyl-cis-trans-isomerase (PPIase) activities in vitro. It is composed of at least three domains, an N-terminal domain which mediates association with the large ribosomal subunit, a central substrate binding and PPIase domain with homology to FKBP proteins, and a C-terminal domain of unknown function. The positioning of TF at the peptide exit channel, together with its ability to interact with nascent chains as short as 57 residues renders TF a prime candidate for being the first chaperone that binds to the nascent polypeptide chains []. This entry represents the C-terminal domain of bacterial trigger factor proteins, which has a multi-helical structure consisting of an irregular array of long and short helices. This domain is structurally similar to the peptide-binding domain of the bacterial porin chaperone SurA.; GO: 0006457 protein folding, 0015031 protein transport; PDB: 1T11_A 3GU0_A 3GTY_X 2NSA_A 1ZXJ_A 1W26_A.
Probab=35.05 E-value=11 Score=27.66 Aligned_cols=35 Identities=23% Similarity=0.518 Sum_probs=22.0
Q ss_pred ccCChHHHHHHHHHHHh-cCCCcchhhhHhhhccCC
Q 031854 26 LKISSQDVEDNICKFAK-KGLTPSQIGVILRDSHGI 60 (152)
Q Consensus 26 l~~~~eEVe~~IvklaK-kG~tpSqIG~iLRD~~GI 60 (152)
+..+.+||++.+..+|. -|.+|.++...+.+....
T Consensus 109 I~v~~eev~~~~~~~a~~~~~~~~~~~~~~~~~~~~ 144 (162)
T PF05698_consen 109 IEVSDEEVEEEIEKLAQQYGMNPEELKEQYEKNKQL 144 (162)
T ss_dssp ----HHHHHHHHHHHHHCSTS-HHHHHHHHHCHHHH
T ss_pred CCCCHHHHHHHHHHHHHHcCCCHHHHHHHHHhChhH
Confidence 56788899998888887 566778777766554433
No 109
>PF14475 Mso1_Sec1_bdg: Sec1-binding region of Mso1
Probab=34.90 E-value=28 Score=22.77 Aligned_cols=14 Identities=7% Similarity=0.197 Sum_probs=10.1
Q ss_pred HHHHHH-HHHhhhhh
Q 031854 119 ESRIHD-WLATTRRQ 132 (152)
Q Consensus 119 ESkI~R-L~kYYk~~ 132 (152)
.+-||| |++||...
T Consensus 19 dT~v~r~l~~yY~~k 33 (41)
T PF14475_consen 19 DTHVHRVLRKYYTEK 33 (41)
T ss_pred hhHHHHHHHHHHHHc
Confidence 345666 78899887
No 110
>PRK09912 L-glyceraldehyde 3-phosphate reductase; Provisional
Probab=34.82 E-value=1.3e+02 Score=25.82 Aligned_cols=63 Identities=10% Similarity=0.132 Sum_probs=39.5
Q ss_pred HHHHHHHHHH-hcCCCcchhhhHhhhccC-CCceeeecchhHHHHHHHc-CC--CCCChhhHHHHHHHHH
Q 031854 32 DVEDNICKFA-KKGLTPSQIGVILRDSHG-IAQVKSVTGSKILRILKAH-GL--APEIPEDLYHLIKKAV 96 (152)
Q Consensus 32 EVe~~Ivkla-KkG~tpSqIG~iLRD~~G-Ip~VK~vtGkkI~~ILk~n-Gl--apeIPEDL~~LIkKAv 96 (152)
+..+.+.++| +.|.||+|+-+.---+++ |. -.+.|.+=.+=|++| +. ..++++|-+..|.+++
T Consensus 265 ~~~~~l~~~a~~~g~t~aq~AL~w~l~~~~v~--~~i~G~~~~~ql~en~~a~~~~~L~~e~~~~l~~~~ 332 (346)
T PRK09912 265 NSLRLLNEMAQQRGQSMAQMALSWLLKDERVT--SVLIGASRAEQLEENVQALNNLTFSTEELAQIDQHI 332 (346)
T ss_pred HHHHHHHHHHHHhCCCHHHHHHHHHHhCCCCe--EEEeCCCCHHHHHHHHhhhcCCCCCHHHHHHHHHhh
Confidence 4445666777 479999999885444543 32 235555544444444 22 2589999998888764
No 111
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=34.72 E-value=44 Score=26.20 Aligned_cols=31 Identities=16% Similarity=0.264 Sum_probs=28.2
Q ss_pred hHHHHHHHHHHHhcCCCcchhhhHhhhccCC
Q 031854 30 SQDVEDNICKFAKKGLTPSQIGVILRDSHGI 60 (152)
Q Consensus 30 ~eEVe~~IvklaKkG~tpSqIG~iLRD~~GI 60 (152)
+.|....|.++-++|.|..||=..+.+.||=
T Consensus 59 A~dmR~~Vr~~i~~G~Sd~eI~~~~v~RYG~ 89 (126)
T TIGR03147 59 AYDLRHEVYSMVNEGKSNQQIIDFMTARFGD 89 (126)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHhcCC
Confidence 5678888999999999999999999999993
No 112
>PF00476 DNA_pol_A: DNA polymerase family A; InterPro: IPR001098 Synonym(s): DNA nucleotidyltransferase (DNA-directed) DNA-directed DNA polymerases(2.7.7.7 from EC) are the key enzymes catalysing the accurate replication of DNA. They require either a small RNA molecule or a protein as a primer for the de novo synthesis of a DNA chain. A number of polymerases belong to this family [, , ].; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 1TKD_A 1TK5_A 2AJQ_F 1T8E_A 1T7P_A 1SKR_A 1X9W_A 1TK8_A 1TK0_A 1SL2_A ....
Probab=34.48 E-value=1e+02 Score=27.02 Aligned_cols=48 Identities=23% Similarity=0.441 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHhcCC---CcchhhhHhhhccCCCceee-------ecchhHHHHHHHc
Q 031854 31 QDVEDNICKFAKKGL---TPSQIGVILRDSHGIAQVKS-------VTGSKILRILKAH 78 (152)
Q Consensus 31 eEVe~~IvklaKkG~---tpSqIG~iLRD~~GIp~VK~-------vtGkkI~~ILk~n 78 (152)
+|+++.+.+++-.-+ ||-|++.+|-|..|+|.++. .|.+..++-|.+.
T Consensus 18 ~~~~~~~~~~~g~~fN~~S~~q~~~~L~~~lgl~~~~~t~~~g~~st~~~~L~~l~~~ 75 (383)
T PF00476_consen 18 RELEAKAYKLAGEEFNPNSPKQLAEVLFEELGLPPTKKTKKKGKPSTDKEVLKKLAED 75 (383)
T ss_dssp HHHHHHHHHHHTSCSSTTTHHHHHHHHHTTSSSTTSSBETTCSEBHCTHHHHHHHCCC
T ss_pred HHHHHHhHHhcCCccCCCCHHHHHHHHHHcCCCCCCCCCcccchhhhHHHHHHHhhhh
Confidence 456677776655434 78899999999999996543 3345555555543
No 113
>PF12188 STAT2_C: Signal transducer and activator of transcription 2 C terminal; InterPro: IPR022756 This region is found in the mammalian signal transducer and activation of transcription (STAT) 2 protein, and is approximately 60 amino acids in length. The family is found in association with PF02865 from PFAM, PF00017 from PFAM, PF01017 from PFAM, PF02864 from PFAM. There is a conserved DLP sequence motif. STATs are involved in transcriptional regulation and are the only regulators known to be modulated by tyrosine phosphorylation. STAT2 forms a trimeric complex with STAT1 and IRF-9 (Interferon Regulatory Factor 9), on activation of the cell by interferon, which is called ISGF3 (Interferon-stimulated gene factor 3). The C-terminal domain of STAT2 contains a nuclear export signal (NES) which allows export of STAT2 into the cytoplasm along with any complexed molecules. ; PDB: 2KA4_B.
Probab=34.21 E-value=12 Score=26.09 Aligned_cols=11 Identities=55% Similarity=1.153 Sum_probs=5.2
Q ss_pred CCCChhhHHHH
Q 031854 81 APEIPEDLYHL 91 (152)
Q Consensus 81 apeIPEDL~~L 91 (152)
.|++|+||.+|
T Consensus 6 EpDLP~DL~hl 16 (56)
T PF12188_consen 6 EPDLPHDLQHL 16 (56)
T ss_dssp -----HHHHTS
T ss_pred CCCccHHHHHh
Confidence 68999999876
No 114
>PF09682 Holin_LLH: Phage holin protein (Holin_LLH); InterPro: IPR010026 This entry represents the Bacteriophage LL-H, Orf107, holin protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This protein family represent one of a large number of mutually dissimilar families of phage holins. It is thought that the temporal precision of holin-mediated lysis may occur through the build-up of a holin oligomer which causes the lysis [].
Probab=34.14 E-value=71 Score=23.53 Aligned_cols=28 Identities=25% Similarity=0.233 Sum_probs=24.1
Q ss_pred hHHHHHHHcCCCCCChhhHHHHHHHHHHH
Q 031854 70 KILRILKAHGLAPEIPEDLYHLIKKAVAI 98 (152)
Q Consensus 70 kI~~ILk~nGlapeIPEDL~~LIkKAv~i 98 (152)
.+.+.|+++|+ .-=+|++..+|.+||.=
T Consensus 76 ~v~~~L~~~gi-~~t~~~i~~~IEaAV~~ 103 (108)
T PF09682_consen 76 YVKERLKKKGI-KVTDEQIEGAIEAAVKE 103 (108)
T ss_pred HHHHHHHHcCC-CCCHHHHHHHHHHHHHH
Confidence 57889999999 55688999999999964
No 115
>PF14420 Clr5: Clr5 domain
Probab=34.08 E-value=49 Score=21.66 Aligned_cols=32 Identities=16% Similarity=0.340 Sum_probs=27.4
Q ss_pred HHHHHHHHHHH-hcCCCcchhhhHhhhccCCCc
Q 031854 31 QDVEDNICKFA-KKGLTPSQIGVILRDSHGIAQ 62 (152)
Q Consensus 31 eEVe~~Ivkla-KkG~tpSqIG~iLRD~~GIp~ 62 (152)
|...+.|.+|. .+|.|-.+|-.++...||.--
T Consensus 6 e~~K~~I~~LY~~e~~tl~~v~~~M~~~~~F~a 38 (54)
T PF14420_consen 6 EPHKEEIERLYIDENKTLEEVMEIMKEEHGFKA 38 (54)
T ss_pred HHHHHHHHHHHHhCCCcHHHHHHHHHHHhCCCc
Confidence 56778899998 699999999999999998743
No 116
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=33.59 E-value=74 Score=30.83 Aligned_cols=59 Identities=25% Similarity=0.416 Sum_probs=40.4
Q ss_pred hHHHHHHHHHHHhcCC---CcchhhhHhhhccCCCc--eeeecc--hhHHHHHHHcCCCCCChhhH
Q 031854 30 SQDVEDNICKFAKKGL---TPSQIGVILRDSHGIAQ--VKSVTG--SKILRILKAHGLAPEIPEDL 88 (152)
Q Consensus 30 ~eEVe~~IvklaKkG~---tpSqIG~iLRD~~GIp~--VK~vtG--kkI~~ILk~nGlapeIPEDL 88 (152)
-.++|+.|.+||-.-+ ||=|+|.+|-|..|.|. -|.=|| ..=..+|++-.-.-+||+-+
T Consensus 227 l~~le~eiy~laG~~FNi~SPKQL~~ILfeKl~Lp~~~kKtktG~yST~~~vLe~L~~~h~i~~~i 292 (593)
T COG0749 227 LAELEEEIYELAGEEFNINSPKQLGEILFEKLGLPPGLKKTKTGNYSTDAEVLEKLADDHPLPKLI 292 (593)
T ss_pred HHHHHHHHHHHhcCcCCCCCHHHHHHHHHHhcCCCccccccCCCCCccHHHHHHHHhhcCccHHHH
Confidence 3578888889987444 78899999999999995 455565 22334555444355666544
No 117
>PF12025 Phage_C: Phage protein C; InterPro: IPR016407 This family of phage proteins is functionally uncharacterised. Proteins in this family are typically between 68 to 86 amino acids in length.; GO: 0019073 viral DNA genome packaging
Probab=33.49 E-value=13 Score=26.60 Aligned_cols=31 Identities=32% Similarity=0.483 Sum_probs=23.0
Q ss_pred hhhhHhhhccCCCceeeec-chhHHHHHHHcCC
Q 031854 49 QIGVILRDSHGIAQVKSVT-GSKILRILKAHGL 80 (152)
Q Consensus 49 qIG~iLRD~~GIp~VK~vt-GkkI~~ILk~nGl 80 (152)
+.|..|+|=+-+-+- .+- -++++.||||.|+
T Consensus 36 m~G~llkdWFryE~h-fvhg~~sllDiLkeRgl 67 (68)
T PF12025_consen 36 MLGALLKDWFRYEDH-FVHGKKSLLDILKERGL 67 (68)
T ss_pred HHHHHHHHHHHHHHH-HhcchHHHHHHHHHccC
Confidence 689999997755542 233 3579999999996
No 118
>PF15051 FAM198: FAM198 protein
Probab=33.48 E-value=37 Score=30.75 Aligned_cols=24 Identities=21% Similarity=0.509 Sum_probs=19.8
Q ss_pred CcCCCCCCCCCCCccCChHHHHHHHH
Q 031854 13 ASALPYKRTPPSWLKISSQDVEDNIC 38 (152)
Q Consensus 13 ~S~~P~~~~~P~Wl~~~~eEVe~~Iv 38 (152)
++.+-|...+|+|+ |+|+|..+..
T Consensus 1 sniRiyse~aPpWf--S~~Di~~Mrl 24 (326)
T PF15051_consen 1 SNIRIYSESAPPWF--SEDDIRKMRL 24 (326)
T ss_pred CCccccCCCCCCcC--CHHHHHHHHH
Confidence 36778999999999 8999987753
No 119
>TIGR00676 fadh2 5,10-methylenetetrahydrofolate reductase, prokaryotic form. This protein is an FAD-containing flavoprotein.
Probab=33.32 E-value=1.8e+02 Score=24.37 Aligned_cols=71 Identities=18% Similarity=0.293 Sum_probs=45.7
Q ss_pred Cceeeecchh-HHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHhHcCCccccchhhhhhHHHHHHHHHhhhhhceeeecc
Q 031854 61 AQVKSVTGSK-ILRILKAHGLAPEIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHDWLATTRRQRSFHLYG 139 (152)
Q Consensus 61 p~VK~vtGkk-I~~ILk~nGlapeIPEDL~~LIkKAv~iRKHLe~n~KD~~sK~~L~LiESkI~RL~kYYk~~~~~~~~~ 139 (152)
|-|-.++..+ +.++++-. .-.||+++..-+.+|- +..+.--..++.+.-.-|.+|..+ ...-+|+|.
T Consensus 190 ~Gi~p~~s~k~~~~~~~~~--Gv~vP~~~~~~l~~~~--------~~~~~~~~~gi~~~~~~~~~l~~~--g~~GiHl~t 257 (272)
T TIGR00676 190 PGIMPITNFKQLLRFAERC--GAEIPAWLVKRLEKYD--------DDPEEVRAVGIEYATDQCEDLIAE--GVPGIHFYT 257 (272)
T ss_pred cccCCcCCHHHHHHHHhcc--CCCCCHHHHHHHHhcC--------CCHHHHHHHHHHHHHHHHHHHHHC--CCCEEEEcC
Confidence 4455666777 77888844 4579999998877751 111111135777776667777664 255678888
Q ss_pred CCCCC
Q 031854 140 NMSQP 144 (152)
Q Consensus 140 ~~~~~ 144 (152)
||++
T Consensus 258 -~n~~ 261 (272)
T TIGR00676 258 -LNRA 261 (272)
T ss_pred -CCCH
Confidence 8865
No 120
>PRK12772 bifunctional flagellar biosynthesis protein FliR/FlhB; Provisional
Probab=33.20 E-value=1.2e+02 Score=29.03 Aligned_cols=60 Identities=22% Similarity=0.417 Sum_probs=45.2
Q ss_pred CCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHH-HHcCCCCCChhhHHHHHHHHHH
Q 031854 21 TPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRIL-KAHGLAPEIPEDLYHLIKKAVA 97 (152)
Q Consensus 21 ~~P~Wl~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~IL-k~nGlapeIPEDL~~LIkKAv~ 97 (152)
.+|-=+-.-.+++-..|.++|+ +||||-|.+ ..+-|-| +.-.+..+||||||.-+-..+.
T Consensus 541 ~aP~VvAKG~d~~A~~Ir~~A~--------------e~~VPive~---~~LAR~Ly~~~evg~~IP~ely~aVA~iL~ 601 (609)
T PRK12772 541 EAPKVVAKGADYVALKIKEIAK--------------ENDVPIIEN---KPLARLIYKKVEIDQEIPQDMYQAVAEILA 601 (609)
T ss_pred CCCEEEEeeCcHHHHHHHHHHH--------------HCCCcEEeC---HHHHHHHHHcCCCCCCCCHHHHHHHHHHHH
Confidence 4565555567888888888886 489999886 4588888 4567888999999976665543
No 121
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=33.12 E-value=56 Score=16.41 Aligned_cols=23 Identities=13% Similarity=0.179 Sum_probs=17.1
Q ss_pred HHHHHHHHHHhcCCCcchhhhHh
Q 031854 32 DVEDNICKFAKKGLTPSQIGVIL 54 (152)
Q Consensus 32 EVe~~IvklaKkG~tpSqIG~iL 54 (152)
+-...|+++...|.+..+|...+
T Consensus 9 ~~~~~i~~~~~~~~s~~~ia~~~ 31 (42)
T cd00569 9 EQIEEARRLLAAGESVAEIARRL 31 (42)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHH
Confidence 34567778888999988887543
No 122
>COG3530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.10 E-value=40 Score=24.37 Aligned_cols=22 Identities=32% Similarity=0.768 Sum_probs=18.1
Q ss_pred HHHHHHHHhcCCCcchhhhHhh
Q 031854 34 EDNICKFAKKGLTPSQIGVILR 55 (152)
Q Consensus 34 e~~IvklaKkG~tpSqIG~iLR 55 (152)
|+-..=+|++|++|-++|..+-
T Consensus 29 e~YLlWFarkgFP~G~lG~Lm~ 50 (71)
T COG3530 29 EEYLLWFARKGFPPGKLGRLMQ 50 (71)
T ss_pred HHHHHHHHHhCCCchHHHHHHH
Confidence 4456778999999999998864
No 123
>PLN02751 glutamyl-tRNA(Gln) amidotransferase
Probab=33.07 E-value=1.3e+02 Score=28.79 Aligned_cols=63 Identities=21% Similarity=0.423 Sum_probs=44.0
Q ss_pred cCChHHHHHHHHHHHhcCCCcchhhh-HhhhccCCCceeeecchhHHHHHHHcCCCCCC-hhhHHHHHHHHHH
Q 031854 27 KISSQDVEDNICKFAKKGLTPSQIGV-ILRDSHGIAQVKSVTGSKILRILKAHGLAPEI-PEDLYHLIKKAVA 97 (152)
Q Consensus 27 ~~~~eEVe~~IvklaKkG~tpSqIG~-iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeI-PEDL~~LIkKAv~ 97 (152)
.++++.+.++| +|...|.=.+.|+. +|.+-+ -+|+....|.+++||..-- +++|..+|+++++
T Consensus 432 ~l~p~~laeLi-~li~~g~Is~~~AK~vl~~~~-------~~~~~p~~iiee~gL~qisD~~~l~~iv~evi~ 496 (544)
T PLN02751 432 KLTPKELAELI-ASIKDGTISGKIGKEILPELL-------AKGGTVKGLVEEKGLVQISDPAEIEAMVDKVLE 496 (544)
T ss_pred CCCHHHHHHHH-HHHHcCCccHHHHHHHHHHHH-------hCCCCHHHHHHhcCCcccCCHHHHHHHHHHHHH
Confidence 36788888875 45555554445543 444433 4578899999999998543 6779999999864
No 124
>TIGR01404 FlhB_rel_III type III secretion protein, YscU/HrpY family. This model represents one of several families of proteins related to bacterial flagellar biosynthesis proteins and involved in bacterial type III protein secretion systems. This family is homologous to, but distinguished from, flagellar biosynthetic protein FlhB (TIGRFAMs model TIGR00328). This model may not identify all type III secretion system FlhB homologs.
Probab=32.31 E-value=1.4e+02 Score=26.57 Aligned_cols=59 Identities=19% Similarity=0.304 Sum_probs=43.9
Q ss_pred CCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHH-HcCCCCCChhhHHHHHHHHH
Q 031854 21 TPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILK-AHGLAPEIPEDLYHLIKKAV 96 (152)
Q Consensus 21 ~~P~Wl~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk-~nGlapeIPEDL~~LIkKAv 96 (152)
.+|-=+---.+++-..|.++|+ +||||-|.+ ..+.|-|= .-.+..+||||||.-+-...
T Consensus 277 ~AP~VvAKG~d~~A~~Ir~iA~--------------e~~VPiven---~pLAR~Ly~~~evg~~IP~ely~aVA~IL 336 (342)
T TIGR01404 277 PLPLIICKGTDAQALAVRAYAE--------------EAGIPVVRD---IPLARQLYRTARVGQYIPEELFEAVAELL 336 (342)
T ss_pred CCCEEEEeeCcHHHHHHHHHHH--------------HcCCCEeeC---HHHHHHHHHcCCCCCcCCHHHHHHHHHHH
Confidence 4555555567888888888886 489999876 45777775 55688999999997665543
No 125
>KOG4279 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=32.30 E-value=44 Score=34.30 Aligned_cols=43 Identities=30% Similarity=0.428 Sum_probs=37.2
Q ss_pred hccCCCceee---ecchhHHHHHHHcCCCCCChhhHHHHHHHHHHH
Q 031854 56 DSHGIAQVKS---VTGSKILRILKAHGLAPEIPEDLYHLIKKAVAI 98 (152)
Q Consensus 56 D~~GIp~VK~---vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv~i 98 (152)
|++||.+++. -.--.+..||+.+.+.|--==-|-|||++||.-
T Consensus 1003 d~~~ia~~~~~lf~f~DaV~~VLR~~~IkPHWMFaLdnli~rAVqa 1048 (1226)
T KOG4279|consen 1003 DTAGIAQINLALFHFSDAVQPVLRRHDIKPHWMFALDNLITRAVQA 1048 (1226)
T ss_pred cccchhhhhhhhccchHHHHHHHHhcCCChhHHHHHHHHHHHHHHH
Confidence 6788888886 455679999999999999999999999999963
No 126
>KOG3089 consensus Predicted DEAD-box-containing helicase [General function prediction only]
Probab=32.05 E-value=59 Score=28.67 Aligned_cols=33 Identities=27% Similarity=0.363 Sum_probs=28.9
Q ss_pred cchhHHHHHHHcCCCCCChhhHHHHHHHHHHHH
Q 031854 67 TGSKILRILKAHGLAPEIPEDLYHLIKKAVAIR 99 (152)
Q Consensus 67 tGkkI~~ILk~nGlapeIPEDL~~LIkKAv~iR 99 (152)
--+||++.++++--.+..||||..|++..++=|
T Consensus 63 kk~Kl~e~~~~~~~~i~sPe~l~~ll~~yi~s~ 95 (271)
T KOG3089|consen 63 KKKKLTEVLAKSEPKIGSPEDLQKLLKDYISSR 95 (271)
T ss_pred HHHHHHHHHhccCCCCCChHHHHHHHHHHHHhh
Confidence 457899999999999999999999999887644
No 127
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=32.03 E-value=1.4e+02 Score=22.22 Aligned_cols=51 Identities=20% Similarity=0.199 Sum_probs=42.3
Q ss_pred HHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHH
Q 031854 36 NICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAV 96 (152)
Q Consensus 36 ~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv 96 (152)
+=..+..-|+|..+|+.-| .++...+.+||.=+.-.|+.|-+|.+.+...+
T Consensus 15 Lq~nf~~~~ls~~~ia~dL----------~~s~~~le~vL~l~~~~~~~vW~lRdyL~~~i 65 (89)
T PF10078_consen 15 LQANFELSGLSLEQIAADL----------GTSPEHLEQVLNLKQPFPEDVWILRDYLNDKI 65 (89)
T ss_pred HHHHHHHcCCCHHHHHHHh----------CCCHHHHHHHHcCCCCCcccchHHHHHHHHHH
Confidence 3345667899999999877 37889999999999888999999998887664
No 128
>PF12832 MFS_1_like: MFS_1 like family
Probab=31.88 E-value=23 Score=24.49 Aligned_cols=15 Identities=47% Similarity=0.888 Sum_probs=12.3
Q ss_pred HHhcCCCcchhhhHh
Q 031854 40 FAKKGLTPSQIGVIL 54 (152)
Q Consensus 40 laKkG~tpSqIG~iL 54 (152)
+...|++++|||++.
T Consensus 27 ~~~~Gl~~~~iGil~ 41 (77)
T PF12832_consen 27 LKQLGLSPSQIGILS 41 (77)
T ss_pred hhhcCCCHHHHHHHH
Confidence 345799999999975
No 129
>PRK14703 glutaminyl-tRNA synthetase/YqeY domain fusion protein; Provisional
Probab=31.67 E-value=1.3e+02 Score=29.82 Aligned_cols=66 Identities=14% Similarity=0.174 Sum_probs=50.2
Q ss_pred CccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCCh-hhHHHHHHHHHH
Q 031854 25 WLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIP-EDLYHLIKKAVA 97 (152)
Q Consensus 25 Wl~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIP-EDL~~LIkKAv~ 97 (152)
-+.++++.+.++|.-++..-+|..++-.+|..-. -+|+++.+|.+++||..--- ++|..+|+++++
T Consensus 659 ~~~l~pe~LaeLv~lV~~g~IS~~~AK~VL~~m~-------~~~~~p~~IIee~GL~qisDe~~Le~iV~eVI~ 725 (771)
T PRK14703 659 ALPFTPAALARLVALVDAGRISTRIAKDVLAELA-------ASGGDPEAIVEAKGLEQVSDAGALEPIVEEVLA 725 (771)
T ss_pred cCCCCHHHHHHHHHHHHcCCccHHHHHHHHHHHH-------hcCCCHHHHHHhcCCcccCCHHHHHHHHHHHHH
Confidence 4567999999998777777777777766665433 34778999999999985444 569999999863
No 130
>PF03433 EspA: EspA-like secreted protein ; InterPro: IPR005095 EspA is the prototypical member of this family. EspA, together with EspB, EspD and Tir are exported by a type III secretion system. These proteins are essential for attaching and effacing lesion formation. EspA is a structural protein and a major component of a large, transiently expressed, filamentous surface organelle which forms a direct link between the bacterium and the host cell [, ].; PDB: 1XOU_A.
Probab=31.64 E-value=16 Score=30.68 Aligned_cols=62 Identities=27% Similarity=0.390 Sum_probs=0.0
Q ss_pred ChHHHHHHHHHHHhcCC-----CcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHH
Q 031854 29 SSQDVEDNICKFAKKGL-----TPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAV 96 (152)
Q Consensus 29 ~~eEVe~~IvklaKkG~-----tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv 96 (152)
.+.+|.+.|.+.+|.|= -|-.+=..+|| +|| .|.|++|...|++||- .++-..=...||-|+
T Consensus 77 maN~vDevIA~~~k~~dk~k~~lp~dVi~Ym~~-ngI----~VdG~si~~Yl~~n~~-~~LdkG~LqaVKaAl 143 (188)
T PF03433_consen 77 MANRVDEVIAEVAKSDDKAKAPLPDDVIDYMRD-NGI----KVDGKSIDDYLKKNGS-GGLDKGQLQAVKAAL 143 (188)
T ss_dssp -------------------------------------------------------------------------
T ss_pred HHHHHHHHHHhccCCCccccccCCHHHHHHHHH-cCC----eecCeeccchhhhhhh-ccCCchhHHHHHHHH
Confidence 45688899999988652 24455567888 888 4799999999999984 455555455555553
No 131
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=31.50 E-value=1.1e+02 Score=22.75 Aligned_cols=49 Identities=22% Similarity=0.374 Sum_probs=37.3
Q ss_pred ChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCC
Q 031854 29 SSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLA 81 (152)
Q Consensus 29 ~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGla 81 (152)
+.+|+.+.++++ +|+-|=--..+|...+| +.+-.+ -.-+.++++..|.-
T Consensus 77 ~~~~~~~~L~~l--~GIG~~tA~~~l~~~~~-~~~~pv-D~~v~r~~~~~~~~ 125 (158)
T cd00056 77 DDPDAREELLAL--PGVGRKTANVVLLFALG-PDAFPV-DTHVRRVLKRLGLI 125 (158)
T ss_pred CCcccHHHHHcC--CCCCHHHHHHHHHHHCC-CCCCcc-chhHHHHHHHhCCC
Confidence 445555555555 78777777888888899 888888 88899999999873
No 132
>PRK04028 glutamyl-tRNA(Gln) amidotransferase subunit E; Validated
Probab=30.77 E-value=1.4e+02 Score=29.00 Aligned_cols=63 Identities=17% Similarity=0.239 Sum_probs=48.1
Q ss_pred CChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHH
Q 031854 28 ISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAV 96 (152)
Q Consensus 28 ~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv 96 (152)
++++.+.+++.-+++..+|-.++-.+|..-+- -.|+.+.+|+++.|+..-=.+.|..+|+.++
T Consensus 519 i~~~~l~~l~~~~~~~~is~~~ak~v~~~~~~------~~~~~~~~IIee~gl~qiSD~eL~~iV~evI 581 (630)
T PRK04028 519 ITDEHIEEVFKLVSEGKIAKEAIEEILKELAE------NPGKSAEEAAEELGLKGLSEEEVEKIIDEIV 581 (630)
T ss_pred CCHHHHHHHHHHHHcCCccHHHHHHHHHHHHh------cCCCCHHHHHHHhCcccCCHHHHHHHHHHHH
Confidence 68899999977777777777777666654431 0167799999999998776678888888885
No 133
>COG1141 Fer Ferredoxin [Energy production and conversion]
Probab=30.41 E-value=29 Score=24.51 Aligned_cols=23 Identities=26% Similarity=0.254 Sum_probs=18.3
Q ss_pred HHHcCCCCCChhhHHHHHHHHHH
Q 031854 75 LKAHGLAPEIPEDLYHLIKKAVA 97 (152)
Q Consensus 75 Lk~nGlapeIPEDL~~LIkKAv~ 97 (152)
+-.+=...++||||++.++.|+.
T Consensus 35 ~~~~~~~~~~~~e~~~~~~~A~~ 57 (68)
T COG1141 35 LDGNIGEGEVPEELEEDAEDAAE 57 (68)
T ss_pred ccCccccccCChHHHHHHHHHHH
Confidence 34445678999999999999974
No 134
>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=30.41 E-value=39 Score=19.85 Aligned_cols=25 Identities=16% Similarity=0.185 Sum_probs=17.7
Q ss_pred hHHHHHHHHHHHh-cCCCcchhhhHh
Q 031854 30 SQDVEDNICKFAK-KGLTPSQIGVIL 54 (152)
Q Consensus 30 ~eEVe~~IvklaK-kG~tpSqIG~iL 54 (152)
++|..+.+-++|+ .|.|-|++=..+
T Consensus 7 ~~~~~~~l~~~a~~~g~s~s~~ir~a 32 (39)
T PF01402_consen 7 PDELYERLDELAKELGRSRSELIREA 32 (39)
T ss_dssp EHHHHHHHHHHHHHHTSSHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHCcCHHHHHHHH
Confidence 4666777777776 789888865443
No 135
>PF11829 DUF3349: Protein of unknown function (DUF3349); InterPro: IPR021784 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 99 to 124 amino acids in length. ; PDB: 2KVC_A 3OL3_B 3OL4_A 2LKY_A.
Probab=30.33 E-value=59 Score=24.43 Aligned_cols=27 Identities=26% Similarity=0.559 Sum_probs=19.6
Q ss_pred cCChHHHHHHHHHHHhcCCCc---chhhhH
Q 031854 27 KISSQDVEDNICKFAKKGLTP---SQIGVI 53 (152)
Q Consensus 27 ~~~~eEVe~~IvklaKkG~tp---SqIG~i 53 (152)
.+|.|||.+.+.+|++.|..+ ..||+.
T Consensus 35 ~Ltd~ev~~Va~~L~~~~~~~~~~~dI~~~ 64 (96)
T PF11829_consen 35 RLTDDEVAEVAAELAARGDPPVDRIDIGVA 64 (96)
T ss_dssp TS-HHHHHHHHHHHHHHTSS-BSCCHHHHH
T ss_pred cCCHHHHHHHHHHHHhcCCCCCCHHHHHHH
Confidence 368999999999999998754 445443
No 136
>PRK12773 flhB flagellar biosynthesis protein FlhB; Reviewed
Probab=30.22 E-value=1.7e+02 Score=28.83 Aligned_cols=61 Identities=21% Similarity=0.355 Sum_probs=46.2
Q ss_pred CCCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHH-HHcCCCCCChhhHHHHHHHHHH
Q 031854 20 RTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRIL-KAHGLAPEIPEDLYHLIKKAVA 97 (152)
Q Consensus 20 ~~~P~Wl~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~IL-k~nGlapeIPEDL~~LIkKAv~ 97 (152)
..+|-=+---.+++-..|.++|+ +||||.|.. ..+-|-| +.-.+..+||||||.-|-..++
T Consensus 576 ~~APiVVAKG~D~lAlrIReiAe--------------E~gVPIVEN---pPLARALY~~veVGq~IP~eLYeAVAeILa 637 (646)
T PRK12773 576 HKAPIVIAKGVDDFALLIIRIAR--------------ENGVPTVED---RLQARGLYEEVELGAEVPQQFYRAIATILS 637 (646)
T ss_pred CCCCEEEEEeCcHHHHHHHHHHH--------------HcCCcEEEC---HHHHHHHHHcCCCCCcCCHHHHHHHHHHHH
Confidence 35565556678889999999886 489999876 4577777 4667889999999976665544
No 137
>TIGR00677 fadh2_euk methylenetetrahydrofolate reductase, eukaryotic type. This protein is an FAD-containing flavoprotein.
Probab=30.09 E-value=3.3e+02 Score=23.26 Aligned_cols=91 Identities=16% Similarity=0.301 Sum_probs=55.1
Q ss_pred CChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchh-HHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHhHcC
Q 031854 28 ISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSK-ILRILKAHGLAPEIPEDLYHLIKKAVAIRKHLERNR 106 (152)
Q Consensus 28 ~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkk-I~~ILk~nGlapeIPEDL~~LIkKAv~iRKHLe~n~ 106 (152)
++++.+++.+.++.+.|.+.- | ||-+-+++..+ +.++-+ =..-.||+++.+-+++|
T Consensus 171 Fd~~~~~~f~~~~~~~gi~~P-I---------i~GI~pi~s~~~~~~~~~--~~Gi~vP~~l~~~l~~~----------- 227 (281)
T TIGR00677 171 YDVDNFLKFVNDCRAIGIDCP-I---------VPGIMPINNYASFLRRAK--WSKTKIPQEIMSRLEPI----------- 227 (281)
T ss_pred ecHHHHHHHHHHHHHcCCCCC-E---------EeeccccCCHHHHHHHHh--cCCCCCCHHHHHHHHhc-----------
Confidence 355555566666665655431 1 45555666655 444422 23468999999887765
Q ss_pred Cccc---cchhhhhhHHHHHHHHHhhhhhceeeeccCCCCC
Q 031854 107 KDKD---SKFRLILVESRIHDWLATTRRQRSFHLYGNMSQP 144 (152)
Q Consensus 107 KD~~---sK~~L~LiESkI~RL~kYYk~~~~~~~~~~~~~~ 144 (152)
+|.+ -..+....=.-|+.|..+ ...-+|.|. ||++
T Consensus 228 ~~~~~~~~~~gi~~a~~~~~~l~~~--G~~giH~~t-~n~~ 265 (281)
T TIGR00677 228 KDDDEAVRDYGIELIVEMCQKLLAS--GIKGLHFYT-LNLE 265 (281)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHC--CCCeeEEec-cCch
Confidence 2221 246777777777887775 466788887 7764
No 138
>PF04926 PAP_RNA-bind: Poly(A) polymerase predicted RNA binding domain; InterPro: IPR007010 In eukaryotes, polyadenylation of pre-mRNA plays an essential role in the initiation step of protein synthesis, as well as in the export and stability of mRNAs. Poly(A) polymerase, the enzyme at the heart of the polyadenylation machinery, is a template-independent RNA polymerase that specifically incorporates ATP at the 3' end of mRNA. The crystal structure of bovine poly(A) polymerase bound to an ATP analogue at 2.5 A resolution has been determined []. The structure revealed expected and unexpected similarities to other proteins. As expected, the catalytic domain of poly(A) polymerase shares substantial structural homology with other nucleotidyl transferases such as DNA polymerase beta and kanamycin transferase. The C-terminal domain unexpectedly folds into a compact domain reminiscent of the RNA-recognition motif fold. The three invariant aspartates of the catalytic triad ligate two of the three active site metals. One of these metals also contacts the adenine ring. Furthermore, conserved, catalytically important residues contact the nucleotide. These contacts, taken together with metal coordination of the adenine base, provide a structural basis for ATP selection by poly(A) polymerase. ; GO: 0003723 RNA binding, 0004652 polynucleotide adenylyltransferase activity, 0043631 RNA polyadenylation, 0005634 nucleus; PDB: 2O1P_A 2HHP_A 3C66_B 1FA0_A 2Q66_A 1Q79_A 1Q78_A 1F5A_A.
Probab=29.97 E-value=23 Score=26.98 Aligned_cols=20 Identities=25% Similarity=0.258 Sum_probs=15.1
Q ss_pred hhhhHHHHHHHHHhhhhhce
Q 031854 115 LILVESRIHDWLATTRRQRS 134 (152)
Q Consensus 115 L~LiESkI~RL~kYYk~~~~ 134 (152)
.-+||||||.|+.-.-+...
T Consensus 26 ~G~VESrlR~Lv~~LE~~~~ 45 (157)
T PF04926_consen 26 SGWVESRLRHLVQKLERNPG 45 (157)
T ss_dssp HHHHHCCHHHHHHHHHTSTT
T ss_pred hhHHHHHHHHHHHHHccCCC
Confidence 34799999999986665443
No 139
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=29.95 E-value=2.1e+02 Score=20.58 Aligned_cols=40 Identities=20% Similarity=0.182 Sum_probs=30.0
Q ss_pred CCCCCCCCCccCChHHHHH--HHHHHHhcCCCcchhhhHhhh
Q 031854 17 PYKRTPPSWLKISSQDVED--NICKFAKKGLTPSQIGVILRD 56 (152)
Q Consensus 17 P~~~~~P~Wl~~~~eEVe~--~IvklaKkG~tpSqIG~iLRD 56 (152)
|..+...-+-.+++++|+. .|..|..-|+|..+|..+|..
T Consensus 28 ~~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~ 69 (113)
T cd01109 28 PVKRDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAEL 69 (113)
T ss_pred CCCcCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 3334444555678888875 488899999999999988864
No 140
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=29.92 E-value=49 Score=22.06 Aligned_cols=20 Identities=30% Similarity=0.474 Sum_probs=16.3
Q ss_pred ccCChHHHHHHHHHHHhcCC
Q 031854 26 LKISSQDVEDNICKFAKKGL 45 (152)
Q Consensus 26 l~~~~eEVe~~IvklaKkG~ 45 (152)
++.+++.|+.++..|-++|+
T Consensus 24 ~~~s~~~ve~mL~~l~~kG~ 43 (69)
T PF09012_consen 24 FGISPEAVEAMLEQLIRKGY 43 (69)
T ss_dssp TT--HHHHHHHHHHHHCCTS
T ss_pred HCcCHHHHHHHHHHHHHCCc
Confidence 56789999999999999996
No 141
>PTZ00081 enolase; Provisional
Probab=29.75 E-value=64 Score=29.60 Aligned_cols=72 Identities=15% Similarity=0.212 Sum_probs=44.3
Q ss_pred CCCCCC--hhhHHHHHHHHHHHHH-----------HHhHcCCccccchhhhh--------hHHHHHHHHHhhhhhceeee
Q 031854 79 GLAPEI--PEDLYHLIKKAVAIRK-----------HLERNRKDKDSKFRLIL--------VESRIHDWLATTRRQRSFHL 137 (152)
Q Consensus 79 GlapeI--PEDL~~LIkKAv~iRK-----------HLe~n~KD~~sK~~L~L--------iESkI~RL~kYYk~~~~~~~ 137 (152)
|.+|.+ +|+-..||..|+.--- |-.+.-+..+.+|.+.. .+---..|+.||.+...-++
T Consensus 219 gfap~~~~~eeal~ll~eAi~~ag~~~~v~i~lD~Aase~~~~~~~~Y~~~f~~~~~~~~~~~s~~eli~~~~~~l~~y~ 298 (439)
T PTZ00081 219 GFAPNIKDPEEALDLLVEAIKKAGYEGKVKICMDVAASEFYDKEKKVYDLDFKNPNNDKSNKLTGEELVELYLDLVKKYP 298 (439)
T ss_pred CcCCCCCCHHHHHHHHHHHHHHcCCcCceEEEEehhhhhhhhccCCceeeeeccccCccccccCHHHHHHHHHHHHhcCC
Confidence 346766 8999999999987321 11111111122444421 11234678999988877777
Q ss_pred ccCCCCCCCCCCC
Q 031854 138 YGNMSQPLPALSW 150 (152)
Q Consensus 138 ~~~~~~~~~~~~~ 150 (152)
+--+-||++.-.|
T Consensus 299 I~~IEDPl~~~D~ 311 (439)
T PTZ00081 299 IVSIEDPFDQDDW 311 (439)
T ss_pred cEEEEcCCCcccH
Confidence 7777899988665
No 142
>cd08642 DNA_pol_A_pol_I_A Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Family A polymerase (polymerase I) functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuclease. P
Probab=29.53 E-value=84 Score=28.55 Aligned_cols=33 Identities=12% Similarity=0.222 Sum_probs=27.7
Q ss_pred hHHHHHHHHHHHhcC--CCcchhhhHhhhccCCCc
Q 031854 30 SQDVEDNICKFAKKG--LTPSQIGVILRDSHGIAQ 62 (152)
Q Consensus 30 ~eEVe~~IvklaKkG--~tpSqIG~iLRD~~GIp~ 62 (152)
.+|+++.|.+++-.. -||-|+|.+|.|+.|.|.
T Consensus 13 k~~l~~~i~~~~g~~n~~SpkQL~~~Lf~~~~l~~ 47 (378)
T cd08642 13 KEELLEEAKELTGLDNPNSPAQLKDWLNEQGGEVD 47 (378)
T ss_pred HHHHHHHHHHHhCCCCCCCHHHHHHHHHHcCCCCC
Confidence 578999999999733 377899999999999874
No 143
>PRK03002 prsA peptidylprolyl isomerase; Reviewed
Probab=29.46 E-value=2.6e+02 Score=23.61 Aligned_cols=47 Identities=19% Similarity=0.353 Sum_probs=31.8
Q ss_pred hhHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHhHcCCccccchhhhhhHHHHHHHHHhhhh
Q 031854 69 SKILRILKAHGLAPEIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHDWLATTRR 131 (152)
Q Consensus 69 kkI~~ILk~nGlapeIPEDL~~LIkKAv~iRKHLe~n~KD~~sK~~L~LiESkI~RL~kYYk~ 131 (152)
..+.+.|+..|+.. .+++.+-|+.-+.+.+.+.. ..+|.-|. +||..
T Consensus 89 ~~f~~~L~~~G~~~--~~~~r~~ir~~l~~~~~~~~-----------~vtd~ei~---~~Y~~ 135 (285)
T PRK03002 89 DQFKNVLKNNGLKD--EADFKNQIKFKLAMNEAIKK-----------SVTEKDVK---DHYKP 135 (285)
T ss_pred HHHHHHHHHcCCCC--HHHHHHHHHHHHHHHHHHhC-----------CCCHHHHH---Hhhcc
Confidence 46888999999852 57888888877766555432 35666665 47753
No 144
>PF09494 Slx4: Slx4 endonuclease; InterPro: IPR018574 The Slx4 protein is a heteromeric structure-specific endonuclease found in fungi. Slx4 with Slx1 acts as a nuclease on branched DNA substrates, particularly simple-Y, 5'-flap, or replication fork structures by cleaving the strand bearing the 5' non-homologous arm at the branch junction and thus generating ligatable nicked products from 5'-flap or replication fork substrates [].
Probab=29.43 E-value=84 Score=21.14 Aligned_cols=40 Identities=20% Similarity=0.276 Sum_probs=32.4
Q ss_pred cCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCC
Q 031854 27 KISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLA 81 (152)
Q Consensus 27 ~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGla 81 (152)
.+.|=+++++...|. ..|+|.++.+.-.++.+.|.++|+.
T Consensus 21 ~YePI~L~el~~~L~---------------~~g~~~~~~~~~~~l~~~lD~~gIt 60 (64)
T PF09494_consen 21 MYEPINLEELHAWLK---------------ASGIGFDRKVDPSKLKEWLDSQGIT 60 (64)
T ss_pred cCCCccHHHHHHHHH---------------HcCCCccceeCHHHHHHHHHHCCce
Confidence 456777777777776 6788999999999999999999874
No 145
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=29.30 E-value=62 Score=25.42 Aligned_cols=31 Identities=10% Similarity=0.160 Sum_probs=28.2
Q ss_pred hHHHHHHHHHHHhcCCCcchhhhHhhhccCC
Q 031854 30 SQDVEDNICKFAKKGLTPSQIGVILRDSHGI 60 (152)
Q Consensus 30 ~eEVe~~IvklaKkG~tpSqIG~iLRD~~GI 60 (152)
+.|....|.++-++|.|..||=..+.+.||=
T Consensus 59 A~dmR~~Vr~~i~~G~sd~eI~~~~v~RYG~ 89 (126)
T PRK10144 59 AVSMRHQVYSMVAEGKSEVEIIGWMTERYGD 89 (126)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHhcCC
Confidence 5678889999999999999999999999993
No 146
>PF12759 HTH_Tnp_IS1: InsA C-terminal domain; InterPro: IPR024431 This entry represents the helix-turn-helix domain found at the C-terminal of InsA.
Probab=29.27 E-value=50 Score=22.06 Aligned_cols=20 Identities=15% Similarity=0.255 Sum_probs=15.3
Q ss_pred HHHHHHHHHHHhcCCCcchh
Q 031854 31 QDVEDNICKFAKKGLTPSQI 50 (152)
Q Consensus 31 eEVe~~IvklaKkG~tpSqI 50 (152)
-+|.++|++||..|.---.+
T Consensus 8 pgikeqIvema~nG~GiRdt 27 (46)
T PF12759_consen 8 PGIKEQIVEMAFNGSGIRDT 27 (46)
T ss_pred ccHHHHHHHHHhcCCcchhh
Confidence 46899999999999653333
No 147
>PF06348 DUF1059: Protein of unknown function (DUF1059); InterPro: IPR009409 This entry consists of short hypothetical archaeal and bacterial proteins of unknown function.
Probab=29.15 E-value=58 Score=21.74 Aligned_cols=18 Identities=50% Similarity=0.931 Sum_probs=13.5
Q ss_pred cCCCCCChhhHHHHHHHHH
Q 031854 78 HGLAPEIPEDLYHLIKKAV 96 (152)
Q Consensus 78 nGlapeIPEDL~~LIkKAv 96 (152)
+|+. ++|+||..-||.++
T Consensus 37 Hg~~-~~~~el~~~ir~~I 54 (57)
T PF06348_consen 37 HGMT-EIPEELREKIRSAI 54 (57)
T ss_pred cCCc-cCCHHHHHHHHHHh
Confidence 4433 78999999888876
No 148
>cd08637 DNA_pol_A_pol_I_C Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Family A polymerase (polymerase I) functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I (pol I) ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuc
Probab=29.03 E-value=1e+02 Score=27.27 Aligned_cols=35 Identities=26% Similarity=0.497 Sum_probs=27.8
Q ss_pred hHHHHHHHHHHHhcCC---CcchhhhHhhhccCCCcee
Q 031854 30 SQDVEDNICKFAKKGL---TPSQIGVILRDSHGIAQVK 64 (152)
Q Consensus 30 ~eEVe~~IvklaKkG~---tpSqIG~iLRD~~GIp~VK 64 (152)
-+|+++.+.+|+...+ ||-|+...|-|..|+|..+
T Consensus 16 ~~~l~~~~~~l~g~~fn~~S~~qv~~~L~~~lgl~~~~ 53 (377)
T cd08637 16 LAELEEEIYELAGEEFNINSPKQLGEVLFEKLGLPVGK 53 (377)
T ss_pred HHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhCCCCCCC
Confidence 4677888888877554 5679999999999999764
No 149
>PRK08156 type III secretion system protein SpaS; Validated
Probab=29.03 E-value=1.7e+02 Score=26.39 Aligned_cols=66 Identities=12% Similarity=0.097 Sum_probs=49.0
Q ss_pred CCCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHH-HcCCCCCChhhHHHHHHHHHHH
Q 031854 20 RTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILK-AHGLAPEIPEDLYHLIKKAVAI 98 (152)
Q Consensus 20 ~~~P~Wl~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk-~nGlapeIPEDL~~LIkKAv~i 98 (152)
..+|-=+---.+++-..|.++|+ +||||-|.. ..+-|-|= .-.+..+|||+||.-+-..++-
T Consensus 272 ~~AP~VvAKG~d~~A~~IreiA~--------------e~~VPiven---~pLARaLY~~vevg~~IP~ely~AVA~iLa~ 334 (361)
T PRK08156 272 APIPFISVRETNQRALAVRAYAE--------------KVGVPVVRD---IKLARRLYKTHRRYSFVSLEDLDEVLRLLIW 334 (361)
T ss_pred CCCCEEEEecCcHHHHHHHHHHH--------------HCCCCEeeC---HHHHHHHHHhCCCCCcCCHHHHHHHHHHHHH
Confidence 34565566677888888988886 489998776 56888885 5578999999999877666554
Q ss_pred HHHH
Q 031854 99 RKHL 102 (152)
Q Consensus 99 RKHL 102 (152)
=--+
T Consensus 335 v~~l 338 (361)
T PRK08156 335 LEQV 338 (361)
T ss_pred HHHH
Confidence 3333
No 150
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=28.97 E-value=1e+02 Score=22.76 Aligned_cols=40 Identities=13% Similarity=0.137 Sum_probs=31.7
Q ss_pred CCCCCCCCCccCChHHHH--HHHHHHHhcCCCcchhhhHhhh
Q 031854 17 PYKRTPPSWLKISSQDVE--DNICKFAKKGLTPSQIGVILRD 56 (152)
Q Consensus 17 P~~~~~P~Wl~~~~eEVe--~~IvklaKkG~tpSqIG~iLRD 56 (152)
|..+..--+=.|+.++|+ ..|..|..-|+|-.+|..+|..
T Consensus 28 p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~ 69 (127)
T cd04784 28 APARSANNYRLYDEEHLERLLFIRRCRSLDMSLDEIRTLLQL 69 (127)
T ss_pred CCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 444555566778999998 6788899999999999998863
No 151
>PF08542 Rep_fac_C: Replication factor C C-terminal domain; InterPro: IPR013748 Replication factor C (RFC) is a multimeric AAA+ protein complex that loads the DNA polymerase processivity clamp PCNA (Proliferating Cell Nuclear Antigen) onto DNA using ATP to drive the reaction []. PCNA functions at multiple levels in directing DNA metabolic pathways []. When bound to DNA, PCNA organises various proteins involved in DNA replication, DNA repair, DNA modification, and chromatin modelling. Replication factor C consists of five subunits in a spiral arrangement: Rfc1, Rfc2, Rfc3, Rfc4, and Rfc5 subunits. Rfc1 and Rfc2 load the PCNA sliding clamp onto DNA, while Rfc3 binds ATP and also acts as a checkpoint sensor. The RFC complex contains four ATP sites (sites A, B, C, and D) located at subunit interfaces. In each ATP site, an arginine residue from one subunit is located near the gamma-phosphate of ATP bound in the adjacent subunit. These arginine residues act as "arginine fingers" that can potentially perform two functions: sensing that ATP is bound and catalyzing ATP hydrolysis []. This entry represents the core domain found in Rfc1-5.; GO: 0003689 DNA clamp loader activity, 0005524 ATP binding, 0006260 DNA replication, 0005663 DNA replication factor C complex; PDB: 1SXJ_B 2CHG_B 2CHV_F 2CHQ_C 1IQP_A.
Probab=28.92 E-value=38 Score=22.98 Aligned_cols=29 Identities=14% Similarity=0.185 Sum_probs=18.6
Q ss_pred cCChHHHHHHHHHHHhcCCCcchhhhHhh
Q 031854 27 KISSQDVEDNICKFAKKGLTPSQIGVILR 55 (152)
Q Consensus 27 ~~~~eEVe~~IvklaKkG~tpSqIG~iLR 55 (152)
+-+-+++.+.+.+|-..|+++++|=.-|.
T Consensus 17 ~~~~~~~~~~~~~l~~~G~s~~~Il~~l~ 45 (89)
T PF08542_consen 17 NGDFKEARKKLYELLVEGYSASDILKQLH 45 (89)
T ss_dssp HTCHHHHHHHHHHHHHTT--HHHHHHHHH
T ss_pred hCCHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 33567777788888888888888754443
No 152
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=28.77 E-value=47 Score=26.95 Aligned_cols=35 Identities=29% Similarity=0.374 Sum_probs=19.8
Q ss_pred CCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCC
Q 031854 44 GLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLA 81 (152)
Q Consensus 44 G~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGla 81 (152)
|+|+|-+-.+|.+. +.|..-|=++|.++.+|.|-.
T Consensus 16 gVS~~TVSrvLn~~---~~vs~~tr~rV~~~a~elgY~ 50 (331)
T PRK14987 16 GVTKMTVSRFLRNP---EQVSVALRGKIAAALDELGYI 50 (331)
T ss_pred CCCHHHhhhhhCCC---CCCCHHHHHHHHHHHHHhCCC
Confidence 66666666666543 345555666666666665543
No 153
>PRK10625 tas putative aldo-keto reductase; Provisional
Probab=28.18 E-value=1.9e+02 Score=24.60 Aligned_cols=61 Identities=20% Similarity=0.330 Sum_probs=37.2
Q ss_pred HHHHHHHH-hcCCCcchhhhHhhhccCCCce-eeecchhHHHHHHHc-C-CCCCChhhHHHHHHHHH
Q 031854 34 EDNICKFA-KKGLTPSQIGVILRDSHGIAQV-KSVTGSKILRILKAH-G-LAPEIPEDLYHLIKKAV 96 (152)
Q Consensus 34 e~~Ivkla-KkG~tpSqIG~iLRD~~GIp~V-K~vtGkkI~~ILk~n-G-lapeIPEDL~~LIkKAv 96 (152)
-+.+.++| +.|.||+|+.+.--=+++ .| -.|.|.+=.+=|++| . +.-+++++.+..|.++.
T Consensus 274 ~~~l~~la~~~g~t~aqval~w~l~~~--~v~~~I~G~~~~~~l~en~~a~~~~L~~~~~~~l~~~~ 338 (346)
T PRK10625 274 VAAYVDIAKRHGLDPAQMALAFVRRQP--FVASTLLGATTMEQLKTNIESLHLTLSEEVLAEIEAVH 338 (346)
T ss_pred HHHHHHHHHHhCCCHHHHHHHHHHhCC--CCeeEEeCCCCHHHHHHHHhhccCCCCHHHHHHHHHHH
Confidence 34566666 589999999874433443 22 235555444444443 1 22468888888888774
No 154
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=28.16 E-value=73 Score=17.13 Aligned_cols=19 Identities=11% Similarity=0.277 Sum_probs=13.5
Q ss_pred ChHHHHHHHHHHHhcCCCc
Q 031854 29 SSQDVEDNICKFAKKGLTP 47 (152)
Q Consensus 29 ~~eEVe~~IvklaKkG~tp 47 (152)
+.+++.+....+.+.|+.|
T Consensus 16 ~~~~a~~~~~~M~~~gv~P 34 (34)
T PF13812_consen 16 DPDAALQLFDEMKEQGVKP 34 (34)
T ss_pred CHHHHHHHHHHHHHhCCCC
Confidence 4566777777777777766
No 155
>TIGR02417 fruct_sucro_rep D-fructose-responsive transcription factor. Members of this family belong the lacI helix-turn-helix family (pfam00356) of DNA-binding transcriptional regulators. All members are from the proteobacteria. Characterized members act as positive and negative transcriptional regulators of fructose and sucrose transport and metabolism. Sucrose is a disaccharide composed of fructose and glucose; D-fructose-1-phosphate rather than an intact sucrose moiety has been shown to act as the inducer.
Probab=28.13 E-value=58 Score=26.26 Aligned_cols=39 Identities=10% Similarity=0.361 Sum_probs=20.1
Q ss_pred CCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCC
Q 031854 44 GLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAP 82 (152)
Q Consensus 44 G~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlap 82 (152)
|+|+|-+-.+|.+.-+-..|..-|=.+|.++.++.|-.|
T Consensus 10 GVS~~TVSrvLn~~~~~~~vs~~tr~rV~~~a~~lgY~p 48 (327)
T TIGR02417 10 GVSKTTASYVINGKAKEYRISQETVERVMAVVREQGYQP 48 (327)
T ss_pred CCCHHHHHHHHcCCCCCCccCHHHHHHHHHHHHHhCCCC
Confidence 566666666665432111355555556666665555433
No 156
>PRK05755 DNA polymerase I; Provisional
Probab=28.03 E-value=1.9e+02 Score=28.46 Aligned_cols=48 Identities=27% Similarity=0.385 Sum_probs=35.4
Q ss_pred hHHHHHHHHHHHhc---CCCcchhhhHhhhccCCCceee-----ecchhHHHHHHH
Q 031854 30 SQDVEDNICKFAKK---GLTPSQIGVILRDSHGIAQVKS-----VTGSKILRILKA 77 (152)
Q Consensus 30 ~eEVe~~IvklaKk---G~tpSqIG~iLRD~~GIp~VK~-----vtGkkI~~ILk~ 77 (152)
.+|+++.|.+++.. --||-|++.+|-|..|+|.++. -|.+.+++-|.+
T Consensus 516 ~~~l~~~~~~~~g~~fn~~S~~ql~~~L~~~lgl~~~~kt~~g~st~~~~L~~l~~ 571 (880)
T PRK05755 516 LAELEQEIYELAGEEFNINSPKQLGEILFEKLGLPVGKKTKTGYSTDAEVLEKLAD 571 (880)
T ss_pred HHHHHHHHHHHhCCCCCCCCHHHHHHHHHHhcCCCCCCCCCCCCCCcHHHHHHHHh
Confidence 45677777777652 2478999999999999998663 567777766654
No 157
>PLN02641 anthranilate phosphoribosyltransferase
Probab=28.01 E-value=55 Score=29.03 Aligned_cols=28 Identities=14% Similarity=0.237 Sum_probs=22.4
Q ss_pred cCChHHHHHHHHHHHhcCCCcchhhhHhh
Q 031854 27 KISSQDVEDNICKFAKKGLTPSQIGVILR 55 (152)
Q Consensus 27 ~~~~eEVe~~IvklaKkG~tpSqIG~iLR 55 (152)
++|.||..+.+..+.. |.+|.|||..|-
T Consensus 16 ~Lt~eEa~~~~~~il~-~~~~~qigAfL~ 43 (343)
T PLN02641 16 DLTEEEAEAALDFLLD-DADEAQISAFLV 43 (343)
T ss_pred CCCHHHHHHHHHHHHc-CCCHHHHHHHHH
Confidence 6788888888888886 689999887653
No 158
>PRK13109 flhB flagellar biosynthesis protein FlhB; Reviewed
Probab=27.52 E-value=2.4e+02 Score=25.28 Aligned_cols=65 Identities=17% Similarity=0.240 Sum_probs=47.1
Q ss_pred CCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHH-HcCCCCCChhhHHHHHHHHHHHH
Q 031854 21 TPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILK-AHGLAPEIPEDLYHLIKKAVAIR 99 (152)
Q Consensus 21 ~~P~Wl~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk-~nGlapeIPEDL~~LIkKAv~iR 99 (152)
.+|-=+-.-.+++-..|.++|+ +||||-|.. ..+.|-|= .-.+.-+|||+||.-+-..+..=
T Consensus 287 ~aP~VvAKG~d~~A~~Ir~~A~--------------e~~VPiven---~pLARaLy~~~evg~~IP~ely~AVA~ILa~v 349 (358)
T PRK13109 287 PAPLVVAKGQDLIALKIREIAE--------------ENGIPVIED---KPLARSLYDAVQVDQVIPAEFYRPVAQILYFL 349 (358)
T ss_pred CCCEEEEEeCcHHHHHHHHHHH--------------HcCCCEEeC---HHHHHHHHHhCCCCCcCCHHHHHHHHHHHHHH
Confidence 4555555567888888888886 489999876 45777776 45688899999998777666544
Q ss_pred HHH
Q 031854 100 KHL 102 (152)
Q Consensus 100 KHL 102 (152)
..|
T Consensus 350 ~~l 352 (358)
T PRK13109 350 FSR 352 (358)
T ss_pred HHH
Confidence 333
No 159
>COG2082 CobH Precorrin isomerase [Coenzyme metabolism]
Probab=27.35 E-value=1e+02 Score=26.18 Aligned_cols=69 Identities=25% Similarity=0.419 Sum_probs=50.0
Q ss_pred CCCCcCCCCCCCCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchh------HHHHHHHcCCCCC
Q 031854 10 GISASALPYKRTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSK------ILRILKAHGLAPE 83 (152)
Q Consensus 10 G~S~S~~P~~~~~P~Wl~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkk------I~~ILk~nGlape 83 (152)
|++.+..|-.. +-|.-++..++.+++.+ .|.|-|.-|+.++++.+-+..=.|.|+- +.+.+++++..|.
T Consensus 82 GI~~~~l~~~~--~v~c~i~d~~~~e~a~~---~g~Trsaa~~~~~~~~~~~~~ivvIGNAPTAL~~l~elie~~~~~pa 156 (210)
T COG2082 82 GITRRRLPALN--PVICYVDDPRVAELAKE---EGITRSAAGMRLAAERGEGGAIVVIGNAPTALFELLELIEEGGIKPA 156 (210)
T ss_pred hcccccccccC--cEEEEecCcchHHHHHh---hCchHHHHHHHHHHHhcCCceEEEEeCCHHHHHHHHHHHHccCCCCc
Confidence 56666665433 77777777776654432 4999999999999999988888899974 5566666656554
No 160
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=27.31 E-value=52 Score=21.30 Aligned_cols=35 Identities=11% Similarity=0.073 Sum_probs=23.7
Q ss_pred CChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCc
Q 031854 28 ISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQ 62 (152)
Q Consensus 28 ~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~ 62 (152)
+.-+++-..|.++...+.|..+|-..|.++|+++-
T Consensus 13 ~~Ln~~a~~Iw~~~~g~~t~~ei~~~l~~~y~~~~ 47 (68)
T PF05402_consen 13 FTLNETAAFIWELLDGPRTVEEIVDALAEEYDVDP 47 (68)
T ss_dssp ----THHHHHHHH--SSS-HHHHHHHHHHHTT--H
T ss_pred ccccHHHHHHHHHccCCCCHHHHHHHHHHHcCCCH
Confidence 36677888899999888999999999999998875
No 161
>PRK13870 transcriptional regulator TraR; Provisional
Probab=26.98 E-value=47 Score=27.28 Aligned_cols=28 Identities=11% Similarity=0.122 Sum_probs=22.7
Q ss_pred cCChHHHHHHHHHHHhcCCCcchhhhHhhh
Q 031854 27 KISSQDVEDNICKFAKKGLTPSQIGVILRD 56 (152)
Q Consensus 27 ~~~~eEVe~~IvklaKkG~tpSqIG~iLRD 56 (152)
.+|+-|.| |...+-.|.|..+||.||-=
T Consensus 173 ~LT~RE~E--~L~W~A~GKT~~EIa~ILgI 200 (234)
T PRK13870 173 WLDPKEAT--YLRWIAVGKTMEEIADVEGV 200 (234)
T ss_pred CCCHHHHH--HHHHHHcCCCHHHHHHHHCC
Confidence 35666655 78999999999999999953
No 162
>PF13910 DUF4209: Domain of unknown function (DUF4209)
Probab=26.77 E-value=27 Score=25.31 Aligned_cols=45 Identities=20% Similarity=0.256 Sum_probs=32.9
Q ss_pred hHhhhccCCCceeeec-----chhHHHHHHHcCCCCCChhhHHHHHHHHH
Q 031854 52 VILRDSHGIAQVKSVT-----GSKILRILKAHGLAPEIPEDLYHLIKKAV 96 (152)
Q Consensus 52 ~iLRD~~GIp~VK~vt-----GkkI~~ILk~nGlapeIPEDL~~LIkKAv 96 (152)
..|+|.+|+...+.-. -+.+.++|....++.-++||+.+++|-..
T Consensus 6 R~l~~~~~~~~~~~~~~~~~~e~~L~dLL~~~~i~~~~g~~~~~~lr~l~ 55 (93)
T PF13910_consen 6 RALGDLAGLKTTKCDKNGIEQEKLLSDLLASEEIKEIFGEDLIFLLRALF 55 (93)
T ss_pred HHHHHHhcccccccCCCcchhhhhHHHHHcChHHHHHcChHHHHHHHHHH
Confidence 3567777777665422 35677888888888888999988887665
No 163
>PRK09526 lacI lac repressor; Reviewed
Probab=26.56 E-value=56 Score=26.45 Aligned_cols=35 Identities=14% Similarity=0.267 Sum_probs=21.4
Q ss_pred CCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCC
Q 031854 44 GLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLA 81 (152)
Q Consensus 44 G~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGla 81 (152)
|+|.|-+-.+|.+. +.|..-|-++|.++.+|-|-.
T Consensus 16 GVS~~TVSrvLn~~---~~vs~~tr~rV~~~a~elgY~ 50 (342)
T PRK09526 16 GVSYQTVSRVLNQA---SHVSAKTREKVEAAMAELNYV 50 (342)
T ss_pred CCCHHHHHHHhcCC---CCCCHHHHHHHHHHHHHHCCC
Confidence 66666666666543 445666666666666666543
No 164
>TIGR01795 CM_mono_cladeE monofunctional chorismate mutase, alpha proteobacterial type. The alpha proteobacterial members are trusted because the pathways of CM are evident and there is only one plausible CM in the genome. In S. coelicolor, however, there is another aparrent monofunctional CM.
Probab=26.55 E-value=89 Score=22.77 Aligned_cols=72 Identities=21% Similarity=0.450 Sum_probs=46.6
Q ss_pred hHHHHHHHHHHHhcCC-CcchhhhHhhhccCCCceeeecc----hhHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHh
Q 031854 30 SQDVEDNICKFAKKGL-TPSQIGVILRDSHGIAQVKSVTG----SKILRILKAHGLAPEIPEDLYHLIKKAVAIRKHLE 103 (152)
Q Consensus 30 ~eEVe~~IvklaKkG~-tpSqIG~iLRD~~GIp~VK~vtG----kkI~~ILk~nGlapeIPEDL~~LIkKAv~iRKHLe 103 (152)
-++|-..|++|-.+=+ -..+||..-.+. |.|-.-+.-= .++.+..++.|+.|++=|.+|.+|-.. ++|.|-+
T Consensus 12 ID~ID~qLv~LL~~R~~~~~~ia~~K~~~-~~~v~dp~Re~~vl~~~~~~a~~~gl~p~~~e~i~~~i~~e-sir~q~~ 88 (94)
T TIGR01795 12 IDNIDAAVIHMLAERFKCTSQVGVLKANA-GLAPADPAREDYQIARLRRLAIDAGLDPEFAEKFLNFIVTE-VIKHHER 88 (94)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhC-CCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHH-HHHHHHH
Confidence 3566666776655444 345677765544 5554432221 245667788899999999999998766 6777643
No 165
>PRK12468 flhB flagellar biosynthesis protein FlhB; Reviewed
Probab=26.55 E-value=2e+02 Score=26.16 Aligned_cols=62 Identities=21% Similarity=0.318 Sum_probs=47.1
Q ss_pred CCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHH-HcCCCCCChhhHHHHHHHHHHHH
Q 031854 21 TPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILK-AHGLAPEIPEDLYHLIKKAVAIR 99 (152)
Q Consensus 21 ~~P~Wl~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk-~nGlapeIPEDL~~LIkKAv~iR 99 (152)
.+|-=+-.-.+++-..|.++|++ ||||-|.. ..+.|-|= .-.+.-+||++||.-|-..++.=
T Consensus 285 ~AP~VvAKG~d~~A~~Ir~~A~e--------------~~VPiven---~pLARaLy~~~evg~~IP~ely~AVA~ILa~V 347 (386)
T PRK12468 285 SAPKVLAKGAGAVALRIRELGAE--------------HRIPLLEA---PPLARALFRHSEVGQHIPATLYAAVAEVLAWV 347 (386)
T ss_pred CCCEEEEeeCcHHHHHHHHHHHH--------------cCCcEEeC---HHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHH
Confidence 45655555778888889888874 89999876 45888885 55788999999998777665543
No 166
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=26.22 E-value=55 Score=21.81 Aligned_cols=22 Identities=32% Similarity=0.500 Sum_probs=18.3
Q ss_pred CCccCChHHHHHHHHHHHhcCC
Q 031854 24 SWLKISSQDVEDNICKFAKKGL 45 (152)
Q Consensus 24 ~Wl~~~~eEVe~~IvklaKkG~ 45 (152)
+++.+++.-|.+.+-+|+++|+
T Consensus 30 ~~L~vs~~tvt~ml~~L~~~Gl 51 (60)
T PF01325_consen 30 ERLGVSPPTVTEMLKRLAEKGL 51 (60)
T ss_dssp HHHTS-HHHHHHHHHHHHHTTS
T ss_pred HHHCCChHHHHHHHHHHHHCCC
Confidence 4678889999999999999996
No 167
>KOG2815 consensus Mitochondrial/choloroplast ribosomal protein S15 [Translation, ribosomal structure and biogenesis]
Probab=26.22 E-value=98 Score=27.13 Aligned_cols=82 Identities=22% Similarity=0.215 Sum_probs=55.8
Q ss_pred ccCCCceeeecch--hHHHHHHHcC------------CCCCChhhHH------------HHHHHHHHHHHHHhHcCCccc
Q 031854 57 SHGIAQVKSVTGS--KILRILKAHG------------LAPEIPEDLY------------HLIKKAVAIRKHLERNRKDKD 110 (152)
Q Consensus 57 ~~GIp~VK~vtGk--kI~~ILk~nG------------lapeIPEDL~------------~LIkKAv~iRKHLe~n~KD~~ 110 (152)
--|++..+.+.-+ +|.+||...+ +.-.-|.+-+ ...-+-.++-.|.+.|+||.+
T Consensus 133 ~~~~~r~~l~~~kr~~~lril~~~n~ss~e~~k~~lk~~~~e~~~~~e~dtgs~~vQ~~~~t~~i~~~~r~~~~Hkkd~~ 212 (256)
T KOG2815|consen 133 LSGKIRIKLLIDKREKILRILRRRNLSSFEKIKIKLKLVRKEPFQRFESDTGSAEVQAAFPTVEIRKLSRHEELHKKDQA 212 (256)
T ss_pred hhchhhHhhcccHHHHHHHHhhhhccccHHHHHHHHHHhccCCcccccccccchhHhHHhHHHHHHHHHHHHHHHHHHHH
Confidence 3366666655443 4777777666 3333333322 233555677889999999999
Q ss_pred cchhhhhhHHHHHHHHHhhhhhceeeec
Q 031854 111 SKFRLILVESRIHDWLATTRRQRSFHLY 138 (152)
Q Consensus 111 sK~~L~LiESkI~RL~kYYk~~~~~~~~ 138 (152)
+.+.|.-.=-+=+|+.+|-.+...---+
T Consensus 213 ~~~~l~~~~qkR~r~Lkyl~~~~~~~y~ 240 (256)
T KOG2815|consen 213 SVRGLRQEVQKRQRALKYLARANRQRYV 240 (256)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCccee
Confidence 9999988888889999998887654433
No 168
>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=26.05 E-value=59 Score=26.18 Aligned_cols=37 Identities=22% Similarity=0.451 Sum_probs=26.0
Q ss_pred cCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCC
Q 031854 43 KGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAP 82 (152)
Q Consensus 43 kG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlap 82 (152)
-|+|+|-+-.+|.+. +.|..-|=.+|.++.++-|-.|
T Consensus 11 agvS~~TVSrvLn~~---~~vs~~tr~rV~~~a~~lgY~p 47 (329)
T TIGR01481 11 AGVSMATVSRVVNGN---PNVKPATRKKVLEVIKRLDYRP 47 (329)
T ss_pred hCCCHHHHHHHhCCC---CCCCHHHHHHHHHHHHHHCCCC
Confidence 377777777777664 4567777777777777777554
No 169
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=26.01 E-value=1.2e+02 Score=16.56 Aligned_cols=33 Identities=18% Similarity=0.247 Sum_probs=17.5
Q ss_pred CCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCC
Q 031854 44 GLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAP 82 (152)
Q Consensus 44 G~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlap 82 (152)
|++++.|...+...+.+ +...+.++.+.-|+.+
T Consensus 21 ~i~~~~i~~~~~~~~~~------~~~~~~~i~~~~~~~~ 53 (56)
T smart00530 21 GVSRSTLSRIENGKRKP------SLETLKKLAKALGVSL 53 (56)
T ss_pred CCCHHHHHHHHCCCCCC------CHHHHHHHHHHhCCCh
Confidence 66666666666555422 4444555555444443
No 170
>TIGR00133 gatB glutamyl-tRNA(Gln) and/or aspartyl-tRNA(Asn) amidotransferase, B subunit. The heterotrimer GatABC is responsible for transferring the NH2 group that converts Glu to Gln, or Asp to Asn after the Glu or Asp has been ligated to the tRNA for Gln or Asn, respectively. In Lactobacillus, GatABC is responsible only for tRNA(Gln). In the Archaea, GatABC is responsible only for tRNA(Asn), while GatDE is responsible for tRNA(Gln). In lineages that include Thermus, Chlamydia, or Acidithiobacillus, the GatABC complex catalyzes both.
Probab=26.00 E-value=2e+02 Score=26.92 Aligned_cols=64 Identities=13% Similarity=0.255 Sum_probs=46.4
Q ss_pred cCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChh-hHHHHHHHHHH
Q 031854 27 KISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPE-DLYHLIKKAVA 97 (152)
Q Consensus 27 ~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIPE-DL~~LIkKAv~ 97 (152)
.++++.+.++|.-++..-+|..++=.+|..-. -+|++..+|.+++|+..---+ .|..+|+++++
T Consensus 368 ~l~p~~l~~Li~lv~~g~Is~~~ak~vl~~~~-------~~~~~~~~ii~~~gl~~isd~~~l~~iv~evl~ 432 (478)
T TIGR00133 368 GLKPSDLAELIKLIKEGKISGKSAKQLIEEML-------ENGGDPSKLIEELGLEQISDEKELIKIIEEVIK 432 (478)
T ss_pred CCCHHHHHHHHHHHHcCCCcHHHHHHHHHHHH-------hcCCCHHHHHHhcCCcccCCHHHHHHHHHHHHH
Confidence 45788888887666666666666666666543 237889999999999853333 69999999864
No 171
>KOG4115 consensus Dynein-associated protein Roadblock [Cell cycle control, cell division, chromosome partitioning; Cell motility]
Probab=25.97 E-value=35 Score=25.98 Aligned_cols=60 Identities=25% Similarity=0.455 Sum_probs=39.1
Q ss_pred hHHHHHHHHHHHh-cCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHh
Q 031854 30 SQDVEDNICKFAK-KGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVAIRKHLE 103 (152)
Q Consensus 30 ~eEVe~~IvklaK-kG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv~iRKHLe 103 (152)
..|||+.+.++-. +|.+ |.++-|..|||.=-...-..-..+. --|-.|..||-++=.-|+
T Consensus 2 ~~~vEe~~~R~qs~~gV~----giiv~d~~GvpikTt~d~~~t~~ya----------~~l~~L~~kars~VrdlD 62 (97)
T KOG4115|consen 2 SAEVEETLKRLQSYKGVT----GIIVVDNAGVPIKTTLDNTTTQQYA----------ALLHPLVEKARSVVRDLD 62 (97)
T ss_pred cHHHHHHHHHHhccCCce----eEEEECCCCcEeEeccCchHHHHHH----------HHHHHHHHHHHHHHHccC
Confidence 3578888888754 7877 9999999999854443333322222 235577788877654443
No 172
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=25.94 E-value=1.4e+02 Score=21.64 Aligned_cols=40 Identities=20% Similarity=0.326 Sum_probs=29.9
Q ss_pred CCCCCCCCCccCChHHHHH--HHHHHHhcCCCcchhhhHhhh
Q 031854 17 PYKRTPPSWLKISSQDVED--NICKFAKKGLTPSQIGVILRD 56 (152)
Q Consensus 17 P~~~~~P~Wl~~~~eEVe~--~IvklaKkG~tpSqIG~iLRD 56 (152)
|.++..-..-.+++++|+. .|..|.+.|++.++|-.+|..
T Consensus 28 p~~~~~~g~R~Y~~~dl~~l~~I~~lr~~G~~l~~I~~~l~~ 69 (108)
T cd04773 28 PDREPETGYRVYDPSDVRDARLIHLLRRGGYLLEQIATVVEQ 69 (108)
T ss_pred CCcCCCCCceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
Confidence 4443334556689999985 578888899999999888853
No 173
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=25.62 E-value=39 Score=20.62 Aligned_cols=24 Identities=17% Similarity=0.338 Sum_probs=13.9
Q ss_pred HHHHHHHHHHHhcCCCcchhhhHh
Q 031854 31 QDVEDNICKFAKKGLTPSQIGVIL 54 (152)
Q Consensus 31 eEVe~~IvklaKkG~tpSqIG~iL 54 (152)
++....|+.|..+|+|..+|...|
T Consensus 4 ~~~R~~ii~l~~~G~s~~~ia~~l 27 (50)
T PF13384_consen 4 EERRAQIIRLLREGWSIREIAKRL 27 (50)
T ss_dssp ------HHHHHHHT--HHHHHHHH
T ss_pred hhHHHHHHHHHHCCCCHHHHHHHH
Confidence 455667888888899999998766
No 174
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=25.58 E-value=56 Score=27.81 Aligned_cols=38 Identities=26% Similarity=0.434 Sum_probs=32.2
Q ss_pred cCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCC
Q 031854 43 KGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPE 83 (152)
Q Consensus 43 kG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlape 83 (152)
-|+|+|-+-.+|.+.- .|+.-|-.||.++.++-|-.|.
T Consensus 10 AGVS~sTVSrvln~~~---~Vs~eTr~kV~~a~~elgY~pN 47 (333)
T COG1609 10 AGVSKATVSRVLNGSP---YVSEETREKVLAAIKELGYRPN 47 (333)
T ss_pred hCCCHHHHHHHHcCCC---CCCHHHHHHHHHHHHHHCCCCC
Confidence 4899998888888774 8888999999999999987765
No 175
>cd01301 rDP_like renal dipeptidase (rDP), best studied in mammals and also called membrane or microsomal dipeptidase, is a membrane-bound glycoprotein hydrolyzing dipeptides and is involved in hydrolytic metabolism of penem and carbapenem beta-lactam antibiotics. Although the biological function of the enzyme is still unknown, it has been suggested to play a role in the renal glutathione metabolism.
Probab=25.28 E-value=1.1e+02 Score=26.46 Aligned_cols=34 Identities=18% Similarity=0.324 Sum_probs=27.6
Q ss_pred CCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhh
Q 031854 22 PPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRD 56 (152)
Q Consensus 22 ~P~Wl~~~~eEVe~~IvklaKkG~tpSqIG~iLRD 56 (152)
+|.|+. ++++...++..|.+.|+|..+|-.++-.
T Consensus 271 ~~~gl~-~~~~~~~l~~~L~~rG~s~~~i~~i~g~ 304 (309)
T cd01301 271 TPGGLE-DVSDLPNLTAELLERGYSEEEIEKIAGG 304 (309)
T ss_pred CccccC-CHHHHHHHHHHHHHcCCCHHHHHHHHhh
Confidence 466664 7889999999999999999999777643
No 176
>PLN03196 MOC1-like protein; Provisional
Probab=25.25 E-value=1.6e+02 Score=27.25 Aligned_cols=57 Identities=19% Similarity=0.254 Sum_probs=39.9
Q ss_pred CChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeee--cc--hhHHHHHHHcCCCCCChhhHHHHHHH
Q 031854 28 ISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSV--TG--SKILRILKAHGLAPEIPEDLYHLIKK 94 (152)
Q Consensus 28 ~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~v--tG--kkI~~ILk~nGlapeIPEDL~~LIkK 94 (152)
.+-+.|.+.|.=|-+.|++.++|+ .| |.+=.. .. ..+.++|++.|+.. +|+-.+|.+
T Consensus 87 ~~~~~~~~~l~~L~s~G~~~~~i~-----~~--P~iL~~~v~~~l~Pvl~fL~~lG~s~---~~i~~lI~~ 147 (487)
T PLN03196 87 STVDVMRERVEFLHKLGLTIEDIN-----EY--PLVLGCSVKKNMIPVLDYLEKLGVTR---SSLPELLRR 147 (487)
T ss_pred ccHHHHHHHHHHHHHcCCChHHhc-----cC--cHHhhcCHhhhhHHHHHHHHHcCCCH---HHHHHHHHh
Confidence 467788888888888999999998 23 655432 21 23678999999874 566655555
No 177
>TIGR02773 addB_Gpos ATP-dependent nuclease subunit B. DNA repair is accomplished by several different systems in prokaryotes. Recombinational repair of double-stranded DNA breaks involves the RecBCD pathway in some lineages, and AddAB (also called RexAB) in other. The AddA protein is conserved between the firmicutes and the alphaproteobacteria, while the partner protein is not. Nevertheless, the partner is designated AddB in both systems. This model describes the AddB protein as found Bacillus subtilis and related species. Although the RexB protein of Streptococcus and Lactococcus is considered to be orthologous, functionally equivalent, and merely named differently, all members of this protein family have a P-loop nucleotide binding motif GxxGxGK[ST] at the N-terminus, unlike RexB proteins, and a CxxCxxxxxC motif at the C-terminus, both of which may be relevant to function.
Probab=25.08 E-value=42 Score=33.73 Aligned_cols=34 Identities=18% Similarity=0.296 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHhc-CCCcchhhhHhhh-------------ccCCCcee
Q 031854 31 QDVEDNICKFAKK-GLTPSQIGVILRD-------------SHGIAQVK 64 (152)
Q Consensus 31 eEVe~~IvklaKk-G~tpSqIG~iLRD-------------~~GIp~VK 64 (152)
+.|.+.|.+|.+. |++++.|.++.|| +||||-.-
T Consensus 319 e~va~~I~~l~~~~g~~~~DIAVL~R~~~~y~~~i~~~f~~~~IP~~i 366 (1158)
T TIGR02773 319 EGVARQILRLTRDKQYRYQDIAILTRDLEDYAKLVEAVFSDYEIPYFI 366 (1158)
T ss_pred HHHHHHHHHHHHcCCCChhheEEEeCCHHHHHHHHHHHHHhCCCCeEE
Confidence 4455677777775 9999999999999 68899653
No 178
>PF08212 Lipocalin_2: Lipocalin-like domain; InterPro: IPR000566 Proteins which transport small hydrophobic molecules such as steroids, bilins, retinoids, and lipids share limited regions of sequence homology and a common tertiary structure architecture [, , , , ]. This is an eight stranded antiparallel beta-barrel with a repeated + 1 topology enclosing a internal ligand binding site [, ]. The name 'lipocalin' has been proposed [] for this protein family, but cytosolic fatty-acid binding proteins are also included. The sequences of most members of the family, the core or kernal lipocalins, are characterised by three short conserved stretches of residues, while others, the outlier lipocalin group, share only one or two of these [, ]. Proteins known to belong to this family include alpha-1-microglobulin (protein HC); alpha-1-acid glycoprotein (orosomucoid) []; aphrodisin; apolipoprotein D; beta-lactoglobulin; complement component C8 gamma chain []; crustacyanin []; epididymal-retinoic acid binding protein (E-RABP) []; insectacyanin; odorant-binding protein (OBP); human pregnancy-associated endometrial alpha-2 globulin; probasin (PB), a rat prostatic protein; prostaglandin D synthase (5.3.99.2 from EC) []; purpurin; Von Ebner's gland protein (VEGP) []; and lizard epididymal secretory protein IV (LESP IV) [].; GO: 0005488 binding; PDB: 3EBW_B 1QWD_A 2ACO_A 3MBT_A.
Probab=24.98 E-value=67 Score=24.02 Aligned_cols=23 Identities=13% Similarity=0.286 Sum_probs=16.7
Q ss_pred CChHHHHHHHHHHHhcCCCcchh
Q 031854 28 ISSQDVEDNICKFAKKGLTPSQI 50 (152)
Q Consensus 28 ~~~eEVe~~IvklaKkG~tpSqI 50 (152)
++++.+.+.+-.+.+.|+.+|++
T Consensus 116 ~~~~~~~~~~~~~~~~G~d~~~l 138 (143)
T PF08212_consen 116 LSEETYAEILDRAKQQGYDVSKL 138 (143)
T ss_dssp --HHHHHHHHHHHHHTT--GGGE
T ss_pred CCHHHHHHHHHHHHHcCCCHHHe
Confidence 57888888888899999999975
No 179
>TIGR00756 PPR pentatricopeptide repeat domain (PPR motif). This family has a similar consensus to the TPR domain (tetratricopeptide), pfam pfam00515, a 33-residue repeat. It is predicted to form a pair of antiparallel helices similar to that of TPR.
Probab=24.94 E-value=1e+02 Score=16.14 Aligned_cols=20 Identities=10% Similarity=0.356 Sum_probs=15.0
Q ss_pred ChHHHHHHHHHHHhcCCCcc
Q 031854 29 SSQDVEDNICKFAKKGLTPS 48 (152)
Q Consensus 29 ~~eEVe~~IvklaKkG~tpS 48 (152)
..++..+...++-+.|+.|+
T Consensus 15 ~~~~a~~~~~~M~~~g~~p~ 34 (35)
T TIGR00756 15 RVEEALELFKEMLERGIEPD 34 (35)
T ss_pred CHHHHHHHHHHHHHcCCCCC
Confidence 35777788888888887775
No 180
>KOG1575 consensus Voltage-gated shaker-like K+ channel, subunit beta/KCNAB [Energy production and conversion]
Probab=24.90 E-value=1.7e+02 Score=26.36 Aligned_cols=47 Identities=17% Similarity=0.308 Sum_probs=35.6
Q ss_pred HHHHHHHHHHHh-cCCCcchhhhH-hhhccCCCceeeecchhHHHHHHHcC
Q 031854 31 QDVEDNICKFAK-KGLTPSQIGVI-LRDSHGIAQVKSVTGSKILRILKAHG 79 (152)
Q Consensus 31 eEVe~~IvklaK-kG~tpSqIG~i-LRD~~GIp~VK~vtGkkI~~ILk~nG 79 (152)
.++-+.+.++|+ .|.|++|+-+. .+++.++ +-++.|-+-.+-|+||=
T Consensus 257 ~~~~~~~~~iA~k~g~T~~qlALawv~~~~~v--~~pIpG~s~ve~l~eni 305 (336)
T KOG1575|consen 257 KPILEALSKIAEKHGCTVPQLALAWVLSNGKV--SSPIPGASKIEQLKENI 305 (336)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHhCCC--EEecCCCCcHHHHHHHH
Confidence 367777888887 58999999864 5677766 77888877666677764
No 181
>PRK02998 prsA peptidylprolyl isomerase; Reviewed
Probab=24.67 E-value=3.3e+02 Score=22.94 Aligned_cols=32 Identities=22% Similarity=0.355 Sum_probs=22.5
Q ss_pred hhHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHH
Q 031854 69 SKILRILKAHGLAPEIPEDLYHLIKKAVAIRKHL 102 (152)
Q Consensus 69 kkI~~ILk~nGlapeIPEDL~~LIkKAv~iRKHL 102 (152)
..+.+.|+..|+.. ++++..-|+.-+.+++-+
T Consensus 87 ~~f~~~L~~~G~~~--~~~~r~~i~~~l~~~~~~ 118 (283)
T PRK02998 87 DNFKSTLEQVGLKN--EDELKEKMKPEIAFEKAI 118 (283)
T ss_pred HHHHHHHHHcCCCc--HHHHHHHHHHHHHHHHHh
Confidence 35678899999863 366777777766666554
No 182
>PF01934 DUF86: Protein of unknown function DUF86; InterPro: IPR008201 This entry describes prokaryotic proteins of unknown function.; PDB: 1YLM_A.
Probab=24.55 E-value=2.6e+02 Score=19.77 Aligned_cols=76 Identities=21% Similarity=0.305 Sum_probs=46.0
Q ss_pred cCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHhHcCCccccchhhhhhHHHH
Q 031854 43 KGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVESRI 122 (152)
Q Consensus 43 kG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv~iRKHLe~n~KD~~sK~~L~LiESkI 122 (152)
-|-+-..|+..+-..+|.+..... +..+|.++|+ ++++...-+++.+++|.-+-..=-+.+-..=...+...+
T Consensus 37 ~~e~~~di~~~i~~~~~~~~p~~~----~~~~L~~~~i---i~~~~~~~l~~~~g~RN~lvH~Y~~id~~~i~~~i~~~l 109 (119)
T PF01934_consen 37 IIEAIIDIAKHIISEEGLGKPGSY----IFEILAEHGI---ISEEPAEPLRKMVGFRNRLVHDYDSIDDEIIYEIIKEDL 109 (119)
T ss_dssp HHHHHHHHHHHHHHHTT----SSH----HHHHHHHTTS---S-HHHHHHHHHHHTTHHHHHT-GGG--HHHHHHHHHHTH
T ss_pred HHHHHhhhHHHHHHHhCCCCCccH----HHHHHHHcCC---ccchhHHHHHHHHHHHHHHccccccCCHHHHHHHHHHHH
Confidence 344455677777778888877665 9999999998 566777778899999988876555554443333443333
Q ss_pred HHH
Q 031854 123 HDW 125 (152)
Q Consensus 123 ~RL 125 (152)
-.|
T Consensus 110 ~~l 112 (119)
T PF01934_consen 110 PDL 112 (119)
T ss_dssp HHH
T ss_pred HHH
Confidence 333
No 183
>PF14907 NTP_transf_5: Uncharacterised nucleotidyltransferase
Probab=24.44 E-value=1.5e+02 Score=23.36 Aligned_cols=55 Identities=13% Similarity=0.242 Sum_probs=45.1
Q ss_pred HHHHHHHHHHHhcCCCcchh-hhHhhhccCCCcee----------eecchhHHHHHHHcCCCCCCh
Q 031854 31 QDVEDNICKFAKKGLTPSQI-GVILRDSHGIAQVK----------SVTGSKILRILKAHGLAPEIP 85 (152)
Q Consensus 31 eEVe~~IvklaKkG~tpSqI-G~iLRD~~GIp~VK----------~vtGkkI~~ILk~nGlapeIP 85 (152)
.|+.++...|.+.|..+--+ |..|.+-|+-|..+ .-.-.+..++|.++|..+.-+
T Consensus 58 ~~~~~i~~~l~~~gI~~~~lKG~~l~~~Y~~~~~R~~~DiDlLV~~~d~~~a~~~L~~~Gy~~~~~ 123 (249)
T PF14907_consen 58 AELQEILAALNANGIPVILLKGAALAQLYPDPGLRPMGDIDLLVPPEDLERAVELLEELGYRIESP 123 (249)
T ss_pred HHHHHHHHHHHHcCCCEEEEchHHHHHhCCCCCCCCCCCeEEEEeCCcHHHHHHHHHHcCCEeccC
Confidence 47778888899999999888 99999999998644 345567899999999887765
No 184
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=24.43 E-value=1.4e+02 Score=21.62 Aligned_cols=50 Identities=24% Similarity=0.332 Sum_probs=35.6
Q ss_pred CChHHHHHHHHHHH----hcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCC
Q 031854 28 ISSQDVEDNICKFA----KKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAP 82 (152)
Q Consensus 28 ~~~eEVe~~Ivkla----KkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlap 82 (152)
.+.+|+|++...+. +.|+|.+++|..+---||. -++-..|.++ +...|.+
T Consensus 4 ~~~~ele~~~~~lk~~R~~lGLTQ~dvA~~lg~~~g~----i~SQstISR~-Es~~ls~ 57 (75)
T smart00352 4 TDPRELEAFAKTFKQRRIKLGFTQADVGLALGALYGP----DFSQTTICRF-EALQLSF 57 (75)
T ss_pred CCHHHHHHHHHHHHHHHHHcCCCHHHHHHHhcccccC----cCCHHHHHHH-HhcCccH
Confidence 36677777665553 4899999999999888887 3666677775 4444443
No 185
>PRK10376 putative oxidoreductase; Provisional
Probab=24.38 E-value=2e+02 Score=23.83 Aligned_cols=59 Identities=14% Similarity=0.201 Sum_probs=35.4
Q ss_pred HHHHHHh-cCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcC--CCCCChhhHHHHHHHH
Q 031854 36 NICKFAK-KGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHG--LAPEIPEDLYHLIKKA 95 (152)
Q Consensus 36 ~IvklaK-kG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nG--lapeIPEDL~~LIkKA 95 (152)
.+.++|+ .|.||+|+...--=+++ |.|-.+.|.+-.+-|++|= +.-+++++...-|.++
T Consensus 225 ~l~~ia~~~~~t~aq~al~w~l~~~-~~~~~i~G~~~~~~l~en~~a~~~~L~~e~~~~l~~~ 286 (290)
T PRK10376 225 TLSDVAASLGATPMQVALAWLLQRS-PNILLIPGTSSVAHLRENLAAAELVLSEEVLAELDGI 286 (290)
T ss_pred HHHHHHHHhCCCHHHHHHHHHHhCC-CCeeEeeCCCCHHHHHHHHhhccCCCCHHHHHHHHHH
Confidence 3444554 59999999874443331 2334577766656666542 2236787777776665
No 186
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=24.32 E-value=72 Score=21.38 Aligned_cols=25 Identities=28% Similarity=0.535 Sum_probs=20.2
Q ss_pred ccCChHHHHHHHHHHHhcCCCcchh
Q 031854 26 LKISSQDVEDNICKFAKKGLTPSQI 50 (152)
Q Consensus 26 l~~~~eEVe~~IvklaKkG~tpSqI 50 (152)
+.++.+|||..|+++-..|.=.+.|
T Consensus 70 l~~~~~~vE~~l~~~I~~~~i~~~I 94 (105)
T PF01399_consen 70 LQLSEEEVESILIDLISNGLIKAKI 94 (105)
T ss_dssp HTCCHHHHHHHHHHHHHTTSSEEEE
T ss_pred hccchHHHHHHHHHHHHCCCEEEEE
Confidence 4567799999999999999766554
No 187
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=24.23 E-value=1.1e+02 Score=22.69 Aligned_cols=40 Identities=18% Similarity=0.196 Sum_probs=31.0
Q ss_pred CCCCCCCCccCChHHHHH--HHHHHHhcCCCcchhhhHhhhc
Q 031854 18 YKRTPPSWLKISSQDVED--NICKFAKKGLTPSQIGVILRDS 57 (152)
Q Consensus 18 ~~~~~P~Wl~~~~eEVe~--~IvklaKkG~tpSqIG~iLRD~ 57 (152)
..+..-..-.+++++|+. .|..|..-|+|-.+|..+|...
T Consensus 29 ~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~ 70 (126)
T cd04783 29 PPRPEGGYRRYPEETVTRLRFIKRAQELGFTLDEIAELLELD 70 (126)
T ss_pred CCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcc
Confidence 344445667789998875 6889999999999999988643
No 188
>PRK10974 glycerol-3-phosphate transporter periplasmic binding protein; Provisional
Probab=24.21 E-value=80 Score=27.15 Aligned_cols=45 Identities=20% Similarity=0.144 Sum_probs=31.0
Q ss_pred hccCCCceeeecchhH-HHHHHHcCCCC-CChhhHHHHHHHHHHHHH
Q 031854 56 DSHGIAQVKSVTGSKI-LRILKAHGLAP-EIPEDLYHLIKKAVAIRK 100 (152)
Q Consensus 56 D~~GIp~VK~vtGkkI-~~ILk~nGlap-eIPEDL~~LIkKAv~iRK 100 (152)
.+||||..-...+-=. ..+|++.|+.| +.|+..-.|+.-|..|.+
T Consensus 136 ~~YglP~~~~~~~l~YNkdlf~~aGi~~~~~P~Twde~~~~a~~l~~ 182 (438)
T PRK10974 136 HLLSQPFNSSTPVLYYNKDAFKKAGLDPEQPPKTWQDLAAYAAKLRA 182 (438)
T ss_pred cEEEeeccCCCceEEEcHHHHHHcCCCCCCCCCCHHHHHHHHHHHHh
Confidence 4799998876655211 26899999975 678777777666655553
No 189
>PF00101 RuBisCO_small: Ribulose bisphosphate carboxylase, small chain; InterPro: IPR000894 RuBisCO (ribulose-1,5-bisphosphate carboxylase/oxygenase) is a bifunctional enzyme that catalyses both the carboxylation and oxygenation of ribulose-1,5-bisphosphate (RuBP) [], thus fixing carbon dioxide as the first step of the Calvin cycle. RuBisCO is the major protein in the stroma of chloroplasts, and in higher plants exists as a complex of 8 large and 8 small subunits. The function of the small subunit is unknown []. While the large subunit is coded for by a single gene, the small subunit is coded for by several different genes, which are distributed in a tissue specific manner. They are transcriptionally regulated by light receptor phytochrome [], which results in RuBisCO being more abundant during the day when it is required. The RuBisCo small subunit consists of a central four-stranded beta-sheet, with two helices packed against it [].; PDB: 1BWV_W 1IWA_P 3AXM_X 1WDD_S 3AXK_T 1IR2_K 1RBL_N 1UZH_J 1RSC_P 1UW9_C ....
Probab=24.15 E-value=57 Score=24.43 Aligned_cols=21 Identities=5% Similarity=0.284 Sum_probs=16.6
Q ss_pred CChHHHHHHHHHHHhcCCCcc
Q 031854 28 ISSQDVEDNICKFAKKGLTPS 48 (152)
Q Consensus 28 ~~~eEVe~~IvklaKkG~tpS 48 (152)
++.+||.++|..|-.+|+.|+
T Consensus 11 l~~~~i~~Qv~~ll~qG~~i~ 31 (99)
T PF00101_consen 11 LTDEEIAKQVRYLLSQGWIIG 31 (99)
T ss_dssp --HHHHHHHHHHHHHTT-EEE
T ss_pred CCHHHHHHHHHhhhhcCceee
Confidence 578999999999999999764
No 190
>PRK00726 murG undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional
Probab=23.90 E-value=1.5e+02 Score=24.41 Aligned_cols=64 Identities=14% Similarity=0.084 Sum_probs=40.0
Q ss_pred ccCCCceeeecch-------hHHHHHHHcCCCCCC------hhhHHHHHHHHH---HHHHHHhHcCCccccchhhhhhHH
Q 031854 57 SHGIAQVKSVTGS-------KILRILKAHGLAPEI------PEDLYHLIKKAV---AIRKHLERNRKDKDSKFRLILVES 120 (152)
Q Consensus 57 ~~GIp~VK~vtGk-------kI~~ILk~nGlapeI------PEDL~~LIkKAv---~iRKHLe~n~KD~~sK~~L~LiES 120 (152)
..|+|.|-.-.|. -..+.+.+.|....+ ||+|.+.|.+.+ ..++-+.++-+.....+...-+..
T Consensus 270 ~~g~Pvv~~~~~~~~~~~~~~~~~~i~~~~~g~~~~~~~~~~~~l~~~i~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~ 349 (357)
T PRK00726 270 AAGLPAILVPLPHAADDHQTANARALVDAGAALLIPQSDLTPEKLAEKLLELLSDPERLEAMAEAARALGKPDAAERLAD 349 (357)
T ss_pred HhCCCEEEecCCCCCcCcHHHHHHHHHHCCCEEEEEcccCCHHHHHHHHHHHHcCHHHHHHHHHHHHhcCCcCHHHHHHH
Confidence 4899998754321 135678888865444 789999998876 445555555554444454444433
No 191
>PF03744 BioW: 6-carboxyhexanoate--CoA ligase; InterPro: IPR005499 This family contains the enzyme 6-carboxyhexanoate--CoA ligase 6.2.1.14 from EC. This enzyme is involved in the first step of biotin synthesis, where it converts pimelate into pimeloyl-CoA []. The enzyme requires magnesium as a cofactor and forms a homodimer [].; GO: 0009102 biotin biosynthetic process
Probab=23.81 E-value=61 Score=27.96 Aligned_cols=58 Identities=17% Similarity=0.407 Sum_probs=40.7
Q ss_pred ChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeec---------------------------chhHHHHHHHcCCC
Q 031854 29 SSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVT---------------------------GSKILRILKAHGLA 81 (152)
Q Consensus 29 ~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vt---------------------------GkkI~~ILk~nGla 81 (152)
+.++|++.+.+|.+++++-|. |.|+-=+++ -.-+..+|++.|+.
T Consensus 22 ~~~~i~~~~~~L~~Ral~H~~---------G~pDfinikie~i~~~i~~i~~Lpv~t~~~~s~ee~~~~a~~lL~~~gi~ 92 (239)
T PF03744_consen 22 EEEDIEETVSELLERALNHSK---------GKPDFINIKIEKIKEPIQYIPALPVRTIEVSSVEEAREFARELLEKAGIS 92 (239)
T ss_pred CHHHHHHHHHHHHHHHhhccC---------CCCCeEEEEEEecCCCceEecCCCceeeecCCHHHHHHHHHHHHHHcCCC
Confidence 689999999999999988753 444322221 12245678888888
Q ss_pred CCChhhHHHHHHHH
Q 031854 82 PEIPEDLYHLIKKA 95 (152)
Q Consensus 82 peIPEDL~~LIkKA 95 (152)
+++.|..+.++.+.
T Consensus 93 ~~~~~~~~~~l~~~ 106 (239)
T PF03744_consen 93 EEAAEKAFELLDSG 106 (239)
T ss_pred HHHHHHHHHHHhcC
Confidence 87777777777655
No 192
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=23.68 E-value=1.8e+02 Score=21.09 Aligned_cols=39 Identities=18% Similarity=0.272 Sum_probs=30.2
Q ss_pred CCCCCCCCCccCChHHHHH--HHHHHHhcCCCcchhhhHhh
Q 031854 17 PYKRTPPSWLKISSQDVED--NICKFAKKGLTPSQIGVILR 55 (152)
Q Consensus 17 P~~~~~P~Wl~~~~eEVe~--~IvklaKkG~tpSqIG~iLR 55 (152)
|..+..--+=.|+.++|+. .|..|.+-|+|.++|..+|.
T Consensus 28 p~~r~~~gyR~Y~~~~i~~l~~I~~lr~~G~sl~eI~~~l~ 68 (123)
T cd04770 28 PPQRSENGYRLYGEADLARLRFIRRAQALGFSLAEIRELLS 68 (123)
T ss_pred CCCCCCCCCccCCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence 4445555566778888874 68899999999999998884
No 193
>PRK09071 hypothetical protein; Validated
Probab=23.55 E-value=78 Score=27.82 Aligned_cols=28 Identities=11% Similarity=0.310 Sum_probs=18.4
Q ss_pred cCChHHHHHHHHHHHhcCCCcchhhhHh
Q 031854 27 KISSQDVEDNICKFAKKGLTPSQIGVIL 54 (152)
Q Consensus 27 ~~~~eEVe~~IvklaKkG~tpSqIG~iL 54 (152)
++|.||.++.+-.+..-.++|+|||..|
T Consensus 20 ~Lt~eEa~~~~~~il~g~~~~~q~aAfL 47 (323)
T PRK09071 20 SLTREEARQAMGMILDGEVEDDQLGAFL 47 (323)
T ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHH
Confidence 3466777777777666667777776544
No 194
>PF13643 DUF4145: Domain of unknown function (DUF4145)
Probab=23.47 E-value=1.5e+02 Score=19.82 Aligned_cols=50 Identities=24% Similarity=0.293 Sum_probs=29.6
Q ss_pred chhHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHhHcCCccccchhhhhh
Q 031854 68 GSKILRILKAHGLAPEIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILV 118 (152)
Q Consensus 68 GkkI~~ILk~nGlapeIPEDL~~LIkKAv~iRKHLe~n~KD~~sK~~L~Li 118 (152)
=.+...-|...|+ |+---|.++-|++.=|---|-.......+++--|.++
T Consensus 37 L~~~I~~l~~~~~-~~~~~~~~~~iR~~GN~aaH~~~~~~~~da~~~l~~~ 86 (87)
T PF13643_consen 37 LNEKINKLRKKGL-PPDIRDWLHAIRKIGNDAAHEEKEITEEDAEDALEFL 86 (87)
T ss_pred HHHHHHHHHHcCC-CHHHHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHh
Confidence 3455667888888 6666667777777777667742333333444444443
No 195
>PF10044 Ret_tiss: Retinal tissue protein; InterPro: IPR018737 Rtp is a family of proteins of approximately 112 amino acids in length which is conserved from nematodes to humans. The proposed tertiary structure is of almost entirely alpha helix interrupted only by loops located at proline residues. Three sites in the protein sequence reveal two types of possible post-translation modification. A serine residue, at position 41, is a candidate for protein kinase C phosphorylation. Glycine residues at position 69 and 91 are probable sites for acetylation by covalent amide linkage of myristate via N-myristoyl transferase. Rtp is differentially expressed in the trout retina between parr and smolt developmental stages (smoltification). It is likely to be a house-keeping protein [].
Probab=23.36 E-value=43 Score=25.19 Aligned_cols=60 Identities=28% Similarity=0.622 Sum_probs=42.4
Q ss_pred CcCCCCCCCCCCCcc-CChHHHHHHHHHHHhcCCCcchhhhHhhh------ccCCCceeeecchhHHHHH
Q 031854 13 ASALPYKRTPPSWLK-ISSQDVEDNICKFAKKGLTPSQIGVILRD------SHGIAQVKSVTGSKILRIL 75 (152)
Q Consensus 13 ~S~~P~~~~~P~Wl~-~~~eEVe~~IvklaKkG~tpSqIG~iLRD------~~GIp~VK~vtGkkI~~IL 75 (152)
.+..|....+|.|.. ++.|++ +.|.+|++ +||+++=...+. |-|+=-.|.+|=.|.++|+
T Consensus 28 ~~~~~~~~~~~~~~~~l~~dD~-~~~~eLs~--Lt~~~L~~~Ik~L~~~aYqLGl~EaKEmtRGK~L~If 94 (95)
T PF10044_consen 28 MSTSPIYQQPPKWLQELTKDDM-EKMNELSS--LTPDQLIEKIKKLQDEAYQLGLEEAKEMTRGKLLNIF 94 (95)
T ss_pred ccCCcccCCCcccccccCHHHH-HHHHHHHc--CCHHHHHHHHHHHHHHHHHHhHHHHHHHHhhhhhhcc
Confidence 345566688899988 677887 58888875 788888776665 3466666666666666665
No 196
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=23.34 E-value=1.8e+02 Score=24.45 Aligned_cols=62 Identities=19% Similarity=0.251 Sum_probs=43.3
Q ss_pred CChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCCh------hhHHHHHHHHHHH
Q 031854 28 ISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIP------EDLYHLIKKAVAI 98 (152)
Q Consensus 28 ~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIP------EDL~~LIkKAv~i 98 (152)
++++++.+.+. + +...|+..|-||.=|+-|=++- -.+||=..|+.|.-| +|+..|+..+..+
T Consensus 142 ~~~~~~~~~l~---~---~~~~Ik~~LLDQ~~iaGiGNiy---a~EiLf~a~I~P~~~~~~Ls~~~~~~L~~~~~~v 209 (274)
T PRK01103 142 FDGEYLAAKLR---K---KKTAIKPALLDQTVVVGVGNIY---ADEALFRAGIHPERPAGSLSRAEAERLVDAIKAV 209 (274)
T ss_pred CCHHHHHHHHh---c---CCccHHHHhhcCCeEecccHhH---HHHHHHHcCCCccCccccCCHHHHHHHHHHHHHH
Confidence 35556655553 3 2368999999997554443333 457999999999877 7888887777665
No 197
>cd01528 RHOD_2 Member of the Rhodanese Homology Domain superfamily, subgroup 2. Subgroup 2 includes uncharacterized putative rhodanese-related domains.
Probab=23.28 E-value=1.5e+02 Score=20.26 Aligned_cols=46 Identities=17% Similarity=0.378 Sum_probs=29.6
Q ss_pred CCCccCChHHHHHHHHHHH------------hcCCCcchhhhHhhhccCCCceeeecch
Q 031854 23 PSWLKISSQDVEDNICKFA------------KKGLTPSQIGVILRDSHGIAQVKSVTGS 69 (152)
Q Consensus 23 P~Wl~~~~eEVe~~Ivkla------------KkG~tpSqIG~iLRD~~GIp~VK~vtGk 69 (152)
|..+.++-+++.+.+-.+. ..|...+.....|+. +|+.+|+.+.|-
T Consensus 35 ~ga~~ip~~~~~~~~~~~~~~~~~~~vv~~c~~g~rs~~~~~~l~~-~G~~~v~~l~GG 92 (101)
T cd01528 35 PGFLHLPMSEIPERSKELDSDNPDKDIVVLCHHGGRSMQVAQWLLR-QGFENVYNLQGG 92 (101)
T ss_pred CCCEecCHHHHHHHHHHhcccCCCCeEEEEeCCCchHHHHHHHHHH-cCCccEEEecCC
Confidence 4444455555555444443 357777777777876 899888887774
No 198
>PF07905 PucR: Purine catabolism regulatory protein-like family; InterPro: IPR012914 This domain is found in the purine catabolism regulatory protein expressed by Bacillus subtilis (PucR, O32138 from SWISSPROT). PucR is thought to be a transcriptional regulator of genes involved in the purine degradation pathway, and may contain a LysR-like DNA-binding domain. It is similar to LysR-type regulators in that it represses its own expression []. The other members of this family are also putative regulatory proteins.
Probab=23.27 E-value=1.7e+02 Score=21.52 Aligned_cols=24 Identities=21% Similarity=0.320 Sum_probs=18.8
Q ss_pred ChHHHHHHHHHHHhcCCCcchhhh
Q 031854 29 SSQDVEDNICKFAKKGLTPSQIGV 52 (152)
Q Consensus 29 ~~eEVe~~IvklaKkG~tpSqIG~ 52 (152)
++++..+.|.+|+++|.+-=-|+.
T Consensus 57 ~~~~~~~~i~~L~~~~~agL~i~~ 80 (123)
T PF07905_consen 57 DEEELREFIRELAEKGAAGLGIKT 80 (123)
T ss_pred CHHHHHHHHHHHHHCCCeEEEEec
Confidence 456799999999999987655543
No 199
>smart00794 AgrD Staphylococcal AgrD protein. This family consists of several AgrD proteins from many Staphylococcus species. The agr locus was initially described in Staphylococcus aureus as an element controlling the production of exoproteins implicated in virulence. Its pattern of action has been shown to be complex, upregulating certain extracellular toxins and enzymes expressed post-exponentially and repressing some exponential-phase surface components. AgrD encodes the precursor of the autoinducing peptide (AIP).The AIP derived from AgrD by the action of AgrB interacts with AgrC in the membrane to activate AgrA, which upregulates transcription both from promoter P2, amplifying the response, and from P3, initiating the production of a novel effector: RNAIII. In S. aureus, delta-hemolysin is the only translation product of RNA III and is not involved in the regulatory functions of the transcript, which is therefore the primary agent for modulating the expression of other operons con
Probab=22.97 E-value=49 Score=22.03 Aligned_cols=12 Identities=42% Similarity=0.877 Sum_probs=9.9
Q ss_pred CCCChhhHHHHH
Q 031854 81 APEIPEDLYHLI 92 (152)
Q Consensus 81 apeIPEDL~~LI 92 (152)
.||+|+.|..|-
T Consensus 33 EpEVPkELt~l~ 44 (45)
T smart00794 33 EPEVPKELTDLY 44 (45)
T ss_pred CCcCcHHHHhhc
Confidence 699999998763
No 200
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=22.79 E-value=3e+02 Score=19.82 Aligned_cols=36 Identities=19% Similarity=0.263 Sum_probs=28.8
Q ss_pred CCCccCChHHHHH--HHHHHHhcCCCcchhhhHhhhcc
Q 031854 23 PSWLKISSQDVED--NICKFAKKGLTPSQIGVILRDSH 58 (152)
Q Consensus 23 P~Wl~~~~eEVe~--~IvklaKkG~tpSqIG~iLRD~~ 58 (152)
.-+=.+++++|.. .|..|..-|+|-++|-.++....
T Consensus 35 ngyR~Y~~~~i~~l~~I~~lr~~G~sl~~i~~l~~~~~ 72 (108)
T cd01107 35 TGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDADN 72 (108)
T ss_pred CCccccCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcCC
Confidence 4566778888875 57888889999999999887754
No 201
>PRK00252 alaS alanyl-tRNA synthetase; Reviewed
Probab=22.69 E-value=1.8e+02 Score=28.93 Aligned_cols=47 Identities=13% Similarity=0.119 Sum_probs=36.8
Q ss_pred CCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHHHH
Q 031854 45 LTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVAI 98 (152)
Q Consensus 45 ~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv~i 98 (152)
.=|......|-|.||+|.= =+..|.+++|+.-++| ..+.+|.++-..
T Consensus 376 ~l~g~~~f~LydtyGfP~d------lt~~~a~e~g~~vd~~-~f~~~~~~~~~~ 422 (865)
T PRK00252 376 VLSGEDAFKLYDTYGFPLD------LTAEIARERGLTVDEE-GFEAAMEEQRER 422 (865)
T ss_pred ccCHHHHHHHHhccCCCHH------HHHHHHHHcCCCcCHH-HHHHHHHHHHHH
Confidence 3477888999999999952 1446899999998888 788888776544
No 202
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=22.56 E-value=1.8e+02 Score=18.79 Aligned_cols=34 Identities=29% Similarity=0.331 Sum_probs=25.4
Q ss_pred CCCCCccCChHHHHH--HHHHHHhcCCCcchhhhHh
Q 031854 21 TPPSWLKISSQDVED--NICKFAKKGLTPSQIGVIL 54 (152)
Q Consensus 21 ~~P~Wl~~~~eEVe~--~IvklaKkG~tpSqIG~iL 54 (152)
+.--.=.++.++|+. .|..|.+.|+|..+|-.+|
T Consensus 31 ~~~g~R~y~~~~l~~l~~i~~l~~~g~~l~~i~~~l 66 (67)
T cd04764 31 TENGRRYYTDEDIELLKKIKTLLEKGLSIKEIKEIL 66 (67)
T ss_pred CCCCceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHh
Confidence 333445578888875 5788889999999997665
No 203
>COG1393 ArsC Arsenate reductase and related proteins, glutaredoxin family [Inorganic ion transport and metabolism]
Probab=22.49 E-value=49 Score=25.00 Aligned_cols=37 Identities=27% Similarity=0.355 Sum_probs=26.7
Q ss_pred ccCCCceeeecchhHHHHHHHcCCCCCC---------hhhHHHHHHHH
Q 031854 57 SHGIAQVKSVTGSKILRILKAHGLAPEI---------PEDLYHLIKKA 95 (152)
Q Consensus 57 ~~GIp~VK~vtGkkI~~ILk~nGlapeI---------PEDL~~LIkKA 95 (152)
-||+|..- |=+|..+.|+++|+++++ .|+|..++++.
T Consensus 5 iy~~p~C~--t~rka~~~L~~~gi~~~~~~y~~~~~s~~eL~~~l~~~ 50 (117)
T COG1393 5 IYGNPNCS--TCRKALAWLEEHGIEYTFIDYLKTPPSREELKKILSKL 50 (117)
T ss_pred EEeCCCCh--HHHHHHHHHHHcCCCcEEEEeecCCCCHHHHHHHHHHc
Confidence 37777776 678888899999988752 36666666554
No 204
>PF11919 DUF3437: Domain of unknown function (DUF3437); InterPro: IPR021843 This presumed domain is functionally uncharacterised. This domain is found in eukaryotes. This domain is typically between 142 to 163 amino acids in length. ; PDB: 3L5Q_6 1VSY_5.
Probab=22.49 E-value=66 Score=23.50 Aligned_cols=33 Identities=24% Similarity=0.649 Sum_probs=21.0
Q ss_pred CCCCCCCCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhh
Q 031854 15 ALPYKRTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRD 56 (152)
Q Consensus 15 ~~P~~~~~P~Wl~~~~eEVe~~IvklaKkG~tpSqIG~iLRD 56 (152)
+-|| ..|.|+ -+.+..||+.+-+|..||...++
T Consensus 19 a~Py--~vP~w~-------P~~l~~La~~~~~~~~I~~tvk~ 51 (90)
T PF11919_consen 19 AFPY--DVPPWM-------PEVLEELARHANDPQPIRTTVKK 51 (90)
T ss_dssp T-S----SS-HH-------HHHHHHHHTTSSS-SSHHHHTHH
T ss_pred HcCC--CCcccH-------HHHHHHHHHHhCCCchHHHHHHH
Confidence 3465 456665 57888899999899988877654
No 205
>PRK09492 treR trehalose repressor; Provisional
Probab=22.40 E-value=77 Score=25.34 Aligned_cols=36 Identities=22% Similarity=0.519 Sum_probs=18.2
Q ss_pred CCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCC
Q 031854 44 GLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAP 82 (152)
Q Consensus 44 G~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlap 82 (152)
|+|+|-+-.+|.+. |.|..-|=.+|.++.++.|-.|
T Consensus 15 gVS~~TVSrvLn~~---~~vs~~tr~rV~~~a~elgY~p 50 (315)
T PRK09492 15 GVGKSTVSRVLNNE---SGVSEETRERVEAVINQHGFSP 50 (315)
T ss_pred CCCHHHHhHHhCCC---CCCCHHHHHHHHHHHHHHCCCc
Confidence 55555555555443 3445555555555555555433
No 206
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=22.24 E-value=72 Score=26.08 Aligned_cols=34 Identities=6% Similarity=0.251 Sum_probs=17.9
Q ss_pred CCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCC
Q 031854 44 GLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGL 80 (152)
Q Consensus 44 G~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGl 80 (152)
|+|+|-+-.+|... +.|..-|-.+|.++.+|-|-
T Consensus 12 GVS~~TVSrvLn~~---~~Vs~~tr~rV~~~a~elgY 45 (343)
T PRK10727 12 GVSVATVSRVINNS---PKASEASRLAVHSAMESLSY 45 (343)
T ss_pred CCCHHHHHHHhCCC---CCCCHHHHHHHHHHHHHHCC
Confidence 55555555555443 33555555555555555553
No 207
>PRK09875 putative hydrolase; Provisional
Probab=22.21 E-value=79 Score=27.33 Aligned_cols=63 Identities=22% Similarity=0.302 Sum_probs=42.3
Q ss_pred CCCCCccC-ChHHHHHHHHHHHhcCCC-----cchhhhHhhh--------------------ccCCCcee----eecchh
Q 031854 21 TPPSWLKI-SSQDVEDNICKFAKKGLT-----PSQIGVILRD--------------------SHGIAQVK----SVTGSK 70 (152)
Q Consensus 21 ~~P~Wl~~-~~eEVe~~IvklaKkG~t-----pSqIG~iLRD--------------------~~GIp~VK----~vtGkk 70 (152)
..|.|+.. +.||+.+.+++-...|+. |..||.+=-+ ..|+|-.- .-.|..
T Consensus 88 ~~p~~~~~~~~e~la~~~i~ei~~Gi~gt~ikaGvIGeiG~~~~~it~~E~kvl~Aaa~a~~~TG~pi~~Ht~~~~~g~e 167 (292)
T PRK09875 88 FFPEHVATRSVQELAQEMVDEIEQGIDGTELKAGIIAEIGSSEGKITPLEEKVFIAAALAHNQTGRPISTHTSFSTMGLE 167 (292)
T ss_pred cCCHHHhcCCHHHHHHHHHHHHHHhhccCCCcccEEEEEecCCCCCCHHHHHHHHHHHHHHHHHCCcEEEcCCCccchHH
Confidence 34777765 899999999998888875 3444433222 24554431 116778
Q ss_pred HHHHHHHcCCCCC
Q 031854 71 ILRILKAHGLAPE 83 (152)
Q Consensus 71 I~~ILk~nGlape 83 (152)
+.++|++.|+.|+
T Consensus 168 ~l~il~e~Gvd~~ 180 (292)
T PRK09875 168 QLALLQAHGVDLS 180 (292)
T ss_pred HHHHHHHcCcCcc
Confidence 8999999998764
No 208
>PLN02900 alanyl-tRNA synthetase
Probab=22.21 E-value=2.1e+02 Score=29.08 Aligned_cols=59 Identities=8% Similarity=0.116 Sum_probs=42.8
Q ss_pred HHHHHHHHHhc--CCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHHHH
Q 031854 33 VEDNICKFAKK--GLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVAI 98 (152)
Q Consensus 33 Ve~~IvklaKk--G~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv~i 98 (152)
+++.|-++.++ +.=|.+.-..|-|.||+|.= =+..|.+|+|+.-+++ ..+.+|.++-..
T Consensus 396 l~~~i~~~~~~~~~~l~g~~af~LydTyGfP~d------lt~~ia~e~g~~vD~~-~F~~~~~~~~~~ 456 (936)
T PLN02900 396 FKKALAAAKANGGPVLSGKDAFLLYDTYGFPVD------LTELMAEERGVTVDME-GFEAAMEEARER 456 (936)
T ss_pred HHHHHHHHhhcCCCcCCHHHHHHHHhccCCCHH------HHHHHHHHcCCeecHH-HHHHHHHHHHHH
Confidence 34444444432 45588999999999999962 1446889999999987 888888777543
No 209
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=22.10 E-value=2e+02 Score=18.64 Aligned_cols=35 Identities=17% Similarity=0.362 Sum_probs=25.7
Q ss_pred CCCCCCccCChHHHHH--HHHHHHhcCCCcchhhhHh
Q 031854 20 RTPPSWLKISSQDVED--NICKFAKKGLTPSQIGVIL 54 (152)
Q Consensus 20 ~~~P~Wl~~~~eEVe~--~IvklaKkG~tpSqIG~iL 54 (152)
++.-..=.+|.+||+. .|..|-+.|+|.++|-.+|
T Consensus 31 r~~~g~R~yt~~di~~l~~i~~l~~~g~~l~~i~~~l 67 (68)
T cd04763 31 RSDGGHRLFNDADIDRILEIKRWIDNGVQVSKVKKLL 67 (68)
T ss_pred cCCCCCcccCHHHHHHHHHHHHHHHcCCCHHHHHHHh
Confidence 3444445678888875 5788888999999987765
No 210
>PF11463 R-HINP1I: R.HinP1I restriction endonuclease; InterPro: IPR021107 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. Hinp1I is a type II restriction endonuclease that recognises and cleaves a palindromic tetranucleotide sequence (G/CGC) resulting in 2 nt 5' overhanging ends []. Structurally HinP1I consists of a conserved catalytic core domain, containing an active site motif SDC18QXK, and a DNA-binding domain []. ; PDB: 1YNM_A 2FKC_A 2FLC_A 2FL3_A 2FKH_B.
Probab=21.95 E-value=66 Score=27.40 Aligned_cols=51 Identities=18% Similarity=0.294 Sum_probs=29.3
Q ss_pred CCChhhHHHHHHHHHHHHHHHhHcCCccccchhhhhhH---HHHHHHHHhhhhhcee
Q 031854 82 PEIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVE---SRIHDWLATTRRQRSF 135 (152)
Q Consensus 82 peIPEDL~~LIkKAv~iRKHLe~n~KD~~sK~~L~LiE---SkI~RL~kYYk~~~~~ 135 (152)
-.+|+|+|.|++--..=-+---+|+| +++|..+.| .-=+++..++...+.+
T Consensus 66 wn~p~~i~~il~~f~ge~~p~~~~~k---~~rrmf~~Efs~~Eq~~il~wf~~Nk~l 119 (205)
T PF11463_consen 66 WNFPDNIYQILQYFTGELKPYIKNPK---DKRRMFITEFSQEEQDRILNWFNKNKIL 119 (205)
T ss_dssp H---HHHHHHHHHHHSSS--SSSTSS---SSS---GGGS-HHHHHHHHHHHHHTHHH
T ss_pred HcCCHHHHHHHHHHcccCCccccCCc---chhhhHHHhhhHHHHHHHHHHHHhccHH
Confidence 46899999998877654443444555 456666666 6677788888776543
No 211
>TIGR01075 uvrD DNA helicase II. Designed to identify uvrD members of the uvrD/rep subfamily.
Probab=21.90 E-value=53 Score=31.11 Aligned_cols=35 Identities=17% Similarity=0.196 Sum_probs=28.8
Q ss_pred hHHHHHHHHHHHhcCCCcchhhhHhhh------------ccCCCcee
Q 031854 30 SQDVEDNICKFAKKGLTPSQIGVILRD------------SHGIAQVK 64 (152)
Q Consensus 30 ~eEVe~~IvklaKkG~tpSqIG~iLRD------------~~GIp~VK 64 (152)
++.|.+.|.+|...|++++.|.+..|. ++|||...
T Consensus 325 a~~ia~~I~~l~~~g~~~~diAVL~R~~~~~~~le~~L~~~gIPy~~ 371 (715)
T TIGR01075 325 ARFVVSRIKTWQRNGGALDECAVLYRSNAQSRVLEEALLQASIPYRI 371 (715)
T ss_pred HHHHHHHHHHHHHcCCCccCEEEEEecCchHHHHHHHHHHcCCCEEE
Confidence 345777788888899999999999998 57999753
No 212
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=21.84 E-value=3.1e+02 Score=19.62 Aligned_cols=41 Identities=29% Similarity=0.287 Sum_probs=30.1
Q ss_pred CCCCCCCCCCccCChHHHHH--HHHHHHh-cCCCcchhhhHhhh
Q 031854 16 LPYKRTPPSWLKISSQDVED--NICKFAK-KGLTPSQIGVILRD 56 (152)
Q Consensus 16 ~P~~~~~P~Wl~~~~eEVe~--~IvklaK-kG~tpSqIG~iLRD 56 (152)
.|..+..+.+-.++.++|+. .|..|.+ .|++-.+|-..|.+
T Consensus 27 ~p~~r~~~g~r~Y~~~dv~~l~~I~~L~~~~G~~l~~I~~~l~~ 70 (95)
T cd04780 27 PEGRRLAPNQAEYSEAHVERLRLIRALQQEGGLPISQIKEVLDA 70 (95)
T ss_pred CCCcCCCCCCeecCHHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 35555556555789998875 4667776 69999999888865
No 213
>PRK01490 tig trigger factor; Provisional
Probab=21.77 E-value=61 Score=28.61 Aligned_cols=52 Identities=23% Similarity=0.424 Sum_probs=26.6
Q ss_pred ccCChHHHHHHHHHHHh-cCCCcchhhhHhhhccCCCcee-eecchhHHHHHHH
Q 031854 26 LKISSQDVEDNICKFAK-KGLTPSQIGVILRDSHGIAQVK-SVTGSKILRILKA 77 (152)
Q Consensus 26 l~~~~eEVe~~IvklaK-kG~tpSqIG~iLRD~~GIp~VK-~vtGkkI~~ILk~ 77 (152)
+..|.+||++.+.++|. -|+++.+|=..+-++-....++ .++-.|+.+.|.+
T Consensus 366 i~vs~eei~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~Kv~~~l~~ 419 (435)
T PRK01490 366 IEVSDEEVKAEIEEMASQYGQPPEVIEFYLKNPQLLAALRADVLEEKVVDFLLE 419 (435)
T ss_pred CCCCHHHHHHHHHHHHHHcCCCHHHHHHHHhChhhHHHHHHHHHHHHHHHHHHH
Confidence 45677788888877775 3555555444433221111222 3444455444444
No 214
>PF14230 DUF4333: Domain of unknown function (DUF4333)
Probab=21.77 E-value=1.1e+02 Score=21.42 Aligned_cols=25 Identities=20% Similarity=0.494 Sum_probs=19.2
Q ss_pred cCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCcee
Q 031854 27 KISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVK 64 (152)
Q Consensus 27 ~~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK 64 (152)
.++.+++|+.|.+ .|.++||++.+.
T Consensus 19 ~ld~~~ve~~v~~-------------~L~~~~G~~~~s 43 (80)
T PF14230_consen 19 VLDKAQVEQGVAQ-------------VLTEQYGVTPVS 43 (80)
T ss_pred eECHHHHHHHHHH-------------HHHHhhCCCCCE
Confidence 5689999987765 566889987664
No 215
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=21.75 E-value=1.5e+02 Score=21.61 Aligned_cols=39 Identities=23% Similarity=0.247 Sum_probs=30.0
Q ss_pred CCCCCCCCCccCChHHHHH--HHHHHHhcCCCcchhhhHhhh
Q 031854 17 PYKRTPPSWLKISSQDVED--NICKFAKKGLTPSQIGVILRD 56 (152)
Q Consensus 17 P~~~~~P~Wl~~~~eEVe~--~IvklaKkG~tpSqIG~iLRD 56 (152)
|.++.. ..=.++.+++.. .|..|.+-|+|.++|..++..
T Consensus 28 p~~~~~-~yR~Y~~~d~~~l~~I~~lr~~G~sl~eI~~~l~~ 68 (116)
T cd04769 28 SPKRSG-NYRVYDAQHVECLRFIKEARQLGFTLAELKAIFAG 68 (116)
T ss_pred CCCCCC-CceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 444443 556678888875 689999999999999988753
No 216
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=21.68 E-value=1.6e+02 Score=21.88 Aligned_cols=39 Identities=21% Similarity=0.341 Sum_probs=30.5
Q ss_pred CCCCCCCCCccCChHHHHH--HHHHHHhcCCCcchhhhHhh
Q 031854 17 PYKRTPPSWLKISSQDVED--NICKFAKKGLTPSQIGVILR 55 (152)
Q Consensus 17 P~~~~~P~Wl~~~~eEVe~--~IvklaKkG~tpSqIG~iLR 55 (152)
|..++.--+=.|+.++|+. .|..|..-|+|-++|..+|.
T Consensus 28 ~~~r~~~g~R~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~ 68 (127)
T cd01108 28 PPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLA 68 (127)
T ss_pred CCCcCCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 3445555677789998875 58889999999999998874
No 217
>PF14842 FliG_N: FliG N-terminal domain; PDB: 3HJL_A 3AJC_A 3USY_B.
Probab=21.67 E-value=89 Score=22.84 Aligned_cols=32 Identities=16% Similarity=0.358 Sum_probs=23.0
Q ss_pred cCChHHHHHHHHHHHh-cCCCcchhhhHhhhcc
Q 031854 27 KISSQDVEDNICKFAK-KGLTPSQIGVILRDSH 58 (152)
Q Consensus 27 ~~~~eEVe~~IvklaK-kG~tpSqIG~iLRD~~ 58 (152)
.++++||+.+...+++ ..+++.++-.+|.+=+
T Consensus 29 ~l~~~ei~~i~~~ma~l~~v~~~~~~~Vl~EF~ 61 (108)
T PF14842_consen 29 HLDEEEIERISREMAKLGSVSPEEVEEVLEEFY 61 (108)
T ss_dssp HS-HHHHHHHHHHHHT-----HHHHHHHHHHHH
T ss_pred cCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHH
Confidence 4689999999999999 5588888888887755
No 218
>TIGR02329 propionate_PrpR propionate catabolism operon regulatory protein PrpR. At least five distinct pathways exists for the catabolism of propionate by way of propionyl-CoA. Members of this family represent the transcriptional regulatory protein PrpR, whose gene is found in most cases divergently transcribed from an operon for the methylcitric acid cycle of propionate catabolism. 2-methylcitric acid, a catabolite by this pathway, is a coactivator of PrpR.
Probab=21.51 E-value=2e+02 Score=26.94 Aligned_cols=49 Identities=10% Similarity=0.245 Sum_probs=36.0
Q ss_pred CChHHHHHHHHHHHhcCCCc---chhhhHhhhccCCCceeeecchhHHHHHH
Q 031854 28 ISSQDVEDNICKFAKKGLTP---SQIGVILRDSHGIAQVKSVTGSKILRILK 76 (152)
Q Consensus 28 ~~~eEVe~~IvklaKkG~tp---SqIG~iLRD~~GIp~VK~vtGkkI~~ILk 76 (152)
.+.+|+++.|.+|.++|+.- ..+..-+=.++|++.|=-..|.+|...++
T Consensus 129 ~~~~e~~~~~~~l~~~G~~~viG~~~~~~~A~~~gl~~ili~s~esi~~a~~ 180 (526)
T TIGR02329 129 VTEEDARSCVNDLRARGIGAVVGAGLITDLAEQAGLHGVFLYSADSVRQAFD 180 (526)
T ss_pred cCHHHHHHHHHHHHHCCCCEEECChHHHHHHHHcCCceEEEecHHHHHHHHH
Confidence 47899999999999999864 23555666778888886666655554444
No 219
>PF05504 Spore_GerAC: Spore germination B3/ GerAC like, C-terminal ; InterPro: IPR008844 The GerAA, -AB, and -AC proteins of the Bacillus subtilis spore are required for the germination response to L-alanine as the sole germinant. Members of GerAC family are thought to be located in the inner spore membrane. Although the function of this family is unclear, they are likely to encode the components of the germination apparatus that respond directly to this germinant, mediating the spore's response [].; GO: 0009847 spore germination, 0016020 membrane; PDB: 3N54_B.
Probab=21.46 E-value=90 Score=23.43 Aligned_cols=28 Identities=25% Similarity=0.425 Sum_probs=18.0
Q ss_pred HHHHHHHHHHH-hcCCCcchhhhHhhhcc
Q 031854 31 QDVEDNICKFA-KKGLTPSQIGVILRDSH 58 (152)
Q Consensus 31 eEVe~~Ivkla-KkG~tpSqIG~iLRD~~ 58 (152)
+++++.|-++- +.|..|-.||..+|-+|
T Consensus 108 ~~~~~~i~k~q~~~~~D~lg~g~~~~~~~ 136 (171)
T PF05504_consen 108 KEIQSLIKKMQKELGVDPLGFGEYLRRKY 136 (171)
T ss_dssp HHHHHHHHHHHHTT----S-HHHHHHHH-
T ss_pred HHHHHHHHHHhhhhCcChHHHHHHHHHHC
Confidence 45666777788 99999999999999877
No 220
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=21.46 E-value=1.4e+02 Score=23.11 Aligned_cols=40 Identities=18% Similarity=0.159 Sum_probs=31.2
Q ss_pred CCCCCCCCCccCChHHHHH--HHHHHHhcCCCcchhhhHhhh
Q 031854 17 PYKRTPPSWLKISSQDVED--NICKFAKKGLTPSQIGVILRD 56 (152)
Q Consensus 17 P~~~~~P~Wl~~~~eEVe~--~IvklaKkG~tpSqIG~iLRD 56 (152)
|.++..--+=.|+.++|+. .|..|..-|+|-++|..+|..
T Consensus 35 p~~r~~~gyR~Y~~~~l~rl~~I~~lr~~G~sL~eI~~ll~~ 76 (144)
T PRK13752 35 EPDKPYGSIRRYGEADVTRVRFVKSAQRLGFSLDEIAELLRL 76 (144)
T ss_pred CCccCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 4555555566778888875 688899999999999998854
No 221
>KOG2598 consensus Phosphomethylpyrimidine kinase [Coenzyme transport and metabolism; Transcription]
Probab=21.43 E-value=2.3e+02 Score=27.28 Aligned_cols=91 Identities=25% Similarity=0.371 Sum_probs=58.8
Q ss_pred CChHHHHHHH--------HHHHhcCCCcchhhhH----hhhccCCCcee-----------eecchhHHHHHHHcC-----
Q 031854 28 ISSQDVEDNI--------CKFAKKGLTPSQIGVI----LRDSHGIAQVK-----------SVTGSKILRILKAHG----- 79 (152)
Q Consensus 28 ~~~eEVe~~I--------vklaKkG~tpSqIG~i----LRD~~GIp~VK-----------~vtGkkI~~ILk~nG----- 79 (152)
++++-|+++| |+--|-||=||+==+. +-+.+.+|.+- ...|+.|..++-|+=
T Consensus 75 lpp~~V~qqidacL~Di~C~VvKTGML~~~~I~~vi~q~l~~~~~~klVvDPVivatsG~~l~~~divsl~~e~l~P~ad 154 (523)
T KOG2598|consen 75 LPPSFVSQQIDACLSDIKCDVVKTGMLPSPEIVKVIEQSLQKFNIPKLVVDPVIVATSGSSLAGKDIVSLFIEELLPFAD 154 (523)
T ss_pred CCHHHHHHHHHHHhhcCcccEEeecCcCchHHHHHHHHHHHhhcCcceeecceEEeccCCcccCCccHHHHHHHhhhhHH
Confidence 3455555554 3445667666542221 22337777653 457888888877764
Q ss_pred -CCCCChhhHHHHHHHHHHHHHHHhHcCCccccchhhhhhHHHHHHHH
Q 031854 80 -LAPEIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHDWL 126 (152)
Q Consensus 80 -lapeIPEDL~~LIkKAv~iRKHLe~n~KD~~sK~~L~LiESkI~RL~ 126 (152)
+.|.|||- ..|-+|+++-.--.++-+...-.-++||++.
T Consensus 155 iltPNI~Ea--------~~Ll~~~~~~~~~i~~v~di~~~~~~ihk~g 194 (523)
T KOG2598|consen 155 ILTPNIPEA--------FILLKKEKREISKIQSVFDIAKDAAKIHKLG 194 (523)
T ss_pred HhCCChHHH--------HHHHhhcccCCcccccHHHHHHHHHHHHhcC
Confidence 67888874 4566776666666777788888888999886
No 222
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=21.40 E-value=81 Score=25.60 Aligned_cols=20 Identities=15% Similarity=0.227 Sum_probs=9.1
Q ss_pred HHHHHHHHHHHh-cCCCcchh
Q 031854 31 QDVEDNICKFAK-KGLTPSQI 50 (152)
Q Consensus 31 eEVe~~IvklaK-kG~tpSqI 50 (152)
+|..+.|.+.|+ -||.|+..
T Consensus 32 ~~tr~rV~~~a~~lgY~pn~~ 52 (327)
T PRK10339 32 EETKHRILEIAEKLEYKTSSA 52 (327)
T ss_pred HHHHHHHHHHHHHhCCCCchh
Confidence 444444444332 45555543
No 223
>PF03825 Nuc_H_symport: Nucleoside H+ symporter
Probab=21.37 E-value=46 Score=29.26 Aligned_cols=16 Identities=31% Similarity=0.748 Sum_probs=13.2
Q ss_pred HHHhcCCCcchhhhHh
Q 031854 39 KFAKKGLTPSQIGVIL 54 (152)
Q Consensus 39 klaKkG~tpSqIG~iL 54 (152)
=|..+|+|++|||+++
T Consensus 28 ~L~~~G~s~~qIG~l~ 43 (400)
T PF03825_consen 28 YLESRGFSGTQIGILL 43 (400)
T ss_pred HHHhCCCCHHHHHHHH
Confidence 4677899999999875
No 224
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=21.26 E-value=79 Score=24.21 Aligned_cols=29 Identities=28% Similarity=0.342 Sum_probs=21.4
Q ss_pred HHHHHHHHHhcCCCcchhhhHhhhccCCC
Q 031854 33 VEDNICKFAKKGLTPSQIGVILRDSHGIA 61 (152)
Q Consensus 33 Ve~~IvklaKkG~tpSqIG~iLRD~~GIp 61 (152)
.++.|.=|.+||+|..+|-..|+..=.-+
T Consensus 23 ~~~k~~FL~sKGLt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 23 LEKKIAFLESKGLTEEEIDEALGRAGSPP 51 (136)
T ss_dssp HHHHHHHHHHCT--HHHHHHHHHHHT--S
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHhcCCcc
Confidence 67888999999999999999998754433
No 225
>PRK11880 pyrroline-5-carboxylate reductase; Reviewed
Probab=21.11 E-value=1.2e+02 Score=24.31 Aligned_cols=65 Identities=18% Similarity=0.292 Sum_probs=45.0
Q ss_pred CChHHHHHHHHHHH--------hcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHHHHH
Q 031854 28 ISSQDVEDNICKFA--------KKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVAIR 99 (152)
Q Consensus 28 ~~~eEVe~~Ivkla--------KkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv~iR 99 (152)
+++++..+.+..+. +.|.+|+++ +|+--.|. =|-....+.|+++|+...+.+-|....+||+.+-
T Consensus 193 l~~~~a~~~~~~~~~g~~~~~~~~~~~~~~l----~~~v~tpg---G~t~~gl~~l~~~g~~~~~~~a~~~~~~ra~~~~ 265 (267)
T PRK11880 193 LPREQARKLAAQTVLGAAKLLLESGEHPAEL----RDNVTSPG---GTTIAALRVLEEKGLRAAVIEAVQAAAKRSKELG 265 (267)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHhcCCCHHHH----HHhCCCCc---HHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHhc
Confidence 45666666655554 467887754 44443332 2334466799999999999999999999998873
No 226
>cd00423 Pterin_binding Pterin binding enzymes. This family includes dihydropteroate synthase (DHPS) and cobalamin-dependent methyltransferases such as methyltetrahydrofolate, corrinoid iron-sulfur protein methyltransferase (MeTr) and methionine synthase (MetH). DHPS, a functional homodimer, catalyzes the condensation of p-aminobenzoic acid (pABA) in the de novo biosynthesis of folate, which is an essential cofactor in both nucleic acid and protein biosynthesis. Prokaryotes (and some lower eukaryotes) must synthesize folate de novo, while higher eukaryotes are able to utilize dietary folate and therefore lack DHPS. Sulfonamide drugs, which are substrate analogs of pABA, target DHPS. Cobalamin-dependent methyltransferases catalyze the transfer of a methyl group via a methyl- cob(III)amide intermediate. These include MeTr, a functional heterodimer, and the folate binding domain of MetH.
Probab=20.87 E-value=81 Score=26.11 Aligned_cols=44 Identities=20% Similarity=0.336 Sum_probs=26.0
Q ss_pred CCCCCCCCCCcCCCCCCCCCCCccCChHHHHHHHHHHHhcCCCcchh
Q 031854 4 MHSRGKGISASALPYKRTPPSWLKISSQDVEDNICKFAKKGLTPSQI 50 (152)
Q Consensus 4 Mh~~~kG~S~S~~P~~~~~P~Wl~~~~eEVe~~IvklaKkG~tpSqI 50 (152)
||.++.|...+..|+ .|.=..--.+.+++.|.++.+.|+++.+|
T Consensus 126 m~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~i~~~~~~Gi~~~~I 169 (258)
T cd00423 126 MHMDGTPQTMQNNPY---YADVVDEVVEFLEERVEAATEAGIPPEDI 169 (258)
T ss_pred ECcCCCCcccccCCC---cchHHHHHHHHHHHHHHHHHHcCCCHHHE
Confidence 677776665444332 12111112466777888888999877665
No 227
>PF13783 DUF4177: Domain of unknown function (DUF4177)
Probab=20.47 E-value=99 Score=20.24 Aligned_cols=20 Identities=25% Similarity=0.539 Sum_probs=17.6
Q ss_pred CChHHHHHHHHHHHhcCCCc
Q 031854 28 ISSQDVEDNICKFAKKGLTP 47 (152)
Q Consensus 28 ~~~eEVe~~IvklaKkG~tp 47 (152)
.+.+++++.+.++|++|---
T Consensus 17 ~~~~~~~~~Ln~~g~eGWeL 36 (61)
T PF13783_consen 17 IDPEDLEEILNEYGKEGWEL 36 (61)
T ss_pred CCHHHHHHHHHHHHhCCcEE
Confidence 68999999999999999643
No 228
>PRK14702 insertion element IS2 transposase InsD; Provisional
Probab=20.43 E-value=2.2e+02 Score=23.82 Aligned_cols=52 Identities=15% Similarity=0.293 Sum_probs=37.3
Q ss_pred cCChHHHHHHHHHHHhcC--CCcchhhhHhhhc---cCCCceeeecchhHHHHHHHcCCC
Q 031854 27 KISSQDVEDNICKFAKKG--LTPSQIGVILRDS---HGIAQVKSVTGSKILRILKAHGLA 81 (152)
Q Consensus 27 ~~~~eEVe~~IvklaKkG--~tpSqIG~iLRD~---~GIp~VK~vtGkkI~~ILk~nGla 81 (152)
....+++.+.|.+++.+. +-.-.|-..|+++ .|++. |.-+.|.++|+++||.
T Consensus 7 ~~~~~~l~~~I~~~~~~~~~yG~rri~~~L~~~~~~~g~~~---v~~krV~rlmr~~gL~ 63 (262)
T PRK14702 7 HTDDTDVLLRIHHVIGELPTYGYRRVWALLRRQAELDGMPA---INAKRVYRLMRQNALL 63 (262)
T ss_pred CcchHHHHHHHHHHHHhCcccChHHHHHHHHhhhcccCccc---cCHHHHHHHHHHhCCc
Confidence 446788888999886542 3334555789885 46533 5668899999999995
No 229
>PRK13317 pantothenate kinase; Provisional
Probab=20.42 E-value=1.9e+02 Score=24.72 Aligned_cols=57 Identities=16% Similarity=0.126 Sum_probs=36.4
Q ss_pred HHHHHHHhcCCCcchhhhHhhhccCC-------CceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHHH
Q 031854 35 DNICKFAKKGLTPSQIGVILRDSHGI-------AQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVA 97 (152)
Q Consensus 35 ~~IvklaKkG~tpSqIG~iLRD~~GI-------p~VK~vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv~ 97 (152)
+.+.+||++|- ++-+...+.|-||. -..=.+.|+ + .-|...|.. +||+..=+-.+|+
T Consensus 144 ~el~~la~~g~-~~~~Dl~v~dIy~~~~~~l~i~s~csvFak-v-~~l~~~g~~---~eDIaasl~~~v~ 207 (277)
T PRK13317 144 EQLIELAKHGD-RNNIDLKVGDIYKGPLPPIPGDLTASNFGK-V-LHHLDSEFT---SSDILAGVIGLVG 207 (277)
T ss_pred HHHHHHHhcCC-CccccceeccccCCCCCCCCCceeEehhhh-h-hhhhccCCC---HHHHHHHHHHHHH
Confidence 34678999994 44588888999987 233366677 3 233344543 7888765555554
No 230
>PF04233 Phage_Mu_F: Phage Mu protein F like protein; InterPro: IPR006528 This domain is found exclusively in phage-related proteins, internally or toward the C terminus. Some of these proteins have been identified as being involved in phage head morphogenesis [, ].
Probab=20.30 E-value=95 Score=21.62 Aligned_cols=30 Identities=23% Similarity=0.491 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHhcCCCcchhhhHhhhccCC
Q 031854 31 QDVEDNICKFAKKGLTPSQIGVILRDSHGI 60 (152)
Q Consensus 31 eEVe~~IvklaKkG~tpSqIG~iLRD~~GI 60 (152)
++|++.|.+-...|.++.+|-..|++..++
T Consensus 1 ~~i~~~v~~~i~~G~~~~~~~~~l~~~~~~ 30 (112)
T PF04233_consen 1 DRIRQAVTQGIERGKSPQEIAKRLRDRGGV 30 (112)
T ss_pred ChHHHHHHHHHHcCCCHHHHHHHHHHHhCc
Confidence 468888888899999999999999999443
No 231
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=20.19 E-value=2.1e+02 Score=20.61 Aligned_cols=39 Identities=21% Similarity=0.151 Sum_probs=29.7
Q ss_pred CCCCCCccCChHHHHHH--HHHH-HhcCCCcchhhhHhhhcc
Q 031854 20 RTPPSWLKISSQDVEDN--ICKF-AKKGLTPSQIGVILRDSH 58 (152)
Q Consensus 20 ~~~P~Wl~~~~eEVe~~--Ivkl-aKkG~tpSqIG~iLRD~~ 58 (152)
+...-.-.+|.+||..+ |..| ...|+|-++|-.+|-+..
T Consensus 31 r~~~g~R~Yt~~di~~l~~I~~llr~~G~~l~~i~~~l~~~~ 72 (99)
T cd04765 31 KRAGGRRYYRPKDVELLLLIKHLLYEKGYTIEGAKQALKEDG 72 (99)
T ss_pred CCCCCCeeeCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHhcc
Confidence 44555667899999976 6665 678999999998887654
No 232
>TIGR00134 gatE_arch glutamyl-tRNA(Gln) amidotransferase, subunit E. The Archaea have an Asp-tRNA(Asn) amidotransferase instead of an Asp--tRNA ligase, but the genes have not been identified. It is likely that this protein replaces gatB in Asp-tRNA(Asn) amidotransferase but that both enzymes share gatA.
Probab=20.08 E-value=3e+02 Score=26.75 Aligned_cols=63 Identities=11% Similarity=0.081 Sum_probs=49.2
Q ss_pred CChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHHH
Q 031854 28 ISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVA 97 (152)
Q Consensus 28 ~~~eEVe~~IvklaKkG~tpSqIG~iLRD~~GIp~VK~vtGkkI~~ILk~nGlapeIPEDL~~LIkKAv~ 97 (152)
++++.+.+++.-++..-+|..++-.+|..-. -+|.+...|.+++||..-=.|+|..+|+.+++
T Consensus 513 ~~~~~l~~l~~~~~~g~is~~~~k~vl~~~~-------~~~~~~~~iiee~gL~qlsdeel~~iV~evI~ 575 (620)
T TIGR00134 513 LELRHLRDAIKLLEVGKIAKEGLREILKCMC-------DEPLAAEDAARKLKLKLLAEEEIESIIQEIIE 575 (620)
T ss_pred CCHHHHHHHHHHHHcCCCcHHHHHHHHHHHH-------hCCCCHHHHHHHcCCcCCCHHHHHHHHHHHHH
Confidence 5789999998888888888888887877655 24456778999999877666788899888864
No 233
>cd08643 DNA_pol_A_pol_I_B Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuclease. Pol I uses its 5
Probab=20.08 E-value=1.4e+02 Score=27.50 Aligned_cols=53 Identities=15% Similarity=0.186 Sum_probs=32.5
Q ss_pred CcchhhhHhhhccCCCcee-eecchhH--HHHHHHcCCCCCChhhHHHHHHHHHHHHHHHhH
Q 031854 46 TPSQIGVILRDSHGIAQVK-SVTGSKI--LRILKAHGLAPEIPEDLYHLIKKAVAIRKHLER 104 (152)
Q Consensus 46 tpSqIG~iLRD~~GIp~VK-~vtGkkI--~~ILk~nGlapeIPEDL~~LIkKAv~iRKHLe~ 104 (152)
||-|||.+|-|..|+|-.+ .-||+-. -.+|++-. -++ -.+|-+...+.|.+..
T Consensus 69 S~~ql~~~L~~~lg~~~~~~t~~G~~std~~vL~~l~--~p~----~~~ileyr~l~K~~st 124 (429)
T cd08643 69 SRKHIAKRLKAKYGWEPQEFTESGEPKVDEDVLSKLD--YPE----AKLLAEYLLVQKRLGQ 124 (429)
T ss_pred CHHHHHHHHHHhcCCCCCCcCCCCCCCcCHHHHHhcc--chH----HHHHHHHHHHHHHHHH
Confidence 7889999999999998554 3456422 25666532 222 3455555556565544
Done!