Query 032468
Match_columns 140
No_of_seqs 124 out of 248
Neff 3.7
Searched_HMMs 46136
Date Fri Mar 29 14:28:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032468.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032468hhsearch_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 6.3E-81 1.4E-85 484.7 14.3 137 4-140 1-137 (148)
2 PRK08561 rps15p 30S ribosomal 100.0 2.9E-77 6.2E-82 465.8 15.5 140 1-140 1-140 (151)
3 KOG0400 40S ribosomal protein 100.0 2E-77 4.3E-82 462.8 9.8 140 1-140 1-140 (151)
4 PF08069 Ribosomal_S13_N: Ribo 100.0 9.3E-38 2E-42 212.2 3.4 60 1-60 1-60 (60)
5 COG0184 RpsO Ribosomal protein 99.9 5.8E-27 1.3E-31 169.5 6.1 81 44-140 1-81 (89)
6 cd00353 Ribosomal_S15p_S13e Ri 99.6 2.9E-15 6.3E-20 105.3 6.2 69 71-139 2-74 (80)
7 PF00312 Ribosomal_S15: Riboso 99.5 6.3E-15 1.4E-19 104.1 5.4 68 66-133 2-69 (83)
8 cd00677 S15_NS1_EPRS_RNA-bind 99.1 9.2E-11 2E-15 74.3 5.4 46 85-130 1-46 (46)
9 TIGR00952 S15_bact ribosomal p 97.4 0.00041 9E-09 50.1 5.6 47 87-133 25-71 (86)
10 CHL00027 rps15 ribosomal prote 97.3 0.00082 1.8E-08 49.2 5.7 48 86-133 24-71 (90)
11 PRK05626 rpsO 30S ribosomal pr 97.2 0.00095 2.1E-08 48.5 5.5 46 88-133 29-74 (89)
12 PTZ00119 40S ribosomal protein 96.7 0.0028 6.1E-08 54.9 5.2 64 70-133 109-176 (302)
13 COG2257 Uncharacterized homolo 95.4 0.12 2.6E-06 38.3 7.6 70 20-106 20-89 (92)
14 PF13565 HTH_32: Homeodomain-l 92.1 0.33 7.1E-06 32.0 4.3 44 30-75 32-77 (77)
15 TIGR00789 flhB_rel flhB C-term 87.6 2.1 4.6E-05 30.5 5.6 60 21-97 16-75 (82)
16 PF13276 HTH_21: HTH-like doma 87.4 1.6 3.4E-05 28.0 4.5 51 31-85 4-57 (60)
17 COG3328 Transposase and inacti 85.5 0.92 2E-05 40.3 3.5 48 9-60 69-116 (379)
18 PF07750 GcrA: GcrA cell cycle 83.6 0.98 2.1E-05 35.6 2.6 25 31-55 5-29 (162)
19 PF00292 PAX: 'Paired box' dom 83.1 0.73 1.6E-05 35.5 1.6 30 30-59 19-48 (125)
20 PHA02591 hypothetical protein; 80.2 1.5 3.3E-05 31.9 2.3 28 27-54 42-69 (83)
21 PF00356 LacI: Bacterial regul 79.5 1.5 3.3E-05 27.9 1.9 41 39-82 4-45 (46)
22 PF13361 UvrD_C: UvrD-like hel 77.9 2 4.4E-05 33.8 2.6 43 31-81 61-103 (351)
23 cd01106 HTH_TipAL-Mta Helix-Tu 75.7 25 0.00054 24.8 7.7 40 17-56 28-69 (103)
24 PRK01322 6-carboxyhexanoate--C 74.9 2.8 6.1E-05 35.6 2.8 78 3-99 6-112 (242)
25 PRK15364 pathogenicity island 74.0 11 0.00024 31.3 6.0 80 30-117 78-162 (196)
26 KOG1802 RNA helicase nonsense 73.4 1.9 4.1E-05 42.2 1.6 51 29-92 708-760 (935)
27 COG1964 Predicted Fe-S oxidore 73.3 11 0.00024 35.0 6.4 78 7-109 69-149 (475)
28 PHA02517 putative transposase 73.2 6.3 0.00014 31.7 4.3 48 30-82 28-78 (277)
29 COG1202 Superfamily II helicas 73.1 2.3 5.1E-05 41.1 2.1 45 33-98 755-799 (830)
30 TIGR00328 flhB flagellar biosy 72.6 14 0.00031 32.4 6.7 61 21-98 278-339 (347)
31 PF15652 Tox-SHH: HNH/Endo VII 72.6 3.3 7.2E-05 31.1 2.4 34 25-58 63-96 (100)
32 PRK13902 alaS alanyl-tRNA synt 70.3 11 0.00024 37.0 6.0 55 36-96 419-474 (900)
33 PF02899 Phage_int_SAM_1: Phag 70.3 5.7 0.00012 25.7 2.9 33 21-53 37-69 (84)
34 PF11740 KfrA_N: Plasmid repli 69.8 8.5 0.00018 27.4 4.0 58 28-92 1-67 (120)
35 PF02885 Glycos_trans_3N: Glyc 69.5 5.1 0.00011 26.5 2.6 29 27-55 14-42 (66)
36 PF13936 HTH_38: Helix-turn-he 68.8 2.9 6.3E-05 25.9 1.2 26 28-54 5-30 (44)
37 smart00354 HTH_LACI helix_turn 68.8 5.8 0.00013 26.4 2.7 39 43-84 10-48 (70)
38 PF10593 Z1: Z1 domain; Inter 68.6 1.3 2.9E-05 36.5 -0.5 58 1-58 172-233 (239)
39 PF13551 HTH_29: Winged helix- 68.5 23 0.00049 24.1 5.7 53 21-79 52-112 (112)
40 PF00872 Transposase_mut: Tran 67.0 4.7 0.0001 35.0 2.5 39 22-61 93-132 (381)
41 PRK05702 flhB flagellar biosyn 66.4 24 0.00051 31.2 6.7 67 21-104 285-352 (359)
42 TIGR03859 PQQ_PqqD coenzyme PQ 66.3 6.1 0.00013 27.3 2.5 53 28-80 27-79 (81)
43 PRK06298 type III secretion sy 65.8 27 0.00059 30.8 7.0 71 21-108 279-351 (356)
44 PF06983 3-dmu-9_3-mt: 3-demet 65.4 3 6.5E-05 30.5 0.9 32 29-61 81-112 (116)
45 KOG3862 Transcription factor P 65.2 12 0.00027 33.0 4.7 50 30-85 27-76 (327)
46 smart00845 GatB_Yqey GatB doma 65.0 30 0.00064 26.1 6.3 64 27-97 38-102 (147)
47 PF11338 DUF3140: Protein of u 64.7 15 0.00032 27.2 4.4 38 65-104 37-75 (92)
48 PF02637 GatB_Yqey: GatB domai 64.5 18 0.00039 27.1 5.0 65 26-97 38-103 (148)
49 KOG3517 Transcription factor P 61.8 5.8 0.00013 34.8 2.1 31 30-60 22-52 (334)
50 TIGR01204 bioW 6-carboxyhexano 61.8 6.3 0.00014 33.4 2.2 62 29-99 15-104 (232)
51 COG3415 Transposase and inacti 60.3 27 0.00059 27.1 5.4 66 14-85 52-117 (138)
52 PF13592 HTH_33: Winged helix- 59.3 8.7 0.00019 25.0 2.2 37 46-86 6-42 (60)
53 PF07508 Recombinase: Recombin 58.4 22 0.00048 24.1 4.2 48 30-78 3-52 (102)
54 PF00196 GerE: Bacterial regul 58.3 11 0.00024 23.8 2.5 25 28-54 4-28 (58)
55 cd08045 TAF4 TATA Binding Prot 57.9 17 0.00037 29.2 4.0 33 65-98 48-80 (212)
56 PF06056 Terminase_5: Putative 56.4 9.7 0.00021 25.3 2.0 26 32-61 1-26 (58)
57 smart00422 HTH_MERR helix_turn 56.2 30 0.00065 21.9 4.3 36 20-55 31-68 (70)
58 smart00550 Zalpha Z-DNA-bindin 56.0 22 0.00049 23.6 3.8 49 28-83 2-54 (68)
59 cd01104 HTH_MlrA-CarA Helix-Tu 55.4 27 0.00059 22.1 4.0 32 23-54 34-67 (68)
60 cd04766 HTH_HspR Helix-Turn-He 53.9 68 0.0015 22.1 6.1 39 16-55 28-69 (91)
61 PF12990 DUF3874: Domain of un 53.9 12 0.00027 26.2 2.3 35 45-80 26-60 (73)
62 COG3028 Uncharacterized protei 53.8 22 0.00048 29.4 4.1 62 44-119 26-87 (187)
63 PF02796 HTH_7: Helix-turn-hel 53.2 9.2 0.0002 23.5 1.4 26 28-54 6-31 (45)
64 TIGR03683 A-tRNA_syn_arch alan 52.7 30 0.00065 34.1 5.5 55 36-96 423-478 (902)
65 COG2445 Uncharacterized conser 52.6 89 0.0019 24.2 7.1 63 49-116 50-112 (138)
66 PF13411 MerR_1: MerR HTH fami 52.3 17 0.00036 23.2 2.6 39 18-56 28-68 (69)
67 cd01392 HTH_LacI Helix-turn-he 52.2 12 0.00026 22.6 1.9 39 43-84 7-45 (52)
68 cd00592 HTH_MerR-like Helix-Tu 51.9 32 0.00069 23.7 4.2 40 17-56 27-68 (100)
69 smart00733 Mterf Mitochondrial 50.7 22 0.00047 18.4 2.6 27 20-46 5-31 (31)
70 PRK13413 mpi multiple promoter 48.3 35 0.00076 26.5 4.3 53 16-81 147-199 (200)
71 COG5352 Uncharacterized protei 47.7 16 0.00035 29.5 2.4 24 31-54 5-28 (169)
72 PRK14810 formamidopyrimidine-D 47.2 63 0.0014 27.0 5.9 71 18-100 131-210 (272)
73 TIGR00180 parB_part ParB-like 46.6 92 0.002 24.2 6.4 55 36-94 94-156 (187)
74 PF04947 Pox_VLTF3: Poxvirus L 46.3 76 0.0016 25.3 6.0 36 28-79 31-66 (171)
75 PF13495 Phage_int_SAM_4: Phag 45.4 23 0.0005 23.1 2.5 30 26-55 39-69 (85)
76 TIGR01293 Kv_beta voltage-depe 44.8 50 0.0011 27.4 5.0 60 34-95 251-316 (317)
77 smart00421 HTH_LUXR helix_turn 44.8 29 0.00063 20.2 2.7 25 28-54 4-28 (58)
78 cd03527 RuBisCO_small Ribulose 44.4 21 0.00045 26.5 2.4 22 27-48 11-32 (99)
79 PLN02389 biotin synthase 43.9 30 0.00066 30.5 3.7 38 22-59 110-147 (379)
80 PF01411 tRNA-synt_2c: tRNA sy 43.8 16 0.00036 33.7 2.1 55 31-91 367-421 (552)
81 PF00690 Cation_ATPase_N: Cati 43.2 14 0.0003 24.2 1.2 53 25-78 1-53 (69)
82 PF10752 DUF2533: Protein of u 43.1 22 0.00048 26.0 2.3 20 30-49 50-69 (84)
83 PF11181 YflT: Heat induced st 42.5 15 0.00034 26.1 1.4 32 29-60 8-39 (103)
84 cd04788 HTH_NolA-AlbR Helix-Tu 42.4 46 0.00099 23.4 3.8 40 17-56 28-69 (96)
85 PF03918 CcmH: Cytochrome C bi 42.1 20 0.00043 27.9 2.0 35 29-64 58-92 (148)
86 PF01244 Peptidase_M19: Membra 42.0 36 0.00078 29.1 3.8 41 23-77 280-320 (320)
87 COG2771 CsgD DNA-binding HTH d 41.2 26 0.00056 21.5 2.2 24 34-57 9-32 (65)
88 COG2082 CobH Precorrin isomera 41.0 44 0.00095 27.9 4.0 69 10-83 82-156 (210)
89 PF15051 FAM198: FAM198 protei 40.5 23 0.0005 31.5 2.4 24 13-38 1-24 (326)
90 PF10929 DUF2811: Protein of u 40.3 26 0.00056 24.0 2.1 22 80-107 2-23 (57)
91 PF12188 STAT2_C: Signal trans 39.8 8.3 0.00018 26.3 -0.3 11 81-91 6-16 (56)
92 PRK12721 secretion system appa 39.8 89 0.0019 27.5 5.9 62 20-98 277-339 (349)
93 PRK10014 DNA-binding transcrip 39.7 28 0.0006 27.9 2.6 37 43-82 16-52 (342)
94 cd01105 HTH_GlnR-like Helix-Tu 39.5 61 0.0013 22.4 4.0 34 24-57 36-71 (88)
95 PRK01584 alanyl-tRNA synthetas 39.4 82 0.0018 29.9 6.0 56 33-95 375-430 (594)
96 PF14361 RsbRD_N: RsbT co-anta 38.9 27 0.00058 24.8 2.2 36 18-54 56-91 (105)
97 cd04782 HTH_BltR Helix-Turn-He 38.6 64 0.0014 22.7 4.1 41 16-56 27-69 (97)
98 cd04786 HTH_MerR-like_sg7 Heli 38.6 1.7E+02 0.0036 21.9 7.7 40 17-56 28-69 (131)
99 KOG4279 Serine/threonine prote 38.3 31 0.00068 34.8 3.2 43 56-98 1003-1048(1226)
100 PRK09108 type III secretion sy 38.0 1.2E+02 0.0027 26.7 6.5 66 21-103 280-345 (353)
101 TIGR00344 alaS alanine--tRNA l 37.4 84 0.0018 30.9 5.9 54 35-96 373-426 (851)
102 PF09682 Holin_LLH: Phage holi 37.4 59 0.0013 23.6 3.9 28 70-98 76-103 (108)
103 PRK05477 gatB aspartyl/glutamy 37.0 1.1E+02 0.0023 28.3 6.2 64 27-97 365-429 (474)
104 PRK09912 L-glyceraldehyde 3-ph 35.9 1.2E+02 0.0027 25.6 6.1 63 32-96 265-332 (346)
105 PF12832 MFS_1_like: MFS_1 lik 35.8 19 0.00041 24.6 1.0 15 40-54 27-41 (77)
106 PF05931 AgrD: Staphylococcal 35.3 22 0.00047 23.2 1.1 12 81-92 33-44 (45)
107 TIGR03147 cyt_nit_nrfF cytochr 35.3 45 0.00098 25.8 3.0 31 30-60 59-89 (126)
108 PF05698 Trigger_C: Bacterial 35.1 13 0.00027 27.1 -0.0 34 26-59 109-143 (162)
109 cd00569 HTH_Hin_like Helix-tur 35.0 53 0.0011 16.3 2.5 23 32-54 9-31 (42)
110 cd04768 HTH_BmrR-like Helix-Tu 34.6 76 0.0017 22.2 4.0 42 16-57 27-70 (96)
111 PF12025 Phage_C: Phage protei 34.5 13 0.00029 26.1 0.0 31 49-80 36-67 (68)
112 PRK02228 V-type ATP synthase s 34.5 38 0.00083 24.3 2.4 62 28-98 27-96 (100)
113 PF09950 DUF2184: Uncharacteri 34.2 59 0.0013 26.8 3.8 53 25-82 102-168 (249)
114 smart00088 PINT motif in prote 34.2 37 0.00081 22.6 2.2 36 26-65 34-69 (88)
115 smart00753 PAM PCI/PINT associ 34.2 37 0.00081 22.6 2.2 36 26-65 34-69 (88)
116 PRK10401 DNA-binding transcrip 34.1 38 0.00083 27.4 2.6 38 43-83 11-48 (346)
117 TIGR00593 pola DNA polymerase 34.1 1.1E+02 0.0025 30.1 6.2 48 30-77 523-578 (887)
118 TIGR02051 MerR Hg(II)-responsi 33.9 1.2E+02 0.0026 22.2 5.0 40 17-56 27-68 (124)
119 PF10078 DUF2316: Uncharacteri 33.4 1.4E+02 0.003 21.8 5.2 51 36-96 15-65 (89)
120 TIGR01404 FlhB_rel_III type II 33.4 1.3E+02 0.0028 26.4 5.9 59 21-96 277-336 (342)
121 cd04784 HTH_CadR-PbrR Helix-Tu 33.1 60 0.0013 23.7 3.3 40 17-56 28-69 (127)
122 KOG1575 Voltage-gated shaker-l 32.9 1.1E+02 0.0023 27.3 5.3 48 31-80 257-306 (336)
123 PF12759 HTH_Tnp_IS1: InsA C-t 32.8 41 0.00089 22.1 2.1 21 31-51 8-28 (46)
124 COG3530 Uncharacterized protei 32.8 42 0.00091 23.8 2.3 22 34-55 29-50 (71)
125 PRK12772 bifunctional flagella 32.6 1.2E+02 0.0026 28.5 6.0 60 21-97 541-601 (609)
126 PLN02751 glutamyl-tRNA(Gln) am 32.6 1.4E+02 0.0031 28.2 6.3 63 27-97 432-496 (544)
127 PF14475 Mso1_Sec1_bdg: Sec1-b 32.5 38 0.00081 21.7 1.8 20 120-139 20-40 (41)
128 PF11829 DUF3349: Protein of u 32.5 54 0.0012 24.2 3.0 21 28-48 36-56 (96)
129 PF14420 Clr5: Clr5 domain 32.5 57 0.0012 21.0 2.8 31 31-61 6-37 (54)
130 PLN02641 anthranilate phosphor 31.9 45 0.00097 29.2 2.9 28 27-55 16-43 (343)
131 PRK15320 transcriptional activ 31.8 87 0.0019 26.9 4.4 70 24-104 157-228 (251)
132 PF01402 RHH_1: Ribbon-helix-h 31.8 38 0.00082 19.6 1.7 25 30-54 7-32 (39)
133 PRK09875 putative hydrolase; P 31.7 45 0.00099 28.4 2.8 63 21-83 88-180 (292)
134 PF00476 DNA_pol_A: DNA polyme 31.7 1.3E+02 0.0029 26.0 5.7 48 31-78 18-75 (383)
135 PF05402 PqqD: Coenzyme PQQ sy 31.7 41 0.00089 21.5 2.0 35 29-63 14-48 (68)
136 PRK12773 flhB flagellar biosyn 31.5 1.6E+02 0.0034 28.6 6.6 61 20-97 576-637 (646)
137 PRK14703 glutaminyl-tRNA synth 31.4 1.4E+02 0.0031 29.2 6.4 67 24-97 658-725 (771)
138 KOG3089 Predicted DEAD-box-con 30.8 65 0.0014 28.0 3.6 33 67-99 63-95 (271)
139 PRK04028 glutamyl-tRNA(Gln) am 30.4 1.5E+02 0.0033 28.4 6.3 64 27-96 518-581 (630)
140 PF03433 EspA: EspA-like secre 30.3 17 0.00037 30.0 0.0 62 29-96 77-143 (188)
141 COG1141 Fer Ferredoxin [Energy 30.2 29 0.00063 24.1 1.1 23 75-97 35-57 (68)
142 PF09012 FeoC: FeoC like trans 30.2 49 0.0011 21.7 2.2 20 26-45 24-43 (69)
143 PRK10625 tas putative aldo-ket 30.0 1.8E+02 0.004 24.4 6.1 62 33-96 273-338 (346)
144 PF08542 Rep_fac_C: Replicatio 29.9 34 0.00075 22.9 1.5 29 27-55 17-45 (89)
145 PF09494 Slx4: Slx4 endonuclea 29.8 85 0.0018 20.8 3.3 40 27-81 21-60 (64)
146 PRK10144 formate-dependent nit 29.5 64 0.0014 25.0 3.1 31 30-60 59-89 (126)
147 COG0749 PolA DNA polymerase I 29.5 99 0.0021 29.6 4.8 59 30-88 227-292 (593)
148 PF06348 DUF1059: Protein of u 29.5 58 0.0012 21.4 2.5 19 77-96 36-54 (57)
149 PF00101 RuBisCO_small: Ribulo 29.5 40 0.00087 24.8 1.9 21 28-48 11-31 (99)
150 PRK08156 type III secretion sy 29.5 1.7E+02 0.0036 26.1 6.0 65 21-102 273-338 (361)
151 PF01325 Fe_dep_repress: Iron 29.4 43 0.00093 22.0 1.8 22 24-45 30-51 (60)
152 cd00056 ENDO3c endonuclease II 29.3 1.3E+02 0.0029 22.0 4.7 48 29-80 77-124 (158)
153 PF13812 PPR_3: Pentatricopept 28.9 70 0.0015 17.0 2.4 19 29-47 16-34 (34)
154 cd01109 HTH_YyaN Helix-Turn-He 28.9 2.2E+02 0.0047 20.3 9.8 40 17-56 28-69 (113)
155 PRK13109 flhB flagellar biosyn 28.8 2.3E+02 0.0049 25.1 6.7 65 21-102 287-352 (358)
156 cd05116 PTKc_Syk Catalytic dom 28.8 1.6E+02 0.0034 22.3 5.1 67 51-129 185-256 (257)
157 PF04926 PAP_RNA-bind: Poly(A) 28.6 24 0.00053 26.5 0.6 17 115-131 26-42 (157)
158 KOG2815 Mitochondrial/cholorop 28.6 1E+02 0.0022 26.6 4.4 45 92-136 194-238 (256)
159 PRK03002 prsA peptidylprolyl i 28.5 2.3E+02 0.0051 23.5 6.5 33 69-103 89-121 (285)
160 cd01301 rDP_like renal dipepti 28.4 96 0.0021 26.5 4.2 35 21-56 270-304 (309)
161 TIGR02417 fruct_sucro_rep D-fr 28.4 62 0.0014 25.8 2.9 39 44-82 10-48 (327)
162 PF13384 HTH_23: Homeodomain-l 28.2 34 0.00075 20.6 1.1 24 31-54 4-27 (50)
163 PLN03196 MOC1-like protein; Pr 28.2 1.2E+02 0.0027 27.6 5.1 57 28-94 87-147 (487)
164 PRK00726 murG undecaprenyldiph 27.7 1.2E+02 0.0025 24.7 4.4 66 57-122 270-351 (357)
165 PRK12468 flhB flagellar biosyn 27.4 1.9E+02 0.0041 25.9 6.0 63 21-100 285-348 (386)
166 PRK14987 gluconate operon tran 27.3 55 0.0012 26.3 2.5 35 44-81 16-50 (331)
167 PRK10974 glycerol-3-phosphate 27.0 68 0.0015 27.3 3.1 45 56-100 136-182 (438)
168 PRK10376 putative oxidoreducta 26.9 1.8E+02 0.0038 23.9 5.4 59 36-95 225-286 (290)
169 PRK09071 hypothetical protein; 26.9 65 0.0014 27.9 2.9 28 27-54 20-47 (323)
170 COG2358 Imp TRAP-type uncharac 26.8 1.2E+02 0.0026 26.8 4.6 51 82-135 260-319 (321)
171 PRK13870 transcriptional regul 26.7 50 0.0011 26.8 2.1 28 27-56 173-200 (234)
172 smart00530 HTH_XRE Helix-turn- 26.6 1.2E+02 0.0025 16.5 4.1 33 44-82 21-53 (56)
173 cd00423 Pterin_binding Pterin 26.6 54 0.0012 26.8 2.3 44 4-50 126-169 (258)
174 PRK13317 pantothenate kinase; 26.4 1.2E+02 0.0027 25.5 4.5 57 35-97 144-207 (277)
175 PF09373 PMBR: Pseudomurein-bi 26.3 61 0.0013 19.1 1.9 17 121-137 13-29 (33)
176 PRK01103 formamidopyrimidine/5 26.3 1.6E+02 0.0034 24.5 5.1 62 28-98 142-209 (274)
177 cd04773 HTH_TioE_rpt2 Second H 26.2 1.4E+02 0.003 21.4 4.2 39 17-55 28-68 (108)
178 cd08642 DNA_pol_A_pol_I_A Poly 26.2 1.1E+02 0.0024 27.4 4.3 33 30-62 13-47 (378)
179 TIGR01795 CM_mono_cladeE monof 26.2 93 0.002 22.3 3.2 71 31-103 13-88 (94)
180 PF13910 DUF4209: Domain of un 26.1 29 0.00063 24.8 0.6 45 52-96 6-55 (93)
181 PF03744 BioW: 6-carboxyhexano 26.1 51 0.0011 28.0 2.2 58 29-95 22-106 (239)
182 cd08637 DNA_pol_A_pol_I_C Poly 26.1 1.3E+02 0.0029 26.2 4.8 35 30-64 16-53 (377)
183 PF11919 DUF3437: Domain of un 26.0 49 0.0011 23.8 1.8 33 15-56 19-51 (90)
184 PF08212 Lipocalin_2: Lipocali 25.9 63 0.0014 23.8 2.4 23 28-50 116-138 (143)
185 TIGR00756 PPR pentatricopeptid 25.8 96 0.0021 16.0 2.6 20 29-48 15-34 (35)
186 PRK05755 DNA polymerase I; Pro 25.8 2.3E+02 0.0051 27.5 6.7 48 30-77 516-571 (880)
187 cd00006 PTS_IIA_man PTS_IIA, P 25.6 2.6E+02 0.0056 20.1 6.1 51 44-97 68-118 (122)
188 PF13643 DUF4145: Domain of un 25.6 1.7E+02 0.0038 19.2 4.3 51 68-119 37-87 (87)
189 TIGR00133 gatB glutamyl-tRNA(G 25.5 2.2E+02 0.0048 26.3 6.2 64 27-97 368-432 (478)
190 PRK09526 lacI lac repressor; R 25.4 66 0.0014 25.8 2.6 35 44-81 16-50 (342)
191 KOG4115 Dynein-associated prot 25.3 36 0.00079 25.5 1.0 60 30-103 2-62 (97)
192 TIGR01481 ccpA catabolite cont 25.2 68 0.0015 25.6 2.6 37 43-82 11-47 (329)
193 cd01107 HTH_BmrR Helix-Turn-He 25.1 2.6E+02 0.0056 19.9 8.0 36 23-58 35-72 (108)
194 TIGR02773 addB_Gpos ATP-depend 25.1 41 0.00089 33.4 1.6 34 31-64 319-366 (1158)
195 COG0013 AlaS Alanyl-tRNA synth 24.4 86 0.0019 31.3 3.6 54 33-92 373-426 (879)
196 COG1609 PurR Transcriptional r 24.3 70 0.0015 26.9 2.7 38 43-83 10-47 (333)
197 PRK02998 prsA peptidylprolyl i 24.0 2.9E+02 0.0062 23.0 6.2 32 69-102 87-118 (283)
198 PF08463 EcoEI_R_C: EcoEI R pr 24.0 60 0.0013 24.3 2.0 15 122-136 110-124 (164)
199 PRK01490 tig trigger factor; P 23.9 57 0.0012 28.4 2.1 52 26-77 366-419 (435)
200 PF14907 NTP_transf_5: Unchara 23.8 1.6E+02 0.0034 22.9 4.4 55 31-85 58-123 (249)
201 PF07905 PucR: Purine cataboli 23.6 1.6E+02 0.0035 21.3 4.2 24 29-52 57-80 (123)
202 PF01399 PCI: PCI domain; Int 23.3 77 0.0017 21.0 2.3 25 26-50 70-94 (105)
203 PF09098 Dehyd-heme_bind: Quin 23.1 68 0.0015 26.1 2.2 26 26-51 49-75 (167)
204 PRK14975 bifunctional 3'-5' ex 23.0 4.2E+02 0.009 24.4 7.5 30 31-61 207-240 (553)
205 smart00352 POU Found in Pit-Oc 23.0 1.7E+02 0.0037 20.8 4.0 50 28-82 4-57 (75)
206 PF03825 Nuc_H_symport: Nucleo 22.9 43 0.00093 29.1 1.1 16 39-54 28-43 (400)
207 cd01528 RHOD_2 Member of the R 22.8 1.5E+02 0.0033 19.9 3.7 46 23-69 35-92 (101)
208 cd04764 HTH_MlrA-like_sg1 Heli 22.7 1.8E+02 0.004 18.4 3.9 33 22-54 32-66 (67)
209 TIGR01075 uvrD DNA helicase II 22.7 47 0.001 31.1 1.4 35 30-64 325-371 (715)
210 TIGR01950 SoxR redox-sensitive 22.6 3.5E+02 0.0076 20.5 7.1 38 19-56 30-69 (142)
211 PF14230 DUF4333: Domain of un 22.6 1E+02 0.0023 21.2 2.9 25 27-64 19-43 (80)
212 PF04282 DUF438: Family of unk 22.6 94 0.002 21.8 2.6 25 27-51 28-52 (71)
213 COG1393 ArsC Arsenate reductas 22.5 50 0.0011 24.6 1.3 36 58-95 6-50 (117)
214 cd04763 HTH_MlrA-like Helix-Tu 22.5 2.1E+02 0.0045 18.3 4.1 35 20-54 31-67 (68)
215 smart00794 AgrD Staphylococcal 22.3 52 0.0011 21.5 1.2 12 81-92 33-44 (45)
216 PF13783 DUF4177: Domain of un 22.3 97 0.0021 20.0 2.5 20 28-47 17-36 (61)
217 cd04783 HTH_MerR1 Helix-Turn-H 22.2 1.4E+02 0.0029 21.8 3.5 40 18-57 29-70 (126)
218 PRK00252 alaS alanyl-tRNA synt 22.2 2E+02 0.0043 28.4 5.5 47 45-98 376-422 (865)
219 PF05504 Spore_GerAC: Spore ge 22.1 88 0.0019 23.2 2.6 28 31-58 108-136 (171)
220 PF14842 FliG_N: FliG N-termin 22.0 91 0.002 22.5 2.5 32 27-58 29-61 (108)
221 PRK13752 putative transcriptio 21.8 1.3E+02 0.0029 22.9 3.5 40 17-56 35-76 (144)
222 TIGR03544 DivI1A_domain DivIVA 21.8 39 0.00084 19.9 0.5 15 27-41 17-31 (34)
223 TIGR02329 propionate_PrpR prop 21.8 2E+02 0.0044 26.5 5.3 49 28-76 129-180 (526)
224 PHA02535 P terminase ATPase su 21.8 4.1E+02 0.0089 25.4 7.3 52 28-90 3-54 (581)
225 TIGR01673 holin_LLH phage holi 21.8 1.7E+02 0.0037 21.8 4.0 30 69-98 74-103 (108)
226 cd04776 HTH_GnyR Helix-Turn-He 21.7 1.9E+02 0.0042 21.1 4.3 33 24-56 33-67 (118)
227 PF01312 Bac_export_2: FlhB Hr 21.6 89 0.0019 27.2 2.8 56 23-95 282-338 (343)
228 PLN02900 alanyl-tRNA synthetas 21.6 2.2E+02 0.0049 28.5 5.8 57 34-97 397-455 (936)
229 PF11463 R-HINP1I: R.HinP1I re 21.6 33 0.00071 28.7 0.2 47 82-131 66-115 (205)
230 PF04233 Phage_Mu_F: Phage Mu 21.5 91 0.002 21.4 2.4 30 31-60 1-30 (112)
231 PF03869 Arc: Arc-like DNA bin 21.4 2.1E+02 0.0047 18.2 3.9 39 83-135 10-48 (50)
232 cd04769 HTH_MerR2 Helix-Turn-H 21.3 2E+02 0.0042 20.7 4.2 39 17-56 28-68 (116)
233 PRK09492 treR trehalose repres 21.2 91 0.002 24.7 2.6 36 44-82 15-50 (315)
234 cd04780 HTH_MerR-like_sg5 Heli 21.2 3.1E+02 0.0066 19.3 6.1 41 16-56 27-70 (95)
235 PF04695 Pex14_N: Peroxisomal 21.0 84 0.0018 23.7 2.3 29 33-61 23-51 (136)
236 cd01108 HTH_CueR Helix-Turn-He 21.0 1.8E+02 0.0038 21.3 4.0 39 17-55 28-68 (127)
237 PRK00283 xerD site-specific ty 20.9 1E+02 0.0022 23.8 2.8 31 24-54 47-77 (299)
238 PRK10727 DNA-binding transcrip 20.9 91 0.002 25.2 2.6 34 44-80 12-45 (343)
239 PF02536 mTERF: mTERF; InterP 20.7 68 0.0015 26.4 1.8 44 20-66 230-273 (345)
240 TIGR01641 phageSPP1_gp7 phage 20.5 72 0.0016 22.3 1.7 29 33-61 1-29 (108)
241 PRK13111 trpA tryptophan synth 20.4 2.9E+02 0.0062 23.1 5.5 51 10-69 117-180 (258)
242 TIGR01523 ATPase-IID_K-Na pota 20.4 93 0.002 31.1 3.0 58 20-78 2-59 (1053)
243 PF02607 B12-binding_2: B12 bi 20.4 79 0.0017 20.6 1.8 26 27-52 14-39 (79)
244 cd04765 HTH_MlrA-like_sg2 Heli 20.3 2.2E+02 0.0048 20.2 4.2 39 20-58 31-72 (99)
245 PRK10339 DNA-binding transcrip 20.3 94 0.002 24.9 2.5 36 44-80 12-47 (327)
No 1
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=100.00 E-value=6.3e-81 Score=484.68 Aligned_cols=137 Identities=84% Similarity=1.298 Sum_probs=136.5
Q ss_pred CCCCCCCCCCcCCCCCCCCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCC
Q 032468 4 MHSRGKGISASALPYKRTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPE 83 (140)
Q Consensus 4 mh~~~kG~S~S~~P~~~~~P~W~~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~ 83 (140)
||++|||+|+|++||++++|+|+++++||||++||+|||+|+||||||++|||||||||||.|||+||++||++||+||+
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 ChhhHHHHHHHHHHHHHHHhHcCCcccchhHHHHHHHHHHHHHHHHHhcCCCCCCCC
Q 032468 84 IPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHRLARYYKKTKKLPPVWK 140 (140)
Q Consensus 84 iPEDL~~LikKAv~~RkHLe~n~kD~~~k~~L~LiESkI~RL~rYYk~~~~LP~~Wk 140 (140)
||||||+||+|||+||||||+|+||+||||+|||||||||||+||||++++||+||+
T Consensus 81 iPeDly~LikKAv~iRkHLe~n~kD~~sK~~LiLiESkI~RL~rYYk~~~~lP~~Wk 137 (148)
T PTZ00072 81 IPEDLYFLIKKAVSIRKHLEKNRKDKDSKFRLILVESRIHRLARYYKRTKQLPPNWK 137 (148)
T ss_pred CchHHHHHHHHHHHHHHHHHHcccchhhhHHHHHHHHHHHHHHHHHhhccCCCCCCc
Confidence 999999999999999999999999999999999999999999999999999999996
No 2
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=100.00 E-value=2.9e-77 Score=465.75 Aligned_cols=140 Identities=53% Similarity=0.891 Sum_probs=139.5
Q ss_pred CCCCCCCCCCCCCcCCCCCCCCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCC
Q 032468 1 MGRMHSRGKGISASALPYKRTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGL 80 (140)
Q Consensus 1 M~rmh~~~kG~S~S~~P~~~~~P~W~~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~ngl 80 (140)
|||||++|||+|+|++||++++|+|+++++||||++||+|||+|+||||||++||||||||+||.|||+||++||++||+
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 CCCChhhHHHHHHHHHHHHHHHhHcCCcccchhHHHHHHHHHHHHHHHHHhcCCCCCCCC
Q 032468 81 APEIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHRLARYYKKTKKLPPVWK 140 (140)
Q Consensus 81 ap~iPEDL~~LikKAv~~RkHLe~n~kD~~~k~~L~LiESkI~RL~rYYk~~~~LP~~Wk 140 (140)
+|+|||||||||+||++|++||+.|+||+||||+|+++|||+|||++||+++++||+||+
T Consensus 81 ~p~iPEDL~~L~~ri~~L~~HL~~nkKD~~skRgL~~~~skrrRLl~Yyk~~~~LP~~Wk 140 (151)
T PRK08561 81 APEIPEDLRNLIKKAVNLRKHLEENPKDLHNKRGLQLIESKIRRLVKYYKRTGVLPADWR 140 (151)
T ss_pred CCCCcHHHHHHHHHHHHHHHHHHhCCCcchhHHHHHHHHHHHHHHHHHHHhcCCCCCCCc
Confidence 999999999999999999999999999999999999999999999999999999999996
No 3
>KOG0400 consensus 40S ribosomal protein S13 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2e-77 Score=462.82 Aligned_cols=140 Identities=81% Similarity=1.261 Sum_probs=139.6
Q ss_pred CCCCCCCCCCCCCcCCCCCCCCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCC
Q 032468 1 MGRMHSRGKGISASALPYKRTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGL 80 (140)
Q Consensus 1 M~rmh~~~kG~S~S~~P~~~~~P~W~~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~ngl 80 (140)
|||||++|||+|+|++||++.+|+|+++++|||.++|++|||||+||||||++|||+||||+|++|||+||++||+.||+
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 CCCChhhHHHHHHHHHHHHHHHhHcCCcccchhHHHHHHHHHHHHHHHHHhcCCCCCCCC
Q 032468 81 APEIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHRLARYYKKTKKLPPVWK 140 (140)
Q Consensus 81 ap~iPEDL~~LikKAv~~RkHLe~n~kD~~~k~~L~LiESkI~RL~rYYk~~~~LP~~Wk 140 (140)
+|+||||||+||+|||++|||||+|+||+|+||||||||||||||+||||++.+||+|||
T Consensus 81 ~PeiPeDLy~likkAv~iRkHLer~RKD~d~K~RLILveSRihRlARYYk~~~~lPp~WK 140 (151)
T KOG0400|consen 81 APEIPEDLYHLIKKAVAIRKHLERNRKDKDAKFRLILVESRIHRLARYYKTKMVLPPNWK 140 (151)
T ss_pred CCCCcHHHHHHHHHHHHHHHHHHHhccccccceEEEeehHHHHHHHHHHHhcccCCCCCC
Confidence 999999999999999999999999999999999999999999999999999999999997
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=9.3e-38 Score=212.22 Aligned_cols=60 Identities=75% Similarity=1.200 Sum_probs=41.8
Q ss_pred CCCCCCCCCCCCCcCCCCCCCCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCC
Q 032468 1 MGRMHSRGKGISASALPYKRTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGI 60 (140)
Q Consensus 1 M~rmh~~~kG~S~S~~P~~~~~P~W~~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GV 60 (140)
|||||++|||+|+|++||++++|+|+++++||||++||+|||+|+||||||++|||||||
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=99.94 E-value=5.8e-27 Score=169.52 Aligned_cols=81 Identities=31% Similarity=0.445 Sum_probs=78.7
Q ss_pred CCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHhHcCCcccchhHHHHHHHHHH
Q 032468 44 GLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIH 123 (140)
Q Consensus 44 G~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~iPEDL~~LikKAv~~RkHLe~n~kD~~~k~~L~LiESkI~ 123 (140)
|+.|||||..|||+||+|.+...+| |||+.+|+++|++|++|++.|+||.||||+|++++||++
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 6789999999999999999999888 999999999999999999999999999999999999999
Q ss_pred HHHHHHHhcCCCCCCCC
Q 032468 124 RLARYYKKTKKLPPVWK 140 (140)
Q Consensus 124 RL~rYYk~~~~LP~~Wk 140 (140)
||++|||+++++|.+|.
T Consensus 65 rLl~Ylk~~~~~~y~~l 81 (89)
T COG0184 65 RLLKYLKRKDVLRYRWL 81 (89)
T ss_pred HHHHHHHhcCcchHHHH
Confidence 99999999999999883
No 6
>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=99.58 E-value=2.9e-15 Score=105.28 Aligned_cols=69 Identities=39% Similarity=0.568 Sum_probs=65.6
Q ss_pred HHHHHHHcCCC----CCChhhHHHHHHHHHHHHHHHhHcCCcccchhHHHHHHHHHHHHHHHHHhcCCCCCCC
Q 032468 71 ILRILKAHGLA----PEIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHRLARYYKKTKKLPPVW 139 (140)
Q Consensus 71 i~~ILk~ngla----p~iPEDL~~LikKAv~~RkHLe~n~kD~~~k~~L~LiESkI~RL~rYYk~~~~LP~~W 139 (140)
+.+|+++.|.. +.+|+++..|..++.+|++||+.|+||++|+++|+.++||.+||.+||++++..|-+|
T Consensus 2 ~~~i~~~~~~~~~DtGs~evQia~LT~rI~~L~~Hl~~~~KD~~~krgL~~lv~kRrrLL~YLk~~~~~~y~~ 74 (80)
T cd00353 2 KQEILKEFGLAEGDTGSPEVQLALLTERIVNLTEHLEKNKKDKHSKRGLLLLVSKRRRLLKYLKRKDRLRYEW 74 (80)
T ss_pred HHHHHHHhCCCCCCCCChHHHHHHHHHHHHHHHHHHHHccccchHHHhHHHHHHHHHHHHHHHHHcCchhHHH
Confidence 56889999988 8999999999999999999999999999999999999999999999999999888766
No 7
>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=99.55 E-value=6.3e-15 Score=104.06 Aligned_cols=68 Identities=22% Similarity=0.327 Sum_probs=65.7
Q ss_pred ecchhHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHhHcCCcccchhHHHHHHHHHHHHHHHHHhcC
Q 032468 66 VTGSKILRILKAHGLAPEIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHRLARYYKKTK 133 (140)
Q Consensus 66 vtG~ki~~ILk~nglap~iPEDL~~LikKAv~~RkHLe~n~kD~~~k~~L~LiESkI~RL~rYYk~~~ 133 (140)
++++.|.++++++|-.+.+|+++..|..++.+|++|++.|+||++|+++|..++||.+||.+||+++.
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 46889999999999999999999999999999999999999999999999999999999999999875
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=99.14 E-value=9.2e-11 Score=74.31 Aligned_cols=46 Identities=35% Similarity=0.478 Sum_probs=44.5
Q ss_pred hhhHHHHHHHHHHHHHHHhHcCCcccchhHHHHHHHHHHHHHHHHH
Q 032468 85 PEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHRLARYYK 130 (140)
Q Consensus 85 PEDL~~LikKAv~~RkHLe~n~kD~~~k~~L~LiESkI~RL~rYYk 130 (140)
|+++..|..++.++..|++.|+||++++++|..++++++||.+||+
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=97.41 E-value=0.00041 Score=50.07 Aligned_cols=47 Identities=30% Similarity=0.490 Sum_probs=41.9
Q ss_pred hHHHHHHHHHHHHHHHhHcCCcccchhHHHHHHHHHHHHHHHHHhcC
Q 032468 87 DLYHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHRLARYYKKTK 133 (140)
Q Consensus 87 DL~~LikKAv~~RkHLe~n~kD~~~k~~L~LiESkI~RL~rYYk~~~ 133 (140)
-...|=.+-.+|..|++.|+||++|+++|...-++=+||.+|-+++.
T Consensus 25 QiA~LT~rI~~L~~Hl~~h~KD~~srrgL~~lv~kRkrlL~YL~~~d 71 (86)
T TIGR00952 25 QIALLTERINQLTEHLKANKKDHHSRRGLLKLVGRRRRLLKYLKRTD 71 (86)
T ss_pred HHHHHHHHHHHHHHHHHHCCCchHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 34566678889999999999999999999999999999999998864
No 10
>CHL00027 rps15 ribosomal protein S15
Probab=97.26 E-value=0.00082 Score=49.18 Aligned_cols=48 Identities=25% Similarity=0.349 Sum_probs=42.4
Q ss_pred hhHHHHHHHHHHHHHHHhHcCCcccchhHHHHHHHHHHHHHHHHHhcC
Q 032468 86 EDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHRLARYYKKTK 133 (140)
Q Consensus 86 EDL~~LikKAv~~RkHLe~n~kD~~~k~~L~LiESkI~RL~rYYk~~~ 133 (140)
--..-|=.+-..+..||+.|+||.+++++|.-.-++=+||.+|.+++.
T Consensus 24 vQiA~LT~rI~~Lt~Hlk~hkKD~~s~RgL~~lv~kRkrLL~YL~r~d 71 (90)
T CHL00027 24 FQVFSFTNKIRRLTSHLELHKKDYSSQRGLRKILGKRQRLLAYLSKKN 71 (90)
T ss_pred HHHHHHHHHHHHHHHHHHHCCCcchhHHHHHHHHHHHHHHHHHHHhCC
Confidence 345566678889999999999999999999999999999999998864
No 11
>PRK05626 rpsO 30S ribosomal protein S15; Reviewed
Probab=97.20 E-value=0.00095 Score=48.47 Aligned_cols=46 Identities=24% Similarity=0.397 Sum_probs=40.9
Q ss_pred HHHHHHHHHHHHHHHhHcCCcccchhHHHHHHHHHHHHHHHHHhcC
Q 032468 88 LYHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHRLARYYKKTK 133 (140)
Q Consensus 88 L~~LikKAv~~RkHLe~n~kD~~~k~~L~LiESkI~RL~rYYk~~~ 133 (140)
..-|=.+-.+|..|++.|+||++++++|...=++=+||-+|-+++.
T Consensus 29 iA~LT~rI~~L~~Hlk~~~KD~~srrgL~~lv~kRkrlL~YL~~~d 74 (89)
T PRK05626 29 VALLTERINHLTEHLKEHKKDHHSRRGLLKMVGQRRKLLDYLKKKD 74 (89)
T ss_pred HHHHHHHHHHHHHHHHHcccchhhHHHHHHHHHhHHHHHHHHHhcC
Confidence 3455668889999999999999999999999999999999998864
No 12
>PTZ00119 40S ribosomal protein S15; Provisional
Probab=96.71 E-value=0.0028 Score=54.89 Aligned_cols=64 Identities=28% Similarity=0.354 Sum_probs=50.4
Q ss_pred hHHHHHHHcCCCC----CChhhHHHHHHHHHHHHHHHhHcCCcccchhHHHHHHHHHHHHHHHHHhcC
Q 032468 70 KILRILKAHGLAP----EIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHRLARYYKKTK 133 (140)
Q Consensus 70 ki~~ILk~nglap----~iPEDL~~LikKAv~~RkHLe~n~kD~~~k~~L~LiESkI~RL~rYYk~~~ 133 (140)
+..+|.++-+..+ ...--..-|=.+-.+|..||+.|+||.+|+++|...-++=+||.+|.+++.
T Consensus 109 rK~eIIkkfqr~~~DTGS~EVQIAiLTeRI~~LTeHLk~hkKD~~SrRGLlkLV~KRRKLLkYLKrkD 176 (302)
T PTZ00119 109 KKLCIRRCLQRRPFDTGSAPVQIGCLTEKILNLRAHLILRCKDHPKKRTMSILLARRQKLMKYLYKTD 176 (302)
T ss_pred HHHHHHHHhcCCCCCCCCHHHHHHHHHHHHHHHHHHHHhCCCccHhHHHHHHHHHHHHHHHHHHHhcC
Confidence 3345555555433 233345667788899999999999999999999999999999999999864
No 13
>COG2257 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]
Probab=95.39 E-value=0.12 Score=38.30 Aligned_cols=70 Identities=23% Similarity=0.424 Sum_probs=60.9
Q ss_pred CCCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHHHHH
Q 032468 20 RTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVAIR 99 (140)
Q Consensus 20 ~~~P~W~~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~iPEDL~~LikKAv~~R 99 (140)
..+|.=+-.-.-+|-+.|++.||+ ||||.+.. ..+.+.|-.-.+..+|||.||.-|-.-...-
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 89998775 5599999999999999999999998888888
Q ss_pred HHHhHcC
Q 032468 100 KHLERNR 106 (140)
Q Consensus 100 kHLe~n~ 106 (140)
.+++.|-
T Consensus 83 ~~~~~~~ 89 (92)
T COG2257 83 YEVDNNV 89 (92)
T ss_pred HHHHccC
Confidence 8887663
No 14
>PF13565 HTH_32: Homeodomain-like domain
Probab=92.08 E-value=0.33 Score=31.99 Aligned_cols=44 Identities=27% Similarity=0.468 Sum_probs=34.3
Q ss_pred hHHHHHHHHHHHhcC--CCcchhhhHhhhccCCCceeeecchhHHHHH
Q 032468 30 SQDVEDNICKFAKKG--LTPSQIGVILRDSHGIAQVKSVTGSKILRIL 75 (140)
Q Consensus 30 ~eeve~~IvklakkG--~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~IL 75 (140)
++|+++.|+++.... .|+.+|-..|.++|||.. .+.-..|-++|
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 677878899987765 899999999999999865 44445555554
No 15
>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=87.56 E-value=2.1 Score=30.46 Aligned_cols=60 Identities=30% Similarity=0.532 Sum_probs=46.5
Q ss_pred CCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHHH
Q 032468 21 TPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVA 97 (140)
Q Consensus 21 ~~P~W~~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~iPEDL~~LikKAv~ 97 (140)
.+|-=+-.-.+++-+.|.++|+ ++|||.+.. ..+.+.|-.-++..+||||||.-+-....
T Consensus 16 ~aP~VvAKG~g~~A~~I~~~A~--------------e~~VPi~~~---~~LAr~L~~~~ig~~IP~~ly~aVAeil~ 75 (82)
T TIGR00789 16 KAPKVVASGVGEVAERIIEIAK--------------KHGIPIVED---PDLVDVLLKLDLDDEIPEELYEVVAEIFA 75 (82)
T ss_pred CCCEEEEEeCCHHHHHHHHHHH--------------HcCCCEEeC---HHHHHHHHhCCCCCccCHHHHHHHHHHHH
Confidence 4555555567788888888887 479999887 45888888889999999999977755443
No 16
>PF13276 HTH_21: HTH-like domain
Probab=87.40 E-value=1.6 Score=28.05 Aligned_cols=51 Identities=22% Similarity=0.311 Sum_probs=39.3
Q ss_pred HHHHHHHHHHHhc---CCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCCh
Q 032468 31 QDVEDNICKFAKK---GLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIP 85 (140)
Q Consensus 31 eeve~~Ivklakk---G~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~iP 85 (140)
+++.+.|.++... -+-.-.|-..|++++|+ .|.-++|.++++++||...++
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 5566667766653 34556888999999987 477888999999999987653
No 17
>COG3328 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=85.48 E-value=0.92 Score=40.33 Aligned_cols=48 Identities=17% Similarity=0.203 Sum_probs=43.5
Q ss_pred CCCCCcCCCCCCCCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCC
Q 032468 9 KGISASALPYKRTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGI 60 (140)
Q Consensus 9 kG~S~S~~P~~~~~P~W~~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GV 60 (140)
|+..+|-.| .++|.+.....+++.|..|..+|+|+.+|...++..|+.
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 566777555 689999999999999999999999999999999999988
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=83.65 E-value=0.98 Score=35.56 Aligned_cols=25 Identities=28% Similarity=0.356 Sum_probs=21.2
Q ss_pred HHHHHHHHHHHhcCCCcchhhhHhh
Q 032468 31 QDVEDNICKFAKKGLTPSQIGVILR 55 (140)
Q Consensus 31 eeve~~IvklakkG~~pSqIG~~LR 55 (140)
||-.+.+.+|+++|+|-|||+..|=
T Consensus 5 de~~~~L~~lw~~G~SasqIA~~lg 29 (162)
T PF07750_consen 5 DERVERLRKLWAEGLSASQIARQLG 29 (162)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHhC
Confidence 4555689999999999999998874
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=83.09 E-value=0.73 Score=35.50 Aligned_cols=30 Identities=37% Similarity=0.657 Sum_probs=23.4
Q ss_pred hHHHHHHHHHHHhcCCCcchhhhHhhhccC
Q 032468 30 SQDVEDNICKFAKKGLTPSQIGVILRDSHG 59 (140)
Q Consensus 30 ~eeve~~IvklakkG~~pSqIG~~LRD~~G 59 (140)
++|+-+.|++||+.|+.|++|-..|+=+||
T Consensus 19 p~~~R~rIvela~~G~rp~~Isr~l~Vs~g 48 (125)
T PF00292_consen 19 PNELRQRIVELAKEGVRPCDISRQLRVSHG 48 (125)
T ss_dssp -HHHHHHHHHHHHTT--HHHHHHHHT--HH
T ss_pred cHHHHHHHHHHhhhcCCHHHHHHHHccchh
Confidence 688999999999999999999999988775
No 20
>PHA02591 hypothetical protein; Provisional
Probab=80.15 E-value=1.5 Score=31.94 Aligned_cols=28 Identities=29% Similarity=0.381 Sum_probs=25.1
Q ss_pred cCChHHHHHHHHHHHhcCCCcchhhhHh
Q 032468 27 KISSQDVEDNICKFAKKGLTPSQIGVIL 54 (140)
Q Consensus 27 ~~~~eeve~~IvklakkG~~pSqIG~~L 54 (140)
--+.|++....-+|++.|+|.+||...|
T Consensus 42 i~~~dd~~~vA~eL~eqGlSqeqIA~~L 69 (83)
T PHA02591 42 VESEDDLISVTHELARKGFTVEKIASLL 69 (83)
T ss_pred EeccchHHHHHHHHHHcCCCHHHHHHHh
Confidence 3478899999999999999999999877
No 21
>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=79.45 E-value=1.5 Score=27.94 Aligned_cols=41 Identities=24% Similarity=0.443 Sum_probs=34.5
Q ss_pred HHHh-cCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCC
Q 032468 39 KFAK-KGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAP 82 (140)
Q Consensus 39 klak-kG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap 82 (140)
++|+ -|+|+|-+-..|.+. |.|..-|-.+|.++.++.|-.|
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 7888899999999999998766
No 22
>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=77.92 E-value=2 Score=33.80 Aligned_cols=43 Identities=26% Similarity=0.495 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCC
Q 032468 31 QDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLA 81 (140)
Q Consensus 31 eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~ngla 81 (140)
+.|.+.|.++...|++|+.|++..|+.. ....|.+.|+++|+.
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 223366666666654
No 23
>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=75.71 E-value=25 Score=24.76 Aligned_cols=40 Identities=25% Similarity=0.406 Sum_probs=32.2
Q ss_pred CCCCCCCCCccCChHHHHHH--HHHHHhcCCCcchhhhHhhh
Q 032468 17 PYKRTPPSWLKISSQDVEDN--ICKFAKKGLTPSQIGVILRD 56 (140)
Q Consensus 17 P~~~~~P~W~~~~~eeve~~--IvklakkG~~pSqIG~~LRD 56 (140)
|.++..-.+-.++.++|..+ |+.|..-|+|.++|..++..
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 44455556778999999875 88899999999999999853
No 24
>PRK01322 6-carboxyhexanoate--CoA ligase; Provisional
Probab=74.93 E-value=2.8 Score=35.60 Aligned_cols=78 Identities=23% Similarity=0.383 Sum_probs=55.3
Q ss_pred CCCCCC--CCCCCcCCCCCCCCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhH---------
Q 032468 3 RMHSRG--KGISASALPYKRTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKI--------- 71 (140)
Q Consensus 3 rmh~~~--kG~S~S~~P~~~~~P~W~~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki--------- 71 (140)
||.+.. +=+||--+=. +.++|++.+.+|.+++++- +.|.|+-=+++=.+|
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 567776544333332
Q ss_pred ------------------HHHHHHcCCCCCChhhHHHHHHHHHHHH
Q 032468 72 ------------------LRILKAHGLAPEIPEDLYHLIKKAVAIR 99 (140)
Q Consensus 72 ------------------~~ILk~nglap~iPEDL~~LikKAv~~R 99 (140)
..+|++.|+.++.+|..+.+|.+--+||
T Consensus 67 LpV~t~~~~~~eea~~~a~~lL~~~gv~~~~~~~~~~~l~~~~~MR 112 (242)
T PRK01322 67 LPIKTIDVKSVEEARALARELLQEEGVSEEAIEKAFELIKEGTNMR 112 (242)
T ss_pred cceeEEecCCHHHHHHHHHHHHHhcCCCHHHHHHHHHHHhcCCCCc
Confidence 4569999999999999999998753443
No 25
>PRK15364 pathogenicity island 2 effector protein SseB; Provisional
Probab=74.04 E-value=11 Score=31.28 Aligned_cols=80 Identities=23% Similarity=0.284 Sum_probs=57.9
Q ss_pred hHHHHHHHHHHHhcCC-----CcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHhH
Q 032468 30 SQDVEDNICKFAKKGL-----TPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVAIRKHLER 104 (140)
Q Consensus 30 ~eeve~~IvklakkG~-----~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~iPEDL~~LikKAv~~RkHLe~ 104 (140)
+.+|.+.|.+++|.|= -|-.+=..+|| +||- |.|++|-..|+++|..+++-.-=...||-|+.-- ..
T Consensus 78 AN~VDevIA~v~k~ddK~k~~LPddVI~Ymrd-NgI~----VdG~sid~Yl~k~~~~~~LdkG~LqAVKAALd~~---sn 149 (196)
T PRK15364 78 SNEMDEVIAKAAKGDAKTKEEVPEDVIKYMRD-NGIL----IDGMTIDDYMAKYGDHGKLDKGGLQAIKAALDND---AN 149 (196)
T ss_pred HHHHHHHHHHHhcCCCcccccCCHHHHHHHHH-cCce----ecccchHHHHhccCCccCCChhhHHHHHHHHHhh---cc
Confidence 5688999999977442 25556678899 8884 7999999999999999999887777888775432 12
Q ss_pred cCCcccchhHHHH
Q 032468 105 NRKDKDSKFRLIL 117 (140)
Q Consensus 105 n~kD~~~k~~L~L 117 (140)
+--|.-+..+|++
T Consensus 150 r~TD~vsQsQLqi 162 (196)
T PRK15364 150 RNTDLMSQGQITI 162 (196)
T ss_pred ccchhhhHHHHHH
Confidence 2345555555554
No 26
>KOG1802 consensus RNA helicase nonsense mRNA reducing factor (pNORF1) [RNA processing and modification]
Probab=73.37 E-value=1.9 Score=42.23 Aligned_cols=51 Identities=35% Similarity=0.625 Sum_probs=39.2
Q ss_pred ChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecch--hHHHHHHHcCCCCCChhhHHHHH
Q 032468 29 SSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGS--KILRILKAHGLAPEIPEDLYHLI 92 (140)
Q Consensus 29 ~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~--ki~~ILk~nglap~iPEDL~~Li 92 (140)
.+-++|.+|-+|-+.|+.|||||+|- +.-|. .|..+|.-+| .++-|||+-|
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 35678999999999999999999873 23333 4788887766 5677888655
No 27
>COG1964 Predicted Fe-S oxidoreductases [General function prediction only]
Probab=73.28 E-value=11 Score=34.97 Aligned_cols=78 Identities=21% Similarity=0.321 Sum_probs=58.3
Q ss_pred CC-CCCCCcCCCCCCCCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhcc-CCCceeeecchhHHHHHHHcCCCCCC
Q 032468 7 RG-KGISASALPYKRTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSH-GIAQVKSVTGSKILRILKAHGLAPEI 84 (140)
Q Consensus 7 ~~-kG~S~S~~P~~~~~P~W~~~~~eeve~~IvklakkG~~pSqIG~~LRD~~-GVp~Vk~vtG~ki~~ILk~nglap~i 84 (140)
.| .|.+-.+-+|...++-=+.-|-|+|++++-.|.+ ++ +.|.+-++||- .|.|
T Consensus 69 ~g~~g~~~~CFa~A~~ag~vYEpt~eqi~~Ml~~lk~--------------e~p~~~~aIq~tGG-----------EPTv 123 (475)
T COG1964 69 EGKFGVNNECFAYAEEAGYIYEPTLEQIREMLRNLKK--------------EHPVGANAVQFTGG-----------EPTL 123 (475)
T ss_pred cCCcCCCCcCcCchhhcCcccCCCHHHHHHHHHHHHh--------------cCCCCCceeEecCC-----------Cccc
Confidence 35 7778888899999888889999999999887655 44 34456677763 7999
Q ss_pred hhhHHHHHHHHHHH-HHHHhHcCCcc
Q 032468 85 PEDLYHLIKKAVAI-RKHLERNRKDK 109 (140)
Q Consensus 85 PEDL~~LikKAv~~-RkHLe~n~kD~ 109 (140)
++||+.||+-|-.. =.|...|..-.
T Consensus 124 r~DL~eiv~~a~e~g~~hVqinTnGi 149 (475)
T COG1964 124 RDDLIEIIKIAREEGYDHVQLNTNGI 149 (475)
T ss_pred hhhHHHHHHHHhhcCccEEEEccCce
Confidence 99999999988654 23555554433
No 28
>PHA02517 putative transposase OrfB; Reviewed
Probab=73.20 E-value=6.3 Score=31.70 Aligned_cols=48 Identities=21% Similarity=0.246 Sum_probs=39.4
Q ss_pred hHHHHHHHHHHHhc---CCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCC
Q 032468 30 SQDVEDNICKFAKK---GLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAP 82 (140)
Q Consensus 30 ~eeve~~Ivklakk---G~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap 82 (140)
.+++.+.|.++..+ .+...+|-..|+++ |+ .+.-++|.++|+++|+..
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 46889999999987 76 367888999999999965
No 29
>COG1202 Superfamily II helicase, archaea-specific [General function prediction only]
Probab=73.12 E-value=2.3 Score=41.12 Aligned_cols=45 Identities=29% Similarity=0.533 Sum_probs=37.2
Q ss_pred HHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHHHH
Q 032468 33 VEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVAI 98 (140)
Q Consensus 33 ve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~iPEDL~~LikKAv~~ 98 (140)
.-+.|++|.-.|.+|+||-.+|++.|||- ..|-|.++-...+|++
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 34789999999999999999999999983 3677777777776655
No 30
>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=72.64 E-value=14 Score=32.38 Aligned_cols=61 Identities=20% Similarity=0.394 Sum_probs=48.8
Q ss_pred CCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHH-HHcCCCCCChhhHHHHHHHHHHH
Q 032468 21 TPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRIL-KAHGLAPEIPEDLYHLIKKAVAI 98 (140)
Q Consensus 21 ~~P~W~~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~IL-k~nglap~iPEDL~~LikKAv~~ 98 (140)
.+|-=+-.-.+++-..|.++|++ ||||-|.. ..+.|-| +.-.+..+|||+||.-+-.....
T Consensus 278 ~aP~vvakG~~~~A~~I~~~A~~--------------~~vPi~~~---~~LAr~Ly~~~~~g~~IP~~ly~aVA~il~~ 339 (347)
T TIGR00328 278 PAPVVVAKGVDELALKIKEIARE--------------NNVPIVEN---PPLARALYRQVEIGQEIPPELYKAVAEVLAY 339 (347)
T ss_pred CCCEEEEeeCcHHHHHHHHHHHH--------------cCCCEEeC---HHHHHHHHHcCCCCCcCCHHHHHHHHHHHHH
Confidence 45666666788899999999886 89999886 4588888 66788899999999888766554
No 31
>PF15652 Tox-SHH: HNH/Endo VII superfamily toxin with a SHH signature
Probab=72.64 E-value=3.3 Score=31.11 Aligned_cols=34 Identities=9% Similarity=0.212 Sum_probs=33.1
Q ss_pred CccCChHHHHHHHHHHHhcCCCcchhhhHhhhcc
Q 032468 25 WLKISSQDVEDNICKFAKKGLTPSQIGVILRDSH 58 (140)
Q Consensus 25 W~~~~~eeve~~IvklakkG~~pSqIG~~LRD~~ 58 (140)
|-....+|+....-+|-+.|++++++=..|+|+|
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 32
>PRK13902 alaS alanyl-tRNA synthetase; Provisional
Probab=70.34 E-value=11 Score=37.03 Aligned_cols=55 Identities=31% Similarity=0.489 Sum_probs=41.8
Q ss_pred HHHHHHhc-CCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHH
Q 032468 36 NICKFAKK-GLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAV 96 (140)
Q Consensus 36 ~Ivklakk-G~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~iPEDL~~LikKAv 96 (140)
++-+++++ +.=|-+.-..|-|.||+|.= + +..|.+++|+.-++|++.+.+|.+.-
T Consensus 419 ~~~~~~~~~~~l~g~~~f~LYDt~G~P~d--l----~~eia~e~g~~vd~p~~F~~~~~~~~ 474 (900)
T PRK13902 419 IVERLAKKKEEIPLDDLIELYDSHGIPPE--I----VKEIAKKKGVEVEVPDNFYSLVAERH 474 (900)
T ss_pred HHHHHHHhcCCCCHHHHhhhhhcCCCCHH--H----HHHHHHHcCCccCchhhHHHHHHHHH
Confidence 34444443 55577888999999999952 1 45789999999999999999986543
No 33
>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=70.29 E-value=5.7 Score=25.74 Aligned_cols=33 Identities=36% Similarity=0.526 Sum_probs=24.5
Q ss_pred CCCCCccCChHHHHHHHHHHHhcCCCcchhhhH
Q 032468 21 TPPSWLKISSQDVEDNICKFAKKGLTPSQIGVI 53 (140)
Q Consensus 21 ~~P~W~~~~~eeve~~IvklakkG~~pSqIG~~ 53 (140)
....|.+++.++|++-+..++++|++|+-|-..
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 457899999999999999999999999887654
No 34
>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=69.79 E-value=8.5 Score=27.41 Aligned_cols=58 Identities=28% Similarity=0.408 Sum_probs=38.0
Q ss_pred CChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHc------C---CCCCChhhHHHHH
Q 032468 28 ISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAH------G---LAPEIPEDLYHLI 92 (140)
Q Consensus 28 ~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~n------g---lap~iPEDL~~Li 92 (140)
+|.++|.+....|...|-.||- ..+|..-|-++- ..|.+.|++- . ..|++|++|...+
T Consensus 1 IT~e~V~~Aa~~L~~~G~~pT~--~~Vr~~lG~GS~-----~ti~~~l~~w~~~~~~~~~~~~~~lP~~l~~~~ 67 (120)
T PF11740_consen 1 ITYEDVIEAADELLAAGKKPTV--RAVRERLGGGSM-----STISKHLKEWREEREAQVSEAAPDLPEALQDAL 67 (120)
T ss_pred CcHHHHHHHHHHHHHcCCCCCH--HHHHHHHCCCCH-----HHHHHHHHHHHHhhhccccccccCCChhHHHHH
Confidence 4789999999999999999974 344555552221 2355555431 1 3678888884433
No 35
>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=69.49 E-value=5.1 Score=26.53 Aligned_cols=29 Identities=14% Similarity=0.237 Sum_probs=22.8
Q ss_pred cCChHHHHHHHHHHHhcCCCcchhhhHhh
Q 032468 27 KISSQDVEDNICKFAKKGLTPSQIGVILR 55 (140)
Q Consensus 27 ~~~~eeve~~IvklakkG~~pSqIG~~LR 55 (140)
.+|.+|+.+.+-.+...-++|.|||-.|-
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 36
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=68.82 E-value=2.9 Score=25.90 Aligned_cols=26 Identities=15% Similarity=0.350 Sum_probs=13.6
Q ss_pred CChHHHHHHHHHHHhcCCCcchhhhHh
Q 032468 28 ISSQDVEDNICKFAKKGLTPSQIGVIL 54 (140)
Q Consensus 28 ~~~eeve~~IvklakkG~~pSqIG~~L 54 (140)
+|.+|... |..|..+|+|.++|+..|
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 778899999999999876
No 37
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=68.82 E-value=5.8 Score=26.35 Aligned_cols=39 Identities=21% Similarity=0.377 Sum_probs=33.3
Q ss_pred cCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCC
Q 032468 43 KGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEI 84 (140)
Q Consensus 43 kG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~i 84 (140)
-|+|.+.|-.+|.+.-+ |..-|-.+|.+++++.|..|..
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 4678888999999999997764
No 38
>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=68.64 E-value=1.3 Score=36.51 Aligned_cols=58 Identities=24% Similarity=0.472 Sum_probs=43.9
Q ss_pred CCCCCCCCCCCCCcCCCCCC-CCCCCccC---ChHHHHHHHHHHHhcCCCcchhhhHhhhcc
Q 032468 1 MGRMHSRGKGISASALPYKR-TPPSWLKI---SSQDVEDNICKFAKKGLTPSQIGVILRDSH 58 (140)
Q Consensus 1 M~rmh~~~kG~S~S~~P~~~-~~P~W~~~---~~eeve~~IvklakkG~~pSqIG~~LRD~~ 58 (140)
||||.+=++|--.-++=|.. ..=+|+.. ..||+.+.|.+++..|.||.++|..+|..-
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 78888888886666666532 22234432 568889999999999999999999998654
No 39
>PF13551 HTH_29: Winged helix-turn helix
Probab=68.52 E-value=23 Score=24.08 Aligned_cols=53 Identities=28% Similarity=0.423 Sum_probs=35.0
Q ss_pred CCCCCccCChHHHHHHHHHHHhc----C---CCcchhhhHh-hhccCCCceeeecchhHHHHHHHcC
Q 032468 21 TPPSWLKISSQDVEDNICKFAKK----G---LTPSQIGVIL-RDSHGIAQVKSVTGSKILRILKAHG 79 (140)
Q Consensus 21 ~~P~W~~~~~eeve~~Ivklakk----G---~~pSqIG~~L-RD~~GVp~Vk~vtG~ki~~ILk~ng 79 (140)
..|.+. +++++. +.|+++... | .|+.+|-..| ..++|+. +.-..|.++|++.|
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 344553 455544 466666654 3 5778888766 7888886 45567999999887
No 40
>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=66.96 E-value=4.7 Score=35.03 Aligned_cols=39 Identities=23% Similarity=0.404 Sum_probs=34.6
Q ss_pred CCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccC-CC
Q 032468 22 PPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHG-IA 61 (140)
Q Consensus 22 ~P~W~~~~~eeve~~IvklakkG~~pSqIG~~LRD~~G-Vp 61 (140)
.|.|-. ..+++++.|..|.-+|+|..+|+.+|.+-|| .+
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 456665 4689999999999999999999999999999 87
No 41
>PRK05702 flhB flagellar biosynthesis protein FlhB; Reviewed
Probab=66.43 E-value=24 Score=31.18 Aligned_cols=67 Identities=25% Similarity=0.426 Sum_probs=51.2
Q ss_pred CCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHH-HcCCCCCChhhHHHHHHHHHHHH
Q 032468 21 TPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILK-AHGLAPEIPEDLYHLIKKAVAIR 99 (140)
Q Consensus 21 ~~P~W~~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk-~nglap~iPEDL~~LikKAv~~R 99 (140)
.+|-=+-.-.+++-..|.++|+ +||||-+.. ..+.|-|= .-.+..+|||+||.-+-.....-
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 4566666677888888988887 689999887 45888884 66788999999998887776655
Q ss_pred HHHhH
Q 032468 100 KHLER 104 (140)
Q Consensus 100 kHLe~ 104 (140)
..++.
T Consensus 348 ~~~~~ 352 (359)
T PRK05702 348 YQLKR 352 (359)
T ss_pred HHHHh
Confidence 54543
No 42
>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=66.29 E-value=6.1 Score=27.34 Aligned_cols=53 Identities=13% Similarity=0.062 Sum_probs=37.3
Q ss_pred CChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCC
Q 032468 28 ISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGL 80 (140)
Q Consensus 28 ~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~ngl 80 (140)
+.-+++-..|.+|-...-|.++|...|-++|+++..-.--=...+..|.++|+
T Consensus 27 ~~Ln~~g~~Iw~lldg~~tv~eI~~~L~~~Y~~~e~~~~dV~~fL~~L~~~gl 79 (81)
T TIGR03859 27 VKLNDSAGEILELCDGKRSLAEIIQELAQRFPAAEEIEDDVIAFLAVARAKHW 79 (81)
T ss_pred eeeChHHHHHHHHccCCCcHHHHHHHHHHHcCChhhHHHHHHHHHHHHHHCcC
Confidence 35678888999999989999999999999998843222111223444556664
No 43
>PRK06298 type III secretion system protein; Validated
Probab=65.79 E-value=27 Score=30.79 Aligned_cols=71 Identities=17% Similarity=0.199 Sum_probs=51.2
Q ss_pred CCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHH-HHcCCCCCChhhHHHHHHHHHHHH
Q 032468 21 TPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRIL-KAHGLAPEIPEDLYHLIKKAVAIR 99 (140)
Q Consensus 21 ~~P~W~~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~IL-k~nglap~iPEDL~~LikKAv~~R 99 (140)
.+|-=+-.-.+++-..|.++|+ +||||-|.. ..+.|-| +.--+..+|||+||.-+-....-=
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 4555555567888888888886 489999886 4588888 456688899999998777666554
Q ss_pred HHHh-HcCCc
Q 032468 100 KHLE-RNRKD 108 (140)
Q Consensus 100 kHLe-~n~kD 108 (140)
-.++ +|+.+
T Consensus 342 ~~l~~~~~~~ 351 (356)
T PRK06298 342 TSLNAQNPNN 351 (356)
T ss_pred HHHhCcCcCC
Confidence 4444 44443
No 44
>PF06983 3-dmu-9_3-mt: 3-demethylubiquinone-9 3-methyltransferase; PDB: 1U7I_A 1TSJ_A 1U69_D 3L20_B 3OMS_A.
Probab=65.42 E-value=3 Score=30.55 Aligned_cols=32 Identities=19% Similarity=0.362 Sum_probs=26.1
Q ss_pred ChHHHHHHHHHHHhcCCCcchhhhHhhhccCCC
Q 032468 29 SSQDVEDNICKFAKKGLTPSQIGVILRDSHGIA 61 (140)
Q Consensus 29 ~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp 61 (140)
+.||++..=.+|+..|-.-|.-| .|.|+|||.
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 45
>KOG3862 consensus Transcription factor PAX2/5/8, contains PAX domain [Transcription]
Probab=65.19 E-value=12 Score=33.01 Aligned_cols=50 Identities=26% Similarity=0.422 Sum_probs=41.1
Q ss_pred hHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCCh
Q 032468 30 SQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIP 85 (140)
Q Consensus 30 ~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~iP 85 (140)
++-|-..|++||..|.-|+-|-..||-+||-|. +.+++.+|.--.+|-.|
T Consensus 27 pd~Vr~rIv~La~~gvrpcdisrQl~vShGcvS------kil~r~yEtgS~~pg~i 76 (327)
T KOG3862|consen 27 PDVVRQRIVELAQNGVRPCDISRQLRVSHGCVS------KILGRYYETGSIRPGVI 76 (327)
T ss_pred chHHHHHHHHHHHcCCcchhHHHHHhhccCCch------hHHHHHHHhcCcccCCC
Confidence 577899999999999999999999999999875 44677777666555444
No 46
>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=65.04 E-value=30 Score=26.12 Aligned_cols=64 Identities=14% Similarity=0.227 Sum_probs=48.8
Q ss_pred cCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChh-hHHHHHHHHHH
Q 032468 27 KISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPE-DLYHLIKKAVA 97 (140)
Q Consensus 27 ~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~iPE-DL~~LikKAv~ 97 (140)
.++++.+.++|.-++..-+|.+++=.+|+.-. -.|..+.++++++|+.+--.| +|..+++.+++
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 46889999998888888888887776776432 125679999999999864444 79999999864
No 47
>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=64.67 E-value=15 Score=27.19 Aligned_cols=38 Identities=26% Similarity=0.641 Sum_probs=32.9
Q ss_pred eecchhHHHHHHHcCCCCCChhhHHHHHHHHHH-HHHHHhH
Q 032468 65 SVTGSKILRILKAHGLAPEIPEDLYHLIKKAVA-IRKHLER 104 (140)
Q Consensus 65 ~vtG~ki~~ILk~nglap~iPEDL~~LikKAv~-~RkHLe~ 104 (140)
.-+|.+|++||..+ ..++-+|=+.-|+|.|. ++.||..
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 57899999999966 56788888999999995 7899988
No 48
>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=64.52 E-value=18 Score=27.10 Aligned_cols=65 Identities=20% Similarity=0.266 Sum_probs=49.2
Q ss_pred ccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCC-hhhHHHHHHHHHH
Q 032468 26 LKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEI-PEDLYHLIKKAVA 97 (140)
Q Consensus 26 ~~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~i-PEDL~~LikKAv~ 97 (140)
+.++++++.++|.-+...-+|.++.-.+|+.-. -+|..+.++.+++|+..-- ++.|..++..+++
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 357999999999888888888888877776654 2388899999999997654 5789999999854
No 49
>KOG3517 consensus Transcription factor PAX1/9 [Transcription]
Probab=61.81 E-value=5.8 Score=34.83 Aligned_cols=31 Identities=32% Similarity=0.523 Sum_probs=28.6
Q ss_pred hHHHHHHHHHHHhcCCCcchhhhHhhhccCC
Q 032468 30 SQDVEDNICKFAKKGLTPSQIGVILRDSHGI 60 (140)
Q Consensus 30 ~eeve~~IvklakkG~~pSqIG~~LRD~~GV 60 (140)
+.++.-.||+||+.|..|..|-..||-+||.
T Consensus 22 Pna~RlrIVELarlGiRPCDISRQLrvSHGC 52 (334)
T KOG3517|consen 22 PNAIRLRIVELARLGIRPCDISRQLRVSHGC 52 (334)
T ss_pred cchhhhhHHHHHHcCCCccchhhhhhhccch
Confidence 4678889999999999999999999999986
No 50
>TIGR01204 bioW 6-carboxyhexanoate--CoA ligase. Alternate name: pimeloyl-CoA synthase.
Probab=61.80 E-value=6.3 Score=33.38 Aligned_cols=62 Identities=16% Similarity=0.294 Sum_probs=45.6
Q ss_pred ChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchh----------------------------HHHHHHHcCC
Q 032468 29 SSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSK----------------------------ILRILKAHGL 80 (140)
Q Consensus 29 ~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~k----------------------------i~~ILk~ngl 80 (140)
+.++|++.+.+|.+++++. +.|.|+-=+++=.+ +..+|++.|+
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 45665543332222 2455999999
Q ss_pred CCCChhhHHHHHHHHHHHH
Q 032468 81 APEIPEDLYHLIKKAVAIR 99 (140)
Q Consensus 81 ap~iPEDL~~LikKAv~~R 99 (140)
.++++|..+.+|.+--+||
T Consensus 86 ~~~~~~~~~~~l~~~~~MR 104 (232)
T TIGR01204 86 SEEVAKKAVEILSKGANMR 104 (232)
T ss_pred CHHHHHHHHHHHhcCCCCc
Confidence 9999999999988754444
No 51
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=60.27 E-value=27 Score=27.15 Aligned_cols=66 Identities=21% Similarity=0.209 Sum_probs=53.1
Q ss_pred cCCCCCCCCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCCh
Q 032468 14 SALPYKRTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIP 85 (140)
Q Consensus 14 S~~P~~~~~P~W~~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~iP 85 (140)
....++...|+++ +.++++.+...+..+-.|...+=.+|--.+||..... .+.++|++-|+...=|
T Consensus 52 l~~~~~~GrP~kl--~~~q~~~l~e~~~~k~wTl~~~~~~l~~e~gv~y~~~----~v~~~l~~~GlsykK~ 117 (138)
T COG3415 52 LPPKPRKGRPRKL--SEEQLEILLERLREKDWTLKELVEELGLEFGVWYHAS----AVRRLLHELGLSYKKP 117 (138)
T ss_pred ccCccCCCCCccc--CHHHHHHHHHHHhcccchHHHHHHHHhhhcCeEEeHH----HHHHHHHHcCCCcCCC
Confidence 3344678899988 6777777777787878999999999988999976553 6899999999987654
No 52
>PF13592 HTH_33: Winged helix-turn helix
Probab=59.29 E-value=8.7 Score=25.00 Aligned_cols=37 Identities=24% Similarity=0.457 Sum_probs=29.7
Q ss_pred CcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChh
Q 032468 46 TPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPE 86 (140)
Q Consensus 46 ~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~iPE 86 (140)
|..+|...+..+|||- ++-..|.++|+..|++..-|-
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 5667888888899885 467789999999999887763
No 53
>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=58.40 E-value=22 Score=24.09 Aligned_cols=48 Identities=27% Similarity=0.353 Sum_probs=37.0
Q ss_pred hHHHHHHHHHHHhcCCCcchhhhHhhhccCC--CceeeecchhHHHHHHHc
Q 032468 30 SQDVEDNICKFAKKGLTPSQIGVILRDSHGI--AQVKSVTGSKILRILKAH 78 (140)
Q Consensus 30 ~eeve~~IvklakkG~~pSqIG~~LRD~~GV--p~Vk~vtG~ki~~ILk~n 78 (140)
..+|...|.++.-.|++..+|...|-+. || |.-+..+...|.+||+.-
T Consensus 3 ea~vVr~if~~~~~g~s~~~I~~~ln~~-gi~~~~~~~W~~~~v~~iL~np 52 (102)
T PF07508_consen 3 EAEVVREIFELYLEGYSLRQIARELNEK-GIPTPRGKKWSKSTVRRILRNP 52 (102)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHhc-CCccccCCcccHHHHHHHHhhh
Confidence 3567788888877999999999999655 44 455567788899998653
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=58.25 E-value=11 Score=23.77 Aligned_cols=25 Identities=12% Similarity=0.445 Sum_probs=18.9
Q ss_pred CChHHHHHHHHHHHhcCCCcchhhhHh
Q 032468 28 ISSQDVEDNICKFAKKGLTPSQIGVIL 54 (140)
Q Consensus 28 ~~~eeve~~IvklakkG~~pSqIG~~L 54 (140)
+|+.|+ .|+.+.-.|+++.+|+..|
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 355554 5999999999999999887
No 55
>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=57.93 E-value=17 Score=29.20 Aligned_cols=33 Identities=42% Similarity=0.538 Sum_probs=27.8
Q ss_pred eecchhHHHHHHHcCCCCCChhhHHHHHHHHHHH
Q 032468 65 SVTGSKILRILKAHGLAPEIPEDLYHLIKKAVAI 98 (140)
Q Consensus 65 ~vtG~ki~~ILk~nglap~iPEDL~~LikKAv~~ 98 (140)
....++|.+|+.++|+. ++.+|+.+||--|+.-
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 45677899999999999 9999999888777654
No 56
>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=56.42 E-value=9.7 Score=25.27 Aligned_cols=26 Identities=19% Similarity=0.354 Sum_probs=22.2
Q ss_pred HHHHHHHHHHhcCCCcchhhhHhhhccCCC
Q 032468 32 DVEDNICKFAKKGLTPSQIGVILRDSHGIA 61 (140)
Q Consensus 32 eve~~IvklakkG~~pSqIG~~LRD~~GVp 61 (140)
||.+....|.-+|+++++|...| |||
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 57888899999999999998765 666
No 57
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=56.16 E-value=30 Score=21.92 Aligned_cols=36 Identities=25% Similarity=0.355 Sum_probs=27.3
Q ss_pred CCCCCCccCChHHHHH--HHHHHHhcCCCcchhhhHhh
Q 032468 20 RTPPSWLKISSQDVED--NICKFAKKGLTPSQIGVILR 55 (140)
Q Consensus 20 ~~~P~W~~~~~eeve~--~IvklakkG~~pSqIG~~LR 55 (140)
+....--.++.+||.. .|..|...|+++++|..+|.
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 3344445678888864 58899999999999988763
No 58
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=55.97 E-value=22 Score=23.64 Aligned_cols=49 Identities=18% Similarity=0.314 Sum_probs=36.4
Q ss_pred CChHHHHHHHHHHHhc--C--CCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCC
Q 032468 28 ISSQDVEDNICKFAKK--G--LTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPE 83 (140)
Q Consensus 28 ~~~eeve~~Ivklakk--G--~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~ 83 (140)
.+++++++.|+++-+. | ++.++|... -||+-. +.++++.-|++.|+.-.
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 4788899999888775 3 777777654 477653 77888888899997543
No 59
>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=55.42 E-value=27 Score=22.14 Aligned_cols=32 Identities=22% Similarity=0.213 Sum_probs=25.0
Q ss_pred CCCccCChHHHHH--HHHHHHhcCCCcchhhhHh
Q 032468 23 PSWLKISSQDVED--NICKFAKKGLTPSQIGVIL 54 (140)
Q Consensus 23 P~W~~~~~eeve~--~IvklakkG~~pSqIG~~L 54 (140)
...-.++.+||.. .|..|.+.|+|..+|...|
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 60
>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=53.93 E-value=68 Score=22.07 Aligned_cols=39 Identities=26% Similarity=0.359 Sum_probs=29.7
Q ss_pred CCCCCCCCCCccCChHHHHH--HHHHHHh-cCCCcchhhhHhh
Q 032468 16 LPYKRTPPSWLKISSQDVED--NICKFAK-KGLTPSQIGVILR 55 (140)
Q Consensus 16 ~P~~~~~P~W~~~~~eeve~--~Ivklak-kG~~pSqIG~~LR 55 (140)
.|. ++....-.+++++|.. .|..|.. .|++.+.|-.+|.
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 3445666689999875 5788888 9999999988886
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=53.85 E-value=12 Score=26.19 Aligned_cols=35 Identities=23% Similarity=0.299 Sum_probs=19.8
Q ss_pred CCcchhhhHhhhccCCCceeeecchhHHHHHHHcCC
Q 032468 45 LTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGL 80 (140)
Q Consensus 45 ~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~ngl 80 (140)
+|+++|=..|.-+++.. .+..+=..+.+||..+|+
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 45555656666666554 444455555666666654
No 62
>COG3028 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=53.84 E-value=22 Score=29.39 Aligned_cols=62 Identities=26% Similarity=0.342 Sum_probs=43.7
Q ss_pred CCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHhHcCCcccchhHHHHHH
Q 032468 44 GLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVE 119 (140)
Q Consensus 44 G~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~iPEDL~~LikKAv~~RkHLe~n~kD~~~k~~L~LiE 119 (140)
+.|-|||- ||-+++ ...|.+|+..=+..=..-.+||||+.-|.-|-++.+|..+ ||+||.|-
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 66777764 444433 2466776665555555678999999999999999999765 56777664
No 63
>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=53.17 E-value=9.2 Score=23.54 Aligned_cols=26 Identities=15% Similarity=0.299 Sum_probs=17.5
Q ss_pred CChHHHHHHHHHHHhcCCCcchhhhHh
Q 032468 28 ISSQDVEDNICKFAKKGLTPSQIGVIL 54 (140)
Q Consensus 28 ~~~eeve~~IvklakkG~~pSqIG~~L 54 (140)
++++ -.+.|++|...|+|.++|-..+
T Consensus 6 ~~~~-~~~~i~~l~~~G~si~~IA~~~ 31 (45)
T PF02796_consen 6 LSKE-QIEEIKELYAEGMSIAEIAKQF 31 (45)
T ss_dssp SSHC-CHHHHHHHHHTT--HHHHHHHT
T ss_pred CCHH-HHHHHHHHHHCCCCHHHHHHHH
Confidence 3444 3567888999999999997643
No 64
>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=52.69 E-value=30 Score=34.14 Aligned_cols=55 Identities=25% Similarity=0.361 Sum_probs=41.0
Q ss_pred HHHHHHhc-CCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHH
Q 032468 36 NICKFAKK-GLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAV 96 (140)
Q Consensus 36 ~Ivklakk-G~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~iPEDL~~LikKAv 96 (140)
++-+++++ +.=|-+.-..|-|.||+|.= =+..|.+++|+.-++|++.+.+|.+.-
T Consensus 423 ~~~~~~~~~~~i~g~~~f~LyDTyGfP~d------l~~eia~e~g~~vd~~~~F~~~~~~~~ 478 (902)
T TIGR03683 423 IVERLLKTKKEIPLDDLIELYDSHGIPPE------IVKEIAAELGAEVEIPDNFYSIVAERH 478 (902)
T ss_pred HHHHHHhcCCcCCHHHHHHHHHccCCCHH------HHHHHHHHcCCcccCCccHHHHHHHHH
Confidence 34445533 23366778899999999952 145789999999999999999987653
No 65
>COG2445 Uncharacterized conserved protein [Function unknown]
Probab=52.56 E-value=89 Score=24.17 Aligned_cols=63 Identities=27% Similarity=0.309 Sum_probs=46.0
Q ss_pred hhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHhHcCCcccchhHHH
Q 032468 49 QIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLI 116 (140)
Q Consensus 49 qIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~iPEDL~~LikKAv~~RkHLe~n~kD~~~k~~L~ 116 (140)
-||..+-+..|.-. +-|...+.++|.++|+ |||+....+++++++|+=|=.-=-+.|...=..
T Consensus 50 Di~~~li~~~~~~~--p~~y~d~~~~L~~~gv---i~~e~~e~L~~~~gfRN~lVH~Y~~vD~~~v~~ 112 (138)
T COG2445 50 DIGNMLISKFGLRD--PGTYDDCIDILVEEGV---IPEEEAEELKKMVGFRNILVHRYWAVDPEKVYR 112 (138)
T ss_pred HHHHHHHHHhCCCC--CCCHHHHHHHHHHcCC---CCHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHH
Confidence 46777777776422 2467889999999997 889999999999999997765444444443333
No 66
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=52.26 E-value=17 Score=23.23 Aligned_cols=39 Identities=26% Similarity=0.395 Sum_probs=28.7
Q ss_pred CCCCCCCCccCChHHHHH--HHHHHHhcCCCcchhhhHhhh
Q 032468 18 YKRTPPSWLKISSQDVED--NICKFAKKGLTPSQIGVILRD 56 (140)
Q Consensus 18 ~~~~~P~W~~~~~eeve~--~IvklakkG~~pSqIG~~LRD 56 (140)
..+..-.+-.++.++|+. .|..|.+.|+|.++|-..|..
T Consensus 28 ~~~~~~g~r~y~~~dv~~l~~i~~l~~~G~sl~~I~~~l~~ 68 (69)
T PF13411_consen 28 PPRDENGYRYYSEEDVERLREIKELRKQGMSLEEIKKLLKQ 68 (69)
T ss_dssp TBESTTSSEEE-HHHHHHHHHHHHHHHTTTHHHHHHHHH--
T ss_pred cccccCceeeccHHHHHHHHHHHHHHHCcCCHHHHHHHHcc
Confidence 333555677889998875 688999999999999888764
No 67
>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=52.20 E-value=12 Score=22.59 Aligned_cols=39 Identities=18% Similarity=0.360 Sum_probs=32.3
Q ss_pred cCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCC
Q 032468 43 KGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEI 84 (140)
Q Consensus 43 kG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~i 84 (140)
-|++++.|-.+|++.. .|..-|-.+|.+++++-|..|+-
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 56778888999999999986653
No 68
>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=51.88 E-value=32 Score=23.71 Aligned_cols=40 Identities=25% Similarity=0.375 Sum_probs=31.7
Q ss_pred CCCCCCCCCccCChHHHHH--HHHHHHhcCCCcchhhhHhhh
Q 032468 17 PYKRTPPSWLKISSQDVED--NICKFAKKGLTPSQIGVILRD 56 (140)
Q Consensus 17 P~~~~~P~W~~~~~eeve~--~IvklakkG~~pSqIG~~LRD 56 (140)
|..+..+.+-.++.+||.. .|..|.+.|++.++|-.+|..
T Consensus 27 ~~~~~~~g~r~y~~~dv~~l~~i~~l~~~g~~~~~i~~~l~~ 68 (100)
T cd00592 27 PPERSENGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLDA 68 (100)
T ss_pred CCCcCCCCCcccCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 3455666788899999984 578888899999999988854
No 69
>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=50.72 E-value=22 Score=18.43 Aligned_cols=27 Identities=15% Similarity=0.277 Sum_probs=21.6
Q ss_pred CCCCCCccCChHHHHHHHHHHHhcCCC
Q 032468 20 RTPPSWLKISSQDVEDNICKFAKKGLT 46 (140)
Q Consensus 20 ~~~P~W~~~~~eeve~~IvklakkG~~ 46 (140)
...|.++.++.+.++..+--|...|++
T Consensus 5 ~~~P~il~~~~~~l~~~~~~l~~~g~~ 31 (31)
T smart00733 5 KKFPQILGYSEKKLKPKVEFLKELGFS 31 (31)
T ss_pred hhCcCcccccHHHhhHHHHHHHHcCCC
Confidence 356999999988888888877777754
No 70
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=48.27 E-value=35 Score=26.52 Aligned_cols=53 Identities=32% Similarity=0.516 Sum_probs=36.9
Q ss_pred CCCCCCCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCC
Q 032468 16 LPYKRTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLA 81 (140)
Q Consensus 16 ~P~~~~~P~W~~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~ngla 81 (140)
+|+- ..|.+..+. +.++.|.++..+|+|.++|-..| || .-..+-+++++.||.
T Consensus 147 rp~g-~~~~~~~~~--~~~~~i~~~~~~g~s~~~iak~l----gi------s~~Tv~r~~k~~~~~ 199 (200)
T PRK13413 147 RPKG-STPKKYKLT--GKEEKIKKLLDKGTSKSEIARKL----GV------SRTTLARFLKTRGLR 199 (200)
T ss_pred CCCC-Ccchhhhcc--hhHHHHHHHHHCCCCHHHHHHHH----CC------CHHHHHHHHHhcccC
Confidence 3653 445554442 33467889999999999999888 43 445678888888763
No 71
>COG5352 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.69 E-value=16 Score=29.52 Aligned_cols=24 Identities=29% Similarity=0.415 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHhcCCCcchhhhHh
Q 032468 31 QDVEDNICKFAKKGLTPSQIGVIL 54 (140)
Q Consensus 31 eeve~~IvklakkG~~pSqIG~~L 54 (140)
||=.+..-||.-.|+|.|||...|
T Consensus 5 dERve~LkKLWseGLSASQIAaQL 28 (169)
T COG5352 5 DERVETLKKLWSEGLSASQIAAQL 28 (169)
T ss_pred HHHHHHHHHHHHcccCHHHHHHHh
Confidence 566778899999999999998766
No 72
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=47.23 E-value=63 Score=27.02 Aligned_cols=71 Identities=21% Similarity=0.261 Sum_probs=50.2
Q ss_pred CCCCCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhc---cCCCceeeecchhHHHHHHHcCCCCCCh------hhH
Q 032468 18 YKRTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDS---HGIAQVKSVTGSKILRILKAHGLAPEIP------EDL 88 (140)
Q Consensus 18 ~~~~~P~W~~~~~eeve~~IvklakkG~~pSqIG~~LRD~---~GVp~Vk~vtG~ki~~ILk~nglap~iP------EDL 88 (140)
+..--|+=+..|.+++.+.+. + +-..|+..|-|| -||+++= -.+||=..|+.|.-| +|+
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 345556666677777766653 2 235699999999 7887764 368999999999887 777
Q ss_pred HHHHHHHHHHHH
Q 032468 89 YHLIKKAVAIRK 100 (140)
Q Consensus 89 ~~LikKAv~~Rk 100 (140)
..|...+..+-.
T Consensus 199 ~~l~~a~~~vl~ 210 (272)
T PRK14810 199 RKLHDAIGEVLR 210 (272)
T ss_pred HHHHHHHHHHHH
Confidence 777665555433
No 73
>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=46.62 E-value=92 Score=24.21 Aligned_cols=55 Identities=15% Similarity=0.326 Sum_probs=30.2
Q ss_pred HHHHHHhcCCCcchhhhHhh---hccCCCc--eee---ecchhHHHHHHHcCCCCCChhhHHHHHHH
Q 032468 36 NICKFAKKGLTPSQIGVILR---DSHGIAQ--VKS---VTGSKILRILKAHGLAPEIPEDLYHLIKK 94 (140)
Q Consensus 36 ~IvklakkG~~pSqIG~~LR---D~~GVp~--Vk~---vtG~ki~~ILk~nglap~iPEDL~~LikK 94 (140)
.+.+..+..+||.+.+.... +.+|.-. +-. ++-..|.+.|.- -++|+++..++..
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 LIENIQREDLSPIEEAQAYKRLLEKFSMTQEDLAKKIGKSRAHITNLLRL----LKLPSEIQSAIPE 156 (187)
T ss_pred HHHHhCccCCCHHHHHHHHHHHHHHhCCCHHHHHHHHCcCHHHHHHHHHH----HcCCHHHHHHHHh
Confidence 34455556777776665442 2344321 111 233345555554 2499999999987
No 74
>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=46.27 E-value=76 Score=25.31 Aligned_cols=36 Identities=19% Similarity=0.291 Sum_probs=27.3
Q ss_pred CChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcC
Q 032468 28 ISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHG 79 (140)
Q Consensus 28 ~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~ng 79 (140)
.+.|=++++..+|++.+++ ...||-..|..|||++|
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 3445566677788888888 45678888999999988
No 75
>PF13495 Phage_int_SAM_4: Phage integrase, N-terminal SAM-like domain; PDB: 2A3V_A.
Probab=45.36 E-value=23 Score=23.09 Aligned_cols=30 Identities=30% Similarity=0.536 Sum_probs=21.0
Q ss_pred ccCChHHHHHHHHHHH-hcCCCcchhhhHhh
Q 032468 26 LKISSQDVEDNICKFA-KKGLTPSQIGVILR 55 (140)
Q Consensus 26 ~~~~~eeve~~Ivkla-kkG~~pSqIG~~LR 55 (140)
-.+++++|++-+..|. .+|++||-|-..++
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 4568999999999999 89999998876654
No 76
>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=44.84 E-value=50 Score=27.38 Aligned_cols=60 Identities=17% Similarity=0.247 Sum_probs=34.0
Q ss_pred HHHHHHHHh-cCCCcchhhhHhhhcc-CCCceeeecchhHHHHHHH----cCCCCCChhhHHHHHHHH
Q 032468 34 EDNICKFAK-KGLTPSQIGVILRDSH-GIAQVKSVTGSKILRILKA----HGLAPEIPEDLYHLIKKA 95 (140)
Q Consensus 34 e~~Ivklak-kG~~pSqIG~~LRD~~-GVp~Vk~vtG~ki~~ILk~----nglap~iPEDL~~LikKA 95 (140)
.+.+.++|+ .|.||+||-+.=-=++ || +-.|.|.+=.+-|++ -.+..+++++-+..|.++
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 6999999876322233 33 134444443333444 333347888888777653
No 77
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=44.79 E-value=29 Score=20.25 Aligned_cols=25 Identities=24% Similarity=0.462 Sum_probs=18.8
Q ss_pred CChHHHHHHHHHHHhcCCCcchhhhHh
Q 032468 28 ISSQDVEDNICKFAKKGLTPSQIGVIL 54 (140)
Q Consensus 28 ~~~eeve~~IvklakkG~~pSqIG~~L 54 (140)
++++|.. |+.+...|++..+|+..|
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 4666664 567778999999999765
No 78
>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=44.40 E-value=21 Score=26.47 Aligned_cols=22 Identities=14% Similarity=0.382 Sum_probs=19.6
Q ss_pred cCChHHHHHHHHHHHhcCCCcc
Q 032468 27 KISSQDVEDNICKFAKKGLTPS 48 (140)
Q Consensus 27 ~~~~eeve~~IvklakkG~~pS 48 (140)
.+|.+||.++|.-+..+|..|+
T Consensus 11 ~lt~~~i~~QI~yll~qG~~~~ 32 (99)
T cd03527 11 PLTDEQIAKQIDYIISNGWAPC 32 (99)
T ss_pred CCCHHHHHHHHHHHHhCCCEEE
Confidence 3589999999999999999875
No 79
>PLN02389 biotin synthase
Probab=43.88 E-value=30 Score=30.47 Aligned_cols=38 Identities=24% Similarity=0.234 Sum_probs=27.6
Q ss_pred CCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccC
Q 032468 22 PPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHG 59 (140)
Q Consensus 22 ~P~W~~~~~eeve~~IvklakkG~~pSqIG~~LRD~~G 59 (140)
.|.|-.+++|||.+.+.++++.|.+---||.-.|+.+|
T Consensus 110 ~~~~~~Ls~EeIl~~a~~~~~~G~~~~~ivts~rg~~~ 147 (379)
T PLN02389 110 VKAQKLMSKDDVLEAAKRAKEAGSTRFCMGAAWRDTVG 147 (379)
T ss_pred CcccccCCHHHHHHHHHHHHHcCCCEEEEEecccCCCC
Confidence 45687889999999999999998875444433444444
No 80
>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=43.81 E-value=16 Score=33.71 Aligned_cols=55 Identities=22% Similarity=0.174 Sum_probs=37.4
Q ss_pred HHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHH
Q 032468 31 QDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHL 91 (140)
Q Consensus 31 eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~iPEDL~~L 91 (140)
+-+++.|-++.+++.=|...-..|-|.||+|. --+..|++++|+.-++|+.-+.+
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 34566666666667778899999999999997 33677899999999998877644
No 81
>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=43.17 E-value=14 Score=24.17 Aligned_cols=53 Identities=17% Similarity=0.354 Sum_probs=38.7
Q ss_pred CccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHc
Q 032468 25 WLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAH 78 (140)
Q Consensus 25 W~~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~n 78 (140)
|...+.|||.+..--=...|+|..|+-. .|.+||--.+......++.+++-+.
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 4578997777777777777666543
No 82
>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=43.14 E-value=22 Score=26.05 Aligned_cols=20 Identities=25% Similarity=0.622 Sum_probs=16.3
Q ss_pred hHHHHHHHHHHHhcCCCcch
Q 032468 30 SQDVEDNICKFAKKGLTPSQ 49 (140)
Q Consensus 30 ~eeve~~IvklakkG~~pSq 49 (140)
-.||.+.|-+|||+|+.|..
T Consensus 50 IN~vT~~mN~LAk~givP~R 69 (84)
T PF10752_consen 50 INEVTKEMNELAKQGIVPTR 69 (84)
T ss_pred HHHHHHHHHHHHHcCCCCcc
Confidence 46788899999999987753
No 83
>PF11181 YflT: Heat induced stress protein YflT
Probab=42.52 E-value=15 Score=26.11 Aligned_cols=32 Identities=16% Similarity=0.298 Sum_probs=28.1
Q ss_pred ChHHHHHHHHHHHhcCCCcchhhhHhhhccCC
Q 032468 29 SSQDVEDNICKFAKKGLTPSQIGVILRDSHGI 60 (140)
Q Consensus 29 ~~eeve~~IvklakkG~~pSqIG~~LRD~~GV 60 (140)
+.+|+.+.|-+|..+||+...|-++-.|..-+
T Consensus 8 ~~~E~~~~I~~L~~~Gy~~ddI~Vva~d~~~~ 39 (103)
T PF11181_consen 8 NEEEALSAIEELKAQGYSEDDIYVVAKDKDRT 39 (103)
T ss_pred CHHHHHHHHHHHHHcCCCcccEEEEEcCchHH
Confidence 78999999999999999999999888766533
No 84
>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=42.41 E-value=46 Score=23.36 Aligned_cols=40 Identities=23% Similarity=0.349 Sum_probs=31.2
Q ss_pred CCCCCCCCCccCChHHHH--HHHHHHHhcCCCcchhhhHhhh
Q 032468 17 PYKRTPPSWLKISSQDVE--DNICKFAKKGLTPSQIGVILRD 56 (140)
Q Consensus 17 P~~~~~P~W~~~~~eeve--~~IvklakkG~~pSqIG~~LRD 56 (140)
|-.+..--+=.++.++|+ ..|..|.+-|+|.++|..+|..
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 434445556678999887 5688999999999999998854
No 85
>PF03918 CcmH: Cytochrome C biogenesis protein; InterPro: IPR005616 Members of this family include NrfF, CcmH, CycL, Ccl2.; PDB: 2KW0_A 2HL7_A.
Probab=42.12 E-value=20 Score=27.95 Aligned_cols=35 Identities=17% Similarity=0.202 Sum_probs=28.1
Q ss_pred ChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCcee
Q 032468 29 SSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVK 64 (140)
Q Consensus 29 ~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk 64 (140)
.+.|..+.|.++-.+|.|..||=..+.+.|| ..|-
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 86
>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=42.00 E-value=36 Score=29.15 Aligned_cols=41 Identities=29% Similarity=0.530 Sum_probs=30.7
Q ss_pred CCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHH
Q 032468 23 PSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKA 77 (140)
Q Consensus 23 P~W~~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~ 77 (140)
|.++. ++.++..++..|.+.|++.++|-.++ |.+..|+|+|
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 55665 57899999999999999999886654 6667777764
No 87
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=41.23 E-value=26 Score=21.50 Aligned_cols=24 Identities=29% Similarity=0.382 Sum_probs=18.8
Q ss_pred HHHHHHHHhcCCCcchhhhHhhhc
Q 032468 34 EDNICKFAKKGLTPSQIGVILRDS 57 (140)
Q Consensus 34 e~~IvklakkG~~pSqIG~~LRD~ 57 (140)
|..|..+...|.++.+|+..|--+
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 88
>COG2082 CobH Precorrin isomerase [Coenzyme metabolism]
Probab=41.04 E-value=44 Score=27.90 Aligned_cols=69 Identities=25% Similarity=0.419 Sum_probs=51.3
Q ss_pred CCCCcCCCCCCCCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchh------HHHHHHHcCCCCC
Q 032468 10 GISASALPYKRTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSK------ILRILKAHGLAPE 83 (140)
Q Consensus 10 G~S~S~~P~~~~~P~W~~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~k------i~~ILk~nglap~ 83 (140)
|++.+..|-.. +-|.-++..++.++..+ .|.|-|.-|+.++++.+.+..-.|.|+- +.+.+++++..|.
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 66666666544 77887777776654432 4999999999999999988888999984 5566666666654
No 89
>PF15051 FAM198: FAM198 protein
Probab=40.50 E-value=23 Score=31.51 Aligned_cols=24 Identities=21% Similarity=0.509 Sum_probs=19.9
Q ss_pred CcCCCCCCCCCCCccCChHHHHHHHH
Q 032468 13 ASALPYKRTPPSWLKISSQDVEDNIC 38 (140)
Q Consensus 13 ~S~~P~~~~~P~W~~~~~eeve~~Iv 38 (140)
++.+-|...+|+|+ |+++|..+..
T Consensus 1 sniRiyse~aPpWf--S~~Di~~Mrl 24 (326)
T PF15051_consen 1 SNIRIYSESAPPWF--SEDDIRKMRL 24 (326)
T ss_pred CCccccCCCCCCcC--CHHHHHHHHH
Confidence 36788999999999 8999987653
No 90
>PF10929 DUF2811: Protein of unknown function (DUF2811); InterPro: IPR021231 This is a bacterial family of uncharacterised proteins.
Probab=40.30 E-value=26 Score=23.96 Aligned_cols=22 Identities=32% Similarity=0.614 Sum_probs=15.7
Q ss_pred CCCCChhhHHHHHHHHHHHHHHHhHcCC
Q 032468 80 LAPEIPEDLYHLIKKAVAIRKHLERNRK 107 (140)
Q Consensus 80 lap~iPEDL~~LikKAv~~RkHLe~n~k 107 (140)
+.-||||+|+.=| +.-+|.||.
T Consensus 2 ~~aeiPe~L~~~m------~~fie~hP~ 23 (57)
T PF10929_consen 2 FEAEIPEDLHQAM------KDFIETHPN 23 (57)
T ss_pred ccccccHHHHHHH------HHHHHcCCC
Confidence 3568999999755 455777764
No 91
>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=39.85 E-value=8.3 Score=26.32 Aligned_cols=11 Identities=55% Similarity=1.153 Sum_probs=5.3
Q ss_pred CCCChhhHHHH
Q 032468 81 APEIPEDLYHL 91 (140)
Q Consensus 81 ap~iPEDL~~L 91 (140)
.|++|+||.+|
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 92
>PRK12721 secretion system apparatus protein SsaU; Reviewed
Probab=39.79 E-value=89 Score=27.51 Aligned_cols=62 Identities=24% Similarity=0.331 Sum_probs=45.8
Q ss_pred CCCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHH-HHcCCCCCChhhHHHHHHHHHHH
Q 032468 20 RTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRIL-KAHGLAPEIPEDLYHLIKKAVAI 98 (140)
Q Consensus 20 ~~~P~W~~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~IL-k~nglap~iPEDL~~LikKAv~~ 98 (140)
..+|-=+---.+++-..|.++|+ +||||-|.+ ..+.|-| +.-.+..+||||||.-+-...+-
T Consensus 277 ~~aP~VvAKG~d~~A~~Ir~iA~--------------e~~VPiven---~pLARaLY~~~~vg~~IP~ely~aVA~ILa~ 339 (349)
T PRK12721 277 TPLPRVLEKGKDAQALHIVKLAE--------------RNGIPVVEN---IPLARALFKEVECGDYIPETLFEPVAALLRM 339 (349)
T ss_pred CCCCEEEEEeCcHHHHHHHHHHH--------------HcCCCEEeC---HHHHHHHHHhCCCCCcCCHHHHHHHHHHHHH
Confidence 34565566667788888888876 479999876 4577766 56778899999999777655544
No 93
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=39.74 E-value=28 Score=27.95 Aligned_cols=37 Identities=16% Similarity=0.468 Sum_probs=31.1
Q ss_pred cCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCC
Q 032468 43 KGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAP 82 (140)
Q Consensus 43 kG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap 82 (140)
-|+|+|-+-..|... |.|..-|..+|.++.++-|-.|
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 6788899999999999988665
No 94
>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=39.47 E-value=61 Score=22.41 Aligned_cols=34 Identities=26% Similarity=0.171 Sum_probs=28.5
Q ss_pred CCccCChHHHH--HHHHHHHhcCCCcchhhhHhhhc
Q 032468 24 SWLKISSQDVE--DNICKFAKKGLTPSQIGVILRDS 57 (140)
Q Consensus 24 ~W~~~~~eeve--~~IvklakkG~~pSqIG~~LRD~ 57 (140)
-.-.++.++|+ ..|..|...|+|..+|-..|...
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 95
>PRK01584 alanyl-tRNA synthetase; Provisional
Probab=39.40 E-value=82 Score=29.93 Aligned_cols=56 Identities=16% Similarity=0.201 Sum_probs=41.2
Q ss_pred HHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHH
Q 032468 33 VEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKA 95 (140)
Q Consensus 33 ve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~iPEDL~~LikKA 95 (140)
+++.|-+|.+.+.=|.+.--.|-|.||+|.= + +..|.+++|+.-++| ....+|+++
T Consensus 375 l~~~i~~~~~~~~~~g~~af~LydTyGfP~d--l----t~~~a~e~g~~vd~~-~f~~~~~~~ 430 (594)
T PRK01584 375 FIKLIPNLGSSKIIPGDIAFKLYDTYGFPYE--I----TEELASEYGFTVDRE-GFDEHFKKH 430 (594)
T ss_pred HHHHHHHhccCCccCHHHHHhhhccCCCCHH--H----HHHHHHHcCCeecHH-HHHHHHHHH
Confidence 3444445443455688999999999999952 1 457899999999998 777777554
No 96
>PF14361 RsbRD_N: RsbT co-antagonist protein rsbRD N-terminal domain
Probab=38.85 E-value=27 Score=24.84 Aligned_cols=36 Identities=22% Similarity=0.382 Sum_probs=24.5
Q ss_pred CCCCCCCCccCChHHHHHHHHHHHhcCCCcchhhhHh
Q 032468 18 YKRTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVIL 54 (140)
Q Consensus 18 ~~~~~P~W~~~~~eeve~~IvklakkG~~pSqIG~~L 54 (140)
+....+.| .-=.+.+++++..-|.+|+|||+....+
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 44566777 2234556666677788999999987543
No 97
>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=38.63 E-value=64 Score=22.67 Aligned_cols=41 Identities=15% Similarity=0.143 Sum_probs=31.3
Q ss_pred CCCCCCCCCCccCChHHHHH--HHHHHHhcCCCcchhhhHhhh
Q 032468 16 LPYKRTPPSWLKISSQDVED--NICKFAKKGLTPSQIGVILRD 56 (140)
Q Consensus 16 ~P~~~~~P~W~~~~~eeve~--~IvklakkG~~pSqIG~~LRD 56 (140)
.|.++..--+=.++.++|.. .|..|..-|+|-++|-.+|..
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 35555555566788888765 588899999999999988864
No 98
>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=38.60 E-value=1.7e+02 Score=21.95 Aligned_cols=40 Identities=15% Similarity=0.248 Sum_probs=32.5
Q ss_pred CCCCCCCCCccCChHHHH--HHHHHHHhcCCCcchhhhHhhh
Q 032468 17 PYKRTPPSWLKISSQDVE--DNICKFAKKGLTPSQIGVILRD 56 (140)
Q Consensus 17 P~~~~~P~W~~~~~eeve--~~IvklakkG~~pSqIG~~LRD 56 (140)
|.++....+=.|+.++|. ..|..|..-|+|-++|..+|-.
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 555666677788988886 5688899999999999999864
No 99
>KOG4279 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=38.34 E-value=31 Score=34.76 Aligned_cols=43 Identities=30% Similarity=0.428 Sum_probs=37.1
Q ss_pred hccCCCceee---ecchhHHHHHHHcCCCCCChhhHHHHHHHHHHH
Q 032468 56 DSHGIAQVKS---VTGSKILRILKAHGLAPEIPEDLYHLIKKAVAI 98 (140)
Q Consensus 56 D~~GVp~Vk~---vtG~ki~~ILk~nglap~iPEDL~~LikKAv~~ 98 (140)
|++||.+++. -.--.+..||+.+.+.|--=--|-|||++||.-
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 445678999999999999999999999999963
No 100
>PRK09108 type III secretion system protein HrcU; Validated
Probab=38.04 E-value=1.2e+02 Score=26.68 Aligned_cols=66 Identities=21% Similarity=0.273 Sum_probs=48.9
Q ss_pred CCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHHHHHH
Q 032468 21 TPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVAIRK 100 (140)
Q Consensus 21 ~~P~W~~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~iPEDL~~LikKAv~~Rk 100 (140)
.+|-=+---.+++-..|.++|+ +||||-|.+ ..+.|-|=.-.+..+|||+||.-+-..++---
T Consensus 280 ~AP~VvAKG~d~~A~~Ir~~A~--------------e~~VPvven---~pLARaLy~~~vg~~IP~ely~aVA~iL~~v~ 342 (353)
T PRK09108 280 PLPRVIAKGVDDGALALRRHAH--------------ALGIPIVGN---PPVARALYRVELDEPIPEELFETVAAILRWVD 342 (353)
T ss_pred CCCEEEEEeCcHHHHHHHHHHH--------------HcCCCEEeC---HHHHHHHhcCCCCCcCCHHHHHHHHHHHHHHH
Confidence 4555555667888888888886 489999876 45788887566888999999988776665544
Q ss_pred HHh
Q 032468 101 HLE 103 (140)
Q Consensus 101 HLe 103 (140)
.++
T Consensus 343 ~l~ 345 (353)
T PRK09108 343 ELG 345 (353)
T ss_pred HHh
Confidence 443
No 101
>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=37.45 E-value=84 Score=30.86 Aligned_cols=54 Identities=20% Similarity=0.239 Sum_probs=40.8
Q ss_pred HHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHH
Q 032468 35 DNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAV 96 (140)
Q Consensus 35 ~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~iPEDL~~LikKAv 96 (140)
+.|-++ +++.=|.+.-..|-|.||+|.= + +..|++|+|+.-++| ..+.+|.++-
T Consensus 373 ~~~~~~-~~~~i~g~~af~LydTyGfP~d--l----t~~~a~e~g~~vd~~-~F~~~~~~~~ 426 (851)
T TIGR00344 373 KLLKKL-GKKELDGEDAFKLYDTYGFPVE--L----TKEIAEERGLTVDIP-GFETLMAEQR 426 (851)
T ss_pred HHHHHh-cCCccCHHHHHHHHHccCCCHH--H----HHHHHHHcCCccCHH-HHHHHHHHHH
Confidence 344444 3455678888999999999952 1 457899999999999 8998886654
No 102
>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=37.44 E-value=59 Score=23.60 Aligned_cols=28 Identities=25% Similarity=0.233 Sum_probs=24.1
Q ss_pred hHHHHHHHcCCCCCChhhHHHHHHHHHHH
Q 032468 70 KILRILKAHGLAPEIPEDLYHLIKKAVAI 98 (140)
Q Consensus 70 ki~~ILk~nglap~iPEDL~~LikKAv~~ 98 (140)
.+.+.|.++|+ .-=+|++.++|.+||.=
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 55688999999999963
No 103
>PRK05477 gatB aspartyl/glutamyl-tRNA amidotransferase subunit B; Validated
Probab=37.02 E-value=1.1e+02 Score=28.30 Aligned_cols=64 Identities=14% Similarity=0.185 Sum_probs=47.2
Q ss_pred cCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCCh-hhHHHHHHHHHH
Q 032468 27 KISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIP-EDLYHLIKKAVA 97 (140)
Q Consensus 27 ~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~iP-EDL~~LikKAv~ 97 (140)
.++++.+.++|.-+...-+|..++-.+|..-. -+|+.+.++.+++|+..--- ++|..+|+++++
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 46899999997666666677777766666433 23778999999999975333 369999999864
No 104
>PRK09912 L-glyceraldehyde 3-phosphate reductase; Provisional
Probab=35.95 E-value=1.2e+02 Score=25.59 Aligned_cols=63 Identities=10% Similarity=0.132 Sum_probs=39.7
Q ss_pred HHHHHHHHHH-hcCCCcchhhhHhhhccC-CCceeeecchhHHHHHHHc-CC--CCCChhhHHHHHHHHH
Q 032468 32 DVEDNICKFA-KKGLTPSQIGVILRDSHG-IAQVKSVTGSKILRILKAH-GL--APEIPEDLYHLIKKAV 96 (140)
Q Consensus 32 eve~~Ivkla-kkG~~pSqIG~~LRD~~G-Vp~Vk~vtG~ki~~ILk~n-gl--ap~iPEDL~~LikKAv 96 (140)
+..+.+.++| +.|.||+|+-+.---+++ |. ..|.|.+=.+-|++| +. ..++++|-+..|.+++
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 4446677777 479999999875444443 32 236665544444444 22 2589999998887754
No 105
>PF12832 MFS_1_like: MFS_1 like family
Probab=35.79 E-value=19 Score=24.56 Aligned_cols=15 Identities=47% Similarity=0.888 Sum_probs=12.4
Q ss_pred HHhcCCCcchhhhHh
Q 032468 40 FAKKGLTPSQIGVIL 54 (140)
Q Consensus 40 lakkG~~pSqIG~~L 54 (140)
+...|++++|||++.
T Consensus 27 ~~~~Gl~~~~iGil~ 41 (77)
T PF12832_consen 27 LKQLGLSPSQIGILS 41 (77)
T ss_pred hhhcCCCHHHHHHHH
Confidence 445799999999975
No 106
>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=35.28 E-value=22 Score=23.19 Aligned_cols=12 Identities=42% Similarity=0.883 Sum_probs=10.2
Q ss_pred CCCChhhHHHHH
Q 032468 81 APEIPEDLYHLI 92 (140)
Q Consensus 81 ap~iPEDL~~Li 92 (140)
.|+|||.|.+|-
T Consensus 33 EpEVP~ELt~l~ 44 (45)
T PF05931_consen 33 EPEVPKELTKLY 44 (45)
T ss_pred CCcCcHHHHhhc
Confidence 699999998873
No 107
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=35.26 E-value=45 Score=25.76 Aligned_cols=31 Identities=16% Similarity=0.264 Sum_probs=28.1
Q ss_pred hHHHHHHHHHHHhcCCCcchhhhHhhhccCC
Q 032468 30 SQDVEDNICKFAKKGLTPSQIGVILRDSHGI 60 (140)
Q Consensus 30 ~eeve~~IvklakkG~~pSqIG~~LRD~~GV 60 (140)
+.|....|.++-.+|.|..||=..+.+.||=
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 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=35.12 E-value=13 Score=27.14 Aligned_cols=34 Identities=24% Similarity=0.506 Sum_probs=21.4
Q ss_pred ccCChHHHHHHHHHHHh-cCCCcchhhhHhhhccC
Q 032468 26 LKISSQDVEDNICKFAK-KGLTPSQIGVILRDSHG 59 (140)
Q Consensus 26 ~~~~~eeve~~Ivklak-kG~~pSqIG~~LRD~~G 59 (140)
+.+|.+||++.+..+|. -|.+|.++...+.+...
T Consensus 109 I~v~~eev~~~~~~~a~~~~~~~~~~~~~~~~~~~ 143 (162)
T PF05698_consen 109 IEVSDEEVEEEIEKLAQQYGMNPEELKEQYEKNKQ 143 (162)
T ss_dssp ----HHHHHHHHHHHHHCSTS-HHHHHHHHHCHHH
T ss_pred CCCCHHHHHHHHHHHHHHcCCCHHHHHHHHHhChh
Confidence 56788888888888887 56677777776655443
No 109
>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=35.03 E-value=53 Score=16.33 Aligned_cols=23 Identities=13% Similarity=0.179 Sum_probs=17.1
Q ss_pred HHHHHHHHHHhcCCCcchhhhHh
Q 032468 32 DVEDNICKFAKKGLTPSQIGVIL 54 (140)
Q Consensus 32 eve~~IvklakkG~~pSqIG~~L 54 (140)
+-...|+++...|.+..+|...+
T Consensus 9 ~~~~~i~~~~~~~~s~~~ia~~~ 31 (42)
T cd00569 9 EQIEEARRLLAAGESVAEIARRL 31 (42)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHH
Confidence 34567778888999999887543
No 110
>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=34.64 E-value=76 Score=22.22 Aligned_cols=42 Identities=17% Similarity=0.150 Sum_probs=33.3
Q ss_pred CCCCCCCCCCccCChHHHHH--HHHHHHhcCCCcchhhhHhhhc
Q 032468 16 LPYKRTPPSWLKISSQDVED--NICKFAKKGLTPSQIGVILRDS 57 (140)
Q Consensus 16 ~P~~~~~P~W~~~~~eeve~--~IvklakkG~~pSqIG~~LRD~ 57 (140)
.|.++..-.+=.++.++|+. .|..|..-|+|-++|-.+|...
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 35555566778889999875 5888999999999999888653
No 111
>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=34.55 E-value=13 Score=26.14 Aligned_cols=31 Identities=32% Similarity=0.483 Sum_probs=22.8
Q ss_pred hhhhHhhhccCCCceeeec-chhHHHHHHHcCC
Q 032468 49 QIGVILRDSHGIAQVKSVT-GSKILRILKAHGL 80 (140)
Q Consensus 49 qIG~~LRD~~GVp~Vk~vt-G~ki~~ILk~ngl 80 (140)
+.|..|+|=+-+-+- .|- -++++.||+|.|+
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 689999997655542 233 3579999999996
No 112
>PRK02228 V-type ATP synthase subunit F; Provisional
Probab=34.52 E-value=38 Score=24.35 Aligned_cols=62 Identities=13% Similarity=0.407 Sum_probs=34.8
Q ss_pred CChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCC---CCh-----hhHHHHHHHHHHH
Q 032468 28 ISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAP---EIP-----EDLYHLIKKAVAI 98 (140)
Q Consensus 28 ~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap---~iP-----EDL~~LikKAv~~ 98 (140)
.+++|+++.+.+|.... .+|+++-.++=...+. ..|.++++ +...| .|| +-+..+++||+.+
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 46689999999985444 5777665554222221 12222222 22221 122 5788999999864
No 113
>PF09950 DUF2184: Uncharacterized protein conserved in bacteria (DUF2184); InterPro: IPR020049 This entry is represented by Bacteriophage T1, Orf47. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=34.25 E-value=59 Score=26.82 Aligned_cols=53 Identities=21% Similarity=0.339 Sum_probs=36.0
Q ss_pred CccCChHHHHHHHHHHHhcC--------------CCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCC
Q 032468 25 WLKISSQDVEDNICKFAKKG--------------LTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAP 82 (140)
Q Consensus 25 W~~~~~eeve~~IvklakkG--------------~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap 82 (140)
|...|++||.+.|-.+..+- ++|++...+ ..+.|..-++.+|++.|++|.++.
T Consensus 102 W~~~T~~eI~~din~~~~~i~~~s~~~~~p~~l~lp~~~~~~L-----~~~~vs~~~~~Tvl~~l~~n~~~~ 168 (249)
T PF09950_consen 102 WATKTPDEILADINAALNAIWTQSGGVHMPDTLLLPPSQYAYL-----SSTRVSDATNMTVLEYLKENNIFT 168 (249)
T ss_pred cccCCHHHHHHHHHHHHHHHHhhccCCcCCCEEEECHHHHhHh-----heeeecCCCCCCHHHHHHHhchhh
Confidence 99999999999988776542 233333222 112333568999999999999543
No 114
>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=34.25 E-value=37 Score=22.59 Aligned_cols=36 Identities=25% Similarity=0.421 Sum_probs=25.1
Q ss_pred ccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceee
Q 032468 26 LKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKS 65 (140)
Q Consensus 26 ~~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~ 65 (140)
+.++.+|||+.|+++...|.=...| -..-|+-.+..
T Consensus 34 ~~l~~~~vE~~i~~~i~~~~l~~~I----D~~~~~v~~~~ 69 (88)
T smart00088 34 LGLSVPEVEKLVSKAIRDGEISAKI----DQVNGIVEFEE 69 (88)
T ss_pred hCcCHHHHHHHHHHHHHCCCeEEEE----cCcCCEEEECC
Confidence 4678899999999999999655544 23344444443
No 115
>smart00753 PAM PCI/PINT associated module.
Probab=34.25 E-value=37 Score=22.59 Aligned_cols=36 Identities=25% Similarity=0.421 Sum_probs=25.1
Q ss_pred ccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceee
Q 032468 26 LKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKS 65 (140)
Q Consensus 26 ~~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~ 65 (140)
+.++.+|||+.|+++...|.=...| -..-|+-.+..
T Consensus 34 ~~l~~~~vE~~i~~~i~~~~l~~~I----D~~~~~v~~~~ 69 (88)
T smart00753 34 LGLSVPEVEKLVSKAIRDGEISAKI----DQVNGIVEFEE 69 (88)
T ss_pred hCcCHHHHHHHHHHHHHCCCeEEEE----cCcCCEEEECC
Confidence 4678899999999999999655544 23344444443
No 116
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=34.12 E-value=38 Score=27.44 Aligned_cols=38 Identities=21% Similarity=0.424 Sum_probs=29.4
Q ss_pred cCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCC
Q 032468 43 KGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPE 83 (140)
Q Consensus 43 kG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~ 83 (140)
-|+|.|-+-..|.+. |.|..-|-++|.++.++.|-.|.
T Consensus 11 aGVS~~TVSrvLn~~---~~Vs~~tr~kV~~~a~elgY~pn 48 (346)
T PRK10401 11 AGVSVATVSRVLNNS---ALVSADTREAVMKAVSELGYRPN 48 (346)
T ss_pred hCCCHHHHHHHHCCC---CCCCHHHHHHHHHHHHHHCCCCC
Confidence 388888888888764 46788888888888888886543
No 117
>TIGR00593 pola DNA polymerase I. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=34.11 E-value=1.1e+02 Score=30.10 Aligned_cols=48 Identities=27% Similarity=0.451 Sum_probs=35.4
Q ss_pred hHHHHHHHHHHHhcC---CCcchhhhHhhhccCCCceee-----ecchhHHHHHHH
Q 032468 30 SQDVEDNICKFAKKG---LTPSQIGVILRDSHGIAQVKS-----VTGSKILRILKA 77 (140)
Q Consensus 30 ~eeve~~IvklakkG---~~pSqIG~~LRD~~GVp~Vk~-----vtG~ki~~ILk~ 77 (140)
-+++++.|.+++..- -||-|+|.+|-+..|+|.++. -|...+++-|.+
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 467788888887543 378899999999999997652 355666666654
No 118
>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=33.86 E-value=1.2e+02 Score=22.22 Aligned_cols=40 Identities=18% Similarity=0.224 Sum_probs=31.5
Q ss_pred CCCCCCCCCccCChHHHHH--HHHHHHhcCCCcchhhhHhhh
Q 032468 17 PYKRTPPSWLKISSQDVED--NICKFAKKGLTPSQIGVILRD 56 (140)
Q Consensus 17 P~~~~~P~W~~~~~eeve~--~IvklakkG~~pSqIG~~LRD 56 (140)
|..+....+-.++.++|+. .|..|..-|+|.++|...|..
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 3445566777788888874 688899999999999998854
No 119
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=33.38 E-value=1.4e+02 Score=21.82 Aligned_cols=51 Identities=20% Similarity=0.199 Sum_probs=41.9
Q ss_pred HHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHH
Q 032468 36 NICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAV 96 (140)
Q Consensus 36 ~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~iPEDL~~LikKAv 96 (140)
+=..+..-|+|..+|..-| .++...+.+||.-+.-.|+.|-+|.+.+...+
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 37888999999998888999999998887654
No 120
>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=33.37 E-value=1.3e+02 Score=26.37 Aligned_cols=59 Identities=19% Similarity=0.304 Sum_probs=43.6
Q ss_pred CCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHH-HcCCCCCChhhHHHHHHHHH
Q 032468 21 TPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILK-AHGLAPEIPEDLYHLIKKAV 96 (140)
Q Consensus 21 ~~P~W~~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk-~nglap~iPEDL~~LikKAv 96 (140)
.+|-=+---.+++-..|.++|+ +||||-|.+ ..+.|-|= .-.+..+|||+||.-+-...
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 56788999999997665443
No 121
>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=33.13 E-value=60 Score=23.67 Aligned_cols=40 Identities=13% Similarity=0.137 Sum_probs=31.7
Q ss_pred CCCCCCCCCccCChHHHH--HHHHHHHhcCCCcchhhhHhhh
Q 032468 17 PYKRTPPSWLKISSQDVE--DNICKFAKKGLTPSQIGVILRD 56 (140)
Q Consensus 17 P~~~~~P~W~~~~~eeve--~~IvklakkG~~pSqIG~~LRD 56 (140)
|..+..--+=.|+.++|+ ..|..|..-|+|-.+|..+|..
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 122
>KOG1575 consensus Voltage-gated shaker-like K+ channel, subunit beta/KCNAB [Energy production and conversion]
Probab=32.94 E-value=1.1e+02 Score=27.25 Aligned_cols=48 Identities=17% Similarity=0.271 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHh-cCCCcchhhhH-hhhccCCCceeeecchhHHHHHHHcCC
Q 032468 31 QDVEDNICKFAK-KGLTPSQIGVI-LRDSHGIAQVKSVTGSKILRILKAHGL 80 (140)
Q Consensus 31 eeve~~Ivklak-kG~~pSqIG~~-LRD~~GVp~Vk~vtG~ki~~ILk~ngl 80 (140)
.++-+.+.++|+ .|.||+|+-+. .+++.++ +-++.|-+-.+-|+||=-
T Consensus 257 ~~~~~~~~~iA~k~g~T~~qlALawv~~~~~v--~~pIpG~s~ve~l~eni~ 306 (336)
T KOG1575|consen 257 KPILEALSKIAEKHGCTVPQLALAWVLSNGKV--SSPIPGASKIEQLKENIG 306 (336)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHhCCC--EEecCCCCcHHHHHHHHh
Confidence 367778888888 58999999874 5777776 788888777777777743
No 123
>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=32.78 E-value=41 Score=22.06 Aligned_cols=21 Identities=14% Similarity=0.251 Sum_probs=15.7
Q ss_pred HHHHHHHHHHHhcCCCcchhh
Q 032468 31 QDVEDNICKFAKKGLTPSQIG 51 (140)
Q Consensus 31 eeve~~IvklakkG~~pSqIG 51 (140)
-+|.++|++||..|..--.+.
T Consensus 8 pgikeqIvema~nG~GiRdta 28 (46)
T PF12759_consen 8 PGIKEQIVEMAFNGSGIRDTA 28 (46)
T ss_pred ccHHHHHHHHHhcCCcchhhH
Confidence 468999999999996533333
No 124
>COG3530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.76 E-value=42 Score=23.81 Aligned_cols=22 Identities=32% Similarity=0.768 Sum_probs=17.8
Q ss_pred HHHHHHHHhcCCCcchhhhHhh
Q 032468 34 EDNICKFAKKGLTPSQIGVILR 55 (140)
Q Consensus 34 e~~IvklakkG~~pSqIG~~LR 55 (140)
|+-..=.|++|++|-++|..+-
T Consensus 29 e~YLlWFarkgFP~G~lG~Lm~ 50 (71)
T COG3530 29 EEYLLWFARKGFPPGKLGRLMQ 50 (71)
T ss_pred HHHHHHHHHhCCCchHHHHHHH
Confidence 3455678999999999999863
No 125
>PRK12772 bifunctional flagellar biosynthesis protein FliR/FlhB; Provisional
Probab=32.64 E-value=1.2e+02 Score=28.54 Aligned_cols=60 Identities=22% Similarity=0.417 Sum_probs=44.9
Q ss_pred CCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHH-HHcCCCCCChhhHHHHHHHHHH
Q 032468 21 TPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRIL-KAHGLAPEIPEDLYHLIKKAVA 97 (140)
Q Consensus 21 ~~P~W~~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~IL-k~nglap~iPEDL~~LikKAv~ 97 (140)
.+|-=+-.-.|++-..|.++|+ +||||-|.+ ..+-|-| +.-.+..+||||||.-+-....
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 4555555667888888888886 589999887 4577877 4667889999999976655443
No 126
>PLN02751 glutamyl-tRNA(Gln) amidotransferase
Probab=32.62 E-value=1.4e+02 Score=28.16 Aligned_cols=63 Identities=19% Similarity=0.388 Sum_probs=43.7
Q ss_pred cCChHHHHHHHHHHHhcCCCcchhhhH-hhhccCCCceeeecchhHHHHHHHcCCCCCC-hhhHHHHHHHHHH
Q 032468 27 KISSQDVEDNICKFAKKGLTPSQIGVI-LRDSHGIAQVKSVTGSKILRILKAHGLAPEI-PEDLYHLIKKAVA 97 (140)
Q Consensus 27 ~~~~eeve~~IvklakkG~~pSqIG~~-LRD~~GVp~Vk~vtG~ki~~ILk~nglap~i-PEDL~~LikKAv~ 97 (140)
.++++.+.++| +|...|.=.+.|+.. |.+-+ -+|+....|.+++||..-- +++|..+++.+++
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 46788888875 455555544555544 33333 4578899999999998543 6779999999864
No 127
>PF14475 Mso1_Sec1_bdg: Sec1-binding region of Mso1
Probab=32.47 E-value=38 Score=21.74 Aligned_cols=20 Identities=35% Similarity=0.883 Sum_probs=16.0
Q ss_pred HHHHH-HHHHHHhcCCCCCCC
Q 032468 120 SRIHR-LARYYKKTKKLPPVW 139 (140)
Q Consensus 120 SkI~R-L~rYYk~~~~LP~~W 139 (140)
+-||| |++||...++=-|+|
T Consensus 20 T~v~r~l~~yY~~k~~~~P~W 40 (41)
T PF14475_consen 20 THVHRVLRKYYTEKGRPFPGW 40 (41)
T ss_pred hHHHHHHHHHHHHcCCCCCCc
Confidence 45666 789999998877888
No 128
>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=32.46 E-value=54 Score=24.25 Aligned_cols=21 Identities=19% Similarity=0.464 Sum_probs=16.9
Q ss_pred CChHHHHHHHHHHHhcCCCcc
Q 032468 28 ISSQDVEDNICKFAKKGLTPS 48 (140)
Q Consensus 28 ~~~eeve~~IvklakkG~~pS 48 (140)
+|.|||.+.+.+|+..|..|.
T Consensus 36 Ltd~ev~~Va~~L~~~~~~~~ 56 (96)
T PF11829_consen 36 LTDDEVAEVAAELAARGDPPV 56 (96)
T ss_dssp S-HHHHHHHHHHHHHHTSS-B
T ss_pred CCHHHHHHHHHHHHhcCCCCC
Confidence 689999999999999997543
No 129
>PF14420 Clr5: Clr5 domain
Probab=32.46 E-value=57 Score=21.01 Aligned_cols=31 Identities=16% Similarity=0.353 Sum_probs=26.8
Q ss_pred HHHHHHHHHHH-hcCCCcchhhhHhhhccCCC
Q 032468 31 QDVEDNICKFA-KKGLTPSQIGVILRDSHGIA 61 (140)
Q Consensus 31 eeve~~Ivkla-kkG~~pSqIG~~LRD~~GVp 61 (140)
|...+.|.+|. .+|.|-.+|-.++...||.-
T Consensus 6 e~~K~~I~~LY~~e~~tl~~v~~~M~~~~~F~ 37 (54)
T PF14420_consen 6 EPHKEEIERLYIDENKTLEEVMEIMKEEHGFK 37 (54)
T ss_pred HHHHHHHHHHHHhCCCcHHHHHHHHHHHhCCC
Confidence 56778889998 69999999999999999874
No 130
>PLN02641 anthranilate phosphoribosyltransferase
Probab=31.90 E-value=45 Score=29.17 Aligned_cols=28 Identities=14% Similarity=0.237 Sum_probs=23.2
Q ss_pred cCChHHHHHHHHHHHhcCCCcchhhhHhh
Q 032468 27 KISSQDVEDNICKFAKKGLTPSQIGVILR 55 (140)
Q Consensus 27 ~~~~eeve~~IvklakkG~~pSqIG~~LR 55 (140)
++|.||..+.+..+.. |.+|.|||..|-
T Consensus 16 ~Lt~eEa~~~~~~il~-~~~~~qigAfL~ 43 (343)
T PLN02641 16 DLTEEEAEAALDFLLD-DADEAQISAFLV 43 (343)
T ss_pred CCCHHHHHHHHHHHHc-CCCHHHHHHHHH
Confidence 6789999988888886 699999987663
No 131
>PRK15320 transcriptional activator SprB; Provisional
Probab=31.77 E-value=87 Score=26.93 Aligned_cols=70 Identities=14% Similarity=0.306 Sum_probs=50.4
Q ss_pred CCccCCh--HHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHHHHHHH
Q 032468 24 SWLKISS--QDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVAIRKH 101 (140)
Q Consensus 24 ~W~~~~~--eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~iPEDL~~LikKAv~~RkH 101 (140)
.|.++.| ++-|-.|.+|--+|+|-.+|...|-- ++|.| -+-..+++++-| +..+|-.|+ +.+.+-.|
T Consensus 157 ~~~~~~~~LSdREIEVL~LLAkG~SNKEIAekL~L-----S~KTV-STYKnRLLeKLg-AkN~~~~~~----~~~~~~~~ 225 (251)
T PRK15320 157 AWWNLPPGVTQAKYALLILLSSGHPAIELAKKFGL-----GTKTV-SIYRKKVMYRLG-MDSSPLSLF----RGLKLDAH 225 (251)
T ss_pred eeecCCCCCCHHHHHHHHHHHcCCCHHHHHHHhcc-----chhhH-HHHHHHHHHHcC-CCCCchHHH----cccchhhh
Confidence 4666543 56677899999999999999999871 12221 234678888888 567888888 55667777
Q ss_pred HhH
Q 032468 102 LER 104 (140)
Q Consensus 102 Le~ 104 (140)
|.+
T Consensus 226 ~~~ 228 (251)
T PRK15320 226 LQR 228 (251)
T ss_pred Hhh
Confidence 765
No 132
>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=31.76 E-value=38 Score=19.62 Aligned_cols=25 Identities=16% Similarity=0.185 Sum_probs=17.9
Q ss_pred hHHHHHHHHHHHh-cCCCcchhhhHh
Q 032468 30 SQDVEDNICKFAK-KGLTPSQIGVIL 54 (140)
Q Consensus 30 ~eeve~~Ivklak-kG~~pSqIG~~L 54 (140)
++|..+.+-++|+ .|.|-|++=..+
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 4667777778776 788888865443
No 133
>PRK09875 putative hydrolase; Provisional
Probab=31.75 E-value=45 Score=28.40 Aligned_cols=63 Identities=22% Similarity=0.302 Sum_probs=42.1
Q ss_pred CCCCCccC-ChHHHHHHHHHHHhcCCC-----cchhhhHhhh--------------------ccCCCcee----eecchh
Q 032468 21 TPPSWLKI-SSQDVEDNICKFAKKGLT-----PSQIGVILRD--------------------SHGIAQVK----SVTGSK 70 (140)
Q Consensus 21 ~~P~W~~~-~~eeve~~IvklakkG~~-----pSqIG~~LRD--------------------~~GVp~Vk----~vtG~k 70 (140)
..|.|+.- +.||+.+.+++-...|+. |..||.+=-+ ..|+|-.- .-.|..
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 34777764 899999999998888875 3444433221 24664431 116677
Q ss_pred HHHHHHHcCCCCC
Q 032468 71 ILRILKAHGLAPE 83 (140)
Q Consensus 71 i~~ILk~nglap~ 83 (140)
+.++|++.|+.|+
T Consensus 168 ~l~il~e~Gvd~~ 180 (292)
T PRK09875 168 QLALLQAHGVDLS 180 (292)
T ss_pred HHHHHHHcCcCcc
Confidence 8999999998764
No 134
>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=31.71 E-value=1.3e+02 Score=26.04 Aligned_cols=48 Identities=23% Similarity=0.441 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHhcCC---CcchhhhHhhhccCCCceee-------ecchhHHHHHHHc
Q 032468 31 QDVEDNICKFAKKGL---TPSQIGVILRDSHGIAQVKS-------VTGSKILRILKAH 78 (140)
Q Consensus 31 eeve~~IvklakkG~---~pSqIG~~LRD~~GVp~Vk~-------vtG~ki~~ILk~n 78 (140)
+++++.+.+++-.-+ ||-|++.+|-+..|+|.++. .|.+..++-|.+.
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 456666666655433 78899999999999996543 3335555555443
No 135
>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=31.68 E-value=41 Score=21.49 Aligned_cols=35 Identities=11% Similarity=0.045 Sum_probs=24.1
Q ss_pred ChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCce
Q 032468 29 SSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQV 63 (140)
Q Consensus 29 ~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~V 63 (140)
.-+++-..|.++...+.|..+|-..|..+|+++--
T Consensus 14 ~Ln~~a~~Iw~~~~g~~t~~ei~~~l~~~y~~~~~ 48 (68)
T PF05402_consen 14 TLNETAAFIWELLDGPRTVEEIVDALAEEYDVDPE 48 (68)
T ss_dssp ---THHHHHHHH--SSS-HHHHHHHHHHHTT--HH
T ss_pred cccHHHHHHHHHccCCCCHHHHHHHHHHHcCCCHH
Confidence 66778888999998889999999999999988753
No 136
>PRK12773 flhB flagellar biosynthesis protein FlhB; Reviewed
Probab=31.55 E-value=1.6e+02 Score=28.64 Aligned_cols=61 Identities=21% Similarity=0.355 Sum_probs=46.1
Q ss_pred CCCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHH-HHcCCCCCChhhHHHHHHHHHH
Q 032468 20 RTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRIL-KAHGLAPEIPEDLYHLIKKAVA 97 (140)
Q Consensus 20 ~~~P~W~~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~IL-k~nglap~iPEDL~~LikKAv~ 97 (140)
..+|-=+---.+++-..|.++|+ +||||.|.. ..+-|-| +.-.+..+||+|||.-|-..++
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 35566666677888889988886 589999886 3477776 5677889999999976655543
No 137
>PRK14703 glutaminyl-tRNA synthetase/YqeY domain fusion protein; Provisional
Probab=31.40 E-value=1.4e+02 Score=29.21 Aligned_cols=67 Identities=13% Similarity=0.177 Sum_probs=50.2
Q ss_pred CCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCCh-hhHHHHHHHHHH
Q 032468 24 SWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIP-EDLYHLIKKAVA 97 (140)
Q Consensus 24 ~W~~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~iP-EDL~~LikKAv~ 97 (140)
+-+.++++.+.++|.-++..-+|..++-.+|..-. -+|.++.+|.+++||..--- +.|..+|+.+++
T Consensus 658 ~~~~l~pe~LaeLv~lV~~g~IS~~~AK~VL~~m~-------~~~~~p~~IIee~GL~qisDe~~Le~iV~eVI~ 725 (771)
T PRK14703 658 AALPFTPAALARLVALVDAGRISTRIAKDVLAELA-------ASGGDPEAIVEAKGLEQVSDAGALEPIVEEVLA 725 (771)
T ss_pred ccCCCCHHHHHHHHHHHHcCCccHHHHHHHHHHHH-------hcCCCHHHHHHhcCCcccCCHHHHHHHHHHHHH
Confidence 34578999999998777777777777766665432 33778999999999985444 569999999863
No 138
>KOG3089 consensus Predicted DEAD-box-containing helicase [General function prediction only]
Probab=30.76 E-value=65 Score=27.96 Aligned_cols=33 Identities=27% Similarity=0.363 Sum_probs=28.6
Q ss_pred cchhHHHHHHHcCCCCCChhhHHHHHHHHHHHH
Q 032468 67 TGSKILRILKAHGLAPEIPEDLYHLIKKAVAIR 99 (140)
Q Consensus 67 tG~ki~~ILk~nglap~iPEDL~~LikKAv~~R 99 (140)
--+||++.+.++--.+..||||..|++..++=+
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 456899999999999999999999998877644
No 139
>PRK04028 glutamyl-tRNA(Gln) amidotransferase subunit E; Validated
Probab=30.40 E-value=1.5e+02 Score=28.41 Aligned_cols=64 Identities=17% Similarity=0.236 Sum_probs=48.1
Q ss_pred cCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHH
Q 032468 27 KISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAV 96 (140)
Q Consensus 27 ~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~iPEDL~~LikKAv 96 (140)
.++++.+.+++.-++...+|-.++-.+|..-+-= .|+.+.+|+++.|+.+-=.+.|..+|+.++
T Consensus 518 ~i~~~~l~~l~~~~~~~~is~~~ak~v~~~~~~~------~~~~~~~IIee~gl~qiSD~eL~~iV~evI 581 (630)
T PRK04028 518 NITDEHIEEVFKLVSEGKIAKEAIEEILKELAEN------PGKSAEEAAEELGLKGLSEEEVEKIIDEIV 581 (630)
T ss_pred cCCHHHHHHHHHHHHcCCccHHHHHHHHHHHHhc------CCCCHHHHHHHhCcccCCHHHHHHHHHHHH
Confidence 3688999999777777777777776666544310 167799999999998766678888888885
No 140
>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=30.26 E-value=17 Score=30.01 Aligned_cols=62 Identities=27% Similarity=0.390 Sum_probs=0.0
Q ss_pred ChHHHHHHHHHHHhcCC-----CcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHH
Q 032468 29 SSQDVEDNICKFAKKGL-----TPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAV 96 (140)
Q Consensus 29 ~~eeve~~IvklakkG~-----~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~iPEDL~~LikKAv 96 (140)
.+.+|.+.|.+.++.|= -|-.+=..+|| +|| .|.|++|...|++||- .++-..=...||-|+
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 45688889999888652 23455567787 888 4799999999999983 455555555555553
No 141
>COG1141 Fer Ferredoxin [Energy production and conversion]
Probab=30.21 E-value=29 Score=24.12 Aligned_cols=23 Identities=26% Similarity=0.254 Sum_probs=18.2
Q ss_pred HHHcCCCCCChhhHHHHHHHHHH
Q 032468 75 LKAHGLAPEIPEDLYHLIKKAVA 97 (140)
Q Consensus 75 Lk~nglap~iPEDL~~LikKAv~ 97 (140)
+-.+=...++||||++.++.|+.
T Consensus 35 ~~~~~~~~~~~~e~~~~~~~A~~ 57 (68)
T COG1141 35 LDGNIGEGEVPEELEEDAEDAAE 57 (68)
T ss_pred ccCccccccCChHHHHHHHHHHH
Confidence 33444678999999999999974
No 142
>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=30.16 E-value=49 Score=21.75 Aligned_cols=20 Identities=30% Similarity=0.474 Sum_probs=16.2
Q ss_pred ccCChHHHHHHHHHHHhcCC
Q 032468 26 LKISSQDVEDNICKFAKKGL 45 (140)
Q Consensus 26 ~~~~~eeve~~IvklakkG~ 45 (140)
++++++.|+.++-.|-++|+
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 143
>PRK10625 tas putative aldo-keto reductase; Provisional
Probab=30.02 E-value=1.8e+02 Score=24.38 Aligned_cols=62 Identities=19% Similarity=0.325 Sum_probs=37.8
Q ss_pred HHHHHHHHH-hcCCCcchhhhHhhhccCCCce-eeecchhHHHHHHHc-C-CCCCChhhHHHHHHHHH
Q 032468 33 VEDNICKFA-KKGLTPSQIGVILRDSHGIAQV-KSVTGSKILRILKAH-G-LAPEIPEDLYHLIKKAV 96 (140)
Q Consensus 33 ve~~Ivkla-kkG~~pSqIG~~LRD~~GVp~V-k~vtG~ki~~ILk~n-g-lap~iPEDL~~LikKAv 96 (140)
..+.+.++| +.|.||+|+-+.--=+++ .| -.|.|.+=.+-|++| . +.-+++++.+..|.++.
T Consensus 273 ~~~~l~~la~~~g~t~aqval~w~l~~~--~v~~~I~G~~~~~~l~en~~a~~~~L~~~~~~~l~~~~ 338 (346)
T PRK10625 273 AVAAYVDIAKRHGLDPAQMALAFVRRQP--FVASTLLGATTMEQLKTNIESLHLTLSEEVLAEIEAVH 338 (346)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHhCC--CCeeEEeCCCCHHHHHHHHhhccCCCCHHHHHHHHHHH
Confidence 345566676 589999998874333443 23 245555544444443 1 22468888888888764
No 144
>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=29.88 E-value=34 Score=22.89 Aligned_cols=29 Identities=14% Similarity=0.185 Sum_probs=18.6
Q ss_pred cCChHHHHHHHHHHHhcCCCcchhhhHhh
Q 032468 27 KISSQDVEDNICKFAKKGLTPSQIGVILR 55 (140)
Q Consensus 27 ~~~~eeve~~IvklakkG~~pSqIG~~LR 55 (140)
+-+-+++.+.+.+|-..|+++++|=..|.
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 145
>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=29.76 E-value=85 Score=20.79 Aligned_cols=40 Identities=20% Similarity=0.276 Sum_probs=32.0
Q ss_pred cCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCC
Q 032468 27 KISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLA 81 (140)
Q Consensus 27 ~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~ngla 81 (140)
.+.|=+++++...|. ..|+|..+.+.-..+.+.|.++|+.
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 456667777777766 6788899999999999999999874
No 146
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=29.55 E-value=64 Score=24.95 Aligned_cols=31 Identities=10% Similarity=0.160 Sum_probs=28.2
Q ss_pred hHHHHHHHHHHHhcCCCcchhhhHhhhccCC
Q 032468 30 SQDVEDNICKFAKKGLTPSQIGVILRDSHGI 60 (140)
Q Consensus 30 ~eeve~~IvklakkG~~pSqIG~~LRD~~GV 60 (140)
+.|....|.++-..|.|..||=-.+.+.||=
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 147
>COG0749 PolA DNA polymerase I - 3'-5' exonuclease and polymerase domains [DNA replication, recombination, and repair]
Probab=29.55 E-value=99 Score=29.56 Aligned_cols=59 Identities=25% Similarity=0.416 Sum_probs=40.1
Q ss_pred hHHHHHHHHHHHhcCC---CcchhhhHhhhccCCCc--eeeecc--hhHHHHHHHcCCCCCChhhH
Q 032468 30 SQDVEDNICKFAKKGL---TPSQIGVILRDSHGIAQ--VKSVTG--SKILRILKAHGLAPEIPEDL 88 (140)
Q Consensus 30 ~eeve~~IvklakkG~---~pSqIG~~LRD~~GVp~--Vk~vtG--~ki~~ILk~nglap~iPEDL 88 (140)
-.++|+.|.+||-.-+ ||=|+|.+|-+..|.|. -|.=|| ..=-.+|++-.-.-+||.-+
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 3578888999987444 78899999999999995 455565 22234555444355666543
No 148
>PF06348 DUF1059: Protein of unknown function (DUF1059); InterPro: IPR009409 This entry consists of short hypothetical archaeal and bacterial proteins of unknown function.
Probab=29.54 E-value=58 Score=21.42 Aligned_cols=19 Identities=47% Similarity=0.875 Sum_probs=13.9
Q ss_pred HcCCCCCChhhHHHHHHHHH
Q 032468 77 AHGLAPEIPEDLYHLIKKAV 96 (140)
Q Consensus 77 ~nglap~iPEDL~~LikKAv 96 (140)
.+|+ -++|+||..-||.++
T Consensus 36 ~Hg~-~~~~~el~~~ir~~I 54 (57)
T PF06348_consen 36 VHGM-TEIPEELREKIRSAI 54 (57)
T ss_pred hcCC-ccCCHHHHHHHHHHh
Confidence 3453 378999999888875
No 149
>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=29.51 E-value=40 Score=24.84 Aligned_cols=21 Identities=5% Similarity=0.284 Sum_probs=16.6
Q ss_pred CChHHHHHHHHHHHhcCCCcc
Q 032468 28 ISSQDVEDNICKFAKKGLTPS 48 (140)
Q Consensus 28 ~~~eeve~~IvklakkG~~pS 48 (140)
++.+||.++|..|-.+|+.|+
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 150
>PRK08156 type III secretion system protein SpaS; Validated
Probab=29.51 E-value=1.7e+02 Score=26.09 Aligned_cols=65 Identities=12% Similarity=0.101 Sum_probs=48.5
Q ss_pred CCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHH-HcCCCCCChhhHHHHHHHHHHHH
Q 032468 21 TPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILK-AHGLAPEIPEDLYHLIKKAVAIR 99 (140)
Q Consensus 21 ~~P~W~~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk-~nglap~iPEDL~~LikKAv~~R 99 (140)
.+|-=+-.-.|++-..|.++|+ +||||-|.+ ..+-|-|= .-.+..+|||+||.-+-..++--
T Consensus 273 ~AP~VvAKG~d~~A~~IreiA~--------------e~~VPiven---~pLARaLY~~vevg~~IP~ely~AVA~iLa~v 335 (361)
T PRK08156 273 PIPFISVRETNQRALAVRAYAE--------------KVGVPVVRD---IKLARRLYKTHRRYSFVSLEDLDEVLRLLIWL 335 (361)
T ss_pred CCCEEEEecCcHHHHHHHHHHH--------------HCCCCEeeC---HHHHHHHHHhCCCCCcCCHHHHHHHHHHHHHH
Confidence 4566666677888888888886 489998876 45888884 56789999999998776665544
Q ss_pred HHH
Q 032468 100 KHL 102 (140)
Q Consensus 100 kHL 102 (140)
-.+
T Consensus 336 ~~l 338 (361)
T PRK08156 336 EQV 338 (361)
T ss_pred HHH
Confidence 333
No 151
>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=29.43 E-value=43 Score=22.00 Aligned_cols=22 Identities=32% Similarity=0.500 Sum_probs=18.4
Q ss_pred CCccCChHHHHHHHHHHHhcCC
Q 032468 24 SWLKISSQDVEDNICKFAKKGL 45 (140)
Q Consensus 24 ~W~~~~~eeve~~IvklakkG~ 45 (140)
+++++++.-|.+.+-+|+++|+
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 4678899999999999999996
No 152
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=29.28 E-value=1.3e+02 Score=22.02 Aligned_cols=48 Identities=23% Similarity=0.387 Sum_probs=37.0
Q ss_pred ChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCC
Q 032468 29 SSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGL 80 (140)
Q Consensus 29 ~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~ngl 80 (140)
+.+++.+.+.++ +|+.|=--..+|...+| +++-++ -.-+.++++..|.
T Consensus 77 ~~~~~~~~L~~l--~GIG~~tA~~~l~~~~~-~~~~pv-D~~v~r~~~~~~~ 124 (158)
T cd00056 77 DDPDAREELLAL--PGVGRKTANVVLLFALG-PDAFPV-DTHVRRVLKRLGL 124 (158)
T ss_pred CCcccHHHHHcC--CCCCHHHHHHHHHHHCC-CCCCcc-chhHHHHHHHhCC
Confidence 445555555555 78888778888888899 888777 8888999999887
No 153
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=28.91 E-value=70 Score=16.96 Aligned_cols=19 Identities=11% Similarity=0.277 Sum_probs=13.2
Q ss_pred ChHHHHHHHHHHHhcCCCc
Q 032468 29 SSQDVEDNICKFAKKGLTP 47 (140)
Q Consensus 29 ~~eeve~~IvklakkG~~p 47 (140)
+.+++.+....+.++|+.|
T Consensus 16 ~~~~a~~~~~~M~~~gv~P 34 (34)
T PF13812_consen 16 DPDAALQLFDEMKEQGVKP 34 (34)
T ss_pred CHHHHHHHHHHHHHhCCCC
Confidence 4566777777777777766
No 154
>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=28.89 E-value=2.2e+02 Score=20.28 Aligned_cols=40 Identities=20% Similarity=0.182 Sum_probs=29.8
Q ss_pred CCCCCCCCCccCChHHHHH--HHHHHHhcCCCcchhhhHhhh
Q 032468 17 PYKRTPPSWLKISSQDVED--NICKFAKKGLTPSQIGVILRD 56 (140)
Q Consensus 17 P~~~~~P~W~~~~~eeve~--~IvklakkG~~pSqIG~~LRD 56 (140)
|..+...-+-.+++++|+. .|..|..-|+|..+|..+|..
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 588899999999999988864
No 155
>PRK13109 flhB flagellar biosynthesis protein FlhB; Reviewed
Probab=28.82 E-value=2.3e+02 Score=25.13 Aligned_cols=65 Identities=17% Similarity=0.240 Sum_probs=46.6
Q ss_pred CCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHH-HcCCCCCChhhHHHHHHHHHHHH
Q 032468 21 TPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILK-AHGLAPEIPEDLYHLIKKAVAIR 99 (140)
Q Consensus 21 ~~P~W~~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk-~nglap~iPEDL~~LikKAv~~R 99 (140)
.+|-=+-.-.+++-..|.++|+ +||||-|.+ ..+.|-|= .-.+..+|||+||.-+-..+..-
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 4455555567788888888776 489999886 45777775 45688999999998776665544
Q ss_pred HHH
Q 032468 100 KHL 102 (140)
Q Consensus 100 kHL 102 (140)
..|
T Consensus 350 ~~l 352 (358)
T PRK13109 350 FSR 352 (358)
T ss_pred HHH
Confidence 333
No 156
>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=28.79 E-value=1.6e+02 Score=22.34 Aligned_cols=67 Identities=22% Similarity=0.455 Sum_probs=37.2
Q ss_pred hhHhhhc--cCCCceeeecchhHHHHHHHcC---CCCCChhhHHHHHHHHHHHHHHHhHcCCcccchhHHHHHHHHHHHH
Q 032468 51 GVILRDS--HGIAQVKSVTGSKILRILKAHG---LAPEIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHRL 125 (140)
Q Consensus 51 G~~LRD~--~GVp~Vk~vtG~ki~~ILk~ng---lap~iPEDL~~LikKAv~~RkHLe~n~kD~~~k~~L~LiESkI~RL 125 (140)
|++|-.- +|-+--....+..+.+.+++.. ..+.+|+++.+||.+..+ .++ +.+-....| +.+|
T Consensus 185 G~~l~el~t~g~~p~~~~~~~~~~~~i~~~~~~~~~~~~~~~l~~li~~~~~------~~p---~~Rp~~~~i---~~~l 252 (257)
T cd05116 185 GVLMWEAFSYGQKPYKGMKGNEVTQMIESGERMECPQRCPPEMYDLMKLCWT------YGV---DERPGFAVV---ELRL 252 (257)
T ss_pred HHHHHHHHhCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHhc------cCc---hhCcCHHHH---HHHH
Confidence 5554443 3444334455666666665432 223467899999988843 333 333444443 6677
Q ss_pred HHHH
Q 032468 126 ARYY 129 (140)
Q Consensus 126 ~rYY 129 (140)
..||
T Consensus 253 ~~~~ 256 (257)
T cd05116 253 RNYY 256 (257)
T ss_pred hccc
Confidence 7776
No 157
>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=28.62 E-value=24 Score=26.55 Aligned_cols=17 Identities=29% Similarity=0.354 Sum_probs=13.4
Q ss_pred HHHHHHHHHHHHHHHHh
Q 032468 115 LILVESRIHRLARYYKK 131 (140)
Q Consensus 115 L~LiESkI~RL~rYYk~ 131 (140)
.-+||||||.|+.-.-+
T Consensus 26 ~G~VESrlR~Lv~~LE~ 42 (157)
T PF04926_consen 26 SGWVESRLRHLVQKLER 42 (157)
T ss_dssp HHHHHCCHHHHHHHHHT
T ss_pred hhHHHHHHHHHHHHHcc
Confidence 45899999999976544
No 158
>KOG2815 consensus Mitochondrial/choloroplast ribosomal protein S15 [Translation, ribosomal structure and biogenesis]
Probab=28.56 E-value=1e+02 Score=26.62 Aligned_cols=45 Identities=18% Similarity=0.220 Sum_probs=37.6
Q ss_pred HHHHHHHHHHHhHcCCcccchhHHHHHHHHHHHHHHHHHhcCCCC
Q 032468 92 IKKAVAIRKHLERNRKDKDSKFRLILVESRIHRLARYYKKTKKLP 136 (140)
Q Consensus 92 ikKAv~~RkHLe~n~kD~~~k~~L~LiESkI~RL~rYYk~~~~LP 136 (140)
.-+-.++-.|.+.|+||.++.+.|.-.=-+=+|+.+|-.+...-+
T Consensus 194 t~~i~~~~r~~~~Hkkd~~~~~~l~~~~qkR~r~Lkyl~~~~~~~ 238 (256)
T KOG2815|consen 194 TVEIRKLSRHEELHKKDQASVRGLRQEVQKRQRALKYLARANRQR 238 (256)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcc
Confidence 345667788999999999999999888788899999988876544
No 159
>PRK03002 prsA peptidylprolyl isomerase; Reviewed
Probab=28.55 E-value=2.3e+02 Score=23.55 Aligned_cols=33 Identities=24% Similarity=0.410 Sum_probs=23.9
Q ss_pred hhHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHh
Q 032468 69 SKILRILKAHGLAPEIPEDLYHLIKKAVAIRKHLE 103 (140)
Q Consensus 69 ~ki~~ILk~nglap~iPEDL~~LikKAv~~RkHLe 103 (140)
..+.+.|+.+|+.. .+++.+-|+.-+.+.+.+.
T Consensus 89 ~~f~~~L~~~G~~~--~~~~r~~ir~~l~~~~~~~ 121 (285)
T PRK03002 89 DQFKNVLKNNGLKD--EADFKNQIKFKLAMNEAIK 121 (285)
T ss_pred HHHHHHHHHcCCCC--HHHHHHHHHHHHHHHHHHh
Confidence 36888899999852 5788888887776655543
No 160
>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=28.41 E-value=96 Score=26.51 Aligned_cols=35 Identities=17% Similarity=0.304 Sum_probs=28.0
Q ss_pred CCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhh
Q 032468 21 TPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRD 56 (140)
Q Consensus 21 ~~P~W~~~~~eeve~~IvklakkG~~pSqIG~~LRD 56 (140)
.+|.|+. ++++...++..|.+.|+|..+|-.++-.
T Consensus 270 ~~~~gl~-~~~~~~~l~~~L~~rG~s~~~i~~i~g~ 304 (309)
T cd01301 270 GTPGGLE-DVSDLPNLTAELLERGYSEEEIEKIAGG 304 (309)
T ss_pred CCccccC-CHHHHHHHHHHHHHcCCCHHHHHHHHhh
Confidence 3466664 7889999999999999999999877643
No 161
>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=28.37 E-value=62 Score=25.82 Aligned_cols=39 Identities=10% Similarity=0.361 Sum_probs=20.2
Q ss_pred CCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCC
Q 032468 44 GLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAP 82 (140)
Q Consensus 44 G~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap 82 (140)
|+|+|-+-.+|.+.-+-..|..-|=.+|.++.++.|-.|
T Consensus 10 GVS~~TVSrvLn~~~~~~~vs~~tr~rV~~~a~~lgY~p 48 (327)
T TIGR02417 10 GVSKTTASYVINGKAKEYRISQETVERVMAVVREQGYQP 48 (327)
T ss_pred CCCHHHHHHHHcCCCCCCccCHHHHHHHHHHHHHhCCCC
Confidence 566666666665432111345555556666665555443
No 162
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=28.23 E-value=34 Score=20.58 Aligned_cols=24 Identities=17% Similarity=0.338 Sum_probs=13.9
Q ss_pred HHHHHHHHHHHhcCCCcchhhhHh
Q 032468 31 QDVEDNICKFAKKGLTPSQIGVIL 54 (140)
Q Consensus 31 eeve~~IvklakkG~~pSqIG~~L 54 (140)
++....|+.|..+|+|..+|...|
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 455667888888899999998776
No 163
>PLN03196 MOC1-like protein; Provisional
Probab=28.22 E-value=1.2e+02 Score=27.56 Aligned_cols=57 Identities=19% Similarity=0.254 Sum_probs=38.9
Q ss_pred CChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeee--cc--hhHHHHHHHcCCCCCChhhHHHHHHH
Q 032468 28 ISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSV--TG--SKILRILKAHGLAPEIPEDLYHLIKK 94 (140)
Q Consensus 28 ~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~v--tG--~ki~~ILk~nglap~iPEDL~~LikK 94 (140)
.+-+.|.+.|.=|-+.|++.++|+ .| |.+=.. .. ..+.++|++.|+.. +|+-.+|.+
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 466778888888888999999998 23 554322 21 23678999999874 566655554
No 164
>PRK00726 murG undecaprenyldiphospho-muramoylpentapeptide beta-N- acetylglucosaminyltransferase; Provisional
Probab=27.68 E-value=1.2e+02 Score=24.75 Aligned_cols=66 Identities=15% Similarity=0.091 Sum_probs=40.3
Q ss_pred ccCCCceeeecch-------hHHHHHHHcCCCCCC------hhhHHHHHHHHH---HHHHHHhHcCCcccchhHHHHHHH
Q 032468 57 SHGIAQVKSVTGS-------KILRILKAHGLAPEI------PEDLYHLIKKAV---AIRKHLERNRKDKDSKFRLILVES 120 (140)
Q Consensus 57 ~~GVp~Vk~vtG~-------ki~~ILk~nglap~i------PEDL~~LikKAv---~~RkHLe~n~kD~~~k~~L~LiES 120 (140)
..|+|.|-.-.|. -..+.+.+.|....+ ||+|.+.|.+.+ ..++-+.++-+.....+...-+..
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 789999888876 445555555554444444444433
Q ss_pred HH
Q 032468 121 RI 122 (140)
Q Consensus 121 kI 122 (140)
.|
T Consensus 350 ~~ 351 (357)
T PRK00726 350 LI 351 (357)
T ss_pred HH
Confidence 33
No 165
>PRK12468 flhB flagellar biosynthesis protein FlhB; Reviewed
Probab=27.41 E-value=1.9e+02 Score=25.94 Aligned_cols=63 Identities=21% Similarity=0.297 Sum_probs=47.4
Q ss_pred CCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHH-HcCCCCCChhhHHHHHHHHHHHH
Q 032468 21 TPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILK-AHGLAPEIPEDLYHLIKKAVAIR 99 (140)
Q Consensus 21 ~~P~W~~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk-~nglap~iPEDL~~LikKAv~~R 99 (140)
.+|-=+-.-.+++-..|.++|+ +||||-|.. ..+.|-|= .-.+..+||++||.-|-..++.-
T Consensus 285 ~AP~VvAKG~d~~A~~Ir~~A~--------------e~~VPiven---~pLARaLy~~~evg~~IP~ely~AVA~ILa~V 347 (386)
T PRK12468 285 SAPKVLAKGAGAVALRIRELGA--------------EHRIPLLEA---PPLARALFRHSEVGQHIPATLYAAVAEVLAWV 347 (386)
T ss_pred CCCEEEEeeCcHHHHHHHHHHH--------------HcCCcEEeC---HHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHH
Confidence 4555566677888888888887 489999886 45888885 56788999999998776665543
Q ss_pred H
Q 032468 100 K 100 (140)
Q Consensus 100 k 100 (140)
-
T Consensus 348 ~ 348 (386)
T PRK12468 348 Y 348 (386)
T ss_pred H
Confidence 3
No 166
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=27.31 E-value=55 Score=26.26 Aligned_cols=35 Identities=29% Similarity=0.374 Sum_probs=19.3
Q ss_pred CCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCC
Q 032468 44 GLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLA 81 (140)
Q Consensus 44 G~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~ngla 81 (140)
|+|+|-+-.+|.+. +.|..-|=.+|.++.+|.|-.
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 66666655555443 345555555555555555543
No 167
>PRK10974 glycerol-3-phosphate transporter periplasmic binding protein; Provisional
Probab=26.99 E-value=68 Score=27.29 Aligned_cols=45 Identities=20% Similarity=0.144 Sum_probs=31.5
Q ss_pred hccCCCceeeecchhH-HHHHHHcCCCC-CChhhHHHHHHHHHHHHH
Q 032468 56 DSHGIAQVKSVTGSKI-LRILKAHGLAP-EIPEDLYHLIKKAVAIRK 100 (140)
Q Consensus 56 D~~GVp~Vk~vtG~ki-~~ILk~nglap-~iPEDL~~LikKAv~~Rk 100 (140)
.+||||..-...+-=. ..+|++.|+.| +.|+..-.|+.-|..|.+
T Consensus 136 ~~YglP~~~~~~~l~YNkdlf~~aGi~~~~~P~Twde~~~~a~~l~~ 182 (438)
T PRK10974 136 HLLSQPFNSSTPVLYYNKDAFKKAGLDPEQPPKTWQDLAAYAAKLRA 182 (438)
T ss_pred cEEEeeccCCCceEEEcHHHHHHcCCCCCCCCCCHHHHHHHHHHHHh
Confidence 3799998876655211 26899999975 688777777766666653
No 168
>PRK10376 putative oxidoreductase; Provisional
Probab=26.95 E-value=1.8e+02 Score=23.90 Aligned_cols=59 Identities=14% Similarity=0.201 Sum_probs=35.5
Q ss_pred HHHHHHh-cCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcC--CCCCChhhHHHHHHHH
Q 032468 36 NICKFAK-KGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHG--LAPEIPEDLYHLIKKA 95 (140)
Q Consensus 36 ~Ivklak-kG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~ng--lap~iPEDL~~LikKA 95 (140)
.+..+|+ .|.||+|+...--=+++ |.+-.+.|.+-.+-|++|= +.-+++++...-|.++
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 59999999884443331 3344577776655565542 2236788777777655
No 169
>PRK09071 hypothetical protein; Validated
Probab=26.87 E-value=65 Score=27.93 Aligned_cols=28 Identities=11% Similarity=0.310 Sum_probs=19.8
Q ss_pred cCChHHHHHHHHHHHhcCCCcchhhhHh
Q 032468 27 KISSQDVEDNICKFAKKGLTPSQIGVIL 54 (140)
Q Consensus 27 ~~~~eeve~~IvklakkG~~pSqIG~~L 54 (140)
++|.||..+.+-.+..-.++|+|||..|
T Consensus 20 ~Lt~eEa~~~~~~il~g~~~~~q~aAfL 47 (323)
T PRK09071 20 SLTREEARQAMGMILDGEVEDDQLGAFL 47 (323)
T ss_pred CCCHHHHHHHHHHHHcCCCCHHHHHHHH
Confidence 3477777777777777777777777654
No 170
>COG2358 Imp TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=26.81 E-value=1.2e+02 Score=26.76 Aligned_cols=51 Identities=22% Similarity=0.287 Sum_probs=32.0
Q ss_pred CCChhhHHHHHHHHHHHHHHHhHcCCcccchhHH----HHHHHHH-----HHHHHHHHhcCCC
Q 032468 82 PEIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRL----ILVESRI-----HRLARYYKKTKKL 135 (140)
Q Consensus 82 p~iPEDL~~LikKAv~~RkHLe~n~kD~~~k~~L----~LiESkI-----~RL~rYYk~~~~L 135 (140)
.++|||+-..|-||+- .|+.+-+ -.|..+.. ..+++-+ -=+.||||..|..
T Consensus 260 ~~v~ed~vY~~tKa~f--en~d~l~-~~h~~~~~l~~~~~a~~g~~iPlHpGA~kyykE~G~~ 319 (321)
T COG2358 260 DDVSEDLVYKLTKALF--ENLDELK-TLHPALEDLKELENAKSGLVIPLHPGAAKYYKEIGVW 319 (321)
T ss_pred CCCCHHHHHHHHHHHH--HhhHHHh-hcChhhhhhhhhhhhhcCCccccChhHHHHHHhcCcC
Confidence 4789999999999865 6666543 22333332 2333332 2358999999983
No 171
>PRK13870 transcriptional regulator TraR; Provisional
Probab=26.68 E-value=50 Score=26.79 Aligned_cols=28 Identities=11% Similarity=0.122 Sum_probs=22.7
Q ss_pred cCChHHHHHHHHHHHhcCCCcchhhhHhhh
Q 032468 27 KISSQDVEDNICKFAKKGLTPSQIGVILRD 56 (140)
Q Consensus 27 ~~~~eeve~~IvklakkG~~pSqIG~~LRD 56 (140)
.+|+-|.| |...+-.|.|..+||.||-=
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 172
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=26.61 E-value=1.2e+02 Score=16.47 Aligned_cols=33 Identities=18% Similarity=0.247 Sum_probs=17.5
Q ss_pred CCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCC
Q 032468 44 GLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAP 82 (140)
Q Consensus 44 G~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap 82 (140)
|++++.|...+...+.+ +...+.++.+.-|+.+
T Consensus 21 ~i~~~~i~~~~~~~~~~------~~~~~~~i~~~~~~~~ 53 (56)
T smart00530 21 GVSRSTLSRIENGKRKP------SLETLKKLAKALGVSL 53 (56)
T ss_pred CCCHHHHHHHHCCCCCC------CHHHHHHHHHHhCCCh
Confidence 66666666666655422 4444555555444443
No 173
>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=26.56 E-value=54 Score=26.82 Aligned_cols=44 Identities=20% Similarity=0.336 Sum_probs=26.1
Q ss_pred CCCCCCCCCCcCCCCCCCCCCCccCChHHHHHHHHHHHhcCCCcchh
Q 032468 4 MHSRGKGISASALPYKRTPPSWLKISSQDVEDNICKFAKKGLTPSQI 50 (140)
Q Consensus 4 mh~~~kG~S~S~~P~~~~~P~W~~~~~eeve~~IvklakkG~~pSqI 50 (140)
||.++.|...+..|+ .|.=..--.+.+++.|..+.+.|+++.+|
T Consensus 126 m~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~i~~~~~~Gi~~~~I 169 (258)
T cd00423 126 MHMDGTPQTMQNNPY---YADVVDEVVEFLEERVEAATEAGIPPEDI 169 (258)
T ss_pred ECcCCCCcccccCCC---cchHHHHHHHHHHHHHHHHHHcCCCHHHE
Confidence 787777765444332 12111112466677788888999877654
No 174
>PRK13317 pantothenate kinase; Provisional
Probab=26.42 E-value=1.2e+02 Score=25.51 Aligned_cols=57 Identities=16% Similarity=0.126 Sum_probs=37.0
Q ss_pred HHHHHHHhcCCCcchhhhHhhhccCC-------CceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHHH
Q 032468 35 DNICKFAKKGLTPSQIGVILRDSHGI-------AQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVA 97 (140)
Q Consensus 35 ~~IvklakkG~~pSqIG~~LRD~~GV-------p~Vk~vtG~ki~~ILk~nglap~iPEDL~~LikKAv~ 97 (140)
+.+.+||++|- ++-+.+.+.|-||. -..-.|.|+ + .-|-..|.. +||+..=+-.+|+
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 44588888888887 445577777 3 334445543 7887765555554
No 175
>PF09373 PMBR: Pseudomurein-binding repeat; InterPro: IPR018975 Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum) is a methanogenic Gram-positive microorganism with a cell wall consisting of pseudomurein. This repeat specifically binds to pseudomurein. This repeat is found at the N terminus of PeiW and PeiP which are pseudomurein binding phage proteins.
Probab=26.30 E-value=61 Score=19.07 Aligned_cols=17 Identities=24% Similarity=0.604 Sum_probs=13.9
Q ss_pred HHHHHHHHHHhcCCCCC
Q 032468 121 RIHRLARYYKKTKKLPP 137 (140)
Q Consensus 121 kI~RL~rYYk~~~~LP~ 137 (140)
-..|...||...|+||.
T Consensus 13 ~a~rv~~f~~~ngRlPn 29 (33)
T PF09373_consen 13 MASRVNNFYESNGRLPN 29 (33)
T ss_pred HHHHHHHHHHHcCCCCC
Confidence 35678899999999985
No 176
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=26.27 E-value=1.6e+02 Score=24.51 Aligned_cols=62 Identities=19% Similarity=0.251 Sum_probs=42.9
Q ss_pred CChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCCh------hhHHHHHHHHHHH
Q 032468 28 ISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIP------EDLYHLIKKAVAI 98 (140)
Q Consensus 28 ~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~iP------EDL~~LikKAv~~ 98 (140)
++++++.+.+. + +-..|+..|-||.=|+-|=++- -.+||=..|+.|.-| +++..|+..+..+
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 45556655553 3 2368999999997444443332 357999999999877 7888887766665
No 177
>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=26.17 E-value=1.4e+02 Score=21.38 Aligned_cols=39 Identities=21% Similarity=0.327 Sum_probs=29.5
Q ss_pred CCCCCCCCCccCChHHHHH--HHHHHHhcCCCcchhhhHhh
Q 032468 17 PYKRTPPSWLKISSQDVED--NICKFAKKGLTPSQIGVILR 55 (140)
Q Consensus 17 P~~~~~P~W~~~~~eeve~--~IvklakkG~~pSqIG~~LR 55 (140)
|.++..-..-.+++++|.. .|..|.+.|++.++|-.+|.
T Consensus 28 p~~~~~~g~R~Y~~~dl~~l~~I~~lr~~G~~l~~I~~~l~ 68 (108)
T cd04773 28 PDREPETGYRVYDPSDVRDARLIHLLRRGGYLLEQIATVVE 68 (108)
T ss_pred CCcCCCCCceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence 4443334566789999875 58888889999999988875
No 178
>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=26.16 E-value=1.1e+02 Score=27.40 Aligned_cols=33 Identities=12% Similarity=0.222 Sum_probs=27.6
Q ss_pred hHHHHHHHHHHHhcC--CCcchhhhHhhhccCCCc
Q 032468 30 SQDVEDNICKFAKKG--LTPSQIGVILRDSHGIAQ 62 (140)
Q Consensus 30 ~eeve~~IvklakkG--~~pSqIG~~LRD~~GVp~ 62 (140)
.+|+++.|.+++-.. -||-|+|.+|.++.|.|.
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 179
>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=26.15 E-value=93 Score=22.33 Aligned_cols=71 Identities=21% Similarity=0.465 Sum_probs=45.3
Q ss_pred HHHHHHHHHHHhcCC-CcchhhhHhhhccCCCceeeecc----hhHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHh
Q 032468 31 QDVEDNICKFAKKGL-TPSQIGVILRDSHGIAQVKSVTG----SKILRILKAHGLAPEIPEDLYHLIKKAVAIRKHLE 103 (140)
Q Consensus 31 eeve~~IvklakkG~-~pSqIG~~LRD~~GVp~Vk~vtG----~ki~~ILk~nglap~iPEDL~~LikKAv~~RkHLe 103 (140)
++|-..|++|-.+=+ -..+||..-.+. |.|-.-+.-= .++.+..++.|+.|++=|.||.+|-.. ++|.|-+
T Consensus 13 D~ID~qLv~LL~~R~~~~~~ia~~K~~~-~~~v~dp~Re~~vl~~~~~~a~~~gl~p~~~e~i~~~i~~e-sir~q~~ 88 (94)
T TIGR01795 13 DNIDAAVIHMLAERFKCTSQVGVLKANA-GLAPADPAREDYQIARLRRLAIDAGLDPEFAEKFLNFIVTE-VIKHHER 88 (94)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhC-CCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHH-HHHHHHH
Confidence 556666666655444 345677765544 5554432211 245666788999999999999998655 6777743
No 180
>PF13910 DUF4209: Domain of unknown function (DUF4209)
Probab=26.13 E-value=29 Score=24.79 Aligned_cols=45 Identities=20% Similarity=0.255 Sum_probs=32.1
Q ss_pred hHhhhccCCCceeee-----cchhHHHHHHHcCCCCCChhhHHHHHHHHH
Q 032468 52 VILRDSHGIAQVKSV-----TGSKILRILKAHGLAPEIPEDLYHLIKKAV 96 (140)
Q Consensus 52 ~~LRD~~GVp~Vk~v-----tG~ki~~ILk~nglap~iPEDL~~LikKAv 96 (140)
..|+|.+|+...+.- .-+-+.++|....++.-++||+.++++-..
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 356777777666442 235677888888888888899888887655
No 181
>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=26.13 E-value=51 Score=28.01 Aligned_cols=58 Identities=17% Similarity=0.387 Sum_probs=41.1
Q ss_pred ChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecc---------------------------hhHHHHHHHcCCC
Q 032468 29 SSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTG---------------------------SKILRILKAHGLA 81 (140)
Q Consensus 29 ~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG---------------------------~ki~~ILk~ngla 81 (140)
+.++|++.+..|.+++++-|. |.|+-=+++= .-+.++|++.|+.
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 689999999999999987753 4444322221 2246678888888
Q ss_pred CCChhhHHHHHHHH
Q 032468 82 PEIPEDLYHLIKKA 95 (140)
Q Consensus 82 p~iPEDL~~LikKA 95 (140)
+++.|..+.++.+.
T Consensus 93 ~~~~~~~~~~l~~~ 106 (239)
T PF03744_consen 93 EEAAEKAFELLDSG 106 (239)
T ss_pred HHHHHHHHHHHhcC
Confidence 88777777777655
No 182
>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=26.07 E-value=1.3e+02 Score=26.25 Aligned_cols=35 Identities=26% Similarity=0.497 Sum_probs=27.8
Q ss_pred hHHHHHHHHHHHhcCC---CcchhhhHhhhccCCCcee
Q 032468 30 SQDVEDNICKFAKKGL---TPSQIGVILRDSHGIAQVK 64 (140)
Q Consensus 30 ~eeve~~IvklakkG~---~pSqIG~~LRD~~GVp~Vk 64 (140)
-+|+++.+.+|+...+ ||-|+...|-|..|+|..+
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 183
>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=25.99 E-value=49 Score=23.81 Aligned_cols=33 Identities=24% Similarity=0.649 Sum_probs=21.3
Q ss_pred CCCCCCCCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhh
Q 032468 15 ALPYKRTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRD 56 (140)
Q Consensus 15 ~~P~~~~~P~W~~~~~eeve~~IvklakkG~~pSqIG~~LRD 56 (140)
+-|| ..|.|+ -+.+..||+.+-+|..||...+.
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 4465 446675 57888899999999999887654
No 184
>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=25.93 E-value=63 Score=23.84 Aligned_cols=23 Identities=13% Similarity=0.286 Sum_probs=16.5
Q ss_pred CChHHHHHHHHHHHhcCCCcchh
Q 032468 28 ISSQDVEDNICKFAKKGLTPSQI 50 (140)
Q Consensus 28 ~~~eeve~~IvklakkG~~pSqI 50 (140)
++++.+.+.+-.+.+.|+.+|++
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 57888888888888999999975
No 185
>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=25.77 E-value=96 Score=16.01 Aligned_cols=20 Identities=10% Similarity=0.356 Sum_probs=14.9
Q ss_pred ChHHHHHHHHHHHhcCCCcc
Q 032468 29 SSQDVEDNICKFAKKGLTPS 48 (140)
Q Consensus 29 ~~eeve~~IvklakkG~~pS 48 (140)
..++..+...++-+.|+.|+
T Consensus 15 ~~~~a~~~~~~M~~~g~~p~ 34 (35)
T TIGR00756 15 RVEEALELFKEMLERGIEPD 34 (35)
T ss_pred CHHHHHHHHHHHHHcCCCCC
Confidence 35677778888888887775
No 186
>PRK05755 DNA polymerase I; Provisional
Probab=25.76 E-value=2.3e+02 Score=27.49 Aligned_cols=48 Identities=27% Similarity=0.385 Sum_probs=35.2
Q ss_pred hHHHHHHHHHHHhc---CCCcchhhhHhhhccCCCceee-----ecchhHHHHHHH
Q 032468 30 SQDVEDNICKFAKK---GLTPSQIGVILRDSHGIAQVKS-----VTGSKILRILKA 77 (140)
Q Consensus 30 ~eeve~~Ivklakk---G~~pSqIG~~LRD~~GVp~Vk~-----vtG~ki~~ILk~ 77 (140)
.+++++.+.+++-. --||-|++.+|-+..|+|.++. -|.+..++-|.+
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 567776666654
No 187
>cd00006 PTS_IIA_man PTS_IIA, PTS system, mannose/sorbose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation. IIA subunits receive phosphoryl groups from HPr and transfer them to IIB subunits, which in turn phosphorylate the substrate.
Probab=25.63 E-value=2.6e+02 Score=20.05 Aligned_cols=51 Identities=22% Similarity=0.292 Sum_probs=34.6
Q ss_pred CCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHHH
Q 032468 44 GLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVA 97 (140)
Q Consensus 44 G~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~iPEDL~~LikKAv~ 97 (140)
|=||.++...+...+ +.+..|+|..+-=+|+.--.... =.++-.++..++.
T Consensus 68 GGSp~n~~~~~~~~~--~~~~visG~nlpmlle~~~~~~~-~~~~~e~~~~~~~ 118 (122)
T cd00006 68 GGSPNNAAARLSMEH--PPVEVIAGVNLPMLLEAARAREL-GLSLDELVENALE 118 (122)
T ss_pred CCCHHHHHHHHHhcC--CCEEEEEccCHHHHHHHHHcccc-CCCHHHHHHHHHH
Confidence 579999998888777 88999999998877765332221 1245555555443
No 188
>PF13643 DUF4145: Domain of unknown function (DUF4145)
Probab=25.59 E-value=1.7e+02 Score=19.25 Aligned_cols=51 Identities=25% Similarity=0.311 Sum_probs=31.4
Q ss_pred chhHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHhHcCCcccchhHHHHHH
Q 032468 68 GSKILRILKAHGLAPEIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVE 119 (140)
Q Consensus 68 G~ki~~ILk~nglap~iPEDL~~LikKAv~~RkHLe~n~kD~~~k~~L~LiE 119 (140)
=.+...-|...|+ |+---|.++-|++.=|---|-.......+++--|.++|
T Consensus 37 L~~~I~~l~~~~~-~~~~~~~~~~iR~~GN~aaH~~~~~~~~da~~~l~~~e 87 (87)
T PF13643_consen 37 LNEKINKLRKKGL-PPDIRDWLHAIRKIGNDAAHEEKEITEEDAEDALEFLE 87 (87)
T ss_pred HHHHHHHHHHcCC-CHHHHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHhC
Confidence 3455667888888 66666677777777777777423334445555554443
No 189
>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=25.52 E-value=2.2e+02 Score=26.31 Aligned_cols=64 Identities=11% Similarity=0.243 Sum_probs=45.9
Q ss_pred cCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCCh-hhHHHHHHHHHH
Q 032468 27 KISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIP-EDLYHLIKKAVA 97 (140)
Q Consensus 27 ~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~iP-EDL~~LikKAv~ 97 (140)
.++++.+.++|.-++..-+|..++=.+|..-. -+|....+|.+++|+..--- ..|..+|+.+++
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 46788888887666666666666666665543 23788999999999985333 369999998864
No 190
>PRK09526 lacI lac repressor; Reviewed
Probab=25.39 E-value=66 Score=25.78 Aligned_cols=35 Identities=14% Similarity=0.267 Sum_probs=20.6
Q ss_pred CCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCC
Q 032468 44 GLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLA 81 (140)
Q Consensus 44 G~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~ngla 81 (140)
|+|.|-+-.+|.+. |.|..-|-++|.++.+|-|-.
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 345556666666666665543
No 191
>KOG4115 consensus Dynein-associated protein Roadblock [Cell cycle control, cell division, chromosome partitioning; Cell motility]
Probab=25.28 E-value=36 Score=25.48 Aligned_cols=60 Identities=25% Similarity=0.450 Sum_probs=37.8
Q ss_pred hHHHHHHHHHHHh-cCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHHh
Q 032468 30 SQDVEDNICKFAK-KGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVAIRKHLE 103 (140)
Q Consensus 30 ~eeve~~Ivklak-kG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~iPEDL~~LikKAv~~RkHLe 103 (140)
..|||+.+-++-. +|.+ |.++-|.+|||.=-...- ..+..- ---|-.|..||-++=.-|+
T Consensus 2 ~~~vEe~~~R~qs~~gV~----giiv~d~~GvpikTt~d~-~~t~~y---------a~~l~~L~~kars~VrdlD 62 (97)
T KOG4115|consen 2 SAEVEETLKRLQSYKGVT----GIIVVDNAGVPIKTTLDN-TTTQQY---------AALLHPLVEKARSVVRDLD 62 (97)
T ss_pred cHHHHHHHHHHhccCCce----eEEEECCCCcEeEeccCc-hHHHHH---------HHHHHHHHHHHHHHHHccC
Confidence 3578888888654 7876 999999999985443322 222221 1235567777776654443
No 192
>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=25.25 E-value=68 Score=25.57 Aligned_cols=37 Identities=22% Similarity=0.451 Sum_probs=25.9
Q ss_pred cCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCC
Q 032468 43 KGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAP 82 (140)
Q Consensus 43 kG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap 82 (140)
-|+|+|-+-.+|.+. +.|..-|=.+|.++.++-|-.|
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 4566777777777777777554
No 193
>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=25.09 E-value=2.6e+02 Score=19.88 Aligned_cols=36 Identities=19% Similarity=0.263 Sum_probs=28.8
Q ss_pred CCCccCChHHHHH--HHHHHHhcCCCcchhhhHhhhcc
Q 032468 23 PSWLKISSQDVED--NICKFAKKGLTPSQIGVILRDSH 58 (140)
Q Consensus 23 P~W~~~~~eeve~--~IvklakkG~~pSqIG~~LRD~~ 58 (140)
..+=.+++++|.. .|..|..-|+|.++|-.++....
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 4566778888865 57888889999999999887754
No 194
>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=25.07 E-value=41 Score=33.36 Aligned_cols=34 Identities=18% Similarity=0.296 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHhc-CCCcchhhhHhhh-------------ccCCCcee
Q 032468 31 QDVEDNICKFAKK-GLTPSQIGVILRD-------------SHGIAQVK 64 (140)
Q Consensus 31 eeve~~Ivklakk-G~~pSqIG~~LRD-------------~~GVp~Vk 64 (140)
+.|.+.|.+|.+. |++++.|.++.|| +||||-.-
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 58999653
No 195
>COG0013 AlaS Alanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=24.36 E-value=86 Score=31.34 Aligned_cols=54 Identities=20% Similarity=0.242 Sum_probs=39.3
Q ss_pred HHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHH
Q 032468 33 VEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLI 92 (140)
Q Consensus 33 ve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~iPEDL~~Li 92 (140)
+++.+-++.+...=+-++-..|-|.||+|. -. +.+|+++.|+.-++|..-+.+.
T Consensus 373 ~~~~~~~~~~~~~l~ge~afkLYDTyGfP~-eL-----t~eia~e~g~~VD~~~f~~~m~ 426 (879)
T COG0013 373 LEKELAKLKKSKTLDGEDAFKLYDTYGFPV-EL-----TEEIAEERGLKVDEPGFEYAME 426 (879)
T ss_pred HHHHHHhhccCCccChHHheeehhcCCCCH-HH-----HHHHHHHcCCeeccccHHHHHH
Confidence 445555565533445677889999999995 22 5679999999999998876443
No 196
>COG1609 PurR Transcriptional regulators [Transcription]
Probab=24.29 E-value=70 Score=26.91 Aligned_cols=38 Identities=26% Similarity=0.434 Sum_probs=30.7
Q ss_pred cCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCC
Q 032468 43 KGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPE 83 (140)
Q Consensus 43 kG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~ 83 (140)
-|+|+|-+-..|.+.- .|..-|-.||.++.++-|-.|.
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 4888888888888764 8888888888888888887764
No 197
>PRK02998 prsA peptidylprolyl isomerase; Reviewed
Probab=24.04 E-value=2.9e+02 Score=23.01 Aligned_cols=32 Identities=22% Similarity=0.355 Sum_probs=22.7
Q ss_pred hhHHHHHHHcCCCCCChhhHHHHHHHHHHHHHHH
Q 032468 69 SKILRILKAHGLAPEIPEDLYHLIKKAVAIRKHL 102 (140)
Q Consensus 69 ~ki~~ILk~nglap~iPEDL~~LikKAv~~RkHL 102 (140)
..+.+.|++.|+.. ++++...|+.-+.+++-+
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 367777777766666654
No 198
>PF08463 EcoEI_R_C: EcoEI R protein C-terminal; InterPro: IPR013670 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 I restriction endonucleases are components of prokaryotic DNA restriction-modification mechanisms that protects the organism against invading foreign DNA. Type I enzymes have three different subunits subunits - M (modification), S (specificity) and R (restriction) - that form multifunctional enzymes with restriction (3.1.21.3 from EC), methylase (2.1.1.72 from EC) and ATPase activities [, ]. The S subunit is required for both restriction and modification and is responsible for recognition of the DNA sequence specific for the system. The M subunit is necessary for modification, and the R subunit is required for restriction. These enzymes use S-Adenosyl-L-methionine (AdoMet) as the methyl group donor in the methylation reaction, and have a requirement for ATP. They recognise asymmetric DNA sequences split into two domains of specific sequence, one 3-4 bp long and another 4-5 bp long, separated by a nonspecific spacer 6-8 bp in length. Cleavage occurs a considerable distance from the recognition sites, rarely less than 400 bp away and up to 7000 bp away. Adenosyl residues are methylated, one on each strand of the recognition sequence. These enzymes are widespread in eubacteria and archaea. In enteric bacteria they have been subdivide into four families: types IA, IB, IC and ID. Type III restriction endonucleases (3.1.21.5 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. Type III enzymes are hetero-oligomeric, multifunctional proteins composed of two subunits, Res and Mod. The Mod subunit recognises the DNA sequence specific for the system and is a modification methyltransferase; as such it is functionally equivalent to the M and S subunits of type I restriction endonuclease. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognise short 5-6 bp long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Type III enzymes belong to the beta-subfamily of N6 adenine methyltransferases, containing the nine motifs that characterise this family, including motif I, the AdoMet binding pocket (FXGXG), and motif IV, the catalytic region (S/D/N (PP) Y/F) [, ]. This entry represents the C-terminal domain found in both the R subunit of type I enzymes and the Res subunit of type III enzymes. The type I enzyme represented is EcoEI, which recognises 5'-GAGN(7)ATGC-3; the R protein (HsdR) is required for both nuclease and ATPase activity [, ]. ; GO: 0003677 DNA binding, 0003824 catalytic activity, 0006304 DNA modification
Probab=24.01 E-value=60 Score=24.32 Aligned_cols=15 Identities=20% Similarity=0.567 Sum_probs=12.0
Q ss_pred HHHHHHHHHhcCCCC
Q 032468 122 IHRLARYYKKTKKLP 136 (140)
Q Consensus 122 I~RL~rYYk~~~~LP 136 (140)
+.+|..||...|.+-
T Consensus 110 L~~i~~~~~~~G~~~ 124 (164)
T PF08463_consen 110 LERILDYYAQNGIIE 124 (164)
T ss_pred HHHHHHHHHHhCccc
Confidence 567899999988764
No 199
>PRK01490 tig trigger factor; Provisional
Probab=23.85 E-value=57 Score=28.44 Aligned_cols=52 Identities=23% Similarity=0.424 Sum_probs=26.8
Q ss_pred ccCChHHHHHHHHHHHh-cCCCcchhhhHhhhccCCCcee-eecchhHHHHHHH
Q 032468 26 LKISSQDVEDNICKFAK-KGLTPSQIGVILRDSHGIAQVK-SVTGSKILRILKA 77 (140)
Q Consensus 26 ~~~~~eeve~~Ivklak-kG~~pSqIG~~LRD~~GVp~Vk-~vtG~ki~~ILk~ 77 (140)
+..|.+||++.+.++|. -|+++.+|=..+-++-....++ .++-.|+.+.|.+
T Consensus 366 i~vs~eei~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~i~~~l~~~Kv~~~l~~ 419 (435)
T PRK01490 366 IEVSDEEVKAEIEEMASQYGQPPEVIEFYLKNPQLLAALRADVLEEKVVDFLLE 419 (435)
T ss_pred CCCCHHHHHHHHHHHHHHcCCCHHHHHHHHhChhhHHHHHHHHHHHHHHHHHHH
Confidence 45677788888888775 3555555444433221111222 3444445444444
No 200
>PF14907 NTP_transf_5: Uncharacterised nucleotidyltransferase
Probab=23.76 E-value=1.6e+02 Score=22.90 Aligned_cols=55 Identities=13% Similarity=0.242 Sum_probs=44.4
Q ss_pred HHHHHHHHHHHhcCCCcchh-hhHhhhccCCCcee----------eecchhHHHHHHHcCCCCCCh
Q 032468 31 QDVEDNICKFAKKGLTPSQI-GVILRDSHGIAQVK----------SVTGSKILRILKAHGLAPEIP 85 (140)
Q Consensus 31 eeve~~IvklakkG~~pSqI-G~~LRD~~GVp~Vk----------~vtG~ki~~ILk~nglap~iP 85 (140)
.|+.++...|.+.|+++--+ |..|.+-|+-|..+ .-.-.+..++|.++|..+.-+
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 46778888899999999888 99999999998644 334567899999999877665
No 201
>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=23.64 E-value=1.6e+02 Score=21.29 Aligned_cols=24 Identities=21% Similarity=0.320 Sum_probs=18.9
Q ss_pred ChHHHHHHHHHHHhcCCCcchhhh
Q 032468 29 SSQDVEDNICKFAKKGLTPSQIGV 52 (140)
Q Consensus 29 ~~eeve~~IvklakkG~~pSqIG~ 52 (140)
++++..+.|.+|+++|.+-=-|+.
T Consensus 57 ~~~~~~~~i~~L~~~~~agL~i~~ 80 (123)
T PF07905_consen 57 DEEELREFIRELAEKGAAGLGIKT 80 (123)
T ss_pred CHHHHHHHHHHHHHCCCeEEEEec
Confidence 456799999999999987655543
No 202
>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=23.34 E-value=77 Score=20.98 Aligned_cols=25 Identities=28% Similarity=0.535 Sum_probs=20.1
Q ss_pred ccCChHHHHHHHHHHHhcCCCcchh
Q 032468 26 LKISSQDVEDNICKFAKKGLTPSQI 50 (140)
Q Consensus 26 ~~~~~eeve~~IvklakkG~~pSqI 50 (140)
+.++.+|||..|+++-..|.=...|
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 3567799999999999999765544
No 203
>PF09098 Dehyd-heme_bind: Quinohemoprotein amine dehydrogenase A, alpha subunit, haem binding; InterPro: IPR015182 Quinohemoprotein amine dehydrogenases (QHNDH) 1.4.99 from EC) are enzymes produced in the periplasmic space of certain Gram-negative bacteria, such as Paracoccus denitrificans and Pseudomonas putida, in response to primary amines, including n-butylamine and benzylamine. QHNDH catalyses the oxidative deamination of a wide range of aliphatic and aromatic amines through formation of a Schiff-base intermediate involving one of the quinone O atoms []. Catalysis requires the presence of a novel redox cofactor, cysteine tryptophylquinone (CTQ). CTQ is derived from the post-translational modification of specific residues, which involves the oxidation of the indole ring of a tryptophan residue to form tryptophylquinone, followed by covalent cross-linking with a cysteine residue []. There is one CTQ per subunit in QHNDH. In addition to CTQ, two haem c cofactors are present in QHNDH that mediate the transfer of the substrate-derived electrons from CTQ to an external electron acceptor, cytochrome c-550 [, ]. QHNDH is a heterotrimer of alpha, beta and gamma subunits. The alpha and beta subunits contain signal peptides necessary for the translocation of QHNDH to the periplasm. The alpha subunit is composed of four domains - domain 1 forming a dihaem cytochrome, and domains 2-4 forming antiparallel beta-barrel structures; the beta subunit is a 7-bladed beta-propeller that provides part of the active site; and the small, catalytic gamma subunit contains the novel cross-linked CTQ cofactor, in addition to additional thioester cross-links between Cys and Asp/Glu residues that encage CTQ. The gamma subunit assumes a globular secondary structure with two short alpha-helices having many turns and bends []. This entry represents the dihaem cytochrome c domain of the QHNDH alpha subunit. The domain contain two cysteine residues that are involved in thioether linkages to haem []. ; PDB: 1PBY_A 1JJU_A 1JMZ_A 1JMX_A.
Probab=23.06 E-value=68 Score=26.14 Aligned_cols=26 Identities=31% Similarity=0.482 Sum_probs=12.4
Q ss_pred ccCChHHHHHHHHHHHh-cCCCcchhh
Q 032468 26 LKISSQDVEDNICKFAK-KGLTPSQIG 51 (140)
Q Consensus 26 ~~~~~eeve~~Ivklak-kG~~pSqIG 51 (140)
+.+|++|-...|--||+ .|+.||+.-
T Consensus 49 l~Is~eer~avVkYLAd~~GLap~Et~ 75 (167)
T PF09098_consen 49 LPISPEERRAVVKYLADTQGLAPSETA 75 (167)
T ss_dssp ----HHHHHHHHHHHHHHT---CGGCT
T ss_pred CCCCHHHHHHHHHHHHHccCCCchhhc
Confidence 34566666666666665 677777653
No 204
>PRK14975 bifunctional 3'-5' exonuclease/DNA polymerase; Provisional
Probab=23.03 E-value=4.2e+02 Score=24.37 Aligned_cols=30 Identities=20% Similarity=0.248 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHhc-C---CCcchhhhHhhhccCCC
Q 032468 31 QDVEDNICKFAKK-G---LTPSQIGVILRDSHGIA 61 (140)
Q Consensus 31 eeve~~Ivklakk-G---~~pSqIG~~LRD~~GVp 61 (140)
+++++.|.+++.. . -||-|++.+| +..|+|
T Consensus 207 ~~l~~~i~~~~g~~~~n~~S~~ql~~~L-~~~g~~ 240 (553)
T PRK14975 207 AELAAEIREALGRPRLNPDSPQQVLRAL-RRAGIE 240 (553)
T ss_pred HHHHHHHHHHhCCCCCCCCCHHHHHHHH-HHCCCC
Confidence 5777777776642 1 4788999999 789998
No 205
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=22.97 E-value=1.7e+02 Score=20.82 Aligned_cols=50 Identities=24% Similarity=0.332 Sum_probs=35.3
Q ss_pred CChHHHHHHHHHHH----hcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCC
Q 032468 28 ISSQDVEDNICKFA----KKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAP 82 (140)
Q Consensus 28 ~~~eeve~~Ivkla----kkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap 82 (140)
.+.+|+|++...+. +.|+|.+++|..+---||. -++-..|.++ +...|.+
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 45677777655543 4899999999999888886 3566667775 4455544
No 206
>PF03825 Nuc_H_symport: Nucleoside H+ symporter
Probab=22.92 E-value=43 Score=29.12 Aligned_cols=16 Identities=31% Similarity=0.748 Sum_probs=13.3
Q ss_pred HHHhcCCCcchhhhHh
Q 032468 39 KFAKKGLTPSQIGVIL 54 (140)
Q Consensus 39 klakkG~~pSqIG~~L 54 (140)
=|..+|+|++|||.++
T Consensus 28 ~L~~~G~s~~qIG~l~ 43 (400)
T PF03825_consen 28 YLESRGFSGTQIGILL 43 (400)
T ss_pred HHHhCCCCHHHHHHHH
Confidence 4677899999999885
No 207
>cd01528 RHOD_2 Member of the Rhodanese Homology Domain superfamily, subgroup 2. Subgroup 2 includes uncharacterized putative rhodanese-related domains.
Probab=22.83 E-value=1.5e+02 Score=19.88 Aligned_cols=46 Identities=17% Similarity=0.378 Sum_probs=29.3
Q ss_pred CCCccCChHHHHHHHHHHH------------hcCCCcchhhhHhhhccCCCceeeecch
Q 032468 23 PSWLKISSQDVEDNICKFA------------KKGLTPSQIGVILRDSHGIAQVKSVTGS 69 (140)
Q Consensus 23 P~W~~~~~eeve~~Ivkla------------kkG~~pSqIG~~LRD~~GVp~Vk~vtG~ 69 (140)
|..+.++-+++.+.+-.+. ..|...+.....|+. +|..+|+.+.|-
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 357777777777775 888888877773
No 208
>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=22.71 E-value=1.8e+02 Score=18.43 Aligned_cols=33 Identities=27% Similarity=0.316 Sum_probs=24.8
Q ss_pred CCCCccCChHHHHH--HHHHHHhcCCCcchhhhHh
Q 032468 22 PPSWLKISSQDVED--NICKFAKKGLTPSQIGVIL 54 (140)
Q Consensus 22 ~P~W~~~~~eeve~--~IvklakkG~~pSqIG~~L 54 (140)
.--.=.++.++|+. .|..|...|+|..+|-.+|
T Consensus 32 ~~g~R~y~~~~l~~l~~i~~l~~~g~~l~~i~~~l 66 (67)
T cd04764 32 ENGRRYYTDEDIELLKKIKTLLEKGLSIKEIKEIL 66 (67)
T ss_pred CCCceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHh
Confidence 33444578888875 5788889999999997665
No 209
>TIGR01075 uvrD DNA helicase II. Designed to identify uvrD members of the uvrD/rep subfamily.
Probab=22.66 E-value=47 Score=31.06 Aligned_cols=35 Identities=17% Similarity=0.196 Sum_probs=28.9
Q ss_pred hHHHHHHHHHHHhcCCCcchhhhHhhh------------ccCCCcee
Q 032468 30 SQDVEDNICKFAKKGLTPSQIGVILRD------------SHGIAQVK 64 (140)
Q Consensus 30 ~eeve~~IvklakkG~~pSqIG~~LRD------------~~GVp~Vk 64 (140)
++.|.+.|..|...|++++.|.+..|. ++|||...
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 345777888888899999999999998 58999653
No 210
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR. SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.
Probab=22.65 E-value=3.5e+02 Score=20.55 Aligned_cols=38 Identities=16% Similarity=0.100 Sum_probs=29.8
Q ss_pred CCCCCCCccCChHHH--HHHHHHHHhcCCCcchhhhHhhh
Q 032468 19 KRTPPSWLKISSQDV--EDNICKFAKKGLTPSQIGVILRD 56 (140)
Q Consensus 19 ~~~~P~W~~~~~eev--e~~IvklakkG~~pSqIG~~LRD 56 (140)
.+..-.+=.|+.++| ...|..|..-|+|..+|..+|..
T Consensus 30 ~r~~~g~R~Y~~~di~~l~~I~~lr~~G~sL~eI~~~l~~ 69 (142)
T TIGR01950 30 IRNSGNQRRYKRDVLRRVAVIKAAQRVGIPLATIGEALAV 69 (142)
T ss_pred ccCCCCCEEECHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 344445666788888 46799999999999999998853
No 211
>PF14230 DUF4333: Domain of unknown function (DUF4333)
Probab=22.59 E-value=1e+02 Score=21.22 Aligned_cols=25 Identities=20% Similarity=0.494 Sum_probs=19.1
Q ss_pred cCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCcee
Q 032468 27 KISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVK 64 (140)
Q Consensus 27 ~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk 64 (140)
.++.+++++.|.+ .|.++||++.+.
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 5688999987765 566888887664
No 212
>PF04282 DUF438: Family of unknown function (DUF438); InterPro: IPR007380 This is a a group of uncharacterised proteins.
Probab=22.57 E-value=94 Score=21.77 Aligned_cols=25 Identities=12% Similarity=0.336 Sum_probs=19.2
Q ss_pred cCChHHHHHHHHHHHhcCCCcchhh
Q 032468 27 KISSQDVEDNICKFAKKGLTPSQIG 51 (140)
Q Consensus 27 ~~~~eeve~~IvklakkG~~pSqIG 51 (140)
++|+.||-..=-+|-+.|+++..|-
T Consensus 28 ~Vs~~EI~~~Eq~Li~eG~~~eeiq 52 (71)
T PF04282_consen 28 DVSASEISAAEQELIQEGMPVEEIQ 52 (71)
T ss_pred CCCHHHHHHHHHHHHHcCCCHHHHH
Confidence 4677888777777888888888774
No 213
>COG1393 ArsC Arsenate reductase and related proteins, glutaredoxin family [Inorganic ion transport and metabolism]
Probab=22.48 E-value=50 Score=24.57 Aligned_cols=36 Identities=28% Similarity=0.381 Sum_probs=25.0
Q ss_pred cCCCceeeecchhHHHHHHHcCCCCCC---------hhhHHHHHHHH
Q 032468 58 HGIAQVKSVTGSKILRILKAHGLAPEI---------PEDLYHLIKKA 95 (140)
Q Consensus 58 ~GVp~Vk~vtG~ki~~ILk~nglap~i---------PEDL~~LikKA 95 (140)
||+|..- |=+|-.+.|+++|+++++ .|+|..++.+.
T Consensus 6 y~~p~C~--t~rka~~~L~~~gi~~~~~~y~~~~~s~~eL~~~l~~~ 50 (117)
T COG1393 6 YGNPNCS--TCRKALAWLEEHGIEYTFIDYLKTPPSREELKKILSKL 50 (117)
T ss_pred EeCCCCh--HHHHHHHHHHHcCCCcEEEEeecCCCCHHHHHHHHHHc
Confidence 6777776 677888888888888752 35666665543
No 214
>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=22.48 E-value=2.1e+02 Score=18.30 Aligned_cols=35 Identities=17% Similarity=0.362 Sum_probs=25.5
Q ss_pred CCCCCCccCChHHHHH--HHHHHHhcCCCcchhhhHh
Q 032468 20 RTPPSWLKISSQDVED--NICKFAKKGLTPSQIGVIL 54 (140)
Q Consensus 20 ~~~P~W~~~~~eeve~--~IvklakkG~~pSqIG~~L 54 (140)
++.-..=.+|.+||.. .|..|-+.|+|.++|-.+|
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 3334444578888764 5788888999999997765
No 215
>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=22.26 E-value=52 Score=21.52 Aligned_cols=12 Identities=42% Similarity=0.877 Sum_probs=10.0
Q ss_pred CCCChhhHHHHH
Q 032468 81 APEIPEDLYHLI 92 (140)
Q Consensus 81 ap~iPEDL~~Li 92 (140)
.||+|+.|.+|-
T Consensus 33 EpEVPkELt~l~ 44 (45)
T smart00794 33 EPEVPKELTDLY 44 (45)
T ss_pred CCcCcHHHHhhc
Confidence 699999998763
No 216
>PF13783 DUF4177: Domain of unknown function (DUF4177)
Probab=22.25 E-value=97 Score=19.99 Aligned_cols=20 Identities=25% Similarity=0.539 Sum_probs=17.6
Q ss_pred CChHHHHHHHHHHHhcCCCc
Q 032468 28 ISSQDVEDNICKFAKKGLTP 47 (140)
Q Consensus 28 ~~~eeve~~IvklakkG~~p 47 (140)
.+.+++++.+.++|++|---
T Consensus 17 ~~~~~~~~~Ln~~g~eGWeL 36 (61)
T PF13783_consen 17 IDPEDLEEILNEYGKEGWEL 36 (61)
T ss_pred CCHHHHHHHHHHHHhCCcEE
Confidence 68999999999999999543
No 217
>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=22.24 E-value=1.4e+02 Score=21.80 Aligned_cols=40 Identities=18% Similarity=0.196 Sum_probs=30.7
Q ss_pred CCCCCCCCccCChHHHHH--HHHHHHhcCCCcchhhhHhhhc
Q 032468 18 YKRTPPSWLKISSQDVED--NICKFAKKGLTPSQIGVILRDS 57 (140)
Q Consensus 18 ~~~~~P~W~~~~~eeve~--~IvklakkG~~pSqIG~~LRD~ 57 (140)
..+..-..-.+++++|+. .|..|..-|+|-.+|..+|...
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 334445666788898865 6889999999999999988643
No 218
>PRK00252 alaS alanyl-tRNA synthetase; Reviewed
Probab=22.23 E-value=2e+02 Score=28.35 Aligned_cols=47 Identities=13% Similarity=0.119 Sum_probs=36.6
Q ss_pred CCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHHHH
Q 032468 45 LTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVAI 98 (140)
Q Consensus 45 ~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~iPEDL~~LikKAv~~ 98 (140)
.=|...-..|-|.||+|.= =+..|++++|+.-++| ..+.+|.++-..
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 1446889999998888 788888766543
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=22.11 E-value=88 Score=23.20 Aligned_cols=28 Identities=25% Similarity=0.425 Sum_probs=17.9
Q ss_pred HHHHHHHHHHH-hcCCCcchhhhHhhhcc
Q 032468 31 QDVEDNICKFA-KKGLTPSQIGVILRDSH 58 (140)
Q Consensus 31 eeve~~Ivkla-kkG~~pSqIG~~LRD~~ 58 (140)
+++.+.|-++- +.|..|-.||..+|-+|
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 99999999999999887
No 220
>PF14842 FliG_N: FliG N-terminal domain; PDB: 3HJL_A 3AJC_A 3USY_B.
Probab=21.99 E-value=91 Score=22.46 Aligned_cols=32 Identities=16% Similarity=0.358 Sum_probs=22.9
Q ss_pred cCChHHHHHHHHHHHh-cCCCcchhhhHhhhcc
Q 032468 27 KISSQDVEDNICKFAK-KGLTPSQIGVILRDSH 58 (140)
Q Consensus 27 ~~~~eeve~~Ivklak-kG~~pSqIG~~LRD~~ 58 (140)
.++++||+.+...+++ ..+++.++-.+|.+=|
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 5588888888887754
No 221
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=21.83 E-value=1.3e+02 Score=22.92 Aligned_cols=40 Identities=18% Similarity=0.159 Sum_probs=31.2
Q ss_pred CCCCCCCCCccCChHHHHH--HHHHHHhcCCCcchhhhHhhh
Q 032468 17 PYKRTPPSWLKISSQDVED--NICKFAKKGLTPSQIGVILRD 56 (140)
Q Consensus 17 P~~~~~P~W~~~~~eeve~--~IvklakkG~~pSqIG~~LRD 56 (140)
|.++..--+=.|+.++|+. .|..|..-|+|-++|..+|..
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 688899999999999998864
No 222
>TIGR03544 DivI1A_domain DivIVA domain. This model describes a domain found in Bacillus subtilis cell division initiation protein DivIVA, and homologs, toward the N-terminus. It is also found as a repeated domain in certain other proteins, including family TIGR03543.
Probab=21.79 E-value=39 Score=19.94 Aligned_cols=15 Identities=13% Similarity=0.220 Sum_probs=6.7
Q ss_pred cCChHHHHHHHHHHH
Q 032468 27 KISSQDVEDNICKFA 41 (140)
Q Consensus 27 ~~~~eeve~~Ivkla 41 (140)
-++++||-+.+-.++
T Consensus 17 GY~~~eVD~fLd~v~ 31 (34)
T TIGR03544 17 GYDAAEVDAFLDRVA 31 (34)
T ss_pred CCCHHHHHHHHHHHH
Confidence 344444444444433
No 223
>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=21.78 E-value=2e+02 Score=26.53 Aligned_cols=49 Identities=10% Similarity=0.245 Sum_probs=35.4
Q ss_pred CChHHHHHHHHHHHhcCCCc---chhhhHhhhccCCCceeeecchhHHHHHH
Q 032468 28 ISSQDVEDNICKFAKKGLTP---SQIGVILRDSHGIAQVKSVTGSKILRILK 76 (140)
Q Consensus 28 ~~~eeve~~IvklakkG~~p---SqIG~~LRD~~GVp~Vk~vtG~ki~~ILk 76 (140)
.+.+|+++.|.+|.++|+.- ..+..-+=.++|++.|=...|.+|...++
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 23555566678888876655555544443
No 224
>PHA02535 P terminase ATPase subunit; Provisional
Probab=21.76 E-value=4.1e+02 Score=25.43 Aligned_cols=52 Identities=19% Similarity=0.243 Sum_probs=38.0
Q ss_pred CChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHH
Q 032468 28 ISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYH 90 (140)
Q Consensus 28 ~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~iPEDL~~ 90 (140)
+|+| +....+.|.-+|+|+++|-..| ||| +.. |..--+.-+-.-..|++=..
T Consensus 3 yt~E-fK~~Av~Ly~~G~sv~eIA~~L----Gv~-~~T-----l~~W~kr~~w~~~~~~~~v~ 54 (581)
T PHA02535 3 YDDD-VRRAAKFLYWQGWTVAEIAEEL----GLK-SRT-----IYSWKERDGWRDLLPEERIE 54 (581)
T ss_pred CCHH-HHHHHHHHHHcCCCHHHHHHHh----CCC-hhH-----HHHHhccccccccCCcccHH
Confidence 4444 6777779988999999999877 888 333 66667777777777766443
No 225
>TIGR01673 holin_LLH phage holin, LL-H family. This model represents a putative phage holin from a number of phage and prophage regions of Gram-positive bacteria. Like other holins, it is small (about 100 amino acids) with stretches of hydrophobic sequence and is encoded adjacent to lytic enzymes.
Probab=21.76 E-value=1.7e+02 Score=21.84 Aligned_cols=30 Identities=23% Similarity=0.135 Sum_probs=25.7
Q ss_pred hhHHHHHHHcCCCCCChhhHHHHHHHHHHH
Q 032468 69 SKILRILKAHGLAPEIPEDLYHLIKKAVAI 98 (140)
Q Consensus 69 ~ki~~ILk~nglap~iPEDL~~LikKAv~~ 98 (140)
+.|...|...|+.-.=+++|.++|.+||.-
T Consensus 74 ~~v~~~L~~~~i~~~t~~~i~~~IE~aV~~ 103 (108)
T TIGR01673 74 NYITEELKKAHIPKPSDAQIEGAIEAAVAE 103 (108)
T ss_pred HHHHHHHHHcCCCCCCHHHHHHHHHHHHHH
Confidence 458899999999666689999999999974
No 226
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. 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=21.70 E-value=1.9e+02 Score=21.08 Aligned_cols=33 Identities=18% Similarity=0.088 Sum_probs=28.4
Q ss_pred CCccCChHHHHHH--HHHHHhcCCCcchhhhHhhh
Q 032468 24 SWLKISSQDVEDN--ICKFAKKGLTPSQIGVILRD 56 (140)
Q Consensus 24 ~W~~~~~eeve~~--IvklakkG~~pSqIG~~LRD 56 (140)
-+=.+++++|+.+ |..|...|+|-++|..+|..
T Consensus 33 gyR~Y~~~~l~~l~~I~~lr~~G~~L~~I~~~l~~ 67 (118)
T cd04776 33 QTRVYSRRDRARLKLILRGKRLGFSLEEIRELLDL 67 (118)
T ss_pred CccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 6777899999876 88999999999999988864
No 227
>PF01312 Bac_export_2: FlhB HrpN YscU SpaS Family; InterPro: IPR006135 Salmonella, and related proteobacteria, secrete large amounts of proteins into the culture media. The major secreted proteins are either flagellar proteins or virulence factors [], secreted through the flagellar or virulence export structures respectively. Both secretion systems penetrate the inner and outer membranes and their components bear substantial sequence similarity. Both the flagellar and needle like pilus look fairly similar to each other []. The type III secretion system is of great interest, as it is used to transport virulence factors from the pathogen directly into the host cell [] and is only triggered when the bacterium comes into close contact with the host. It is believed that the family of type III flagellar and pilus inner membrane proteins are used as structural moieties in a complex with several other subunits []. One such set of inner membrane proteins, labeled "S" here for nomenclature purposes, includes the Salmonella and Shigella SpaS, the Yersinia YscU, Rhizobium Y4YO, and the Erwinia HrcU genes, Salmonella FlhB and Escherichia coli EscU [, , , ]. Many of the proteins, in this entry, undergo autocatalytic cleavage promoted by cyclization of a conserved asparagine. These proteins belong to the MEROPS peptidase family N6. ; GO: 0009306 protein secretion, 0016020 membrane; PDB: 3C03_C 3BZT_A 3BZV_B 3BZP_A 3BZX_B 3BZL_B 3C00_A 3BZR_A 3BZY_A 3BZO_A ....
Probab=21.61 E-value=89 Score=27.20 Aligned_cols=56 Identities=25% Similarity=0.449 Sum_probs=33.1
Q ss_pred CCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHcC-CCCCChhhHHHHHHHH
Q 032468 23 PSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHG-LAPEIPEDLYHLIKKA 95 (140)
Q Consensus 23 P~W~~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~ng-lap~iPEDL~~LikKA 95 (140)
|-=+-.-.+++-..|.++|+ +||||-|.+ ..+.|-|=.+. +..+|||+||.-+-..
T Consensus 282 P~vvAKG~d~~A~~Ir~~A~--------------~~~VPiven---~pLARaLy~~~~~g~~IP~ely~aVA~i 338 (343)
T PF01312_consen 282 PIVVAKGADELALRIREIAR--------------EHGVPIVEN---PPLARALYRTVEVGQEIPEELYEAVAEI 338 (343)
T ss_dssp EEEEEEEECHHHHHHHHHHH--------------HHT--EEE----HHHHHHHHHHS-TTSB--GGGHHHHHHH
T ss_pred CEEeeeccHHHHHHHHHHHH--------------HcCCCeeeC---HHHHHHHHhcCCCCCcCCHHHHHHHHHH
Confidence 33333445666666766665 478888776 45777776654 7889999999665443
No 228
>PLN02900 alanyl-tRNA synthetase
Probab=21.61 E-value=2.2e+02 Score=28.46 Aligned_cols=57 Identities=9% Similarity=0.134 Sum_probs=41.7
Q ss_pred HHHHHHHHhc--CCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCCCChhhHHHHHHHHHH
Q 032468 34 EDNICKFAKK--GLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAPEIPEDLYHLIKKAVA 97 (140)
Q Consensus 34 e~~Ivklakk--G~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap~iPEDL~~LikKAv~ 97 (140)
++.|-++.++ +.=|.+.--.|-|.||+|.= =+..|.+|+|+.-+++ ..+.+|.++-.
T Consensus 397 ~~~i~~~~~~~~~~l~g~~af~LydTyGfP~d------lt~~ia~e~g~~vD~~-~F~~~~~~~~~ 455 (936)
T PLN02900 397 KKALAAAKANGGPVLSGKDAFLLYDTYGFPVD------LTELMAEERGVTVDME-GFEAAMEEARE 455 (936)
T ss_pred HHHHHHHhhcCCCcCCHHHHHHHHhccCCCHH------HHHHHHHHcCCeecHH-HHHHHHHHHHH
Confidence 3444444332 45588999999999999952 1446889999999988 88888877653
No 229
>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=21.58 E-value=33 Score=28.69 Aligned_cols=47 Identities=21% Similarity=0.441 Sum_probs=23.2
Q ss_pred CCChhhHHHHHHHHHHHHHHHhHcCCcccchhHHHHHH---HHHHHHHHHHHh
Q 032468 82 PEIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVE---SRIHRLARYYKK 131 (140)
Q Consensus 82 p~iPEDL~~LikKAv~~RkHLe~n~kD~~~k~~L~LiE---SkI~RL~rYYk~ 131 (140)
-.+|+|+|.|++--..=-+---+|+| +++|+-+.| .-=+++..+|..
T Consensus 66 wn~p~~i~~il~~f~ge~~p~~~~~k---~~rrmf~~Efs~~Eq~~il~wf~~ 115 (205)
T PF11463_consen 66 WNFPDNIYQILQYFTGELKPYIKNPK---DKRRMFITEFSQEEQDRILNWFNK 115 (205)
T ss_dssp H---HHHHHHHHHHHSSS--SSSTSS---SSS---GGGS-HHHHHHHHHHHHH
T ss_pred HcCCHHHHHHHHHHcccCCccccCCc---chhhhHHHhhhHHHHHHHHHHHHh
Confidence 46899999999876654443444555 455555555 444455555443
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=21.46 E-value=91 Score=21.45 Aligned_cols=30 Identities=23% Similarity=0.491 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHhcCCCcchhhhHhhhccCC
Q 032468 31 QDVEDNICKFAKKGLTPSQIGVILRDSHGI 60 (140)
Q Consensus 31 eeve~~IvklakkG~~pSqIG~~LRD~~GV 60 (140)
++|.+.|.+-...|.++.+|-..|++..++
T Consensus 1 ~~i~~~v~~~i~~G~~~~~~~~~l~~~~~~ 30 (112)
T PF04233_consen 1 DRIRQAVTQGIERGKSPQEIAKRLRDRGGV 30 (112)
T ss_pred ChHHHHHHHHHHcCCCHHHHHHHHHHHhCc
Confidence 468888888889999999999999999554
No 231
>PF03869 Arc: Arc-like DNA binding domain; InterPro: IPR005569 Arc repressor act by the cooperative binding of two Arc repressor dimers to a 21-base-pair operator site. Each Arc dimer uses an antiparallel beta-sheet to recognise bases in the major groove [].; GO: 0003677 DNA binding; PDB: 3QOQ_D 1MNT_B 1QTG_B 1BDV_A 1PAR_C 1BDT_C 1ARR_B 1MYL_F 1MYK_A 1NLA_B ....
Probab=21.45 E-value=2.1e+02 Score=18.23 Aligned_cols=39 Identities=28% Similarity=0.483 Sum_probs=24.6
Q ss_pred CChhhHHHHHHHHHHHHHHHhHcCCcccchhHHHHHHHHHHHHHHHHHhcCCC
Q 032468 83 EIPEDLYHLIKKAVAIRKHLERNRKDKDSKFRLILVESRIHRLARYYKKTKKL 135 (140)
Q Consensus 83 ~iPEDL~~LikKAv~~RkHLe~n~kD~~~k~~L~LiESkI~RL~rYYk~~~~L 135 (140)
-||++|+.-|+.+ =+.|.+-.++- =|++|-.++++.|.+
T Consensus 10 RlP~~l~~~lk~~------A~~~gRS~NsE--------Iv~~L~~~l~~e~~i 48 (50)
T PF03869_consen 10 RLPEELKEKLKER------AEENGRSMNSE--------IVQRLEEALKKEGRI 48 (50)
T ss_dssp ECEHHHHHHHHHH------HHHTTS-HHHH--------HHHHHHHHHHHCTSS
T ss_pred ECCHHHHHHHHHH------HHHhCCChHHH--------HHHHHHHHHhccccC
Confidence 3899999888765 23444444332 266777777777765
No 232
>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=21.34 E-value=2e+02 Score=20.71 Aligned_cols=39 Identities=23% Similarity=0.247 Sum_probs=30.0
Q ss_pred CCCCCCCCCccCChHHHHH--HHHHHHhcCCCcchhhhHhhh
Q 032468 17 PYKRTPPSWLKISSQDVED--NICKFAKKGLTPSQIGVILRD 56 (140)
Q Consensus 17 P~~~~~P~W~~~~~eeve~--~IvklakkG~~pSqIG~~LRD 56 (140)
|.++.. ..=.++.+++.. .|..|..-|+|.++|..++..
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 666678888875 699999999999999988753
No 233
>PRK09492 treR trehalose repressor; Provisional
Probab=21.19 E-value=91 Score=24.67 Aligned_cols=36 Identities=22% Similarity=0.519 Sum_probs=18.4
Q ss_pred CCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCCCC
Q 032468 44 GLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGLAP 82 (140)
Q Consensus 44 G~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~nglap 82 (140)
|+|+|-+-.+|.+. |.|..-|=.+|.++.++.|-.|
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 234
>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=21.16 E-value=3.1e+02 Score=19.33 Aligned_cols=41 Identities=29% Similarity=0.287 Sum_probs=30.0
Q ss_pred CCCCCCCCCCccCChHHHHH--HHHHHHh-cCCCcchhhhHhhh
Q 032468 16 LPYKRTPPSWLKISSQDVED--NICKFAK-KGLTPSQIGVILRD 56 (140)
Q Consensus 16 ~P~~~~~P~W~~~~~eeve~--~Ivklak-kG~~pSqIG~~LRD 56 (140)
.|..+..+.+-.++.++|+. .|..|.+ .|++-.+|-..|..
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 45556666555789998875 5667776 69999999888764
No 235
>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=21.02 E-value=84 Score=23.72 Aligned_cols=29 Identities=28% Similarity=0.342 Sum_probs=21.3
Q ss_pred HHHHHHHHHhcCCCcchhhhHhhhccCCC
Q 032468 33 VEDNICKFAKKGLTPSQIGVILRDSHGIA 61 (140)
Q Consensus 33 ve~~IvklakkG~~pSqIG~~LRD~~GVp 61 (140)
.++.|.=|.+||+|..+|-..|+..=.-+
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 67888899999999999999998754433
No 236
>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=21.00 E-value=1.8e+02 Score=21.34 Aligned_cols=39 Identities=21% Similarity=0.341 Sum_probs=30.4
Q ss_pred CCCCCCCCCccCChHHHHH--HHHHHHhcCCCcchhhhHhh
Q 032468 17 PYKRTPPSWLKISSQDVED--NICKFAKKGLTPSQIGVILR 55 (140)
Q Consensus 17 P~~~~~P~W~~~~~eeve~--~IvklakkG~~pSqIG~~LR 55 (140)
|..++.--+=.|+.++|+. .|..|..-|+|-++|..+|.
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 3444555677789998875 68889999999999998885
No 237
>PRK00283 xerD site-specific tyrosine recombinase XerD; Reviewed
Probab=20.94 E-value=1e+02 Score=23.77 Aligned_cols=31 Identities=16% Similarity=0.257 Sum_probs=26.5
Q ss_pred CCccCChHHHHHHHHHHHhcCCCcchhhhHh
Q 032468 24 SWLKISSQDVEDNICKFAKKGLTPSQIGVIL 54 (140)
Q Consensus 24 ~W~~~~~eeve~~IvklakkG~~pSqIG~~L 54 (140)
.|-++++++|++.+..+.+.|++++.+...+
T Consensus 47 ~~~~l~~~~i~~~~~~~~~~~~~~~t~~~~~ 77 (299)
T PRK00283 47 SLAEATRDDLQAFLAELAEGGYKATSSARRL 77 (299)
T ss_pred ChHHCCHHHHHHHHHHHHhCCCCHHHHHHHH
Confidence 5778899999999999998899998886543
No 238
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=20.92 E-value=91 Score=25.22 Aligned_cols=34 Identities=6% Similarity=0.251 Sum_probs=17.2
Q ss_pred CCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCC
Q 032468 44 GLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGL 80 (140)
Q Consensus 44 G~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~ngl 80 (140)
|+|+|-+-..|... |.|..-|-.+|.++.++-|-
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 55555555555433 33455555555555555543
No 239
>PF02536 mTERF: mTERF; InterPro: IPR003690 This family currently contains one sequence of known function human mitochondrial transcription termination factor (mTERF), a multizipper protein but binds to DNA as a monomer, with evidence pointing to intramolecular leucine zipper interactions []. The precursors contain a mitochondrial targeting sequence, and the mature mTERF exhibits three leucine zippers, of which one is bipartite, and two widely spaced basic domains. Both basic domains and the three leucine zipper motifs are necessary for DNA binding. The leucine zippers are not implicated in a dimerisation role as in other leucine zippers []. The rest of the family consists of hypothetical proteins none of which have any functional information.; PDB: 3M66_A 3OPG_A 3MVA_O 3MVB_O 3N7Q_A 3N6S_A.
Probab=20.69 E-value=68 Score=26.42 Aligned_cols=44 Identities=20% Similarity=0.323 Sum_probs=30.5
Q ss_pred CCCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeee
Q 032468 20 RTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSV 66 (140)
Q Consensus 20 ~~~P~W~~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~v 66 (140)
...|.++.++.+.+...|--|.+-|+|-.||+.+++.. |++=..
T Consensus 230 ~~~p~il~~~~~~l~~~i~~L~~lG~s~~ei~~mv~~~---P~iL~~ 273 (345)
T PF02536_consen 230 KKFPQILSLSEEKLKPKIEFLQSLGFSEEEIAKMVRRF---PQILSY 273 (345)
T ss_dssp -------THHHHHHHHHHHHHHTTT--HHHHHHHHHHS---GGGGGS
T ss_pred cccccccccchHhHHHHHHHHHHhcCcHHHHHHHHHhC---cchhhc
Confidence 45799999999999999999999999999999999877 654433
No 240
>TIGR01641 phageSPP1_gp7 phage putative head morphogenesis protein, SPP1 gp7 family. This model describes a region of about 110 amino acids found exclusively in phage-related proteins, internally or toward the C-terminus. One member, gp7 of phage SPP1, appears involved in head morphogenesis.
Probab=20.46 E-value=72 Score=22.35 Aligned_cols=29 Identities=31% Similarity=0.549 Sum_probs=22.4
Q ss_pred HHHHHHHHHhcCCCcchhhhHhhhccCCC
Q 032468 33 VEDNICKFAKKGLTPSQIGVILRDSHGIA 61 (140)
Q Consensus 33 ve~~IvklakkG~~pSqIG~~LRD~~GVp 61 (140)
|++.|.+=-.+|.++.+|-..|++.+|+-
T Consensus 1 ~~~~l~~gi~~G~~~~~iak~i~~~~~~~ 29 (108)
T TIGR01641 1 VEDILADGVQRGLGPNELAKRLRKELGVQ 29 (108)
T ss_pred ChHHHHHHHHcCCCHHHHHHHHHHHHCcc
Confidence 35556666667999999999999998643
No 241
>PRK13111 trpA tryptophan synthase subunit alpha; Provisional
Probab=20.44 E-value=2.9e+02 Score=23.12 Aligned_cols=51 Identities=22% Similarity=0.395 Sum_probs=33.6
Q ss_pred CCCCcCCCCCCCCCCCccCChHHHHHHHHHHHhcCCCcc----------hhhhHhhhccCCC---ceeeecch
Q 032468 10 GISASALPYKRTPPSWLKISSQDVEDNICKFAKKGLTPS----------QIGVILRDSHGIA---QVKSVTGS 69 (140)
Q Consensus 10 G~S~S~~P~~~~~P~W~~~~~eeve~~IvklakkG~~pS----------qIG~~LRD~~GVp---~Vk~vtG~ 69 (140)
|..|...| ++..||+++.+..+.+.|+.+- .|-.+....-|.= .+.-+||.
T Consensus 117 GvdGviip---------DLp~ee~~~~~~~~~~~gl~~I~lvap~t~~eri~~i~~~s~gfIY~vs~~GvTG~ 180 (258)
T PRK13111 117 GVDGLIIP---------DLPPEEAEELRAAAKKHGLDLIFLVAPTTTDERLKKIASHASGFVYYVSRAGVTGA 180 (258)
T ss_pred CCcEEEEC---------CCCHHHHHHHHHHHHHcCCcEEEEeCCCCCHHHHHHHHHhCCCcEEEEeCCCCCCc
Confidence 55666665 6677999999999999996433 3666666666632 22345665
No 242
>TIGR01523 ATPase-IID_K-Na potassium and/or sodium efflux P-type ATPase, fungal-type. The Leishmania sequence (GP|3192903), which falls between trusted and noise in this model, may very well turn out to be an active potassium pump.
Probab=20.42 E-value=93 Score=31.07 Aligned_cols=58 Identities=12% Similarity=0.110 Sum_probs=41.7
Q ss_pred CCCCCCccCChHHHHHHHHHHHhcCCCcchhhhHhhhccCCCceeeecchhHHHHHHHc
Q 032468 20 RTPPSWLKISSQDVEDNICKFAKKGLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAH 78 (140)
Q Consensus 20 ~~~P~W~~~~~eeve~~IvklakkG~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~n 78 (140)
.+.|+|...+.+||.+..--=..+|+|.+|.- ..|.+||--.+..-.+.++.+++-++
T Consensus 2 ~~~~~~~~~~~~~v~~~l~t~~~~GLs~~ea~-~rl~~~G~N~l~~~~~~s~~~~~l~q 59 (1053)
T TIGR01523 2 AEFNAYFSDIADEAAEFIGTSIPEGLTHDEAQ-HRLKEVGENRLEADSGIDAKAMLLHQ 59 (1053)
T ss_pred CCCCchhhCCHHHHHHHhCcCcccCCCHHHHH-HHHHHcCCCCCCCCCCCCHHHHHHHH
Confidence 36799999999999887532224699999954 56678998777766666666555443
No 243
>PF02607 B12-binding_2: B12 binding domain; InterPro: IPR003759 Cobalamin-dependent methionine synthase (2.1.1.13 from EC) is a large modular protein that catalyses methyl transfer from methyltetrahydrofolate (CH3-H4folate) to homocysteine. During the catalytic cycle, it supports three distinct methyl transfer reactions, each involving the cobalamin (vitamin B12) cofactor and a substrate bound to its own functional unit []. The cobalamin cofactor plays an essential role in this reaction, accepting the methyl group from CH3-H4folate to form methylcob(III)alamin, and in turn donating the methyl group to homocysteine to generate methionine and cob(I)alamin. Methionine synthase is a large enzyme composed of four structurally and functionally distinct modules: the first two modules bind homocysteine and CH3-H4folate, the third module binds the cobalamin cofactor and the C-terminal module binds S-adenosylmethionine. The cobalamin-binding module is composed of two structurally distinct domains: a 4-helical bundle cap domain (residues 651-740 in the Escherichia coli enzyme) and an alpha/beta B12-binding domain (residues 741-896) (IPR006158 from INTERPRO). The 4-helical bundle forms a cap over the alpha/beta domain, which acts to shield the methyl ligand of cobalamin from solvent []. Furthermore, in the conversion to the active conformation of this enzyme, the 4-helical cap rotates to allow the cobalamin cofactor to bind the activation domain (IPR004223 from INTERPRO). The alpha/beta domain is a common cobalamin-binding motif, whereas the 4-helical bundle domain with its methyl cap is a distinctive feature of methionine synthases. This entry represents the 4-helical bundle cap domain. This domain is also present in other shorter proteins that bind to B12, and is always found N terminus to the alpha/beta B12-binding domain.; GO: 0008705 methionine synthase activity, 0031419 cobalamin binding, 0046872 metal ion binding, 0009086 methionine biosynthetic process; PDB: 3EZX_A 3BUL_A 1K7Y_A 1BMT_A 3IV9_A 1K98_A 3IVA_A 2I2X_P.
Probab=20.39 E-value=79 Score=20.61 Aligned_cols=26 Identities=15% Similarity=0.158 Sum_probs=20.1
Q ss_pred cCChHHHHHHHHHHHhcCCCcchhhh
Q 032468 27 KISSQDVEDNICKFAKKGLTPSQIGV 52 (140)
Q Consensus 27 ~~~~eeve~~IvklakkG~~pSqIG~ 52 (140)
..+.+++++.+-++...|++|..|=.
T Consensus 14 ~~d~~~~~~~~~~~l~~g~~~~~i~~ 39 (79)
T PF02607_consen 14 AGDEEEAEALLEEALAQGYPPEDIIE 39 (79)
T ss_dssp TT-CCHHHHHHHHHHHCSSSTTHHHH
T ss_pred hCCHHHHHHHHHHHHHcCCCHHHHHH
Confidence 45778899999999988988877644
No 244
>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=20.35 E-value=2.2e+02 Score=20.22 Aligned_cols=39 Identities=21% Similarity=0.151 Sum_probs=29.6
Q ss_pred CCCCCCccCChHHHHHH--HHHH-HhcCCCcchhhhHhhhcc
Q 032468 20 RTPPSWLKISSQDVEDN--ICKF-AKKGLTPSQIGVILRDSH 58 (140)
Q Consensus 20 ~~~P~W~~~~~eeve~~--Ivkl-akkG~~pSqIG~~LRD~~ 58 (140)
+...-.-.+|.+||..+ |..| ...|+|-++|-..|-...
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 44556667899999976 6665 678999999998887654
No 245
>PRK10339 DNA-binding transcriptional repressor EbgR; Provisional
Probab=20.31 E-value=94 Score=24.95 Aligned_cols=36 Identities=25% Similarity=0.392 Sum_probs=16.0
Q ss_pred CCCcchhhhHhhhccCCCceeeecchhHHHHHHHcCC
Q 032468 44 GLTPSQIGVILRDSHGIAQVKSVTGSKILRILKAHGL 80 (140)
Q Consensus 44 G~~pSqIG~~LRD~~GVp~Vk~vtG~ki~~ILk~ngl 80 (140)
|+|+|-+-..|.+.-++ .|..-|=.+|.++.++-|-
T Consensus 12 gVS~~TVSrvln~~~~~-~vs~~tr~rV~~~a~~lgY 47 (327)
T PRK10339 12 GVSLATVSRVLNDDPTL-NVKEETKHRILEIAEKLEY 47 (327)
T ss_pred CCCHHhhhhhhcCCCCC-CcCHHHHHHHHHHHHHhCC
Confidence 44554444444433221 2444444444444444443
Done!