Query psy9269
Match_columns 148
No_of_seqs 130 out of 829
Neff 7.1
Searched_HMMs 46136
Date Fri Aug 16 23:07:35 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9269.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9269hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0952|consensus 100.0 2.7E-36 5.9E-41 271.2 4.4 145 1-147 494-643 (1230)
2 KOG0951|consensus 99.9 2E-27 4.4E-32 216.8 3.9 142 1-147 705-851 (1674)
3 PRK02362 ski2-like helicase; P 99.9 4E-23 8.8E-28 185.5 12.3 125 2-147 403-536 (737)
4 PRK00254 ski2-like helicase; P 99.9 1.3E-22 2.7E-27 181.9 10.5 125 3-147 394-528 (720)
5 PRK01172 ski2-like helicase; P 99.9 2.2E-21 4.8E-26 172.6 11.2 122 2-146 383-511 (674)
6 KOG0951|consensus 99.8 4.3E-21 9.3E-26 175.9 5.0 117 1-126 1497-1613(1674)
7 COG1204 Superfamily II helicas 99.4 2.1E-13 4.5E-18 123.5 6.6 120 9-146 422-548 (766)
8 COG1202 Superfamily II helicas 95.1 0.012 2.7E-07 52.6 2.0 42 84-126 620-661 (830)
9 PRK11131 ATP-dependent RNA hel 90.6 0.65 1.4E-05 45.3 6.2 60 81-140 456-519 (1294)
10 PF10264 Stork_head: Winged he 89.2 1.3 2.7E-05 29.7 5.0 66 19-108 14-79 (80)
11 smart00847 HA2 Helicase associ 88.4 0.97 2.1E-05 29.9 4.2 52 86-141 2-57 (92)
12 PF04408 HA2: Helicase associa 88.4 0.99 2.1E-05 30.9 4.3 38 85-126 1-38 (102)
13 COG1321 TroR Mn-dependent tran 88.0 0.57 1.2E-05 35.0 3.1 77 40-126 8-85 (154)
14 PF14338 Mrr_N: Mrr N-terminal 86.4 5.7 0.00012 26.6 7.1 76 25-114 9-88 (92)
15 TIGR01967 DEAH_box_HrpA ATP-de 86.3 1.6 3.4E-05 42.7 5.7 45 81-126 449-493 (1283)
16 PF06969 HemN_C: HemN C-termin 85.7 0.89 1.9E-05 28.3 2.6 30 81-111 36-65 (66)
17 PF14947 HTH_45: Winged helix- 82.8 2.1 4.5E-05 27.9 3.5 35 81-116 34-68 (77)
18 PRK03902 manganese transport t 82.2 1.9 4.1E-05 31.2 3.5 36 81-116 37-72 (142)
19 smart00529 HTH_DTXR Helix-turn 80.1 2.9 6.3E-05 27.7 3.6 38 81-118 14-51 (96)
20 PHA01735 hypothetical protein 76.0 3.4 7.3E-05 27.0 2.8 34 13-46 9-44 (76)
21 PRK09333 30S ribosomal protein 73.8 6.5 0.00014 29.4 4.2 30 81-111 96-125 (150)
22 PF10915 DUF2709: Protein of u 72.9 2.2 4.8E-05 33.3 1.6 68 81-148 50-122 (238)
23 COG3432 Predicted transcriptio 72.7 5.3 0.00012 27.6 3.3 33 81-113 46-81 (95)
24 PRK05256 condesin subunit E; P 70.6 24 0.00052 28.2 6.9 71 28-108 108-182 (238)
25 KOG3411|consensus 70.1 5.9 0.00013 29.1 3.1 31 81-111 98-128 (143)
26 PF13463 HTH_27: Winged helix 69.8 3 6.6E-05 25.7 1.5 30 81-110 33-68 (68)
27 PF14394 DUF4423: Domain of un 69.0 5.5 0.00012 30.1 3.0 45 81-126 56-100 (171)
28 PRK13767 ATP-dependent helicas 68.1 16 0.00034 34.5 6.3 42 10-52 416-459 (876)
29 PF01090 Ribosomal_S19e: Ribos 67.5 7.5 0.00016 28.7 3.3 32 81-112 95-126 (139)
30 PF13601 HTH_34: Winged helix 64.8 5.1 0.00011 26.4 1.8 39 81-119 29-74 (80)
31 COG4742 Predicted transcriptio 64.1 7.1 0.00015 31.7 2.9 34 83-117 43-76 (260)
32 PF14277 DUF4364: Domain of un 63.8 8.3 0.00018 29.0 3.0 36 83-118 36-75 (163)
33 KOG4385|consensus 63.8 5.9 0.00013 35.0 2.5 26 34-61 388-413 (581)
34 PF13182 DUF4007: Protein of u 62.7 17 0.00036 29.7 4.9 74 42-126 13-92 (286)
35 PF01638 HxlR: HxlR-like helix 60.9 9.2 0.0002 25.4 2.6 34 81-114 34-73 (90)
36 PF09681 Phage_rep_org_N: N-te 60.5 12 0.00025 26.9 3.2 34 78-111 65-98 (121)
37 PRK11050 manganese transport r 60.0 12 0.00026 27.5 3.3 36 81-116 66-101 (152)
38 PTZ00095 40S ribosomal protein 59.8 17 0.00038 27.6 4.1 31 81-111 120-151 (169)
39 PRK03573 transcriptional regul 59.6 12 0.00025 26.7 3.1 35 81-115 61-101 (144)
40 PRK11512 DNA-binding transcrip 58.3 12 0.00026 26.8 3.0 34 81-114 69-108 (144)
41 TIGR02147 Fsuc_second hypothet 57.9 9 0.0002 31.2 2.5 45 81-126 154-198 (271)
42 TIGR02337 HpaR homoprotocatech 56.7 15 0.00032 25.3 3.2 33 81-113 57-95 (118)
43 PF09821 AAA_assoc_C: C-termin 56.3 12 0.00026 26.7 2.7 32 86-118 17-48 (120)
44 PF05402 PqqD: Coenzyme PQQ sy 54.0 41 0.0009 20.6 4.7 48 24-97 21-68 (68)
45 cd00092 HTH_CRP helix_turn_hel 52.7 21 0.00045 21.6 3.1 27 81-107 40-66 (67)
46 COG1846 MarR Transcriptional r 52.3 17 0.00036 24.3 2.8 39 81-119 51-95 (126)
47 smart00347 HTH_MARR helix_turn 51.6 20 0.00044 23.1 3.0 36 81-116 39-80 (101)
48 COG1733 Predicted transcriptio 51.4 17 0.00036 25.9 2.7 33 81-113 52-90 (120)
49 TIGR01714 phage_rep_org_N phag 51.3 20 0.00044 25.6 3.1 32 80-111 65-96 (119)
50 PF03551 PadR: Transcriptional 50.6 14 0.00031 23.4 2.1 33 81-113 32-72 (75)
51 PF02981 FokI_N: Restriction e 50.5 24 0.00052 26.2 3.5 32 86-117 112-144 (145)
52 TIGR01970 DEAH_box_HrpB ATP-de 49.4 43 0.00093 31.5 5.8 42 81-126 381-422 (819)
53 cd00186 TOP1Ac DNA Topoisomera 49.2 37 0.00079 28.7 4.9 32 85-117 305-336 (381)
54 COG2238 RPS19A Ribosomal prote 48.4 21 0.00045 26.5 2.8 30 81-111 96-125 (147)
55 TIGR01889 Staph_reg_Sar staphy 46.6 21 0.00046 24.4 2.6 32 81-112 58-95 (109)
56 PF01726 LexA_DNA_bind: LexA D 46.6 73 0.0016 20.0 5.6 22 80-101 40-61 (65)
57 PRK05799 coproporphyrinogen II 46.4 45 0.00098 27.8 5.0 33 82-115 334-366 (374)
58 PF14502 HTH_41: Helix-turn-he 46.3 24 0.00053 21.3 2.4 22 81-102 21-42 (48)
59 PF10007 DUF2250: Uncharacteri 45.6 25 0.00054 24.1 2.7 26 81-106 36-61 (92)
60 PF04288 MukE: MukE-like famil 45.5 25 0.00054 28.0 3.1 31 78-108 141-174 (235)
61 PF13730 HTH_36: Helix-turn-he 45.4 62 0.0013 18.9 5.0 29 67-96 27-55 (55)
62 PF03882 KicB: KicB killing fa 45.4 15 0.00032 31.8 1.9 44 82-125 73-122 (440)
63 PRK13347 coproporphyrinogen II 44.2 1.5E+02 0.0032 25.6 8.0 31 85-116 403-433 (453)
64 PRK10870 transcriptional repre 44.0 28 0.00061 26.1 3.2 36 81-116 86-127 (176)
65 TIGR02647 DNA conserved hypoth 43.6 36 0.00079 22.5 3.2 34 81-116 34-67 (77)
66 smart00419 HTH_CRP helix_turn_ 43.2 28 0.0006 19.4 2.4 24 81-105 23-46 (48)
67 KOG0925|consensus 43.2 47 0.001 29.9 4.7 37 105-141 453-492 (699)
68 PF13545 HTH_Crp_2: Crp-like h 42.0 42 0.00091 20.8 3.3 45 66-112 29-73 (76)
69 PRK05776 DNA topoisomerase I; 41.4 54 0.0012 30.1 5.0 32 85-117 496-527 (670)
70 PRK08599 coproporphyrinogen II 40.4 59 0.0013 27.1 4.8 35 81-116 334-368 (377)
71 PF00126 HTH_1: Bacterial regu 40.1 28 0.00062 21.1 2.2 18 93-111 43-60 (60)
72 PF03444 HrcA_DNA-bdg: Winged 38.9 47 0.001 22.1 3.2 33 81-113 38-72 (78)
73 PRK13777 transcriptional regul 38.7 39 0.00084 25.9 3.2 35 81-115 74-114 (185)
74 PRK11664 ATP-dependent RNA hel 38.6 42 0.00092 31.5 4.0 42 81-126 384-425 (812)
75 smart00611 SEC63 Domain of unk 38.5 22 0.00047 28.7 1.9 20 128-147 30-49 (312)
76 TIGR01056 topB DNA topoisomera 38.4 70 0.0015 29.3 5.3 32 85-117 523-554 (660)
77 PF08499 PDEase_I_N: 3'5'-cycl 38.1 25 0.00054 22.2 1.7 23 27-51 10-32 (59)
78 KOG0923|consensus 37.5 62 0.0013 30.3 4.6 60 81-145 652-715 (902)
79 COG3095 MukE Uncharacterized p 37.4 36 0.00078 26.4 2.8 30 79-108 149-180 (238)
80 PF00392 GntR: Bacterial regul 37.2 42 0.0009 20.5 2.7 21 81-101 39-59 (64)
81 PF09202 Rio2_N: Rio2, N-termi 37.2 73 0.0016 21.1 4.0 36 76-111 34-71 (82)
82 KOG1165|consensus 36.5 42 0.00092 28.9 3.3 67 35-126 108-188 (449)
83 PF11630 DUF3254: Protein of u 36.5 66 0.0014 22.4 3.7 26 19-45 75-100 (100)
84 PF01131 Topoisom_bac: DNA top 36.0 33 0.00072 29.1 2.7 33 85-117 337-369 (403)
85 PF04458 DUF505: Protein of un 36.0 25 0.00055 31.8 2.0 33 83-115 467-499 (591)
86 PRK06294 coproporphyrinogen II 35.7 54 0.0012 27.5 3.9 33 82-115 331-363 (370)
87 smart00346 HTH_ICLR helix_turn 35.5 53 0.0011 21.1 3.1 30 81-110 35-65 (91)
88 KOG0924|consensus 35.3 77 0.0017 29.9 4.9 58 81-142 743-803 (1042)
89 cd07377 WHTH_GntR Winged helix 34.9 58 0.0013 19.2 3.0 21 81-101 40-60 (66)
90 PRK07561 DNA topoisomerase I s 34.8 72 0.0016 30.1 4.9 32 85-117 490-521 (859)
91 PF04919 DUF655: Protein of un 34.5 64 0.0014 24.9 3.7 41 2-42 100-149 (181)
92 PRK05260 condesin subunit F; P 34.1 15 0.00032 31.9 0.2 44 83-126 74-123 (440)
93 PF01978 TrmB: Sugar-specific 34.1 28 0.0006 21.6 1.5 20 81-100 37-56 (68)
94 PRK11402 DNA-binding transcrip 33.9 1.9E+02 0.0041 22.3 6.5 25 81-105 48-73 (241)
95 PF14117 DUF4287: Domain of un 33.8 84 0.0018 19.8 3.6 26 23-48 18-44 (61)
96 PF08222 HTH_CodY: CodY helix- 33.1 53 0.0012 20.7 2.5 20 81-100 19-38 (61)
97 smart00437 TOP1Ac Bacterial DN 32.9 27 0.00058 28.1 1.5 27 85-112 232-258 (259)
98 PRK07726 DNA topoisomerase III 32.9 95 0.0021 28.4 5.2 41 85-126 520-564 (658)
99 PTZ00407 DNA topoisomerase IA; 32.8 40 0.00087 31.7 2.8 34 85-118 601-634 (805)
100 PF04433 SWIRM: SWIRM domain; 32.7 1.4E+02 0.0031 19.4 5.1 17 81-97 69-85 (86)
101 COG4344 Uncharacterized protei 32.7 38 0.00083 25.5 2.2 27 82-108 47-73 (175)
102 PF09382 RQC: RQC domain; Int 32.3 84 0.0018 20.9 3.8 33 81-113 57-93 (106)
103 COG1643 HrpA HrpA-like helicas 31.6 1.1E+02 0.0025 29.0 5.6 42 81-126 433-474 (845)
104 TIGR03433 padR_acidobact trans 31.4 68 0.0015 21.6 3.2 32 82-113 41-80 (100)
105 TIGR01884 cas_HTH CRISPR locus 31.3 40 0.00086 25.7 2.2 30 81-110 172-203 (203)
106 PF09339 HTH_IclR: IclR helix- 30.8 58 0.0013 19.1 2.5 20 81-100 33-52 (52)
107 COG5631 Predicted transcriptio 30.4 85 0.0018 24.1 3.8 46 81-126 114-162 (199)
108 PRK09057 coproporphyrinogen II 30.4 52 0.0011 27.7 2.9 32 85-116 342-373 (380)
109 PF00627 UBA: UBA/TS-N domain; 30.4 90 0.0019 17.0 3.1 20 23-44 18-37 (37)
110 PRK06319 DNA topoisomerase I/S 30.4 88 0.0019 29.6 4.7 32 85-117 501-532 (860)
111 PRK08898 coproporphyrinogen II 29.8 60 0.0013 27.5 3.2 32 83-115 355-386 (394)
112 PRK14165 winged helix-turn-hel 29.0 67 0.0015 25.3 3.2 37 81-117 36-76 (217)
113 PRK05628 coproporphyrinogen II 28.9 81 0.0018 26.3 3.9 32 84-116 337-368 (375)
114 PF00325 Crp: Bacterial regula 28.9 74 0.0016 17.4 2.4 16 81-96 17-32 (32)
115 TIGR01051 topA_bact DNA topois 28.6 1.1E+02 0.0024 27.7 4.8 41 85-126 483-530 (610)
116 PRK07219 DNA topoisomerase I; 28.2 1E+02 0.0022 28.9 4.7 40 85-126 499-545 (822)
117 PRK08629 coproporphyrinogen II 28.1 1.1E+02 0.0025 26.3 4.7 34 81-115 374-407 (433)
118 PRK09416 lstR lineage-specific 28.1 69 0.0015 23.5 2.9 35 81-115 78-116 (135)
119 COG0550 TopA Topoisomerase IA 27.9 55 0.0012 29.6 2.8 32 85-117 475-506 (570)
120 COG1491 Predicted RNA-binding 27.5 92 0.002 24.3 3.6 42 1-42 113-163 (202)
121 PRK05582 DNA topoisomerase I; 27.2 1.2E+02 0.0026 27.7 4.8 32 85-117 477-508 (650)
122 PRK00082 hrcA heat-inducible t 27.0 45 0.00098 27.9 2.0 38 81-121 42-80 (339)
123 KOG4244|consensus 26.6 2.4E+02 0.0052 23.2 5.9 48 66-117 199-246 (281)
124 TIGR01054 rgy reverse gyrase. 26.5 1.2E+02 0.0026 29.8 5.0 32 85-117 1096-1127(1171)
125 TIGR02606 antidote_CC2985 puta 26.2 1.2E+02 0.0027 19.2 3.5 27 16-42 5-31 (69)
126 PRK04172 pheS phenylalanyl-tRN 26.1 78 0.0017 27.7 3.4 35 81-115 35-71 (489)
127 cd05394 RasGAP_RASA2 RASA2 (or 26.0 3.9E+02 0.0085 22.3 7.9 69 21-95 158-230 (313)
128 TIGR01610 phage_O_Nterm phage 25.7 83 0.0018 21.1 2.8 20 81-100 62-81 (95)
129 COG1568 Predicted methyltransf 25.6 84 0.0018 26.3 3.2 33 82-115 50-82 (354)
130 PF01325 Fe_dep_repress: Iron 25.6 73 0.0016 19.6 2.3 33 68-101 25-57 (60)
131 PRK05660 HemN family oxidoredu 25.6 73 0.0016 26.8 3.0 31 84-115 339-369 (378)
132 KOG1956|consensus 25.3 98 0.0021 28.6 3.8 41 82-122 506-547 (758)
133 PRK08780 DNA topoisomerase I; 25.3 66 0.0014 30.1 2.9 32 85-117 497-528 (780)
134 TIGR01057 topA_arch DNA topois 25.1 1.4E+02 0.003 27.0 4.9 40 85-126 490-536 (618)
135 PRK11523 DNA-binding transcrip 25.0 1.8E+02 0.0039 22.6 5.0 24 81-104 47-71 (253)
136 PF12802 MarR_2: MarR family; 24.9 60 0.0013 19.2 1.8 20 81-100 36-55 (62)
137 PF01337 Barstar: Barstar (bar 24.9 83 0.0018 20.5 2.7 26 31-62 5-30 (90)
138 PRK06599 DNA topoisomerase I; 24.8 1.5E+02 0.0032 27.2 5.0 41 85-126 491-538 (675)
139 PF09114 MotA_activ: Transcrip 24.6 86 0.0019 21.5 2.6 31 81-112 47-77 (96)
140 KOG0926|consensus 24.6 97 0.0021 29.8 3.7 42 81-126 750-791 (1172)
141 PRK07379 coproporphyrinogen II 24.3 1.7E+02 0.0037 24.8 5.0 34 81-115 351-386 (400)
142 cd02977 ArsC_family Arsenate R 23.8 2.3E+02 0.0049 18.8 5.3 65 81-145 10-89 (105)
143 PRK10225 DNA-binding transcrip 23.7 2.1E+02 0.0046 22.2 5.2 24 81-104 48-72 (257)
144 PHA03061 putative DNA-binding 23.7 43 0.00092 27.5 1.2 46 48-102 129-174 (311)
145 COG5407 SEC63 Preprotein trans 23.4 23 0.0005 31.4 -0.4 31 117-147 226-260 (610)
146 PRK10421 DNA-binding transcrip 22.9 2.2E+02 0.0047 22.1 5.1 24 81-104 41-65 (253)
147 PF13309 HTH_22: HTH domain 22.6 1.7E+02 0.0037 18.1 3.6 35 85-126 28-62 (64)
148 cd00090 HTH_ARSR Arsenical Res 22.6 68 0.0015 18.9 1.8 32 81-113 35-69 (78)
149 PF03289 Pox_I1: Poxvirus prot 22.4 45 0.00098 27.4 1.1 44 49-101 131-174 (312)
150 PRK08208 coproporphyrinogen II 22.3 83 0.0018 26.9 2.8 30 84-114 379-408 (430)
151 smart00418 HTH_ARSR helix_turn 22.2 1.2E+02 0.0025 17.3 2.8 21 81-101 25-45 (66)
152 PRK09990 DNA-binding transcrip 22.2 2.4E+02 0.0051 21.8 5.2 24 81-104 46-70 (251)
153 smart00345 HTH_GNTR helix_turn 22.1 1.2E+02 0.0026 17.3 2.8 21 81-101 35-55 (60)
154 PHA03362 single-stranded bindi 21.5 2.6E+02 0.0057 27.7 6.1 62 48-126 838-915 (1189)
155 smart00733 Mterf Mitochondrial 20.9 1.2E+02 0.0026 14.6 2.4 14 82-95 17-30 (31)
156 cd04447 DEP_BRCC3 DEP (Disheve 20.6 2.8E+02 0.006 19.0 4.5 41 37-97 32-72 (92)
157 TIGR01638 Atha_cystat_rel Arab 20.5 18 0.00039 24.9 -1.4 42 81-122 17-58 (92)
158 PF00395 SLH: S-layer homology 20.4 92 0.002 17.5 1.9 23 85-107 14-36 (45)
159 TIGR03147 cyt_nit_nrfF cytochr 20.1 1.5E+02 0.0033 21.4 3.4 32 17-50 58-89 (126)
No 1
>KOG0952|consensus
Probab=100.00 E-value=2.7e-36 Score=271.18 Aligned_cols=145 Identities=30% Similarity=0.542 Sum_probs=133.4
Q ss_pred ChHHHhhcCCCceeccccHHHHHHHHHHHHhCCcCCHHHHHHHHHhHHHHHHHhhCCCCCCCCCCCChHHHHHHHhhhhH
Q psy9269 1 ERYEKLVEGREPVESSLHRHLVEHLNSEIVLKTISDVSVAVEWLRSTFFFVRVLSNPGHYGFPAGLSSEELQSRLQGKNS 80 (148)
Q Consensus 1 ~~Y~~ll~~~~pIES~L~~~L~~~lnaeIa~g~i~s~~~~~~wl~~TFly~Rl~~nP~~Yg~~~~~~~~~~~~~l~~~~~ 80 (148)
++|++++.++.||||+|+.+|.||+||||++|||+|+++|++||++||+|+||++||.+||+..+ .-..++.+..++.
T Consensus 494 ~~Y~sLl~~~~piES~~~~~L~dnLnAEi~LgTVt~VdeAVeWL~yTylYVRm~KNP~~Ygi~~~--~l~~dp~l~s~~~ 571 (1230)
T KOG0952|consen 494 DHYESLLTGQNPIESQLLPCLIDNLNAEISLGTVTNVDEAVEWLKYTYLYVRMRKNPMAYGISYE--ELEPDPRLESHRR 571 (1230)
T ss_pred HHHHHHHcCCChhHHHHHHHHHHhhhhheeeceeecHHHHHHHhhceeEEEEeccChHHhhhhhh--cccCCchHHHHHH
Confidence 58999999999999999999999999999999999999999999999999999999999998753 1112466777777
Q ss_pred hHHHHHHHHhhhCCceeecCC-CccccChhhHHHHhcCCCHHHHHhc----cCCCCHHHHHHhhhCCCCCCC
Q psy9269 81 GLCMRELNGLSRYNLITMNDG-FDILPTVTGSIMAKFCIGFNTMVAF----TGWEKAQKDLALLTTLPLATS 147 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~-~~i~~T~lG~i~S~~YI~~~T~~~~----~~~~s~~~lL~ll~~s~e~~~ 147 (148)
++|..+++.|.+.+||..|.. +.+.||++||+||+|||+++||+.| ++.+++.++|+++|++.||+.
T Consensus 572 ~l~~~~~~~L~~~qmi~~D~~t~~~~stdlGR~aS~yYik~ETme~~nn~~k~~~se~~iL~lis~aeEfs~ 643 (1230)
T KOG0952|consen 572 ELCLVAAMELDKVQMIRFDERTGYLKSTDLGRVASNYYIKYETMETFNNLPKSFYSEDDILALISMAEEFSQ 643 (1230)
T ss_pred HHHHHHHHHhhhhheEEEecccceEcccchhhhhhhhhhhhHHHHHHHhcccccCCHHHHHHHHHhhHhhhh
Confidence 999999999999999999987 8899999999999999999999999 557999999999999999973
No 2
>KOG0951|consensus
Probab=99.93 E-value=2e-27 Score=216.81 Aligned_cols=142 Identities=25% Similarity=0.379 Sum_probs=133.9
Q ss_pred ChHHHhhcCCCceeccccHHHHHHHHHHHHhCCcCCHHHHHHHHHhHHHHHHHhhCCCCCCCCCCCChHHHHHHHhhhhH
Q psy9269 1 ERYEKLVEGREPVESSLHRHLVEHLNSEIVLKTISDVSVAVEWLRSTFFFVRVLSNPGHYGFPAGLSSEELQSRLQGKNS 80 (148)
Q Consensus 1 ~~Y~~ll~~~~pIES~L~~~L~~~lnaeIa~g~i~s~~~~~~wl~~TFly~Rl~~nP~~Yg~~~~~~~~~~~~~l~~~~~ 80 (148)
.+|.++++++.||||++.+.|.|.+||||+.| +++.+|+++|+.+||||+||.+||..||+.++.+ +..++.++.
T Consensus 705 qyyls~mn~qLpiesq~~~rl~d~lnaeiv~G-v~~~~d~~~wl~yTylyvRm~~~p~ly~~~~~~~----d~~le~~r~ 779 (1674)
T KOG0951|consen 705 QYYLSLMNQQLPIESQFVSRLADCLNAEIVLG-VRSARDAVDWLGYTYLYVRMVRNPTLYGVSPEAS----DRLLEQRRA 779 (1674)
T ss_pred hhhHHhhhhcCCChHHHHHHhhhhhhhhhhcc-hhhHHHHHhhhcceeeEEeeccCchhccCCcccc----hHHHHHHHh
Confidence 37999999999999999999999999999999 9999999999999999999999999999986544 577888888
Q ss_pred hHHHHHHHHhhhCCceeecCC-CccccChhhHHHHhcCCCHHHHHhc----cCCCCHHHHHHhhhCCCCCCC
Q psy9269 81 GLCMRELNGLSRYNLITMNDG-FDILPTVTGSIMAKFCIGFNTMVAF----TGWEKAQKDLALLTTLPLATS 147 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~-~~i~~T~lG~i~S~~YI~~~T~~~~----~~~~s~~~lL~ll~~s~e~~~ 147 (148)
+++++++..|.++|+|-++.. |.+++|++|+|+|+|||.+.||..+ ++.+++.+++++++++.||..
T Consensus 780 ~lvhsa~~ll~~~~li~yd~~s~~~~~telg~ias~yyi~~~s~~~yn~~L~~~~~~i~lfrifs~seEfk~ 851 (1674)
T KOG0951|consen 780 DLVHSAATLLDKAGLIKYDRKSGAIQATELGRIASSYYITHGSMATYNELLKETMSEIDLFRIFSKSEEFKY 851 (1674)
T ss_pred hhHHHHHhhHhhcCccccccccCcccchhhccccceeeeecchHHHHHhhhhhhhccchhhhhhhhcccccc
Confidence 999999999999999999987 8999999999999999999999999 788999999999999999964
No 3
>PRK02362 ski2-like helicase; Provisional
Probab=99.89 E-value=4e-23 Score=185.47 Aligned_cols=125 Identities=20% Similarity=0.223 Sum_probs=109.2
Q ss_pred hHHHhh-cCCCceecccc--HHHHHHHHHHHHhCCcCCHHHHHHHHHhHHHHHHHhhCCCCCCCCCCCChHHHHHHHhhh
Q psy9269 2 RYEKLV-EGREPVESSLH--RHLVEHLNSEIVLKTISDVSVAVEWLRSTFFFVRVLSNPGHYGFPAGLSSEELQSRLQGK 78 (148)
Q Consensus 2 ~Y~~ll-~~~~pIES~L~--~~L~~~lnaeIa~g~i~s~~~~~~wl~~TFly~Rl~~nP~~Yg~~~~~~~~~~~~~l~~~ 78 (148)
+|++++ ++++||||+|. ..|++|+||||++|++.+.+|+++|+++||||+|. +. ...++
T Consensus 403 ~~~~~l~~~~~~i~S~l~~~~~l~~~lla~I~~~~~~~~~d~~~~l~~Tf~~~~~---~~-------------~~~l~-- 464 (737)
T PRK02362 403 LFERYIWADPEDVRSKLATEPALRTHVLSTIASGFARTRDGLLEFLEATFYATQT---DD-------------TGRLE-- 464 (737)
T ss_pred HHHHHHhCCCCceeecCCChhhHHHHHHHHHHhCccCCHHHHHHHHHhChHHhhc---cc-------------hHHHH--
Confidence 477877 69999999996 58999999999999999999999999999999842 10 23566
Q ss_pred hHhHHHHHHHHhhhCCceeecCCCccccChhhHHHHhcCCCHHHHHhc----cC--CCCHHHHHHhhhCCCCCCC
Q psy9269 79 NSGLCMRELNGLSRYNLITMNDGFDILPTVTGSIMAKFCIGFNTMVAF----TG--WEKAQKDLALLTTLPLATS 147 (148)
Q Consensus 79 ~~~~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~YI~~~T~~~~----~~--~~s~~~lL~ll~~s~e~~~ 147 (148)
++|+++++.|.++|||+.++ +.+.||++|+++|+|||+|.|+..| .. ..++.++|++||.+|||..
T Consensus 465 --~~v~~~l~~L~~~~~i~~~~-~~~~~t~lG~~~s~~~l~~~t~~~~~~~l~~~~~~~~~~~l~~i~~~~e~~~ 536 (737)
T PRK02362 465 --RVVDDVLDFLERNGMIEEDG-ETLEATELGHLVSRLYIDPLSAAEIIDGLEAAKKPTDLGLLHLVCSTPDMYE 536 (737)
T ss_pred --HHHHHHHHHHHHCCCeeecC-CeEeEChHHHHHHHhcCCHHHHHHHHHHhhhcccCchHHHHHHhhcCccccc
Confidence 89999999999999999876 6799999999999999999999999 22 2478999999999999964
No 4
>PRK00254 ski2-like helicase; Provisional
Probab=99.88 E-value=1.3e-22 Score=181.88 Aligned_cols=125 Identities=18% Similarity=0.158 Sum_probs=108.9
Q ss_pred HHHhh-cCCCceecccc--HHHHHHHHHHHHhCCcCCHHHHHHHHHhHHHHHHHhhCCCCCCCCCCCChHHHHHHHhhhh
Q psy9269 3 YEKLV-EGREPVESSLH--RHLVEHLNSEIVLKTISDVSVAVEWLRSTFFFVRVLSNPGHYGFPAGLSSEELQSRLQGKN 79 (148)
Q Consensus 3 Y~~ll-~~~~pIES~L~--~~L~~~lnaeIa~g~i~s~~~~~~wl~~TFly~Rl~~nP~~Yg~~~~~~~~~~~~~l~~~~ 79 (148)
|++++ +.|+++.|.|. +.|++|+|++|+.|++.+.+|+++||++||+|. +||.+|+ +.
T Consensus 394 ~~~~~~~~pe~l~s~l~~es~l~~~ll~~i~~~~~~~~~~~~~~l~~Tf~~~---~~~~~~~-------------~~--- 454 (720)
T PRK00254 394 MERYIFGKPEKLFSMLSNESAFRSQVLALITNFGVSNFKELVNFLERTFYAH---QRKDLYS-------------LE--- 454 (720)
T ss_pred HHHHHhCCchhhhccCCchHHHHHHHHHHHHhCCCCCHHHHHHHHHhCHHHH---hhcChHh-------------HH---
Confidence 55553 56677888886 579999999999999999999999999999996 7888765 23
Q ss_pred HhHHHHHHHHhhhCCceeecCCCccccChhhHHHHhcCCCHHHHHhc----c---CCCCHHHHHHhhhCCCCCCC
Q psy9269 80 SGLCMRELNGLSRYNLITMNDGFDILPTVTGSIMAKFCIGFNTMVAF----T---GWEKAQKDLALLTTLPLATS 147 (148)
Q Consensus 80 ~~~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~YI~~~T~~~~----~---~~~s~~~lL~ll~~s~e~~~ 147 (148)
+.+++++..|.++|||+.++++.+.||++|+++|+|||+|+|+..| . ..+++.++|++||.+|||..
T Consensus 455 -~~v~~~l~~L~~~~~i~~~~~~~~~~t~lG~~~s~~~i~~~t~~~~~~~l~~~~~~~~~~~~l~~~~~~~e~~~ 528 (720)
T PRK00254 455 -EKAKEIVYFLLENEFIDIDLEDRFIPLPLGIRTSQLYIDPLTAKKFKDAFPKIEKNPNPLGIFQLIASTPDMTP 528 (720)
T ss_pred -HHHHHHHHHHHHCCCeEEcCCCCEeeChHHHHHHHHhCCHHHHHHHHHHHHhhccCCCHHHHHHHhhCCccccc
Confidence 6788899999999999998767899999999999999999999999 2 26789999999999999964
No 5
>PRK01172 ski2-like helicase; Provisional
Probab=99.86 E-value=2.2e-21 Score=172.61 Aligned_cols=122 Identities=13% Similarity=0.092 Sum_probs=106.0
Q ss_pred hHHHhh-cCCCceeccccH--HHHHHHHHHHHhCCcCCHHHHHHHHHhHHHHHHHhhCCCCCCCCCCCChHHHHHHHhhh
Q psy9269 2 RYEKLV-EGREPVESSLHR--HLVEHLNSEIVLKTISDVSVAVEWLRSTFFFVRVLSNPGHYGFPAGLSSEELQSRLQGK 78 (148)
Q Consensus 2 ~Y~~ll-~~~~pIES~L~~--~L~~~lnaeIa~g~i~s~~~~~~wl~~TFly~Rl~~nP~~Yg~~~~~~~~~~~~~l~~~ 78 (148)
+|++++ ++|+||||+|.. .++.++++||+.|.+.+++|+++|+++||+|+ +|+. +.++
T Consensus 383 ~~~~~l~~~~~pi~S~l~~~~~~~~~~l~~i~~g~~~~~~d~~~~l~~tf~~~---~~~~--------------~~l~-- 443 (674)
T PRK01172 383 AAKKYLSGEPEPVISYMGSQRKVRFNTLAAISMGLASSMEDLILFYNETLMAI---QNGV--------------DEID-- 443 (674)
T ss_pred HHHHHHcCCCCceeecCCCcccHHHHHHHHHHhcccCCHHHHHHHHHhhhhHh---cCch--------------HHHH--
Confidence 467777 899999999985 46666779999999999999999999999998 4421 2455
Q ss_pred hHhHHHHHHHHhhhCCceeecCCCccccChhhHHHHhcCCCHHHHHhc----cCCCCHHHHHHhhhCCCCCC
Q psy9269 79 NSGLCMRELNGLSRYNLITMNDGFDILPTVTGSIMAKFCIGFNTMVAF----TGWEKAQKDLALLTTLPLAT 146 (148)
Q Consensus 79 ~~~~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~YI~~~T~~~~----~~~~s~~~lL~ll~~s~e~~ 146 (148)
+.|+++++.|.++|||+.+ +.+.||++|++||+|||+|+|+..| ...++..++|++||.+|||.
T Consensus 444 --~~v~~~l~~L~~~~~i~~~--~~~~~t~lG~~~s~~~l~~~t~~~~~~~l~~~~~~~~~l~~~~~~~e~~ 511 (674)
T PRK01172 444 --YYIESSLKFLKENGFIKGD--VTLRATRLGKLTSDLYIDPESALILKSAFDHDYDEDLALYYISLCREII 511 (674)
T ss_pred --HHHHHHHHHHHHCCCcccC--CcEeECHHHHHHHHhCCCHHHHHHHHHHhhccCCHHHHHHHhhcCcccc
Confidence 8999999999999999844 4699999999999999999999999 55678999999999999994
No 6
>KOG0951|consensus
Probab=99.82 E-value=4.3e-21 Score=175.87 Aligned_cols=117 Identities=34% Similarity=0.507 Sum_probs=108.3
Q ss_pred ChHHHhhcCCCceeccccHHHHHHHHHHHHhCCcCCHHHHHHHHHhHHHHHHHhhCCCCCCCCCCCChHHHHHHHhhhhH
Q psy9269 1 ERYEKLVEGREPVESSLHRHLVEHLNSEIVLKTISDVSVAVEWLRSTFFFVRVLSNPGHYGFPAGLSSEELQSRLQGKNS 80 (148)
Q Consensus 1 ~~Y~~ll~~~~pIES~L~~~L~~~lnaeIa~g~i~s~~~~~~wl~~TFly~Rl~~nP~~Yg~~~~~~~~~~~~~l~~~~~ 80 (148)
.+|++|+.+|.|+||+|...|.|+.|+||+.++|.|.+||++||.|||+|+|+.+||.||++. +.+.+.++..|+
T Consensus 1497 ~yykkfl~e~lPves~lq~~lhd~~n~ei~~~tienkqd~vd~lt~s~~yrr~~~np~yy~l~-~v~~~~~S~~lS---- 1571 (1674)
T KOG0951|consen 1497 EYYKKFLYEPLPVESHLQHCLHDNFNAEIVTKTIENKQDAVDYLTWSFMYRRLPQNPNYYNLQ-GVSHRHLSDFLS---- 1571 (1674)
T ss_pred HHHHHhccCcCchHHHHHHHHHhhhhHHHHHHHHHhHHHHHHHHHHHHhhhccccCcceeccc-ccchhhhhhHHH----
Confidence 379999999999999999999999999999999999999999999999999999999999988 567777766676
Q ss_pred hHHHHHHHHhhhCCceeecCCCccccChhhHHHHhcCCCHHHHHhc
Q psy9269 81 GLCMRELNGLSRYNLITMNDGFDILPTVTGSIMAKFCIGFNTMVAF 126 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~YI~~~T~~~~ 126 (148)
++++.++..|++++||+++.... -+|.|+|+|||++-|+..|
T Consensus 1572 ~lvet~l~dl~~s~~i~v~dad~----~l~~Ias~y~i~y~ti~~f 1613 (1674)
T KOG0951|consen 1572 ELVETTLNDLEESKCIEVDDEDD----SLGMIASYYYISYITIERF 1613 (1674)
T ss_pred HHHHHHHHHhhcCceEEeecccc----ccchhhhhceeeeEeeehh
Confidence 99999999999999999887533 2999999999999999988
No 7
>COG1204 Superfamily II helicase [General function prediction only]
Probab=99.42 E-value=2.1e-13 Score=123.45 Aligned_cols=120 Identities=28% Similarity=0.292 Sum_probs=97.6
Q ss_pred CCCceeccccHHHHHHHHHHHHhCCcCCHHHHHHHHHhHHHHHHHhhCCCCCCCCCCCChHHHHHHHhhhhHhHHHHHHH
Q psy9269 9 GREPVESSLHRHLVEHLNSEIVLKTISDVSVAVEWLRSTFFFVRVLSNPGHYGFPAGLSSEELQSRLQGKNSGLCMRELN 88 (148)
Q Consensus 9 ~~~pIES~L~~~L~~~lnaeIa~g~i~s~~~~~~wl~~TFly~Rl~~nP~~Yg~~~~~~~~~~~~~l~~~~~~~v~~~l~ 88 (148)
.++|++|+|.. ++ |+++..+++.+..++++|+..||||.|+..||..|+.. .++ ..+..++.
T Consensus 422 ~~e~~~s~l~~---~~-~~~~~l~~v~~~~~~v~~~~~~~f~~~t~~~~~~~~~~----------~~~----~~i~~~~~ 483 (766)
T COG1204 422 EPEPIESKLGD---EL-NLRTFLLGVISVGDAVSWLELTDFYERTFYNPQTYGEG----------MLR----EEILASLR 483 (766)
T ss_pred CcchHHHhhcc---cc-cchheEEEEEeccchhhHHHHHHHHHHHHhhhhhcccc----------chH----HHHHHHHH
Confidence 34445555443 33 99999999999999999999999999999999998752 233 67888999
Q ss_pred HhhhCCceeecCCCccccChhhHHHHhcCCCHHHHHhc-----cCC--CCHHHHHHhhhCCCCCC
Q psy9269 89 GLSRYNLITMNDGFDILPTVTGSIMAKFCIGFNTMVAF-----TGW--EKAQKDLALLTTLPLAT 146 (148)
Q Consensus 89 ~L~~~~lI~~~~~~~i~~T~lG~i~S~~YI~~~T~~~~-----~~~--~s~~~lL~ll~~s~e~~ 146 (148)
.|.+++++.......+.+|++|+.+|++||+|+||..| ... .++.+++++++.+|||.
T Consensus 484 ~L~~~~~~~~~~~~~~~ate~g~~~s~~yi~~~sa~~~~~~l~~~~~~~~~~~~l~~is~~pd~~ 548 (766)
T COG1204 484 YLEENGLILDADWEALHATELGKLVSRLYIDPESAKIFRDLLAELALEPTEIGLLYLISLTPDLM 548 (766)
T ss_pred HHHhccceeeccccccchhHHHHHhhhccCCHHHHHHHHHHHHHhccccchHHHhhhhhcCccch
Confidence 99999733333336799999999999999999999999 111 48999999999999985
No 8
>COG1202 Superfamily II helicase, archaea-specific [General function prediction only]
Probab=95.11 E-value=0.012 Score=52.60 Aligned_cols=42 Identities=21% Similarity=0.254 Sum_probs=38.4
Q ss_pred HHHHHHhhhCCceeecCCCccccChhhHHHHhcCCCHHHHHhc
Q psy9269 84 MRELNGLSRYNLITMNDGFDILPTVTGSIMAKFCIGFNTMVAF 126 (148)
Q Consensus 84 ~~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~YI~~~T~~~~ 126 (148)
+.++..|++.|||..++ +.+.||++|+++|.+++.|.++..+
T Consensus 620 ~k~l~~Lee~g~i~~~G-~~v~~T~yGrava~~Fl~p~~a~~I 661 (830)
T COG1202 620 KKALSKLEEYGMIKKKG-NIVRPTPYGRAVAMSFLGPSEAEFI 661 (830)
T ss_pred HHHHHHHHhcCCeeccC-CEeeeccccceeEEeecCchHHHHH
Confidence 46778999999999876 5799999999999999999999998
No 9
>PRK11131 ATP-dependent RNA helicase HrpA; Provisional
Probab=90.61 E-value=0.65 Score=45.26 Aligned_cols=60 Identities=10% Similarity=0.002 Sum_probs=45.3
Q ss_pred hHHHHHHHHhhhCCceeecCC-CccccChhhHHHHhcCCCHHHHHhc---cCCCCHHHHHHhhh
Q psy9269 81 GLCMRELNGLSRYNLITMNDG-FDILPTVTGSIMAKFCIGFNTMVAF---TGWEKAQKDLALLT 140 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~-~~i~~T~lG~i~S~~YI~~~T~~~~---~~~~s~~~lL~ll~ 140 (148)
+-+..++..|.+.|.|..+++ +....|++|+.||++.|+|.-.+++ ...-...+++-+.|
T Consensus 456 ~~i~~al~~L~~LgAld~~~~~~~~~LT~lG~~la~LPldPrlakmLl~a~~~~c~~evl~IaA 519 (1294)
T PRK11131 456 RNIQDGVRLLEELGAITTDEQASAYKLTPLGRQLAQLPVDPRLARMVLEAQKHGCVREVMIITS 519 (1294)
T ss_pred HHHHHHHHHHHHCCCCCccccCCCccCcHHHHHHHhCCCChHHHHHHHHhhhcCCHHHHHHHHH
Confidence 567889999999999975532 3468999999999999999999988 22224445555444
No 10
>PF10264 Stork_head: Winged helix Storkhead-box1 domain; InterPro: IPR019391 In humans the Storkhead-box protein controls polyploidization of extravillus trophoblast and is implicated in pre-eclampsia []. This entry represents the conserved N-terminal winged-helix domain, which is likely to bind DNA.
Probab=89.22 E-value=1.3 Score=29.72 Aligned_cols=66 Identities=14% Similarity=0.018 Sum_probs=51.2
Q ss_pred HHHHHHHHHHHHhCCcCCHHHHHHHHHhHHHHHHHhhCCCCCCCCCCCChHHHHHHHhhhhHhHHHHHHHHhhhCCceee
Q psy9269 19 RHLVEHLNSEIVLKTISDVSVAVEWLRSTFFFVRVLSNPGHYGFPAGLSSEELQSRLQGKNSGLCMRELNGLSRYNLITM 98 (148)
Q Consensus 19 ~~L~~~lnaeIa~g~i~s~~~~~~wl~~TFly~Rl~~nP~~Yg~~~~~~~~~~~~~l~~~~~~~v~~~l~~L~~~~lI~~ 98 (148)
+.|+..|-..=+.|..-+.+.+++||..-|=.+ .-|+. +.+..+|..|.+.|-|..
T Consensus 14 EvlC~~I~dln~~~~~at~E~l~~~L~~~yp~i---~~Ps~---------------------e~l~~~L~~Li~erkIY~ 69 (80)
T PF10264_consen 14 EVLCWVISDLNAAGQPATQETLREHLRKHYPGI---AIPSQ---------------------EVLYNTLGTLIKERKIYH 69 (80)
T ss_pred HHHHHHHHHHhccCCcchHHHHHHHHHHhCCCC---CCCCH---------------------HHHHHHHHHHHHcCceee
Confidence 567777777778899999999999999877322 11211 788899999999999988
Q ss_pred cCCCccccCh
Q psy9269 99 NDGFDILPTV 108 (148)
Q Consensus 99 ~~~~~i~~T~ 108 (148)
.++|.+..|+
T Consensus 70 tg~GYfivtP 79 (80)
T PF10264_consen 70 TGEGYFIVTP 79 (80)
T ss_pred CCCceEeeCC
Confidence 8777777665
No 11
>smart00847 HA2 Helicase associated domain (HA2) Add an annotation. This presumed domain is about 90 amino acid residues in length. It is found is a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding.
Probab=88.39 E-value=0.97 Score=29.86 Aligned_cols=52 Identities=13% Similarity=0.008 Sum_probs=38.3
Q ss_pred HHHHhhhCCceeecCCCccccChhhHHHHhcCCCHHHHHhc---cCC-CCHHHHHHhhhC
Q psy9269 86 ELNGLSRYNLITMNDGFDILPTVTGSIMAKFCIGFNTMVAF---TGW-EKAQKDLALLTT 141 (148)
Q Consensus 86 ~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~YI~~~T~~~~---~~~-~s~~~lL~ll~~ 141 (148)
++..|...|.|..+ + ..|++|+.||.+=++|.=.+++ ... ....+++.+++.
T Consensus 2 A~~~L~~LgAld~~--~--~lT~lG~~m~~lPl~Prla~~Ll~a~~~~~c~~~~~~i~a~ 57 (92)
T smart00847 2 ALELLYELGALDDD--G--RLTPLGRKMAELPLDPRLAKMLLAAAELFGCLDEILTIAAM 57 (92)
T ss_pred HHHHHHHCCCcCCC--C--CcCHHHHHHHHCCCChHHHHHHHHHHhhcCcHHHHHHHHHH
Confidence 56678888998632 3 7999999999999999999888 221 245566666553
No 12
>PF04408 HA2: Helicase associated domain (HA2); InterPro: IPR007502 This presumed domain is about 90 amino acid residues in length. It is found as a diverse set of RNA helicases. Its function is unknown, however it seems likely to be involved in nucleic acid binding.; GO: 0004386 helicase activity; PDB: 3I4U_A 2XAU_B 3KX2_B.
Probab=88.37 E-value=0.99 Score=30.88 Aligned_cols=38 Identities=16% Similarity=0.069 Sum_probs=28.6
Q ss_pred HHHHHhhhCCceeecCCCccccChhhHHHHhcCCCHHHHHhc
Q psy9269 85 RELNGLSRYNLITMNDGFDILPTVTGSIMAKFCIGFNTMVAF 126 (148)
Q Consensus 85 ~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~YI~~~T~~~~ 126 (148)
++++.|...|.|..+ -..|++|+.++++=++|.=.+++
T Consensus 1 ~A~~~L~~Lgald~~----~~lT~lG~~~~~lPl~p~~a~~L 38 (102)
T PF04408_consen 1 KALELLKSLGALDEN----GNLTPLGRKMSQLPLDPRLAKML 38 (102)
T ss_dssp -HHHHHHHTTSB-TT----S-B-HHHHHHTTSSS-HHHHHHH
T ss_pred CHHHHHHHCCCCCCC----CCcCHHHHHHHHCCCchHhHhHh
Confidence 367789999999422 38899999999999999998887
No 13
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=88.02 E-value=0.57 Score=34.97 Aligned_cols=77 Identities=13% Similarity=0.160 Sum_probs=51.7
Q ss_pred HHHHHHhHHHHHHHhhCCCCCCCCCCCChHHHHHHHhhhhHhHHHHHHHHhhhCCceeecCCCccccChhhH-HHHhcCC
Q psy9269 40 AVEWLRSTFFFVRVLSNPGHYGFPAGLSSEELQSRLQGKNSGLCMRELNGLSRYNLITMNDGFDILPTVTGS-IMAKFCI 118 (148)
Q Consensus 40 ~~~wl~~TFly~Rl~~nP~~Yg~~~~~~~~~~~~~l~~~~~~~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~-i~S~~YI 118 (148)
.-++|+.-|...+ .+.| ....++...|.+. ..-|.+.++.|.+.|+|.+.+.+.+..|+.|+ ++...+=
T Consensus 8 ~edYL~~Iy~l~~-~~~~--------~~~~diA~~L~Vs-p~sVt~ml~rL~~~GlV~~~~y~gi~LT~~G~~~a~~~~r 77 (154)
T COG1321 8 EEDYLETIYELLE-EKGF--------ARTKDIAERLKVS-PPSVTEMLKRLERLGLVEYEPYGGVTLTEKGREKAKELLR 77 (154)
T ss_pred HHHHHHHHHHHHh-ccCc--------ccHHHHHHHhCCC-cHHHHHHHHHHHHCCCeEEecCCCeEEChhhHHHHHHHHH
Confidence 3467777766553 1111 1223344444422 24566789999999999998888899999999 7766776
Q ss_pred CHHHHHhc
Q psy9269 119 GFNTMVAF 126 (148)
Q Consensus 119 ~~~T~~~~ 126 (148)
.+.+...|
T Consensus 78 ~hrlle~f 85 (154)
T COG1321 78 KHRLLERF 85 (154)
T ss_pred HHHHHHHH
Confidence 77777777
No 14
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=86.40 E-value=5.7 Score=26.57 Aligned_cols=76 Identities=16% Similarity=-0.000 Sum_probs=48.4
Q ss_pred HHHHHHh-CCcCCHHHHHHHHHhHHHHH---HHhhCCCCCCCCCCCChHHHHHHHhhhhHhHHHHHHHHhhhCCceeecC
Q psy9269 25 LNSEIVL-KTISDVSVAVEWLRSTFFFV---RVLSNPGHYGFPAGLSSEELQSRLQGKNSGLCMRELNGLSRYNLITMND 100 (148)
Q Consensus 25 lnaeIa~-g~i~s~~~~~~wl~~TFly~---Rl~~nP~~Yg~~~~~~~~~~~~~l~~~~~~~v~~~l~~L~~~~lI~~~~ 100 (148)
++..++. |...+..|+.+.+...|-.. +-..-|+ +.. ..... .-+.=++..|...|+|+...
T Consensus 9 iL~~L~~~g~~~~~~ei~~~v~~~~~ls~e~~~~~~~s------g~~----~~~~~----~ri~Wa~~~L~~aGli~~~~ 74 (92)
T PF14338_consen 9 ILEALKDLGGSASRKEIYERVAERFGLSDEERNERLPS------GQG----YSRFK----NRIRWARSYLKKAGLIERPK 74 (92)
T ss_pred HHHHHHHcCCCcCHHHHHHHHHHHhCCCHHHHHHHccc------CCc----chhHH----HhHHHHHHHHHHCCCccCCC
Confidence 3444444 88899999999998776211 0000000 000 01222 55667888999999998755
Q ss_pred CCccccChhhHHHH
Q psy9269 101 GFDILPTVTGSIMA 114 (148)
Q Consensus 101 ~~~i~~T~lG~i~S 114 (148)
.|.+..|+.|+-+-
T Consensus 75 rG~~~iT~~G~~~l 88 (92)
T PF14338_consen 75 RGIWRITEKGRKAL 88 (92)
T ss_pred CCceEECHhHHHHH
Confidence 58999999998653
No 15
>TIGR01967 DEAH_box_HrpA ATP-dependent helicase HrpA. This model represents HrpA, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria and a few high-GC Gram-positive bacteria. HrpA is about 1300 amino acids long, while its paralog HrpB, also uncharacterized, is about 800 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing.
Probab=86.35 E-value=1.6 Score=42.70 Aligned_cols=45 Identities=9% Similarity=0.013 Sum_probs=39.1
Q ss_pred hHHHHHHHHhhhCCceeecCCCccccChhhHHHHhcCCCHHHHHhc
Q psy9269 81 GLCMRELNGLSRYNLITMNDGFDILPTVTGSIMAKFCIGFNTMVAF 126 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~YI~~~T~~~~ 126 (148)
.-+..++..|.+.|.|..++ +....|++|+.||++.++|.-.+++
T Consensus 449 ~~i~~A~~~L~~LGAld~~~-~~~~LT~lGr~ma~LPldPrlarmL 493 (1283)
T TIGR01967 449 RAIRDGFRLLEELGALDDDE-AEPQLTPIGRQLAQLPVDPRLARML 493 (1283)
T ss_pred HHHHHHHHHHHHCCCCCCCC-CCccccHHHHHHhhcCCChHHHHHH
Confidence 56788999999999997544 3468999999999999999999998
No 16
>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.
Probab=85.67 E-value=0.89 Score=28.34 Aligned_cols=30 Identities=20% Similarity=0.208 Sum_probs=23.9
Q ss_pred hHHHHHHHHhhhCCceeecCCCccccChhhH
Q psy9269 81 GLCMRELNGLSRYNLITMNDGFDILPTVTGS 111 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~ 111 (148)
+.....+..|.+.|+|+.++ +.+.+|+-|+
T Consensus 36 ~~~~~~l~~l~~~Gll~~~~-~~l~lT~~G~ 65 (66)
T PF06969_consen 36 EEFQKELEELQEDGLLEIDG-GRLRLTEKGR 65 (66)
T ss_dssp HH-HHHHHHHHHTTSEEE-S-SEEEE-TTTG
T ss_pred HHHHHHHHHHHHCCCEEEeC-CEEEECcccC
Confidence 55577899999999999988 7899999996
No 17
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=82.75 E-value=2.1 Score=27.90 Aligned_cols=35 Identities=20% Similarity=0.077 Sum_probs=27.8
Q ss_pred hHHHHHHHHhhhCCceeecCCCccccChhhHHHHhc
Q psy9269 81 GLCMRELNGLSRYNLITMNDGFDILPTVTGSIMAKF 116 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~ 116 (148)
..+...++.|.+.|+|..++ +.+..|+-|+-+-.-
T Consensus 34 ~~~~~yL~~L~~~gLI~~~~-~~Y~lTekG~~~l~~ 68 (77)
T PF14947_consen 34 STLKKYLKELEEKGLIKKKD-GKYRLTEKGKEFLEE 68 (77)
T ss_dssp HHHHHHHHHHHHTTSEEEET-TEEEE-HHHHHHHHH
T ss_pred HHHHHHHHHHHHCcCeeCCC-CEEEECccHHHHHHH
Confidence 56778899999999997644 789999999976543
No 18
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=82.17 E-value=1.9 Score=31.16 Aligned_cols=36 Identities=11% Similarity=0.114 Sum_probs=28.6
Q ss_pred hHHHHHHHHhhhCCceeecCCCccccChhhHHHHhc
Q psy9269 81 GLCMRELNGLSRYNLITMNDGFDILPTVTGSIMAKF 116 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~ 116 (148)
.-|...++.|++.|+|.....+.+.+|+-|+.++..
T Consensus 37 ~svs~~l~~L~~~Gli~~~~~~~i~LT~~G~~~a~~ 72 (142)
T PRK03902 37 SSVTKMVQKLDKDEYLIYEKYRGLVLTPKGKKIGKR 72 (142)
T ss_pred hHHHHHHHHHHHCCCEEEecCceEEECHHHHHHHHH
Confidence 456678899999999987655679999999876544
No 19
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=80.10 E-value=2.9 Score=27.68 Aligned_cols=38 Identities=18% Similarity=0.135 Sum_probs=31.0
Q ss_pred hHHHHHHHHhhhCCceeecCCCccccChhhHHHHhcCC
Q psy9269 81 GLCMRELNGLSRYNLITMNDGFDILPTVTGSIMAKFCI 118 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~YI 118 (148)
.-+..+++.|++.|+|...++..+.+|+.|.....-..
T Consensus 14 stvs~~l~~L~~~glI~r~~~~~~~lT~~g~~~~~~~~ 51 (96)
T smart00529 14 PTVTQMLKKLEKDGLVEYEPYRGITLTEKGRRLARRLL 51 (96)
T ss_pred HHHHHHHHHHHHCCCEEEcCCCceEechhHHHHHHHHH
Confidence 45678899999999999988667999999988764443
No 20
>PHA01735 hypothetical protein
Probab=76.03 E-value=3.4 Score=26.98 Aligned_cols=34 Identities=29% Similarity=0.427 Sum_probs=28.2
Q ss_pred eeccccHHHHHHHHHHHHhCCcCC--HHHHHHHHHh
Q psy9269 13 VESSLHRHLVEHLNSEIVLKTISD--VSVAVEWLRS 46 (148)
Q Consensus 13 IES~L~~~L~~~lnaeIa~g~i~s--~~~~~~wl~~ 46 (148)
.-|-||..+.+-+.+-|.+|..++ ...|++||+.
T Consensus 9 ~fs~LH~~lt~El~~RiksgeATtaDL~AA~d~Lk~ 44 (76)
T PHA01735 9 QFDELHQLLTNELLSRIKSGEATTADLRAACDWLKS 44 (76)
T ss_pred HHHHHHHHHHHHHHHHHhcCcccHHHHHHHHHHHHH
Confidence 447788999999999999998764 5678999964
No 21
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=73.84 E-value=6.5 Score=29.38 Aligned_cols=30 Identities=17% Similarity=0.152 Sum_probs=24.5
Q ss_pred hHHHHHHHHhhhCCceeecCCCccccChhhH
Q psy9269 81 GLCMRELNGLSRYNLITMNDGFDILPTVTGS 111 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~ 111 (148)
.++..+|..|++.|+|+.++.| =..|+-|+
T Consensus 96 ~iiR~~LqqLE~~glVek~~~G-R~lT~~G~ 125 (150)
T PRK09333 96 SIIRKILQQLEKAGLVEKTKKG-RVITPKGR 125 (150)
T ss_pred HHHHHHHHHHHHCCCeeeCCCC-CEeCHHHH
Confidence 6889999999999999987744 44777775
No 22
>PF10915 DUF2709: Protein of unknown function (DUF2709); InterPro: IPR024484 Members of this family appear restricted to Chlamydiales. Their function is unknown.
Probab=72.85 E-value=2.2 Score=33.32 Aligned_cols=68 Identities=13% Similarity=-0.007 Sum_probs=47.6
Q ss_pred hHHHHHHHHhhhCCceeecCC--CccccChhhHHHHhcCCCHHHHHhc--cCCCCHHH-HHHhhhCCCCCCCC
Q psy9269 81 GLCMRELNGLSRYNLITMNDG--FDILPTVTGSIMAKFCIGFNTMVAF--TGWEKAQK-DLALLTTLPLATSR 148 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~--~~i~~T~lG~i~S~~YI~~~T~~~~--~~~~s~~~-lL~ll~~s~e~~~~ 148 (148)
.-.+.+++.|++-|=|..+.+ =.+--.....-..+-||-|-|.+.| .-..+.+| +-+++++|||=|.|
T Consensus 50 qs~e~ai~~lE~e~KlWreteI~I~~g~p~VNE~TkkIYICPFTGKVF~DNt~~nPQDAIYDWvSkCPeN~ER 122 (238)
T PF10915_consen 50 QSAEDAIRILEEEGKLWRETEIKIQSGKPSVNEQTKKIYICPFTGKVFGDNTHPNPQDAIYDWVSKCPENTER 122 (238)
T ss_pred cCHHHHHHHHHHhcchheeeeEEEecCCcccccccceEEEcCCcCccccCCCCCChHHHHHHHHhhCCccchh
Confidence 456788999999887776543 0122234555667899999999999 22245444 55999999997765
No 23
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=72.70 E-value=5.3 Score=27.57 Aligned_cols=33 Identities=18% Similarity=0.029 Sum_probs=27.2
Q ss_pred hHHHHHHHHhhhCCceeecCCC---ccccChhhHHH
Q psy9269 81 GLCMRELNGLSRYNLITMNDGF---DILPTVTGSIM 113 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~~---~i~~T~lG~i~ 113 (148)
....+.++.|.+.|+|...+++ .+..|+.|+..
T Consensus 46 ~~~~~yi~~L~~~Gli~~~~~~~~~~y~lT~KG~~f 81 (95)
T COG3432 46 KRAQKYIEMLVEKGLIIKQDNGRRKVYELTEKGKRF 81 (95)
T ss_pred HHHHHHHHHHHhCCCEEeccCCccceEEEChhHHHH
Confidence 5667888899999988777654 69999999865
No 24
>PRK05256 condesin subunit E; Provisional
Probab=70.58 E-value=24 Score=28.17 Aligned_cols=71 Identities=20% Similarity=0.134 Sum_probs=41.5
Q ss_pred HHHhCCcCCHHHHHHHHHhHHHHHHHhh--CCCCCCCCCCCChHHHHHHHhhhhHhHHHHHHHHhhhCCcee-ecCC-Cc
Q psy9269 28 EIVLKTISDVSVAVEWLRSTFFFVRVLS--NPGHYGFPAGLSSEELQSRLQGKNSGLCMRELNGLSRYNLIT-MNDG-FD 103 (148)
Q Consensus 28 eIa~g~i~s~~~~~~wl~~TFly~Rl~~--nP~~Yg~~~~~~~~~~~~~l~~~~~~~v~~~l~~L~~~~lI~-~~~~-~~ 103 (148)
-.+.+.|-+.+++.+=|.+--=-.|+.+ ||..=|- +.. ...|. +.|..++..|.+.|||. ++.+ +.
T Consensus 108 rLa~~gift~qeL~deL~~ladE~kllklvn~R~~Gs--DlD----~~Kl~----ekvr~sLrrLrRlgmI~~l~~d~~k 177 (238)
T PRK05256 108 RLAHEGIFTQQELYDELLTLADEAKLLKLVNNRSTGS--DLD----KQKLQ----EKVRTSLNRLRRLGMVWFMGHDSSK 177 (238)
T ss_pred HHhcCCceeHHHHHHHHHHhhcHHHHHHHhcCCCCcc--hhh----HHHHH----HHHHHHHHHHHhccceeeecCCCce
Confidence 3455566666666655544333333333 4443321 111 13344 89999999999999999 4433 66
Q ss_pred cccCh
Q psy9269 104 ILPTV 108 (148)
Q Consensus 104 i~~T~ 108 (148)
|.+|+
T Consensus 178 F~ite 182 (238)
T PRK05256 178 FRITE 182 (238)
T ss_pred EEecH
Confidence 77765
No 25
>KOG3411|consensus
Probab=70.09 E-value=5.9 Score=29.05 Aligned_cols=31 Identities=16% Similarity=0.222 Sum_probs=25.2
Q ss_pred hHHHHHHHHhhhCCceeecCCCccccChhhH
Q psy9269 81 GLCMRELNGLSRYNLITMNDGFDILPTVTGS 111 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~ 111 (148)
.+.+.+|..|+..|+|+.+++|.=..|+-|+
T Consensus 98 ~i~rkvlQ~Le~~~~ve~hp~gGR~lt~~Gq 128 (143)
T KOG3411|consen 98 GIARKVLQALEKMGIVEKHPKGGRRLTEQGQ 128 (143)
T ss_pred HHHHHHHHHHHhCCceeeCCCCcceeCcccc
Confidence 7888999999999999999986455555554
No 26
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=69.78 E-value=3 Score=25.65 Aligned_cols=30 Identities=17% Similarity=0.119 Sum_probs=21.7
Q ss_pred hHHHHHHHHhhhCCceeecCC------CccccChhh
Q psy9269 81 GLCMRELNGLSRYNLITMNDG------FDILPTVTG 110 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~------~~i~~T~lG 110 (148)
.-+...++.|.+.|+|+..++ ..+..|+.|
T Consensus 33 ~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~~G 68 (68)
T PF13463_consen 33 STVSRIIKKLEEKGLVEKERDPHDKRSKRYRLTPAG 68 (68)
T ss_dssp HHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-HHH
T ss_pred HHHHHHHHHHHHCCCEEecCCCCcCCeeEEEeCCCC
Confidence 345688999999999965532 247888887
No 27
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=69.00 E-value=5.5 Score=30.09 Aligned_cols=45 Identities=13% Similarity=0.048 Sum_probs=33.5
Q ss_pred hHHHHHHHHhhhCCceeecCCCccccChhhHHHHhcCCCHHHHHhc
Q psy9269 81 GLCMRELNGLSRYNLITMNDGFDILPTVTGSIMAKFCIGFNTMVAF 126 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~YI~~~T~~~~ 126 (148)
+-+.++|+.|.+.|+|+.+++|.+..|+-.- .+-..+.+..+..|
T Consensus 56 ~ev~~sL~~L~~~gli~k~~~g~y~~t~~~l-~~~~~~~~~avr~~ 100 (171)
T PF14394_consen 56 EEVRDSLEFLEKLGLIKKDGDGKYVQTDKSL-TTSSEIPSEAVRSY 100 (171)
T ss_pred HHHHHHHHHHHHCCCeEECCCCcEEEeccee-eCCCCCcHHHHHHH
Confidence 6788999999999999999887888877532 24455555555555
No 28
>PRK13767 ATP-dependent helicase; Provisional
Probab=68.11 E-value=16 Score=34.48 Aligned_cols=42 Identities=14% Similarity=0.162 Sum_probs=32.9
Q ss_pred CCceeccc--cHHHHHHHHHHHHhCCcCCHHHHHHHHHhHHHHHH
Q psy9269 10 REPVESSL--HRHLVEHLNSEIVLKTISDVSVAVEWLRSTFFFVR 52 (148)
Q Consensus 10 ~~pIES~L--~~~L~~~lnaeIa~g~i~s~~~~~~wl~~TFly~R 52 (148)
.+|+.+.. ...|..|+.+.++.| .-+.+++.+|++.||.|..
T Consensus 416 ie~~~~~~~~~dvl~q~i~~~~~~~-~~~~~~~~~~~~~~~~~~~ 459 (876)
T PRK13767 416 IDRVHIPKNPLDVLAQHIVGMAIER-PWDIEEAYNIVRRAYPYRD 459 (876)
T ss_pred CCCCCCCCCcHHHHHHHHHHHHHcC-CCCHHHHHHHHhccCCccc
Confidence 34444443 357999999988886 5699999999999999973
No 29
>PF01090 Ribosomal_S19e: Ribosomal protein S19e; InterPro: IPR001266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family includes a number of eukaryotic and archaebacterial ribosomal proteins; mammalian S19, Drosophila S19, Ascaris lumbricoides S19g (ALEP-1) and S19s, yeast YS16 (RP55A and RP55B), Aspergillus S16 and Haloarcula marismortui HS12.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZ6_S 3U5G_T 3U5C_T 3O30_M 3O2Z_M 3IZB_S 2XZN_T 2XZM_T 2V7F_A.
Probab=67.49 E-value=7.5 Score=28.67 Aligned_cols=32 Identities=16% Similarity=0.090 Sum_probs=25.3
Q ss_pred hHHHHHHHHhhhCCceeecCCCccccChhhHH
Q psy9269 81 GLCMRELNGLSRYNLITMNDGFDILPTVTGSI 112 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~i 112 (148)
.++..+|.+|++.|+|+.++++.=..|+-|+-
T Consensus 95 ~iiR~~LqqLE~~glv~k~~~~GR~lT~~G~~ 126 (139)
T PF01090_consen 95 SIIRKILQQLEKAGLVEKDPKGGRRLTPKGQR 126 (139)
T ss_dssp HHHHHHHHHHHHTTSEEEETTTEEEE-HHHHH
T ss_pred HHHHHHHHHHHHCCCEEecCCCCCEECHHHHH
Confidence 68999999999999999986533467777774
No 30
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=64.77 E-value=5.1 Score=26.36 Aligned_cols=39 Identities=13% Similarity=0.041 Sum_probs=28.3
Q ss_pred hHHHHHHHHhhhCCceeecCC-------CccccChhhHHHHhcCCC
Q psy9269 81 GLCMRELNGLSRYNLITMNDG-------FDILPTVTGSIMAKFCIG 119 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~-------~~i~~T~lG~i~S~~YI~ 119 (148)
.-+...+..|+++|+|+.... ..+..|+-|+-+=.-|+.
T Consensus 29 g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~~~~~~~~ 74 (80)
T PF13601_consen 29 GNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGREAFERYVA 74 (80)
T ss_dssp HHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHHHHHHHHH
Confidence 345577889999999998654 248899999987655543
No 31
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=64.06 E-value=7.1 Score=31.70 Aligned_cols=34 Identities=12% Similarity=0.137 Sum_probs=28.2
Q ss_pred HHHHHHHhhhCCceeecCCCccccChhhHHHHhcC
Q psy9269 83 CMRELNGLSRYNLITMNDGFDILPTVTGSIMAKFC 117 (148)
Q Consensus 83 v~~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~Y 117 (148)
+.-.|+.|.+.|+|..++ +.+..|+.|+++..-.
T Consensus 43 i~pqiKkL~~~~LV~~~~-~~Y~LS~~G~iiv~km 76 (260)
T COG4742 43 ILPQIKKLKDKGLVVQEG-DRYSLSSLGKIIVEKM 76 (260)
T ss_pred HHHHHHHHhhCCCEEecC-CEEEecchHHHHHHHH
Confidence 345577999999999886 7899999999997543
No 32
>PF14277 DUF4364: Domain of unknown function (DUF4364)
Probab=63.84 E-value=8.3 Score=29.01 Aligned_cols=36 Identities=22% Similarity=0.178 Sum_probs=29.0
Q ss_pred HHHHHHHhhhCCceeecC--C--CccccChhhHHHHhcCC
Q psy9269 83 CMRELNGLSRYNLITMND--G--FDILPTVTGSIMAKFCI 118 (148)
Q Consensus 83 v~~~l~~L~~~~lI~~~~--~--~~i~~T~lG~i~S~~YI 118 (148)
+.+++.+|.++|+|..+. + ..+..|+-|+-+..++.
T Consensus 36 lqq~l~eL~es~~i~~~~~~~~~~~y~iTe~G~~tl~~F~ 75 (163)
T PF14277_consen 36 LQQALSELVESGLITLETDSDNKTRYSITEKGKETLEFFE 75 (163)
T ss_pred HHHHHHHHHHCCCEEEeeccCCCcEEEECHhhHHHHHHHH
Confidence 567899999999999752 2 57899999998776653
No 33
>KOG4385|consensus
Probab=63.75 E-value=5.9 Score=34.97 Aligned_cols=26 Identities=19% Similarity=0.460 Sum_probs=22.1
Q ss_pred cCCHHHHHHHHHhHHHHHHHhhCCCCCC
Q psy9269 34 ISDVSVAVEWLRSTFFFVRVLSNPGHYG 61 (148)
Q Consensus 34 i~s~~~~~~wl~~TFly~Rl~~nP~~Yg 61 (148)
-.+..|+.+||++||-|.| +|+..+.
T Consensus 388 QLTLNEIY~WFTrtFAYFR--RNaATWK 413 (581)
T KOG4385|consen 388 QLTLNEIYNWFTRTFAYFR--RNAATWK 413 (581)
T ss_pred hccHHHHHHHHHHHHHHHh--ccchhHh
Confidence 4578999999999999986 7888765
No 34
>PF13182 DUF4007: Protein of unknown function (DUF4007)
Probab=62.74 E-value=17 Score=29.69 Aligned_cols=74 Identities=14% Similarity=0.170 Sum_probs=49.6
Q ss_pred HHHHhHHHHHHHhhCCCCCCCCCCCChHHHH--HHHhhhhHhHHHHHHHHhhhCCceeecCCCccccChhhHHHH----h
Q psy9269 42 EWLRSTFFFVRVLSNPGHYGFPAGLSSEELQ--SRLQGKNSGLCMRELNGLSRYNLITMNDGFDILPTVTGSIMA----K 115 (148)
Q Consensus 42 ~wl~~TFly~Rl~~nP~~Yg~~~~~~~~~~~--~~l~~~~~~~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S----~ 115 (148)
.||+.-|=+++ ++|..+.-. +.+. ..=+ ++|...--.|...|+|+.+.++.-.+|++|+++- .
T Consensus 13 ~WL~K~~~~v~--~~~~~F~~~-----~a~~~lGvGk----NMV~siryWl~a~gli~~~~~~~~~~T~lG~~i~~g~Dp 81 (286)
T PF13182_consen 13 GWLKKGYDAVE--NDPDVFSDE-----DAIVRLGVGK----NMVKSIRYWLRAFGLIEEDNKGKRKLTPLGELIFDGNDP 81 (286)
T ss_pred HHHHHHHHHHh--cCcccccch-----hHHHHcCCCH----hHHHHHHHHHHHcCCcccCCCCCcccCHHHHHHHhcCCC
Confidence 48888876653 567665411 1111 0111 6777777799999999988764459999999998 5
Q ss_pred cCCCHHHHHhc
Q psy9269 116 FCIGFNTMVAF 126 (148)
Q Consensus 116 ~YI~~~T~~~~ 126 (148)
|--++.|.=.+
T Consensus 82 ylE~~~TlWll 92 (286)
T PF13182_consen 82 YLEDPGTLWLL 92 (286)
T ss_pred cccChHhHHHH
Confidence 55577776555
No 35
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=60.88 E-value=9.2 Score=25.39 Aligned_cols=34 Identities=15% Similarity=0.092 Sum_probs=25.3
Q ss_pred hHHHHHHHHhhhCCceeecCC------CccccChhhHHHH
Q psy9269 81 GLCMRELNGLSRYNLITMNDG------FDILPTVTGSIMA 114 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~------~~i~~T~lG~i~S 114 (148)
.++.+.|+.|++.|+|+.... -.+..|+.|+-.-
T Consensus 34 ~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~~G~~l~ 73 (90)
T PF01638_consen 34 KVLSQRLKELEEAGLVERRVYPEVPPRVEYSLTEKGKELL 73 (90)
T ss_dssp HHHHHHHHHHHHTTSEEEEEESSSSSEEEEEE-HHHHHHH
T ss_pred HHHHHHHHHHHHcchhhcccccCCCCCCccCCCcCHHHHH
Confidence 677788999999999986532 2478899998553
No 36
>PF09681 Phage_rep_org_N: N-terminal phage replisome organiser (Phage_rep_org_N); InterPro: IPR010056 This entry is represented by the N-terminal domain of Bacteriophage A500, Gp45. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. The proteins in this entry contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The low-complexity region is adjacent to this N-terminal domain.
Probab=60.55 E-value=12 Score=26.87 Aligned_cols=34 Identities=12% Similarity=0.040 Sum_probs=28.2
Q ss_pred hhHhHHHHHHHHhhhCCceeecCCCccccChhhH
Q psy9269 78 KNSGLCMRELNGLSRYNLITMNDGFDILPTVTGS 111 (148)
Q Consensus 78 ~~~~~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~ 111 (148)
+-.+.|+.||..|.+.|||+..++|.+..+....
T Consensus 65 ~~~~~V~~AL~~f~k~glIe~~ed~~i~i~~~~~ 98 (121)
T PF09681_consen 65 RPVDTVRLALAVFQKLGLIEIDEDGVIYIPNWEK 98 (121)
T ss_pred CCHHHHHHHHHHHHHCCCEEEecCCeEEeecHHH
Confidence 3347889999999999999998888888777655
No 37
>PRK11050 manganese transport regulator MntR; Provisional
Probab=59.96 E-value=12 Score=27.49 Aligned_cols=36 Identities=22% Similarity=0.215 Sum_probs=29.5
Q ss_pred hHHHHHHHHhhhCCceeecCCCccccChhhHHHHhc
Q psy9269 81 GLCMRELNGLSRYNLITMNDGFDILPTVTGSIMAKF 116 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~ 116 (148)
.-+...++.|++.|+|.....+.+.+|+.|+.....
T Consensus 66 stVsr~l~~Le~~GlI~r~~~~~v~LT~~G~~l~~~ 101 (152)
T PRK11050 66 PTVAKMLKRLARDGLVEMRPYRGVFLTPEGEKLAQE 101 (152)
T ss_pred HHHHHHHHHHHHCCCEEEecCCceEECchHHHHHHH
Confidence 567889999999999987765568999999887443
No 38
>PTZ00095 40S ribosomal protein S19; Provisional
Probab=59.77 E-value=17 Score=27.64 Aligned_cols=31 Identities=13% Similarity=0.019 Sum_probs=24.8
Q ss_pred hHHHHHHHHhhhCCceeecCC-CccccChhhH
Q psy9269 81 GLCMRELNGLSRYNLITMNDG-FDILPTVTGS 111 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~-~~i~~T~lG~ 111 (148)
.++..+|.+|++.|+|+.+++ +.=..|+-|+
T Consensus 120 ~iiR~~LQqLE~~glVek~~~~~GR~lT~~Gr 151 (169)
T PTZ00095 120 KILRWICQQLEKLGLVEQGPKKKGRRLTRKGC 151 (169)
T ss_pred HHHHHHHHHHHHCCCEEecCCCCCCEECHhHH
Confidence 788999999999999998753 3346777776
No 39
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=59.56 E-value=12 Score=26.75 Aligned_cols=35 Identities=20% Similarity=0.121 Sum_probs=28.2
Q ss_pred hHHHHHHHHhhhCCceeecCC------CccccChhhHHHHh
Q psy9269 81 GLCMRELNGLSRYNLITMNDG------FDILPTVTGSIMAK 115 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~------~~i~~T~lG~i~S~ 115 (148)
.-+...++.|++.|+|+...+ -.+.+|+-|+-+-.
T Consensus 61 ~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~ 101 (144)
T PRK03573 61 PSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLIS 101 (144)
T ss_pred hhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChHHHHHHH
Confidence 456788999999999998654 35899999997654
No 40
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=58.28 E-value=12 Score=26.79 Aligned_cols=34 Identities=18% Similarity=0.162 Sum_probs=27.6
Q ss_pred hHHHHHHHHhhhCCceeecCC------CccccChhhHHHH
Q psy9269 81 GLCMRELNGLSRYNLITMNDG------FDILPTVTGSIMA 114 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~------~~i~~T~lG~i~S 114 (148)
.-+...++.|++.|+|+...+ -.+.+|+-|+-+-
T Consensus 69 ~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~~ 108 (144)
T PRK11512 69 GALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAIC 108 (144)
T ss_pred HHHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHHHH
Confidence 456788999999999998654 2489999999763
No 41
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=57.89 E-value=9 Score=31.18 Aligned_cols=45 Identities=16% Similarity=0.002 Sum_probs=34.0
Q ss_pred hHHHHHHHHhhhCCceeecCCCccccChhhHHHHhcCCCHHHHHhc
Q psy9269 81 GLCMRELNGLSRYNLITMNDGFDILPTVTGSIMAKFCIGFNTMVAF 126 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~YI~~~T~~~~ 126 (148)
+-|.++|+.|.+.|||..+++|.+.+|+- .+.+-..+.+..+..|
T Consensus 154 ~ev~~sL~~L~~~glikk~~~g~y~~t~~-~l~~~~~~~~~avr~~ 198 (271)
T TIGR02147 154 EQVKESLDLLERLGLIKKNEDGFYKQTDK-AVSTGDEVIPLAVRQY 198 (271)
T ss_pred HHHHHHHHHHHHCCCeeECCCCcEEeecc-eeecCCccchHHHHHH
Confidence 56889999999999999988788888876 3445555666555554
No 42
>TIGR02337 HpaR homoprotocatechuate degradation operon regulator, HpaR. This Helix-Turn-Helix transcriptional regulator is a member of the MarR family (pfam01047) and is found in association with operons for the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate.
Probab=56.74 E-value=15 Score=25.32 Aligned_cols=33 Identities=24% Similarity=0.124 Sum_probs=26.7
Q ss_pred hHHHHHHHHhhhCCceeecCC------CccccChhhHHH
Q psy9269 81 GLCMRELNGLSRYNLITMNDG------FDILPTVTGSIM 113 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~------~~i~~T~lG~i~ 113 (148)
..+...++.|++.|+|+...+ -.+.+|+-|+-+
T Consensus 57 ~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~ 95 (118)
T TIGR02337 57 PSLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQAL 95 (118)
T ss_pred hhHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHH
Confidence 467789999999999997653 258899999865
No 43
>PF09821 AAA_assoc_C: C-terminal AAA-associated domain; InterPro: IPR018632 Members of this family are found in various prokaryotic ABC transporters, predominantly involved in nitrate, sulphonate and bicarbonate translocation.
Probab=56.30 E-value=12 Score=26.70 Aligned_cols=32 Identities=19% Similarity=0.107 Sum_probs=26.5
Q ss_pred HHHHhhhCCceeecCCCccccChhhHHHHhcCC
Q psy9269 86 ELNGLSRYNLITMNDGFDILPTVTGSIMAKFCI 118 (148)
Q Consensus 86 ~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~YI 118 (148)
+++.++-.||++..+ |.+..|+.|+..+..-+
T Consensus 17 ~~eAaelLgf~~~~~-Gdi~LT~~G~~f~~a~~ 48 (120)
T PF09821_consen 17 IVEAAELLGFAEVEE-GDIRLTPLGRRFAEADI 48 (120)
T ss_pred HHHHHHHcCCeeecC-CcEEeccchHHHHHCCh
Confidence 455667779999987 89999999999887765
No 44
>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=54.03 E-value=41 Score=20.60 Aligned_cols=48 Identities=15% Similarity=0.079 Sum_probs=28.0
Q ss_pred HHHHHHHhCCcCCHHHHHHHHHhHHHHHHHhhCCCCCCCCCCCChHHHHHHHhhhhHhHHHHHHHHhhhCCcee
Q psy9269 24 HLNSEIVLKTISDVSVAVEWLRSTFFFVRVLSNPGHYGFPAGLSSEELQSRLQGKNSGLCMRELNGLSRYNLIT 97 (148)
Q Consensus 24 ~lnaeIa~g~i~s~~~~~~wl~~TFly~Rl~~nP~~Yg~~~~~~~~~~~~~l~~~~~~~v~~~l~~L~~~~lI~ 97 (148)
.|-..+ .|. +|++++++.+...| +.. + +.++ +-+...+..|.+.|+|+
T Consensus 21 ~Iw~~~-~g~-~t~~ei~~~l~~~y------------~~~----~----~~~~----~dv~~fl~~L~~~glIe 68 (68)
T PF05402_consen 21 FIWELL-DGP-RTVEEIVDALAEEY------------DVD----P----EEAE----EDVEEFLEQLREKGLIE 68 (68)
T ss_dssp HHHHH---SS-S-HHHHHHHHHHHT------------T------H----HHHH----HHHHHHHHHHHHTT---
T ss_pred HHHHHc-cCC-CCHHHHHHHHHHHc------------CCC----H----HHHH----HHHHHHHHHHHHCcCcC
Confidence 333444 443 79999999998875 222 2 2234 66778888999999884
No 45
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=52.70 E-value=21 Score=21.57 Aligned_cols=27 Identities=19% Similarity=0.073 Sum_probs=20.9
Q ss_pred hHHHHHHHHhhhCCceeecCCCccccC
Q psy9269 81 GLCMRELNGLSRYNLITMNDGFDILPT 107 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~~~i~~T 107 (148)
.-+...++.|.+.|+|...+.+.+..+
T Consensus 40 ~tv~r~l~~L~~~g~i~~~~~~~~~l~ 66 (67)
T cd00092 40 ETVSRTLKELEEEGLISRRGRGKYRVN 66 (67)
T ss_pred HHHHHHHHHHHHCCCEEecCCCeEEeC
Confidence 667889999999999998764445544
No 46
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=52.32 E-value=17 Score=24.26 Aligned_cols=39 Identities=18% Similarity=0.074 Sum_probs=31.0
Q ss_pred hHHHHHHHHhhhCCceeecCC------CccccChhhHHHHhcCCC
Q psy9269 81 GLCMRELNGLSRYNLITMNDG------FDILPTVTGSIMAKFCIG 119 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~------~~i~~T~lG~i~S~~YI~ 119 (148)
..+...++.|++.|+|....+ -.+..|+-|+-...-...
T Consensus 51 ~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~~~~~~~ 95 (126)
T COG1846 51 STVTRLLKRLEDKGLIERLRDPEDRRAVLVRLTEKGRELLEQLLP 95 (126)
T ss_pred HHHHHHHHHHHHCCCeeecCCccccceeeEEECccHHHHHHHhcc
Confidence 567789999999999997765 247899999987665555
No 47
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=51.62 E-value=20 Score=23.10 Aligned_cols=36 Identities=19% Similarity=0.121 Sum_probs=26.9
Q ss_pred hHHHHHHHHhhhCCceeecCC------CccccChhhHHHHhc
Q psy9269 81 GLCMRELNGLSRYNLITMNDG------FDILPTVTGSIMAKF 116 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~------~~i~~T~lG~i~S~~ 116 (148)
.-+...++.|++.|+|+...+ ..+.+|+.|...-..
T Consensus 39 ~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~lT~~g~~~~~~ 80 (101)
T smart00347 39 STVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEEGRELIEE 80 (101)
T ss_pred hhHHHHHHHHHHCCCeEecCCCCCCCeEEEEECHhHHHHHHH
Confidence 456688999999999986643 247889998765443
No 48
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=51.35 E-value=17 Score=25.89 Aligned_cols=33 Identities=18% Similarity=0.103 Sum_probs=26.1
Q ss_pred hHHHHHHHHhhhCCceeecCC------CccccChhhHHH
Q psy9269 81 GLCMRELNGLSRYNLITMNDG------FDILPTVTGSIM 113 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~------~~i~~T~lG~i~ 113 (148)
.+..+.|+.|++.|+|....- -.+..|+.|+-.
T Consensus 52 k~Ls~~Lk~Le~~Glv~R~~~~~~PprveY~LT~~G~~L 90 (120)
T COG1733 52 KMLSRRLKELEEDGLVERVVYPEEPPRVEYRLTEKGRDL 90 (120)
T ss_pred HHHHHHHHHHHHCCCEEeeecCCCCceeEEEEhhhHHHH
Confidence 677789999999999987642 247889999844
No 49
>TIGR01714 phage_rep_org_N phage replisome organizer, putative, N-terminal region. This model represents the N-terminal domain of a small family of phage proteins. The protein contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The region covered by this model is N-terminal to the low-complexity region.
Probab=51.35 E-value=20 Score=25.65 Aligned_cols=32 Identities=22% Similarity=0.116 Sum_probs=26.4
Q ss_pred HhHHHHHHHHhhhCCceeecCCCccccChhhH
Q psy9269 80 SGLCMRELNGLSRYNLITMNDGFDILPTVTGS 111 (148)
Q Consensus 80 ~~~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~ 111 (148)
.+.|+-|+..|.+.|||+..++|.+..+....
T Consensus 65 ~~~V~~Al~~f~k~glIe~~d~g~i~i~~~~~ 96 (119)
T TIGR01714 65 VGDIRITLQTLESLGLIEKKNNGDIFLENWEK 96 (119)
T ss_pred HHHHHHHHHHHHHCCCEEEecCCcEEehhHHH
Confidence 36789999999999999998777777777643
No 50
>PF03551 PadR: Transcriptional regulator PadR-like family; InterPro: IPR005149 Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response [].; PDB: 1XMA_B 2ESH_A 2DQL_B 3L9F_C 3ELK_B 4EJO_B 3L7W_A 3HHH_A 1YG2_A 3F8B_A ....
Probab=50.63 E-value=14 Score=23.44 Aligned_cols=33 Identities=21% Similarity=-0.001 Sum_probs=25.6
Q ss_pred hHHHHHHHHhhhCCceeecCC--------CccccChhhHHH
Q psy9269 81 GLCMRELNGLSRYNLITMNDG--------FDILPTVTGSIM 113 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~--------~~i~~T~lG~i~ 113 (148)
.-+..+|+.|++.|+|+.... ..+..|+-|+-.
T Consensus 32 g~lY~~L~~Le~~gli~~~~~~~~~~~~rk~Y~iT~~G~~~ 72 (75)
T PF03551_consen 32 GSLYPALKRLEEEGLIESRWEEEGNGRPRKYYRITEKGREE 72 (75)
T ss_dssp HHHHHHHHHHHHTTSEEEEEEEETTSSEEEEEEESHHHHHH
T ss_pred hHHHHHHHHHHhCCCEEEeeeccCCCCCCEEEEECHHHHHH
Confidence 456788999999999986532 247899999864
No 51
>PF02981 FokI_N: Restriction endonuclease FokI, recognition domain; InterPro: IPR004234 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 []. Thie entry represents the type IIS restriction endonuclease FokI (3.1.21.4 from EC), which is a member of an unusual class of bipartite restriction enzymes that recognise a specific DNA sequence and cleave DNA nonspecifically a short distance away from that sequence []. FokI contains amino- and carboxy-terminal domains corresponding to the DNA-recognition and cleavage functions (IPR004233 from INTERPRO), respectively. The recognition domain is made of three smaller subdomains (D1, D2 and D3) which are evolutionarily related to the helix-turn-helix-containing DNA-binding domain of the catabolite gene activator protein CAP []. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system; PDB: 1FOK_A 2FOK_B.
Probab=50.53 E-value=24 Score=26.17 Aligned_cols=32 Identities=13% Similarity=-0.057 Sum_probs=24.4
Q ss_pred HHHHhhhCCceeecCC-CccccChhhHHHHhcC
Q psy9269 86 ELNGLSRYNLITMNDG-FDILPTVTGSIMAKFC 117 (148)
Q Consensus 86 ~l~~L~~~~lI~~~~~-~~i~~T~lG~i~S~~Y 117 (148)
-|+.=...|||.++.+ +++..|++|+..++.|
T Consensus 112 flrwAvslgfl~~~~~~Dtf~IT~lG~~~~~~~ 144 (145)
T PF02981_consen 112 FLRWAVSLGFLDYDRETDTFSITELGKKYVKSN 144 (145)
T ss_dssp HHHHHHHTTSEEEETTTTEEEE-HHHHHHHHS-
T ss_pred eeeeeeeeCceeeccCCCEEEeehhHHHHhhcc
Confidence 4455566799999877 7899999999988754
No 52
>TIGR01970 DEAH_box_HrpB ATP-dependent helicase HrpB. This model represents HrpB, one of two related but uncharacterized DEAH-box ATP-dependent helicases in many Proteobacteria, but also in a few species of other lineages. The member from Rhizobium meliloti has been designated HelO. HrpB is typically about 800 residues in length, while its paralog HrpA (TIGR01967), also uncharacterized, is about 1300 amino acids long. Related characterized eukarotic proteins are RNA helicases associated with pre-mRNA processing.
Probab=49.41 E-value=43 Score=31.50 Aligned_cols=42 Identities=14% Similarity=-0.030 Sum_probs=35.5
Q ss_pred hHHHHHHHHhhhCCceeecCCCccccChhhHHHHhcCCCHHHHHhc
Q psy9269 81 GLCMRELNGLSRYNLITMNDGFDILPTVTGSIMAKFCIGFNTMVAF 126 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~YI~~~T~~~~ 126 (148)
.-+..++..|...|.|..+ + ..|++|+.||.+=++|.=.+++
T Consensus 381 ~~i~~a~~~L~~lgald~~--~--~lT~~G~~~~~lp~~p~l~~~l 422 (819)
T TIGR01970 381 VALAAARQLLQRLGALDAQ--G--RLTAHGKAMAALGCHPRLAAML 422 (819)
T ss_pred HHHHHHHHHHHHCCCCCCC--C--CcCHHHHHHHhcCCCHHHHHHH
Confidence 4567889999999998633 3 4799999999999999999888
No 53
>cd00186 TOP1Ac DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand.
Probab=49.24 E-value=37 Score=28.72 Aligned_cols=32 Identities=13% Similarity=0.190 Sum_probs=25.5
Q ss_pred HHHHHhhhCCceeecCCCccccChhhHHHHhcC
Q psy9269 85 RELNGLSRYNLITMNDGFDILPTVTGSIMAKFC 117 (148)
Q Consensus 85 ~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~Y 117 (148)
..|..|.+.|.|..++ +.+.||++|+.+-..+
T Consensus 305 ~iI~~L~~r~Yi~~~~-k~l~pT~~G~~li~~l 336 (381)
T cd00186 305 SIIETLLDRGYVEKEK-KKLIPTELGFAVIELL 336 (381)
T ss_pred HHHHHHHhCCcEEeeC-CEEeECHHHHHHHHHH
Confidence 4566788899999766 5799999999886554
No 54
>COG2238 RPS19A Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis]
Probab=48.35 E-value=21 Score=26.50 Aligned_cols=30 Identities=17% Similarity=0.151 Sum_probs=24.2
Q ss_pred hHHHHHHHHhhhCCceeecCCCccccChhhH
Q psy9269 81 GLCMRELNGLSRYNLITMNDGFDILPTVTGS 111 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~ 111 (148)
.+++.++.+|++.|+|+..++| =..|+-|+
T Consensus 96 sI~RkilqqLE~~G~V~k~~~G-R~ltp~Gr 125 (147)
T COG2238 96 SIIRKVLQQLEKAGLVEKTPKG-RVLTPKGR 125 (147)
T ss_pred hHHHHHHHHHHHCCceeecCCC-ceeCccch
Confidence 7899999999999999987743 44566666
No 55
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=46.63 E-value=21 Score=24.41 Aligned_cols=32 Identities=9% Similarity=0.046 Sum_probs=25.3
Q ss_pred hHHHHHHHHhhhCCceeecCC------CccccChhhHH
Q psy9269 81 GLCMRELNGLSRYNLITMNDG------FDILPTVTGSI 112 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~------~~i~~T~lG~i 112 (148)
.-+...++.|++.|+|....+ -.+.+|+-|+-
T Consensus 58 stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~lT~~G~~ 95 (109)
T TIGR01889 58 SALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQRS 95 (109)
T ss_pred HHHHHHHHHHHHCCCEeccCCcccCCeEEEEECHHHHH
Confidence 566788999999999997554 24789999964
No 56
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=46.62 E-value=73 Score=20.05 Aligned_cols=22 Identities=27% Similarity=0.416 Sum_probs=18.6
Q ss_pred HhHHHHHHHHhhhCCceeecCC
Q psy9269 80 SGLCMRELNGLSRYNLITMNDG 101 (148)
Q Consensus 80 ~~~v~~~l~~L~~~~lI~~~~~ 101 (148)
..-|...|+.|++.|+|..++.
T Consensus 40 ~~tv~~~L~~Le~kG~I~r~~~ 61 (65)
T PF01726_consen 40 TSTVQRHLKALERKGYIRRDPG 61 (65)
T ss_dssp HHHHHHHHHHHHHTTSEEEGCC
T ss_pred hHHHHHHHHHHHHCcCccCCCC
Confidence 3678889999999999998763
No 57
>PRK05799 coproporphyrinogen III oxidase; Provisional
Probab=46.42 E-value=45 Score=27.76 Aligned_cols=33 Identities=12% Similarity=0.123 Sum_probs=27.6
Q ss_pred HHHHHHHHhhhCCceeecCCCccccChhhHHHHh
Q psy9269 82 LCMRELNGLSRYNLITMNDGFDILPTVTGSIMAK 115 (148)
Q Consensus 82 ~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~ 115 (148)
.....++.|.+.|++..++ +.+.+|+-|+..+.
T Consensus 334 ~~~~~l~~l~~~gl~~~~~-~~~~lT~~G~~~~~ 366 (374)
T PRK05799 334 VYGEVINKYIKLGLLIEKE-GRIYLSERGIEVSN 366 (374)
T ss_pred HHHHHHHHHHHCCCEEEEC-CEEEEChhHHHHHH
Confidence 4556788999999999876 68999999998764
No 58
>PF14502 HTH_41: Helix-turn-helix domain
Probab=46.27 E-value=24 Score=21.28 Aligned_cols=22 Identities=18% Similarity=0.117 Sum_probs=19.0
Q ss_pred hHHHHHHHHhhhCCceeecCCC
Q psy9269 81 GLCMRELNGLSRYNLITMNDGF 102 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~~ 102 (148)
-.|.+||+.|++.|.|..+..|
T Consensus 21 GtiQ~Alk~Le~~gaI~Le~rG 42 (48)
T PF14502_consen 21 GTIQNALKFLEENGAIKLESRG 42 (48)
T ss_pred hHHHHHHHHHHHCCcEEeeecC
Confidence 5788999999999999987653
No 59
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=45.64 E-value=25 Score=24.06 Aligned_cols=26 Identities=19% Similarity=0.175 Sum_probs=20.1
Q ss_pred hHHHHHHHHhhhCCceeecCCCcccc
Q psy9269 81 GLCMRELNGLSRYNLITMNDGFDILP 106 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~~~i~~ 106 (148)
+.|+.+++.|++.|+|+......+..
T Consensus 36 ~~v~~~l~~Le~~GLler~~g~~iK~ 61 (92)
T PF10007_consen 36 EEVREALEKLEEMGLLERVEGKTIKR 61 (92)
T ss_pred HHHHHHHHHHHHCCCeEEecCcccch
Confidence 57889999999999999876433333
No 60
>PF04288 MukE: MukE-like family; InterPro: IPR007385 This family contains MukE, which are proteins involved in the segregation and condensation of prokaryotic chromosomes. MukE along with MukF (IPR005582 from INTERPRO) interact with MukB (IPR007406 from INTERPRO) in vivo forming a complex, which is required for chromosome condensation and segregation in Escherichia coli []. The Muk complex appears to be similar to the SMC-ScpA-ScpB complex in other prokaryotes where MukB is the homologue of SMC []. ScpA (IPR003768 from INTERPRO) and ScpB (IPR005234 from INTERPRO) have little sequence similarity to MukE or MukF, though they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. ; GO: 0007059 chromosome segregation, 0030261 chromosome condensation, 0005737 cytoplasm; PDB: 3EUK_M 3EUH_D 3RPU_Z.
Probab=45.45 E-value=25 Score=28.00 Aligned_cols=31 Identities=19% Similarity=0.080 Sum_probs=24.3
Q ss_pred hhHhHHHHHHHHhhhCCceeecCC---CccccCh
Q psy9269 78 KNSGLCMRELNGLSRYNLITMNDG---FDILPTV 108 (148)
Q Consensus 78 ~~~~~v~~~l~~L~~~~lI~~~~~---~~i~~T~ 108 (148)
+..+.|..++..|...|||...++ +.|.+|+
T Consensus 141 Kl~Ekvr~sL~rLrRlgmI~~~g~~d~~kF~ite 174 (235)
T PF04288_consen 141 KLQEKVRTSLRRLRRLGMIYFVGDQDSQKFRITE 174 (235)
T ss_dssp CHHHHHHHHHHHHHHTTSEEESS-SSSSEEEE-G
T ss_pred HHHHHHHHHHHHHHhcCceEeeccCcccceeecH
Confidence 334899999999999999998862 6777776
No 61
>PF13730 HTH_36: Helix-turn-helix domain
Probab=45.40 E-value=62 Score=18.89 Aligned_cols=29 Identities=28% Similarity=0.280 Sum_probs=19.8
Q ss_pred ChHHHHHHHhhhhHhHHHHHHHHhhhCCce
Q psy9269 67 SSEELQSRLQGKNSGLCMRELNGLSRYNLI 96 (148)
Q Consensus 67 ~~~~~~~~l~~~~~~~v~~~l~~L~~~~lI 96 (148)
+.+.+...+... .+-|.++++.|++.|+|
T Consensus 27 S~~~la~~~g~s-~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 27 SQETLAKDLGVS-RRTVQRAIKELEEKGLI 55 (55)
T ss_pred CHHHHHHHHCcC-HHHHHHHHHHHHHCcCC
Confidence 444444444322 47788999999999986
No 62
>PF03882 KicB: KicB killing factor; InterPro: IPR005582 This family contains MukF, which are proteins involved in chromosome condensation, segregation and cell cycle progression. MukE (IPR007385 from INTERPRO) along with MukF interact with MukB (IPR007406 from INTERPRO) in vivo forming a complex, which is required for chromosome condensation and segregation in Escherichia coli []. The Muk complex appears to be similar to the SMC-ScpA-ScpB complex in other prokaryotes where MukB is the homologue of SMC []. ScpA (IPR003768 from INTERPRO) and ScpB (IPR005234 from INTERPRO) have little sequence similarity to MukE or MukF, though they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. ; GO: 0005509 calcium ion binding, 0006260 DNA replication, 0007059 chromosome segregation, 0005737 cytoplasm; PDB: 1T98_B 3RPU_X 3EUH_B 3EUK_J 3EUJ_B.
Probab=45.37 E-value=15 Score=31.81 Aligned_cols=44 Identities=16% Similarity=0.092 Sum_probs=31.0
Q ss_pred HHHHHHHHhhhCCceeecC------CCccccChhhHHHHhcCCCHHHHHh
Q psy9269 82 LCMRELNGLSRYNLITMND------GFDILPTVTGSIMAKFCIGFNTMVA 125 (148)
Q Consensus 82 ~v~~~l~~L~~~~lI~~~~------~~~i~~T~lG~i~S~~YI~~~T~~~ 125 (148)
=+.++|+.|.+.+|+..-. .+.+..|++|--++.|||..+-...
T Consensus 73 RANNAIndlv~QrlLsRf~se~~eg~~iYRLT~L~~gI~dyyirqrefs~ 122 (440)
T PF03882_consen 73 RANNAINDLVRQRLLSRFTSEFTEGASIYRLTPLGIGISDYYIRQREFST 122 (440)
T ss_dssp HHHHHHHHHHHTTSEEEEE-SSSTTSEEEEE-HHHHHHHHHHHS-----H
T ss_pred HHHHHHHHHHHHHHHHHhccccccccceeeechhhhchhHHHHHHHHHhH
Confidence 3568999999999997432 2568999999999999998765443
No 63
>PRK13347 coproporphyrinogen III oxidase; Provisional
Probab=44.23 E-value=1.5e+02 Score=25.59 Aligned_cols=31 Identities=23% Similarity=0.231 Sum_probs=26.1
Q ss_pred HHHHHhhhCCceeecCCCccccChhhHHHHhc
Q psy9269 85 RELNGLSRYNLITMNDGFDILPTVTGSIMAKF 116 (148)
Q Consensus 85 ~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~ 116 (148)
..+..|++.|+|..++ +.+..|+.|+..++.
T Consensus 403 ~~l~~l~~~gl~~~~~-~~~~lT~~G~~~~~~ 433 (453)
T PRK13347 403 ARLEPLAADGLVTIDG-GGIRVTPEGRPLIRA 433 (453)
T ss_pred HHHHHHHHCCCEEEEC-CEEEECcchhHHHHH
Confidence 5788999999999887 579999999987643
No 64
>PRK10870 transcriptional repressor MprA; Provisional
Probab=44.03 E-value=28 Score=26.07 Aligned_cols=36 Identities=14% Similarity=0.125 Sum_probs=28.5
Q ss_pred hHHHHHHHHhhhCCceeecCC------CccccChhhHHHHhc
Q psy9269 81 GLCMRELNGLSRYNLITMNDG------FDILPTVTGSIMAKF 116 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~------~~i~~T~lG~i~S~~ 116 (148)
.-+...++.|++.|+|+...+ -.+.+|+-|+-.-.-
T Consensus 86 ~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~~~~ 127 (176)
T PRK10870 86 TNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEFLRE 127 (176)
T ss_pred HHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHHH
Confidence 456778999999999998654 258999999876544
No 65
>TIGR02647 DNA conserved hypothetical protein TIGR02647. Members of this family are found, so far, only in the Gammaproteobacteria. The function is unknown. The location on the chromosome usually is not far from housekeeping genes rather than in what is clearly, say, a prophage region. Some members have been annotated in public databases as DNA-binding protein inhibitor Id-2-related protein, putative transcriptional regulator, or hypothetical DNA binding protein.
Probab=43.63 E-value=36 Score=22.55 Aligned_cols=34 Identities=21% Similarity=0.049 Sum_probs=25.8
Q ss_pred hHHHHHHHHhhhCCceeecCCCccccChhhHHHHhc
Q psy9269 81 GLCMRELNGLSRYNLITMNDGFDILPTVTGSIMAKF 116 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~ 116 (148)
.-+-.+++.|.+.|+|.-.. |. ..|+.|.-+|.+
T Consensus 34 p~~i~a~~RLheKGLI~~pd-Gg-yLT~~G~~~aEh 67 (77)
T TIGR02647 34 PAAVAAAARLHEKGLTTQPD-GG-YLTSLGLEAAEH 67 (77)
T ss_pred HHHHHHHHHHHHcCCccCCC-CC-EecHHHHHHHHH
Confidence 34457899999999998544 44 889999887743
No 66
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=43.23 E-value=28 Score=19.43 Aligned_cols=24 Identities=25% Similarity=0.260 Sum_probs=18.8
Q ss_pred hHHHHHHHHhhhCCceeecCCCccc
Q psy9269 81 GLCMRELNGLSRYNLITMNDGFDIL 105 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~~~i~ 105 (148)
.-+...++.|++.|+|..+. +.+.
T Consensus 23 ~tv~~~l~~L~~~g~l~~~~-~~~~ 46 (48)
T smart00419 23 ETVSRTLKRLEKEGLISREG-GRIV 46 (48)
T ss_pred HHHHHHHHHHHHCCCEEEeC-CEEE
Confidence 56788999999999998765 4443
No 67
>KOG0925|consensus
Probab=43.20 E-value=47 Score=29.93 Aligned_cols=37 Identities=16% Similarity=0.109 Sum_probs=26.3
Q ss_pred ccChhhHHHHhcCCCHHHHHhc--cCC-CCHHHHHHhhhC
Q psy9269 105 LPTVTGSIMAKFCIGFNTMVAF--TGW-EKAQKDLALLTT 141 (148)
Q Consensus 105 ~~T~lG~i~S~~YI~~~T~~~~--~~~-~s~~~lL~ll~~ 141 (148)
..|++|.+||.|=++|.=++++ ... -...++|.+-++
T Consensus 453 nLT~lG~imSEFPLdPqLAkmLi~S~efnCsnEiLsisAM 492 (699)
T KOG0925|consen 453 NLTSLGEIMSEFPLDPQLAKMLIGSCEFNCSNEILSISAM 492 (699)
T ss_pred ccchhhhhhhcCCCChHHHHHHhhcCCCCchHHHHHHHhc
Confidence 4689999999999999999998 111 233455554443
No 68
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=41.96 E-value=42 Score=20.85 Aligned_cols=45 Identities=20% Similarity=0.178 Sum_probs=31.3
Q ss_pred CChHHHHHHHhhhhHhHHHHHHHHhhhCCceeecCCCccccChhhHH
Q psy9269 66 LSSEELQSRLQGKNSGLCMRELNGLSRYNLITMNDGFDILPTVTGSI 112 (148)
Q Consensus 66 ~~~~~~~~~l~~~~~~~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~i 112 (148)
.+.+.+...+... ..-+.+.++.|++.|+|+... +.+..++.-++
T Consensus 29 lt~~~iA~~~g~s-r~tv~r~l~~l~~~g~I~~~~-~~i~I~d~~~L 73 (76)
T PF13545_consen 29 LTQEEIADMLGVS-RETVSRILKRLKDEGIIEVKR-GKIIILDPERL 73 (76)
T ss_dssp SSHHHHHHHHTSC-HHHHHHHHHHHHHTTSEEEET-TEEEESSHHHH
T ss_pred CCHHHHHHHHCCC-HHHHHHHHHHHHHCCCEEEcC-CEEEECCHHHH
Confidence 4555665544433 355889999999999999887 56776665543
No 69
>PRK05776 DNA topoisomerase I; Provisional
Probab=41.42 E-value=54 Score=30.08 Aligned_cols=32 Identities=25% Similarity=0.114 Sum_probs=26.1
Q ss_pred HHHHHhhhCCceeecCCCccccChhhHHHHhcC
Q psy9269 85 RELNGLSRYNLITMNDGFDILPTVTGSIMAKFC 117 (148)
Q Consensus 85 ~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~Y 117 (148)
..|..|.+-|.|..++ +.+.||++|+.+...+
T Consensus 496 ~iI~~L~~R~Yv~~~~-k~l~pT~~G~~v~~~L 527 (670)
T PRK05776 496 RIIETLFKRGYLTSNG-KYIEVTPLGFGVAEVL 527 (670)
T ss_pred HHHHHHHhCCCEEeeC-CEEeECHHHHHHHHHH
Confidence 4566788999998765 6799999999987665
No 70
>PRK08599 coproporphyrinogen III oxidase; Provisional
Probab=40.36 E-value=59 Score=27.15 Aligned_cols=35 Identities=14% Similarity=0.181 Sum_probs=28.2
Q ss_pred hHHHHHHHHhhhCCceeecCCCccccChhhHHHHhc
Q psy9269 81 GLCMRELNGLSRYNLITMNDGFDILPTVTGSIMAKF 116 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~ 116 (148)
+.....+..|.+.|++..++ +.+.+|+.|+..+..
T Consensus 334 ~~~~~~~~~l~~~gl~~~~~-~~~~lt~~G~~~~~~ 368 (377)
T PRK08599 334 DVFGETIQELQEQGLLEEDD-DHVRLTKKGKFLGNE 368 (377)
T ss_pred HHHHHHHHHHHHCCCEEEEC-CEEEECccHhHHHHH
Confidence 34566788999999999877 689999999977543
No 71
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 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, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=40.09 E-value=28 Score=21.08 Aligned_cols=18 Identities=17% Similarity=0.102 Sum_probs=11.9
Q ss_pred CCceeecCCCccccChhhH
Q psy9269 93 YNLITMNDGFDILPTVTGS 111 (148)
Q Consensus 93 ~~lI~~~~~~~i~~T~lG~ 111 (148)
..++.... +.+.||+.|+
T Consensus 43 ~~Lf~r~~-~~~~lT~~G~ 60 (60)
T PF00126_consen 43 VPLFERSG-RGLRLTEAGE 60 (60)
T ss_dssp S-SEEECS-SSEEE-HHHH
T ss_pred CeEEEECC-CCeeEChhhC
Confidence 36776666 4699999996
No 72
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=38.90 E-value=47 Score=22.05 Aligned_cols=33 Identities=15% Similarity=0.123 Sum_probs=25.2
Q ss_pred hHHHHHHHHhhhCCceeecC--CCccccChhhHHH
Q psy9269 81 GLCMRELNGLSRYNLITMND--GFDILPTVTGSIM 113 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~--~~~i~~T~lG~i~ 113 (148)
--|.+.+..|++.|+|+-.+ .+...||.-|-.+
T Consensus 38 aTIRN~M~~Le~lGlve~~p~~s~GriPT~~aYr~ 72 (78)
T PF03444_consen 38 ATIRNEMADLEELGLVESQPHPSGGRIPTDKAYRA 72 (78)
T ss_pred HHHHHHHHHHHHCCCccCCCCCCCCCCcCHHHHHH
Confidence 56778888999999998432 3668899888643
No 73
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=38.66 E-value=39 Score=25.89 Aligned_cols=35 Identities=14% Similarity=0.039 Sum_probs=27.8
Q ss_pred hHHHHHHHHhhhCCceeecCC------CccccChhhHHHHh
Q psy9269 81 GLCMRELNGLSRYNLITMNDG------FDILPTVTGSIMAK 115 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~------~~i~~T~lG~i~S~ 115 (148)
.-+...++.|++.|+|....+ -.+.+|+-|+-+-.
T Consensus 74 sTvtr~l~rLE~kGlI~R~~~~~DrR~~~I~LTekG~~l~~ 114 (185)
T PRK13777 74 STAFNFSKKLEERGYLTFSKKEDDKRNTYIELTEKGEELLL 114 (185)
T ss_pred hhHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHH
Confidence 457788999999999997643 35899999997744
No 74
>PRK11664 ATP-dependent RNA helicase HrpB; Provisional
Probab=38.56 E-value=42 Score=31.48 Aligned_cols=42 Identities=12% Similarity=-0.063 Sum_probs=35.7
Q ss_pred hHHHHHHHHhhhCCceeecCCCccccChhhHHHHhcCCCHHHHHhc
Q psy9269 81 GLCMRELNGLSRYNLITMNDGFDILPTVTGSIMAKFCIGFNTMVAF 126 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~YI~~~T~~~~ 126 (148)
.-++.++..|...|.|.-+ | ..|++|+.||.+=++|.=.+++
T Consensus 384 ~~~~~A~~~L~~lgald~~--g--~lT~~G~~m~~lp~~Prla~~l 425 (812)
T PRK11664 384 AALAAAKRLLQQLGALDGQ--G--RLTARGRKMAALGNDPRLAAML 425 (812)
T ss_pred HHHHHHHHHHHHCCCCCCC--C--CcCHHHHHHHhcCCchHHHHHH
Confidence 4567899999999998632 3 5799999999999999998888
No 75
>smart00611 SEC63 Domain of unknown function in Sec63p, Brr2p and other proteins.
Probab=38.54 E-value=22 Score=28.67 Aligned_cols=20 Identities=10% Similarity=-0.062 Sum_probs=17.1
Q ss_pred CCCCHHHHHHhhhCCCCCCC
Q psy9269 128 GWEKAQKDLALLTTLPLATS 147 (148)
Q Consensus 128 ~~~s~~~lL~ll~~s~e~~~ 147 (148)
+.++..++|++||.|+||..
T Consensus 30 ~~~~~~~lL~~ls~a~Ef~~ 49 (312)
T smart00611 30 PKMTTKDLLRILSMSSEFDQ 49 (312)
T ss_pred CCCCHHHHHHHHhCcHhhCC
Confidence 34688999999999999964
No 76
>TIGR01056 topB DNA topoisomerase III, bacteria and conjugative plasmid. This model describes topoisomerase III from bacteria and its equivalents encoded on plasmids. The gene is designated topB if found in the bacterial chromosome, traE on conjugative plasmid RP4, etc. These enzymes are involved in the control of DNA topology. DNA topoisomerase III belongs to the type I topoisomerases, which are ATP-independent.
Probab=38.37 E-value=70 Score=29.29 Aligned_cols=32 Identities=16% Similarity=0.218 Sum_probs=26.1
Q ss_pred HHHHHhhhCCceeecCCCccccChhhHHHHhcC
Q psy9269 85 RELNGLSRYNLITMNDGFDILPTVTGSIMAKFC 117 (148)
Q Consensus 85 ~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~Y 117 (148)
..|..|.+.|.|+.++ ..+.||++|+.+....
T Consensus 523 ~iI~~L~~R~Yv~~~~-k~l~pT~~G~~v~~~L 554 (660)
T TIGR01056 523 DIIENLFKRGFIQKKK-NKIYITKNGKLLCLLL 554 (660)
T ss_pred HHHHHHHhCCCEEeeC-CEEEEcHHHHHHHHHh
Confidence 3566788899999766 5799999999987665
No 77
>PF08499 PDEase_I_N: 3'5'-cyclic nucleotide phosphodiesterase N-terminal; InterPro: IPR013706 The cyclic nucleotide phosphodiesterases (PDE) comprise a group of enzymes that degrade the phosphodiester bond in the second messenger molecules cAMP and cGMP. They are divided into 11 families. They regulate the localisation, duration and amplitude of cyclic nucleotide signalling within subcellular domains. PDEs are therefore important for signal transduction. PDE enzymes are often targets for pharmacological inhibition due to their unique tissue distribution, structural properties, and functional properties. Inhibitors include: Roflumilast for chronic obstructive pulmonary disease and asthma [], Sildenafil for erectile dysfunction [] and Cilostazol for peripheral arterial occlusive disease [], amongst others. Retinal 3',5'-cGMP phosphodiesterase is located in photoreceptor outer segments: it is light activated, playing a pivotal role in signal transduction. In rod cells, PDE is oligomeric, comprising an alpha-, a beta- and 2 gamma-subunits, while in cones, PDE is a homodimer of alpha chains, which are associated with several smaller subunits. Both rod and cone PDEs catalyse the hydrolysis of cAMP or cGMP to the corresponding nucleoside 5' monophosphates, both enzymes also binding cGMP with high affinity. The cGMP-binding sites are located in the N-terminal half of the protein sequence, while the catalytic core resides in the C-terminal portion. This domain is found to the N terminus of the calcium/calmodulin-dependent 3'5'-cyclic nucleotide phosphodiesterase domain (IPR002073 from INTERPRO).; GO: 0004114 3',5'-cyclic-nucleotide phosphodiesterase activity
Probab=38.13 E-value=25 Score=22.17 Aligned_cols=23 Identities=35% Similarity=0.486 Sum_probs=15.2
Q ss_pred HHHHhCCcCCHHHHHHHHHhHHHHH
Q psy9269 27 SEIVLKTISDVSVAVEWLRSTFFFV 51 (148)
Q Consensus 27 aeIa~g~i~s~~~~~~wl~~TFly~ 51 (148)
+||..-.+. +|+.+||..||=-.
T Consensus 10 ~~i~~dsvp--~eVr~WLasTFtrq 32 (59)
T PF08499_consen 10 SEIQSDSVP--DEVRDWLASTFTRQ 32 (59)
T ss_pred hhcccccCC--HHHHHHHHHHHHhh
Confidence 455554443 45889999999543
No 78
>KOG0923|consensus
Probab=37.50 E-value=62 Score=30.27 Aligned_cols=60 Identities=13% Similarity=0.037 Sum_probs=43.1
Q ss_pred hHHHHHHHHhhhCCceeecCCCccccChhhHHHHhcCCCHHHHHhc----cCCCCHHHHHHhhhCCCCC
Q psy9269 81 GLCMRELNGLSRYNLITMNDGFDILPTVTGSIMAKFCIGFNTMVAF----TGWEKAQKDLALLTTLPLA 145 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~YI~~~T~~~~----~~~~s~~~lL~ll~~s~e~ 145 (148)
+-+..+|..|...|-+. ..-..|.+||.|+.|=++|.=.+++ +-. +..+++.+.++.+..
T Consensus 652 etL~~aLE~LyaLGALn----~~GeLTk~GrrMaEfP~dPmlsKmi~as~ky~-cs~EiitiaamlS~~ 715 (902)
T KOG0923|consen 652 ETLLKALEQLYALGALN----HLGELTKLGRRMAEFPVDPMLSKMIVASEKYK-CSEEIITIAAMLSVG 715 (902)
T ss_pred HHHHHHHHHHHHhhccc----cccchhhhhhhhhhcCCCHHHHhHHhhhcccc-chHHHHHHHHHHhcC
Confidence 34557788888888764 2357899999999999999999998 222 335666666655443
No 79
>COG3095 MukE Uncharacterized protein involved in chromosome partitioning [Cell division and chromosome partitioning]
Probab=37.41 E-value=36 Score=26.40 Aligned_cols=30 Identities=17% Similarity=0.013 Sum_probs=24.1
Q ss_pred hHhHHHHHHHHhhhCCceeecCC--CccccCh
Q psy9269 79 NSGLCMRELNGLSRYNLITMNDG--FDILPTV 108 (148)
Q Consensus 79 ~~~~v~~~l~~L~~~~lI~~~~~--~~i~~T~ 108 (148)
+.+.|..++..|...|||...++ |.|..|+
T Consensus 149 l~ekvr~sl~rlrrlgmi~~~g~~sgkf~ite 180 (238)
T COG3095 149 LQEKVRSSLNRLRRLGMVWFMGHDSGKFRITE 180 (238)
T ss_pred HHHHHHHHHHHHHHhceeEEeccCCCceeeeH
Confidence 33899999999999999987653 6676665
No 80
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=37.19 E-value=42 Score=20.52 Aligned_cols=21 Identities=24% Similarity=0.213 Sum_probs=18.5
Q ss_pred hHHHHHHHHhhhCCceeecCC
Q psy9269 81 GLCMRELNGLSRYNLITMNDG 101 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~ 101 (148)
..+.+++..|++.|+|...+.
T Consensus 39 ~tvr~al~~L~~~g~i~~~~~ 59 (64)
T PF00392_consen 39 TTVREALRRLEAEGLIERRPG 59 (64)
T ss_dssp HHHHHHHHHHHHTTSEEEETT
T ss_pred cHHHHHHHHHHHCCcEEEECC
Confidence 678899999999999998765
No 81
>PF09202 Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This N-terminal domain is found in RIO2 kinases, and is structurally homologous to the winged helix (wHTH) domain. It adopts a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1TQP_A 1ZAR_A 1TQI_A 1ZAO_A 1TQM_A.
Probab=37.15 E-value=73 Score=21.12 Aligned_cols=36 Identities=19% Similarity=0.240 Sum_probs=25.1
Q ss_pred hhhhHhHHHHHHHHhhhCCceeecCC--CccccChhhH
Q psy9269 76 QGKNSGLCMRELNGLSRYNLITMNDG--FDILPTVTGS 111 (148)
Q Consensus 76 ~~~~~~~v~~~l~~L~~~~lI~~~~~--~~i~~T~lG~ 111 (148)
.+....-+...+..|.+.|+|..... ..+..|..|-
T Consensus 34 s~l~~~~~~~~L~~L~~~kLv~~~~~~Y~GYrLT~~GY 71 (82)
T PF09202_consen 34 SGLSEGEVEKRLKRLVKLKLVSRRNKPYDGYRLTFLGY 71 (82)
T ss_dssp HT--HHHHHHHHHHHHHTTSEEEE-SSS-EEEE-HHHH
T ss_pred hCcCHHHHHHHHHHHHhcCCccccCCCcceEEEeecch
Confidence 33445788899999999999998653 3478888884
No 82
>KOG1165|consensus
Probab=36.54 E-value=42 Score=28.88 Aligned_cols=67 Identities=15% Similarity=0.013 Sum_probs=44.8
Q ss_pred CCHHHHHHHHHhHHHHHHHhhCCCCCCCCCCCChHHHHHHHhhhhHhHHHHHHHHhhhCCceeecCC-------------
Q psy9269 35 SDVSVAVEWLRSTFFFVRVLSNPGHYGFPAGLSSEELQSRLQGKNSGLCMRELNGLSRYNLITMNDG------------- 101 (148)
Q Consensus 35 ~s~~~~~~wl~~TFly~Rl~~nP~~Yg~~~~~~~~~~~~~l~~~~~~~v~~~l~~L~~~~lI~~~~~------------- 101 (148)
-|.||+.||--.+|=-.-+. .+.. .+| .-+..+.+..+|..|-+
T Consensus 108 PSLEDLFD~CgR~FSvKTV~---------------miA~-------Qmi-~rie~vH~k~LIYRDIKPdNFLIGrp~~k~ 164 (449)
T KOG1165|consen 108 PSLEDLFDLCGRRFSVKTVA---------------MIAK-------QMI-TRIEYVHEKDLIYRDIKPDNFLIGRPGTKD 164 (449)
T ss_pred cCHHHHHHHhcCcccHHhHH---------------HHHH-------HHH-HHHHHHHhcceeecccCccceeecCCCCCC
Confidence 58999999998888432111 1111 222 23556777888876532
Q ss_pred -CccccChhhHHHHhcCCCHHHHHhc
Q psy9269 102 -FDILPTVTGSIMAKFCIGFNTMVAF 126 (148)
Q Consensus 102 -~~i~~T~lG~i~S~~YI~~~T~~~~ 126 (148)
+.|..-++| |++.|+||+|-+.+
T Consensus 165 ~n~IhiiDFG--mAK~YrDp~TkqHI 188 (449)
T KOG1165|consen 165 ANVIHIIDFG--MAKEYRDPKTKQHI 188 (449)
T ss_pred CceEEEEecc--chhhhcCccccccC
Confidence 346667777 78999999999998
No 83
>PF11630 DUF3254: Protein of unknown function (DUF3254); InterPro: IPR024509 Anti-lipopolysaccharide factor binds to bacterial LPS and may specifically inhibit the LPS-mediated activation of the hemolymph coagulation. It has a strong antibacterial effect, especially on the growth of Gram-negative bacteria [,]. This entry also includes the antibacterial protein Scygonadin, which has antibacterial activity against the Gram-positive bacterium Micrococcus luteus [].; PDB: 2JOB_A.
Probab=36.53 E-value=66 Score=22.41 Aligned_cols=26 Identities=15% Similarity=0.240 Sum_probs=21.6
Q ss_pred HHHHHHHHHHHHhCCcCCHHHHHHHHH
Q psy9269 19 RHLVEHLNSEIVLKTISDVSVAVEWLR 45 (148)
Q Consensus 19 ~~L~~~lnaeIa~g~i~s~~~~~~wl~ 45 (148)
...+|++--.++.|-| +.+||-.||+
T Consensus 75 ~a~rDFv~kA~~~gLi-T~eeA~~wL~ 100 (100)
T PF11630_consen 75 KATRDFVRKAFQAGLI-TEEEAQPWLN 100 (100)
T ss_dssp HHHHHHHHHHHHHT-S--HHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCc-cHHHHHHhhC
Confidence 5799999999999977 8999999985
No 84
>PF01131 Topoisom_bac: DNA topoisomerase; InterPro: IPR013497 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. Type IA topoisomerases are comprised of four domains that together form a toroidal structure with a central hole large enough to accommodate single- and double-stranded DNA: an N-terminal alpha/beta Toprim domain, domain 2 and the C-terminal domain 4 are winged-helix domains, and domain 3 is a beta-barrel. Domains 1 (Toprim) and 3 form the active site of the enzyme, while the winged helix domains 2 and 4 form a single-strand DNA-binding groove [, ]. This entry represents the central portion of the enzyme, which covers domains 2 and 3 in topoisomerase type IA enzymes. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome; PDB: 1CYY_A 3PWT_A 1CY4_A 1CY9_A 1ECL_A 1CY7_A 1CY8_A 1CY6_A 1MW8_X 1CY0_A ....
Probab=36.03 E-value=33 Score=29.15 Aligned_cols=33 Identities=18% Similarity=0.300 Sum_probs=25.1
Q ss_pred HHHHHhhhCCceeecCCCccccChhhHHHHhcC
Q psy9269 85 RELNGLSRYNLITMNDGFDILPTVTGSIMAKFC 117 (148)
Q Consensus 85 ~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~Y 117 (148)
..|..|.+.|.|..+.++.+.||+.|+.+-...
T Consensus 337 ~iI~~L~~r~Yi~~~k~~~l~~T~~G~~li~~l 369 (403)
T PF01131_consen 337 SIIEKLIKRGYIERSKGKKLIPTPKGRALIEAL 369 (403)
T ss_dssp HHHHHHHHTTSEEE-ETTEEEEBHHHHHHHHHH
T ss_pred HHHHHhhccceeecccCceeeeehHHHHHHHHH
Confidence 455678889999997547899999999876543
No 85
>PF04458 DUF505: Protein of unknown function (DUF505); InterPro: IPR007548 This is a family of uncharacterised prokaryotic proteins.
Probab=35.97 E-value=25 Score=31.77 Aligned_cols=33 Identities=18% Similarity=0.252 Sum_probs=28.9
Q ss_pred HHHHHHHhhhCCceeecCCCccccChhhHHHHh
Q psy9269 83 CMRELNGLSRYNLITMNDGFDILPTVTGSIMAK 115 (148)
Q Consensus 83 v~~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~ 115 (148)
+..||+.|+..|+|..=++|.+..|+.|+.+-+
T Consensus 467 i~~AL~kLEArGfI~~Lp~g~iilTeaG~~ik~ 499 (591)
T PF04458_consen 467 IIEALEKLEARGFIEILPNGMIILTEAGELIKR 499 (591)
T ss_pred HHHHHHHHHhcchHHHcCCCcEEEehhhHHHHH
Confidence 344999999999999988899999999998754
No 86
>PRK06294 coproporphyrinogen III oxidase; Provisional
Probab=35.69 E-value=54 Score=27.49 Aligned_cols=33 Identities=18% Similarity=0.114 Sum_probs=27.4
Q ss_pred HHHHHHHHhhhCCceeecCCCccccChhhHHHHh
Q psy9269 82 LCMRELNGLSRYNLITMNDGFDILPTVTGSIMAK 115 (148)
Q Consensus 82 ~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~ 115 (148)
.....++.|++.|++..++ +.+..|+.|+..+.
T Consensus 331 ~~~~~l~~~~~~gll~~~~-~~i~lT~~G~~~~~ 363 (370)
T PRK06294 331 LTSELIMHPIIQELFTKND-QALSLNKKGRLFHD 363 (370)
T ss_pred HHHHHHHHHHHCCCEEEEC-CEEEECcchhhHHH
Confidence 3456788999999999877 67999999998764
No 87
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=35.47 E-value=53 Score=21.07 Aligned_cols=30 Identities=13% Similarity=-0.015 Sum_probs=22.0
Q ss_pred hHHHHHHHHhhhCCceeecCC-CccccChhh
Q psy9269 81 GLCMRELNGLSRYNLITMNDG-FDILPTVTG 110 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~-~~i~~T~lG 110 (148)
.-|...+..|++.|+|..+++ +.+.+++-+
T Consensus 35 ~tv~r~l~~L~~~g~l~~~~~~~~y~l~~~~ 65 (91)
T smart00346 35 STAHRLLNTLQELGYVEQDGQNGRYRLGPKV 65 (91)
T ss_pred HHHHHHHHHHHHCCCeeecCCCCceeecHHH
Confidence 567888999999999998743 455555433
No 88
>KOG0924|consensus
Probab=35.28 E-value=77 Score=29.88 Aligned_cols=58 Identities=14% Similarity=0.058 Sum_probs=41.5
Q ss_pred hHHHHHHHHhhhCCceeecCCCccccChhhHHHHhcCCCHHHHHhc---cCCCCHHHHHHhhhCC
Q psy9269 81 GLCMRELNGLSRYNLITMNDGFDILPTVTGSIMAKFCIGFNTMVAF---TGWEKAQKDLALLTTL 142 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~YI~~~T~~~~---~~~~s~~~lL~ll~~s 142 (148)
+.+.+++..|-..|-|.. .=..|++|+-|+.|=+||.=.+++ ...-...++|.++++-
T Consensus 743 d~~~~sly~Lw~LGAl~~----~g~LT~lG~~MvefpLDP~lsKmll~a~~~Gc~dEilsIvSmL 803 (1042)
T KOG0924|consen 743 DNLLNSLYQLWTLGALDN----TGQLTPLGRKMVEFPLDPPLSKMLLMAARMGCSDEILSIVSML 803 (1042)
T ss_pred HHHHHHHHHHHHhhcccc----CCccchhhHHhhhCCCCchHHHHHHHHhccCcHHHHHHHHHHh
Confidence 455667777777777653 236799999999999999988887 2223456677666653
No 89
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=34.88 E-value=58 Score=19.20 Aligned_cols=21 Identities=19% Similarity=0.202 Sum_probs=17.5
Q ss_pred hHHHHHHHHhhhCCceeecCC
Q psy9269 81 GLCMRELNGLSRYNLITMNDG 101 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~ 101 (148)
.-+..++..|++.|+|+..++
T Consensus 40 ~~v~~~l~~L~~~G~i~~~~~ 60 (66)
T cd07377 40 TTVREALRELEAEGLVERRPG 60 (66)
T ss_pred HHHHHHHHHHHHCCCEEecCC
Confidence 667889999999999986653
No 90
>PRK07561 DNA topoisomerase I subunit omega; Validated
Probab=34.77 E-value=72 Score=30.13 Aligned_cols=32 Identities=9% Similarity=0.219 Sum_probs=25.6
Q ss_pred HHHHHhhhCCceeecCCCccccChhhHHHHhcC
Q psy9269 85 RELNGLSRYNLITMNDGFDILPTVTGSIMAKFC 117 (148)
Q Consensus 85 ~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~Y 117 (148)
..|..|.+.|.|..++ +.+.||++|+.+..+.
T Consensus 490 ~iI~~L~~R~Yv~~~~-~~l~pT~~G~~v~~~l 521 (859)
T PRK07561 490 SIISTIQDRGYVRLEN-RRFYPEKMGRIVTDRL 521 (859)
T ss_pred HHHHHHhhcCeEEeeC-CEEeecHHHHHHHHHH
Confidence 4567788889998766 6799999999976554
No 91
>PF04919 DUF655: Protein of unknown function (DUF655); InterPro: IPR007003 This family includes several uncharacterised archaeal proteins.; PDB: 2I5H_A.
Probab=34.47 E-value=64 Score=24.87 Aligned_cols=41 Identities=17% Similarity=0.251 Sum_probs=28.6
Q ss_pred hHHHhhcCCCceecccc---------HHHHHHHHHHHHhCCcCCHHHHHH
Q psy9269 2 RYEKLVEGREPVESSLH---------RHLVEHLNSEIVLKTISDVSVAVE 42 (148)
Q Consensus 2 ~Y~~ll~~~~pIES~L~---------~~L~~~lnaeIa~g~i~s~~~~~~ 42 (148)
+|..|+|...||..+|| +.+...|+.|-..+...|++|.-+
T Consensus 100 ~FV~FfN~A~PIt~RlH~LeLLPGIGKK~m~~ILeERkkkpFeSFeDi~~ 149 (181)
T PF04919_consen 100 RFVDFFNEAQPITLRLHSLELLPGIGKKTMWKILEERKKKPFESFEDIEE 149 (181)
T ss_dssp HHHHHH-----B-SSSBGGGGSTT--HHHHHHHHHHHHHS---SHHHHHH
T ss_pred HHHHHhhcCCCChHHHHHHhhcccccHHHHHHHHHHHccCCCCCHHHHHH
Confidence 58899999999999999 378999999999999999999886
No 92
>PRK05260 condesin subunit F; Provisional
Probab=34.12 E-value=15 Score=31.88 Aligned_cols=44 Identities=16% Similarity=0.116 Sum_probs=32.1
Q ss_pred HHHHHHHhhhCCceeec------CCCccccChhhHHHHhcCCCHHHHHhc
Q psy9269 83 CMRELNGLSRYNLITMN------DGFDILPTVTGSIMAKFCIGFNTMVAF 126 (148)
Q Consensus 83 v~~~l~~L~~~~lI~~~------~~~~i~~T~lG~i~S~~YI~~~T~~~~ 126 (148)
+.++|+.|.+.+|+..- +.+.+..|++|.=++.|||.-+-....
T Consensus 74 AnNAIn~lv~QRlL~Rf~se~~~g~~iYRLTpLa~gi~dyyirqrefs~l 123 (440)
T PRK05260 74 ANNAINDLVRQRLLNRFTSEQAEGNAIYRLTPLGIGITDYYIRQREFSTL 123 (440)
T ss_pred HHHHHHHHHHHHHHHhcccccccccceeeccHhhccchHHHHhhHHHhHH
Confidence 45677777777776532 225789999999999999987765543
No 93
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=34.11 E-value=28 Score=21.56 Aligned_cols=20 Identities=20% Similarity=0.345 Sum_probs=17.7
Q ss_pred hHHHHHHHHhhhCCceeecC
Q psy9269 81 GLCMRELNGLSRYNLITMND 100 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~ 100 (148)
.-|..+++.|.+.|+|+..+
T Consensus 37 ~~v~~~L~~L~~~GlV~~~~ 56 (68)
T PF01978_consen 37 STVYRALKSLEEKGLVEREE 56 (68)
T ss_dssp HHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHHHHCCCEEEEc
Confidence 67789999999999999775
No 94
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=33.94 E-value=1.9e+02 Score=22.30 Aligned_cols=25 Identities=8% Similarity=0.025 Sum_probs=20.8
Q ss_pred hHHHHHHHHhhhCCceeecCC-Cccc
Q psy9269 81 GLCMRELNGLSRYNLITMNDG-FDIL 105 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~-~~i~ 105 (148)
.-|.+||+.|++.|+|..... |+|.
T Consensus 48 ~TvR~Al~~L~~eGli~r~~G~GTfV 73 (241)
T PRK11402 48 ITIRKAISDLVADGVLIRWQGKGTFV 73 (241)
T ss_pred HHHHHHHHHHHHCCCEEEecCceeEE
Confidence 568899999999999998765 6654
No 95
>PF14117 DUF4287: Domain of unknown function (DUF4287)
Probab=33.85 E-value=84 Score=19.79 Aligned_cols=26 Identities=12% Similarity=0.210 Sum_probs=19.3
Q ss_pred HHHHHHHHhC-CcCCHHHHHHHHHhHH
Q psy9269 23 EHLNSEIVLK-TISDVSVAVEWLRSTF 48 (148)
Q Consensus 23 ~~lnaeIa~g-~i~s~~~~~~wl~~TF 48 (148)
++..+.+..+ ....-.|.++||+..|
T Consensus 18 ~~W~~~~~~~~~~~k~~e~v~WLK~eh 44 (61)
T PF14117_consen 18 DEWLALAREGGPLTKHGEIVAWLKDEH 44 (61)
T ss_pred HHHHHHHHHhCCCCcHHHHHHHHHHHH
Confidence 3444555555 8889999999999885
No 96
>PF08222 HTH_CodY: CodY helix-turn-helix domain; InterPro: IPR013198 This family consists of the C-terminal helix-turn-helix domain found in several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions []. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk [].; PDB: 2B0L_C.
Probab=33.07 E-value=53 Score=20.70 Aligned_cols=20 Identities=15% Similarity=0.227 Sum_probs=17.3
Q ss_pred hHHHHHHHHhhhCCceeecC
Q psy9269 81 GLCMRELNGLSRYNLITMND 100 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~ 100 (148)
..+.++++.|+.+|.|+-..
T Consensus 19 SvIVNALRKleSaGvIesrS 38 (61)
T PF08222_consen 19 SVIVNALRKLESAGVIESRS 38 (61)
T ss_dssp HHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHHHhcCceeecc
Confidence 78889999999999998543
No 97
>smart00437 TOP1Ac Bacterial DNA topoisomerase I DNA-binding domain. Bacterial DNA topoisomerase I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase alpha subunit
Probab=32.93 E-value=27 Score=28.07 Aligned_cols=27 Identities=19% Similarity=0.246 Sum_probs=21.7
Q ss_pred HHHHHhhhCCceeecCCCccccChhhHH
Q psy9269 85 RELNGLSRYNLITMNDGFDILPTVTGSI 112 (148)
Q Consensus 85 ~~l~~L~~~~lI~~~~~~~i~~T~lG~i 112 (148)
..|+.|.+.|.|...+ +.+.||+.|+.
T Consensus 232 ~iIe~L~~r~Yi~~~~-k~l~~T~~G~~ 258 (259)
T smart00437 232 EIIETLLDRGYVTKEK-KKLIPTELGIA 258 (259)
T ss_pred HHHHHHHhCCcEEeeC-CEEeEccceec
Confidence 4566788999999766 57999999974
No 98
>PRK07726 DNA topoisomerase III; Provisional
Probab=32.85 E-value=95 Score=28.35 Aligned_cols=41 Identities=10% Similarity=0.030 Sum_probs=29.6
Q ss_pred HHHHHhhhCCceeecCCCccccChhhHHHHhcC----CCHHHHHhc
Q psy9269 85 RELNGLSRYNLITMNDGFDILPTVTGSIMAKFC----IGFNTMVAF 126 (148)
Q Consensus 85 ~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~Y----I~~~T~~~~ 126 (148)
..|..|.+.|.|...+ +.+.||++|+.+-... ++|+.-..+
T Consensus 520 ~iIe~L~~R~Yi~~~~-k~l~pT~~G~~li~~l~~~l~~p~~Ta~~ 564 (658)
T PRK07726 520 GIIEKLFKRGYLEKKG-KYIHATDKGKQLIDALPEELTSPDMTAKW 564 (658)
T ss_pred HHHHHHHhCCCEEecC-CEEEECHHHHHHHHHHHHHcCChhhHHHH
Confidence 3566788999998766 5799999999886654 445444433
No 99
>PTZ00407 DNA topoisomerase IA; Provisional
Probab=32.81 E-value=40 Score=31.71 Aligned_cols=34 Identities=15% Similarity=0.059 Sum_probs=27.5
Q ss_pred HHHHHhhhCCceeecCCCccccChhhHHHHhcCC
Q psy9269 85 RELNGLSRYNLITMNDGFDILPTVTGSIMAKFCI 118 (148)
Q Consensus 85 ~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~YI 118 (148)
..|..|.+.|.|..++++.+.||++|+.+-.++-
T Consensus 601 sIIetL~~R~YV~~~~kkrl~PT~lG~~Li~~L~ 634 (805)
T PTZ00407 601 MIVKTLLARGYIAVNPKGRCETTPVGRMLVETAK 634 (805)
T ss_pred HHHHHHHhcCCEEeccCceeeecHHHHHHHHHHH
Confidence 4567888999999873368999999999987763
No 100
>PF04433 SWIRM: SWIRM domain; InterPro: IPR007526 The SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in eukaryotic chromosomal proteins. It is named after the proteins SWI3, RSC8 and MOIRA in which it was first recognised. This domain is predicted to mediate protein-protein interactions in the assembly of chromatin-protein complexes. The SWIRM domain can be linked to different domains, such as the ZZ-type zinc finger (IPR000433 from INTERPRO), the Myb DNA-binding domain (IPR001005 from INTERPRO), the HORMA domain (IPR003511 from INTERPRO), the amino-oxidase domain, the chromo domain (IPR000953 from INTERPRO), and the JAB1/PAD1 domain.; GO: 0005515 protein binding; PDB: 2Z3Y_A 2UXN_A 2Y48_A 2HKO_A 2XAF_A 2X0L_A 2XAJ_A 2UXX_A 2V1D_A 2L3D_A ....
Probab=32.69 E-value=1.4e+02 Score=19.35 Aligned_cols=17 Identities=29% Similarity=0.323 Sum_probs=14.7
Q ss_pred hHHHHHHHHhhhCCcee
Q psy9269 81 GLCMRELNGLSRYNLIT 97 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~ 97 (148)
..+..+.++|+.+|+|-
T Consensus 69 ~~~~ri~~FL~~~G~IN 85 (86)
T PF04433_consen 69 NKIRRIYDFLERWGLIN 85 (86)
T ss_dssp HHHHHHHHHHHHTTSSS
T ss_pred HHHHHHHHHHHHcCccC
Confidence 67788999999999984
No 101
>COG4344 Uncharacterized protein conserved in archaea [Function unknown]
Probab=32.66 E-value=38 Score=25.47 Aligned_cols=27 Identities=26% Similarity=0.166 Sum_probs=20.2
Q ss_pred HHHHHHHHhhhCCceeecCCCccccCh
Q psy9269 82 LCMRELNGLSRYNLITMNDGFDILPTV 108 (148)
Q Consensus 82 ~v~~~l~~L~~~~lI~~~~~~~i~~T~ 108 (148)
-|+..+++|.+.|+|++..+.+++-|+
T Consensus 47 ~i~e~l~dL~elGLier~tgttiKrte 73 (175)
T COG4344 47 RIREYLKDLKELGLIERYTGTTIKRTE 73 (175)
T ss_pred HHHHHHHHHHHcCCeeeccCchhhhhH
Confidence 467889999999999987654444443
No 102
>PF09382 RQC: RQC domain; InterPro: IPR018982 This entry represents the RQC domain, which is a DNA-binding domain found only in RecQ family enzymes. RecQ family helicases can unwind G4 DNA, and play important roles at G-rich domains of the genome, including the telomeres, rDNA, and immunoglobulin switch regions. This domain has a helix-turn-helix structure and acts as a high affinity G4 DNA binding domain []. Binding of RecQ to Holliday junctions involves both the RQC and the HRDC domains.; GO: 0043140 ATP-dependent 3'-5' DNA helicase activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1OYW_A 1OYY_A 3AAF_A 2AXL_A 2V1X_B 2WWY_B.
Probab=32.26 E-value=84 Score=20.95 Aligned_cols=33 Identities=15% Similarity=0.078 Sum_probs=22.9
Q ss_pred hHHHHHHHHhhhCCceeecCC----CccccChhhHHH
Q psy9269 81 GLCMRELNGLSRYNLITMNDG----FDILPTVTGSIM 113 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~----~~i~~T~lG~i~ 113 (148)
..++..++.|...|++..+.+ ..+.+|+-|+-.
T Consensus 57 ~~~~~li~~Li~~g~L~~~~~~~~~~~l~~~~~~~~~ 93 (106)
T PF09382_consen 57 DDWERLIRQLILEGYLSEDNGGFAYPYLKLTPKGKEL 93 (106)
T ss_dssp HHHHHHHHHHHHTTSEEEEECCCCTEEEEE-GGGHHH
T ss_pred HHHHHHHHHHHHcCCceecCCcccccEEEECHHHHHH
Confidence 556677888999999976543 357788877643
No 103
>COG1643 HrpA HrpA-like helicases [DNA replication, recombination, and repair]
Probab=31.63 E-value=1.1e+02 Score=28.97 Aligned_cols=42 Identities=12% Similarity=0.002 Sum_probs=35.7
Q ss_pred hHHHHHHHHhhhCCceeecCCCccccChhhHHHHhcCCCHHHHHhc
Q psy9269 81 GLCMRELNGLSRYNLITMNDGFDILPTVTGSIMAKFCIGFNTMVAF 126 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~YI~~~T~~~~ 126 (148)
.-+..++..|...|.+..++ ..|++|+-||.+=++|.=+.+.
T Consensus 433 ~~i~~A~~~L~~LGAld~~g----~LT~lG~~ms~lpldprLA~mL 474 (845)
T COG1643 433 AAIQAALTLLQELGALDDSG----KLTPLGKQMSLLPLDPRLARML 474 (845)
T ss_pred HHHHHHHHHHHHcCCcCCCC----CCCHHHHHHHhCCCChHHHHHH
Confidence 45568888999999987543 3899999999999999999888
No 104
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=31.37 E-value=68 Score=21.60 Aligned_cols=32 Identities=19% Similarity=0.082 Sum_probs=23.7
Q ss_pred HHHHHHHHhhhCCceeec--CC------CccccChhhHHH
Q psy9269 82 LCMRELNGLSRYNLITMN--DG------FDILPTVTGSIM 113 (148)
Q Consensus 82 ~v~~~l~~L~~~~lI~~~--~~------~~i~~T~lG~i~ 113 (148)
-+..+|+.|++.|+|+.. ++ -.+..|+-|+-.
T Consensus 41 tlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~iT~~Gr~~ 80 (100)
T TIGR03433 41 SLYPALHRLERRGWIAAEWGESENNRRAKFYRLTAAGRKQ 80 (100)
T ss_pred cHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECHHHHHH
Confidence 456789999999999973 11 247888888854
No 105
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=31.34 E-value=40 Score=25.70 Aligned_cols=30 Identities=20% Similarity=0.154 Sum_probs=24.1
Q ss_pred hHHHHHHHHhhhCCceeecCC--CccccChhh
Q psy9269 81 GLCMRELNGLSRYNLITMNDG--FDILPTVTG 110 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~--~~i~~T~lG 110 (148)
..+...++.|++.|+|...++ ..+.+|+.|
T Consensus 172 stv~r~L~~Le~~GlI~r~~~r~~~~~lT~~G 203 (203)
T TIGR01884 172 STISRHLRELEKKGLVEQKGRKGKRYSLTKLG 203 (203)
T ss_pred HHHHHHHHHHHHCCCEEEEcCCccEEEeCCCC
Confidence 567788999999999998862 457888876
No 106
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=30.77 E-value=58 Score=19.05 Aligned_cols=20 Identities=15% Similarity=0.122 Sum_probs=16.7
Q ss_pred hHHHHHHHHhhhCCceeecC
Q psy9269 81 GLCMRELNGLSRYNLITMND 100 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~ 100 (148)
.-+...+..|.+.|+|+.++
T Consensus 33 stv~r~L~tL~~~g~v~~dp 52 (52)
T PF09339_consen 33 STVHRLLQTLVEEGYVERDP 52 (52)
T ss_dssp HHHHHHHHHHHHTTSEEECS
T ss_pred HHHHHHHHHHHHCcCeecCc
Confidence 56778899999999998764
No 107
>COG5631 Predicted transcription regulator, contains HTH domain (MarR family) [Transcription]
Probab=30.44 E-value=85 Score=24.06 Aligned_cols=46 Identities=15% Similarity=0.006 Sum_probs=38.2
Q ss_pred hHHHHHHHHhhhCCceeecCCC---ccccChhhHHHHhcCCCHHHHHhc
Q psy9269 81 GLCMRELNGLSRYNLITMNDGF---DILPTVTGSIMAKFCIGFNTMVAF 126 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~~---~i~~T~lG~i~S~~YI~~~T~~~~ 126 (148)
.++.-+|+.|.+.|+|+....| +++.|++|..+--.|-+-......
T Consensus 114 h~itYslrKL~k~gLit~t~~gkevTy~vTa~G~~acarYa~IRe~lLi 162 (199)
T COG5631 114 HNITYSLRKLLKGGLITRTGSGKEVTYEVTALGHRACARYADIREVLLI 162 (199)
T ss_pred hhHHHHHHHHHhccceecCCCCceEEEEEecchHHHHHHHHHHHHHHHH
Confidence 3456689999999999977653 589999999999899888887777
No 108
>PRK09057 coproporphyrinogen III oxidase; Provisional
Probab=30.42 E-value=52 Score=27.67 Aligned_cols=32 Identities=22% Similarity=0.282 Sum_probs=26.4
Q ss_pred HHHHHhhhCCceeecCCCccccChhhHHHHhc
Q psy9269 85 RELNGLSRYNLITMNDGFDILPTVTGSIMAKF 116 (148)
Q Consensus 85 ~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~ 116 (148)
..++.|.+.|++..++++.+.+|+.|+..+..
T Consensus 342 ~~l~~l~~~gl~~~~~~~~~~lT~~G~~~~d~ 373 (380)
T PRK09057 342 ERLADLIEEGLIERDGGSRLRATPAGRLVLDA 373 (380)
T ss_pred HHHHHHHHCCCEEEcCCCEEEECcchhHHHHH
Confidence 57889999999998764479999999987653
No 109
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=30.41 E-value=90 Score=16.98 Aligned_cols=20 Identities=25% Similarity=0.406 Sum_probs=13.9
Q ss_pred HHHHHHHHhCCcCCHHHHHHHH
Q psy9269 23 EHLNSEIVLKTISDVSVAVEWL 44 (148)
Q Consensus 23 ~~lnaeIa~g~i~s~~~~~~wl 44 (148)
+..-|....+. +++.|++||
T Consensus 18 ~~~~AL~~~~~--nve~A~~~L 37 (37)
T PF00627_consen 18 QAREALRACNG--NVERAVDWL 37 (37)
T ss_dssp HHHHHHHHTTT--SHHHHHHHH
T ss_pred HHHHHHHHcCC--CHHHHHHhC
Confidence 34455566654 899999987
No 110
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=30.37 E-value=88 Score=29.62 Aligned_cols=32 Identities=19% Similarity=0.316 Sum_probs=25.4
Q ss_pred HHHHHhhhCCceeecCCCccccChhhHHHHhcC
Q psy9269 85 RELNGLSRYNLITMNDGFDILPTVTGSIMAKFC 117 (148)
Q Consensus 85 ~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~Y 117 (148)
..|..|.+.|.|..++ +.|.||++|+.+..+.
T Consensus 501 ~iI~~L~~R~Yv~~~~-k~l~pT~~G~~v~~~L 532 (860)
T PRK06319 501 TIMNKIQSREYTLKEN-QRLRPTELGKIISQFL 532 (860)
T ss_pred HHHHHHhhCCeEEccC-CEEEECHHHHHHHHHH
Confidence 4566788899998665 6799999999976544
No 111
>PRK08898 coproporphyrinogen III oxidase; Provisional
Probab=29.78 E-value=60 Score=27.48 Aligned_cols=32 Identities=19% Similarity=0.215 Sum_probs=26.8
Q ss_pred HHHHHHHhhhCCceeecCCCccccChhhHHHHh
Q psy9269 83 CMRELNGLSRYNLITMNDGFDILPTVTGSIMAK 115 (148)
Q Consensus 83 v~~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~ 115 (148)
+...++.|++.|++..++ +.+..|+-|+..+.
T Consensus 355 ~~~~l~~l~~~gll~~~~-~~~~LT~~G~~~~d 386 (394)
T PRK08898 355 IEPQLAAAEQRGLLERDH-TRIRPTPLGQRFLN 386 (394)
T ss_pred HHHHHHHHHHCCCEEEEC-CEEEEChhHhHHHH
Confidence 456788999999999876 67999999998764
No 112
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=29.04 E-value=67 Score=25.28 Aligned_cols=37 Identities=22% Similarity=-0.043 Sum_probs=28.2
Q ss_pred hHHHHHHHHhhhCCceeecCC---CccccChhhHH-HHhcC
Q psy9269 81 GLCMRELNGLSRYNLITMNDG---FDILPTVTGSI-MAKFC 117 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~---~~i~~T~lG~i-~S~~Y 117 (148)
.-+.+.++.|++.|+|+...+ ..+..|+-|+- ..+-|
T Consensus 36 ~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LTekG~~ll~~~~ 76 (217)
T PRK14165 36 KTAARILKQLEDEGYITRTIVPRGQLITITEKGLDVLYNEY 76 (217)
T ss_pred HHHHHHHHHHHHCCCEEEEEcCCceEEEECHHHHHHHHHHH
Confidence 567788999999999987643 56899999984 34444
No 113
>PRK05628 coproporphyrinogen III oxidase; Validated
Probab=28.91 E-value=81 Score=26.30 Aligned_cols=32 Identities=13% Similarity=0.154 Sum_probs=26.9
Q ss_pred HHHHHHhhhCCceeecCCCccccChhhHHHHhc
Q psy9269 84 MRELNGLSRYNLITMNDGFDILPTVTGSIMAKF 116 (148)
Q Consensus 84 ~~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~ 116 (148)
...++.|.+.|++..++ +.+..|+.|+..+..
T Consensus 337 ~~~l~~l~~~gl~~~~~-~~~~lT~~G~~~~~~ 368 (375)
T PRK05628 337 RARAARVVADGLLAAEG-GRLVLTLRGRLLADA 368 (375)
T ss_pred HHHHHHHHHCCCEEEEC-CEEEEChhhhHHHHH
Confidence 46788999999999877 689999999987643
No 114
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 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. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=28.88 E-value=74 Score=17.39 Aligned_cols=16 Identities=38% Similarity=0.372 Sum_probs=14.1
Q ss_pred hHHHHHHHHhhhCCce
Q psy9269 81 GLCMRELNGLSRYNLI 96 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI 96 (148)
+.|..++..|++.|+|
T Consensus 17 ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 17 ETVSRILKKLERQGLI 32 (32)
T ss_dssp HHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHHHHHcCCC
Confidence 7788899999999986
No 115
>TIGR01051 topA_bact DNA topoisomerase I, bacterial. This model describes DNA topoisomerase I among the members of bacteria. DNA topoisomerase I transiently cleaves one DNA strand and thus relaxes negatively supercoiled DNA during replication, transcription and recombination events.
Probab=28.59 E-value=1.1e+02 Score=27.71 Aligned_cols=41 Identities=7% Similarity=0.235 Sum_probs=29.4
Q ss_pred HHHHHhhhCCceeecCCCccccChhhHHHHhc-------CCCHHHHHhc
Q psy9269 85 RELNGLSRYNLITMNDGFDILPTVTGSIMAKF-------CIGFNTMVAF 126 (148)
Q Consensus 85 ~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~-------YI~~~T~~~~ 126 (148)
..|..|.+.|.|...+ +.+.||++|+.+-.. ..+|+.-..+
T Consensus 483 ~iIe~L~~r~Yi~~~~-~~l~pT~~G~~li~~l~~~~~~l~~p~lTa~~ 530 (610)
T TIGR01051 483 SIISTIQDRGYVKKEN-KRLYPTELGFAVTDLLEKHFGDVVDYDFTAKM 530 (610)
T ss_pred HHHHHHhhCCeEEeeC-CEEeECHHHHHHHHHHHHhhhhhcCHHHHHHH
Confidence 4566788899998765 679999999985433 3556555444
No 116
>PRK07219 DNA topoisomerase I; Validated
Probab=28.19 E-value=1e+02 Score=28.94 Aligned_cols=40 Identities=10% Similarity=0.076 Sum_probs=28.9
Q ss_pred HHHHHhhhCCceeecCCCccccChhhHHHHhcC-------CCHHHHHhc
Q psy9269 85 RELNGLSRYNLITMNDGFDILPTVTGSIMAKFC-------IGFNTMVAF 126 (148)
Q Consensus 85 ~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~Y-------I~~~T~~~~ 126 (148)
..|..|.+.|.| .++ +.+.||++|+.+-..+ ++|+.-..+
T Consensus 499 ~iI~~L~~R~Yv-~~~-~~l~pT~~G~~l~~~l~~~~~~l~~~~~Ta~~ 545 (822)
T PRK07219 499 DIIEKLYKRGYV-IEG-DPPRPTDLGIAVIEALEKYAPEIVSEEMTAQL 545 (822)
T ss_pred HHHHHHHhcCcE-ecC-CEeeecHHHHHHHHHHHHhchhhcChhHHHHH
Confidence 456678889999 554 6899999999866555 456555444
No 117
>PRK08629 coproporphyrinogen III oxidase; Provisional
Probab=28.12 E-value=1.1e+02 Score=26.32 Aligned_cols=34 Identities=18% Similarity=0.116 Sum_probs=27.3
Q ss_pred hHHHHHHHHhhhCCceeecCCCccccChhhHHHHh
Q psy9269 81 GLCMRELNGLSRYNLITMNDGFDILPTVTGSIMAK 115 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~ 115 (148)
......+..|++.|++..++ +.+..|+.|+..+.
T Consensus 374 ~~~~~~l~~l~~~Gll~~~~-~~l~lT~~G~~~~d 407 (433)
T PRK08629 374 KALFKEMLLLKLIGAIKNDP-GDLIVTDFGKYLGV 407 (433)
T ss_pred HHHHHHHHHHHHCCCEEEEC-CEEEECcchhHHHH
Confidence 34556778899999999876 68999999997753
No 118
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=28.12 E-value=69 Score=23.48 Aligned_cols=35 Identities=20% Similarity=0.090 Sum_probs=26.2
Q ss_pred hHHHHHHHHhhhCCceeecCC----CccccChhhHHHHh
Q psy9269 81 GLCMRELNGLSRYNLITMNDG----FDILPTVTGSIMAK 115 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~----~~i~~T~lG~i~S~ 115 (148)
.-+.-+|..|++.|+|..... -.+..|+.|+.+-.
T Consensus 78 GtIYp~L~RLE~~GlI~s~~~~~~RK~Y~ITe~Gre~L~ 116 (135)
T PRK09416 78 GSLYTLLHRLEQNRFIQSSWDHEGAKYYQLTDKGNKMLR 116 (135)
T ss_pred ccHHHHHHHHHHCCCeEEeecCCCceEEEECHHHHHHHH
Confidence 346678999999999986432 35789999986543
No 119
>COG0550 TopA Topoisomerase IA [DNA replication, recombination, and repair]
Probab=27.86 E-value=55 Score=29.55 Aligned_cols=32 Identities=13% Similarity=0.253 Sum_probs=26.8
Q ss_pred HHHHHhhhCCceeecCCCccccChhhHHHHhcC
Q psy9269 85 RELNGLSRYNLITMNDGFDILPTVTGSIMAKFC 117 (148)
Q Consensus 85 ~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~Y 117 (148)
..+..|.+-|.|..++ +.+.||++|+++....
T Consensus 475 ~iI~~L~~RgYv~~~~-~~~~pT~~G~~v~~~L 506 (570)
T COG0550 475 SIIETLQKRGYVEKKG-KRLVPTELGEAVIELL 506 (570)
T ss_pred HHHHHHhcCCcEEecC-CeeEEcHHHHHHHHHH
Confidence 4677899999999877 6899999999987654
No 120
>COG1491 Predicted RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=27.54 E-value=92 Score=24.27 Aligned_cols=42 Identities=21% Similarity=0.283 Sum_probs=37.2
Q ss_pred ChHHHhhcCCCceeccccH---------HHHHHHHHHHHhCCcCCHHHHHH
Q psy9269 1 ERYEKLVEGREPVESSLHR---------HLVEHLNSEIVLKTISDVSVAVE 42 (148)
Q Consensus 1 ~~Y~~ll~~~~pIES~L~~---------~L~~~lnaeIa~g~i~s~~~~~~ 42 (148)
+++.+|+|+.+||.-+||. ....+|+.|---+...|++|+-+
T Consensus 113 ~rFV~fFN~A~PIt~RLH~LELLpGiGkK~m~~ILeERkkkpFeSFeDi~~ 163 (202)
T COG1491 113 DRFVKFFNEAEPITLRLHQLELLPGIGKKTMWAILEERKKKPFESFEDIKE 163 (202)
T ss_pred hHHHHHhcccCcchHHHHHHHhcccccHHHHHHHHHHHhcCCCcCHHHHHH
Confidence 4688999999999999983 67889999999999999999876
No 121
>PRK05582 DNA topoisomerase I; Validated
Probab=27.20 E-value=1.2e+02 Score=27.65 Aligned_cols=32 Identities=13% Similarity=0.366 Sum_probs=25.0
Q ss_pred HHHHHhhhCCceeecCCCccccChhhHHHHhcC
Q psy9269 85 RELNGLSRYNLITMNDGFDILPTVTGSIMAKFC 117 (148)
Q Consensus 85 ~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~Y 117 (148)
..|..|.+.|.|...+ +.+.||+.|+.+-..+
T Consensus 477 ~iI~~L~~r~Yi~~~~-k~l~pT~~G~~l~~~l 508 (650)
T PRK05582 477 PTISTIQKRGYVKLEK-KRLVPTELGEIVNELL 508 (650)
T ss_pred HHHHHHHhCCeEEeeC-CEEeecHHHHHHHHHH
Confidence 4567888999998665 6799999999874433
No 122
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=26.95 E-value=45 Score=27.85 Aligned_cols=38 Identities=13% Similarity=0.243 Sum_probs=29.7
Q ss_pred hHHHHHHHHhhhCCceeecCC-CccccChhhHHHHhcCCCHH
Q psy9269 81 GLCMRELNGLSRYNLITMNDG-FDILPTVTGSIMAKFCIGFN 121 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~-~~i~~T~lG~i~S~~YI~~~ 121 (148)
.-|++.+..|++.|++..... ..-.||+.|- +||++..
T Consensus 42 aTIR~dm~~Le~~G~l~~~h~sagrIPT~kGY---R~YVd~L 80 (339)
T PRK00082 42 ATIRNDMADLEELGLLEKPHTSSGRIPTDKGY---RYFVDHL 80 (339)
T ss_pred HHHHHHHHHHHhCCCcCCCcCCCCCCcCHHHH---HHHHHHh
Confidence 567788899999999985543 4478999998 6887754
No 123
>KOG4244|consensus
Probab=26.58 E-value=2.4e+02 Score=23.25 Aligned_cols=48 Identities=15% Similarity=0.054 Sum_probs=30.0
Q ss_pred CChHHHHHHHhhhhHhHHHHHHHHhhhCCceeecCCCccccChhhHHHHhcC
Q psy9269 66 LSSEELQSRLQGKNSGLCMRELNGLSRYNLITMNDGFDILPTVTGSIMAKFC 117 (148)
Q Consensus 66 ~~~~~~~~~l~~~~~~~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~Y 117 (148)
.+...+++.+. +-+...-+.|.+.+++--++-..+.+|-+|.+++-||
T Consensus 199 f~~~Ei~ell~----rDlr~i~~~Lg~KkflfGdkit~~DatvFgqLa~v~Y 246 (281)
T KOG4244|consen 199 FESAEIDELLH----RDLRAISDYLGDKKFLFGDKITPADATVFGQLAQVYY 246 (281)
T ss_pred cCHHHHHHHHH----HHHHHHHHHhCCCccccCCCCCcceeeehhhhhheec
Confidence 34444554444 3333333455555666544335688999999999999
No 124
>TIGR01054 rgy reverse gyrase. Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.
Probab=26.54 E-value=1.2e+02 Score=29.80 Aligned_cols=32 Identities=16% Similarity=0.161 Sum_probs=25.2
Q ss_pred HHHHHhhhCCceeecCCCccccChhhHHHHhcC
Q psy9269 85 RELNGLSRYNLITMNDGFDILPTVTGSIMAKFC 117 (148)
Q Consensus 85 ~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~Y 117 (148)
..+..|.+.|.|..+. +.+.||++|+.+-.+.
T Consensus 1096 ~II~~L~~R~YV~~~~-k~l~pT~lG~~v~~~L 1127 (1171)
T TIGR01054 1096 TIVEKLLRRGYVVESK-GFLIPTKLGIEVYNYL 1127 (1171)
T ss_pred HHHHHhhccCcEEeeC-CEEeECHHHHHHHHHH
Confidence 3456788889998655 6899999999886654
No 125
>TIGR02606 antidote_CC2985 putative addiction module antidote protein, CC2985 family. This bacterial protein family has a very similar seed alignment to that of Pfam model pfam03693 but is a more stringent model with higher cutoff scores. Proteins that score above the trusted cutoff to this model almost invariably are found adjacent to a ParE family protein (pfam05016), where ParE is the killing partner of an addiction module for plasmid stabilization. Members of this family, therefore, are putative addiction module antidote proteins. Some are encoded on plasmids or in prophage regions, but others appear chromosomal. A genome may contain several identical copies, such as the four in Magnetococcus sp. MC-1. This family is named for one member, CC2985 of Caulobacter crescentus CB15.
Probab=26.18 E-value=1.2e+02 Score=19.22 Aligned_cols=27 Identities=26% Similarity=0.287 Sum_probs=23.5
Q ss_pred cccHHHHHHHHHHHHhCCcCCHHHHHH
Q psy9269 16 SLHRHLVEHLNSEIVLKTISDVSVAVE 42 (148)
Q Consensus 16 ~L~~~L~~~lnaeIa~g~i~s~~~~~~ 42 (148)
.|.+.+.+++.+.|.+|.-.|..|++.
T Consensus 5 sL~~~~~~~i~~~V~sG~Y~s~SEVir 31 (69)
T TIGR02606 5 SLGEHLESFIRSQVQSGRYGSASEVVR 31 (69)
T ss_pred ecCHHHHHHHHHHHHCCCCCCHHHHHH
Confidence 355789999999999999999999885
No 126
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=26.06 E-value=78 Score=27.73 Aligned_cols=35 Identities=20% Similarity=0.169 Sum_probs=29.3
Q ss_pred hHHHHHHHHhhhCCceeecCC--CccccChhhHHHHh
Q psy9269 81 GLCMRELNGLSRYNLITMNDG--FDILPTVTGSIMAK 115 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~--~~i~~T~lG~i~S~ 115 (148)
.-|..+++.|++.|+|+..+. ..+..|+-|+-+..
T Consensus 35 ~tVt~~i~~Le~kGlV~~~~~~~~~i~LTeeG~~~~~ 71 (489)
T PRK04172 35 EAVMRAAEWLEEKGLVKVEERVEEVYVLTEEGKKYAE 71 (489)
T ss_pred HHHHHHHHHHHhCCCEEEEeeeEEEEEECHHHHHHHH
Confidence 567788999999999998764 56889999998765
No 127
>cd05394 RasGAP_RASA2 RASA2 (or GAP1(m)) is a member of the GAP1 family of Ras GTPase-activating proteins that includes GAP1_IP4BP (or RASA3), CAPRI, and RASAL. In vitro, RASA2 has been shown to bind inositol 1,3,4,5-tetrakisphosphate (IP4), the water soluble inositol head group of the lipid second messenger phosphatidylinositol 3,4,5-trisphosphate (PIP3). In vivo studies also demonstrated that RASA2 binds PIP3, and it is recruited to the plasma membrane following agonist stimulation of PI 3-kinase. Furthermore, the membrane translocation is a consequence of the ability of its pleckstrin homology (PH) domain to bind PIP3.
Probab=25.99 E-value=3.9e+02 Score=22.31 Aligned_cols=69 Identities=14% Similarity=0.199 Sum_probs=43.0
Q ss_pred HHHHHHHHHHhCCcCCHHHHHHHHHhHHHHHHHhh----CCCCCCCCCCCChHHHHHHHhhhhHhHHHHHHHHhhhCCc
Q psy9269 21 LVEHLNSEIVLKTISDVSVAVEWLRSTFFFVRVLS----NPGHYGFPAGLSSEELQSRLQGKNSGLCMRELNGLSRYNL 95 (148)
Q Consensus 21 L~~~lnaeIa~g~i~s~~~~~~wl~~TFly~Rl~~----nP~~Yg~~~~~~~~~~~~~l~~~~~~~v~~~l~~L~~~~l 95 (148)
+..++...+....- +.++.....-..|+|-|..- +|..+|+..+.........| -+|.++|..|...+.
T Consensus 158 i~~~lr~~v~~rFp-~~~~~~~~aVsgFlFLRF~cPAIlSP~lf~L~~~~p~~~~~RtL-----tLIaKvLQnLAN~~~ 230 (313)
T cd05394 158 IFYSLRHMAVKRFP-NDPHVQYSAVSSFVFLRFFAVAVVSPHTFHLRPHHPDAQTSRTL-----TLISKTIQTLGSWGS 230 (313)
T ss_pred HHHHHHHHHHHHCC-ChHhhHHHHHHHHHHHHHhhhhhcCcccccccCCCCChhhhHHH-----HHHHHHHHHHhCccc
Confidence 44445444444333 33566667888999998876 89999986543322223334 477888888876554
No 128
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=25.65 E-value=83 Score=21.06 Aligned_cols=20 Identities=15% Similarity=0.190 Sum_probs=17.8
Q ss_pred hHHHHHHHHhhhCCceeecC
Q psy9269 81 GLCMRELNGLSRYNLITMND 100 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~ 100 (148)
.-|..+|+.|++.|+|....
T Consensus 62 ~tVsr~L~~Le~~GlI~r~~ 81 (95)
T TIGR01610 62 THVSDAIKSLARRRIIFRQG 81 (95)
T ss_pred HHHHHHHHHHHHCCCeeeec
Confidence 67889999999999999765
No 129
>COG1568 Predicted methyltransferases [General function prediction only]
Probab=25.59 E-value=84 Score=26.32 Aligned_cols=33 Identities=18% Similarity=0.190 Sum_probs=27.8
Q ss_pred HHHHHHHHhhhCCceeecCCCccccChhhHHHHh
Q psy9269 82 LCMRELNGLSRYNLITMNDGFDILPTVTGSIMAK 115 (148)
Q Consensus 82 ~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~ 115 (148)
++...+..|.+-|+|..++ |.+..|+.|+=.+.
T Consensus 50 ~v~~i~~~l~~egiv~~~~-g~v~~TekG~E~~e 82 (354)
T COG1568 50 LVASILEILEDEGIVKIEE-GGVELTEKGEELAE 82 (354)
T ss_pred HHHHHHHHHHhcCcEEEec-CcEeehhhhHHHHH
Confidence 5667788999999999998 56999999986654
No 130
>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=25.58 E-value=73 Score=19.60 Aligned_cols=33 Identities=15% Similarity=0.177 Sum_probs=21.9
Q ss_pred hHHHHHHHhhhhHhHHHHHHHHhhhCCceeecCC
Q psy9269 68 SEELQSRLQGKNSGLCMRELNGLSRYNLITMNDG 101 (148)
Q Consensus 68 ~~~~~~~l~~~~~~~v~~~l~~L~~~~lI~~~~~ 101 (148)
..+|...|.... .-+.+.+..|++.|+|.+++.
T Consensus 25 ~~~iA~~L~vs~-~tvt~ml~~L~~~GlV~~~~y 57 (60)
T PF01325_consen 25 TKDIAERLGVSP-PTVTEMLKRLAEKGLVEYEPY 57 (60)
T ss_dssp HHHHHHHHTS-H-HHHHHHHHHHHHTTSEEEETT
T ss_pred HHHHHHHHCCCh-HHHHHHHHHHHHCCCEEecCC
Confidence 344444443222 446778999999999998874
No 131
>PRK05660 HemN family oxidoreductase; Provisional
Probab=25.58 E-value=73 Score=26.80 Aligned_cols=31 Identities=13% Similarity=0.042 Sum_probs=26.3
Q ss_pred HHHHHHhhhCCceeecCCCccccChhhHHHHh
Q psy9269 84 MRELNGLSRYNLITMNDGFDILPTVTGSIMAK 115 (148)
Q Consensus 84 ~~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~ 115 (148)
...++.|.+.|++..++ +.+..|+-|+..+.
T Consensus 339 ~~~l~~l~~~gl~~~~~-~~~~lt~~G~~~~d 369 (378)
T PRK05660 339 RPQLDEALAQGYLTETA-DHWQITEHGKLFLN 369 (378)
T ss_pred HHHHHHHHHCCCEEEeC-CEEEECcchhHHHH
Confidence 45788999999999876 68999999997764
No 132
>KOG1956|consensus
Probab=25.31 E-value=98 Score=28.63 Aligned_cols=41 Identities=12% Similarity=0.115 Sum_probs=32.6
Q ss_pred HHHHHHHHhhhCCceee-cCCCccccChhhHHHHhcCCCHHH
Q psy9269 82 LCMRELNGLSRYNLITM-NDGFDILPTVTGSIMAKFCIGFNT 122 (148)
Q Consensus 82 ~v~~~l~~L~~~~lI~~-~~~~~i~~T~lG~i~S~~YI~~~T 122 (148)
-+.+.++.+++-+.|.. ++++.|.||.+|...+..|=++-+
T Consensus 506 T~aehi~kiq~R~Yv~~~~~~~~~~P~~lg~aLv~gyd~~g~ 547 (758)
T KOG1956|consen 506 TIAEHIEKIQERGYVTKKNKVGRFVPTFLGVALVEGYDDMGL 547 (758)
T ss_pred hHHHHHHHHHhhcceeeeccccccCchHHHHHHHHhHHhhhh
Confidence 34566778999999998 565789999999999999865543
No 133
>PRK08780 DNA topoisomerase I; Provisional
Probab=25.28 E-value=66 Score=30.08 Aligned_cols=32 Identities=22% Similarity=0.273 Sum_probs=25.2
Q ss_pred HHHHHhhhCCceeecCCCccccChhhHHHHhcC
Q psy9269 85 RELNGLSRYNLITMNDGFDILPTVTGSIMAKFC 117 (148)
Q Consensus 85 ~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~Y 117 (148)
..|..|.+.|.|..++ +.+.||++|+.+..+.
T Consensus 497 ~iI~~L~~R~Yv~~~~-k~l~pT~~G~~v~~~L 528 (780)
T PRK08780 497 SIISTLQFRKYVEMEG-RRFRPTDVGRAVNKFL 528 (780)
T ss_pred HHHHHHHhCCcEeccC-CEEeecHHHHHHHHHH
Confidence 4566788889998766 5799999999975543
No 134
>TIGR01057 topA_arch DNA topoisomerase I, archaeal. This model describes topoisomerase I from archaea. These enzymes are involved in the control of DNA topology. DNA topoisomerase I belongs to the type I topoisomerases, which are ATP-independent.
Probab=25.14 E-value=1.4e+02 Score=27.02 Aligned_cols=40 Identities=20% Similarity=0.120 Sum_probs=29.3
Q ss_pred HHHHHhhhCCceeecCCCccccChhhHHHHhcC-------CCHHHHHhc
Q psy9269 85 RELNGLSRYNLITMNDGFDILPTVTGSIMAKFC-------IGFNTMVAF 126 (148)
Q Consensus 85 ~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~Y-------I~~~T~~~~ 126 (148)
..|..|.+.|.|+.+ +.+.||+.|+..-..+ ++|+.-..+
T Consensus 490 ~iIe~L~~r~Yi~~~--~~l~pT~~G~~li~~l~~~~~~l~~p~~Ta~~ 536 (618)
T TIGR01057 490 RIIETLYKRGYIEGK--KSIKVTPLGEAVIETLQRYCPEIISEELTRRF 536 (618)
T ss_pred HHHHHHHhCCcEeEC--CEEeeehHHHHHHHHHHHhchhhcChhhHHHH
Confidence 356678889999854 5799999999887655 566654444
No 135
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=24.96 E-value=1.8e+02 Score=22.61 Aligned_cols=24 Identities=8% Similarity=-0.044 Sum_probs=20.3
Q ss_pred hHHHHHHHHhhhCCceeecCC-Ccc
Q psy9269 81 GLCMRELNGLSRYNLITMNDG-FDI 104 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~-~~i 104 (148)
.-|.+|+..|+..|+|+..++ |.+
T Consensus 47 tpVREAL~~L~~eGlV~~~~~~G~~ 71 (253)
T PRK11523 47 TVVREAIIMLEVEGYVEVRKGSGIH 71 (253)
T ss_pred HHHHHHHHHHHHCCCEEEecCCeeE
Confidence 678899999999999998876 543
No 136
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=24.93 E-value=60 Score=19.20 Aligned_cols=20 Identities=15% Similarity=0.209 Sum_probs=16.8
Q ss_pred hHHHHHHHHhhhCCceeecC
Q psy9269 81 GLCMRELNGLSRYNLITMND 100 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~ 100 (148)
.-+...++.|++.|+|+...
T Consensus 36 ~~vs~~v~~L~~~Glv~r~~ 55 (62)
T PF12802_consen 36 STVSRIVKRLEKKGLVERER 55 (62)
T ss_dssp HHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHHHHCCCEEEeC
Confidence 56678899999999998764
No 137
>PF01337 Barstar: Barstar (barnase inhibitor); InterPro: IPR000468 Barstar is a small single chain protein. Barnase is the extracellular ribonuclease IPR001887 from INTERPRO of Bacillus amyloliquefaciens, and barstar its specific intracellular inhibitor [, ]. Expression of barstar is necessary to counter the lethal effect of expressed active barnase. The structure of the barnase-barstar complex is known [].; PDB: 2CX6_A 1B2U_F 1A19_A 1X1U_F 1B27_E 1X1W_F 1BGS_E 1X1Y_D 1B3S_D 1B2S_D ....
Probab=24.89 E-value=83 Score=20.52 Aligned_cols=26 Identities=19% Similarity=0.204 Sum_probs=19.2
Q ss_pred hCCcCCHHHHHHHHHhHHHHHHHhhCCCCCCC
Q psy9269 31 LKTISDVSVAVEWLRSTFFFVRVLSNPGHYGF 62 (148)
Q Consensus 31 ~g~i~s~~~~~~wl~~TFly~Rl~~nP~~Yg~ 62 (148)
...|+|+++..+.++..| .-|.|||-
T Consensus 5 g~~i~~~~~~~~~l~~~l------~fP~yfG~ 30 (90)
T PF01337_consen 5 GRKIRDKEDFYDALAEAL------DFPDYFGR 30 (90)
T ss_dssp CCC-SSHHHHHHHHHHHT------T--TTSSS
T ss_pred CCCCCCHHHHHHHHHHHc------CCCchhcC
Confidence 346899999999999888 77999983
No 138
>PRK06599 DNA topoisomerase I; Validated
Probab=24.77 E-value=1.5e+02 Score=27.19 Aligned_cols=41 Identities=15% Similarity=0.367 Sum_probs=29.2
Q ss_pred HHHHHhhhCCceeecCCCccccChhhHHHHhc-------CCCHHHHHhc
Q psy9269 85 RELNGLSRYNLITMNDGFDILPTVTGSIMAKF-------CIGFNTMVAF 126 (148)
Q Consensus 85 ~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~-------YI~~~T~~~~ 126 (148)
..|..|.+.|.|...+ +.+.||++|+.+-.. .++|+--..+
T Consensus 491 ~iIe~L~~r~Yi~~~~-~~l~~T~~G~~l~~~l~~~~~~l~~p~lTa~~ 538 (675)
T PRK06599 491 SIISTLQDREYVELEK-KRFIPTDLGRIVNDFLVEHFPKYVDYDFTAGL 538 (675)
T ss_pred HHHHHHhhCCeEEeeC-CEEeecHHHHHHHHHHHHhchhhCCHHHHHHH
Confidence 4566788899998765 689999999985332 3566655544
No 139
>PF09114 MotA_activ: Transcription factor MotA, activation domain; InterPro: IPR015198 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the N-terminal (activation) domain of MotA factors that binds sigma70. The N-terminal domain adopts an almost completely alpha-helical topology, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2 [].; PDB: 1BJA_B 1I1S_A.
Probab=24.62 E-value=86 Score=21.54 Aligned_cols=31 Identities=16% Similarity=0.070 Sum_probs=24.5
Q ss_pred hHHHHHHHHhhhCCceeecCCCccccChhhHH
Q psy9269 81 GLCMRELNGLSRYNLITMNDGFDILPTVTGSI 112 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~i 112 (148)
..|.+-+.-|.+.|+|+..+|| +..|..|.-
T Consensus 47 ~~V~SNIGvLIKkglIEKSGDG-lv~T~~g~~ 77 (96)
T PF09114_consen 47 ASVNSNIGVLIKKGLIEKSGDG-LVITEEGMD 77 (96)
T ss_dssp HHHHHHHHHHHHTTSEEEETTE-EEE-HHHHH
T ss_pred hHHHHhHHHHHHcCcccccCCc-eEEechHHH
Confidence 4566678899999999999977 888888863
No 140
>KOG0926|consensus
Probab=24.58 E-value=97 Score=29.75 Aligned_cols=42 Identities=14% Similarity=-0.004 Sum_probs=33.5
Q ss_pred hHHHHHHHHhhhCCceeecCCCccccChhhHHHHhcCCCHHHHHhc
Q psy9269 81 GLCMRELNGLSRYNLITMNDGFDILPTVTGSIMAKFCIGFNTMVAF 126 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~YI~~~T~~~~ 126 (148)
..++.|.+.|...|-+..+ | ..|++|+.||.|=++|+=.+++
T Consensus 750 ~~L~~Aer~L~~LgALd~~--g--~lT~lGk~mS~FPlsPrfsKmL 791 (1172)
T KOG0926|consen 750 SALEKAERRLKALGALDSN--G--GLTKLGKAMSLFPLSPRFSKML 791 (1172)
T ss_pred HHHHHHHHHHHHhcccccc--C--CcccccchhcccccChhHHHHH
Confidence 3455777778777877653 3 6799999999999999988887
No 141
>PRK07379 coproporphyrinogen III oxidase; Provisional
Probab=24.25 E-value=1.7e+02 Score=24.83 Aligned_cols=34 Identities=9% Similarity=0.076 Sum_probs=27.3
Q ss_pred hHHHHHHHHhhhCCceeecCCCc-cccCh-hhHHHHh
Q psy9269 81 GLCMRELNGLSRYNLITMNDGFD-ILPTV-TGSIMAK 115 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~~~-i~~T~-lG~i~S~ 115 (148)
+.....+..|.+.|++..++ +. +..|+ -|...+.
T Consensus 351 ~~~~~~l~~l~~~gll~~~~-~~~~~lT~~~G~~~~~ 386 (400)
T PRK07379 351 EQILQCLQPYFQQGWVELEG-DRRLRLTDPEGFLFSN 386 (400)
T ss_pred HHHHHHHHHHHHCCCEEEeC-CeEEEECchHHhHHHH
Confidence 34567788999999999877 67 99995 8987764
No 142
>cd02977 ArsC_family Arsenate Reductase (ArsC) family; composed of TRX-fold arsenic reductases and similar proteins including the transcriptional regulator, Spx. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from glutathione (GSH) via glutaredoxin (GRX), through a single catalytic cysteine. This family of predominantly bacterial enzymes is unrelated to two other families of arsenate reductases which show similarity to low-molecular-weight acid phosphatases and phosphotyrosyl phosphatases. Spx is a general regulator that exerts negative and positive control over transcription initiation by binding to the C-terminal domain of the alpha subunit of RNA polymerase.
Probab=23.81 E-value=2.3e+02 Score=18.83 Aligned_cols=65 Identities=12% Similarity=0.086 Sum_probs=44.3
Q ss_pred hHHHHHHHHhhhCCcee--ecCC-CccccChhhHHHHhcCCCHHHHHhc------------cCCCCHHHHHHhhhCCCCC
Q psy9269 81 GLCMRELNGLSRYNLIT--MNDG-FDILPTVTGSIMAKFCIGFNTMVAF------------TGWEKAQKDLALLTTLPLA 145 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~--~~~~-~~i~~T~lG~i~S~~YI~~~T~~~~------------~~~~s~~~lL~ll~~s~e~ 145 (148)
..|..+.+.|.+.|+=. .+-. +....+++-++.++.-..++.+-.- ...+++.+++.+|+..|..
T Consensus 10 ~~c~ka~~~L~~~~i~~~~idi~~~~~~~~~l~~~~~~~~~~~~~li~~~~~~~~~l~~~~~~~ls~~e~~~~l~~~p~L 89 (105)
T cd02977 10 STSRKALAWLEEHGIEYEFIDYLKEPPTKEELKELLAKLGLGVEDLFNTRGTPYRKLGLADKDELSDEEALELMAEHPKL 89 (105)
T ss_pred HHHHHHHHHHHHcCCCcEEEeeccCCCCHHHHHHHHHhcCCCHHHHHhcCCchHHHcCCccccCCCHHHHHHHHHhCcCe
Confidence 46788889999888532 2111 3466678888888777655544332 1357899999999998875
No 143
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=23.68 E-value=2.1e+02 Score=22.21 Aligned_cols=24 Identities=17% Similarity=0.040 Sum_probs=20.3
Q ss_pred hHHHHHHHHhhhCCceeecCC-Ccc
Q psy9269 81 GLCMRELNGLSRYNLITMNDG-FDI 104 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~-~~i 104 (148)
.-|.+|+..|+..|+|+..++ |.+
T Consensus 48 tpVREAL~~L~~eGlV~~~~~~G~~ 72 (257)
T PRK10225 48 TVVREALIMLEIKGLVEVRRGAGIY 72 (257)
T ss_pred HHHHHHHHHHHHCCCEEEecCCEEE
Confidence 678899999999999998876 543
No 144
>PHA03061 putative DNA-binding virion core protein; Provisional
Probab=23.68 E-value=43 Score=27.49 Aligned_cols=46 Identities=13% Similarity=0.224 Sum_probs=31.3
Q ss_pred HHHHHHhhCCCCCCCCCCCChHHHHHHHhhhhHhHHHHHHHHhhhCCceeecCCC
Q psy9269 48 FFFVRVLSNPGHYGFPAGLSSEELQSRLQGKNSGLCMRELNGLSRYNLITMNDGF 102 (148)
Q Consensus 48 Fly~Rl~~nP~~Yg~~~~~~~~~~~~~l~~~~~~~v~~~l~~L~~~~lI~~~~~~ 102 (148)
-|.-|++.+|..+-+++- ...+++ +.+++.+++|.++|.|..++..
T Consensus 129 ~La~RLk~~a~~f~f~g~--~Y~le~-------~kiedlINql~kn~~I~lDek~ 174 (311)
T PHA03061 129 VLAARLKTSASSFEFNGH--TYHLEN-------DKIEDLINQLVKNGAIILDEKS 174 (311)
T ss_pred HHHHHhCCCcceEEECCe--EEEecc-------ccHHHHHHHHHhcCCeeeeccc
Confidence 356788888887655421 111111 6678888999999999998863
No 145
>COG5407 SEC63 Preprotein translocase subunit Sec63 [Intracellular trafficking and secretion]
Probab=23.38 E-value=23 Score=31.39 Aligned_cols=31 Identities=26% Similarity=0.238 Sum_probs=25.5
Q ss_pred CCCHHHHHhc----cCCCCHHHHHHhhhCCCCCCC
Q psy9269 117 CIGFNTMVAF----TGWEKAQKDLALLTTLPLATS 147 (148)
Q Consensus 117 YI~~~T~~~~----~~~~s~~~lL~ll~~s~e~~~ 147 (148)
-|.+.||..| .+..+...+|++++.+.|+|+
T Consensus 226 gvh~vT~~~f~~~~~~SlTlDelLslfasskElt~ 260 (610)
T COG5407 226 GVHFVTMEMFYERIDGSLTLDELLSLFASSKELTR 260 (610)
T ss_pred ceeeeeHHHHHHhhcccchHHHHHHHHhhhHHHHH
Confidence 4677888888 445789999999999999875
No 146
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=22.89 E-value=2.2e+02 Score=22.13 Aligned_cols=24 Identities=13% Similarity=0.043 Sum_probs=20.2
Q ss_pred hHHHHHHHHhhhCCceeecCC-Ccc
Q psy9269 81 GLCMRELNGLSRYNLITMNDG-FDI 104 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~-~~i 104 (148)
.-|.+||..|+..|+|+..++ |.+
T Consensus 41 tpVREAL~~Le~~GlV~~~~~~G~~ 65 (253)
T PRK10421 41 NSLREALAKLVSEGVLLSRRGGGTF 65 (253)
T ss_pred HHHHHHHHHHHHCCCEEEeCCCeEE
Confidence 678899999999999998776 544
No 147
>PF13309 HTH_22: HTH domain
Probab=22.61 E-value=1.7e+02 Score=18.15 Aligned_cols=35 Identities=11% Similarity=0.166 Sum_probs=28.1
Q ss_pred HHHHHhhhCCceeecCCCccccChhhHHHHhcCCCHHHHHhc
Q psy9269 85 RELNGLSRYNLITMNDGFDILPTVTGSIMAKFCIGFNTMVAF 126 (148)
Q Consensus 85 ~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~YI~~~T~~~~ 126 (148)
+.+..|.+.|+-.+.+ ....++..+-|+.-|+..|
T Consensus 28 ~iV~~L~~~G~F~lKg-------av~~vA~~L~iS~~TVY~Y 62 (64)
T PF13309_consen 28 EIVRQLYEKGIFLLKG-------AVEYVAEKLGISRATVYRY 62 (64)
T ss_pred HHHHHHHHCCCcccCc-------HHHHHHHHHCCCHHHHHHH
Confidence 5677999999988776 4778888889998888654
No 148
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=22.57 E-value=68 Score=18.94 Aligned_cols=32 Identities=16% Similarity=0.075 Sum_probs=21.9
Q ss_pred hHHHHHHHHhhhCCceeecCC---CccccChhhHHH
Q psy9269 81 GLCMRELNGLSRYNLITMNDG---FDILPTVTGSIM 113 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~---~~i~~T~lG~i~ 113 (148)
.-+...++.|.+.|+|....+ ..+..|+ |+-.
T Consensus 35 ~~i~~~l~~L~~~g~i~~~~~~~~~~~~~~~-g~~~ 69 (78)
T cd00090 35 STVSRHLKKLEEAGLVESRREGRRVYYSLTD-AERL 69 (78)
T ss_pred hHHHHHHHHHHHCCCeEEEEeccEEEEEeCC-chHH
Confidence 456788899999999986543 3355565 5543
No 149
>PF03289 Pox_I1: Poxvirus protein I1; InterPro: IPR004969 Proteins in this group show homology to vaccinia virus I1L (Late) encoded protein.
Probab=22.44 E-value=45 Score=27.35 Aligned_cols=44 Identities=14% Similarity=0.263 Sum_probs=30.4
Q ss_pred HHHHHhhCCCCCCCCCCCChHHHHHHHhhhhHhHHHHHHHHhhhCCceeecCC
Q psy9269 49 FFVRVLSNPGHYGFPAGLSSEELQSRLQGKNSGLCMRELNGLSRYNLITMNDG 101 (148)
Q Consensus 49 ly~Rl~~nP~~Yg~~~~~~~~~~~~~l~~~~~~~v~~~l~~L~~~~lI~~~~~ 101 (148)
|.-|++.+|..+-+.+. ...+++ +.+++.+++|.++|.|..++.
T Consensus 131 La~RLk~~a~~f~f~~~--~Y~le~-------~kiedlINql~kn~~I~lDek 174 (312)
T PF03289_consen 131 LASRLKTSASSFEFNGH--TYHLEA-------DKIEDLINQLVKNGAISLDEK 174 (312)
T ss_pred HHHHhCCCcceEEECCe--EEEecc-------ccHHHHHHHHhhcCCeeeecc
Confidence 56788888877654421 111111 667888999999999999986
No 150
>PRK08208 coproporphyrinogen III oxidase; Validated
Probab=22.27 E-value=83 Score=26.94 Aligned_cols=30 Identities=20% Similarity=0.125 Sum_probs=25.3
Q ss_pred HHHHHHhhhCCceeecCCCccccChhhHHHH
Q psy9269 84 MRELNGLSRYNLITMNDGFDILPTVTGSIMA 114 (148)
Q Consensus 84 ~~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S 114 (148)
...++.|.+.|++..++ +.+..|+-|+..+
T Consensus 379 ~~~l~~l~~~gll~~~~-~~l~lT~~G~~~~ 408 (430)
T PRK08208 379 FPELELLIDRGWLEQNG-GRLRLTEEGLALS 408 (430)
T ss_pred HHHHHHHHHCCCEEEEC-CEEEECcchhhHH
Confidence 45788999999999877 6899999998764
No 151
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=22.19 E-value=1.2e+02 Score=17.28 Aligned_cols=21 Identities=14% Similarity=0.155 Sum_probs=16.4
Q ss_pred hHHHHHHHHhhhCCceeecCC
Q psy9269 81 GLCMRELNGLSRYNLITMNDG 101 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~ 101 (148)
.-+...++.|.+.|+|....+
T Consensus 25 ~~v~~~l~~L~~~g~i~~~~~ 45 (66)
T smart00418 25 STVSHHLKKLREAGLVESRRE 45 (66)
T ss_pred HHHHHHHHHHHHCCCeeeeec
Confidence 356788889999999986653
No 152
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=22.16 E-value=2.4e+02 Score=21.82 Aligned_cols=24 Identities=17% Similarity=0.111 Sum_probs=20.2
Q ss_pred hHHHHHHHHhhhCCceeecCC-Ccc
Q psy9269 81 GLCMRELNGLSRYNLITMNDG-FDI 104 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~-~~i 104 (148)
.-|.+||..|+..|+|+..++ |.+
T Consensus 46 tpVREAL~~L~~eGlV~~~~~~G~~ 70 (251)
T PRK09990 46 SALREGLTVLRGRGIIETAQGRGSF 70 (251)
T ss_pred HHHHHHHHHHHHCCCEEEeCCCeeE
Confidence 678899999999999998876 443
No 153
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=22.12 E-value=1.2e+02 Score=17.31 Aligned_cols=21 Identities=19% Similarity=0.210 Sum_probs=17.5
Q ss_pred hHHHHHHHHhhhCCceeecCC
Q psy9269 81 GLCMRELNGLSRYNLITMNDG 101 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~ 101 (148)
.-+..+++.|++.|+|...++
T Consensus 35 ~tv~~~l~~L~~~g~i~~~~~ 55 (60)
T smart00345 35 TTVREALSRLEAEGLVQRRPG 55 (60)
T ss_pred HHHHHHHHHHHHCCCEEEecC
Confidence 567889999999999986653
No 154
>PHA03362 single-stranded binding protein UL29; Provisional
Probab=21.53 E-value=2.6e+02 Score=27.70 Aligned_cols=62 Identities=19% Similarity=0.320 Sum_probs=35.5
Q ss_pred HHHHHHhhC--CCCCCCCCCCChHHHHHHHhhhhHhHHHHHHHHhhhCCceeecCCCccccChhhHHH------------
Q psy9269 48 FFFVRVLSN--PGHYGFPAGLSSEELQSRLQGKNSGLCMRELNGLSRYNLITMNDGFDILPTVTGSIM------------ 113 (148)
Q Consensus 48 Fly~Rl~~n--P~~Yg~~~~~~~~~~~~~l~~~~~~~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~i~------------ 113 (148)
+||.++++| |.- +. ..++.+ +. .+|...-+.-.+..+|. +.|+.+|..+
T Consensus 838 ~fW~~~~~N~lP~~--v~----~~e~~e-~~----~fVk~~s~~Y~e~N~Id------i~P~~i~~ya~~~~~N~iL~~c 900 (1189)
T PHA03362 838 WFWTLLQRNQLPAS--LL----SKEDIE-TI----AFVKRFTDEYAAINFIN------LTPNNIGELAQFYFANLILKYC 900 (1189)
T ss_pred HHHHHHHhccCCCC--Cc----chhHHH-HH----HHHHHhhhhhhhcceee------cCcchHHHHHHHHHHHHHHHHc
Confidence 378999999 842 21 112222 22 46666666677777776 4555555544
Q ss_pred --HhcCCCHHHHHhc
Q psy9269 114 --AKFCIGFNTMVAF 126 (148)
Q Consensus 114 --S~~YI~~~T~~~~ 126 (148)
+.|||.-.|..+-
T Consensus 901 gh~~y~i~~lta~l~ 915 (1189)
T PHA03362 901 DHSQYFINTLTAILV 915 (1189)
T ss_pred CCchhhhcchhhhcc
Confidence 3556666665555
No 155
>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=20.87 E-value=1.2e+02 Score=14.56 Aligned_cols=14 Identities=7% Similarity=-0.005 Sum_probs=8.1
Q ss_pred HHHHHHHHhhhCCc
Q psy9269 82 LCMRELNGLSRYNL 95 (148)
Q Consensus 82 ~v~~~l~~L~~~~l 95 (148)
.+...++.|.+.|+
T Consensus 17 ~l~~~~~~l~~~g~ 30 (31)
T smart00733 17 KLKPKVEFLKELGF 30 (31)
T ss_pred HhhHHHHHHHHcCC
Confidence 34456667766654
No 156
>cd04447 DEP_BRCC3 DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in BBRC3-like proteins. BBRC3, also known as DEPDC1B, is a DEP containing protein of unknown function.
Probab=20.60 E-value=2.8e+02 Score=19.00 Aligned_cols=41 Identities=24% Similarity=0.427 Sum_probs=25.2
Q ss_pred HHHHHHHHHhHHHHHHHhhCCCCCCCCCCCChHHHHHHHhhhhHhHHHHHHHHhhhCCcee
Q psy9269 37 VSVAVEWLRSTFFFVRVLSNPGHYGFPAGLSSEELQSRLQGKNSGLCMRELNGLSRYNLIT 97 (148)
Q Consensus 37 ~~~~~~wl~~TFly~Rl~~nP~~Yg~~~~~~~~~~~~~l~~~~~~~v~~~l~~L~~~~lI~ 97 (148)
=.||+|||-... .+||. +|- +.+. .-+-+.+..|.+++.|+
T Consensus 32 gsEAVDwL~~~l-----~~n~~-fg~--~vtR------------~~av~l~qkll~~hVie 72 (92)
T cd04447 32 ASEAVDWLHELL-----RSNSN-FGP--EVTR------------QQTVQLLKKFLKNHVIE 72 (92)
T ss_pred hHHHHHHHHHHH-----Hhccc-cCC--CCCH------------HHHHHHHHHHHHcCCch
Confidence 458999998764 25666 342 2222 22334467788888886
No 157
>TIGR01638 Atha_cystat_rel Arabidopsis thaliana cystatin-related protein. This model represents a family similar in sequence and probably homologous to a large family of cysteine proteinase inhibitors, or cystatins, as described by pfam model pfam00031. Cystatins may help plants resist attack by insects.
Probab=20.50 E-value=18 Score=24.85 Aligned_cols=42 Identities=12% Similarity=0.086 Sum_probs=29.7
Q ss_pred hHHHHHHHHhhhCCceeecCCCccccChhhHHHHhcCCCHHH
Q psy9269 81 GLCMRELNGLSRYNLITMNDGFDILPTVTGSIMAKFCIGFNT 122 (148)
Q Consensus 81 ~~v~~~l~~L~~~~lI~~~~~~~i~~T~lG~i~S~~YI~~~T 122 (148)
+++..+++.+.+.+--.++-...+.++.-|--...+||.+.-
T Consensus 17 ~la~~al~k~N~~~~t~lEfV~vVrAn~~~~~g~~~yITF~A 58 (92)
T TIGR01638 17 RLSYVASKKYNDTKFLNLELVEVVRANYRGGAKSKSYITFEA 58 (92)
T ss_pred HHHHHHHHHhhhhcCceEEEEEEEEEEeeccceEEEEEEEEE
Confidence 888999999987754333322456777777788888887653
No 158
>PF00395 SLH: S-layer homology domain; InterPro: IPR001119 S-layers are paracrystalline mono-layered assemblies of (glyco)proteins which coat the surface of bacteria [, ]. Several S-layer proteins and some other cell wall proteins contain one or more copies of a domain of about 50-60 residues, which has been called SLH (for S-layer homology). Although it was originally proposed that SLH domains bind to peptidoglycan, it is now evident that pyruvylated secondary cell wall polymers (SCWPs), which are either teichoic acids, teichuronic acids, lipoteichoic acids or lipoglycans, serve as the anchoring structures for SLH motifs in the Gram-positive cell wall [, ]. However, the study of S-layer protein SbpA of Bacillus sphaericus revealed that SLH motifs are not sufficient for specific binding to SCWPs. Thus, the molecular basis explaining SLH affinity and specificity of interaction with cell wall polymers are not completely elucidated [].; PDB: 3PYW_A.
Probab=20.42 E-value=92 Score=17.48 Aligned_cols=23 Identities=13% Similarity=0.130 Sum_probs=13.6
Q ss_pred HHHHHhhhCCceeecCCCccccC
Q psy9269 85 RELNGLSRYNLITMNDGFDILPT 107 (148)
Q Consensus 85 ~~l~~L~~~~lI~~~~~~~i~~T 107 (148)
.++..|.+.|++.-.+++.|.|-
T Consensus 14 ~~i~~~~~~gi~~G~~~~~f~P~ 36 (45)
T PF00395_consen 14 EAIQWLYQLGIISGYSDGTFNPN 36 (45)
T ss_dssp HHHHHHHHTTSS---TTS---TT
T ss_pred HHHHHHHHcCCcccCCCCeECCC
Confidence 67788999999987776777663
No 159
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=20.11 E-value=1.5e+02 Score=21.39 Aligned_cols=32 Identities=9% Similarity=0.080 Sum_probs=27.0
Q ss_pred ccHHHHHHHHHHHHhCCcCCHHHHHHHHHhHHHH
Q psy9269 17 LHRHLVEHLNSEIVLKTISDVSVAVEWLRSTFFF 50 (148)
Q Consensus 17 L~~~L~~~lnaeIa~g~i~s~~~~~~wl~~TFly 50 (148)
+...++..+-..|..| .|-+++++|+...|--
T Consensus 58 iA~dmR~~Vr~~i~~G--~Sd~eI~~~~v~RYG~ 89 (126)
T TIGR03147 58 IAYDLRHEVYSMVNEG--KSNQQIIDFMTARFGD 89 (126)
T ss_pred HHHHHHHHHHHHHHcC--CCHHHHHHHHHHhcCC
Confidence 3467999999999998 5999999999988753
Done!