Query psy5605
Match_columns 152
No_of_seqs 101 out of 319
Neff 4.2
Searched_HMMs 46136
Date Fri Aug 16 21:49:05 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy5605.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/5605hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01090 Ribosomal_S19e: Ribos 100.0 3.3E-68 7.2E-73 414.2 9.9 130 2-131 10-139 (139)
2 PTZ00095 40S ribosomal protein 100.0 8.7E-67 1.9E-71 416.9 12.3 132 2-133 35-167 (169)
3 PRK09333 30S ribosomal protein 100.0 1.4E-65 3E-70 403.7 12.9 132 2-134 11-142 (150)
4 KOG3411|consensus 100.0 2.3E-65 4.9E-70 396.7 11.0 129 2-130 13-141 (143)
5 COG2238 RPS19A Ribosomal prote 100.0 1.7E-63 3.6E-68 389.2 11.5 130 3-133 12-141 (147)
6 PF03444 HrcA_DNA-bdg: Winged 97.4 0.00038 8.2E-09 50.2 4.8 57 52-122 15-75 (78)
7 PF08461 HTH_12: Ribonuclease 97.3 0.00045 9.7E-09 47.4 4.4 63 49-120 3-66 (66)
8 TIGR02702 SufR_cyano iron-sulf 96.8 0.0054 1.2E-07 49.1 7.5 60 48-121 5-72 (203)
9 PF14947 HTH_45: Winged helix- 96.8 0.0064 1.4E-07 42.3 6.7 60 48-123 10-69 (77)
10 COG3388 Predicted transcriptio 96.6 0.0078 1.7E-07 45.3 6.4 73 45-132 15-87 (101)
11 COG1420 HrcA Transcriptional r 96.6 0.0047 1E-07 54.7 5.8 63 45-119 7-75 (346)
12 PRK11512 DNA-binding transcrip 96.6 0.02 4.4E-07 43.1 8.5 65 48-126 44-114 (144)
13 TIGR02337 HpaR homoprotocatech 96.6 0.029 6.2E-07 40.9 9.0 68 49-130 33-106 (118)
14 COG1725 Predicted transcriptio 96.5 0.011 2.5E-07 45.7 6.8 60 86-145 49-108 (125)
15 smart00529 HTH_DTXR Helix-turn 96.2 0.012 2.5E-07 41.0 5.0 43 84-126 11-53 (96)
16 PRK11050 manganese transport r 96.2 0.03 6.6E-07 43.4 7.7 63 49-125 42-104 (152)
17 smart00347 HTH_MARR helix_turn 96.1 0.052 1.1E-06 36.8 7.6 67 49-129 15-87 (101)
18 COG1846 MarR Transcriptional r 96.0 0.053 1.1E-06 37.6 7.6 65 47-125 25-95 (126)
19 PF13463 HTH_27: Winged helix 96.0 0.013 2.9E-07 38.2 4.2 54 49-116 8-68 (68)
20 smart00418 HTH_ARSR helix_turn 95.9 0.033 7.2E-07 34.4 5.7 59 49-122 2-64 (66)
21 smart00346 HTH_ICLR helix_turn 95.9 0.11 2.3E-06 35.6 8.6 60 44-117 5-66 (91)
22 PF05491 RuvB_C: Holliday junc 95.8 0.014 3.1E-07 41.9 4.1 68 40-121 7-74 (76)
23 TIGR01889 Staph_reg_Sar staphy 95.7 0.066 1.4E-06 38.9 7.3 68 49-130 30-107 (109)
24 PF01638 HxlR: HxlR-like helix 95.7 0.04 8.6E-07 39.0 6.0 64 47-124 8-77 (90)
25 PRK10870 transcriptional repre 95.7 0.093 2E-06 41.5 8.5 65 49-127 60-132 (176)
26 PRK13777 transcriptional regul 95.4 0.12 2.7E-06 41.9 8.4 66 48-127 49-120 (185)
27 PRK03911 heat-inducible transc 95.3 0.025 5.3E-07 48.8 4.4 64 46-121 5-75 (260)
28 PRK03573 transcriptional regul 95.3 0.17 3.6E-06 37.9 8.3 64 49-126 36-106 (144)
29 TIGR03433 padR_acidobact trans 95.2 0.081 1.7E-06 38.2 6.2 49 81-129 34-90 (100)
30 TIGR00331 hrcA heat shock gene 95.2 0.044 9.6E-07 47.9 5.7 58 54-123 17-76 (337)
31 PF13601 HTH_34: Winged helix 94.8 0.056 1.2E-06 38.1 4.3 62 52-127 8-76 (80)
32 PRK03902 manganese transport t 94.7 0.16 3.5E-06 38.3 6.9 57 53-123 17-73 (142)
33 TIGR03338 phnR_burk phosphonat 94.6 0.14 3.1E-06 40.2 6.7 65 45-123 15-85 (212)
34 PRK00082 hrcA heat-inducible t 94.4 0.11 2.3E-06 45.6 6.1 59 53-123 18-80 (339)
35 COG3432 Predicted transcriptio 94.0 0.083 1.8E-06 39.4 4.0 42 82-123 41-85 (95)
36 PF09339 HTH_IclR: IclR helix- 93.9 0.14 3E-06 32.7 4.5 49 44-106 3-52 (52)
37 PRK09834 DNA-binding transcrip 93.9 0.47 1E-05 39.3 8.6 66 44-123 11-78 (263)
38 PF14338 Mrr_N: Mrr N-terminal 93.7 0.081 1.8E-06 37.6 3.4 37 85-121 53-89 (92)
39 PRK11414 colanic acid/biofilm 93.7 0.27 5.8E-06 39.2 6.7 50 60-123 36-85 (221)
40 PRK05638 threonine synthase; V 93.4 0.24 5.3E-06 44.2 6.6 75 31-123 363-441 (442)
41 TIGR02719 repress_PhaQ poly-be 93.2 0.33 7.2E-06 38.0 6.3 45 84-128 55-107 (138)
42 PF10711 DUF2513: Hypothetical 93.2 0.16 3.5E-06 37.0 4.3 50 77-126 25-83 (102)
43 PRK09990 DNA-binding transcrip 92.8 0.25 5.3E-06 40.1 5.3 45 60-118 33-77 (251)
44 COG1693 Repressor of nif and g 92.8 0.11 2.4E-06 45.9 3.4 70 49-127 11-83 (325)
45 COG1321 TroR Mn-dependent tran 92.7 0.18 3.9E-06 39.8 4.2 53 56-122 22-74 (154)
46 PRK11534 DNA-binding transcrip 92.6 0.48 1E-05 37.7 6.6 50 59-122 31-80 (224)
47 PF02082 Rrf2: Transcriptional 92.6 0.39 8.5E-06 33.3 5.4 45 58-116 25-71 (83)
48 PF03551 PadR: Transcriptional 92.5 0.1 2.2E-06 35.4 2.3 41 81-121 26-74 (75)
49 cd07377 WHTH_GntR Winged helix 92.2 0.19 4E-06 31.9 3.1 39 61-113 28-66 (66)
50 PF01047 MarR: MarR family; I 92.0 0.49 1.1E-05 30.1 4.9 51 47-111 6-58 (59)
51 smart00345 HTH_GNTR helix_turn 92.0 0.48 1E-05 29.4 4.8 36 60-109 22-57 (60)
52 PF12840 HTH_20: Helix-turn-he 92.0 0.42 9.1E-06 31.3 4.7 47 47-107 13-59 (61)
53 COG1802 GntR Transcriptional r 92.0 0.65 1.4E-05 37.3 6.7 64 45-122 20-89 (230)
54 TIGR01884 cas_HTH CRISPR locus 91.8 0.53 1.1E-05 37.7 5.9 55 48-116 147-203 (203)
55 PF00392 GntR: Bacterial regul 91.7 0.78 1.7E-05 30.2 5.8 37 60-110 26-62 (64)
56 TIGR02812 fadR_gamma fatty aci 91.6 0.34 7.3E-06 38.9 4.6 42 60-115 32-73 (235)
57 cd00090 HTH_ARSR Arsenical Res 91.5 1 2.3E-05 28.1 6.0 61 48-124 11-74 (78)
58 PRK10225 DNA-binding transcrip 91.4 0.53 1.1E-05 38.3 5.6 59 45-117 13-78 (257)
59 TIGR02944 suf_reg_Xantho FeS a 91.4 1.1 2.3E-05 33.2 6.8 68 46-127 11-83 (130)
60 PF12802 MarR_2: MarR family; 91.3 0.7 1.5E-05 29.4 5.1 47 47-107 8-56 (62)
61 PF09114 MotA_activ: Transcrip 91.3 2 4.3E-05 32.3 8.0 78 45-135 17-94 (96)
62 PRK10421 DNA-binding transcrip 91.2 0.57 1.2E-05 38.1 5.7 33 83-115 37-69 (253)
63 PRK15090 DNA-binding transcrip 91.1 0.87 1.9E-05 37.4 6.7 58 44-115 14-72 (257)
64 PRK11523 DNA-binding transcrip 90.5 0.45 9.9E-06 38.7 4.5 33 84-116 44-76 (253)
65 TIGR02277 PaaX_trns_reg phenyl 90.2 0.36 7.7E-06 41.2 3.7 45 84-128 32-79 (280)
66 PRK11014 transcriptional repre 90.0 0.96 2.1E-05 34.2 5.6 43 58-114 25-69 (141)
67 PRK04984 fatty acid metabolism 89.9 0.9 2E-05 36.4 5.7 41 60-114 33-73 (239)
68 TIGR00738 rrf2_super rrf2 fami 89.9 2.4 5.2E-05 31.0 7.5 48 57-118 24-73 (132)
69 COG1733 Predicted transcriptio 89.8 1.3 2.8E-05 33.6 6.1 63 49-125 28-96 (120)
70 COG3355 Predicted transcriptio 89.5 1.7 3.8E-05 33.8 6.8 65 55-133 39-117 (126)
71 PF01726 LexA_DNA_bind: LexA D 89.5 0.28 6.1E-06 33.5 2.1 40 58-110 25-64 (65)
72 PF09382 RQC: RQC domain; Int 89.4 1.6 3.5E-05 30.9 6.1 76 46-121 6-95 (106)
73 PRK11569 transcriptional repre 89.3 2.3 5.1E-05 35.4 7.9 58 44-115 28-87 (274)
74 PRK03837 transcriptional regul 89.2 2.6 5.7E-05 33.6 7.8 42 60-115 39-80 (241)
75 PF08220 HTH_DeoR: DeoR-like h 89.1 1.2 2.5E-05 29.3 4.8 48 46-107 2-49 (57)
76 PRK10163 DNA-binding transcrip 89.0 2.7 5.8E-05 35.1 8.1 58 44-115 25-84 (271)
77 TIGR02010 IscR iron-sulfur clu 88.1 1.9 4.1E-05 32.5 6.0 45 57-115 24-70 (135)
78 COG1485 Predicted ATPase [Gene 88.0 0.91 2E-05 41.0 4.9 97 40-150 55-168 (367)
79 PRK07379 coproporphyrinogen II 87.9 0.71 1.5E-05 40.8 4.1 59 57-130 334-395 (400)
80 smart00420 HTH_DEOR helix_turn 87.8 2.1 4.6E-05 25.7 5.1 46 48-107 4-49 (53)
81 PF06969 HemN_C: HemN C-termin 87.6 1.2 2.7E-05 29.1 4.2 52 52-117 14-65 (66)
82 PRK14165 winged helix-turn-hel 87.5 1.1 2.3E-05 37.5 4.7 48 84-131 33-83 (217)
83 PRK09464 pdhR transcriptional 87.4 0.58 1.3E-05 38.0 3.1 41 60-114 36-76 (254)
84 cd00092 HTH_CRP helix_turn_hel 87.2 0.85 1.9E-05 29.2 3.2 44 57-114 24-67 (67)
85 PF10007 DUF2250: Uncharacteri 87.0 1.7 3.6E-05 32.1 5.0 44 49-106 12-55 (92)
86 PRK08629 coproporphyrinogen II 86.5 4.4 9.5E-05 36.5 8.4 71 56-140 356-426 (433)
87 COG1695 Predicted transcriptio 86.1 1.8 4E-05 32.2 4.9 44 84-127 42-93 (138)
88 COG2186 FadR Transcriptional r 86.0 2.5 5.5E-05 34.9 6.1 32 83-114 45-76 (241)
89 PRK08599 coproporphyrinogen II 85.8 3.3 7.2E-05 35.9 7.1 62 53-128 313-374 (377)
90 PRK09416 lstR lineage-specific 85.8 1.2 2.6E-05 35.1 3.9 43 83-125 74-120 (135)
91 TIGR02018 his_ut_repres histid 85.5 3.1 6.7E-05 33.4 6.3 59 43-115 3-68 (230)
92 PF13412 HTH_24: Winged helix- 85.1 3.4 7.4E-05 25.5 5.1 42 48-103 7-48 (48)
93 smart00550 Zalpha Z-DNA-bindin 85.0 3.7 8.1E-05 27.8 5.6 46 48-107 10-57 (68)
94 PRK09057 coproporphyrinogen II 84.8 3.8 8.3E-05 35.9 7.0 58 55-128 322-379 (380)
95 PF01978 TrmB: Sugar-specific 84.6 1.5 3.4E-05 28.9 3.5 47 47-107 11-57 (68)
96 PF12793 SgrR_N: Sugar transpo 84.1 1.9 4.2E-05 32.4 4.3 39 58-110 19-57 (115)
97 COG1414 IclR Transcriptional r 83.9 4.5 9.8E-05 33.6 6.8 77 44-135 4-92 (246)
98 PRK09802 DNA-binding transcrip 83.7 2.4 5.2E-05 35.7 5.1 55 44-113 17-71 (269)
99 PRK13509 transcriptional repre 83.4 6.2 0.00014 32.8 7.4 56 45-114 6-61 (251)
100 TIGR02787 codY_Gpos GTP-sensin 83.3 1.2 2.7E-05 38.4 3.2 40 83-122 209-250 (251)
101 TIGR02325 C_P_lyase_phnF phosp 83.3 1.3 2.8E-05 35.3 3.2 61 42-116 9-76 (238)
102 PF13814 Replic_Relax: Replica 82.8 3.1 6.8E-05 32.0 5.1 61 51-122 2-72 (191)
103 PF14394 DUF4423: Domain of un 82.6 3.5 7.6E-05 32.9 5.4 87 39-141 22-114 (171)
104 COG4901 Ribosomal protein S25 82.2 1.3 2.7E-05 33.9 2.6 40 58-112 59-98 (107)
105 PRK11920 rirA iron-responsive 82.2 1.6 3.5E-05 34.0 3.3 45 58-116 24-70 (153)
106 TIGR02431 pcaR_pcaU beta-ketoa 82.0 5.6 0.00012 32.4 6.5 57 44-115 9-66 (248)
107 PRK10857 DNA-binding transcrip 81.7 5.1 0.00011 31.7 6.0 45 57-115 24-70 (164)
108 PRK14999 histidine utilization 81.6 11 0.00023 30.5 8.0 61 42-116 13-80 (241)
109 PRK10434 srlR DNA-bindng trans 80.6 9.5 0.00021 31.8 7.5 54 45-113 6-59 (256)
110 PRK08208 coproporphyrinogen II 80.2 2.7 5.9E-05 37.4 4.4 62 56-132 359-420 (430)
111 PRK05628 coproporphyrinogen II 79.8 2.6 5.5E-05 36.6 4.0 38 90-128 337-374 (375)
112 smart00419 HTH_CRP helix_turn_ 79.4 2.5 5.4E-05 25.3 2.8 22 85-106 21-42 (48)
113 PRK05799 coproporphyrinogen II 79.3 3.2 7E-05 35.8 4.5 58 57-128 316-373 (374)
114 TIGR02147 Fsuc_second hypothet 78.9 14 0.00031 31.7 8.2 85 40-140 121-211 (271)
115 PRK10906 DNA-binding transcrip 78.6 7.4 0.00016 32.5 6.3 55 45-114 6-60 (252)
116 COG1959 Predicted transcriptio 78.5 7.1 0.00015 30.4 5.8 45 58-116 25-71 (150)
117 PF09012 FeoC: FeoC like trans 78.5 4.2 9.2E-05 27.3 4.0 41 53-107 9-49 (69)
118 TIGR02404 trehalos_R_Bsub treh 78.2 2.4 5.1E-05 34.0 3.1 33 83-115 35-67 (233)
119 PRK09334 30S ribosomal protein 77.6 2.7 5.9E-05 30.8 3.0 24 83-106 52-75 (86)
120 PRK09764 DNA-binding transcrip 77.4 2.7 5.8E-05 34.1 3.3 61 42-116 6-73 (240)
121 PRK13347 coproporphyrinogen II 77.4 3.4 7.4E-05 37.1 4.2 64 52-127 375-438 (453)
122 PF14277 DUF4364: Domain of un 77.3 5.6 0.00012 31.7 5.0 53 88-140 35-91 (163)
123 PRK05283 deoxyribose-phosphate 77.3 3 6.6E-05 35.8 3.7 74 22-100 160-250 (257)
124 COG2188 PhnF Transcriptional r 76.9 9.9 0.00022 31.1 6.5 33 83-115 42-74 (236)
125 PRK05660 HemN family oxidoredu 76.9 3.1 6.8E-05 36.4 3.7 58 57-129 320-377 (378)
126 COG1349 GlpR Transcriptional r 76.3 11 0.00024 31.4 6.7 56 45-115 6-61 (253)
127 TIGR01610 phage_O_Nterm phage 76.0 11 0.00023 27.0 5.7 48 45-106 26-81 (95)
128 PRK06582 coproporphyrinogen II 75.3 10 0.00023 33.6 6.6 61 53-128 328-389 (390)
129 PRK09249 coproporphyrinogen II 74.8 3.6 7.8E-05 36.9 3.6 37 92-129 404-440 (453)
130 PF04703 FaeA: FaeA-like prote 74.7 3.5 7.7E-05 28.2 2.8 38 56-107 13-50 (62)
131 PRK06294 coproporphyrinogen II 74.5 4.5 9.9E-05 35.3 4.1 38 89-127 332-369 (370)
132 PRK10079 phosphonate metabolis 74.3 3.3 7.1E-05 33.5 3.0 59 42-115 13-78 (241)
133 TIGR00637 ModE_repress ModE mo 73.7 14 0.00031 26.8 6.0 36 85-120 29-71 (99)
134 PRK09058 coproporphyrinogen II 73.6 5.2 0.00011 36.0 4.3 43 89-132 398-440 (449)
135 TIGR00538 hemN oxygen-independ 73.6 4 8.7E-05 36.5 3.6 39 92-131 404-442 (455)
136 PF01022 HTH_5: Bacterial regu 73.5 12 0.00026 23.2 4.9 41 49-104 7-47 (47)
137 TIGR03339 phn_lysR aminoethylp 73.5 16 0.00035 28.7 6.7 47 87-135 26-75 (279)
138 PRK11402 DNA-binding transcrip 72.7 4.2 9.1E-05 32.8 3.3 61 42-116 10-77 (241)
139 PRK06266 transcription initiat 71.7 32 0.00068 27.7 8.1 42 48-103 26-67 (178)
140 PRK11886 bifunctional biotin-- 71.7 12 0.00026 31.8 5.9 59 43-115 3-62 (319)
141 PRK08898 coproporphyrinogen II 71.6 6.1 0.00013 34.9 4.2 59 55-128 335-393 (394)
142 PRK04172 pheS phenylalanyl-tRN 71.3 8.3 0.00018 35.2 5.1 66 47-126 9-76 (489)
143 PF09821 AAA_assoc_C: C-termin 70.8 9 0.0002 29.1 4.5 31 91-122 16-46 (120)
144 COG2524 Predicted transcriptio 70.7 3.5 7.6E-05 36.3 2.5 35 87-121 40-76 (294)
145 COG0635 HemN Coproporphyrinoge 70.3 20 0.00042 32.4 7.2 83 30-131 331-413 (416)
146 PF03297 Ribosomal_S25: S25 ri 70.0 4.4 9.5E-05 30.6 2.6 36 57-106 58-93 (105)
147 COG2255 RuvB Holliday junction 69.9 13 0.00028 33.4 5.8 68 40-121 259-326 (332)
148 PRK10086 DNA-binding transcrip 68.4 15 0.00033 30.2 5.7 47 88-136 44-93 (311)
149 TIGR00122 birA_repr_reg BirA b 68.1 27 0.00058 23.0 5.9 52 49-115 5-56 (69)
150 COG2512 Predicted membrane-ass 67.7 5 0.00011 34.3 2.8 77 15-110 171-248 (258)
151 PRK11242 DNA-binding transcrip 67.2 21 0.00046 28.5 6.2 49 87-137 30-81 (296)
152 PRK10411 DNA-binding transcrip 67.1 15 0.00033 30.4 5.5 52 45-110 5-56 (240)
153 PRK09986 DNA-binding transcrip 67.0 20 0.00043 28.7 6.0 49 87-137 36-87 (294)
154 PRK00080 ruvB Holliday junctio 66.8 12 0.00025 31.8 4.8 65 40-121 261-325 (328)
155 TIGR00635 ruvB Holliday juncti 65.8 15 0.00033 30.2 5.2 50 56-120 253-303 (305)
156 PF00126 HTH_1: Bacterial regu 65.7 9 0.0002 24.8 3.1 32 85-117 26-60 (60)
157 PRK10082 cell density-dependen 65.3 24 0.00052 28.8 6.2 44 87-132 40-86 (303)
158 PF14178 YppF: YppF-like prote 63.9 11 0.00024 26.2 3.3 33 32-68 14-46 (60)
159 PRK12423 LexA repressor; Provi 63.7 8.3 0.00018 30.9 3.2 36 59-107 26-61 (202)
160 TIGR02424 TF_pcaQ pca operon t 63.6 27 0.00058 28.2 6.2 44 87-132 32-78 (300)
161 TIGR01594 holin_lambda phage h 63.6 6.4 0.00014 29.6 2.4 35 34-72 1-44 (107)
162 TIGR02698 CopY_TcrY copper tra 62.7 20 0.00044 27.1 5.0 52 48-110 8-59 (130)
163 PRK09906 DNA-binding transcrip 61.9 24 0.00051 28.4 5.6 46 88-135 31-79 (296)
164 COG1542 Uncharacterized conser 61.8 4.4 9.5E-05 38.4 1.4 92 14-119 380-489 (593)
165 PRK14997 LysR family transcrip 61.6 22 0.00049 28.7 5.4 46 88-135 32-80 (301)
166 COG4533 ABC-type uncharacteriz 61.5 23 0.00049 33.9 6.1 59 59-131 24-88 (564)
167 PRK08446 coproporphyrinogen II 61.2 11 0.00023 32.7 3.7 37 89-128 313-349 (350)
168 TIGR02036 dsdC D-serine deamin 61.1 34 0.00074 28.0 6.5 47 87-135 37-86 (302)
169 PRK10837 putative DNA-binding 60.7 37 0.00079 27.1 6.4 45 87-133 32-79 (290)
170 TIGR00498 lexA SOS regulatory 60.2 14 0.0003 29.1 3.9 46 50-108 15-62 (199)
171 PF13089 PP_kinase_N: Polyphos 60.2 9.9 0.00021 28.2 2.9 49 94-147 53-108 (109)
172 PF07848 PaaX: PaaX-like prote 60.0 9.6 0.00021 26.5 2.6 61 45-116 1-70 (70)
173 PRK11716 DNA-binding transcrip 59.4 45 0.00098 25.9 6.6 45 87-133 6-53 (269)
174 PF01325 Fe_dep_repress: Iron 59.0 43 0.00093 22.2 5.6 40 56-109 20-59 (60)
175 PRK13626 transcriptional regul 59.0 8.8 0.00019 35.1 2.9 40 57-110 22-61 (552)
176 TIGR03042 PS_II_psbQ_bact phot 58.9 18 0.00038 28.8 4.2 17 38-61 61-77 (142)
177 PRK11151 DNA-binding transcrip 58.8 46 0.001 27.0 6.8 47 87-135 30-79 (305)
178 PF13730 HTH_36: Helix-turn-he 58.7 9.6 0.00021 23.9 2.3 20 83-102 36-55 (55)
179 PF08222 HTH_CodY: CodY helix- 58.3 14 0.00031 25.7 3.1 21 86-106 18-38 (61)
180 PRK10141 DNA-binding transcrip 57.0 83 0.0018 23.8 9.1 60 48-122 20-83 (117)
181 PF03965 Penicillinase_R: Peni 56.8 67 0.0015 23.3 6.8 50 48-107 7-56 (115)
182 PRK10341 DNA-binding transcrip 56.6 43 0.00094 27.5 6.4 46 87-134 36-84 (312)
183 PRK12681 cysB transcriptional 55.9 38 0.00082 28.4 6.0 46 88-134 32-80 (324)
184 PRK11233 nitrogen assimilation 55.5 48 0.001 27.1 6.4 47 87-135 30-79 (305)
185 PF11313 DUF3116: Protein of u 54.8 17 0.00037 26.6 3.3 42 84-125 39-83 (85)
186 PRK11013 DNA-binding transcrip 54.7 40 0.00086 27.7 5.8 44 86-131 32-78 (309)
187 PRK09791 putative DNA-binding 54.3 64 0.0014 26.1 6.9 43 87-131 34-79 (302)
188 PRK11139 DNA-binding transcrip 54.1 50 0.0011 26.7 6.3 47 87-135 35-84 (297)
189 PRK11057 ATP-dependent DNA hel 54.0 41 0.00089 31.4 6.4 105 39-144 410-552 (607)
190 PRK10632 transcriptional regul 53.7 54 0.0012 26.9 6.5 46 87-134 31-79 (309)
191 PRK04424 fatty acid biosynthes 53.5 19 0.00041 28.8 3.6 47 45-105 8-54 (185)
192 PF07381 DUF1495: Winged helix 53.2 11 0.00024 27.7 2.0 29 94-122 57-89 (90)
193 PRK03601 transcriptional regul 50.6 79 0.0017 25.5 6.9 45 88-134 31-78 (275)
194 PRK10094 DNA-binding transcrip 50.2 57 0.0012 26.9 6.1 46 87-134 31-79 (308)
195 PRK00215 LexA repressor; Valid 50.2 18 0.00038 28.6 3.0 50 58-120 23-74 (205)
196 PRK15421 DNA-binding transcrip 49.9 56 0.0012 27.2 6.1 46 87-134 31-79 (317)
197 PF03836 RasGAP_C: RasGAP C-te 49.7 5.5 0.00012 30.6 0.0 34 88-129 8-41 (142)
198 PF03969 AFG1_ATPase: AFG1-lik 48.7 53 0.0011 29.2 6.0 85 48-150 60-165 (362)
199 TIGR03337 phnR transcriptional 47.7 21 0.00046 28.2 3.1 32 85-116 38-69 (231)
200 smart00344 HTH_ASNC helix_turn 47.5 52 0.0011 23.0 4.8 42 48-103 7-48 (108)
201 PRK15481 transcriptional regul 47.1 22 0.00047 31.0 3.3 32 83-114 40-71 (431)
202 TIGR03418 chol_sulf_TF putativ 46.5 61 0.0013 26.0 5.6 43 87-131 30-75 (291)
203 CHL00180 rbcR LysR transcripti 45.9 72 0.0016 26.0 6.0 43 87-131 34-79 (305)
204 PRK12684 transcriptional regul 45.6 59 0.0013 26.8 5.5 43 89-132 33-78 (313)
205 PRK11074 putative DNA-binding 45.1 1.1E+02 0.0024 24.9 7.0 43 87-131 31-76 (300)
206 PF08279 HTH_11: HTH domain; 44.1 77 0.0017 19.6 5.2 48 45-106 1-50 (55)
207 PRK11062 nhaR transcriptional 43.4 93 0.002 25.3 6.3 42 88-131 34-78 (296)
208 KOG1767|consensus 42.9 16 0.00035 28.1 1.6 24 83-106 71-94 (110)
209 PRK09508 leuO leucine transcri 42.7 71 0.0015 26.2 5.6 46 85-132 49-97 (314)
210 smart00427 H2B Histone H2B. 42.3 55 0.0012 24.2 4.3 38 87-134 5-42 (89)
211 PRK09213 pur operon repressor; 41.9 1.2E+02 0.0027 26.1 7.1 75 45-127 8-91 (271)
212 PRK04214 rbn ribonuclease BN/u 41.7 94 0.002 27.7 6.5 55 44-112 292-350 (412)
213 PLN02956 PSII-Q subunit 41.6 48 0.001 27.6 4.3 25 114-138 135-159 (185)
214 PRK12679 cbl transcriptional r 41.5 1E+02 0.0022 25.5 6.3 46 87-134 31-80 (316)
215 PF04408 HA2: Helicase associa 41.4 20 0.00043 25.6 1.9 26 91-120 1-26 (102)
216 PRK11482 putative DNA-binding 40.8 73 0.0016 26.5 5.4 43 87-131 58-103 (317)
217 PRK12683 transcriptional regul 39.8 1.2E+02 0.0026 25.0 6.5 46 87-134 31-80 (309)
218 TIGR00373 conserved hypothetic 38.7 1.9E+02 0.0041 22.6 8.8 43 47-103 17-59 (158)
219 PRK10676 DNA-binding transcrip 38.4 77 0.0017 26.7 5.2 65 40-120 15-86 (263)
220 PRK13348 chromosome replicatio 38.4 1.4E+02 0.0031 23.9 6.6 37 87-125 31-70 (294)
221 PF09397 Ftsk_gamma: Ftsk gamm 38.2 1.3E+02 0.0029 20.7 6.3 51 40-107 5-55 (65)
222 PRK15092 DNA-binding transcrip 38.1 1.1E+02 0.0024 25.5 6.1 44 88-133 41-87 (310)
223 PF10264 Stork_head: Winged he 37.3 82 0.0018 22.8 4.5 35 81-115 46-80 (80)
224 TIGR03298 argP transcriptional 37.2 1.3E+02 0.0028 24.1 6.2 37 87-125 30-69 (292)
225 COG2345 Predicted transcriptio 36.8 1.7E+02 0.0036 24.7 6.9 59 47-119 14-80 (218)
226 PF08432 Vfa1: AAA-ATPase Vps4 36.5 9 0.00019 30.8 -0.7 13 34-46 28-40 (182)
227 COG1568 Predicted methyltransf 36.2 32 0.0007 31.0 2.7 38 83-121 45-82 (354)
228 PRK09801 transcriptional activ 36.1 1.4E+02 0.0029 24.8 6.3 47 87-135 35-84 (310)
229 TIGR02647 DNA conserved hypoth 36.1 75 0.0016 23.1 4.1 37 82-121 30-66 (77)
230 TIGR02716 C20_methyl_CrtF C-20 35.1 67 0.0015 26.8 4.3 52 56-122 21-72 (306)
231 COG1339 Transcriptional regula 35.0 72 0.0016 27.2 4.4 42 87-128 34-78 (214)
232 COG3327 PaaX Phenylacetic acid 35.0 51 0.0011 29.2 3.6 45 85-129 41-88 (291)
233 PRK15243 transcriptional regul 34.7 1.5E+02 0.0032 25.1 6.4 45 87-133 33-80 (297)
234 PF09681 Phage_rep_org_N: N-te 34.3 94 0.002 23.7 4.7 60 41-114 28-95 (121)
235 TIGR01743 purR_Bsub pur operon 34.2 2E+02 0.0043 24.9 7.1 75 45-127 6-89 (268)
236 PRK12680 transcriptional regul 34.2 89 0.0019 26.3 5.0 45 87-133 31-79 (327)
237 COG3398 Uncharacterized protei 34.0 41 0.00088 29.1 2.9 27 84-111 200-226 (240)
238 cd00772 ProRS_core Prolyl-tRNA 34.0 80 0.0017 26.5 4.6 41 93-133 7-48 (264)
239 smart00847 HA2 Helicase associ 33.3 31 0.00068 23.5 1.7 25 92-120 2-26 (92)
240 TIGR02066 dsrB sulfite reducta 32.9 28 0.0006 30.7 1.8 111 21-133 10-133 (341)
241 PRK12682 transcriptional regul 32.9 1.9E+02 0.0041 23.6 6.6 40 87-127 31-74 (309)
242 PLN00158 histone H2B; Provisio 32.6 93 0.002 24.1 4.4 42 83-134 27-68 (116)
243 PF03975 CheD: CheD chemotacti 32.0 57 0.0012 24.1 3.1 58 86-148 20-82 (114)
244 PRK10681 DNA-binding transcrip 31.5 1.2E+02 0.0026 25.1 5.3 42 45-100 8-49 (252)
245 smart00351 PAX Paired Box doma 31.3 91 0.002 23.3 4.1 82 44-146 22-110 (125)
246 PRK03635 chromosome replicatio 30.7 1.4E+02 0.0031 24.1 5.5 39 88-129 32-73 (294)
247 PF09202 Rio2_N: Rio2, N-termi 30.2 54 0.0012 23.4 2.6 38 83-120 35-74 (82)
248 cd08768 Cdc6_C Winged-helix do 30.2 44 0.00096 22.5 2.1 23 84-106 44-66 (87)
249 PF02909 TetR_C: Tetracyclin r 30.2 1.4E+02 0.0031 21.2 4.9 59 35-104 2-62 (139)
250 PF15129 FAM150: FAM150 family 30.2 36 0.00078 26.6 1.8 17 41-57 103-119 (123)
251 PRK13493 chemoreceptor glutami 29.9 1.1E+02 0.0023 25.7 4.7 53 87-148 100-157 (213)
252 PF05119 Terminase_4: Phage te 29.8 1.9E+02 0.0041 19.9 5.9 50 87-145 34-83 (100)
253 PF14337 DUF4393: Domain of un 29.6 63 0.0014 25.2 3.1 77 16-105 53-133 (186)
254 COG4344 Uncharacterized protei 28.7 81 0.0018 25.9 3.6 39 87-125 46-104 (175)
255 PHA00738 putative HTH transcri 28.7 1.6E+02 0.0034 22.5 5.0 48 49-111 17-64 (108)
256 PTZ00463 histone H2B; Provisio 28.4 2.1E+02 0.0046 22.2 5.7 42 83-134 28-69 (117)
257 COG3668 ParE Plasmid stabiliza 28.3 76 0.0016 22.1 3.1 18 111-128 5-22 (98)
258 COG1654 BirA Biotin operon rep 28.0 79 0.0017 22.6 3.1 30 85-114 32-62 (79)
259 PRK06474 hypothetical protein; 27.8 1.7E+02 0.0038 23.2 5.4 46 48-106 15-61 (178)
260 cd04252 AAK_NAGK-fArgBP AAK_NA 27.3 1.6E+02 0.0034 24.4 5.2 62 80-148 32-93 (248)
261 PF09079 Cdc6_C: CDC6, C termi 27.3 54 0.0012 22.4 2.1 22 85-106 38-59 (85)
262 PRK15279 type III secretion pr 26.9 2.4E+02 0.0051 24.2 6.2 83 62-148 47-139 (240)
263 PHA02943 hypothetical protein; 26.6 2.5E+02 0.0054 23.1 6.1 54 39-107 6-59 (165)
264 COG0583 LysR Transcriptional r 26.2 3.1E+02 0.0068 21.2 6.6 45 89-135 32-79 (297)
265 smart00843 Ftsk_gamma This dom 26.1 2.2E+02 0.0049 19.6 5.4 50 40-106 4-53 (63)
266 PF07042 TrfA: TrfA protein; 25.9 39 0.00086 29.5 1.5 40 58-104 231-270 (282)
267 TIGR01389 recQ ATP-dependent D 25.4 1.4E+02 0.0031 27.5 5.1 73 49-121 408-492 (591)
268 PF14629 ORC4_C: Origin recogn 25.4 73 0.0016 25.1 2.8 37 82-118 149-186 (203)
269 PF14502 HTH_41: Helix-turn-he 25.3 81 0.0018 20.9 2.5 27 83-110 17-43 (48)
270 PF04458 DUF505: Protein of un 25.3 53 0.0011 31.7 2.3 41 83-123 326-370 (591)
271 COG4626 Phage terminase-like p 25.2 1.2E+02 0.0027 29.0 4.7 50 92-149 392-455 (546)
272 PF14557 AphA_like: Putative A 25.1 1.1E+02 0.0025 25.3 3.9 44 83-126 43-92 (175)
273 PRK00135 scpB segregation and 25.1 1.6E+02 0.0035 24.0 4.8 64 19-104 69-133 (188)
274 PF14542 Acetyltransf_CG: GCN5 24.7 1E+02 0.0022 21.2 3.2 24 127-150 39-62 (78)
275 COG4754 Uncharacterized conser 24.4 62 0.0014 26.3 2.2 32 90-122 46-77 (157)
276 PF04458 DUF505: Protein of un 24.4 68 0.0015 31.0 2.8 97 17-119 390-497 (591)
277 PF13545 HTH_Crp_2: Crp-like h 24.0 95 0.0021 20.1 2.8 25 82-106 38-62 (76)
278 PRK10263 DNA translocase FtsK; 24.0 2.3E+02 0.0049 30.2 6.6 83 4-106 1253-1341(1355)
279 PF09929 DUF2161: Uncharacteri 23.7 64 0.0014 25.0 2.1 22 99-120 97-118 (118)
280 TIGR02873 spore_ylxY probable 23.5 2.7E+02 0.0058 23.6 6.1 75 75-149 174-263 (268)
281 smart00190 IL4_13 Interleukins 23.3 2.1E+02 0.0045 22.8 4.9 17 41-57 68-84 (138)
282 PF15447 NTS: N-terminal segme 23.3 44 0.00095 20.9 0.9 18 116-133 2-19 (37)
283 PF13182 DUF4007: Protein of u 23.2 54 0.0012 28.1 1.8 38 83-120 38-76 (286)
284 PF04182 B-block_TFIIIC: B-blo 22.7 66 0.0014 22.0 1.8 22 86-107 32-53 (75)
285 PF09661 DUF2398: Protein of u 22.5 1.6E+02 0.0035 26.3 4.7 50 62-115 309-358 (368)
286 PF15398 DUF4619: Domain of un 22.0 29 0.00062 30.8 -0.1 64 29-116 56-123 (296)
287 PF01121 CoaE: Dephospho-CoA k 21.9 3.5E+02 0.0076 21.4 6.1 79 44-144 28-106 (180)
288 PF02002 TFIIE_alpha: TFIIE al 21.7 1.5E+02 0.0033 21.0 3.7 44 46-103 15-58 (105)
289 COG3265 GntK Gluconate kinase 21.6 3.7E+02 0.008 22.0 6.2 111 13-133 25-159 (161)
290 PRK13490 chemoreceptor glutami 21.4 1.3E+02 0.0028 24.0 3.5 58 87-148 68-130 (162)
291 PRK02539 hypothetical protein; 21.3 76 0.0017 23.4 2.0 24 90-116 42-65 (85)
292 COG1510 Predicted transcriptio 21.3 1E+02 0.0022 25.5 3.0 46 52-111 34-81 (177)
293 PF03480 SBP_bac_7: Bacterial 21.2 1.8E+02 0.0038 23.9 4.4 38 111-148 218-262 (286)
294 COG4465 CodY Pleiotropic trans 21.2 1.2E+02 0.0027 26.4 3.5 22 85-106 217-238 (261)
295 PF02477 Nairo_nucleo: Nucleoc 21.1 1.5E+02 0.0032 27.5 4.2 52 89-145 251-304 (442)
296 PRK15431 ferrous iron transpor 20.8 2.4E+02 0.0051 20.4 4.4 41 52-106 10-50 (78)
297 PF02985 HEAT: HEAT repeat; I 20.7 74 0.0016 17.9 1.5 12 37-49 10-21 (31)
298 COG5631 Predicted transcriptio 20.6 1.5E+02 0.0033 24.8 3.8 39 86-124 113-154 (199)
299 PF03849 Tfb2: Transcription f 20.5 1.9E+02 0.0042 25.8 4.7 57 30-106 24-80 (366)
300 PLN02512 acetylglutamate kinas 20.3 2.7E+02 0.0059 23.9 5.5 62 82-149 85-146 (309)
301 PRK13494 chemoreceptor glutami 20.2 1.7E+02 0.0037 23.5 4.0 55 86-148 73-132 (163)
302 PF14113 DUF4285: Domain of un 20.2 1.3E+02 0.0028 22.4 3.1 28 30-57 28-55 (115)
303 PRK13491 chemoreceptor glutami 20.2 1.8E+02 0.0039 24.3 4.2 53 87-148 76-133 (199)
304 PTZ00362 hypothetical protein; 20.1 38 0.00082 31.9 0.3 22 7-28 323-346 (479)
305 PF06414 Zeta_toxin: Zeta toxi 20.1 2.8E+02 0.0061 21.5 5.2 65 83-147 24-97 (199)
306 COG2138 Sirohydrochlorin ferro 20.1 1.4E+02 0.0031 25.2 3.7 37 113-149 14-69 (245)
307 COG0640 ArsR Predicted transcr 20.1 2.4E+02 0.0053 17.8 8.0 50 49-112 30-79 (110)
No 1
>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=100.00 E-value=3.3e-68 Score=414.20 Aligned_cols=130 Identities=52% Similarity=0.931 Sum_probs=118.6
Q ss_pred chHHHhhhccccCCCCCCCcchhhhcccCCcCCCCCCCchHHHHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCcc
Q psy5605 2 VSVSYIGFRPSKSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHF 81 (152)
Q Consensus 2 ~~I~~~A~~LKk~gki~~PeW~d~vKTg~~KElaP~d~DW~YiRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~ 81 (152)
.||++||+|||++|+|++|+|+||||||++||+||+||||||+||||||||||++||+||++|+++|||++|||++|+||
T Consensus 10 ~fI~~~A~~LK~~gki~~P~w~d~vKTg~~kE~~P~~~DW~Y~RaASilRklY~~g~~GV~~lr~~YGg~k~~G~~p~h~ 89 (139)
T PF01090_consen 10 EFIKALAEFLKKSGKIEPPEWADIVKTGSHKELAPYDPDWWYIRAASILRKLYIRGPVGVGRLRKIYGGRKRRGVRPSHF 89 (139)
T ss_dssp HHHHHHHHHHTCSSTS--TSCGGGTSSSSS-SSTTCHHTHHHHHHHHHHHHHHHCTSB-HHHHHHHH--EEEETSSCCEE
T ss_pred HHHHHHHHHHHHcCCcCCcchHHHHhhcccccCCCCCCCeeeeeHHHHHHHHHHhcCcchHHHHHHhCCCCCCCCCCCCC
Confidence 48999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHHHHH
Q psy5605 82 CRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSK 131 (152)
Q Consensus 82 ~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~ 131 (152)
++|||+|||+||||||++|||++++++||+|||+||++||+||.+|++++
T Consensus 90 ~~asg~iiR~~LqqLE~~glv~k~~~~GR~lT~~G~~~lD~iA~~v~~~~ 139 (139)
T PF01090_consen 90 VKASGSIIRKILQQLEKAGLVEKDPKGGRRLTPKGQRDLDRIAGQVAKEL 139 (139)
T ss_dssp --CHHHHHHHHHHHHHHTTSEEEETTTEEEE-HHHHHHHHHHHHHHHHHH
T ss_pred CCCCcHHHHHHHHHHHHCCCEEecCCCCCEECHHHHHHHHHHHHHHHHcC
Confidence 99999999999999999999999998999999999999999999998764
No 2
>PTZ00095 40S ribosomal protein S19; Provisional
Probab=100.00 E-value=8.7e-67 Score=416.87 Aligned_cols=132 Identities=35% Similarity=0.610 Sum_probs=128.2
Q ss_pred chHHHhhhccccCCCCCCCcchhhhcccCCcCCCCCCCchHHHHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCcc
Q psy5605 2 VSVSYIGFRPSKSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHF 81 (152)
Q Consensus 2 ~~I~~~A~~LKk~gki~~PeW~d~vKTg~~KElaP~d~DW~YiRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~ 81 (152)
.||++||+|||++|+|++|+|+||||||++||+||+||||||+||||||||||++||+||++|+++|||++|||++|+||
T Consensus 35 ~fI~~~A~~LK~~gki~~P~W~d~vKTg~~KElaP~d~DW~YiRaASilRkiYlrgpvGV~~Lrk~YGg~krrG~~P~h~ 114 (169)
T PTZ00095 35 RFIKAFAQHFKLEGKIFVPKCTEIVKTSHGRELAPQNPDWYYIRCAAVLRALYLRPDVGYGGLRKRFSSKKRRGSAPNHT 114 (169)
T ss_pred HHHHHHHHHHHHcCCCCCCcchhhhcccccccCCCCCccHHHHHHHHHHHHHHhcCCccHHHHHHHHCCCCCCCCCCCcc
Confidence 48999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCchhHHHHHHHHHHhCCcceecCC-CCceeCcchHhhHHHHHHHHHHHHHH
Q psy5605 82 CRSSGSVARKALQALEQVNIIEKSDD-GGRKITSHGRRDMDRIAAQIRVSKKE 133 (152)
Q Consensus 82 ~~asg~iiR~~LQqLE~~glVek~~~-gGR~lT~~G~~~LD~iA~~i~~~~~~ 133 (152)
++|||+|||+||||||++|||+++++ +||+|||+||++||+||.+|++++..
T Consensus 115 ~~aSg~iiR~~LQqLE~~glVek~~~~~GR~lT~~Gr~~LD~iA~~v~~~l~~ 167 (169)
T PTZ00095 115 VRASGKILRWICQQLEKLGLVEQGPKKKGRRLTRKGCNFANAFARQVTIRKFG 167 (169)
T ss_pred cCCchHHHHHHHHHHHHCCCEEecCCCCCCEECHhHHHHHHHHHHHHHHHHhc
Confidence 99999999999999999999999964 89999999999999999999987754
No 3
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=100.00 E-value=1.4e-65 Score=403.70 Aligned_cols=132 Identities=38% Similarity=0.713 Sum_probs=129.1
Q ss_pred chHHHhhhccccCCCCCCCcchhhhcccCCcCCCCCCCchHHHHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCcc
Q psy5605 2 VSVSYIGFRPSKSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHF 81 (152)
Q Consensus 2 ~~I~~~A~~LKk~gki~~PeW~d~vKTg~~KElaP~d~DW~YiRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~ 81 (152)
.||++||+|||++|+|++|+|+||||||++||+||+||||||+||||||||||++||+||++|+++|||+||||++|+||
T Consensus 11 ~~I~~~A~~LK~~~ki~~P~W~~~vKTg~~kE~~P~~~DW~Y~R~AsIlR~vY~~gpvGV~~L~~~yGg~k~~G~~P~h~ 90 (150)
T PRK09333 11 LLIERLAEYLKNVDEIKPPEWAAFVKTGVHKERPPEQEDWWYVRAASILRKVYIDGPVGVERLRTAYGGRKNRGVRPEHF 90 (150)
T ss_pred HHHHHHHHHHHhcCCcCCCcchhhhcccccccCCCCCCchHHHHHHHHHHHHHHcCCccHHHHHHHHCCCcCCCCCCCcc
Confidence 48999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHHHHHHHH
Q psy5605 82 CRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEA 134 (152)
Q Consensus 82 ~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~ 134 (152)
++|||+|||++|||||++|||++++ +||+||++||++||+||.+|++++.+.
T Consensus 91 ~~~sg~iiR~~LqqLE~~glVek~~-~GR~lT~~G~~~LD~iA~~i~~~~~~~ 142 (150)
T PRK09333 91 VKGSGSIIRKILQQLEKAGLVEKTK-KGRVITPKGRSLLDNLAAEVKKELAEE 142 (150)
T ss_pred ccCccHHHHHHHHHHHHCCCeeeCC-CCCEeCHHHHHHHHHHHHHHHHHHHhh
Confidence 9999999999999999999999999 899999999999999999999988654
No 4
>KOG3411|consensus
Probab=100.00 E-value=2.3e-65 Score=396.70 Aligned_cols=129 Identities=60% Similarity=1.030 Sum_probs=127.0
Q ss_pred chHHHhhhccccCCCCCCCcchhhhcccCCcCCCCCCCchHHHHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCcc
Q psy5605 2 VSVSYIGFRPSKSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHF 81 (152)
Q Consensus 2 ~~I~~~A~~LKk~gki~~PeW~d~vKTg~~KElaP~d~DW~YiRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~ 81 (152)
.|+++||.|||++|||++|+|+|+||||.+||+||+||||||+|||||+||||+++|+||+.|+++|||+||||++|+||
T Consensus 13 ~f~~a~asfLK~sgkv~vp~~~DivKtg~~kElAP~D~dWfytRaASiaRhiylR~~~gvg~~~KiYGg~krrGvrPsh~ 92 (143)
T KOG3411|consen 13 KFTKAYASFLKRSGKVEVPQWVDIVKTGKGKELAPYDPDWYYTRAASIARHIYLRGPVGVGALTKIYGGSKRRGVRPSHF 92 (143)
T ss_pred HHHHHHHHHHHhcCCccCcchhhhhhcccCcccCCCCccHHHHHHHHHHHHHHhccccchhHHHHHhcccccCCCCChhh
Confidence 48999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHHHH
Q psy5605 82 CRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVS 130 (152)
Q Consensus 82 ~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~ 130 (152)
+.+||+|+|++||+||++||||++++|||+||++||+|||+||++|.++
T Consensus 93 ~~as~~i~rkvlQ~Le~~~~ve~hp~gGR~lt~~GqrdldrIa~~i~~~ 141 (143)
T KOG3411|consen 93 CDASGGIARKVLQALEKMGIVEKHPKGGRRLTEQGQRDLDRIAGQIREE 141 (143)
T ss_pred hccccHHHHHHHHHHHhCCceeeCCCCcceeCcccchhHHHHHHHHHhc
Confidence 9999999999999999999999999999999999999999999999865
No 5
>COG2238 RPS19A Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.7e-63 Score=389.16 Aligned_cols=130 Identities=41% Similarity=0.751 Sum_probs=128.3
Q ss_pred hHHHhhhccccCCCCCCCcchhhhcccCCcCCCCCCCchHHHHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccC
Q psy5605 3 SVSYIGFRPSKSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFC 82 (152)
Q Consensus 3 ~I~~~A~~LKk~gki~~PeW~d~vKTg~~KElaP~d~DW~YiRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~ 82 (152)
+|+++|++||++++|++|+|+||||||.+||+||.|+||||+||||||||||++||+||++|++.|||++|||++|+||+
T Consensus 12 lI~~lA~~LK~~~kv~pP~wa~~vKTG~~kE~~P~~~DWwY~RaASilRkiyi~gpvGi~rL~t~YGg~k~rG~rP~~~~ 91 (147)
T COG2238 12 LIEALASYLKETGKVKPPEWADIVKTGVHKERPPEQEDWWYVRAASILRKIYIDGPVGIERLRTAYGGRKNRGSRPEKFR 91 (147)
T ss_pred HHHHHHHHHHhcCCcCChhhhhhhhccccccCCCCCCchHHHHHHHHHHHHHhcCchhHHHHHHHHCccccCCCCchhhh
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHHHHHHH
Q psy5605 83 RSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKE 133 (152)
Q Consensus 83 ~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~ 133 (152)
+|||+|+|++|||||++|||++++ +||+|||+||++||+||.+|++++.+
T Consensus 92 ~gsgsI~RkilqqLE~~G~V~k~~-~GR~ltp~GrsllD~~a~ei~eel~~ 141 (147)
T COG2238 92 KGSGSIIRKVLQQLEKAGLVEKTP-KGRVLTPKGRSLLDRIATEIKEELEE 141 (147)
T ss_pred cCCchHHHHHHHHHHHCCceeecC-CCceeCccchhHHHHHHHHHHHHhcc
Confidence 999999999999999999999999 79999999999999999999999876
No 6
>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=97.35 E-value=0.00038 Score=50.22 Aligned_cols=57 Identities=32% Similarity=0.623 Sum_probs=46.6
Q ss_pred hHhhc--CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceec--CCCCceeCcchHhhHHH
Q psy5605 52 HIYMR--SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKS--DDGGRKITSHGRRDMDR 122 (152)
Q Consensus 52 kiYl~--g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~--~~gGR~lT~~G~~~LD~ 122 (152)
..|++ .|||-..+....+ -|..-||+.++.||++|||++. +.+||+-|.+|-+.+++
T Consensus 15 ~~Y~~~~~PVgSk~ia~~l~--------------~s~aTIRN~M~~Le~lGlve~~p~~s~GriPT~~aYr~~~~ 75 (78)
T PF03444_consen 15 ELYIETGEPVGSKTIAEELG--------------RSPATIRNEMADLEELGLVESQPHPSGGRIPTDKAYRALNR 75 (78)
T ss_pred HHHHhcCCCcCHHHHHHHHC--------------CChHHHHHHHHHHHHCCCccCCCCCCCCCCcCHHHHHHHcc
Confidence 45764 6999999998753 2347899999999999999964 46899999999998864
No 7
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=97.28 E-value=0.00045 Score=47.45 Aligned_cols=63 Identities=27% Similarity=0.400 Sum_probs=50.6
Q ss_pred HHhhHhh-cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhH
Q psy5605 49 LARHIYM-RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDM 120 (152)
Q Consensus 49 ilRkiYl-~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~L 120 (152)
||+.|+- .+|+|-..|+....-+ | ..-|-.-+|.-|..||..|++++.-.+||.||++|...|
T Consensus 3 IL~~L~~~~~P~g~~~l~~~L~~~---g------~~~se~avRrrLr~me~~Glt~~~g~~G~~iT~~G~~~L 66 (66)
T PF08461_consen 3 ILRILAESDKPLGRKQLAEELKLR---G------EELSEEAVRRRLRAMERDGLTRKVGRQGRIITEKGLDEL 66 (66)
T ss_pred HHHHHHHcCCCCCHHHHHHHHHhc---C------hhhhHHHHHHHHHHHHHCCCccccCCcccccCHHHHhhC
Confidence 6777775 4789999999887432 2 234557899999999999999987778999999998764
No 8
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=96.84 E-value=0.0054 Score=49.10 Aligned_cols=60 Identities=18% Similarity=0.320 Sum_probs=48.8
Q ss_pred HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC---CCCc-----eeCcchHhh
Q psy5605 48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD---DGGR-----KITSHGRRD 119 (152)
Q Consensus 48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~---~gGR-----~lT~~G~~~ 119 (152)
+||..|.-.+++.+..|....|- +.+-+|..|+.||+.|||+..+ ..|| .||++|+..
T Consensus 5 ~IL~~L~~~~~~t~~eLA~~lgi--------------s~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~G~~~ 70 (203)
T TIGR02702 5 DILSYLLKQGQATAAALAEALAI--------------SPQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSRQGREQ 70 (203)
T ss_pred HHHHHHHHcCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCeEEeecccCCCCCceEEEECcchhhh
Confidence 57777777899999999998743 3578999999999999998763 2478 999999875
Q ss_pred HH
Q psy5605 120 MD 121 (152)
Q Consensus 120 LD 121 (152)
+.
T Consensus 71 ~~ 72 (203)
T TIGR02702 71 FP 72 (203)
T ss_pred cc
Confidence 43
No 9
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=96.81 E-value=0.0064 Score=42.31 Aligned_cols=60 Identities=18% Similarity=0.306 Sum_probs=42.0
Q ss_pred HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHH
Q psy5605 48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRI 123 (152)
Q Consensus 48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~i 123 (152)
.||.-+- .++.....+.. .+.=|-+.+...|..|++.|+|++. ++.-.||++|...|+.+
T Consensus 10 ~IL~~l~-~~~~~~t~i~~--------------~~~L~~~~~~~yL~~L~~~gLI~~~-~~~Y~lTekG~~~l~~l 69 (77)
T PF14947_consen 10 DILKILS-KGGAKKTEIMY--------------KANLNYSTLKKYLKELEEKGLIKKK-DGKYRLTEKGKEFLEEL 69 (77)
T ss_dssp HHHHHH--TT-B-HHHHHT--------------TST--HHHHHHHHHHHHHTTSEEEE-TTEEEE-HHHHHHHHHH
T ss_pred HHHHHHH-cCCCCHHHHHH--------------HhCcCHHHHHHHHHHHHHCcCeeCC-CCEEEECccHHHHHHHH
Confidence 4454443 66666665553 2556778999999999999999774 46899999999999988
No 10
>COG3388 Predicted transcriptional regulator [Transcription]
Probab=96.62 E-value=0.0078 Score=45.31 Aligned_cols=73 Identities=25% Similarity=0.371 Sum_probs=60.7
Q ss_pred HHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHH
Q psy5605 45 RCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIA 124 (152)
Q Consensus 45 RaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA 124 (152)
|--+++..+-=.+|+|+..|+..-| .|+|. +|+.|.=||+.++|.-+. .|-.+|+.+-.++++|-
T Consensus 15 RHl~Vl~~v~eeqPiGI~klS~~TG-------mp~HK-------VRYSLRVLEq~~iI~PS~-~GAi~td~~~e~ie~i~ 79 (101)
T COG3388 15 RHLSVLKVVLEEQPIGIIKLSDETG-------MPEHK-------VRYSLRVLEQENIISPSR-QGAILTDDFPEFIEEII 79 (101)
T ss_pred HHHHHHHHHHHhCCceeEeechhcC-------Cchhh-------hhhhhhhhhhcCccCccc-cCCccCccHHHHHHHHH
Confidence 5556676666789999999999876 48876 799999999999998777 59999999999999998
Q ss_pred HHHHHHHH
Q psy5605 125 AQIRVSKK 132 (152)
Q Consensus 125 ~~i~~~~~ 132 (152)
+++-+-+.
T Consensus 80 ~dl~ei~e 87 (101)
T COG3388 80 GDLSEINE 87 (101)
T ss_pred HHHHHHHH
Confidence 88754333
No 11
>COG1420 HrcA Transcriptional regulator of heat shock gene [Transcription]
Probab=96.58 E-value=0.0047 Score=54.70 Aligned_cols=63 Identities=33% Similarity=0.533 Sum_probs=51.7
Q ss_pred HHHHHHhhH---hhc--CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC-CCceeCcchHh
Q psy5605 45 RCAALARHI---YMR--SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD-GGRKITSHGRR 118 (152)
Q Consensus 45 RaASilRki---Yl~--g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~-gGR~lT~~G~~ 118 (152)
|-..|||.| |+. -|||-..|.+.|+ -.-|..-||+.+++||++|+++|... .||+-|..|-+
T Consensus 7 Rq~~IL~aIV~~Yi~t~ePVGSk~L~e~~~------------l~~SsATIRN~Ma~LE~~GlI~k~HtSsGRvPT~~Gyr 74 (346)
T COG1420 7 RQRLILRAIVEDYLATGEPVGSKTLSEKYN------------LDLSSATIRNEMADLEKLGLIEKPHTSSGRVPTDKGYR 74 (346)
T ss_pred HHHHHHHHHHHHHHhcCCccchHHHHHHhC------------CCCCchhHHHHHHHHHHCCCccCccccCCcCCcHhHHH
Confidence 556677654 764 5999999999984 24677899999999999999998764 79999999976
Q ss_pred h
Q psy5605 119 D 119 (152)
Q Consensus 119 ~ 119 (152)
.
T Consensus 75 ~ 75 (346)
T COG1420 75 Y 75 (346)
T ss_pred H
Confidence 4
No 12
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=96.56 E-value=0.02 Score=43.08 Aligned_cols=65 Identities=14% Similarity=0.124 Sum_probs=47.9
Q ss_pred HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHH
Q psy5605 48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMD 121 (152)
Q Consensus 48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD 121 (152)
.||..|+-.+++....|+...|- +.+-+=.+++.||+.|||++.++ ++| .||++|+..++
T Consensus 44 ~vL~~l~~~~~~t~~eLa~~l~i--------------~~~tvsr~l~~Le~~GlI~R~~~~~DrR~~~l~LT~~G~~~~~ 109 (144)
T PRK11512 44 KVLCSIRCAACITPVELKKVLSV--------------DLGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICE 109 (144)
T ss_pred HHHHHHHHcCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEeccCcccCCeeEeEEChhHHHHHH
Confidence 35666676777888888887643 33556678899999999997653 455 58999999988
Q ss_pred HHHHH
Q psy5605 122 RIAAQ 126 (152)
Q Consensus 122 ~iA~~ 126 (152)
++...
T Consensus 110 ~~~~~ 114 (144)
T PRK11512 110 QCHQL 114 (144)
T ss_pred HHHHH
Confidence 76443
No 13
>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=96.56 E-value=0.029 Score=40.85 Aligned_cols=68 Identities=13% Similarity=0.141 Sum_probs=52.0
Q ss_pred HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHHH
Q psy5605 49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMDR 122 (152)
Q Consensus 49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD~ 122 (152)
||..|+-.+++.+..|+...|-. .+-+-.+++.||+.|||+..++ +.| .||++|++.+++
T Consensus 33 iL~~l~~~~~~t~~ela~~~~~~--------------~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~LT~~G~~~~~~ 98 (118)
T TIGR02337 33 ILRILAEQGSMEFTQLANQACIL--------------RPSLTGILARLERDGLVTRLKASNDQRRVYISLTPKGQALYAS 98 (118)
T ss_pred HHHHHHHcCCcCHHHHHHHhCCC--------------chhHHHHHHHHHHCCCEEeccCCCCCCeeEEEECHhHHHHHHH
Confidence 66667778888999999887542 2345688999999999997653 344 699999999998
Q ss_pred HHHHHHHH
Q psy5605 123 IAAQIRVS 130 (152)
Q Consensus 123 iA~~i~~~ 130 (152)
+.....+.
T Consensus 99 ~~~~~~~~ 106 (118)
T TIGR02337 99 LSPQIEEI 106 (118)
T ss_pred hhHHHHHH
Confidence 87665443
No 14
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=96.50 E-value=0.011 Score=45.75 Aligned_cols=60 Identities=20% Similarity=0.351 Sum_probs=51.3
Q ss_pred hhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHHHHHHHHHHHHHhhcCce
Q psy5605 86 GSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEAALQALAAQGIT 145 (152)
Q Consensus 86 g~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~~~~~~~~~~~~ 145 (152)
-.-+.++.|.||..|+|++....|..+|++++..+|..=.+..++..+.--..+.+.|++
T Consensus 49 pnTv~raY~eLE~eG~i~t~rg~G~fV~~~~~~~~~~~~~~~~~~~l~~~I~~~~~~G~s 108 (125)
T COG1725 49 PNTVQRAYQELEREGIVETKRGKGTFVTEDAKEILDQLKRELAEEELEEFIEEAKALGLS 108 (125)
T ss_pred HHHHHHHHHHHHHCCCEEEecCeeEEEcCCchhhHHHHHHHHHHHHHHHHHHHHHHcCCC
Confidence 367889999999999999998889999999999888887777777777777777777775
No 15
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=96.20 E-value=0.012 Score=41.02 Aligned_cols=43 Identities=26% Similarity=0.343 Sum_probs=37.1
Q ss_pred CchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHH
Q psy5605 84 SSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQ 126 (152)
Q Consensus 84 asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~ 126 (152)
-|.+-++.+++.||+.|||++.++++-.||+.|+...+.+...
T Consensus 11 is~stvs~~l~~L~~~glI~r~~~~~~~lT~~g~~~~~~~~~~ 53 (96)
T smart00529 11 VSPPTVTQMLKKLEKDGLVEYEPYRGITLTEKGRRLARRLLRK 53 (96)
T ss_pred CChHHHHHHHHHHHHCCCEEEcCCCceEechhHHHHHHHHHHH
Confidence 3567899999999999999999977999999999988776543
No 16
>PRK11050 manganese transport regulator MntR; Provisional
Probab=96.19 E-value=0.03 Score=43.37 Aligned_cols=63 Identities=17% Similarity=0.168 Sum_probs=51.1
Q ss_pred HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHH
Q psy5605 49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAA 125 (152)
Q Consensus 49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~ 125 (152)
|++.++-.+++.+..|...+| -|.+-+...++.||+.|||...+.+|-.||++|+..+..+..
T Consensus 42 I~~~l~~~~~~t~~eLA~~l~--------------is~stVsr~l~~Le~~GlI~r~~~~~v~LT~~G~~l~~~~~~ 104 (152)
T PRK11050 42 IADLIAEVGEARQVDIAARLG--------------VSQPTVAKMLKRLARDGLVEMRPYRGVFLTPEGEKLAQESRE 104 (152)
T ss_pred HHHHHHhcCCCCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEecCCceEECchHHHHHHHHHH
Confidence 445555568888888888873 456789999999999999998877789999999998887663
No 17
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=96.07 E-value=0.052 Score=36.78 Aligned_cols=67 Identities=22% Similarity=0.342 Sum_probs=51.0
Q ss_pred HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCC------CceeCcchHhhHHH
Q psy5605 49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDG------GRKITSHGRRDMDR 122 (152)
Q Consensus 49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~g------GR~lT~~G~~~LD~ 122 (152)
|+..|+..+++.+..+....+- |..-+...|+.|++.|||+...++ .-.||++|.+.+..
T Consensus 15 il~~l~~~~~~~~~~la~~~~~--------------s~~~i~~~l~~L~~~g~v~~~~~~~~~r~~~~~lT~~g~~~~~~ 80 (101)
T smart00347 15 VLRILYEEGPLSVSELAKRLGV--------------SPSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEEGRELIEE 80 (101)
T ss_pred HHHHHHHcCCcCHHHHHHHHCC--------------CchhHHHHHHHHHHCCCeEecCCCCCCCeEEEEECHhHHHHHHH
Confidence 6777888888999999887631 233477999999999999876542 35699999998888
Q ss_pred HHHHHHH
Q psy5605 123 IAAQIRV 129 (152)
Q Consensus 123 iA~~i~~ 129 (152)
+...+..
T Consensus 81 ~~~~~~~ 87 (101)
T smart00347 81 LLEARHE 87 (101)
T ss_pred HHHHHHH
Confidence 7666543
No 18
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=96.02 E-value=0.053 Score=37.62 Aligned_cols=65 Identities=23% Similarity=0.401 Sum_probs=49.5
Q ss_pred HHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhH
Q psy5605 47 AALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDM 120 (152)
Q Consensus 47 ASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~L 120 (152)
..++..||..++.+.+.|+...+ -+.+-+=.+++.||+.|||+..++ ++| .||++|+..+
T Consensus 25 ~~~L~~l~~~~~~~~~~la~~l~--------------i~~~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~~ 90 (126)
T COG1846 25 YQVLLALYEAGGITVKELAERLG--------------LDRSTVTRLLKRLEDKGLIERLRDPEDRRAVLVRLTEKGRELL 90 (126)
T ss_pred HHHHHHHHHhCCCcHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCeeecCCccccceeeEEECccHHHHH
Confidence 45777888888766566766653 344667778999999999996653 455 7999999999
Q ss_pred HHHHH
Q psy5605 121 DRIAA 125 (152)
Q Consensus 121 D~iA~ 125 (152)
.++..
T Consensus 91 ~~~~~ 95 (126)
T COG1846 91 EQLLP 95 (126)
T ss_pred HHhcc
Confidence 88776
No 19
>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=96.00 E-value=0.013 Score=38.17 Aligned_cols=54 Identities=24% Similarity=0.421 Sum_probs=38.8
Q ss_pred HHhhHh-hcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcch
Q psy5605 49 LARHIY-MRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHG 116 (152)
Q Consensus 49 ilRkiY-l~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G 116 (152)
||+.|+ -.++.....|+...|- +..-+..++++|++.|||++.++ .+| .|||+|
T Consensus 8 vL~~l~~~~~~~t~~~l~~~~~~--------------~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~LT~~G 68 (68)
T PF13463_consen 8 VLRALAHSDGPMTQSDLAERLGI--------------SKSTVSRIIKKLEEKGLVEKERDPHDKRSKRYRLTPAG 68 (68)
T ss_dssp HHHHHT--TS-BEHHHHHHHTT----------------HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE-HHH
T ss_pred HHHHHHccCCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEecCCCCcCCeeEEEeCCCC
Confidence 677888 7789999999998743 44566799999999999986643 455 578877
No 20
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=95.92 E-value=0.033 Score=34.42 Aligned_cols=59 Identities=17% Similarity=0.280 Sum_probs=43.4
Q ss_pred HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCC---CceeCc-chHhhHHH
Q psy5605 49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDG---GRKITS-HGRRDMDR 122 (152)
Q Consensus 49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~g---GR~lT~-~G~~~LD~ 122 (152)
|++.++ .+++.+..+...+| -|.+-++.+|++|++.|+|+...++ .-.+|+ .|...++.
T Consensus 2 il~~l~-~~~~~~~~i~~~l~--------------is~~~v~~~l~~L~~~g~i~~~~~~~~~~~~~~~~~~~~~~~~ 64 (66)
T smart00418 2 ILKLLA-EGELCVCELAEILG--------------LSQSTVSHHLKKLREAGLVESRREGKRVYYSLTDEKVADLLEE 64 (66)
T ss_pred HHHHhh-cCCccHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCeeeeecCCEEEEEEchHHHHHHHHh
Confidence 566677 88999999999985 3446799999999999999976642 234666 55554443
No 21
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=95.90 E-value=0.11 Score=35.62 Aligned_cols=60 Identities=18% Similarity=0.273 Sum_probs=48.8
Q ss_pred HHHHHHHhhHhhc-CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC-CCceeCcchH
Q psy5605 44 TRCAALARHIYMR-SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD-GGRKITSHGR 117 (152)
Q Consensus 44 iRaASilRkiYl~-g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~-gGR~lT~~G~ 117 (152)
-|+-.|+..|.-. +++++..+....|- +.+-++..|+.|++.|+|+.++. +...|++...
T Consensus 5 ~r~~~Il~~l~~~~~~~t~~~ia~~l~i--------------~~~tv~r~l~~L~~~g~l~~~~~~~~y~l~~~~~ 66 (91)
T smart00346 5 ERGLAVLRALAEEPGGLTLAELAERLGL--------------SKSTAHRLLNTLQELGYVEQDGQNGRYRLGPKVL 66 (91)
T ss_pred HHHHHHHHHHHhCCCCcCHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCeeecCCCCceeecHHHH
Confidence 3788899988877 79999999999743 56889999999999999998753 4567877544
No 22
>PF05491 RuvB_C: Holliday junction DNA helicase ruvB C-terminus; InterPro: IPR008823 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the C-terminal region of the proteins; it is thought to be a helicase DNA-binding domain.; GO: 0003677 DNA binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3PFI_B 1IXR_C 1HQC_B 1IXS_B 1IN8_A 1IN4_A 1IN5_A 1J7K_A 1IN6_A 1IN7_A.
Probab=95.84 E-value=0.014 Score=41.93 Aligned_cols=68 Identities=19% Similarity=0.277 Sum_probs=45.6
Q ss_pred chHHHHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhh
Q psy5605 40 DWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRD 119 (152)
Q Consensus 40 DW~YiRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~ 119 (152)
|+.=.|.-..+..-|--||+|+..|+..-|-- ...|.=.+=-=|-+.|+|++++ .||++|++|.+-
T Consensus 7 d~~D~~yL~~l~~~f~ggPvGl~tlA~~l~ed-------------~~Tie~v~EPyLiq~G~I~RT~-rGR~~T~~a~~~ 72 (76)
T PF05491_consen 7 DELDRRYLKTLIENFKGGPVGLDTLAAALGED-------------KETIEDVIEPYLIQIGFIQRTP-RGRVATPKAYEH 72 (76)
T ss_dssp BHHHHHHHHHHHHCSTTS-B-HHHHHHHTTS--------------HHHHHHTTHHHHHHTTSEEEET-TEEEE-HHHHHH
T ss_pred CHHHHHHHHHHHHHcCCCCeeHHHHHHHHCCC-------------HhHHHHHhhHHHHHhhhHhhCc-cHHHhHHHHHHH
Confidence 45555655667777788999999999876432 2233333334566799999999 599999999876
Q ss_pred HH
Q psy5605 120 MD 121 (152)
Q Consensus 120 LD 121 (152)
|.
T Consensus 73 l~ 74 (76)
T PF05491_consen 73 LG 74 (76)
T ss_dssp TT
T ss_pred hC
Confidence 53
No 23
>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=95.72 E-value=0.066 Score=38.93 Aligned_cols=68 Identities=15% Similarity=0.168 Sum_probs=50.7
Q ss_pred HHhhHh----hcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHh
Q psy5605 49 LARHIY----MRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRR 118 (152)
Q Consensus 49 ilRkiY----l~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~ 118 (152)
+|..|+ -.+++....|+..-+- +.+-+=.++..||+.|||.+.++ +.| .||++|++
T Consensus 30 vL~~l~~~~~~~~~~t~~eL~~~l~~--------------~~stvs~~i~~Le~kg~I~r~~~~~D~R~~~i~lT~~G~~ 95 (109)
T TIGR01889 30 ILYYLGKLENNEGKLTLKEIIKEILI--------------KQSALVKIIKKLSKKGYLSKERSEDDERKVIISINKEQRS 95 (109)
T ss_pred HHHHHHhhhccCCcCcHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEeccCCcccCCeEEEEECHHHHH
Confidence 666666 3467888888887632 33556678899999999997653 344 29999999
Q ss_pred hHHHHHHHHHHH
Q psy5605 119 DMDRIAAQIRVS 130 (152)
Q Consensus 119 ~LD~iA~~i~~~ 130 (152)
.++.+-.++-+-
T Consensus 96 ~~~~~~~~~~~~ 107 (109)
T TIGR01889 96 KIESLISEIEQI 107 (109)
T ss_pred HHHHHHHHHHHH
Confidence 999998887543
No 24
>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=95.71 E-value=0.04 Score=38.96 Aligned_cols=64 Identities=16% Similarity=0.276 Sum_probs=49.1
Q ss_pred HHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCC------CceeCcchHhhH
Q psy5605 47 AALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDG------GRKITSHGRRDM 120 (152)
Q Consensus 47 ASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~g------GR~lT~~G~~~L 120 (152)
..|++.++. |+...+.|.+.- ...|.+++-.-|+.||+.|+|++.... -..||+.|++++
T Consensus 8 ~~IL~~l~~-g~~rf~el~~~l-------------~~is~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~~G~~l~ 73 (90)
T PF01638_consen 8 LLILRALFQ-GPMRFSELQRRL-------------PGISPKVLSQRLKELEEAGLVERRVYPEVPPRVEYSLTEKGKELL 73 (90)
T ss_dssp HHHHHHHTT-SSEEHHHHHHHS-------------TTS-HHHHHHHHHHHHHTTSEEEEEESSSSSEEEEEE-HHHHHHH
T ss_pred HHHHHHHHh-CCCcHHHHHHhc-------------chhHHHHHHHHHHHHHHcchhhcccccCCCCCCccCCCcCHHHHH
Confidence 568888888 888888888764 246789999999999999999976432 278999999988
Q ss_pred HHHH
Q psy5605 121 DRIA 124 (152)
Q Consensus 121 D~iA 124 (152)
+-+.
T Consensus 74 ~~l~ 77 (90)
T PF01638_consen 74 PVLE 77 (90)
T ss_dssp HHHH
T ss_pred HHHH
Confidence 6543
No 25
>PRK10870 transcriptional repressor MprA; Provisional
Probab=95.66 E-value=0.093 Score=41.51 Aligned_cols=65 Identities=15% Similarity=0.220 Sum_probs=45.9
Q ss_pred HHhhHhhc--CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCce----eCcchHhhH
Q psy5605 49 LARHIYMR--SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGRK----ITSHGRRDM 120 (152)
Q Consensus 49 ilRkiYl~--g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR~----lT~~G~~~L 120 (152)
+|..|+-. +++.+..|+...|- +.+-+=.+++.||+.|||++.+ +++|. ||++|+..+
T Consensus 60 iL~~L~~~~~~~it~~eLa~~l~l--------------~~~tvsr~v~rLe~kGlV~R~~~~~DrR~~~v~LT~~G~~~~ 125 (176)
T PRK10870 60 ALITLESQENHSIQPSELSCALGS--------------SRTNATRIADELEKRGWIERRESDNDRRCLHLQLTEKGHEFL 125 (176)
T ss_pred HHHHHhcCCCCCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHH
Confidence 45555532 34566677776642 3356667889999999999765 45777 999999999
Q ss_pred HHHHHHH
Q psy5605 121 DRIAAQI 127 (152)
Q Consensus 121 D~iA~~i 127 (152)
+++-...
T Consensus 126 ~~i~~~~ 132 (176)
T PRK10870 126 REVLPPQ 132 (176)
T ss_pred HHHHHHH
Confidence 9975443
No 26
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=95.36 E-value=0.12 Score=41.91 Aligned_cols=66 Identities=17% Similarity=0.119 Sum_probs=48.5
Q ss_pred HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceec--CCCCc----eeCcchHhhHH
Q psy5605 48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKS--DDGGR----KITSHGRRDMD 121 (152)
Q Consensus 48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~--~~gGR----~lT~~G~~~LD 121 (152)
.||-.||-.+++....|++..+- ..+-+-.+++.||+.|||+.. ++..| .||++|+..++
T Consensus 49 ~iL~~L~~~~~itq~eLa~~l~l--------------~~sTvtr~l~rLE~kGlI~R~~~~~DrR~~~I~LTekG~~l~~ 114 (185)
T PRK13777 49 HILWIAYHLKGASISEIAKFGVM--------------HVSTAFNFSKKLEERGYLTFSKKEDDKRNTYIELTEKGEELLL 114 (185)
T ss_pred HHHHHHHhCCCcCHHHHHHHHCC--------------CHhhHHHHHHHHHHCCCEEecCCCCCCCeeEEEECHHHHHHHH
Confidence 36667788888888999886432 123355689999999999965 43444 39999999999
Q ss_pred HHHHHH
Q psy5605 122 RIAAQI 127 (152)
Q Consensus 122 ~iA~~i 127 (152)
++...+
T Consensus 115 ~l~~~~ 120 (185)
T PRK13777 115 ETMEEY 120 (185)
T ss_pred HHHHHH
Confidence 876543
No 27
>PRK03911 heat-inducible transcription repressor; Provisional
Probab=95.30 E-value=0.025 Score=48.85 Aligned_cols=64 Identities=17% Similarity=0.350 Sum_probs=49.9
Q ss_pred HHHHHhh---Hhhc--CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC-CCCceeCcchHhh
Q psy5605 46 CAALARH---IYMR--SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD-DGGRKITSHGRRD 119 (152)
Q Consensus 46 aASilRk---iYl~--g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~-~gGR~lT~~G~~~ 119 (152)
--.||+. -|+. .|||-..|.+.|+- .-|.+-||+.++.||++|++++.. ..||.-|.+|-+.
T Consensus 5 ~~~IL~~iV~~Yi~t~~PVGSk~L~~~~~l------------~~SsATIRn~m~~LE~~G~L~qpHtSsGRIPT~~gyr~ 72 (260)
T PRK03911 5 KDLLLDSIIQTYLQDNEPIGSNELKSLMNL------------KISAATIRNYFKKLSDEGLLTQLHISGGRIPTIKAMKN 72 (260)
T ss_pred HHHHHHHHHHHHhccCCccCHHHHHHHcCC------------CCCcHHHHHHHHHHHHCcCccCCcCCCCcCCCHHHHHH
Confidence 3344443 4664 59999999998853 356689999999999999998765 4799999999864
Q ss_pred -HH
Q psy5605 120 -MD 121 (152)
Q Consensus 120 -LD 121 (152)
+|
T Consensus 73 Yvd 75 (260)
T PRK03911 73 YWQ 75 (260)
T ss_pred HHH
Confidence 44
No 28
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=95.25 E-value=0.17 Score=37.86 Aligned_cols=64 Identities=17% Similarity=0.187 Sum_probs=44.1
Q ss_pred HHhhHhhc-CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCc----eeCcchHhhHH
Q psy5605 49 LARHIYMR-SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGR----KITSHGRRDMD 121 (152)
Q Consensus 49 ilRkiYl~-g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR----~lT~~G~~~LD 121 (152)
+|..|+-. ++.....|+...|- +.+-+=.+++.||+.|||++.++ +.| .||++|+..++
T Consensus 36 vL~~l~~~~~~~t~~eLa~~l~~--------------~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~LT~~G~~~~~ 101 (144)
T PRK03573 36 TLHNIHQLPPEQSQIQLAKAIGI--------------EQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLIS 101 (144)
T ss_pred HHHHHHHcCCCCCHHHHHHHhCC--------------ChhhHHHHHHHHHHCCCEeeecCCCCcCeeeeEEChHHHHHHH
Confidence 44455543 34566677766543 23455688999999999997753 455 49999999998
Q ss_pred HHHHH
Q psy5605 122 RIAAQ 126 (152)
Q Consensus 122 ~iA~~ 126 (152)
.+...
T Consensus 102 ~~~~~ 106 (144)
T PRK03573 102 EVEAV 106 (144)
T ss_pred HHHHH
Confidence 76544
No 29
>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=95.19 E-value=0.081 Score=38.23 Aligned_cols=49 Identities=18% Similarity=0.277 Sum_probs=36.7
Q ss_pred cCCCchhHHHHHHHHHHhCCcceec--C-CCCc-----eeCcchHhhHHHHHHHHHH
Q psy5605 81 FCRSSGSVARKALQALEQVNIIEKS--D-DGGR-----KITSHGRRDMDRIAAQIRV 129 (152)
Q Consensus 81 ~~~asg~iiR~~LQqLE~~glVek~--~-~gGR-----~lT~~G~~~LD~iA~~i~~ 129 (152)
+..-+-+-+-.+|..||+.|||+.. + .+|| .||++|+..|+........
T Consensus 34 ~~~i~~gtlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~iT~~Gr~~l~~~~~~~~~ 90 (100)
T TIGR03433 34 VLQVEEGSLYPALHRLERRGWIAAEWGESENNRRAKFYRLTAAGRKQLAAETESWAR 90 (100)
T ss_pred ccccCCCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEECHHHHHHHHHHHHHHHH
Confidence 3344556688899999999999973 2 2232 5999999999998777643
No 30
>TIGR00331 hrcA heat shock gene repressor HrcA. In Bacillus subtilis, hrcA is the first gene of the dnaK operon and so is itself a heat shock gene.
Probab=95.18 E-value=0.044 Score=47.88 Aligned_cols=58 Identities=31% Similarity=0.444 Sum_probs=47.2
Q ss_pred hhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCC-CceeCcchHhh-HHHH
Q psy5605 54 YMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDG-GRKITSHGRRD-MDRI 123 (152)
Q Consensus 54 Yl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~g-GR~lT~~G~~~-LD~i 123 (152)
--.+|+|+..|.+.|+- .-|..-||+-+.+||+.|++++.-.+ ||.-|.+|-+. .|.+
T Consensus 17 ~~~~pv~s~~l~~~~~~------------~vS~aTiR~d~~~Le~~G~l~~~h~sagript~kGYR~yv~~~ 76 (337)
T TIGR00331 17 KTGQPVGSKTLLEKYNL------------GLSSATIRNDMADLEDLGFIEKPHTSSGRIPTDKGYRYYVDHL 76 (337)
T ss_pred hcCCCcCHHHHHhhcCC------------CCChHHHHHHHHHHHHCCCccCCCCCCCcCcChhHHHHHHHHh
Confidence 34689999999999743 45678999999999999999987654 99999998876 4443
No 31
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=94.78 E-value=0.056 Score=38.07 Aligned_cols=62 Identities=19% Similarity=0.350 Sum_probs=43.0
Q ss_pred hHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CC-----ceeCcchHhhHHHHH
Q psy5605 52 HIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GG-----RKITSHGRRDMDRIA 124 (152)
Q Consensus 52 kiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gG-----R~lT~~G~~~LD~iA 124 (152)
-++-.+.+-...|+..- .-+.+-+.+-|+.||++|+|+..+. ++ -.||++|+..+++.-
T Consensus 8 ~L~~~~~~~f~~L~~~l--------------~lt~g~Ls~hL~~Le~~GyV~~~k~~~~~~p~t~~~lT~~Gr~~~~~~~ 73 (80)
T PF13601_consen 8 LLYANEEATFSELKEEL--------------GLTDGNLSKHLKKLEEAGYVEVEKEFEGRRPRTWYSLTDKGREAFERYV 73 (80)
T ss_dssp HHHHHSEEEHHHHHHHT--------------T--HHHHHHHHHHHHHTTSEEEEEE-SSS--EEEEEE-HHHHHHHHHHH
T ss_pred HHhhcCCCCHHHHHHHh--------------CcCHHHHHHHHHHHHHCCCEEEEEeccCCCCeEEEEECHHHHHHHHHHH
Confidence 34445666666666664 4566788899999999999986542 33 269999999988876
Q ss_pred HHH
Q psy5605 125 AQI 127 (152)
Q Consensus 125 ~~i 127 (152)
..+
T Consensus 74 ~~L 76 (80)
T PF13601_consen 74 AAL 76 (80)
T ss_dssp HHH
T ss_pred HHH
Confidence 554
No 32
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=94.68 E-value=0.16 Score=38.33 Aligned_cols=57 Identities=18% Similarity=0.209 Sum_probs=43.0
Q ss_pred HhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHH
Q psy5605 53 IYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRI 123 (152)
Q Consensus 53 iYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~i 123 (152)
+.-.|++-+..|+...| -|.+-++..|+.||+.|||.....+|=.||++|+.....+
T Consensus 17 ~~~~~~~~~~ela~~l~--------------vs~~svs~~l~~L~~~Gli~~~~~~~i~LT~~G~~~a~~~ 73 (142)
T PRK03902 17 IEEKGYARVSDIAEALS--------------VHPSSVTKMVQKLDKDEYLIYEKYRGLVLTPKGKKIGKRL 73 (142)
T ss_pred HhcCCCcCHHHHHHHhC--------------CChhHHHHHHHHHHHCCCEEEecCceEEECHHHHHHHHHH
Confidence 33457777777777653 2345677778999999999976667899999999876655
No 33
>TIGR03338 phnR_burk phosphonate utilization associated transcriptional regulator. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Polaromonas, Burkholderia, Ralstonia and Verminephrobacter.
Probab=94.60 E-value=0.14 Score=40.20 Aligned_cols=65 Identities=15% Similarity=0.250 Sum_probs=47.9
Q ss_pred HHHHHHhhHhhcCC------cchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHh
Q psy5605 45 RCAALARHIYMRSP------VGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRR 118 (152)
Q Consensus 45 RaASilRkiYl~g~------vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~ 118 (152)
.++..+|..-+.|. +.-..|+..|| -|.+-+|.+|+.||..|||+..+..|-.+++-...
T Consensus 15 ~v~~~l~~~I~~g~l~pG~~L~e~~La~~lg--------------VSRtpVReAL~~L~~eGlv~~~~~~G~~V~~~~~~ 80 (212)
T TIGR03338 15 LVQDEIERAILSGELPPGAKLNESDIAARLG--------------VSRGPVREAFRALEEAGLVRNEKNRGVFVREISLA 80 (212)
T ss_pred HHHHHHHHHHHcCCCCCCCEecHHHHHHHhC--------------CChHHHHHHHHHHHHCCCEEEecCCCeEEecCCHH
Confidence 34445555544442 34456788874 57899999999999999999999889888887777
Q ss_pred hHHHH
Q psy5605 119 DMDRI 123 (152)
Q Consensus 119 ~LD~i 123 (152)
++..+
T Consensus 81 ~~~ei 85 (212)
T TIGR03338 81 EADEI 85 (212)
T ss_pred HHHHH
Confidence 66543
No 34
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=94.44 E-value=0.11 Score=45.56 Aligned_cols=59 Identities=34% Similarity=0.563 Sum_probs=46.8
Q ss_pred Hhh--cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC-CCceeCcchHhh-HHHH
Q psy5605 53 IYM--RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD-GGRKITSHGRRD-MDRI 123 (152)
Q Consensus 53 iYl--~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~-gGR~lT~~G~~~-LD~i 123 (152)
.|+ .+|+|+..|.+.|+= .-|..-||+-+..||++|++++.-. .||.-|.+|-+. +|.+
T Consensus 18 ~yi~~~~pv~s~~l~~~~~l------------~~S~aTIR~dm~~Le~~G~l~~~h~sagrIPT~kGYR~YVd~L 80 (339)
T PRK00082 18 DYIATGEPVGSKTLSKRYGL------------GVSSATIRNDMADLEELGLLEKPHTSSGRIPTDKGYRYFVDHL 80 (339)
T ss_pred HHHhcCCCcCHHHHHHHhCC------------CCChHHHHHHHHHHHhCCCcCCCcCCCCCCcCHHHHHHHHHHh
Confidence 354 589999999988632 3456889999999999999997654 599999999764 4444
No 35
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=94.02 E-value=0.083 Score=39.38 Aligned_cols=42 Identities=24% Similarity=0.359 Sum_probs=34.1
Q ss_pred CCCchhHHHHHHHHHHhCCcceecCCC---CceeCcchHhhHHHH
Q psy5605 82 CRSSGSVARKALQALEQVNIIEKSDDG---GRKITSHGRRDMDRI 123 (152)
Q Consensus 82 ~~asg~iiR~~LQqLE~~glVek~~~g---GR~lT~~G~~~LD~i 123 (152)
+.=+=.+++++++.|++.|++++.+++ .-.||++|.++|.++
T Consensus 41 aNlny~~~~~yi~~L~~~Gli~~~~~~~~~~y~lT~KG~~fle~y 85 (95)
T COG3432 41 ANLNYKRAQKYIEMLVEKGLIIKQDNGRRKVYELTEKGKRFLEKY 85 (95)
T ss_pred cCcCHHHHHHHHHHHHhCCCEEeccCCccceEEEChhHHHHHHHH
Confidence 444558999999999999998888754 357999999997654
No 36
>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=93.93 E-value=0.14 Score=32.70 Aligned_cols=49 Identities=16% Similarity=0.323 Sum_probs=40.4
Q ss_pred HHHHHHHhhHhhc-CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC
Q psy5605 44 TRCAALARHIYMR-SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD 106 (152)
Q Consensus 44 iRaASilRkiYl~-g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~ 106 (152)
-|+.+||+.|.-. +++++..+...-| =+.+-+..+|+.|++.|||++++
T Consensus 3 ~ral~iL~~l~~~~~~~t~~eia~~~g--------------l~~stv~r~L~tL~~~g~v~~dp 52 (52)
T PF09339_consen 3 ERALRILEALAESGGPLTLSEIARALG--------------LPKSTVHRLLQTLVEEGYVERDP 52 (52)
T ss_dssp HHHHHHHHCHHCTBSCEEHHHHHHHHT--------------S-HHHHHHHHHHHHHTTSEEECS
T ss_pred HHHHHHHHHHHcCCCCCCHHHHHHHHC--------------cCHHHHHHHHHHHHHCcCeecCc
Confidence 4888999988865 4589999999865 34578999999999999999875
No 37
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=93.88 E-value=0.47 Score=39.28 Aligned_cols=66 Identities=15% Similarity=0.217 Sum_probs=52.6
Q ss_pred HHHHHHHhhHhhcC-CcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC-CCceeCcchHhhHH
Q psy5605 44 TRCAALARHIYMRS-PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD-GGRKITSHGRRDMD 121 (152)
Q Consensus 44 iRaASilRkiYl~g-~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~-gGR~lT~~G~~~LD 121 (152)
-|+..||+.|.-.+ ++++..|.+..| -+.+-+..+|+.|++.|||+++++ +...||++..+.-.
T Consensus 11 ~ral~iL~~l~~~~~~ls~~eia~~lg--------------l~kstv~RlL~tL~~~g~v~~~~~~~~Y~Lg~~~~~l~~ 76 (263)
T PRK09834 11 SRGLMVLRALNRLDGGATVGLLAELTG--------------LHRTTVRRLLETLQEEGYVRRSASDDSFRLTLKVRQLSE 76 (263)
T ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCEEEecCCCcEEEcHHHHHHHH
Confidence 38889999887654 599999999974 345789999999999999999864 56789988876544
Q ss_pred HH
Q psy5605 122 RI 123 (152)
Q Consensus 122 ~i 123 (152)
.+
T Consensus 77 ~~ 78 (263)
T PRK09834 77 GF 78 (263)
T ss_pred hh
Confidence 43
No 38
>PF14338 Mrr_N: Mrr N-terminal domain
Probab=93.72 E-value=0.081 Score=37.58 Aligned_cols=37 Identities=27% Similarity=0.373 Sum_probs=31.9
Q ss_pred chhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHH
Q psy5605 85 SGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMD 121 (152)
Q Consensus 85 sg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD 121 (152)
.-+-++.+++.|.++|+|++...|--.||+.|++.|-
T Consensus 53 ~~~ri~Wa~~~L~~aGli~~~~rG~~~iT~~G~~~l~ 89 (92)
T PF14338_consen 53 FKNRIRWARSYLKKAGLIERPKRGIWRITEKGRKALA 89 (92)
T ss_pred HHHhHHHHHHHHHHCCCccCCCCCceEECHhHHHHHh
Confidence 3457899999999999999877667999999999874
No 39
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=93.69 E-value=0.27 Score=39.17 Aligned_cols=50 Identities=24% Similarity=0.296 Sum_probs=38.6
Q ss_pred chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHH
Q psy5605 60 GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRI 123 (152)
Q Consensus 60 GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~i 123 (152)
-...|+..|| -|..-+|.+|+.||..|||+..+..|-.+++-...++..+
T Consensus 36 ~e~~La~~lg--------------VSRtpVREAL~~L~~eGLV~~~~~~g~~v~~~~~~~~~ei 85 (221)
T PRK11414 36 ITKNLAEQLG--------------MSITPVREALLRLVSVNALSVAPAQAFTVPEVSKRQLDEI 85 (221)
T ss_pred CHHHHHHHHC--------------CCchhHHHHHHHHHHCCCEEecCCCceeecCCCHHHHHHH
Confidence 3456778774 5778999999999999999999877877766655555443
No 40
>PRK05638 threonine synthase; Validated
Probab=93.40 E-value=0.24 Score=44.22 Aligned_cols=75 Identities=17% Similarity=0.245 Sum_probs=54.1
Q ss_pred CcCCCCCCCchHHHHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCc
Q psy5605 31 FKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGR 110 (152)
Q Consensus 31 ~KElaP~d~DW~YiRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR 110 (152)
+||.-+.++.+. .||+.|. +++.-+..|.+..+. .-|.+.++..|+.||+.|||+.....||
T Consensus 363 ~~~~~~~~~~r~-----~IL~~L~-~~~~~~~el~~~l~~------------~~s~~~v~~hL~~Le~~GLV~~~~~~g~ 424 (442)
T PRK05638 363 GREKFTIGGTKL-----EILKILS-EREMYGYEIWKALGK------------PLKYQAVYQHIKELEELGLIEEAYRKGR 424 (442)
T ss_pred chhhhcccchHH-----HHHHHHh-hCCccHHHHHHHHcc------------cCCcchHHHHHHHHHHCCCEEEeecCCC
Confidence 344444555544 4666554 678889999998863 1477899999999999999986422344
Q ss_pred e----eCcchHhhHHHH
Q psy5605 111 K----ITSHGRRDMDRI 123 (152)
Q Consensus 111 ~----lT~~G~~~LD~i 123 (152)
+ ||++|+..+..+
T Consensus 425 ~~~Y~Lt~~g~~~l~~~ 441 (442)
T PRK05638 425 RVYYKLTEKGRRLLENL 441 (442)
T ss_pred cEEEEECcHHHHHHHhc
Confidence 3 999999998764
No 41
>TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor. Members of this family are transcriptional regulatory proteins found in the vicinity of poly-beta-hydroxybutyrate (PHB) operons in several species of Bacillus. This protein appears to have repressor activity modulated by PHB itself. This protein belongs to the larger PadR family (see pfam03551).
Probab=93.24 E-value=0.33 Score=38.03 Aligned_cols=45 Identities=20% Similarity=0.304 Sum_probs=34.8
Q ss_pred CchhHHHHHHHHHHhCCcceec---CCCCc-----eeCcchHhhHHHHHHHHH
Q psy5605 84 SSGSVARKALQALEQVNIIEKS---DDGGR-----KITSHGRRDMDRIAAQIR 128 (152)
Q Consensus 84 asg~iiR~~LQqLE~~glVek~---~~gGR-----~lT~~G~~~LD~iA~~i~ 128 (152)
.+-+-+=.+|+.||+.|||+.. ..+|| .||+.|++.|+....+..
T Consensus 55 v~~GtLYp~L~RLE~~GlI~~~~~~~~~gp~RK~Y~LTe~Gr~~L~~~~~~w~ 107 (138)
T TIGR02719 55 VDQGNVYRTLRKLEKDNLISSQWDTSAEGPAKRIYSLTDAGEQYLSMCANSFE 107 (138)
T ss_pred CCcChHHHHHHHHHHCCCEEEEeeecCCCCCcEEEEECHHHHHHHHHHHHHHH
Confidence 4456677899999999999863 22354 499999999999887753
No 42
>PF10711 DUF2513: Hypothetical protein (DUF2513); InterPro: IPR019650 The function of this family is not known.
Probab=93.23 E-value=0.16 Score=37.03 Aligned_cols=50 Identities=24% Similarity=0.291 Sum_probs=40.2
Q ss_pred CCCccCCCchhHHHHHHHHHHhCCcceecCCC---C------ceeCcchHhhHHHHHHH
Q psy5605 77 CPSHFCRSSGSVARKALQALEQVNIIEKSDDG---G------RKITSHGRRDMDRIAAQ 126 (152)
Q Consensus 77 ~P~h~~~asg~iiR~~LQqLE~~glVek~~~g---G------R~lT~~G~~~LD~iA~~ 126 (152)
.+..+..-+-.-+-+-+++|.++|+|+-.... | ..||.+|..+||.|=.+
T Consensus 25 ~~~~~~~y~~~~i~YHl~lL~eagli~~~~~~~~~~~~~~~i~~LT~~GHdFLd~IRd~ 83 (102)
T PF10711_consen 25 EEDEIDGYSKEEIAYHLKLLDEAGLIEGSVSGTMNGPYSFIIKRLTWSGHDFLDAIRDD 83 (102)
T ss_pred chhcccCCCHHHHHHHHHHHHHCCCeeeccccccCCccchhhcccChhHHHHHHHhcCc
Confidence 45556667777999999999999999976532 2 48999999999998655
No 43
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=92.82 E-value=0.25 Score=40.05 Aligned_cols=45 Identities=24% Similarity=0.316 Sum_probs=36.2
Q ss_pred chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHh
Q psy5605 60 GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRR 118 (152)
Q Consensus 60 GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~ 118 (152)
.-..|+..|| -|...+|.+|+.||..|||+..+..|-.+++-...
T Consensus 33 sE~eLa~~~g--------------VSRtpVREAL~~L~~eGlV~~~~~~G~~V~~~~~~ 77 (251)
T PRK09990 33 SERRLCEKLG--------------FSRSALREGLTVLRGRGIIETAQGRGSFVARLNRV 77 (251)
T ss_pred CHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEeCCCeeEEecCCcc
Confidence 4457777774 58899999999999999999999878777765443
No 44
>COG1693 Repressor of nif and glnA expression [Transcription]
Probab=92.81 E-value=0.11 Score=45.94 Aligned_cols=70 Identities=23% Similarity=0.425 Sum_probs=52.1
Q ss_pred HHhhHhhc-CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHH--HHH
Q psy5605 49 LARHIYMR-SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDR--IAA 125 (152)
Q Consensus 49 ilRkiYl~-g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~--iA~ 125 (152)
|||=|-=. .|+|-......-- +||+. =+---+|+=||-||+.|+++|+--.||.||++|-+.|.+ +..
T Consensus 11 Il~il~esd~plgak~Ia~el~---kRGy~------igeRavRYhlk~lderglt~kvgyagr~iTe~Gl~el~~~~~~~ 81 (325)
T COG1693 11 ILRILAESDEPLGAKIIALELR---KRGYN------IGERAVRYHLKKLDERGLTRKVGYAGREITEKGLKELKRALISE 81 (325)
T ss_pred HHHHHHhcCCccchHHHHHHHH---hcccc------hhHHHHHHHHHHHhhccchhhccccceeehHhhHHHHhhhhhHH
Confidence 45555543 4888887776652 22543 233468999999999999999988899999999999998 555
Q ss_pred HH
Q psy5605 126 QI 127 (152)
Q Consensus 126 ~i 127 (152)
++
T Consensus 82 R~ 83 (325)
T COG1693 82 RL 83 (325)
T ss_pred HH
Confidence 54
No 45
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=92.71 E-value=0.18 Score=39.75 Aligned_cols=53 Identities=21% Similarity=0.359 Sum_probs=42.7
Q ss_pred cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHH
Q psy5605 56 RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDR 122 (152)
Q Consensus 56 ~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~ 122 (152)
.|++.++.++..-+ +. .+-+-..|+.|++.|||+..+.+|=.||++|.+..-.
T Consensus 22 ~~~~~~~diA~~L~------Vs--------p~sVt~ml~rL~~~GlV~~~~y~gi~LT~~G~~~a~~ 74 (154)
T COG1321 22 KGFARTKDIAERLK------VS--------PPSVTEMLKRLERLGLVEYEPYGGVTLTEKGREKAKE 74 (154)
T ss_pred cCcccHHHHHHHhC------CC--------cHHHHHHHHHHHHCCCeEEecCCCeEEChhhHHHHHH
Confidence 57788888888752 33 3567788999999999999999999999999865443
No 46
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=92.64 E-value=0.48 Score=37.71 Aligned_cols=50 Identities=14% Similarity=0.232 Sum_probs=39.4
Q ss_pred cchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHH
Q psy5605 59 VGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDR 122 (152)
Q Consensus 59 vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~ 122 (152)
+....|+..|| -|..-+|.+|+.||..|+|+..+..|-.+++-...++..
T Consensus 31 L~e~eLae~lg--------------VSRtpVREAL~~L~~eGlv~~~~~~G~~V~~~~~~~~~e 80 (224)
T PRK11534 31 LRMSLLTSRYA--------------LGVGPLREALSQLVAERLVTVVNQKGYRVASMSEQELLD 80 (224)
T ss_pred CCHHHHHHHHC--------------CChHHHHHHHHHHHHCCCEEEeCCCceEeCCCCHHHHHH
Confidence 34567777774 467899999999999999999998887887766665544
No 47
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=92.59 E-value=0.39 Score=33.30 Aligned_cols=45 Identities=36% Similarity=0.527 Sum_probs=35.1
Q ss_pred CcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCceeCcch
Q psy5605 58 PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGRKITSHG 116 (152)
Q Consensus 58 ~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR~lT~~G 116 (152)
++.+..++..+| -+-..+|+++++|++.|+|+..+ .||-.|+..-
T Consensus 25 ~~s~~eiA~~~~--------------i~~~~l~kil~~L~~~Gli~s~~G~~GGy~L~~~~ 71 (83)
T PF02082_consen 25 PVSSKEIAERLG--------------ISPSYLRKILQKLKKAGLIESSRGRGGGYRLARPP 71 (83)
T ss_dssp -BEHHHHHHHHT--------------S-HHHHHHHHHHHHHTTSEEEETSTTSEEEESS-C
T ss_pred CCCHHHHHHHHC--------------cCHHHHHHHHHHHhhCCeeEecCCCCCceeecCCH
Confidence 488999999874 46689999999999999999665 4788887643
No 48
>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=92.53 E-value=0.1 Score=35.41 Aligned_cols=41 Identities=32% Similarity=0.475 Sum_probs=32.2
Q ss_pred cCCCchhHHHHHHHHHHhCCcceecCC---CC-----ceeCcchHhhHH
Q psy5605 81 FCRSSGSVARKALQALEQVNIIEKSDD---GG-----RKITSHGRRDMD 121 (152)
Q Consensus 81 ~~~asg~iiR~~LQqLE~~glVek~~~---gG-----R~lT~~G~~~LD 121 (152)
+..-|-+-+=.+|+.||+.|||+.... +| -.||++|+..|.
T Consensus 26 ~~~i~~g~lY~~L~~Le~~gli~~~~~~~~~~~~rk~Y~iT~~G~~~l~ 74 (75)
T PF03551_consen 26 FWKISPGSLYPALKRLEEEGLIESRWEEEGNGRPRKYYRITEKGREELR 74 (75)
T ss_dssp TEETTHHHHHHHHHHHHHTTSEEEEEEEETTSSEEEEEEESHHHHHHHH
T ss_pred CcccChhHHHHHHHHHHhCCCEEEeeeccCCCCCCEEEEECHHHHHHhc
Confidence 345667888999999999999985542 22 469999999876
No 49
>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=92.24 E-value=0.19 Score=31.91 Aligned_cols=39 Identities=23% Similarity=0.419 Sum_probs=31.0
Q ss_pred hhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeC
Q psy5605 61 VKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKIT 113 (152)
Q Consensus 61 V~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT 113 (152)
+..|+..|| -|..-++++|+.|++.|+|+..++.|-.||
T Consensus 28 ~~~la~~~~--------------is~~~v~~~l~~L~~~G~i~~~~~~~~~l~ 66 (66)
T cd07377 28 ERELAEELG--------------VSRTTVREALRELEAEGLVERRPGRGTFVA 66 (66)
T ss_pred HHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEecCCCeEEeC
Confidence 667777763 467899999999999999998776666664
No 50
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=92.02 E-value=0.49 Score=30.15 Aligned_cols=51 Identities=22% Similarity=0.359 Sum_probs=40.0
Q ss_pred HHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCce
Q psy5605 47 AALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGRK 111 (152)
Q Consensus 47 ASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR~ 111 (152)
..+|..||-.|++.+..|....+- +.+-+-.++++||+.|||++.. +..|.
T Consensus 6 ~~iL~~l~~~~~~~~~~la~~~~~--------------~~~~~t~~i~~L~~~g~I~r~~~~~D~R~ 58 (59)
T PF01047_consen 6 FRILRILYENGGITQSELAEKLGI--------------SRSTVTRIIKRLEKKGLIERERDPDDRRQ 58 (59)
T ss_dssp HHHHHHHHHHSSEEHHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEEEEETTETTS
T ss_pred HHHHHHHHHcCCCCHHHHHHHHCC--------------ChhHHHHHHHHHHHCCCEEeccCCCCCCc
Confidence 357888999999999999998744 5567778899999999998664 33453
No 51
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=91.99 E-value=0.48 Score=29.38 Aligned_cols=36 Identities=19% Similarity=0.356 Sum_probs=28.7
Q ss_pred chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCC
Q psy5605 60 GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGG 109 (152)
Q Consensus 60 GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gG 109 (152)
.+..|+..| .-|.+-+|.+|++|++.|+|+..+++|
T Consensus 22 s~~~la~~~--------------~vs~~tv~~~l~~L~~~g~i~~~~~~g 57 (60)
T smart00345 22 SERELAAQL--------------GVSRTTVREALSRLEAEGLVQRRPGSG 57 (60)
T ss_pred CHHHHHHHH--------------CCCHHHHHHHHHHHHHCCCEEEecCCe
Confidence 566677776 346789999999999999999877544
No 52
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=91.98 E-value=0.42 Score=31.28 Aligned_cols=47 Identities=23% Similarity=0.344 Sum_probs=39.3
Q ss_pred HHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC
Q psy5605 47 AALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD 107 (152)
Q Consensus 47 ASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~ 107 (152)
..|++.|-..+|..++.|....| -+.+-+.+=|+.||++|+|+....
T Consensus 13 ~~Il~~L~~~~~~t~~ela~~l~--------------~~~~t~s~hL~~L~~aGli~~~~~ 59 (61)
T PF12840_consen 13 LRILRLLASNGPMTVSELAEELG--------------ISQSTVSYHLKKLEEAGLIEVERE 59 (61)
T ss_dssp HHHHHHHHHCSTBEHHHHHHHHT--------------S-HHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHHHHHHhcCCCCCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCeEEecc
Confidence 35888887899999999999986 345678899999999999998763
No 53
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=91.95 E-value=0.65 Score=37.26 Aligned_cols=64 Identities=16% Similarity=0.217 Sum_probs=51.7
Q ss_pred HHHHHHhhHhhcC------CcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHh
Q psy5605 45 RCAALARHIYMRS------PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRR 118 (152)
Q Consensus 45 RaASilRkiYl~g------~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~ 118 (152)
.+...+|.-=+.| .+....|+..||- |..-+|.+|+.|+..|+|+..+..|-.+++-..+
T Consensus 20 ~vy~~Lr~~Il~g~l~pG~~l~e~~La~~~gv--------------SrtPVReAL~rL~~eGlv~~~p~rG~~V~~~~~~ 85 (230)
T COG1802 20 QVYEELREAILSGELAPGERLSEEELAEELGV--------------SRTPVREALRRLEAEGLVEIEPNRGAFVAPLSLA 85 (230)
T ss_pred HHHHHHHHHHHhCCCCCCCCccHHHHHHHhCC--------------CCccHHHHHHHHHHCCCeEecCCCCCeeCCCCHH
Confidence 4445555555544 5778889999964 6678999999999999999999889999999888
Q ss_pred hHHH
Q psy5605 119 DMDR 122 (152)
Q Consensus 119 ~LD~ 122 (152)
+++.
T Consensus 86 ~~~e 89 (230)
T COG1802 86 EARE 89 (230)
T ss_pred HHHH
Confidence 8887
No 54
>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=91.80 E-value=0.53 Score=37.67 Aligned_cols=55 Identities=22% Similarity=0.295 Sum_probs=44.3
Q ss_pred HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCC--CceeCcch
Q psy5605 48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDG--GRKITSHG 116 (152)
Q Consensus 48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~g--GR~lT~~G 116 (152)
.|+..+.-+|++.+..+....|- |.+-+++.|+.||+.|||+..++. .-.||++|
T Consensus 147 ~IL~~l~~~g~~s~~eia~~l~i--------------s~stv~r~L~~Le~~GlI~r~~~r~~~~~lT~~G 203 (203)
T TIGR01884 147 KVLEVLKAEGEKSVKNIAKKLGK--------------SLSTISRHLRELEKKGLVEQKGRKGKRYSLTKLG 203 (203)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEEcCCccEEEeCCCC
Confidence 67877777789999999999853 456889999999999999988632 34578876
No 55
>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=91.71 E-value=0.78 Score=30.20 Aligned_cols=37 Identities=24% Similarity=0.407 Sum_probs=29.7
Q ss_pred chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCc
Q psy5605 60 GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGR 110 (152)
Q Consensus 60 GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR 110 (152)
....|...| .-|...+|.+|+.|++.|+|+..+..|-
T Consensus 26 s~~~la~~~--------------~vsr~tvr~al~~L~~~g~i~~~~~~G~ 62 (64)
T PF00392_consen 26 SERELAERY--------------GVSRTTVREALRRLEAEGLIERRPGRGT 62 (64)
T ss_dssp -HHHHHHHH--------------TS-HHHHHHHHHHHHHTTSEEEETTTEE
T ss_pred CHHHHHHHh--------------ccCCcHHHHHHHHHHHCCcEEEECCceE
Confidence 667788887 4688999999999999999999886553
No 56
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=91.58 E-value=0.34 Score=38.88 Aligned_cols=42 Identities=14% Similarity=0.281 Sum_probs=35.5
Q ss_pred chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcc
Q psy5605 60 GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSH 115 (152)
Q Consensus 60 GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~ 115 (152)
.-..|+..|| -|..-+|.+|+.||..|+|+..+..|-.+++-
T Consensus 32 sE~~La~~lg--------------VSRtpVREAL~~Le~eGlV~~~~~~G~~V~~~ 73 (235)
T TIGR02812 32 AERELSELIG--------------VTRTTLREVLQRLARDGWLTIQHGKPTKVNNF 73 (235)
T ss_pred CHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCEEEeCCCccEecCc
Confidence 4557777774 57899999999999999999999888888773
No 57
>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=91.48 E-value=1 Score=28.14 Aligned_cols=61 Identities=18% Similarity=0.271 Sum_probs=45.0
Q ss_pred HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC---CCceeCcchHhhHHHHH
Q psy5605 48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD---GGRKITSHGRRDMDRIA 124 (152)
Q Consensus 48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~---gGR~lT~~G~~~LD~iA 124 (152)
.|+..++-.+ +....+.+..| -+.+-++..|.+|++.|+|..... .-..+|+ |+..++.+.
T Consensus 11 ~il~~l~~~~-~~~~ei~~~~~--------------i~~~~i~~~l~~L~~~g~i~~~~~~~~~~~~~~~-g~~~~~~~~ 74 (78)
T cd00090 11 RILRLLLEGP-LTVSELAERLG--------------LSQSTVSRHLKKLEEAGLVESRREGRRVYYSLTD-AERLLALLE 74 (78)
T ss_pred HHHHHHHHCC-cCHHHHHHHHC--------------cCHhHHHHHHHHHHHCCCeEEEEeccEEEEEeCC-chHHHHHHH
Confidence 3565566555 88888888763 345778999999999999986553 2357898 888777654
No 58
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=91.39 E-value=0.53 Score=38.35 Aligned_cols=59 Identities=17% Similarity=0.334 Sum_probs=43.0
Q ss_pred HHHHHHhhHhhcC------Cc-chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchH
Q psy5605 45 RCAALARHIYMRS------PV-GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGR 117 (152)
Q Consensus 45 RaASilRkiYl~g------~v-GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~ 117 (152)
..+..+|.-=+.| .+ ....|+..|| -|..-+|.+|+.||..|||+..+..|-.+++...
T Consensus 13 ~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~~g--------------VSRtpVREAL~~L~~eGlV~~~~~~G~~V~~~~~ 78 (257)
T PRK10225 13 EVGAMIRDLIIKTPYNPGERLPPEREIAEMLD--------------VTRTVVREALIMLEIKGLVEVRRGAGIYVLDSSG 78 (257)
T ss_pred HHHHHHHHHHHhCCCCCCCcCcCHHHHHHHhC--------------CCHHHHHHHHHHHHHCCCEEEecCCEEEEeCCCc
Confidence 4444455554554 24 3567888884 5789999999999999999999977877766543
No 59
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=91.36 E-value=1.1 Score=33.23 Aligned_cols=68 Identities=13% Similarity=0.253 Sum_probs=46.6
Q ss_pred HHHHHhhHhhc--CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCceeCcch-HhhH
Q psy5605 46 CAALARHIYMR--SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGRKITSHG-RRDM 120 (152)
Q Consensus 46 aASilRkiYl~--g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR~lT~~G-~~~L 120 (152)
|-.++..+... +++.+..|+..+| -|.+.++++|+.|++.|+|+... ++|..|.... +-.+
T Consensus 11 al~~l~~la~~~~~~~s~~eia~~l~--------------is~~~v~~~l~~L~~~Gli~~~~g~~ggy~l~~~~~~it~ 76 (130)
T TIGR02944 11 ATLVLTTLAQNDSQPYSAAEIAEQTG--------------LNAPTVSKILKQLSLAGIVTSKRGVEGGYTLARAPRDITV 76 (130)
T ss_pred HHHHHHHHHhCCCCCccHHHHHHHHC--------------cCHHHHHHHHHHHHHCCcEEecCCCCCChhhcCCccccCH
Confidence 34455555543 4688888888874 56789999999999999998653 5677776644 2224
Q ss_pred HHHHHHH
Q psy5605 121 DRIAAQI 127 (152)
Q Consensus 121 D~iA~~i 127 (152)
++|...+
T Consensus 77 ~~v~~~l 83 (130)
T TIGR02944 77 ADIVKAV 83 (130)
T ss_pred HHHHHHH
Confidence 4444443
No 60
>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=91.33 E-value=0.7 Score=29.45 Aligned_cols=47 Identities=15% Similarity=0.217 Sum_probs=38.2
Q ss_pred HHHHhhHhhcCC--cchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC
Q psy5605 47 AALARHIYMRSP--VGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD 107 (152)
Q Consensus 47 ASilRkiYl~g~--vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~ 107 (152)
..||..|+-.++ +.+..|+...|- +.+-+-.+++.||+.|||++.++
T Consensus 8 ~~vL~~l~~~~~~~~t~~~la~~l~~--------------~~~~vs~~v~~L~~~Glv~r~~~ 56 (62)
T PF12802_consen 8 FRVLMALARHPGEELTQSELAERLGI--------------SKSTVSRIVKRLEKKGLVERERD 56 (62)
T ss_dssp HHHHHHHHHSTTSGEEHHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEEEE-
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEeCC
Confidence 368889999988 899999998743 44677889999999999997764
No 61
>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=91.29 E-value=2 Score=32.29 Aligned_cols=78 Identities=17% Similarity=0.158 Sum_probs=57.5
Q ss_pred HHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHH
Q psy5605 45 RCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIA 124 (152)
Q Consensus 45 RaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA 124 (152)
.+++|+-.+|-+.=+..+.++..- +...+-..+-+=.+-|-+-|||||+-| |-++|..|+..+-++|
T Consensus 17 ~~~~ilI~v~Kk~Fit~~ev~e~l------------~~~~~~~~V~SNIGvLIKkglIEKSGD-Glv~T~~g~~Ii~~AA 83 (96)
T PF09114_consen 17 NAANILIQVAKKNFITASEVREAL------------ATEMNKASVNSNIGVLIKKGLIEKSGD-GLVITEEGMDIIIQAA 83 (96)
T ss_dssp HHHHHHHHHHHSTTB-HHHHHH-T-------------TTS-HHHHHHHHHHHHHTTSEEEETT-EEEE-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHHccCCHHHHHHHH------------HHHhhhhHHHHhHHHHHHcCcccccCC-ceEEechHHHHHHHHH
Confidence 578888888888777777777643 123455666666799999999999996 7999999999999988
Q ss_pred HHHHHHHHHHH
Q psy5605 125 AQIRVSKKEAA 135 (152)
Q Consensus 125 ~~i~~~~~~~~ 135 (152)
.--..+..++.
T Consensus 84 ~l~a~en~pel 94 (96)
T PF09114_consen 84 ELWAQENAPEL 94 (96)
T ss_dssp HHHHHHTHHHH
T ss_pred HHHHhcCChhh
Confidence 77666665543
No 62
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=91.23 E-value=0.57 Score=38.14 Aligned_cols=33 Identities=24% Similarity=0.244 Sum_probs=28.8
Q ss_pred CCchhHHHHHHHHHHhCCcceecCCCCceeCcc
Q psy5605 83 RSSGSVARKALQALEQVNIIEKSDDGGRKITSH 115 (152)
Q Consensus 83 ~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~ 115 (152)
.-|..-+|.+|+.||..|||+..+.+|-.+++-
T Consensus 37 gVSRtpVREAL~~Le~~GlV~~~~~~G~~V~~~ 69 (253)
T PRK10421 37 GVSRNSLREALAKLVSEGVLLSRRGGGTFIRWR 69 (253)
T ss_pred CCCHHHHHHHHHHHHHCCCEEEeCCCeEEEecC
Confidence 358899999999999999999988778887764
No 63
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=91.13 E-value=0.87 Score=37.38 Aligned_cols=58 Identities=10% Similarity=0.182 Sum_probs=46.4
Q ss_pred HHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC-CCceeCcc
Q psy5605 44 TRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD-GGRKITSH 115 (152)
Q Consensus 44 iRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~-gGR~lT~~ 115 (152)
-|+-.||..|.-.+++++..|++.-| -+.+-+..+|+.|++.|||+.++. +...|+++
T Consensus 14 ~r~l~IL~~l~~~~~l~l~eia~~lg--------------l~kstv~Rll~tL~~~G~l~~~~~~~~Y~lG~~ 72 (257)
T PRK15090 14 LKVFGILQALGEEREIGITELSQRVM--------------MSKSTVYRFLQTMKTLGYVAQEGESEKYSLTLK 72 (257)
T ss_pred HHHHHHHHHhhcCCCCCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCEEEcCCCCcEEecHH
Confidence 38889999988778899999999864 345788999999999999998864 44555544
No 64
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=90.50 E-value=0.45 Score=38.72 Aligned_cols=33 Identities=27% Similarity=0.342 Sum_probs=28.1
Q ss_pred CchhHHHHHHHHHHhCCcceecCCCCceeCcch
Q psy5605 84 SSGSVARKALQALEQVNIIEKSDDGGRKITSHG 116 (152)
Q Consensus 84 asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G 116 (152)
-|..-+|.+|+.||..|+|+..+..|-.+++--
T Consensus 44 VSRtpVREAL~~L~~eGlV~~~~~~G~~V~~~~ 76 (253)
T PRK11523 44 VSRTVVREAIIMLEVEGYVEVRKGSGIHVVSNQ 76 (253)
T ss_pred CCHHHHHHHHHHHHHCCCEEEecCCeeEEecCC
Confidence 578999999999999999999987776666543
No 65
>TIGR02277 PaaX_trns_reg phenylacetic acid degradation operon negative regulatory protein PaaX. This transcriptional regulator is always found in association with operons believed to be involved in the degradation of phenylacetic acid. The gene product has been shown to bind to the promoter sites and repress their transcription.
Probab=90.15 E-value=0.36 Score=41.24 Aligned_cols=45 Identities=20% Similarity=0.254 Sum_probs=38.2
Q ss_pred CchhHHHHHHHHHHhCCcceecCC---CCceeCcchHhhHHHHHHHHH
Q psy5605 84 SSGSVARKALQALEQVNIIEKSDD---GGRKITSHGRRDMDRIAAQIR 128 (152)
Q Consensus 84 asg~iiR~~LQqLE~~glVek~~~---gGR~lT~~G~~~LD~iA~~i~ 128 (152)
=+...+|.+|.-|++.|||+.... +...||++|++.++..+..|.
T Consensus 32 i~~~~vr~al~RL~~~G~l~~~~~grr~~Y~LT~~g~~~l~~~~~rIy 79 (280)
T TIGR02277 32 INERLVRTAVSRLVAQGWLQSERKGRRSFYSLTDKGRRRFAAAAQRIY 79 (280)
T ss_pred CCcchHHHHHHHHHHCCCEEeeecCCCCEEEECHHHHHHHHHHhhhhc
Confidence 355789999999999999997654 467899999999999887764
No 66
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=90.04 E-value=0.96 Score=34.24 Aligned_cols=43 Identities=19% Similarity=0.368 Sum_probs=34.3
Q ss_pred CcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCceeCc
Q psy5605 58 PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGRKITS 114 (152)
Q Consensus 58 ~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR~lT~ 114 (152)
++.+..|+..+| -|...+|++|++|++.|||+..++ ||-.|+.
T Consensus 25 ~~s~~~ia~~~~--------------is~~~vrk~l~~L~~~Glv~s~~G~~GG~~l~~ 69 (141)
T PRK11014 25 MTSISEVTEVYG--------------VSRNHMVKIINQLSRAGYVTAVRGKNGGIRLGK 69 (141)
T ss_pred ccCHHHHHHHHC--------------cCHHHHHHHHHHHHhCCEEEEecCCCCCeeecC
Confidence 567788888874 467899999999999999997774 4656664
No 67
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=89.92 E-value=0.9 Score=36.41 Aligned_cols=41 Identities=15% Similarity=0.289 Sum_probs=34.1
Q ss_pred chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCc
Q psy5605 60 GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITS 114 (152)
Q Consensus 60 GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~ 114 (152)
.-..|+..|| -|.+-+|.+|+.||..|+|+..+..|-.+++
T Consensus 33 sE~eLae~~g--------------VSRt~VReAL~~L~~eGlv~~~~g~G~~V~~ 73 (239)
T PRK04984 33 AERELSELIG--------------VTRTTLREVLQRLARDGWLTIQHGKPTKVNN 73 (239)
T ss_pred CHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEeCCCeeEeCC
Confidence 3456777774 6889999999999999999999987877765
No 68
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=89.87 E-value=2.4 Score=31.04 Aligned_cols=48 Identities=27% Similarity=0.437 Sum_probs=37.8
Q ss_pred CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceec--CCCCceeCcchHh
Q psy5605 57 SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKS--DDGGRKITSHGRR 118 (152)
Q Consensus 57 g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~--~~gGR~lT~~G~~ 118 (152)
+|+.+..|+..+| -+.+.+|++|+.|++.|||... ..||-.|+.....
T Consensus 24 ~~~s~~eia~~~~--------------i~~~~v~~il~~L~~~gli~~~~g~~ggy~l~~~~~~ 73 (132)
T TIGR00738 24 GPVSVKEIAERQG--------------ISRSYLEKILRTLRRAGLVESVRGPGGGYRLARPPEE 73 (132)
T ss_pred CcCcHHHHHHHHC--------------cCHHHHHHHHHHHHHCCcEEeccCCCCCccCCCCHHH
Confidence 4788889988874 4678999999999999999864 3457788766543
No 69
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=89.78 E-value=1.3 Score=33.61 Aligned_cols=63 Identities=21% Similarity=0.358 Sum_probs=47.1
Q ss_pred HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC------CCceeCcchHhhHHH
Q psy5605 49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD------GGRKITSHGRRDMDR 122 (152)
Q Consensus 49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~------gGR~lT~~G~~~LD~ 122 (152)
|++++.- |+.--+.|++.-++ =|.+++=.-|+.||+.|+|++..- -...||+.|++++.-
T Consensus 28 Il~~L~~-g~~RF~eL~r~i~~-------------Is~k~Ls~~Lk~Le~~Glv~R~~~~~~PprveY~LT~~G~~L~~v 93 (120)
T COG1733 28 ILRDLFD-GPKRFNELRRSIGG-------------ISPKMLSRRLKELEEDGLVERVVYPEEPPRVEYRLTEKGRDLLPV 93 (120)
T ss_pred HHHHHhc-CCCcHHHHHHHccc-------------cCHHHHHHHHHHHHHCCCEEeeecCCCCceeEEEEhhhHHHHHHH
Confidence 5666665 77677777776543 566888888999999999997752 268899999998765
Q ss_pred HHH
Q psy5605 123 IAA 125 (152)
Q Consensus 123 iA~ 125 (152)
+..
T Consensus 94 l~~ 96 (120)
T COG1733 94 LLA 96 (120)
T ss_pred HHH
Confidence 543
No 70
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=89.53 E-value=1.7 Score=33.82 Aligned_cols=65 Identities=23% Similarity=0.399 Sum_probs=47.4
Q ss_pred hcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC---CCCc-----------eeCcchHhhH
Q psy5605 55 MRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD---DGGR-----------KITSHGRRDM 120 (152)
Q Consensus 55 l~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~---~gGR-----------~lT~~G~~~L 120 (152)
.+||..|..|+..- .=+.|-+-++||.|..+|+|++.+ ++|| .++....++|
T Consensus 39 ~~~~~tvdelae~l--------------nr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~~i~~ee~k~~i~~~l 104 (126)
T COG3355 39 ENGPLTVDELAEIL--------------NRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKPIDPEEIKKKILKDL 104 (126)
T ss_pred hcCCcCHHHHHHHH--------------CccHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEecCCHHHHHHHHHHHH
Confidence 47999999999985 456788999999999999998664 3343 2455566667
Q ss_pred HHHHHHHHHHHHH
Q psy5605 121 DRIAAQIRVSKKE 133 (152)
Q Consensus 121 D~iA~~i~~~~~~ 133 (152)
|..+.++...+.+
T Consensus 105 ~~w~~~~~~~i~~ 117 (126)
T COG3355 105 DEWYDKMKQLIEE 117 (126)
T ss_pred HHHHHHHHHHHHH
Confidence 7666666554443
No 71
>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=89.51 E-value=0.28 Score=33.55 Aligned_cols=40 Identities=28% Similarity=0.434 Sum_probs=30.5
Q ss_pred CcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCc
Q psy5605 58 PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGR 110 (152)
Q Consensus 58 ~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR 110 (152)
|..|..++..+|- .|-+-+..-|++||+.|+|+.++...|
T Consensus 25 ~Pt~rEIa~~~g~-------------~S~~tv~~~L~~Le~kG~I~r~~~~~R 64 (65)
T PF01726_consen 25 PPTVREIAEALGL-------------KSTSTVQRHLKALERKGYIRRDPGKAR 64 (65)
T ss_dssp ---HHHHHHHHTS-------------SSHHHHHHHHHHHHHTTSEEEGCCSCC
T ss_pred CCCHHHHHHHhCC-------------CChHHHHHHHHHHHHCcCccCCCCCCC
Confidence 5577777777754 577889999999999999999986444
No 72
>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=89.42 E-value=1.6 Score=30.90 Aligned_cols=76 Identities=11% Similarity=0.221 Sum_probs=51.2
Q ss_pred HHHHHhhHh-hcCCcchhhHHHHhCCCCCCCCCCCc------cCC---CchhHHHHHHHHHHhCCcceecCC--C--Cce
Q psy5605 46 CAALARHIY-MRSPVGVKTVTKIFGGRKRNGVCPSH------FCR---SSGSVARKALQALEQVNIIEKSDD--G--GRK 111 (152)
Q Consensus 46 aASilRkiY-l~g~vGV~~L~~~YGg~krrG~~P~h------~~~---asg~iiR~~LQqLE~~glVek~~~--g--GR~ 111 (152)
|..|++-|+ +.+.+|...+..++=|.++......+ |-. =|..-++.++++|...|+++...+ . -=.
T Consensus 6 a~~il~~V~~~~~~~~~~~ivdvlrGs~~~~i~~~~~~~l~~yG~gk~~~~~~~~~li~~Li~~g~L~~~~~~~~~~~l~ 85 (106)
T PF09382_consen 6 AKKILSCVQRLKQRFGLSQIVDVLRGSKSKKIREKGHDQLPTYGIGKDMSKDDWERLIRQLILEGYLSEDNGGFAYPYLK 85 (106)
T ss_dssp HHHHHHHHHHTTT-S-HHHHHHHHTT-S-CCCHHTTGGGSTTTTTTTTS-HHHHHHHHHHHHHTTSEEEEECCCCTEEEE
T ss_pred HHHHHHHHHHHhccccHHHHHHHHHhccchhhhhcCCCcCcccCCcccCCHHHHHHHHHHHHHcCCceecCCcccccEEE
Confidence 446677777 46789999999999998887754322 211 245689999999999999976653 1 346
Q ss_pred eCcchHhhHH
Q psy5605 112 ITSHGRRDMD 121 (152)
Q Consensus 112 lT~~G~~~LD 121 (152)
+|++|++.|.
T Consensus 86 ~~~~~~~~l~ 95 (106)
T PF09382_consen 86 LTPKGKELLN 95 (106)
T ss_dssp E-GGGHHHHC
T ss_pred ECHHHHHHHC
Confidence 8999998875
No 73
>PRK11569 transcriptional repressor IclR; Provisional
Probab=89.30 E-value=2.3 Score=35.42 Aligned_cols=58 Identities=21% Similarity=0.300 Sum_probs=46.4
Q ss_pred HHHHHHHhhHhh-cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC-CCceeCcc
Q psy5605 44 TRCAALARHIYM-RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD-GGRKITSH 115 (152)
Q Consensus 44 iRaASilRkiYl-~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~-gGR~lT~~ 115 (152)
-|+..||+.|-- .+|+++..|.+.-|- +.+-+..+|+.|++.|||+.+++ +...|.+.
T Consensus 28 ~ral~IL~~l~~~~~~~~lseia~~lgl--------------pksTv~RlL~tL~~~G~l~~~~~~~~Y~lG~~ 87 (274)
T PRK11569 28 TRGLKLLEWIAESNGSVALTELAQQAGL--------------PNSTTHRLLTTMQQQGFVRQVGELGHWAIGAH 87 (274)
T ss_pred HHHHHHHHHHHhCCCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEcCCCCeEecCHH
Confidence 599999999875 578999999998653 45789999999999999998875 33455544
No 74
>PRK03837 transcriptional regulator NanR; Provisional
Probab=89.20 E-value=2.6 Score=33.63 Aligned_cols=42 Identities=21% Similarity=0.399 Sum_probs=34.5
Q ss_pred chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcc
Q psy5605 60 GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSH 115 (152)
Q Consensus 60 GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~ 115 (152)
....|+..|| -|.+.+|.+|+.||..|||+..+..|-.+++-
T Consensus 39 ~E~~Lae~~g--------------VSRt~VREAL~~L~~eGlv~~~~~~G~~V~~~ 80 (241)
T PRK03837 39 SERELMAFFG--------------VGRPAVREALQALKRKGLVQISHGERARVSRP 80 (241)
T ss_pred CHHHHHHHhC--------------CCHHHHHHHHHHHHHCCCEEEecCCceeEecC
Confidence 4567888874 68899999999999999999988767666653
No 75
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=89.13 E-value=1.2 Score=29.28 Aligned_cols=48 Identities=23% Similarity=0.374 Sum_probs=41.3
Q ss_pred HHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC
Q psy5605 46 CAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD 107 (152)
Q Consensus 46 aASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~ 107 (152)
-..|+..|--++.+.+..|...|| -|-.=||.=|+.||+.|+|.+.-+
T Consensus 2 ~~~Il~~l~~~~~~s~~ela~~~~--------------VS~~TiRRDl~~L~~~g~i~r~~G 49 (57)
T PF08220_consen 2 QQQILELLKEKGKVSVKELAEEFG--------------VSEMTIRRDLNKLEKQGLIKRTHG 49 (57)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCEEEEcC
Confidence 345777788899999999999994 467889999999999999998884
No 76
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=89.05 E-value=2.7 Score=35.09 Aligned_cols=58 Identities=14% Similarity=0.116 Sum_probs=45.6
Q ss_pred HHHHHHHhhHhh-cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCC-ceeCcc
Q psy5605 44 TRCAALARHIYM-RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGG-RKITSH 115 (152)
Q Consensus 44 iRaASilRkiYl-~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gG-R~lT~~ 115 (152)
-|+.+||+.|.- .+++++..+++.-|- +.+-+..+|+.|+..|||+.++..| ..|++.
T Consensus 25 ~r~l~IL~~~~~~~~~~tl~eIa~~lgl--------------pkStv~RlL~tL~~~G~l~~~~~~~~Y~lG~~ 84 (271)
T PRK10163 25 ERGIAILQYLEKSGGSSSVSDISLNLDL--------------PLSTTFRLLKVLQAADFVYQDSQLGWWHIGLG 84 (271)
T ss_pred HHHHHHHHHHHhCCCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEEcCCCCeEEecHH
Confidence 388999999875 467999999998654 4578899999999999999986433 345544
No 77
>TIGR02010 IscR iron-sulfur cluster assembly transcription factor IscR. This model describes IscR, an iron-sulfur binding transcription factor of the ISC iron-sulfur cluster assembly system.
Probab=88.08 E-value=1.9 Score=32.48 Aligned_cols=45 Identities=16% Similarity=0.259 Sum_probs=35.6
Q ss_pred CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceec--CCCCceeCcc
Q psy5605 57 SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKS--DDGGRKITSH 115 (152)
Q Consensus 57 g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~--~~gGR~lT~~ 115 (152)
+++.+..++..+ .-+...++++|++|.++|||+.. +.||-.|+..
T Consensus 24 ~~~s~~~ia~~~--------------~ip~~~l~kil~~L~~~glv~s~~G~~Ggy~l~~~ 70 (135)
T TIGR02010 24 GPVTLADISERQ--------------GISLSYLEQLFAKLRKAGLVKSVRGPGGGYQLGRP 70 (135)
T ss_pred CcCcHHHHHHHH--------------CcCHHHHHHHHHHHHHCCceEEEeCCCCCEeccCC
Confidence 478888888876 45678999999999999999853 3467777654
No 78
>COG1485 Predicted ATPase [General function prediction only]
Probab=88.02 E-value=0.91 Score=41.04 Aligned_cols=97 Identities=23% Similarity=0.322 Sum_probs=65.2
Q ss_pred chHHHHHHHHHhhHhhcCCcchhh---HHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcch
Q psy5605 40 DWFYTRCAALARHIYMRSPVGVKT---VTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHG 116 (152)
Q Consensus 40 DW~YiRaASilRkiYl~g~vGV~~---L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G 116 (152)
-|+|-|.....|-||+.||||.|. |-..|.+-.-..-+.-||+ ..++.+-|.|..+. |+. .-+
T Consensus 55 ~~lf~r~~~~~~GlYl~GgVGrGKT~LMD~Fy~~lp~~~k~R~HFh----~FM~~vH~~l~~l~--------g~~--dpl 120 (367)
T COG1485 55 GWLFGRDHGPVRGLYLWGGVGRGKTMLMDLFYESLPGERKRRLHFH----RFMARVHQRLHTLQ--------GQT--DPL 120 (367)
T ss_pred ccccccCCCCCceEEEECCCCccHHHHHHHHHhhCCccccccccHH----HHHHHHHHHHHHHc--------CCC--Ccc
Confidence 699999889999999999999986 5667766554444455654 47888888888776 222 223
Q ss_pred HhhHHHHHHH-------------HHHHH-HHHHHHHHhhcCceeeccC
Q psy5605 117 RRDMDRIAAQ-------------IRVSK-KEAALQALAAQGITVVPTG 150 (152)
Q Consensus 117 ~~~LD~iA~~-------------i~~~~-~~~~~~~~~~~~~~~~~~~ 150 (152)
...-|++|.+ |...+ ----..+|-++||++|-|.
T Consensus 121 ~~iA~~~~~~~~vLCfDEF~VtDI~DAMiL~rL~~~Lf~~GV~lvaTS 168 (367)
T COG1485 121 PPIADELAAETRVLCFDEFEVTDIADAMILGRLLEALFARGVVLVATS 168 (367)
T ss_pred HHHHHHHHhcCCEEEeeeeeecChHHHHHHHHHHHHHHHCCcEEEEeC
Confidence 3444555544 22222 2233568889999999875
No 79
>PRK07379 coproporphyrinogen III oxidase; Provisional
Probab=87.86 E-value=0.71 Score=40.83 Aligned_cols=59 Identities=20% Similarity=0.203 Sum_probs=43.8
Q ss_pred CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCc--eeCc-chHhhHHHHHHHHHHH
Q psy5605 57 SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGR--KITS-HGRRDMDRIAAQIRVS 130 (152)
Q Consensus 57 g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR--~lT~-~G~~~LD~iA~~i~~~ 130 (152)
.++-...+...||.. .-......|++|++.||++.+. +| +||+ +|+-.+|.|+.+++..
T Consensus 334 ~Gl~~~~~~~~~g~~-------------~~~~~~~~l~~l~~~gll~~~~--~~~~~lT~~~G~~~~~~i~~~~~~~ 395 (400)
T PRK07379 334 EGVSLSALTERFGKE-------------IVEQILQCLQPYFQQGWVELEG--DRRLRLTDPEGFLFSNTVLASLFEA 395 (400)
T ss_pred CCcCHHHHHHHHCCC-------------HHHHHHHHHHHHHHCCCEEEeC--CeEEEECchHHhHHHHHHHHHHHHH
Confidence 445566677777531 2234567789999999998654 55 8995 9999999999999843
No 80
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=87.83 E-value=2.1 Score=25.72 Aligned_cols=46 Identities=17% Similarity=0.361 Sum_probs=36.3
Q ss_pred HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC
Q psy5605 48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD 107 (152)
Q Consensus 48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~ 107 (152)
.|+..+.-++++.+..|+..+| -|.+-+++.|+.|++.|+|+...+
T Consensus 4 ~il~~l~~~~~~s~~~l~~~l~--------------~s~~tv~~~l~~L~~~g~i~~~~~ 49 (53)
T smart00420 4 QILELLAQQGKVSVEELAELLG--------------VSEMTIRRDLNKLEEQGLLTRVHG 49 (53)
T ss_pred HHHHHHHHcCCcCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEeec
Confidence 3566666678899999999983 245678999999999999997763
No 81
>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=87.65 E-value=1.2 Score=29.11 Aligned_cols=52 Identities=19% Similarity=0.326 Sum_probs=37.0
Q ss_pred hHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchH
Q psy5605 52 HIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGR 117 (152)
Q Consensus 52 kiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~ 117 (152)
.+=+..++-+..+...||.. --......|+.|++.|||+.+. +.=+||++|+
T Consensus 14 ~LR~~~Gi~~~~~~~~~g~~-------------~~~~~~~~l~~l~~~Gll~~~~-~~l~lT~~G~ 65 (66)
T PF06969_consen 14 GLRCNEGIDLSEFEQRFGID-------------FAEEFQKELEELQEDGLLEIDG-GRLRLTEKGR 65 (66)
T ss_dssp HHHHHSEEEHHHHHHHTT---------------THHH-HHHHHHHHHTTSEEE-S-SEEEE-TTTG
T ss_pred HHHhHCCcCHHHHHHHHCcC-------------HHHHHHHHHHHHHHCCCEEEeC-CEEEECcccC
Confidence 34456788888999998764 2244577899999999999887 4778999996
No 82
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=87.53 E-value=1.1 Score=37.54 Aligned_cols=48 Identities=21% Similarity=0.088 Sum_probs=38.3
Q ss_pred CchhHHHHHHHHHHhCCcceecCC---CCceeCcchHhhHHHHHHHHHHHH
Q psy5605 84 SSGSVARKALQALEQVNIIEKSDD---GGRKITSHGRRDMDRIAAQIRVSK 131 (152)
Q Consensus 84 asg~iiR~~LQqLE~~glVek~~~---gGR~lT~~G~~~LD~iA~~i~~~~ 131 (152)
-|.+-+-..|+.||+.|||+...+ .--.||++|+..+++...+....+
T Consensus 33 iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~LTekG~~ll~~~~~d~~~if 83 (217)
T PRK14165 33 TSSKTAARILKQLEDEGYITRTIVPRGQLITITEKGLDVLYNEYADYSRIF 83 (217)
T ss_pred cCHHHHHHHHHHHHHCCCEEEEEcCCceEEEECHHHHHHHHHHHHHHHHHh
Confidence 466778889999999999987653 245799999999988887765544
No 83
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=87.43 E-value=0.58 Score=37.96 Aligned_cols=41 Identities=27% Similarity=0.396 Sum_probs=33.4
Q ss_pred chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCc
Q psy5605 60 GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITS 114 (152)
Q Consensus 60 GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~ 114 (152)
.-..|+..| .-|...+|.+|+.||..|||+..+.+|-.+++
T Consensus 36 sE~eLa~~l--------------gVSRtpVREAL~~L~~eGlv~~~~~~G~~V~~ 76 (254)
T PRK09464 36 PERELAKQF--------------DVSRPSLREAIQRLEAKGLLLRRQGGGTFVQS 76 (254)
T ss_pred CHHHHHHHh--------------CCCHHHHHHHHHHHHHCCCEEEecCceeEEec
Confidence 345577777 46889999999999999999999877866655
No 84
>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=87.25 E-value=0.85 Score=29.22 Aligned_cols=44 Identities=16% Similarity=0.399 Sum_probs=32.4
Q ss_pred CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCc
Q psy5605 57 SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITS 114 (152)
Q Consensus 57 g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~ 114 (152)
+++....|....| -|.+-+..+|++|++.|+|+....++-.|+|
T Consensus 24 ~~~s~~ela~~~g--------------~s~~tv~r~l~~L~~~g~i~~~~~~~~~l~~ 67 (67)
T cd00092 24 LPLTRQEIADYLG--------------LTRETVSRTLKELEEEGLISRRGRGKYRVNP 67 (67)
T ss_pred CCcCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEecCCCeEEeCC
Confidence 4556666666654 3567889999999999999988755566654
No 85
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=87.04 E-value=1.7 Score=32.07 Aligned_cols=44 Identities=20% Similarity=0.406 Sum_probs=36.0
Q ss_pred HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC
Q psy5605 49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD 106 (152)
Q Consensus 49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~ 106 (152)
||.++|-.||---..+++.. ...-.-++.+|..||++|||+..+
T Consensus 12 IL~hl~~~~~Dy~k~ia~~l--------------~~~~~~v~~~l~~Le~~GLler~~ 55 (92)
T PF10007_consen 12 ILQHLKKAGPDYAKSIARRL--------------KIPLEEVREALEKLEEMGLLERVE 55 (92)
T ss_pred HHHHHHHHCCCcHHHHHHHH--------------CCCHHHHHHHHHHHHHCCCeEEec
Confidence 88899988886666666653 455678999999999999999887
No 86
>PRK08629 coproporphyrinogen III oxidase; Provisional
Probab=86.46 E-value=4.4 Score=36.53 Aligned_cols=71 Identities=14% Similarity=0.136 Sum_probs=51.0
Q ss_pred cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHHHHHHHHH
Q psy5605 56 RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEAA 135 (152)
Q Consensus 56 ~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~~ 135 (152)
.+++-...+...||.. ........|++|+..|++..+. +.=.||++|+-.+|.|..+++.-+-+.+
T Consensus 356 ~~gld~~~f~~~~g~~-------------~~~~~~~~l~~l~~~Gll~~~~-~~l~lT~~G~~~~d~i~~~f~~g~~~~r 421 (433)
T PRK08629 356 SGRLSIKYFRETFGVN-------------LDKALFKEMLLLKLIGAIKNDP-GDLIVTDFGKYLGVVMMKEFYTGMDNVR 421 (433)
T ss_pred hCCcCHHHHHHHHCCC-------------HHHHHHHHHHHHHHCCCEEEEC-CEEEECcchhHHHHHHHHHHHhChHHHH
Confidence 4566677888887631 2345677889999999999765 2458999999999999999985333333
Q ss_pred HHHHh
Q psy5605 136 LQALA 140 (152)
Q Consensus 136 ~~~~~ 140 (152)
.++.+
T Consensus 422 ~~~~~ 426 (433)
T PRK08629 422 AQFRD 426 (433)
T ss_pred HHHHh
Confidence 34333
No 87
>COG1695 Predicted transcriptional regulators [Transcription]
Probab=86.07 E-value=1.8 Score=32.20 Aligned_cols=44 Identities=23% Similarity=0.400 Sum_probs=33.2
Q ss_pred CchhHHHHHHHHHHhCCcceecC--CCC------ceeCcchHhhHHHHHHHH
Q psy5605 84 SSGSVARKALQALEQVNIIEKSD--DGG------RKITSHGRRDMDRIAAQI 127 (152)
Q Consensus 84 asg~iiR~~LQqLE~~glVek~~--~gG------R~lT~~G~~~LD~iA~~i 127 (152)
.|-+-|=-+|+.||+.|||+... .++ -.||++|+..|.+...+.
T Consensus 42 ~s~gtiYp~L~~Le~~Gli~~~~~~~~~g~~rk~Y~lTe~G~~~l~~~~~~~ 93 (138)
T COG1695 42 PSPGTIYPLLKRLEKEGLIESRWEESGGGPPRKYYRLTEKGKEELAELREEW 93 (138)
T ss_pred CCCCcHHHHHHHHHHCCCeEEEecccCCCCCceEEEECHHHHHHHHHHHHHH
Confidence 34455667899999999999652 122 379999999999877654
No 88
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=85.95 E-value=2.5 Score=34.90 Aligned_cols=32 Identities=28% Similarity=0.402 Sum_probs=26.6
Q ss_pred CCchhHHHHHHHHHHhCCcceecCCCCceeCc
Q psy5605 83 RSSGSVARKALQALEQVNIIEKSDDGGRKITS 114 (152)
Q Consensus 83 ~asg~iiR~~LQqLE~~glVek~~~gGR~lT~ 114 (152)
.-|+.++|-+|+.||..|||+..++.|=.+++
T Consensus 45 gVSR~~vREAl~~L~a~Glve~r~G~Gt~V~~ 76 (241)
T COG2186 45 GVSRTVVREALKRLEAKGLVEIRQGSGTFVRP 76 (241)
T ss_pred CCCcHHHHHHHHHHHHCCCeeecCCCceEecC
Confidence 35889999999999999999988876655543
No 89
>PRK08599 coproporphyrinogen III oxidase; Provisional
Probab=85.84 E-value=3.3 Score=35.86 Aligned_cols=62 Identities=18% Similarity=0.260 Sum_probs=47.6
Q ss_pred HhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHH
Q psy5605 53 IYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIR 128 (152)
Q Consensus 53 iYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~ 128 (152)
+....++-...++..||.. ........+.+|++.||++.+. +.=+||++|+-.+|.|+.+++
T Consensus 313 Lr~~~gl~~~~~~~~~~~~-------------~~~~~~~~~~~l~~~gl~~~~~-~~~~lt~~G~~~~~~i~~~~~ 374 (377)
T PRK08599 313 LRKKSGVSKARFEEKFGQS-------------FEDVFGETIQELQEQGLLEEDD-DHVRLTKKGKFLGNEVFEAFL 374 (377)
T ss_pred HHhhCCcCHHHHHHHHCcC-------------HHHHHHHHHHHHHHCCCEEEEC-CEEEECccHhHHHHHHHHHHh
Confidence 3345667777788777531 2355677889999999999766 467899999999999998875
No 90
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=85.78 E-value=1.2 Score=35.12 Aligned_cols=43 Identities=23% Similarity=0.309 Sum_probs=33.3
Q ss_pred CCchhHHHHHHHHHHhCCcceecCCC-C---ceeCcchHhhHHHHHH
Q psy5605 83 RSSGSVARKALQALEQVNIIEKSDDG-G---RKITSHGRRDMDRIAA 125 (152)
Q Consensus 83 ~asg~iiR~~LQqLE~~glVek~~~g-G---R~lT~~G~~~LD~iA~ 125 (152)
..|-+-|=-+|+.||+.|||+....+ . -.||+.|+..|+....
T Consensus 74 ~~s~GtIYp~L~RLE~~GlI~s~~~~~~RK~Y~ITe~Gre~L~e~~~ 120 (135)
T PRK09416 74 EGNEGSLYTLLHRLEQNRFIQSSWDHEGAKYYQLTDKGNKMLRKAEK 120 (135)
T ss_pred cCCCccHHHHHHHHHHCCCeEEeecCCCceEEEECHHHHHHHHHHHh
Confidence 33556677899999999999865432 2 3699999999998765
No 91
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=85.53 E-value=3.1 Score=33.37 Aligned_cols=59 Identities=15% Similarity=0.218 Sum_probs=42.4
Q ss_pred HHHHHHHHhhHhhcCCc-------chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcc
Q psy5605 43 YTRCAALARHIYMRSPV-------GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSH 115 (152)
Q Consensus 43 YiRaASilRkiYl~g~v-------GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~ 115 (152)
|.+.+..||+-=..|.. +-..|+..|| -|..-+|++|+.|++.|+|.+.++.|-.+++.
T Consensus 3 y~qi~~~l~~~I~~g~~~~g~~LPsE~eLa~~~~--------------VSR~TVR~Al~~L~~eGli~r~~G~GtfV~~~ 68 (230)
T TIGR02018 3 YQRIKQDILERIRSGEWPPGHRIPSEHELVAQYG--------------CSRMTVNRALRELTDAGLLERRQGVGTFVAEP 68 (230)
T ss_pred HHHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEecCCEEEEccC
Confidence 45555555544444321 4457777774 57899999999999999999999778777643
No 92
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=85.06 E-value=3.4 Score=25.49 Aligned_cols=42 Identities=21% Similarity=0.302 Sum_probs=34.2
Q ss_pred HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcce
Q psy5605 48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIE 103 (152)
Q Consensus 48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVe 103 (152)
.|+..|+-+|++....++...| =|.+-+++.|++|++.|+|+
T Consensus 7 ~Il~~l~~~~~~t~~ela~~~~--------------is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 7 KILNYLRENPRITQKELAEKLG--------------ISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHCTTS-HHHHHHHHT--------------S-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHcCCCCHHHHHHHhC--------------CCHHHHHHHHHHHHHCcCcC
Confidence 4777777789999999999874 46688999999999999985
No 93
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=84.96 E-value=3.7 Score=27.78 Aligned_cols=46 Identities=13% Similarity=0.113 Sum_probs=37.8
Q ss_pred HHHhhHhhcCC--cchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC
Q psy5605 48 ALARHIYMRSP--VGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD 107 (152)
Q Consensus 48 SilRkiYl~g~--vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~ 107 (152)
.||..|.-+|+ +....|.+..|= +.+.++..|..||+.|+|++...
T Consensus 10 ~IL~~L~~~g~~~~ta~eLa~~lgl--------------~~~~v~r~L~~L~~~G~V~~~~~ 57 (68)
T smart00550 10 KILEFLENSGDETSTALQLAKNLGL--------------PKKEVNRVLYSLEKKGKVCKQGG 57 (68)
T ss_pred HHHHHHHHCCCCCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCEEecCC
Confidence 57777777777 999999998754 34689999999999999998763
No 94
>PRK09057 coproporphyrinogen III oxidase; Provisional
Probab=84.77 E-value=3.8 Score=35.88 Aligned_cols=58 Identities=19% Similarity=0.308 Sum_probs=44.9
Q ss_pred hcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHH
Q psy5605 55 MRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIR 128 (152)
Q Consensus 55 l~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~ 128 (152)
...++-...+...||-.- ....|+.|++.|+++.+.++.=+||++|+-.+|.|+.+++
T Consensus 322 ~~~gid~~~~~~~~g~~~----------------~~~~l~~l~~~gl~~~~~~~~~~lT~~G~~~~d~i~~~~~ 379 (380)
T PRK09057 322 LREGIDLARYAALSGRPL----------------DPERLADLIEEGLIERDGGSRLRATPAGRLVLDAVVADLA 379 (380)
T ss_pred HhCCCCHHHHHHHHCCCc----------------hHHHHHHHHHCCCEEEcCCCEEEECcchhHHHHHHHHHHh
Confidence 346778889999987431 0247899999999997653346899999999999998874
No 95
>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=84.64 E-value=1.5 Score=28.94 Aligned_cols=47 Identities=19% Similarity=0.331 Sum_probs=37.5
Q ss_pred HHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC
Q psy5605 47 AALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD 107 (152)
Q Consensus 47 ASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~ 107 (152)
+.|...|--+|+..+..+++.- .-+.+-++.+|+.|++.|||+..+.
T Consensus 11 ~~vy~~Ll~~~~~t~~eIa~~l--------------~i~~~~v~~~L~~L~~~GlV~~~~~ 57 (68)
T PF01978_consen 11 AKVYLALLKNGPATAEEIAEEL--------------GISRSTVYRALKSLEEKGLVEREEG 57 (68)
T ss_dssp HHHHHHHHHHCHEEHHHHHHHH--------------TSSHHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHHHHHHHHcCCCCHHHHHHHH--------------CcCHHHHHHHHHHHHHCCCEEEEcC
Confidence 3455555567999999999885 4567889999999999999998873
No 96
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=84.08 E-value=1.9 Score=32.44 Aligned_cols=39 Identities=21% Similarity=0.244 Sum_probs=31.5
Q ss_pred CcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCc
Q psy5605 58 PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGR 110 (152)
Q Consensus 58 ~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR 110 (152)
++.+..|+....+ |..-+|.+|++|++.|||+-.|.-||
T Consensus 19 ~vtl~elA~~l~c--------------S~Rn~r~lLkkm~~~gWi~W~pg~GR 57 (115)
T PF12793_consen 19 EVTLDELAELLFC--------------SRRNARTLLKKMQEEGWITWQPGRGR 57 (115)
T ss_pred ceeHHHHHHHhCC--------------CHHHHHHHHHHHHHCCCeeeeCCCCC
Confidence 4677888887644 55668999999999999999997565
No 97
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=83.92 E-value=4.5 Score=33.57 Aligned_cols=77 Identities=17% Similarity=0.289 Sum_probs=54.6
Q ss_pred HHHHHHHhhHhhcCCc--chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCC-ceeCc----ch
Q psy5605 44 TRCAALARHIYMRSPV--GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGG-RKITS----HG 116 (152)
Q Consensus 44 iRaASilRkiYl~g~v--GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gG-R~lT~----~G 116 (152)
.|+..||..|.- +|. ++..|.+.-| -+.+=++.+|+.|++.|||+.+++.| -.|++ -|
T Consensus 4 ~ral~iL~~l~~-~~~~l~l~ela~~~g--------------lpksT~~RlL~tL~~~G~v~~d~~~g~Y~Lg~~~~~lg 68 (246)
T COG1414 4 ERALAILDLLAE-GPGGLSLAELAERLG--------------LPKSTVHRLLQTLVELGYVEQDPEDGRYRLGPRLLELG 68 (246)
T ss_pred HHHHHHHHHHHh-CCCCCCHHHHHHHhC--------------cCHHHHHHHHHHHHHCCCEEEcCCCCcEeehHHHHHHH
Confidence 488889988886 444 5999999864 34578999999999999999999644 44544 45
Q ss_pred HhhHHH-----HHHHHHHHHHHHH
Q psy5605 117 RRDMDR-----IAAQIRVSKKEAA 135 (152)
Q Consensus 117 ~~~LD~-----iA~~i~~~~~~~~ 135 (152)
...+++ +|..+++++.+..
T Consensus 69 ~~~l~~~~l~~~a~p~l~~L~~~t 92 (246)
T COG1414 69 AAALSSLDLVSLARPLLEELAEET 92 (246)
T ss_pred HHHHhcCCHHHHhHHHHHHHHHHh
Confidence 555554 5555555554443
No 98
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=83.74 E-value=2.4 Score=35.72 Aligned_cols=55 Identities=24% Similarity=0.376 Sum_probs=47.2
Q ss_pred HHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeC
Q psy5605 44 TRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKIT 113 (152)
Q Consensus 44 iRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT 113 (152)
-|-..|+..|--++.+.+..|...|| -|..-||.=|..||+.|++.... ||..+.
T Consensus 17 eR~~~Il~~L~~~~~vtv~eLa~~l~--------------VS~~TIRRDL~~Le~~G~l~r~~-GGa~~~ 71 (269)
T PRK09802 17 ERREQIIQRLRQQGSVQVNDLSALYG--------------VSTVTIRNDLAFLEKQGIAVRAY-GGALIC 71 (269)
T ss_pred HHHHHHHHHHHHcCCEeHHHHHHHHC--------------CCHHHHHHHHHHHHhCCCeEEEe-CCEEec
Confidence 47788888888899999999999983 56688999999999999999888 676654
No 99
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=83.37 E-value=6.2 Score=32.78 Aligned_cols=56 Identities=25% Similarity=0.329 Sum_probs=45.3
Q ss_pred HHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCc
Q psy5605 45 RCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITS 114 (152)
Q Consensus 45 RaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~ 114 (152)
|-..|++.|--+|.+.+..|+..+| -|..-||+=|++||+.|++.+.-.|-..+++
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l~--------------vS~~TirRdL~~Le~~g~i~r~~gga~~~~~ 61 (251)
T PRK13509 6 RHQILLELLAQLGFVTVEKVIERLG--------------ISPATARRDINKLDESGKLKKVRNGAEAITQ 61 (251)
T ss_pred HHHHHHHHHHHcCCcCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCEEEecCCccccCC
Confidence 6677888888889999999999984 4667889999999999999987744333443
No 100
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=83.33 E-value=1.2 Score=38.39 Aligned_cols=40 Identities=25% Similarity=0.311 Sum_probs=34.0
Q ss_pred CCchhHHHHHHHHHHhCCcceecC-C-CCceeCcchHhhHHH
Q psy5605 83 RSSGSVARKALQALEQVNIIEKSD-D-GGRKITSHGRRDMDR 122 (152)
Q Consensus 83 ~asg~iiR~~LQqLE~~glVek~~-~-gGR~lT~~G~~~LD~ 122 (152)
.-|.+.+|.+++.||++|+|+..+ . .|-.+.+-...++|.
T Consensus 209 GVSRs~ireAlrkLE~aGvIe~r~LG~kGt~V~~l~~~~~~e 250 (251)
T TIGR02787 209 GITRSVIVNALRKLESAGVIESRSLGMKGTYIKVLNDKLIEE 250 (251)
T ss_pred CCCHHHHHHHHHHHHHCCCEEeccCCCCccEeCCCChhhhhc
Confidence 357899999999999999999988 5 487888887777775
No 101
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=83.30 E-value=1.3 Score=35.31 Aligned_cols=61 Identities=13% Similarity=0.245 Sum_probs=45.2
Q ss_pred HHHHHHHHHhhHhhcCCc-------chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCc
Q psy5605 42 FYTRCAALARHIYMRSPV-------GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITS 114 (152)
Q Consensus 42 ~YiRaASilRkiYl~g~v-------GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~ 114 (152)
-|...+..++.-=..|.. .-..|+..|| -|..-+|++|+.|+..|+|+..++.|-.+++
T Consensus 9 ~y~~i~~~l~~~I~~g~~~~G~~LPsE~eLa~~~~--------------VSR~TvR~Al~~L~~eGli~r~~G~GtfV~~ 74 (238)
T TIGR02325 9 LWRQIADKIEQEIAAGHLRAGDYLPAEMQLAERFG--------------VNRHTVRRAIAALVERGLLRAEQGRGTFVAA 74 (238)
T ss_pred HHHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEecCCEEEECC
Confidence 466766666655444432 3456777774 5789999999999999999999987888875
Q ss_pred ch
Q psy5605 115 HG 116 (152)
Q Consensus 115 ~G 116 (152)
..
T Consensus 75 ~~ 76 (238)
T TIGR02325 75 RR 76 (238)
T ss_pred Cc
Confidence 54
No 102
>PF13814 Replic_Relax: Replication-relaxation
Probab=82.77 E-value=3.1 Score=31.97 Aligned_cols=61 Identities=16% Similarity=0.328 Sum_probs=44.7
Q ss_pred hhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC-----CC-----ceeCcchHhhH
Q psy5605 51 RHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD-----GG-----RKITSHGRRDM 120 (152)
Q Consensus 51 RkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~-----gG-----R~lT~~G~~~L 120 (152)
+-||-.+.+....|...++...+. .+-+|..|++|++.|+|+.... +| -.||+.|.+.+
T Consensus 2 ~~L~~~r~lt~~Qi~~l~~~~~~~-----------~~~~~rrL~~L~~~glv~~~~~~~~~~~g~~~~vy~Lt~~G~~~l 70 (191)
T PF13814_consen 2 RLLARHRFLTTDQIARLLFPSSKS-----------ERTARRRLKRLRELGLVDRFRRRVGARGGSQPYVYYLTPAGARLL 70 (191)
T ss_pred hhHHHhcCcCHHHHHHHHcCCCcc-----------hHHHHHHHHHHhhCCcEEeecccccccCCCcceEEEECHHHHHHH
Confidence 446666677788888888553221 1278999999999999986653 13 37999999999
Q ss_pred HH
Q psy5605 121 DR 122 (152)
Q Consensus 121 D~ 122 (152)
+.
T Consensus 71 ~~ 72 (191)
T PF13814_consen 71 AD 72 (191)
T ss_pred Hh
Confidence 74
No 103
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=82.64 E-value=3.5 Score=32.87 Aligned_cols=87 Identities=21% Similarity=0.274 Sum_probs=54.4
Q ss_pred CchHHHHHHHHHhhHh-hcCCc-chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcch
Q psy5605 39 PDWFYTRCAALARHIY-MRSPV-GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHG 116 (152)
Q Consensus 39 ~DW~YiRaASilRkiY-l~g~v-GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G 116 (152)
++|||.- +|-+- +.+.. -...|.+.- +| .-|-.=+|.+|+-|+++|+|+++.+|.-..|.+.
T Consensus 22 ~~W~~~~----ir~l~~l~~~~~d~~~iak~l--------~p----~is~~ev~~sL~~L~~~gli~k~~~g~y~~t~~~ 85 (171)
T PF14394_consen 22 SSWYHPA----IRELLPLMPFAPDPEWIAKRL--------RP----KISAEEVRDSLEFLEKLGLIKKDGDGKYVQTDKS 85 (171)
T ss_pred hhhHHHH----HHHHhhcCCCCCCHHHHHHHh--------cC----CCCHHHHHHHHHHHHHCCCeEECCCCcEEEecce
Confidence 4688753 44433 33322 455555543 23 4566789999999999999999998665655543
Q ss_pred H----hhHHHHHHHHHHHHHHHHHHHHhh
Q psy5605 117 R----RDMDRIAAQIRVSKKEAALQALAA 141 (152)
Q Consensus 117 ~----~~LD~iA~~i~~~~~~~~~~~~~~ 141 (152)
- ...-....+.-.++-+.+.+||..
T Consensus 86 l~~~~~~~~~avr~~h~q~~~lA~~al~~ 114 (171)
T PF14394_consen 86 LTTSSEIPSEAVRSYHKQMLELAQEALDR 114 (171)
T ss_pred eeCCCCCcHHHHHHHHHHHHHHHHHHHHh
Confidence 3 344444455556666666666653
No 104
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=82.21 E-value=1.3 Score=33.94 Aligned_cols=40 Identities=28% Similarity=0.410 Sum_probs=30.8
Q ss_pred CcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCcee
Q psy5605 58 PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKI 112 (152)
Q Consensus 58 ~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~l 112 (152)
-|.+..|...|| =++||.|.+|..||+.|+|....+ +|+.
T Consensus 59 ~VTpy~la~r~g--------------I~~SvAr~vLR~LeeeGvv~lvsk-nrR~ 98 (107)
T COG4901 59 VVTPYVLASRYG--------------INGSVARIVLRHLEEEGVVQLVSK-NRRQ 98 (107)
T ss_pred eecHHHHHHHhc--------------cchHHHHHHHHHHHhCCceeeecc-Cccc
Confidence 455666777774 468999999999999999987763 5543
No 105
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=82.21 E-value=1.6 Score=33.99 Aligned_cols=45 Identities=18% Similarity=0.304 Sum_probs=35.8
Q ss_pred CcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCceeCcch
Q psy5605 58 PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGRKITSHG 116 (152)
Q Consensus 58 ~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR~lT~~G 116 (152)
++.+..++..+ .-|.+.++++||+|.++|||+... +||-.|+..-
T Consensus 24 ~~s~~eIA~~~--------------~is~~~L~kIl~~L~~aGlv~S~rG~~GGy~La~~p 70 (153)
T PRK11920 24 LSRIPEIARAY--------------GVSELFLFKILQPLVEAGLVETVRGRNGGVRLGRPA 70 (153)
T ss_pred cCcHHHHHHHH--------------CcCHHHHHHHHHHHHHCCCEEeecCCCCCeeecCCH
Confidence 56777787776 356789999999999999999765 4788887654
No 106
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=82.03 E-value=5.6 Score=32.37 Aligned_cols=57 Identities=18% Similarity=0.166 Sum_probs=44.7
Q ss_pred HHHHHHHhhHhh-cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcc
Q psy5605 44 TRCAALARHIYM-RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSH 115 (152)
Q Consensus 44 iRaASilRkiYl-~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~ 115 (152)
-|+-.||.-|-- .+|+++..|.+.-|- +.+-+..+|+.|++.|||+++. +.-.|++.
T Consensus 9 ~ral~IL~~l~~~~~~~~l~eia~~lgl--------------pksT~~RlL~tL~~~G~l~~~~-~~Y~lG~~ 66 (248)
T TIGR02431 9 ARGLAVIEAFGAERPRLTLTDVAEATGL--------------TRAAARRFLLTLVELGYVTSDG-RLFWLTPR 66 (248)
T ss_pred HHHHHHHHHHhcCCCCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCCEEeCC-CEEEecHH
Confidence 378888888864 678999999998653 4578899999999999999864 44556554
No 107
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=81.68 E-value=5.1 Score=31.72 Aligned_cols=45 Identities=16% Similarity=0.220 Sum_probs=36.0
Q ss_pred CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceec--CCCCceeCcc
Q psy5605 57 SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKS--DDGGRKITSH 115 (152)
Q Consensus 57 g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~--~~gGR~lT~~ 115 (152)
+|+.+..++..+ .-+...++++|++|.++|||+.. ++||-.|...
T Consensus 24 ~~vs~~eIA~~~--------------~ip~~~l~kIl~~L~~aGLv~s~rG~~GGy~Lar~ 70 (164)
T PRK10857 24 GPVPLADISERQ--------------GISLSYLEQLFSRLRKNGLVSSVRGPGGGYLLGKD 70 (164)
T ss_pred CcCcHHHHHHHH--------------CcCHHHHHHHHHHHHHCCCEEeCCCCCCCeeccCC
Confidence 478888888887 45678999999999999999853 4578777644
No 108
>PRK14999 histidine utilization repressor; Provisional
Probab=81.58 E-value=11 Score=30.52 Aligned_cols=61 Identities=13% Similarity=0.147 Sum_probs=45.9
Q ss_pred HHHHHHHHHhhHhhcCC------c-chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCc
Q psy5605 42 FYTRCAALARHIYMRSP------V-GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITS 114 (152)
Q Consensus 42 ~YiRaASilRkiYl~g~------v-GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~ 114 (152)
.|...+..||+-=..|. + +-..|+..|| -|..-+|++|+.|+..|+|.+.++.|--+++
T Consensus 13 ly~qi~~~i~~~I~~g~~~~G~~LPsE~eLa~~~g--------------VSR~TVR~Al~~L~~eGli~r~~GkGTfV~~ 78 (241)
T PRK14999 13 FYETVKQDICKKIAGGVWQPHDRIPSEAELVAQYG--------------FSRMTINRALRELTDEGWLVRLQGVGTFVAE 78 (241)
T ss_pred HHHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEecCcEEEECC
Confidence 46677666665544442 2 5567888884 5789999999999999999999977887765
Q ss_pred ch
Q psy5605 115 HG 116 (152)
Q Consensus 115 ~G 116 (152)
..
T Consensus 79 ~~ 80 (241)
T PRK14999 79 PK 80 (241)
T ss_pred CC
Confidence 43
No 109
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=80.64 E-value=9.5 Score=31.78 Aligned_cols=54 Identities=24% Similarity=0.409 Sum_probs=45.6
Q ss_pred HHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeC
Q psy5605 45 RCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKIT 113 (152)
Q Consensus 45 RaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT 113 (152)
|-..|+..|--+|.+.+..|...|| -|..-||.=|+.||+.|+|...- ||=++.
T Consensus 6 R~~~Il~~L~~~~~v~v~eLa~~l~--------------VS~~TIRRDL~~Le~~g~l~r~~-Gga~~~ 59 (256)
T PRK10434 6 RQAAILEYLQKQGKTSVEELAQYFD--------------TTGTTIRKDLVILEHAGTVIRTY-GGVVLN 59 (256)
T ss_pred HHHHHHHHHHHcCCEEHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEEE-CCEEcC
Confidence 6778888888899999999999984 57788999999999999999887 454443
No 110
>PRK08208 coproporphyrinogen III oxidase; Validated
Probab=80.23 E-value=2.7 Score=37.45 Aligned_cols=62 Identities=18% Similarity=0.213 Sum_probs=46.3
Q ss_pred cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHHHHHH
Q psy5605 56 RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKK 132 (152)
Q Consensus 56 ~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~ 132 (152)
..++-...+...||.. + .. ....|++|++.|||+.+. +.=+||++|+-..|.|+.+++..-.
T Consensus 359 ~~gl~~~~~~~~~g~~------~-------~~-~~~~l~~l~~~gll~~~~-~~l~lT~~G~~~~d~i~~~~~~~~~ 420 (430)
T PRK08208 359 AQGLDLADYRQRFGSD------P-------LR-DFPELELLIDRGWLEQNG-GRLRLTEEGLALSDAIGPVFISPEV 420 (430)
T ss_pred hCCcCHHHHHHHHCCC------H-------HH-HHHHHHHHHHCCCEEEEC-CEEEECcchhhHHHHHHHHHcCHHH
Confidence 4567777788887631 1 12 345789999999999765 3568999999999999999875443
No 111
>PRK05628 coproporphyrinogen III oxidase; Validated
Probab=79.79 E-value=2.6 Score=36.61 Aligned_cols=38 Identities=16% Similarity=0.199 Sum_probs=32.3
Q ss_pred HHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHH
Q psy5605 90 RKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIR 128 (152)
Q Consensus 90 R~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~ 128 (152)
+..|++|++.|++..+. +.=+||++|+-.+|.|+..++
T Consensus 337 ~~~l~~l~~~gl~~~~~-~~~~lT~~G~~~~~~i~~~~~ 374 (375)
T PRK05628 337 RARAARVVADGLLAAEG-GRLVLTLRGRLLADAVVRDLL 374 (375)
T ss_pred HHHHHHHHHCCCEEEEC-CEEEEChhhhHHHHHHHHHHh
Confidence 56889999999998766 357899999999999988763
No 112
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=79.45 E-value=2.5 Score=25.27 Aligned_cols=22 Identities=18% Similarity=0.401 Sum_probs=19.1
Q ss_pred chhHHHHHHHHHHhCCcceecC
Q psy5605 85 SGSVARKALQALEQVNIIEKSD 106 (152)
Q Consensus 85 sg~iiR~~LQqLE~~glVek~~ 106 (152)
|.+-++.+|++|++.|+|+...
T Consensus 21 s~~tv~~~l~~L~~~g~l~~~~ 42 (48)
T smart00419 21 TRETVSRTLKRLEKEGLISREG 42 (48)
T ss_pred CHHHHHHHHHHHHHCCCEEEeC
Confidence 5577899999999999998765
No 113
>PRK05799 coproporphyrinogen III oxidase; Provisional
Probab=79.34 E-value=3.2 Score=35.83 Aligned_cols=58 Identities=12% Similarity=0.216 Sum_probs=41.5
Q ss_pred CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHH
Q psy5605 57 SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIR 128 (152)
Q Consensus 57 g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~ 128 (152)
.++-...+...||.. -.......|+.|++.||++.+. +.=+||++|+-.+|.|+.++.
T Consensus 316 ~g~~~~~~~~~~~~~-------------~~~~~~~~l~~l~~~gl~~~~~-~~~~lT~~G~~~~~~i~~~~~ 373 (374)
T PRK05799 316 KGICIEDFKKRFGKN-------------IYEVYGEVINKYIKLGLLIEKE-GRIYLSERGIEVSNSIMSDFL 373 (374)
T ss_pred CCcCHHHHHHHHCcC-------------HHHHHHHHHHHHHHCCCEEEEC-CEEEEChhHHHHHHHHHHHHh
Confidence 345555666666531 1123556689999999999665 346899999999999998763
No 114
>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=78.94 E-value=14 Score=31.69 Aligned_cols=85 Identities=22% Similarity=0.343 Sum_probs=52.0
Q ss_pred chHHHHHHHHHhhHh-hcC-CcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcc--
Q psy5605 40 DWFYTRCAALARHIY-MRS-PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSH-- 115 (152)
Q Consensus 40 DW~YiRaASilRkiY-l~g-~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~-- 115 (152)
+|||. ++|-+- +.+ ..-+..|.+.-+ | .-|-.=+|.+|+-|+++|+|+++.+|--+.|.+
T Consensus 121 ~W~~~----virel~~~~~~~~~~~~ia~~l~--------p----~is~~ev~~sL~~L~~~glikk~~~g~y~~t~~~l 184 (271)
T TIGR02147 121 HWYNS----VIRELLGVMPFADDPEELAKRCF--------P----KISAEQVKESLDLLERLGLIKKNEDGFYKQTDKAV 184 (271)
T ss_pred HHHHH----HHHHHhhcCCCCCCHHHHHHHhC--------C----CCCHHHHHHHHHHHHHCCCeeECCCCcEEeeccee
Confidence 78876 666665 222 224556776642 2 235577999999999999999998653444432
Q ss_pred --hHhhHHHHHHHHHHHHHHHHHHHHh
Q psy5605 116 --GRRDMDRIAAQIRVSKKEAALQALA 140 (152)
Q Consensus 116 --G~~~LD~iA~~i~~~~~~~~~~~~~ 140 (152)
|.........+...++-+.+.+||.
T Consensus 185 ~~~~~~~~~avr~~h~q~l~lA~~al~ 211 (271)
T TIGR02147 185 STGDEVIPLAVRQYQKQMIDLAKEALD 211 (271)
T ss_pred ecCCccchHHHHHHHHHHHHHHHHHHH
Confidence 3333344444455555555555554
No 115
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=78.60 E-value=7.4 Score=32.47 Aligned_cols=55 Identities=24% Similarity=0.335 Sum_probs=45.2
Q ss_pred HHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCc
Q psy5605 45 RCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITS 114 (152)
Q Consensus 45 RaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~ 114 (152)
|-..|+.-|--++.+.+..|...| .-|-.-||+=|..||+.|++.+.- ||=.+.+
T Consensus 6 R~~~Il~~l~~~~~~~~~ela~~l--------------~vS~~TiRRdL~~Le~~g~l~r~~-GGa~~~~ 60 (252)
T PRK10906 6 RHDAIIELVKQQGYVSTEELVEHF--------------SVSPQTIRRDLNDLAEQNKILRHH-GGAALPS 60 (252)
T ss_pred HHHHHHHHHHHcCCEeHHHHHHHh--------------CCCHHHHHHHHHHHHHCCCEEEec-CCEEecC
Confidence 666788888888999999999998 356788999999999999999877 4544443
No 116
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=78.53 E-value=7.1 Score=30.36 Aligned_cols=45 Identities=20% Similarity=0.306 Sum_probs=35.4
Q ss_pred CcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC--CCCceeCcch
Q psy5605 58 PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD--DGGRKITSHG 116 (152)
Q Consensus 58 ~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~--~gGR~lT~~G 116 (152)
++.+..++..+ .-|.+.++++|++|.++|+|+... +||-+|...-
T Consensus 25 ~~s~~~IA~~~--------------~is~~~L~kil~~L~kaGlV~S~rG~~GGy~Lar~~ 71 (150)
T COG1959 25 PVSSAEIAERQ--------------GISPSYLEKILSKLRKAGLVKSVRGKGGGYRLARPP 71 (150)
T ss_pred cccHHHHHHHh--------------CcCHHHHHHHHHHHHHcCCEEeecCCCCCccCCCCh
Confidence 56678888776 346689999999999999998664 5788887543
No 117
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=78.53 E-value=4.2 Score=27.27 Aligned_cols=41 Identities=22% Similarity=0.244 Sum_probs=32.7
Q ss_pred HhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC
Q psy5605 53 IYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD 107 (152)
Q Consensus 53 iYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~ 107 (152)
|=-+|.+.+..|++.| ..|...++..|.+|+..|.|++...
T Consensus 9 l~~~~~~S~~eLa~~~--------------~~s~~~ve~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 9 LRERGRVSLAELAREF--------------GISPEAVEAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp HHHS-SEEHHHHHHHT--------------T--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred HHHcCCcCHHHHHHHH--------------CcCHHHHHHHHHHHHHCCcEEEecC
Confidence 4457889999999988 4677999999999999999997763
No 118
>TIGR02404 trehalos_R_Bsub trehalose operon repressor, B. subtilis-type. This family consists of repressors of the GntR family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gram-positive lineages and does not include the TreR from E. coli.
Probab=78.20 E-value=2.4 Score=34.04 Aligned_cols=33 Identities=27% Similarity=0.359 Sum_probs=28.8
Q ss_pred CCchhHHHHHHHHHHhCCcceecCCCCceeCcc
Q psy5605 83 RSSGSVARKALQALEQVNIIEKSDDGGRKITSH 115 (152)
Q Consensus 83 ~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~ 115 (152)
.-|..-+|++|+.|+..|+|+..++.|--+++.
T Consensus 35 gVSR~TVR~Al~~L~~eGli~r~~G~GTfV~~~ 67 (233)
T TIGR02404 35 GASRETVRKALNLLTEAGYIQKIQGKGSIVLNR 67 (233)
T ss_pred CCCHHHHHHHHHHHHHCCCEEEeCCceEEEecC
Confidence 468899999999999999999999878887653
No 119
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=77.60 E-value=2.7 Score=30.79 Aligned_cols=24 Identities=29% Similarity=0.284 Sum_probs=20.5
Q ss_pred CCchhHHHHHHHHHHhCCcceecC
Q psy5605 83 RSSGSVARKALQALEQVNIIEKSD 106 (152)
Q Consensus 83 ~asg~iiR~~LQqLE~~glVek~~ 106 (152)
+=.||++|.+|.+||+-|+|....
T Consensus 52 kI~~SlAr~~Lr~L~~kG~Ik~V~ 75 (86)
T PRK09334 52 GIKISVAKKVLRELEKRGVLVLYS 75 (86)
T ss_pred cchHHHHHHHHHHHHHCCCEEEEe
Confidence 346899999999999999997554
No 120
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=77.43 E-value=2.7 Score=34.09 Aligned_cols=61 Identities=23% Similarity=0.336 Sum_probs=44.3
Q ss_pred HHHHHHHHHhhHhhcCCc-------chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCc
Q psy5605 42 FYTRCAALARHIYMRSPV-------GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITS 114 (152)
Q Consensus 42 ~YiRaASilRkiYl~g~v-------GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~ 114 (152)
.|...+..|+.-=..|.. .-..|+..|| -|..-+|.+|+.|+..|+|.+.+..|-.+++
T Consensus 6 ly~qi~~~L~~~I~~g~~~~G~~LPsE~eL~~~~~--------------VSR~TvR~Al~~L~~eGli~r~~G~GtfV~~ 71 (240)
T PRK09764 6 LYRQIADRIREQIARGELKPGDALPTESALQTEFG--------------VSRVTVRQALRQLVEQQILESIQGSGTYVKE 71 (240)
T ss_pred HHHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEecCceeEEcc
Confidence 356666666655444422 3456777773 5789999999999999999999977877776
Q ss_pred ch
Q psy5605 115 HG 116 (152)
Q Consensus 115 ~G 116 (152)
..
T Consensus 72 ~~ 73 (240)
T PRK09764 72 ER 73 (240)
T ss_pred cc
Confidence 54
No 121
>PRK13347 coproporphyrinogen III oxidase; Provisional
Probab=77.38 E-value=3.4 Score=37.09 Aligned_cols=64 Identities=20% Similarity=0.298 Sum_probs=46.2
Q ss_pred hHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHH
Q psy5605 52 HIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQI 127 (152)
Q Consensus 52 kiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i 127 (152)
.|-...++-...+...||-. +..+ .. ....|++|++.|||+.+. ++=+||++|+-.+|.|+..+
T Consensus 375 ~L~~~~~ld~~~~~~~~g~~------~~~~----~~-~~~~l~~l~~~gl~~~~~-~~~~lT~~G~~~~~~i~~~f 438 (453)
T PRK13347 375 TLMCNFPVDLAAIAARHGFF------ARYF----LD-ELARLEPLAADGLVTIDG-GGIRVTPEGRPLIRAVAAAF 438 (453)
T ss_pred HHHhhCCcCHHHHHHHHCCC------HHHH----HH-HHHHHHHHHHCCCEEEEC-CEEEECcchhHHHHHHHHHH
Confidence 45555667777888888642 1111 01 245789999999999765 35689999999999999866
No 122
>PF14277 DUF4364: Domain of unknown function (DUF4364)
Probab=77.32 E-value=5.6 Score=31.72 Aligned_cols=53 Identities=23% Similarity=0.284 Sum_probs=40.4
Q ss_pred HHHHHHHHHHhCCcceec--CC--CCceeCcchHhhHHHHHHHHHHHHHHHHHHHHh
Q psy5605 88 VARKALQALEQVNIIEKS--DD--GGRKITSHGRRDMDRIAAQIRVSKKEAALQALA 140 (152)
Q Consensus 88 iiR~~LQqLE~~glVek~--~~--gGR~lT~~G~~~LD~iA~~i~~~~~~~~~~~~~ 140 (152)
-+..+|..|++.|+|... .+ .=-.||++|+..|+-+..+|=...++.-.++|.
T Consensus 35 ~lqq~l~eL~es~~i~~~~~~~~~~~y~iTe~G~~tl~~F~~~Ip~~i~~~i~~~l~ 91 (163)
T PF14277_consen 35 TLQQALSELVESGLITLETDSDNKTRYSITEKGKETLEFFENRIPESIREDIDEYLK 91 (163)
T ss_pred HHHHHHHHHHHCCCEEEeeccCCCcEEEECHhhHHHHHHHHHhCCHHHHHHHHHHHH
Confidence 466789999999999965 22 246899999999999888876666665555554
No 123
>PRK05283 deoxyribose-phosphate aldolase; Provisional
Probab=77.28 E-value=3 Score=35.81 Aligned_cols=74 Identities=18% Similarity=0.198 Sum_probs=43.5
Q ss_pred chhhhcccCCcCCCCCCCchHHHHHHHHHhhHh----hcCCcch------hhHHHH--h--CCCCCCC---CCCCccCCC
Q psy5605 22 WVDIVKSAKFKELAPYDPDWFYTRCAALARHIY----MRSPVGV------KTVTKI--F--GGRKRNG---VCPSHFCRS 84 (152)
Q Consensus 22 W~d~vKTg~~KElaP~d~DW~YiRaASilRkiY----l~g~vGV------~~L~~~--Y--Gg~krrG---~~P~h~~~a 84 (152)
=+|||||+++..-.+..+. ...+||..- ..+.+|| ..+... | -|+..-| ..|+.|+-|
T Consensus 160 GADFVKTSTGf~~~gAt~e-----dv~lm~~~i~~~~~~~~vgIKAsGGIrt~~~A~~~i~ag~~~lg~~~~~~~~fR~G 234 (257)
T PRK05283 160 GADFIKTSTGKVPVNATLE-----AARIMLEVIRDMGVAKTVGFKPAGGVRTAEDAAQYLALADEILGADWADARHFRFG 234 (257)
T ss_pred CCCEEEcCCCCCCCCCCHH-----HHHHHHHHHHhcccCCCeeEEccCCCCCHHHHHHHHHHHHHHhChhhcCcccEeee
Confidence 4799999999876666642 233444332 1233444 222100 0 1111112 469999999
Q ss_pred chhHHHHHHHHHHhCC
Q psy5605 85 SGSVARKALQALEQVN 100 (152)
Q Consensus 85 sg~iiR~~LQqLE~~g 100 (152)
+.+++=.+|+.||..-
T Consensus 235 ~Ssll~~~~~~~~~~~ 250 (257)
T PRK05283 235 ASSLLASLLKTLGHGD 250 (257)
T ss_pred hHHhHHHHHHHHhccc
Confidence 9999999999886643
No 124
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=76.93 E-value=9.9 Score=31.10 Aligned_cols=33 Identities=27% Similarity=0.311 Sum_probs=28.9
Q ss_pred CCchhHHHHHHHHHHhCCcceecCCCCceeCcc
Q psy5605 83 RSSGSVARKALQALEQVNIIEKSDDGGRKITSH 115 (152)
Q Consensus 83 ~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~ 115 (152)
.-|+--+|++|++|++.|+|....+.|--+++.
T Consensus 42 ~VSR~TvRkAL~~L~~eGli~r~~G~GtfV~~~ 74 (236)
T COG2188 42 GVSRMTVRKALDELVEEGLIVRRQGKGTFVASP 74 (236)
T ss_pred CCcHHHHHHHHHHHHHCCcEEEEecCeeEEcCc
Confidence 357889999999999999999998778877775
No 125
>PRK05660 HemN family oxidoreductase; Provisional
Probab=76.90 E-value=3.1 Score=36.45 Aligned_cols=58 Identities=12% Similarity=0.106 Sum_probs=42.9
Q ss_pred CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHHH
Q psy5605 57 SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRV 129 (152)
Q Consensus 57 g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~~ 129 (152)
.++-+..+...||.. + .. ....++.|++.||++.+. +.=+||++|+-++|.|+..++.
T Consensus 320 ~G~~~~~~~~~~g~~------~-------~~-~~~~l~~l~~~gl~~~~~-~~~~lt~~G~~~~d~i~~~~~~ 377 (378)
T PRK05660 320 EAAPRADFEAYTGLP------E-------SV-IRPQLDEALAQGYLTETA-DHWQITEHGKLFLNDLLELFLA 377 (378)
T ss_pred cCCCHHHHHHHHCCC------H-------HH-HHHHHHHHHHCCCEEEeC-CEEEECcchhHHHHHHHHHHhc
Confidence 456666777777642 1 11 356889999999998655 3467899999999999988764
No 126
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=76.32 E-value=11 Score=31.41 Aligned_cols=56 Identities=21% Similarity=0.415 Sum_probs=45.4
Q ss_pred HHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcc
Q psy5605 45 RCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSH 115 (152)
Q Consensus 45 RaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~ 115 (152)
|=-.|+.-|=-+|-+-|..|...|| -|..-||+=|..||+.|++.+.- ||=.+.+.
T Consensus 6 R~~~Il~~l~~~g~v~v~eLa~~~~--------------VS~~TIRRDL~~Le~~g~l~R~h-GGa~~~~~ 61 (253)
T COG1349 6 RHQKILELLKEKGKVSVEELAELFG--------------VSEMTIRRDLNELEEQGLLLRVH-GGAVLPDS 61 (253)
T ss_pred HHHHHHHHHHHcCcEEHHHHHHHhC--------------CCHHHHHHhHHHHHHCCcEEEEe-CCEecCCC
Confidence 5556777777789999999999984 57789999999999999999988 45444433
No 127
>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=76.00 E-value=11 Score=27.05 Aligned_cols=48 Identities=19% Similarity=0.222 Sum_probs=31.7
Q ss_pred HHHHHHhhHh--------hcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC
Q psy5605 45 RCAALARHIY--------MRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD 106 (152)
Q Consensus 45 RaASilRkiY--------l~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~ 106 (152)
|-|++|-.|. ...++.-..|....| .|..-+..+|++||+.|||+...
T Consensus 26 r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~g--------------~sr~tVsr~L~~Le~~GlI~r~~ 81 (95)
T TIGR01610 26 REFRVLLAIIRLTYGWNKKQDRVTATVIAELTG--------------LSRTHVSDAIKSLARRRIIFRQG 81 (95)
T ss_pred HHHHHHHHHHHHHhCccccCCccCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCeeeec
Confidence 5555554444 344555555555543 45566889999999999998665
No 128
>PRK06582 coproporphyrinogen III oxidase; Provisional
Probab=75.34 E-value=10 Score=33.56 Aligned_cols=61 Identities=11% Similarity=0.214 Sum_probs=44.9
Q ss_pred HhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHH-HHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHH
Q psy5605 53 IYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVA-RKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIR 128 (152)
Q Consensus 53 iYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~ii-R~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~ 128 (152)
|-+..++-+..+...||-. + .... ...|++|++.||++. . +.=.||++|+-..|.|+.+++
T Consensus 328 LR~~~Gl~~~~~~~~~g~~------~-------~~~~~~~~l~~l~~~gll~~-~-~~l~lT~~G~~~~d~i~~~~~ 389 (390)
T PRK06582 328 LRLSKGINISTLEQKLNTK------L-------ENILDMNNLKHYQALDLIRL-D-ENIYLTDKGLMLHSYIVPRLI 389 (390)
T ss_pred HHhhCCCCHHHHHHHHCcC------H-------HHhhhHHHHHHHHHCCCEEE-C-CEEEECcchhHHHHHHHHHHh
Confidence 3345677888888888631 1 1111 467889999999997 3 457899999999999998764
No 129
>PRK09249 coproporphyrinogen III oxidase; Provisional
Probab=74.76 E-value=3.6 Score=36.89 Aligned_cols=37 Identities=27% Similarity=0.391 Sum_probs=31.7
Q ss_pred HHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHHH
Q psy5605 92 ALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRV 129 (152)
Q Consensus 92 ~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~~ 129 (152)
.|++|++.||++.+. +.=+||++|+-.+|.|+..+-.
T Consensus 404 ~l~~l~~~gll~~~~-~~~~lT~~G~~~~d~i~~~f~~ 440 (453)
T PRK09249 404 RLAPLEADGLVELDE-NGITVTPKGRLLVRNIAMAFDA 440 (453)
T ss_pred HHHHHHHCCCEEEEC-CEEEECccchHHHHHHHHHHHH
Confidence 478999999999776 4678999999999999987655
No 130
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=74.70 E-value=3.5 Score=28.22 Aligned_cols=38 Identities=26% Similarity=0.329 Sum_probs=28.9
Q ss_pred cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC
Q psy5605 56 RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD 107 (152)
Q Consensus 56 ~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~ 107 (152)
++|+-...+....| =|-.-+|+.|++||+.|.|++.+-
T Consensus 13 ~~p~~T~eiA~~~g--------------ls~~~aR~yL~~Le~eG~V~~~~~ 50 (62)
T PF04703_consen 13 NGPLKTREIADALG--------------LSIYQARYYLEKLEKEGKVERSPV 50 (62)
T ss_dssp TS-EEHHHHHHHHT--------------S-HHHHHHHHHHHHHCTSEEEES-
T ss_pred CCCCCHHHHHHHhC--------------CCHHHHHHHHHHHHHCCCEEEecC
Confidence 66777777777753 456789999999999999998873
No 131
>PRK06294 coproporphyrinogen III oxidase; Provisional
Probab=74.47 E-value=4.5 Score=35.34 Aligned_cols=38 Identities=21% Similarity=0.245 Sum_probs=31.9
Q ss_pred HHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHH
Q psy5605 89 ARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQI 127 (152)
Q Consensus 89 iR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i 127 (152)
....+++|++.||++.+. +.=.||++|+-.+|.|+.++
T Consensus 332 ~~~~l~~~~~~gll~~~~-~~i~lT~~G~~~~~~i~~~~ 369 (370)
T PRK06294 332 TSELIMHPIIQELFTKND-QALSLNKKGRLFHDTIAEEI 369 (370)
T ss_pred HHHHHHHHHHCCCEEEEC-CEEEECcchhhHHHHHHHHh
Confidence 456788999999998765 35689999999999998865
No 132
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=74.28 E-value=3.3 Score=33.53 Aligned_cols=59 Identities=14% Similarity=0.196 Sum_probs=42.3
Q ss_pred HHHHHHHHHhhHhhcCC-------cchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCc
Q psy5605 42 FYTRCAALARHIYMRSP-------VGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITS 114 (152)
Q Consensus 42 ~YiRaASilRkiYl~g~-------vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~ 114 (152)
.|...+..||+- |.+- -+=..|+..| .-|..-+|++|+.|+..|+|+..++.|-.+++
T Consensus 13 ~Y~qi~~~L~~~-I~~~~~~G~~LPsE~eLa~~~--------------~VSR~TVR~Al~~L~~eGli~r~~G~GtfV~~ 77 (241)
T PRK10079 13 RYQEIAAKLEQE-LRQHYRCGDYLPAEQQLAARY--------------EVNRHTLRRAIDQLVEKGWVQRRQGVGVLVLM 77 (241)
T ss_pred HHHHHHHHHHHH-HhcccCCCCcCCCHHHHHHHH--------------CCCHHHHHHHHHHHHHCCCEEEecCCEEEEec
Confidence 466766666654 2221 1334566666 46889999999999999999999977877764
Q ss_pred c
Q psy5605 115 H 115 (152)
Q Consensus 115 ~ 115 (152)
.
T Consensus 78 ~ 78 (241)
T PRK10079 78 R 78 (241)
T ss_pred C
Confidence 3
No 133
>TIGR00637 ModE_repress ModE molybdate transport repressor domain. ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.
Probab=73.67 E-value=14 Score=26.81 Aligned_cols=36 Identities=25% Similarity=0.405 Sum_probs=27.1
Q ss_pred chhHHHHHHHHHHh---CCcceecC----CCCceeCcchHhhH
Q psy5605 85 SGSVARKALQALEQ---VNIIEKSD----DGGRKITSHGRRDM 120 (152)
Q Consensus 85 sg~iiR~~LQqLE~---~glVek~~----~gGR~lT~~G~~~L 120 (152)
|-+-+-..+++||+ ..|++..+ .+|-.||+.|+..+
T Consensus 29 S~stvs~~I~~LE~~lg~~Lf~R~~~g~~~~g~~lT~~G~~l~ 71 (99)
T TIGR00637 29 SYKSAWDYIRAMNNLSGEPLVERATGGKGGGGAVLTEYGQRLI 71 (99)
T ss_pred CHHHHHHHHHHHHHHhCCCeEEecCCCCCCCCeeECHHHHHHH
Confidence 34556677899998 35677775 24899999999987
No 134
>PRK09058 coproporphyrinogen III oxidase; Provisional
Probab=73.60 E-value=5.2 Score=36.02 Aligned_cols=43 Identities=16% Similarity=0.105 Sum_probs=35.8
Q ss_pred HHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHHHHHH
Q psy5605 89 ARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKK 132 (152)
Q Consensus 89 iR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~ 132 (152)
....|++|++.||++.+. +.=+||++|+-..|.|+..+..-+.
T Consensus 398 ~~~~l~~~~~~Gll~~~~-~~l~lT~~G~~~~~~i~~~~~~~l~ 440 (449)
T PRK09058 398 LAPLLAQWQQAGLVELSS-DCLRLTLAGRFWAVNLTQGLIEILQ 440 (449)
T ss_pred HHHHHHHHHHCCCEEEEC-CEEEECCCcccHHHHHHHHHHHHHH
Confidence 445789999999999765 4678999999999999998876543
No 135
>TIGR00538 hemN oxygen-independent coproporphyrinogen III oxidase. This model represents HemN, the oxygen-independent coproporphyrinogen III oxidase that replaces HemF function under anaerobic conditions. Several species, including E. coli, Helicobacter pylori, and Aquifex aeolicus, have both a member of this family and a member of another, closely related family for which there is no evidence of coproporphyrinogen III oxidase activity. Members of this family have a perfectly conserved motif PYRT[SC]YP in a region N-terminal to the region of homology with the related uncharacterized protein.
Probab=73.59 E-value=4 Score=36.52 Aligned_cols=39 Identities=23% Similarity=0.348 Sum_probs=32.4
Q ss_pred HHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHHHHH
Q psy5605 92 ALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSK 131 (152)
Q Consensus 92 ~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~ 131 (152)
.|++|+..||++.+. +.=+||++|+-.+|.|+.++-.-+
T Consensus 404 ~l~~l~~~gll~~~~-~~~~lT~~G~~~~~~i~~~f~~~~ 442 (455)
T TIGR00538 404 LLKPLEEDGLLDVDE-KGIEVTPKGRLLIRNIAMVFDTYL 442 (455)
T ss_pred HHHHHHhCCCEEEEC-CEEEECcCChHHHHHHHHHHHHHh
Confidence 478899999999765 467899999999999998885433
No 136
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=73.53 E-value=12 Score=23.22 Aligned_cols=41 Identities=22% Similarity=0.413 Sum_probs=32.0
Q ss_pred HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCccee
Q psy5605 49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEK 104 (152)
Q Consensus 49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek 104 (152)
|+..|. .||..+..|....| -|.+.+.+=|..|+++|+|++
T Consensus 7 Il~~L~-~~~~~~~el~~~l~--------------~s~~~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 7 ILKLLS-EGPLTVSELAEELG--------------LSQSTVSHHLKKLREAGLVEK 47 (47)
T ss_dssp HHHHHT-TSSEEHHHHHHHHT--------------S-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHH-hCCCchhhHHHhcc--------------ccchHHHHHHHHHHHCcCeeC
Confidence 443333 48999999999874 466889999999999999985
No 137
>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).
Probab=73.45 E-value=16 Score=28.69 Aligned_cols=47 Identities=19% Similarity=0.340 Sum_probs=33.5
Q ss_pred hHHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHHHHHHHHHHHH
Q psy5605 87 SVARKALQALEQ---VNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEAA 135 (152)
Q Consensus 87 ~iiR~~LQqLE~---~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~~ 135 (152)
+-+=+.+++||+ ..|++... .|=.||+.|+.++. .|.++.....+..
T Consensus 26 savS~~i~~LE~~lg~~Lf~R~~-~~~~lT~~G~~l~~-~a~~~l~~~~~~~ 75 (279)
T TIGR03339 26 PTVTDQVRKLEERYGVELFHRNG-RRLELTDAGHRLLP-IVERLFQQEAEAE 75 (279)
T ss_pred hHHHHHHHHHHHHhCCccEEEcC-CeEEEChhHHHHHH-HHHHHHHHHHHHH
Confidence 345567899998 46777765 58999999999994 5566666544433
No 138
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=72.72 E-value=4.2 Score=32.82 Aligned_cols=61 Identities=13% Similarity=0.121 Sum_probs=44.2
Q ss_pred HHHHHHHHHhhHhhcCCc-------chhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCc
Q psy5605 42 FYTRCAALARHIYMRSPV-------GVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITS 114 (152)
Q Consensus 42 ~YiRaASilRkiYl~g~v-------GV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~ 114 (152)
-|...+..++.-=..|-. +=..|+..|| -|..-+|++|+.|++.|+|.+..+.|--+++
T Consensus 10 ~y~qI~~~i~~~I~~G~~~~g~kLPsE~eLa~~~~--------------VSR~TvR~Al~~L~~eGli~r~~G~GTfV~~ 75 (241)
T PRK11402 10 LYATVRQRLLDDIAQGVYQAGQQIPTENELCTQYN--------------VSRITIRKAISDLVADGVLIRWQGKGTFVQS 75 (241)
T ss_pred HHHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCEEEecCceeEECC
Confidence 356666666554444422 3356777774 5789999999999999999999977877776
Q ss_pred ch
Q psy5605 115 HG 116 (152)
Q Consensus 115 ~G 116 (152)
..
T Consensus 76 ~~ 77 (241)
T PRK11402 76 QK 77 (241)
T ss_pred Cc
Confidence 54
No 139
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=71.74 E-value=32 Score=27.73 Aligned_cols=42 Identities=14% Similarity=0.178 Sum_probs=35.4
Q ss_pred HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcce
Q psy5605 48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIE 103 (152)
Q Consensus 48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVe 103 (152)
-|+..|.-+|.+....|+..-|- +..-+|++|+.|++.|||.
T Consensus 26 ~Vl~~L~~~g~~tdeeLA~~Lgi--------------~~~~VRk~L~~L~e~gLv~ 67 (178)
T PRK06266 26 EVLKALIKKGEVTDEEIAEQTGI--------------KLNTVRKILYKLYDARLAD 67 (178)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCeE
Confidence 37777777889999999988753 4578999999999999998
No 140
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=71.68 E-value=12 Score=31.85 Aligned_cols=59 Identities=19% Similarity=0.168 Sum_probs=45.4
Q ss_pred HHHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCc-ceecCCCCceeCcc
Q psy5605 43 YTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNI-IEKSDDGGRKITSH 115 (152)
Q Consensus 43 YiRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~gl-Vek~~~gGR~lT~~ 115 (152)
|-|...|++.|.-..++....|+..+| -|.+-++..++.|++.|+ +...+.+|-.|.+.
T Consensus 3 ~~r~~~il~~L~~~~~~s~~~LA~~lg--------------vsr~tV~~~l~~L~~~G~~i~~~~~~Gy~L~~~ 62 (319)
T PRK11886 3 YTVMLQLLSLLADGDFHSGEQLGEELG--------------ISRAAIWKHIQTLEEWGLDIFSVKGKGYRLAEP 62 (319)
T ss_pred ccHHHHHHHHHHcCCCcCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCceEEecCCeEEecCc
Confidence 347788888887777888889999885 466889999999999999 44444447776444
No 141
>PRK08898 coproporphyrinogen III oxidase; Provisional
Probab=71.62 E-value=6.1 Score=34.86 Aligned_cols=59 Identities=17% Similarity=0.161 Sum_probs=41.8
Q ss_pred hcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHH
Q psy5605 55 MRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIR 128 (152)
Q Consensus 55 l~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~ 128 (152)
+..++-...+...||-. ..-+...|+.|++.|+++.+. +.=+||++|+-.+|.|+.+++
T Consensus 335 ~~~Gld~~~f~~~~g~~--------------~~~~~~~l~~l~~~gll~~~~-~~~~LT~~G~~~~d~i~~~~~ 393 (394)
T PRK08898 335 LTDGVPAHLFQERTGLP--------------LAAIEPQLAAAEQRGLLERDH-TRIRPTPLGQRFLNDLQELFL 393 (394)
T ss_pred HhCCcCHHHHHHHHCCC--------------HHHHHHHHHHHHHCCCEEEEC-CEEEEChhHhHHHHHHHHHHh
Confidence 34555566666666521 122345789999999998655 234899999999999998764
No 142
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=71.27 E-value=8.3 Score=35.22 Aligned_cols=66 Identities=9% Similarity=0.139 Sum_probs=49.4
Q ss_pred HHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCceeCcchHhhHHHHH
Q psy5605 47 AALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGRKITSHGRRDMDRIA 124 (152)
Q Consensus 47 ASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR~lT~~G~~~LD~iA 124 (152)
..||..|.-.+++....|+...|- +.+-+-.++..||+.|||+.... .--.||++|++.++++.
T Consensus 9 ~~vL~~L~~~~~~s~~eLA~~l~l--------------~~~tVt~~i~~Le~kGlV~~~~~~~~~i~LTeeG~~~~~~g~ 74 (489)
T PRK04172 9 KKVLKALKELKEATLEELAEKLGL--------------PPEAVMRAAEWLEEKGLVKVEERVEEVYVLTEEGKKYAEEGL 74 (489)
T ss_pred HHHHHHHHhCCCCCHHHHHHHhCc--------------CHHHHHHHHHHHHhCCCEEEEeeeEEEEEECHHHHHHHHhcC
Confidence 357778888888888889887642 22444556789999999997652 35679999999999765
Q ss_pred HH
Q psy5605 125 AQ 126 (152)
Q Consensus 125 ~~ 126 (152)
-+
T Consensus 75 pE 76 (489)
T PRK04172 75 PE 76 (489)
T ss_pred HH
Confidence 44
No 143
>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=70.80 E-value=9 Score=29.13 Aligned_cols=31 Identities=26% Similarity=0.391 Sum_probs=26.7
Q ss_pred HHHHHHHhCCcceecCCCCceeCcchHhhHHH
Q psy5605 91 KALQALEQVNIIEKSDDGGRKITSHGRRDMDR 122 (152)
Q Consensus 91 ~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~ 122 (152)
.++..+|-+|+|+... |-=.||+.|+++.+.
T Consensus 16 p~~eAaelLgf~~~~~-Gdi~LT~~G~~f~~a 46 (120)
T PF09821_consen 16 PIVEAAELLGFAEVEE-GDIRLTPLGRRFAEA 46 (120)
T ss_pred HHHHHHHHcCCeeecC-CcEEeccchHHHHHC
Confidence 5778999999999876 678999999998864
No 144
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=70.72 E-value=3.5 Score=36.31 Aligned_cols=35 Identities=26% Similarity=0.441 Sum_probs=30.2
Q ss_pred hHHHHHHHHHHhCCcceecC--CCCceeCcchHhhHH
Q psy5605 87 SVARKALQALEQVNIIEKSD--DGGRKITSHGRRDMD 121 (152)
Q Consensus 87 ~iiR~~LQqLE~~glVek~~--~gGR~lT~~G~~~LD 121 (152)
.-+|+.+|.|..+||||-.+ +||.+-|.+.-..|+
T Consensus 40 GTVRNqmq~LkaLgLVegvpGPkGGY~PT~kAYe~L~ 76 (294)
T COG2524 40 GTVRNQMQSLKALGLVEGVPGPKGGYKPTSKAYEALS 76 (294)
T ss_pred chHHHHHHHHHhcCccccccCCCCCccccHHHHHHhc
Confidence 56899999999999999665 689999998877665
No 145
>COG0635 HemN Coproporphyrinogen III oxidase and related Fe-S oxidoreductases [Coenzyme metabolism]
Probab=70.29 E-value=20 Score=32.39 Aligned_cols=83 Identities=22% Similarity=0.188 Sum_probs=60.0
Q ss_pred CCcCCCCCCCchHHHHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCC
Q psy5605 30 KFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGG 109 (152)
Q Consensus 30 ~~KElaP~d~DW~YiRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gG 109 (152)
...+++|.|. +|-+ ++=.+=+.-++-+..+...||- -. -..+...|+.++..|+++.+. +.
T Consensus 331 ~~~~l~~~d~----~~e~-~i~gLr~~~gv~~~~~~~~~~~-~~------------~~~~~~~l~~~~~~Gll~~~~-~~ 391 (416)
T COG0635 331 EGEELTPDDL----IREA-LILGLRLNFGVDLAELEERFGI-FK------------FAEILELLAELIADGLLELDG-DR 391 (416)
T ss_pred eeeeCCHHHH----HHHH-HHHHHHHhcCCCHHHHHHHhCc-ch------------hhhHHHHHHHHHhCCCEEecC-CE
Confidence 4556676663 1211 2223445567888888888864 21 367888999999999999888 47
Q ss_pred ceeCcchHhhHHHHHHHHHHHH
Q psy5605 110 RKITSHGRRDMDRIAAQIRVSK 131 (152)
Q Consensus 110 R~lT~~G~~~LD~iA~~i~~~~ 131 (152)
-+||+.|+-++|.|+......+
T Consensus 392 ~~lt~~g~~~~~~i~~~f~~~~ 413 (416)
T COG0635 392 LRLTEKGRLLLRSIAEAFDAYL 413 (416)
T ss_pred EEECCcchhHHHHHHHHHHHHh
Confidence 8999999999999998876544
No 146
>PF03297 Ribosomal_S25: S25 ribosomal protein; InterPro: IPR004977 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 [, ]. The S25 ribosomal protein is a component of the 40S ribosomal subunit.; PDB: 2XZM_8 2XZN_8 3O30_Q 3U5G_Z 3IZB_V 3U5C_Z 3O2Z_Q 3IZ6_V.
Probab=70.01 E-value=4.4 Score=30.59 Aligned_cols=36 Identities=28% Similarity=0.429 Sum_probs=29.3
Q ss_pred CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC
Q psy5605 57 SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD 106 (152)
Q Consensus 57 g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~ 106 (152)
.-|....|+..| +=++|+.|.+|+.||+-|+|....
T Consensus 58 K~ITp~~lserl--------------kI~~SlAr~~Lr~L~~kG~Ik~V~ 93 (105)
T PF03297_consen 58 KLITPSVLSERL--------------KINGSLARKALRELESKGLIKPVS 93 (105)
T ss_dssp SCECHHHHHHHH--------------CCSCHHHHHHHHHHHHCCSSEEEE
T ss_pred cEeeHHHHHHhH--------------hhHHHHHHHHHHHHHHCCCEEEEe
Confidence 347777888887 346799999999999999997654
No 147
>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]
Probab=69.93 E-value=13 Score=33.39 Aligned_cols=68 Identities=18% Similarity=0.259 Sum_probs=48.7
Q ss_pred chHHHHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhh
Q psy5605 40 DWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRD 119 (152)
Q Consensus 40 DW~YiRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~ 119 (152)
||.=.+--+.+-.-|--||||+..++-.-|--. ..|-=.+=-=|-..|++++++ .||++|+++.+.
T Consensus 259 d~~D~k~L~~li~~f~GgPVGl~tia~~lge~~-------------~TiEdv~EPyLiq~gfi~RTp-RGR~aT~~ay~h 324 (332)
T COG2255 259 DEIDRKYLRALIEQFGGGPVGLDTIAAALGEDR-------------DTIEDVIEPYLIQQGFIQRTP-RGRIATAKAYEH 324 (332)
T ss_pred cHHHHHHHHHHHHHhCCCCccHHHHHHHhcCch-------------hHHHHHHhHHHHHhchhhhCC-CcceecHHHHHH
Confidence 676666666666667779999999999876532 122222333466789999999 599999999876
Q ss_pred HH
Q psy5605 120 MD 121 (152)
Q Consensus 120 LD 121 (152)
|-
T Consensus 325 l~ 326 (332)
T COG2255 325 LG 326 (332)
T ss_pred hc
Confidence 53
No 148
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=68.38 E-value=15 Score=30.25 Aligned_cols=47 Identities=15% Similarity=0.217 Sum_probs=33.7
Q ss_pred HHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHHHHHHHHHHHHH
Q psy5605 88 VARKALQALEQ---VNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEAAL 136 (152)
Q Consensus 88 iiR~~LQqLE~---~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~~~ 136 (152)
-+=+.+++||+ .-|.+.+. .|=.||+.|+.+++. |.++.....+...
T Consensus 44 avS~~I~~LE~~lG~~LF~R~~-r~~~LT~~G~~l~~~-a~~~l~~~~~~~~ 93 (311)
T PRK10086 44 AVSHRINQLEEELGIKLFVRSH-RKVELTEEGKRVFWA-LKSSLDTLNQEIL 93 (311)
T ss_pred HHHHHHHHHHHHhCCeeEEEcC-CCcccCHhHHHHHHH-HHHHHHHHHHHHH
Confidence 34456789998 45667666 589999999999987 6667666554433
No 149
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=68.09 E-value=27 Score=23.00 Aligned_cols=52 Identities=15% Similarity=0.220 Sum_probs=37.8
Q ss_pred HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcc
Q psy5605 49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSH 115 (152)
Q Consensus 49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~ 115 (152)
|++.+- +++..+..|+..+| -|..-|+..++.|++.|+.....+.|..|.+.
T Consensus 5 il~~L~-~~~~~~~eLa~~l~--------------vS~~tv~~~l~~L~~~g~~i~~~~~g~~l~~~ 56 (69)
T TIGR00122 5 LLALLA-DNPFSGEKLGEALG--------------MSRTAVNKHIQTLREWGVDVLTVGKGYRLPPP 56 (69)
T ss_pred HHHHHH-cCCcCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCCeEEecCCceEecCc
Confidence 455433 66778889998874 45688999999999999964334567777443
No 150
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=67.74 E-value=5 Score=34.34 Aligned_cols=77 Identities=17% Similarity=0.162 Sum_probs=49.7
Q ss_pred CCCCCCcchhhhcccCCcCCCCCCCchHHHHHHHHHhhHhhcCC-cchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHH
Q psy5605 15 GKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSP-VGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKAL 93 (152)
Q Consensus 15 gki~~PeW~d~vKTg~~KElaP~d~DW~YiRaASilRkiYl~g~-vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~L 93 (152)
+.+..|.|....++...-+..|.++|= -.++.-|=-+|+ +-=..|++.-| -|.+=+-.+|
T Consensus 171 ~~~~~~~~~~~~~~~~~~~~~~L~~~e-----~~il~~i~~~GGri~Q~eL~r~lg--------------lsktTvsR~L 231 (258)
T COG2512 171 APVIEPLLSRGDELRVLVNEYDLNEDE-----KEILDLIRERGGRITQAELRRALG--------------LSKTTVSRIL 231 (258)
T ss_pred chhhhhccccccccccccccCCCCHHH-----HHHHHHHHHhCCEEeHHHHHHhhC--------------CChHHHHHHH
Confidence 335556777777776666655555541 245544444555 44556666643 3456677899
Q ss_pred HHHHhCCcceecCCCCc
Q psy5605 94 QALEQVNIIEKSDDGGR 110 (152)
Q Consensus 94 QqLE~~glVek~~~gGR 110 (152)
+.||++|+||+.+.|++
T Consensus 232 ~~LEk~GlIe~~K~G~~ 248 (258)
T COG2512 232 RRLEKRGLIEKEKKGRT 248 (258)
T ss_pred HHHHhCCceEEEEeCCe
Confidence 99999999999986543
No 151
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=67.24 E-value=21 Score=28.54 Aligned_cols=49 Identities=12% Similarity=0.196 Sum_probs=34.6
Q ss_pred hHHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHHHHHHHHHHHHHH
Q psy5605 87 SVARKALQALEQ---VNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEAALQ 137 (152)
Q Consensus 87 ~iiR~~LQqLE~---~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~~~~ 137 (152)
+-+=+.+++||+ ..|+..+. .|-.||+.|+.+++.+ .+++.+..+...+
T Consensus 30 savS~~i~~LE~~lg~~Lf~R~~-~~~~lT~~G~~l~~~~-~~il~~~~~~~~~ 81 (296)
T PRK11242 30 PTLSQQIRQLEESLGVQLFDRSG-RTVRLTDAGEVYLRYA-RRALQDLEAGRRA 81 (296)
T ss_pred hHHHHHHHHHHHHhCCeeEeEcC-CceeechhHHHHHHHH-HHHHHHHHHHHHH
Confidence 445567899998 46777765 5899999999998764 5555555554443
No 152
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=67.13 E-value=15 Score=30.35 Aligned_cols=52 Identities=13% Similarity=0.234 Sum_probs=42.0
Q ss_pred HHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCc
Q psy5605 45 RCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGR 110 (152)
Q Consensus 45 RaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR 110 (152)
|--.|+..|--++.+.+..|...+| -|..=||+-|.+||+.|++....+++.
T Consensus 5 R~~~Il~~l~~~~~~~~~eLa~~l~--------------VS~~TiRRdL~~L~~~~~l~r~~Gga~ 56 (240)
T PRK10411 5 RQQAIVDLLLNHTSLTTEALAEQLN--------------VSKETIRRDLNELQTQGKILRNHGRAK 56 (240)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCEEEecCeEE
Confidence 4456777777789999999999994 566789999999999999988664443
No 153
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=67.01 E-value=20 Score=28.69 Aligned_cols=49 Identities=10% Similarity=0.165 Sum_probs=34.8
Q ss_pred hHHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHHHHHHHHHHHHHH
Q psy5605 87 SVARKALQALEQ---VNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEAALQ 137 (152)
Q Consensus 87 ~iiR~~LQqLE~---~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~~~~ 137 (152)
+-+-+.+++||+ ..|++.+. +|-.||+.|+..+.. |.++...+.....+
T Consensus 36 ~avS~~i~~LE~~lg~~Lf~R~~-r~~~lT~~G~~l~~~-a~~~l~~~~~~~~~ 87 (294)
T PRK09986 36 PPLSIHIKELEDQLGTPLFIRHS-RSVVLTHAGKILMEE-SRRLLDNAEQSLAR 87 (294)
T ss_pred CHHHHHHHHHHHHhCCeeEeeCC-CceeECHhHHHHHHH-HHHHHHHHHHHHHH
Confidence 446677899998 36777765 589999999999965 55566655554443
No 154
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=66.80 E-value=12 Score=31.82 Aligned_cols=65 Identities=22% Similarity=0.321 Sum_probs=44.3
Q ss_pred chHHHHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhh
Q psy5605 40 DWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRD 119 (152)
Q Consensus 40 DW~YiRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~ 119 (152)
|..|+| .+...|-.+|+|+..++..-|-.. ..+.+.+=..|-..|+|++.+ .||++|++|.+.
T Consensus 261 ~~~~l~---~~~~~~~~~~~~~~~~a~~lg~~~-------------~~~~~~~e~~Li~~~li~~~~-~gr~~~~~~~~~ 323 (328)
T PRK00080 261 DRKYLR---TIIEKFGGGPVGLDTLAAALGEER-------------DTIEDVYEPYLIQQGFIQRTP-RGRVATPKAYEH 323 (328)
T ss_pred HHHHHH---HHHHHcCCCceeHHHHHHHHCCCc-------------chHHHHhhHHHHHcCCcccCC-chHHHHHHHHHH
Confidence 344554 334445678999999988875421 122222323888899998776 699999999987
Q ss_pred HH
Q psy5605 120 MD 121 (152)
Q Consensus 120 LD 121 (152)
|.
T Consensus 324 ~~ 325 (328)
T PRK00080 324 LG 325 (328)
T ss_pred hC
Confidence 74
No 155
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=65.81 E-value=15 Score=30.24 Aligned_cols=50 Identities=22% Similarity=0.412 Sum_probs=39.1
Q ss_pred cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHH-HHHhCCcceecCCCCceeCcchHhhH
Q psy5605 56 RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQ-ALEQVNIIEKSDDGGRKITSHGRRDM 120 (152)
Q Consensus 56 ~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQ-qLE~~glVek~~~gGR~lT~~G~~~L 120 (152)
.+++++..++...|- +..-++.++. .|-+.|+|++.. .||..|++|...|
T Consensus 253 ~~~~~~~~ia~~lg~--------------~~~~~~~~~e~~Li~~~li~~~~-~g~~~~~~~~~~~ 303 (305)
T TIGR00635 253 GGPVGLKTLAAALGE--------------DADTIEDVYEPYLLQIGFLQRTP-RGRIATELAYEHL 303 (305)
T ss_pred CCcccHHHHHHHhCC--------------CcchHHHhhhHHHHHcCCcccCC-chhhhhHHHHHHh
Confidence 457999999998865 2244666667 699999998555 6999999998866
No 156
>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=65.72 E-value=9 Score=24.84 Aligned_cols=32 Identities=31% Similarity=0.542 Sum_probs=23.8
Q ss_pred chhHHHHHHHHHHh---CCcceecCCCCceeCcchH
Q psy5605 85 SGSVARKALQALEQ---VNIIEKSDDGGRKITSHGR 117 (152)
Q Consensus 85 sg~iiR~~LQqLE~---~glVek~~~gGR~lT~~G~ 117 (152)
|-+-+...+++||+ ..|++... +|=.||+.|+
T Consensus 26 s~~~vs~~i~~LE~~lg~~Lf~r~~-~~~~lT~~G~ 60 (60)
T PF00126_consen 26 SQSAVSRQIKQLEEELGVPLFERSG-RGLRLTEAGE 60 (60)
T ss_dssp SHHHHHHHHHHHHHHHTS-SEEECS-SSEEE-HHHH
T ss_pred cchHHHHHHHHHHHHhCCeEEEECC-CCeeEChhhC
Confidence 44677888999998 57888776 4789999986
No 157
>PRK10082 cell density-dependent motility repressor; Provisional
Probab=65.27 E-value=24 Score=28.82 Aligned_cols=44 Identities=14% Similarity=0.227 Sum_probs=31.7
Q ss_pred hHHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHHHHHHHHH
Q psy5605 87 SVARKALQALEQ---VNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKK 132 (152)
Q Consensus 87 ~iiR~~LQqLE~---~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~ 132 (152)
+-+-+.+++||+ ..|++.+. .|-.||+.|+.+++. |..+.....
T Consensus 40 pavS~~I~~LE~~lG~~Lf~R~~-r~~~lT~~G~~l~~~-a~~~l~~~e 86 (303)
T PRK10082 40 PAFSRRIRALEQAIGVELFNRQV-TPLQLSEQGKIFHSQ-IRHLLQQLE 86 (303)
T ss_pred HHHHHHHHHHHHHcCCEEEEecC-CCCccCHHHHHHHHH-HHHHHHHHH
Confidence 456677899998 35566665 588999999999986 455554443
No 158
>PF14178 YppF: YppF-like protein
Probab=63.88 E-value=11 Score=26.17 Aligned_cols=33 Identities=18% Similarity=0.456 Sum_probs=22.4
Q ss_pred cCCCCCCCchHHHHHHHHHhhHhhcCCcchhhHHHHh
Q psy5605 32 KELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIF 68 (152)
Q Consensus 32 KElaP~d~DW~YiRaASilRkiYl~g~vGV~~L~~~Y 68 (152)
|+..|.+-| ----.+|+.||.|-+.+...|..+
T Consensus 14 k~y~p~~~N----eLLDFar~~Yi~gei~i~eYR~lv 46 (60)
T PF14178_consen 14 KKYEPEDMN----ELLDFARKLYIQGEISINEYRNLV 46 (60)
T ss_pred hccCcccHH----HHHHHHHHHHHhCcccHHHHHHHH
Confidence 556666643 122457899999999997766654
No 159
>PRK12423 LexA repressor; Provisional
Probab=63.66 E-value=8.3 Score=30.95 Aligned_cols=36 Identities=36% Similarity=0.486 Sum_probs=28.9
Q ss_pred cchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC
Q psy5605 59 VGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD 107 (152)
Q Consensus 59 vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~ 107 (152)
-.+..|+..+|= .|.+.+|..|+.||+.|+|+..+.
T Consensus 26 Ps~~eia~~~g~-------------~s~~~v~~~l~~L~~~G~l~~~~~ 61 (202)
T PRK12423 26 PSLAEIAQAFGF-------------ASRSVARKHVQALAEAGLIEVVPN 61 (202)
T ss_pred CCHHHHHHHhCC-------------CChHHHHHHHHHHHHCCCEEecCC
Confidence 377777777641 466889999999999999999885
No 160
>TIGR02424 TF_pcaQ pca operon transcription factor PcaQ. Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria.
Probab=63.60 E-value=27 Score=28.17 Aligned_cols=44 Identities=18% Similarity=0.289 Sum_probs=31.7
Q ss_pred hHHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHHHHHHHHH
Q psy5605 87 SVARKALQALEQ---VNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKK 132 (152)
Q Consensus 87 ~iiR~~LQqLE~---~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~ 132 (152)
+-+=+.+++||+ ..|.+.+. +|-.||+.|+.+++.+ .++.....
T Consensus 32 ~avS~~I~~LE~~lg~~LF~R~~-~~~~lT~~G~~l~~~a-~~~l~~~~ 78 (300)
T TIGR02424 32 PAVSKTLRELEEILGTPLFERDR-RGIRLTRYGELFLRHA-GASLAALR 78 (300)
T ss_pred HHHHHHHHHHHHHhCCeEEEEcC-CCccccHhHHHHHHHH-HHHHHHHH
Confidence 456667899998 46777766 5899999999998654 44544433
No 161
>TIGR01594 holin_lambda phage holin, lambda family. This model represents one of a large number of mutally dissimilar families of phage holins. Holins act against the host cell membrane to allow lytic enzymes of the phage to reach the bacterial cell wall. This family includes the product of the S gene of phage lambda.
Probab=63.58 E-value=6.4 Score=29.59 Aligned_cols=35 Identities=26% Similarity=0.327 Sum_probs=21.9
Q ss_pred CCCCCCchHHHHHHHHHh--hHhhcCC-------cchhhHHHHhCCCC
Q psy5605 34 LAPYDPDWFYTRCAALAR--HIYMRSP-------VGVKTVTKIFGGRK 72 (152)
Q Consensus 34 laP~d~DW~YiRaASilR--kiYl~g~-------vGV~~L~~~YGg~k 72 (152)
++|.||||| |.++. +.+.++| +.+.-||-.|+|..
T Consensus 1 mm~~~P~~W----~~ll~~l~~~~~~~i~g~~lA~~mA~LR~~Y~g~~ 44 (107)
T TIGR01594 1 MMIKEPDLW----AALLSWLQDAWRSQGQGALLALAIAYLRIRYMGGK 44 (107)
T ss_pred CCCCCccHH----HHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHcCcc
Confidence 478899988 33333 3344432 44677889998754
No 162
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=62.72 E-value=20 Score=27.14 Aligned_cols=52 Identities=15% Similarity=0.295 Sum_probs=40.4
Q ss_pred HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCc
Q psy5605 48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGR 110 (152)
Q Consensus 48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR 110 (152)
.||+-|+-.||+.+..+....+.. +| -+-+-++.+|.-|++-|+|+.... ||
T Consensus 8 ~VM~vlW~~~~~t~~eI~~~l~~~--~~--------~~~tTv~T~L~rL~~KG~v~~~k~-gr 59 (130)
T TIGR02698 8 EVMRVVWTLGETTSRDIIRILAEK--KD--------WSDSTIKTLLGRLVDKGCLTTEKE-GR 59 (130)
T ss_pred HHHHHHHcCCCCCHHHHHHHHhhc--cC--------CcHHHHHHHHHHHHHCCceeeecC-CC
Confidence 588889999999999988877532 22 234678999999999999987753 55
No 163
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=61.95 E-value=24 Score=28.42 Aligned_cols=46 Identities=17% Similarity=0.232 Sum_probs=32.6
Q ss_pred HHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHHHHHHHHHHHH
Q psy5605 88 VARKALQALEQ---VNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEAA 135 (152)
Q Consensus 88 iiR~~LQqLE~---~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~~ 135 (152)
-+=+.+++||+ ..|.+... +|=.||+.|+..++. |.++.+.+.+..
T Consensus 31 avSr~i~~LE~~lg~~Lf~R~~-~~~~lT~~G~~l~~~-a~~~l~~~~~~~ 79 (296)
T PRK09906 31 SLSQQIKDLENCVGVPLLVRDK-RKVALTAAGEVFLQD-ARAILEQAEKAK 79 (296)
T ss_pred HHHHHHHHHHHHhCCeeeeeCC-CcceEcHhHHHHHHH-HHHHHHHHHHHH
Confidence 34456788998 46777765 589999999999974 566655554433
No 164
>COG1542 Uncharacterized conserved protein [Function unknown]
Probab=61.76 E-value=4.4 Score=38.45 Aligned_cols=92 Identities=18% Similarity=0.244 Sum_probs=63.3
Q ss_pred CCCCCCCcchhhhc-ccCCcCCCCCCCchHHHHHHHH-HhhHhh----------------cCCcchhhHHHHhCCCCCCC
Q psy5605 14 SGKMKVPEWVDIVK-SAKFKELAPYDPDWFYTRCAAL-ARHIYM----------------RSPVGVKTVTKIFGGRKRNG 75 (152)
Q Consensus 14 ~gki~~PeW~d~vK-Tg~~KElaP~d~DW~YiRaASi-lRkiYl----------------~g~vGV~~L~~~YGg~krrG 75 (152)
+.....|+|..-.+ -|--+.-+|.+.-=+|.+.|-- =|+=|+ +.+.=|+.++..||
T Consensus 380 ef~aPn~EW~eqa~~eglVs~gAiT~kGrl~akls~tikRkP~LT~~e~kvl~kiP~~~ikrg~liedi~~~~g------ 453 (593)
T COG1542 380 EFDAPNAEWYEQAKEEGLVSRGAITEKGRLYAKLSKTIKRKPYLTKYEIKVLIKIPRKYIKRGELIEDIQGHVG------ 453 (593)
T ss_pred ccCCCCHHHHHHHHhcccccccCcCcchhHHHHHHHHHhcCcccchhHHHHHHhccccccchhhHHHHHHhhcC------
Confidence 34456678876543 4566667788888888886642 233333 33334444444444
Q ss_pred CCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhh
Q psy5605 76 VCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRD 119 (152)
Q Consensus 76 ~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~ 119 (152)
+-..=++.+|..||.-|+|+--+.+|=.||..||-.
T Consensus 454 --------~~eeev~~sl~kleskgfveeL~n~gv~LTeaGe~~ 489 (593)
T COG1542 454 --------GDEEEVIKSLGKLESKGFVEELPNKGVKLTEAGELV 489 (593)
T ss_pred --------ccHHHHHHHHHHHhhcchHHHhccCcEEeehhhHHH
Confidence 334568899999999999999999999999999854
No 165
>PRK14997 LysR family transcriptional regulator; Provisional
Probab=61.64 E-value=22 Score=28.71 Aligned_cols=46 Identities=17% Similarity=0.292 Sum_probs=31.8
Q ss_pred HHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHHHHHHHHHHHH
Q psy5605 88 VARKALQALEQ---VNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEAA 135 (152)
Q Consensus 88 iiR~~LQqLE~---~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~~ 135 (152)
-+=..+++||+ ..|.+.+. .|-.||+.|+.++.. |.++...+....
T Consensus 32 avS~~I~~LE~~lG~~LF~R~~-r~~~lT~~G~~l~~~-a~~il~~~~~~~ 80 (301)
T PRK14997 32 KLSRRIAQLEERLGVRLIQRTT-RQFNVTEVGQTFYEH-CKAMLVEAQAAQ 80 (301)
T ss_pred HHHHHHHHHHHHhCCEeeeecc-CcceEcHhHHHHHHH-HHHHHHHHHHHH
Confidence 34456799998 35566665 589999999999965 455555554433
No 166
>COG4533 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=61.45 E-value=23 Score=33.91 Aligned_cols=59 Identities=14% Similarity=0.172 Sum_probs=44.0
Q ss_pred cchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCc------eeCcchHhhHHHHHHHHHHHH
Q psy5605 59 VGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGR------KITSHGRRDMDRIAAQIRVSK 131 (152)
Q Consensus 59 vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR------~lT~~G~~~LD~iA~~i~~~~ 131 (152)
+.+..|+.... .|...+|..|+||++.||++-.+.-|| .+..++...+-..|++..+.-
T Consensus 24 ~tl~eLA~~lf--------------CS~Rh~R~lL~q~q~~gWL~W~p~~GRGkrSrL~flr~~e~L~~q~a~~~le~g 88 (564)
T COG4533 24 TTLNELADILF--------------CSRRHARTLLRQMQEAGWLTWQPQAGRGKRSRLTFLRTPEALLLQLAEKLLEQG 88 (564)
T ss_pred eeHHHHHHHhc--------------cCHHHHHHHHHHHHHcCCEEeccCCCCCcceeEEEecChHHHHHHHHHHHHhcC
Confidence 55666666653 456679999999999999999986454 355678888888888876543
No 167
>PRK08446 coproporphyrinogen III oxidase; Provisional
Probab=61.25 E-value=11 Score=32.69 Aligned_cols=37 Identities=19% Similarity=0.114 Sum_probs=29.4
Q ss_pred HHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHH
Q psy5605 89 ARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIR 128 (152)
Q Consensus 89 iR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~ 128 (152)
.-..|++|++.||++.+. +| ||++|.-+.|.|+..+.
T Consensus 313 ~~~~l~~l~~~gl~~~~~--~~-l~~~g~~~~d~i~~~~~ 349 (350)
T PRK08446 313 EEKKVKILIEENKLFIKN--NR-LYNKDFFLADEIALFLL 349 (350)
T ss_pred HHHHHHHHHHCCCEEeeC--CE-EcccchhhHHHHHHHhh
Confidence 345778999999998554 44 99999999999987653
No 168
>TIGR02036 dsdC D-serine deaminase transcriptional activator. This family, part of the LysR family of transcriptional regulators, activates transcription of the gene for D-serine deaminase, dsdA. Trusted members of this family so far are found adjacent to dsdA and only in Gammaproteobacteria, including E. coli, Vibrio cholerae, and Colwellia psychrerythraea.
Probab=61.15 E-value=34 Score=28.01 Aligned_cols=47 Identities=15% Similarity=0.204 Sum_probs=33.3
Q ss_pred hHHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHHHHHHHHHHHH
Q psy5605 87 SVARKALQALEQ---VNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEAA 135 (152)
Q Consensus 87 ~iiR~~LQqLE~---~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~~ 135 (152)
+-+=.-+++||+ ..|++.+. .|=.||+.|+.++..+- +++..+.+..
T Consensus 37 pavS~~I~~LE~~lg~~Lf~R~~-r~~~lT~~G~~l~~~a~-~~l~~~~~~~ 86 (302)
T TIGR02036 37 SAISHRINQLEEELGIQLFVRSH-RKVELTHEGKRIYWALK-SSLDTLNQEI 86 (302)
T ss_pred HHHHHHHHHHHHHhCCceEEECC-CceeECHhHHHHHHHHH-HHHHHHHHHH
Confidence 445566799998 46777776 59999999998886654 5555544433
No 169
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=60.67 E-value=37 Score=27.07 Aligned_cols=45 Identities=27% Similarity=0.305 Sum_probs=33.2
Q ss_pred hHHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHHHHHHHHHH
Q psy5605 87 SVARKALQALEQ---VNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKE 133 (152)
Q Consensus 87 ~iiR~~LQqLE~---~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~ 133 (152)
+-+-+.+++||+ ..|.+... .|=.||+.|+..++. |.++.....+
T Consensus 32 pavS~~I~~LE~~lg~~Lf~R~~-r~~~lT~~G~~l~~~-a~~~l~~~~~ 79 (290)
T PRK10837 32 SAVSAALTDLEGQLGVQLFDRVG-KRLVVNEHGRLLYPR-ALALLEQAVE 79 (290)
T ss_pred cHHHHHHHHHHHHhCCccEeecC-CeEEECHhHHHHHHH-HHHHHHHHHH
Confidence 345567799998 46777766 488899999999985 5666665543
No 170
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=60.24 E-value=14 Score=29.07 Aligned_cols=46 Identities=26% Similarity=0.359 Sum_probs=33.4
Q ss_pred HhhHhhcC--CcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCC
Q psy5605 50 ARHIYMRS--PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDG 108 (152)
Q Consensus 50 lRkiYl~g--~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~g 108 (152)
+++.|.++ |.++..|...+|- .|.+-++..|+.||+.|+|++..+.
T Consensus 15 l~~~~~~~~~~~~~~ela~~~~~-------------~s~~tv~~~l~~L~~~g~i~~~~~~ 62 (199)
T TIGR00498 15 IRAHIESTGYPPSIREIARAVGL-------------RSPSAAEEHLKALERKGYIERDPGK 62 (199)
T ss_pred HHHHHHhcCCCCcHHHHHHHhCC-------------CChHHHHHHHHHHHHCCCEecCCCC
Confidence 33444444 4566788888753 3568899999999999999988743
No 171
>PF13089 PP_kinase_N: Polyphosphate kinase N-terminal domain; PDB: 2O8R_A 1XDP_A 1XDO_B.
Probab=60.20 E-value=9.9 Score=28.20 Aligned_cols=49 Identities=20% Similarity=0.365 Sum_probs=27.2
Q ss_pred HHHHhCCcceecCCCCceeCcchHhhHHHHHHHHHHHHHH-------HHHHHHhhcCceee
Q psy5605 94 QALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKE-------AALQALAAQGITVV 147 (152)
Q Consensus 94 QqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~-------~~~~~~~~~~~~~~ 147 (152)
+++..+|.-..+++ -+||+-+ |+.|...+..-..+ .-..+|+++||.++
T Consensus 53 k~~~~~g~~~~~~~---g~tP~eq--L~~I~~~v~~l~~~q~~~~~~~Llp~L~~~GI~ll 108 (109)
T PF13089_consen 53 KRQIEAGVKKRDPD---GLTPQEQ--LDAIRKRVHELVEEQYEIYNEELLPELAEEGIHLL 108 (109)
T ss_dssp HHHCCHHHCC---S------HHHH--HHHHHHHHHHHHHHHHHHHHHTHHHHHHCTTEEEE
T ss_pred HHHHHhccCCCCcC---CCCHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEe
Confidence 44444454444443 2555444 88888877543332 36679999999886
No 172
>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT). PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid []. The gene product has been shown to bind to the promoter sites and repress their transcription []. ; PDB: 3KFW_X 3L09_B.
Probab=60.01 E-value=9.6 Score=26.46 Aligned_cols=61 Identities=23% Similarity=0.329 Sum_probs=39.3
Q ss_pred HHHHHHhhHh---hc---CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCC---CceeCcc
Q psy5605 45 RCAALARHIY---MR---SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDG---GRKITSH 115 (152)
Q Consensus 45 RaASilRkiY---l~---g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~g---GR~lT~~ 115 (152)
|+-|++--+| +. +++-++.|-...+. --=+-+-+|.+|--|-+.||++....| .-.||++
T Consensus 1 ~a~Sli~tl~Gdy~~~~g~~i~~~~Li~ll~~-----------~Gv~e~avR~alsRl~~~G~L~~~r~Gr~~~Y~Lt~~ 69 (70)
T PF07848_consen 1 RARSLIVTLLGDYLRPRGGWIWVASLIRLLAA-----------FGVSESAVRTALSRLVRRGWLESERRGRRSYYRLTER 69 (70)
T ss_dssp -HHHHHHHHHHHHCCTTTS-EEHHHHHHHHCC-----------TT--HHHHHHHHHHHHHTTSEEEECCCTEEEEEE-HH
T ss_pred CcceehHHHHHHHhccCCCceeHHHHHHHHHH-----------cCCChHHHHHHHHHHHHcCceeeeecCccceEeeCCC
Confidence 3446666666 33 35666666666532 123457899999999999999988864 3678887
Q ss_pred h
Q psy5605 116 G 116 (152)
Q Consensus 116 G 116 (152)
|
T Consensus 70 g 70 (70)
T PF07848_consen 70 G 70 (70)
T ss_dssp H
T ss_pred C
Confidence 6
No 173
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=59.38 E-value=45 Score=25.91 Aligned_cols=45 Identities=16% Similarity=0.172 Sum_probs=31.9
Q ss_pred hHHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHHHHHHHHHH
Q psy5605 87 SVARKALQALEQ---VNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKE 133 (152)
Q Consensus 87 ~iiR~~LQqLE~---~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~ 133 (152)
+-+=..+++||+ ..|.+.+. .|=.||+.|+.+++.+. ++...+.+
T Consensus 6 pavS~~I~~LE~~lg~~Lf~R~~-r~~~lT~~G~~l~~~a~-~~l~~~~~ 53 (269)
T PRK11716 6 STLSRQIQRLEEELGQPLFVRDN-RSVTLTEAGEELRPFAQ-QTLLQWQQ 53 (269)
T ss_pred HHHHHHHHHHHHHhCCeeEEecC-CceeECHhHHHHHHHHH-HHHHHHHH
Confidence 345567889998 46777766 58899999999998754 44443333
No 174
>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=59.05 E-value=43 Score=22.23 Aligned_cols=40 Identities=23% Similarity=0.341 Sum_probs=31.1
Q ss_pred cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCC
Q psy5605 56 RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGG 109 (152)
Q Consensus 56 ~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gG 109 (152)
.+++....++...|= |.+-+=..++.|++.|||+..+.+|
T Consensus 20 ~~~v~~~~iA~~L~v--------------s~~tvt~ml~~L~~~GlV~~~~y~g 59 (60)
T PF01325_consen 20 GGPVRTKDIAERLGV--------------SPPTVTEMLKRLAEKGLVEYEPYKG 59 (60)
T ss_dssp TSSBBHHHHHHHHTS---------------HHHHHHHHHHHHHTTSEEEETTTE
T ss_pred CCCccHHHHHHHHCC--------------ChHHHHHHHHHHHHCCCEEecCCCC
Confidence 378888999988743 3355667899999999999988654
No 175
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=59.02 E-value=8.8 Score=35.06 Aligned_cols=40 Identities=15% Similarity=0.273 Sum_probs=32.1
Q ss_pred CCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCc
Q psy5605 57 SPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGR 110 (152)
Q Consensus 57 g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR 110 (152)
..+.+..|+....+ |...+|.+|++|++.|||+-.+.-||
T Consensus 22 ~~~~l~~la~~l~c--------------s~R~~~~~l~~~~~~gwl~w~~~~GR 61 (552)
T PRK13626 22 QETTLNELAELLNC--------------SRRHMRTLLNTMQQRGWLTWQAEAGR 61 (552)
T ss_pred ceeeHHHHHHHhcC--------------ChhHHHHHHHHHHHCCCeeeecCCCC
Confidence 35778888887754 44568999999999999999987665
No 176
>TIGR03042 PS_II_psbQ_bact photosystem II protein PsbQ. This protein through the member sll1638 from Synechocystis sp. PCC 6803, was shown to be part of the cyanobacteria photosystem II. It is homologous to (but quite diverged from) the chloroplast PsbQ protein, called oxygen-evolving enhancer protein 3 (OEE3). We designate this cyanobacteria protein PsbQ by homology.
Probab=58.85 E-value=18 Score=28.78 Aligned_cols=17 Identities=35% Similarity=0.899 Sum_probs=13.9
Q ss_pred CCchHHHHHHHHHhhHhhcCCcch
Q psy5605 38 DPDWFYTRCAALARHIYMRSPVGV 61 (152)
Q Consensus 38 d~DW~YiRaASilRkiYl~g~vGV 61 (152)
+.||-|+| =|||||.|-
T Consensus 61 kk~W~~vr-------n~irgp~g~ 77 (142)
T TIGR03042 61 KEDWVFTR-------NLIHGPMGE 77 (142)
T ss_pred hcchHHHH-------HHHhccHHH
Confidence 46999999 688998765
No 177
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=58.77 E-value=46 Score=27.02 Aligned_cols=47 Identities=19% Similarity=0.192 Sum_probs=33.9
Q ss_pred hHHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHHHHHHHHHHHH
Q psy5605 87 SVARKALQALEQ---VNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEAA 135 (152)
Q Consensus 87 ~iiR~~LQqLE~---~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~~ 135 (152)
+-+-+.+++||+ ..|.+.+. .|=.||+.|+..++. |.++...+....
T Consensus 30 pavS~~i~~LE~~lg~~LF~R~~-r~~~lT~~G~~l~~~-a~~~l~~~~~~~ 79 (305)
T PRK11151 30 PTLSGQIRKLEDELGVMLLERTS-RKVLFTQAGLLLVDQ-ARTVLREVKVLK 79 (305)
T ss_pred hHHHHHHHHHHHHhCchheeeCC-CceeECccHHHHHHH-HHHHHHHHHHHH
Confidence 456677899998 46667665 599999999999876 455655555443
No 178
>PF13730 HTH_36: Helix-turn-helix domain
Probab=58.74 E-value=9.6 Score=23.88 Aligned_cols=20 Identities=25% Similarity=0.415 Sum_probs=17.0
Q ss_pred CCchhHHHHHHHHHHhCCcc
Q psy5605 83 RSSGSVARKALQALEQVNII 102 (152)
Q Consensus 83 ~asg~iiR~~LQqLE~~glV 102 (152)
.-|.+=++++++.||+.|||
T Consensus 36 g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 36 GVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CcCHHHHHHHHHHHHHCcCC
Confidence 44677899999999999986
No 179
>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=58.31 E-value=14 Score=25.68 Aligned_cols=21 Identities=38% Similarity=0.469 Sum_probs=18.6
Q ss_pred hhHHHHHHHHHHhCCcceecC
Q psy5605 86 GSVARKALQALEQVNIIEKSD 106 (152)
Q Consensus 86 g~iiR~~LQqLE~~glVek~~ 106 (152)
+|+|=++|..||.+|+|+.-.
T Consensus 18 RSvIVNALRKleSaGvIesrS 38 (61)
T PF08222_consen 18 RSVIVNALRKLESAGVIESRS 38 (61)
T ss_dssp HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHHHHhcCceeecc
Confidence 589999999999999999554
No 180
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=56.99 E-value=83 Score=23.79 Aligned_cols=60 Identities=10% Similarity=0.150 Sum_probs=41.2
Q ss_pred HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCc----eeCcchHhhHHH
Q psy5605 48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGR----KITSHGRRDMDR 122 (152)
Q Consensus 48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR----~lT~~G~~~LD~ 122 (152)
.|++.|.-.++..|+.|...+|- +.+-+=+=|+-|+++|||+.... || .|.+.....++.
T Consensus 20 ~IL~~L~~~~~~~v~ela~~l~l--------------sqstvS~HL~~L~~AGLV~~~r~-Gr~~~Y~l~~~~~~~~~~ 83 (117)
T PRK10141 20 GIVLLLRESGELCVCDLCTALDQ--------------SQPKISRHLALLRESGLLLDRKQ-GKWVHYRLSPHIPAWAAK 83 (117)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCc--------------CHHHHHHHHHHHHHCCceEEEEE-cCEEEEEECchHHHHHHH
Confidence 46666655588999999998854 22334455799999999998885 54 466654444444
No 181
>PF03965 Penicillinase_R: Penicillinase repressor; InterPro: IPR005650 Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis []. BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth []. MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected []. At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2G9W_A 2K4B_A 1XSD_A 1SD4_A 1SD7_A 1SD6_A 2P7C_B 1P6R_A 1OKR_B 2D45_B ....
Probab=56.76 E-value=67 Score=23.27 Aligned_cols=50 Identities=8% Similarity=0.137 Sum_probs=40.4
Q ss_pred HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC
Q psy5605 48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD 107 (152)
Q Consensus 48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~ 107 (152)
-||+-|.-.|++.+..+....... ++ -+-+-++..|.-|++-|+|+....
T Consensus 7 ~IM~~lW~~~~~t~~eI~~~l~~~--~~--------~~~sTv~t~L~rL~~Kg~l~~~~~ 56 (115)
T PF03965_consen 7 EIMEILWESGEATVREIHEALPEE--RS--------WAYSTVQTLLNRLVEKGFLTREKI 56 (115)
T ss_dssp HHHHHHHHHSSEEHHHHHHHHCTT--SS----------HHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHHHHHHhCCCCCHHHHHHHHHhc--cc--------cchhHHHHHHHHHHhCCceeEeec
Confidence 478888889999999999998654 22 244789999999999999998875
No 182
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=56.62 E-value=43 Score=27.49 Aligned_cols=46 Identities=22% Similarity=0.374 Sum_probs=32.7
Q ss_pred hHHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHHHHHHHHHHH
Q psy5605 87 SVARKALQALEQ---VNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEA 134 (152)
Q Consensus 87 ~iiR~~LQqLE~---~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~ 134 (152)
+-+-..+++||+ ..|.+.+. +|=.||+.|+.+++. |.++...+...
T Consensus 36 pavS~~I~~LE~~lg~~LF~R~~-r~~~lT~~G~~l~~~-a~~il~~~~~~ 84 (312)
T PRK10341 36 PAVSKIINDIEDYFGVELIVRKN-TGVTLTPAGQVLLSR-SESITREMKNM 84 (312)
T ss_pred HHHHHHHHHHHHHhCCeEEEEcC-CCceEChhHHHHHHH-HHHHHHHHHHH
Confidence 446667899998 35666666 589999999999986 45555544333
No 183
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=55.90 E-value=38 Score=28.42 Aligned_cols=46 Identities=20% Similarity=0.230 Sum_probs=31.0
Q ss_pred HHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHHHHHHHHHHH
Q psy5605 88 VARKALQALEQ---VNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEA 134 (152)
Q Consensus 88 iiR~~LQqLE~---~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~ 134 (152)
-+=..+++||+ ..|.+....+-..||+.|+.+++. |.++.....+.
T Consensus 32 avS~~I~~LE~~lG~~LF~R~~r~~~~LT~~G~~l~~~-a~~il~~~~~~ 80 (324)
T PRK12681 32 GISKQVRMLEDELGIQIFARSGKHLTQVTPAGEEIIRI-AREILSKVESI 80 (324)
T ss_pred HHHHHHHHHHHHhCCEeEEECCCCCCccCHHHHHHHHH-HHHHHHHHHHH
Confidence 45566799998 467777663223699999999965 45565555443
No 184
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=55.45 E-value=48 Score=27.11 Aligned_cols=47 Identities=15% Similarity=0.165 Sum_probs=33.9
Q ss_pred hHHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHHHHHHHHHHHH
Q psy5605 87 SVARKALQALEQ---VNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEAA 135 (152)
Q Consensus 87 ~iiR~~LQqLE~---~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~~ 135 (152)
+-+-+.+++||+ ..|++.+. .|=.||+.|+.++... .++.....+..
T Consensus 30 ~avS~~I~~LE~~lg~~LF~R~~-r~v~lT~~G~~l~~~a-~~~l~~~~~~~ 79 (305)
T PRK11233 30 PALSQQVATLEGELNQQLLIRTK-RGVTPTEAGKILYTHA-RAILRQCEQAQ 79 (305)
T ss_pred hHHHHHHHHHHHHhCCceEEeCC-CCceECHhHHHHHHHH-HHHHHHHHHHH
Confidence 456677899998 46777776 5899999999988764 45555554443
No 185
>PF11313 DUF3116: Protein of unknown function (DUF3116); InterPro: IPR021464 This family of proteins with unknown function appears to be restricted to Bacillales.
Probab=54.77 E-value=17 Score=26.61 Aligned_cols=42 Identities=14% Similarity=0.136 Sum_probs=31.9
Q ss_pred CchhHHHHHHHHHHhCCcceecCC---CCceeCcchHhhHHHHHH
Q psy5605 84 SSGSVARKALQALEQVNIIEKSDD---GGRKITSHGRRDMDRIAA 125 (152)
Q Consensus 84 asg~iiR~~LQqLE~~glVek~~~---gGR~lT~~G~~~LD~iA~ 125 (152)
-+.+=+=.++=.||..|+|..... .--.+|++|...|++|-.
T Consensus 39 ~TKNelL~~vYWLE~ngyI~R~~~~~~~rY~~T~kG~~ll~~~~~ 83 (85)
T PF11313_consen 39 FTKNELLYTVYWLEENGYIFRDNNNNEKRYSLTEKGKELLAEIKN 83 (85)
T ss_pred ccHHHHHHHHHHHhhcCeeEeecCCCcceeEEeccHHHHHHHHHh
Confidence 334455577789999999985542 247899999999999854
No 186
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=54.67 E-value=40 Score=27.65 Aligned_cols=44 Identities=16% Similarity=0.271 Sum_probs=32.7
Q ss_pred hhHHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHHHHHHHH
Q psy5605 86 GSVARKALQALEQ---VNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSK 131 (152)
Q Consensus 86 g~iiR~~LQqLE~---~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~ 131 (152)
-+-+-+.+++||+ ..|++.+. +|=.||+.|+.+++.+ .++...+
T Consensus 32 qsavS~~Ik~LE~~lg~~Lf~R~~-~~v~LT~~G~~l~~~a-~~~l~~~ 78 (309)
T PRK11013 32 QPTVSRELARFEKVIGLKLFERVR-GRLHPTVQGLRLFEEV-QRSYYGL 78 (309)
T ss_pred cHHHHHHHHHHHHHhCceeeeecC-CCcccCHHHHHHHHHH-HHHHHHH
Confidence 3567788999998 46777666 5789999999998865 4554433
No 187
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=54.34 E-value=64 Score=26.14 Aligned_cols=43 Identities=19% Similarity=0.244 Sum_probs=31.8
Q ss_pred hHHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHHHHHHHH
Q psy5605 87 SVARKALQALEQ---VNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSK 131 (152)
Q Consensus 87 ~iiR~~LQqLE~---~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~ 131 (152)
+-+=+.+++||+ ..|++... +|=.||+.|+.+++.+.. +...+
T Consensus 34 ~avS~~i~~LE~~lG~~LF~R~~-r~~~lT~~G~~l~~~a~~-~l~~~ 79 (302)
T PRK09791 34 PALTKSIQELEEGLAAQLFFRRS-KGVTLTDAGESFYQHASL-ILEEL 79 (302)
T ss_pred HHHHHHHHHHHHHhCCeEEEEcC-CCceECccHHHHHHHHHH-HHHHH
Confidence 455667899998 46777766 589999999999987654 44433
No 188
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=54.12 E-value=50 Score=26.70 Aligned_cols=47 Identities=19% Similarity=0.278 Sum_probs=33.4
Q ss_pred hHHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHHHHHHHHHHHH
Q psy5605 87 SVARKALQALEQ---VNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEAA 135 (152)
Q Consensus 87 ~iiR~~LQqLE~---~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~~ 135 (152)
+-+=+.+++||+ ..|++... .|=.||+.|+.++.. |.++...+.+..
T Consensus 35 ~avS~~i~~LE~~lg~~Lf~R~~-r~l~lT~~G~~l~~~-~~~~l~~~~~~~ 84 (297)
T PRK11139 35 AAVSHQIKALEDFLGLKLFRRRN-RSLLLTEEGQRYFLD-IREIFDQLAEAT 84 (297)
T ss_pred HHHHHHHHHHHHHhCchheEecC-CceeECHhHHHHHHH-HHHHHHHHHHHH
Confidence 456677899998 36777666 588999999998877 445555444443
No 189
>PRK11057 ATP-dependent DNA helicase RecQ; Provisional
Probab=54.04 E-value=41 Score=31.43 Aligned_cols=105 Identities=10% Similarity=0.141 Sum_probs=69.8
Q ss_pred CchHHHHHHHHHhhHh-hcCCcchhhHHHHhCCCCCCCCCCC------cc---CCCchhHHHHHHHHHHhCCcceecCC-
Q psy5605 39 PDWFYTRCAALARHIY-MRSPVGVKTVTKIFGGRKRNGVCPS------HF---CRSSGSVARKALQALEQVNIIEKSDD- 107 (152)
Q Consensus 39 ~DW~YiRaASilRkiY-l~g~vGV~~L~~~YGg~krrG~~P~------h~---~~asg~iiR~~LQqLE~~glVek~~~- 107 (152)
-|+. .-+..++.-+| +.+..|.+.+...+-|.++.-++-. .| ..-+..-++.++++|...|+++...+
T Consensus 410 ~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~l~~~~~~~~~~~~ 488 (607)
T PRK11057 410 YDGL-EDAQKALSCIYRVNQRFGMGYVVEVLRGANNQRIRDYGHDKLKVYGIGRDKSHEHWVSVIRQLIHLGLVTQNIAQ 488 (607)
T ss_pred cccH-HHHHHHHHHHHHhcCCCCcceeeeeeeccCcchhhhcccccCCccCcCCcCCHHHHHHHHHHHHHcCCceeccCc
Confidence 3654 44566777777 5678899999988888766554332 22 12234588999999999999986653
Q ss_pred -CCceeCcchHhhHHH--------------------------HHHHHHHHHHHHHHHHHhhcCc
Q psy5605 108 -GGRKITSHGRRDMDR--------------------------IAAQIRVSKKEAALQALAAQGI 144 (152)
Q Consensus 108 -gGR~lT~~G~~~LD~--------------------------iA~~i~~~~~~~~~~~~~~~~~ 144 (152)
..=.||++|+..|.. .-..+++++++.+++...++|+
T Consensus 489 ~~~l~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~Lr~~R~~~a~~~~~ 552 (607)
T PRK11057 489 HSALQLTEAARPVLRGEVSLQLAVPRIVALKPRAMQKSFGGNYDRKLFAKLRKLRKSIADEENI 552 (607)
T ss_pred cceEEECHHHHHHhcCCceEEEecccccccccccccccccccchHHHHHHHHHHHHHHHHHcCC
Confidence 245678777765542 1134667777777776555554
No 190
>PRK10632 transcriptional regulator; Provisional
Probab=53.72 E-value=54 Score=26.93 Aligned_cols=46 Identities=17% Similarity=0.258 Sum_probs=32.4
Q ss_pred hHHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHHHHHHHHHHH
Q psy5605 87 SVARKALQALEQ---VNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEA 134 (152)
Q Consensus 87 ~iiR~~LQqLE~---~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~ 134 (152)
+-+=..+++||+ ..|.+.+. .|-.||+.|+.+++.. .++.....+.
T Consensus 31 pavS~~I~~LE~~lg~~Lf~R~~-r~i~lT~~G~~l~~~a-~~il~~~~~~ 79 (309)
T PRK10632 31 SSISQTVSKLEDELQVKLLNRST-RSIGLTEAGRIYYQGC-RRMLHEVQDV 79 (309)
T ss_pred HHHHHHHHHHHHHhCCeeecccC-CCceechhHHHHHHHH-HHHHHHHHHH
Confidence 456677899998 46666666 5899999999988664 4555444433
No 191
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=53.47 E-value=19 Score=28.78 Aligned_cols=47 Identities=21% Similarity=0.134 Sum_probs=41.7
Q ss_pred HHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceec
Q psy5605 45 RCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKS 105 (152)
Q Consensus 45 RaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~ 105 (152)
|-..|+..|--+|.+.+..|...|| -|..-||.=|++||+.|+|...
T Consensus 8 R~~~Il~~l~~~~~~~~~~La~~~~--------------vS~~TiRRDl~~L~~~g~~~r~ 54 (185)
T PRK04424 8 RQKALQELIEENPFITDEELAEKFG--------------VSIQTIRLDRMELGIPELRERI 54 (185)
T ss_pred HHHHHHHHHHHCCCEEHHHHHHHHC--------------cCHHHHHHHHHHHhcchHHHHH
Confidence 7778888888899999999999984 6789999999999999999744
No 192
>PF07381 DUF1495: Winged helix DNA-binding domain (DUF1495); InterPro: IPR010863 This family consists of several hypothetical archaeal proteins of around 110 residues in length. The function of this family is unknown, although one sequence (Q8U3W1 from SWISSPROT) is described as a putative HTH transcription regulator.
Probab=53.19 E-value=11 Score=27.73 Aligned_cols=29 Identities=24% Similarity=0.577 Sum_probs=21.6
Q ss_pred HHHHhCCcc-eecCCCC---ceeCcchHhhHHH
Q psy5605 94 QALEQVNII-EKSDDGG---RKITSHGRRDMDR 122 (152)
Q Consensus 94 QqLE~~glV-ek~~~gG---R~lT~~G~~~LD~ 122 (152)
.+|..+||| ++...+| -+||++|.+..|-
T Consensus 57 ~SLv~lGLV~~~~~~~g~k~Y~lT~~G~~~~~~ 89 (90)
T PF07381_consen 57 DSLVGLGLVEEEEEKGGFKYYRLTEKGKRIAEM 89 (90)
T ss_pred hhHHHcCCeeEeeecCCeeEEEeChhhhhHHhc
Confidence 578999999 4444333 5799999988763
No 193
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=50.61 E-value=79 Score=25.49 Aligned_cols=45 Identities=18% Similarity=0.271 Sum_probs=32.1
Q ss_pred HHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHHHHHHHHHHH
Q psy5605 88 VARKALQALEQ---VNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEA 134 (152)
Q Consensus 88 iiR~~LQqLE~---~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~ 134 (152)
-+=+-+++||+ ..|++.+. .|=.||++|+.+++.+. ++.....+.
T Consensus 31 avS~~I~~LE~~lG~~LF~R~~-r~~~lT~~G~~l~~~a~-~~l~~~~~~ 78 (275)
T PRK03601 31 AVSFRIRQLENQLGVNLFTRHR-NNIRLTAAGERLLPYAE-TLMNTWQAA 78 (275)
T ss_pred HHHHHHHHHHHHhCCceEEECC-CceEECHhHHHHHHHHH-HHHHHHHHH
Confidence 34456799998 46777776 58899999999888765 455444433
No 194
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=50.19 E-value=57 Score=26.92 Aligned_cols=46 Identities=11% Similarity=0.135 Sum_probs=32.5
Q ss_pred hHHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHHHHHHHHHHH
Q psy5605 87 SVARKALQALEQ---VNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEA 134 (152)
Q Consensus 87 ~iiR~~LQqLE~---~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~ 134 (152)
+-+=..+++||+ ..|++.+. .|-.||+.|+..++.+ .++...+...
T Consensus 31 pavS~~I~~LE~~lg~~Lf~R~~-r~~~lT~~G~~l~~~a-~~il~~~~~~ 79 (308)
T PRK10094 31 ATISYRIKLLEENTGVALFFRTT-RSVTLTAAGEHLLSQA-RDWLSWLESM 79 (308)
T ss_pred HHHHHHHHHHHHHhCCEEEeeCC-CceeECHhHHHHHHHH-HHHHHHHHHH
Confidence 345567899998 45667666 5899999999998764 4555544443
No 195
>PRK00215 LexA repressor; Validated
Probab=50.18 E-value=18 Score=28.60 Aligned_cols=50 Identities=20% Similarity=0.376 Sum_probs=36.1
Q ss_pred CcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCc--eeCcchHhhH
Q psy5605 58 PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGR--KITSHGRRDM 120 (152)
Q Consensus 58 ~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR--~lT~~G~~~L 120 (152)
+.++..|+...|- .+.+-+...|+.||+.|+|+..++.+| .|++.|+..+
T Consensus 23 ~~s~~ela~~~~~-------------~~~~tv~~~l~~L~~~g~i~~~~~~~r~~~l~~~~~~~~ 74 (205)
T PRK00215 23 PPSRREIADALGL-------------RSPSAVHEHLKALERKGFIRRDPGRSRAIEVAAPAQLEL 74 (205)
T ss_pred CCCHHHHHHHhCC-------------CChHHHHHHHHHHHHCCCEEeCCCCcceEEecccccccc
Confidence 5688899988754 134567788999999999999886654 3555565543
No 196
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=49.87 E-value=56 Score=27.23 Aligned_cols=46 Identities=20% Similarity=0.222 Sum_probs=32.5
Q ss_pred hHHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHHHHHHHHHHH
Q psy5605 87 SVARKALQALEQ---VNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEA 134 (152)
Q Consensus 87 ~iiR~~LQqLE~---~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~ 134 (152)
+-+-..+++||+ ..|++.+. .|=.||+.|+.+++. |.+++..+.+.
T Consensus 31 paVS~~Ik~LE~~lg~~LF~R~~-r~v~lT~~G~~l~~~-a~~il~~~~~~ 79 (317)
T PRK15421 31 SALSHQFSDLEQRLGFRLFVRKS-QPLRFTPQGEILLQL-ANQVLPQISQA 79 (317)
T ss_pred HHHHHHHHHHHHHhCCEEEEecC-CCceECHhHHHHHHH-HHHHHHHHHHH
Confidence 446667899998 45667665 588999999999876 45555555443
No 197
>PF03836 RasGAP_C: RasGAP C-terminus; InterPro: IPR000593 Ras GTPase-activating protein (rasGAP) is a major contributor to the down-regulation of ras by facilitating GTP hydrolysis of activated ras. In addition, GAP participates in the down-stream effector system of the ras signalling pathway. Abnormal signal transduction involving activated ras genes plays a major role in the development of a variety of tumours. Depending on the precise genetic alteration, its location within the gene and the effects it exerts on protein function, rasGAP can theoretically function as either an oncogene or as a tumour suppressor gene [].; GO: 0005099 Ras GTPase activator activity, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 3ISU_A 3IEZ_A 4EZA_B 1X0H_A.
Probab=49.67 E-value=5.5 Score=30.62 Aligned_cols=34 Identities=26% Similarity=0.389 Sum_probs=0.0
Q ss_pred HHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHHH
Q psy5605 88 VARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRV 129 (152)
Q Consensus 88 iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~~ 129 (152)
-+..-|..||.+|+|....+ =|..|+.||.+|..
T Consensus 8 ~~l~~l~~LE~~G~v~~~n~--------yQ~lln~IA~dI~~ 41 (142)
T PF03836_consen 8 KILENLKELESLGIVSRSNN--------YQDLLNDIAKDIRN 41 (142)
T ss_dssp ------------------------------------------
T ss_pred HHHHHHHHHHHCCCCCCccc--------HHHHHHHHHHHHhC
Confidence 45566789999999987642 24589999999854
No 198
>PF03969 AFG1_ATPase: AFG1-like ATPase; InterPro: IPR005654 ATPase family gene 1 (AFG1) ATPase is a 377 amino acid putative protein with an ATPase motif typical of the protein family including SEC18p PAS1, CDC48-VCP and TBP. AFG1 also has substantial homology to these proteins outside the ATPase domain []. This family of proteins contains a P-loop motif.; GO: 0005524 ATP binding
Probab=48.68 E-value=53 Score=29.20 Aligned_cols=85 Identities=16% Similarity=0.266 Sum_probs=48.1
Q ss_pred HHHhhHhhcCCcchhh---HHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHH
Q psy5605 48 ALARHIYMRSPVGVKT---VTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIA 124 (152)
Q Consensus 48 SilRkiYl~g~vGV~~---L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA 124 (152)
+.-|-|||.||||.|. |--.|..-.-..-+.-||. ..+..+-+.|-+.. .+..-|+.+|
T Consensus 60 ~~~~GlYl~G~vG~GKT~Lmd~f~~~lp~~~k~R~HFh----~Fm~~vh~~l~~~~--------------~~~~~l~~va 121 (362)
T PF03969_consen 60 PPPKGLYLWGPVGRGKTMLMDLFYDSLPIKRKRRVHFH----EFMLDVHSRLHQLR--------------GQDDPLPQVA 121 (362)
T ss_pred CCCceEEEECCCCCchhHHHHHHHHhCCcccccccccc----HHHHHHHHHHHHHh--------------CCCccHHHHH
Confidence 3457899999999986 3445555443334555664 34555555555544 1111233333
Q ss_pred HHH-----------------HHH-HHHHHHHHHhhcCceeeccC
Q psy5605 125 AQI-----------------RVS-KKEAALQALAAQGITVVPTG 150 (152)
Q Consensus 125 ~~i-----------------~~~-~~~~~~~~~~~~~~~~~~~~ 150 (152)
.++ ..+ +-+.-..+|-++|+.+|-|.
T Consensus 122 ~~l~~~~~lLcfDEF~V~DiaDAmil~rLf~~l~~~gvvlVaTS 165 (362)
T PF03969_consen 122 DELAKESRLLCFDEFQVTDIADAMILKRLFEALFKRGVVLVATS 165 (362)
T ss_pred HHHHhcCCEEEEeeeeccchhHHHHHHHHHHHHHHCCCEEEecC
Confidence 333 212 23444567888999998774
No 199
>TIGR03337 phnR transcriptional regulator protein. This family of proteins are members of the GntR family (pfam00392) containing an N-terminal helix-turn-helix (HTH) motif. This clade is found adjacent to or inside of operons for the degradation of 2-aminoethylphosphonate (AEP) in Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii.
Probab=47.67 E-value=21 Score=28.20 Aligned_cols=32 Identities=28% Similarity=0.360 Sum_probs=27.5
Q ss_pred chhHHHHHHHHHHhCCcceecCCCCceeCcch
Q psy5605 85 SGSVARKALQALEQVNIIEKSDDGGRKITSHG 116 (152)
Q Consensus 85 sg~iiR~~LQqLE~~glVek~~~gGR~lT~~G 116 (152)
|...+|.+|..|+..|+|......|..+++..
T Consensus 38 sr~Tvr~Al~~L~~eGli~~~~g~Gt~V~~~~ 69 (231)
T TIGR03337 38 TRVTIREALQQLEAEGLIYREDRRGWFVSPPR 69 (231)
T ss_pred CHHHHHHHHHHHHHCCeEEEeCCCEEEECCcc
Confidence 47899999999999999999887787777543
No 200
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=47.53 E-value=52 Score=23.02 Aligned_cols=42 Identities=17% Similarity=0.295 Sum_probs=35.2
Q ss_pred HHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcce
Q psy5605 48 ALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIE 103 (152)
Q Consensus 48 SilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVe 103 (152)
.|++.+.-++++....|.+..| -|.+-++..++.|++.|+|.
T Consensus 7 ~il~~L~~~~~~~~~~la~~l~--------------~s~~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 7 KILEELQKDARISLAELAKKVG--------------LSPSTVHNRVKRLEEEGVIK 48 (108)
T ss_pred HHHHHHHHhCCCCHHHHHHHHC--------------cCHHHHHHHHHHHHHCCCee
Confidence 4777777788888888888863 45688999999999999998
No 201
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=47.13 E-value=22 Score=30.97 Aligned_cols=32 Identities=13% Similarity=0.178 Sum_probs=26.9
Q ss_pred CCchhHHHHHHHHHHhCCcceecCCCCceeCc
Q psy5605 83 RSSGSVARKALQALEQVNIIEKSDDGGRKITS 114 (152)
Q Consensus 83 ~asg~iiR~~LQqLE~~glVek~~~gGR~lT~ 114 (152)
.-|.+-+|.++++||+.|+|+..+..|-.+.+
T Consensus 40 ~vsr~tv~~a~~~L~~~g~i~~~~~~G~~v~~ 71 (431)
T PRK15481 40 GVNRNTVAAAYKRLVTAGLAQSQGRNGTVIRG 71 (431)
T ss_pred CCCHHHHHHHHHHHHHCCCEEEeCCCceEEcc
Confidence 46889999999999999999988766766653
No 202
>TIGR03418 chol_sulf_TF putative choline sulfate-utilization transcription factor. Members of this protein family are transcription factors of the LysR family. Their genes typically are divergently transcribed from choline-sulfatase genes. That enzyme makes choline, a precursor to the osmoprotectant glycine-betaine, available by hydrolysis of choline sulfate.
Probab=46.52 E-value=61 Score=25.96 Aligned_cols=43 Identities=16% Similarity=0.301 Sum_probs=30.0
Q ss_pred hHHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHHHHHHHH
Q psy5605 87 SVARKALQALEQ---VNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSK 131 (152)
Q Consensus 87 ~iiR~~LQqLE~---~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~ 131 (152)
+-+=..+++||+ ..|.+.+. .|-.||+.|+.+++.+. ++....
T Consensus 30 pavS~~Ik~LE~~lg~~LF~R~~-r~~~lT~~G~~l~~~a~-~il~~~ 75 (291)
T TIGR03418 30 PAVSQQVKRLEEELGTPLFERGH-RGIELTEDGQRLFEAVR-AGLDTI 75 (291)
T ss_pred HHHHHHHHHHHHHhCcHHhhcCC-CceeEcHhHHHHHHHHH-HHHHHH
Confidence 345566799998 35666655 58999999999888755 444433
No 203
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=45.86 E-value=72 Score=26.01 Aligned_cols=43 Identities=14% Similarity=0.188 Sum_probs=30.5
Q ss_pred hHHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHHHHHHHH
Q psy5605 87 SVARKALQALEQ---VNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSK 131 (152)
Q Consensus 87 ~iiR~~LQqLE~---~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~ 131 (152)
+-+-+.+++||+ ..|++.+. .|=.||+.|+.+++... ++....
T Consensus 34 pavS~~i~~LE~~lg~~Lf~R~~-r~~~lT~~G~~l~~~a~-~ll~~~ 79 (305)
T CHL00180 34 PAVSLQIKNLEKQLNIPLFDRSK-NKASLTEAGELLLRYGN-RILALC 79 (305)
T ss_pred hHHHHHHHHHHHHhCCEEEEecC-CCceECHhHHHHHHHHH-HHHHHH
Confidence 345667899998 35666665 48999999999988754 444433
No 204
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=45.60 E-value=59 Score=26.83 Aligned_cols=43 Identities=26% Similarity=0.326 Sum_probs=27.9
Q ss_pred HHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHHHHHHHHH
Q psy5605 89 ARKALQALEQ---VNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKK 132 (152)
Q Consensus 89 iR~~LQqLE~---~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~ 132 (152)
+=..+++||+ ..|.+.+..+...||+.|+..++.+ .++.....
T Consensus 33 vS~~ik~LE~~lg~~Lf~R~~r~~~~lT~~G~~l~~~a-~~il~~~~ 78 (313)
T PRK12684 33 VSKAIIELEDELGVEIFTRHGKRLRGLTEPGRIILASV-ERILQEVE 78 (313)
T ss_pred HHHHHHHHHHHhCCeeEEEcCCcccccChhHHHHHHHH-HHHHHHHH
Confidence 4456788998 4566665532257999999888754 44544443
No 205
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=45.12 E-value=1.1e+02 Score=24.85 Aligned_cols=43 Identities=16% Similarity=0.227 Sum_probs=30.9
Q ss_pred hHHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHHHHHHHH
Q psy5605 87 SVARKALQALEQ---VNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSK 131 (152)
Q Consensus 87 ~iiR~~LQqLE~---~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~ 131 (152)
+-+-..+++||+ .-|.+.+. .|=.||+.|+.++..+ .++...+
T Consensus 31 pavS~~I~~LE~~lg~~LF~R~~-r~~~lT~~G~~l~~~~-~~~l~~~ 76 (300)
T PRK11074 31 SAVSYTVRQLEEWLAVPLFERRH-RDVELTPAGEWFVKEA-RSVIKKM 76 (300)
T ss_pred HHHHHHHHHHHHHhCCeeEEeCC-CCceECccHHHHHHHH-HHHHHHH
Confidence 456677899998 46667665 5889999999998654 4444433
No 206
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=44.09 E-value=77 Score=19.62 Aligned_cols=48 Identities=19% Similarity=0.345 Sum_probs=35.9
Q ss_pred HHHHHHhhHhh-cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCC-cceecC
Q psy5605 45 RCAALARHIYM-RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVN-IIEKSD 106 (152)
Q Consensus 45 RaASilRkiYl-~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~g-lVek~~ 106 (152)
|-..|+.-|.- .+++....|+..+| -|..-|++-++.|++.| .|+..+
T Consensus 1 R~~~il~~L~~~~~~it~~eLa~~l~--------------vS~rTi~~~i~~L~~~~~~I~~~~ 50 (55)
T PF08279_consen 1 RQKQILKLLLESKEPITAKELAEELG--------------VSRRTIRRDIKELREWGIPIESKR 50 (55)
T ss_dssp HHHHHHHHHHHTTTSBEHHHHHHHCT--------------S-HHHHHHHHHHHHHTT-EEEEET
T ss_pred CHHHHHHHHHHcCCCcCHHHHHHHhC--------------CCHHHHHHHHHHHHHCCCeEEeeC
Confidence 44567877764 45699999999974 46788999999999999 444444
No 207
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=43.35 E-value=93 Score=25.30 Aligned_cols=42 Identities=14% Similarity=0.154 Sum_probs=29.8
Q ss_pred HHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHHHHHHHH
Q psy5605 88 VARKALQALEQ---VNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSK 131 (152)
Q Consensus 88 iiR~~LQqLE~---~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~ 131 (152)
-+=..+++||+ ..|.+... +|=.||+.|+.++..+.. +....
T Consensus 34 avS~~I~~LE~~lg~~Lf~R~~-r~~~lT~~G~~l~~~a~~-il~~~ 78 (296)
T PRK11062 34 TITGQIKALEERLQGKLFKRKG-RGLEPTELGELVFRYADK-MFTLS 78 (296)
T ss_pred HHHHHHHHHHHHcCccceeecC-CceeECHhHHHHHHHHHH-HHHHH
Confidence 34455789998 46677766 589999999999876554 44443
No 208
>KOG1767|consensus
Probab=42.94 E-value=16 Score=28.08 Aligned_cols=24 Identities=33% Similarity=0.555 Sum_probs=20.5
Q ss_pred CCchhHHHHHHHHHHhCCcceecC
Q psy5605 83 RSSGSVARKALQALEQVNIIEKSD 106 (152)
Q Consensus 83 ~asg~iiR~~LQqLE~~glVek~~ 106 (152)
+=.||+.|.+|+.|+.-|+|....
T Consensus 71 kIngsLAr~alr~L~~kG~Ik~Vs 94 (110)
T KOG1767|consen 71 KINGSLARAALRELSNKGVIKQVS 94 (110)
T ss_pred hhchHHHHHHHHHHHhcchHHHHh
Confidence 456899999999999999997544
No 209
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=42.74 E-value=71 Score=26.22 Aligned_cols=46 Identities=15% Similarity=0.115 Sum_probs=32.6
Q ss_pred chhHHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHHHHHHHHH
Q psy5605 85 SGSVARKALQALEQ---VNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKK 132 (152)
Q Consensus 85 sg~iiR~~LQqLE~---~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~ 132 (152)
|-+-+-+.+++||+ ..|++.+. .|=.||+.|+.++.. |.++...+.
T Consensus 49 sQpavS~~I~~LE~~lg~~LF~R~~-r~~~lT~~G~~l~~~-~~~~l~~~~ 97 (314)
T PRK09508 49 SQPAVSNAVARLKVMFNDELFVRYG-RGIQPTARARQLFGP-VRQALQLVQ 97 (314)
T ss_pred CHHHHHHHHHHHHHhhCCCcEEEcC-CCCcCcHHHHHHHHH-HHHHHHHHH
Confidence 33556677899998 46777776 488999999998866 445554443
No 210
>smart00427 H2B Histone H2B.
Probab=42.28 E-value=55 Score=24.18 Aligned_cols=38 Identities=18% Similarity=0.093 Sum_probs=29.6
Q ss_pred hHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHHHHHHHH
Q psy5605 87 SVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEA 134 (152)
Q Consensus 87 ~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~ 134 (152)
.-|.++|+| .+|+. .||.+.+..||.+..++++....+
T Consensus 5 ~Yi~kvLKq--------Vhpd~--giS~kam~imnSfvnDiferIa~E 42 (89)
T smart00427 5 IYIYKVLKQ--------VHPDT--GISSKAMSIMNSFVNDIFERIAAE 42 (89)
T ss_pred HHHHHHHHH--------hCCCc--cccHHHHHHHHHHHHHHHHHHHHH
Confidence 346677776 46754 599999999999999999877544
No 211
>PRK09213 pur operon repressor; Provisional
Probab=41.93 E-value=1.2e+02 Score=26.09 Aligned_cols=75 Identities=11% Similarity=0.284 Sum_probs=49.0
Q ss_pred HHHHHHhhHhhcC--CcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCceeCcc-----
Q psy5605 45 RCAALARHIYMRS--PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGRKITSH----- 115 (152)
Q Consensus 45 RaASilRkiYl~g--~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR~lT~~----- 115 (152)
|...+.+.+--++ -+.+..|+..|+..|-- ---.=.||+.+|++ +.+|.++..+. ||-+.+|.
T Consensus 8 r~~~~~~~l~~~p~~~~~l~~f~~~~~~aks~-------ised~~i~~~~~~~-~~~g~~~t~~ga~ggv~~~p~~~~~~ 79 (271)
T PRK09213 8 RLVDMTKYLLENPNKLISLTFFAERYGAAKSS-------ISEDLVIIKETFEK-QGIGTLETVPGAAGGVKYIPSISEEE 79 (271)
T ss_pred HHHHHHHHHHhCCCceEcHHHHHHHhccccch-------hhhhHHHHHHHHHh-cCCceEEEeCCCCCCeEEEcCCCHHH
Confidence 4455554444443 48999999999875421 00112489999987 57899998884 67666653
Q ss_pred hHhhHHHHHHHH
Q psy5605 116 GRRDMDRIAAQI 127 (152)
Q Consensus 116 G~~~LD~iA~~i 127 (152)
.++.|+.++.++
T Consensus 80 a~~~~~~L~~~L 91 (271)
T PRK09213 80 AREFVEELCERL 91 (271)
T ss_pred HHHHHHHHHHHH
Confidence 666677776655
No 212
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=41.72 E-value=94 Score=27.70 Aligned_cols=55 Identities=9% Similarity=0.139 Sum_probs=38.2
Q ss_pred HHHHHHHhhHh--h--cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCcee
Q psy5605 44 TRCAALARHIY--M--RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKI 112 (152)
Q Consensus 44 iRaASilRkiY--l--~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~l 112 (152)
..+-.++.+++ . ..|+....|++.. ..+-.+++.+|.+|+++|||...++++-.+
T Consensus 292 ~~al~iL~~l~~~~~~g~~~t~~~La~~l--------------~~~~~~v~~iL~~L~~agLI~~~~~g~~~l 350 (412)
T PRK04214 292 YDLLRLLGRLDQARKHGKALDVDEIRRLE--------------PMGYDELGELLCELARIGLLRRGERGQWVL 350 (412)
T ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHh--------------CCCHHHHHHHHHHHHhCCCeEecCCCceEe
Confidence 44556888876 2 2356666776654 345579999999999999998776554333
No 213
>PLN02956 PSII-Q subunit
Probab=41.65 E-value=48 Score=27.59 Aligned_cols=25 Identities=16% Similarity=0.209 Sum_probs=19.0
Q ss_pred cchHhhHHHHHHHHHHHHHHHHHHH
Q psy5605 114 SHGRRDMDRIAAQIRVSKKEAALQA 138 (152)
Q Consensus 114 ~~G~~~LD~iA~~i~~~~~~~~~~~ 138 (152)
|+=|..+.++|.++++.+.+.+.+|
T Consensus 135 p~Drk~a~~La~~LFd~l~~LD~AA 159 (185)
T PLN02956 135 GKDRPQLRRLYSDLFNSVTKLDYAA 159 (185)
T ss_pred HhHhHHHHHHHHHHHHHHHHHHHHH
Confidence 4557778888888888888777766
No 214
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=41.48 E-value=1e+02 Score=25.51 Aligned_cols=46 Identities=17% Similarity=0.203 Sum_probs=29.3
Q ss_pred hHHHHHHHHHHh---CCcceecCCCCc-eeCcchHhhHHHHHHHHHHHHHHH
Q psy5605 87 SVARKALQALEQ---VNIIEKSDDGGR-KITSHGRRDMDRIAAQIRVSKKEA 134 (152)
Q Consensus 87 ~iiR~~LQqLE~---~glVek~~~gGR-~lT~~G~~~LD~iA~~i~~~~~~~ 134 (152)
+-+=..+++||+ ..|.+... +|. .||+.|+.+++. |.++.....+.
T Consensus 31 ~avSr~I~~LE~~lg~~LF~R~~-~~~~~lT~~G~~l~~~-a~~il~~~~~~ 80 (316)
T PRK12679 31 SGVSRHIRELEDELGIEIFIRRG-KRLLGMTEPGKALLVI-AERILNEASNV 80 (316)
T ss_pred hHHHHHHHHHHHHhCCEEEEECC-CcccccCHhHHHHHHH-HHHHHHHHHHH
Confidence 345566799998 34555544 243 799999998765 44555554443
No 215
>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=41.38 E-value=20 Score=25.58 Aligned_cols=26 Identities=27% Similarity=0.498 Sum_probs=17.7
Q ss_pred HHHHHHHhCCcceecCCCCceeCcchHhhH
Q psy5605 91 KALQALEQVNIIEKSDDGGRKITSHGRRDM 120 (152)
Q Consensus 91 ~~LQqLE~~glVek~~~gGR~lT~~G~~~L 120 (152)
++++.|..+|.|+.+. .||+-|+...
T Consensus 1 ~A~~~L~~Lgald~~~----~lT~lG~~~~ 26 (102)
T PF04408_consen 1 KALELLKSLGALDENG----NLTPLGRKMS 26 (102)
T ss_dssp -HHHHHHHTTSB-TTS-----B-HHHHHHT
T ss_pred CHHHHHHHCCCCCCCC----CcCHHHHHHH
Confidence 4789999999995433 8999998753
No 216
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=40.77 E-value=73 Score=26.53 Aligned_cols=43 Identities=19% Similarity=0.083 Sum_probs=29.8
Q ss_pred hHHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHHHHHHHH
Q psy5605 87 SVARKALQALEQ---VNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSK 131 (152)
Q Consensus 87 ~iiR~~LQqLE~---~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~ 131 (152)
+-+-+.+++||+ .-|.+... .|=.||+.|+..+..+. ++...+
T Consensus 58 pavS~~I~~LE~~lG~~LF~R~~-r~v~lT~~G~~l~~~~~-~~l~~l 103 (317)
T PRK11482 58 SAISQSIQKLRVIFPDPLFIRKG-QGVTPTAYATHLHEYIS-QGLESI 103 (317)
T ss_pred HHHHHHHHHHHHHhCCcceEecC-CCccCCHHHHHHHHHHH-HHHHHH
Confidence 456677899998 35566554 58899999998887743 444433
No 217
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=39.83 E-value=1.2e+02 Score=25.03 Aligned_cols=46 Identities=17% Similarity=0.286 Sum_probs=30.2
Q ss_pred hHHHHHHHHHHh---CCcceecCCCC-ceeCcchHhhHHHHHHHHHHHHHHH
Q psy5605 87 SVARKALQALEQ---VNIIEKSDDGG-RKITSHGRRDMDRIAAQIRVSKKEA 134 (152)
Q Consensus 87 ~iiR~~LQqLE~---~glVek~~~gG-R~lT~~G~~~LD~iA~~i~~~~~~~ 134 (152)
+-+=+.+++||+ ..|++.+. +| ..||+.|+.+++.+ .+++....+.
T Consensus 31 pavS~~I~~LE~~lg~~Lf~R~~-r~~~~lT~~G~~l~~~a-~~il~~~~~~ 80 (309)
T PRK12683 31 SGVSKQIKDLEDELGVEIFIRRG-KRLTGLTEPGKELLQIV-ERMLLDAENL 80 (309)
T ss_pred HHHHHHHHHHHHHhCCeeEeeCC-CCcCCcCHHHHHHHHHH-HHHHHHHHHH
Confidence 345667899998 35666554 34 36999999988664 4555544443
No 218
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=38.71 E-value=1.9e+02 Score=22.64 Aligned_cols=43 Identities=16% Similarity=0.147 Sum_probs=34.5
Q ss_pred HHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcce
Q psy5605 47 AALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIE 103 (152)
Q Consensus 47 ASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVe 103 (152)
--|+..|..++.+....|+..-|- +-+.+|++|+.|.+.|+|.
T Consensus 17 v~Vl~aL~~~~~~tdEeLa~~Lgi--------------~~~~VRk~L~~L~e~~Lv~ 59 (158)
T TIGR00373 17 GLVLFSLGIKGEFTDEEISLELGI--------------KLNEVRKALYALYDAGLAD 59 (158)
T ss_pred HHHHHHHhccCCCCHHHHHHHHCC--------------CHHHHHHHHHHHHHCCCce
Confidence 346667777888888888888754 3478999999999999994
No 219
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=38.44 E-value=77 Score=26.72 Aligned_cols=65 Identities=23% Similarity=0.324 Sum_probs=40.1
Q ss_pred chHHHHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHh-C--CcceecC----CCCcee
Q psy5605 40 DWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQ-V--NIIEKSD----DGGRKI 112 (152)
Q Consensus 40 DW~YiRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~-~--glVek~~----~gGR~l 112 (152)
.+|=.|-..+++.|.-.|.+ ..-++.-| =|-+-+=..+++||+ + -|++... .+|=.|
T Consensus 15 ~~~~~~~l~~l~~v~~~gS~--s~AA~~l~--------------~s~~a~s~~i~~le~~lg~~L~~r~~gg~~g~~~~l 78 (263)
T PRK10676 15 LFADPRRISLLKQIALTGSI--SQGAKLAG--------------ISYKSAWDAINEMNQLSEHILVERATGGKGGGGAVL 78 (263)
T ss_pred cccCHHHHHHHHHHHHHCCH--HHHHHHhC--------------CCHHHHHHHHHHHHHHhCCCeEEEecCCCCCCCcEE
Confidence 34446666777777777642 22222221 122445567788988 3 4577663 246789
Q ss_pred CcchHhhH
Q psy5605 113 TSHGRRDM 120 (152)
Q Consensus 113 T~~G~~~L 120 (152)
|+.|+.++
T Consensus 79 T~~G~~l~ 86 (263)
T PRK10676 79 TRYGERLI 86 (263)
T ss_pred CHHHHHHH
Confidence 99999999
No 220
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=38.38 E-value=1.4e+02 Score=23.94 Aligned_cols=37 Identities=19% Similarity=0.315 Sum_probs=27.5
Q ss_pred hHHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHH
Q psy5605 87 SVARKALQALEQ---VNIIEKSDDGGRKITSHGRRDMDRIAA 125 (152)
Q Consensus 87 ~iiR~~LQqLE~---~glVek~~~gGR~lT~~G~~~LD~iA~ 125 (152)
+-+=+.+++||+ ..|++.. +|-.||+.|+.+++.+-.
T Consensus 31 ~avS~~i~~LE~~lg~~Lf~R~--r~i~lT~~G~~l~~~a~~ 70 (294)
T PRK13348 31 SAVSQRIKALEESLGQPLLVRG--RPCRPTPAGQRLLRHLRQ 70 (294)
T ss_pred hHHHHHHHHHHHHhCceeeecC--CCCccChhHHHHHHHHHH
Confidence 345566799998 3566664 489999999999887664
No 221
>PF09397 Ftsk_gamma: Ftsk gamma domain; InterPro: IPR018541 This domain directs oriented DNA translocation and forms a winged helix structure []. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding []. ; PDB: 2VE9_B 2VE8_E 2J5O_A 2J5P_A.
Probab=38.19 E-value=1.3e+02 Score=20.68 Aligned_cols=51 Identities=14% Similarity=0.244 Sum_probs=33.3
Q ss_pred chHHHHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC
Q psy5605 40 DWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD 107 (152)
Q Consensus 40 DW~YiRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~ 107 (152)
|=.|-.|..++. -.+.+.++.|.+.|+= |. +=.-.++.+||+.|+|.....
T Consensus 5 D~ly~~a~~~V~---~~~~~S~S~lQR~~rI-------------Gy-nrAariid~LE~~GiVs~~~~ 55 (65)
T PF09397_consen 5 DPLYEEAVEFVI---EEGKASISLLQRKFRI-------------GY-NRAARIIDQLEEEGIVSPANG 55 (65)
T ss_dssp STTHHHHHHHHH---HCTCECHHHHHHHHT---------------H-HHHHHHHHHHHHCTSBE---T
T ss_pred cHHHHHHHHHHH---HcCCccHHHHHHHhCC-------------CH-HHHHHHHHHHHHCCCCCCCCC
Confidence 445667666654 3788999999998832 22 223468899999999986653
No 222
>PRK15092 DNA-binding transcriptional repressor LrhA; Provisional
Probab=38.05 E-value=1.1e+02 Score=25.46 Aligned_cols=44 Identities=20% Similarity=0.292 Sum_probs=30.9
Q ss_pred HHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHHHHHHHHHH
Q psy5605 88 VARKALQALEQ---VNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKE 133 (152)
Q Consensus 88 iiR~~LQqLE~---~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~ 133 (152)
-+=.-+++||+ ..|++.+. .|-.||+.|+.+++.+. ++...+.+
T Consensus 41 avS~~I~~LE~~lG~~LF~R~~-~~~~LT~~G~~l~~~a~-~il~~~~~ 87 (310)
T PRK15092 41 AVSQQMQRLEQLVGKELFARHG-RNKLLTEHGIQLLGYAR-KILRFNDE 87 (310)
T ss_pred HHHHHHHHHHHHhCcceEEECC-CCceECHhHHHHHHHHH-HHHHHHHH
Confidence 34445688997 46777766 48899999999887654 45554443
No 223
>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=37.32 E-value=82 Score=22.83 Aligned_cols=35 Identities=20% Similarity=0.155 Sum_probs=28.6
Q ss_pred cCCCchhHHHHHHHHHHhCCcceecCCCCceeCcc
Q psy5605 81 FCRSSGSVARKALQALEQVNIIEKSDDGGRKITSH 115 (152)
Q Consensus 81 ~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~ 115 (152)
-..-|-.+++.+|.+|-+.+-|=.+..|=..+||+
T Consensus 46 i~~Ps~e~l~~~L~~Li~erkIY~tg~GYfivtP~ 80 (80)
T PF10264_consen 46 IAIPSQEVLYNTLGTLIKERKIYHTGEGYFIVTPQ 80 (80)
T ss_pred CCCCCHHHHHHHHHHHHHcCceeeCCCceEeeCCC
Confidence 44678899999999999999998777555777875
No 224
>TIGR03298 argP transcriptional regulator, ArgP family. ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (PubMed:10589831). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity (PubMed: 15150242).
Probab=37.23 E-value=1.3e+02 Score=24.11 Aligned_cols=37 Identities=19% Similarity=0.307 Sum_probs=29.0
Q ss_pred hHHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHH
Q psy5605 87 SVARKALQALEQ---VNIIEKSDDGGRKITSHGRRDMDRIAA 125 (152)
Q Consensus 87 ~iiR~~LQqLE~---~glVek~~~gGR~lT~~G~~~LD~iA~ 125 (152)
+-+=+.+++||+ ..|++.. +|=.||+.|+.+++.+-.
T Consensus 30 pavS~~I~~LE~~lg~~Lf~R~--r~~~lT~~G~~l~~~~~~ 69 (292)
T TIGR03298 30 SAVSQRIKALEERLGQPLLVRT--QPCRATEAGQRLLRHARQ 69 (292)
T ss_pred HHHHHHHHHHHHHhCchheecC--CCCcCCHhHHHHHHHHHH
Confidence 445667899998 4677774 489999999999987655
No 225
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=36.84 E-value=1.7e+02 Score=24.74 Aligned_cols=59 Identities=25% Similarity=0.455 Sum_probs=45.0
Q ss_pred HHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC-C--Cc-----eeCcchHh
Q psy5605 47 AALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD-G--GR-----KITSHGRR 118 (152)
Q Consensus 47 ASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~-g--GR-----~lT~~G~~ 118 (152)
..|+.-+--+||+.++.+...-|= |..-+|.=|+.||+.|+|+.... + || .||.+|.+
T Consensus 14 ~~il~lL~~~g~~sa~elA~~Lgi--------------s~~avR~HL~~Le~~Glv~~~~~~~g~GRP~~~y~Lt~~g~~ 79 (218)
T COG2345 14 ERILELLKKSGPVSADELAEELGI--------------SPMAVRRHLDDLEAEGLVEVERQQGGRGRPAKLYRLTEKGRE 79 (218)
T ss_pred HHHHHHHhccCCccHHHHHHHhCC--------------CHHHHHHHHHHHHhCcceeeeeccCCCCCCceeeeecccchh
Confidence 345555556899999999999754 44678999999999999986532 2 54 79999986
Q ss_pred h
Q psy5605 119 D 119 (152)
Q Consensus 119 ~ 119 (152)
.
T Consensus 80 ~ 80 (218)
T COG2345 80 Q 80 (218)
T ss_pred h
Confidence 3
No 226
>PF08432 Vfa1: AAA-ATPase Vps4-associated protein 1; InterPro: IPR013640 This is a family of fungal proteins of unknown function.
Probab=36.49 E-value=9 Score=30.78 Aligned_cols=13 Identities=31% Similarity=0.708 Sum_probs=10.5
Q ss_pred CCCCCCchHHHHH
Q psy5605 34 LAPYDPDWFYTRC 46 (152)
Q Consensus 34 laP~d~DW~YiRa 46 (152)
..|.++||||+.-
T Consensus 28 ~t~~~~DfFY~C~ 40 (182)
T PF08432_consen 28 ITPDNKDFFYVCP 40 (182)
T ss_pred ecCCCCCeEEeCc
Confidence 3588899999874
No 227
>COG1568 Predicted methyltransferases [General function prediction only]
Probab=36.18 E-value=32 Score=31.01 Aligned_cols=38 Identities=21% Similarity=0.348 Sum_probs=30.7
Q ss_pred CCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHH
Q psy5605 83 RSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMD 121 (152)
Q Consensus 83 ~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD 121 (152)
..+=-+.=.++..||..|+|+.++ +|=.||.+|..+..
T Consensus 45 ~~plp~v~~i~~~l~~egiv~~~~-g~v~~TekG~E~~e 82 (354)
T COG1568 45 DLPLPLVASILEILEDEGIVKIEE-GGVELTEKGEELAE 82 (354)
T ss_pred cCCchHHHHHHHHHHhcCcEEEec-CcEeehhhhHHHHH
Confidence 444456667889999999999988 57999999997654
No 228
>PRK09801 transcriptional activator TtdR; Provisional
Probab=36.11 E-value=1.4e+02 Score=24.79 Aligned_cols=47 Identities=23% Similarity=0.378 Sum_probs=32.0
Q ss_pred hHHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHHHHHHHHHHHH
Q psy5605 87 SVARKALQALEQ---VNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEAA 135 (152)
Q Consensus 87 ~iiR~~LQqLE~---~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~~ 135 (152)
+-+=..+++||+ .-|.+... .|=.||+.|+..+.. |.++.....+..
T Consensus 35 pavS~~I~~LE~~LG~~Lf~R~~-r~~~lT~~G~~l~~~-a~~il~~~~~l~ 84 (310)
T PRK09801 35 AFVTKRIQILENTLATTLLNRSA-RGVALTESGQRCYEH-ALEILTQYQRLV 84 (310)
T ss_pred HHHHHHHHHHHHHhCCEeeeecC-CCCcccHhHHHHHHH-HHHHHHHHHHHH
Confidence 445566799998 34566665 589999999988876 455555544443
No 229
>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=36.06 E-value=75 Score=23.09 Aligned_cols=37 Identities=22% Similarity=0.268 Sum_probs=27.9
Q ss_pred CCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHH
Q psy5605 82 CRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMD 121 (152)
Q Consensus 82 ~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD 121 (152)
..|+.+++ .+++.|=+-|||. +|+ |..||+.|...-+
T Consensus 30 ~dA~p~~i-~a~~RLheKGLI~-~pd-GgyLT~~G~~~aE 66 (77)
T TIGR02647 30 STASPAAV-AAAARLHEKGLTT-QPD-GGYLTSLGLEAAE 66 (77)
T ss_pred ccCCHHHH-HHHHHHHHcCCcc-CCC-CCEecHHHHHHHH
Confidence 56777766 4779999999996 444 4499999987543
No 230
>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU. Members of this protein family are the S-adenosylmethionine-depenedent C-20 methyltransferase BchU, part of the pathway of bacteriochlorophyll c production in photosynthetic green sulfur bacteria. The position modified by this enzyme represents the difference between bacteriochlorophylls c and d; strains lacking this protein can only produced bacteriochlorophyll d.
Probab=35.06 E-value=67 Score=26.81 Aligned_cols=52 Identities=21% Similarity=0.258 Sum_probs=41.3
Q ss_pred cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHH
Q psy5605 56 RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDR 122 (152)
Q Consensus 56 ~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~ 122 (152)
.||..+..|+..-| ..-.-++..|..|..+|+++++. +.-.+|+.+...|+.
T Consensus 21 ~gp~t~~eLA~~~~--------------~~~~~~~~lL~~L~~lgll~~~~-~~y~~t~~~~~~l~~ 72 (306)
T TIGR02716 21 EGPKDLATLAADTG--------------SVPPRLEMLLETLRQMRVINLED-GKWSLTEFADYMFSP 72 (306)
T ss_pred cCCCCHHHHHHHcC--------------CChHHHHHHHHHHHhCCCeEecC-CcEecchhHHhhccC
Confidence 47888888887643 33357999999999999999875 689999999877753
No 231
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=35.03 E-value=72 Score=27.17 Aligned_cols=42 Identities=21% Similarity=0.261 Sum_probs=29.9
Q ss_pred hHHHHHHHHHHhCCcceecC-CCC--ceeCcchHhhHHHHHHHHH
Q psy5605 87 SVARKALQALEQVNIIEKSD-DGG--RKITSHGRRDMDRIAAQIR 128 (152)
Q Consensus 87 ~iiR~~LQqLE~~glVek~~-~gG--R~lT~~G~~~LD~iA~~i~ 128 (152)
.-.=.+|++||+.|+|+... +.| =.+|++|...|-..=.++.
T Consensus 34 qta~R~l~~le~~~~I~R~~~~~Gq~i~iTekG~~~L~~~~~d~~ 78 (214)
T COG1339 34 QTAARKLKELEDEGYITRTISKRGQLITITEKGIDLLYKEYEDLS 78 (214)
T ss_pred HHHHHHHHhhccCCcEEEEecCCCcEEEehHhHHHHHHHHHHHHH
Confidence 33345789999999998664 334 5789999988766554443
No 232
>COG3327 PaaX Phenylacetic acid-responsive transcriptional repressor [Transcription]
Probab=34.96 E-value=51 Score=29.17 Aligned_cols=45 Identities=20% Similarity=0.297 Sum_probs=36.3
Q ss_pred chhHHHHHHHHHHhCCcceecCCC--C-ceeCcchHhhHHHHHHHHHH
Q psy5605 85 SGSVARKALQALEQVNIIEKSDDG--G-RKITSHGRRDMDRIAAQIRV 129 (152)
Q Consensus 85 sg~iiR~~LQqLE~~glVek~~~g--G-R~lT~~G~~~LD~iA~~i~~ 129 (152)
|-..+|.+|.-|-++||+.....| + .+||.+|+..+-+-+..|..
T Consensus 41 sE~~vRaal~Rm~kaG~l~~er~grks~Y~LSDkgl~r~~~a~~riy~ 88 (291)
T COG3327 41 SETTVRAALSRMVKAGWLVGEREGRKSFYRLSDKGLARQRRAARRIYP 88 (291)
T ss_pred cHHHHHHHHHHHHhccchheeecccccceeecHHHHHHHHHHhhhhcC
Confidence 345789999999999999866532 2 57899999999998888754
No 233
>PRK15243 transcriptional regulator SpvR; Provisional
Probab=34.66 E-value=1.5e+02 Score=25.14 Aligned_cols=45 Identities=9% Similarity=0.105 Sum_probs=31.2
Q ss_pred hHHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHHHHHHHHHH
Q psy5605 87 SVARKALQALEQ---VNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKE 133 (152)
Q Consensus 87 ~iiR~~LQqLE~---~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~ 133 (152)
+-+=..+++||+ ..|.+... .|=.||+.|+..+.. |.++.....+
T Consensus 33 pavS~~Ik~LE~eLG~~LF~R~~-r~~~LT~aG~~ll~~-a~~il~~~~~ 80 (297)
T PRK15243 33 TPLSRVISDLERELKQRLFIRKN-GTLIPTEFAQTIYRK-VKSHYIFLHA 80 (297)
T ss_pred HHHHHHHHHHHHHhCCccEEeCC-CCeeECHHHHHHHHH-HHHHHHHHHH
Confidence 446677899998 35666655 488999999998876 4555444433
No 234
>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=34.31 E-value=94 Score=23.68 Aligned_cols=60 Identities=20% Similarity=0.349 Sum_probs=41.1
Q ss_pred hHHHHHHHHH------hhHhhcC--CcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCcee
Q psy5605 41 WFYTRCAALA------RHIYMRS--PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKI 112 (152)
Q Consensus 41 W~YiRaASil------RkiYl~g--~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~l 112 (152)
.+|+|.-... =+||+.+ |.-.+.|+..+ .-+-..+|.+|+-|++.|+|+..+++--.+
T Consensus 28 ~i~lkLlllsgk~n~~G~L~~~~~ipy~~e~LA~~~--------------~~~~~~V~~AL~~f~k~glIe~~ed~~i~i 93 (121)
T PF09681_consen 28 VIWLKLLLLSGKLNDEGKLYLSGNIPYTAEMLALEF--------------DRPVDTVRLALAVFQKLGLIEIDEDGVIYI 93 (121)
T ss_pred HHHHHHHHHhcccCCCCEEEECCCCCCcHHHHHHHH--------------CCCHHHHHHHHHHHHHCCCEEEecCCeEEe
Confidence 5566644444 1245543 66777777776 334578999999999999999988764555
Q ss_pred Cc
Q psy5605 113 TS 114 (152)
Q Consensus 113 T~ 114 (152)
+.
T Consensus 94 ~~ 95 (121)
T PF09681_consen 94 PN 95 (121)
T ss_pred ec
Confidence 54
No 235
>TIGR01743 purR_Bsub pur operon repressor, Bacillus subtilis type. This model represents the puring operon repressor PurR of low-GC Gram-positive bacteria. This homodimeric repressor contains a large region homologous to phosphoribosyltransferases and is inhibited by 5-phosphoribosyl 1-pyrophosphate.
Probab=34.21 E-value=2e+02 Score=24.87 Aligned_cols=75 Identities=8% Similarity=0.165 Sum_probs=48.5
Q ss_pred HHHHHHhhHhhcC--CcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC--CCceeCcc-----
Q psy5605 45 RCAALARHIYMRS--PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD--GGRKITSH----- 115 (152)
Q Consensus 45 RaASilRkiYl~g--~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~--gGR~lT~~----- 115 (152)
|...+.+.+--++ -+.+..|+..|+..|-- ---.=.|||.+|++ +.+|.++..+. ||-+.+|.
T Consensus 6 r~~~~t~~l~~~p~~~~~l~~f~~~~~~aks~-------ised~~i~~~~~~~-~~~g~~~t~~ga~ggv~~~p~~~~~~ 77 (268)
T TIGR01743 6 RLVDLTNYLITNPNKLIPLNFFSERYESAKSS-------ISEDIVIIKETFEK-FGIGKLLTVPGAAGGVKYIPKMSQAE 77 (268)
T ss_pred HHHHHHHHHHhCCCceEcHHHHHHHhccccch-------hhhhHHHHHHHHHh-cCCceEEEeCCCCCCeEEEeCCCHHH
Confidence 4455555444443 48899999999875421 00112489999987 57899998884 67666654
Q ss_pred hHhhHHHHHHHH
Q psy5605 116 GRRDMDRIAAQI 127 (152)
Q Consensus 116 G~~~LD~iA~~i 127 (152)
.+.+|++++..+
T Consensus 78 ~~~~~~~l~~~l 89 (268)
T TIGR01743 78 AEEFVEELCQSL 89 (268)
T ss_pred HHHHHHHHHHHH
Confidence 555666666554
No 236
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=34.20 E-value=89 Score=26.27 Aligned_cols=45 Identities=18% Similarity=0.239 Sum_probs=30.6
Q ss_pred hHHHHHHHHHHh---CCcceecCCCCc-eeCcchHhhHHHHHHHHHHHHHH
Q psy5605 87 SVARKALQALEQ---VNIIEKSDDGGR-KITSHGRRDMDRIAAQIRVSKKE 133 (152)
Q Consensus 87 ~iiR~~LQqLE~---~glVek~~~gGR-~lT~~G~~~LD~iA~~i~~~~~~ 133 (152)
+-+=..+++||+ ..|++.+.. |- .||+.|+.+++.... +...+.+
T Consensus 31 pavS~~I~~LE~~lG~~LF~R~~r-~v~~LT~~G~~l~~~a~~-il~~~~~ 79 (327)
T PRK12680 31 PGLSKQLKQLEDELGFLLFVRKGR-SLESVTPAGVEVIERARA-VLSEANN 79 (327)
T ss_pred hHHHHHHHHHHHHhCCeEEEECCC-cCCccCccHHHHHHHHHH-HHHHHHH
Confidence 345567899998 456677663 54 499999999988654 4444433
No 237
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=34.02 E-value=41 Score=29.07 Aligned_cols=27 Identities=30% Similarity=0.422 Sum_probs=22.7
Q ss_pred CchhHHHHHHHHHHhCCcceecCCCCce
Q psy5605 84 SSGSVARKALQALEQVNIIEKSDDGGRK 111 (152)
Q Consensus 84 asg~iiR~~LQqLE~~glVek~~~gGR~ 111 (152)
=|..-+++.+..||..|+|.++.. ||+
T Consensus 200 ls~aTV~~~lk~l~~~Gii~~~~~-Gr~ 226 (240)
T COG3398 200 LSVATVAYHLKKLEELGIIPEDRE-GRS 226 (240)
T ss_pred ccHHHHHHHHHHHHHcCCCccccc-Cce
Confidence 467889999999999999998874 554
No 238
>cd00772 ProRS_core Prolyl-tRNA synthetase (ProRS) class II core catalytic domain. ProRS is a homodimer. It is responsible for the attachment of proline to the 3' OH group of ribose of the appropriate tRNA. This domain is primarily responsible for ATP-dependent formation of the enzyme bound aminoacyl-adenylate. Class II assignment is based upon its structure and the presence of three characteristic sequence motifs in the core domain.
Probab=33.97 E-value=80 Score=26.46 Aligned_cols=41 Identities=15% Similarity=0.234 Sum_probs=33.6
Q ss_pred HHHHHhCCcceec-CCCCceeCcchHhhHHHHHHHHHHHHHH
Q psy5605 93 LQALEQVNIIEKS-DDGGRKITSHGRRDMDRIAAQIRVSKKE 133 (152)
Q Consensus 93 LQqLE~~glVek~-~~gGR~lT~~G~~~LD~iA~~i~~~~~~ 133 (152)
-|=|.++|+|+.. ..|-+.+.|.|.+.+++|-.-+.+.+++
T Consensus 7 ~~~l~~ag~~~~~~~~G~~~~lP~g~~i~~~I~~~i~~~~~~ 48 (264)
T cd00772 7 LEHIGKAELADQGPGRGIINFLPLAKAILDKIENVLDKMFKE 48 (264)
T ss_pred HHHHHhcCCccccCCCCEEEECCcHHHHHHHHHHHHHHHHHH
Confidence 3568899999988 5577999999999999998887766554
No 239
>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=33.29 E-value=31 Score=23.46 Aligned_cols=25 Identities=28% Similarity=0.550 Sum_probs=19.8
Q ss_pred HHHHHHhCCcceecCCCCceeCcchHhhH
Q psy5605 92 ALQALEQVNIIEKSDDGGRKITSHGRRDM 120 (152)
Q Consensus 92 ~LQqLE~~glVek~~~gGR~lT~~G~~~L 120 (152)
+++.|..+|-++.+ | .||+-|+...
T Consensus 2 A~~~L~~LgAld~~---~-~lT~lG~~m~ 26 (92)
T smart00847 2 ALELLYELGALDDD---G-RLTPLGRKMA 26 (92)
T ss_pred HHHHHHHCCCcCCC---C-CcCHHHHHHH
Confidence 57889999999652 3 8999999853
No 240
>TIGR02066 dsrB sulfite reductase, dissimilatory-type beta subunit. This model describes the beta subunit of sulfite reductase.
Probab=32.91 E-value=28 Score=30.73 Aligned_cols=111 Identities=14% Similarity=0.117 Sum_probs=71.4
Q ss_pred cchhhhcccCCcCCCCCCCchHHHHHHHHHhhHhhcCCcchhhHHHHhCCC-CCCCCCCCcc-CCCchhHHHHHHHHHHh
Q psy5605 21 EWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGR-KRNGVCPSHF-CRSSGSVARKALQALEQ 98 (152)
Q Consensus 21 eW~d~vKTg~~KElaP~d~DW~YiRaASilRkiYl~g~vGV~~L~~~YGg~-krrG~~P~h~-~~asg~iiR~~LQqLE~ 98 (152)
.|..++|-|.-....|.+.+-|++|..--. .+....=-.+..+...||.- -+-.++-+-. ..-...=+-.+++.|++
T Consensus 10 ~~~~~~~~gv~~~~~~~~~~~~mvRv~ip~-~lt~eqLr~LAdiaekyg~g~i~lTtrQnI~l~~I~~edl~~i~~~L~~ 88 (341)
T TIGR02066 10 KYHEVVKPGVIKHVAESGDVIYTVKAGTPR-LLSVDTLRKLCDIADKYSDGYLRWTIRNNVEFLVSDESKIQPLIDELEE 88 (341)
T ss_pred EEcccCCCcEEEEECCCCCcEEEEEeCCCc-ccCHHHHHHHHHHHHHhCCCeEEEeccCCEEEecCCHHHHHHHHHHHHh
Confidence 588999999999999999999999976544 44433334567778889742 2222222110 11224567889999999
Q ss_pred CCcceecCCCC--c-eeC--------cchHhhHHHHHHHHHHHHHH
Q psy5605 99 VNIIEKSDDGG--R-KIT--------SHGRRDMDRIAAQIRVSKKE 133 (152)
Q Consensus 99 ~glVek~~~gG--R-~lT--------~~G~~~LD~iA~~i~~~~~~ 133 (152)
.|+-.... ++ | .+| +.|--+-+.++..+...+.+
T Consensus 89 ~Gl~~~~~-G~~vrrni~aC~G~~~C~~a~~dt~~l~~~l~~~l~~ 133 (341)
T TIGR02066 89 VGFPVGGT-GDAVKGNIVHTQGWLHCHIPAIDASGIVKAVMDELYE 133 (341)
T ss_pred ccCCCCCC-CCccccccccCcCCCCCCcchhchHHHHHHHHHHHHH
Confidence 99864221 21 3 454 55667788887777665544
No 241
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=32.88 E-value=1.9e+02 Score=23.61 Aligned_cols=40 Identities=23% Similarity=0.304 Sum_probs=27.9
Q ss_pred hHHHHHHHHHHh---CCcceecCCCCc-eeCcchHhhHHHHHHHH
Q psy5605 87 SVARKALQALEQ---VNIIEKSDDGGR-KITSHGRRDMDRIAAQI 127 (152)
Q Consensus 87 ~iiR~~LQqLE~---~glVek~~~gGR-~lT~~G~~~LD~iA~~i 127 (152)
+-+=+.+++||+ ..|++... .|- .||+.|+.+++.+..-+
T Consensus 31 ~avSr~I~~LE~~lg~~LF~R~~-~~~~~lT~~G~~l~~~~~~~l 74 (309)
T PRK12682 31 PGVSKAIIELEEELGIEIFIRHG-KRLKGLTEPGKAVLDVIERIL 74 (309)
T ss_pred HHHHHHHHHHHHHhCCeeEEECC-CCcCccCHhHHHHHHHHHHHH
Confidence 345566799998 45666655 354 69999999998765443
No 242
>PLN00158 histone H2B; Provisional
Probab=32.63 E-value=93 Score=24.14 Aligned_cols=42 Identities=17% Similarity=0.070 Sum_probs=33.0
Q ss_pred CCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHHHHHHHH
Q psy5605 83 RSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEA 134 (152)
Q Consensus 83 ~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~ 134 (152)
.....-|-++|+| .+|+. .||.+.+..||.+..+|++.+..+
T Consensus 27 esy~~YI~kVLKQ--------VhPd~--gIS~kaM~ImnSfvnDiferIA~E 68 (116)
T PLN00158 27 ETYKIYIYKVLKQ--------VHPDT--GISSKAMSIMNSFINDIFEKIATE 68 (116)
T ss_pred ccHHHHHHHHHHH--------hCCCC--CccHHHHHHHHHHHHHHHHHHHHH
Confidence 4455668888887 46755 489999999999999999877544
No 243
>PF03975 CheD: CheD chemotactic sensory transduction; InterPro: IPR005659 CheD deamidates glutamine residues to glutamate on methyl-accepting chemotaxis receptors (MCPs). CheD-mediated MCP deamidation is required for productive communication of the conformational signals of the chemoreceptors to the cheA kinase []. CheC is a CheY-P phosphatase (CheY controls flagellar rotation and is activated by phosphorylation). The activity of CheC is enhanced by its interaction with CheD, forming a CheC-CheD heterodimer. It is suggested that CheC exerts its effect on MCP methylation in Bacillus subtilis by controlling the binding of CheD to the MCPs [].; GO: 0050568 protein-glutamine glutaminase activity, 0006935 chemotaxis; PDB: 2F9Z_D.
Probab=32.00 E-value=57 Score=24.12 Aligned_cols=58 Identities=24% Similarity=0.266 Sum_probs=32.7
Q ss_pred hhHHHHHHHHHHhCCcce-----ecCCCCceeCcchHhhHHHHHHHHHHHHHHHHHHHHhhcCceeec
Q psy5605 86 GSVARKALQALEQVNIIE-----KSDDGGRKITSHGRRDMDRIAAQIRVSKKEAALQALAAQGITVVP 148 (152)
Q Consensus 86 g~iiR~~LQqLE~~glVe-----k~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~~~~~~~~~~~~~~~ 148 (152)
..-|...+++|+++|--. |--.|+.++.. .......|-..+.+..++.|++.||.++-
T Consensus 20 d~ai~~ll~~m~~~Ga~~~~l~aklfGGa~m~~~-----~~~~~~~IG~rNv~~a~~~L~~~gi~I~a 82 (114)
T PF03975_consen 20 DTAIELLLDEMEKRGARPSRLEAKLFGGANMFPG-----MNSSSFNIGERNVEAARELLAEEGIPIVA 82 (114)
T ss_dssp HHHHHHHHHHHHTTT--GGG-EEEEEE----S-----------SS-HHHHHHHHHHHHHHHTT--EEE
T ss_pred HHHHHHHHHHHHHcCCCHHHeEEEEeeCcccccc-----cccccCCHHHHHHHHHHHHHHHCCCcEEE
Confidence 357888999999998532 22245667665 33344556677888899999999999874
No 244
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=31.50 E-value=1.2e+02 Score=25.07 Aligned_cols=42 Identities=19% Similarity=0.237 Sum_probs=36.7
Q ss_pred HHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCC
Q psy5605 45 RCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVN 100 (152)
Q Consensus 45 RaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~g 100 (152)
|-..|+..|=-+|.+.|..|...|| -|..-||+=|..||+.+
T Consensus 8 R~~~I~~~l~~~~~v~v~eLa~~~~--------------VS~~TIRRDL~~Le~~~ 49 (252)
T PRK10681 8 RIGQLLQALKRSDKLHLKDAAALLG--------------VSEMTIRRDLNAHSAPV 49 (252)
T ss_pred HHHHHHHHHHHcCCCcHHHHHHHhC--------------CCHHHHHHHHHHhhcCe
Confidence 7778888888899999999999984 56788999999999755
No 245
>smart00351 PAX Paired Box domain.
Probab=31.27 E-value=91 Score=23.28 Aligned_cols=82 Identities=17% Similarity=0.140 Sum_probs=48.3
Q ss_pred HHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCC---ceeCcchHhhH
Q psy5605 44 TRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGG---RKITSHGRRDM 120 (152)
Q Consensus 44 iRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gG---R~lT~~G~~~L 120 (152)
.|+.-|+ +|. .+.....+++.||- |.+-+.++++...+-|.++--+.+| +.+|+ ...
T Consensus 22 ~R~riv~--~~~-~G~s~~~iA~~~gv--------------s~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~---~~~ 81 (125)
T smart00351 22 ERQRIVE--LAQ-NGVRPCDISRQLCV--------------SHGCVSKILGRYYETGSIRPGAIGGSKPKVATP---KVV 81 (125)
T ss_pred HHHHHHH--HHH-cCCCHHHHHHHHCc--------------CHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCH---HHH
Confidence 4543332 343 66778888888853 5678888999999999988655444 33333 222
Q ss_pred HHHHHHHHH----HHHHHHHHHHhhcCcee
Q psy5605 121 DRIAAQIRV----SKKEAALQALAAQGITV 146 (152)
Q Consensus 121 D~iA~~i~~----~~~~~~~~~~~~~~~~~ 146 (152)
+.|...+.+ .+.|. .+.|+++||.+
T Consensus 82 ~~I~~~~~~~p~~t~~el-~~~L~~~gv~~ 110 (125)
T smart00351 82 KKIADYKQENPGIFAWEI-RDRLLSEGVCD 110 (125)
T ss_pred HHHHHHHHHCCCCCHHHH-HHHHHHcCCCc
Confidence 333332222 23333 34577888866
No 246
>PRK03635 chromosome replication initiation inhibitor protein; Validated
Probab=30.72 E-value=1.4e+02 Score=24.10 Aligned_cols=39 Identities=18% Similarity=0.328 Sum_probs=27.5
Q ss_pred HHHHHHHHHHh---CCcceecCCCCceeCcchHhhHHHHHHHHHH
Q psy5605 88 VARKALQALEQ---VNIIEKSDDGGRKITSHGRRDMDRIAAQIRV 129 (152)
Q Consensus 88 iiR~~LQqLE~---~glVek~~~gGR~lT~~G~~~LD~iA~~i~~ 129 (152)
-+=..+++||+ ..|.+.. .|-.||+.|+.++..+-. +..
T Consensus 32 avS~~I~~LE~~lg~~LF~R~--~~~~lT~~G~~l~~~a~~-~~~ 73 (294)
T PRK03635 32 AVSQRIKALEERVGQVLLVRT--QPCRPTEAGQRLLRHARQ-VRL 73 (294)
T ss_pred HHHHHHHHHHHHhCceeeecC--CCCccCHHHHHHHHHHHH-HHH
Confidence 34455789998 3556664 499999999999876644 543
No 247
>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=30.24 E-value=54 Score=23.40 Aligned_cols=38 Identities=18% Similarity=0.309 Sum_probs=27.0
Q ss_pred CCchhHHHHHHHHHHhCCcceecCC--CCceeCcchHhhH
Q psy5605 83 RSSGSVARKALQALEQVNIIEKSDD--GGRKITSHGRRDM 120 (152)
Q Consensus 83 ~asg~iiR~~LQqLE~~glVek~~~--gGR~lT~~G~~~L 120 (152)
+=+.+-+.++|++|-+.|+|..... .|-+||-.|-..|
T Consensus 35 ~l~~~~~~~~L~~L~~~kLv~~~~~~Y~GYrLT~~GYD~L 74 (82)
T PF09202_consen 35 GLSEGEVEKRLKRLVKLKLVSRRNKPYDGYRLTFLGYDYL 74 (82)
T ss_dssp T--HHHHHHHHHHHHHTTSEEEE-SSS-EEEE-HHHHHHH
T ss_pred CcCHHHHHHHHHHHHhcCCccccCCCcceEEEeecchhHH
Confidence 3445677889999999999997543 4999999996543
No 248
>cd08768 Cdc6_C Winged-helix domain of essential DNA replication protein Cell division control protein (Cdc6), which mediates DNA binding. This model characterizes the winged-helix, C-terminal domain of the Cell division control protein (Cdc6_C). Cdc6 (also known as Cell division cycle 6 or Cdc18) functions as a regulator at the early stages of DNA replication, by helping to recruit and load the Minichromosome Maintenance Complex (MCM) onto DNA and may have additional roles in the control of mitotic entry. Precise duplication of chromosomal DNA is required for genomic stability during replication. Cdc6 has an essential role in DNA replication and irregular expression of Cdc6 may lead to genomic instability. Cdc6 over-expression is observed in many cancerous lesions. DNA replication begins when an origin recognition complex (ORC) binds to a replication origin site on the chromatin. Studies indicate that Cdc6 interacts with ORC through the Orc1 subunit, and that this association increases
Probab=30.24 E-value=44 Score=22.52 Aligned_cols=23 Identities=17% Similarity=0.206 Sum_probs=18.5
Q ss_pred CchhHHHHHHHHHHhCCcceecC
Q psy5605 84 SSGSVARKALQALEQVNIIEKSD 106 (152)
Q Consensus 84 asg~iiR~~LQqLE~~glVek~~ 106 (152)
-+-.-++.+|+.||.+|+|+...
T Consensus 44 l~~~~~~~~l~~L~~~gli~~~~ 66 (87)
T cd08768 44 LTQRRISDLLSELEMLGLLETEV 66 (87)
T ss_pred CcHHHHHHHHHHHHHcCCeEEEE
Confidence 34467888999999999998654
No 249
>PF02909 TetR_C: Tetracyclin repressor, C-terminal all-alpha domain; InterPro: IPR004111 The antibiotic tetracycline has a broad spectrum of activity, acting to inhibit bacterial protein synthesis by binding to the 30S ribosomal subunit, which prevents the association of the aminoacyl-tRNA to the ribosomal acceptor A site. Tetracycline binding is reversible, therefore diluting out the antibiotic can reverse its effects. Tetracycline resistance genes are often located on mobile elements, such as plasmids, transposons and/or conjugative transposons, which can sometimes be transferred between bacterial species. In certain cases, tetracycline can enhance the transfer of these elements, thereby promoting resistance amongst a bacterial colony. There are three types of tetracycline resistance: tetracycline efflux, ribosomal protection, and tetracycline modification [, ]: Tetracycline efflux proteins belong to the major facilitator superfamily. Efflux proteins are membrane-associated proteins that recognise and export tetracycline from the cell. They are found in both Gram-positive and Gram-negative bacteria []. There are at least 22 different tetracycline efflux proteins, grouped according to sequence similarity: Group 1 are Tet(A), Tet(B), Tet(C), Tet(D), Tet(E), Tet(G), Tet(H), Tet(J), Tet(Z) and Tet(30); Group 2 are Tet(K) and Tet(L); Group 3 are Otr(B) and Tcr(3); Group 4 is TetA(P); Group 5 is Tet(V). In addition, there are the efflux proteins Tet(31), Tet(33), Tet(V), Tet(Y), Tet(34), and Tet(35). Ribosomal protection proteins are cytoplasmic proteins that display homology with the elongation factors EF-Tu and EF-G. Protection proteins bind the ribosome, causing an alteration in ribosomal conformation that prevents tetracycline from binding. There are at least ten ribosomal protection proteins: Tet(M), Tet(O), Tet(S), Tet(W), Tet(32), Tet(36), Tet(Q), Tet(T), Otr(A), and TetB(P). Both Tet(M) and Tet(O) have ribosome-dependent GTPase activity, the hydrolysis of GTP providing the energy for the ribosomal conformational changes. Tetracycline modification proteins include the enzymes Tet(37) and Tet(X), both of which inactivate tetracycline. In addition, there are the tetracycline resistance proteins Tet(U) and Otr(C). The expression of several of these tet genes is controlled by a family of tetracycline transcriptional regulators known as TetR. TetR family regulators are involved in the transcriptional control of multidrug efflux pumps, pathways for the biosynthesis of antibiotics, response to osmotic stress and toxic chemicals, control of catabolic pathways, differentiation processes, and pathogenicity []. The TetR proteins identified in over 115 genera of bacteria and archaea share a common helix-turn-helix (HTH) structure in their DNA-binding domain. However, TetR proteins can work in different ways: they can bind a target operator directly to exert their effect (e.g. TetR binds Tet(A) gene to repress it in the absence of tetracycline), or they can be involved in complex regulatory cascades in which the TetR protein can either be modulated by another regulator or TetR can trigger the cellular response. This entry represents the C-terminal domain found in the tetracycline transcriptional repressor TetR, which binds to the Tet(A) gene to repress its expression in the absence of tetracycline []. Tet(A) is a membrane-associated efflux protein that exports tetracycline from the cell before it can attach to ribosomes and inhibit polypeptide chain growth. TetR occurs as a homodimer and uses two helix-turn-helix (HTH) motifs to bind tandem DNA operators, thereby blocking the expression of the associated genes, TetA and TetR. The structure of the class D TetR repressor protein [] involves 10 alpha-helices, with connecting turns and loops. The three N-terminal helices constitute the DNA-binding HTH domain, which has an inverse orientation compared with HTH motifs in other DNA-binding proteins. The core of the protein, formed by helices 5-10, is responsible for dimerisation and contains, for each monomer, a binding pocket that accommodates tetracycline in the presence of a divalent cation.; GO: 0045892 negative regulation of transcription, DNA-dependent; PDB: 2Y30_B 3ZQL_C 2Y31_B 2Y2Z_A 2VPR_A 3B6A_A 3B6C_A 2OPT_A 2NS7_B 2NS8_C ....
Probab=30.22 E-value=1.4e+02 Score=21.19 Aligned_cols=59 Identities=17% Similarity=0.158 Sum_probs=38.3
Q ss_pred CCCCCch--HHHHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCccee
Q psy5605 35 APYDPDW--FYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEK 104 (152)
Q Consensus 35 aP~d~DW--~YiRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek 104 (152)
|+.+.|| +....|.-+|..|++-|-.+.-+... | .....+-.++-.+|+.|...|+=..
T Consensus 2 P~~~~~W~~~l~~~a~~~r~~~~~hP~~~~~~~~~----------~-~~~p~~l~~~e~~l~~L~~aG~~~~ 62 (139)
T PF02909_consen 2 PDPGDDWRERLRALARAYRAALLRHPWLAELLLAR----------P-PPGPNALRLMEAMLRALRDAGFSPE 62 (139)
T ss_dssp -CTTSEHHHHHHHHHHHHHHHHHTSTTHHHHHHTS----------S-CTSHHHHHHHHHHHHHHHHTTEEHH
T ss_pred ccCCCCHHHHHHHHHHHHHHHHHHCcCHHHHHHhc----------C-CCChhHHHHHHHHHHHHHHcCcCHH
Confidence 3344466 56777888999999988666544431 1 1223344566689999999998643
No 250
>PF15129 FAM150: FAM150 family
Probab=30.18 E-value=36 Score=26.58 Aligned_cols=17 Identities=29% Similarity=0.647 Sum_probs=13.8
Q ss_pred hHHHHHHHHHhhHhhcC
Q psy5605 41 WFYTRCAALARHIYMRS 57 (152)
Q Consensus 41 W~YiRaASilRkiYl~g 57 (152)
=||.|||++|-++.+.+
T Consensus 103 ayykrcarlltrla~sp 119 (123)
T PF15129_consen 103 AYYKRCARLLTRLAVSP 119 (123)
T ss_pred HHHHHHHHHHHHhccCc
Confidence 48999999998887653
No 251
>PRK13493 chemoreceptor glutamine deamidase CheD; Provisional
Probab=29.85 E-value=1.1e+02 Score=25.71 Aligned_cols=53 Identities=13% Similarity=0.062 Sum_probs=39.5
Q ss_pred hHHHHHHHHHHhCCcc-----eecCCCCceeCcchHhhHHHHHHHHHHHHHHHHHHHHhhcCceeec
Q psy5605 87 SVARKALQALEQVNII-----EKSDDGGRKITSHGRRDMDRIAAQIRVSKKEAALQALAAQGITVVP 148 (152)
Q Consensus 87 ~iiR~~LQqLE~~glV-----ek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~~~~~~~~~~~~~~~ 148 (152)
.-|...+++|+++|-- -|--.|+.++... ..|-..+.+..++.|++.||.|+-
T Consensus 100 ~Am~~Li~~m~~~Ga~~~~l~aKifGGA~m~~~~---------~~IG~rNi~~a~~~L~~~gI~Iva 157 (213)
T PRK13493 100 YAMEVLINRLLSMGAERERLKFKLFGGAHLMGYQ---------SLVGEKNVEFVLEYAKREKLNVVA 157 (213)
T ss_pred HHHHHHHHHHHHcCCCHHHeEEEEEeCccccccc---------ccHhHHHHHHHHHHHHHcCCcEEE
Confidence 3678888899988753 2334567777532 248889999999999999999974
No 252
>PF05119 Terminase_4: Phage terminase, small subunit; InterPro: IPR006448 This entry is represented by Streptococcus phage 7201, Orf21. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This group of sequences describe the distinct family of phage (and integrated prophage) putative terminase small subunit sequnces. Members tend to be encoded by the gene adjacent to the phage terminase large subunit gene.
Probab=29.81 E-value=1.9e+02 Score=19.92 Aligned_cols=50 Identities=20% Similarity=0.227 Sum_probs=31.7
Q ss_pred hHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHHHHHHHHHHHHHhhcCce
Q psy5605 87 SVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEAALQALAAQGIT 145 (152)
Q Consensus 87 ~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~~~~~~~~~~~~ 145 (152)
+..|.+..+|++.|++..+++|+-+.+| +-.+..+..++-.+.+.+-|+|
T Consensus 34 ~~~~~~~~~l~~~G~~~~~~~G~~~~nP---------~~~~~~~~~~~~~~l~~~lGLt 83 (100)
T PF05119_consen 34 SRYREAEKELKKEGFVVETKNGNPKKNP---------AVSILNKAMKQMRSLASELGLT 83 (100)
T ss_pred HHHHHHHHHHHHcCceeeCCCCCcccCH---------HHHHHHHHHHHHHHHHHHcCCC
Confidence 6788999999999999666654233333 2234444555555555666665
No 253
>PF14337 DUF4393: Domain of unknown function (DUF4393)
Probab=29.58 E-value=63 Score=25.18 Aligned_cols=77 Identities=22% Similarity=0.271 Sum_probs=49.0
Q ss_pred CCCCCcchhhhcccCCcCCCCCCCchHHHHHHHHHhhHhhcCCcchhhHHHHh-CCCCCCCCCCCccCCC---chhHHHH
Q psy5605 16 KMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIF-GGRKRNGVCPSHFCRS---SGSVARK 91 (152)
Q Consensus 16 ki~~PeW~d~vKTg~~KElaP~d~DW~YiRaASilRkiYl~g~vGV~~L~~~Y-Gg~krrG~~P~h~~~a---sg~iiR~ 91 (152)
..--|.+++++| ++.|.| |.+|+.+|-.+..-+...+..+ .+...+-..++.+..+ +-..+-.
T Consensus 53 ~~~hp~fv~Ii~-----qLsp~E--------A~iL~~l~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 119 (186)
T PF14337_consen 53 DDVHPSFVEIIK-----QLSPDE--------ARILKYLYDNNQIPIVDVRLRRKNGPGSRIVLSNISLVGEEASPDNIPS 119 (186)
T ss_pred ccccHHHHHHHH-----hCCHHH--------HHHHHHHHhcCCCcceeeeeeecCCccceeecccccccccccchHHHHH
Confidence 345677888864 788877 7899999966554444433333 1111111223322222 5578999
Q ss_pred HHHHHHhCCcceec
Q psy5605 92 ALQALEQVNIIEKS 105 (152)
Q Consensus 92 ~LQqLE~~glVek~ 105 (152)
.|+.|+.+|||+-.
T Consensus 120 ~l~nL~rLGLi~~~ 133 (186)
T PF14337_consen 120 YLDNLERLGLIEIP 133 (186)
T ss_pred HHHHHHHCCCceec
Confidence 99999999999877
No 254
>COG4344 Uncharacterized protein conserved in archaea [Function unknown]
Probab=28.74 E-value=81 Score=25.93 Aligned_cols=39 Identities=18% Similarity=0.322 Sum_probs=29.4
Q ss_pred hHHHHHHHHHHhCCcceecCCC--------------------CceeCcchHhhHHHHHH
Q psy5605 87 SVARKALQALEQVNIIEKSDDG--------------------GRKITSHGRRDMDRIAA 125 (152)
Q Consensus 87 ~iiR~~LQqLE~~glVek~~~g--------------------GR~lT~~G~~~LD~iA~ 125 (152)
--||.+|..|+++|+++-..+. =-+||.+|.-.|-.|-.
T Consensus 46 ~~i~e~l~dL~elGLier~tgttiKrteAKfKksaEVHKHHTYYrl~rege~~lr~i~~ 104 (175)
T COG4344 46 PRIREYLKDLKELGLIERYTGTTIKRTEAKFKKSAEVHKHHTYYRLNREGEAVLREITP 104 (175)
T ss_pred HHHHHHHHHHHHcCCeeeccCchhhhhHHHHHHhHHHHhchhhheechhHHHHHHhcCH
Confidence 4689999999999999966521 14688888877766655
No 255
>PHA00738 putative HTH transcription regulator
Probab=28.72 E-value=1.6e+02 Score=22.53 Aligned_cols=48 Identities=17% Similarity=0.153 Sum_probs=33.1
Q ss_pred HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCce
Q psy5605 49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRK 111 (152)
Q Consensus 49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~ 111 (152)
|+..|.-.++..|+.|...++- |..-+=+=|+-|+++|+|+.... ||.
T Consensus 17 IL~lL~~~e~~~V~eLae~l~l--------------SQptVS~HLKvLreAGLV~srK~-Gr~ 64 (108)
T PHA00738 17 ILELIAENYILSASLISHTLLL--------------SYTTVLRHLKILNEQGYIELYKE-GRT 64 (108)
T ss_pred HHHHHHHcCCccHHHHHHhhCC--------------CHHHHHHHHHHHHHCCceEEEEE-CCE
Confidence 4444443457889999988742 33444455899999999998874 654
No 256
>PTZ00463 histone H2B; Provisional
Probab=28.40 E-value=2.1e+02 Score=22.24 Aligned_cols=42 Identities=17% Similarity=0.065 Sum_probs=31.9
Q ss_pred CCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHHHHHHHH
Q psy5605 83 RSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEA 134 (152)
Q Consensus 83 ~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~ 134 (152)
.....-|-++|+| .+|+. .||.+.+..|+.+..+|++.+..+
T Consensus 28 esy~~YI~KVLKq--------VhPd~--gIS~kaM~ImnSfvnDifErIA~E 69 (117)
T PTZ00463 28 DSYGLYIFKVLKQ--------VHPDT--GISRKSMNIMNSFLVDTFEKIATE 69 (117)
T ss_pred chHHHHHHHHHHh--------hCCCC--CccHHHHHHHHHHHHHHHHHHHHH
Confidence 3444557777777 46754 489999999999999999877544
No 257
>COG3668 ParE Plasmid stabilization system protein [General function prediction only]
Probab=28.31 E-value=76 Score=22.14 Aligned_cols=18 Identities=22% Similarity=0.368 Sum_probs=16.9
Q ss_pred eeCcchHhhHHHHHHHHH
Q psy5605 111 KITSHGRRDMDRIAAQIR 128 (152)
Q Consensus 111 ~lT~~G~~~LD~iA~~i~ 128 (152)
.+|+..++||+.|+.-+.
T Consensus 5 ~~s~~A~~dl~~I~~~~~ 22 (98)
T COG3668 5 ILSPAAEADLEDIADYIA 22 (98)
T ss_pred EccHHHHHHHHHHHHHHH
Confidence 689999999999999997
No 258
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=28.01 E-value=79 Score=22.57 Aligned_cols=30 Identities=23% Similarity=0.312 Sum_probs=23.6
Q ss_pred chhHHHHHHHHHHhCCc-ceecCCCCceeCc
Q psy5605 85 SGSVARKALQALEQVNI-IEKSDDGGRKITS 114 (152)
Q Consensus 85 sg~iiR~~LQqLE~~gl-Vek~~~gGR~lT~ 114 (152)
|+.-|=+.+|+|++.|+ |+.....|+.|..
T Consensus 32 SRtaVwK~Iq~Lr~~G~~I~s~~~kGY~L~~ 62 (79)
T COG1654 32 SRTAVWKHIQQLREEGVDIESVRGKGYLLPQ 62 (79)
T ss_pred cHHHHHHHHHHHHHhCCceEecCCCceeccC
Confidence 56677888999999998 4666666998864
No 259
>PRK06474 hypothetical protein; Provisional
Probab=27.79 E-value=1.7e+02 Score=23.18 Aligned_cols=46 Identities=11% Similarity=0.157 Sum_probs=34.2
Q ss_pred HHHhhHhhcCC-cchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC
Q psy5605 48 ALARHIYMRSP-VGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD 106 (152)
Q Consensus 48 SilRkiYl~g~-vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~ 106 (152)
.|++-|.-.++ ..+..+....+ .-|.+-+=+-|+.|++.|+|+..+
T Consensus 15 ~Il~~L~~~~~~~ta~el~~~l~-------------~is~aTvYrhL~~L~e~GLI~~~~ 61 (178)
T PRK06474 15 KICQVLMRNKEGLTPLELVKILK-------------DVPQATLYRHLQTMVDSGILHVVK 61 (178)
T ss_pred HHHHHHHhCCCCCCHHHHHHHhc-------------CCCHHHHHHHHHHHHHCCCEEEee
Confidence 36666666554 88988888753 255667777899999999999765
No 260
>cd04252 AAK_NAGK-fArgBP AAK_NAGK-fArgBP: N-Acetyl-L-glutamate kinase (NAGK) of the fungal arginine-biosynthetic pathway (fArgBP). The nuclear-encoded, mitochondrial polyprotein precursor with an N-terminal NAGK (ArgB) domain (this CD), a central DUF619 domain, and a C-terminal reductase domain (ArgC, N-Acetylglutamate Phosphate Reductase, NAGPR). The precursor is cleaved in the mitochondria into two distinct enzymes (NAGK-DUF619 and NAGPR). Native molecular weights of these proteins indicate that the kinase is an octamer whereas the reductase is a dimer. This CD also includes some gamma-proteobacteria (Xanthomonas and Xylella) NAG kinases with an N-terminal NAGK (ArgB) domain (this CD) and a C-terminal DUF619 domain. The DUF619 domain is described as a putative distant homolog of the acetyltransferase, ArgA, predicted to function in NAG synthase association in fungi. Eukaryotic sequences have an N-terminal mitochondrial transit peptide. Members of this NAG kinase domain CD belong to th
Probab=27.32 E-value=1.6e+02 Score=24.38 Aligned_cols=62 Identities=15% Similarity=0.232 Sum_probs=40.3
Q ss_pred ccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHHHHHHHHHHHHHhhcCceeec
Q psy5605 80 HFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEAALQALAAQGITVVP 148 (152)
Q Consensus 80 h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~~~~~~~~~~~~~~~ 148 (152)
--..|.|+-|-..+.+ .|+=.+-. +|.++|++ ..|+.+-. .+.++...-.++|.++|+..+|
T Consensus 32 VlVHGgg~~i~~~~~~---~gi~~~~~-~g~RvT~~--~~l~~v~~-al~~vn~~iv~~l~~~g~~a~~ 93 (248)
T cd04252 32 IVVHGAGPQLNEELEA---AGVEPEYV-DGLRVTDP--ETLAVARK-VFLEENLKLVEALERNGARARP 93 (248)
T ss_pred EEEeCCCHHHHHHHHH---cCCCcEee-CCcccCCH--HHHHHHHH-HHHHHHHHHHHHHHhCCCCccc
Confidence 4466777777765554 45544333 47888876 45554443 3347777888889999998776
No 261
>PF09079 Cdc6_C: CDC6, C terminal ; InterPro: IPR015163 The C-terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity []. ; PDB: 2QBY_A 2V1U_A 1W5T_A 1W5S_B 1FNN_B.
Probab=27.30 E-value=54 Score=22.42 Aligned_cols=22 Identities=27% Similarity=0.232 Sum_probs=17.4
Q ss_pred chhHHHHHHHHHHhCCcceecC
Q psy5605 85 SGSVARKALQALEQVNIIEKSD 106 (152)
Q Consensus 85 sg~iiR~~LQqLE~~glVek~~ 106 (152)
|-.=++..|.+||.+|+|+...
T Consensus 38 s~~r~~~~l~eL~~~gli~~~~ 59 (85)
T PF09079_consen 38 SYRRFSDYLSELEMLGLIESER 59 (85)
T ss_dssp -HHHHHHHHHHHHHTTSEEEEE
T ss_pred CHHHHHHHHHHHHhCCCeEEEe
Confidence 3355788899999999998665
No 262
>PRK15279 type III secretion protein SopE; Provisional
Probab=26.91 E-value=2.4e+02 Score=24.18 Aligned_cols=83 Identities=23% Similarity=0.353 Sum_probs=56.9
Q ss_pred hhHHHHhCCCCCCCCCCCccCCCchh----------HHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHHHHH
Q psy5605 62 KTVTKIFGGRKRNGVCPSHFCRSSGS----------VARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSK 131 (152)
Q Consensus 62 ~~L~~~YGg~krrG~~P~h~~~asg~----------iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~ 131 (152)
.+|+..|-+-++--..|.||.+||-+ |=-.+||.|-.+.+=. .+-.=..-++....-+-..|..+.
T Consensus 47 ~~lS~RF~~h~~td~~~ThfhRG~AsegRavLt~k~VK~fmlq~L~sldirg----~askDp~yarQt~EA~lsavyS~~ 122 (240)
T PRK15279 47 SKLSERFISHKNTESSATHFHRGSASEGRAVLTNKVVKDFMLQTLNDIDIRG----SASKDPAYASQTREAILSAVYSKN 122 (240)
T ss_pred HHHHHHHHhccCCCCCCceeecCccccccccCChHHHHHHHHHHhhhhcccC----ccccChHHHHHHHHHHHHHHHHHh
Confidence 57888888888888899999999877 3335566666654321 122223456677777777778777
Q ss_pred HHHHHHHHhhcCceeec
Q psy5605 132 KEAALQALAAQGITVVP 148 (152)
Q Consensus 132 ~~~~~~~~~~~~~~~~~ 148 (152)
+.+--.+|...|+.+-|
T Consensus 123 Kd~~c~ll~skg~~i~p 139 (240)
T PRK15279 123 KDQCCNLLISKGINIAP 139 (240)
T ss_pred HHHHHHHHHhcCCCchH
Confidence 77777777777777655
No 263
>PHA02943 hypothetical protein; Provisional
Probab=26.61 E-value=2.5e+02 Score=23.07 Aligned_cols=54 Identities=24% Similarity=0.210 Sum_probs=42.0
Q ss_pred CchHHHHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC
Q psy5605 39 PDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD 107 (152)
Q Consensus 39 ~DW~YiRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~ 107 (152)
.|=...|.--|++-| -.|...+..+.+..|= |-+=+|++|..||+.|.|++.+-
T Consensus 6 sd~v~~R~~eILE~L-k~G~~TtseIAkaLGl--------------S~~qa~~~LyvLErEG~VkrV~~ 59 (165)
T PHA02943 6 SDTVHTRMIKTLRLL-ADGCKTTSRIANKLGV--------------SHSMARNALYQLAKEGMVLKVEI 59 (165)
T ss_pred hHHHHHHHHHHHHHH-hcCCccHHHHHHHHCC--------------CHHHHHHHHHHHHHcCceEEEee
Confidence 355566777788877 5666778888887653 55779999999999999999884
No 264
>COG0583 LysR Transcriptional regulator [Transcription]
Probab=26.20 E-value=3.1e+02 Score=21.25 Aligned_cols=45 Identities=22% Similarity=0.420 Sum_probs=29.0
Q ss_pred HHHHHHHHHh-CC--cceecCCCCceeCcchHhhHHHHHHHHHHHHHHHH
Q psy5605 89 ARKALQALEQ-VN--IIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEAA 135 (152)
Q Consensus 89 iR~~LQqLE~-~g--lVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~~ 135 (152)
+=..+++||+ +| |.+... +|=.||+.|+..++.+ .++...+.+..
T Consensus 32 vS~~I~~LE~~lg~~Lf~R~~-~~~~lT~~G~~l~~~a-~~~l~~~~~~~ 79 (297)
T COG0583 32 VSRQIKRLEEELGVPLFERTT-RRVRLTEAGERLLERA-RRILAELEEAL 79 (297)
T ss_pred HHHHHHHHHHHhCchheeecC-CceeeCHhHHHHHHHH-HHHHHHHHHHH
Confidence 5567899998 33 444444 3468999999988764 45554444443
No 265
>smart00843 Ftsk_gamma This domain directs oriented DNA translocation and forms a winged helix structure. Mutated proteins with substitutions in the FtsK gamma DNA-recognition helix are impaired in DNA binding.
Probab=26.13 E-value=2.2e+02 Score=19.56 Aligned_cols=50 Identities=14% Similarity=0.213 Sum_probs=34.3
Q ss_pred chHHHHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC
Q psy5605 40 DWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD 106 (152)
Q Consensus 40 DW~YiRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~ 106 (152)
|=.|-.|..++.. .+-..++.|.+.|.- |. +=.-.++.+||+.|+|...+
T Consensus 4 D~ly~~a~~~V~~---~~~~S~S~lQR~~~I-------------Gy-nrAariid~lE~~GiV~p~~ 53 (63)
T smart00843 4 DELYDEAVELVIE---TQKASTSLLQRRLRI-------------GY-NRAARLIDQLEEEGIVGPAN 53 (63)
T ss_pred cHHHHHHHHHHHH---hCCCChHHHHHHHhc-------------ch-hHHHHHHHHHHHCcCCCCCC
Confidence 4467777766543 577788888887732 21 22456889999999997654
No 266
>PF07042 TrfA: TrfA protein; InterPro: IPR010751 This family consists of several bacterial TrfA proteins. The trfA operon of broad-host-range IncP plasmids is essential to activate the origin of vegetative replication in diverse species. The trfA operon encodes two ORFs. The first ORF is highly conserved and encodes a putative single-stranded DNA binding protein (Ssb). The second, trfA, contains two translational starts as in the IncP alpha plasmids, generating related polypeptides of 406 (TrfA1) and 282 (TrfA2) amino acids. TrfA2 is very similar to the IncP alpha product, whereas the N-terminal region of TrfA1 shows very little similarity to the equivalent region of IncP alpha TrfA1. This region has been implicated in the ability of IncP alpha plasmids to replicate efficiently in Pseudomonas aeruginosa [].
Probab=25.94 E-value=39 Score=29.47 Aligned_cols=40 Identities=25% Similarity=0.445 Sum_probs=33.0
Q ss_pred CcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCccee
Q psy5605 58 PVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEK 104 (152)
Q Consensus 58 ~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek 104 (152)
|+.|+.|+..-|+... ++.+|... ++.+|..|++.|+|+.
T Consensus 231 P~kvetl~~lcGS~~~---~l~~FR~~----Lk~AL~eL~~~g~v~~ 270 (282)
T PF07042_consen 231 PIKVETLRELCGSESS---RLRKFRQQ----LKKALDELVAVGFVSS 270 (282)
T ss_pred CccHHHHHHHcCCCcc---CHHHHHHH----HHHHHHHHHhcCceeE
Confidence 8999999999888643 46677544 9999999999999974
No 267
>TIGR01389 recQ ATP-dependent DNA helicase RecQ. The ATP-dependent DNA helicase RecQ of E. coli is about 600 residues long. This model represents bacterial proteins with a high degree of similarity in domain architecture and in primary sequence to E. coli RecQ. The model excludes eukaryotic and archaeal proteins with RecQ-like regions, as well as more distantly related bacterial helicases related to RecQ.
Probab=25.41 E-value=1.4e+02 Score=27.50 Aligned_cols=73 Identities=18% Similarity=0.256 Sum_probs=46.8
Q ss_pred HHhhHh-hcCCcchhhHHHHhCCCCCCCCC------CC---ccCCCchhHHHHHHHHHHhCCcceecCCC--CceeCcch
Q psy5605 49 LARHIY-MRSPVGVKTVTKIFGGRKRNGVC------PS---HFCRSSGSVARKALQALEQVNIIEKSDDG--GRKITSHG 116 (152)
Q Consensus 49 ilRkiY-l~g~vGV~~L~~~YGg~krrG~~------P~---h~~~asg~iiR~~LQqLE~~glVek~~~g--GR~lT~~G 116 (152)
|+..+| +.+..|++.+...+-|.++.-.. .+ -...-+...++.++++|...|+++....+ .=.||+++
T Consensus 408 ~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~~~~~~~~~ 487 (591)
T TIGR01389 408 ALSCVYRMGQRFGVGYIIEVLRGSKNDKILQKGHDQLSTYGIGKDYTQKEWRSLIDQLIAEGLLTENDEIYIGLQLTEAA 487 (591)
T ss_pred HHHHHHHhcCCCchhHhHHHHhCccchhHHhcCcccCCccCcCCCCCHHHHHHHHHHHHHcCCceeccCcCceEEeccch
Confidence 444455 45677888888888443332111 11 12334678999999999999999876532 44567777
Q ss_pred HhhHH
Q psy5605 117 RRDMD 121 (152)
Q Consensus 117 ~~~LD 121 (152)
+..|+
T Consensus 488 ~~~l~ 492 (591)
T TIGR01389 488 RKVLK 492 (591)
T ss_pred hhhcc
Confidence 66654
No 268
>PF14629 ORC4_C: Origin recognition complex (ORC) subunit 4 C-terminus
Probab=25.39 E-value=73 Score=25.09 Aligned_cols=37 Identities=22% Similarity=0.176 Sum_probs=27.9
Q ss_pred CCCchhHHHHHHHHHHhCCccee-cCCCCceeCcchHh
Q psy5605 82 CRSSGSVARKALQALEQVNIIEK-SDDGGRKITSHGRR 118 (152)
Q Consensus 82 ~~asg~iiR~~LQqLE~~glVek-~~~gGR~lT~~G~~ 118 (152)
..-+..+++++++.|.++|+|.- ....+..+....|.
T Consensus 149 ~~~~k~v~~~a~E~L~~l~Ll~~~~~~~~~~~~~e~r~ 186 (203)
T PF14629_consen 149 KVWSKPVALKAWEHLLSLELLKPNYDGSSNNVQKEFRM 186 (203)
T ss_pred ccCCHHHHHHHHHHHHHCCCceecccCCCCccCccceE
Confidence 45678899999999999999987 23346666666543
No 269
>PF14502 HTH_41: Helix-turn-helix domain
Probab=25.30 E-value=81 Score=20.90 Aligned_cols=27 Identities=26% Similarity=0.299 Sum_probs=22.1
Q ss_pred CCchhHHHHHHHHHHhCCcceecCCCCc
Q psy5605 83 RSSGSVARKALQALEQVNIIEKSDDGGR 110 (152)
Q Consensus 83 ~asg~iiR~~LQqLE~~glVek~~~gGR 110 (152)
.-|...|-++|+-||+.|-|.-... ||
T Consensus 17 ~vs~GtiQ~Alk~Le~~gaI~Le~r-Gh 43 (48)
T PF14502_consen 17 GVSRGTIQNALKFLEENGAIKLESR-GH 43 (48)
T ss_pred CcchhHHHHHHHHHHHCCcEEeeec-Cc
Confidence 4577899999999999999987663 44
No 270
>PF04458 DUF505: Protein of unknown function (DUF505); InterPro: IPR007548 This is a family of uncharacterised prokaryotic proteins.
Probab=25.27 E-value=53 Score=31.73 Aligned_cols=41 Identities=24% Similarity=0.263 Sum_probs=33.1
Q ss_pred CCchhHHHHHHHHHHhCCcceecCCC----CceeCcchHhhHHHH
Q psy5605 83 RSSGSVARKALQALEQVNIIEKSDDG----GRKITSHGRRDMDRI 123 (152)
Q Consensus 83 ~asg~iiR~~LQqLE~~glVek~~~g----GR~lT~~G~~~LD~i 123 (152)
+..=.++|.+|..||.-+||+...++ -..||+-|++.++..
T Consensus 326 ~~~~d~l~~~Ly~LEsf~LI~~~~~~~Gk~vY~lTe~Gekvle~~ 370 (591)
T PF04458_consen 326 RKNFDDLRESLYSLESFGLIESEVDEKGKDVYWLTEYGEKVLEDQ 370 (591)
T ss_pred hcchhHHHHHHHHHHhhhhHHhhhhccCceeEEechhHHHHHHhh
Confidence 34445789999999999999876643 378999999999966
No 271
>COG4626 Phage terminase-like protein, large subunit [General function prediction only]
Probab=25.24 E-value=1.2e+02 Score=28.97 Aligned_cols=50 Identities=24% Similarity=0.187 Sum_probs=37.3
Q ss_pred HHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHHHHHHH--------------HHHHHHhhcCceeecc
Q psy5605 92 ALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKE--------------AALQALAAQGITVVPT 149 (152)
Q Consensus 92 ~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~--------------~~~~~~~~~~~~~~~~ 149 (152)
.||+++++|++.. |+-+--+.|.|..-+.+..++ .-..+|+.+||.+||-
T Consensus 392 ~~~ew~k~G~lTi--------t~~~~id~~~I~ew~~~~~~~~~i~~v~~D~~g~~~~~~~l~~~g~~lv~i 455 (546)
T COG4626 392 RLQEWVKAGDLTI--------TRRDLIDYAEIVEWFMEIREKFLIKLVGFDPSGAGEFRDALAEAGIKVVGI 455 (546)
T ss_pred hHHHHHhcCceEE--------eCCCccCHHHHHHHHHHHHHhCCccEEeecccchHHHHHHHHhCCCceeec
Confidence 6999999999954 444667888888887665433 2346799999998873
No 272
>PF14557 AphA_like: Putative AphA-like transcriptional regulator
Probab=25.08 E-value=1.1e+02 Score=25.25 Aligned_cols=44 Identities=20% Similarity=0.319 Sum_probs=33.8
Q ss_pred CCchhHHHHHHHHHHhCCcceecCCC------CceeCcchHhhHHHHHHH
Q psy5605 83 RSSGSVARKALQALEQVNIIEKSDDG------GRKITSHGRRDMDRIAAQ 126 (152)
Q Consensus 83 ~asg~iiR~~LQqLE~~glVek~~~g------GR~lT~~G~~~LD~iA~~ 126 (152)
-.|-.++=.++.-|+..|+|+-.... =-.||++||..|+.+-++
T Consensus 43 gps~~Ll~~sie~Lr~eGlve~~~g~g~e~~a~l~iT~~Gr~~l~~Llt~ 92 (175)
T PF14557_consen 43 GPSLDLLGTSIELLREEGLVEAVDGEGMEDNALLAITDAGRRELQTLLTA 92 (175)
T ss_pred cCchhhhhhHHHHHHhcCCcccccccCCCccceeeeCcchHHHHHHHHhC
Confidence 34556777889999999999977421 247999999999886544
No 273
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=25.05 E-value=1.6e+02 Score=23.99 Aligned_cols=64 Identities=17% Similarity=0.183 Sum_probs=42.6
Q ss_pred CCcchhhhcccCCcCC-CCCCCchHHHHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHH
Q psy5605 19 VPEWVDIVKSAKFKEL-APYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALE 97 (152)
Q Consensus 19 ~PeW~d~vKTg~~KEl-aP~d~DW~YiRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE 97 (152)
-|+..++|+--..... ++... -+--+|--|+.++|+.-..+.++.|-. + -.++++|-
T Consensus 69 k~e~~~~v~~~~~~~~~~~LS~-----aaLEtLaiIay~qPiTr~eI~~irGv~------~-----------~~ii~~L~ 126 (188)
T PRK00135 69 KEENADYLQKLVKTPIKQSLSQ-----AALEVLAIIAYKQPITRIEIDEIRGVN------S-----------DGALQTLL 126 (188)
T ss_pred cHHHHHHHHHHhcccccCCCCH-----HHHHHHHHHHHcCCcCHHHHHHHHCCC------H-----------HHHHHHHH
Confidence 4666666654322211 12221 234578889999999999999987542 1 56789999
Q ss_pred hCCccee
Q psy5605 98 QVNIIEK 104 (152)
Q Consensus 98 ~~glVek 104 (152)
+.|||+.
T Consensus 127 ~~gLI~e 133 (188)
T PRK00135 127 AKGLIKE 133 (188)
T ss_pred HCCCeEE
Confidence 9999974
No 274
>PF14542 Acetyltransf_CG: GCN5-related N-acetyl-transferase; PDB: 2H5M_A 2Q44_A 1XMT_A 2Q4Y_A 2IL4_A 2EVN_A 1R57_A.
Probab=24.68 E-value=1e+02 Score=21.17 Aligned_cols=24 Identities=42% Similarity=0.451 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHhhcCceeeccC
Q psy5605 127 IRVSKKEAALQALAAQGITVVPTG 150 (152)
Q Consensus 127 i~~~~~~~~~~~~~~~~~~~~~~~ 150 (152)
+...+.+...+-..++|..|+|+-
T Consensus 39 ia~~L~~~~l~~a~~~~~kv~p~C 62 (78)
T PF14542_consen 39 IAKKLVEAALDYARENGLKVVPTC 62 (78)
T ss_dssp HHHHHHHHHHHHHHHTT-EEEETS
T ss_pred HHHHHHHHHHHHHHHCCCEEEEEC
Confidence 344555666677788999999974
No 275
>COG4754 Uncharacterized conserved protein [Function unknown]
Probab=24.42 E-value=62 Score=26.32 Aligned_cols=32 Identities=9% Similarity=0.274 Sum_probs=26.2
Q ss_pred HHHHHHHHhCCcceecCCCCceeCcchHhhHHH
Q psy5605 90 RKALQALEQVNIIEKSDDGGRKITSHGRRDMDR 122 (152)
Q Consensus 90 R~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~ 122 (152)
=.|.-.++.+|+|+-.. |.=.||++|+..+++
T Consensus 46 ~piv~ta~~Lglv~~e~-GDiilT~~Gk~~v~~ 77 (157)
T COG4754 46 MPIVETASLLGLVTAES-GDIILTDEGKEYVES 77 (157)
T ss_pred HHHHHHHHhcCceeccC-CCEEEehhhHHHHhC
Confidence 34667888899998666 678999999999875
No 276
>PF04458 DUF505: Protein of unknown function (DUF505); InterPro: IPR007548 This is a family of uncharacterised prokaryotic proteins.
Probab=24.38 E-value=68 Score=31.03 Aligned_cols=97 Identities=22% Similarity=0.241 Sum_probs=57.2
Q ss_pred CCCCcchhhhc-ccCCcCCCCCCCchHHHHHHHHH-hhHhhcCCcchhhHHHHhCCCCCCCC-CC--------CccCCCc
Q psy5605 17 MKVPEWVDIVK-SAKFKELAPYDPDWFYTRCAALA-RHIYMRSPVGVKTVTKIFGGRKRNGV-CP--------SHFCRSS 85 (152)
Q Consensus 17 i~~PeW~d~vK-Tg~~KElaP~d~DW~YiRaASil-RkiYl~g~vGV~~L~~~YGg~krrG~-~P--------~h~~~as 85 (152)
...++|+.-.+ -|.-..-.|.+.-+||.+.|.=+ |+-|+..- =..-|.+. -++|+ .. +|. ..-
T Consensus 390 ~P~~eWv~~A~eeglvg~g~pT~sG~~ya~LA~~i~R~P~lTr~-E~~vl~ki----P~~~~i~~~~~~e~~~d~~-~~e 463 (591)
T PF04458_consen 390 APNREWVEEAREEGLVGTGEPTESGRFYAELARHIKRLPHLTRY-EMEVLHKI----PDKGYIHREELVEFIKDHV-GKE 463 (591)
T ss_pred CCcHHHHHHHHHccccCCCCCCcchHHHHHHHhhhhhcccccHH-HHHHHHhC----CccccccHHHHHHHhhccc-ccc
Confidence 44446665322 23444456889999999988765 66666420 00111111 11110 00 111 111
Q ss_pred hhHHHHHHHHHHhCCcceecCCCCceeCcchHhh
Q psy5605 86 GSVARKALQALEQVNIIEKSDDGGRKITSHGRRD 119 (152)
Q Consensus 86 g~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~ 119 (152)
..=++.+|..||.-|+|+--++|+=.+|+.|+..
T Consensus 464 e~~i~~AL~kLEArGfI~~Lp~g~iilTeaG~~i 497 (591)
T PF04458_consen 464 EEEIIEALEKLEARGFIEILPNGMIILTEAGELI 497 (591)
T ss_pred hHHHHHHHHHHHhcchHHHcCCCcEEEehhhHHH
Confidence 2235669999999999999999999999999753
No 277
>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=24.02 E-value=95 Score=20.14 Aligned_cols=25 Identities=24% Similarity=0.254 Sum_probs=20.6
Q ss_pred CCCchhHHHHHHHHHHhCCcceecC
Q psy5605 82 CRSSGSVARKALQALEQVNIIEKSD 106 (152)
Q Consensus 82 ~~asg~iiR~~LQqLE~~glVek~~ 106 (152)
...|..-+=.+|+.|++.|+|+...
T Consensus 38 ~g~sr~tv~r~l~~l~~~g~I~~~~ 62 (76)
T PF13545_consen 38 LGVSRETVSRILKRLKDEGIIEVKR 62 (76)
T ss_dssp HTSCHHHHHHHHHHHHHTTSEEEET
T ss_pred HCCCHHHHHHHHHHHHHCCCEEEcC
Confidence 3456677888999999999999665
No 278
>PRK10263 DNA translocase FtsK; Provisional
Probab=23.99 E-value=2.3e+02 Score=30.20 Aligned_cols=83 Identities=16% Similarity=0.202 Sum_probs=53.6
Q ss_pred HHHhhhccccCCCCCCCcchhhhcccCCcC------CCCCCCchHHHHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCC
Q psy5605 4 VSYIGFRPSKSGKMKVPEWVDIVKSAKFKE------LAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVC 77 (152)
Q Consensus 4 I~~~A~~LKk~gki~~PeW~d~vKTg~~KE------laP~d~DW~YiRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~ 77 (152)
|+++.+|+|.++ .|++.+-+-.....+ -.-.+.|=.|-.|.+++ --.+-+.++.|.+.|.-
T Consensus 1253 i~~vv~~~k~~~---~p~y~~~~~~~~~~~~~~~~~~~~~~~D~l~~~a~~~v---~~~~~~S~S~lQR~~~i------- 1319 (1355)
T PRK10263 1253 VHAVVQDWKARG---RPQYVDGITSDSESEGGAGGFDGAEELDPLFDQAVQFV---TEKRKASISGVQRQFRI------- 1319 (1355)
T ss_pred HHHHHHHHHhcC---CCchhhhhcccccccccccCcCCCccccHHHHHHHHHH---HhcCccCHHHHHHHhhc-------
Confidence 778999999886 466654332111111 11123466777777665 34678899999988732
Q ss_pred CCccCCCchhHHHHHHHHHHhCCcceecC
Q psy5605 78 PSHFCRSSGSVARKALQALEQVNIIEKSD 106 (152)
Q Consensus 78 P~h~~~asg~iiR~~LQqLE~~glVek~~ 106 (152)
|. +-..+++.+||+.|+|....
T Consensus 1320 ------Gy-nRAariid~lE~~Giv~p~~ 1341 (1355)
T PRK10263 1320 ------GY-NRAARIIEQMEAQGIVSEQG 1341 (1355)
T ss_pred ------Ch-HHHHHHHHHHHHCCcCCCCC
Confidence 22 23467899999999998755
No 279
>PF09929 DUF2161: Uncharacterized conserved protein (DUF2161); InterPro: IPR018679 This family of various hypothetical prokaryotic proteins has no known function.
Probab=23.71 E-value=64 Score=25.05 Aligned_cols=22 Identities=23% Similarity=0.386 Sum_probs=19.1
Q ss_pred CCcceecCCCCceeCcchHhhH
Q psy5605 99 VNIIEKSDDGGRKITSHGRRDM 120 (152)
Q Consensus 99 ~glVek~~~gGR~lT~~G~~~L 120 (152)
=||.|..+.|=-.||++|+..|
T Consensus 97 YGWFeRv~rGvY~LT~~G~~al 118 (118)
T PF09929_consen 97 YGWFERVERGVYALTPAGRAAL 118 (118)
T ss_pred ccceeeeccceEecCcchhhcC
Confidence 4999999987799999999764
No 280
>TIGR02873 spore_ylxY probable sporulation protein, polysaccharide deacetylase family. Members of this protein family are most closely related to TIGR02764, a subset of polysaccharide deacetylase family proteins found in a species if and only if the species forms endospores like those of Bacillus subtilis or Clostridium tetani. This family is likewise restricted to spore-formers, but is not universal among them in having sequences with full-length matches to the model.
Probab=23.53 E-value=2.7e+02 Score=23.57 Aligned_cols=75 Identities=17% Similarity=0.225 Sum_probs=44.7
Q ss_pred CCCCCccCCCchhHHHHHHHHHHhCCccee--cCCCCceeCcchHhhHHHHHHHH-------------HHHHHHHHHHHH
Q psy5605 75 GVCPSHFCRSSGSVARKALQALEQVNIIEK--SDDGGRKITSHGRRDMDRIAAQI-------------RVSKKEAALQAL 139 (152)
Q Consensus 75 G~~P~h~~~asg~iiR~~LQqLE~~glVek--~~~gGR~lT~~G~~~LD~iA~~i-------------~~~~~~~~~~~~ 139 (152)
|..|..|+..+|+.-..+++.|.++|+.-- +-+..--.++......+++-.++ ..+.-+.-...|
T Consensus 174 G~~p~~fRpP~G~~n~~~~~~l~~~G~~~v~Wsvd~~Dw~~~~~~~i~~~v~~~~~~G~IILmHd~~~T~~aL~~iI~~L 253 (268)
T TIGR02873 174 GVTPKWFAPPSGSFNDNVVQIAADLQMGTIMWTVDTIDWKNPSPSVMVNRVLSKIHPGAMVLMHPTASSTEGLEEMITII 253 (268)
T ss_pred CCCCCEEECCCCCCCHHHHHHHHHCCCeEEEeccCCCCCCCCCHHHHHHHHHhcCCCCcEEEEcCCccHHHHHHHHHHHH
Confidence 346777888888888889999999888542 22111112233334444443321 123455666778
Q ss_pred hhcCceeecc
Q psy5605 140 AAQGITVVPT 149 (152)
Q Consensus 140 ~~~~~~~~~~ 149 (152)
.++|.++|+.
T Consensus 254 k~kGy~fvtl 263 (268)
T TIGR02873 254 KEKGYKIGTI 263 (268)
T ss_pred HHCCCEEEeH
Confidence 8899888763
No 281
>smart00190 IL4_13 Interleukins 4 and 13. Interleukins-4 and -13 are cytokines involved in inflammatory and immune responses. IL-4 stimulates B and T cells.
Probab=23.26 E-value=2.1e+02 Score=22.84 Aligned_cols=17 Identities=18% Similarity=0.477 Sum_probs=14.6
Q ss_pred hHHHHHHHHHhhHhhcC
Q psy5605 41 WFYTRCAALARHIYMRS 57 (152)
Q Consensus 41 W~YiRaASilRkiYl~g 57 (152)
=.|-||+-+||++|.+.
T Consensus 68 e~~CrA~~vLr~~y~~~ 84 (138)
T smart00190 68 ELFCRALKVLRNFYFHN 84 (138)
T ss_pred hHhhHHHHHHHHHHHhh
Confidence 45899999999999863
No 282
>PF15447 NTS: N-terminal segments of PfEMP1; PDB: 2XU0_A 2YK0_A.
Probab=23.25 E-value=44 Score=20.87 Aligned_cols=18 Identities=28% Similarity=0.407 Sum_probs=14.0
Q ss_pred hHhhHHHHHHHHHHHHHH
Q psy5605 116 GRRDMDRIAAQIRVSKKE 133 (152)
Q Consensus 116 G~~~LD~iA~~i~~~~~~ 133 (152)
.+..||+|+.+|.++.++
T Consensus 2 Ak~vLd~IG~~I~~~v~~ 19 (37)
T PF15447_consen 2 AKNVLDRIGKEIYKKVKK 19 (37)
T ss_dssp HHHHHHHHHHHHHHHCC-
T ss_pred HHHHHHHHHHHHHHHHhH
Confidence 477899999999876544
No 283
>PF13182 DUF4007: Protein of unknown function (DUF4007)
Probab=23.22 E-value=54 Score=28.07 Aligned_cols=38 Identities=24% Similarity=0.347 Sum_probs=28.6
Q ss_pred CCchh-HHHHHHHHHHhCCcceecCCCCceeCcchHhhH
Q psy5605 83 RSSGS-VARKALQALEQVNIIEKSDDGGRKITSHGRRDM 120 (152)
Q Consensus 83 ~asg~-iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~L 120 (152)
-|-|+ .+..+--=|...|+++.+.++++.+|+-|+..+
T Consensus 38 lGvGkNMV~siryWl~a~gli~~~~~~~~~~T~lG~~i~ 76 (286)
T PF13182_consen 38 LGVGKNMVKSIRYWLRAFGLIEEDNKGKRKLTPLGELIF 76 (286)
T ss_pred cCCCHhHHHHHHHHHHHcCCcccCCCCCcccCHHHHHHH
Confidence 34444 344444457789999999877789999999999
No 284
>PF04182 B-block_TFIIIC: B-block binding subunit of TFIIIC; InterPro: IPR007309 Yeast transcription factor IIIC (TFIIIC) is a multisubunit protein complex that interacts with two control elements of class III promoters called the A and B blocks. This family represents the subunit within TFIIIC involved in B-block binding []. Although defined as a yeast protein, it is also found in a number of other organisms.
Probab=22.70 E-value=66 Score=21.96 Aligned_cols=22 Identities=23% Similarity=0.143 Sum_probs=18.0
Q ss_pred hhHHHHHHHHHHhCCcceecCC
Q psy5605 86 GSVARKALQALEQVNIIEKSDD 107 (152)
Q Consensus 86 g~iiR~~LQqLE~~glVek~~~ 107 (152)
..-+-+.++.||+.|||.+.+-
T Consensus 32 ~r~i~~~~k~L~~~gLI~k~~~ 53 (75)
T PF04182_consen 32 PRSIFYRLKKLEKKGLIVKQSV 53 (75)
T ss_pred chHHHHHHHHHHHCCCEEEEEe
Confidence 3557788999999999998763
No 285
>PF09661 DUF2398: Protein of unknown function (DUF2398); InterPro: IPR013494 Proteins in this family are encoded within a conserved gene four-gene neighbourhood found sporadically in a phylogenetically broad range of bacteria including: Nocardia farcinica, Symbiobacterium thermophilum, Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. (strain EbN1) (Aromatoleum aromaticum (strain EbN1)) and Ralstonia solanacearum (Betaproteobacteria).
Probab=22.45 E-value=1.6e+02 Score=26.29 Aligned_cols=50 Identities=16% Similarity=0.219 Sum_probs=35.9
Q ss_pred hhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcc
Q psy5605 62 KTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSH 115 (152)
Q Consensus 62 ~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~ 115 (152)
..|+..||..=++ .....+...+++.++..|+..|+++..+++|=.|.|.
T Consensus 309 ~~l~~~~~~~W~k----~~~~~~~~~L~~~vl~~L~~~~L~~~~~~~~v~l~Pa 358 (368)
T PF09661_consen 309 AELRERYGSGWSK----EYREMDPEELAEEVLELLEEWGLARVDGDGGVVLLPA 358 (368)
T ss_pred HHHHHHhhccccc----ccccCCHHHHHHHHHHHHHHCCCceECCCCeEEEccc
Confidence 4556666654433 3334567889999999999999999888765566653
No 286
>PF15398 DUF4619: Domain of unknown function (DUF4619)
Probab=22.04 E-value=29 Score=30.75 Aligned_cols=64 Identities=22% Similarity=0.459 Sum_probs=43.1
Q ss_pred cCCcCCCCCCCchHHHHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHH----HHHHHHHhCCccee
Q psy5605 29 AKFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVAR----KALQALEQVNIIEK 104 (152)
Q Consensus 29 g~~KElaP~d~DW~YiRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR----~~LQqLE~~glVek 104 (152)
....+|||.-+.|| =|..++=|-+|++=|+ ..+..|||+ .=||.||.+++-..
T Consensus 56 ~~egQLPPLret~y-Grys~v~r~m~FDIpl----------------------e~~EtSIIKrHPPRRlQkLEp~~lP~~ 112 (296)
T PF15398_consen 56 ALEGQLPPLRETWY-GRYSTVPRAMYFDIPL----------------------ENGETSIIKRHPPRRLQKLEPIDLPQV 112 (296)
T ss_pred ccccCCCchhhccc-cccccCCCceeeeecc----------------------cCCcccccccCCCccccccCCCCCCcc
Confidence 34589999998876 7888888888887442 235667777 35788888876543
Q ss_pred cCCCCceeCcch
Q psy5605 105 SDDGGRKITSHG 116 (152)
Q Consensus 105 ~~~gGR~lT~~G 116 (152)
.. .+|.++++.
T Consensus 113 it-s~rll~q~e 123 (296)
T PF15398_consen 113 IT-SERLLSQQE 123 (296)
T ss_pred cc-hhhhhhHHH
Confidence 33 244454443
No 287
>PF01121 CoaE: Dephospho-CoA kinase; InterPro: IPR001977 This family contains dephospho-CoA kinases (2.7.1.24 from EC), which catalyzes the final step in CoA biosynthesis, the phosphorylation of the 3'-hydroxyl group of ribose using ATP as a phosphate donor. The crystal structures of a number of the proteins in this entry have been determined, including the structure of the protein from Haemophilus influenzae to 2.0-A resolution in a comlex with ATP. The protein consists of three domains: the nucleotide-binding domain with a five-stranded parallel beta-sheet, the substrate-binding alpha-helical domain, and the lid domain formed by a pair of alpha-helices; the overall topology of the protein resembles the structures of other nucleotide kinases [].; GO: 0004140 dephospho-CoA kinase activity, 0005524 ATP binding, 0015937 coenzyme A biosynthetic process; PDB: 1VHL_A 1N3B_A 1VIY_A 1VHT_B 1T3H_B 1UF9_C 2F6R_A 2GRJ_D 2IF2_C 1JJV_A.
Probab=21.91 E-value=3.5e+02 Score=21.43 Aligned_cols=79 Identities=15% Similarity=0.299 Sum_probs=54.9
Q ss_pred HHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHH
Q psy5605 44 TRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRI 123 (152)
Q Consensus 44 iRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~i 123 (152)
+-|=.+.+.+|-.++.+...|...||.. .....|.|-|..|-++ |=. .|+-++.|+.|
T Consensus 28 idaD~i~~~l~~~~~~~~~~l~~~FG~~---------il~~~g~idR~~L~~~-----vF~--------d~~~~~~L~~i 85 (180)
T PF01121_consen 28 IDADEIAHELYEPGSEGYKALKERFGEE---------ILDEDGEIDRKKLAEI-----VFS--------DPEKLKKLENI 85 (180)
T ss_dssp EEHHHHHHHCTSCTCHHHHHHHHHHGGG---------GBETTSSB-HHHHHHH-----HTT--------SHHHHHHHHHH
T ss_pred ECccHHHHHHhhcCHHHHHHHHHHcCcc---------ccCCCCCChHHHHHHH-----Hhc--------CHHHHHHHHHH
Confidence 4455789999999999999999999843 3345678888888775 222 24568899999
Q ss_pred HHHHHHHHHHHHHHHHhhcCc
Q psy5605 124 AAQIRVSKKEAALQALAAQGI 144 (152)
Q Consensus 124 A~~i~~~~~~~~~~~~~~~~~ 144 (152)
-+-.+.+.-+...+....+.+
T Consensus 86 ihP~I~~~~~~~~~~~~~~~~ 106 (180)
T PF01121_consen 86 IHPLIREEIEKFIKRNKSEKV 106 (180)
T ss_dssp HHHHHHHHHHHHHHHCHSTSE
T ss_pred HhHHHHHHHHHHHHhccCCCE
Confidence 998766555555554444333
No 288
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=21.67 E-value=1.5e+02 Score=20.99 Aligned_cols=44 Identities=11% Similarity=0.138 Sum_probs=28.1
Q ss_pred HHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcce
Q psy5605 46 CAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIE 103 (152)
Q Consensus 46 aASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVe 103 (152)
++-|++-|..+|.+-=..|++.- .=.-+.+|++|+.|.+.|+|.
T Consensus 15 ~~~Il~~L~~~~~l~de~la~~~--------------~l~~~~vRkiL~~L~~~~lv~ 58 (105)
T PF02002_consen 15 AVRILDALLRKGELTDEDLAKKL--------------GLKPKEVRKILYKLYEDGLVS 58 (105)
T ss_dssp THHHHHHHHHH--B-HHHHHHTT---------------S-HHHHHHHHHHHHHHSS-E
T ss_pred HHHHHHHHHHcCCcCHHHHHHHh--------------CCCHHHHHHHHHHHHHCCCeE
Confidence 34566666666666666666653 234589999999999999995
No 289
>COG3265 GntK Gluconate kinase [Carbohydrate transport and metabolism]
Probab=21.59 E-value=3.7e+02 Score=21.99 Aligned_cols=111 Identities=15% Similarity=0.152 Sum_probs=71.7
Q ss_pred cCCCCCCCcchhhhcccCCcCCCCCCCchHHHHHHHHHhhHhhcCC---cchhhHHHHhCCCCCCCC-------------
Q psy5605 13 KSGKMKVPEWVDIVKSAKFKELAPYDPDWFYTRCAALARHIYMRSP---VGVKTVTKIFGGRKRNGV------------- 76 (152)
Q Consensus 13 k~gki~~PeW~d~vKTg~~KElaP~d~DW~YiRaASilRkiYl~g~---vGV~~L~~~YGg~krrG~------------- 76 (152)
+-..+-+|+ ++-|-+.+--|--+|.-+|--+...-++..+-.+. +.-++|.+.|-..-|.++
T Consensus 25 dGDdlHp~a--Ni~KM~~GiPL~DdDR~pWL~~l~~~~~~~~~~~~~~vi~CSALKr~YRD~LR~~~~~~~Fv~L~g~~~ 102 (161)
T COG3265 25 DGDDLHPPA--NIEKMSAGIPLNDDDRWPWLEALGDAAASLAQKNKHVVIACSALKRSYRDLLREANPGLRFVYLDGDFD 102 (161)
T ss_pred cccccCCHH--HHHHHhCCCCCCcchhhHHHHHHHHHHHHhhcCCCceEEecHHHHHHHHHHHhccCCCeEEEEecCCHH
Confidence 345677887 55566666555433434677777777777776654 455889999988877775
Q ss_pred --------CCCccCCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHHHHHHH
Q psy5605 77 --------CPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKE 133 (152)
Q Consensus 77 --------~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~ 133 (152)
|..||-++ +.+.+=|-.||.-+ -++ .+||=.=-..++.+..+++.-+++
T Consensus 103 ~i~~Rm~~R~gHFM~~--~ll~SQfa~LE~P~---~de---~vi~idi~~~~e~vv~~~~~~l~~ 159 (161)
T COG3265 103 LILERMKARKGHFMPA--SLLDSQFATLEEPG---ADE---DVLTIDIDQPPEEVVAQALAWLKE 159 (161)
T ss_pred HHHHHHHhcccCCCCH--HHHHHHHHHhcCCC---CCC---CEEEeeCCCCHHHHHHHHHHHHhc
Confidence 66787776 56666666666433 233 355555555677777777665543
No 290
>PRK13490 chemoreceptor glutamine deamidase CheD; Provisional
Probab=21.35 E-value=1.3e+02 Score=24.02 Aligned_cols=58 Identities=12% Similarity=0.152 Sum_probs=40.7
Q ss_pred hHHHHHHHHHHhCCcce-----ecCCCCceeCcchHhhHHHHHHHHHHHHHHHHHHHHhhcCceeec
Q psy5605 87 SVARKALQALEQVNIIE-----KSDDGGRKITSHGRRDMDRIAAQIRVSKKEAALQALAAQGITVVP 148 (152)
Q Consensus 87 ~iiR~~LQqLE~~glVe-----k~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~~~~~~~~~~~~~~~ 148 (152)
.-|...+++|+++|--. |--.|+.++.....+.. ..|-..+.+..++.|++.||.++-
T Consensus 68 ~ai~~Li~~m~~~Ga~~~~l~aKifGGA~m~~~~~~~~~----~~IG~rNv~~a~~~L~~~gI~i~a 130 (162)
T PRK13490 68 LAIPILIEKMEKLGANKRNLKAKIAGGASMFNFSDKSMV----MDIGNRNGKAVKKKLKELSIPILA 130 (162)
T ss_pred HHHHHHHHHHHHcCCCHHHEEEEEEeCccccCCCCcccc----CChhHHHHHHHHHHHHHcCCcEEE
Confidence 46788888999988642 33346677764432211 247788899999999999999874
No 291
>PRK02539 hypothetical protein; Provisional
Probab=21.27 E-value=76 Score=23.37 Aligned_cols=24 Identities=21% Similarity=0.512 Sum_probs=18.3
Q ss_pred HHHHHHHHhCCcceecCCCCceeCcch
Q psy5605 90 RKALQALEQVNIIEKSDDGGRKITSHG 116 (152)
Q Consensus 90 R~~LQqLE~~glVek~~~gGR~lT~~G 116 (152)
....+||+.+.+|+ + .|--+||+=
T Consensus 42 ~~~~~~L~~i~ivD--~-~G~dVTP~K 65 (85)
T PRK02539 42 RSVRHHIEGIKIVD--E-EGNDVTPEK 65 (85)
T ss_pred HHHHHHhccceEEC--C-CCCCCCHHH
Confidence 34568999999994 4 377899983
No 292
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=21.26 E-value=1e+02 Score=25.52 Aligned_cols=46 Identities=28% Similarity=0.528 Sum_probs=35.0
Q ss_pred hHhh-cCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCC-CCce
Q psy5605 52 HIYM-RSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDD-GGRK 111 (152)
Q Consensus 52 kiYl-~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~-gGR~ 111 (152)
-+|+ ++|+.++.++.+-|-.+ +-+=..+..||..++|++... |-|+
T Consensus 34 ilyls~~Pmtl~Ei~E~lg~Sk--------------s~vS~~lkkL~~~~lV~~~~~~G~Rk 81 (177)
T COG1510 34 ILYLSRKPLTLDEIAEALGMSK--------------SNVSMGLKKLQDWNLVKKVFEKGDRK 81 (177)
T ss_pred hheecCCCccHHHHHHHHCCCc--------------chHHHHHHHHHhcchHHhhhccCcch
Confidence 4788 88999999999987642 334567899999999997653 4454
No 293
>PF03480 SBP_bac_7: Bacterial extracellular solute-binding protein, family 7; InterPro: IPR018389 This family of proteins are involved in binding extracellular solutes for transport across the bacterial cytoplasmic membrane. This family includes a C4-dicarboxylate-binding protein DctP [, ] and the sialic acid-binding protein SiaP. The structure of the SiaP receptor has revealed an overall topology similar to ATP binding cassette ESR (extracytoplasmic solute receptors) proteins []. Upon binding of sialic acid, SiaP undergoes domain closure about a hinge region and kinking of an alpha-helix hinge component [].; GO: 0006810 transport, 0030288 outer membrane-bounded periplasmic space; PDB: 2HZK_C 2HZL_B 2HPG_C 2XWI_A 2XWK_A 2WX9_A 2CEY_A 2WYP_A 3B50_A 2CEX_B ....
Probab=21.25 E-value=1.8e+02 Score=23.92 Aligned_cols=38 Identities=26% Similarity=0.466 Sum_probs=26.3
Q ss_pred eeCcchHhhHHHHHHHHHH-------HHHHHHHHHHhhcCceeec
Q psy5605 111 KITSHGRRDMDRIAAQIRV-------SKKEAALQALAAQGITVVP 148 (152)
Q Consensus 111 ~lT~~G~~~LD~iA~~i~~-------~~~~~~~~~~~~~~~~~~~ 148 (152)
.|+++=|..|++.+.+... +..+...+.|.++|++|+.
T Consensus 218 ~L~~e~q~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~ 262 (286)
T PF03480_consen 218 SLPDEDQEALDDAADEAEARAREYYEAEDEEALKELEENGVTVVE 262 (286)
T ss_dssp HS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEE
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCcCEEeC
Confidence 5778888888888877633 3445556678889999975
No 294
>COG4465 CodY Pleiotropic transcriptional repressor [Transcription]
Probab=21.20 E-value=1.2e+02 Score=26.36 Aligned_cols=22 Identities=36% Similarity=0.471 Sum_probs=19.4
Q ss_pred chhHHHHHHHHHHhCCcceecC
Q psy5605 85 SGSVARKALQALEQVNIIEKSD 106 (152)
Q Consensus 85 sg~iiR~~LQqLE~~glVek~~ 106 (152)
.+|||=++|..||.+|+||...
T Consensus 217 TRSVIVNALRKlESAGvIeSRS 238 (261)
T COG4465 217 TRSVIVNALRKLESAGVIESRS 238 (261)
T ss_pred hHHHHHHHHHHhhhcCceeecc
Confidence 4689999999999999998655
No 295
>PF02477 Nairo_nucleo: Nucleocapsid N protein; InterPro: IPR003486 The nucleoprotein of the ssRNA negative-strand Nairovirus is an internal part of the virus particle.; GO: 0019013 viral nucleocapsid; PDB: 3U3I_A.
Probab=21.11 E-value=1.5e+02 Score=27.54 Aligned_cols=52 Identities=19% Similarity=0.291 Sum_probs=29.5
Q ss_pred HHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHHHHH--HHHHHHHHhhcCce
Q psy5605 89 ARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSK--KEAALQALAAQGIT 145 (152)
Q Consensus 89 iR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~--~~~~~~~~~~~~~~ 145 (152)
||..|.+|+ |||+.+++. .=--+|.+.++.+-.++.+.. .+. -.||.+||-.
T Consensus 251 ~k~~l~~l~--~w~~~~kd~--~e~~k~~elv~~~~k~l~~a~~L~k~-s~a~raQGaq 304 (442)
T PF02477_consen 251 IKKTLLDLK--KWVEDNKDE--VEDGKGDELVKTLTKHLAKATELSKK-STAFRAQGAQ 304 (442)
T ss_dssp HHHHHHHHH--HHHHHTGGG--S-HHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHT-
T ss_pred HHHHHHHHH--HHHHhchHh--hhcccHHHHHHHHHHHHHHHHHHhcC-chHHHhccCc
Confidence 455555555 699977752 222345777777777665433 222 2467788743
No 296
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=20.85 E-value=2.4e+02 Score=20.39 Aligned_cols=41 Identities=12% Similarity=0.234 Sum_probs=34.2
Q ss_pred hHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC
Q psy5605 52 HIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD 106 (152)
Q Consensus 52 kiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~ 106 (152)
.|-++|-+....|+..| ..+-..|+-.|..|+.+|-|++.+
T Consensus 10 ~l~~~gr~s~~~Ls~~~--------------~~p~~~VeaMLe~l~~kGkverv~ 50 (78)
T PRK15431 10 LLALRGRMEAAQISQTL--------------NTPQPMINAMLQQLESMGKAVRIQ 50 (78)
T ss_pred HHHHcCcccHHHHHHHH--------------CcCHHHHHHHHHHHHHCCCeEeec
Confidence 34567888888888887 456689999999999999999886
No 297
>PF02985 HEAT: HEAT repeat; InterPro: IPR000357 The HEAT repeat is a tandemly repeated, 37-47 amino acid long module occurring in a number of cytoplasmic proteins, including the four name-giving proteins huntingtin, elongation factor 3 (EF3), the 65 Kd alpha regulatory subunit of protein phosphatase 2A (PP2A) and the yeast PI3-kinase TOR1 []. Arrays of HEAT repeats consists of 3 to 36 units forming a rod-like helical structure and appear to function as protein-protein interaction surfaces. It has been noted that many HEAT repeat-containing proteins are involved in intracellular transport processes. In the crystal structure of PP2A PR65/A [], the HEAT repeats consist of pairs of antiparallel alpha helices [].; GO: 0005515 protein binding; PDB: 3FGA_A 2PF4_C 2IAE_A 2BKU_D 3EA5_B 3ND2_A 2BPT_A 2NYL_A 2NPP_D 2PKG_B ....
Probab=20.67 E-value=74 Score=17.92 Aligned_cols=12 Identities=42% Similarity=0.235 Sum_probs=7.4
Q ss_pred CCCchHHHHHHHH
Q psy5605 37 YDPDWFYTRCAAL 49 (152)
Q Consensus 37 ~d~DW~YiRaASi 49 (152)
.||||. +|.|++
T Consensus 10 ~D~~~~-VR~~a~ 21 (31)
T PF02985_consen 10 NDPSPE-VRQAAA 21 (31)
T ss_dssp T-SSHH-HHHHHH
T ss_pred CCCCHH-HHHHHH
Confidence 477777 776665
No 298
>COG5631 Predicted transcription regulator, contains HTH domain (MarR family) [Transcription]
Probab=20.56 E-value=1.5e+02 Score=24.76 Aligned_cols=39 Identities=23% Similarity=0.321 Sum_probs=30.1
Q ss_pred hhHHHHHHHHHHhCCcceecCCC---CceeCcchHhhHHHHH
Q psy5605 86 GSVARKALQALEQVNIIEKSDDG---GRKITSHGRRDMDRIA 124 (152)
Q Consensus 86 g~iiR~~LQqLE~~glVek~~~g---GR~lT~~G~~~LD~iA 124 (152)
-.+|-+.|..|++.|||+....| --.+|+.|.+.--+.|
T Consensus 113 th~itYslrKL~k~gLit~t~~gkevTy~vTa~G~~acarYa 154 (199)
T COG5631 113 THNITYSLRKLLKGGLITRTGSGKEVTYEVTALGHRACARYA 154 (199)
T ss_pred chhHHHHHHHHHhccceecCCCCceEEEEEecchHHHHHHHH
Confidence 35788999999999999977642 3468899987666554
No 299
>PF03849 Tfb2: Transcription factor Tfb2; InterPro: IPR004598 Members of this family are part of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. The core-TFIIH basal transcription factor complex has six subunits, this is the p52 subunit.; GO: 0006281 DNA repair, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=20.46 E-value=1.9e+02 Score=25.77 Aligned_cols=57 Identities=23% Similarity=0.458 Sum_probs=41.7
Q ss_pred CCcCCCCCCCchHHHHHHHHHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecC
Q psy5605 30 KFKELAPYDPDWFYTRCAALARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSD 106 (152)
Q Consensus 30 ~~KElaP~d~DW~YiRaASilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~ 106 (152)
.+|++||.-..+ |+|=+|+..|+....+...- +|++ .+-...+++.|.++.++...+
T Consensus 24 IfR~LP~LAK~~-------VmrLL~~~~pv~~~~l~~Wv--------~~~~-----~~~~~~al~~L~~L~Ii~~~~ 80 (366)
T PF03849_consen 24 IFRSLPPLAKQY-------VMRLLFVEQPVPQADLESWV--------KPES-----KKEHDEALKRLRSLHIIQESE 80 (366)
T ss_pred HHHhccHHHHHH-------HHHHHhcCCCcCHHHHHHHh--------Cccc-----hHHHHHHHHHHhhCeeEeecc
Confidence 445555544321 67889999999999998875 3433 567789999999999997554
No 300
>PLN02512 acetylglutamate kinase
Probab=20.34 E-value=2.7e+02 Score=23.90 Aligned_cols=62 Identities=16% Similarity=0.205 Sum_probs=37.6
Q ss_pred CCCchhHHHHHHHHHHhCCcceecCCCCceeCcchHhhHHHHHHHHHHHHHHHHHHHHhhcCceeecc
Q psy5605 82 CRSSGSVARKALQALEQVNIIEKSDDGGRKITSHGRRDMDRIAAQIRVSKKEAALQALAAQGITVVPT 149 (152)
Q Consensus 82 ~~asg~iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~~~~~~~~~~~~~~~~ 149 (152)
..|.|+.+.. .|++.|+-.+.. .|.++|+. ..|+-+-..+..++.+.--++|.++|+..++.
T Consensus 85 VHGgG~~i~~---~~~~~gi~~~~~-~G~rvT~~--~~lei~~~~l~g~ln~~lv~~L~~~Gv~av~l 146 (309)
T PLN02512 85 VHGGGPEINS---WLKKVGIEPQFK-NGLRVTDA--ETMEVVEMVLVGKVNKSLVSLINKAGGTAVGL 146 (309)
T ss_pred EECCcHHHHH---HHHHcCCCCcCC-CCCcCCCH--HHHHHHHHHHhhHHHHHHHHHHHHcCCCeEEe
Confidence 4466665544 445566554333 47777776 44544433334566667778899999987764
No 301
>PRK13494 chemoreceptor glutamine deamidase CheD; Provisional
Probab=20.24 E-value=1.7e+02 Score=23.53 Aligned_cols=55 Identities=15% Similarity=0.164 Sum_probs=40.6
Q ss_pred hhHHHHHHHHHHhCCcce-----ecCCCCceeCcchHhhHHHHHHHHHHHHHHHHHHHHhhcCceeec
Q psy5605 86 GSVARKALQALEQVNIIE-----KSDDGGRKITSHGRRDMDRIAAQIRVSKKEAALQALAAQGITVVP 148 (152)
Q Consensus 86 g~iiR~~LQqLE~~glVe-----k~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~~~~~~~~~~~~~~~ 148 (152)
..-+...+++|+++|--. |--.|++++.+. ...|-..+.+..++.|++.||.++-
T Consensus 73 d~ai~~Ll~~m~~~Ga~~~~l~aKifGGa~m~~~~--------~~~IG~rNv~~a~~~L~~~gI~i~a 132 (163)
T PRK13494 73 VYAIPMLIDAMLENGASKSNLKAKLFGGTNFMAKG--------TIKVGLENSEFAVNTLNKYGIPILA 132 (163)
T ss_pred HHHHHHHHHHHHHcCCCHHHeEEEEEeCcccCCcc--------cCChHHHHHHHHHHHHHHcCCcEEE
Confidence 456788889999988643 333567777632 1247888999999999999999874
No 302
>PF14113 DUF4285: Domain of unknown function (DUF4285)
Probab=20.23 E-value=1.3e+02 Score=22.45 Aligned_cols=28 Identities=18% Similarity=0.337 Sum_probs=23.4
Q ss_pred CCcCCCCCCCchHHHHHHHHHhhHhhcC
Q psy5605 30 KFKELAPYDPDWFYTRCAALARHIYMRS 57 (152)
Q Consensus 30 ~~KElaP~d~DW~YiRaASilRkiYl~g 57 (152)
..+...|.|-.||++|+..++--|..++
T Consensus 28 ~~~~~~~~~g~~y~~ra~~l~~~L~~~~ 55 (115)
T PF14113_consen 28 LGRTVSGADGKWYIYRAEELANWLKKKP 55 (115)
T ss_pred cceeccCCCCCchhhHHHHHHHHHHHCC
Confidence 4677778888999999999998887773
No 303
>PRK13491 chemoreceptor glutamine deamidase CheD; Provisional
Probab=20.17 E-value=1.8e+02 Score=24.30 Aligned_cols=53 Identities=17% Similarity=0.137 Sum_probs=39.2
Q ss_pred hHHHHHHHHHHhCCcce-----ecCCCCceeCcchHhhHHHHHHHHHHHHHHHHHHHHhhcCceeec
Q psy5605 87 SVARKALQALEQVNIIE-----KSDDGGRKITSHGRRDMDRIAAQIRVSKKEAALQALAAQGITVVP 148 (152)
Q Consensus 87 ~iiR~~LQqLE~~glVe-----k~~~gGR~lT~~G~~~LD~iA~~i~~~~~~~~~~~~~~~~~~~~~ 148 (152)
.-|...|++|+++|--. |--.|++++.. ...|-..+.+..++.|+..||.++-
T Consensus 76 ~Ai~~Li~~m~~~Ga~~~~L~AKifGGA~M~~~---------~~~IG~rNie~a~~~L~~~GI~iva 133 (199)
T PRK13491 76 HAMELLINALLKLGAARQRIEAKIFGGAMMTPQ---------LGAIGQANAAFARRYLRDEGIRCTA 133 (199)
T ss_pred HHHHHHHHHHHHcCCCHHHeEEEEEeCcccccc---------cccHHHHHHHHHHHHHHHcCCcEEE
Confidence 45788888899988542 33346666641 1258888999999999999999874
No 304
>PTZ00362 hypothetical protein; Provisional
Probab=20.13 E-value=38 Score=31.89 Aligned_cols=22 Identities=27% Similarity=0.348 Sum_probs=18.2
Q ss_pred hhhccccCCC--CCCCcchhhhcc
Q psy5605 7 IGFRPSKSGK--MKVPEWVDIVKS 28 (152)
Q Consensus 7 ~A~~LKk~gk--i~~PeW~d~vKT 28 (152)
+|-+||+.|+ |.+|.|.++=+-
T Consensus 323 LAi~LKq~~KC~IvpP~Wm~ie~L 346 (479)
T PTZ00362 323 IAKELSHFGLVTVEFPFWFYIKNL 346 (479)
T ss_pred ehhhhcccCceEEeCcccccHHHH
Confidence 6889999988 889999987544
No 305
>PF06414 Zeta_toxin: Zeta toxin; InterPro: IPR010488 This entry represents a domain originally identified in bacterial zeta toxin proteins, where it comprises the whole protein []. It has subsequently been found in a number of other proteins, such as polynucleotide kinase and 2',3'-cyclic-nucleotide 3'-phosphodiesterase. It appears to function as a kinase domain [, ].; GO: 0005524 ATP binding, 0016301 kinase activity; PDB: 2P5T_H 1GVN_B 3Q8X_D.
Probab=20.12 E-value=2.8e+02 Score=21.55 Aligned_cols=65 Identities=14% Similarity=0.165 Sum_probs=37.4
Q ss_pred CCchh--HHHHHHHHHHhCCcceecCCCCceeCcchHhhHH-------HHHHHHHHHHHHHHHHHHhhcCceee
Q psy5605 83 RSSGS--VARKALQALEQVNIIEKSDDGGRKITSHGRRDMD-------RIAAQIRVSKKEAALQALAAQGITVV 147 (152)
Q Consensus 83 ~asg~--iiR~~LQqLE~~glVek~~~gGR~lT~~G~~~LD-------~iA~~i~~~~~~~~~~~~~~~~~~~~ 147 (152)
.|||+ +++.++.++..-+.|--++|.=|..-|.-...+. .....-...+.+...+.+..+|..++
T Consensus 24 ~GsGKSt~~~~~~~~~~~~~~v~i~~D~~r~~~p~~~~~~~~~~~~~~~~~~~~a~~~~~~~~~~a~~~~~nii 97 (199)
T PF06414_consen 24 PGSGKSTLARQLLEEFGGGGIVVIDADEFRQFHPDYDELLKADPDEASELTQKEASRLAEKLIEYAIENRYNII 97 (199)
T ss_dssp TTSTTHHHHHHHHHHT-TT-SEEE-GGGGGGGSTTHHHHHHHHCCCTHHHHHHHHHHHHHHHHHHHHHCT--EE
T ss_pred CCCCHHHHHHHhhhhccCCCeEEEehHHHHHhccchhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHcCCCEE
Confidence 45554 8888888887778887777766777777665333 33444444455555555556666554
No 306
>COG2138 Sirohydrochlorin ferrochelatase [Inorganic ion transport and metabolism]
Probab=20.11 E-value=1.4e+02 Score=25.22 Aligned_cols=37 Identities=43% Similarity=0.567 Sum_probs=24.2
Q ss_pred CcchHhhHHHHHHHH------------HHHHH----HHHHHHHhhcC---ceeecc
Q psy5605 113 TSHGRRDMDRIAAQI------------RVSKK----EAALQALAAQG---ITVVPT 149 (152)
Q Consensus 113 T~~G~~~LD~iA~~i------------~~~~~----~~~~~~~~~~~---~~~~~~ 149 (152)
+|.|+..+..++..+ +-++. ++..++|.++| |.|||-
T Consensus 14 ~p~~~~~~~~~a~~~~~~~~~~~v~~~f~e~~~P~l~~~~~al~~~G~~~ivvVPl 69 (245)
T COG2138 14 LPRGREVAEAIAARLEERGDFPPVRVAFLELAEPSLREALQALVARGVDRIVVVPL 69 (245)
T ss_pred CccHHHHHHHHHHHHHhhcCCccchhHHHHhcCCCHHHHHHHHHhcCCCeEEEeeh
Confidence 355566666666643 22232 66788999999 889984
No 307
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=20.10 E-value=2.4e+02 Score=17.78 Aligned_cols=50 Identities=14% Similarity=0.238 Sum_probs=33.9
Q ss_pred HHhhHhhcCCcchhhHHHHhCCCCCCCCCCCccCCCchhHHHHHHHHHHhCCcceecCCCCcee
Q psy5605 49 LARHIYMRSPVGVKTVTKIFGGRKRNGVCPSHFCRSSGSVARKALQALEQVNIIEKSDDGGRKI 112 (152)
Q Consensus 49 ilRkiYl~g~vGV~~L~~~YGg~krrG~~P~h~~~asg~iiR~~LQqLE~~glVek~~~gGR~l 112 (152)
|++.+.-..+..+..+.... .-+.+.+.+-|..|+++|+|+....++..+
T Consensus 30 il~~l~~~~~~~~~~l~~~~--------------~~~~~~v~~hL~~L~~~glv~~~~~~~~~~ 79 (110)
T COG0640 30 ILSLLAEGGELTVGELAEAL--------------GLSQSTVSHHLKVLREAGLVELRREGRLRL 79 (110)
T ss_pred HHHHHHhcCCccHHHHHHHH--------------CCChhHHHHHHHHHHHCCCeEEEecccEEE
Confidence 34333333566777787776 445567777788899999999877555444
Done!