Query 046522
Match_columns 115
No_of_seqs 100 out of 280
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 12:58:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046522.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046522hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3490 Transcription elongati 100.0 7.7E-51 1.7E-55 289.9 7.4 106 9-115 2-107 (111)
2 cd07973 Spt4 Transcription elo 100.0 1.8E-49 3.9E-54 279.3 8.9 97 14-110 1-98 (98)
3 COG5204 SPT4 Transcription elo 100.0 3.9E-43 8.4E-48 248.7 4.8 99 16-114 9-107 (112)
4 PF06093 Spt4: Spt4/RpoE2 zinc 100.0 5.3E-42 1.2E-46 232.3 1.6 77 16-92 1-77 (77)
5 PRK06393 rpoE DNA-directed RNA 100.0 6.9E-30 1.5E-34 168.2 5.6 61 14-92 3-63 (64)
6 PRK08351 DNA-directed RNA poly 99.9 3E-27 6.5E-32 154.4 5.5 59 16-92 3-61 (61)
7 COG2093 DNA-directed RNA polym 99.9 3.2E-24 6.9E-29 140.8 5.0 63 14-92 2-64 (64)
8 COG3364 Zn-ribbon containing p 93.8 0.0088 1.9E-07 43.3 -1.5 23 18-40 4-27 (112)
9 PF07754 DUF1610: Domain of un 92.0 0.086 1.9E-06 28.7 1.1 22 19-40 1-23 (24)
10 PF09845 DUF2072: Zn-ribbon co 88.7 0.2 4.3E-06 37.4 1.0 23 18-40 3-26 (131)
11 TIGR00615 recR recombination p 86.9 1.2 2.7E-05 34.9 4.5 64 14-99 51-121 (195)
12 PRK13844 recombination protein 86.6 1.3 2.8E-05 35.0 4.5 64 14-99 55-125 (200)
13 PRK00398 rpoP DNA-directed RNA 85.5 0.36 7.8E-06 28.9 0.7 25 16-40 3-28 (46)
14 PF02591 DUF164: Putative zinc 84.8 0.51 1.1E-05 29.3 1.1 24 17-40 23-53 (56)
15 PF10571 UPF0547: Uncharacteri 84.6 0.64 1.4E-05 25.4 1.4 22 17-41 1-22 (26)
16 cd00350 rubredoxin_like Rubred 84.5 0.61 1.3E-05 26.4 1.3 23 18-41 3-25 (33)
17 PRK00076 recR recombination pr 83.3 1.9 4.2E-05 33.8 4.1 55 14-90 51-106 (196)
18 PF13248 zf-ribbon_3: zinc-rib 82.0 0.62 1.3E-05 25.1 0.6 21 17-40 3-23 (26)
19 PRK11788 tetratricopeptide rep 81.8 0.84 1.8E-05 36.1 1.6 24 16-42 354-377 (389)
20 cd00729 rubredoxin_SM Rubredox 79.7 1.2 2.5E-05 25.6 1.3 24 17-41 3-26 (34)
21 COG1579 Zn-ribbon protein, pos 78.9 0.74 1.6E-05 37.2 0.4 27 16-42 197-231 (239)
22 PF09567 RE_MamI: MamI restric 78.6 1.2 2.7E-05 37.0 1.6 58 15-91 81-138 (314)
23 PRK10475 23S rRNA pseudouridin 78.4 7.7 0.00017 31.7 6.2 49 60-110 111-159 (290)
24 cd02554 PseudoU_synth_RluF Pse 77.0 12 0.00027 28.0 6.5 48 60-109 44-91 (164)
25 TIGR02827 RNR_anaer_Bdell anae 76.4 1.7 3.6E-05 39.1 1.9 44 15-73 531-574 (586)
26 COG1996 RPC10 DNA-directed RNA 74.9 1.4 3.1E-05 27.7 0.8 25 16-40 6-31 (49)
27 PF15645 Tox-PLDMTX: Dermonecr 74.9 1.5 3.2E-05 32.6 1.0 47 47-93 54-104 (135)
28 COG2888 Predicted Zn-ribbon RN 73.5 1.6 3.5E-05 28.7 0.8 25 16-40 9-34 (61)
29 PRK10700 23S rRNA pseudouridyl 73.0 16 0.00034 29.7 6.6 49 60-110 114-162 (289)
30 PRK13130 H/ACA RNA-protein com 72.4 2.3 5E-05 27.3 1.3 22 14-40 3-24 (56)
31 PRK14890 putative Zn-ribbon RN 72.1 2.4 5.1E-05 27.7 1.3 26 15-40 6-32 (59)
32 PRK03681 hypA hydrogenase nick 71.9 2.4 5.1E-05 30.2 1.4 25 16-40 70-94 (114)
33 TIGR00375 conserved hypothetic 71.7 1.5 3.1E-05 37.5 0.4 38 15-53 239-278 (374)
34 PF03604 DNA_RNApol_7kD: DNA d 70.6 2.9 6.4E-05 23.9 1.4 23 18-40 2-24 (32)
35 PRK08271 anaerobic ribonucleos 70.2 1.3 2.9E-05 40.0 -0.2 43 15-72 565-607 (623)
36 PF13240 zinc_ribbon_2: zinc-r 69.4 2.1 4.5E-05 22.6 0.5 19 19-40 2-20 (23)
37 PRK06266 transcription initiat 69.2 2 4.2E-05 32.9 0.6 24 14-40 115-143 (178)
38 COG1645 Uncharacterized Zn-fin 68.8 2.6 5.6E-05 31.4 1.1 20 17-40 29-51 (131)
39 PF13597 NRDD: Anaerobic ribon 68.2 0.87 1.9E-05 40.2 -1.7 47 15-77 490-536 (546)
40 PRK15103 paraquat-inducible me 67.8 3.6 7.8E-05 35.3 2.0 25 13-40 218-242 (419)
41 cd04883 ACT_AcuB C-terminal AC 67.0 10 0.00022 23.2 3.4 28 84-111 42-69 (72)
42 PRK15364 pathogenicity island 66.7 6.9 0.00015 31.0 3.2 21 90-110 94-114 (196)
43 COG0353 RecR Recombinational D 66.7 11 0.00025 29.8 4.4 56 14-90 52-107 (198)
44 TIGR00373 conserved hypothetic 65.3 2.1 4.5E-05 32.0 0.0 24 14-40 107-135 (158)
45 TIGR00155 pqiA_fam integral me 64.8 5.5 0.00012 34.0 2.5 29 12-40 9-40 (403)
46 smart00659 RPOLCX RNA polymera 64.3 3.6 7.7E-05 25.0 0.9 23 18-40 4-26 (44)
47 PRK12380 hydrogenase nickel in 63.3 3.8 8.3E-05 29.0 1.1 24 16-40 70-93 (113)
48 PF12172 DUF35_N: Rubredoxin-l 62.6 3 6.6E-05 23.7 0.4 22 16-40 11-32 (37)
49 PRK00564 hypA hydrogenase nick 62.0 4.2 9.2E-05 29.0 1.1 25 16-40 71-95 (117)
50 COG1592 Rubrerythrin [Energy p 61.4 4.9 0.00011 30.9 1.4 23 16-40 134-156 (166)
51 cd02566 PseudoU_synth_RluE Pse 61.0 31 0.00067 25.4 5.6 48 60-109 44-91 (168)
52 smart00531 TFIIE Transcription 60.5 3.2 7E-05 30.3 0.3 27 14-40 97-130 (147)
53 TIGR02605 CxxC_CxxC_SSSS putat 60.4 6.2 0.00013 23.6 1.5 26 16-41 5-34 (52)
54 PRK10144 formate-dependent nit 60.2 3.6 7.8E-05 30.4 0.5 39 70-113 55-96 (126)
55 PRK03824 hypA hydrogenase nick 60.2 4.9 0.00011 29.3 1.2 15 15-29 69-83 (135)
56 TIGR02487 NrdD anaerobic ribon 59.8 4.2 9.1E-05 36.2 0.9 24 14-40 522-545 (579)
57 PF13192 Thioredoxin_3: Thiore 59.0 9.7 0.00021 24.3 2.4 58 33-97 7-67 (76)
58 COG2995 PqiA Uncharacterized p 58.5 6.5 0.00014 34.3 1.8 26 13-40 217-242 (418)
59 cd00730 rubredoxin Rubredoxin; 58.4 5.7 0.00012 24.7 1.1 12 18-29 3-14 (50)
60 COG1096 Predicted RNA-binding 58.2 3.9 8.4E-05 32.2 0.4 26 16-42 149-174 (188)
61 PRK08579 anaerobic ribonucleos 58.0 2.3 5E-05 38.5 -1.0 23 15-40 567-589 (625)
62 PRK00420 hypothetical protein; 58.0 5.2 0.00011 28.9 1.0 24 17-40 24-47 (112)
63 cd01675 RNR_III Class III ribo 57.1 8.9 0.00019 34.0 2.5 22 15-40 518-539 (555)
64 PF01155 HypA: Hydrogenase exp 57.1 3.3 7.2E-05 29.2 -0.1 24 16-40 70-93 (113)
65 TIGR00595 priA primosomal prot 56.0 42 0.00091 29.3 6.4 27 67-95 268-294 (505)
66 PF08535 KorB: KorB domain; I 55.6 14 0.00031 24.6 2.8 27 69-108 16-42 (93)
67 COG1379 PHP family phosphoeste 55.1 2.9 6.2E-05 36.1 -0.9 42 15-56 245-288 (403)
68 PF15288 zf-CCHC_6: Zinc knuck 55.0 6.2 0.00013 23.9 0.8 26 35-64 3-29 (40)
69 PRK11394 23S rRNA pseudouridin 54.9 49 0.0011 26.1 6.1 49 60-110 83-131 (217)
70 COG0375 HybF Zn finger protein 54.7 6.1 0.00013 28.8 0.9 24 16-40 70-93 (115)
71 cd04882 ACT_Bt0572_2 C-termina 54.4 21 0.00046 21.0 3.2 24 85-110 41-64 (65)
72 COG3357 Predicted transcriptio 54.1 7 0.00015 27.8 1.1 25 16-40 58-83 (97)
73 cd02985 TRX_CDSP32 TRX family, 54.1 9.5 0.00021 25.4 1.7 72 30-107 21-103 (103)
74 PRK07111 anaerobic ribonucleos 53.8 6.1 0.00013 36.4 1.0 43 14-72 678-720 (735)
75 TIGR00093 pseudouridine syntha 53.8 63 0.0014 22.7 6.0 44 60-104 9-52 (128)
76 cd03026 AhpF_NTD_C TRX-GRX-lik 53.7 4.1 9E-05 27.3 -0.1 51 30-87 18-70 (89)
77 TIGR03147 cyt_nit_nrfF cytochr 53.5 5.3 0.00012 29.5 0.4 39 70-113 55-96 (126)
78 TIGR00100 hypA hydrogenase nic 51.1 8.1 0.00018 27.4 1.1 25 16-41 70-94 (115)
79 cd02556 PseudoU_synth_RluB Pse 50.9 70 0.0015 23.4 6.1 44 60-104 47-90 (167)
80 PRK08402 replication factor A; 50.0 10 0.00022 32.2 1.6 50 15-66 211-261 (355)
81 COG1198 PriA Primosomal protei 49.4 9.1 0.0002 35.5 1.3 33 62-96 485-517 (730)
82 COG1187 RsuA 16S rRNA uridine- 49.1 56 0.0012 26.5 5.7 49 60-110 112-160 (248)
83 PRK12496 hypothetical protein; 49.0 9.1 0.0002 28.8 1.1 23 17-40 128-150 (164)
84 PF07282 OrfB_Zn_ribbon: Putat 48.6 7 0.00015 24.6 0.4 28 15-42 27-55 (69)
85 COG0675 Transposase and inacti 48.4 7.9 0.00017 29.7 0.7 22 16-41 309-330 (364)
86 PF12773 DZR: Double zinc ribb 48.3 12 0.00026 22.1 1.4 27 15-41 11-37 (50)
87 smart00839 ELFV_dehydrog Gluta 47.7 20 0.00044 24.7 2.6 23 91-113 32-54 (102)
88 PRK05580 primosome assembly pr 47.4 62 0.0014 29.3 6.3 29 65-95 434-462 (679)
89 smart00661 RPOL9 RNA polymeras 46.6 11 0.00024 22.2 1.0 25 18-42 2-29 (52)
90 COG5591 Uncharacterized conser 46.4 13 0.00029 26.7 1.5 34 72-108 28-61 (103)
91 COG2260 Predicted Zn-ribbon RN 46.2 11 0.00023 24.7 1.0 21 15-40 4-24 (59)
92 cd02555 PSSA_1 PSSA_1: Pseudou 45.8 83 0.0018 23.6 5.9 44 60-104 58-101 (177)
93 PF01783 Ribosomal_L32p: Ribos 45.5 12 0.00027 23.4 1.1 23 15-41 25-47 (56)
94 PHA02278 thioredoxin-like prot 45.4 18 0.0004 24.8 2.1 70 30-105 20-102 (103)
95 TIGR00155 pqiA_fam integral me 45.2 14 0.0003 31.6 1.8 25 14-40 213-237 (403)
96 PRK02935 hypothetical protein; 45.0 11 0.00025 27.3 1.0 22 35-56 72-94 (110)
97 cd04902 ACT_3PGDH-xct C-termin 45.0 42 0.00092 20.2 3.6 27 84-110 40-67 (73)
98 CHL00174 accD acetyl-CoA carbo 44.6 8.9 0.00019 31.9 0.5 37 16-52 38-76 (296)
99 KOG3895 Synaptic vesicle prote 44.5 27 0.00059 30.7 3.4 33 63-97 92-125 (488)
100 PRK15103 paraquat-inducible me 44.3 14 0.00031 31.7 1.7 27 14-40 8-37 (419)
101 cd01121 Sms Sms (bacterial rad 44.3 11 0.00024 31.7 1.0 20 18-40 2-21 (372)
102 PF13453 zf-TFIIB: Transcripti 43.9 9.7 0.00021 22.1 0.5 22 19-40 2-26 (41)
103 smart00834 CxxC_CXXC_SSSS Puta 43.7 14 0.00031 20.6 1.2 25 16-40 5-33 (41)
104 PF11922 DUF3440: Domain of un 43.2 20 0.00042 28.2 2.2 19 93-111 102-120 (181)
105 PF11823 DUF3343: Protein of u 43.1 29 0.00062 22.2 2.6 25 87-111 43-67 (73)
106 TIGR00515 accD acetyl-CoA carb 42.7 9.7 0.00021 31.3 0.5 26 16-41 26-53 (285)
107 cd02870 PseudoU_synth_RsuA_lik 42.5 1.2E+02 0.0026 21.5 6.5 47 60-108 45-91 (146)
108 COG4279 Uncharacterized conser 42.3 7.6 0.00017 32.1 -0.2 27 87-113 91-118 (266)
109 PF02150 RNA_POL_M_15KD: RNA p 41.2 6.2 0.00013 22.7 -0.7 24 17-41 2-28 (35)
110 PF11023 DUF2614: Protein of u 40.9 12 0.00025 27.5 0.5 22 18-40 71-92 (114)
111 COG4260 Membrane protease subu 40.7 16 0.00036 31.0 1.5 27 14-40 313-341 (345)
112 TIGR03769 P_ac_wall_RPT actino 40.3 20 0.00044 21.3 1.5 11 83-93 11-21 (41)
113 PRK12286 rpmF 50S ribosomal pr 39.8 17 0.00036 23.2 1.1 22 15-40 26-47 (57)
114 PRK06764 hypothetical protein; 39.4 20 0.00043 25.5 1.5 17 82-98 81-97 (105)
115 COG4357 Zinc finger domain con 38.9 14 0.00029 26.7 0.6 27 14-40 60-87 (105)
116 cd02948 TRX_NDPK TRX domain, T 38.8 27 0.00058 23.1 2.1 68 30-105 23-101 (102)
117 COG1110 Reverse gyrase [DNA re 38.4 14 0.00031 36.0 0.9 87 15-106 693-787 (1187)
118 PF03433 EspA: EspA-like secre 38.0 11 0.00023 29.8 0.0 21 90-110 94-114 (188)
119 PF10058 DUF2296: Predicted in 37.7 28 0.00061 21.9 1.9 29 14-42 20-53 (54)
120 PRK05580 primosome assembly pr 37.7 7.7 0.00017 35.0 -0.9 34 35-68 423-460 (679)
121 TIGR02620 cas_VVA1548 putative 37.6 31 0.00067 24.4 2.3 22 90-111 37-58 (93)
122 KOG2324 Prolyl-tRNA synthetase 37.6 17 0.00037 31.9 1.1 87 15-110 226-322 (457)
123 PRK11823 DNA repair protein Ra 37.5 20 0.00044 30.7 1.6 24 14-40 5-28 (446)
124 COG1400 SEC65 Signal recogniti 37.3 27 0.00058 24.6 1.9 30 83-114 23-53 (93)
125 COG0266 Nei Formamidopyrimidin 37.0 19 0.0004 29.8 1.2 28 13-40 242-272 (273)
126 TIGR00416 sms DNA repair prote 36.8 20 0.00043 31.0 1.4 24 14-40 5-28 (454)
127 PF03990 DUF348: Domain of unk 36.0 27 0.00058 20.5 1.5 21 95-115 16-36 (43)
128 COG1656 Uncharacterized conser 35.4 43 0.00093 25.9 2.9 43 67-114 12-55 (165)
129 PF09723 Zn-ribbon_8: Zinc rib 35.2 25 0.00054 20.6 1.3 25 16-40 5-33 (42)
130 KOG3084 NADH pyrophosphatase I 35.1 37 0.00081 29.1 2.8 73 35-110 152-244 (345)
131 TIGR00595 priA primosomal prot 35.0 18 0.0004 31.5 1.0 42 17-62 241-285 (505)
132 PF09124 Endonuc-dimeris: T4 r 34.7 35 0.00076 21.8 2.0 19 97-115 19-37 (54)
133 PF08772 NOB1_Zn_bind: Nin one 34.6 18 0.00039 24.2 0.7 23 15-41 8-32 (73)
134 COG1658 Small primase-like pro 34.6 30 0.00064 25.5 1.9 27 58-86 54-82 (127)
135 KOG4020 Protein DRE2, required 34.6 24 0.00053 29.0 1.5 32 9-40 181-223 (257)
136 PRK08270 anaerobic ribonucleos 34.6 19 0.00041 32.8 1.0 23 14-40 624-646 (656)
137 TIGR00412 redox_disulf_2 small 34.2 15 0.00033 23.4 0.3 11 30-40 4-14 (76)
138 COG1439 Predicted nucleic acid 33.8 20 0.00044 27.9 0.9 23 15-40 138-160 (177)
139 TIGR01031 rpmF_bact ribosomal 33.5 21 0.00046 22.5 0.8 22 15-40 25-46 (55)
140 PRK14559 putative protein seri 33.2 21 0.00046 32.6 1.1 33 17-64 28-60 (645)
141 PF12090 Spt20: Spt20 family; 33.2 39 0.00084 25.9 2.4 35 66-111 36-71 (182)
142 TIGR02187 GlrX_arch Glutaredox 33.0 44 0.00096 25.3 2.7 58 34-97 32-100 (215)
143 PHA02942 putative transposase; 32.8 20 0.00043 30.4 0.8 25 15-42 324-351 (383)
144 cd04476 RPA1_DBD_C RPA1_DBD_C: 32.7 21 0.00045 26.0 0.8 27 14-40 32-58 (166)
145 PRK05654 acetyl-CoA carboxylas 32.7 22 0.00049 29.2 1.1 25 16-40 27-53 (292)
146 cd03005 PDI_a_ERp46 PDIa famil 32.6 30 0.00066 22.0 1.5 53 30-89 22-80 (102)
147 PRK06386 replication factor A; 32.2 22 0.00049 30.3 1.0 57 16-80 236-292 (358)
148 PF06677 Auto_anti-p27: Sjogre 32.0 22 0.00048 21.3 0.7 9 19-27 20-28 (41)
149 PRK09381 trxA thioredoxin; Pro 32.0 52 0.0011 21.5 2.6 70 30-104 27-105 (109)
150 PRK14704 anaerobic ribonucleos 31.9 23 0.0005 32.1 1.1 22 15-40 558-579 (618)
151 COG1066 Sms Predicted ATP-depe 31.8 28 0.0006 30.9 1.5 23 15-40 6-28 (456)
152 TIGR00411 redox_disulf_1 small 31.7 51 0.0011 20.1 2.4 67 31-104 6-79 (82)
153 PRK00762 hypA hydrogenase nick 31.6 27 0.00059 25.1 1.2 23 17-40 71-99 (124)
154 cd02550 PseudoU_synth_Rsu_Rlu_ 31.5 68 0.0015 22.9 3.4 43 60-103 46-88 (154)
155 PF09986 DUF2225: Uncharacteri 31.0 26 0.00055 27.3 1.1 10 34-43 49-58 (214)
156 KOG4207 Predicted splicing fac 30.9 62 0.0013 26.5 3.3 33 83-115 10-49 (256)
157 COG3088 CcmH Uncharacterized p 30.6 20 0.00042 27.5 0.4 42 67-113 56-100 (153)
158 PF09912 DUF2141: Uncharacteri 30.3 36 0.00077 23.9 1.7 15 80-94 48-62 (112)
159 PRK07218 replication factor A; 30.1 37 0.00081 29.5 2.0 43 16-65 297-339 (423)
160 PRK10445 endonuclease VIII; Pr 29.8 31 0.00067 27.6 1.4 27 14-40 233-262 (263)
161 PF03918 CcmH: Cytochrome C bi 29.4 14 0.00029 27.6 -0.6 39 70-113 55-96 (148)
162 cd04908 ACT_Bt0572_1 N-termina 29.3 68 0.0015 19.5 2.7 24 88-111 42-65 (66)
163 KOG2907 RNA polymerase I trans 29.1 32 0.00068 25.3 1.2 13 19-31 28-40 (116)
164 PF07295 DUF1451: Protein of u 28.9 36 0.00077 25.5 1.5 26 15-40 111-137 (146)
165 PRK14894 glycyl-tRNA synthetas 28.8 34 0.00073 30.9 1.6 28 12-40 84-111 (539)
166 TIGR01384 TFS_arch transcripti 28.8 27 0.00059 23.6 0.8 22 18-42 2-25 (104)
167 TIGR01126 pdi_dom protein disu 28.6 57 0.0012 20.5 2.3 68 30-104 19-99 (102)
168 cd02973 TRX_GRX_like Thioredox 28.6 26 0.00057 21.0 0.7 11 30-40 5-15 (67)
169 TIGR00354 polC DNA polymerase, 28.5 51 0.0011 32.1 2.7 70 15-102 624-697 (1095)
170 cd02960 AGR Anterior Gradient 28.4 11 0.00025 27.5 -1.2 81 31-114 30-111 (130)
171 PRK14873 primosome assembly pr 27.9 30 0.00064 31.6 1.1 42 16-62 410-454 (665)
172 PF06906 DUF1272: Protein of u 27.8 16 0.00036 23.7 -0.4 8 33-40 41-48 (57)
173 PRK14873 primosome assembly pr 27.7 16 0.00034 33.3 -0.6 57 36-104 413-469 (665)
174 TIGR03831 YgiT_finger YgiT-typ 27.5 36 0.00078 19.2 1.1 27 36-66 1-27 (46)
175 PF10164 DUF2367: Uncharacteri 27.4 34 0.00073 24.4 1.1 14 18-31 51-64 (98)
176 PF01927 Mut7-C: Mut7-C RNAse 27.3 1.3E+02 0.0027 21.8 4.2 46 65-114 4-49 (147)
177 PRK04031 DNA primase; Provisio 27.2 1.1E+02 0.0024 26.8 4.4 39 71-111 346-384 (408)
178 cd01076 NAD_bind_1_Glu_DH NAD( 27.1 61 0.0013 25.3 2.6 23 91-113 136-158 (227)
179 COG2816 NPY1 NTP pyrophosphohy 26.8 1.4E+02 0.003 24.9 4.7 84 14-110 109-199 (279)
180 COG4704 Uncharacterized protei 26.7 16 0.00036 27.8 -0.6 23 70-95 75-97 (151)
181 PF02357 NusG: Transcription t 26.7 34 0.00074 22.2 1.0 22 87-108 4-25 (92)
182 COG4031 Predicted metal-bindin 26.2 31 0.00067 27.8 0.8 17 19-40 3-19 (227)
183 PF04760 IF2_N: Translation in 25.7 84 0.0018 18.8 2.6 24 71-109 7-31 (54)
184 cd00616 AHBA_syn 3-amino-5-hyd 25.7 83 0.0018 24.5 3.2 26 84-109 267-295 (352)
185 cd02984 TRX_PICOT TRX domain, 25.7 28 0.0006 22.1 0.4 67 30-103 20-96 (97)
186 PF12647 RNHCP: RNHCP domain; 25.7 36 0.00079 24.0 1.0 28 17-44 5-36 (92)
187 PF08029 HisG_C: HisG, C-termi 25.7 81 0.0018 20.9 2.7 25 83-107 37-63 (75)
188 PRK01103 formamidopyrimidine/5 25.7 41 0.00089 26.9 1.4 27 14-40 243-272 (274)
189 PRK10996 thioredoxin 2; Provis 25.6 55 0.0012 23.2 2.0 29 70-98 95-129 (139)
190 cd07249 MMCE Methylmalonyl-CoA 25.6 1.7E+02 0.0036 18.8 4.2 46 62-111 49-98 (128)
191 PRK12366 replication factor A; 25.5 40 0.00086 30.5 1.4 60 15-80 531-592 (637)
192 PF08862 DUF1829: Domain of un 25.4 1.1E+02 0.0023 20.7 3.3 46 67-112 29-84 (88)
193 COG1282 PntB NAD/NADP transhyd 25.4 74 0.0016 28.1 3.0 40 71-111 329-369 (463)
194 COG2126 RPL37A Ribosomal prote 25.1 60 0.0013 21.3 1.9 40 1-42 1-40 (61)
195 TIGR02098 MJ0042_CXXC MJ0042 f 25.0 38 0.00082 18.9 0.8 6 35-40 27-32 (38)
196 PF02132 RecR: RecR protein; 25.0 11 0.00025 22.0 -1.4 21 15-40 16-36 (41)
197 cd02957 Phd_like Phosducin (Ph 24.9 41 0.0009 22.6 1.2 53 30-89 30-83 (113)
198 PF09538 FYDLN_acid: Protein o 24.9 58 0.0013 23.2 1.9 21 15-40 8-33 (108)
199 PRK11486 flagellar biosynthesi 24.6 48 0.001 24.4 1.5 27 70-96 35-61 (124)
200 COG0178 UvrA Excinuclease ATPa 24.4 1.1E+02 0.0024 29.5 4.1 82 15-103 244-342 (935)
201 PF09413 DUF2007: Domain of un 24.4 54 0.0012 20.2 1.5 17 98-114 14-30 (67)
202 PF03374 ANT: Phage antirepres 24.0 1.2E+02 0.0026 20.4 3.3 26 71-111 28-53 (111)
203 cd05313 NAD_bind_2_Glu_DH NAD( 24.0 74 0.0016 25.7 2.6 23 91-113 154-176 (254)
204 cd02956 ybbN ybbN protein fami 23.8 76 0.0016 20.1 2.2 53 30-89 18-73 (96)
205 COG1058 CinA Predicted nucleot 23.7 1.6E+02 0.0036 23.9 4.6 40 65-106 18-57 (255)
206 COG5636 Uncharacterized conser 23.4 96 0.0021 25.6 3.1 25 13-40 235-259 (284)
207 cd00474 SUI1_eIF1 The SUI1/eIF 23.2 81 0.0018 20.9 2.3 23 87-109 48-70 (77)
208 PRK05452 anaerobic nitric oxid 23.2 61 0.0013 28.1 2.1 16 14-29 423-438 (479)
209 PRK11032 hypothetical protein; 23.1 48 0.001 25.3 1.3 27 15-41 123-150 (160)
210 PF11121 DUF2639: Protein of u 23.1 58 0.0013 19.7 1.4 15 99-113 8-22 (40)
211 PF00301 Rubredoxin: Rubredoxi 23.0 50 0.0011 20.2 1.1 12 18-29 3-14 (47)
212 PHA02085 hypothetical protein 23.0 22 0.00047 24.8 -0.5 26 56-81 7-32 (87)
213 PF09652 Cas_VVA1548: Putative 22.8 79 0.0017 22.3 2.2 22 90-111 37-58 (93)
214 PF05495 zf-CHY: CHY zinc fing 22.7 30 0.00065 22.5 0.1 26 15-40 40-68 (71)
215 PRK14892 putative transcriptio 22.6 66 0.0014 22.7 1.9 27 15-41 20-50 (99)
216 KOG4354 N-acetyl-gamma-glutamy 22.5 42 0.00091 28.3 0.9 41 47-95 111-163 (340)
217 cd04718 BAH_plant_2 BAH, or Br 22.4 1.1E+02 0.0023 23.3 3.0 23 68-91 50-72 (148)
218 PF05093 CIAPIN1: Cytokine-ind 22.3 50 0.0011 23.5 1.2 23 16-44 67-89 (100)
219 TIGR00334 5S_RNA_mat_M5 ribonu 22.3 98 0.0021 24.0 2.9 53 58-110 46-112 (174)
220 cd02965 HyaE HyaE family; HyaE 22.3 1.2E+02 0.0027 21.5 3.2 61 31-98 34-106 (111)
221 COG1328 NrdD Oxygen-sensitive 22.2 52 0.0011 30.6 1.6 24 14-40 639-662 (700)
222 COG5257 GCD11 Translation init 22.0 96 0.0021 27.1 3.0 47 15-77 56-104 (415)
223 PRK09521 exosome complex RNA-b 21.9 38 0.00083 25.5 0.6 29 14-42 146-175 (189)
224 KOG0907 Thioredoxin [Posttrans 21.7 87 0.0019 21.7 2.3 71 30-106 27-105 (106)
225 TIGR01068 thioredoxin thioredo 21.6 1.2E+02 0.0026 18.8 2.8 69 30-105 20-99 (101)
226 PF14690 zf-ISL3: zinc-finger 21.6 76 0.0016 18.2 1.7 7 35-41 4-10 (47)
227 PF01186 Lysyl_oxidase: Lysyl 21.5 45 0.00099 26.6 0.9 27 74-101 149-175 (205)
228 PF14447 Prok-RING_4: Prokaryo 21.3 53 0.0011 21.1 1.0 21 20-40 23-46 (55)
229 PF11020 DUF2610: Domain of un 21.0 91 0.002 21.6 2.2 39 56-104 14-55 (82)
230 cd02553 PseudoU_synth_RsuA Pse 20.9 3.4E+02 0.0074 19.8 5.9 48 60-109 47-94 (167)
231 PRK00423 tfb transcription ini 20.9 56 0.0012 26.6 1.4 10 15-24 10-19 (310)
232 PRK00481 NAD-dependent deacety 20.9 60 0.0013 25.3 1.5 24 17-40 123-149 (242)
233 PF02887 PK_C: Pyruvate kinase 20.7 2.3E+02 0.0051 19.2 4.3 35 64-102 43-79 (117)
234 PF02927 CelD_N: N-terminal ig 20.7 74 0.0016 21.2 1.7 12 83-94 76-87 (91)
235 cd00272 Chemokine_CC Chemokine 20.7 69 0.0015 19.6 1.5 22 55-78 33-54 (57)
236 TIGR02905 spore_yutH spore coa 20.6 1.3E+02 0.0029 24.0 3.5 30 84-113 28-64 (313)
237 PRK04023 DNA polymerase II lar 20.5 53 0.0012 32.1 1.3 83 15-102 625-722 (1121)
238 TIGR02538 type_IV_pilB type IV 20.5 62 0.0013 28.6 1.7 11 31-41 486-496 (564)
239 PRK14811 formamidopyrimidine-D 20.3 55 0.0012 26.3 1.2 27 14-40 233-262 (269)
240 PRK14487 cbb3-type cytochrome 20.3 1.8E+02 0.0039 23.4 4.1 43 69-111 115-166 (217)
241 PF14803 Nudix_N_2: Nudix N-te 20.1 53 0.0012 18.8 0.8 17 9-25 15-31 (34)
242 COG1545 Predicted nucleic-acid 20.0 55 0.0012 23.9 1.1 22 17-41 30-51 (140)
No 1
>KOG3490 consensus Transcription elongation factor SPT4 [Transcription]
Probab=100.00 E-value=7.7e-51 Score=289.89 Aligned_cols=106 Identities=48% Similarity=0.995 Sum_probs=102.4
Q ss_pred CCCCCccccccccCcccccchhhccCCCCCCCCCCCCCCcccccccCCCccceEEEEeCCChhHHHHHHhcCCCCCeeeE
Q 046522 9 PTSFGHELRACLRCRLVKTYDQFRESGCENCPFFKMDEDHERVVDCTTPNFNGIISVMDPTRSWAARWLRIGRFVPGCYT 88 (115)
Q Consensus 9 p~~~~r~lrAC~~C~~I~t~~qf~~~gCpnC~~l~m~~~~d~v~~~tT~~f~G~I~i~dP~~SwVAk~l~i~~~~pG~YA 88 (115)
|.. .+++|||+.|++|+|.++|.++|||||++|+|+||.++|.||||++|+|+|++|+|++|||||||||++|+||+||
T Consensus 2 ~~~-~~~lRACllCs~Vkt~~~F~~dGC~Nc~~l~mkgn~e~V~ecTS~nF~GiIa~m~Pt~SWVakWqri~~f~~G~YA 80 (111)
T KOG3490|consen 2 PKD-LRKLRACLLCSIVKTLNGFRKDGCENCPMLNMKGNVENVYECTSPNFDGIIAMMSPTESWVAKWQRIGRFTPGMYA 80 (111)
T ss_pred cch-hhhhhhhhhhhhhhhhhhhhhcCCCCchhhhhccCcceeEEecCCCccceeeeeCccHHHHHHHHhhccccCceEE
Confidence 444 3699999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEecCCCcHHHHHHHHhcCCeecCCCC
Q 046522 89 LAVSEALPEDLQNLCEDERVQYVPPKR 115 (115)
Q Consensus 89 i~V~g~lp~~i~~~l~~~gi~y~prd~ 115 (115)
|+|+|.||++++++|+++||.|+|||+
T Consensus 81 i~VsG~Lpe~~v~~l~~~g~~Yk~Rd~ 107 (111)
T KOG3490|consen 81 ISVSGVLPEEVVESLKSRGVHYKSRDG 107 (111)
T ss_pred EEecccCCHHHHHHHHhcceeeecccc
Confidence 999999999999999999999999985
No 2
>cd07973 Spt4 Transcription elongation factor Spt4. Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 compl
Probab=100.00 E-value=1.8e-49 Score=279.35 Aligned_cols=97 Identities=55% Similarity=1.093 Sum_probs=94.9
Q ss_pred ccccccccCcccccchhhccCCCCCCC-CCCCCCCcccccccCCCccceEEEEeCCChhHHHHHHhcCCCCCeeeEEEec
Q 046522 14 HELRACLRCRLVKTYDQFRESGCENCP-FFKMDEDHERVVDCTTPNFNGIISVMDPTRSWAARWLRIGRFVPGCYTLAVS 92 (115)
Q Consensus 14 r~lrAC~~C~~I~t~~qf~~~gCpnC~-~l~m~~~~d~v~~~tT~~f~G~I~i~dP~~SwVAk~l~i~~~~pG~YAi~V~ 92 (115)
|++|||+.|++|+|.+||..+|||||+ +++|+|++|+|+||||++|+|+|+||||++|||||||||++++||+|||+|+
T Consensus 1 r~lrAC~~C~~I~~~~qf~~~gCpnC~~~l~~~g~~~~v~~~tT~~f~G~i~i~dP~~SwVAk~l~i~~~~pG~YAi~V~ 80 (98)
T cd07973 1 RGLRACLLCSLIKTEDQFERDGCPNCEGYLDMKGNHERVYDCTSPNFEGIIALMDPEKSWVARWQRIDKFVPGIYAISVS 80 (98)
T ss_pred CCCchhccCCcccccccccCCCCCCCcchhccCCCccccccccCCCcceEEEEECCchhHHHHHhCCCCCCCCeEEEEec
Confidence 478999999999999999999999996 9999999999999999999999999999999999999999999999999999
Q ss_pred CCCcHHHHHHHHhcCCee
Q 046522 93 EALPEDLQNLCEDERVQY 110 (115)
Q Consensus 93 g~lp~~i~~~l~~~gi~y 110 (115)
|+||++|+++||++||.|
T Consensus 81 g~lp~~i~~~l~~~~i~y 98 (98)
T cd07973 81 GRLPEDIVEELESRGIIY 98 (98)
T ss_pred CcCCHHHHHHHHHcCCCC
Confidence 999999999999999987
No 3
>COG5204 SPT4 Transcription elongation factor SPT4 [Transcription]
Probab=100.00 E-value=3.9e-43 Score=248.70 Aligned_cols=99 Identities=41% Similarity=0.877 Sum_probs=97.6
Q ss_pred ccccccCcccccchhhccCCCCCCCCCCCCCCcccccccCCCccceEEEEeCCChhHHHHHHhcCCCCCeeeEEEecCCC
Q 046522 16 LRACLRCRLVKTYDQFRESGCENCPFFKMDEDHERVVDCTTPNFNGIISVMDPTRSWAARWLRIGRFVPGCYTLAVSEAL 95 (115)
Q Consensus 16 lrAC~~C~~I~t~~qf~~~gCpnC~~l~m~~~~d~v~~~tT~~f~G~I~i~dP~~SwVAk~l~i~~~~pG~YAi~V~g~l 95 (115)
.|||+.|++|+|.+.|.++|||||+.+.|+|+-++|.+|||+.|+|+|+|+.|.+|||||||+|+.|.||+||++|.|.|
T Consensus 9 sRACl~Cgiv~t~n~F~~dGCpNc~~l~~~~gV~~ve~~TSp~FeGvvam~~Pt~SWVakWqrid~f~~GlYA~~V~G~L 88 (112)
T COG5204 9 SRACLGCGIVKTLNGFRKDGCPNCPMLNMKGGVTNVEECTSPKFEGVVAMLQPTNSWVAKWQRIDEFRKGLYAMVVEGAL 88 (112)
T ss_pred hhhhhhcceeeecccccccCCCCCcccccccCccceeeecCcchHHHHHHhcccHHHHHHHhhhcccccceeEEEEcccC
Confidence 49999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cHHHHHHHHhcCCeecCCC
Q 046522 96 PEDLQNLCEDERVQYVPPK 114 (115)
Q Consensus 96 p~~i~~~l~~~gi~y~prd 114 (115)
|+|+++.|+++||.|+||+
T Consensus 89 ~edvve~L~~~g~~Y~pR~ 107 (112)
T COG5204 89 SEDVVEDLEQHGRIYYPRT 107 (112)
T ss_pred CHHHHHHHHHhCccccCCC
Confidence 9999999999999999997
No 4
>PF06093 Spt4: Spt4/RpoE2 zinc finger; InterPro: IPR022800 This entry consists of several eukaryotic transcription elongation Spt4 proteins as well as archaebacterial RpoE2 []. Three transcription-elongation factors Spt4, Spt5, and Spt6 are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. Spt4 and Spt5 are tightly associated in a complex, while the physical association of the Spt4-Spt5 complex with Spt6 is considerably weaker. It has been demonstrated that Spt4, Spt5, and Spt6 play roles in transcription elongation in both yeast and humans including a role in activation by Tat. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles []. RpoE2 is one of 13 subunits in the archaeal RNA polymerase. These proteins contain a C4-type zinc finger, and the structure has been solved in []. The structure reveals that Spt4-Spt5 binding is governed by an acid-dipole interaction between Spt5 and Spt4, and the complex binds to and travels along the elongating RNA polymerase. The Spt4-Spt5 complex is likely to be an ancient, core component of the transcription elongation machinery. ; PDB: 2EXU_A 3H7H_A 3LPE_F 3P8B_A 1RYQ_A 3QQC_E.
Probab=100.00 E-value=5.3e-42 Score=232.28 Aligned_cols=77 Identities=65% Similarity=1.417 Sum_probs=69.1
Q ss_pred ccccccCcccccchhhccCCCCCCCCCCCCCCcccccccCCCccceEEEEeCCChhHHHHHHhcCCCCCeeeEEEec
Q 046522 16 LRACLRCRLVKTYDQFRESGCENCPFFKMDEDHERVVDCTTPNFNGIISVMDPTRSWAARWLRIGRFVPGCYTLAVS 92 (115)
Q Consensus 16 lrAC~~C~~I~t~~qf~~~gCpnC~~l~m~~~~d~v~~~tT~~f~G~I~i~dP~~SwVAk~l~i~~~~pG~YAi~V~ 92 (115)
||||+.|++|+|.+||+++|||||++|+|++++|++.+|||++|+|+|+||||++||||||||+++++||+|||+|+
T Consensus 1 lrAC~~C~~i~t~~qF~~~gCpnC~~l~~~~~~~~~~~~tT~~f~G~i~i~~P~~SwvAk~~rl~~~~pG~YAi~V~ 77 (77)
T PF06093_consen 1 LRACLRCRLIKTEDQFRDEGCPNCPFLQMKGDRDRVSDCTTPNFEGMIAIMDPEKSWVAKWQRLGKFVPGCYAIKVR 77 (77)
T ss_dssp EEEETTT-BEECCCHHHHH--TTTHHHH-TCHCHHCHCCEESSEEEEEEES-TTT-HHHHHTTCTTSSSEEEEEEE-
T ss_pred CcccccCCcccCHhHccCCCCCCCccccccCCcCcccccCCCCCcCEEEECCCchhHHHHhhccCCCCCCEEEEEeC
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999999995
No 5
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=99.96 E-value=6.9e-30 Score=168.19 Aligned_cols=61 Identities=28% Similarity=0.525 Sum_probs=55.3
Q ss_pred ccccccccCcccccchhhccCCCCCCCCCCCCCCcccccccCCCccceEEEEeCCChhHHHHHHhcCCCCCeeeEEEec
Q 046522 14 HELRACLRCRLVKTYDQFRESGCENCPFFKMDEDHERVVDCTTPNFNGIISVMDPTRSWAARWLRIGRFVPGCYTLAVS 92 (115)
Q Consensus 14 r~lrAC~~C~~I~t~~qf~~~gCpnC~~l~m~~~~d~v~~~tT~~f~G~I~i~dP~~SwVAk~l~i~~~~pG~YAi~V~ 92 (115)
+.++||++||+|++.+ .||+|+ +++ ||++|+|+|+|+||++|||||||||+ +||+|||+|+
T Consensus 3 ~~~~AC~~C~~i~~~~-----~Cp~Cg------s~~-----~S~~w~G~v~i~dPe~S~vAk~~~i~--~pG~YAlkVr 63 (64)
T PRK06393 3 VQYRACKKCKRLTPEK-----TCPVHG------DEK-----TTTEWFGFLIITEPEGSAIAKRAGIT--EPGMYAIKVR 63 (64)
T ss_pred chhhhHhhCCcccCCC-----cCCCCC------CCc-----CCcCcceEEEEECCchhHHHHHhCCC--CCCeEEEEee
Confidence 5789999999999644 599998 333 89999999999999999999999999 7999999996
No 6
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=99.94 E-value=3e-27 Score=154.39 Aligned_cols=59 Identities=27% Similarity=0.557 Sum_probs=52.9
Q ss_pred ccccccCcccccchhhccCCCCCCCCCCCCCCcccccccCCCccceEEEEeCCChhHHHHHHhcCCCCCeeeEEEec
Q 046522 16 LRACLRCRLVKTYDQFRESGCENCPFFKMDEDHERVVDCTTPNFNGIISVMDPTRSWAARWLRIGRFVPGCYTLAVS 92 (115)
Q Consensus 16 lrAC~~C~~I~t~~qf~~~gCpnC~~l~m~~~~d~v~~~tT~~f~G~I~i~dP~~SwVAk~l~i~~~~pG~YAi~V~ 92 (115)
++||++|++|++.+ .||||+ +++ +|++|.|+|+|+||++|||||+|+|+ +||+|||+|+
T Consensus 3 ~kAC~~C~~i~~~~-----~CP~Cg------s~~-----~T~~W~G~viI~dPe~S~IAk~l~i~--~pG~YAlkVr 61 (61)
T PRK08351 3 EKACRHCHYITTED-----RCPVCG------SRD-----LSDEWFDLVIIIDVENSRIAKKLGAK--VPGKYAIRVR 61 (61)
T ss_pred hhhhhhCCcccCCC-----cCCCCc------CCc-----cccccccEEEEeCCcHhHHHHHhCCC--CCCeEEEEeC
Confidence 57999999999755 499998 333 89999999999999999999999997 6999999985
No 7
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=99.90 E-value=3.2e-24 Score=140.82 Aligned_cols=63 Identities=30% Similarity=0.604 Sum_probs=56.7
Q ss_pred ccccccccCcccccchhhccCCCCCCCCCCCCCCcccccccCCCccceEEEEeCCChhHHHHHHhcCCCCCeeeEEEec
Q 046522 14 HELRACLRCRLVKTYDQFRESGCENCPFFKMDEDHERVVDCTTPNFNGIISVMDPTRSWAARWLRIGRFVPGCYTLAVS 92 (115)
Q Consensus 14 r~lrAC~~C~~I~t~~qf~~~gCpnC~~l~m~~~~d~v~~~tT~~f~G~I~i~dP~~SwVAk~l~i~~~~pG~YAi~V~ 92 (115)
..++||++|++|++.+. +.||+|+ +++ +|++|.|+|+|+||++|.|||.++++ +||+|||+|+
T Consensus 2 ~~~kAC~~Ck~l~~~d~---e~CP~Cg------s~~-----~te~W~G~~iIidpe~SeIAkrlgi~--~Pg~yAl~V~ 64 (64)
T COG2093 2 STEKACKNCKRLTPEDT---EICPVCG------STD-----LTEEWFGLLIIIDPEKSEIAKRLGIK--IPGKYALRVR 64 (64)
T ss_pred chhHHHhhccccCCCCC---ccCCCCC------Ccc-----cchhhccEEEEEcCcHHHHHHHhCCC--CCceEEEEeC
Confidence 36799999999999876 5699998 444 99999999999999999999999998 5999999985
No 8
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=93.80 E-value=0.0088 Score=43.28 Aligned_cols=23 Identities=35% Similarity=0.628 Sum_probs=18.1
Q ss_pred ccccCcccccc-hhhccCCCCCCC
Q 046522 18 ACLRCRLVKTY-DQFRESGCENCP 40 (115)
Q Consensus 18 AC~~C~~I~t~-~qf~~~gCpnC~ 40 (115)
-|.+|+-|-.. +.-...|||+|+
T Consensus 4 ~CtrCG~vf~~g~~~il~GCp~CG 27 (112)
T COG3364 4 QCTRCGEVFDDGSEEILSGCPKCG 27 (112)
T ss_pred eecccccccccccHHHHccCcccc
Confidence 49999998776 444458999999
No 9
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=91.96 E-value=0.086 Score=28.73 Aligned_cols=22 Identities=23% Similarity=0.437 Sum_probs=14.5
Q ss_pred cccCcccccchh-hccCCCCCCC
Q 046522 19 CLRCRLVKTYDQ-FRESGCENCP 40 (115)
Q Consensus 19 C~~C~~I~t~~q-f~~~gCpnC~ 40 (115)
|..|+..+.... ...-.||||+
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG 23 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCG 23 (24)
T ss_pred CccCCCcccCcccCceEeCCCCC
Confidence 678876665543 3334699998
No 10
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=88.67 E-value=0.2 Score=37.36 Aligned_cols=23 Identities=30% Similarity=0.580 Sum_probs=17.6
Q ss_pred ccccCcccccchh-hccCCCCCCC
Q 046522 18 ACLRCRLVKTYDQ-FRESGCENCP 40 (115)
Q Consensus 18 AC~~C~~I~t~~q-f~~~gCpnC~ 40 (115)
-|.+|+-+-.... -..+|||+|+
T Consensus 3 ~Ct~Cg~~f~dgs~eil~GCP~CG 26 (131)
T PF09845_consen 3 QCTKCGRVFEDGSKEILSGCPECG 26 (131)
T ss_pred ccCcCCCCcCCCcHHHHccCcccC
Confidence 4999999876543 2347999999
No 11
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=86.90 E-value=1.2 Score=34.92 Aligned_cols=64 Identities=28% Similarity=0.494 Sum_probs=41.7
Q ss_pred ccccccccCcccccchhhccCCCCCCCCCCCCCCcccccccCCCccceEEEEe-CCChhHHHHHHhcCCCCCeeeEEE--
Q 046522 14 HELRACLRCRLVKTYDQFRESGCENCPFFKMDEDHERVVDCTTPNFNGIISVM-DPTRSWAARWLRIGRFVPGCYTLA-- 90 (115)
Q Consensus 14 r~lrAC~~C~~I~t~~qf~~~gCpnC~~l~m~~~~d~v~~~tT~~f~G~I~i~-dP~~SwVAk~l~i~~~~pG~YAi~-- 90 (115)
.+.+-|..|+.+.+.+ -|+.|.. +..-.+.|.|+ +|.+=|.-...+ .-.|.|-|-
T Consensus 51 ~~i~~C~~C~~lse~~-----~C~IC~d--------------~~Rd~~~iCVVE~~~Dv~aiE~~~---~y~G~YhVL~G 108 (195)
T TIGR00615 51 ENLRTCSVCGAISDQE-----VCNICSD--------------ERRDNSVICVVEDPKDVFALEKTK---EFRGRYHVLGG 108 (195)
T ss_pred HcCCcCCCCCCCCCCC-----cCCCCCC--------------CCCCCCEEEEECCHHHHHHHHhhC---ccceEEEEccC
Confidence 3678999999998754 4999972 22336677776 554444444443 248999876
Q ss_pred ----ecCCCcHHH
Q 046522 91 ----VSEALPEDL 99 (115)
Q Consensus 91 ----V~g~lp~~i 99 (115)
+.|.-|+++
T Consensus 109 ~iSPldgigp~~l 121 (195)
T TIGR00615 109 HISPLDGIGPEDL 121 (195)
T ss_pred ccCccCCCChhhc
Confidence 467767654
No 12
>PRK13844 recombination protein RecR; Provisional
Probab=86.62 E-value=1.3 Score=34.98 Aligned_cols=64 Identities=17% Similarity=0.318 Sum_probs=40.9
Q ss_pred ccccccccCcccccchhhccCCCCCCCCCCCCCCcccccccCCCccceEEEEe-CCChhHHHHHHhcCCCCCeeeEEE--
Q 046522 14 HELRACLRCRLVKTYDQFRESGCENCPFFKMDEDHERVVDCTTPNFNGIISVM-DPTRSWAARWLRIGRFVPGCYTLA-- 90 (115)
Q Consensus 14 r~lrAC~~C~~I~t~~qf~~~gCpnC~~l~m~~~~d~v~~~tT~~f~G~I~i~-dP~~SwVAk~l~i~~~~pG~YAi~-- 90 (115)
.+.+.|..|+.+.+.+ -|+.|.. +....+.|.|+ +|.+=|.-...+ .-.|.|-|-
T Consensus 55 ~~i~~C~~C~~lte~~-----~C~IC~d--------------~~Rd~~~iCVVE~~~Dv~aiE~t~---~y~G~YhVL~G 112 (200)
T PRK13844 55 ANIKKCVYCQALTEDD-----VCNICSN--------------TNRDDTKLCIIESMLDMIAIEEAG---IYRGKYFVLNG 112 (200)
T ss_pred HhCCcCCCCCCCCCCC-----CCCCCCC--------------CCCCCCEEEEECCHHHHHHHHhhC---ccceEEEEccC
Confidence 4678999999998754 4999972 23346777776 444433333332 248999875
Q ss_pred ----ecCCCcHHH
Q 046522 91 ----VSEALPEDL 99 (115)
Q Consensus 91 ----V~g~lp~~i 99 (115)
+.|.-|+++
T Consensus 113 ~ispl~gi~p~~l 125 (200)
T PRK13844 113 RISPLDGIGPSEL 125 (200)
T ss_pred ccCccCCCChhhc
Confidence 466666654
No 13
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=85.49 E-value=0.36 Score=28.89 Aligned_cols=25 Identities=24% Similarity=0.558 Sum_probs=19.5
Q ss_pred ccccccCcccccchhhc-cCCCCCCC
Q 046522 16 LRACLRCRLVKTYDQFR-ESGCENCP 40 (115)
Q Consensus 16 lrAC~~C~~I~t~~qf~-~~gCpnC~ 40 (115)
...|.+|+...+.+... .-.||+|+
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG 28 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCG 28 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCC
Confidence 35699999988777655 35699999
No 14
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=84.75 E-value=0.51 Score=29.30 Aligned_cols=24 Identities=25% Similarity=0.596 Sum_probs=19.0
Q ss_pred cccccCcccccchhhcc-------CCCCCCC
Q 046522 17 RACLRCRLVKTYDQFRE-------SGCENCP 40 (115)
Q Consensus 17 rAC~~C~~I~t~~qf~~-------~gCpnC~ 40 (115)
.+|..|++-++.+.+.+ --||||+
T Consensus 23 ~~C~gC~~~l~~~~~~~i~~~~~i~~Cp~Cg 53 (56)
T PF02591_consen 23 GTCSGCHMELPPQELNEIRKGDEIVFCPNCG 53 (56)
T ss_pred CccCCCCEEcCHHHHHHHHcCCCeEECcCCC
Confidence 69999999998875532 2499998
No 15
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=84.60 E-value=0.64 Score=25.45 Aligned_cols=22 Identities=18% Similarity=0.582 Sum_probs=17.4
Q ss_pred cccccCcccccchhhccCCCCCCCC
Q 046522 17 RACLRCRLVKTYDQFRESGCENCPF 41 (115)
Q Consensus 17 rAC~~C~~I~t~~qf~~~gCpnC~~ 41 (115)
+-|..|+-+++.+. +-||+||+
T Consensus 1 K~CP~C~~~V~~~~---~~Cp~CG~ 22 (26)
T PF10571_consen 1 KTCPECGAEVPESA---KFCPHCGY 22 (26)
T ss_pred CcCCCCcCCchhhc---CcCCCCCC
Confidence 35889999988775 45999994
No 16
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=84.50 E-value=0.61 Score=26.35 Aligned_cols=23 Identities=17% Similarity=0.405 Sum_probs=16.7
Q ss_pred ccccCcccccchhhccCCCCCCCC
Q 046522 18 ACLRCRLVKTYDQFRESGCENCPF 41 (115)
Q Consensus 18 AC~~C~~I~t~~qf~~~gCpnC~~ 41 (115)
-|..|++|-..+. ....||.|+.
T Consensus 3 ~C~~CGy~y~~~~-~~~~CP~Cg~ 25 (33)
T cd00350 3 VCPVCGYIYDGEE-APWVCPVCGA 25 (33)
T ss_pred ECCCCCCEECCCc-CCCcCcCCCC
Confidence 5999999966552 2246999983
No 17
>PRK00076 recR recombination protein RecR; Reviewed
Probab=83.34 E-value=1.9 Score=33.80 Aligned_cols=55 Identities=22% Similarity=0.399 Sum_probs=36.0
Q ss_pred ccccccccCcccccchhhccCCCCCCCCCCCCCCcccccccCCCccceEEEEe-CCChhHHHHHHhcCCCCCeeeEEE
Q 046522 14 HELRACLRCRLVKTYDQFRESGCENCPFFKMDEDHERVVDCTTPNFNGIISVM-DPTRSWAARWLRIGRFVPGCYTLA 90 (115)
Q Consensus 14 r~lrAC~~C~~I~t~~qf~~~gCpnC~~l~m~~~~d~v~~~tT~~f~G~I~i~-dP~~SwVAk~l~i~~~~pG~YAi~ 90 (115)
.+.+-|..|+.+.+.+. |+.|.. +..-.++|.|+ +|.+=|.-...+ .-.|.|-|-
T Consensus 51 ~~i~~C~~C~~lse~~~-----C~IC~d--------------~~Rd~~~icVVE~~~Dv~aiE~s~---~y~G~YhVL 106 (196)
T PRK00076 51 EKIKHCSVCGNLTEQDP-----CEICSD--------------PRRDQSLICVVESPADVLAIERTG---EYRGLYHVL 106 (196)
T ss_pred HcCCcCCCCCCcCCCCc-----CCCCCC--------------CCCCCCEEEEECCHHHHHHHHhhC---cCceEEEEe
Confidence 36788999999987654 999972 22236666666 555444444443 247999875
No 18
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=82.04 E-value=0.62 Score=25.06 Aligned_cols=21 Identities=29% Similarity=0.505 Sum_probs=15.2
Q ss_pred cccccCcccccchhhccCCCCCCC
Q 046522 17 RACLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 17 rAC~~C~~I~t~~qf~~~gCpnC~ 40 (115)
+.|.+|+.....+. .-||+|+
T Consensus 3 ~~Cp~Cg~~~~~~~---~fC~~CG 23 (26)
T PF13248_consen 3 MFCPNCGAEIDPDA---KFCPNCG 23 (26)
T ss_pred CCCcccCCcCCccc---ccChhhC
Confidence 57899998655443 3499998
No 19
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=81.77 E-value=0.84 Score=36.07 Aligned_cols=24 Identities=17% Similarity=0.523 Sum_probs=19.2
Q ss_pred ccccccCcccccchhhccCCCCCCCCC
Q 046522 16 LRACLRCRLVKTYDQFRESGCENCPFF 42 (115)
Q Consensus 16 lrAC~~C~~I~t~~qf~~~gCpnC~~l 42 (115)
.-+|..|+++.+.=+|. ||+|+..
T Consensus 354 ~~~c~~cg~~~~~~~~~---c~~c~~~ 377 (389)
T PRK11788 354 RYRCRNCGFTARTLYWH---CPSCKAW 377 (389)
T ss_pred CEECCCCCCCCccceeE---CcCCCCc
Confidence 46799999998866654 9999933
No 20
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=79.65 E-value=1.2 Score=25.56 Aligned_cols=24 Identities=17% Similarity=0.473 Sum_probs=17.3
Q ss_pred cccccCcccccchhhccCCCCCCCC
Q 046522 17 RACLRCRLVKTYDQFRESGCENCPF 41 (115)
Q Consensus 17 rAC~~C~~I~t~~qf~~~gCpnC~~ 41 (115)
--|..|++|...+. .-+.||.|+.
T Consensus 3 ~~C~~CG~i~~g~~-~p~~CP~Cg~ 26 (34)
T cd00729 3 WVCPVCGYIHEGEE-APEKCPICGA 26 (34)
T ss_pred EECCCCCCEeECCc-CCCcCcCCCC
Confidence 35999999976543 1257999983
No 21
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=78.95 E-value=0.74 Score=37.22 Aligned_cols=27 Identities=19% Similarity=0.445 Sum_probs=19.4
Q ss_pred ccccccCcccccchhhc----c---CCCCCCC-CC
Q 046522 16 LRACLRCRLVKTYDQFR----E---SGCENCP-FF 42 (115)
Q Consensus 16 lrAC~~C~~I~t~~qf~----~---~gCpnC~-~l 42 (115)
-++|-.|+++++..... + -.||+|| +|
T Consensus 197 g~~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgRIL 231 (239)
T COG1579 197 GRVCGGCHMKLPSQTLSKVRKKDEIVFCPYCGRIL 231 (239)
T ss_pred CCcccCCeeeecHHHHHHHhcCCCCccCCccchHH
Confidence 48999999999865211 0 2699999 54
No 22
>PF09567 RE_MamI: MamI restriction endonuclease; InterPro: IPR019067 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the MamI restriction endonuclease which recognises and cleaves GATNN^NNATC. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=78.60 E-value=1.2 Score=36.98 Aligned_cols=58 Identities=16% Similarity=0.346 Sum_probs=40.0
Q ss_pred cccccccCcccccchhhccCCCCCCCCCCCCCCcccccccCCCccceEEEEeCCChhHHHHHHhcCCCCCeeeEEEe
Q 046522 15 ELRACLRCRLVKTYDQFRESGCENCPFFKMDEDHERVVDCTTPNFNGIISVMDPTRSWAARWLRIGRFVPGCYTLAV 91 (115)
Q Consensus 15 ~lrAC~~C~~I~t~~qf~~~gCpnC~~l~m~~~~d~v~~~tT~~f~G~I~i~dP~~SwVAk~l~i~~~~pG~YAi~V 91 (115)
+++-|.+|+..+..=+ .-||||+..+-+. -+.+.| ++.+-+ +-+.+..|+ |-+|-+-+
T Consensus 81 Ql~~C~~CGa~V~~~e---~~Cp~C~StnI~r-------~DdSkW--l~~ir~--d~E~~e~L~-----P~~~ylvl 138 (314)
T PF09567_consen 81 QLGKCNNCGANVSRLE---ESCPNCGSTNIKR-------KDDSKW--LFGIRS--DDEFEEYLN-----PRMIYLVL 138 (314)
T ss_pred hhhhhccccceeeehh---hcCCCCCcccccc-------cCCcce--eccccc--HHHHHHhcC-----ccEEEEEE
Confidence 6889999999887543 4599998554333 257888 666644 345677775 77777665
No 23
>PRK10475 23S rRNA pseudouridine synthase F; Provisional
Probab=78.42 E-value=7.7 Score=31.71 Aligned_cols=49 Identities=16% Similarity=0.240 Sum_probs=38.8
Q ss_pred ceEEEEeCCChhHHHHHHhcCCCCCeeeEEEecCCCcHHHHHHHHhcCCee
Q 046522 60 NGIISVMDPTRSWAARWLRIGRFVPGCYTLAVSEALPEDLQNLCEDERVQY 110 (115)
Q Consensus 60 ~G~I~i~dP~~SwVAk~l~i~~~~pG~YAi~V~g~lp~~i~~~l~~~gi~y 110 (115)
+|+|.+.+-. .+..+.++=...++=.|-+.|.|.++++.++.|. +||..
T Consensus 111 sGLLLlT~dg-~~~~~L~~p~~~i~K~Y~v~V~g~~~~~~l~~l~-~Gv~l 159 (290)
T PRK10475 111 QGLIFLTNHG-DLVNKILRAGNDHEKEYLVTVDKPITDEFIRGMG-AGVPI 159 (290)
T ss_pred cceEEEecCH-HHHHHhhCcCCCCCeEEEEEECCCCCHHHHHHHh-CCcEE
Confidence 7999997764 4777776644457889999999999999999885 57765
No 24
>cd02554 PseudoU_synth_RluF PseudoU_synth_RluF_like: Pseudouridine synthase, Escherichia coli RluF like. This group is comprised of bacterial proteins similar to Escherichia coli RluF. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluF makes psi2604 in 23S RNA. psi2604 has only been detected in E. coli. It is absent from other eubacteria despite a precursor U at that site and from eukarya and archea which lack a precursor U at that site.
Probab=76.96 E-value=12 Score=27.97 Aligned_cols=48 Identities=13% Similarity=0.216 Sum_probs=36.5
Q ss_pred ceEEEEeCCChhHHHHHHhcCCCCCeeeEEEecCCCcHHHHHHHHhcCCe
Q 046522 60 NGIISVMDPTRSWAARWLRIGRFVPGCYTLAVSEALPEDLQNLCEDERVQ 109 (115)
Q Consensus 60 ~G~I~i~dP~~SwVAk~l~i~~~~pG~YAi~V~g~lp~~i~~~l~~~gi~ 109 (115)
+|++.+.+- ..+..+.+.-...++-.|-+.|.|.+.++.+..|.. |+.
T Consensus 44 sGlll~t~d-g~~~~~L~~p~~~~~K~Y~V~v~~~l~~~~l~~l~~-G~~ 91 (164)
T cd02554 44 EGLILLTND-GDLVNKILHADNNHEKEYLVTVNKPITDEFIEGMSN-GVV 91 (164)
T ss_pred eeEEEEEcC-HHHHHHHhhhhcCCCeEEEEEECCCCCHHHHHHHhC-CCE
Confidence 799999775 345555555455679999999999999998888854 554
No 25
>TIGR02827 RNR_anaer_Bdell anaerobic ribonucleoside-triphosphate reductase. Members of this family belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are pair with genes for an acitivating protein that creates a glycine radical. Members of this family, though related, fall outside the scope of TIGR02487, a functionally equivalent protein set; no genome has members in both familes. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons.
Probab=76.36 E-value=1.7 Score=39.15 Aligned_cols=44 Identities=11% Similarity=0.321 Sum_probs=31.1
Q ss_pred cccccccCcccccchhhccCCCCCCCCCCCCCCcccccccCCCccceEEEEeCCChhHH
Q 046522 15 ELRACLRCRLVKTYDQFRESGCENCPFFKMDEDHERVVDCTTPNFNGIISVMDPTRSWA 73 (115)
Q Consensus 15 ~lrAC~~C~~I~t~~qf~~~gCpnC~~l~m~~~~d~v~~~tT~~f~G~I~i~dP~~SwV 73 (115)
+.--|..|+.+.....| .||.|+. . .++.|+=+++.+.|-++|-
T Consensus 531 ~~siC~~CGy~~g~~~~---~CP~CGs------~------~~ev~sRv~GYl~~v~~wN 574 (586)
T TIGR02827 531 KITICNDCHHIDKRTLH---RCPVCGS------A------NIDYGTRVIGYLKRVSAFS 574 (586)
T ss_pred CCeecCCCCCcCCCcCC---cCcCCCC------c------cceEEEeecceecCccccc
Confidence 56789999997543333 4999982 2 2567888888888876664
No 26
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=74.92 E-value=1.4 Score=27.66 Aligned_cols=25 Identities=28% Similarity=0.468 Sum_probs=18.8
Q ss_pred ccccccCcccccchhhcc-CCCCCCC
Q 046522 16 LRACLRCRLVKTYDQFRE-SGCENCP 40 (115)
Q Consensus 16 lrAC~~C~~I~t~~qf~~-~gCpnC~ 40 (115)
.--|..|+...+..|-.. -.||.|+
T Consensus 6 ~Y~C~~Cg~~~~~~~~~~~irCp~Cg 31 (49)
T COG1996 6 EYKCARCGREVELDQETRGIRCPYCG 31 (49)
T ss_pred EEEhhhcCCeeehhhccCceeCCCCC
Confidence 457999999987555333 4699998
No 27
>PF15645 Tox-PLDMTX: Dermonecrotoxin of the Papain-like fold
Probab=74.85 E-value=1.5 Score=32.60 Aligned_cols=47 Identities=21% Similarity=0.254 Sum_probs=36.2
Q ss_pred CcccccccCCCccceEE----EEeCCChhHHHHHHhcCCCCCeeeEEEecC
Q 046522 47 DHERVVDCTTPNFNGII----SVMDPTRSWAARWLRIGRFVPGCYTLAVSE 93 (115)
Q Consensus 47 ~~d~v~~~tT~~f~G~I----~i~dP~~SwVAk~l~i~~~~pG~YAi~V~g 93 (115)
+.+-|.|-|...|.+.- .|+.|+++|+.||+.-.+.....|.=-++.
T Consensus 54 g~eyV~D~Ta~QF~~~~~~~~p~i~~~~~W~~~~~~~~~~k~i~y~~~~~~ 104 (135)
T PF15645_consen 54 GKEYVFDPTAHQFSNKGNDNGPIILPEDAWKKRYQQANNEKLIRYKDFVNA 104 (135)
T ss_pred CEEEEEeCcHHHhhccCCCCCceEecHHHHHHHHHHHhhhceEEeeecccc
Confidence 44556666777788777 778999999999999777788888755553
No 28
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=73.49 E-value=1.6 Score=28.68 Aligned_cols=25 Identities=20% Similarity=0.364 Sum_probs=17.6
Q ss_pred ccccccCcccc-cchhhccCCCCCCC
Q 046522 16 LRACLRCRLVK-TYDQFRESGCENCP 40 (115)
Q Consensus 16 lrAC~~C~~I~-t~~qf~~~gCpnC~ 40 (115)
..-|..|+.++ ..+.+..--||||+
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPnCG 34 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPNCG 34 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCCCC
Confidence 46799999988 44433333599998
No 29
>PRK10700 23S rRNA pseudouridylate synthase B; Provisional
Probab=73.03 E-value=16 Score=29.69 Aligned_cols=49 Identities=18% Similarity=0.171 Sum_probs=37.8
Q ss_pred ceEEEEeCCChhHHHHHHhcCCCCCeeeEEEecCCCcHHHHHHHHhcCCee
Q 046522 60 NGIISVMDPTRSWAARWLRIGRFVPGCYTLAVSEALPEDLQNLCEDERVQY 110 (115)
Q Consensus 60 ~G~I~i~dP~~SwVAk~l~i~~~~pG~YAi~V~g~lp~~i~~~l~~~gi~y 110 (115)
+|+|.+.+- ..+..+.+.-+..++=.|-+.|.|.++++.++.| .+|+..
T Consensus 114 sGLLLlTnd-g~~~~~L~~p~~~i~K~Y~v~V~G~~~~~~l~~l-~~Gv~l 162 (289)
T PRK10700 114 CGLLLFTTD-GELANRLMHPSREVEREYAVRVFGQVDDAKLRQL-SRGVQL 162 (289)
T ss_pred ceEEEEEcC-HHHHHHHhCccCCCCeEEEEEEccCCCHHHHHHH-HcCCEe
Confidence 699888765 4666666665556899999999999999888777 467654
No 30
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=72.36 E-value=2.3 Score=27.32 Aligned_cols=22 Identities=23% Similarity=0.641 Sum_probs=17.7
Q ss_pred ccccccccCcccccchhhccCCCCCCC
Q 046522 14 HELRACLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 14 r~lrAC~~C~~I~t~~qf~~~gCpnC~ 40 (115)
..+|.|..|+...-. +.||+||
T Consensus 3 s~mr~C~~CgvYTLk-----~~CP~CG 24 (56)
T PRK13130 3 SKIRKCPKCGVYTLK-----EICPVCG 24 (56)
T ss_pred ccceECCCCCCEEcc-----ccCcCCC
Confidence 368999999988763 3499999
No 31
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=72.07 E-value=2.4 Score=27.72 Aligned_cols=26 Identities=23% Similarity=0.419 Sum_probs=17.8
Q ss_pred cccccccCcccccchh-hccCCCCCCC
Q 046522 15 ELRACLRCRLVKTYDQ-FRESGCENCP 40 (115)
Q Consensus 15 ~lrAC~~C~~I~t~~q-f~~~gCpnC~ 40 (115)
....|..|+..+.... ...-.||||+
T Consensus 6 ~~~~CtSCg~~i~~~~~~~~F~CPnCG 32 (59)
T PRK14890 6 EPPKCTSCGIEIAPREKAVKFLCPNCG 32 (59)
T ss_pred cCccccCCCCcccCCCccCEeeCCCCC
Confidence 4567999998877443 3233599997
No 32
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=71.86 E-value=2.4 Score=30.16 Aligned_cols=25 Identities=24% Similarity=0.376 Sum_probs=17.6
Q ss_pred ccccccCcccccchhhccCCCCCCC
Q 046522 16 LRACLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 16 lrAC~~C~~I~t~~qf~~~gCpnC~ 40 (115)
.--|..|+...+..++....||.|+
T Consensus 70 ~~~C~~Cg~~~~~~~~~~~~CP~Cg 94 (114)
T PRK03681 70 ECWCETCQQYVTLLTQRVRRCPQCH 94 (114)
T ss_pred EEEcccCCCeeecCCccCCcCcCcC
Confidence 3459999987766543323599999
No 33
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=71.69 E-value=1.5 Score=37.49 Aligned_cols=38 Identities=16% Similarity=0.251 Sum_probs=28.2
Q ss_pred cccccccCcccccchhhc--cCCCCCCCCCCCCCCcccccc
Q 046522 15 ELRACLRCRLVKTYDQFR--ESGCENCPFFKMDEDHERVVD 53 (115)
Q Consensus 15 ~lrAC~~C~~I~t~~qf~--~~gCpnC~~l~m~~~~d~v~~ 53 (115)
.+-+|+.|+...+.++=. ...|| |+..--+|-.|||.+
T Consensus 239 h~~~c~~C~~~~~~~~~~~~~~~Cp-CG~~i~~GV~~Rv~e 278 (374)
T TIGR00375 239 HQTACEACGEPAVSEDAETACANCP-CGGRIKKGVSDRLRE 278 (374)
T ss_pred chhhhcccCCcCCchhhhhcCCCCC-CCCcceechHHHHHH
Confidence 467999999999877621 13499 995566777887776
No 34
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=70.58 E-value=2.9 Score=23.90 Aligned_cols=23 Identities=17% Similarity=0.372 Sum_probs=15.9
Q ss_pred ccccCcccccchhhccCCCCCCC
Q 046522 18 ACLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 18 AC~~C~~I~t~~qf~~~gCpnC~ 40 (115)
-|..|+...+.+.-..-.||+|+
T Consensus 2 ~C~~Cg~~~~~~~~~~irC~~CG 24 (32)
T PF03604_consen 2 ICGECGAEVELKPGDPIRCPECG 24 (32)
T ss_dssp BESSSSSSE-BSTSSTSSBSSSS
T ss_pred CCCcCCCeeEcCCCCcEECCcCC
Confidence 48889988876543234799998
No 35
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=70.18 E-value=1.3 Score=40.00 Aligned_cols=43 Identities=12% Similarity=0.414 Sum_probs=27.8
Q ss_pred cccccccCcccccchhhccCCCCCCCCCCCCCCcccccccCCCccceEEEEeCCChhH
Q 046522 15 ELRACLRCRLVKTYDQFRESGCENCPFFKMDEDHERVVDCTTPNFNGIISVMDPTRSW 72 (115)
Q Consensus 15 ~lrAC~~C~~I~t~~qf~~~gCpnC~~l~m~~~~d~v~~~tT~~f~G~I~i~dP~~Sw 72 (115)
+.--|..|+++.+... ..||+|+. .+ ++.|+=+++.+.|-++|
T Consensus 565 ~~~iC~~CG~~~~g~~---~~CP~CGs------~~------~ev~~RV~GYl~~v~~w 607 (623)
T PRK08271 565 KITICNDCHHIDKRTG---KRCPICGS------EN------IDYYTRVIGYLKRVSAF 607 (623)
T ss_pred CCccCCCCCCcCCCCC---cCCcCCCC------cc------hhHHHHHhhhhcCcccc
Confidence 5678999999844443 35999983 22 34566666666665444
No 36
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=69.38 E-value=2.1 Score=22.63 Aligned_cols=19 Identities=32% Similarity=0.632 Sum_probs=12.4
Q ss_pred cccCcccccchhhccCCCCCCC
Q 046522 19 CLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 19 C~~C~~I~t~~qf~~~gCpnC~ 40 (115)
|.+|+.-...+. +-||+|+
T Consensus 2 Cp~CG~~~~~~~---~fC~~CG 20 (23)
T PF13240_consen 2 CPNCGAEIEDDA---KFCPNCG 20 (23)
T ss_pred CcccCCCCCCcC---cchhhhC
Confidence 677777665543 3388887
No 37
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=69.21 E-value=2 Score=32.89 Aligned_cols=24 Identities=29% Similarity=0.746 Sum_probs=18.8
Q ss_pred ccccccccCcccccch-----hhccCCCCCCC
Q 046522 14 HELRACLRCRLVKTYD-----QFRESGCENCP 40 (115)
Q Consensus 14 r~lrAC~~C~~I~t~~-----qf~~~gCpnC~ 40 (115)
..+--|.+|+.-.|.+ .| .||+|+
T Consensus 115 ~~~Y~Cp~C~~rytf~eA~~~~F---~Cp~Cg 143 (178)
T PRK06266 115 NMFFFCPNCHIRFTFDEAMEYGF---RCPQCG 143 (178)
T ss_pred CCEEECCCCCcEEeHHHHhhcCC---cCCCCC
Confidence 4678899999877765 45 399999
No 38
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=68.85 E-value=2.6 Score=31.40 Aligned_cols=20 Identities=25% Similarity=0.702 Sum_probs=15.5
Q ss_pred cccccCcccccchhhccCC---CCCCC
Q 046522 17 RACLRCRLVKTYDQFRESG---CENCP 40 (115)
Q Consensus 17 rAC~~C~~I~t~~qf~~~g---CpnC~ 40 (115)
..|..|+.-+-. ++| ||+|+
T Consensus 29 ~hCp~Cg~PLF~----KdG~v~CPvC~ 51 (131)
T COG1645 29 KHCPKCGTPLFR----KDGEVFCPVCG 51 (131)
T ss_pred hhCcccCCccee----eCCeEECCCCC
Confidence 579999988744 344 99998
No 39
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=68.21 E-value=0.87 Score=40.18 Aligned_cols=47 Identities=13% Similarity=0.377 Sum_probs=18.2
Q ss_pred cccccccCcccccchhhccCCCCCCCCCCCCCCcccccccCCCccceEEEEeCCChhHHHHHH
Q 046522 15 ELRACLRCRLVKTYDQFRESGCENCPFFKMDEDHERVVDCTTPNFNGIISVMDPTRSWAARWL 77 (115)
Q Consensus 15 ~lrAC~~C~~I~t~~qf~~~gCpnC~~l~m~~~~d~v~~~tT~~f~G~I~i~dP~~SwVAk~l 77 (115)
..--|..|+.+... .+ .||.|+. ++ ++.|+=+++-+.|-++|-+=.+
T Consensus 490 ~~~~C~~CG~~~~~-~~---~CP~CGs------~~------~~~~~Rv~GYl~~v~~~n~gK~ 536 (546)
T PF13597_consen 490 PIDICPDCGYIGGE-GD---KCPKCGS------EN------IEVYSRVTGYLRPVSRWNKGKQ 536 (546)
T ss_dssp -EEEETTT---S---EE---E-CCC----------------EEEEB-SSSS-BTTS-------
T ss_pred CcccccCCCcCCCC-CC---CCCCCCC------cc------cceEEEeeccccCccccCHHHH
Confidence 45679999998775 44 4999983 32 3444444444558777765433
No 40
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=67.84 E-value=3.6 Score=35.32 Aligned_cols=25 Identities=32% Similarity=0.688 Sum_probs=19.6
Q ss_pred CccccccccCcccccchhhccCCCCCCC
Q 046522 13 GHELRACLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 13 ~r~lrAC~~C~~I~t~~qf~~~gCpnC~ 40 (115)
..++.+|..|+++.+.++ ..||.|+
T Consensus 218 ~~~l~~C~~Cd~l~~~~~---a~CpRC~ 242 (419)
T PRK15103 218 RQGLRSCSCCTAILPADQ---PVCPRCH 242 (419)
T ss_pred ccCCCcCCCCCCCCCCCC---CCCCCCC
Confidence 356889999999976443 3699999
No 41
>cd04883 ACT_AcuB C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. This CD includes the C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. AcuB is putatively involved in the anaerobic catabolism of acetoin, and related proteins. Studies report the induction of AcuB by nitrate respiration and also by fermentation. Since acetoin can be secreted and later serve as a source of carbon, it has been proposed that, during anaerobic growth when other carbon sources are exhausted, the induction of the AcuB protein results in acetoin catabolism. AcuB-like proteins have two N-terminal tandem CBS domains and a single C-terminal ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=66.98 E-value=10 Score=23.20 Aligned_cols=28 Identities=7% Similarity=0.027 Sum_probs=23.0
Q ss_pred CeeeEEEecCCCcHHHHHHHHhcCCeec
Q 046522 84 PGCYTLAVSEALPEDLQNLCEDERVQYV 111 (115)
Q Consensus 84 pG~YAi~V~g~lp~~i~~~l~~~gi~y~ 111 (115)
.+.+.++|.+..++++.+.|+++|.+..
T Consensus 42 ~~~v~i~v~~~~~~~~~~~L~~~G~~v~ 69 (72)
T cd04883 42 NKILVFRVQTMNPRPIIEDLRRAGYEVL 69 (72)
T ss_pred eEEEEEEEecCCHHHHHHHHHHCCCeee
Confidence 4456777888889999999999998764
No 42
>PRK15364 pathogenicity island 2 effector protein SseB; Provisional
Probab=66.75 E-value=6.9 Score=30.95 Aligned_cols=21 Identities=24% Similarity=0.423 Sum_probs=19.1
Q ss_pred EecCCCcHHHHHHHHhcCCee
Q 046522 90 AVSEALPEDLQNLCEDERVQY 110 (115)
Q Consensus 90 ~V~g~lp~~i~~~l~~~gi~y 110 (115)
+..+.||+|+++.|.++||..
T Consensus 94 K~k~~LPddVI~YmrdNgI~V 114 (196)
T PRK15364 94 KTKEEVPEDVIKYMRDNGILI 114 (196)
T ss_pred cccccCCHHHHHHHHHcCcee
Confidence 678999999999999999974
No 43
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=66.71 E-value=11 Score=29.83 Aligned_cols=56 Identities=18% Similarity=0.355 Sum_probs=37.0
Q ss_pred ccccccccCcccccchhhccCCCCCCCCCCCCCCcccccccCCCccceEEEEeCCChhHHHHHHhcCCCCCeeeEEE
Q 046522 14 HELRACLRCRLVKTYDQFRESGCENCPFFKMDEDHERVVDCTTPNFNGIISVMDPTRSWAARWLRIGRFVPGCYTLA 90 (115)
Q Consensus 14 r~lrAC~~C~~I~t~~qf~~~gCpnC~~l~m~~~~d~v~~~tT~~f~G~I~i~dP~~SwVAk~l~i~~~~pG~YAi~ 90 (115)
++.+-|..|+.+.+.+. |..|.. .+-+.+=+.+|-+|++=|.-...+. -.|.|-|-
T Consensus 52 ~~i~~C~~C~~~te~d~-----C~ICsd-------------~~Rd~~~icVVe~p~Dv~a~E~~~~---f~G~YhVL 107 (198)
T COG0353 52 ENIKHCSVCGNLTESDP-----CDICSD-------------ESRDKSQLCVVEEPKDVLALEKTGE---FRGLYHVL 107 (198)
T ss_pred hcCccccccCCcCCCCc-----CcCcCC-------------cccCCceEEEEcchHHHHHHHHhcc---cCeeEEEe
Confidence 46788999999988664 999962 2333342333447766666666643 37888764
No 44
>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=65.28 E-value=2.1 Score=31.99 Aligned_cols=24 Identities=21% Similarity=0.524 Sum_probs=18.4
Q ss_pred ccccccccCcccccch-----hhccCCCCCCC
Q 046522 14 HELRACLRCRLVKTYD-----QFRESGCENCP 40 (115)
Q Consensus 14 r~lrAC~~C~~I~t~~-----qf~~~gCpnC~ 40 (115)
..+--|.+|+.-.|.+ .| .||+|+
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~~~~F---~Cp~Cg 135 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAMELNF---TCPRCG 135 (158)
T ss_pred CCeEECCCCCcEeeHHHHHHcCC---cCCCCC
Confidence 4678899999776665 34 499999
No 45
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=64.82 E-value=5.5 Score=34.01 Aligned_cols=29 Identities=14% Similarity=0.488 Sum_probs=20.2
Q ss_pred CCccccccccCcccccchhhcc---CCCCCCC
Q 046522 12 FGHELRACLRCRLVKTYDQFRE---SGCENCP 40 (115)
Q Consensus 12 ~~r~lrAC~~C~~I~t~~qf~~---~gCpnC~ 40 (115)
...++.+|..|.++........ --||.|+
T Consensus 9 ~~~~~~~C~~Cd~l~~~~~l~~g~~a~CpRCg 40 (403)
T TIGR00155 9 PAAKHILCSQCDMLVALPRIESGQKAACPRCG 40 (403)
T ss_pred CCCCeeeCCCCCCcccccCCCCCCeeECCCCC
Confidence 3356889999999985442221 2499999
No 46
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=64.26 E-value=3.6 Score=24.96 Aligned_cols=23 Identities=17% Similarity=0.421 Sum_probs=16.5
Q ss_pred ccccCcccccchhhccCCCCCCC
Q 046522 18 ACLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 18 AC~~C~~I~t~~qf~~~gCpnC~ 40 (115)
-|..|+.-.+.+.-..-.||+|+
T Consensus 4 ~C~~Cg~~~~~~~~~~irC~~CG 26 (44)
T smart00659 4 ICGECGRENEIKSKDVVRCRECG 26 (44)
T ss_pred ECCCCCCEeecCCCCceECCCCC
Confidence 58899987776632224699998
No 47
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=63.29 E-value=3.8 Score=29.05 Aligned_cols=24 Identities=25% Similarity=0.566 Sum_probs=17.0
Q ss_pred ccccccCcccccchhhccCCCCCCC
Q 046522 16 LRACLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 16 lrAC~~C~~I~t~~qf~~~gCpnC~ 40 (115)
.--|..|+..-+.+++. ..||+|+
T Consensus 70 ~~~C~~Cg~~~~~~~~~-~~CP~Cg 93 (113)
T PRK12380 70 QAWCWDCSQVVEIHQHD-AQCPHCH 93 (113)
T ss_pred EEEcccCCCEEecCCcC-ccCcCCC
Confidence 35699999766665443 2499999
No 48
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=62.60 E-value=3 Score=23.68 Aligned_cols=22 Identities=23% Similarity=0.507 Sum_probs=12.6
Q ss_pred ccccccCcccccchhhccCCCCCCC
Q 046522 16 LRACLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 16 lrAC~~C~~I~t~~qf~~~gCpnC~ 40 (115)
..-|..|+.+.-.-+ ..||+|+
T Consensus 11 ~~rC~~Cg~~~~pPr---~~Cp~C~ 32 (37)
T PF12172_consen 11 GQRCRDCGRVQFPPR---PVCPHCG 32 (37)
T ss_dssp EEE-TTT--EEES-----SEETTTT
T ss_pred EEEcCCCCCEecCCC---cCCCCcC
Confidence 467999999854443 4599997
No 49
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=62.03 E-value=4.2 Score=28.99 Aligned_cols=25 Identities=24% Similarity=0.468 Sum_probs=17.8
Q ss_pred ccccccCcccccchhhccCCCCCCC
Q 046522 16 LRACLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 16 lrAC~~C~~I~t~~qf~~~gCpnC~ 40 (115)
.--|..|+..-+..++..-.||.|+
T Consensus 71 ~~~C~~Cg~~~~~~~~~~~~CP~Cg 95 (117)
T PRK00564 71 ELECKDCSHVFKPNALDYGVCEKCH 95 (117)
T ss_pred EEEhhhCCCccccCCccCCcCcCCC
Confidence 4569999977776554223499999
No 50
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=61.42 E-value=4.9 Score=30.89 Aligned_cols=23 Identities=17% Similarity=0.452 Sum_probs=17.8
Q ss_pred ccccccCcccccchhhccCCCCCCC
Q 046522 16 LRACLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 16 lrAC~~C~~I~t~~qf~~~gCpnC~ 40 (115)
.--|..|+++...+ --..||+|+
T Consensus 134 ~~vC~vCGy~~~ge--~P~~CPiCg 156 (166)
T COG1592 134 VWVCPVCGYTHEGE--APEVCPICG 156 (166)
T ss_pred EEEcCCCCCcccCC--CCCcCCCCC
Confidence 46799999998652 235799998
No 51
>cd02566 PseudoU_synth_RluE PseudoU_synth_RluE: Pseudouridine synthase, Escherichia coli RluE. This group is comprised of bacterial proteins similar to E. coli RluE. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. Escherichia coli RluE makes psi2457 in 23S RNA. psi2457 is not universally conserved.
Probab=60.97 E-value=31 Score=25.39 Aligned_cols=48 Identities=19% Similarity=0.187 Sum_probs=33.4
Q ss_pred ceEEEEeCCChhHHHHHHhcCCCCCeeeEEEecCCCcHHHHHHHHhcCCe
Q 046522 60 NGIISVMDPTRSWAARWLRIGRFVPGCYTLAVSEALPEDLQNLCEDERVQ 109 (115)
Q Consensus 60 ~G~I~i~dP~~SwVAk~l~i~~~~pG~YAi~V~g~lp~~i~~~l~~~gi~ 109 (115)
+|+|.+.+-. .+.+++..-...+.-.|-+.|.|.++++..+.|. .|+.
T Consensus 44 sGlll~a~d~-~~~~~l~~~~~~v~K~Y~a~v~g~~~~~~~~~l~-~g~~ 91 (168)
T cd02566 44 EGLLLLTDDG-RLQHRITDPSFKHPKTYYVQVEGVPTEDALEQLR-NGVE 91 (168)
T ss_pred eEEEEEEeCH-HHHHHHHCCCCCCCEEEEEEECCcCCHHHHHHHh-CCcE
Confidence 7999997653 3444444433347889999999999988766554 3553
No 52
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=60.54 E-value=3.2 Score=30.35 Aligned_cols=27 Identities=19% Similarity=0.469 Sum_probs=17.4
Q ss_pred ccccccccCcccccchhhcc-------CCCCCCC
Q 046522 14 HELRACLRCRLVKTYDQFRE-------SGCENCP 40 (115)
Q Consensus 14 r~lrAC~~C~~I~t~~qf~~-------~gCpnC~ 40 (115)
+..--|.+|+..-+.+.... -.||+|+
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg 130 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCG 130 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCC
Confidence 35677899987766543221 1399998
No 53
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=60.41 E-value=6.2 Score=23.62 Aligned_cols=26 Identities=19% Similarity=0.220 Sum_probs=15.8
Q ss_pred ccccccCcccccchhhcc----CCCCCCCC
Q 046522 16 LRACLRCRLVKTYDQFRE----SGCENCPF 41 (115)
Q Consensus 16 lrAC~~C~~I~t~~qf~~----~gCpnC~~ 41 (115)
...|..|+..-+..+-.. ..||+|+.
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEEeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 356999998544332111 26999983
No 54
>PRK10144 formate-dependent nitrite reductase complex subunit NrfF; Provisional
Probab=60.21 E-value=3.6 Score=30.39 Aligned_cols=39 Identities=18% Similarity=0.280 Sum_probs=29.9
Q ss_pred hhHHHHHHhcCCCCCeeeEEEecCCCcHHHHHHHHhc---CCeecCC
Q 046522 70 RSWAARWLRIGRFVPGCYTLAVSEALPEDLQNLCEDE---RVQYVPP 113 (115)
Q Consensus 70 ~SwVAk~l~i~~~~pG~YAi~V~g~lp~~i~~~l~~~---gi~y~pr 113 (115)
+|-+|+-+|.. .|..-..|.=.++|++.|-++ -|-|.|+
T Consensus 55 na~iA~dmR~~-----Vr~~i~~G~sd~eI~~~~v~RYG~~Vl~~Pp 96 (126)
T PRK10144 55 NAPVAVSMRHQ-----VYSMVAEGKSEVEIIGWMTERYGDFVRYNPP 96 (126)
T ss_pred CCHHHHHHHHH-----HHHHHHcCCCHHHHHHHHHHhcCCeEEecCC
Confidence 57899988854 233445899999999999988 4677775
No 55
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=60.19 E-value=4.9 Score=29.32 Aligned_cols=15 Identities=13% Similarity=0.288 Sum_probs=11.5
Q ss_pred cccccccCcccccch
Q 046522 15 ELRACLRCRLVKTYD 29 (115)
Q Consensus 15 ~lrAC~~C~~I~t~~ 29 (115)
..--|..|+..-+.+
T Consensus 69 ~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCRNCGNEWSLK 83 (135)
T ss_pred eEEECCCCCCEEecc
Confidence 446799999887765
No 56
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=59.75 E-value=4.2 Score=36.20 Aligned_cols=24 Identities=17% Similarity=0.441 Sum_probs=16.6
Q ss_pred ccccccccCcccccchhhccCCCCCCC
Q 046522 14 HELRACLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 14 r~lrAC~~C~~I~t~~qf~~~gCpnC~ 40 (115)
.++--|..|+++-... ...||.|+
T Consensus 522 ~~~~~C~~CG~~g~~~---~~~CP~Cg 545 (579)
T TIGR02487 522 PPVDVCEDCGYTGEGL---NDKCPKCG 545 (579)
T ss_pred cCCccCCCCCCCCCCC---CCcCcCCC
Confidence 3567899999843332 23599998
No 57
>PF13192 Thioredoxin_3: Thioredoxin domain; PDB: 1ZYP_B 1ZYN_A 1HYU_A 1ILO_A 1J08_F 2YWM_B 2AYT_B 2HLS_B 1A8L_A 2K8S_B ....
Probab=59.04 E-value=9.7 Score=24.30 Aligned_cols=58 Identities=14% Similarity=0.272 Sum_probs=30.2
Q ss_pred cCCCCCCCCCCCCCCcccccccCCCccceEEEEeCCChhHHHHHHhcCCCCCeeeE---EEecCCCcH
Q 046522 33 ESGCENCPFFKMDEDHERVVDCTTPNFNGIISVMDPTRSWAARWLRIGRFVPGCYT---LAVSEALPE 97 (115)
Q Consensus 33 ~~gCpnC~~l~m~~~~d~v~~~tT~~f~G~I~i~dP~~SwVAk~l~i~~~~pG~YA---i~V~g~lp~ 97 (115)
..+||+|..+ .........+..--+-+.+-+..--++..|+.. +|..+- ++-.|+.|.
T Consensus 7 ~~~C~~C~~~------~~~~~~~~~~~~i~~ei~~~~~~~~~~~ygv~~-vPalvIng~~~~~G~~p~ 67 (76)
T PF13192_consen 7 SPGCPYCPEL------VQLLKEAAEELGIEVEIIDIEDFEEIEKYGVMS-VPALVINGKVVFVGRVPS 67 (76)
T ss_dssp CSSCTTHHHH------HHHHHHHHHHTTEEEEEEETTTHHHHHHTT-SS-SSEEEETTEEEEESS--H
T ss_pred CCCCCCcHHH------HHHHHHHHHhcCCeEEEEEccCHHHHHHcCCCC-CCEEEECCEEEEEecCCC
Confidence 3579999821 222223344444335666765555556667654 787743 455665553
No 58
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=58.50 E-value=6.5 Score=34.33 Aligned_cols=26 Identities=35% Similarity=0.787 Sum_probs=21.9
Q ss_pred CccccccccCcccccchhhccCCCCCCC
Q 046522 13 GHELRACLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 13 ~r~lrAC~~C~~I~t~~qf~~~gCpnC~ 40 (115)
..+.++|..|+++...++ +-.||.|+
T Consensus 217 ~~~~~~C~~C~~~~~~~~--~~~CpRC~ 242 (418)
T COG2995 217 REGLRSCLCCHYILPHDA--EPRCPRCG 242 (418)
T ss_pred cccceecccccccCCHhh--CCCCCCCC
Confidence 347899999999999874 45699999
No 59
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=58.42 E-value=5.7 Score=24.74 Aligned_cols=12 Identities=17% Similarity=0.418 Sum_probs=9.3
Q ss_pred ccccCcccccch
Q 046522 18 ACLRCRLVKTYD 29 (115)
Q Consensus 18 AC~~C~~I~t~~ 29 (115)
-|..|++|-..+
T Consensus 3 ~C~~CgyiYd~~ 14 (50)
T cd00730 3 ECRICGYIYDPA 14 (50)
T ss_pred CCCCCCeEECCC
Confidence 488999988754
No 60
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=58.19 E-value=3.9 Score=32.20 Aligned_cols=26 Identities=27% Similarity=0.420 Sum_probs=19.2
Q ss_pred ccccccCcccccchhhccCCCCCCCCC
Q 046522 16 LRACLRCRLVKTYDQFRESGCENCPFF 42 (115)
Q Consensus 16 lrAC~~C~~I~t~~qf~~~gCpnC~~l 42 (115)
+--|.+|+-.+-. .+..-.||||+..
T Consensus 149 ~A~CsrC~~~L~~-~~~~l~Cp~Cg~t 174 (188)
T COG1096 149 YARCSRCRAPLVK-KGNMLKCPNCGNT 174 (188)
T ss_pred EEEccCCCcceEE-cCcEEECCCCCCE
Confidence 3569999988876 4444569999944
No 61
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=58.03 E-value=2.3 Score=38.47 Aligned_cols=23 Identities=22% Similarity=0.520 Sum_probs=17.0
Q ss_pred cccccccCcccccchhhccCCCCCCC
Q 046522 15 ELRACLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 15 ~lrAC~~C~~I~t~~qf~~~gCpnC~ 40 (115)
..--|..|+....... ..||+|+
T Consensus 567 ~~~~C~~CG~~~~g~~---~~CP~CG 589 (625)
T PRK08579 567 AITVCNKCGRSTTGLY---TRCPRCG 589 (625)
T ss_pred CCccCCCCCCccCCCC---CcCcCCC
Confidence 5678999999544443 3599998
No 62
>PRK00420 hypothetical protein; Validated
Probab=57.99 E-value=5.2 Score=28.93 Aligned_cols=24 Identities=21% Similarity=0.169 Sum_probs=16.6
Q ss_pred cccccCcccccchhhccCCCCCCC
Q 046522 17 RACLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 17 rAC~~C~~I~t~~qf~~~gCpnC~ 40 (115)
..|..|+..+....=-..-||+|+
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg 47 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHG 47 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCC
Confidence 689999988775210123599999
No 63
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=57.10 E-value=8.9 Score=33.96 Aligned_cols=22 Identities=18% Similarity=0.434 Sum_probs=16.3
Q ss_pred cccccccCcccccchhhccCCCCCCC
Q 046522 15 ELRACLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 15 ~lrAC~~C~~I~t~~qf~~~gCpnC~ 40 (115)
.. -|..|+++..... ..||.|+
T Consensus 518 ~~-~C~~CG~~~~~~~---~~CP~CG 539 (555)
T cd01675 518 ID-ICNDCGYIGEGEG---FKCPKCG 539 (555)
T ss_pred Cc-cCCCCCCCCcCCC---CCCcCCC
Confidence 44 8999999764344 3599998
No 64
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=57.05 E-value=3.3 Score=29.20 Aligned_cols=24 Identities=25% Similarity=0.524 Sum_probs=17.6
Q ss_pred ccccccCcccccchhhccCCCCCCC
Q 046522 16 LRACLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 16 lrAC~~C~~I~t~~qf~~~gCpnC~ 40 (115)
.--|..|+..-+.+++. .-||+|+
T Consensus 70 ~~~C~~Cg~~~~~~~~~-~~CP~Cg 93 (113)
T PF01155_consen 70 RARCRDCGHEFEPDEFD-FSCPRCG 93 (113)
T ss_dssp EEEETTTS-EEECHHCC-HH-SSSS
T ss_pred cEECCCCCCEEecCCCC-CCCcCCc
Confidence 35699999998888764 4599998
No 65
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=55.99 E-value=42 Score=29.31 Aligned_cols=27 Identities=11% Similarity=0.129 Sum_probs=12.4
Q ss_pred CCChhHHHHHHhcCCCCCeeeEEEecCCC
Q 046522 67 DPTRSWAARWLRIGRFVPGCYTLAVSEAL 95 (115)
Q Consensus 67 dP~~SwVAk~l~i~~~~pG~YAi~V~g~l 95 (115)
.+..-++++.++ +.-||.=.+++.++.
T Consensus 268 g~Gte~~~e~l~--~~fp~~~v~~~d~d~ 294 (505)
T TIGR00595 268 GYGTEQVEEELA--KLFPGARIARIDSDT 294 (505)
T ss_pred cccHHHHHHHHH--hhCCCCcEEEEeccc
Confidence 444455555554 223554334444444
No 66
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=55.55 E-value=14 Score=24.62 Aligned_cols=27 Identities=33% Similarity=0.738 Sum_probs=18.1
Q ss_pred ChhHHHHHHhcCCCCCeeeEEEecCCCcHHHHHHHHhcCC
Q 046522 69 TRSWAARWLRIGRFVPGCYTLAVSEALPEDLQNLCEDERV 108 (115)
Q Consensus 69 ~~SwVAk~l~i~~~~pG~YAi~V~g~lp~~i~~~l~~~gi 108 (115)
..|||++.+.+- +||++|.+.+++..+
T Consensus 16 s~s~Vs~~l~Ll-------------~lP~~i~~~v~~g~~ 42 (93)
T PF08535_consen 16 SRSWVSNHLALL-------------DLPEEIKELVRSGRI 42 (93)
T ss_dssp -HHHHHHHHGGG-------------S--HHHHHHHHTTS-
T ss_pred CHHHHHHHHHHH-------------cCCHHHHHHHHcCCC
Confidence 468999988765 599999888876544
No 67
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=55.06 E-value=2.9 Score=36.06 Aligned_cols=42 Identities=21% Similarity=0.381 Sum_probs=29.9
Q ss_pred cccccccCcccccchhhcc--CCCCCCCCCCCCCCcccccccCC
Q 046522 15 ELRACLRCRLVKTYDQFRE--SGCENCPFFKMDEDHERVVDCTT 56 (115)
Q Consensus 15 ~lrAC~~C~~I~t~~qf~~--~gCpnC~~l~m~~~~d~v~~~tT 56 (115)
.+-||.+|+..-+.+.-.. -.||+|+..--+|-+||+.+-.+
T Consensus 245 ~~TAC~rC~t~y~le~A~~~~wrCpkCGg~ikKGV~dRv~ELad 288 (403)
T COG1379 245 HLTACSRCYTRYSLEEAKSLRWRCPKCGGKIKKGVSDRVLELAD 288 (403)
T ss_pred hHHHHHHhhhccCcchhhhhcccCcccccchhhhHHHHHHHhhc
Confidence 5789999996655443222 35999996666888999887443
No 68
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=55.02 E-value=6.2 Score=23.88 Aligned_cols=26 Identities=27% Similarity=0.706 Sum_probs=20.3
Q ss_pred CCCCCC-CCCCCCCcccccccCCCccceEEE
Q 046522 35 GCENCP-FFKMDEDHERVVDCTTPNFNGIIS 64 (115)
Q Consensus 35 gCpnC~-~l~m~~~~d~v~~~tT~~f~G~I~ 64 (115)
.|.+|+ |.+|..|+. |.-..|.|..+
T Consensus 3 kC~~CG~~GH~~t~k~----CP~~~~~~a~~ 29 (40)
T PF15288_consen 3 KCKNCGAFGHMRTNKR----CPMYCWSGALA 29 (40)
T ss_pred cccccccccccccCcc----CCCCCCCCCCC
Confidence 499999 999988886 77777776543
No 69
>PRK11394 23S rRNA pseudouridine synthase E; Provisional
Probab=54.90 E-value=49 Score=26.12 Aligned_cols=49 Identities=16% Similarity=0.221 Sum_probs=36.8
Q ss_pred ceEEEEeCCChhHHHHHHhcCCCCCeeeEEEecCCCcHHHHHHHHhcCCee
Q 046522 60 NGIISVMDPTRSWAARWLRIGRFVPGCYTLAVSEALPEDLQNLCEDERVQY 110 (115)
Q Consensus 60 ~G~I~i~dP~~SwVAk~l~i~~~~pG~YAi~V~g~lp~~i~~~l~~~gi~y 110 (115)
+|+|.+.+- ..+..+...-+..+.-.|-+.|.|.++++..+.| .+|+..
T Consensus 83 sGllLlt~d-~~~~~~L~~~~~~i~K~Y~~~v~g~~~~~~l~~l-~~Gv~i 131 (217)
T PRK11394 83 EGLLVLTNN-GALQARLTQPGKRTGKIYYVQVEGIPTQDALEAL-RNGVTL 131 (217)
T ss_pred eeEEEEECC-HHHHHHHhCcccCCCEEEEEEECCCCCHHHHHHH-hCCeEE
Confidence 688888665 5666777666667889999999999999887765 345443
No 70
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=54.65 E-value=6.1 Score=28.79 Aligned_cols=24 Identities=21% Similarity=0.510 Sum_probs=18.2
Q ss_pred ccccccCcccccchhhccCCCCCCC
Q 046522 16 LRACLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 16 lrAC~~C~~I~t~~qf~~~gCpnC~ 40 (115)
.--|..|+-..+.+.+.-. ||.|+
T Consensus 70 ~~~C~~C~~~~~~e~~~~~-CP~C~ 93 (115)
T COG0375 70 ECWCLDCGQEVELEELDYR-CPKCG 93 (115)
T ss_pred EEEeccCCCeecchhheeE-CCCCC
Confidence 3459999777777766544 99999
No 71
>cd04882 ACT_Bt0572_2 C-terminal ACT domain of a novel protein composed of just two ACT domains. Included in this CD is the C-terminal ACT domain of a novel protein composed of just two ACT domains, as seen in the yet uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related proteins. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=54.45 E-value=21 Score=21.02 Aligned_cols=24 Identities=8% Similarity=0.158 Sum_probs=18.7
Q ss_pred eeeEEEecCCCcHHHHHHHHhcCCee
Q 046522 85 GCYTLAVSEALPEDLQNLCEDERVQY 110 (115)
Q Consensus 85 G~YAi~V~g~lp~~i~~~l~~~gi~y 110 (115)
+.+.+++.+ ++++.+.|+++|..+
T Consensus 41 ~~v~~~ve~--~~~~~~~L~~~G~~v 64 (65)
T cd04882 41 ALLIFRTED--IEKAIEVLQERGVEL 64 (65)
T ss_pred EEEEEEeCC--HHHHHHHHHHCCceE
Confidence 455566665 899999999999764
No 72
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=54.08 E-value=7 Score=27.83 Aligned_cols=25 Identities=24% Similarity=0.639 Sum_probs=18.6
Q ss_pred ccccccCcccccchhhcc-CCCCCCC
Q 046522 16 LRACLRCRLVKTYDQFRE-SGCENCP 40 (115)
Q Consensus 16 lrAC~~C~~I~t~~qf~~-~gCpnC~ 40 (115)
.-+|..|++.--.+.-.. ..||.|.
T Consensus 58 Pa~CkkCGfef~~~~ik~pSRCP~CK 83 (97)
T COG3357 58 PARCKKCGFEFRDDKIKKPSRCPKCK 83 (97)
T ss_pred ChhhcccCccccccccCCcccCCcch
Confidence 358999999876654432 5799998
No 73
>cd02985 TRX_CDSP32 TRX family, chloroplastic drought-induced stress protein of 32 kD (CDSP32); CDSP32 is composed of two TRX domains, a C-terminal TRX domain which contains a redox active CXXC motif and an N-terminal TRX-like domain which contains an SXXS sequence instead of the redox active motif. CDSP32 is a stress-inducible TRX, i.e., it acts as a TRX by reducing protein disulfides and is induced by environmental and oxidative stress conditions. It plays a critical role in plastid defense against oxidative damage, a role related to its function as a physiological electron donor to BAS1, a plastidic 2-cys peroxiredoxin. Plants lacking CDSP32 exhibit decreased photosystem II photochemical efficiencies and chlorophyll retention compared to WT controls, as well as an increased proportion of BAS1 in its overoxidized monomeric form.
Probab=54.06 E-value=9.5 Score=25.45 Aligned_cols=72 Identities=10% Similarity=-0.002 Sum_probs=41.9
Q ss_pred hhccCCCCCCCCCCCCCCcccccccCCCccceE-EEEeCCChh----HHHHHHhcCC------CCCeeeEEEecCCCcHH
Q 046522 30 QFRESGCENCPFFKMDEDHERVVDCTTPNFNGI-ISVMDPTRS----WAARWLRIGR------FVPGCYTLAVSEALPED 98 (115)
Q Consensus 30 qf~~~gCpnC~~l~m~~~~d~v~~~tT~~f~G~-I~i~dP~~S----wVAk~l~i~~------~~pG~YAi~V~g~lp~~ 98 (115)
.|....|+.|..+ ...=+. ....|.++ ++.+|-+++ .+|+..+|.. +..|.-..+..|..|++
T Consensus 21 ~F~a~wC~~C~~~--~p~l~~----la~~~~~v~~~~vd~d~~~~~~~l~~~~~V~~~Pt~~~~~~G~~v~~~~G~~~~~ 94 (103)
T cd02985 21 EFALKHSGPSVKI--YPTMVK----LSRTCNDVVFLLVNGDENDSTMELCRREKIIEVPHFLFYKDGEKIHEEEGIGPDE 94 (103)
T ss_pred EEECCCCHhHHHH--hHHHHH----HHHHCCCCEEEEEECCCChHHHHHHHHcCCCcCCEEEEEeCCeEEEEEeCCCHHH
Confidence 4667789999822 111111 23334332 333454433 6888888876 34566556678888888
Q ss_pred HHHHHHhcC
Q 046522 99 LQNLCEDER 107 (115)
Q Consensus 99 i~~~l~~~g 107 (115)
+...+...|
T Consensus 95 l~~~~~~~~ 103 (103)
T cd02985 95 LIGDVLYYG 103 (103)
T ss_pred HHHHHHhcC
Confidence 887765443
No 74
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=53.78 E-value=6.1 Score=36.40 Aligned_cols=43 Identities=14% Similarity=0.401 Sum_probs=27.1
Q ss_pred ccccccccCcccccchhhccCCCCCCCCCCCCCCcccccccCCCccceEEEEeCCChhH
Q 046522 14 HELRACLRCRLVKTYDQFRESGCENCPFFKMDEDHERVVDCTTPNFNGIISVMDPTRSW 72 (115)
Q Consensus 14 r~lrAC~~C~~I~t~~qf~~~gCpnC~~l~m~~~~d~v~~~tT~~f~G~I~i~dP~~Sw 72 (115)
..+--|..|+++... . ..||+|+. . ..+-|+=+++.+.|-+.|
T Consensus 678 ~~~~~C~~CG~~~~~-~---~~CP~CG~------~------~~~~~~Ri~GYl~~v~~w 720 (735)
T PRK07111 678 HPVDRCPVCGYLGVI-E---DKCPKCGS------T------NIQRIRRITGYLGTLDRF 720 (735)
T ss_pred CCCeecCCCCCCCCc-C---ccCcCCCC------c------cceeeehhhhhccchhhc
Confidence 356789999986653 2 35999983 1 244555555555664444
No 75
>TIGR00093 pseudouridine synthase. This model identifies panels of pseudouridine synthase enzymes that RNA modifications involved in maturing the protein translation apparatus. Counts per genome vary: two in Staphylococcus aureus, three in Pseudomonas putida, four in E. coli, etc.
Probab=53.78 E-value=63 Score=22.65 Aligned_cols=44 Identities=11% Similarity=0.225 Sum_probs=30.9
Q ss_pred ceEEEEeCCChhHHHHHHhcCCCCCeeeEEEecCCCcHHHHHHHH
Q 046522 60 NGIISVMDPTRSWAARWLRIGRFVPGCYTLAVSEALPEDLQNLCE 104 (115)
Q Consensus 60 ~G~I~i~dP~~SwVAk~l~i~~~~pG~YAi~V~g~lp~~i~~~l~ 104 (115)
+|+|.+.+- ..+..+...-...+.=.|-+.|.|.++++.++.+.
T Consensus 9 SGlll~akd-~~~~~~L~~~~~~i~K~Y~a~v~g~~~~~~~~~~~ 52 (128)
T TIGR00093 9 EGLLLLTND-GELVHRLTHPGHHCEKTYLVTVEGPVTDEDLEALR 52 (128)
T ss_pred EEEEEEEeC-HHHHHHHhCCCCCCCeEEEEEECCCCCHHHHHHHh
Confidence 799998663 33444444434457889999999999988776554
No 76
>cd03026 AhpF_NTD_C TRX-GRX-like family, Alkyl hydroperoxide reductase F subunit (AhpF) N-terminal domain (NTD) subfamily, C-terminal TRX-fold subdomain; AhpF is a homodimeric flavoenzyme which catalyzes the NADH-dependent reduction of the peroxiredoxin AhpC, which then reduces hydrogen peroxide and organic hydroperoxides. AhpF contains an NTD containing two contiguous TRX-fold subdomains similar to Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). It also contains a catalytic core similar to TRX reductase containing FAD and NADH binding domains with an active site disulfide. The proposed mechanism of action of AhpF is similar to a TRX/TRX reductase system. The flow of reducing equivalents goes from NADH - catalytic core of AhpF - NTD of AhpF - AhpC - peroxide substrates. The catalytic CXXC motif of the NTD of AhpF is contained in its C-terminal TRX subdomain.
Probab=53.69 E-value=4.1 Score=27.28 Aligned_cols=51 Identities=20% Similarity=0.297 Sum_probs=28.9
Q ss_pred hhccCCCCCCCCC-CCCCCcccccccCCCccceEEEEeCCC-hhHHHHHHhcCCCCCeee
Q 046522 30 QFRESGCENCPFF-KMDEDHERVVDCTTPNFNGIISVMDPT-RSWAARWLRIGRFVPGCY 87 (115)
Q Consensus 30 qf~~~gCpnC~~l-~m~~~~d~v~~~tT~~f~G~I~i~dP~-~SwVAk~l~i~~~~pG~Y 87 (115)
.|...+||+|... ++- +.+.. .+++++ +.++|-. ...+|+..++.. +|..+
T Consensus 18 ~F~~~~C~~C~~~~~~~---~~l~~-~~~~i~--~~~vd~~~~~e~a~~~~V~~-vPt~v 70 (89)
T cd03026 18 TYVSLSCHNCPDVVQAL---NLMAV-LNPNIE--HEMIDGALFQDEVEERGIMS-VPAIF 70 (89)
T ss_pred EEECCCCCCcHHHHHHH---HHHHH-HCCCce--EEEEEhHhCHHHHHHcCCcc-CCEEE
Confidence 5777899999821 111 11211 233333 3333433 357899999875 88886
No 77
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=53.54 E-value=5.3 Score=29.47 Aligned_cols=39 Identities=23% Similarity=0.258 Sum_probs=29.3
Q ss_pred hhHHHHHHhcCCCCCeeeEEEecCCCcHHHHHHHHhc---CCeecCC
Q 046522 70 RSWAARWLRIGRFVPGCYTLAVSEALPEDLQNLCEDE---RVQYVPP 113 (115)
Q Consensus 70 ~SwVAk~l~i~~~~pG~YAi~V~g~lp~~i~~~l~~~---gi~y~pr 113 (115)
+|-+|+-+|.. .|..-..|.=.++|++.|-++ -|-|.|+
T Consensus 55 ~a~iA~dmR~~-----Vr~~i~~G~Sd~eI~~~~v~RYG~~Vly~Pp 96 (126)
T TIGR03147 55 NSPIAYDLRHE-----VYSMVNEGKSNQQIIDFMTARFGDFVLYNPP 96 (126)
T ss_pred CCHHHHHHHHH-----HHHHHHcCCCHHHHHHHHHHhcCCeEEecCC
Confidence 56889888744 233345899999999999988 4677775
No 78
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=51.11 E-value=8.1 Score=27.39 Aligned_cols=25 Identities=16% Similarity=0.200 Sum_probs=18.1
Q ss_pred ccccccCcccccchhhccCCCCCCCC
Q 046522 16 LRACLRCRLVKTYDQFRESGCENCPF 41 (115)
Q Consensus 16 lrAC~~C~~I~t~~qf~~~gCpnC~~ 41 (115)
.--|..|+..-+..++. ..||.|+.
T Consensus 70 ~~~C~~Cg~~~~~~~~~-~~CP~Cgs 94 (115)
T TIGR00100 70 ECECEDCSEEVSPEIDL-YRCPKCHG 94 (115)
T ss_pred EEEcccCCCEEecCCcC-ccCcCCcC
Confidence 35699999877776542 35999993
No 79
>cd02556 PseudoU_synth_RluB PseudoU_synth_RluB: Pseudouridine synthase, Escherichia coli RluB like. This group is comprised of bacterial and eukaryotic proteins similar to E. coli RluB. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RluB makes psi2605 in 23S RNA. psi2605 has been detected in eubacteria but, not in eukarya and archea despite the presence of a precursor U at that site.
Probab=50.85 E-value=70 Score=23.45 Aligned_cols=44 Identities=11% Similarity=0.187 Sum_probs=31.1
Q ss_pred ceEEEEeCCChhHHHHHHhcCCCCCeeeEEEecCCCcHHHHHHHH
Q 046522 60 NGIISVMDPTRSWAARWLRIGRFVPGCYTLAVSEALPEDLQNLCE 104 (115)
Q Consensus 60 ~G~I~i~dP~~SwVAk~l~i~~~~pG~YAi~V~g~lp~~i~~~l~ 104 (115)
+|+|.+.+-. .+..+.+.-+..+.=.|-+.|.|.++++.++.+.
T Consensus 47 sGLll~ak~~-~~~~~L~~~~~~i~K~Y~a~V~g~~~~~~~~~~~ 90 (167)
T cd02556 47 EGLLLFTNDG-ELANRLMHPSNEIEREYAVRVFGQVTDEQLKSLK 90 (167)
T ss_pred eeEEEEECCH-HHHHHHhCCcCCCCeEEEEEECccCCHHHHHHHH
Confidence 7999987653 3444444333457889999999999888766554
No 80
>PRK08402 replication factor A; Reviewed
Probab=49.97 E-value=10 Score=32.16 Aligned_cols=50 Identities=22% Similarity=0.292 Sum_probs=29.8
Q ss_pred cccccccCcccccchhhcc-CCCCCCCCCCCCCCcccccccCCCccceEEEEe
Q 046522 15 ELRACLRCRLVKTYDQFRE-SGCENCPFFKMDEDHERVVDCTTPNFNGIISVM 66 (115)
Q Consensus 15 ~lrAC~~C~~I~t~~qf~~-~gCpnC~~l~m~~~~d~v~~~tT~~f~G~I~i~ 66 (115)
-+.||..|...++.++-.. -.|++|+- ..+...-+..+.=.+++|.+-+.
T Consensus 211 ~y~aCp~CnKkv~~~~~~~~~~Ce~~~~--v~p~~ryil~~~l~D~TG~~~vt 261 (355)
T PRK08402 211 VYDACPECRRKVDYDPATDTWICPEHGE--VEPIKITILDFGLDDGTGYIRVT 261 (355)
T ss_pred eEecCCCCCeEEEEecCCCCEeCCCCCC--cCcceeEEEEEEEEcCCCcEEEE
Confidence 4689999999987433111 13999971 23344444444555666666554
No 81
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=49.37 E-value=9.1 Score=35.48 Aligned_cols=33 Identities=15% Similarity=0.332 Sum_probs=21.3
Q ss_pred EEEEeCCChhHHHHHHhcCCCCCeeeEEEecCCCc
Q 046522 62 IISVMDPTRSWAARWLRIGRFVPGCYTLAVSEALP 96 (115)
Q Consensus 62 ~I~i~dP~~SwVAk~l~i~~~~pG~YAi~V~g~lp 96 (115)
.+.-.-+---+|++.++ +.-|+.=-+++..+..
T Consensus 485 ~L~~~G~GterieeeL~--~~FP~~rv~r~d~Dtt 517 (730)
T COG1198 485 HLRAVGPGTERIEEELK--RLFPGARIIRIDSDTT 517 (730)
T ss_pred eeEEecccHHHHHHHHH--HHCCCCcEEEEccccc
Confidence 34455677778888876 5567766666655544
No 82
>COG1187 RsuA 16S rRNA uridine-516 pseudouridylate synthase and related pseudouridylate synthases [Translation, ribosomal structure and biogenesis]
Probab=49.07 E-value=56 Score=26.48 Aligned_cols=49 Identities=16% Similarity=0.190 Sum_probs=38.4
Q ss_pred ceEEEEeCCChhHHHHHHhcCCCCCeeeEEEecCCCcHHHHHHHHhcCCee
Q 046522 60 NGIISVMDPTRSWAARWLRIGRFVPGCYTLAVSEALPEDLQNLCEDERVQY 110 (115)
Q Consensus 60 ~G~I~i~dP~~SwVAk~l~i~~~~pG~YAi~V~g~lp~~i~~~l~~~gi~y 110 (115)
+|++.+.|- --|..+.++=...++=.|.++|.|.+.++.++.|.+ ||.+
T Consensus 112 eGLLLLTnD-G~la~rL~~P~~~~~K~Y~v~v~g~~~~~~l~~l~~-Gv~l 160 (248)
T COG1187 112 EGLLLLTND-GELAHRLMHPSSEVEKEYLVRVEGPVTEEDLEKLRK-GVTL 160 (248)
T ss_pred eeEEEEeCC-HHHHHHhcCCCCCCCEEEEEEEecCCCHHHHHHHhC-CcEe
Confidence 799998775 356666666566799999999999999999998874 5544
No 83
>PRK12496 hypothetical protein; Provisional
Probab=49.03 E-value=9.1 Score=28.80 Aligned_cols=23 Identities=26% Similarity=0.596 Sum_probs=15.7
Q ss_pred cccccCcccccchhhccCCCCCCC
Q 046522 17 RACLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 17 rAC~~C~~I~t~~qf~~~gCpnC~ 40 (115)
.-|..|+..-+.+- ..+-||+||
T Consensus 128 ~~C~gC~~~~~~~~-~~~~C~~CG 150 (164)
T PRK12496 128 KVCKGCKKKYPEDY-PDDVCEICG 150 (164)
T ss_pred EECCCCCccccCCC-CCCcCCCCC
Confidence 56999997765331 113499999
No 84
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=48.56 E-value=7 Score=24.59 Aligned_cols=28 Identities=29% Similarity=0.484 Sum_probs=18.0
Q ss_pred cccccccCcccccch-hhccCCCCCCCCC
Q 046522 15 ELRACLRCRLVKTYD-QFRESGCENCPFF 42 (115)
Q Consensus 15 ~lrAC~~C~~I~t~~-qf~~~gCpnC~~l 42 (115)
.-+.|..|+.+.... .-..-.||+|++.
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCE
Confidence 457899999887761 1111259999843
No 85
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=48.43 E-value=7.9 Score=29.73 Aligned_cols=22 Identities=27% Similarity=0.730 Sum_probs=16.1
Q ss_pred ccccccCcccccchhhccCCCCCCCC
Q 046522 16 LRACLRCRLVKTYDQFRESGCENCPF 41 (115)
Q Consensus 16 lrAC~~C~~I~t~~qf~~~gCpnC~~ 41 (115)
-+-|-.|+. .....|. ||+|++
T Consensus 309 S~~C~~cg~-~~~r~~~---C~~cg~ 330 (364)
T COG0675 309 SKTCPCCGH-LSGRLFK---CPRCGF 330 (364)
T ss_pred cccccccCC-ccceeEE---CCCCCC
Confidence 477999999 4444443 999994
No 86
>PF12773 DZR: Double zinc ribbon
Probab=48.26 E-value=12 Score=22.10 Aligned_cols=27 Identities=19% Similarity=0.379 Sum_probs=17.9
Q ss_pred cccccccCcccccchhhccCCCCCCCC
Q 046522 15 ELRACLRCRLVKTYDQFRESGCENCPF 41 (115)
Q Consensus 15 ~lrAC~~C~~I~t~~qf~~~gCpnC~~ 41 (115)
..+-|..|+.-+....-...-||+|+.
T Consensus 11 ~~~fC~~CG~~l~~~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 11 DAKFCPHCGTPLPPPDQSKKICPNCGA 37 (50)
T ss_pred cccCChhhcCChhhccCCCCCCcCCcC
Confidence 357899999888722212245999983
No 87
>smart00839 ELFV_dehydrog Glutamate/Leucine/Phenylalanine/Valine dehydrogenase. Glutamate, leucine, phenylalanine and valine dehydrogenases are structurally and functionally related. They contain a Gly-rich region containing a conserved Lys residue, which has been implicated in the catalytic activity, in each case a reversible oxidative deamination reaction.
Probab=47.73 E-value=20 Score=24.74 Aligned_cols=23 Identities=26% Similarity=0.527 Sum_probs=20.3
Q ss_pred ecCCCcHHHHHHHHhcCCeecCC
Q 046522 91 VSEALPEDLQNLCEDERVQYVPP 113 (115)
Q Consensus 91 V~g~lp~~i~~~l~~~gi~y~pr 113 (115)
-++.+.++..+.|+++||.|.|.
T Consensus 32 AN~~~t~~a~~~L~~rGi~~~PD 54 (102)
T smart00839 32 ANMPLTDEADDILEDRGVLYAPD 54 (102)
T ss_pred CCCCCCHHHHHHHHHCCCEEcCc
Confidence 37788888999999999999984
No 88
>PRK05580 primosome assembly protein PriA; Validated
Probab=47.43 E-value=62 Score=29.30 Aligned_cols=29 Identities=14% Similarity=0.189 Sum_probs=16.6
Q ss_pred EeCCChhHHHHHHhcCCCCCeeeEEEecCCC
Q 046522 65 VMDPTRSWAARWLRIGRFVPGCYTLAVSEAL 95 (115)
Q Consensus 65 i~dP~~SwVAk~l~i~~~~pG~YAi~V~g~l 95 (115)
...+.--++++.++ +..||.=.+++.++.
T Consensus 434 ~~g~G~e~~~e~l~--~~fp~~~v~~~~~d~ 462 (679)
T PRK05580 434 PVGPGTERLEEELA--ELFPEARILRIDRDT 462 (679)
T ss_pred EeeccHHHHHHHHH--HhCCCCcEEEEeccc
Confidence 34556677777775 335664444555554
No 89
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=46.62 E-value=11 Score=22.25 Aligned_cols=25 Identities=16% Similarity=0.410 Sum_probs=16.0
Q ss_pred ccccCcccccchhhc---cCCCCCCCCC
Q 046522 18 ACLRCRLVKTYDQFR---ESGCENCPFF 42 (115)
Q Consensus 18 AC~~C~~I~t~~qf~---~~gCpnC~~l 42 (115)
-|..|+-++...... .--||.|++.
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~ 29 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYE 29 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCe
Confidence 478888777665431 1249999854
No 90
>COG5591 Uncharacterized conserved protein [Function unknown]
Probab=46.41 E-value=13 Score=26.71 Aligned_cols=34 Identities=21% Similarity=0.390 Sum_probs=26.2
Q ss_pred HHHHHHhcCCCCCeeeEEEecCCCcHHHHHHHHhcCC
Q 046522 72 WAARWLRIGRFVPGCYTLAVSEALPEDLQNLCEDERV 108 (115)
Q Consensus 72 wVAk~l~i~~~~pG~YAi~V~g~lp~~i~~~l~~~gi 108 (115)
|+....-|+ +|+|++.++.+.|.....-.+..|.
T Consensus 28 w~sa~afiD---dgCye~p~~~e~g~~akaKV~pqgy 61 (103)
T COG5591 28 WKSAEAFID---DGCYELPVTDENGNVAKAKVDPQGY 61 (103)
T ss_pred hhhhhheeC---CCceecccccccchHHhheeCccce
Confidence 666677777 9999999999999777666665553
No 91
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=46.16 E-value=11 Score=24.69 Aligned_cols=21 Identities=24% Similarity=0.602 Sum_probs=16.4
Q ss_pred cccccccCcccccchhhccCCCCCCC
Q 046522 15 ELRACLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 15 ~lrAC~~C~~I~t~~qf~~~gCpnC~ 40 (115)
.+|-|..|+.-.-. +.||.|+
T Consensus 4 ~~rkC~~cg~YTLk-----e~Cp~CG 24 (59)
T COG2260 4 LIRKCPKCGRYTLK-----EKCPVCG 24 (59)
T ss_pred hhhcCcCCCceeec-----ccCCCCC
Confidence 46889999987654 3599998
No 92
>cd02555 PSSA_1 PSSA_1: Pseudouridine synthase, a subgroup of the RsuA family. This group is comprised of bacterial proteins assigned to the RsuA family of pseudouridine synthases. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. The TruA family is comprised of proteins related to Escherichia coli RsuA.
Probab=45.80 E-value=83 Score=23.63 Aligned_cols=44 Identities=9% Similarity=0.054 Sum_probs=32.6
Q ss_pred ceEEEEeCCChhHHHHHHhcCCCCCeeeEEEecCCCcHHHHHHHH
Q 046522 60 NGIISVMDPTRSWAARWLRIGRFVPGCYTLAVSEALPEDLQNLCE 104 (115)
Q Consensus 60 ~G~I~i~dP~~SwVAk~l~i~~~~pG~YAi~V~g~lp~~i~~~l~ 104 (115)
+|++.+.+- ..+..+...-...++-.|-+.|.|.++++-+..|.
T Consensus 58 sGLLl~t~d-~~~~~~L~~~~~~i~K~Y~v~v~g~~~~~~l~~l~ 101 (177)
T cd02555 58 SGLLVFSQD-GRVLRKLIGDASRLEQEYLVEVRGELTAGGLERLN 101 (177)
T ss_pred eeEEEEECC-HHHHHHHhChhcCCCEEEEEEEcccCCHHHHHHHh
Confidence 799999774 45666655544558889999999999887555554
No 93
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=45.46 E-value=12 Score=23.38 Aligned_cols=23 Identities=26% Similarity=0.612 Sum_probs=16.8
Q ss_pred cccccccCcccccchhhccCCCCCCCC
Q 046522 15 ELRACLRCRLVKTYDQFRESGCENCPF 41 (115)
Q Consensus 15 ~lrAC~~C~~I~t~~qf~~~gCpnC~~ 41 (115)
.+-.|..|+-+.-... -|++||+
T Consensus 25 ~l~~c~~cg~~~~~H~----vc~~cG~ 47 (56)
T PF01783_consen 25 NLVKCPNCGEPKLPHR----VCPSCGY 47 (56)
T ss_dssp SEEESSSSSSEESTTS----BCTTTBB
T ss_pred ceeeeccCCCEecccE----eeCCCCe
Confidence 5678999997765443 4999983
No 94
>PHA02278 thioredoxin-like protein
Probab=45.38 E-value=18 Score=24.80 Aligned_cols=70 Identities=11% Similarity=0.163 Sum_probs=43.9
Q ss_pred hhccCCCCCCCCCCCCCCcccccccCCCccc--eEEEEeCCCh-----hHHHHHHhcCC------CCCeeeEEEecCCCc
Q 046522 30 QFRESGCENCPFFKMDEDHERVVDCTTPNFN--GIISVMDPTR-----SWAARWLRIGR------FVPGCYTLAVSEALP 96 (115)
Q Consensus 30 qf~~~gCpnC~~l~m~~~~d~v~~~tT~~f~--G~I~i~dP~~-----SwVAk~l~i~~------~~pG~YAi~V~g~lp 96 (115)
.|+...|+.|... .. +.+-+..... .-+..+|-++ ..+|+.++|.. |..|.--=++.|..+
T Consensus 20 ~F~A~WCgpCk~m--~p----~l~~l~~~~~~~~~~~~vdvd~~~~d~~~l~~~~~I~~iPT~i~fk~G~~v~~~~G~~~ 93 (103)
T PHA02278 20 MITQDNCGKCEIL--KS----VIPMFQESGDIKKPILTLNLDAEDVDREKAVKLFDIMSTPVLIGYKDGQLVKKYEDQVT 93 (103)
T ss_pred EEECCCCHHHHhH--HH----HHHHHHhhhcCCceEEEEECCccccccHHHHHHCCCccccEEEEEECCEEEEEEeCCCC
Confidence 4677889999832 11 1112222222 2245555543 46899999876 345665567889999
Q ss_pred HHHHHHHHh
Q 046522 97 EDLQNLCED 105 (115)
Q Consensus 97 ~~i~~~l~~ 105 (115)
.+-+.+||+
T Consensus 94 ~~~l~~~~~ 102 (103)
T PHA02278 94 PMQLQELES 102 (103)
T ss_pred HHHHHhhhc
Confidence 998888875
No 95
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=45.19 E-value=14 Score=31.58 Aligned_cols=25 Identities=32% Similarity=0.647 Sum_probs=18.9
Q ss_pred ccccccccCcccccchhhccCCCCCCC
Q 046522 14 HELRACLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 14 r~lrAC~~C~~I~t~~qf~~~gCpnC~ 40 (115)
..+.+|-.|+++....+ +--||.|+
T Consensus 213 ~~~~~C~~Cd~~~~~~~--~a~CpRC~ 237 (403)
T TIGR00155 213 LKLRSCSACHTTILPAQ--EPVCPRCS 237 (403)
T ss_pred cCCCcCCCCCCccCCCC--CcCCcCCC
Confidence 35789999999765443 23599999
No 96
>PRK02935 hypothetical protein; Provisional
Probab=45.05 E-value=11 Score=27.33 Aligned_cols=22 Identities=23% Similarity=0.439 Sum_probs=13.9
Q ss_pred CCCCCC-CCCCCCCcccccccCC
Q 046522 35 GCENCP-FFKMDEDHERVVDCTT 56 (115)
Q Consensus 35 gCpnC~-~l~m~~~~d~v~~~tT 56 (115)
.||||+ ...|-|..|..-.|-+
T Consensus 72 ~CP~C~K~TKmLGrvD~CM~C~~ 94 (110)
T PRK02935 72 ICPSCEKPTKMLGRVDACMHCNQ 94 (110)
T ss_pred ECCCCCchhhhccceeecCcCCC
Confidence 377777 6666666666665544
No 97
>cd04902 ACT_3PGDH-xct C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH). The C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with an extended C-terminal (xct) region from bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback-controlled by the end product L-serine in an allosteric manner. Some 3PGDH enzymes have an additional domain formed by an extended C-terminal region. This additional domain introduces significant asymmetry to the homotetramer. Adjacent ACT (regulatory) domains interact, creating two serine-binding sites, however, this asymmetric arrangement results in the formation of two different and distinct domain interfaces between iden
Probab=45.02 E-value=42 Score=20.16 Aligned_cols=27 Identities=15% Similarity=0.233 Sum_probs=20.5
Q ss_pred CeeeEEEecCCCcHHHHHHHHhc-CCee
Q 046522 84 PGCYTLAVSEALPEDLQNLCEDE-RVQY 110 (115)
Q Consensus 84 pG~YAi~V~g~lp~~i~~~l~~~-gi~y 110 (115)
-+.+.+.|.+..|+++.++|.+. |+.+
T Consensus 40 ~~~~~i~v~~~~~~~~~~~l~~~~~v~~ 67 (73)
T cd04902 40 EALMVLSVDEPVPDEVLEELRALPGILS 67 (73)
T ss_pred EEEEEEEeCCCCCHHHHHHHHcCCCccE
Confidence 34566678889999999999985 7654
No 98
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=44.55 E-value=8.9 Score=31.94 Aligned_cols=37 Identities=16% Similarity=0.384 Sum_probs=26.2
Q ss_pred ccccccCcccccchhhcc--CCCCCCCCCCCCCCccccc
Q 046522 16 LRACLRCRLVKTYDQFRE--SGCENCPFFKMDEDHERVV 52 (115)
Q Consensus 16 lrAC~~C~~I~t~~qf~~--~gCpnC~~l~m~~~~d~v~ 52 (115)
..-|..|+-+...+++.+ ..||+|++-.--.-++++.
T Consensus 38 w~kc~~C~~~~~~~~l~~~~~vcp~c~~h~rltAreRI~ 76 (296)
T CHL00174 38 WVQCENCYGLNYKKFLKSKMNICEQCGYHLKMSSSDRIE 76 (296)
T ss_pred eeECCCccchhhHHHHHHcCCCCCCCCCCcCCCHHHHHH
Confidence 577999999999998866 4799999422223344443
No 99
>KOG3895 consensus Synaptic vesicle protein Synapsin [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=44.51 E-value=27 Score=30.70 Aligned_cols=33 Identities=27% Similarity=0.732 Sum_probs=22.8
Q ss_pred EEEeCCChhHHHHHHhcCCCCCeeeEEEe-cCCCcH
Q 046522 63 ISVMDPTRSWAARWLRIGRFVPGCYTLAV-SEALPE 97 (115)
Q Consensus 63 I~i~dP~~SwVAk~l~i~~~~pG~YAi~V-~g~lp~ 97 (115)
++|-+|..-| ||+.+ +|++-|.|+|+| ++++.|
T Consensus 92 LVID~~H~DW-sKyFr-gkkvhgey~IrVEQaefse 125 (488)
T KOG3895|consen 92 LVIDEPHTDW-SKYFR-GKKVHGEYDIRVEQAEFSE 125 (488)
T ss_pred EEecCCcccH-HHHhc-CCccccceEEEeeecccch
Confidence 3444555455 78887 566999999999 565544
No 100
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=44.31 E-value=14 Score=31.72 Aligned_cols=27 Identities=15% Similarity=0.577 Sum_probs=19.0
Q ss_pred ccccccccCcccccchhhcc---CCCCCCC
Q 046522 14 HELRACLRCRLVKTYDQFRE---SGCENCP 40 (115)
Q Consensus 14 r~lrAC~~C~~I~t~~qf~~---~gCpnC~ 40 (115)
..+.+|..|+++.....-.. --||.|+
T Consensus 8 ~~~~~C~~Cd~l~~~~~l~~g~~a~CpRCg 37 (419)
T PRK15103 8 AKHILCPQCDMLVALPRLEHGQKAACPRCG 37 (419)
T ss_pred CCcccCCCCCceeecCCCCCCCeeECCCCC
Confidence 35689999999986442211 2499999
No 101
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=44.25 E-value=11 Score=31.75 Aligned_cols=20 Identities=25% Similarity=0.780 Sum_probs=15.3
Q ss_pred ccccCcccccchhhccCCCCCCC
Q 046522 18 ACLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 18 AC~~C~~I~t~~qf~~~gCpnC~ 40 (115)
-|..|++.-+ +|.. .||+|+
T Consensus 2 ~c~~cg~~~~--~~~g-~cp~c~ 21 (372)
T cd01121 2 VCSECGYVSP--KWLG-KCPECG 21 (372)
T ss_pred CCCCCCCCCC--CccE-ECcCCC
Confidence 5999999876 4432 499998
No 102
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=43.89 E-value=9.7 Score=22.11 Aligned_cols=22 Identities=23% Similarity=0.483 Sum_probs=11.9
Q ss_pred cccCcccccchhhc---cCCCCCCC
Q 046522 19 CLRCRLVKTYDQFR---ESGCENCP 40 (115)
Q Consensus 19 C~~C~~I~t~~qf~---~~gCpnC~ 40 (115)
|.+|+-.+....+. -+.||+|+
T Consensus 2 CP~C~~~l~~~~~~~~~id~C~~C~ 26 (41)
T PF13453_consen 2 CPRCGTELEPVRLGDVEIDVCPSCG 26 (41)
T ss_pred cCCCCcccceEEECCEEEEECCCCC
Confidence 55565554444332 24688887
No 103
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=43.71 E-value=14 Score=20.65 Aligned_cols=25 Identities=20% Similarity=0.279 Sum_probs=15.8
Q ss_pred ccccccCcccccchhh----ccCCCCCCC
Q 046522 16 LRACLRCRLVKTYDQF----RESGCENCP 40 (115)
Q Consensus 16 lrAC~~C~~I~t~~qf----~~~gCpnC~ 40 (115)
.-.|..|+...+..+- ....||.|+
T Consensus 5 ~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg 33 (41)
T smart00834 5 EYRCEDCGHTFEVLQKISDDPLATCPECG 33 (41)
T ss_pred EEEcCCCCCEEEEEEecCCCCCCCCCCCC
Confidence 3468999985543321 123699998
No 104
>PF11922 DUF3440: Domain of unknown function (DUF3440); InterPro: IPR021845 This presumed domain is functionally uncharacterised. This domain is found in bacteria. This domain is typically between 53 to 190 amino acids in length. This domain is found associated with PF01507 from PFAM. This domain has a conserved KND sequence motif.
Probab=43.19 E-value=20 Score=28.18 Aligned_cols=19 Identities=16% Similarity=0.274 Sum_probs=17.1
Q ss_pred CCCcHHHHHHHHhcCCeec
Q 046522 93 EALPEDLQNLCEDERVQYV 111 (115)
Q Consensus 93 g~lp~~i~~~l~~~gi~y~ 111 (115)
|.||++.+++|+++|+...
T Consensus 102 ~~lpde~i~~L~~~~~~~~ 120 (181)
T PF11922_consen 102 GCLPDETIQELEEAGIPIE 120 (181)
T ss_pred CCCCHHHHHHHHhcCCcee
Confidence 8999999999999988754
No 105
>PF11823 DUF3343: Protein of unknown function (DUF3343); InterPro: IPR021778 This family of proteins are functionally uncharacterised. This protein is found in bacteria and archaea. Proteins in this family are typically between 78 to 102 amino acids in length.
Probab=43.09 E-value=29 Score=22.23 Aligned_cols=25 Identities=16% Similarity=0.335 Sum_probs=22.6
Q ss_pred eEEEecCCCcHHHHHHHHhcCCeec
Q 046522 87 YTLAVSEALPEDLQNLCEDERVQYV 111 (115)
Q Consensus 87 YAi~V~g~lp~~i~~~l~~~gi~y~ 111 (115)
+||++..+--+.+.+.|+++||.|.
T Consensus 43 ~al~~~~~d~~~i~~~l~~~~i~~~ 67 (73)
T PF11823_consen 43 LALRFEPEDLEKIKEILEENGIEYE 67 (73)
T ss_pred EEEEEChhhHHHHHHHHHHCCCCee
Confidence 7899999999999999999999874
No 106
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=42.71 E-value=9.7 Score=31.28 Aligned_cols=26 Identities=19% Similarity=0.531 Sum_probs=21.7
Q ss_pred ccccccCcccccchhhcc--CCCCCCCC
Q 046522 16 LRACLRCRLVKTYDQFRE--SGCENCPF 41 (115)
Q Consensus 16 lrAC~~C~~I~t~~qf~~--~gCpnC~~ 41 (115)
...|-.|+-++..+++.+ ..||+|++
T Consensus 26 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~ 53 (285)
T TIGR00515 26 WTKCPKCGQVLYTKELERNLEVCPKCDH 53 (285)
T ss_pred eeECCCCcchhhHHHHHhhCCCCCCCCC
Confidence 578999999998887755 47999993
No 107
>cd02870 PseudoU_synth_RsuA_like Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA. The RsuA subfamily includes Pseudouridine Synthase similar to Ribosomal small subunit pseudouridine 516 synthase. Most of the proteins in this family are bacterial proteins.
Probab=42.48 E-value=1.2e+02 Score=21.45 Aligned_cols=47 Identities=17% Similarity=0.130 Sum_probs=32.4
Q ss_pred ceEEEEeCCChhHHHHHHhcCCCCCeeeEEEecCCCcHHHHHHHHhcCC
Q 046522 60 NGIISVMDPTRSWAARWLRIGRFVPGCYTLAVSEALPEDLQNLCEDERV 108 (115)
Q Consensus 60 ~G~I~i~dP~~SwVAk~l~i~~~~pG~YAi~V~g~lp~~i~~~l~~~gi 108 (115)
+|+|.+.+-. .+..+...-+..+.-.|-+.|.|.++++....+. .|+
T Consensus 45 sGlll~ak~~-~~~~~l~~~~~~i~K~Y~a~v~g~~~~~~~~~~~-~~~ 91 (146)
T cd02870 45 EGLLLLTNDG-ELANRLTHPRYGVEKTYLVKVRGVPSEEELRRLR-AGV 91 (146)
T ss_pred eeEEEEeCCH-HHHHHhhCccCCCCeEEEEEECCCCCHHHHHHHH-CCe
Confidence 7999987653 3344444433457889999999999987766654 444
No 108
>COG4279 Uncharacterized conserved protein [Function unknown]
Probab=42.34 E-value=7.6 Score=32.07 Aligned_cols=27 Identities=19% Similarity=0.448 Sum_probs=23.1
Q ss_pred eEEE-ecCCCcHHHHHHHHhcCCeecCC
Q 046522 87 YTLA-VSEALPEDLQNLCEDERVQYVPP 113 (115)
Q Consensus 87 YAi~-V~g~lp~~i~~~l~~~gi~y~pr 113 (115)
||-+ ..|++|++|++.+-+.|+.-.|.
T Consensus 91 ~aakLL~gemP~sIedvf~~~GL~LfP~ 118 (266)
T COG4279 91 YAAKLLSGEMPESIEDVFVGNGLSLFPF 118 (266)
T ss_pred HHHHHhcCCCCchHHHHHHhcCcccCCC
Confidence 4444 48999999999999999999886
No 109
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=41.23 E-value=6.2 Score=22.69 Aligned_cols=24 Identities=21% Similarity=0.551 Sum_probs=11.3
Q ss_pred cccccCcccccchhhccCC---CCCCCC
Q 046522 17 RACLRCRLVKTYDQFRESG---CENCPF 41 (115)
Q Consensus 17 rAC~~C~~I~t~~qf~~~g---CpnC~~ 41 (115)
+-|..|+=++-...= +.+ |++|++
T Consensus 2 ~FCp~C~nlL~p~~~-~~~~~~C~~C~Y 28 (35)
T PF02150_consen 2 RFCPECGNLLYPKED-KEKRVACRTCGY 28 (35)
T ss_dssp -BETTTTSBEEEEEE-TTTTEEESSSS-
T ss_pred eeCCCCCccceEcCC-CccCcCCCCCCC
Confidence 446666655544321 123 777763
No 110
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=40.92 E-value=12 Score=27.47 Aligned_cols=22 Identities=23% Similarity=0.558 Sum_probs=9.6
Q ss_pred ccccCcccccchhhccCCCCCCC
Q 046522 18 ACLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 18 AC~~C~~I~t~~qf~~~gCpnC~ 40 (115)
-|.+|+-..-.=- +.+.|..|+
T Consensus 71 ~CP~C~K~TKmLG-r~D~CM~C~ 92 (114)
T PF11023_consen 71 ECPNCGKQTKMLG-RVDACMHCK 92 (114)
T ss_pred ECCCCCChHhhhc-hhhccCcCC
Confidence 3666665431100 113466665
No 111
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=40.73 E-value=16 Score=30.97 Aligned_cols=27 Identities=30% Similarity=0.511 Sum_probs=17.7
Q ss_pred ccccccccCcccccchhh--ccCCCCCCC
Q 046522 14 HELRACLRCRLVKTYDQF--RESGCENCP 40 (115)
Q Consensus 14 r~lrAC~~C~~I~t~~qf--~~~gCpnC~ 40 (115)
.++.-|.+|++..+.+-= ..+-||+|+
T Consensus 313 ~k~nfc~ncG~~~t~~~~ng~a~fcp~cg 341 (345)
T COG4260 313 AKLNFCLNCGCGTTADFDNGKAKFCPECG 341 (345)
T ss_pred cccccccccCcccccCCccchhhhChhhc
Confidence 356789999987776310 113499997
No 112
>TIGR03769 P_ac_wall_RPT actinobacterial surface-anchored protein domain. This model describes a repeat domain that one to three times in Actinobacterial proteins, some of which have LPXTG-type sortase recognition motifs for covalent attachment to the Gram-positive cell wall. Where it occurs with duplication in an LPXTG-anchored protein, it tends to be adjacent to the substrate-binding protein of the gene trio of an ABC transporter system, where that substrate-binding protein has a single copy of this same domain. This arrangement suggests a substrate-binding relay system, with the LPXTG protein acting as a substrate receptor.
Probab=40.33 E-value=20 Score=21.28 Aligned_cols=11 Identities=55% Similarity=0.924 Sum_probs=9.3
Q ss_pred CCeeeEEEecC
Q 046522 83 VPGCYTLAVSE 93 (115)
Q Consensus 83 ~pG~YAi~V~g 93 (115)
.||.|.|.++.
T Consensus 11 ~PG~Y~l~~~a 21 (41)
T TIGR03769 11 KPGTYTLTVQA 21 (41)
T ss_pred CCeEEEEEEEE
Confidence 59999999854
No 113
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=39.81 E-value=17 Score=23.20 Aligned_cols=22 Identities=27% Similarity=0.543 Sum_probs=13.2
Q ss_pred cccccccCcccccchhhccCCCCCCC
Q 046522 15 ELRACLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 15 ~lrAC~~C~~I~t~~qf~~~gCpnC~ 40 (115)
.+-.|..|+-.+-.-. -||+|+
T Consensus 26 ~l~~C~~CG~~~~~H~----vC~~CG 47 (57)
T PRK12286 26 GLVECPNCGEPKLPHR----VCPSCG 47 (57)
T ss_pred cceECCCCCCccCCeE----ECCCCC
Confidence 3556777776554332 377777
No 114
>PRK06764 hypothetical protein; Provisional
Probab=39.36 E-value=20 Score=25.51 Aligned_cols=17 Identities=29% Similarity=0.514 Sum_probs=13.7
Q ss_pred CCCeeeEEEecCCCcHH
Q 046522 82 FVPGCYTLAVSEALPED 98 (115)
Q Consensus 82 ~~pG~YAi~V~g~lp~~ 98 (115)
..||.|-|+|+|-+=+|
T Consensus 81 ~kpg~yvirvngciy~d 97 (105)
T PRK06764 81 SKPGKYVIRVNGCIYND 97 (105)
T ss_pred cCCccEEEEEccEEeee
Confidence 47999999999976544
No 115
>COG4357 Zinc finger domain containing protein (CHY type) [Function unknown]
Probab=38.94 E-value=14 Score=26.68 Aligned_cols=27 Identities=22% Similarity=0.501 Sum_probs=22.7
Q ss_pred ccccccccCcccccchhhcc-CCCCCCC
Q 046522 14 HELRACLRCRLVKTYDQFRE-SGCENCP 40 (115)
Q Consensus 14 r~lrAC~~C~~I~t~~qf~~-~gCpnC~ 40 (115)
.+.--|-.|+-.+|.+++.. .-||||.
T Consensus 60 ~~~iiCGvC~~~LT~~EY~~~~~Cp~C~ 87 (105)
T COG4357 60 PKAIICGVCRKLLTRAEYGMCGSCPYCQ 87 (105)
T ss_pred CccEEhhhhhhhhhHHHHhhcCCCCCcC
Confidence 35678999999999999875 5699998
No 116
>cd02948 TRX_NDPK TRX domain, TRX and NDP-kinase (NDPK) fusion protein family; most members of this group are fusion proteins which contain one redox active TRX domain containing a CXXC motif and three NDPK domains, and are characterized as intermediate chains (ICs) of axonemal outer arm dynein. Dyneins are molecular motors that generate force against microtubules to produce cellular movement, and are divided into two classes: axonemal and cytoplasmic. They are supramolecular complexes consisting of three protein groups classified according to size: dynein heavy, intermediate and light chains. Axonemal dyneins form two structures, the inner and outer arms, which are attached to doublet microtubules throughout the cilia and flagella. The human homolog is the sperm-specific Sptrx-2, presumed to be a component of the human sperm axoneme architecture. Included in this group is another human protein, TRX-like protein 2, a smaller fusion protein containing one TRX and one NDPK domain, which
Probab=38.82 E-value=27 Score=23.13 Aligned_cols=68 Identities=10% Similarity=0.094 Sum_probs=40.8
Q ss_pred hhccCCCCCCC-CCCCCCCcccccccCCCccc--e-EEEEeCCChhHHHHHHhcCCCCC-------eeeEEEecCCCcHH
Q 046522 30 QFRESGCENCP-FFKMDEDHERVVDCTTPNFN--G-IISVMDPTRSWAARWLRIGRFVP-------GCYTLAVSEALPED 98 (115)
Q Consensus 30 qf~~~gCpnC~-~l~m~~~~d~v~~~tT~~f~--G-~I~i~dP~~SwVAk~l~i~~~~p-------G~YAi~V~g~lp~~ 98 (115)
.|+...|+.|. +.. +.+-....|. . .++.+|-+..-+|+.+++.. +| |.---++.|.-|++
T Consensus 23 ~F~a~wC~~Ck~~~p-------~l~~~~~~~~~~~~~~~~vd~d~~~~~~~~~v~~-~Pt~~~~~~g~~~~~~~G~~~~~ 94 (102)
T cd02948 23 DVYQEWCGPCKAVVS-------LFKKIKNELGDDLLHFATAEADTIDTLKRYRGKC-EPTFLFYKNGELVAVIRGANAPL 94 (102)
T ss_pred EEECCcCHhHHHHhH-------HHHHHHHHcCCCcEEEEEEeCCCHHHHHHcCCCc-CcEEEEEECCEEEEEEecCChHH
Confidence 46777899998 221 1111233443 2 35555665677888888776 44 54444566667777
Q ss_pred HHHHHHh
Q 046522 99 LQNLCED 105 (115)
Q Consensus 99 i~~~l~~ 105 (115)
+.+.+++
T Consensus 95 ~~~~i~~ 101 (102)
T cd02948 95 LNKTITE 101 (102)
T ss_pred HHHHHhh
Confidence 7776653
No 117
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=38.35 E-value=14 Score=36.01 Aligned_cols=87 Identities=15% Similarity=0.337 Sum_probs=57.7
Q ss_pred cccccccCcccccchhhccCCCCCCCCCCCCCCccccc--ccCCCccceEEEEeCCCh-----hH-HHHHHhcCCCCCee
Q 046522 15 ELRACLRCRLVKTYDQFRESGCENCPFFKMDEDHERVV--DCTTPNFNGIISVMDPTR-----SW-AARWLRIGRFVPGC 86 (115)
Q Consensus 15 ~lrAC~~C~~I~t~~qf~~~gCpnC~~l~m~~~~d~v~--~~tT~~f~G~I~i~dP~~-----Sw-VAk~l~i~~~~pG~ 86 (115)
..+-|+.|+...+.++ +-||+|+.....+..+.+. --...+-+=+++=.||+. .| |+-.+ .-+.|-.
T Consensus 693 tIKrC~dcg~q~~~~~---~~cP~Cgs~~v~d~~~~ve~lRelA~EvDeVlIgTDPDtEGEKIawDv~~~l--~Py~~ni 767 (1187)
T COG1110 693 TIKRCRDCGEQFVDSE---DKCPRCGSRNVEDKTETVEALRELALEVDEILIGTDPDTEGEKIAWDVFNYL--RPYNPNV 767 (1187)
T ss_pred HHHHHhhcCceecccc---ccCCCCCCccccccHHHHHHHHHHHhhcCEEEEcCCCCCccchhHHHHHHhh--CcCCCce
Confidence 4688999999888774 4699999543333332211 112334455666678864 23 33334 3568999
Q ss_pred eEEEecCCCcHHHHHHHHhc
Q 046522 87 YTLAVSEALPEDLQNLCEDE 106 (115)
Q Consensus 87 YAi~V~g~lp~~i~~~l~~~ 106 (115)
|-+.-..-=+.-|.++|++.
T Consensus 768 kR~eFHEVTrrAIleAl~n~ 787 (1187)
T COG1110 768 KRIEFHEVTRRAILEALKNP 787 (1187)
T ss_pred eEEEeeeecHHHHHHHHhCc
Confidence 99998888888899988864
No 118
>PF03433 EspA: EspA-like secreted protein ; InterPro: IPR005095 EspA is the prototypical member of this family. EspA, together with EspB, EspD and Tir are exported by a type III secretion system. These proteins are essential for attaching and effacing lesion formation. EspA is a structural protein and a major component of a large, transiently expressed, filamentous surface organelle which forms a direct link between the bacterium and the host cell [, ].; PDB: 1XOU_A.
Probab=38.04 E-value=11 Score=29.76 Aligned_cols=21 Identities=19% Similarity=0.458 Sum_probs=0.0
Q ss_pred EecCCCcHHHHHHHHhcCCee
Q 046522 90 AVSEALPEDLQNLCEDERVQY 110 (115)
Q Consensus 90 ~V~g~lp~~i~~~l~~~gi~y 110 (115)
+....||+|+++.|+++||..
T Consensus 94 k~k~~lp~dVi~Ym~~ngI~V 114 (188)
T PF03433_consen 94 KAKAPLPDDVIDYMRDNGIKV 114 (188)
T ss_dssp ---------------------
T ss_pred cccccCCHHHHHHHHHcCCee
Confidence 467899999999999999974
No 119
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=37.74 E-value=28 Score=21.85 Aligned_cols=29 Identities=17% Similarity=0.388 Sum_probs=17.3
Q ss_pred ccccccccCcccccch---hh--ccCCCCCCCCC
Q 046522 14 HELRACLRCRLVKTYD---QF--RESGCENCPFF 42 (115)
Q Consensus 14 r~lrAC~~C~~I~t~~---qf--~~~gCpnC~~l 42 (115)
|.-.-|.+|+..--.. .| ..-.||+|+++
T Consensus 20 r~aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 20 RYALICSKCFSHNGLAPKEEFEEIQYRCPYCGAL 53 (54)
T ss_pred ceeEECcccchhhcccccccCCceEEEcCCCCCc
Confidence 5667799997643222 11 11259999853
No 120
>PRK05580 primosome assembly protein PriA; Validated
Probab=37.67 E-value=7.7 Score=35.02 Aligned_cols=34 Identities=21% Similarity=0.339 Sum_probs=20.6
Q ss_pred CCCCCCCCCC---CCCcccccccCCCccceE-EEEeCC
Q 046522 35 GCENCPFFKM---DEDHERVVDCTTPNFNGI-ISVMDP 68 (115)
Q Consensus 35 gCpnC~~l~m---~~~~d~v~~~tT~~f~G~-I~i~dP 68 (115)
.||+|+...+ .-..+++.+.....|-|. |..+|-
T Consensus 423 ~Cp~Cg~~~l~~~g~G~e~~~e~l~~~fp~~~v~~~~~ 460 (679)
T PRK05580 423 ACPECGSTDLVPVGPGTERLEEELAELFPEARILRIDR 460 (679)
T ss_pred CCCCCcCCeeEEeeccHHHHHHHHHHhCCCCcEEEEec
Confidence 5888873322 235667777777777764 444553
No 121
>TIGR02620 cas_VVA1548 putative CRISPR-associated protein, VVA1548 family. This model represents a conserved domain of about 95 amino acids exclusively in species with CRISPR (Clustered Regularly Interspaced Short Palidromic Repeats). In all bacterial species with members so far (Vibrio vulnificus YJ016, Mannheimia succiniciproducens MBEL55E, and Nitrosomonas europaea ATCC 19718) and but not in the archaeon Methanothermobacter thermautotrophicus str. Delta H, the gene for this protein is in the midst of a cluster of Cas protein gene near CRISPR repeats.
Probab=37.61 E-value=31 Score=24.42 Aligned_cols=22 Identities=23% Similarity=0.256 Sum_probs=20.5
Q ss_pred EecCCCcHHHHHHHHhcCCeec
Q 046522 90 AVSEALPEDLQNLCEDERVQYV 111 (115)
Q Consensus 90 ~V~g~lp~~i~~~l~~~gi~y~ 111 (115)
+|-|.||-.+..++-++|..|.
T Consensus 37 ~ViGtLPv~Laa~vc~kGa~y~ 58 (93)
T TIGR02620 37 KVIGTLPVSLAADICKKGARYF 58 (93)
T ss_pred EEEEeCCHHHHHHHHhCCcEEE
Confidence 7899999999999999999884
No 122
>KOG2324 consensus Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=37.60 E-value=17 Score=31.92 Aligned_cols=87 Identities=22% Similarity=0.432 Sum_probs=52.4
Q ss_pred cccccccCcccccchhhccC---CCCCCCCCCCCCCcccccccCCCccceEEEEeCCChhHH--HHHHhcCCCCC-----
Q 046522 15 ELRACLRCRLVKTYDQFRES---GCENCPFFKMDEDHERVVDCTTPNFNGIISVMDPTRSWA--ARWLRIGRFVP----- 84 (115)
Q Consensus 15 ~lrAC~~C~~I~t~~qf~~~---gCpnC~~l~m~~~~d~v~~~tT~~f~G~I~i~dP~~SwV--Ak~l~i~~~~p----- 84 (115)
.+.-|.+|++-+..+.+... .||+|.... + .-|+.-=-|-+-++-.+-|-. |+..+... .|
T Consensus 226 ~l~~C~~C~~s~n~e~~~~sk~~~Cp~C~~~~-------L-~~~~~IEVgHtF~LG~kYS~~lna~f~~~~g-Kpe~l~M 296 (457)
T KOG2324|consen 226 TLMSCPSCGYSKNSEDLDLSKIASCPKCNEGR-------L-TKTKSIEVGHTFLLGTKYSKPLNAKFVNVEG-KPEFLHM 296 (457)
T ss_pred ceeecCcCCccCchhhhcCCccccCCcccCCC-------c-ccccceEEEEEEEeccccccccCceeeeecC-CcceEEe
Confidence 57889999999988877554 599997211 1 123333345555554444432 44333332 45
Q ss_pred eeeEEEecCCCcHHHHHHHHhcCCee
Q 046522 85 GCYTLAVSEALPEDLQNLCEDERVQY 110 (115)
Q Consensus 85 G~YAi~V~g~lp~~i~~~l~~~gi~y 110 (115)
|+|-|-|+.-|+--+.-.=-++|.+|
T Consensus 297 gCyGIGVtRllaAa~evls~~~~lrw 322 (457)
T KOG2324|consen 297 GCYGIGVTRLLAAAAEVLSDDKGLRW 322 (457)
T ss_pred cceeccHHHHHHHHHHHhcccccccc
Confidence 99999998877765543333446554
No 123
>PRK11823 DNA repair protein RadA; Provisional
Probab=37.45 E-value=20 Score=30.73 Aligned_cols=24 Identities=17% Similarity=0.310 Sum_probs=18.1
Q ss_pred ccccccccCcccccchhhccCCCCCCC
Q 046522 14 HELRACLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 14 r~lrAC~~C~~I~t~~qf~~~gCpnC~ 40 (115)
+...-|..|++-...=+| .||.|+
T Consensus 5 ~~~y~C~~Cg~~~~~~~g---~Cp~C~ 28 (446)
T PRK11823 5 KTAYVCQECGAESPKWLG---RCPECG 28 (446)
T ss_pred CCeEECCcCCCCCcccCe---eCcCCC
Confidence 456779999998664443 399998
No 124
>COG1400 SEC65 Signal recognition particle 19 kDa protein [Intracellular trafficking and secretion]
Probab=37.34 E-value=27 Score=24.58 Aligned_cols=30 Identities=17% Similarity=0.191 Sum_probs=23.0
Q ss_pred CCeeeEEEecCCCcHHHHHHHHhcCCee-cCCC
Q 046522 83 VPGCYTLAVSEALPEDLQNLCEDERVQY-VPPK 114 (115)
Q Consensus 83 ~pG~YAi~V~g~lp~~i~~~l~~~gi~y-~prd 114 (115)
+|=.+| |.--..++|.+.|++.|+.| +++|
T Consensus 23 vpk~la--V~~P~~~ei~~a~~~LGl~~~v~~d 53 (93)
T COG1400 23 VPKELA--VENPSLEEIAEALRELGLKPKVERD 53 (93)
T ss_pred cchhhc--ccCCCHHHHHHHHHHcCCCeeechh
Confidence 444444 45667899999999999999 6666
No 125
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=36.96 E-value=19 Score=29.75 Aligned_cols=28 Identities=21% Similarity=0.380 Sum_probs=19.7
Q ss_pred CccccccccCcccccchhhcc---CCCCCCC
Q 046522 13 GHELRACLRCRLVKTYDQFRE---SGCENCP 40 (115)
Q Consensus 13 ~r~lrAC~~C~~I~t~~qf~~---~gCpnC~ 40 (115)
.|.-..|..|+-+.....+.. --||+|+
T Consensus 242 gR~GepC~~CGt~I~k~~~~gR~t~~CP~CQ 272 (273)
T COG0266 242 GRAGEPCRRCGTPIEKIKLGGRSTFYCPVCQ 272 (273)
T ss_pred cCCCCCCCccCCEeEEEEEcCCcCEeCCCCC
Confidence 345678999998877665433 1399996
No 126
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=36.76 E-value=20 Score=30.97 Aligned_cols=24 Identities=21% Similarity=0.320 Sum_probs=18.2
Q ss_pred ccccccccCcccccchhhccCCCCCCC
Q 046522 14 HELRACLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 14 r~lrAC~~C~~I~t~~qf~~~gCpnC~ 40 (115)
|....|..|++--..=.| .||.|+
T Consensus 5 ~~~y~C~~Cg~~~~~~~g---~Cp~C~ 28 (454)
T TIGR00416 5 KSKFVCQHCGADSPKWQG---KCPACH 28 (454)
T ss_pred CCeEECCcCCCCCccccE---ECcCCC
Confidence 456789999997664443 399999
No 127
>PF03990 DUF348: Domain of unknown function (DUF348) ; InterPro: IPR007137 This domain normally occurs as tandem repeats; however it is found as a single copy in the Saccharomyces cerevisiae (Baker's yeast) DNA-binding nuclear protein YCR593 (P25357 from SWISSPROT).
Probab=35.95 E-value=27 Score=20.46 Aligned_cols=21 Identities=0% Similarity=0.028 Sum_probs=17.0
Q ss_pred CcHHHHHHHHhcCCeecCCCC
Q 046522 95 LPEDLQNLCEDERVQYVPPKR 115 (115)
Q Consensus 95 lp~~i~~~l~~~gi~y~prd~ 115 (115)
....+.+.|++.||.+.+.|+
T Consensus 16 ~a~tV~~~L~~~gI~l~~~D~ 36 (43)
T PF03990_consen 16 TASTVGDALKELGITLGEEDK 36 (43)
T ss_pred CCCCHHHHHHhCCCCCCCCCE
Confidence 345678899999999988874
No 128
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=35.35 E-value=43 Score=25.88 Aligned_cols=43 Identities=21% Similarity=0.309 Sum_probs=25.3
Q ss_pred CCChhHHHHHHhcCCCCCeeeEEEec-CCCcHHHHHHHHhcCCeecCCC
Q 046522 67 DPTRSWAARWLRIGRFVPGCYTLAVS-EALPEDLQNLCEDERVQYVPPK 114 (115)
Q Consensus 67 dP~~SwVAk~l~i~~~~pG~YAi~V~-g~lp~~i~~~l~~~gi~y~prd 114 (115)
|--=-|+||||||-. |...+. ..-+++|+......|.-..-||
T Consensus 12 D~mLG~LARwLRllG-----ydt~~~~~~~d~~i~~i~~~e~rIllTRD 55 (165)
T COG1656 12 DAMLGKLARWLRLLG-----YDTVYSSNESDDEIILIAKKEGRILLTRD 55 (165)
T ss_pred HHhHHHHHHHHHHcC-----CceeeeccCCcHHHHHHHhcCCeEEEecc
Confidence 444468999999875 444433 3445555555555565555555
No 129
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=35.24 E-value=25 Score=20.64 Aligned_cols=25 Identities=16% Similarity=0.324 Sum_probs=14.4
Q ss_pred ccccccCcccc----cchhhccCCCCCCC
Q 046522 16 LRACLRCRLVK----TYDQFRESGCENCP 40 (115)
Q Consensus 16 lrAC~~C~~I~----t~~qf~~~gCpnC~ 40 (115)
.-.|..|+-.- +..+-....||.|+
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg 33 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSISEDDPVPCPECG 33 (42)
T ss_pred EEEeCCCCCEEEEEEEcCCCCCCcCCCCC
Confidence 35688898332 22221124699998
No 130
>KOG3084 consensus NADH pyrophosphatase I of the Nudix family of hydrolases [Replication, recombination and repair]
Probab=35.06 E-value=37 Score=29.06 Aligned_cols=73 Identities=16% Similarity=0.299 Sum_probs=43.5
Q ss_pred CCCCCC---CCCCCCCccccc--ccCCC-----ccceEE--EEeCCChhH--HHHHHhcCCCCCeeeEE-----EecCCC
Q 046522 35 GCENCP---FFKMDEDHERVV--DCTTP-----NFNGII--SVMDPTRSW--AARWLRIGRFVPGCYTL-----AVSEAL 95 (115)
Q Consensus 35 gCpnC~---~l~m~~~~d~v~--~~tT~-----~f~G~I--~i~dP~~Sw--VAk~l~i~~~~pG~YAi-----~V~g~l 95 (115)
-||-|+ +-.+.|...... .|++. .++=+| .|++|+.+- .+| -..+.||+|+. .+...+
T Consensus 152 FCp~CG~~tkp~e~g~k~~Cs~~~C~~~n~~yPr~dPvVIm~li~~d~~~~LL~R---~~r~~~gl~t~lAGFlEpGES~ 228 (345)
T KOG3084|consen 152 FCPGCGSPTKPEEAGTKLQCSDETCPSCNVIYPRTDPVVIMLLIDHDGKHALLGR---QKRYPPGLWTCLAGFLEPGESI 228 (345)
T ss_pred cCcccCCCcccccCCccceeecccCCcCCeeccCCCCeEEEEEEcCCCCEeeeec---ccCCCCchhhhhhccCCccccH
Confidence 477777 445555555555 56542 233333 457887653 344 23578999985 456666
Q ss_pred cHHHHHHHHhc-CCee
Q 046522 96 PEDLQNLCEDE-RVQY 110 (115)
Q Consensus 96 p~~i~~~l~~~-gi~y 110 (115)
-|-++.|-.+. ||..
T Consensus 229 eeav~REtwEEtGi~V 244 (345)
T KOG3084|consen 229 EEAVRRETWEETGIEV 244 (345)
T ss_pred HHHHHHHHHHHhCcee
Confidence 67666666554 8764
No 131
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=35.00 E-value=18 Score=31.49 Aligned_cols=42 Identities=19% Similarity=0.313 Sum_probs=23.4
Q ss_pred cccccCcccccchhhccCCCCCCCCCCCC---CCcccccccCCCccceE
Q 046522 17 RACLRCRLVKTYDQFRESGCENCPFFKMD---EDHERVVDCTTPNFNGI 62 (115)
Q Consensus 17 rAC~~C~~I~t~~qf~~~gCpnC~~l~m~---~~~d~v~~~tT~~f~G~ 62 (115)
.-|-.|+...... ..||+|+...+. -+.+++.+.....|-|.
T Consensus 241 l~Ch~Cg~~~~~~----~~Cp~C~s~~l~~~g~Gte~~~e~l~~~fp~~ 285 (505)
T TIGR00595 241 LRCHYCGYQEPIP----KTCPQCGSEDLVYKGYGTEQVEEELAKLFPGA 285 (505)
T ss_pred EEcCCCcCcCCCC----CCCCCCCCCeeEeecccHHHHHHHHHhhCCCC
Confidence 3455555444322 358999843222 24567777777777663
No 132
>PF09124 Endonuc-dimeris: T4 recombination endonuclease VII, dimerisation; InterPro: IPR015208 This entry represents a dimerisation domain predominantly found in Bacteriophage T4 recombination endonuclease VII. It adopts a helical secondary structure, with three alpha helices oriented parallel to each other. As well as mediating dimerisation of the protein, this domain is also involved in binding to the DNA major groove []. ; PDB: 1EN7_B 1E7L_B 2QNF_A 2QNC_A 1E7D_A.
Probab=34.73 E-value=35 Score=21.85 Aligned_cols=19 Identities=5% Similarity=0.093 Sum_probs=12.1
Q ss_pred HHHHHHHHhcCCeecCCCC
Q 046522 97 EDLQNLCEDERVQYVPPKR 115 (115)
Q Consensus 97 ~~i~~~l~~~gi~y~prd~ 115 (115)
+|.+.+|.+.|+.|-+-|+
T Consensus 19 ~eMiaem~~~G~~y~~~~t 37 (54)
T PF09124_consen 19 PEMIAEMDSYGFEYNEKDT 37 (54)
T ss_dssp HHHHHHHHHTT----TTS-
T ss_pred HHHHHHHHHhCCcCCcccc
Confidence 5789999999999987664
No 133
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=34.64 E-value=18 Score=24.24 Aligned_cols=23 Identities=26% Similarity=0.569 Sum_probs=10.6
Q ss_pred cccccccCcccccc--hhhccCCCCCCCC
Q 046522 15 ELRACLRCRLVKTY--DQFRESGCENCPF 41 (115)
Q Consensus 15 ~lrAC~~C~~I~t~--~qf~~~gCpnC~~ 41 (115)
-..-|..|-.+... .+| ||+||.
T Consensus 8 ~vlrC~aCf~~t~~~~k~F----Cp~CGn 32 (73)
T PF08772_consen 8 WVLRCHACFKITKDMTKQF----CPKCGN 32 (73)
T ss_dssp EEEE-SSS--EES-SS--S-----SSS--
T ss_pred eeEEccccccCcCCCCcee----CcccCC
Confidence 34668889888763 355 999993
No 134
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]
Probab=34.63 E-value=30 Score=25.49 Aligned_cols=27 Identities=30% Similarity=0.764 Sum_probs=20.7
Q ss_pred ccceEEEEeCCCh--hHHHHHHhcCCCCCee
Q 046522 58 NFNGIISVMDPTR--SWAARWLRIGRFVPGC 86 (115)
Q Consensus 58 ~f~G~I~i~dP~~--SwVAk~l~i~~~~pG~ 86 (115)
.+.|+|+++||+. +-++||+- .+.||.
T Consensus 54 ~~k~VIILTD~D~~Ge~Irk~l~--~~l~~~ 82 (127)
T COG1658 54 KYKGVIILTDPDRKGERIRKKLK--EYLPGA 82 (127)
T ss_pred ccCCEEEEeCCCcchHHHHHHHH--HHhccc
Confidence 6999999999987 67888774 345553
No 135
>KOG4020 consensus Protein DRE2, required for cell viability [Function unknown]
Probab=34.62 E-value=24 Score=28.98 Aligned_cols=32 Identities=28% Similarity=0.502 Sum_probs=21.3
Q ss_pred CCCCCccccccccCcccccchhh-----------ccCCCCCCC
Q 046522 9 PTSFGHELRACLRCRLVKTYDQF-----------RESGCENCP 40 (115)
Q Consensus 9 p~~~~r~lrAC~~C~~I~t~~qf-----------~~~gCpnC~ 40 (115)
+.+..++-|||.+|.-=+-+++. ...+|-||-
T Consensus 181 ~~~~~kKkkaCk~CtcGl~Ee~E~Eks~~q~s~~~~s~CGnCy 223 (257)
T KOG4020|consen 181 SCSPGKKKKACKNCTCGLAEEEEKEKSREQISSNPKSACGNCY 223 (257)
T ss_pred CCCCcccchhhhcCCcccHHHHHhhhhhhhhccCcccccCccc
Confidence 34445778999999765554433 124799996
No 136
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=34.59 E-value=19 Score=32.79 Aligned_cols=23 Identities=13% Similarity=0.346 Sum_probs=17.0
Q ss_pred ccccccccCcccccchhhccCCCCCCC
Q 046522 14 HELRACLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 14 r~lrAC~~C~~I~t~~qf~~~gCpnC~ 40 (115)
.++--|..|+++. ...| .||+|+
T Consensus 624 ~~~~~C~~CG~~~-g~~~---~CP~CG 646 (656)
T PRK08270 624 PTFSICPKHGYLS-GEHE---FCPKCG 646 (656)
T ss_pred CCCcccCCCCCcC-CCCC---CCcCCc
Confidence 3567899999964 3343 599998
No 137
>TIGR00412 redox_disulf_2 small redox-active disulfide protein 2. This small protein is found in three archaeal species so far (Methanococcus jannaschii, Archeoglobus fulgidus, and Methanobacterium thermoautotrophicum) as well as in Anabaena PCC7120. It is homologous to thioredoxins, glutaredoxins, and protein disulfide isomerases, and shares with them a redox-active disulfide. The redox active disulfide region CXXC motif resembles neither thioredoxin nor glutaredoxin. A closely related protein found in the same three Archaea, described by redox_disulf_1, has a glutaredoxin-like CP[YH]C sequence; it has been characterized in functional assays as redox-active but unlikely to be a thioredoxin or glutaredoxin.
Probab=34.19 E-value=15 Score=23.43 Aligned_cols=11 Identities=45% Similarity=1.084 Sum_probs=8.9
Q ss_pred hhccCCCCCCC
Q 046522 30 QFRESGCENCP 40 (115)
Q Consensus 30 qf~~~gCpnC~ 40 (115)
+|+..+||+|.
T Consensus 4 ~~~a~~C~~C~ 14 (76)
T TIGR00412 4 QIYGTGCANCQ 14 (76)
T ss_pred EEECCCCcCHH
Confidence 36668999998
No 138
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=33.80 E-value=20 Score=27.93 Aligned_cols=23 Identities=17% Similarity=0.326 Sum_probs=18.0
Q ss_pred cccccccCcccccchhhccCCCCCCC
Q 046522 15 ELRACLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 15 ~lrAC~~C~~I~t~~qf~~~gCpnC~ 40 (115)
-..-|..|+.+-+.+ .+-||.||
T Consensus 138 w~~rC~GC~~~f~~~---~~~Cp~CG 160 (177)
T COG1439 138 WRLRCHGCKRIFPEP---KDFCPICG 160 (177)
T ss_pred eeEEEecCceecCCC---CCcCCCCC
Confidence 457899999998832 24599998
No 139
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=33.48 E-value=21 Score=22.48 Aligned_cols=22 Identities=27% Similarity=0.584 Sum_probs=14.1
Q ss_pred cccccccCcccccchhhccCCCCCCC
Q 046522 15 ELRACLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 15 ~lrAC~~C~~I~t~~qf~~~gCpnC~ 40 (115)
.+-.|..|+-.+-.-. -||+|+
T Consensus 25 ~l~~C~~cG~~~~~H~----vc~~cG 46 (55)
T TIGR01031 25 TLVVCPNCGEFKLPHR----VCPSCG 46 (55)
T ss_pred cceECCCCCCcccCee----ECCccC
Confidence 4566888876554332 388887
No 140
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=33.22 E-value=21 Score=32.56 Aligned_cols=33 Identities=27% Similarity=0.518 Sum_probs=19.2
Q ss_pred cccccCcccccchhhccCCCCCCCCCCCCCCcccccccCCCccceEEE
Q 046522 17 RACLRCRLVKTYDQFRESGCENCPFFKMDEDHERVVDCTTPNFNGIIS 64 (115)
Q Consensus 17 rAC~~C~~I~t~~qf~~~gCpnC~~l~m~~~~d~v~~~tT~~f~G~I~ 64 (115)
+.|..|+...+.+. +-||+||.. +..-|..+|+
T Consensus 28 ~~Cp~CG~~~~~~~---~fC~~CG~~------------~~~~~~~~~~ 60 (645)
T PRK14559 28 KPCPQCGTEVPVDE---AHCPNCGAE------------TGTIWWAIIA 60 (645)
T ss_pred CcCCCCCCCCCccc---ccccccCCc------------ccchhhhhcc
Confidence 34666666655443 237777622 4555888876
No 141
>PF12090 Spt20: Spt20 family; InterPro: IPR021950 This presumed domain is found in the Spt20 proteins from both human and yeast. The Spt20 protein is part of the SAGA complex which is a large cmplex mediating histone deacetylation. Yeast Spt20 has been shown to play a role in structural integrity of the SAGA complex as as no intact SAGA could be purified in spt20 deletion strains.
Probab=33.17 E-value=39 Score=25.86 Aligned_cols=35 Identities=29% Similarity=0.432 Sum_probs=26.2
Q ss_pred eCCChhHHHHHHh-cCCCCCeeeEEEecCCCcHHHHHHHHhcCCeec
Q 046522 66 MDPTRSWAARWLR-IGRFVPGCYTLAVSEALPEDLQNLCEDERVQYV 111 (115)
Q Consensus 66 ~dP~~SwVAk~l~-i~~~~pG~YAi~V~g~lp~~i~~~l~~~gi~y~ 111 (115)
+-|-+|-+..+|. |+ .|+||.++++.|++.+|+|.
T Consensus 36 ~~pY~~~~k~~L~~I~-----------~~~iP~~Lle~l~~~~v~FY 71 (182)
T PF12090_consen 36 SFPYNSPMKEFLEYID-----------AGEIPHDLLELLDDANVPFY 71 (182)
T ss_pred eecCCchHHHHHHHHH-----------cCCCCHHHHHHHHhCCCeeE
Confidence 3466676655553 34 79999999999999998663
No 142
>TIGR02187 GlrX_arch Glutaredoxin-like domain protein. This family of archaeal proteins contains a C-terminal domain with homology to bacterial and eukaryotic glutaredoxins, including a CPYC motif. There is an N-terminal domain which has even more distant homology to glutaredoxins. The name "glutaredoxin" may be inappropriate in the sense of working in tandem with glutathione and glutathione reductase which may not be present in the archaea. The overall domain structure appears to be related to bacterial alkylhydroperoxide reductases, but the homology may be distant enough that the function of this family is wholly different.
Probab=32.99 E-value=44 Score=25.26 Aligned_cols=58 Identities=16% Similarity=0.254 Sum_probs=33.2
Q ss_pred CCCCCCCCCCCCCCcccccccCCCccceE-EEEeC---CChhHHHHHHhcCC------CCCeeeE-EEecCCCcH
Q 046522 34 SGCENCPFFKMDEDHERVVDCTTPNFNGI-ISVMD---PTRSWAARWLRIGR------FVPGCYT-LAVSEALPE 97 (115)
Q Consensus 34 ~gCpnC~~l~m~~~~d~v~~~tT~~f~G~-I~i~d---P~~SwVAk~l~i~~------~~pG~YA-i~V~g~lp~ 97 (115)
.+||.|..+ ..+.+-.+..+.++ |.+++ ++...+|+.++|.. +..|..- .+..|-.+.
T Consensus 32 ~wC~~C~~~------~p~l~~la~~~~~~~i~~v~vd~~~~~~l~~~~~V~~~Pt~~~f~~g~~~~~~~~G~~~~ 100 (215)
T TIGR02187 32 EGCQYCKET------EQLLEELSEVSPKLKLEIYDFDTPEDKEEAEKYGVERVPTTIILEEGKDGGIRYTGIPAG 100 (215)
T ss_pred CCCCchHHH------HHHHHHHHhhCCCceEEEEecCCcccHHHHHHcCCCccCEEEEEeCCeeeEEEEeecCCH
Confidence 579999822 22333345555554 33333 35788999998875 3345542 355666554
No 143
>PHA02942 putative transposase; Provisional
Probab=32.84 E-value=20 Score=30.36 Aligned_cols=25 Identities=20% Similarity=0.541 Sum_probs=17.0
Q ss_pred cccccccCcccccc---hhhccCCCCCCCCC
Q 046522 15 ELRACLRCRLVKTY---DQFRESGCENCPFF 42 (115)
Q Consensus 15 ~lrAC~~C~~I~t~---~qf~~~gCpnC~~l 42 (115)
.-+-|..|+.+... ..|. ||+||+.
T Consensus 324 TSq~Cs~CG~~~~~l~~r~f~---C~~CG~~ 351 (383)
T PHA02942 324 SSVSCPKCGHKMVEIAHRYFH---CPSCGYE 351 (383)
T ss_pred CCccCCCCCCccCcCCCCEEE---CCCCCCE
Confidence 34789999977542 2343 9999953
No 144
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=32.68 E-value=21 Score=26.01 Aligned_cols=27 Identities=22% Similarity=0.363 Sum_probs=18.3
Q ss_pred ccccccccCcccccchhhccCCCCCCC
Q 046522 14 HELRACLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 14 r~lrAC~~C~~I~t~~qf~~~gCpnC~ 40 (115)
--+.||..|+--+..+.-..--|++|+
T Consensus 32 ~~Y~aC~~C~kkv~~~~~~~~~C~~C~ 58 (166)
T cd04476 32 WWYPACPGCNKKVVEEGNGTYRCEKCN 58 (166)
T ss_pred eEEccccccCcccEeCCCCcEECCCCC
Confidence 357999999887775430011399998
No 145
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=32.67 E-value=22 Score=29.23 Aligned_cols=25 Identities=20% Similarity=0.509 Sum_probs=21.9
Q ss_pred ccccccCcccccchhhcc--CCCCCCC
Q 046522 16 LRACLRCRLVKTYDQFRE--SGCENCP 40 (115)
Q Consensus 16 lrAC~~C~~I~t~~qf~~--~gCpnC~ 40 (115)
...|..|+-+.-..++.+ ..||.|+
T Consensus 27 ~~~c~~c~~~~~~~~l~~~~~vc~~c~ 53 (292)
T PRK05654 27 WTKCPSCGQVLYRKELEANLNVCPKCG 53 (292)
T ss_pred eeECCCccchhhHHHHHhcCCCCCCCC
Confidence 678999999999888866 4799999
No 146
>cd03005 PDI_a_ERp46 PDIa family, endoplasmic reticulum protein 46 (ERp46) subfamily; ERp46 is an ER-resident protein containing three redox active TRX domains. Yeast complementation studies show that ERp46 can substitute for protein disulfide isomerase (PDI) function in vivo. It has been detected in many tissues, however, transcript and protein levels do not correlate in all tissues, suggesting regulation at a posttranscriptional level. An identical protein, named endoPDI, has been identified as an endothelial PDI that is highly expressed in the endothelium of tumors and hypoxic lesions. It has a protective effect on cells exposed to hypoxia.
Probab=32.58 E-value=30 Score=21.99 Aligned_cols=53 Identities=15% Similarity=0.225 Sum_probs=27.8
Q ss_pred hhccCCCCCCCCCCCCCCcccccccCCCccce-----EEEEeCC-ChhHHHHHHhcCCCCCeeeEE
Q 046522 30 QFRESGCENCPFFKMDEDHERVVDCTTPNFNG-----IISVMDP-TRSWAARWLRIGRFVPGCYTL 89 (115)
Q Consensus 30 qf~~~gCpnC~~l~m~~~~d~v~~~tT~~f~G-----~I~i~dP-~~SwVAk~l~i~~~~pG~YAi 89 (115)
.|+...|+.|... .. ..+-....|.| .++-+|- +..-+++.+++.. +|-.+.+
T Consensus 22 ~f~a~wC~~C~~~--~p----~~~~~~~~~~~~~~~~~~~~vd~~~~~~~~~~~~v~~-~Pt~~~~ 80 (102)
T cd03005 22 KFFAPWCGHCKRL--AP----TWEQLAKKFNNENPSVKIAKVDCTQHRELCSEFQVRG-YPTLLLF 80 (102)
T ss_pred EEECCCCHHHHHh--CH----HHHHHHHHHhccCCcEEEEEEECCCChhhHhhcCCCc-CCEEEEE
Confidence 3667789999822 11 11123334443 2233343 3457888888765 5554444
No 147
>PRK06386 replication factor A; Reviewed
Probab=32.21 E-value=22 Score=30.25 Aligned_cols=57 Identities=12% Similarity=0.197 Sum_probs=31.2
Q ss_pred ccccccCcccccchhhccCCCCCCCCCCCCCCcccccccCCCccceEEEEeCCChhHHHHHHhcC
Q 046522 16 LRACLRCRLVKTYDQFRESGCENCPFFKMDEDHERVVDCTTPNFNGIISVMDPTRSWAARWLRIG 80 (115)
Q Consensus 16 lrAC~~C~~I~t~~qf~~~gCpnC~~l~m~~~~d~v~~~tT~~f~G~I~i~dP~~SwVAk~l~i~ 80 (115)
...|..|+.++... .||.|+- ..+.-|...--.=++=+|.+.++=. ..-+++.+|++
T Consensus 236 i~rCP~C~R~l~~g-----~C~~HG~--v~~~~dlr~k~vLDDGtg~~~~~l~-~e~~e~l~G~~ 292 (358)
T PRK06386 236 FTKCSVCNKIIEDG-----VCKDHPD--APVYLDIFGYFTISDGTGFVTCYAN-KDSFLPYININ 292 (358)
T ss_pred EecCcCCCeEccCC-----cCCCCCC--CCCeeEEEEEEEEECCCCeEEEEEC-hHHhHHHhCCC
Confidence 58999999999853 3999992 2223331111122223445544333 34456666655
No 148
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=32.03 E-value=22 Score=21.27 Aligned_cols=9 Identities=22% Similarity=0.504 Sum_probs=4.1
Q ss_pred cccCccccc
Q 046522 19 CLRCRLVKT 27 (115)
Q Consensus 19 C~~C~~I~t 27 (115)
|..|+..+-
T Consensus 20 Cp~C~~PL~ 28 (41)
T PF06677_consen 20 CPDCGTPLM 28 (41)
T ss_pred cCCCCCeeE
Confidence 444544443
No 149
>PRK09381 trxA thioredoxin; Provisional
Probab=31.98 E-value=52 Score=21.53 Aligned_cols=70 Identities=13% Similarity=0.215 Sum_probs=34.6
Q ss_pred hhccCCCCCCCCCCCCCCcccccccCCCccceEEEEeCCC-hhHHHHHHhcCCCCCeeeEE-------EecCCCcHHH-H
Q 046522 30 QFRESGCENCPFFKMDEDHERVVDCTTPNFNGIISVMDPT-RSWAARWLRIGRFVPGCYTL-------AVSEALPEDL-Q 100 (115)
Q Consensus 30 qf~~~gCpnC~~l~m~~~~d~v~~~tT~~f~G~I~i~dP~-~SwVAk~l~i~~~~pG~YAi-------~V~g~lp~~i-~ 100 (115)
.|...+||.|... ...=+.+.+.....+ .+ +.+|-+ ..-+++.+++.. +|..+-+ +..|.++.+. .
T Consensus 27 ~f~~~~C~~C~~~--~p~~~~l~~~~~~~~-~~-~~vd~~~~~~~~~~~~v~~-~Pt~~~~~~G~~~~~~~G~~~~~~l~ 101 (109)
T PRK09381 27 DFWAEWCGPCKMI--APILDEIADEYQGKL-TV-AKLNIDQNPGTAPKYGIRG-IPTLLLFKNGEVAATKVGALSKGQLK 101 (109)
T ss_pred EEECCCCHHHHHH--hHHHHHHHHHhCCCc-EE-EEEECCCChhHHHhCCCCc-CCEEEEEeCCeEEEEecCCCCHHHHH
Confidence 4667789999822 111122222222221 22 333333 356677788765 6665443 3456665544 4
Q ss_pred HHHH
Q 046522 101 NLCE 104 (115)
Q Consensus 101 ~~l~ 104 (115)
..++
T Consensus 102 ~~i~ 105 (109)
T PRK09381 102 EFLD 105 (109)
T ss_pred HHHH
Confidence 4444
No 150
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=31.90 E-value=23 Score=32.13 Aligned_cols=22 Identities=18% Similarity=0.522 Sum_probs=15.7
Q ss_pred cccccccCcccccchhhccCCCCCCC
Q 046522 15 ELRACLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 15 ~lrAC~~C~~I~t~~qf~~~gCpnC~ 40 (115)
++--|..|++ ..... ..||+|+
T Consensus 558 ~~~~C~~CGy-~g~~~---~~CP~CG 579 (618)
T PRK14704 558 PVDRCKCCSY-HGVIG---NECPSCG 579 (618)
T ss_pred CCeecCCCCC-CCCcC---ccCcCCC
Confidence 5678999998 33222 3599998
No 151
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=31.79 E-value=28 Score=30.86 Aligned_cols=23 Identities=22% Similarity=0.603 Sum_probs=18.5
Q ss_pred cccccccCcccccchhhccCCCCCCC
Q 046522 15 ELRACLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 15 ~lrAC~~C~~I~t~~qf~~~gCpnC~ 40 (115)
....|..|++.-+ +|.. .||+|+
T Consensus 6 t~f~C~~CG~~s~--KW~G-kCp~Cg 28 (456)
T COG1066 6 TAFVCQECGYVSP--KWLG-KCPACG 28 (456)
T ss_pred cEEEcccCCCCCc--cccc-cCCCCC
Confidence 5678999999866 5643 499998
No 152
>TIGR00411 redox_disulf_1 small redox-active disulfide protein 1. This protein is homologous to a family of proteins that includes thioredoxins, glutaredoxins, protein-disulfide isomerases, and others, some of which have several such domains. The sequence of this protein at the redox-active disufide site, CPYC, matches glutaredoxins rather than thioredoxins, although its overall sequence seems closer to thioredoxins. It is suggested to be a ribonucleotide-reducing system component distinct from thioredoxin or glutaredoxin.
Probab=31.71 E-value=51 Score=20.11 Aligned_cols=67 Identities=21% Similarity=0.245 Sum_probs=32.6
Q ss_pred hccCCCCCCCCCCCCCCcccccccCCCccce---EEEEeCCChhHHHHHHhcCCCCCeeeE---EEecCCC-cHHHHHHH
Q 046522 31 FRESGCENCPFFKMDEDHERVVDCTTPNFNG---IISVMDPTRSWAARWLRIGRFVPGCYT---LAVSEAL-PEDLQNLC 103 (115)
Q Consensus 31 f~~~gCpnC~~l~m~~~~d~v~~~tT~~f~G---~I~i~dP~~SwVAk~l~i~~~~pG~YA---i~V~g~l-p~~i~~~l 103 (115)
|...+||.|... ..+.+-...++.+ ++-|--.+....++..++.. +|-.+- .+..|.. ++++.+.|
T Consensus 6 f~~~~C~~C~~~------~~~l~~l~~~~~~~~~~~~vd~~~~~~~~~~~~v~~-vPt~~~~g~~~~~G~~~~~~l~~~l 78 (82)
T TIGR00411 6 FTSPTCPYCPAA------KRVVEEVAKEMGDAVEVEYINVMENPQKAMEYGIMA-VPAIVINGDVEFIGAPTKEELVEAI 78 (82)
T ss_pred EECCCCcchHHH------HHHHHHHHHHhcCceEEEEEeCccCHHHHHHcCCcc-CCEEEECCEEEEecCCCHHHHHHHH
Confidence 556789999821 1122112222322 23332335566777777764 454331 2455654 44444444
Q ss_pred H
Q 046522 104 E 104 (115)
Q Consensus 104 ~ 104 (115)
+
T Consensus 79 ~ 79 (82)
T TIGR00411 79 K 79 (82)
T ss_pred H
Confidence 4
No 153
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=31.60 E-value=27 Score=25.06 Aligned_cols=23 Identities=22% Similarity=0.456 Sum_probs=13.6
Q ss_pred cccccCcccccchhh-----c-cCCCCCCC
Q 046522 17 RACLRCRLVKTYDQF-----R-ESGCENCP 40 (115)
Q Consensus 17 rAC~~C~~I~t~~qf-----~-~~gCpnC~ 40 (115)
--| .|+..-+.+.| . ...||.|+
T Consensus 71 ~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cg 99 (124)
T PRK00762 71 IEC-ECGYEGVVDEDEIDHYAAVIECPVCG 99 (124)
T ss_pred EEe-eCcCcccccccchhccccCCcCcCCC
Confidence 458 99966332211 1 13599999
No 154
>cd02550 PseudoU_synth_Rsu_Rlu_like PseudoU_synth_Rsu_Rlu: Pseudouridine synthase, Rsu/Rlu family. This group is comprised of eukaryotic, bacterial and archeal proteins similar to eight site specific Escherichia coli pseudouridine synthases: RsuA, RluA, RluB, RluC, RluD, RluE, RluF and TruA. Pseudouridine synthases catalyze the isomerization of specific uridines in a n RNA molecule to pseudouridines (5-ribosyluracil, psi) requiring no cofactors. E. coli RluC for example makes psi955, 2504 and 2580 in 23S RNA. Some psi sites such as psi1917 in 23S RNA made by RluD are universally conserved. Other psi sites occur in a more restricted fashion, for example psi2819 in 21S mitochondrial ribosomal RNA made by S. cerevisiae Pus5p is only found in mitochondrial large subunit rRNAs from some other species and in gram negative bacteria. The E. coli counterpart of this psi residue is psi2580 in 23S rRNA. psi2604in 23S RNA made by RluF has only been detected in E.coli.
Probab=31.47 E-value=68 Score=22.92 Aligned_cols=43 Identities=16% Similarity=0.156 Sum_probs=32.0
Q ss_pred ceEEEEeCCChhHHHHHHhcCCCCCeeeEEEecCCCcHHHHHHH
Q 046522 60 NGIISVMDPTRSWAARWLRIGRFVPGCYTLAVSEALPEDLQNLC 103 (115)
Q Consensus 60 ~G~I~i~dP~~SwVAk~l~i~~~~pG~YAi~V~g~lp~~i~~~l 103 (115)
+|+|.+.+- ..+..+....+..+.=.|-+.|.|.++++....+
T Consensus 46 SGlll~ak~-~~~~~~l~~~~~~v~K~Y~a~v~g~~~~~~~~~~ 88 (154)
T cd02550 46 SGLLLLTND-GRLQRRLTEPRREIEKEYLVTVRGELDEEGIEDL 88 (154)
T ss_pred eeEEEEEcC-HHHHHHHhhhhccCcEEEEEEEEeecCcchheec
Confidence 799988765 4556666666666888999999999987654433
No 155
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=30.98 E-value=26 Score=27.30 Aligned_cols=10 Identities=20% Similarity=0.597 Sum_probs=7.7
Q ss_pred CCCCCCCCCC
Q 046522 34 SGCENCPFFK 43 (115)
Q Consensus 34 ~gCpnC~~l~ 43 (115)
..||+|++..
T Consensus 49 ~vCP~CgyA~ 58 (214)
T PF09986_consen 49 WVCPHCGYAA 58 (214)
T ss_pred EECCCCCCcc
Confidence 3699999764
No 156
>KOG4207 consensus Predicted splicing factor, SR protein superfamily [RNA processing and modification]
Probab=30.87 E-value=62 Score=26.51 Aligned_cols=33 Identities=33% Similarity=0.534 Sum_probs=26.8
Q ss_pred CCeeeEEEe----cCCCcHHHHHHHHhc---CCeecCCCC
Q 046522 83 VPGCYTLAV----SEALPEDLQNLCEDE---RVQYVPPKR 115 (115)
Q Consensus 83 ~pG~YAi~V----~g~lp~~i~~~l~~~---gi~y~prd~ 115 (115)
|-|+|.|+| ...-|+++....|.. |=.|+|||+
T Consensus 10 v~gm~SLkVdNLTyRTspd~LrrvFekYG~vgDVyIPrdr 49 (256)
T KOG4207|consen 10 VEGMTSLKVDNLTYRTSPDDLRRVFEKYGRVGDVYIPRDR 49 (256)
T ss_pred cccceeEEecceeccCCHHHHHHHHHHhCcccceeccccc
Confidence 678888887 456789999999887 457999986
No 157
>COG3088 CcmH Uncharacterized protein involved in biosynthesis of c-type cytochromes [Posttranslational modification, protein turnover, chaperones]
Probab=30.55 E-value=20 Score=27.50 Aligned_cols=42 Identities=24% Similarity=0.253 Sum_probs=33.3
Q ss_pred CCChhHHHHHHhcCCCCCeeeEEEecCCCcHHHHHHHHhc---CCeecCC
Q 046522 67 DPTRSWAARWLRIGRFVPGCYTLAVSEALPEDLQNLCEDE---RVQYVPP 113 (115)
Q Consensus 67 dP~~SwVAk~l~i~~~~pG~YAi~V~g~lp~~i~~~l~~~---gi~y~pr 113 (115)
+-.++.||+=+|+. .|-+-.+|+=-.+|++.|=++ =+.|.|+
T Consensus 56 adSnA~IA~DlR~~-----V~e~l~eGkS~~qIid~mVaRYG~FVly~Pp 100 (153)
T COG3088 56 ADSNAPIARDLRHQ-----VYELLQEGKSDQQIIDYMVARYGEFVLYKPP 100 (153)
T ss_pred hhhccHHHHHHHHH-----HHHHHHcCCcHHHHHHHHHHhhcceeeecCC
Confidence 44579999999976 455567899999999999887 4778776
No 158
>PF09912 DUF2141: Uncharacterized protein conserved in bacteria (DUF2141); InterPro: IPR018673 This family of conserved hypothetical proteins has no known function.
Probab=30.31 E-value=36 Score=23.87 Aligned_cols=15 Identities=33% Similarity=0.603 Sum_probs=11.1
Q ss_pred CCCCCeeeEEEecCC
Q 046522 80 GRFVPGCYTLAVSEA 94 (115)
Q Consensus 80 ~~~~pG~YAi~V~g~ 94 (115)
..-.||.|||.|--+
T Consensus 48 ~~lp~G~YAi~v~hD 62 (112)
T PF09912_consen 48 EDLPPGTYAIAVFHD 62 (112)
T ss_pred CCCCCccEEEEEEEe
Confidence 345699999998543
No 159
>PRK07218 replication factor A; Provisional
Probab=30.08 E-value=37 Score=29.48 Aligned_cols=43 Identities=14% Similarity=0.352 Sum_probs=27.8
Q ss_pred ccccccCcccccchhhccCCCCCCCCCCCCCCcccccccCCCccceEEEE
Q 046522 16 LRACLRCRLVKTYDQFRESGCENCPFFKMDEDHERVVDCTTPNFNGIISV 65 (115)
Q Consensus 16 lrAC~~C~~I~t~~qf~~~gCpnC~~l~m~~~~d~v~~~tT~~f~G~I~i 65 (115)
...|..|+.++... .||.|+ ...+..|....-.=++=.|.+.+
T Consensus 297 i~rCP~C~r~v~~~-----~C~~hG--~ve~~~dlrik~vLDDGtg~~~~ 339 (423)
T PRK07218 297 IERCPECGRVIQKG-----QCRSHG--AVEGEDDLRIKAILDDGTGSVTV 339 (423)
T ss_pred eecCcCccccccCC-----cCCCCC--CcCCeeeeEEEEEEECCCCeEEE
Confidence 58999999999643 499999 33455554433333444566655
No 160
>PRK10445 endonuclease VIII; Provisional
Probab=29.76 E-value=31 Score=27.58 Aligned_cols=27 Identities=22% Similarity=0.480 Sum_probs=15.1
Q ss_pred ccccccccCcccccchhhcc---CCCCCCC
Q 046522 14 HELRACLRCRLVKTYDQFRE---SGCENCP 40 (115)
Q Consensus 14 r~lrAC~~C~~I~t~~qf~~---~gCpnC~ 40 (115)
|.-..|.+|+-.......-. --||+|+
T Consensus 233 r~g~~Cp~Cg~~I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 233 RDGEACERCGGIIEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCCCCEeEEEEECCCCcEECCCCc
Confidence 34567888876654433211 1388875
No 161
>PF03918 CcmH: Cytochrome C biogenesis protein; InterPro: IPR005616 Members of this family include NrfF, CcmH, CycL, Ccl2.; PDB: 2KW0_A 2HL7_A.
Probab=29.45 E-value=14 Score=27.62 Aligned_cols=39 Identities=21% Similarity=0.226 Sum_probs=24.1
Q ss_pred hhHHHHHHhcCCCCCeeeEEEecCCCcHHHHHHHHhc---CCeecCC
Q 046522 70 RSWAARWLRIGRFVPGCYTLAVSEALPEDLQNLCEDE---RVQYVPP 113 (115)
Q Consensus 70 ~SwVAk~l~i~~~~pG~YAi~V~g~lp~~i~~~l~~~---gi~y~pr 113 (115)
+|-+|+-+|-. +|..--.|.=.++|+++|-++ -|-|.|+
T Consensus 55 ~a~~A~dmR~~-----I~~~l~~G~s~~eI~~~~v~rYG~~Vl~~Pp 96 (148)
T PF03918_consen 55 NAPIARDMRRE-----IREMLAEGKSDEEIIDYFVERYGEFVLYEPP 96 (148)
T ss_dssp -SHHHHHHHHH-----HHHHHHHT--HHHHHHHHHHHHTTT-EES--
T ss_pred CcHHHHHHHHH-----HHHHHHcCCCHHHHHHHHHHhcCcceeecCC
Confidence 58888888743 222334888999999999887 4667775
No 162
>cd04908 ACT_Bt0572_1 N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains. Included in this CD is the N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains as seen in the uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related ACT domains. These tandem ACT domain proteins belong to the superfamily of ACT regulatory domains.
Probab=29.26 E-value=68 Score=19.53 Aligned_cols=24 Identities=8% Similarity=0.104 Sum_probs=17.9
Q ss_pred EEEecCCCcHHHHHHHHhcCCeec
Q 046522 88 TLAVSEALPEDLQNLCEDERVQYV 111 (115)
Q Consensus 88 Ai~V~g~lp~~i~~~l~~~gi~y~ 111 (115)
.+++..+.++.+.+.|+++|.+.+
T Consensus 42 ~~rl~~~~~~~~~~~L~~~G~~v~ 65 (66)
T cd04908 42 ILRLIVSDPDKAKEALKEAGFAVK 65 (66)
T ss_pred EEEEEECCHHHHHHHHHHCCCEEE
Confidence 334444668899999999998764
No 163
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=29.15 E-value=32 Score=25.29 Aligned_cols=13 Identities=38% Similarity=1.055 Sum_probs=7.0
Q ss_pred cccCcccccchhh
Q 046522 19 CLRCRLVKTYDQF 31 (115)
Q Consensus 19 C~~C~~I~t~~qf 31 (115)
|.+|+..-+.++|
T Consensus 28 C~~Ck~~~~v~~~ 40 (116)
T KOG2907|consen 28 CIRCKIEYPVSQF 40 (116)
T ss_pred eccccccCCHHHh
Confidence 5555555554444
No 164
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=28.92 E-value=36 Score=25.47 Aligned_cols=26 Identities=15% Similarity=0.365 Sum_probs=18.8
Q ss_pred cccccccCcccccchhhcc-CCCCCCC
Q 046522 15 ELRACLRCRLVKTYDQFRE-SGCENCP 40 (115)
Q Consensus 15 ~lrAC~~C~~I~t~~qf~~-~gCpnC~ 40 (115)
....|.+|+..+....-.. .-||.|+
T Consensus 111 G~l~C~~Cg~~~~~~~~~~l~~Cp~C~ 137 (146)
T PF07295_consen 111 GTLVCENCGHEVELTHPERLPPCPKCG 137 (146)
T ss_pred ceEecccCCCEEEecCCCcCCCCCCCC
Confidence 4678999998877653211 3699998
No 165
>PRK14894 glycyl-tRNA synthetase; Provisional
Probab=28.78 E-value=34 Score=30.95 Aligned_cols=28 Identities=29% Similarity=0.682 Sum_probs=21.7
Q ss_pred CCccccccccCcccccchhhccCCCCCCC
Q 046522 12 FGHELRACLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 12 ~~r~lrAC~~C~~I~t~~qf~~~gCpnC~ 40 (115)
|.-.+.+|+.|+...-.++.. ..||+|+
T Consensus 84 F~DpmV~CkkCk~ryRaD~Li-ikCP~CG 111 (539)
T PRK14894 84 FNDPLVDCRDCKMRWRADHIQ-GVCPNCG 111 (539)
T ss_pred CCCceeECCCCCccccCccce-eeCCCCC
Confidence 334689999999888777653 3599998
No 166
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=28.77 E-value=27 Score=23.63 Aligned_cols=22 Identities=23% Similarity=0.630 Sum_probs=15.6
Q ss_pred ccccCcccccch--hhccCCCCCCCCC
Q 046522 18 ACLRCRLVKTYD--QFRESGCENCPFF 42 (115)
Q Consensus 18 AC~~C~~I~t~~--qf~~~gCpnC~~l 42 (115)
-|..|+-++... ++ -|++|++.
T Consensus 2 fC~~Cg~~l~~~~~~~---~C~~C~~~ 25 (104)
T TIGR01384 2 FCPKCGSLMTPKNGVY---VCPSCGYE 25 (104)
T ss_pred CCcccCcccccCCCeE---ECcCCCCc
Confidence 488898888653 33 49999944
No 167
>TIGR01126 pdi_dom protein disulfide-isomerase domain. This model describes a domain of eukaryotic protein disulfide isomerases, generally found in two copies. The high cutoff for total score reflects the expectation of finding both copies. The domain is similar to thioredoxin but the redox-active disulfide region motif is APWCGHCK.
Probab=28.64 E-value=57 Score=20.46 Aligned_cols=68 Identities=12% Similarity=0.221 Sum_probs=35.3
Q ss_pred hhccCCCCCCCCCCCCCCcccccccCCCccce-----EEEEeCCChhHHHHHHhcCCCCCeeeEE-------EecCCCcH
Q 046522 30 QFRESGCENCPFFKMDEDHERVVDCTTPNFNG-----IISVMDPTRSWAARWLRIGRFVPGCYTL-------AVSEALPE 97 (115)
Q Consensus 30 qf~~~gCpnC~~l~m~~~~d~v~~~tT~~f~G-----~I~i~dP~~SwVAk~l~i~~~~pG~YAi-------~V~g~lp~ 97 (115)
.|....|+.|..+. ..-+. ....|.| ++.+--.+..-+++.++|.. +|-.|-+ +..|..+.
T Consensus 19 ~f~~~~C~~c~~~~--~~~~~----~~~~~~~~~~~~~~~~d~~~~~~~~~~~~i~~-~P~~~~~~~~~~~~~~~g~~~~ 91 (102)
T TIGR01126 19 EFYAPWCGHCKNLA--PEYEK----LAKELKGDPDIVLAKVDATAEKDLASRFGVSG-FPTIKFFPKGKKPVDYEGGRDL 91 (102)
T ss_pred EEECCCCHHHHhhC--hHHHH----HHHHhccCCceEEEEEEccchHHHHHhCCCCc-CCEEEEecCCCcceeecCCCCH
Confidence 35566799997321 11111 2334444 33333445678888888865 6644433 44555554
Q ss_pred H-HHHHHH
Q 046522 98 D-LQNLCE 104 (115)
Q Consensus 98 ~-i~~~l~ 104 (115)
+ +...++
T Consensus 92 ~~l~~~i~ 99 (102)
T TIGR01126 92 EAIVEFVN 99 (102)
T ss_pred HHHHHHHH
Confidence 3 444444
No 168
>cd02973 TRX_GRX_like Thioredoxin (TRX)-Glutaredoxin (GRX)-like family; composed of archaeal and bacterial proteins that show similarity to both TRX and GRX, including the C-terminal TRX-fold subdomain of Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO). All members contain a redox-active CXXC motif and may function as PDOs. The archaeal proteins Mj0307 and Mt807 show structures more similar to GRX, but activities more similar to TRX. Some members of the family are similar to PfPDO in that they contain a second CXXC motif located in a second TRX-fold subdomain at the N-terminus; the superimposable N- and C-terminal TRX subdomains form a compact structure. PfPDO is postulated to be the archaeal counterpart of bacterial DsbA and eukaryotic protein disulfide isomerase (PDI). The C-terminal CXXC motif of PfPDO is required for its oxidase, reductase and isomerase activities. Also included in the family is the C-terminal TRX-fold subdomain of the N-terminal domain (NTD) of bacteri
Probab=28.56 E-value=26 Score=21.00 Aligned_cols=11 Identities=36% Similarity=0.960 Sum_probs=9.1
Q ss_pred hhccCCCCCCC
Q 046522 30 QFRESGCENCP 40 (115)
Q Consensus 30 qf~~~gCpnC~ 40 (115)
.|...+||.|.
T Consensus 5 ~f~~~~C~~C~ 15 (67)
T cd02973 5 VFVSPTCPYCP 15 (67)
T ss_pred EEECCCCCCcH
Confidence 46678999998
No 169
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=28.45 E-value=51 Score=32.15 Aligned_cols=70 Identities=19% Similarity=0.359 Sum_probs=41.8
Q ss_pred cccccccCcccccchhhccCCCCCCCCCCCCCCcccccccCCCccceEEEEeCCChhHHHHHHhcCC----CCCeeeEEE
Q 046522 15 ELRACLRCRLVKTYDQFRESGCENCPFFKMDEDHERVVDCTTPNFNGIISVMDPTRSWAARWLRIGR----FVPGCYTLA 90 (115)
Q Consensus 15 ~lrAC~~C~~I~t~~qf~~~gCpnC~~l~m~~~~d~v~~~tT~~f~G~I~i~dP~~SwVAk~l~i~~----~~pG~YAi~ 90 (115)
..|-|..|+...... .||.|+.- |...+-.-+ -++..+-|-+-..++.. .+.|.--+.
T Consensus 624 ~~RKCPkCG~yTlk~-----rCP~CG~~------------Te~~~pc~~-~i~l~~~~~~A~~~lg~~~~~~~KGVkgl~ 685 (1095)
T TIGR00354 624 AIRKCPQCGKESFWL-----KCPVCGEL------------TEQLYYGKR-KVDLRELYEEAIANLGEYKFDTIKGVKGMT 685 (1095)
T ss_pred EEEECCCCCcccccc-----cCCCCCCc------------cccccceeE-EecHHHHHHHHHHHhCCCCccccccceecc
Confidence 468999999986644 49999821 334444433 34665555554444433 245555555
Q ss_pred ecCCCcHHHHHH
Q 046522 91 VSEALPEDLQNL 102 (115)
Q Consensus 91 V~g~lp~~i~~~ 102 (115)
=...+||-++.-
T Consensus 686 S~~k~pEPlEKG 697 (1095)
T TIGR00354 686 SKTKIPEPLEKG 697 (1095)
T ss_pred cCCCCCcchHhh
Confidence 566777766653
No 170
>cd02960 AGR Anterior Gradient (AGR) family; members of this family are similar to secreted proteins encoded by the cement gland-specific genes XAG-1 and XAG-2, expressed in the anterior region of dorsal ectoderm of Xenopus. They are implicated in the formation of the cement gland and the induction of forebrain fate. The human homologs, hAG-2 and hAG-3, are secreted proteins associated with estrogen-positive breast tumors. Yeast two-hybrid studies identified the metastasis-associated C4.4a protein and dystroglycan as binding partners, indicating possible roles in the development and progression of breast cancer. hAG-2 has also been implicated in prostate cancer. Its gene was cloned as an androgen-inducible gene and it was shown to be overexpressed in prostate cancer cells at the mRNA and protein levels. AGR proteins contain one conserved cysteine corresponding to the first cysteine in the CXXC motif of TRX. They show high sequence similarity to ERp19.
Probab=28.40 E-value=11 Score=27.52 Aligned_cols=81 Identities=16% Similarity=0.236 Sum_probs=48.6
Q ss_pred hccCCCCCCCCCCC-CCCcccccccCCCccceEEEEeCCChhHHHHHHhcCCCCCeeeEEEecCCCcHHHHHHHHhcCCe
Q 046522 31 FRESGCENCPFFKM-DEDHERVVDCTTPNFNGIISVMDPTRSWAARWLRIGRFVPGCYTLAVSEALPEDLQNLCEDERVQ 109 (115)
Q Consensus 31 f~~~gCpnC~~l~m-~~~~d~v~~~tT~~f~G~I~i~dP~~SwVAk~l~i~~~~pG~YAi~V~g~lp~~i~~~l~~~gi~ 109 (115)
|..+.||.|..++- .-+...|.+-...+|--+-...+..++-.+. -..++|-.+=+.-.|++...|...+.++.-.
T Consensus 30 f~sdwC~~Ck~l~k~~f~~~eV~~~l~~~Fv~V~l~~d~td~~~~~---~g~~vPtivFld~~g~vi~~i~Gy~~~~~~~ 106 (130)
T cd02960 30 HHLEDCPHSQALKKAFAEHKEIQKLAQEDFIMLNLVHETTDKNLSP---DGQYVPRIMFVDPSLTVRADITGRYSNRLYT 106 (130)
T ss_pred EeCCcCHhHHHHHHHhhCCHHHHHHHHhCeEEEEEEeccCCCCcCc---cCcccCeEEEECCCCCCcccccccccCccce
Confidence 56688999983321 1233445554445662211222222111111 1246888888888999999998888888888
Q ss_pred ecCCC
Q 046522 110 YVPPK 114 (115)
Q Consensus 110 y~prd 114 (115)
|-|-|
T Consensus 107 y~~~~ 111 (130)
T cd02960 107 YEPAD 111 (130)
T ss_pred eCcCc
Confidence 88765
No 171
>PRK14873 primosome assembly protein PriA; Provisional
Probab=27.86 E-value=30 Score=31.62 Aligned_cols=42 Identities=17% Similarity=0.304 Sum_probs=21.3
Q ss_pred ccccccCcccccchhhccCCCCCCCCC---CCCCCcccccccCCCccceE
Q 046522 16 LRACLRCRLVKTYDQFRESGCENCPFF---KMDEDHERVVDCTTPNFNGI 62 (115)
Q Consensus 16 lrAC~~C~~I~t~~qf~~~gCpnC~~l---~m~~~~d~v~~~tT~~f~G~ 62 (115)
..-|-.|++-.. ...||+|+.. .+.-.++++.+.....|-|.
T Consensus 410 ~l~Ch~CG~~~~-----p~~Cp~Cgs~~l~~~g~Gter~eeeL~~~FP~~ 454 (665)
T PRK14873 410 TPRCRWCGRAAP-----DWRCPRCGSDRLRAVVVGARRTAEELGRAFPGV 454 (665)
T ss_pred eeECCCCcCCCc-----CccCCCCcCCcceeeeccHHHHHHHHHHHCCCC
Confidence 445777766332 1247777622 22334455555555555543
No 172
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=27.79 E-value=16 Score=23.68 Aligned_cols=8 Identities=38% Similarity=0.945 Sum_probs=6.5
Q ss_pred cCCCCCCC
Q 046522 33 ESGCENCP 40 (115)
Q Consensus 33 ~~gCpnC~ 40 (115)
...||||+
T Consensus 41 ~~~CPNCg 48 (57)
T PF06906_consen 41 NGVCPNCG 48 (57)
T ss_pred cCcCcCCC
Confidence 35699998
No 173
>PRK14873 primosome assembly protein PriA; Provisional
Probab=27.75 E-value=16 Score=33.32 Aligned_cols=57 Identities=16% Similarity=0.243 Sum_probs=31.4
Q ss_pred CCCCCCCCCCCCcccccccCCCccceEEEEeCCChhHHHHHHhcCCCCCeeeEEEecCCCcHHHHHHHH
Q 046522 36 CENCPFFKMDEDHERVVDCTTPNFNGIISVMDPTRSWAARWLRIGRFVPGCYTLAVSEALPEDLQNLCE 104 (115)
Q Consensus 36 CpnC~~l~m~~~~d~v~~~tT~~f~G~I~i~dP~~SwVAk~l~i~~~~pG~YAi~V~g~lp~~i~~~l~ 104 (115)
|..|++.. ....+-.|-+.+| ..+-+-...++..++ +.-||.=-+++.+ +++++.+.
T Consensus 413 Ch~CG~~~---~p~~Cp~Cgs~~l----~~~g~Gter~eeeL~--~~FP~~~V~r~d~---d~~l~~~~ 469 (665)
T PRK14873 413 CRWCGRAA---PDWRCPRCGSDRL----RAVVVGARRTAEELG--RAFPGVPVVTSGG---DQVVDTVD 469 (665)
T ss_pred CCCCcCCC---cCccCCCCcCCcc----eeeeccHHHHHHHHH--HHCCCCCEEEECh---HHHHHhhc
Confidence 55555432 1345556655554 344667788998887 4467643334433 34555554
No 174
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=27.52 E-value=36 Score=19.20 Aligned_cols=27 Identities=19% Similarity=0.384 Sum_probs=14.8
Q ss_pred CCCCCCCCCCCCcccccccCCCccceEEEEe
Q 046522 36 CENCPFFKMDEDHERVVDCTTPNFNGIISVM 66 (115)
Q Consensus 36 CpnC~~l~m~~~~d~v~~~tT~~f~G~I~i~ 66 (115)
||.|+...+..... -.+-.+.|-+.++
T Consensus 1 C~~C~~~~~~~~~~----~~~~~~~~~~~~i 27 (46)
T TIGR03831 1 CPICGGEELEGKTT----TETYEYGGELIVI 27 (46)
T ss_pred CCCCCCceecceEE----EEEEEeCCEEEEE
Confidence 89997443333321 1344567777766
No 175
>PF10164 DUF2367: Uncharacterized conserved protein (DUF2367); InterPro: IPR019317 This is a highly conserved set of proteins which contains three pairs of cysteine residues within a length of 42 amino acids and is rich in proline residues towards the N terminus. It includes a membrane protein that has been found to be highly expressed in the mouse brain and consequently, several members have been assigned as brain protein i3 (Bri3). Their function is unknown.
Probab=27.43 E-value=34 Score=24.44 Aligned_cols=14 Identities=36% Similarity=0.714 Sum_probs=6.0
Q ss_pred ccccCcccccchhh
Q 046522 18 ACLRCRLVKTYDQF 31 (115)
Q Consensus 18 AC~~C~~I~t~~qf 31 (115)
.|..|+.-+-++.|
T Consensus 51 gCp~CrvG~le~~f 64 (98)
T PF10164_consen 51 GCPACRVGVLEDSF 64 (98)
T ss_pred CCCCCceeeecccc
Confidence 34444444444433
No 176
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=27.30 E-value=1.3e+02 Score=21.85 Aligned_cols=46 Identities=24% Similarity=0.367 Sum_probs=29.3
Q ss_pred EeCCChhHHHHHHhcCCCCCeeeEEEecCCCcHHHHHHHHhcCCeecCCC
Q 046522 65 VMDPTRSWAARWLRIGRFVPGCYTLAVSEALPEDLQNLCEDERVQYVPPK 114 (115)
Q Consensus 65 i~dP~~SwVAk~l~i~~~~pG~YAi~V~g~lp~~i~~~l~~~gi~y~prd 114 (115)
|+|-.=..+|||||+- |.=|+-+.+.-..+|+....+.|....-||
T Consensus 4 l~D~~L~~Lar~LR~l----G~Dt~~~~~~~D~~il~~A~~e~RillTrd 49 (147)
T PF01927_consen 4 LVDAMLGRLARWLRLL----GYDTLYSRDIDDDEILELAREEGRILLTRD 49 (147)
T ss_pred EEeCCHHHHHHHHHHC----CCcEEEeCCCChHHHHHHhhhCCeEEEECC
Confidence 4566667899999854 566666665555566665555566555444
No 177
>PRK04031 DNA primase; Provisional
Probab=27.18 E-value=1.1e+02 Score=26.80 Aligned_cols=39 Identities=15% Similarity=0.256 Sum_probs=32.0
Q ss_pred hHHHHHHhcCCCCCeeeEEEecCCCcHHHHHHHHhcCCeec
Q 046522 71 SWAARWLRIGRFVPGCYTLAVSEALPEDLQNLCEDERVQYV 111 (115)
Q Consensus 71 SwVAk~l~i~~~~pG~YAi~V~g~lp~~i~~~l~~~gi~y~ 111 (115)
+.+...+. ...++.|||-+.|.+.+-+++.+.++||.|.
T Consensus 346 ~dl~~~l~--~~~~~~~~iv~DgiitQrl~D~a~~kgv~~i 384 (408)
T PRK04031 346 RDLVDKLE--EAEDKVYAIVFDGIITQRLLDLASEKGVKYL 384 (408)
T ss_pred HHHHHHHH--hcCCCCeEEEECCeecHHHHHHHHHCCCcEE
Confidence 44555554 3347999999999999999999999999885
No 178
>cd01076 NAD_bind_1_Glu_DH NAD(P) binding domain of glutamate dehydrogenase, subgroup 1. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NADP+. Glutamate DH is a multidomain enzyme that catalyzes the reaction from glutamate to 2-oxyoglutarate and ammonia in the presence of NAD or NADP. It is present in all organisms. Enzymes involved in ammonia assimilation are typically NADP+-dependent, while those involved in glutamate catabolism are generally NAD+-dependent. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids
Probab=27.09 E-value=61 Score=25.30 Aligned_cols=23 Identities=13% Similarity=0.247 Sum_probs=20.4
Q ss_pred ecCCCcHHHHHHHHhcCCeecCC
Q 046522 91 VSEALPEDLQNLCEDERVQYVPP 113 (115)
Q Consensus 91 V~g~lp~~i~~~l~~~gi~y~pr 113 (115)
-+..+.++..+.|+++||.|.|.
T Consensus 136 AN~~~t~~a~~~L~~rGi~~~PD 158 (227)
T cd01076 136 ANGPTTPEADEILHERGVLVVPD 158 (227)
T ss_pred CCCCCCHHHHHHHHHCCCEEECh
Confidence 37788899999999999999984
No 179
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=26.79 E-value=1.4e+02 Score=24.89 Aligned_cols=84 Identities=23% Similarity=0.334 Sum_probs=45.9
Q ss_pred ccccccccCcccccchh-hccCCCCCCCCCCCCCCcccccccCCCccceEEEEeCCChhHHHHHHhcCCCCCeeeEEE--
Q 046522 14 HELRACLRCRLVKTYDQ-FRESGCENCPFFKMDEDHERVVDCTTPNFNGIISVMDPTRSWAARWLRIGRFVPGCYTLA-- 90 (115)
Q Consensus 14 r~lrAC~~C~~I~t~~q-f~~~gCpnC~~l~m~~~~d~v~~~tT~~f~G~I~i~dP~~SwVAk~l~i~~~~pG~YAi~-- 90 (115)
++.|-|-+|+-=+...+ -..-.||+|+.... .+ |.+ -=+|++.+=++=-+| |-..+.||+|++-
T Consensus 109 ~~~RFCg~CG~~~~~~~~g~~~~C~~cg~~~f--PR------~dP--~vIv~v~~~~~ilLa---~~~~h~~g~yS~LAG 175 (279)
T COG2816 109 RSHRFCGRCGTKTYPREGGWARVCPKCGHEHF--PR------IDP--CVIVAVIRGDEILLA---RHPRHFPGMYSLLAG 175 (279)
T ss_pred hhCcCCCCCCCcCccccCceeeeCCCCCCccC--CC------CCC--eEEEEEecCCceeec---CCCCCCCcceeeeee
Confidence 56788999986544332 12247999983211 11 222 123344455442333 3345569999975
Q ss_pred ---ecCCCcHHHHHH-HHhcCCee
Q 046522 91 ---VSEALPEDLQNL-CEDERVQY 110 (115)
Q Consensus 91 ---V~g~lp~~i~~~-l~~~gi~y 110 (115)
+...+-+-+..| +|+-||..
T Consensus 176 FVE~GETlE~AV~REv~EE~Gi~V 199 (279)
T COG2816 176 FVEPGETLEQAVAREVFEEVGIKV 199 (279)
T ss_pred cccCCccHHHHHHHHHHHhhCeEE
Confidence 455565555554 45557754
No 180
>COG4704 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.73 E-value=16 Score=27.77 Aligned_cols=23 Identities=17% Similarity=0.323 Sum_probs=14.7
Q ss_pred hhHHHHHHhcCCCCCeeeEEEecCCC
Q 046522 70 RSWAARWLRIGRFVPGCYTLAVSEAL 95 (115)
Q Consensus 70 ~SwVAk~l~i~~~~pG~YAi~V~g~l 95 (115)
+|--++..++. ||.|||.+--++
T Consensus 75 dpv~~~f~~Lk---~G~YAvaa~qD~ 97 (151)
T COG4704 75 DPVSKSFYGLK---PGKYAVAAFQDE 97 (151)
T ss_pred CchhheeecCC---CccEEEEEEEec
Confidence 34444555555 999999974443
No 181
>PF02357 NusG: Transcription termination factor nusG; InterPro: IPR006645 This sequence is identified by the NGN domain and is represented by the bacterial antitermination protein NusG. This protein influences transcription termination and anti-termination and acts as a component of the transcription complex. In addition to this, it interacts with the termination factor Rho and RNA polymerase [, ].; GO: 0032968 positive regulation of transcription elongation from RNA polymerase II promoter; PDB: 1NZ8_A 2OUG_C 1NPP_B 1M1G_D 1NPR_A 1M1H_A 2XHA_A 2XHC_A 2K06_A.
Probab=26.68 E-value=34 Score=22.21 Aligned_cols=22 Identities=14% Similarity=0.256 Sum_probs=17.0
Q ss_pred eEEEecCCCcHHHHHHHHhcCC
Q 046522 87 YTLAVSEALPEDLQNLCEDERV 108 (115)
Q Consensus 87 YAi~V~g~lp~~i~~~l~~~gi 108 (115)
|+|.+.-.--+.+.+.|+++||
T Consensus 4 Yvl~~~~~~E~~v~~~L~~~~i 25 (92)
T PF02357_consen 4 YVLRTKPGKEQKVAERLERQGI 25 (92)
T ss_dssp EEEEESTTTHHHHHHHHCHHHH
T ss_pred EEEEEECChHHHHHHHHHHcCC
Confidence 7888877767778888877776
No 182
>COG4031 Predicted metal-binding protein [General function prediction only]
Probab=26.16 E-value=31 Score=27.76 Aligned_cols=17 Identities=41% Similarity=0.972 Sum_probs=13.8
Q ss_pred cccCcccccchhhccCCCCCCC
Q 046522 19 CLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 19 C~~C~~I~t~~qf~~~gCpnC~ 40 (115)
| +|+.-++.-.| |+||+
T Consensus 3 C-rCG~~l~~p~~----Cl~Cg 19 (227)
T COG4031 3 C-RCGAELSSPAF----CLNCG 19 (227)
T ss_pred c-ccCCcccccch----hcccC
Confidence 7 89888776665 99998
No 183
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=25.74 E-value=84 Score=18.78 Aligned_cols=24 Identities=13% Similarity=0.094 Sum_probs=17.5
Q ss_pred hHHHHHHhcCCCCCeeeEEEecCCCcHHHHHHH-HhcCCe
Q 046522 71 SWAARWLRIGRFVPGCYTLAVSEALPEDLQNLC-EDERVQ 109 (115)
Q Consensus 71 SwVAk~l~i~~~~pG~YAi~V~g~lp~~i~~~l-~~~gi~ 109 (115)
+.+|+.++++ +.++++.| ++.||.
T Consensus 7 ~elAk~l~v~---------------~~~ii~~l~~~~Gi~ 31 (54)
T PF04760_consen 7 SELAKELGVP---------------SKEIIKKLFKELGIM 31 (54)
T ss_dssp THHHHHHSSS---------------HHHHHHHH-HHHTS-
T ss_pred HHHHHHHCcC---------------HHHHHHHHHHhCCcC
Confidence 5678888766 67888888 557887
No 184
>cd00616 AHBA_syn 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary metabolites. Some well studied proteins in this CD are AHBA_synthase, protein product of pleiotropic regulatory gene degT, Arnb aminotransferase and pilin glycosylation protein. The prototype of this family, the AHBA_synthase, is a dimeric PLP dependent enzyme. AHBA_syn is the terminal enzyme of 3-amino-5-hydroxybenzoic acid (AHBA) formation which is involved in the biosynthesis of ansamycin antibiotics, including rifamycin B. Some members of this CD are involved in 4-amino-6-deoxy-monosaccharide D-perosamine synthesis. Perosamine is an important element in the glycosylation of several cell products, such as antibiotics and lipopolysaccharides of gram-positive and gram-negative bacteria. The pilin glycosylation protein
Probab=25.73 E-value=83 Score=24.49 Aligned_cols=26 Identities=8% Similarity=0.206 Sum_probs=22.2
Q ss_pred CeeeEEEec---CCCcHHHHHHHHhcCCe
Q 046522 84 PGCYTLAVS---EALPEDLQNLCEDERVQ 109 (115)
Q Consensus 84 pG~YAi~V~---g~lp~~i~~~l~~~gi~ 109 (115)
+++|.+.+. +.-++++.+.|+++||.
T Consensus 267 ~~~~~~~~~~~~~~~~~~v~~~L~~~gI~ 295 (352)
T cd00616 267 YHLYVIRLDPEAGESRDELIEALKEAGIE 295 (352)
T ss_pred eEEEEEEECCcCCCCHHHHHHHHHHCCCC
Confidence 368888887 67899999999999994
No 185
>cd02984 TRX_PICOT TRX domain, PICOT (for PKC-interacting cousin of TRX) subfamily; PICOT is a protein that interacts with protein kinase C (PKC) theta, a calcium independent PKC isoform selectively expressed in skeletal muscle and T lymphocytes. PICOT contains an N-terminal TRX-like domain, which does not contain the catalytic CXXC motif, followed by one to three glutaredoxin domains. The TRX-like domain is required for interaction with PKC theta. PICOT inhibits the activation of c-Jun N-terminal kinase and the transcription factors, AP-1 and NF-kB, induced by PKC theta or T-cell activating stimuli.
Probab=25.71 E-value=28 Score=22.10 Aligned_cols=67 Identities=19% Similarity=0.240 Sum_probs=36.5
Q ss_pred hhccCCCCCCCCCCCCCCcccccccCCCccc-e-EEEEeC-CChhHHHHHHhcCCCCC-------eeeEEEecCCCcHHH
Q 046522 30 QFRESGCENCPFFKMDEDHERVVDCTTPNFN-G-IISVMD-PTRSWAARWLRIGRFVP-------GCYTLAVSEALPEDL 99 (115)
Q Consensus 30 qf~~~gCpnC~~l~m~~~~d~v~~~tT~~f~-G-~I~i~d-P~~SwVAk~l~i~~~~p-------G~YAi~V~g~lp~~i 99 (115)
.|....|+.|... .. +.+-.+..+. . .+.-+| -+...+++.+++.. +| |.-.-++.|..++++
T Consensus 20 ~f~~~~C~~C~~~--~~----~l~~l~~~~~~~i~~~~vd~~~~~~~~~~~~i~~-~Pt~~~~~~g~~~~~~~g~~~~~l 92 (97)
T cd02984 20 HFWAPWAEPCKQM--NQ----VFEELAKEAFPSVLFLSIEAEELPEISEKFEITA-VPTFVFFRNGTIVDRVSGADPKEL 92 (97)
T ss_pred EEECCCCHHHHHH--hH----HHHHHHHHhCCceEEEEEccccCHHHHHhcCCcc-ccEEEEEECCEEEEEEeCCCHHHH
Confidence 4666789999822 11 1122233322 1 222234 33566788888876 55 554445677777777
Q ss_pred HHHH
Q 046522 100 QNLC 103 (115)
Q Consensus 100 ~~~l 103 (115)
.+.+
T Consensus 93 ~~~~ 96 (97)
T cd02984 93 AKKV 96 (97)
T ss_pred HHhh
Confidence 6654
No 186
>PF12647 RNHCP: RNHCP domain; InterPro: IPR024439 This domain is found in uncharacterised bacterial proteins. It is typically between 94 and 143 amino acids in length and has a conserved RNHCP sequence motif.
Probab=25.71 E-value=36 Score=23.96 Aligned_cols=28 Identities=18% Similarity=0.465 Sum_probs=19.2
Q ss_pred cccccCcccccchhh---ccCCCCCCC-CCCC
Q 046522 17 RACLRCRLVKTYDQF---RESGCENCP-FFKM 44 (115)
Q Consensus 17 rAC~~C~~I~t~~qf---~~~gCpnC~-~l~m 44 (115)
-.|..|++.++.... ..+-||+|- +++.
T Consensus 5 F~C~~CG~~V~p~~~g~~~RNHCP~CL~S~Hv 36 (92)
T PF12647_consen 5 FTCVHCGLTVSPLAAGSAHRNHCPSCLSSLHV 36 (92)
T ss_pred cCccccCCCcccCCCCCCccCcCccccccccc
Confidence 579999997755321 236799998 4443
No 187
>PF08029 HisG_C: HisG, C-terminal domain; InterPro: IPR013115 ATP phosphoribosyltransferase (2.4.2.17 from EC) is the enzyme that catalyzes the first step in the biosynthesis of histidine in bacteria, fungi and plants as shown below. It is a member of the larger phosphoribosyltransferase superfamily of enzymes which catalyse the condensation of 5-phospho-alpha-D-ribose 1-diphosphate with nitrogenous bases in the presence of divalent metal ions []. ATP + 5-phospho-alpha-D-ribose 1-diphosphate = 1-(5-phospho-D-ribosyl)-ATP + diphosphate Histidine biosynthesis is an energetically expensive process and ATP phosphoribosyltransferase activity is subject to control at several levels. Transcriptional regulation is based primarily on nutrient conditions and determines the amount of enzyme present in the cell, while feedback inihibition rapidly modulates activity in response to cellular conditions. The enzyme has been shown to be inhibited by 1-(5-phospho-D-ribosyl)-ATP, histidine, ppGpp (a signal associated with adverse environmental conditions) and ADP and AMP (which reflect the overall energy status of the cell). As this pathway of histidine biosynthesis is present only in prokayrotes, plants and fungi, this enzyme is a promising target for the development of novel antimicrobial compounds and herbicides. This entry represents the C-terminal portion of ATP phosphoribosyltransferase. The enzyme itself exists in equilibrium between an active dimeric form, an inactive hexameric form and higher aggregates [, ]. Interconversion between the various forms is largely reversible and is influenced by the binding of the natural substrates and inhibitors of the enzyme. This domain is not directly involved in catalysis but appears to be responsible for the formation of hexamers induced by the binding of inhibitors to the enzyme, thus regulating activity.; GO: 0000287 magnesium ion binding, 0003879 ATP phosphoribosyltransferase activity, 0000105 histidine biosynthetic process, 0005737 cytoplasm; PDB: 1Q1K_A 1H3D_A 2VD3_B 1NH7_A 1NH8_A.
Probab=25.67 E-value=81 Score=20.92 Aligned_cols=25 Identities=16% Similarity=0.025 Sum_probs=21.3
Q ss_pred CCeeeEEE--ecCCCcHHHHHHHHhcC
Q 046522 83 VPGCYTLA--VSEALPEDLQNLCEDER 107 (115)
Q Consensus 83 ~pG~YAi~--V~g~lp~~i~~~l~~~g 107 (115)
-+|-|||. |..+.=-+++++|+..|
T Consensus 37 ~~~w~AV~~vV~~~~~~~~~~~Lk~~G 63 (75)
T PF08029_consen 37 DEDWVAVHAVVPEKQVWDLMDKLKAAG 63 (75)
T ss_dssp STTEEEEEEEEECCCHHHHHHHHHCTT
T ss_pred CCCEEEEEEEecHHHHHHHHHHHHHcC
Confidence 47899999 68888889999999886
No 188
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=25.65 E-value=41 Score=26.89 Aligned_cols=27 Identities=22% Similarity=0.316 Sum_probs=15.0
Q ss_pred ccccccccCcccccchhhcc---CCCCCCC
Q 046522 14 HELRACLRCRLVKTYDQFRE---SGCENCP 40 (115)
Q Consensus 14 r~lrAC~~C~~I~t~~qf~~---~gCpnC~ 40 (115)
|.-..|.+|+--......-. --||+|+
T Consensus 243 R~g~pC~~Cg~~I~~~~~~gR~t~~CP~CQ 272 (274)
T PRK01103 243 REGEPCRRCGTPIEKIKQGGRSTFFCPRCQ 272 (274)
T ss_pred CCCCCCCCCCCeeEEEEECCCCcEECcCCC
Confidence 34467999985443221110 1399996
No 189
>PRK10996 thioredoxin 2; Provisional
Probab=25.62 E-value=55 Score=23.19 Aligned_cols=29 Identities=21% Similarity=0.238 Sum_probs=16.8
Q ss_pred hhHHHHHHhcCC------CCCeeeEEEecCCCcHH
Q 046522 70 RSWAARWLRIGR------FVPGCYTLAVSEALPED 98 (115)
Q Consensus 70 ~SwVAk~l~i~~------~~pG~YAi~V~g~lp~~ 98 (115)
...+++.++|.. +..|...-++.|.++++
T Consensus 95 ~~~l~~~~~V~~~Ptlii~~~G~~v~~~~G~~~~e 129 (139)
T PRK10996 95 ERELSARFRIRSIPTIMIFKNGQVVDMLNGAVPKA 129 (139)
T ss_pred CHHHHHhcCCCccCEEEEEECCEEEEEEcCCCCHH
Confidence 356677777655 23455555566666655
No 190
>cd07249 MMCE Methylmalonyl-CoA epimerase (MMCE). MMCE, also called methylmalonyl-CoA racemase (EC 5.1.99.1) interconverts (2R)-methylmalonyl-CoA and (2S)-methylmalonyl-CoA. MMCE has been found in bacteria, archaea, and in animals. In eukaryotes, MMCE is an essential enzyme in a pathway that converts propionyl-CoA to succinyl-CoA, and is important in the breakdown of odd-chain length fatty acids, branched-chain amino acids, and other metabolites. In bacteria, MMCE participates in the reverse pathway for propionate fermentation, glyoxylate regeneration, and the biosynthesis of polyketide antibiotics. MMCE is closely related to glyoxalase I and type I extradiol dioxygenases.
Probab=25.56 E-value=1.7e+02 Score=18.75 Aligned_cols=46 Identities=17% Similarity=0.247 Sum_probs=27.8
Q ss_pred EEEEeCCCh--hHHHHHHhcCCCCCeee--EEEecCCCcHHHHHHHHhcCCeec
Q 046522 62 IISVMDPTR--SWAARWLRIGRFVPGCY--TLAVSEALPEDLQNLCEDERVQYV 111 (115)
Q Consensus 62 ~I~i~dP~~--SwVAk~l~i~~~~pG~Y--Ai~V~g~lp~~i~~~l~~~gi~y~ 111 (115)
.+.|+.|.. +-.+.+.. ...+|.+ |+.|.+ -+++.+.|.++|+++.
T Consensus 49 ~l~l~~~~~~~~~~~~~~~--~~~~g~~h~~f~v~d--~~~~~~~l~~~G~~~~ 98 (128)
T cd07249 49 QIELIEPLDDDSPIAKFLE--KRGEGLHHIAFEVDD--IDAALARLKAQGVRLL 98 (128)
T ss_pred EEEEEEECCCCCcHHHHHh--cCCCceEEEEEEeCC--HHHHHHHHHHCCCeee
Confidence 345555432 33333322 3357775 555654 6888999999999875
No 191
>PRK12366 replication factor A; Reviewed
Probab=25.47 E-value=40 Score=30.51 Aligned_cols=60 Identities=18% Similarity=0.227 Sum_probs=34.7
Q ss_pred cccccccCcccccch--hhccCCCCCCCCCCCCCCcccccccCCCccceEEEEeCCChhHHHHHHhcC
Q 046522 15 ELRACLRCRLVKTYD--QFRESGCENCPFFKMDEDHERVVDCTTPNFNGIISVMDPTRSWAARWLRIG 80 (115)
Q Consensus 15 ~lrAC~~C~~I~t~~--qf~~~gCpnC~~l~m~~~~d~v~~~tT~~f~G~I~i~dP~~SwVAk~l~i~ 80 (115)
-+.||..|.-.+... +| .||.|+-. ++...-+..+.=.+++|-+-++-- ..-..+.+|++
T Consensus 531 ~y~aCp~CnkKv~~~~g~~---~C~~c~~~--~p~~~~~l~~~i~D~TG~~~~t~f-~e~ae~l~G~s 592 (637)
T PRK12366 531 ILYLCPNCRKRVEEVDGEY---ICEFCGEV--EPNELLMLNFTLDDGTGTINCRFY-GKNVEKLLGMS 592 (637)
T ss_pred EEecccccCeEeEcCCCcE---ECCCCCCC--CCcEEEEEEEEEEcCCCCEEEEEE-hHHhHHHhCCC
Confidence 479999999888643 23 39999832 334344444555566666655433 22334444544
No 192
>PF08862 DUF1829: Domain of unknown function DUF1829; InterPro: IPR014961 This short protein is usually associated with IPR014960 from INTERPRO.
Probab=25.43 E-value=1.1e+02 Score=20.72 Aligned_cols=46 Identities=20% Similarity=0.401 Sum_probs=30.8
Q ss_pred CCChhHHHH----HHhc----CCCCCeeeEEE--ecCCCcHHHHHHHHhcCCeecC
Q 046522 67 DPTRSWAAR----WLRI----GRFVPGCYTLA--VSEALPEDLQNLCEDERVQYVP 112 (115)
Q Consensus 67 dP~~SwVAk----~l~i----~~~~pG~YAi~--V~g~lp~~i~~~l~~~gi~y~p 112 (115)
+|.++-++. |.-+ ....+-.|+|- ....+.+++++.|++.+|...|
T Consensus 29 np~~~~~~~~~f~w~D~~~~~~~~~~~~~ii~ND~e~~i~~~~~~a~~~y~I~~i~ 84 (88)
T PF08862_consen 29 NPNKNNIANAIFAWEDTKKRNRKSNSKFYIILNDSEKPISEDIINALEQYNIKPIP 84 (88)
T ss_pred CcCHhHHHHHHHHHhhhhhhccCCCceEEEEECCCCCccCHHHHHHHHHCCCceec
Confidence 466655544 3333 11345667764 3457889999999999999876
No 193
>COG1282 PntB NAD/NADP transhydrogenase beta subunit [Energy production and conversion]
Probab=25.39 E-value=74 Score=28.12 Aligned_cols=40 Identities=20% Similarity=0.254 Sum_probs=32.0
Q ss_pred hHHHHHHhcCCCCCeeeEEE-ecCCCcHHHHHHHHhcCCeec
Q 046522 71 SWAARWLRIGRFVPGCYTLA-VSEALPEDLQNLCEDERVQYV 111 (115)
Q Consensus 71 SwVAk~l~i~~~~pG~YAi~-V~g~lp~~i~~~l~~~gi~y~ 111 (115)
.++|+.|+-. -++=+|||- |-|++|-+.--.|.+..++|-
T Consensus 329 ~E~~~~L~~~-Gv~VrfaIHPVAGRmPGHMNVLLAEA~VpYd 369 (463)
T COG1282 329 AEITEKLRAR-GVNVRFAIHPVAGRMPGHMNVLLAEAKVPYD 369 (463)
T ss_pred HHHHHHHHhc-CCeeeEeecccccCCCcchhhhhhhccCCHH
Confidence 4666666643 489999999 999999988888888888873
No 194
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=25.10 E-value=60 Score=21.32 Aligned_cols=40 Identities=18% Similarity=0.266 Sum_probs=26.9
Q ss_pred CCCCCCCCCCCCCccccccccCcccccchhhccCCCCCCCCC
Q 046522 1 MGSAPAQIPTSFGHELRACLRCRLVKTYDQFRESGCENCPFF 42 (115)
Q Consensus 1 m~~~~~~~p~~~~r~lrAC~~C~~I~t~~qf~~~gCpnC~~l 42 (115)
|+..-+.+-....+..--|++|+.---.-+ ++.|.-|+|.
T Consensus 1 MskGT~S~GKrnk~tH~~CRRCGr~syhv~--k~~CaaCGfg 40 (61)
T COG2126 1 MSKGTPSFGKRNKKTHIRCRRCGRRSYHVR--KKYCAACGFG 40 (61)
T ss_pred CCCCCccccccCCcceehhhhccchheeec--cceecccCCC
Confidence 555555555554466778999997644333 4579999975
No 195
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=25.05 E-value=38 Score=18.91 Aligned_cols=6 Identities=33% Similarity=1.132 Sum_probs=4.6
Q ss_pred CCCCCC
Q 046522 35 GCENCP 40 (115)
Q Consensus 35 gCpnC~ 40 (115)
.||+|+
T Consensus 27 ~C~~C~ 32 (38)
T TIGR02098 27 RCGKCG 32 (38)
T ss_pred ECCCCC
Confidence 488887
No 196
>PF02132 RecR: RecR protein; InterPro: IPR023628 The bacterial protein RecR seems to play a role in a recombinational process of DNA repair []. It may act with RecF and RecO. RecR's structure consists of a N-terminal helix-hairpin-helix (HhH) motif, followed by a Cys4 zinc-finger motif, a Toprim domain and a Walker B motif []. This entry represents the C4-type zinc finger.; PDB: 1VDD_D 2V1C_B.
Probab=24.96 E-value=11 Score=22.04 Aligned_cols=21 Identities=29% Similarity=0.714 Sum_probs=11.9
Q ss_pred cccccccCcccccchhhccCCCCCCC
Q 046522 15 ELRACLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 15 ~lrAC~~C~~I~t~~qf~~~gCpnC~ 40 (115)
+.+-|..|+.+.+.+ -|+.|.
T Consensus 16 ~i~~C~~C~nlse~~-----~C~IC~ 36 (41)
T PF02132_consen 16 NIKFCSICGNLSEED-----PCEICS 36 (41)
T ss_dssp H-EE-SSS--EESSS-----S-HHHH
T ss_pred cCCccCCCCCcCCCC-----cCcCCC
Confidence 567899999887755 388886
No 197
>cd02957 Phd_like Phosducin (Phd)-like family; composed of Phd and Phd-like proteins (PhLP), characterized as cytosolic regulators of G protein functions. Phd and PhLPs specifically bind G protein betagamma (Gbg)-subunits with high affinity, resulting in the solubilization of Gbg from the plasma membrane and impeding G protein-mediated signal transduction by inhibiting the formation of a functional G protein trimer (G protein alphabetagamma). Phd also inhibits the GTPase activity of G protein alpha. Phd can be phosphorylated by protein kinase A and G protein-coupled receptor kinase 2, leading to its inactivation. Phd was originally isolated from the retina, where it is highly expressed and has been implicated to play an important role in light adaptation. It is also found in the pineal gland, liver, spleen, striated muscle and the brain. The C-terminal domain of Phd adopts a thioredoxin fold, but it does not contain a CXXC motif. Phd interacts with G protein beta mostly through the N-te
Probab=24.92 E-value=41 Score=22.61 Aligned_cols=53 Identities=13% Similarity=0.381 Sum_probs=33.2
Q ss_pred hhccCCCCCCCCCCCCCCcccccccCCCccceE-EEEeCCChhHHHHHHhcCCCCCeeeEE
Q 046522 30 QFRESGCENCPFFKMDEDHERVVDCTTPNFNGI-ISVMDPTRSWAARWLRIGRFVPGCYTL 89 (115)
Q Consensus 30 qf~~~gCpnC~~l~m~~~~d~v~~~tT~~f~G~-I~i~dP~~SwVAk~l~i~~~~pG~YAi 89 (115)
.|+...|+.|..+ ..+.+-....+.++ ++-+|-++.-+|+.++|.. +|-....
T Consensus 30 ~F~a~~c~~C~~l------~~~l~~la~~~~~v~f~~vd~~~~~l~~~~~i~~-~Pt~~~f 83 (113)
T cd02957 30 HFYEPGFPRCKIL------DSHLEELAAKYPETKFVKINAEKAFLVNYLDIKV-LPTLLVY 83 (113)
T ss_pred EEeCCCCCcHHHH------HHHHHHHHHHCCCcEEEEEEchhhHHHHhcCCCc-CCEEEEE
Confidence 4777889999832 22333345566663 3446776668888888865 6754443
No 198
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=24.86 E-value=58 Score=23.17 Aligned_cols=21 Identities=29% Similarity=0.752 Sum_probs=15.1
Q ss_pred cccccccCcccccchhhcc-----CCCCCCC
Q 046522 15 ELRACLRCRLVKTYDQFRE-----SGCENCP 40 (115)
Q Consensus 15 ~lrAC~~C~~I~t~~qf~~-----~gCpnC~ 40 (115)
.-|.|..|+. .||. -.||.|+
T Consensus 8 tKR~Cp~CG~-----kFYDLnk~PivCP~CG 33 (108)
T PF09538_consen 8 TKRTCPSCGA-----KFYDLNKDPIVCPKCG 33 (108)
T ss_pred CcccCCCCcc-----hhccCCCCCccCCCCC
Confidence 3488999975 5654 1599998
No 199
>PRK11486 flagellar biosynthesis protein FliO; Provisional
Probab=24.58 E-value=48 Score=24.36 Aligned_cols=27 Identities=19% Similarity=0.323 Sum_probs=21.6
Q ss_pred hhHHHHHHhcCCCCCeeeEEEecCCCc
Q 046522 70 RSWAARWLRIGRFVPGCYTLAVSEALP 96 (115)
Q Consensus 70 ~SwVAk~l~i~~~~pG~YAi~V~g~lp 96 (115)
-.|+.|.+++.....|...++|.+.+|
T Consensus 35 ~aWLlkR~~~~~~~~~~~~lkVva~~s 61 (124)
T PRK11486 35 AAWLVKRLGFAPKRTGVRGLKISASAS 61 (124)
T ss_pred HHHHHHHcCCCCCCCCCcceEEEEeec
Confidence 369999998776567778899988775
No 200
>COG0178 UvrA Excinuclease ATPase subunit [DNA replication, recombination, and repair]
Probab=24.40 E-value=1.1e+02 Score=29.52 Aligned_cols=82 Identities=22% Similarity=0.309 Sum_probs=51.8
Q ss_pred cccccccCcccccch---hh--cc--CCCCCCCCCC--CCCCcccccccCC-CccceEEEEeCCChhHHHHH-------H
Q 046522 15 ELRACLRCRLVKTYD---QF--RE--SGCENCPFFK--MDEDHERVVDCTT-PNFNGIISVMDPTRSWAARW-------L 77 (115)
Q Consensus 15 ~lrAC~~C~~I~t~~---qf--~~--~gCpnC~~l~--m~~~~d~v~~~tT-~~f~G~I~i~dP~~SwVAk~-------l 77 (115)
...||..|++..++= -| .. --||.|.-+. ..-|.+.+.+..+ +-=+|.|....+.++|-..+ +
T Consensus 244 ~~~acp~~g~~~~eleprlFSFNsP~GaCp~C~GlG~~~~~D~~~vi~d~~lsl~egai~~~~~~~~~~~~~l~~l~~~~ 323 (935)
T COG0178 244 ENFACPVCGFSIPELEPRLFSFNSPFGACPTCDGLGVKLEVDPDLVIPDPNLSLNEGAIAPWGNTNSYYLQMLQALAEHY 323 (935)
T ss_pred cccCCCccCcccCCCCcccccCCCCCCCCCcCCCcceeeeeChhhcCCCCCCChhcCCeecCcCCCchHHHHHHHHHHHc
Confidence 457999999987653 12 22 2499998432 3345566666644 33578888888887775433 4
Q ss_pred hcCCCCCeeeEEEecCCCcHHHHHHH
Q 046522 78 RIGRFVPGCYTLAVSEALPEDLQNLC 103 (115)
Q Consensus 78 ~i~~~~pG~YAi~V~g~lp~~i~~~l 103 (115)
+++..+| -.+||+++.+.+
T Consensus 324 ~~d~~~P-------~~~L~~e~~~~i 342 (935)
T COG0178 324 GFDLDTP-------WKDLPEEQQDII 342 (935)
T ss_pred CCCccCc-------hhhCCHHHHHHH
Confidence 4444344 357888887765
No 201
>PF09413 DUF2007: Domain of unknown function (DUF2007); InterPro: IPR018551 This is a family of proteins with unknown function. ; PDB: 2HFV_A.
Probab=24.37 E-value=54 Score=20.17 Aligned_cols=17 Identities=12% Similarity=0.171 Sum_probs=10.4
Q ss_pred HHHHHHHhcCCeecCCC
Q 046522 98 DLQNLCEDERVQYVPPK 114 (115)
Q Consensus 98 ~i~~~l~~~gi~y~prd 114 (115)
-+...|+++||.|.-+|
T Consensus 14 ~i~~~L~~~gI~~~v~~ 30 (67)
T PF09413_consen 14 LIKGLLEENGIPAFVKN 30 (67)
T ss_dssp HHHHHHHHTT--EE--S
T ss_pred HHHHHHHhCCCcEEEEC
Confidence 36788999999997554
No 202
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=23.98 E-value=1.2e+02 Score=20.43 Aligned_cols=26 Identities=27% Similarity=0.274 Sum_probs=22.4
Q ss_pred hHHHHHHhcCCCCCeeeEEEecCCCcHHHHHHHHhcCCeec
Q 046522 71 SWAARWLRIGRFVPGCYTLAVSEALPEDLQNLCEDERVQYV 111 (115)
Q Consensus 71 SwVAk~l~i~~~~pG~YAi~V~g~lp~~i~~~l~~~gi~y~ 111 (115)
+.+||.++|. +..+.+.|.++|+-|+
T Consensus 28 ~~~AK~L~i~---------------~~~l~~~Lr~~g~l~~ 53 (111)
T PF03374_consen 28 REAAKLLGIG---------------RNKLFQWLREKGWLYR 53 (111)
T ss_pred HHHHHHhCCC---------------HHHHHHHHHhCCceEE
Confidence 7788888666 6789999999999998
No 203
>cd05313 NAD_bind_2_Glu_DH NAD(P) binding domain of glutamate dehydrogenase, subgroup 2. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NADP+. Glutamate DH is a multidomain enzyme that catalyzes the reaction from glutamate to 2-oxyoglutarate and ammonia in the presence of NAD or NADP. It is present in all organisms. Enzymes involved in ammonia asimilation are typically NADP+-dependent, while those involved in glutamate catabolism are generally NAD+-dependent. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids t
Probab=23.97 E-value=74 Score=25.74 Aligned_cols=23 Identities=9% Similarity=0.186 Sum_probs=20.7
Q ss_pred ecCCCcHHHHHHHHhcCCeecCC
Q 046522 91 VSEALPEDLQNLCEDERVQYVPP 113 (115)
Q Consensus 91 V~g~lp~~i~~~l~~~gi~y~pr 113 (115)
=++.+.++..+.|+++||.|.|.
T Consensus 154 AN~p~t~~a~~~L~~rGI~vvPD 176 (254)
T cd05313 154 ANMPCTAEAIEVFRQAGVLFAPG 176 (254)
T ss_pred CCCCCCHHHHHHHHHCCcEEECc
Confidence 37889999999999999999984
No 204
>cd02956 ybbN ybbN protein family; ybbN is a hypothetical protein containing a redox-inactive TRX-like domain. Its gene has been sequenced from several gammaproteobacteria and actinobacteria.
Probab=23.82 E-value=76 Score=20.08 Aligned_cols=53 Identities=11% Similarity=0.153 Sum_probs=27.5
Q ss_pred hhccCCCCCCCCCCCCCCcccccccCCCccceE---EEEeCCChhHHHHHHhcCCCCCeeeEE
Q 046522 30 QFRESGCENCPFFKMDEDHERVVDCTTPNFNGI---ISVMDPTRSWAARWLRIGRFVPGCYTL 89 (115)
Q Consensus 30 qf~~~gCpnC~~l~m~~~~d~v~~~tT~~f~G~---I~i~dP~~SwVAk~l~i~~~~pG~YAi 89 (115)
.|+...|+.|..+. .. ..-....|.|- +.|---+..-+++.+++.. +|-.+-+
T Consensus 18 ~f~a~wC~~C~~~~--~~----~~~~~~~~~~~~~~~~vd~~~~~~l~~~~~i~~-~Pt~~~~ 73 (96)
T cd02956 18 DFWAPRSPPSKELL--PL----LERLAEEYQGQFVLAKVNCDAQPQIAQQFGVQA-LPTVYLF 73 (96)
T ss_pred EEECCCChHHHHHH--HH----HHHHHHHhCCcEEEEEEeccCCHHHHHHcCCCC-CCEEEEE
Confidence 46677899998221 11 11123334332 2332223467888888865 5554444
No 205
>COG1058 CinA Predicted nucleotide-utilizing enzyme related to molybdopterin-biosynthesis enzyme MoeA [General function prediction only]
Probab=23.72 E-value=1.6e+02 Score=23.94 Aligned_cols=40 Identities=10% Similarity=0.100 Sum_probs=31.6
Q ss_pred EeCCChhHHHHHHhcCCCCCeeeEEEecCCCcHHHHHHHHhc
Q 046522 65 VMDPTRSWAARWLRIGRFVPGCYTLAVSEALPEDLQNLCEDE 106 (115)
Q Consensus 65 i~dP~~SwVAk~l~i~~~~pG~YAi~V~g~lp~~i~~~l~~~ 106 (115)
++|.+-.|+|+.|.--. =-.|-+.+.|+-|++|.+.|...
T Consensus 18 ivdtNa~~la~~L~~~G--~~v~~~~~VgD~~~~I~~~l~~a 57 (255)
T COG1058 18 IVDTNAAFLADELTELG--VDLARITTVGDNPDRIVEALREA 57 (255)
T ss_pred eecchHHHHHHHHHhcC--ceEEEEEecCCCHHHHHHHHHHH
Confidence 46888999999995322 23677889999999999998765
No 206
>COG5636 Uncharacterized conserved protein, contains Zn-ribbon-like motif [Function unknown]
Probab=23.35 E-value=96 Score=25.58 Aligned_cols=25 Identities=44% Similarity=0.773 Sum_probs=17.6
Q ss_pred CccccccccCcccccchhhccCCCCCCC
Q 046522 13 GHELRACLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 13 ~r~lrAC~~C~~I~t~~qf~~~gCpnC~ 40 (115)
+++.-||-+|.+ -+.|+=.|||.=+
T Consensus 235 ~K~Vs~CGnCyl---GDAFRCSGCPylG 259 (284)
T COG5636 235 GKKVSACGNCYL---GDAFRCSGCPYLG 259 (284)
T ss_pred cccccccccccc---cccceecCCCccC
Confidence 456789999998 6788744444444
No 207
>cd00474 SUI1_eIF1 The SUI1/eIF1 (eukaryotic initiation factor 1) fold is found in eukaryotes, archaea, and some bacteria and is thought to play an important role in accurate initiator codon recognition during translation initiation. This fold, which includes two antiparallel alpha helices packed against the same side of a five-strand beta sheet, is structurally similar to other RNA-binding domains suggesting that SUI1/eIF1 may bind RNA. Point mutations in the yeast eIF1 implicate the protein in maintaining accurate start-site selection but its mechanism of action is unknown.
Probab=23.24 E-value=81 Score=20.94 Aligned_cols=23 Identities=0% Similarity=0.011 Sum_probs=20.7
Q ss_pred eEEEecCCCcHHHHHHHHhcCCe
Q 046522 87 YTLAVSEALPEDLQNLCEDERVQ 109 (115)
Q Consensus 87 YAi~V~g~lp~~i~~~l~~~gi~ 109 (115)
-.|.++|+-.+.+.+.|.+.|+.
T Consensus 48 ~~I~lQGD~r~~v~~~L~~~g~~ 70 (77)
T cd00474 48 EVIELQGDQRKKIKEFLIKMGFA 70 (77)
T ss_pred CEEEEeCcHHHHHHHHHHHcCCC
Confidence 47889999999999999999874
No 208
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=23.23 E-value=61 Score=28.10 Aligned_cols=16 Identities=13% Similarity=0.237 Sum_probs=12.7
Q ss_pred ccccccccCcccccch
Q 046522 14 HELRACLRCRLVKTYD 29 (115)
Q Consensus 14 r~lrAC~~C~~I~t~~ 29 (115)
...--|..|++|-..+
T Consensus 423 ~~~~~c~~c~~~yd~~ 438 (479)
T PRK05452 423 GPRMQCSVCQWIYDPA 438 (479)
T ss_pred CCeEEECCCCeEECCC
Confidence 4456899999998875
No 209
>PRK11032 hypothetical protein; Provisional
Probab=23.11 E-value=48 Score=25.28 Aligned_cols=27 Identities=15% Similarity=0.332 Sum_probs=18.7
Q ss_pred cccccccCcccccchhhcc-CCCCCCCC
Q 046522 15 ELRACLRCRLVKTYDQFRE-SGCENCPF 41 (115)
Q Consensus 15 ~lrAC~~C~~I~t~~qf~~-~gCpnC~~ 41 (115)
....|..|+.-+....-.. .-||+|+.
T Consensus 123 G~LvC~~Cg~~~~~~~p~~i~pCp~C~~ 150 (160)
T PRK11032 123 GNLVCEKCHHHLAFYTPEVLPLCPKCGH 150 (160)
T ss_pred ceEEecCCCCEEEecCCCcCCCCCCCCC
Confidence 4578999998776543222 46999983
No 210
>PF11121 DUF2639: Protein of unknown function (DUF2639); InterPro: IPR022580 This family is conserved in the Bacillaceae family. Several members are named as being YflJ, but the function is not known.
Probab=23.09 E-value=58 Score=19.74 Aligned_cols=15 Identities=0% Similarity=-0.184 Sum_probs=12.6
Q ss_pred HHHHHHhcCCeecCC
Q 046522 99 LQNLCEDERVQYVPP 113 (115)
Q Consensus 99 i~~~l~~~gi~y~pr 113 (115)
.+++|...||.++|.
T Consensus 8 ~V~eLKk~GI~~h~~ 22 (40)
T PF11121_consen 8 YVKELKKLGIRRHEG 22 (40)
T ss_pred HHHHHHHhCccccch
Confidence 478999999999884
No 211
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=22.99 E-value=50 Score=20.24 Aligned_cols=12 Identities=25% Similarity=0.512 Sum_probs=8.7
Q ss_pred ccccCcccccch
Q 046522 18 ACLRCRLVKTYD 29 (115)
Q Consensus 18 AC~~C~~I~t~~ 29 (115)
.|..|++|-..+
T Consensus 3 ~C~~CgyvYd~~ 14 (47)
T PF00301_consen 3 QCPVCGYVYDPE 14 (47)
T ss_dssp EETTTSBEEETT
T ss_pred CCCCCCEEEcCC
Confidence 488888886654
No 212
>PHA02085 hypothetical protein
Probab=22.95 E-value=22 Score=24.77 Aligned_cols=26 Identities=8% Similarity=0.200 Sum_probs=20.6
Q ss_pred CCccceEEEEeCCChhHHHHHHhcCC
Q 046522 56 TPNFNGIISVMDPTRSWAARWLRIGR 81 (115)
Q Consensus 56 T~~f~G~I~i~dP~~SwVAk~l~i~~ 81 (115)
|+.-.|.-+-+.|-++|||..||.+-
T Consensus 7 S~e~R~~Fa~~~~~N~~IAe~mGmdw 32 (87)
T PHA02085 7 SEEHKAMFARRHDCNQWIADKMGTDW 32 (87)
T ss_pred CHhHHHHHHhhchhhHHHHHHhcCCc
Confidence 45556666777899999999999875
No 213
>PF09652 Cas_VVA1548: Putative CRISPR-associated protein (Cas_VVA1548); InterPro: IPR013443 Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) are a family of DNA direct repeats separated by regularly sized non-repetitive spacer sequences that are found in most bacterial and archaeal genomes []. CRISPRs appear to provide acquired resistance against bacteriophages, possibly acting with an RNA interference-like mechanism to inhibit gene functions of invasive DNA elements [, ]. Differences in the number and type of spacers between CRISPR repeats correlate with phage sensitivity. It is thought that following phage infection, bacteria integrate new spacers derived from phage genomic sequences, and that the removal or addition of particular spacers modifies the phage-resistance phenotype of the cell. Therefore, the specificity of CRISPRs may be determined by spacer-phage sequence similarity. In addition, there are many protein families known as CRISPR-associated sequences (Cas), which are encoded in the vicinity of CRISPR loci []. CRISPR/cas gene regions can be quite large, with up to 20 different, tandem-arranged cas genes next to a CRISPR cluster or filling the region between two repeat clusters. Cas genes and CRISPRs are found on mobile genetic elements such as plasmids, and have undergone extensive horizontal transfer. Cas proteins are thought to be involved in the propagation and functioning of CRISPRs. Some Cas proteins show similarity to helicases and repair proteins, although the functions of most are unknown. Cas families can be divided into subtypes according to operon organisation and phylogeny. This entry represents a conserved region of about 95 amino acids found exclusively in species with CRISPR repeats. In all bacterial species that contain this entry, the genes encoding the proteins are in the midst of a cluster of cas genes.
Probab=22.78 E-value=79 Score=22.32 Aligned_cols=22 Identities=23% Similarity=0.312 Sum_probs=20.1
Q ss_pred EecCCCcHHHHHHHHhcCCeec
Q 046522 90 AVSEALPEDLQNLCEDERVQYV 111 (115)
Q Consensus 90 ~V~g~lp~~i~~~l~~~gi~y~ 111 (115)
.|-|.||-.+..++-++|..|.
T Consensus 37 ~ViGtLPvhLaA~vc~kGa~y~ 58 (93)
T PF09652_consen 37 VVIGTLPVHLAAEVCEKGARYY 58 (93)
T ss_pred EEEEeCcHHHHHHHHhCCcEEE
Confidence 6889999999999999998884
No 214
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=22.65 E-value=30 Score=22.51 Aligned_cols=26 Identities=23% Similarity=0.533 Sum_probs=16.3
Q ss_pred cccccccCcccccchhhccC---CCCCCC
Q 046522 15 ELRACLRCRLVKTYDQFRES---GCENCP 40 (115)
Q Consensus 15 ~lrAC~~C~~I~t~~qf~~~---gCpnC~ 40 (115)
....|..|+..++.++..-. -||.|+
T Consensus 40 ~~v~Cg~C~~~~~~~~~~c~~~~~C~~C~ 68 (71)
T PF05495_consen 40 KRVICGKCRTEQPIDEYSCGADYFCPICG 68 (71)
T ss_dssp -EEEETTT--EEES-SBTT--SEEETTTT
T ss_pred cCeECCCCCCccChhhhhcCCCccCcCcC
Confidence 36889999999998764222 488887
No 215
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=22.57 E-value=66 Score=22.66 Aligned_cols=27 Identities=22% Similarity=0.541 Sum_probs=15.2
Q ss_pred cccccccCc-cccc--chhh-ccCCCCCCCC
Q 046522 15 ELRACLRCR-LVKT--YDQF-RESGCENCPF 41 (115)
Q Consensus 15 ~lrAC~~C~-~I~t--~~qf-~~~gCpnC~~ 41 (115)
++--|..|+ ..++ .+.- ..-.||+|++
T Consensus 20 t~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~ 50 (99)
T PRK14892 20 KIFECPRCGKVSISVKIKKNIAIITCGNCGL 50 (99)
T ss_pred cEeECCCCCCeEeeeecCCCcceEECCCCCC
Confidence 577899999 3222 0000 0124999993
No 216
>KOG4354 consensus N-acetyl-gamma-glutamyl-phosphate reductase [Amino acid transport and metabolism]
Probab=22.48 E-value=42 Score=28.32 Aligned_cols=41 Identities=24% Similarity=0.582 Sum_probs=23.9
Q ss_pred CcccccccCCCccceEEEEeCCChhHH------------HHHHhcCCCCCeeeEEEecCCC
Q 046522 47 DHERVVDCTTPNFNGIISVMDPTRSWA------------ARWLRIGRFVPGCYTLAVSEAL 95 (115)
Q Consensus 47 ~~d~v~~~tT~~f~G~I~i~dP~~SwV------------Ak~l~i~~~~pG~YAi~V~g~l 95 (115)
.+.++.| .+.+|.| .|+++|+ ++--.|. -||+||--.+=-|
T Consensus 111 gks~iid-lsad~rf-----~p~~~w~YGLpElndRe~i~na~~ia--NPGCYaTgsQl~l 163 (340)
T KOG4354|consen 111 GKSRIID-LSADWRF-----QPHKEWVYGLPELNDREDIKNARLIA--NPGCYATGSQLPL 163 (340)
T ss_pred Cceeeee-cchhhcC-----CcchheeecCcccccHHHHhhhhhcc--CCCcccccCcccc
Confidence 3334443 5666665 5777875 3333444 4999997654433
No 217
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=22.45 E-value=1.1e+02 Score=23.26 Aligned_cols=23 Identities=26% Similarity=0.326 Sum_probs=17.1
Q ss_pred CChhHHHHHHhcCCCCCeeeEEEe
Q 046522 68 PTRSWAARWLRIGRFVPGCYTLAV 91 (115)
Q Consensus 68 P~~SwVAk~l~i~~~~pG~YAi~V 91 (115)
..+.|||+..+|-.- +|.+-+.|
T Consensus 50 ~~~~~vArIekiW~~-~G~~~~~g 72 (148)
T cd04718 50 SGDLWLARIEKLWEE-NGTYWYAA 72 (148)
T ss_pred cCchHHHHHHHHHhc-cCceEEEE
Confidence 467899999998664 48876555
No 218
>PF05093 CIAPIN1: Cytokine-induced anti-apoptosis inhibitor 1, Fe-S biogenesis; InterPro: IPR007785 Anamorsin, subsequently named CIAPIN1 for cytokine-induced anti-apoptosis inhibitor 1, in humans is the homologue of yeast Dre2, a conserved soluble eukaryotic Fe-S cluster protein, that functions in cytosolic Fe-S protein biogenesis. It is found in both the cytoplasm and in the mitochondrial intermembrane space (IMS) []. CIAPIN1 is found to be up-regulated in hepatocellular cancer, is considered to be a downstream effector of the receptor tyrosine kinase-Ras signalling pathway, and is essential in mouse definitive haematopoiesis []. In addition, it has also anti-apoptotic effects in the cell. It is involved in negative control of cell death upon cytokine withdrawal and promotes development of hematopoietic cells [].
Probab=22.30 E-value=50 Score=23.52 Aligned_cols=23 Identities=39% Similarity=1.034 Sum_probs=17.5
Q ss_pred ccccccCcccccchhhccCCCCCCCCCCC
Q 046522 16 LRACLRCRLVKTYDQFRESGCENCPFFKM 44 (115)
Q Consensus 16 lrAC~~C~~I~t~~qf~~~gCpnC~~l~m 44 (115)
--+|-+|.| -|-|+ |-.|+++.|
T Consensus 67 ~ssCGsC~L---GDAFR---Ca~CPYlGl 89 (100)
T PF05093_consen 67 KSSCGSCYL---GDAFR---CAGCPYLGL 89 (100)
T ss_pred cCccccccc---cccce---ecCCCcCCC
Confidence 378999998 77887 777776644
No 219
>TIGR00334 5S_RNA_mat_M5 ribonuclease M5. This family of orthologous proteins shows a weak but significant similarity to the central region of the DnaG-type DNA primase. The region of similarity is termed the Toprim (topoisomerase-primase) domain and is also shared by RecR, OLD family nucleases, and type IA and II topoisomerases.
Probab=22.29 E-value=98 Score=24.00 Aligned_cols=53 Identities=23% Similarity=0.269 Sum_probs=34.3
Q ss_pred ccceEEEEeCCChh------HHHHHHhc--CCCCCeeeE------EEecCCCcHHHHHHHHhcCCee
Q 046522 58 NFNGIISVMDPTRS------WAARWLRI--GRFVPGCYT------LAVSEALPEDLQNLCEDERVQY 110 (115)
Q Consensus 58 ~f~G~I~i~dP~~S------wVAk~l~i--~~~~pG~YA------i~V~g~lp~~i~~~l~~~gi~y 110 (115)
.-.|+|+++||+.+ ++.+.+.- ..|+|=.|| |-|..--|++|.+.|++....+
T Consensus 46 ~~rgVIIfTDpD~~GekIRk~i~~~vp~~khafi~~~~a~~~~~~iGVE~As~e~I~~AL~~~~~~~ 112 (174)
T TIGR00334 46 KKQGVIILTDPDFPGEKIRKKIEQHLPGYENCFIPKHLAKPNKKKIGVEEASVEAIIAALENVHEET 112 (174)
T ss_pred hcCCEEEEeCCCCchHHHHHHHHHHCCCCeEEeeeHHhcCcCCCCcccCCCCHHHHHHHHHHhcccc
Confidence 35899999999864 44443320 013444444 3466667999999999877543
No 220
>cd02965 HyaE HyaE family; HyaE is also called HupG and HoxO. They are proteins serving a critical role in the assembly of multimeric [NiFe] hydrogenases, the enzymes that catalyze the oxidation of molecular hydrogen to enable microorganisms to utilize hydrogen as the sole energy source. The E. coli HyaE protein is a chaperone that specifically interacts with the twin-arginine translocation (Tat) signal peptide of the [NiFe] hydrogenase-1 beta subunit precursor. Tat signal peptides target precursor proteins to the Tat protein export system, which facilitates the transport of fully folded proteins across the inner membrane. HyaE may be involved in regulating the traffic of [NiFe] hydrogenase-1 on the Tat transport pathway.
Probab=22.27 E-value=1.2e+02 Score=21.47 Aligned_cols=61 Identities=15% Similarity=0.049 Sum_probs=36.7
Q ss_pred hccC--CCCCCCCCCCCCCcccccccCCCccceEE---EEeCCChhHHHHHHhcCCCCCee-------eEEEecCCCcHH
Q 046522 31 FRES--GCENCPFFKMDEDHERVVDCTTPNFNGII---SVMDPTRSWAARWLRIGRFVPGC-------YTLAVSEALPED 98 (115)
Q Consensus 31 f~~~--gCpnC~~l~m~~~~d~v~~~tT~~f~G~I---~i~dP~~SwVAk~l~i~~~~pG~-------YAi~V~g~lp~~ 98 (115)
|..+ .||-|... .-+.+-....|.|.+ .+-.-++..+|...+|.. +|-. .-=+..|..+.+
T Consensus 34 f~~~~~~cp~c~~i------~P~leela~e~~~~v~f~kVdid~~~~la~~f~V~s-IPTli~fkdGk~v~~~~G~~~~~ 106 (111)
T cd02965 34 LAGDPVRFPEVLDV------AVVLPELLKAFPGRFRAAVVGRADEQALAARFGVLR-TPALLFFRDGRYVGVLAGIRDWD 106 (111)
T ss_pred ecCCcccCcchhhh------HhHHHHHHHHCCCcEEEEEEECCCCHHHHHHcCCCc-CCEEEEEECCEEEEEEeCccCHH
Confidence 4555 59999833 234445677788743 333444569999999876 5544 333445555543
No 221
>COG1328 NrdD Oxygen-sensitive ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]
Probab=22.22 E-value=52 Score=30.56 Aligned_cols=24 Identities=21% Similarity=0.537 Sum_probs=18.3
Q ss_pred ccccccccCcccccchhhccCCCCCCC
Q 046522 14 HELRACLRCRLVKTYDQFRESGCENCP 40 (115)
Q Consensus 14 r~lrAC~~C~~I~t~~qf~~~gCpnC~ 40 (115)
...+-|-.|++... |...+||+|+
T Consensus 639 ~~i~~C~~cg~~~~---~~~~~Cp~CG 662 (700)
T COG1328 639 TPISVCNRCGYSGE---GLRTRCPKCG 662 (700)
T ss_pred CCceeeccCCcccc---cccccCCCCC
Confidence 46889999999754 3335699998
No 222
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=21.98 E-value=96 Score=27.14 Aligned_cols=47 Identities=23% Similarity=0.478 Sum_probs=28.8
Q ss_pred cccccccCcccccchhhccCCCCCCCCCCCCCCcccccccCCCccceEEEEeCCCh--hHHHHHH
Q 046522 15 ELRACLRCRLVKTYDQFRESGCENCPFFKMDEDHERVVDCTTPNFNGIISVMDPTR--SWAARWL 77 (115)
Q Consensus 15 ~lrAC~~C~~I~t~~qf~~~gCpnC~~l~m~~~~d~v~~~tT~~f~G~I~i~dP~~--SwVAk~l 77 (115)
+.+-|-.|..=.... .+..||||+ ...+|.=-|+++|--- --+|-.|
T Consensus 56 ~i~kC~~c~~~~~y~--~~~~C~~cg--------------~~~~l~R~VSfVDaPGHe~LMATML 104 (415)
T COG5257 56 KIYKCPECYRPECYT--TEPKCPNCG--------------AETELVRRVSFVDAPGHETLMATML 104 (415)
T ss_pred ceEeCCCCCCCcccc--cCCCCCCCC--------------CCccEEEEEEEeeCCchHHHHHHHh
Confidence 568899998642211 134699998 2347777888876422 3445554
No 223
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=21.93 E-value=38 Score=25.54 Aligned_cols=29 Identities=31% Similarity=0.484 Sum_probs=22.7
Q ss_pred ccccc-cccCcccccchhhccCCCCCCCCC
Q 046522 14 HELRA-CLRCRLVKTYDQFRESGCENCPFF 42 (115)
Q Consensus 14 r~lrA-C~~C~~I~t~~qf~~~gCpnC~~l 42 (115)
..+.| |..|+-.+..-.|..--||+|+..
T Consensus 146 Gvv~a~~~~~g~~~~~~~~~~~~c~~~~~~ 175 (189)
T PRK09521 146 GVIYAMCSRCRTPLVKKGENELKCPNCGNI 175 (189)
T ss_pred eEEEEEccccCCceEECCCCEEECCCCCCE
Confidence 35677 888999888888766679999844
No 224
>KOG0907 consensus Thioredoxin [Posttranslational modification, protein turnover, chaperones]
Probab=21.68 E-value=87 Score=21.75 Aligned_cols=71 Identities=13% Similarity=0.180 Sum_probs=51.1
Q ss_pred hhccCCCCCCCCCCCCCCcccccccCCCccceEEEE-eCCC-hhHHHHHHhcCC------CCCeeeEEEecCCCcHHHHH
Q 046522 30 QFRESGCENCPFFKMDEDHERVVDCTTPNFNGIISV-MDPT-RSWAARWLRIGR------FVPGCYTLAVSEALPEDLQN 101 (115)
Q Consensus 30 qf~~~gCpnC~~l~m~~~~d~v~~~tT~~f~G~I~i-~dP~-~SwVAk~l~i~~------~~pG~YAi~V~g~lp~~i~~ 101 (115)
.|+...|+=|..+. -...-++..|..++.+ +|-+ ...+|+.+++.. +..|.=..++.|-.++++++
T Consensus 27 dF~a~wCgPCk~i~------P~~~~La~~y~~v~Flkvdvde~~~~~~~~~V~~~PTf~f~k~g~~~~~~vGa~~~~l~~ 100 (106)
T KOG0907|consen 27 DFYATWCGPCKAIA------PKFEKLAEKYPDVVFLKVDVDELEEVAKEFNVKAMPTFVFYKGGEEVDEVVGANKAELEK 100 (106)
T ss_pred EEECCCCcchhhhh------hHHHHHHHHCCCCEEEEEecccCHhHHHhcCceEeeEEEEEECCEEEEEEecCCHHHHHH
Confidence 47778899999442 1333478888886666 3443 477888888766 46788888899999998887
Q ss_pred HHHhc
Q 046522 102 LCEDE 106 (115)
Q Consensus 102 ~l~~~ 106 (115)
.++..
T Consensus 101 ~i~~~ 105 (106)
T KOG0907|consen 101 KIAKH 105 (106)
T ss_pred HHHhc
Confidence 77653
No 225
>TIGR01068 thioredoxin thioredoxin. Several proteins, such as protein disulfide isomerase, have two or more copies of a domain closely related to thioredoxin. This model is designed to recognize authentic thioredoxin, a small protein that should be hit exactly once by this model.
Probab=21.57 E-value=1.2e+02 Score=18.76 Aligned_cols=69 Identities=17% Similarity=0.318 Sum_probs=36.3
Q ss_pred hhccCCCCCCCCCCCCCCcccccccCCCccce--EEEEeCC-ChhHHHHHHhcCCCCCeeeEE-------EecCCCc-HH
Q 046522 30 QFRESGCENCPFFKMDEDHERVVDCTTPNFNG--IISVMDP-TRSWAARWLRIGRFVPGCYTL-------AVSEALP-ED 98 (115)
Q Consensus 30 qf~~~gCpnC~~l~m~~~~d~v~~~tT~~f~G--~I~i~dP-~~SwVAk~l~i~~~~pG~YAi-------~V~g~lp-~~ 98 (115)
.|....|+.|... ..........|.+ .++.+|= ++.-+++.+++.. +|-...+ .+.|..+ ++
T Consensus 20 ~f~~~~C~~C~~~------~~~l~~~~~~~~~~~~~~~vd~~~~~~~~~~~~v~~-~P~~~~~~~g~~~~~~~g~~~~~~ 92 (101)
T TIGR01068 20 DFWAPWCGPCKMI------APILEELAKEYEGKVKFVKLNVDENPDIAAKYGIRS-IPTLLLFKNGKEVDRSVGALPKAA 92 (101)
T ss_pred EEECCCCHHHHHh------CHHHHHHHHHhcCCeEEEEEECCCCHHHHHHcCCCc-CCEEEEEeCCcEeeeecCCCCHHH
Confidence 3556779999822 1112223445554 2333443 3345778888875 5544433 3445555 66
Q ss_pred HHHHHHh
Q 046522 99 LQNLCED 105 (115)
Q Consensus 99 i~~~l~~ 105 (115)
+.+.|++
T Consensus 93 l~~~l~~ 99 (101)
T TIGR01068 93 LKQLINK 99 (101)
T ss_pred HHHHHHh
Confidence 6666654
No 226
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=21.56 E-value=76 Score=18.16 Aligned_cols=7 Identities=29% Similarity=0.871 Sum_probs=5.6
Q ss_pred CCCCCCC
Q 046522 35 GCENCPF 41 (115)
Q Consensus 35 gCpnC~~ 41 (115)
-||+|+.
T Consensus 4 ~Cp~Cg~ 10 (47)
T PF14690_consen 4 RCPHCGS 10 (47)
T ss_pred cCCCcCC
Confidence 4999994
No 227
>PF01186 Lysyl_oxidase: Lysyl oxidase ; InterPro: IPR001695 Lysyl oxidase (1.4.3.13 from EC) (LOX) [] is an extracellular copper-dependent enzyme that catalyses the oxidative deamination of peptidyl lysine residues in precursors of various collagens and elastins, yielding alpha-aminoadipic-delta-semialdehyde. The deaminated lysines are then able to form semialdehyde cross-links, resulting in the formation of insoluble collagen and elastin fibres in the extracellular matrix []. The active site of LOX resides towards the C terminus: this region also binds a single copper atom in an octahedral coordination complex involving at least 3 His residues []. Four histidine residues are clustered in a central region of the enzyme. This region is thought to be involved in cooper-binding and is called the 'copper-talon' [].; GO: 0005507 copper ion binding, 0016641 oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor, 0055114 oxidation-reduction process
Probab=21.53 E-value=45 Score=26.57 Aligned_cols=27 Identities=33% Similarity=0.635 Sum_probs=20.2
Q ss_pred HHHHhcCCCCCeeeEEEecCCCcHHHHH
Q 046522 74 ARWLRIGRFVPGCYTLAVSEALPEDLQN 101 (115)
Q Consensus 74 Ak~l~i~~~~pG~YAi~V~g~lp~~i~~ 101 (115)
.+|+-|+.-.||.|.++|.-. |+..+.
T Consensus 149 cQWiDITdvp~G~Y~l~V~vN-P~~~v~ 175 (205)
T PF01186_consen 149 CQWIDITDVPPGTYILQVTVN-PEYRVA 175 (205)
T ss_pred ccceeecCCCCccEEEEEecC-Cccccc
Confidence 478999888999999998654 444333
No 228
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=21.30 E-value=53 Score=21.11 Aligned_cols=21 Identities=29% Similarity=0.612 Sum_probs=12.9
Q ss_pred ccCcccccchhhcc---CCCCCCC
Q 046522 20 LRCRLVKTYDQFRE---SGCENCP 40 (115)
Q Consensus 20 ~~C~~I~t~~qf~~---~gCpnC~ 40 (115)
+-|+-+....-|-. +|||-|+
T Consensus 23 ~pCgH~I~~~~f~~~rYngCPfC~ 46 (55)
T PF14447_consen 23 LPCGHLICDNCFPGERYNGCPFCG 46 (55)
T ss_pred ccccceeeccccChhhccCCCCCC
Confidence 34454555554432 7999998
No 229
>PF11020 DUF2610: Domain of unknown function (DUF2610); InterPro: IPR021277 This family is conserved in Proteobacteria. One member is annotated as being elongation factor P but this could not be confirmed.
Probab=20.98 E-value=91 Score=21.61 Aligned_cols=39 Identities=23% Similarity=0.340 Sum_probs=24.9
Q ss_pred CCccceEEEEeCCChhH---HHHHHhcCCCCCeeeEEEecCCCcHHHHHHHH
Q 046522 56 TPNFNGIISVMDPTRSW---AARWLRIGRFVPGCYTLAVSEALPEDLQNLCE 104 (115)
Q Consensus 56 T~~f~G~I~i~dP~~Sw---VAk~l~i~~~~pG~YAi~V~g~lp~~i~~~l~ 104 (115)
++-|.=+|+==+|...- -++||.-++ .|.+|++|.+.|.
T Consensus 14 ~a~F~iYIG~P~~~~HPl~~Q~~WLskeR----------gG~IP~~V~~sl~ 55 (82)
T PF11020_consen 14 RAPFAIYIGEPKPDHHPLQFQATWLSKER----------GGQIPEKVMDSLS 55 (82)
T ss_pred cCceeEEeCCCCCCCCchHHHHHHHHHhh----------CCCCCHHHHHHHH
Confidence 55566334333444444 467886543 6899999999875
No 230
>cd02553 PseudoU_synth_RsuA PseudoU_synth_RsuA: Pseudouridine synthase, Escherichia coli RsuA like. This group is comprised of eukaryotic and bacterial proteins similar to Escherichia coli RsuA. Pseudouridine synthases catalyze the isomerization of specific uridines in an RNA molecule to pseudouridines (5-ribosyluracil, psi). No cofactors are required. E.coli RsuA makes psi516 in 16S RNA. Psi at this position is not generally conserved in other organisms.
Probab=20.95 E-value=3.4e+02 Score=19.80 Aligned_cols=48 Identities=23% Similarity=0.324 Sum_probs=30.7
Q ss_pred ceEEEEeCCChhHHHHHHhcCCCCCeeeEEEecCCCcHHHHHHHHhcCCe
Q 046522 60 NGIISVMDPTRSWAARWLRIGRFVPGCYTLAVSEALPEDLQNLCEDERVQ 109 (115)
Q Consensus 60 ~G~I~i~dP~~SwVAk~l~i~~~~pG~YAi~V~g~lp~~i~~~l~~~gi~ 109 (115)
+|++.+.+-. ....+.+.-...+.-.|-+.|.|.++++....+. .|+.
T Consensus 47 SGlll~ak~~-~~~~~l~~~~~~i~K~Y~a~V~G~~~~~~~~~~~-~~~~ 94 (167)
T cd02553 47 TGLLLLTNDG-QLAHRLTSPKKHVPKTYEVTLAGPLTEDDIEAFA-EGVL 94 (167)
T ss_pred EEEEEEEeCH-HHHHHhhCCcCCCceEEEEEEccCCCHHHHHHHH-CCeE
Confidence 7999996532 2233333323457789999999999877655443 3443
No 231
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=20.88 E-value=56 Score=26.65 Aligned_cols=10 Identities=30% Similarity=0.580 Sum_probs=6.2
Q ss_pred cccccccCcc
Q 046522 15 ELRACLRCRL 24 (115)
Q Consensus 15 ~lrAC~~C~~ 24 (115)
....|..|+-
T Consensus 10 ~~~~Cp~Cg~ 19 (310)
T PRK00423 10 EKLVCPECGS 19 (310)
T ss_pred cCCcCcCCCC
Confidence 3456777864
No 232
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=20.87 E-value=60 Score=25.25 Aligned_cols=24 Identities=21% Similarity=0.696 Sum_probs=16.6
Q ss_pred cccccCcccccchhhccC---CCCCCC
Q 046522 17 RACLRCRLVKTYDQFRES---GCENCP 40 (115)
Q Consensus 17 rAC~~C~~I~t~~qf~~~---gCpnC~ 40 (115)
--|..|+.....+..... -||+|+
T Consensus 123 ~~C~~C~~~~~~~~~~~~~~p~C~~Cg 149 (242)
T PRK00481 123 ARCTKCGQTYDLDEYLKPEPPRCPKCG 149 (242)
T ss_pred eeeCCCCCCcChhhhccCCCCCCCCCC
Confidence 449999987665544432 499997
No 233
>PF02887 PK_C: Pyruvate kinase, alpha/beta domain; InterPro: IPR015795 Pyruvate kinase (2.7.1.40 from EC) (PK) catalyses the final step in glycolysis [], the conversion of phosphoenolpyruvate to pyruvate with concomitant phosphorylation of ADP to ATP: ADP + phosphoenolpyruvate = ATP + pyruvate The enzyme, which is found in all living organisms, requires both magnesium and potassium ions for its activity. In vertebrates, there are four tissue-specific isozymes: L (liver), R (red cells), M1 (muscle, heart and brain), and M2 (early foetal tissue). In plants, PK exists as cytoplasmic and plastid isozymes, while most bacteria and lower eukaryotes have one form, except in certain bacteria, such as Escherichia coli, that have two isozymes. All isozymes appear to be tetramers of identical subunits of ~500 residues. PK helps control the rate of glycolysis, along with phosphofructokinase (IPR000023 from INTERPRO) and hexokinase (IPR001312 from INTERPRO). PK possesses allosteric sites for numerous effectors, yet the isozymes respond differently, in keeping with their different tissue distributions []. The activity of L-type (liver) PK is increased by fructose-1,6-bisphosphate (F1,6BP) and lowered by ATP and alanine (gluconeogenic precursor), therefore when glucose levels are high, glycolysis is promoted, and when levels are low, gluconeogenesis is promoted. L-type PK is also hormonally regulated, being activated by insulin and inhibited by glucagon, which covalently modifies the PK enzyme. M1-type (muscle, brain) PK is inhibited by ATP, but F1,6BP and alanine have no effect, which correlates with the function of muscle and brain, as opposed to the liver. The structure of several pyruvate kinases from various organisms have been determined [, ]. The protein comprises three-four domains: a small N-terminal helical domain (absent in bacterial PK), a beta/alpha-barrel domain, a beta-barrel domain (inserted within the beta/alpha-barrel domain), and a 3-layer alpha/beta/alpha sandwich domain. This entry represents the 3-layer alpha/beta/alpha sandwich domain. This domain has a similar topology to the archaeal hypothetical protein, MTH1675 from Methanobacterium thermoautotrophicum.; PDB: 3QTG_B 1VP8_A 1T57_C 3N25_A 1AQF_C 2G50_B 1F3X_G 1A5U_F 1A49_E 1F3W_C ....
Probab=20.75 E-value=2.3e+02 Score=19.21 Aligned_cols=35 Identities=26% Similarity=0.269 Sum_probs=22.3
Q ss_pred EEeCCChhHHHHHHhcCCCCCeeeEEEecCCC--cHHHHHH
Q 046522 64 SVMDPTRSWAARWLRIGRFVPGCYTLAVSEAL--PEDLQNL 102 (115)
Q Consensus 64 ~i~dP~~SwVAk~l~i~~~~pG~YAi~V~g~l--p~~i~~~ 102 (115)
..+-|+ -++++++.+. -|.|.+-+.... ++++++.
T Consensus 43 iavt~~-~~~~r~l~l~---~GV~p~~~~~~~~~~~~~~~~ 79 (117)
T PF02887_consen 43 IAVTPN-ESVARQLSLY---WGVYPVLIEEFDKDTEELIAE 79 (117)
T ss_dssp EEEESS-HHHHHHGGGS---TTEEEEECSSHSHSHHHHHHH
T ss_pred EEEcCc-HHHHhhhhcc---cceEEEEeccccccHHHHHHH
Confidence 333443 4599999877 899998765554 4554443
No 234
>PF02927 CelD_N: N-terminal ig-like domain of cellulase; InterPro: IPR004197 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Cellulases (Endoglucanases) 3.2.1.4 from EC catalyse the endohydrolysis of 1,4-beta-D-glucosidic linkages in cellulose. This is the N-terminal ig-like domain of cellulase, enzymes containing this domain belong to family 9 of the glycoside hydrolases (GH9 from CAZY).; GO: 0008810 cellulase activity, 0005975 carbohydrate metabolic process; PDB: 1CLC_A 1WMX_B 2C24_B 1RQ5_A 3K4Z_A 3H7L_B 3RX5_A 3RX8_A 3H2W_A 3RX7_A ....
Probab=20.74 E-value=74 Score=21.19 Aligned_cols=12 Identities=42% Similarity=0.756 Sum_probs=9.5
Q ss_pred CCeeeEEEecCC
Q 046522 83 VPGCYTLAVSEA 94 (115)
Q Consensus 83 ~pG~YAi~V~g~ 94 (115)
.||.|.|+|.|.
T Consensus 76 ~~G~Y~i~~~~~ 87 (91)
T PF02927_consen 76 TPGTYYIRVGGA 87 (91)
T ss_dssp S-EEEEEEETTE
T ss_pred CCEEEEEEECCc
Confidence 799999999763
No 235
>cd00272 Chemokine_CC Chemokine_CC: 1 of 4 subgroup designations based on the arrangement of the two N-terminal cysteine residues; includes a number of secreted growth factors and interferons involved in mitogenic, chemotactic, and inflammatory activity; some members (e.g. 2HCC) contain an additional disulfide bond which is thought to compensate for the highly conserved Trp missing in these; chemotatic for monocytes, macrophages, eosinophils, basophils, and T cells, but not neutrophils; exist as monomers and dimers, but are believed to be functional as monomers; found only in vertebrates and a few viruses; a subgroup of CC, identified by an N-terminal DCCL motif (Exodus-1, Exodus-2, and Exodus-3), has been shown to inhibit specific types of human cancer cell growth in a mouse model. See CDs: Chemokine (cd00169) for the general alignment of chemokines, or Chemokine_CXC (cd00273), Chemokine_C (cd00271), and Chemokine_CX3C (cd00274) for the additional chemokine subgroups, and Chemokine_C
Probab=20.67 E-value=69 Score=19.60 Aligned_cols=22 Identities=23% Similarity=0.678 Sum_probs=15.5
Q ss_pred CCCccceEEEEeCCChhHHHHHHh
Q 046522 55 TTPNFNGIISVMDPTRSWAARWLR 78 (115)
Q Consensus 55 tT~~f~G~I~i~dP~~SwVAk~l~ 78 (115)
+|.+ .+.|.+ ||+..||-+.+.
T Consensus 33 ~tk~-g~~iC~-dP~~~WVk~~i~ 54 (57)
T cd00272 33 KTKR-GREVCA-DPKQKWVQRYMK 54 (57)
T ss_pred EeCC-CCEEeC-CCChHHHHHHHH
Confidence 4544 335554 999999999874
No 236
>TIGR02905 spore_yutH spore coat protein YutH. Members of this family are homologs of the Bacillus subtilis spore coat protein CotS. Members of this family, designated YutH, are found only in the family Bacillaceae from among the endospore-forming members of the Firmicutes branch of the Bacteria.
Probab=20.61 E-value=1.3e+02 Score=24.03 Aligned_cols=30 Identities=13% Similarity=0.202 Sum_probs=22.9
Q ss_pred CeeeEEEecCCCcH-------HHHHHHHhcCCeecCC
Q 046522 84 PGCYTLAVSEALPE-------DLQNLCEDERVQYVPP 113 (115)
Q Consensus 84 pG~YAi~V~g~lp~-------~i~~~l~~~gi~y~pr 113 (115)
-|.|++++....++ +..+.|.++|+.+.|+
T Consensus 28 ~g~y~Lk~~e~~~~~~l~f~~~~~~~L~~~G~~~v~~ 64 (313)
T TIGR02905 28 NQAYLIVPVDGLEEEELAELMAMSDYLQQAGDETVLE 64 (313)
T ss_pred CceEEEEEecCCCHHHHHHHHHHHHHHHHcCCCcccc
Confidence 89999998766665 3577888999876653
No 237
>PRK04023 DNA polymerase II large subunit; Validated
Probab=20.53 E-value=53 Score=32.11 Aligned_cols=83 Identities=17% Similarity=0.269 Sum_probs=40.6
Q ss_pred cccccccCcccccchhhccCCCCCCCCC-C---------CCCCcccccccCCCccceEEEEeCCChhHHHHHHhcCC--C
Q 046522 15 ELRACLRCRLVKTYDQFRESGCENCPFF-K---------MDEDHERVVDCTTPNFNGIISVMDPTRSWAARWLRIGR--F 82 (115)
Q Consensus 15 ~lrAC~~C~~I~t~~qf~~~gCpnC~~l-~---------m~~~~d~v~~~tT~~f~G~I~i~dP~~SwVAk~l~i~~--~ 82 (115)
..|-|..|+.... .| .||+|+.. . ...+.+.+-.|-+..=.+.-.-+|..+=|-.-..++.. .
T Consensus 625 g~RfCpsCG~~t~--~f---rCP~CG~~Te~i~fCP~CG~~~~~y~CPKCG~El~~~s~~~i~l~~~~~~A~~~lg~~~~ 699 (1121)
T PRK04023 625 GRRKCPSCGKETF--YR---RCPFCGTHTEPVYRCPRCGIEVEEDECEKCGREPTPYSKRKIDLKELYDRALENLGERKN 699 (1121)
T ss_pred cCccCCCCCCcCC--cc---cCCCCCCCCCcceeCccccCcCCCCcCCCCCCCCCccceEEecHHHHHHHHHHHhCCcCC
Confidence 4577888888753 22 38888721 0 00011112223333334444456665545444433332 1
Q ss_pred ---CCeeeEEEecCCCcHHHHHH
Q 046522 83 ---VPGCYTLAVSEALPEDLQNL 102 (115)
Q Consensus 83 ---~pG~YAi~V~g~lp~~i~~~ 102 (115)
+.|.--+.=...+||-++.-
T Consensus 700 ~~~~KGVkgl~S~~k~~EPlEKG 722 (1121)
T PRK04023 700 FDEVKGVKGLTSKDKIPEPLEKG 722 (1121)
T ss_pred ccccccceecccCCCCCcchHhh
Confidence 45555555566677766553
No 238
>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB. This model describes a protein of type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly and is closely related to GspE (TIGR02533) of type II secretion, also called the main terminal branch of the general secretion pathway. Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.
Probab=20.46 E-value=62 Score=28.62 Aligned_cols=11 Identities=27% Similarity=1.002 Sum_probs=8.1
Q ss_pred hccCCCCCCCC
Q 046522 31 FRESGCENCPF 41 (115)
Q Consensus 31 f~~~gCpnC~~ 41 (115)
|...||+.|..
T Consensus 486 ~~~~gC~~C~~ 496 (564)
T TIGR02538 486 YGPVGCDECSN 496 (564)
T ss_pred ecCCCCcccCC
Confidence 44579999974
No 239
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=20.33 E-value=55 Score=26.28 Aligned_cols=27 Identities=22% Similarity=0.362 Sum_probs=16.6
Q ss_pred ccccccccCcccccchhhcc---CCCCCCC
Q 046522 14 HELRACLRCRLVKTYDQFRE---SGCENCP 40 (115)
Q Consensus 14 r~lrAC~~C~~I~t~~qf~~---~gCpnC~ 40 (115)
|.-+.|.+|+--......-. --||+|+
T Consensus 233 R~g~pC~~Cg~~I~~~~~~gR~ty~Cp~CQ 262 (269)
T PRK14811 233 REGQPCPRCGTPIEKIVVGGRGTHFCPQCQ 262 (269)
T ss_pred CCcCCCCcCCCeeEEEEECCCCcEECCCCc
Confidence 44578999986554332111 1399998
No 240
>PRK14487 cbb3-type cytochrome c oxidase subunit II; Provisional
Probab=20.27 E-value=1.8e+02 Score=23.43 Aligned_cols=43 Identities=23% Similarity=0.343 Sum_probs=27.8
Q ss_pred ChhHHHHHHhcCC-CCCee----eEEEecCCCc-HHHHHHHHhc---CCeec
Q 046522 69 TRSWAARWLRIGR-FVPGC----YTLAVSEALP-EDLQNLCEDE---RVQYV 111 (115)
Q Consensus 69 ~~SwVAk~l~i~~-~~pG~----YAi~V~g~lp-~~i~~~l~~~---gi~y~ 111 (115)
...|...|+.--. -+||. |.---..+|- +++.+.|+.. |++|-
T Consensus 115 s~~w~~~hl~nP~~v~PgS~MPay~~L~~~~ld~~~~~~~l~~l~~~gvPYt 166 (217)
T PRK14487 115 SDEWHRNHLINPRSVVPESNMPAYPWLAENDLDGTDTAEKMTALRVVGVPYT 166 (217)
T ss_pred CHHHHHHHHhCcccCCCCCCCCCCcccccccCCHHHHHHHHHHhhhcCCCCC
Confidence 3589999997543 36885 7644455555 4566555554 88884
No 241
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=20.07 E-value=53 Score=18.83 Aligned_cols=17 Identities=24% Similarity=0.542 Sum_probs=6.7
Q ss_pred CCCCCccccccccCccc
Q 046522 9 PTSFGHELRACLRCRLV 25 (115)
Q Consensus 9 p~~~~r~lrAC~~C~~I 25 (115)
|....+.-..|..|+.|
T Consensus 15 p~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 15 PEGDDRERLVCPACGFI 31 (34)
T ss_dssp -TT-SS-EEEETTTTEE
T ss_pred CCCCCccceECCCCCCE
Confidence 33333444455555544
No 242
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=20.02 E-value=55 Score=23.93 Aligned_cols=22 Identities=23% Similarity=0.495 Sum_probs=16.5
Q ss_pred cccccCcccccchhhccCCCCCCCC
Q 046522 17 RACLRCRLVKTYDQFRESGCENCPF 41 (115)
Q Consensus 17 rAC~~C~~I~t~~qf~~~gCpnC~~ 41 (115)
--|.+|+.+--.-+ .-||+|+.
T Consensus 30 ~kC~~CG~v~~PPr---~~Cp~C~~ 51 (140)
T COG1545 30 TKCKKCGRVYFPPR---AYCPKCGS 51 (140)
T ss_pred EEcCCCCeEEcCCc---ccCCCCCC
Confidence 46999998865554 34999983
Done!