Query 042101
Match_columns 380
No_of_seqs 245 out of 1742
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 02:52:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042101.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042101hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK05667 dnaG DNA primase; Val 100.0 1.6E-42 3.6E-47 362.4 25.1 273 65-376 3-372 (580)
2 TIGR01391 dnaG DNA primase, ca 100.0 3E-42 6.5E-47 349.0 24.4 264 74-376 16-373 (415)
3 PHA02540 61 DNA primase; Provi 100.0 1.6E-40 3.4E-45 324.1 21.9 256 70-366 9-322 (337)
4 COG0358 DnaG DNA primase (bact 100.0 4.4E-39 9.6E-44 337.7 20.1 260 67-364 3-352 (568)
5 PHA02415 DNA primase domain-co 100.0 6.5E-30 1.4E-34 265.6 21.6 271 74-373 13-360 (930)
6 PRK08624 hypothetical protein; 100.0 4.2E-30 9.1E-35 251.6 18.4 250 72-363 14-359 (373)
7 TIGR00646 MG010 DNA primase-re 100.0 2.4E-29 5.2E-34 230.9 19.3 173 168-365 29-216 (218)
8 PHA02031 putative DnaG-like pr 99.9 5.8E-26 1.3E-30 213.2 14.5 215 114-360 32-263 (266)
9 TIGR02760 TraI_TIGR conjugativ 99.6 9.3E-14 2E-18 162.6 19.9 169 163-366 1680-1878(1960)
10 PF13155 Toprim_2: Toprim-like 99.5 1.4E-14 3.1E-19 117.3 7.8 85 242-349 1-96 (96)
11 PRK07078 hypothetical protein; 99.5 8.2E-13 1.8E-17 142.4 19.0 149 196-363 135-299 (759)
12 cd03364 TOPRIM_DnaG_primases T 99.4 6E-13 1.3E-17 104.4 9.2 75 239-332 1-78 (79)
13 PF13662 Toprim_4: Toprim doma 99.3 2.1E-12 4.5E-17 101.8 6.0 71 239-325 1-72 (81)
14 PF13362 Toprim_3: Toprim doma 99.3 2.1E-11 4.5E-16 99.0 9.1 91 240-355 1-96 (96)
15 cd01029 TOPRIM_primases TOPRIM 99.2 4.8E-11 1E-15 93.2 8.5 68 239-325 1-69 (79)
16 COG4643 Uncharacterized protei 99.2 6.4E-10 1.4E-14 107.1 14.1 142 196-361 161-310 (366)
17 PRK04031 DNA primase; Provisio 99.1 2.4E-10 5.1E-15 113.6 11.2 103 235-369 166-268 (408)
18 PF01807 zf-CHC2: CHC2 zinc fi 99.1 1.8E-11 3.9E-16 100.0 2.0 54 74-141 15-68 (97)
19 PF08275 Toprim_N: DNA primase 99.0 5E-10 1.1E-14 96.1 5.3 70 166-235 11-127 (128)
20 smart00493 TOPRIM topoisomeras 98.9 8.6E-09 1.9E-13 79.6 8.0 71 239-325 1-73 (76)
21 cd01027 TOPRIM_RNase_M5_like T 98.9 8.5E-09 1.8E-13 81.5 7.9 68 239-325 2-71 (81)
22 smart00400 ZnF_CHCC zinc finge 98.8 1.9E-09 4E-14 78.9 3.0 37 95-141 1-37 (55)
23 PF12965 DUF3854: Domain of un 98.7 2.9E-07 6.2E-12 79.2 11.2 112 238-357 10-130 (130)
24 KOG2373 Predicted mitochondria 98.4 6.9E-07 1.5E-11 87.4 8.3 177 173-373 37-233 (514)
25 cd00188 TOPRIM Topoisomerase-p 98.2 9.9E-06 2.1E-10 61.6 7.9 69 239-324 1-72 (83)
26 PF08273 Prim_Zn_Ribbon: Zinc- 97.8 2.2E-05 4.7E-10 53.5 2.7 35 95-138 2-38 (40)
27 PF01751 Toprim: Toprim domain 97.3 0.00083 1.8E-08 54.7 7.4 82 240-324 1-85 (100)
28 smart00778 Prim_Zn_Ribbon Zinc 97.3 0.00016 3.6E-09 48.3 2.2 33 95-138 2-35 (37)
29 COG1658 Small primase-like pro 97.2 0.00081 1.8E-08 57.4 5.6 73 238-325 9-81 (127)
30 PRK04017 hypothetical protein; 97.1 0.0015 3.2E-08 56.2 6.7 71 237-325 21-91 (132)
31 PF13154 DUF3991: Protein of u 96.9 0.0025 5.5E-08 49.6 5.6 49 171-219 1-57 (77)
32 TIGR00334 5S_RNA_mat_M5 ribonu 96.6 0.0065 1.4E-07 54.6 7.3 107 239-367 3-111 (174)
33 PRK14719 bifunctional RNAse/5- 95.7 0.012 2.6E-07 59.1 4.8 100 238-362 23-125 (360)
34 COG4026 Uncharacterized protei 95.3 0.085 1.8E-06 48.9 8.2 82 239-336 8-97 (290)
35 TIGR03655 anti_R_Lar restricti 94.1 0.047 1E-06 39.4 2.7 34 97-139 2-38 (53)
36 cd01025 TOPRIM_recR TOPRIM_rec 93.7 0.62 1.3E-05 39.0 9.1 79 240-325 2-83 (112)
37 PRK09710 lar restriction allev 91.8 0.22 4.8E-06 37.3 3.4 35 96-140 6-40 (64)
38 TIGR00615 recR recombination p 91.5 1.8 3.9E-05 39.8 9.8 90 237-333 77-169 (195)
39 PRK00076 recR recombination pr 90.9 2.2 4.9E-05 39.2 9.9 93 237-336 77-175 (196)
40 PRK13844 recombination protein 90.6 2.8 6.1E-05 38.7 10.2 89 237-333 81-172 (200)
41 COG0353 RecR Recombinational D 90.0 3.1 6.7E-05 38.2 9.9 91 236-333 77-170 (198)
42 PF14354 Lar_restr_allev: Rest 87.4 0.68 1.5E-05 34.0 3.2 29 97-135 4-37 (61)
43 PTZ00255 60S ribosomal protein 86.3 0.53 1.1E-05 37.8 2.2 27 96-135 36-62 (90)
44 PF01780 Ribosomal_L37ae: Ribo 85.7 0.84 1.8E-05 36.7 3.1 27 96-135 35-61 (90)
45 TIGR00280 L37a ribosomal prote 85.5 0.76 1.6E-05 37.0 2.7 27 96-135 35-61 (91)
46 COG1997 RPL43A Ribosomal prote 84.3 0.91 2E-05 36.1 2.6 28 96-136 35-62 (89)
47 PRK03976 rpl37ae 50S ribosomal 84.2 1.1 2.4E-05 36.0 3.1 27 96-135 36-62 (90)
48 PF11781 RRN7: RNA polymerase 81.3 1.3 2.8E-05 29.5 2.1 26 96-135 8-33 (36)
49 PF05129 Elf1: Transcription e 80.5 1.6 3.4E-05 34.4 2.7 33 96-137 22-56 (81)
50 PF12760 Zn_Tnp_IS1595: Transp 77.7 3.3 7.1E-05 28.8 3.4 27 97-135 19-45 (46)
51 cd01026 TOPRIM_OLD TOPRIM_OLD: 76.4 7.7 0.00017 31.1 5.7 59 238-314 3-70 (97)
52 PF08271 TF_Zn_Ribbon: TFIIB z 76.4 3.5 7.5E-05 28.2 3.1 26 98-135 2-27 (43)
53 TIGR00311 aIF-2beta translatio 76.0 6.2 0.00013 34.1 5.3 51 65-139 80-130 (133)
54 PF07282 OrfB_Zn_ribbon: Putat 73.6 4.8 0.0001 30.1 3.6 52 73-139 7-58 (69)
55 cd01028 TOPRIM_TopoIA TOPRIM_T 73.0 14 0.00031 31.8 6.9 42 294-335 86-129 (142)
56 PRK03988 translation initiatio 70.4 10 0.00022 33.0 5.3 51 65-139 85-135 (138)
57 PRK06319 DNA topoisomerase I/S 70.1 65 0.0014 36.4 12.9 91 239-334 3-110 (860)
58 PRK12336 translation initiatio 69.8 9.6 0.00021 35.2 5.4 52 65-140 81-132 (201)
59 PRK08780 DNA topoisomerase I; 68.7 59 0.0013 36.3 12.1 81 239-324 3-99 (780)
60 cd03362 TOPRIM_TopoIA_TopoIII 67.0 19 0.00041 31.4 6.5 41 294-334 94-137 (151)
61 PF03811 Zn_Tnp_IS1: InsA N-te 66.2 5.9 0.00013 26.3 2.3 28 97-133 6-35 (36)
62 COG3593 Predicted ATP-dependen 64.9 11 0.00023 40.5 5.1 83 224-324 378-473 (581)
63 COG4888 Uncharacterized Zn rib 64.1 7.3 0.00016 31.9 2.9 35 96-137 22-56 (104)
64 PRK07561 DNA topoisomerase I s 63.7 91 0.002 35.2 12.5 41 294-334 82-124 (859)
65 PRK14892 putative transcriptio 63.5 8 0.00017 31.7 3.1 32 96-137 21-52 (99)
66 cd03363 TOPRIM_TopoIA_TopoI TO 63.4 30 0.00065 29.2 6.8 41 294-334 68-109 (123)
67 COG0550 TopA Topoisomerase IA 62.5 1E+02 0.0022 33.1 12.0 95 240-334 2-115 (570)
68 KOG0402 60S ribosomal protein 61.4 3.5 7.5E-05 32.6 0.6 27 96-135 36-62 (92)
69 PF01873 eIF-5_eIF-2B: Domain 60.1 15 0.00033 31.3 4.4 48 65-136 76-123 (125)
70 PRK05582 DNA topoisomerase I; 59.0 1.2E+02 0.0026 33.0 12.1 86 240-325 4-100 (650)
71 cd03361 TOPRIM_TopoIA_RevGyr T 56.7 43 0.00093 29.9 7.0 41 294-334 114-156 (170)
72 smart00653 eIF2B_5 domain pres 54.8 28 0.0006 29.0 5.0 48 65-136 63-110 (110)
73 PF14097 SpoVAE: Stage V sporu 54.6 34 0.00073 30.8 5.7 54 301-368 1-54 (180)
74 PRK06599 DNA topoisomerase I; 54.6 1.8E+02 0.0038 32.0 12.5 96 239-334 3-114 (675)
75 KOG3214 Uncharacterized Zn rib 53.1 8.3 0.00018 31.5 1.5 36 96-138 23-58 (109)
76 PRK05776 DNA topoisomerase I; 50.3 54 0.0012 35.9 7.7 42 293-334 91-133 (670)
77 COG1198 PriA Primosomal protei 49.1 31 0.00067 38.1 5.6 62 66-140 405-475 (730)
78 PF01927 Mut7-C: Mut7-C RNAse 47.4 32 0.00069 29.9 4.5 29 71-104 71-99 (147)
79 PF02150 RNA_POL_M_15KD: RNA p 46.9 29 0.00063 22.7 3.1 30 98-139 3-32 (35)
80 PRK00432 30S ribosomal protein 46.2 14 0.0003 26.3 1.6 27 96-136 20-46 (50)
81 PHA00626 hypothetical protein 44.7 19 0.00041 26.4 2.1 33 98-138 2-34 (59)
82 PF04606 Ogr_Delta: Ogr/Delta- 43.0 12 0.00025 26.2 0.8 38 98-138 1-38 (47)
83 TIGR01051 topA_bact DNA topois 42.2 78 0.0017 34.2 7.4 40 294-333 65-106 (610)
84 PRK07219 DNA topoisomerase I; 41.4 85 0.0018 35.2 7.7 41 294-334 93-136 (822)
85 KOG2767 Translation initiation 40.6 21 0.00045 35.7 2.4 50 68-140 82-131 (400)
86 smart00661 RPOL9 RNA polymeras 40.5 22 0.00049 24.7 2.0 31 98-139 2-32 (52)
87 TIGR01056 topB DNA topoisomera 40.0 95 0.0021 33.9 7.6 41 294-334 89-134 (660)
88 PF01921 tRNA-synt_1f: tRNA sy 39.7 24 0.00051 35.6 2.7 40 95-140 173-212 (360)
89 PF09151 DUF1936: Domain of un 39.7 40 0.00087 21.6 2.8 32 97-135 2-34 (36)
90 PRK00750 lysK lysyl-tRNA synth 39.2 57 0.0012 34.5 5.6 38 95-139 174-211 (510)
91 COG2888 Predicted Zn-ribbon RN 39.1 44 0.00095 24.8 3.3 30 96-137 27-60 (61)
92 PRK07726 DNA topoisomerase III 38.6 80 0.0017 34.5 6.8 41 294-334 88-129 (658)
93 PF14447 Prok-RING_4: Prokaryo 38.3 13 0.00029 27.1 0.6 13 91-104 35-47 (55)
94 PF03470 zf-XS: XS zinc finger 38.2 19 0.00042 24.9 1.3 6 99-104 1-6 (43)
95 PF01096 TFIIS_C: Transcriptio 37.3 27 0.00059 23.4 1.9 30 98-135 2-36 (39)
96 TIGR01054 rgy reverse gyrase. 37.3 1E+02 0.0022 36.2 7.6 41 294-334 715-757 (1171)
97 PRK14973 DNA topoisomerase I; 37.3 95 0.0021 35.4 7.3 41 294-334 92-136 (936)
98 PRK09401 reverse gyrase; Revie 36.5 1.1E+02 0.0025 35.8 7.9 41 294-334 715-757 (1176)
99 KOG2593 Transcription initiati 36.1 21 0.00046 36.6 1.7 53 71-135 109-161 (436)
100 PF13707 RloB: RloB-like prote 35.7 1.9E+02 0.0042 25.4 7.8 12 298-309 59-70 (183)
101 PF14803 Nudix_N_2: Nudix N-te 35.1 33 0.0007 22.5 1.9 29 98-135 2-30 (34)
102 cd00674 LysRS_core_class_I cat 33.6 73 0.0016 32.1 5.1 38 95-140 168-205 (353)
103 TIGR02443 conserved hypothetic 33.5 75 0.0016 23.6 3.8 35 96-139 9-43 (59)
104 COG1998 RPS31 Ribosomal protei 33.4 28 0.00061 24.8 1.5 28 96-136 19-46 (51)
105 PF09664 DUF2399: Protein of u 33.4 2.8E+02 0.0061 24.3 8.3 71 238-325 18-92 (152)
106 COG3677 Transposase and inacti 33.4 27 0.00058 29.9 1.7 37 96-140 30-66 (129)
107 PF04216 FdhE: Protein involve 32.8 36 0.00077 33.0 2.7 35 96-139 172-209 (290)
108 PF13719 zinc_ribbon_5: zinc-r 32.8 35 0.00075 22.5 1.8 30 97-137 3-35 (37)
109 PRK07220 DNA topoisomerase I; 32.3 1.3E+02 0.0028 33.4 7.3 31 294-324 93-123 (740)
110 TIGR00467 lysS_arch lysyl-tRNA 32.1 83 0.0018 33.3 5.5 36 95-139 167-202 (515)
111 smart00440 ZnF_C2C2 C2C2 Zinc 31.9 58 0.0013 21.9 2.8 31 98-136 2-37 (40)
112 PF09862 DUF2089: Protein of u 31.5 41 0.00089 28.3 2.5 20 99-135 1-20 (113)
113 PF10058 DUF2296: Predicted in 31.0 92 0.002 22.5 3.9 50 72-135 3-52 (54)
114 PF09526 DUF2387: Probable met 30.7 77 0.0017 24.3 3.7 36 96-140 8-43 (71)
115 TIGR01057 topA_arch DNA topois 30.3 1.2E+02 0.0026 32.8 6.5 42 293-334 88-130 (618)
116 PF01458 UPF0051: Uncharacteri 30.2 39 0.00084 31.5 2.4 24 163-186 201-224 (229)
117 PHA02942 putative transposase; 29.6 42 0.00091 34.1 2.7 47 77-139 308-354 (383)
118 PF11672 DUF3268: Protein of u 29.5 34 0.00073 28.2 1.6 39 97-140 3-44 (102)
119 PRK00464 nrdR transcriptional 28.7 40 0.00087 29.9 2.1 14 125-140 28-41 (154)
120 PF10367 Vps39_2: Vacuolar sor 28.6 43 0.00094 26.7 2.2 30 96-129 78-107 (109)
121 cd00223 TOPRIM_TopoIIB_SPO TOP 28.3 2.4E+02 0.0053 24.5 7.1 68 239-321 1-73 (160)
122 TIGR00686 phnA alkylphosphonat 27.2 52 0.0011 27.4 2.3 27 97-137 3-29 (109)
123 COG1656 Uncharacterized conser 27.1 55 0.0012 29.3 2.6 29 71-104 77-105 (165)
124 PF13453 zf-TFIIB: Transcripti 27.0 68 0.0015 21.5 2.5 11 123-135 17-27 (41)
125 PRK14891 50S ribosomal protein 26.2 49 0.0011 28.4 2.1 31 97-134 5-38 (131)
126 TIGR02098 MJ0042_CXXC MJ0042 f 25.4 56 0.0012 21.3 1.9 30 97-137 3-35 (38)
127 TIGR02159 PA_CoA_Oxy4 phenylac 25.2 38 0.00083 29.7 1.3 72 61-139 65-142 (146)
128 PF14353 CpXC: CpXC protein 25.1 87 0.0019 26.3 3.5 14 125-140 38-51 (128)
129 PF14255 Cys_rich_CPXG: Cystei 25.0 66 0.0014 23.2 2.3 7 98-104 2-8 (52)
130 cd01458 vWA_ku Ku70/Ku80 N-ter 25.0 1.8E+02 0.004 26.5 5.9 51 299-350 128-184 (218)
131 PF04216 FdhE: Protein involve 24.9 48 0.001 32.1 2.1 37 97-140 212-251 (290)
132 PRK10220 hypothetical protein; 24.7 72 0.0016 26.6 2.7 28 97-138 4-31 (111)
133 PF03119 DNA_ligase_ZBD: NAD-d 24.5 64 0.0014 20.0 1.9 25 98-133 1-26 (28)
134 COG2824 PhnA Uncharacterized Z 23.8 74 0.0016 26.4 2.6 28 97-138 4-31 (112)
135 TIGR01981 sufD FeS assembly pr 23.6 64 0.0014 32.4 2.8 24 163-186 321-344 (366)
136 PRK14890 putative Zn-ribbon RN 23.5 1.4E+02 0.003 22.1 3.7 32 94-137 23-58 (59)
137 PF08274 PhnA_Zn_Ribbon: PhnA 23.4 64 0.0014 20.5 1.7 24 98-135 4-27 (30)
138 PF08063 PADR1: PADR1 (NUC008) 23.4 62 0.0013 23.5 1.9 23 96-130 14-36 (55)
139 TIGR03830 CxxCG_CxxCG_HTH puta 23.1 2E+02 0.0044 23.6 5.4 11 124-136 30-40 (127)
140 KOG2846 Predicted membrane pro 23.0 69 0.0015 31.8 2.7 52 71-139 203-254 (328)
141 COG1779 C4-type Zn-finger prot 23.0 92 0.002 28.8 3.3 37 94-137 12-53 (201)
142 KOG2923 Uncharacterized conser 22.5 61 0.0013 24.4 1.7 32 92-135 18-52 (67)
143 PF02330 MAM33: Mitochondrial 22.2 63 0.0014 29.6 2.2 19 167-185 162-180 (204)
144 PTZ00407 DNA topoisomerase IA; 21.2 2.5E+02 0.0054 31.6 6.8 29 296-324 122-150 (805)
145 PF09983 DUF2220: Uncharacteri 21.2 4.2E+02 0.0092 23.7 7.4 70 237-324 42-111 (181)
146 KOG4498 Uncharacterized conser 20.7 1.2E+02 0.0025 28.0 3.5 54 69-130 71-124 (197)
No 1
>PRK05667 dnaG DNA primase; Validated
Probab=100.00 E-value=1.6e-42 Score=362.41 Aligned_cols=273 Identities=24% Similarity=0.366 Sum_probs=206.5
Q ss_pred ccchhhHHHHH------HHHHHhCCccccCCCCCceeeecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCCcc
Q 042101 65 TIDISKLTEVK------QKLKLVGINCDDSCIPGRYAHLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGR 138 (380)
Q Consensus 65 ~~~~~~~~~~~------~~l~~~gi~~~~~~~~G~~~~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~G~ 138 (380)
+++.+.+++|+ +++..+ +++++ +|++|.++||||++ ++|||+|++++ +.||||+ ||.+||
T Consensus 3 ~i~~~~i~~i~~~~dI~~vi~~~-v~Lkk---~G~~~~~~CPfH~e------ktpSf~V~~~k--~~~~CF~--Cg~~Gd 68 (580)
T PRK05667 3 RIPPEFIEELRARVDIVDVIGEY-VKLKK---AGRNYKGLCPFHDE------KTPSFTVSPDK--QFYHCFG--CGAGGD 68 (580)
T ss_pred CCCHHHHHHHHhcCCHHHHHHHh-cceee---cCCceeecCCCCCC------CCCceEEECCC--CeEEECC--CCCCCC
Confidence 34555555544 455554 88877 89999999999985 78999999864 9999999 999999
Q ss_pred cccC-----Cc---c------------chhc--cch--h-hhh---hh--cc---CC-CcccHHHHHHHHhCCCCHHHHh
Q 042101 139 AFAG-----SN---K------------IRKV--MSS--R-QVA---EK--SL---GL-EPLGEKLIAYLGERMISEGTLQ 184 (380)
Q Consensus 139 v~~~-----~~---e------------~~~~--~~~--~-~~~---~~--~~---~~-~pl~~~~~~YL~~RGIs~eti~ 184 (380)
++.. .. + .... .+. + +.. +. .+ .+ .+.++.+++||.+|||++++++
T Consensus 69 ~i~fv~~~~~~sf~eAv~~La~~~gi~~~~~~~~~~~~~~~l~~~~~~a~~~y~~~L~~~~~~~a~~YL~~RGls~~~i~ 148 (580)
T PRK05667 69 VIKFLMEYEGLSFVEAVEELADRAGIELPYEDQQERSRRQRLYEIMELAAKFYQQQLRTPEGAEARQYLYKRGLSEETIE 148 (580)
T ss_pred HHHHHHHHhCCCHHHHHHHHHHHhCCCCCchhhhhhhhHHHHHHHHHHHHHHHHHHHcCccchHHHHHHHHcCCCHHHHH
Confidence 9852 10 1 0000 000 0 000 00 00 12 4667789999999999999999
Q ss_pred hcceEEecC-------------------------------C-------cEEEEE-ecCCCEEEEEeeecCC---Cccccc
Q 042101 185 RNSVMQRLH-------------------------------D-------QAIAFP-YWHNGVLVGCKYRSME---RKFRQE 222 (380)
Q Consensus 185 ~f~~g~~~~-------------------------------g-------~~I~fP-~~~~G~vv~~~~R~~~---Kkf~~~ 222 (380)
+|++||+++ | +||+|| +|.+|++|+|++|.++ .||.+.
T Consensus 149 ~f~lGyap~~~~~L~~~l~~~~~~~~~l~~~GL~~~~~~~~~~yd~Fr~RimfPI~d~~G~vigF~GR~l~~~~pKYlNS 228 (580)
T PRK05667 149 RFGIGYAPDGWDALLKHLGGKGFSEKELEEAGLLIKNEDGGGPYDRFRNRIMFPIRDLRGRVIGFGGRVLGDDKPKYLNS 228 (580)
T ss_pred HhCCccCCChHHHHHHHHHhcCCCHHHHHHCCceEecCCCCCcchhcCCeEEEEEECCCCcEEEEEeeecCCCCCeeeCC
Confidence 999998641 2 289999 5789999999999985 578775
Q ss_pred c-----CCCCccccccccC----CCCEEEEEechhHHHHHHHhCCCcEEEcCCCCCCCccCCCCCCCcccchhhhhHHHH
Q 042101 223 K-----GTEKWLYGLDDIN----ETAEVIIVEGEIDKLSVEEAGFQNCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCK 293 (380)
Q Consensus 223 ~-----~~~~~Lfgl~~i~----~~~~iiIvEG~~DaLSl~q~G~~~~Vs~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~ 293 (380)
+ .++..|||++.++ +.+.||||||++||||++|+|+.|||++ .|+..+ . +|+
T Consensus 229 pet~iF~K~~~LYgl~~a~~~i~~~~~viivEG~~Dvisl~q~Gi~naVA~-lGtalt--~----------------~~~ 289 (580)
T PRK05667 229 PETPLFHKGRVLYGLDEARKAIAKKKQVIVVEGYMDVIALHQAGITNAVAS-LGTALT--E----------------EHL 289 (580)
T ss_pred CCCCCccCCccccCccHHHHhcccCCeEEEEeeHHHHHHHHHcCCCcEEEe-CCCCCC--H----------------HHH
Confidence 5 3678999998754 5789999999999999999999999976 465321 1 244
Q ss_pred hhcCCC-CeEEEEeCCChhhHHHHHHHHHH---hC--CCceEEEEcCCCCCCCCCCCHHHHHHhcChHHHHHHHHhccCC
Q 042101 294 EHLDKV-SRIILGTDADTPGHALAEELARR---LG--KDRCWRVRWPKKDEFSYFKDANEVLKCLGPGALREVIENAELY 367 (380)
Q Consensus 294 ~~L~~~-~~Ivl~~DnD~AG~~aa~~la~~---L~--~~~v~iv~lP~~~~~~~~KD~ND~L~~~g~~~l~~~i~~A~~~ 367 (380)
.+|.+. .+||+|||+|.||++||.++++. +. ...++++.+|+ +|||||+++++|.++|+++|++|.++
T Consensus 290 ~~L~r~~~~vil~~D~D~AG~~aa~r~~~~~~~l~~~g~~v~vv~lp~------gkDpdd~l~~~G~~~~~~~i~~a~~~ 363 (580)
T PRK05667 290 KLLRRLTDEVILCFDGDKAGRKAALRALELALPLLKDGRQVRVAFLPD------GKDPDDLVRKEGPEAFRALLEQAIPL 363 (580)
T ss_pred HHHHhcCCeEEEEeCCCHHHHHHHHHHHHHHHHHHhCCceEEEEECCC------CCChHHHHHHhCHHHHHHHHHcCCCH
Confidence 555443 58999999999999999998877 42 23688999997 49999999999999999999999998
Q ss_pred Cccchhhhh
Q 042101 368 QLHVSEEAL 376 (380)
Q Consensus 368 ~~~~~~~~~ 376 (380)
....+...+
T Consensus 364 ~~f~~~~~~ 372 (580)
T PRK05667 364 SEFLIRRLI 372 (580)
T ss_pred HHHHHHHHH
Confidence 766555443
No 2
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=100.00 E-value=3e-42 Score=348.95 Aligned_cols=264 Identities=25% Similarity=0.356 Sum_probs=200.2
Q ss_pred HHHHHHHhCCccccCCCCCceeeecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCCcccccCC-----c---c
Q 042101 74 VKQKLKLVGINCDDSCIPGRYAHLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGRAFAGS-----N---K 145 (380)
Q Consensus 74 ~~~~l~~~gi~~~~~~~~G~~~~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~G~v~~~~-----~---e 145 (380)
|.+++.++ +++++ .|++|.++||||++ ++|||+|++++ +.||||+ ||.+||+++.- . +
T Consensus 16 i~~vi~~~-~~l~~---~G~~~~~~CPfh~e------k~pSf~v~~~k--~~~~Cf~--Cg~~Gd~i~fv~~~~~~sf~e 81 (415)
T TIGR01391 16 IVDVISEY-VKLKK---KGRNYVGLCPFHHE------KTPSFSVSPEK--QFYHCFG--CGAGGDAIKFLMEIEGISFVE 81 (415)
T ss_pred HHHHHHhh-Cceee---cCCceEeeCCCCCC------CCCeEEEEcCC--CcEEECC--CCCCCCHHHHHHHHhCCCHHH
Confidence 55566666 88876 89999999999985 78999999864 8999999 99999998511 0 0
Q ss_pred ------------chhc---cc------hh-hhh---h---h----ccCCCcccHHHHHHHHhCCCCHHHHhhcceEEecC
Q 042101 146 ------------IRKV---MS------SR-QVA---E---K----SLGLEPLGEKLIAYLGERMISEGTLQRNSVMQRLH 193 (380)
Q Consensus 146 ------------~~~~---~~------~~-~~~---~---~----~~~~~pl~~~~~~YL~~RGIs~eti~~f~~g~~~~ 193 (380)
.... .. .+ +.. . . .+...+.+..+++||.+|||+++++++|++||.++
T Consensus 82 A~~~La~~~gi~l~~~~~~~~~~~~~~~~~~l~~~~~~a~~~y~~~L~~~~~~~~a~~YL~~RGis~e~i~~f~lGyap~ 161 (415)
T TIGR01391 82 AVEELAKRAGIDLPFEKDQQEKKEQKSKRKKLYELLELAAKFFKNQLKHTPENRAALDYLQSRGLSDETIDRFELGYAPN 161 (415)
T ss_pred HHHHHHHHcCCCCCcccccchhhhhhhHHHHHHHHHHHHHHHHHHHhccCccchHHHHHHHHcCCCHHHHHHcCCCCCCC
Confidence 0000 00 00 000 0 0 01123335678999999999999999999998531
Q ss_pred -------------------------------C-------cEEEEE-ecCCCEEEEEeeecCC---CccccccC-----CC
Q 042101 194 -------------------------------D-------QAIAFP-YWHNGVLVGCKYRSME---RKFRQEKG-----TE 226 (380)
Q Consensus 194 -------------------------------g-------~~I~fP-~~~~G~vv~~~~R~~~---Kkf~~~~~-----~~ 226 (380)
| +||+|| +|.+|++++|++|.++ .||.+.+. ++
T Consensus 162 ~~~~l~~~l~~k~~~~~~~l~~~Gl~~~~~~g~~~d~Fr~RiifPi~d~~G~vvgf~gR~~~~~~pKYlNspet~~f~K~ 241 (415)
T TIGR01391 162 NWDFLFDFLQNKKGFDLELLAEAGLLVKKENGKYYDRFRNRIMFPIHDPKGRVVGFGGRALGDEKPKYLNSPETPLFKKS 241 (415)
T ss_pred cHHHHHHHHHhccCCCHHHHHHCCCeEECCCCCeeeecCCeEEEEEECCCCCEEEEEeeecCCCCCceeCCCCCCCccCC
Confidence 1 289999 5799999999999985 47877543 57
Q ss_pred Ccccccccc----CCCCEEEEEechhHHHHHHHhCCCcEEEcCCCCCCCccCCCCCCCcccchhhhhHHHHhhcCC-CCe
Q 042101 227 KWLYGLDDI----NETAEVIIVEGEIDKLSVEEAGFQNCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLDK-VSR 301 (380)
Q Consensus 227 ~~Lfgl~~i----~~~~~iiIvEG~~DaLSl~q~G~~~~Vs~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~~~L~~-~~~ 301 (380)
..|||++.+ .+.+.|+||||++||||++++|++++|++. |+.... +++++|.+ .++
T Consensus 242 ~~lygl~~a~~~~~~~~~viivEG~~Daisl~~~G~~~aVA~~-Gtalt~------------------~~~~~l~r~~~~ 302 (415)
T TIGR01391 242 ELLYGLHKARKEIRKEKELILVEGYMDVIALHQAGIKNAVASL-GTALTE------------------EHIKLLKRYADE 302 (415)
T ss_pred ccccCHhHHHHhhccCCcEEEEecHHHHHHHHHCCCCcEEECC-CCCCcH------------------HHHHHHHhhCCe
Confidence 899999865 357789999999999999999999999864 553211 23455544 369
Q ss_pred EEEEeCCChhhHHHHHHHHHHhCC--CceEEEEcCCCCCCCCCCCHHHHHHhcChHHHHHHHHhccCCCccchhhhh
Q 042101 302 IILGTDADTPGHALAEELARRLGK--DRCWRVRWPKKDEFSYFKDANEVLKCLGPGALREVIENAELYQLHVSEEAL 376 (380)
Q Consensus 302 Ivl~~DnD~AG~~aa~~la~~L~~--~~v~iv~lP~~~~~~~~KD~ND~L~~~g~~~l~~~i~~A~~~~~~~~~~~~ 376 (380)
||||+|+|.||++||.++++.|.. ..++++.||. +|||||+|+++|.++|+++|++|.++....++..+
T Consensus 303 vvl~~D~D~aG~~aa~r~~~~l~~~g~~v~v~~lp~------gkDpdd~l~~~g~~~~~~~l~~a~~~~~f~~~~~~ 373 (415)
T TIGR01391 303 IILCFDGDKAGRKAALRAIELLLPLGINVKVIKLPG------GKDPDEYLRKEGVEALKKLLENSKSLIEFLIARLL 373 (415)
T ss_pred EEEEeCCCHHHHHHHHHHHHHHHHcCCeEEEEECCC------CCCHHHHHHHhCHHHHHHHHhcCCCHHHHHHHHHH
Confidence 999999999999999998888742 3688889986 49999999999999999999999987655554433
No 3
>PHA02540 61 DNA primase; Provisional
Probab=100.00 E-value=1.6e-40 Score=324.11 Aligned_cols=256 Identities=19% Similarity=0.271 Sum_probs=184.2
Q ss_pred hHHHHHHHHHHhCCccccCCCCCceeeecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCCcccccCCc-----
Q 042101 70 KLTEVKQKLKLVGINCDDSCIPGRYAHLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGRAFAGSN----- 144 (380)
Q Consensus 70 ~~~~~~~~l~~~gi~~~~~~~~G~~~~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~G~v~~~~~----- 144 (380)
++.+++..|.+ +++ +|. |+++||||++ +.++|++|||+|++++..++||||+ ||++||++.+-.
T Consensus 9 ~~~~~~~~f~~----~~~---~~~-~~~~CPf~~d-s~~~~~kpsF~V~p~k~~~~yhCFg--CGa~Gd~i~Flme~e~l 77 (337)
T PHA02540 9 RASPHLPKFKQ----VRR---SSF-YNFRCPICGD-SQKDKNKARGWIYEKKDGGVFKCHN--CGYHRPFGNFLKDYEPD 77 (337)
T ss_pred HHHHHHhhhhe----ecc---Cce-EEecCCCCCC-ccccCcCCcEEEeccCCceEEEecC--CCCCCCHHHHHHHhcCC
Confidence 45556666665 554 565 9999999999 6677899999999987556999999 999999985210
Q ss_pred ---cc----h---------h--ccch---hh---hhh----hccCCCcccHHHHHHHHhCCCCHHHHhhcceEEe-----
Q 042101 145 ---KI----R---------K--VMSS---RQ---VAE----KSLGLEPLGEKLIAYLGERMISEGTLQRNSVMQR----- 191 (380)
Q Consensus 145 ---e~----~---------~--~~~~---~~---~~~----~~~~~~pl~~~~~~YL~~RGIs~eti~~f~~g~~----- 191 (380)
|. . . .+.. .+ ... ..+...+.+..+++||.+|||++++++.++.-..
T Consensus 78 sf~Eav~~la~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~a~~YL~~RGi~~~~~~~~~~~~~~~~l~ 157 (337)
T PHA02540 78 LYREYIMERFKERGTGKGRPVPKPKFEFKKEKKVIEKLPFCERLDTLPEDHPIIKYVENRCIPKDKWKLLYFTREWQKLV 157 (337)
T ss_pred ChHHHHHHHHHHhCCccccCCCCCChhHHHHHHHHHHHHHHHHHHhCcccHHHHHHHHHcCCCHHHHHhcCCCccHHHHH
Confidence 10 0 0 0000 00 000 0112356677899999999999999998633100
Q ss_pred -----------cCCcEEEEE-ecCCCEEEEEeeecCC----Ccccccc--CCCCccccccccCCCCEEEEEechhHHHHH
Q 042101 192 -----------LHDQAIAFP-YWHNGVLVGCKYRSME----RKFRQEK--GTEKWLYGLDDINETAEVIIVEGEIDKLSV 253 (380)
Q Consensus 192 -----------~~g~~I~fP-~~~~G~vv~~~~R~~~----Kkf~~~~--~~~~~Lfgl~~i~~~~~iiIvEG~~DaLSl 253 (380)
.+.+||||| +|.+|++|+|++|.++ .||++.+ .++..|||++.+++.+.+|||||+||||+
T Consensus 158 ~~l~~~~~~~~~d~~RImFPI~d~~G~vigFgGR~l~~~~~pKYlNSp~f~K~~~LYGl~~a~~~~~vilvEGYmDvi~- 236 (337)
T PHA02540 158 NSIKPDTYKKEKPEPRLVIPIFNKDGKIESFQGRALRKDAPQKYITIKADEEATKIYGLDRIDPGKTVYVVEGPIDSLF- 236 (337)
T ss_pred HHHhhccCchhccCCeeEEEEECCCCCEEEEEeEECCCCCCCCeeeCCcccccccccChhHhccCCEEEEEeCCcceee-
Confidence 012499999 5899999999999995 3788754 47889999999988899999999999997
Q ss_pred HHhCCCcEEEcCCCCCCCccCCCCCCCcccchhhhhHHHHhhcCCCCeEEEEeCCChhhHHHHHHHHHHhCCCceEEEEc
Q 042101 254 EEAGFQNCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLDKVSRIILGTDADTPGHALAEELARRLGKDRCWRVRW 333 (380)
Q Consensus 254 ~q~G~~~~Vs~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~~~L~~~~~Ivl~~DnD~AG~~aa~~la~~L~~~~v~iv~l 333 (380)
+.|+|+. .|++.+. +|. .-.++|||+|||| ||++|+.+..+.|-...+.++.|
T Consensus 237 ----i~naVAt-lGTaLT~------------------~~~---~~~~~vvl~~D~D-a~~~at~r~~~~l~~~g~~v~v~ 289 (337)
T PHA02540 237 ----LPNSIAI-TGGDLDL------------------NEV---PFKDTRVWVLDNE-PRHPDTIKRISKLIDAGEKVVIW 289 (337)
T ss_pred ----eccceee-CccccCH------------------hHh---CccceEEEEECCc-hhHHHHHHHHHHHHHCCCeEEEe
Confidence 4788875 5664221 122 1136999999999 77788877777774333556667
Q ss_pred CCCCCCCCCCCHHHHHHhcCh--HHHHHHHHhccC
Q 042101 334 PKKDEFSYFKDANEVLKCLGP--GALREVIENAEL 366 (380)
Q Consensus 334 P~~~~~~~~KD~ND~L~~~g~--~~l~~~i~~A~~ 366 (380)
|.+ +...|||||+++++|. +++.++|+++.-
T Consensus 290 ~~~--~~~~kDpde~i~~~G~~~~~~~~~i~~n~~ 322 (337)
T PHA02540 290 DKC--PWPSKDINDMIMKGGATPEDIMEYIKSNTY 322 (337)
T ss_pred cCC--CCCCcCHHHHHHhcCCCHHHHHHHHHHccc
Confidence 652 1246999999999875 999999988754
No 4
>COG0358 DnaG DNA primase (bacterial type) [DNA replication, recombination, and repair]
Probab=100.00 E-value=4.4e-39 Score=337.69 Aligned_cols=260 Identities=22% Similarity=0.358 Sum_probs=195.1
Q ss_pred chhhHHHHHHHH-----HHhCCccccCCCCCceeeecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCCccccc
Q 042101 67 DISKLTEVKQKL-----KLVGINCDDSCIPGRYAHLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGRAFA 141 (380)
Q Consensus 67 ~~~~~~~~~~~l-----~~~gi~~~~~~~~G~~~~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~G~v~~ 141 (380)
..+.+++|++.+ ....|++++ .|++|.++||||++ |||||+|++++ |+||||+ ||++||++.
T Consensus 3 ~~~~i~~l~~~~dIvdvI~~~v~Lkk---~G~~y~~lCPFH~E------ktPSf~V~~~k--~~yhCFG--Cg~~Gd~i~ 69 (568)
T COG0358 3 PREFIDELRERIDIVDVIGEYVKLKK---QGANYTGLCPFHAE------KTPSFTVSPEK--GFYHCFG--CGAGGDAIK 69 (568)
T ss_pred CHHHHHHHHHcCCHHHHHhhheEeee---cCCCceeECcCCCC------CCCCceEeCCC--CeEecCC--CCCCccHHH
Confidence 344555555422 224478876 89999999999984 89999999865 9999999 999999985
Q ss_pred CCc--------cc----h---------h---ccchh-hhhh--h---cc---CCCcccHHHHHHHHhCCCCHHHHhhcce
Q 042101 142 GSN--------KI----R---------K---VMSSR-QVAE--K---SL---GLEPLGEKLIAYLGERMISEGTLQRNSV 188 (380)
Q Consensus 142 ~~~--------e~----~---------~---~~~~~-~~~~--~---~~---~~~pl~~~~~~YL~~RGIs~eti~~f~~ 188 (380)
+-. ++ . . ..+.+ +... + .+ .+.+.+.+++.||.+||++.+++++|++
T Consensus 70 Fl~~~~g~sf~eav~~La~~~gi~~~~~~~~~~~~~~~l~~~~~~~~~fy~~~L~~~~~~a~~yL~~Rgls~~~i~~f~i 149 (568)
T COG0358 70 FLMELLGLSFDEAVLQLAGRAGIELPYEKGKRIEKRQKLYDGKEEAAIFYQSSLDPEGAAALKYLETRGLAAELIAHFRL 149 (568)
T ss_pred HHHHhcCCCHHHHHHHHHHHhCCCCCccccccchhHHHHHHHHHHHHHHHHHHHHhchHHHHHHHHHcCCCHHHHHHhCC
Confidence 211 10 0 0 00000 0000 0 00 1226667889999999999999999999
Q ss_pred EEecC----------------------------C-------cEEEEE-ecCCCEEEEEeeecCC---Ccccccc-----C
Q 042101 189 MQRLH----------------------------D-------QAIAFP-YWHNGVLVGCKYRSME---RKFRQEK-----G 224 (380)
Q Consensus 189 g~~~~----------------------------g-------~~I~fP-~~~~G~vv~~~~R~~~---Kkf~~~~-----~ 224 (380)
||+++ | +||+|| ++..|++|+|++|.++ .||++.+ .
T Consensus 150 G~ap~~~~~~~~~~k~~~~~~~l~~~Gl~~~~~~~~ydrFr~RImfPI~d~~g~vigFggR~l~~~~~KYlNspet~if~ 229 (568)
T COG0358 150 GYAPPNDSLLPFLAKKEYREEKLEDLGLLKRKEGKIYDRFRNRIMFPIRDLRGDVIGFGGRVLGDDKPKYLNSPETELFK 229 (568)
T ss_pred CCCCCchHHHHHHhcCCcCHHHHHHCCCeecCCCceeehhcCeeEEeccCCCCCEEeeeccccCCCCCcccCCCCCcCcc
Confidence 95421 1 299999 5799999999999994 5788865 4
Q ss_pred CCCccccccccC----CCCEEEEEechhHHHHHHHhCCCcEEEcCCCCCCCccCCCCCCCcccchhhhhHHHHhhcCCC-
Q 042101 225 TEKWLYGLDDIN----ETAEVIIVEGEIDKLSVEEAGFQNCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLDKV- 299 (380)
Q Consensus 225 ~~~~Lfgl~~i~----~~~~iiIvEG~~DaLSl~q~G~~~~Vs~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~~~L~~~- 299 (380)
+++.|||++.+. +.++||||||+||||+++++|+.|||++ .|++.+. +|+..|.+.
T Consensus 230 Kg~~Lyg~~~a~~~~~~~~~iivVEGymDViaL~~aGi~naVA~-lGTalt~------------------ehi~~L~r~~ 290 (568)
T COG0358 230 KGEELYGLDPARKKIAKADQIIVVEGYMDVIALHKAGIKNAVAS-LGTALTE------------------EHIKLLSRGK 290 (568)
T ss_pred CcHHhhCHHHHHHhhccCCeEEEEechHHHHHHHHcCCcceeec-ccccCCH------------------HHHHHHHhcC
Confidence 788999998653 4788999999999999999999999986 5765221 355666554
Q ss_pred CeEEEEeCCChhhHHHHHHHHHHh---CCCceEEEEcCCCCCCCCCCCHHHHHHhcChHHHHHHHHhc
Q 042101 300 SRIILGTDADTPGHALAEELARRL---GKDRCWRVRWPKKDEFSYFKDANEVLKCLGPGALREVIENA 364 (380)
Q Consensus 300 ~~Ivl~~DnD~AG~~aa~~la~~L---~~~~v~iv~lP~~~~~~~~KD~ND~L~~~g~~~l~~~i~~A 364 (380)
.+|++|||+|.||++||.++.+.. ....++++.+|.| +||+|+++++|.++|.+.+.++
T Consensus 291 ~~vil~fDgD~AG~~Aa~ral~~~~~~~~~~v~v~~~P~G------kDpDel~~k~g~~al~~~l~~~ 352 (568)
T COG0358 291 KKVILCFDGDRAGRKAAKRALQLVLPLDFVGVFVILLPDG------KDPDELIRKEGAEALRKKLPNE 352 (568)
T ss_pred CCEEEEeCChHHHHHHHHHHHHHhhhhccCCeEEEECCCC------CChHHHHHHhChHHHHHHHHhC
Confidence 679999999999999988766633 2222889999974 9999999999999999999885
No 5
>PHA02415 DNA primase domain-containing protein
Probab=99.97 E-value=6.5e-30 Score=265.62 Aligned_cols=271 Identities=19% Similarity=0.231 Sum_probs=184.1
Q ss_pred HHHHHHHhCCccccCCCCCceeeecCCCCCCCCCCCCccceEEEEEcC--CccEEEeCCccCCCCcccccCCc-------
Q 042101 74 VKQKLKLVGINCDDSCIPGRYAHLLCPKCKGGGRSLERSLSVHIIQDG--DFAMWRCFRVDCGWAGRAFAGSN------- 144 (380)
Q Consensus 74 ~~~~l~~~gi~~~~~~~~G~~~~~~CPfc~~~~~~~eks~s~~v~~d~--~~g~~~Cf~~~CG~~G~v~~~~~------- 144 (380)
|.+++...|++..+ .|+++.++||||.+ ++|||+|+.+. ....||||+ ||.+||+++.-.
T Consensus 13 IVDVLerLGLkp~r---~G~~a~YlCPFHnE------KTPSFsVn~~~~~k~NiWyCFG--CG~GGDaIDFVmkieglSF 81 (930)
T PHA02415 13 LHDLADRLGLKRGR---GGDKALYHSPQHED------KSPSLSIYVNHPKHGTGWRDHS--ADAGGSCIDLVIHARGGTV 81 (930)
T ss_pred HHHHHHHcCCEEee---CCCeeeeeCCCCCC------CCCceEEeecccccCcEEEEeC--CCCCCCHHHHHHHHhCCCH
Confidence 77788888887754 68888899999974 89999998742 234799999 999999985211
Q ss_pred -cc------------hhc-cchhhhhhh-cc---CCCcccHHHHHHHHhCCCCHHHHhh-cceEEe-------------c
Q 042101 145 -KI------------RKV-MSSRQVAEK-SL---GLEPLGEKLIAYLGERMISEGTLQR-NSVMQR-------------L 192 (380)
Q Consensus 145 -e~------------~~~-~~~~~~~~~-~~---~~~pl~~~~~~YL~~RGIs~eti~~-f~~g~~-------------~ 192 (380)
++ ... ...++..+. .+ ...+-...+.+||.+|||++++|++ +..|.. .
T Consensus 82 ~EAVe~Lae~~GI~lp~ps~s~kekK~Ka~Fl~~r~~ad~rrA~AYLK~RGIS~EVI~~cIk~GlIg~~~W~s~rv~agd 161 (930)
T PHA02415 82 ADAVRYLHDAYGIPLDRPAPAERREKSTVEYIADRCLAERERVREYLGGRGISAAAIDAAFAARSLGFNTWTSSKVAAGE 161 (930)
T ss_pred HHHHHHHHHHcCCCCCCccccccchhhhhhhhHhhhccchHHHHHHHHhcCCCHHHHHHHHHcCcccccccccccccccc
Confidence 10 000 000000000 11 0112256799999999999999997 544311 0
Q ss_pred ---CCc--EEEEEecCCCEEEEEeeecCCCcccccc----CCCCcccccccc----CCCCEEEEEechhHHHHHHHhCCC
Q 042101 193 ---HDQ--AIAFPYWHNGVLVGCKYRSMERKFRQEK----GTEKWLYGLDDI----NETAEVIIVEGEIDKLSVEEAGFQ 259 (380)
Q Consensus 193 ---~g~--~I~fP~~~~G~vv~~~~R~~~Kkf~~~~----~~~~~Lfgl~~i----~~~~~iiIvEG~~DaLSl~q~G~~ 259 (380)
+|. .++||++.+|.++..+.|.++..|.... .++...|+++.. ...++|+||||+|||||++++|++
T Consensus 162 ~gygg~nAAFIVpf~rdGtvv~v~~Rg~d~afkG~vKanf~Gs~~G~gW~~p~~~L~~a~eVwIvEGiIDAISL~q~Gi~ 241 (930)
T PHA02415 162 VGHAGPAAAFIVREPADGRVVAVDMRYVDPALNGGVKTQTQGDKAGYGWTADARRLDKAKRVFIVESAINALSIDTCAMP 241 (930)
T ss_pred cccCCCceEEEecccCCceEEEeeeccccccccCCccccCCCCCCCCccCCCccccCCCCEEEEEechHhHHHHHHcCch
Confidence 122 4578999999999999998765443221 224555666532 346799999999999999999998
Q ss_pred cEEEcC-CCCCCCccCCCCCCCcccchhhhhHHHHhhcCCCCeEEEEeCCChh------------hHHHHHHHHHHhCCC
Q 042101 260 NCVSVP-SGAPPKVSNRELPPREKDTGYQYLWNCKEHLDKVSRIILGTDADTP------------GHALAEELARRLGKD 326 (380)
Q Consensus 260 ~~Vs~~-~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~~~L~~~~~Ivl~~DnD~A------------G~~aa~~la~~L~~~ 326 (380)
++.+++ .|..+. .. . .++.+ ..++|+||+|||+| |++||.++.++|...
T Consensus 242 avAaVAL~GLan~-~~------------i----D~~~l-~~KrVvlcLDNDea~~~~~~~~g~rpG~eAA~~l~e~lta~ 303 (930)
T PHA02415 242 GAAALALRGLANV-DA------------I----DFSSL-RGKQVVICLDNDEPFEDGHPRAGHRPGPEAAWALYERLASL 303 (930)
T ss_pred hHHHHHHcCcCCC-ch------------h----hchhh-cCceEEEEecCCccccccCcccccCccHHHHHHHHHHHhhc
Confidence 532222 343211 10 0 02233 47899999999998 999999999998422
Q ss_pred --ceEEEE---cCC----C-CCCCCCCCHHHHHHhcChHHHHHHHHhccCCCccchh
Q 042101 327 --RCWRVR---WPK----K-DEFSYFKDANEVLKCLGPGALREVIENAELYQLHVSE 373 (380)
Q Consensus 327 --~v~iv~---lP~----~-~~~~~~KD~ND~L~~~g~~~l~~~i~~A~~~~~~~~~ 373 (380)
.+..|. |-+ + .......|+||+|+.+|.+++...++.-+||-|+|+.
T Consensus 304 ~i~~~lvd~~~w~~~~~~~~~~~~~~~d~nd~l~~~g~~~~~~~l~~~~~wli~g~~ 360 (930)
T PHA02415 304 NISAVLVDQAGWLADLADGETKQQPINDVNDYLQLRGPEELARALEQLEPWLIAGLA 360 (930)
T ss_pred CCceEEeehhhhhhhcccccccccccccHHHHHHHhCHHHHHHHHHhccccccCCCC
Confidence 334443 322 1 0112346999999999999999999999999999875
No 6
>PRK08624 hypothetical protein; Provisional
Probab=99.97 E-value=4.2e-30 Score=251.58 Aligned_cols=250 Identities=23% Similarity=0.302 Sum_probs=165.0
Q ss_pred HHHHHHHHHhCCccccCCCCCce-eeecCCCCCCCCCCCCccceEEEEEcCCccEEEeC-CccCCCCcccccCCcc----
Q 042101 72 TEVKQKLKLVGINCDDSCIPGRY-AHLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCF-RVDCGWAGRAFAGSNK---- 145 (380)
Q Consensus 72 ~~~~~~l~~~gi~~~~~~~~G~~-~~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf-~~~CG~~G~v~~~~~e---- 145 (380)
+.|..+|...|..... .+.|.. |.++|+++++ .|+|++|++++ |+|||| + ||++|||+.+-.+
T Consensus 14 ~~i~~il~~~g~~~~l-~k~G~~~y~~~CH~e~~------pS~sv~v~pek--q~yhCF~G--CGa~GDVf~Fv~~~~~m 82 (373)
T PRK08624 14 EDIIKILEEVGCENVR-GKDGNTIAETACHNDGG------GSTKLYYYIEN--DNFHCYTR--CGDIFDVFELLCKRLKM 82 (373)
T ss_pred HHHHHHHHHhccccee-ccCCcchhheecCCCCC------CCceEEEcCCC--CEEEEeCC--CCCCCceeeehhhhhhc
Confidence 3588899998886654 357888 7999966542 55556667764 999999 9 9999999863211
Q ss_pred ---------c----hh--------ccchh--hhh--------------h-hcc--CCCcccHHHHHHH--------HhCC
Q 042101 146 ---------I----RK--------VMSSR--QVA--------------E-KSL--GLEPLGEKLIAYL--------GERM 177 (380)
Q Consensus 146 ---------~----~~--------~~~~~--~~~--------------~-~~~--~~~pl~~~~~~YL--------~~RG 177 (380)
+ .+ ..... +.. . ..+ .+..+.+.++.|+ .+||
T Consensus 83 e~~~lsF~eAve~LA~~aGI~l~~~~~~~~~~~~~~~~~d~~~~~~~~k~~~~~~~l~~~~e~~l~~f~~~~~~~~l~RG 162 (373)
T PRK08624 83 EGKALSFSKAIRKITKILGLSYFYEPKQQGIKPSFLKILDWVWTGKKEKKEKIQPQLKSFNENILNQFVKIPNRKWLDEG 162 (373)
T ss_pred cccCCCHHHHHHHHHHHhCcccccCcccccchhhhHhHHHHHhhhhhhhhHHHHHHHHHHHHHHHHHhhcccHHHHHHcC
Confidence 0 00 00000 000 0 000 0111233344443 3799
Q ss_pred CCHHHHhhcceEEecCC--cEEEEEe-cCCCEEEEEeeecCCC------cccc----cc----CCCCcccccccc----C
Q 042101 178 ISEGTLQRNSVMQRLHD--QAIAFPY-WHNGVLVGCKYRSMER------KFRQ----EK----GTEKWLYGLDDI----N 236 (380)
Q Consensus 178 Is~eti~~f~~g~~~~g--~~I~fP~-~~~G~vv~~~~R~~~K------kf~~----~~----~~~~~Lfgl~~i----~ 236 (380)
|+++|+++|++||..|- +||+||+ |.+|++|||++|.++. ||.+ .+ .++..|||++.+ +
T Consensus 163 Is~etik~F~lGy~~D~Fr~RImFPI~d~~GrvIGFgGR~l~~~~~~~~KY~p~y~Nst~~~F~Kg~~LYGl~~Ak~~ir 242 (373)
T PRK08624 163 ISEKTQKYWEIKFYLDVISQRIIIPHRDESGELIGIRGRLLDKELVDKNKYFPIYVNDTGYNHPKGKILYGLWQNKKYIK 242 (373)
T ss_pred CCHHHHHHhCCCccccccCCeeEEEEECCCCCEEEEeCeEcCCCccccccccccCCCCcccccccchhhcCHHHHHHHhc
Confidence 99999999999987663 5999995 7999999999999952 3432 11 267899999864 4
Q ss_pred CCCEEEEEechhHHH---HHHHhCCCcEEEcCCCCCCCccCCCCCCCcccchhhhhHHHHhhcCCC--CeEEEEeCC---
Q 042101 237 ETAEVIIVEGEIDKL---SVEEAGFQNCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLDKV--SRIILGTDA--- 308 (380)
Q Consensus 237 ~~~~iiIvEG~~DaL---Sl~q~G~~~~Vs~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~~~L~~~--~~Ivl~~Dn--- 308 (380)
+.+.+|||||+|||| +++++| .++|++ +|++. +. +|+..|.+. ++|+||||+
T Consensus 243 k~~~vIivEGymDVI~~~a~~~~G-~naVA~-lGTal--T~----------------~q~~lL~r~~~~~Vil~~Dgd~~ 302 (373)
T PRK08624 243 EKKKVIIVESEKSVLFSDKFYGEG-NFVVAI-CGSNI--SE----------------VQAEKLLRLGVEEVTIALDKEYM 302 (373)
T ss_pred cCCeEEEEeccHHHHHHHHHhcCC-CcEEEC-ChhhC--CH----------------HHHHHHHhcCCCcEEEEecCCcc
Confidence 678999999999999 888999 888876 56642 21 356777665 599999999
Q ss_pred ChhhHHHHHHH------HHHhCC-CceEEEEcCCCCCCCCCCCHHHHHHh------cChHHHHHHHHh
Q 042101 309 DTPGHALAEEL------ARRLGK-DRCWRVRWPKKDEFSYFKDANEVLKC------LGPGALREVIEN 363 (380)
Q Consensus 309 D~AG~~aa~~l------a~~L~~-~~v~iv~lP~~~~~~~~KD~ND~L~~------~g~~~l~~~i~~ 363 (380)
|.+|.++...+ ...|.+ -+++.+. |++.+|.. .|.+.|.++++.
T Consensus 303 d~~~~~~~~~~~ki~k~~~~~~~~~~~~~~~-----------d~~g~l~~~~~~~~~~~~~~~~l~~~ 359 (373)
T PRK08624 303 DVTEEEVYEYIKKLMKPVKTFAPYVNIYILK-----------DEAGLLKYKDSPPDDNKDTLEELMSV 359 (373)
T ss_pred ccchHHHHHHHHHHHHHHHhcCcceEEEEEe-----------cchhhhccCCCCccCCHHHHHHHHHh
Confidence 67775554433 223332 2344443 44445532 366778877744
No 7
>TIGR00646 MG010 DNA primase-related protein. The DNA primase DnaG of E. coli and its apparent orthologs in other eubacterial species are approximately 600 residues in length. Within this set, a conspicuous outlier in percent identity, as seen in a UPGMA difference tree, is the branch containing the Mycoplasmas. This lineage is also unique in containing the small, DNA primase-related protein modelled by this alignment, which is homologous to the central third of DNA primase. Several small regions of sequence similarity specifically to Mycoplasma sequences rather than to all DnaG homologs suggests that the divergence of this protein from DnaG post-dated the separation of bacterial lineages. The function of this DNA primase-related protein is unknown.
Probab=99.97 E-value=2.4e-29 Score=230.86 Aligned_cols=173 Identities=19% Similarity=0.276 Sum_probs=141.2
Q ss_pred HHHHHHHhCCCCHHHHhhcc--eEEecCCcEEEEE-ecCCCEEEEEeeecCC--Ccccccc-----CCCCcccccccc-C
Q 042101 168 KLIAYLGERMISEGTLQRNS--VMQRLHDQAIAFP-YWHNGVLVGCKYRSME--RKFRQEK-----GTEKWLYGLDDI-N 236 (380)
Q Consensus 168 ~~~~YL~~RGIs~eti~~f~--~g~~~~g~~I~fP-~~~~G~vv~~~~R~~~--Kkf~~~~-----~~~~~Lfgl~~i-~ 236 (380)
.+.+||+++|+++..+-..| +.|+...+||||| ++.+|++|||++|.++ +||++.+ .++..|||++.. .
T Consensus 29 ~l~~~l~~~g~~~~~~~~~G~~~~y~~~~~RimFPI~d~~G~vvgFgGR~l~~~~KYlNspet~~f~K~~~Lygl~~~~~ 108 (218)
T TIGR00646 29 CAMNYLKKRGFNLQDFLKVGGGLAYLGEKEWLNLPLYNFDGNLIGFLNRKVGFEKEFLYLPFNKPPSKSEAFLGLKELPI 108 (218)
T ss_pred HHHHHHHHcCCCHHHHHHcCCCEEecccCCEEEEEEECCCCCEEEEeccCCCCCCCcccCCCCCCcccchhhcCcchhhc
Confidence 57999999999999888876 4566555699999 5899999999999995 6888854 368899999654 4
Q ss_pred CCCEEEEEechhHHHHHHHhCCCcEEEcCCCCCCCccCCCCCCCcccchhhhhHHHHhhcCC--CCeEEEEeCCChhhHH
Q 042101 237 ETAEVIIVEGEIDKLSVEEAGFQNCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLDK--VSRIILGTDADTPGHA 314 (380)
Q Consensus 237 ~~~~iiIvEG~~DaLSl~q~G~~~~Vs~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~~~L~~--~~~Ivl~~DnD~AG~~ 314 (380)
+.+++|||||+|||||++|+|+.++|++ +|+..+. +|...|.+ .++|+||+|||.||++
T Consensus 109 k~~~vilvEGymDVIsl~qaGi~naVAs-lGTALT~------------------~q~~lLkr~~~~~Iil~~D~D~AG~~ 169 (218)
T TIGR00646 109 EDNSIYLVEGDFDWLAFRKAGILNCLPL-CGLTISD------------------KQMKFFKQKKIEKIFICFDNDFAGKN 169 (218)
T ss_pred CCCEEEEEecHHHHHHHHHCCCCeEEEc-CchHhHH------------------HHHHHHhccCCCEEEEEeCCCHHHHH
Confidence 6789999999999999999999998864 5664221 24555555 4799999999999999
Q ss_pred HHHHHHHHhC--CCceEEEEcCCCCCCCCCCCHHHHHHhcChHHHHHHHHhcc
Q 042101 315 LAEELARRLG--KDRCWRVRWPKKDEFSYFKDANEVLKCLGPGALREVIENAE 365 (380)
Q Consensus 315 aa~~la~~L~--~~~v~iv~lP~~~~~~~~KD~ND~L~~~g~~~l~~~i~~A~ 365 (380)
|+.++.+.|. ...++++.+|. .+|||||+|+.++ +.+.++|.++.
T Consensus 170 Aa~r~~~~L~~~G~~v~vv~lP~-----~~KDwNEllk~~~-~~w~~~l~~~~ 216 (218)
T TIGR00646 170 AAANLEEILKKAGFITKVIEIKA-----AAKDWNDLFLLNN-KNWAAALRDHL 216 (218)
T ss_pred HHHHHHHHHHHCCCeEEEEeCCC-----cCCChhHHHHHhh-hhHHHHHHhhh
Confidence 9999988884 34688898986 5799999999865 77888888764
No 8
>PHA02031 putative DnaG-like primase
Probab=99.94 E-value=5.8e-26 Score=213.18 Aligned_cols=215 Identities=14% Similarity=0.055 Sum_probs=151.4
Q ss_pred eEEEEEcCCccEEEeCCccCCCCcccccCCccchh--ccchhhhhhhc---cCCCcccHHHHHHHHhCCCCHHHHhhcce
Q 042101 114 SVHIIQDGDFAMWRCFRVDCGWAGRAFAGSNKIRK--VMSSRQVAEKS---LGLEPLGEKLIAYLGERMISEGTLQRNSV 188 (380)
Q Consensus 114 s~~v~~d~~~g~~~Cf~~~CG~~G~v~~~~~e~~~--~~~~~~~~~~~---~~~~pl~~~~~~YL~~RGIs~eti~~f~~ 188 (380)
.+.++.+...+..+|++ |+.+|.+..-..-... .+++....++. ....|.-..+..||.++||+.+.+..-++
T Consensus 32 ~~~~~~~~~~w~ayc~r--c~~~~~~~~~~~~~~~~~~~~~~~~~p~d~~~~~~~~~w~~L~~~L~~kG~~~~~l~~~~~ 109 (266)
T PHA02031 32 AMTLYNNPDRWVAYCYR--CKEGGKVEKTHVRRVQCADQERFMPWPEDASDISQADAYQSLYGLLLSKGIDPNMMEPGLP 109 (266)
T ss_pred eeEEecCcchHHHHHHh--hcccchhhHHHHHHHHHHHHHhhCCCCCChhhhhcCChHHHHHHHHHHCCCCHHHHHhcCC
Confidence 46777666678999999 9998887421100000 00001111110 11123334678999999999998876432
Q ss_pred -EEecCCcEEEEEecCCCEEEEEeeecCC---CccccccCCCCcccccccc-CCCCEEEEEechhHHHHHHH---hCCCc
Q 042101 189 -MQRLHDQAIAFPYWHNGVLVGCKYRSME---RKFRQEKGTEKWLYGLDDI-NETAEVIIVEGEIDKLSVEE---AGFQN 260 (380)
Q Consensus 189 -g~~~~g~~I~fP~~~~G~vv~~~~R~~~---Kkf~~~~~~~~~Lfgl~~i-~~~~~iiIvEG~~DaLSl~q---~G~~~ 260 (380)
.|+.--+|||||+.. +|++|.++ +||.|.+.....|||++.. ...+.+||||||||||++++ +|+.|
T Consensus 110 ~~yDrFr~RimFPI~d-----gFgGR~l~~~~PKYLN~~SP~~~l~~~~~~~~~~~~vIlvEGYmDVI~l~~a~~aG~~n 184 (266)
T PHA02031 110 LEYSERQGRLIFRTDA-----GWLGRATADQQPKWVGYGYPAPDYVGWPPELSMPRPVVLTEDYLSALKVRWACNKPEVF 184 (266)
T ss_pred cceeeeCCEEEEeecc-----ccccccCCCCCCCcCCCCCCcHHHhhchhhhccCCeEEEEcCcHHHHHHHHHHhcCcce
Confidence 354444699999754 89999984 5898843336689998754 36789999999999999976 69999
Q ss_pred EEEcCCCCCCCccCCCCCCCcccchhhhhHHHHhhcCC--CCeEEEEeCCChhhHHHHHHHHHHhC--CCceEEEEcCCC
Q 042101 261 CVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLDK--VSRIILGTDADTPGHALAEELARRLG--KDRCWRVRWPKK 336 (380)
Q Consensus 261 ~Vs~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~~~L~~--~~~Ivl~~DnD~AG~~aa~~la~~L~--~~~v~iv~lP~~ 336 (380)
+|+. .|+..+. +|+..|.+ .++|+||||+|.||++|+.+..+.|. ...++|+.+|+|
T Consensus 185 aVA~-LGTALT~------------------~q~~~L~r~~~~~Vil~fDgD~AG~~Aa~ra~~~l~~~~~~v~vv~lP~g 245 (266)
T PHA02031 185 AVAL-LGTRLRD------------------RLAAILLQQTCPRVLIFLDGDPAGVDGSAGAMRRLRPLLIEGQVIITPDG 245 (266)
T ss_pred EEEC-CcccCCH------------------HHHHHHHhcCCCCEEEEeCCCHHHHHHHHHHHHHHHHcCCceEEEECCCC
Confidence 9975 5764221 34566655 48999999999999999999887763 246899999975
Q ss_pred CCCCCCCCHHHHHHhcChHHHHHH
Q 042101 337 DEFSYFKDANEVLKCLGPGALREV 360 (380)
Q Consensus 337 ~~~~~~KD~ND~L~~~g~~~l~~~ 360 (380)
+||+|++++.+.+.+...
T Consensus 246 ------~DPDd~ir~~i~eal~~~ 263 (266)
T PHA02031 246 ------FDPKDLEREQIRELLIGR 263 (266)
T ss_pred ------CChHHHHHHHHHHHHhcc
Confidence 999999988776666544
No 9
>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI. This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.
Probab=99.56 E-value=9.3e-14 Score=162.63 Aligned_cols=169 Identities=17% Similarity=0.200 Sum_probs=114.5
Q ss_pred Ccc-cHHHHHHH-HhCCCCHHHHhhcceEEec-----C----CcEEEEE-ecCCCEEEEEeeecCCC------cccccc-
Q 042101 163 EPL-GEKLIAYL-GERMISEGTLQRNSVMQRL-----H----DQAIAFP-YWHNGVLVGCKYRSMER------KFRQEK- 223 (380)
Q Consensus 163 ~pl-~~~~~~YL-~~RGIs~eti~~f~~g~~~-----~----g~~I~fP-~~~~G~vv~~~~R~~~K------kf~~~~- 223 (380)
.|+ +..+..|| ..|||+. +..+.++|.+ + ..+++|| +|.+|++++++.+.+++ ++...+
T Consensus 1680 ~pi~gt~A~~YL~~~RGI~~--~~~~~LrfhP~~y~~~~~~~~Paliapv~D~~G~i~gv~rt~L~p~~g~~~k~l~~~k 1757 (1960)
T TIGR02760 1680 QELKGTLAEKYLKQHRGLAS--IDNDDIRFHPTVYSSDKKNKHPALIAAARNEKGEITGIQITYLDKDDANKDKDMDNNK 1757 (1960)
T ss_pred CCCCCHHHHHHHHhcCCCCC--CCccceEECcccccCCCCCcCCeEEEEEECCCCCEEEEEEEEccCCCCCCCccCCCcc
Confidence 354 45789999 8999975 4567787765 2 1289999 58999999999999861 333321
Q ss_pred ----CCCCccccccccCCCCEEEEEechhHHHHHHHhCC--CcEEEcCCCCCCCccCCCCCCCcccchhhhhHHHHhhcC
Q 042101 224 ----GTEKWLYGLDDINETAEVIIVEGEIDKLSVEEAGF--QNCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLD 297 (380)
Q Consensus 224 ----~~~~~Lfgl~~i~~~~~iiIvEG~~DaLSl~q~G~--~~~Vs~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~~~L~ 297 (380)
.+...+++++.....+.++|+||++|+||+++++. .+++++ .|+. .+.. +..-.
T Consensus 1758 r~~G~k~g~~v~l~~~~~~~~liiaEGiEtaLS~~~a~~~~~~vvA~-lg~~-~l~~------------------i~~~~ 1817 (1960)
T TIGR02760 1758 RVKGSISGQFVVINKGMQGDRSYIAEGIETGLSIALANPKATVVIAV-GGKN-NLSP------------------IIPKF 1817 (1960)
T ss_pred cccccccCcEEEecCCCCCCeEEEEcCHHHHHHHHHhCCCCccEEEE-CCcc-cccc------------------ccCCC
Confidence 12233445443344678999999999999999974 455654 3442 1110 01011
Q ss_pred CCCeEEEEeCCC--hh-hHHHHHHHHHHhCC--CceEEEEcCCCCCCCCCCCHHHHHHhcChHHHHHHHHhccC
Q 042101 298 KVSRIILGTDAD--TP-GHALAEELARRLGK--DRCWRVRWPKKDEFSYFKDANEVLKCLGPGALREVIENAEL 366 (380)
Q Consensus 298 ~~~~Ivl~~DnD--~A-G~~aa~~la~~L~~--~~v~iv~lP~~~~~~~~KD~ND~L~~~g~~~l~~~i~~A~~ 366 (380)
..++||||+||| .+ |++|+.++++++.. ..++++ +| .||||+ |.+++.+.|+.+.+
T Consensus 1818 ~~~~viI~~D~D~~~a~G~~Aa~k~~~~l~~~G~~v~i~-~P--------~Dfnd~----g~~~~~~~l~~~~~ 1878 (1960)
T TIGR02760 1818 IPKNVVIVLDNDGEEAKSQRAIEKIINKFKQDNISARIV-FP--------DDWNDI----GEEELQKQLMRAIS 1878 (1960)
T ss_pred CCceEEEEeCCCCcccchHHHHHHHHHHHHhCCCeeEEe-CC--------chhhhh----hHHHHHHHHHHhhh
Confidence 247999999999 45 99999999998843 245555 66 388888 56777777766544
No 10
>PF13155 Toprim_2: Toprim-like
Probab=99.54 E-value=1.4e-14 Score=117.27 Aligned_cols=85 Identities=29% Similarity=0.389 Sum_probs=60.0
Q ss_pred EEEechhHHHHHHHhCCCcE----EEcCCCCCCCccCCCCCCCcccchhhhhHHHHhhc--CCCCeEEEEeCCChhhHHH
Q 042101 242 IIVEGEIDKLSVEEAGFQNC----VSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHL--DKVSRIILGTDADTPGHAL 315 (380)
Q Consensus 242 iIvEG~~DaLSl~q~G~~~~----Vs~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~~~L--~~~~~Ivl~~DnD~AG~~a 315 (380)
|||||++|+||++|++..+. +++++++.... .....+| .+.++|++|+|||+||+++
T Consensus 1 ~v~Eg~iDaLS~~~~~~~~~~~~~~~l~~~~~~~~-----------------~~~~~~l~~~~~~~i~l~~DnD~aG~~~ 63 (96)
T PF13155_consen 1 VVFEGPIDALSYYQLGKENIKDNSLSLAGGGTLSE-----------------KQQIKFLKENPYKKIVLAFDNDEAGRKA 63 (96)
T ss_pred cEEeCHHHHHHHHHhCchhcCCceEEEECCchHHH-----------------HHHHHHHHhCCCCcEEEEeCCCHHHHHH
Confidence 69999999999999987542 45554432110 0123444 3347899999999999999
Q ss_pred HHHHHHHhCCC-----ceEEEEcCCCCCCCCCCCHHHHH
Q 042101 316 AEELARRLGKD-----RCWRVRWPKKDEFSYFKDANEVL 349 (380)
Q Consensus 316 a~~la~~L~~~-----~v~iv~lP~~~~~~~~KD~ND~L 349 (380)
++++.+.|... .+.+..+|. .|||||+|
T Consensus 64 ~~~~~~~l~~~~~~~~~~~~~~~~~------~KD~Nd~L 96 (96)
T PF13155_consen 64 AEKLQKELKEEGFPNIKVRIEDPPD------GKDWNDYL 96 (96)
T ss_pred HHHHHHHHHhhCCCcceeeecCCCC------CcCchhhC
Confidence 99999888532 344445554 49999986
No 11
>PRK07078 hypothetical protein; Validated
Probab=99.50 E-value=8.2e-13 Score=142.43 Aligned_cols=149 Identities=21% Similarity=0.275 Sum_probs=103.9
Q ss_pred EEEEEe-cCCCEEEEEeeecCC----Ccc--cccc------CCCCccccccccCCCCEEEEEechhHHHHHHHhCCCcEE
Q 042101 196 AIAFPY-WHNGVLVGCKYRSME----RKF--RQEK------GTEKWLYGLDDINETAEVIIVEGEIDKLSVEEAGFQNCV 262 (380)
Q Consensus 196 ~I~fP~-~~~G~vv~~~~R~~~----Kkf--~~~~------~~~~~Lfgl~~i~~~~~iiIvEG~~DaLSl~q~G~~~~V 262 (380)
...++| |.+|+++....|... |.| +.++ .....|||++.+.....|+|||||.||.+++++|+. ++
T Consensus 135 ~~~~~Y~D~~G~~~~~v~R~~~~~~~K~fr~~~g~~~~~~~~~~~pLy~lp~l~~a~~V~lvEGEk~adal~~~g~~-at 213 (759)
T PRK07078 135 TAKWDYLDAAGKLIAVVYRYDPPGRRKEFRPWDAKRRKMAPPEPRPLYNQPGLLSAEQVVLVEGEKCAQALIDAGVV-AT 213 (759)
T ss_pred eeEEEEECCCCCEEEEEEeecCCCCCceeecccCCcceecCCCCcCCcCchhhhcCCeEEEEeChHHHHHHHhcCCe-EE
Confidence 445666 788999888888652 444 2222 234578999988777899999999999999999886 45
Q ss_pred EcCCCCCCCccCCCCCCCcccchhhhhHHHHhhcCCCCeEEEEeCCChhhHHHHHHHHHHhCC--CceEEEEcCCCCCCC
Q 042101 263 SVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLDKVSRIILGTDADTPGHALAEELARRLGK--DRCWRVRWPKKDEFS 340 (380)
Q Consensus 263 s~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~~~L~~~~~Ivl~~DnD~AG~~aa~~la~~L~~--~~v~iv~lP~~~~~~ 340 (380)
+.+.|+..... +.. +..|.+ ++|||+.|||++|+++|+++++.|.. ..+.++.+|. ++.+
T Consensus 214 t~~~Ga~~~~~-----------~~d-----~~~L~g-~~VvI~pD~D~~G~~~a~~va~~l~~~g~~~~~v~~p~-~~~~ 275 (759)
T PRK07078 214 TAMHGANAPVD-----------KTD-----WSPLAG-KAVLIWPDRDKPGWEYADRAAQAILSAGASSCAVLLPP-EDLP 275 (759)
T ss_pred ecCCCCCCCcc-----------ccc-----ccccCC-CEEEEEcCCChHHHHHHHHHHHHHHhcCCeEEEEEecC-cccC
Confidence 55667742211 011 233554 79999999999999999999998832 2344444553 2234
Q ss_pred CCCCHHHHHHh-cChHHHHHHHHh
Q 042101 341 YFKDANEVLKC-LGPGALREVIEN 363 (380)
Q Consensus 341 ~~KD~ND~L~~-~g~~~l~~~i~~ 363 (380)
.++|++|++.. ++.++|..+.+.
T Consensus 276 ~~~D~aD~~~~G~~~~~~~~~~~~ 299 (759)
T PRK07078 276 EGWDAADAIAEGFDVAGFLAHGER 299 (759)
T ss_pred cCCCHHHHHHcCCCHHHHHhhccc
Confidence 67999999998 355666666653
No 12
>cd03364 TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. E. coli DnaG is a single subunit enzyme.
Probab=99.44 E-value=6e-13 Score=104.41 Aligned_cols=75 Identities=28% Similarity=0.352 Sum_probs=57.8
Q ss_pred CEEEEEechhHHHHHHHhCCCcEEEcCCCCCCCccCCCCCCCcccchhhhhHHHHhhcCC-CCeEEEEeCCChhhHHHHH
Q 042101 239 AEVIIVEGEIDKLSVEEAGFQNCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLDK-VSRIILGTDADTPGHALAE 317 (380)
Q Consensus 239 ~~iiIvEG~~DaLSl~q~G~~~~Vs~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~~~L~~-~~~Ivl~~DnD~AG~~aa~ 317 (380)
++|+||||++|+||++++|+.++|++. |+... ..++++|.+ .++|+||+|||.+|+++++
T Consensus 1 ~~v~i~EG~~D~ls~~~~g~~~~va~~-G~~~~------------------~~~~~~L~~~~~~vii~~D~D~aG~~a~~ 61 (79)
T cd03364 1 KKVILVEGYMDVIALHQAGIKNVVASL-GTALT------------------EEQAELLKRLAKEVILAFDGDEAGQKAAL 61 (79)
T ss_pred CeEEEEeCHHHHHHHHHcCCCCEEECC-CccCc------------------HHHHHHHHhcCCeEEEEECCCHHHHHHHH
Confidence 469999999999999999998888764 44211 023456655 4899999999999999999
Q ss_pred HHHHHhCC--CceEEEE
Q 042101 318 ELARRLGK--DRCWRVR 332 (380)
Q Consensus 318 ~la~~L~~--~~v~iv~ 332 (380)
++.++|.. ..++++.
T Consensus 62 ~~~~~l~~~g~~~~~~~ 78 (79)
T cd03364 62 RALELLLKLGLNVRVLT 78 (79)
T ss_pred HHHHHHHHCCCeEEEEe
Confidence 99999853 2455553
No 13
>PF13662 Toprim_4: Toprim domain; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A.
Probab=99.33 E-value=2.1e-12 Score=101.82 Aligned_cols=71 Identities=41% Similarity=0.678 Sum_probs=49.5
Q ss_pred CEEEEEechhHHHHHHHhCCCcEEEcCCCCCCCccCCCCCCCcccchhhhhHHHHhhcCC-CCeEEEEeCCChhhHHHHH
Q 042101 239 AEVIIVEGEIDKLSVEEAGFQNCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLDK-VSRIILGTDADTPGHALAE 317 (380)
Q Consensus 239 ~~iiIvEG~~DaLSl~q~G~~~~Vs~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~~~L~~-~~~Ivl~~DnD~AG~~aa~ 317 (380)
+.++||||++|+|+++++|+++++++.+|+.+... +.. ...+.. .++|+||+|+|.+|++++.
T Consensus 1 k~viIvEG~~D~~~l~~~g~~~~v~~~g~~~~~~~-------------~~~---~~~~~~~~~~Vii~~D~D~~G~~~a~ 64 (81)
T PF13662_consen 1 KEVIIVEGEFDAIALEQAGYKNVVAVLGGNLSPLD-------------QIL---REKLEKKVKEVIIAFDNDKAGEKAAQ 64 (81)
T ss_dssp --EEEESSHHHHHHHHHTT-TTEEEESSSS---HH-------------HHH---HHHHH---SEEEEEEESSHHHHHHHH
T ss_pred CEEEEECCHHHHHHHHHhCCCeEEEECCCCCChHH-------------HhC---hHhhhccCceEEEEeCcCHHHHHHHH
Confidence 46999999999999999999998887544321211 111 122222 6899999999999999999
Q ss_pred HHHHHhCC
Q 042101 318 ELARRLGK 325 (380)
Q Consensus 318 ~la~~L~~ 325 (380)
++.+.|..
T Consensus 65 ~i~~~l~~ 72 (81)
T PF13662_consen 65 KIAKKLLP 72 (81)
T ss_dssp HHHHHHG-
T ss_pred HHHHHHHh
Confidence 99998853
No 14
>PF13362 Toprim_3: Toprim domain
Probab=99.27 E-value=2.1e-11 Score=99.03 Aligned_cols=91 Identities=29% Similarity=0.276 Sum_probs=64.4
Q ss_pred EEEEEechhHHHHH-HHhCCCcEEEcCCCCCCCccCCCCCCCcccchhhhhHHHHhhcCCCCeEEEEeCCChh--hHHHH
Q 042101 240 EVIIVEGEIDKLSV-EEAGFQNCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLDKVSRIILGTDADTP--GHALA 316 (380)
Q Consensus 240 ~iiIvEG~~DaLSl-~q~G~~~~Vs~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~~~L~~~~~Ivl~~DnD~A--G~~aa 316 (380)
.++|+||+.|+||+ ++.....++++. ++. .+. .+......++|+|+.|||.+ |++++
T Consensus 1 tl~i~EG~etals~~~~~~~~~~~a~~-~~~-nl~------------------~~~~~~~~~~vii~~D~D~~~~G~~~a 60 (96)
T PF13362_consen 1 TLIIAEGIETALSIAQQATGVPVVAAL-GAG-NLK------------------NVAIPEPGRRVIIAADNDKANEGQKAA 60 (96)
T ss_pred CEEEEEhHHHHHHHHHhcCCCeEEEEE-Chh-hhh------------------hhcCCCCCCeEEEEECCCCchhhHHHH
Confidence 47999999999999 555555566653 332 111 01222467899999999999 99999
Q ss_pred HHHHHHhCCC--ceEEEEcCCCCCCCCCCCHHHHHHhcChH
Q 042101 317 EELARRLGKD--RCWRVRWPKKDEFSYFKDANEVLKCLGPG 355 (380)
Q Consensus 317 ~~la~~L~~~--~v~iv~lP~~~~~~~~KD~ND~L~~~g~~ 355 (380)
.++++++... .+.++..+. .++||||+|+.+|.|
T Consensus 61 ~~~~~~~~~~g~~~~~~~p~~-----~g~D~ND~l~~~G~e 96 (96)
T PF13362_consen 61 EKAAERLEAAGIAVSIVEPGP-----EGKDWNDLLQARGKE 96 (96)
T ss_pred HHHHHHHHhCCCeEEEECCCC-----CCchHHHHHHhhCCC
Confidence 9999998632 345554412 358999999998853
No 15
>cd01029 TOPRIM_primases TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. The prototypical bacterial primase. Escherichia coli DnaG is a single subunit enzyme.
Probab=99.22 E-value=4.8e-11 Score=93.16 Aligned_cols=68 Identities=32% Similarity=0.414 Sum_probs=52.3
Q ss_pred CEEEEEechhHHHHHHHhCCCcEEEcCCCCCCCccCCCCCCCcccchhhhhHHHHhhcCCC-CeEEEEeCCChhhHHHHH
Q 042101 239 AEVIIVEGEIDKLSVEEAGFQNCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLDKV-SRIILGTDADTPGHALAE 317 (380)
Q Consensus 239 ~~iiIvEG~~DaLSl~q~G~~~~Vs~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~~~L~~~-~~Ivl~~DnD~AG~~aa~ 317 (380)
+.++||||++|+||++++|+.+++++ .|+... ..++..+.+. ++|+||+|||.+|++++.
T Consensus 1 ~~v~i~EG~~Dals~~~~~~~~~~~~-~g~~~~------------------~~~~~~l~~~~~~vii~~D~D~~G~~~~~ 61 (79)
T cd01029 1 DEVIIVEGYMDVLALHQAGIKNVVAA-LGTANT------------------EEQLRLLKRFARTVILAFDNDEAGKKAAA 61 (79)
T ss_pred CEEEEEeCHHHHHHHHHcCCCCEEEC-CCccCc------------------HHHHHHHHhcCCEEEEEECCCHHHHHHHH
Confidence 46899999999999999999777765 354311 0123445454 999999999999999999
Q ss_pred HHHHHhCC
Q 042101 318 ELARRLGK 325 (380)
Q Consensus 318 ~la~~L~~ 325 (380)
++.+.+..
T Consensus 62 ~~~~~~~~ 69 (79)
T cd01029 62 RALELLLA 69 (79)
T ss_pred HHHHHHHH
Confidence 98888753
No 16
>COG4643 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=99.15 E-value=6.4e-10 Score=107.13 Aligned_cols=142 Identities=23% Similarity=0.197 Sum_probs=84.7
Q ss_pred EEEEEecCCCEEEEEeeecCC--CccccccCCCCcccccc-ccCCCCEEEEEechhHHHHHHHhCCCcEEEcCCCCCCCc
Q 042101 196 AIAFPYWHNGVLVGCKYRSME--RKFRQEKGTEKWLYGLD-DINETAEVIIVEGEIDKLSVEEAGFQNCVSVPSGAPPKV 272 (380)
Q Consensus 196 ~I~fP~~~~G~vv~~~~R~~~--Kkf~~~~~~~~~Lfgl~-~i~~~~~iiIvEG~~DaLSl~q~G~~~~Vs~~~Ga~~~~ 272 (380)
.++.+.|.+|++++.+.-..| |+|..++-+....+-+. ......++||+||+-.+++++++-... |....-+. +
T Consensus 161 slip~~d~~Gel~~lq~I~~dG~Krf~~Ggr~kg~f~p~~g~~~~aa~lvi~EGyATal~i~~~~ga~-v~aAi~ag-N- 237 (366)
T COG4643 161 SLIPLRDADGELTGLQLIQPDGTKRFLKGGRVKGCFIPLGGLAGPAARLVIAEGYATALSISQATGAP-VAAAIDAG-N- 237 (366)
T ss_pred ceEEEEcCCCCEeeeEEEcCCccceeccCCcccceeeecCCCcccccceEEeechhHHHHHHHHhhhh-HHhhhhcc-c-
Confidence 444558999999999986665 78866543222222222 122356699999999999999984221 21111121 0
Q ss_pred cCCCCCCCcccchhhhhHHHHhhcCCCCeEEEEeCCCh-----hhHHHHHHHHHHhCCCceEEEEcCCCCCCCCCCCHHH
Q 042101 273 SNRELPPREKDTGYQYLWNCKEHLDKVSRIILGTDADT-----PGHALAEELARRLGKDRCWRVRWPKKDEFSYFKDANE 347 (380)
Q Consensus 273 ~~~~Lp~~~~~~~~~~l~~~~~~L~~~~~Ivl~~DnD~-----AG~~aa~~la~~L~~~~v~iv~lP~~~~~~~~KD~ND 347 (380)
|-.+. +-| +..+ +...|+||.|+|. +|+..|++.+..... . +.+|.- ..-||+|
T Consensus 238 ----ll~VA-----~al--~~~~--Pda~iIIaAD~D~~~~nnpG~t~A~eaA~Avng---~-~~lP~~----~~adwpD 296 (366)
T COG4643 238 ----LLAVA-----SAL--RKKF--PDAQIIIAADDDINTANNPGLTKAEEAAQAVNG---T-VALPPF----GPADWPD 296 (366)
T ss_pred ----HHHHH-----HHH--HHhC--CCcceEEEeccccccCCCcchHHHHHHHHhhCc---e-eecCCC----CCCcCcc
Confidence 10000 000 1111 3479999999998 699999998887654 2 334431 2258888
Q ss_pred HHHhcChHHHHHHH
Q 042101 348 VLKCLGPGALREVI 361 (380)
Q Consensus 348 ~L~~~g~~~l~~~i 361 (380)
+....+..+.+..+
T Consensus 297 ~~tq~n~la~r~~~ 310 (366)
T COG4643 297 GFTQFNDLATRCAF 310 (366)
T ss_pred hhhhcchhhhhhhh
Confidence 88876655444443
No 17
>PRK04031 DNA primase; Provisional
Probab=99.15 E-value=2.4e-10 Score=113.55 Aligned_cols=103 Identities=21% Similarity=0.344 Sum_probs=80.4
Q ss_pred cCCCCEEEEEechhHHHHHHHhCCCcEEEcCCCCCCCccCCCCCCCcccchhhhhHHHHhhcCCCCeEEEEeCCChhhHH
Q 042101 235 INETAEVIIVEGEIDKLSVEEAGFQNCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLDKVSRIILGTDADTPGHA 314 (380)
Q Consensus 235 i~~~~~iiIvEG~~DaLSl~q~G~~~~Vs~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~~~L~~~~~Ivl~~DnD~AG~~ 314 (380)
+...+.+|||||++|+++|+++|+.|+|++ .|+.. + .+...|.+.++|++|+|+|.||+.
T Consensus 166 i~k~~~iIVVEG~~DVi~L~~aGi~nvVAt-~GT~l--~-----------------~~i~~l~k~~~Vil~~DgD~aGe~ 225 (408)
T PRK04031 166 VDDSDAIIVVEGRADVLNLLRYGIKNAIAV-EGTNV--P-----------------ETIIELSKKKTVTAFLDGDRGGEL 225 (408)
T ss_pred cccCCeEEEEeCHHHHHHHHhcccceEEEe-CCccc--H-----------------HHHHHHhcCCCEEEEECCCHHHHH
Confidence 346789999999999999999999999986 46631 1 122333347899999999999999
Q ss_pred HHHHHHHHhCCCceEEEEcCCCCCCCCCCCHHHHHHhcChHHHHHHHHhccCCCc
Q 042101 315 LAEELARRLGKDRCWRVRWPKKDEFSYFKDANEVLKCLGPGALREVIENAELYQL 369 (380)
Q Consensus 315 aa~~la~~L~~~~v~iv~lP~~~~~~~~KD~ND~L~~~g~~~l~~~i~~A~~~~~ 369 (380)
+.+.+.+ ... ..++...|+| +|+.++ ..+++.++|.++.|+.-
T Consensus 226 I~k~l~~-v~~-~d~VaraP~G------~dVE~l----s~eeI~kAL~~~~p~~~ 268 (408)
T PRK04031 226 ILKELLQ-VAD-IDYVARAPPG------KEVEEL----TKKEIAKALRNKVPVEQ 268 (408)
T ss_pred HHHHHHh-hcc-eeEEecCCCC------CChhhC----CHHHHHHHHHhcCCHHH
Confidence 9888876 332 4578888864 899888 57899999999888643
No 18
>PF01807 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 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. This entry represents CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0003896 DNA primase activity, 0008270 zinc ion binding, 0006260 DNA replication; PDB: 1D0Q_B 2AU3_A.
Probab=99.13 E-value=1.8e-11 Score=100.00 Aligned_cols=54 Identities=26% Similarity=0.501 Sum_probs=35.8
Q ss_pred HHHHHHHhCCccccCCCCCceeeecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCCccccc
Q 042101 74 VKQKLKLVGINCDDSCIPGRYAHLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGRAFA 141 (380)
Q Consensus 74 ~~~~l~~~gi~~~~~~~~G~~~~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~G~v~~ 141 (380)
|.+++..+ +++++ .|+.|.++||||++ ++|||+|++++ +.||||+ ||.+||+++
T Consensus 15 i~~v~~~~-~~l~~---~G~~~~~~CPfH~d------~~pS~~i~~~k--~~~~Cf~--Cg~~Gd~i~ 68 (97)
T PF01807_consen 15 IVDVIERY-IKLKR---RGREYRCLCPFHDD------KTPSFSINPDK--NRFKCFG--CGKGGDVID 68 (97)
T ss_dssp HHHHHCCC-S--EE---ETTEEEE--SSS--------SS--EEEETTT--TEEEETT--T--EE-HHH
T ss_pred HHHHHHHh-ccccc---cCCeEEEECcCCCC------CCCceEEECCC--CeEEECC--CCCCCcHHh
Confidence 55566666 88877 89999999999986 67999998864 8999999 999999984
No 19
>PF08275 Toprim_N: DNA primase catalytic core, N-terminal domain; InterPro: IPR013264 This is the N-terminal, catalytic core domain of DNA primases. DNA primase (2.7.7 from EC) is a nucleotidyltransferase which synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork. It can also prime the leading strand and has been implicated in cell division []. ; PDB: 1EQN_E 1DD9_A 3B39_B 1DDE_A 2AU3_A.
Probab=98.99 E-value=5e-10 Score=96.07 Aligned_cols=70 Identities=27% Similarity=0.448 Sum_probs=50.1
Q ss_pred cHHHHHHHHhCCCCHHHHhhcceEEecC------------------------------C-------cEEEEEe-cCCCEE
Q 042101 166 GEKLIAYLGERMISEGTLQRNSVMQRLH------------------------------D-------QAIAFPY-WHNGVL 207 (380)
Q Consensus 166 ~~~~~~YL~~RGIs~eti~~f~~g~~~~------------------------------g-------~~I~fP~-~~~G~v 207 (380)
..++++||.+|||++++|+.|++||++. + +|||||+ |..|+|
T Consensus 11 ~~~a~~YL~~Rgl~~e~i~~F~lGyap~~~~~l~~~l~~~~~~~~~l~~~GL~~~~~~~~~~d~F~~RiifPI~d~~G~v 90 (128)
T PF08275_consen 11 GKEALEYLKKRGLSDETIKKFQLGYAPGNWDSLLEYLKKKGFSLEELLEAGLIRKNENGGYYDFFRGRIIFPIRDERGRV 90 (128)
T ss_dssp HHHHHHHHHHTT--HHHHHHTT-EEE-SCSCHHHHHHCCCCHHHHHHCCTTCEECCTTTEEEETTTTEEEEEEE-TTS-E
T ss_pred hHHHHHHHHHcCCCHHHHHHhCCCcccCcHHHHHHHHHhccccHHHHHHCCCcEEcCCCCcccccCCeEEEEEEcCCCCE
Confidence 3469999999999999999999999741 1 2999995 799999
Q ss_pred EEEeeecCC----Ccccccc-----CCCCcccccccc
Q 042101 208 VGCKYRSME----RKFRQEK-----GTEKWLYGLDDI 235 (380)
Q Consensus 208 v~~~~R~~~----Kkf~~~~-----~~~~~Lfgl~~i 235 (380)
|+|.+|.++ .||++.+ .++..|||++.+
T Consensus 91 vgF~gR~l~~~~~pKYlNs~et~if~K~~~Lyg~~~A 127 (128)
T PF08275_consen 91 VGFGGRRLDDENPPKYLNSPETPIFKKSRILYGLDQA 127 (128)
T ss_dssp EEEEEEESSSSSS-SEEE---BTTB-GGG-EETHHHH
T ss_pred EEEecccCCCCCCCceECCCCCccccCCceecCcccc
Confidence 999999994 4788754 367899998754
No 20
>smart00493 TOPRIM topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins.
Probab=98.87 E-value=8.6e-09 Score=79.58 Aligned_cols=71 Identities=35% Similarity=0.403 Sum_probs=48.7
Q ss_pred CEEEEEechhHHHHHHHhCCCc--EEEcCCCCCCCccCCCCCCCcccchhhhhHHHHhhcCCCCeEEEEeCCChhhHHHH
Q 042101 239 AEVIIVEGEIDKLSVEEAGFQN--CVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLDKVSRIILGTDADTPGHALA 316 (380)
Q Consensus 239 ~~iiIvEG~~DaLSl~q~G~~~--~Vs~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~~~L~~~~~Ivl~~DnD~AG~~aa 316 (380)
++++||||++|++++++++..+ ++++ .|...... .++.+. +.... .+|+||+|+|.+|++++
T Consensus 1 ~~l~ivEg~~da~~~~~~~~~~~~~~~~-~G~~~~~~-----------~~~~l~---~~~~~-~~Iii~~D~D~~G~~~~ 64 (76)
T smart00493 1 KVLIIVEGPADAIALEKAGGFGGNVVAL-GGHLLKKE-----------IIKLLK---RLAKK-KEVILATDPDREGEAIA 64 (76)
T ss_pred CEEEEEcCHHHHHHHHHhcCCCEEEEEE-eeeecHHH-----------HHHHHH---HHhcC-CEEEEEcCCChhHHHHH
Confidence 4699999999999999998853 3333 34321100 112221 11222 68999999999999999
Q ss_pred HHHHHHhCC
Q 042101 317 EELARRLGK 325 (380)
Q Consensus 317 ~~la~~L~~ 325 (380)
.++.+.+..
T Consensus 65 ~~i~~~l~~ 73 (76)
T smart00493 65 WKLAELLKP 73 (76)
T ss_pred HHHHHHhhh
Confidence 999988754
No 21
>cd01027 TOPRIM_RNase_M5_like TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in Ribonuclease M5: (RNase M5) and other small primase-like proteins from bacteria and archaea. RNase M5 catalyzes the maturation of 5S rRNA in low G+C Gram-positive bacteria. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=98.87 E-value=8.5e-09 Score=81.48 Aligned_cols=68 Identities=29% Similarity=0.428 Sum_probs=53.0
Q ss_pred CEEEEEechhHHHHHHHhCC-CcEEEcCCCCCCCccCCCCCCCcccchhhhhHHHHhhcCC-CCeEEEEeCCChhhHHHH
Q 042101 239 AEVIIVEGEIDKLSVEEAGF-QNCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLDK-VSRIILGTDADTPGHALA 316 (380)
Q Consensus 239 ~~iiIvEG~~DaLSl~q~G~-~~~Vs~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~~~L~~-~~~Ivl~~DnD~AG~~aa 316 (380)
+.+|||||..|+++++++|+ .+++++ .|+.... ++.+.+.+ .++|+|++|+|.+|++++
T Consensus 2 ~~vIiVEG~~D~~~l~~~g~~~~~i~t-~Gt~~~~------------------~~~~~l~~~~~~VIiltD~D~aG~~i~ 62 (81)
T cd01027 2 GEVIIVEGKNDTESLKKLGIEAEIIET-NGSIINK------------------ETIELIKKAYRGVIILTDPDRKGEKIR 62 (81)
T ss_pred CeEEEEEchHHHHHHHHhCCCccEEEE-CCCcCCH------------------HHHHHHHHhCCEEEEEECCCHHHHHHH
Confidence 47899999999999999999 777765 4553210 12333333 689999999999999999
Q ss_pred HHHHHHhCC
Q 042101 317 EELARRLGK 325 (380)
Q Consensus 317 ~~la~~L~~ 325 (380)
.++.+.|..
T Consensus 63 ~~~~~~l~~ 71 (81)
T cd01027 63 KKLSEYLSG 71 (81)
T ss_pred HHHHHHhcc
Confidence 999999953
No 22
>smart00400 ZnF_CHCC zinc finger.
Probab=98.84 E-value=1.9e-09 Score=78.89 Aligned_cols=37 Identities=27% Similarity=0.580 Sum_probs=31.9
Q ss_pred eeecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCCccccc
Q 042101 95 AHLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGRAFA 141 (380)
Q Consensus 95 ~~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~G~v~~ 141 (380)
|.++||||++ ++|||.|+++ ++.||||+ ||.+||+++
T Consensus 1 ~~~~cPfh~d------~~pSf~v~~~--kn~~~Cf~--cg~gGd~i~ 37 (55)
T smart00400 1 YKGLCPFHGE------KTPSFSVSPD--KQFFHCFG--CGAGGNVIS 37 (55)
T ss_pred CcccCcCCCC------CCCCEEEECC--CCEEEEeC--CCCCCCHHH
Confidence 4678999985 7899999875 48999999 999999984
No 23
>PF12965 DUF3854: Domain of unknown function (DUF3854); InterPro: IPR024385 This is a family of uncharacterised proteins, found by clustering human gut metagenomic sequences [].
Probab=98.66 E-value=2.9e-07 Score=79.21 Aligned_cols=112 Identities=18% Similarity=0.207 Sum_probs=72.6
Q ss_pred CCEEEEEechhHHHHHHHhCCCcEEEcCCCCCCCccCCCCCCCcccchhhhhHHHHhhc-CCCCeEEEEeCCC------h
Q 042101 238 TAEVIIVEGEIDKLSVEEAGFQNCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHL-DKVSRIILGTDAD------T 310 (380)
Q Consensus 238 ~~~iiIvEG~~DaLSl~q~G~~~~Vs~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~~~L-~~~~~Ivl~~DnD------~ 310 (380)
.-+|+||||..-|.++.+.|+. ++++|+-.+.. ....... .+.... .|-..+..+ .+.++|+||||.| .
T Consensus 10 ~~pi~ItEG~kKA~al~s~G~~-aIalpGV~~~~-~~~~~~~-~~~~~~-~L~p~L~~~~~~gr~v~iaFD~D~~~~Tn~ 85 (130)
T PF12965_consen 10 NIPIWITEGAKKAGALLSQGYP-AIALPGVNNGY-RWPKDEG-DKIGKR-RLIPELAKLAKPGREVYIAFDADTKPKTNK 85 (130)
T ss_pred CccEEEEechHHHHHHHcCCce-EEEeCceeccc-ccccccc-ccccch-hcchhHHHhccCCceEEEEecCCCccchhH
Confidence 5679999999999999999885 68887333211 0000000 000001 111123333 3568999999999 3
Q ss_pred hhHHHHHHHHHHhCC--CceEEEEcCCCCCCCCCCCHHHHHHhcChHHH
Q 042101 311 PGHALAEELARRLGK--DRCWRVRWPKKDEFSYFKDANEVLKCLGPGAL 357 (380)
Q Consensus 311 AG~~aa~~la~~L~~--~~v~iv~lP~~~~~~~~KD~ND~L~~~g~~~l 357 (380)
.=.+|..++++.|.. ..++++.||.+ .+|-.+|+|.++|++.|
T Consensus 86 ~V~~a~~~l~~~L~~~G~~v~~~~w~~~----~~KGiDD~l~~~G~~~f 130 (130)
T PF12965_consen 86 NVRRAIKRLGKLLKEAGCKVKIITWPPG----EGKGIDDLLAAKGPDAF 130 (130)
T ss_pred HHHHHHHHHHHHHHHCCCEEEEEEeCCC----CCCCHhHHHHhcCcccC
Confidence 345666777777742 36889999953 57999999999997754
No 24
>KOG2373 consensus Predicted mitochondrial DNA helicase twinkle [Replication, recombination and repair]
Probab=98.42 E-value=6.9e-07 Score=87.37 Aligned_cols=177 Identities=24% Similarity=0.256 Sum_probs=122.9
Q ss_pred HHhCCCCHHHHhhcceEEecC--Cc-EEEEE-ec---CCCE-EEEEee-ecC-----CCcccc-----ccCCCCcccccc
Q 042101 173 LGERMISEGTLQRNSVMQRLH--DQ-AIAFP-YW---HNGV-LVGCKY-RSM-----ERKFRQ-----EKGTEKWLYGLD 233 (380)
Q Consensus 173 L~~RGIs~eti~~f~~g~~~~--g~-~I~fP-~~---~~G~-vv~~~~-R~~-----~Kkf~~-----~~~~~~~Lfgl~ 233 (380)
|.--.|+.+++.+|.++|... |+ .+.|| |. ..+. ..|.++ |.. ...|-- ...+...+||++
T Consensus 37 ~glt~i~~~tl~rf~Vry~~p~~~qp~~~FP~~~~~tp~~~~~~GlK~l~e~~~~~~g~~ye~~~~~~~r~a~~~~fGL~ 116 (514)
T KOG2373|consen 37 LGLTNISFETLARFNVRYQTPTYGQPAILFPRYRGMTPRLRIPMGLKLLREVGDRMEGENYELPDETSVRQAFNGVFGLH 116 (514)
T ss_pred hccchhhhhhhccccccccCcccCCCccccccccccCccchhhhhhHHHHHhhhccccccCCCCcccchhhhhcceecee
Confidence 333568889999999998653 33 88999 32 2222 223331 111 112210 113456889998
Q ss_pred ccC-CCCEEEEEechhHHHHHHHhCCCcEEEcCCCCCCCccCCCCCCCcccchhhhhHHHHhhcCCCCeEEEEeCCChhh
Q 042101 234 DIN-ETAEVIIVEGEIDKLSVEEAGFQNCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLDKVSRIILGTDADTPG 312 (380)
Q Consensus 234 ~i~-~~~~iiIvEG~~DaLSl~q~G~~~~Vs~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~~~L~~~~~Ivl~~DnD~AG 312 (380)
.+. ....++|+--+.|+|+++++..-.++++|.|... ||. .++++|+++++||+|+--|...
T Consensus 117 l~~rrd~~vVltsne~D~lal~~~t~~~t~~LP~g~~~------lP~-----------~~LPyLE~F~~i~fWl~~d~~s 179 (514)
T KOG2373|consen 117 LATRRDRSVVLTSNERDALALYEATKALTFALPHGEIL------LPQ-----------LVLPYLEEFDKIYFWLPVDHVS 179 (514)
T ss_pred ecccccceEEEeecchhHHHHhhhcCceEEEccccccc------CcH-----------HHHHHHHhhheEEEEecccccc
Confidence 774 4678999999999999999965557889988632 343 2578999999999999999999
Q ss_pred HHHHHHHHHHhCCCceEEEEcCCCCCCCCCCCHHHHHHhcChHHHHHHHHhccCCCccchh
Q 042101 313 HALAEELARRLGKDRCWRVRWPKKDEFSYFKDANEVLKCLGPGALREVIENAELYQLHVSE 373 (380)
Q Consensus 313 ~~aa~~la~~L~~~~v~iv~lP~~~~~~~~KD~ND~L~~~g~~~l~~~i~~A~~~~~~~~~ 373 (380)
++||+.++..|...+|..|+..+ .-|.-+....+.-.+..++.+|.|+-..++.
T Consensus 180 w~aAk~fa~kLn~~rClLvrp~e-------~~p~p~~al~~rlnl~~il~~a~p~~hk~i~ 233 (514)
T KOG2373|consen 180 WSAAKDFASKLNTLRCLLVRPEE-------RPPEPVRALDHRLNLNSILNSAVPMRHKGIR 233 (514)
T ss_pred hHHHHHHHhhcCcceEEEECCCC-------CCcchhhhhcccccHHHHHhhhchhhhhhhh
Confidence 99999999999888898876432 2222333334567888899999988766554
No 25
>cd00188 TOPRIM Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=98.16 E-value=9.9e-06 Score=61.62 Aligned_cols=69 Identities=32% Similarity=0.410 Sum_probs=47.1
Q ss_pred CEEEEEechhHHHHHHHhCCC--cEEEcCCCCCCCccCCCCCCCcccchhhhhHHHHhhcCC-CCeEEEEeCCChhhHHH
Q 042101 239 AEVIIVEGEIDKLSVEEAGFQ--NCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLDK-VSRIILGTDADTPGHAL 315 (380)
Q Consensus 239 ~~iiIvEG~~DaLSl~q~G~~--~~Vs~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~~~L~~-~~~Ivl~~DnD~AG~~a 315 (380)
+.++||||+.|++++.+++.. .++++ .|.... .. ...+..+.+ ..+|++++|+|.+|+..
T Consensus 1 ~~viivEg~~d~~~l~~~~~~~~~~~~~-~G~~~~---------------~~-~~~~~~~~~~~~~v~i~~D~D~~g~~~ 63 (83)
T cd00188 1 KKLIIVEGPSDALALAQAGGYGGAVVAL-GGHALN---------------KT-RELLKRLLGEAKEVIIATDADREGEAI 63 (83)
T ss_pred CEEEEEecHHHHHHHHHHcCCCEEEEEE-ccEEcH---------------HH-HHHHHHHhcCCCEEEEEcCCChhHHHH
Confidence 368999999999999999884 34443 343210 00 011223323 58999999999999988
Q ss_pred HHHHHHHhC
Q 042101 316 AEELARRLG 324 (380)
Q Consensus 316 a~~la~~L~ 324 (380)
+..+.+.+.
T Consensus 64 ~~~~~~~~~ 72 (83)
T cd00188 64 ALRLLELLK 72 (83)
T ss_pred HHHHHHHHH
Confidence 877776654
No 26
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=97.75 E-value=2.2e-05 Score=53.46 Aligned_cols=35 Identities=37% Similarity=0.764 Sum_probs=20.6
Q ss_pred eeecCCCCCCCCCCCCccceEEEEEcC-CccEEEeCCccCCC-Ccc
Q 042101 95 AHLLCPKCKGGGRSLERSLSVHIIQDG-DFAMWRCFRVDCGW-AGR 138 (380)
Q Consensus 95 ~~~~CPfc~~~~~~~eks~s~~v~~d~-~~g~~~Cf~~~CG~-~G~ 138 (380)
++.+||.|++ +| .|.||+|+ .+|.|+|+. |+. .|+
T Consensus 2 ~h~pCP~CGG---~D----rFri~~d~~~~G~~~C~~--C~~~~GD 38 (40)
T PF08273_consen 2 KHGPCPICGG---KD----RFRIFDDKDGRGTWICRQ--CGGDAGD 38 (40)
T ss_dssp EEE--TTTT----TT----TEEEETT----S-EEETT--TTBE---
T ss_pred CCCCCCCCcC---cc----ccccCcCcccCCCEECCC--CCCcCCC
Confidence 5799999997 43 58889885 569999999 954 554
No 27
>PF01751 Toprim: Toprim domain; InterPro: IPR006171 This is a conserved region from DNA primase. This corresponds to the Toprim (topoisomerase-primase) domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR/M DNA repair proteins []. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase 2.7.7.6 from EC is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division []. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases []. Type II DNA topoisomerases catalyse the relaxation of DNA supercoiling by causing transient double strand breaks.; PDB: 2ZJT_A 3IG0_A 3M4I_A 3NUH_B 1GKU_B 1GL9_C 3PWT_A 1CY4_A 1ECL_A 1CY7_A ....
Probab=97.34 E-value=0.00083 Score=54.73 Aligned_cols=82 Identities=30% Similarity=0.336 Sum_probs=50.7
Q ss_pred EEEEEechhHHHHHHHhCC--CcEEEcCCCCCCCccCCCCCCCcc-cchhhhhHHHHhhcCCCCeEEEEeCCChhhHHHH
Q 042101 240 EVIIVEGEIDKLSVEEAGF--QNCVSVPSGAPPKVSNRELPPREK-DTGYQYLWNCKEHLDKVSRIILGTDADTPGHALA 316 (380)
Q Consensus 240 ~iiIvEG~~DaLSl~q~G~--~~~Vs~~~Ga~~~~~~~~Lp~~~~-~~~~~~l~~~~~~L~~~~~Ivl~~DnD~AG~~aa 316 (380)
+|+||||..|+.++.++.. ...|....|....+. -|..-. ..+...+......+.+..+||+|.|.|..|+..+
T Consensus 1 ~liIvE~ps~a~~i~~~l~~~~~~v~~~~Ghl~~~~---~~~~~~~~~~~~~i~~l~~~~~~~~~iiiatD~D~EGe~Ia 77 (100)
T PF01751_consen 1 ELIIVEKPSDAKAIAKALGGEEYIVIATSGHLLELA---KPEDYDPKDKKKQIKNLKKLLKKADEIIIATDPDREGELIA 77 (100)
T ss_dssp EEEEESSHHHHHHHHHHSSTTTEEEEEESSSSEEST---TSSHHHCHTTHHHHHHHHHHHHSCSEEEEEC-SSHHHHHHH
T ss_pred CEEEEeCHHHHHHHHHHcCCCCEEEEEeCCcccccc---cccccccccccccchhhHHHhhhccEeeecCCCChHHHHHH
Confidence 5899999999999999965 223333345422111 000000 0011112233344567899999999999999999
Q ss_pred HHHHHHhC
Q 042101 317 EELARRLG 324 (380)
Q Consensus 317 ~~la~~L~ 324 (380)
..+.+.++
T Consensus 78 ~~i~~~~~ 85 (100)
T PF01751_consen 78 WEIIELLG 85 (100)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHh
Confidence 99988874
No 28
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=97.29 E-value=0.00016 Score=48.33 Aligned_cols=33 Identities=36% Similarity=0.759 Sum_probs=24.8
Q ss_pred eeecCCCCCCCCCCCCccceEEEEEcC-CccEEEeCCccCCCCcc
Q 042101 95 AHLLCPKCKGGGRSLERSLSVHIIQDG-DFAMWRCFRVDCGWAGR 138 (380)
Q Consensus 95 ~~~~CPfc~~~~~~~eks~s~~v~~d~-~~g~~~Cf~~~CG~~G~ 138 (380)
++.+||.|++ +| .|. +.|+ .+|.|+|+. |++ |+
T Consensus 2 ~~~pCP~CGG---~D----rFr-~~d~~g~G~~~C~~--Cg~-gd 35 (37)
T smart00778 2 RHGPCPNCGG---SD----RFR-FDDKDGRGTWFCSV--CGA-GD 35 (37)
T ss_pred CccCCCCCCC---cc----ccc-cccCCCCcCEEeCC--CCC-CC
Confidence 3689999997 43 466 5554 569999999 998 44
No 29
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]
Probab=97.15 E-value=0.00081 Score=57.45 Aligned_cols=73 Identities=25% Similarity=0.296 Sum_probs=53.2
Q ss_pred CCEEEEEechhHHHHHHHhCCCcEEEcCCCCCCCccCCCCCCCcccchhhhhHHHHhhcCCCCeEEEEeCCChhhHHHHH
Q 042101 238 TAEVIIVEGEIDKLSVEEAGFQNCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLDKVSRIILGTDADTPGHALAE 317 (380)
Q Consensus 238 ~~~iiIvEG~~DaLSl~q~G~~~~Vs~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~~~L~~~~~Ivl~~DnD~AG~~aa~ 317 (380)
.+.+|||||--|..++.+++..+++-+.+.+.... +.+. .+......+.|+|.+|.|..|.+.++
T Consensus 9 ~~~vIVVEGK~D~~~l~~~~~~~~i~~~g~~i~~~--------------~~ie-~i~~~~~~k~VIILTD~D~~Ge~Irk 73 (127)
T COG1658 9 LKEVIVVEGKDDTASLKRLGDAGVIITNGSAINSL--------------ETIE-LIKKAQKYKGVIILTDPDRKGERIRK 73 (127)
T ss_pred cCceEEEeCCcHHHHHHHhcCCceEEEcCCccchH--------------HHHH-HHHHhhccCCEEEEeCCCcchHHHHH
Confidence 36899999999999999999887665532221100 1111 12222357899999999999999999
Q ss_pred HHHHHhCC
Q 042101 318 ELARRLGK 325 (380)
Q Consensus 318 ~la~~L~~ 325 (380)
++.+.|+.
T Consensus 74 ~l~~~l~~ 81 (127)
T COG1658 74 KLKEYLPG 81 (127)
T ss_pred HHHHHhcc
Confidence 99999975
No 30
>PRK04017 hypothetical protein; Provisional
Probab=97.11 E-value=0.0015 Score=56.25 Aligned_cols=71 Identities=28% Similarity=0.328 Sum_probs=51.6
Q ss_pred CCCEEEEEechhHHHHHHHhCCCcEEEcCCCCCCCccCCCCCCCcccchhhhhHHHHhhcCCCCeEEEEeCCChhhHHHH
Q 042101 237 ETAEVIIVEGEIDKLSVEEAGFQNCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLDKVSRIILGTDADTPGHALA 316 (380)
Q Consensus 237 ~~~~iiIvEG~~DaLSl~q~G~~~~Vs~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~~~L~~~~~Ivl~~DnD~AG~~aa 316 (380)
..+.+|||||--|.-++.++|+...+-..+|.+. +. .. + ......+.|+|.+|.|.+|.+.+
T Consensus 21 ~~g~vIVVEGk~D~~~L~~lGv~~~iI~t~g~~~--~~-------------~~-e--~ia~~~r~VIILTD~D~~GekIr 82 (132)
T PRK04017 21 EAGAPIIVEGKRDVESLRKLGVEGEIIKVSRTPL--AE-------------IA-E--LIASRGKEVIILTDFDRKGEELA 82 (132)
T ss_pred CCCCEEEEeCccHHHHHHHcCCCccEEEECCeec--ch-------------HH-H--HHHhcCCeEEEEECCCcchHHHH
Confidence 3557899999999999999999643333344421 10 00 1 11346789999999999999999
Q ss_pred HHHHHHhCC
Q 042101 317 EELARRLGK 325 (380)
Q Consensus 317 ~~la~~L~~ 325 (380)
+++.+.|..
T Consensus 83 ~~l~~~l~~ 91 (132)
T PRK04017 83 KKLSEYLQG 91 (132)
T ss_pred HHHHHHHHh
Confidence 999998853
No 31
>PF13154 DUF3991: Protein of unknown function (DUF3991)
Probab=96.86 E-value=0.0025 Score=49.65 Aligned_cols=49 Identities=29% Similarity=0.409 Sum_probs=38.3
Q ss_pred HHHHh-CCCCHHHHhhc---ceEEecCCcEEEEE-ecCCCEEEEEeeecC---CCcc
Q 042101 171 AYLGE-RMISEGTLQRN---SVMQRLHDQAIAFP-YWHNGVLVGCKYRSM---ERKF 219 (380)
Q Consensus 171 ~YL~~-RGIs~eti~~f---~~g~~~~g~~I~fP-~~~~G~vv~~~~R~~---~Kkf 219 (380)
+||.+ |||++++++.| ++-+...-..++|| ++.+|+++++..|.. ++.|
T Consensus 1 ~YL~~~RgI~~~~v~~~~~~g~i~~d~~~N~vF~~~d~~g~~~ga~~rGt~~~~~~~ 57 (77)
T PF13154_consen 1 AYLTEERGIDPEIVDAFINQGLIYQDKYGNVVFVGYDENGKPVGAELRGTYGKRKPF 57 (77)
T ss_pred CchhhhcCcCHHHHHHHHHCCCEEEcCCccEEEEEECCCCCEEEEEEECCCCCCCCc
Confidence 48887 99999999998 33444333488899 578999999999998 3455
No 32
>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=96.65 E-value=0.0065 Score=54.62 Aligned_cols=107 Identities=21% Similarity=0.266 Sum_probs=66.2
Q ss_pred CEEEEEechhHHHHHHHhCCCcEEEcCCCCCCCccCCCCCCCcccchhhhhHHHHhhcCCCCeEEEEeCCChhhHHHHHH
Q 042101 239 AEVIIVEGEIDKLSVEEAGFQNCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLDKVSRIILGTDADTPGHALAEE 318 (380)
Q Consensus 239 ~~iiIvEG~~DaLSl~q~G~~~~Vs~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~~~L~~~~~Ivl~~DnD~AG~~aa~~ 318 (380)
++||||||--|...+.++---.++.. +|+.. +. + ..+ .+..+...+.|+|+.|.|.+|.+-.+.
T Consensus 3 kevIVVEGK~D~~~lk~~~d~~~I~T-~Gs~i--~~------~---~i~----~i~~~~~~rgVIIfTDpD~~GekIRk~ 66 (174)
T TIGR00334 3 KEIIVVEGKDDQARIKQAFDVDVIET-NGSAL--KD------E---TIN----LIKKAQKKQGVIILTDPDFPGEKIRKK 66 (174)
T ss_pred CeEEEEecchHHHHHHHhcCceEEEE-CCCcc--CH------H---HHH----HHHHHhhcCCEEEEeCCCCchHHHHHH
Confidence 58999999999999988832234443 55531 11 0 111 123334567899999999999999999
Q ss_pred HHHHhCCCceEEEEcCCCCCCCCCCC-HHHHHHh-cChHHHHHHHHhccCC
Q 042101 319 LARRLGKDRCWRVRWPKKDEFSYFKD-ANEVLKC-LGPGALREVIENAELY 367 (380)
Q Consensus 319 la~~L~~~~v~iv~lP~~~~~~~~KD-~ND~L~~-~g~~~l~~~i~~A~~~ 367 (380)
+.+.++. +.-+.+|.. .... -.++=.. -.+++++++|+++...
T Consensus 67 i~~~vp~--~khafi~~~----~a~~~~~~iGVE~As~e~I~~AL~~~~~~ 111 (174)
T TIGR00334 67 IEQHLPG--YENCFIPKH----LAKPNKKKIGVEEASVEAIIAALENVHEE 111 (174)
T ss_pred HHHHCCC--CeEEeeeHH----hcCcCCCCcccCCCCHHHHHHHHHHhccc
Confidence 9999874 333334431 0110 0011111 2478888888887764
No 33
>PRK14719 bifunctional RNAse/5-amino-6-(5-phosphoribosylamino)uracil reductase; Provisional
Probab=95.75 E-value=0.012 Score=59.07 Aligned_cols=100 Identities=21% Similarity=0.237 Sum_probs=64.1
Q ss_pred CCEEEEEechhHHHHHHHhCCC-cEEEcCCCCCCCccCCCCCCCcccchhhhhHHHHhhc--CCCCeEEEEeCCChhhHH
Q 042101 238 TAEVIIVEGEIDKLSVEEAGFQ-NCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHL--DKVSRIILGTDADTPGHA 314 (380)
Q Consensus 238 ~~~iiIvEG~~DaLSl~q~G~~-~~Vs~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~~~L--~~~~~Ivl~~DnD~AG~~ 314 (380)
.+.+|||||.=|..||..+|+. +.+.++ +.+. ..|.+.+ .++++||+++|-|.+|+.
T Consensus 23 ~~~~ilveg~~d~~~l~~lgi~g~~i~~s-~~p~-------------------~~cad~ii~~gi~rVVi~~D~d~~G~~ 82 (360)
T PRK14719 23 KGIPILVEGPNDILSLKNLKINANFITVS-NTPV-------------------FQIADDLIAENISEVILLTDFDRAGRV 82 (360)
T ss_pred CCCEEEEEcchHHHHHHHcCCCCcEEEEe-CCch-------------------HHHHHHHHHcCCCEEEEEECCCCCCCc
Confidence 4579999999999999999996 445442 2221 0234443 367899999999999999
Q ss_pred HHHHHHHHhCCCceEEEEcCCCCCCCCCCCHHHHHHhcChHHHHHHHH
Q 042101 315 LAEELARRLGKDRCWRVRWPKKDEFSYFKDANEVLKCLGPGALREVIE 362 (380)
Q Consensus 315 aa~~la~~L~~~~v~iv~lP~~~~~~~~KD~ND~L~~~g~~~l~~~i~ 362 (380)
.+.++.+.|....+.+...-. +..+.+|.-... .-|.|...+.
T Consensus 83 ~~~~~~~~L~~aGi~V~~~l~----~e~~~l~~~~~~-~ie~~~~~~~ 125 (360)
T PRK14719 83 YAKNIMEEFQSRGIKVNNLIR----KEIIKYSRGDLK-DIESLYPYIS 125 (360)
T ss_pred cchHHHHHHHHCCCEEEeehH----HHHHHHhHHhhh-cchhhhhhhe
Confidence 998888888644444432221 122333332222 3456666666
No 34
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=95.34 E-value=0.085 Score=48.95 Aligned_cols=82 Identities=27% Similarity=0.355 Sum_probs=52.3
Q ss_pred CEEEEEechhHHHHHHHh------CCCcEEEcCCCCCCCccCCCCCCCcccchhhhhHHHHhhcCCCCeEEEEeCCChhh
Q 042101 239 AEVIIVEGEIDKLSVEEA------GFQNCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLDKVSRIILGTDADTPG 312 (380)
Q Consensus 239 ~~iiIvEG~~DaLSl~q~------G~~~~Vs~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~~~L~~~~~Ivl~~DnD~AG 312 (380)
+.=|||||..|+=++..+ |-..-+.+++- +|-.. +.-......+..-|+||.|.|..|
T Consensus 8 DVRIiVEGAsDvE~iSkalQr~aLG~eYnITisSI---------iPTT~-------~eIA~raaeGADlvlIATDaD~~G 71 (290)
T COG4026 8 DVRIIVEGASDVEVISKALQRLALGSEYNITISSI---------IPTTN-------VEIAKRAAEGADLVLIATDADRVG 71 (290)
T ss_pred eEEEEeeccchHHHHHHHHHHhhhcccceeEEEee---------ccCch-------HHHHHHhhccCCEEEEeecCcchh
Confidence 345899999999887766 22211222111 11100 001123344667899999999999
Q ss_pred HHHHHHHHHHhCC--CceEEEEcCCC
Q 042101 313 HALAEELARRLGK--DRCWRVRWPKK 336 (380)
Q Consensus 313 ~~aa~~la~~L~~--~~v~iv~lP~~ 336 (380)
++.|+++.+.|.. +.+..+.+|-|
T Consensus 72 ReLA~kf~eeLrg~VGhiERmK~PiG 97 (290)
T COG4026 72 RELAEKFFEELRGMVGHIERMKIPIG 97 (290)
T ss_pred HHHHHHHHHHHHHhhhhhheeccCCC
Confidence 9999999998842 35667888986
No 35
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=94.10 E-value=0.047 Score=39.42 Aligned_cols=34 Identities=24% Similarity=0.413 Sum_probs=22.1
Q ss_pred ecCCCCCCCCCCCCccceEEE--EEcC-CccEEEeCCccCCCCccc
Q 042101 97 LLCPKCKGGGRSLERSLSVHI--IQDG-DFAMWRCFRVDCGWAGRA 139 (380)
Q Consensus 97 ~~CPfc~~~~~~~eks~s~~v--~~d~-~~g~~~Cf~~~CG~~G~v 139 (380)
.+|||||+ ++ ..+. +.++ ..+.|+|-. ||+.+.+
T Consensus 2 kPCPfCGg---~~----~~~~~~~~~~~~~~~~~C~~--Cga~~~~ 38 (53)
T TIGR03655 2 KPCPFCGG---AD----VYLRRGFDPLDLSHYFECST--CGASGPV 38 (53)
T ss_pred CCCCCCCC---cc----eeeEeccCCCCCEEEEECCC--CCCCccc
Confidence 47999997 32 1122 2222 346778999 9998876
No 36
>cd01025 TOPRIM_recR TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in Escherichia coli RecR. RecR participates in the RecFOR pathway of homologous recombinational repair in prokaryotes. This pathway provides a single-stranded DNA molecule coated with RecA to allow invasion of a homologous molecule. The RecFOR system directs the loading of RecA onto gapped DNA coated with SSB protein. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). In RecR sequences this glutamate in the first turn of the TOPRIM domain is semiconserved, the DXD motif is not conserved.
Probab=93.69 E-value=0.62 Score=39.05 Aligned_cols=79 Identities=27% Similarity=0.374 Sum_probs=50.0
Q ss_pred EEEEEechhHHHHHHHhCC-CcEEEcCCCCCCCccCCCCCCCcccchhhhhHHHHhhcC--CCCeEEEEeCCChhhHHHH
Q 042101 240 EVIIVEGEIDKLSVEEAGF-QNCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLD--KVSRIILGTDADTPGHALA 316 (380)
Q Consensus 240 ~iiIvEG~~DaLSl~q~G~-~~~Vs~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~~~L~--~~~~Ivl~~DnD~AG~~aa 316 (380)
.|.|||-.-|++++.+.|. ....-|-+|.-+.+.- ..+. +..+. +-.+.++ ..++|+||+|.|.-|+.-|
T Consensus 2 ~lcVVE~~~Dv~~iE~~~~y~G~Y~VL~G~ispl~g--i~p~--~l~i~---~L~~ri~~~~i~EVIlA~~pt~EGe~Ta 74 (112)
T cd01025 2 KLCVVEEPRDVLAIEESGEYRGLYHVLGGLISPLDG--IGPD--DLNID---KLLERIAKGQVKEVILATNPTVEGEATA 74 (112)
T ss_pred EEEEECCHHHHHHHHhhCccceEEEEeCCCcCCCCC--CCcc--ccCHH---HHHHHHhcCCCcEEEEecCCCchHHHHH
Confidence 5889999999999999874 3322233443222111 0010 11111 2223333 3589999999999999999
Q ss_pred HHHHHHhCC
Q 042101 317 EELARRLGK 325 (380)
Q Consensus 317 ~~la~~L~~ 325 (380)
.-+.+.|..
T Consensus 75 ~yi~~~l~~ 83 (112)
T cd01025 75 LYIAKLLKD 83 (112)
T ss_pred HHHHHHHhH
Confidence 999888864
No 37
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=91.75 E-value=0.22 Score=37.28 Aligned_cols=35 Identities=20% Similarity=0.249 Sum_probs=22.5
Q ss_pred eecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCCcccc
Q 042101 96 HLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGRAF 140 (380)
Q Consensus 96 ~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~G~v~ 140 (380)
..+||||+. . ...+-....-..+.|.. ||+.+-..
T Consensus 6 lKPCPFCG~---~-----~~~v~~~~g~~~v~C~~--CgA~~~~~ 40 (64)
T PRK09710 6 VKPCPFCGC---P-----SVTVKAISGYYRAKCNG--CESRTGYG 40 (64)
T ss_pred ccCCCCCCC---c-----eeEEEecCceEEEEcCC--CCcCcccc
Confidence 468999996 2 23333222234578999 99987665
No 38
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=91.47 E-value=1.8 Score=39.78 Aligned_cols=90 Identities=23% Similarity=0.226 Sum_probs=57.2
Q ss_pred CCCEEEEEechhHHHHHHHhCCCc-EEEcCCCCCCCccCCCCCCCcccchhhhhHHHHhhcC--CCCeEEEEeCCChhhH
Q 042101 237 ETAEVIIVEGEIDKLSVEEAGFQN-CVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLD--KVSRIILGTDADTPGH 313 (380)
Q Consensus 237 ~~~~iiIvEG~~DaLSl~q~G~~~-~Vs~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~~~L~--~~~~Ivl~~DnD~AG~ 313 (380)
+...|.|||...|++++.+.|... ..-|-+|.-+.+... .+. +..+.-| .+.+. ..++|+||++.+--|+
T Consensus 77 d~~~iCVVE~~~Dv~aiE~~~~y~G~YhVL~G~iSPldgi--gp~--~l~i~~L---~~Ri~~~~v~EVIlAt~~tvEGe 149 (195)
T TIGR00615 77 DNSVICVVEDPKDVFALEKTKEFRGRYHVLGGHISPLDGI--GPE--DLTIAAL---LKRLQEESVKEVILATNPTVEGE 149 (195)
T ss_pred CCCEEEEECCHHHHHHHHhhCccceEEEEccCccCccCCC--Chh--hcCHHHH---HHHHhcCCCcEEEEeCCCCchHH
Confidence 456799999999999999997633 333334442222211 111 1122222 23343 4789999999999999
Q ss_pred HHHHHHHHHhCCCceEEEEc
Q 042101 314 ALAEELARRLGKDRCWRVRW 333 (380)
Q Consensus 314 ~aa~~la~~L~~~~v~iv~l 333 (380)
.-|.-+++.|....+++.++
T Consensus 150 ~Ta~yi~~~lk~~~ikvtRl 169 (195)
T TIGR00615 150 ATALYIARLLQPFGVKVTRI 169 (195)
T ss_pred HHHHHHHHHhhhcCCcEEee
Confidence 99999998886544444443
No 39
>PRK00076 recR recombination protein RecR; Reviewed
Probab=90.93 E-value=2.2 Score=39.24 Aligned_cols=93 Identities=27% Similarity=0.306 Sum_probs=57.8
Q ss_pred CCCEEEEEechhHHHHHHHhCCCc-EEEcCCCCCCCccCCCCCCCcccchhhhhHHHHhhc-CCCCeEEEEeCCChhhHH
Q 042101 237 ETAEVIIVEGEIDKLSVEEAGFQN-CVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHL-DKVSRIILGTDADTPGHA 314 (380)
Q Consensus 237 ~~~~iiIvEG~~DaLSl~q~G~~~-~Vs~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~~~L-~~~~~Ivl~~DnD~AG~~ 314 (380)
+...|.|||-..|++++.+.|... ..-|-+|.-+.+.-. -+. +..+.-| .+.+ ...++|+||++.+--|+.
T Consensus 77 d~~~icVVE~~~Dv~aiE~s~~y~G~YhVL~G~ispl~gi--~p~--~l~i~~L---~~ri~~~v~EVIlA~~pt~EGe~ 149 (196)
T PRK00076 77 DQSLICVVESPADVLAIERTGEYRGLYHVLGGLLSPLDGI--GPE--DLNIDEL---LERLDGEVKEVILATNPTVEGEA 149 (196)
T ss_pred CCCEEEEECCHHHHHHHHhhCcCceEEEEecCCcCCCCCC--Ccc--ccCHHHH---HHHHhCCCCEEEEeCCCCchHHH
Confidence 466799999999999999997633 222333432221111 011 1122222 2333 357999999999999999
Q ss_pred HHHHHHHHhCCCceEEEE----cCCC
Q 042101 315 LAEELARRLGKDRCWRVR----WPKK 336 (380)
Q Consensus 315 aa~~la~~L~~~~v~iv~----lP~~ 336 (380)
-|.-+.+.|....+++.+ +|-|
T Consensus 150 Ta~yi~~~lk~~~ikvtRiA~GiP~G 175 (196)
T PRK00076 150 TAHYIARLLKPLGVKVTRLAHGVPVG 175 (196)
T ss_pred HHHHHHHHHHHcCCCeeeeeeCCCCC
Confidence 999998888643343333 5654
No 40
>PRK13844 recombination protein RecR; Provisional
Probab=90.56 E-value=2.8 Score=38.68 Aligned_cols=89 Identities=20% Similarity=0.317 Sum_probs=58.1
Q ss_pred CCCEEEEEechhHHHHHHHhCCCc-EEEcCCCCCCCccCCCCCCCcccchhhhhHHHHhhcC--CCCeEEEEeCCChhhH
Q 042101 237 ETAEVIIVEGEIDKLSVEEAGFQN-CVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLD--KVSRIILGTDADTPGH 313 (380)
Q Consensus 237 ~~~~iiIvEG~~DaLSl~q~G~~~-~Vs~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~~~L~--~~~~Ivl~~DnD~AG~ 313 (380)
+...|.|||...|++++...|..+ ..-|-+|.-+.+.-. .+. +..+.-| .+.+. ..++|+||+..+--|+
T Consensus 81 d~~~iCVVE~~~Dv~aiE~t~~y~G~YhVL~G~ispl~gi--~p~--~l~i~~L---~~Ri~~~~v~EVIlAt~~t~EGe 153 (200)
T PRK13844 81 DDTKLCIIESMLDMIAIEEAGIYRGKYFVLNGRISPLDGI--GPS--ELKLDIL---QQIIADRKIDEVILAISPTVEGE 153 (200)
T ss_pred CCCEEEEECCHHHHHHHHhhCccceEEEEccCccCccCCC--Chh--hcCHHHH---HHHHhcCCCcEEEEeCCCCccHH
Confidence 456799999999999999997633 333334432222211 111 1122222 23332 4789999999999999
Q ss_pred HHHHHHHHHhCCCceEEEEc
Q 042101 314 ALAEELARRLGKDRCWRVRW 333 (380)
Q Consensus 314 ~aa~~la~~L~~~~v~iv~l 333 (380)
.-|.-+++.|.. .+++.++
T Consensus 154 ~Ta~yi~~~lk~-~vkvtRl 172 (200)
T PRK13844 154 TTAHFISQMIAK-DIKISRI 172 (200)
T ss_pred HHHHHHHHHhcC-CCcEEee
Confidence 999999999976 6666554
No 41
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=90.03 E-value=3.1 Score=38.16 Aligned_cols=91 Identities=23% Similarity=0.229 Sum_probs=56.4
Q ss_pred CCCCEEEEEechhHHHHHHHhCCC-cEEEcCCCCCCCccCCCCCCCcccchhhhhHHHHhhcCCCC--eEEEEeCCChhh
Q 042101 236 NETAEVIIVEGEIDKLSVEEAGFQ-NCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLDKVS--RIILGTDADTPG 312 (380)
Q Consensus 236 ~~~~~iiIvEG~~DaLSl~q~G~~-~~Vs~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~~~L~~~~--~Ivl~~DnD~AG 312 (380)
++...|.|||-.-|++++.++|.. ...-|-+|.-+.++-+ .+.+ . .|..-+..+.... +|+||.+.---|
T Consensus 77 Rd~~~icVVe~p~Dv~a~E~~~~f~G~YhVL~G~lspl~gi--gpe~--l---~i~~L~~Rl~~~~~~EvIlAtnpTvEG 149 (198)
T COG0353 77 RDKSQLCVVEEPKDVLALEKTGEFRGLYHVLGGLLSPLDGI--GPED--L---NIDELLQRLAEGSIKEVILATNPTVEG 149 (198)
T ss_pred cCCceEEEEcchHHHHHHHHhcccCeeEEEecCccCcccCC--Cccc--c---cHHHHHHHHhcCCCceEEEecCCCccc
Confidence 346689999999999999999743 2222334432222111 1111 1 1222233443443 999999999999
Q ss_pred HHHHHHHHHHhCCCceEEEEc
Q 042101 313 HALAEELARRLGKDRCWRVRW 333 (380)
Q Consensus 313 ~~aa~~la~~L~~~~v~iv~l 333 (380)
+.-|.-+++.|....+++.++
T Consensus 150 eaTA~YI~~~l~~~~ikvtRl 170 (198)
T COG0353 150 EATALYIARLLKPLGLKVTRL 170 (198)
T ss_pred hHHHHHHHHHHhhcCCeEEEE
Confidence 999999999987544544443
No 42
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=87.43 E-value=0.68 Score=33.99 Aligned_cols=29 Identities=38% Similarity=0.658 Sum_probs=17.4
Q ss_pred ecCCCCCCCCCCCCccceEEEEEcCCc-----cEEEeCCccCCC
Q 042101 97 LLCPKCKGGGRSLERSLSVHIIQDGDF-----AMWRCFRVDCGW 135 (380)
Q Consensus 97 ~~CPfc~~~~~~~eks~s~~v~~d~~~-----g~~~Cf~~~CG~ 135 (380)
.+|||||. +.+.+..+... ...+|.. ||+
T Consensus 4 kPCPFCG~--------~~~~~~~~~~~~~~~~~~V~C~~--Cga 37 (61)
T PF14354_consen 4 KPCPFCGS--------ADVLIRQDEGFDYGMYYYVECTD--CGA 37 (61)
T ss_pred cCCCCCCC--------cceEeecccCCCCCCEEEEEcCC--CCC
Confidence 57999964 12444332211 3456999 998
No 43
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=86.29 E-value=0.53 Score=37.82 Aligned_cols=27 Identities=30% Similarity=0.770 Sum_probs=19.2
Q ss_pred eecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCC
Q 042101 96 HLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGW 135 (380)
Q Consensus 96 ~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~ 135 (380)
...||||+. .++... ..|+|+|-. |+.
T Consensus 36 ~y~CpfCgk--------~~vkR~---a~GIW~C~~--C~~ 62 (90)
T PTZ00255 36 KYFCPFCGK--------HAVKRQ---AVGIWRCKG--CKK 62 (90)
T ss_pred CccCCCCCC--------Cceeee---eeEEEEcCC--CCC
Confidence 467999985 123332 359999999 986
No 44
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=85.74 E-value=0.84 Score=36.68 Aligned_cols=27 Identities=33% Similarity=0.934 Sum_probs=18.9
Q ss_pred eecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCC
Q 042101 96 HLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGW 135 (380)
Q Consensus 96 ~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~ 135 (380)
+..||||+. . ++... ..|+|+|-. ||.
T Consensus 35 ky~Cp~Cgk---~-----~vkR~---a~GIW~C~~--C~~ 61 (90)
T PF01780_consen 35 KYTCPFCGK---T-----SVKRV---ATGIWKCKK--CGK 61 (90)
T ss_dssp -BEESSSSS---S-----EEEEE---ETTEEEETT--TTE
T ss_pred CCcCCCCCC---c-----eeEEe---eeEEeecCC--CCC
Confidence 467999995 1 34332 359999999 985
No 45
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=85.53 E-value=0.76 Score=36.98 Aligned_cols=27 Identities=30% Similarity=0.800 Sum_probs=19.2
Q ss_pred eecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCC
Q 042101 96 HLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGW 135 (380)
Q Consensus 96 ~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~ 135 (380)
...||||+. +++... ..|+|+|-. ||.
T Consensus 35 ~y~CpfCgk--------~~vkR~---a~GIW~C~~--C~~ 61 (91)
T TIGR00280 35 KYVCPFCGK--------KTVKRG---STGIWTCRK--CGA 61 (91)
T ss_pred CccCCCCCC--------CceEEE---eeEEEEcCC--CCC
Confidence 467999985 123332 359999999 986
No 46
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=84.26 E-value=0.91 Score=36.14 Aligned_cols=28 Identities=29% Similarity=0.801 Sum_probs=19.4
Q ss_pred eecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCC
Q 042101 96 HLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWA 136 (380)
Q Consensus 96 ~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~ 136 (380)
.-.||+|+. + .+.. . .+|+|.|-. ||+.
T Consensus 35 ~~~Cp~C~~------~--~VkR--~-a~GIW~C~k--Cg~~ 62 (89)
T COG1997 35 KHVCPFCGR------T--TVKR--I-ATGIWKCRK--CGAK 62 (89)
T ss_pred CCcCCCCCC------c--ceee--e-ccCeEEcCC--CCCe
Confidence 457999985 1 1222 1 469999999 9974
No 47
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=84.20 E-value=1.1 Score=35.97 Aligned_cols=27 Identities=30% Similarity=0.874 Sum_probs=19.0
Q ss_pred eecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCC
Q 042101 96 HLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGW 135 (380)
Q Consensus 96 ~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~ 135 (380)
...||||+. +++... ..|+|+|-. |+.
T Consensus 36 ~y~CpfCgk--------~~vkR~---a~GIW~C~~--C~~ 62 (90)
T PRK03976 36 KHVCPVCGR--------PKVKRV---GTGIWECRK--CGA 62 (90)
T ss_pred CccCCCCCC--------CceEEE---EEEEEEcCC--CCC
Confidence 467999974 134332 359999999 986
No 48
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=81.31 E-value=1.3 Score=29.45 Aligned_cols=26 Identities=27% Similarity=0.625 Sum_probs=18.8
Q ss_pred eecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCC
Q 042101 96 HLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGW 135 (380)
Q Consensus 96 ~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~ 135 (380)
.-.||.|+. .++... .|.|+|-+ ||.
T Consensus 8 ~~~C~~C~~---------~~~~~~---dG~~yC~~--cG~ 33 (36)
T PF11781_consen 8 NEPCPVCGS---------RWFYSD---DGFYYCDR--CGH 33 (36)
T ss_pred CCcCCCCCC---------eEeEcc---CCEEEhhh--Cce
Confidence 456999996 244433 38999999 986
No 49
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=80.48 E-value=1.6 Score=34.43 Aligned_cols=33 Identities=30% Similarity=0.569 Sum_probs=17.2
Q ss_pred eecCCCCCCCCCCCCccceEEEEEcC--CccEEEeCCccCCCCc
Q 042101 96 HLLCPKCKGGGRSLERSLSVHIIQDG--DFAMWRCFRVDCGWAG 137 (380)
Q Consensus 96 ~~~CPfc~~~~~~~eks~s~~v~~d~--~~g~~~Cf~~~CG~~G 137 (380)
.-.||||+. ++| +.|..|+ ..+.-.|-. ||..-
T Consensus 22 ~F~CPfC~~-----~~s--V~v~idkk~~~~~~~C~~--Cg~~~ 56 (81)
T PF05129_consen 22 VFDCPFCNH-----EKS--VSVKIDKKEGIGILSCRV--CGESF 56 (81)
T ss_dssp ----TTT-------SS---EEEEEETTTTEEEEEESS--S--EE
T ss_pred eEcCCcCCC-----CCe--EEEEEEccCCEEEEEecC--CCCeE
Confidence 467999985 344 5555554 468999999 98743
No 50
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=77.71 E-value=3.3 Score=28.78 Aligned_cols=27 Identities=22% Similarity=0.604 Sum_probs=18.3
Q ss_pred ecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCC
Q 042101 97 LLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGW 135 (380)
Q Consensus 97 ~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~ 135 (380)
..||.|+. . .++.-+..+.|.|.. |+.
T Consensus 19 ~~CP~Cg~---~-------~~~~~~~~~~~~C~~--C~~ 45 (46)
T PF12760_consen 19 FVCPHCGS---T-------KHYRLKTRGRYRCKA--CRK 45 (46)
T ss_pred CCCCCCCC---e-------eeEEeCCCCeEECCC--CCC
Confidence 45999996 1 222222358999999 985
No 51
>cd01026 TOPRIM_OLD TOPRIM_OLD: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in bacterial and archaeal nucleases of the OLD (overcome lysogenization defect) family. The bacteriophage P2 OLD protein, which has DNase as well as RNase activity, consists of an N-terminal ABC-type ATPase domain and a C-terminal Toprim domain; the nuclease activity of OLD is stimulated by ATP, though the ATPase activity is not DNA-dependent. Functional details on OLD are scant and further experimentation is required to define the relationship between the ATPase and Toprim nuclease domains. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general acid in strand cleavage by nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=76.37 E-value=7.7 Score=31.07 Aligned_cols=59 Identities=20% Similarity=0.388 Sum_probs=35.6
Q ss_pred CCEEEEEechhHHHHHHHh----CC----CcEEEcCCCCCCCccCCCCCCCcccchhhhhHHHHhhcCCC-CeEEEEeCC
Q 042101 238 TAEVIIVEGEIDKLSVEEA----GF----QNCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLDKV-SRIILGTDA 308 (380)
Q Consensus 238 ~~~iiIvEG~~DaLSl~q~----G~----~~~Vs~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~~~L~~~-~~Ivl~~Dn 308 (380)
++.+++|||..|.+.+..+ |. .++.-++.|.. .. ..| ..+|... -++++.+|+
T Consensus 3 a~~vIlVEG~tE~~~l~~~~~~~~~~~~~~~i~ii~~gG~-~~-------------~~~----~~ll~~~~i~~~vi~D~ 64 (97)
T cd01026 3 ADKVILVEGDSEEILLPALAKKLGLDLDEAGISIIPVGGK-NF-------------KPF----IKLLNALGIPVAVLTDL 64 (97)
T ss_pred CCeEEEEecHHHHHHHHHHHHHhCCCHHHCCEEEEEeCCc-ch-------------HHH----HHHHHHcCCCEEEEEeC
Confidence 4689999999999998776 22 12122333332 21 011 2333332 478999999
Q ss_pred ChhhHH
Q 042101 309 DTPGHA 314 (380)
Q Consensus 309 D~AG~~ 314 (380)
|..+..
T Consensus 65 D~~~~~ 70 (97)
T cd01026 65 DAKRNE 70 (97)
T ss_pred CCCCCc
Confidence 987754
No 52
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 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. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=76.36 E-value=3.5 Score=28.17 Aligned_cols=26 Identities=31% Similarity=0.707 Sum_probs=18.4
Q ss_pred cCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCC
Q 042101 98 LCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGW 135 (380)
Q Consensus 98 ~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~ 135 (380)
.||.|+. +. +..|..+|.+.|-. ||.
T Consensus 2 ~Cp~Cg~---------~~-~~~D~~~g~~vC~~--CG~ 27 (43)
T PF08271_consen 2 KCPNCGS---------KE-IVFDPERGELVCPN--CGL 27 (43)
T ss_dssp SBTTTSS---------SE-EEEETTTTEEEETT--T-B
T ss_pred CCcCCcC---------Cc-eEEcCCCCeEECCC--CCC
Confidence 5999985 12 33455679999999 976
No 53
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=76.03 E-value=6.2 Score=34.10 Aligned_cols=51 Identities=16% Similarity=0.367 Sum_probs=30.8
Q ss_pred ccchhhHHHHHHHHHHhCCccccCCCCCceeeecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCCccc
Q 042101 65 TIDISKLTEVKQKLKLVGINCDDSCIPGRYAHLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGRA 139 (380)
Q Consensus 65 ~~~~~~~~~~~~~l~~~gi~~~~~~~~G~~~~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~G~v 139 (380)
+|+...+..+++.+.. .| -+||.|+. .+. .+. .++...+.+|.+ ||+...+
T Consensus 80 ~~~~~~i~~~L~~yI~-------------~y-VlC~~C~s-PdT-----~l~--k~~r~~~l~C~A--CGa~~~v 130 (133)
T TIGR00311 80 KFTHFLLNERIEDYVR-------------KY-VICRECNR-PDT-----RII--KEGRVSLLKCEA--CGAKAPL 130 (133)
T ss_pred ecCHHHHHHHHHHHHh-------------he-EECCCCCC-CCc-----EEE--EeCCeEEEeccc--CCCCCcc
Confidence 3666666665555543 12 58999986 221 232 232223559999 9998876
No 54
>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=73.58 E-value=4.8 Score=30.10 Aligned_cols=52 Identities=19% Similarity=0.453 Sum_probs=33.4
Q ss_pred HHHHHHHHhCCccccCCCCCceeeecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCCccc
Q 042101 73 EVKQKLKLVGINCDDSCIPGRYAHLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGRA 139 (380)
Q Consensus 73 ~~~~~l~~~gi~~~~~~~~G~~~~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~G~v 139 (380)
-|.......|+.+.. . .-.+.-..||.||. ..++ ......|+|.. ||...+.
T Consensus 7 ~L~yka~~~G~~v~~-v-~~~~TSq~C~~CG~---~~~~--------~~~~r~~~C~~--Cg~~~~r 58 (69)
T PF07282_consen 7 RLEYKAEEYGIQVVE-V-DEAYTSQTCPRCGH---RNKK--------RRSGRVFTCPN--CGFEMDR 58 (69)
T ss_pred HHHHHHHHhCCEEEE-E-CCCCCccCccCccc---cccc--------ccccceEEcCC--CCCEECc
Confidence 455667778998765 2 22234578999997 2212 11236899999 9987553
No 55
>cd01028 TOPRIM_TopoIA TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IA family of DNA topoisomerases (TopoIA). This subgroup contains proteins similar to the Type I DNA topoisomerases: E. coli topisomerases I and III, eukaryotic topoisomerase III and, ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA. These enzymes cleave one strand of the DNA duplex, covalently link to the 5' phosphoryl end of the DNA break and allow the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general b
Probab=72.98 E-value=14 Score=31.79 Aligned_cols=42 Identities=26% Similarity=0.325 Sum_probs=33.5
Q ss_pred hhcCCCCeEEEEeCCChhhHHHHHHHHHHhCC--CceEEEEcCC
Q 042101 294 EHLDKVSRIILGTDADTPGHALAEELARRLGK--DRCWRVRWPK 335 (380)
Q Consensus 294 ~~L~~~~~Ivl~~DnD~AG~~aa~~la~~L~~--~~v~iv~lP~ 335 (380)
.++.+..+||+|.|.|.-|+.-+..+.+.++. ..++.+.+..
T Consensus 86 ~l~~~~d~iiiAtD~DrEGE~I~~~i~~~~~~~~~~v~R~~fss 129 (142)
T cd01028 86 KLAKKADEIVLATDPDREGELIAWEILEVLKCDNKPVKRAWFSE 129 (142)
T ss_pred HHHhcCCEEEEcCCCCcchHHHHHHHHHHhCCCCCCeEEEEEcc
Confidence 44556789999999999999999999998874 3566666653
No 56
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=70.37 E-value=10 Score=33.02 Aligned_cols=51 Identities=18% Similarity=0.442 Sum_probs=32.0
Q ss_pred ccchhhHHHHHHHHHHhCCccccCCCCCceeeecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCCccc
Q 042101 65 TIDISKLTEVKQKLKLVGINCDDSCIPGRYAHLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGRA 139 (380)
Q Consensus 65 ~~~~~~~~~~~~~l~~~gi~~~~~~~~G~~~~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~G~v 139 (380)
+|+...++.+++.+.. .| -+||-|+. .+. .+ ..++..-+-+|.+ ||+...+
T Consensus 85 ~~~~~~i~~~L~~yI~-------------~y-VlC~~C~s-pdT-----~l--~k~~r~~~l~C~A--CGa~~~V 135 (138)
T PRK03988 85 KFSPRVINEKIDRYVK-------------EY-VICPECGS-PDT-----KL--IKEGRIWVLKCEA--CGAETPV 135 (138)
T ss_pred eeCHHHHHHHHHHHHH-------------hc-EECCCCCC-CCc-----EE--EEcCCeEEEEccc--CCCCCcC
Confidence 4666667766555544 12 58999986 211 22 2233345789999 9998766
No 57
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=70.11 E-value=65 Score=36.39 Aligned_cols=91 Identities=22% Similarity=0.284 Sum_probs=55.0
Q ss_pred CEEEEEechhHHHHHHHh-CCCcEEEcCCCCCCCccCCCCCCC------cc---------cchhhhhHHHHhhcCCCCeE
Q 042101 239 AEVIIVEGEIDKLSVEEA-GFQNCVSVPSGAPPKVSNRELPPR------EK---------DTGYQYLWNCKEHLDKVSRI 302 (380)
Q Consensus 239 ~~iiIvEG~~DaLSl~q~-G~~~~Vs~~~Ga~~~~~~~~Lp~~------~~---------~~~~~~l~~~~~~L~~~~~I 302 (380)
..|||||..-=|=++..+ |-...|..+.|--- +||.. +. ..+...+......+.....|
T Consensus 3 ~~LvIvEsP~kak~I~~~Lg~~~~V~as~GHl~-----dLp~~~~~~~~~~~f~p~y~~~~~k~~~~~~ik~~~k~ad~i 77 (860)
T PRK06319 3 KSLIIVESPAKIKTLQKLLGEGFIFASSLGHIV-----DLPAKEFGIDIENDFEPDYQILPDKEEVINKICKLAKKCDVV 77 (860)
T ss_pred CeEEEEeCHHHHHHHHHHhCCCCEEEecccCcc-----cCCcccCCcCCCCCCCcceEECccHHHHHHHHHHHHHhCCEE
Confidence 469999999888887776 43334433344211 11110 00 01112222233444567899
Q ss_pred EEEeCCChhhHHHHHHHHHHhCC-CceEEEEcC
Q 042101 303 ILGTDADTPGHALAEELARRLGK-DRCWRVRWP 334 (380)
Q Consensus 303 vl~~DnD~AG~~aa~~la~~L~~-~~v~iv~lP 334 (380)
|||.|.|.-|+.-+..+.+.|+. ..++.+.+-
T Consensus 78 ilAtDpDREGE~I~~~i~~~l~~~~~v~Rv~f~ 110 (860)
T PRK06319 78 YLSPDPDREGEAIAWHIANQLPKNTKIQRISFN 110 (860)
T ss_pred EECCCCCcchHHHHHHHHHHcCCCCCeeEEEEc
Confidence 99999999999999999999874 245555443
No 58
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=69.80 E-value=9.6 Score=35.21 Aligned_cols=52 Identities=13% Similarity=0.251 Sum_probs=32.3
Q ss_pred ccchhhHHHHHHHHHHhCCccccCCCCCceeeecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCCcccc
Q 042101 65 TIDISKLTEVKQKLKLVGINCDDSCIPGRYAHLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGRAF 140 (380)
Q Consensus 65 ~~~~~~~~~~~~~l~~~gi~~~~~~~~G~~~~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~G~v~ 140 (380)
+|+...+..+++.+.. .| -+||.|+. .+. .+. .+...-+.+|.+ ||+...+.
T Consensus 81 ~~~~~~i~~~l~~yi~-------------~y-V~C~~C~~-pdT-----~l~--k~~~~~~l~C~a--CGa~~~v~ 132 (201)
T PRK12336 81 KFTEEDIQAAIDAYVD-------------EY-VICSECGL-PDT-----RLV--KEDRVLMLRCDA--CGAHRPVK 132 (201)
T ss_pred eeCHHHHHHHHHHHHH-------------he-EECCCCCC-CCc-----EEE--EcCCeEEEEccc--CCCCcccc
Confidence 3566666666555544 13 58999986 211 232 233334669999 99998885
No 59
>PRK08780 DNA topoisomerase I; Provisional
Probab=68.69 E-value=59 Score=36.30 Aligned_cols=81 Identities=25% Similarity=0.318 Sum_probs=50.8
Q ss_pred CEEEEEechhHHHHHHHh-CCCcEEEcCCCCCCCccCCCCCCCcc--c-------------chhhhhHHHHhhcCCCCeE
Q 042101 239 AEVIIVEGEIDKLSVEEA-GFQNCVSVPSGAPPKVSNRELPPREK--D-------------TGYQYLWNCKEHLDKVSRI 302 (380)
Q Consensus 239 ~~iiIvEG~~DaLSl~q~-G~~~~Vs~~~Ga~~~~~~~~Lp~~~~--~-------------~~~~~l~~~~~~L~~~~~I 302 (380)
..|||||..-=|-.+..+ |-...|..+.|-- .+||..+. + .+...+......+.....|
T Consensus 3 ~~LiIvEsPskAk~I~~~Lg~~y~V~as~GHi-----~dL~~~~~~vd~~~~f~~~y~~~~~k~~~~~~lk~~~k~ad~v 77 (780)
T PRK08780 3 KHLVIVESPAKAKTINKYLGKDFTVLASYGHV-----RDLVPKEGAVDPENGFAMRYDLIDKNEKHVEAIAKAAKSADDL 77 (780)
T ss_pred CeEEEEeCHHHHHHHHHHcCCCCEEEeccCCc-----ccCCCcccCCChhhCCceEEEEcCchHHHHHHHHHHHHhCCEE
Confidence 469999999988888777 4333454444531 12221110 0 0111122222334567899
Q ss_pred EEEeCCChhhHHHHHHHHHHhC
Q 042101 303 ILGTDADTPGHALAEELARRLG 324 (380)
Q Consensus 303 vl~~DnD~AG~~aa~~la~~L~ 324 (380)
|||.|.|.-|+.-+..+.+.|+
T Consensus 78 ilAtD~DREGE~Ia~~i~~~l~ 99 (780)
T PRK08780 78 YLATDPDREGEAISWHLAEILK 99 (780)
T ss_pred EECCCCCcccHHHHHHHHHHhc
Confidence 9999999999999999999985
No 60
>cd03362 TOPRIM_TopoIA_TopoIII TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=66.98 E-value=19 Score=31.35 Aligned_cols=41 Identities=20% Similarity=0.309 Sum_probs=32.7
Q ss_pred hhcCCCCeEEEEeCCChhhHHHHHHHHHHhCC---CceEEEEcC
Q 042101 294 EHLDKVSRIILGTDADTPGHALAEELARRLGK---DRCWRVRWP 334 (380)
Q Consensus 294 ~~L~~~~~Ivl~~DnD~AG~~aa~~la~~L~~---~~v~iv~lP 334 (380)
.++++...||+|.|.|.-|+.-+..+.+.++. ..++.+.+.
T Consensus 94 ~l~~~ad~ii~atD~DrEGE~I~~~i~~~~~~~~~~~v~R~~fs 137 (151)
T cd03362 94 KLAKRADEIVIATDADREGELIGREILEYAKCVKRKPVKRAWFS 137 (151)
T ss_pred HHHhCCCeEEEccCCCccccHHHHHHHHHhCCCCCCcEEEEEEc
Confidence 44567789999999999999999999998875 345666554
No 61
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=66.21 E-value=5.9 Score=26.30 Aligned_cols=28 Identities=25% Similarity=0.694 Sum_probs=16.4
Q ss_pred ecCCCCCCCCCCCCccceEEEEE--cCCccEEEeCCccC
Q 042101 97 LLCPKCKGGGRSLERSLSVHIIQ--DGDFAMWRCFRVDC 133 (380)
Q Consensus 97 ~~CPfc~~~~~~~eks~s~~v~~--d~~~g~~~Cf~~~C 133 (380)
..||+|+. .+ ++.-+- ....+.|.|.. |
T Consensus 6 v~CP~C~s---~~----~v~k~G~~~~G~qryrC~~--C 35 (36)
T PF03811_consen 6 VHCPRCQS---TE----GVKKNGKSPSGHQRYRCKD--C 35 (36)
T ss_pred eeCCCCCC---CC----cceeCCCCCCCCEeEecCc--C
Confidence 46999986 11 122111 11357999998 8
No 62
>COG3593 Predicted ATP-dependent endonuclease of the OLD family [DNA replication, recombination, and repair]
Probab=64.88 E-value=11 Score=40.49 Aligned_cols=83 Identities=19% Similarity=0.285 Sum_probs=49.7
Q ss_pred CCCCccccccccC----CCCEEEEEechhHHHHHH----HhCCC---cEEE-cCCCCCCCccCCCCCCCcccchhhhhHH
Q 042101 224 GTEKWLYGLDDIN----ETAEVIIVEGEIDKLSVE----EAGFQ---NCVS-VPSGAPPKVSNRELPPREKDTGYQYLWN 291 (380)
Q Consensus 224 ~~~~~Lfgl~~i~----~~~~iiIvEG~~DaLSl~----q~G~~---~~Vs-~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~ 291 (380)
++...-|.++..+ =++.+|+|||+.++|-+. ++|+. .-+. ++. +++... .|
T Consensus 378 ~~r~i~r~l~~trs~~lFAr~vIlVEG~aE~ill~~la~~~~~~L~~~gi~VI~~-~gs~~k-------------~f--- 440 (581)
T COG3593 378 DKRRIKRHLDATRSSLLFARGVILVEGEAEVILLPELARQCGIDLEKEGIIVIEF-AGSGLK-------------PF--- 440 (581)
T ss_pred chhhhhhhcccccchhhhhceeEEEeccchhhhHHHHHHHhccccccCcEEEEee-cccCcH-------------HH---
Confidence 3344555555433 267899999999999877 33442 1122 232 222211 11
Q ss_pred HHhhcCCC-CeEEEEeCCChhhHHHHHHHHHHhC
Q 042101 292 CKEHLDKV-SRIILGTDADTPGHALAEELARRLG 324 (380)
Q Consensus 292 ~~~~L~~~-~~Ivl~~DnD~AG~~aa~~la~~L~ 324 (380)
..+.+.+ -++++..|+|++|.++..+.-..+.
T Consensus 441 -~kf~~~~gI~~~vitD~D~~g~~~~~~~~~l~~ 473 (581)
T COG3593 441 -IKFAEAMGIRVHVITDGDEAGKKYEATVRDLLK 473 (581)
T ss_pred -HHHhhccCceEEEEecCCcccchhhhhhhhcch
Confidence 2222333 4899999999999999887765554
No 63
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=64.10 E-value=7.3 Score=31.89 Aligned_cols=35 Identities=23% Similarity=0.505 Sum_probs=23.7
Q ss_pred eecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCCc
Q 042101 96 HLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAG 137 (380)
Q Consensus 96 ~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~G 137 (380)
.-.||||+. ++.-|-.|-.-...++-+|-. ||..-
T Consensus 22 ~FtCp~Cgh-----e~vs~ctvkk~~~~g~~~Cg~--CGls~ 56 (104)
T COG4888 22 TFTCPRCGH-----EKVSSCTVKKTVNIGTAVCGN--CGLSF 56 (104)
T ss_pred eEecCccCC-----eeeeEEEEEecCceeEEEccc--CcceE
Confidence 568999996 454444443322468999999 99853
No 64
>PRK07561 DNA topoisomerase I subunit omega; Validated
Probab=63.70 E-value=91 Score=35.20 Aligned_cols=41 Identities=29% Similarity=0.358 Sum_probs=32.1
Q ss_pred hhcCCCCeEEEEeCCChhhHHHHHHHHHHhC-C-CceEEEEcC
Q 042101 294 EHLDKVSRIILGTDADTPGHALAEELARRLG-K-DRCWRVRWP 334 (380)
Q Consensus 294 ~~L~~~~~Ivl~~DnD~AG~~aa~~la~~L~-~-~~v~iv~lP 334 (380)
..+....+||||.|.|.-|+.-+..+.+.|+ . ..++.+.+-
T Consensus 82 ~~~k~ad~iilAtD~DREGE~I~~~i~~~l~~~~~~v~Ri~f~ 124 (859)
T PRK07561 82 KAAKDADELYLATDPDREGEAIAWHLLEVLGGDDVPVKRVVFN 124 (859)
T ss_pred HHHhcCCEEEECCCCCccchHHHHHHHHHhCCCCCCeEEEEEc
Confidence 4445678999999999999999999999997 3 245555553
No 65
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=63.46 E-value=8 Score=31.71 Aligned_cols=32 Identities=25% Similarity=0.589 Sum_probs=23.2
Q ss_pred eecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCCc
Q 042101 96 HLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAG 137 (380)
Q Consensus 96 ~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~G 137 (380)
...||||+. . ++.|-.++..++-.|-. ||..-
T Consensus 21 ~f~CP~Cge------~--~v~v~~~k~~~h~~C~~--CG~y~ 52 (99)
T PRK14892 21 IFECPRCGK------V--SISVKIKKNIAIITCGN--CGLYT 52 (99)
T ss_pred EeECCCCCC------e--EeeeecCCCcceEECCC--CCCcc
Confidence 467999985 2 45554455678999999 99853
No 66
>cd03363 TOPRIM_TopoIA_TopoI TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=63.38 E-value=30 Score=29.20 Aligned_cols=41 Identities=34% Similarity=0.363 Sum_probs=31.6
Q ss_pred hhcCCCCeEEEEeCCChhhHHHHHHHHHHhCC-CceEEEEcC
Q 042101 294 EHLDKVSRIILGTDADTPGHALAEELARRLGK-DRCWRVRWP 334 (380)
Q Consensus 294 ~~L~~~~~Ivl~~DnD~AG~~aa~~la~~L~~-~~v~iv~lP 334 (380)
.++.+..+||+|.|.|.-|+.-+..+.+.++. .++..+.+.
T Consensus 68 ~l~~~~~eiiiAtD~drEGe~i~~~i~~~~~~~~~v~Rl~~s 109 (123)
T cd03363 68 KLAKKADEIYLATDPDREGEAIAWHLAEVLKLKKNVKRVVFN 109 (123)
T ss_pred HHHhcCCEEEEcCCCCcchHHHHHHHHHHcCCCCCeEEEEEc
Confidence 44456789999999999999999999998874 345555443
No 67
>COG0550 TopA Topoisomerase IA [DNA replication, recombination, and repair]
Probab=62.45 E-value=1e+02 Score=33.12 Aligned_cols=95 Identities=23% Similarity=0.297 Sum_probs=55.9
Q ss_pred EEEEEechhHHHHHHHh-CCCcEEEcCCCCCCCccC---------CCCC---CC--cccc-hhhhhHHHHhhcCCCCeEE
Q 042101 240 EVIIVEGEIDKLSVEEA-GFQNCVSVPSGAPPKVSN---------RELP---PR--EKDT-GYQYLWNCKEHLDKVSRII 303 (380)
Q Consensus 240 ~iiIvEG~~DaLSl~q~-G~~~~Vs~~~Ga~~~~~~---------~~Lp---~~--~~~~-~~~~l~~~~~~L~~~~~Iv 303 (380)
.+||||..-=|-++... |-..+|..+.|---.+.. ..++ +. -... +..++.+......+..+||
T Consensus 2 ~LiIvEsPskAk~Ia~~Lg~~~~V~as~GHi~dl~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~v~~lk~~ak~ad~v~ 81 (570)
T COG0550 2 RLIIVESPSKAKTIAKYLGKGYVVTASVGHLRDLPFPEEYKGWVDVDLPIFEPKYIIKPGKKKKVVKKLKKLAKKADEVY 81 (570)
T ss_pred eEEEEeCHHHHHHHHHhcCCCcEEEEcccccccCCChhhccCCcCCcccccccceeccchhhHHHHHHHHHHhccCCEEE
Confidence 68999999999998887 433344333442100000 0111 10 0011 2223333333445678999
Q ss_pred EEeCCChhhHHHHHHHHHHhCCC---ceEEEEcC
Q 042101 304 LGTDADTPGHALAEELARRLGKD---RCWRVRWP 334 (380)
Q Consensus 304 l~~DnD~AG~~aa~~la~~L~~~---~v~iv~lP 334 (380)
||.|.|.-|..-+..+.+.++.. .++.+.+-
T Consensus 82 lAtD~DREGE~I~~~i~~~l~~~~~~~~~R~~F~ 115 (570)
T COG0550 82 LATDPDREGEAIGWHILEVLKLKNPSKVKRVVFS 115 (570)
T ss_pred ECCCCCcchHHHHHHHHHHhCccCCCceeEEEEe
Confidence 99999999999999999999743 35555543
No 68
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=61.45 E-value=3.5 Score=32.55 Aligned_cols=27 Identities=22% Similarity=0.674 Sum_probs=18.1
Q ss_pred eecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCC
Q 042101 96 HLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGW 135 (380)
Q Consensus 96 ~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~ 135 (380)
+..|+|||. ++ +.. ..-|+|.|-+ |..
T Consensus 36 ky~CsfCGK------~~--vKR---~AvGiW~C~~--C~k 62 (92)
T KOG0402|consen 36 KYTCSFCGK------KT--VKR---KAVGIWKCGS--CKK 62 (92)
T ss_pred hhhhhhcch------hh--hhh---hceeEEecCC--ccc
Confidence 468999996 11 211 1248999999 975
No 69
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=60.12 E-value=15 Score=31.32 Aligned_cols=48 Identities=21% Similarity=0.585 Sum_probs=29.7
Q ss_pred ccchhhHHHHHHHHHHhCCccccCCCCCceeeecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCC
Q 042101 65 TIDISKLTEVKQKLKLVGINCDDSCIPGRYAHLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWA 136 (380)
Q Consensus 65 ~~~~~~~~~~~~~l~~~gi~~~~~~~~G~~~~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~ 136 (380)
+|+...|.++++.+.. .| .+||.|+. |--.+..++....-+|.+ ||+.
T Consensus 76 ~~~~~~i~~~L~~fI~-------------~y-VlC~~C~s--------pdT~l~k~~r~~~l~C~a--CGa~ 123 (125)
T PF01873_consen 76 RFSSKQIQDLLDKFIK-------------EY-VLCPECGS--------PDTELIKEGRLIFLKCKA--CGAS 123 (125)
T ss_dssp SSSCCHHHHHHHHHHC-------------HH-SSCTSTSS--------SSEEEEEETTCCEEEETT--TSCE
T ss_pred ecCHHHHHHHHHHHHH-------------HE-EEcCCCCC--------CccEEEEcCCEEEEEecc--cCCc
Confidence 4555666665555543 12 58999986 212333334467899999 9974
No 70
>PRK05582 DNA topoisomerase I; Validated
Probab=58.97 E-value=1.2e+02 Score=33.04 Aligned_cols=86 Identities=23% Similarity=0.254 Sum_probs=50.6
Q ss_pred EEEEEechhHHHHHHHh-CCCcEEEcCCCCCCCccC--CCCCCCc-c-------cchhhhhHHHHhhcCCCCeEEEEeCC
Q 042101 240 EVIIVEGEIDKLSVEEA-GFQNCVSVPSGAPPKVSN--RELPPRE-K-------DTGYQYLWNCKEHLDKVSRIILGTDA 308 (380)
Q Consensus 240 ~iiIvEG~~DaLSl~q~-G~~~~Vs~~~Ga~~~~~~--~~Lp~~~-~-------~~~~~~l~~~~~~L~~~~~Ivl~~Dn 308 (380)
.|||+|-.-=|-.+..+ |....|+.+.|--..+.. ...++.+ . ..+...+.....++.....||+|.|.
T Consensus 4 ~LiIaEkps~a~~ia~~lg~~~~V~~~~GHl~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ik~l~~~~d~ii~AtD~ 83 (650)
T PRK05582 4 KLVIVESPAKAKTIEKYLGKNYKVVASMGHIRDLPKSQLGIDIENNFEPKYITIRGKGPVIKELKKAAKKAKKVYLATDP 83 (650)
T ss_pred eEEEEeCHHHHHHHHHHcCCCCEEEeccCchhcCCCccCCCCcccCCceeeEECCcHHHHHHHHHHHHhcCCEEEECCCC
Confidence 58999998777777666 444455544453111100 0000111 0 00112233333455667899999999
Q ss_pred ChhhHHHHHHHHHHhCC
Q 042101 309 DTPGHALAEELARRLGK 325 (380)
Q Consensus 309 D~AG~~aa~~la~~L~~ 325 (380)
|.-|+.-+..+.+.++.
T Consensus 84 DrEGE~I~~~i~~~~~~ 100 (650)
T PRK05582 84 DREGEAIAWHLAHILGL 100 (650)
T ss_pred CcchHHHHHHHHHHhCC
Confidence 99999999999998873
No 71
>cd03361 TOPRIM_TopoIA_RevGyr TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to the ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=56.67 E-value=43 Score=29.93 Aligned_cols=41 Identities=24% Similarity=0.316 Sum_probs=32.0
Q ss_pred hhcCCCCeEEEEeCCChhhHHHHHHHHHHhCC--CceEEEEcC
Q 042101 294 EHLDKVSRIILGTDADTPGHALAEELARRLGK--DRCWRVRWP 334 (380)
Q Consensus 294 ~~L~~~~~Ivl~~DnD~AG~~aa~~la~~L~~--~~v~iv~lP 334 (380)
.++++..+||||.|.|.-|+.-+..+.+.++. .++..+.+.
T Consensus 114 ~l~~~~~~iiiatD~drEGe~I~~~i~~~~~~~~~~v~R~~fs 156 (170)
T cd03361 114 ELALEVDEVLIATDPDTEGEKIAWDVYLALRPYNKNIKRAEFH 156 (170)
T ss_pred HHHhhCCEEEEecCCCccHHHHHHHHHHHhccCCCCeEEEEEe
Confidence 44467889999999999999999999998863 345555543
No 72
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=54.85 E-value=28 Score=29.05 Aligned_cols=48 Identities=19% Similarity=0.447 Sum_probs=28.8
Q ss_pred ccchhhHHHHHHHHHHhCCccccCCCCCceeeecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCC
Q 042101 65 TIDISKLTEVKQKLKLVGINCDDSCIPGRYAHLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWA 136 (380)
Q Consensus 65 ~~~~~~~~~~~~~l~~~gi~~~~~~~~G~~~~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~ 136 (380)
+|+...+.++++.+.. .| -+||-|+. .+. .+.. ++..-.-+|.+ ||+.
T Consensus 63 ~~~~~~i~~~l~~yI~-------------~y-VlC~~C~s-pdT-----~l~k--~~r~~~l~C~a--CGa~ 110 (110)
T smart00653 63 RFTPKKLQDLLRRYIK-------------EY-VLCPECGS-PDT-----ELIK--ENRLFFLKCEA--CGAR 110 (110)
T ss_pred eeCHHHHHHHHHHHHH-------------hc-EECCCCCC-CCc-----EEEE--eCCeEEEEccc--cCCC
Confidence 4666667766555544 12 58999986 211 2222 23345778999 9973
No 73
>PF14097 SpoVAE: Stage V sporulation protein AE1
Probab=54.65 E-value=34 Score=30.84 Aligned_cols=54 Identities=26% Similarity=0.374 Sum_probs=37.2
Q ss_pred eEEEEeCCChhhHHHHHHHHHHhCCCceEEEEcCCCCCCCCCCCHHHHHHhcChHHHHHHHHhccCCC
Q 042101 301 RIILGTDADTPGHALAEELARRLGKDRCWRVRWPKKDEFSYFKDANEVLKCLGPGALREVIENAELYQ 368 (380)
Q Consensus 301 ~Ivl~~DnD~AG~~aa~~la~~L~~~~v~iv~lP~~~~~~~~KD~ND~L~~~g~~~l~~~i~~A~~~~ 368 (380)
+|+|..|+|..-+++.+.+++.+|. +| +....| .|.-+ ..+++.++|.+|..=|
T Consensus 1 kVIlvTDGD~~A~ravE~aa~~iGg-RC--IS~S~G-------NPT~l----sG~elV~lIk~a~~DP 54 (180)
T PF14097_consen 1 KVILVTDGDEYAKRAVEIAAKNIGG-RC--ISQSAG-------NPTPL----SGEELVELIKQAPHDP 54 (180)
T ss_pred CEEEEECChHHHHHHHHHHHHHhCc-EE--EeccCC-------CCCcC----CHHHHHHHHHhCCCCC
Confidence 5899999999999999999999986 44 223221 11111 3477777777776544
No 74
>PRK06599 DNA topoisomerase I; Validated
Probab=54.60 E-value=1.8e+02 Score=31.95 Aligned_cols=96 Identities=21% Similarity=0.239 Sum_probs=52.9
Q ss_pred CEEEEEechhHHHHHHHh-CCCcEEEcCCCCCCCcc--CCCCCCCc--------ccchhhhhHHHHhhcCCCCeEEEEeC
Q 042101 239 AEVIIVEGEIDKLSVEEA-GFQNCVSVPSGAPPKVS--NRELPPRE--------KDTGYQYLWNCKEHLDKVSRIILGTD 307 (380)
Q Consensus 239 ~~iiIvEG~~DaLSl~q~-G~~~~Vs~~~Ga~~~~~--~~~Lp~~~--------~~~~~~~l~~~~~~L~~~~~Ivl~~D 307 (380)
..|||+|-.-=|-.+..+ |....|+.+.|--..+. ...+.+.. ...+.+.+.....++....+||+|.|
T Consensus 3 ~~LiIaEKPs~ak~Ia~~lg~~~~V~~~~GHl~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ik~l~~~~d~iiiAtD 82 (675)
T PRK06599 3 KKLVIVESPAKAKTIKKYLGKDYKVLASFGHVRDLPKKKGGVDPDNDFAPKYEIIEGKEKVVDALKKAAKKADAVYLATD 82 (675)
T ss_pred CeEEEEeCHHHHHHHHHHcCCCCEEEecccchhcCCccccCCCcccCCCceEEECCcHHHHHHHHHHHHhhCCEEEECCC
Confidence 358888888777776665 33334443344211110 00000000 00011223333345566789999999
Q ss_pred CChhhHHHHHHHHHHhC---C--CceEEEEcC
Q 042101 308 ADTPGHALAEELARRLG---K--DRCWRVRWP 334 (380)
Q Consensus 308 nD~AG~~aa~~la~~L~---~--~~v~iv~lP 334 (380)
.|.-|+.-+..+.+.++ . ..++.+.+-
T Consensus 83 ~DrEGE~I~~~i~~~~~~~~~~~~~v~Rl~~s 114 (675)
T PRK06599 83 PDREGEAIAWHIAEVLKEAKLKDKNVKRVVFN 114 (675)
T ss_pred CCcchHHHHHHHHHHHHhhcCCCCCeeEEEEc
Confidence 99999999999988883 2 245555553
No 75
>KOG3214 consensus Uncharacterized Zn ribbon-containing protein [Function unknown]
Probab=53.14 E-value=8.3 Score=31.53 Aligned_cols=36 Identities=19% Similarity=0.344 Sum_probs=24.5
Q ss_pred eecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCCcc
Q 042101 96 HLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGR 138 (380)
Q Consensus 96 ~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~G~ 138 (380)
...||||.. +++-+..+-.....|.-+|-- |+.+..
T Consensus 23 ~FnClfcnH-----ek~v~~~~Dk~~~iG~~sC~i--C~esFq 58 (109)
T KOG3214|consen 23 QFNCLFCNH-----EKSVSCTLDKKHNIGKASCRI--CEESFQ 58 (109)
T ss_pred eeccCcccc-----ccceeeeehhhcCcceeeeee--hhhhhc
Confidence 466999986 565444443222568999999 987543
No 76
>PRK05776 DNA topoisomerase I; Provisional
Probab=50.32 E-value=54 Score=35.92 Aligned_cols=42 Identities=17% Similarity=0.282 Sum_probs=32.4
Q ss_pred HhhcCCCCeEEEEeCCChhhHHHHHHHHHHhCC-CceEEEEcC
Q 042101 293 KEHLDKVSRIILGTDADTPGHALAEELARRLGK-DRCWRVRWP 334 (380)
Q Consensus 293 ~~~L~~~~~Ivl~~DnD~AG~~aa~~la~~L~~-~~v~iv~lP 334 (380)
..++....+||+|.|.|.-|+.-+..+.+.++. ..++.+.+-
T Consensus 91 k~l~k~ad~iiiAtD~DREGE~I~~~i~~~~~~~~~v~R~~fs 133 (670)
T PRK05776 91 SSLSKYADEFINACDYDIEGSVIGYLIIKYLGDPKKAKRMKFS 133 (670)
T ss_pred HHHHhcCCEEEECCCCChhHHHHHHHHHHHhCCCCCeeEEEEc
Confidence 344566789999999999999999999999973 245555543
No 77
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=49.14 E-value=31 Score=38.08 Aligned_cols=62 Identities=16% Similarity=0.259 Sum_probs=37.6
Q ss_pred cchhhHHHHHHHHHHhCCccccCCCCCcee---------eecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCC
Q 042101 66 IDISKLTEVKQKLKLVGINCDDSCIPGRYA---------HLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWA 136 (380)
Q Consensus 66 ~~~~~~~~~~~~l~~~gi~~~~~~~~G~~~---------~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~ 136 (380)
|+..-++.|++.|..-.--+--.-+.|+.. ...||.|+. ++.... .++...||. ||..
T Consensus 405 lS~~Ll~~i~~~l~~geQ~llflnRRGys~~l~C~~Cg~v~~Cp~Cd~---------~lt~H~--~~~~L~CH~--Cg~~ 471 (730)
T COG1198 405 LSPALLEAIRKTLERGEQVLLFLNRRGYAPLLLCRDCGYIAECPNCDS---------PLTLHK--ATGQLRCHY--CGYQ 471 (730)
T ss_pred CCHHHHHHHHHHHhcCCeEEEEEccCCccceeecccCCCcccCCCCCc---------ceEEec--CCCeeEeCC--CCCC
Confidence 666778899998886322111001256543 355666654 344333 358999999 9998
Q ss_pred cccc
Q 042101 137 GRAF 140 (380)
Q Consensus 137 G~v~ 140 (380)
..+.
T Consensus 472 ~~~p 475 (730)
T COG1198 472 EPIP 475 (730)
T ss_pred CCCC
Confidence 6664
No 78
>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=47.43 E-value=32 Score=29.92 Aligned_cols=29 Identities=24% Similarity=0.495 Sum_probs=21.5
Q ss_pred HHHHHHHHHHhCCccccCCCCCceeeecCCCCCC
Q 042101 71 LTEVKQKLKLVGINCDDSCIPGRYAHLLCPKCKG 104 (380)
Q Consensus 71 ~~~~~~~l~~~gi~~~~~~~~G~~~~~~CPfc~~ 104 (380)
.++|.+++..+++.+.. . .....||.|++
T Consensus 71 ~~QL~ev~~~~~l~~~~---~--~~~sRC~~CN~ 99 (147)
T PF01927_consen 71 EEQLREVLERFGLKLRL---D--PIFSRCPKCNG 99 (147)
T ss_pred HHHHHHHHHHcCCcccc---C--CCCCccCCCCc
Confidence 45688888899988743 1 22579999997
No 79
>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=46.90 E-value=29 Score=22.74 Aligned_cols=30 Identities=23% Similarity=0.654 Sum_probs=19.3
Q ss_pred cCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCCccc
Q 042101 98 LCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGRA 139 (380)
Q Consensus 98 ~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~G~v 139 (380)
.||.|+. -+.+..++.+.. .|.. ||+...+
T Consensus 3 FCp~C~n---------lL~p~~~~~~~~-~C~~--C~Y~~~~ 32 (35)
T PF02150_consen 3 FCPECGN---------LLYPKEDKEKRV-ACRT--CGYEEPI 32 (35)
T ss_dssp BETTTTS---------BEEEEEETTTTE-EESS--SS-EEE-
T ss_pred eCCCCCc---------cceEcCCCccCc-CCCC--CCCccCC
Confidence 6999986 355555554444 8999 9985443
No 80
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=46.22 E-value=14 Score=26.35 Aligned_cols=27 Identities=26% Similarity=0.997 Sum_probs=18.8
Q ss_pred eecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCC
Q 042101 96 HLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWA 136 (380)
Q Consensus 96 ~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~ 136 (380)
...||-|+. .|.. +. ...|+|-. ||..
T Consensus 20 ~~fCP~Cg~---------~~m~-~~--~~r~~C~~--Cgyt 46 (50)
T PRK00432 20 NKFCPRCGS---------GFMA-EH--LDRWHCGK--CGYT 46 (50)
T ss_pred cCcCcCCCc---------chhe-cc--CCcEECCC--cCCE
Confidence 458999985 2333 22 37899999 9974
No 81
>PHA00626 hypothetical protein
Probab=44.68 E-value=19 Score=26.40 Aligned_cols=33 Identities=24% Similarity=0.526 Sum_probs=19.8
Q ss_pred cCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCCcc
Q 042101 98 LCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGR 138 (380)
Q Consensus 98 ~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~G~ 138 (380)
.||-||. ++-.-+-.+. +..+.|.|.. ||....
T Consensus 2 ~CP~CGS----~~Ivrcg~cr--~~snrYkCkd--CGY~ft 34 (59)
T PHA00626 2 SCPKCGS----GNIAKEKTMR--GWSDDYVCCD--CGYNDS 34 (59)
T ss_pred CCCCCCC----ceeeeeceec--ccCcceEcCC--CCCeec
Confidence 5999995 1111122221 2358999999 998543
No 82
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=43.00 E-value=12 Score=26.17 Aligned_cols=38 Identities=21% Similarity=0.387 Sum_probs=21.3
Q ss_pred cCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCCcc
Q 042101 98 LCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGR 138 (380)
Q Consensus 98 ~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~G~ 138 (380)
.||.||.+-.. .+ |..+.+.-..-.|.|..-.||+...
T Consensus 1 ~CP~Cg~~a~i-r~--S~~~s~~~~~~Y~qC~N~~Cg~tfv 38 (47)
T PF04606_consen 1 RCPHCGSKARI-RT--SRQLSPLTRELYCQCTNPECGHTFV 38 (47)
T ss_pred CcCCCCCeeEE-EE--chhhCcceEEEEEEECCCcCCCEEE
Confidence 49999972110 01 2222222234678898878998654
No 83
>TIGR01051 topA_bact DNA topoisomerase I, bacterial. This model describes DNA topoisomerase I among the members of bacteria. DNA topoisomerase I transiently cleaves one DNA strand and thus relaxes negatively supercoiled DNA during replication, transcription and recombination events.
Probab=42.16 E-value=78 Score=34.21 Aligned_cols=40 Identities=33% Similarity=0.396 Sum_probs=30.8
Q ss_pred hhcCCCCeEEEEeCCChhhHHHHHHHHHHhCC-Cce-EEEEc
Q 042101 294 EHLDKVSRIILGTDADTPGHALAEELARRLGK-DRC-WRVRW 333 (380)
Q Consensus 294 ~~L~~~~~Ivl~~DnD~AG~~aa~~la~~L~~-~~v-~iv~l 333 (380)
.++....+||+|.|.|.-|+.-+..+.+.++. ..+ +.+.+
T Consensus 65 ~l~~~~d~ii~AtD~DrEGE~I~~~i~~~~~~~~~~~~Rl~~ 106 (610)
T TIGR01051 65 TLAKKADEVYLATDPDREGEAIAWHLAEVLKPKDPVYKRIVF 106 (610)
T ss_pred HHHhcCCEEEECCCCCcchhHHHHHHHHHhCCCCCCceEEEE
Confidence 44566789999999999999999999988873 233 44544
No 84
>PRK07219 DNA topoisomerase I; Validated
Probab=41.38 E-value=85 Score=35.25 Aligned_cols=41 Identities=22% Similarity=0.338 Sum_probs=28.4
Q ss_pred hhcCCCCeEEEEeCCChhhHHHH---HHHHHHhCCCceEEEEcC
Q 042101 294 EHLDKVSRIILGTDADTPGHALA---EELARRLGKDRCWRVRWP 334 (380)
Q Consensus 294 ~~L~~~~~Ivl~~DnD~AG~~aa---~~la~~L~~~~v~iv~lP 334 (380)
.++....+||+|.|.|.-|+.-+ ..+.+.+....++.+.+-
T Consensus 93 ~l~~~ad~iiiAtD~DREGE~I~~ei~~i~~~~~~~~v~R~~fs 136 (822)
T PRK07219 93 KLAKDADEIIIATDYDREGELIGKEAYHILREVCQVPVKRARFS 136 (822)
T ss_pred HHHhcCCEEEEcCCCChhHHHHHHHHHHHHHhcCCCceeEEEEc
Confidence 44456789999999999999988 555555432345555553
No 85
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=40.59 E-value=21 Score=35.70 Aligned_cols=50 Identities=22% Similarity=0.468 Sum_probs=33.2
Q ss_pred hhhHHHHHHHHHHhCCccccCCCCCceeeecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCCcccc
Q 042101 68 ISKLTEVKQKLKLVGINCDDSCIPGRYAHLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGRAF 140 (380)
Q Consensus 68 ~~~~~~~~~~l~~~gi~~~~~~~~G~~~~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~G~v~ 140 (380)
+++|-.|.+-|.. + ..+||+|+.+ .--+.|.. +.+-...|-+ ||..+++.
T Consensus 82 ~~KLqdlLdgFIk------K--------FVlC~~C~NP------ETel~itk-~q~i~~~CkA--CG~r~~~d 131 (400)
T KOG2767|consen 82 ASKLQDLLDGFIK------K--------FVLCPSCENP------ETELIITK-KQTISLKCKA--CGFRSDMD 131 (400)
T ss_pred HHHHHHHHHHHHH------H--------heeCcCCCCC------ceeEEecc-cchhhhHHHH--cCCccccc
Confidence 3556666666654 1 3689999872 11355554 2345789999 99999875
No 86
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=40.54 E-value=22 Score=24.73 Aligned_cols=31 Identities=23% Similarity=0.632 Sum_probs=18.9
Q ss_pred cCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCCccc
Q 042101 98 LCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGRA 139 (380)
Q Consensus 98 ~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~G~v 139 (380)
.||.||. -++...+.....|.|-. ||..-.+
T Consensus 2 FCp~Cg~---------~l~~~~~~~~~~~vC~~--Cg~~~~~ 32 (52)
T smart00661 2 FCPKCGN---------MLIPKEGKEKRRFVCRK--CGYEEPI 32 (52)
T ss_pred CCCCCCC---------ccccccCCCCCEEECCc--CCCeEEC
Confidence 5999985 12222221224899999 9986544
No 87
>TIGR01056 topB DNA topoisomerase III, bacteria and conjugative plasmid. This model describes topoisomerase III from bacteria and its equivalents encoded on plasmids. The gene is designated topB if found in the bacterial chromosome, traE on conjugative plasmid RP4, etc. These enzymes are involved in the control of DNA topology. DNA topoisomerase III belongs to the type I topoisomerases, which are ATP-independent.
Probab=39.99 E-value=95 Score=33.94 Aligned_cols=41 Identities=29% Similarity=0.410 Sum_probs=31.8
Q ss_pred hhcC--CCCeEEEEeCCChhhHHHHHHHHHHhCC-C--ceEEEEcC
Q 042101 294 EHLD--KVSRIILGTDADTPGHALAEELARRLGK-D--RCWRVRWP 334 (380)
Q Consensus 294 ~~L~--~~~~Ivl~~DnD~AG~~aa~~la~~L~~-~--~v~iv~lP 334 (380)
.++. ....||+|.|.|.-|+.-+..+.+.++. . .++.+.+-
T Consensus 89 ~l~k~~~ad~Ii~AtDpDREGE~I~~~i~~~l~~~~~~~v~Ri~f~ 134 (660)
T TIGR01056 89 RILKENKVDEVVIATDPDREGELIAREILDYLKVTDKVTIKRLWIS 134 (660)
T ss_pred HHhhhcCCCEEEECCCCCcchHHHHHHHHHHhCCCCCCceEEEEec
Confidence 4445 6789999999999999999999999873 2 45555554
No 88
>PF01921 tRNA-synt_1f: tRNA synthetases class I (K); InterPro: IPR002904 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Lysyl-tRNA synthetase (6.1.1.6 from EC) is an alpha 2 homodimer that belong to both class I and class II. In eubacteria and eukaryota lysyl-tRNA synthetases belong to class II in the same family as aspartyl tRNA synthetase. The class Ic lysyl-tRNA synthetase family is present in archaea and in a number of bacterial groups that include the alphaproteobacteria and spirochaetes[]. A refined crystal structures shows that the active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding [].; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IRX_A.
Probab=39.71 E-value=24 Score=35.63 Aligned_cols=40 Identities=23% Similarity=0.424 Sum_probs=21.7
Q ss_pred eeecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCCcccc
Q 042101 95 AHLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGRAF 140 (380)
Q Consensus 95 ~~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~G~v~ 140 (380)
+.-.||.||. =+ .++-..+.++..+-.|.|-. ||..|.+.
T Consensus 173 f~piC~~cGr---i~-tt~v~~~d~~~~~v~Y~c~~--cG~~g~~~ 212 (360)
T PF01921_consen 173 FLPICEKCGR---ID-TTEVTEYDPEGGTVTYRCEE--CGHEGEVD 212 (360)
T ss_dssp EEEEETTTEE------EEEEEEE--SSSEEEEE--T--TS---EEE
T ss_pred eeeeccccCC---cc-cceeeEeecCCCEEEEEecC--CCCEEEEe
Confidence 5788999983 11 33344444456678999999 99988764
No 89
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=39.68 E-value=40 Score=21.64 Aligned_cols=32 Identities=28% Similarity=0.726 Sum_probs=13.8
Q ss_pred ecCCCCCCCCCCCCccceEEEEEcC-CccEEEeCCccCCC
Q 042101 97 LLCPKCKGGGRSLERSLSVHIIQDG-DFAMWRCFRVDCGW 135 (380)
Q Consensus 97 ~~CPfc~~~~~~~eks~s~~v~~d~-~~g~~~Cf~~~CG~ 135 (380)
-+||.||- |- -.-||..+ +--+|+|....|..
T Consensus 2 hlcpkcgv-gv------l~pvy~~kgeikvfrcsnpacdy 34 (36)
T PF09151_consen 2 HLCPKCGV-GV------LEPVYNQKGEIKVFRCSNPACDY 34 (36)
T ss_dssp -B-TTTSS-SB------EEEEE-TTS-EEEEEES-TT---
T ss_pred ccCCccCc-eE------EEEeecCCCcEEEEEcCCCcccc
Confidence 37999996 21 23466554 22366666544543
No 90
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=39.22 E-value=57 Score=34.47 Aligned_cols=38 Identities=21% Similarity=0.560 Sum_probs=23.2
Q ss_pred eeecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCCccc
Q 042101 95 AHLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGRA 139 (380)
Q Consensus 95 ~~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~G~v 139 (380)
+.-.||.||. ...++-..+..+..+-.|.| . ||..|-+
T Consensus 174 ~~pic~~cg~----~~~~~~~~~d~~~~~v~y~~-~--cG~~~~~ 211 (510)
T PRK00750 174 FLPICPKCGK----VLTTPVISYDAEAGTVTYDC-E--CGHEGEV 211 (510)
T ss_pred eeeeCCCCCc----cceEEEEEEeCCCCEEEEEc-C--CCCEEEE
Confidence 5789999985 33333333333333457777 5 8887655
No 91
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=39.05 E-value=44 Score=24.82 Aligned_cols=30 Identities=33% Similarity=0.792 Sum_probs=20.0
Q ss_pred eecCCCCCCCCCCCCccceEEEEEcC----CccEEEeCCccCCCCc
Q 042101 96 HLLCPKCKGGGRSLERSLSVHIIQDG----DFAMWRCFRVDCGWAG 137 (380)
Q Consensus 96 ~~~CPfc~~~~~~~eks~s~~v~~d~----~~g~~~Cf~~~CG~~G 137 (380)
+-.||-||+ ..|+-.. ....|.|-. ||+.|
T Consensus 27 ~F~CPnCGe----------~~I~Rc~~CRk~g~~Y~Cp~--CGF~G 60 (61)
T COG2888 27 KFPCPNCGE----------VEIYRCAKCRKLGNPYRCPK--CGFEG 60 (61)
T ss_pred EeeCCCCCc----------eeeehhhhHHHcCCceECCC--cCccC
Confidence 678999996 2333221 234788888 98876
No 92
>PRK07726 DNA topoisomerase III; Provisional
Probab=38.56 E-value=80 Score=34.47 Aligned_cols=41 Identities=27% Similarity=0.389 Sum_probs=32.3
Q ss_pred hhcCCCCeEEEEeCCChhhHHHHHHHHHHhCC-CceEEEEcC
Q 042101 294 EHLDKVSRIILGTDADTPGHALAEELARRLGK-DRCWRVRWP 334 (380)
Q Consensus 294 ~~L~~~~~Ivl~~DnD~AG~~aa~~la~~L~~-~~v~iv~lP 334 (380)
.++.....||+|.|.|.-|+.-+..+.+.++. ..++.+.+-
T Consensus 88 ~l~~~~d~Ii~AtD~DREGE~I~~~i~~~~~~~~~v~Rl~~s 129 (658)
T PRK07726 88 KLLKQATEIVIATDADREGELIAREILDYCGVRKPIKRLWIS 129 (658)
T ss_pred HHHhhCCeEEEcCCCCccccHHHHHHHHHhCCCCCeEEEEEc
Confidence 44567789999999999999999999999874 345555553
No 93
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=38.32 E-value=13 Score=27.05 Aligned_cols=13 Identities=38% Similarity=0.833 Sum_probs=9.2
Q ss_pred CCceeeecCCCCCC
Q 042101 91 PGRYAHLLCPKCKG 104 (380)
Q Consensus 91 ~G~~~~~~CPfc~~ 104 (380)
.|..|.+ ||||+.
T Consensus 35 ~~~rYng-CPfC~~ 47 (55)
T PF14447_consen 35 PGERYNG-CPFCGT 47 (55)
T ss_pred ChhhccC-CCCCCC
Confidence 4555654 999986
No 94
>PF03470 zf-XS: XS zinc finger domain; InterPro: IPR005381 This domain is a putative nucleic acid binding zinc finger and is found at the N terminus of proteins that also contain an adjacent XS domain IPR005380 from INTERPRO and in some proteins a C-terminal XH domain IPR005379 from INTERPRO.
Probab=38.21 E-value=19 Score=24.92 Aligned_cols=6 Identities=67% Similarity=1.846 Sum_probs=5.5
Q ss_pred CCCCCC
Q 042101 99 CPKCKG 104 (380)
Q Consensus 99 CPfc~~ 104 (380)
||||.+
T Consensus 1 CP~C~~ 6 (43)
T PF03470_consen 1 CPFCPG 6 (43)
T ss_pred CCCCCC
Confidence 999987
No 95
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 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. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=37.34 E-value=27 Score=23.35 Aligned_cols=30 Identities=33% Similarity=0.712 Sum_probs=15.8
Q ss_pred cCCCCCCCCCCCCccceEEEEE----c-CCccEEEeCCccCCC
Q 042101 98 LCPKCKGGGRSLERSLSVHIIQ----D-GDFAMWRCFRVDCGW 135 (380)
Q Consensus 98 ~CPfc~~~~~~~eks~s~~v~~----d-~~~g~~~Cf~~~CG~ 135 (380)
.||.|+. ++. -|+-.. | ..+-+|.|.. ||.
T Consensus 2 ~Cp~Cg~-----~~a-~~~~~Q~rsaDE~~T~fy~C~~--C~~ 36 (39)
T PF01096_consen 2 KCPKCGH-----NEA-VFFQIQTRSADEPMTLFYVCCN--CGH 36 (39)
T ss_dssp --SSS-S-----SEE-EEEEESSSSSSSSSEEEEEESS--STE
T ss_pred CCcCCCC-----CeE-EEEEeeccCCCCCCeEEEEeCC--CCC
Confidence 5999986 122 222111 1 2456999999 986
No 96
>TIGR01054 rgy reverse gyrase. Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.
Probab=37.31 E-value=1e+02 Score=36.17 Aligned_cols=41 Identities=29% Similarity=0.424 Sum_probs=31.8
Q ss_pred hhcCCCCeEEEEeCCChhhHHHHHHHHHHhCC--CceEEEEcC
Q 042101 294 EHLDKVSRIILGTDADTPGHALAEELARRLGK--DRCWRVRWP 334 (380)
Q Consensus 294 ~~L~~~~~Ivl~~DnD~AG~~aa~~la~~L~~--~~v~iv~lP 334 (380)
..+....+||+|.|.|.-|+.-+..+.+.+.. .+++.+.+-
T Consensus 715 ~l~~~~d~ViiATDpDrEGE~Ia~~i~~~l~~~~~~i~R~~f~ 757 (1171)
T TIGR01054 715 ELAHEVDEVFIGTDPDTEGEKIGWDLALLLSPYNPNVKRAEFH 757 (1171)
T ss_pred HHHhcCCEEEECCCCCccHHHHHHHHHHHhcccCCCeEEEEEc
Confidence 34456789999999999999999999998753 356666554
No 97
>PRK14973 DNA topoisomerase I; Provisional
Probab=37.31 E-value=95 Score=35.43 Aligned_cols=41 Identities=24% Similarity=0.302 Sum_probs=30.8
Q ss_pred hhcCCCCeEEEEeCCChhhHHHHHHHHHHhCC----CceEEEEcC
Q 042101 294 EHLDKVSRIILGTDADTPGHALAEELARRLGK----DRCWRVRWP 334 (380)
Q Consensus 294 ~~L~~~~~Ivl~~DnD~AG~~aa~~la~~L~~----~~v~iv~lP 334 (380)
.++.+...||+|.|.|.-|+.-+..+.+.++. ..++.+.+.
T Consensus 92 ~l~k~ad~IiiAtD~DREGE~I~~~i~e~~~~~~~~~~v~R~~fs 136 (936)
T PRK14973 92 KLAKKADRVTIATDFDTEGELIGKEAYELVRAVNPKVPIDRARFS 136 (936)
T ss_pred HHHHhCCEEEECCCCCcchHHHHHHHHHHhhhccCCCceEEEEEc
Confidence 44456789999999999999999888888853 245555543
No 98
>PRK09401 reverse gyrase; Reviewed
Probab=36.46 E-value=1.1e+02 Score=35.76 Aligned_cols=41 Identities=27% Similarity=0.357 Sum_probs=31.9
Q ss_pred hhcCCCCeEEEEeCCChhhHHHHHHHHHHhCC--CceEEEEcC
Q 042101 294 EHLDKVSRIILGTDADTPGHALAEELARRLGK--DRCWRVRWP 334 (380)
Q Consensus 294 ~~L~~~~~Ivl~~DnD~AG~~aa~~la~~L~~--~~v~iv~lP 334 (380)
.++....+||+|.|.|.-|+.-+..+.+.++. .+++.+.+-
T Consensus 715 ~l~~~~d~IiiAtDpDrEGE~Ia~~i~~~l~~~~~~i~R~~f~ 757 (1176)
T PRK09401 715 ELALEVDEVLIATDPDTEGEKIAWDLYLLLSPYNSNIKRIEFH 757 (1176)
T ss_pred HHHhcCCEEEEccCcChhHHHHHHHHHHHhcccCCCEEEEEee
Confidence 33456789999999999999999999999873 356555553
No 99
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=36.05 E-value=21 Score=36.59 Aligned_cols=53 Identities=23% Similarity=0.525 Sum_probs=27.0
Q ss_pred HHHHHHHHHHhCCccccCCCCCceeeecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCC
Q 042101 71 LTEVKQKLKLVGINCDDSCIPGRYAHLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGW 135 (380)
Q Consensus 71 ~~~~~~~l~~~gi~~~~~~~~G~~~~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~ 135 (380)
|..+++.|..- ++. .-..-...||+|.. .-+.=--.+ +. +..++.|||.. |+.
T Consensus 109 lh~m~krled~---~~d---~t~~~~Y~Cp~C~k-kyt~Lea~~--L~-~~~~~~F~C~~--C~g 161 (436)
T KOG2593|consen 109 LHQMRKRLEDR---LRD---DTNVAGYVCPNCQK-KYTSLEALQ--LL-DNETGEFHCEN--CGG 161 (436)
T ss_pred HHHHHHHHHHH---hhh---ccccccccCCcccc-chhhhHHHH--hh-cccCceEEEec--CCC
Confidence 55666666663 221 11112457999985 100000011 11 22468999999 975
No 100
>PF13707 RloB: RloB-like protein
Probab=35.69 E-value=1.9e+02 Score=25.38 Aligned_cols=12 Identities=17% Similarity=0.116 Sum_probs=11.0
Q ss_pred CCCeEEEEeCCC
Q 042101 298 KVSRIILGTDAD 309 (380)
Q Consensus 298 ~~~~Ivl~~DnD 309 (380)
.+..|++++|.|
T Consensus 59 ~~d~v~~V~D~D 70 (183)
T PF13707_consen 59 EYDEVWCVFDRD 70 (183)
T ss_pred CCCEEEEEEeCC
Confidence 578999999999
No 101
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=35.08 E-value=33 Score=22.48 Aligned_cols=29 Identities=34% Similarity=0.827 Sum_probs=14.7
Q ss_pred cCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCC
Q 042101 98 LCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGW 135 (380)
Q Consensus 98 ~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~ 135 (380)
.||.||. ...+.|-...+.-.+.|-+ ||+
T Consensus 2 fC~~CG~-------~l~~~ip~gd~r~R~vC~~--Cg~ 30 (34)
T PF14803_consen 2 FCPQCGG-------PLERRIPEGDDRERLVCPA--CGF 30 (34)
T ss_dssp B-TTT---------B-EEE--TT-SS-EEEETT--TTE
T ss_pred ccccccC-------hhhhhcCCCCCccceECCC--CCC
Confidence 5999996 1344443222467999999 986
No 102
>cd00674 LysRS_core_class_I catalytic core domain of class I lysyl tRNA synthetase. Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity.
Probab=33.57 E-value=73 Score=32.05 Aligned_cols=38 Identities=16% Similarity=0.301 Sum_probs=25.5
Q ss_pred eeecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCCcccc
Q 042101 95 AHLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGRAF 140 (380)
Q Consensus 95 ~~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~G~v~ 140 (380)
+.-.||-||. . .++-..+..+..+-.|.| . ||..|-+.
T Consensus 168 ~~p~c~~cg~----~-~~~v~~~d~~~~~v~y~c-~--cG~~g~~~ 205 (353)
T cd00674 168 FMPYCEKCGK----D-TTTVEAYDAKAGTVTYKC-E--CGHEETVD 205 (353)
T ss_pred eeeecCCcCc----c-eeEEEEEeCCCCeEEEEc-C--CCCEEEEe
Confidence 5788999984 2 133334444445679999 7 99988763
No 103
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=33.46 E-value=75 Score=23.56 Aligned_cols=35 Identities=17% Similarity=0.689 Sum_probs=24.1
Q ss_pred eecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCCccc
Q 042101 96 HLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGRA 139 (380)
Q Consensus 96 ~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~G~v 139 (380)
...||-|+. -| ++.++.+....+--|-. ||+....
T Consensus 9 GA~CP~C~~---~D----tl~~~~e~~~e~vECv~--Cg~~~~~ 43 (59)
T TIGR02443 9 GAVCPACSA---QD----TLAMWKENNIELVECVE--CGYQEQQ 43 (59)
T ss_pred cccCCCCcC---cc----EEEEEEeCCceEEEecc--CCCcccc
Confidence 478999987 32 34555444446789999 9997554
No 104
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=33.44 E-value=28 Score=24.85 Aligned_cols=28 Identities=29% Similarity=0.855 Sum_probs=20.1
Q ss_pred eecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCC
Q 042101 96 HLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWA 136 (380)
Q Consensus 96 ~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~ 136 (380)
+..||-||. | +|.-. +.-.|+|=. ||..
T Consensus 19 ~~~CPrCG~-g-------vfmA~---H~dR~~CGk--CgyT 46 (51)
T COG1998 19 NRFCPRCGP-G-------VFMAD---HKDRWACGK--CGYT 46 (51)
T ss_pred cccCCCCCC-c-------chhhh---cCceeEecc--ccce
Confidence 578999996 1 35442 345899999 9974
No 105
>PF09664 DUF2399: Protein of unknown function C-terminus (DUF2399); InterPro: IPR024465 This domain is found in archaeal, bacterial and eukaryotic proteins. Its function is unknown.
Probab=33.38 E-value=2.8e+02 Score=24.28 Aligned_cols=71 Identities=24% Similarity=0.343 Sum_probs=44.9
Q ss_pred CCEEEEEechhHHHHHHHh-CC--CcEEEcCCCCCCCccCCCCCCCcccchhhhhHHHHhhcC-CCCeEEEEeCCChhhH
Q 042101 238 TAEVIIVEGEIDKLSVEEA-GF--QNCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLD-KVSRIILGTDADTPGH 313 (380)
Q Consensus 238 ~~~iiIvEG~~DaLSl~q~-G~--~~~Vs~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~~~L~-~~~~Ivl~~DnD~AG~ 313 (380)
...|+|||-..=.=++... +. ...|+. .|-.+... +..+..|. ..-+++...|.|.+|.
T Consensus 18 ~~~V~VvENp~Vf~~~~~~~~~~~~pLVCt-~G~p~~A~----------------~~LL~~L~~~g~~l~y~GDfDp~Gl 80 (152)
T PF09664_consen 18 SGRVYVVENPAVFSALADELGASCPPLVCT-SGQPSAAA----------------RRLLDRLAAAGARLYYSGDFDPEGL 80 (152)
T ss_pred CCEEEEEecHHHHHHHHHhcCCCCCeEEEc-CCcHHHHH----------------HHHHHHHHhCCCEEEEecCCCHHHH
Confidence 4559999987655444444 33 223433 35432110 01234443 3459999999999999
Q ss_pred HHHHHHHHHhCC
Q 042101 314 ALAEELARRLGK 325 (380)
Q Consensus 314 ~aa~~la~~L~~ 325 (380)
.-|.++.++++.
T Consensus 81 ~IA~~l~~r~~~ 92 (152)
T PF09664_consen 81 RIANRLIQRYGA 92 (152)
T ss_pred HHHHHHHHHhCC
Confidence 999999999875
No 106
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=33.36 E-value=27 Score=29.94 Aligned_cols=37 Identities=22% Similarity=0.480 Sum_probs=22.5
Q ss_pred eecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCCcccc
Q 042101 96 HLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGRAF 140 (380)
Q Consensus 96 ~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~G~v~ 140 (380)
+.-||+|+. .+ -.+.. .+.. ..+.|.|.. |+...+..
T Consensus 30 ~~~cP~C~s-~~-~~k~g---~~~~-~~qRyrC~~--C~~tf~~~ 66 (129)
T COG3677 30 KVNCPRCKS-SN-VVKIG---GIRR-GHQRYKCKS--CGSTFTVE 66 (129)
T ss_pred cCcCCCCCc-cc-eeeEC---Cccc-cccccccCC--cCcceeee
Confidence 467999986 11 01110 1112 368999999 99976664
No 107
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=32.82 E-value=36 Score=33.04 Aligned_cols=35 Identities=23% Similarity=0.502 Sum_probs=16.5
Q ss_pred eecCCCCCCCCCCCCccceEEEEEcC---CccEEEeCCccCCCCccc
Q 042101 96 HLLCPKCKGGGRSLERSLSVHIIQDG---DFAMWRCFRVDCGWAGRA 139 (380)
Q Consensus 96 ~~~CPfc~~~~~~~eks~s~~v~~d~---~~g~~~Cf~~~CG~~G~v 139 (380)
++.||.||. .|.+.+-..+ ..-..+|-- ||..-.+
T Consensus 172 ~g~CPvCGs-------~P~~s~l~~~~~~G~R~L~Cs~--C~t~W~~ 209 (290)
T PF04216_consen 172 RGYCPVCGS-------PPVLSVLRGGEREGKRYLHCSL--CGTEWRF 209 (290)
T ss_dssp -SS-TTT----------EEEEEEE------EEEEEETT--T--EEE-
T ss_pred CCcCCCCCC-------cCceEEEecCCCCccEEEEcCC--CCCeeee
Confidence 689999996 2445544332 135889988 8875443
No 108
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=32.80 E-value=35 Score=22.53 Aligned_cols=30 Identities=27% Similarity=0.645 Sum_probs=21.3
Q ss_pred ecCCCCCCCCCCCCccceEEEEEc---CCccEEEeCCccCCCCc
Q 042101 97 LLCPKCKGGGRSLERSLSVHIIQD---GDFAMWRCFRVDCGWAG 137 (380)
Q Consensus 97 ~~CPfc~~~~~~~eks~s~~v~~d---~~~g~~~Cf~~~CG~~G 137 (380)
..||-|+- .|.|.++ ...+..+|-. |+...
T Consensus 3 i~CP~C~~---------~f~v~~~~l~~~~~~vrC~~--C~~~f 35 (37)
T PF13719_consen 3 ITCPNCQT---------RFRVPDDKLPAGGRKVRCPK--CGHVF 35 (37)
T ss_pred EECCCCCc---------eEEcCHHHcccCCcEEECCC--CCcEe
Confidence 46999985 4666554 2356899999 98743
No 109
>PRK07220 DNA topoisomerase I; Validated
Probab=32.34 E-value=1.3e+02 Score=33.35 Aligned_cols=31 Identities=19% Similarity=0.267 Sum_probs=25.5
Q ss_pred hhcCCCCeEEEEeCCChhhHHHHHHHHHHhC
Q 042101 294 EHLDKVSRIILGTDADTPGHALAEELARRLG 324 (380)
Q Consensus 294 ~~L~~~~~Ivl~~DnD~AG~~aa~~la~~L~ 324 (380)
.++....+||||.|.|.-|+.-+..+.+.++
T Consensus 93 ~l~k~ad~viiAtD~DREGE~I~~~i~~~l~ 123 (740)
T PRK07220 93 KLGKEADRVTIATDYDREGELIGVEALNIIK 123 (740)
T ss_pred HHHhcCCEEEECCCCCccHHHHHHHHHHHHH
Confidence 3445678999999999999999988777765
No 110
>TIGR00467 lysS_arch lysyl-tRNA synthetase, archaeal and spirochete. This model represents the lysyl-tRNA synthetases that are class I amino-acyl tRNA synthetases. It includes archaeal and spirochete examples of the enzyme. All other known examples are class IIc amino-acyl tRNA synthetases and seem to form a separate orthologous set.
Probab=32.07 E-value=83 Score=33.34 Aligned_cols=36 Identities=14% Similarity=0.339 Sum_probs=24.4
Q ss_pred eeecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCCccc
Q 042101 95 AHLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGRA 139 (380)
Q Consensus 95 ~~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~G~v 139 (380)
+.-.||-||. . -++-..+..+. +-.|.| . ||..|-+
T Consensus 167 ~~pic~~cGr----v-~~~~~~~~~~~-~v~Y~c-~--cG~~g~~ 202 (515)
T TIGR00467 167 ISVFCENCGR----D-TTTVNNYDNEY-SIEYSC-E--CGNQESV 202 (515)
T ss_pred eeeecCCcCc----c-CceEEEecCCc-eEEEEc-C--CCCEEEE
Confidence 5789999985 2 33444444443 689999 6 9987765
No 111
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=31.88 E-value=58 Score=21.92 Aligned_cols=31 Identities=26% Similarity=0.712 Sum_probs=19.1
Q ss_pred cCCCCCCCCCCCCccceEEEE-----EcCCccEEEeCCccCCCC
Q 042101 98 LCPKCKGGGRSLERSLSVHII-----QDGDFAMWRCFRVDCGWA 136 (380)
Q Consensus 98 ~CPfc~~~~~~~eks~s~~v~-----~d~~~g~~~Cf~~~CG~~ 136 (380)
.||.|+. +...|+-. +++.+-+|.|-. ||..
T Consensus 2 ~Cp~C~~------~~a~~~q~Q~RsaDE~mT~fy~C~~--C~~~ 37 (40)
T smart00440 2 PCPKCGN------REATFFQLQTRSADEPMTVFYVCTK--CGHR 37 (40)
T ss_pred cCCCCCC------CeEEEEEEcccCCCCCCeEEEEeCC--CCCE
Confidence 6999985 12233321 123456999999 9863
No 112
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=31.46 E-value=41 Score=28.26 Aligned_cols=20 Identities=35% Similarity=1.007 Sum_probs=15.9
Q ss_pred CCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCC
Q 042101 99 CPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGW 135 (380)
Q Consensus 99 CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~ 135 (380)
||.|++ .+.| -.++|-. |+.
T Consensus 1 CPvCg~---------~l~v------t~l~C~~--C~t 20 (113)
T PF09862_consen 1 CPVCGG---------ELVV------TRLKCPS--CGT 20 (113)
T ss_pred CCCCCC---------ceEE------EEEEcCC--CCC
Confidence 999997 3666 3689999 976
No 113
>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=31.00 E-value=92 Score=22.51 Aligned_cols=50 Identities=20% Similarity=0.342 Sum_probs=29.9
Q ss_pred HHHHHHHHHhCCccccCCCCCceeeecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCC
Q 042101 72 TEVKQKLKLVGINCDDSCIPGRYAHLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGW 135 (380)
Q Consensus 72 ~~~~~~l~~~gi~~~~~~~~G~~~~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~ 135 (380)
+.|.+.|..-+=.. ....|...|+-|.. + +. +..-.+.+.-.|.|-. ||.
T Consensus 3 Dki~d~L~G~d~~~-----~~~r~aLIC~~C~~--h---NG--la~~~~~~~i~y~C~~--Cg~ 52 (54)
T PF10058_consen 3 DKILDVLLGDDPTS-----PSNRYALICSKCFS--H---NG--LAPKEEFEEIQYRCPY--CGA 52 (54)
T ss_pred HHHHHHHhCCCCcc-----ccCceeEECcccch--h---hc--ccccccCCceEEEcCC--CCC
Confidence 44666666544422 34467899999975 1 11 2212233446999999 986
No 114
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=30.65 E-value=77 Score=24.32 Aligned_cols=36 Identities=22% Similarity=0.655 Sum_probs=25.5
Q ss_pred eecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCCcccc
Q 042101 96 HLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGRAF 140 (380)
Q Consensus 96 ~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~G~v~ 140 (380)
...||-|+. -| ++.++.+.....--|-. ||+.....
T Consensus 8 Ga~CP~C~~---~D----~i~~~~e~~ve~vECV~--CGy~e~~~ 43 (71)
T PF09526_consen 8 GAVCPKCQA---MD----TIMMWRENGVEYVECVE--CGYTERQP 43 (71)
T ss_pred CccCCCCcC---cc----EEEEEEeCCceEEEecC--CCCeeccC
Confidence 478999987 33 45665554456889999 99975543
No 115
>TIGR01057 topA_arch DNA topoisomerase I, archaeal. This model describes topoisomerase I from archaea. These enzymes are involved in the control of DNA topology. DNA topoisomerase I belongs to the type I topoisomerases, which are ATP-independent.
Probab=30.29 E-value=1.2e+02 Score=32.79 Aligned_cols=42 Identities=14% Similarity=0.220 Sum_probs=32.2
Q ss_pred HhhcCCCCeEEEEeCCChhhHHHHHHHHHHhCC-CceEEEEcC
Q 042101 293 KEHLDKVSRIILGTDADTPGHALAEELARRLGK-DRCWRVRWP 334 (380)
Q Consensus 293 ~~~L~~~~~Ivl~~DnD~AG~~aa~~la~~L~~-~~v~iv~lP 334 (380)
..++.+..+||+|.|.|.-|+.-+..+.+.++. ..++.+.+-
T Consensus 88 k~l~~~~d~ii~AtD~DREGE~I~~~i~~~~~~~~~v~Rl~~~ 130 (618)
T TIGR01057 88 SKLAKGADEYINACDYDIEGEVIGFKALKYFCGVERAKRMKFS 130 (618)
T ss_pred HHHHhcCCEEEECCCCCccHHHHHHHHHHHhccCCCceEEEEc
Confidence 345567889999999999999999999998853 345555443
No 116
>PF01458 UPF0051: Uncharacterized protein family (UPF0051); InterPro: IPR000825 Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] []. FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems. The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins [, ]. It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly []. The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA []. SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA [], acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets. In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins []. Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen []. This entry represents SufB and SufD proteins that form part of the SufBCD complex in the SUF system. No specific functions have been assigned to these proteins.; GO: 0016226 iron-sulfur cluster assembly; PDB: 1VH4_B 2ZU0_A 4DN7_A.
Probab=30.23 E-value=39 Score=31.46 Aligned_cols=24 Identities=25% Similarity=0.321 Sum_probs=17.5
Q ss_pred CcccHHHHHHHHhCCCCHHHHhhc
Q 042101 163 EPLGEKLIAYLGERMISEGTLQRN 186 (380)
Q Consensus 163 ~pl~~~~~~YL~~RGIs~eti~~f 186 (380)
..+.++.+=||..|||+++.+++.
T Consensus 201 G~idee~LFYL~SRGl~~~eA~~L 224 (229)
T PF01458_consen 201 GQIDEEQLFYLMSRGLSEEEARKL 224 (229)
T ss_dssp EES-HHHHHHHHCTT--HHHHHHH
T ss_pred ecCCHHHHHHHHHcCCCHHHHHHH
Confidence 457788999999999999988763
No 117
>PHA02942 putative transposase; Provisional
Probab=29.64 E-value=42 Score=34.10 Aligned_cols=47 Identities=23% Similarity=0.603 Sum_probs=29.9
Q ss_pred HHHHhCCccccCCCCCceeeecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCCccc
Q 042101 77 KLKLVGINCDDSCIPGRYAHLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGRA 139 (380)
Q Consensus 77 ~l~~~gi~~~~~~~~G~~~~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~G~v 139 (380)
....+|+.+.. ..+- +.-..||.||. .. +.+ ....|.|-. ||...|-
T Consensus 308 KA~~~G~~Vv~-V~p~-yTSq~Cs~CG~---~~-~~l--------~~r~f~C~~--CG~~~dr 354 (383)
T PHA02942 308 QAKKHGMIVEF-VNPS-YSSVSCPKCGH---KM-VEI--------AHRYFHCPS--CGYENDR 354 (383)
T ss_pred HHHHhCCEEEE-ECCC-CCCccCCCCCC---cc-CcC--------CCCEEECCC--CCCEeCc
Confidence 55568887765 2232 23478999996 21 111 125899999 9997664
No 118
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=29.51 E-value=34 Score=28.24 Aligned_cols=39 Identities=21% Similarity=0.394 Sum_probs=22.6
Q ss_pred ecCCCCCCCCCCCCccceEEEEEcC---CccEEEeCCccCCCCcccc
Q 042101 97 LLCPKCKGGGRSLERSLSVHIIQDG---DFAMWRCFRVDCGWAGRAF 140 (380)
Q Consensus 97 ~~CPfc~~~~~~~eks~s~~v~~d~---~~g~~~Cf~~~CG~~G~v~ 140 (380)
..||+||. +-+-.++-.||+.. ....|.|-. |++.-.+.
T Consensus 3 ~~CpYCg~---~~~l~~~~~iYg~~~~~~~~~y~C~~--C~AyVG~H 44 (102)
T PF11672_consen 3 IICPYCGG---PAELVDGSEIYGHRYDDGPYLYVCTP--CDAYVGCH 44 (102)
T ss_pred cccCCCCC---eeEEcccchhcCccCCCCceeEECCC--CCceeeee
Confidence 47999997 21211222345422 234699999 98855443
No 119
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=28.67 E-value=40 Score=29.86 Aligned_cols=14 Identities=29% Similarity=0.624 Sum_probs=10.9
Q ss_pred EEEeCCccCCCCcccc
Q 042101 125 MWRCFRVDCGWAGRAF 140 (380)
Q Consensus 125 ~~~Cf~~~CG~~G~v~ 140 (380)
.++|-. ||......
T Consensus 28 ~~~c~~--c~~~f~~~ 41 (154)
T PRK00464 28 RRECLA--CGKRFTTF 41 (154)
T ss_pred eeeccc--cCCcceEe
Confidence 599999 99876653
No 120
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=28.55 E-value=43 Score=26.66 Aligned_cols=30 Identities=17% Similarity=0.403 Sum_probs=18.8
Q ss_pred eecCCCCCCCCCCCCccceEEEEEcCCccEEEeC
Q 042101 96 HLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCF 129 (380)
Q Consensus 96 ~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf 129 (380)
...|+.|+.+ = ...-|.+||+++--+++|+
T Consensus 78 ~~~C~vC~k~---l-~~~~f~~~p~~~v~H~~C~ 107 (109)
T PF10367_consen 78 STKCSVCGKP---L-GNSVFVVFPCGHVVHYSCI 107 (109)
T ss_pred CCCccCcCCc---C-CCceEEEeCCCeEEecccc
Confidence 4679999971 1 1135889998633455554
No 121
>cd00223 TOPRIM_TopoIIB_SPO TOPRIM_TopoIIB_SPO: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IIB family of DNA topoisomerases and Spo11. This subgroup contains proteins similar to Sulfolobus shibatae topoisomerase VI (TopoVI) and Saccharomyces cerevisiae meiotic recombination factor: Spo11. Type II DNA topoisomerases catalyze the ATP-dependent transport of one DNA duplex through another, in the process generating transient double strand breaks via covalent attachments to both DNA strands at the 5' positions. TopoVI enzymes are heterotetramers found in archaea and plants. Spo11 plays a role in generating the double strand breaks that initiate homologous recombination during meiosis. S. shibatae TopoVI relaxes both positive and negative supercoils, and in addition has a strong decatenase activity. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspart
Probab=28.35 E-value=2.4e+02 Score=24.53 Aligned_cols=68 Identities=22% Similarity=0.319 Sum_probs=40.8
Q ss_pred CEEEEEechhHHHHHHHhCCC---cEEEcCCCCCCCccCCCCCCCcccchhhhhHHHHhhcCC--CCeEEEEeCCChhhH
Q 042101 239 AEVIIVEGEIDKLSVEEAGFQ---NCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLDK--VSRIILGTDADTPGH 313 (380)
Q Consensus 239 ~~iiIvEG~~DaLSl~q~G~~---~~Vs~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~~~L~~--~~~Ivl~~DnD~AG~ 313 (380)
+.|+|||-+.=.-.+.+.++. +++-+.++.-.... ..++| ..|.. .-.++.+.|.|..|.
T Consensus 1 ~~ilvVEk~avf~~L~~~~~~~~~~~ilit~kG~P~~~-----------tr~~l----~~L~~~~~~~~~~l~D~DP~Gi 65 (160)
T cd00223 1 DFVLVVEKEAVFQRLIEEGFHERNNCILITGKGYPDRA-----------TRRFL----RRLHEELDLPVYILVDGDPYGI 65 (160)
T ss_pred CEEEEEecHHHHHHHHHcCccccCCEEEEEcCCcCCHH-----------HHHHH----HHHHHhhCCCEEEEECCCcchh
Confidence 368999998777777777664 55544322211111 11222 22211 237899999999998
Q ss_pred HHHHHHHH
Q 042101 314 ALAEELAR 321 (380)
Q Consensus 314 ~aa~~la~ 321 (380)
.-+..+..
T Consensus 66 ~I~~~y~~ 73 (160)
T cd00223 66 SILLTYKY 73 (160)
T ss_pred hhhHHHHh
Confidence 87776654
No 122
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=27.17 E-value=52 Score=27.37 Aligned_cols=27 Identities=30% Similarity=0.602 Sum_probs=21.6
Q ss_pred ecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCCc
Q 042101 97 LLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAG 137 (380)
Q Consensus 97 ~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~G 137 (380)
-.||.|+. -+.|.|+ ..|-|-- |++..
T Consensus 3 p~CP~C~s----------eytY~dg--~~~iCpe--C~~EW 29 (109)
T TIGR00686 3 PPCPKCNS----------EYTYHDG--TQLICPS--CLYEW 29 (109)
T ss_pred CcCCcCCC----------cceEecC--CeeECcc--ccccc
Confidence 36999984 5889986 6899999 98753
No 123
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=27.08 E-value=55 Score=29.34 Aligned_cols=29 Identities=21% Similarity=0.382 Sum_probs=17.8
Q ss_pred HHHHHHHHHHhCCccccCCCCCceeeecCCCCCC
Q 042101 71 LTEVKQKLKLVGINCDDSCIPGRYAHLLCPKCKG 104 (380)
Q Consensus 71 ~~~~~~~l~~~gi~~~~~~~~G~~~~~~CPfc~~ 104 (380)
.+.+.+.++.+|..-.- ..-...||.|++
T Consensus 77 ~~Ql~e~~~~~~l~~~~-----~~e~~RCp~CN~ 105 (165)
T COG1656 77 EEQLAEFLARLGLKPRL-----FPEFSRCPECNG 105 (165)
T ss_pred HHHHHHHHHHhccchhc-----ccccccCcccCC
Confidence 44566776666665411 112578999997
No 124
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=26.99 E-value=68 Score=21.46 Aligned_cols=11 Identities=27% Similarity=0.516 Sum_probs=8.3
Q ss_pred ccEEEeCCccCCC
Q 042101 123 FAMWRCFRVDCGW 135 (380)
Q Consensus 123 ~g~~~Cf~~~CG~ 135 (380)
--+++|.+ ||.
T Consensus 17 ~~id~C~~--C~G 27 (41)
T PF13453_consen 17 VEIDVCPS--CGG 27 (41)
T ss_pred EEEEECCC--CCe
Confidence 35889999 964
No 125
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=26.23 E-value=49 Score=28.38 Aligned_cols=31 Identities=16% Similarity=0.299 Sum_probs=21.7
Q ss_pred ecCCCCCC---CCCCCCccceEEEEEcCCccEEEeCCccCC
Q 042101 97 LLCPKCKG---GGRSLERSLSVHIIQDGDFAMWRCFRVDCG 134 (380)
Q Consensus 97 ~~CPfc~~---~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG 134 (380)
.+|=|||. +|+- ..||-.|+ +.+|.|.+ +|-
T Consensus 5 e~CsFcG~kIyPG~G-----~~fVR~DG-kvf~Fcss-KC~ 38 (131)
T PRK14891 5 RTCDYTGEEIEPGTG-----TMFVRKDG-TVLHFVDS-KCE 38 (131)
T ss_pred eeecCcCCcccCCCC-----cEEEecCC-CEEEEecH-HHH
Confidence 47999987 3332 47777664 67899987 784
No 126
>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=25.45 E-value=56 Score=21.25 Aligned_cols=30 Identities=30% Similarity=0.720 Sum_probs=20.1
Q ss_pred ecCCCCCCCCCCCCccceEEEEEcC---CccEEEeCCccCCCCc
Q 042101 97 LLCPKCKGGGRSLERSLSVHIIQDG---DFAMWRCFRVDCGWAG 137 (380)
Q Consensus 97 ~~CPfc~~~~~~~eks~s~~v~~d~---~~g~~~Cf~~~CG~~G 137 (380)
..||.|+. .|.|..+. ......|=. ||..-
T Consensus 3 ~~CP~C~~---------~~~v~~~~~~~~~~~v~C~~--C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKT---------SFRVVDSQLGANGGKVRCGK--CGHVW 35 (38)
T ss_pred EECCCCCC---------EEEeCHHHcCCCCCEEECCC--CCCEE
Confidence 57999986 46665432 234788988 98743
No 127
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=25.15 E-value=38 Score=29.65 Aligned_cols=72 Identities=21% Similarity=0.334 Sum_probs=41.1
Q ss_pred CCCcccchhhHH-HHHHHHHHhCCccccC-CCCCc---eeeecCCCCCCCCCCCCccceEEEEEcC-CccEEEeCCccCC
Q 042101 61 HKDDTIDISKLT-EVKQKLKLVGINCDDS-CIPGR---YAHLLCPKCKGGGRSLERSLSVHIIQDG-DFAMWRCFRVDCG 134 (380)
Q Consensus 61 ~~~~~~~~~~~~-~~~~~l~~~gi~~~~~-~~~G~---~~~~~CPfc~~~~~~~eks~s~~v~~d~-~~g~~~Cf~~~CG 134 (380)
..+-.+++.++. +-++.|+.+||.-... ...+. ...-.||.||. .+ +--.+.|--. =+..|+|.. |.
T Consensus 65 ~~~p~Wt~d~it~~gr~~l~~~giapp~~~~~~~~~~~~~~~~cp~c~s-~~----t~~~s~fg~t~cka~~~c~~--c~ 137 (146)
T TIGR02159 65 SLDPPWTTDWITEDAREKLREYGIAPPAGHYVVGVSPEPPSVQCPRCGS-AD----TTITSIFGPTACKALYRCRA--CK 137 (146)
T ss_pred eeCCCCChHHCCHHHHHHHHhcCccCCCccCCCcccCCCCCCcCCCCCC-CC----cEeecCCCChhhHHHhhhhh--hC
Confidence 444557777766 6899999999954320 00110 01358999997 22 2112222110 136899999 97
Q ss_pred CCccc
Q 042101 135 WAGRA 139 (380)
Q Consensus 135 ~~G~v 139 (380)
.-.+.
T Consensus 138 epf~~ 142 (146)
T TIGR02159 138 EPFEY 142 (146)
T ss_pred CcHhh
Confidence 65443
No 128
>PF14353 CpXC: CpXC protein
Probab=25.13 E-value=87 Score=26.27 Aligned_cols=14 Identities=29% Similarity=0.496 Sum_probs=11.5
Q ss_pred EEEeCCccCCCCcccc
Q 042101 125 MWRCFRVDCGWAGRAF 140 (380)
Q Consensus 125 ~~~Cf~~~CG~~G~v~ 140 (380)
.|.|-. ||..+.+.
T Consensus 38 ~~~CP~--Cg~~~~~~ 51 (128)
T PF14353_consen 38 SFTCPS--CGHKFRLE 51 (128)
T ss_pred EEECCC--CCCceecC
Confidence 889999 99987764
No 129
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=24.99 E-value=66 Score=23.16 Aligned_cols=7 Identities=43% Similarity=1.189 Sum_probs=6.1
Q ss_pred cCCCCCC
Q 042101 98 LCPKCKG 104 (380)
Q Consensus 98 ~CPfc~~ 104 (380)
.||+||.
T Consensus 2 ~CPyCge 8 (52)
T PF14255_consen 2 QCPYCGE 8 (52)
T ss_pred CCCCCCC
Confidence 5999997
No 130
>cd01458 vWA_ku Ku70/Ku80 N-terminal domain. The Ku78 heterodimer (composed of Ku70 and Ku80) contributes to genomic integrity through its ability to bind DNA double-strand breaks (DSB) in a preferred orientation. DSB's are repaired by either homologues recombination or non-homologues end joining and facilitate repair by the non-homologous end-joining pathway (NHEJ). The Ku heterodimer is required for accurate process that tends to preserve the sequence at the junction. Ku78 is found in all three kingdoms of life. However, only the eukaryotic proteins have a vWA domain fused to them at their N-termini. The vWA domain is not involved in DNA binding but may very likey mediate Ku78's interactions with other proteins. Members of this subgroup lack the conserved MIDAS motif.
Probab=24.98 E-value=1.8e+02 Score=26.47 Aligned_cols=51 Identities=25% Similarity=0.218 Sum_probs=28.1
Q ss_pred CCeEEEEeCCChh-h-----HHHHHHHHHHhCCCceEEEEcCCCCCCCCCCCHHHHHH
Q 042101 299 VSRIILGTDADTP-G-----HALAEELARRLGKDRCWRVRWPKKDEFSYFKDANEVLK 350 (380)
Q Consensus 299 ~~~Ivl~~DnD~A-G-----~~aa~~la~~L~~~~v~iv~lP~~~~~~~~KD~ND~L~ 350 (380)
.++|+|..|+|.+ | ...+..+++.|....+.+..++-+.. .+.-|++.++.
T Consensus 128 ~k~IvL~TDg~~p~~~~~~~~~~~~~~a~~l~~~gI~i~~i~i~~~-~~~f~~~~fy~ 184 (218)
T cd01458 128 HKRIFLFTNNDDPHGGDSIKDSQAAVKAEDLKDKGIELELFPLSSP-GKKFDVSKFYK 184 (218)
T ss_pred ccEEEEECCCCCCCCCCHHHHHHHHHHHHHHHhCCcEEEEEecCCC-CCCCChhHHHH
Confidence 4789999999887 2 34455666666543444433332210 11246665554
No 131
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=24.89 E-value=48 Score=32.13 Aligned_cols=37 Identities=16% Similarity=0.429 Sum_probs=16.7
Q ss_pred ecCCCCCCCCCCCCccceEEEE-Ec--CCccEEEeCCccCCCCcccc
Q 042101 97 LLCPKCKGGGRSLERSLSVHII-QD--GDFAMWRCFRVDCGWAGRAF 140 (380)
Q Consensus 97 ~~CPfc~~~~~~~eks~s~~v~-~d--~~~g~~~Cf~~~CG~~G~v~ 140 (380)
..||+||. .+.. ++..+ .+ ..-....|-. |+..-.++
T Consensus 212 ~~Cp~Cg~---~~~~--~l~~~~~e~~~~~rve~C~~--C~~YlK~v 251 (290)
T PF04216_consen 212 IKCPYCGN---TDHE--KLEYFTVEGEPAYRVEVCES--CGSYLKTV 251 (290)
T ss_dssp TS-TTT------SS---EEE--------SEEEEEETT--TTEEEEEE
T ss_pred CCCcCCCC---CCCc--ceeeEecCCCCcEEEEECCc--ccchHHHH
Confidence 56899987 2222 23332 22 2335888988 97754444
No 132
>PRK10220 hypothetical protein; Provisional
Probab=24.68 E-value=72 Score=26.62 Aligned_cols=28 Identities=29% Similarity=0.647 Sum_probs=22.2
Q ss_pred ecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCCcc
Q 042101 97 LLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGR 138 (380)
Q Consensus 97 ~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~G~ 138 (380)
-.||.|+. -+.|.|. ..|-|-- |+...+
T Consensus 4 P~CP~C~s----------eytY~d~--~~~vCpe--C~hEW~ 31 (111)
T PRK10220 4 PHCPKCNS----------EYTYEDN--GMYICPE--CAHEWN 31 (111)
T ss_pred CcCCCCCC----------cceEcCC--CeEECCc--ccCcCC
Confidence 46999984 5889886 6899999 987543
No 133
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 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. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=24.53 E-value=64 Score=20.03 Aligned_cols=25 Identities=24% Similarity=0.505 Sum_probs=10.6
Q ss_pred cCCCCCCCCCCCCccceEEEEEcCCccEEEeCCc-cC
Q 042101 98 LCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRV-DC 133 (380)
Q Consensus 98 ~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~-~C 133 (380)
.||.|+. .+.-.+ +.-.|+|-+. .|
T Consensus 1 ~CP~C~s---------~l~~~~--~ev~~~C~N~l~C 26 (28)
T PF03119_consen 1 TCPVCGS---------KLVREE--GEVDIRCPNPLSC 26 (28)
T ss_dssp B-TTT-----------BEEE-C--CTTCEEE--CGC-
T ss_pred CcCCCCC---------EeEcCC--CCEeEECCCCCcC
Confidence 4999985 133222 2358999875 55
No 134
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=23.78 E-value=74 Score=26.45 Aligned_cols=28 Identities=29% Similarity=0.596 Sum_probs=22.0
Q ss_pred ecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCCcc
Q 042101 97 LLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGR 138 (380)
Q Consensus 97 ~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~G~ 138 (380)
-.||.|++ -++|.|. +.|.|-. |++..+
T Consensus 4 p~cp~c~s----------EytYed~--~~~~cpe--c~~ew~ 31 (112)
T COG2824 4 PPCPKCNS----------EYTYEDG--GQLICPE--CAHEWN 31 (112)
T ss_pred CCCCccCC----------ceEEecC--ceEeCch--hccccc
Confidence 47999974 5889886 6999999 987533
No 135
>TIGR01981 sufD FeS assembly protein SufD, group 1. This protein, SufD, forms a cytosolic complex SufBCD. This complex enhances the cysteine desulfurase of SufSE. The system, together with SufA, is believed to act in iron-sulfur cluster formation during oxidative stress. SufB and SufD are homologous. Note that SufC belongs to the family of ABC transporter ATP binding proteins, so this protein, encoded by an adjacent gene, has often been annotated as a transporter component.
Probab=23.60 E-value=64 Score=32.42 Aligned_cols=24 Identities=25% Similarity=0.364 Sum_probs=20.6
Q ss_pred CcccHHHHHHHHhCCCCHHHHhhc
Q 042101 163 EPLGEKLIAYLGERMISEGTLQRN 186 (380)
Q Consensus 163 ~pl~~~~~~YL~~RGIs~eti~~f 186 (380)
..+.++.+-||+.|||+++.+++.
T Consensus 321 G~ldee~LFYL~SRGi~~~eA~~l 344 (366)
T TIGR01981 321 GQIDDEQLFYLRSRGIDEEEARRL 344 (366)
T ss_pred cCCCHHHHHHHHHcCCCHHHHHHH
Confidence 456678899999999999998875
No 136
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=23.52 E-value=1.4e+02 Score=22.14 Aligned_cols=32 Identities=31% Similarity=0.768 Sum_probs=19.3
Q ss_pred eeeecCCCCCCCCCCCCccceEEEEEc----CCccEEEeCCccCCCCc
Q 042101 94 YAHLLCPKCKGGGRSLERSLSVHIIQD----GDFAMWRCFRVDCGWAG 137 (380)
Q Consensus 94 ~~~~~CPfc~~~~~~~eks~s~~v~~d----~~~g~~~Cf~~~CG~~G 137 (380)
.-+-.||-||. .-|+-- +....|.|-. ||+.|
T Consensus 23 ~~~F~CPnCG~----------~~I~RC~~CRk~~~~Y~CP~--CGF~G 58 (59)
T PRK14890 23 AVKFLCPNCGE----------VIIYRCEKCRKQSNPYTCPK--CGFEG 58 (59)
T ss_pred cCEeeCCCCCC----------eeEeechhHHhcCCceECCC--CCCcC
Confidence 44678999986 112211 1224788888 88766
No 137
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=23.37 E-value=64 Score=20.52 Aligned_cols=24 Identities=33% Similarity=0.816 Sum_probs=13.2
Q ss_pred cCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCC
Q 042101 98 LCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGW 135 (380)
Q Consensus 98 ~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~ 135 (380)
.||.|+. =+.|.|+ ..|.|-- |+.
T Consensus 4 ~Cp~C~s----------e~~y~D~--~~~vCp~--C~~ 27 (30)
T PF08274_consen 4 KCPLCGS----------EYTYEDG--ELLVCPE--CGH 27 (30)
T ss_dssp --TTT---------------EE-S--SSEEETT--TTE
T ss_pred CCCCCCC----------cceeccC--CEEeCCc--ccc
Confidence 6999985 2445665 7899999 975
No 138
>PF08063 PADR1: PADR1 (NUC008) domain; InterPro: IPR012982 This domain is found in poly(ADP-ribose)-synthetases []. The function of this domain is unknown.; GO: 0003950 NAD+ ADP-ribosyltransferase activity, 0005634 nucleus; PDB: 2JVN_A 4DQY_E 2RIQ_A.
Probab=23.37 E-value=62 Score=23.49 Aligned_cols=23 Identities=39% Similarity=0.840 Sum_probs=13.0
Q ss_pred eecCCCCCCCCCCCCccceEEEEEcCCccEEEeCC
Q 042101 96 HLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFR 130 (380)
Q Consensus 96 ~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~ 130 (380)
-..||.|++ ..++.+. ..|+|.+
T Consensus 14 l~~Cp~C~~----------~~l~~~~--~~Y~C~G 36 (55)
T PF08063_consen 14 LEPCPKCKG----------GQLYFDG--SGYKCTG 36 (55)
T ss_dssp E---SSSSE-----------EEEEET--TEEEEES
T ss_pred CCCCCCCCC----------CeEEecC--CccEeCc
Confidence 367999986 2333343 4899998
No 139
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=23.13 E-value=2e+02 Score=23.55 Aligned_cols=11 Identities=36% Similarity=0.912 Sum_probs=7.8
Q ss_pred cEEEeCCccCCCC
Q 042101 124 AMWRCFRVDCGWA 136 (380)
Q Consensus 124 g~~~Cf~~~CG~~ 136 (380)
-.|+|-. ||..
T Consensus 30 ~~~~C~~--CGe~ 40 (127)
T TIGR03830 30 PGWYCPA--CGEE 40 (127)
T ss_pred eeeECCC--CCCE
Confidence 3678888 8763
No 140
>KOG2846 consensus Predicted membrane protein [Function unknown]
Probab=23.00 E-value=69 Score=31.80 Aligned_cols=52 Identities=17% Similarity=0.386 Sum_probs=32.9
Q ss_pred HHHHHHHHHHhCCccccCCCCCceeeecCCCCCCCCCCCCccceEEEEEcCCccEEEeCCccCCCCccc
Q 042101 71 LTEVKQKLKLVGINCDDSCIPGRYAHLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFRVDCGWAGRA 139 (380)
Q Consensus 71 ~~~~~~~l~~~gi~~~~~~~~G~~~~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~~~CG~~G~v 139 (380)
++.|.++|..- .++..|...|+.|.. | +. +....+-.--.|+|+. |++.-..
T Consensus 203 ~DRI~d~lvGd--------sP~~ryALIC~~C~~--H---NG--la~~ee~~yi~F~C~~--Cn~LN~~ 254 (328)
T KOG2846|consen 203 FDRILDYLVGD--------SPNNRYALICSQCHH--H---NG--LARKEEYEYITFRCPH--CNALNPA 254 (328)
T ss_pred HHHHHHHHhcC--------CCcchhhhcchhhcc--c---cC--cCChhhcCceEEECcc--ccccCCC
Confidence 45777777762 156678999999975 1 11 2222222346899999 9875443
No 141
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=22.97 E-value=92 Score=28.77 Aligned_cols=37 Identities=24% Similarity=0.538 Sum_probs=21.4
Q ss_pred eeeecCCCCCCCCCCCCccceEEEEEcCCc-----cEEEeCCccCCCCc
Q 042101 94 YAHLLCPKCKGGGRSLERSLSVHIIQDGDF-----AMWRCFRVDCGWAG 137 (380)
Q Consensus 94 ~~~~~CPfc~~~~~~~eks~s~~v~~d~~~-----g~~~Cf~~~CG~~G 137 (380)
.....||.|+. . =....+++.-... .+++|-+ ||+.-
T Consensus 12 ~~~~~CPvCg~---~--l~~~~~~~~IPyFG~V~i~t~~C~~--CgYR~ 53 (201)
T COG1779 12 ETRIDCPVCGG---T--LKAHMYLYDIPYFGEVLISTGVCER--CGYRS 53 (201)
T ss_pred eeeecCCcccc---e--eeEEEeeecCCccceEEEEEEEccc--cCCcc
Confidence 35789999995 1 1111222221112 4899999 99853
No 142
>KOG2923 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.51 E-value=61 Score=24.41 Aligned_cols=32 Identities=22% Similarity=0.479 Sum_probs=22.1
Q ss_pred CceeeecCCCCCCCCCCCCccceEEEEEcC---CccEEEeCCccCCC
Q 042101 92 GRYAHLLCPKCKGGGRSLERSLSVHIIQDG---DFAMWRCFRVDCGW 135 (380)
Q Consensus 92 G~~~~~~CPfc~~~~~~~eks~s~~v~~d~---~~g~~~Cf~~~CG~ 135 (380)
-+.|..+|| ||+ .|.|..+. ...+-.|-+ |.-
T Consensus 18 ~~~y~yPCp-CGD---------rf~It~edL~~ge~Va~Cps--CSL 52 (67)
T KOG2923|consen 18 NQTYYYPCP-CGD---------RFQITLEDLENGEDVARCPS--CSL 52 (67)
T ss_pred CCeEEcCCC-CCC---------eeeecHHHHhCCCeeecCCC--ceE
Confidence 346788999 776 37776542 346889999 854
No 143
>PF02330 MAM33: Mitochondrial glycoprotein; InterPro: IPR003428 This mitochondrial matrix protein family contains members of the MAM33 family which bind to the globular 'heads' of C1Q.; GO: 0005759 mitochondrial matrix; PDB: 3QV0_A 1YQF_F 3JV1_A 1P32_A 3RPX_A.
Probab=22.15 E-value=63 Score=29.56 Aligned_cols=19 Identities=32% Similarity=0.433 Sum_probs=15.2
Q ss_pred HHHHHHHHhCCCCHHHHhh
Q 042101 167 EKLIAYLGERMISEGTLQR 185 (380)
Q Consensus 167 ~~~~~YL~~RGIs~eti~~ 185 (380)
....+||.+|||+.+++..
T Consensus 162 ~~~~~yLeeRGId~~la~f 180 (204)
T PF02330_consen 162 DAFMNYLEERGIDEELANF 180 (204)
T ss_dssp HHHHHHHHHTT-SHHHHHH
T ss_pred HHHHHHHHHhCCCHHHHHH
Confidence 4678999999999998765
No 144
>PTZ00407 DNA topoisomerase IA; Provisional
Probab=21.24 E-value=2.5e+02 Score=31.57 Aligned_cols=29 Identities=34% Similarity=0.503 Sum_probs=25.9
Q ss_pred cCCCCeEEEEeCCChhhHHHHHHHHHHhC
Q 042101 296 LDKVSRIILGTDADTPGHALAEELARRLG 324 (380)
Q Consensus 296 L~~~~~Ivl~~DnD~AG~~aa~~la~~L~ 324 (380)
+.....||+|.|.|.-|+.-+..+.+.++
T Consensus 122 ak~ad~IIlATDpDREGE~Ia~hIle~l~ 150 (805)
T PTZ00407 122 ADNVTEIILATDPDREGELIAVHALQTIK 150 (805)
T ss_pred HhcCCEEEECCCCCcchHHHHHHHHHHhc
Confidence 45678999999999999999999998886
No 145
>PF09983 DUF2220: Uncharacterized protein conserved in bacteria C-term(DUF2220); InterPro: IPR024534 This is a domain of unknown function that is found predominantly in hypothetical bacterial proteins.
Probab=21.20 E-value=4.2e+02 Score=23.67 Aligned_cols=70 Identities=21% Similarity=0.171 Sum_probs=46.6
Q ss_pred CCCEEEEEechhHHHHHHHhCCCcEEEcCCCCCCCccCCCCCCCcccchhhhhHHHHhhcCCCCeEEEEeCCChhhHHHH
Q 042101 237 ETAEVIIVEGEIDKLSVEEAGFQNCVSVPSGAPPKVSNRELPPREKDTGYQYLWNCKEHLDKVSRIILGTDADTPGHALA 316 (380)
Q Consensus 237 ~~~~iiIvEG~~DaLSl~q~G~~~~Vs~~~Ga~~~~~~~~Lp~~~~~~~~~~l~~~~~~L~~~~~Ivl~~DnD~AG~~aa 316 (380)
..+.|+|||-.....++.+... .++....|-.... ... .++++... .|+-|.|-|..|-.-.
T Consensus 42 ~~~~vliVEN~~tf~~~~~~~~-~~~Iyg~G~~~~~------------~~~----~~~~~~~~-~~~ywGDiD~~G~~I~ 103 (181)
T PF09983_consen 42 PPRRVLIVENLTTFYSLPELPN-GLVIYGGGFAISS------------SRR----FLKWLQPK-PVYYWGDIDPGGLRIL 103 (181)
T ss_pred CCCEEEEEeCHHHHHHHHhcCC-eEEEECCCcCcHH------------HHH----HHhhcCCC-ceEEeccCCHhHHHHH
Confidence 4689999999999999886542 2232333432110 011 12455555 9999999999999988
Q ss_pred HHHHHHhC
Q 042101 317 EELARRLG 324 (380)
Q Consensus 317 ~~la~~L~ 324 (380)
.++.+.+.
T Consensus 104 ~~lr~~~p 111 (181)
T PF09983_consen 104 ERLRRKFP 111 (181)
T ss_pred HHHHHhCC
Confidence 88887763
No 146
>KOG4498 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.71 E-value=1.2e+02 Score=27.97 Aligned_cols=54 Identities=15% Similarity=0.132 Sum_probs=39.8
Q ss_pred hhHHHHHHHHHHhCCccccCCCCCceeeecCCCCCCCCCCCCccceEEEEEcCCccEEEeCC
Q 042101 69 SKLTEVKQKLKLVGINCDDSCIPGRYAHLLCPKCKGGGRSLERSLSVHIIQDGDFAMWRCFR 130 (380)
Q Consensus 69 ~~~~~~~~~l~~~gi~~~~~~~~G~~~~~~CPfc~~~~~~~eks~s~~v~~d~~~g~~~Cf~ 130 (380)
+.|.++++.|.++|+.+-- ..+| .+...=+||.. +-.+--||.|.+++.|.|..
T Consensus 71 adLa~l~~~ld~~Gv~Li~-vg~g-~~~~~~~f~~q------~~f~gevylD~~~~~Y~~le 124 (197)
T KOG4498|consen 71 ADLASLKDLLDELGVVLIA-VGPG-SHVQFEDFWDQ------TYFSGEVYLDPHRGFYKPLE 124 (197)
T ss_pred HHHHHHHHHHHHhCCEEEE-Eecc-ceeecchhhcc------cCcceeEEEcCccceechhh
Confidence 4577899999999999865 2233 46778899975 22345688888888888887
Done!