Query 011230
Match_columns 490
No_of_seqs 280 out of 674
Neff 5.3
Searched_HMMs 46136
Date Thu Mar 28 23:02:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/011230.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/011230hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2703 C4-type Zn-finger prot 100.0 1E-148 2E-153 1127.2 31.5 450 1-487 1-458 (460)
2 TIGR00310 ZPR1_znf ZPR1 zinc f 100.0 2.8E-67 6.1E-72 500.5 21.4 188 287-480 2-192 (192)
3 TIGR00310 ZPR1_znf ZPR1 zinc f 100.0 3.4E-65 7.4E-70 486.2 22.6 184 33-222 2-189 (192)
4 smart00709 Zpr1 Duplicated dom 100.0 6.6E-60 1.4E-64 438.7 19.8 159 32-192 1-160 (160)
5 PF03367 zf-ZPR1: ZPR1 zinc-fi 100.0 7.6E-60 1.6E-64 438.9 15.6 160 31-192 1-161 (161)
6 smart00709 Zpr1 Duplicated dom 100.0 6.1E-59 1.3E-63 432.2 18.9 160 286-447 1-160 (160)
7 PF03367 zf-ZPR1: ZPR1 zinc-fi 100.0 6E-58 1.3E-62 426.2 14.4 160 285-447 1-161 (161)
8 TIGR00340 zpr1_rel ZPR1-relate 100.0 2.5E-56 5.4E-61 415.4 19.2 157 34-196 1-159 (163)
9 TIGR00340 zpr1_rel ZPR1-relate 100.0 5.8E-55 1.3E-59 406.3 18.1 156 288-450 1-158 (163)
10 KOG2703 C4-type Zn-finger prot 100.0 3.2E-55 7E-60 445.7 15.6 200 278-480 32-231 (460)
11 COG1779 C4-type Zn-finger prot 100.0 1.9E-51 4.1E-56 388.0 14.2 194 278-479 7-201 (201)
12 COG1779 C4-type Zn-finger prot 100.0 2.6E-47 5.7E-52 359.9 15.9 191 23-220 6-197 (201)
13 PF10571 UPF0547: Uncharacteri 94.6 0.015 3.1E-07 39.0 0.8 24 33-71 2-25 (26)
14 PF14353 CpXC: CpXC protein 93.8 0.021 4.6E-07 51.2 0.6 40 32-71 2-49 (128)
15 PF14353 CpXC: CpXC protein 92.1 0.046 1E-06 49.0 0.3 40 286-325 2-49 (128)
16 PF10571 UPF0547: Uncharacteri 92.0 0.069 1.5E-06 35.8 0.9 24 287-325 2-25 (26)
17 PF09986 DUF2225: Uncharacteri 90.9 0.27 5.8E-06 48.4 4.1 46 30-75 4-63 (214)
18 COG1326 Uncharacterized archae 90.7 0.28 6.1E-06 47.7 3.9 83 28-132 3-94 (201)
19 PF09986 DUF2225: Uncharacteri 90.6 0.27 5.8E-06 48.3 3.9 45 285-329 5-63 (214)
20 PHA00626 hypothetical protein 89.7 0.43 9.3E-06 37.7 3.5 49 33-91 2-50 (59)
21 PHA00626 hypothetical protein 89.2 0.51 1.1E-05 37.3 3.6 50 286-345 1-50 (59)
22 PRK00464 nrdR transcriptional 88.7 0.45 9.8E-06 44.8 3.6 45 286-331 1-45 (154)
23 PRK00398 rpoP DNA-directed RNA 88.0 0.38 8.3E-06 35.9 2.1 29 31-70 3-31 (46)
24 PF10058 DUF2296: Predicted in 87.5 0.61 1.3E-05 36.5 3.1 36 27-70 18-54 (54)
25 PRK03824 hypA hydrogenase nick 86.4 0.39 8.4E-06 44.1 1.7 50 30-79 69-126 (135)
26 PRK00464 nrdR transcriptional 86.2 0.96 2.1E-05 42.6 4.2 46 33-79 2-47 (154)
27 PRK14890 putative Zn-ribbon RN 85.6 0.34 7.3E-06 38.7 0.8 34 30-69 24-57 (59)
28 PRK05978 hypothetical protein; 85.6 0.36 7.7E-06 45.2 1.1 32 30-71 32-63 (148)
29 PRK12336 translation initiatio 84.8 3.3 7E-05 40.5 7.3 72 286-365 99-176 (201)
30 smart00440 ZnF_C2C2 C2C2 Zinc 84.4 1.7 3.8E-05 31.8 4.0 39 33-72 2-40 (40)
31 PRK03824 hypA hydrogenase nick 84.3 0.5 1.1E-05 43.3 1.4 48 284-331 69-124 (135)
32 PF13248 zf-ribbon_3: zinc-rib 84.3 0.43 9.3E-06 31.7 0.7 24 285-323 2-25 (26)
33 COG2888 Predicted Zn-ribbon RN 83.3 0.56 1.2E-05 37.5 1.1 35 29-69 25-59 (61)
34 PRK00398 rpoP DNA-directed RNA 83.0 0.96 2.1E-05 33.7 2.2 29 286-325 4-32 (46)
35 COG0484 DnaJ DnaJ-class molecu 81.9 7.8 0.00017 41.5 9.2 38 31-73 159-196 (371)
36 smart00440 ZnF_C2C2 C2C2 Zinc 81.5 2.4 5.2E-05 31.0 3.8 39 287-326 2-40 (40)
37 COG1326 Uncharacterized archae 81.1 2.3 5E-05 41.5 4.6 83 282-384 3-94 (201)
38 PRK05978 hypothetical protein; 80.9 0.68 1.5E-05 43.4 0.9 37 283-329 31-67 (148)
39 COG0484 DnaJ DnaJ-class molecu 80.5 7.9 0.00017 41.4 8.7 39 284-327 158-196 (371)
40 COG1996 RPC10 DNA-directed RNA 79.9 0.91 2E-05 35.0 1.1 31 29-70 4-34 (49)
41 PF09862 DUF2089: Protein of u 79.5 1.6 3.4E-05 39.3 2.6 75 34-144 1-79 (113)
42 PF13240 zinc_ribbon_2: zinc-r 79.4 0.77 1.7E-05 29.8 0.5 8 288-295 2-9 (23)
43 COG1594 RPB9 DNA-directed RNA 78.5 2.3 4.9E-05 38.1 3.4 40 31-72 72-112 (113)
44 PF04606 Ogr_Delta: Ogr/Delta- 78.3 1.4 3.1E-05 33.1 1.8 36 287-325 1-38 (47)
45 PF04606 Ogr_Delta: Ogr/Delta- 77.6 1.7 3.7E-05 32.7 2.0 36 33-71 1-38 (47)
46 TIGR01384 TFS_arch transcripti 77.3 4.1 8.8E-05 35.2 4.6 43 29-72 60-102 (104)
47 TIGR00244 transcriptional regu 76.6 4.6 9.9E-05 37.9 4.9 64 32-101 1-64 (147)
48 PF13453 zf-TFIIB: Transcripti 76.2 3.4 7.3E-05 30.1 3.2 27 287-322 1-27 (41)
49 PRK12336 translation initiatio 75.6 7.6 0.00016 38.0 6.4 71 32-113 99-176 (201)
50 PF07282 OrfB_Zn_ribbon: Putat 75.6 1.7 3.7E-05 34.6 1.7 29 31-70 28-56 (69)
51 smart00531 TFIIE Transcription 75.5 0.85 1.8E-05 42.2 -0.2 33 29-71 97-134 (147)
52 PRK14292 chaperone protein Dna 75.5 19 0.00041 38.1 9.9 33 32-67 158-190 (371)
53 TIGR03831 YgiT_finger YgiT-typ 75.2 3.2 6.9E-05 30.1 2.9 36 34-70 1-42 (46)
54 smart00661 RPOL9 RNA polymeras 75.1 2.4 5.3E-05 31.8 2.3 29 33-70 2-30 (52)
55 COG1997 RPL43A Ribosomal prote 74.4 2.3 5.1E-05 36.5 2.2 36 31-81 35-70 (89)
56 PF01096 TFIIS_C: Transcriptio 74.1 2.8 6E-05 30.5 2.3 37 287-324 2-38 (39)
57 PRK14284 chaperone protein Dna 73.7 18 0.00038 38.8 9.2 26 108-133 295-326 (391)
58 COG1997 RPL43A Ribosomal prote 73.4 2.5 5.3E-05 36.4 2.1 40 280-334 30-69 (89)
59 KOG2907 RNA polymerase I trans 72.9 1.5 3.3E-05 39.2 0.8 43 28-72 71-114 (116)
60 PF09862 DUF2089: Protein of u 72.7 3 6.4E-05 37.5 2.5 19 378-396 61-79 (113)
61 PRK03988 translation initiatio 72.6 3.7 8E-05 38.0 3.3 32 286-325 103-134 (138)
62 PF13824 zf-Mss51: Zinc-finger 72.5 1.6 3.5E-05 34.4 0.7 24 33-70 1-24 (55)
63 PRK14284 chaperone protein Dna 72.5 12 0.00026 40.0 7.6 26 360-385 295-326 (391)
64 PF13453 zf-TFIIB: Transcripti 72.4 5 0.00011 29.2 3.3 28 33-69 1-28 (41)
65 PF01096 TFIIS_C: Transcriptio 72.2 4.1 8.8E-05 29.6 2.8 36 33-70 2-38 (39)
66 PF07282 OrfB_Zn_ribbon: Putat 72.2 2.3 5.1E-05 33.8 1.7 29 285-324 28-56 (69)
67 TIGR01206 lysW lysine biosynth 71.9 2.7 5.8E-05 33.0 1.8 32 286-327 3-34 (54)
68 PF10058 DUF2296: Predicted in 71.2 3.8 8.2E-05 32.1 2.6 35 282-324 19-54 (54)
69 TIGR03831 YgiT_finger YgiT-typ 71.1 4.5 9.7E-05 29.3 2.8 35 288-323 1-41 (46)
70 smart00659 RPOLCX RNA polymera 71.1 1.8 4E-05 32.4 0.7 26 287-324 4-29 (44)
71 KOG2846 Predicted membrane pro 71.0 1.8 3.9E-05 45.3 0.9 40 28-75 217-257 (328)
72 smart00653 eIF2B_5 domain pres 70.5 2.7 5.8E-05 37.5 1.8 30 286-323 81-110 (110)
73 TIGR03830 CxxCG_CxxCG_HTH puta 70.5 3.8 8.2E-05 36.0 2.8 36 288-323 1-40 (127)
74 TIGR03830 CxxCG_CxxCG_HTH puta 69.7 3.9 8.4E-05 35.9 2.7 37 34-70 1-41 (127)
75 KOG2907 RNA polymerase I trans 69.1 2.7 5.9E-05 37.7 1.5 43 282-326 71-114 (116)
76 TIGR00100 hypA hydrogenase nic 68.8 2.4 5.2E-05 37.8 1.1 37 30-79 69-105 (115)
77 smart00531 TFIIE Transcription 68.8 1.4 3E-05 40.7 -0.4 35 283-327 97-136 (147)
78 TIGR01206 lysW lysine biosynth 68.0 5 0.00011 31.5 2.6 30 32-70 3-32 (54)
79 PRK14297 chaperone protein Dna 67.7 43 0.00092 35.7 10.4 26 108-133 289-318 (380)
80 PF07754 DUF1610: Domain of un 67.6 3 6.4E-05 27.6 1.1 10 59-68 15-24 (24)
81 TIGR02443 conserved hypothetic 67.6 4.1 8.9E-05 32.6 2.1 36 286-328 10-45 (59)
82 PHA02942 putative transposase; 67.6 3.1 6.7E-05 44.5 1.8 33 32-76 326-359 (383)
83 TIGR02443 conserved hypothetic 67.6 4.9 0.00011 32.2 2.5 34 32-72 10-43 (59)
84 COG5415 Predicted integral mem 66.9 2.5 5.5E-05 41.8 0.9 37 31-75 192-229 (251)
85 PF03604 DNA_RNApol_7kD: DNA d 66.6 4.2 9.2E-05 28.6 1.8 25 33-69 2-26 (32)
86 TIGR00311 aIF-2beta translatio 66.3 5.7 0.00012 36.6 3.1 31 286-324 98-128 (133)
87 PF05876 Terminase_GpA: Phage 66.1 5.5 0.00012 44.6 3.5 47 282-328 197-243 (557)
88 TIGR00100 hypA hydrogenase nic 65.7 2.8 6.1E-05 37.4 0.9 36 284-332 69-104 (115)
89 PRK06266 transcription initiat 65.4 1.6 3.5E-05 41.8 -0.7 34 30-73 116-149 (178)
90 PF07191 zinc-ribbons_6: zinc- 65.4 9.7 0.00021 31.5 3.9 47 286-332 2-48 (70)
91 COG2888 Predicted Zn-ribbon RN 65.2 7.5 0.00016 31.2 3.1 9 315-323 51-59 (61)
92 PRK03681 hypA hydrogenase nick 65.0 2.8 6.1E-05 37.4 0.8 38 30-79 69-106 (114)
93 TIGR00373 conserved hypothetic 64.8 1.6 3.4E-05 41.1 -0.9 35 30-74 108-142 (158)
94 TIGR01031 rpmF_bact ribosomal 64.6 3.6 7.7E-05 32.3 1.2 22 32-69 27-48 (55)
95 PRK00564 hypA hydrogenase nick 64.3 4.2 9E-05 36.4 1.8 38 30-79 70-107 (117)
96 COG0675 Transposase and inacti 64.2 3.8 8.3E-05 40.9 1.7 32 32-79 310-342 (364)
97 PF14803 Nudix_N_2: Nudix N-te 62.8 4.6 0.0001 28.8 1.4 30 33-69 2-31 (34)
98 PRK12286 rpmF 50S ribosomal pr 62.3 4.4 9.5E-05 32.1 1.3 23 32-70 28-50 (57)
99 PF05876 Terminase_GpA: Phage 61.8 7.5 0.00016 43.5 3.6 93 28-141 197-289 (557)
100 PTZ00037 DnaJ_C chaperone prot 61.8 40 0.00087 36.6 9.0 33 32-67 167-199 (421)
101 PHA02942 putative transposase; 61.8 4.8 0.0001 43.1 2.0 28 286-325 326-353 (383)
102 PHA02998 RNA polymerase subuni 61.7 11 0.00023 36.6 4.0 48 25-74 136-185 (195)
103 PRK12380 hydrogenase nickel in 59.9 4.2 9.1E-05 36.2 1.0 37 30-79 69-105 (113)
104 PF09526 DUF2387: Probable met 59.8 6.4 0.00014 32.5 2.0 34 286-326 9-42 (71)
105 PF09526 DUF2387: Probable met 59.6 7.3 0.00016 32.2 2.3 33 32-71 9-41 (71)
106 PF09855 DUF2082: Nucleic-acid 59.5 14 0.00031 29.9 3.9 38 287-329 2-49 (64)
107 TIGR01384 TFS_arch transcripti 59.3 13 0.00028 32.0 3.9 42 284-326 61-102 (104)
108 PRK14892 putative transcriptio 58.7 7.6 0.00016 34.1 2.3 32 32-71 22-53 (99)
109 COG1594 RPB9 DNA-directed RNA 58.1 8.7 0.00019 34.3 2.7 40 285-326 72-112 (113)
110 PF12760 Zn_Tnp_IS1595: Transp 57.9 7.1 0.00015 29.1 1.8 28 32-69 19-46 (46)
111 KOG2767 Translation initiation 57.7 4 8.7E-05 43.2 0.5 33 286-325 97-129 (400)
112 PRK14704 anaerobic ribonucleos 57.5 4.6 0.0001 45.9 1.0 25 30-70 558-582 (618)
113 PRK12380 hydrogenase nickel in 57.5 4.8 0.0001 35.8 0.9 35 284-331 69-103 (113)
114 PRK00432 30S ribosomal protein 57.2 8.4 0.00018 29.7 2.1 32 280-323 15-46 (50)
115 PRK14298 chaperone protein Dna 57.1 38 0.00082 36.2 7.7 77 32-134 159-235 (377)
116 PRK03681 hypA hydrogenase nick 57.1 4.1 8.8E-05 36.3 0.4 36 284-331 69-104 (114)
117 PF14690 zf-ISL3: zinc-finger 56.6 26 0.00057 25.5 4.7 35 32-66 3-47 (47)
118 PF01155 HypA: Hydrogenase exp 56.6 3.7 7.9E-05 36.5 0.0 37 30-79 69-105 (113)
119 PRK14296 chaperone protein Dna 56.4 61 0.0013 34.5 9.1 26 108-133 291-320 (372)
120 PF14205 Cys_rich_KTR: Cystein 55.9 9.4 0.0002 30.1 2.2 29 32-69 5-37 (55)
121 PRK14291 chaperone protein Dna 55.7 32 0.00069 36.7 6.9 32 286-324 174-205 (382)
122 PRK14892 putative transcriptio 55.7 8.4 0.00018 33.8 2.1 32 286-325 22-53 (99)
123 PF12760 Zn_Tnp_IS1595: Transp 55.5 7.7 0.00017 28.9 1.6 28 286-323 19-46 (46)
124 PHA02998 RNA polymerase subuni 55.0 17 0.00037 35.3 4.2 44 284-328 142-185 (195)
125 PRK14282 chaperone protein Dna 54.6 44 0.00096 35.4 7.7 37 286-325 170-206 (369)
126 COG4469 CoiA Competence protei 54.3 5.1 0.00011 42.1 0.7 26 285-310 25-50 (342)
127 PRK10767 chaperone protein Dna 54.3 49 0.0011 35.0 8.0 26 360-385 279-308 (371)
128 TIGR03829 YokU_near_AblA uncha 54.3 5.8 0.00012 34.3 0.8 22 60-81 35-56 (89)
129 TIGR02349 DnaJ_bact chaperone 54.2 87 0.0019 32.9 9.8 27 108-134 284-314 (354)
130 TIGR00373 conserved hypothetic 53.6 2.8 6.2E-05 39.3 -1.2 35 285-329 109-143 (158)
131 COG0675 Transposase and inacti 53.6 7.4 0.00016 38.9 1.6 22 286-323 310-331 (364)
132 TIGR00311 aIF-2beta translatio 53.0 11 0.00023 34.8 2.5 32 32-71 98-129 (133)
133 PF01873 eIF-5_eIF-2B: Domain 52.4 10 0.00023 34.5 2.3 31 286-324 94-124 (125)
134 PF00684 DnaJ_CXXCXGXG: DnaJ c 52.4 25 0.00055 28.0 4.2 36 32-70 16-51 (66)
135 PRK14292 chaperone protein Dna 52.4 41 0.0009 35.6 7.1 37 286-325 158-194 (371)
136 KOG2906 RNA polymerase III sub 52.2 12 0.00027 32.9 2.5 30 287-325 3-32 (105)
137 PRK06266 transcription initiat 52.1 3.3 7.2E-05 39.7 -1.1 32 286-327 118-149 (178)
138 PRK14282 chaperone protein Dna 51.7 60 0.0013 34.5 8.1 21 114-134 226-246 (369)
139 TIGR03655 anti_R_Lar restricti 51.4 18 0.00039 27.8 3.1 35 287-325 3-37 (53)
140 PF13597 NRDD: Anaerobic ribon 51.4 7.3 0.00016 43.6 1.3 32 28-75 488-519 (546)
141 PRK07111 anaerobic ribonucleos 51.2 7.7 0.00017 45.0 1.5 28 30-73 679-706 (735)
142 PRK00564 hypA hydrogenase nick 51.0 6.4 0.00014 35.2 0.6 36 285-332 71-106 (117)
143 PF08274 PhnA_Zn_Ribbon: PhnA 50.8 3.9 8.5E-05 28.4 -0.6 27 31-69 2-28 (30)
144 KOG2906 RNA polymerase III sub 50.7 14 0.00031 32.6 2.6 13 58-70 19-31 (105)
145 TIGR02487 NrdD anaerobic ribon 50.6 7.5 0.00016 43.8 1.3 29 30-73 523-551 (579)
146 KOG2767 Translation initiation 50.3 6.5 0.00014 41.7 0.6 33 32-71 97-129 (400)
147 PRK14288 chaperone protein Dna 50.1 52 0.0011 35.0 7.4 21 114-134 209-229 (369)
148 PF01921 tRNA-synt_1f: tRNA sy 50.1 13 0.00029 39.6 3.0 39 29-71 172-210 (360)
149 PF05180 zf-DNL: DNL zinc fing 49.9 8.3 0.00018 31.5 1.1 26 58-84 2-27 (66)
150 KOG2846 Predicted membrane pro 49.9 9.1 0.0002 40.2 1.6 42 280-329 215-257 (328)
151 PRK14291 chaperone protein Dna 49.7 49 0.0011 35.3 7.1 21 114-134 225-245 (382)
152 KOG2691 RNA polymerase II subu 49.7 24 0.00052 31.6 4.0 42 30-72 72-113 (113)
153 PRK14296 chaperone protein Dna 49.5 65 0.0014 34.3 8.0 76 33-134 168-243 (372)
154 PRK03988 translation initiatio 49.1 19 0.00041 33.4 3.4 32 32-71 103-134 (138)
155 COG1645 Uncharacterized Zn-fin 48.8 9.2 0.0002 35.3 1.3 33 29-74 26-58 (131)
156 PRK04023 DNA polymerase II lar 48.4 9.6 0.00021 45.4 1.7 72 32-146 627-698 (1121)
157 PF00684 DnaJ_CXXCXGXG: DnaJ c 48.2 26 0.00055 28.0 3.7 34 287-323 17-50 (66)
158 TIGR00244 transcriptional regu 48.0 21 0.00046 33.5 3.6 96 286-396 1-97 (147)
159 PRK04023 DNA polymerase II lar 47.8 9.5 0.00021 45.4 1.5 75 281-396 622-696 (1121)
160 PRK14289 chaperone protein Dna 47.6 54 0.0012 35.0 7.1 21 114-134 228-248 (386)
161 COG4469 CoiA Competence protei 47.2 8.3 0.00018 40.6 0.9 28 31-58 25-52 (342)
162 COG1327 Predicted transcriptio 47.0 13 0.00029 35.0 2.1 98 32-146 1-99 (156)
163 PRK09263 anaerobic ribonucleos 46.6 8.5 0.00018 44.5 0.9 29 31-70 641-669 (711)
164 COG1645 Uncharacterized Zn-fin 46.5 9.8 0.00021 35.1 1.1 34 284-330 27-60 (131)
165 PRK14289 chaperone protein Dna 46.3 50 0.0011 35.2 6.6 35 286-323 172-206 (386)
166 PF07191 zinc-ribbons_6: zinc- 46.1 24 0.00052 29.2 3.2 46 32-77 2-47 (70)
167 COG5415 Predicted integral mem 46.1 9.7 0.00021 37.8 1.1 36 286-329 193-229 (251)
168 PRK14704 anaerobic ribonucleos 45.1 10 0.00022 43.2 1.2 24 285-324 559-582 (618)
169 TIGR02349 DnaJ_bact chaperone 44.7 1E+02 0.0022 32.3 8.6 19 367-385 295-313 (354)
170 PRK14278 chaperone protein Dna 44.5 66 0.0014 34.3 7.2 21 114-134 213-233 (378)
171 TIGR00686 phnA alkylphosphonat 44.5 18 0.00039 32.3 2.4 31 32-74 3-33 (109)
172 PRK14290 chaperone protein Dna 44.5 79 0.0017 33.5 7.7 35 286-323 166-200 (365)
173 PF01921 tRNA-synt_1f: tRNA sy 44.5 13 0.00029 39.6 1.9 44 278-325 167-210 (360)
174 PRK04296 thymidine kinase; Pro 44.4 22 0.00047 33.8 3.2 46 278-323 133-187 (190)
175 COG1571 Predicted DNA-binding 44.4 9.7 0.00021 41.4 0.9 34 31-76 350-383 (421)
176 PRK00762 hypA hydrogenase nick 44.3 22 0.00047 32.2 3.0 43 30-79 69-111 (124)
177 PRK14281 chaperone protein Dna 44.2 59 0.0013 34.9 6.7 21 114-134 236-256 (397)
178 PRK14283 chaperone protein Dna 44.0 1.6E+02 0.0035 31.3 10.0 26 108-133 287-316 (378)
179 COG1856 Uncharacterized homolo 43.6 9 0.00019 38.6 0.4 29 300-328 4-36 (275)
180 TIGR00515 accD acetyl-CoA carb 43.5 5.6 0.00012 41.0 -1.0 32 30-71 25-56 (285)
181 PF13717 zinc_ribbon_4: zinc-r 43.4 15 0.00033 26.2 1.4 10 60-69 25-34 (36)
182 TIGR02827 RNR_anaer_Bdell anae 43.2 13 0.00029 42.1 1.7 29 30-73 531-559 (586)
183 PF13005 zf-IS66: zinc-finger 43.1 29 0.00063 25.5 3.0 37 285-321 2-47 (47)
184 PRK05654 acetyl-CoA carboxylas 43.0 5.8 0.00012 41.1 -1.0 32 30-71 26-57 (292)
185 COG0777 AccD Acetyl-CoA carbox 42.8 6.7 0.00015 40.4 -0.6 72 366-439 128-206 (294)
186 PF01783 Ribosomal_L32p: Ribos 42.5 5.6 0.00012 31.1 -0.9 22 32-69 27-48 (56)
187 COG1571 Predicted DNA-binding 42.5 12 0.00025 40.8 1.1 48 97-144 184-231 (421)
188 CHL00174 accD acetyl-CoA carbo 41.9 6.1 0.00013 41.0 -1.0 32 30-71 37-68 (296)
189 PF14354 Lar_restr_allev: Rest 41.3 30 0.00065 26.8 3.0 33 287-322 5-37 (61)
190 smart00653 eIF2B_5 domain pres 41.2 23 0.0005 31.6 2.6 30 32-69 81-110 (110)
191 PRK08271 anaerobic ribonucleos 41.1 11 0.00024 42.9 0.8 29 30-73 565-593 (623)
192 PF01155 HypA: Hydrogenase exp 41.1 5.3 0.00012 35.4 -1.4 36 284-332 69-104 (113)
193 PRK00762 hypA hydrogenase nick 40.1 24 0.00051 31.9 2.6 42 284-332 69-110 (124)
194 PRK14288 chaperone protein Dna 40.0 81 0.0017 33.6 6.9 33 286-325 157-189 (369)
195 PF10071 DUF2310: Zn-ribbon-co 39.9 12 0.00026 38.2 0.7 76 112-189 3-101 (258)
196 PRK09678 DNA-binding transcrip 39.9 20 0.00043 29.8 1.9 39 286-327 2-42 (72)
197 COG2824 PhnA Uncharacterized Z 39.8 60 0.0013 29.1 4.9 32 32-75 4-35 (112)
198 PRK04296 thymidine kinase; Pro 39.6 28 0.00061 33.1 3.2 45 25-69 134-187 (190)
199 TIGR00280 L37a ribosomal prote 39.5 26 0.00056 30.4 2.6 37 30-81 34-70 (91)
200 PF10071 DUF2310: Zn-ribbon-co 39.4 12 0.00027 38.1 0.7 35 27-69 216-250 (258)
201 COG1545 Predicted nucleic-acid 39.4 44 0.00095 30.8 4.3 46 28-91 26-72 (140)
202 PRK07111 anaerobic ribonucleos 39.2 15 0.00033 42.6 1.5 27 285-327 680-706 (735)
203 PRK08270 anaerobic ribonucleos 39.2 17 0.00036 41.8 1.7 28 29-73 624-651 (656)
204 PRK14294 chaperone protein Dna 38.9 1.3E+02 0.0028 32.0 8.2 26 108-133 281-310 (366)
205 PRK14279 chaperone protein Dna 38.6 80 0.0017 33.9 6.7 32 286-324 191-222 (392)
206 TIGR00515 accD acetyl-CoA carb 38.1 6.9 0.00015 40.4 -1.4 32 284-325 25-56 (285)
207 PRK14276 chaperone protein Dna 37.9 1.2E+02 0.0027 32.3 8.0 21 114-134 220-240 (380)
208 PF11023 DUF2614: Protein of u 37.9 14 0.0003 33.3 0.7 28 30-70 68-95 (114)
209 PF05180 zf-DNL: DNL zinc fing 37.8 16 0.00035 29.9 1.0 27 311-338 1-27 (66)
210 CHL00174 accD acetyl-CoA carbo 37.7 7.1 0.00015 40.6 -1.3 32 284-325 37-68 (296)
211 TIGR01385 TFSII transcription 37.6 34 0.00074 35.6 3.6 39 31-71 258-297 (299)
212 PRK14295 chaperone protein Dna 37.5 91 0.002 33.4 6.9 21 114-134 236-256 (389)
213 PRK05654 acetyl-CoA carboxylas 37.3 7.3 0.00016 40.3 -1.3 32 284-325 26-57 (292)
214 PRK10767 chaperone protein Dna 37.3 86 0.0019 33.2 6.6 20 114-133 212-231 (371)
215 PRK09710 lar restriction allev 37.2 34 0.00073 27.9 2.7 29 33-69 8-36 (64)
216 TIGR02098 MJ0042_CXXC MJ0042 f 36.6 17 0.00036 25.7 0.8 12 59-70 1-12 (38)
217 COG1885 Uncharacterized protei 36.6 36 0.00077 30.4 3.0 39 53-91 42-80 (115)
218 TIGR02487 NrdD anaerobic ribon 36.6 18 0.00038 40.9 1.4 28 285-327 524-551 (579)
219 PRK14300 chaperone protein Dna 36.3 1E+02 0.0022 32.8 7.0 33 285-324 162-194 (372)
220 PRK14290 chaperone protein Dna 36.1 1.5E+02 0.0032 31.5 8.2 21 114-134 222-242 (365)
221 COG1655 Uncharacterized protei 36.0 17 0.00036 36.7 1.0 37 30-70 18-72 (267)
222 PRK09678 DNA-binding transcrip 35.7 28 0.0006 28.9 2.1 39 32-73 2-42 (72)
223 PF02150 RNA_POL_M_15KD: RNA p 35.4 23 0.00049 25.2 1.3 27 288-324 4-30 (35)
224 PRK14285 chaperone protein Dna 35.4 82 0.0018 33.4 6.1 32 286-324 164-195 (365)
225 PF13894 zf-C2H2_4: C2H2-type 35.4 18 0.00038 21.9 0.7 12 61-72 1-12 (24)
226 PF08271 TF_Zn_Ribbon: TFIIB z 35.3 39 0.00084 24.7 2.6 31 33-73 2-32 (43)
227 PRK14294 chaperone protein Dna 35.0 1E+02 0.0022 32.6 6.8 21 114-134 214-234 (366)
228 COG1655 Uncharacterized protei 34.9 18 0.0004 36.5 1.1 38 283-324 17-72 (267)
229 PRK14301 chaperone protein Dna 34.6 93 0.002 33.1 6.4 21 114-134 214-234 (373)
230 TIGR00280 L37a ribosomal prote 34.6 34 0.00074 29.7 2.5 39 281-334 31-69 (91)
231 COG0333 RpmF Ribosomal protein 34.6 21 0.00045 28.5 1.1 23 31-69 27-49 (57)
232 PRK14279 chaperone protein Dna 34.5 1.1E+02 0.0024 32.8 6.9 21 114-134 243-263 (392)
233 PRK14300 chaperone protein Dna 34.3 1.4E+02 0.0031 31.7 7.7 21 114-134 215-235 (372)
234 COG1096 Predicted RNA-binding 34.3 28 0.00061 34.0 2.2 33 278-323 142-174 (188)
235 PF06054 CoiA: Competence prot 34.2 17 0.00037 38.7 0.8 36 283-320 28-63 (375)
236 COG0375 HybF Zn finger protein 34.1 26 0.00056 31.7 1.8 39 30-81 69-107 (115)
237 PF13597 NRDD: Anaerobic ribon 34.1 17 0.00038 40.7 0.9 29 284-328 490-518 (546)
238 PF05907 DUF866: Eukaryotic pr 34.0 23 0.00049 33.6 1.5 47 280-326 25-76 (161)
239 PRK10220 hypothetical protein; 33.9 34 0.00074 30.7 2.4 30 32-73 4-33 (111)
240 PTZ00255 60S ribosomal protein 33.8 36 0.00078 29.5 2.5 39 281-334 32-70 (90)
241 PRK00750 lysK lysyl-tRNA synth 33.5 48 0.001 36.9 4.2 42 280-326 170-211 (510)
242 cd01675 RNR_III Class III ribo 33.5 19 0.00041 40.4 1.1 26 33-73 520-545 (555)
243 PRK14287 chaperone protein Dna 33.4 1.7E+02 0.0037 31.1 8.1 22 113-134 211-232 (371)
244 COG3877 Uncharacterized protei 33.4 32 0.0007 30.8 2.2 24 30-68 5-28 (122)
245 PRK02935 hypothetical protein; 33.4 24 0.00052 31.5 1.4 27 284-323 69-95 (110)
246 PRK09263 anaerobic ribonucleos 33.3 17 0.00036 42.2 0.6 28 286-324 642-669 (711)
247 PRK00420 hypothetical protein; 33.3 20 0.00043 32.2 0.9 27 284-322 22-48 (112)
248 PF12773 DZR: Double zinc ribb 33.2 18 0.00039 26.9 0.5 28 31-70 12-39 (50)
249 TIGR02827 RNR_anaer_Bdell anae 33.2 22 0.00047 40.4 1.4 27 285-327 532-559 (586)
250 PF06138 Chordopox_E11: Chordo 32.9 51 0.0011 30.4 3.5 29 155-183 32-61 (130)
251 PF10122 Mu-like_Com: Mu-like 32.7 24 0.00052 27.6 1.1 36 286-331 5-40 (51)
252 TIGR02300 FYDLN_acid conserved 32.7 16 0.00035 33.6 0.2 28 30-70 8-36 (129)
253 PF09538 FYDLN_acid: Protein o 32.7 15 0.00033 32.7 0.1 29 30-71 8-37 (108)
254 PRK14280 chaperone protein Dna 32.7 1.7E+02 0.0036 31.3 7.9 21 114-134 217-237 (376)
255 COG0777 AccD Acetyl-CoA carbox 32.6 12 0.00027 38.5 -0.5 34 28-71 25-58 (294)
256 PF10609 ParA: ParA/MinD ATPas 32.5 19 0.00042 30.5 0.7 13 59-71 64-76 (81)
257 COG2816 NPY1 NTP pyrophosphohy 32.4 47 0.001 34.4 3.6 44 287-348 113-156 (279)
258 PRK14276 chaperone protein Dna 32.4 1.6E+02 0.0034 31.5 7.7 36 286-324 164-199 (380)
259 PF01873 eIF-5_eIF-2B: Domain 32.3 38 0.00081 30.9 2.6 31 32-70 94-124 (125)
260 TIGR01385 TFSII transcription 32.3 46 0.00099 34.7 3.5 39 285-324 258-296 (299)
261 PF00265 TK: Thymidine kinase; 32.2 21 0.00046 34.0 1.0 38 5-48 117-154 (176)
262 PRK14278 chaperone protein Dna 32.2 1.3E+02 0.0029 32.0 7.1 35 286-323 157-191 (378)
263 PRK03976 rpl37ae 50S ribosomal 32.2 40 0.00086 29.3 2.5 39 281-334 32-70 (90)
264 PRK14293 chaperone protein Dna 32.1 1.2E+02 0.0025 32.4 6.6 20 115-134 218-237 (374)
265 PRK00750 lysK lysyl-tRNA synth 31.6 60 0.0013 36.1 4.5 39 28-71 172-210 (510)
266 PHA03001 putative virion core 31.5 57 0.0012 30.1 3.6 30 155-184 31-61 (132)
267 PRK14285 chaperone protein Dna 31.3 1.2E+02 0.0025 32.3 6.4 21 114-134 216-236 (365)
268 PF05907 DUF866: Eukaryotic pr 31.1 51 0.0011 31.2 3.3 46 27-72 26-76 (161)
269 PF00265 TK: Thymidine kinase; 30.7 23 0.0005 33.7 1.0 25 278-302 130-154 (176)
270 PF06750 DiS_P_DiS: Bacterial 30.2 13 0.00027 32.1 -0.8 38 30-71 32-69 (92)
271 PRK14277 chaperone protein Dna 30.0 1.4E+02 0.003 31.9 6.8 21 114-134 229-249 (386)
272 COG1096 Predicted RNA-binding 29.9 49 0.0011 32.4 3.0 32 25-69 143-174 (188)
273 COG1856 Uncharacterized homolo 29.8 26 0.00055 35.5 1.1 27 46-72 4-34 (275)
274 PF09723 Zn-ribbon_8: Zinc rib 29.8 36 0.00077 25.0 1.6 19 60-78 5-23 (42)
275 PRK14295 chaperone protein Dna 29.7 2.8E+02 0.006 29.8 9.0 27 108-134 303-334 (389)
276 PRK14298 chaperone protein Dna 29.6 56 0.0012 34.9 3.7 34 286-322 159-192 (377)
277 cd04476 RPA1_DBD_C RPA1_DBD_C: 29.4 44 0.00095 31.0 2.6 31 284-326 33-63 (166)
278 PF01780 Ribosomal_L37ae: Ribo 29.0 13 0.00029 32.1 -0.8 38 282-334 32-69 (90)
279 COG3478 Predicted nucleic-acid 28.9 42 0.00092 27.5 2.0 11 59-69 39-49 (68)
280 COG5349 Uncharacterized protei 28.4 16 0.00034 33.4 -0.6 32 30-71 20-51 (126)
281 smart00834 CxxC_CXXC_SSSS Puta 28.1 40 0.00087 23.7 1.6 11 58-68 24-34 (41)
282 PRK14281 chaperone protein Dna 28.0 1.1E+02 0.0024 32.8 5.7 34 286-322 180-213 (397)
283 PRK03922 hypothetical protein; 28.0 60 0.0013 29.2 3.0 39 53-91 42-80 (113)
284 PRK08271 anaerobic ribonucleos 27.9 27 0.0006 39.9 1.1 28 285-327 566-593 (623)
285 PRK14297 chaperone protein Dna 27.3 1.5E+02 0.0034 31.5 6.6 35 286-323 166-200 (380)
286 PF04216 FdhE: Protein involve 27.0 42 0.00091 34.3 2.2 43 283-326 170-223 (290)
287 PF13909 zf-H2C2_5: C2H2-type 26.8 29 0.00062 21.9 0.6 11 61-71 1-11 (24)
288 PRK01110 rpmF 50S ribosomal pr 26.5 37 0.00081 27.1 1.3 22 32-70 28-49 (60)
289 cd02660 Peptidase_C19D A subfa 26.5 91 0.002 31.5 4.5 90 281-373 130-252 (328)
290 PF05502 Dynactin_p62: Dynacti 26.4 39 0.00084 37.4 1.9 42 286-327 53-99 (483)
291 PF06054 CoiA: Competence prot 26.3 31 0.00067 36.8 1.1 36 29-66 28-63 (375)
292 PF05129 Elf1: Transcription e 26.2 37 0.0008 28.6 1.3 34 286-324 23-56 (81)
293 PTZ00037 DnaJ_C chaperone prot 26.0 1.4E+02 0.0031 32.4 6.1 26 360-385 291-323 (421)
294 PF09297 zf-NADH-PPase: NADH p 25.5 38 0.00083 23.2 1.1 10 60-69 21-30 (32)
295 PRK08270 anaerobic ribonucleos 25.5 34 0.00075 39.3 1.3 26 285-327 626-651 (656)
296 PTZ00293 thymidine kinase; Pro 25.4 57 0.0012 32.4 2.7 41 278-321 130-176 (211)
297 TIGR00467 lysS_arch lysyl-tRNA 25.3 64 0.0014 36.1 3.3 40 280-326 163-202 (515)
298 PF13719 zinc_ribbon_5: zinc-r 25.0 36 0.00077 24.3 0.9 25 59-85 1-25 (37)
299 PF09567 RE_MamI: MamI restric 24.8 56 0.0012 33.5 2.5 63 33-122 84-160 (314)
300 TIGR00467 lysS_arch lysyl-tRNA 24.8 71 0.0015 35.7 3.6 37 28-71 165-201 (515)
301 cd02661 Peptidase_C19E A subfa 24.6 1.3E+02 0.0028 29.7 5.1 86 283-373 133-236 (304)
302 PF00096 zf-C2H2: Zinc finger, 24.6 28 0.0006 21.5 0.2 11 61-71 1-11 (23)
303 PRK08579 anaerobic ribonucleos 24.6 31 0.00067 39.5 0.7 29 30-73 567-595 (625)
304 TIGR03825 FliH_bacil flagellar 24.6 1.5E+02 0.0033 29.7 5.6 64 131-195 161-227 (255)
305 PF06138 Chordopox_E11: Chordo 24.5 84 0.0018 29.0 3.3 29 409-437 32-61 (130)
306 PF06044 DRP: Dam-replacing fa 24.5 48 0.001 33.7 2.0 39 31-77 31-69 (254)
307 COG2023 RPR2 RNase P subunit R 24.4 72 0.0016 28.5 2.8 34 286-325 57-93 (105)
308 PF13465 zf-H2C2_2: Zinc-finge 24.3 27 0.00058 22.9 0.1 10 61-70 15-24 (26)
309 PHA03001 putative virion core 23.7 90 0.002 28.8 3.4 30 409-438 31-61 (132)
310 COG3677 Transposase and inacti 23.4 51 0.0011 30.1 1.8 40 27-72 26-65 (129)
311 TIGR00595 priA primosomal prot 23.3 45 0.00097 37.0 1.7 11 287-297 224-234 (505)
312 COG3049 Penicillin V acylase a 23.2 1E+02 0.0023 32.8 4.2 22 172-193 158-179 (353)
313 COG3677 Transposase and inacti 23.2 51 0.0011 30.1 1.7 42 280-327 25-66 (129)
314 COG4306 Uncharacterized protei 23.1 37 0.0008 31.3 0.8 40 286-325 40-79 (160)
315 COG3877 Uncharacterized protei 22.8 61 0.0013 29.1 2.1 20 379-399 70-89 (122)
316 KOG2879 Predicted E3 ubiquitin 22.5 44 0.00094 34.6 1.3 31 281-321 235-283 (298)
317 PF04216 FdhE: Protein involve 22.4 47 0.001 33.9 1.5 43 30-73 171-224 (290)
318 COG1198 PriA Primosomal protei 22.4 47 0.001 38.7 1.6 10 314-323 462-471 (730)
319 PF08921 DUF1904: Domain of un 22.3 1.4E+02 0.003 26.6 4.2 55 159-216 17-72 (108)
320 KOG3022 Predicted ATPase, nucl 22.2 37 0.00081 35.3 0.8 43 302-344 209-255 (300)
321 COG5595 Zn-ribbon-containing, 22.2 33 0.00072 33.9 0.4 72 112-186 3-97 (256)
322 PRK14873 primosome assembly pr 22.1 50 0.0011 38.1 1.8 15 178-192 260-274 (665)
323 cd01675 RNR_III Class III ribo 22.0 39 0.00086 37.9 0.9 27 286-327 519-545 (555)
324 COG1998 RPS31 Ribosomal protei 22.0 66 0.0014 25.1 1.8 34 279-323 13-46 (51)
325 cd02664 Peptidase_C19H A subfa 21.6 1.6E+02 0.0035 30.2 5.3 91 281-373 106-212 (327)
326 PF05605 zf-Di19: Drought indu 21.5 37 0.0008 25.9 0.4 8 61-68 3-10 (54)
327 cd02668 Peptidase_C19L A subfa 21.5 1.7E+02 0.0038 29.8 5.5 90 282-373 126-234 (324)
328 COG1885 Uncharacterized protei 21.2 66 0.0014 28.8 2.0 36 313-348 48-83 (115)
329 PF14584 DUF4446: Protein of u 21.2 3E+02 0.0065 25.9 6.5 61 129-193 42-116 (151)
330 COG5222 Uncharacterized conser 21.2 19 0.0004 37.6 -1.6 44 284-327 273-323 (427)
331 TIGR00630 uvra excinuclease AB 21.2 61 0.0013 38.8 2.3 31 32-68 737-767 (924)
332 PF11672 DUF3268: Protein of u 21.1 64 0.0014 28.6 1.9 12 285-296 2-13 (102)
333 PF13754 Big_3_4: Bacterial Ig 20.9 67 0.0015 24.6 1.8 20 171-190 22-41 (54)
334 COG1675 TFA1 Transcription ini 20.8 22 0.00047 34.4 -1.2 37 30-76 112-148 (176)
335 PF14122 YokU: YokU-like prote 20.7 51 0.0011 28.4 1.1 23 60-82 35-57 (87)
336 PLN03165 chaperone protein dna 20.7 1.3E+02 0.0028 27.0 3.8 32 287-324 54-85 (111)
337 TIGR02605 CxxC_CxxC_SSSS putat 20.6 67 0.0015 24.0 1.7 9 62-70 28-36 (52)
338 KOG2593 Transcription initiati 20.6 34 0.00073 37.3 0.0 31 30-67 127-160 (436)
339 COG1435 Tdk Thymidine kinase [ 20.4 32 0.00069 34.0 -0.2 42 27-68 140-190 (201)
340 cd07241 Glo_EDI_BRP_like_3 Thi 20.4 1.8E+02 0.0039 24.0 4.5 14 176-189 109-122 (125)
341 PLN03165 chaperone protein dna 20.3 1.5E+02 0.0032 26.7 4.0 32 33-70 54-85 (111)
342 PF05502 Dynactin_p62: Dynacti 20.2 72 0.0016 35.4 2.5 65 285-349 298-377 (483)
343 KOG3262 H/ACA small nucleolar 20.1 39 0.00084 33.1 0.3 36 278-313 50-85 (215)
344 PTZ00073 60S ribosomal protein 20.1 45 0.00098 29.0 0.7 34 283-330 14-47 (91)
No 1
>KOG2703 consensus C4-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=1.1e-148 Score=1127.24 Aligned_cols=450 Identities=52% Similarity=0.861 Sum_probs=422.1
Q ss_pred CCCCcccccccccchhccc--------cCCCCCCceEEeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccc
Q 011230 1 MENNKEEIVDVGSVVEAVS--------ADDSDAPLYQVESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNE 72 (490)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~--------~~~~~~~v~eies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnE 72 (490)
|++++++|.++|++|+.++ ++..+++++|++|+||+||++|+|||++|+||||||||||||+|||||+|||+
T Consensus 1 ~~~~~~~~~~~~~~a~~v~~~ik~~~~ed~~~~~~~EvES~Cm~Cg~nG~TRlllT~IP~fREvVimSF~CpHCG~kN~e 80 (460)
T KOG2703|consen 1 SENKEDLFIPPGEAAANVSPLIKREGAEDVEGNPVQEVESLCMNCGENGTTRLLLTSIPYFREVVIMSFECPHCGHKNNE 80 (460)
T ss_pred CCccccCCCChhHhhcccchhhhhhhhhhhhcCchHHHHHhhhhcccCCceeEEEeecchhheeeeEEeecCccCCcccc
Confidence 4567889999999999874 35588999999999999999999999999999999999999999999999999
Q ss_pred eeeccccCCcceEEEEEeeCCCcccccceEEecCccEEEEeeeeeEeCCCCCCCceeeHHHHHHHHHHHHHHhhHHHhcC
Q 011230 73 VQFAGEIQPRGCNYSLKVPSSDQKMFHRQVVKSESATIKIPELDFEIPPEAQRGSLSTVEGILVRAADELEALQEERKKL 152 (490)
Q Consensus 73 vq~~g~i~~kG~r~tl~V~~~~~~DLnR~VvkS~~ati~IPEL~~eI~p~~~~G~iTTVEGlL~~~~~~L~~~~~~r~~~ 152 (490)
||+++.+|++|+||+|+|. +.+|||||||||++|+|+||||+||||+.+|+|.||||||+|.|++++|+++|+.|+..
T Consensus 81 iQ~a~~iQ~~Gvri~l~V~--s~EDlnRqVvkSe~Asi~IpEldlEIP~~Sq~GslTTVEGiL~r~~d~LsqdQekRr~~ 158 (460)
T KOG2703|consen 81 IQSAEEIQEGGVRIELRVQ--SVEDLNRQVVKSESASIEIPELDLEIPAKSQKGSLTTVEGILERVIDGLSQDQEKRRIT 158 (460)
T ss_pred ccchhccccCceEEEEEec--cHHHhhhHhhhcccceeecccceeeccccccCCceeehHHHHHHHHHHHhhhhhhhccc
Confidence 9999999999999999999 99999999999999999999999999999999999999999999999999999999999
Q ss_pred CHHHHHHHHHHHHHHHHhhcCCCcEEEEEECCCCCeeeecCCCCCCCCCeeEEEecCCHHHHHHcCCCCCCCccCCCCCC
Q 011230 153 DPQTAEAIDQFLLKLRACAKGDSTFTFILDDPAGNSFIENLYAPSPDPSLNIKFYERTPEQQALLGYLVDPSQQGESSNV 232 (490)
Q Consensus 153 ~~e~~~ki~~~i~kL~~~~~g~~pFTliidDPsGNS~I~~~~ap~~D~~~~~~~y~Rt~eq~~~LGl~~~~~~~~~~~~~ 232 (490)
+|+.+++|++|+.||+.++.+..|||||++||+|||||+++.+|..||+|++.+|.||.+||+.|||...++.+.+-
T Consensus 159 ~pa~a~~Id~fi~kl~s~k~~~~pftlildDp~GNS~iEnp~~p~~dp~~~~~~y~Rt~eqne~lgl~~~~~~e~~~--- 235 (460)
T KOG2703|consen 159 DPATAKQIDDFIVKLKSLKELTTPFTLILDDPTGNSFIENPHAPRVDPRLKIVHYLRTLEQNELLGLVDKNQEESEV--- 235 (460)
T ss_pred CHHHHHHHHHHHHHHHHHhhcCCceEEEecCCCCCccccCCCCCCCCCcceeEEEecCHhHHHhhccccccchhhhc---
Confidence 99999999999999999999999999999999999999999999999999999999999999999999776544220
Q ss_pred CCCCCCCCCCCCCCCCCCccccccccccccCCcHHHHHhhhccCCCCcceEeeccCcCCccccceeEEEeecCCCCcEEE
Q 011230 233 VPSEGLSSTSDKREPRGSVGAVAGHRAIAQSNSAEIADALFRYSAPEEVMTFPSTCGACAASCETRMFMTRIPYFQEVIV 312 (490)
Q Consensus 233 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ev~~~~s~Cp~C~~~~~t~m~~~~IP~FkeviI 312 (490)
.+. ++.++. .+.++ +++||+.|++.||+|.+++.|+|++++|||||||||
T Consensus 236 ~k~------------------------~a~~~~-~di~~-----~~~EV~~F~t~Cp~C~~pcet~Mk~~~IPhFkeVIi 285 (460)
T KOG2703|consen 236 LKP------------------------IAASEA-TDIED-----APNEVLTFPTTCPSCTAPCETNMKLTDIPHFKEVII 285 (460)
T ss_pred ccc------------------------cccccc-chhhc-----cccceEEccCCCCCCCCchhccceeccCCcceeEEE
Confidence 000 001111 11222 389999999999999999999999999999999999
Q ss_pred EEeecCCCCCCccccccCCCCCCCCeEEEEEEcCcccccceeeeeCceeEEecceeeeecCCCccceeEeHHHHHHHHHH
Q 011230 313 MASTCDACGYRNSELKPGGRIPEKGKRITLFVKNINDLSRDLIKSDTAGVKIPELDLELAGGTLGGIVTTVEGLITKISE 392 (490)
Q Consensus 313 msf~C~~CGyr~nEVk~gg~i~~kG~ritL~V~~~eDL~R~VlKS~ta~v~IPEL~lei~pGtl~G~~TTVEGlL~~i~d 392 (490)
||++|++||||+||||+||+|+++|+||||+|.+.+||+||||||+||++.||||+|++.+|+|||+||||||||.++++
T Consensus 286 Mst~Cd~CGyksnEvKsGGai~~~G~ritl~~~~~~DlsRDvlKseTcs~~IPEl~lel~~~~LgGrfTTiEGLl~~~~e 365 (460)
T KOG2703|consen 286 MSTVCDRCGYKSNEVKSGGAIPDKGRRITLKVEDAEDLSRDVLKSETCSLSIPELDLELGGGTLGGRFTTIEGLLTQIRE 365 (460)
T ss_pred EeecccccCCccccccCCCCcCCCCcEEEEEecchHhhhHHHhhccccceeccccceeccCccccceeeeHHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhccCcCCCCCCCHHHHHHHHHHHHHHHHhhcCCCceEEEEEcCCCCccccCCCCCCCCCCCeEEEEecCCHHHHHhc
Q 011230 393 SLERVHGFSFGDSLDENKRTKWQDFKAKLNKLLSVEESWTLILDDALANSFIAPVTDDIKDDHQLTFEEYERSWEQNEEL 472 (490)
Q Consensus 393 ~L~~~~~~~~gds~~~e~~~k~~~fl~~L~~~~~g~~~fTlIidDP~GnS~I~~~~~~p~~Dp~l~~~~Y~RT~eqne~L 472 (490)
+|.. ++|..+||+++..+++|.+|+++|.++++|+.|||||||||+||||| ||+|||++||+|++|+|+|||||||+|
T Consensus 366 ~l~~-~~f~~~DS~~~~~~~~~~~F~~~l~~~i~~~~~~tlIldDp~~~syv-q~~~ap~~dp~lt~E~Y~Rt~eqNeeL 443 (460)
T KOG2703|consen 366 QLDG-RSFTFGDSMDEGQKARWQEFLAKLDDIIAGKLPATLILDDPLGNSYV-QNVYAPDDDPNLTVEEYERTYEQNEEL 443 (460)
T ss_pred HHhc-CceeccccCCHHHHHHHHHHHHHHHHHHhcccceEEEeecCCcCccc-ccccCCCCCCcccHHHhhhhhhhhhhc
Confidence 9998 56878999999999999999999999999999999999999999999 999999999999999999999999999
Q ss_pred CCCCCCCCchhhhcc
Q 011230 473 GLNDIDTSSADAAYN 487 (490)
Q Consensus 473 Gl~dm~~e~y~~~~~ 487 (490)
||||||||||++++.
T Consensus 444 GlnDmkte~yE~~~~ 458 (460)
T KOG2703|consen 444 GLNDMKTENYEEDEP 458 (460)
T ss_pred CccccccccccccCC
Confidence 999999999988754
No 2
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=100.00 E-value=2.8e-67 Score=500.50 Aligned_cols=188 Identities=34% Similarity=0.616 Sum_probs=180.7
Q ss_pred cCcCCccccceeEEEee-cCCCCcEEEEEeecCCCCCCccccccCCCCCCCCeEEEEEEcCcccccceeeeeCceeEEec
Q 011230 287 TCGACAASCETRMFMTR-IPYFQEVIVMASTCDACGYRNSELKPGGRIPEKGKRITLFVKNINDLSRDLIKSDTAGVKIP 365 (490)
Q Consensus 287 ~Cp~C~~~~~t~m~~~~-IP~FkeviImsf~C~~CGyr~nEVk~gg~i~~kG~ritL~V~~~eDL~R~VlKS~ta~v~IP 365 (490)
.||+||+++.++|++++ |||||+||||||.|+|||||+|||+++|+++++ ||+|+|++++||+|+||||++|+|.||
T Consensus 2 ~Cp~C~~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~ev~~~g~~~p~--r~~l~V~~~~DL~r~VvkS~tati~IP 79 (192)
T TIGR00310 2 DCPSCGGECETVMKTVNDIPYFGEVLETSTICEHCGYRSNDVKTLGAKEPK--RYILKIDDEADLNRRVVKSESATIRIP 79 (192)
T ss_pred cCCCCCCCCEEEEEEEcCCCCcceEEEEEEECCCCCCccceeEECCCCCCE--EEEEEECChhcccceEEEcCCcEEEcc
Confidence 59999999999999999 999999999999999999999999999999866 999999999999999999999999999
Q ss_pred ceeeeecCC-CccceeEeHHHHHHHHHHHHhhccCcCCCCCCCHHHHHHHHHHHHHHHHhhcCCCceEEEEEcCCCCccc
Q 011230 366 ELDLELAGG-TLGGIVTTVEGLITKISESLERVHGFSFGDSLDENKRTKWQDFKAKLNKLLSVEESWTLILDDALANSFI 444 (490)
Q Consensus 366 EL~lei~pG-tl~G~~TTVEGlL~~i~d~L~~~~~~~~gds~~~e~~~k~~~fl~~L~~~~~g~~~fTlIidDP~GnS~I 444 (490)
||+|+|+|| +++|+||||||||+++++.|+.... .|+.+++.++||++|+++|+++++|+.|||||||||+|||||
T Consensus 80 El~lei~pg~~~~G~iTTVEGlL~~~~~~L~~~~~---~d~~~~e~~~k~~~~i~kL~~~~~g~~pfTlIidDP~GNS~I 156 (192)
T TIGR00310 80 ELGLDIEPGPTSGGFITNLEGVLRRVEEELETAIR---WQSEDEETKKRAEEILERLKEAIEGKEKFTVILEDPLGGSYI 156 (192)
T ss_pred ceEEEECCCccCCceEEeeHhHHHHHHHHHHhhhh---ccccCHHHHHHHHHHHHHHHHHHhCCCCEEEEEECCCCCeee
Confidence 999999999 4899999999999999999998532 267788999999999999999999999999999999999999
Q ss_pred cCCCCCCCCCCC-eEEEEecCCHHHHHhcCCCCCCCC
Q 011230 445 APVTDDIKDDHQ-LTFEEYERSWEQNEELGLNDIDTS 480 (490)
Q Consensus 445 ~~~~~~p~~Dp~-l~~~~Y~RT~eqne~LGl~dm~~e 480 (490)
+|++||+.||+ |++++|.||+|||++|||+||+||
T Consensus 157 -~~~~a~~~d~~~~~~~~y~rt~eq~~~lGl~~~~~e 192 (192)
T TIGR00310 157 -QNVYAPKEILSEEEIEDLKTGKEINEDLGLSDEEVE 192 (192)
T ss_pred -ecCCCCCCCCcccEeeecCCCHHHHHhcCCcccccC
Confidence 99999999999 999999999999999999999997
No 3
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=100.00 E-value=3.4e-65 Score=486.18 Aligned_cols=184 Identities=38% Similarity=0.609 Sum_probs=178.2
Q ss_pred cCCccCCCceEEEEEee-cCCccceEEEEeecCCCCCCccceeeccccCCcceEEEEEeeCCCcccccceEEecCccEEE
Q 011230 33 LCMRCGENGVTRFLLTL-IPHFRKVLLSAFECPHCGERNNEVQFAGEIQPRGCNYSLKVPSSDQKMFHRQVVKSESATIK 111 (490)
Q Consensus 33 ~Cp~Cg~~g~trlllt~-IP~F~eviimSf~C~~CGyrnnEvq~~g~i~~kG~r~tl~V~~~~~~DLnR~VvkS~~ati~ 111 (490)
.||+||++|+|++++|+ |||||+||||||.|+||||||||||++|+++|+ ||+|+|+ +++||+||||||++|+|+
T Consensus 2 ~Cp~C~~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~ev~~~g~~~p~--r~~l~V~--~~~DL~r~VvkS~tati~ 77 (192)
T TIGR00310 2 DCPSCGGECETVMKTVNDIPYFGEVLETSTICEHCGYRSNDVKTLGAKEPK--RYILKID--DEADLNRRVVKSESATIR 77 (192)
T ss_pred cCCCCCCCCEEEEEEEcCCCCcceEEEEEEECCCCCCccceeEECCCCCCE--EEEEEEC--ChhcccceEEEcCCcEEE
Confidence 59999999999999999 999999999999999999999999999999997 9999999 999999999999999999
Q ss_pred EeeeeeEeCCC-CCCCceeeHHHHHHHHHHHHHHhhHHHh-cCCHHHHHHHHHHHHHHHHhhcCCCcEEEEEECCCCCee
Q 011230 112 IPELDFEIPPE-AQRGSLSTVEGILVRAADELEALQEERK-KLDPQTAEAIDQFLLKLRACAKGDSTFTFILDDPAGNSF 189 (490)
Q Consensus 112 IPEL~~eI~p~-~~~G~iTTVEGlL~~~~~~L~~~~~~r~-~~~~e~~~ki~~~i~kL~~~~~g~~pFTliidDPsGNS~ 189 (490)
||||+|||||+ +++|+||||||+|++++++|+... ++ +.+++.++|+++|+++|+++++|+.|||||||||+||||
T Consensus 78 IPEl~lei~pg~~~~G~iTTVEGlL~~~~~~L~~~~--~~d~~~~e~~~k~~~~i~kL~~~~~g~~pfTlIidDP~GNS~ 155 (192)
T TIGR00310 78 IPELGLDIEPGPTSGGFITNLEGVLRRVEEELETAI--RWQSEDEETKKRAEEILERLKEAIEGKEKFTVILEDPLGGSY 155 (192)
T ss_pred ccceEEEECCCccCCceEEeeHhHHHHHHHHHHhhh--hccccCHHHHHHHHHHHHHHHHHHhCCCCEEEEEECCCCCee
Confidence 99999999996 799999999999999999999975 55 789999999999999999999999999999999999999
Q ss_pred eecCCCCCCCCC-eeEEEecCCHHHHHHcCCCCC
Q 011230 190 IENLYAPSPDPS-LNIKFYERTPEQQALLGYLVD 222 (490)
Q Consensus 190 I~~~~ap~~D~~-~~~~~y~Rt~eq~~~LGl~~~ 222 (490)
|+|++||..||+ |++++|.||++||++|||...
T Consensus 156 I~~~~a~~~d~~~~~~~~y~rt~eq~~~lGl~~~ 189 (192)
T TIGR00310 156 IQNVYAPKEILSEEEIEDLKTGKEINEDLGLSDE 189 (192)
T ss_pred eecCCCCCCCCcccEeeecCCCHHHHHhcCCccc
Confidence 999999999999 999999999999999999753
No 4
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=100.00 E-value=6.6e-60 Score=438.68 Aligned_cols=159 Identities=55% Similarity=0.904 Sum_probs=154.5
Q ss_pred ccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccceeeccccCCcceEEEEEeeCCCcccccceEEecCccEEE
Q 011230 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEIQPRGCNYSLKVPSSDQKMFHRQVVKSESATIK 111 (490)
Q Consensus 32 s~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEvq~~g~i~~kG~r~tl~V~~~~~~DLnR~VvkS~~ati~ 111 (490)
|+||+||++|+||+++|+||||||||||||.|+||||||||||++|+++|+|+||+|+|+ +++||||+||||++|+|+
T Consensus 1 s~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~~ev~~~~~~~p~G~r~~l~V~--~~~DL~r~VvkS~ta~i~ 78 (160)
T smart00709 1 SDCPSCGGNGTTRMLLTSIPYFREVIIMSFECEHCGYRNNEVKSGGAIEPKGTRITLKVE--SPEDLNRDVVKSETATIS 78 (160)
T ss_pred CcCCCCCCCCEEEEEEecCCCcceEEEEEEECCCCCCccceEEECcccCCCceEEEEEEC--ChhhccceEEEcCCcEEE
Confidence 689999999999999999999999999999999999999999999999999999999999 999999999999999999
Q ss_pred EeeeeeEeCCCCCCCceeeHHHHHHHHHHHHHHh-hHHHhcCCHHHHHHHHHHHHHHHHhhcCCCcEEEEEECCCCCeee
Q 011230 112 IPELDFEIPPEAQRGSLSTVEGILVRAADELEAL-QEERKKLDPQTAEAIDQFLLKLRACAKGDSTFTFILDDPAGNSFI 190 (490)
Q Consensus 112 IPEL~~eI~p~~~~G~iTTVEGlL~~~~~~L~~~-~~~r~~~~~e~~~ki~~~i~kL~~~~~g~~pFTliidDPsGNS~I 190 (490)
||||+|||||++++|+||||||+|++++++|+.. ++.++..+++.++|+++|+++|+++++|+.|||||||||+|||||
T Consensus 79 IPEl~~ei~pg~~~g~itTVEGlL~~i~~~L~~~~~~~~~~~~~e~~~k~~~~~~~L~~~~~g~~~fTliidDP~GnS~I 158 (160)
T smart00709 79 IPELDLEIPPGPLGGFITTVEGLLSRVREVLSQAIQETRDDSDPETKEKIDEFLEKLKELIEGKEPFTLILDDPAGNSYI 158 (160)
T ss_pred eeeeeEEecCCCCCcEEEehHHHHHHHHHHHHhhhhhhcccCCHHHHHHHHHHHHHHHHHHcCCCCEEEEEECCCCceec
Confidence 9999999999889999999999999999999998 666766789999999999999999999999999999999999999
Q ss_pred ec
Q 011230 191 EN 192 (490)
Q Consensus 191 ~~ 192 (490)
+|
T Consensus 159 ~~ 160 (160)
T smart00709 159 QN 160 (160)
T ss_pred cC
Confidence 85
No 5
>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 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 ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.
Probab=100.00 E-value=7.6e-60 Score=438.93 Aligned_cols=160 Identities=54% Similarity=0.916 Sum_probs=139.9
Q ss_pred eccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccceeeccccCCcceEEEEEeeCCCcccccceEEecCccEE
Q 011230 31 ESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEIQPRGCNYSLKVPSSDQKMFHRQVVKSESATI 110 (490)
Q Consensus 31 es~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEvq~~g~i~~kG~r~tl~V~~~~~~DLnR~VvkS~~ati 110 (490)
+|+||+||++|.||+++|+|||||+||||||.|+||||||||||++|+++|+|+||+|+|+ +++||||+||||++|+|
T Consensus 1 ~s~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~~ev~~~~~~~~~G~r~tl~V~--~~~DL~r~VvkS~~ati 78 (161)
T PF03367_consen 1 ESLCPNCGENGTTRILLTDIPYFKEVIIMSFECEHCGYKNNEVKSGGQIQPKGVRITLKVE--SPEDLNRQVVKSDTATI 78 (161)
T ss_dssp -EE-TTTSSCCEEEEEEEEETTTEEEEEEEEE-TTT--EEEEEEEECSS-SSEEEEEEEE---SHHHHC-EEEE-TT-EE
T ss_pred CCcCCCCCCCcEEEEEEEcCCCCceEEEEEeECCCCCCEeeeEEECccCCCCceEEEEEEC--CHHHhcceEEecCcEEE
Confidence 5899999999999999999999999999999999999999999999999999999999999 99999999999999999
Q ss_pred EEeeeeeEe-CCCCCCCceeeHHHHHHHHHHHHHHhhHHHhcCCHHHHHHHHHHHHHHHHhhcCCCcEEEEEECCCCCee
Q 011230 111 KIPELDFEI-PPEAQRGSLSTVEGILVRAADELEALQEERKKLDPQTAEAIDQFLLKLRACAKGDSTFTFILDDPAGNSF 189 (490)
Q Consensus 111 ~IPEL~~eI-~p~~~~G~iTTVEGlL~~~~~~L~~~~~~r~~~~~e~~~ki~~~i~kL~~~~~g~~pFTliidDPsGNS~ 189 (490)
+||||+||| |+++++|+||||||+|++++++|+..++.|++.+++.++++++|+++|+++++|+.|||||||||+||||
T Consensus 79 ~IPEl~~ei~P~~~~~g~iTTVEGlL~~i~~~L~~~~~~~~~~~~e~~~~~~~~i~~L~~~~~g~~pfTlIidDP~GnS~ 158 (161)
T PF03367_consen 79 EIPELGLEIEPGPSQGGFITTVEGLLMRIIDNLERLQPERDSDDPEEKEKIEEFIEKLDELIEGKRPFTLIIDDPSGNSF 158 (161)
T ss_dssp EEGGGTEEE--TTTT-SEEEEHHHHHHHHHHHHHTTHHCCCHH-HHHHHHHHHHHHHHHHHHCTSS-EEEEEEETTS--E
T ss_pred EEeecceEEccCCCCCceEEehHHHHHHHHHHHHhhhhccccCCHHHHHHHHHHHHHHHHHHcCCCCEEEEEECCCCcce
Confidence 999999999 5689999999999999999999999999888889999999999999999999999999999999999999
Q ss_pred eec
Q 011230 190 IEN 192 (490)
Q Consensus 190 I~~ 192 (490)
|+|
T Consensus 159 I~n 161 (161)
T PF03367_consen 159 IQN 161 (161)
T ss_dssp E--
T ss_pred ecC
Confidence 986
No 6
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=100.00 E-value=6.1e-59 Score=432.21 Aligned_cols=160 Identities=49% Similarity=0.836 Sum_probs=153.0
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCccccccCCCCCCCCeEEEEEEcCcccccceeeeeCceeEEec
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRIPEKGKRITLFVKNINDLSRDLIKSDTAGVKIP 365 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEVk~gg~i~~kG~ritL~V~~~eDL~R~VlKS~ta~v~IP 365 (490)
+.||+||+++.|+|++++||||||||||||.|+|||||+||||++|+++++|+||+|+|++++||+|+|+||++|+|+||
T Consensus 1 s~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~~ev~~~~~~~p~G~r~~l~V~~~~DL~r~VvkS~ta~i~IP 80 (160)
T smart00709 1 SDCPSCGGNGTTRMLLTSIPYFREVIIMSFECEHCGYRNNEVKSGGAIEPKGTRITLKVESPEDLNRDVVKSETATISIP 80 (160)
T ss_pred CcCCCCCCCCEEEEEEecCCCcceEEEEEEECCCCCCccceEEECcccCCCceEEEEEECChhhccceEEEcCCcEEEee
Confidence 57999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceeeeecCCCccceeEeHHHHHHHHHHHHhhccCcCCCCCCCHHHHHHHHHHHHHHHHhhcCCCceEEEEEcCCCCcccc
Q 011230 366 ELDLELAGGTLGGIVTTVEGLITKISESLERVHGFSFGDSLDENKRTKWQDFKAKLNKLLSVEESWTLILDDALANSFIA 445 (490)
Q Consensus 366 EL~lei~pGtl~G~~TTVEGlL~~i~d~L~~~~~~~~gds~~~e~~~k~~~fl~~L~~~~~g~~~fTlIidDP~GnS~I~ 445 (490)
||+|+|+||+++|+||||||||++++++|+....+..+++ +++.++|+++|+++|+++++|+.|||||||||+|||||
T Consensus 81 El~~ei~pg~~~g~itTVEGlL~~i~~~L~~~~~~~~~~~-~~e~~~k~~~~~~~L~~~~~g~~~fTliidDP~GnS~I- 158 (160)
T smart00709 81 ELDLEIPPGPLGGFITTVEGLLSRVREVLSQAIQETRDDS-DPETKEKIDEFLEKLKELIEGKEPFTLILDDPAGNSYI- 158 (160)
T ss_pred eeeEEecCCCCCcEEEehHHHHHHHHHHHHhhhhhhcccC-CHHHHHHHHHHHHHHHHHHcCCCCEEEEEECCCCceec-
Confidence 9999999999999999999999999999998755545665 78889999999999999999999999999999999999
Q ss_pred CC
Q 011230 446 PV 447 (490)
Q Consensus 446 ~~ 447 (490)
+|
T Consensus 159 ~~ 160 (160)
T smart00709 159 QN 160 (160)
T ss_pred cC
Confidence 65
No 7
>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 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 ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.
Probab=100.00 E-value=6e-58 Score=426.21 Aligned_cols=160 Identities=47% Similarity=0.813 Sum_probs=136.7
Q ss_pred eccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCccccccCCCCCCCCeEEEEEEcCcccccceeeeeCceeEEe
Q 011230 285 PSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRIPEKGKRITLFVKNINDLSRDLIKSDTAGVKI 364 (490)
Q Consensus 285 ~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEVk~gg~i~~kG~ritL~V~~~eDL~R~VlKS~ta~v~I 364 (490)
++.||+||+++.++|++++|||||+||||||.|++||||+|||+++|+++++|+||||+|++++||+|+|+||++|+|+|
T Consensus 1 ~s~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~~ev~~~~~~~~~G~r~tl~V~~~~DL~r~VvkS~~ati~I 80 (161)
T PF03367_consen 1 ESLCPNCGENGTTRILLTDIPYFKEVIIMSFECEHCGYKNNEVKSGGQIQPKGVRITLKVESPEDLNRQVVKSDTATIEI 80 (161)
T ss_dssp -EE-TTTSSCCEEEEEEEEETTTEEEEEEEEE-TTT--EEEEEEEECSS-SSEEEEEEEE-SHHHHC-EEEE-TT-EEEE
T ss_pred CCcCCCCCCCcEEEEEEEcCCCCceEEEEEeECCCCCCEeeeEEECccCCCCceEEEEEECCHHHhcceEEecCcEEEEE
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred cceeeeecCC-CccceeEeHHHHHHHHHHHHhhccCcCCCCCCCHHHHHHHHHHHHHHHHhhcCCCceEEEEEcCCCCcc
Q 011230 365 PELDLELAGG-TLGGIVTTVEGLITKISESLERVHGFSFGDSLDENKRTKWQDFKAKLNKLLSVEESWTLILDDALANSF 443 (490)
Q Consensus 365 PEL~lei~pG-tl~G~~TTVEGlL~~i~d~L~~~~~~~~gds~~~e~~~k~~~fl~~L~~~~~g~~~fTlIidDP~GnS~ 443 (490)
|||+|+|.|| +++|+||||||||++++++|+..++ .+++.+++.+++|++|+++|+++++|+.|||||||||+||||
T Consensus 81 PEl~~ei~P~~~~~g~iTTVEGlL~~i~~~L~~~~~--~~~~~~~e~~~~~~~~i~~L~~~~~g~~pfTlIidDP~GnS~ 158 (161)
T PF03367_consen 81 PELGLEIEPGPSQGGFITTVEGLLMRIIDNLERLQP--ERDSDDPEEKEKIEEFIEKLDELIEGKRPFTLIIDDPSGNSF 158 (161)
T ss_dssp GGGTEEE--TTTT-SEEEEHHHHHHHHHHHHHTTHH--CCCHH-HHHHHHHHHHHHHHHHHHCTSS-EEEEEEETTS--E
T ss_pred eecceEEccCCCCCceEEehHHHHHHHHHHHHhhhh--ccccCCHHHHHHHHHHHHHHHHHHcCCCCEEEEEECCCCcce
Confidence 9999999755 6799999999999999999999776 467888999999999999999999999999999999999999
Q ss_pred ccCC
Q 011230 444 IAPV 447 (490)
Q Consensus 444 I~~~ 447 (490)
| +|
T Consensus 159 I-~n 161 (161)
T PF03367_consen 159 I-QN 161 (161)
T ss_dssp E---
T ss_pred e-cC
Confidence 9 76
No 8
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=100.00 E-value=2.5e-56 Score=415.44 Aligned_cols=157 Identities=34% Similarity=0.601 Sum_probs=149.6
Q ss_pred CCccCCCceEE-EEEeecCCccceEEEEeecCCCCCCccceeeccccCCcceEEEEEeeCCCcccccceEEecCccEEEE
Q 011230 34 CMRCGENGVTR-FLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEIQPRGCNYSLKVPSSDQKMFHRQVVKSESATIKI 112 (490)
Q Consensus 34 Cp~Cg~~g~tr-lllt~IP~F~eviimSf~C~~CGyrnnEvq~~g~i~~kG~r~tl~V~~~~~~DLnR~VvkS~~ati~I 112 (490)
||+||.++.+. +++|+|||||+||||||.|+||||||||||++|+++| +||+|+|+ +++||+||||||++|+|+|
T Consensus 1 CP~Cg~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~ev~~~~~~~p--~r~~l~V~--~~~DL~r~VvkS~ta~i~I 76 (163)
T TIGR00340 1 CPVCGSRTLKAVTYDYDIPYFGKIMLSTYICEKCGYRSTDVYQLEEKEP--VRYIIKIE--NEDDLFTLVYRSRSATIRI 76 (163)
T ss_pred CCCCCCcceEeeeEeccCCCcceEEEEEEECCCCCCchhheeEcCCcCC--EEEEEEEC--ChhhccceEEEcCCcEEEc
Confidence 99999886665 7999999999999999999999999999999999999 89999999 9999999999999999999
Q ss_pred eeeeeEeCCCC-CCCceeeHHHHHHHHHHHHHHhhHHHhcCCHHHHHHHHHHHHHHHHhhcCCCcEEEEEECCCCCeeee
Q 011230 113 PELDFEIPPEA-QRGSLSTVEGILVRAADELEALQEERKKLDPQTAEAIDQFLLKLRACAKGDSTFTFILDDPAGNSFIE 191 (490)
Q Consensus 113 PEL~~eI~p~~-~~G~iTTVEGlL~~~~~~L~~~~~~r~~~~~e~~~ki~~~i~kL~~~~~g~~pFTliidDPsGNS~I~ 191 (490)
|||+|||||++ ++|+||||||+|++++++|+... |+..+++.++|+++|+++|+++++|+.|||||||||+|||||+
T Consensus 77 PEl~lei~pg~~~~G~iTTVEGlL~~i~~~L~~~~--~~~~~~e~~~k~~~~l~kL~~~~~g~~pfTlIldDP~GNS~I~ 154 (163)
T TIGR00340 77 PELGIKIEPGPASQGYISNIEGVLERIEEVLDTAS--DDDEDDEAVKKCEEILKRIREVIEGKFKFTLIIEDPFGNSFIE 154 (163)
T ss_pred cceeEEecCCCcCCceEEehHhHHHHHHHHHHHhh--hcccCHHHHHHHHHHHHHHHHHHhCCCCeEEEEECCCCCeeec
Confidence 99999999966 89999999999999999999874 7777899999999999999999999999999999999999999
Q ss_pred cCCCC
Q 011230 192 NLYAP 196 (490)
Q Consensus 192 ~~~ap 196 (490)
++++.
T Consensus 155 ~~~~~ 159 (163)
T TIGR00340 155 SEKAI 159 (163)
T ss_pred CCCcc
Confidence 98774
No 9
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=100.00 E-value=5.8e-55 Score=406.31 Aligned_cols=156 Identities=25% Similarity=0.537 Sum_probs=144.8
Q ss_pred CcCCcccccee-EEEeecCCCCcEEEEEeecCCCCCCccccccCCCCCCCCeEEEEEEcCcccccceeeeeCceeEEecc
Q 011230 288 CGACAASCETR-MFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRIPEKGKRITLFVKNINDLSRDLIKSDTAGVKIPE 366 (490)
Q Consensus 288 Cp~C~~~~~t~-m~~~~IP~FkeviImsf~C~~CGyr~nEVk~gg~i~~kG~ritL~V~~~eDL~R~VlKS~ta~v~IPE 366 (490)
||+||+++.+. |++++|||||+||||||.|+|||||+||||++|++++ +||+|+|++++||+|+|+||++|+|+|||
T Consensus 1 CP~Cg~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~ev~~~~~~~p--~r~~l~V~~~~DL~r~VvkS~ta~i~IPE 78 (163)
T TIGR00340 1 CPVCGSRTLKAVTYDYDIPYFGKIMLSTYICEKCGYRSTDVYQLEEKEP--VRYIIKIENEDDLFTLVYRSRSATIRIPE 78 (163)
T ss_pred CCCCCCcceEeeeEeccCCCcceEEEEEEECCCCCCchhheeEcCCcCC--EEEEEEECChhhccceEEEcCCcEEEccc
Confidence 99999986544 8999999999999999999999999999999999975 99999999999999999999999999999
Q ss_pred eeeeecCCCc-cceeEeHHHHHHHHHHHHhhccCcCCCCCCCHHHHHHHHHHHHHHHHhhcCCCceEEEEEcCCCCcccc
Q 011230 367 LDLELAGGTL-GGIVTTVEGLITKISESLERVHGFSFGDSLDENKRTKWQDFKAKLNKLLSVEESWTLILDDALANSFIA 445 (490)
Q Consensus 367 L~lei~pGtl-~G~~TTVEGlL~~i~d~L~~~~~~~~gds~~~e~~~k~~~fl~~L~~~~~g~~~fTlIidDP~GnS~I~ 445 (490)
|+|+|+||++ +|+||||||||++++++|+.... +..+++.+++|++|+++|+++++|+.|||||||||+|||||
T Consensus 79 l~lei~pg~~~~G~iTTVEGlL~~i~~~L~~~~~----~~~~~e~~~k~~~~l~kL~~~~~g~~pfTlIldDP~GNS~I- 153 (163)
T TIGR00340 79 LGIKIEPGPASQGYISNIEGVLERIEEVLDTASD----DDEDDEAVKKCEEILKRIREVIEGKFKFTLIIEDPFGNSFI- 153 (163)
T ss_pred eeEEecCCCcCCceEEehHhHHHHHHHHHHHhhh----cccCHHHHHHHHHHHHHHHHHHhCCCCeEEEEECCCCCeee-
Confidence 9999999995 89999999999999999997522 23367889999999999999999999999999999999999
Q ss_pred CCCCC
Q 011230 446 PVTDD 450 (490)
Q Consensus 446 ~~~~~ 450 (490)
+|+.+
T Consensus 154 ~~~~~ 158 (163)
T TIGR00340 154 ESEKA 158 (163)
T ss_pred cCCCc
Confidence 77655
No 10
>KOG2703 consensus C4-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=3.2e-55 Score=445.67 Aligned_cols=200 Identities=37% Similarity=0.614 Sum_probs=191.9
Q ss_pred CCcceEeeccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCccccccCCCCCCCCeEEEEEEcCcccccceeeee
Q 011230 278 PEEVMTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRIPEKGKRITLFVKNINDLSRDLIKS 357 (490)
Q Consensus 278 ~~ev~~~~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEVk~gg~i~~kG~ritL~V~~~eDL~R~VlKS 357 (490)
.+.++++++.||+|+++|.|||++|+||||+|||||||.|+|||+|||||++++.|+++|+||+|+|.+.+||+|+|+||
T Consensus 32 ~~~~~EvES~Cm~Cg~nG~TRlllT~IP~fREvVimSF~CpHCG~kN~eiQ~a~~iQ~~Gvri~l~V~s~EDlnRqVvkS 111 (460)
T KOG2703|consen 32 GNPVQEVESLCMNCGENGTTRLLLTSIPYFREVVIMSFECPHCGHKNNEIQSAEEIQEGGVRIELRVQSVEDLNRQVVKS 111 (460)
T ss_pred cCchHHHHHhhhhcccCCceeEEEeecchhheeeeEEeecCccCCccccccchhccccCceEEEEEeccHHHhhhHhhhc
Confidence 45688999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CceeEEecceeeeecCCCccceeEeHHHHHHHHHHHHhhccCcCCCCCCCHHHHHHHHHHHHHHHHhhcCCCceEEEEEc
Q 011230 358 DTAGVKIPELDLELAGGTLGGIVTTVEGLITKISESLERVHGFSFGDSLDENKRTKWQDFKAKLNKLLSVEESWTLILDD 437 (490)
Q Consensus 358 ~ta~v~IPEL~lei~pGtl~G~~TTVEGlL~~i~d~L~~~~~~~~gds~~~e~~~k~~~fl~~L~~~~~g~~~fTlIidD 437 (490)
++|+|+||||+|||++-++.|.+|||||+|.|+++.|++.|.. .+..+++.+++++.|+.+|+.++.+..|||||++|
T Consensus 112 e~Asi~IpEldlEIP~~Sq~GslTTVEGiL~r~~d~LsqdQek--Rr~~~pa~a~~Id~fi~kl~s~k~~~~pftlildD 189 (460)
T KOG2703|consen 112 ESASIEIPELDLEIPAKSQKGSLTTVEGILERVIDGLSQDQEK--RRITDPATAKQIDDFIVKLKSLKELTTPFTLILDD 189 (460)
T ss_pred ccceeecccceeeccccccCCceeehHHHHHHHHHHHhhhhhh--hcccCHHHHHHHHHHHHHHHHHhhcCCceEEEecC
Confidence 9999999999999999999999999999999999999998875 45678899999999999999999899999999999
Q ss_pred CCCCccccCCCCCCCCCCCeEEEEecCCHHHHHhcCCCCCCCC
Q 011230 438 ALANSFIAPVTDDIKDDHQLTFEEYERSWEQNEELGLNDIDTS 480 (490)
Q Consensus 438 P~GnS~I~~~~~~p~~Dp~l~~~~Y~RT~eqne~LGl~dm~~e 480 (490)
|+||||| +|+.+|.+||+|++.+|.||.+||+.|||.+..-+
T Consensus 190 p~GNS~i-Enp~~p~~dp~~~~~~y~Rt~eqne~lgl~~~~~~ 231 (460)
T KOG2703|consen 190 PTGNSFI-ENPHAPRVDPRLKIVHYLRTLEQNELLGLVDKNQE 231 (460)
T ss_pred CCCCccc-cCCCCCCCCCcceeEEEecCHhHHHhhccccccch
Confidence 9999999 99999999999999999999999999999987644
No 11
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=1.9e-51 Score=387.97 Aligned_cols=194 Identities=28% Similarity=0.508 Sum_probs=183.9
Q ss_pred CCcceEeeccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCccccccCCCCCCCCeEEEEEEcCcccccceeeee
Q 011230 278 PEEVMTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRIPEKGKRITLFVKNINDLSRDLIKS 357 (490)
Q Consensus 278 ~~ev~~~~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEVk~gg~i~~kG~ritL~V~~~eDL~R~VlKS 357 (490)
+.++.++...||+||+.+.++|++++||||++|+||+..|++||||++||+.+++.. |+||+|+|++++||+++|+||
T Consensus 7 ~~~~~~~~~~CPvCg~~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~DV~~~e~~e--P~r~~lkve~~edL~~~V~RS 84 (201)
T COG1779 7 PKEEFETRIDCPVCGGTLKAHMYLYDIPYFGEVLISTGVCERCGYRSTDVKTLEERE--PRRYTLKVESEEDLSARVVRS 84 (201)
T ss_pred cceeeeeeecCCcccceeeEEEeeecCCccceEEEEEEEccccCCcccceeecccCC--CeEEEEEeCCHHHhhhheeec
Confidence 567889999999999999999999999999999999999999999999999999976 599999999999999999999
Q ss_pred CceeEEecceeeeecCCCcc-ceeEeHHHHHHHHHHHHhhccCcCCCCCCCHHHHHHHHHHHHHHHHhhcCCCceEEEEE
Q 011230 358 DTAGVKIPELDLELAGGTLG-GIVTTVEGLITKISESLERVHGFSFGDSLDENKRTKWQDFKAKLNKLLSVEESWTLILD 436 (490)
Q Consensus 358 ~ta~v~IPEL~lei~pGtl~-G~~TTVEGlL~~i~d~L~~~~~~~~gds~~~e~~~k~~~fl~~L~~~~~g~~~fTlIid 436 (490)
.+|+|+||||+++|.||+++ |+||||||+|.|+.+.|..+..|. .+++.++|+++++.++.+++.|+.+|||||+
T Consensus 85 ~s~~I~IPELg~~iePG~~s~G~ITtIEGvL~rv~e~l~~a~~~~----~~dE~~~k~~e~~~~i~~~ieg~~~fTlIie 160 (201)
T COG1779 85 KSATIYIPELGLEIEPGPASEGFITTIEGVLERVYEVLETAIKLA----EDDESKKKAEELLKRIDEAIEGKRKFTLIIE 160 (201)
T ss_pred CCccEEcccCceEeccccccCceEehHHHHHHHHHHHHHHHHhcc----cchHHHHHHHHHHHHHHHHhccCccEEEEEE
Confidence 99999999999999999997 999999999999999999866553 2348899999999999999999999999999
Q ss_pred cCCCCccccCCCCCCCCCCCeEEEEecCCHHHHHhcCCCCCCC
Q 011230 437 DALANSFIAPVTDDIKDDHQLTFEEYERSWEQNEELGLNDIDT 479 (490)
Q Consensus 437 DP~GnS~I~~~~~~p~~Dp~l~~~~Y~RT~eqne~LGl~dm~~ 479 (490)
||+||||| ++.+|+..++.++..+|.||. ++..+|+++|+.
T Consensus 161 Dp~G~S~I-~~~~a~~e~l~~ee~~~lktg-~~~~~~~~~~~~ 201 (201)
T COG1779 161 DPLGNSAI-ISEKAPDEKLSKEEAEKLKTG-MNVIDGDGDMKE 201 (201)
T ss_pred CCCCCcee-eccccccCCccHHHHHHhcCC-ceEecccCcccC
Confidence 99999999 899999999999999999999 999999999973
No 12
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=2.6e-47 Score=359.89 Aligned_cols=191 Identities=32% Similarity=0.465 Sum_probs=181.0
Q ss_pred CCCCceEEeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccceeeccccCCcceEEEEEeeCCCcccccceE
Q 011230 23 SDAPLYQVESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEIQPRGCNYSLKVPSSDQKMFHRQV 102 (490)
Q Consensus 23 ~~~~v~eies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEvq~~g~i~~kG~r~tl~V~~~~~~DLnR~V 102 (490)
....+++....||+||....+.+++++||||++|++|+..|++||||++||..+++..| .||+|+|+ +++||+++|
T Consensus 6 ~~~~~~~~~~~CPvCg~~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~DV~~~e~~eP--~r~~lkve--~~edL~~~V 81 (201)
T COG1779 6 FPKEEFETRIDCPVCGGTLKAHMYLYDIPYFGEVLISTGVCERCGYRSTDVKTLEEREP--RRYTLKVE--SEEDLSARV 81 (201)
T ss_pred ccceeeeeeecCCcccceeeEEEeeecCCccceEEEEEEEccccCCcccceeecccCCC--eEEEEEeC--CHHHhhhhe
Confidence 44567888999999999999999999999999999999999999999999999999999 89999999 999999999
Q ss_pred EecCccEEEEeeeeeEeCC-CCCCCceeeHHHHHHHHHHHHHHhhHHHhcCCHHHHHHHHHHHHHHHHhhcCCCcEEEEE
Q 011230 103 VKSESATIKIPELDFEIPP-EAQRGSLSTVEGILVRAADELEALQEERKKLDPQTAEAIDQFLLKLRACAKGDSTFTFIL 181 (490)
Q Consensus 103 vkS~~ati~IPEL~~eI~p-~~~~G~iTTVEGlL~~~~~~L~~~~~~r~~~~~e~~~ki~~~i~kL~~~~~g~~pFTlii 181 (490)
+||.+|+|+||||+++|.| +.+.|+||||||+|.|+.+.|+.+. +|..++|..+|+++++.+|.++++|+.+|||||
T Consensus 82 ~RS~s~~I~IPELg~~iePG~~s~G~ITtIEGvL~rv~e~l~~a~--~~~~~dE~~~k~~e~~~~i~~~ieg~~~fTlIi 159 (201)
T COG1779 82 VRSKSATIYIPELGLEIEPGPASEGFITTIEGVLERVYEVLETAI--KLAEDDESKKKAEELLKRIDEAIEGKRKFTLII 159 (201)
T ss_pred eecCCccEEcccCceEeccccccCceEehHHHHHHHHHHHHHHHH--hcccchHHHHHHHHHHHHHHHHhccCccEEEEE
Confidence 9999999999999999999 6677999999999999999999987 677777999999999999999999999999999
Q ss_pred ECCCCCeeeecCCCCCCCCCeeEEEecCCHHHHHHcCCC
Q 011230 182 DDPAGNSFIENLYAPSPDPSLNIKFYERTPEQQALLGYL 220 (490)
Q Consensus 182 dDPsGNS~I~~~~ap~~D~~~~~~~y~Rt~eq~~~LGl~ 220 (490)
+||+|||+|.+.+|+..++......|-||. ++..+|+.
T Consensus 160 eDp~G~S~I~~~~a~~e~l~~ee~~~lktg-~~~~~~~~ 197 (201)
T COG1779 160 EDPLGNSAIISEKAPDEKLSKEEAEKLKTG-MNVIDGDG 197 (201)
T ss_pred ECCCCCceeeccccccCCccHHHHHHhcCC-ceEecccC
Confidence 999999999999999999999999999999 99888874
No 13
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=94.55 E-value=0.015 Score=39.01 Aligned_cols=24 Identities=46% Similarity=0.841 Sum_probs=19.6
Q ss_pred cCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCcc
Q 011230 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNN 71 (490)
Q Consensus 33 ~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnn 71 (490)
.||.|+ .+|-+.+-.||||||...
T Consensus 2 ~CP~C~---------------~~V~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECG---------------AEVPESAKFCPHCGYDFE 25 (26)
T ss_pred cCCCCc---------------CCchhhcCcCCCCCCCCc
Confidence 499995 566778899999999763
No 14
>PF14353 CpXC: CpXC protein
Probab=93.83 E-value=0.021 Score=51.16 Aligned_cols=40 Identities=25% Similarity=0.597 Sum_probs=29.3
Q ss_pred ccCCccCCCceEEEEEe----ecCCccceEE----EEeecCCCCCCcc
Q 011230 32 SLCMRCGENGVTRFLLT----LIPHFRKVLL----SAFECPHCGERNN 71 (490)
Q Consensus 32 s~Cp~Cg~~g~trlllt----~IP~F~evii----mSf~C~~CGyrnn 71 (490)
..||+||......+... .-|-+++-|+ .+|.||+||.+..
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~ 49 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFR 49 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCcee
Confidence 47999999887766432 4455555554 5899999999874
No 15
>PF14353 CpXC: CpXC protein
Probab=92.13 E-value=0.046 Score=48.98 Aligned_cols=40 Identities=28% Similarity=0.565 Sum_probs=28.0
Q ss_pred ccCcCCccccceeEE-Ee---ecCCCCcEEE----EEeecCCCCCCcc
Q 011230 286 STCGACAASCETRMF-MT---RIPYFQEVIV----MASTCDACGYRNS 325 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~-~~---~IP~FkeviI----msf~C~~CGyr~n 325 (490)
..||+|++....... .+ .-|-+++=|+ .+++|++||++..
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~ 49 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFR 49 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCcee
Confidence 479999998765553 22 3354555544 6899999999874
No 16
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=92.05 E-value=0.069 Score=35.80 Aligned_cols=24 Identities=42% Similarity=0.798 Sum_probs=18.7
Q ss_pred cCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCcc
Q 011230 287 TCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNS 325 (490)
Q Consensus 287 ~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~n 325 (490)
.||.|++. |-+.+-.|++|||...
T Consensus 2 ~CP~C~~~---------------V~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAE---------------VPESAKFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCC---------------chhhcCcCCCCCCCCc
Confidence 49999754 4667889999999753
No 17
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=90.89 E-value=0.27 Score=48.36 Aligned_cols=46 Identities=26% Similarity=0.634 Sum_probs=31.1
Q ss_pred EeccCCccCCCceEEEEEe---ec--------CCccc---eEEEEeecCCCCCCccceee
Q 011230 30 VESLCMRCGENGVTRFLLT---LI--------PHFRK---VLLSAFECPHCGERNNEVQF 75 (490)
Q Consensus 30 ies~Cp~Cg~~g~trlllt---~I--------P~F~e---viimSf~C~~CGyrnnEvq~ 75 (490)
-+..||+|++.-++..+.+ ++ |+|++ .+.....||||||-..+-.+
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~~F 63 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEEDF 63 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccccc
Confidence 3567999998866654433 11 44444 46777889999998765543
No 18
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=90.69 E-value=0.28 Score=47.67 Aligned_cols=83 Identities=13% Similarity=0.261 Sum_probs=54.0
Q ss_pred eEEeccCCccCCCceE--EEEEeecCCccceEEEEeecCCCCCCccceeeccccCCcceEEEEEeeCCCcccccceEEec
Q 011230 28 YQVESLCMRCGENGVT--RFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEIQPRGCNYSLKVPSSDQKMFHRQVVKS 105 (490)
Q Consensus 28 ~eies~Cp~Cg~~g~t--rlllt~IP~F~eviimSf~C~~CGyrnnEvq~~g~i~~kG~r~tl~V~~~~~~DLnR~VvkS 105 (490)
.++...||+|| ...+ .++..+.+. ...+|..||+=+.+ .-.-|+.++..+.|. +-=+|
T Consensus 3 ~~iy~~Cp~Cg-~eev~hEVik~~g~~------~lvrC~eCG~V~~~----~i~~~k~~~v~viVS---------~~~~S 62 (201)
T COG1326 3 EEIYIECPSCG-SEEVSHEVIKERGRE------PLVRCEECGTVHPA----IIKTPKPVRVRVIVS---------RHEES 62 (201)
T ss_pred ceEEEECCCCC-cchhhHHHHHhcCCc------eEEEccCCCcEeec----eeeccccceEEEEEe---------cCCcc
Confidence 46778999999 4444 555555554 45699999997754 333455566777776 33367
Q ss_pred CccEEEEeeee-------eEeCCCCCCCceeeHH
Q 011230 106 ESATIKIPELD-------FEIPPEAQRGSLSTVE 132 (490)
Q Consensus 106 ~~ati~IPEL~-------~eI~p~~~~G~iTTVE 132 (490)
-+-.+++|+.+ |++. .-+..||++|
T Consensus 63 ~~~~vel~~gE~l~vGDei~vd--~e~veITSIE 94 (201)
T COG1326 63 FTKEVELDPGETLKVGDEIEVD--GEEVEITSIE 94 (201)
T ss_pred cceeEecCCCCeEecCCEEEEc--CCEEEEEEEe
Confidence 77777777644 4443 3457788877
No 19
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=90.60 E-value=0.27 Score=48.33 Aligned_cols=45 Identities=22% Similarity=0.463 Sum_probs=30.5
Q ss_pred eccCcCCccccceeEEEe--------e---cCCCCc---EEEEEeecCCCCCCcccccc
Q 011230 285 PSTCGACAASCETRMFMT--------R---IPYFQE---VIVMASTCDACGYRNSELKP 329 (490)
Q Consensus 285 ~s~Cp~C~~~~~t~m~~~--------~---IP~Fke---viImsf~C~~CGyr~nEVk~ 329 (490)
...||+|++.-.+..... + =|+|++ .+-...+||||||-..+-..
T Consensus 5 ~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~~F 63 (214)
T PF09986_consen 5 KITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEEDF 63 (214)
T ss_pred ceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccccc
Confidence 467999998866554322 1 155554 46677899999998776543
No 20
>PHA00626 hypothetical protein
Probab=89.68 E-value=0.43 Score=37.74 Aligned_cols=49 Identities=20% Similarity=0.433 Sum_probs=28.9
Q ss_pred cCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccceeeccccCCcceEEEEEee
Q 011230 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEIQPRGCNYSLKVP 91 (490)
Q Consensus 33 ~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEvq~~g~i~~kG~r~tl~V~ 91 (490)
.||+||..-.+|--..+-|- -.+.|+.|||+.+---+ .++|.---++|+
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~s------nrYkCkdCGY~ft~~~~----~~~~~~~~~~~~ 50 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWS------DDYVCCDCGYNDSKDAF----GERGKNEFVRIN 50 (59)
T ss_pred CCCCCCCceeeeeceecccC------cceEcCCCCCeechhhh----hhccccceEEec
Confidence 69999975444432222211 35899999999975433 345543444443
No 21
>PHA00626 hypothetical protein
Probab=89.25 E-value=0.51 Score=37.34 Aligned_cols=50 Identities=24% Similarity=0.373 Sum_probs=31.7
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCccccccCCCCCCCCeEEEEEEc
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRIPEKGKRITLFVK 345 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEVk~gg~i~~kG~ritL~V~ 345 (490)
..||.||+.-.++-..++-|- --+.|+.|||+.+.--.| ++|+---++|+
T Consensus 1 m~CP~CGS~~Ivrcg~cr~~s------nrYkCkdCGY~ft~~~~~----~~~~~~~~~~~ 50 (59)
T PHA00626 1 MSCPKCGSGNIAKEKTMRGWS------DDYVCCDCGYNDSKDAFG----ERGKNEFVRIN 50 (59)
T ss_pred CCCCCCCCceeeeeceecccC------cceEcCCCCCeechhhhh----hccccceEEec
Confidence 369999996555544433322 247899999998876544 45654444444
No 22
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=88.74 E-value=0.45 Score=44.77 Aligned_cols=45 Identities=18% Similarity=0.224 Sum_probs=31.4
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCccccccCC
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGG 331 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEVk~gg 331 (490)
+.||.||.+-+--.-..-++- +-+|-+.-.|+.||++.+-....+
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~-~~~~~~~~~c~~c~~~f~~~e~~~ 45 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAED-GNAIRRRRECLACGKRFTTFERVE 45 (154)
T ss_pred CcCCCCCCCCCEeEeccccCC-CCceeeeeeccccCCcceEeEecc
Confidence 369999988632222222222 568888899999999999876544
No 23
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=87.97 E-value=0.38 Score=35.87 Aligned_cols=29 Identities=34% Similarity=0.642 Sum_probs=18.6
Q ss_pred eccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCc
Q 011230 31 ESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (490)
Q Consensus 31 es~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrn 70 (490)
+-.|++||..-.. .|. .. .+.||+||.+.
T Consensus 3 ~y~C~~CG~~~~~------~~~-~~----~~~Cp~CG~~~ 31 (46)
T PRK00398 3 EYKCARCGREVEL------DEY-GT----GVRCPYCGYRI 31 (46)
T ss_pred EEECCCCCCEEEE------CCC-CC----ceECCCCCCeE
Confidence 4579999864221 111 11 78999999764
No 24
>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=87.45 E-value=0.61 Score=36.46 Aligned_cols=36 Identities=28% Similarity=0.743 Sum_probs=25.4
Q ss_pred ceEEeccCCccCC-CceEEEEEeecCCccceEEEEeecCCCCCCc
Q 011230 27 LYQVESLCMRCGE-NGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (490)
Q Consensus 27 v~eies~Cp~Cg~-~g~trlllt~IP~F~eviimSf~C~~CGyrn 70 (490)
-.-..-.|.+|+. ||... .--|.++ +|.|++||+.|
T Consensus 18 ~~r~aLIC~~C~~hNGla~-----~~~~~~i---~y~C~~Cg~~N 54 (54)
T PF10058_consen 18 SNRYALICSKCFSHNGLAP-----KEEFEEI---QYRCPYCGALN 54 (54)
T ss_pred cCceeEECcccchhhcccc-----cccCCce---EEEcCCCCCcC
Confidence 3456677999995 67664 1224444 99999999976
No 25
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=86.41 E-value=0.39 Score=44.07 Aligned_cols=50 Identities=22% Similarity=0.472 Sum_probs=34.1
Q ss_pred EeccCCccCCCceEE--------EEEeecCCccceEEEEeecCCCCCCccceeecccc
Q 011230 30 VESLCMRCGENGVTR--------FLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEI 79 (490)
Q Consensus 30 ies~Cp~Cg~~g~tr--------lllt~IP~F~eviimSf~C~~CGyrnnEvq~~g~i 79 (490)
....|++||..-... .+-+.|-|..|++-..+.||+||-.+-+|..+.++
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G~el 126 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEIVKGRGV 126 (135)
T ss_pred eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcEEecCceE
Confidence 567899999543322 12334556667777778999999888777666554
No 26
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=86.21 E-value=0.96 Score=42.62 Aligned_cols=46 Identities=17% Similarity=0.282 Sum_probs=30.4
Q ss_pred cCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccceeecccc
Q 011230 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEI 79 (490)
Q Consensus 33 ~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEvq~~g~i 79 (490)
.||.||.+-+--.----++- |.+|-+.-.|+.||++.+-+......
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~-~~~~~~~~~c~~c~~~f~~~e~~~~~ 47 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAED-GNAIRRRRECLACGKRFTTFERVELV 47 (154)
T ss_pred cCCCCCCCCCEeEeccccCC-CCceeeeeeccccCCcceEeEeccCc
Confidence 69999976422111111222 56888889999999999877665554
No 27
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=85.65 E-value=0.34 Score=38.66 Aligned_cols=34 Identities=38% Similarity=0.778 Sum_probs=22.4
Q ss_pred EeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCC
Q 011230 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGER 69 (490)
Q Consensus 30 ies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyr 69 (490)
+.-.||+||+..+.|- ..=|+-- ..+.||.|||.
T Consensus 24 ~~F~CPnCG~~~I~RC-----~~CRk~~-~~Y~CP~CGF~ 57 (59)
T PRK14890 24 VKFLCPNCGEVIIYRC-----EKCRKQS-NPYTCPKCGFE 57 (59)
T ss_pred CEeeCCCCCCeeEeec-----hhHHhcC-CceECCCCCCc
Confidence 5678999987655554 2222222 36789999996
No 28
>PRK05978 hypothetical protein; Provisional
Probab=85.64 E-value=0.36 Score=45.23 Aligned_cols=32 Identities=34% Similarity=0.691 Sum_probs=25.9
Q ss_pred EeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCcc
Q 011230 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNN 71 (490)
Q Consensus 30 ies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnn 71 (490)
+...||+||+- ..|+--+-|.-.|++||.+..
T Consensus 32 l~grCP~CG~G----------~LF~g~Lkv~~~C~~CG~~~~ 63 (148)
T PRK05978 32 FRGRCPACGEG----------KLFRAFLKPVDHCAACGEDFT 63 (148)
T ss_pred HcCcCCCCCCC----------cccccccccCCCccccCCccc
Confidence 67899999876 336677778999999999875
No 29
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=84.77 E-value=3.3 Score=40.52 Aligned_cols=72 Identities=21% Similarity=0.385 Sum_probs=45.7
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCcccc-----c-cCCCCCCCCeEEEEEEcCcccccceeeeeCc
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSEL-----K-PGGRIPEKGKRITLFVKNINDLSRDLIKSDT 359 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEV-----k-~gg~i~~kG~ritL~V~~~eDL~R~VlKS~t 359 (490)
..|+.|+.+- |.+... +. ++...|..||++..=- . +..+--.+|..++++|++...-.+-|.+-+.
T Consensus 99 V~C~~C~~pd-T~l~k~-----~~--~~~l~C~aCGa~~~v~~~~~~~~~~~~~~~~~e~~~v~Ie~l~~~G~GVak~~g 170 (201)
T PRK12336 99 VICSECGLPD-TRLVKE-----DR--VLMLRCDACGAHRPVKKRKASSETQREAIEEGKTYEVEITGTGRKGDGVAKKGK 170 (201)
T ss_pred EECCCCCCCC-cEEEEc-----CC--eEEEEcccCCCCccccccccccCCCCCCCccCCEEEEEEEEccCCCceEEEECC
Confidence 5799999986 444322 22 4558999999965311 1 1121123456678888888777777877666
Q ss_pred eeEEec
Q 011230 360 AGVKIP 365 (490)
Q Consensus 360 a~v~IP 365 (490)
-++.+|
T Consensus 171 ~~vfV~ 176 (201)
T PRK12336 171 YTIFVP 176 (201)
T ss_pred EEEEeC
Confidence 667766
No 30
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=84.36 E-value=1.7 Score=31.76 Aligned_cols=39 Identities=26% Similarity=0.531 Sum_probs=24.8
Q ss_pred cCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccc
Q 011230 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNE 72 (490)
Q Consensus 33 ~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnE 72 (490)
.||.||.+...-+ ...+=---|=...-|.|..||++..+
T Consensus 2 ~Cp~C~~~~a~~~-q~Q~RsaDE~mT~fy~C~~C~~~w~~ 40 (40)
T smart00440 2 PCPKCGNREATFF-QLQTRSADEPMTVFYVCTKCGHRWRE 40 (40)
T ss_pred cCCCCCCCeEEEE-EEcccCCCCCCeEEEEeCCCCCEeCC
Confidence 6999986543322 22222234666678999999998653
No 31
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=84.31 E-value=0.5 Score=43.34 Aligned_cols=48 Identities=23% Similarity=0.456 Sum_probs=33.1
Q ss_pred eeccCcCCcccccee--------EEEeecCCCCcEEEEEeecCCCCCCccccccCC
Q 011230 284 FPSTCGACAASCETR--------MFMTRIPYFQEVIVMASTCDACGYRNSELKPGG 331 (490)
Q Consensus 284 ~~s~Cp~C~~~~~t~--------m~~~~IP~FkeviImsf~C~~CGyr~nEVk~gg 331 (490)
....|++||..-... +.-+.|-|..|++-..+.||+||-.+-+|..|-
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G~ 124 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEIVKGR 124 (135)
T ss_pred eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcEEecCc
Confidence 457899999654332 233344455777777789999998888886653
No 32
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=84.30 E-value=0.43 Score=31.66 Aligned_cols=24 Identities=29% Similarity=0.670 Sum_probs=16.2
Q ss_pred eccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCC
Q 011230 285 PSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYR 323 (490)
Q Consensus 285 ~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr 323 (490)
+..||+||+.... -+-.|++||.+
T Consensus 2 ~~~Cp~Cg~~~~~---------------~~~fC~~CG~~ 25 (26)
T PF13248_consen 2 EMFCPNCGAEIDP---------------DAKFCPNCGAK 25 (26)
T ss_pred cCCCcccCCcCCc---------------ccccChhhCCC
Confidence 4569999885321 15678888875
No 33
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=83.33 E-value=0.56 Score=37.51 Aligned_cols=35 Identities=29% Similarity=0.600 Sum_probs=21.6
Q ss_pred EEeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCC
Q 011230 29 QVESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGER 69 (490)
Q Consensus 29 eies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyr 69 (490)
-+.-.||+||+.-++|-..-+- + =-...||.|||+
T Consensus 25 ~v~F~CPnCGe~~I~Rc~~CRk--~----g~~Y~Cp~CGF~ 59 (61)
T COG2888 25 AVKFPCPNCGEVEIYRCAKCRK--L----GNPYRCPKCGFE 59 (61)
T ss_pred eeEeeCCCCCceeeehhhhHHH--c----CCceECCCcCcc
Confidence 4667899998766665421110 0 013589999996
No 34
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=83.04 E-value=0.96 Score=33.69 Aligned_cols=29 Identities=28% Similarity=0.663 Sum_probs=19.3
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCcc
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNS 325 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~n 325 (490)
..|++||..... +-... .+.|++||.+..
T Consensus 4 y~C~~CG~~~~~-------~~~~~----~~~Cp~CG~~~~ 32 (46)
T PRK00398 4 YKCARCGREVEL-------DEYGT----GVRCPYCGYRIL 32 (46)
T ss_pred EECCCCCCEEEE-------CCCCC----ceECCCCCCeEE
Confidence 469999987432 11111 789999997643
No 35
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=81.94 E-value=7.8 Score=41.48 Aligned_cols=38 Identities=18% Similarity=0.440 Sum_probs=27.0
Q ss_pred eccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccce
Q 011230 31 ESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEV 73 (490)
Q Consensus 31 es~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEv 73 (490)
...|+.|+-.|.++...-. =++.|.-.|+.|+=+-..|
T Consensus 159 ~~tC~tC~G~G~v~~~~~~-----g~~~~~~~C~~C~G~G~~i 196 (371)
T COG0484 159 PKTCPTCNGSGQVRTVQRT-----GFFSFQQTCPTCNGTGKII 196 (371)
T ss_pred CCcCCCCCCcCeEEEEEee-----eEEEEEEECCCCccceeEC
Confidence 4679999999988775433 3466777888887655555
No 36
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=81.52 E-value=2.4 Score=31.00 Aligned_cols=39 Identities=26% Similarity=0.486 Sum_probs=25.6
Q ss_pred cCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCccc
Q 011230 287 TCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSE 326 (490)
Q Consensus 287 ~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nE 326 (490)
.||.||+...+ .....+=--.|=+..-+.|.+||++-.|
T Consensus 2 ~Cp~C~~~~a~-~~q~Q~RsaDE~mT~fy~C~~C~~~w~~ 40 (40)
T smart00440 2 PCPKCGNREAT-FFQLQTRSADEPMTVFYVCTKCGHRWRE 40 (40)
T ss_pred cCCCCCCCeEE-EEEEcccCCCCCCeEEEEeCCCCCEeCC
Confidence 69999865432 2233333345667778999999998643
No 37
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=81.13 E-value=2.3 Score=41.52 Aligned_cols=83 Identities=22% Similarity=0.320 Sum_probs=50.2
Q ss_pred eEeeccCcCCccccce--eEEEeecCCCCcEEEEEeecCCCCCCccccccCCCCCCCCeEEEEEEcCcccccceeeeeCc
Q 011230 282 MTFPSTCGACAASCET--RMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRIPEKGKRITLFVKNINDLSRDLIKSDT 359 (490)
Q Consensus 282 ~~~~s~Cp~C~~~~~t--~m~~~~IP~FkeviImsf~C~~CGyr~nEVk~gg~i~~kG~ritL~V~~~eDL~R~VlKS~t 359 (490)
.++-..||+|+ ...+ .......++ ....|..||+=+.+.. ..++.+++.+-|..-+ +|.+
T Consensus 3 ~~iy~~Cp~Cg-~eev~hEVik~~g~~------~lvrC~eCG~V~~~~i----~~~k~~~v~viVS~~~-------~S~~ 64 (201)
T COG1326 3 EEIYIECPSCG-SEEVSHEVIKERGRE------PLVRCEECGTVHPAII----KTPKPVRVRVIVSRHE-------ESFT 64 (201)
T ss_pred ceEEEECCCCC-cchhhHHHHHhcCCc------eEEEccCCCcEeecee----eccccceEEEEEecCC-------cccc
Confidence 35567899999 4333 233333443 4679999999775532 2356667766665332 4777
Q ss_pred eeEEeccee-------eeecCCCccceeEeHH
Q 011230 360 AGVKIPELD-------LELAGGTLGGIVTTVE 384 (490)
Q Consensus 360 a~v~IPEL~-------lei~pGtl~G~~TTVE 384 (490)
-.+++|+.+ |++... ...||++|
T Consensus 65 ~~vel~~gE~l~vGDei~vd~e--~veITSIE 94 (201)
T COG1326 65 KEVELDPGETLKVGDEIEVDGE--EVEITSIE 94 (201)
T ss_pred eeEecCCCCeEecCCEEEEcCC--EEEEEEEe
Confidence 778887644 333322 36677766
No 38
>PRK05978 hypothetical protein; Provisional
Probab=80.93 E-value=0.68 Score=43.38 Aligned_cols=37 Identities=24% Similarity=0.591 Sum_probs=28.6
Q ss_pred EeeccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCcccccc
Q 011230 283 TFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKP 329 (490)
Q Consensus 283 ~~~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEVk~ 329 (490)
-+...||+||+- ..|+--+-|.-.|++||.+..-...
T Consensus 31 Gl~grCP~CG~G----------~LF~g~Lkv~~~C~~CG~~~~~~~a 67 (148)
T PRK05978 31 GFRGRCPACGEG----------KLFRAFLKPVDHCAACGEDFTHHRA 67 (148)
T ss_pred HHcCcCCCCCCC----------cccccccccCCCccccCCccccCCc
Confidence 356789999976 2366777799999999998766544
No 39
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=80.47 E-value=7.9 Score=41.41 Aligned_cols=39 Identities=23% Similarity=0.477 Sum_probs=25.8
Q ss_pred eeccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCcccc
Q 011230 284 FPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSEL 327 (490)
Q Consensus 284 ~~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEV 327 (490)
-+..|+.|+..|.+++..-. =++.|...|+.|+=+-..|
T Consensus 158 ~~~tC~tC~G~G~v~~~~~~-----g~~~~~~~C~~C~G~G~~i 196 (371)
T COG0484 158 DPKTCPTCNGSGQVRTVQRT-----GFFSFQQTCPTCNGTGKII 196 (371)
T ss_pred CCCcCCCCCCcCeEEEEEee-----eEEEEEEECCCCccceeEC
Confidence 34568888888877665433 4566777888887544444
No 40
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=79.86 E-value=0.91 Score=35.00 Aligned_cols=31 Identities=32% Similarity=0.714 Sum_probs=20.2
Q ss_pred EEeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCc
Q 011230 29 QVESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (490)
Q Consensus 29 eies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrn 70 (490)
...-.|+.||+.-. + .-...-..||+||||-
T Consensus 4 ~~~Y~C~~Cg~~~~-------~----~~~~~~irCp~Cg~rI 34 (49)
T COG1996 4 MMEYKCARCGREVE-------L----DQETRGIRCPYCGSRI 34 (49)
T ss_pred eEEEEhhhcCCeee-------h----hhccCceeCCCCCcEE
Confidence 35668999987630 0 1133456899999974
No 41
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=79.47 E-value=1.6 Score=39.28 Aligned_cols=75 Identities=23% Similarity=0.518 Sum_probs=40.1
Q ss_pred CCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccceeeccccCCcceEEEEEeeCCCcccc--cceEEecCccEEE
Q 011230 34 CMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEIQPRGCNYSLKVPSSDQKMF--HRQVVKSESATIK 111 (490)
Q Consensus 34 Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEvq~~g~i~~kG~r~tl~V~~~~~~DL--nR~VvkS~~ati~ 111 (490)
||+|| ++.+|....|++||-.- -|.+.. -+-.+. +++|| =+..+|+.. .++
T Consensus 1 CPvCg---------------~~l~vt~l~C~~C~t~i-----~G~F~l---~~~~~L---~~E~~~Fi~~Fi~~rG-nlK 53 (113)
T PF09862_consen 1 CPVCG---------------GELVVTRLKCPSCGTEI-----EGEFEL---PWFARL---SPEQLEFIKLFIKNRG-NLK 53 (113)
T ss_pred CCCCC---------------CceEEEEEEcCCCCCEE-----Eeeecc---chhhcC---CHHHHHHHHHHHHhcC-CHH
Confidence 99998 45677788999998432 333322 012222 33343 234444422 222
Q ss_pred E--eeeeeEeCCCCCCCceeeHHHHHHHHHHHHHH
Q 011230 112 I--PELDFEIPPEAQRGSLSTVEGILVRAADELEA 144 (490)
Q Consensus 112 I--PEL~~eI~p~~~~G~iTTVEGlL~~~~~~L~~ 144 (490)
= -+|++.. -||-.-|.+++..|..
T Consensus 54 e~e~~lgiSY---------PTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 54 EMEKELGISY---------PTVRNRLDKIIEKLGY 79 (113)
T ss_pred HHHHHHCCCc---------HHHHHHHHHHHHHhCC
Confidence 1 1133333 3677778888777776
No 42
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=79.41 E-value=0.77 Score=29.82 Aligned_cols=8 Identities=38% Similarity=0.962 Sum_probs=6.0
Q ss_pred CcCCcccc
Q 011230 288 CGACAASC 295 (490)
Q Consensus 288 Cp~C~~~~ 295 (490)
||+||+..
T Consensus 2 Cp~CG~~~ 9 (23)
T PF13240_consen 2 CPNCGAEI 9 (23)
T ss_pred CcccCCCC
Confidence 78888765
No 43
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=78.54 E-value=2.3 Score=38.06 Aligned_cols=40 Identities=25% Similarity=0.453 Sum_probs=27.4
Q ss_pred eccCCccCCC-ceEEEEEeecCCccceEEEEeecCCCCCCccc
Q 011230 31 ESLCMRCGEN-GVTRFLLTLIPHFRKVLLSAFECPHCGERNNE 72 (490)
Q Consensus 31 es~Cp~Cg~~-g~trlllt~IP~F~eviimSf~C~~CGyrnnE 72 (490)
.-.||.||.+ ....++.++- =.|=.-..+.|.+|||+.++
T Consensus 72 ~~~CpkCg~~ea~y~~~QtRs--aDEp~T~Fy~C~~Cg~~wre 112 (113)
T COG1594 72 KEKCPKCGNKEAYYWQLQTRS--ADEPETRFYKCTRCGYRWRE 112 (113)
T ss_pred cccCCCCCCceeEEEeeehhc--cCCCceEEEEecccCCEeec
Confidence 3479999965 4445555543 34445557999999999865
No 44
>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=78.30 E-value=1.4 Score=33.14 Aligned_cols=36 Identities=22% Similarity=0.482 Sum_probs=27.1
Q ss_pred cCcCCccccceeEEEeecCCCCcEEEEEeecCC--CCCCcc
Q 011230 287 TCGACAASCETRMFMTRIPYFQEVIVMASTCDA--CGYRNS 325 (490)
Q Consensus 287 ~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~--CGyr~n 325 (490)
.||.||..+.++--.-.-|.++| .-..|.+ ||+...
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~~~~~---~Y~qC~N~~Cg~tfv 38 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSPLTRE---LYCQCTNPECGHTFV 38 (47)
T ss_pred CcCCCCCeeEEEEchhhCcceEE---EEEEECCCcCCCEEE
Confidence 49999999877765555556666 7788988 998754
No 45
>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=77.56 E-value=1.7 Score=32.69 Aligned_cols=36 Identities=28% Similarity=0.526 Sum_probs=27.8
Q ss_pred cCCccCCCceEEEEEeecCCccceEEEEeecCC--CCCCcc
Q 011230 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPH--CGERNN 71 (490)
Q Consensus 33 ~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~--CGyrnn 71 (490)
.||.||.....|--...-|.+++ .-+.|.+ ||+...
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~~~~~---~Y~qC~N~~Cg~tfv 38 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSPLTRE---LYCQCTNPECGHTFV 38 (47)
T ss_pred CcCCCCCeeEEEEchhhCcceEE---EEEEECCCcCCCEEE
Confidence 49999998887765555666776 6789988 999764
No 46
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=77.30 E-value=4.1 Score=35.17 Aligned_cols=43 Identities=19% Similarity=0.385 Sum_probs=28.0
Q ss_pred EEeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccc
Q 011230 29 QVESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNE 72 (490)
Q Consensus 29 eies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnE 72 (490)
.+...||.||.+...-+ ...+----|=+-.-|.|..|||+..|
T Consensus 60 ~~~~~Cp~Cg~~~a~f~-~~Q~RsadE~~T~fy~C~~C~~~w~~ 102 (104)
T TIGR01384 60 TTRVECPKCGHKEAYYW-LLQTRRADEPETRFYKCTKCGYVWRE 102 (104)
T ss_pred cccCCCCCCCCCeeEEE-EeccCCCCCCcEEEEEeCCCCCeeEe
Confidence 45789999986643222 12222234556678999999998765
No 47
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=76.56 E-value=4.6 Score=37.89 Aligned_cols=64 Identities=23% Similarity=0.324 Sum_probs=43.4
Q ss_pred ccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccceeeccccCCcceEEEEEeeCCCcccccce
Q 011230 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEIQPRGCNYSLKVPSSDQKMFHRQ 101 (490)
Q Consensus 32 s~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEvq~~g~i~~kG~r~tl~V~~~~~~DLnR~ 101 (490)
..||-||.+ .|+.+-.+.--=+..|---=+|+.||+|++..--.+...+ ..+|=. |..+.++|+
T Consensus 1 M~CP~C~~~-dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErve~~~l----~ViKkd-G~re~Fdr~ 64 (147)
T TIGR00244 1 MHCPFCQHH-NTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELLPP----TVIKQD-GVREPFNRE 64 (147)
T ss_pred CCCCCCCCC-CCEeeeccccCCCCeeeecccCCccCCccceeeecccccc----EEEcCC-CCCCCCCHH
Confidence 369999865 6777666665667778888899999999987655554433 233332 455666665
No 48
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=76.21 E-value=3.4 Score=30.10 Aligned_cols=27 Identities=30% Similarity=0.749 Sum_probs=18.0
Q ss_pred cCcCCccccceeEEEeecCCCCcEEEEEeecCCCCC
Q 011230 287 TCGACAASCETRMFMTRIPYFQEVIVMASTCDACGY 322 (490)
Q Consensus 287 ~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGy 322 (490)
.||.|+..... +.+ .+ +..-.|++||-
T Consensus 1 ~CP~C~~~l~~----~~~---~~--~~id~C~~C~G 27 (41)
T PF13453_consen 1 KCPRCGTELEP----VRL---GD--VEIDVCPSCGG 27 (41)
T ss_pred CcCCCCcccce----EEE---CC--EEEEECCCCCe
Confidence 59999886433 333 55 45567999984
No 49
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=75.65 E-value=7.6 Score=37.99 Aligned_cols=71 Identities=24% Similarity=0.437 Sum_probs=43.3
Q ss_pred ccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccceeecc-------ccCCcceEEEEEeeCCCcccccceEEe
Q 011230 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAG-------EIQPRGCNYSLKVPSSDQKMFHRQVVK 104 (490)
Q Consensus 32 s~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEvq~~g-------~i~~kG~r~tl~V~~~~~~DLnR~Vvk 104 (490)
.+|+.|+.+ .|.|... +. ++...|..||.+.. |+.-- +--.+|..++++|+ +...-.+-|.+
T Consensus 99 V~C~~C~~p-dT~l~k~-----~~--~~~l~C~aCGa~~~-v~~~~~~~~~~~~~~~~~e~~~v~Ie--~l~~~G~GVak 167 (201)
T PRK12336 99 VICSECGLP-DTRLVKE-----DR--VLMLRCDACGAHRP-VKKRKASSETQREAIEEGKTYEVEIT--GTGRKGDGVAK 167 (201)
T ss_pred EECCCCCCC-CcEEEEc-----CC--eEEEEcccCCCCcc-ccccccccCCCCCCCccCCEEEEEEE--EccCCCceEEE
Confidence 789999876 5666433 22 44689999999754 22211 11123455778887 55555555776
Q ss_pred cCccEEEEe
Q 011230 105 SESATIKIP 113 (490)
Q Consensus 105 S~~ati~IP 113 (490)
-+..++.+|
T Consensus 168 ~~g~~vfV~ 176 (201)
T PRK12336 168 KGKYTIFVP 176 (201)
T ss_pred ECCEEEEeC
Confidence 666666665
No 50
>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=75.62 E-value=1.7 Score=34.61 Aligned_cols=29 Identities=31% Similarity=0.738 Sum_probs=19.9
Q ss_pred eccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCc
Q 011230 31 ESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (490)
Q Consensus 31 es~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrn 70 (490)
...||.||..... ..---.|.|++||+..
T Consensus 28 Sq~C~~CG~~~~~-----------~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 28 SQTCPRCGHRNKK-----------RRSGRVFTCPNCGFEM 56 (69)
T ss_pred ccCccCccccccc-----------ccccceEEcCCCCCEE
Confidence 4569999966444 1223468999999963
No 51
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=75.49 E-value=0.85 Score=42.16 Aligned_cols=33 Identities=27% Similarity=0.582 Sum_probs=20.6
Q ss_pred EEeccCCccCCCceEEEEEeecCCccceEEE-----EeecCCCCCCcc
Q 011230 29 QVESLCMRCGENGVTRFLLTLIPHFRKVLLS-----AFECPHCGERNN 71 (490)
Q Consensus 29 eies~Cp~Cg~~g~trlllt~IP~F~eviim-----Sf~C~~CGyrnn 71 (490)
...-.||+||..-. |-+.+.. .|.||+||..=-
T Consensus 97 ~~~Y~Cp~C~~~y~----------~~ea~~~~d~~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 97 NAYYKCPNCQSKYT----------FLEANQLLDMDGTFTCPRCGEELE 134 (147)
T ss_pred CcEEECcCCCCEee----------HHHHHHhcCCCCcEECCCCCCEEE
Confidence 35678999984311 2333322 399999998643
No 52
>PRK14292 chaperone protein DnaJ; Provisional
Probab=75.47 E-value=19 Score=38.14 Aligned_cols=33 Identities=27% Similarity=0.495 Sum_probs=20.0
Q ss_pred ccCCccCCCceEEEEEeecCCccceEEEEeecCCCC
Q 011230 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCG 67 (490)
Q Consensus 32 s~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CG 67 (490)
..|+.|+..|..++....+|.+ + .+...|+.|+
T Consensus 158 ~~C~~C~G~G~~~~~~~~~~g~--~-~~~~~C~~C~ 190 (371)
T PRK14292 158 KTCPTCRGAGAVRAQARTIFGV--V-ETQQPCPTCR 190 (371)
T ss_pred ccCCCCCCccEEEEEEeccCce--E-EEeeecCCCc
Confidence 4577777777666655555533 2 3466788883
No 53
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=75.17 E-value=3.2 Score=30.06 Aligned_cols=36 Identities=28% Similarity=0.522 Sum_probs=19.1
Q ss_pred CCccCCCc---eEEEEEeecCCccceEE---EEeecCCCCCCc
Q 011230 34 CMRCGENG---VTRFLLTLIPHFRKVLL---SAFECPHCGERN 70 (490)
Q Consensus 34 Cp~Cg~~g---~trlllt~IP~F~evii---mSf~C~~CGyrn 70 (490)
||.|+... .++-+.+.. -=+-+++ -.+.|++||-..
T Consensus 1 C~~C~~~~~~~~~~~~~~~~-~~~~~~i~~vp~~~C~~CGE~~ 42 (46)
T TIGR03831 1 CPICGGEELEGKTTTETYEY-GGELIVIENVPALVCPQCGEEY 42 (46)
T ss_pred CCCCCCceecceEEEEEEEe-CCEEEEEeCCCccccccCCCEe
Confidence 99996432 222233333 2233333 356799999653
No 54
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=75.10 E-value=2.4 Score=31.77 Aligned_cols=29 Identities=24% Similarity=0.705 Sum_probs=17.2
Q ss_pred cCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCc
Q 011230 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (490)
Q Consensus 33 ~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrn 70 (490)
.||.||.....+ -... -.-+.|++|||..
T Consensus 2 FCp~Cg~~l~~~-------~~~~--~~~~vC~~Cg~~~ 30 (52)
T smart00661 2 FCPKCGNMLIPK-------EGKE--KRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCCccccc-------cCCC--CCEEECCcCCCeE
Confidence 599998732111 1111 0267899999964
No 55
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=74.43 E-value=2.3 Score=36.50 Aligned_cols=36 Identities=31% Similarity=0.716 Sum_probs=25.3
Q ss_pred eccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccceeeccccCC
Q 011230 31 ESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEIQP 81 (490)
Q Consensus 31 es~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEvq~~g~i~~ 81 (490)
.-.||.|++...-|+ -+- -+.|.+|||+. .+|.+.|
T Consensus 35 ~~~Cp~C~~~~VkR~-a~G----------IW~C~kCg~~f----AGgay~P 70 (89)
T COG1997 35 KHVCPFCGRTTVKRI-ATG----------IWKCRKCGAKF----AGGAYTP 70 (89)
T ss_pred CCcCCCCCCcceeee-ccC----------eEEcCCCCCee----ccccccc
Confidence 457999998844443 222 38999999987 3666666
No 56
>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=74.15 E-value=2.8 Score=30.48 Aligned_cols=37 Identities=19% Similarity=0.362 Sum_probs=21.5
Q ss_pred cCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCc
Q 011230 287 TCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRN 324 (490)
Q Consensus 287 ~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~ 324 (490)
.||.||+....-+ ...+=-=.|-...-+.|-.||++-
T Consensus 2 ~Cp~Cg~~~a~~~-~~Q~rsaDE~~T~fy~C~~C~~~w 38 (39)
T PF01096_consen 2 KCPKCGHNEAVFF-QIQTRSADEPMTLFYVCCNCGHRW 38 (39)
T ss_dssp --SSS-SSEEEEE-EESSSSSSSSSEEEEEESSSTEEE
T ss_pred CCcCCCCCeEEEE-EeeccCCCCCCeEEEEeCCCCCee
Confidence 6999998643222 333322356667778899999863
No 57
>PRK14284 chaperone protein DnaJ; Provisional
Probab=73.66 E-value=18 Score=38.77 Aligned_cols=26 Identities=35% Similarity=0.602 Sum_probs=17.1
Q ss_pred cEEEEeee------eeEeCCCCCCCceeeHHH
Q 011230 108 ATIKIPEL------DFEIPPEAQRGSLSTVEG 133 (490)
Q Consensus 108 ati~IPEL------~~eI~p~~~~G~iTTVEG 133 (490)
++++||-| .+.||++++.|.+-.|.|
T Consensus 295 ~~~~v~tld~g~~i~v~Ip~g~~~g~~~~i~g 326 (391)
T PRK14284 295 MKKEIPTLLKEGTCRLTIPEGIQSGTILKVRG 326 (391)
T ss_pred CeEEEeecCCCcEEEEEECCccCCCeEEEECC
Confidence 55666644 377777777777776654
No 58
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=73.41 E-value=2.5 Score=36.37 Aligned_cols=40 Identities=25% Similarity=0.499 Sum_probs=26.3
Q ss_pred cceEeeccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCccccccCCCCC
Q 011230 280 EVMTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRIP 334 (490)
Q Consensus 280 ev~~~~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEVk~gg~i~ 334 (490)
+.+.-...||.|+++..-|. -+-| +.|.+|||+. .||++.
T Consensus 30 ~~~~~~~~Cp~C~~~~VkR~-a~GI----------W~C~kCg~~f----AGgay~ 69 (89)
T COG1997 30 AQQRAKHVCPFCGRTTVKRI-ATGI----------WKCRKCGAKF----AGGAYT 69 (89)
T ss_pred HHHhcCCcCCCCCCcceeee-ccCe----------EEcCCCCCee----cccccc
Confidence 34555678999999843332 2333 7899999975 355544
No 59
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=72.88 E-value=1.5 Score=39.24 Aligned_cols=43 Identities=19% Similarity=0.420 Sum_probs=27.2
Q ss_pred eEEeccCCccCCCce-EEEEEeecCCccceEEEEeecCCCCCCccc
Q 011230 28 YQVESLCMRCGENGV-TRFLLTLIPHFRKVLLSAFECPHCGERNNE 72 (490)
Q Consensus 28 ~eies~Cp~Cg~~g~-trlllt~IP~F~eviimSf~C~~CGyrnnE 72 (490)
..|+-.||.||...+ ..-+.++=--=+.- .-+.|+.|+||.+|
T Consensus 71 a~I~~kCpkCghe~m~Y~T~QlRSADEGQT--VFYTC~kC~~k~~e 114 (116)
T KOG2907|consen 71 AVIKHKCPKCGHEEMSYHTLQLRSADEGQT--VFYTCPKCKYKFTE 114 (116)
T ss_pred cchhccCcccCCchhhhhhhhcccccCCce--EEEEcCccceeeec
Confidence 358899999996543 22222322222333 35899999999875
No 60
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=72.66 E-value=3 Score=37.52 Aligned_cols=19 Identities=32% Similarity=0.186 Sum_probs=15.5
Q ss_pred ceeEeHHHHHHHHHHHHhh
Q 011230 378 GIVTTVEGLITKISESLER 396 (490)
Q Consensus 378 G~~TTVEGlL~~i~d~L~~ 396 (490)
=.+-||-.-|.+++..|..
T Consensus 61 iSYPTvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 61 ISYPTVRNRLDKIIEKLGY 79 (113)
T ss_pred CCcHHHHHHHHHHHHHhCC
Confidence 3567899999999998876
No 61
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=72.65 E-value=3.7 Score=38.05 Aligned_cols=32 Identities=19% Similarity=0.490 Sum_probs=22.5
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCcc
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNS 325 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~n 325 (490)
..||.|+.+-+.-.+. +. ++...|..||.+..
T Consensus 103 VlC~~C~spdT~l~k~------~r--~~~l~C~ACGa~~~ 134 (138)
T PRK03988 103 VICPECGSPDTKLIKE------GR--IWVLKCEACGAETP 134 (138)
T ss_pred EECCCCCCCCcEEEEc------CC--eEEEEcccCCCCCc
Confidence 5699999986333322 23 66789999999753
No 62
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=72.51 E-value=1.6 Score=34.43 Aligned_cols=24 Identities=38% Similarity=0.825 Sum_probs=17.5
Q ss_pred cCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCc
Q 011230 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (490)
Q Consensus 33 ~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrn 70 (490)
+||.|++.. -.-..|.||.||+-.
T Consensus 1 ~Cpv~~~~~--------------~~~v~~~Cp~cGipt 24 (55)
T PF13824_consen 1 LCPVCKKDL--------------PAHVNFECPDCGIPT 24 (55)
T ss_pred CCCCCcccc--------------ccccCCcCCCCCCcC
Confidence 589998654 233489999999853
No 63
>PRK14284 chaperone protein DnaJ; Provisional
Probab=72.50 E-value=12 Score=40.03 Aligned_cols=26 Identities=31% Similarity=0.542 Sum_probs=18.0
Q ss_pred eeEEecce------eeeecCCCccceeEeHHH
Q 011230 360 AGVKIPEL------DLELAGGTLGGIVTTVEG 385 (490)
Q Consensus 360 a~v~IPEL------~lei~pGtl~G~~TTVEG 385 (490)
+++.||-| .+.|++|+..|..-.|.|
T Consensus 295 ~~~~v~tld~g~~i~v~Ip~g~~~g~~~~i~g 326 (391)
T PRK14284 295 MKKEIPTLLKEGTCRLTIPEGIQSGTILKVRG 326 (391)
T ss_pred CeEEEeecCCCcEEEEEECCccCCCeEEEECC
Confidence 55666643 478888888777776664
No 64
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=72.36 E-value=5 Score=29.18 Aligned_cols=28 Identities=29% Similarity=0.597 Sum_probs=18.1
Q ss_pred cCCccCCCceEEEEEeecCCccceEEEEeecCCCCCC
Q 011230 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGER 69 (490)
Q Consensus 33 ~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyr 69 (490)
.||.|+....... + .+ +....|++||--
T Consensus 1 ~CP~C~~~l~~~~----~---~~--~~id~C~~C~G~ 28 (41)
T PF13453_consen 1 KCPRCGTELEPVR----L---GD--VEIDVCPSCGGI 28 (41)
T ss_pred CcCCCCcccceEE----E---CC--EEEEECCCCCeE
Confidence 4999976533322 2 55 445779999853
No 65
>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=72.22 E-value=4.1 Score=29.61 Aligned_cols=36 Identities=28% Similarity=0.566 Sum_probs=20.7
Q ss_pred cCCccCCCceEEE-EEeecCCccceEEEEeecCCCCCCc
Q 011230 33 LCMRCGENGVTRF-LLTLIPHFRKVLLSAFECPHCGERN 70 (490)
Q Consensus 33 ~Cp~Cg~~g~trl-llt~IP~F~eviimSf~C~~CGyrn 70 (490)
.||+||.+...-+ ..++= =-|-...-|.|-.||++.
T Consensus 2 ~Cp~Cg~~~a~~~~~Q~rs--aDE~~T~fy~C~~C~~~w 38 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQIQTRS--ADEPMTLFYVCCNCGHRW 38 (39)
T ss_dssp --SSS-SSEEEEEEESSSS--SSSSSEEEEEESSSTEEE
T ss_pred CCcCCCCCeEEEEEeeccC--CCCCCeEEEEeCCCCCee
Confidence 5999997654333 22322 245556678899999874
No 66
>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=72.22 E-value=2.3 Score=33.84 Aligned_cols=29 Identities=24% Similarity=0.532 Sum_probs=20.6
Q ss_pred eccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCc
Q 011230 285 PSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRN 324 (490)
Q Consensus 285 ~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~ 324 (490)
...||.||..... ..-.-.|.|++||+..
T Consensus 28 Sq~C~~CG~~~~~-----------~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 28 SQTCPRCGHRNKK-----------RRSGRVFTCPNCGFEM 56 (69)
T ss_pred ccCccCccccccc-----------ccccceEEcCCCCCEE
Confidence 3459999987644 2233468999999963
No 67
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=71.87 E-value=2.7 Score=33.02 Aligned_cols=32 Identities=34% Similarity=0.717 Sum_probs=21.2
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCcccc
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSEL 327 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEV 327 (490)
..||.||+.... .=+.-+++| .|+.||... ||
T Consensus 3 ~~CP~CG~~iev-----~~~~~GeiV----~Cp~CGael-eV 34 (54)
T TIGR01206 3 FECPDCGAEIEL-----ENPELGELV----ICDECGAEL-EV 34 (54)
T ss_pred cCCCCCCCEEec-----CCCccCCEE----eCCCCCCEE-EE
Confidence 479999995421 223346765 899999854 44
No 68
>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=71.22 E-value=3.8 Score=32.07 Aligned_cols=35 Identities=23% Similarity=0.494 Sum_probs=23.5
Q ss_pred eEeeccCcCCcc-ccceeEEEeecCCCCcEEEEEeecCCCCCCc
Q 011230 282 MTFPSTCGACAA-SCETRMFMTRIPYFQEVIVMASTCDACGYRN 324 (490)
Q Consensus 282 ~~~~s~Cp~C~~-~~~t~m~~~~IP~FkeviImsf~C~~CGyr~ 324 (490)
..+...|+.|+. +|... .--|.++ .|.|++||+.|
T Consensus 19 ~r~aLIC~~C~~hNGla~-----~~~~~~i---~y~C~~Cg~~N 54 (54)
T PF10058_consen 19 NRYALICSKCFSHNGLAP-----KEEFEEI---QYRCPYCGALN 54 (54)
T ss_pred CceeEECcccchhhcccc-----cccCCce---EEEcCCCCCcC
Confidence 345667999974 56433 2224444 99999999865
No 69
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=71.11 E-value=4.5 Score=29.27 Aligned_cols=35 Identities=20% Similarity=0.380 Sum_probs=18.7
Q ss_pred CcCCccc-c--ceeEEEeecCCCCcEEE---EEeecCCCCCC
Q 011230 288 CGACAAS-C--ETRMFMTRIPYFQEVIV---MASTCDACGYR 323 (490)
Q Consensus 288 Cp~C~~~-~--~t~m~~~~IP~FkeviI---msf~C~~CGyr 323 (490)
||.|+.. . .++.+.+.. -=+-++| -++.|++||-.
T Consensus 1 C~~C~~~~~~~~~~~~~~~~-~~~~~~i~~vp~~~C~~CGE~ 41 (46)
T TIGR03831 1 CPICGGEELEGKTTTETYEY-GGELIVIENVPALVCPQCGEE 41 (46)
T ss_pred CCCCCCceecceEEEEEEEe-CCEEEEEeCCCccccccCCCE
Confidence 8999643 2 232333333 2233333 24579999964
No 70
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=71.07 E-value=1.8 Score=32.43 Aligned_cols=26 Identities=35% Similarity=0.825 Sum_probs=16.7
Q ss_pred cCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCc
Q 011230 287 TCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRN 324 (490)
Q Consensus 287 ~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~ 324 (490)
.|..||..-... .-....|++||+|-
T Consensus 4 ~C~~Cg~~~~~~------------~~~~irC~~CG~rI 29 (44)
T smart00659 4 ICGECGRENEIK------------SKDVVRCRECGYRI 29 (44)
T ss_pred ECCCCCCEeecC------------CCCceECCCCCceE
Confidence 588888764322 12457888888863
No 71
>KOG2846 consensus Predicted membrane protein [Function unknown]
Probab=71.00 E-value=1.8 Score=45.30 Aligned_cols=40 Identities=28% Similarity=0.589 Sum_probs=30.1
Q ss_pred eEEeccCCccC-CCceEEEEEeecCCccceEEEEeecCCCCCCccceee
Q 011230 28 YQVESLCMRCG-ENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQF 75 (490)
Q Consensus 28 ~eies~Cp~Cg-~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEvq~ 75 (490)
.-.--.|.+|+ .||..+. -.-|| .+|.|+||+..|-..+.
T Consensus 217 ~ryALIC~~C~~HNGla~~--ee~~y------i~F~C~~Cn~LN~~~k~ 257 (328)
T KOG2846|consen 217 NRYALICSQCHHHNGLARK--EEYEY------ITFRCPHCNALNPAKKS 257 (328)
T ss_pred chhhhcchhhccccCcCCh--hhcCc------eEEECccccccCCCcCC
Confidence 34566799999 6888776 33333 58999999999977665
No 72
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=70.48 E-value=2.7 Score=37.47 Aligned_cols=30 Identities=27% Similarity=0.738 Sum_probs=21.7
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCC
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYR 323 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr 323 (490)
..|+.|+.| .|.|... +. ++...|..||.+
T Consensus 81 VlC~~C~sp-dT~l~k~-----~r--~~~l~C~aCGa~ 110 (110)
T smart00653 81 VLCPECGSP-DTELIKE-----NR--LFFLKCEACGAR 110 (110)
T ss_pred EECCCCCCC-CcEEEEe-----CC--eEEEEccccCCC
Confidence 569999999 4555433 22 566789999985
No 73
>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=70.47 E-value=3.8 Score=35.97 Aligned_cols=36 Identities=25% Similarity=0.363 Sum_probs=21.5
Q ss_pred CcCCcc-ccceeEEEeecCCCCcE---EEEEeecCCCCCC
Q 011230 288 CGACAA-SCETRMFMTRIPYFQEV---IVMASTCDACGYR 323 (490)
Q Consensus 288 Cp~C~~-~~~t~m~~~~IP~Fkev---iImsf~C~~CGyr 323 (490)
||.|++ ..........+.|=++. .+-.+.|+.||-.
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~G~~~~v~~~~~~C~~CGe~ 40 (127)
T TIGR03830 1 CPICGSGELVRDVKDEPYTYKGESITIGVPGWYCPACGEE 40 (127)
T ss_pred CCCCCCccceeeeecceEEEcCEEEEEeeeeeECCCCCCE
Confidence 999985 44433333334444442 3357889999863
No 74
>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=69.74 E-value=3.9 Score=35.91 Aligned_cols=37 Identities=24% Similarity=0.450 Sum_probs=22.2
Q ss_pred CCccCC-CceEEEEEeecCCccc---eEEEEeecCCCCCCc
Q 011230 34 CMRCGE-NGVTRFLLTLIPHFRK---VLLSAFECPHCGERN 70 (490)
Q Consensus 34 Cp~Cg~-~g~trlllt~IP~F~e---viimSf~C~~CGyrn 70 (490)
||.|++ ..........+.|=++ |.+-.+.|++||-..
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~G~~~~v~~~~~~C~~CGe~~ 41 (127)
T TIGR03830 1 CPICGSGELVRDVKDEPYTYKGESITIGVPGWYCPACGEEL 41 (127)
T ss_pred CCCCCCccceeeeecceEEEcCEEEEEeeeeeECCCCCCEE
Confidence 999984 4443333333444444 334578999998744
No 75
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=69.15 E-value=2.7 Score=37.69 Aligned_cols=43 Identities=19% Similarity=0.357 Sum_probs=28.0
Q ss_pred eEeeccCcCCcccc-ceeEEEeecCCCCcEEEEEeecCCCCCCccc
Q 011230 282 MTFPSTCGACAASC-ETRMFMTRIPYFQEVIVMASTCDACGYRNSE 326 (490)
Q Consensus 282 ~~~~s~Cp~C~~~~-~t~m~~~~IP~FkeviImsf~C~~CGyr~nE 326 (490)
-.++-.||.||++. ..+.+.++=--=+.. +-+.|++|+||..|
T Consensus 71 a~I~~kCpkCghe~m~Y~T~QlRSADEGQT--VFYTC~kC~~k~~e 114 (116)
T KOG2907|consen 71 AVIKHKCPKCGHEEMSYHTLQLRSADEGQT--VFYTCPKCKYKFTE 114 (116)
T ss_pred cchhccCcccCCchhhhhhhhcccccCCce--EEEEcCccceeeec
Confidence 36778899999873 333333333333333 45789999999875
No 76
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=68.84 E-value=2.4 Score=37.83 Aligned_cols=37 Identities=27% Similarity=0.466 Sum_probs=25.6
Q ss_pred EeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccceeecccc
Q 011230 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEI 79 (490)
Q Consensus 30 ies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEvq~~g~i 79 (490)
....|..||.... ++.+ .|.||+||-.+-+|..+.++
T Consensus 69 ~~~~C~~Cg~~~~-------~~~~------~~~CP~Cgs~~~~i~~G~El 105 (115)
T TIGR00100 69 VECECEDCSEEVS-------PEID------LYRCPKCHGIMLQVRAGKEL 105 (115)
T ss_pred cEEEcccCCCEEe-------cCCc------CccCcCCcCCCcEEecCCeE
Confidence 4567999985422 1111 47899999988888777664
No 77
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=68.80 E-value=1.4 Score=40.75 Aligned_cols=35 Identities=26% Similarity=0.434 Sum_probs=21.8
Q ss_pred EeeccCcCCccccceeEEEeecCCCCcEEEE-----EeecCCCCCCcccc
Q 011230 283 TFPSTCGACAASCETRMFMTRIPYFQEVIVM-----ASTCDACGYRNSEL 327 (490)
Q Consensus 283 ~~~s~Cp~C~~~~~t~m~~~~IP~FkeviIm-----sf~C~~CGyr~nEV 327 (490)
...-.||+|+..-. |-+.+.. .|.|++||..--+.
T Consensus 97 ~~~Y~Cp~C~~~y~----------~~ea~~~~d~~~~f~Cp~Cg~~l~~~ 136 (147)
T smart00531 97 NAYYKCPNCQSKYT----------FLEANQLLDMDGTFTCPRCGEELEED 136 (147)
T ss_pred CcEEECcCCCCEee----------HHHHHHhcCCCCcEECCCCCCEEEEc
Confidence 44556999986532 2233322 39999999865443
No 78
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=67.97 E-value=5 Score=31.50 Aligned_cols=30 Identities=27% Similarity=0.568 Sum_probs=19.6
Q ss_pred ccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCc
Q 011230 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (490)
Q Consensus 32 s~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrn 70 (490)
..||.||+.. -+ .=+.-+++| .|+.||-..
T Consensus 3 ~~CP~CG~~i----ev-~~~~~GeiV----~Cp~CGael 32 (54)
T TIGR01206 3 FECPDCGAEI----EL-ENPELGELV----ICDECGAEL 32 (54)
T ss_pred cCCCCCCCEE----ec-CCCccCCEE----eCCCCCCEE
Confidence 4799998732 11 223347766 899999854
No 79
>PRK14297 chaperone protein DnaJ; Provisional
Probab=67.70 E-value=43 Score=35.70 Aligned_cols=26 Identities=31% Similarity=0.749 Sum_probs=17.7
Q ss_pred cEEEEee----eeeEeCCCCCCCceeeHHH
Q 011230 108 ATIKIPE----LDFEIPPEAQRGSLSTVEG 133 (490)
Q Consensus 108 ati~IPE----L~~eI~p~~~~G~iTTVEG 133 (490)
++++||- +.+.|||+++.|.+-.|.|
T Consensus 289 ~~~~i~~ldg~~~v~ip~g~~~g~~~ri~g 318 (380)
T PRK14297 289 TEIKVPTVDGEVKYEVPAGTQPGTVFRLKG 318 (380)
T ss_pred CcEEEEcCCCcEEEEECCCcCCCCEEEEcC
Confidence 4556665 4577888777787776665
No 80
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=67.64 E-value=3 Score=27.64 Aligned_cols=10 Identities=50% Similarity=1.341 Sum_probs=7.4
Q ss_pred EEeecCCCCC
Q 011230 59 SAFECPHCGE 68 (490)
Q Consensus 59 mSf~C~~CGy 68 (490)
..|.||+||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 4678888875
No 81
>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=67.58 E-value=4.1 Score=32.62 Aligned_cols=36 Identities=25% Similarity=0.587 Sum_probs=25.0
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCccccc
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELK 328 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEVk 328 (490)
..||.|+..-...|...+ =+-.-.|-.|||+...-.
T Consensus 10 A~CP~C~~~Dtl~~~~e~-------~~e~vECv~Cg~~~~~~~ 45 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKEN-------NIELVECVECGYQEQQKD 45 (59)
T ss_pred ccCCCCcCccEEEEEEeC-------CceEEEeccCCCccccCC
Confidence 569999998877664332 223468999999875543
No 82
>PHA02942 putative transposase; Provisional
Probab=67.58 E-value=3.1 Score=44.49 Aligned_cols=33 Identities=33% Similarity=0.774 Sum_probs=20.4
Q ss_pred ccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCC-ccceeec
Q 011230 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGER-NNEVQFA 76 (490)
Q Consensus 32 s~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyr-nnEvq~~ 76 (490)
..||.||.... ++ --+ .|.|++|||. |.|+..+
T Consensus 326 q~Cs~CG~~~~-~l------~~r-----~f~C~~CG~~~drD~nAA 359 (383)
T PHA02942 326 VSCPKCGHKMV-EI------AHR-----YFHCPSCGYENDRDVIAI 359 (383)
T ss_pred ccCCCCCCccC-cC------CCC-----EEECCCCCCEeCcHHHHH
Confidence 56999996432 10 011 6999999995 4454433
No 83
>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=67.56 E-value=4.9 Score=32.19 Aligned_cols=34 Identities=18% Similarity=0.506 Sum_probs=24.1
Q ss_pred ccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccc
Q 011230 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNE 72 (490)
Q Consensus 32 s~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnE 72 (490)
..||.|+..-+.+|+.. -=+-.-+|=.|||+...
T Consensus 10 A~CP~C~~~Dtl~~~~e-------~~~e~vECv~Cg~~~~~ 43 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKE-------NNIELVECVECGYQEQQ 43 (59)
T ss_pred ccCCCCcCccEEEEEEe-------CCceEEEeccCCCcccc
Confidence 57999998877766432 22334689999998753
No 84
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=66.90 E-value=2.5 Score=41.78 Aligned_cols=37 Identities=35% Similarity=0.798 Sum_probs=26.9
Q ss_pred eccCCccC-CCceEEEEEeecCCccceEEEEeecCCCCCCccceee
Q 011230 31 ESLCMRCG-ENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQF 75 (490)
Q Consensus 31 es~Cp~Cg-~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEvq~ 75 (490)
.-.||.|+ .||-.++--. =+.-|.|+||..+|-++..
T Consensus 192 alIC~~C~hhngl~~~~ek--------~~~efiC~~Cn~~n~~~~~ 229 (251)
T COG5415 192 ALICPQCHHHNGLYRLAEK--------PIIEFICPHCNHKNDEVKE 229 (251)
T ss_pred hhccccccccccccccccc--------cchheecccchhhcCcccc
Confidence 34699998 6888876332 2337999999999965543
No 85
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=66.56 E-value=4.2 Score=28.59 Aligned_cols=25 Identities=32% Similarity=0.905 Sum_probs=14.5
Q ss_pred cCCccCCCceEEEEEeecCCccceEEEEeecCCCCCC
Q 011230 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGER 69 (490)
Q Consensus 33 ~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyr 69 (490)
.|..||..-. |.. ++. ..|++||||
T Consensus 2 ~C~~Cg~~~~-------~~~-~~~----irC~~CG~R 26 (32)
T PF03604_consen 2 ICGECGAEVE-------LKP-GDP----IRCPECGHR 26 (32)
T ss_dssp BESSSSSSE--------BST-SST----SSBSSSS-S
T ss_pred CCCcCCCeeE-------cCC-CCc----EECCcCCCe
Confidence 5888886532 222 232 389999987
No 86
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=66.26 E-value=5.7 Score=36.57 Aligned_cols=31 Identities=23% Similarity=0.477 Sum_probs=21.4
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCc
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRN 324 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~ 324 (490)
..||.|+.|-+.-.+. +. ++...|..||++.
T Consensus 98 VlC~~C~sPdT~l~k~------~r--~~~l~C~ACGa~~ 128 (133)
T TIGR00311 98 VICRECNRPDTRIIKE------GR--VSLLKCEACGAKA 128 (133)
T ss_pred EECCCCCCCCcEEEEe------CC--eEEEecccCCCCC
Confidence 5799999986443321 23 3456999999975
No 87
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=66.10 E-value=5.5 Score=44.59 Aligned_cols=47 Identities=13% Similarity=0.154 Sum_probs=30.9
Q ss_pred eEeeccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCccccc
Q 011230 282 MTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELK 328 (490)
Q Consensus 282 ~~~~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEVk 328 (490)
..+...||+||..-..++.....|.=..-=-.-+.|+|||..-.|-.
T Consensus 197 r~~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e~~ 243 (557)
T PF05876_consen 197 RRYYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEEHD 243 (557)
T ss_pred eEEEccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCHHH
Confidence 38999999999876555443333310012235678999999988743
No 88
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=65.65 E-value=2.8 Score=37.37 Aligned_cols=36 Identities=14% Similarity=0.337 Sum_probs=25.0
Q ss_pred eeccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCccccccCCC
Q 011230 284 FPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGR 332 (490)
Q Consensus 284 ~~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEVk~gg~ 332 (490)
....|+.|++.... +.+ .+.||+||-.+-+|.+|-+
T Consensus 69 ~~~~C~~Cg~~~~~-------~~~------~~~CP~Cgs~~~~i~~G~E 104 (115)
T TIGR00100 69 VECECEDCSEEVSP-------EID------LYRCPKCHGIMLQVRAGKE 104 (115)
T ss_pred cEEEcccCCCEEec-------CCc------CccCcCCcCCCcEEecCCe
Confidence 34679999965322 111 4789999998888876643
No 89
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=65.43 E-value=1.6 Score=41.84 Aligned_cols=34 Identities=32% Similarity=0.729 Sum_probs=23.7
Q ss_pred EeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccce
Q 011230 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEV 73 (490)
Q Consensus 30 ies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEv 73 (490)
..-.||+||.. +. |-|.+-..|.||.||..=.+.
T Consensus 116 ~~Y~Cp~C~~r----yt------f~eA~~~~F~Cp~Cg~~L~~~ 149 (178)
T PRK06266 116 MFFFCPNCHIR----FT------FDEAMEYGFRCPQCGEMLEEY 149 (178)
T ss_pred CEEECCCCCcE----Ee------HHHHhhcCCcCCCCCCCCeec
Confidence 45679999832 21 345666799999999765554
No 90
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=65.40 E-value=9.7 Score=31.53 Aligned_cols=47 Identities=23% Similarity=0.266 Sum_probs=23.2
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCccccccCCC
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGR 332 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEVk~gg~ 332 (490)
..||.|+.+...+--.+.=++=..-+.+-..|+.||..---+|.=|+
T Consensus 2 ~~CP~C~~~L~~~~~~~~C~~C~~~~~~~a~CPdC~~~Le~LkACGA 48 (70)
T PF07191_consen 2 NTCPKCQQELEWQGGHYHCEACQKDYKKEAFCPDCGQPLEVLKACGA 48 (70)
T ss_dssp -B-SSS-SBEEEETTEEEETTT--EEEEEEE-TTT-SB-EEEEETTE
T ss_pred CcCCCCCCccEEeCCEEECccccccceecccCCCcccHHHHHHHhcc
Confidence 35777777654444344445555566667777777776666665543
No 91
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=65.23 E-value=7.5 Score=31.25 Aligned_cols=9 Identities=33% Similarity=1.180 Sum_probs=7.0
Q ss_pred eecCCCCCC
Q 011230 315 STCDACGYR 323 (490)
Q Consensus 315 f~C~~CGyr 323 (490)
..|++|||+
T Consensus 51 Y~Cp~CGF~ 59 (61)
T COG2888 51 YRCPKCGFE 59 (61)
T ss_pred eECCCcCcc
Confidence 478888885
No 92
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=64.99 E-value=2.8 Score=37.35 Aligned_cols=38 Identities=16% Similarity=0.380 Sum_probs=23.7
Q ss_pred EeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccceeecccc
Q 011230 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEI 79 (490)
Q Consensus 30 ies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEvq~~g~i 79 (490)
....|+.||.. +.++. ...|.||+||-.+.++-.+.++
T Consensus 69 ~~~~C~~Cg~~-------~~~~~-----~~~~~CP~Cgs~~~~i~~G~El 106 (114)
T PRK03681 69 AECWCETCQQY-------VTLLT-----QRVRRCPQCHGDMLRIVADDGL 106 (114)
T ss_pred cEEEcccCCCe-------eecCC-----ccCCcCcCcCCCCcEEccCCeE
Confidence 45679999852 11110 1116899999888777666553
No 93
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=64.83 E-value=1.6 Score=41.06 Aligned_cols=35 Identities=26% Similarity=0.582 Sum_probs=24.2
Q ss_pred EeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCcccee
Q 011230 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQ 74 (490)
Q Consensus 30 ies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEvq 74 (490)
..-.||+|+. |+. |-|.+-..|.||.||..-.+..
T Consensus 108 ~~Y~Cp~c~~----r~t------f~eA~~~~F~Cp~Cg~~L~~~d 142 (158)
T TIGR00373 108 MFFICPNMCV----RFT------FNEAMELNFTCPRCGAMLDYLD 142 (158)
T ss_pred CeEECCCCCc----Eee------HHHHHHcCCcCCCCCCEeeecc
Confidence 5568999973 221 4566667999999997654443
No 94
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=64.59 E-value=3.6 Score=32.31 Aligned_cols=22 Identities=41% Similarity=0.922 Sum_probs=16.3
Q ss_pred ccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCC
Q 011230 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGER 69 (490)
Q Consensus 32 s~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyr 69 (490)
+.||+||+ ..+.-..|++|||=
T Consensus 27 ~~C~~cG~----------------~~~~H~vc~~cG~Y 48 (55)
T TIGR01031 27 VVCPNCGE----------------FKLPHRVCPSCGYY 48 (55)
T ss_pred eECCCCCC----------------cccCeeECCccCeE
Confidence 55999963 44556789999973
No 95
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=64.31 E-value=4.2 Score=36.43 Aligned_cols=38 Identities=21% Similarity=0.329 Sum_probs=24.6
Q ss_pred EeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccceeecccc
Q 011230 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEI 79 (490)
Q Consensus 30 ies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEvq~~g~i 79 (490)
....|..||......- + ..+.||+||-.+-+|..+.++
T Consensus 70 ~~~~C~~Cg~~~~~~~-------~-----~~~~CP~Cgs~~~~i~~G~El 107 (117)
T PRK00564 70 VELECKDCSHVFKPNA-------L-----DYGVCEKCHSKNVIITQGNEM 107 (117)
T ss_pred CEEEhhhCCCccccCC-------c-----cCCcCcCCCCCceEEecCCEE
Confidence 3456999985422211 1 114599999988888777665
No 96
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=64.22 E-value=3.8 Score=40.91 Aligned_cols=32 Identities=34% Similarity=0.709 Sum_probs=21.6
Q ss_pred ccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCC-ccceeecccc
Q 011230 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGER-NNEVQFAGEI 79 (490)
Q Consensus 32 s~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyr-nnEvq~~g~i 79 (490)
..||.||. .---.|.|++||+. |.|+..+--|
T Consensus 310 ~~C~~cg~----------------~~~r~~~C~~cg~~~~rD~naa~Ni 342 (364)
T COG0675 310 KTCPCCGH----------------LSGRLFKCPRCGFVHDRDVNAALNI 342 (364)
T ss_pred ccccccCC----------------ccceeEECCCCCCeehhhHHHHHHH
Confidence 67999997 11346899999995 4555444333
No 97
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=62.82 E-value=4.6 Score=28.78 Aligned_cols=30 Identities=33% Similarity=0.687 Sum_probs=13.5
Q ss_pred cCCccCCCceEEEEEeecCCccceEEEEeecCCCCCC
Q 011230 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGER 69 (490)
Q Consensus 33 ~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyr 69 (490)
-||.||.....+ ||-=.+ -.-..|+.|||=
T Consensus 2 fC~~CG~~l~~~-----ip~gd~--r~R~vC~~Cg~I 31 (34)
T PF14803_consen 2 FCPQCGGPLERR-----IPEGDD--RERLVCPACGFI 31 (34)
T ss_dssp B-TTT--B-EEE-------TT-S--S-EEEETTTTEE
T ss_pred ccccccChhhhh-----cCCCCC--ccceECCCCCCE
Confidence 499998774444 451111 124679999973
No 98
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=62.30 E-value=4.4 Score=32.08 Aligned_cols=23 Identities=39% Similarity=0.800 Sum_probs=16.7
Q ss_pred ccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCc
Q 011230 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (490)
Q Consensus 32 s~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrn 70 (490)
+.||+||+ ..+.-..|++|||=+
T Consensus 28 ~~C~~CG~----------------~~~~H~vC~~CG~Y~ 50 (57)
T PRK12286 28 VECPNCGE----------------PKLPHRVCPSCGYYK 50 (57)
T ss_pred eECCCCCC----------------ccCCeEECCCCCcCC
Confidence 56999964 334467899999844
No 99
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=61.84 E-value=7.5 Score=43.55 Aligned_cols=93 Identities=17% Similarity=0.252 Sum_probs=49.0
Q ss_pred eEEeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccceeeccccCCcceEEEEEeeCCCcccccceEEecCc
Q 011230 28 YQVESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEIQPRGCNYSLKVPSSDQKMFHRQVVKSES 107 (490)
Q Consensus 28 ~eies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEvq~~g~i~~kG~r~tl~V~~~~~~DLnR~VvkS~~ 107 (490)
......||+||..-..+.--.+.|.=..-=-.-+.|+|||..-.|-+-.-.+ .+| +|.-. .+ ..++.+
T Consensus 197 r~~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e~~k~~m~-~~G-~Wv~~----~~------~~~~~~ 264 (557)
T PF05876_consen 197 RRYYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEEHDKRRMV-RRG-RWVAT----NP------DRRPRH 264 (557)
T ss_pred eEEEccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCHHHHhhcc-CCe-EEEec----cc------cCCCCE
Confidence 4789999999976443322111121001123468999999998875433322 233 23222 22 222333
Q ss_pred cEEEEeeeeeEeCCCCCCCceeeHHHHHHHHHHH
Q 011230 108 ATIKIPELDFEIPPEAQRGSLSTVEGILVRAADE 141 (490)
Q Consensus 108 ati~IPEL~~eI~p~~~~G~iTTVEGlL~~~~~~ 141 (490)
+ +|-|.. .-..+.+-..|..+.++.
T Consensus 265 ~-------gf~i~~--l~Sp~~sw~~ia~~~l~A 289 (557)
T PF05876_consen 265 V-------GFHINA--LYSPFVSWAEIAREFLEA 289 (557)
T ss_pred E-------EEEeee--eecccCCHHHHHHHHHhh
Confidence 3 444443 122336777777777776
No 100
>PTZ00037 DnaJ_C chaperone protein; Provisional
Probab=61.81 E-value=40 Score=36.63 Aligned_cols=33 Identities=15% Similarity=0.438 Sum_probs=17.0
Q ss_pred ccCCccCCCceEEEEEeecCCccceEEEEeecCCCC
Q 011230 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCG 67 (490)
Q Consensus 32 s~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CG 67 (490)
..|+.|+..|.. +....+.. -+.-+...|+.|+
T Consensus 167 ~~C~~C~G~G~~-~~~~~~g~--~~~q~~~~C~~C~ 199 (421)
T PTZ00037 167 VDCKLCNGQGIR-VQIRQMGS--MIHQTQSTCNSCN 199 (421)
T ss_pred ccCCCCCCCCeE-EEEEeecc--eeeEEEEeCCCCC
Confidence 357777777752 22222211 2334566777774
No 101
>PHA02942 putative transposase; Provisional
Probab=61.81 E-value=4.8 Score=43.05 Aligned_cols=28 Identities=29% Similarity=0.707 Sum_probs=18.5
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCcc
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNS 325 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~n 325 (490)
..||.||..... .. . =.|.|++|||..+
T Consensus 326 q~Cs~CG~~~~~------l~--~----r~f~C~~CG~~~d 353 (383)
T PHA02942 326 VSCPKCGHKMVE------IA--H----RYFHCPSCGYEND 353 (383)
T ss_pred ccCCCCCCccCc------CC--C----CEEECCCCCCEeC
Confidence 459999975421 00 1 1699999999643
No 102
>PHA02998 RNA polymerase subunit; Provisional
Probab=61.69 E-value=11 Score=36.63 Aligned_cols=48 Identities=17% Similarity=0.286 Sum_probs=31.6
Q ss_pred CCceE-EeccCCccCCCceE-EEEEeecCCccceEEEEeecCCCCCCcccee
Q 011230 25 APLYQ-VESLCMRCGENGVT-RFLLTLIPHFRKVLLSAFECPHCGERNNEVQ 74 (490)
Q Consensus 25 ~~v~e-ies~Cp~Cg~~g~t-rlllt~IP~F~eviimSf~C~~CGyrnnEvq 74 (490)
..+.. ++..||.||....+ .++.|+ --.|=...-+.|..||++..-=+
T Consensus 136 nvlpkkt~v~CPkCg~~~A~f~qlQTR--SADEPmT~FYkC~~CG~~wkppk 185 (195)
T PHA02998 136 NVLDEKYNTPCPNCKSKNTTPMMIQTR--AADEPPLVRHACRDCKKHFKPPK 185 (195)
T ss_pred eccCcccCCCCCCCCCCceEEEEEeec--cCCCCceEEEEcCCCCCccCCcc
Confidence 33444 77899999955333 333343 24666677889999999876433
No 103
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=59.85 E-value=4.2 Score=36.19 Aligned_cols=37 Identities=19% Similarity=0.513 Sum_probs=24.0
Q ss_pred EeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccceeecccc
Q 011230 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEI 79 (490)
Q Consensus 30 ies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEvq~~g~i 79 (490)
....|..||...... . ..|.||+||-.+-+|..+.++
T Consensus 69 ~~~~C~~Cg~~~~~~-------~------~~~~CP~Cgs~~~~i~~G~El 105 (113)
T PRK12380 69 AQAWCWDCSQVVEIH-------Q------HDAQCPHCHGERLRVDTGDSL 105 (113)
T ss_pred cEEEcccCCCEEecC-------C------cCccCcCCCCCCcEEccCCeE
Confidence 345799998442211 1 234699999888777666554
No 104
>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=59.79 E-value=6.4 Score=32.53 Aligned_cols=34 Identities=26% Similarity=0.530 Sum_probs=24.0
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCccc
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSE 326 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nE 326 (490)
..||.|+..-...|...+ =+---.|=+|||+...
T Consensus 9 a~CP~C~~~D~i~~~~e~-------~ve~vECV~CGy~e~~ 42 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWREN-------GVEYVECVECGYTERQ 42 (71)
T ss_pred ccCCCCcCccEEEEEEeC-------CceEEEecCCCCeecc
Confidence 469999998766664333 2455689999997653
No 105
>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=59.64 E-value=7.3 Score=32.19 Aligned_cols=33 Identities=18% Similarity=0.433 Sum_probs=23.3
Q ss_pred ccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCcc
Q 011230 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNN 71 (490)
Q Consensus 32 s~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnn 71 (490)
..||.|+..-+.++... -=+-.-+|=+|||+..
T Consensus 9 a~CP~C~~~D~i~~~~e-------~~ve~vECV~CGy~e~ 41 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWRE-------NGVEYVECVECGYTER 41 (71)
T ss_pred ccCCCCcCccEEEEEEe-------CCceEEEecCCCCeec
Confidence 57999998766665333 2245568999999764
No 106
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=59.45 E-value=14 Score=29.92 Aligned_cols=38 Identities=24% Similarity=0.546 Sum_probs=22.7
Q ss_pred cCcCCcccc----cee------EEEeecCCCCcEEEEEeecCCCCCCcccccc
Q 011230 287 TCGACAASC----ETR------MFMTRIPYFQEVIVMASTCDACGYRNSELKP 329 (490)
Q Consensus 287 ~Cp~C~~~~----~t~------m~~~~IP~FkeviImsf~C~~CGyr~nEVk~ 329 (490)
.||.||..- ..+ .++.+|.+=+ -.+-.|.+|||- |+-.
T Consensus 2 ~C~KCg~~~~e~~~v~~tgg~~skiFdvq~~~---f~~v~C~~CGYT--E~Y~ 49 (64)
T PF09855_consen 2 KCPKCGNEEYESGEVRATGGGLSKIFDVQNKK---FTTVSCTNCGYT--EFYK 49 (64)
T ss_pred CCCCCCCcceecceEEccCCeeEEEEEecCcE---EEEEECCCCCCE--EEEe
Confidence 599997541 222 2445666532 335579999995 5544
No 107
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=59.32 E-value=13 Score=32.04 Aligned_cols=42 Identities=19% Similarity=0.282 Sum_probs=27.0
Q ss_pred eeccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCccc
Q 011230 284 FPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSE 326 (490)
Q Consensus 284 ~~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nE 326 (490)
....||.||+....-+ ...+---.|=+-.-|.|.+|||+-.|
T Consensus 61 ~~~~Cp~Cg~~~a~f~-~~Q~RsadE~~T~fy~C~~C~~~w~~ 102 (104)
T TIGR01384 61 TRVECPKCGHKEAYYW-LLQTRRADEPETRFYKCTKCGYVWRE 102 (104)
T ss_pred ccCCCCCCCCCeeEEE-EeccCCCCCCcEEEEEeCCCCCeeEe
Confidence 3568999987642221 22232235566778999999998654
No 108
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=58.68 E-value=7.6 Score=34.12 Aligned_cols=32 Identities=25% Similarity=0.569 Sum_probs=19.9
Q ss_pred ccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCcc
Q 011230 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNN 71 (490)
Q Consensus 32 s~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnn 71 (490)
..||+||+. ...+ .|. + -+-.-.|+.|||.+.
T Consensus 22 f~CP~Cge~-~v~v---~~~--k--~~~h~~C~~CG~y~~ 53 (99)
T PRK14892 22 FECPRCGKV-SISV---KIK--K--NIAIITCGNCGLYTE 53 (99)
T ss_pred eECCCCCCe-Eeee---ecC--C--CcceEECCCCCCccC
Confidence 569999943 2222 111 1 255778999999764
No 109
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=58.13 E-value=8.7 Score=34.34 Aligned_cols=40 Identities=28% Similarity=0.450 Sum_probs=27.1
Q ss_pred eccCcCCccc-cceeEEEeecCCCCcEEEEEeecCCCCCCccc
Q 011230 285 PSTCGACAAS-CETRMFMTRIPYFQEVIVMASTCDACGYRNSE 326 (490)
Q Consensus 285 ~s~Cp~C~~~-~~t~m~~~~IP~FkeviImsf~C~~CGyr~nE 326 (490)
...||.||.. ....++.+.- =.|=.-..+.|.+|||+-++
T Consensus 72 ~~~CpkCg~~ea~y~~~QtRs--aDEp~T~Fy~C~~Cg~~wre 112 (113)
T COG1594 72 KEKCPKCGNKEAYYWQLQTRS--ADEPETRFYKCTRCGYRWRE 112 (113)
T ss_pred cccCCCCCCceeEEEeeehhc--cCCCceEEEEecccCCEeec
Confidence 4579999865 5455555543 34445556899999998754
No 110
>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=57.91 E-value=7.1 Score=29.08 Aligned_cols=28 Identities=21% Similarity=0.648 Sum_probs=18.7
Q ss_pred ccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCC
Q 011230 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGER 69 (490)
Q Consensus 32 s~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyr 69 (490)
..||.||..-..++ .+ ...|.|.+|++.
T Consensus 19 ~~CP~Cg~~~~~~~--~~--------~~~~~C~~C~~q 46 (46)
T PF12760_consen 19 FVCPHCGSTKHYRL--KT--------RGRYRCKACRKQ 46 (46)
T ss_pred CCCCCCCCeeeEEe--CC--------CCeEECCCCCCc
Confidence 34999986633333 22 568999999874
No 111
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=57.71 E-value=4 Score=43.18 Aligned_cols=33 Identities=27% Similarity=0.810 Sum_probs=20.9
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCcc
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNS 325 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~n 325 (490)
..||.|+.|- |.+..+. +. -.+..|..||||+.
T Consensus 97 VlC~~C~NPE-Tel~itk----~q--~i~~~CkACG~r~~ 129 (400)
T KOG2767|consen 97 VLCPSCENPE-TELIITK----KQ--TISLKCKACGFRSD 129 (400)
T ss_pred eeCcCCCCCc-eeEEecc----cc--hhhhHHHHcCCccc
Confidence 5799999884 2222221 11 13678999999864
No 112
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=57.53 E-value=4.6 Score=45.88 Aligned_cols=25 Identities=36% Similarity=0.850 Sum_probs=18.8
Q ss_pred EeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCc
Q 011230 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (490)
Q Consensus 30 ies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrn 70 (490)
--+.|+.||-.|.. .+.||+||-++
T Consensus 558 ~~~~C~~CGy~g~~----------------~~~CP~CG~~d 582 (618)
T PRK14704 558 PVDRCKCCSYHGVI----------------GNECPSCGNED 582 (618)
T ss_pred CCeecCCCCCCCCc----------------CccCcCCCCCC
Confidence 34789999865542 29999999865
No 113
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=57.45 E-value=4.8 Score=35.85 Aligned_cols=35 Identities=17% Similarity=0.382 Sum_probs=23.3
Q ss_pred eeccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCccccccCC
Q 011230 284 FPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGG 331 (490)
Q Consensus 284 ~~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEVk~gg 331 (490)
....|+.||+...... ..+.||+||-.+-+|.+|-
T Consensus 69 ~~~~C~~Cg~~~~~~~-------------~~~~CP~Cgs~~~~i~~G~ 103 (113)
T PRK12380 69 AQAWCWDCSQVVEIHQ-------------HDAQCPHCHGERLRVDTGD 103 (113)
T ss_pred cEEEcccCCCEEecCC-------------cCccCcCCCCCCcEEccCC
Confidence 3467999996532211 2336999998888887654
No 114
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=57.20 E-value=8.4 Score=29.66 Aligned_cols=32 Identities=25% Similarity=0.509 Sum_probs=21.3
Q ss_pred cceEeeccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCC
Q 011230 280 EVMTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYR 323 (490)
Q Consensus 280 ev~~~~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr 323 (490)
.|.-...-||.||.. -| .++. -.+.|..|||.
T Consensus 15 ~v~~~~~fCP~Cg~~---~m----~~~~-----~r~~C~~Cgyt 46 (50)
T PRK00432 15 KVKRKNKFCPRCGSG---FM----AEHL-----DRWHCGKCGYT 46 (50)
T ss_pred EEEEccCcCcCCCcc---hh----eccC-----CcEECCCcCCE
Confidence 354455689999974 22 2333 37889999995
No 115
>PRK14298 chaperone protein DnaJ; Provisional
Probab=57.11 E-value=38 Score=36.15 Aligned_cols=77 Identities=19% Similarity=0.378 Sum_probs=44.1
Q ss_pred ccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccceeeccccCCcceEEEEEeeCCCcccccceEEecCccEEE
Q 011230 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEIQPRGCNYSLKVPSSDQKMFHRQVVKSESATIK 111 (490)
Q Consensus 32 s~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEvq~~g~i~~kG~r~tl~V~~~~~~DLnR~VvkS~~ati~ 111 (490)
..|+.|+..|....... .|+.. +.+...|+.|+=+---+. . .++.- . .+-+++ .
T Consensus 159 ~~C~~C~G~G~~~~~~~-~~~g~--~~~~~~C~~C~G~G~~~~------~-----~C~~C---~---G~g~v~------~ 212 (377)
T PRK14298 159 KRCPTCGGTGQVTTTRS-TPLGQ--FVTTTTCSTCHGRGQVIE------S-----PCPVC---S---GTGKVR------K 212 (377)
T ss_pred CcCCCCCCccEEEEEEe-cCcee--EEEEEeCCCCCCCCcccC------C-----CCCCC---C---CccEEE------E
Confidence 45888877776554433 55543 367889999976542211 0 01111 0 011111 1
Q ss_pred EeeeeeEeCCCCCCCceeeHHHH
Q 011230 112 IPELDFEIPPEAQRGSLSTVEGI 134 (490)
Q Consensus 112 IPEL~~eI~p~~~~G~iTTVEGl 134 (490)
--.|.+.|||++..|..-.++|.
T Consensus 213 ~~~l~V~IppG~~~G~~i~~~g~ 235 (377)
T PRK14298 213 TRKITVNVPAGADSGLRLKLSGE 235 (377)
T ss_pred EEEEEecCCCCCCCCCEEEEecc
Confidence 13567889999999988888764
No 116
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=57.07 E-value=4.1 Score=36.33 Aligned_cols=36 Identities=11% Similarity=0.207 Sum_probs=23.1
Q ss_pred eeccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCccccccCC
Q 011230 284 FPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGG 331 (490)
Q Consensus 284 ~~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEVk~gg 331 (490)
....|+.|++. +.++.+ ..+.||+||-.+.++..|-
T Consensus 69 ~~~~C~~Cg~~-------~~~~~~-----~~~~CP~Cgs~~~~i~~G~ 104 (114)
T PRK03681 69 AECWCETCQQY-------VTLLTQ-----RVRRCPQCHGDMLRIVADD 104 (114)
T ss_pred cEEEcccCCCe-------eecCCc-----cCCcCcCcCCCCcEEccCC
Confidence 34679999962 222210 1167999998888886654
No 117
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=56.64 E-value=26 Score=25.55 Aligned_cols=35 Identities=20% Similarity=0.544 Sum_probs=21.5
Q ss_pred ccCCccCCC-----ceEEEEEeecCCccceEEEE-----eecCCC
Q 011230 32 SLCMRCGEN-----GVTRFLLTLIPHFRKVLLSA-----FECPHC 66 (490)
Q Consensus 32 s~Cp~Cg~~-----g~trlllt~IP~F~eviimS-----f~C~~C 66 (490)
..||.||.. |...-....+|+++.-+++- |.|++|
T Consensus 3 ~~Cp~Cg~~~~~~~g~~~r~i~~l~~~~~~~~L~i~~~R~~C~~C 47 (47)
T PF14690_consen 3 PRCPHCGSPSVHRHGYKTRRIRHLPIGGRPVYLRIRKRRYRCKNC 47 (47)
T ss_pred ccCCCcCCCceECCceEEEEEeecccCCEEEEEEEEeEEEECcCC
Confidence 469999854 33333455777777655543 566666
No 118
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=56.58 E-value=3.7 Score=36.46 Aligned_cols=37 Identities=30% Similarity=0.720 Sum_probs=21.8
Q ss_pred EeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccceeecccc
Q 011230 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEI 79 (490)
Q Consensus 30 ies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEvq~~g~i 79 (490)
....|..||..... ..+. +.||+||-.+-+|..+.++
T Consensus 69 ~~~~C~~Cg~~~~~-------~~~~------~~CP~Cgs~~~~i~~G~el 105 (113)
T PF01155_consen 69 ARARCRDCGHEFEP-------DEFD------FSCPRCGSPDVEIISGREL 105 (113)
T ss_dssp -EEEETTTS-EEEC-------HHCC------HH-SSSSSS-EEEEESS-E
T ss_pred CcEECCCCCCEEec-------CCCC------CCCcCCcCCCcEEccCCeE
Confidence 45679999966322 1121 4599999998888777664
No 119
>PRK14296 chaperone protein DnaJ; Provisional
Probab=56.41 E-value=61 Score=34.54 Aligned_cols=26 Identities=23% Similarity=0.464 Sum_probs=20.0
Q ss_pred cEEEEeeee----eEeCCCCCCCceeeHHH
Q 011230 108 ATIKIPELD----FEIPPEAQRGSLSTVEG 133 (490)
Q Consensus 108 ati~IPEL~----~eI~p~~~~G~iTTVEG 133 (490)
+++.||-|+ +.|||.++-|.+-.|.|
T Consensus 291 ~~~~i~tldG~~~v~ip~~t~~g~~~ri~G 320 (372)
T PRK14296 291 NEIIIKTLDGDIKYKLPKSINSNELIIINN 320 (372)
T ss_pred CEEEeeCCCCCEEEEECCccCCCcEEEEcC
Confidence 677888654 77888888888888753
No 120
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=55.86 E-value=9.4 Score=30.14 Aligned_cols=29 Identities=31% Similarity=0.860 Sum_probs=17.6
Q ss_pred ccCCccCCCceEEE----EEeecCCccceEEEEeecCCCCCC
Q 011230 32 SLCMRCGENGVTRF----LLTLIPHFRKVLLSAFECPHCGER 69 (490)
Q Consensus 32 s~Cp~Cg~~g~trl----llt~IP~F~eviimSf~C~~CGyr 69 (490)
.+||.||..-.+++ .|.+.|.| ||.|-..
T Consensus 5 i~CP~CgnKTR~kir~DT~LkNfPly---------CpKCK~E 37 (55)
T PF14205_consen 5 ILCPICGNKTRLKIREDTVLKNFPLY---------CPKCKQE 37 (55)
T ss_pred EECCCCCCccceeeecCceecccccc---------CCCCCce
Confidence 47999985443443 23455544 8888653
No 121
>PRK14291 chaperone protein DnaJ; Provisional
Probab=55.72 E-value=32 Score=36.69 Aligned_cols=32 Identities=25% Similarity=0.524 Sum_probs=20.7
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCc
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRN 324 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~ 324 (490)
..|+.|+..|..... .-.+.+...|++|+-+-
T Consensus 174 ~~C~~C~G~G~~~~~-------~g~~~~~~~C~~C~G~G 205 (382)
T PRK14291 174 KVCPTCGGSGEIYQR-------GGFFRISQTCPTCGGEG 205 (382)
T ss_pred ccCCCCCCceEEEEe-------cceEEEEecCCCCCCce
Confidence 457777766644333 12356788999998665
No 122
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=55.71 E-value=8.4 Score=33.84 Aligned_cols=32 Identities=22% Similarity=0.506 Sum_probs=19.8
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCcc
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNS 325 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~n 325 (490)
..||+||... ..+.|.. -+-...|..|||...
T Consensus 22 f~CP~Cge~~----v~v~~~k----~~~h~~C~~CG~y~~ 53 (99)
T PRK14892 22 FECPRCGKVS----ISVKIKK----NIAIITCGNCGLYTE 53 (99)
T ss_pred eECCCCCCeE----eeeecCC----CcceEECCCCCCccC
Confidence 4599999532 1222222 256689999998654
No 123
>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=55.48 E-value=7.7 Score=28.91 Aligned_cols=28 Identities=21% Similarity=0.433 Sum_probs=19.6
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCC
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYR 323 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr 323 (490)
..||.||..-..++.. ...+.|.+|++.
T Consensus 19 ~~CP~Cg~~~~~~~~~----------~~~~~C~~C~~q 46 (46)
T PF12760_consen 19 FVCPHCGSTKHYRLKT----------RGRYRCKACRKQ 46 (46)
T ss_pred CCCCCCCCeeeEEeCC----------CCeEECCCCCCc
Confidence 3499999873333322 678999999974
No 124
>PHA02998 RNA polymerase subunit; Provisional
Probab=55.00 E-value=17 Score=35.27 Aligned_cols=44 Identities=16% Similarity=0.338 Sum_probs=29.9
Q ss_pred eeccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCccccc
Q 011230 284 FPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELK 328 (490)
Q Consensus 284 ~~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEVk 328 (490)
....||.|+.... ...+..+=--.|=...-+.|..||++..-=+
T Consensus 142 t~v~CPkCg~~~A-~f~qlQTRSADEPmT~FYkC~~CG~~wkppk 185 (195)
T PHA02998 142 YNTPCPNCKSKNT-TPMMIQTRAADEPPLVRHACRDCKKHFKPPK 185 (195)
T ss_pred cCCCCCCCCCCce-EEEEEeeccCCCCceEEEEcCCCCCccCCcc
Confidence 5688999986532 2233333334677778899999999876444
No 125
>PRK14282 chaperone protein DnaJ; Provisional
Probab=54.57 E-value=44 Score=35.42 Aligned_cols=37 Identities=24% Similarity=0.405 Sum_probs=21.4
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCcc
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNS 325 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~n 325 (490)
..|+.|+..|...+....-|.| +.+...|+.|+=+-.
T Consensus 170 ~~C~~C~G~G~~~~~~~~~~G~---~~~~~~C~~C~G~G~ 206 (369)
T PRK14282 170 VTCPKCHGTGRIREERRSFFGV---FVSERTCERCGGTGK 206 (369)
T ss_pred cCCCCCCCcCEEEEEEEccCcc---eEEEEECCCCCCcce
Confidence 4577777777443333222333 345779999975443
No 126
>COG4469 CoiA Competence protein CoiA-like family, contains a predicted nuclease domain [General function prediction only]
Probab=54.35 E-value=5.1 Score=42.11 Aligned_cols=26 Identities=23% Similarity=0.392 Sum_probs=22.9
Q ss_pred eccCcCCccccceeEEEeecCCCCcE
Q 011230 285 PSTCGACAASCETRMFMTRIPYFQEV 310 (490)
Q Consensus 285 ~s~Cp~C~~~~~t~m~~~~IP~Fkev 310 (490)
.--||+||++...+.=...||||--.
T Consensus 25 ~ffCPaC~~~l~lK~G~~k~pHFAHk 50 (342)
T COG4469 25 RFFCPACGSQLILKQGLIKIPHFAHK 50 (342)
T ss_pred ccccCCCCCeeeeecCccccchhhhh
Confidence 46799999999999999999999554
No 127
>PRK10767 chaperone protein DnaJ; Provisional
Probab=54.33 E-value=49 Score=35.02 Aligned_cols=26 Identities=23% Similarity=0.558 Sum_probs=17.5
Q ss_pred eeEEecc----eeeeecCCCccceeEeHHH
Q 011230 360 AGVKIPE----LDLELAGGTLGGIVTTVEG 385 (490)
Q Consensus 360 a~v~IPE----L~lei~pGtl~G~~TTVEG 385 (490)
+++.||- +.+.|+||+..|..-+|.|
T Consensus 279 ~~~~i~~ldG~i~v~ip~g~~~g~~~~i~g 308 (371)
T PRK10767 279 GEIEVPTLDGRVKLKIPEGTQTGKLFRLRG 308 (371)
T ss_pred CeEEEecCCCcEEEEeCCCCCCCCEEEECC
Confidence 4556653 5678888887777776754
No 128
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=54.31 E-value=5.8 Score=34.28 Aligned_cols=22 Identities=27% Similarity=0.625 Sum_probs=18.1
Q ss_pred EeecCCCCCCccceeeccccCC
Q 011230 60 AFECPHCGERNNEVQFAGEIQP 81 (490)
Q Consensus 60 Sf~C~~CGyrnnEvq~~g~i~~ 81 (490)
+..|+|||...-+-..+.+|+.
T Consensus 35 a~~C~~CGe~y~~dev~~eIE~ 56 (89)
T TIGR03829 35 SISCSHCGMEYQDDTTVKEIED 56 (89)
T ss_pred cccccCCCcEeecHHHHHHHHh
Confidence 6789999998877777777765
No 129
>TIGR02349 DnaJ_bact chaperone protein DnaJ. This model represents bacterial forms of DnaJ, part of the DnaK-DnaJ-GrpE chaperone system. The three components typically are encoded by consecutive genes. DnaJ homologs occur in many genomes, typically not near DnaK and GrpE-like genes; most such genes are not included by this family. Eukaryotic (mitochondrial and chloroplast) forms are not included in the scope of this family.
Probab=54.21 E-value=87 Score=32.87 Aligned_cols=27 Identities=26% Similarity=0.621 Sum_probs=17.0
Q ss_pred cEEEEee----eeeEeCCCCCCCceeeHHHH
Q 011230 108 ATIKIPE----LDFEIPPEAQRGSLSTVEGI 134 (490)
Q Consensus 108 ati~IPE----L~~eI~p~~~~G~iTTVEGl 134 (490)
+++.|+- +.+.||++++.|.+.+|.|.
T Consensus 284 ~~~~i~~ldG~i~v~ip~g~~~g~~~~i~g~ 314 (354)
T TIGR02349 284 GEIEVPTLDGDVKLKIPAGTQSGTVFRLKGK 314 (354)
T ss_pred CeEEEecCCceEEEEECCcccCCcEEEECCC
Confidence 3444544 45777777777777777653
No 130
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=53.61 E-value=2.8 Score=39.35 Aligned_cols=35 Identities=23% Similarity=0.363 Sum_probs=23.9
Q ss_pred eccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCcccccc
Q 011230 285 PSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKP 329 (490)
Q Consensus 285 ~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEVk~ 329 (490)
--.||+|+..-. |-|.+-..|.|+.||..-.++.+
T Consensus 109 ~Y~Cp~c~~r~t----------f~eA~~~~F~Cp~Cg~~L~~~dn 143 (158)
T TIGR00373 109 FFICPNMCVRFT----------FNEAMELNFTCPRCGAMLDYLDN 143 (158)
T ss_pred eEECCCCCcEee----------HHHHHHcCCcCCCCCCEeeeccC
Confidence 345999995421 45555679999999986555443
No 131
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=53.57 E-value=7.4 Score=38.87 Aligned_cols=22 Identities=27% Similarity=0.708 Sum_probs=16.8
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCC
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYR 323 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr 323 (490)
..||.||. .--=.+.|++||+.
T Consensus 310 ~~C~~cg~----------------~~~r~~~C~~cg~~ 331 (364)
T COG0675 310 KTCPCCGH----------------LSGRLFKCPRCGFV 331 (364)
T ss_pred ccccccCC----------------ccceeEECCCCCCe
Confidence 46999999 11345899999995
No 132
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=52.97 E-value=11 Score=34.79 Aligned_cols=32 Identities=25% Similarity=0.727 Sum_probs=21.9
Q ss_pred ccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCcc
Q 011230 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNN 71 (490)
Q Consensus 32 s~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnn 71 (490)
.+|+.|+.+- |.|... +. ++...|..||.+..
T Consensus 98 VlC~~C~sPd-T~l~k~-----~r--~~~l~C~ACGa~~~ 129 (133)
T TIGR00311 98 VICRECNRPD-TRIIKE-----GR--VSLLKCEACGAKAP 129 (133)
T ss_pred EECCCCCCCC-cEEEEe-----CC--eEEEecccCCCCCc
Confidence 7899999874 555321 23 34569999999753
No 133
>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=52.38 E-value=10 Score=34.46 Aligned_cols=31 Identities=23% Similarity=0.569 Sum_probs=21.9
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCc
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRN 324 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~ 324 (490)
..||.|+.+- |.+... +.+ +...|..||.+.
T Consensus 94 VlC~~C~spd-T~l~k~-----~r~--~~l~C~aCGa~~ 124 (125)
T PF01873_consen 94 VLCPECGSPD-TELIKE-----GRL--IFLKCKACGASR 124 (125)
T ss_dssp SSCTSTSSSS-EEEEEE-----TTC--CEEEETTTSCEE
T ss_pred EEcCCCCCCc-cEEEEc-----CCE--EEEEecccCCcC
Confidence 5799999984 555333 333 457899999864
No 134
>PF00684 DnaJ_CXXCXGXG: DnaJ central domain; InterPro: IPR001305 The hsp70 chaperone machine performs many diverse roles in the cell, including folding of nascent proteins, translocation of polypeptides across organelle membranes, coordinating responses to stress, and targeting selected proteins for degradation. DnaJ is a member of the hsp40 family of molecular chaperones, which is also called the J-protein family, the members of which regulate the activity of hsp70s. DnaJ (hsp40) binds to DnaK (hsp70) and stimulates its ATPase activity, generating the ADP-bound state of DnaK, which interacts stably with the polypeptide substrate []. Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation []. DnaJ consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acid residues, a glycine and phenylalanine-rich domain ('G/F' domain), a central cysteine rich domain (CR-type zinc finger) containing four repeats of a CXXCXGXG motif which can coordinate two zinc atom and a C-terminal domain (CTD) []. This entry represents the central cysteine-rich (CR) domain of DnaJ proteins. This central cysteine rich domain (CR-type zinc finger) has an overall V-shaped extended beta-hairpin topology and contains four repeats of the motif CXXCXGXG where X is any amino acid. The isolated cysteine rich domain folds in zinc dependent fashion. Each set of two repeats binds one unit of zinc. Although this domain has been implicated in substrate binding, no evidence of specific interaction between the isolated DnaJ cysteine rich domain and various hydrophobic peptides has been found [].; GO: 0031072 heat shock protein binding, 0051082 unfolded protein binding; PDB: 1NLT_A 2CTT_A 1EXK_A.
Probab=52.38 E-value=25 Score=28.03 Aligned_cols=36 Identities=25% Similarity=0.523 Sum_probs=25.2
Q ss_pred ccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCc
Q 011230 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (490)
Q Consensus 32 s~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrn 70 (490)
..|+.|+-.|....... .|++ ++.+...|++|+=+-
T Consensus 16 ~~C~~C~G~G~~~~~~~-~~~~--~~~~~~~C~~C~G~G 51 (66)
T PF00684_consen 16 KTCPQCNGSGQVTRRQQ-TPGG--VFQMQQTCPKCGGTG 51 (66)
T ss_dssp EE-TTSSSSSEEEEEEE-SSST--TEEEEEE-TTTSSSS
T ss_pred cCCcCCCCeeEEEEEEe-CCCe--EEEEEEECCCCccee
Confidence 48999999998877766 4443 466788899998543
No 135
>PRK14292 chaperone protein DnaJ; Provisional
Probab=52.37 E-value=41 Score=35.60 Aligned_cols=37 Identities=19% Similarity=0.360 Sum_probs=24.1
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCcc
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNS 325 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~n 325 (490)
..|+.|+..|..++....+|.+ +-+...|+.|+=+-.
T Consensus 158 ~~C~~C~G~G~~~~~~~~~~g~---~~~~~~C~~C~G~G~ 194 (371)
T PRK14292 158 KTCPTCRGAGAVRAQARTIFGV---VETQQPCPTCRGEGQ 194 (371)
T ss_pred ccCCCCCCccEEEEEEeccCce---EEEeeecCCCcccce
Confidence 4577777777666666666543 335779999965443
No 136
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=52.25 E-value=12 Score=32.89 Aligned_cols=30 Identities=20% Similarity=0.451 Sum_probs=22.3
Q ss_pred cCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCcc
Q 011230 287 TCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNS 325 (490)
Q Consensus 287 ~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~n 325 (490)
-||.||..+ ++.- ++. -+.|.|..|+|-.+
T Consensus 3 FCP~Cgn~L-----ive~---g~~-~~rf~C~tCpY~~~ 32 (105)
T KOG2906|consen 3 FCPTCGNML-----IVES---GES-CNRFSCRTCPYVFP 32 (105)
T ss_pred ccCCCCCEE-----EEec---CCe-EeeEEcCCCCceee
Confidence 499999654 3333 555 89999999999654
No 137
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=52.08 E-value=3.3 Score=39.74 Aligned_cols=32 Identities=25% Similarity=0.501 Sum_probs=22.6
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCcccc
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSEL 327 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEV 327 (490)
-.||+|+..-. |-|.+-..|.|+.||..-.++
T Consensus 118 Y~Cp~C~~ryt----------f~eA~~~~F~Cp~Cg~~L~~~ 149 (178)
T PRK06266 118 FFCPNCHIRFT----------FDEAMEYGFRCPQCGEMLEEY 149 (178)
T ss_pred EECCCCCcEEe----------HHHHhhcCCcCCCCCCCCeec
Confidence 45999995431 345555699999999866554
No 138
>PRK14282 chaperone protein DnaJ; Provisional
Probab=51.73 E-value=60 Score=34.45 Aligned_cols=21 Identities=19% Similarity=0.409 Sum_probs=16.4
Q ss_pred eeeeEeCCCCCCCceeeHHHH
Q 011230 114 ELDFEIPPEAQRGSLSTVEGI 134 (490)
Q Consensus 114 EL~~eI~p~~~~G~iTTVEGl 134 (490)
.|.+.|||++..|..-.++|.
T Consensus 226 ~l~V~Ip~G~~~G~~i~~~g~ 246 (369)
T PRK14282 226 RTTVKIPAGVEDGTVLRITGG 246 (369)
T ss_pred EEEEEeCCCCCCCCEEEEecc
Confidence 577888898888888877763
No 139
>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=51.41 E-value=18 Score=27.75 Aligned_cols=35 Identities=17% Similarity=0.282 Sum_probs=19.4
Q ss_pred cCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCcc
Q 011230 287 TCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNS 325 (490)
Q Consensus 287 ~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~n 325 (490)
.||-||....+ .. .....++.--+ +.|..||+...
T Consensus 3 PCPfCGg~~~~--~~-~~~~~~~~~~~-~~C~~Cga~~~ 37 (53)
T TIGR03655 3 PCPFCGGADVY--LR-RGFDPLDLSHY-FECSTCGASGP 37 (53)
T ss_pred CCCCCCCccee--eE-eccCCCCCEEE-EECCCCCCCcc
Confidence 69999987641 11 11111222222 38999999744
No 140
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=51.38 E-value=7.3 Score=43.60 Aligned_cols=32 Identities=34% Similarity=0.629 Sum_probs=15.3
Q ss_pred eEEeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccceee
Q 011230 28 YQVESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQF 75 (490)
Q Consensus 28 ~eies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEvq~ 75 (490)
+---+.|+.||..+ + . .+.||+||-++.++-.
T Consensus 488 n~~~~~C~~CG~~~-------------~--~-~~~CP~CGs~~~~~~~ 519 (546)
T PF13597_consen 488 NPPIDICPDCGYIG-------------G--E-GDKCPKCGSENIEVYS 519 (546)
T ss_dssp E--EEEETTT---S------------------EEE-CCC----EEEEB
T ss_pred ecCcccccCCCcCC-------------C--C-CCCCCCCCCcccceEE
Confidence 34457899998432 1 2 8899999999866644
No 141
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=51.21 E-value=7.7 Score=45.01 Aligned_cols=28 Identities=36% Similarity=0.699 Sum_probs=19.1
Q ss_pred EeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccce
Q 011230 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEV 73 (490)
Q Consensus 30 ies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEv 73 (490)
--+.|+.||-.+.. .+.||+||-.+.++
T Consensus 679 ~~~~C~~CG~~~~~----------------~~~CP~CG~~~~~~ 706 (735)
T PRK07111 679 PVDRCPVCGYLGVI----------------EDKCPKCGSTNIQR 706 (735)
T ss_pred CCeecCCCCCCCCc----------------CccCcCCCCcccee
Confidence 44789999843321 28999999765444
No 142
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=50.99 E-value=6.4 Score=35.24 Aligned_cols=36 Identities=17% Similarity=0.468 Sum_probs=23.8
Q ss_pred eccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCccccccCCC
Q 011230 285 PSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGR 332 (490)
Q Consensus 285 ~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEVk~gg~ 332 (490)
...|..||+....... ..+.||+||-.+-++.+|.+
T Consensus 71 ~~~C~~Cg~~~~~~~~------------~~~~CP~Cgs~~~~i~~G~E 106 (117)
T PRK00564 71 ELECKDCSHVFKPNAL------------DYGVCEKCHSKNVIITQGNE 106 (117)
T ss_pred EEEhhhCCCccccCCc------------cCCcCcCCCCCceEEecCCE
Confidence 3679999965422211 11459999998888876643
No 143
>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=50.78 E-value=3.9 Score=28.40 Aligned_cols=27 Identities=26% Similarity=0.607 Sum_probs=12.1
Q ss_pred eccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCC
Q 011230 31 ESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGER 69 (490)
Q Consensus 31 es~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyr 69 (490)
.+.||.|+..-+. .=+. -|.||.||+.
T Consensus 2 ~p~Cp~C~se~~y--------~D~~----~~vCp~C~~e 28 (30)
T PF08274_consen 2 LPKCPLCGSEYTY--------EDGE----LLVCPECGHE 28 (30)
T ss_dssp S---TTT-----E--------E-SS----SEEETTTTEE
T ss_pred CCCCCCCCCccee--------ccCC----EEeCCccccc
Confidence 3689999866444 1133 3569999974
No 144
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=50.72 E-value=14 Score=32.55 Aligned_cols=13 Identities=23% Similarity=0.473 Sum_probs=6.8
Q ss_pred EEEeecCCCCCCc
Q 011230 58 LSAFECPHCGERN 70 (490)
Q Consensus 58 imSf~C~~CGyrn 70 (490)
.+.|.|..|+|-.
T Consensus 19 ~~rf~C~tCpY~~ 31 (105)
T KOG2906|consen 19 CNRFSCRTCPYVF 31 (105)
T ss_pred EeeEEcCCCCcee
Confidence 4555555555543
No 145
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=50.61 E-value=7.5 Score=43.81 Aligned_cols=29 Identities=34% Similarity=0.764 Sum_probs=20.2
Q ss_pred EeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccce
Q 011230 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEV 73 (490)
Q Consensus 30 ies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEv 73 (490)
--+.|+.||-.|... .+.||+||-++-++
T Consensus 523 ~~~~C~~CG~~g~~~---------------~~~CP~Cgs~~~~~ 551 (579)
T TIGR02487 523 PVDVCEDCGYTGEGL---------------NDKCPKCGSHDIEV 551 (579)
T ss_pred CCccCCCCCCCCCCC---------------CCcCcCCCCcccee
Confidence 347899998543321 28899999877444
No 146
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=50.32 E-value=6.5 Score=41.67 Aligned_cols=33 Identities=27% Similarity=0.698 Sum_probs=23.3
Q ss_pred ccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCcc
Q 011230 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNN 71 (490)
Q Consensus 32 s~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnn 71 (490)
.+||.|+.+ .|.+..+. .. -.+..|..||||..
T Consensus 97 VlC~~C~NP-ETel~itk----~q--~i~~~CkACG~r~~ 129 (400)
T KOG2767|consen 97 VLCPSCENP-ETELIITK----KQ--TISLKCKACGFRSD 129 (400)
T ss_pred eeCcCCCCC-ceeEEecc----cc--hhhhHHHHcCCccc
Confidence 689999755 67666553 11 12789999999863
No 147
>PRK14288 chaperone protein DnaJ; Provisional
Probab=50.11 E-value=52 Score=34.98 Aligned_cols=21 Identities=19% Similarity=0.221 Sum_probs=16.6
Q ss_pred eeeeEeCCCCCCCceeeHHHH
Q 011230 114 ELDFEIPPEAQRGSLSTVEGI 134 (490)
Q Consensus 114 EL~~eI~p~~~~G~iTTVEGl 134 (490)
.|.+.|||++..|..-+++|.
T Consensus 209 ~l~V~IP~G~~~G~~i~l~g~ 229 (369)
T PRK14288 209 EIDAIIPEGIDDQNRMVLKNK 229 (369)
T ss_pred EEEEecCCCCCCCCEEEEccC
Confidence 577889999889987777764
No 148
>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=50.07 E-value=13 Score=39.57 Aligned_cols=39 Identities=18% Similarity=0.408 Sum_probs=21.9
Q ss_pred EEeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCcc
Q 011230 29 QVESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNN 71 (490)
Q Consensus 29 eies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnn 71 (490)
-+.-.|++||+-.+|.+.-++. +-=...+.|++||++..
T Consensus 172 Pf~piC~~cGri~tt~v~~~d~----~~~~v~Y~c~~cG~~g~ 210 (360)
T PF01921_consen 172 PFLPICEKCGRIDTTEVTEYDP----EGGTVTYRCEECGHEGE 210 (360)
T ss_dssp SEEEEETTTEE--EEEEEEE------SSSEEEEE--TTS---E
T ss_pred eeeeeccccCCcccceeeEeec----CCCEEEEEecCCCCEEE
Confidence 4678899999977787765553 11234899999999763
No 149
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 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. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=49.95 E-value=8.3 Score=31.55 Aligned_cols=26 Identities=23% Similarity=0.537 Sum_probs=17.9
Q ss_pred EEEeecCCCCCCccceeeccccCCcce
Q 011230 58 LSAFECPHCGERNNEVQFAGEIQPRGC 84 (490)
Q Consensus 58 imSf~C~~CGyrnnEvq~~g~i~~kG~ 84 (490)
.+.|.|.-||.|+....+--++ .+|+
T Consensus 2 ~l~FTC~~C~~Rs~~~~sk~aY-~~Gv 27 (66)
T PF05180_consen 2 QLTFTCNKCGTRSAKMFSKQAY-HKGV 27 (66)
T ss_dssp EEEEEETTTTEEEEEEEEHHHH-HTSE
T ss_pred eEEEEcCCCCCccceeeCHHHH-hCCe
Confidence 5678888888888776665555 3564
No 150
>KOG2846 consensus Predicted membrane protein [Function unknown]
Probab=49.91 E-value=9.1 Score=40.19 Aligned_cols=42 Identities=19% Similarity=0.393 Sum_probs=29.9
Q ss_pred cceEeeccCcCCc-cccceeEEEeecCCCCcEEEEEeecCCCCCCcccccc
Q 011230 280 EVMTFPSTCGACA-ASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKP 329 (490)
Q Consensus 280 ev~~~~s~Cp~C~-~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEVk~ 329 (490)
+-..+...|+.|+ ++|-.+- -+-|| .+|.|.||+..|-..|.
T Consensus 215 P~~ryALIC~~C~~HNGla~~--ee~~y------i~F~C~~Cn~LN~~~k~ 257 (328)
T KOG2846|consen 215 PNNRYALICSQCHHHNGLARK--EEYEY------ITFRCPHCNALNPAKKS 257 (328)
T ss_pred CcchhhhcchhhccccCcCCh--hhcCc------eEEECccccccCCCcCC
Confidence 3445667899996 5675443 22333 68999999999988876
No 151
>PRK14291 chaperone protein DnaJ; Provisional
Probab=49.68 E-value=49 Score=35.33 Aligned_cols=21 Identities=33% Similarity=0.559 Sum_probs=17.4
Q ss_pred eeeeEeCCCCCCCceeeHHHH
Q 011230 114 ELDFEIPPEAQRGSLSTVEGI 134 (490)
Q Consensus 114 EL~~eI~p~~~~G~iTTVEGl 134 (490)
.|.+.|||+...|..-+++|.
T Consensus 225 ~l~V~Ip~G~~~G~~i~~~g~ 245 (382)
T PRK14291 225 TIKVRIPPGVDNGSKLRVPGK 245 (382)
T ss_pred EEEEEeCCCCCCCCEEEEecC
Confidence 478889999999988888764
No 152
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=49.67 E-value=24 Score=31.59 Aligned_cols=42 Identities=21% Similarity=0.503 Sum_probs=24.6
Q ss_pred EeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccc
Q 011230 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNE 72 (490)
Q Consensus 30 ies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnE 72 (490)
-.-.||+||..-. -+....---=.+-+..-|.|-+||++..|
T Consensus 72 s~~~C~~C~~~ea-vffQ~~~~r~d~~m~l~yvC~~C~h~wte 113 (113)
T KOG2691|consen 72 SDKHCPKCGHREA-VFFQAQTRRADEAMRLFYVCCSCGHRWTE 113 (113)
T ss_pred ccccCCccCCcce-EEEecccccccceEEEEEEeccccccccC
Confidence 5567999996521 12122111123445556889999998764
No 153
>PRK14296 chaperone protein DnaJ; Provisional
Probab=49.51 E-value=65 Score=34.31 Aligned_cols=76 Identities=12% Similarity=0.192 Sum_probs=41.0
Q ss_pred cCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccceeeccccCCcceEEEEEeeCCCcccccceEEecCccEEEE
Q 011230 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEIQPRGCNYSLKVPSSDQKMFHRQVVKSESATIKI 112 (490)
Q Consensus 33 ~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEvq~~g~i~~kG~r~tl~V~~~~~~DLnR~VvkS~~ati~I 112 (490)
.|+.|+..|..+... .+.+| ++-+...|+.|+=+-.-+... ++.. -.+.+++. -
T Consensus 168 ~C~~C~G~G~~~~~~-~~g~~--~~q~~~~C~~C~G~G~~~~~~-----------C~~C------~G~g~v~~------~ 221 (372)
T PRK14296 168 ICNNCHGTGEVLVQK-NMGFF--QFQQSAKCNVCNGAGKIIKNK-----------CKNC------KGKGKYLE------R 221 (372)
T ss_pred cCCCCCCCceEEEEE-eccce--EEEEEecCCCcCCcceeeccc-----------ccCC------CCceEEEE------E
Confidence 477777777554443 33332 334567899997654322110 1111 00111111 1
Q ss_pred eeeeeEeCCCCCCCceeeHHHH
Q 011230 113 PELDFEIPPEAQRGSLSTVEGI 134 (490)
Q Consensus 113 PEL~~eI~p~~~~G~iTTVEGl 134 (490)
-.+.+.|||++..|..-+++|.
T Consensus 222 ~~~~V~Ip~G~~~G~~i~~~g~ 243 (372)
T PRK14296 222 KKIEVNIPKGIRPNQQIKLSQK 243 (372)
T ss_pred EEEEEEECCCCCCCCEEEEecc
Confidence 3467888899899988888764
No 154
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=49.08 E-value=19 Score=33.38 Aligned_cols=32 Identities=22% Similarity=0.692 Sum_probs=22.7
Q ss_pred ccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCcc
Q 011230 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNN 71 (490)
Q Consensus 32 s~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnn 71 (490)
.+|+.|+.+ .|.|... +. ++.-.|..||.+..
T Consensus 103 VlC~~C~sp-dT~l~k~-----~r--~~~l~C~ACGa~~~ 134 (138)
T PRK03988 103 VICPECGSP-DTKLIKE-----GR--IWVLKCEACGAETP 134 (138)
T ss_pred EECCCCCCC-CcEEEEc-----CC--eEEEEcccCCCCCc
Confidence 689999986 4555321 23 56789999999753
No 155
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=48.77 E-value=9.2 Score=35.27 Aligned_cols=33 Identities=33% Similarity=0.680 Sum_probs=20.6
Q ss_pred EEeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCcccee
Q 011230 29 QVESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQ 74 (490)
Q Consensus 29 eies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEvq 74 (490)
-..-.||.||-+ .|+ ===-..||.|||+-+-+.
T Consensus 26 ML~~hCp~Cg~P-----------LF~--KdG~v~CPvC~~~~~~v~ 58 (131)
T COG1645 26 MLAKHCPKCGTP-----------LFR--KDGEVFCPVCGYREVVVE 58 (131)
T ss_pred HHHhhCcccCCc-----------cee--eCCeEECCCCCceEEEee
Confidence 356789999844 343 111235999999765443
No 156
>PRK04023 DNA polymerase II large subunit; Validated
Probab=48.39 E-value=9.6 Score=45.40 Aligned_cols=72 Identities=18% Similarity=0.251 Sum_probs=45.1
Q ss_pred ccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccceeeccccCCcceEEEEEeeCCCcccccceEEecCccEEE
Q 011230 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEIQPRGCNYSLKVPSSDQKMFHRQVVKSESATIK 111 (490)
Q Consensus 32 s~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEvq~~g~i~~kG~r~tl~V~~~~~~DLnR~VvkS~~ati~ 111 (490)
-.||.||..+ ..|.||+||-+...+.+=.. .....++ -.
T Consensus 627 RfCpsCG~~t-----------------~~frCP~CG~~Te~i~fCP~---------------CG~~~~~---------y~ 665 (1121)
T PRK04023 627 RKCPSCGKET-----------------FYRRCPFCGTHTEPVYRCPR---------------CGIEVEE---------DE 665 (1121)
T ss_pred ccCCCCCCcC-----------------CcccCCCCCCCCCcceeCcc---------------ccCcCCC---------Cc
Confidence 4699999773 46999999998332221111 1111111 22
Q ss_pred EeeeeeEeCCCCCCCceeeHHHHHHHHHHHHHHhh
Q 011230 112 IPELDFEIPPEAQRGSLSTVEGILVRAADELEALQ 146 (490)
Q Consensus 112 IPEL~~eI~p~~~~G~iTTVEGlL~~~~~~L~~~~ 146 (490)
-|.=++++++. .-.--++-.++.++.++|....
T Consensus 666 CPKCG~El~~~--s~~~i~l~~~~~~A~~~lg~~~ 698 (1121)
T PRK04023 666 CEKCGREPTPY--SKRKIDLKELYDRALENLGERK 698 (1121)
T ss_pred CCCCCCCCCcc--ceEEecHHHHHHHHHHHhCCcC
Confidence 57788888874 2334678889999988887643
No 157
>PF00684 DnaJ_CXXCXGXG: DnaJ central domain; InterPro: IPR001305 The hsp70 chaperone machine performs many diverse roles in the cell, including folding of nascent proteins, translocation of polypeptides across organelle membranes, coordinating responses to stress, and targeting selected proteins for degradation. DnaJ is a member of the hsp40 family of molecular chaperones, which is also called the J-protein family, the members of which regulate the activity of hsp70s. DnaJ (hsp40) binds to DnaK (hsp70) and stimulates its ATPase activity, generating the ADP-bound state of DnaK, which interacts stably with the polypeptide substrate []. Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation []. DnaJ consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acid residues, a glycine and phenylalanine-rich domain ('G/F' domain), a central cysteine rich domain (CR-type zinc finger) containing four repeats of a CXXCXGXG motif which can coordinate two zinc atom and a C-terminal domain (CTD) []. This entry represents the central cysteine-rich (CR) domain of DnaJ proteins. This central cysteine rich domain (CR-type zinc finger) has an overall V-shaped extended beta-hairpin topology and contains four repeats of the motif CXXCXGXG where X is any amino acid. The isolated cysteine rich domain folds in zinc dependent fashion. Each set of two repeats binds one unit of zinc. Although this domain has been implicated in substrate binding, no evidence of specific interaction between the isolated DnaJ cysteine rich domain and various hydrophobic peptides has been found [].; GO: 0031072 heat shock protein binding, 0051082 unfolded protein binding; PDB: 1NLT_A 2CTT_A 1EXK_A.
Probab=48.19 E-value=26 Score=28.01 Aligned_cols=34 Identities=32% Similarity=0.506 Sum_probs=23.8
Q ss_pred cCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCC
Q 011230 287 TCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYR 323 (490)
Q Consensus 287 ~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr 323 (490)
.|+.|+..|...+... .|++ ++.+...|++|+=+
T Consensus 17 ~C~~C~G~G~~~~~~~-~~~~--~~~~~~~C~~C~G~ 50 (66)
T PF00684_consen 17 TCPQCNGSGQVTRRQQ-TPGG--VFQMQQTCPKCGGT 50 (66)
T ss_dssp E-TTSSSSSEEEEEEE-SSST--TEEEEEE-TTTSSS
T ss_pred CCcCCCCeeEEEEEEe-CCCe--EEEEEEECCCCcce
Confidence 6999999997777665 4443 56788899999753
No 158
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=48.02 E-value=21 Score=33.54 Aligned_cols=96 Identities=15% Similarity=0.167 Sum_probs=53.9
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCccccccCCCCCCCCeEEEEEEcCcccccceee-eeCceeEEe
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRIPEKGKRITLFVKNINDLSRDLI-KSDTAGVKI 364 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEVk~gg~i~~kG~ritL~V~~~eDL~R~Vl-KS~ta~v~I 364 (490)
+.||-|+.+- |+..-...--=+..|---=.|..||+|++-.-- ++..+..+.=+=-..+.++|+=| ++=....
T Consensus 1 M~CP~C~~~d-tkViDSR~~~dg~~IRRRReC~~C~~RFTTyEr---ve~~~l~ViKkdG~re~Fdr~Kl~~gl~~Ac-- 74 (147)
T TIGR00244 1 MHCPFCQHHN-TRVLDSRLVEDGQSIRRRRECLECHERFTTFER---AELLPPTVIKQDGVREPFNREKLLRGMVRAC-- 74 (147)
T ss_pred CCCCCCCCCC-CEeeeccccCCCCeeeecccCCccCCccceeee---ccccccEEEcCCCCCCCCCHHHHHHHHHHHh--
Confidence 4699999864 233333333345677777899999999987754 33334333333335566666522 2111110
Q ss_pred cceeeeecCCCccceeEeHHHHHHHHHHHHhh
Q 011230 365 PELDLELAGGTLGGIVTTVEGLITKISESLER 396 (490)
Q Consensus 365 PEL~lei~pGtl~G~~TTVEGlL~~i~d~L~~ 396 (490)
..-+. ....+|-++..|...|..
T Consensus 75 -------~KRpV--s~e~ie~~v~~Ie~~l~~ 97 (147)
T TIGR00244 75 -------EKRPV--SFDDLEHAINHIEAQLRA 97 (147)
T ss_pred -------cCCCC--CHHHHHHHHHHHHHHHHH
Confidence 11110 124577788888888766
No 159
>PRK04023 DNA polymerase II large subunit; Validated
Probab=47.84 E-value=9.5 Score=45.45 Aligned_cols=75 Identities=15% Similarity=0.175 Sum_probs=47.4
Q ss_pred ceEeeccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCccccccCCCCCCCCeEEEEEEcCcccccceeeeeCce
Q 011230 281 VMTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRIPEKGKRITLFVKNINDLSRDLIKSDTA 360 (490)
Q Consensus 281 v~~~~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEVk~gg~i~~kG~ritL~V~~~eDL~R~VlKS~ta 360 (490)
|-.-.-.||+||+.+ ..|.|++||.++..++.=... +....
T Consensus 622 VEVg~RfCpsCG~~t-----------------~~frCP~CG~~Te~i~fCP~C----------------------G~~~~ 662 (1121)
T PRK04023 622 VEIGRRKCPSCGKET-----------------FYRRCPFCGTHTEPVYRCPRC----------------------GIEVE 662 (1121)
T ss_pred ecccCccCCCCCCcC-----------------CcccCCCCCCCCCcceeCccc----------------------cCcCC
Confidence 334445799999983 458999999985444321111 11111
Q ss_pred eEEecceeeeecCCCccceeEeHHHHHHHHHHHHhh
Q 011230 361 GVKIPELDLELAGGTLGGIVTTVEGLITKISESLER 396 (490)
Q Consensus 361 ~v~IPEL~lei~pGtl~G~~TTVEGlL~~i~d~L~~ 396 (490)
.-..|.=++++.+++ -+--++-.++.+..++|..
T Consensus 663 ~y~CPKCG~El~~~s--~~~i~l~~~~~~A~~~lg~ 696 (1121)
T PRK04023 663 EDECEKCGREPTPYS--KRKIDLKELYDRALENLGE 696 (1121)
T ss_pred CCcCCCCCCCCCccc--eEEecHHHHHHHHHHHhCC
Confidence 123688888888864 3345788888888888865
No 160
>PRK14289 chaperone protein DnaJ; Provisional
Probab=47.64 E-value=54 Score=34.98 Aligned_cols=21 Identities=19% Similarity=0.376 Sum_probs=17.1
Q ss_pred eeeeEeCCCCCCCceeeHHHH
Q 011230 114 ELDFEIPPEAQRGSLSTVEGI 134 (490)
Q Consensus 114 EL~~eI~p~~~~G~iTTVEGl 134 (490)
.+.+.|||+++.|.+-++.|.
T Consensus 228 ~~~V~Ip~G~~~G~~i~l~g~ 248 (386)
T PRK14289 228 VITVKIPAGVAEGMQLSMNGK 248 (386)
T ss_pred EEEEEeCCCCCCCCEEEEecc
Confidence 467788899999999888764
No 161
>COG4469 CoiA Competence protein CoiA-like family, contains a predicted nuclease domain [General function prediction only]
Probab=47.16 E-value=8.3 Score=40.61 Aligned_cols=28 Identities=32% Similarity=0.552 Sum_probs=24.1
Q ss_pred eccCCccCCCceEEEEEeecCCccceEE
Q 011230 31 ESLCMRCGENGVTRFLLTLIPHFRKVLL 58 (490)
Q Consensus 31 es~Cp~Cg~~g~trlllt~IP~F~evii 58 (490)
.--||+||++...+.=+.+||||--.=+
T Consensus 25 ~ffCPaC~~~l~lK~G~~k~pHFAHk~l 52 (342)
T COG4469 25 RFFCPACGSQLILKQGLIKIPHFAHKSL 52 (342)
T ss_pred ccccCCCCCeeeeecCccccchhhhhhh
Confidence 3689999999999999999999976544
No 162
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=46.99 E-value=13 Score=35.03 Aligned_cols=98 Identities=19% Similarity=0.239 Sum_probs=53.5
Q ss_pred ccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccceeeccccCCcceEEEEEeeCCCcccccce-EEecCccEE
Q 011230 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEIQPRGCNYSLKVPSSDQKMFHRQ-VVKSESATI 110 (490)
Q Consensus 32 s~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEvq~~g~i~~kG~r~tl~V~~~~~~DLnR~-VvkS~~ati 110 (490)
..||-|+.+ .|+..-.+.--=+..|---=+|++||.|++..--+.-..+ +.+|=. |..+.++|+ ++++-...
T Consensus 1 M~CPfC~~~-~tkViDSR~~edg~aIRRRReC~~C~~RFTTfE~~El~~~----~VvKkd-g~Re~F~r~Kl~~gl~~A- 73 (156)
T COG1327 1 MKCPFCGHE-DTKVIDSRPAEEGNAIRRRRECLECGERFTTFERAELRPL----IVVKKD-GRREPFDREKLRRGLIRA- 73 (156)
T ss_pred CCCCCCCCC-CCeeeecccccccchhhhhhcccccccccchhheeeeccc----eEECcC-CCcCCCCHHHHHHHHHHH-
Confidence 369999866 4555444443445555556789999999987655444433 222222 344455554 22221111
Q ss_pred EEeeeeeEeCCCCCCCceeeHHHHHHHHHHHHHHhh
Q 011230 111 KIPELDFEIPPEAQRGSLSTVEGILVRAADELEALQ 146 (490)
Q Consensus 111 ~IPEL~~eI~p~~~~G~iTTVEGlL~~~~~~L~~~~ 146 (490)
.+=-| =.-..||.++..+...|....
T Consensus 74 ------~~KRp----Vs~e~ie~~v~~ie~~Lr~~g 99 (156)
T COG1327 74 ------CEKRP----VSSEQIEEAVSHIERQLRSSG 99 (156)
T ss_pred ------HhcCC----CCHHHHHHHHHHHHHHHHhcC
Confidence 11111 012357888888888887754
No 163
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=46.62 E-value=8.5 Score=44.51 Aligned_cols=29 Identities=31% Similarity=0.786 Sum_probs=19.0
Q ss_pred eccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCc
Q 011230 31 ESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (490)
Q Consensus 31 es~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrn 70 (490)
-+.|+.||-.|...+ .-..+.||+||-++
T Consensus 641 ~~~C~~CG~~Ge~~~-----------~~~~~~CP~CG~~~ 669 (711)
T PRK09263 641 IDECYECGFTGEFEC-----------TEKGFTCPKCGNHD 669 (711)
T ss_pred CcccCCCCCCccccC-----------CCCCCcCcCCCCCC
Confidence 378999986554432 11138899999765
No 164
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=46.47 E-value=9.8 Score=35.09 Aligned_cols=34 Identities=26% Similarity=0.563 Sum_probs=24.0
Q ss_pred eeccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCccccccC
Q 011230 284 FPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPG 330 (490)
Q Consensus 284 ~~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEVk~g 330 (490)
+...||.||.|..- +-++| .|+.|||+-+-|+.-
T Consensus 27 L~~hCp~Cg~PLF~--------KdG~v-----~CPvC~~~~~~v~~e 60 (131)
T COG1645 27 LAKHCPKCGTPLFR--------KDGEV-----FCPVCGYREVVVEEE 60 (131)
T ss_pred HHhhCcccCCccee--------eCCeE-----ECCCCCceEEEeecc
Confidence 44569999988622 23555 599999987777653
No 165
>PRK14289 chaperone protein DnaJ; Provisional
Probab=46.29 E-value=50 Score=35.23 Aligned_cols=35 Identities=23% Similarity=0.417 Sum_probs=19.8
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCC
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYR 323 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr 323 (490)
..|+.|+..|...+.. ..+ ++-+. +...|++|+=+
T Consensus 172 ~~C~~C~G~G~~~~~~-~~~-~G~~~-~~~~C~~C~G~ 206 (386)
T PRK14289 172 ETCPTCKGSGSVTRVQ-NTI-LGTMQ-TQSTCPTCNGE 206 (386)
T ss_pred CcCCCCcCeEEEEEEE-ecc-cceEE-EEEecCCCCcc
Confidence 4467776666444433 332 22232 58899999655
No 166
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=46.08 E-value=24 Score=29.24 Aligned_cols=46 Identities=17% Similarity=0.247 Sum_probs=19.5
Q ss_pred ccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccceeecc
Q 011230 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAG 77 (490)
Q Consensus 32 s~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEvq~~g 77 (490)
..||.|+.....+--.+.=++=..-+.+-..||.||-.---+|.=|
T Consensus 2 ~~CP~C~~~L~~~~~~~~C~~C~~~~~~~a~CPdC~~~Le~LkACG 47 (70)
T PF07191_consen 2 NTCPKCQQELEWQGGHYHCEACQKDYKKEAFCPDCGQPLEVLKACG 47 (70)
T ss_dssp -B-SSS-SBEEEETTEEEETTT--EEEEEEE-TTT-SB-EEEEETT
T ss_pred CcCCCCCCccEEeCCEEECccccccceecccCCCcccHHHHHHHhc
Confidence 4577776654433323333444444555666777766555554443
No 167
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=46.06 E-value=9.7 Score=37.82 Aligned_cols=36 Identities=22% Similarity=0.453 Sum_probs=25.7
Q ss_pred ccCcCCc-cccceeEEEeecCCCCcEEEEEeecCCCCCCcccccc
Q 011230 286 STCGACA-ASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKP 329 (490)
Q Consensus 286 s~Cp~C~-~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEVk~ 329 (490)
-.||.|+ ++|-.+.-.. =|.-|.|+||..++.+++.
T Consensus 193 lIC~~C~hhngl~~~~ek--------~~~efiC~~Cn~~n~~~~~ 229 (251)
T COG5415 193 LICPQCHHHNGLYRLAEK--------PIIEFICPHCNHKNDEVKE 229 (251)
T ss_pred hccccccccccccccccc--------cchheecccchhhcCcccc
Confidence 4699996 5676654332 2338999999999977764
No 168
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=45.15 E-value=10 Score=43.21 Aligned_cols=24 Identities=21% Similarity=0.641 Sum_probs=18.4
Q ss_pred eccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCc
Q 011230 285 PSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRN 324 (490)
Q Consensus 285 ~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~ 324 (490)
-+.|+.||..|... +.||+||-++
T Consensus 559 ~~~C~~CGy~g~~~----------------~~CP~CG~~d 582 (618)
T PRK14704 559 VDRCKCCSYHGVIG----------------NECPSCGNED 582 (618)
T ss_pred CeecCCCCCCCCcC----------------ccCcCCCCCC
Confidence 36799999876421 8999999765
No 169
>TIGR02349 DnaJ_bact chaperone protein DnaJ. This model represents bacterial forms of DnaJ, part of the DnaK-DnaJ-GrpE chaperone system. The three components typically are encoded by consecutive genes. DnaJ homologs occur in many genomes, typically not near DnaK and GrpE-like genes; most such genes are not included by this family. Eukaryotic (mitochondrial and chloroplast) forms are not included in the scope of this family.
Probab=44.70 E-value=1e+02 Score=32.33 Aligned_cols=19 Identities=32% Similarity=0.625 Sum_probs=12.2
Q ss_pred eeeeecCCCccceeEeHHH
Q 011230 367 LDLELAGGTLGGIVTTVEG 385 (490)
Q Consensus 367 L~lei~pGtl~G~~TTVEG 385 (490)
+.+.|++|+..|...++.|
T Consensus 295 i~v~ip~g~~~g~~~~i~g 313 (354)
T TIGR02349 295 VKLKIPAGTQSGTVFRLKG 313 (354)
T ss_pred EEEEECCcccCCcEEEECC
Confidence 4567777766666666654
No 170
>PRK14278 chaperone protein DnaJ; Provisional
Probab=44.54 E-value=66 Score=34.30 Aligned_cols=21 Identities=19% Similarity=0.303 Sum_probs=17.0
Q ss_pred eeeeEeCCCCCCCceeeHHHH
Q 011230 114 ELDFEIPPEAQRGSLSTVEGI 134 (490)
Q Consensus 114 EL~~eI~p~~~~G~iTTVEGl 134 (490)
.|.+.|||+...|..-.+.|.
T Consensus 213 ~~~V~Ip~G~~~G~~i~~~g~ 233 (378)
T PRK14278 213 EITVKIPAGVGDGMRIRLAAQ 233 (378)
T ss_pred EEEEEECCCCCCCcEEEEccC
Confidence 578899999999988877653
No 171
>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=44.52 E-value=18 Score=32.35 Aligned_cols=31 Identities=23% Similarity=0.399 Sum_probs=22.1
Q ss_pred ccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCcccee
Q 011230 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQ 74 (490)
Q Consensus 32 s~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEvq 74 (490)
-.||.|+.+-++.. ++. |.||.|||..+.-.
T Consensus 3 p~CP~C~seytY~d--------g~~----~iCpeC~~EW~~~~ 33 (109)
T TIGR00686 3 PPCPKCNSEYTYHD--------GTQ----LICPSCLYEWNENE 33 (109)
T ss_pred CcCCcCCCcceEec--------CCe----eECccccccccccc
Confidence 36999987755443 333 67999999987653
No 172
>PRK14290 chaperone protein DnaJ; Provisional
Probab=44.51 E-value=79 Score=33.50 Aligned_cols=35 Identities=31% Similarity=0.587 Sum_probs=20.1
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCC
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYR 323 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr 323 (490)
..|+.|+..|...+.. -|.| -+..+...|++|+=+
T Consensus 166 ~~C~~C~G~G~~~~~~--~~g~-~~~~~~~~C~~C~G~ 200 (365)
T PRK14290 166 ITCPTCHGTGQQRIVR--GQGF-FRMVTVTTCRTCGGR 200 (365)
T ss_pred ccCCCCCCcCEEEEEe--ccCe-EEEEEEEeCCCCCCc
Confidence 4577777777555544 2333 123346789999643
No 173
>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=44.46 E-value=13 Score=39.58 Aligned_cols=44 Identities=20% Similarity=0.366 Sum_probs=24.1
Q ss_pred CCcceEeeccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCcc
Q 011230 278 PEEVMTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNS 325 (490)
Q Consensus 278 ~~ev~~~~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~n 325 (490)
+..-.-|.-.|+.||+-.+|.+.-++.- -=...+.|+.||++-.
T Consensus 167 ~~~y~Pf~piC~~cGri~tt~v~~~d~~----~~~v~Y~c~~cG~~g~ 210 (360)
T PF01921_consen 167 PETYSPFLPICEKCGRIDTTEVTEYDPE----GGTVTYRCEECGHEGE 210 (360)
T ss_dssp -TT--SEEEEETTTEE--EEEEEEE--S----SSEEEEE--TTS---E
T ss_pred CCCeeeeeeeccccCCcccceeeEeecC----CCEEEEEecCCCCEEE
Confidence 3344557888999999888888777642 2246799999999743
No 174
>PRK04296 thymidine kinase; Provisional
Probab=44.38 E-value=22 Score=33.84 Aligned_cols=46 Identities=11% Similarity=0.244 Sum_probs=35.7
Q ss_pred CCcceEeeccCcCCccccceeEEEee---cCCCCcEEE------EEeecCCCCCC
Q 011230 278 PEEVMTFPSTCGACAASCETRMFMTR---IPYFQEVIV------MASTCDACGYR 323 (490)
Q Consensus 278 ~~ev~~~~s~Cp~C~~~~~t~m~~~~---IP~FkeviI------msf~C~~CGyr 323 (490)
.+.|.++...|+.||+++..++..++ .++-+++|. ....|.+|-+.
T Consensus 133 aD~V~~l~~vC~~Cg~~a~~~~r~~~~~~~~~~~~~~~ig~~e~Y~~~Cr~c~~~ 187 (190)
T PRK04296 133 ADKVTELKAICVHCGRKATMNQRLIDGGPAVYEGPQVLVGGNESYEAVCRKHYKE 187 (190)
T ss_pred cCeEEEeeEEccccCCccceEEEEeCCCCccCCCCEEEECCcCcEEehhHHhhhc
Confidence 46899999999999999998888883 446677774 44578777653
No 175
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=44.36 E-value=9.7 Score=41.35 Aligned_cols=34 Identities=29% Similarity=0.688 Sum_probs=22.9
Q ss_pred eccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccceeec
Q 011230 31 ESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFA 76 (490)
Q Consensus 31 es~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEvq~~ 76 (490)
.-.||.||......- .- -|.|+.||+|.++...-
T Consensus 350 ~p~Cp~Cg~~m~S~G---------~~---g~rC~kCg~~~~~~~~~ 383 (421)
T COG1571 350 NPVCPRCGGRMKSAG---------RN---GFRCKKCGTRARETLIK 383 (421)
T ss_pred CCCCCccCCchhhcC---------CC---CcccccccccCCccccc
Confidence 348999985533322 11 47899999998877654
No 176
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=44.35 E-value=22 Score=32.16 Aligned_cols=43 Identities=35% Similarity=0.699 Sum_probs=24.7
Q ss_pred EeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccceeecccc
Q 011230 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEI 79 (490)
Q Consensus 30 ies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEvq~~g~i 79 (490)
....| .||....... ..+.+| ...+.||+||-.+-+|..+.++
T Consensus 69 ~~~~C-~Cg~~~~~~~--~~~~~~----~~~~~CP~Cgs~~~~i~~G~El 111 (124)
T PRK00762 69 VEIEC-ECGYEGVVDE--DEIDHY----AAVIECPVCGNKRAHILGGREC 111 (124)
T ss_pred eeEEe-eCcCcccccc--cchhcc----ccCCcCcCCCCCCCEEecCCeE
Confidence 45679 9995522210 011111 0146799999878777766655
No 177
>PRK14281 chaperone protein DnaJ; Provisional
Probab=44.15 E-value=59 Score=34.92 Aligned_cols=21 Identities=24% Similarity=0.472 Sum_probs=17.2
Q ss_pred eeeeEeCCCCCCCceeeHHHH
Q 011230 114 ELDFEIPPEAQRGSLSTVEGI 134 (490)
Q Consensus 114 EL~~eI~p~~~~G~iTTVEGl 134 (490)
.|.+.|||++..|..-++.|.
T Consensus 236 ~~~V~Ip~G~~~G~~i~~~g~ 256 (397)
T PRK14281 236 TVKVTVPAGVQDGNYLTLRGQ 256 (397)
T ss_pred EEEEecCCCCCCCCEEEEecc
Confidence 467889999999988888764
No 178
>PRK14283 chaperone protein DnaJ; Provisional
Probab=43.99 E-value=1.6e+02 Score=31.30 Aligned_cols=26 Identities=27% Similarity=0.658 Sum_probs=16.5
Q ss_pred cEEEEe----eeeeEeCCCCCCCceeeHHH
Q 011230 108 ATIKIP----ELDFEIPPEAQRGSLSTVEG 133 (490)
Q Consensus 108 ati~IP----EL~~eI~p~~~~G~iTTVEG 133 (490)
.++.|| .+.+.||++++.|.+-.|.|
T Consensus 287 ~~~~i~tldG~i~v~ip~g~~~g~~~ri~g 316 (378)
T PRK14283 287 DTVDVPTIDGPVELKIPAGTQSGTTFRLKG 316 (378)
T ss_pred CeEEEEcCCceEEEEeCCCCCCCCEEEECC
Confidence 445566 35577777777777766664
No 179
>COG1856 Uncharacterized homolog of biotin synthetase [Function unknown]
Probab=43.60 E-value=9 Score=38.64 Aligned_cols=29 Identities=24% Similarity=0.418 Sum_probs=22.8
Q ss_pred EEeecCCCCcEEE----EEeecCCCCCCccccc
Q 011230 300 FMTRIPYFQEVIV----MASTCDACGYRNSELK 328 (490)
Q Consensus 300 ~~~~IP~FkeviI----msf~C~~CGyr~nEVk 328 (490)
+.+++|+|..|-+ .+++|+|||.+.=+=+
T Consensus 4 l~v~~~k~~sISVTG~yC~lnC~HCg~~~L~~M 36 (275)
T COG1856 4 LTVDPPKFISISVTGAYCSLNCPHCGRHYLEHM 36 (275)
T ss_pred cccCCCCCceEEEeccceEecChHHHHHHHHHh
Confidence 4578899999877 4899999998765543
No 180
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=43.46 E-value=5.6 Score=41.03 Aligned_cols=32 Identities=22% Similarity=0.472 Sum_probs=21.1
Q ss_pred EeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCcc
Q 011230 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNN 71 (490)
Q Consensus 30 ies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnn 71 (490)
.-..||.|++... -+++---.+.||+|||+..
T Consensus 25 ~~~~c~~c~~~~~----------~~~l~~~~~vc~~c~~h~r 56 (285)
T TIGR00515 25 VWTKCPKCGQVLY----------TKELERNLEVCPKCDHHMR 56 (285)
T ss_pred CeeECCCCcchhh----------HHHHHhhCCCCCCCCCcCc
Confidence 4678999986532 2233233478999999754
No 181
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=43.39 E-value=15 Score=26.24 Aligned_cols=10 Identities=30% Similarity=0.969 Sum_probs=5.8
Q ss_pred EeecCCCCCC
Q 011230 60 AFECPHCGER 69 (490)
Q Consensus 60 Sf~C~~CGyr 69 (490)
...|+.||..
T Consensus 25 ~v~C~~C~~~ 34 (36)
T PF13717_consen 25 KVRCSKCGHV 34 (36)
T ss_pred EEECCCCCCE
Confidence 4566666653
No 182
>TIGR02827 RNR_anaer_Bdell anaerobic ribonucleoside-triphosphate reductase. Members of this family belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are pair with genes for an acitivating protein that creates a glycine radical. Members of this family, though related, fall outside the scope of TIGR02487, a functionally equivalent protein set; no genome has members in both familes. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons.
Probab=43.25 E-value=13 Score=42.06 Aligned_cols=29 Identities=24% Similarity=0.621 Sum_probs=18.9
Q ss_pred EeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccce
Q 011230 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEV 73 (490)
Q Consensus 30 ies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEv 73 (490)
--+.|+.||.- -++. .+.||+||-++.|+
T Consensus 531 ~~siC~~CGy~------------~g~~---~~~CP~CGs~~~ev 559 (586)
T TIGR02827 531 KITICNDCHHI------------DKRT---LHRCPVCGSANIDY 559 (586)
T ss_pred CCeecCCCCCc------------CCCc---CCcCcCCCCccceE
Confidence 44789999851 0111 38999999765444
No 183
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=43.11 E-value=29 Score=25.47 Aligned_cols=37 Identities=24% Similarity=0.567 Sum_probs=22.6
Q ss_pred eccCcCCcccc----ce-eEEEeecC----CCCcEEEEEeecCCCC
Q 011230 285 PSTCGACAASC----ET-RMFMTRIP----YFQEVIVMASTCDACG 321 (490)
Q Consensus 285 ~s~Cp~C~~~~----~t-~m~~~~IP----~FkeviImsf~C~~CG 321 (490)
+..||.||... .. .....+|| +..+.+.....|.+||
T Consensus 2 ~~~C~~Cg~~l~~ig~~~~~q~l~~~p~~~~V~e~~~~~y~C~~C~ 47 (47)
T PF13005_consen 2 PRACPDCGGELKEIGEEKVRQVLDLPPAKPEVTEHVRHKYACPCCG 47 (47)
T ss_pred CCcCCCCCceeeECCceeeEEEEeecccceEEEEEEeceEECCCCC
Confidence 35699998764 22 23333332 2256667788899997
No 184
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=43.04 E-value=5.8 Score=41.06 Aligned_cols=32 Identities=22% Similarity=0.532 Sum_probs=21.0
Q ss_pred EeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCcc
Q 011230 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNN 71 (490)
Q Consensus 30 ies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnn 71 (490)
+=..||.|++.... +++---.+.||+|||...
T Consensus 26 ~~~~c~~c~~~~~~----------~~l~~~~~vc~~c~~h~r 57 (292)
T PRK05654 26 LWTKCPSCGQVLYR----------KELEANLNVCPKCGHHMR 57 (292)
T ss_pred CeeECCCccchhhH----------HHHHhcCCCCCCCCCCee
Confidence 46889999865322 222222469999999763
No 185
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=42.84 E-value=6.7 Score=40.40 Aligned_cols=72 Identities=21% Similarity=0.343 Sum_probs=36.8
Q ss_pred ceeeeecCCCccceeEeHHHHHHHHHHHHhhccCcC----C-CCCCCHHHH--HHHHHHHHHHHHhhcCCCceEEEEEcC
Q 011230 366 ELDLELAGGTLGGIVTTVEGLITKISESLERVHGFS----F-GDSLDENKR--TKWQDFKAKLNKLLSVEESWTLILDDA 438 (490)
Q Consensus 366 EL~lei~pGtl~G~~TTVEGlL~~i~d~L~~~~~~~----~-gds~~~e~~--~k~~~fl~~L~~~~~g~~~fTlIidDP 438 (490)
-.||....|++|..+ =|-+...+...++...|+. . |--+.+... -.+.+.-..|+.+.+-..||-.+|.||
T Consensus 128 v~df~FmgGSmGsVv--Geki~ra~E~A~e~k~P~v~f~aSGGARMQEg~lSLMQMaktsaAl~~l~ea~lpyIsVLt~P 205 (294)
T COG0777 128 VMDFAFMGGSMGSVV--GEKITRAIERAIEDKLPLVLFSASGGARMQEGILSLMQMAKTSAALKRLSEAGLPYISVLTDP 205 (294)
T ss_pred EEeccccccchhHHH--HHHHHHHHHHHHHhCCCEEEEecCcchhHhHHHHHHHHHHHHHHHHHHHHhcCCceEEEecCC
Confidence 345555555554322 2345555555677767762 1 111111111 122233333444445567999999999
Q ss_pred C
Q 011230 439 L 439 (490)
Q Consensus 439 ~ 439 (490)
.
T Consensus 206 T 206 (294)
T COG0777 206 T 206 (294)
T ss_pred C
Confidence 7
No 186
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=42.55 E-value=5.6 Score=31.14 Aligned_cols=22 Identities=45% Similarity=1.056 Sum_probs=16.4
Q ss_pred ccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCC
Q 011230 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGER 69 (490)
Q Consensus 32 s~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyr 69 (490)
+.||+||+ ..+|| ..|++|||=
T Consensus 27 ~~c~~cg~--------~~~~H--------~vc~~cG~y 48 (56)
T PF01783_consen 27 VKCPNCGE--------PKLPH--------RVCPSCGYY 48 (56)
T ss_dssp EESSSSSS--------EESTT--------SBCTTTBBS
T ss_pred eeeccCCC--------Eeccc--------EeeCCCCeE
Confidence 67999974 34466 689999853
No 187
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=42.49 E-value=12 Score=40.76 Aligned_cols=48 Identities=13% Similarity=0.160 Sum_probs=28.7
Q ss_pred cccceEEecCccEEEEeeeeeEeCCCCCCCceeeHHHHHHHHHHHHHH
Q 011230 97 MFHRQVVKSESATIKIPELDFEIPPEAQRGSLSTVEGILVRAADELEA 144 (490)
Q Consensus 97 DLnR~VvkS~~ati~IPEL~~eI~p~~~~G~iTTVEGlL~~~~~~L~~ 144 (490)
.+.++-.-=.+..|-.-++.+-|||.++.-.+.=|+|.--++...+..
T Consensus 184 e~d~~~~p~tfdnvD~~~~~~~i~P~t~~PVl~GIRg~~p~~l~~a~~ 231 (421)
T COG1571 184 EMDKETFPFTFDNVDVQNLYPLIPPHTPNPVLYGIRGAVPEVLLKAMS 231 (421)
T ss_pred HHHhccCCeeEeeeeccccccccCCCCCCCEEEEEecCCHHHHHHHHH
Confidence 344443333334455555677888877888888888865444444443
No 188
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=41.87 E-value=6.1 Score=41.02 Aligned_cols=32 Identities=16% Similarity=0.256 Sum_probs=21.2
Q ss_pred EeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCcc
Q 011230 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNN 71 (490)
Q Consensus 30 ies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnn 71 (490)
+-..||+|++.... +++---...||+|||...
T Consensus 37 lw~kc~~C~~~~~~----------~~l~~~~~vcp~c~~h~r 68 (296)
T CHL00174 37 LWVQCENCYGLNYK----------KFLKSKMNICEQCGYHLK 68 (296)
T ss_pred CeeECCCccchhhH----------HHHHHcCCCCCCCCCCcC
Confidence 46789999865332 222223468999999764
No 189
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=41.29 E-value=30 Score=26.76 Aligned_cols=33 Identities=15% Similarity=0.300 Sum_probs=17.5
Q ss_pred cCcCCccccceeEEEeecCCCCcEEEEEeecCCCCC
Q 011230 287 TCGACAASCETRMFMTRIPYFQEVIVMASTCDACGY 322 (490)
Q Consensus 287 ~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGy 322 (490)
.||-||............. .+.. ....|..||.
T Consensus 5 PCPFCG~~~~~~~~~~~~~-~~~~--~~V~C~~Cga 37 (61)
T PF14354_consen 5 PCPFCGSADVLIRQDEGFD-YGMY--YYVECTDCGA 37 (61)
T ss_pred CCCCCCCcceEeecccCCC-CCCE--EEEEcCCCCC
Confidence 5999976643222211111 1111 5566999998
No 190
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=41.16 E-value=23 Score=31.59 Aligned_cols=30 Identities=33% Similarity=0.784 Sum_probs=21.8
Q ss_pred ccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCC
Q 011230 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGER 69 (490)
Q Consensus 32 s~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyr 69 (490)
.+|+.|+.+ .|+|... +. ++.-.|..||.+
T Consensus 81 VlC~~C~sp-dT~l~k~-----~r--~~~l~C~aCGa~ 110 (110)
T smart00653 81 VLCPECGSP-DTELIKE-----NR--LFFLKCEACGAR 110 (110)
T ss_pred EECCCCCCC-CcEEEEe-----CC--eEEEEccccCCC
Confidence 689999887 5666443 22 456789999975
No 191
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=41.11 E-value=11 Score=42.88 Aligned_cols=29 Identities=28% Similarity=0.655 Sum_probs=19.5
Q ss_pred EeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccce
Q 011230 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEV 73 (490)
Q Consensus 30 ies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEv 73 (490)
--+.|+.||..+. + ..+.||+||-++.|+
T Consensus 565 ~~~iC~~CG~~~~-----------g----~~~~CP~CGs~~~ev 593 (623)
T PRK08271 565 KITICNDCHHIDK-----------R----TGKRCPICGSENIDY 593 (623)
T ss_pred CCccCCCCCCcCC-----------C----CCcCCcCCCCcchhH
Confidence 4478999985311 0 138999999876554
No 192
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=41.07 E-value=5.3 Score=35.42 Aligned_cols=36 Identities=25% Similarity=0.592 Sum_probs=21.5
Q ss_pred eeccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCccccccCCC
Q 011230 284 FPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGR 332 (490)
Q Consensus 284 ~~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEVk~gg~ 332 (490)
....|..||+.....- +. +.||+||-.+-+|.+|.+
T Consensus 69 ~~~~C~~Cg~~~~~~~-------~~------~~CP~Cgs~~~~i~~G~e 104 (113)
T PF01155_consen 69 ARARCRDCGHEFEPDE-------FD------FSCPRCGSPDVEIISGRE 104 (113)
T ss_dssp -EEEETTTS-EEECHH-------CC------HH-SSSSSS-EEEEESS-
T ss_pred CcEECCCCCCEEecCC-------CC------CCCcCCcCCCcEEccCCe
Confidence 4477999998753221 11 349999999888977643
No 193
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=40.12 E-value=24 Score=31.93 Aligned_cols=42 Identities=17% Similarity=0.433 Sum_probs=24.4
Q ss_pred eeccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCccccccCCC
Q 011230 284 FPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGR 332 (490)
Q Consensus 284 ~~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEVk~gg~ 332 (490)
....| .||+...... ..+.+| ...+.||+||-.+-+|..|-+
T Consensus 69 ~~~~C-~Cg~~~~~~~--~~~~~~----~~~~~CP~Cgs~~~~i~~G~E 110 (124)
T PRK00762 69 VEIEC-ECGYEGVVDE--DEIDHY----AAVIECPVCGNKRAHILGGRE 110 (124)
T ss_pred eeEEe-eCcCcccccc--cchhcc----ccCCcCcCCCCCCCEEecCCe
Confidence 44679 9996643221 111111 014679999987888876543
No 194
>PRK14288 chaperone protein DnaJ; Provisional
Probab=39.99 E-value=81 Score=33.55 Aligned_cols=33 Identities=30% Similarity=0.569 Sum_probs=21.4
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCcc
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNS 325 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~n 325 (490)
..|+.|+..|...+.. .| +.+...|+.|+-+--
T Consensus 157 ~~C~~C~G~G~~~~~~----g~---~~~~~~C~~C~G~G~ 189 (369)
T PRK14288 157 ETCKQCNGQGQVFMRQ----GF---MSFAQTCGACQGKGK 189 (369)
T ss_pred cCCCCCCCCcEEEEEe----ce---EEEEEecCCCCCCce
Confidence 4588888888655433 22 346669999976643
No 195
>PF10071 DUF2310: Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); InterPro: IPR016908 This group represents uncharacterised conserved proteins.
Probab=39.94 E-value=12 Score=38.20 Aligned_cols=76 Identities=24% Similarity=0.232 Sum_probs=47.6
Q ss_pred EeeeeeEeCCCCCCCceeeHHHHHHHHHHHHHHhh----------------------HHHhcCCHHHH-HHHHHHHHHHH
Q 011230 112 IPELDFEIPPEAQRGSLSTVEGILVRAADELEALQ----------------------EERKKLDPQTA-EAIDQFLLKLR 168 (490)
Q Consensus 112 IPEL~~eI~p~~~~G~iTTVEGlL~~~~~~L~~~~----------------------~~r~~~~~e~~-~ki~~~i~kL~ 168 (490)
|-||-|+. - ...-.+.-++..|..+++.|...- |+.++.+|... ....+-+++|.
T Consensus 3 v~el~F~~-~-~~~~~~~~~~~~i~~~l~~lr~NGQIlGRe~p~~~~~~~f~~rvvcPe~dSL~~~~~s~~V~~al~~l~ 80 (258)
T PF10071_consen 3 VAELFFEQ-C-FADTDISAVEHAINQLLDALRYNGQILGREFPLAFQENEFRVRVVCPEQDSLHPKYNSPYVNEALQKLE 80 (258)
T ss_pred EEEEEccc-c-cCCCCHHHHHHHHHHHHHHHHhcCeeeccccceEEecCEEEEEEeCCCcchhchhhCCHHHHHHHHHHH
Confidence 55777774 1 124456778888999988887642 22333444432 45666677777
Q ss_pred HhhcCCCcEEEEEECCCCCee
Q 011230 169 ACAKGDSTFTFILDDPAGNSF 189 (490)
Q Consensus 169 ~~~~g~~pFTliidDPsGNS~ 189 (490)
++--+...|.+|=+|...+.-
T Consensus 81 ~~gl~~p~~~~ig~d~~s~~t 101 (258)
T PF10071_consen 81 EAGLLFPKFQIIGEDLNSEET 101 (258)
T ss_pred HhCCCCceeEEecccCCcccc
Confidence 776666678887777554433
No 196
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=39.85 E-value=20 Score=29.77 Aligned_cols=39 Identities=13% Similarity=0.167 Sum_probs=25.7
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecC--CCCCCcccc
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCD--ACGYRNSEL 327 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~--~CGyr~nEV 327 (490)
..||.||....++--..--+. +.-.-..|. .||+++.-.
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~---~~~~Y~qC~N~eCg~tF~t~ 42 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDT---TKERYHQCQNVNCSATFITY 42 (72)
T ss_pred ccCCCCCCccEEEEChhcChh---hheeeeecCCCCCCCEEEEE
Confidence 369999988855443333333 555678898 899887544
No 197
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=39.78 E-value=60 Score=29.10 Aligned_cols=32 Identities=22% Similarity=0.393 Sum_probs=24.3
Q ss_pred ccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccceee
Q 011230 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQF 75 (490)
Q Consensus 32 s~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEvq~ 75 (490)
-+||.|+...+++. -. .|.||.|+|..+++-.
T Consensus 4 p~cp~c~sEytYed----------~~--~~~cpec~~ew~~~~~ 35 (112)
T COG2824 4 PPCPKCNSEYTYED----------GG--QLICPECAHEWNENEA 35 (112)
T ss_pred CCCCccCCceEEec----------Cc--eEeCchhccccccccc
Confidence 36999998876654 12 6889999999996643
No 198
>PRK04296 thymidine kinase; Provisional
Probab=39.59 E-value=28 Score=33.08 Aligned_cols=45 Identities=13% Similarity=0.249 Sum_probs=32.9
Q ss_pred CCceEEeccCCccCCCceEEEEEe---ecCCccceEEE------EeecCCCCCC
Q 011230 25 APLYQVESLCMRCGENGVTRFLLT---LIPHFRKVLLS------AFECPHCGER 69 (490)
Q Consensus 25 ~~v~eies~Cp~Cg~~g~trlllt---~IP~F~eviim------Sf~C~~CGyr 69 (490)
..|.++...|+.||+.+....-++ ..++-+++|+. .-.|.+|-+.
T Consensus 134 D~V~~l~~vC~~Cg~~a~~~~r~~~~~~~~~~~~~~~ig~~e~Y~~~Cr~c~~~ 187 (190)
T PRK04296 134 DKVTELKAICVHCGRKATMNQRLIDGGPAVYEGPQVLVGGNESYEAVCRKHYKE 187 (190)
T ss_pred CeEEEeeEEccccCCccceEEEEeCCCCccCCCCEEEECCcCcEEehhHHhhhc
Confidence 348899999999999888877766 24566777754 3467777653
No 199
>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=39.47 E-value=26 Score=30.45 Aligned_cols=37 Identities=27% Similarity=0.626 Sum_probs=25.7
Q ss_pred EeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccceeeccccCC
Q 011230 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEIQP 81 (490)
Q Consensus 30 ies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEvq~~g~i~~ 81 (490)
-.-.||-||+....|. -.=-+.|.+||+.. .+|...|
T Consensus 34 a~y~CpfCgk~~vkR~-----------a~GIW~C~~C~~~~----AGGAy~p 70 (91)
T TIGR00280 34 AKYVCPFCGKKTVKRG-----------STGIWTCRKCGAKF----AGGAYTP 70 (91)
T ss_pred cCccCCCCCCCceEEE-----------eeEEEEcCCCCCEE----eCCcccc
Confidence 3467999997654443 34458999999975 4666654
No 200
>PF10071 DUF2310: Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); InterPro: IPR016908 This group represents uncharacterised conserved proteins.
Probab=39.43 E-value=12 Score=38.12 Aligned_cols=35 Identities=23% Similarity=0.479 Sum_probs=23.6
Q ss_pred ceEEeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCC
Q 011230 27 LYQVESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGER 69 (490)
Q Consensus 27 v~eies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyr 69 (490)
..|....||.||++ .++ +-|.|. |.-|.|++|--=
T Consensus 216 ~~e~~r~CP~Cg~~--W~L---~~plh~---iFdFKCD~CRLV 250 (258)
T PF10071_consen 216 ASEQARKCPSCGGD--WRL---KEPLHD---IFDFKCDPCRLV 250 (258)
T ss_pred HHhhCCCCCCCCCc--ccc---CCchhh---ceeccCCcceee
Confidence 34678999999975 332 224433 568999999653
No 201
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=39.36 E-value=44 Score=30.84 Aligned_cols=46 Identities=26% Similarity=0.517 Sum_probs=30.9
Q ss_pred eEEeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCcc-ceeeccccCCcceEEEEEee
Q 011230 28 YQVESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNN-EVQFAGEIQPRGCNYSLKVP 91 (490)
Q Consensus 28 ~eies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnn-Evq~~g~i~~kG~r~tl~V~ 91 (490)
..+-+.|++||.- .. |- .-.|++||.+.+ |.-- +..+|+.+|++|.
T Consensus 26 kl~g~kC~~CG~v---~~-----PP-------r~~Cp~C~~~~~~E~ve---ls~~G~V~t~Tv~ 72 (140)
T COG1545 26 KLLGTKCKKCGRV---YF-----PP-------RAYCPKCGSETELEWVE---LSGEGKVETYTVV 72 (140)
T ss_pred cEEEEEcCCCCeE---Ec-----CC-------cccCCCCCCCCceEEEE---eCCCeEEEEEEEE
Confidence 3577999999732 11 22 346999999952 4433 3347888888886
No 202
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=39.19 E-value=15 Score=42.59 Aligned_cols=27 Identities=22% Similarity=0.497 Sum_probs=18.6
Q ss_pred eccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCcccc
Q 011230 285 PSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSEL 327 (490)
Q Consensus 285 ~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEV 327 (490)
-+.|+.||..+.. .+.||+||-.+.+|
T Consensus 680 ~~~C~~CG~~~~~----------------~~~CP~CG~~~~~~ 706 (735)
T PRK07111 680 VDRCPVCGYLGVI----------------EDKCPKCGSTNIQR 706 (735)
T ss_pred CeecCCCCCCCCc----------------CccCcCCCCcccee
Confidence 3679999965432 18999999754444
No 203
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=39.18 E-value=17 Score=41.80 Aligned_cols=28 Identities=32% Similarity=0.568 Sum_probs=17.6
Q ss_pred EEeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccce
Q 011230 29 QVESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEV 73 (490)
Q Consensus 29 eies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEv 73 (490)
---+.|+.||.- -++ -+.||+|| +..||
T Consensus 624 ~~~~~C~~CG~~------------~g~----~~~CP~CG-~~~~v 651 (656)
T PRK08270 624 PTFSICPKHGYL------------SGE----HEFCPKCG-EETEV 651 (656)
T ss_pred CCCcccCCCCCc------------CCC----CCCCcCCc-Cccce
Confidence 345679999842 111 39999999 33443
No 204
>PRK14294 chaperone protein DnaJ; Provisional
Probab=38.94 E-value=1.3e+02 Score=31.95 Aligned_cols=26 Identities=31% Similarity=0.632 Sum_probs=18.4
Q ss_pred cEEEEee----eeeEeCCCCCCCceeeHHH
Q 011230 108 ATIKIPE----LDFEIPPEAQRGSLSTVEG 133 (490)
Q Consensus 108 ati~IPE----L~~eI~p~~~~G~iTTVEG 133 (490)
+++.|+- +.++|||+++.|.+-.|.|
T Consensus 281 ~~~~i~tldG~~~v~ip~g~~~g~~iri~G 310 (366)
T PRK14294 281 AQIEVPTLEGERELKIPKGTQPGDIFRFKG 310 (366)
T ss_pred CeEEEECCCCcEEEEECCCcCCCCEEEECC
Confidence 5666664 3578888878888777765
No 205
>PRK14279 chaperone protein DnaJ; Provisional
Probab=38.57 E-value=80 Score=33.90 Aligned_cols=32 Identities=16% Similarity=0.332 Sum_probs=19.5
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCc
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRN 324 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~ 324 (490)
..|+.|+..|...... + .+-|...|+.|+=+-
T Consensus 191 ~~C~~C~G~G~~~~~~------g-~~~~~~~C~~C~G~G 222 (392)
T PRK14279 191 KVCPTCNGSGVISRNQ------G-AFGFSEPCTDCRGTG 222 (392)
T ss_pred CCCCCCcceEEEEEEe------c-ceEEEEecCCCCcee
Confidence 4577777776443332 1 224779999997543
No 206
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=38.09 E-value=6.9 Score=40.37 Aligned_cols=32 Identities=19% Similarity=0.350 Sum_probs=21.1
Q ss_pred eeccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCcc
Q 011230 284 FPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNS 325 (490)
Q Consensus 284 ~~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~n 325 (490)
+-..||.|++....+ ++----.+|++|||...
T Consensus 25 ~~~~c~~c~~~~~~~----------~l~~~~~vc~~c~~h~r 56 (285)
T TIGR00515 25 VWTKCPKCGQVLYTK----------ELERNLEVCPKCDHHMR 56 (285)
T ss_pred CeeECCCCcchhhHH----------HHHhhCCCCCCCCCcCc
Confidence 356799999875322 22222378999999754
No 207
>PRK14276 chaperone protein DnaJ; Provisional
Probab=37.88 E-value=1.2e+02 Score=32.25 Aligned_cols=21 Identities=19% Similarity=0.439 Sum_probs=16.2
Q ss_pred eeeeEeCCCCCCCceeeHHHH
Q 011230 114 ELDFEIPPEAQRGSLSTVEGI 134 (490)
Q Consensus 114 EL~~eI~p~~~~G~iTTVEGl 134 (490)
.|.+.|||++..|..-++.|.
T Consensus 220 ~l~V~Ip~G~~~G~~i~l~G~ 240 (380)
T PRK14276 220 TVSVKIPAGVETGQQIRLQGQ 240 (380)
T ss_pred EEEEEeCCCccCCcEEEEecc
Confidence 356778898889988877764
No 208
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=37.86 E-value=14 Score=33.28 Aligned_cols=28 Identities=32% Similarity=0.734 Sum_probs=18.3
Q ss_pred EeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCc
Q 011230 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (490)
Q Consensus 30 ies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrn 70 (490)
+...||+||+.- ++ ++.+ -.|.||+-.=
T Consensus 68 v~V~CP~C~K~T--Km-------LGr~----D~CM~C~~pL 95 (114)
T PF11023_consen 68 VQVECPNCGKQT--KM-------LGRV----DACMHCKEPL 95 (114)
T ss_pred eeeECCCCCChH--hh-------hchh----hccCcCCCcC
Confidence 445699999762 22 3444 4799998643
No 209
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 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. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=37.85 E-value=16 Score=29.91 Aligned_cols=27 Identities=26% Similarity=0.535 Sum_probs=21.2
Q ss_pred EEEEeecCCCCCCccccccCCCCCCCCe
Q 011230 311 IVMASTCDACGYRNSELKPGGRIPEKGK 338 (490)
Q Consensus 311 iImsf~C~~CGyr~nEVk~gg~i~~kG~ 338 (490)
+.|.|.|..||.|+....+--++ .+|+
T Consensus 1 ~~l~FTC~~C~~Rs~~~~sk~aY-~~Gv 27 (66)
T PF05180_consen 1 YQLTFTCNKCGTRSAKMFSKQAY-HKGV 27 (66)
T ss_dssp EEEEEEETTTTEEEEEEEEHHHH-HTSE
T ss_pred CeEEEEcCCCCCccceeeCHHHH-hCCe
Confidence 46899999999999988775554 3665
No 210
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=37.72 E-value=7.1 Score=40.57 Aligned_cols=32 Identities=19% Similarity=0.506 Sum_probs=21.6
Q ss_pred eeccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCcc
Q 011230 284 FPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNS 325 (490)
Q Consensus 284 ~~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~n 325 (490)
+-+.||+|++....+- .---..+|++|||...
T Consensus 37 lw~kc~~C~~~~~~~~----------l~~~~~vcp~c~~h~r 68 (296)
T CHL00174 37 LWVQCENCYGLNYKKF----------LKSKMNICEQCGYHLK 68 (296)
T ss_pred CeeECCCccchhhHHH----------HHHcCCCCCCCCCCcC
Confidence 3678999998763332 2222368999999654
No 211
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=37.57 E-value=34 Score=35.61 Aligned_cols=39 Identities=23% Similarity=0.460 Sum_probs=25.2
Q ss_pred eccCCccCCCceEEE-EEeecCCccceEEEEeecCCCCCCcc
Q 011230 31 ESLCMRCGENGVTRF-LLTLIPHFRKVLLSAFECPHCGERNN 71 (490)
Q Consensus 31 es~Cp~Cg~~g~trl-llt~IP~F~eviimSf~C~~CGyrnn 71 (490)
...|+.||....+-+ +.++ --.|=+-.-|.|..||++..
T Consensus 258 ~~~C~~C~~~~~~~~q~Qtr--saDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 258 LFTCGKCKQKKCTYYQLQTR--SADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred cccCCCCCCccceEEEeccc--CCCCCCeEEEEcCCCCCeee
Confidence 468999996544322 2232 23455666789999999863
No 212
>PRK14295 chaperone protein DnaJ; Provisional
Probab=37.52 E-value=91 Score=33.44 Aligned_cols=21 Identities=19% Similarity=0.390 Sum_probs=16.7
Q ss_pred eeeeEeCCCCCCCceeeHHHH
Q 011230 114 ELDFEIPPEAQRGSLSTVEGI 134 (490)
Q Consensus 114 EL~~eI~p~~~~G~iTTVEGl 134 (490)
.|.+.|||+...|..-+++|.
T Consensus 236 ~l~V~Ip~G~~~G~~i~l~g~ 256 (389)
T PRK14295 236 TMQVRIPAGVSDGQRIRLRGK 256 (389)
T ss_pred EEEEEeCCCCCCCCEEEEccc
Confidence 367888899899988887764
No 213
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=37.33 E-value=7.3 Score=40.33 Aligned_cols=32 Identities=16% Similarity=0.396 Sum_probs=21.2
Q ss_pred eeccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCcc
Q 011230 284 FPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNS 325 (490)
Q Consensus 284 ~~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~n 325 (490)
+-..||.|++....+- .---..+|++|||...
T Consensus 26 ~~~~c~~c~~~~~~~~----------l~~~~~vc~~c~~h~r 57 (292)
T PRK05654 26 LWTKCPSCGQVLYRKE----------LEANLNVCPKCGHHMR 57 (292)
T ss_pred CeeECCCccchhhHHH----------HHhcCCCCCCCCCCee
Confidence 3567999998753322 2122368999999764
No 214
>PRK10767 chaperone protein DnaJ; Provisional
Probab=37.27 E-value=86 Score=33.21 Aligned_cols=20 Identities=25% Similarity=0.486 Sum_probs=15.3
Q ss_pred eeeeEeCCCCCCCceeeHHH
Q 011230 114 ELDFEIPPEAQRGSLSTVEG 133 (490)
Q Consensus 114 EL~~eI~p~~~~G~iTTVEG 133 (490)
.|.+.|||++..|..-.+.|
T Consensus 212 ~l~V~Ip~G~~~G~~i~~~g 231 (371)
T PRK10767 212 TLSVKIPAGVDTGDRIRLSG 231 (371)
T ss_pred eEEEecCCCCCCCcEEEEec
Confidence 46778888888888777765
No 215
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=37.17 E-value=34 Score=27.93 Aligned_cols=29 Identities=28% Similarity=0.516 Sum_probs=19.1
Q ss_pred cCCccCCCceEEEEEeecCCccceEEEEeecCCCCCC
Q 011230 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGER 69 (490)
Q Consensus 33 ~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyr 69 (490)
.||.||.+-.+-- ..-+|| .|.|..||-+
T Consensus 8 PCPFCG~~~~~v~--~~~g~~------~v~C~~CgA~ 36 (64)
T PRK09710 8 PCPFCGCPSVTVK--AISGYY------RAKCNGCESR 36 (64)
T ss_pred CCCCCCCceeEEE--ecCceE------EEEcCCCCcC
Confidence 6999997743322 223444 5999999974
No 216
>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=36.64 E-value=17 Score=25.66 Aligned_cols=12 Identities=25% Similarity=0.778 Sum_probs=7.4
Q ss_pred EEeecCCCCCCc
Q 011230 59 SAFECPHCGERN 70 (490)
Q Consensus 59 mSf~C~~CGyrn 70 (490)
|-+.|||||-++
T Consensus 1 M~~~CP~C~~~~ 12 (38)
T TIGR02098 1 MRIQCPNCKTSF 12 (38)
T ss_pred CEEECCCCCCEE
Confidence 446677777653
No 217
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=36.59 E-value=36 Score=30.39 Aligned_cols=39 Identities=23% Similarity=0.416 Sum_probs=28.9
Q ss_pred ccceEEEEeecCCCCCCccceeeccccCCcceEEEEEee
Q 011230 53 FRKVLLSAFECPHCGERNNEVQFAGEIQPRGCNYSLKVP 91 (490)
Q Consensus 53 F~eviimSf~C~~CGyrnnEvq~~g~i~~kG~r~tl~V~ 91 (490)
|=+|=+=+..||+||-...-+-.++...--|..++++|=
T Consensus 42 yV~ie~G~t~CP~Cg~~~e~~fvva~~aLVgl~l~mkVF 80 (115)
T COG1885 42 YVEIEVGSTSCPKCGEPFESAFVVANTALVGLILSMKVF 80 (115)
T ss_pred eEEEecccccCCCCCCccceeEEEecceeEEEEEEEEEe
Confidence 345556677888888887777777777777888888875
No 218
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=36.56 E-value=18 Score=40.89 Aligned_cols=28 Identities=25% Similarity=0.620 Sum_probs=20.2
Q ss_pred eccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCcccc
Q 011230 285 PSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSEL 327 (490)
Q Consensus 285 ~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEV 327 (490)
-+.|+.||..+... .+.|++||-++-+|
T Consensus 524 ~~~C~~CG~~g~~~---------------~~~CP~Cgs~~~~~ 551 (579)
T TIGR02487 524 VDVCEDCGYTGEGL---------------NDKCPKCGSHDIEV 551 (579)
T ss_pred CccCCCCCCCCCCC---------------CCcCcCCCCcccee
Confidence 37799999765332 17899999876555
No 219
>PRK14300 chaperone protein DnaJ; Provisional
Probab=36.28 E-value=1e+02 Score=32.80 Aligned_cols=33 Identities=27% Similarity=0.513 Sum_probs=20.0
Q ss_pred eccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCc
Q 011230 285 PSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRN 324 (490)
Q Consensus 285 ~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~ 324 (490)
...|+.|+..|...+. ++- +-|...|+.|.=+-
T Consensus 162 ~~~C~~C~G~G~~~~~------~g~-~~~~~~C~~C~G~G 194 (372)
T PRK14300 162 VTTCDACSGVGATRMQ------QGF-FTIEQACHKCQGNG 194 (372)
T ss_pred CccCCCccCeEEEEEe------ece-EEEEEeCCCCCccc
Confidence 3567778777755442 122 23777999996443
No 220
>PRK14290 chaperone protein DnaJ; Provisional
Probab=36.15 E-value=1.5e+02 Score=31.46 Aligned_cols=21 Identities=24% Similarity=0.358 Sum_probs=17.3
Q ss_pred eeeeEeCCCCCCCceeeHHHH
Q 011230 114 ELDFEIPPEAQRGSLSTVEGI 134 (490)
Q Consensus 114 EL~~eI~p~~~~G~iTTVEGl 134 (490)
.|.+.|||++..|..-.++|.
T Consensus 222 ~~~V~Ip~G~~~G~~i~~~g~ 242 (365)
T PRK14290 222 DISVKIPKGATDNLRLRVKGK 242 (365)
T ss_pred EEEEEECCCCCCCcEEEEccc
Confidence 678889999999988877764
No 221
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.96 E-value=17 Score=36.72 Aligned_cols=37 Identities=27% Similarity=0.528 Sum_probs=22.4
Q ss_pred EeccCCccCCC--------ceEEEEEeec----------CCccceEEEEeecCCCCCCc
Q 011230 30 VESLCMRCGEN--------GVTRFLLTLI----------PHFRKVLLSAFECPHCGERN 70 (490)
Q Consensus 30 ies~Cp~Cg~~--------g~trlllt~I----------P~F~eviimSf~C~~CGyrn 70 (490)
-...||+|+-. |..|++--++ |+|=+|+ .||.|+|--
T Consensus 18 k~ieCPvC~tkFkkeev~tgsiRiiagDld~~lkygninP~fY~Vv----vCP~C~yAa 72 (267)
T COG1655 18 KTIECPVCNTKFKKEEVKTGSIRIIAGDLDFFLKYGNINPYFYDVV----VCPICYYAA 72 (267)
T ss_pred ceeccCcccchhhhhheeccceeEecccccceeeccccCCceeEEE----EcchhhHHH
Confidence 45679999833 3334432222 5555554 599999954
No 222
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=35.67 E-value=28 Score=28.95 Aligned_cols=39 Identities=13% Similarity=0.180 Sum_probs=25.2
Q ss_pred ccCCccCCCceEEEEEeecCCccceEEEEeecC--CCCCCccce
Q 011230 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECP--HCGERNNEV 73 (490)
Q Consensus 32 s~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~--~CGyrnnEv 73 (490)
..||.||....+|---..-+. +.-.-..|. +||+++.-.
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~---~~~~Y~qC~N~eCg~tF~t~ 42 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDT---TKERYHQCQNVNCSATFITY 42 (72)
T ss_pred ccCCCCCCccEEEEChhcChh---hheeeeecCCCCCCCEEEEE
Confidence 369999987755443222232 455678998 999987543
No 223
>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=35.42 E-value=23 Score=25.24 Aligned_cols=27 Identities=30% Similarity=0.687 Sum_probs=15.1
Q ss_pred CcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCc
Q 011230 288 CGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRN 324 (490)
Q Consensus 288 Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~ 324 (490)
||.|+.....+-- ++..+ .|..|||..
T Consensus 4 Cp~C~nlL~p~~~-------~~~~~---~C~~C~Y~~ 30 (35)
T PF02150_consen 4 CPECGNLLYPKED-------KEKRV---ACRTCGYEE 30 (35)
T ss_dssp ETTTTSBEEEEEE-------TTTTE---EESSSS-EE
T ss_pred CCCCCccceEcCC-------CccCc---CCCCCCCcc
Confidence 8999876532221 11111 899999953
No 224
>PRK14285 chaperone protein DnaJ; Provisional
Probab=35.38 E-value=82 Score=33.44 Aligned_cols=32 Identities=22% Similarity=0.317 Sum_probs=19.2
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCc
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRN 324 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~ 324 (490)
..|+.|+..|...+ -| +-+ -+...|+.|+=+-
T Consensus 164 ~~C~~C~G~G~~~~----~~--G~~-~~~~~C~~C~G~G 195 (365)
T PRK14285 164 SICNMCNGSGRVMQ----GG--GFF-RVTTTCPKCYGNG 195 (365)
T ss_pred ccCCCccCceeEEe----cC--cee-EEeeecCCCCCcc
Confidence 34777766664433 22 323 5788999996544
No 225
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=35.36 E-value=18 Score=21.90 Aligned_cols=12 Identities=42% Similarity=1.168 Sum_probs=7.4
Q ss_pred eecCCCCCCccc
Q 011230 61 FECPHCGERNNE 72 (490)
Q Consensus 61 f~C~~CGyrnnE 72 (490)
|.|+.||+..+.
T Consensus 1 ~~C~~C~~~~~~ 12 (24)
T PF13894_consen 1 FQCPICGKSFRS 12 (24)
T ss_dssp EE-SSTS-EESS
T ss_pred CCCcCCCCcCCc
Confidence 678999887653
No 226
>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=35.29 E-value=39 Score=24.70 Aligned_cols=31 Identities=29% Similarity=0.667 Sum_probs=17.5
Q ss_pred cCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccce
Q 011230 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEV 73 (490)
Q Consensus 33 ~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEv 73 (490)
.||+||... +.++ +.=++ +.|+.||.--.|-
T Consensus 2 ~Cp~Cg~~~----~~~D-~~~g~-----~vC~~CG~Vl~e~ 32 (43)
T PF08271_consen 2 KCPNCGSKE----IVFD-PERGE-----LVCPNCGLVLEEN 32 (43)
T ss_dssp SBTTTSSSE----EEEE-TTTTE-----EEETTT-BBEE-T
T ss_pred CCcCCcCCc----eEEc-CCCCe-----EECCCCCCEeecc
Confidence 599998643 2233 44444 4699999754443
No 227
>PRK14294 chaperone protein DnaJ; Provisional
Probab=34.97 E-value=1e+02 Score=32.63 Aligned_cols=21 Identities=24% Similarity=0.417 Sum_probs=16.7
Q ss_pred eeeeEeCCCCCCCceeeHHHH
Q 011230 114 ELDFEIPPEAQRGSLSTVEGI 134 (490)
Q Consensus 114 EL~~eI~p~~~~G~iTTVEGl 134 (490)
.|.+.|||++..|..-+++|.
T Consensus 214 ~l~V~Ip~G~~~G~~i~~~g~ 234 (366)
T PRK14294 214 TVQVKIPAGVDTGSRLRLRGE 234 (366)
T ss_pred eEEEecCCCCcCCcEEEEccC
Confidence 456788999999988888764
No 228
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.90 E-value=18 Score=36.45 Aligned_cols=38 Identities=26% Similarity=0.656 Sum_probs=22.9
Q ss_pred EeeccCcCCcccc--------ceeEEEeec----------CCCCcEEEEEeecCCCCCCc
Q 011230 283 TFPSTCGACAASC--------ETRMFMTRI----------PYFQEVIVMASTCDACGYRN 324 (490)
Q Consensus 283 ~~~s~Cp~C~~~~--------~t~m~~~~I----------P~FkeviImsf~C~~CGyr~ 324 (490)
.-...||+|+-.- ..|+.--++ |+|=+| .+||.|+|-.
T Consensus 17 kk~ieCPvC~tkFkkeev~tgsiRiiagDld~~lkygninP~fY~V----vvCP~C~yAa 72 (267)
T COG1655 17 KKTIECPVCNTKFKKEEVKTGSIRIIAGDLDFFLKYGNINPYFYDV----VVCPICYYAA 72 (267)
T ss_pred hceeccCcccchhhhhheeccceeEecccccceeeccccCCceeEE----EEcchhhHHH
Confidence 3446799997543 334332222 555555 5799999964
No 229
>PRK14301 chaperone protein DnaJ; Provisional
Probab=34.63 E-value=93 Score=33.12 Aligned_cols=21 Identities=33% Similarity=0.491 Sum_probs=16.1
Q ss_pred eeeeEeCCCCCCCceeeHHHH
Q 011230 114 ELDFEIPPEAQRGSLSTVEGI 134 (490)
Q Consensus 114 EL~~eI~p~~~~G~iTTVEGl 134 (490)
.+.+.|||++..|..-++.|.
T Consensus 214 ~l~V~Ip~G~~~G~~i~~~g~ 234 (373)
T PRK14301 214 ELKVRIPAGVDTGSRLRLRGE 234 (373)
T ss_pred EEEEEeCCCCcCCCEEEEecc
Confidence 356778899889988877764
No 230
>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=34.62 E-value=34 Score=29.74 Aligned_cols=39 Identities=21% Similarity=0.358 Sum_probs=27.1
Q ss_pred ceEeeccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCccccccCCCCC
Q 011230 281 VMTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRIP 334 (490)
Q Consensus 281 v~~~~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEVk~gg~i~ 334 (490)
.+.-...||-|++.. ++.+-.=-+.|.+||+. ..||++.
T Consensus 31 ~q~a~y~CpfCgk~~-----------vkR~a~GIW~C~~C~~~----~AGGAy~ 69 (91)
T TIGR00280 31 QQKAKYVCPFCGKKT-----------VKRGSTGIWTCRKCGAK----FAGGAYT 69 (91)
T ss_pred HHhcCccCCCCCCCc-----------eEEEeeEEEEcCCCCCE----EeCCccc
Confidence 345567899999875 34444555899999995 4466654
No 231
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=34.61 E-value=21 Score=28.48 Aligned_cols=23 Identities=39% Similarity=0.739 Sum_probs=16.0
Q ss_pred eccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCC
Q 011230 31 ESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGER 69 (490)
Q Consensus 31 es~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyr 69 (490)
-+.|++||+ ..+.--.|.+|||-
T Consensus 27 ~~~c~~cG~----------------~~l~Hrvc~~cg~Y 49 (57)
T COG0333 27 LSVCPNCGE----------------YKLPHRVCLKCGYY 49 (57)
T ss_pred ceeccCCCC----------------cccCceEcCCCCCc
Confidence 367999964 33344679999974
No 232
>PRK14279 chaperone protein DnaJ; Provisional
Probab=34.50 E-value=1.1e+02 Score=32.85 Aligned_cols=21 Identities=24% Similarity=0.547 Sum_probs=16.8
Q ss_pred eeeeEeCCCCCCCceeeHHHH
Q 011230 114 ELDFEIPPEAQRGSLSTVEGI 134 (490)
Q Consensus 114 EL~~eI~p~~~~G~iTTVEGl 134 (490)
.+.+.|||++..|..-+++|.
T Consensus 243 ~~~V~Ip~G~~~G~~i~~~g~ 263 (392)
T PRK14279 243 TINVRIPPGVEDGQRIRLAGQ 263 (392)
T ss_pred eeEEEeCCCCCCCcEEEEeCC
Confidence 567889999999988877764
No 233
>PRK14300 chaperone protein DnaJ; Provisional
Probab=34.32 E-value=1.4e+02 Score=31.74 Aligned_cols=21 Identities=24% Similarity=0.403 Sum_probs=16.7
Q ss_pred eeeeEeCCCCCCCceeeHHHH
Q 011230 114 ELDFEIPPEAQRGSLSTVEGI 134 (490)
Q Consensus 114 EL~~eI~p~~~~G~iTTVEGl 134 (490)
.+.+.|||++..|..-.+.|.
T Consensus 215 ~~~V~Ip~G~~~G~~i~l~g~ 235 (372)
T PRK14300 215 NLSVNIPAGVENGTRIRHTGE 235 (372)
T ss_pred EEEEEECCCCCCCcEEEEecc
Confidence 578889999999987777664
No 234
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=34.27 E-value=28 Score=33.98 Aligned_cols=33 Identities=18% Similarity=0.428 Sum_probs=24.6
Q ss_pred CCcceEeeccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCC
Q 011230 278 PEEVMTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYR 323 (490)
Q Consensus 278 ~~ev~~~~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr 323 (490)
.+..-.+-+.|+.|+.++.-+ =+...|+.||+.
T Consensus 142 ~~dlGVI~A~CsrC~~~L~~~-------------~~~l~Cp~Cg~t 174 (188)
T COG1096 142 GNDLGVIYARCSRCRAPLVKK-------------GNMLKCPNCGNT 174 (188)
T ss_pred CCcceEEEEEccCCCcceEEc-------------CcEEECCCCCCE
Confidence 456778899999999986322 245689999973
No 235
>PF06054 CoiA: Competence protein CoiA-like family; InterPro: IPR010330 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. Many of the members of this family are described as transcription factors. CoiA falls within a competence-specific operon in Streptococcus. CoiA is an uncharacterised protein.
Probab=34.18 E-value=17 Score=38.74 Aligned_cols=36 Identities=19% Similarity=0.259 Sum_probs=27.6
Q ss_pred EeeccCcCCccccceeEEEeecCCCCcEEEEEeecCCC
Q 011230 283 TFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDAC 320 (490)
Q Consensus 283 ~~~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~C 320 (490)
.-.-.||.|+++...+.-...+|||.-.-. ..|+.+
T Consensus 28 ~~~~~CP~C~~~v~lk~G~~k~~HFAH~~~--~~c~~~ 63 (375)
T PF06054_consen 28 KGKYFCPGCGEPVILKKGKKKIPHFAHKSK--SDCPFF 63 (375)
T ss_pred CCcEECCCCCCeeEEEEcCcccceeeecCC--CCCCcc
Confidence 334569999999999999999999987643 246433
No 236
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=34.10 E-value=26 Score=31.67 Aligned_cols=39 Identities=26% Similarity=0.575 Sum_probs=26.0
Q ss_pred EeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccceeeccccCC
Q 011230 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEIQP 81 (490)
Q Consensus 30 ies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEvq~~g~i~~ 81 (490)
.+-.|..|+..-. .+ ..-+.||+||-.+-.|..+....=
T Consensus 69 ~~~~C~~C~~~~~-----------~e--~~~~~CP~C~s~~~~i~~G~el~i 107 (115)
T COG0375 69 AECWCLDCGQEVE-----------LE--ELDYRCPKCGSINLRIIGGDELII 107 (115)
T ss_pred cEEEeccCCCeec-----------ch--hheeECCCCCCCceEEecCCeeEE
Confidence 4567999964321 12 223449999999988887776643
No 237
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=34.07 E-value=17 Score=40.66 Aligned_cols=29 Identities=24% Similarity=0.458 Sum_probs=14.1
Q ss_pred eeccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCccccc
Q 011230 284 FPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELK 328 (490)
Q Consensus 284 ~~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEVk 328 (490)
--+.|+.||..+. . .+.||.||-++.+|-
T Consensus 490 ~~~~C~~CG~~~~---------------~-~~~CP~CGs~~~~~~ 518 (546)
T PF13597_consen 490 PIDICPDCGYIGG---------------E-GDKCPKCGSENIEVY 518 (546)
T ss_dssp -EEEETTT---S------------------EEE-CCC----EEEE
T ss_pred CcccccCCCcCCC---------------C-CCCCCCCCCcccceE
Confidence 3477999996431 2 788999999886664
No 238
>PF05907 DUF866: Eukaryotic protein of unknown function (DUF866); InterPro: IPR008584 This family consists of a number of hypothetical eukaryotic proteins of unknown function with an average length of around 165 residues.; PDB: 1ZSO_B.
Probab=33.98 E-value=23 Score=33.58 Aligned_cols=47 Identities=19% Similarity=0.275 Sum_probs=29.5
Q ss_pred cceEeeccCcCCcccc-----ceeEEEeecCCCCcEEEEEeecCCCCCCccc
Q 011230 280 EVMTFPSTCGACAASC-----ETRMFMTRIPYFQEVIVMASTCDACGYRNSE 326 (490)
Q Consensus 280 ev~~~~s~Cp~C~~~~-----~t~m~~~~IP~FkeviImsf~C~~CGyr~nE 326 (490)
-.+.|...|.+|+..- .++.-.++||..|-..=+.+.|..|+..++=
T Consensus 25 ~~~~fkvkCt~CgE~~~k~V~i~~~e~~e~~gsrG~aNfv~KCk~C~re~si 76 (161)
T PF05907_consen 25 FEWFFKVKCTSCGEVHPKWVYINRFEKHEIPGSRGTANFVMKCKFCKRESSI 76 (161)
T ss_dssp --EEEEEEETTSS--EEEEEEE-TT-BEE-TTSS-EESEEE--SSSS--EEE
T ss_pred CEEEEEEEECCCCCccCcceEeecceEEecCCCccceEeEecCcCcCCccEE
Confidence 4588999999998643 3455678899999999999999999876654
No 239
>PRK10220 hypothetical protein; Provisional
Probab=33.88 E-value=34 Score=30.72 Aligned_cols=30 Identities=20% Similarity=0.551 Sum_probs=21.1
Q ss_pred ccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccce
Q 011230 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEV 73 (490)
Q Consensus 32 s~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEv 73 (490)
-.||.|+.+-++-. ++ -|.||.|||..+.-
T Consensus 4 P~CP~C~seytY~d--------~~----~~vCpeC~hEW~~~ 33 (111)
T PRK10220 4 PHCPKCNSEYTYED--------NG----MYICPECAHEWNDA 33 (111)
T ss_pred CcCCCCCCcceEcC--------CC----eEECCcccCcCCcc
Confidence 36999987644433 33 37899999998754
No 240
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=33.80 E-value=36 Score=29.54 Aligned_cols=39 Identities=18% Similarity=0.306 Sum_probs=26.7
Q ss_pred ceEeeccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCccccccCCCCC
Q 011230 281 VMTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRIP 334 (490)
Q Consensus 281 v~~~~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEVk~gg~i~ 334 (490)
.+.-...||-|++.. ++.+-+=-+.|.+||+. ..||+..
T Consensus 32 ~q~a~y~CpfCgk~~-----------vkR~a~GIW~C~~C~~~----~AGGAy~ 70 (90)
T PTZ00255 32 SQHAKYFCPFCGKHA-----------VKRQAVGIWRCKGCKKT----VAGGAWT 70 (90)
T ss_pred HHhCCccCCCCCCCc-----------eeeeeeEEEEcCCCCCE----EeCCccc
Confidence 345567899999875 33444455899999995 3466653
No 241
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=33.51 E-value=48 Score=36.88 Aligned_cols=42 Identities=17% Similarity=0.346 Sum_probs=29.4
Q ss_pred cceEeeccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCccc
Q 011230 280 EVMTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSE 326 (490)
Q Consensus 280 ev~~~~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nE 326 (490)
.-.-|.-.||.||+-.+|.+.-++... + ...+.| .||++..-
T Consensus 170 ~~~P~~pic~~cg~~~~~~~~~~d~~~-~---~v~y~~-~cG~~~~~ 211 (510)
T PRK00750 170 TYSPFLPICPKCGKVLTTPVISYDAEA-G---TVTYDC-ECGHEGEV 211 (510)
T ss_pred CeeeeeeeCCCCCccceEEEEEEeCCC-C---EEEEEc-CCCCEEEE
Confidence 445688899999999988887665432 2 223578 59997543
No 242
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=33.49 E-value=19 Score=40.39 Aligned_cols=26 Identities=42% Similarity=1.055 Sum_probs=18.7
Q ss_pred cCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccce
Q 011230 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEV 73 (490)
Q Consensus 33 ~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEv 73 (490)
.|..||..+. + ..+.||+||-++.++
T Consensus 520 ~C~~CG~~~~-----------~----~~~~CP~CGs~~~~~ 545 (555)
T cd01675 520 ICNDCGYIGE-----------G----EGFKCPKCGSEDVEV 545 (555)
T ss_pred cCCCCCCCCc-----------C----CCCCCcCCCCcCceE
Confidence 8999986543 1 129999999887444
No 243
>PRK14287 chaperone protein DnaJ; Provisional
Probab=33.43 E-value=1.7e+02 Score=31.13 Aligned_cols=22 Identities=18% Similarity=0.440 Sum_probs=17.1
Q ss_pred eeeeeEeCCCCCCCceeeHHHH
Q 011230 113 PELDFEIPPEAQRGSLSTVEGI 134 (490)
Q Consensus 113 PEL~~eI~p~~~~G~iTTVEGl 134 (490)
-.|.+.|||++..|..-++.|.
T Consensus 211 ~~l~V~Ip~G~~~G~~i~~~G~ 232 (371)
T PRK14287 211 KKINVKVPAGIDHGQQLRVSGQ 232 (371)
T ss_pred EEEEEEECCcCCCCCEEEEccC
Confidence 4577888899899988877753
No 244
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.40 E-value=32 Score=30.80 Aligned_cols=24 Identities=33% Similarity=0.934 Sum_probs=17.7
Q ss_pred EeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCC
Q 011230 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGE 68 (490)
Q Consensus 30 ies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGy 68 (490)
+--.||+|| ++.|+.-..|+.|+-
T Consensus 5 ~~~~cPvcg---------------~~~iVTeL~c~~~et 28 (122)
T COG3877 5 VINRCPVCG---------------RKLIVTELKCSNCET 28 (122)
T ss_pred CCCCCCccc---------------ccceeEEEecCCCCc
Confidence 446799998 445666778988874
No 245
>PRK02935 hypothetical protein; Provisional
Probab=33.36 E-value=24 Score=31.48 Aligned_cols=27 Identities=19% Similarity=0.580 Sum_probs=17.1
Q ss_pred eeccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCC
Q 011230 284 FPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYR 323 (490)
Q Consensus 284 ~~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr 323 (490)
....||+|+++. +|+ +. .-.|-||+-.
T Consensus 69 vqV~CP~C~K~T--KmL-------Gr----vD~CM~C~~P 95 (110)
T PRK02935 69 VQVICPSCEKPT--KML-------GR----VDACMHCNQP 95 (110)
T ss_pred eeeECCCCCchh--hhc-------cc----eeecCcCCCc
Confidence 345799999985 331 11 1268899854
No 246
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=33.33 E-value=17 Score=42.18 Aligned_cols=28 Identities=29% Similarity=0.564 Sum_probs=17.4
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCc
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRN 324 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~ 324 (490)
+.|+.||..|+..+ + -..+.||+||-++
T Consensus 642 ~~C~~CG~~Ge~~~--~---------~~~~~CP~CG~~~ 669 (711)
T PRK09263 642 DECYECGFTGEFEC--T---------EKGFTCPKCGNHD 669 (711)
T ss_pred cccCCCCCCccccC--C---------CCCCcCcCCCCCC
Confidence 66888887664433 0 1127788888654
No 247
>PRK00420 hypothetical protein; Validated
Probab=33.30 E-value=20 Score=32.24 Aligned_cols=27 Identities=19% Similarity=0.401 Sum_probs=17.8
Q ss_pred eeccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCC
Q 011230 284 FPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGY 322 (490)
Q Consensus 284 ~~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGy 322 (490)
....||.||.+. |+- =--...|+.||-
T Consensus 22 l~~~CP~Cg~pL-----------f~l-k~g~~~Cp~Cg~ 48 (112)
T PRK00420 22 LSKHCPVCGLPL-----------FEL-KDGEVVCPVHGK 48 (112)
T ss_pred ccCCCCCCCCcc-----------eec-CCCceECCCCCC
Confidence 557899999764 320 011347999998
No 248
>PF12773 DZR: Double zinc ribbon
Probab=33.24 E-value=18 Score=26.94 Aligned_cols=28 Identities=32% Similarity=0.632 Sum_probs=17.7
Q ss_pred eccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCc
Q 011230 31 ESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (490)
Q Consensus 31 es~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrn 70 (490)
...|++||.... ........|++||+.+
T Consensus 12 ~~fC~~CG~~l~------------~~~~~~~~C~~Cg~~~ 39 (50)
T PF12773_consen 12 AKFCPHCGTPLP------------PPDQSKKICPNCGAEN 39 (50)
T ss_pred ccCChhhcCChh------------hccCCCCCCcCCcCCC
Confidence 456888886644 2222345699998864
No 249
>TIGR02827 RNR_anaer_Bdell anaerobic ribonucleoside-triphosphate reductase. Members of this family belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are pair with genes for an acitivating protein that creates a glycine radical. Members of this family, though related, fall outside the scope of TIGR02487, a functionally equivalent protein set; no genome has members in both familes. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons.
Probab=33.19 E-value=22 Score=40.40 Aligned_cols=27 Identities=26% Similarity=0.589 Sum_probs=18.6
Q ss_pred eccCcCCccc-cceeEEEeecCCCCcEEEEEeecCCCCCCcccc
Q 011230 285 PSTCGACAAS-CETRMFMTRIPYFQEVIVMASTCDACGYRNSEL 327 (490)
Q Consensus 285 ~s~Cp~C~~~-~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEV 327 (490)
-+.|+.||.- +.. .+.||+||-++.||
T Consensus 532 ~siC~~CGy~~g~~----------------~~~CP~CGs~~~ev 559 (586)
T TIGR02827 532 ITICNDCHHIDKRT----------------LHRCPVCGSANIDY 559 (586)
T ss_pred CeecCCCCCcCCCc----------------CCcCcCCCCccceE
Confidence 3679999982 211 28999999765444
No 250
>PF06138 Chordopox_E11: Chordopoxvirus E11 protein; InterPro: IPR009201 This group represents a virion core protein, vaccinia E11L type.
Probab=32.94 E-value=51 Score=30.35 Aligned_cols=29 Identities=24% Similarity=0.466 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHHHHHhhcCCC-cEEEEEEC
Q 011230 155 QTAEAIDQFLLKLRACAKGDS-TFTFILDD 183 (490)
Q Consensus 155 e~~~ki~~~i~kL~~~~~g~~-pFTliidD 183 (490)
+....++.||+.|.+++..+. .|+|+|.|
T Consensus 32 ~~~~Av~~Fl~~L~kyI~veeStFylvvrd 61 (130)
T PF06138_consen 32 EARRAVKHFLSVLKKYIDVEESTFYLVVRD 61 (130)
T ss_pred hHHHHHHHHHHHHHhhEEecccEEEEEEec
Confidence 556789999999999999876 99999999
No 251
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=32.73 E-value=24 Score=27.56 Aligned_cols=36 Identities=22% Similarity=0.471 Sum_probs=24.0
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCccccccCC
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGG 331 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEVk~gg 331 (490)
..|++|++-.-. -+++.-....|+.||- -|.|+...
T Consensus 5 iRC~~CnklLa~---------~g~~~~leIKCpRC~t-iN~~~a~~ 40 (51)
T PF10122_consen 5 IRCGHCNKLLAK---------AGEVIELEIKCPRCKT-INHVRATS 40 (51)
T ss_pred eeccchhHHHhh---------hcCccEEEEECCCCCc-cceEeccC
Confidence 458889876411 1356667889999986 56676544
No 252
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=32.72 E-value=16 Score=33.59 Aligned_cols=28 Identities=29% Similarity=0.549 Sum_probs=18.1
Q ss_pred EeccCCccCCCceEEEE-EeecCCccceEEEEeecCCCCCCc
Q 011230 30 VESLCMRCGENGVTRFL-LTLIPHFRKVLLSAFECPHCGERN 70 (490)
Q Consensus 30 ies~Cp~Cg~~g~trll-lt~IP~F~eviimSf~C~~CGyrn 70 (490)
..-.||+||+ |+| |.+-| ..||.||...
T Consensus 8 tKr~Cp~cg~----kFYDLnk~p---------~vcP~cg~~~ 36 (129)
T TIGR02300 8 TKRICPNTGS----KFYDLNRRP---------AVSPYTGEQF 36 (129)
T ss_pred ccccCCCcCc----cccccCCCC---------ccCCCcCCcc
Confidence 4567999974 333 33433 3699999864
No 253
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=32.68 E-value=15 Score=32.70 Aligned_cols=29 Identities=34% Similarity=0.871 Sum_probs=18.0
Q ss_pred EeccCCccCCCceEEEE-EeecCCccceEEEEeecCCCCCCcc
Q 011230 30 VESLCMRCGENGVTRFL-LTLIPHFRKVLLSAFECPHCGERNN 71 (490)
Q Consensus 30 ies~Cp~Cg~~g~trll-lt~IP~F~eviimSf~C~~CGyrnn 71 (490)
..-.||+||+ |+| |-+-| ..||.||.-..
T Consensus 8 tKR~Cp~CG~----kFYDLnk~P---------ivCP~CG~~~~ 37 (108)
T PF09538_consen 8 TKRTCPSCGA----KFYDLNKDP---------IVCPKCGTEFP 37 (108)
T ss_pred CcccCCCCcc----hhccCCCCC---------ccCCCCCCccC
Confidence 4567999974 332 33333 24999998654
No 254
>PRK14280 chaperone protein DnaJ; Provisional
Probab=32.66 E-value=1.7e+02 Score=31.26 Aligned_cols=21 Identities=24% Similarity=0.487 Sum_probs=15.7
Q ss_pred eeeeEeCCCCCCCceeeHHHH
Q 011230 114 ELDFEIPPEAQRGSLSTVEGI 134 (490)
Q Consensus 114 EL~~eI~p~~~~G~iTTVEGl 134 (490)
.|.+.|||++..|..-++.|.
T Consensus 217 ~i~V~Ip~G~~~G~~i~l~G~ 237 (376)
T PRK14280 217 KINVKIPAGVDNGQQIRVSGE 237 (376)
T ss_pred EEEEEeCCCCcCCcEEEEccc
Confidence 456778898888887777653
No 255
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=32.58 E-value=12 Score=38.49 Aligned_cols=34 Identities=24% Similarity=0.432 Sum_probs=23.6
Q ss_pred eEEeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCcc
Q 011230 28 YQVESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNN 71 (490)
Q Consensus 28 ~eies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnn 71 (490)
..+-..||.|++-. |-+|+----..||.|||...
T Consensus 25 e~lw~KCp~c~~~~----------y~~eL~~n~~vcp~c~~h~r 58 (294)
T COG0777 25 EGLWTKCPSCGEML----------YRKELESNLKVCPKCGHHMR 58 (294)
T ss_pred CCceeECCCcccee----------eHHHHHhhhhcccccCcccc
Confidence 34668999998653 33444444578999999764
No 256
>PF10609 ParA: ParA/MinD ATPase like; InterPro: IPR019591 This entry represents ATPases involved in plasmid partitioning []. It also contains cytosolic Fe-S cluster assembling factors, NBP35 and CFD1 which are required for biogenesis and export of both ribosomal subunits probably through assembling the ISCs in RLI1, a protein which performs rRNA processing and ribosome export [, , ].; PDB: 2PH1_A 3KB1_B.
Probab=32.53 E-value=19 Score=30.48 Aligned_cols=13 Identities=69% Similarity=1.341 Sum_probs=7.1
Q ss_pred EEeecCCCCCCcc
Q 011230 59 SAFECPHCGERNN 71 (490)
Q Consensus 59 mSf~C~~CGyrnn 71 (490)
..|.|||||.+.+
T Consensus 64 s~~~Cp~Cg~~~~ 76 (81)
T PF10609_consen 64 SYFVCPHCGERIY 76 (81)
T ss_dssp -EEE-TTT--EEE
T ss_pred CccCCCCCCCeec
Confidence 4689999998754
No 257
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=32.41 E-value=47 Score=34.36 Aligned_cols=44 Identities=23% Similarity=0.376 Sum_probs=29.9
Q ss_pred cCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCccccccCCCCCCCCeEEEEEEcCcc
Q 011230 287 TCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRIPEKGKRITLFVKNIN 348 (490)
Q Consensus 287 ~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEVk~gg~i~~kG~ritL~V~~~e 348 (490)
-|+.||.+...+.- + .+-.|++||...--. + .|+-|.+-+...+
T Consensus 113 FCg~CG~~~~~~~~--------g---~~~~C~~cg~~~fPR-----~--dP~vIv~v~~~~~ 156 (279)
T COG2816 113 FCGRCGTKTYPREG--------G---WARVCPKCGHEHFPR-----I--DPCVIVAVIRGDE 156 (279)
T ss_pred CCCCCCCcCccccC--------c---eeeeCCCCCCccCCC-----C--CCeEEEEEecCCc
Confidence 49999887644432 2 245899999876554 2 3788888776665
No 258
>PRK14276 chaperone protein DnaJ; Provisional
Probab=32.39 E-value=1.6e+02 Score=31.48 Aligned_cols=36 Identities=31% Similarity=0.523 Sum_probs=20.9
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCc
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRN 324 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~ 324 (490)
..|+.|+..|...+. ..++ |+-+. +...|+.|+=+-
T Consensus 164 ~~C~~C~G~G~~~~~-~~~~-~G~~~-~~~~C~~C~G~G 199 (380)
T PRK14276 164 VTCGKCHGSGVITVD-TQTP-LGMMR-RQVTCDVCHGTG 199 (380)
T ss_pred ccCCCCCCeeEEEEE-EecC-CceEE-EEEECCCCCCCC
Confidence 458888777755443 3333 23333 366999996543
No 259
>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=32.29 E-value=38 Score=30.89 Aligned_cols=31 Identities=26% Similarity=0.682 Sum_probs=22.0
Q ss_pred ccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCc
Q 011230 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (490)
Q Consensus 32 s~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrn 70 (490)
.+|+.|+.+ .|.|... +.+ +...|..||.+.
T Consensus 94 VlC~~C~sp-dT~l~k~-----~r~--~~l~C~aCGa~~ 124 (125)
T PF01873_consen 94 VLCPECGSP-DTELIKE-----GRL--IFLKCKACGASR 124 (125)
T ss_dssp SSCTSTSSS-SEEEEEE-----TTC--CEEEETTTSCEE
T ss_pred EEcCCCCCC-ccEEEEc-----CCE--EEEEecccCCcC
Confidence 789999877 5666443 333 457899999864
No 260
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=32.26 E-value=46 Score=34.70 Aligned_cols=39 Identities=28% Similarity=0.474 Sum_probs=24.8
Q ss_pred eccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCc
Q 011230 285 PSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRN 324 (490)
Q Consensus 285 ~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~ 324 (490)
...||.|++.-.+- +...+=--.|=+-.-+.|-.||++-
T Consensus 258 ~~~C~~C~~~~~~~-~q~QtrsaDEpmT~f~~C~~Cg~~w 296 (299)
T TIGR01385 258 LFTCGKCKQKKCTY-YQLQTRSADEPMTTFVTCEECGNRW 296 (299)
T ss_pred cccCCCCCCccceE-EEecccCCCCCCeEEEEcCCCCCee
Confidence 46899998653222 2222323356666678999999974
No 261
>PF00265 TK: Thymidine kinase; InterPro: IPR001267 Thymidine kinase (TK) (2.7.1.21 from EC) is an ubiquitous enzyme that catalyzes the ATP-dependent phosphorylation of thymidine. Two different families of Thymidine kinase have been identified [, ] and are represented in this entry; one groups together Thymidine kinase from herpesviruses, as well as cytosolic thymidylate kinases and the second family groups Thymidine kinase from various sources that include, vertebrates, bacteria, the Bacteriophage T4, poxviruses, African swine fever virus (ASFV) and Fish lymphocystis disease virus (FLDV). The major capsid protein of insect iridescent viruses also belongs to this family.; GO: 0004797 thymidine kinase activity, 0005524 ATP binding; PDB: 1XX6_B 2J9R_A 2J87_B 3E2I_A 2JA1_A 2UZ3_B 2B8T_B 2WVJ_A 1W4R_F 1XBT_F ....
Probab=32.24 E-value=21 Score=34.00 Aligned_cols=38 Identities=11% Similarity=0.255 Sum_probs=22.3
Q ss_pred cccccccccchhccccCCCCCCceEEeccCCccCCCceEEEEEe
Q 011230 5 KEEIVDVGSVVEAVSADDSDAPLYQVESLCMRCGENGVTRFLLT 48 (490)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~v~eies~Cp~Cg~~g~trlllt 48 (490)
.+.|.++.....- ...|.++.+.|+.||+.+.....+.
T Consensus 117 ~~~F~~~~~Ll~~------Ad~i~kl~avC~~Cg~~A~~t~R~~ 154 (176)
T PF00265_consen 117 GEPFGGSPRLLPL------ADKITKLKAVCEVCGRKATFTQRIV 154 (176)
T ss_dssp SSB-TTHHHHHHH-------SEEEEE-EE-TTTSSEE-EEEEEE
T ss_pred cCcchhHHHHHhh------CCeEEEeccEECCCCCceeEEEEEc
Confidence 3456666554432 2348899999999999877666555
No 262
>PRK14278 chaperone protein DnaJ; Provisional
Probab=32.24 E-value=1.3e+02 Score=32.01 Aligned_cols=35 Identities=20% Similarity=0.551 Sum_probs=19.8
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCC
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYR 323 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr 323 (490)
..|+.|+..|...+... ..|+-+. +...|+.|+=+
T Consensus 157 ~~C~~C~G~G~~~~~~~--~~~g~~~-~~~~C~~C~G~ 191 (378)
T PRK14278 157 VTCDTCGGRGEVQTVQR--SFLGQVM-TSRPCPTCRGV 191 (378)
T ss_pred eecCCccCceEEEEEEe--ccceeEE-EEEECCCCCcc
Confidence 35777777764333322 2334443 56689999643
No 263
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=32.20 E-value=40 Score=29.29 Aligned_cols=39 Identities=23% Similarity=0.429 Sum_probs=27.2
Q ss_pred ceEeeccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCccccccCCCCC
Q 011230 281 VMTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRIP 334 (490)
Q Consensus 281 v~~~~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEVk~gg~i~ 334 (490)
.+.-...||-|++.. ++.+-+=-+.|.+||+.. .||+..
T Consensus 32 ~q~a~y~CpfCgk~~-----------vkR~a~GIW~C~~C~~~~----AGGAy~ 70 (90)
T PRK03976 32 KMRAKHVCPVCGRPK-----------VKRVGTGIWECRKCGAKF----AGGAYT 70 (90)
T ss_pred HHhcCccCCCCCCCc-----------eEEEEEEEEEcCCCCCEE----eCCccc
Confidence 345567899998765 455555668999999953 466543
No 264
>PRK14293 chaperone protein DnaJ; Provisional
Probab=32.14 E-value=1.2e+02 Score=32.36 Aligned_cols=20 Identities=30% Similarity=0.491 Sum_probs=14.9
Q ss_pred eeeEeCCCCCCCceeeHHHH
Q 011230 115 LDFEIPPEAQRGSLSTVEGI 134 (490)
Q Consensus 115 L~~eI~p~~~~G~iTTVEGl 134 (490)
+.++|||+++.|..-.+.|.
T Consensus 218 ~~V~IppG~~~G~~i~l~g~ 237 (374)
T PRK14293 218 LKINIPAGVDTGTRLRVSGE 237 (374)
T ss_pred EEEEeCCCCCCCCEEEEccC
Confidence 46778888888887777653
No 265
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=31.63 E-value=60 Score=36.14 Aligned_cols=39 Identities=18% Similarity=0.479 Sum_probs=26.8
Q ss_pred eEEeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCcc
Q 011230 28 YQVESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNN 71 (490)
Q Consensus 28 ~eies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnn 71 (490)
.-+.-.|++||+-.+|.+.-++... +. ..+.| .||++..
T Consensus 172 ~P~~pic~~cg~~~~~~~~~~d~~~-~~---v~y~~-~cG~~~~ 210 (510)
T PRK00750 172 SPFLPICPKCGKVLTTPVISYDAEA-GT---VTYDC-ECGHEGE 210 (510)
T ss_pred eeeeeeCCCCCccceEEEEEEeCCC-CE---EEEEc-CCCCEEE
Confidence 3577889999999888875554321 22 24688 5999764
No 266
>PHA03001 putative virion core protein; Provisional
Probab=31.45 E-value=57 Score=30.08 Aligned_cols=30 Identities=30% Similarity=0.491 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHHHHHhhcCCC-cEEEEEECC
Q 011230 155 QTAEAIDQFLLKLRACAKGDS-TFTFILDDP 184 (490)
Q Consensus 155 e~~~ki~~~i~kL~~~~~g~~-pFTliidDP 184 (490)
+..+.++.||+.|.+++..++ .|+|+|.|-
T Consensus 31 ~~~ka~~~fl~~L~kYi~v~eStFylvvrd~ 61 (132)
T PHA03001 31 EMRKAINKFLELLKKYIHVDKSTFYLVVKDK 61 (132)
T ss_pred hHHHHHHHHHHHHHhhEEecccEEEEEEecC
Confidence 556789999999999999876 999999986
No 267
>PRK14285 chaperone protein DnaJ; Provisional
Probab=31.27 E-value=1.2e+02 Score=32.32 Aligned_cols=21 Identities=14% Similarity=0.371 Sum_probs=16.3
Q ss_pred eeeeEeCCCCCCCceeeHHHH
Q 011230 114 ELDFEIPPEAQRGSLSTVEGI 134 (490)
Q Consensus 114 EL~~eI~p~~~~G~iTTVEGl 134 (490)
.+.+.|||++..|..-.++|.
T Consensus 216 ~~~V~Ip~G~~~G~~i~~~g~ 236 (365)
T PRK14285 216 TIELKIPAGIDDNQQIKMRGK 236 (365)
T ss_pred EEEEEECCCCCCCCEEEEeec
Confidence 567888888888888777764
No 268
>PF05907 DUF866: Eukaryotic protein of unknown function (DUF866); InterPro: IPR008584 This family consists of a number of hypothetical eukaryotic proteins of unknown function with an average length of around 165 residues.; PDB: 1ZSO_B.
Probab=31.11 E-value=51 Score=31.24 Aligned_cols=46 Identities=20% Similarity=0.330 Sum_probs=28.4
Q ss_pred ceEEeccCCccCCCceEEEE-----EeecCCccceEEEEeecCCCCCCccc
Q 011230 27 LYQVESLCMRCGENGVTRFL-----LTLIPHFRKVLLSAFECPHCGERNNE 72 (490)
Q Consensus 27 v~eies~Cp~Cg~~g~trll-----lt~IP~F~eviimSf~C~~CGyrnnE 72 (490)
..-+...|.+||+.-...++ .+.+|..|-..=+.+.|..|+..++=
T Consensus 26 ~~~fkvkCt~CgE~~~k~V~i~~~e~~e~~gsrG~aNfv~KCk~C~re~si 76 (161)
T PF05907_consen 26 EWFFKVKCTSCGEVHPKWVYINRFEKHEIPGSRGTANFVMKCKFCKRESSI 76 (161)
T ss_dssp -EEEEEEETTSS--EEEEEEE-TT-BEE-TTSS-EESEEE--SSSS--EEE
T ss_pred EEEEEEEECCCCCccCcceEeecceEEecCCCccceEeEecCcCcCCccEE
Confidence 46788999999976443333 45899999888899999999877653
No 269
>PF00265 TK: Thymidine kinase; InterPro: IPR001267 Thymidine kinase (TK) (2.7.1.21 from EC) is an ubiquitous enzyme that catalyzes the ATP-dependent phosphorylation of thymidine. Two different families of Thymidine kinase have been identified [, ] and are represented in this entry; one groups together Thymidine kinase from herpesviruses, as well as cytosolic thymidylate kinases and the second family groups Thymidine kinase from various sources that include, vertebrates, bacteria, the Bacteriophage T4, poxviruses, African swine fever virus (ASFV) and Fish lymphocystis disease virus (FLDV). The major capsid protein of insect iridescent viruses also belongs to this family.; GO: 0004797 thymidine kinase activity, 0005524 ATP binding; PDB: 1XX6_B 2J9R_A 2J87_B 3E2I_A 2JA1_A 2UZ3_B 2B8T_B 2WVJ_A 1W4R_F 1XBT_F ....
Probab=30.70 E-value=23 Score=33.73 Aligned_cols=25 Identities=8% Similarity=0.373 Sum_probs=18.2
Q ss_pred CCcceEeeccCcCCccccceeEEEe
Q 011230 278 PEEVMTFPSTCGACAASCETRMFMT 302 (490)
Q Consensus 278 ~~ev~~~~s~Cp~C~~~~~t~m~~~ 302 (490)
.++|.++.+.|..||+++..+...+
T Consensus 130 Ad~i~kl~avC~~Cg~~A~~t~R~~ 154 (176)
T PF00265_consen 130 ADKITKLKAVCEVCGRKATFTQRIV 154 (176)
T ss_dssp -SEEEEE-EE-TTTSSEE-EEEEEE
T ss_pred CCeEEEeccEECCCCCceeEEEEEc
Confidence 4689999999999999987777666
No 270
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=30.15 E-value=13 Score=32.08 Aligned_cols=38 Identities=32% Similarity=0.484 Sum_probs=27.9
Q ss_pred EeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCcc
Q 011230 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNN 71 (490)
Q Consensus 30 ies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnn 71 (490)
-.|.|++|++..... ..||-|.=++. -.+|.+|+-+-+
T Consensus 32 ~rS~C~~C~~~L~~~---~lIPi~S~l~l-rGrCr~C~~~I~ 69 (92)
T PF06750_consen 32 PRSHCPHCGHPLSWW---DLIPILSYLLL-RGRCRYCGAPIP 69 (92)
T ss_pred CCCcCcCCCCcCccc---ccchHHHHHHh-CCCCcccCCCCC
Confidence 369999998664433 46787776655 789999997654
No 271
>PRK14277 chaperone protein DnaJ; Provisional
Probab=30.04 E-value=1.4e+02 Score=31.93 Aligned_cols=21 Identities=24% Similarity=0.521 Sum_probs=16.2
Q ss_pred eeeeEeCCCCCCCceeeHHHH
Q 011230 114 ELDFEIPPEAQRGSLSTVEGI 134 (490)
Q Consensus 114 EL~~eI~p~~~~G~iTTVEGl 134 (490)
.|.+.|||++..|..-+++|.
T Consensus 229 ~l~V~Ip~G~~~G~~i~~~g~ 249 (386)
T PRK14277 229 KIKVNIPAGIDDGQMITLRGE 249 (386)
T ss_pred EEEEecCCCccCCcEEEEccc
Confidence 356778888889988888764
No 272
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=29.85 E-value=49 Score=32.36 Aligned_cols=32 Identities=28% Similarity=0.637 Sum_probs=22.3
Q ss_pred CCceEEeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCC
Q 011230 25 APLYQVESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGER 69 (490)
Q Consensus 25 ~~v~eies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyr 69 (490)
+..-.|-+.|.+|+..... + =+...||.||+.
T Consensus 143 ~dlGVI~A~CsrC~~~L~~----------~---~~~l~Cp~Cg~t 174 (188)
T COG1096 143 NDLGVIYARCSRCRAPLVK----------K---GNMLKCPNCGNT 174 (188)
T ss_pred CcceEEEEEccCCCcceEE----------c---CcEEECCCCCCE
Confidence 4455789999999865332 1 235679999974
No 273
>COG1856 Uncharacterized homolog of biotin synthetase [Function unknown]
Probab=29.83 E-value=26 Score=35.52 Aligned_cols=27 Identities=33% Similarity=0.732 Sum_probs=21.4
Q ss_pred EEeecCCccceEE----EEeecCCCCCCccc
Q 011230 46 LLTLIPHFRKVLL----SAFECPHCGERNNE 72 (490)
Q Consensus 46 llt~IP~F~evii----mSf~C~~CGyrnnE 72 (490)
+..+.|+|..|-+ .+|.|+|||-+.-+
T Consensus 4 l~v~~~k~~sISVTG~yC~lnC~HCg~~~L~ 34 (275)
T COG1856 4 LTVDPPKFISISVTGAYCSLNCPHCGRHYLE 34 (275)
T ss_pred cccCCCCCceEEEeccceEecChHHHHHHHH
Confidence 4567888988876 48999999987643
No 274
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=29.82 E-value=36 Score=24.97 Aligned_cols=19 Identities=26% Similarity=0.642 Sum_probs=10.3
Q ss_pred EeecCCCCCCccceeeccc
Q 011230 60 AFECPHCGERNNEVQFAGE 78 (490)
Q Consensus 60 Sf~C~~CGyrnnEvq~~g~ 78 (490)
.|.|+.||.....+++.++
T Consensus 5 ey~C~~Cg~~fe~~~~~~~ 23 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSISE 23 (42)
T ss_pred EEEeCCCCCEEEEEEEcCC
Confidence 4555555555555555444
No 275
>PRK14295 chaperone protein DnaJ; Provisional
Probab=29.69 E-value=2.8e+02 Score=29.79 Aligned_cols=27 Identities=26% Similarity=0.666 Sum_probs=19.1
Q ss_pred cEEEEee-----eeeEeCCCCCCCceeeHHHH
Q 011230 108 ATIKIPE-----LDFEIPPEAQRGSLSTVEGI 134 (490)
Q Consensus 108 ati~IPE-----L~~eI~p~~~~G~iTTVEGl 134 (490)
+++.||- +.+.|||+++.|.+-.|.|-
T Consensus 303 ~~~~I~tldG~~~~v~ip~g~~~g~~iri~G~ 334 (389)
T PRK14295 303 AEVRVPTLGGPPVTVKLPPGTPNGRVLRVRGK 334 (389)
T ss_pred CeEEEECCCCCEEEEEECCccCCCcEEEECCC
Confidence 5666764 55788888888888777653
No 276
>PRK14298 chaperone protein DnaJ; Provisional
Probab=29.61 E-value=56 Score=34.87 Aligned_cols=34 Identities=24% Similarity=0.515 Sum_probs=21.8
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCC
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGY 322 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGy 322 (490)
..|+.|+..|...+..- .|... +.+...|+.|+=
T Consensus 159 ~~C~~C~G~G~~~~~~~-~~~g~--~~~~~~C~~C~G 192 (377)
T PRK14298 159 KRCPTCGGTGQVTTTRS-TPLGQ--FVTTTTCSTCHG 192 (377)
T ss_pred CcCCCCCCccEEEEEEe-cCcee--EEEEEeCCCCCC
Confidence 55888887775554443 55432 357888888853
No 277
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=29.43 E-value=44 Score=31.00 Aligned_cols=31 Identities=13% Similarity=0.352 Sum_probs=20.1
Q ss_pred eeccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCccc
Q 011230 284 FPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSE 326 (490)
Q Consensus 284 ~~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nE 326 (490)
+=..||.|++.... .+. -++.|+.|+-...+
T Consensus 33 ~Y~aC~~C~kkv~~------~~~------~~~~C~~C~~~~~~ 63 (166)
T cd04476 33 WYPACPGCNKKVVE------EGN------GTYRCEKCNKSVPN 63 (166)
T ss_pred EEccccccCcccEe------CCC------CcEECCCCCCcCCC
Confidence 44569999885421 111 57899999876533
No 278
>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=29.00 E-value=13 Score=32.11 Aligned_cols=38 Identities=24% Similarity=0.465 Sum_probs=23.3
Q ss_pred eEeeccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCccccccCCCCC
Q 011230 282 MTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRIP 334 (490)
Q Consensus 282 ~~~~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEVk~gg~i~ 334 (490)
+.-.-.||.|++...-|. - .=-+.|.+||++ ..||+..
T Consensus 32 q~~ky~Cp~Cgk~~vkR~---a--------~GIW~C~~C~~~----~AGGAy~ 69 (90)
T PF01780_consen 32 QHAKYTCPFCGKTSVKRV---A--------TGIWKCKKCGKK----FAGGAYT 69 (90)
T ss_dssp HHS-BEESSSSSSEEEEE---E--------TTEEEETTTTEE----EE-BSSS
T ss_pred HhCCCcCCCCCCceeEEe---e--------eEEeecCCCCCE----EeCCCcc
Confidence 344567999999873222 1 222899999974 4566654
No 279
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=28.94 E-value=42 Score=27.50 Aligned_cols=11 Identities=27% Similarity=0.803 Sum_probs=8.5
Q ss_pred EEeecCCCCCC
Q 011230 59 SAFECPHCGER 69 (490)
Q Consensus 59 mSf~C~~CGyr 69 (490)
....|..|||.
T Consensus 39 ~~itCk~CgYt 49 (68)
T COG3478 39 IVITCKNCGYT 49 (68)
T ss_pred EEEEeccCCch
Confidence 35689999994
No 280
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.39 E-value=16 Score=33.42 Aligned_cols=32 Identities=38% Similarity=0.782 Sum_probs=24.2
Q ss_pred EeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCcc
Q 011230 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNN 71 (490)
Q Consensus 30 ies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnn 71 (490)
+...||+||+- || |+--+-.+-.|+.||....
T Consensus 20 l~grCP~CGeG---rL-------F~gFLK~~p~C~aCG~dyg 51 (126)
T COG5349 20 LRGRCPRCGEG---RL-------FRGFLKVVPACEACGLDYG 51 (126)
T ss_pred hcCCCCCCCCc---hh-------hhhhcccCchhhhcccccc
Confidence 56789999753 33 6666667789999998764
No 281
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=28.12 E-value=40 Score=23.74 Aligned_cols=11 Identities=36% Similarity=0.896 Sum_probs=6.9
Q ss_pred EEEeecCCCCC
Q 011230 58 LSAFECPHCGE 68 (490)
Q Consensus 58 imSf~C~~CGy 68 (490)
--...||+||-
T Consensus 24 ~~~~~CP~Cg~ 34 (41)
T smart00834 24 DPLATCPECGG 34 (41)
T ss_pred CCCCCCCCCCC
Confidence 33456777776
No 282
>PRK14281 chaperone protein DnaJ; Provisional
Probab=28.04 E-value=1.1e+02 Score=32.84 Aligned_cols=34 Identities=29% Similarity=0.483 Sum_probs=19.1
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCC
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGY 322 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGy 322 (490)
..|+.|+..|..++...-.|.| +.+...|+.|+-
T Consensus 180 ~~C~~C~G~G~~~~~~~~~~g~---~~~~~~C~~C~G 213 (397)
T PRK14281 180 ETCPTCHGSGEVRQASKTMFGQ---FVNITACPTCGG 213 (397)
T ss_pred ccCCCCCCCcEEEEEEecccce---EEEEEecCCCcc
Confidence 4577787777554433333332 234558888843
No 283
>PRK03922 hypothetical protein; Provisional
Probab=27.97 E-value=60 Score=29.19 Aligned_cols=39 Identities=23% Similarity=0.382 Sum_probs=27.1
Q ss_pred ccceEEEEeecCCCCCCccceeeccccCCcceEEEEEee
Q 011230 53 FRKVLLSAFECPHCGERNNEVQFAGEIQPRGCNYSLKVP 91 (490)
Q Consensus 53 F~eviimSf~C~~CGyrnnEvq~~g~i~~kG~r~tl~V~ 91 (490)
|=||=+-+..||+||+...-+..+..-.--|..++++|=
T Consensus 42 yVeievG~~~cP~cge~~~~afvvA~taLVgL~lemkVF 80 (113)
T PRK03922 42 YVEVEVGLTICPKCGEPFDSAFVVADTALVGLLLEMKVF 80 (113)
T ss_pred eEEEecCcccCCCCCCcCCcEEEEeccceEEEEEEEEEe
Confidence 455666677788888877777666666666777777764
No 284
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=27.92 E-value=27 Score=39.85 Aligned_cols=28 Identities=21% Similarity=0.579 Sum_probs=18.7
Q ss_pred eccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCcccc
Q 011230 285 PSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSEL 327 (490)
Q Consensus 285 ~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEV 327 (490)
-+.|+.||..+. + ..+.||+||-++.||
T Consensus 566 ~~iC~~CG~~~~-----------g----~~~~CP~CGs~~~ev 593 (623)
T PRK08271 566 ITICNDCHHIDK-----------R----TGKRCPICGSENIDY 593 (623)
T ss_pred CccCCCCCCcCC-----------C----CCcCCcCCCCcchhH
Confidence 367999997521 0 128999999766554
No 285
>PRK14297 chaperone protein DnaJ; Provisional
Probab=27.27 E-value=1.5e+02 Score=31.49 Aligned_cols=35 Identities=31% Similarity=0.714 Sum_probs=19.5
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCC
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYR 323 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr 323 (490)
..|+.|+..|...+. ..++ ++ .+.+...|+.|+=+
T Consensus 166 ~~C~~C~G~G~~~~~-~~~~-~G-~~~~~~~C~~C~G~ 200 (380)
T PRK14297 166 KTCDKCGGTGQIRVQ-RNTP-LG-SFVSTTTCDKCGGS 200 (380)
T ss_pred ccCCCccCeEEEEEE-EEcC-Cc-eeEEEEeCCCCCCC
Confidence 456777666643332 2332 33 34467789999643
No 286
>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=27.02 E-value=42 Score=34.29 Aligned_cols=43 Identities=14% Similarity=0.196 Sum_probs=14.8
Q ss_pred EeeccCcCCccccceeEEEeecC-CCCcEEEE----------EeecCCCCCCccc
Q 011230 283 TFPSTCGACAASCETRMFMTRIP-YFQEVIVM----------ASTCDACGYRNSE 326 (490)
Q Consensus 283 ~~~s~Cp~C~~~~~t~m~~~~IP-~FkeviIm----------sf~C~~CGyr~nE 326 (490)
.....||+||..-..-+..-.-+ .+ .-+.. -..|++||-.+.+
T Consensus 170 w~~g~CPvCGs~P~~s~l~~~~~~G~-R~L~Cs~C~t~W~~~R~~Cp~Cg~~~~~ 223 (290)
T PF04216_consen 170 WQRGYCPVCGSPPVLSVLRGGEREGK-RYLHCSLCGTEWRFVRIKCPYCGNTDHE 223 (290)
T ss_dssp TT-SS-TTT---EEEEEEE------E-EEEEETTT--EEE--TTS-TTT---SS-
T ss_pred ccCCcCCCCCCcCceEEEecCCCCcc-EEEEcCCCCCeeeecCCCCcCCCCCCCc
Confidence 34589999997633333322222 21 22222 2479999987655
No 287
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=26.78 E-value=29 Score=21.86 Aligned_cols=11 Identities=36% Similarity=1.265 Sum_probs=7.2
Q ss_pred eecCCCCCCcc
Q 011230 61 FECPHCGERNN 71 (490)
Q Consensus 61 f~C~~CGyrnn 71 (490)
|.|+.|.|..+
T Consensus 1 y~C~~C~y~t~ 11 (24)
T PF13909_consen 1 YKCPHCSYSTS 11 (24)
T ss_dssp EE-SSSS-EES
T ss_pred CCCCCCCCcCC
Confidence 68999999765
No 288
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=26.51 E-value=37 Score=27.12 Aligned_cols=22 Identities=32% Similarity=0.452 Sum_probs=14.2
Q ss_pred ccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCc
Q 011230 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (490)
Q Consensus 32 s~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrn 70 (490)
+.|++||+ .+ +|| -.|+ |||-+
T Consensus 28 ~~c~~cg~---~~-----~pH--------~vc~-cG~Y~ 49 (60)
T PRK01110 28 SVDKTTGE---YH-----LPH--------HVSP-KGYYK 49 (60)
T ss_pred eEcCCCCc---ee-----ccc--------eecC-CcccC
Confidence 67999963 22 244 4599 99543
No 289
>cd02660 Peptidase_C19D A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=26.50 E-value=91 Score=31.51 Aligned_cols=90 Identities=19% Similarity=0.272 Sum_probs=50.0
Q ss_pred ceEeeccCcCCccccce----eEEEeecCC--------------------------CCcEEEEE--eecCCCCCCccccc
Q 011230 281 VMTFPSTCGACAASCET----RMFMTRIPY--------------------------FQEVIVMA--STCDACGYRNSELK 328 (490)
Q Consensus 281 v~~~~s~Cp~C~~~~~t----~m~~~~IP~--------------------------FkeviIms--f~C~~CGyr~nEVk 328 (490)
.+.-...|..|++.... ..+..+||. |+.-.+.. +.|+.||.+..-.+
T Consensus 130 ~~~~~~~C~~C~~~s~~~e~f~~lsl~i~~~~~~~~~~~~~~~~~~~sl~~~L~~~~~~e~~~~~~~~C~~C~~~~~~~~ 209 (328)
T cd02660 130 SLQSSVTCQRCGGVSTTVDPFLDLSLDIPNKSTPSWALGESGVSGTPTLSDCLDRFTRPEKLGDFAYKCSGCGSTQEATK 209 (328)
T ss_pred EEEeeeEcCCCCCccceecccceeeeeccccccccccccccCCCCCCCHHHHHHHhcCccccCCCCccCCCCCCccceEE
Confidence 34556689999865432 335566664 22223333 37999998754333
Q ss_pred cCCCCCCCCeEEEEEEcCccc-ccceeeeeCceeEEecceeeeecC
Q 011230 329 PGGRIPEKGKRITLFVKNIND-LSRDLIKSDTAGVKIPELDLELAG 373 (490)
Q Consensus 329 ~gg~i~~kG~ritL~V~~~eD-L~R~VlKS~ta~v~IPEL~lei~p 373 (490)
.. .+..-|.-+.+++..-.- ......| -...|.+|+ .|.|.+
T Consensus 210 ~~-~i~~lP~~Lii~lkRf~~~~~~~~~K-~~~~v~fp~-~Ldl~~ 252 (328)
T cd02660 210 QL-SIKKLPPVLCFQLKRFEHSLNKTSRK-IDTYVQFPL-ELNMTP 252 (328)
T ss_pred EE-EecCCCceeEEEEEeEEecCCCCCcC-CCcEEeCCC-Eechhh
Confidence 32 255667777777653321 1112223 345788896 366655
No 290
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=26.38 E-value=39 Score=37.43 Aligned_cols=42 Identities=14% Similarity=0.212 Sum_probs=27.9
Q ss_pred ccCcCCccccceeEEEeec-----CCCCcEEEEEeecCCCCCCcccc
Q 011230 286 STCGACAASCETRMFMTRI-----PYFQEVIVMASTCDACGYRNSEL 327 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~I-----P~FkeviImsf~C~~CGyr~nEV 327 (490)
-.||.|..++.++...+.- ..=..--...+.|.+|-|-+.||
T Consensus 53 f~CP~C~~~L~~~~~~~~~~~~~~~~~~~~~~~~l~C~~C~Wss~~i 99 (483)
T PF05502_consen 53 FDCPICFSPLSVRASDTPPSPPDPSSDSGGKPYYLSCSYCRWSSRDI 99 (483)
T ss_pred ccCCCCCCcceeEecccccccccccccCCCCCEEEECCCceeecccc
Confidence 3599999998887766500 00001123468999999999987
No 291
>PF06054 CoiA: Competence protein CoiA-like family; InterPro: IPR010330 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. Many of the members of this family are described as transcription factors. CoiA falls within a competence-specific operon in Streptococcus. CoiA is an uncharacterised protein.
Probab=26.32 E-value=31 Score=36.83 Aligned_cols=36 Identities=28% Similarity=0.506 Sum_probs=28.0
Q ss_pred EEeccCCccCCCceEEEEEeecCCccceEEEEeecCCC
Q 011230 29 QVESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHC 66 (490)
Q Consensus 29 eies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~C 66 (490)
.-.-.||.|++....|.=..++|||.-.-. -.|+.+
T Consensus 28 ~~~~~CP~C~~~v~lk~G~~k~~HFAH~~~--~~c~~~ 63 (375)
T PF06054_consen 28 KGKYFCPGCGEPVILKKGKKKIPHFAHKSK--SDCPFF 63 (375)
T ss_pred CCcEECCCCCCeeEEEEcCcccceeeecCC--CCCCcc
Confidence 345789999999999998999999998744 246433
No 292
>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=26.24 E-value=37 Score=28.64 Aligned_cols=34 Identities=15% Similarity=0.264 Sum_probs=16.5
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCc
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRN 324 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~ 324 (490)
-.||.|++.......+ -+.--+-...|..||.+.
T Consensus 23 F~CPfC~~~~sV~v~i-----dkk~~~~~~~C~~Cg~~~ 56 (81)
T PF05129_consen 23 FDCPFCNHEKSVSVKI-----DKKEGIGILSCRVCGESF 56 (81)
T ss_dssp ---TTT--SS-EEEEE-----ETTTTEEEEEESSS--EE
T ss_pred EcCCcCCCCCeEEEEE-----EccCCEEEEEecCCCCeE
Confidence 4599999664444333 233556677899997654
No 293
>PTZ00037 DnaJ_C chaperone protein; Provisional
Probab=25.97 E-value=1.4e+02 Score=32.42 Aligned_cols=26 Identities=15% Similarity=0.134 Sum_probs=15.9
Q ss_pred eeEEecce-----eeeecCC--CccceeEeHHH
Q 011230 360 AGVKIPEL-----DLELAGG--TLGGIVTTVEG 385 (490)
Q Consensus 360 a~v~IPEL-----~lei~pG--tl~G~~TTVEG 385 (490)
+++.||-| .+.++|| +.-|.+-.|.|
T Consensus 291 ~~i~I~tLdG~~l~I~ip~g~vt~pg~~~~I~g 323 (421)
T PTZ00037 291 FVFYITHLDGRKLLVNTPPGEVVKPGDIKVINN 323 (421)
T ss_pred CEEEeeCCCCCeEEEEeCCCcccCCCcEEEeCC
Confidence 45677744 4666777 55566666654
No 294
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=25.55 E-value=38 Score=23.22 Aligned_cols=10 Identities=50% Similarity=1.245 Sum_probs=5.9
Q ss_pred EeecCCCCCC
Q 011230 60 AFECPHCGER 69 (490)
Q Consensus 60 Sf~C~~CGyr 69 (490)
+-.|++||..
T Consensus 21 ~r~C~~Cg~~ 30 (32)
T PF09297_consen 21 ARRCPSCGHE 30 (32)
T ss_dssp -EEESSSS-E
T ss_pred EeECCCCcCE
Confidence 5578888864
No 295
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=25.48 E-value=34 Score=39.29 Aligned_cols=26 Identities=27% Similarity=0.498 Sum_probs=17.3
Q ss_pred eccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCcccc
Q 011230 285 PSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSEL 327 (490)
Q Consensus 285 ~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEV 327 (490)
-+.|+.||... ++ .+.||+|| +..||
T Consensus 626 ~~~C~~CG~~~------------g~----~~~CP~CG-~~~~v 651 (656)
T PRK08270 626 FSICPKHGYLS------------GE----HEFCPKCG-EETEV 651 (656)
T ss_pred CcccCCCCCcC------------CC----CCCCcCCc-Cccce
Confidence 36799999731 11 28999999 33444
No 296
>PTZ00293 thymidine kinase; Provisional
Probab=25.39 E-value=57 Score=32.35 Aligned_cols=41 Identities=17% Similarity=0.392 Sum_probs=31.0
Q ss_pred CCcceEeeccCcCCccccceeEEEeecCCCCcEEE------EEeecCCCC
Q 011230 278 PEEVMTFPSTCGACAASCETRMFMTRIPYFQEVIV------MASTCDACG 321 (490)
Q Consensus 278 ~~ev~~~~s~Cp~C~~~~~t~m~~~~IP~FkeviI------msf~C~~CG 321 (490)
.+.|.++.+.|..||+++...+.+++ =+++++ ....|.+|-
T Consensus 130 AD~V~kl~aiC~~CG~~A~~t~R~~~---~~~~v~IGg~e~Y~a~CR~c~ 176 (211)
T PTZ00293 130 AERVTKLTAVCMFCGKEASFSKRIVQ---SEQIELIGGEDKYIATCRKCF 176 (211)
T ss_pred hCEEEEcceEchhhCCcceeEEEEcC---CCCEEEECCcccEEehhhhhh
Confidence 46899999999999999887777665 245544 356788886
No 297
>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=25.32 E-value=64 Score=36.09 Aligned_cols=40 Identities=18% Similarity=0.405 Sum_probs=26.5
Q ss_pred cceEeeccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCccc
Q 011230 280 EVMTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSE 326 (490)
Q Consensus 280 ev~~~~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nE 326 (490)
.-+-|.-.|+.||+-.. .+.-++.=. -..+.| .||++..-
T Consensus 163 ~~~P~~pic~~cGrv~~-~~~~~~~~~-----~v~Y~c-~cG~~g~~ 202 (515)
T TIGR00467 163 NWYPISVFCENCGRDTT-TVNNYDNEY-----SIEYSC-ECGNQESV 202 (515)
T ss_pred CceeeeeecCCcCccCc-eEEEecCCc-----eEEEEc-CCCCEEEE
Confidence 34558889999999865 333444322 266789 59997543
No 298
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=24.99 E-value=36 Score=24.35 Aligned_cols=25 Identities=24% Similarity=0.521 Sum_probs=14.5
Q ss_pred EEeecCCCCCCccceeeccccCCcceE
Q 011230 59 SAFECPHCGERNNEVQFAGEIQPRGCN 85 (490)
Q Consensus 59 mSf~C~~CGyrnnEvq~~g~i~~kG~r 85 (490)
|-..||+|+.+.+ | +..++.+.|.+
T Consensus 1 M~i~CP~C~~~f~-v-~~~~l~~~~~~ 25 (37)
T PF13719_consen 1 MIITCPNCQTRFR-V-PDDKLPAGGRK 25 (37)
T ss_pred CEEECCCCCceEE-c-CHHHcccCCcE
Confidence 4568888888764 2 23344455543
No 299
>PF09567 RE_MamI: MamI restriction endonuclease; InterPro: IPR019067 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the MamI restriction endonuclease which recognises and cleaves GATNN^NNATC. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=24.79 E-value=56 Score=33.51 Aligned_cols=63 Identities=33% Similarity=0.577 Sum_probs=38.2
Q ss_pred cCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCcccee--------------eccccCCcceEEEEEeeCCCcccc
Q 011230 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQ--------------FAGEIQPRGCNYSLKVPSSDQKMF 98 (490)
Q Consensus 33 ~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEvq--------------~~g~i~~kG~r~tl~V~~~~~~DL 98 (490)
.|-+||.+ |...--+||.||-.|-..+ ++.-+.| .+|-|-+- +..|+
T Consensus 84 ~C~~CGa~---------------V~~~e~~Cp~C~StnI~r~DdSkWl~~ir~d~E~~e~L~P--~~~ylvlf--d~~d~ 144 (314)
T PF09567_consen 84 KCNNCGAN---------------VSRLEESCPNCGSTNIKRKDDSKWLFGIRSDDEFEEYLNP--RMIYLVLF--DFPDF 144 (314)
T ss_pred hhccccce---------------eeehhhcCCCCCcccccccCCcceecccccHHHHHHhcCc--cEEEEEEe--cccCC
Confidence 58888743 3444567888887663322 2334444 56666666 66676
Q ss_pred cceEEecCccEEEEeeeeeEeCCC
Q 011230 99 HRQVVKSESATIKIPELDFEIPPE 122 (490)
Q Consensus 99 nR~VvkS~~ati~IPEL~~eI~p~ 122 (490)
|++..|+|-- ++|-|.
T Consensus 145 ------~d~~~IRi~~--W~Vd~~ 160 (314)
T PF09567_consen 145 ------SDSNDIRIRI--WEVDPQ 160 (314)
T ss_pred ------CCcccceEEE--EEeccC
Confidence 6667777754 566663
No 300
>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=24.76 E-value=71 Score=35.74 Aligned_cols=37 Identities=22% Similarity=0.549 Sum_probs=24.3
Q ss_pred eEEeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCcc
Q 011230 28 YQVESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNN 71 (490)
Q Consensus 28 ~eies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnn 71 (490)
.-+.-.|++||+-.++.. -++. .. -..+.| .||++..
T Consensus 165 ~P~~pic~~cGrv~~~~~-~~~~---~~--~v~Y~c-~cG~~g~ 201 (515)
T TIGR00467 165 YPISVFCENCGRDTTTVN-NYDN---EY--SIEYSC-ECGNQES 201 (515)
T ss_pred eeeeeecCCcCccCceEE-EecC---Cc--eEEEEc-CCCCEEE
Confidence 347888999999855333 3332 12 257799 5999864
No 301
>cd02661 Peptidase_C19E A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=24.64 E-value=1.3e+02 Score=29.71 Aligned_cols=86 Identities=16% Similarity=0.223 Sum_probs=45.9
Q ss_pred EeeccCcCCccccce----eEEEeecC-----------CCCcEEEEE---eecCCCCCCccccccCCCCCCCCeEEEEEE
Q 011230 283 TFPSTCGACAASCET----RMFMTRIP-----------YFQEVIVMA---STCDACGYRNSELKPGGRIPEKGKRITLFV 344 (490)
Q Consensus 283 ~~~s~Cp~C~~~~~t----~m~~~~IP-----------~FkeviIms---f~C~~CGyr~nEVk~gg~i~~kG~ritL~V 344 (490)
.-...|..|+..-.. ......|| ||+.-.+-. ..|+.||.+..-.+.- .+..-|..+.+++
T Consensus 133 ~~~~~C~~C~~~s~~~e~~~~l~l~i~~~~~l~~~l~~~~~~e~~~~~~~~~C~~C~~~~~~~~~~-~i~~~P~iL~i~l 211 (304)
T cd02661 133 RSQVKCLNCKHVSNTYDPFLDLSLDIKGADSLEDALEQFTKPEQLDGENKYKCERCKKKVKASKQL-TIHRAPNVLTIHL 211 (304)
T ss_pred eeeEEeCCCCCCcCccccceeeeeecCCCCcHHHHHHHhcCceeeCCCCCeeCCCCCCccceEEEE-EEecCCcEEEEEE
Confidence 445679999865432 24556677 343322222 6899999875433221 1445567777777
Q ss_pred cCcccccceeeeeCceeEEecceeeeecC
Q 011230 345 KNINDLSRDLIKSDTAGVKIPELDLELAG 373 (490)
Q Consensus 345 ~~~eDL~R~VlKS~ta~v~IPEL~lei~p 373 (490)
.--.- + ..+.-...|.+|+ .|.+.+
T Consensus 212 ~Rf~~-~--~~~Ki~~~v~f~~-~L~l~~ 236 (304)
T cd02661 212 KRFSN-F--RGGKINKQISFPE-TLDLSP 236 (304)
T ss_pred ecccc-C--CccccCCeEecCC-eechhh
Confidence 53221 1 1222344578886 344443
No 302
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 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. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=24.63 E-value=28 Score=21.47 Aligned_cols=11 Identities=36% Similarity=1.214 Sum_probs=8.1
Q ss_pred eecCCCCCCcc
Q 011230 61 FECPHCGERNN 71 (490)
Q Consensus 61 f~C~~CGyrnn 71 (490)
|.|+.||...+
T Consensus 1 y~C~~C~~~f~ 11 (23)
T PF00096_consen 1 YKCPICGKSFS 11 (23)
T ss_dssp EEETTTTEEES
T ss_pred CCCCCCCCccC
Confidence 67888887654
No 303
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=24.62 E-value=31 Score=39.48 Aligned_cols=29 Identities=31% Similarity=0.771 Sum_probs=18.3
Q ss_pred EeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccce
Q 011230 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEV 73 (490)
Q Consensus 30 ies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEv 73 (490)
--+.|+.||... -++ .+.||+||-++-++
T Consensus 567 ~~~~C~~CG~~~-----------~g~----~~~CP~CGs~~~~v 595 (625)
T PRK08579 567 AITVCNKCGRST-----------TGL----YTRCPRCGSEDVEV 595 (625)
T ss_pred CCccCCCCCCcc-----------CCC----CCcCcCCCCchhHH
Confidence 347899998621 011 38999999755433
No 304
>TIGR03825 FliH_bacil flagellar assembly protein FliH. This bacillus clade of FliH proteins is not found by the Pfam FliH model pfam02108, but is closely related to the sequences identified by that model. Sequences identified by this model are observed in flagellar operons in an analogous position relative to other flagellar operon genes.
Probab=24.57 E-value=1.5e+02 Score=29.69 Aligned_cols=64 Identities=13% Similarity=0.247 Sum_probs=43.3
Q ss_pred HHHHHHHHHHHHHHhhHHHhcCCHHHHHHHHHHHHHHHHhhcCCCcEEEEEECC---CCCeeeecCCC
Q 011230 131 VEGILVRAADELEALQEERKKLDPQTAEAIDQFLLKLRACAKGDSTFTFILDDP---AGNSFIENLYA 195 (490)
Q Consensus 131 VEGlL~~~~~~L~~~~~~r~~~~~e~~~ki~~~i~kL~~~~~g~~pFTliidDP---sGNS~I~~~~a 195 (490)
+..++..++..|.......-..+|+.++.+....+.|.....+...+. |+.|| -|...|+.+.+
T Consensus 161 i~~lv~~al~~l~~~~~i~I~v~p~d~~~v~~~~~~l~~~~~~~~~i~-i~~D~~l~~GgcvIEt~~G 227 (255)
T TIGR03825 161 FQALVRQVLSEVREFDEVSIYVHPHWYERVAAQKDELQSILPACEHLA-VYPDEKLPDGGCYVETNFG 227 (255)
T ss_pred HHHHHHHHHHhccCCCcEEEEECHHHHHHHHHhHHHHHhhcCCCCceE-EEeCCCCCCCCeEEEcCCc
Confidence 345555555555443322334689999999888888888877766776 45565 68999998765
No 305
>PF06138 Chordopox_E11: Chordopoxvirus E11 protein; InterPro: IPR009201 This group represents a virion core protein, vaccinia E11L type.
Probab=24.54 E-value=84 Score=29.00 Aligned_cols=29 Identities=31% Similarity=0.536 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHHHHhhcCCC-ceEEEEEc
Q 011230 409 NKRTKWQDFKAKLNKLLSVEE-SWTLILDD 437 (490)
Q Consensus 409 e~~~k~~~fl~~L~~~~~g~~-~fTlIidD 437 (490)
+....++.||+.|++++..+. .|+|+|.|
T Consensus 32 ~~~~Av~~Fl~~L~kyI~veeStFylvvrd 61 (130)
T PF06138_consen 32 EARRAVKHFLSVLKKYIDVEESTFYLVVRD 61 (130)
T ss_pred hHHHHHHHHHHHHHhhEEecccEEEEEEec
Confidence 456789999999999999987 99999999
No 306
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=24.51 E-value=48 Score=33.73 Aligned_cols=39 Identities=28% Similarity=0.730 Sum_probs=15.0
Q ss_pred eccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccceeecc
Q 011230 31 ESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAG 77 (490)
Q Consensus 31 es~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEvq~~g 77 (490)
.+.||+||..-..++ +-.+- +--|.|++|+... |+++-.
T Consensus 31 n~yCP~Cg~~~L~~f-----~NN~P--VaDF~C~~C~eey-ELKSk~ 69 (254)
T PF06044_consen 31 NMYCPNCGSKPLSKF-----ENNRP--VADFYCPNCNEEY-ELKSKK 69 (254)
T ss_dssp H---TTT--SS-EE---------------EEE-TTT--EE-EEEEEE
T ss_pred CCcCCCCCChhHhhc-----cCCCc--cceeECCCCchHH-hhhhhc
Confidence 478999997644444 44443 3579999998743 555543
No 307
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=24.39 E-value=72 Score=28.49 Aligned_cols=34 Identities=21% Similarity=0.388 Sum_probs=20.5
Q ss_pred ccCcCCcc---ccceeEEEeecCCCCcEEEEEeecCCCCCCcc
Q 011230 286 STCGACAA---SCETRMFMTRIPYFQEVIVMASTCDACGYRNS 325 (490)
Q Consensus 286 s~Cp~C~~---~~~t~m~~~~IP~FkeviImsf~C~~CGyr~n 325 (490)
+.|..|+. +|.+--....=++ .++.|..||+.-.
T Consensus 57 ~~CkkC~t~Lvpg~n~rvR~~~~~------v~vtC~~CG~~~R 93 (105)
T COG2023 57 TICKKCYTPLVPGKNARVRLRKGR------VVVTCLECGTIRR 93 (105)
T ss_pred HhccccCcccccCcceEEEEcCCe------EEEEecCCCcEEE
Confidence 67999987 4432222222222 6778999998643
No 308
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=24.28 E-value=27 Score=22.88 Aligned_cols=10 Identities=40% Similarity=1.305 Sum_probs=7.4
Q ss_pred eecCCCCCCc
Q 011230 61 FECPHCGERN 70 (490)
Q Consensus 61 f~C~~CGyrn 70 (490)
|.|+.||++.
T Consensus 15 ~~C~~C~k~F 24 (26)
T PF13465_consen 15 YKCPYCGKSF 24 (26)
T ss_dssp EEESSSSEEE
T ss_pred CCCCCCcCee
Confidence 6788888764
No 309
>PHA03001 putative virion core protein; Provisional
Probab=23.74 E-value=90 Score=28.84 Aligned_cols=30 Identities=23% Similarity=0.455 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHHHHhhcCCC-ceEEEEEcC
Q 011230 409 NKRTKWQDFKAKLNKLLSVEE-SWTLILDDA 438 (490)
Q Consensus 409 e~~~k~~~fl~~L~~~~~g~~-~fTlIidDP 438 (490)
+.++.++.||+.|++++..+. .|+|+|.|-
T Consensus 31 ~~~ka~~~fl~~L~kYi~v~eStFylvvrd~ 61 (132)
T PHA03001 31 EMRKAINKFLELLKKYIHVDKSTFYLVVKDK 61 (132)
T ss_pred hHHHHHHHHHHHHHhhEEecccEEEEEEecC
Confidence 456789999999999999887 999999986
No 310
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=23.40 E-value=51 Score=30.10 Aligned_cols=40 Identities=20% Similarity=0.414 Sum_probs=25.1
Q ss_pred ceEEeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccc
Q 011230 27 LYQVESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNE 72 (490)
Q Consensus 27 v~eies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnE 72 (490)
+....-.||.|+..-.-+. =|+.+- ...|.|++||+..+.
T Consensus 26 ~~~~~~~cP~C~s~~~~k~----g~~~~~--~qRyrC~~C~~tf~~ 65 (129)
T COG3677 26 MQITKVNCPRCKSSNVVKI----GGIRRG--HQRYKCKSCGSTFTV 65 (129)
T ss_pred hhcccCcCCCCCccceeeE----CCcccc--ccccccCCcCcceee
Confidence 3445678999974322221 133333 779999999997763
No 311
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.34 E-value=45 Score=36.97 Aligned_cols=11 Identities=27% Similarity=0.579 Sum_probs=5.9
Q ss_pred cCcCCccccce
Q 011230 287 TCGACAASCET 297 (490)
Q Consensus 287 ~Cp~C~~~~~t 297 (490)
.||+|..+.+.
T Consensus 224 ~C~~C~~~l~~ 234 (505)
T TIGR00595 224 CCPNCDVSLTY 234 (505)
T ss_pred CCCCCCCceEE
Confidence 46666555433
No 312
>COG3049 Penicillin V acylase and related amidases [Cell envelope biogenesis, outer membrane]
Probab=23.18 E-value=1e+02 Score=32.85 Aligned_cols=22 Identities=27% Similarity=0.460 Sum_probs=18.8
Q ss_pred cCCCcEEEEEECCCCCeeeecC
Q 011230 172 KGDSTFTFILDDPAGNSFIENL 193 (490)
Q Consensus 172 ~g~~pFTliidDPsGNS~I~~~ 193 (490)
.|..|+++++-|++|-|.|..+
T Consensus 158 ~~~~plH~s~sDasG~S~iiE~ 179 (353)
T COG3049 158 EGVAPLHYSLSDASGDSAIIEP 179 (353)
T ss_pred CCCCceeEEEEcCCCCeEEEEE
Confidence 3456999999999999998865
No 313
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=23.16 E-value=51 Score=30.13 Aligned_cols=42 Identities=14% Similarity=0.243 Sum_probs=28.1
Q ss_pred cceEeeccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCcccc
Q 011230 280 EVMTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSEL 327 (490)
Q Consensus 280 ev~~~~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEV 327 (490)
.+......||.|+..-..+. =|+.+- .-.|.|.+||+-.+.-
T Consensus 25 ~~~~~~~~cP~C~s~~~~k~----g~~~~~--~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 25 RMQITKVNCPRCKSSNVVKI----GGIRRG--HQRYKCKSCGSTFTVE 66 (129)
T ss_pred hhhcccCcCCCCCccceeeE----CCcccc--ccccccCCcCcceeee
Confidence 46667789999987642221 133333 7789999999976654
No 314
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.05 E-value=37 Score=31.34 Aligned_cols=40 Identities=23% Similarity=0.420 Sum_probs=20.8
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCcc
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNS 325 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~n 325 (490)
+.||.|..+..-..+.--+=.|+-=--.-..|.+||.|.-
T Consensus 40 ~qcp~csasirgd~~vegvlglg~dye~psfchncgs~fp 79 (160)
T COG4306 40 TQCPICSASIRGDYYVEGVLGLGGDYEPPSFCHNCGSRFP 79 (160)
T ss_pred hcCCccCCcccccceeeeeeccCCCCCCcchhhcCCCCCC
Confidence 5699998774333332222122111112234999998764
No 315
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.79 E-value=61 Score=29.12 Aligned_cols=20 Identities=10% Similarity=0.112 Sum_probs=14.2
Q ss_pred eeEeHHHHHHHHHHHHhhccC
Q 011230 379 IVTTVEGLITKISESLERVHG 399 (490)
Q Consensus 379 ~~TTVEGlL~~i~d~L~~~~~ 399 (490)
.+-||-|-|..+...+.. +|
T Consensus 70 sYptvR~kld~vlramgy-~p 89 (122)
T COG3877 70 SYPTVRTKLDEVLRAMGY-NP 89 (122)
T ss_pred ccHHHHHHHHHHHHHcCC-CC
Confidence 355788888888887765 44
No 316
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=22.45 E-value=44 Score=34.61 Aligned_cols=31 Identities=32% Similarity=0.625 Sum_probs=0.0
Q ss_pred ceEeeccCcCCccccceeEEEeecCCCCcEEE------------------EEeecCCCC
Q 011230 281 VMTFPSTCGACAASCETRMFMTRIPYFQEVIV------------------MASTCDACG 321 (490)
Q Consensus 281 v~~~~s~Cp~C~~~~~t~m~~~~IP~FkeviI------------------msf~C~~CG 321 (490)
..+-.+.||.||+. |-..-++- .||.|+.||
T Consensus 235 ~~t~~~~C~~Cg~~----------PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg 283 (298)
T KOG2879|consen 235 TGTSDTECPVCGEP----------PTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCG 283 (298)
T ss_pred cccCCceeeccCCC----------CCCCeeeccccceeehhhhhhhhcchhhcccCccC
No 317
>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=22.41 E-value=47 Score=33.92 Aligned_cols=43 Identities=26% Similarity=0.455 Sum_probs=14.9
Q ss_pred EeccCCccCCCceEEEEEeecC-CccceEEE----------EeecCCCCCCccce
Q 011230 30 VESLCMRCGENGVTRFLLTLIP-HFRKVLLS----------AFECPHCGERNNEV 73 (490)
Q Consensus 30 ies~Cp~Cg~~g~trlllt~IP-~F~eviim----------Sf~C~~CGyrnnEv 73 (490)
-...||+||..-..-.+.-.-+ .+ .-+.. -..|++||-.+.+-
T Consensus 171 ~~g~CPvCGs~P~~s~l~~~~~~G~-R~L~Cs~C~t~W~~~R~~Cp~Cg~~~~~~ 224 (290)
T PF04216_consen 171 QRGYCPVCGSPPVLSVLRGGEREGK-RYLHCSLCGTEWRFVRIKCPYCGNTDHEK 224 (290)
T ss_dssp T-SS-TTT---EEEEEEE------E-EEEEETTT--EEE--TTS-TTT---SS-E
T ss_pred cCCcCCCCCCcCceEEEecCCCCcc-EEEEcCCCCCeeeecCCCCcCCCCCCCcc
Confidence 4589999997633333222221 22 22222 24799999877553
No 318
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=22.37 E-value=47 Score=38.74 Aligned_cols=10 Identities=40% Similarity=1.152 Sum_probs=6.8
Q ss_pred EeecCCCCCC
Q 011230 314 ASTCDACGYR 323 (490)
Q Consensus 314 sf~C~~CGyr 323 (490)
...|.+|||.
T Consensus 462 ~L~CH~Cg~~ 471 (730)
T COG1198 462 QLRCHYCGYQ 471 (730)
T ss_pred eeEeCCCCCC
Confidence 3467777776
No 319
>PF08921 DUF1904: Domain of unknown function (DUF1904); InterPro: IPR015017 This entry represents a family of hypothetical bacterial proteins. ; PDB: 1U9D_B.
Probab=22.31 E-value=1.4e+02 Score=26.60 Aligned_cols=55 Identities=16% Similarity=0.200 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHhhcCCC-cEEEEEECCCCCeeeecCCCCCCCCCeeEEEecCCHHHHHH
Q 011230 159 AIDQFLLKLRACAKGDS-TFTFILDDPAGNSFIENLYAPSPDPSLNIKFYERTPEQQAL 216 (490)
Q Consensus 159 ki~~~i~kL~~~~~g~~-pFTliidDPsGNS~I~~~~ap~~D~~~~~~~y~Rt~eq~~~ 216 (490)
-=+.+++.|.++..... -|||.... ..||.+-..-..-|.+.+.+|.|..|....
T Consensus 17 ~S~~LideLa~i~~~p~e~ftlE~i~---s~~i~~G~~~~~~pfVEV~WF~R~qe~qd~ 72 (108)
T PF08921_consen 17 LSKELIDELAEICGCPRENFTLEWIN---STFIFDGEISEGYPFVEVLWFDRGQEVQDK 72 (108)
T ss_dssp HHHHHHHHHHHHHT--GGG-EEEE----------TT-B-----EEEEEES---HHHHHH
T ss_pred HhHHHHHHHHHHHCCCcceEEEEEec---eEEEEcCcccccceeEEEEEecCCHHHHHH
Confidence 33456888888888765 99998876 456655443345578999999999987754
No 320
>KOG3022 consensus Predicted ATPase, nucleotide-binding [Cell cycle control, cell division, chromosome partitioning]
Probab=22.25 E-value=37 Score=35.28 Aligned_cols=43 Identities=26% Similarity=0.366 Sum_probs=30.2
Q ss_pred eecCCCCcEEEEE-eecCCCCCCccccccCCCC---CCCCeEEEEEE
Q 011230 302 TRIPYFQEVIVMA-STCDACGYRNSELKPGGRI---PEKGKRITLFV 344 (490)
Q Consensus 302 ~~IP~FkeviIms-f~C~~CGyr~nEVk~gg~i---~~kG~ritL~V 344 (490)
+.||-++=|-=|| |.|+|||.+++=..++|+- +..|..+--.|
T Consensus 209 ~~I~ilGvVENMs~f~Cp~C~~~~~iF~~gGg~~l~~~~glp~Lg~i 255 (300)
T KOG3022|consen 209 AGIPILGVVENMSGFVCPKCGHSTNIFGSGGGERLAEELGLPLLGSL 255 (300)
T ss_pred cCCceEEEEeccccccCCCCCCcceeccCccHHHHHHHcCCCeEeec
Confidence 4567777777665 8999999999988887763 44454444433
No 321
>COG5595 Zn-ribbon-containing, possibly nucleic-acid-binding protein [General function prediction only]
Probab=22.18 E-value=33 Score=33.90 Aligned_cols=72 Identities=22% Similarity=0.308 Sum_probs=42.4
Q ss_pred EeeeeeEeCCCCCCCceeeHHHHHHHHHHHHHHh----------------------hHHHhcCCHHHH-HHHHHHHHHHH
Q 011230 112 IPELDFEIPPEAQRGSLSTVEGILVRAADELEAL----------------------QEERKKLDPQTA-EAIDQFLLKLR 168 (490)
Q Consensus 112 IPEL~~eI~p~~~~G~iTTVEGlL~~~~~~L~~~----------------------~~~r~~~~~e~~-~ki~~~i~kL~ 168 (490)
+-|+.|+..+. -.|+.|--+|+.++|.+... +|+..+..|+.. +-++.-+.++.
T Consensus 3 lie~~fr~t~~---~~i~~~~~lln~lidqwryngqiigreiplyl~~~~~~vr~icpeq~sl~p~~nn~~ve~al~~a~ 79 (256)
T COG5595 3 LIELEFRCTDN---TTISAVDKLLNGLIDQWRYNGQIIGREIPLYLGDGVGYVRAICPEQESLHPKFNNEYVEAALSRAS 79 (256)
T ss_pred eEEEEEEecCC---cchhhHHHHHHHHHHHHHhcCEEecccceEEEecccceeeeeccchhccCcccchHHHHHHHhhhh
Confidence 55788888763 45566667788888877653 233344455422 34455555555
Q ss_pred HhhcCCCcEEEEEECCCC
Q 011230 169 ACAKGDSTFTFILDDPAG 186 (490)
Q Consensus 169 ~~~~g~~pFTliidDPsG 186 (490)
++---...|.|+=||-..
T Consensus 80 kcgl~fd~fq~~gdd~ns 97 (256)
T COG5595 80 KCGLIFDGFQLVGDDFNS 97 (256)
T ss_pred hcceeccccEEeccccCc
Confidence 443223478888777543
No 322
>PRK14873 primosome assembly protein PriA; Provisional
Probab=22.11 E-value=50 Score=38.09 Aligned_cols=15 Identities=13% Similarity=0.096 Sum_probs=10.1
Q ss_pred EEEEECCCCCeeeec
Q 011230 178 TFILDDPAGNSFIEN 192 (490)
Q Consensus 178 TliidDPsGNS~I~~ 192 (490)
-|||||....||-+.
T Consensus 260 LIIvdEEhd~sykq~ 274 (665)
T PRK14873 260 LVAIWDDGDDLLAEP 274 (665)
T ss_pred EEEEEcCCchhhcCC
Confidence 356677777888653
No 323
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=22.01 E-value=39 Score=37.93 Aligned_cols=27 Identities=26% Similarity=0.612 Sum_probs=19.6
Q ss_pred ccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCcccc
Q 011230 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSEL 327 (490)
Q Consensus 286 s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEV 327 (490)
..|..||..++ + ..+.||+||-++.+|
T Consensus 519 ~~C~~CG~~~~-----------~----~~~~CP~CGs~~~~~ 545 (555)
T cd01675 519 DICNDCGYIGE-----------G----EGFKCPKCGSEDVEV 545 (555)
T ss_pred ccCCCCCCCCc-----------C----CCCCCcCCCCcCceE
Confidence 37999998653 1 128999999887554
No 324
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=21.99 E-value=66 Score=25.10 Aligned_cols=34 Identities=26% Similarity=0.565 Sum_probs=21.3
Q ss_pred CcceEeeccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCC
Q 011230 279 EEVMTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYR 323 (490)
Q Consensus 279 ~ev~~~~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr 323 (490)
+.|....-.||.||.-.. | -+-++ -..|-.|||-
T Consensus 13 ~kv~rk~~~CPrCG~gvf--m-----A~H~d----R~~CGkCgyT 46 (51)
T COG1998 13 EKVKRKNRFCPRCGPGVF--M-----ADHKD----RWACGKCGYT 46 (51)
T ss_pred CcEEEccccCCCCCCcch--h-----hhcCc----eeEeccccce
Confidence 346777788999995321 1 11122 5689999983
No 325
>cd02664 Peptidase_C19H A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=21.65 E-value=1.6e+02 Score=30.24 Aligned_cols=91 Identities=16% Similarity=0.259 Sum_probs=50.2
Q ss_pred ceEeeccCcCCccccc----eeEEEeecC--------CC-CcEEE--EEeecCCCCCCccccccCCCCCCCCeEEEEEEc
Q 011230 281 VMTFPSTCGACAASCE----TRMFMTRIP--------YF-QEVIV--MASTCDACGYRNSELKPGGRIPEKGKRITLFVK 345 (490)
Q Consensus 281 v~~~~s~Cp~C~~~~~----t~m~~~~IP--------~F-keviI--msf~C~~CGyr~nEVk~gg~i~~kG~ritL~V~ 345 (490)
.......|..|+.... ...+...|| |+ .|++- ..+.|+.||.+..-.+. -.|..-|.-+.|++.
T Consensus 106 ~~~~~i~C~~C~~~s~~~e~f~~l~L~i~sl~~~l~~~~~~E~l~g~n~~~C~~C~~~~~a~k~-~~i~~lP~vLii~Lk 184 (327)
T cd02664 106 KLSTTIRCLNCNSTSARTERFRDLDLSFPSVQDLLNYFLSPEKLTGDNQYYCEKCASLQDAEKE-MKVTGAPEYLILTLL 184 (327)
T ss_pred EeEeEEEcCCCCCEecccccceeeecCCCCHHHHHHHhcCeeEccCCCceeCCccCCccceeEE-EEcccCChhhEEEee
Confidence 4556678999985432 234556666 22 23331 23889999976544443 235556666666664
Q ss_pred Ccc-cccceeeeeCceeEEecceeeeecC
Q 011230 346 NIN-DLSRDLIKSDTAGVKIPELDLELAG 373 (490)
Q Consensus 346 ~~e-DL~R~VlKS~ta~v~IPEL~lei~p 373 (490)
--. |......+--...|.+|+ .|.+++
T Consensus 185 RF~~~~~~~~~~Ki~~~v~fp~-~ldl~~ 212 (327)
T cd02664 185 RFSYDQKTHVREKIMDNVSINE-VLSLPV 212 (327)
T ss_pred eeEEccccCcceecCceEecCC-EEecCc
Confidence 322 333222233356788886 255554
No 326
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=21.53 E-value=37 Score=25.93 Aligned_cols=8 Identities=63% Similarity=1.792 Sum_probs=3.8
Q ss_pred eecCCCCC
Q 011230 61 FECPHCGE 68 (490)
Q Consensus 61 f~C~~CGy 68 (490)
|.||.||.
T Consensus 3 f~CP~C~~ 10 (54)
T PF05605_consen 3 FTCPYCGK 10 (54)
T ss_pred cCCCCCCC
Confidence 44444444
No 327
>cd02668 Peptidase_C19L A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=21.52 E-value=1.7e+02 Score=29.78 Aligned_cols=90 Identities=13% Similarity=0.267 Sum_probs=51.3
Q ss_pred eEeeccCcCCccccc----eeEEEeecCC-----------CCcEEE---EEeecCCCCCCccccccCCCCCCCCeEEEEE
Q 011230 282 MTFPSTCGACAASCE----TRMFMTRIPY-----------FQEVIV---MASTCDACGYRNSELKPGGRIPEKGKRITLF 343 (490)
Q Consensus 282 ~~~~s~Cp~C~~~~~----t~m~~~~IP~-----------FkeviI---msf~C~~CGyr~nEVk~gg~i~~kG~ritL~ 343 (490)
......|..|+.... .....++||. |+.-.+ -.+.|+.||.+..-.+.. .|..-|.-+.++
T Consensus 126 ~~~~~~C~~C~~~s~~~e~f~~l~l~i~~~~sl~~~L~~~~~~e~l~g~~~~~C~~C~~~~~a~k~~-~i~~lP~iLii~ 204 (324)
T cd02668 126 YSYVTQCSKCGRESSLPSKFYELELQLKGHKTLEECIDEFLKEEQLTGDNQYFCESCNSKTDATRRI-RLTTLPPTLNFQ 204 (324)
T ss_pred EEEEEEeCCCCCccccccccEEEEEEecccCCHHHHHHHhhCceecCCCccccCCCCCceeeeEEEE-EecCCCCeEEEE
Confidence 455678999986532 2335566773 332222 237899999876544432 255566666776
Q ss_pred EcCc-ccccceeeeeCceeEEecceeeeecC
Q 011230 344 VKNI-NDLSRDLIKSDTAGVKIPELDLELAG 373 (490)
Q Consensus 344 V~~~-eDL~R~VlKS~ta~v~IPEL~lei~p 373 (490)
+.-- -|......+--...|.+|+ .|.|.+
T Consensus 205 LkRf~~d~~~~~~~Ki~~~v~fp~-~Ldl~~ 234 (324)
T cd02668 205 LLRFVFDRKTGAKKKLNASISFPE-ILDMGE 234 (324)
T ss_pred EEcceeecccCcceeCCcEEECCC-eEechh
Confidence 6422 1222223344567788995 555554
No 328
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=21.25 E-value=66 Score=28.76 Aligned_cols=36 Identities=17% Similarity=0.179 Sum_probs=17.2
Q ss_pred EEeecCCCCCCccccccCCCCCCCCeEEEEEEcCcc
Q 011230 313 MASTCDACGYRNSELKPGGRIPEKGKRITLFVKNIN 348 (490)
Q Consensus 313 msf~C~~CGyr~nEVk~gg~i~~kG~ritL~V~~~e 348 (490)
=++.|++||-...-+.-.+...--|.-++++|=|.+
T Consensus 48 G~t~CP~Cg~~~e~~fvva~~aLVgl~l~mkVFNae 83 (115)
T COG1885 48 GSTSCPKCGEPFESAFVVANTALVGLILSMKVFNAE 83 (115)
T ss_pred ccccCCCCCCccceeEEEecceeEEEEEEEEEecCC
Confidence 344444444444444433334444566666665443
No 329
>PF14584 DUF4446: Protein of unknown function (DUF4446)
Probab=21.24 E-value=3e+02 Score=25.90 Aligned_cols=61 Identities=28% Similarity=0.479 Sum_probs=43.9
Q ss_pred eeHHHHHHHHHHHHHHhhHHHhcCCHHHHHHHHHHHHHHHHhhc--------------CCCcEEEEEECCCCCeeeecC
Q 011230 129 STVEGILVRAADELEALQEERKKLDPQTAEAIDQFLLKLRACAK--------------GDSTFTFILDDPAGNSFIENL 193 (490)
Q Consensus 129 TTVEGlL~~~~~~L~~~~~~r~~~~~e~~~ki~~~i~kL~~~~~--------------g~~pFTliidDPsGNS~I~~~ 193 (490)
.++|.+|.+..+.++.....- .+..++++.+-++++.... |+..|.|-+-|-.||-+|-+-
T Consensus 42 ~~lE~~l~~~~~~~~~~~~~~----~~~~~~~~~l~~~~~~~~~kvgvvRYnAF~dmGg~LSFslAlLD~~~nGvVlts 116 (151)
T PF14584_consen 42 KNLEDLLNELFDQIDELKEEL----EELEKRIEELEEKLRNCVQKVGVVRYNAFEDMGGDLSFSLALLDDNNNGVVLTS 116 (151)
T ss_pred ccHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHhccceEEEEEccCcccccccceeeeEEEeCCCCEEEEEe
Confidence 478999988888888876432 2344555555555554432 566999999999999999873
No 330
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=21.23 E-value=19 Score=37.64 Aligned_cols=44 Identities=18% Similarity=0.327 Sum_probs=31.5
Q ss_pred eeccCcCCccccceeEE--EeecCCCCcEEE-----EEeecCCCCCCcccc
Q 011230 284 FPSTCGACAASCETRMF--MTRIPYFQEVIV-----MASTCDACGYRNSEL 327 (490)
Q Consensus 284 ~~s~Cp~C~~~~~t~m~--~~~IP~FkeviI-----msf~C~~CGyr~nEV 327 (490)
+.-.||.|+.-...-|+ --++-+-+|+|- |-|.|+.|..|+.=+
T Consensus 273 i~LkCplc~~Llrnp~kT~cC~~~fc~eci~~al~dsDf~CpnC~rkdvll 323 (427)
T COG5222 273 ISLKCPLCHCLLRNPMKTPCCGHTFCDECIGTALLDSDFKCPNCSRKDVLL 323 (427)
T ss_pred ccccCcchhhhhhCcccCccccchHHHHHHhhhhhhccccCCCcccccchh
Confidence 45789999876544443 355666788887 999999998775433
No 331
>TIGR00630 uvra excinuclease ABC, A subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=21.19 E-value=61 Score=38.80 Aligned_cols=31 Identities=23% Similarity=0.555 Sum_probs=24.1
Q ss_pred ccCCccCCCceEEEEEeecCCccceEEEEeecCCCCC
Q 011230 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGE 68 (490)
Q Consensus 32 s~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGy 68 (490)
..||.|...|..++ +.-|+.++ ...|+.|+=
T Consensus 737 G~C~~C~G~G~~~~---~~~f~~~~---~~~C~~C~G 767 (924)
T TIGR00630 737 GRCEACQGDGVIKI---EMHFLPDV---YVPCEVCKG 767 (924)
T ss_pred CCCCCCccceEEEE---EccCCCCc---ccCCCCcCC
Confidence 55999999999874 55666665 569999963
No 332
>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=21.06 E-value=64 Score=28.57 Aligned_cols=12 Identities=33% Similarity=0.830 Sum_probs=7.3
Q ss_pred eccCcCCccccc
Q 011230 285 PSTCGACAASCE 296 (490)
Q Consensus 285 ~s~Cp~C~~~~~ 296 (490)
+..||-||.+..
T Consensus 2 p~~CpYCg~~~~ 13 (102)
T PF11672_consen 2 PIICPYCGGPAE 13 (102)
T ss_pred CcccCCCCCeeE
Confidence 345777776653
No 333
>PF13754 Big_3_4: Bacterial Ig-like domain (group 3)
Probab=20.89 E-value=67 Score=24.62 Aligned_cols=20 Identities=40% Similarity=0.464 Sum_probs=17.5
Q ss_pred hcCCCcEEEEEECCCCCeee
Q 011230 171 AKGDSTFTFILDDPAGNSFI 190 (490)
Q Consensus 171 ~~g~~pFTliidDPsGNS~I 190 (490)
.+|...|++...|.+||+--
T Consensus 22 ~dG~y~itv~a~D~AGN~s~ 41 (54)
T PF13754_consen 22 ADGTYTITVTATDAAGNTST 41 (54)
T ss_pred CCccEEEEEEEEeCCCCCCC
Confidence 47888999999999999853
No 334
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=20.82 E-value=22 Score=34.38 Aligned_cols=37 Identities=27% Similarity=0.652 Sum_probs=24.5
Q ss_pred EeccCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCccceeec
Q 011230 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFA 76 (490)
Q Consensus 30 ies~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrnnEvq~~ 76 (490)
.--.||+|+-. + -|.|-..+-|.||.||--=.+..+.
T Consensus 112 ~~y~C~~~~~r----~------sfdeA~~~~F~Cp~Cg~~L~~~d~s 148 (176)
T COG1675 112 NYYVCPNCHVK----Y------SFDEAMELGFTCPKCGEDLEEYDSS 148 (176)
T ss_pred CceeCCCCCCc----c------cHHHHHHhCCCCCCCCchhhhccch
Confidence 33568998632 1 2677777889999999654444433
No 335
>PF14122 YokU: YokU-like protein
Probab=20.68 E-value=51 Score=28.42 Aligned_cols=23 Identities=26% Similarity=0.537 Sum_probs=18.0
Q ss_pred EeecCCCCCCccceeeccccCCc
Q 011230 60 AFECPHCGERNNEVQFAGEIQPR 82 (490)
Q Consensus 60 Sf~C~~CGyrnnEvq~~g~i~~k 82 (490)
+..|.+||.-.-+=+...+|+.+
T Consensus 35 ~i~C~~CgmvYq~d~vi~EIEdq 57 (87)
T PF14122_consen 35 AIICSNCGMVYQDDEVIKEIEDQ 57 (87)
T ss_pred eeeecCCCcEEehhHHHHHHhhh
Confidence 68999999988777667777663
No 336
>PLN03165 chaperone protein dnaJ-related; Provisional
Probab=20.66 E-value=1.3e+02 Score=27.00 Aligned_cols=32 Identities=19% Similarity=0.242 Sum_probs=22.7
Q ss_pred cCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCc
Q 011230 287 TCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRN 324 (490)
Q Consensus 287 ~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~ 324 (490)
.|+.|+..|...+.. -| ..-+...|+.|+=+-
T Consensus 54 ~C~~C~G~G~v~~~~--~g----~~q~~~~C~~C~G~G 85 (111)
T PLN03165 54 VCRFCVGSGNVTVEL--GG----GEKEVSKCINCDGAG 85 (111)
T ss_pred CCCCCcCcCeEEEEe--CC----cEEEEEECCCCCCcc
Confidence 799999888665433 23 245688999998765
No 337
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=20.57 E-value=67 Score=24.03 Aligned_cols=9 Identities=44% Similarity=1.401 Sum_probs=6.4
Q ss_pred ecCCCCCCc
Q 011230 62 ECPHCGERN 70 (490)
Q Consensus 62 ~C~~CGyrn 70 (490)
.||.||-.+
T Consensus 28 ~CP~Cg~~~ 36 (52)
T TIGR02605 28 TCPECGGEK 36 (52)
T ss_pred CCCCCCCCc
Confidence 588888643
No 338
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=20.55 E-value=34 Score=37.33 Aligned_cols=31 Identities=23% Similarity=0.576 Sum_probs=17.1
Q ss_pred EeccCCccCCCceEEEEEeecCCccceEEE---EeecCCCC
Q 011230 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLS---AFECPHCG 67 (490)
Q Consensus 30 ies~Cp~Cg~~g~trlllt~IP~F~eviim---Sf~C~~CG 67 (490)
-.-.||+|.+.-. -| . --.+|-| +|.|..||
T Consensus 127 ~~Y~Cp~C~kkyt-~L---e---a~~L~~~~~~~F~C~~C~ 160 (436)
T KOG2593|consen 127 AGYVCPNCQKKYT-SL---E---ALQLLDNETGEFHCENCG 160 (436)
T ss_pred ccccCCccccchh-hh---H---HHHhhcccCceEEEecCC
Confidence 3457999975411 11 0 0122333 88999997
No 339
>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]
Probab=20.43 E-value=32 Score=33.96 Aligned_cols=42 Identities=14% Similarity=0.293 Sum_probs=0.0
Q ss_pred ceEEeccCCccCCCceEEEEEee---cCCccceEEEE------eecCCCCC
Q 011230 27 LYQVESLCMRCGENGVTRFLLTL---IPHFRKVLLSA------FECPHCGE 68 (490)
Q Consensus 27 v~eies~Cp~Cg~~g~trlllt~---IP~F~eviimS------f~C~~CGy 68 (490)
+.++...|..||+..+..+-+.+ -+|++++|+.- -.|.+|.+
T Consensus 140 v~kL~aIC~~Cg~~At~~~Rl~~~~~a~~~~~~i~IGg~e~Y~a~CR~h~~ 190 (201)
T COG1435 140 VTKLKAICNVCGRKATRTLRLINGGPAVYEGPQILIGGNESYEARCRKHHK 190 (201)
T ss_pred HHHHHHHHHHhCCcceEEEEecCCCCCccCCCeEEECCCcceeehhhhhhh
No 340
>cd07241 Glo_EDI_BRP_like_3 This conserved domain belongs to a superfamily including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. This protein family belongs to a conserved domain superfamily that is found in a variety of structurally related metalloproteins, including the bleomycin resistance protein, glyoxalase I, and type I ring-cleaving dioxygenases. A bound metal ion is required for protein activities for the members of this superfamily. A variety of metal ions have been found in the catalytic centers of these proteins including Fe(II), Mn(II), Zn(II), Ni(II) and Mg(II). The protein superfamily contains members with or without domain swapping. The proteins of this family share three conserved metal binding amino acids with the type I extradiol dioxygenases, which shows no domain swapping.
Probab=20.35 E-value=1.8e+02 Score=24.03 Aligned_cols=14 Identities=29% Similarity=0.612 Sum_probs=11.1
Q ss_pred cEEEEEECCCCCee
Q 011230 176 TFTFILDDPAGNSF 189 (490)
Q Consensus 176 pFTliidDPsGNS~ 189 (490)
.+..++.||.||.+
T Consensus 109 ~~~~~~~DPdG~~i 122 (125)
T cd07241 109 YYESVILDPEGNRI 122 (125)
T ss_pred eEEEEEECCCCCEE
Confidence 45677999999975
No 341
>PLN03165 chaperone protein dnaJ-related; Provisional
Probab=20.33 E-value=1.5e+02 Score=26.68 Aligned_cols=32 Identities=19% Similarity=0.286 Sum_probs=22.6
Q ss_pred cCCccCCCceEEEEEeecCCccceEEEEeecCCCCCCc
Q 011230 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (490)
Q Consensus 33 ~Cp~Cg~~g~trlllt~IP~F~eviimSf~C~~CGyrn 70 (490)
.|+.|+..|.....+ -| ..-+...|+.|+=+-
T Consensus 54 ~C~~C~G~G~v~~~~--~g----~~q~~~~C~~C~G~G 85 (111)
T PLN03165 54 VCRFCVGSGNVTVEL--GG----GEKEVSKCINCDGAG 85 (111)
T ss_pred CCCCCcCcCeEEEEe--CC----cEEEEEECCCCCCcc
Confidence 789998888766433 23 245688999998765
No 342
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=20.17 E-value=72 Score=35.35 Aligned_cols=65 Identities=14% Similarity=0.154 Sum_probs=34.8
Q ss_pred eccCcCCcccc----------ceeEEEeecCCCCcEEEEEeecCCCC----CCccccccCCC-CCCCCeEEEEEEcCccc
Q 011230 285 PSTCGACAASC----------ETRMFMTRIPYFQEVIVMASTCDACG----YRNSELKPGGR-IPEKGKRITLFVKNIND 349 (490)
Q Consensus 285 ~s~Cp~C~~~~----------~t~m~~~~IP~FkeviImsf~C~~CG----yr~nEVk~gg~-i~~kG~ritL~V~~~eD 349 (490)
.-.|+.|.+.. ..++.+.-+=|..+|-|+.+.-..=+ ........... ..-+...+.|.+.|+-.
T Consensus 298 SkRC~~C~h~L~KPe~~p~S~kFkI~l~A~~yiP~i~i~~l~~~~~~~~~~~~~~~~~~~~~L~p~~~~~~~Lt~~NPl~ 377 (483)
T PF05502_consen 298 SKRCRQCRHILSKPEFKPTSTKFKIKLFAINYIPRIRIRPLPPSPSSSPSTSPSPPAVPVDNLRPGKPYQFLLTFTNPLF 377 (483)
T ss_pred ehhhhcccCceECCCCCCcchhhhHHhHHHHhCCeEEEEeccCccccCcccccccccccccccCCCCceEEEEEecCCCC
Confidence 34699997643 23445666778888999854432211 00000000111 12345678889888864
No 343
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=20.14 E-value=39 Score=33.14 Aligned_cols=36 Identities=28% Similarity=0.537 Sum_probs=29.9
Q ss_pred CCcceEeeccCcCCccccceeEEEeecCCCCcEEEE
Q 011230 278 PEEVMTFPSTCGACAASCETRMFMTRIPYFQEVIVM 313 (490)
Q Consensus 278 ~~ev~~~~s~Cp~C~~~~~t~m~~~~IP~FkeviIm 313 (490)
++||.++-.-=..|....++++-..+||||.-=|..
T Consensus 50 p~evvelg~flh~Cegd~Vck~~~~kIPyfNAPIyl 85 (215)
T KOG3262|consen 50 PEEVVELGKFLHMCEGDLVCKLTNKKIPYFNAPIYL 85 (215)
T ss_pred chhhhhhhhhhhhcCCceEEeeccccCCCCCCceee
Confidence 567778777778899999999999999999766654
No 344
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=20.08 E-value=45 Score=28.95 Aligned_cols=34 Identities=18% Similarity=0.466 Sum_probs=23.8
Q ss_pred EeeccCcCCccccceeEEEeecCCCCcEEEEEeecCCCCCCccccccC
Q 011230 283 TFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPG 330 (490)
Q Consensus 283 ~~~s~Cp~C~~~~~t~m~~~~IP~FkeviImsf~C~~CGyr~nEVk~g 330 (490)
...+.|..||...--.-+. .|.+|||++.-+...
T Consensus 14 ktHtlCrRCG~~syH~qK~--------------~CasCGypsak~R~Y 47 (91)
T PTZ00073 14 KTHTLCRRCGKRSFHVQKK--------------RCASCGYPSAKMRRY 47 (91)
T ss_pred cCcchhcccCccccccccc--------------cchhcCCchhhcccc
Confidence 4567899999876322222 399999988777654
Done!