Query 017546
Match_columns 369
No_of_seqs 256 out of 641
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 09:32:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017546.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017546hhsearch_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-108 2E-113 809.9 22.2 334 1-369 1-342 (460)
2 TIGR00310 ZPR1_znf ZPR1 zinc f 100.0 9.8E-68 2.1E-72 485.9 22.6 185 33-222 2-189 (192)
3 smart00709 Zpr1 Duplicated dom 100.0 1.9E-62 4.1E-67 439.6 19.8 159 32-192 1-160 (160)
4 PF03367 zf-ZPR1: ZPR1 zinc-fi 100.0 1.7E-62 3.6E-67 440.4 15.9 160 31-192 1-161 (161)
5 KOG2703 C4-type Zn-finger prot 100.0 2.5E-61 5.4E-66 475.0 13.7 200 21-222 248-448 (460)
6 TIGR00340 zpr1_rel ZPR1-relate 100.0 2.4E-58 5.3E-63 414.0 19.2 157 34-196 1-159 (163)
7 COG1779 C4-type Zn-finger prot 100.0 1.7E-48 3.8E-53 356.0 15.8 191 23-220 6-197 (201)
8 smart00709 Zpr1 Duplicated dom 100.0 7.8E-33 1.7E-37 248.4 8.3 84 286-369 1-84 (160)
9 PF03367 zf-ZPR1: ZPR1 zinc-fi 100.0 1.3E-32 2.7E-37 247.2 5.9 84 286-369 2-85 (161)
10 TIGR00340 zpr1_rel ZPR1-relate 100.0 1.8E-30 3.8E-35 233.7 7.7 80 288-369 1-81 (163)
11 TIGR00310 ZPR1_znf ZPR1 zinc f 100.0 4.7E-30 1E-34 236.4 8.3 81 287-369 2-83 (192)
12 COG1779 C4-type Zn-finger prot 100.0 2.5E-29 5.5E-34 230.2 7.4 88 280-369 9-96 (201)
13 PF10571 UPF0547: Uncharacteri 94.5 0.016 3.4E-07 37.5 0.8 24 33-71 2-25 (26)
14 PF10571 UPF0547: Uncharacteri 94.4 0.018 3.8E-07 37.3 0.9 24 287-325 2-25 (26)
15 PF14353 CpXC: CpXC protein 93.0 0.026 5.7E-07 48.6 -0.2 40 32-71 2-49 (128)
16 PF09986 DUF2225: Uncharacteri 92.6 0.12 2.5E-06 48.9 3.5 43 285-327 5-61 (214)
17 PRK00464 nrdR transcriptional 92.4 0.12 2.6E-06 46.8 3.3 47 286-333 1-47 (154)
18 PHA00626 hypothetical protein 92.4 0.18 3.9E-06 38.5 3.6 50 32-91 1-50 (59)
19 PF14353 CpXC: CpXC protein 91.3 0.041 8.8E-07 47.4 -1.0 41 286-326 2-50 (128)
20 COG1326 Uncharacterized archae 91.2 0.31 6.8E-06 45.7 4.7 84 28-132 3-94 (201)
21 smart00440 ZnF_C2C2 C2C2 Zinc 90.5 0.38 8.1E-06 33.9 3.4 39 287-326 2-40 (40)
22 PF13248 zf-ribbon_3: zinc-rib 90.2 0.13 2.8E-06 32.9 0.8 24 285-323 2-25 (26)
23 PHA00626 hypothetical protein 89.8 0.37 7.9E-06 36.9 3.1 51 286-346 1-51 (59)
24 PRK12336 translation initiatio 89.4 1.4 2.9E-05 41.5 7.3 72 286-365 99-176 (201)
25 PF09986 DUF2225: Uncharacteri 88.9 0.49 1.1E-05 44.7 4.1 45 31-75 5-63 (214)
26 PRK03824 hypA hydrogenase nick 88.7 0.25 5.4E-06 43.6 1.8 50 30-79 69-126 (135)
27 PF04606 Ogr_Delta: Ogr/Delta- 88.1 0.29 6.4E-06 35.5 1.5 36 287-325 1-38 (47)
28 PF10058 DUF2296: Predicted in 87.8 0.56 1.2E-05 35.3 2.9 35 28-70 19-54 (54)
29 PRK00464 nrdR transcriptional 87.5 0.8 1.7E-05 41.5 4.3 46 32-79 1-47 (154)
30 PRK00398 rpoP DNA-directed RNA 87.2 0.45 9.8E-06 34.1 2.0 29 31-70 3-31 (46)
31 COG1997 RPL43A Ribosomal prote 86.2 0.65 1.4E-05 38.4 2.7 36 31-81 35-70 (89)
32 TIGR01206 lysW lysine biosynth 86.2 0.53 1.1E-05 35.6 2.0 33 285-326 2-34 (54)
33 PF01096 TFIIS_C: Transcriptio 86.1 0.5 1.1E-05 33.1 1.7 37 287-324 2-38 (39)
34 PRK05978 hypothetical protein; 86.0 0.33 7.1E-06 43.8 1.0 37 283-329 31-67 (148)
35 PRK05978 hypothetical protein; 86.0 0.35 7.6E-06 43.6 1.2 33 30-72 32-64 (148)
36 PF13240 zinc_ribbon_2: zinc-r 85.9 0.32 6.9E-06 30.5 0.6 22 287-323 1-22 (23)
37 PRK00398 rpoP DNA-directed RNA 85.0 0.72 1.6E-05 33.1 2.2 29 286-325 4-32 (46)
38 COG0484 DnaJ DnaJ-class molecu 84.7 5.8 0.00013 40.8 9.3 38 31-73 159-196 (371)
39 smart00440 ZnF_C2C2 C2C2 Zinc 83.4 2.1 4.6E-05 30.1 4.0 39 33-72 2-40 (40)
40 PRK12336 translation initiatio 83.4 4.3 9.4E-05 38.1 7.2 71 32-113 99-176 (201)
41 PRK03824 hypA hydrogenase nick 81.7 0.96 2.1E-05 39.9 2.1 50 284-333 69-126 (135)
42 TIGR00244 transcriptional regu 81.5 2.8 6.2E-05 37.8 5.0 64 32-101 1-64 (147)
43 TIGR01384 TFS_arch transcripti 81.1 1.8 3.9E-05 35.8 3.5 41 285-326 62-102 (104)
44 KOG2907 RNA polymerase I trans 80.9 0.7 1.5E-05 39.9 0.9 42 283-326 72-114 (116)
45 TIGR00244 transcriptional regu 80.3 1.9 4.2E-05 38.9 3.5 49 286-335 1-49 (147)
46 TIGR00311 aIF-2beta translatio 80.3 1.9 4E-05 38.2 3.4 32 286-325 98-129 (133)
47 PF04606 Ogr_Delta: Ogr/Delta- 79.9 1.5 3.2E-05 31.8 2.2 36 33-71 1-38 (47)
48 COG1327 Predicted transcriptio 79.9 1.6 3.6E-05 39.5 2.9 98 32-146 1-99 (156)
49 PF09855 DUF2082: Nucleic-acid 79.8 2.8 6E-05 32.8 3.8 34 287-323 2-45 (64)
50 PRK03988 translation initiatio 79.7 1.9 4.1E-05 38.4 3.3 32 286-325 103-134 (138)
51 COG1594 RPB9 DNA-directed RNA 79.7 1.6 3.6E-05 37.4 2.8 41 285-326 72-112 (113)
52 COG1997 RPL43A Ribosomal prote 79.5 0.81 1.8E-05 37.9 0.8 41 280-335 30-70 (89)
53 COG1996 RPC10 DNA-directed RNA 79.4 0.73 1.6E-05 34.3 0.4 30 30-70 5-34 (49)
54 PRK14890 putative Zn-ribbon RN 79.3 0.93 2E-05 34.9 1.0 28 287-323 27-57 (59)
55 PF13453 zf-TFIIB: Transcripti 79.2 2.2 4.8E-05 29.8 2.9 29 287-324 1-29 (41)
56 PRK14292 chaperone protein Dna 78.9 14 0.0003 37.5 9.7 33 32-67 158-190 (371)
57 TIGR03831 YgiT_finger YgiT-typ 78.6 2.5 5.4E-05 29.4 3.0 37 288-324 1-42 (46)
58 PF09862 DUF2089: Protein of u 78.2 1.9 4E-05 37.3 2.7 15 130-144 65-79 (113)
59 COG3478 Predicted nucleic-acid 78.2 2.6 5.6E-05 33.2 3.2 37 286-323 5-49 (68)
60 PRK14284 chaperone protein Dna 78.2 13 0.00028 38.1 9.2 26 108-133 295-326 (391)
61 PF07282 OrfB_Zn_ribbon: Putat 77.6 1.4 3.1E-05 33.7 1.6 30 285-325 28-57 (69)
62 PRK14892 putative transcriptio 77.4 1.3 2.8E-05 37.5 1.4 33 286-326 22-54 (99)
63 TIGR03831 YgiT_finger YgiT-typ 77.1 3 6.5E-05 29.0 3.1 35 34-69 1-41 (46)
64 PF09862 DUF2089: Protein of u 76.9 2.1 4.5E-05 37.1 2.6 21 288-323 1-21 (113)
65 smart00653 eIF2B_5 domain pres 76.6 2.6 5.7E-05 36.1 3.1 30 286-323 81-110 (110)
66 COG1645 Uncharacterized Zn-fin 76.0 1.5 3.3E-05 38.8 1.6 36 285-333 28-63 (131)
67 smart00661 RPOL9 RNA polymeras 76.0 2.3 5E-05 30.6 2.3 11 60-70 20-30 (52)
68 KOG2907 RNA polymerase I trans 75.3 1.3 2.9E-05 38.3 1.0 42 29-72 72-114 (116)
69 TIGR01384 TFS_arch transcripti 74.9 5.5 0.00012 32.9 4.6 43 29-72 60-102 (104)
70 COG2888 Predicted Zn-ribbon RN 74.8 3.6 7.8E-05 31.9 3.1 9 315-323 51-59 (61)
71 PF01783 Ribosomal_L32p: Ribos 74.7 1.8 4E-05 32.6 1.5 22 32-69 27-48 (56)
72 smart00659 RPOLCX RNA polymera 74.7 1.4 3E-05 31.9 0.8 26 287-324 4-29 (44)
73 TIGR03830 CxxCG_CxxCG_HTH puta 74.5 2.4 5.3E-05 35.6 2.4 39 288-326 1-43 (127)
74 PF07282 OrfB_Zn_ribbon: Putat 74.4 2 4.3E-05 32.9 1.7 29 31-70 28-56 (69)
75 PF01096 TFIIS_C: Transcriptio 74.4 2.9 6.3E-05 29.2 2.4 36 33-70 2-38 (39)
76 COG1594 RPB9 DNA-directed RNA 73.7 3.8 8.2E-05 35.2 3.4 40 31-72 72-112 (113)
77 PF05876 Terminase_GpA: Phage 73.2 3.1 6.7E-05 44.7 3.4 46 282-327 197-242 (557)
78 PRK00432 30S ribosomal protein 73.2 1.7 3.6E-05 32.2 0.9 32 281-324 16-47 (50)
79 smart00531 TFIIE Transcription 73.1 1 2.2E-05 40.0 -0.3 31 30-70 98-133 (147)
80 PRK14892 putative transcriptio 72.5 2.8 6.1E-05 35.4 2.3 32 32-71 22-53 (99)
81 TIGR00100 hypA hydrogenase nic 72.5 1.8 4E-05 37.1 1.2 36 31-79 70-105 (115)
82 PHA02998 RNA polymerase subuni 71.8 4.9 0.00011 37.5 3.9 42 284-326 142-183 (195)
83 PF13453 zf-TFIIB: Transcripti 71.5 5.7 0.00012 27.7 3.3 27 33-68 1-27 (41)
84 TIGR00100 hypA hydrogenase nic 71.3 2.6 5.6E-05 36.1 1.8 39 283-334 68-106 (115)
85 PF13824 zf-Mss51: Zinc-finger 71.1 1.9 4.1E-05 32.8 0.8 24 33-70 1-24 (55)
86 KOG2846 Predicted membrane pro 69.9 2.1 4.7E-05 43.1 1.2 39 29-75 218-257 (328)
87 PRK03681 hypA hydrogenase nick 69.7 2.1 4.5E-05 36.7 0.9 37 31-79 70-106 (114)
88 TIGR03830 CxxCG_CxxCG_HTH puta 69.4 4.4 9.6E-05 34.0 2.9 36 34-69 1-40 (127)
89 PRK00564 hypA hydrogenase nick 69.4 2.9 6.3E-05 36.0 1.7 41 283-335 69-109 (117)
90 PF07754 DUF1610: Domain of un 69.1 2.7 5.8E-05 26.9 1.1 10 59-68 15-24 (24)
91 TIGR02443 conserved hypothetic 68.6 4.7 0.0001 31.1 2.5 34 32-72 10-43 (59)
92 PF01873 eIF-5_eIF-2B: Domain 67.8 3.8 8.3E-05 35.9 2.2 31 286-324 94-124 (125)
93 PHA02942 putative transposase; 67.7 3.1 6.7E-05 42.7 1.8 31 32-74 326-357 (383)
94 PF14803 Nudix_N_2: Nudix N-te 67.5 2.9 6.3E-05 28.7 1.1 29 288-323 3-31 (34)
95 PRK14297 chaperone protein Dna 67.2 46 0.001 34.0 10.2 26 108-133 289-318 (380)
96 TIGR01206 lysW lysine biosynth 66.0 6.8 0.00015 29.6 2.9 30 32-70 3-32 (54)
97 PRK00564 hypA hydrogenase nick 66.0 4.7 0.0001 34.7 2.3 37 31-79 71-107 (117)
98 PF12760 Zn_Tnp_IS1595: Transp 65.8 4.5 9.7E-05 29.0 1.8 27 33-69 20-46 (46)
99 TIGR02443 conserved hypothetic 65.7 4.4 9.5E-05 31.3 1.8 34 285-326 9-43 (59)
100 KOG2906 RNA polymerase III sub 65.5 4.7 0.0001 34.2 2.2 30 287-325 3-32 (105)
101 PRK12380 hydrogenase nickel in 64.9 3.1 6.8E-05 35.6 1.0 36 31-79 70-105 (113)
102 smart00531 TFIIE Transcription 64.7 1.8 3.8E-05 38.5 -0.6 38 285-327 99-136 (147)
103 PTZ00037 DnaJ_C chaperone prot 64.5 42 0.0009 35.1 9.3 26 108-133 291-323 (421)
104 PRK09678 DNA-binding transcrip 64.3 4.3 9.2E-05 32.5 1.6 38 286-326 2-41 (72)
105 COG4469 CoiA Competence protei 63.8 2.7 5.8E-05 42.6 0.5 26 285-310 25-50 (342)
106 PF14354 Lar_restr_allev: Rest 63.6 7.4 0.00016 29.0 2.8 33 287-322 5-37 (61)
107 PF14205 Cys_rich_KTR: Cystein 63.4 5.3 0.00011 30.4 1.9 21 287-307 6-30 (55)
108 PHA02942 putative transposase; 63.1 4.5 9.8E-05 41.5 2.0 28 286-325 326-353 (383)
109 PF03604 DNA_RNApol_7kD: DNA d 63.0 2 4.4E-05 29.1 -0.4 26 287-324 2-27 (32)
110 PF05876 Terminase_GpA: Phage 62.9 7.3 0.00016 41.9 3.6 94 27-141 196-289 (557)
111 PF07191 zinc-ribbons_6: zinc- 62.8 7.3 0.00016 31.1 2.6 47 286-332 2-48 (70)
112 PRK12380 hydrogenase nickel in 62.5 4.7 0.0001 34.4 1.7 39 282-333 67-105 (113)
113 COG0675 Transposase and inacti 62.5 4.4 9.6E-05 38.6 1.7 28 32-75 310-338 (364)
114 KOG2691 RNA polymerase II subu 61.6 11 0.00023 32.6 3.6 41 285-326 73-113 (113)
115 PF09526 DUF2387: Probable met 61.4 7.1 0.00015 31.1 2.4 33 32-71 9-41 (71)
116 PRK14296 chaperone protein Dna 61.3 51 0.0011 33.7 9.2 26 108-133 291-320 (372)
117 PF09526 DUF2387: Probable met 61.2 9.2 0.0002 30.4 3.0 34 286-326 9-42 (71)
118 PRK06266 transcription initiat 60.3 2.2 4.7E-05 39.4 -0.8 33 31-73 117-149 (178)
119 TIGR00373 conserved hypothetic 60.2 2 4.3E-05 38.8 -1.0 34 31-74 109-142 (158)
120 COG1327 Predicted transcriptio 60.1 6.3 0.00014 35.9 2.1 49 286-335 1-49 (156)
121 COG1571 Predicted DNA-binding 60.0 4.2 9.1E-05 42.5 1.1 48 97-144 184-231 (421)
122 PRK14282 chaperone protein Dna 59.8 41 0.00089 34.2 8.2 20 114-133 226-245 (369)
123 PRK03681 hypA hydrogenase nick 59.6 4.9 0.00011 34.4 1.3 40 282-333 67-106 (114)
124 PRK14298 chaperone protein Dna 59.5 31 0.00066 35.3 7.2 36 32-70 159-194 (377)
125 PRK14704 anaerobic ribonucleos 59.3 4.2 9E-05 44.4 1.0 24 31-70 559-582 (618)
126 PRK03988 translation initiatio 59.0 11 0.00024 33.6 3.5 32 32-71 103-134 (138)
127 PRK14291 chaperone protein Dna 59.0 31 0.00067 35.3 7.2 21 114-134 225-245 (382)
128 PRK14288 chaperone protein Dna 58.9 32 0.0007 35.0 7.3 31 33-70 158-188 (369)
129 COG0675 Transposase and inacti 58.5 5.4 0.00012 38.0 1.6 22 286-323 310-331 (364)
130 PF01155 HypA: Hydrogenase exp 58.5 3.2 7E-05 35.4 -0.0 36 31-79 70-105 (113)
131 TIGR01031 rpmF_bact ribosomal 58.3 5.3 0.00012 30.2 1.1 22 32-69 27-48 (55)
132 COG1655 Uncharacterized protei 58.1 5.3 0.00011 38.8 1.3 42 283-324 17-72 (267)
133 PRK14296 chaperone protein Dna 58.0 43 0.00092 34.2 8.0 35 33-70 168-202 (372)
134 PF01780 Ribosomal_L37ae: Ribo 57.4 7 0.00015 32.6 1.8 35 32-81 36-70 (90)
135 TIGR03655 anti_R_Lar restricti 56.8 17 0.00037 26.8 3.6 35 33-71 3-37 (53)
136 PF05180 zf-DNL: DNL zinc fing 56.4 5.2 0.00011 31.5 0.8 27 57-84 1-27 (66)
137 COG4888 Uncharacterized Zn rib 56.4 10 0.00023 32.3 2.7 40 281-325 18-57 (104)
138 PF14690 zf-ISL3: zinc-finger 56.2 32 0.0007 24.0 4.9 35 32-66 3-47 (47)
139 PRK00762 hypA hydrogenase nick 56.1 13 0.00027 32.3 3.3 43 30-79 69-111 (124)
140 COG5415 Predicted integral mem 56.0 5.1 0.00011 38.4 0.9 36 32-75 193-229 (251)
141 PRK12286 rpmF 50S ribosomal pr 55.7 6.6 0.00014 29.9 1.3 23 32-70 28-50 (57)
142 PF00684 DnaJ_CXXCXGXG: DnaJ c 55.7 21 0.00046 27.3 4.1 36 32-70 16-51 (66)
143 PF02150 RNA_POL_M_15KD: RNA p 55.4 6.8 0.00015 26.8 1.2 27 288-324 4-30 (35)
144 TIGR00373 conserved hypothetic 55.4 2.6 5.6E-05 38.1 -1.2 33 287-329 111-143 (158)
145 PRK14298 chaperone protein Dna 55.4 64 0.0014 33.0 8.8 15 28-42 181-195 (377)
146 PRK14281 chaperone protein Dna 55.0 37 0.00081 34.9 7.0 35 33-70 181-215 (397)
147 PF07191 zinc-ribbons_6: zinc- 54.8 24 0.00051 28.2 4.3 46 32-77 2-47 (70)
148 PHA02998 RNA polymerase subuni 54.8 18 0.00039 33.9 4.2 42 30-73 142-184 (195)
149 KOG2767 Translation initiation 54.5 5.1 0.00011 41.0 0.6 33 286-325 97-129 (400)
150 PF13717 zinc_ribbon_4: zinc-r 54.5 7.8 0.00017 26.7 1.4 23 60-84 2-24 (36)
151 PRK07111 anaerobic ribonucleos 54.2 7 0.00015 43.6 1.7 27 31-73 680-706 (735)
152 PF01155 HypA: Hydrogenase exp 53.8 3.3 7.1E-05 35.3 -0.7 40 281-333 66-105 (113)
153 PF08271 TF_Zn_Ribbon: TFIIB z 53.1 17 0.00038 25.5 3.0 36 286-331 1-36 (43)
154 COG1326 Uncharacterized archae 52.9 16 0.00035 34.6 3.6 38 283-327 4-43 (201)
155 KOG2906 RNA polymerase III sub 52.3 15 0.00033 31.2 3.0 13 58-70 19-31 (105)
156 PRK06266 transcription initiat 51.9 3.4 7.3E-05 38.1 -1.0 33 287-329 119-151 (178)
157 PRK04296 thymidine kinase; Pro 51.7 13 0.00028 33.9 2.8 45 279-323 134-187 (190)
158 PF08274 PhnA_Zn_Ribbon: PhnA 51.6 3.7 7.9E-05 27.5 -0.6 26 32-69 3-28 (30)
159 PRK14289 chaperone protein Dna 51.6 46 0.00099 34.0 7.0 35 33-70 173-207 (386)
160 PF13005 zf-IS66: zinc-finger 51.3 19 0.00041 25.4 3.0 36 286-321 3-47 (47)
161 TIGR02487 NrdD anaerobic ribon 51.2 7.4 0.00016 42.1 1.3 28 31-73 524-551 (579)
162 TIGR01385 TFSII transcription 51.0 15 0.00032 36.8 3.2 40 285-325 258-297 (299)
163 PF13597 NRDD: Anaerobic ribon 50.9 7.2 0.00016 41.9 1.1 29 31-75 491-519 (546)
164 PRK04023 DNA polymerase II lar 50.9 8.8 0.00019 44.1 1.8 9 32-40 627-635 (1121)
165 COG4469 CoiA Competence protei 50.4 7.1 0.00015 39.6 0.9 34 32-70 26-59 (342)
166 TIGR00280 L37a ribosomal prote 50.1 14 0.00031 30.8 2.5 40 281-335 31-70 (91)
167 COG1998 RPS31 Ribosomal protei 49.9 12 0.00026 28.1 1.8 33 280-323 14-46 (51)
168 PRK09263 anaerobic ribonucleos 49.2 7.6 0.00016 43.1 1.0 28 32-70 642-669 (711)
169 PTZ00255 60S ribosomal protein 48.8 15 0.00033 30.6 2.5 40 281-335 32-71 (90)
170 COG0777 AccD Acetyl-CoA carbox 48.1 4.7 0.0001 40.0 -0.7 33 283-325 26-58 (294)
171 KOG2767 Translation initiation 48.0 7.6 0.00016 39.8 0.7 33 32-71 97-129 (400)
172 TIGR00311 aIF-2beta translatio 47.6 18 0.0004 32.0 3.0 32 32-71 98-129 (133)
173 CHL00174 accD acetyl-CoA carbo 47.4 3.3 7.2E-05 41.3 -1.9 32 30-71 37-68 (296)
174 PF00684 DnaJ_CXXCXGXG: DnaJ c 47.2 22 0.00047 27.3 3.0 34 286-322 16-49 (66)
175 COG3877 Uncharacterized protei 47.1 15 0.00032 31.8 2.1 27 283-324 4-30 (122)
176 PRK14278 chaperone protein Dna 47.1 60 0.0013 33.2 7.0 35 33-70 158-192 (378)
177 PRK14294 chaperone protein Dna 46.6 1E+02 0.0022 31.4 8.5 26 108-133 281-310 (366)
178 PF12773 DZR: Double zinc ribb 46.5 7.7 0.00017 27.8 0.4 25 287-323 14-38 (50)
179 CHL00174 accD acetyl-CoA carbo 46.4 4.3 9.4E-05 40.5 -1.3 32 284-325 37-68 (296)
180 TIGR00515 accD acetyl-CoA carb 46.3 4.3 9.2E-05 40.3 -1.3 31 285-325 26-56 (285)
181 COG0777 AccD Acetyl-CoA carbox 46.3 5.1 0.00011 39.8 -0.8 33 29-71 26-58 (294)
182 PF05129 Elf1: Transcription e 45.9 9.1 0.0002 31.0 0.7 35 285-324 22-56 (81)
183 TIGR02827 RNR_anaer_Bdell anae 45.8 12 0.00025 40.8 1.8 27 31-73 532-559 (586)
184 PRK03976 rpl37ae 50S ribosomal 45.3 19 0.00041 30.0 2.5 40 281-335 32-71 (90)
185 PRK09710 lar restriction allev 45.2 23 0.00049 27.9 2.8 29 33-69 8-36 (64)
186 PRK09678 DNA-binding transcrip 44.9 20 0.00043 28.7 2.5 37 32-71 2-40 (72)
187 smart00653 eIF2B_5 domain pres 44.9 20 0.00043 30.8 2.7 30 32-69 81-110 (110)
188 TIGR00686 phnA alkylphosphonat 44.9 15 0.00032 31.7 1.9 29 287-327 4-32 (109)
189 COG3677 Transposase and inacti 44.7 14 0.0003 32.5 1.7 43 280-328 25-67 (129)
190 PRK10767 chaperone protein Dna 44.2 61 0.0013 32.9 6.5 32 33-71 161-192 (371)
191 PRK05654 acetyl-CoA carboxylas 44.2 3.9 8.5E-05 40.6 -2.0 32 30-71 26-57 (292)
192 TIGR00515 accD acetyl-CoA carb 44.0 4 8.7E-05 40.5 -1.9 32 30-71 25-56 (285)
193 PRK14295 chaperone protein Dna 44.0 72 0.0016 32.8 7.1 32 32-70 184-215 (389)
194 PRK05654 acetyl-CoA carboxylas 43.6 5 0.00011 39.9 -1.3 31 285-325 27-57 (292)
195 TIGR03829 YokU_near_AblA uncha 43.4 24 0.00052 29.4 2.9 22 60-81 35-56 (89)
196 COG0375 HybF Zn finger protein 43.3 20 0.00042 31.2 2.4 47 282-343 67-113 (115)
197 PRK14276 chaperone protein Dna 43.2 96 0.0021 31.7 7.8 35 33-70 165-199 (380)
198 PF09297 zf-NADH-PPase: NADH p 43.0 8 0.00017 25.6 -0.0 25 288-323 6-30 (32)
199 PRK10767 chaperone protein Dna 43.0 1.3E+02 0.0029 30.5 8.7 26 108-133 279-308 (371)
200 COG0484 DnaJ DnaJ-class molecu 42.8 29 0.00064 35.8 4.0 39 284-327 158-196 (371)
201 COG1856 Uncharacterized homolo 42.6 9.8 0.00021 37.1 0.5 27 46-72 4-34 (275)
202 PRK14283 chaperone protein Dna 42.3 1.9E+02 0.0042 29.4 9.9 26 108-133 287-316 (378)
203 PRK14285 chaperone protein Dna 42.2 73 0.0016 32.4 6.7 31 33-70 165-195 (365)
204 KOG2691 RNA polymerase II subu 42.1 39 0.00085 29.2 4.0 42 30-72 72-113 (113)
205 PRK08270 anaerobic ribonucleos 41.9 15 0.00032 40.5 1.8 26 31-73 626-651 (656)
206 PRK14290 chaperone protein Dna 41.8 1.2E+02 0.0026 30.9 8.2 21 114-134 222-242 (365)
207 PRK14287 chaperone protein Dna 41.7 1.1E+02 0.0024 31.1 8.0 36 33-71 157-192 (371)
208 PTZ00255 60S ribosomal protein 41.3 27 0.00058 29.2 2.8 36 31-81 36-71 (90)
209 PRK04296 thymidine kinase; Pro 40.9 28 0.0006 31.7 3.2 44 25-68 134-186 (190)
210 PRK14279 chaperone protein Dna 40.3 85 0.0018 32.3 6.9 20 115-134 244-263 (392)
211 TIGR02098 MJ0042_CXXC MJ0042 f 40.1 14 0.0003 25.0 0.8 11 59-69 1-11 (38)
212 PF13894 zf-C2H2_4: C2H2-type 39.5 14 0.0003 21.5 0.7 12 61-72 1-12 (24)
213 PF10071 DUF2310: Zn-ribbon-co 39.4 11 0.00024 37.0 0.4 75 112-188 3-100 (258)
214 TIGR02349 DnaJ_bact chaperone 39.4 87 0.0019 31.5 6.7 20 115-134 218-237 (354)
215 PRK14301 chaperone protein Dna 39.4 1.5E+02 0.0033 30.3 8.5 27 108-134 281-311 (373)
216 PRK14294 chaperone protein Dna 39.2 86 0.0019 31.8 6.7 20 115-134 215-234 (366)
217 PF06054 CoiA: Competence prot 39.1 12 0.00026 38.3 0.5 34 285-320 30-63 (375)
218 PRK14301 chaperone protein Dna 39.0 75 0.0016 32.5 6.2 31 33-70 163-193 (373)
219 PRK14300 chaperone protein Dna 38.8 1.1E+02 0.0025 31.1 7.5 32 32-70 163-194 (372)
220 PF06138 Chordopox_E11: Chordo 38.6 37 0.0008 30.1 3.4 29 155-183 32-61 (130)
221 COG4306 Uncharacterized protei 38.4 14 0.00031 32.9 0.8 41 285-334 39-90 (160)
222 PRK14280 chaperone protein Dna 38.3 1.3E+02 0.0027 30.8 7.8 36 33-71 162-197 (376)
223 COG0375 HybF Zn finger protein 38.3 22 0.00048 30.9 2.0 38 31-81 70-107 (115)
224 PRK04023 DNA polymerase II lar 38.1 18 0.00039 41.7 1.8 15 280-294 621-635 (1121)
225 PRK08271 anaerobic ribonucleos 37.9 16 0.00034 40.2 1.2 28 31-73 566-593 (623)
226 PF11672 DUF3268: Protein of u 37.6 20 0.00044 30.5 1.6 41 285-325 2-42 (102)
227 PHA03001 putative virion core 37.5 40 0.00087 29.9 3.5 30 155-184 31-61 (132)
228 PF05191 ADK_lid: Adenylate ki 37.1 13 0.00029 25.6 0.4 8 287-294 3-10 (36)
229 PF01873 eIF-5_eIF-2B: Domain 36.9 27 0.00058 30.6 2.3 31 32-70 94-124 (125)
230 PRK14293 chaperone protein Dna 36.8 91 0.002 31.8 6.5 35 33-70 162-196 (374)
231 PRK10220 hypothetical protein; 36.8 26 0.00056 30.3 2.1 29 287-327 5-33 (111)
232 KOG3507 DNA-directed RNA polym 36.7 15 0.00032 28.5 0.5 30 283-324 18-47 (62)
233 PF10071 DUF2310: Zn-ribbon-co 36.5 12 0.00026 36.8 0.0 36 27-70 216-251 (258)
234 PF05502 Dynactin_p62: Dynacti 36.4 23 0.0005 37.6 2.2 35 33-74 54-100 (483)
235 PRK13130 H/ACA RNA-protein com 36.0 19 0.00042 27.5 1.1 16 280-295 12-27 (56)
236 PF04216 FdhE: Protein involve 35.4 24 0.00051 34.6 2.0 10 285-294 172-181 (290)
237 PRK14277 chaperone protein Dna 35.2 1.2E+02 0.0026 31.0 7.1 34 34-70 175-208 (386)
238 PRK00762 hypA hydrogenase nick 34.6 34 0.00073 29.7 2.6 46 282-334 67-112 (124)
239 PF13909 zf-H2C2_5: C2H2-type 34.6 18 0.00038 21.9 0.6 11 61-71 1-11 (24)
240 COG2824 PhnA Uncharacterized Z 34.6 26 0.00056 30.2 1.8 31 33-75 5-35 (112)
241 PF05180 zf-DNL: DNL zinc fing 34.2 19 0.00041 28.4 0.8 27 311-338 1-27 (66)
242 PF10621 FpoO: F420H2 dehydrog 34.0 26 0.00057 30.4 1.7 37 284-320 59-97 (119)
243 PF01921 tRNA-synt_1f: tRNA sy 33.8 26 0.00057 36.0 2.0 45 277-325 166-210 (360)
244 PF01921 tRNA-synt_1f: tRNA sy 33.8 30 0.00065 35.6 2.4 39 29-71 172-210 (360)
245 PF10122 Mu-like_Com: Mu-like 33.7 24 0.00051 26.6 1.2 37 286-332 5-41 (51)
246 TIGR00280 L37a ribosomal prote 33.4 42 0.0009 28.1 2.8 36 31-81 35-70 (91)
247 PRK01110 rpmF 50S ribosomal pr 33.3 27 0.00059 26.8 1.6 22 32-70 28-49 (60)
248 COG5349 Uncharacterized protei 33.2 13 0.00028 32.7 -0.3 33 30-72 20-52 (126)
249 PF10609 ParA: ParA/MinD ATPas 33.1 19 0.00041 29.4 0.7 13 59-71 64-76 (81)
250 PF03119 DNA_ligase_ZBD: NAD-d 33.0 18 0.00038 23.6 0.4 10 287-296 1-10 (28)
251 COG3809 Uncharacterized protei 32.9 21 0.00047 29.2 1.0 26 287-322 3-29 (88)
252 cd01675 RNR_III Class III ribo 32.8 23 0.0005 38.1 1.5 26 33-73 520-545 (555)
253 PRK14278 chaperone protein Dna 32.8 2.4E+02 0.0053 28.8 8.9 26 108-133 280-310 (378)
254 PF05907 DUF866: Eukaryotic pr 32.6 32 0.0007 31.3 2.2 47 280-326 25-76 (161)
255 PF01927 Mut7-C: Mut7-C RNAse 32.5 28 0.0006 30.8 1.7 43 280-322 86-132 (147)
256 COG1885 Uncharacterized protei 32.3 49 0.0011 28.5 3.1 39 53-91 42-80 (115)
257 PF04475 DUF555: Protein of un 32.3 44 0.00096 28.5 2.8 35 280-314 42-76 (102)
258 PF00265 TK: Thymidine kinase; 32.2 21 0.00045 32.7 0.9 24 279-302 131-154 (176)
259 PRK00750 lysK lysyl-tRNA synth 32.1 58 0.0013 34.8 4.3 43 278-325 168-210 (510)
260 TIGR01385 TFSII transcription 31.7 50 0.0011 33.0 3.6 38 31-70 258-296 (299)
261 TIGR00357 methionine-R-sulfoxi 31.7 76 0.0016 28.3 4.3 55 287-342 42-116 (134)
262 COG2816 NPY1 NTP pyrophosphohy 31.2 64 0.0014 32.1 4.2 44 287-348 113-156 (279)
263 PF09723 Zn-ribbon_8: Zinc rib 31.0 34 0.00074 24.1 1.7 19 60-78 5-23 (42)
264 PTZ00293 thymidine kinase; Pro 30.7 39 0.00084 32.2 2.5 40 279-321 131-176 (211)
265 PRK14300 chaperone protein Dna 30.4 65 0.0014 32.8 4.2 29 285-320 162-190 (372)
266 TIGR00622 ssl1 transcription f 30.2 26 0.00056 30.4 1.1 48 280-327 10-68 (112)
267 PRK04136 rpl40e 50S ribosomal 30.1 29 0.00063 25.8 1.2 24 285-323 14-37 (48)
268 PF06054 CoiA: Competence prot 29.9 25 0.00055 36.0 1.2 32 31-64 30-61 (375)
269 PRK03976 rpl37ae 50S ribosomal 29.7 53 0.0012 27.4 2.8 36 31-81 36-71 (90)
270 PRK14295 chaperone protein Dna 29.7 3.2E+02 0.007 28.1 9.1 27 108-134 303-334 (389)
271 COG3877 Uncharacterized protei 29.3 44 0.00094 29.0 2.3 24 30-68 5-28 (122)
272 PRK14704 anaerobic ribonucleos 28.8 28 0.0006 38.2 1.3 24 285-324 559-582 (618)
273 smart00834 CxxC_CXXC_SSSS Puta 28.5 41 0.00088 22.7 1.7 9 60-68 26-34 (41)
274 PRK14559 putative protein seri 28.3 22 0.00049 39.1 0.5 15 313-327 40-54 (645)
275 COG0333 RpmF Ribosomal protein 28.3 30 0.00065 26.5 1.0 23 285-323 27-49 (57)
276 PRK00750 lysK lysyl-tRNA synth 28.2 95 0.0021 33.2 5.1 39 28-71 172-210 (510)
277 PRK14714 DNA polymerase II lar 28.1 30 0.00064 41.0 1.4 14 281-294 663-676 (1337)
278 TIGR01562 FdhE formate dehydro 28.1 69 0.0015 32.2 3.8 69 280-361 179-256 (305)
279 cd04476 RPA1_DBD_C RPA1_DBD_C: 27.8 30 0.00066 30.7 1.2 29 284-324 33-61 (166)
280 PRK14282 chaperone protein Dna 27.8 69 0.0015 32.6 3.9 33 286-321 170-202 (369)
281 PF13719 zinc_ribbon_5: zinc-r 27.7 30 0.00065 23.8 0.9 25 59-85 1-25 (37)
282 PF07295 DUF1451: Protein of u 27.5 33 0.00071 30.9 1.3 40 274-324 101-140 (146)
283 PF00096 zf-C2H2: Zinc finger, 27.2 22 0.00049 21.0 0.2 11 61-71 1-11 (23)
284 PRK12496 hypothetical protein; 27.2 42 0.00091 30.5 2.0 32 280-324 122-153 (164)
285 PTZ00073 60S ribosomal protein 27.1 27 0.00059 29.2 0.7 34 284-331 15-48 (91)
286 PF13465 zf-H2C2_2: Zinc-finge 26.6 22 0.00048 22.4 0.0 10 61-70 15-24 (26)
287 PRK03564 formate dehydrogenase 26.6 1.1E+02 0.0024 30.8 5.0 14 281-294 183-196 (309)
288 PF04423 Rad50_zn_hook: Rad50 26.5 24 0.00051 26.0 0.2 12 285-296 20-31 (54)
289 COG3357 Predicted transcriptio 26.1 39 0.00084 28.5 1.4 13 314-326 58-70 (97)
290 PRK14292 chaperone protein Dna 25.9 69 0.0015 32.5 3.5 33 286-321 158-190 (371)
291 PRK08665 ribonucleotide-diphos 25.8 30 0.00065 38.8 0.9 25 286-323 725-749 (752)
292 COG2260 Predicted Zn-ribbon RN 25.6 39 0.00084 26.2 1.2 16 280-295 12-27 (59)
293 TIGR00467 lysS_arch lysyl-tRNA 25.6 75 0.0016 34.1 3.8 41 278-325 161-201 (515)
294 COG3529 Predicted nucleic-acid 25.6 16 0.00036 28.5 -0.8 34 285-326 10-44 (66)
295 PRK07111 anaerobic ribonucleos 25.5 37 0.0008 38.0 1.6 24 285-324 680-703 (735)
296 PF05907 DUF866: Eukaryotic pr 25.4 72 0.0016 29.0 3.2 46 26-71 25-75 (161)
297 PF05502 Dynactin_p62: Dynacti 25.2 45 0.00097 35.5 2.0 44 286-329 53-101 (483)
298 PF02563 Poly_export: Polysacc 25.1 61 0.0013 25.6 2.4 32 337-368 16-47 (82)
299 PRK00241 nudC NADH pyrophospha 24.9 38 0.00082 32.9 1.3 27 287-324 101-127 (256)
300 KOG3262 H/ACA small nucleolar 24.8 25 0.00053 33.3 0.0 63 277-345 49-111 (215)
301 PF14584 DUF4446: Protein of u 24.7 2.9E+02 0.0062 25.0 6.8 59 130-192 43-115 (151)
302 PRK03922 hypothetical protein; 24.4 81 0.0018 27.4 3.1 39 53-91 42-80 (113)
303 PF06044 DRP: Dam-replacing fa 24.3 50 0.0011 32.4 2.0 39 31-77 31-69 (254)
304 COG1096 Predicted RNA-binding 24.3 59 0.0013 30.6 2.4 31 280-323 144-174 (188)
305 PRK08579 anaerobic ribonucleos 24.2 33 0.00071 37.8 0.8 28 31-73 568-595 (625)
306 COG1435 Tdk Thymidine kinase [ 24.0 21 0.00045 33.9 -0.6 44 279-322 138-190 (201)
307 TIGR00630 uvra excinuclease AB 23.9 53 0.0011 37.8 2.4 31 32-68 737-767 (924)
308 PF10083 DUF2321: Uncharacteri 23.9 18 0.00039 33.1 -1.0 31 285-324 39-78 (158)
309 PF04216 FdhE: Protein involve 23.8 52 0.0011 32.2 2.1 43 30-73 171-224 (290)
310 PRK14284 chaperone protein Dna 23.7 1.4E+02 0.0031 30.6 5.3 31 286-323 176-206 (391)
311 cd00042 CY Substituted updates 23.6 1.1E+02 0.0023 24.8 3.6 31 33-63 70-105 (105)
312 PF06827 zf-FPG_IleRS: Zinc fi 23.4 89 0.0019 20.1 2.5 8 59-66 20-27 (30)
313 COG1198 PriA Primosomal protei 23.4 35 0.00077 38.2 0.9 13 179-191 316-329 (730)
314 PF02563 Poly_export: Polysacc 23.3 1.8E+02 0.0039 22.9 4.8 53 83-143 16-68 (82)
315 PLN03165 chaperone protein dna 23.2 1.3E+02 0.0028 26.0 4.1 32 33-70 54-85 (111)
316 PRK14277 chaperone protein Dna 23.2 95 0.0021 31.8 3.9 33 286-321 173-205 (386)
317 cd07241 Glo_EDI_BRP_like_3 Thi 23.1 1.4E+02 0.003 23.6 4.1 14 176-189 109-122 (125)
318 PRK03922 hypothetical protein; 23.0 79 0.0017 27.5 2.7 35 280-314 44-78 (113)
319 PF13754 Big_3_4: Bacterial Ig 23.0 57 0.0012 24.0 1.7 19 171-189 22-40 (54)
320 PF05605 zf-Di19: Drought indu 22.8 34 0.00074 25.0 0.5 8 286-293 32-39 (54)
321 PRK03564 formate dehydrogenase 22.8 79 0.0017 31.9 3.1 35 285-322 226-260 (309)
322 TIGR00354 polC DNA polymerase, 22.7 54 0.0012 37.9 2.1 28 280-324 620-647 (1095)
323 COG1096 Predicted RNA-binding 22.7 67 0.0015 30.3 2.4 33 24-69 142-174 (188)
324 PRK14281 chaperone protein Dna 22.4 93 0.002 32.0 3.7 33 286-321 180-212 (397)
325 PF00265 TK: Thymidine kinase; 22.1 37 0.0008 31.0 0.6 24 25-48 131-154 (176)
326 TIGR00595 priA primosomal prot 22.0 42 0.00091 35.7 1.1 13 285-297 222-234 (505)
327 TIGR02605 CxxC_CxxC_SSSS putat 21.8 63 0.0014 23.2 1.7 9 62-70 28-36 (52)
328 TIGR02487 NrdD anaerobic ribon 21.8 50 0.0011 35.9 1.6 28 285-327 524-551 (579)
329 cd00729 rubredoxin_SM Rubredox 21.5 49 0.0011 22.4 1.0 13 314-326 2-14 (34)
330 COG5595 Zn-ribbon-containing, 21.5 35 0.00076 32.6 0.3 30 112-144 3-32 (256)
331 PF14206 Cys_rich_CPCC: Cystei 21.4 54 0.0012 26.6 1.3 18 61-78 21-38 (78)
332 COG2023 RPR2 RNase P subunit R 21.3 94 0.002 26.7 2.8 35 286-326 57-94 (105)
333 PRK14873 primosome assembly pr 20.7 54 0.0012 36.3 1.6 14 178-191 260-273 (665)
334 PRK11032 hypothetical protein; 20.6 55 0.0012 30.0 1.4 40 274-324 113-152 (160)
335 KOG2879 Predicted E3 ubiquitin 20.2 69 0.0015 32.0 2.1 39 25-70 233-286 (298)
336 TIGR00575 dnlj DNA ligase, NAD 20.2 70 0.0015 35.3 2.3 16 281-296 388-403 (652)
337 COG2023 RPR2 RNase P subunit R 20.1 1.1E+02 0.0024 26.3 3.0 34 32-71 57-93 (105)
338 TIGR00467 lysS_arch lysyl-tRNA 20.1 1.1E+02 0.0024 32.9 3.7 37 28-71 165-201 (515)
339 COG1435 Tdk Thymidine kinase [ 20.1 30 0.00065 32.9 -0.4 43 26-68 139-190 (201)
No 1
>KOG2703 consensus C4-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=1.1e-108 Score=809.88 Aligned_cols=334 Identities=50% Similarity=0.828 Sum_probs=307.1
Q ss_pred CCCCcccccccccchhccC--------CCCCCCCceEEeccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccc
Q 017546 1 MENNKEEIVDVGSVVEAVS--------ADDSDAPLYQVESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNE 72 (369)
Q Consensus 1 ~~~~~~~~~~~g~~~~~~~--------~~~~~~~v~eies~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnE 72 (369)
|+.+..+|.++|.+|.+.+ ++..+++++|++|+||+||++|+|||++|+||||||||||||.|||||+||||
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 3556779999998888774 34578899999999999999999999999999999999999999999999999
Q ss_pred eeeCcccCCcceEEEEEeeCCCcccccceeeeecceEEEeecceeEeCCCCCcceEEehHHHHHHHHHHHHHhhHhhhcC
Q 017546 73 VQFAGEIQPRGCNYSLKVPSSDQKMFHRQVVKSESATIKIPELDFEIPPEAQRGSLSTVEGILVRAADELEALQEERKKL 152 (369)
Q Consensus 73 Vq~~g~i~~kG~r~tL~V~~~~~~DLnR~VvKS~~ati~IPELd~eI~p~~~~G~iTTVEGlL~~i~~~L~~~~~~r~~~ 152 (369)
||+++.||++|+||+|+|. +.+||||+||||++|+|+||||+||||+.+|+|.||||||+|.|++++|+++|+.||..
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 CHHHHHHHHHHHHHHHHhhcCCCceEEEEeCCCCCcceecCCCCCCCCCeEEEEecCCHHHHHHcCCCCCCCccCCCCCC
Q 017546 153 DPQTAEAIDQFLLKLRACAKGDSTFTFILDDPAGNSFIENLYAPSPDPSLNIKFYERTPEQQALLGYLVDPSQQGESSNV 232 (369)
Q Consensus 153 ~~e~~~ki~~~i~kL~~~~~g~~pFTliidDPsGNS~I~~~~ap~~Dp~~~~~~y~Rt~eqn~~LGl~~~~~~~~~~~~~ 232 (369)
+|+.+++|++|+.||+.++.+..|||||+|||+|||||+++.+|.+||+|++.+|.||.+||+.|||...++.+.+-
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 99999999999999999999999999999999999999999999999999999999999999999999776533211
Q ss_pred CCCCCCCCCCCCCCCCCCccccccccccccCCchhhhhhhhccCCCcceeeeeccCccCcccccceeEEEecCCCCeEEE
Q 017546 233 VPSEGLSSTSDKREPRGSVGAVAGHRAIAQSNSAEIADALFRYSAPEEVMTFPSTCGACAASCETRMFMTRIPYFQEVIV 312 (369)
Q Consensus 233 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ev~~~~~~Cp~C~~~~~~~m~~~~IP~F~evii 312 (369)
.+.. +.....+.+++ +.||+.|+++||+|.++++|+|++++|||||+|||
T Consensus 236 ----------~k~~------------a~~~~~di~~~--------~~EV~~F~t~Cp~C~~pcet~Mk~~~IPhFkeVIi 285 (460)
T KOG2703|consen 236 ----------LKPI------------AASEATDIEDA--------PNEVLTFPTTCPSCTAPCETNMKLTDIPHFKEVII 285 (460)
T ss_pred ----------cccc------------cccccchhhcc--------ccceEEccCCCCCCCCchhccceeccCCcceeEEE
Confidence 1110 01111223333 44999999999999999999999999999999999
Q ss_pred EEeeCCCCCCCccccccCCccCCCceEEEEEecCcCcccceeeeecceeEEecccCC
Q 017546 313 MASTCDACGYRNSELKPGGRIPEKGKRITLFVKNINDLSRDLIKVCNGAIQLISIAV 369 (369)
Q Consensus 313 ms~~C~~CGyk~~eVk~~g~~~~~g~ritl~V~~~~DL~r~VlkS~ta~i~IPElg~ 369 (369)
||++|++||||+||||+||+|++||+||||+|.+.+||+||||||+||++.||||++
T Consensus 286 Mst~Cd~CGyksnEvKsGGai~~~G~ritl~~~~~~DlsRDvlKseTcs~~IPEl~l 342 (460)
T KOG2703|consen 286 MSTVCDRCGYKSNEVKSGGAIPDKGRRITLKVEDAEDLSRDVLKSETCSLSIPELDL 342 (460)
T ss_pred EeecccccCCccccccCCCCcCCCCcEEEEEecchHhhhHHHhhccccceeccccce
Confidence 999999999999999999999999999999999999999999999999999999974
No 2
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=100.00 E-value=9.8e-68 Score=485.89 Aligned_cols=185 Identities=37% Similarity=0.604 Sum_probs=177.7
Q ss_pred cCCCCCCCceEEEEEee-cCCcceEEEEEeeCCCCCCCccceeeCcccCCcceEEEEEeeCCCcccccceeeeecceEEE
Q 017546 33 LCMRCGENGVTRFLLTL-IPHFRKVLLSAFECPHCGERNNEVQFAGEIQPRGCNYSLKVPSSDQKMFHRQVVKSESATIK 111 (369)
Q Consensus 33 ~Cp~Cg~~g~tr~llt~-IP~FkeiiImSf~C~~CGyrnnEVq~~g~i~~kG~r~tL~V~~~~~~DLnR~VvKS~~ati~ 111 (369)
.||+||++|+|+|++|+ ||||||||||||.|+||||||||||++|+++|+ ||+|+|+ +++||+|+||||++|+|+
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 eecceeEeCCC-CCcceEEehHHHHHHHHHHHHHhhHhhhcCCHHHHHHHHHHHHHHHHhhcCCCceEEEEeCCCCCcce
Q 017546 112 IPELDFEIPPE-AQRGSLSTVEGILVRAADELEALQEERKKLDPQTAEAIDQFLLKLRACAKGDSTFTFILDDPAGNSFI 190 (369)
Q Consensus 112 IPELd~eI~p~-~~~G~iTTVEGlL~~i~~~L~~~~~~r~~~~~e~~~ki~~~i~kL~~~~~g~~pFTliidDPsGNS~I 190 (369)
||||+|||||| +++|+||||||+|++++++|+.... +++.+++.++|+++|+++|+++++|+.|||||||||+|||||
T Consensus 78 IPEl~lei~pg~~~~G~iTTVEGlL~~~~~~L~~~~~-~d~~~~e~~~k~~~~i~kL~~~~~g~~pfTlIidDP~GNS~I 156 (192)
T TIGR00310 78 IPELGLDIEPGPTSGGFITNLEGVLRRVEEELETAIR-WQSEDEETKKRAEEILERLKEAIEGKEKFTVILEDPLGGSYI 156 (192)
T ss_pred ccceEEEECCCccCCceEEeeHhHHHHHHHHHHhhhh-ccccCHHHHHHHHHHHHHHHHHHhCCCCEEEEEECCCCCeee
Confidence 99999999997 7999999999999999999998742 237889999999999999999999999999999999999999
Q ss_pred ecCCCCCCCCC-eEEEEecCCHHHHHHcCCCCC
Q 017546 191 ENLYAPSPDPS-LNIKFYERTPEQQALLGYLVD 222 (369)
Q Consensus 191 ~~~~ap~~Dp~-~~~~~y~Rt~eqn~~LGl~~~ 222 (369)
+|++||..||+ |++++|.||+|||++|||...
T Consensus 157 ~~~~a~~~d~~~~~~~~y~rt~eq~~~lGl~~~ 189 (192)
T TIGR00310 157 QNVYAPKEILSEEEIEDLKTGKEINEDLGLSDE 189 (192)
T ss_pred ecCCCCCCCCcccEeeecCCCHHHHHhcCCccc
Confidence 99999999999 999999999999999999643
No 3
>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=1.9e-62 Score=439.64 Aligned_cols=159 Identities=55% Similarity=0.904 Sum_probs=154.3
Q ss_pred ccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccceeeCcccCCcceEEEEEeeCCCcccccceeeeecceEEE
Q 017546 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEIQPRGCNYSLKVPSSDQKMFHRQVVKSESATIK 111 (369)
Q Consensus 32 s~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEVq~~g~i~~kG~r~tL~V~~~~~~DLnR~VvKS~~ati~ 111 (369)
|+||+||++|+|||++|+||||||||||||.|+||||||||||++|+++|+|+||+|+|+ +++||||+||||++|+|+
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 eecceeEeCCCCCcceEEehHHHHHHHHHHHHHh-hHhhhcCCHHHHHHHHHHHHHHHHhhcCCCceEEEEeCCCCCcce
Q 017546 112 IPELDFEIPPEAQRGSLSTVEGILVRAADELEAL-QEERKKLDPQTAEAIDQFLLKLRACAKGDSTFTFILDDPAGNSFI 190 (369)
Q Consensus 112 IPELd~eI~p~~~~G~iTTVEGlL~~i~~~L~~~-~~~r~~~~~e~~~ki~~~i~kL~~~~~g~~pFTliidDPsGNS~I 190 (369)
||||+|||||++++|+||||||+|++++++|+.. ++.++..+++.++|+++|+++|+++++|+.|||||||||+|||||
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 9999999999999999999999999999999988 666766789999999999999999999999999999999999999
Q ss_pred ec
Q 017546 191 EN 192 (369)
Q Consensus 191 ~~ 192 (369)
+|
T Consensus 159 ~~ 160 (160)
T smart00709 159 QN 160 (160)
T ss_pred cC
Confidence 85
No 4
>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=1.7e-62 Score=440.41 Aligned_cols=160 Identities=54% Similarity=0.916 Sum_probs=140.0
Q ss_pred eccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccceeeCcccCCcceEEEEEeeCCCcccccceeeeecceEE
Q 017546 31 ESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEIQPRGCNYSLKVPSSDQKMFHRQVVKSESATI 110 (369)
Q Consensus 31 es~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEVq~~g~i~~kG~r~tL~V~~~~~~DLnR~VvKS~~ati 110 (369)
+|+||+||++|.|||++|+||||||||||||.|+||||||||||++|+++|+|+||+|+|+ +++||||+||||++|+|
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 EeecceeEe-CCCCCcceEEehHHHHHHHHHHHHHhhHhhhcCCHHHHHHHHHHHHHHHHhhcCCCceEEEEeCCCCCcc
Q 017546 111 KIPELDFEI-PPEAQRGSLSTVEGILVRAADELEALQEERKKLDPQTAEAIDQFLLKLRACAKGDSTFTFILDDPAGNSF 189 (369)
Q Consensus 111 ~IPELd~eI-~p~~~~G~iTTVEGlL~~i~~~L~~~~~~r~~~~~e~~~ki~~~i~kL~~~~~g~~pFTliidDPsGNS~ 189 (369)
+||||+||| |+++++|+||||||+|++++++|+..++.|++.+++.++++++|+++|+++++|+.|||||||||+||||
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 5679999999999999999999999999888999999999999999999999999999999999999999
Q ss_pred eec
Q 017546 190 IEN 192 (369)
Q Consensus 190 I~~ 192 (369)
|+|
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 5
>KOG2703 consensus C4-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=2.5e-61 Score=475.05 Aligned_cols=200 Identities=36% Similarity=0.597 Sum_probs=191.8
Q ss_pred CCCCCCceEEeccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccceeeCcccCCcceEEEEEeeCCCcccccc
Q 017546 21 DDSDAPLYQVESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEIQPRGCNYSLKVPSSDQKMFHR 100 (369)
Q Consensus 21 ~~~~~~v~eies~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEVq~~g~i~~kG~r~tL~V~~~~~~DLnR 100 (369)
++..++|..|.+.||+|..+..|+|.+|+||||+||||||..|++||||+||||+||+|.++|+||||+|. +.+||.|
T Consensus 248 ~~~~~EV~~F~t~Cp~C~~pcet~Mk~~~IPhFkeVIiMst~Cd~CGyksnEvKsGGai~~~G~ritl~~~--~~~DlsR 325 (460)
T KOG2703|consen 248 EDAPNEVLTFPTTCPSCTAPCETNMKLTDIPHFKEVIIMSTVCDRCGYKSNEVKSGGAIPDKGRRITLKVE--DAEDLSR 325 (460)
T ss_pred hccccceEEccCCCCCCCCchhccceeccCCcceeEEEEeecccccCCccccccCCCCcCCCCcEEEEEec--chHhhhH
Confidence 34568999999999999999999999999999999999999999999999999999999999999999999 9999999
Q ss_pred eeeeecceEEEeecceeEeCCCCCcceEEehHHHHHHHHHHHHH-hhHhhhcCCHHHHHHHHHHHHHHHHhhcCCCceEE
Q 017546 101 QVVKSESATIKIPELDFEIPPEAQRGSLSTVEGILVRAADELEA-LQEERKKLDPQTAEAIDQFLLKLRACAKGDSTFTF 179 (369)
Q Consensus 101 ~VvKS~~ati~IPELd~eI~p~~~~G~iTTVEGlL~~i~~~L~~-~~~~r~~~~~e~~~ki~~~i~kL~~~~~g~~pFTl 179 (369)
+|+||+||+++||||+||+.+++++|.||||||||.++.+.|.. ...+.+++++...++|.+|+++|.+++.|+.||||
T Consensus 326 DvlKseTcs~~IPEl~lel~~~~LgGrfTTiEGLl~~~~e~l~~~~f~~~DS~~~~~~~~~~~F~~~l~~~i~~~~~~tl 405 (460)
T KOG2703|consen 326 DVLKSETCSLSIPELDLELGGGTLGGRFTTIEGLLTQIREQLDGRSFTFGDSMDEGQKARWQEFLAKLDDIIAGKLPATL 405 (460)
T ss_pred HHhhccccceeccccceeccCccccceeeeHHHHHHHHHHHHhcCceeccccCCHHHHHHHHHHHHHHHHHHhcccceEE
Confidence 99999999999999999999999999999999999999999976 23345899999999999999999999999999999
Q ss_pred EEeCCCCCcceecCCCCCCCCCeEEEEecCCHHHHHHcCCCCC
Q 017546 180 ILDDPAGNSFIENLYAPSPDPSLNIKFYERTPEQQALLGYLVD 222 (369)
Q Consensus 180 iidDPsGNS~I~~~~ap~~Dp~~~~~~y~Rt~eqn~~LGl~~~ 222 (369)
|||||+|||||+|.+||++||+|++++|+||+|||++|||..-
T Consensus 406 IldDp~~~syvq~~~ap~~dp~lt~E~Y~Rt~eqNeeLGlnDm 448 (460)
T KOG2703|consen 406 ILDDPLGNSYVQNVYAPDDDPNLTVEEYERTYEQNEELGLNDM 448 (460)
T ss_pred EeecCCcCcccccccCCCCCCcccHHHhhhhhhhhhhcCcccc
Confidence 9999999999999999999999999999999999999999754
No 6
>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=2.4e-58 Score=413.97 Aligned_cols=157 Identities=34% Similarity=0.601 Sum_probs=148.5
Q ss_pred CCCCCCCceEE-EEEeecCCcceEEEEEeeCCCCCCCccceeeCcccCCcceEEEEEeeCCCcccccceeeeecceEEEe
Q 017546 34 CMRCGENGVTR-FLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEIQPRGCNYSLKVPSSDQKMFHRQVVKSESATIKI 112 (369)
Q Consensus 34 Cp~Cg~~g~tr-~llt~IP~FkeiiImSf~C~~CGyrnnEVq~~g~i~~kG~r~tL~V~~~~~~DLnR~VvKS~~ati~I 112 (369)
||+||+++.+. |++|+||||||||||||.|+||||||||||++|+++| +||+|+|+ +++||+||||||++|+|+|
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 99999987655 8999999999999999999999999999999999999 89999999 9999999999999999999
Q ss_pred ecceeEeCCCC-CcceEEehHHHHHHHHHHHHHhhHhhhcCCHHHHHHHHHHHHHHHHhhcCCCceEEEEeCCCCCccee
Q 017546 113 PELDFEIPPEA-QRGSLSTVEGILVRAADELEALQEERKKLDPQTAEAIDQFLLKLRACAKGDSTFTFILDDPAGNSFIE 191 (369)
Q Consensus 113 PELd~eI~p~~-~~G~iTTVEGlL~~i~~~L~~~~~~r~~~~~e~~~ki~~~i~kL~~~~~g~~pFTliidDPsGNS~I~ 191 (369)
|||+|||||++ ++|+||||||+|++++++|+... |+..+++.++|+++|+++|+++++|+.|||||||||+|||||+
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 99999999977 79999999999999999999763 4466889999999999999999999999999999999999999
Q ss_pred cCCCC
Q 017546 192 NLYAP 196 (369)
Q Consensus 192 ~~~ap 196 (369)
++.+.
T Consensus 155 ~~~~~ 159 (163)
T TIGR00340 155 SEKAI 159 (163)
T ss_pred CCCcc
Confidence 98773
No 7
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=100.00 E-value=1.7e-48 Score=355.99 Aligned_cols=191 Identities=31% Similarity=0.457 Sum_probs=178.7
Q ss_pred CCCCceEEeccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccceeeCcccCCcceEEEEEeeCCCccccccee
Q 017546 23 SDAPLYQVESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEIQPRGCNYSLKVPSSDQKMFHRQV 102 (369)
Q Consensus 23 ~~~~v~eies~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEVq~~g~i~~kG~r~tL~V~~~~~~DLnR~V 102 (369)
....+.+....||+||....+.+++++||||++|+||+..|++||||++||+.++++.| +||+|+|+ +++||+++|
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 34567788899999999889999999999999999999999999999999999999999 89999999 999999999
Q ss_pred eeecceEEEeecceeEeCCCCC-cceEEehHHHHHHHHHHHHHhhHhhhcCCHHHHHHHHHHHHHHHHhhcCCCceEEEE
Q 017546 103 VKSESATIKIPELDFEIPPEAQ-RGSLSTVEGILVRAADELEALQEERKKLDPQTAEAIDQFLLKLRACAKGDSTFTFIL 181 (369)
Q Consensus 103 vKS~~ati~IPELd~eI~p~~~-~G~iTTVEGlL~~i~~~L~~~~~~r~~~~~e~~~ki~~~i~kL~~~~~g~~pFTlii 181 (369)
+||.+|+|+||||+++|.||+. .|+||||||+|.|+.+.|+....+ ..++|..+|+++++.+++++++|+.+|||||
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 VRSKSATIYIPELGLEIEPGPASEGFITTIEGVLERVYEVLETAIKL--AEDDESKKKAEELLKRIDEAIEGKRKFTLII 159 (201)
T ss_pred eecCCccEEcccCceEeccccccCceEehHHHHHHHHHHHHHHHHhc--ccchHHHHHHHHHHHHHHHHhccCccEEEEE
Confidence 9999999999999999999654 599999999999999999987766 3445889999999999999999999999999
Q ss_pred eCCCCCcceecCCCCCCCCCeEEEEecCCHHHHHHcCCC
Q 017546 182 DDPAGNSFIENLYAPSPDPSLNIKFYERTPEQQALLGYL 220 (369)
Q Consensus 182 dDPsGNS~I~~~~ap~~Dp~~~~~~y~Rt~eqn~~LGl~ 220 (369)
+||+|||||.+.+|+..++..+..+|.||. ++..+|+.
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 99988864
No 8
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=99.98 E-value=7.8e-33 Score=248.37 Aligned_cols=84 Identities=46% Similarity=0.873 Sum_probs=82.2
Q ss_pred ccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCccccccCCccCCCceEEEEEecCcCcccceeeeecceeEEec
Q 017546 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRIPEKGKRITLFVKNINDLSRDLIKVCNGAIQLI 365 (369)
Q Consensus 286 ~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~eVk~~g~~~~~g~ritl~V~~~~DL~r~VlkS~ta~i~IP 365 (369)
+.||+||+++.++|++++|||||+||||||.|++||||+|||+++|+++|+|+||||+|++++||+|+|+||+||+|.||
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 46999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCC
Q 017546 366 SIAV 369 (369)
Q Consensus 366 Elg~ 369 (369)
|||+
T Consensus 81 El~~ 84 (160)
T smart00709 81 ELDL 84 (160)
T ss_pred eeeE
Confidence 9985
No 9
>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=99.97 E-value=1.3e-32 Score=247.23 Aligned_cols=84 Identities=43% Similarity=0.841 Sum_probs=73.5
Q ss_pred ccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCccccccCCccCCCceEEEEEecCcCcccceeeeecceeEEec
Q 017546 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRIPEKGKRITLFVKNINDLSRDLIKVCNGAIQLI 365 (369)
Q Consensus 286 ~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~eVk~~g~~~~~g~ritl~V~~~~DL~r~VlkS~ta~i~IP 365 (369)
+.||+||+++.++|++|+|||||+||||||.|++||||+|||+++|+++|+|+||||+|++++||+|+|+||+||+|+||
T Consensus 2 s~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~~ev~~~~~~~~~G~r~tl~V~~~~DL~r~VvkS~~ati~IP 81 (161)
T PF03367_consen 2 SLCPNCGENGTTRILLTDIPYFKEVIIMSFECEHCGYKNNEVKSGGQIQPKGVRITLKVESPEDLNRQVVKSDTATIEIP 81 (161)
T ss_dssp EE-TTTSSCCEEEEEEEEETTTEEEEEEEEE-TTT--EEEEEEEECSS-SSEEEEEEEE-SHHHHC-EEEE-TT-EEEEG
T ss_pred CcCCCCCCCcEEEEEEEcCCCCceEEEEEeECCCCCCEeeeEEECccCCCCceEEEEEECCHHHhcceEEecCcEEEEEe
Confidence 67999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccCC
Q 017546 366 SIAV 369 (369)
Q Consensus 366 Elg~ 369 (369)
|||+
T Consensus 82 El~~ 85 (161)
T PF03367_consen 82 ELGL 85 (161)
T ss_dssp GGTE
T ss_pred ecce
Confidence 9985
No 10
>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=99.96 E-value=1.8e-30 Score=233.74 Aligned_cols=80 Identities=20% Similarity=0.482 Sum_probs=76.8
Q ss_pred CccCcccccce-eEEEecCCCCeEEEEEeeCCCCCCCccccccCCccCCCceEEEEEecCcCcccceeeeecceeEEecc
Q 017546 288 CGACAASCETR-MFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRIPEKGKRITLFVKNINDLSRDLIKVCNGAIQLIS 366 (369)
Q Consensus 288 Cp~C~~~~~~~-m~~~~IP~F~eviims~~C~~CGyk~~eVk~~g~~~~~g~ritl~V~~~~DL~r~VlkS~ta~i~IPE 366 (369)
||+||+++.+. |++++|||||+||||||.|++||||+|||+++|+++| +||||+|++++||+|+|+||+||+|.|||
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 99999985555 8999999999999999999999999999999999999 99999999999999999999999999999
Q ss_pred cCC
Q 017546 367 IAV 369 (369)
Q Consensus 367 lg~ 369 (369)
||+
T Consensus 79 l~l 81 (163)
T TIGR00340 79 LGI 81 (163)
T ss_pred eeE
Confidence 985
No 11
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=99.96 E-value=4.7e-30 Score=236.44 Aligned_cols=81 Identities=33% Similarity=0.691 Sum_probs=79.3
Q ss_pred cCccCcccccceeEEEe-cCCCCeEEEEEeeCCCCCCCccccccCCccCCCceEEEEEecCcCcccceeeeecceeEEec
Q 017546 287 TCGACAASCETRMFMTR-IPYFQEVIVMASTCDACGYRNSELKPGGRIPEKGKRITLFVKNINDLSRDLIKVCNGAIQLI 365 (369)
Q Consensus 287 ~Cp~C~~~~~~~m~~~~-IP~F~eviims~~C~~CGyk~~eVk~~g~~~~~g~ritl~V~~~~DL~r~VlkS~ta~i~IP 365 (369)
.||+||+++.++|++++ |||||+||||||.|++||||+|||+++|+++| +||+|+|++++||+|+|+||+||+|.||
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 DCPSCGGECETVMKTVNDIPYFGEVLETSTICEHCGYRSNDVKTLGAKEP--KRYILKIDDEADLNRRVVKSESATIRIP 79 (192)
T ss_pred cCCCCCCCCEEEEEEEcCCCCcceEEEEEEECCCCCCccceeEECCCCCC--EEEEEEECChhcccceEEEcCCcEEEcc
Confidence 69999999999999999 99999999999999999999999999999999 5999999999999999999999999999
Q ss_pred ccCC
Q 017546 366 SIAV 369 (369)
Q Consensus 366 Elg~ 369 (369)
|||+
T Consensus 80 El~l 83 (192)
T TIGR00310 80 ELGL 83 (192)
T ss_pred ceEE
Confidence 9985
No 12
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=99.96 E-value=2.5e-29 Score=230.23 Aligned_cols=88 Identities=27% Similarity=0.586 Sum_probs=86.4
Q ss_pred ceeeeeccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCccccccCCccCCCceEEEEEecCcCcccceeeeecc
Q 017546 280 EVMTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRIPEKGKRITLFVKNINDLSRDLIKVCN 359 (369)
Q Consensus 280 ev~~~~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~eVk~~g~~~~~g~ritl~V~~~~DL~r~VlkS~t 359 (369)
++.++...||+||+.+.++|++|+|||||+|+||++.|++||||++||+++|+++| +||+|+|++++||+++|+||.|
T Consensus 9 ~~~~~~~~CPvCg~~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~DV~~~e~~eP--~r~~lkve~~edL~~~V~RS~s 86 (201)
T COG1779 9 EEFETRIDCPVCGGTLKAHMYLYDIPYFGEVLISTGVCERCGYRSTDVKTLEEREP--RRYTLKVESEEDLSARVVRSKS 86 (201)
T ss_pred eeeeeeecCCcccceeeEEEeeecCCccceEEEEEEEccccCCcccceeecccCCC--eEEEEEeCCHHHhhhheeecCC
Confidence 78899999999999999999999999999999999999999999999999999999 9999999999999999999999
Q ss_pred eeEEecccCC
Q 017546 360 GAIQLISIAV 369 (369)
Q Consensus 360 a~i~IPElg~ 369 (369)
|+|+|||||+
T Consensus 87 ~~I~IPELg~ 96 (201)
T COG1779 87 ATIYIPELGL 96 (201)
T ss_pred ccEEcccCce
Confidence 9999999996
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=94.49 E-value=0.016 Score=37.52 Aligned_cols=24 Identities=46% Similarity=0.841 Sum_probs=19.5
Q ss_pred cCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCcc
Q 017546 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNN 71 (369)
Q Consensus 33 ~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnn 71 (369)
.||.|+ ++|-+.+-.|+||||...
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 566788899999999763
No 14
>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=94.40 E-value=0.018 Score=37.29 Aligned_cols=24 Identities=42% Similarity=0.798 Sum_probs=19.3
Q ss_pred cCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCcc
Q 017546 287 TCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNS 325 (369)
Q Consensus 287 ~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~ 325 (369)
.||.|++. |-+.+..|++|||.+.
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 59999855 4567889999999764
No 15
>PF14353 CpXC: CpXC protein
Probab=92.96 E-value=0.026 Score=48.55 Aligned_cols=40 Identities=25% Similarity=0.566 Sum_probs=28.8
Q ss_pred ccCCCCCCCceEEE----EEeecCCcceEEE----EEeeCCCCCCCcc
Q 017546 32 SLCMRCGENGVTRF----LLTLIPHFRKVLL----SAFECPHCGERNN 71 (369)
Q Consensus 32 s~Cp~Cg~~g~tr~----llt~IP~FkeiiI----mSf~C~~CGyrnn 71 (369)
-.||+||+.....+ -...-|=+++=|+ .+|.||+||.+..
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 46999999876543 3334566666665 5799999999874
No 16
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=92.56 E-value=0.12 Score=48.85 Aligned_cols=43 Identities=23% Similarity=0.497 Sum_probs=30.1
Q ss_pred eccCccCcccccceeEE--------Ee---cCCCCe---EEEEEeeCCCCCCCcccc
Q 017546 285 PSTCGACAASCETRMFM--------TR---IPYFQE---VIVMASTCDACGYRNSEL 327 (369)
Q Consensus 285 ~~~Cp~C~~~~~~~m~~--------~~---IP~F~e---viims~~C~~CGyk~~eV 327 (369)
...||+|++...++... ++ =|+|+. .+-..++|++|||-..+-
T Consensus 5 ~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 5 KITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred ceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 46899999987665421 11 255554 467789999999987754
No 17
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=92.43 E-value=0.12 Score=46.78 Aligned_cols=47 Identities=17% Similarity=0.221 Sum_probs=32.8
Q ss_pred ccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCccccccCCcc
Q 017546 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRI 333 (369)
Q Consensus 286 ~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~eVk~~g~~ 333 (369)
+.||.||.+...-....-++- |.+|-+.-.|.+||++++-....+..
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~-~~~~~~~~~c~~c~~~f~~~e~~~~~ 47 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAED-GNAIRRRRECLACGKRFTTFERVELV 47 (154)
T ss_pred CcCCCCCCCCCEeEeccccCC-CCceeeeeeccccCCcceEeEeccCc
Confidence 479999988522222222233 77888889999999999877665554
No 18
>PHA00626 hypothetical protein
Probab=92.41 E-value=0.18 Score=38.51 Aligned_cols=50 Identities=18% Similarity=0.377 Sum_probs=30.7
Q ss_pred ccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccceeeCcccCCcceEEEEEee
Q 017546 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEIQPRGCNYSLKVP 91 (369)
Q Consensus 32 s~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEVq~~g~i~~kG~r~tL~V~ 91 (369)
..||+||..-.+|--..+-|- -.+.|+.|||+.+.- +..++|.---++|+
T Consensus 1 m~CP~CGS~~Ivrcg~cr~~s------nrYkCkdCGY~ft~~----~~~~~~~~~~~~~~ 50 (59)
T PHA00626 1 MSCPKCGSGNIAKEKTMRGWS------DDYVCCDCGYNDSKD----AFGERGKNEFVRIN 50 (59)
T ss_pred CCCCCCCCceeeeeceecccC------cceEcCCCCCeechh----hhhhccccceEEec
Confidence 369999986555533322221 238999999999754 44445544445554
No 19
>PF14353 CpXC: CpXC protein
Probab=91.28 E-value=0.041 Score=47.36 Aligned_cols=41 Identities=27% Similarity=0.528 Sum_probs=28.9
Q ss_pred ccCccCcccccceeE-EEe---cCCCCeEE----EEEeeCCCCCCCccc
Q 017546 286 STCGACAASCETRMF-MTR---IPYFQEVI----VMASTCDACGYRNSE 326 (369)
Q Consensus 286 ~~Cp~C~~~~~~~m~-~~~---IP~F~evi----ims~~C~~CGyk~~e 326 (369)
.+||+||+....... .++ -|-+++-| +..++|++||++..=
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~ 50 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRL 50 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceec
Confidence 479999999877663 333 35444444 468999999998863
No 20
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=91.24 E-value=0.31 Score=45.72 Aligned_cols=84 Identities=14% Similarity=0.277 Sum_probs=53.8
Q ss_pred eEEeccCCCCCCCceE-EEEEeecCCcceEEEEEeeCCCCCCCccceeeCcccCCcceEEEEEeeCCCcccccceeeeec
Q 017546 28 YQVESLCMRCGENGVT-RFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEIQPRGCNYSLKVPSSDQKMFHRQVVKSE 106 (369)
Q Consensus 28 ~eies~Cp~Cg~~g~t-r~llt~IP~FkeiiImSf~C~~CGyrnnEVq~~g~i~~kG~r~tL~V~~~~~~DLnR~VvKS~ 106 (369)
.++...||+||..-++ .++..+.+. ....|..||+=+.+ .-.-|+-++..+-|. +.=+|.
T Consensus 3 ~~iy~~Cp~Cg~eev~hEVik~~g~~------~lvrC~eCG~V~~~----~i~~~k~~~v~viVS---------~~~~S~ 63 (201)
T COG1326 3 EEIYIECPSCGSEEVSHEVIKERGRE------PLVRCEECGTVHPA----IIKTPKPVRVRVIVS---------RHEESF 63 (201)
T ss_pred ceEEEECCCCCcchhhHHHHHhcCCc------eEEEccCCCcEeec----eeeccccceEEEEEe---------cCCccc
Confidence 4677889999933332 344444544 44799999996643 444456666777775 333577
Q ss_pred ceEEEeecce-------eEeCCCCCcceEEehH
Q 017546 107 SATIKIPELD-------FEIPPEAQRGSLSTVE 132 (369)
Q Consensus 107 ~ati~IPELd-------~eI~p~~~~G~iTTVE 132 (369)
+-.+++|+.+ |++.. -+..||++|
T Consensus 64 ~~~vel~~gE~l~vGDei~vd~--e~veITSIE 94 (201)
T COG1326 64 TKEVELDPGETLKVGDEIEVDG--EEVEITSIE 94 (201)
T ss_pred ceeEecCCCCeEecCCEEEEcC--CEEEEEEEe
Confidence 7788888654 44443 467888887
No 21
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=90.45 E-value=0.38 Score=33.94 Aligned_cols=39 Identities=23% Similarity=0.468 Sum_probs=26.2
Q ss_pred cCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCccc
Q 017546 287 TCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSE 326 (369)
Q Consensus 287 ~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~e 326 (369)
.||.||+.- .......+=--.|=...-+.|-+|||+..|
T Consensus 2 ~Cp~C~~~~-a~~~q~Q~RsaDE~mT~fy~C~~C~~~w~~ 40 (40)
T smart00440 2 PCPKCGNRE-ATFFQLQTRSADEPMTVFYVCTKCGHRWRE 40 (40)
T ss_pred cCCCCCCCe-EEEEEEcccCCCCCCeEEEEeCCCCCEeCC
Confidence 699998663 233344444445666677899999998754
No 22
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=90.22 E-value=0.13 Score=32.94 Aligned_cols=24 Identities=29% Similarity=0.670 Sum_probs=17.2
Q ss_pred eccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCC
Q 017546 285 PSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYR 323 (369)
Q Consensus 285 ~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk 323 (369)
...||+||+.... -+..|.+||.+
T Consensus 2 ~~~Cp~Cg~~~~~---------------~~~fC~~CG~~ 25 (26)
T PF13248_consen 2 EMFCPNCGAEIDP---------------DAKFCPNCGAK 25 (26)
T ss_pred cCCCcccCCcCCc---------------ccccChhhCCC
Confidence 4679999986422 26679999976
No 23
>PHA00626 hypothetical protein
Probab=89.80 E-value=0.37 Score=36.86 Aligned_cols=51 Identities=24% Similarity=0.371 Sum_probs=30.1
Q ss_pred ccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCccccccCCccCCCceEEEEEecC
Q 017546 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRIPEKGKRITLFVKN 346 (369)
Q Consensus 286 ~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~eVk~~g~~~~~g~ritl~V~~ 346 (369)
+.||.||+.-.++-..+.-|- --+.|..|||+++----| +.|+---++|..
T Consensus 1 m~CP~CGS~~Ivrcg~cr~~s------nrYkCkdCGY~ft~~~~~----~~~~~~~~~~~~ 51 (59)
T PHA00626 1 MSCPKCGSGNIAKEKTMRGWS------DDYVCCDCGYNDSKDAFG----ERGKNEFVRINK 51 (59)
T ss_pred CCCCCCCCceeeeeceecccC------cceEcCCCCCeechhhhh----hccccceEEech
Confidence 479999986444433332221 346899999999865433 344444445543
No 24
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=89.39 E-value=1.4 Score=41.46 Aligned_cols=72 Identities=21% Similarity=0.351 Sum_probs=46.7
Q ss_pred ccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCcccc-----c-cCCccCCCceEEEEEecCcCcccceeeeecc
Q 017546 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSEL-----K-PGGRIPEKGKRITLFVKNINDLSRDLIKVCN 359 (369)
Q Consensus 286 ~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~eV-----k-~~g~~~~~g~ritl~V~~~~DL~r~VlkS~t 359 (369)
..||.|+.+ .|.+..- +. ++...|..||++..=- . +.++--.+|..++++|++...-.+-|.|-+.
T Consensus 99 V~C~~C~~p-dT~l~k~-----~~--~~~l~C~aCGa~~~v~~~~~~~~~~~~~~~~~e~~~v~Ie~l~~~G~GVak~~g 170 (201)
T PRK12336 99 VICSECGLP-DTRLVKE-----DR--VLMLRCDACGAHRPVKKRKASSETQREAIEEGKTYEVEITGTGRKGDGVAKKGK 170 (201)
T ss_pred EECCCCCCC-CcEEEEc-----CC--eEEEEcccCCCCccccccccccCCCCCCCccCCEEEEEEEEccCCCceEEEECC
Confidence 569999998 5666432 23 4458999999976421 1 1121122566788999888776666777666
Q ss_pred eeEEec
Q 017546 360 GAIQLI 365 (369)
Q Consensus 360 a~i~IP 365 (369)
-.+.+|
T Consensus 171 ~~vfV~ 176 (201)
T PRK12336 171 YTIFVP 176 (201)
T ss_pred EEEEeC
Confidence 666665
No 25
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=88.94 E-value=0.49 Score=44.66 Aligned_cols=45 Identities=29% Similarity=0.668 Sum_probs=29.6
Q ss_pred eccCCCCCCCceEEEEEe-ec----------CCcce---EEEEEeeCCCCCCCccceee
Q 017546 31 ESLCMRCGENGVTRFLLT-LI----------PHFRK---VLLSAFECPHCGERNNEVQF 75 (369)
Q Consensus 31 es~Cp~Cg~~g~tr~llt-~I----------P~Fke---iiImSf~C~~CGyrnnEVq~ 75 (369)
+..||+|++.-.+..+.+ .+ |+|+. .+.....||||||-..+-.+
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 456999998865443222 22 45544 46777899999998765543
No 26
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=88.68 E-value=0.25 Score=43.56 Aligned_cols=50 Identities=22% Similarity=0.472 Sum_probs=35.2
Q ss_pred EeccCCCCCCCceEE--------EEEeecCCcceEEEEEeeCCCCCCCccceeeCccc
Q 017546 30 VESLCMRCGENGVTR--------FLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEI 79 (369)
Q Consensus 30 ies~Cp~Cg~~g~tr--------~llt~IP~FkeiiImSf~C~~CGyrnnEVq~~g~i 79 (369)
....|++||..-... .+-+.|-|-.|++-..+.||+||-++-+|..|.++
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G~el 126 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEIVKGRGV 126 (135)
T ss_pred eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcEEecCceE
Confidence 457899999654322 23345556677777778999999888888777654
No 27
>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=88.09 E-value=0.29 Score=35.48 Aligned_cols=36 Identities=22% Similarity=0.482 Sum_probs=27.6
Q ss_pred cCccCcccccceeEEEecCCCCeEEEEEeeCCC--CCCCcc
Q 017546 287 TCGACAASCETRMFMTRIPYFQEVIVMASTCDA--CGYRNS 325 (369)
Q Consensus 287 ~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~--CGyk~~ 325 (369)
.||.||+.+.++--...-|.+++ ....|.+ ||+.+.
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 49999999877765555666666 7788988 998764
No 28
>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=87.84 E-value=0.56 Score=35.35 Aligned_cols=35 Identities=29% Similarity=0.785 Sum_probs=24.4
Q ss_pred eEEeccCCCCC-CCceEEEEEeecCCcceEEEEEeeCCCCCCCc
Q 017546 28 YQVESLCMRCG-ENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (369)
Q Consensus 28 ~eies~Cp~Cg-~~g~tr~llt~IP~FkeiiImSf~C~~CGyrn 70 (369)
.-..-.|.+|+ .||... .--|.++ +|.|++||+.|
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 34566799997 467553 2224444 89999999976
No 29
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=87.51 E-value=0.8 Score=41.50 Aligned_cols=46 Identities=17% Similarity=0.236 Sum_probs=31.2
Q ss_pred ccCCCCCCCce-EEEEEeecCCcceEEEEEeeCCCCCCCccceeeCccc
Q 017546 32 SLCMRCGENGV-TRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEI 79 (369)
Q Consensus 32 s~Cp~Cg~~g~-tr~llt~IP~FkeiiImSf~C~~CGyrnnEVq~~g~i 79 (369)
..||.||.+-+ .+---+.=| +..|-+.-.|+.||++.+-+...+..
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~--~~~~~~~~~c~~c~~~f~~~e~~~~~ 47 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAED--GNAIRRRRECLACGKRFTTFERVELV 47 (154)
T ss_pred CcCCCCCCCCCEeEeccccCC--CCceeeeeeccccCCcceEeEeccCc
Confidence 36999997652 222111112 55888889999999999877666554
No 30
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=87.16 E-value=0.45 Score=34.11 Aligned_cols=29 Identities=34% Similarity=0.642 Sum_probs=18.4
Q ss_pred eccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCc
Q 017546 31 ESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (369)
Q Consensus 31 es~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrn 70 (369)
+-.|++||..-.. .+. .. .+.||+||.+.
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 3469999975221 111 11 79999999754
No 31
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=86.19 E-value=0.65 Score=38.45 Aligned_cols=36 Identities=31% Similarity=0.728 Sum_probs=26.7
Q ss_pred eccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccceeeCcccCC
Q 017546 31 ESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEIQP 81 (369)
Q Consensus 31 es~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEVq~~g~i~~ 81 (369)
.-.||.|+.+.+ +=.-+-| +.|.+|||+. .+|+..|
T Consensus 35 ~~~Cp~C~~~~V-kR~a~GI----------W~C~kCg~~f----AGgay~P 70 (89)
T COG1997 35 KHVCPFCGRTTV-KRIATGI----------WKCRKCGAKF----AGGAYTP 70 (89)
T ss_pred CCcCCCCCCcce-eeeccCe----------EEcCCCCCee----ccccccc
Confidence 356999999844 3345566 9999999987 4777666
No 32
>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=86.16 E-value=0.53 Score=35.58 Aligned_cols=33 Identities=30% Similarity=0.622 Sum_probs=22.5
Q ss_pred eccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCccc
Q 017546 285 PSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSE 326 (369)
Q Consensus 285 ~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~e 326 (369)
...||.||+.... .=+.-++++ .|+.||...-=
T Consensus 2 ~~~CP~CG~~iev-----~~~~~GeiV----~Cp~CGaeleV 34 (54)
T TIGR01206 2 QFECPDCGAEIEL-----ENPELGELV----ICDECGAELEV 34 (54)
T ss_pred ccCCCCCCCEEec-----CCCccCCEE----eCCCCCCEEEE
Confidence 3589999986532 223446755 89999987643
No 33
>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=86.11 E-value=0.5 Score=33.10 Aligned_cols=37 Identities=22% Similarity=0.441 Sum_probs=22.2
Q ss_pred cCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCc
Q 017546 287 TCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRN 324 (369)
Q Consensus 287 ~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~ 324 (369)
.||.||+.- ..+.+..+=--.|-...-+.|-+||++.
T Consensus 2 ~Cp~Cg~~~-a~~~~~Q~rsaDE~~T~fy~C~~C~~~w 38 (39)
T PF01096_consen 2 KCPKCGHNE-AVFFQIQTRSADEPMTLFYVCCNCGHRW 38 (39)
T ss_dssp --SSS-SSE-EEEEEESSSSSSSSSEEEEEESSSTEEE
T ss_pred CCcCCCCCe-EEEEEeeccCCCCCCeEEEEeCCCCCee
Confidence 699999873 3333444433455566677899999875
No 34
>PRK05978 hypothetical protein; Provisional
Probab=86.01 E-value=0.33 Score=43.78 Aligned_cols=37 Identities=24% Similarity=0.591 Sum_probs=28.4
Q ss_pred eeeccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCcccccc
Q 017546 283 TFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKP 329 (369)
Q Consensus 283 ~~~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~eVk~ 329 (369)
-+...||.||+- .-|+.-+-|.-.|++||.+..-...
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 457789999876 3456777799999999998765543
No 35
>PRK05978 hypothetical protein; Provisional
Probab=86.01 E-value=0.35 Score=43.58 Aligned_cols=33 Identities=33% Similarity=0.669 Sum_probs=26.0
Q ss_pred EeccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccc
Q 017546 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNE 72 (369)
Q Consensus 30 ies~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnE 72 (369)
+...||+||+-. .|+--+-|.-.|++||.+..-
T Consensus 32 l~grCP~CG~G~----------LF~g~Lkv~~~C~~CG~~~~~ 64 (148)
T PRK05978 32 FRGRCPACGEGK----------LFRAFLKPVDHCAACGEDFTH 64 (148)
T ss_pred HcCcCCCCCCCc----------ccccccccCCCccccCCcccc
Confidence 568899999763 356667788999999998753
No 36
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=85.91 E-value=0.32 Score=30.48 Aligned_cols=22 Identities=32% Similarity=0.720 Sum_probs=14.5
Q ss_pred cCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCC
Q 017546 287 TCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYR 323 (369)
Q Consensus 287 ~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk 323 (369)
.||.||++..-.. -.|.+||++
T Consensus 1 ~Cp~CG~~~~~~~---------------~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIEDDA---------------KFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCCcC---------------cchhhhCCc
Confidence 3888888764332 238888875
No 37
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=85.00 E-value=0.72 Score=33.06 Aligned_cols=29 Identities=28% Similarity=0.663 Sum_probs=19.4
Q ss_pred ccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCcc
Q 017546 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNS 325 (369)
Q Consensus 286 ~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~ 325 (369)
..||+||+.... +-... .+.|++||.+..
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 22111 789999997654
No 38
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=84.67 E-value=5.8 Score=40.83 Aligned_cols=38 Identities=18% Similarity=0.440 Sum_probs=26.1
Q ss_pred eccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccce
Q 017546 31 ESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEV 73 (369)
Q Consensus 31 es~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEV 73 (369)
...|+.|+..|.++...-. =++.|.-.|+.|+=+-..|
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 3569999888877665433 4566777888887655555
No 39
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=83.45 E-value=2.1 Score=30.12 Aligned_cols=39 Identities=26% Similarity=0.531 Sum_probs=24.5
Q ss_pred cCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccc
Q 017546 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNE 72 (369)
Q Consensus 33 ~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnE 72 (369)
.||.||.+...-+ ...+=--.|=...-|.|..||++-.|
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 5999986654322 22222234555666999999997643
No 40
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=83.35 E-value=4.3 Score=38.08 Aligned_cols=71 Identities=24% Similarity=0.416 Sum_probs=43.8
Q ss_pred ccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccceee-------CcccCCcceEEEEEeeCCCcccccceeee
Q 017546 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQF-------AGEIQPRGCNYSLKVPSSDQKMFHRQVVK 104 (369)
Q Consensus 32 s~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEVq~-------~g~i~~kG~r~tL~V~~~~~~DLnR~VvK 104 (369)
.+|+.|+.+ .|.|... + =++...|..||.+.. |+. ..+--.+|..++++|+ +...-.+-|.+
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-----D--RVLMLRCDACGAHRP-VKKRKASSETQREAIEEGKTYEVEIT--GTGRKGDGVAK 167 (201)
T ss_pred EECCCCCCC-CcEEEEc-----C--CeEEEEcccCCCCcc-ccccccccCCCCCCCccCCEEEEEEE--EccCCCceEEE
Confidence 689999986 4555432 1 244589999999753 222 1111134556788887 55555555776
Q ss_pred ecceEEEee
Q 017546 105 SESATIKIP 113 (369)
Q Consensus 105 S~~ati~IP 113 (369)
-+..++.+|
T Consensus 168 ~~g~~vfV~ 176 (201)
T PRK12336 168 KGKYTIFVP 176 (201)
T ss_pred ECCEEEEeC
Confidence 666666665
No 41
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=81.73 E-value=0.96 Score=39.86 Aligned_cols=50 Identities=22% Similarity=0.452 Sum_probs=32.9
Q ss_pred eeccCccCcccccce--------eEEEecCCCCeEEEEEeeCCCCCCCccccccCCcc
Q 017546 284 FPSTCGACAASCETR--------MFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRI 333 (369)
Q Consensus 284 ~~~~Cp~C~~~~~~~--------m~~~~IP~F~eviims~~C~~CGyk~~eVk~~g~~ 333 (369)
....|+.||...... +.-+.+=|..+++-..+.|++||-..-+|..|...
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G~el 126 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEIVKGRGV 126 (135)
T ss_pred eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcEEecCceE
Confidence 456899999664332 12233334466666668899999888788666543
No 42
>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=81.47 E-value=2.8 Score=37.81 Aligned_cols=64 Identities=23% Similarity=0.324 Sum_probs=44.3
Q ss_pred ccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccceeeCcccCCcceEEEEEeeCCCcccccce
Q 017546 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEIQPRGCNYSLKVPSSDQKMFHRQ 101 (369)
Q Consensus 32 s~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEVq~~g~i~~kG~r~tL~V~~~~~~DLnR~ 101 (369)
+.||-||.+ .|+..-.+.--=+..|---=+|+.||+|++..--.+...+ ..+|=. |..+.++|+
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 469999865 5666666655556677788899999999997655555433 233322 677788886
No 43
>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=81.13 E-value=1.8 Score=35.83 Aligned_cols=41 Identities=20% Similarity=0.357 Sum_probs=27.3
Q ss_pred eccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCccc
Q 017546 285 PSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSE 326 (369)
Q Consensus 285 ~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~e 326 (369)
...||.||+.-. ......+---.|=.-.-+.|-+|||+..|
T Consensus 62 ~~~Cp~Cg~~~a-~f~~~Q~RsadE~~T~fy~C~~C~~~w~~ 102 (104)
T TIGR01384 62 RVECPKCGHKEA-YYWLLQTRRADEPETRFYKCTKCGYVWRE 102 (104)
T ss_pred cCCCCCCCCCee-EEEEeccCCCCCCcEEEEEeCCCCCeeEe
Confidence 468999997632 22233443345556677899999999865
No 44
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=80.92 E-value=0.7 Score=39.94 Aligned_cols=42 Identities=19% Similarity=0.400 Sum_probs=27.5
Q ss_pred eeeccCccCccc-ccceeEEEecCCCCeEEEEEeeCCCCCCCccc
Q 017546 283 TFPSTCGACAAS-CETRMFMTRIPYFQEVIVMASTCDACGYRNSE 326 (369)
Q Consensus 283 ~~~~~Cp~C~~~-~~~~m~~~~IP~F~eviims~~C~~CGyk~~e 326 (369)
.+.-.||.||++ +..+..++.=--=|..+ -+.|.+|+||..+
T Consensus 72 ~I~~kCpkCghe~m~Y~T~QlRSADEGQTV--FYTC~kC~~k~~e 114 (116)
T KOG2907|consen 72 VIKHKCPKCGHEEMSYHTLQLRSADEGQTV--FYTCPKCKYKFTE 114 (116)
T ss_pred chhccCcccCCchhhhhhhhcccccCCceE--EEEcCccceeeec
Confidence 556689999987 33344444333334443 4689999999875
No 45
>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=80.29 E-value=1.9 Score=38.89 Aligned_cols=49 Identities=20% Similarity=0.352 Sum_probs=33.1
Q ss_pred ccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCccccccCCccCC
Q 017546 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRIPE 335 (369)
Q Consensus 286 ~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~eVk~~g~~~~ 335 (369)
+.||-||++ .++..-...--=|..|=---.|.+||+|++-.-..+..++
T Consensus 1 M~CP~C~~~-dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErve~~~l 49 (147)
T TIGR00244 1 MHCPFCQHH-NTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELLPP 49 (147)
T ss_pred CCCCCCCCC-CCEeeeccccCCCCeeeecccCCccCCccceeeecccccc
Confidence 579999987 3444333333446677778899999999986644444433
No 46
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=80.27 E-value=1.9 Score=38.23 Aligned_cols=32 Identities=28% Similarity=0.680 Sum_probs=22.6
Q ss_pred ccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCcc
Q 017546 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNS 325 (369)
Q Consensus 286 ~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~ 325 (369)
+.||.|+.+ .|.+..- +.+ +...|..||++..
T Consensus 98 VlC~~C~sP-dT~l~k~-----~r~--~~l~C~ACGa~~~ 129 (133)
T TIGR00311 98 VICRECNRP-DTRIIKE-----GRV--SLLKCEACGAKAP 129 (133)
T ss_pred EECCCCCCC-CcEEEEe-----CCe--EEEecccCCCCCc
Confidence 569999998 4555431 343 4569999999763
No 47
>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=79.93 E-value=1.5 Score=31.83 Aligned_cols=36 Identities=28% Similarity=0.526 Sum_probs=27.6
Q ss_pred cCCCCCCCceEEEEEeecCCcceEEEEEeeCCC--CCCCcc
Q 017546 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPH--CGERNN 71 (369)
Q Consensus 33 ~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~--CGyrnn 71 (369)
.||.||.....|--...-|.++| .-+.|.+ ||+...
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 49999999887765555666777 6688988 998763
No 48
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=79.91 E-value=1.6 Score=39.54 Aligned_cols=98 Identities=18% Similarity=0.220 Sum_probs=55.2
Q ss_pred ccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccceeeCcccCCcceEEEEEeeCCCcccccce-eeeecceEE
Q 017546 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEIQPRGCNYSLKVPSSDQKMFHRQ-VVKSESATI 110 (369)
Q Consensus 32 s~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEVq~~g~i~~kG~r~tL~V~~~~~~DLnR~-VvKS~~ati 110 (369)
+.||-|+.+. |+..--+---=+.-|---=.|++||.|++..--+.-..+ +.+|=. |..+.++|+ ++++
T Consensus 1 M~CPfC~~~~-tkViDSR~~edg~aIRRRReC~~C~~RFTTfE~~El~~~----~VvKkd-g~Re~F~r~Kl~~g----- 69 (156)
T COG1327 1 MKCPFCGHED-TKVIDSRPAEEGNAIRRRRECLECGERFTTFERAELRPL----IVVKKD-GRREPFDREKLRRG----- 69 (156)
T ss_pred CCCCCCCCCC-Ceeeecccccccchhhhhhcccccccccchhheeeeccc----eEECcC-CCcCCCCHHHHHHH-----
Confidence 4699998774 344333333334445555689999999987755554433 222222 466677776 3333
Q ss_pred EeecceeEeCCCCCcceEEehHHHHHHHHHHHHHhh
Q 017546 111 KIPELDFEIPPEAQRGSLSTVEGILVRAADELEALQ 146 (369)
Q Consensus 111 ~IPELd~eI~p~~~~G~iTTVEGlL~~i~~~L~~~~ 146 (369)
|......- .=.-..||.++..|...|.+..
T Consensus 70 ----l~~A~~KR--pVs~e~ie~~v~~ie~~Lr~~g 99 (156)
T COG1327 70 ----LIRACEKR--PVSSEQIEEAVSHIERQLRSSG 99 (156)
T ss_pred ----HHHHHhcC--CCCHHHHHHHHHHHHHHHHhcC
Confidence 11111110 0012268888888888887643
No 49
>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=79.80 E-value=2.8 Score=32.77 Aligned_cols=34 Identities=24% Similarity=0.579 Sum_probs=21.0
Q ss_pred cCccCcccc-c---ce------eEEEecCCCCeEEEEEeeCCCCCCC
Q 017546 287 TCGACAASC-E---TR------MFMTRIPYFQEVIVMASTCDACGYR 323 (369)
Q Consensus 287 ~Cp~C~~~~-~---~~------m~~~~IP~F~eviims~~C~~CGyk 323 (369)
.||.||..- + .+ .++.+|.+= . -.+.+|.+|||-
T Consensus 2 ~C~KCg~~~~e~~~v~~tgg~~skiFdvq~~-~--f~~v~C~~CGYT 45 (64)
T PF09855_consen 2 KCPKCGNEEYESGEVRATGGGLSKIFDVQNK-K--FTTVSCTNCGYT 45 (64)
T ss_pred CCCCCCCcceecceEEccCCeeEEEEEecCc-E--EEEEECCCCCCE
Confidence 599998652 1 11 144566662 2 345679999995
No 50
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=79.72 E-value=1.9 Score=38.39 Aligned_cols=32 Identities=22% Similarity=0.681 Sum_probs=23.4
Q ss_pred ccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCcc
Q 017546 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNS 325 (369)
Q Consensus 286 ~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~ 325 (369)
+.||.|+.+ .|.+..- +. ++...|..||++..
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 569999998 5665331 44 56779999999864
No 51
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=79.67 E-value=1.6 Score=37.43 Aligned_cols=41 Identities=24% Similarity=0.455 Sum_probs=26.6
Q ss_pred eccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCccc
Q 017546 285 PSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSE 326 (369)
Q Consensus 285 ~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~e 326 (369)
...||.||.. +....+.++=--.+=.-..+.|.+|||+.++
T Consensus 72 ~~~CpkCg~~-ea~y~~~QtRsaDEp~T~Fy~C~~Cg~~wre 112 (113)
T COG1594 72 KEKCPKCGNK-EAYYWQLQTRSADEPETRFYKCTRCGYRWRE 112 (113)
T ss_pred cccCCCCCCc-eeEEEeeehhccCCCceEEEEecccCCEeec
Confidence 4579999876 2233344444434444556899999999875
No 52
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=79.46 E-value=0.81 Score=37.89 Aligned_cols=41 Identities=17% Similarity=0.391 Sum_probs=28.7
Q ss_pred ceeeeeccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCccccccCCccCC
Q 017546 280 EVMTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRIPE 335 (369)
Q Consensus 280 ev~~~~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~eVk~~g~~~~ 335 (369)
+.+.-...||.|+++.. +.+--=-|.|.+|||++. ||+..|
T Consensus 30 ~~~~~~~~Cp~C~~~~V-----------kR~a~GIW~C~kCg~~fA----Ggay~P 70 (89)
T COG1997 30 AQQRAKHVCPFCGRTTV-----------KRIATGIWKCRKCGAKFA----GGAYTP 70 (89)
T ss_pred HHHhcCCcCCCCCCcce-----------eeeccCeEEcCCCCCeec----cccccc
Confidence 45566778999998843 233334589999999874 666655
No 53
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=79.38 E-value=0.73 Score=34.27 Aligned_cols=30 Identities=37% Similarity=0.740 Sum_probs=18.9
Q ss_pred EeccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCc
Q 017546 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (369)
Q Consensus 30 ies~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrn 70 (369)
..=.|+.||+.- .+ .-..+-..|++||||-
T Consensus 5 ~~Y~C~~Cg~~~---~~--------~~~~~~irCp~Cg~rI 34 (49)
T COG1996 5 MEYKCARCGREV---EL--------DQETRGIRCPYCGSRI 34 (49)
T ss_pred EEEEhhhcCCee---eh--------hhccCceeCCCCCcEE
Confidence 445799998763 00 1123447899999873
No 54
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=79.28 E-value=0.93 Score=34.95 Aligned_cols=28 Identities=32% Similarity=0.734 Sum_probs=17.7
Q ss_pred cCccCccccccee---EEEecCCCCeEEEEEeeCCCCCCC
Q 017546 287 TCGACAASCETRM---FMTRIPYFQEVIVMASTCDACGYR 323 (369)
Q Consensus 287 ~Cp~C~~~~~~~m---~~~~IP~F~eviims~~C~~CGyk 323 (369)
.||+||+....+= -....|| .|++|||.
T Consensus 27 ~CPnCG~~~I~RC~~CRk~~~~Y---------~CP~CGF~ 57 (59)
T PRK14890 27 LCPNCGEVIIYRCEKCRKQSNPY---------TCPKCGFE 57 (59)
T ss_pred eCCCCCCeeEeechhHHhcCCce---------ECCCCCCc
Confidence 6899987643332 2233444 89999985
No 55
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=79.18 E-value=2.2 Score=29.83 Aligned_cols=29 Identities=28% Similarity=0.600 Sum_probs=18.7
Q ss_pred cCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCc
Q 017546 287 TCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRN 324 (369)
Q Consensus 287 ~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~ 324 (369)
+||.|+..+. .+.+ ++ +..-.|++||--.
T Consensus 1 ~CP~C~~~l~----~~~~---~~--~~id~C~~C~G~W 29 (41)
T PF13453_consen 1 KCPRCGTELE----PVRL---GD--VEIDVCPSCGGIW 29 (41)
T ss_pred CcCCCCcccc----eEEE---CC--EEEEECCCCCeEE
Confidence 5999987533 3333 44 4556799998543
No 56
>PRK14292 chaperone protein DnaJ; Provisional
Probab=78.87 E-value=14 Score=37.51 Aligned_cols=33 Identities=27% Similarity=0.495 Sum_probs=19.3
Q ss_pred ccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCC
Q 017546 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCG 67 (369)
Q Consensus 32 s~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CG 67 (369)
..|+.|+..|..++....+|.+ + -+...|+.|+
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 3466666666555555555533 2 3456788883
No 57
>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=78.56 E-value=2.5 Score=29.38 Aligned_cols=37 Identities=30% Similarity=0.566 Sum_probs=19.4
Q ss_pred CccCccc-ccceeEEEecCCCCeEEEE----EeeCCCCCCCc
Q 017546 288 CGACAAS-CETRMFMTRIPYFQEVIVM----ASTCDACGYRN 324 (369)
Q Consensus 288 Cp~C~~~-~~~~m~~~~IP~F~eviim----s~~C~~CGyk~ 324 (369)
||.|+.. .......+.+=|=+..++. ++.|++||-..
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~~~~~~i~~vp~~~C~~CGE~~ 42 (46)
T TIGR03831 1 CPICGGEELEGKTTTETYEYGGELIVIENVPALVCPQCGEEY 42 (46)
T ss_pred CCCCCCceecceEEEEEEEeCCEEEEEeCCCccccccCCCEe
Confidence 9999643 3333322222222333333 56799999654
No 58
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=78.22 E-value=1.9 Score=37.35 Aligned_cols=15 Identities=27% Similarity=0.255 Sum_probs=11.8
Q ss_pred ehHHHHHHHHHHHHH
Q 017546 130 TVEGILVRAADELEA 144 (369)
Q Consensus 130 TVEGlL~~i~~~L~~ 144 (369)
||-.-|.+++..|..
T Consensus 65 TvR~rLd~ii~~lg~ 79 (113)
T PF09862_consen 65 TVRNRLDKIIEKLGY 79 (113)
T ss_pred HHHHHHHHHHHHhCC
Confidence 777888888888775
No 59
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=78.18 E-value=2.6 Score=33.17 Aligned_cols=37 Identities=19% Similarity=0.468 Sum_probs=20.4
Q ss_pred ccCccCcccccceeEEEecC--CCCeEE------EEEeeCCCCCCC
Q 017546 286 STCGACAASCETRMFMTRIP--YFQEVI------VMASTCDACGYR 323 (369)
Q Consensus 286 ~~Cp~C~~~~~~~m~~~~IP--~F~evi------ims~~C~~CGyk 323 (369)
..||.||..- ...+.+..| .+..++ -.+..|.+|||.
T Consensus 5 ~kCpKCgn~~-~~ekei~~tg~~lskifdvq~n~f~~itCk~CgYt 49 (68)
T COG3478 5 FKCPKCGNTN-YEEKEIAATGGGLSKIFDVQNNKFIVITCKNCGYT 49 (68)
T ss_pred ccCCCcCCcc-hhhceeeccCCCcceeEEecccEEEEEEeccCCch
Confidence 3599998652 222333333 122222 245689999994
No 60
>PRK14284 chaperone protein DnaJ; Provisional
Probab=78.15 E-value=13 Score=38.15 Aligned_cols=26 Identities=35% Similarity=0.602 Sum_probs=16.8
Q ss_pred eEEEeecc------eeEeCCCCCcceEEehHH
Q 017546 108 ATIKIPEL------DFEIPPEAQRGSLSTVEG 133 (369)
Q Consensus 108 ati~IPEL------d~eI~p~~~~G~iTTVEG 133 (369)
++++||-| .+.||++++.|..-.|.|
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 45566544 367777777777776664
No 61
>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=77.58 E-value=1.4 Score=33.70 Aligned_cols=30 Identities=23% Similarity=0.520 Sum_probs=21.1
Q ss_pred eccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCcc
Q 017546 285 PSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNS 325 (369)
Q Consensus 285 ~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~ 325 (369)
...||.||..... ..---.+.|++||+..+
T Consensus 28 Sq~C~~CG~~~~~-----------~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 28 SQTCPRCGHRNKK-----------RRSGRVFTCPNCGFEMD 57 (69)
T ss_pred ccCccCccccccc-----------ccccceEEcCCCCCEEC
Confidence 4569999987643 23334689999999643
No 62
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=77.35 E-value=1.3 Score=37.46 Aligned_cols=33 Identities=21% Similarity=0.435 Sum_probs=19.8
Q ss_pred ccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCccc
Q 017546 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSE 326 (369)
Q Consensus 286 ~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~e 326 (369)
..||.||+.. . .+.|.. -+-..+|.+|||...-
T Consensus 22 f~CP~Cge~~-v---~v~~~k----~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 22 FECPRCGKVS-I---SVKIKK----NIAIITCGNCGLYTEF 54 (99)
T ss_pred eECCCCCCeE-e---eeecCC----CcceEECCCCCCccCE
Confidence 4699999531 1 111111 2556799999987543
No 63
>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=77.07 E-value=3 Score=28.95 Aligned_cols=35 Identities=29% Similarity=0.550 Sum_probs=19.2
Q ss_pred CCCCCCCc---eEEEEEeecCCcceEEE---EEeeCCCCCCC
Q 017546 34 CMRCGENG---VTRFLLTLIPHFRKVLL---SAFECPHCGER 69 (369)
Q Consensus 34 Cp~Cg~~g---~tr~llt~IP~FkeiiI---mSf~C~~CGyr 69 (369)
||.|+... .++.+.+.. -=+-++| -++.|++||-.
T Consensus 1 C~~C~~~~~~~~~~~~~~~~-~~~~~~i~~vp~~~C~~CGE~ 41 (46)
T TIGR03831 1 CPICGGEELEGKTTTETYEY-GGELIVIENVPALVCPQCGEE 41 (46)
T ss_pred CCCCCCceecceEEEEEEEe-CCEEEEEeCCCccccccCCCE
Confidence 89996443 233333333 2233334 24679999964
No 64
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=76.89 E-value=2.1 Score=37.09 Aligned_cols=21 Identities=29% Similarity=0.893 Sum_probs=17.1
Q ss_pred CccCcccccceeEEEecCCCCeEEEEEeeCCCCCCC
Q 017546 288 CGACAASCETRMFMTRIPYFQEVIVMASTCDACGYR 323 (369)
Q Consensus 288 Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk 323 (369)
||+||++ .++....|++||-.
T Consensus 1 CPvCg~~---------------l~vt~l~C~~C~t~ 21 (113)
T PF09862_consen 1 CPVCGGE---------------LVVTRLKCPSCGTE 21 (113)
T ss_pred CCCCCCc---------------eEEEEEEcCCCCCE
Confidence 9999965 46788899999854
No 65
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=76.57 E-value=2.6 Score=36.12 Aligned_cols=30 Identities=27% Similarity=0.738 Sum_probs=22.3
Q ss_pred ccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCC
Q 017546 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYR 323 (369)
Q Consensus 286 ~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk 323 (369)
+.||.|+.+ +|.+..- +. ++...|..||++
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 469999999 6666443 33 456789999985
No 66
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=76.05 E-value=1.5 Score=38.81 Aligned_cols=36 Identities=25% Similarity=0.529 Sum_probs=25.9
Q ss_pred eccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCccccccCCcc
Q 017546 285 PSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRI 333 (369)
Q Consensus 285 ~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~eVk~~g~~ 333 (369)
...||.||.|+.-+ =|+| .|+.||||..=|+.-..-
T Consensus 28 ~~hCp~Cg~PLF~K--------dG~v-----~CPvC~~~~~~v~~e~~~ 63 (131)
T COG1645 28 AKHCPKCGTPLFRK--------DGEV-----FCPVCGYREVVVEEEEEE 63 (131)
T ss_pred HhhCcccCCcceee--------CCeE-----ECCCCCceEEEeeccccc
Confidence 55799999886542 2665 599999988777655443
No 67
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=76.02 E-value=2.3 Score=30.60 Aligned_cols=11 Identities=36% Similarity=0.981 Sum_probs=9.2
Q ss_pred EeeCCCCCCCc
Q 017546 60 AFECPHCGERN 70 (369)
Q Consensus 60 Sf~C~~CGyrn 70 (369)
-+.|++|||..
T Consensus 20 ~~vC~~Cg~~~ 30 (52)
T smart00661 20 RFVCRKCGYEE 30 (52)
T ss_pred EEECCcCCCeE
Confidence 57899999964
No 68
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=75.34 E-value=1.3 Score=38.27 Aligned_cols=42 Identities=19% Similarity=0.429 Sum_probs=27.4
Q ss_pred EEeccCCCCCCCce-EEEEEeecCCcceEEEEEeeCCCCCCCccc
Q 017546 29 QVESLCMRCGENGV-TRFLLTLIPHFRKVLLSAFECPHCGERNNE 72 (369)
Q Consensus 29 eies~Cp~Cg~~g~-tr~llt~IP~FkeiiImSf~C~~CGyrnnE 72 (369)
.|+-.||.||.... +..+.++=- .|==-.-+.|+.|+||.+|
T Consensus 72 ~I~~kCpkCghe~m~Y~T~QlRSA--DEGQTVFYTC~kC~~k~~e 114 (116)
T KOG2907|consen 72 VIKHKCPKCGHEEMSYHTLQLRSA--DEGQTVFYTCPKCKYKFTE 114 (116)
T ss_pred chhccCcccCCchhhhhhhhcccc--cCCceEEEEcCccceeeec
Confidence 58899999998764 233333322 2222334899999999875
No 69
>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=74.95 E-value=5.5 Score=32.93 Aligned_cols=43 Identities=19% Similarity=0.385 Sum_probs=27.5
Q ss_pred EEeccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccc
Q 017546 29 QVESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNE 72 (369)
Q Consensus 29 eies~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnE 72 (369)
.+...||.||.+...-+ ...+---.|=.-.-|.|..|||+-.|
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 35789999997754222 12222234555566999999998654
No 70
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=74.78 E-value=3.6 Score=31.89 Aligned_cols=9 Identities=33% Similarity=1.180 Sum_probs=7.2
Q ss_pred eeCCCCCCC
Q 017546 315 STCDACGYR 323 (369)
Q Consensus 315 ~~C~~CGyk 323 (369)
..|++|||+
T Consensus 51 Y~Cp~CGF~ 59 (61)
T COG2888 51 YRCPKCGFE 59 (61)
T ss_pred eECCCcCcc
Confidence 479999985
No 71
>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=74.75 E-value=1.8 Score=32.55 Aligned_cols=22 Identities=45% Similarity=1.056 Sum_probs=17.5
Q ss_pred ccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCC
Q 017546 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGER 69 (369)
Q Consensus 32 s~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyr 69 (369)
+.||+||+ ..+|| ..|++|||=
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 67999985 45688 899999853
No 72
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=74.69 E-value=1.4 Score=31.89 Aligned_cols=26 Identities=35% Similarity=0.825 Sum_probs=17.1
Q ss_pred cCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCc
Q 017546 287 TCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRN 324 (369)
Q Consensus 287 ~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~ 324 (369)
.|..||...... --....|.+||||.
T Consensus 4 ~C~~Cg~~~~~~------------~~~~irC~~CG~rI 29 (44)
T smart00659 4 ICGECGRENEIK------------SKDVVRCRECGYRI 29 (44)
T ss_pred ECCCCCCEeecC------------CCCceECCCCCceE
Confidence 588888764332 12457888888874
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=74.45 E-value=2.4 Score=35.62 Aligned_cols=39 Identities=23% Similarity=0.350 Sum_probs=23.7
Q ss_pred CccCcc-cccceeEEEecCCCCe---EEEEEeeCCCCCCCccc
Q 017546 288 CGACAA-SCETRMFMTRIPYFQE---VIVMASTCDACGYRNSE 326 (369)
Q Consensus 288 Cp~C~~-~~~~~m~~~~IP~F~e---viims~~C~~CGyk~~e 326 (369)
||.||+ .+......+.+.|=|. |.+-.+.|+.||-..-+
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~G~~~~v~~~~~~C~~CGe~~~~ 43 (127)
T TIGR03830 1 CPICGSGELVRDVKDEPYTYKGESITIGVPGWYCPACGEELLD 43 (127)
T ss_pred CCCCCCccceeeeecceEEEcCEEEEEeeeeeECCCCCCEEEc
Confidence 999985 4443444444444444 23357899999965433
No 74
>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=74.41 E-value=2 Score=32.87 Aligned_cols=29 Identities=31% Similarity=0.738 Sum_probs=19.7
Q ss_pred eccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCc
Q 017546 31 ESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (369)
Q Consensus 31 es~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrn 70 (369)
...||.||..... ..---.|.|++||+..
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 4569999976544 1122349999999963
No 75
>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=74.37 E-value=2.9 Score=29.20 Aligned_cols=36 Identities=28% Similarity=0.566 Sum_probs=20.7
Q ss_pred cCCCCCCCceEEE-EEeecCCcceEEEEEeeCCCCCCCc
Q 017546 33 LCMRCGENGVTRF-LLTLIPHFRKVLLSAFECPHCGERN 70 (369)
Q Consensus 33 ~Cp~Cg~~g~tr~-llt~IP~FkeiiImSf~C~~CGyrn 70 (369)
.||+||.+...-+ ..++= =.|=...-|.|-.||++-
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 5999998754332 33332 345556668899999863
No 76
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=73.74 E-value=3.8 Score=35.20 Aligned_cols=40 Identities=25% Similarity=0.442 Sum_probs=27.1
Q ss_pred eccCCCCCCCc-eEEEEEeecCCcceEEEEEeeCCCCCCCccc
Q 017546 31 ESLCMRCGENG-VTRFLLTLIPHFRKVLLSAFECPHCGERNNE 72 (369)
Q Consensus 31 es~Cp~Cg~~g-~tr~llt~IP~FkeiiImSf~C~~CGyrnnE 72 (369)
.-.||.||.+- ...++.++= =.|=.-..+.|.+|||+-++
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 34799999764 345555553 34444556999999998764
No 77
>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=73.21 E-value=3.1 Score=44.68 Aligned_cols=46 Identities=13% Similarity=0.153 Sum_probs=30.8
Q ss_pred eeeeccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCcccc
Q 017546 282 MTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSEL 327 (369)
Q Consensus 282 ~~~~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~eV 327 (369)
..|-..||.||..-...+..+..|.=..-=-..+.|++||....|-
T Consensus 197 r~~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e~ 242 (557)
T PF05876_consen 197 RRYYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEEH 242 (557)
T ss_pred eEEEccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCHH
Confidence 3889999999988665544333332001223467899999999884
No 78
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=73.19 E-value=1.7 Score=32.24 Aligned_cols=32 Identities=25% Similarity=0.506 Sum_probs=20.5
Q ss_pred eeeeeccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCc
Q 017546 281 VMTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRN 324 (369)
Q Consensus 281 v~~~~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~ 324 (369)
|.....-||.||.. -| .++. -.+.|.+|||..
T Consensus 16 v~~~~~fCP~Cg~~---~m----~~~~-----~r~~C~~Cgyt~ 47 (50)
T PRK00432 16 VKRKNKFCPRCGSG---FM----AEHL-----DRWHCGKCGYTE 47 (50)
T ss_pred EEEccCcCcCCCcc---hh----eccC-----CcEECCCcCCEE
Confidence 33344579999974 11 2333 367899999963
No 79
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=73.06 E-value=1 Score=40.03 Aligned_cols=31 Identities=29% Similarity=0.603 Sum_probs=19.3
Q ss_pred EeccCCCCCCCceEEEEEeecCCcceEEEE-----EeeCCCCCCCc
Q 017546 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLS-----AFECPHCGERN 70 (369)
Q Consensus 30 ies~Cp~Cg~~g~tr~llt~IP~FkeiiIm-----Sf~C~~CGyrn 70 (369)
..-.||+||..-+ |-|.+.. .|.||+||..=
T Consensus 98 ~~Y~Cp~C~~~y~----------~~ea~~~~d~~~~f~Cp~Cg~~l 133 (147)
T smart00531 98 AYYKCPNCQSKYT----------FLEANQLLDMDGTFTCPRCGEEL 133 (147)
T ss_pred cEEECcCCCCEee----------HHHHHHhcCCCCcEECCCCCCEE
Confidence 3456999984321 2233322 39999999754
No 80
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=72.55 E-value=2.8 Score=35.41 Aligned_cols=32 Identities=25% Similarity=0.584 Sum_probs=19.4
Q ss_pred ccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCcc
Q 017546 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNN 71 (369)
Q Consensus 32 s~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnn 71 (369)
..||+||+.. ... +|. + -+-.-.|+.|||.+.
T Consensus 22 f~CP~Cge~~-v~v---~~~--k--~~~h~~C~~CG~y~~ 53 (99)
T PRK14892 22 FECPRCGKVS-ISV---KIK--K--NIAIITCGNCGLYTE 53 (99)
T ss_pred eECCCCCCeE-eee---ecC--C--CcceEECCCCCCccC
Confidence 4599999532 111 111 1 244589999999764
No 81
>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=72.47 E-value=1.8 Score=37.06 Aligned_cols=36 Identities=25% Similarity=0.472 Sum_probs=25.7
Q ss_pred eccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccceeeCccc
Q 017546 31 ESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEI 79 (369)
Q Consensus 31 es~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEVq~~g~i 79 (369)
...|.+||+.... +.+ .|.||+||-.+-+|..|.+.
T Consensus 70 ~~~C~~Cg~~~~~-------~~~------~~~CP~Cgs~~~~i~~G~El 105 (115)
T TIGR00100 70 ECECEDCSEEVSP-------EID------LYRCPKCHGIMLQVRAGKEL 105 (115)
T ss_pred EEEcccCCCEEec-------CCc------CccCcCCcCCCcEEecCCeE
Confidence 4779999954321 111 47899999988888877665
No 82
>PHA02998 RNA polymerase subunit; Provisional
Probab=71.84 E-value=4.9 Score=37.51 Aligned_cols=42 Identities=17% Similarity=0.389 Sum_probs=30.7
Q ss_pred eeccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCccc
Q 017546 284 FPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSE 326 (369)
Q Consensus 284 ~~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~e 326 (369)
....||.|++. .....+.++=--.|=...-+.|..||++..-
T Consensus 142 t~v~CPkCg~~-~A~f~qlQTRSADEPmT~FYkC~~CG~~wkp 183 (195)
T PHA02998 142 YNTPCPNCKSK-NTTPMMIQTRAADEPPLVRHACRDCKKHFKP 183 (195)
T ss_pred cCCCCCCCCCC-ceEEEEEeeccCCCCceEEEEcCCCCCccCC
Confidence 46799999876 3344455565556777778899999998753
No 83
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=71.52 E-value=5.7 Score=27.74 Aligned_cols=27 Identities=30% Similarity=0.661 Sum_probs=17.1
Q ss_pred cCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCC
Q 017546 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGE 68 (369)
Q Consensus 33 ~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGy 68 (369)
.||.|+.....+ .+ .+ +....|++||-
T Consensus 1 ~CP~C~~~l~~~----~~---~~--~~id~C~~C~G 27 (41)
T PF13453_consen 1 KCPRCGTELEPV----RL---GD--VEIDVCPSCGG 27 (41)
T ss_pred CcCCCCcccceE----EE---CC--EEEEECCCCCe
Confidence 499998643322 22 45 44577999984
No 84
>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=71.25 E-value=2.6 Score=36.12 Aligned_cols=39 Identities=13% Similarity=0.306 Sum_probs=27.3
Q ss_pred eeeccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCccccccCCccC
Q 017546 283 TFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRIP 334 (369)
Q Consensus 283 ~~~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~eVk~~g~~~ 334 (369)
.....|+.||+... ++.+ .+.|++||-..-+|..|....
T Consensus 68 p~~~~C~~Cg~~~~-------~~~~------~~~CP~Cgs~~~~i~~G~El~ 106 (115)
T TIGR00100 68 PVECECEDCSEEVS-------PEID------LYRCPKCHGIMLQVRAGKELN 106 (115)
T ss_pred CcEEEcccCCCEEe-------cCCc------CccCcCCcCCCcEEecCCeEE
Confidence 44678999996532 2221 468999999888887776543
No 85
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=71.08 E-value=1.9 Score=32.82 Aligned_cols=24 Identities=38% Similarity=0.825 Sum_probs=17.3
Q ss_pred cCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCc
Q 017546 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (369)
Q Consensus 33 ~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrn 70 (369)
+||.|++.. -.-..|.||.||+-.
T Consensus 1 ~Cpv~~~~~--------------~~~v~~~Cp~cGipt 24 (55)
T PF13824_consen 1 LCPVCKKDL--------------PAHVNFECPDCGIPT 24 (55)
T ss_pred CCCCCcccc--------------ccccCCcCCCCCCcC
Confidence 588887754 233569999999854
No 86
>KOG2846 consensus Predicted membrane protein [Function unknown]
Probab=69.91 E-value=2.1 Score=43.12 Aligned_cols=39 Identities=28% Similarity=0.616 Sum_probs=28.5
Q ss_pred EEeccCCCCC-CCceEEEEEeecCCcceEEEEEeeCCCCCCCccceee
Q 017546 29 QVESLCMRCG-ENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQF 75 (369)
Q Consensus 29 eies~Cp~Cg-~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEVq~ 75 (369)
-.--.|.+|+ +||..+. -.-|| .+|.|+||+..|-..+.
T Consensus 218 ryALIC~~C~~HNGla~~--ee~~y------i~F~C~~Cn~LN~~~k~ 257 (328)
T KOG2846|consen 218 RYALICSQCHHHNGLARK--EEYEY------ITFRCPHCNALNPAKKS 257 (328)
T ss_pred hhhhcchhhccccCcCCh--hhcCc------eEEECccccccCCCcCC
Confidence 3456799997 6887664 23333 57999999999987766
No 87
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=69.73 E-value=2.1 Score=36.69 Aligned_cols=37 Identities=16% Similarity=0.381 Sum_probs=24.0
Q ss_pred eccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccceeeCccc
Q 017546 31 ESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEI 79 (369)
Q Consensus 31 es~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEVq~~g~i 79 (369)
...|+.||+. +.++ -...|.||+||-.+-++..|.++
T Consensus 70 ~~~C~~Cg~~-------~~~~-----~~~~~~CP~Cgs~~~~i~~G~El 106 (114)
T PRK03681 70 ECWCETCQQY-------VTLL-----TQRVRRCPQCHGDMLRIVADDGL 106 (114)
T ss_pred EEEcccCCCe-------eecC-----CccCCcCcCcCCCCcEEccCCeE
Confidence 4679999952 1111 00116899999888888766554
No 88
>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=69.41 E-value=4.4 Score=34.02 Aligned_cols=36 Identities=25% Similarity=0.490 Sum_probs=20.6
Q ss_pred CCCCCC-CceEEEEEeecCCcce---EEEEEeeCCCCCCC
Q 017546 34 CMRCGE-NGVTRFLLTLIPHFRK---VLLSAFECPHCGER 69 (369)
Q Consensus 34 Cp~Cg~-~g~tr~llt~IP~Fke---iiImSf~C~~CGyr 69 (369)
||.|++ ..........+.|=++ |.+-.+.|+.||-.
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~G~~~~v~~~~~~C~~CGe~ 40 (127)
T TIGR03830 1 CPICGSGELVRDVKDEPYTYKGESITIGVPGWYCPACGEE 40 (127)
T ss_pred CCCCCCccceeeeecceEEEcCEEEEEeeeeeECCCCCCE
Confidence 999985 3333333333334333 23356889999873
No 89
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=69.39 E-value=2.9 Score=35.96 Aligned_cols=41 Identities=15% Similarity=0.403 Sum_probs=27.2
Q ss_pred eeeccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCccccccCCccCC
Q 017546 283 TFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRIPE 335 (369)
Q Consensus 283 ~~~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~eVk~~g~~~~ 335 (369)
.....|+.||........ ..+.|++||-..-++..|....=
T Consensus 69 p~~~~C~~Cg~~~~~~~~------------~~~~CP~Cgs~~~~i~~G~El~I 109 (117)
T PRK00564 69 KVELECKDCSHVFKPNAL------------DYGVCEKCHSKNVIITQGNEMRL 109 (117)
T ss_pred CCEEEhhhCCCccccCCc------------cCCcCcCCCCCceEEecCCEEEE
Confidence 346789999965432211 11459999999888887766543
No 90
>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=69.12 E-value=2.7 Score=26.86 Aligned_cols=10 Identities=50% Similarity=1.341 Sum_probs=7.2
Q ss_pred EEeeCCCCCC
Q 017546 59 SAFECPHCGE 68 (369)
Q Consensus 59 mSf~C~~CGy 68 (369)
..|.||+||+
T Consensus 15 v~f~CPnCG~ 24 (24)
T PF07754_consen 15 VPFPCPNCGF 24 (24)
T ss_pred ceEeCCCCCC
Confidence 3578888875
No 91
>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=68.57 E-value=4.7 Score=31.14 Aligned_cols=34 Identities=18% Similarity=0.506 Sum_probs=23.9
Q ss_pred ccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccc
Q 017546 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNE 72 (369)
Q Consensus 32 s~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnE 72 (369)
..||.|+..-+.+|... -=+-.-+|-.|||+...
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 46999999877766432 22234789999998753
No 92
>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=67.81 E-value=3.8 Score=35.86 Aligned_cols=31 Identities=23% Similarity=0.633 Sum_probs=22.6
Q ss_pred ccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCc
Q 017546 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRN 324 (369)
Q Consensus 286 ~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~ 324 (369)
+.||.|+.+ +|.+..- +.+ +...|..||.+.
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 579999998 5666443 444 456899999874
No 93
>PHA02942 putative transposase; Provisional
Probab=67.68 E-value=3.1 Score=42.67 Aligned_cols=31 Identities=35% Similarity=0.856 Sum_probs=19.6
Q ss_pred ccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCC-cccee
Q 017546 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGER-NNEVQ 74 (369)
Q Consensus 32 s~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyr-nnEVq 74 (369)
..||.||.... ++ -=+ .|.|++|||. |.|+-
T Consensus 326 q~Cs~CG~~~~-~l------~~r-----~f~C~~CG~~~drD~n 357 (383)
T PHA02942 326 VSCPKCGHKMV-EI------AHR-----YFHCPSCGYENDRDVI 357 (383)
T ss_pred ccCCCCCCccC-cC------CCC-----EEECCCCCCEeCcHHH
Confidence 55999997532 10 001 5999999995 34443
No 94
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=67.54 E-value=2.9 Score=28.68 Aligned_cols=29 Identities=34% Similarity=0.733 Sum_probs=13.4
Q ss_pred CccCcccccceeEEEecCCCCeEEEEEeeCCCCCCC
Q 017546 288 CGACAASCETRMFMTRIPYFQEVIVMASTCDACGYR 323 (369)
Q Consensus 288 Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk 323 (369)
||.||.+++ ..||-=.+ -.-.+|++|||=
T Consensus 3 C~~CG~~l~-----~~ip~gd~--r~R~vC~~Cg~I 31 (34)
T PF14803_consen 3 CPQCGGPLE-----RRIPEGDD--RERLVCPACGFI 31 (34)
T ss_dssp -TTT--B-E-----EE--TT-S--S-EEEETTTTEE
T ss_pred cccccChhh-----hhcCCCCC--ccceECCCCCCE
Confidence 999999864 34452111 134679999973
No 95
>PRK14297 chaperone protein DnaJ; Provisional
Probab=67.15 E-value=46 Score=33.96 Aligned_cols=26 Identities=31% Similarity=0.749 Sum_probs=17.4
Q ss_pred eEEEeec----ceeEeCCCCCcceEEehHH
Q 017546 108 ATIKIPE----LDFEIPPEAQRGSLSTVEG 133 (369)
Q Consensus 108 ati~IPE----Ld~eI~p~~~~G~iTTVEG 133 (369)
++++||- +.+.||++++.|....|.|
T Consensus 289 ~~~~i~~ldg~~~v~ip~g~~~g~~~ri~g 318 (380)
T PRK14297 289 TEIKVPTVDGEVKYEVPAGTQPGTVFRLKG 318 (380)
T ss_pred CcEEEEcCCCcEEEEECCCcCCCCEEEEcC
Confidence 4455665 4577888777777776655
No 96
>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=66.00 E-value=6.8 Score=29.63 Aligned_cols=30 Identities=27% Similarity=0.568 Sum_probs=19.3
Q ss_pred ccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCc
Q 017546 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (369)
Q Consensus 32 s~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrn 70 (369)
..||.||+.- -+ .=+.-+++| .|+.||-.-
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 4699999732 11 223346765 899999854
No 97
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=65.99 E-value=4.7 Score=34.70 Aligned_cols=37 Identities=19% Similarity=0.308 Sum_probs=24.9
Q ss_pred eccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccceeeCccc
Q 017546 31 ESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEI 79 (369)
Q Consensus 31 es~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEVq~~g~i 79 (369)
...|..||......- + ..+.||+||-.+-+|..|.++
T Consensus 71 ~~~C~~Cg~~~~~~~-------~-----~~~~CP~Cgs~~~~i~~G~El 107 (117)
T PRK00564 71 ELECKDCSHVFKPNA-------L-----DYGVCEKCHSKNVIITQGNEM 107 (117)
T ss_pred EEEhhhCCCccccCC-------c-----cCCcCcCCCCCceEEecCCEE
Confidence 367999995532211 0 114599999999888877765
No 98
>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=65.82 E-value=4.5 Score=29.00 Aligned_cols=27 Identities=22% Similarity=0.679 Sum_probs=18.7
Q ss_pred cCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCC
Q 017546 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGER 69 (369)
Q Consensus 33 ~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyr 69 (369)
.||.||....+++-- ...|.|.+|+++
T Consensus 20 ~CP~Cg~~~~~~~~~----------~~~~~C~~C~~q 46 (46)
T PF12760_consen 20 VCPHCGSTKHYRLKT----------RGRYRCKACRKQ 46 (46)
T ss_pred CCCCCCCeeeEEeCC----------CCeEECCCCCCc
Confidence 499999773333322 556999999874
No 99
>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=65.74 E-value=4.4 Score=31.30 Aligned_cols=34 Identities=29% Similarity=0.657 Sum_probs=22.8
Q ss_pred eccCccCcccccceeE-EEecCCCCeEEEEEeeCCCCCCCccc
Q 017546 285 PSTCGACAASCETRMF-MTRIPYFQEVIVMASTCDACGYRNSE 326 (369)
Q Consensus 285 ~~~Cp~C~~~~~~~m~-~~~IP~F~eviims~~C~~CGyk~~e 326 (369)
-+.||.|+..=...|. .-++ -...|-.|||+..-
T Consensus 9 GA~CP~C~~~Dtl~~~~e~~~--------e~vECv~Cg~~~~~ 43 (59)
T TIGR02443 9 GAVCPACSAQDTLAMWKENNI--------ELVECVECGYQEQQ 43 (59)
T ss_pred cccCCCCcCccEEEEEEeCCc--------eEEEeccCCCcccc
Confidence 3579999987555553 2223 23679999998754
No 100
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=65.48 E-value=4.7 Score=34.20 Aligned_cols=30 Identities=20% Similarity=0.398 Sum_probs=22.2
Q ss_pred cCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCcc
Q 017546 287 TCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNS 325 (369)
Q Consensus 287 ~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~ 325 (369)
-||.||..+...- ++. -+.|.|..|+|-++
T Consensus 3 FCP~Cgn~Live~--------g~~-~~rf~C~tCpY~~~ 32 (105)
T KOG2906|consen 3 FCPTCGNMLIVES--------GES-CNRFSCRTCPYVFP 32 (105)
T ss_pred ccCCCCCEEEEec--------CCe-EeeEEcCCCCceee
Confidence 3999996653322 444 79999999999765
No 101
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=64.86 E-value=3.1 Score=35.55 Aligned_cols=36 Identities=19% Similarity=0.492 Sum_probs=24.3
Q ss_pred eccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccceeeCccc
Q 017546 31 ESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEI 79 (369)
Q Consensus 31 es~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEVq~~g~i 79 (369)
...|..||......- ..|.||+||-.+-+|..|.+.
T Consensus 70 ~~~C~~Cg~~~~~~~-------------~~~~CP~Cgs~~~~i~~G~El 105 (113)
T PRK12380 70 QAWCWDCSQVVEIHQ-------------HDAQCPHCHGERLRVDTGDSL 105 (113)
T ss_pred EEEcccCCCEEecCC-------------cCccCcCCCCCCcEEccCCeE
Confidence 467999995432111 225699999888888777654
No 102
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=64.69 E-value=1.8 Score=38.48 Aligned_cols=38 Identities=18% Similarity=0.270 Sum_probs=20.8
Q ss_pred eccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCcccc
Q 017546 285 PSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSEL 327 (369)
Q Consensus 285 ~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~eV 327 (369)
--.||.||...... +.....+- -..|.|++||..--+-
T Consensus 99 ~Y~Cp~C~~~y~~~----ea~~~~d~-~~~f~Cp~Cg~~l~~~ 136 (147)
T smart00531 99 YYKCPNCQSKYTFL----EANQLLDM-DGTFTCPRCGEELEED 136 (147)
T ss_pred EEECcCCCCEeeHH----HHHHhcCC-CCcEECCCCCCEEEEc
Confidence 34699999764321 11111000 1239999999875443
No 103
>PTZ00037 DnaJ_C chaperone protein; Provisional
Probab=64.51 E-value=42 Score=35.07 Aligned_cols=26 Identities=23% Similarity=0.510 Sum_probs=16.8
Q ss_pred eEEEeecce-----eEeCCC--CCcceEEehHH
Q 017546 108 ATIKIPELD-----FEIPPE--AQRGSLSTVEG 133 (369)
Q Consensus 108 ati~IPELd-----~eI~p~--~~~G~iTTVEG 133 (369)
.++.||-|+ +.|||+ ++-|.+-.|.|
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 456677543 566776 67777777655
No 104
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=64.30 E-value=4.3 Score=32.45 Aligned_cols=38 Identities=13% Similarity=0.171 Sum_probs=26.5
Q ss_pred ccCccCcccccceeEEEecCCCCeEEEEEeeCC--CCCCCccc
Q 017546 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCD--ACGYRNSE 326 (369)
Q Consensus 286 ~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~--~CGyk~~e 326 (369)
+.||.||....++--.+--+. +......|. .||+++.-
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~---~~~~Y~qC~N~eCg~tF~t 41 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDT---TKERYHQCQNVNCSATFIT 41 (72)
T ss_pred ccCCCCCCccEEEEChhcChh---hheeeeecCCCCCCCEEEE
Confidence 579999998855543333333 556678998 99998753
No 105
>COG4469 CoiA Competence protein CoiA-like family, contains a predicted nuclease domain [General function prediction only]
Probab=63.84 E-value=2.7 Score=42.59 Aligned_cols=26 Identities=23% Similarity=0.392 Sum_probs=22.8
Q ss_pred eccCccCcccccceeEEEecCCCCeE
Q 017546 285 PSTCGACAASCETRMFMTRIPYFQEV 310 (369)
Q Consensus 285 ~~~Cp~C~~~~~~~m~~~~IP~F~ev 310 (369)
.--||+||+++..+.-...||||--.
T Consensus 25 ~ffCPaC~~~l~lK~G~~k~pHFAHk 50 (342)
T COG4469 25 RFFCPACGSQLILKQGLIKIPHFAHK 50 (342)
T ss_pred ccccCCCCCeeeeecCccccchhhhh
Confidence 45799999999999999999999654
No 106
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=63.56 E-value=7.4 Score=28.99 Aligned_cols=33 Identities=18% Similarity=0.328 Sum_probs=18.1
Q ss_pred cCccCcccccceeEEEecCCCCeEEEEEeeCCCCCC
Q 017546 287 TCGACAASCETRMFMTRIPYFQEVIVMASTCDACGY 322 (369)
Q Consensus 287 ~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGy 322 (369)
.||-||.............+ +.. ....|..||.
T Consensus 5 PCPFCG~~~~~~~~~~~~~~-~~~--~~V~C~~Cga 37 (61)
T PF14354_consen 5 PCPFCGSADVLIRQDEGFDY-GMY--YYVECTDCGA 37 (61)
T ss_pred CCCCCCCcceEeecccCCCC-CCE--EEEEcCCCCC
Confidence 59999876432222111111 111 5667999998
No 107
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=63.39 E-value=5.3 Score=30.42 Aligned_cols=21 Identities=14% Similarity=0.642 Sum_probs=11.7
Q ss_pred cCccCccccccee----EEEecCCC
Q 017546 287 TCGACAASCETRM----FMTRIPYF 307 (369)
Q Consensus 287 ~Cp~C~~~~~~~m----~~~~IP~F 307 (369)
.||.||...-+++ .+-+.|.|
T Consensus 6 ~CP~CgnKTR~kir~DT~LkNfPly 30 (55)
T PF14205_consen 6 LCPICGNKTRLKIREDTVLKNFPLY 30 (55)
T ss_pred ECCCCCCccceeeecCceecccccc
Confidence 4777776544433 35555554
No 108
>PHA02942 putative transposase; Provisional
Probab=63.06 E-value=4.5 Score=41.51 Aligned_cols=28 Identities=25% Similarity=0.641 Sum_probs=18.7
Q ss_pred ccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCcc
Q 017546 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNS 325 (369)
Q Consensus 286 ~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~ 325 (369)
-.||.||.... +.=.. .|.|.+|||..+
T Consensus 326 q~Cs~CG~~~~--------~l~~r----~f~C~~CG~~~d 353 (383)
T PHA02942 326 VSCPKCGHKMV--------EIAHR----YFHCPSCGYEND 353 (383)
T ss_pred ccCCCCCCccC--------cCCCC----EEECCCCCCEeC
Confidence 46999997532 11011 599999999654
No 109
>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=62.99 E-value=2 Score=29.11 Aligned_cols=26 Identities=35% Similarity=0.813 Sum_probs=14.5
Q ss_pred cCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCc
Q 017546 287 TCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRN 324 (369)
Q Consensus 287 ~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~ 324 (369)
.|..||+... |.. ++ ...|.+||||.
T Consensus 2 ~C~~Cg~~~~-------~~~-~~----~irC~~CG~RI 27 (32)
T PF03604_consen 2 ICGECGAEVE-------LKP-GD----PIRCPECGHRI 27 (32)
T ss_dssp BESSSSSSE--------BST-SS----TSSBSSSS-SE
T ss_pred CCCcCCCeeE-------cCC-CC----cEECCcCCCeE
Confidence 4777877643 221 22 24888888874
No 110
>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=62.93 E-value=7.3 Score=41.88 Aligned_cols=94 Identities=17% Similarity=0.250 Sum_probs=49.6
Q ss_pred ceEEeccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccceeeCcccCCcceEEEEEeeCCCcccccceeeeec
Q 017546 27 LYQVESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEIQPRGCNYSLKVPSSDQKMFHRQVVKSE 106 (369)
Q Consensus 27 v~eies~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEVq~~g~i~~kG~r~tL~V~~~~~~DLnR~VvKS~ 106 (369)
...+...||+||+.-..++--.+.|-=..-=-.-+.|+|||..-.|-+-.-.. .+| ++.-. .+ ...+.
T Consensus 196 qr~~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e~~k~~m~-~~G-~Wv~~----~~------~~~~~ 263 (557)
T PF05876_consen 196 QRRYYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEEHDKRRMV-RRG-RWVAT----NP------DRRPR 263 (557)
T ss_pred ceEEEccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCHHHHhhcc-CCe-EEEec----cc------cCCCC
Confidence 34788999999987654432222221001123458999999998875433322 233 22221 22 22222
Q ss_pred ceEEEeecceeEeCCCCCcceEEehHHHHHHHHHH
Q 017546 107 SATIKIPELDFEIPPEAQRGSLSTVEGILVRAADE 141 (369)
Q Consensus 107 ~ati~IPELd~eI~p~~~~G~iTTVEGlL~~i~~~ 141 (369)
+ .+|-|.. .-..+.+-..|..+.++.
T Consensus 264 ~-------~gf~i~~--l~Sp~~sw~~ia~~~l~A 289 (557)
T PF05876_consen 264 H-------VGFHINA--LYSPFVSWAEIAREFLEA 289 (557)
T ss_pred E-------EEEEeee--eecccCCHHHHHHHHHhh
Confidence 3 3444443 122346777777777776
No 111
>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=62.76 E-value=7.3 Score=31.07 Aligned_cols=47 Identities=23% Similarity=0.266 Sum_probs=28.4
Q ss_pred ccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCccccccCCc
Q 017546 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGR 332 (369)
Q Consensus 286 ~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~eVk~~g~ 332 (369)
..||.|+.++..+--.|.=++=..-..+-..|+.||...--+|.=|+
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 36888888866655566666666777788888888887777776665
No 112
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=62.53 E-value=4.7 Score=34.44 Aligned_cols=39 Identities=15% Similarity=0.348 Sum_probs=25.5
Q ss_pred eeeeccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCccccccCCcc
Q 017546 282 MTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRI 333 (369)
Q Consensus 282 ~~~~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~eVk~~g~~ 333 (369)
......|+.||...... . ..+.|++||-..-+|..|...
T Consensus 67 vp~~~~C~~Cg~~~~~~-------~------~~~~CP~Cgs~~~~i~~G~El 105 (113)
T PRK12380 67 KPAQAWCWDCSQVVEIH-------Q------HDAQCPHCHGERLRVDTGDSL 105 (113)
T ss_pred eCcEEEcccCCCEEecC-------C------cCccCcCCCCCCcEEccCCeE
Confidence 34467899999653221 1 223599999888788666543
No 113
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=62.52 E-value=4.4 Score=38.61 Aligned_cols=28 Identities=32% Similarity=0.776 Sum_probs=19.3
Q ss_pred ccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCC-ccceee
Q 017546 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGER-NNEVQF 75 (369)
Q Consensus 32 s~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyr-nnEVq~ 75 (369)
..|+.||. .---.|.|++||+. +.|+-.
T Consensus 310 ~~C~~cg~----------------~~~r~~~C~~cg~~~~rD~na 338 (364)
T COG0675 310 KTCPCCGH----------------LSGRLFKCPRCGFVHDRDVNA 338 (364)
T ss_pred ccccccCC----------------ccceeEECCCCCCeehhhHHH
Confidence 57999998 11345999999995 344433
No 114
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=61.56 E-value=11 Score=32.56 Aligned_cols=41 Identities=22% Similarity=0.439 Sum_probs=24.5
Q ss_pred eccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCccc
Q 017546 285 PSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSE 326 (369)
Q Consensus 285 ~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~e 326 (369)
...||.||..-. -.++..----.+-+-.-++|-+||++..|
T Consensus 73 ~~~C~~C~~~ea-vffQ~~~~r~d~~m~l~yvC~~C~h~wte 113 (113)
T KOG2691|consen 73 DKHCPKCGHREA-VFFQAQTRRADEAMRLFYVCCSCGHRWTE 113 (113)
T ss_pred cccCCccCCcce-EEEecccccccceEEEEEEeccccccccC
Confidence 447999987621 22222222223345556789999999865
No 115
>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=61.36 E-value=7.1 Score=31.06 Aligned_cols=33 Identities=18% Similarity=0.425 Sum_probs=23.3
Q ss_pred ccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCcc
Q 017546 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNN 71 (369)
Q Consensus 32 s~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnn 71 (369)
..||.|+..-+.+|...+ =+---+|=+|||+..
T Consensus 9 a~CP~C~~~D~i~~~~e~-------~ve~vECV~CGy~e~ 41 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWREN-------GVEYVECVECGYTER 41 (71)
T ss_pred ccCCCCcCccEEEEEEeC-------CceEEEecCCCCeec
Confidence 469999988766653332 244578999999764
No 116
>PRK14296 chaperone protein DnaJ; Provisional
Probab=61.28 E-value=51 Score=33.67 Aligned_cols=26 Identities=23% Similarity=0.464 Sum_probs=19.7
Q ss_pred eEEEeecce----eEeCCCCCcceEEehHH
Q 017546 108 ATIKIPELD----FEIPPEAQRGSLSTVEG 133 (369)
Q Consensus 108 ati~IPELd----~eI~p~~~~G~iTTVEG 133 (369)
+++.||-|+ +.||++++-|.+-.|.|
T Consensus 291 ~~~~i~tldG~~~v~ip~~t~~g~~~ri~G 320 (372)
T PRK14296 291 NEIIIKTLDGDIKYKLPKSINSNELIIINN 320 (372)
T ss_pred CEEEeeCCCCCEEEEECCccCCCcEEEEcC
Confidence 577788654 77888888888887754
No 117
>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=61.25 E-value=9.2 Score=30.41 Aligned_cols=34 Identities=26% Similarity=0.530 Sum_probs=22.3
Q ss_pred ccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCccc
Q 017546 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSE 326 (369)
Q Consensus 286 ~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~e 326 (369)
+.||.|++.=...|..-+ =+-.-.|=+|||+..-
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 579999987544443222 1344689999998654
No 118
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=60.32 E-value=2.2 Score=39.39 Aligned_cols=33 Identities=30% Similarity=0.625 Sum_probs=22.3
Q ss_pred eccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccce
Q 017546 31 ESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEV 73 (369)
Q Consensus 31 es~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEV 73 (369)
.-.||+|+..-+ |-|.+-..|.||.||..=.+.
T Consensus 117 ~Y~Cp~C~~ryt----------f~eA~~~~F~Cp~Cg~~L~~~ 149 (178)
T PRK06266 117 FFFCPNCHIRFT----------FDEAMEYGFRCPQCGEMLEEY 149 (178)
T ss_pred EEECCCCCcEEe----------HHHHhhcCCcCCCCCCCCeec
Confidence 346999984321 345555689999999765544
No 119
>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=60.24 E-value=2 Score=38.77 Aligned_cols=34 Identities=21% Similarity=0.434 Sum_probs=22.8
Q ss_pred eccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCcccee
Q 017546 31 ESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQ 74 (369)
Q Consensus 31 es~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEVq 74 (369)
.=.||+|+..-+ |-|.+-..|.||.||..-.+..
T Consensus 109 ~Y~Cp~c~~r~t----------f~eA~~~~F~Cp~Cg~~L~~~d 142 (158)
T TIGR00373 109 FFICPNMCVRFT----------FNEAMELNFTCPRCGAMLDYLD 142 (158)
T ss_pred eEECCCCCcEee----------HHHHHHcCCcCCCCCCEeeecc
Confidence 346999984311 4555556899999997644443
No 120
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=60.10 E-value=6.3 Score=35.89 Aligned_cols=49 Identities=20% Similarity=0.342 Sum_probs=29.9
Q ss_pred ccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCccccccCCccCC
Q 017546 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRIPE 335 (369)
Q Consensus 286 ~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~eVk~~g~~~~ 335 (369)
+.||-|+++ .++..--..--=|.-|==--.|.+||.|++-.-..+-.++
T Consensus 1 M~CPfC~~~-~tkViDSR~~edg~aIRRRReC~~C~~RFTTfE~~El~~~ 49 (156)
T COG1327 1 MKCPFCGHE-DTKVIDSRPAEEGNAIRRRRECLECGERFTTFERAELRPL 49 (156)
T ss_pred CCCCCCCCC-CCeeeecccccccchhhhhhcccccccccchhheeeeccc
Confidence 579999987 3343222222224455555679999999986655554433
No 121
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=60.00 E-value=4.2 Score=42.46 Aligned_cols=48 Identities=13% Similarity=0.160 Sum_probs=29.4
Q ss_pred cccceeeeecceEEEeecceeEeCCCCCcceEEehHHHHHHHHHHHHH
Q 017546 97 MFHRQVVKSESATIKIPELDFEIPPEAQRGSLSTVEGILVRAADELEA 144 (369)
Q Consensus 97 DLnR~VvKS~~ati~IPELd~eI~p~~~~G~iTTVEGlL~~i~~~L~~ 144 (369)
.+.++-.-=-+..|-.-++.+-|||.++.-.+.=|+|.--+....+..
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 444443333333444555677888888888888888876555554443
No 122
>PRK14282 chaperone protein DnaJ; Provisional
Probab=59.75 E-value=41 Score=34.21 Aligned_cols=20 Identities=20% Similarity=0.504 Sum_probs=14.3
Q ss_pred cceeEeCCCCCcceEEehHH
Q 017546 114 ELDFEIPPEAQRGSLSTVEG 133 (369)
Q Consensus 114 ELd~eI~p~~~~G~iTTVEG 133 (369)
.|.+.|||+...|..-.++|
T Consensus 226 ~l~V~Ip~G~~~G~~i~~~g 245 (369)
T PRK14282 226 RTTVKIPAGVEDGTVLRITG 245 (369)
T ss_pred EEEEEeCCCCCCCCEEEEec
Confidence 36677778777777777765
No 123
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=59.58 E-value=4.9 Score=34.42 Aligned_cols=40 Identities=10% Similarity=0.193 Sum_probs=25.5
Q ss_pred eeeeccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCccccccCCcc
Q 017546 282 MTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRI 333 (369)
Q Consensus 282 ~~~~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~eVk~~g~~ 333 (369)
......|+.||.. +.++.+ ..+.|++||-..-++..|.+.
T Consensus 67 ~p~~~~C~~Cg~~-------~~~~~~-----~~~~CP~Cgs~~~~i~~G~El 106 (114)
T PRK03681 67 QEAECWCETCQQY-------VTLLTQ-----RVRRCPQCHGDMLRIVADDGL 106 (114)
T ss_pred eCcEEEcccCCCe-------eecCCc-----cCCcCcCcCCCCcEEccCCeE
Confidence 3446789999963 222211 015799999888888666543
No 124
>PRK14298 chaperone protein DnaJ; Provisional
Probab=59.50 E-value=31 Score=35.33 Aligned_cols=36 Identities=22% Similarity=0.489 Sum_probs=23.0
Q ss_pred ccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCc
Q 017546 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (369)
Q Consensus 32 s~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrn 70 (369)
..|+.|+..|...... ..|+.- +.+...|+.|+=+-
T Consensus 159 ~~C~~C~G~G~~~~~~-~~~~g~--~~~~~~C~~C~G~G 194 (377)
T PRK14298 159 KRCPTCGGTGQVTTTR-STPLGQ--FVTTTTCSTCHGRG 194 (377)
T ss_pred CcCCCCCCccEEEEEE-ecCcee--EEEEEeCCCCCCCC
Confidence 4577777777544433 356543 35888999997654
No 125
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=59.29 E-value=4.2 Score=44.44 Aligned_cols=24 Identities=38% Similarity=0.911 Sum_probs=18.7
Q ss_pred eccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCc
Q 017546 31 ESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (369)
Q Consensus 31 es~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrn 70 (369)
-+.|+.||..|.. .+.||+||-++
T Consensus 559 ~~~C~~CGy~g~~----------------~~~CP~CG~~d 582 (618)
T PRK14704 559 VDRCKCCSYHGVI----------------GNECPSCGNED 582 (618)
T ss_pred CeecCCCCCCCCc----------------CccCcCCCCCC
Confidence 3789999976642 19999999865
No 126
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=58.99 E-value=11 Score=33.55 Aligned_cols=32 Identities=22% Similarity=0.723 Sum_probs=22.4
Q ss_pred ccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCcc
Q 017546 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNN 71 (369)
Q Consensus 32 s~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnn 71 (369)
.+|+.|+.+- |.|..- +. ++...|..||.+..
T Consensus 103 VlC~~C~spd-T~l~k~-----~r--~~~l~C~ACGa~~~ 134 (138)
T PRK03988 103 VICPECGSPD-TKLIKE-----GR--IWVLKCEACGAETP 134 (138)
T ss_pred EECCCCCCCC-cEEEEc-----CC--eEEEEcccCCCCCc
Confidence 6799999874 554321 22 56689999999763
No 127
>PRK14291 chaperone protein DnaJ; Provisional
Probab=58.98 E-value=31 Score=35.30 Aligned_cols=21 Identities=33% Similarity=0.559 Sum_probs=16.0
Q ss_pred cceeEeCCCCCcceEEehHHH
Q 017546 114 ELDFEIPPEAQRGSLSTVEGI 134 (369)
Q Consensus 114 ELd~eI~p~~~~G~iTTVEGl 134 (369)
.|.+.|||+...|..-+++|.
T Consensus 225 ~l~V~Ip~G~~~G~~i~~~g~ 245 (382)
T PRK14291 225 TIKVRIPPGVDNGSKLRVPGK 245 (382)
T ss_pred EEEEEeCCCCCCCCEEEEecC
Confidence 377788888888887777764
No 128
>PRK14288 chaperone protein DnaJ; Provisional
Probab=58.88 E-value=32 Score=35.02 Aligned_cols=31 Identities=23% Similarity=0.505 Sum_probs=18.4
Q ss_pred cCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCc
Q 017546 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (369)
Q Consensus 33 ~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrn 70 (369)
.|+.|+..|..++.. .| +.+...|+.|+=+-
T Consensus 158 ~C~~C~G~G~~~~~~----g~---~~~~~~C~~C~G~G 188 (369)
T PRK14288 158 TCKQCNGQGQVFMRQ----GF---MSFAQTCGACQGKG 188 (369)
T ss_pred CCCCCCCCcEEEEEe----ce---EEEEEecCCCCCCc
Confidence 466776666544332 22 24556899998764
No 129
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=58.53 E-value=5.4 Score=38.01 Aligned_cols=22 Identities=27% Similarity=0.708 Sum_probs=16.6
Q ss_pred ccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCC
Q 017546 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYR 323 (369)
Q Consensus 286 ~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk 323 (369)
..||.||. .--=.+.|++||+.
T Consensus 310 ~~C~~cg~----------------~~~r~~~C~~cg~~ 331 (364)
T COG0675 310 KTCPCCGH----------------LSGRLFKCPRCGFV 331 (364)
T ss_pred ccccccCC----------------ccceeEECCCCCCe
Confidence 47999998 11235789999995
No 130
>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=58.51 E-value=3.2 Score=35.36 Aligned_cols=36 Identities=31% Similarity=0.714 Sum_probs=22.3
Q ss_pred eccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccceeeCccc
Q 017546 31 ESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEI 79 (369)
Q Consensus 31 es~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEVq~~g~i 79 (369)
...|..||.... +..+. +.||+||-.+-+|.+|.+.
T Consensus 70 ~~~C~~Cg~~~~-------~~~~~------~~CP~Cgs~~~~i~~G~el 105 (113)
T PF01155_consen 70 RARCRDCGHEFE-------PDEFD------FSCPRCGSPDVEIISGREL 105 (113)
T ss_dssp EEEETTTS-EEE-------CHHCC------HH-SSSSSS-EEEEESS-E
T ss_pred cEECCCCCCEEe-------cCCCC------CCCcCCcCCCcEEccCCeE
Confidence 467999997632 11111 4599999999888887765
No 131
>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=58.35 E-value=5.3 Score=30.16 Aligned_cols=22 Identities=45% Similarity=1.067 Sum_probs=16.3
Q ss_pred ccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCC
Q 017546 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGER 69 (369)
Q Consensus 32 s~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyr 69 (369)
+.|++||+. ..|| ..|++|||=
T Consensus 27 ~~C~~cG~~--------~~~H--------~vc~~cG~Y 48 (55)
T TIGR01031 27 VVCPNCGEF--------KLPH--------RVCPSCGYY 48 (55)
T ss_pred eECCCCCCc--------ccCe--------eECCccCeE
Confidence 459999863 3455 899999973
No 132
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=58.08 E-value=5.3 Score=38.81 Aligned_cols=42 Identities=14% Similarity=0.310 Sum_probs=23.9
Q ss_pred eeeccCccCcccccceeEEE-----------ecCCCCeE---EEEEeeCCCCCCCc
Q 017546 283 TFPSTCGACAASCETRMFMT-----------RIPYFQEV---IVMASTCDACGYRN 324 (369)
Q Consensus 283 ~~~~~Cp~C~~~~~~~m~~~-----------~IP~F~ev---iims~~C~~CGyk~ 324 (369)
.-...||+|+-...-+|..+ .-|-||+| +--.++|+.|+|-.
T Consensus 17 kk~ieCPvC~tkFkkeev~tgsiRiiagDld~~lkygninP~fY~VvvCP~C~yAa 72 (267)
T COG1655 17 KKTIECPVCNTKFKKEEVKTGSIRIIAGDLDFFLKYGNINPYFYDVVVCPICYYAA 72 (267)
T ss_pred hceeccCcccchhhhhheeccceeEecccccceeeccccCCceeEEEEcchhhHHH
Confidence 34568999976544433221 11233333 23346899999964
No 133
>PRK14296 chaperone protein DnaJ; Provisional
Probab=58.01 E-value=43 Score=34.23 Aligned_cols=35 Identities=17% Similarity=0.425 Sum_probs=20.8
Q ss_pred cCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCc
Q 017546 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (369)
Q Consensus 33 ~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrn 70 (369)
.|+.|+..|..+... .+.+| ++-+...|+.|+=+-
T Consensus 168 ~C~~C~G~G~~~~~~-~~g~~--~~q~~~~C~~C~G~G 202 (372)
T PRK14296 168 ICNNCHGTGEVLVQK-NMGFF--QFQQSAKCNVCNGAG 202 (372)
T ss_pred cCCCCCCCceEEEEE-eccce--EEEEEecCCCcCCcc
Confidence 477777777544443 33332 334667899997654
No 134
>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=57.42 E-value=7 Score=32.58 Aligned_cols=35 Identities=34% Similarity=0.752 Sum_probs=24.4
Q ss_pred ccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccceeeCcccCC
Q 017546 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEIQP 81 (369)
Q Consensus 32 s~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEVq~~g~i~~ 81 (369)
-.||.||+..+-|. -+-| +.|.+||+.. .+|+..|
T Consensus 36 y~Cp~Cgk~~vkR~-a~GI----------W~C~~C~~~~----AGGAy~~ 70 (90)
T PF01780_consen 36 YTCPFCGKTSVKRV-ATGI----------WKCKKCGKKF----AGGAYTP 70 (90)
T ss_dssp BEESSSSSSEEEEE-ETTE----------EEETTTTEEE----E-BSSSS
T ss_pred CcCCCCCCceeEEe-eeEE----------eecCCCCCEE----eCCCccc
Confidence 46999999874443 3334 9999999865 5777665
No 135
>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=56.75 E-value=17 Score=26.78 Aligned_cols=35 Identities=29% Similarity=0.438 Sum_probs=19.2
Q ss_pred cCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCcc
Q 017546 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNN 71 (369)
Q Consensus 33 ~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnn 71 (369)
.||-||....+ +.. ....+..--+ |.|..||+.-.
T Consensus 3 PCPfCGg~~~~--~~~-~~~~~~~~~~-~~C~~Cga~~~ 37 (53)
T TIGR03655 3 PCPFCGGADVY--LRR-GFDPLDLSHY-FECSTCGASGP 37 (53)
T ss_pred CCCCCCCccee--eEe-ccCCCCCEEE-EECCCCCCCcc
Confidence 69999876542 111 1111122212 48999999753
No 136
>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=56.36 E-value=5.2 Score=31.53 Aligned_cols=27 Identities=22% Similarity=0.517 Sum_probs=20.3
Q ss_pred EEEEeeCCCCCCCccceeeCcccCCcce
Q 017546 57 LLSAFECPHCGERNNEVQFAGEIQPRGC 84 (369)
Q Consensus 57 iImSf~C~~CGyrnnEVq~~g~i~~kG~ 84 (369)
..+.|.|..||.|+....+--+. .+|+
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 36789999999999877666555 4675
No 137
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=56.36 E-value=10 Score=32.26 Aligned_cols=40 Identities=20% Similarity=0.416 Sum_probs=27.1
Q ss_pred eeeeeccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCcc
Q 017546 281 VMTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNS 325 (369)
Q Consensus 281 v~~~~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~ 325 (369)
++.-..+||.||+.... .+.++ +.+-+-..+|..||-++-
T Consensus 18 ~L~k~FtCp~Cghe~vs-~ctvk----k~~~~g~~~Cg~CGls~e 57 (104)
T COG4888 18 VLPKTFTCPRCGHEKVS-SCTVK----KTVNIGTAVCGNCGLSFE 57 (104)
T ss_pred cCCceEecCccCCeeee-EEEEE----ecCceeEEEcccCcceEE
Confidence 44556689999987432 22332 455677889999998763
No 138
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=56.24 E-value=32 Score=24.03 Aligned_cols=35 Identities=17% Similarity=0.485 Sum_probs=20.5
Q ss_pred ccCCCCCCCc-----eEEEEEeecCCcceEEEEE-----eeCCCC
Q 017546 32 SLCMRCGENG-----VTRFLLTLIPHFRKVLLSA-----FECPHC 66 (369)
Q Consensus 32 s~Cp~Cg~~g-----~tr~llt~IP~FkeiiImS-----f~C~~C 66 (369)
..||.||... ...-.....|+++.-+++- |.|++|
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 4689998654 2233445677766555443 556655
No 139
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=56.13 E-value=13 Score=32.34 Aligned_cols=43 Identities=35% Similarity=0.699 Sum_probs=25.3
Q ss_pred EeccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccceeeCccc
Q 017546 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEI 79 (369)
Q Consensus 30 ies~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEVq~~g~i 79 (369)
....| .||....... ..+.+| ...+.||+||-.+-+|..|.++
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 34679 9996532210 011111 0136899999888888777665
No 140
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=56.03 E-value=5.1 Score=38.38 Aligned_cols=36 Identities=39% Similarity=0.831 Sum_probs=26.1
Q ss_pred ccCCCCC-CCceEEEEEeecCCcceEEEEEeeCCCCCCCccceee
Q 017546 32 SLCMRCG-ENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQF 75 (369)
Q Consensus 32 s~Cp~Cg-~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEVq~ 75 (369)
-.||.|+ +||-.++--..| .-|.|+||..+|.+++.
T Consensus 193 lIC~~C~hhngl~~~~ek~~--------~efiC~~Cn~~n~~~~~ 229 (251)
T COG5415 193 LICPQCHHHNGLYRLAEKPI--------IEFICPHCNHKNDEVKE 229 (251)
T ss_pred hccccccccccccccccccc--------hheecccchhhcCcccc
Confidence 4699996 678777643333 26999999999966544
No 141
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=55.72 E-value=6.6 Score=29.92 Aligned_cols=23 Identities=43% Similarity=0.998 Sum_probs=16.9
Q ss_pred ccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCc
Q 017546 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (369)
Q Consensus 32 s~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrn 70 (369)
+.|++||+. ..|| ..|++|||=+
T Consensus 28 ~~C~~CG~~--------~~~H--------~vC~~CG~Y~ 50 (57)
T PRK12286 28 VECPNCGEP--------KLPH--------RVCPSCGYYK 50 (57)
T ss_pred eECCCCCCc--------cCCe--------EECCCCCcCC
Confidence 559999864 2344 8999999854
No 142
>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=55.65 E-value=21 Score=27.35 Aligned_cols=36 Identities=25% Similarity=0.523 Sum_probs=23.9
Q ss_pred ccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCc
Q 017546 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (369)
Q Consensus 32 s~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrn 70 (369)
..|+.|+..|....... .|++ ++.+...|++|+=+-
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 37999999987766655 4444 456678899997543
No 143
>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=55.41 E-value=6.8 Score=26.84 Aligned_cols=27 Identities=26% Similarity=0.671 Sum_probs=15.4
Q ss_pred CccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCc
Q 017546 288 CGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRN 324 (369)
Q Consensus 288 Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~ 324 (369)
||.||..+..+- ---+.+ .|..|||..
T Consensus 4 Cp~C~nlL~p~~-----~~~~~~-----~C~~C~Y~~ 30 (35)
T PF02150_consen 4 CPECGNLLYPKE-----DKEKRV-----ACRTCGYEE 30 (35)
T ss_dssp ETTTTSBEEEEE-----ETTTTE-----EESSSS-EE
T ss_pred CCCCCccceEcC-----CCccCc-----CCCCCCCcc
Confidence 999987653221 111112 899999964
No 144
>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=55.36 E-value=2.6 Score=38.06 Aligned_cols=33 Identities=24% Similarity=0.451 Sum_probs=22.4
Q ss_pred cCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCcccccc
Q 017546 287 TCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKP 329 (369)
Q Consensus 287 ~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~eVk~ 329 (369)
.||.|+.... |-+.+-..|.|+.||..-.+...
T Consensus 111 ~Cp~c~~r~t----------f~eA~~~~F~Cp~Cg~~L~~~dn 143 (158)
T TIGR00373 111 ICPNMCVRFT----------FNEAMELNFTCPRCGAMLDYLDN 143 (158)
T ss_pred ECCCCCcEee----------HHHHHHcCCcCCCCCCEeeeccC
Confidence 5999986642 23444468999999976555443
No 145
>PRK14298 chaperone protein DnaJ; Provisional
Probab=55.35 E-value=64 Score=33.00 Aligned_cols=15 Identities=20% Similarity=0.629 Sum_probs=10.1
Q ss_pred eEEeccCCCCCCCce
Q 017546 28 YQVESLCMRCGENGV 42 (369)
Q Consensus 28 ~eies~Cp~Cg~~g~ 42 (369)
..+.+.|+.|+..|.
T Consensus 181 ~~~~~~C~~C~G~G~ 195 (377)
T PRK14298 181 FVTTTTCSTCHGRGQ 195 (377)
T ss_pred EEEEEeCCCCCCCCc
Confidence 356677888876664
No 146
>PRK14281 chaperone protein DnaJ; Provisional
Probab=54.98 E-value=37 Score=34.92 Aligned_cols=35 Identities=23% Similarity=0.509 Sum_probs=19.5
Q ss_pred cCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCc
Q 017546 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (369)
Q Consensus 33 ~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrn 70 (369)
.|+.|+..|..+......|.| +.+...|+.|+=+-
T Consensus 181 ~C~~C~G~G~~~~~~~~~~g~---~~~~~~C~~C~G~G 215 (397)
T PRK14281 181 TCPTCHGSGEVRQASKTMFGQ---FVNITACPTCGGEG 215 (397)
T ss_pred cCCCCCCCcEEEEEEecccce---EEEEEecCCCccee
Confidence 467776666544333333322 22455899997654
No 147
>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=54.85 E-value=24 Score=28.20 Aligned_cols=46 Identities=17% Similarity=0.247 Sum_probs=17.2
Q ss_pred ccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccceeeCc
Q 017546 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAG 77 (369)
Q Consensus 32 s~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEVq~~g 77 (369)
..||.|+.....+--.+.=++=..-+.+-..||.||-.---+|.=|
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 3466665553322222333333334445555666665554444443
No 148
>PHA02998 RNA polymerase subunit; Provisional
Probab=54.77 E-value=18 Score=33.87 Aligned_cols=42 Identities=17% Similarity=0.309 Sum_probs=29.1
Q ss_pred EeccCCCCCCCceE-EEEEeecCCcceEEEEEeeCCCCCCCccce
Q 017546 30 VESLCMRCGENGVT-RFLLTLIPHFRKVLLSAFECPHCGERNNEV 73 (369)
Q Consensus 30 ies~Cp~Cg~~g~t-r~llt~IP~FkeiiImSf~C~~CGyrnnEV 73 (369)
.+..||.|+....+ .++.|+ --.|=...-+.|..||++..-=
T Consensus 142 t~v~CPkCg~~~A~f~qlQTR--SADEPmT~FYkC~~CG~~wkpp 184 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTR--AADEPPLVRHACRDCKKHFKPP 184 (195)
T ss_pred cCCCCCCCCCCceEEEEEeec--cCCCCceEEEEcCCCCCccCCc
Confidence 67889999966443 344444 2456666779999999987543
No 149
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=54.52 E-value=5.1 Score=40.99 Aligned_cols=33 Identities=30% Similarity=0.876 Sum_probs=21.0
Q ss_pred ccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCcc
Q 017546 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNS 325 (369)
Q Consensus 286 ~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~ 325 (369)
+.||.|+.| +|.+.... +. -.+..|..||||+.
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 469999988 44332221 11 12568999999974
No 150
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=54.51 E-value=7.8 Score=26.66 Aligned_cols=23 Identities=26% Similarity=0.729 Sum_probs=10.4
Q ss_pred EeeCCCCCCCccceeeCcccCCcce
Q 017546 60 AFECPHCGERNNEVQFAGEIQPRGC 84 (369)
Q Consensus 60 Sf~C~~CGyrnnEVq~~g~i~~kG~ 84 (369)
-+.||+|+.+++ | +.+.|.++|.
T Consensus 2 ~i~Cp~C~~~y~-i-~d~~ip~~g~ 24 (36)
T PF13717_consen 2 IITCPNCQAKYE-I-DDEKIPPKGR 24 (36)
T ss_pred EEECCCCCCEEe-C-CHHHCCCCCc
Confidence 345555555542 1 2333444443
No 151
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=54.22 E-value=7 Score=43.57 Aligned_cols=27 Identities=37% Similarity=0.747 Sum_probs=19.2
Q ss_pred eccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccce
Q 017546 31 ESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEV 73 (369)
Q Consensus 31 es~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEV 73 (369)
-+.|++||..+.. .+.||+||-.+-+|
T Consensus 680 ~~~C~~CG~~~~~----------------~~~CP~CG~~~~~~ 706 (735)
T PRK07111 680 VDRCPVCGYLGVI----------------EDKCPKCGSTNIQR 706 (735)
T ss_pred CeecCCCCCCCCc----------------CccCcCCCCcccee
Confidence 3789999965431 19999999765444
No 152
>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=53.80 E-value=3.3 Score=35.30 Aligned_cols=40 Identities=20% Similarity=0.434 Sum_probs=23.5
Q ss_pred eeeeeccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCccccccCCcc
Q 017546 281 VMTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRI 333 (369)
Q Consensus 281 v~~~~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~eVk~~g~~ 333 (369)
.......|..||+.....- .+ +.|++||-..-+|.+|...
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~-----~~--------~~CP~Cgs~~~~i~~G~el 105 (113)
T PF01155_consen 66 EVPARARCRDCGHEFEPDE-----FD--------FSCPRCGSPDVEIISGREL 105 (113)
T ss_dssp EE--EEEETTTS-EEECHH-----CC--------HH-SSSSSS-EEEEESS-E
T ss_pred ecCCcEECCCCCCEEecCC-----CC--------CCCcCCcCCCcEEccCCeE
Confidence 3445778999998753322 11 3399999998888777654
No 153
>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=53.09 E-value=17 Score=25.50 Aligned_cols=36 Identities=22% Similarity=0.406 Sum_probs=21.6
Q ss_pred ccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCccccccCC
Q 017546 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGG 331 (369)
Q Consensus 286 ~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~eVk~~g 331 (369)
+.||.||... ..++ +.=+++ +|..||+--.|-..-.
T Consensus 1 m~Cp~Cg~~~----~~~D-~~~g~~-----vC~~CG~Vl~e~~i~~ 36 (43)
T PF08271_consen 1 MKCPNCGSKE----IVFD-PERGEL-----VCPNCGLVLEENIIDE 36 (43)
T ss_dssp ESBTTTSSSE----EEEE-TTTTEE-----EETTT-BBEE-TTBSC
T ss_pred CCCcCCcCCc----eEEc-CCCCeE-----ECCCCCCEeecccccC
Confidence 3699999863 2333 444554 7999998766654433
No 154
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=52.94 E-value=16 Score=34.55 Aligned_cols=38 Identities=21% Similarity=0.420 Sum_probs=23.4
Q ss_pred eeeccCccCcccccc--eeEEEecCCCCeEEEEEeeCCCCCCCcccc
Q 017546 283 TFPSTCGACAASCET--RMFMTRIPYFQEVIVMASTCDACGYRNSEL 327 (369)
Q Consensus 283 ~~~~~Cp~C~~~~~~--~m~~~~IP~F~eviims~~C~~CGyk~~eV 327 (369)
+.-..||+|| ..++ .......+. ....|.+||+=+.+.
T Consensus 4 ~iy~~Cp~Cg-~eev~hEVik~~g~~------~lvrC~eCG~V~~~~ 43 (201)
T COG1326 4 EIYIECPSCG-SEEVSHEVIKERGRE------PLVRCEECGTVHPAI 43 (201)
T ss_pred eEEEECCCCC-cchhhHHHHHhcCCc------eEEEccCCCcEeece
Confidence 4456799999 3333 222222333 456899999988664
No 155
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=52.33 E-value=15 Score=31.22 Aligned_cols=13 Identities=23% Similarity=0.473 Sum_probs=7.0
Q ss_pred EEEeeCCCCCCCc
Q 017546 58 LSAFECPHCGERN 70 (369)
Q Consensus 58 ImSf~C~~CGyrn 70 (369)
.+.|.|..|+|-.
T Consensus 19 ~~rf~C~tCpY~~ 31 (105)
T KOG2906|consen 19 CNRFSCRTCPYVF 31 (105)
T ss_pred EeeEEcCCCCcee
Confidence 4555555555543
No 156
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=51.88 E-value=3.4 Score=38.14 Aligned_cols=33 Identities=24% Similarity=0.510 Sum_probs=22.8
Q ss_pred cCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCcccccc
Q 017546 287 TCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKP 329 (369)
Q Consensus 287 ~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~eVk~ 329 (369)
.||.|+.... |-+.+-..|.|+.||.--.+...
T Consensus 119 ~Cp~C~~ryt----------f~eA~~~~F~Cp~Cg~~L~~~dn 151 (178)
T PRK06266 119 FCPNCHIRFT----------FDEAMEYGFRCPQCGEMLEEYDN 151 (178)
T ss_pred ECCCCCcEEe----------HHHHhhcCCcCCCCCCCCeeccc
Confidence 5999987643 22344468999999987666543
No 157
>PRK04296 thymidine kinase; Provisional
Probab=51.68 E-value=13 Score=33.94 Aligned_cols=45 Identities=11% Similarity=0.247 Sum_probs=34.3
Q ss_pred cceeeeeccCccCcccccceeEEEe---cCCCCeEEE------EEeeCCCCCCC
Q 017546 279 EEVMTFPSTCGACAASCETRMFMTR---IPYFQEVIV------MASTCDACGYR 323 (369)
Q Consensus 279 ~ev~~~~~~Cp~C~~~~~~~m~~~~---IP~F~evii------ms~~C~~CGyk 323 (369)
+.|.++...|..||+++..+...++ .++-++++. ....|.+|=+.
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 3799999999999999888888773 456677774 44678887553
No 158
>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=51.60 E-value=3.7 Score=27.52 Aligned_cols=26 Identities=27% Similarity=0.618 Sum_probs=11.4
Q ss_pred ccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCC
Q 017546 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGER 69 (369)
Q Consensus 32 s~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyr 69 (369)
+.||.|+..-+. .- + .-|.|+.||+.
T Consensus 3 p~Cp~C~se~~y--~D------~----~~~vCp~C~~e 28 (30)
T PF08274_consen 3 PKCPLCGSEYTY--ED------G----ELLVCPECGHE 28 (30)
T ss_dssp ---TTT-----E--E-------S----SSEEETTTTEE
T ss_pred CCCCCCCCccee--cc------C----CEEeCCccccc
Confidence 579999877544 11 1 12779999873
No 159
>PRK14289 chaperone protein DnaJ; Provisional
Probab=51.56 E-value=46 Score=34.04 Aligned_cols=35 Identities=17% Similarity=0.440 Sum_probs=18.2
Q ss_pred cCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCc
Q 017546 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (369)
Q Consensus 33 ~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrn 70 (369)
.|+.|+..|..++ .+..+ ++-+. +...|++|+=+-
T Consensus 173 ~C~~C~G~G~~~~-~~~~~-~G~~~-~~~~C~~C~G~G 207 (386)
T PRK14289 173 TCPTCKGSGSVTR-VQNTI-LGTMQ-TQSTCPTCNGEG 207 (386)
T ss_pred cCCCCcCeEEEEE-EEecc-cceEE-EEEecCCCCccc
Confidence 3555555553333 22222 23332 478999997653
No 160
>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=51.26 E-value=19 Score=25.41 Aligned_cols=36 Identities=19% Similarity=0.491 Sum_probs=22.1
Q ss_pred ccCccCcccccc-----eeEEEecC----CCCeEEEEEeeCCCCC
Q 017546 286 STCGACAASCET-----RMFMTRIP----YFQEVIVMASTCDACG 321 (369)
Q Consensus 286 ~~Cp~C~~~~~~-----~m~~~~IP----~F~eviims~~C~~CG 321 (369)
..||.||..+.- ....+++| +..+.+.....|..||
T Consensus 3 ~~C~~Cg~~l~~ig~~~~~q~l~~~p~~~~V~e~~~~~y~C~~C~ 47 (47)
T PF13005_consen 3 RACPDCGGELKEIGEEKVRQVLDLPPAKPEVTEHVRHKYACPCCG 47 (47)
T ss_pred CcCCCCCceeeECCceeeEEEEeecccceEEEEEEeceEECCCCC
Confidence 469999887542 12334433 2245566778898887
No 161
>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=51.16 E-value=7.4 Score=42.08 Aligned_cols=28 Identities=36% Similarity=0.813 Sum_probs=20.2
Q ss_pred eccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccce
Q 017546 31 ESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEV 73 (369)
Q Consensus 31 es~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEV 73 (369)
-+.|..||..|... .+.||+||-++-++
T Consensus 524 ~~~C~~CG~~g~~~---------------~~~CP~Cgs~~~~~ 551 (579)
T TIGR02487 524 VDVCEDCGYTGEGL---------------NDKCPKCGSHDIEV 551 (579)
T ss_pred CccCCCCCCCCCCC---------------CCcCcCCCCcccee
Confidence 37899999755321 18899999877444
No 162
>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=51.01 E-value=15 Score=36.80 Aligned_cols=40 Identities=25% Similarity=0.454 Sum_probs=25.6
Q ss_pred eccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCcc
Q 017546 285 PSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNS 325 (369)
Q Consensus 285 ~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~ 325 (369)
...||.||+.-. ..+...+=--.|=+-.-+.|-.||++..
T Consensus 258 ~~~C~~C~~~~~-~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 258 LFTCGKCKQKKC-TYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred cccCCCCCCccc-eEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 568999986632 2233333333455566678999999864
No 163
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=50.85 E-value=7.2 Score=41.87 Aligned_cols=29 Identities=38% Similarity=0.708 Sum_probs=14.9
Q ss_pred eccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccceee
Q 017546 31 ESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQF 75 (369)
Q Consensus 31 es~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEVq~ 75 (369)
-+.|++||..+. . .+.||+||-++.+|-.
T Consensus 491 ~~~C~~CG~~~~---------------~-~~~CP~CGs~~~~~~~ 519 (546)
T PF13597_consen 491 IDICPDCGYIGG---------------E-GDKCPKCGSENIEVYS 519 (546)
T ss_dssp EEEETTT---S------------------EEE-CCC----EEEEB
T ss_pred cccccCCCcCCC---------------C-CCCCCCCCCcccceEE
Confidence 478999996431 1 7899999999866654
No 164
>PRK04023 DNA polymerase II large subunit; Validated
Probab=50.85 E-value=8.8 Score=44.15 Aligned_cols=9 Identities=33% Similarity=0.992 Sum_probs=6.7
Q ss_pred ccCCCCCCC
Q 017546 32 SLCMRCGEN 40 (369)
Q Consensus 32 s~Cp~Cg~~ 40 (369)
-.|+.||..
T Consensus 627 RfCpsCG~~ 635 (1121)
T PRK04023 627 RKCPSCGKE 635 (1121)
T ss_pred ccCCCCCCc
Confidence 468888876
No 165
>COG4469 CoiA Competence protein CoiA-like family, contains a predicted nuclease domain [General function prediction only]
Probab=50.43 E-value=7.1 Score=39.63 Aligned_cols=34 Identities=32% Similarity=0.529 Sum_probs=27.0
Q ss_pred ccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCc
Q 017546 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (369)
Q Consensus 32 s~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrn 70 (369)
--||+||++...|.=+.+||||--.=+- +|-+-+
T Consensus 26 ffCPaC~~~l~lK~G~~k~pHFAHk~l~-----~C~~~~ 59 (342)
T COG4469 26 FFCPACGSQLILKQGLIKIPHFAHKSLK-----ACAFFN 59 (342)
T ss_pred cccCCCCCeeeeecCccccchhhhhhhh-----hccccC
Confidence 5799999999999999999999765433 555544
No 166
>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=50.09 E-value=14 Score=30.83 Aligned_cols=40 Identities=20% Similarity=0.347 Sum_probs=29.1
Q ss_pred eeeeeccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCccccccCCccCC
Q 017546 281 VMTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRIPE 335 (369)
Q Consensus 281 v~~~~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~eVk~~g~~~~ 335 (369)
.+.-.-.||.||+.. ++.+-.=-|.|.+||+.. .||+..|
T Consensus 31 ~q~a~y~CpfCgk~~-----------vkR~a~GIW~C~~C~~~~----AGGAy~p 70 (91)
T TIGR00280 31 QQKAKYVCPFCGKKT-----------VKRGSTGIWTCRKCGAKF----AGGAYTP 70 (91)
T ss_pred HHhcCccCCCCCCCc-----------eEEEeeEEEEcCCCCCEE----eCCcccc
Confidence 445567899999763 355666669999999975 4676665
No 167
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=49.92 E-value=12 Score=28.08 Aligned_cols=33 Identities=21% Similarity=0.486 Sum_probs=21.3
Q ss_pred ceeeeeccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCC
Q 017546 280 EVMTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYR 323 (369)
Q Consensus 280 ev~~~~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk 323 (369)
.|....-.||.||.-...-- -++ -+.|..|||-
T Consensus 14 kv~rk~~~CPrCG~gvfmA~-------H~d----R~~CGkCgyT 46 (51)
T COG1998 14 KVKRKNRFCPRCGPGVFMAD-------HKD----RWACGKCGYT 46 (51)
T ss_pred cEEEccccCCCCCCcchhhh-------cCc----eeEeccccce
Confidence 46666778999995322111 122 6789999994
No 168
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=49.23 E-value=7.6 Score=43.12 Aligned_cols=28 Identities=32% Similarity=0.846 Sum_probs=19.1
Q ss_pred ccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCc
Q 017546 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (369)
Q Consensus 32 s~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrn 70 (369)
+.|++||..|...+ .-..+.||+||-++
T Consensus 642 ~~C~~CG~~Ge~~~-----------~~~~~~CP~CG~~~ 669 (711)
T PRK09263 642 DECYECGFTGEFEC-----------TEKGFTCPKCGNHD 669 (711)
T ss_pred cccCCCCCCccccC-----------CCCCCcCcCCCCCC
Confidence 78999997664332 11128999999775
No 169
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=48.83 E-value=15 Score=30.61 Aligned_cols=40 Identities=18% Similarity=0.277 Sum_probs=28.4
Q ss_pred eeeeeccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCccccccCCccCC
Q 017546 281 VMTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRIPE 335 (369)
Q Consensus 281 v~~~~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~eVk~~g~~~~ 335 (369)
.+.-.-.||.||+.. ++.+-.=-+.|.+||++.. ||+..|
T Consensus 32 ~q~a~y~CpfCgk~~-----------vkR~a~GIW~C~~C~~~~A----GGAy~~ 71 (90)
T PTZ00255 32 SQHAKYFCPFCGKHA-----------VKRQAVGIWRCKGCKKTVA----GGAWTL 71 (90)
T ss_pred HHhCCccCCCCCCCc-----------eeeeeeEEEEcCCCCCEEe----CCcccc
Confidence 345567899999763 2455556699999999754 666655
No 170
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=48.14 E-value=4.7 Score=40.01 Aligned_cols=33 Identities=18% Similarity=0.396 Sum_probs=22.7
Q ss_pred eeeccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCcc
Q 017546 283 TFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNS 325 (369)
Q Consensus 283 ~~~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~ 325 (369)
..-++||.|+..... +|+----.+|++|||...
T Consensus 26 ~lw~KCp~c~~~~y~----------~eL~~n~~vcp~c~~h~r 58 (294)
T COG0777 26 GLWTKCPSCGEMLYR----------KELESNLKVCPKCGHHMR 58 (294)
T ss_pred CceeECCCccceeeH----------HHHHhhhhcccccCcccc
Confidence 345689999976533 343334578999999764
No 171
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=48.04 E-value=7.6 Score=39.77 Aligned_cols=33 Identities=27% Similarity=0.698 Sum_probs=23.0
Q ss_pred ccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCcc
Q 017546 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNN 71 (369)
Q Consensus 32 s~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnn 71 (369)
.+||.|+.+ .|-+..+. +. -.+..|-.||||..
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 689999865 56665554 11 13579999999864
No 172
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=47.59 E-value=18 Score=31.98 Aligned_cols=32 Identities=25% Similarity=0.727 Sum_probs=21.7
Q ss_pred ccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCcc
Q 017546 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNN 71 (369)
Q Consensus 32 s~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnn 71 (369)
.+|+.|+.+- |.+..- +. ++...|..||.+..
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 6899999875 444321 22 34569999999753
No 173
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=47.43 E-value=3.3 Score=41.33 Aligned_cols=32 Identities=16% Similarity=0.256 Sum_probs=21.3
Q ss_pred EeccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCcc
Q 017546 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNN 71 (369)
Q Consensus 30 ies~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnn 71 (369)
+-..||+|++.-.. ++.---...||+|||...
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 46789999876422 222222379999999764
No 174
>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=47.20 E-value=22 Score=27.28 Aligned_cols=34 Identities=32% Similarity=0.509 Sum_probs=22.2
Q ss_pred ccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCC
Q 017546 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGY 322 (369)
Q Consensus 286 ~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGy 322 (369)
..||.|+-.+...+... .|++ ++.+...|+.|+=
T Consensus 16 ~~C~~C~G~G~~~~~~~-~~~~--~~~~~~~C~~C~G 49 (66)
T PF00684_consen 16 KTCPQCNGSGQVTRRQQ-TPGG--VFQMQQTCPKCGG 49 (66)
T ss_dssp EE-TTSSSSSEEEEEEE-SSST--TEEEEEE-TTTSS
T ss_pred cCCcCCCCeeEEEEEEe-CCCe--EEEEEEECCCCcc
Confidence 47999988876655544 4443 5677888999974
No 175
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.09 E-value=15 Score=31.83 Aligned_cols=27 Identities=22% Similarity=0.550 Sum_probs=20.2
Q ss_pred eeeccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCc
Q 017546 283 TFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRN 324 (369)
Q Consensus 283 ~~~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~ 324 (369)
.+.-.||+||+. .|+.-..|.+||-..
T Consensus 4 ~~~~~cPvcg~~---------------~iVTeL~c~~~etTV 30 (122)
T COG3877 4 KVINRCPVCGRK---------------LIVTELKCSNCETTV 30 (122)
T ss_pred CCCCCCCccccc---------------ceeEEEecCCCCceE
Confidence 456689999965 467778899998543
No 176
>PRK14278 chaperone protein DnaJ; Provisional
Probab=47.06 E-value=60 Score=33.22 Aligned_cols=35 Identities=23% Similarity=0.604 Sum_probs=18.9
Q ss_pred cCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCc
Q 017546 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (369)
Q Consensus 33 ~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrn 70 (369)
.|+.|+..|....... .+|+-+. ++..|+.|+=+-
T Consensus 158 ~C~~C~G~G~~~~~~~--~~~g~~~-~~~~C~~C~G~G 192 (378)
T PRK14278 158 TCDTCGGRGEVQTVQR--SFLGQVM-TSRPCPTCRGVG 192 (378)
T ss_pred ecCCccCceEEEEEEe--ccceeEE-EEEECCCCCccc
Confidence 4667766664333221 2344444 455899996543
No 177
>PRK14294 chaperone protein DnaJ; Provisional
Probab=46.57 E-value=1e+02 Score=31.39 Aligned_cols=26 Identities=31% Similarity=0.632 Sum_probs=17.8
Q ss_pred eEEEeec----ceeEeCCCCCcceEEehHH
Q 017546 108 ATIKIPE----LDFEIPPEAQRGSLSTVEG 133 (369)
Q Consensus 108 ati~IPE----Ld~eI~p~~~~G~iTTVEG 133 (369)
.++.|+- +.++||++++.|.+-.|.|
T Consensus 281 ~~~~i~tldG~~~v~ip~g~~~g~~iri~G 310 (366)
T PRK14294 281 AQIEVPTLEGERELKIPKGTQPGDIFRFKG 310 (366)
T ss_pred CeEEEECCCCcEEEEECCCcCCCCEEEECC
Confidence 4566664 3577888777787777765
No 178
>PF12773 DZR: Double zinc ribbon
Probab=46.49 E-value=7.7 Score=27.77 Aligned_cols=25 Identities=20% Similarity=0.465 Sum_probs=16.4
Q ss_pred cCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCC
Q 017546 287 TCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYR 323 (369)
Q Consensus 287 ~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk 323 (369)
-||.||.++. .-......|.+||+.
T Consensus 14 fC~~CG~~l~------------~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 14 FCPHCGTPLP------------PPDQSKKICPNCGAE 38 (50)
T ss_pred CChhhcCChh------------hccCCCCCCcCCcCC
Confidence 4888888765 222234568888885
No 179
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=46.42 E-value=4.3 Score=40.53 Aligned_cols=32 Identities=19% Similarity=0.506 Sum_probs=21.7
Q ss_pred eeccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCcc
Q 017546 284 FPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNS 325 (369)
Q Consensus 284 ~~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~ 325 (369)
+-++||.|++....+. +---..+|++|||...
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 3578999998764432 2223479999999654
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=46.29 E-value=4.3 Score=40.26 Aligned_cols=31 Identities=19% Similarity=0.360 Sum_probs=20.9
Q ss_pred eccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCcc
Q 017546 285 PSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNS 325 (369)
Q Consensus 285 ~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~ 325 (369)
-.+||.|++....+ ++---..+|++|||...
T Consensus 26 ~~~c~~c~~~~~~~----------~l~~~~~vc~~c~~h~r 56 (285)
T TIGR00515 26 WTKCPKCGQVLYTK----------ELERNLEVCPKCDHHMR 56 (285)
T ss_pred eeECCCCcchhhHH----------HHHhhCCCCCCCCCcCc
Confidence 56799999875432 22222378999999754
No 181
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=46.25 E-value=5.1 Score=39.79 Aligned_cols=33 Identities=24% Similarity=0.484 Sum_probs=22.9
Q ss_pred EEeccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCcc
Q 017546 29 QVESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNN 71 (369)
Q Consensus 29 eies~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnn 71 (369)
.+-..||.|++.-. -+|+----..|++|||...
T Consensus 26 ~lw~KCp~c~~~~y----------~~eL~~n~~vcp~c~~h~r 58 (294)
T COG0777 26 GLWTKCPSCGEMLY----------RKELESNLKVCPKCGHHMR 58 (294)
T ss_pred CceeECCCccceee----------HHHHHhhhhcccccCcccc
Confidence 45678999987643 3444333489999999764
No 182
>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=45.95 E-value=9.1 Score=31.05 Aligned_cols=35 Identities=14% Similarity=0.282 Sum_probs=16.1
Q ss_pred eccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCc
Q 017546 285 PSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRN 324 (369)
Q Consensus 285 ~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~ 324 (369)
...||.||+.-.....+- ++--+-...|..||..+
T Consensus 22 ~F~CPfC~~~~sV~v~id-----kk~~~~~~~C~~Cg~~~ 56 (81)
T PF05129_consen 22 VFDCPFCNHEKSVSVKID-----KKEGIGILSCRVCGESF 56 (81)
T ss_dssp ----TTT--SS-EEEEEE-----TTTTEEEEEESSS--EE
T ss_pred eEcCCcCCCCCeEEEEEE-----ccCCEEEEEecCCCCeE
Confidence 447999996644444332 33445667899997665
No 183
>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=45.81 E-value=12 Score=40.83 Aligned_cols=27 Identities=30% Similarity=0.731 Sum_probs=18.7
Q ss_pred eccCCCCCC-CceEEEEEeecCCcceEEEEEeeCCCCCCCccce
Q 017546 31 ESLCMRCGE-NGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEV 73 (369)
Q Consensus 31 es~Cp~Cg~-~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEV 73 (369)
-+.|+.||. .|.. .+.||+||-++-|+
T Consensus 532 ~siC~~CGy~~g~~----------------~~~CP~CGs~~~ev 559 (586)
T TIGR02827 532 ITICNDCHHIDKRT----------------LHRCPVCGSANIDY 559 (586)
T ss_pred CeecCCCCCcCCCc----------------CCcCcCCCCccceE
Confidence 378999996 2211 28999999765444
No 184
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=45.27 E-value=19 Score=30.05 Aligned_cols=40 Identities=23% Similarity=0.421 Sum_probs=29.0
Q ss_pred eeeeeccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCccccccCCccCC
Q 017546 281 VMTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRIPE 335 (369)
Q Consensus 281 v~~~~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~eVk~~g~~~~ 335 (369)
.+.-.-.||.||+.. ++.+-.=-+.|.+||+... ||+..|
T Consensus 32 ~q~a~y~CpfCgk~~-----------vkR~a~GIW~C~~C~~~~A----GGAy~~ 71 (90)
T PRK03976 32 KMRAKHVCPVCGRPK-----------VKRVGTGIWECRKCGAKFA----GGAYTP 71 (90)
T ss_pred HHhcCccCCCCCCCc-----------eEEEEEEEEEcCCCCCEEe----CCcccc
Confidence 345567899998653 3666667799999999754 666655
No 185
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=45.19 E-value=23 Score=27.85 Aligned_cols=29 Identities=28% Similarity=0.516 Sum_probs=19.6
Q ss_pred cCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCC
Q 017546 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGER 69 (369)
Q Consensus 33 ~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyr 69 (369)
.||.||.+-.+-- ..-+|| .|.|..||-+
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 5999998854322 123444 4999999974
No 186
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=44.92 E-value=20 Score=28.69 Aligned_cols=37 Identities=14% Similarity=0.200 Sum_probs=23.8
Q ss_pred ccCCCCCCCceEEEEEeecCCcceEEEEEeeCC--CCCCCcc
Q 017546 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECP--HCGERNN 71 (369)
Q Consensus 32 s~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~--~CGyrnn 71 (369)
..||.||....+|---..-+. +.-.-..|. +||+++.
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~---~~~~Y~qC~N~eCg~tF~ 40 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDT---TKERYHQCQNVNCSATFI 40 (72)
T ss_pred ccCCCCCCccEEEEChhcChh---hheeeeecCCCCCCCEEE
Confidence 369999988755433222233 444568898 8998874
No 187
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=44.91 E-value=20 Score=30.76 Aligned_cols=30 Identities=33% Similarity=0.784 Sum_probs=21.5
Q ss_pred ccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCC
Q 017546 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGER 69 (369)
Q Consensus 32 s~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyr 69 (369)
.+|+.|+.+ .|+|... +. ++...|..||.+
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 689999988 5665443 22 455789999975
No 188
>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=44.91 E-value=15 Score=31.68 Aligned_cols=29 Identities=21% Similarity=0.426 Sum_probs=20.5
Q ss_pred cCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCcccc
Q 017546 287 TCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSEL 327 (369)
Q Consensus 287 ~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~eV 327 (369)
.||.|+..-.+.+ +.. +.|+.|||-.+.-
T Consensus 4 ~CP~C~seytY~d--------g~~----~iCpeC~~EW~~~ 32 (109)
T TIGR00686 4 PCPKCNSEYTYHD--------GTQ----LICPSCLYEWNEN 32 (109)
T ss_pred cCCcCCCcceEec--------CCe----eECcccccccccc
Confidence 6999987743322 332 6799999998765
No 189
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=44.66 E-value=14 Score=32.46 Aligned_cols=43 Identities=14% Similarity=0.208 Sum_probs=29.6
Q ss_pred ceeeeeccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCccccc
Q 017546 280 EVMTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELK 328 (369)
Q Consensus 280 ev~~~~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~eVk 328 (369)
.++.....||.|+..- ....=|+... ...+.|.+||+-+++--
T Consensus 25 ~~~~~~~~cP~C~s~~----~~k~g~~~~~--~qRyrC~~C~~tf~~~~ 67 (129)
T COG3677 25 RMQITKVNCPRCKSSN----VVKIGGIRRG--HQRYKCKSCGSTFTVET 67 (129)
T ss_pred hhhcccCcCCCCCccc----eeeECCcccc--ccccccCCcCcceeeec
Confidence 4566779999998763 1122233333 78899999999888653
No 190
>PRK10767 chaperone protein DnaJ; Provisional
Probab=44.24 E-value=61 Score=32.92 Aligned_cols=32 Identities=25% Similarity=0.570 Sum_probs=18.1
Q ss_pred cCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCcc
Q 017546 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNN 71 (369)
Q Consensus 33 ~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnn 71 (369)
.|+.|+..|..+... + .+.+...|++|+=+-.
T Consensus 161 ~C~~C~G~G~~~~~~------g-~~~~~~~C~~C~G~G~ 192 (371)
T PRK10767 161 TCPTCHGAGQVRMQQ------G-FFTVQQTCPTCHGRGK 192 (371)
T ss_pred cCCCCCCeeEEEEee------c-eEEEEEeCCCCCCcee
Confidence 466666666433322 1 1236669999976543
No 191
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=44.23 E-value=3.9 Score=40.64 Aligned_cols=32 Identities=22% Similarity=0.501 Sum_probs=21.1
Q ss_pred EeccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCcc
Q 017546 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNN 71 (369)
Q Consensus 30 ies~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnn 71 (369)
+=..||.|++.-. -++.---.+.||+|||...
T Consensus 26 ~~~~c~~c~~~~~----------~~~l~~~~~vc~~c~~h~r 57 (292)
T PRK05654 26 LWTKCPSCGQVLY----------RKELEANLNVCPKCGHHMR 57 (292)
T ss_pred CeeECCCccchhh----------HHHHHhcCCCCCCCCCCee
Confidence 4678999987532 2222222379999999764
No 192
>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=43.98 E-value=4 Score=40.46 Aligned_cols=32 Identities=22% Similarity=0.460 Sum_probs=21.3
Q ss_pred EeccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCcc
Q 017546 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNN 71 (369)
Q Consensus 30 ies~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnn 71 (369)
+=..||+|++.- |-+++---.+.||+|||+..
T Consensus 25 ~~~~c~~c~~~~----------~~~~l~~~~~vc~~c~~h~r 56 (285)
T TIGR00515 25 VWTKCPKCGQVL----------YTKELERNLEVCPKCDHHMR 56 (285)
T ss_pred CeeECCCCcchh----------hHHHHHhhCCCCCCCCCcCc
Confidence 457899998753 22233223379999999864
No 193
>PRK14295 chaperone protein DnaJ; Provisional
Probab=43.98 E-value=72 Score=32.81 Aligned_cols=32 Identities=25% Similarity=0.515 Sum_probs=18.6
Q ss_pred ccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCc
Q 017546 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (369)
Q Consensus 32 s~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrn 70 (369)
..|+.|+..|...... -.| .+...|+.|+=+-
T Consensus 184 ~~C~~C~G~G~~~~~~---g~~----~~~~~C~~C~G~G 215 (389)
T PRK14295 184 RVCPTCSGTGQVSRNS---GGF----SLSEPCPDCKGRG 215 (389)
T ss_pred cCCCCCCCEeEEEEEe---cce----EEEEecCCCccee
Confidence 3466676666433322 222 4667999997654
No 194
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=43.63 E-value=5 Score=39.88 Aligned_cols=31 Identities=16% Similarity=0.387 Sum_probs=20.9
Q ss_pred eccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCcc
Q 017546 285 PSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNS 325 (369)
Q Consensus 285 ~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~ 325 (369)
-.+||.|++....+- +---..+|++|||...
T Consensus 27 ~~~c~~c~~~~~~~~----------l~~~~~vc~~c~~h~r 57 (292)
T PRK05654 27 WTKCPSCGQVLYRKE----------LEANLNVCPKCGHHMR 57 (292)
T ss_pred eeECCCccchhhHHH----------HHhcCCCCCCCCCCee
Confidence 568999998754332 2122368999999764
No 195
>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=43.44 E-value=24 Score=29.39 Aligned_cols=22 Identities=27% Similarity=0.625 Sum_probs=17.1
Q ss_pred EeeCCCCCCCccceeeCcccCC
Q 017546 60 AFECPHCGERNNEVQFAGEIQP 81 (369)
Q Consensus 60 Sf~C~~CGyrnnEVq~~g~i~~ 81 (369)
+..|+|||...-+-.-+.+|..
T Consensus 35 a~~C~~CGe~y~~dev~~eIE~ 56 (89)
T TIGR03829 35 SISCSHCGMEYQDDTTVKEIED 56 (89)
T ss_pred cccccCCCcEeecHHHHHHHHh
Confidence 5789999988776666777755
No 196
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=43.28 E-value=20 Score=31.25 Aligned_cols=47 Identities=23% Similarity=0.355 Sum_probs=31.6
Q ss_pred eeeeccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCccccccCCccCCCceEEEEE
Q 017546 282 MTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRIPEKGKRITLF 343 (369)
Q Consensus 282 ~~~~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~eVk~~g~~~~~g~ritl~ 343 (369)
......|..|+.+... + .+.+.|++||-.+-.|..|....= ++|++.
T Consensus 67 ~p~~~~C~~C~~~~~~-----------e--~~~~~CP~C~s~~~~i~~G~el~i--~~ieve 113 (115)
T COG0375 67 EPAECWCLDCGQEVEL-----------E--ELDYRCPKCGSINLRIIGGDELII--KSIEVE 113 (115)
T ss_pred eccEEEeccCCCeecc-----------h--hheeECCCCCCCceEEecCCeeEE--EEEEEe
Confidence 3446789999765432 1 122339999999999988887765 555554
No 197
>PRK14276 chaperone protein DnaJ; Provisional
Probab=43.25 E-value=96 Score=31.72 Aligned_cols=35 Identities=23% Similarity=0.474 Sum_probs=19.4
Q ss_pred cCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCc
Q 017546 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (369)
Q Consensus 33 ~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrn 70 (369)
.|+.|+..|..++. ..++ |+-+. +...|+.|+=+-
T Consensus 165 ~C~~C~G~G~~~~~-~~~~-~G~~~-~~~~C~~C~G~G 199 (380)
T PRK14276 165 TCGKCHGSGVITVD-TQTP-LGMMR-RQVTCDVCHGTG 199 (380)
T ss_pred cCCCCCCeeEEEEE-EecC-CceEE-EEEECCCCCCCC
Confidence 47777666654333 3333 23333 356999996543
No 198
>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=43.02 E-value=8 Score=25.62 Aligned_cols=25 Identities=32% Similarity=0.693 Sum_probs=11.6
Q ss_pred CccCcccccceeEEEecCCCCeEEEEEeeCCCCCCC
Q 017546 288 CGACAASCETRMFMTRIPYFQEVIVMASTCDACGYR 323 (369)
Q Consensus 288 Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk 323 (369)
||.||.+..... - -.+..|+.||..
T Consensus 6 C~~CG~~t~~~~------~-----g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 6 CGRCGAPTKPAP------G-----GWARRCPSCGHE 30 (32)
T ss_dssp -TTT--BEEE-S------S-----SS-EEESSSS-E
T ss_pred cCcCCccccCCC------C-----cCEeECCCCcCE
Confidence 899988753211 1 145678888864
No 199
>PRK10767 chaperone protein DnaJ; Provisional
Probab=42.95 E-value=1.3e+02 Score=30.49 Aligned_cols=26 Identities=31% Similarity=0.662 Sum_probs=18.0
Q ss_pred eEEEeec----ceeEeCCCCCcceEEehHH
Q 017546 108 ATIKIPE----LDFEIPPEAQRGSLSTVEG 133 (369)
Q Consensus 108 ati~IPE----Ld~eI~p~~~~G~iTTVEG 133 (369)
+++.||- +.+.||++++.|.+-+|.|
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 4566654 4577888888888777765
No 200
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=42.77 E-value=29 Score=35.80 Aligned_cols=39 Identities=23% Similarity=0.477 Sum_probs=26.5
Q ss_pred eeccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCcccc
Q 017546 284 FPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSEL 327 (369)
Q Consensus 284 ~~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~eV 327 (369)
-+..||.|+..+.+++..-. -+..|...|+.|+=+=..|
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 45678888888776664322 4567888888887654444
No 201
>COG1856 Uncharacterized homolog of biotin synthetase [Function unknown]
Probab=42.60 E-value=9.8 Score=37.07 Aligned_cols=27 Identities=33% Similarity=0.732 Sum_probs=21.6
Q ss_pred EEeecCCcceEEE----EEeeCCCCCCCccc
Q 017546 46 LLTLIPHFRKVLL----SAFECPHCGERNNE 72 (369)
Q Consensus 46 llt~IP~FkeiiI----mSf~C~~CGyrnnE 72 (369)
+..+.|+|..|-+ .+|.|+|||-+.=+
T Consensus 4 l~v~~~k~~sISVTG~yC~lnC~HCg~~~L~ 34 (275)
T COG1856 4 LTVDPPKFISISVTGAYCSLNCPHCGRHYLE 34 (275)
T ss_pred cccCCCCCceEEEeccceEecChHHHHHHHH
Confidence 5567899998876 48999999987643
No 202
>PRK14283 chaperone protein DnaJ; Provisional
Probab=42.29 E-value=1.9e+02 Score=29.44 Aligned_cols=26 Identities=27% Similarity=0.658 Sum_probs=15.6
Q ss_pred eEEEee----cceeEeCCCCCcceEEehHH
Q 017546 108 ATIKIP----ELDFEIPPEAQRGSLSTVEG 133 (369)
Q Consensus 108 ati~IP----ELd~eI~p~~~~G~iTTVEG 133 (369)
.++.|| .+.+.||++++.|.+-.|.|
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 344555 34566777666776666664
No 203
>PRK14285 chaperone protein DnaJ; Provisional
Probab=42.15 E-value=73 Score=32.43 Aligned_cols=31 Identities=19% Similarity=0.373 Sum_probs=17.6
Q ss_pred cCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCc
Q 017546 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (369)
Q Consensus 33 ~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrn 70 (369)
.|+.|+..|..+. -| +-+ -+...|+.|+=+-
T Consensus 165 ~C~~C~G~G~~~~----~~--G~~-~~~~~C~~C~G~G 195 (365)
T PRK14285 165 ICNMCNGSGRVMQ----GG--GFF-RVTTTCPKCYGNG 195 (365)
T ss_pred cCCCccCceeEEe----cC--cee-EEeeecCCCCCcc
Confidence 4666655554332 22 223 5678899997544
No 204
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=42.07 E-value=39 Score=29.20 Aligned_cols=42 Identities=21% Similarity=0.503 Sum_probs=23.9
Q ss_pred EeccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccc
Q 017546 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNE 72 (369)
Q Consensus 30 ies~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnE 72 (369)
-.-.||+||..-. -.....---=.+-+..-|.|-+||++.+|
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 3467999986521 12222111123344455889999998754
No 205
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=41.88 E-value=15 Score=40.49 Aligned_cols=26 Identities=35% Similarity=0.655 Sum_probs=17.3
Q ss_pred eccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccce
Q 017546 31 ESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEV 73 (369)
Q Consensus 31 es~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEV 73 (369)
-+.|+.||.-+ ++ -+.||+|| +..||
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 47899999521 11 29999999 33444
No 206
>PRK14290 chaperone protein DnaJ; Provisional
Probab=41.83 E-value=1.2e+02 Score=30.85 Aligned_cols=21 Identities=24% Similarity=0.358 Sum_probs=16.5
Q ss_pred cceeEeCCCCCcceEEehHHH
Q 017546 114 ELDFEIPPEAQRGSLSTVEGI 134 (369)
Q Consensus 114 ELd~eI~p~~~~G~iTTVEGl 134 (369)
.|.+.||||+..|..-.++|.
T Consensus 222 ~~~V~Ip~G~~~G~~i~~~g~ 242 (365)
T PRK14290 222 DISVKIPKGATDNLRLRVKGK 242 (365)
T ss_pred EEEEEECCCCCCCcEEEEccc
Confidence 477888898888887777764
No 207
>PRK14287 chaperone protein DnaJ; Provisional
Probab=41.75 E-value=1.1e+02 Score=31.14 Aligned_cols=36 Identities=28% Similarity=0.659 Sum_probs=17.8
Q ss_pred cCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCcc
Q 017546 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNN 71 (369)
Q Consensus 33 ~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnn 71 (369)
.|+.|+..|... ...+++ |+-+. +...|+.|+=+-.
T Consensus 157 ~C~~C~G~G~~~-~~~~~~-~G~~~-~~~~C~~C~G~G~ 192 (371)
T PRK14287 157 TCSHCGGSGQLN-VEQNTP-FGRVV-NRRVCHHCEGTGK 192 (371)
T ss_pred ccCCCCCEEEEE-EEEecC-CceEE-EEEeCCCCCCCCc
Confidence 355555555332 222333 23233 3568888876543
No 208
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=41.31 E-value=27 Score=29.18 Aligned_cols=36 Identities=25% Similarity=0.516 Sum_probs=25.3
Q ss_pred eccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccceeeCcccCC
Q 017546 31 ESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEIQP 81 (369)
Q Consensus 31 es~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEVq~~g~i~~ 81 (369)
.-.||.||+..+-|. -+-| +.|.+||+.. .+|+..|
T Consensus 36 ~y~CpfCgk~~vkR~-a~GI----------W~C~~C~~~~----AGGAy~~ 71 (90)
T PTZ00255 36 KYFCPFCGKHAVKRQ-AVGI----------WRCKGCKKTV----AGGAWTL 71 (90)
T ss_pred CccCCCCCCCceeee-eeEE----------EEcCCCCCEE----eCCcccc
Confidence 457999998764443 2244 9999999965 4666654
No 209
>PRK04296 thymidine kinase; Provisional
Probab=40.86 E-value=28 Score=31.73 Aligned_cols=44 Identities=14% Similarity=0.252 Sum_probs=32.0
Q ss_pred CCceEEeccCCCCCCCceEEEEEe---ecCCcceEEEE------EeeCCCCCC
Q 017546 25 APLYQVESLCMRCGENGVTRFLLT---LIPHFRKVLLS------AFECPHCGE 68 (369)
Q Consensus 25 ~~v~eies~Cp~Cg~~g~tr~llt---~IP~FkeiiIm------Sf~C~~CGy 68 (369)
..|.++...|+.||++......++ ..++-+++|+. .-.|.+|-+
T Consensus 134 D~V~~l~~vC~~Cg~~a~~~~r~~~~~~~~~~~~~~~ig~~e~Y~~~Cr~c~~ 186 (190)
T PRK04296 134 DKVTELKAICVHCGRKATMNQRLIDGGPAVYEGPQVLVGGNESYEAVCRKHYK 186 (190)
T ss_pred CeEEEeeEEccccCCccceEEEEeCCCCccCCCCEEEECCcCcEEehhHHhhh
Confidence 458899999999999887777666 24566777754 345777754
No 210
>PRK14279 chaperone protein DnaJ; Provisional
Probab=40.32 E-value=85 Score=32.32 Aligned_cols=20 Identities=25% Similarity=0.576 Sum_probs=13.5
Q ss_pred ceeEeCCCCCcceEEehHHH
Q 017546 115 LDFEIPPEAQRGSLSTVEGI 134 (369)
Q Consensus 115 Ld~eI~p~~~~G~iTTVEGl 134 (369)
+.+.|||++..|..-+++|.
T Consensus 244 ~~V~Ip~G~~~G~~i~~~g~ 263 (392)
T PRK14279 244 INVRIPPGVEDGQRIRLAGQ 263 (392)
T ss_pred eEEEeCCCCCCCcEEEEeCC
Confidence 56667777777776666654
No 211
>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=40.07 E-value=14 Score=25.04 Aligned_cols=11 Identities=27% Similarity=0.942 Sum_probs=6.2
Q ss_pred EEeeCCCCCCC
Q 017546 59 SAFECPHCGER 69 (369)
Q Consensus 59 mSf~C~~CGyr 69 (369)
|-+.||+||-+
T Consensus 1 M~~~CP~C~~~ 11 (38)
T TIGR02098 1 MRIQCPNCKTS 11 (38)
T ss_pred CEEECCCCCCE
Confidence 34566666654
No 212
>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=39.52 E-value=14 Score=21.45 Aligned_cols=12 Identities=42% Similarity=1.168 Sum_probs=7.3
Q ss_pred eeCCCCCCCccc
Q 017546 61 FECPHCGERNNE 72 (369)
Q Consensus 61 f~C~~CGyrnnE 72 (369)
|.|+.||+..+.
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 679999887653
No 213
>PF10071 DUF2310: Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); InterPro: IPR016908 This group represents uncharacterised conserved proteins.
Probab=39.42 E-value=11 Score=36.97 Aligned_cols=75 Identities=25% Similarity=0.251 Sum_probs=46.2
Q ss_pred eecceeEeCCCCCcceEEehHHHHHHHHHHHHHh-hH---------------------hhhcCCHHHH-HHHHHHHHHHH
Q 017546 112 IPELDFEIPPEAQRGSLSTVEGILVRAADELEAL-QE---------------------ERKKLDPQTA-EAIDQFLLKLR 168 (369)
Q Consensus 112 IPELd~eI~p~~~~G~iTTVEGlL~~i~~~L~~~-~~---------------------~r~~~~~e~~-~ki~~~i~kL~ 168 (369)
+-||-|+. - ...-.+.-+|..|..+++.|... |- +.++.+++-. ....+.+++|.
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 45677774 1 12445667889999999998753 21 1123333222 45666677777
Q ss_pred HhhcCCCceEEEEeCCCCCc
Q 017546 169 ACAKGDSTFTFILDDPAGNS 188 (369)
Q Consensus 169 ~~~~g~~pFTliidDPsGNS 188 (369)
++--+...|.++=+|-..+.
T Consensus 81 ~~gl~~p~~~~ig~d~~s~~ 100 (258)
T PF10071_consen 81 EAGLLFPKFQIIGEDLNSEE 100 (258)
T ss_pred HhCCCCceeEEecccCCccc
Confidence 77766667888877765544
No 214
>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=39.39 E-value=87 Score=31.52 Aligned_cols=20 Identities=25% Similarity=0.441 Sum_probs=13.9
Q ss_pred ceeEeCCCCCcceEEehHHH
Q 017546 115 LDFEIPPEAQRGSLSTVEGI 134 (369)
Q Consensus 115 Ld~eI~p~~~~G~iTTVEGl 134 (369)
|.+.|||++..|..-.++|.
T Consensus 218 l~V~Ip~G~~~G~~i~~~g~ 237 (354)
T TIGR02349 218 ITVKIPAGVDTGQRLRVSGK 237 (354)
T ss_pred EEEEECCCCCCCCEEEEecC
Confidence 56777777777776666653
No 215
>PRK14301 chaperone protein DnaJ; Provisional
Probab=39.35 E-value=1.5e+02 Score=30.27 Aligned_cols=27 Identities=26% Similarity=0.586 Sum_probs=17.4
Q ss_pred eEEEeec----ceeEeCCCCCcceEEehHHH
Q 017546 108 ATIKIPE----LDFEIPPEAQRGSLSTVEGI 134 (369)
Q Consensus 108 ati~IPE----Ld~eI~p~~~~G~iTTVEGl 134 (369)
+++.||- +.+.||++++.|..-.|.|-
T Consensus 281 ~~~~v~tldG~i~v~ip~g~~~g~~~ri~g~ 311 (373)
T PRK14301 281 DRIEVPTLDDPVTLDIPKGTQSGEVFRLRGK 311 (373)
T ss_pred CeEEEecCCccEEEEECCCcCCCcEEEEcCC
Confidence 4555654 34777777777777777653
No 216
>PRK14294 chaperone protein DnaJ; Provisional
Probab=39.24 E-value=86 Score=31.84 Aligned_cols=20 Identities=25% Similarity=0.439 Sum_probs=13.7
Q ss_pred ceeEeCCCCCcceEEehHHH
Q 017546 115 LDFEIPPEAQRGSLSTVEGI 134 (369)
Q Consensus 115 Ld~eI~p~~~~G~iTTVEGl 134 (369)
|.+.|||++..|..-+++|.
T Consensus 215 l~V~Ip~G~~~G~~i~~~g~ 234 (366)
T PRK14294 215 VQVKIPAGVDTGSRLRLRGE 234 (366)
T ss_pred EEEecCCCCcCCcEEEEccC
Confidence 45667777777777777653
No 217
>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=39.12 E-value=12 Score=38.33 Aligned_cols=34 Identities=21% Similarity=0.324 Sum_probs=26.4
Q ss_pred eccCccCcccccceeEEEecCCCCeEEEEEeeCCCC
Q 017546 285 PSTCGACAASCETRMFMTRIPYFQEVIVMASTCDAC 320 (369)
Q Consensus 285 ~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~C 320 (369)
.-.||.|+.+...+.-...+|||--.-. ..|+.+
T Consensus 30 ~~~CP~C~~~v~lk~G~~k~~HFAH~~~--~~c~~~ 63 (375)
T PF06054_consen 30 KYFCPGCGEPVILKKGKKKIPHFAHKSK--SDCPFF 63 (375)
T ss_pred cEECCCCCCeeEEEEcCcccceeeecCC--CCCCcc
Confidence 4579999999999999999999987633 346433
No 218
>PRK14301 chaperone protein DnaJ; Provisional
Probab=38.96 E-value=75 Score=32.46 Aligned_cols=31 Identities=29% Similarity=0.621 Sum_probs=17.8
Q ss_pred cCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCc
Q 017546 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (369)
Q Consensus 33 ~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrn 70 (369)
.|+.|+..|...... . .+.++..|+.|+=+-
T Consensus 163 ~C~~C~G~G~v~~~~----G---~~~~~~~C~~C~G~G 193 (373)
T PRK14301 163 TCRHCGGSGQVRQSQ----G---FFQIAVPCPVCRGEG 193 (373)
T ss_pred ccCCccCeeEEEEEe----e---eEEEEEeCCCCCcee
Confidence 466666555433221 1 235689999997544
No 219
>PRK14300 chaperone protein DnaJ; Provisional
Probab=38.80 E-value=1.1e+02 Score=31.09 Aligned_cols=32 Identities=22% Similarity=0.435 Sum_probs=18.7
Q ss_pred ccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCc
Q 017546 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (369)
Q Consensus 32 s~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrn 70 (369)
..|+.|+..|..++. ++- +-|...|++|.=+-
T Consensus 163 ~~C~~C~G~G~~~~~------~g~-~~~~~~C~~C~G~G 194 (372)
T PRK14300 163 TTCDACSGVGATRMQ------QGF-FTIEQACHKCQGNG 194 (372)
T ss_pred ccCCCccCeEEEEEe------ece-EEEEEeCCCCCccc
Confidence 457777666654432 122 23677999996544
No 220
>PF06138 Chordopox_E11: Chordopoxvirus E11 protein; InterPro: IPR009201 This group represents a virion core protein, vaccinia E11L type.
Probab=38.63 E-value=37 Score=30.13 Aligned_cols=29 Identities=24% Similarity=0.466 Sum_probs=25.9
Q ss_pred HHHHHHHHHHHHHHHhhcCCC-ceEEEEeC
Q 017546 155 QTAEAIDQFLLKLRACAKGDS-TFTFILDD 183 (369)
Q Consensus 155 e~~~ki~~~i~kL~~~~~g~~-pFTliidD 183 (369)
+....++.||+.|++++..+. .|+|+|.|
T Consensus 32 ~~~~Av~~Fl~~L~kyI~veeStFylvvrd 61 (130)
T PF06138_consen 32 EARRAVKHFLSVLKKYIDVEESTFYLVVRD 61 (130)
T ss_pred hHHHHHHHHHHHHHhhEEecccEEEEEEec
Confidence 456789999999999999876 99999999
No 221
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.43 E-value=14 Score=32.86 Aligned_cols=41 Identities=32% Similarity=0.532 Sum_probs=26.1
Q ss_pred eccCccCccccccee---------EEEecCCCCeEEEEEeeCCCCCCCc--cccccCCccC
Q 017546 285 PSTCGACAASCETRM---------FMTRIPYFQEVIVMASTCDACGYRN--SELKPGGRIP 334 (369)
Q Consensus 285 ~~~Cp~C~~~~~~~m---------~~~~IP~F~eviims~~C~~CGyk~--~eVk~~g~~~ 334 (369)
-+.||.|..+.--.. ..|++|-| |.+||.|+ .+-|..|+.+
T Consensus 39 i~qcp~csasirgd~~vegvlglg~dye~psf---------chncgs~fpwterkiaga~e 90 (160)
T COG4306 39 ITQCPICSASIRGDYYVEGVLGLGGDYEPPSF---------CHNCGSRFPWTERKIAGAVE 90 (160)
T ss_pred HhcCCccCCcccccceeeeeeccCCCCCCcch---------hhcCCCCCCcHHHHHhHHHH
Confidence 457999987642222 34667764 99999775 4555555543
No 222
>PRK14280 chaperone protein DnaJ; Provisional
Probab=38.26 E-value=1.3e+02 Score=30.83 Aligned_cols=36 Identities=31% Similarity=0.779 Sum_probs=18.4
Q ss_pred cCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCcc
Q 017546 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNN 71 (369)
Q Consensus 33 ~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnn 71 (369)
.|+.|+..|... ....++ |+-+. +...|+.|+=+-.
T Consensus 162 ~C~~C~G~G~~~-~~~~~~-~g~~~-~~~~C~~C~G~G~ 197 (376)
T PRK14280 162 TCSHCGGSGQVS-VEQNTP-FGRVV-NRQTCPHCNGTGQ 197 (376)
T ss_pred cCCCCCCEEEEE-EEeecC-CceEE-EEEEcCCCCCCCc
Confidence 355555555332 223333 23232 5679999976543
No 223
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=38.26 E-value=22 Score=30.90 Aligned_cols=38 Identities=26% Similarity=0.589 Sum_probs=25.9
Q ss_pred eccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccceeeCcccCC
Q 017546 31 ESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEIQP 81 (369)
Q Consensus 31 es~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEVq~~g~i~~ 81 (369)
+-.|..|+..-. .+ ..-+.||+||-.+-.|..|....=
T Consensus 70 ~~~C~~C~~~~~-----------~e--~~~~~CP~C~s~~~~i~~G~el~i 107 (115)
T COG0375 70 ECWCLDCGQEVE-----------LE--ELDYRCPKCGSINLRIIGGDELII 107 (115)
T ss_pred EEEeccCCCeec-----------ch--hheeECCCCCCCceEEecCCeeEE
Confidence 467999965421 12 222449999999999988877643
No 224
>PRK04023 DNA polymerase II large subunit; Validated
Probab=38.07 E-value=18 Score=41.72 Aligned_cols=15 Identities=27% Similarity=0.468 Sum_probs=9.8
Q ss_pred ceeeeeccCccCccc
Q 017546 280 EVMTFPSTCGACAAS 294 (369)
Q Consensus 280 ev~~~~~~Cp~C~~~ 294 (369)
+|-...-.||.||+.
T Consensus 621 eVEVg~RfCpsCG~~ 635 (1121)
T PRK04023 621 EVEIGRRKCPSCGKE 635 (1121)
T ss_pred eecccCccCCCCCCc
Confidence 344445678888876
No 225
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=37.94 E-value=16 Score=40.17 Aligned_cols=28 Identities=29% Similarity=0.699 Sum_probs=19.2
Q ss_pred eccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccce
Q 017546 31 ESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEV 73 (369)
Q Consensus 31 es~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEV 73 (369)
-+.|+.||..+. + ..+.||+||-++-|+
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 378999996421 0 129999999866554
No 226
>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=37.61 E-value=20 Score=30.49 Aligned_cols=41 Identities=15% Similarity=0.107 Sum_probs=22.4
Q ss_pred eccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCcc
Q 017546 285 PSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNS 325 (369)
Q Consensus 285 ~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~ 325 (369)
+..||-||.+....--..--|+.-.---+.+.|+.|+-..-
T Consensus 2 p~~CpYCg~~~~l~~~~~iYg~~~~~~~~~y~C~~C~AyVG 42 (102)
T PF11672_consen 2 PIICPYCGGPAELVDGSEIYGHRYDDGPYLYVCTPCDAYVG 42 (102)
T ss_pred CcccCCCCCeeEEcccchhcCccCCCCceeEECCCCCceee
Confidence 56899999886553311112232100112289999986543
No 227
>PHA03001 putative virion core protein; Provisional
Probab=37.49 E-value=40 Score=29.94 Aligned_cols=30 Identities=30% Similarity=0.491 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHHHHhhcCCC-ceEEEEeCC
Q 017546 155 QTAEAIDQFLLKLRACAKGDS-TFTFILDDP 184 (369)
Q Consensus 155 e~~~ki~~~i~kL~~~~~g~~-pFTliidDP 184 (369)
+.++.++.||+.|++++..++ .|+|+|.|-
T Consensus 31 ~~~ka~~~fl~~L~kYi~v~eStFylvvrd~ 61 (132)
T PHA03001 31 EMRKAINKFLELLKKYIHVDKSTFYLVVKDK 61 (132)
T ss_pred hHHHHHHHHHHHHHhhEEecccEEEEEEecC
Confidence 456789999999999999876 999999985
No 228
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=37.09 E-value=13 Score=25.64 Aligned_cols=8 Identities=25% Similarity=0.771 Sum_probs=5.5
Q ss_pred cCccCccc
Q 017546 287 TCGACAAS 294 (369)
Q Consensus 287 ~Cp~C~~~ 294 (369)
.||.||+.
T Consensus 3 ~C~~Cg~~ 10 (36)
T PF05191_consen 3 ICPKCGRI 10 (36)
T ss_dssp EETTTTEE
T ss_pred CcCCCCCc
Confidence 47777765
No 229
>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=36.91 E-value=27 Score=30.58 Aligned_cols=31 Identities=26% Similarity=0.682 Sum_probs=21.5
Q ss_pred ccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCc
Q 017546 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (369)
Q Consensus 32 s~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrn 70 (369)
.+|+.|+.+ .|.|... +.+ +...|..||.+.
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 689999977 4555433 222 347899999864
No 230
>PRK14293 chaperone protein DnaJ; Provisional
Probab=36.81 E-value=91 Score=31.77 Aligned_cols=35 Identities=31% Similarity=0.649 Sum_probs=18.3
Q ss_pred cCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCc
Q 017546 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (369)
Q Consensus 33 ~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrn 70 (369)
.|+.|+..|..+. .+.+|+ + .+.+...|++|+=+-
T Consensus 162 ~C~~C~G~G~~~~-~~~~~~-g-~~~~~~~C~~C~G~G 196 (374)
T PRK14293 162 TCSTCGGAGQVRR-ATRTPF-G-SFTQVSECPTCNGTG 196 (374)
T ss_pred eCCCCCCcceEEE-EEecCc-c-eEEEEeeCCCCCcce
Confidence 4666666664333 333332 2 222456899996543
No 231
>PRK10220 hypothetical protein; Provisional
Probab=36.76 E-value=26 Score=30.33 Aligned_cols=29 Identities=14% Similarity=0.382 Sum_probs=20.0
Q ss_pred cCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCcccc
Q 017546 287 TCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSEL 327 (369)
Q Consensus 287 ~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~eV 327 (369)
.||.|+..-.+.+ +. -+.|+.|||-.+.-
T Consensus 5 ~CP~C~seytY~d--------~~----~~vCpeC~hEW~~~ 33 (111)
T PRK10220 5 HCPKCNSEYTYED--------NG----MYICPECAHEWNDA 33 (111)
T ss_pred cCCCCCCcceEcC--------CC----eEECCcccCcCCcc
Confidence 6999987643222 22 37899999988654
No 232
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=36.67 E-value=15 Score=28.54 Aligned_cols=30 Identities=33% Similarity=0.763 Sum_probs=20.6
Q ss_pred eeeccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCc
Q 017546 283 TFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRN 324 (369)
Q Consensus 283 ~~~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~ 324 (369)
.+.-.|..||.....+- |+| +.|..||||.
T Consensus 18 ~miYiCgdC~~en~lk~--------~D~----irCReCG~RI 47 (62)
T KOG3507|consen 18 TMIYICGDCGQENTLKR--------GDV----IRCRECGYRI 47 (62)
T ss_pred cEEEEeccccccccccC--------CCc----EehhhcchHH
Confidence 33446999998755443 444 5899999984
No 233
>PF10071 DUF2310: Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); InterPro: IPR016908 This group represents uncharacterised conserved proteins.
Probab=36.45 E-value=12 Score=36.79 Aligned_cols=36 Identities=19% Similarity=0.410 Sum_probs=23.7
Q ss_pred ceEEeccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCc
Q 017546 27 LYQVESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (369)
Q Consensus 27 v~eies~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrn 70 (369)
..|....||.||++=...- |.|. |+-|.|++|--=+
T Consensus 216 ~~e~~r~CP~Cg~~W~L~~-----plh~---iFdFKCD~CRLVS 251 (258)
T PF10071_consen 216 ASEQARKCPSCGGDWRLKE-----PLHD---IFDFKCDPCRLVS 251 (258)
T ss_pred HHhhCCCCCCCCCccccCC-----chhh---ceeccCCcceeec
Confidence 3467899999998643222 3332 4569999996543
No 234
>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=36.44 E-value=23 Score=37.59 Aligned_cols=35 Identities=20% Similarity=0.283 Sum_probs=25.2
Q ss_pred cCCCCCCCceEEEEEe------------ecCCcceEEEEEeeCCCCCCCcccee
Q 017546 33 LCMRCGENGVTRFLLT------------LIPHFRKVLLSAFECPHCGERNNEVQ 74 (369)
Q Consensus 33 ~Cp~Cg~~g~tr~llt------------~IP~FkeiiImSf~C~~CGyrnnEVq 74 (369)
.||.|.....++..-+ .=||| |.|.+|.|.+.||-
T Consensus 54 ~CP~C~~~L~~~~~~~~~~~~~~~~~~~~~~~~-------l~C~~C~Wss~~ig 100 (483)
T PF05502_consen 54 DCPICFSPLSVRASDTPPSPPDPSSDSGGKPYY-------LSCSYCRWSSRDIG 100 (483)
T ss_pred cCCCCCCcceeEecccccccccccccCCCCCEE-------EECCCceeeccccC
Confidence 5888887776665554 23443 89999999988763
No 235
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=36.01 E-value=19 Score=27.45 Aligned_cols=16 Identities=25% Similarity=0.584 Sum_probs=9.8
Q ss_pred ceeeeeccCccCcccc
Q 017546 280 EVMTFPSTCGACAASC 295 (369)
Q Consensus 280 ev~~~~~~Cp~C~~~~ 295 (369)
.+|++...||.||.+.
T Consensus 12 gvYTLk~~CP~CG~~t 27 (56)
T PRK13130 12 GVYTLKEICPVCGGKT 27 (56)
T ss_pred CCEEccccCcCCCCCC
Confidence 4566666666666653
No 236
>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=35.42 E-value=24 Score=34.58 Aligned_cols=10 Identities=20% Similarity=0.704 Sum_probs=3.5
Q ss_pred eccCccCccc
Q 017546 285 PSTCGACAAS 294 (369)
Q Consensus 285 ~~~Cp~C~~~ 294 (369)
...||+||..
T Consensus 172 ~g~CPvCGs~ 181 (290)
T PF04216_consen 172 RGYCPVCGSP 181 (290)
T ss_dssp -SS-TTT---
T ss_pred CCcCCCCCCc
Confidence 4567777665
No 237
>PRK14277 chaperone protein DnaJ; Provisional
Probab=35.23 E-value=1.2e+02 Score=31.04 Aligned_cols=34 Identities=21% Similarity=0.435 Sum_probs=17.5
Q ss_pred CCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCc
Q 017546 34 CMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (369)
Q Consensus 34 Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrn 70 (369)
|+.|+..|. .+....++ |+-+..+ ..|+.|+=+-
T Consensus 175 C~~C~G~G~-~~~~~~~~-~G~~~~~-~~C~~C~G~G 208 (386)
T PRK14277 175 CPVCHGTGQ-VRTRQNTP-FGRIVNI-RTCDRCHGEG 208 (386)
T ss_pred CCCCCCEEE-EEEEEecc-CceEEEE-EECCCCCcce
Confidence 555544442 23333443 3444434 5999997654
No 238
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=34.63 E-value=34 Score=29.69 Aligned_cols=46 Identities=15% Similarity=0.400 Sum_probs=27.3
Q ss_pred eeeeccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCccccccCCccC
Q 017546 282 MTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRIP 334 (369)
Q Consensus 282 ~~~~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~eVk~~g~~~ 334 (369)
......| .||+...... ..+.+| ...+.|++||-..-++..|....
T Consensus 67 vp~~~~C-~Cg~~~~~~~--~~~~~~----~~~~~CP~Cgs~~~~i~~G~El~ 112 (124)
T PRK00762 67 IPVEIEC-ECGYEGVVDE--DEIDHY----AAVIECPVCGNKRAHILGGRECN 112 (124)
T ss_pred cCeeEEe-eCcCcccccc--cchhcc----ccCCcCcCCCCCCCEEecCCeEE
Confidence 3456789 9997643321 111111 01367999998777887665543
No 239
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=34.59 E-value=18 Score=21.94 Aligned_cols=11 Identities=36% Similarity=1.265 Sum_probs=7.4
Q ss_pred eeCCCCCCCcc
Q 017546 61 FECPHCGERNN 71 (369)
Q Consensus 61 f~C~~CGyrnn 71 (369)
|.|+.|.|..+
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 68999999875
No 240
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=34.56 E-value=26 Score=30.24 Aligned_cols=31 Identities=23% Similarity=0.389 Sum_probs=23.5
Q ss_pred cCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccceee
Q 017546 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQF 75 (369)
Q Consensus 33 ~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEVq~ 75 (369)
+||.|+...+++.. . .|.||.|++.-+++-.
T Consensus 5 ~cp~c~sEytYed~----------~--~~~cpec~~ew~~~~~ 35 (112)
T COG2824 5 PCPKCNSEYTYEDG----------G--QLICPECAHEWNENEA 35 (112)
T ss_pred CCCccCCceEEecC----------c--eEeCchhccccccccc
Confidence 69999888766542 2 4899999999996543
No 241
>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=34.15 E-value=19 Score=28.40 Aligned_cols=27 Identities=26% Similarity=0.517 Sum_probs=19.9
Q ss_pred EEEEeeCCCCCCCccccccCCccCCCce
Q 017546 311 IVMASTCDACGYRNSELKPGGRIPEKGK 338 (369)
Q Consensus 311 iims~~C~~CGyk~~eVk~~g~~~~~g~ 338 (369)
..+.|+|..||.|+....+--+.. +|+
T Consensus 1 ~~l~FTC~~C~~Rs~~~~sk~aY~-~Gv 27 (66)
T PF05180_consen 1 YQLTFTCNKCGTRSAKMFSKQAYH-KGV 27 (66)
T ss_dssp EEEEEEETTTTEEEEEEEEHHHHH-TSE
T ss_pred CeEEEEcCCCCCccceeeCHHHHh-CCe
Confidence 368899999999998776655543 455
No 242
>PF10621 FpoO: F420H2 dehydrogenase subunit FpoO ; InterPro: IPR018288 This entry represents the FpoO subunit of membrane-bound multi-subunit F420H2 dehydrogenase, which oxidises the reduced coenzyme F420H2 to coenzyme F420 and feeds the electrons via an FeS cluster into an energy-conserving electron transport chain [, ]. This enzyme plays a role in the methanogenic pathway in methanogenic archaea. Reduced coenzyme F420H2 is the major cytoplasmic electron carrier of methanogens and a reversible hydride donor, much like NADH []. F420H2 + COB-S-S-CoM = F420 + CoM-SH + CoB-SH Where CoB-S-S-CoM (the heterosulphide of 2-mercaptoethanesulphonate and 7-mercaptoheptanoylthreonine phosphate) is the terminal electron acceptor of the methanogenic pathway, and is reduced with the concomitant generation of a transmembrane proton potential and ATP synthesis. The FpoO subunit of F420H2 dehydrogenase probably participates in the reduction of methanophenazine, where it acts as a special mechanism for the reduction of the methanogenic cofactor [].
Probab=34.02 E-value=26 Score=30.38 Aligned_cols=37 Identities=22% Similarity=0.459 Sum_probs=27.5
Q ss_pred eeccCccCcccccceeEEEecCCCCeEEEE--EeeCCCC
Q 017546 284 FPSTCGACAASCETRMFMTRIPYFQEVIVM--ASTCDAC 320 (369)
Q Consensus 284 ~~~~Cp~C~~~~~~~m~~~~IP~F~eviim--s~~C~~C 320 (369)
-..+|-.||+++..--..++||-|++.++- .-.|-+|
T Consensus 59 ~~gKC~LCG~kt~l~~VevqIPsFskg~~~~~~~lC~~C 97 (119)
T PF10621_consen 59 RSGKCDLCGKKTQLYPVEVQIPSFSKGSVKKDVHLCRRC 97 (119)
T ss_pred cccceeccCCcceeeEEeeecCCcccccchhHHHHHHHH
Confidence 356899999998777789999999876653 2344444
No 243
>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=33.79 E-value=26 Score=36.02 Aligned_cols=45 Identities=20% Similarity=0.375 Sum_probs=24.4
Q ss_pred CCcceeeeeccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCcc
Q 017546 277 APEEVMTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNS 325 (369)
Q Consensus 277 ~~~ev~~~~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~ 325 (369)
.++.-+-|..-|+.||+-..|.+..++.-. + ...+.|+.||++-.
T Consensus 166 ~~~~y~Pf~piC~~cGri~tt~v~~~d~~~-~---~v~Y~c~~cG~~g~ 210 (360)
T PF01921_consen 166 RPETYSPFLPICEKCGRIDTTEVTEYDPEG-G---TVTYRCEECGHEGE 210 (360)
T ss_dssp --TT--SEEEEETTTEE--EEEEEEE--SS-S---EEEEE--TTS---E
T ss_pred CCCCeeeeeeeccccCCcccceeeEeecCC-C---EEEEEecCCCCEEE
Confidence 445567788999999997778887776433 2 35789999999753
No 244
>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=33.77 E-value=30 Score=35.58 Aligned_cols=39 Identities=18% Similarity=0.408 Sum_probs=21.1
Q ss_pred EEeccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCcc
Q 017546 29 QVESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNN 71 (369)
Q Consensus 29 eies~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnn 71 (369)
-+.-.|++||+-.+|.+.-++. +-=...+.|++||++..
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 3667899999866677665553 22235699999999753
No 245
>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=33.72 E-value=24 Score=26.59 Aligned_cols=37 Identities=22% Similarity=0.451 Sum_probs=24.8
Q ss_pred ccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCccccccCCc
Q 017546 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGR 332 (369)
Q Consensus 286 ~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~eVk~~g~ 332 (369)
..|+.|++-+.. -+++.-....|+.||- .|.|+....
T Consensus 5 iRC~~CnklLa~---------~g~~~~leIKCpRC~t-iN~~~a~~~ 41 (51)
T PF10122_consen 5 IRCGHCNKLLAK---------AGEVIELEIKCPRCKT-INHVRATSP 41 (51)
T ss_pred eeccchhHHHhh---------hcCccEEEEECCCCCc-cceEeccCC
Confidence 469999887532 1456677889999984 556665543
No 246
>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=33.41 E-value=42 Score=28.12 Aligned_cols=36 Identities=33% Similarity=0.677 Sum_probs=25.2
Q ss_pred eccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccceeeCcccCC
Q 017546 31 ESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEIQP 81 (369)
Q Consensus 31 es~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEVq~~g~i~~ 81 (369)
.-.||.||+..+-|. -+-| +.|.+||+.. .+|+..|
T Consensus 35 ~y~CpfCgk~~vkR~-a~GI----------W~C~~C~~~~----AGGAy~p 70 (91)
T TIGR00280 35 KYVCPFCGKKTVKRG-STGI----------WTCRKCGAKF----AGGAYTP 70 (91)
T ss_pred CccCCCCCCCceEEE-eeEE----------EEcCCCCCEE----eCCcccc
Confidence 357999997764332 3344 9999999965 4777655
No 247
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=33.26 E-value=27 Score=26.80 Aligned_cols=22 Identities=32% Similarity=0.422 Sum_probs=15.3
Q ss_pred ccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCc
Q 017546 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (369)
Q Consensus 32 s~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrn 70 (369)
+.|++||+. ..|| -.|+ |||-+
T Consensus 28 ~~c~~cg~~--------~~pH--------~vc~-cG~Y~ 49 (60)
T PRK01110 28 SVDKTTGEY--------HLPH--------HVSP-KGYYK 49 (60)
T ss_pred eEcCCCCce--------eccc--------eecC-CcccC
Confidence 569999753 3455 6799 99543
No 248
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.17 E-value=13 Score=32.75 Aligned_cols=33 Identities=33% Similarity=0.660 Sum_probs=23.7
Q ss_pred EeccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccc
Q 017546 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNE 72 (369)
Q Consensus 30 ies~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnE 72 (369)
+...||+||+--- |+--+-.+-.|+.||.....
T Consensus 20 l~grCP~CGeGrL----------F~gFLK~~p~C~aCG~dyg~ 52 (126)
T COG5349 20 LRGRCPRCGEGRL----------FRGFLKVVPACEACGLDYGF 52 (126)
T ss_pred hcCCCCCCCCchh----------hhhhcccCchhhhccccccC
Confidence 4678999996532 55555556789999987653
No 249
>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=33.08 E-value=19 Score=29.40 Aligned_cols=13 Identities=69% Similarity=1.341 Sum_probs=6.9
Q ss_pred EEeeCCCCCCCcc
Q 017546 59 SAFECPHCGERNN 71 (369)
Q Consensus 59 mSf~C~~CGyrnn 71 (369)
..|.|+|||.+.+
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 4589999998754
No 250
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=32.99 E-value=18 Score=23.65 Aligned_cols=10 Identities=30% Similarity=0.743 Sum_probs=5.2
Q ss_pred cCccCccccc
Q 017546 287 TCGACAASCE 296 (369)
Q Consensus 287 ~Cp~C~~~~~ 296 (369)
.||+||.++.
T Consensus 1 ~CP~C~s~l~ 10 (28)
T PF03119_consen 1 TCPVCGSKLV 10 (28)
T ss_dssp B-TTT--BEE
T ss_pred CcCCCCCEeE
Confidence 4999998764
No 251
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.86 E-value=21 Score=29.25 Aligned_cols=26 Identities=19% Similarity=0.382 Sum_probs=16.0
Q ss_pred cCccCccccccee-EEEecCCCCeEEEEEeeCCCCCC
Q 017546 287 TCGACAASCETRM-FMTRIPYFQEVIVMASTCDACGY 322 (369)
Q Consensus 287 ~Cp~C~~~~~~~m-~~~~IP~F~eviims~~C~~CGy 322 (369)
.||+|+..+.... .-++|- .|+.|+=
T Consensus 3 lCP~C~v~l~~~~rs~vEiD----------~CPrCrG 29 (88)
T COG3809 3 LCPICGVELVMSVRSGVEID----------YCPRCRG 29 (88)
T ss_pred ccCcCCceeeeeeecCceee----------eCCcccc
Confidence 5999988764332 333443 3888863
No 252
>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=32.84 E-value=23 Score=38.14 Aligned_cols=26 Identities=42% Similarity=1.068 Sum_probs=18.9
Q ss_pred cCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccce
Q 017546 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEV 73 (369)
Q Consensus 33 ~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEV 73 (369)
.|..||..+. ++ .+.||+||-++-++
T Consensus 520 ~C~~CG~~~~-----------~~----~~~CP~CGs~~~~~ 545 (555)
T cd01675 520 ICNDCGYIGE-----------GE----GFKCPKCGSEDVEV 545 (555)
T ss_pred cCCCCCCCCc-----------CC----CCCCcCCCCcCceE
Confidence 8999997543 11 29999999887444
No 253
>PRK14278 chaperone protein DnaJ; Provisional
Probab=32.82 E-value=2.4e+02 Score=28.79 Aligned_cols=26 Identities=35% Similarity=0.721 Sum_probs=18.0
Q ss_pred eEEEeecc-----eeEeCCCCCcceEEehHH
Q 017546 108 ATIKIPEL-----DFEIPPEAQRGSLSTVEG 133 (369)
Q Consensus 108 ati~IPEL-----d~eI~p~~~~G~iTTVEG 133 (369)
+++.||-| .+.||++++.|.+-.|.|
T Consensus 280 ~~~~i~tld~~~i~v~ip~g~~~g~~lrl~g 310 (378)
T PRK14278 280 TTVTVEAILDGPSEITIPPGTQPGSVITLRG 310 (378)
T ss_pred CeEEEecCCCCeEEEEeCCCcCCCcEEEECC
Confidence 56666654 477888777787776665
No 254
>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=32.63 E-value=32 Score=31.27 Aligned_cols=47 Identities=19% Similarity=0.275 Sum_probs=28.2
Q ss_pred ceeeeeccCccCcccc-----cceeEEEecCCCCeEEEEEeeCCCCCCCccc
Q 017546 280 EVMTFPSTCGACAASC-----ETRMFMTRIPYFQEVIVMASTCDACGYRNSE 326 (369)
Q Consensus 280 ev~~~~~~Cp~C~~~~-----~~~m~~~~IP~F~eviims~~C~~CGyk~~e 326 (369)
-.+.|...|.+||..- .+..-.+++|..+-.-=+.+.|..|+...+=
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 4578999999998642 2234577899998888899999999876654
No 255
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=32.46 E-value=28 Score=30.79 Aligned_cols=43 Identities=21% Similarity=0.321 Sum_probs=26.2
Q ss_pred ceeeeeccCccCcccccceeE---EEecCC-CCeEEEEEeeCCCCCC
Q 017546 280 EVMTFPSTCGACAASCETRMF---MTRIPY-FQEVIVMASTCDACGY 322 (369)
Q Consensus 280 ev~~~~~~Cp~C~~~~~~~m~---~~~IP~-F~eviims~~C~~CGy 322 (369)
+.-.+.+.|+.||.++..-.+ .-.+|. ..+-.-.-+.|+.||.
T Consensus 86 ~~~~~~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~k 132 (147)
T PF01927_consen 86 RLDPIFSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGK 132 (147)
T ss_pred ccCCCCCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCC
Confidence 344556899999987643222 122333 2333445899999995
No 256
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=32.32 E-value=49 Score=28.51 Aligned_cols=39 Identities=23% Similarity=0.416 Sum_probs=26.7
Q ss_pred cceEEEEEeeCCCCCCCccceeeCcccCCcceEEEEEee
Q 017546 53 FRKVLLSAFECPHCGERNNEVQFAGEIQPRGCNYSLKVP 91 (369)
Q Consensus 53 FkeiiImSf~C~~CGyrnnEVq~~g~i~~kG~r~tL~V~ 91 (369)
|=||=+=+..||+||-...-+--++...--|..++++|=
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 345555566777777776666666666667777888875
No 257
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=32.32 E-value=44 Score=28.46 Aligned_cols=35 Identities=11% Similarity=0.297 Sum_probs=25.4
Q ss_pred ceeeeeccCccCcccccceeEEEecCCCCeEEEEE
Q 017546 280 EVMTFPSTCGACAASCETRMFMTRIPYFQEVIVMA 314 (369)
Q Consensus 280 ev~~~~~~Cp~C~~~~~~~m~~~~IP~F~eviims 314 (369)
||-...+.||.||.++..-+..-+.-..+=++.|-
T Consensus 42 eIevG~~~cP~Cge~~~~a~vva~taLVgL~l~mk 76 (102)
T PF04475_consen 42 EIEVGDTICPKCGEELDSAFVVADTALVGLILEMK 76 (102)
T ss_pred EEecCcccCCCCCCccCceEEEeccceEEEEEEEE
Confidence 45556778999999987777777766666666664
No 258
>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=32.20 E-value=21 Score=32.66 Aligned_cols=24 Identities=8% Similarity=0.384 Sum_probs=17.1
Q ss_pred cceeeeeccCccCcccccceeEEE
Q 017546 279 EEVMTFPSTCGACAASCETRMFMT 302 (369)
Q Consensus 279 ~ev~~~~~~Cp~C~~~~~~~m~~~ 302 (369)
++|..+.+.|..||+++..+...+
T Consensus 131 d~i~kl~avC~~Cg~~A~~t~R~~ 154 (176)
T PF00265_consen 131 DKITKLKAVCEVCGRKATFTQRIV 154 (176)
T ss_dssp SEEEEE-EE-TTTSSEE-EEEEEE
T ss_pred CeEEEeccEECCCCCceeEEEEEc
Confidence 579999999999999976666555
No 259
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=32.11 E-value=58 Score=34.75 Aligned_cols=43 Identities=19% Similarity=0.364 Sum_probs=31.1
Q ss_pred CcceeeeeccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCcc
Q 017546 278 PEEVMTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNS 325 (369)
Q Consensus 278 ~~ev~~~~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~ 325 (369)
++.-+-|.--||.||+-..+.+..++... +.| .+.| .||++..
T Consensus 168 ~~~~~P~~pic~~cg~~~~~~~~~~d~~~-~~v---~y~~-~cG~~~~ 210 (510)
T PRK00750 168 QATYSPFLPICPKCGKVLTTPVISYDAEA-GTV---TYDC-ECGHEGE 210 (510)
T ss_pred CCCeeeeeeeCCCCCccceEEEEEEeCCC-CEE---EEEc-CCCCEEE
Confidence 44567789999999999888887676543 333 3478 6999854
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=31.72 E-value=50 Score=33.04 Aligned_cols=38 Identities=24% Similarity=0.398 Sum_probs=24.5
Q ss_pred eccCCCCCCCceEE-EEEeecCCcceEEEEEeeCCCCCCCc
Q 017546 31 ESLCMRCGENGVTR-FLLTLIPHFRKVLLSAFECPHCGERN 70 (369)
Q Consensus 31 es~Cp~Cg~~g~tr-~llt~IP~FkeiiImSf~C~~CGyrn 70 (369)
.-.|+.||+...+- .+.|+ --.|=+-.-|.|..||++-
T Consensus 258 ~~~C~~C~~~~~~~~q~Qtr--saDEpmT~f~~C~~Cg~~w 296 (299)
T TIGR01385 258 LFTCGKCKQKKCTYYQLQTR--SADEPMTTFVTCEECGNRW 296 (299)
T ss_pred cccCCCCCCccceEEEeccc--CCCCCCeEEEEcCCCCCee
Confidence 36799999765433 23333 2345555568999999874
No 261
>TIGR00357 methionine-R-sulfoxide reductase. This model describes a domain found in PilB, a protein important for pilin expression, N-terminal to a domain coextensive to with the known peptide methionine sulfoxide reductase (MsrA), a protein repair enzyme, of E. coli. Among the early completed genomes, this module is found if and only if MsrA is also found, whether N-terminal to MsrA (as for Helicobacter pylori), C-terminal (as for Treponema pallidum), or in a separate polypeptide. Although the function of this region is not clear, an auxiliary function to MsrA is suggested.
Probab=31.68 E-value=76 Score=28.33 Aligned_cols=55 Identities=16% Similarity=0.195 Sum_probs=39.3
Q ss_pred cCccCcccccceeEEEec----CCCCeEE----------------EEEeeCCCCCCCccccccCCccCCCceEEEE
Q 017546 287 TCGACAASCETRMFMTRI----PYFQEVI----------------VMASTCDACGYRNSELKPGGRIPEKGKRITL 342 (369)
Q Consensus 287 ~Cp~C~~~~~~~m~~~~I----P~F~evi----------------ims~~C~~CGyk~~eVk~~g~~~~~g~ritl 342 (369)
.|.+||.++..-...++- |-|-+-| -.-..|.+||-.---|...|. .|.|.|+-+
T Consensus 42 ~C~~Cg~pLF~S~~KfdSg~GWPSF~~~i~~~~V~~~~D~s~gm~RtEv~C~~Cg~HLGHVF~DGP-~ptg~RyCI 116 (134)
T TIGR00357 42 VDITCGEPLFSSEDKFDSGCGWPSFYKPISEEVVAYERDESHGMIRTEVRCRNCDAHLGHVFDDGP-EPTGLRYCI 116 (134)
T ss_pred EccCCCCccccccchhcCCCCCcCcCcccCCCceEEeecCCCCcEEEEEEecCCCCccCcccCCCC-CCCCceEee
Confidence 588888887665555554 6664433 244789999999888888876 678888764
No 262
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=31.23 E-value=64 Score=32.13 Aligned_cols=44 Identities=23% Similarity=0.407 Sum_probs=31.0
Q ss_pred cCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCccccccCCccCCCceEEEEEecCcC
Q 017546 287 TCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRIPEKGKRITLFVKNIN 348 (369)
Q Consensus 287 ~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~eVk~~g~~~~~g~ritl~V~~~~ 348 (369)
-|+.||.+...+. ++ .+..|.+||..+--. +.| .-|.+-+...+
T Consensus 113 FCg~CG~~~~~~~--------~g---~~~~C~~cg~~~fPR-----~dP--~vIv~v~~~~~ 156 (279)
T COG2816 113 FCGRCGTKTYPRE--------GG---WARVCPKCGHEHFPR-----IDP--CVIVAVIRGDE 156 (279)
T ss_pred CCCCCCCcCcccc--------Cc---eeeeCCCCCCccCCC-----CCC--eEEEEEecCCc
Confidence 3888888765443 22 356899999988655 788 77777776654
No 263
>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=30.97 E-value=34 Score=24.07 Aligned_cols=19 Identities=26% Similarity=0.642 Sum_probs=11.1
Q ss_pred EeeCCCCCCCccceeeCcc
Q 017546 60 AFECPHCGERNNEVQFAGE 78 (369)
Q Consensus 60 Sf~C~~CGyrnnEVq~~g~ 78 (369)
.|.|+.||.....+++.++
T Consensus 5 ey~C~~Cg~~fe~~~~~~~ 23 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSISE 23 (42)
T ss_pred EEEeCCCCCEEEEEEEcCC
Confidence 4566666666655555554
No 264
>PTZ00293 thymidine kinase; Provisional
Probab=30.67 E-value=39 Score=32.18 Aligned_cols=40 Identities=18% Similarity=0.399 Sum_probs=30.1
Q ss_pred cceeeeeccCccCcccccceeEEEecCCCCeEEE------EEeeCCCCC
Q 017546 279 EEVMTFPSTCGACAASCETRMFMTRIPYFQEVIV------MASTCDACG 321 (369)
Q Consensus 279 ~ev~~~~~~Cp~C~~~~~~~m~~~~IP~F~evii------ms~~C~~CG 321 (369)
+.|.++.+.|..||+++..+...++ =++++. ....|.+|=
T Consensus 131 D~V~kl~aiC~~CG~~A~~t~R~~~---~~~~v~IGg~e~Y~a~CR~c~ 176 (211)
T PTZ00293 131 ERVTKLTAVCMFCGKEASFSKRIVQ---SEQIELIGGEDKYIATCRKCF 176 (211)
T ss_pred CEEEEcceEchhhCCcceeEEEEcC---CCCEEEECCcccEEehhhhhh
Confidence 4799999999999999776666665 244444 456788886
No 265
>PRK14300 chaperone protein DnaJ; Provisional
Probab=30.41 E-value=65 Score=32.82 Aligned_cols=29 Identities=31% Similarity=0.615 Sum_probs=16.5
Q ss_pred eccCccCcccccceeEEEecCCCCeEEEEEeeCCCC
Q 017546 285 PSTCGACAASCETRMFMTRIPYFQEVIVMASTCDAC 320 (369)
Q Consensus 285 ~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~C 320 (369)
...||.|+..+...+. ++-+- |...|+.|
T Consensus 162 ~~~C~~C~G~G~~~~~------~g~~~-~~~~C~~C 190 (372)
T PRK14300 162 VTTCDACSGVGATRMQ------QGFFT-IEQACHKC 190 (372)
T ss_pred CccCCCccCeEEEEEe------eceEE-EEEeCCCC
Confidence 3567777666543331 23333 66788888
No 266
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=30.17 E-value=26 Score=30.36 Aligned_cols=48 Identities=19% Similarity=0.366 Sum_probs=35.8
Q ss_pred ceeeeeccCccCcccccc--ee-----EEEecCCCCeEEEE----EeeCCCCCCCcccc
Q 017546 280 EVMTFPSTCGACAASCET--RM-----FMTRIPYFQEVIVM----ASTCDACGYRNSEL 327 (369)
Q Consensus 280 ev~~~~~~Cp~C~~~~~~--~m-----~~~~IP~F~eviim----s~~C~~CGyk~~eV 327 (369)
.|=++|+.||+||-.+.. ++ .++-+|-|.+|-.. +..|-.|+-+..+.
T Consensus 10 kvC~LP~~CpiCgLtLVss~HLARSyHHLfPl~~f~ev~~~~~~~~~~C~~C~~~f~~~ 68 (112)
T TIGR00622 10 KVCELPVECPICGLTLILSTHLARSYHHLFPLKAFQEIPLEEYNGSRFCFGCQGPFPKP 68 (112)
T ss_pred CccCCCCcCCcCCCEEeccchHHHhhhccCCCcccccccccccCCCCcccCcCCCCCCc
Confidence 466899999999987643 22 57888999887432 34699999887764
No 267
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=30.09 E-value=29 Score=25.80 Aligned_cols=24 Identities=38% Similarity=0.861 Sum_probs=18.5
Q ss_pred eccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCC
Q 017546 285 PSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYR 323 (369)
Q Consensus 285 ~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk 323 (369)
...|..|++....+ ++.|-.|||+
T Consensus 14 k~ICrkC~ARnp~~---------------A~~CRKCg~~ 37 (48)
T PRK04136 14 KKICMRCNARNPWR---------------ATKCRKCGYK 37 (48)
T ss_pred ccchhcccCCCCcc---------------ccccccCCCC
Confidence 45699998876433 8999999984
No 268
>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=29.91 E-value=25 Score=35.96 Aligned_cols=32 Identities=34% Similarity=0.649 Sum_probs=26.3
Q ss_pred eccCCCCCCCceEEEEEeecCCcceEEEEEeeCC
Q 017546 31 ESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECP 64 (369)
Q Consensus 31 es~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~ 64 (369)
.-.||.|++....|.-..++|||.-.-.. .|+
T Consensus 30 ~~~CP~C~~~v~lk~G~~k~~HFAH~~~~--~c~ 61 (375)
T PF06054_consen 30 KYFCPGCGEPVILKKGKKKIPHFAHKSKS--DCP 61 (375)
T ss_pred cEECCCCCCeeEEEEcCcccceeeecCCC--CCC
Confidence 46799999999999999999999887443 454
No 269
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=29.69 E-value=53 Score=27.43 Aligned_cols=36 Identities=36% Similarity=0.743 Sum_probs=24.5
Q ss_pred eccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccceeeCcccCC
Q 017546 31 ESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAGEIQP 81 (369)
Q Consensus 31 es~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEVq~~g~i~~ 81 (369)
.-.||.||+..+-|. -+-| +.|.+||+.. .+|+..|
T Consensus 36 ~y~CpfCgk~~vkR~-a~GI----------W~C~~C~~~~----AGGAy~~ 71 (90)
T PRK03976 36 KHVCPVCGRPKVKRV-GTGI----------WECRKCGAKF----AGGAYTP 71 (90)
T ss_pred CccCCCCCCCceEEE-EEEE----------EEcCCCCCEE----eCCcccc
Confidence 457999987654332 2333 9999999965 4666654
No 270
>PRK14295 chaperone protein DnaJ; Provisional
Probab=29.68 E-value=3.2e+02 Score=28.08 Aligned_cols=27 Identities=26% Similarity=0.666 Sum_probs=19.2
Q ss_pred eEEEeec-----ceeEeCCCCCcceEEehHHH
Q 017546 108 ATIKIPE-----LDFEIPPEAQRGSLSTVEGI 134 (369)
Q Consensus 108 ati~IPE-----Ld~eI~p~~~~G~iTTVEGl 134 (369)
.+++||- +.+.||++++.|..-.|.|-
T Consensus 303 ~~~~I~tldG~~~~v~ip~g~~~g~~iri~G~ 334 (389)
T PRK14295 303 AEVRVPTLGGPPVTVKLPPGTPNGRVLRVRGK 334 (389)
T ss_pred CeEEEECCCCCEEEEEECCccCCCcEEEECCC
Confidence 5666763 55788888888888777654
No 271
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.27 E-value=44 Score=28.98 Aligned_cols=24 Identities=29% Similarity=0.874 Sum_probs=17.3
Q ss_pred EeccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCC
Q 017546 30 VESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGE 68 (369)
Q Consensus 30 ies~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGy 68 (369)
+...||+||+ +.|+.-..|+.|+-
T Consensus 5 ~~~~cPvcg~---------------~~iVTeL~c~~~et 28 (122)
T COG3877 5 VINRCPVCGR---------------KLIVTELKCSNCET 28 (122)
T ss_pred CCCCCCcccc---------------cceeEEEecCCCCc
Confidence 4467999984 45666678888874
No 272
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=28.78 E-value=28 Score=38.22 Aligned_cols=24 Identities=21% Similarity=0.661 Sum_probs=17.4
Q ss_pred eccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCc
Q 017546 285 PSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRN 324 (369)
Q Consensus 285 ~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~ 324 (369)
-+.|+.||..+.. .+.|+.||-+.
T Consensus 559 ~~~C~~CGy~g~~----------------~~~CP~CG~~d 582 (618)
T PRK14704 559 VDRCKCCSYHGVI----------------GNECPSCGNED 582 (618)
T ss_pred CeecCCCCCCCCc----------------CccCcCCCCCC
Confidence 5679999876532 18899999654
No 273
>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=28.53 E-value=41 Score=22.72 Aligned_cols=9 Identities=44% Similarity=1.228 Sum_probs=5.9
Q ss_pred EeeCCCCCC
Q 017546 60 AFECPHCGE 68 (369)
Q Consensus 60 Sf~C~~CGy 68 (369)
...||+||-
T Consensus 26 ~~~CP~Cg~ 34 (41)
T smart00834 26 LATCPECGG 34 (41)
T ss_pred CCCCCCCCC
Confidence 456777775
No 274
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=28.34 E-value=22 Score=39.12 Aligned_cols=15 Identities=20% Similarity=0.627 Sum_probs=10.3
Q ss_pred EEeeCCCCCCCcccc
Q 017546 313 MASTCDACGYRNSEL 327 (369)
Q Consensus 313 ms~~C~~CGyk~~eV 327 (369)
-+..|++||++...+
T Consensus 40 ~~~fC~~CG~~~~~~ 54 (645)
T PRK14559 40 DEAHCPNCGAETGTI 54 (645)
T ss_pred ccccccccCCcccch
Confidence 455688888876654
No 275
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=28.32 E-value=30 Score=26.55 Aligned_cols=23 Identities=35% Similarity=0.891 Sum_probs=16.3
Q ss_pred eccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCC
Q 017546 285 PSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYR 323 (369)
Q Consensus 285 ~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk 323 (369)
...||+||.. .+|| -+|.+|||=
T Consensus 27 ~~~c~~cG~~--------~l~H--------rvc~~cg~Y 49 (57)
T COG0333 27 LSVCPNCGEY--------KLPH--------RVCLKCGYY 49 (57)
T ss_pred ceeccCCCCc--------ccCc--------eEcCCCCCc
Confidence 3569999854 2355 789999963
No 276
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=28.16 E-value=95 Score=33.17 Aligned_cols=39 Identities=21% Similarity=0.516 Sum_probs=26.3
Q ss_pred eEEeccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCcc
Q 017546 28 YQVESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNN 71 (369)
Q Consensus 28 ~eies~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnn 71 (369)
.-+.-.|++||+-.+|.+.-++... +.| .+.| .||++..
T Consensus 172 ~P~~pic~~cg~~~~~~~~~~d~~~-~~v---~y~~-~cG~~~~ 210 (510)
T PRK00750 172 SPFLPICPKCGKVLTTPVISYDAEA-GTV---TYDC-ECGHEGE 210 (510)
T ss_pred eeeeeeCCCCCccceEEEEEEeCCC-CEE---EEEc-CCCCEEE
Confidence 3577889999998888775554321 222 3578 5999764
No 277
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=28.13 E-value=30 Score=40.95 Aligned_cols=14 Identities=21% Similarity=0.446 Sum_probs=9.2
Q ss_pred eeeeeccCccCccc
Q 017546 281 VMTFPSTCGACAAS 294 (369)
Q Consensus 281 v~~~~~~Cp~C~~~ 294 (369)
|--....||.||+.
T Consensus 663 VEV~~rkCPkCG~~ 676 (1337)
T PRK14714 663 VEVGRRRCPSCGTE 676 (1337)
T ss_pred EEEEEEECCCCCCc
Confidence 33446678888875
No 278
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=28.08 E-value=69 Score=32.21 Aligned_cols=69 Identities=16% Similarity=0.209 Sum_probs=0.0
Q ss_pred ceeeeeccCccCcccccceeEEEecCCCCeEEEE-------EeeCCCCCCCccccccCCccCCCceEEEEEecCc--Ccc
Q 017546 280 EVMTFPSTCGACAASCETRMFMTRIPYFQEVIVM-------ASTCDACGYRNSELKPGGRIPEKGKRITLFVKNI--NDL 350 (369)
Q Consensus 280 ev~~~~~~Cp~C~~~~~~~m~~~~IP~F~eviim-------s~~C~~CGyk~~eVk~~g~~~~~g~ritl~V~~~--~DL 350 (369)
++......||+||.. |....|..- -..|.-|+...+-+...=......+++.+.--+. +.
T Consensus 179 ~~~~~~~~CPvCGs~----------P~~s~~~~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~~~l~y~~~e~~~~~- 247 (305)
T TIGR01562 179 ETRESRTLCPACGSP----------PVASMVRQGGKETGLRYLSCSLCATEWHYVRVKCSHCEESKHLAYLSLEHDAEK- 247 (305)
T ss_pred cccCCCCcCCCCCCh----------hhhhhhcccCCCCCceEEEcCCCCCcccccCccCCCCCCCCceeeEeecCCCCC-
Q ss_pred cceeeeeccee
Q 017546 351 SRDLIKVCNGA 361 (369)
Q Consensus 351 ~r~VlkS~ta~ 361 (369)
.-+|-++|.
T Consensus 248 --~~~r~e~C~ 256 (305)
T TIGR01562 248 --AVLKAETCD 256 (305)
T ss_pred --cceEEeecc
No 279
>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=27.79 E-value=30 Score=30.72 Aligned_cols=29 Identities=14% Similarity=0.397 Sum_probs=19.5
Q ss_pred eeccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCc
Q 017546 284 FPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRN 324 (369)
Q Consensus 284 ~~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~ 324 (369)
+=..||.|++..... +. -.+.|++|+-..
T Consensus 33 ~Y~aC~~C~kkv~~~------~~------~~~~C~~C~~~~ 61 (166)
T cd04476 33 WYPACPGCNKKVVEE------GN------GTYRCEKCNKSV 61 (166)
T ss_pred EEccccccCcccEeC------CC------CcEECCCCCCcC
Confidence 445699998764321 11 578999998665
No 280
>PRK14282 chaperone protein DnaJ; Provisional
Probab=27.76 E-value=69 Score=32.57 Aligned_cols=33 Identities=30% Similarity=0.581 Sum_probs=17.4
Q ss_pred ccCccCcccccceeEEEecCCCCeEEEEEeeCCCCC
Q 017546 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACG 321 (369)
Q Consensus 286 ~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CG 321 (369)
..||.|+..+... ....+++ +-+ .+...|+.|+
T Consensus 170 ~~C~~C~G~G~~~-~~~~~~~-G~~-~~~~~C~~C~ 202 (369)
T PRK14282 170 VTCPKCHGTGRIR-EERRSFF-GVF-VSERTCERCG 202 (369)
T ss_pred cCCCCCCCcCEEE-EEEEccC-cce-EEEEECCCCC
Confidence 4577776665332 2333332 333 3466888885
No 281
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=27.73 E-value=30 Score=23.77 Aligned_cols=25 Identities=24% Similarity=0.521 Sum_probs=14.6
Q ss_pred EEeeCCCCCCCccceeeCcccCCcceE
Q 017546 59 SAFECPHCGERNNEVQFAGEIQPRGCN 85 (369)
Q Consensus 59 mSf~C~~CGyrnnEVq~~g~i~~kG~r 85 (369)
|-..||+|+.+.+ | +..++.+.|.+
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 4567888887764 2 33445555543
No 282
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=27.48 E-value=33 Score=30.90 Aligned_cols=40 Identities=28% Similarity=0.516 Sum_probs=27.3
Q ss_pred ccCCCcceeeeeccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCc
Q 017546 274 RYSAPEEVMTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRN 324 (369)
Q Consensus 274 ~~~~~~ev~~~~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~ 324 (369)
.|.+.+-|......|-.||+...... ...|| .|++||...
T Consensus 101 ~Y~sGE~~g~G~l~C~~Cg~~~~~~~-~~~l~----------~Cp~C~~~~ 140 (146)
T PF07295_consen 101 VYHSGEVVGPGTLVCENCGHEVELTH-PERLP----------PCPKCGHTE 140 (146)
T ss_pred CeecCcEecCceEecccCCCEEEecC-CCcCC----------CCCCCCCCe
Confidence 46666667777889999998754322 23344 599999764
No 283
>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=27.23 E-value=22 Score=21.00 Aligned_cols=11 Identities=36% Similarity=1.214 Sum_probs=8.1
Q ss_pred eeCCCCCCCcc
Q 017546 61 FECPHCGERNN 71 (369)
Q Consensus 61 f~C~~CGyrnn 71 (369)
|.|+.||...+
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 284
>PRK12496 hypothetical protein; Provisional
Probab=27.21 E-value=42 Score=30.50 Aligned_cols=32 Identities=22% Similarity=0.640 Sum_probs=20.9
Q ss_pred ceeeeeccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCc
Q 017546 280 EVMTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRN 324 (369)
Q Consensus 280 ev~~~~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~ 324 (369)
++..+.-.|+.||+... .+.|+ -.|+.||.+.
T Consensus 122 ~~~~w~~~C~gC~~~~~-----~~~~~--------~~C~~CG~~~ 153 (164)
T PRK12496 122 KVIKWRKVCKGCKKKYP-----EDYPD--------DVCEICGSPV 153 (164)
T ss_pred hheeeeEECCCCCcccc-----CCCCC--------CcCCCCCChh
Confidence 56778888999996531 11121 3699999764
No 285
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=27.10 E-value=27 Score=29.18 Aligned_cols=34 Identities=18% Similarity=0.483 Sum_probs=23.1
Q ss_pred eeccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCccccccCC
Q 017546 284 FPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGG 331 (369)
Q Consensus 284 ~~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~eVk~~g 331 (369)
-.+.|.-||....-.-+ -.|.+|||++.-.....
T Consensus 15 tHtlCrRCG~~syH~qK--------------~~CasCGypsak~R~Yn 48 (91)
T PTZ00073 15 THTLCRRCGKRSFHVQK--------------KRCASCGYPSAKMRRYN 48 (91)
T ss_pred CcchhcccCcccccccc--------------ccchhcCCchhhccccc
Confidence 45679999987532222 23999999887665543
No 286
>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=26.62 E-value=22 Score=22.37 Aligned_cols=10 Identities=40% Similarity=1.305 Sum_probs=7.6
Q ss_pred eeCCCCCCCc
Q 017546 61 FECPHCGERN 70 (369)
Q Consensus 61 f~C~~CGyrn 70 (369)
|.|+.||++.
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 7788888764
No 287
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=26.57 E-value=1.1e+02 Score=30.82 Aligned_cols=14 Identities=14% Similarity=0.275 Sum_probs=10.9
Q ss_pred eeeeeccCccCccc
Q 017546 281 VMTFPSTCGACAAS 294 (369)
Q Consensus 281 v~~~~~~Cp~C~~~ 294 (369)
+......||+||..
T Consensus 183 ~~~~~~~CPvCGs~ 196 (309)
T PRK03564 183 YGEQRQFCPVCGSM 196 (309)
T ss_pred cccCCCCCCCCCCc
Confidence 34467899999986
No 288
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=26.49 E-value=24 Score=25.96 Aligned_cols=12 Identities=17% Similarity=0.584 Sum_probs=6.1
Q ss_pred eccCccCccccc
Q 017546 285 PSTCGACAASCE 296 (369)
Q Consensus 285 ~~~Cp~C~~~~~ 296 (369)
...||+|+.++.
T Consensus 20 ~~~CPlC~r~l~ 31 (54)
T PF04423_consen 20 KGCCPLCGRPLD 31 (54)
T ss_dssp SEE-TTT--EE-
T ss_pred CCcCCCCCCCCC
Confidence 348999998864
No 289
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=26.14 E-value=39 Score=28.47 Aligned_cols=13 Identities=23% Similarity=0.917 Sum_probs=7.9
Q ss_pred EeeCCCCCCCccc
Q 017546 314 ASTCDACGYRNSE 326 (369)
Q Consensus 314 s~~C~~CGyk~~e 326 (369)
-..|.+|||-+++
T Consensus 58 Pa~CkkCGfef~~ 70 (97)
T COG3357 58 PARCKKCGFEFRD 70 (97)
T ss_pred ChhhcccCccccc
Confidence 3456666666666
No 290
>PRK14292 chaperone protein DnaJ; Provisional
Probab=25.91 E-value=69 Score=32.53 Aligned_cols=33 Identities=24% Similarity=0.438 Sum_probs=18.5
Q ss_pred ccCccCcccccceeEEEecCCCCeEEEEEeeCCCCC
Q 017546 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACG 321 (369)
Q Consensus 286 ~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CG 321 (369)
..|+.|+..+...+....+| +-+- +...|..|+
T Consensus 158 ~~C~~C~G~G~~~~~~~~~~--g~~~-~~~~C~~C~ 190 (371)
T PRK14292 158 KTCPTCRGAGAVRAQARTIF--GVVE-TQQPCPTCR 190 (371)
T ss_pred ccCCCCCCccEEEEEEeccC--ceEE-EeeecCCCc
Confidence 44666665554444444444 4443 466888883
No 291
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=25.81 E-value=30 Score=38.81 Aligned_cols=25 Identities=28% Similarity=0.810 Sum_probs=15.8
Q ss_pred ccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCC
Q 017546 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYR 323 (369)
Q Consensus 286 ~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk 323 (369)
..||.||.++... . =..+|.+|||-
T Consensus 725 ~~Cp~Cg~~l~~~---------~----GC~~C~~CG~s 749 (752)
T PRK08665 725 GACPECGSILEHE---------E----GCVVCHSCGYS 749 (752)
T ss_pred CCCCCCCcccEEC---------C----CCCcCCCCCCC
Confidence 3699998553211 1 12489999994
No 292
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=25.64 E-value=39 Score=26.17 Aligned_cols=16 Identities=19% Similarity=0.495 Sum_probs=12.4
Q ss_pred ceeeeeccCccCcccc
Q 017546 280 EVMTFPSTCGACAASC 295 (369)
Q Consensus 280 ev~~~~~~Cp~C~~~~ 295 (369)
.+|++...||.||...
T Consensus 12 g~YTLke~Cp~CG~~t 27 (59)
T COG2260 12 GRYTLKEKCPVCGGDT 27 (59)
T ss_pred CceeecccCCCCCCcc
Confidence 5778888899998763
No 293
>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=25.63 E-value=75 Score=34.12 Aligned_cols=41 Identities=20% Similarity=0.446 Sum_probs=27.5
Q ss_pred CcceeeeeccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCcc
Q 017546 278 PEEVMTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNS 325 (369)
Q Consensus 278 ~~ev~~~~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~ 325 (369)
++.-+-|.--||.||+-.. .+..++.=. . ..+.| .||++-.
T Consensus 161 ~~~~~P~~pic~~cGrv~~-~~~~~~~~~--~---v~Y~c-~cG~~g~ 201 (515)
T TIGR00467 161 EENWYPISVFCENCGRDTT-TVNNYDNEY--S---IEYSC-ECGNQES 201 (515)
T ss_pred CCCceeeeeecCCcCccCc-eEEEecCCc--e---EEEEc-CCCCEEE
Confidence 3456778999999999855 444554322 2 45689 5999854
No 294
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=25.63 E-value=16 Score=28.47 Aligned_cols=34 Identities=26% Similarity=0.463 Sum_probs=23.6
Q ss_pred eccCccCccccccee-EEEecCCCCeEEEEEeeCCCCCCCccc
Q 017546 285 PSTCGACAASCETRM-FMTRIPYFQEVIVMASTCDACGYRNSE 326 (369)
Q Consensus 285 ~~~Cp~C~~~~~~~m-~~~~IP~F~eviims~~C~~CGyk~~e 326 (369)
-+.||.|...-...| ..-++|+ -.|-.|||...+
T Consensus 10 GA~CP~C~~~Dtl~mW~En~ve~--------vECV~CG~~~~~ 44 (66)
T COG3529 10 GAVCPACQAQDTLAMWRENNVEI--------VECVKCGHHMRE 44 (66)
T ss_pred cCCCcccchhhHHHHHHhcCCce--------EehhhcchHhhh
Confidence 357999987655555 4555665 469999997644
No 295
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=25.53 E-value=37 Score=38.00 Aligned_cols=24 Identities=25% Similarity=0.591 Sum_probs=16.4
Q ss_pred eccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCc
Q 017546 285 PSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRN 324 (369)
Q Consensus 285 ~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~ 324 (369)
-+.|+.||..+.. .+.|+.||-..
T Consensus 680 ~~~C~~CG~~~~~----------------~~~CP~CG~~~ 703 (735)
T PRK07111 680 VDRCPVCGYLGVI----------------EDKCPKCGSTN 703 (735)
T ss_pred CeecCCCCCCCCc----------------CccCcCCCCcc
Confidence 5679999865421 17899998643
No 296
>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=25.38 E-value=72 Score=28.99 Aligned_cols=46 Identities=24% Similarity=0.400 Sum_probs=27.5
Q ss_pred CceEEeccCCCCCCCce-----EEEEEeecCCcceEEEEEeeCCCCCCCcc
Q 017546 26 PLYQVESLCMRCGENGV-----TRFLLTLIPHFRKVLLSAFECPHCGERNN 71 (369)
Q Consensus 26 ~v~eies~Cp~Cg~~g~-----tr~llt~IP~FkeiiImSf~C~~CGyrnn 71 (369)
-..-+...|.+||+.-. ++.-.+.+|..|-..=+.+.|..|+..++
T Consensus 25 ~~~~fkvkCt~CgE~~~k~V~i~~~e~~e~~gsrG~aNfv~KCk~C~re~s 75 (161)
T PF05907_consen 25 FEWFFKVKCTSCGEVHPKWVYINRFEKHEIPGSRGTANFVMKCKFCKRESS 75 (161)
T ss_dssp --EEEEEEETTSS--EEEEEEE-TT-BEE-TTSS-EESEEE--SSSS--EE
T ss_pred CEEEEEEEECCCCCccCcceEeecceEEecCCCccceEeEecCcCcCCccE
Confidence 34678889999997543 23456689999998899999999987765
No 297
>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=25.24 E-value=45 Score=35.50 Aligned_cols=44 Identities=16% Similarity=0.229 Sum_probs=28.4
Q ss_pred ccCccCcccccceeEEEec-C----CCCeEEEEEeeCCCCCCCcccccc
Q 017546 286 STCGACAASCETRMFMTRI-P----YFQEVIVMASTCDACGYRNSELKP 329 (369)
Q Consensus 286 ~~Cp~C~~~~~~~m~~~~I-P----~F~eviims~~C~~CGyk~~eVk~ 329 (369)
..||.|..++.+......- | .=..--...+.|.+|-|-+.||-.
T Consensus 53 f~CP~C~~~L~~~~~~~~~~~~~~~~~~~~~~~~l~C~~C~Wss~~igi 101 (483)
T PF05502_consen 53 FDCPICFSPLSVRASDTPPSPPDPSSDSGGKPYYLSCSYCRWSSRDIGI 101 (483)
T ss_pred ccCCCCCCcceeEecccccccccccccCCCCCEEEECCCceeeccccCc
Confidence 3699999998877755400 0 000012345899999999998743
No 298
>PF02563 Poly_export: Polysaccharide biosynthesis/export protein; InterPro: IPR003715 The extracellular polysaccharide colanic acid (CA) is produced by species of the family Enterobacteriaceae. In Escherichia coli (strain K12) the CA cluster comprises 19 genes. The wzx gene encodes a protein with multiple transmembrane segments that may function in export of the CA repeat unit from the cytoplasm into the periplasm in a process analogous to O-unit export. The CA gene clusters may be involved in the export of polysaccharide from the cell [].; GO: 0015159 polysaccharide transmembrane transporter activity, 0015774 polysaccharide transport, 0016020 membrane; PDB: 2W8I_E 2W8H_E 2J58_D.
Probab=25.12 E-value=61 Score=25.61 Aligned_cols=32 Identities=25% Similarity=0.264 Sum_probs=26.3
Q ss_pred ceEEEEEecCcCcccceeeeecceeEEecccC
Q 017546 337 GKRITLFVKNINDLSRDLIKVCNGAIQLISIA 368 (369)
Q Consensus 337 g~ritl~V~~~~DL~r~VlkS~ta~i~IPElg 368 (369)
|-++.+.|-...+|++.+.-+..++|.+|.+|
T Consensus 16 GD~l~i~v~~~~~l~~~~~V~~dG~I~lP~iG 47 (82)
T PF02563_consen 16 GDVLRISVFGWPELSGEYTVDPDGTISLPLIG 47 (82)
T ss_dssp T-EEEEEETT-HHHCCSEE--TTSEEEETTTE
T ss_pred CCEEEEEEecCCCcccceEECCCCcEeecccc
Confidence 77899999999999999999999999999987
No 299
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=24.92 E-value=38 Score=32.87 Aligned_cols=27 Identities=30% Similarity=0.554 Sum_probs=16.8
Q ss_pred cCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCc
Q 017546 287 TCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRN 324 (369)
Q Consensus 287 ~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~ 324 (369)
-||.||.+.... -+. ....|.+||..+
T Consensus 101 fC~~CG~~~~~~--------~~~---~~~~C~~c~~~~ 127 (256)
T PRK00241 101 FCGYCGHPMHPS--------KTE---WAMLCPHCRERY 127 (256)
T ss_pred cccccCCCCeec--------CCc---eeEECCCCCCEE
Confidence 499999875432 122 235688888654
No 300
>KOG3262 consensus H/ACA small nucleolar RNP component GAR1 [Translation, ribosomal structure and biogenesis]
Probab=24.77 E-value=25 Score=33.27 Aligned_cols=63 Identities=22% Similarity=0.395 Sum_probs=41.5
Q ss_pred CCcceeeeeccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCccccccCCccCCCceEEEEEec
Q 017546 277 APEEVMTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSELKPGGRIPEKGKRITLFVK 345 (369)
Q Consensus 277 ~~~ev~~~~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~eVk~~g~~~~~g~ritl~V~ 345 (369)
.|+||.++-.-=..|...+..+.-..+||||.--|.....= .=| |.-|| .+.+.+ .-+|+|..
T Consensus 49 pp~evvelg~flh~Cegd~Vck~~~~kIPyfNAPIylenk~-qIG-KVDEI--fG~i~d--~~fsIK~~ 111 (215)
T KOG3262|consen 49 PPEEVVELGKFLHMCEGDLVCKLTNKKIPYFNAPIYLENKE-QIG-KVDEI--FGPIND--VHFSIKPS 111 (215)
T ss_pred CchhhhhhhhhhhhcCCceEEeeccccCCCCCCceeecchh-hhc-chhhh--cccccc--cEEEEecC
Confidence 45677777777778888888899999999997766544321 111 34444 566666 55555543
No 301
>PF14584 DUF4446: Protein of unknown function (DUF4446)
Probab=24.67 E-value=2.9e+02 Score=24.98 Aligned_cols=59 Identities=29% Similarity=0.492 Sum_probs=40.7
Q ss_pred ehHHHHHHHHHHHHHhhHhhhcCCHHHHHHHHHHHHHHHHhh--------------cCCCceEEEEeCCCCCcceec
Q 017546 130 TVEGILVRAADELEALQEERKKLDPQTAEAIDQFLLKLRACA--------------KGDSTFTFILDDPAGNSFIEN 192 (369)
Q Consensus 130 TVEGlL~~i~~~L~~~~~~r~~~~~e~~~ki~~~i~kL~~~~--------------~g~~pFTliidDPsGNS~I~~ 192 (369)
++|.+|.+..++++..+..- .+..++++.+-.+++... .|+..|.|-+-|-.||-||-+
T Consensus 43 ~lE~~l~~~~~~~~~~~~~~----~~~~~~~~~l~~~~~~~~~kvgvvRYnAF~dmGg~LSFslAlLD~~~nGvVlt 115 (151)
T PF14584_consen 43 NLEDLLNELFDQIDELKEEL----EELEKRIEELEEKLRNCVQKVGVVRYNAFEDMGGDLSFSLALLDDNNNGVVLT 115 (151)
T ss_pred cHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHhccceEEEEEccCcccccccceeeeEEEeCCCCEEEEE
Confidence 78999988888887765431 223344555445554332 256799999999999999965
No 302
>PRK03922 hypothetical protein; Provisional
Probab=24.43 E-value=81 Score=27.36 Aligned_cols=39 Identities=23% Similarity=0.382 Sum_probs=25.2
Q ss_pred cceEEEEEeeCCCCCCCccceeeCcccCCcceEEEEEee
Q 017546 53 FRKVLLSAFECPHCGERNNEVQFAGEIQPRGCNYSLKVP 91 (369)
Q Consensus 53 FkeiiImSf~C~~CGyrnnEVq~~g~i~~kG~r~tL~V~ 91 (369)
|=||=+-+..||+||+...-+--+....=-|..++++|=
T Consensus 42 yVeievG~~~cP~cge~~~~afvvA~taLVgL~lemkVF 80 (113)
T PRK03922 42 YVEVEVGLTICPKCGEPFDSAFVVADTALVGLLLEMKVF 80 (113)
T ss_pred eEEEecCcccCCCCCCcCCcEEEEeccceEEEEEEEEEe
Confidence 455566667777777776666665555556766766664
No 303
>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=24.28 E-value=50 Score=32.37 Aligned_cols=39 Identities=28% Similarity=0.715 Sum_probs=15.6
Q ss_pred eccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccceeeCc
Q 017546 31 ESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEVQFAG 77 (369)
Q Consensus 31 es~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEVq~~g 77 (369)
.+.||+||..-..+. +-.+ -+--|.|+.|+-.. |+++-.
T Consensus 31 n~yCP~Cg~~~L~~f-----~NN~--PVaDF~C~~C~eey-ELKSk~ 69 (254)
T PF06044_consen 31 NMYCPNCGSKPLSKF-----ENNR--PVADFYCPNCNEEY-ELKSKK 69 (254)
T ss_dssp H---TTT--SS-EE---------------EEE-TTT--EE-EEEEEE
T ss_pred CCcCCCCCChhHhhc-----cCCC--ccceeECCCCchHH-hhhhhc
Confidence 478999997744333 2222 24569999999743 677654
No 304
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=24.26 E-value=59 Score=30.64 Aligned_cols=31 Identities=19% Similarity=0.463 Sum_probs=21.9
Q ss_pred ceeeeeccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCC
Q 017546 280 EVMTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYR 323 (369)
Q Consensus 280 ev~~~~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk 323 (369)
+.-..-+.|+.|+..+.-. -+...|++||+.
T Consensus 144 dlGVI~A~CsrC~~~L~~~-------------~~~l~Cp~Cg~t 174 (188)
T COG1096 144 DLGVIYARCSRCRAPLVKK-------------GNMLKCPNCGNT 174 (188)
T ss_pred cceEEEEEccCCCcceEEc-------------CcEEECCCCCCE
Confidence 4556778899999886432 244579999974
No 305
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=24.19 E-value=33 Score=37.75 Aligned_cols=28 Identities=32% Similarity=0.797 Sum_probs=18.0
Q ss_pred eccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCccce
Q 017546 31 ESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNNEV 73 (369)
Q Consensus 31 es~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnnEV 73 (369)
-+.|+.||... -++ .+.||+||-++-++
T Consensus 568 ~~~C~~CG~~~-----------~g~----~~~CP~CGs~~~~v 595 (625)
T PRK08579 568 ITVCNKCGRST-----------TGL----YTRCPRCGSEDVEV 595 (625)
T ss_pred CccCCCCCCcc-----------CCC----CCcCcCCCCchhHH
Confidence 47899999621 011 38999999755443
No 306
>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]
Probab=23.96 E-value=21 Score=33.90 Aligned_cols=44 Identities=14% Similarity=0.367 Sum_probs=33.1
Q ss_pred cceeeeeccCccCcccccceeEEEe---cCCCCeEEEEE------eeCCCCCC
Q 017546 279 EEVMTFPSTCGACAASCETRMFMTR---IPYFQEVIVMA------STCDACGY 322 (369)
Q Consensus 279 ~ev~~~~~~Cp~C~~~~~~~m~~~~---IP~F~eviims------~~C~~CGy 322 (369)
+.|.++.+-|..||++......+.+ -+|+++.|+.. ..|.+|-+
T Consensus 138 Dkv~kL~aIC~~Cg~~At~~~Rl~~~~~a~~~~~~i~IGg~e~Y~a~CR~h~~ 190 (201)
T COG1435 138 DKVTKLKAICNVCGRKATRTLRLINGGPAVYEGPQILIGGNESYEARCRKHHK 190 (201)
T ss_pred HHHHHHHHHHHHhCCcceEEEEecCCCCCccCCCeEEECCCcceeehhhhhhh
Confidence 3688999999999999765555555 45779888764 57877754
No 307
>TIGR00630 uvra excinuclease ABC, A subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.91 E-value=53 Score=37.81 Aligned_cols=31 Identities=23% Similarity=0.555 Sum_probs=23.5
Q ss_pred ccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCC
Q 017546 32 SLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGE 68 (369)
Q Consensus 32 s~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGy 68 (369)
..||.|...|..++ +.-|+.++ ...|+.|+=
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 45999999998774 55566664 579999973
No 308
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=23.89 E-value=18 Score=33.07 Aligned_cols=31 Identities=23% Similarity=0.547 Sum_probs=18.9
Q ss_pred eccCccCcccccceeE---------EEecCCCCeEEEEEeeCCCCCCCc
Q 017546 285 PSTCGACAASCETRMF---------MTRIPYFQEVIVMASTCDACGYRN 324 (369)
Q Consensus 285 ~~~Cp~C~~~~~~~m~---------~~~IP~F~eviims~~C~~CGyk~ 324 (369)
-..||+|+.+..-..+ .+..| ..|.+||..+
T Consensus 39 I~~Cp~C~~~IrG~y~v~gv~~~g~~~~~P---------sYC~~CGkpy 78 (158)
T PF10083_consen 39 ITSCPNCSTPIRGDYHVEGVFGLGGHYEAP---------SYCHNCGKPY 78 (158)
T ss_pred HHHCcCCCCCCCCceecCCeeeeCCCCCCC---------hhHHhCCCCC
Confidence 4579999887432221 12333 3599999765
No 309
>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=23.79 E-value=52 Score=32.17 Aligned_cols=43 Identities=26% Similarity=0.447 Sum_probs=14.4
Q ss_pred EeccCCCCCCCceEEEEEeecC-CcceEEE----------EEeeCCCCCCCccce
Q 017546 30 VESLCMRCGENGVTRFLLTLIP-HFRKVLL----------SAFECPHCGERNNEV 73 (369)
Q Consensus 30 ies~Cp~Cg~~g~tr~llt~IP-~FkeiiI----------mSf~C~~CGyrnnEV 73 (369)
....||+||..-..-++.-.-+ .+ --+. .-..|++||-.+.+-
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 3489999998743322222222 21 1111 125799999877653
No 310
>PRK14284 chaperone protein DnaJ; Provisional
Probab=23.67 E-value=1.4e+02 Score=30.57 Aligned_cols=31 Identities=32% Similarity=0.527 Sum_probs=17.0
Q ss_pred ccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCC
Q 017546 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYR 323 (369)
Q Consensus 286 ~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk 323 (369)
..||.|+..+...+.. +- +.+...|+.|+=+
T Consensus 176 ~~C~~C~G~G~v~~~~------G~-~~~~~~C~~C~G~ 206 (391)
T PRK14284 176 KVCDRCKGSGQVVQSR------GF-FSMASTCPECGGE 206 (391)
T ss_pred eecCccCCeeEEEEEe------ce-EEEEEECCCCCCC
Confidence 3466666555433222 32 2366788888544
No 311
>cd00042 CY Substituted updates: Jan 30, 2002
Probab=23.57 E-value=1.1e+02 Score=24.75 Aligned_cols=31 Identities=23% Similarity=0.327 Sum_probs=25.8
Q ss_pred cCCCC-----CCCceEEEEEeecCCcceEEEEEeeC
Q 017546 33 LCMRC-----GENGVTRFLLTLIPHFRKVLLSAFEC 63 (369)
Q Consensus 33 ~Cp~C-----g~~g~tr~llt~IP~FkeiiImSf~C 63 (369)
.|+.| +..+..+...+..|..++.-+.+|.|
T Consensus 70 ~~~~c~~~~~~~~~~C~~~V~~~pw~~~~~l~~~~C 105 (105)
T cd00042 70 DCPDCKLLEEGKKKFCTAKVWEKPWENFKELLSFKC 105 (105)
T ss_pred ccccccccccCCCEEEEEEEEecCCCCceeeeeccC
Confidence 38888 44567788899999999999999988
No 312
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 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 domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=23.43 E-value=89 Score=20.12 Aligned_cols=8 Identities=50% Similarity=1.510 Sum_probs=4.7
Q ss_pred EEeeCCCC
Q 017546 59 SAFECPHC 66 (369)
Q Consensus 59 mSf~C~~C 66 (369)
.++.|++|
T Consensus 20 ~~~~C~rC 27 (30)
T PF06827_consen 20 STYLCPRC 27 (30)
T ss_dssp EEEE-TTT
T ss_pred CCeECcCC
Confidence 46777777
No 313
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=23.36 E-value=35 Score=38.19 Aligned_cols=13 Identities=23% Similarity=0.424 Sum_probs=7.1
Q ss_pred EEEeCCCC-Cccee
Q 017546 179 FILDDPAG-NSFIE 191 (369)
Q Consensus 179 liidDPsG-NS~I~ 191 (369)
|||-|--. +||=+
T Consensus 316 LIIvDEEHD~sYKq 329 (730)
T COG1198 316 LIIVDEEHDSSYKQ 329 (730)
T ss_pred EEEEeccccccccC
Confidence 55555554 55644
No 314
>PF02563 Poly_export: Polysaccharide biosynthesis/export protein; InterPro: IPR003715 The extracellular polysaccharide colanic acid (CA) is produced by species of the family Enterobacteriaceae. In Escherichia coli (strain K12) the CA cluster comprises 19 genes. The wzx gene encodes a protein with multiple transmembrane segments that may function in export of the CA repeat unit from the cytoplasm into the periplasm in a process analogous to O-unit export. The CA gene clusters may be involved in the export of polysaccharide from the cell [].; GO: 0015159 polysaccharide transmembrane transporter activity, 0015774 polysaccharide transport, 0016020 membrane; PDB: 2W8I_E 2W8H_E 2J58_D.
Probab=23.32 E-value=1.8e+02 Score=22.87 Aligned_cols=53 Identities=17% Similarity=0.178 Sum_probs=34.4
Q ss_pred ceEEEEEeeCCCcccccceeeeecceEEEeecceeEeCCCCCcceEEehHHHHHHHHHHHH
Q 017546 83 GCNYSLKVPSSDQKMFHRQVVKSESATIKIPELDFEIPPEAQRGSLSTVEGILVRAADELE 143 (369)
Q Consensus 83 G~r~tL~V~~~~~~DLnR~VvKS~~ati~IPELd~eI~p~~~~G~iTTVEGlL~~i~~~L~ 143 (369)
|=++.+.|- ...+|++.+.-+...+|.+|.++ .|.. .|. |++-+=..+...|.
T Consensus 16 GD~l~i~v~--~~~~l~~~~~V~~dG~I~lP~iG-~v~v---~G~--T~~e~~~~I~~~l~ 68 (82)
T PF02563_consen 16 GDVLRISVF--GWPELSGEYTVDPDGTISLPLIG-PVKV---AGL--TLEEAEEEIKQRLQ 68 (82)
T ss_dssp T-EEEEEET--T-HHHCCSEE--TTSEEEETTTE-EEE----TT----HHHHHHHHHHHHT
T ss_pred CCEEEEEEe--cCCCcccceEECCCCcEeecccc-eEEE---CCC--CHHHHHHHHHHHHH
Confidence 567889998 78889999999999999999988 4443 444 66655555555544
No 315
>PLN03165 chaperone protein dnaJ-related; Provisional
Probab=23.17 E-value=1.3e+02 Score=25.98 Aligned_cols=32 Identities=19% Similarity=0.286 Sum_probs=22.0
Q ss_pred cCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCc
Q 017546 33 LCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERN 70 (369)
Q Consensus 33 ~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrn 70 (369)
.|+.|+..|.....+ -| ..-+...|+.|+=+-
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 788888888655433 23 245678999998765
No 316
>PRK14277 chaperone protein DnaJ; Provisional
Probab=23.16 E-value=95 Score=31.80 Aligned_cols=33 Identities=27% Similarity=0.652 Sum_probs=17.5
Q ss_pred ccCccCcccccceeEEEecCCCCeEEEEEeeCCCCC
Q 017546 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACG 321 (369)
Q Consensus 286 ~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CG 321 (369)
..|+.|+..+. .+....++ |+-+..+ ..|+.|+
T Consensus 173 ~~C~~C~G~G~-~~~~~~~~-~G~~~~~-~~C~~C~ 205 (386)
T PRK14277 173 VTCPVCHGTGQ-VRTRQNTP-FGRIVNI-RTCDRCH 205 (386)
T ss_pred ccCCCCCCEEE-EEEEEecc-CceEEEE-EECCCCC
Confidence 34666655542 23344444 4555444 5888884
No 317
>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=23.10 E-value=1.4e+02 Score=23.62 Aligned_cols=14 Identities=29% Similarity=0.612 Sum_probs=10.9
Q ss_pred ceEEEEeCCCCCcc
Q 017546 176 TFTFILDDPAGNSF 189 (369)
Q Consensus 176 pFTliidDPsGNS~ 189 (369)
.+...+.||.||.+
T Consensus 109 ~~~~~~~DPdG~~i 122 (125)
T cd07241 109 YYESVILDPEGNRI 122 (125)
T ss_pred eEEEEEECCCCCEE
Confidence 45677899999975
No 318
>PRK03922 hypothetical protein; Provisional
Probab=22.97 E-value=79 Score=27.45 Aligned_cols=35 Identities=14% Similarity=0.281 Sum_probs=23.2
Q ss_pred ceeeeeccCccCcccccceeEEEecCCCCeEEEEE
Q 017546 280 EVMTFPSTCGACAASCETRMFMTRIPYFQEVIVMA 314 (369)
Q Consensus 280 ev~~~~~~Cp~C~~~~~~~m~~~~IP~F~eviims 314 (369)
||--..+.||.||.+...-+..-+.-..|=++-|.
T Consensus 44 eievG~~~cP~cge~~~~afvvA~taLVgL~lemk 78 (113)
T PRK03922 44 EVEVGLTICPKCGEPFDSAFVVADTALVGLLLEMK 78 (113)
T ss_pred EEecCcccCCCCCCcCCcEEEEeccceEEEEEEEE
Confidence 44455678999998877666666665555555553
No 319
>PF13754 Big_3_4: Bacterial Ig-like domain (group 3)
Probab=22.96 E-value=57 Score=23.99 Aligned_cols=19 Identities=42% Similarity=0.499 Sum_probs=17.0
Q ss_pred hcCCCceEEEEeCCCCCcc
Q 017546 171 AKGDSTFTFILDDPAGNSF 189 (369)
Q Consensus 171 ~~g~~pFTliidDPsGNS~ 189 (369)
.+|...|++...|.+||+-
T Consensus 22 ~dG~y~itv~a~D~AGN~s 40 (54)
T PF13754_consen 22 ADGTYTITVTATDAAGNTS 40 (54)
T ss_pred CCccEEEEEEEEeCCCCCC
Confidence 4788899999999999985
No 320
>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=22.80 E-value=34 Score=25.04 Aligned_cols=8 Identities=25% Similarity=0.908 Sum_probs=4.4
Q ss_pred ccCccCcc
Q 017546 286 STCGACAA 293 (369)
Q Consensus 286 ~~Cp~C~~ 293 (369)
..||.|.+
T Consensus 32 v~CPiC~~ 39 (54)
T PF05605_consen 32 VVCPICSS 39 (54)
T ss_pred ccCCCchh
Confidence 35666644
No 321
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=22.75 E-value=79 Score=31.90 Aligned_cols=35 Identities=23% Similarity=0.586 Sum_probs=20.4
Q ss_pred eccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCC
Q 017546 285 PSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGY 322 (369)
Q Consensus 285 ~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGy 322 (369)
.+.||.||........ .+.- .+=-+-.-+|+.||-
T Consensus 226 R~~C~~Cg~~~~l~y~--~~~~-~~~~~r~e~C~~C~~ 260 (309)
T PRK03564 226 RVKCSNCEQSGKLHYW--SLDS-EQAAVKAESCGDCGT 260 (309)
T ss_pred CccCCCCCCCCceeee--eecC-CCcceEeeecccccc
Confidence 6789999975332222 2221 111257788999973
No 322
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=22.67 E-value=54 Score=37.93 Aligned_cols=28 Identities=25% Similarity=0.496 Sum_probs=0.0
Q ss_pred ceeeeeccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCc
Q 017546 280 EVMTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRN 324 (369)
Q Consensus 280 ev~~~~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~ 324 (369)
+|-...-.||.||... +...|+.||-++
T Consensus 620 ~vev~~RKCPkCG~yT-----------------lk~rCP~CG~~T 647 (1095)
T TIGR00354 620 EVEIAIRKCPQCGKES-----------------FWLKCPVCGELT 647 (1095)
T ss_pred EEEEEEEECCCCCccc-----------------ccccCCCCCCcc
No 323
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=22.66 E-value=67 Score=30.25 Aligned_cols=33 Identities=27% Similarity=0.619 Sum_probs=22.9
Q ss_pred CCCceEEeccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCC
Q 017546 24 DAPLYQVESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGER 69 (369)
Q Consensus 24 ~~~v~eies~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyr 69 (369)
.+..-.+-+.|.+|+....- + =+...||.||+.
T Consensus 142 ~~dlGVI~A~CsrC~~~L~~----------~---~~~l~Cp~Cg~t 174 (188)
T COG1096 142 GNDLGVIYARCSRCRAPLVK----------K---GNMLKCPNCGNT 174 (188)
T ss_pred CCcceEEEEEccCCCcceEE----------c---CcEEECCCCCCE
Confidence 34566789999999876422 1 234679999974
No 324
>PRK14281 chaperone protein DnaJ; Provisional
Probab=22.39 E-value=93 Score=32.04 Aligned_cols=33 Identities=30% Similarity=0.603 Sum_probs=16.8
Q ss_pred ccCccCcccccceeEEEecCCCCeEEEEEeeCCCCC
Q 017546 286 STCGACAASCETRMFMTRIPYFQEVIVMASTCDACG 321 (369)
Q Consensus 286 ~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CG 321 (369)
..|+.|+..+...+...-.| +-+ .+...|+.|+
T Consensus 180 ~~C~~C~G~G~~~~~~~~~~--g~~-~~~~~C~~C~ 212 (397)
T PRK14281 180 ETCPTCHGSGEVRQASKTMF--GQF-VNITACPTCG 212 (397)
T ss_pred ccCCCCCCCcEEEEEEeccc--ceE-EEEEecCCCc
Confidence 45777766664433222222 222 2455788884
No 325
>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=22.10 E-value=37 Score=31.03 Aligned_cols=24 Identities=13% Similarity=0.422 Sum_probs=16.2
Q ss_pred CCceEEeccCCCCCCCceEEEEEe
Q 017546 25 APLYQVESLCMRCGENGVTRFLLT 48 (369)
Q Consensus 25 ~~v~eies~Cp~Cg~~g~tr~llt 48 (369)
..|.++.+.|+.||+.+.....++
T Consensus 131 d~i~kl~avC~~Cg~~A~~t~R~~ 154 (176)
T PF00265_consen 131 DKITKLKAVCEVCGRKATFTQRIV 154 (176)
T ss_dssp SEEEEE-EE-TTTSSEE-EEEEEE
T ss_pred CeEEEeccEECCCCCceeEEEEEc
Confidence 458899999999999876655554
No 326
>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=21.99 E-value=42 Score=35.66 Aligned_cols=13 Identities=23% Similarity=0.371 Sum_probs=7.1
Q ss_pred eccCccCcccccc
Q 017546 285 PSTCGACAASCET 297 (369)
Q Consensus 285 ~~~Cp~C~~~~~~ 297 (369)
...||.|+.++..
T Consensus 222 ~~~C~~C~~~l~~ 234 (505)
T TIGR00595 222 ILCCPNCDVSLTY 234 (505)
T ss_pred ccCCCCCCCceEE
Confidence 3457777655443
No 327
>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=21.76 E-value=63 Score=23.17 Aligned_cols=9 Identities=44% Similarity=1.401 Sum_probs=6.2
Q ss_pred eCCCCCCCc
Q 017546 62 ECPHCGERN 70 (369)
Q Consensus 62 ~C~~CGyrn 70 (369)
.||.||-.+
T Consensus 28 ~CP~Cg~~~ 36 (52)
T TIGR02605 28 TCPECGGEK 36 (52)
T ss_pred CCCCCCCCc
Confidence 588888643
No 328
>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=21.75 E-value=50 Score=35.86 Aligned_cols=28 Identities=25% Similarity=0.620 Sum_probs=19.1
Q ss_pred eccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCcccc
Q 017546 285 PSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRNSEL 327 (369)
Q Consensus 285 ~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~~eV 327 (369)
-+.|+.||..+... .+.|+.||-+.-+|
T Consensus 524 ~~~C~~CG~~g~~~---------------~~~CP~Cgs~~~~~ 551 (579)
T TIGR02487 524 VDVCEDCGYTGEGL---------------NDKCPKCGSHDIEV 551 (579)
T ss_pred CccCCCCCCCCCCC---------------CCcCcCCCCcccee
Confidence 57799998754321 17899999765444
No 329
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=21.52 E-value=49 Score=22.42 Aligned_cols=13 Identities=31% Similarity=0.815 Sum_probs=10.2
Q ss_pred EeeCCCCCCCccc
Q 017546 314 ASTCDACGYRNSE 326 (369)
Q Consensus 314 s~~C~~CGyk~~e 326 (369)
.+.|..|||-...
T Consensus 2 ~~~C~~CG~i~~g 14 (34)
T cd00729 2 VWVCPVCGYIHEG 14 (34)
T ss_pred eEECCCCCCEeEC
Confidence 4789999997653
No 330
>COG5595 Zn-ribbon-containing, possibly nucleic-acid-binding protein [General function prediction only]
Probab=21.45 E-value=35 Score=32.63 Aligned_cols=30 Identities=23% Similarity=0.375 Sum_probs=20.9
Q ss_pred eecceeEeCCCCCcceEEehHHHHHHHHHHHHH
Q 017546 112 IPELDFEIPPEAQRGSLSTVEGILVRAADELEA 144 (369)
Q Consensus 112 IPELd~eI~p~~~~G~iTTVEGlL~~i~~~L~~ 144 (369)
+-|+.|+..+. -.+..+--+|..++|.+.-
T Consensus 3 lie~~fr~t~~---~~i~~~~~lln~lidqwry 32 (256)
T COG5595 3 LIELEFRCTDN---TTISAVDKLLNGLIDQWRY 32 (256)
T ss_pred eEEEEEEecCC---cchhhHHHHHHHHHHHHHh
Confidence 45788888762 4566667778888887764
No 331
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=21.42 E-value=54 Score=26.64 Aligned_cols=18 Identities=28% Similarity=0.427 Sum_probs=14.2
Q ss_pred eeCCCCCCCccceeeCcc
Q 017546 61 FECPHCGERNNEVQFAGE 78 (369)
Q Consensus 61 f~C~~CGyrnnEVq~~g~ 78 (369)
-.|+-|+|.+.-+|....
T Consensus 21 dIC~VC~WEdD~~q~~~p 38 (78)
T PF14206_consen 21 DICPVCFWEDDGVQLRDP 38 (78)
T ss_pred eECCCCCcccCCccccCC
Confidence 569999999988876543
No 332
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=21.33 E-value=94 Score=26.72 Aligned_cols=35 Identities=20% Similarity=0.327 Sum_probs=20.9
Q ss_pred ccCccCccccc---ceeEEEecCCCCeEEEEEeeCCCCCCCccc
Q 017546 286 STCGACAASCE---TRMFMTRIPYFQEVIVMASTCDACGYRNSE 326 (369)
Q Consensus 286 ~~Cp~C~~~~~---~~m~~~~IP~F~eviims~~C~~CGyk~~e 326 (369)
+.|..|+..+. +--.-..=++ .++.|..||+.-.-
T Consensus 57 ~~CkkC~t~Lvpg~n~rvR~~~~~------v~vtC~~CG~~~R~ 94 (105)
T COG2023 57 TICKKCYTPLVPGKNARVRLRKGR------VVVTCLECGTIRRY 94 (105)
T ss_pred HhccccCcccccCcceEEEEcCCe------EEEEecCCCcEEEe
Confidence 56999988532 2112222222 67789999986543
No 333
>PRK14873 primosome assembly protein PriA; Provisional
Probab=20.73 E-value=54 Score=36.30 Aligned_cols=14 Identities=14% Similarity=0.124 Sum_probs=9.9
Q ss_pred EEEEeCCCCCccee
Q 017546 178 TFILDDPAGNSFIE 191 (369)
Q Consensus 178 TliidDPsGNS~I~ 191 (369)
-|||||....||-+
T Consensus 260 LIIvdEEhd~sykq 273 (665)
T PRK14873 260 LVAIWDDGDDLLAE 273 (665)
T ss_pred EEEEEcCCchhhcC
Confidence 46667777788864
No 334
>PRK11032 hypothetical protein; Provisional
Probab=20.62 E-value=55 Score=30.00 Aligned_cols=40 Identities=23% Similarity=0.355 Sum_probs=27.2
Q ss_pred ccCCCcceeeeeccCccCcccccceeEEEecCCCCeEEEEEeeCCCCCCCc
Q 017546 274 RYSAPEEVMTFPSTCGACAASCETRMFMTRIPYFQEVIVMASTCDACGYRN 324 (369)
Q Consensus 274 ~~~~~~ev~~~~~~Cp~C~~~~~~~m~~~~IP~F~eviims~~C~~CGyk~ 324 (369)
.|.+.+-|--....|-.||+.... .+...|| -|++||...
T Consensus 113 ~Y~sGEvvg~G~LvC~~Cg~~~~~-~~p~~i~----------pCp~C~~~~ 152 (160)
T PRK11032 113 VYHSGEVVGLGNLVCEKCHHHLAF-YTPEVLP----------LCPKCGHDQ 152 (160)
T ss_pred eeecceeeecceEEecCCCCEEEe-cCCCcCC----------CCCCCCCCe
Confidence 465666666778899999987422 2344455 499999754
No 335
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=20.23 E-value=69 Score=32.03 Aligned_cols=39 Identities=36% Similarity=0.718 Sum_probs=25.1
Q ss_pred CCceEEeccCCCCCCCceEEEEEeecCCcce-------------EEE--EEeeCCCCCCCc
Q 017546 25 APLYQVESLCMRCGENGVTRFLLTLIPHFRK-------------VLL--SAFECPHCGERN 70 (369)
Q Consensus 25 ~~v~eies~Cp~Cg~~g~tr~llt~IP~Fke-------------iiI--mSf~C~~CGyrn 70 (369)
....+-...||.||+.-+ |||--- -.. .||.||.||-.-
T Consensus 233 ss~~t~~~~C~~Cg~~Pt-------iP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~ 286 (298)
T KOG2879|consen 233 SSTGTSDTECPVCGEPPT-------IPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENV 286 (298)
T ss_pred cccccCCceeeccCCCCC-------CCeeeccccceeehhhhhhhhcchhhcccCccCCCC
Confidence 445566788999998753 344222 122 359999999743
No 336
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=20.19 E-value=70 Score=35.34 Aligned_cols=16 Identities=25% Similarity=0.779 Sum_probs=13.3
Q ss_pred eeeeeccCccCccccc
Q 017546 281 VMTFPSTCGACAASCE 296 (369)
Q Consensus 281 v~~~~~~Cp~C~~~~~ 296 (369)
.+.+|..||+||.++.
T Consensus 388 ~~~~P~~CP~C~s~l~ 403 (652)
T TIGR00575 388 PIRFPTHCPSCGSPLV 403 (652)
T ss_pred CCCCCCCCCCCCCEeE
Confidence 4678999999998864
No 337
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=20.12 E-value=1.1e+02 Score=26.28 Aligned_cols=34 Identities=18% Similarity=0.424 Sum_probs=20.7
Q ss_pred ccCCCCCC---CceEEEEEeecCCcceEEEEEeeCCCCCCCcc
Q 017546 32 SLCMRCGE---NGVTRFLLTLIPHFRKVLLSAFECPHCGERNN 71 (369)
Q Consensus 32 s~Cp~Cg~---~g~tr~llt~IP~FkeiiImSf~C~~CGyrnn 71 (369)
..|..|+. +|.+--.-.+=+. .++.|..||+.-.
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 5543211111111 5688999998643
No 338
>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=20.09 E-value=1.1e+02 Score=32.94 Aligned_cols=37 Identities=22% Similarity=0.541 Sum_probs=23.8
Q ss_pred eEEeccCCCCCCCceEEEEEeecCCcceEEEEEeeCCCCCCCcc
Q 017546 28 YQVESLCMRCGENGVTRFLLTLIPHFRKVLLSAFECPHCGERNN 71 (369)
Q Consensus 28 ~eies~Cp~Cg~~g~tr~llt~IP~FkeiiImSf~C~~CGyrnn 71 (369)
.-+.-.|++||+-.++.. -++.= . -..+.| .||++..
T Consensus 165 ~P~~pic~~cGrv~~~~~-~~~~~---~--~v~Y~c-~cG~~g~ 201 (515)
T TIGR00467 165 YPISVFCENCGRDTTTVN-NYDNE---Y--SIEYSC-ECGNQES 201 (515)
T ss_pred eeeeeecCCcCccCceEE-EecCC---c--eEEEEc-CCCCEEE
Confidence 347788999998755333 33321 2 256789 4999764
No 339
>COG1435 Tdk Thymidine kinase [Nucleotide transport and metabolism]
Probab=20.07 E-value=30 Score=32.86 Aligned_cols=43 Identities=14% Similarity=0.281 Sum_probs=32.3
Q ss_pred CceEEeccCCCCCCCceEEEEEee---cCCcceEEEEE------eeCCCCCC
Q 017546 26 PLYQVESLCMRCGENGVTRFLLTL---IPHFRKVLLSA------FECPHCGE 68 (369)
Q Consensus 26 ~v~eies~Cp~Cg~~g~tr~llt~---IP~FkeiiImS------f~C~~CGy 68 (369)
.|.++...|..||+..+..+.+.+ -+|++++|+.- -.|.+|.+
T Consensus 139 kv~kL~aIC~~Cg~~At~~~Rl~~~~~a~~~~~~i~IGg~e~Y~a~CR~h~~ 190 (201)
T COG1435 139 KVTKLKAICNVCGRKATRTLRLINGGPAVYEGPQILIGGNESYEARCRKHHK 190 (201)
T ss_pred HHHHHHHHHHHhCCcceEEEEecCCCCCccCCCeEEECCCcceeehhhhhhh
Confidence 466889999999999766555555 56789888764 56777765
Done!