Query 039987
Match_columns 105
No_of_seqs 98 out of 109
Neff 2.5
Searched_HMMs 46136
Date Fri Mar 29 03:58:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/039987.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/039987hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF06839 zf-GRF: GRF zinc fing 99.6 1.5E-16 3.2E-21 96.1 4.2 38 13-52 1-44 (45)
2 KOG1956 DNA topoisomerase III 97.9 4.6E-06 1E-10 75.3 1.5 38 12-50 718-758 (758)
3 PF01396 zf-C4_Topoisom: Topoi 97.1 0.001 2.2E-08 39.5 4.0 34 13-52 2-38 (39)
4 PF05325 DUF730: Protein of un 96.9 0.00098 2.1E-08 49.3 3.5 66 6-77 14-88 (122)
5 smart00440 ZnF_C2C2 C2C2 Zinc 96.4 0.0068 1.5E-07 36.2 3.9 36 14-50 2-39 (40)
6 PRK00464 nrdR transcriptional 96.2 0.0038 8.3E-08 46.7 2.7 33 14-46 2-36 (154)
7 PF01096 TFIIS_C: Transcriptio 95.6 0.017 3.6E-07 34.3 3.0 34 13-46 1-36 (39)
8 TIGR01384 TFS_arch transcripti 95.5 0.021 4.5E-07 38.4 3.7 40 12-52 62-103 (104)
9 KOG4399 C2HC-type Zn-finger pr 95.1 0.016 3.4E-07 48.7 2.6 44 10-56 11-61 (325)
10 COG1594 RPB9 DNA-directed RNA 94.0 0.058 1.3E-06 38.3 3.0 38 12-50 72-111 (113)
11 TIGR03655 anti_R_Lar restricti 93.7 0.095 2.1E-06 32.3 3.2 35 12-47 1-35 (53)
12 PF12760 Zn_Tnp_IS1595: Transp 93.6 0.086 1.9E-06 31.6 2.8 27 13-46 19-45 (46)
13 smart00661 RPOL9 RNA polymeras 92.7 0.17 3.7E-06 29.8 3.2 32 14-51 2-33 (52)
14 PF01927 Mut7-C: Mut7-C RNAse 92.6 0.14 3E-06 36.8 3.1 39 12-52 91-138 (147)
15 PF04216 FdhE: Protein involve 92.2 0.098 2.1E-06 41.0 2.1 37 12-50 172-208 (290)
16 PHA00626 hypothetical protein 91.9 0.14 3E-06 34.3 2.3 37 14-53 2-38 (59)
17 KOG2907 RNA polymerase I trans 91.0 0.12 2.7E-06 38.2 1.5 38 10-47 72-111 (116)
18 PF09855 DUF2082: Nucleic-acid 90.5 0.37 7.9E-06 31.8 3.2 43 14-56 2-54 (64)
19 PF04606 Ogr_Delta: Ogr/Delta- 90.2 0.25 5.4E-06 29.9 2.1 32 14-46 1-35 (47)
20 PF14353 CpXC: CpXC protein 89.7 0.32 7E-06 33.6 2.5 32 13-46 2-46 (128)
21 TIGR01385 TFSII transcription 89.6 0.47 1E-05 38.7 3.8 40 9-49 255-296 (299)
22 KOG2906 RNA polymerase III sub 89.4 0.24 5.1E-06 36.3 1.8 39 12-51 65-105 (105)
23 PF04216 FdhE: Protein involve 89.1 0.22 4.8E-06 39.0 1.6 75 2-80 201-277 (290)
24 KOG2691 RNA polymerase II subu 89.1 0.41 8.8E-06 35.5 2.8 45 5-50 63-112 (113)
25 PRK00432 30S ribosomal protein 88.3 0.49 1.1E-05 29.6 2.5 30 12-50 20-49 (50)
26 PHA02998 RNA polymerase subuni 88.2 0.6 1.3E-05 37.3 3.4 39 12-51 143-183 (195)
27 PRK09678 DNA-binding transcrip 87.7 0.49 1.1E-05 31.9 2.3 33 13-46 2-37 (72)
28 KOG1294 Apurinic/apyrimidinic 84.6 0.54 1.2E-05 39.2 1.5 20 23-42 299-318 (335)
29 PF07282 OrfB_Zn_ribbon: Putat 84.6 0.78 1.7E-05 28.5 1.9 28 12-47 28-55 (69)
30 PRK07220 DNA topoisomerase I; 84.3 1.2 2.5E-05 40.0 3.6 36 12-53 635-672 (740)
31 COG2888 Predicted Zn-ribbon RN 84.0 0.7 1.5E-05 31.1 1.6 30 12-46 27-58 (61)
32 PF03811 Zn_Tnp_IS1: InsA N-te 83.6 1.4 3E-05 26.2 2.6 33 11-45 4-36 (36)
33 PRK14890 putative Zn-ribbon RN 83.1 1.1 2.3E-05 29.9 2.2 32 10-46 23-56 (59)
34 PF11672 DUF3268: Protein of u 82.8 1.5 3.3E-05 31.3 3.1 40 12-52 2-45 (102)
35 PF14354 Lar_restr_allev: Rest 82.1 2 4.3E-05 26.2 3.0 35 11-46 2-37 (61)
36 PF14803 Nudix_N_2: Nudix N-te 80.1 1.7 3.8E-05 25.5 2.1 31 14-48 2-32 (34)
37 PRK03564 formate dehydrogenase 79.8 2.2 4.8E-05 35.3 3.4 30 12-42 187-216 (309)
38 PF10058 DUF2296: Predicted in 79.3 1.8 3.8E-05 27.5 2.1 36 7-47 18-53 (54)
39 TIGR02098 MJ0042_CXXC MJ0042 f 78.5 2.1 4.4E-05 24.2 2.1 31 13-46 3-33 (38)
40 TIGR01562 FdhE formate dehydro 77.7 2.9 6.4E-05 34.5 3.5 44 2-45 214-259 (305)
41 PRK06599 DNA topoisomerase I; 75.5 2.3 5.1E-05 37.5 2.5 35 12-51 585-622 (675)
42 COG0675 Transposase and inacti 75.0 2.3 5.1E-05 31.1 2.1 40 12-70 309-348 (364)
43 PF08271 TF_Zn_Ribbon: TFIIB z 74.9 3.5 7.7E-05 24.1 2.5 35 14-55 2-36 (43)
44 COG3677 Transposase and inacti 74.8 2.5 5.4E-05 30.6 2.1 64 12-78 30-99 (129)
45 COG1656 Uncharacterized conser 74.8 1.6 3.5E-05 33.8 1.2 38 12-51 97-143 (165)
46 PRK08173 DNA topoisomerase III 73.9 1.9 4.1E-05 39.6 1.6 29 12-50 624-652 (862)
47 COG1571 Predicted DNA-binding 73.6 1.8 3.9E-05 37.6 1.3 30 11-49 349-378 (421)
48 PRK05582 DNA topoisomerase I; 73.0 3.5 7.5E-05 36.2 2.9 35 13-52 612-649 (650)
49 PF13453 zf-TFIIB: Transcripti 72.5 4.7 0.0001 23.5 2.6 27 14-46 1-27 (41)
50 PHA02942 putative transposase; 72.0 3.4 7.3E-05 34.4 2.5 40 13-67 326-365 (383)
51 PRK09710 lar restriction allev 71.6 5.2 0.00011 27.0 2.9 29 12-46 6-35 (64)
52 PF13408 Zn_ribbon_recom: Reco 70.8 5.4 0.00012 23.3 2.6 27 12-43 5-31 (58)
53 TIGR01562 FdhE formate dehydro 70.2 3 6.4E-05 34.4 1.8 33 12-44 184-216 (305)
54 PF13824 zf-Mss51: Zinc-finger 70.0 2.8 6.1E-05 27.3 1.3 24 14-48 1-24 (55)
55 PRK07220 DNA topoisomerase I; 69.6 5.4 0.00012 35.8 3.5 35 12-51 589-626 (740)
56 PF05876 Terminase_GpA: Phage 69.5 4.1 8.8E-05 35.3 2.6 41 6-46 194-237 (557)
57 PF08274 PhnA_Zn_Ribbon: PhnA 69.1 2.9 6.3E-05 24.2 1.1 28 12-49 2-29 (30)
58 PRK12380 hydrogenase nickel in 68.2 2.3 4.9E-05 29.9 0.7 27 12-48 70-96 (113)
59 PRK03564 formate dehydrogenase 68.1 4.7 0.0001 33.5 2.6 37 12-48 226-262 (309)
60 COG0551 TopA Zn-finger domain 67.8 7.7 0.00017 27.3 3.3 41 12-56 60-103 (140)
61 TIGR00100 hypA hydrogenase nic 66.6 2.7 5.8E-05 29.6 0.8 26 12-47 70-95 (115)
62 PRK05582 DNA topoisomerase I; 66.1 6.9 0.00015 34.4 3.4 34 12-51 571-607 (650)
63 PF13719 zinc_ribbon_5: zinc-r 66.1 5.2 0.00011 23.2 1.8 32 12-46 2-33 (37)
64 PRK06319 DNA topoisomerase I/S 65.8 5.6 0.00012 36.4 2.8 30 12-46 592-624 (860)
65 PF14206 Cys_rich_CPCC: Cystei 65.3 8.1 0.00018 26.5 2.9 32 13-54 2-33 (78)
66 PRK14892 putative transcriptio 64.8 10 0.00023 26.8 3.5 40 12-56 21-60 (99)
67 COG1198 PriA Primosomal protei 64.1 4.6 9.9E-05 37.0 1.9 55 35-90 472-552 (730)
68 PF02150 RNA_POL_M_15KD: RNA p 63.1 10 0.00023 22.0 2.7 29 13-48 2-30 (35)
69 PF09538 FYDLN_acid: Protein o 62.1 5.4 0.00012 28.4 1.7 11 12-22 26-36 (108)
70 PRK14810 formamidopyrimidine-D 61.1 8.2 0.00018 30.5 2.6 28 12-45 244-271 (272)
71 PF09986 DUF2225: Uncharacteri 59.9 3.2 6.9E-05 31.8 0.2 14 39-52 49-62 (214)
72 PF05265 DUF723: Protein of un 59.0 5.3 0.00012 26.6 1.1 29 12-45 32-60 (60)
73 PF09723 Zn-ribbon_8: Zinc rib 57.6 8.8 0.00019 22.7 1.8 14 10-23 24-37 (42)
74 smart00531 TFIIE Transcription 57.2 5.3 0.00011 28.7 0.9 39 12-52 99-137 (147)
75 PRK00564 hypA hydrogenase nick 56.5 6 0.00013 27.9 1.1 26 12-46 71-96 (117)
76 PRK10445 endonuclease VIII; Pr 56.5 12 0.00025 29.5 2.8 28 12-45 235-262 (263)
77 PHA02446 hypothetical protein 54.7 5.9 0.00013 30.7 0.9 31 12-42 62-92 (166)
78 PRK07726 DNA topoisomerase III 54.7 12 0.00027 33.0 3.0 34 12-51 610-645 (658)
79 PRK14724 DNA topoisomerase III 54.6 12 0.00025 35.2 2.9 59 11-82 754-823 (987)
80 PRK14811 formamidopyrimidine-D 53.7 14 0.0003 29.3 2.8 27 13-45 236-262 (269)
81 COG1997 RPL43A Ribosomal prote 53.7 14 0.0003 26.4 2.6 32 12-52 35-66 (89)
82 PF07754 DUF1610: Domain of un 53.4 7.2 0.00015 21.8 0.8 9 38-46 16-24 (24)
83 PRK01103 formamidopyrimidine/5 53.2 14 0.00029 29.0 2.7 27 13-45 246-272 (274)
84 PRK00398 rpoP DNA-directed RNA 52.4 9.9 0.00021 22.4 1.4 27 12-46 3-29 (46)
85 PF09788 Tmemb_55A: Transmembr 51.8 13 0.00029 30.7 2.5 26 12-42 85-110 (256)
86 TIGR02159 PA_CoA_Oxy4 phenylac 51.4 5 0.00011 29.6 0.0 33 12-45 105-137 (146)
87 TIGR00577 fpg formamidopyrimid 51.2 15 0.00033 28.9 2.7 27 13-45 246-272 (272)
88 PRK03681 hypA hydrogenase nick 50.8 7.7 0.00017 27.3 0.9 27 12-47 70-96 (114)
89 PRK03824 hypA hydrogenase nick 50.8 6.7 0.00014 28.3 0.6 11 36-46 105-115 (135)
90 TIGR02605 CxxC_CxxC_SSSS putat 49.9 14 0.00031 21.8 1.9 18 11-28 25-42 (52)
91 PRK07219 DNA topoisomerase I; 49.3 19 0.00042 32.7 3.4 32 12-49 688-722 (822)
92 COG4332 Uncharacterized protei 49.2 11 0.00023 30.4 1.6 36 11-46 16-57 (203)
93 COG1998 RPS31 Ribosomal protei 48.4 14 0.0003 24.2 1.7 32 12-51 19-50 (51)
94 cd03031 GRX_GRX_like Glutaredo 48.4 22 0.00048 26.2 3.0 30 13-45 111-140 (147)
95 PRK13945 formamidopyrimidine-D 48.1 18 0.00039 28.6 2.7 27 13-45 255-281 (282)
96 PRK07219 DNA topoisomerase I; 47.4 20 0.00042 32.7 3.1 35 12-51 602-639 (822)
97 smart00834 CxxC_CXXC_SSSS Puta 47.3 12 0.00026 20.8 1.1 11 10-20 24-34 (41)
98 PF13717 zinc_ribbon_4: zinc-r 47.1 18 0.00039 20.9 1.9 30 12-45 2-32 (36)
99 TIGR00311 aIF-2beta translatio 46.8 22 0.00047 26.2 2.7 30 12-47 97-127 (133)
100 PRK08173 DNA topoisomerase III 46.2 17 0.00038 33.5 2.6 57 10-79 724-787 (862)
101 PRK04179 rpl37e 50S ribosomal 45.8 12 0.00026 25.1 1.2 20 2-21 7-26 (62)
102 PF01907 Ribosomal_L37e: Ribos 45.3 6.3 0.00014 25.9 -0.2 19 2-21 6-24 (55)
103 PF06827 zf-FPG_IleRS: Zinc fi 45.2 25 0.00054 19.1 2.2 26 13-44 2-27 (30)
104 COG2126 RPL37A Ribosomal prote 43.7 15 0.00032 24.8 1.4 34 2-47 7-40 (61)
105 TIGR00595 priA primosomal prot 43.3 14 0.00029 31.7 1.4 21 69-89 308-329 (505)
106 cd00350 rubredoxin_like Rubred 43.2 13 0.00028 21.0 0.9 9 37-45 16-24 (33)
107 PRK14973 DNA topoisomerase I; 42.8 19 0.00041 33.8 2.4 33 12-50 588-623 (936)
108 PRK14973 DNA topoisomerase I; 41.8 19 0.0004 33.9 2.1 36 13-52 636-671 (936)
109 COG2740 Predicted nucleic-acid 41.5 9.1 0.0002 26.8 0.1 53 28-85 37-89 (95)
110 PF13913 zf-C2HC_2: zinc-finge 41.4 13 0.00029 20.0 0.7 10 11-20 1-10 (25)
111 PRK06319 DNA topoisomerase I/S 41.2 30 0.00066 31.8 3.3 36 12-52 693-733 (860)
112 cd00974 DSRD Desulforedoxin (D 40.9 22 0.00047 19.9 1.6 12 37-48 3-14 (34)
113 PF10263 SprT-like: SprT-like 39.9 22 0.00048 24.6 1.8 28 12-45 123-150 (157)
114 PF13465 zf-H2C2_2: Zinc-finge 39.6 16 0.00035 19.4 0.9 12 35-46 11-22 (26)
115 PTZ00073 60S ribosomal protein 39.4 18 0.00039 25.9 1.3 33 2-46 7-39 (91)
116 TIGR00319 desulf_FeS4 desulfof 39.2 24 0.00053 19.7 1.6 13 36-48 5-17 (34)
117 PRK12286 rpmF 50S ribosomal pr 39.2 30 0.00065 22.2 2.2 23 12-47 27-49 (57)
118 TIGR01051 topA_bact DNA topois 39.1 32 0.00069 30.2 3.1 29 12-46 574-605 (610)
119 TIGR01057 topA_arch DNA topois 38.9 29 0.00063 30.4 2.8 26 12-43 589-614 (618)
120 TIGR00244 transcriptional regu 38.9 27 0.00058 26.7 2.2 69 14-82 2-92 (147)
121 PRK14724 DNA topoisomerase III 38.7 19 0.00042 33.8 1.7 29 12-50 643-678 (987)
122 PF09526 DUF2387: Probable met 38.4 31 0.00068 23.0 2.3 37 13-53 9-45 (71)
123 PRK07561 DNA topoisomerase I s 38.0 27 0.00058 32.0 2.5 35 12-52 587-627 (859)
124 PF03884 DUF329: Domain of unk 37.8 17 0.00037 23.6 0.9 35 13-54 3-41 (57)
125 TIGR00310 ZPR1_znf ZPR1 zinc f 37.7 46 0.00099 25.7 3.4 34 13-47 1-39 (192)
126 PF01780 Ribosomal_L37ae: Ribo 37.5 77 0.0017 22.4 4.2 36 12-56 35-71 (90)
127 PF08772 NOB1_Zn_bind: Nin one 36.6 25 0.00055 23.7 1.7 23 12-35 24-46 (73)
128 TIGR00340 zpr1_rel ZPR1-relate 36.6 42 0.00091 25.4 3.0 32 15-47 1-37 (163)
129 PRK00241 nudC NADH pyrophospha 36.4 32 0.0007 27.0 2.5 32 12-51 99-130 (256)
130 smart00647 IBR In Between Ring 36.4 48 0.001 19.3 2.7 29 12-46 18-48 (64)
131 PRK12336 translation initiatio 36.3 37 0.00081 26.0 2.7 35 12-52 98-133 (201)
132 PRK04023 DNA polymerase II lar 35.9 24 0.00051 34.5 1.9 8 39-46 664-671 (1121)
133 PF13909 zf-H2C2_5: C2H2-type 35.7 22 0.00049 17.9 1.0 9 39-47 1-9 (24)
134 COG1779 C4-type Zn-finger prot 35.1 50 0.0011 26.5 3.3 35 12-47 14-52 (201)
135 PF14369 zf-RING_3: zinc-finge 35.0 25 0.00055 20.4 1.3 10 12-21 21-30 (35)
136 PF12773 DZR: Double zinc ribb 35.0 25 0.00055 20.5 1.3 31 7-46 7-37 (50)
137 COG4311 SoxD Sarcosine oxidase 34.6 25 0.00055 25.5 1.5 26 12-37 3-28 (97)
138 COG1326 Uncharacterized archae 34.6 17 0.00038 29.2 0.7 33 12-48 6-40 (201)
139 PF06397 Desulfoferrod_N: Desu 33.9 22 0.00048 21.3 0.9 12 36-47 4-15 (36)
140 smart00653 eIF2B_5 domain pres 33.2 49 0.0011 23.5 2.7 28 13-46 81-109 (110)
141 PRK05580 primosome assembly pr 33.1 25 0.00054 31.2 1.5 21 68-88 475-496 (679)
142 COG0266 Nei Formamidopyrimidin 33.0 39 0.00086 27.8 2.5 27 13-45 246-272 (273)
143 PRK11823 DNA repair protein Ra 32.9 28 0.00061 29.3 1.7 23 12-46 7-29 (446)
144 PF09297 zf-NADH-PPase: NADH p 32.6 19 0.00041 19.9 0.5 9 13-21 4-12 (32)
145 cd00279 YlxR Ylxr homologs; gr 32.5 31 0.00066 23.1 1.5 48 27-81 30-79 (79)
146 cd00674 LysRS_core_class_I cat 32.1 52 0.0011 27.5 3.1 36 12-50 169-204 (353)
147 PF09862 DUF2089: Protein of u 31.6 46 0.001 24.2 2.4 40 15-66 1-47 (113)
148 PRK00418 DNA gyrase inhibitor; 31.3 35 0.00075 22.7 1.6 36 12-54 6-45 (62)
149 PRK00750 lysK lysyl-tRNA synth 30.9 68 0.0015 27.7 3.7 37 12-50 175-211 (510)
150 COG4888 Uncharacterized Zn rib 30.6 95 0.0021 22.8 3.9 52 13-66 23-75 (104)
151 PF01873 eIF-5_eIF-2B: Domain 30.6 72 0.0016 23.1 3.3 30 13-47 94-123 (125)
152 TIGR01031 rpmF_bact ribosomal 30.3 49 0.0011 20.9 2.1 24 12-48 26-49 (55)
153 PRK06260 threonine synthase; V 30.2 35 0.00075 27.9 1.8 7 38-44 19-25 (397)
154 PF05184 SapB_1: Saposin-like 29.3 35 0.00076 18.7 1.2 26 59-84 12-37 (39)
155 PRK03988 translation initiatio 28.5 64 0.0014 23.8 2.8 30 12-47 102-132 (138)
156 PTZ00255 60S ribosomal protein 28.2 56 0.0012 23.1 2.3 29 12-48 36-64 (90)
157 TIGR03831 YgiT_finger YgiT-typ 28.1 64 0.0014 17.9 2.2 13 15-27 1-13 (46)
158 PF03119 DNA_ligase_ZBD: NAD-d 27.7 24 0.00052 19.7 0.3 21 14-42 1-21 (28)
159 PF01921 tRNA-synt_1f: tRNA sy 27.6 33 0.00072 29.2 1.3 41 12-53 174-214 (360)
160 TIGR00416 sms DNA repair prote 27.6 40 0.00087 28.6 1.8 24 12-47 7-30 (454)
161 PRK15103 paraquat-inducible me 27.6 57 0.0012 27.7 2.6 36 11-52 9-44 (419)
162 TIGR00373 conserved hypothetic 26.6 41 0.00088 24.8 1.4 17 32-49 103-119 (158)
163 PF04828 GFA: Glutathione-depe 26.4 84 0.0018 19.2 2.7 37 32-68 42-79 (92)
164 cd00729 rubredoxin_SM Rubredox 26.4 73 0.0016 18.2 2.2 11 38-48 2-12 (34)
165 PRK05776 DNA topoisomerase I; 26.2 58 0.0013 29.2 2.6 33 12-48 596-635 (670)
166 PF15616 TerY-C: TerY-C metal 26.2 34 0.00073 25.5 1.0 14 13-26 78-91 (131)
167 PHA02540 61 DNA primase; Provi 26.0 32 0.0007 28.8 0.9 34 12-45 27-62 (337)
168 PF04296 DUF448: Protein of un 25.9 29 0.00063 22.7 0.5 43 28-77 30-74 (78)
169 PF07649 C1_3: C1-like domain; 25.8 39 0.00086 18.3 1.0 12 36-47 13-24 (30)
170 TIGR01056 topB DNA topoisomera 25.7 52 0.0011 29.4 2.2 33 12-51 611-653 (660)
171 PF11287 DUF3088: Protein of u 25.5 46 0.00099 24.5 1.5 15 31-46 15-29 (112)
172 CHL00174 accD acetyl-CoA carbo 25.2 16 0.00035 30.3 -1.0 28 12-46 38-65 (296)
173 COG2051 RPS27A Ribosomal prote 24.8 39 0.00085 23.1 1.0 28 12-46 19-46 (67)
174 COG0777 AccD Acetyl-CoA carbox 24.5 26 0.00057 29.6 0.1 30 12-48 28-57 (294)
175 PRK14283 chaperone protein Dna 23.9 96 0.0021 25.5 3.3 33 12-44 163-195 (378)
176 COG1439 Predicted nucleic acid 23.7 61 0.0013 25.4 2.0 25 11-36 152-176 (177)
177 PF05180 zf-DNL: DNL zinc fing 23.2 26 0.00057 23.4 -0.1 34 14-48 6-39 (66)
178 PRK07591 threonine synthase; V 23.2 54 0.0012 27.3 1.7 23 12-45 18-40 (421)
179 TIGR00686 phnA alkylphosphonat 22.8 80 0.0017 23.3 2.4 32 12-53 2-33 (109)
180 TIGR01391 dnaG DNA primase, ca 22.8 72 0.0016 26.6 2.4 30 12-46 34-63 (415)
181 PRK14282 chaperone protein Dna 22.5 1.2E+02 0.0025 24.9 3.5 17 12-28 169-185 (369)
182 PF10122 Mu-like_Com: Mu-like 21.9 51 0.0011 21.4 1.1 10 12-21 24-33 (51)
183 TIGR00320 dfx_rbo desulfoferro 21.8 62 0.0014 23.4 1.6 13 36-48 5-17 (125)
184 KOG2462 C2H2-type Zn-finger pr 21.8 42 0.0009 28.1 0.8 32 13-45 188-222 (279)
185 PRK05654 acetyl-CoA carboxylas 21.7 19 0.00041 29.3 -1.2 30 12-48 27-56 (292)
186 smart00400 ZnF_CHCC zinc finge 21.6 89 0.0019 18.8 2.1 27 14-45 4-30 (55)
187 PRK06266 transcription initiat 21.2 62 0.0014 24.4 1.6 14 32-45 111-124 (178)
188 PF13894 zf-C2H2_4: C2H2-type 21.2 53 0.0011 15.4 0.8 7 39-45 1-7 (24)
189 COG1327 Predicted transcriptio 21.0 63 0.0014 25.1 1.6 69 14-82 2-92 (156)
190 PF00684 DnaJ_CXXCXGXG: DnaJ c 20.8 1.6E+02 0.0034 18.4 3.1 19 11-29 14-32 (66)
191 PRK02655 psbI photosystem II r 20.5 51 0.0011 20.5 0.8 10 28-37 26-35 (38)
192 PRK13899 type IV secretion sys 20.5 40 0.00086 23.4 0.4 20 26-45 76-95 (97)
193 COG3024 Uncharacterized protei 20.5 69 0.0015 21.8 1.5 37 12-54 7-46 (65)
194 KOG1024 Receptor-like protein 20.2 70 0.0015 29.2 1.9 37 48-84 304-341 (563)
195 PF04695 Pex14_N: Peroxisomal 20.2 52 0.0011 23.6 0.9 23 61-83 27-49 (136)
No 1
>PF06839 zf-GRF: GRF zinc finger; InterPro: IPR010666 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 presumed zinc-binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to IPR000380 from INTERPRO. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=99.65 E-value=1.5e-16 Score=96.08 Aligned_cols=38 Identities=47% Similarity=1.070 Sum_probs=35.0
Q ss_pred ccccccCCceeEEEeec-CCCCCCCceEeCC-----CCCeeEecCC
Q 039987 13 KACEKCFNSSKVLRTSH-TRENPNRKFWKCK-----GCGAFKWDDD 52 (105)
Q Consensus 13 ~~Cp~Cg~~~avlrTSk-T~~NPGRkFY~Cp-----sC~FFqW~De 52 (105)
+.|+ || .+++++||+ |++||||+||+|| +|+||+|.|+
T Consensus 1 p~C~-Cg-~~~~~~~s~k~~~N~GR~Fy~C~~~~~~~C~fF~W~De 44 (45)
T PF06839_consen 1 PKCP-CG-EPAVRRTSKKTGPNPGRRFYKCPNYKDKGCNFFQWEDE 44 (45)
T ss_pred CCCC-CC-CEeEEEEEeCCCCCCCCcceECCCCCCCCcCCEEeccC
Confidence 4788 95 889999998 9999999999999 5999999997
No 2
>KOG1956 consensus DNA topoisomerase III alpha [Replication, recombination and repair]
Probab=97.89 E-value=4.6e-06 Score=75.29 Aligned_cols=38 Identities=32% Similarity=0.719 Sum_probs=32.3
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCC---CCCeeEec
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCK---GCGAFKWD 50 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~Cp---sC~FFqW~ 50 (105)
...| .|+-..+.+++.+|++|.||+||+|+ +|+||+|+
T Consensus 718 ~~~c-~c~~ra~~l~v~k~~~nrGR~f~sc~~~k~c~ff~w~ 758 (758)
T KOG1956|consen 718 EVTC-GCGTRAVKLLVAKTEPNRGRKFYSCLPEKSCNFFAWE 758 (758)
T ss_pred cccc-CCcchhhhhhhhccCccCCCCCcccCCCCCcceEeeC
Confidence 4455 48655788888999999999999999 69999996
No 3
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=97.09 E-value=0.001 Score=39.54 Aligned_cols=34 Identities=29% Similarity=0.483 Sum_probs=29.0
Q ss_pred ccccccCCceeEEEeecCCCCCCCceEeCC---CCCeeEecCC
Q 039987 13 KACEKCFNSSKVLRTSHTRENPNRKFWKCK---GCGAFKWDDD 52 (105)
Q Consensus 13 ~~Cp~Cg~~~avlrTSkT~~NPGRkFY~Cp---sC~FFqW~De 52 (105)
..||.|+ .+.++++++.+ .||.|. .|.+..|..+
T Consensus 2 ~~CP~Cg-~~lv~r~~k~g-----~F~~Cs~yP~C~~~~~~~~ 38 (39)
T PF01396_consen 2 EKCPKCG-GPLVLRRGKKG-----KFLGCSNYPECKYTEPLPK 38 (39)
T ss_pred cCCCCCC-ceeEEEECCCC-----CEEECCCCCCcCCeEeCCC
Confidence 5799997 77888888766 999999 7999999764
No 4
>PF05325 DUF730: Protein of unknown function (DUF730); InterPro: IPR007989 This family consists of several uncharacterised Arabidopsis thaliana proteins of unknown function.
Probab=96.93 E-value=0.00098 Score=49.31 Aligned_cols=66 Identities=26% Similarity=0.534 Sum_probs=50.2
Q ss_pred ccCccccccccccCCceeEEEeecCCCCCCCceEeCC---------CCCeeEecCCCCCCccchhhhhhhhccccchhhh
Q 039987 6 SDNRTQLKACEKCFNSSKVLRTSHTRENPNRKFWKCK---------GCGAFKWDDDRKSSECNDFRGMVDRNMSENKIDI 76 (105)
Q Consensus 6 ~~n~~~l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~Cp---------sC~FFqW~De~~~~~~~~~~~~~~~n~~~~~~~~ 76 (105)
+|++.+++-|- | +...++-||+.+-..|.-||.|| +|+|=.|+-..--++ | .|++.-+.|-|-|+
T Consensus 14 rrdkgv~ie~d-c-nakvvvats~dpvts~klyfscpyeisdg~g~~~gfkrwwtvalcde---f-dmikee~~emkkdl 87 (122)
T PF05325_consen 14 RRDKGVPIECD-C-NAKVVVATSRDPVTSGKLYFSCPYEISDGPGRGCGFKRWWTVALCDE---F-DMIKEETIEMKKDL 87 (122)
T ss_pred ccCCCcceecc-C-CceEEEEeccCCcccceeeecCccccccCCCCCccceeEEeeeechh---h-hHHHHHHHHHHHHH
Confidence 56778899995 8 56689999999999999999999 799999996543332 2 35555566666665
Q ss_pred H
Q 039987 77 L 77 (105)
Q Consensus 77 ~ 77 (105)
-
T Consensus 88 e 88 (122)
T PF05325_consen 88 E 88 (122)
T ss_pred H
Confidence 3
No 5
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=96.38 E-value=0.0068 Score=36.18 Aligned_cols=36 Identities=28% Similarity=0.771 Sum_probs=29.7
Q ss_pred cccccCCceeEEEee--cCCCCCCCceEeCCCCCeeEec
Q 039987 14 ACEKCFNSSKVLRTS--HTRENPNRKFWKCKGCGAFKWD 50 (105)
Q Consensus 14 ~Cp~Cg~~~avlrTS--kT~~NPGRkFY~CpsC~FFqW~ 50 (105)
.||.|++..++..++ +....|=-.||.|..|+. +|.
T Consensus 2 ~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~-~w~ 39 (40)
T smart00440 2 PCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGH-RWR 39 (40)
T ss_pred cCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCC-EeC
Confidence 699999999998874 557778889999999984 564
No 6
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=96.23 E-value=0.0038 Score=46.73 Aligned_cols=33 Identities=24% Similarity=0.481 Sum_probs=24.9
Q ss_pred cccccCCceeEEEeecC--CCCCCCceEeCCCCCe
Q 039987 14 ACEKCFNSSKVLRTSHT--RENPNRKFWKCKGCGA 46 (105)
Q Consensus 14 ~Cp~Cg~~~avlrTSkT--~~NPGRkFY~CpsC~F 46 (105)
+||.||.....+++|+- +-|--|+||.||.|++
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~ 36 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGK 36 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCC
Confidence 69999755547888874 4567788899996654
No 7
>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=95.57 E-value=0.017 Score=34.25 Aligned_cols=34 Identities=26% Similarity=0.663 Sum_probs=26.0
Q ss_pred ccccccCCceeEEEe--ecCCCCCCCceEeCCCCCe
Q 039987 13 KACEKCFNSSKVLRT--SHTRENPNRKFWKCKGCGA 46 (105)
Q Consensus 13 ~~Cp~Cg~~~avlrT--SkT~~NPGRkFY~CpsC~F 46 (105)
+.||.|+...++... .+....|=-.||.|..|+.
T Consensus 1 ~~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~ 36 (39)
T PF01096_consen 1 IKCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGH 36 (39)
T ss_dssp S--SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTE
T ss_pred CCCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCC
Confidence 479999999998887 4457788999999999984
No 8
>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=95.52 E-value=0.021 Score=38.38 Aligned_cols=40 Identities=25% Similarity=0.657 Sum_probs=32.9
Q ss_pred cccccccCCceeEEEee--cCCCCCCCceEeCCCCCeeEecCC
Q 039987 12 LKACEKCFNSSKVLRTS--HTRENPNRKFWKCKGCGAFKWDDD 52 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTS--kT~~NPGRkFY~CpsC~FFqW~De 52 (105)
...||.||...|+..+. +....|=-.||.|..|++ +|.+.
T Consensus 62 ~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~-~w~~~ 103 (104)
T TIGR01384 62 RVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGY-VWREY 103 (104)
T ss_pred cCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCC-eeEeC
Confidence 57899999999988874 446778889999999995 78763
No 9
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=95.13 E-value=0.016 Score=48.72 Aligned_cols=44 Identities=20% Similarity=0.476 Sum_probs=37.7
Q ss_pred cccccccccCCceeEEEeecCCCCCCCceEeCC-------CCCeeEecCCCCCC
Q 039987 10 TQLKACEKCFNSSKVLRTSHTRENPNRKFWKCK-------GCGAFKWDDDRKSS 56 (105)
Q Consensus 10 ~~l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~Cp-------sC~FFqW~De~~~~ 56 (105)
+|-+.|| -+|+++..-+|.+---|+||+|. -|+||+|.|+.-.|
T Consensus 11 ~~~P~C~---HGP~LLF~K~~~~E~~~~F~ACs~~R~d~kfC~F~~~~d~~~~g 61 (325)
T KOG4399|consen 11 VPAPLCP---HGPTLLFVKVTQKEETRRFYACSACRMDDKFCHFFMFEDEFFDG 61 (325)
T ss_pred CCCCcCC---CCCeEEEEEccCcchheeeehhhhhhcchhccchhhhcccccCc
Confidence 4456666 48999999999999999999999 69999999997665
No 10
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=93.98 E-value=0.058 Score=38.32 Aligned_cols=38 Identities=29% Similarity=0.803 Sum_probs=31.9
Q ss_pred cccccccCCceeEEEee--cCCCCCCCceEeCCCCCeeEec
Q 039987 12 LKACEKCFNSSKVLRTS--HTRENPNRKFWKCKGCGAFKWD 50 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTS--kT~~NPGRkFY~CpsC~FFqW~ 50 (105)
...||.||+..+...+. +....|==+||+|..|++ .|.
T Consensus 72 ~~~CpkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~-~wr 111 (113)
T COG1594 72 KEKCPKCGNKEAYYWQLQTRSADEPETRFYKCTRCGY-RWR 111 (113)
T ss_pred cccCCCCCCceeEEEeeehhccCCCceEEEEecccCC-Eee
Confidence 35699999999999884 448899999999999996 564
No 11
>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=93.70 E-value=0.095 Score=32.26 Aligned_cols=35 Identities=26% Similarity=0.493 Sum_probs=21.8
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCCee
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAF 47 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FF 47 (105)
|+.||-||+. +....+..+..-++..|.|..|+.-
T Consensus 1 LkPCPfCGg~-~~~~~~~~~~~~~~~~~~C~~Cga~ 35 (53)
T TIGR03655 1 LKPCPFCGGA-DVYLRRGFDPLDLSHYFECSTCGAS 35 (53)
T ss_pred CCCCCCCCCc-ceeeEeccCCCCCEEEEECCCCCCC
Confidence 6789999765 4433333343344445579988763
No 12
>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=93.57 E-value=0.086 Score=31.61 Aligned_cols=27 Identities=22% Similarity=0.573 Sum_probs=19.2
Q ss_pred ccccccCCceeEEEeecCCCCCCCceEeCCCCCe
Q 039987 13 KACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGA 46 (105)
Q Consensus 13 ~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~F 46 (105)
++||+||......+++ |.-|+|.+|+.
T Consensus 19 ~~CP~Cg~~~~~~~~~-------~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGSTKHYRLKT-------RGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCeeeEEeCC-------CCeEECCCCCC
Confidence 6799998663333333 88999998873
No 13
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=92.73 E-value=0.17 Score=29.84 Aligned_cols=32 Identities=22% Similarity=0.485 Sum_probs=20.4
Q ss_pred cccccCCceeEEEeecCCCCCCCceEeCCCCCeeEecC
Q 039987 14 ACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKWDD 51 (105)
Q Consensus 14 ~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFqW~D 51 (105)
-||.||+ ++..+.. .++..|.||.|++-...+
T Consensus 2 FCp~Cg~----~l~~~~~--~~~~~~vC~~Cg~~~~~~ 33 (52)
T smart00661 2 FCPKCGN----MLIPKEG--KEKRRFVCRKCGYEEPIE 33 (52)
T ss_pred CCCCCCC----ccccccC--CCCCEEECCcCCCeEECC
Confidence 5999974 2222222 234589999999876554
No 14
>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=92.59 E-value=0.14 Score=36.79 Aligned_cols=39 Identities=28% Similarity=0.834 Sum_probs=27.8
Q ss_pred cccccccCCceeEEEeecC---------CCCCCCceEeCCCCCeeEecCC
Q 039987 12 LKACEKCFNSSKVLRTSHT---------RENPNRKFWKCKGCGAFKWDDD 52 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT---------~~NPGRkFY~CpsC~FFqW~De 52 (105)
.-.|+.|+ .+ +..+++. ..+....||.||+|+=..|...
T Consensus 91 ~sRC~~CN-~~-L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~Gs 138 (147)
T PF01927_consen 91 FSRCPKCN-GP-LRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEGS 138 (147)
T ss_pred CCccCCCC-cE-eeechhhccccccCccccccCCeEEECCCCCCEecccc
Confidence 57899995 43 3333444 2356778999999999999753
No 15
>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=92.21 E-value=0.098 Score=40.95 Aligned_cols=37 Identities=16% Similarity=0.504 Sum_probs=20.3
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCCeeEec
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKWD 50 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFqW~ 50 (105)
...||-||..|..-.....+. .|+|+..|.-|++ +|.
T Consensus 172 ~g~CPvCGs~P~~s~l~~~~~-~G~R~L~Cs~C~t-~W~ 208 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLRGGER-EGKRYLHCSLCGT-EWR 208 (290)
T ss_dssp -SS-TTT---EEEEEEE-------EEEEEETTT---EEE
T ss_pred CCcCCCCCCcCceEEEecCCC-CccEEEEcCCCCC-eee
Confidence 579999998888888877766 8999999997763 554
No 16
>PHA00626 hypothetical protein
Probab=91.94 E-value=0.14 Score=34.25 Aligned_cols=37 Identities=22% Similarity=0.354 Sum_probs=23.7
Q ss_pred cccccCCceeEEEeecCCCCCCCceEeCCCCCeeEecCCC
Q 039987 14 ACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKWDDDR 53 (105)
Q Consensus 14 ~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFqW~De~ 53 (105)
.||.||....+ +-. +- +.-|.-|.|+.|+|+.=.|.-
T Consensus 2 ~CP~CGS~~Iv-rcg-~c-r~~snrYkCkdCGY~ft~~~~ 38 (59)
T PHA00626 2 SCPKCGSGNIA-KEK-TM-RGWSDDYVCCDCGYNDSKDAF 38 (59)
T ss_pred CCCCCCCceee-eec-ee-cccCcceEcCCCCCeechhhh
Confidence 69999743332 221 21 122677999999999877753
No 17
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=91.04 E-value=0.12 Score=38.23 Aligned_cols=38 Identities=18% Similarity=0.391 Sum_probs=29.1
Q ss_pred cccccccccCCceeEEEeecC-CCCCCC-ceEeCCCCCee
Q 039987 10 TQLKACEKCFNSSKVLRTSHT-RENPNR-KFWKCKGCGAF 47 (105)
Q Consensus 10 ~~l~~Cp~Cg~~~avlrTSkT-~~NPGR-kFY~CpsC~FF 47 (105)
+...+||+||.....--|--+ +++-|- .||+|+.|.|=
T Consensus 72 ~I~~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k 111 (116)
T KOG2907|consen 72 VIKHKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYK 111 (116)
T ss_pred chhccCcccCCchhhhhhhhcccccCCceEEEEcCcccee
Confidence 336789999999888888333 566665 69999999874
No 18
>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=90.47 E-value=0.37 Score=31.85 Aligned_cols=43 Identities=26% Similarity=0.466 Sum_probs=29.5
Q ss_pred cccccCCceeEEEe-ecCCCCCC-------Cce--EeCCCCCeeEecCCCCCC
Q 039987 14 ACEKCFNSSKVLRT-SHTRENPN-------RKF--WKCKGCGAFKWDDDRKSS 56 (105)
Q Consensus 14 ~Cp~Cg~~~avlrT-SkT~~NPG-------RkF--Y~CpsC~FFqW~De~~~~ 56 (105)
.||+|++....... +-|+.+-+ |+| ..|+.|++=+|-....+.
T Consensus 2 ~C~KCg~~~~e~~~v~~tgg~~skiFdvq~~~f~~v~C~~CGYTE~Y~~~~~~ 54 (64)
T PF09855_consen 2 KCPKCGNEEYESGEVRATGGGLSKIFDVQNKKFTTVSCTNCGYTEFYKAKTSN 54 (64)
T ss_pred CCCCCCCcceecceEEccCCeeEEEEEecCcEEEEEECCCCCCEEEEeecCcc
Confidence 69999987766555 33455443 334 579999999998765443
No 19
>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=90.21 E-value=0.25 Score=29.94 Aligned_cols=32 Identities=28% Similarity=0.612 Sum_probs=23.6
Q ss_pred cccccCCceeEEEeecC-CCCCCCceEeCC--CCCe
Q 039987 14 ACEKCFNSSKVLRTSHT-RENPNRKFWKCK--GCGA 46 (105)
Q Consensus 14 ~Cp~Cg~~~avlrTSkT-~~NPGRkFY~Cp--sC~F 46 (105)
.||.|| .++.++||+. .+.-...+|.|. .|+.
T Consensus 1 ~CP~Cg-~~a~ir~S~~~s~~~~~~Y~qC~N~~Cg~ 35 (47)
T PF04606_consen 1 RCPHCG-SKARIRTSRQLSPLTRELYCQCTNPECGH 35 (47)
T ss_pred CcCCCC-CeeEEEEchhhCcceEEEEEEECCCcCCC
Confidence 499996 6689999877 555666677888 4653
No 20
>PF14353 CpXC: CpXC protein
Probab=89.65 E-value=0.32 Score=33.61 Aligned_cols=32 Identities=22% Similarity=0.494 Sum_probs=20.2
Q ss_pred ccccccCCceeEEEeecCCCCCCCc-------------eEeCCCCCe
Q 039987 13 KACEKCFNSSKVLRTSHTRENPNRK-------------FWKCKGCGA 46 (105)
Q Consensus 13 ~~Cp~Cg~~~avlrTSkT~~NPGRk-------------FY~CpsC~F 46 (105)
+.||.|+. ....+.+|.=|.... .|+||+||.
T Consensus 2 itCP~C~~--~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~ 46 (128)
T PF14353_consen 2 ITCPHCGH--EFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGH 46 (128)
T ss_pred cCCCCCCC--eeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCC
Confidence 68999963 233334454554444 599998874
No 21
>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=89.59 E-value=0.47 Score=38.74 Aligned_cols=40 Identities=28% Similarity=0.671 Sum_probs=31.7
Q ss_pred ccccccccccCCceeEEEee--cCCCCCCCceEeCCCCCeeEe
Q 039987 9 RTQLKACEKCFNSSKVLRTS--HTRENPNRKFWKCKGCGAFKW 49 (105)
Q Consensus 9 ~~~l~~Cp~Cg~~~avlrTS--kT~~NPGRkFY~CpsC~FFqW 49 (105)
...+..||.|+...++.... +....|=-.||.|..|+. +|
T Consensus 255 ~t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~-~w 296 (299)
T TIGR01385 255 VTDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGN-RW 296 (299)
T ss_pred CcccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCC-ee
Confidence 44589999999888887664 456778899999999984 44
No 22
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=89.43 E-value=0.24 Score=36.30 Aligned_cols=39 Identities=21% Similarity=0.663 Sum_probs=32.3
Q ss_pred cccccccCCceeEEEe--ecCCCCCCCceEeCCCCCeeEecC
Q 039987 12 LKACEKCFNSSKVLRT--SHTRENPNRKFWKCKGCGAFKWDD 51 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrT--SkT~~NPGRkFY~CpsC~FFqW~D 51 (105)
...||.||...|.... .++..-|--.||+|-.|++ +|.|
T Consensus 65 ~~~Cp~Cgh~rayF~qlQtRSADEPmT~FYkC~~C~~-~Wre 105 (105)
T KOG2906|consen 65 EATCPTCGHERAYFMQLQTRSADEPMTTFYKCCKCKH-RWRE 105 (105)
T ss_pred cCcCCCCCCCceEEEEeeeccCCCcHhHhhhhhcccc-cccC
Confidence 6789999998887655 6678889999999999984 6764
No 23
>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=89.14 E-value=0.22 Score=38.97 Aligned_cols=75 Identities=23% Similarity=0.343 Sum_probs=35.4
Q ss_pred ccccccCccccccccccCCceeEEEeec-CCCCCCCceEeCCCCC-eeEecCCCCCCccchhhhhhhhccccchhhhHhH
Q 039987 2 SFSTSDNRTQLKACEKCFNSSKVLRTSH-TRENPNRKFWKCKGCG-AFKWDDDRKSSECNDFRGMVDRNMSENKIDILLG 79 (105)
Q Consensus 2 ~~~~~~n~~~l~~Cp~Cg~~~avlrTSk-T~~NPGRkFY~CpsC~-FFqW~De~~~~~~~~~~~~~~~n~~~~~~~~~~~ 79 (105)
|++.+.=+.+.+.||.||+.....+..- .+..++-+-+.|..|+ +++=-|........ .+--.+---.+||+..
T Consensus 201 s~C~t~W~~~R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK~vd~~~~~~~~----~~~dDl~tl~LD~~a~ 276 (290)
T PF04216_consen 201 SLCGTEWRFVRIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLKTVDREKDPELD----PVADDLATLHLDLLAQ 276 (290)
T ss_dssp TTT--EEE--TTS-TTT---SS-EEE--------SEEEEEETTTTEEEEEEETTT-TT------HHHHHHTTHHHHHHHH
T ss_pred CCCCCeeeecCCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHHHHhhhhCcccc----hhhHHhhhhhHHHHHH
Confidence 3455555666889999999988888877 5888899999999997 44444533222221 1222333345666665
Q ss_pred h
Q 039987 80 E 80 (105)
Q Consensus 80 ~ 80 (105)
|
T Consensus 277 e 277 (290)
T PF04216_consen 277 E 277 (290)
T ss_dssp H
T ss_pred h
Confidence 4
No 24
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=89.06 E-value=0.41 Score=35.46 Aligned_cols=45 Identities=31% Similarity=0.652 Sum_probs=35.8
Q ss_pred cccCccc---cccccccCCceeEEEeecC--CCCCCCceEeCCCCCeeEec
Q 039987 5 TSDNRTQ---LKACEKCFNSSKVLRTSHT--RENPNRKFWKCKGCGAFKWD 50 (105)
Q Consensus 5 ~~~n~~~---l~~Cp~Cg~~~avlrTSkT--~~NPGRkFY~CpsC~FFqW~ 50 (105)
++|+.+| ++.||+|+-..++...+.| ..--=|-||.|-+|++ .|.
T Consensus 63 ~~DPTLPrts~~~C~~C~~~eavffQ~~~~r~d~~m~l~yvC~~C~h-~wt 112 (113)
T KOG2691|consen 63 ASDPTLPRTSDKHCPKCGHREAVFFQAQTRRADEAMRLFYVCCSCGH-RWT 112 (113)
T ss_pred ccCCCcCccccccCCccCCcceEEEecccccccceEEEEEEeccccc-ccc
Confidence 4677776 7899999999999998655 5566789999999874 453
No 25
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=88.35 E-value=0.49 Score=29.60 Aligned_cols=30 Identities=23% Similarity=0.664 Sum_probs=20.9
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCCeeEec
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKWD 50 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFqW~ 50 (105)
...||.||+. .+.-.. ..|.|+.|+|-.|.
T Consensus 20 ~~fCP~Cg~~--~m~~~~-------~r~~C~~Cgyt~~~ 49 (50)
T PRK00432 20 NKFCPRCGSG--FMAEHL-------DRWHCGKCGYTEFK 49 (50)
T ss_pred cCcCcCCCcc--hheccC-------CcEECCCcCCEEec
Confidence 5689999754 332222 46899999998774
No 26
>PHA02998 RNA polymerase subunit; Provisional
Probab=88.22 E-value=0.6 Score=37.26 Aligned_cols=39 Identities=13% Similarity=0.405 Sum_probs=31.5
Q ss_pred cccccccCCceeEEEe--ecCCCCCCCceEeCCCCCeeEecC
Q 039987 12 LKACEKCFNSSKVLRT--SHTRENPNRKFWKCKGCGAFKWDD 51 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrT--SkT~~NPGRkFY~CpsC~FFqW~D 51 (105)
...||.|++..+...+ .+...-|-=.||+|..|+. +|.-
T Consensus 143 ~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~-~wkp 183 (195)
T PHA02998 143 NTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKK-HFKP 183 (195)
T ss_pred CCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCC-ccCC
Confidence 5789999999888555 6667888899999999985 5543
No 27
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=87.74 E-value=0.49 Score=31.92 Aligned_cols=33 Identities=24% Similarity=0.603 Sum_probs=25.4
Q ss_pred ccccccCCceeEEEeecC-CCCCCCceEeCC--CCCe
Q 039987 13 KACEKCFNSSKVLRTSHT-RENPNRKFWKCK--GCGA 46 (105)
Q Consensus 13 ~~Cp~Cg~~~avlrTSkT-~~NPGRkFY~Cp--sC~F 46 (105)
-.||.|| ..+.++||+. +..--|+.|.|. .|+.
T Consensus 2 m~CP~Cg-~~a~irtSr~~s~~~~~~Y~qC~N~eCg~ 37 (72)
T PRK09678 2 FHCPLCQ-HAAHARTSRYITDTTKERYHQCQNVNCSA 37 (72)
T ss_pred ccCCCCC-CccEEEEChhcChhhheeeeecCCCCCCC
Confidence 3699996 5578888877 556778999999 6664
No 28
>KOG1294 consensus Apurinic/apyrimidinic endonuclease and related enzymes [Replication, recombination and repair]
Probab=84.60 E-value=0.54 Score=39.17 Aligned_cols=20 Identities=25% Similarity=0.546 Sum_probs=17.6
Q ss_pred eEEEeecCCCCCCCceEeCC
Q 039987 23 KVLRTSHTRENPNRKFWKCK 42 (105)
Q Consensus 23 avlrTSkT~~NPGRkFY~Cp 42 (105)
-.+++|++..|+||+||-|+
T Consensus 299 dy~~Vsk~~~n~~r~~~Ic~ 318 (335)
T KOG1294|consen 299 DYILVSKPGPNNGRRFYICS 318 (335)
T ss_pred eEEEecCcCCCCCceeeeec
Confidence 45566999999999999999
No 29
>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=84.55 E-value=0.78 Score=28.53 Aligned_cols=28 Identities=18% Similarity=0.648 Sum_probs=20.8
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCCee
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAF 47 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FF 47 (105)
-..||.||.. ...++..+-|.||.|++.
T Consensus 28 Sq~C~~CG~~--------~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 28 SQTCPRCGHR--------NKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred ccCccCcccc--------cccccccceEEcCCCCCE
Confidence 4579999733 112777889999999987
No 30
>PRK07220 DNA topoisomerase I; Validated
Probab=84.25 E-value=1.2 Score=39.97 Aligned_cols=36 Identities=19% Similarity=0.417 Sum_probs=23.6
Q ss_pred cccccccCCceeEEEeecCCCCCCCc--eEeCCCCCeeEecCCC
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRK--FWKCKGCGAFKWDDDR 53 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRk--FY~CpsC~FFqW~De~ 53 (105)
...||.||.. .+... +.|++ ||.||.|+|..|....
T Consensus 635 ~~~Cp~Cg~~-~~k~~-----~~g~~~~~~~Cp~C~~~~~~~~~ 672 (740)
T PRK07220 635 DKVCEAHGLN-HIRII-----NGGKRPWDLGCPQCNFIEWQKKQ 672 (740)
T ss_pred CCCCCCCCCc-eEEEE-----ecCCccceeeCCCCCCccccCCc
Confidence 3679999643 22222 22333 8999999999887644
No 31
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=84.02 E-value=0.7 Score=31.07 Aligned_cols=30 Identities=23% Similarity=0.566 Sum_probs=18.2
Q ss_pred cccccccCCceeEEEe--ecCCCCCCCceEeCCCCCe
Q 039987 12 LKACEKCFNSSKVLRT--SHTRENPNRKFWKCKGCGA 46 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrT--SkT~~NPGRkFY~CpsC~F 46 (105)
--.||.|| +..+.|- .+.-.| .|+||.|+|
T Consensus 27 ~F~CPnCG-e~~I~Rc~~CRk~g~----~Y~Cp~CGF 58 (61)
T COG2888 27 KFPCPNCG-EVEIYRCAKCRKLGN----PYRCPKCGF 58 (61)
T ss_pred EeeCCCCC-ceeeehhhhHHHcCC----ceECCCcCc
Confidence 45688885 3333333 333444 499999998
No 32
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=83.61 E-value=1.4 Score=26.16 Aligned_cols=33 Identities=18% Similarity=0.529 Sum_probs=22.3
Q ss_pred ccccccccCCceeEEEeecCCCCCCCceEeCCCCC
Q 039987 11 QLKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCG 45 (105)
Q Consensus 11 ~l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~ 45 (105)
..+.||.|.....+.+--+ ...|.+=|.|.+|.
T Consensus 4 i~v~CP~C~s~~~v~k~G~--~~~G~qryrC~~C~ 36 (36)
T PF03811_consen 4 IDVHCPRCQSTEGVKKNGK--SPSGHQRYRCKDCR 36 (36)
T ss_pred EeeeCCCCCCCCcceeCCC--CCCCCEeEecCcCC
Confidence 3789999965443554322 23588999999884
No 33
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=83.12 E-value=1.1 Score=29.86 Aligned_cols=32 Identities=22% Similarity=0.495 Sum_probs=19.6
Q ss_pred cccccccccCCceeEEEee--cCCCCCCCceEeCCCCCe
Q 039987 10 TQLKACEKCFNSSKVLRTS--HTRENPNRKFWKCKGCGA 46 (105)
Q Consensus 10 ~~l~~Cp~Cg~~~avlrTS--kT~~NPGRkFY~CpsC~F 46 (105)
.+.-.||.|| +..+.|-+ +.-.| -|+||.|||
T Consensus 23 ~~~F~CPnCG-~~~I~RC~~CRk~~~----~Y~CP~CGF 56 (59)
T PRK14890 23 AVKFLCPNCG-EVIIYRCEKCRKQSN----PYTCPKCGF 56 (59)
T ss_pred cCEeeCCCCC-CeeEeechhHHhcCC----ceECCCCCC
Confidence 3456788885 43344442 23333 499999998
No 34
>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=82.79 E-value=1.5 Score=31.26 Aligned_cols=40 Identities=15% Similarity=0.262 Sum_probs=25.4
Q ss_pred cccccccCCceeEEEeecC--CCC--CCCceEeCCCCCeeEecCC
Q 039987 12 LKACEKCFNSSKVLRTSHT--REN--PNRKFWKCKGCGAFKWDDD 52 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT--~~N--PGRkFY~CpsC~FFqW~De 52 (105)
.+.||.|| .++.+.++.. +.. .+.-+|.|..|+-..-.-+
T Consensus 2 p~~CpYCg-~~~~l~~~~~iYg~~~~~~~~~y~C~~C~AyVG~H~ 45 (102)
T PF11672_consen 2 PIICPYCG-GPAELVDGSEIYGHRYDDGPYLYVCTPCDAYVGCHP 45 (102)
T ss_pred CcccCCCC-CeeEEcccchhcCccCCCCceeEECCCCCceeeeeC
Confidence 47899996 5677766322 222 2444699998876665543
No 35
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=82.15 E-value=2 Score=26.18 Aligned_cols=35 Identities=31% Similarity=0.562 Sum_probs=21.0
Q ss_pred ccccccccCCceeEEEeecCCCCCCC-ceEeCCCCCe
Q 039987 11 QLKACEKCFNSSKVLRTSHTRENPNR-KFWKCKGCGA 46 (105)
Q Consensus 11 ~l~~Cp~Cg~~~avlrTSkT~~NPGR-kFY~CpsC~F 46 (105)
+|+.||-|| .+.+........+.|= -+-.|..|+.
T Consensus 2 ~LkPCPFCG-~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPFCG-SADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCCCC-CcceEeecccCCCCCCEEEEEcCCCCC
Confidence 488999994 4444444433333332 4556998977
No 36
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=80.14 E-value=1.7 Score=25.53 Aligned_cols=31 Identities=26% Similarity=0.527 Sum_probs=16.9
Q ss_pred cccccCCceeEEEeecCCCCCCCceEeCCCCCeeE
Q 039987 14 ACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFK 48 (105)
Q Consensus 14 ~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFq 48 (105)
-||.|| .+...+ .++.-+|.=+.|++|++..
T Consensus 2 fC~~CG-~~l~~~---ip~gd~r~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 2 FCPQCG-GPLERR---IPEGDDRERLVCPACGFIH 32 (34)
T ss_dssp B-TTT---B-EEE-----TT-SS-EEEETTTTEEE
T ss_pred cccccc-Chhhhh---cCCCCCccceECCCCCCEE
Confidence 599996 443333 3444577889999999864
No 37
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=79.80 E-value=2.2 Score=35.34 Aligned_cols=30 Identities=10% Similarity=0.236 Sum_probs=19.9
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCC
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCK 42 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~Cp 42 (105)
...||-||..|..-...- +..-|.|+..|.
T Consensus 187 ~~~CPvCGs~P~~s~v~~-~~~~G~RyL~Cs 216 (309)
T PRK03564 187 RQFCPVCGSMPVSSVVQI-GTTQGLRYLHCN 216 (309)
T ss_pred CCCCCCCCCcchhheeec-cCCCCceEEEcC
Confidence 568888887774443322 335688888888
No 38
>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=79.26 E-value=1.8 Score=27.55 Aligned_cols=36 Identities=33% Similarity=0.728 Sum_probs=22.6
Q ss_pred cCccccccccccCCceeEEEeecCCCCCCCceEeCCCCCee
Q 039987 7 DNRTQLKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAF 47 (105)
Q Consensus 7 ~n~~~l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FF 47 (105)
.|+..+| |+.|..-.-... ...+.---|+||.|++|
T Consensus 18 ~~r~aLI-C~~C~~hNGla~----~~~~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 18 SNRYALI-CSKCFSHNGLAP----KEEFEEIQYRCPYCGAL 53 (54)
T ss_pred cCceeEE-Ccccchhhcccc----cccCCceEEEcCCCCCc
Confidence 4555555 999965433333 23334447999999986
No 39
>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=78.47 E-value=2.1 Score=24.18 Aligned_cols=31 Identities=26% Similarity=0.448 Sum_probs=16.8
Q ss_pred ccccccCCceeEEEeecCCCCCCCceEeCCCCCe
Q 039987 13 KACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGA 46 (105)
Q Consensus 13 ~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~F 46 (105)
+.||.|+ ..-.+-.+.-+.+. . -.+||.|+-
T Consensus 3 ~~CP~C~-~~~~v~~~~~~~~~-~-~v~C~~C~~ 33 (38)
T TIGR02098 3 IQCPNCK-TSFRVVDSQLGANG-G-KVRCGKCGH 33 (38)
T ss_pred EECCCCC-CEEEeCHHHcCCCC-C-EEECCCCCC
Confidence 5799995 32222222223333 2 578998874
No 40
>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=77.72 E-value=2.9 Score=34.46 Aligned_cols=44 Identities=20% Similarity=0.307 Sum_probs=29.9
Q ss_pred ccccccCccccccccccCCceeEEEeecCC--CCCCCceEeCCCCC
Q 039987 2 SFSTSDNRTQLKACEKCFNSSKVLRTSHTR--ENPNRKFWKCKGCG 45 (105)
Q Consensus 2 ~~~~~~n~~~l~~Cp~Cg~~~avlrTSkT~--~NPGRkFY~CpsC~ 45 (105)
|++.+.=..+...||.||+..-+-.-+-.+ ..++-+-..|..|+
T Consensus 214 slC~teW~~~R~~C~~Cg~~~~l~y~~~e~~~~~~~~r~e~C~~C~ 259 (305)
T TIGR01562 214 SLCATEWHYVRVKCSHCEESKHLAYLSLEHDAEKAVLKAETCDSCQ 259 (305)
T ss_pred CCCCCcccccCccCCCCCCCCceeeEeecCCCCCcceEEeeccccc
Confidence 455555566789999998764332223233 46889999999886
No 41
>PRK06599 DNA topoisomerase I; Validated
Probab=75.46 E-value=2.3 Score=37.49 Aligned_cols=35 Identities=29% Similarity=0.469 Sum_probs=25.0
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCC---CCCeeEecC
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCK---GCGAFKWDD 51 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~Cp---sC~FFqW~D 51 (105)
...||.|++...+++.++. | +||.|. .|++..|..
T Consensus 585 ~~~CP~C~~~~l~~k~~k~----g-~F~~Cs~~p~C~~~~~~~ 622 (675)
T PRK06599 585 DETCPKCGGGPLVLKLGKN----G-KFLGCSGYPECKYTKNIT 622 (675)
T ss_pred CccccccCCCcceEEecCC----C-ceeeCCCCCccCCCCCCc
Confidence 4789999655566654433 2 499997 799998853
No 42
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=75.03 E-value=2.3 Score=31.08 Aligned_cols=40 Identities=25% Similarity=0.512 Sum_probs=27.3
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCCeeEecCCCCCCccchhhhhhhhccc
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKWDDDRKSSECNDFRGMVDRNMS 70 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFqW~De~~~~~~~~~~~~~~~n~~ 70 (105)
-+.||.||. .-.+-|.||.|++..=.| -|+..|+.++-.+
T Consensus 309 S~~C~~cg~-------------~~~r~~~C~~cg~~~~rD------~naa~Ni~~~~~~ 348 (364)
T COG0675 309 SKTCPCCGH-------------LSGRLFKCPRCGFVHDRD------VNAALNIARRALG 348 (364)
T ss_pred cccccccCC-------------ccceeEECCCCCCeehhh------HHHHHHHHHHhcc
Confidence 478999974 446789999999875443 4555666655543
No 43
>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=74.93 E-value=3.5 Score=24.15 Aligned_cols=35 Identities=20% Similarity=0.434 Sum_probs=22.7
Q ss_pred cccccCCceeEEEeecCCCCCCCceEeCCCCCeeEecCCCCC
Q 039987 14 ACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKWDDDRKS 55 (105)
Q Consensus 14 ~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFqW~De~~~ 55 (105)
+||.|+... + ..++.+-.+.|+.||.-.=.+...+
T Consensus 2 ~Cp~Cg~~~-~------~~D~~~g~~vC~~CG~Vl~e~~i~~ 36 (43)
T PF08271_consen 2 KCPNCGSKE-I------VFDPERGELVCPNCGLVLEENIIDE 36 (43)
T ss_dssp SBTTTSSSE-E------EEETTTTEEEETTT-BBEE-TTBSC
T ss_pred CCcCCcCCc-e------EEcCCCCeEECCCCCCEeecccccC
Confidence 699997654 2 2347888999999997655444433
No 44
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=74.82 E-value=2.5 Score=30.59 Aligned_cols=64 Identities=20% Similarity=0.344 Sum_probs=37.2
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCCe-eEecCCCCCCc-----cchhhhhhhhccccchhhhHh
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGA-FKWDDDRKSSE-----CNDFRGMVDRNMSENKIDILL 78 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~F-FqW~De~~~~~-----~~~~~~~~~~n~~~~~~~~~~ 78 (105)
-+.||.|+... +.+.. ....|.+=|+|++|++ |.=.+...... .-....|+.-|++-..+.=++
T Consensus 30 ~~~cP~C~s~~-~~k~g--~~~~~~qRyrC~~C~~tf~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~a~~l 99 (129)
T COG3677 30 KVNCPRCKSSN-VVKIG--GIRRGHQRYKCKSCGSTFTVETGSPLSKALYKIKLQAVTLYMLGLGIRDIARTL 99 (129)
T ss_pred cCcCCCCCccc-eeeEC--CccccccccccCCcCcceeeeccCcccccchHHHHHHHHHHHcCCCcccHHHHh
Confidence 58999996443 33332 3344588999999986 33333322223 223456666677766655443
No 45
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=74.76 E-value=1.6 Score=33.78 Aligned_cols=38 Identities=21% Similarity=0.740 Sum_probs=27.3
Q ss_pred cccccccCCceeEEEeecCC---C------CCCCceEeCCCCCeeEecC
Q 039987 12 LKACEKCFNSSKVLRTSHTR---E------NPNRKFWKCKGCGAFKWDD 51 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~---~------NPGRkFY~CpsC~FFqW~D 51 (105)
.-.||.|+ + .++.+|+.. + -.-..||.||.|+=-.|..
T Consensus 97 ~~RCp~CN-~-~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW~G 143 (165)
T COG1656 97 FSRCPECN-G-ELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIYWKG 143 (165)
T ss_pred cccCcccC-C-EeccCcHHHHhhccchhhhhcccceeECCCCcccccCc
Confidence 56899994 4 355566553 1 2345799999999999965
No 46
>PRK08173 DNA topoisomerase III; Validated
Probab=73.87 E-value=1.9 Score=39.60 Aligned_cols=29 Identities=21% Similarity=0.424 Sum_probs=20.8
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCCeeEec
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKWD 50 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFqW~ 50 (105)
...||.||.. + .-+.++|.|.+|+|..|.
T Consensus 624 ~~~CP~Cg~~--~--------~~~~~~~~Cs~C~f~~~~ 652 (862)
T PRK08173 624 QTPCPNCGGV--V--------KENYRRFACTKCDFSISK 652 (862)
T ss_pred cccCCccccc--c--------cccCceeEcCCCCcccch
Confidence 3689999743 1 112446999999999995
No 47
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=73.60 E-value=1.8 Score=37.61 Aligned_cols=30 Identities=23% Similarity=0.556 Sum_probs=21.9
Q ss_pred ccccccccCCceeEEEeecCCCCCCCceEeCCCCCeeEe
Q 039987 11 QLKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKW 49 (105)
Q Consensus 11 ~l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFqW 49 (105)
..++||.||+ +-+..||.=|+|+.|+.=.=
T Consensus 349 ~~p~Cp~Cg~---------~m~S~G~~g~rC~kCg~~~~ 378 (421)
T COG1571 349 VNPVCPRCGG---------RMKSAGRNGFRCKKCGTRAR 378 (421)
T ss_pred cCCCCCccCC---------chhhcCCCCcccccccccCC
Confidence 3789999973 33456777899999987543
No 48
>PRK05582 DNA topoisomerase I; Validated
Probab=72.97 E-value=3.5 Score=36.22 Aligned_cols=35 Identities=37% Similarity=0.781 Sum_probs=22.9
Q ss_pred ccccccCCceeEEEeecCCCCCCCceEeCC---CCCeeEecCC
Q 039987 13 KACEKCFNSSKVLRTSHTRENPNRKFWKCK---GCGAFKWDDD 52 (105)
Q Consensus 13 ~~Cp~Cg~~~avlrTSkT~~NPGRkFY~Cp---sC~FFqW~De 52 (105)
..||.|+ ...+++.. ..|+.||.|. +|+|+.|.-+
T Consensus 612 ~~CP~C~-~~l~l~k~----k~gk~f~~Cs~~p~C~~~~~~~~ 649 (650)
T PRK05582 612 VKCPKCG-GQIVERKS----KKGRKFYGCSRYPECDFVSWDKP 649 (650)
T ss_pred CCCCCCC-CceEEEcC----CCCceeeccCCCCCCCcccCCCC
Confidence 5788885 33444322 2466799995 7999988643
No 49
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=72.47 E-value=4.7 Score=23.46 Aligned_cols=27 Identities=19% Similarity=0.508 Sum_probs=17.6
Q ss_pred cccccCCceeEEEeecCCCCCCCceEeCCCCCe
Q 039987 14 ACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGA 46 (105)
Q Consensus 14 ~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~F 46 (105)
.||+|+. ....+.. .+=.-+.|++|+=
T Consensus 1 ~CP~C~~--~l~~~~~----~~~~id~C~~C~G 27 (41)
T PF13453_consen 1 KCPRCGT--ELEPVRL----GDVEIDVCPSCGG 27 (41)
T ss_pred CcCCCCc--ccceEEE----CCEEEEECCCCCe
Confidence 5999964 2222222 6678899998863
No 50
>PHA02942 putative transposase; Provisional
Probab=72.03 E-value=3.4 Score=34.36 Aligned_cols=40 Identities=18% Similarity=0.480 Sum_probs=25.6
Q ss_pred ccccccCCceeEEEeecCCCCCCCceEeCCCCCeeEecCCCCCCccchhhhhhhh
Q 039987 13 KACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKWDDDRKSSECNDFRGMVDR 67 (105)
Q Consensus 13 ~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFqW~De~~~~~~~~~~~~~~~ 67 (105)
..||.||... . .++.+.|.|+.||+-. ..|-|+..|+..+
T Consensus 326 q~Cs~CG~~~--------~-~l~~r~f~C~~CG~~~------drD~nAA~NI~~r 365 (383)
T PHA02942 326 VSCPKCGHKM--------V-EIAHRYFHCPSCGYEN------DRDVIAIMNLNGR 365 (383)
T ss_pred ccCCCCCCcc--------C-cCCCCEEECCCCCCEe------CcHHHHHHHHHHH
Confidence 6799997431 1 2345589999999853 2345566666554
No 51
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=71.55 E-value=5.2 Score=26.98 Aligned_cols=29 Identities=28% Similarity=0.631 Sum_probs=19.9
Q ss_pred cccccccCCceeEEEeecCCCCCCCce-EeCCCCCe
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKF-WKCKGCGA 46 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkF-Y~CpsC~F 46 (105)
++.||-||.....++.+ |.-| +.|.+|+-
T Consensus 6 lKPCPFCG~~~~~v~~~------~g~~~v~C~~CgA 35 (64)
T PRK09710 6 VKPCPFCGCPSVTVKAI------SGYYRAKCNGCES 35 (64)
T ss_pred ccCCCCCCCceeEEEec------CceEEEEcCCCCc
Confidence 78999997555554443 3344 88998875
No 52
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=70.79 E-value=5.4 Score=23.33 Aligned_cols=27 Identities=22% Similarity=0.572 Sum_probs=18.0
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCC
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKG 43 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~Cps 43 (105)
++.|+.|| .+....+. + .++..|.|.+
T Consensus 5 ~l~C~~CG-~~m~~~~~-~---~~~~yy~C~~ 31 (58)
T PF13408_consen 5 LLRCGHCG-SKMTRRKR-K---GKYRYYRCSN 31 (58)
T ss_pred cEEcccCC-cEeEEEEC-C---CCceEEEcCC
Confidence 68999996 43444332 2 4558899994
No 53
>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=70.16 E-value=3 Score=34.44 Aligned_cols=33 Identities=12% Similarity=0.356 Sum_probs=23.2
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCC
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGC 44 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC 44 (105)
...||-||..|..-.....+...|.|+..|.-|
T Consensus 184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC 216 (305)
T TIGR01562 184 RTLCPACGSPPVASMVRQGGKETGLRYLSCSLC 216 (305)
T ss_pred CCcCCCCCChhhhhhhcccCCCCCceEEEcCCC
Confidence 569999987775443333345678999999944
No 54
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=69.98 E-value=2.8 Score=27.34 Aligned_cols=24 Identities=25% Similarity=0.667 Sum_probs=18.0
Q ss_pred cccccCCceeEEEeecCCCCCCCceEeCCCCCeeE
Q 039987 14 ACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFK 48 (105)
Q Consensus 14 ~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFq 48 (105)
.||-|+.+. |++.-|.||.||+=.
T Consensus 1 ~Cpv~~~~~-----------~~~v~~~Cp~cGipt 24 (55)
T PF13824_consen 1 LCPVCKKDL-----------PAHVNFECPDCGIPT 24 (55)
T ss_pred CCCCCcccc-----------ccccCCcCCCCCCcC
Confidence 478775442 999999999777654
No 55
>PRK07220 DNA topoisomerase I; Validated
Probab=69.58 E-value=5.4 Score=35.84 Aligned_cols=35 Identities=23% Similarity=0.382 Sum_probs=24.9
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCC---CCCeeEecC
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCK---GCGAFKWDD 51 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~Cp---sC~FFqW~D 51 (105)
...||.|| ...+++.++. |.+||.|. .|.|-.|-.
T Consensus 589 ~~~CP~Cg-~~l~~r~~r~----g~~f~gCs~yp~C~~~~~l~ 626 (740)
T PRK07220 589 IGKCPLCG-SDLMVRRSKR----GSRFIGCEGYPECTFSLPLP 626 (740)
T ss_pred ccccccCC-CeeeEEecCC----CceEEEcCCCCCCCceeeCC
Confidence 46899996 4555555432 35699996 799999853
No 56
>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=69.50 E-value=4.1 Score=35.34 Aligned_cols=41 Identities=22% Similarity=0.488 Sum_probs=27.8
Q ss_pred ccCccccccccccCCceeEEEe--ecCCC-CCCCceEeCCCCCe
Q 039987 6 SDNRTQLKACEKCFNSSKVLRT--SHTRE-NPNRKFWKCKGCGA 46 (105)
Q Consensus 6 ~~n~~~l~~Cp~Cg~~~avlrT--SkT~~-NPGRkFY~CpsC~F 46 (105)
++.+.=.+.||+||....+..- .++.. .|..-.|.||+|+-
T Consensus 194 sdqr~~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~ 237 (557)
T PF05876_consen 194 SDQRRYYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGC 237 (557)
T ss_pred CCceEEEccCCCCCCCccccccceeecCCCCccceEEECCCCcC
Confidence 3444347899999866554422 34332 79999999998874
No 57
>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=69.13 E-value=2.9 Score=24.17 Aligned_cols=28 Identities=25% Similarity=0.723 Sum_probs=13.4
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCCeeEe
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKW 49 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFqW 49 (105)
+++||.|+..... ...--|.||.|+. +|
T Consensus 2 ~p~Cp~C~se~~y---------~D~~~~vCp~C~~-ew 29 (30)
T PF08274_consen 2 LPKCPLCGSEYTY---------EDGELLVCPECGH-EW 29 (30)
T ss_dssp S---TTT-----E---------E-SSSEEETTTTE-EE
T ss_pred CCCCCCCCCccee---------ccCCEEeCCcccc-cC
Confidence 6789999755443 4455688888874 44
No 58
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=68.22 E-value=2.3 Score=29.89 Aligned_cols=27 Identities=15% Similarity=0.279 Sum_probs=17.5
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCCeeE
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFK 48 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFq 48 (105)
...|+.|+.. -.+...+|.||.|+=+.
T Consensus 70 ~~~C~~Cg~~----------~~~~~~~~~CP~Cgs~~ 96 (113)
T PRK12380 70 QAWCWDCSQV----------VEIHQHDAQCPHCHGER 96 (113)
T ss_pred EEEcccCCCE----------EecCCcCccCcCCCCCC
Confidence 6789999622 22333677899998543
No 59
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=68.14 E-value=4.7 Score=33.46 Aligned_cols=37 Identities=27% Similarity=0.435 Sum_probs=26.6
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCCeeE
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFK 48 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFq 48 (105)
...||.||+..-+..-+-.+.+++-+-+.|..|+-..
T Consensus 226 R~~C~~Cg~~~~l~y~~~~~~~~~~r~e~C~~C~~Yl 262 (309)
T PRK03564 226 RVKCSNCEQSGKLHYWSLDSEQAAVKAESCGDCGTYL 262 (309)
T ss_pred CccCCCCCCCCceeeeeecCCCcceEeeecccccccc
Confidence 5689999865433333556667899999999998653
No 60
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=67.79 E-value=7.7 Score=27.27 Aligned_cols=41 Identities=20% Similarity=0.379 Sum_probs=29.7
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCC---CCCeeEecCCCCCC
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCK---GCGAFKWDDDRKSS 56 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~Cp---sC~FFqW~De~~~~ 56 (105)
-+.||.|+....+++.++- |+.||.|- .|+|-.|.......
T Consensus 60 ~~~Cp~C~~~~~~~k~~~~----~~~f~~~~~~Pkc~~~~~~~~~~~~ 103 (140)
T COG0551 60 GVKCPKCGKGLLVLKKGRF----GKNFLGCSNYPKCRFTEKPKPKEKK 103 (140)
T ss_pred ceeCCCCCCCceEEEeccC----CceEEeecCCCcCceeecCCccccc
Confidence 5899999755555555533 37899777 99999999875443
No 61
>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=66.64 E-value=2.7 Score=29.55 Aligned_cols=26 Identities=23% Similarity=0.713 Sum_probs=16.3
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCCee
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAF 47 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FF 47 (105)
...|+.|+.. -.+...++.||.|+=.
T Consensus 70 ~~~C~~Cg~~----------~~~~~~~~~CP~Cgs~ 95 (115)
T TIGR00100 70 ECECEDCSEE----------VSPEIDLYRCPKCHGI 95 (115)
T ss_pred EEEcccCCCE----------EecCCcCccCcCCcCC
Confidence 6789999622 1122237889999843
No 62
>PRK05582 DNA topoisomerase I; Validated
Probab=66.14 E-value=6.9 Score=34.39 Aligned_cols=34 Identities=29% Similarity=0.444 Sum_probs=22.8
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCC---CCCeeEecC
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCK---GCGAFKWDD 51 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~Cp---sC~FFqW~D 51 (105)
...||.|+ ...+.+..+. | +||.|. .|+|..|..
T Consensus 571 ~~~CP~Cg-~~l~~~~~k~----g-kf~~Cs~~~~C~~~~~~~ 607 (650)
T PRK05582 571 GEDCPKCG-SPMVIKMGRY----G-KFIACSNFPDCRNTKPIV 607 (650)
T ss_pred CCCCCCCC-CEeEEEecCC----C-ceeecCCccccccCCCcc
Confidence 46899996 3333333222 2 699998 699998854
No 63
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=66.06 E-value=5.2 Score=23.18 Aligned_cols=32 Identities=19% Similarity=0.552 Sum_probs=17.7
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCCe
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGA 46 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~F 46 (105)
.+.||.|+ ......-+.--++.+-.+|+.|+-
T Consensus 2 ~i~CP~C~---~~f~v~~~~l~~~~~~vrC~~C~~ 33 (37)
T PF13719_consen 2 IITCPNCQ---TRFRVPDDKLPAGGRKVRCPKCGH 33 (37)
T ss_pred EEECCCCC---ceEEcCHHHcccCCcEEECCCCCc
Confidence 46899995 222332221114444789998863
No 64
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=65.76 E-value=5.6 Score=36.43 Aligned_cols=30 Identities=27% Similarity=0.556 Sum_probs=22.7
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCC---CCCe
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCK---GCGA 46 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~Cp---sC~F 46 (105)
...||.|++...+++.++.+ .||.|. .|.+
T Consensus 592 ~~~CP~Cg~~~L~~k~gr~G-----~Fl~Cs~yP~C~~ 624 (860)
T PRK06319 592 EIDCPKCHKGKLVKIWAKNR-----YFYGCSEYPECDY 624 (860)
T ss_pred CcccCCCCCcceeEEecCCC-----ceeeccCCccccc
Confidence 57899998777777776653 599997 5754
No 65
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=65.29 E-value=8.1 Score=26.47 Aligned_cols=32 Identities=22% Similarity=0.418 Sum_probs=20.3
Q ss_pred ccccccCCceeEEEeecCCCCCCCceEeCCCCCeeEecCCCC
Q 039987 13 KACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKWDDDRK 54 (105)
Q Consensus 13 ~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFqW~De~~ 54 (105)
..||+||-. .+.+ .++--|..||-|+ |+|+..
T Consensus 2 ~~CPCCg~~---Tl~~----~~~~~ydIC~VC~---WEdD~~ 33 (78)
T PF14206_consen 2 YPCPCCGYY---TLEE----RGEGTYDICPVCF---WEDDGV 33 (78)
T ss_pred ccCCCCCcE---Eecc----CCCcCceECCCCC---cccCCc
Confidence 479999732 1222 2233499999995 888754
No 66
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=64.78 E-value=10 Score=26.80 Aligned_cols=40 Identities=15% Similarity=0.367 Sum_probs=26.3
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCCeeEecCCCCCC
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKWDDDRKSS 56 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFqW~De~~~~ 56 (105)
+..||.|+ ...+ .... +. |+--..|+.|++..=..-...+
T Consensus 21 ~f~CP~Cg-e~~v-~v~~-~k--~~~h~~C~~CG~y~~~~V~~l~ 60 (99)
T PRK14892 21 IFECPRCG-KVSI-SVKI-KK--NIAIITCGNCGLYTEFEVPSVY 60 (99)
T ss_pred EeECCCCC-CeEe-eeec-CC--CcceEECCCCCCccCEECCccc
Confidence 67899996 3222 2222 22 7999999999998766544444
No 67
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=64.13 E-value=4.6 Score=37.04 Aligned_cols=55 Identities=20% Similarity=0.408 Sum_probs=35.8
Q ss_pred CCceEeCCCCCeeEec-------------------------CCCCCCccchhhhhhhhccccchhhhHhHhh-hhcCcee
Q 039987 35 NRKFWKCKGCGAFKWD-------------------------DDRKSSECNDFRGMVDRNMSENKIDILLGEV-CKLGHQM 88 (105)
Q Consensus 35 GRkFY~CpsC~FFqW~-------------------------De~~~~~~~~~~~~~~~n~~~~~~~~~~~~~-~~~~~~~ 88 (105)
.+.+..||.|+=..|. |.+.-..++..+.+++ .+..+++|||+|-- -.-||..
T Consensus 472 ~~~p~~Cp~Cgs~~L~~~G~GterieeeL~~~FP~~rv~r~d~Dtt~~k~~~~~~l~-~~~~ge~dILiGTQmiaKG~~f 550 (730)
T COG1198 472 EPIPQSCPECGSEHLRAVGPGTERIEEELKRLFPGARIIRIDSDTTRRKGALEDLLD-QFANGEADILIGTQMIAKGHDF 550 (730)
T ss_pred CCCCCCCCCCCCCeeEEecccHHHHHHHHHHHCCCCcEEEEccccccchhhHHHHHH-HHhCCCCCeeecchhhhcCCCc
Confidence 5678889999888776 4444445555555554 47788999999842 2335544
Q ss_pred ee
Q 039987 89 EC 90 (105)
Q Consensus 89 ~~ 90 (105)
.=
T Consensus 551 p~ 552 (730)
T COG1198 551 PN 552 (730)
T ss_pred cc
Confidence 43
No 68
>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=63.09 E-value=10 Score=21.96 Aligned_cols=29 Identities=24% Similarity=0.557 Sum_probs=15.6
Q ss_pred ccccccCCceeEEEeecCCCCCCCceEeCCCCCeeE
Q 039987 13 KACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFK 48 (105)
Q Consensus 13 ~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFq 48 (105)
.-||.|++- ......+. ++. .|+.|++-+
T Consensus 2 ~FCp~C~nl-L~p~~~~~----~~~--~C~~C~Y~~ 30 (35)
T PF02150_consen 2 RFCPECGNL-LYPKEDKE----KRV--ACRTCGYEE 30 (35)
T ss_dssp -BETTTTSB-EEEEEETT----TTE--EESSSS-EE
T ss_pred eeCCCCCcc-ceEcCCCc----cCc--CCCCCCCcc
Confidence 469999744 22222222 222 999998865
No 69
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=62.07 E-value=5.4 Score=28.41 Aligned_cols=11 Identities=27% Similarity=0.428 Sum_probs=6.4
Q ss_pred cccccccCCce
Q 039987 12 LKACEKCFNSS 22 (105)
Q Consensus 12 l~~Cp~Cg~~~ 22 (105)
.++||+||...
T Consensus 26 PivCP~CG~~~ 36 (108)
T PF09538_consen 26 PIVCPKCGTEF 36 (108)
T ss_pred CccCCCCCCcc
Confidence 56677775443
No 70
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=61.10 E-value=8.2 Score=30.47 Aligned_cols=28 Identities=21% Similarity=0.394 Sum_probs=18.3
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCC
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCG 45 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~ 45 (105)
-..||.||.. . .+. +-. ||.-|=||.|.
T Consensus 244 g~pCprCG~~-I-~~~-~~~---gR~t~~CP~CQ 271 (272)
T PRK14810 244 GEPCLNCKTP-I-RRV-VVA---GRSSHYCPHCQ 271 (272)
T ss_pred CCcCCCCCCe-e-EEE-EEC---CCccEECcCCc
Confidence 3579999633 2 222 111 79999999884
No 71
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=59.85 E-value=3.2 Score=31.82 Aligned_cols=14 Identities=36% Similarity=1.163 Sum_probs=11.1
Q ss_pred EeCCCCCeeEecCC
Q 039987 39 WKCKGCGAFKWDDD 52 (105)
Q Consensus 39 Y~CpsC~FFqW~De 52 (105)
+.||.|||--+..+
T Consensus 49 ~vCP~CgyA~~~~~ 62 (214)
T PF09986_consen 49 WVCPHCGYAAFEED 62 (214)
T ss_pred EECCCCCCcccccc
Confidence 68999999777654
No 72
>PF05265 DUF723: Protein of unknown function (DUF723); InterPro: IPR007929 This family contains several uncharacterised proteins from Neisseria meningitidis. These proteins may have a role in DNA binding.
Probab=58.98 E-value=5.3 Score=26.58 Aligned_cols=29 Identities=24% Similarity=0.345 Sum_probs=18.8
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCC
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCG 45 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~ 45 (105)
-+.||.+|+...-...+-...+ +.||.|+
T Consensus 32 tI~CP~HG~~~~s~~~~~~~sk-----~GCP~Cg 60 (60)
T PF05265_consen 32 TIRCPKHGNFTCSTFNSFIKSK-----HGCPECG 60 (60)
T ss_pred EEECCCCCcEEeccHHhhhhhc-----cCCCCCC
Confidence 7899999876554444333333 4599885
No 73
>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=57.60 E-value=8.8 Score=22.66 Aligned_cols=14 Identities=14% Similarity=0.396 Sum_probs=8.1
Q ss_pred cccccccccCCcee
Q 039987 10 TQLKACEKCFNSSK 23 (105)
Q Consensus 10 ~~l~~Cp~Cg~~~a 23 (105)
.+...||.||+..+
T Consensus 24 ~~~~~CP~Cg~~~~ 37 (42)
T PF09723_consen 24 DDPVPCPECGSTEV 37 (42)
T ss_pred CCCCcCCCCCCCce
Confidence 34667777765333
No 74
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=57.18 E-value=5.3 Score=28.72 Aligned_cols=39 Identities=18% Similarity=0.417 Sum_probs=20.2
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCCeeEecCC
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKWDDD 52 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFqW~De 52 (105)
.-.||.|+.. -....+-.-.+|.+. |.||.||-=.=.++
T Consensus 99 ~Y~Cp~C~~~-y~~~ea~~~~d~~~~-f~Cp~Cg~~l~~~d 137 (147)
T smart00531 99 YYKCPNCQSK-YTFLEANQLLDMDGT-FTCPRCGEELEEDD 137 (147)
T ss_pred EEECcCCCCE-eeHHHHHHhcCCCCc-EECCCCCCEEEEcC
Confidence 5679999532 222222221123333 88998886544443
No 75
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=56.54 E-value=6 Score=27.93 Aligned_cols=26 Identities=15% Similarity=0.432 Sum_probs=15.5
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCCe
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGA 46 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~F 46 (105)
...|..|+.. .+-+.+.|.+||.|+=
T Consensus 71 ~~~C~~Cg~~---------~~~~~~~~~~CP~Cgs 96 (117)
T PRK00564 71 ELECKDCSHV---------FKPNALDYGVCEKCHS 96 (117)
T ss_pred EEEhhhCCCc---------cccCCccCCcCcCCCC
Confidence 6678888621 1222335567998873
No 76
>PRK10445 endonuclease VIII; Provisional
Probab=56.51 E-value=12 Score=29.46 Aligned_cols=28 Identities=36% Similarity=0.710 Sum_probs=18.7
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCC
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCG 45 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~ 45 (105)
-..||.||..-...... ||.-|=||.|.
T Consensus 235 g~~Cp~Cg~~I~~~~~~------gR~t~~CP~CQ 262 (263)
T PRK10445 235 GEACERCGGIIEKTTLS------SRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCCEeEEEEEC------CCCcEECCCCc
Confidence 35799997432222222 79999999884
No 77
>PHA02446 hypothetical protein
Probab=54.69 E-value=5.9 Score=30.65 Aligned_cols=31 Identities=19% Similarity=0.481 Sum_probs=26.1
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCC
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCK 42 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~Cp 42 (105)
+-.||.||...-++.|-.-.+.|.|-|-.||
T Consensus 62 ~q~cp~cg~dawv~~~g~~eahpd~l~qecp 92 (166)
T PHA02446 62 QQQCPLCGQDAWVIHTGIVEAHPDKLLQECP 92 (166)
T ss_pred hhcCCCcccceeEeecCccccCcHHHHHhCC
Confidence 6789999766556666778999999999999
No 78
>PRK07726 DNA topoisomerase III; Provisional
Probab=54.67 E-value=12 Score=33.02 Aligned_cols=34 Identities=21% Similarity=0.376 Sum_probs=21.7
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCC--CCCeeEecC
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCK--GCGAFKWDD 51 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~Cp--sC~FFqW~D 51 (105)
...||.|++ +.+.+.++. | +||.|. .|.|..|..
T Consensus 610 ~~~CP~C~~-~~~~~~~~~----~-~f~~Cs~~~~~~~~~~~ 645 (658)
T PRK07726 610 GPKCPDCGK-PMLKVKGKN----G-KMLVCQDRECGKRKNVS 645 (658)
T ss_pred cccccccCc-cceeecccC----C-eeEecCCCccccccccc
Confidence 468999964 333322222 3 599999 477778855
No 79
>PRK14724 DNA topoisomerase III; Provisional
Probab=54.60 E-value=12 Score=35.23 Aligned_cols=59 Identities=20% Similarity=0.242 Sum_probs=34.3
Q ss_pred ccccccccCCceeEEEeecCCCCCCCceEeCC-----------CCCeeEecCCCCCCccchhhhhhhhccccchhhhHhH
Q 039987 11 QLKACEKCFNSSKVLRTSHTRENPNRKFWKCK-----------GCGAFKWDDDRKSSECNDFRGMVDRNMSENKIDILLG 79 (105)
Q Consensus 11 ~l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~Cp-----------sC~FFqW~De~~~~~~~~~~~~~~~n~~~~~~~~~~~ 79 (105)
++..||.||+. ++. +.++|.|. +|.|-.|.-- .+ +.+-+..+.+=+...+.|++.|
T Consensus 754 ~~g~CPkCg~~--v~e--------~gk~y~Cs~~~~~~~~~~~~C~f~i~k~i--~g-K~is~~~~~kLl~~GkT~ll~g 820 (987)
T PRK14724 754 SLGPCPKCGAP--VFE--------HGSNYVCEKSVPTLAQPTPSCTFKSGQVI--LQ-QPIEREQMQKLLATGKTDLLDK 820 (987)
T ss_pred cccCCCCCCCc--eEe--------ecceEEcCCCcccccCCCCCCCceecccc--cC-cCCCHHHHHHHHhcCCcccccc
Confidence 47899999744 221 57799997 3998877632 11 1133333333344666666665
Q ss_pred hhh
Q 039987 80 EVC 82 (105)
Q Consensus 80 ~~~ 82 (105)
=+-
T Consensus 821 f~s 823 (987)
T PRK14724 821 FVS 823 (987)
T ss_pred cee
Confidence 444
No 80
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=53.73 E-value=14 Score=29.25 Aligned_cols=27 Identities=19% Similarity=0.375 Sum_probs=18.0
Q ss_pred ccccccCCceeEEEeecCCCCCCCceEeCCCCC
Q 039987 13 KACEKCFNSSKVLRTSHTRENPNRKFWKCKGCG 45 (105)
Q Consensus 13 ~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~ 45 (105)
..||.||.. ....+- . ||.-|=||.|.
T Consensus 236 ~pC~~Cg~~-I~~~~~--~---gR~ty~Cp~CQ 262 (269)
T PRK14811 236 QPCPRCGTP-IEKIVV--G---GRGTHFCPQCQ 262 (269)
T ss_pred CCCCcCCCe-eEEEEE--C---CCCcEECCCCc
Confidence 479999633 222221 1 79999999884
No 81
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=53.73 E-value=14 Score=26.41 Aligned_cols=32 Identities=34% Similarity=0.811 Sum_probs=23.7
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCCeeEecCC
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKWDDD 52 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFqW~De 52 (105)
.-.||.|+ .+.+.|.+ -.-|.|..|++ .|...
T Consensus 35 ~~~Cp~C~-~~~VkR~a-------~GIW~C~kCg~-~fAGg 66 (89)
T COG1997 35 KHVCPFCG-RTTVKRIA-------TGIWKCRKCGA-KFAGG 66 (89)
T ss_pred CCcCCCCC-Ccceeeec-------cCeEEcCCCCC-eeccc
Confidence 67899996 55777775 35799999996 45544
No 82
>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=53.38 E-value=7.2 Score=21.76 Aligned_cols=9 Identities=33% Similarity=0.973 Sum_probs=6.3
Q ss_pred eEeCCCCCe
Q 039987 38 FWKCKGCGA 46 (105)
Q Consensus 38 FY~CpsC~F 46 (105)
-|.||.|||
T Consensus 16 ~f~CPnCG~ 24 (24)
T PF07754_consen 16 PFPCPNCGF 24 (24)
T ss_pred eEeCCCCCC
Confidence 477777775
No 83
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=53.22 E-value=14 Score=29.05 Aligned_cols=27 Identities=19% Similarity=0.468 Sum_probs=17.9
Q ss_pred ccccccCCceeEEEeecCCCCCCCceEeCCCCC
Q 039987 13 KACEKCFNSSKVLRTSHTRENPNRKFWKCKGCG 45 (105)
Q Consensus 13 ~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~ 45 (105)
..||.||.. ....+- . ||.-|=||.|.
T Consensus 246 ~pC~~Cg~~-I~~~~~--~---gR~t~~CP~CQ 272 (274)
T PRK01103 246 EPCRRCGTP-IEKIKQ--G---GRSTFFCPRCQ 272 (274)
T ss_pred CCCCCCCCe-eEEEEE--C---CCCcEECcCCC
Confidence 469999633 222221 1 89999999884
No 84
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=52.36 E-value=9.9 Score=22.45 Aligned_cols=27 Identities=19% Similarity=0.305 Sum_probs=14.8
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCCe
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGA 46 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~F 46 (105)
.-+|+.||.. .. ....+ .-.+||.||.
T Consensus 3 ~y~C~~CG~~-~~-~~~~~------~~~~Cp~CG~ 29 (46)
T PRK00398 3 EYKCARCGRE-VE-LDEYG------TGVRCPYCGY 29 (46)
T ss_pred EEECCCCCCE-EE-ECCCC------CceECCCCCC
Confidence 3578888632 11 11111 1578998876
No 85
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=51.80 E-value=13 Score=30.65 Aligned_cols=26 Identities=27% Similarity=0.699 Sum_probs=20.3
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCC
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCK 42 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~Cp 42 (105)
-++|+.| ++ -|.-..+=||+|+.+||
T Consensus 85 VVkC~~C-nE----ATPIr~aPpGKKYVRCP 110 (256)
T PF09788_consen 85 VVKCSVC-NE----ATPIRNAPPGKKYVRCP 110 (256)
T ss_pred eEECCCC-Cc----cccccCCCCCCeeEecC
Confidence 6788888 44 35556778999999999
No 86
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=51.38 E-value=5 Score=29.63 Aligned_cols=33 Identities=21% Similarity=0.507 Sum_probs=27.5
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCC
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCG 45 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~ 45 (105)
.+.||+|| ..-..+.|.=++..=|--|+|.+|.
T Consensus 105 ~~~cp~c~-s~~t~~~s~fg~t~cka~~~c~~c~ 137 (146)
T TIGR02159 105 SVQCPRCG-SADTTITSIFGPTACKALYRCRACK 137 (146)
T ss_pred CCcCCCCC-CCCcEeecCCCChhhHHHhhhhhhC
Confidence 48999996 5577777888999999999998874
No 87
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=51.18 E-value=15 Score=28.90 Aligned_cols=27 Identities=19% Similarity=0.384 Sum_probs=18.0
Q ss_pred ccccccCCceeEEEeecCCCCCCCceEeCCCCC
Q 039987 13 KACEKCFNSSKVLRTSHTRENPNRKFWKCKGCG 45 (105)
Q Consensus 13 ~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~ 45 (105)
..||.||.. ....+- . ||.-|=||.|.
T Consensus 246 ~pC~~Cg~~-I~~~~~--~---gR~t~~CP~CQ 272 (272)
T TIGR00577 246 EPCRRCGTP-IEKIKV--G---GRGTHFCPQCQ 272 (272)
T ss_pred CCCCCCCCe-eEEEEE--C---CCCCEECCCCC
Confidence 479999633 322221 1 79999999883
No 88
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=50.79 E-value=7.7 Score=27.26 Aligned_cols=27 Identities=19% Similarity=0.350 Sum_probs=16.2
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCCee
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAF 47 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FF 47 (105)
...|+.|+. +-+-+.+.++.||.|+=+
T Consensus 70 ~~~C~~Cg~---------~~~~~~~~~~~CP~Cgs~ 96 (114)
T PRK03681 70 ECWCETCQQ---------YVTLLTQRVRRCPQCHGD 96 (114)
T ss_pred EEEcccCCC---------eeecCCccCCcCcCcCCC
Confidence 567988962 112223344789999843
No 89
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=50.78 E-value=6.7 Score=28.32 Aligned_cols=11 Identities=45% Similarity=1.171 Sum_probs=8.8
Q ss_pred CceEeCCCCCe
Q 039987 36 RKFWKCKGCGA 46 (105)
Q Consensus 36 RkFY~CpsC~F 46 (105)
+.++.||.|+=
T Consensus 105 ~~~~~CP~Cgs 115 (135)
T PRK03824 105 HAFLKCPKCGS 115 (135)
T ss_pred ccCcCCcCCCC
Confidence 67788999873
No 90
>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=49.89 E-value=14 Score=21.77 Aligned_cols=18 Identities=22% Similarity=0.290 Sum_probs=10.0
Q ss_pred ccccccccCCceeEEEee
Q 039987 11 QLKACEKCFNSSKVLRTS 28 (105)
Q Consensus 11 ~l~~Cp~Cg~~~avlrTS 28 (105)
.++.||.||...+....|
T Consensus 25 ~~~~CP~Cg~~~~~r~~s 42 (52)
T TIGR02605 25 PLATCPECGGEKLRRLLS 42 (52)
T ss_pred CCCCCCCCCCCceeEEec
Confidence 356788876544433334
No 91
>PRK07219 DNA topoisomerase I; Validated
Probab=49.29 E-value=19 Score=32.69 Aligned_cols=32 Identities=19% Similarity=0.397 Sum_probs=22.0
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCC---CCCeeEe
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCK---GCGAFKW 49 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~Cp---sC~FFqW 49 (105)
...||.|+ ...+++.++. |. ||.|. .|++..+
T Consensus 688 ~~~CP~Cg-~~l~~k~gr~----G~-F~~Cs~yp~C~~~~~ 722 (822)
T PRK07219 688 IGPCPKCG-GELAIKQLKY----GS-FLGCTNYPKCKYTLP 722 (822)
T ss_pred cccCCCCC-CeeEEEcCCC----CC-eeeCCCCCCCCceee
Confidence 56899996 4455544443 44 99997 7988765
No 92
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=49.19 E-value=11 Score=30.43 Aligned_cols=36 Identities=25% Similarity=0.481 Sum_probs=27.2
Q ss_pred ccccccccCCceeEEEeecCCCCCCCc------eEeCCCCCe
Q 039987 11 QLKACEKCFNSSKVLRTSHTRENPNRK------FWKCKGCGA 46 (105)
Q Consensus 11 ~l~~Cp~Cg~~~avlrTSkT~~NPGRk------FY~CpsC~F 46 (105)
+.+.|++||.+.+..-.-+-.-|-.++ -|+|-.|+.
T Consensus 16 ~~k~C~~Cg~kr~f~cSg~fRvNAq~K~LDvWlIYkC~~Cd~ 57 (203)
T COG4332 16 PAKRCNSCGVKRAFTCSGKFRVNAQGKVLDVWLIYKCTHCDY 57 (203)
T ss_pred hhhhCcccCCcceeeecCcEEEcCCCcEEEEEEEEEeeccCC
Confidence 378999999887776665556676666 499998875
No 93
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=48.43 E-value=14 Score=24.16 Aligned_cols=32 Identities=25% Similarity=0.697 Sum_probs=21.6
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCCeeEecC
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKWDD 51 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFqW~D 51 (105)
...||+||.+ +..-...+ -|.|..|++-+|..
T Consensus 19 ~~~CPrCG~g--vfmA~H~d------R~~CGkCgyTe~~~ 50 (51)
T COG1998 19 NRFCPRCGPG--VFMADHKD------RWACGKCGYTEFKK 50 (51)
T ss_pred cccCCCCCCc--chhhhcCc------eeEeccccceEeec
Confidence 5789999743 22222111 59999999999964
No 94
>cd03031 GRX_GRX_like Glutaredoxin (GRX) family, GRX-like domain containing protein subfamily; composed of uncharacterized eukaryotic proteins containing a GRX-like domain having only one conserved cysteine, aligning to the C-terminal cysteine of the CXXC motif of GRXs. This subfamily is predominantly composed of plant proteins. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins via a redox active CXXC motif using a similar dithiol mechanism employed by TRXs. GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. Proteins containing only the C-terminal cysteine are generally redox inactive.
Probab=48.39 E-value=22 Score=26.15 Aligned_cols=30 Identities=20% Similarity=0.533 Sum_probs=15.5
Q ss_pred ccccccCCceeEEEeecCCCCCCCceEeCCCCC
Q 039987 13 KACEKCFNSSKVLRTSHTRENPNRKFWKCKGCG 45 (105)
Q Consensus 13 ~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~ 45 (105)
+.|+.|. +...+..+... .+..|-+||.||
T Consensus 111 v~C~~C~-Gs~k~~~~~~~--~~~~~~rC~~Cn 140 (147)
T cd03031 111 VPCSECN-GSCKVFAENAT--AAGGFLRCPECN 140 (147)
T ss_pred EECCCCC-CcceEEeccCc--ccccEEECCCCC
Confidence 4556663 44544443311 344577777665
No 95
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=48.12 E-value=18 Score=28.62 Aligned_cols=27 Identities=26% Similarity=0.445 Sum_probs=18.2
Q ss_pred ccccccCCceeEEEeecCCCCCCCceEeCCCCC
Q 039987 13 KACEKCFNSSKVLRTSHTRENPNRKFWKCKGCG 45 (105)
Q Consensus 13 ~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~ 45 (105)
..||.||.. ....+- -||.-|=||.|.
T Consensus 255 ~pC~~Cg~~-I~~~~~-----~gR~t~~CP~CQ 281 (282)
T PRK13945 255 KPCRKCGTP-IERIKL-----AGRSTHWCPNCQ 281 (282)
T ss_pred CCCCcCCCe-eEEEEE-----CCCccEECCCCc
Confidence 579999633 222221 379999999884
No 96
>PRK07219 DNA topoisomerase I; Validated
Probab=47.43 E-value=20 Score=32.68 Aligned_cols=35 Identities=14% Similarity=0.352 Sum_probs=24.7
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCC---CCCeeEecC
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCK---GCGAFKWDD 51 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~Cp---sC~FFqW~D 51 (105)
...||.|+ ...+++.++. |-+||.|. .|+|-.|-.
T Consensus 602 ~~~CP~Cg-~~l~~r~~~~----g~~F~gCs~yp~C~~t~~lp 639 (822)
T PRK07219 602 IGKCPECG-GDLIIIRTDK----GSRFVGCSGYPDCRNTFPLP 639 (822)
T ss_pred cCcCCCCC-CcceeeeccC----CceeeecCCCcCCCCeeecC
Confidence 57899996 4455554432 33699997 699998854
No 97
>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=47.33 E-value=12 Score=20.82 Aligned_cols=11 Identities=27% Similarity=0.694 Sum_probs=8.9
Q ss_pred cccccccccCC
Q 039987 10 TQLKACEKCFN 20 (105)
Q Consensus 10 ~~l~~Cp~Cg~ 20 (105)
..++.||.||+
T Consensus 24 ~~~~~CP~Cg~ 34 (41)
T smart00834 24 DPLATCPECGG 34 (41)
T ss_pred CCCCCCCCCCC
Confidence 45889999975
No 98
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=47.07 E-value=18 Score=20.94 Aligned_cols=30 Identities=20% Similarity=0.590 Sum_probs=16.5
Q ss_pred cccccccCCceeEEEeecC-CCCCCCceEeCCCCC
Q 039987 12 LKACEKCFNSSKVLRTSHT-RENPNRKFWKCKGCG 45 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT-~~NPGRkFY~CpsC~ 45 (105)
.+.||.|+ +.-...-. -+ ++.+=.+|+.|+
T Consensus 2 ~i~Cp~C~---~~y~i~d~~ip-~~g~~v~C~~C~ 32 (36)
T PF13717_consen 2 IITCPNCQ---AKYEIDDEKIP-PKGRKVRCSKCG 32 (36)
T ss_pred EEECCCCC---CEEeCCHHHCC-CCCcEEECCCCC
Confidence 36799995 22333222 22 333467888886
No 99
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=46.76 E-value=22 Score=26.16 Aligned_cols=30 Identities=27% Similarity=0.598 Sum_probs=19.9
Q ss_pred cccccccCCceeEEEeecCCCCCCCc-eEeCCCCCee
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRK-FWKCKGCGAF 47 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRk-FY~CpsC~FF 47 (105)
-+.|+.|++. -..++-. +|. |-+|..||..
T Consensus 97 yVlC~~C~sP-dT~l~k~-----~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 97 YVICRECNRP-DTRIIKE-----GRVSLLKCEACGAK 127 (133)
T ss_pred eEECCCCCCC-CcEEEEe-----CCeEEEecccCCCC
Confidence 3789999754 4444421 566 5699999864
No 100
>PRK08173 DNA topoisomerase III; Validated
Probab=46.23 E-value=17 Score=33.54 Aligned_cols=57 Identities=21% Similarity=0.355 Sum_probs=32.2
Q ss_pred cccccccccCCceeEEEeecCCCCCCCceEeCC-------CCCeeEecCCCCCCccchhhhhhhhccccchhhhHhH
Q 039987 10 TQLKACEKCFNSSKVLRTSHTRENPNRKFWKCK-------GCGAFKWDDDRKSSECNDFRGMVDRNMSENKIDILLG 79 (105)
Q Consensus 10 ~~l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~Cp-------sC~FFqW~De~~~~~~~~~~~~~~~n~~~~~~~~~~~ 79 (105)
..++.||.|+.. +.. +.++|.|. +|+|-.|.- ..+. .+....+.+=+...+.|++.|
T Consensus 724 ~~~g~CPkCg~~--v~e--------~~k~y~Cs~~~~~~~~C~f~i~k~--i~gK-~it~~~~kkLL~~Gkt~ll~g 787 (862)
T PRK08173 724 EPVGACPKCGGR--VFE--------HGMSYVCEKSVGPPKTCDFRSGKV--ILQQ-EISREQMAKLLADGKTDLLPG 787 (862)
T ss_pred ccccCCCCCCCe--eEe--------eceEEEeCCCcCCCCCCCeeeCce--ecCc-cCCHHHHHHHHHcCCcccccc
Confidence 347899999743 221 23499997 399998842 1121 133333333334666666555
No 101
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=45.82 E-value=12 Score=25.15 Aligned_cols=20 Identities=15% Similarity=0.378 Sum_probs=15.1
Q ss_pred ccccccCccccccccccCCc
Q 039987 2 SFSTSDNRTQLKACEKCFNS 21 (105)
Q Consensus 2 ~~~~~~n~~~l~~Cp~Cg~~ 21 (105)
||+-++|+-.-+.|.+||..
T Consensus 7 SfGKr~~k~tHt~CrRCG~~ 26 (62)
T PRK04179 7 SMGKRNKGKTHIRCRRCGRH 26 (62)
T ss_pred ccccccCCcccchhcccCcc
Confidence 78777776458999999643
No 102
>PF01907 Ribosomal_L37e: Ribosomal protein L37e; InterPro: IPR001569 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 [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of proteins of 56 to 96 amino-acid residues that share a highly conserved region located in the N-terminal part.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A19_A 4A1D_A 4A18_A 4A1B_A 1S1I_Y 3O5H_d 3IZS_l 3O58_d 2ZKR_2 3IZR_l ....
Probab=45.35 E-value=6.3 Score=25.91 Aligned_cols=19 Identities=32% Similarity=0.648 Sum_probs=12.0
Q ss_pred ccccccCccccccccccCCc
Q 039987 2 SFSTSDNRTQLKACEKCFNS 21 (105)
Q Consensus 2 ~~~~~~n~~~l~~Cp~Cg~~ 21 (105)
||+-++|++ -+.|.+||..
T Consensus 6 S~Gkr~~kt-H~~CrRCG~~ 24 (55)
T PF01907_consen 6 SFGKRHNKT-HTLCRRCGRR 24 (55)
T ss_dssp HHTTS-S-S-EEE-TTTSSE
T ss_pred CccccCCcc-EeeecccCCe
Confidence 677777774 8999999643
No 103
>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=45.20 E-value=25 Score=19.06 Aligned_cols=26 Identities=23% Similarity=0.701 Sum_probs=13.1
Q ss_pred ccccccCCceeEEEeecCCCCCCCceEeCCCC
Q 039987 13 KACEKCFNSSKVLRTSHTRENPNRKFWKCKGC 44 (105)
Q Consensus 13 ~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC 44 (105)
.+||+|++....+.. -||..|-|+.|
T Consensus 2 ~~C~rC~~~~~~~~~------~~r~~~~C~rC 27 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGI------NGRSTYLCPRC 27 (30)
T ss_dssp SB-TTT--BBEEEEE------TTEEEEE-TTT
T ss_pred CcCccCCCcceEeEe------cCCCCeECcCC
Confidence 379999754222222 46777888766
No 104
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=43.72 E-value=15 Score=24.79 Aligned_cols=34 Identities=26% Similarity=0.529 Sum_probs=21.6
Q ss_pred ccccccCccccccccccCCceeEEEeecCCCCCCCceEeCCCCCee
Q 039987 2 SFSTSDNRTQLKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAF 47 (105)
Q Consensus 2 ~~~~~~n~~~l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FF 47 (105)
||+-.++ -.-+.|-+||...--+++. .|.+|+|=
T Consensus 7 S~GKrnk-~tH~~CRRCGr~syhv~k~-----------~CaaCGfg 40 (61)
T COG2126 7 SFGKRNK-KTHIRCRRCGRRSYHVRKK-----------YCAACGFG 40 (61)
T ss_pred cccccCC-cceehhhhccchheeeccc-----------eecccCCC
Confidence 5665666 4489999997554433332 47788874
No 105
>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=43.26 E-value=14 Score=31.67 Aligned_cols=21 Identities=33% Similarity=0.656 Sum_probs=12.7
Q ss_pred cccchhhhHhHh-hhhcCceee
Q 039987 69 MSENKIDILLGE-VCKLGHQME 89 (105)
Q Consensus 69 ~~~~~~~~~~~~-~~~~~~~~~ 89 (105)
+.++++|||+|- +..-||..+
T Consensus 308 f~~g~~~ILVgT~~i~kG~d~~ 329 (505)
T TIGR00595 308 FANGKADILIGTQMIAKGHHFP 329 (505)
T ss_pred HhcCCCCEEEeCcccccCCCCC
Confidence 456788999874 334455443
No 106
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=43.16 E-value=13 Score=20.97 Aligned_cols=9 Identities=44% Similarity=1.258 Sum_probs=5.0
Q ss_pred ceEeCCCCC
Q 039987 37 KFWKCKGCG 45 (105)
Q Consensus 37 kFY~CpsC~ 45 (105)
..|+||.|+
T Consensus 16 ~~~~CP~Cg 24 (33)
T cd00350 16 APWVCPVCG 24 (33)
T ss_pred CCCcCcCCC
Confidence 455566554
No 107
>PRK14973 DNA topoisomerase I; Provisional
Probab=42.83 E-value=19 Score=33.79 Aligned_cols=33 Identities=15% Similarity=0.319 Sum_probs=21.0
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCC---CCCeeEec
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCK---GCGAFKWD 50 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~Cp---sC~FFqW~ 50 (105)
.+.||.||. +.+++.. .+ | +||.|. .|.|..+-
T Consensus 588 ~~~CP~CG~-~l~ik~~---k~-g-kFigCS~Yp~Ck~t~~L 623 (936)
T PRK14973 588 IGPCPVCGK-DLRIKHI---GS-S-QFIGCSGYPDCTFNIGL 623 (936)
T ss_pred cccCCcccc-cceeecc---cC-c-eeEECCCCCCCCccccC
Confidence 468999964 4443322 22 3 499998 69877543
No 108
>PRK14973 DNA topoisomerase I; Provisional
Probab=41.80 E-value=19 Score=33.86 Aligned_cols=36 Identities=11% Similarity=0.193 Sum_probs=23.3
Q ss_pred ccccccCCceeEEEeecCCCCCCCceEeCCCCCeeEecCC
Q 039987 13 KACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKWDDD 52 (105)
Q Consensus 13 ~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFqW~De 52 (105)
..||.||. +. ++.-+++ ..-.|..||.|++-+|..+
T Consensus 636 ~~Cp~CG~-p~-~~~~r~G--r~g~fl~CP~C~~~~~~~~ 671 (936)
T PRK14973 636 EVCPIHHL-NH-VRLIRKG--ARPWDIGCPLCSHIESNTE 671 (936)
T ss_pred CCCCCCCC-Cc-eEEeecC--CCcccccCccccchhhccc
Confidence 47999974 32 2222332 1123999999999999765
No 109
>COG2740 Predicted nucleic-acid-binding protein implicated in transcription termination [Transcription]
Probab=41.46 E-value=9.1 Score=26.76 Aligned_cols=53 Identities=19% Similarity=0.280 Sum_probs=33.7
Q ss_pred ecCCCCCCCceEeCCCCCeeEecCCCCCCccchhhhhhhhccccchhhhHhHhhhhcC
Q 039987 28 SHTRENPNRKFWKCKGCGAFKWDDDRKSSECNDFRGMVDRNMSENKIDILLGEVCKLG 85 (105)
Q Consensus 28 SkT~~NPGRkFY~CpsC~FFqW~De~~~~~~~~~~~~~~~n~~~~~~~~~~~~~~~~~ 85 (105)
--+.+.|||-+|-|+++.-. +.--..++|..-++.++|+.-.|.+...+-.+.
T Consensus 37 d~~~k~~GRGaYv~~~~~~~-----~~a~kk~~f~ra~~~~~~~~~~~~l~~~l~~~~ 89 (95)
T COG2740 37 DPTGKLPGRGAYVCPDRECI-----EKAKKKKLFSRALKAKVSDSLYDELIQLLAELE 89 (95)
T ss_pred ccccCCCCceEEEeCCHHHH-----HHHHHHHHHHHHHhccCCHHHHHHHHHHHHHhc
Confidence 34578999999999954321 122366777777888888444555555544443
No 110
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=41.42 E-value=13 Score=19.97 Aligned_cols=10 Identities=30% Similarity=0.660 Sum_probs=7.6
Q ss_pred ccccccccCC
Q 039987 11 QLKACEKCFN 20 (105)
Q Consensus 11 ~l~~Cp~Cg~ 20 (105)
++..||.||.
T Consensus 1 ~l~~C~~CgR 10 (25)
T PF13913_consen 1 ELVPCPICGR 10 (25)
T ss_pred CCCcCCCCCC
Confidence 4678999964
No 111
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=41.15 E-value=30 Score=31.83 Aligned_cols=36 Identities=28% Similarity=0.540 Sum_probs=24.7
Q ss_pred cccccc--cCCceeEEEeecCCCCCCCceEeCC---CCCeeEecCC
Q 039987 12 LKACEK--CFNSSKVLRTSHTRENPNRKFWKCK---GCGAFKWDDD 52 (105)
Q Consensus 12 l~~Cp~--Cg~~~avlrTSkT~~NPGRkFY~Cp---sC~FFqW~De 52 (105)
.+.||. |+ ...+++.++ .|..||.|. .|.|..|.-+
T Consensus 693 ~~~CP~~~C~-g~l~~r~gr----~G~~f~~Cs~yp~C~~~~~~~~ 733 (860)
T PRK06319 693 TVPCPAIGCT-GHIVKRRSR----FNKMFYSCSEYPACSVIGNSID 733 (860)
T ss_pred CCCCCCcCCC-CcEEEEecC----CCCeeeccCCCCCCceeeccCC
Confidence 468995 65 445555443 366699997 8999977654
No 112
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=40.93 E-value=22 Score=19.94 Aligned_cols=12 Identities=33% Similarity=0.941 Sum_probs=10.3
Q ss_pred ceEeCCCCCeeE
Q 039987 37 KFWKCKGCGAFK 48 (105)
Q Consensus 37 kFY~CpsC~FFq 48 (105)
+||+|..|+...
T Consensus 3 ~~ykC~~CGniv 14 (34)
T cd00974 3 EVYKCEICGNIV 14 (34)
T ss_pred cEEEcCCCCcEE
Confidence 699999998776
No 113
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=39.89 E-value=22 Score=24.56 Aligned_cols=28 Identities=29% Similarity=0.713 Sum_probs=16.1
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCC
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCG 45 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~ 45 (105)
.-.|+.|+.. +.+..+. .+.-|.|+.|+
T Consensus 123 ~~~C~~C~~~--~~r~~~~----~~~~~~C~~C~ 150 (157)
T PF10263_consen 123 VYRCPSCGRE--YKRHRRS----KRKRYRCGRCG 150 (157)
T ss_pred EEEcCCCCCE--eeeeccc----chhhEECCCCC
Confidence 6678888633 2222222 33349999876
No 114
>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=39.57 E-value=16 Score=19.41 Aligned_cols=12 Identities=42% Similarity=0.891 Sum_probs=9.0
Q ss_pred CCceEeCCCCCe
Q 039987 35 NRKFWKCKGCGA 46 (105)
Q Consensus 35 GRkFY~CpsC~F 46 (105)
|-+.|.|+.|+-
T Consensus 11 ~~k~~~C~~C~k 22 (26)
T PF13465_consen 11 GEKPYKCPYCGK 22 (26)
T ss_dssp SSSSEEESSSSE
T ss_pred CCCCCCCCCCcC
Confidence 556799998864
No 115
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=39.39 E-value=18 Score=25.93 Aligned_cols=33 Identities=27% Similarity=0.652 Sum_probs=21.8
Q ss_pred ccccccCccccccccccCCceeEEEeecCCCCCCCceEeCCCCCe
Q 039987 2 SFSTSDNRTQLKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGA 46 (105)
Q Consensus 2 ~~~~~~n~~~l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~F 46 (105)
||+-++|++ -+.|.+||...--+.-+ .|.+|+|
T Consensus 7 SfGKr~~kt-HtlCrRCG~~syH~qK~-----------~CasCGy 39 (91)
T PTZ00073 7 SFGKRHGKT-HTLCRRCGKRSFHVQKK-----------RCASCGY 39 (91)
T ss_pred ccccccCcC-cchhcccCccccccccc-----------cchhcCC
Confidence 677777765 89999997442222212 3888988
No 116
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=39.20 E-value=24 Score=19.69 Aligned_cols=13 Identities=31% Similarity=0.882 Sum_probs=10.7
Q ss_pred CceEeCCCCCeeE
Q 039987 36 RKFWKCKGCGAFK 48 (105)
Q Consensus 36 RkFY~CpsC~FFq 48 (105)
-+||+|..|+...
T Consensus 5 ~~~ykC~~Cgniv 17 (34)
T TIGR00319 5 GQVYKCEVCGNIV 17 (34)
T ss_pred CcEEEcCCCCcEE
Confidence 4699999988776
No 117
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=39.18 E-value=30 Score=22.17 Aligned_cols=23 Identities=30% Similarity=0.808 Sum_probs=15.6
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCCee
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAF 47 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FF 47 (105)
+..||.||. +-+.=..|+.|||.
T Consensus 27 l~~C~~CG~-------------~~~~H~vC~~CG~Y 49 (57)
T PRK12286 27 LVECPNCGE-------------PKLPHRVCPSCGYY 49 (57)
T ss_pred ceECCCCCC-------------ccCCeEECCCCCcC
Confidence 778999962 23445678888764
No 118
>TIGR01051 topA_bact DNA topoisomerase I, bacterial. This model describes DNA topoisomerase I among the members of bacteria. DNA topoisomerase I transiently cleaves one DNA strand and thus relaxes negatively supercoiled DNA during replication, transcription and recombination events.
Probab=39.15 E-value=32 Score=30.23 Aligned_cols=29 Identities=21% Similarity=0.515 Sum_probs=17.8
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCC---CCe
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKG---CGA 46 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~Cps---C~F 46 (105)
...||.|+ .+...+..++ | +||.|.+ |+|
T Consensus 574 ~~~CP~Cg-~~~~~~~~~~----g-kf~gCs~y~~C~~ 605 (610)
T TIGR01051 574 SQDCPLCG-RPMVVKLGKY----G-PFLACSNFPECKY 605 (610)
T ss_pred CCCCCCCC-CeeEEEecCC----C-ceeeCCCCCCCCC
Confidence 46899996 4444333333 3 5999984 654
No 119
>TIGR01057 topA_arch DNA topoisomerase I, archaeal. This model describes topoisomerase I from archaea. These enzymes are involved in the control of DNA topology. DNA topoisomerase I belongs to the type I topoisomerases, which are ATP-independent.
Probab=38.92 E-value=29 Score=30.40 Aligned_cols=26 Identities=23% Similarity=0.533 Sum_probs=15.9
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCC
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKG 43 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~Cps 43 (105)
...||.|+ .+.+.+..+. | +||.|.+
T Consensus 589 ~~~CPkCg-~~l~~~~~k~----g-~f~gCs~ 614 (618)
T TIGR01057 589 VGKCPKCG-GKLVSKYAKK----G-RFVGCSN 614 (618)
T ss_pred cCCCCcCC-CeeeeeecCC----c-cEEECCC
Confidence 46799996 4444332222 2 6999974
No 120
>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=38.90 E-value=27 Score=26.68 Aligned_cols=69 Identities=19% Similarity=0.319 Sum_probs=47.1
Q ss_pred cccccCCceeEEEeecCC--CCCCCceEeCCCCCe----eEecCC------------CCCCccchhhhhh----hhcccc
Q 039987 14 ACEKCFNSSKVLRTSHTR--ENPNRKFWKCKGCGA----FKWDDD------------RKSSECNDFRGMV----DRNMSE 71 (105)
Q Consensus 14 ~Cp~Cg~~~avlrTSkT~--~NPGRkFY~CpsC~F----FqW~De------------~~~~~~~~~~~~~----~~n~~~ 71 (105)
.||.|+.....+.-|+.. .|-=|+==.|++|+. |..-+. +..+..++.+|+. ++.+|.
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErve~~~l~ViKkdG~re~Fdr~Kl~~gl~~Ac~KRpVs~ 81 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELLPPTVIKQDGVREPFNREKLLRGMVRACEKRPVSF 81 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeeccccccEEEcCCCCCCCCCHHHHHHHHHHHhcCCCCCH
Confidence 699999877777777763 334566678998873 333332 3344566666654 689999
Q ss_pred chhhhHhHhhh
Q 039987 72 NKIDILLGEVC 82 (105)
Q Consensus 72 ~~~~~~~~~~~ 82 (105)
..||-++.++-
T Consensus 82 e~ie~~v~~Ie 92 (147)
T TIGR00244 82 DDLEHAINHIE 92 (147)
T ss_pred HHHHHHHHHHH
Confidence 99998876653
No 121
>PRK14724 DNA topoisomerase III; Provisional
Probab=38.70 E-value=19 Score=33.82 Aligned_cols=29 Identities=24% Similarity=0.512 Sum_probs=20.1
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCC-------CCCeeEec
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCK-------GCGAFKWD 50 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~Cp-------sC~FFqW~ 50 (105)
...||.|++. . .-+.++|.|. +|+|-.|.
T Consensus 643 ~~~CP~Cg~~-~---------~~~~~~~~Cs~~~~~~~~C~f~~~k 678 (987)
T PRK14724 643 STPCPNCGGV-V---------KENYRRYACTGANGAGEGCGFSFTK 678 (987)
T ss_pred cccCCccccc-c---------cccCceeecCCCcCCCCCCCcccch
Confidence 3689999743 1 1234569998 49999995
No 122
>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=38.36 E-value=31 Score=23.02 Aligned_cols=37 Identities=19% Similarity=0.435 Sum_probs=25.5
Q ss_pred ccccccCCceeEEEeecCCCCCCCceEeCCCCCeeEecCCC
Q 039987 13 KACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKWDDDR 53 (105)
Q Consensus 13 ~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFqW~De~ 53 (105)
-+||.|+... .+.-|++.+ ...-.|-+|+|-+=..+.
T Consensus 9 a~CP~C~~~D--~i~~~~e~~--ve~vECV~CGy~e~~~~~ 45 (71)
T PF09526_consen 9 AVCPKCQAMD--TIMMWRENG--VEYVECVECGYTERQPDQ 45 (71)
T ss_pred ccCCCCcCcc--EEEEEEeCC--ceEEEecCCCCeeccCCc
Confidence 4799996544 333445554 777889999998766554
No 123
>PRK07561 DNA topoisomerase I subunit omega; Validated
Probab=37.98 E-value=27 Score=32.03 Aligned_cols=35 Identities=23% Similarity=0.397 Sum_probs=26.1
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCC------CCCeeEecCC
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCK------GCGAFKWDDD 52 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~Cp------sC~FFqW~De 52 (105)
...||.||. ..++++++.+ .||.|. .|.+-.|-..
T Consensus 587 ~~~CP~Cg~-~l~~r~gr~G-----~Fl~Cs~y~~~p~C~~~~~l~~ 627 (859)
T PRK07561 587 DRDCPTCGR-GMGIRTGKTG-----VFLGCSGYALKERCKTTRNLTP 627 (859)
T ss_pred cccCcccCC-cceEEecCCC-----CeeeccCCcCCCCCCCCCCCCc
Confidence 478999964 4667776654 399997 5998888654
No 124
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=37.76 E-value=17 Score=23.63 Aligned_cols=35 Identities=29% Similarity=0.676 Sum_probs=18.4
Q ss_pred ccccccCCceeEEEeecCCCCCCCceEeCC-CC---CeeEecCCCC
Q 039987 13 KACEKCFNSSKVLRTSHTRENPNRKFWKCK-GC---GAFKWDDDRK 54 (105)
Q Consensus 13 ~~Cp~Cg~~~avlrTSkT~~NPGRkFY~Cp-sC---~FFqW~De~~ 54 (105)
+.||.|+ + .+.++..||=|.| |. .| .+-.|.++..
T Consensus 3 v~CP~C~-k----~~~~~~~n~~rPF--CS~RCk~iDLg~W~~e~Y 41 (57)
T PF03884_consen 3 VKCPICG-K----PVEWSPENPFRPF--CSERCKLIDLGRWANEEY 41 (57)
T ss_dssp EE-TTT-------EEE-SSSSS--SS--SSHHHHHHHHS-SSSSS-
T ss_pred ccCCCCC-C----eecccCCCCcCCc--ccHhhcccCHHHHhcCCc
Confidence 5799995 3 2455688888888 44 44 4667887743
No 125
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=37.74 E-value=46 Score=25.74 Aligned_cols=34 Identities=15% Similarity=0.133 Sum_probs=18.8
Q ss_pred ccccccCCceeEEEeecC--CCCCCCc---eEeCCCCCee
Q 039987 13 KACEKCFNSSKVLRTSHT--RENPNRK---FWKCKGCGAF 47 (105)
Q Consensus 13 ~~Cp~Cg~~~avlrTSkT--~~NPGRk---FY~CpsC~FF 47 (105)
+.||.|+. ....+.-.+ -+--|.- -+.|++|||=
T Consensus 1 ~~Cp~C~~-~~~~~~~~~~~IP~F~evii~sf~C~~CGyr 39 (192)
T TIGR00310 1 IDCPSCGG-ECETVMKTVNDIPYFGEVLETSTICEHCGYR 39 (192)
T ss_pred CcCCCCCC-CCEEEEEEEcCCCCcceEEEEEEECCCCCCc
Confidence 35999963 333333222 2333443 4789999974
No 126
>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=37.52 E-value=77 Score=22.41 Aligned_cols=36 Identities=36% Similarity=0.721 Sum_probs=24.0
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCCeeEecCC-CCCC
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKWDDD-RKSS 56 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFqW~De-~~~~ 56 (105)
.-.||.|+ ...+.+++ + --|.|.+|+. .|... ..|.
T Consensus 35 ky~Cp~Cg-k~~vkR~a-~------GIW~C~~C~~-~~AGGAy~~~ 71 (90)
T PF01780_consen 35 KYTCPFCG-KTSVKRVA-T------GIWKCKKCGK-KFAGGAYTPS 71 (90)
T ss_dssp -BEESSSS-SSEEEEEE-T------TEEEETTTTE-EEE-BSSSSS
T ss_pred CCcCCCCC-CceeEEee-e------EEeecCCCCC-EEeCCCcccc
Confidence 34799995 66788887 2 3699999995 55544 3343
No 127
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=36.64 E-value=25 Score=23.71 Aligned_cols=23 Identities=26% Similarity=0.436 Sum_probs=8.7
Q ss_pred cccccccCCceeEEEeecCCCCCC
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPN 35 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPG 35 (105)
..-||+||+. .+.++|-+...-|
T Consensus 24 k~FCp~CGn~-TL~rvsvsv~~~G 46 (73)
T PF08772_consen 24 KQFCPKCGNA-TLKRVSVSVDEDG 46 (73)
T ss_dssp --S-SSS--S---EEEE-B--SS-
T ss_pred ceeCcccCCC-cceEEEEEECCCC
Confidence 6789999866 6777766643333
No 128
>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=36.58 E-value=42 Score=25.38 Aligned_cols=32 Identities=19% Similarity=0.476 Sum_probs=17.8
Q ss_pred ccccCCceeEEEeecCCCCC--CCc---eEeCCCCCee
Q 039987 15 CEKCFNSSKVLRTSHTRENP--NRK---FWKCKGCGAF 47 (105)
Q Consensus 15 Cp~Cg~~~avlrTSkT~~NP--GRk---FY~CpsC~FF 47 (105)
||-||+. +...+..+..-| |.- -+.|++|||=
T Consensus 1 CP~Cg~~-~~~~~~~~~~IP~F~evii~sf~C~~CGyr 37 (163)
T TIGR00340 1 CPVCGSR-TLKAVTYDYDIPYFGKIMLSTYICEKCGYR 37 (163)
T ss_pred CCCCCCc-ceEeeeEeccCCCcceEEEEEEECCCCCCc
Confidence 8889654 333322333333 332 4788889873
No 129
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=36.42 E-value=32 Score=27.02 Aligned_cols=32 Identities=13% Similarity=0.204 Sum_probs=20.1
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCCeeEecC
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKWDD 51 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFqW~D 51 (105)
..-||.||.. ... ..+..--.|++|+...|-.
T Consensus 99 ~~fC~~CG~~-~~~-------~~~~~~~~C~~c~~~~yp~ 130 (256)
T PRK00241 99 HRFCGYCGHP-MHP-------SKTEWAMLCPHCRERYYPR 130 (256)
T ss_pred CccccccCCC-Cee-------cCCceeEECCCCCCEECCC
Confidence 4579999743 221 1233345799999888753
No 130
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=36.39 E-value=48 Score=19.34 Aligned_cols=29 Identities=28% Similarity=0.580 Sum_probs=18.7
Q ss_pred ccccc--ccCCceeEEEeecCCCCCCCceEeCCCCCe
Q 039987 12 LKACE--KCFNSSKVLRTSHTRENPNRKFWKCKGCGA 46 (105)
Q Consensus 12 l~~Cp--~Cg~~~avlrTSkT~~NPGRkFY~CpsC~F 46 (105)
..-|| .|+ .++...+ +++-....|+.|++
T Consensus 18 ~~~CP~~~C~--~~~~~~~----~~~~~~v~C~~C~~ 48 (64)
T smart00647 18 LKWCPAPDCS--AAIIVTE----EEGCNRVTCPKCGF 48 (64)
T ss_pred ccCCCCCCCc--ceEEecC----CCCCCeeECCCCCC
Confidence 56799 884 2343332 56777889987753
No 131
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=36.32 E-value=37 Score=26.00 Aligned_cols=35 Identities=20% Similarity=0.455 Sum_probs=22.6
Q ss_pred cccccccCCceeEEEeecCCCCCCCc-eEeCCCCCeeEecCC
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRK-FWKCKGCGAFKWDDD 52 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRk-FY~CpsC~FFqW~De 52 (105)
-+.|+.|++. -..++- . +|. |-+|..||...=-+.
T Consensus 98 yV~C~~C~~p-dT~l~k-~----~~~~~l~C~aCGa~~~v~~ 133 (201)
T PRK12336 98 YVICSECGLP-DTRLVK-E----DRVLMLRCDACGAHRPVKK 133 (201)
T ss_pred eEECCCCCCC-CcEEEE-c----CCeEEEEcccCCCCccccc
Confidence 3789999764 444432 1 355 559999998755443
No 132
>PRK04023 DNA polymerase II large subunit; Validated
Probab=35.90 E-value=24 Score=34.52 Aligned_cols=8 Identities=38% Similarity=1.045 Sum_probs=4.4
Q ss_pred EeCCCCCe
Q 039987 39 WKCKGCGA 46 (105)
Q Consensus 39 Y~CpsC~F 46 (105)
|.||.|++
T Consensus 664 y~CPKCG~ 671 (1121)
T PRK04023 664 DECEKCGR 671 (1121)
T ss_pred CcCCCCCC
Confidence 44555655
No 133
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=35.74 E-value=22 Score=17.90 Aligned_cols=9 Identities=33% Similarity=0.877 Sum_probs=5.2
Q ss_pred EeCCCCCee
Q 039987 39 WKCKGCGAF 47 (105)
Q Consensus 39 Y~CpsC~FF 47 (105)
|+|+.|.|.
T Consensus 1 y~C~~C~y~ 9 (24)
T PF13909_consen 1 YKCPHCSYS 9 (24)
T ss_dssp EE-SSSS-E
T ss_pred CCCCCCCCc
Confidence 678888765
No 134
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=35.06 E-value=50 Score=26.50 Aligned_cols=35 Identities=14% Similarity=0.112 Sum_probs=23.5
Q ss_pred cccccccCCceeEEEeecC-CCCCCC---ceEeCCCCCee
Q 039987 12 LKACEKCFNSSKVLRTSHT-RENPNR---KFWKCKGCGAF 47 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT-~~NPGR---kFY~CpsC~FF 47 (105)
..-||.||+ ...+.+.-. -+--|+ ..+.|..|||=
T Consensus 14 ~~~CPvCg~-~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR 52 (201)
T COG1779 14 RIDCPVCGG-TLKAHMYLYDIPYFGEVLISTGVCERCGYR 52 (201)
T ss_pred eecCCcccc-eeeEEEeeecCCccceEEEEEEEccccCCc
Confidence 789999975 444444322 555576 46789999974
No 135
>PF14369 zf-RING_3: zinc-finger
Probab=35.03 E-value=25 Score=20.43 Aligned_cols=10 Identities=30% Similarity=0.753 Sum_probs=6.2
Q ss_pred cccccccCCc
Q 039987 12 LKACEKCFNS 21 (105)
Q Consensus 12 l~~Cp~Cg~~ 21 (105)
.+.||.|+++
T Consensus 21 ~~~CP~C~~g 30 (35)
T PF14369_consen 21 DVACPRCHGG 30 (35)
T ss_pred CcCCcCCCCc
Confidence 4467777654
No 136
>PF12773 DZR: Double zinc ribbon
Probab=34.96 E-value=25 Score=20.46 Aligned_cols=31 Identities=29% Similarity=0.563 Sum_probs=18.3
Q ss_pred cCccccccccccCCceeEEEeecCCCCCCCceEeCCCCCe
Q 039987 7 DNRTQLKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGA 46 (105)
Q Consensus 7 ~n~~~l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~F 46 (105)
.+......|+.||.... .+....+.|+.|+-
T Consensus 7 ~~~~~~~fC~~CG~~l~---------~~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 7 PNPDDAKFCPHCGTPLP---------PPDQSKKICPNCGA 37 (50)
T ss_pred cCCccccCChhhcCChh---------hccCCCCCCcCCcC
Confidence 34445677888863322 44455667777764
No 137
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=34.63 E-value=25 Score=25.49 Aligned_cols=26 Identities=19% Similarity=0.163 Sum_probs=21.0
Q ss_pred cccccccCCceeEEEeecCCCCCCCc
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRK 37 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRk 37 (105)
||.||.||-.+-.-.|-+-+++.-|.
T Consensus 3 LI~CP~Cg~R~e~EFt~~G~A~i~RP 28 (97)
T COG4311 3 LIPCPYCGERPEEEFTYAGDAHIARP 28 (97)
T ss_pred eecCCCCCCCchhheeecccccccCC
Confidence 89999998877777777777777775
No 138
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=34.58 E-value=17 Score=29.16 Aligned_cols=33 Identities=18% Similarity=0.512 Sum_probs=21.4
Q ss_pred cccccccCCcee--EEEeecCCCCCCCceEeCCCCCeeE
Q 039987 12 LKACEKCFNSSK--VLRTSHTRENPNRKFWKCKGCGAFK 48 (105)
Q Consensus 12 l~~Cp~Cg~~~a--vlrTSkT~~NPGRkFY~CpsC~FFq 48 (105)
.+.||.|+.... .+.+.+.. + .-+.|+.||.+.
T Consensus 6 y~~Cp~Cg~eev~hEVik~~g~-~---~lvrC~eCG~V~ 40 (201)
T COG1326 6 YIECPSCGSEEVSHEVIKERGR-E---PLVRCEECGTVH 40 (201)
T ss_pred EEECCCCCcchhhHHHHHhcCC-c---eEEEccCCCcEe
Confidence 568999974433 23333222 2 689999999875
No 139
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=33.90 E-value=22 Score=21.32 Aligned_cols=12 Identities=42% Similarity=1.237 Sum_probs=7.1
Q ss_pred CceEeCCCCCee
Q 039987 36 RKFWKCKGCGAF 47 (105)
Q Consensus 36 RkFY~CpsC~FF 47 (105)
.+||+|..|+=.
T Consensus 4 ~~~YkC~~CGni 15 (36)
T PF06397_consen 4 GEFYKCEHCGNI 15 (36)
T ss_dssp TEEEE-TTT--E
T ss_pred ccEEEccCCCCE
Confidence 479999988743
No 140
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=33.24 E-value=49 Score=23.53 Aligned_cols=28 Identities=39% Similarity=0.799 Sum_probs=18.0
Q ss_pred ccccccCCceeEEEeecCCCCCCCc-eEeCCCCCe
Q 039987 13 KACEKCFNSSKVLRTSHTRENPNRK-FWKCKGCGA 46 (105)
Q Consensus 13 ~~Cp~Cg~~~avlrTSkT~~NPGRk-FY~CpsC~F 46 (105)
+.|+.|++..-.+... +|. |-+|.+||.
T Consensus 81 VlC~~C~spdT~l~k~------~r~~~l~C~aCGa 109 (110)
T smart00653 81 VLCPECGSPDTELIKE------NRLFFLKCEACGA 109 (110)
T ss_pred EECCCCCCCCcEEEEe------CCeEEEEccccCC
Confidence 7899997554333332 455 667988873
No 141
>PRK05580 primosome assembly protein PriA; Validated
Probab=33.15 E-value=25 Score=31.18 Aligned_cols=21 Identities=29% Similarity=0.624 Sum_probs=13.0
Q ss_pred ccccchhhhHhHh-hhhcCcee
Q 039987 68 NMSENKIDILLGE-VCKLGHQM 88 (105)
Q Consensus 68 n~~~~~~~~~~~~-~~~~~~~~ 88 (105)
.+.++++|||+|- +..-||..
T Consensus 475 ~f~~g~~~ILVgT~~iakG~d~ 496 (679)
T PRK05580 475 QFARGEADILIGTQMLAKGHDF 496 (679)
T ss_pred HHhcCCCCEEEEChhhccCCCC
Confidence 4556788999883 34445543
No 142
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=32.96 E-value=39 Score=27.77 Aligned_cols=27 Identities=19% Similarity=0.596 Sum_probs=18.5
Q ss_pred ccccccCCceeEEEeecCCCCCCCceEeCCCCC
Q 039987 13 KACEKCFNSSKVLRTSHTRENPNRKFWKCKGCG 45 (105)
Q Consensus 13 ~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~ 45 (105)
..|+.||..-..+..+ ||-+|=||.|.
T Consensus 246 epC~~CGt~I~k~~~~------gR~t~~CP~CQ 272 (273)
T COG0266 246 EPCRRCGTPIEKIKLG------GRSTFYCPVCQ 272 (273)
T ss_pred CCCCccCCEeEEEEEc------CCcCEeCCCCC
Confidence 4699996433333323 89999999884
No 143
>PRK11823 DNA repair protein RadA; Provisional
Probab=32.92 E-value=28 Score=29.31 Aligned_cols=23 Identities=26% Similarity=0.687 Sum_probs=16.4
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCCe
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGA 46 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~F 46 (105)
.-+|..||.. -.+-+|+||+|+=
T Consensus 7 ~y~C~~Cg~~------------~~~~~g~Cp~C~~ 29 (446)
T PRK11823 7 AYVCQECGAE------------SPKWLGRCPECGA 29 (446)
T ss_pred eEECCcCCCC------------CcccCeeCcCCCC
Confidence 4678888744 2456889999964
No 144
>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=32.59 E-value=19 Score=19.93 Aligned_cols=9 Identities=22% Similarity=0.748 Sum_probs=4.1
Q ss_pred ccccccCCc
Q 039987 13 KACEKCFNS 21 (105)
Q Consensus 13 ~~Cp~Cg~~ 21 (105)
.-|+.||+.
T Consensus 4 rfC~~CG~~ 12 (32)
T PF09297_consen 4 RFCGRCGAP 12 (32)
T ss_dssp SB-TTT--B
T ss_pred cccCcCCcc
Confidence 458999744
No 145
>cd00279 YlxR Ylxr homologs; group of conserved hypothetical bacterial proteins of unknown function; structure revealed putative RNA binding cleft; proteins are encoded by an operon that includes other proteins involved in transcription and/or translation
Probab=32.51 E-value=31 Score=23.12 Aligned_cols=48 Identities=23% Similarity=0.353 Sum_probs=32.3
Q ss_pred eecCCCCCCCceEeCC--CCCeeEecCCCCCCccchhhhhhhhccccchhhhHhHhh
Q 039987 27 TSHTRENPNRKFWKCK--GCGAFKWDDDRKSSECNDFRGMVDRNMSENKIDILLGEV 81 (105)
Q Consensus 27 TSkT~~NPGRkFY~Cp--sC~FFqW~De~~~~~~~~~~~~~~~n~~~~~~~~~~~~~ 81 (105)
.-.+++.|||-+|-|+ .|- . .--..+.|.--++.++++.-.|-|..+|
T Consensus 30 ~D~~~k~~GRGaYvc~~~~c~----~---~a~kk~~l~Ralk~~v~~~~~~~L~~~v 79 (79)
T cd00279 30 PDPTGKLPGRGAYVCADRECI----E---KAKKKKLFNRAFKAKVSDSVYDELIEYV 79 (79)
T ss_pred ECCCCCCCCCeEEEcCCHHHH----H---HHHHhCHHHHHhCCCCCHHHHHHHHHhC
Confidence 3446778999999999 442 1 1115567777777788777777776553
No 146
>cd00674 LysRS_core_class_I catalytic core domain of class I lysyl tRNA synthetase. Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity.
Probab=32.13 E-value=52 Score=27.49 Aligned_cols=36 Identities=22% Similarity=0.434 Sum_probs=23.8
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCCeeEec
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKWD 50 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFqW~ 50 (105)
++.||.||.. .+..|+. +...|..-|.|. ||.=-+.
T Consensus 169 ~p~c~~cg~~-~~~v~~~-d~~~~~v~y~c~-cG~~g~~ 204 (353)
T cd00674 169 MPYCEKCGKD-TTTVEAY-DAKAGTVTYKCE-CGHEETV 204 (353)
T ss_pred eeecCCcCcc-eeEEEEE-eCCCCeEEEEcC-CCCEEEE
Confidence 8999999733 3444444 555678999996 5544444
No 147
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=31.58 E-value=46 Score=24.19 Aligned_cols=40 Identities=20% Similarity=0.413 Sum_probs=24.6
Q ss_pred ccccCCceeEEEeecCCCCCCCceEeCCCCCee-------EecCCCCCCccchhhhhhh
Q 039987 15 CEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAF-------KWDDDRKSSECNDFRGMVD 66 (105)
Q Consensus 15 Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FF-------qW~De~~~~~~~~~~~~~~ 66 (105)
||.||+... .|. ++|++|+.- -|-....+++-.|++..++
T Consensus 1 CPvCg~~l~--vt~----------l~C~~C~t~i~G~F~l~~~~~L~~E~~~Fi~~Fi~ 47 (113)
T PF09862_consen 1 CPVCGGELV--VTR----------LKCPSCGTEIEGEFELPWFARLSPEQLEFIKLFIK 47 (113)
T ss_pred CCCCCCceE--EEE----------EEcCCCCCEEEeeeccchhhcCCHHHHHHHHHHHH
Confidence 899974433 332 678877642 3545555557777777665
No 148
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=31.32 E-value=35 Score=22.71 Aligned_cols=36 Identities=25% Similarity=0.593 Sum_probs=24.4
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCC-CC---CeeEecCCCC
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCK-GC---GAFKWDDDRK 54 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~Cp-sC---~FFqW~De~~ 54 (105)
.+.||.|+ ++ +.|+..||=|.| |. .| .+-.|.++..
T Consensus 6 ~v~CP~C~-k~----~~w~~~~~~rPF--CS~RCk~IDLg~W~~e~y 45 (62)
T PRK00418 6 TVNCPTCG-KP----VEWGEISPFRPF--CSKRCQLIDLGEWAAEEK 45 (62)
T ss_pred cccCCCCC-Cc----ccccCCCCcCCc--ccHHHHhhhHHHHHcCCc
Confidence 57899995 32 345677898887 33 44 4667888754
No 149
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=30.92 E-value=68 Score=27.71 Aligned_cols=37 Identities=22% Similarity=0.322 Sum_probs=24.3
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCCeeEec
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKWD 50 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFqW~ 50 (105)
++.||.||...-+..++. +...|..-|.|. ||.=-+.
T Consensus 175 ~pic~~cg~~~~~~~~~~-d~~~~~v~y~~~-cG~~~~~ 211 (510)
T PRK00750 175 LPICPKCGKVLTTPVISY-DAEAGTVTYDCE-CGHEGEV 211 (510)
T ss_pred eeeCCCCCccceEEEEEE-eCCCCEEEEEcC-CCCEEEE
Confidence 899999975433333343 666778899997 5544433
No 150
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=30.64 E-value=95 Score=22.81 Aligned_cols=52 Identities=19% Similarity=0.196 Sum_probs=32.6
Q ss_pred ccccccCCceeEEEeecCCCCCCCceEeCCCCCeeEecCCCCCC-ccchhhhhhh
Q 039987 13 KACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKWDDDRKSS-ECNDFRGMVD 66 (105)
Q Consensus 13 ~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFqW~De~~~~-~~~~~~~~~~ 66 (105)
-.||.|+....+.-|-+... ++-+-.|..|+.-.=++..... +.++.+..+|
T Consensus 23 FtCp~Cghe~vs~ctvkk~~--~~g~~~Cg~CGls~e~ev~~l~~~vDvYs~wvD 75 (104)
T COG4888 23 FTCPRCGHEKVSSCTVKKTV--NIGTAVCGNCGLSFECEVPELSEPVDVYSAWVD 75 (104)
T ss_pred EecCccCCeeeeEEEEEecC--ceeEEEcccCcceEEEeccccccchhHHHHHHH
Confidence 35999987666655543333 4668999999875555544333 6665555443
No 151
>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=30.63 E-value=72 Score=23.09 Aligned_cols=30 Identities=30% Similarity=0.546 Sum_probs=20.0
Q ss_pred ccccccCCceeEEEeecCCCCCCCceEeCCCCCee
Q 039987 13 KACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAF 47 (105)
Q Consensus 13 ~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FF 47 (105)
+.||.|++. -..++.. -+--|-+|..||.-
T Consensus 94 VlC~~C~sp-dT~l~k~----~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 94 VLCPECGSP-DTELIKE----GRLIFLKCKACGAS 123 (125)
T ss_dssp SSCTSTSSS-SEEEEEE----TTCCEEEETTTSCE
T ss_pred EEcCCCCCC-ccEEEEc----CCEEEEEecccCCc
Confidence 789999754 4444433 33467789988853
No 152
>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=30.29 E-value=49 Score=20.94 Aligned_cols=24 Identities=29% Similarity=0.663 Sum_probs=15.8
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCCeeE
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFK 48 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFq 48 (105)
+..||.||. +-+.=+.|+.|+|..
T Consensus 26 l~~C~~cG~-------------~~~~H~vc~~cG~Y~ 49 (55)
T TIGR01031 26 LVVCPNCGE-------------FKLPHRVCPSCGYYK 49 (55)
T ss_pred ceECCCCCC-------------cccCeeECCccCeEC
Confidence 778998862 334556777777653
No 153
>PRK06260 threonine synthase; Validated
Probab=30.23 E-value=35 Score=27.86 Aligned_cols=7 Identities=29% Similarity=1.274 Sum_probs=3.8
Q ss_pred eEeCCCC
Q 039987 38 FWKCKGC 44 (105)
Q Consensus 38 FY~CpsC 44 (105)
.|+||.|
T Consensus 19 ~~~Cp~c 25 (397)
T PRK06260 19 IYTCPEC 25 (397)
T ss_pred cccCCCC
Confidence 4555555
No 154
>PF05184 SapB_1: Saposin-like type B, region 1; InterPro: IPR007856 Synonym(s):cerebroside sulphate activator, CSAct Saposin B is a small non-enzymatic glycoprotein required for the breakdown of cerebroside sulphates (sulphatides) in lysosomes. Saposin B contains three intramolecular disulphide bridges, exists as a dimer and is remarkably heat, protease, and pH stable. The crystal structure of human saposin B reveals an unusual shell-like dimer consisting of a monolayer of alpha-helices enclosing a large hydrophobic cavity. Although the secondary structure of saposin B is similar to that of the known monomeric members of the saposin-like superfamily, the helices are repacked into a different tertiary arrangement to form the homodimer. A comparison of the two forms of the saposin B dimer suggests that extraction of target lipids from membranes involves a conformational change that facilitates access to the inner cavity [].; GO: 0006629 lipid metabolic process; PDB: 1N69_C 1QDM_C 4DDJ_A 2DOB_A 1OF9_A 2Z9A_A 1M12_A 2GTG_A 1SN6_A 2QYP_B ....
Probab=29.26 E-value=35 Score=18.70 Aligned_cols=26 Identities=19% Similarity=0.446 Sum_probs=21.0
Q ss_pred chhhhhhhhccccchhhhHhHhhhhc
Q 039987 59 NDFRGMVDRNMSENKIDILLGEVCKL 84 (105)
Q Consensus 59 ~~~~~~~~~n~~~~~~~~~~~~~~~~ 84 (105)
+.+..++..|.++..|=-.|-++|..
T Consensus 12 ~~i~~~l~~~~t~~~I~~~l~~~C~~ 37 (39)
T PF05184_consen 12 KEIEKLLKNNKTEEEIKKALEKACNK 37 (39)
T ss_dssp HHHHHHHHSTCHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHcCccHHHHHHHHHHHHhh
Confidence 35677888899999998888888863
No 155
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=28.47 E-value=64 Score=23.82 Aligned_cols=30 Identities=27% Similarity=0.537 Sum_probs=20.2
Q ss_pred cccccccCCceeEEEeecCCCCCCCc-eEeCCCCCee
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRK-FWKCKGCGAF 47 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRk-FY~CpsC~FF 47 (105)
-+.|+.|++. -..++- . +|. |-+|..||..
T Consensus 102 yVlC~~C~sp-dT~l~k-~----~r~~~l~C~ACGa~ 132 (138)
T PRK03988 102 YVICPECGSP-DTKLIK-E----GRIWVLKCEACGAE 132 (138)
T ss_pred cEECCCCCCC-CcEEEE-c----CCeEEEEcccCCCC
Confidence 4789999754 444442 1 664 7899999864
No 156
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=28.17 E-value=56 Score=23.09 Aligned_cols=29 Identities=31% Similarity=0.647 Sum_probs=22.0
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCCeeE
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFK 48 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFq 48 (105)
.-.||-|+ .+.+.+++- --|.|.+|++-.
T Consensus 36 ~y~CpfCg-k~~vkR~a~-------GIW~C~~C~~~~ 64 (90)
T PTZ00255 36 KYFCPFCG-KHAVKRQAV-------GIWRCKGCKKTV 64 (90)
T ss_pred CccCCCCC-CCceeeeee-------EEEEcCCCCCEE
Confidence 45799996 677877763 579999998643
No 157
>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=28.09 E-value=64 Score=17.92 Aligned_cols=13 Identities=23% Similarity=0.330 Sum_probs=6.8
Q ss_pred ccccCCceeEEEe
Q 039987 15 CEKCFNSSKVLRT 27 (105)
Q Consensus 15 Cp~Cg~~~avlrT 27 (105)
||.|++......+
T Consensus 1 C~~C~~~~~~~~~ 13 (46)
T TIGR03831 1 CPICGGEELEGKT 13 (46)
T ss_pred CCCCCCceecceE
Confidence 6777544443333
No 158
>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=27.69 E-value=24 Score=19.66 Aligned_cols=21 Identities=14% Similarity=0.445 Sum_probs=9.8
Q ss_pred cccccCCceeEEEeecCCCCCCCceEeCC
Q 039987 14 ACEKCFNSSKVLRTSHTRENPNRKFWKCK 42 (105)
Q Consensus 14 ~Cp~Cg~~~avlrTSkT~~NPGRkFY~Cp 42 (105)
.||.|+.. ++ ..+|-..|+|+
T Consensus 1 ~CP~C~s~--l~------~~~~ev~~~C~ 21 (28)
T PF03119_consen 1 TCPVCGSK--LV------REEGEVDIRCP 21 (28)
T ss_dssp B-TTT--B--EE------E-CCTTCEEE-
T ss_pred CcCCCCCE--eE------cCCCCEeEECC
Confidence 48999522 22 34556677776
No 159
>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=27.64 E-value=33 Score=29.19 Aligned_cols=41 Identities=24% Similarity=0.340 Sum_probs=22.7
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCCeeEecCCC
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKWDDDR 53 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFqW~De~ 53 (105)
++.|+.||...-+..++ -+..-+...|+|++||.=-+.|-.
T Consensus 174 ~piC~~cGri~tt~v~~-~d~~~~~v~Y~c~~cG~~g~~~i~ 214 (360)
T PF01921_consen 174 LPICEKCGRIDTTEVTE-YDPEGGTVTYRCEECGHEGEVDIT 214 (360)
T ss_dssp EEEETTTEE--EEEEEE-E--SSSEEEEE--TTS---EEETT
T ss_pred eeeccccCCcccceeeE-eecCCCEEEEEecCCCCEEEEecC
Confidence 88999997422333333 344578999999999987777654
No 160
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=27.59 E-value=40 Score=28.60 Aligned_cols=24 Identities=25% Similarity=0.526 Sum_probs=16.9
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCCee
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAF 47 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FF 47 (105)
.-+|..||-. -.+-+|+||+|+=|
T Consensus 7 ~y~C~~Cg~~------------~~~~~g~Cp~C~~w 30 (454)
T TIGR00416 7 KFVCQHCGAD------------SPKWQGKCPACHAW 30 (454)
T ss_pred eEECCcCCCC------------CccccEECcCCCCc
Confidence 4678888743 24568999999643
No 161
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=27.56 E-value=57 Score=27.71 Aligned_cols=36 Identities=19% Similarity=0.288 Sum_probs=24.6
Q ss_pred ccccccccCCceeEEEeecCCCCCCCceEeCCCCCeeEecCC
Q 039987 11 QLKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKWDDD 52 (105)
Q Consensus 11 ~l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFqW~De 52 (105)
.+..||.|+ ......+-+||.+ ..||.|+.--+...
T Consensus 9 ~~~~C~~Cd-----~l~~~~~l~~g~~-a~CpRCg~~L~~~~ 44 (419)
T PRK15103 9 KHILCPQCD-----MLVALPRLEHGQK-AACPRCGTTLTVRW 44 (419)
T ss_pred CcccCCCCC-----ceeecCCCCCCCe-eECCCCCCCCcCCC
Confidence 367899995 2234456677776 56999998776544
No 162
>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=26.59 E-value=41 Score=24.76 Aligned_cols=17 Identities=18% Similarity=0.454 Sum_probs=12.4
Q ss_pred CCCCCceEeCCCCCeeEe
Q 039987 32 ENPNRKFWKCKGCGAFKW 49 (105)
Q Consensus 32 ~NPGRkFY~CpsC~FFqW 49 (105)
..-+..||.||.|+ -+|
T Consensus 103 ~e~~~~~Y~Cp~c~-~r~ 119 (158)
T TIGR00373 103 FETNNMFFICPNMC-VRF 119 (158)
T ss_pred hccCCCeEECCCCC-cEe
Confidence 45578899999887 344
No 163
>PF04828 GFA: Glutathione-dependent formaldehyde-activating enzyme; InterPro: IPR006913 The GFA family consists mainly of glutathione-dependent formaldehyde-activating enzymes, but also includes centromere protein V and a fission yeast protein described as uncharacterised lyase. Glutathione-dependent formaldehyde-activating enzyme catalyse the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione. All known members of this family contain 5 strongly conserved cysteine residues.; GO: 0016846 carbon-sulfur lyase activity, 0008152 metabolic process; PDB: 3FAC_B 1XA8_A 1X6M_B.
Probab=26.43 E-value=84 Score=19.17 Aligned_cols=37 Identities=19% Similarity=0.364 Sum_probs=25.2
Q ss_pred CCCCCceEeCCCCCeeEec-CCCCCCccchhhhhhhhc
Q 039987 32 ENPNRKFWKCKGCGAFKWD-DDRKSSECNDFRGMVDRN 68 (105)
Q Consensus 32 ~NPGRkFY~CpsC~FFqW~-De~~~~~~~~~~~~~~~n 68 (105)
.-++.+.+-|+.||-..|. ++..++...+.-++++.-
T Consensus 42 s~~~~~r~FC~~CGs~l~~~~~~~~~~~~V~~g~ld~~ 79 (92)
T PF04828_consen 42 SGKGVERYFCPTCGSPLFSEDERDPDLVGVNAGTLDDP 79 (92)
T ss_dssp TTSSCEEEEETTT--EEEEEESSTTTEEEEEGGGBTT-
T ss_pred CCCcCcCcccCCCCCeeecccCCCCCEEEEEeEeeCCC
Confidence 5677778999988877774 566677777777777653
No 164
>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=26.41 E-value=73 Score=18.19 Aligned_cols=11 Identities=36% Similarity=1.141 Sum_probs=6.3
Q ss_pred eEeCCCCCeeE
Q 039987 38 FWKCKGCGAFK 48 (105)
Q Consensus 38 FY~CpsC~FFq 48 (105)
.|.|+-||+..
T Consensus 2 ~~~C~~CG~i~ 12 (34)
T cd00729 2 VWVCPVCGYIH 12 (34)
T ss_pred eEECCCCCCEe
Confidence 46666666553
No 165
>PRK05776 DNA topoisomerase I; Provisional
Probab=26.25 E-value=58 Score=29.25 Aligned_cols=33 Identities=9% Similarity=0.099 Sum_probs=20.7
Q ss_pred cccccccCCcee----EEEeecCCCCCCCceEeCC---CCCeeE
Q 039987 12 LKACEKCFNSSK----VLRTSHTRENPNRKFWKCK---GCGAFK 48 (105)
Q Consensus 12 l~~Cp~Cg~~~a----vlrTSkT~~NPGRkFY~Cp---sC~FFq 48 (105)
...||.||. +. +++-++. ++ -+|+.|. .|.+=.
T Consensus 596 ~~~Cp~Cg~-~l~~~~~~~~~~~--~~-~~f~~c~~~p~c~~~~ 635 (670)
T PRK05776 596 VGKCKICGR-EAYKDGLCKYHYE--AK-KRLVKAYEEWKERTGY 635 (670)
T ss_pred CCcCCCCCC-ccccCceEEeccc--CC-ccceecCCCccccCCC
Confidence 468999974 44 4544432 11 2799998 687543
No 166
>PF15616 TerY-C: TerY-C metal binding domain
Probab=26.21 E-value=34 Score=25.48 Aligned_cols=14 Identities=21% Similarity=0.392 Sum_probs=11.0
Q ss_pred ccccccCCceeEEE
Q 039987 13 KACEKCFNSSKVLR 26 (105)
Q Consensus 13 ~~Cp~Cg~~~avlr 26 (105)
+-||+||+..+.+.
T Consensus 78 PgCP~CGn~~~fa~ 91 (131)
T PF15616_consen 78 PGCPHCGNQYAFAV 91 (131)
T ss_pred CCCCCCcChhcEEE
Confidence 89999998856554
No 167
>PHA02540 61 DNA primase; Provisional
Probab=26.03 E-value=32 Score=28.82 Aligned_cols=34 Identities=24% Similarity=0.466 Sum_probs=22.1
Q ss_pred cccccccCCceeEEEeecCCCCCCCc--eEeCCCCC
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRK--FWKCKGCG 45 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRk--FY~CpsC~ 45 (105)
...||-|+..+--..|..=--+|.++ ||.|=+||
T Consensus 27 ~~~CPf~~ds~~~~~kpsF~V~p~k~~~~yhCFgCG 62 (337)
T PHA02540 27 NFRCPICGDSQKDKNKARGWIYEKKDGGVFKCHNCG 62 (337)
T ss_pred EecCCCCCCccccCcCCcEEEeccCCceEEEecCCC
Confidence 67899997543333333234456666 99999886
No 168
>PF04296 DUF448: Protein of unknown function (DUF448); InterPro: IPR007393 This entry represents a group of uncharacterised proteins. Some member sequences retain zinc-binding residues. The structure of the hypothetical cytosolic protein SP0554 from Streptococcus pneumoniae revealed an alpha+beta fold that could have evolved from a glucocorticoid receptor-like zinc finger domain [].; PDB: 1G2R_A.
Probab=25.92 E-value=29 Score=22.74 Aligned_cols=43 Identities=14% Similarity=0.336 Sum_probs=20.8
Q ss_pred ecCCCCCCCceEeCCC--CCeeEecCCCCCCccchhhhhhhhccccchhhhH
Q 039987 28 SHTRENPNRKFWKCKG--CGAFKWDDDRKSSECNDFRGMVDRNMSENKIDIL 77 (105)
Q Consensus 28 SkT~~NPGRkFY~Cps--C~FFqW~De~~~~~~~~~~~~~~~n~~~~~~~~~ 77 (105)
--+.+-|||-+|-|++ |- .... ..+.|.--++.+++++-.|.|
T Consensus 30 D~~~k~~GRGaYvc~~~~c~----~~a~---kkk~l~ra~k~~v~~~~~~~L 74 (78)
T PF04296_consen 30 DPSGKLPGRGAYVCPDPECL----EKAK---KKKALNRAFKTKVPEEVYEQL 74 (78)
T ss_dssp ETTS---SEEEEEES-HHHH----HHHH---HHTHHHHHHTS---HHHHHHH
T ss_pred CCCCCCCCCeEEEcCCHHHH----HHHH---HHCHHHHHHCCCCCHHHHHHH
Confidence 3456899999999994 41 1111 335555556666666555544
No 169
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=25.80 E-value=39 Score=18.30 Aligned_cols=12 Identities=25% Similarity=0.692 Sum_probs=5.8
Q ss_pred CceEeCCCCCee
Q 039987 36 RKFWKCKGCGAF 47 (105)
Q Consensus 36 RkFY~CpsC~FF 47 (105)
..+|.|+.|+|.
T Consensus 13 ~~~Y~C~~Cdf~ 24 (30)
T PF07649_consen 13 GWFYRCSECDFD 24 (30)
T ss_dssp --EEE-TTT---
T ss_pred CceEECccCCCc
Confidence 579999999985
No 170
>TIGR01056 topB DNA topoisomerase III, bacteria and conjugative plasmid. This model describes topoisomerase III from bacteria and its equivalents encoded on plasmids. The gene is designated topB if found in the bacterial chromosome, traE on conjugative plasmid RP4, etc. These enzymes are involved in the control of DNA topology. DNA topoisomerase III belongs to the type I topoisomerases, which are ATP-independent.
Probab=25.67 E-value=52 Score=29.41 Aligned_cols=33 Identities=15% Similarity=0.272 Sum_probs=21.3
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCC----------CCCeeEecC
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCK----------GCGAFKWDD 51 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~Cp----------sC~FFqW~D 51 (105)
...|| || ...+.+.++. | +|+.|. +|+|=.|..
T Consensus 611 ~~~cp-cg-~~l~~~~~~~----g-~f~~c~~~p~C~~~~~~c~~~~~~~ 653 (660)
T TIGR01056 611 KEPVS-CG-GIAKCPAKDN----G-RLIDCKKFPECTEYGNGCEFTIPKK 653 (660)
T ss_pred CccCC-CC-CceeeeecCC----C-eeecCCCCCCccCcCCCCeEEccHH
Confidence 56799 96 5566554432 4 499987 477777765
No 171
>PF11287 DUF3088: Protein of unknown function (DUF3088); InterPro: IPR021439 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=25.54 E-value=46 Score=24.46 Aligned_cols=15 Identities=33% Similarity=1.037 Sum_probs=10.9
Q ss_pred CCCCCCceEeCCCCCe
Q 039987 31 RENPNRKFWKCKGCGA 46 (105)
Q Consensus 31 ~~NPGRkFY~CpsC~F 46 (105)
++-||.+|| ||.|.-
T Consensus 15 ~~~PG~~f~-Cp~c~~ 29 (112)
T PF11287_consen 15 PAGPGQRFY-CPHCAA 29 (112)
T ss_pred CCCCCceEE-CCchHH
Confidence 455999888 787753
No 172
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=25.17 E-value=16 Score=30.27 Aligned_cols=28 Identities=25% Similarity=0.633 Sum_probs=17.7
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCCe
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGA 46 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~F 46 (105)
-.+||.|+. .+. .+.-.+.+|.||.|++
T Consensus 38 w~kc~~C~~---~~~----~~~l~~~~~vcp~c~~ 65 (296)
T CHL00174 38 WVQCENCYG---LNY----KKFLKSKMNICEQCGY 65 (296)
T ss_pred eeECCCccc---hhh----HHHHHHcCCCCCCCCC
Confidence 678999952 121 1224456799998876
No 173
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=24.75 E-value=39 Score=23.06 Aligned_cols=28 Identities=29% Similarity=0.542 Sum_probs=19.1
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCCe
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGA 46 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~F 46 (105)
.+.||.|++.+.+.--+-| -.+|..|+-
T Consensus 19 ~VkCpdC~N~q~vFshast-------~V~C~~CG~ 46 (67)
T COG2051 19 RVKCPDCGNEQVVFSHAST-------VVTCLICGT 46 (67)
T ss_pred EEECCCCCCEEEEeccCce-------EEEeccccc
Confidence 6899999998776544332 256777763
No 174
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=24.49 E-value=26 Score=29.56 Aligned_cols=30 Identities=20% Similarity=0.488 Sum_probs=20.3
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCCeeE
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFK 48 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFq 48 (105)
-.+||.|+ .++-+. .-++.++.||.|+++.
T Consensus 28 w~KCp~c~---~~~y~~----eL~~n~~vcp~c~~h~ 57 (294)
T COG0777 28 WTKCPSCG---EMLYRK----ELESNLKVCPKCGHHM 57 (294)
T ss_pred eeECCCcc---ceeeHH----HHHhhhhcccccCccc
Confidence 57899996 334433 3455689999888764
No 175
>PRK14283 chaperone protein DnaJ; Provisional
Probab=23.88 E-value=96 Score=25.48 Aligned_cols=33 Identities=21% Similarity=0.448 Sum_probs=17.6
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCC
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGC 44 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC 44 (105)
...|+.|.+...+..+.....-......+|+.|
T Consensus 163 ~~~C~~C~G~G~~~~~~~~~~g~~~~~~~C~~C 195 (378)
T PRK14283 163 VKTCPTCGGTGQVKQVRNTILGQMMNVTTCPDC 195 (378)
T ss_pred CccCCCcCCccEEEEEEeccCceEEEEEECCCC
Confidence 567888866655444443332233334567744
No 176
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=23.72 E-value=61 Score=25.41 Aligned_cols=25 Identities=16% Similarity=0.232 Sum_probs=17.3
Q ss_pred ccccccccCCceeEEEeecCCCCCCC
Q 039987 11 QLKACEKCFNSSKVLRTSHTRENPNR 36 (105)
Q Consensus 11 ~l~~Cp~Cg~~~avlrTSkT~~NPGR 36 (105)
+...||.|| .+.++++.++..+.|+
T Consensus 152 ~~~~Cp~CG-~~~~~~~~~~~~~~~~ 176 (177)
T COG1439 152 PKDFCPICG-SPLKRKRVKSRSSKGE 176 (177)
T ss_pred CCCcCCCCC-CceEEeeechhhcccC
Confidence 467899996 4466666666666554
No 177
>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=23.22 E-value=26 Score=23.42 Aligned_cols=34 Identities=21% Similarity=0.390 Sum_probs=23.3
Q ss_pred cccccCCceeEEEeecCCCCCCCceEeCCCCCeeE
Q 039987 14 ACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFK 48 (105)
Q Consensus 14 ~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFq 48 (105)
.|..|+ .......|+-.=+.|=.+-+||+|.-..
T Consensus 6 TC~~C~-~Rs~~~~sk~aY~~GvViv~C~gC~~~H 39 (66)
T PF05180_consen 6 TCNKCG-TRSAKMFSKQAYHKGVVIVQCPGCKNRH 39 (66)
T ss_dssp EETTTT-EEEEEEEEHHHHHTSEEEEE-TTS--EE
T ss_pred EcCCCC-CccceeeCHHHHhCCeEEEECCCCccee
Confidence 588885 4455555877888899999999997543
No 178
>PRK07591 threonine synthase; Validated
Probab=23.21 E-value=54 Score=27.26 Aligned_cols=23 Identities=17% Similarity=0.332 Sum_probs=13.8
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCC
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCG 45 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~ 45 (105)
--+|..||.. -.+... |+||.|+
T Consensus 18 ~l~C~~Cg~~----------~~~~~~-~~C~~cg 40 (421)
T PRK07591 18 ALKCRECGAE----------YPLGPI-HVCEECF 40 (421)
T ss_pred EEEeCCCCCc----------CCCCCC-ccCCCCC
Confidence 3678888622 122333 8898885
No 179
>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=22.84 E-value=80 Score=23.26 Aligned_cols=32 Identities=22% Similarity=0.609 Sum_probs=20.9
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCCeeEecCCC
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFKWDDDR 53 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFqW~De~ 53 (105)
++.||.|...-.. +...-|.||.|++ .|....
T Consensus 2 lp~CP~C~seytY---------~dg~~~iCpeC~~-EW~~~~ 33 (109)
T TIGR00686 2 LPPCPKCNSEYTY---------HDGTQLICPSCLY-EWNENE 33 (109)
T ss_pred CCcCCcCCCcceE---------ecCCeeECccccc-cccccc
Confidence 6899999643211 1223599999984 787553
No 180
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=22.80 E-value=72 Score=26.61 Aligned_cols=30 Identities=27% Similarity=0.768 Sum_probs=20.6
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCCe
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGA 46 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~F 46 (105)
-..||-|+.+...... ||.+.+|.|-+|+.
T Consensus 34 ~~~CPfh~ek~pSf~v-----~~~k~~~~Cf~Cg~ 63 (415)
T TIGR01391 34 VGLCPFHHEKTPSFSV-----SPEKQFYHCFGCGA 63 (415)
T ss_pred EeeCCCCCCCCCeEEE-----EcCCCcEEECCCCC
Confidence 3579999655433333 57788999998874
No 181
>PRK14282 chaperone protein DnaJ; Provisional
Probab=22.46 E-value=1.2e+02 Score=24.94 Aligned_cols=17 Identities=18% Similarity=0.598 Sum_probs=9.0
Q ss_pred cccccccCCceeEEEee
Q 039987 12 LKACEKCFNSSKVLRTS 28 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTS 28 (105)
...|+.|.+.-.+..+.
T Consensus 169 ~~~C~~C~G~G~~~~~~ 185 (369)
T PRK14282 169 YVTCPKCHGTGRIREER 185 (369)
T ss_pred CcCCCCCCCcCEEEEEE
Confidence 45677775554444433
No 182
>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=21.87 E-value=51 Score=21.39 Aligned_cols=10 Identities=20% Similarity=0.511 Sum_probs=8.1
Q ss_pred cccccccCCc
Q 039987 12 LKACEKCFNS 21 (105)
Q Consensus 12 l~~Cp~Cg~~ 21 (105)
.|+||+|+..
T Consensus 24 eIKCpRC~ti 33 (51)
T PF10122_consen 24 EIKCPRCKTI 33 (51)
T ss_pred EEECCCCCcc
Confidence 7999999644
No 183
>TIGR00320 dfx_rbo desulfoferrodoxin. This protein is described in some articles as rubredoxin oxidoreductase (rbo), and its gene shares an operon with the rubredoxin gene in Desulfovibrio vulgaris Hildenborough.
Probab=21.81 E-value=62 Score=23.36 Aligned_cols=13 Identities=31% Similarity=0.851 Sum_probs=11.0
Q ss_pred CceEeCCCCCeeE
Q 039987 36 RKFWKCKGCGAFK 48 (105)
Q Consensus 36 RkFY~CpsC~FFq 48 (105)
-+||+|+.|+...
T Consensus 5 ~~fYkC~~CGniv 17 (125)
T TIGR00320 5 LQVYKCEVCGNIV 17 (125)
T ss_pred CcEEECCCCCcEE
Confidence 4699999998876
No 184
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=21.78 E-value=42 Score=28.14 Aligned_cols=32 Identities=28% Similarity=0.563 Sum_probs=22.6
Q ss_pred ccccccCCceeE---EEeecCCCCCCCceEeCCCCC
Q 039987 13 KACEKCFNSSKV---LRTSHTRENPNRKFWKCKGCG 45 (105)
Q Consensus 13 ~~Cp~Cg~~~av---lrTSkT~~NPGRkFY~CpsC~ 45 (105)
-.|+-|| +.-- +++-.....-|=|+|.|+.|+
T Consensus 188 c~C~iCG-KaFSRPWLLQGHiRTHTGEKPF~C~hC~ 222 (279)
T KOG2462|consen 188 CECGICG-KAFSRPWLLQGHIRTHTGEKPFSCPHCG 222 (279)
T ss_pred ccccccc-ccccchHHhhcccccccCCCCccCCccc
Confidence 3577774 3222 556667777889999999886
No 185
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=21.75 E-value=19 Score=29.33 Aligned_cols=30 Identities=23% Similarity=0.503 Sum_probs=17.1
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCCeeE
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCGAFK 48 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~FFq 48 (105)
-.+||.|+. .+.+..-.. .++.||.|++..
T Consensus 27 ~~~c~~c~~---~~~~~~l~~----~~~vc~~c~~h~ 56 (292)
T PRK05654 27 WTKCPSCGQ---VLYRKELEA----NLNVCPKCGHHM 56 (292)
T ss_pred eeECCCccc---hhhHHHHHh----cCCCCCCCCCCe
Confidence 568999852 232222233 367899777643
No 186
>smart00400 ZnF_CHCC zinc finger.
Probab=21.56 E-value=89 Score=18.76 Aligned_cols=27 Identities=26% Similarity=0.762 Sum_probs=18.3
Q ss_pred cccccCCceeEEEeecCCCCCCCceEeCCCCC
Q 039987 14 ACEKCFNSSKVLRTSHTRENPNRKFWKCKGCG 45 (105)
Q Consensus 14 ~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~ 45 (105)
+||-|..+.+.... |+.+..|.|-+|+
T Consensus 4 ~cPfh~d~~pSf~v-----~~~kn~~~Cf~cg 30 (55)
T smart00400 4 LCPFHGEKTPSFSV-----SPDKQFFHCFGCG 30 (55)
T ss_pred cCcCCCCCCCCEEE-----ECCCCEEEEeCCC
Confidence 58888766555544 3556678888884
No 187
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=21.24 E-value=62 Score=24.40 Aligned_cols=14 Identities=36% Similarity=0.842 Sum_probs=10.4
Q ss_pred CCCCCceEeCCCCC
Q 039987 32 ENPNRKFWKCKGCG 45 (105)
Q Consensus 32 ~NPGRkFY~CpsC~ 45 (105)
..-...||.||.|+
T Consensus 111 ~e~~~~~Y~Cp~C~ 124 (178)
T PRK06266 111 EEENNMFFFCPNCH 124 (178)
T ss_pred hccCCCEEECCCCC
Confidence 34456899999776
No 188
>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=21.22 E-value=53 Score=15.37 Aligned_cols=7 Identities=43% Similarity=1.407 Sum_probs=2.9
Q ss_pred EeCCCCC
Q 039987 39 WKCKGCG 45 (105)
Q Consensus 39 Y~CpsC~ 45 (105)
|.|+-|+
T Consensus 1 ~~C~~C~ 7 (24)
T PF13894_consen 1 FQCPICG 7 (24)
T ss_dssp EE-SSTS
T ss_pred CCCcCCC
Confidence 4455444
No 189
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=21.03 E-value=63 Score=25.12 Aligned_cols=69 Identities=22% Similarity=0.391 Sum_probs=47.4
Q ss_pred cccccCCceeEEEeecC--CCCCCCceEeCCCCCe----eEec----------CC--CCCCccchhhhhh----hhcccc
Q 039987 14 ACEKCFNSSKVLRTSHT--RENPNRKFWKCKGCGA----FKWD----------DD--RKSSECNDFRGMV----DRNMSE 71 (105)
Q Consensus 14 ~Cp~Cg~~~avlrTSkT--~~NPGRkFY~CpsC~F----FqW~----------De--~~~~~~~~~~~~~----~~n~~~ 71 (105)
+||.|+.....+.-|+. +-|-=|+==.|+.|+. |.=. |+ +..+.-++++||. ++..|.
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTTfE~~El~~~~VvKkdg~Re~F~r~Kl~~gl~~A~~KRpVs~ 81 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTTFERAELRPLIVVKKDGRREPFDREKLRRGLIRACEKRPVSS 81 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccchhheeeeccceEECcCCCcCCCCHHHHHHHHHHHHhcCCCCH
Confidence 69999877777777876 5556677788998873 2111 22 3344666777765 588999
Q ss_pred chhhhHhHhhh
Q 039987 72 NKIDILLGEVC 82 (105)
Q Consensus 72 ~~~~~~~~~~~ 82 (105)
..|+-++..+.
T Consensus 82 e~ie~~v~~ie 92 (156)
T COG1327 82 EQIEEAVSHIE 92 (156)
T ss_pred HHHHHHHHHHH
Confidence 88887776654
No 190
>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=20.77 E-value=1.6e+02 Score=18.42 Aligned_cols=19 Identities=32% Similarity=0.639 Sum_probs=11.6
Q ss_pred ccccccccCCceeEEEeec
Q 039987 11 QLKACEKCFNSSKVLRTSH 29 (105)
Q Consensus 11 ~l~~Cp~Cg~~~avlrTSk 29 (105)
....|+.|.+.-.+..+..
T Consensus 14 ~~~~C~~C~G~G~~~~~~~ 32 (66)
T PF00684_consen 14 KPKTCPQCNGSGQVTRRQQ 32 (66)
T ss_dssp T-EE-TTSSSSSEEEEEEE
T ss_pred CCcCCcCCCCeeEEEEEEe
Confidence 3678999977666666554
No 191
>PRK02655 psbI photosystem II reaction center I protein I; Provisional
Probab=20.54 E-value=51 Score=20.47 Aligned_cols=10 Identities=50% Similarity=0.753 Sum_probs=7.4
Q ss_pred ecCCCCCCCc
Q 039987 28 SHTRENPNRK 37 (105)
Q Consensus 28 SkT~~NPGRk 37 (105)
+-.+.||||+
T Consensus 26 nDP~RnP~rk 35 (38)
T PRK02655 26 SDPTRNPGRK 35 (38)
T ss_pred CCCCCCCCcc
Confidence 3457899987
No 192
>PRK13899 type IV secretion system protein VirB3; Provisional
Probab=20.51 E-value=40 Score=23.39 Aligned_cols=20 Identities=15% Similarity=0.317 Sum_probs=15.6
Q ss_pred EeecCCCCCCCceEeCCCCC
Q 039987 26 RTSHTRENPNRKFWKCKGCG 45 (105)
Q Consensus 26 rTSkT~~NPGRkFY~CpsC~ 45 (105)
+++++++.++|+||.+.+.+
T Consensus 76 ~~~~~~r~~Nr~~WG~~SY~ 95 (97)
T PRK13899 76 KMQKCSKCPNRFYHGANSYD 95 (97)
T ss_pred HHhhcCCCCCcCccCccccC
Confidence 45677878999999987654
No 193
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.49 E-value=69 Score=21.78 Aligned_cols=37 Identities=24% Similarity=0.486 Sum_probs=24.0
Q ss_pred cccccccCCceeEEEeecCCCCCCCceEeCCCCC---eeEecCCCC
Q 039987 12 LKACEKCFNSSKVLRTSHTRENPNRKFWKCKGCG---AFKWDDDRK 54 (105)
Q Consensus 12 l~~Cp~Cg~~~avlrTSkT~~NPGRkFY~CpsC~---FFqW~De~~ 54 (105)
.+.||.|| ++ +-|.+.||=|.|- +..|. +=.|.++.+
T Consensus 7 ~v~CP~Cg-kp----v~w~~~s~frPFC-SkRCklIDLg~Wa~eey 46 (65)
T COG3024 7 TVPCPTCG-KP----VVWGEESPFRPFC-SKRCKLIDLGEWAAEEY 46 (65)
T ss_pred cccCCCCC-Cc----ccccccCCcCcch-hHhhhhcchhhhhccCc
Confidence 57899995 43 2467888888872 22554 446877643
No 194
>KOG1024 consensus Receptor-like protein tyrosine kinase RYK/derailed [Signal transduction mechanisms]
Probab=20.24 E-value=70 Score=29.17 Aligned_cols=37 Identities=19% Similarity=0.309 Sum_probs=32.1
Q ss_pred EecCCCCCC-ccchhhhhhhhccccchhhhHhHhhhhc
Q 039987 48 KWDDDRKSS-ECNDFRGMVDRNMSENKIDILLGEVCKL 84 (105)
Q Consensus 48 qW~De~~~~-~~~~~~~~~~~n~~~~~~~~~~~~~~~~ 84 (105)
.|.|+..+- ...++-.+|+.|.|+-.+|.+|-|-|+|
T Consensus 304 I~~eEdt~n~~q~v~vKTvk~~AS~iQv~~~L~es~ll 341 (563)
T KOG1024|consen 304 IWREEDTYNDCQEVLVKTVKQHASQIQVNLLLQESMLL 341 (563)
T ss_pred eecccCCcchHHHHHHHHHHhcccHHHHHHHHHHHHHH
Confidence 588876666 6678889999999999999999999986
No 195
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=20.19 E-value=52 Score=23.56 Aligned_cols=23 Identities=22% Similarity=0.345 Sum_probs=16.4
Q ss_pred hhhhhhhccccchhhhHhHhhhh
Q 039987 61 FRGMVDRNMSENKIDILLGEVCK 83 (105)
Q Consensus 61 ~~~~~~~n~~~~~~~~~~~~~~~ 83 (105)
+.=|-.|++++..||.+|+++=.
T Consensus 27 ~~FL~sKGLt~~EI~~al~~a~~ 49 (136)
T PF04695_consen 27 IAFLESKGLTEEEIDEALGRAGS 49 (136)
T ss_dssp HHHHHHCT--HHHHHHHHHHHT-
T ss_pred HHHHHcCCCCHHHHHHHHHhcCC
Confidence 44567899999999999998643
Done!