Query 041503
Match_columns 99
No_of_seqs 110 out of 277
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 07:49:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041503.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041503hhsearch_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 99.7 2.5E-17 5.5E-22 97.7 3.7 38 13-51 1-44 (45)
2 KOG1956 DNA topoisomerase III 98.0 3.6E-06 7.8E-11 73.4 2.8 36 13-49 719-758 (758)
3 PF05325 DUF730: Protein of un 97.4 0.00079 1.7E-08 47.2 7.0 39 13-52 21-68 (122)
4 PF01396 zf-C4_Topoisom: Topoi 97.3 0.00036 7.7E-09 40.3 3.4 34 13-51 2-38 (39)
5 PRK00464 nrdR transcriptional 97.0 0.00043 9.3E-09 50.7 2.4 31 14-44 2-35 (154)
6 TIGR03655 anti_R_Lar restricti 96.0 0.0075 1.6E-07 36.4 2.7 33 13-45 2-34 (53)
7 PF04606 Ogr_Delta: Ogr/Delta- 95.3 0.0095 2.1E-07 35.3 1.4 31 14-44 1-34 (47)
8 KOG4399 C2HC-type Zn-finger pr 95.3 0.012 2.7E-07 47.3 2.4 42 10-53 11-59 (325)
9 PF01096 TFIIS_C: Transcriptio 94.9 0.027 5.9E-07 32.3 2.4 33 13-45 1-36 (39)
10 PRK09678 DNA-binding transcrip 94.9 0.02 4.3E-07 37.4 2.0 32 13-44 2-36 (72)
11 COG2888 Predicted Zn-ribbon RN 94.2 0.022 4.7E-07 36.4 0.9 29 13-45 28-58 (61)
12 smart00440 ZnF_C2C2 C2C2 Zinc 94.1 0.061 1.3E-06 31.0 2.7 32 14-45 2-36 (40)
13 PF03884 DUF329: Domain of unk 94.0 0.012 2.5E-07 37.0 -0.6 34 13-52 3-40 (57)
14 PF12760 Zn_Tnp_IS1595: Transp 93.9 0.058 1.3E-06 31.6 2.4 27 13-45 19-45 (46)
15 PF11672 DUF3268: Protein of u 93.8 0.18 3.9E-06 34.9 5.0 66 13-80 3-73 (102)
16 PRK14890 putative Zn-ribbon RN 93.6 0.039 8.4E-07 35.0 1.3 29 13-45 26-56 (59)
17 PF01927 Mut7-C: Mut7-C RNAse 93.5 0.066 1.4E-06 38.1 2.5 40 13-52 92-139 (147)
18 PRK00418 DNA gyrase inhibitor; 93.4 0.021 4.5E-07 36.5 -0.2 35 12-52 6-44 (62)
19 PF13408 Zn_ribbon_recom: Reco 93.3 0.075 1.6E-06 31.3 2.2 28 10-41 3-30 (58)
20 TIGR01384 TFS_arch transcripti 92.9 0.12 2.6E-06 34.4 2.9 38 12-50 62-102 (104)
21 PF07282 OrfB_Zn_ribbon: Putat 92.4 0.089 1.9E-06 32.5 1.7 27 13-46 29-55 (69)
22 PHA00626 hypothetical protein 92.3 0.13 2.7E-06 32.6 2.3 36 14-51 2-37 (59)
23 PF14803 Nudix_N_2: Nudix N-te 92.3 0.16 3.5E-06 28.7 2.5 31 14-47 2-32 (34)
24 smart00661 RPOL9 RNA polymeras 91.9 0.23 5E-06 28.9 3.0 34 14-52 2-35 (52)
25 PRK06266 transcription initiat 91.4 0.13 2.8E-06 38.2 1.9 20 72-91 154-173 (178)
26 COG1594 RPB9 DNA-directed RNA 91.1 0.18 4E-06 35.0 2.3 33 13-45 73-108 (113)
27 PF04216 FdhE: Protein involve 90.7 0.13 2.9E-06 40.0 1.5 30 13-43 173-203 (290)
28 KOG2907 RNA polymerase I trans 90.0 0.2 4.3E-06 35.6 1.7 40 7-46 69-111 (116)
29 PRK09710 lar restriction allev 89.5 0.41 8.8E-06 30.8 2.7 31 10-45 4-35 (64)
30 COG3024 Uncharacterized protei 89.0 0.33 7.1E-06 31.3 2.0 37 12-52 7-45 (65)
31 PF14353 CpXC: CpXC protein 88.9 0.34 7.4E-06 33.3 2.2 32 13-44 2-45 (128)
32 PF04977 DivIC: Septum formati 88.9 2.2 4.7E-05 26.3 5.8 29 61-89 21-49 (80)
33 TIGR02098 MJ0042_CXXC MJ0042 f 88.6 0.37 8E-06 26.7 1.8 31 13-45 3-33 (38)
34 PRK07220 DNA topoisomerase I; 88.3 0.38 8.3E-06 42.5 2.6 36 13-51 636-671 (740)
35 smart00531 TFIIE Transcription 88.0 0.27 5.8E-06 35.0 1.3 39 12-51 99-137 (147)
36 PF13453 zf-TFIIB: Transcripti 87.9 0.52 1.1E-05 26.8 2.2 32 14-51 1-32 (41)
37 PF05377 FlaC_arch: Flagella a 87.8 1.9 4.2E-05 26.9 4.9 30 59-88 2-31 (55)
38 PF14354 Lar_restr_allev: Rest 87.7 0.67 1.4E-05 27.9 2.7 34 12-45 3-37 (61)
39 PRK00888 ftsB cell division pr 87.3 2.8 6E-05 28.7 5.9 43 56-98 26-77 (105)
40 PRK01343 zinc-binding protein; 87.1 0.25 5.4E-06 31.0 0.6 32 11-52 8-43 (57)
41 COG1571 Predicted DNA-binding 86.6 0.35 7.5E-06 40.8 1.3 32 12-51 350-381 (421)
42 PF05876 Terminase_GpA: Phage 86.5 0.54 1.2E-05 40.2 2.5 32 13-44 201-236 (557)
43 COG1997 RPL43A Ribosomal prote 86.3 0.59 1.3E-05 31.8 2.1 32 13-52 36-67 (89)
44 PF04977 DivIC: Septum formati 86.2 3 6.5E-05 25.7 5.2 42 58-99 25-68 (80)
45 PF01780 Ribosomal_L37ae: Ribo 86.1 4.2 9.2E-05 27.6 6.2 32 13-52 36-67 (90)
46 COG1656 Uncharacterized conser 86.1 0.35 7.6E-06 36.1 1.0 39 13-52 98-145 (165)
47 PF10571 UPF0547: Uncharacteri 85.9 0.39 8.4E-06 25.5 0.9 9 14-22 2-10 (26)
48 PHA02998 RNA polymerase subuni 85.9 0.77 1.7E-05 35.1 2.8 34 12-45 143-179 (195)
49 PF04880 NUDE_C: NUDE protein, 85.6 0.55 1.2E-05 35.0 1.9 34 55-88 12-48 (166)
50 PRK12380 hydrogenase nickel in 85.5 0.35 7.6E-06 33.4 0.7 25 13-46 71-95 (113)
51 PRK00420 hypothetical protein; 85.5 3.1 6.7E-05 29.2 5.5 31 13-51 24-54 (112)
52 PF03811 Zn_Tnp_IS1: InsA N-te 84.9 1.1 2.4E-05 25.5 2.5 31 13-44 6-36 (36)
53 PRK03564 formate dehydrogenase 84.8 0.96 2.1E-05 36.6 3.0 30 12-41 187-216 (309)
54 PRK00888 ftsB cell division pr 84.3 3.7 8.1E-05 28.0 5.4 14 65-78 49-62 (105)
55 TIGR02159 PA_CoA_Oxy4 phenylac 84.1 0.34 7.3E-06 35.1 0.1 33 12-44 105-137 (146)
56 PRK14892 putative transcriptio 83.5 1.1 2.3E-05 30.8 2.4 32 12-47 21-52 (99)
57 PRK00432 30S ribosomal protein 83.4 0.99 2.2E-05 27.2 2.0 29 13-49 21-49 (50)
58 PF09788 Tmemb_55A: Transmembr 82.9 0.68 1.5E-05 36.8 1.4 26 12-41 85-110 (256)
59 PHA02942 putative transposase; 82.7 0.88 1.9E-05 37.3 2.1 27 13-47 326-352 (383)
60 COG0675 Transposase and inacti 82.6 0.91 2E-05 33.9 2.0 27 13-51 310-336 (364)
61 TIGR01385 TFSII transcription 82.4 1.4 3.1E-05 35.3 3.1 35 11-45 257-294 (299)
62 KOG2906 RNA polymerase III sub 81.7 0.78 1.7E-05 32.0 1.2 36 13-49 66-104 (105)
63 PF14205 Cys_rich_KTR: Cystein 81.6 1.1 2.4E-05 28.0 1.8 31 13-44 5-35 (55)
64 TIGR03830 CxxCG_CxxCG_HTH puta 81.6 2.4 5.1E-05 28.4 3.5 15 35-49 29-43 (127)
65 TIGR00100 hypA hydrogenase nic 81.3 0.69 1.5E-05 31.9 0.8 24 13-45 71-94 (115)
66 COG3677 Transposase and inacti 81.3 1.2 2.6E-05 31.6 2.0 32 11-44 29-60 (129)
67 PRK07220 DNA topoisomerase I; 80.7 1.5 3.2E-05 38.9 2.8 33 13-49 590-625 (740)
68 PRK14810 formamidopyrimidine-D 80.5 1.4 3E-05 34.3 2.4 27 13-44 245-271 (272)
69 KOG3896 Dynactin, subunit p62 80.2 2.4 5.2E-05 35.6 3.7 48 42-89 107-164 (449)
70 TIGR00340 zpr1_rel ZPR1-relate 80.1 1.6 3.4E-05 32.3 2.4 31 15-45 1-36 (163)
71 PRK00564 hypA hydrogenase nick 79.9 0.95 2.1E-05 31.4 1.2 24 13-44 72-95 (117)
72 PRK00398 rpoP DNA-directed RNA 79.5 1.8 4E-05 25.0 2.1 26 13-45 4-29 (46)
73 PRK05582 DNA topoisomerase I; 79.4 1.3 2.8E-05 38.4 2.1 34 13-50 612-648 (650)
74 PRK14973 DNA topoisomerase I; 79.3 1.4 3E-05 40.3 2.3 37 13-52 636-672 (936)
75 COG1867 TRM1 N2,N2-dimethylgua 79.2 6 0.00013 33.1 5.8 69 13-89 241-315 (380)
76 TIGR00577 fpg formamidopyrimid 79.1 1.7 3.8E-05 33.8 2.5 27 13-44 246-272 (272)
77 PRK01103 formamidopyrimidine/5 78.9 1.8 3.8E-05 33.7 2.5 27 13-44 246-272 (274)
78 PRK07726 DNA topoisomerase III 78.9 1.4 3E-05 38.5 2.0 33 13-50 611-645 (658)
79 PRK14811 formamidopyrimidine-D 78.8 1.7 3.7E-05 33.8 2.4 27 13-44 236-262 (269)
80 PRK08173 DNA topoisomerase III 78.3 1.3 2.7E-05 40.1 1.7 28 13-49 625-652 (862)
81 smart00834 CxxC_CXXC_SSSS Puta 77.9 2.3 5E-05 23.3 2.2 16 13-28 6-21 (41)
82 PF08271 TF_Zn_Ribbon: TFIIB z 77.7 1.2 2.7E-05 25.4 1.0 28 14-47 2-29 (43)
83 PRK10445 endonuclease VIII; Pr 77.1 2.1 4.6E-05 33.2 2.4 27 13-44 236-262 (263)
84 COG2174 RPL34A Ribosomal prote 76.8 0.77 1.7E-05 31.5 -0.0 32 12-43 34-77 (93)
85 KOG2691 RNA polymerase II subu 76.8 3.2 6.9E-05 29.4 3.0 34 12-45 73-109 (113)
86 PRK03824 hypA hydrogenase nick 76.7 1.6 3.4E-05 31.0 1.5 34 12-45 70-115 (135)
87 PF07716 bZIP_2: Basic region 76.4 11 0.00023 22.4 5.0 26 61-86 29-54 (54)
88 PF09036 Bcr-Abl_Oligo: Bcr-Ab 76.3 9.9 0.00021 25.3 5.1 30 67-96 29-58 (79)
89 PRK03681 hypA hydrogenase nick 76.2 1.3 2.8E-05 30.6 0.9 26 13-46 71-96 (114)
90 PRK03976 rpl37ae 50S ribosomal 75.5 7.2 0.00016 26.5 4.4 26 13-45 37-62 (90)
91 PF09723 Zn-ribbon_8: Zinc rib 75.3 2.1 4.6E-05 24.6 1.5 17 14-30 7-23 (42)
92 TIGR00280 L37a ribosomal prote 75.2 9.6 0.00021 26.0 5.0 26 13-45 36-61 (91)
93 KOG4317 Predicted Zn-finger pr 74.9 1.7 3.6E-05 36.1 1.4 28 1-47 2-29 (383)
94 TIGR01562 FdhE formate dehydro 74.9 1.9 4.2E-05 34.7 1.7 30 12-41 184-214 (305)
95 PF05502 Dynactin_p62: Dynacti 74.3 6.2 0.00013 33.5 4.7 54 13-69 53-116 (483)
96 PF02150 RNA_POL_M_15KD: RNA p 73.5 2.5 5.4E-05 23.6 1.5 28 14-47 3-30 (35)
97 cd00632 Prefoldin_beta Prefold 72.7 15 0.00032 24.5 5.4 28 62-89 75-102 (105)
98 PF14255 Cys_rich_CPXG: Cystei 72.6 3.5 7.6E-05 25.2 2.1 28 13-42 1-29 (52)
99 PRK13945 formamidopyrimidine-D 72.5 3.3 7.2E-05 32.4 2.5 27 13-44 255-281 (282)
100 PF04728 LPP: Lipoprotein leuc 72.4 21 0.00045 22.3 5.7 31 57-87 3-33 (56)
101 PTZ00255 60S ribosomal protein 71.7 13 0.00027 25.3 4.9 27 13-46 37-63 (90)
102 PF04216 FdhE: Protein involve 71.7 5.3 0.00012 31.1 3.5 41 12-52 211-254 (290)
103 smart00338 BRLZ basic region l 71.7 19 0.00041 21.9 5.3 30 60-89 29-58 (65)
104 COG0551 TopA Zn-finger domain 71.6 3.4 7.3E-05 28.8 2.2 29 12-45 17-48 (140)
105 PF01166 TSC22: TSC-22/dip/bun 71.6 4 8.6E-05 25.9 2.2 25 62-86 12-36 (59)
106 PF13824 zf-Mss51: Zinc-finger 71.5 2.7 5.9E-05 26.2 1.5 24 14-47 1-24 (55)
107 PF07106 TBPIP: Tat binding pr 71.0 20 0.00043 25.6 6.1 32 58-89 73-104 (169)
108 TIGR00310 ZPR1_znf ZPR1 zinc f 70.9 4.1 8.9E-05 30.7 2.6 32 14-45 2-38 (192)
109 PF09986 DUF2225: Uncharacteri 70.9 8.8 0.00019 29.0 4.4 41 12-52 5-63 (214)
110 PF06005 DUF904: Protein of un 70.7 18 0.00039 23.3 5.3 16 57-72 18-33 (72)
111 TIGR00311 aIF-2beta translatio 70.5 3.6 7.9E-05 29.4 2.1 30 13-47 98-128 (133)
112 PRK05582 DNA topoisomerase I; 70.2 3.2 7E-05 36.1 2.1 33 13-50 572-607 (650)
113 PF08826 DMPK_coil: DMPK coile 70.1 24 0.00053 22.2 6.2 18 72-89 40-57 (61)
114 smart00709 Zpr1 Duplicated dom 70.0 4.5 9.9E-05 29.6 2.6 8 15-22 3-10 (160)
115 PF13719 zinc_ribbon_5: zinc-r 70.0 3.4 7.3E-05 23.1 1.5 30 13-44 3-32 (37)
116 COG1998 RPS31 Ribosomal protei 69.1 3.5 7.7E-05 25.4 1.6 31 13-50 20-50 (51)
117 PRK07219 DNA topoisomerase I; 69.0 4.7 0.0001 36.1 3.0 36 12-51 602-640 (822)
118 COG0551 TopA Zn-finger domain 67.9 5.5 0.00012 27.7 2.6 38 12-53 60-101 (140)
119 PF12773 DZR: Double zinc ribb 67.7 3.9 8.5E-05 23.5 1.5 27 11-45 11-37 (50)
120 PF07334 IFP_35_N: Interferon- 67.4 14 0.0003 24.4 4.2 23 67-89 3-25 (76)
121 COG2919 Septum formation initi 67.2 20 0.00043 24.7 5.3 39 61-99 61-101 (117)
122 PF02996 Prefoldin: Prefoldin 67.2 13 0.00027 24.7 4.2 49 42-90 66-117 (120)
123 PF00170 bZIP_1: bZIP transcri 67.2 25 0.00054 21.3 5.2 26 62-87 31-56 (64)
124 PF01921 tRNA-synt_1f: tRNA sy 67.1 3.1 6.8E-05 34.4 1.4 40 13-52 175-214 (360)
125 PF10058 DUF2296: Predicted in 66.7 4.2 9E-05 24.9 1.6 31 13-46 23-53 (54)
126 PF04420 CHD5: CHD5-like prote 66.5 15 0.00033 26.5 4.8 36 57-92 40-87 (161)
127 COG3883 Uncharacterized protei 66.4 21 0.00046 28.5 5.9 22 63-84 72-93 (265)
128 cd00890 Prefoldin Prefoldin is 66.4 21 0.00046 23.7 5.2 48 42-89 76-126 (129)
129 PF04508 Pox_A_type_inc: Viral 65.8 11 0.00024 19.7 2.8 18 72-89 2-19 (23)
130 KOG2264 Exostosin EXT1L [Signa 65.2 17 0.00037 32.8 5.5 26 68-93 104-129 (907)
131 PF07754 DUF1610: Domain of un 65.2 3.3 7.1E-05 21.8 0.8 8 38-45 17-24 (24)
132 PF14197 Cep57_CLD_2: Centroso 64.9 23 0.00049 22.6 4.8 25 68-92 44-68 (69)
133 TIGR02605 CxxC_CxxC_SSSS putat 64.2 6.6 0.00014 22.8 2.1 8 13-20 27-34 (52)
134 COG1326 Uncharacterized archae 64.1 3.5 7.6E-05 31.8 1.1 31 13-47 7-40 (201)
135 PF09862 DUF2089: Protein of u 63.9 12 0.00026 26.3 3.6 19 15-44 1-19 (113)
136 TIGR02894 DNA_bind_RsfA transc 63.8 22 0.00047 26.6 5.1 27 63-89 103-129 (161)
137 PF02403 Seryl_tRNA_N: Seryl-t 63.6 22 0.00047 23.4 4.8 32 59-90 69-100 (108)
138 TIGR00244 transcriptional regu 63.5 25 0.00054 25.9 5.4 39 14-52 2-47 (147)
139 PRK10884 SH3 domain-containing 63.5 31 0.00067 26.2 6.1 14 76-89 137-150 (206)
140 TIGR02209 ftsL_broad cell divi 63.4 30 0.00065 21.6 5.2 29 61-89 28-56 (85)
141 KOG1294 Apurinic/apyrimidinic 63.4 3.9 8.4E-05 33.4 1.3 22 20-41 297-318 (335)
142 PF12443 AKNA: AT-hook-contain 62.8 9.2 0.0002 26.7 2.9 36 55-90 43-78 (106)
143 smart00659 RPOLCX RNA polymera 62.7 6.3 0.00014 23.1 1.8 10 14-23 4-13 (44)
144 PF12709 Kinetocho_Slk19: Cent 62.6 22 0.00049 24.0 4.6 24 66-89 51-74 (87)
145 PF14193 DUF4315: Domain of un 62.6 31 0.00066 22.9 5.3 29 57-85 1-29 (83)
146 PF13600 DUF4140: N-terminal d 62.3 28 0.00062 22.7 5.1 31 57-87 70-100 (104)
147 cd00350 rubredoxin_like Rubred 62.2 4.4 9.5E-05 22.1 1.0 9 36-44 16-24 (33)
148 KOG4797 Transcriptional regula 62.1 19 0.0004 25.7 4.3 24 63-86 66-89 (123)
149 smart00338 BRLZ basic region l 62.1 27 0.00059 21.1 4.7 23 66-88 28-50 (65)
150 PRK07219 DNA topoisomerase I; 62.0 7.4 0.00016 34.9 2.8 32 12-48 688-722 (822)
151 PF03367 zf-ZPR1: ZPR1 zinc-fi 61.8 4.4 9.5E-05 29.6 1.2 10 14-23 3-12 (161)
152 PF01920 Prefoldin_2: Prefoldi 61.4 32 0.0007 22.0 5.2 30 61-90 66-95 (106)
153 PF08432 Vfa1: AAA-ATPase Vps4 61.2 24 0.00052 26.0 5.0 26 13-41 14-40 (182)
154 PRK14973 DNA topoisomerase I; 61.2 5.9 0.00013 36.4 2.1 31 13-48 589-622 (936)
155 PRK06319 DNA topoisomerase I/S 60.8 8.3 0.00018 34.9 3.0 35 13-51 694-733 (860)
156 PF05180 zf-DNL: DNL zinc fing 60.4 3.3 7.1E-05 26.6 0.3 37 13-49 5-41 (66)
157 cd03031 GRX_GRX_like Glutaredo 60.4 9.1 0.0002 27.6 2.6 30 13-44 111-140 (147)
158 PRK00241 nudC NADH pyrophospha 59.7 7.6 0.00016 30.1 2.2 30 13-49 100-129 (256)
159 PF13015 PRKCSH_1: Glucosidase 59.4 12 0.00026 27.3 3.1 28 62-89 1-28 (154)
160 COG1675 TFA1 Transcription ini 59.1 7 0.00015 29.4 1.9 18 72-89 150-167 (176)
161 PF13815 Dzip-like_N: Iguana/D 59.1 22 0.00047 24.3 4.3 21 67-87 90-110 (118)
162 PRK14724 DNA topoisomerase III 59.1 8.5 0.00019 35.5 2.8 30 12-50 755-795 (987)
163 PF10883 DUF2681: Protein of u 59.0 52 0.0011 22.1 5.9 41 55-95 21-61 (87)
164 COG2433 Uncharacterized conser 58.9 23 0.0005 31.6 5.2 30 60-89 432-461 (652)
165 cd00974 DSRD Desulforedoxin (D 58.8 7.1 0.00015 21.2 1.4 12 36-47 3-14 (34)
166 PRK06599 DNA topoisomerase I; 58.6 7 0.00015 34.2 2.1 34 12-50 585-622 (675)
167 CHL00174 accD acetyl-CoA carbo 58.3 3.3 7.2E-05 33.4 0.0 27 13-45 39-65 (296)
168 COG0266 Nei Formamidopyrimidin 58.3 8.5 0.00018 30.8 2.3 27 13-44 246-272 (273)
169 PF11461 RILP: Rab interacting 58.3 17 0.00037 23.0 3.3 26 64-89 3-28 (60)
170 TIGR00319 desulf_FeS4 desulfof 58.3 7.3 0.00016 21.1 1.4 13 35-47 5-17 (34)
171 PRK12336 translation initiatio 58.1 8.4 0.00018 29.0 2.2 35 13-52 99-134 (201)
172 PF08772 NOB1_Zn_bind: Nin one 57.9 6.1 0.00013 25.7 1.2 25 10-34 22-46 (73)
173 COG2956 Predicted N-acetylgluc 57.8 6.8 0.00015 32.8 1.8 23 13-46 355-377 (389)
174 PF10018 Med4: Vitamin-D-recep 57.5 35 0.00076 25.1 5.4 34 58-91 30-63 (188)
175 PF11853 DUF3373: Protein of u 57.1 12 0.00026 32.2 3.2 19 65-83 32-50 (489)
176 KOG4684 Uncharacterized conser 57.0 5.6 0.00012 31.6 1.1 26 12-41 100-125 (275)
177 PRK11546 zraP zinc resistance 56.4 42 0.00092 24.4 5.5 18 66-83 91-108 (143)
178 PF14712 Snapin_Pallidin: Snap 56.4 46 0.001 21.2 5.3 33 56-88 13-45 (92)
179 PRK14714 DNA polymerase II lar 56.4 6.4 0.00014 37.6 1.5 38 13-50 668-705 (1337)
180 PF03962 Mnd1: Mnd1 family; I 56.1 55 0.0012 24.3 6.3 30 61-90 66-95 (188)
181 PF13717 zinc_ribbon_4: zinc-r 55.9 8.8 0.00019 21.4 1.5 30 13-44 3-32 (36)
182 PF08172 CASP_C: CASP C termin 55.7 27 0.00059 27.3 4.7 24 66-89 95-118 (248)
183 TIGR01056 topB DNA topoisomera 55.4 8.7 0.00019 33.7 2.1 33 12-50 611-653 (660)
184 PF03119 DNA_ligase_ZBD: NAD-d 55.3 6.2 0.00014 21.0 0.8 21 14-41 1-21 (28)
185 PRK15396 murein lipoprotein; P 54.9 59 0.0013 21.4 5.6 30 57-86 25-54 (78)
186 PRK08116 hypothetical protein; 54.8 9.1 0.0002 29.6 2.0 35 8-44 12-46 (268)
187 TIGR02338 gimC_beta prefoldin, 54.7 45 0.00098 22.4 5.2 26 65-90 75-100 (110)
188 PF13863 DUF4200: Domain of un 54.7 62 0.0013 21.6 6.0 25 65-89 82-106 (126)
189 PF12548 DUF3740: Sulfatase pr 54.5 27 0.00058 25.4 4.2 45 31-77 74-126 (145)
190 PHA02107 hypothetical protein 54.5 16 0.00034 28.1 3.1 21 66-90 186-206 (216)
191 PHA02446 hypothetical protein 54.4 5.4 0.00012 29.2 0.6 29 13-41 63-92 (166)
192 PF13909 zf-H2C2_5: C2H2-type 54.3 7 0.00015 19.2 0.9 10 38-47 1-10 (24)
193 PRK08173 DNA topoisomerase III 54.2 12 0.00026 34.0 2.8 29 12-49 726-761 (862)
194 PRK05776 DNA topoisomerase I; 54.1 9.9 0.00021 33.5 2.3 36 13-51 597-639 (670)
195 PF00170 bZIP_1: bZIP transcri 54.1 47 0.001 20.1 5.5 26 61-86 37-62 (64)
196 PF14931 IFT20: Intraflagellar 54.0 62 0.0013 22.7 5.9 25 61-85 84-108 (120)
197 PF12808 Mto2_bdg: Micro-tubul 53.8 29 0.00063 21.3 3.7 26 68-93 26-51 (52)
198 PF10186 Atg14: UV radiation r 53.7 57 0.0012 24.3 6.1 11 32-43 7-17 (302)
199 smart00647 IBR In Between Ring 53.6 15 0.00032 21.4 2.4 30 10-44 16-47 (64)
200 PLN02678 seryl-tRNA synthetase 53.4 38 0.00083 28.7 5.6 30 61-90 75-104 (448)
201 PF05529 Bap31: B-cell recepto 53.3 32 0.0007 25.0 4.6 10 72-81 162-171 (192)
202 TIGR01057 topA_arch DNA topois 53.1 11 0.00023 32.7 2.2 25 13-42 590-614 (618)
203 PRK14127 cell division protein 53.0 42 0.00091 23.4 4.8 23 67-89 40-62 (109)
204 PF08274 PhnA_Zn_Ribbon: PhnA 52.9 7.9 0.00017 21.2 1.0 25 13-45 3-27 (30)
205 TIGR01051 topA_bact DNA topois 52.9 12 0.00025 32.5 2.5 28 13-45 575-605 (610)
206 PF05615 THOC7: Tho complex su 52.7 54 0.0012 22.7 5.4 28 68-95 85-112 (139)
207 PHA02540 61 DNA primase; Provi 52.7 7.4 0.00016 31.8 1.2 32 13-44 28-62 (337)
208 PRK07561 DNA topoisomerase I s 52.7 10 0.00023 34.2 2.2 34 13-51 588-627 (859)
209 PRK14127 cell division protein 52.3 61 0.0013 22.5 5.6 29 60-88 40-68 (109)
210 PF01025 GrpE: GrpE; InterPro 52.2 65 0.0014 22.5 5.9 35 58-92 19-53 (165)
211 PRK00750 lysK lysyl-tRNA synth 52.1 12 0.00027 31.7 2.5 33 13-46 176-208 (510)
212 COG4049 Uncharacterized protei 52.0 6.1 0.00013 25.2 0.5 11 34-44 14-24 (65)
213 PF03833 PolC_DP2: DNA polymer 51.9 4.8 0.0001 37.0 0.0 38 9-46 652-689 (900)
214 PRK14154 heat shock protein Gr 51.9 57 0.0012 25.1 5.9 36 54-89 49-84 (208)
215 PRK03564 formate dehydrogenase 51.7 13 0.00029 30.1 2.5 40 13-52 227-268 (309)
216 PF11853 DUF3373: Protein of u 51.5 19 0.00041 31.1 3.5 24 64-88 25-48 (489)
217 TIGR01834 PHA_synth_III_E poly 51.4 30 0.00065 28.3 4.5 26 64-89 289-314 (320)
218 PRK14724 DNA topoisomerase III 50.9 9.7 0.00021 35.1 1.8 28 13-49 644-678 (987)
219 smart00067 GHA Glycoprotein ho 50.9 8.7 0.00019 26.0 1.1 29 15-47 2-30 (87)
220 PF08172 CASP_C: CASP C termin 50.8 43 0.00093 26.2 5.1 32 60-91 2-33 (248)
221 PRK00448 polC DNA polymerase I 50.7 9.7 0.00021 36.6 1.8 24 28-51 899-922 (1437)
222 PF11544 Spc42p: Spindle pole 50.3 55 0.0012 21.6 4.8 23 65-87 13-35 (76)
223 PF09332 Mcm10: Mcm10 replicat 50.0 8.1 0.00017 31.8 1.0 35 13-54 286-320 (344)
224 KOG2462 C2H2-type Zn-finger pr 50.0 8.5 0.00018 31.0 1.1 32 13-44 188-222 (279)
225 PRK03988 translation initiatio 49.8 15 0.00032 26.5 2.2 30 13-47 103-133 (138)
226 TIGR02209 ftsL_broad cell divi 49.7 62 0.0013 20.2 5.6 25 60-84 34-58 (85)
227 KOG1962 B-cell receptor-associ 49.6 32 0.0007 26.7 4.2 30 62-91 149-178 (216)
228 KOG0402 60S ribosomal protein 49.1 21 0.00045 24.4 2.7 26 13-45 37-62 (92)
229 COG4332 Uncharacterized protei 49.0 12 0.00026 28.8 1.8 36 10-45 15-57 (203)
230 TIGR01405 polC_Gram_pos DNA po 48.7 11 0.00023 35.7 1.7 24 28-51 674-697 (1213)
231 PF13815 Dzip-like_N: Iguana/D 48.7 74 0.0016 21.6 5.6 29 63-91 79-107 (118)
232 PF13600 DUF4140: N-terminal d 48.6 65 0.0014 21.0 5.1 33 62-94 68-100 (104)
233 PF06305 DUF1049: Protein of u 48.4 31 0.00067 20.7 3.3 22 68-89 45-66 (68)
234 PF08946 Osmo_CC: Osmosensory 48.3 44 0.00096 20.2 3.8 22 62-83 17-38 (46)
235 PF14577 SEO_C: Sieve element 48.2 9.9 0.00022 29.8 1.2 15 13-27 215-229 (235)
236 KOG4119 G protein gamma subuni 48.2 61 0.0013 21.1 4.7 35 55-89 5-39 (71)
237 PF06005 DUF904: Protein of un 48.2 72 0.0016 20.5 5.5 24 59-82 13-36 (72)
238 PF10398 DUF2443: Protein of u 48.1 24 0.00052 23.5 2.9 16 62-77 55-70 (79)
239 PRK06319 DNA topoisomerase I/S 48.0 14 0.00029 33.5 2.2 29 13-46 646-677 (860)
240 PRK11239 hypothetical protein; 47.9 43 0.00092 26.1 4.6 60 25-87 148-213 (215)
241 TIGR01031 rpmF_bact ribosomal 47.7 15 0.00032 22.5 1.7 23 13-47 27-49 (55)
242 COG1996 RPC10 DNA-directed RNA 47.5 11 0.00023 23.0 1.0 11 37-47 24-34 (49)
243 PF08232 Striatin: Striatin fa 47.5 87 0.0019 22.1 5.9 36 58-93 33-68 (134)
244 TIGR01391 dnaG DNA primase, ca 47.5 13 0.00029 30.6 1.9 28 13-44 35-62 (415)
245 PF11287 DUF3088: Protein of u 47.4 11 0.00024 26.5 1.3 13 31-44 16-28 (112)
246 TIGR00515 accD acetyl-CoA carb 47.4 5.4 0.00012 31.8 -0.4 27 13-45 27-53 (285)
247 TIGR00219 mreC rod shape-deter 47.3 81 0.0017 24.8 6.2 32 61-92 70-101 (283)
248 PRK13922 rod shape-determining 47.0 76 0.0016 24.2 5.9 24 60-83 72-95 (276)
249 PF14182 YgaB: YgaB-like prote 46.9 85 0.0018 20.9 5.3 23 65-87 48-70 (79)
250 TIGR02894 DNA_bind_RsfA transc 46.7 56 0.0012 24.4 4.9 29 60-88 107-135 (161)
251 PF09151 DUF1936: Domain of un 46.6 17 0.00038 20.6 1.7 30 14-45 3-34 (36)
252 TIGR01206 lysW lysine biosynth 46.6 22 0.00048 21.8 2.4 27 13-44 3-29 (54)
253 PF06044 DRP: Dam-replacing fa 46.4 11 0.00024 30.0 1.3 28 13-44 32-60 (254)
254 COG3058 FdhE Uncharacterized p 46.3 12 0.00027 30.4 1.5 31 11-41 184-215 (308)
255 PRK05431 seryl-tRNA synthetase 46.0 61 0.0013 26.9 5.6 28 62-89 71-98 (425)
256 PF07798 DUF1640: Protein of u 46.0 73 0.0016 23.1 5.5 26 67-92 76-101 (177)
257 KOG4191 Histone acetyltransfer 45.8 42 0.0009 29.2 4.6 32 57-88 401-432 (516)
258 KOG2991 Splicing regulator [RN 45.7 41 0.00088 27.5 4.4 32 66-97 266-300 (330)
259 COG1384 LysS Lysyl-tRNA synthe 45.7 17 0.00036 31.7 2.3 35 13-50 172-207 (521)
260 PF07106 TBPIP: Tat binding pr 45.6 42 0.00091 23.9 4.1 22 59-80 81-102 (169)
261 PF11802 CENP-K: Centromere-as 45.6 78 0.0017 25.4 5.9 29 67-95 99-127 (268)
262 PF07334 IFP_35_N: Interferon- 45.6 59 0.0013 21.4 4.4 27 60-86 3-29 (76)
263 PRK10803 tol-pal system protei 45.4 77 0.0017 24.6 5.8 26 64-89 61-86 (263)
264 TIGR00293 prefoldin, archaeal 45.4 72 0.0016 21.4 5.1 46 42-87 75-123 (126)
265 PF14817 HAUS5: HAUS augmin-li 45.3 73 0.0016 28.3 6.2 35 57-91 79-113 (632)
266 PF14982 UPF0731: UPF0731 fami 45.3 28 0.00062 23.0 2.8 25 28-52 34-58 (79)
267 PF01920 Prefoldin_2: Prefoldi 45.1 80 0.0017 20.1 6.2 32 57-88 69-100 (106)
268 PF06827 zf-FPG_IleRS: Zinc fi 45.0 28 0.00062 18.1 2.4 27 13-44 2-28 (30)
269 cd00632 Prefoldin_beta Prefold 44.9 79 0.0017 20.9 5.1 31 62-92 68-98 (105)
270 TIGR00414 serS seryl-tRNA synt 44.7 68 0.0015 26.6 5.7 30 61-90 73-102 (418)
271 PF01873 eIF-5_eIF-2B: Domain 44.6 23 0.0005 24.9 2.6 29 13-45 94-122 (125)
272 PRK06443 chorismate mutase; Va 44.4 70 0.0015 24.2 5.2 35 55-89 3-37 (177)
273 PF14389 Lzipper-MIP1: Leucine 44.2 70 0.0015 21.0 4.7 34 57-90 54-87 (88)
274 KOG4603 TBP-1 interacting prot 44.2 66 0.0014 24.7 5.1 19 72-90 117-135 (201)
275 PRK05667 dnaG DNA primase; Val 44.0 16 0.00034 31.7 1.9 29 13-45 37-65 (580)
276 PF10458 Val_tRNA-synt_C: Valy 44.0 69 0.0015 19.6 4.4 20 70-89 3-22 (66)
277 PF05082 Rop-like: Rop-like; 43.9 60 0.0013 20.9 4.1 23 65-87 3-25 (66)
278 KOG1002 Nucleotide excision re 43.8 35 0.00076 30.6 4.0 43 8-53 532-591 (791)
279 PRK12286 rpmF 50S ribosomal pr 43.8 17 0.00036 22.5 1.5 22 13-46 28-49 (57)
280 TIGR00416 sms DNA repair prote 43.5 13 0.00027 31.2 1.2 24 13-47 8-31 (454)
281 cd00674 LysRS_core_class_I cat 43.5 23 0.0005 29.0 2.7 36 13-50 170-205 (353)
282 PF06397 Desulfoferrod_N: Desu 43.4 12 0.00026 21.4 0.7 12 35-46 4-15 (36)
283 PF06717 DUF1202: Protein of u 43.2 82 0.0018 25.8 5.7 42 44-87 127-168 (308)
284 PRK09413 IS2 repressor TnpA; R 43.1 83 0.0018 21.3 5.1 15 63-77 77-91 (121)
285 smart00653 eIF2B_5 domain pres 42.9 21 0.00046 24.6 2.1 28 13-45 81-109 (110)
286 PF07926 TPR_MLP1_2: TPR/MLP1/ 42.9 97 0.0021 21.4 5.5 33 59-91 5-37 (132)
287 COG3439 Uncharacterized conser 42.9 40 0.00086 24.2 3.6 11 42-52 86-96 (137)
288 PRK00762 hypA hydrogenase nick 42.8 12 0.00027 26.0 0.9 27 13-44 71-99 (124)
289 PF08317 Spc7: Spc7 kinetochor 42.6 81 0.0018 25.0 5.6 21 67-87 240-260 (325)
290 PRK13169 DNA replication intia 42.5 77 0.0017 22.0 4.9 21 62-82 13-33 (110)
291 PF05529 Bap31: B-cell recepto 42.5 75 0.0016 23.0 5.1 13 77-89 160-172 (192)
292 PF07649 C1_3: C1-like domain; 42.3 13 0.00029 19.5 0.8 13 35-47 13-25 (30)
293 COG2433 Uncharacterized conser 42.1 76 0.0016 28.5 5.8 26 61-86 440-465 (652)
294 KOG4253 Tryptophan-rich basic 42.1 84 0.0018 23.8 5.3 19 72-90 71-89 (175)
295 PF04645 DUF603: Protein of un 41.9 80 0.0017 24.1 5.2 8 62-69 117-124 (181)
296 TIGR03831 YgiT_finger YgiT-typ 41.7 17 0.00037 20.0 1.3 7 15-21 1-7 (46)
297 PF12709 Kinetocho_Slk19: Cent 41.5 92 0.002 21.0 5.0 33 55-87 46-79 (87)
298 PF10263 SprT-like: SprT-like 41.4 18 0.0004 24.9 1.6 27 13-44 124-150 (157)
299 cd00584 Prefoldin_alpha Prefol 41.3 96 0.0021 20.9 5.2 45 42-86 76-123 (129)
300 TIGR02338 gimC_beta prefoldin, 41.3 1.1E+02 0.0023 20.5 5.4 32 58-89 75-106 (110)
301 PF07047 OPA3: Optic atrophy 3 41.1 55 0.0012 23.0 4.0 24 68-91 109-132 (134)
302 PF05308 Mito_fiss_reg: Mitoch 40.7 32 0.0007 27.0 3.1 21 55-75 120-140 (253)
303 PF08317 Spc7: Spc7 kinetochor 40.5 80 0.0017 25.1 5.3 10 65-74 217-226 (325)
304 COG1422 Predicted membrane pro 40.4 71 0.0015 24.6 4.8 23 55-77 70-92 (201)
305 PRK03947 prefoldin subunit alp 40.4 1.1E+02 0.0025 20.9 5.5 30 60-89 104-133 (140)
306 cd04476 RPA1_DBD_C RPA1_DBD_C: 40.3 18 0.00039 25.6 1.5 24 13-44 35-58 (166)
307 PF13465 zf-H2C2_2: Zinc-finge 39.9 14 0.00031 18.8 0.7 11 34-44 11-21 (26)
308 COG1579 Zn-ribbon protein, pos 39.7 97 0.0021 24.3 5.5 29 60-88 106-134 (239)
309 PRK10698 phage shock protein P 39.1 1.4E+02 0.003 22.7 6.2 35 59-93 101-135 (222)
310 PF03980 Nnf1: Nnf1 ; InterPr 39.1 1.1E+02 0.0024 20.3 5.1 27 64-90 80-106 (109)
311 PF04102 SlyX: SlyX; InterPro 38.7 98 0.0021 19.3 5.8 23 66-88 20-42 (69)
312 COG4238 Murein lipoprotein [Ce 38.6 1.2E+02 0.0026 20.2 5.3 37 55-91 23-59 (78)
313 PRK04023 DNA polymerase II lar 38.4 23 0.00051 33.4 2.2 14 85-98 717-730 (1121)
314 COG4985 ABC-type phosphate tra 38.4 66 0.0014 25.9 4.4 31 60-90 217-247 (289)
315 PF01486 K-box: K-box region; 38.3 78 0.0017 20.7 4.3 18 45-62 37-54 (100)
316 COG0576 GrpE Molecular chapero 38.3 1.5E+02 0.0032 22.2 6.2 36 57-92 43-78 (193)
317 PF07407 Seadorna_VP6: Seadorn 38.2 63 0.0014 27.2 4.5 32 57-88 32-63 (420)
318 KOG3335 Predicted coiled-coil 38.1 99 0.0021 23.6 5.2 29 62-90 104-132 (181)
319 PRK12495 hypothetical protein; 38.0 20 0.00043 28.2 1.5 28 13-49 43-70 (226)
320 PF11365 DUF3166: Protein of u 37.9 1.3E+02 0.0027 20.6 5.3 24 72-97 23-46 (96)
321 smart00132 LIM Zinc-binding do 37.9 13 0.00028 19.2 0.3 30 14-44 1-34 (39)
322 TIGR01562 FdhE formate dehydro 37.8 33 0.00071 27.7 2.8 41 12-52 224-268 (305)
323 PLN00180 NDF6 (NDH-dependent f 37.5 39 0.00085 25.5 2.9 50 38-91 107-178 (180)
324 COG1163 DRG Predicted GTPase [ 37.4 88 0.0019 26.2 5.2 34 57-90 6-45 (365)
325 PRK14011 prefoldin subunit alp 37.4 1.5E+02 0.0032 21.4 5.9 33 58-90 96-128 (144)
326 PRK05771 V-type ATP synthase s 37.3 1E+02 0.0023 26.6 5.9 32 62-93 98-129 (646)
327 PF09889 DUF2116: Uncharacteri 37.0 15 0.00033 23.0 0.6 11 13-23 4-14 (59)
328 TIGR01242 26Sp45 26S proteasom 36.8 1.1E+02 0.0024 24.2 5.6 24 65-88 14-37 (364)
329 COG4311 SoxD Sarcosine oxidase 36.8 22 0.00048 24.6 1.4 25 12-36 3-28 (97)
330 PF14265 DUF4355: Domain of un 36.7 1.3E+02 0.0029 20.2 5.4 23 71-93 49-71 (125)
331 PF11488 Lge1: Transcriptional 36.6 1.2E+02 0.0025 19.5 5.1 26 63-88 29-54 (80)
332 PRK11788 tetratricopeptide rep 36.5 23 0.00049 27.1 1.6 25 11-46 353-377 (389)
333 PF05377 FlaC_arch: Flagella a 36.5 1.1E+02 0.0023 19.0 5.2 24 60-83 17-40 (55)
334 PRK09413 IS2 repressor TnpA; R 36.3 73 0.0016 21.5 4.0 23 66-88 73-95 (121)
335 COG2919 Septum formation initi 36.3 1.3E+02 0.0028 20.6 5.2 33 57-89 50-82 (117)
336 PRK02655 psbI photosystem II r 36.1 19 0.00042 20.9 0.9 12 25-36 23-35 (38)
337 COG4391 Uncharacterized protei 35.8 19 0.00041 23.0 0.9 14 9-22 45-58 (62)
338 KOG2391 Vacuolar sorting prote 35.8 1.1E+02 0.0025 25.6 5.6 28 68-95 239-266 (365)
339 smart00746 TRASH metallochaper 35.8 9.7 0.00021 18.5 -0.4 9 15-23 1-9 (39)
340 PF08912 Rho_Binding: Rho Bind 35.6 1.2E+02 0.0027 19.6 5.2 25 60-84 6-30 (69)
341 COG3879 Uncharacterized protei 35.5 1.2E+02 0.0027 24.0 5.5 32 60-91 53-84 (247)
342 PF13240 zinc_ribbon_2: zinc-r 35.4 17 0.00037 18.4 0.5 9 14-22 1-9 (23)
343 TIGR00373 conserved hypothetic 35.3 22 0.00048 25.7 1.3 14 31-44 103-116 (158)
344 PF03112 DUF244: Uncharacteriz 35.3 40 0.00086 25.1 2.6 8 45-52 45-52 (158)
345 PF11336 DUF3138: Protein of u 35.2 61 0.0013 28.2 4.0 25 64-88 25-49 (514)
346 PRK00423 tfb transcription ini 35.1 38 0.00083 26.8 2.7 31 10-46 9-39 (310)
347 PF15269 zf-C2H2_7: Zinc-finge 35.1 22 0.00047 21.8 1.0 17 30-46 12-29 (54)
348 PHA01750 hypothetical protein 34.9 1.3E+02 0.0029 19.7 4.8 20 65-84 43-62 (75)
349 cd01675 RNR_III Class III ribo 34.9 18 0.0004 31.0 0.9 24 10-44 516-539 (555)
350 TIGR00467 lysS_arch lysyl-tRNA 34.8 36 0.00078 29.3 2.7 35 13-50 169-203 (515)
351 PF01807 zf-CHC2: CHC2 zinc fi 34.7 31 0.00067 22.8 1.8 28 13-44 34-61 (97)
352 TIGR00320 dfx_rbo desulfoferro 34.7 25 0.00054 24.7 1.4 13 35-47 5-17 (125)
353 PRK09343 prefoldin subunit bet 34.6 1.4E+02 0.0031 20.5 5.2 24 66-89 80-103 (121)
354 PF08606 Prp19: Prp19/Pso4-lik 34.6 1.3E+02 0.0028 19.5 5.2 31 60-90 11-41 (70)
355 COG0068 HypF Hydrogenase matur 34.5 30 0.00065 31.4 2.2 22 31-52 162-191 (750)
356 PF05557 MAD: Mitotic checkpoi 34.4 65 0.0014 28.3 4.2 38 57-94 503-540 (722)
357 COG1382 GimC Prefoldin, chaper 34.1 1.5E+02 0.0032 21.0 5.3 17 71-87 91-107 (119)
358 COG0777 AccD Acetyl-CoA carbox 34.0 12 0.00026 30.4 -0.3 30 13-48 29-58 (294)
359 COG1439 Predicted nucleic acid 33.9 26 0.00056 26.5 1.5 22 13-34 154-175 (177)
360 COG2740 Predicted nucleic-acid 33.9 31 0.00068 23.3 1.8 20 24-43 34-53 (95)
361 PF02591 DUF164: Putative zinc 33.8 19 0.00041 21.4 0.6 12 10-21 44-55 (56)
362 TIGR02231 conserved hypothetic 33.8 1.1E+02 0.0023 25.7 5.3 22 66-87 147-168 (525)
363 COG3937 Uncharacterized conser 33.8 63 0.0014 22.7 3.3 23 65-87 84-106 (108)
364 PRK05580 primosome assembly pr 33.7 68 0.0015 28.2 4.2 37 13-49 391-433 (679)
365 PF01783 Ribosomal_L32p: Ribos 33.7 14 0.0003 22.5 -0.0 9 12-20 26-34 (56)
366 PF08646 Rep_fac-A_C: Replicat 33.6 24 0.00052 24.4 1.2 24 13-44 19-44 (146)
367 PRK05654 acetyl-CoA carboxylas 33.4 10 0.00022 30.3 -0.8 27 13-45 28-54 (292)
368 PRK12366 replication factor A; 33.4 27 0.00058 30.6 1.7 23 13-44 533-555 (637)
369 PF11023 DUF2614: Protein of u 33.1 15 0.00031 26.1 0.0 25 12-45 69-93 (114)
370 PF04999 FtsL: Cell division p 32.9 1.3E+02 0.0029 19.3 4.7 24 65-88 43-66 (97)
371 PF08537 NBP1: Fungal Nap bind 32.8 1.4E+02 0.0031 24.6 5.7 35 59-93 177-211 (323)
372 PF08792 A2L_zn_ribbon: A2L zi 32.8 56 0.0012 18.0 2.4 26 12-44 3-28 (33)
373 KOG2264 Exostosin EXT1L [Signa 32.7 88 0.0019 28.5 4.7 16 65-80 108-123 (907)
374 PF13334 DUF4094: Domain of un 32.6 1.3E+02 0.0027 20.3 4.6 30 62-91 64-93 (95)
375 TIGR03847 conserved hypothetic 32.3 22 0.00048 27.0 0.9 12 11-22 155-166 (177)
376 PF07820 TraC: TraC-like prote 32.3 1.1E+02 0.0023 21.0 4.2 18 67-84 5-22 (92)
377 TIGR02977 phageshock_pspA phag 32.2 1.9E+02 0.0041 21.6 6.0 32 61-92 103-134 (219)
378 COG3599 DivIVA Cell division i 32.2 1.4E+02 0.0031 22.8 5.4 32 62-93 35-66 (212)
379 PTZ00454 26S protease regulato 32.2 1.2E+02 0.0026 25.0 5.2 25 65-89 37-61 (398)
380 PF07061 Swi5: Swi5; InterPro 32.1 1.2E+02 0.0025 20.0 4.2 26 61-86 4-29 (83)
381 PF11932 DUF3450: Protein of u 32.1 1.5E+02 0.0033 22.4 5.5 13 65-77 57-69 (251)
382 PRK09973 putative outer membra 31.9 1.6E+02 0.0035 19.7 5.6 31 57-87 24-54 (85)
383 PF02318 FYVE_2: FYVE-type zin 31.6 1.7E+02 0.0036 19.8 6.1 17 77-93 26-42 (118)
384 CHL00024 psbI photosystem II p 31.5 26 0.00057 20.1 0.9 12 25-36 23-35 (36)
385 PF07412 Geminin: Geminin; In 31.5 93 0.002 24.0 4.2 18 66-83 134-151 (200)
386 TIGR03545 conserved hypothetic 31.4 1.6E+02 0.0034 25.7 6.0 29 64-92 219-247 (555)
387 COG3074 Uncharacterized protei 31.3 1.6E+02 0.0035 19.5 5.5 16 59-74 20-35 (79)
388 PF09726 Macoilin: Transmembra 31.2 1.4E+02 0.003 26.8 5.7 31 58-88 546-576 (697)
389 PF12548 DUF3740: Sulfatase pr 31.2 88 0.0019 22.7 3.8 23 68-91 110-132 (145)
390 PF13935 Ead_Ea22: Ead/Ea22-li 31.1 1.6E+02 0.0036 20.6 5.2 20 73-92 92-111 (139)
391 PF10234 Cluap1: Clusterin-ass 31.1 2E+02 0.0043 23.0 6.1 29 66-94 185-213 (267)
392 PRK06260 threonine synthase; V 30.9 32 0.0007 27.8 1.7 8 13-20 20-27 (397)
393 COG5509 Uncharacterized small 30.9 1.2E+02 0.0025 19.5 3.9 24 66-89 27-50 (65)
394 PF13248 zf-ribbon_3: zinc-rib 30.8 23 0.0005 18.2 0.6 9 13-21 3-11 (26)
395 PF10601 zf-LITAF-like: LITAF- 30.8 32 0.0007 21.4 1.4 18 12-29 7-24 (73)
396 PF04576 Zein-binding: Zein-bi 30.8 1.1E+02 0.0024 20.9 4.1 23 71-93 6-28 (94)
397 COG1645 Uncharacterized Zn-fin 30.8 31 0.00066 24.9 1.4 23 13-44 29-51 (131)
398 KOG3478 Prefoldin subunit 6, K 30.7 1.2E+02 0.0026 21.7 4.3 27 66-92 78-104 (120)
399 TIGR01242 26Sp45 26S proteasom 30.7 1.4E+02 0.003 23.7 5.2 32 60-91 2-33 (364)
400 PRK10803 tol-pal system protei 30.6 1.4E+02 0.003 23.2 5.1 24 60-83 64-87 (263)
401 PF00261 Tropomyosin: Tropomyo 30.5 1.7E+02 0.0037 22.0 5.5 29 62-90 202-230 (237)
402 KOG2077 JNK/SAPK-associated pr 30.5 1.2E+02 0.0026 27.6 5.2 17 74-90 353-369 (832)
403 smart00787 Spc7 Spc7 kinetocho 30.5 1.6E+02 0.0034 23.7 5.5 23 66-88 234-256 (312)
404 PF11544 Spc42p: Spindle pole 30.5 1.6E+02 0.0036 19.4 5.2 24 60-83 15-38 (76)
405 KOG4010 Coiled-coil protein TP 30.4 1.9E+02 0.0042 22.4 5.7 37 63-99 43-84 (208)
406 PF08826 DMPK_coil: DMPK coile 30.3 1.4E+02 0.0031 18.6 5.3 32 59-90 3-37 (61)
407 PHA02109 hypothetical protein 30.3 1.5E+02 0.0032 23.1 5.1 35 62-97 198-232 (233)
408 PF06906 DUF1272: Protein of u 30.0 22 0.00048 22.4 0.5 13 13-25 42-54 (57)
409 PF04201 TPD52: Tumour protein 30.0 2.3E+02 0.0049 21.2 5.9 36 63-98 28-68 (162)
410 PF06156 DUF972: Protein of un 29.7 1.9E+02 0.0041 19.8 6.2 24 65-88 23-46 (107)
411 PRK11020 hypothetical protein; 29.6 1.9E+02 0.0042 20.6 5.2 20 58-77 32-51 (118)
412 cd00279 YlxR Ylxr homologs; gr 29.6 34 0.00074 22.2 1.3 13 29-41 33-45 (79)
413 PF10211 Ax_dynein_light: Axon 29.5 1.9E+02 0.0042 21.4 5.5 16 68-83 131-146 (189)
414 PRK02195 V-type ATP synthase s 29.4 1.7E+02 0.0036 22.0 5.2 30 58-87 32-61 (201)
415 PF14952 zf-tcix: Putative tre 29.4 25 0.00054 21.1 0.6 10 11-20 10-19 (44)
416 PF14818 DUF4482: Domain of un 29.4 1.4E+02 0.0031 21.8 4.7 35 57-91 17-54 (141)
417 PF04799 Fzo_mitofusin: fzo-li 29.4 1.7E+02 0.0037 22.0 5.2 58 22-83 61-139 (171)
418 PF05103 DivIVA: DivIVA protei 29.3 31 0.00067 23.1 1.2 20 65-84 33-52 (131)
419 PRK00295 hypothetical protein; 29.2 1.5E+02 0.0033 18.6 6.2 23 66-88 21-43 (68)
420 PF02050 FliJ: Flagellar FliJ 29.2 1.5E+02 0.0032 18.5 6.2 33 61-93 56-88 (123)
421 PF07047 OPA3: Optic atrophy 3 29.2 1.1E+02 0.0024 21.4 4.1 19 64-82 112-130 (134)
422 PF08657 DASH_Spc34: DASH comp 28.9 1.7E+02 0.0036 23.1 5.3 33 57-89 180-212 (259)
423 PF07412 Geminin: Geminin; In 28.9 1.4E+02 0.003 23.1 4.7 24 65-88 126-149 (200)
424 PF14257 DUF4349: Domain of un 28.8 1.3E+02 0.0029 22.7 4.7 7 71-77 176-182 (262)
425 COG2176 PolC DNA polymerase II 28.8 42 0.00092 32.5 2.2 29 24-52 901-929 (1444)
426 KOG3335 Predicted coiled-coil 28.7 1.2E+02 0.0026 23.2 4.3 30 60-89 109-138 (181)
427 TIGR02231 conserved hypothetic 28.7 1.4E+02 0.0029 25.1 5.1 31 57-87 71-101 (525)
428 PF08209 Sgf11: Sgf11 (transcr 28.7 25 0.00054 19.6 0.5 11 12-22 4-14 (33)
429 KOG2041 WD40 repeat protein [G 28.7 51 0.0011 30.8 2.6 35 13-47 1132-1166(1189)
430 PF05207 zf-CSL: CSL zinc fing 28.6 20 0.00043 21.7 0.1 34 13-49 19-52 (55)
431 PF05766 NinG: Bacteriophage L 28.5 80 0.0017 24.0 3.4 77 13-90 88-187 (189)
432 PLN03166 60S ribosomal protein 28.4 35 0.00075 23.3 1.3 26 13-38 42-79 (96)
433 PRK07218 replication factor A; 28.3 30 0.00065 29.1 1.1 19 13-44 298-316 (423)
434 KOG4657 Uncharacterized conser 28.3 1.3E+02 0.0029 23.9 4.6 29 60-88 89-117 (246)
435 COG1938 Archaeal enzymes of AT 28.3 99 0.0021 24.4 3.9 24 68-91 208-231 (244)
436 COG1327 Predicted transcriptio 28.3 42 0.00091 25.0 1.8 31 14-44 2-35 (156)
437 PRK14155 heat shock protein Gr 28.1 2.7E+02 0.0058 21.3 6.2 35 57-91 20-54 (208)
438 KOG0976 Rho/Rac1-interacting s 27.9 1.2E+02 0.0026 28.7 4.9 32 62-93 481-512 (1265)
439 PF07926 TPR_MLP1_2: TPR/MLP1/ 27.9 1.7E+02 0.0036 20.2 4.7 29 60-88 101-129 (132)
440 TIGR00155 pqiA_fam integral me 27.8 50 0.0011 27.4 2.3 32 11-52 214-245 (403)
441 PF09538 FYDLN_acid: Protein o 27.8 46 0.001 22.9 1.8 10 35-44 24-33 (108)
442 PF10482 CtIP_N: Tumour-suppre 27.8 74 0.0016 22.8 2.9 23 66-88 98-120 (120)
443 PF04859 DUF641: Plant protein 27.7 1.2E+02 0.0026 21.7 4.0 13 65-77 102-114 (131)
444 COG0718 Uncharacterized protei 27.7 64 0.0014 22.4 2.5 32 66-97 7-38 (105)
445 PF10186 Atg14: UV radiation r 27.7 2.5E+02 0.0054 20.9 5.9 17 71-87 84-100 (302)
446 PRK07737 fliD flagellar cappin 27.6 1.5E+02 0.0032 25.2 5.2 26 59-84 443-468 (501)
447 PRK08270 anaerobic ribonucleos 27.6 32 0.0007 30.4 1.2 22 11-44 625-646 (656)
448 PF07028 DUF1319: Protein of u 27.3 1.7E+02 0.0036 21.1 4.7 16 72-87 61-76 (126)
449 PF00831 Ribosomal_L29: Riboso 27.3 1.4E+02 0.0029 18.0 3.7 19 76-94 12-30 (58)
450 COG3416 Uncharacterized protei 27.3 1.2E+02 0.0025 24.0 4.1 30 57-86 48-77 (233)
451 PF14723 SSFA2_C: Sperm-specif 27.2 2.2E+02 0.0049 21.6 5.5 32 66-97 147-178 (179)
452 COG5185 HEC1 Protein involved 27.2 98 0.0021 27.4 4.0 32 60-91 333-364 (622)
453 cd01107 HTH_BmrR Helix-Turn-He 27.2 1.9E+02 0.004 19.1 4.7 6 34-39 36-41 (108)
454 PF15188 CCDC-167: Coiled-coil 27.2 1.3E+02 0.0028 20.1 3.9 32 58-89 37-68 (85)
455 PF11382 DUF3186: Protein of u 27.1 1.5E+02 0.0033 23.5 4.9 29 61-89 36-64 (308)
456 PF13094 CENP-Q: CENP-Q, a CEN 27.1 2.3E+02 0.0049 20.0 5.4 18 72-89 63-80 (160)
457 PRK00736 hypothetical protein; 27.1 1.7E+02 0.0036 18.4 6.2 23 66-88 21-43 (68)
458 PRK02935 hypothetical protein; 27.1 23 0.00051 24.9 0.2 24 12-44 70-93 (110)
459 KOG3156 Uncharacterized membra 27.0 1E+02 0.0022 24.1 3.8 23 71-93 116-138 (220)
460 PRK09239 chorismate mutase; Pr 27.0 2E+02 0.0044 19.4 5.3 34 54-87 7-40 (104)
461 COG4839 FtsL Protein required 26.8 1.7E+02 0.0037 20.9 4.6 27 63-89 66-92 (120)
462 PRK02195 V-type ATP synthase s 26.8 2.7E+02 0.0059 20.8 6.1 29 65-93 127-155 (201)
463 COG2260 Predicted Zn-ribbon RN 26.7 28 0.00062 22.0 0.6 12 13-24 18-29 (59)
464 PRK07111 anaerobic ribonucleos 26.7 30 0.00066 31.0 0.9 23 11-45 679-701 (735)
465 PRK04179 rpl37e 50S ribosomal 26.7 46 0.001 21.2 1.5 32 4-45 6-40 (62)
466 PF01813 ATP-synt_D: ATP synth 26.6 1.9E+02 0.0041 21.1 5.0 30 58-87 23-52 (196)
467 PRK13848 conjugal transfer pro 26.6 2.1E+02 0.0046 19.8 4.9 16 68-83 7-22 (98)
468 smart00400 ZnF_CHCC zinc finge 26.6 49 0.0011 19.4 1.6 27 14-44 4-30 (55)
469 PF09738 DUF2051: Double stran 26.6 1.2E+02 0.0026 24.5 4.2 34 66-99 221-254 (302)
470 PF00816 Histone_HNS: H-NS his 26.5 1.8E+02 0.0038 18.7 4.4 15 62-76 3-17 (93)
471 KOG2767 Translation initiation 26.5 26 0.00056 29.5 0.4 36 13-51 97-132 (400)
472 PRK05771 V-type ATP synthase s 26.4 2.3E+02 0.0051 24.5 6.2 21 65-85 223-243 (646)
473 PF13913 zf-C2HC_2: zinc-finge 26.2 32 0.00069 17.6 0.6 9 13-21 3-11 (25)
474 PRK04860 hypothetical protein; 26.2 23 0.00051 25.9 0.1 38 13-51 120-158 (160)
475 PF05600 DUF773: Protein of un 26.1 1.8E+02 0.0038 25.0 5.4 32 59-90 462-493 (507)
476 PRK02119 hypothetical protein; 26.0 1.8E+02 0.0039 18.5 6.2 24 66-89 25-48 (73)
477 PF12718 Tropomyosin_1: Tropom 26.0 2.4E+02 0.0053 20.0 6.1 20 70-89 34-53 (143)
478 PF10825 DUF2752: Protein of u 25.9 30 0.00065 20.7 0.5 8 13-20 10-17 (52)
479 PHA03162 hypothetical protein; 25.9 1.3E+02 0.0027 22.0 3.8 22 66-87 15-36 (135)
480 COG1579 Zn-ribbon protein, pos 25.9 1.7E+02 0.0038 22.9 4.9 18 71-88 52-69 (239)
481 TIGR00686 phnA alkylphosphonat 25.7 29 0.00063 24.4 0.5 30 13-51 3-32 (109)
482 PRK14140 heat shock protein Gr 25.7 3E+02 0.0064 20.8 6.0 26 63-88 43-68 (191)
483 PRK09039 hypothetical protein; 25.7 1.9E+02 0.0041 23.4 5.2 19 69-87 142-160 (343)
484 PRK14143 heat shock protein Gr 25.6 3E+02 0.0065 21.4 6.2 29 60-88 70-98 (238)
485 PF04296 DUF448: Protein of un 25.6 28 0.00061 22.2 0.4 14 29-42 32-45 (78)
486 PF08181 DegQ: DegQ (SacQ) fam 25.5 1.4E+02 0.0031 17.8 3.4 14 64-77 18-31 (46)
487 KOG0977 Nuclear envelope prote 25.4 1.8E+02 0.0038 25.7 5.3 32 60-91 165-196 (546)
488 PF02388 FemAB: FemAB family; 25.3 2.4E+02 0.0051 23.1 5.8 19 73-91 275-293 (406)
489 PF01302 CAP_GLY: CAP-Gly doma 25.3 32 0.00068 21.5 0.6 15 34-48 49-64 (69)
490 PF04194 PDCD2_C: Programmed c 25.2 51 0.0011 23.8 1.7 19 3-21 88-106 (164)
491 PRK02793 phi X174 lysis protei 25.1 1.9E+02 0.0041 18.3 6.2 39 57-95 15-53 (72)
492 PF10146 zf-C4H2: Zinc finger- 25.1 2.2E+02 0.0048 22.0 5.3 33 57-89 60-92 (230)
493 KOG3277 Uncharacterized conser 25.1 39 0.00084 25.4 1.1 33 15-47 82-114 (165)
494 PF04475 DUF555: Protein of un 25.0 50 0.0011 23.0 1.6 21 9-29 44-66 (102)
495 PF04111 APG6: Autophagy prote 25.0 3.2E+02 0.0069 21.8 6.4 39 57-95 50-88 (314)
496 TIGR01807 CM_P2 chorismate mut 24.9 1.8E+02 0.0039 18.1 4.7 28 60-87 2-29 (76)
497 PF04568 IATP: Mitochondrial A 24.9 2.3E+02 0.0051 19.3 5.4 35 55-89 53-94 (100)
498 COG1779 C4-type Zn-finger prot 24.9 54 0.0012 25.3 1.9 30 15-45 17-51 (201)
499 PF04981 NMD3: NMD3 family ; 24.7 26 0.00057 26.5 0.2 19 15-43 1-19 (236)
500 PF10211 Ax_dynein_light: Axon 24.7 2.9E+02 0.0064 20.4 5.9 36 60-95 123-158 (189)
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=99.68 E-value=2.5e-17 Score=97.72 Aligned_cols=38 Identities=42% Similarity=0.907 Sum_probs=35.9
Q ss_pred ccccCccccceeeeec-CCCCCCcceeeCC-----CCCeeEeccC
Q 041503 13 QVCNECGGQIELFTSH-TTKNPNRKFWKCR-----VCKNFQWAED 51 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~-t~~NPgR~Fy~C~-----~C~fF~W~De 51 (99)
|.| .||.+++++||+ +.+||||+||+|| .|+||+|+||
T Consensus 1 p~C-~Cg~~~~~~~s~k~~~N~GR~Fy~C~~~~~~~C~fF~W~De 44 (45)
T PF06839_consen 1 PKC-PCGEPAVRRTSKKTGPNPGRRFYKCPNYKDKGCNFFQWEDE 44 (45)
T ss_pred CCC-CCCCEeEEEEEeCCCCCCCCcceECCCCCCCCcCCEEeccC
Confidence 589 699999999999 9999999999999 5999999997
No 2
>KOG1956 consensus DNA topoisomerase III alpha [Replication, recombination and repair]
Probab=98.00 E-value=3.6e-06 Score=73.44 Aligned_cols=36 Identities=36% Similarity=0.932 Sum_probs=33.6
Q ss_pred ccccCccc-cceeeeecCCCCCCcceeeCC---CCCeeEec
Q 041503 13 QVCNECGG-QIELFTSHTTKNPNRKFWKCR---VCKNFQWA 49 (99)
Q Consensus 13 ~~Cp~Cg~-~~~~~tS~t~~NPgR~Fy~C~---~C~fF~W~ 49 (99)
+.| .||. .+.+++.++..|-||+||+|+ +|.||.|+
T Consensus 719 ~~c-~c~~ra~~l~v~k~~~nrGR~f~sc~~~k~c~ff~w~ 758 (758)
T KOG1956|consen 719 VTC-GCGTRAVKLLVAKTEPNRGRKFYSCLPEKSCNFFAWE 758 (758)
T ss_pred ccc-CCcchhhhhhhhccCccCCCCCcccCCCCCcceEeeC
Confidence 899 9998 888899999999999999999 59999995
No 3
>PF05325 DUF730: Protein of unknown function (DUF730); InterPro: IPR007989 This family consists of several uncharacterised Arabidopsis thaliana proteins of unknown function.
Probab=97.43 E-value=0.00079 Score=47.20 Aligned_cols=39 Identities=18% Similarity=0.507 Sum_probs=36.2
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCC---------CCCeeEeccCC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCR---------VCKNFQWAEDR 52 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~---------~C~fF~W~De~ 52 (99)
+.| .|+..+++-||..+-..|..||.|| +|+|-.|.--+
T Consensus 21 ie~-dcnakvvvats~dpvts~klyfscpyeisdg~g~~~gfkrwwtva 68 (122)
T PF05325_consen 21 IEC-DCNAKVVVATSRDPVTSGKLYFSCPYEISDGPGRGCGFKRWWTVA 68 (122)
T ss_pred eec-cCCceEEEEeccCCcccceeeecCccccccCCCCCccceeEEeee
Confidence 889 9999999999999999999999999 89999998554
No 4
>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=97.30 E-value=0.00036 Score=40.28 Aligned_cols=34 Identities=29% Similarity=0.610 Sum_probs=29.0
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCC---CCCeeEeccC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCR---VCKNFQWAED 51 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~---~C~fF~W~De 51 (99)
..||.||..++++.++.. .||.|. .|+|..|...
T Consensus 2 ~~CP~Cg~~lv~r~~k~g-----~F~~Cs~yP~C~~~~~~~~ 38 (39)
T PF01396_consen 2 EKCPKCGGPLVLRRGKKG-----KFLGCSNYPECKYTEPLPK 38 (39)
T ss_pred cCCCCCCceeEEEECCCC-----CEEECCCCCCcCCeEeCCC
Confidence 579999988888887765 999998 7999999764
No 5
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=97.03 E-value=0.00043 Score=50.71 Aligned_cols=31 Identities=26% Similarity=0.509 Sum_probs=23.7
Q ss_pred cccCccccc-eeeeecC--CCCCCcceeeCCCCC
Q 041503 14 VCNECGGQI-ELFTSHT--TKNPNRKFWKCRVCK 44 (99)
Q Consensus 14 ~Cp~Cg~~~-~~~tS~t--~~NPgR~Fy~C~~C~ 44 (99)
+||.||.+. .+..|+- +.|--|+||.||.|+
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~ 35 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACG 35 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccC
Confidence 799999877 6666653 355678899999776
No 6
>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=95.98 E-value=0.0075 Score=36.42 Aligned_cols=33 Identities=18% Similarity=0.482 Sum_probs=25.1
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCe
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKN 45 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~f 45 (99)
.-||.||.....+.+.....-++.+|.|..|+.
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga 34 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDLSHYFECSTCGA 34 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCCEEEEECCCCCC
Confidence 469999998886665555555677778998884
No 7
>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=95.35 E-value=0.0095 Score=35.30 Aligned_cols=31 Identities=23% Similarity=0.575 Sum_probs=25.2
Q ss_pred cccCccccceeeeecCCC-CCCcceeeCC--CCC
Q 041503 14 VCNECGGQIELFTSHTTK-NPNRKFWKCR--VCK 44 (99)
Q Consensus 14 ~Cp~Cg~~~~~~tS~t~~-NPgR~Fy~C~--~C~ 44 (99)
.||.||.++.+++|+... .-...||.|. .|+
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~~Cg 34 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSPLTRELYCQCTNPECG 34 (47)
T ss_pred CcCCCCCeeEEEEchhhCcceEEEEEEECCCcCC
Confidence 599999999999998774 4457788998 576
No 8
>KOG4399 consensus C2HC-type Zn-finger protein [General function prediction only]
Probab=95.32 E-value=0.012 Score=47.31 Aligned_cols=42 Identities=26% Similarity=0.598 Sum_probs=35.3
Q ss_pred CCcccccCccccceeeeecCCCCCCcceeeCC-------CCCeeEeccCCc
Q 041503 10 NSLQVCNECGGQIELFTSHTTKNPNRKFWKCR-------VCKNFQWAEDRK 53 (99)
Q Consensus 10 ~~~~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~-------~C~fF~W~De~~ 53 (99)
+..+.||. +++.+++..|.+---|+||.|. -|+||.|.|+..
T Consensus 11 ~~~P~C~H--GP~LLF~K~~~~E~~~~F~ACs~~R~d~kfC~F~~~~d~~~ 59 (325)
T KOG4399|consen 11 VPAPLCPH--GPTLLFVKVTQKEETRRFYACSACRMDDKFCHFFMFEDEFF 59 (325)
T ss_pred CCCCcCCC--CCeEEEEEccCcchheeeehhhhhhcchhccchhhhccccc
Confidence 44577865 7889999999988899999999 589999999973
No 9
>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=94.89 E-value=0.027 Score=32.29 Aligned_cols=33 Identities=24% Similarity=0.670 Sum_probs=22.3
Q ss_pred ccccCccccceeee---ecCCCCCCcceeeCCCCCe
Q 041503 13 QVCNECGGQIELFT---SHTTKNPNRKFWKCRVCKN 45 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~t---S~t~~NPgR~Fy~C~~C~f 45 (99)
+.||.||..-..++ .++.+.|--.||.|..|+.
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 46999997544433 4456889999999999984
No 10
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=94.85 E-value=0.02 Score=37.37 Aligned_cols=32 Identities=19% Similarity=0.448 Sum_probs=27.0
Q ss_pred ccccCccccceeeeecCCC-CCCcceeeCC--CCC
Q 041503 13 QVCNECGGQIELFTSHTTK-NPNRKFWKCR--VCK 44 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~-NPgR~Fy~C~--~C~ 44 (99)
..||.||..+.+++|+... .--++||.|. .|+
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~~~~~Y~qC~N~eCg 36 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDTTKERYHQCQNVNCS 36 (72)
T ss_pred ccCCCCCCccEEEEChhcChhhheeeeecCCCCCC
Confidence 4799999999999998774 4568999999 776
No 11
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=94.17 E-value=0.022 Score=36.35 Aligned_cols=29 Identities=24% Similarity=0.548 Sum_probs=21.3
Q ss_pred ccccCccccceeeee--cCCCCCCcceeeCCCCCe
Q 041503 13 QVCNECGGQIELFTS--HTTKNPNRKFWKCRVCKN 45 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS--~t~~NPgR~Fy~C~~C~f 45 (99)
..||.||...+.+-. +...|| |+||.|+|
T Consensus 28 F~CPnCGe~~I~Rc~~CRk~g~~----Y~Cp~CGF 58 (61)
T COG2888 28 FPCPNCGEVEIYRCAKCRKLGNP----YRCPKCGF 58 (61)
T ss_pred eeCCCCCceeeehhhhHHHcCCc----eECCCcCc
Confidence 789999977666543 333444 99999998
No 12
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=94.13 E-value=0.061 Score=31.00 Aligned_cols=32 Identities=25% Similarity=0.810 Sum_probs=24.1
Q ss_pred cccCcccc-ceeee--ecCCCCCCcceeeCCCCCe
Q 041503 14 VCNECGGQ-IELFT--SHTTKNPNRKFWKCRVCKN 45 (99)
Q Consensus 14 ~Cp~Cg~~-~~~~t--S~t~~NPgR~Fy~C~~C~f 45 (99)
.||.||.. ++-+. .++.+.|--.||.|..|++
T Consensus 2 ~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~ 36 (40)
T smart00440 2 PCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGH 36 (40)
T ss_pred cCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCC
Confidence 69999975 44333 3556888899999999984
No 13
>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=93.95 E-value=0.012 Score=36.96 Aligned_cols=34 Identities=38% Similarity=0.857 Sum_probs=21.2
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCC-CCC---eeEeccCC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCR-VCK---NFQWAEDR 52 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~-~C~---fF~W~De~ 52 (99)
+.||.||+++. ++..||-|+| |. .|+ +-.|.++.
T Consensus 3 v~CP~C~k~~~----~~~~n~~rPF--CS~RCk~iDLg~W~~e~ 40 (57)
T PF03884_consen 3 VKCPICGKPVE----WSPENPFRPF--CSERCKLIDLGRWANEE 40 (57)
T ss_dssp EE-TTT--EEE-----SSSSS--SS--SSHHHHHHHHS-SSSSS
T ss_pred ccCCCCCCeec----ccCCCCcCCc--ccHhhcccCHHHHhcCC
Confidence 67999998765 4688999999 55 564 88999887
No 14
>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=93.93 E-value=0.058 Score=31.58 Aligned_cols=27 Identities=26% Similarity=0.746 Sum_probs=20.4
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCe
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKN 45 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~f 45 (99)
+.||.||.....++.. +..|+|..|+.
T Consensus 19 ~~CP~Cg~~~~~~~~~------~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGSTKHYRLKT------RGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCeeeEEeCC------CCeEECCCCCC
Confidence 7799999874444443 88999998873
No 15
>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=93.80 E-value=0.18 Score=34.89 Aligned_cols=66 Identities=20% Similarity=0.322 Sum_probs=36.0
Q ss_pred ccccCccccceeeeecCCCCC-----CcceeeCCCCCeeEeccCCccchhhHHHHHHHHHHHHHHHHHHHHHH
Q 041503 13 QVCNECGGQIELFTSHTTKNP-----NRKFWKCRVCKNFQWAEDRKFSNEKIDLLVEEVRKLTLEIERLSDKF 80 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NP-----gR~Fy~C~~C~fF~W~De~~~~~~k~~~l~~ei~e~~~ei~~l~~k~ 80 (99)
+.||.||.++++.. ...-=| +--+|.|..|+-++=+-..+ .-|..-+...++|+...+.-++=+++
T Consensus 3 ~~CpYCg~~~~l~~-~~~iYg~~~~~~~~~y~C~~C~AyVG~H~~t-~~PlGtLAd~~lR~~R~~ah~~fd~l 73 (102)
T PF11672_consen 3 IICPYCGGPAELVD-GSEIYGHRYDDGPYLYVCTPCDAYVGCHPGT-DIPLGTLADAELRRARKAAHRAFDPL 73 (102)
T ss_pred cccCCCCCeeEEcc-cchhcCccCCCCceeEECCCCCceeeeeCCC-CCcCcccCCHHHHHHHHHHHHHHHHH
Confidence 68999999888744 333222 22359999998665554432 12222222335665544444433333
No 16
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=93.56 E-value=0.039 Score=34.99 Aligned_cols=29 Identities=24% Similarity=0.524 Sum_probs=20.4
Q ss_pred ccccCccccceeeeec--CCCCCCcceeeCCCCCe
Q 041503 13 QVCNECGGQIELFTSH--TTKNPNRKFWKCRVCKN 45 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~--t~~NPgR~Fy~C~~C~f 45 (99)
..||.||...+.+=.+ ...| -|+||.|+|
T Consensus 26 F~CPnCG~~~I~RC~~CRk~~~----~Y~CP~CGF 56 (59)
T PRK14890 26 FLCPNCGEVIIYRCEKCRKQSN----PYTCPKCGF 56 (59)
T ss_pred eeCCCCCCeeEeechhHHhcCC----ceECCCCCC
Confidence 8899999875555332 2232 399999998
No 17
>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=93.47 E-value=0.066 Score=38.09 Aligned_cols=40 Identities=20% Similarity=0.700 Sum_probs=29.1
Q ss_pred ccccCccccceeeeec--------CCCCCCcceeeCCCCCeeEeccCC
Q 041503 13 QVCNECGGQIELFTSH--------TTKNPNRKFWKCRVCKNFQWAEDR 52 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~--------t~~NPgR~Fy~C~~C~fF~W~De~ 52 (99)
..||.|+.+....... ...++...||.||+|+=..|...+
T Consensus 92 sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~GsH 139 (147)
T PF01927_consen 92 SRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEGSH 139 (147)
T ss_pred CccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEeccccc
Confidence 6899999854433222 234567789999999999998765
No 18
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=93.38 E-value=0.021 Score=36.48 Aligned_cols=35 Identities=31% Similarity=0.723 Sum_probs=27.4
Q ss_pred cccccCccccceeeeecCCCCCCcceeeCC-CC---CeeEeccCC
Q 041503 12 LQVCNECGGQIELFTSHTTKNPNRKFWKCR-VC---KNFQWAEDR 52 (99)
Q Consensus 12 ~~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~-~C---~fF~W~De~ 52 (99)
.+.||.||+++. ++..||-|+| |. .| .+-.|.++.
T Consensus 6 ~v~CP~C~k~~~----w~~~~~~rPF--CS~RCk~IDLg~W~~e~ 44 (62)
T PRK00418 6 TVNCPTCGKPVE----WGEISPFRPF--CSKRCQLIDLGEWAAEE 44 (62)
T ss_pred cccCCCCCCccc----ccCCCCcCCc--ccHHHHhhhHHHHHcCC
Confidence 478999999754 4678999998 44 55 488999886
No 19
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=93.30 E-value=0.075 Score=31.26 Aligned_cols=28 Identities=18% Similarity=0.653 Sum_probs=21.5
Q ss_pred CCcccccCccccceeeeecCCCCCCcceeeCC
Q 041503 10 NSLQVCNECGGQIELFTSHTTKNPNRKFWKCR 41 (99)
Q Consensus 10 ~~~~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~ 41 (99)
.+.+.|+.||......+.+ .++.+|.|.
T Consensus 3 ~g~l~C~~CG~~m~~~~~~----~~~~yy~C~ 30 (58)
T PF13408_consen 3 SGLLRCGHCGSKMTRRKRK----GKYRYYRCS 30 (58)
T ss_pred CCcEEcccCCcEeEEEECC----CCceEEEcC
Confidence 3568999999988875433 455999999
No 20
>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=92.86 E-value=0.12 Score=34.43 Aligned_cols=38 Identities=26% Similarity=0.761 Sum_probs=28.1
Q ss_pred cccccCccccceeee---ecCCCCCCcceeeCCCCCeeEecc
Q 041503 12 LQVCNECGGQIELFT---SHTTKNPNRKFWKCRVCKNFQWAE 50 (99)
Q Consensus 12 ~~~Cp~Cg~~~~~~t---S~t~~NPgR~Fy~C~~C~fF~W~D 50 (99)
...||.||..-..+. -++.+.|-=.||.|..|++ +|.|
T Consensus 62 ~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~-~w~~ 102 (104)
T TIGR01384 62 RVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGY-VWRE 102 (104)
T ss_pred cCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCC-eeEe
Confidence 389999997544444 3455778899999999996 5654
No 21
>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=92.39 E-value=0.089 Score=32.51 Aligned_cols=27 Identities=22% Similarity=0.566 Sum_probs=23.1
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCee
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNF 46 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF 46 (99)
..||.||..... ++..+-|.||.|++.
T Consensus 29 q~C~~CG~~~~~-------~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 29 QTCPRCGHRNKK-------RRSGRVFTCPNCGFE 55 (69)
T ss_pred cCccCccccccc-------ccccceEEcCCCCCE
Confidence 679999987665 778889999999987
No 22
>PHA00626 hypothetical protein
Probab=92.33 E-value=0.13 Score=32.64 Aligned_cols=36 Identities=17% Similarity=0.285 Sum_probs=23.2
Q ss_pred cccCccccceeeeecCCCCCCcceeeCCCCCeeEeccC
Q 041503 14 VCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQWAED 51 (99)
Q Consensus 14 ~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~W~De 51 (99)
.||.||..-+++ +.+-.. -|.-|+|+.|+|+-=.|.
T Consensus 2 ~CP~CGS~~Ivr-cg~cr~-~snrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 2 SCPKCGSGNIAK-EKTMRG-WSDDYVCCDCGYNDSKDA 37 (59)
T ss_pred CCCCCCCceeee-eceecc-cCcceEcCCCCCeechhh
Confidence 699999854442 222222 255699999998865554
No 23
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=92.31 E-value=0.16 Score=28.65 Aligned_cols=31 Identities=26% Similarity=0.635 Sum_probs=17.4
Q ss_pred cccCccccceeeeecCCCCCCcceeeCCCCCeeE
Q 041503 14 VCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQ 47 (99)
Q Consensus 14 ~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~ 47 (99)
.||.||.++...+-.. =+|.=+.|+.|++..
T Consensus 2 fC~~CG~~l~~~ip~g---d~r~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEG---DDRERLVCPACGFIH 32 (34)
T ss_dssp B-TTT--B-EEE--TT----SS-EEEETTTTEEE
T ss_pred ccccccChhhhhcCCC---CCccceECCCCCCEE
Confidence 5999999987776532 256667899999864
No 24
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=91.94 E-value=0.23 Score=28.90 Aligned_cols=34 Identities=21% Similarity=0.509 Sum_probs=22.5
Q ss_pred cccCccccceeeeecCCCCCCcceeeCCCCCeeEeccCC
Q 041503 14 VCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQWAEDR 52 (99)
Q Consensus 14 ~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~W~De~ 52 (99)
.||.||..+... . ..++.+|.||.|+|-...+..
T Consensus 2 FCp~Cg~~l~~~--~---~~~~~~~vC~~Cg~~~~~~~~ 35 (52)
T smart00661 2 FCPKCGNMLIPK--E---GKEKRRFVCRKCGYEEPIEQK 35 (52)
T ss_pred CCCCCCCccccc--c---CCCCCEEECCcCCCeEECCCc
Confidence 589999844322 1 112358899999987776654
No 25
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=91.40 E-value=0.13 Score=38.19 Aligned_cols=20 Identities=25% Similarity=0.415 Sum_probs=12.9
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 041503 72 EIERLSDKFRLLHKELEHTQ 91 (99)
Q Consensus 72 ei~~l~~k~~~l~~El~~~~ 91 (99)
.++.|+++|..|++|+.+..
T Consensus 154 ~~~~l~~~I~~l~~~~~~~~ 173 (178)
T PRK06266 154 LIKELKEQIKELEEELKLNP 173 (178)
T ss_pred HHHHHHHHHHHHHHHhcccc
Confidence 35666667777777776543
No 26
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=91.09 E-value=0.18 Score=35.02 Aligned_cols=33 Identities=24% Similarity=0.821 Sum_probs=26.3
Q ss_pred ccccCccc-cceeee--ecCCCCCCcceeeCCCCCe
Q 041503 13 QVCNECGG-QIELFT--SHTTKNPNRKFWKCRVCKN 45 (99)
Q Consensus 13 ~~Cp~Cg~-~~~~~t--S~t~~NPgR~Fy~C~~C~f 45 (99)
..||.||. .+.-++ .++.+.|-=+||+|..|+|
T Consensus 73 ~~CpkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~ 108 (113)
T COG1594 73 EKCPKCGNKEAYYWQLQTRSADEPETRFYKCTRCGY 108 (113)
T ss_pred ccCCCCCCceeEEEeeehhccCCCceEEEEecccCC
Confidence 67999996 455554 4556999999999999996
No 27
>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=90.74 E-value=0.13 Score=40.02 Aligned_cols=30 Identities=17% Similarity=0.630 Sum_probs=15.3
Q ss_pred ccccCcccc-ceeeeecCCCCCCcceeeCCCC
Q 041503 13 QVCNECGGQ-IELFTSHTTKNPNRKFWKCRVC 43 (99)
Q Consensus 13 ~~Cp~Cg~~-~~~~tS~t~~NPgR~Fy~C~~C 43 (99)
..||-||.. ..-.+..... .|+||..|.-|
T Consensus 173 g~CPvCGs~P~~s~l~~~~~-~G~R~L~Cs~C 203 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGER-EGKRYLHCSLC 203 (290)
T ss_dssp SS-TTT---EEEEEEE-------EEEEEETTT
T ss_pred CcCCCCCCcCceEEEecCCC-CccEEEEcCCC
Confidence 799999974 5555555555 89999999833
No 28
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=89.99 E-value=0.2 Score=35.58 Aligned_cols=40 Identities=18% Similarity=0.476 Sum_probs=25.9
Q ss_pred CCCCCcccccCccccceeeee---cCCCCCCcceeeCCCCCee
Q 041503 7 ESRNSLQVCNECGGQIELFTS---HTTKNPNRKFWKCRVCKNF 46 (99)
Q Consensus 7 ~~~~~~~~Cp~Cg~~~~~~tS---~t~~NPgR~Fy~C~~C~fF 46 (99)
++.+-.-+||.||-.-..+.. ++.+---=-||.|+.|+|=
T Consensus 69 ~ga~I~~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k 111 (116)
T KOG2907|consen 69 DGAVIKHKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYK 111 (116)
T ss_pred cccchhccCcccCCchhhhhhhhcccccCCceEEEEcCcccee
Confidence 344444899999975444433 3334444689999999873
No 29
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=89.50 E-value=0.41 Score=30.80 Aligned_cols=31 Identities=19% Similarity=0.490 Sum_probs=21.7
Q ss_pred CCcccccCccccceeeeecCCCCCCcce-eeCCCCCe
Q 041503 10 NSLQVCNECGGQIELFTSHTTKNPNRKF-WKCRVCKN 45 (99)
Q Consensus 10 ~~~~~Cp~Cg~~~~~~tS~t~~NPgR~F-y~C~~C~f 45 (99)
+++.-||+||...+.... ++..| +.|.+|+-
T Consensus 4 d~lKPCPFCG~~~~~v~~-----~~g~~~v~C~~CgA 35 (64)
T PRK09710 4 DNVKPCPFCGCPSVTVKA-----ISGYYRAKCNGCES 35 (64)
T ss_pred ccccCCCCCCCceeEEEe-----cCceEEEEcCCCCc
Confidence 455789999987666653 23344 78888875
No 30
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=88.99 E-value=0.33 Score=31.33 Aligned_cols=37 Identities=24% Similarity=0.638 Sum_probs=28.2
Q ss_pred cccccCccccceeeeecCCCCCCccee--eCCCCCeeEeccCC
Q 041503 12 LQVCNECGGQIELFTSHTTKNPNRKFW--KCRVCKNFQWAEDR 52 (99)
Q Consensus 12 ~~~Cp~Cg~~~~~~tS~t~~NPgR~Fy--~C~~C~fF~W~De~ 52 (99)
.+.||-||+++ .|++.||-|+|- +|..=.+=.|.++.
T Consensus 7 ~v~CP~Cgkpv----~w~~~s~frPFCSkRCklIDLg~Wa~ee 45 (65)
T COG3024 7 TVPCPTCGKPV----VWGEESPFRPFCSKRCKLIDLGEWAAEE 45 (65)
T ss_pred cccCCCCCCcc----cccccCCcCcchhHhhhhcchhhhhccC
Confidence 48999999986 488999999993 23333467898886
No 31
>PF14353 CpXC: CpXC protein
Probab=88.93 E-value=0.34 Score=33.27 Aligned_cols=32 Identities=25% Similarity=0.734 Sum_probs=21.1
Q ss_pred ccccCcccc--ceeee-ecCCCCCC--------cc-eeeCCCCC
Q 041503 13 QVCNECGGQ--IELFT-SHTTKNPN--------RK-FWKCRVCK 44 (99)
Q Consensus 13 ~~Cp~Cg~~--~~~~t-S~t~~NPg--------R~-Fy~C~~C~ 44 (99)
+.||.||.. +.+++ .++..+|. .- .|+||+|+
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg 45 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCG 45 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCC
Confidence 579999974 44444 34456662 22 49999997
No 32
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []. These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle
Probab=88.92 E-value=2.2 Score=26.32 Aligned_cols=29 Identities=34% Similarity=0.454 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 61 LLVEEVRKLTLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 61 ~l~~ei~e~~~ei~~l~~k~~~l~~El~~ 89 (99)
.+..++.++..+++.++++++.|+.|++.
T Consensus 21 ~~~~ei~~l~~~i~~l~~e~~~L~~ei~~ 49 (80)
T PF04977_consen 21 QLNQEIAELQKEIEELKKENEELKEEIER 49 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445555555566665555555555544
No 33
>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=88.55 E-value=0.37 Score=26.67 Aligned_cols=31 Identities=19% Similarity=0.445 Sum_probs=20.4
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCe
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKN 45 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~f 45 (99)
+.||.||..-.+-.+.-..+.+ -.+||.|+.
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~--~v~C~~C~~ 33 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGG--KVRCGKCGH 33 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCC--EEECCCCCC
Confidence 5799999875555444433333 678999983
No 34
>PRK07220 DNA topoisomerase I; Validated
Probab=88.27 E-value=0.38 Score=42.47 Aligned_cols=36 Identities=17% Similarity=0.357 Sum_probs=23.7
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCeeEeccC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQWAED 51 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~W~De 51 (99)
..||.||.+.+... +. ..++.||.||.|+|..|...
T Consensus 636 ~~Cp~Cg~~~~k~~-~~--g~~~~~~~Cp~C~~~~~~~~ 671 (740)
T PRK07220 636 KVCEAHGLNHIRII-NG--GKRPWDLGCPQCNFIEWQKK 671 (740)
T ss_pred CCCCCCCCceEEEE-ec--CCccceeeCCCCCCccccCC
Confidence 57999997543222 11 11223899999999888753
No 35
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=88.02 E-value=0.27 Score=35.01 Aligned_cols=39 Identities=13% Similarity=0.384 Sum_probs=24.7
Q ss_pred cccccCccccceeeeecCCCCCCcceeeCCCCCeeEeccC
Q 041503 12 LQVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQWAED 51 (99)
Q Consensus 12 ~~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~W~De 51 (99)
...||.||......-+....+|.+. |.||.|+--.=.++
T Consensus 99 ~Y~Cp~C~~~y~~~ea~~~~d~~~~-f~Cp~Cg~~l~~~d 137 (147)
T smart00531 99 YYKCPNCQSKYTFLEANQLLDMDGT-FTCPRCGEELEEDD 137 (147)
T ss_pred EEECcCCCCEeeHHHHHHhcCCCCc-EECCCCCCEEEEcC
Confidence 4789999976554444443345333 89999985444444
No 36
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=87.95 E-value=0.52 Score=26.80 Aligned_cols=32 Identities=22% Similarity=0.590 Sum_probs=22.1
Q ss_pred cccCccccceeeeecCCCCCCcceeeCCCCCeeEeccC
Q 041503 14 VCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQWAED 51 (99)
Q Consensus 14 ~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~W~De 51 (99)
+||.|+..+..... ++=.-+.|++|+= .|.|.
T Consensus 1 ~CP~C~~~l~~~~~-----~~~~id~C~~C~G-~W~d~ 32 (41)
T PF13453_consen 1 KCPRCGTELEPVRL-----GDVEIDVCPSCGG-IWFDA 32 (41)
T ss_pred CcCCCCcccceEEE-----CCEEEEECCCCCe-EEccH
Confidence 59999986554433 6678899999973 34444
No 37
>PF05377 FlaC_arch: Flagella accessory protein C (FlaC); InterPro: IPR008039 Although archaeal flagella appear superficially similar to those of bacteria, they are quite distinct []. In several archaea, the flagellin genes are followed immediately by the flagellar accessory genes flaCDEFGHIJ. The gene products may have a role in translocation, secretion, or assembly of the flagellum. FlaC is a protein whose exact role is unknown but it has been shown to be membrane-associated (by immuno-blotting fractionated cells) [].
Probab=87.81 E-value=1.9 Score=26.88 Aligned_cols=30 Identities=20% Similarity=0.325 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 59 IDLLVEEVRKLTLEIERLSDKFRLLHKELE 88 (99)
Q Consensus 59 ~~~l~~ei~e~~~ei~~l~~k~~~l~~El~ 88 (99)
++.|++++..+...+..++++++.++.+++
T Consensus 2 i~elEn~~~~~~~~i~tvk~en~~i~~~ve 31 (55)
T PF05377_consen 2 IDELENELPRIESSINTVKKENEEISESVE 31 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345555555555555555555555555444
No 38
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=87.71 E-value=0.67 Score=27.89 Aligned_cols=34 Identities=21% Similarity=0.411 Sum_probs=21.8
Q ss_pred cccccCccccceeeeecCCCCCCc-ceeeCCCCCe
Q 041503 12 LQVCNECGGQIELFTSHTTKNPNR-KFWKCRVCKN 45 (99)
Q Consensus 12 ~~~Cp~Cg~~~~~~tS~t~~NPgR-~Fy~C~~C~f 45 (99)
+.-||+||.+.+........+.+- -|..|..|+.
T Consensus 3 LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 3 LKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 357999976665555544444433 5566998987
No 39
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=87.29 E-value=2.8 Score=28.65 Aligned_cols=43 Identities=14% Similarity=0.069 Sum_probs=21.6
Q ss_pred hhhHHHHHHHHHHHHHHHHH-------HHHHHHHHHH--HHHHHHHHHhhcC
Q 041503 56 NEKIDLLVEEVRKLTLEIER-------LSDKFRLLHK--ELEHTQLRSKYGL 98 (99)
Q Consensus 56 ~~k~~~l~~ei~e~~~ei~~-------l~~k~~~l~~--El~~~~~~~~~~~ 98 (99)
|.....+.+++.++..++.+ |++++..|+. +.-++.-|.++|+
T Consensus 26 ~~~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~~~dyiEe~AR~~Lg~ 77 (105)
T PRK00888 26 ILDYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKGGQEAIEERARNELGM 77 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCcHHHHHHHHHHHcCC
Confidence 33444455555544444444 4444444443 3445555666665
No 40
>PRK01343 zinc-binding protein; Provisional
Probab=87.08 E-value=0.25 Score=31.04 Aligned_cols=32 Identities=25% Similarity=0.667 Sum_probs=23.5
Q ss_pred CcccccCccccceeeeecCCCCCCcceeeCC-CCC---eeEeccCC
Q 041503 11 SLQVCNECGGQIELFTSHTTKNPNRKFWKCR-VCK---NFQWAEDR 52 (99)
Q Consensus 11 ~~~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~-~C~---fF~W~De~ 52 (99)
..+.||-||+++. ++-|+| |. .|+ |-.|.++.
T Consensus 8 p~~~CP~C~k~~~--------~~~rPF--CS~RC~~iDLg~W~~e~ 43 (57)
T PRK01343 8 PTRPCPECGKPST--------REAYPF--CSERCRDIDLNRWLSGS 43 (57)
T ss_pred CCCcCCCCCCcCc--------CCCCcc--cCHHHhhhhHHHHhCCC
Confidence 4588999999853 467766 33 554 88999886
No 41
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=86.61 E-value=0.35 Score=40.76 Aligned_cols=32 Identities=28% Similarity=0.684 Sum_probs=23.4
Q ss_pred cccccCccccceeeeecCCCCCCcceeeCCCCCeeEeccC
Q 041503 12 LQVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQWAED 51 (99)
Q Consensus 12 ~~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~W~De 51 (99)
.++||.||..+ +.-||.-|+|+.|+.-.=.+.
T Consensus 350 ~p~Cp~Cg~~m--------~S~G~~g~rC~kCg~~~~~~~ 381 (421)
T COG1571 350 NPVCPRCGGRM--------KSAGRNGFRCKKCGTRARETL 381 (421)
T ss_pred CCCCCccCCch--------hhcCCCCcccccccccCCccc
Confidence 38999999754 445777999999986544433
No 42
>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=86.52 E-value=0.54 Score=40.18 Aligned_cols=32 Identities=22% Similarity=0.478 Sum_probs=23.8
Q ss_pred ccccCccccceee---eecCCC-CCCcceeeCCCCC
Q 041503 13 QVCNECGGQIELF---TSHTTK-NPNRKFWKCRVCK 44 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~---tS~t~~-NPgR~Fy~C~~C~ 44 (99)
+.||+||..-.+. +.+... .|..-.|.||+|+
T Consensus 201 vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg 236 (557)
T PF05876_consen 201 VPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCG 236 (557)
T ss_pred ccCCCCCCCccccccceeecCCCCccceEEECCCCc
Confidence 8999999744433 445443 7899999999885
No 43
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=86.29 E-value=0.59 Score=31.84 Aligned_cols=32 Identities=31% Similarity=0.718 Sum_probs=25.8
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCeeEeccCC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQWAEDR 52 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~W~De~ 52 (99)
..||.||...+.+++.. -|.|..|++ .|....
T Consensus 36 ~~Cp~C~~~~VkR~a~G-------IW~C~kCg~-~fAGga 67 (89)
T COG1997 36 HVCPFCGRTTVKRIATG-------IWKCRKCGA-KFAGGA 67 (89)
T ss_pred CcCCCCCCcceeeeccC-------eEEcCCCCC-eecccc
Confidence 78999999999999875 799999984 455443
No 44
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []. These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle
Probab=86.18 E-value=3 Score=25.67 Aligned_cols=42 Identities=26% Similarity=0.374 Sum_probs=29.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHH-H-HHHHHHHHHHhhcCC
Q 041503 58 KIDLLVEEVRKLTLEIERLSDKFRLL-H-KELEHTQLRSKYGLS 99 (99)
Q Consensus 58 k~~~l~~ei~e~~~ei~~l~~k~~~l-~-~El~~~~~~~~~~~~ 99 (99)
....+.+++.++..+.+.|+++++.| . .+--+..-+.+||++
T Consensus 25 ei~~l~~~i~~l~~e~~~L~~ei~~l~~~~~~ie~~AR~~lgm~ 68 (80)
T PF04977_consen 25 EIAELQKEIEELKKENEELKEEIERLKNDPDYIEKVAREKLGMV 68 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHcCCc
Confidence 34667778899999999999999988 2 333344445577763
No 45
>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=86.08 E-value=4.2 Score=27.62 Aligned_cols=32 Identities=25% Similarity=0.636 Sum_probs=25.1
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCeeEeccCC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQWAEDR 52 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~W~De~ 52 (99)
-.||.||...+.+++.. -|.|..|++ .|...+
T Consensus 36 y~Cp~Cgk~~vkR~a~G-------IW~C~~C~~-~~AGGA 67 (90)
T PF01780_consen 36 YTCPFCGKTSVKRVATG-------IWKCKKCGK-KFAGGA 67 (90)
T ss_dssp BEESSSSSSEEEEEETT-------EEEETTTTE-EEE-BS
T ss_pred CcCCCCCCceeEEeeeE-------EeecCCCCC-EEeCCC
Confidence 67999999999999875 699999994 555444
No 46
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=86.07 E-value=0.35 Score=36.14 Aligned_cols=39 Identities=26% Similarity=0.721 Sum_probs=27.8
Q ss_pred ccccCccccceeeeecCC---------CCCCcceeeCCCCCeeEeccCC
Q 041503 13 QVCNECGGQIELFTSHTT---------KNPNRKFWKCRVCKNFQWAEDR 52 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~---------~NPgR~Fy~C~~C~fF~W~De~ 52 (99)
..||.|+.+.... |... .-+-..||+||.|+=..|..-+
T Consensus 98 ~RCp~CN~~L~~v-s~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW~GsH 145 (165)
T COG1656 98 SRCPECNGELEKV-SREEVKEKVPEKVYRNYEEFYRCPKCGKIYWKGSH 145 (165)
T ss_pred ccCcccCCEeccC-cHHHHhhccchhhhhcccceeECCCCcccccCchH
Confidence 6899999865433 3322 1234679999999999998765
No 47
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=85.94 E-value=0.39 Score=25.54 Aligned_cols=9 Identities=44% Similarity=1.390 Sum_probs=6.2
Q ss_pred cccCccccc
Q 041503 14 VCNECGGQI 22 (99)
Q Consensus 14 ~Cp~Cg~~~ 22 (99)
.||.|+..+
T Consensus 2 ~CP~C~~~V 10 (26)
T PF10571_consen 2 TCPECGAEV 10 (26)
T ss_pred cCCCCcCCc
Confidence 577777655
No 48
>PHA02998 RNA polymerase subunit; Provisional
Probab=85.91 E-value=0.77 Score=35.11 Aligned_cols=34 Identities=21% Similarity=0.530 Sum_probs=26.6
Q ss_pred cccccCcccc-ce--eeeecCCCCCCcceeeCCCCCe
Q 041503 12 LQVCNECGGQ-IE--LFTSHTTKNPNRKFWKCRVCKN 45 (99)
Q Consensus 12 ~~~Cp~Cg~~-~~--~~tS~t~~NPgR~Fy~C~~C~f 45 (99)
...||.||.. +. ...-++.+-|-=.||+|..|++
T Consensus 143 ~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~ 179 (195)
T PHA02998 143 NTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKK 179 (195)
T ss_pred CCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCC
Confidence 4789999964 33 4446677899999999999984
No 49
>PF04880 NUDE_C: NUDE protein, C-terminal conserved region; InterPro: IPR006964 This domain represents the C-terminal conserved region of NUDE proteins. Emericella nidulans (Aspergillus nidulans) NUDE, acts in the cytoplasmic dynein/dynactin pathway and is required for distribution of nuclei []. It is a homologue of the nuclear distribution protein RO11 of Neurospora crassa. NUDE interacts with the NUDF via an N-terminal coiled coil domain; this is the only domain which is absolutely required for NUDE function.; PDB: 2V66_B 2V71_B.
Probab=85.65 E-value=0.55 Score=34.98 Aligned_cols=34 Identities=38% Similarity=0.506 Sum_probs=14.9
Q ss_pred chhhHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHH
Q 041503 55 SNEKIDLLVEEVR---KLTLEIERLSDKFRLLHKELE 88 (99)
Q Consensus 55 ~~~k~~~l~~ei~---e~~~ei~~l~~k~~~l~~El~ 88 (99)
+-++.++|+.||+ .|.++.-+|++..+.|++||.
T Consensus 12 AIERnalLE~ELdEKE~L~~~~QRLkDE~RDLKqEl~ 48 (166)
T PF04880_consen 12 AIERNALLESELDEKENLREEVQRLKDELRDLKQELI 48 (166)
T ss_dssp HHHHHHHHHHHHHHHHHHHHCH---------------
T ss_pred HHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5578899999886 466788899999999999993
No 50
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=85.53 E-value=0.35 Score=33.36 Aligned_cols=25 Identities=16% Similarity=0.434 Sum_probs=17.3
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCee
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNF 46 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF 46 (99)
..|+.||... .+...||.||.|+-+
T Consensus 71 ~~C~~Cg~~~---------~~~~~~~~CP~Cgs~ 95 (113)
T PRK12380 71 AWCWDCSQVV---------EIHQHDAQCPHCHGE 95 (113)
T ss_pred EEcccCCCEE---------ecCCcCccCcCCCCC
Confidence 7899999322 233467889999844
No 51
>PRK00420 hypothetical protein; Validated
Probab=85.46 E-value=3.1 Score=29.17 Aligned_cols=31 Identities=16% Similarity=0.294 Sum_probs=20.8
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCeeEeccC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQWAED 51 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~W~De 51 (99)
..||.||.+...+ +-|. .-||.|+-+.=+..
T Consensus 24 ~~CP~Cg~pLf~l------k~g~--~~Cp~Cg~~~~v~~ 54 (112)
T PRK00420 24 KHCPVCGLPLFEL------KDGE--VVCPVHGKVYIVKS 54 (112)
T ss_pred CCCCCCCCcceec------CCCc--eECCCCCCeeeecc
Confidence 6899999877654 2222 35999997655543
No 52
>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=84.94 E-value=1.1 Score=25.45 Aligned_cols=31 Identities=13% Similarity=0.484 Sum_probs=20.8
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCK 44 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~ 44 (99)
++||.|+..-.+. -+....-|..=|+|..|+
T Consensus 6 v~CP~C~s~~~v~-k~G~~~~G~qryrC~~C~ 36 (36)
T PF03811_consen 6 VHCPRCQSTEGVK-KNGKSPSGHQRYRCKDCR 36 (36)
T ss_pred eeCCCCCCCCcce-eCCCCCCCCEeEecCcCC
Confidence 7899999865221 223334478889999885
No 53
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=84.77 E-value=0.96 Score=36.59 Aligned_cols=30 Identities=17% Similarity=0.379 Sum_probs=21.2
Q ss_pred cccccCccccceeeeecCCCCCCcceeeCC
Q 041503 12 LQVCNECGGQIELFTSHTTKNPNRKFWKCR 41 (99)
Q Consensus 12 ~~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~ 41 (99)
...||-||...+.-+.......|.||..|.
T Consensus 187 ~~~CPvCGs~P~~s~v~~~~~~G~RyL~Cs 216 (309)
T PRK03564 187 RQFCPVCGSMPVSSVVQIGTTQGLRYLHCN 216 (309)
T ss_pred CCCCCCCCCcchhheeeccCCCCceEEEcC
Confidence 489999998654333333445799999998
No 54
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=84.33 E-value=3.7 Score=28.00 Aligned_cols=14 Identities=29% Similarity=0.339 Sum_probs=6.7
Q ss_pred HHHHHHHHHHHHHH
Q 041503 65 EVRKLTLEIERLSD 78 (99)
Q Consensus 65 ei~e~~~ei~~l~~ 78 (99)
+..+|..+|+.|++
T Consensus 49 ~n~~L~~eI~~L~~ 62 (105)
T PRK00888 49 RNDQLFAEIDDLKG 62 (105)
T ss_pred HHHHHHHHHHHhhC
Confidence 33344455555543
No 55
>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=84.05 E-value=0.34 Score=35.07 Aligned_cols=33 Identities=27% Similarity=0.604 Sum_probs=30.3
Q ss_pred cccccCccccceeeeecCCCCCCcceeeCCCCC
Q 041503 12 LQVCNECGGQIELFTSHTTKNPNRKFWKCRVCK 44 (99)
Q Consensus 12 ~~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~ 44 (99)
.+.||.||-.-...+|.=...+-|.-|+|..|.
T Consensus 105 ~~~cp~c~s~~t~~~s~fg~t~cka~~~c~~c~ 137 (146)
T TIGR02159 105 SVQCPRCGSADTTITSIFGPTACKALYRCRACK 137 (146)
T ss_pred CCcCCCCCCCCcEeecCCCChhhHHHhhhhhhC
Confidence 389999999999999999999999999999886
No 56
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=83.53 E-value=1.1 Score=30.81 Aligned_cols=32 Identities=22% Similarity=0.494 Sum_probs=22.1
Q ss_pred cccccCccccceeeeecCCCCCCcceeeCCCCCeeE
Q 041503 12 LQVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQ 47 (99)
Q Consensus 12 ~~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~ 47 (99)
.+.||.||.. .+.+... + |+.-..|+.|++..
T Consensus 21 ~f~CP~Cge~-~v~v~~~-k--~~~h~~C~~CG~y~ 52 (99)
T PRK14892 21 IFECPRCGKV-SISVKIK-K--NIAIITCGNCGLYT 52 (99)
T ss_pred EeECCCCCCe-EeeeecC-C--CcceEECCCCCCcc
Confidence 3899999953 2222222 2 79999999999764
No 57
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=83.44 E-value=0.99 Score=27.23 Aligned_cols=29 Identities=21% Similarity=0.657 Sum_probs=19.8
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCeeEec
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQWA 49 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~W~ 49 (99)
..||.||.. .+.... ..+.|+.|+|-.|.
T Consensus 21 ~fCP~Cg~~-~m~~~~-------~r~~C~~Cgyt~~~ 49 (50)
T PRK00432 21 KFCPRCGSG-FMAEHL-------DRWHCGKCGYTEFK 49 (50)
T ss_pred CcCcCCCcc-hheccC-------CcEECCCcCCEEec
Confidence 689999975 222221 46789999987663
No 58
>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=82.95 E-value=0.68 Score=36.78 Aligned_cols=26 Identities=19% Similarity=0.608 Sum_probs=20.7
Q ss_pred cccccCccccceeeeecCCCCCCcceeeCC
Q 041503 12 LQVCNECGGQIELFTSHTTKNPNRKFWKCR 41 (99)
Q Consensus 12 ~~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~ 41 (99)
+++|+.|++...++ ..=||++|.|||
T Consensus 85 VVkC~~CnEATPIr----~aPpGKKYVRCP 110 (256)
T PF09788_consen 85 VVKCSVCNEATPIR----NAPPGKKYVRCP 110 (256)
T ss_pred eEECCCCCcccccc----CCCCCCeeEecC
Confidence 38999999876664 345799999999
No 59
>PHA02942 putative transposase; Provisional
Probab=82.73 E-value=0.88 Score=37.27 Aligned_cols=27 Identities=19% Similarity=0.668 Sum_probs=20.0
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCeeE
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQ 47 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~ 47 (99)
..||.||.... .++.+.|.|+.|+|-.
T Consensus 326 q~Cs~CG~~~~--------~l~~r~f~C~~CG~~~ 352 (383)
T PHA02942 326 VSCPKCGHKMV--------EIAHRYFHCPSCGYEN 352 (383)
T ss_pred ccCCCCCCccC--------cCCCCEEECCCCCCEe
Confidence 67999997542 2345689999999854
No 60
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=82.61 E-value=0.91 Score=33.89 Aligned_cols=27 Identities=22% Similarity=0.570 Sum_probs=21.5
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCeeEeccC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQWAED 51 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~W~De 51 (99)
..||.||. .-.+-|.||.|++..=.|.
T Consensus 310 ~~C~~cg~------------~~~r~~~C~~cg~~~~rD~ 336 (364)
T COG0675 310 KTCPCCGH------------LSGRLFKCPRCGFVHDRDV 336 (364)
T ss_pred ccccccCC------------ccceeEECCCCCCeehhhH
Confidence 78999999 4467889999998765554
No 61
>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=82.39 E-value=1.4 Score=35.27 Aligned_cols=35 Identities=23% Similarity=0.661 Sum_probs=26.3
Q ss_pred CcccccCcccc-ceeee--ecCCCCCCcceeeCCCCCe
Q 041503 11 SLQVCNECGGQ-IELFT--SHTTKNPNRKFWKCRVCKN 45 (99)
Q Consensus 11 ~~~~Cp~Cg~~-~~~~t--S~t~~NPgR~Fy~C~~C~f 45 (99)
....||.||.. ++-+. .++.+.|=-.||.|..|++
T Consensus 257 ~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~ 294 (299)
T TIGR01385 257 DLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGN 294 (299)
T ss_pred ccccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCC
Confidence 35899999974 44443 3455788899999999984
No 62
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=81.72 E-value=0.78 Score=32.03 Aligned_cols=36 Identities=28% Similarity=0.851 Sum_probs=28.1
Q ss_pred ccccCcccc---ceeeeecCCCCCCcceeeCCCCCeeEec
Q 041503 13 QVCNECGGQ---IELFTSHTTKNPNRKFWKCRVCKNFQWA 49 (99)
Q Consensus 13 ~~Cp~Cg~~---~~~~tS~t~~NPgR~Fy~C~~C~fF~W~ 49 (99)
..||.||-. -..+.-++.+-|-=.||+|-.|+| .|-
T Consensus 66 ~~Cp~Cgh~rayF~qlQtRSADEPmT~FYkC~~C~~-~Wr 104 (105)
T KOG2906|consen 66 ATCPTCGHERAYFMQLQTRSADEPMTTFYKCCKCKH-RWR 104 (105)
T ss_pred CcCCCCCCCceEEEEeeeccCCCcHhHhhhhhcccc-ccc
Confidence 789999964 344456788999999999999985 454
No 63
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=81.59 E-value=1.1 Score=28.00 Aligned_cols=31 Identities=29% Similarity=0.494 Sum_probs=18.2
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCK 44 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~ 44 (99)
+.||.||....+.+-....=-+=+ .-||.|+
T Consensus 5 i~CP~CgnKTR~kir~DT~LkNfP-lyCpKCK 35 (55)
T PF14205_consen 5 ILCPICGNKTRLKIREDTVLKNFP-LYCPKCK 35 (55)
T ss_pred EECCCCCCccceeeecCceecccc-ccCCCCC
Confidence 679999977655554433222222 3378776
No 64
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=81.57 E-value=2.4 Score=28.35 Aligned_cols=15 Identities=20% Similarity=0.441 Sum_probs=9.8
Q ss_pred cceeeCCCCCeeEec
Q 041503 35 RKFWKCRVCKNFQWA 49 (99)
Q Consensus 35 R~Fy~C~~C~fF~W~ 49 (99)
-..|.|+.|+=-...
T Consensus 29 ~~~~~C~~CGe~~~~ 43 (127)
T TIGR03830 29 VPGWYCPACGEELLD 43 (127)
T ss_pred eeeeECCCCCCEEEc
Confidence 456789999844333
No 65
>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=81.32 E-value=0.69 Score=31.93 Aligned_cols=24 Identities=21% Similarity=0.884 Sum_probs=16.4
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCe
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKN 45 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~f 45 (99)
..|+.||.... +...++.||.|+-
T Consensus 71 ~~C~~Cg~~~~---------~~~~~~~CP~Cgs 94 (115)
T TIGR00100 71 CECEDCSEEVS---------PEIDLYRCPKCHG 94 (115)
T ss_pred EEcccCCCEEe---------cCCcCccCcCCcC
Confidence 78999994322 2233789999984
No 66
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=81.28 E-value=1.2 Score=31.57 Aligned_cols=32 Identities=16% Similarity=0.362 Sum_probs=21.8
Q ss_pred CcccccCccccceeeeecCCCCCCcceeeCCCCC
Q 041503 11 SLQVCNECGGQIELFTSHTTKNPNRKFWKCRVCK 44 (99)
Q Consensus 11 ~~~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~ 44 (99)
+.+.||.|+..-+.. .....-|..=|+|+.|+
T Consensus 29 ~~~~cP~C~s~~~~k--~g~~~~~~qRyrC~~C~ 60 (129)
T COG3677 29 TKVNCPRCKSSNVVK--IGGIRRGHQRYKCKSCG 60 (129)
T ss_pred ccCcCCCCCccceee--ECCccccccccccCCcC
Confidence 348999999877222 22233347789999998
No 67
>PRK07220 DNA topoisomerase I; Validated
Probab=80.68 E-value=1.5 Score=38.86 Aligned_cols=33 Identities=21% Similarity=0.417 Sum_probs=24.4
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCC---CCCeeEec
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCR---VCKNFQWA 49 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~---~C~fF~W~ 49 (99)
..||.||..++++.++. |.+||.|. .|+|..|.
T Consensus 590 ~~CP~Cg~~l~~r~~r~----g~~f~gCs~yp~C~~~~~l 625 (740)
T PRK07220 590 GKCPLCGSDLMVRRSKR----GSRFIGCEGYPECTFSLPL 625 (740)
T ss_pred cccccCCCeeeEEecCC----CceEEEcCCCCCCCceeeC
Confidence 58999998766654432 35699996 69988885
No 68
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=80.53 E-value=1.4 Score=34.35 Aligned_cols=27 Identities=22% Similarity=0.495 Sum_probs=21.5
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCK 44 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~ 44 (99)
..||.||.++...+.. ||.-|=||.|+
T Consensus 245 ~pCprCG~~I~~~~~~-----gR~t~~CP~CQ 271 (272)
T PRK14810 245 EPCLNCKTPIRRVVVA-----GRSSHYCPHCQ 271 (272)
T ss_pred CcCCCCCCeeEEEEEC-----CCccEECcCCc
Confidence 6799999877555443 69999999996
No 69
>KOG3896 consensus Dynactin, subunit p62 [Cell motility]
Probab=80.17 E-value=2.4 Score=35.62 Aligned_cols=48 Identities=25% Similarity=0.407 Sum_probs=35.7
Q ss_pred CCCeeEeccCC---------ccchhhHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 42 VCKNFQWAEDR---------KFSNEKID-LLVEEVRKLTLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 42 ~C~fF~W~De~---------~~~~~k~~-~l~~ei~e~~~ei~~l~~k~~~l~~El~~ 89 (99)
.|.|-.|-.-. +=+||... .+.+-+.++.+=+.+|..+++++..++++
T Consensus 107 ~C~~CRWtsRdvg~~Dq~vatg~Wp~~Enp~~~r~n~l~eY~q~Laek~Ek~e~drkK 164 (449)
T KOG3896|consen 107 VCQYCRWTSRDVGQEDQSVATGSWPTKENPLVNRLNELTEYMQRLAEKIEKAEKDRKK 164 (449)
T ss_pred eeeeeeccccccCCcccccccCCCCCCCCHHHHHHHHHHHHHHHHHHHHHhhHHHHhc
Confidence 57888887433 12898764 44667888888888898888898888887
No 70
>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=80.12 E-value=1.6 Score=32.26 Aligned_cols=31 Identities=19% Similarity=0.434 Sum_probs=15.6
Q ss_pred ccCccccceeeeecCCCCCC-c----ceeeCCCCCe
Q 041503 15 CNECGGQIELFTSHTTKNPN-R----KFWKCRVCKN 45 (99)
Q Consensus 15 Cp~Cg~~~~~~tS~t~~NPg-R----~Fy~C~~C~f 45 (99)
||.||......+-...+-|. | --|.|++|+|
T Consensus 1 CP~Cg~~~~~~~~~~~~IP~F~evii~sf~C~~CGy 36 (163)
T TIGR00340 1 CPVCGSRTLKAVTYDYDIPYFGKIMLSTYICEKCGY 36 (163)
T ss_pred CCCCCCcceEeeeEeccCCCcceEEEEEEECCCCCC
Confidence 66666654444334444443 1 1356666654
No 71
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=79.90 E-value=0.95 Score=31.36 Aligned_cols=24 Identities=21% Similarity=0.592 Sum_probs=15.4
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCK 44 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~ 44 (99)
..|+.||... .-+...|++||.|+
T Consensus 72 ~~C~~Cg~~~--------~~~~~~~~~CP~Cg 95 (117)
T PRK00564 72 LECKDCSHVF--------KPNALDYGVCEKCH 95 (117)
T ss_pred EEhhhCCCcc--------ccCCccCCcCcCCC
Confidence 7898899322 11233566799998
No 72
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=79.50 E-value=1.8 Score=24.97 Aligned_cols=26 Identities=31% Similarity=0.586 Sum_probs=17.2
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCe
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKN 45 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~f 45 (99)
.+||.||.....-...+ -.+||.|+.
T Consensus 4 y~C~~CG~~~~~~~~~~-------~~~Cp~CG~ 29 (46)
T PRK00398 4 YKCARCGREVELDEYGT-------GVRCPYCGY 29 (46)
T ss_pred EECCCCCCEEEECCCCC-------ceECCCCCC
Confidence 57999998665532221 468998884
No 73
>PRK05582 DNA topoisomerase I; Validated
Probab=79.40 E-value=1.3 Score=38.43 Aligned_cols=34 Identities=38% Similarity=0.849 Sum_probs=22.4
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCC---CCCeeEecc
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCR---VCKNFQWAE 50 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~---~C~fF~W~D 50 (99)
..||.|+.....+.. .-|+.|+.|. .|+|+.|.-
T Consensus 612 ~~CP~C~~~l~l~k~----k~gk~f~~Cs~~p~C~~~~~~~ 648 (650)
T PRK05582 612 VKCPKCGGQIVERKS----KKGRKFYGCSRYPECDFVSWDK 648 (650)
T ss_pred CCCCCCCCceEEEcC----CCCceeeccCCCCCCCcccCCC
Confidence 467888765544322 2356799995 799998853
No 74
>PRK14973 DNA topoisomerase I; Provisional
Probab=79.34 E-value=1.4 Score=40.30 Aligned_cols=37 Identities=11% Similarity=0.153 Sum_probs=26.3
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCeeEeccCC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQWAEDR 52 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~W~De~ 52 (99)
..||.||.+.++.+ +.. ..-.|..||.|++..|..+.
T Consensus 636 ~~Cp~CG~p~~~~~-r~G--r~g~fl~CP~C~~~~~~~~~ 672 (936)
T PRK14973 636 EVCPIHHLNHVRLI-RKG--ARPWDIGCPLCSHIESNTES 672 (936)
T ss_pred CCCCCCCCCceEEe-ecC--CCcccccCccccchhhcccc
Confidence 46999999855554 221 22249999999999998663
No 75
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=79.23 E-value=6 Score=33.10 Aligned_cols=69 Identities=20% Similarity=0.355 Sum_probs=32.3
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCC-eeEeccCCccchhhHHHHHHHHHHHHHH-----HHHHHHHHHHHHHH
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCK-NFQWAEDRKFSNEKIDLLVEEVRKLTLE-----IERLSDKFRLLHKE 86 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~-fF~W~De~~~~~~k~~~l~~ei~e~~~e-----i~~l~~k~~~l~~E 86 (99)
.+|+.|| .+......... +||.|+ .|.-..+...+--....+.+++.+..++ -++...-++.+++|
T Consensus 241 ~~c~~cg-----~~~~~~~~~~~---~c~~Cg~~~~~~GPlW~GpL~d~~f~e~~l~~~~~~~l~~~~~~~klL~~i~~E 312 (380)
T COG1867 241 YHCSRCG-----EIVGSFREVDE---KCPHCGGKVHLAGPLWLGPLHDEEFIEEMLEIAEGLELGTKKRALKLLKLIKKE 312 (380)
T ss_pred EEccccc-----ceecccccccc---cCCcccccceeccCcccCcccCHHHHHHHHHHhhccccccHHHHHHHHHHHHhh
Confidence 7899999 22222222222 399888 4444444332222223444444433221 12334344455566
Q ss_pred HHH
Q 041503 87 LEH 89 (99)
Q Consensus 87 l~~ 89 (99)
+..
T Consensus 313 ~~~ 315 (380)
T COG1867 313 LDI 315 (380)
T ss_pred cCC
Confidence 654
No 76
>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=79.15 E-value=1.7 Score=33.79 Aligned_cols=27 Identities=30% Similarity=0.653 Sum_probs=22.0
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCK 44 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~ 44 (99)
..||.||.++...+.. ||.-|=||.|+
T Consensus 246 ~pC~~Cg~~I~~~~~~-----gR~t~~CP~CQ 272 (272)
T TIGR00577 246 EPCRRCGTPIEKIKVG-----GRGTHFCPQCQ 272 (272)
T ss_pred CCCCCCCCeeEEEEEC-----CCCCEECCCCC
Confidence 5799999887665554 79999999995
No 77
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=78.91 E-value=1.8 Score=33.68 Aligned_cols=27 Identities=30% Similarity=0.731 Sum_probs=21.4
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCK 44 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~ 44 (99)
..||.||.++...+.. ||.-|=||.|+
T Consensus 246 ~pC~~Cg~~I~~~~~~-----gR~t~~CP~CQ 272 (274)
T PRK01103 246 EPCRRCGTPIEKIKQG-----GRSTFFCPRCQ 272 (274)
T ss_pred CCCCCCCCeeEEEEEC-----CCCcEECcCCC
Confidence 5699999876654443 79999999996
No 78
>PRK07726 DNA topoisomerase III; Provisional
Probab=78.86 E-value=1.4 Score=38.47 Aligned_cols=33 Identities=18% Similarity=0.468 Sum_probs=22.9
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCC--CCCeeEecc
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCR--VCKNFQWAE 50 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~--~C~fF~W~D 50 (99)
..||.||...+...++. -+||.|. .|.|+.|..
T Consensus 611 ~~CP~C~~~~~~~~~~~-----~~f~~Cs~~~~~~~~~~~ 645 (658)
T PRK07726 611 PKCPDCGKPMLKVKGKN-----GKMLVCQDRECGKRKNVS 645 (658)
T ss_pred ccccccCccceeecccC-----CeeEecCCCccccccccc
Confidence 67999998754332222 2599999 488778865
No 79
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=78.77 E-value=1.7 Score=33.85 Aligned_cols=27 Identities=33% Similarity=0.650 Sum_probs=21.9
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCK 44 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~ 44 (99)
..||.||.++...+.. ||.-|=||.|+
T Consensus 236 ~pC~~Cg~~I~~~~~~-----gR~ty~Cp~CQ 262 (269)
T PRK14811 236 QPCPRCGTPIEKIVVG-----GRGTHFCPQCQ 262 (269)
T ss_pred CCCCcCCCeeEEEEEC-----CCCcEECCCCc
Confidence 5699999887665554 79999999996
No 80
>PRK08173 DNA topoisomerase III; Validated
Probab=78.27 E-value=1.3 Score=40.09 Aligned_cols=28 Identities=25% Similarity=0.621 Sum_probs=21.0
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCeeEec
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQWA 49 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~W~ 49 (99)
..||.||..+ ..+ ..+|.|.+|+|..|.
T Consensus 625 ~~CP~Cg~~~-------~~~--~~~~~Cs~C~f~~~~ 652 (862)
T PRK08173 625 TPCPNCGGVV-------KEN--YRRFACTKCDFSISK 652 (862)
T ss_pred ccCCcccccc-------ccc--CceeEcCCCCcccch
Confidence 5799999863 112 335999999999994
No 81
>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=77.93 E-value=2.3 Score=23.33 Aligned_cols=16 Identities=25% Similarity=0.717 Sum_probs=8.6
Q ss_pred ccccCccccceeeeec
Q 041503 13 QVCNECGGQIELFTSH 28 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~ 28 (99)
..||.||....+..+.
T Consensus 6 y~C~~Cg~~fe~~~~~ 21 (41)
T smart00834 6 YRCEDCGHTFEVLQKI 21 (41)
T ss_pred EEcCCCCCEEEEEEec
Confidence 3566666655554443
No 82
>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=77.71 E-value=1.2 Score=25.42 Aligned_cols=28 Identities=25% Similarity=0.517 Sum_probs=19.3
Q ss_pred cccCccccceeeeecCCCCCCcceeeCCCCCeeE
Q 041503 14 VCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQ 47 (99)
Q Consensus 14 ~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~ 47 (99)
+||.||.... ..++.+-.+.|+.|+...
T Consensus 2 ~Cp~Cg~~~~------~~D~~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 2 KCPNCGSKEI------VFDPERGELVCPNCGLVL 29 (43)
T ss_dssp SBTTTSSSEE------EEETTTTEEEETTT-BBE
T ss_pred CCcCCcCCce------EEcCCCCeEECCCCCCEe
Confidence 6889987552 223778888999998654
No 83
>PRK10445 endonuclease VIII; Provisional
Probab=77.11 E-value=2.1 Score=33.21 Aligned_cols=27 Identities=41% Similarity=0.911 Sum_probs=21.9
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCK 44 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~ 44 (99)
..||.||.++...+.. ||.-|=||.|+
T Consensus 236 ~~Cp~Cg~~I~~~~~~-----gR~t~~CP~CQ 262 (263)
T PRK10445 236 EACERCGGIIEKTTLS-----SRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCEeEEEEEC-----CCCcEECCCCc
Confidence 6799999887655553 69999999996
No 84
>COG2174 RPL34A Ribosomal protein L34E [Translation, ribosomal structure and biogenesis]
Probab=76.84 E-value=0.77 Score=31.48 Aligned_cols=32 Identities=31% Similarity=0.701 Sum_probs=25.3
Q ss_pred cccccCccccc----------eeeeecCCCCCCcce--eeCCCC
Q 041503 12 LQVCNECGGQI----------ELFTSHTTKNPNRKF--WKCRVC 43 (99)
Q Consensus 12 ~~~Cp~Cg~~~----------~~~tS~t~~NPgR~F--y~C~~C 43 (99)
.++|+.||.+. ....|+|.+-|+|+| |-|+.|
T Consensus 34 ~p~C~~cg~pL~Gi~r~RP~e~~r~skt~krp~RpYGG~lc~~c 77 (93)
T COG2174 34 IPKCAICGRPLGGIPRGRPREFRRLSKTKKRPERPYGGYLCANC 77 (93)
T ss_pred CCcccccCCccCCccCCCcHHHHhccccccCcCCCcCceecHHH
Confidence 38999999742 346799999999999 777766
No 85
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=76.76 E-value=3.2 Score=29.39 Aligned_cols=34 Identities=26% Similarity=0.688 Sum_probs=26.6
Q ss_pred cccccCccc-cceeeeecCCC--CCCcceeeCCCCCe
Q 041503 12 LQVCNECGG-QIELFTSHTTK--NPNRKFWKCRVCKN 45 (99)
Q Consensus 12 ~~~Cp~Cg~-~~~~~tS~t~~--NPgR~Fy~C~~C~f 45 (99)
...||.||. .++-+.+.|.+ --=|.||.|-.|++
T Consensus 73 ~~~C~~C~~~eavffQ~~~~r~d~~m~l~yvC~~C~h 109 (113)
T KOG2691|consen 73 DKHCPKCGHREAVFFQAQTRRADEAMRLFYVCCSCGH 109 (113)
T ss_pred cccCCccCCcceEEEecccccccceEEEEEEeccccc
Confidence 378999996 68888887763 33499999999875
No 86
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=76.65 E-value=1.6 Score=30.98 Aligned_cols=34 Identities=24% Similarity=0.610 Sum_probs=19.6
Q ss_pred cccccCccccceeee-----ecCCCCC-------CcceeeCCCCCe
Q 041503 12 LQVCNECGGQIELFT-----SHTTKNP-------NRKFWKCRVCKN 45 (99)
Q Consensus 12 ~~~Cp~Cg~~~~~~t-----S~t~~NP-------gR~Fy~C~~C~f 45 (99)
...|+.||.....-- --+..+| .+.|++||.|+-
T Consensus 70 ~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs 115 (135)
T PRK03824 70 VLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGS 115 (135)
T ss_pred EEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCC
Confidence 389999995432210 0011222 268899999983
No 87
>PF07716 bZIP_2: Basic region leucine zipper; InterPro: IPR011700 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotes are proteins that contain a basic region mediating sequence-specific DNA-binding, followed by a leucine zipper region (see IPR002158 from INTERPRO), which is required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NWQ_A 1H89_B 1H88_A 1GTW_B 2E43_A 1IO4_A 1GU4_B 2E42_A 1H8A_B 1GU5_B ....
Probab=76.42 E-value=11 Score=22.40 Aligned_cols=26 Identities=35% Similarity=0.426 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 61 LLVEEVRKLTLEIERLSDKFRLLHKE 86 (99)
Q Consensus 61 ~l~~ei~e~~~ei~~l~~k~~~l~~E 86 (99)
.++.+|.+|..+...|..++..|+.|
T Consensus 29 ~le~~~~~L~~en~~L~~~i~~L~~E 54 (54)
T PF07716_consen 29 ELEQEVQELEEENEQLRQEIAQLERE 54 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 34445566666666666666666544
No 88
>PF09036 Bcr-Abl_Oligo: Bcr-Abl oncoprotein oligomerisation domain; InterPro: IPR015123 This entry represents the oligomerisation domain of the breakpoint cluster region oncoprotein Bcr, and the Bcr/Abl (Abelson-leukemia-virus) fusion protein created by a reciprocal (9;22) fusion []. Brc displays serine/threonine protein kinase activity (2.7.11.1 from EC), acting as a GTPase-activating protein for RAC1 and CDC42. Brc promotes the exchange of RAC or CDC42-bound GDP by GTP, thereby activating them []. The Bcr/Abl fusion protein loses some of the regulatory function of Bcr with regards to small Rho-like GTPases with negative consequences on cell motility, in particular on the capacity to adhere to endothelial cells []. The Bcr, Bcr/Abl oncoprotein oligomerisation domain consists of a short N-terminal helix (alpha-1), a flexible loop and a long C-terminal helix (alpha-2). Together these form an N-shaped structure, with the loop allowing the two helices to assume a parallel orientation. The monomeric domains associate into a dimer through the formation of an antiparallel coiled coil between the alpha-2 helices and domain swapping of two alpha-1 helices, where one alpha-1 helix swings back and packs against the alpha-2 helix from the second monomer. Two dimers then associate into a tetramer. The oligomerisation domain is essential for the oncogenicity of the Bcr-Abl protein []. ; GO: 0004674 protein serine/threonine kinase activity, 0005096 GTPase activator activity, 0006468 protein phosphorylation, 0007165 signal transduction; PDB: 1K1F_C.
Probab=76.28 E-value=9.9 Score=25.31 Aligned_cols=30 Identities=27% Similarity=0.472 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 041503 67 RKLTLEIERLSDKFRLLHKELEHTQLRSKY 96 (99)
Q Consensus 67 ~e~~~ei~~l~~k~~~l~~El~~~~~~~~~ 96 (99)
..+..|+++-++.|+.|++||++++.+-+|
T Consensus 29 gd~e~eLerCK~sirrLeqevnkERFrmiY 58 (79)
T PF09036_consen 29 GDIEQELERCKASIRRLEQEVNKERFRMIY 58 (79)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356667888888899999999999988877
No 89
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=76.20 E-value=1.3 Score=30.60 Aligned_cols=26 Identities=15% Similarity=0.463 Sum_probs=16.7
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCee
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNF 46 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF 46 (99)
..|+.||... .-+.+.++.||.|+=+
T Consensus 71 ~~C~~Cg~~~--------~~~~~~~~~CP~Cgs~ 96 (114)
T PRK03681 71 CWCETCQQYV--------TLLTQRVRRCPQCHGD 96 (114)
T ss_pred EEcccCCCee--------ecCCccCCcCcCcCCC
Confidence 7899999521 1123445789999843
No 90
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=75.49 E-value=7.2 Score=26.51 Aligned_cols=26 Identities=31% Similarity=0.781 Sum_probs=21.7
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCe
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKN 45 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~f 45 (99)
-.||.||...+.+++.. -|.|..|++
T Consensus 37 y~CpfCgk~~vkR~a~G-------IW~C~~C~~ 62 (90)
T PRK03976 37 HVCPVCGRPKVKRVGTG-------IWECRKCGA 62 (90)
T ss_pred ccCCCCCCCceEEEEEE-------EEEcCCCCC
Confidence 67999999999888763 578999985
No 91
>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=75.32 E-value=2.1 Score=24.55 Aligned_cols=17 Identities=35% Similarity=0.827 Sum_probs=7.3
Q ss_pred cccCccccceeeeecCC
Q 041503 14 VCNECGGQIELFTSHTT 30 (99)
Q Consensus 14 ~Cp~Cg~~~~~~tS~t~ 30 (99)
+|+.||..-.++.+-++
T Consensus 7 ~C~~Cg~~fe~~~~~~~ 23 (42)
T PF09723_consen 7 RCEECGHEFEVLQSISE 23 (42)
T ss_pred EeCCCCCEEEEEEEcCC
Confidence 34444444444444333
No 92
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=75.18 E-value=9.6 Score=25.95 Aligned_cols=26 Identities=35% Similarity=0.752 Sum_probs=21.5
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCe
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKN 45 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~f 45 (99)
-.||.||...+.+++.. -|.|..|++
T Consensus 36 y~CpfCgk~~vkR~a~G-------IW~C~~C~~ 61 (91)
T TIGR00280 36 YVCPFCGKKTVKRGSTG-------IWTCRKCGA 61 (91)
T ss_pred ccCCCCCCCceEEEeeE-------EEEcCCCCC
Confidence 67999999988888753 578999985
No 93
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=74.92 E-value=1.7 Score=36.06 Aligned_cols=28 Identities=32% Similarity=0.711 Sum_probs=17.9
Q ss_pred CCCCCCCCCCCcccccCccccceeeeecCCCCCCcceeeCCCCCeeE
Q 041503 1 MSSSTNESRNSLQVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQ 47 (99)
Q Consensus 1 mSSSs~~~~~~~~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~ 47 (99)
|++||+ ..||-||.. | |+ |+||.|+|-.
T Consensus 2 ~pts~~------~~C~ic~vq-----------~-~~-YtCPRCn~~Y 29 (383)
T KOG4317|consen 2 MPTSSF------LACGICGVQ-----------K-RE-YTCPRCNLLY 29 (383)
T ss_pred CCCCce------eeccccccc-----------c-cc-ccCCCCCccc
Confidence 566665 457777753 2 33 8999888643
No 94
>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=74.86 E-value=1.9 Score=34.73 Aligned_cols=30 Identities=17% Similarity=0.436 Sum_probs=21.3
Q ss_pred cccccCccccceeee-ecCCCCCCcceeeCC
Q 041503 12 LQVCNECGGQIELFT-SHTTKNPNRKFWKCR 41 (99)
Q Consensus 12 ~~~Cp~Cg~~~~~~t-S~t~~NPgR~Fy~C~ 41 (99)
...||-||...+.-+ .......|.||..|.
T Consensus 184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL~Cs 214 (305)
T TIGR01562 184 RTLCPACGSPPVASMVRQGGKETGLRYLSCS 214 (305)
T ss_pred CCcCCCCCChhhhhhhcccCCCCCceEEEcC
Confidence 469999998655433 333356789999988
No 95
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=74.27 E-value=6.2 Score=33.48 Aligned_cols=54 Identities=22% Similarity=0.433 Sum_probs=33.3
Q ss_pred ccccCccccceeeeecC--------CCCCC-cceeeCCCCCeeEecc-CCccchhhHHHHHHHHHHH
Q 041503 13 QVCNECGGQIELFTSHT--------TKNPN-RKFWKCRVCKNFQWAE-DRKFSNEKIDLLVEEVRKL 69 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t--------~~NPg-R~Fy~C~~C~fF~W~D-e~~~~~~k~~~l~~ei~e~ 69 (99)
..||.|.-...+..+.+ ..+++ .-|+.|+.|+ |.- +..+.+.|-..|.+.+.++
T Consensus 53 f~CP~C~~~L~~~~~~~~~~~~~~~~~~~~~~~~l~C~~C~---Wss~~igi~Fdkpt~l~~QL~kl 116 (483)
T PF05502_consen 53 FDCPICFSPLSVRASDTPPSPPDPSSDSGGKPYYLSCSYCR---WSSRDIGIKFDKPTGLRAQLSKL 116 (483)
T ss_pred ccCCCCCCcceeEecccccccccccccCCCCCEEEECCCce---eeccccCccccCchhHHHHHHhh
Confidence 88999998877776665 12333 4556877775 543 2334556666666655544
No 96
>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=73.55 E-value=2.5 Score=23.63 Aligned_cols=28 Identities=25% Similarity=0.593 Sum_probs=18.0
Q ss_pred cccCccccceeeeecCCCCCCcceeeCCCCCeeE
Q 041503 14 VCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQ 47 (99)
Q Consensus 14 ~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~ 47 (99)
-||.||-............ .|+.|++-.
T Consensus 3 FCp~C~nlL~p~~~~~~~~------~C~~C~Y~~ 30 (35)
T PF02150_consen 3 FCPECGNLLYPKEDKEKRV------ACRTCGYEE 30 (35)
T ss_dssp BETTTTSBEEEEEETTTTE------EESSSS-EE
T ss_pred eCCCCCccceEcCCCccCc------CCCCCCCcc
Confidence 5899998766554443322 899998764
No 97
>cd00632 Prefoldin_beta Prefoldin beta; Prefoldin is a hexameric molecular chaperone complex, composed of two evolutionarily related subunits (alpha and beta), which are found in both eukaryotes and archaea. Prefoldin binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The hexameric structure consists of a double beta barrel assembly with six protruding coiled-coils. The alpha prefoldin subunits have two beta hairpin structures while the beta prefoldin subunits (this CD) have only one hairpin that is most similar to the second hairpin of the alpha subunit. The prefoldin hexamer consists of two alpha and four beta subunits and is assembled from the beta hairpins of all six subunits. The alpha subunits initially dimerize providing a structural nucleus for the assembly of the beta subunits. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the st
Probab=72.69 E-value=15 Score=24.47 Aligned_cols=28 Identities=18% Similarity=0.433 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 62 LVEEVRKLTLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 62 l~~ei~e~~~ei~~l~~k~~~l~~El~~ 89 (99)
+..+|+.+...+..+.+++..++.+|.+
T Consensus 75 le~~i~~l~~~~~~l~~~~~elk~~l~~ 102 (105)
T cd00632 75 IELRIKRLERQEEDLQEKLKELQEKIQQ 102 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344555555555555555555555544
No 98
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=72.58 E-value=3.5 Score=25.21 Aligned_cols=28 Identities=25% Similarity=0.701 Sum_probs=20.6
Q ss_pred ccccCccccceeeeecCCCCCCccee-eCCC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFW-KCRV 42 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy-~C~~ 42 (99)
+.||+||....+.+-.+.. +..|+ -|+.
T Consensus 1 i~CPyCge~~~~~iD~s~~--~Q~yiEDC~v 29 (52)
T PF14255_consen 1 IQCPYCGEPIEILIDPSAG--DQEYIEDCQV 29 (52)
T ss_pred CCCCCCCCeeEEEEecCCC--CeeEEeehhh
Confidence 4699999999988877766 45554 4663
No 99
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=72.54 E-value=3.3 Score=32.39 Aligned_cols=27 Identities=30% Similarity=0.671 Sum_probs=21.5
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCK 44 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~ 44 (99)
..||.||.++...+. -||.-|=||.|+
T Consensus 255 ~pC~~Cg~~I~~~~~-----~gR~t~~CP~CQ 281 (282)
T PRK13945 255 KPCRKCGTPIERIKL-----AGRSTHWCPNCQ 281 (282)
T ss_pred CCCCcCCCeeEEEEE-----CCCccEECCCCc
Confidence 579999987765554 269999999996
No 100
>PF04728 LPP: Lipoprotein leucine-zipper; InterPro: IPR006817 This repeating sequence, NAKVDQLSNDV, is found in the enterobacterial outer membrane lipoprotein LPP. The outer membrane lipoprotein is the most abundant protein in an Escherichia coli cell. The messenger RNA for the lipoprotein of the E. coli outer membrane codes for a putative precursor, prolipoprotein, which has 20 additional amino acid residues extending from the amino terminus of the lipoprotein.; GO: 0019867 outer membrane; PDB: 1JCC_A 2GUV_C 2GUS_A 1JCD_A 1KFM_A 1T8Z_D 1KFN_A 1EQ7_A.
Probab=72.42 E-value=21 Score=22.31 Aligned_cols=31 Identities=29% Similarity=0.508 Sum_probs=18.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 57 EKIDLLVEEVRKLTLEIERLSDKFRLLHKEL 87 (99)
Q Consensus 57 ~k~~~l~~ei~e~~~ei~~l~~k~~~l~~El 87 (99)
.|++-|.++|.+|..++..|...+..|+.|+
T Consensus 3 akid~Ls~dVq~L~~kvdqLs~dv~~lr~~v 33 (56)
T PF04728_consen 3 AKIDQLSSDVQTLNSKVDQLSSDVNALRADV 33 (56)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3556666666666666666655555555554
No 101
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=71.70 E-value=13 Score=25.31 Aligned_cols=27 Identities=26% Similarity=0.684 Sum_probs=22.0
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCee
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNF 46 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF 46 (99)
-.||.||...+.+++. --|.|..|++-
T Consensus 37 y~CpfCgk~~vkR~a~-------GIW~C~~C~~~ 63 (90)
T PTZ00255 37 YFCPFCGKHAVKRQAV-------GIWRCKGCKKT 63 (90)
T ss_pred ccCCCCCCCceeeeee-------EEEEcCCCCCE
Confidence 6899999998888876 36889999853
No 102
>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=71.67 E-value=5.3 Score=31.09 Aligned_cols=41 Identities=17% Similarity=0.319 Sum_probs=21.9
Q ss_pred cccccCcccc--ceeeeecCCCCCCcceeeCCCCC-eeEeccCC
Q 041503 12 LQVCNECGGQ--IELFTSHTTKNPNRKFWKCRVCK-NFQWAEDR 52 (99)
Q Consensus 12 ~~~Cp~Cg~~--~~~~tS~t~~NPgR~Fy~C~~C~-fF~W~De~ 52 (99)
...||.||.. .....-..+..|+-+-+.|..|+ |++=.|..
T Consensus 211 R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK~vd~~ 254 (290)
T PF04216_consen 211 RIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLKTVDRE 254 (290)
T ss_dssp TTS-TTT---SS-EEE--------SEEEEEETTTTEEEEEEETT
T ss_pred CCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHHHHhhh
Confidence 3789999963 33333336788899999999998 77777743
No 103
>smart00338 BRLZ basic region leucin zipper.
Probab=71.66 E-value=19 Score=21.89 Aligned_cols=30 Identities=37% Similarity=0.499 Sum_probs=17.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 60 DLLVEEVRKLTLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 60 ~~l~~ei~e~~~ei~~l~~k~~~l~~El~~ 89 (99)
..|+.++..+..+...|..++..|..|+..
T Consensus 29 ~~Le~~~~~L~~en~~L~~~~~~l~~e~~~ 58 (65)
T smart00338 29 EELERKVEQLEAENERLKKEIERLRRELEK 58 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444555666666666666666666655543
No 104
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=71.65 E-value=3.4 Score=28.81 Aligned_cols=29 Identities=24% Similarity=0.520 Sum_probs=22.0
Q ss_pred cccccCccccceeeeecCCCCCCcceeeCC---CCCe
Q 041503 12 LQVCNECGGQIELFTSHTTKNPNRKFWKCR---VCKN 45 (99)
Q Consensus 12 ~~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~---~C~f 45 (99)
...||.||...+++..... +|+.|. .|.+
T Consensus 17 ~~~Cp~Cg~~m~~~~~~~g-----~f~gCs~yP~C~~ 48 (140)
T COG0551 17 GQICPKCGKNMVKKFGKYG-----IFLGCSNYPKCDY 48 (140)
T ss_pred CccCCcCCCeeEEEEccCC-----eEEEeCCCCCCCC
Confidence 3789999999988887742 777776 5665
No 105
>PF01166 TSC22: TSC-22/dip/bun family; InterPro: IPR000580 Several eukaryotic proteins are evolutionary related and are thought to be involved in transcriptional regulation. These proteins are highly similar in a region of about 50 residues that include a conserved leucine-zipper domain most probably involved in homo- or hetero-dimerisation. Proteins containing this signature include: Vertebrate protein TSC-22 [], a transcriptional regulator which seems to act on C-type natriuretic peptide (CNP) promoter. Mammalian protein DIP (DSIP-immunoreactive peptide) [], a protein whose function is not yet known. Drosophila protein bunched [] (gene bun) (also known as shortsighted), a probable transcription factor required for peripheral nervous system morphogenesis, eye development and oogenesis. Caenorhabditis elegans hypothetical protein T18D3.7. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1DIP_B.
Probab=71.59 E-value=4 Score=25.89 Aligned_cols=25 Identities=32% Similarity=0.407 Sum_probs=18.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 62 LVEEVRKLTLEIERLSDKFRLLHKE 86 (99)
Q Consensus 62 l~~ei~e~~~ei~~l~~k~~~l~~E 86 (99)
++.||+-++..|.+|..++..|+.|
T Consensus 12 VrEEVevLK~~I~eL~~~n~~Le~E 36 (59)
T PF01166_consen 12 VREEVEVLKEQIAELEERNSQLEEE 36 (59)
T ss_dssp -TTSHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3457888888899998888887554
No 106
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=71.49 E-value=2.7 Score=26.17 Aligned_cols=24 Identities=21% Similarity=0.596 Sum_probs=18.3
Q ss_pred cccCccccceeeeecCCCCCCcceeeCCCCCeeE
Q 041503 14 VCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQ 47 (99)
Q Consensus 14 ~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~ 47 (99)
.||.|+... |++.-|.||.|++=.
T Consensus 1 ~Cpv~~~~~----------~~~v~~~Cp~cGipt 24 (55)
T PF13824_consen 1 LCPVCKKDL----------PAHVNFECPDCGIPT 24 (55)
T ss_pred CCCCCcccc----------ccccCCcCCCCCCcC
Confidence 477777654 899999999777644
No 107
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=70.99 E-value=20 Score=25.63 Aligned_cols=32 Identities=25% Similarity=0.400 Sum_probs=19.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 58 KIDLLVEEVRKLTLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 58 k~~~l~~ei~e~~~ei~~l~~k~~~l~~El~~ 89 (99)
....+..+|.++..++..|+..+..|+.||..
T Consensus 73 el~~ld~ei~~L~~el~~l~~~~k~l~~eL~~ 104 (169)
T PF07106_consen 73 ELAELDAEIKELREELAELKKEVKSLEAELAS 104 (169)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455556666666666666666666666543
No 108
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=70.89 E-value=4.1 Score=30.75 Aligned_cols=32 Identities=25% Similarity=0.524 Sum_probs=18.0
Q ss_pred cccCccccceeeeecCCCCCC--c---ceeeCCCCCe
Q 041503 14 VCNECGGQIELFTSHTTKNPN--R---KFWKCRVCKN 45 (99)
Q Consensus 14 ~Cp~Cg~~~~~~tS~t~~NPg--R---~Fy~C~~C~f 45 (99)
.||.||.....+...+..-|. . --|.|++|+|
T Consensus 2 ~Cp~C~~~~~~~~~~~~~IP~F~evii~sf~C~~CGy 38 (192)
T TIGR00310 2 DCPSCGGECETVMKTVNDIPYFGEVLETSTICEHCGY 38 (192)
T ss_pred cCCCCCCCCEEEEEEEcCCCCcceEEEEEEECCCCCC
Confidence 588888665444444432443 1 1367887765
No 109
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=70.85 E-value=8.8 Score=28.96 Aligned_cols=41 Identities=20% Similarity=0.492 Sum_probs=24.3
Q ss_pred cccccCccccceeeee--------cCCCCCCcce----------eeCCCCCeeEeccCC
Q 041503 12 LQVCNECGGQIELFTS--------HTTKNPNRKF----------WKCRVCKNFQWAEDR 52 (99)
Q Consensus 12 ~~~Cp~Cg~~~~~~tS--------~t~~NPgR~F----------y~C~~C~fF~W~De~ 52 (99)
...||-|+..-..-.. +.+..+...| +.||+|+|--...+-
T Consensus 5 ~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~~F 63 (214)
T PF09986_consen 5 KITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEEDF 63 (214)
T ss_pred ceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccccc
Confidence 3789999974332222 2233333332 689999987766553
No 110
>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.
Probab=70.72 E-value=18 Score=23.27 Aligned_cols=16 Identities=38% Similarity=0.364 Sum_probs=9.9
Q ss_pred hhHHHHHHHHHHHHHH
Q 041503 57 EKIDLLVEEVRKLTLE 72 (99)
Q Consensus 57 ~k~~~l~~ei~e~~~e 72 (99)
..+++|+.||.++..+
T Consensus 18 eti~~Lq~e~eeLke~ 33 (72)
T PF06005_consen 18 ETIALLQMENEELKEK 33 (72)
T ss_dssp HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3456666677766665
No 111
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=70.51 E-value=3.6 Score=29.41 Aligned_cols=30 Identities=23% Similarity=0.545 Sum_probs=22.5
Q ss_pred ccccCccccceeeeecCCCCCCcc-eeeCCCCCeeE
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRK-FWKCRVCKNFQ 47 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~-Fy~C~~C~fF~ 47 (99)
+.||.||.+=..++.. +|. |-+|..|+...
T Consensus 98 VlC~~C~sPdT~l~k~-----~r~~~l~C~ACGa~~ 128 (133)
T TIGR00311 98 VICRECNRPDTRIIKE-----GRVSLLKCEACGAKA 128 (133)
T ss_pred EECCCCCCCCcEEEEe-----CCeEEEecccCCCCC
Confidence 8999999987666642 466 46999998643
No 112
>PRK05582 DNA topoisomerase I; Validated
Probab=70.19 E-value=3.2 Score=36.07 Aligned_cols=33 Identities=24% Similarity=0.545 Sum_probs=23.2
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCC---CCCeeEecc
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCR---VCKNFQWAE 50 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~---~C~fF~W~D 50 (99)
..||.||...+....+. | +||.|. .|+|..|..
T Consensus 572 ~~CP~Cg~~l~~~~~k~----g-kf~~Cs~~~~C~~~~~~~ 607 (650)
T PRK05582 572 EDCPKCGSPMVIKMGRY----G-KFIACSNFPDCRNTKPIV 607 (650)
T ss_pred CCCCCCCCEeEEEecCC----C-ceeecCCccccccCCCcc
Confidence 68999997655442222 2 699997 599988754
No 113
>PF08826 DMPK_coil: DMPK coiled coil domain like; InterPro: IPR014930 This domain is found in the myotonic dystrophy protein kinase (DMPK) and adopts a coiled coil structure. It plays a role in dimerisation []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1WT6_D.
Probab=70.09 E-value=24 Score=22.16 Aligned_cols=18 Identities=28% Similarity=0.410 Sum_probs=9.0
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 041503 72 EIERLSDKFRLLHKELEH 89 (99)
Q Consensus 72 ei~~l~~k~~~l~~El~~ 89 (99)
....|.+++..|++|+++
T Consensus 40 rn~eL~~ei~~L~~e~ee 57 (61)
T PF08826_consen 40 RNRELEQEIERLKKEMEE 57 (61)
T ss_dssp HHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 344445555555555554
No 114
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=69.98 E-value=4.5 Score=29.61 Aligned_cols=8 Identities=50% Similarity=1.319 Sum_probs=4.1
Q ss_pred ccCccccc
Q 041503 15 CNECGGQI 22 (99)
Q Consensus 15 Cp~Cg~~~ 22 (99)
||.||...
T Consensus 3 Cp~C~~~~ 10 (160)
T smart00709 3 CPSCGGNG 10 (160)
T ss_pred CCCCCCCC
Confidence 55555443
No 115
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=69.97 E-value=3.4 Score=23.14 Aligned_cols=30 Identities=13% Similarity=0.416 Sum_probs=19.5
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCK 44 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~ 44 (99)
+.||.|+..-.+--++- -++.+-.+|+.|+
T Consensus 3 i~CP~C~~~f~v~~~~l--~~~~~~vrC~~C~ 32 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKL--PAGGRKVRCPKCG 32 (37)
T ss_pred EECCCCCceEEcCHHHc--ccCCcEEECCCCC
Confidence 67999987554433332 2445578999887
No 116
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=69.11 E-value=3.5 Score=25.42 Aligned_cols=31 Identities=19% Similarity=0.690 Sum_probs=21.4
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCeeEecc
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQWAE 50 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~W~D 50 (99)
..||.||..+.+ +...+ -|.|..|++-.|..
T Consensus 20 ~~CPrCG~gvfm--A~H~d-----R~~CGkCgyTe~~~ 50 (51)
T COG1998 20 RFCPRCGPGVFM--ADHKD-----RWACGKCGYTEFKK 50 (51)
T ss_pred ccCCCCCCcchh--hhcCc-----eeEeccccceEeec
Confidence 789999965443 22222 47799999988864
No 117
>PRK07219 DNA topoisomerase I; Validated
Probab=68.95 E-value=4.7 Score=36.10 Aligned_cols=36 Identities=25% Similarity=0.623 Sum_probs=26.1
Q ss_pred cccccCccccceeeeecCCCCCCcceeeCC---CCCeeEeccC
Q 041503 12 LQVCNECGGQIELFTSHTTKNPNRKFWKCR---VCKNFQWAED 51 (99)
Q Consensus 12 ~~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~---~C~fF~W~De 51 (99)
...||.||....+..++. |-+||.|. .|+|-.|...
T Consensus 602 ~~~CP~Cg~~l~~r~~~~----g~~F~gCs~yp~C~~t~~lp~ 640 (822)
T PRK07219 602 IGKCPECGGDLIIIRTDK----GSRFVGCSGYPDCRNTFPLPS 640 (822)
T ss_pred cCcCCCCCCcceeeeccC----CceeeecCCCcCCCCeeecCC
Confidence 367999998766554432 33699997 5999999654
No 118
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=67.88 E-value=5.5 Score=27.74 Aligned_cols=38 Identities=18% Similarity=0.445 Sum_probs=27.2
Q ss_pred cccccCccc-cceeeeecCCCCCCcceeeCC---CCCeeEeccCCc
Q 041503 12 LQVCNECGG-QIELFTSHTTKNPNRKFWKCR---VCKNFQWAEDRK 53 (99)
Q Consensus 12 ~~~Cp~Cg~-~~~~~tS~t~~NPgR~Fy~C~---~C~fF~W~De~~ 53 (99)
...||.||. ..++..++- |+.||.|- .|+|..|.....
T Consensus 60 ~~~Cp~C~~~~~~~k~~~~----~~~f~~~~~~Pkc~~~~~~~~~~ 101 (140)
T COG0551 60 GVKCPKCGKGLLVLKKGRF----GKNFLGCSNYPKCRFTEKPKPKE 101 (140)
T ss_pred ceeCCCCCCCceEEEeccC----CceEEeecCCCcCceeecCCccc
Confidence 388999996 455554443 36788765 899999987753
No 119
>PF12773 DZR: Double zinc ribbon
Probab=67.71 E-value=3.9 Score=23.54 Aligned_cols=27 Identities=22% Similarity=0.631 Sum_probs=18.9
Q ss_pred CcccccCccccceeeeecCCCCCCcceeeCCCCCe
Q 041503 11 SLQVCNECGGQIELFTSHTTKNPNRKFWKCRVCKN 45 (99)
Q Consensus 11 ~~~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~f 45 (99)
+...||.||.++. .+....+.|+.|+.
T Consensus 11 ~~~fC~~CG~~l~--------~~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 11 DAKFCPHCGTPLP--------PPDQSKKICPNCGA 37 (50)
T ss_pred cccCChhhcCChh--------hccCCCCCCcCCcC
Confidence 3478899998777 44555666887764
No 120
>PF07334 IFP_35_N: Interferon-induced 35 kDa protein (IFP 35) N-terminus; InterPro: IPR009938 This entry represents the N terminus of interferon-induced 35 kDa protein (IFP 35) (approximately 80 residues long), which contains a leucine zipper motif in an alpha helical configuration []. This group of proteins also includes N-myc-interactor (Nmi), a homologous interferon-induced protein.
Probab=67.38 E-value=14 Score=24.43 Aligned_cols=23 Identities=26% Similarity=0.439 Sum_probs=12.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 041503 67 RKLTLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 67 ~e~~~ei~~l~~k~~~l~~El~~ 89 (99)
.++.+|..+|+..+++|+.||.+
T Consensus 3 ~ei~eEn~~Lk~eiqkle~ELq~ 25 (76)
T PF07334_consen 3 HEIQEENARLKEEIQKLEAELQQ 25 (76)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445555555555555555543
No 121
>COG2919 Septum formation initiator [Cell division and chromosome partitioning]
Probab=67.25 E-value=20 Score=24.67 Aligned_cols=39 Identities=23% Similarity=0.280 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHhhcCC
Q 041503 61 LLVEEVRKLTLEIERLSDKFRLLHKE--LEHTQLRSKYGLS 99 (99)
Q Consensus 61 ~l~~ei~e~~~ei~~l~~k~~~l~~E--l~~~~~~~~~~~~ 99 (99)
.+.+|+.++..+-..|++++..|+.+ .-+++-++.||++
T Consensus 61 ~~~~e~~~L~~~~~~l~~ei~~L~dg~~~i~e~AR~~l~~~ 101 (117)
T COG2919 61 AQQAELEKLSARNTALEAEIKDLKDGRDYIEERARSELGMS 101 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcccHHHHHHHHHHHhCCC
Confidence 33445555655566666666666554 3445556666654
No 122
>PF02996 Prefoldin: Prefoldin subunit; InterPro: IPR004127 This entry comprises of several prefoldin subunits. Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal alpha subunit, eukaryotic prefoldin subunits 3 and 5 and the UXT (ubiquitously expressed transcript) family. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 1FXK_C 2ZDI_C.
Probab=67.16 E-value=13 Score=24.71 Aligned_cols=49 Identities=20% Similarity=0.277 Sum_probs=29.6
Q ss_pred CCCeeEeccCC---ccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 42 VCKNFQWAEDR---KFSNEKIDLLVEEVRKLTLEIERLSDKFRLLHKELEHT 90 (99)
Q Consensus 42 ~C~fF~W~De~---~~~~~k~~~l~~ei~e~~~ei~~l~~k~~~l~~El~~~ 90 (99)
+++||...+-. .|--.++..|...++++..++..+++++..+...+..-
T Consensus 66 G~~~~vE~s~~eA~~~l~~r~~~l~~~~~~l~~~~~~~~~~~~~~~~~l~~~ 117 (120)
T PF02996_consen 66 GAGYYVEMSLEEAIEFLKKRIKELEEQLEKLEKELAELQAQIEQLEQTLQQL 117 (120)
T ss_dssp ETTEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHH
T ss_pred eCCeEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 57777776554 12334445555566666667777777766666665543
No 123
>PF00170 bZIP_1: bZIP transcription factor cAMP response element binding (CREB) protein signature fos transforming protein signature jun transcription factor signature; InterPro: IPR011616 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotic are proteins that contain a basic region mediating sequence-specific DNA-binding followed by a leucine zipper region (see IPR002158 from INTERPRO) required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2H7H_B 2OQQ_B 1S9K_E 1JNM_A 1JUN_A 1FOS_H 1A02_J 1T2K_C 1CI6_A 1DH3_C ....
Probab=67.16 E-value=25 Score=21.30 Aligned_cols=26 Identities=38% Similarity=0.505 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 62 LVEEVRKLTLEIERLSDKFRLLHKEL 87 (99)
Q Consensus 62 l~~ei~e~~~ei~~l~~k~~~l~~El 87 (99)
|+..+..+..+...|..++..|..++
T Consensus 31 Le~~~~~L~~en~~L~~~~~~L~~~~ 56 (64)
T PF00170_consen 31 LEEKVEELESENEELKKELEQLKKEI 56 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444455555555554444444443
No 124
>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=67.11 E-value=3.1 Score=34.38 Aligned_cols=40 Identities=13% Similarity=0.298 Sum_probs=23.5
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCeeEeccCC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQWAEDR 52 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~W~De~ 52 (99)
+.|+.||+.....+..-+..-+.-.|+|+.|+.-.+.|-.
T Consensus 175 piC~~cGri~tt~v~~~d~~~~~v~Y~c~~cG~~g~~~i~ 214 (360)
T PF01921_consen 175 PICEKCGRIDTTEVTEYDPEGGTVTYRCEECGHEGEVDIT 214 (360)
T ss_dssp EEETTTEE--EEEEEEE--SSSEEEEE--TTS---EEETT
T ss_pred eeccccCCcccceeeEeecCCCEEEEEecCCCCEEEEecC
Confidence 8999999954444444444568999999999987777664
No 125
>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=66.71 E-value=4.2 Score=24.90 Aligned_cols=31 Identities=16% Similarity=0.480 Sum_probs=20.9
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCee
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNF 46 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF 46 (99)
..|+.|...--+.- ...+.---|+||.|++|
T Consensus 23 LIC~~C~~hNGla~---~~~~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 23 LICSKCFSHNGLAP---KEEFEEIQYRCPYCGAL 53 (54)
T ss_pred EECcccchhhcccc---cccCCceEEEcCCCCCc
Confidence 78999987544433 23333447999999986
No 126
>PF04420 CHD5: CHD5-like protein; InterPro: IPR007514 Members of this family are probably coiled-coil proteins that are similar to the CHD5 (Congenital heart disease 5) protein. The exact molecular function of these eukaryotic proteins is unknown.; PDB: 3SJA_H 3SJC_D 3SJB_D 3ZS8_D 3VLC_E.
Probab=66.50 E-value=15 Score=26.52 Aligned_cols=36 Identities=28% Similarity=0.380 Sum_probs=24.4
Q ss_pred hhHHHHHHHHHHHHHHH------------HHHHHHHHHHHHHHHHHHH
Q 041503 57 EKIDLLVEEVRKLTLEI------------ERLSDKFRLLHKELEHTQL 92 (99)
Q Consensus 57 ~k~~~l~~ei~e~~~ei------------~~l~~k~~~l~~El~~~~~ 92 (99)
.+...++.|+.++..|+ .+++.|+.++.+||++..-
T Consensus 40 ~~~~~l~~Ei~~l~~E~~~iS~qDeFAkwaKl~Rk~~kl~~el~~~~~ 87 (161)
T PF04420_consen 40 KEQRQLRKEILQLKRELNAISAQDEFAKWAKLNRKLDKLEEELEKLNK 87 (161)
T ss_dssp HHHHHHHHHHHHHHHHHTTS-TTTSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44456666777776544 3467788888888887544
No 127
>COG3883 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=66.44 E-value=21 Score=28.50 Aligned_cols=22 Identities=23% Similarity=0.365 Sum_probs=9.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 041503 63 VEEVRKLTLEIERLSDKFRLLH 84 (99)
Q Consensus 63 ~~ei~e~~~ei~~l~~k~~~l~ 84 (99)
..+|.++..+|+.|+.+|..+.
T Consensus 72 ~~~i~~~~~eik~l~~eI~~~~ 93 (265)
T COG3883 72 QKEIDQSKAEIKKLQKEIAELK 93 (265)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444444444444444443
No 128
>cd00890 Prefoldin Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=66.36 E-value=21 Score=23.71 Aligned_cols=48 Identities=21% Similarity=0.369 Sum_probs=28.7
Q ss_pred CCCeeEeccCCc---cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 42 VCKNFQWAEDRK---FSNEKIDLLVEEVRKLTLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 42 ~C~fF~W~De~~---~~~~k~~~l~~ei~e~~~ei~~l~~k~~~l~~El~~ 89 (99)
+.++|.-.+-.. +--.+++.|..++.++..++..+++++..++..|..
T Consensus 76 G~~~~ve~~~~eA~~~l~~r~~~l~~~~~~l~~~~~~~~~~~~~l~~~l~~ 126 (129)
T cd00890 76 GTGVYVEKSLEEAIEFLKKRLETLEKQIEKLEKQLEKLQDQITELQEELQQ 126 (129)
T ss_pred cCCEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 556666554431 222344555666777777777777777777665543
No 129
>PF04508 Pox_A_type_inc: Viral A-type inclusion protein repeat ; InterPro: IPR007596 The repeat is found in the A-type inclusion protein of the Poxvirus family [].; GO: 0016032 viral reproduction
Probab=65.79 E-value=11 Score=19.67 Aligned_cols=18 Identities=28% Similarity=0.567 Sum_probs=12.5
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 041503 72 EIERLSDKFRLLHKELEH 89 (99)
Q Consensus 72 ei~~l~~k~~~l~~El~~ 89 (99)
|+.+++.+|..|+.+|.+
T Consensus 2 E~~rlr~rI~dLer~L~~ 19 (23)
T PF04508_consen 2 EMNRLRNRISDLERQLSE 19 (23)
T ss_pred hHHHHHHHHHHHHHHHHH
Confidence 566777777777777764
No 130
>KOG2264 consensus Exostosin EXT1L [Signal transduction mechanisms]
Probab=65.24 E-value=17 Score=32.82 Aligned_cols=26 Identities=31% Similarity=0.461 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 68 KLTLEIERLSDKFRLLHKELEHTQLR 93 (99)
Q Consensus 68 e~~~ei~~l~~k~~~l~~El~~~~~~ 93 (99)
++..+|++++.|++++++++...++-
T Consensus 104 el~seI~~~n~kiEelk~~i~~~q~e 129 (907)
T KOG2264|consen 104 ELNSEIEEINTKIEELKRLIPQKQLE 129 (907)
T ss_pred HHHhHHHHHHHHHHHHHHHHHHhHHH
Confidence 66677999999999998888776653
No 131
>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=65.21 E-value=3.3 Score=21.79 Aligned_cols=8 Identities=25% Similarity=0.779 Sum_probs=4.4
Q ss_pred eeCCCCCe
Q 041503 38 WKCRVCKN 45 (99)
Q Consensus 38 y~C~~C~f 45 (99)
|.||.|+|
T Consensus 17 f~CPnCG~ 24 (24)
T PF07754_consen 17 FPCPNCGF 24 (24)
T ss_pred EeCCCCCC
Confidence 55665553
No 132
>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89
Probab=64.88 E-value=23 Score=22.60 Aligned_cols=25 Identities=28% Similarity=0.288 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 68 KLTLEIERLSDKFRLLHKELEHTQL 92 (99)
Q Consensus 68 e~~~ei~~l~~k~~~l~~El~~~~~ 92 (99)
..-.++.+|++++..|++||++...
T Consensus 44 ~a~~e~~~Lk~E~e~L~~el~~~r~ 68 (69)
T PF14197_consen 44 DAYEENNKLKEENEALRKELEELRA 68 (69)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 3445788888888888899887654
No 133
>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=64.20 E-value=6.6 Score=22.80 Aligned_cols=8 Identities=63% Similarity=1.610 Sum_probs=4.3
Q ss_pred ccccCccc
Q 041503 13 QVCNECGG 20 (99)
Q Consensus 13 ~~Cp~Cg~ 20 (99)
+.||.||.
T Consensus 27 ~~CP~Cg~ 34 (52)
T TIGR02605 27 ATCPECGG 34 (52)
T ss_pred CCCCCCCC
Confidence 45555554
No 134
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=64.12 E-value=3.5 Score=31.77 Aligned_cols=31 Identities=19% Similarity=0.645 Sum_probs=20.6
Q ss_pred ccccCcc-ccc--eeeeecCCCCCCcceeeCCCCCeeE
Q 041503 13 QVCNECG-GQI--ELFTSHTTKNPNRKFWKCRVCKNFQ 47 (99)
Q Consensus 13 ~~Cp~Cg-~~~--~~~tS~t~~NPgR~Fy~C~~C~fF~ 47 (99)
..||.|| ..+ .+...+... .-++|..|+.+.
T Consensus 7 ~~Cp~Cg~eev~hEVik~~g~~----~lvrC~eCG~V~ 40 (201)
T COG1326 7 IECPSCGSEEVSHEVIKERGRE----PLVRCEECGTVH 40 (201)
T ss_pred EECCCCCcchhhHHHHHhcCCc----eEEEccCCCcEe
Confidence 6899999 344 333332222 789999999775
No 135
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=63.93 E-value=12 Score=26.29 Aligned_cols=19 Identities=37% Similarity=1.015 Sum_probs=13.8
Q ss_pred ccCccccceeeeecCCCCCCcceeeCCCCC
Q 041503 15 CNECGGQIELFTSHTTKNPNRKFWKCRVCK 44 (99)
Q Consensus 15 Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~ 44 (99)
||.||.+..+.- ++|++|+
T Consensus 1 CPvCg~~l~vt~-----------l~C~~C~ 19 (113)
T PF09862_consen 1 CPVCGGELVVTR-----------LKCPSCG 19 (113)
T ss_pred CCCCCCceEEEE-----------EEcCCCC
Confidence 899998766543 4588886
No 136
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=63.76 E-value=22 Score=26.58 Aligned_cols=27 Identities=33% Similarity=0.358 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 63 VEEVRKLTLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 63 ~~ei~e~~~ei~~l~~k~~~l~~El~~ 89 (99)
..|...+..++++|+.++..|++|+++
T Consensus 103 ~~e~~~l~~e~~~l~~~~e~Le~e~~~ 129 (161)
T TIGR02894 103 QKENERLKNQNESLQKRNEELEKELEK 129 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555556666666666666666554
No 137
>PF02403 Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal domain; InterPro: IPR015866 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. This entry represents the N-terminal domain of Seryl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Seryl-tRNA synthetase (6.1.1.11 from EC) exists as monomer and belongs to class IIa [].; GO: 0000166 nucleotide binding, 0004828 serine-tRNA ligase activity, 0005524 ATP binding, 0006434 seryl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 3QO8_A 3QO5_A 3QO7_A 3QNE_A 3LSQ_A 3LSS_A 2DQ3_B 1SET_A 1SER_A 1SRY_B ....
Probab=63.64 E-value=22 Score=23.43 Aligned_cols=32 Identities=31% Similarity=0.483 Sum_probs=20.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 59 IDLLVEEVRKLTLEIERLSDKFRLLHKELEHT 90 (99)
Q Consensus 59 ~~~l~~ei~e~~~ei~~l~~k~~~l~~El~~~ 90 (99)
.+.|.+++.+++.+|..+.++...+..++..-
T Consensus 69 ~~~l~~e~~~lk~~i~~le~~~~~~e~~l~~~ 100 (108)
T PF02403_consen 69 AEELKAEVKELKEEIKELEEQLKELEEELNEL 100 (108)
T ss_dssp THHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555666667777777776666666665543
No 138
>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=63.52 E-value=25 Score=25.86 Aligned_cols=39 Identities=23% Similarity=0.422 Sum_probs=27.1
Q ss_pred cccCccc-cceeeeecCCCCC--CcceeeCCCCC----eeEeccCC
Q 041503 14 VCNECGG-QIELFTSHTTKNP--NRKFWKCRVCK----NFQWAEDR 52 (99)
Q Consensus 14 ~Cp~Cg~-~~~~~tS~t~~NP--gR~Fy~C~~C~----fF~W~De~ 52 (99)
+||.||- ...+.=|+..+.- =|+=-.|+.|+ -|...+..
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErve~~ 47 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELL 47 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeecccc
Confidence 6999997 5666667765443 37777899887 45555553
No 139
>PRK10884 SH3 domain-containing protein; Provisional
Probab=63.50 E-value=31 Score=26.23 Aligned_cols=14 Identities=21% Similarity=0.257 Sum_probs=6.4
Q ss_pred HHHHHHHHHHHHHH
Q 041503 76 LSDKFRLLHKELEH 89 (99)
Q Consensus 76 l~~k~~~l~~El~~ 89 (99)
|+.+++.|++||+.
T Consensus 137 L~~~n~~L~~~l~~ 150 (206)
T PRK10884 137 LKEENQKLKNQLIV 150 (206)
T ss_pred HHHHHHHHHHHHHH
Confidence 44444444444443
No 140
>TIGR02209 ftsL_broad cell division protein FtsL. This model represents FtsL, both forms similar to that in E. coli and similar to that in B. subtilis. FtsL is one of the later proteins active in cell division septum formation. FtsL is small, low in complexity, and highly divergent. The scope of this model is broader than that of the Pfam model pfam04999.3 for FtsL, as this one includes FtsL from Bacillus subtilis and related species.
Probab=63.41 E-value=30 Score=21.65 Aligned_cols=29 Identities=38% Similarity=0.590 Sum_probs=18.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 61 LLVEEVRKLTLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 61 ~l~~ei~e~~~ei~~l~~k~~~l~~El~~ 89 (99)
.+.+++..+..+++.+++++..|+.|+..
T Consensus 28 ~~~~~~~~~~~~~~~l~~en~~L~~ei~~ 56 (85)
T TIGR02209 28 QLNNELQKLQLEIDKLQKEWRDLQLEVAE 56 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33446666667777777777777766654
No 141
>KOG1294 consensus Apurinic/apyrimidinic endonuclease and related enzymes [Replication, recombination and repair]
Probab=63.39 E-value=3.9 Score=33.42 Aligned_cols=22 Identities=23% Similarity=0.412 Sum_probs=18.8
Q ss_pred ccceeeeecCCCCCCcceeeCC
Q 041503 20 GQIELFTSHTTKNPNRKFWKCR 41 (99)
Q Consensus 20 ~~~~~~tS~t~~NPgR~Fy~C~ 41 (99)
.-.-+.||++..|+||+||-|+
T Consensus 297 r~dy~~Vsk~~~n~~r~~~Ic~ 318 (335)
T KOG1294|consen 297 RCDYILVSKPGPNNGRRFYICS 318 (335)
T ss_pred ceeEEEecCcCCCCCceeeeec
Confidence 3456678999999999999998
No 142
>PF12443 AKNA: AT-hook-containing transcription factor; InterPro: IPR022150 This domain family is found in eukaryotes, and is approximately 110 amino acids in length. This family contains a transcription factor which regulates the expression of the costimulatory molecules on lymphocytes.
Probab=62.75 E-value=9.2 Score=26.73 Aligned_cols=36 Identities=28% Similarity=0.299 Sum_probs=30.8
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 55 SNEKIDLLVEEVRKLTLEIERLSDKFRLLHKELEHT 90 (99)
Q Consensus 55 ~~~k~~~l~~ei~e~~~ei~~l~~k~~~l~~El~~~ 90 (99)
.+.++.-+++||-+|.+.+++|+++++.+.++++-+
T Consensus 43 ~f~~~~ege~~~qkL~eqteeLK~kvqe~sk~i~~~ 78 (106)
T PF12443_consen 43 IFDKIREGEQMIQKLGEQTEELKDKVQEFSKRIEQD 78 (106)
T ss_pred ccCcchHHHHHHHHHHHHHHHHHHHHHHHhcCcCCC
Confidence 566777888899999999999999999999887644
No 143
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=62.65 E-value=6.3 Score=23.10 Aligned_cols=10 Identities=50% Similarity=1.272 Sum_probs=5.2
Q ss_pred cccCccccce
Q 041503 14 VCNECGGQIE 23 (99)
Q Consensus 14 ~Cp~Cg~~~~ 23 (99)
.|..||....
T Consensus 4 ~C~~Cg~~~~ 13 (44)
T smart00659 4 ICGECGRENE 13 (44)
T ss_pred ECCCCCCEee
Confidence 4555665433
No 144
>PF12709 Kinetocho_Slk19: Central kinetochore-associated; InterPro: IPR024312 This is a family of proteins integrally involved in the central kinetochore. Slk19 is a yeast member and it may play an important role in the timing of nuclear migration. It may also participate, directly or indirectly, in the maintenance of centromeric tensile strength during mitotic stagnation, for instance during activation of checkpoint controls, when cells need to preserve nuclear integrity until cell cycle progression can be resumed [].
Probab=62.65 E-value=22 Score=23.99 Aligned_cols=24 Identities=29% Similarity=0.317 Sum_probs=11.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 66 VRKLTLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 66 i~e~~~ei~~l~~k~~~l~~El~~ 89 (99)
|+++..++..|.+.+..|+.+|+.
T Consensus 51 v~~L~~e~~~l~~E~e~L~~~l~~ 74 (87)
T PF12709_consen 51 VDELENENKALKRENEQLKKKLDT 74 (87)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444444444444444444444443
No 145
>PF14193 DUF4315: Domain of unknown function (DUF4315)
Probab=62.63 E-value=31 Score=22.92 Aligned_cols=29 Identities=21% Similarity=0.377 Sum_probs=21.1
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 57 EKIDLLVEEVRKLTLEIERLSDKFRLLHK 85 (99)
Q Consensus 57 ~k~~~l~~ei~e~~~ei~~l~~k~~~l~~ 85 (99)
+|++-|.+||.+....|.+++++++.|..
T Consensus 1 ~KleKi~~eieK~k~Kiae~Q~rlK~Le~ 29 (83)
T PF14193_consen 1 NKLEKIRAEIEKTKEKIAELQARLKELEA 29 (83)
T ss_pred ChHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 36677888888777778777777766643
No 146
>PF13600 DUF4140: N-terminal domain of unknown function (DUF4140)
Probab=62.30 E-value=28 Score=22.71 Aligned_cols=31 Identities=26% Similarity=0.409 Sum_probs=16.4
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 57 EKIDLLVEEVRKLTLEIERLSDKFRLLHKEL 87 (99)
Q Consensus 57 ~k~~~l~~ei~e~~~ei~~l~~k~~~l~~El 87 (99)
+....|+++++++..++..+++++..++..+
T Consensus 70 ~~~~~l~~~l~~l~~~~~~~~~~~~~~~~~~ 100 (104)
T PF13600_consen 70 PELKELEEELEALEDELAALQDEIQALEAQI 100 (104)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444555555555555555555555554443
No 147
>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=62.16 E-value=4.4 Score=22.06 Aligned_cols=9 Identities=44% Similarity=1.210 Sum_probs=5.5
Q ss_pred ceeeCCCCC
Q 041503 36 KFWKCRVCK 44 (99)
Q Consensus 36 ~Fy~C~~C~ 44 (99)
..++||.|+
T Consensus 16 ~~~~CP~Cg 24 (33)
T cd00350 16 APWVCPVCG 24 (33)
T ss_pred CCCcCcCCC
Confidence 556666665
No 148
>KOG4797 consensus Transcriptional regulator [Transcription]
Probab=62.10 E-value=19 Score=25.73 Aligned_cols=24 Identities=33% Similarity=0.430 Sum_probs=16.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 63 VEEVRKLTLEIERLSDKFRLLHKE 86 (99)
Q Consensus 63 ~~ei~e~~~ei~~l~~k~~~l~~E 86 (99)
+.||+-+++.|.+|..++..|+.|
T Consensus 66 REEVe~Lk~qI~eL~er~~~Le~E 89 (123)
T KOG4797|consen 66 REEVEVLKEQIRELEERNSALERE 89 (123)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 446777777777777777777555
No 149
>smart00338 BRLZ basic region leucin zipper.
Probab=62.09 E-value=27 Score=21.14 Aligned_cols=23 Identities=30% Similarity=0.491 Sum_probs=10.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 041503 66 VRKLTLEIERLSDKFRLLHKELE 88 (99)
Q Consensus 66 i~e~~~ei~~l~~k~~~l~~El~ 88 (99)
+.+|..++..|.+++..|..++.
T Consensus 28 ~~~Le~~~~~L~~en~~L~~~~~ 50 (65)
T smart00338 28 IEELERKVEQLEAENERLKKEIE 50 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444444555555555544443
No 150
>PRK07219 DNA topoisomerase I; Validated
Probab=62.00 E-value=7.4 Score=34.89 Aligned_cols=32 Identities=25% Similarity=0.590 Sum_probs=21.8
Q ss_pred cccccCccccceeeeecCCCCCCcceeeCC---CCCeeEe
Q 041503 12 LQVCNECGGQIELFTSHTTKNPNRKFWKCR---VCKNFQW 48 (99)
Q Consensus 12 ~~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~---~C~fF~W 48 (99)
...||.||..+.+..++. |. ||.|. .|+|..+
T Consensus 688 ~~~CP~Cg~~l~~k~gr~----G~-F~~Cs~yp~C~~~~~ 722 (822)
T PRK07219 688 IGPCPKCGGELAIKQLKY----GS-FLGCTNYPKCKYTLP 722 (822)
T ss_pred cccCCCCCCeeEEEcCCC----CC-eeeCCCCCCCCceee
Confidence 367999987655543332 44 99996 6987765
No 151
>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.
Probab=61.82 E-value=4.4 Score=29.60 Aligned_cols=10 Identities=30% Similarity=0.890 Sum_probs=4.4
Q ss_pred cccCccccce
Q 041503 14 VCNECGGQIE 23 (99)
Q Consensus 14 ~Cp~Cg~~~~ 23 (99)
.||.||....
T Consensus 3 ~Cp~C~~~~~ 12 (161)
T PF03367_consen 3 LCPNCGENGT 12 (161)
T ss_dssp E-TTTSSCCE
T ss_pred cCCCCCCCcE
Confidence 4555555433
No 152
>PF01920 Prefoldin_2: Prefoldin subunit; InterPro: IPR002777 Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal beta subunit, eukaryotic prefoldin subunits 1, 2, 4 and 6. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 2ZDI_B 3AEI_B 2ZQM_A 1FXK_A.
Probab=61.38 E-value=32 Score=21.99 Aligned_cols=30 Identities=33% Similarity=0.526 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 61 LLVEEVRKLTLEIERLSDKFRLLHKELEHT 90 (99)
Q Consensus 61 ~l~~ei~e~~~ei~~l~~k~~~l~~El~~~ 90 (99)
.|...+..+..+|+.|+.+...+..++++.
T Consensus 66 ~L~~~~~~~~~~i~~l~~~~~~l~~~l~~~ 95 (106)
T PF01920_consen 66 ELEERIEKLEKEIKKLEKQLKYLEKKLKEL 95 (106)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344455566666666666666665555543
No 153
>PF08432 Vfa1: AAA-ATPase Vps4-associated protein 1; InterPro: IPR013640 This is a family of fungal proteins of unknown function.
Probab=61.22 E-value=24 Score=26.00 Aligned_cols=26 Identities=23% Similarity=0.497 Sum_probs=14.4
Q ss_pred ccccCcccc-ceeeeecCCCCCCcceeeCC
Q 041503 13 QVCNECGGQ-IELFTSHTTKNPNRKFWKCR 41 (99)
Q Consensus 13 ~~Cp~Cg~~-~~~~tS~t~~NPgR~Fy~C~ 41 (99)
.-|--|.++ ..+++ |+.|+ =-||.||
T Consensus 14 k~C~IC~KpsttVL~--t~~~~-DfFY~C~ 40 (182)
T PF08432_consen 14 KACFICYKPSTTVLI--TPDNK-DFFYVCP 40 (182)
T ss_pred CceeEecCCCceEEe--cCCCC-CeEEeCc
Confidence 345456664 33333 33333 4799999
No 154
>PRK14973 DNA topoisomerase I; Provisional
Probab=61.19 E-value=5.9 Score=36.37 Aligned_cols=31 Identities=19% Similarity=0.416 Sum_probs=20.2
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCC---CCCeeEe
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCR---VCKNFQW 48 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~---~C~fF~W 48 (99)
..||.||..+.+... ++ | +||.|. .|+|...
T Consensus 589 ~~CP~CG~~l~ik~~---k~-g-kFigCS~Yp~Ck~t~~ 622 (936)
T PRK14973 589 GPCPVCGKDLRIKHI---GS-S-QFIGCSGYPDCTFNIG 622 (936)
T ss_pred ccCCcccccceeecc---cC-c-eeEECCCCCCCCcccc
Confidence 689999987554422 22 2 388887 5887644
No 155
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=60.81 E-value=8.3 Score=34.86 Aligned_cols=35 Identities=29% Similarity=0.550 Sum_probs=24.6
Q ss_pred ccccC--ccccceeeeecCCCCCCcceeeCC---CCCeeEeccC
Q 041503 13 QVCNE--CGGQIELFTSHTTKNPNRKFWKCR---VCKNFQWAED 51 (99)
Q Consensus 13 ~~Cp~--Cg~~~~~~tS~t~~NPgR~Fy~C~---~C~fF~W~De 51 (99)
+.||. ||...+++.++ -|..||.|. .|.|+.|.-+
T Consensus 694 ~~CP~~~C~g~l~~r~gr----~G~~f~~Cs~yp~C~~~~~~~~ 733 (860)
T PRK06319 694 VPCPAIGCTGHIVKRRSR----FNKMFYSCSEYPACSVIGNSID 733 (860)
T ss_pred CCCCCcCCCCcEEEEecC----CCCeeeccCCCCCCceeeccCC
Confidence 67884 78776655443 266699997 7998877654
No 156
>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=60.45 E-value=3.3 Score=26.62 Aligned_cols=37 Identities=24% Similarity=0.440 Sum_probs=29.2
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCeeEec
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQWA 49 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~W~ 49 (99)
..|..|+......+|+..-+-|=-+-+||+|+-..-.
T Consensus 5 FTC~~C~~Rs~~~~sk~aY~~GvViv~C~gC~~~HlI 41 (66)
T PF05180_consen 5 FTCNKCGTRSAKMFSKQAYHKGVVIVQCPGCKNRHLI 41 (66)
T ss_dssp EEETTTTEEEEEEEEHHHHHTSEEEEE-TTS--EEES
T ss_pred EEcCCCCCccceeeCHHHHhCCeEEEECCCCcceeee
Confidence 4688999999999999999999999999999854433
No 157
>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=60.44 E-value=9.1 Score=27.58 Aligned_cols=30 Identities=30% Similarity=0.814 Sum_probs=22.8
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCK 44 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~ 44 (99)
+.|+.|+....++..... ....|-+||.|+
T Consensus 111 v~C~~C~Gs~k~~~~~~~--~~~~~~rC~~Cn 140 (147)
T cd03031 111 VPCSECNGSCKVFAENAT--AAGGFLRCPECN 140 (147)
T ss_pred EECCCCCCcceEEeccCc--ccccEEECCCCC
Confidence 788889988888876533 445689999885
No 158
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=59.67 E-value=7.6 Score=30.11 Aligned_cols=30 Identities=17% Similarity=0.501 Sum_probs=20.5
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCeeEec
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQWA 49 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~W~ 49 (99)
..||.||.+.... +-+++ ..|+.|++..+-
T Consensus 100 ~fC~~CG~~~~~~------~~~~~-~~C~~c~~~~yp 129 (256)
T PRK00241 100 RFCGYCGHPMHPS------KTEWA-MLCPHCRERYYP 129 (256)
T ss_pred ccccccCCCCeec------CCcee-EECCCCCCEECC
Confidence 6899999976653 22333 469988877664
No 159
>PF13015 PRKCSH_1: Glucosidase II beta subunit-like protein
Probab=59.42 E-value=12 Score=27.29 Aligned_cols=28 Identities=25% Similarity=0.420 Sum_probs=22.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 62 LVEEVRKLTLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 62 l~~ei~e~~~ei~~l~~k~~~l~~El~~ 89 (99)
|+.+|+++..++..++.+++.++.+|+.
T Consensus 1 ~~~~~~~~e~~~~~l~~~i~~~~~~l~~ 28 (154)
T PF13015_consen 1 LEKEIDEAERKLSDLESKIRELEDDLNK 28 (154)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 3567888888888888888888888764
No 160
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=59.13 E-value=7 Score=29.36 Aligned_cols=18 Identities=44% Similarity=0.626 Sum_probs=10.5
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 041503 72 EIERLSDKFRLLHKELEH 89 (99)
Q Consensus 72 ei~~l~~k~~~l~~El~~ 89 (99)
.|+.|.++++.+..||+.
T Consensus 150 ~i~~l~~~i~~l~~~l~~ 167 (176)
T COG1675 150 EIEELESELDELEEELER 167 (176)
T ss_pred HHHHHHHHHHHHHHHHhc
Confidence 455566666666566554
No 161
>PF13815 Dzip-like_N: Iguana/Dzip1-like DAZ-interacting protein N-terminal
Probab=59.12 E-value=22 Score=24.32 Aligned_cols=21 Identities=33% Similarity=0.578 Sum_probs=8.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 041503 67 RKLTLEIERLSDKFRLLHKEL 87 (99)
Q Consensus 67 ~e~~~ei~~l~~k~~~l~~El 87 (99)
+.+..++++++.++.++..|+
T Consensus 90 ~~~~~~~~~l~~~~~~~~~~~ 110 (118)
T PF13815_consen 90 QELQQEIEKLKQKLKKQKEEI 110 (118)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 333344444444444443333
No 162
>PRK14724 DNA topoisomerase III; Provisional
Probab=59.08 E-value=8.5 Score=35.46 Aligned_cols=30 Identities=20% Similarity=0.411 Sum_probs=22.5
Q ss_pred cccccCccccceeeeecCCCCCCcceeeCCC-----------CCeeEecc
Q 041503 12 LQVCNECGGQIELFTSHTTKNPNRKFWKCRV-----------CKNFQWAE 50 (99)
Q Consensus 12 ~~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~-----------C~fF~W~D 50 (99)
...||.||..+.. +..+|.|.. |+|-.|.-
T Consensus 755 ~g~CPkCg~~v~e---------~gk~y~Cs~~~~~~~~~~~~C~f~i~k~ 795 (987)
T PRK14724 755 LGPCPKCGAPVFE---------HGSNYVCEKSVPTLAQPTPSCTFKSGQV 795 (987)
T ss_pred ccCCCCCCCceEe---------ecceEEcCCCcccccCCCCCCCceeccc
Confidence 4789999987431 577999973 99887753
No 163
>PF10883 DUF2681: Protein of unknown function (DUF2681); InterPro: IPR020274 This entry contains membrane proteins with no known function.
Probab=58.96 E-value=52 Score=22.11 Aligned_cols=41 Identities=20% Similarity=0.191 Sum_probs=29.6
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 041503 55 SNEKIDLLVEEVRKLTLEIERLSDKFRLLHKELEHTQLRSK 95 (99)
Q Consensus 55 ~~~k~~~l~~ei~e~~~ei~~l~~k~~~l~~El~~~~~~~~ 95 (99)
.|=+..-+..++.+|..|.+.|+.++..-..+++....+-|
T Consensus 21 ~~~k~~ka~~~~~kL~~en~qlk~Ek~~~~~qvkn~~vrqk 61 (87)
T PF10883_consen 21 LWWKVKKAKKQNAKLQKENEQLKTEKAVAETQVKNAKVRQK 61 (87)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444555667888888888888888888888887776654
No 164
>COG2433 Uncharacterized conserved protein [Function unknown]
Probab=58.92 E-value=23 Score=31.65 Aligned_cols=30 Identities=37% Similarity=0.462 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 60 DLLVEEVRKLTLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 60 ~~l~~ei~e~~~ei~~l~~k~~~l~~El~~ 89 (99)
..|+.|+++|+.++++|++.+.+|+.+|+.
T Consensus 432 e~l~~e~~~L~~~~ee~k~eie~L~~~l~~ 461 (652)
T COG2433 432 ERLEEENSELKRELEELKREIEKLESELER 461 (652)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344556666666666666666666666653
No 165
>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=58.75 E-value=7.1 Score=21.20 Aligned_cols=12 Identities=33% Similarity=1.035 Sum_probs=10.1
Q ss_pred ceeeCCCCCeeE
Q 041503 36 KFWKCRVCKNFQ 47 (99)
Q Consensus 36 ~Fy~C~~C~fF~ 47 (99)
.||+|..|+.+.
T Consensus 3 ~~ykC~~CGniv 14 (34)
T cd00974 3 EVYKCEICGNIV 14 (34)
T ss_pred cEEEcCCCCcEE
Confidence 599999998665
No 166
>PRK06599 DNA topoisomerase I; Validated
Probab=58.59 E-value=7 Score=34.19 Aligned_cols=34 Identities=32% Similarity=0.628 Sum_probs=22.6
Q ss_pred cccccCcc-ccceeeeecCCCCCCcceeeCC---CCCeeEecc
Q 041503 12 LQVCNECG-GQIELFTSHTTKNPNRKFWKCR---VCKNFQWAE 50 (99)
Q Consensus 12 ~~~Cp~Cg-~~~~~~tS~t~~NPgR~Fy~C~---~C~fF~W~D 50 (99)
...||.|| ..++....+ ..+||.|. .|+|..|..
T Consensus 585 ~~~CP~C~~~~l~~k~~k-----~g~F~~Cs~~p~C~~~~~~~ 622 (675)
T PRK06599 585 DETCPKCGGGPLVLKLGK-----NGKFLGCSGYPECKYTKNIT 622 (675)
T ss_pred CccccccCCCcceEEecC-----CCceeeCCCCCccCCCCCCc
Confidence 47899995 454443222 22499996 799988853
No 167
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=58.34 E-value=3.3 Score=33.39 Aligned_cols=27 Identities=22% Similarity=0.329 Sum_probs=18.3
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCe
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKN 45 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~f 45 (99)
.+||.|+...-..- -.+.+|.||.|++
T Consensus 39 ~kc~~C~~~~~~~~------l~~~~~vcp~c~~ 65 (296)
T CHL00174 39 VQCENCYGLNYKKF------LKSKMNICEQCGY 65 (296)
T ss_pred eECCCccchhhHHH------HHHcCCCCCCCCC
Confidence 89999997543221 2355789998874
No 168
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=58.31 E-value=8.5 Score=30.76 Aligned_cols=27 Identities=33% Similarity=0.784 Sum_probs=21.9
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCK 44 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~ 44 (99)
.-|+.||..+..-+-. ||.+|=||.|.
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 6799999877665554 79999999996
No 169
>PF11461 RILP: Rab interacting lysosomal protein; InterPro: IPR021563 RILP contains a domain which contains two coiled-coil regions and is found mainly in the cytosol. RILP is recruited onto late endosomal and lysosomal membranes by Rab7 and acts as a downstream effector of Rab7. This recruitment process is important for phagosome maturation and fusion with late endosomes and lysosomes. ; PDB: 1YHN_B.
Probab=58.31 E-value=17 Score=22.96 Aligned_cols=26 Identities=31% Similarity=0.422 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 64 EEVRKLTLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 64 ~ei~e~~~ei~~l~~k~~~l~~El~~ 89 (99)
.|++++=-|-.+|+++.-.|+.||.-
T Consensus 3 ~ELr~VL~ERNeLK~~v~~leEEL~~ 28 (60)
T PF11461_consen 3 QELREVLQERNELKARVFLLEEELAY 28 (60)
T ss_dssp TTHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46777777888888888888888863
No 170
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=58.30 E-value=7.3 Score=21.10 Aligned_cols=13 Identities=38% Similarity=0.945 Sum_probs=10.5
Q ss_pred cceeeCCCCCeeE
Q 041503 35 RKFWKCRVCKNFQ 47 (99)
Q Consensus 35 R~Fy~C~~C~fF~ 47 (99)
-.||+|..|+.+.
T Consensus 5 ~~~ykC~~Cgniv 17 (34)
T TIGR00319 5 GQVYKCEVCGNIV 17 (34)
T ss_pred CcEEEcCCCCcEE
Confidence 4699999998665
No 171
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=58.05 E-value=8.4 Score=28.98 Aligned_cols=35 Identities=23% Similarity=0.578 Sum_probs=25.9
Q ss_pred ccccCccccceeeeecCCCCCCcc-eeeCCCCCeeEeccCC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRK-FWKCRVCKNFQWAEDR 52 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~-Fy~C~~C~fF~W~De~ 52 (99)
+.||.|+.+=..++.. +|. |-+|..|+...=++..
T Consensus 99 V~C~~C~~pdT~l~k~-----~~~~~l~C~aCGa~~~v~~~ 134 (201)
T PRK12336 99 VICSECGLPDTRLVKE-----DRVLMLRCDACGAHRPVKKR 134 (201)
T ss_pred EECCCCCCCCcEEEEc-----CCeEEEEcccCCCCcccccc
Confidence 8999999976666643 356 5599999977666554
No 172
>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=57.86 E-value=6.1 Score=25.73 Aligned_cols=25 Identities=20% Similarity=0.324 Sum_probs=11.3
Q ss_pred CCcccccCccccceeeeecCCCCCC
Q 041503 10 NSLQVCNECGGQIELFTSHTTKNPN 34 (99)
Q Consensus 10 ~~~~~Cp~Cg~~~~~~tS~t~~NPg 34 (99)
....-||.||.....++|-+.+..|
T Consensus 22 ~~k~FCp~CGn~TL~rvsvsv~~~G 46 (73)
T PF08772_consen 22 MTKQFCPKCGNATLKRVSVSVDEDG 46 (73)
T ss_dssp SS--S-SSS--S--EEEE-B--SS-
T ss_pred CCceeCcccCCCcceEEEEEECCCC
Confidence 3448899999999999998876555
No 173
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=57.75 E-value=6.8 Score=32.80 Aligned_cols=23 Identities=26% Similarity=1.008 Sum_probs=14.9
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCee
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNF 46 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF 46 (99)
-.|..||..+..+ ||-||+|+-|
T Consensus 355 YRC~~CGF~a~~l-----------~W~CPsC~~W 377 (389)
T COG2956 355 YRCQNCGFTAHTL-----------YWHCPSCRAW 377 (389)
T ss_pred ceecccCCcceee-----------eeeCCCcccc
Confidence 5677777665543 6777777743
No 174
>PF10018 Med4: Vitamin-D-receptor interacting Mediator subunit 4; InterPro: IPR019258 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Members of this family represent the Med4 subunit of the Mediator (Med) complex [, ]. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=57.50 E-value=35 Score=25.05 Aligned_cols=34 Identities=24% Similarity=0.361 Sum_probs=19.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 58 KIDLLVEEVRKLTLEIERLSDKFRLLHKELEHTQ 91 (99)
Q Consensus 58 k~~~l~~ei~e~~~ei~~l~~k~~~l~~El~~~~ 91 (99)
++..|.+|+..++..|+.+-.++...++||...-
T Consensus 30 ~I~~L~~e~~~ld~~i~~~~~~L~~~~~~L~~~~ 63 (188)
T PF10018_consen 30 RIQQLRAEIEELDEQIRDILKQLKEARKELRTLP 63 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445555666666666666666666666665543
No 175
>PF11853 DUF3373: Protein of unknown function (DUF3373); InterPro: IPR021803 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 472 to 574 amino acids in length.
Probab=57.12 E-value=12 Score=32.23 Aligned_cols=19 Identities=21% Similarity=0.303 Sum_probs=8.9
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 041503 65 EVRKLTLEIERLSDKFRLL 83 (99)
Q Consensus 65 ei~e~~~ei~~l~~k~~~l 83 (99)
+|++|+.||++|++|...|
T Consensus 32 kie~L~kql~~Lk~q~~~l 50 (489)
T PF11853_consen 32 KIEALKKQLEELKAQQDDL 50 (489)
T ss_pred HHHHHHHHHHHHHHhhccc
Confidence 4444444444444444433
No 176
>KOG4684 consensus Uncharacterized conserved protein, contains C4-type Zn-finger [General function prediction only]
Probab=57.02 E-value=5.6 Score=31.61 Aligned_cols=26 Identities=19% Similarity=0.639 Sum_probs=20.9
Q ss_pred cccccCccccceeeeecCCCCCCcceeeCC
Q 041503 12 LQVCNECGGQIELFTSHTTKNPNRKFWKCR 41 (99)
Q Consensus 12 ~~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~ 41 (99)
+++|..|++...++- .-||++|.+||
T Consensus 100 VVKC~~CnEATPIrn----APpGKKYVRCP 125 (275)
T KOG4684|consen 100 VVKCHSCNEATPIRN----APPGKKYVRCP 125 (275)
T ss_pred eEeecccCccccCCC----CCCCCceeecC
Confidence 389988988776653 45899999999
No 177
>PRK11546 zraP zinc resistance protein; Provisional
Probab=56.43 E-value=42 Score=24.44 Aligned_cols=18 Identities=22% Similarity=0.390 Sum_probs=11.5
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 041503 66 VRKLTLEIERLSDKFRLL 83 (99)
Q Consensus 66 i~e~~~ei~~l~~k~~~l 83 (99)
|+++..||..|++++..+
T Consensus 91 I~aL~kEI~~Lr~kL~e~ 108 (143)
T PRK11546 91 INAVAKEMENLRQSLDEL 108 (143)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 556666777777666643
No 178
>PF14712 Snapin_Pallidin: Snapin/Pallidin
Probab=56.42 E-value=46 Score=21.25 Aligned_cols=33 Identities=21% Similarity=0.358 Sum_probs=19.8
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 56 NEKIDLLVEEVRKLTLEIERLSDKFRLLHKELE 88 (99)
Q Consensus 56 ~~k~~~l~~ei~e~~~ei~~l~~k~~~l~~El~ 88 (99)
.|..+.+.+-|.++...-..|.++++.+..+|.
T Consensus 13 ~P~l~~~~~~l~el~~sQ~~L~~~i~~~~~~L~ 45 (92)
T PF14712_consen 13 EPDLDRLDQQLQELRQSQEELLQQIDRLNEKLK 45 (92)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 466666666666665555555556666555554
No 179
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=56.35 E-value=6.4 Score=37.61 Aligned_cols=38 Identities=13% Similarity=0.261 Sum_probs=19.4
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCeeEecc
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQWAE 50 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~W~D 50 (99)
.+||.||..........=..+--.-|.||.|+.-.=.|
T Consensus 668 rkCPkCG~~t~~~fCP~CGs~te~vy~CPsCGaev~~d 705 (1337)
T PRK14714 668 RRCPSCGTETYENRCPDCGTHTEPVYVCPDCGAEVPPD 705 (1337)
T ss_pred EECCCCCCccccccCcccCCcCCCceeCccCCCccCCC
Confidence 77888887433222111111111246899888754344
No 180
>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast). The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].
Probab=56.14 E-value=55 Score=24.33 Aligned_cols=30 Identities=30% Similarity=0.400 Sum_probs=17.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 61 LLVEEVRKLTLEIERLSDKFRLLHKELEHT 90 (99)
Q Consensus 61 ~l~~ei~e~~~ei~~l~~k~~~l~~El~~~ 90 (99)
.+...+.++..+++.+++++..++.+|+..
T Consensus 66 ~~~~~~~~l~~~~~~~~~~i~~l~~~i~~~ 95 (188)
T PF03962_consen 66 KRQNKLEKLQKEIEELEKKIEELEEKIEEA 95 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334455666666666666666666666554
No 181
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=55.91 E-value=8.8 Score=21.40 Aligned_cols=30 Identities=20% Similarity=0.562 Sum_probs=19.0
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCK 44 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~ 44 (99)
+.||.|+..-.+--++-+ |+.+=.+|+.|+
T Consensus 3 i~Cp~C~~~y~i~d~~ip--~~g~~v~C~~C~ 32 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIP--PKGRKVRCSKCG 32 (36)
T ss_pred EECCCCCCEEeCCHHHCC--CCCcEEECCCCC
Confidence 578888875544433332 444567888887
No 182
>PF08172 CASP_C: CASP C terminal; InterPro: IPR012955 This domain is the C-terminal region of the CASP family of proteins. These are Golgi membrane proteins which are thought to have a role in vesicle transport [].; GO: 0006891 intra-Golgi vesicle-mediated transport, 0030173 integral to Golgi membrane
Probab=55.74 E-value=27 Score=27.25 Aligned_cols=24 Identities=21% Similarity=0.326 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 66 VRKLTLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 66 i~e~~~ei~~l~~k~~~l~~El~~ 89 (99)
+.||.+|+.++++++..|+.|++.
T Consensus 95 n~ELE~elr~~~~~~~~L~~Ev~~ 118 (248)
T PF08172_consen 95 NAELEEELRKQQQTISSLRREVES 118 (248)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444555555555555555443
No 183
>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=55.40 E-value=8.7 Score=33.71 Aligned_cols=33 Identities=15% Similarity=0.347 Sum_probs=21.6
Q ss_pred cccccCccccceeeeecCCCCCCcceeeCC----------CCCeeEecc
Q 041503 12 LQVCNECGGQIELFTSHTTKNPNRKFWKCR----------VCKNFQWAE 50 (99)
Q Consensus 12 ~~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~----------~C~fF~W~D 50 (99)
...|| ||...+...++. | +|+.|. +|+|=.|..
T Consensus 611 ~~~cp-cg~~l~~~~~~~----g-~f~~c~~~p~C~~~~~~c~~~~~~~ 653 (660)
T TIGR01056 611 KEPVS-CGGIAKCPAKDN----G-RLIDCKKFPECTEYGNGCEFTIPKK 653 (660)
T ss_pred CccCC-CCCceeeeecCC----C-eeecCCCCCCccCcCCCCeEEccHH
Confidence 36798 998877664432 3 488886 466666654
No 184
>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=55.29 E-value=6.2 Score=21.02 Aligned_cols=21 Identities=19% Similarity=0.616 Sum_probs=10.8
Q ss_pred cccCccccceeeeecCCCCCCcceeeCC
Q 041503 14 VCNECGGQIELFTSHTTKNPNRKFWKCR 41 (99)
Q Consensus 14 ~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~ 41 (99)
.||.||..++ +.+|...|+|+
T Consensus 1 ~CP~C~s~l~-------~~~~ev~~~C~ 21 (28)
T PF03119_consen 1 TCPVCGSKLV-------REEGEVDIRCP 21 (28)
T ss_dssp B-TTT--BEE-------E-CCTTCEEE-
T ss_pred CcCCCCCEeE-------cCCCCEeEECC
Confidence 4889997766 23556677776
No 185
>PRK15396 murein lipoprotein; Provisional
Probab=54.89 E-value=59 Score=21.38 Aligned_cols=30 Identities=27% Similarity=0.526 Sum_probs=17.7
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 57 EKIDLLVEEVRKLTLEIERLSDKFRLLHKE 86 (99)
Q Consensus 57 ~k~~~l~~ei~e~~~ei~~l~~k~~~l~~E 86 (99)
++.+.|.++|..+..++.++......++.+
T Consensus 25 ~kvd~LssqV~~L~~kvdql~~dv~~~~~~ 54 (78)
T PRK15396 25 AKIDQLSSDVQTLNAKVDQLSNDVNAMRSD 54 (78)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455666666666666666665555555553
No 186
>PRK08116 hypothetical protein; Validated
Probab=54.84 E-value=9.1 Score=29.56 Aligned_cols=35 Identities=23% Similarity=0.360 Sum_probs=21.0
Q ss_pred CCCCcccccCccccceeeeecCCCCCCcceeeCCCCC
Q 041503 8 SRNSLQVCNECGGQIELFTSHTTKNPNRKFWKCRVCK 44 (99)
Q Consensus 8 ~~~~~~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~ 44 (99)
...+...||.||.+....+. ..++.+.+..|+.|.
T Consensus 12 ~~~~~~~C~~Cg~~~~~~~~--~~~~~~~~~~~c~C~ 46 (268)
T PRK08116 12 EEDGGEYCEVCGKRIEKVVE--LLGKNRIVPIMCECE 46 (268)
T ss_pred ccccCccCcCCCCcceeeec--ccCcceecCCCCCCh
Confidence 34566899999986654332 233344444577774
No 187
>TIGR02338 gimC_beta prefoldin, beta subunit, archaeal. Chaperonins are cytosolic, ATP-dependent molecular chaperones, with a conserved toroidal architecture, that assist in the folding of nascent and/or denatured polypeptide chains. The group I chaperonin system consists of GroEL and GroES, and is found (usually) in bacteria and organelles of bacterial origin. The group II chaperonin system, called the thermosome in Archaea and TRiC or CCT in the Eukaryota, is structurally similar but only distantly related. Prefoldin, also called GimC, is a complex in Archaea and Eukaryota, that works with group II chaperonins. Members of this protein family are the archaeal clade of the beta class of prefoldin subunit. Closely related, but outside the scope of this family are the eukaryotic beta-class prefoldin subunits, Gim-1,3,4 and 6. The alpha class prefoldin subunits are more distantly related.
Probab=54.74 E-value=45 Score=22.36 Aligned_cols=26 Identities=19% Similarity=0.308 Sum_probs=14.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 65 EVRKLTLEIERLSDKFRLLHKELEHT 90 (99)
Q Consensus 65 ei~e~~~ei~~l~~k~~~l~~El~~~ 90 (99)
.++.+...|+.|..+...+++.+++.
T Consensus 75 r~e~ie~~i~~lek~~~~l~~~l~e~ 100 (110)
T TIGR02338 75 KKETLELRVKTLQRQEERLREQLKEL 100 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44455555555555555555555543
No 188
>PF13863 DUF4200: Domain of unknown function (DUF4200)
Probab=54.73 E-value=62 Score=21.60 Aligned_cols=25 Identities=36% Similarity=0.603 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 65 EVRKLTLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 65 ei~e~~~ei~~l~~k~~~l~~El~~ 89 (99)
||.++..+|..|+..+..+...|++
T Consensus 82 ei~~l~~~l~~l~~~~~k~e~~l~~ 106 (126)
T PF13863_consen 82 EIKKLKAELEELKSEISKLEEKLEE 106 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5556666666666666666555554
No 189
>PF12548 DUF3740: Sulfatase protein; InterPro: IPR024609 This uncharacterised domain is found in the C-terminal region of extracellular sulphatase proteins.
Probab=54.55 E-value=27 Score=25.41 Aligned_cols=45 Identities=18% Similarity=0.283 Sum_probs=21.5
Q ss_pred CCCCcceeeCC-------CCCeeEeccCCccchhhH-HHHHHHHHHHHHHHHHHH
Q 041503 31 KNPNRKFWKCR-------VCKNFQWAEDRKFSNEKI-DLLVEEVRKLTLEIERLS 77 (99)
Q Consensus 31 ~NPgR~Fy~C~-------~C~fF~W~De~~~~~~k~-~~l~~ei~e~~~ei~~l~ 77 (99)
.|+-+..++|- .|.--+..|.- +|-+- .-|+.||+.|..+|+.|+
T Consensus 74 ~~~i~~t~rC~Il~n~tVnCs~~iY~d~~--aWk~hr~~ID~eIe~Lq~Ki~~LK 126 (145)
T PF12548_consen 74 PNSIQVTHRCFILPNDTVNCSNVIYQDPK--AWKDHRLHIDHEIETLQDKIKNLK 126 (145)
T ss_pred cccccceeeEEEecCCcEeccHhhhcCHH--HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44456667874 56543333332 67442 333444444444444444
No 190
>PHA02107 hypothetical protein
Probab=54.53 E-value=16 Score=28.07 Aligned_cols=21 Identities=29% Similarity=0.458 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 66 VRKLTLEIERLSDKFRLLHKELEHT 90 (99)
Q Consensus 66 i~e~~~ei~~l~~k~~~l~~El~~~ 90 (99)
|.|++.||++|+ ++++|+|+.
T Consensus 186 i~EID~EI~~LQ----A~RKEiEDN 206 (216)
T PHA02107 186 ISEIDEEIKELQ----ARRKEIEDN 206 (216)
T ss_pred HhHHhHHHHHHH----HHHHHHHHH
Confidence 668999998888 889998753
No 191
>PHA02446 hypothetical protein
Probab=54.41 E-value=5.4 Score=29.16 Aligned_cols=29 Identities=24% Similarity=0.535 Sum_probs=23.8
Q ss_pred ccccCcccccee-eeecCCCCCCcceeeCC
Q 041503 13 QVCNECGGQIEL-FTSHTTKNPNRKFWKCR 41 (99)
Q Consensus 13 ~~Cp~Cg~~~~~-~tS~t~~NPgR~Fy~C~ 41 (99)
..||-||..+-+ .+-.-+..|.|.|-.||
T Consensus 63 q~cp~cg~dawv~~~g~~eahpd~l~qecp 92 (166)
T PHA02446 63 QQCPLCGQDAWVIHTGIVEAHPDKLLQECP 92 (166)
T ss_pred hcCCCcccceeEeecCccccCcHHHHHhCC
Confidence 689999997644 44566789999999999
No 192
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=54.35 E-value=7 Score=19.17 Aligned_cols=10 Identities=30% Similarity=0.776 Sum_probs=6.0
Q ss_pred eeCCCCCeeE
Q 041503 38 WKCRVCKNFQ 47 (99)
Q Consensus 38 y~C~~C~fF~ 47 (99)
|+|+.|.|.-
T Consensus 1 y~C~~C~y~t 10 (24)
T PF13909_consen 1 YKCPHCSYST 10 (24)
T ss_dssp EE-SSSS-EE
T ss_pred CCCCCCCCcC
Confidence 7888888754
No 193
>PRK08173 DNA topoisomerase III; Validated
Probab=54.22 E-value=12 Score=34.01 Aligned_cols=29 Identities=21% Similarity=0.523 Sum_probs=21.1
Q ss_pred cccccCccccceeeeecCCCCCCcceeeCCC-------CCeeEec
Q 041503 12 LQVCNECGGQIELFTSHTTKNPNRKFWKCRV-------CKNFQWA 49 (99)
Q Consensus 12 ~~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~-------C~fF~W~ 49 (99)
...||.||..+.. +..+|.|.. |+|-.|.
T Consensus 726 ~g~CPkCg~~v~e---------~~k~y~Cs~~~~~~~~C~f~i~k 761 (862)
T PRK08173 726 VGACPKCGGRVFE---------HGMSYVCEKSVGPPKTCDFRSGK 761 (862)
T ss_pred ccCCCCCCCeeEe---------eceEEEeCCCcCCCCCCCeeeCc
Confidence 4789999986431 233899973 9999884
No 194
>PRK05776 DNA topoisomerase I; Provisional
Probab=54.11 E-value=9.9 Score=33.47 Aligned_cols=36 Identities=11% Similarity=0.078 Sum_probs=24.0
Q ss_pred ccccCccccc----eeeeecCCCCCCcceeeCC---CCCeeEeccC
Q 041503 13 QVCNECGGQI----ELFTSHTTKNPNRKFWKCR---VCKNFQWAED 51 (99)
Q Consensus 13 ~~Cp~Cg~~~----~~~tS~t~~NPgR~Fy~C~---~C~fF~W~De 51 (99)
..||.||.++ ++..++. ++ -+|+.|. .|++=.+...
T Consensus 597 ~~Cp~Cg~~l~~~~~~~~~~~--~~-~~f~~c~~~p~c~~~~~~~~ 639 (670)
T PRK05776 597 GKCKICGREAYKDGLCKYHYE--AK-KRLVKAYEEWKERTGYDHKE 639 (670)
T ss_pred CcCCCCCCccccCceEEeccc--CC-ccceecCCCccccCCCCcch
Confidence 6899999876 4443332 22 3799997 7987665554
No 195
>PF00170 bZIP_1: bZIP transcription factor cAMP response element binding (CREB) protein signature fos transforming protein signature jun transcription factor signature; InterPro: IPR011616 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotic are proteins that contain a basic region mediating sequence-specific DNA-binding followed by a leucine zipper region (see IPR002158 from INTERPRO) required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2H7H_B 2OQQ_B 1S9K_E 1JNM_A 1JUN_A 1FOS_H 1A02_J 1T2K_C 1CI6_A 1DH3_C ....
Probab=54.08 E-value=47 Score=20.05 Aligned_cols=26 Identities=31% Similarity=0.392 Sum_probs=11.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 61 LLVEEVRKLTLEIERLSDKFRLLHKE 86 (99)
Q Consensus 61 ~l~~ei~e~~~ei~~l~~k~~~l~~E 86 (99)
.|..+...+..++..|...+..|..|
T Consensus 37 ~L~~en~~L~~~~~~L~~~~~~L~~e 62 (64)
T PF00170_consen 37 ELESENEELKKELEQLKKEIQSLKSE 62 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 33344444444444444444444443
No 196
>PF14931 IFT20: Intraflagellar transport complex B, subunit 20
Probab=53.99 E-value=62 Score=22.71 Aligned_cols=25 Identities=28% Similarity=0.462 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 61 LLVEEVRKLTLEIERLSDKFRLLHK 85 (99)
Q Consensus 61 ~l~~ei~e~~~ei~~l~~k~~~l~~ 85 (99)
.++..|.+...|+++|+..++.|++
T Consensus 84 ~lq~~I~Ek~~eLERl~~E~~sL~k 108 (120)
T PF14931_consen 84 QLQALIAEKKMELERLRSEYESLQK 108 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445677888888888888887743
No 197
>PF12808 Mto2_bdg: Micro-tubular organiser Mto1 C-term Mto2-binding region; InterPro: IPR024545 This domain occurs at the C terminus of microtubule organising proteins in both budding and fission fungi. In Schizosaccharomyces pombe it has been shown to interact with the Mto2p protein, an interaction which is critical for anchoring the cytokinetic actin ring to the medial region of the cell and for proper coordination of mitosis with cytokinesis [, ].
Probab=53.82 E-value=29 Score=21.29 Aligned_cols=26 Identities=31% Similarity=0.413 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 68 KLTLEIERLSDKFRLLHKELEHTQLR 93 (99)
Q Consensus 68 e~~~ei~~l~~k~~~l~~El~~~~~~ 93 (99)
....+|.+|...++.|+.||+..++.
T Consensus 26 ~a~~rl~~l~~EN~~Lr~eL~~~r~~ 51 (52)
T PF12808_consen 26 AARKRLSKLEGENRLLRAELERLRSR 51 (52)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 44567888888888888999888765
No 198
>PF10186 Atg14: UV radiation resistance protein and autophagy-related subunit 14; InterPro: IPR018791 Class III phosphatidylinositol 3-kinase (PI3-kinase) regulates multiple membrane trafficking. In yeast, two distinct PI3-kinase complexes are known: complex I (Vps34, Vps15, Vps30/Atg6, and Atg14) is involved in autophagy, and complex II (Vps34, Vps15, Vps30/Atg6, and Vps38) functions in the vacuolar protein sorting pathway. In mammals, the counterparts of Vps34, Vps15, and Vps30/Atg6 are Vps34, p150, and Beclin 1, respectively. Mammalian UV irradiation resistance-associated gene (UVRAG) has been identified as identical to yeast Vps38 []. The Atg14 (autophagy-related protein 14) proteins are hydrophilic proteins and have a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole []. This entry represents Atg14 and UVRAG, which bind Beclin 1 to forms two distinct PI3-kinase complexes. This entry also includes Bakor (beclin-1-associated autophagy-related key regulator), also known as autophagy-related protein 14-like protein, which share sequence similarity to the yeast Atg14 protein []. Barkor positively regulates autophagy through its interaction with Beclin-1, with decreased levels of autophagosome formation observed when Barkor expression is eliminated []. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. ; GO: 0010508 positive regulation of autophagy
Probab=53.66 E-value=57 Score=24.35 Aligned_cols=11 Identities=45% Similarity=1.307 Sum_probs=6.5
Q ss_pred CCCcceeeCCCC
Q 041503 32 NPNRKFWKCRVC 43 (99)
Q Consensus 32 NPgR~Fy~C~~C 43 (99)
+++++|| |++|
T Consensus 7 ~~~~~~~-C~~C 17 (302)
T PF10186_consen 7 NSRRRFY-CANC 17 (302)
T ss_pred CCCCCeE-CHHH
Confidence 5556665 6655
No 199
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=53.58 E-value=15 Score=21.42 Aligned_cols=30 Identities=20% Similarity=0.480 Sum_probs=19.6
Q ss_pred CCccccc--CccccceeeeecCCCCCCcceeeCCCCC
Q 041503 10 NSLQVCN--ECGGQIELFTSHTTKNPNRKFWKCRVCK 44 (99)
Q Consensus 10 ~~~~~Cp--~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~ 44 (99)
.....|| .|+..+..- .+++-....|+.|+
T Consensus 16 ~~~~~CP~~~C~~~~~~~-----~~~~~~~v~C~~C~ 47 (64)
T smart00647 16 PDLKWCPAPDCSAAIIVT-----EEEGCNRVTCPKCG 47 (64)
T ss_pred CCccCCCCCCCcceEEec-----CCCCCCeeECCCCC
Confidence 3446798 887655432 15666778898775
No 200
>PLN02678 seryl-tRNA synthetase
Probab=53.43 E-value=38 Score=28.66 Aligned_cols=30 Identities=20% Similarity=0.274 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 61 LLVEEVRKLTLEIERLSDKFRLLHKELEHT 90 (99)
Q Consensus 61 ~l~~ei~e~~~ei~~l~~k~~~l~~El~~~ 90 (99)
.|.+++++++.+|..|.++...++.+|.+.
T Consensus 75 ~l~~~~~~Lk~ei~~le~~~~~~~~~l~~~ 104 (448)
T PLN02678 75 ELIAETKELKKEITEKEAEVQEAKAALDAK 104 (448)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334455566666666666666666666553
No 201
>PF05529 Bap31: B-cell receptor-associated protein 31-like ; InterPro: IPR008417 Bap31 is a polytopic integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8. Bap31 is cleaved within its cytosolic domain, generating pro-apoptotic p20 Bap31 [].; GO: 0006886 intracellular protein transport, 0005783 endoplasmic reticulum, 0016021 integral to membrane
Probab=53.29 E-value=32 Score=24.98 Aligned_cols=10 Identities=40% Similarity=0.737 Sum_probs=3.7
Q ss_pred HHHHHHHHHH
Q 041503 72 EIERLSDKFR 81 (99)
Q Consensus 72 ei~~l~~k~~ 81 (99)
|+++|++++.
T Consensus 162 ei~~lk~el~ 171 (192)
T PF05529_consen 162 EIEKLKKELE 171 (192)
T ss_pred HHHHHHHHHH
Confidence 3333333333
No 202
>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=53.08 E-value=11 Score=32.73 Aligned_cols=25 Identities=24% Similarity=0.598 Sum_probs=16.5
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRV 42 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~ 42 (99)
..||.||..++....++ -.||.|.+
T Consensus 590 ~~CPkCg~~l~~~~~k~-----g~f~gCs~ 614 (618)
T TIGR01057 590 GKCPKCGGKLVSKYAKK-----GRFVGCSN 614 (618)
T ss_pred CCCCcCCCeeeeeecCC-----ccEEECCC
Confidence 57999998755432221 26999974
No 203
>PRK14127 cell division protein GpsB; Provisional
Probab=52.99 E-value=42 Score=23.36 Aligned_cols=23 Identities=22% Similarity=0.330 Sum_probs=11.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 041503 67 RKLTLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 67 ~e~~~ei~~l~~k~~~l~~El~~ 89 (99)
..+..++.+|+.++..|+.+|.+
T Consensus 40 e~l~~e~~~Lk~e~~~l~~~l~e 62 (109)
T PRK14127 40 EAFQKEIEELQQENARLKAQVDE 62 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445555555555555555544
No 204
>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=52.95 E-value=7.9 Score=21.20 Aligned_cols=25 Identities=20% Similarity=0.628 Sum_probs=9.4
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCe
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKN 45 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~f 45 (99)
++||.|+..-.. +..--|.||.|.+
T Consensus 3 p~Cp~C~se~~y--------~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 3 PKCPLCGSEYTY--------EDGELLVCPECGH 27 (30)
T ss_dssp ---TTT-----E--------E-SSSEEETTTTE
T ss_pred CCCCCCCCccee--------ccCCEEeCCcccc
Confidence 567777754333 3444566666653
No 205
>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=52.87 E-value=12 Score=32.50 Aligned_cols=28 Identities=29% Similarity=0.593 Sum_probs=18.3
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCC---CCCe
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCR---VCKN 45 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~---~C~f 45 (99)
..||.||..+.....++ | +||.|. .|+|
T Consensus 575 ~~CP~Cg~~~~~~~~~~----g-kf~gCs~y~~C~~ 605 (610)
T TIGR01051 575 QDCPLCGRPMVVKLGKY----G-PFLACSNFPECKY 605 (610)
T ss_pred CCCCCCCCeeEEEecCC----C-ceeeCCCCCCCCC
Confidence 67999998644332222 3 599997 4875
No 206
>PF05615 THOC7: Tho complex subunit 7; InterPro: IPR008501 The Tho complex (THOC) is involved in transcription elongation and mRNA export from the nucleus []. This entry represents the subunit THOC7, which is found in higher eukaryotes, and the non-homologous subunit Mft1p found in yeast. The funtions of these subunits are unknown, and it is not known if these subunits are functionally equivalent.
Probab=52.71 E-value=54 Score=22.66 Aligned_cols=28 Identities=25% Similarity=0.368 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 041503 68 KLTLEIERLSDKFRLLHKELEHTQLRSK 95 (99)
Q Consensus 68 e~~~ei~~l~~k~~~l~~El~~~~~~~~ 95 (99)
++..+|+.++++|..|+.+|.+.+....
T Consensus 85 ~i~~~i~~~k~~ie~lk~~L~~ak~~r~ 112 (139)
T PF05615_consen 85 EIEQEIEQAKKEIEELKEELEEAKRVRQ 112 (139)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5667888889999999999998876554
No 207
>PHA02540 61 DNA primase; Provisional
Probab=52.71 E-value=7.4 Score=31.84 Aligned_cols=32 Identities=19% Similarity=0.400 Sum_probs=20.2
Q ss_pred ccccCcccccee-eeecCCCCCCcc--eeeCCCCC
Q 041503 13 QVCNECGGQIEL-FTSHTTKNPNRK--FWKCRVCK 44 (99)
Q Consensus 13 ~~Cp~Cg~~~~~-~tS~t~~NPgR~--Fy~C~~C~ 44 (99)
..||.||....- .+..---+|.+. ||.|-+|+
T Consensus 28 ~~CPf~~ds~~~~~kpsF~V~p~k~~~~yhCFgCG 62 (337)
T PHA02540 28 FRCPICGDSQKDKNKARGWIYEKKDGGVFKCHNCG 62 (337)
T ss_pred ecCCCCCCccccCcCCcEEEeccCCceEEEecCCC
Confidence 689999984422 111112345555 99999997
No 208
>PRK07561 DNA topoisomerase I subunit omega; Validated
Probab=52.68 E-value=10 Score=34.17 Aligned_cols=34 Identities=26% Similarity=0.521 Sum_probs=25.9
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCC------CCCeeEeccC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCR------VCKNFQWAED 51 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~------~C~fF~W~De 51 (99)
..||.||..+.+++.+.. .||.|. .|+|-.|...
T Consensus 588 ~~CP~Cg~~l~~r~gr~G-----~Fl~Cs~y~~~p~C~~~~~l~~ 627 (859)
T PRK07561 588 RDCPTCGRGMGIRTGKTG-----VFLGCSGYALKERCKTTRNLTP 627 (859)
T ss_pred ccCcccCCcceEEecCCC-----CeeeccCCcCCCCCCCCCCCCc
Confidence 789999988766655542 499997 5998888654
No 209
>PRK14127 cell division protein GpsB; Provisional
Probab=52.26 E-value=61 Score=22.54 Aligned_cols=29 Identities=24% Similarity=0.373 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 60 DLLVEEVRKLTLEIERLSDKFRLLHKELE 88 (99)
Q Consensus 60 ~~l~~ei~e~~~ei~~l~~k~~~l~~El~ 88 (99)
..+..|+.+|..++.+|++++..++..+.
T Consensus 40 e~l~~e~~~Lk~e~~~l~~~l~e~~~~~~ 68 (109)
T PRK14127 40 EAFQKEIEELQQENARLKAQVDELTKQVS 68 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 45556888888888888888887776554
No 210
>PF01025 GrpE: GrpE; InterPro: IPR000740 Molecular chaperones are a diverse family of proteins that function to protect proteins in the intracellular milieu from irreversible aggregation during synthesis and in times of cellular stress. The bacterial molecular chaperone DnaK is an enzyme that couples cycles of ATP binding, hydrolysis, and ADP release by an N-terminal ATP-hydrolysing domain to cycles of sequestration and release of unfolded proteins by a C-terminal substrate binding domain. In prokaryotes the grpE protein. Dimeric GrpE is the co-chaperone for DnaK, and acts as a nucleotide exchange factor, stimulating the rate of ADP release 5000-fold []. DnaK is itself a weak ATPase; ATP hydrolysis by DnaK is stimulated by its interaction with another co-chaperone, DnaJ. Thus the co-chaperones DnaJ and GrpE are capable of tightly regulating the nucleotide-bound and substrate-bound state of DnaK in ways that are necessary for the normal housekeeping functions and stress-related functions of the DnaK molecular chaperone cycle. The X-ray crystal structure of GrpE in complex with the ATPase domain of DnaK revealed that GrpE is an asymmetric homodimer, bent in a manner that favours extensive contacts with only one DnaKATPase monomer []. GrpE does not actively compete for the atomic positions occupied by the nucleotide. GrpE and ADP mutually reduce one another's affinity for DnaK 200-fold, and ATP instantly dissociates GrpE from DnaK.; GO: 0000774 adenyl-nucleotide exchange factor activity, 0042803 protein homodimerization activity, 0051087 chaperone binding, 0006457 protein folding; PDB: 3A6M_A 4ANI_A 1DKG_B.
Probab=52.16 E-value=65 Score=22.51 Aligned_cols=35 Identities=26% Similarity=0.405 Sum_probs=24.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 58 KIDLLVEEVRKLTLEIERLSDKFRLLHKELEHTQL 92 (99)
Q Consensus 58 k~~~l~~ei~e~~~ei~~l~~k~~~l~~El~~~~~ 92 (99)
+.+.+..+++++...+.++.+.++.+++.+.++..
T Consensus 19 ~l~~l~~~~~~l~~~~~r~~ae~en~~~r~~~e~~ 53 (165)
T PF01025_consen 19 ELEELEKEIEELKERLLRLQAEFENYRKRLEKEKE 53 (165)
T ss_dssp CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34556667777777777777777777777766543
No 211
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=52.08 E-value=12 Score=31.70 Aligned_cols=33 Identities=15% Similarity=0.458 Sum_probs=24.4
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCee
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNF 46 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF 46 (99)
+.||.||+.....+..-+...|.-.|.|. |+.=
T Consensus 176 pic~~cg~~~~~~~~~~d~~~~~v~y~~~-cG~~ 208 (510)
T PRK00750 176 PICPKCGKVLTTPVISYDAEAGTVTYDCE-CGHE 208 (510)
T ss_pred eeCCCCCccceEEEEEEeCCCCEEEEEcC-CCCE
Confidence 99999999877666444566677889987 4433
No 212
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=51.95 E-value=6.1 Score=25.24 Aligned_cols=11 Identities=27% Similarity=0.909 Sum_probs=7.6
Q ss_pred CcceeeCCCCC
Q 041503 34 NRKFWKCRVCK 44 (99)
Q Consensus 34 gR~Fy~C~~C~ 44 (99)
|-.|++||.|+
T Consensus 14 GE~~lrCPRC~ 24 (65)
T COG4049 14 GEEFLRCPRCG 24 (65)
T ss_pred CceeeeCCchh
Confidence 55677777776
No 213
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=51.94 E-value=4.8 Score=36.99 Aligned_cols=38 Identities=13% Similarity=0.259 Sum_probs=0.0
Q ss_pred CCCcccccCccccceeeeecCCCCCCcceeeCCCCCee
Q 041503 9 RNSLQVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNF 46 (99)
Q Consensus 9 ~~~~~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF 46 (99)
..+.-+||.||......+...=..+-.+-|.||.|+.-
T Consensus 652 ei~~r~Cp~Cg~~t~~~~Cp~CG~~T~~~~~Cp~C~~~ 689 (900)
T PF03833_consen 652 EIGRRRCPKCGKETFYNRCPECGSHTEPVYVCPDCGIE 689 (900)
T ss_dssp --------------------------------------
T ss_pred eeecccCcccCCcchhhcCcccCCccccceeccccccc
Confidence 34457899999876665554334444567888877653
No 214
>PRK14154 heat shock protein GrpE; Provisional
Probab=51.86 E-value=57 Score=25.07 Aligned_cols=36 Identities=6% Similarity=0.227 Sum_probs=24.8
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 54 FSNEKIDLLVEEVRKLTLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 54 ~~~~k~~~l~~ei~e~~~ei~~l~~k~~~l~~El~~ 89 (99)
.++|.+..|.++|.++..+++++++++.-+.-|.+-
T Consensus 49 ~~~~~~~~l~~el~~le~e~~elkd~~lRl~ADfeN 84 (208)
T PRK14154 49 LEFPSREKLEGQLTRMERKVDEYKTQYLRAQAEMDN 84 (208)
T ss_pred ccCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 477888888777777777777776666665555543
No 215
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=51.67 E-value=13 Score=30.08 Aligned_cols=40 Identities=15% Similarity=0.223 Sum_probs=27.5
Q ss_pred ccccCccccc-eeeeecCCCCCCcceeeCCCCC-eeEeccCC
Q 041503 13 QVCNECGGQI-ELFTSHTTKNPNRKFWKCRVCK-NFQWAEDR 52 (99)
Q Consensus 13 ~~Cp~Cg~~~-~~~tS~t~~NPgR~Fy~C~~C~-fF~W~De~ 52 (99)
..||.||..- ..+.+-...+++-+-+.|..|+ |++=.|..
T Consensus 227 ~~C~~Cg~~~~l~y~~~~~~~~~~r~e~C~~C~~YlK~~~~~ 268 (309)
T PRK03564 227 VKCSNCEQSGKLHYWSLDSEQAAVKAESCGDCGTYLKILYQE 268 (309)
T ss_pred ccCCCCCCCCceeeeeecCCCcceEeeecccccccceecccc
Confidence 8999999732 2233444456888999999998 66655443
No 216
>PF11853 DUF3373: Protein of unknown function (DUF3373); InterPro: IPR021803 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 472 to 574 amino acids in length.
Probab=51.55 E-value=19 Score=31.10 Aligned_cols=24 Identities=21% Similarity=0.432 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 64 EEVRKLTLEIERLSDKFRLLHKELE 88 (99)
Q Consensus 64 ~ei~e~~~ei~~l~~k~~~l~~El~ 88 (99)
+|+..++ +|++|++|+++|+++++
T Consensus 25 ~~~~~~q-kie~L~kql~~Lk~q~~ 48 (489)
T PF11853_consen 25 DDIDLLQ-KIEALKKQLEELKAQQD 48 (489)
T ss_pred hhhHHHH-HHHHHHHHHHHHHHhhc
Confidence 3555555 88888888888888755
No 217
>TIGR01834 PHA_synth_III_E poly(R)-hydroxyalkanoic acid synthase, class III, PhaE subunit. This model represents the PhaE subunit of the heterodimeric class (class III) of polymerase for poly(R)-hydroxyalkanoic acids (PHAs), carbon and energy storage polymers of many bacteria. The most common PHA is polyhydroxybutyrate but about 150 different constituent hydroxyalkanoic acids (HAs) have been identified in various species. This model must be designated subfamily to indicate the heterogeneity of PHAs.
Probab=51.42 E-value=30 Score=28.34 Aligned_cols=26 Identities=23% Similarity=0.363 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 64 EEVRKLTLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 64 ~ei~e~~~ei~~l~~k~~~l~~El~~ 89 (99)
.||+++-..|.+|+..++.|+++|.+
T Consensus 289 sElDe~~krL~ELrR~vr~L~k~l~~ 314 (320)
T TIGR01834 289 SELDEAHQRIQQLRREVKSLKKRLGD 314 (320)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 36777777888888888888888765
No 218
>PRK14724 DNA topoisomerase III; Provisional
Probab=50.93 E-value=9.7 Score=35.12 Aligned_cols=28 Identities=25% Similarity=0.591 Sum_probs=20.4
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCC-------CCCeeEec
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCR-------VCKNFQWA 49 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~-------~C~fF~W~ 49 (99)
..||.||..+. . +.++|.|. .|+|-.|.
T Consensus 644 ~~CP~Cg~~~~-------~--~~~~~~Cs~~~~~~~~C~f~~~k 678 (987)
T PRK14724 644 TPCPNCGGVVK-------E--NYRRYACTGANGAGEGCGFSFTK 678 (987)
T ss_pred ccCCccccccc-------c--cCceeecCCCcCCCCCCCcccch
Confidence 57999998641 1 24469998 49999984
No 219
>smart00067 GHA Glycoprotein hormone alpha chain homologues. Also called gonadotropins. Glycoprotein hormones consist of two glycosylated chains (alpha and beta) of similar topology.
Probab=50.92 E-value=8.7 Score=25.95 Aligned_cols=29 Identities=24% Similarity=0.502 Sum_probs=20.9
Q ss_pred ccCccccceeeeecCCCCCCcceeeCCCCCeeE
Q 041503 15 CNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQ 47 (99)
Q Consensus 15 Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~ 47 (99)
||.|...-..+.|+ |||+-|.|-+|-|-.
T Consensus 2 C~EC~L~~N~~FS~----~~~PiyQC~GCCFSr 30 (87)
T smart00067 2 CPECTLKENKIFSK----PGAPIYQCMGCCFSR 30 (87)
T ss_pred CccceeccccccCC----CCCceeEecceeccc
Confidence 55666555555554 899999999998754
No 220
>PF08172 CASP_C: CASP C terminal; InterPro: IPR012955 This domain is the C-terminal region of the CASP family of proteins. These are Golgi membrane proteins which are thought to have a role in vesicle transport [].; GO: 0006891 intra-Golgi vesicle-mediated transport, 0030173 integral to Golgi membrane
Probab=50.75 E-value=43 Score=26.17 Aligned_cols=32 Identities=22% Similarity=0.306 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 60 DLLVEEVRKLTLEIERLSDKFRLLHKELEHTQ 91 (99)
Q Consensus 60 ~~l~~ei~e~~~ei~~l~~k~~~l~~El~~~~ 91 (99)
+.|+.++.++..+++++++-+.+|+.||...+
T Consensus 2 ~~lq~~l~~l~~~~~~~~~L~~kLE~DL~~~~ 33 (248)
T PF08172_consen 2 EELQKELSELEAKLEEQKELNAKLENDLAKVQ 33 (248)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 35677888999999999988888888887754
No 221
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=50.66 E-value=9.7 Score=36.61 Aligned_cols=24 Identities=29% Similarity=0.476 Sum_probs=21.5
Q ss_pred cCCCCCCcceeeCCCCCeeEeccC
Q 041503 28 HTTKNPNRKFWKCRVCKNFQWAED 51 (99)
Q Consensus 28 ~t~~NPgR~Fy~C~~C~fF~W~De 51 (99)
=|+-||=++-|.||.|+++.|.++
T Consensus 899 ITeVdPL~phy~C~~C~~~ef~~~ 922 (1437)
T PRK00448 899 ITEVNPLPPHYVCPNCKYSEFFTD 922 (1437)
T ss_pred CCCcCCCCccccCccccccccccc
Confidence 477899999999999999999766
No 222
>PF11544 Spc42p: Spindle pole body component Spc42p; InterPro: IPR021611 Spc42p is a 42kDa component of the S.cerevisiae spindle body that localises to the electron dense central region of the SPB. Spc42p is a phosphoprotein which forms a polymeric layer at the periphery of the SPB central plaque. This functions during SPB duplication and also facilitates the attachment of the SPB to the nuclear membrane. ; PDB: 2Q6Q_B.
Probab=50.29 E-value=55 Score=21.64 Aligned_cols=23 Identities=26% Similarity=0.271 Sum_probs=9.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 041503 65 EVRKLTLEIERLSDKFRLLHKEL 87 (99)
Q Consensus 65 ei~e~~~ei~~l~~k~~~l~~El 87 (99)
.++....||.+|+.-+..|+..|
T Consensus 13 kL~~K~eEI~rLn~lv~sLR~KL 35 (76)
T PF11544_consen 13 KLNDKQEEIDRLNILVGSLRGKL 35 (76)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444444444444444443333
No 223
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=50.01 E-value=8.1 Score=31.81 Aligned_cols=35 Identities=20% Similarity=0.685 Sum_probs=12.9
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCeeEeccCCcc
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQWAEDRKF 54 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~W~De~~~ 54 (99)
+.|++||..++.+ ..=|.. .|+.|+-+.|.-...+
T Consensus 286 FkC~~C~~Rt~sl----~r~P~~---~C~~Cg~~~wer~~M~ 320 (344)
T PF09332_consen 286 FKCKDCGNRTISL----ERLPKK---HCSNCGSSKWERTGML 320 (344)
T ss_dssp EE-T-TS-EEEES----SSS--S-----TTT-S---EEE---
T ss_pred EECCCCCCeeeec----ccCCCC---CCCcCCcCceeehhhh
Confidence 6787788765433 222433 5778888888866543
No 224
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=49.98 E-value=8.5 Score=31.04 Aligned_cols=32 Identities=25% Similarity=0.613 Sum_probs=21.3
Q ss_pred ccccCccccce---eeeecCCCCCCcceeeCCCCC
Q 041503 13 QVCNECGGQIE---LFTSHTTKNPNRKFWKCRVCK 44 (99)
Q Consensus 13 ~~Cp~Cg~~~~---~~tS~t~~NPgR~Fy~C~~C~ 44 (99)
-.|+.||+.-- ++.-.....-|-+.|.|+.|+
T Consensus 188 c~C~iCGKaFSRPWLLQGHiRTHTGEKPF~C~hC~ 222 (279)
T KOG2462|consen 188 CECGICGKAFSRPWLLQGHIRTHTGEKPFSCPHCG 222 (279)
T ss_pred cccccccccccchHHhhcccccccCCCCccCCccc
Confidence 46777776544 555555566677788888876
No 225
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=49.76 E-value=15 Score=26.45 Aligned_cols=30 Identities=27% Similarity=0.598 Sum_probs=22.8
Q ss_pred ccccCccccceeeeecCCCCCCcc-eeeCCCCCeeE
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRK-FWKCRVCKNFQ 47 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~-Fy~C~~C~fF~ 47 (99)
+.||.||.+=..++.. +|. |-+|..|+...
T Consensus 103 VlC~~C~spdT~l~k~-----~r~~~l~C~ACGa~~ 133 (138)
T PRK03988 103 VICPECGSPDTKLIKE-----GRIWVLKCEACGAET 133 (138)
T ss_pred EECCCCCCCCcEEEEc-----CCeEEEEcccCCCCC
Confidence 8999999977666642 564 78999998643
No 226
>TIGR02209 ftsL_broad cell division protein FtsL. This model represents FtsL, both forms similar to that in E. coli and similar to that in B. subtilis. FtsL is one of the later proteins active in cell division septum formation. FtsL is small, low in complexity, and highly divergent. The scope of this model is broader than that of the Pfam model pfam04999.3 for FtsL, as this one includes FtsL from Bacillus subtilis and related species.
Probab=49.72 E-value=62 Score=20.16 Aligned_cols=25 Identities=28% Similarity=0.186 Sum_probs=12.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 60 DLLVEEVRKLTLEIERLSDKFRLLH 84 (99)
Q Consensus 60 ~~l~~ei~e~~~ei~~l~~k~~~l~ 84 (99)
..++.+++++..+..+|+.++..|.
T Consensus 34 ~~~~~~~~~l~~en~~L~~ei~~l~ 58 (85)
T TIGR02209 34 QKLQLEIDKLQKEWRDLQLEVAELS 58 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 3444455555555555555555543
No 227
>KOG1962 consensus B-cell receptor-associated protein and related proteins [Defense mechanisms]
Probab=49.62 E-value=32 Score=26.70 Aligned_cols=30 Identities=37% Similarity=0.505 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 62 LVEEVRKLTLEIERLSDKFRLLHKELEHTQ 91 (99)
Q Consensus 62 l~~ei~e~~~ei~~l~~k~~~l~~El~~~~ 91 (99)
+.+|.++..++++.|+++.++..++|++.+
T Consensus 149 ~~~~~~~~~~~~~kL~~el~~~~~~Le~~~ 178 (216)
T KOG1962|consen 149 LEEENDKLKADLEKLETELEKKQKKLEKAQ 178 (216)
T ss_pred hhhhHHHHHhhHHHHHHHHHHHHHHHHHHH
Confidence 444566666677777777777777776654
No 228
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=49.06 E-value=21 Score=24.39 Aligned_cols=26 Identities=31% Similarity=0.756 Sum_probs=18.7
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCe
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKN 45 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~f 45 (99)
-.|++||+..+.+.+-. -|.|..|+-
T Consensus 37 y~CsfCGK~~vKR~AvG-------iW~C~~C~k 62 (92)
T KOG0402|consen 37 YTCSFCGKKTVKRKAVG-------IWKCGSCKK 62 (92)
T ss_pred hhhhhcchhhhhhhcee-------EEecCCccc
Confidence 57999998766665543 577888873
No 229
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=49.04 E-value=12 Score=28.81 Aligned_cols=36 Identities=28% Similarity=0.551 Sum_probs=23.3
Q ss_pred CCcccccCccccceeeeecCC-CCCCcce------eeCCCCCe
Q 041503 10 NSLQVCNECGGQIELFTSHTT-KNPNRKF------WKCRVCKN 45 (99)
Q Consensus 10 ~~~~~Cp~Cg~~~~~~tS~t~-~NPgR~F------y~C~~C~f 45 (99)
-....||.||..-.-.-|..- -|-+++. |+|-.|++
T Consensus 15 q~~k~C~~Cg~kr~f~cSg~fRvNAq~K~LDvWlIYkC~~Cd~ 57 (203)
T COG4332 15 QPAKRCNSCGVKRAFTCSGKFRVNAQGKVLDVWLIYKCTHCDY 57 (203)
T ss_pred hhhhhCcccCCcceeeecCcEEEcCCCcEEEEEEEEEeeccCC
Confidence 334899999975444333332 4555554 99999973
No 230
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=48.68 E-value=11 Score=35.68 Aligned_cols=24 Identities=29% Similarity=0.491 Sum_probs=21.5
Q ss_pred cCCCCCCcceeeCCCCCeeEeccC
Q 041503 28 HTTKNPNRKFWKCRVCKNFQWAED 51 (99)
Q Consensus 28 ~t~~NPgR~Fy~C~~C~fF~W~De 51 (99)
=|+-||=++-|.||.|+++.|.++
T Consensus 674 ITeVdPL~phy~c~~c~~~ef~~~ 697 (1213)
T TIGR01405 674 ITEVNPLPPHYLCPNCKYSEFITD 697 (1213)
T ss_pred CCCcCCCcccccCccccccccccc
Confidence 477899999999999999999876
No 231
>PF13815 Dzip-like_N: Iguana/Dzip1-like DAZ-interacting protein N-terminal
Probab=48.68 E-value=74 Score=21.65 Aligned_cols=29 Identities=14% Similarity=0.360 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 63 VEEVRKLTLEIERLSDKFRLLHKELEHTQ 91 (99)
Q Consensus 63 ~~ei~e~~~ei~~l~~k~~~l~~El~~~~ 91 (99)
...+..+..++..+++++..++.++.+..
T Consensus 79 ~~~~~~l~~~~~~~~~~~~~l~~~~~~~~ 107 (118)
T PF13815_consen 79 SSQLEQLEERLQELQQEIEKLKQKLKKQK 107 (118)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33455666666666666666666665544
No 232
>PF13600 DUF4140: N-terminal domain of unknown function (DUF4140)
Probab=48.56 E-value=65 Score=20.97 Aligned_cols=33 Identities=24% Similarity=0.370 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 62 LVEEVRKLTLEIERLSDKFRLLHKELEHTQLRS 94 (99)
Q Consensus 62 l~~ei~e~~~ei~~l~~k~~~l~~El~~~~~~~ 94 (99)
...++.++..+++.+++++.++..++.-.....
T Consensus 68 ~~~~~~~l~~~l~~l~~~~~~~~~~~~~~~~~~ 100 (104)
T PF13600_consen 68 DSPELKELEEELEALEDELAALQDEIQALEAQI 100 (104)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344788888889999988888887776555443
No 233
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=48.40 E-value=31 Score=20.72 Aligned_cols=22 Identities=41% Similarity=0.635 Sum_probs=15.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 041503 68 KLTLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 68 e~~~ei~~l~~k~~~l~~El~~ 89 (99)
....++++++++++++++|+++
T Consensus 45 ~~r~~~~~~~k~l~~le~e~~~ 66 (68)
T PF06305_consen 45 RLRRRIRRLRKELKKLEKELEQ 66 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHHHh
Confidence 5556677777777777777765
No 234
>PF08946 Osmo_CC: Osmosensory transporter coiled coil; InterPro: IPR015041 The osmosensory transporter coiled coil is a C-terminal domain found in various bacterial osmoprotective transporters, such as ProP, Proline/betaine transporter, Proline permease 2 and the citrate proton symporters. It adopts an antiparallel coiled-coil structure, and is essential for osmosensory and osmoprotectant transporter function []. ; PDB: 1R48_B.
Probab=48.33 E-value=44 Score=20.17 Aligned_cols=22 Identities=18% Similarity=0.321 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 041503 62 LVEEVRKLTLEIERLSDKFRLL 83 (99)
Q Consensus 62 l~~ei~e~~~ei~~l~~k~~~l 83 (99)
++.-|+.++.+|++|++|-+.|
T Consensus 17 IEqkiedid~qIaeLe~KR~~L 38 (46)
T PF08946_consen 17 IEQKIEDIDEQIAELEAKRQRL 38 (46)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHhHHHHHHHHHHHHHHHHHH
Confidence 3444778888888888665544
No 235
>PF14577 SEO_C: Sieve element occlusion C-terminus
Probab=48.24 E-value=9.9 Score=29.84 Aligned_cols=15 Identities=47% Similarity=0.937 Sum_probs=13.3
Q ss_pred ccccCccccceeeee
Q 041503 13 QVCNECGGQIELFTS 27 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS 27 (99)
+.||.||+++..+++
T Consensus 215 i~CpeC~R~MEk~v~ 229 (235)
T PF14577_consen 215 IVCPECGRPMEKFVM 229 (235)
T ss_pred eECCCCCCchhhcee
Confidence 999999999987775
No 236
>KOG4119 consensus G protein gamma subunit [Signal transduction mechanisms]
Probab=48.24 E-value=61 Score=21.11 Aligned_cols=35 Identities=31% Similarity=0.217 Sum_probs=26.9
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 55 SNEKIDLLVEEVRKLTLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 55 ~~~k~~~l~~ei~e~~~ei~~l~~k~~~l~~El~~ 89 (99)
+|.+...+..+|.+|..|..--+-++.+...||.+
T Consensus 5 ~~~~~~q~k~~VeqLk~e~~~~R~~vS~a~~el~~ 39 (71)
T KOG4119|consen 5 SNSKKPQMKKEVEQLKLEANIERIKVSKAAAELLE 39 (71)
T ss_pred cccchHHHHHHHHHHHHHHHhhHhhHHHHHHHHHH
Confidence 45666777888888888877777788888888765
No 237
>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.
Probab=48.19 E-value=72 Score=20.46 Aligned_cols=24 Identities=33% Similarity=0.354 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 59 IDLLVEEVRKLTLEIERLSDKFRL 82 (99)
Q Consensus 59 ~~~l~~ei~e~~~ei~~l~~k~~~ 82 (99)
+..+..-|..+..++++|+.++..
T Consensus 13 i~~aveti~~Lq~e~eeLke~n~~ 36 (72)
T PF06005_consen 13 IQQAVETIALLQMENEELKEKNNE 36 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Confidence 334444556666677777665333
No 238
>PF10398 DUF2443: Protein of unknown function (DUF2443); InterPro: IPR019469 This entry represents a small group of highly conserved proteins from bacteria, in particular Helicobacter species. The structure is a bundle of alpha helices. The function is not known. ; PDB: 1ZKE_F.
Probab=48.08 E-value=24 Score=23.48 Aligned_cols=16 Identities=44% Similarity=0.559 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHHHHHH
Q 041503 62 LVEEVRKLTLEIERLS 77 (99)
Q Consensus 62 l~~ei~e~~~ei~~l~ 77 (99)
+..||+++++.|..|+
T Consensus 55 ideeV~~LKe~IdaLN 70 (79)
T PF10398_consen 55 IDEEVEKLKEHIDALN 70 (79)
T ss_dssp HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3446666666676666
No 239
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=48.03 E-value=14 Score=33.54 Aligned_cols=29 Identities=24% Similarity=0.726 Sum_probs=19.3
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCC---CCCee
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCR---VCKNF 46 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~---~C~fF 46 (99)
..||.||..+++...+.. .||.|. .|++.
T Consensus 646 ~~CP~Cg~~m~lK~gr~G-----~Fl~Cs~yP~Ck~~ 677 (860)
T PRK06319 646 SPCPLCGGEMKVRHGRFG-----TFLGCENYPECRGI 677 (860)
T ss_pred CcCccCCCeeEEecCCCC-----ceeeCCCCcccccc
Confidence 579999987777655443 377774 56544
No 240
>PRK11239 hypothetical protein; Provisional
Probab=47.87 E-value=43 Score=26.13 Aligned_cols=60 Identities=20% Similarity=0.314 Sum_probs=35.2
Q ss_pred eeecCCCCCCcceeeCC--CCCeeEeccCCc----cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 25 FTSHTTKNPNRKFWKCR--VCKNFQWAEDRK----FSNEKIDLLVEEVRKLTLEIERLSDKFRLLHKEL 87 (99)
Q Consensus 25 ~tS~t~~NPgR~Fy~C~--~C~fF~W~De~~----~~~~k~~~l~~ei~e~~~ei~~l~~k~~~l~~El 87 (99)
++.+-+.-||+|=-+-. -|+- .|... .+-...+.|+++|.++..|+..|++++..|..++
T Consensus 148 lV~~LpR~pG~RE~Ry~hLl~g~---v~~~~~~~~~~~~~~~~Le~rv~~Le~eva~L~~~l~~l~~~~ 213 (215)
T PRK11239 148 FVVRLAREPGKRESRYMHLFSGE---VDDQPAVTDMSNAVDGDLQARVEALEIEVAELKQRLDSLLAHL 213 (215)
T ss_pred eeeecCCCCCcchHHHHHHhcCC---ccccccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45566677776643322 2321 12111 1223445677888888888888888888776654
No 241
>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=47.65 E-value=15 Score=22.48 Aligned_cols=23 Identities=26% Similarity=0.694 Sum_probs=15.1
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCeeE
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQ 47 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~ 47 (99)
..||.||.. -++-+.|+.|+|+.
T Consensus 27 ~~C~~cG~~------------~~~H~vc~~cG~Y~ 49 (55)
T TIGR01031 27 VVCPNCGEF------------KLPHRVCPSCGYYK 49 (55)
T ss_pred eECCCCCCc------------ccCeeECCccCeEC
Confidence 678888863 34455677787654
No 242
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=47.50 E-value=11 Score=22.99 Aligned_cols=11 Identities=18% Similarity=0.347 Sum_probs=5.9
Q ss_pred eeeCCCCCeeE
Q 041503 37 FWKCRVCKNFQ 47 (99)
Q Consensus 37 Fy~C~~C~fF~ 47 (99)
-.+||.|++=+
T Consensus 24 ~irCp~Cg~rI 34 (49)
T COG1996 24 GIRCPYCGSRI 34 (49)
T ss_pred ceeCCCCCcEE
Confidence 35566666433
No 243
>PF08232 Striatin: Striatin family; InterPro: IPR013258 This domain is associated with the N terminus of striatin. Striatin is an intracellular protein which has a caveolin-binding motif, a coiled-coil structure, a calmodulin-binding site, and a WD (IPR001680 from INTERPRO) repeat domain []. It acts as a scaffold protein [] and is involved in signalling pathways [, ].
Probab=47.48 E-value=87 Score=22.10 Aligned_cols=36 Identities=19% Similarity=0.287 Sum_probs=21.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 58 KIDLLVEEVRKLTLEIERLSDKFRLLHKELEHTQLR 93 (99)
Q Consensus 58 k~~~l~~ei~e~~~ei~~l~~k~~~l~~El~~~~~~ 93 (99)
+|+.|+.|.+.+..-.+.|...|.-|+..|+.++..
T Consensus 33 rIa~LEGE~r~~e~l~~dL~rrIkMLE~aLkqER~k 68 (134)
T PF08232_consen 33 RIAFLEGERRGQENLKKDLKRRIKMLEYALKQERAK 68 (134)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445555566655555556666666666666666554
No 244
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=47.47 E-value=13 Score=30.57 Aligned_cols=28 Identities=21% Similarity=0.602 Sum_probs=21.0
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCK 44 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~ 44 (99)
..||.|+....-+.. ||.+.+|.|-+|+
T Consensus 35 ~~CPfh~ek~pSf~v----~~~k~~~~Cf~Cg 62 (415)
T TIGR01391 35 GLCPFHHEKTPSFSV----SPEKQFYHCFGCG 62 (415)
T ss_pred eeCCCCCCCCCeEEE----EcCCCcEEECCCC
Confidence 679999976544444 4677899999887
No 245
>PF11287 DUF3088: Protein of unknown function (DUF3088); InterPro: IPR021439 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=47.44 E-value=11 Score=26.54 Aligned_cols=13 Identities=31% Similarity=1.101 Sum_probs=10.4
Q ss_pred CCCCcceeeCCCCC
Q 041503 31 KNPNRKFWKCRVCK 44 (99)
Q Consensus 31 ~NPgR~Fy~C~~C~ 44 (99)
+-||++|| ||.|.
T Consensus 16 ~~PG~~f~-Cp~c~ 28 (112)
T PF11287_consen 16 AGPGQRFY-CPHCA 28 (112)
T ss_pred CCCCceEE-CCchH
Confidence 34999998 89885
No 246
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=47.38 E-value=5.4 Score=31.78 Aligned_cols=27 Identities=22% Similarity=0.535 Sum_probs=17.1
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCe
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKN 45 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~f 45 (99)
.+||.|+...-..- -.+.||.||.|++
T Consensus 27 ~~c~~c~~~~~~~~------l~~~~~vc~~c~~ 53 (285)
T TIGR00515 27 TKCPKCGQVLYTKE------LERNLEVCPKCDH 53 (285)
T ss_pred eECCCCcchhhHHH------HHhhCCCCCCCCC
Confidence 78999987543211 2245688998863
No 247
>TIGR00219 mreC rod shape-determining protein MreC. MreC (murein formation C) is involved in the rod shape determination in E. coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped. Cells defective in MreC are round. Species with MreC include many of the Proteobacteria, Gram-positives, and spirochetes.
Probab=47.33 E-value=81 Score=24.81 Aligned_cols=32 Identities=22% Similarity=0.304 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 61 LLVEEVRKLTLEIERLSDKFRLLHKELEHTQL 92 (99)
Q Consensus 61 ~l~~ei~e~~~ei~~l~~k~~~l~~El~~~~~ 92 (99)
.+.+|-++|..++.+|+++.+.+..||+.+--
T Consensus 70 ~l~~EN~~Lr~e~~~l~~~~~~~~~~l~~EN~ 101 (283)
T TIGR00219 70 NLEYENYKLRQELLKKNQQLEILTQNLKQENV 101 (283)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34456667777766665555554444444433
No 248
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=47.04 E-value=76 Score=24.22 Aligned_cols=24 Identities=29% Similarity=0.254 Sum_probs=14.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 60 DLLVEEVRKLTLEIERLSDKFRLL 83 (99)
Q Consensus 60 ~~l~~ei~e~~~ei~~l~~k~~~l 83 (99)
..+.+|.++|..|+.+|+.+...+
T Consensus 72 ~~l~~en~~L~~e~~~l~~~~~~~ 95 (276)
T PRK13922 72 FDLREENEELKKELLELESRLQEL 95 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344446666666666666555544
No 249
>PF14182 YgaB: YgaB-like protein
Probab=46.87 E-value=85 Score=20.93 Aligned_cols=23 Identities=17% Similarity=0.404 Sum_probs=9.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 041503 65 EVRKLTLEIERLSDKFRLLHKEL 87 (99)
Q Consensus 65 ei~e~~~ei~~l~~k~~~l~~El 87 (99)
||+....+++.++..|++...|+
T Consensus 48 EI~~mkk~Lk~Iq~~Fe~QTeeV 70 (79)
T PF14182_consen 48 EISQMKKELKEIQRVFEKQTEEV 70 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 44444444444444444444433
No 250
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=46.71 E-value=56 Score=24.41 Aligned_cols=29 Identities=21% Similarity=0.279 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 60 DLLVEEVRKLTLEIERLSDKFRLLHKELE 88 (99)
Q Consensus 60 ~~l~~ei~e~~~ei~~l~~k~~~l~~El~ 88 (99)
..|..|+.++..+++.|..++..|.+++.
T Consensus 107 ~~l~~e~~~l~~~~e~Le~e~~~L~~~~~ 135 (161)
T TIGR02894 107 ERLKNQNESLQKRNEELEKELEKLRQRLS 135 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45666777777777777777777766553
No 251
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=46.62 E-value=17 Score=20.56 Aligned_cols=30 Identities=20% Similarity=0.545 Sum_probs=14.5
Q ss_pred cccCccccceeeeecCCCCCCcceeeCC--CCCe
Q 041503 14 VCNECGGQIELFTSHTTKNPNRKFWKCR--VCKN 45 (99)
Q Consensus 14 ~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~--~C~f 45 (99)
.||.||..+..-+-+.. -.=+-|+|. .|.|
T Consensus 3 lcpkcgvgvl~pvy~~k--geikvfrcsnpacdy 34 (36)
T PF09151_consen 3 LCPKCGVGVLEPVYNQK--GEIKVFRCSNPACDY 34 (36)
T ss_dssp B-TTTSSSBEEEEE-TT--S-EEEEEES-TT---
T ss_pred cCCccCceEEEEeecCC--CcEEEEEcCCCcccc
Confidence 68999986655443321 123567776 6764
No 252
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=46.56 E-value=22 Score=21.81 Aligned_cols=27 Identities=30% Similarity=0.668 Sum_probs=15.3
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCK 44 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~ 44 (99)
..||.||..+.+-.. -.|- -..||.|+
T Consensus 3 ~~CP~CG~~iev~~~----~~Ge-iV~Cp~CG 29 (54)
T TIGR01206 3 FECPDCGAEIELENP----ELGE-LVICDECG 29 (54)
T ss_pred cCCCCCCCEEecCCC----ccCC-EEeCCCCC
Confidence 468888875544111 1122 45788777
No 253
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=46.36 E-value=11 Score=30.01 Aligned_cols=28 Identities=29% Similarity=0.903 Sum_probs=8.4
Q ss_pred ccccCcccc-ceeeeecCCCCCCcceeeCCCCC
Q 041503 13 QVCNECGGQ-IELFTSHTTKNPNRKFWKCRVCK 44 (99)
Q Consensus 13 ~~Cp~Cg~~-~~~~tS~t~~NPgR~Fy~C~~C~ 44 (99)
..||.||.. ...+ ....|-.-|| |+.|+
T Consensus 32 ~yCP~Cg~~~L~~f---~NN~PVaDF~-C~~C~ 60 (254)
T PF06044_consen 32 MYCPNCGSKPLSKF---ENNRPVADFY-CPNCN 60 (254)
T ss_dssp ---TTT--SS-EE-----------EEE--TTT-
T ss_pred CcCCCCCChhHhhc---cCCCccceeE-CCCCc
Confidence 789999975 4444 2233555565 78774
No 254
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=46.28 E-value=12 Score=30.44 Aligned_cols=31 Identities=19% Similarity=0.496 Sum_probs=24.4
Q ss_pred CcccccCccc-cceeeeecCCCCCCcceeeCC
Q 041503 11 SLQVCNECGG-QIELFTSHTTKNPNRKFWKCR 41 (99)
Q Consensus 11 ~~~~Cp~Cg~-~~~~~tS~t~~NPgR~Fy~C~ 41 (99)
....||-||. ++.-.|--+..-.|=||-.|.
T Consensus 184 ~~~~CPvCGS~PvaSmV~~g~~~~GlRYL~Cs 215 (308)
T COG3058 184 SRQYCPVCGSMPVASMVQIGETEQGLRYLHCS 215 (308)
T ss_pred ccccCCCcCCCCcceeeeecCccccchhhhhh
Confidence 3479999996 555566666689999999998
No 255
>PRK05431 seryl-tRNA synthetase; Provisional
Probab=45.99 E-value=61 Score=26.92 Aligned_cols=28 Identities=39% Similarity=0.561 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 62 LVEEVRKLTLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 62 l~~ei~e~~~ei~~l~~k~~~l~~El~~ 89 (99)
+.+++++++.+|+.++++..++..++.+
T Consensus 71 l~~~~~~l~~~~~~~~~~~~~~~~~~~~ 98 (425)
T PRK05431 71 LIAEVKELKEEIKALEAELDELEAELEE 98 (425)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3334444455555555555555444444
No 256
>PF07798 DUF1640: Protein of unknown function (DUF1640); InterPro: IPR024461 This family consists of uncharacterised proteins.
Probab=45.98 E-value=73 Score=23.10 Aligned_cols=26 Identities=27% Similarity=0.300 Sum_probs=15.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 67 RKLTLEIERLSDKFRLLHKELEHTQL 92 (99)
Q Consensus 67 ~e~~~ei~~l~~k~~~l~~El~~~~~ 92 (99)
.++..+.+.|+..+.+|+.+|.++-.
T Consensus 76 ~~lr~~~e~L~~eie~l~~~L~~ei~ 101 (177)
T PF07798_consen 76 AELRSENEKLQREIEKLRQELREEIN 101 (177)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555666666666666666666543
No 257
>KOG4191 consensus Histone acetyltransferases PCAF/SAGA/ADA, subunit TADA3L/NGG1 [Chromatin structure and dynamics]
Probab=45.81 E-value=42 Score=29.19 Aligned_cols=32 Identities=28% Similarity=0.364 Sum_probs=25.7
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 57 EKIDLLVEEVRKLTLEIERLSDKFRLLHKELE 88 (99)
Q Consensus 57 ~k~~~l~~ei~e~~~ei~~l~~k~~~l~~El~ 88 (99)
.+.+.+.+|+|+++.+|+.+.+.+++++..|-
T Consensus 401 dddDEvlaeLR~lqaeLk~vS~~N~k~k~~Ll 432 (516)
T KOG4191|consen 401 DDDDEVLAELRKLQAELKAVSAHNRKKKHDLL 432 (516)
T ss_pred cchHHHHHHHHHHHHHHHHHHhhhHHHHHHHH
Confidence 34578899999999999999888887776553
No 258
>KOG2991 consensus Splicing regulator [RNA processing and modification]
Probab=45.73 E-value=41 Score=27.48 Aligned_cols=32 Identities=25% Similarity=0.461 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH---HHHhhc
Q 041503 66 VRKLTLEIERLSDKFRLLHKELEHTQ---LRSKYG 97 (99)
Q Consensus 66 i~e~~~ei~~l~~k~~~l~~El~~~~---~~~~~~ 97 (99)
|.+|++..++++.+|--|+++|++++ -+.+.|
T Consensus 266 m~eLdedVEgmqsTiliLQq~Lketr~~Iq~l~k~ 300 (330)
T KOG2991|consen 266 MEELDEDVEGMQSTILILQQKLKETRKEIQRLKKG 300 (330)
T ss_pred HHHHHHHHhcchhhHHHHHHHHHHHHHHHHHHHHH
Confidence 45888888999999999999999887 555554
No 259
>COG1384 LysS Lysyl-tRNA synthetase (class I) [Translation, ribosomal structure and biogenesis]
Probab=45.69 E-value=17 Score=31.73 Aligned_cols=35 Identities=14% Similarity=0.444 Sum_probs=24.7
Q ss_pred ccccCccc-cceeeeecCCCCCCcceeeCCCCCeeEecc
Q 041503 13 QVCNECGG-QIELFTSHTTKNPNRKFWKCRVCKNFQWAE 50 (99)
Q Consensus 13 ~~Cp~Cg~-~~~~~tS~t~~NPgR~Fy~C~~C~fF~W~D 50 (99)
+.||.||+ ..+.-+++... |+--|+|. |++=-|+|
T Consensus 172 piC~kcGri~~t~v~~~d~~--~~v~Y~Ce-~Gh~g~v~ 207 (521)
T COG1384 172 PICEKCGRILTTPVIEWDGE--GTVEYRCE-CGHEGEVD 207 (521)
T ss_pred ccccccCCcceeEEEEecCC--ceEEEEec-CCccceee
Confidence 99999999 55555566544 99999998 34444443
No 260
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=45.64 E-value=42 Score=23.93 Aligned_cols=22 Identities=32% Similarity=0.457 Sum_probs=9.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 041503 59 IDLLVEEVRKLTLEIERLSDKF 80 (99)
Q Consensus 59 ~~~l~~ei~e~~~ei~~l~~k~ 80 (99)
+..|..++.++..++..|++++
T Consensus 81 i~~L~~el~~l~~~~k~l~~eL 102 (169)
T PF07106_consen 81 IKELREELAELKKEVKSLEAEL 102 (169)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444444444444333333
No 261
>PF11802 CENP-K: Centromere-associated protein K; InterPro: IPR020993 Cenp-K is one of seven new Cenp-A-nucleosome distal (CAD) centromere components (the others being Cenp-L, Cenp-O, Cenp-P, Cenp-Q, Cenp-R and Cenp-S) that are identified as assembling on the Cenp-A nucleosome associated complex, NAC []. The Cenp-A NAC is essential, as disruption of the complex causes errors of chromosome alignment and segregation that preclude cell survival despite continued centromere-derived mitotic checkpoint signalling. Cenp-K is centromere-associated through its interaction with one or more components of the Cenp-A NAC.; GO: 0005634 nucleus
Probab=45.61 E-value=78 Score=25.43 Aligned_cols=29 Identities=21% Similarity=0.278 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 041503 67 RKLTLEIERLSDKFRLLHKELEHTQLRSK 95 (99)
Q Consensus 67 ~e~~~ei~~l~~k~~~l~~El~~~~~~~~ 95 (99)
.++..-+.-.++|..+|+.+|++++.|+.
T Consensus 99 ~eLe~vLs~~q~KnekLke~LerEq~wL~ 127 (268)
T PF11802_consen 99 SELEMVLSTVQSKNEKLKEDLEREQQWLD 127 (268)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35555566678999999999999999863
No 262
>PF07334 IFP_35_N: Interferon-induced 35 kDa protein (IFP 35) N-terminus; InterPro: IPR009938 This entry represents the N terminus of interferon-induced 35 kDa protein (IFP 35) (approximately 80 residues long), which contains a leucine zipper motif in an alpha helical configuration []. This group of proteins also includes N-myc-interactor (Nmi), a homologous interferon-induced protein.
Probab=45.56 E-value=59 Score=21.44 Aligned_cols=27 Identities=26% Similarity=0.374 Sum_probs=20.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 60 DLLVEEVRKLTLEIERLSDKFRLLHKE 86 (99)
Q Consensus 60 ~~l~~ei~e~~~ei~~l~~k~~~l~~E 86 (99)
+.|..|..+|+.+|..|++..+.+..|
T Consensus 3 ~ei~eEn~~Lk~eiqkle~ELq~~~~~ 29 (76)
T PF07334_consen 3 HEIQEENARLKEEIQKLEAELQQNKRE 29 (76)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 456667778888888887777777766
No 263
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=45.39 E-value=77 Score=24.58 Aligned_cols=26 Identities=12% Similarity=0.240 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 64 EEVRKLTLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 64 ~ei~e~~~ei~~l~~k~~~l~~El~~ 89 (99)
+.|+.+..||.+|+-+++.+.-+|+.
T Consensus 61 ~ql~~lq~ev~~LrG~~E~~~~~l~~ 86 (263)
T PRK10803 61 QQLSDNQSDIDSLRGQIQENQYQLNQ 86 (263)
T ss_pred HHHHHHHHHHHHHhhHHHHHHHHHHH
Confidence 34555566666666666655555554
No 264
>TIGR00293 prefoldin, archaeal alpha subunit/eukaryotic subunit 5. This model finds a set of small proteins from the Archaea and from Aquifex aeolicus that may represent two orthologous groups. The proteins are predicted to be mostly coiled coil, and may hit large numbers of proteins that contain coiled coil regions.
Probab=45.38 E-value=72 Score=21.42 Aligned_cols=46 Identities=17% Similarity=0.286 Sum_probs=19.4
Q ss_pred CCCeeEeccCCc---cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 42 VCKNFQWAEDRK---FSNEKIDLLVEEVRKLTLEIERLSDKFRLLHKEL 87 (99)
Q Consensus 42 ~C~fF~W~De~~---~~~~k~~~l~~ei~e~~~ei~~l~~k~~~l~~El 87 (99)
+.+||...+-.. +-=.++..|...++++...+..+++++..+...|
T Consensus 75 G~g~~vE~~~~eA~~~l~~~~~~l~~~~~~l~~~l~~l~~~~~~i~~~l 123 (126)
T TIGR00293 75 GSGYYVEKDAEEAIEFLKKRIEELEKAIEKLQEALAELASRAQQLEQEA 123 (126)
T ss_pred CCCEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 556665554331 1112223333344444444444444444444333
No 265
>PF14817 HAUS5: HAUS augmin-like complex subunit 5
Probab=45.32 E-value=73 Score=28.32 Aligned_cols=35 Identities=23% Similarity=0.359 Sum_probs=24.8
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 57 EKIDLLVEEVRKLTLEIERLSDKFRLLHKELEHTQ 91 (99)
Q Consensus 57 ~k~~~l~~ei~e~~~ei~~l~~k~~~l~~El~~~~ 91 (99)
.+...|..+|.++..+|.++.+.|+.+..|+..+-
T Consensus 79 ~~r~~L~~everLraei~~l~~~I~~~e~e~~~~e 113 (632)
T PF14817_consen 79 RRRRELEKEVERLRAEIQELDKEIESREREVSRQE 113 (632)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45566666777888888888777777777766543
No 266
>PF14982 UPF0731: UPF0731 family
Probab=45.26 E-value=28 Score=22.99 Aligned_cols=25 Identities=12% Similarity=0.314 Sum_probs=21.4
Q ss_pred cCCCCCCcceeeCCCCCeeEeccCC
Q 041503 28 HTTKNPNRKFWKCRVCKNFQWAEDR 52 (99)
Q Consensus 28 ~t~~NPgR~Fy~C~~C~fF~W~De~ 52 (99)
.++-||.|+.-+||+|+..---|-.
T Consensus 34 ~kE~~p~RqLrRCpgsHCLTitdvP 58 (79)
T PF14982_consen 34 GKEHSPTRQLRRCPGSHCLTITDVP 58 (79)
T ss_pred CcccCccchhccCCCcceeEeeccc
Confidence 6788999999999998887777765
No 267
>PF01920 Prefoldin_2: Prefoldin subunit; InterPro: IPR002777 Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal beta subunit, eukaryotic prefoldin subunits 1, 2, 4 and 6. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 2ZDI_B 3AEI_B 2ZQM_A 1FXK_A.
Probab=45.09 E-value=80 Score=20.10 Aligned_cols=32 Identities=34% Similarity=0.549 Sum_probs=24.5
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 57 EKIDLLVEEVRKLTLEIERLSDKFRLLHKELE 88 (99)
Q Consensus 57 ~k~~~l~~ei~e~~~ei~~l~~k~~~l~~El~ 88 (99)
.+.+.+..+|..+..+++.+..++.+++..|.
T Consensus 69 ~~~~~~~~~i~~l~~~~~~l~~~l~~~~~~l~ 100 (106)
T PF01920_consen 69 ERIEKLEKEIKKLEKQLKYLEKKLKELKKKLY 100 (106)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44566777888888888888888888877765
No 268
>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=44.97 E-value=28 Score=18.11 Aligned_cols=27 Identities=26% Similarity=0.551 Sum_probs=14.4
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCK 44 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~ 44 (99)
.+||.|+........ -+|..|=|+.|.
T Consensus 2 ~~C~rC~~~~~~~~~-----~~r~~~~C~rCq 28 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGI-----NGRSTYLCPRCQ 28 (30)
T ss_dssp SB-TTT--BBEEEEE-----TTEEEEE-TTTC
T ss_pred CcCccCCCcceEeEe-----cCCCCeECcCCc
Confidence 368999987544433 357777787764
No 269
>cd00632 Prefoldin_beta Prefoldin beta; Prefoldin is a hexameric molecular chaperone complex, composed of two evolutionarily related subunits (alpha and beta), which are found in both eukaryotes and archaea. Prefoldin binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The hexameric structure consists of a double beta barrel assembly with six protruding coiled-coils. The alpha prefoldin subunits have two beta hairpin structures while the beta prefoldin subunits (this CD) have only one hairpin that is most similar to the second hairpin of the alpha subunit. The prefoldin hexamer consists of two alpha and four beta subunits and is assembled from the beta hairpins of all six subunits. The alpha subunits initially dimerize providing a structural nucleus for the assembly of the beta subunits. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the st
Probab=44.94 E-value=79 Score=20.89 Aligned_cols=31 Identities=29% Similarity=0.381 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 62 LVEEVRKLTLEIERLSDKFRLLHKELEHTQL 92 (99)
Q Consensus 62 l~~ei~e~~~ei~~l~~k~~~l~~El~~~~~ 92 (99)
|...+..+..+++++..++..+.+++++-.-
T Consensus 68 Le~~~e~le~~i~~l~~~~~~l~~~~~elk~ 98 (105)
T cd00632 68 LKERLETIELRIKRLERQEEDLQEKLKELQE 98 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445678888888888888888888776543
No 270
>TIGR00414 serS seryl-tRNA synthetase. This model represents the seryl-tRNA synthetase found in most organisms. This protein is a class II tRNA synthetase, and is recognized by the pfam model tRNA-synt_2b. The seryl-tRNA synthetases of two archaeal species, Methanococcus jannaschii and Methanobacterium thermoautotrophicum, differ considerably and are included in a different model.
Probab=44.71 E-value=68 Score=26.58 Aligned_cols=30 Identities=27% Similarity=0.441 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 61 LLVEEVRKLTLEIERLSDKFRLLHKELEHT 90 (99)
Q Consensus 61 ~l~~ei~e~~~ei~~l~~k~~~l~~El~~~ 90 (99)
.|.+++++++.+|..|.++..++..++.+.
T Consensus 73 ~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~ 102 (418)
T TIGR00414 73 EIKKELKELKEELTELSAALKALEAELQDK 102 (418)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344455555556666665555555555543
No 271
>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=44.61 E-value=23 Score=24.94 Aligned_cols=29 Identities=28% Similarity=0.647 Sum_probs=21.9
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCe
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKN 45 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~f 45 (99)
+.||.|+.+=..++.. -+--|-+|..|+.
T Consensus 94 VlC~~C~spdT~l~k~----~r~~~l~C~aCGa 122 (125)
T PF01873_consen 94 VLCPECGSPDTELIKE----GRLIFLKCKACGA 122 (125)
T ss_dssp SSCTSTSSSSEEEEEE----TTCCEEEETTTSC
T ss_pred EEcCCCCCCccEEEEc----CCEEEEEecccCC
Confidence 8999999987666665 2346778988874
No 272
>PRK06443 chorismate mutase; Validated
Probab=44.39 E-value=70 Score=24.25 Aligned_cols=35 Identities=23% Similarity=0.200 Sum_probs=27.1
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 55 SNEKIDLLVEEVRKLTLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 55 ~~~k~~~l~~ei~e~~~ei~~l~~k~~~l~~El~~ 89 (99)
.|.+.+.++.+|++++.+|-+|=++=..+-.|+-+
T Consensus 3 ~~~dLeeLR~eID~ID~eIL~LL~kRm~la~eIg~ 37 (177)
T PRK06443 3 HFIDMEDLRSEILENTMDIIELIEKRRELARMIGI 37 (177)
T ss_pred ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 57778889999999999998887666666565543
No 273
>PF14389 Lzipper-MIP1: Leucine-zipper of ternary complex factor MIP1
Probab=44.25 E-value=70 Score=21.02 Aligned_cols=34 Identities=29% Similarity=0.378 Sum_probs=24.6
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 57 EKIDLLVEEVRKLTLEIERLSDKFRLLHKELEHT 90 (99)
Q Consensus 57 ~k~~~l~~ei~e~~~ei~~l~~k~~~l~~El~~~ 90 (99)
++...|..||--+-++|..|..++..|.-.|-++
T Consensus 54 ~~~keLL~EIA~lE~eV~~LE~~v~~L~~~l~~q 87 (88)
T PF14389_consen 54 KKAKELLEEIALLEAEVAKLEQKVLSLYRQLFQQ 87 (88)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3456677788888888888888888777666543
No 274
>KOG4603 consensus TBP-1 interacting protein [Signal transduction mechanisms]
Probab=44.21 E-value=66 Score=24.74 Aligned_cols=19 Identities=21% Similarity=0.349 Sum_probs=11.0
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 041503 72 EIERLSDKFRLLHKELEHT 90 (99)
Q Consensus 72 ei~~l~~k~~~l~~El~~~ 90 (99)
-+++++.++.+|.+|+..-
T Consensus 117 t~eemQe~i~~L~kev~~~ 135 (201)
T KOG4603|consen 117 TTEEMQEEIQELKKEVAGY 135 (201)
T ss_pred ChHHHHHHHHHHHHHHHHH
Confidence 3445566666666666543
No 275
>PRK05667 dnaG DNA primase; Validated
Probab=44.02 E-value=16 Score=31.74 Aligned_cols=29 Identities=24% Similarity=0.621 Sum_probs=21.6
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCe
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKN 45 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~f 45 (99)
..||.|+....-+.. ||.+.+|.|-+|+-
T Consensus 37 ~~CPfH~ektpSf~V----~~~k~~~~CF~Cg~ 65 (580)
T PRK05667 37 GLCPFHDEKTPSFTV----SPDKQFYHCFGCGA 65 (580)
T ss_pred ecCCCCCCCCCceEE----ECCCCeEEECCCCC
Confidence 679999976544444 46788999998873
No 276
>PF10458 Val_tRNA-synt_C: Valyl tRNA synthetase tRNA binding arm; InterPro: IPR019499 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. This entry represents the C-terminal domain of Valyl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Valyl-tRNA synthetase (6.1.1.9 from EC) is an alpha monomer that belongs to class Ia.; GO: 0000166 nucleotide binding, 0004832 valine-tRNA ligase activity, 0005524 ATP binding, 0006438 valyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IVS_B 1GAX_B.
Probab=44.01 E-value=69 Score=19.64 Aligned_cols=20 Identities=45% Similarity=0.650 Sum_probs=9.8
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 041503 70 TLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 70 ~~ei~~l~~k~~~l~~El~~ 89 (99)
+.|+++|..++.++++++..
T Consensus 3 ~~E~~rL~Kel~kl~~~i~~ 22 (66)
T PF10458_consen 3 EAEIERLEKELEKLEKEIER 22 (66)
T ss_dssp HHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 34455555555555555443
No 277
>PF05082 Rop-like: Rop-like; InterPro: IPR007774 This family contains several uncharacterised bacterial proteins. These proteins are found in nitrogen fixation operons, so are likely to play a role in this process.; PDB: 3CSX_A 2JS5_B.
Probab=43.87 E-value=60 Score=20.87 Aligned_cols=23 Identities=22% Similarity=0.413 Sum_probs=14.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 041503 65 EVRKLTLEIERLSDKFRLLHKEL 87 (99)
Q Consensus 65 ei~e~~~ei~~l~~k~~~l~~El 87 (99)
+|.+++.++++|+.+--.+..||
T Consensus 3 d~~eLk~evkKL~~~A~~~kmdL 25 (66)
T PF05082_consen 3 DIEELKKEVKKLNRKATQAKMDL 25 (66)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHH
Confidence 56666667777665555555444
No 278
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=43.81 E-value=35 Score=30.58 Aligned_cols=43 Identities=19% Similarity=0.283 Sum_probs=30.1
Q ss_pred CCCCcccccCccccceeeeecC-----------------CCCCCcceeeCCCCCeeEeccCCc
Q 041503 8 SRNSLQVCNECGGQIELFTSHT-----------------TKNPNRKFWKCRVCKNFQWAEDRK 53 (99)
Q Consensus 8 ~~~~~~~Cp~Cg~~~~~~tS~t-----------------~~NPgR~Fy~C~~C~fF~W~De~~ 53 (99)
.+.+++.|..|..++.-++..+ ..|-| ..||.|+.-.=.|.-.
T Consensus 532 enk~~~~C~lc~d~aed~i~s~ChH~FCrlCi~eyv~~f~~~~n---vtCP~C~i~LsiDlse 591 (791)
T KOG1002|consen 532 ENKGEVECGLCHDPAEDYIESSCHHKFCRLCIKEYVESFMENNN---VTCPVCHIGLSIDLSE 591 (791)
T ss_pred cccCceeecccCChhhhhHhhhhhHHHHHHHHHHHHHhhhcccC---CCCccccccccccccc
Confidence 3455689988998877766544 34444 7899999777777643
No 279
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=43.80 E-value=17 Score=22.47 Aligned_cols=22 Identities=23% Similarity=0.616 Sum_probs=14.6
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCee
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNF 46 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF 46 (99)
..||.||... ++-..|+.|+|+
T Consensus 28 ~~C~~CG~~~------------~~H~vC~~CG~Y 49 (57)
T PRK12286 28 VECPNCGEPK------------LPHRVCPSCGYY 49 (57)
T ss_pred eECCCCCCcc------------CCeEECCCCCcC
Confidence 6788888643 334557778765
No 280
>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=43.51 E-value=13 Score=31.17 Aligned_cols=24 Identities=29% Similarity=0.739 Sum_probs=16.0
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCeeE
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQ 47 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~ 47 (99)
..|..||.... +.+++||.|+-|-
T Consensus 8 y~C~~Cg~~~~-----------~~~g~Cp~C~~w~ 31 (454)
T TIGR00416 8 FVCQHCGADSP-----------KWQGKCPACHAWN 31 (454)
T ss_pred EECCcCCCCCc-----------cccEECcCCCCcc
Confidence 67877876433 5677888887443
No 281
>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=43.51 E-value=23 Score=28.98 Aligned_cols=36 Identities=17% Similarity=0.482 Sum_probs=22.5
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCeeEecc
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQWAE 50 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~W~D 50 (99)
|.||.||+..+..++. +...+.-.|+|. |+.=.+.|
T Consensus 170 p~c~~cg~~~~~v~~~-d~~~~~v~y~c~-cG~~g~~~ 205 (353)
T cd00674 170 PYCEKCGKDTTTVEAY-DAKAGTVTYKCE-CGHEETVD 205 (353)
T ss_pred eecCCcCcceeEEEEE-eCCCCeEEEEcC-CCCEEEEe
Confidence 9999999543333333 344567899995 65444443
No 282
>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=43.43 E-value=12 Score=21.38 Aligned_cols=12 Identities=42% Similarity=1.099 Sum_probs=7.3
Q ss_pred cceeeCCCCCee
Q 041503 35 RKFWKCRVCKNF 46 (99)
Q Consensus 35 R~Fy~C~~C~fF 46 (99)
..||+|..|+-.
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 479999999844
No 283
>PF06717 DUF1202: Protein of unknown function (DUF1202); InterPro: IPR009592 This family consists of several hypothetical bacterial proteins of around 335 residues in length. Members of this family are found exclusively in Escherichia coli and Salmonella species and are often referred to as YggM proteins. The function of this family is unknown.
Probab=43.20 E-value=82 Score=25.81 Aligned_cols=42 Identities=14% Similarity=0.192 Sum_probs=27.8
Q ss_pred CeeEeccCCccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 44 KNFQWAEDRKFSNEKIDLLVEEVRKLTLEIERLSDKFRLLHKEL 87 (99)
Q Consensus 44 ~fF~W~De~~~~~~k~~~l~~ei~e~~~ei~~l~~k~~~l~~El 87 (99)
+|.+|.|+... -+.+.|.+++.+.+..|.+|+.++.+|.++.
T Consensus 127 KYLIvn~~~F~--~rf~~Ied~~~~kK~~I~~L~~qisaLdkqi 168 (308)
T PF06717_consen 127 KYLIVNDQDFN--YRFNQIEDEYNRKKNKIPGLNKQISALDKQI 168 (308)
T ss_pred cEEEecchhHH--HHHHHHHHHHHHHhhhhHHHHHHHHHHHHHH
Confidence 89999988632 3445666666666666666666666665554
No 284
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=43.15 E-value=83 Score=21.27 Aligned_cols=15 Identities=7% Similarity=0.326 Sum_probs=7.0
Q ss_pred HHHHHHHHHHHHHHH
Q 041503 63 VEEVRKLTLEIERLS 77 (99)
Q Consensus 63 ~~ei~e~~~ei~~l~ 77 (99)
+.|+++|..++++|+
T Consensus 77 ~~ei~~L~~el~~L~ 91 (121)
T PRK09413 77 MKQIKELQRLLGKKT 91 (121)
T ss_pred HHHHHHHHHHHHHHH
Confidence 334444444444444
No 285
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=42.92 E-value=21 Score=24.65 Aligned_cols=28 Identities=36% Similarity=0.786 Sum_probs=20.3
Q ss_pred ccccCccccceeeeecCCCCCCcc-eeeCCCCCe
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRK-FWKCRVCKN 45 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~-Fy~C~~C~f 45 (99)
+.||.|+.+=..++-. +|. |-+|..|+.
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 8999999986655544 455 667888863
No 286
>PF07926 TPR_MLP1_2: TPR/MLP1/MLP2-like protein; InterPro: IPR012929 This domain is found in a number of proteins, including TPR protein (P12270 from SWISSPROT) and yeast myosin-like proteins 1 (MLP1, Q02455 from SWISSPROT) and 2 (MLP2, P40457 from SWISSPROT). These proteins share a number of features; for example, they all have coiled-coil regions and all three are associated with nuclear pores [, , ]. TPR is thought to be a component of nuclear pore complex- attached intranuclear filaments [], and is implicated in nuclear protein import []. Moreover, its N-terminal region is involved in the activation of oncogenic kinases, possibly by mediating the dimerisation of kinase domains or by targeting these kinases to the nuclear pore complex []. MLP1 and MLP2 are involved in the process of telomere length regulation, where they are thought to interact with proteins such as Tel1p and modulate their activity []. ; GO: 0006606 protein import into nucleus, 0005643 nuclear pore
Probab=42.91 E-value=97 Score=21.41 Aligned_cols=33 Identities=21% Similarity=0.379 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 59 IDLLVEEVRKLTLEIERLSDKFRLLHKELEHTQ 91 (99)
Q Consensus 59 ~~~l~~ei~e~~~ei~~l~~k~~~l~~El~~~~ 91 (99)
.+.|.+++..+...+.....++..++.||+...
T Consensus 5 ~~~l~~e~~~~~~~~~~~~~~~~~~~~dl~~q~ 37 (132)
T PF07926_consen 5 LSSLQSELQRLKEQEEDAEEQLQSLREDLESQA 37 (132)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456677777777777778888888888877654
No 287
>COG3439 Uncharacterized conserved protein [Function unknown]
Probab=42.87 E-value=40 Score=24.17 Aligned_cols=11 Identities=9% Similarity=0.603 Sum_probs=9.8
Q ss_pred CCCeeEeccCC
Q 041503 42 VCKNFQWAEDR 52 (99)
Q Consensus 42 ~C~fF~W~De~ 52 (99)
.|+++.|+|+.
T Consensus 86 Pcrv~V~e~~~ 96 (137)
T COG3439 86 PCRVLVYEDED 96 (137)
T ss_pred CeEEEEEEcCC
Confidence 79999999776
No 288
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=42.78 E-value=12 Score=26.02 Aligned_cols=27 Identities=26% Similarity=0.532 Sum_probs=14.8
Q ss_pred ccccCccccceeeeecCCCCCCc--ceeeCCCCC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNR--KFWKCRVCK 44 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR--~Fy~C~~C~ 44 (99)
..| .||..-..-- ..+.+ .|+.||.|+
T Consensus 71 ~~C-~Cg~~~~~~~----~~~~~~~~~~~CP~Cg 99 (124)
T PRK00762 71 IEC-ECGYEGVVDE----DEIDHYAAVIECPVCG 99 (124)
T ss_pred EEe-eCcCcccccc----cchhccccCCcCcCCC
Confidence 789 9994321110 11112 257899998
No 289
>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association [].
Probab=42.59 E-value=81 Score=25.04 Aligned_cols=21 Identities=29% Similarity=0.379 Sum_probs=8.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 041503 67 RKLTLEIERLSDKFRLLHKEL 87 (99)
Q Consensus 67 ~e~~~ei~~l~~k~~~l~~El 87 (99)
.++..+|+.+.+++.++..|+
T Consensus 240 ~~l~~~i~~~~~~k~~l~~eI 260 (325)
T PF08317_consen 240 EELEEKIEELEEQKQELLAEI 260 (325)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 333344444444444444433
No 290
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=42.53 E-value=77 Score=22.04 Aligned_cols=21 Identities=19% Similarity=0.226 Sum_probs=8.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 041503 62 LVEEVRKLTLEIERLSDKFRL 82 (99)
Q Consensus 62 l~~ei~e~~~ei~~l~~k~~~ 82 (99)
++..|.++..++++|++.+..
T Consensus 13 le~~l~~l~~el~~LK~~~~e 33 (110)
T PRK13169 13 LEQNLGVLLKELGALKKQLAE 33 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 333334444444444433333
No 291
>PF05529 Bap31: B-cell receptor-associated protein 31-like ; InterPro: IPR008417 Bap31 is a polytopic integral protein of the endoplasmic reticulum membrane and a substrate of caspase-8. Bap31 is cleaved within its cytosolic domain, generating pro-apoptotic p20 Bap31 [].; GO: 0006886 intracellular protein transport, 0005783 endoplasmic reticulum, 0016021 integral to membrane
Probab=42.52 E-value=75 Score=23.04 Aligned_cols=13 Identities=46% Similarity=0.641 Sum_probs=5.3
Q ss_pred HHHHHHHHHHHHH
Q 041503 77 SDKFRLLHKELEH 89 (99)
Q Consensus 77 ~~k~~~l~~El~~ 89 (99)
+.+++++++||++
T Consensus 160 ~~ei~~lk~el~~ 172 (192)
T PF05529_consen 160 SEEIEKLKKELEK 172 (192)
T ss_pred HHHHHHHHHHHHH
Confidence 3344444444433
No 292
>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=42.28 E-value=13 Score=19.49 Aligned_cols=13 Identities=23% Similarity=0.552 Sum_probs=5.8
Q ss_pred cceeeCCCCCeeE
Q 041503 35 RKFWKCRVCKNFQ 47 (99)
Q Consensus 35 R~Fy~C~~C~fF~ 47 (99)
..+|.|+.|+|..
T Consensus 13 ~~~Y~C~~Cdf~l 25 (30)
T PF07649_consen 13 GWFYRCSECDFDL 25 (30)
T ss_dssp --EEE-TTT----
T ss_pred CceEECccCCCcc
Confidence 4799999999864
No 293
>COG2433 Uncharacterized conserved protein [Function unknown]
Probab=42.11 E-value=76 Score=28.51 Aligned_cols=26 Identities=31% Similarity=0.484 Sum_probs=10.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 61 LLVEEVRKLTLEIERLSDKFRLLHKE 86 (99)
Q Consensus 61 ~l~~ei~e~~~ei~~l~~k~~~l~~E 86 (99)
.|..+|++++.+|+.|+++...++.+
T Consensus 440 ~L~~~~ee~k~eie~L~~~l~~~~r~ 465 (652)
T COG2433 440 ELKRELEELKREIEKLESELERFRRE 465 (652)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444444444444444444433333
No 294
>KOG4253 consensus Tryptophan-rich basic nuclear protein [General function prediction only]
Probab=42.07 E-value=84 Score=23.75 Aligned_cols=19 Identities=42% Similarity=0.520 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 041503 72 EIERLSDKFRLLHKELEHT 90 (99)
Q Consensus 72 ei~~l~~k~~~l~~El~~~ 90 (99)
.-.+|+.|+.+|-+|+|..
T Consensus 71 kwaRlnRKi~kl~~ele~q 89 (175)
T KOG4253|consen 71 KWARLNRKINKLDKELETQ 89 (175)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3457888999999999654
No 295
>PF04645 DUF603: Protein of unknown function, DUF603; InterPro: IPR006739 This family includes several uncharacterised proteins from Borrelia species.
Probab=41.95 E-value=80 Score=24.06 Aligned_cols=8 Identities=25% Similarity=0.310 Sum_probs=3.0
Q ss_pred HHHHHHHH
Q 041503 62 LVEEVRKL 69 (99)
Q Consensus 62 l~~ei~e~ 69 (99)
|+.+|..+
T Consensus 117 L~~kI~~L 124 (181)
T PF04645_consen 117 LRLKISSL 124 (181)
T ss_pred HHHHHHHH
Confidence 33334333
No 296
>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=41.73 E-value=17 Score=19.99 Aligned_cols=7 Identities=57% Similarity=1.630 Sum_probs=4.1
Q ss_pred ccCcccc
Q 041503 15 CNECGGQ 21 (99)
Q Consensus 15 Cp~Cg~~ 21 (99)
||.||..
T Consensus 1 C~~C~~~ 7 (46)
T TIGR03831 1 CPICGGE 7 (46)
T ss_pred CCCCCCc
Confidence 5677543
No 297
>PF12709 Kinetocho_Slk19: Central kinetochore-associated; InterPro: IPR024312 This is a family of proteins integrally involved in the central kinetochore. Slk19 is a yeast member and it may play an important role in the timing of nuclear migration. It may also participate, directly or indirectly, in the maintenance of centromeric tensile strength during mitotic stagnation, for instance during activation of checkpoint controls, when cells need to preserve nuclear integrity until cell cycle progression can be resumed [].
Probab=41.48 E-value=92 Score=21.02 Aligned_cols=33 Identities=33% Similarity=0.317 Sum_probs=24.8
Q ss_pred chhh-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 55 SNEK-IDLLVEEVRKLTLEIERLSDKFRLLHKEL 87 (99)
Q Consensus 55 ~~~k-~~~l~~ei~e~~~ei~~l~~k~~~l~~El 87 (99)
.|.+ ++.|..++..+..|++.|+.++.....|-
T Consensus 46 rwek~v~~L~~e~~~l~~E~e~L~~~l~~e~~Ek 79 (87)
T PF12709_consen 46 RWEKKVDELENENKALKRENEQLKKKLDTEREEK 79 (87)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3543 46677788888889998988888877663
No 298
>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=41.39 E-value=18 Score=24.90 Aligned_cols=27 Identities=26% Similarity=0.689 Sum_probs=17.1
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCK 44 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~ 44 (99)
..|+.||....... + . ++.-|+|+.|+
T Consensus 124 ~~C~~C~~~~~r~~-~--~--~~~~~~C~~C~ 150 (157)
T PF10263_consen 124 YRCPSCGREYKRHR-R--S--KRKRYRCGRCG 150 (157)
T ss_pred EEcCCCCCEeeeec-c--c--chhhEECCCCC
Confidence 78999997652221 1 1 34449999886
No 299
>cd00584 Prefoldin_alpha Prefoldin alpha subunit; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=41.34 E-value=96 Score=20.91 Aligned_cols=45 Identities=24% Similarity=0.378 Sum_probs=19.8
Q ss_pred CCCeeEeccCCc---cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 42 VCKNFQWAEDRK---FSNEKIDLLVEEVRKLTLEIERLSDKFRLLHKE 86 (99)
Q Consensus 42 ~C~fF~W~De~~---~~~~k~~~l~~ei~e~~~ei~~l~~k~~~l~~E 86 (99)
+.++|.-.+-.. +--.++..|...++++...+..+++++..+...
T Consensus 76 G~g~~vE~~~~eA~~~l~~r~~~l~~~~~~l~~~l~~l~~~~~~~~~~ 123 (129)
T cd00584 76 GTGYYVEKDLEEAIEFLDKKIEELTKQIEKLQKELAKLKDQINTLEAE 123 (129)
T ss_pred CCCEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455555554331 122233333444445555555555444444333
No 300
>TIGR02338 gimC_beta prefoldin, beta subunit, archaeal. Chaperonins are cytosolic, ATP-dependent molecular chaperones, with a conserved toroidal architecture, that assist in the folding of nascent and/or denatured polypeptide chains. The group I chaperonin system consists of GroEL and GroES, and is found (usually) in bacteria and organelles of bacterial origin. The group II chaperonin system, called the thermosome in Archaea and TRiC or CCT in the Eukaryota, is structurally similar but only distantly related. Prefoldin, also called GimC, is a complex in Archaea and Eukaryota, that works with group II chaperonins. Members of this protein family are the archaeal clade of the beta class of prefoldin subunit. Closely related, but outside the scope of this family are the eukaryotic beta-class prefoldin subunits, Gim-1,3,4 and 6. The alpha class prefoldin subunits are more distantly related.
Probab=41.29 E-value=1.1e+02 Score=20.50 Aligned_cols=32 Identities=25% Similarity=0.417 Sum_probs=23.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 58 KIDLLVEEVRKLTLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 58 k~~~l~~ei~e~~~ei~~l~~k~~~l~~El~~ 89 (99)
++..++..|..+...++.++.++.+++..|.+
T Consensus 75 r~e~ie~~i~~lek~~~~l~~~l~e~q~~l~~ 106 (110)
T TIGR02338 75 KKETLELRVKTLQRQEERLREQLKELQEKIQE 106 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34556667788888888888888888777754
No 301
>PF07047 OPA3: Optic atrophy 3 protein (OPA3); InterPro: IPR010754 OPA3 deficiency causes type III 3-methylglutaconic aciduria (MGA) in humans. This disease manifests with early bilateral optic atrophy, spasticity, extrapyramidal dysfunction, ataxia, and cognitive deficits, but normal longevity []. This family consists of several optic atrophy 3 (OPA3) proteins and related proteins from other eukaryotic species, the function is unknown.
Probab=41.12 E-value=55 Score=22.98 Aligned_cols=24 Identities=25% Similarity=0.470 Sum_probs=14.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 68 KLTLEIERLSDKFRLLHKELEHTQ 91 (99)
Q Consensus 68 e~~~ei~~l~~k~~~l~~El~~~~ 91 (99)
++..+++.|+.++..|..++++.+
T Consensus 109 ~~~~~l~~L~~~i~~L~~~~~~~~ 132 (134)
T PF07047_consen 109 ELQERLEELEERIEELEEQVEKQQ 132 (134)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Confidence 444566667777777766666543
No 302
>PF05308 Mito_fiss_reg: Mitochondrial fission regulator; InterPro: IPR007972 This family consists of several uncharacterised eukaryotic proteins of unknown function.
Probab=40.72 E-value=32 Score=27.01 Aligned_cols=21 Identities=29% Similarity=0.477 Sum_probs=13.5
Q ss_pred chhhHHHHHHHHHHHHHHHHH
Q 041503 55 SNEKIDLLVEEVRKLTLEIER 75 (99)
Q Consensus 55 ~~~k~~~l~~ei~e~~~ei~~ 75 (99)
+..|+++|++|+..|..+|..
T Consensus 120 AlqKIsALEdELs~LRaQIA~ 140 (253)
T PF05308_consen 120 ALQKISALEDELSRLRAQIAK 140 (253)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 556777777776666665543
No 303
>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association [].
Probab=40.55 E-value=80 Score=25.07 Aligned_cols=10 Identities=40% Similarity=0.431 Sum_probs=3.6
Q ss_pred HHHHHHHHHH
Q 041503 65 EVRKLTLEIE 74 (99)
Q Consensus 65 ei~e~~~ei~ 74 (99)
++.++..+|+
T Consensus 217 eL~~~~~~i~ 226 (325)
T PF08317_consen 217 ELAEQKEEIE 226 (325)
T ss_pred HHHHHHHHHH
Confidence 3333333333
No 304
>COG1422 Predicted membrane protein [Function unknown]
Probab=40.43 E-value=71 Score=24.65 Aligned_cols=23 Identities=17% Similarity=0.287 Sum_probs=15.0
Q ss_pred chhhHHHHHHHHHHHHHHHHHHH
Q 041503 55 SNEKIDLLVEEVRKLTLEIERLS 77 (99)
Q Consensus 55 ~~~k~~~l~~ei~e~~~ei~~l~ 77 (99)
.|++-..++.+++|.++++++.+
T Consensus 70 D~ekm~~~qk~m~efq~e~~eA~ 92 (201)
T COG1422 70 DQEKMKELQKMMKEFQKEFREAQ 92 (201)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHH
Confidence 66776667776666666665553
No 305
>PRK03947 prefoldin subunit alpha; Reviewed
Probab=40.41 E-value=1.1e+02 Score=20.93 Aligned_cols=30 Identities=23% Similarity=0.437 Sum_probs=15.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 60 DLLVEEVRKLTLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 60 ~~l~~ei~e~~~ei~~l~~k~~~l~~El~~ 89 (99)
+.|...++++...+..+++++..+...|.+
T Consensus 104 ~~l~~~~~~l~~~l~~~~~~~~~~~~~l~~ 133 (140)
T PRK03947 104 EELEKALEKLEEALQKLASRIAQLAQELQQ 133 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333444555555566666555555555543
No 306
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=40.33 E-value=18 Score=25.56 Aligned_cols=24 Identities=21% Similarity=0.621 Sum_probs=15.4
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCK 44 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~ 44 (99)
+-||.|++.+.-- +. .-|.|+.|+
T Consensus 35 ~aC~~C~kkv~~~-------~~-~~~~C~~C~ 58 (166)
T cd04476 35 PACPGCNKKVVEE-------GN-GTYRCEKCN 58 (166)
T ss_pred ccccccCcccEeC-------CC-CcEECCCCC
Confidence 6788888764321 11 568888776
No 307
>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=39.86 E-value=14 Score=18.78 Aligned_cols=11 Identities=36% Similarity=0.830 Sum_probs=8.5
Q ss_pred CcceeeCCCCC
Q 041503 34 NRKFWKCRVCK 44 (99)
Q Consensus 34 gR~Fy~C~~C~ 44 (99)
|-+.|.|+.|+
T Consensus 11 ~~k~~~C~~C~ 21 (26)
T PF13465_consen 11 GEKPYKCPYCG 21 (26)
T ss_dssp SSSSEEESSSS
T ss_pred CCCCCCCCCCc
Confidence 55669999887
No 308
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=39.69 E-value=97 Score=24.33 Aligned_cols=29 Identities=34% Similarity=0.489 Sum_probs=14.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 60 DLLVEEVRKLTLEIERLSDKFRLLHKELE 88 (99)
Q Consensus 60 ~~l~~ei~e~~~ei~~l~~k~~~l~~El~ 88 (99)
..|+.|+.++..+++++.+++..++..+.
T Consensus 106 ~~le~el~~l~~~~~~l~~~i~~l~~~~~ 134 (239)
T COG1579 106 NSLEDELAELMEEIEKLEKEIEDLKERLE 134 (239)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44455555555555555555544444443
No 309
>PRK10698 phage shock protein PspA; Provisional
Probab=39.12 E-value=1.4e+02 Score=22.71 Aligned_cols=35 Identities=26% Similarity=0.347 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 59 IDLLVEEVRKLTLEIERLSDKFRLLHKELEHTQLR 93 (99)
Q Consensus 59 ~~~l~~ei~e~~~ei~~l~~k~~~l~~El~~~~~~ 93 (99)
.+.|.+++......+..|+.++..|+..|++...+
T Consensus 101 ~~~l~~~~~~~~~~~~~L~~~l~~L~~ki~eak~k 135 (222)
T PRK10698 101 IATLEHEVTLVDETLARMKKEIGELENKLSETRAR 135 (222)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555566666677777777777777777665543
No 310
>PF03980 Nnf1: Nnf1 ; InterPro: IPR007128 NNF1 is an essential yeast gene required for proper spindle orientation, nucleolar and nuclear envelope structure and mRNA export [].
Probab=39.07 E-value=1.1e+02 Score=20.25 Aligned_cols=27 Identities=19% Similarity=0.377 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 64 EEVRKLTLEIERLSDKFRLLHKELEHT 90 (99)
Q Consensus 64 ~ei~e~~~ei~~l~~k~~~l~~El~~~ 90 (99)
.++..|+..+..++..+..|..+|...
T Consensus 80 ~~~~~L~~~l~~l~~eN~~L~~~i~~~ 106 (109)
T PF03980_consen 80 KEREQLNARLQELEEENEALAEEIQEQ 106 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 356677777777777777777777653
No 311
>PF04102 SlyX: SlyX; InterPro: IPR007236 The SlyX protein has no known function. It is short, less than 80 amino acids, and its gene is found close to the slyD gene. The SlyX protein has a conserved PPH(Y/W) motif at its C terminus. The protein may be a coiled-coil structure.; PDB: 3EFG_A.
Probab=38.74 E-value=98 Score=19.29 Aligned_cols=23 Identities=13% Similarity=0.277 Sum_probs=10.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 041503 66 VRKLTLEIERLSDKFRLLHKELE 88 (99)
Q Consensus 66 i~e~~~ei~~l~~k~~~l~~El~ 88 (99)
|++|+..+-++..+|..|+..|.
T Consensus 20 ie~Ln~~v~~Qq~~I~~L~~~l~ 42 (69)
T PF04102_consen 20 IEELNDVVTEQQRQIDRLQRQLR 42 (69)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 44554444444444444444443
No 312
>COG4238 Murein lipoprotein [Cell envelope biogenesis, outer membrane]
Probab=38.64 E-value=1.2e+02 Score=20.21 Aligned_cols=37 Identities=24% Similarity=0.506 Sum_probs=25.3
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 55 SNEKIDLLVEEVRKLTLEIERLSDKFRLLHKELEHTQ 91 (99)
Q Consensus 55 ~~~k~~~l~~ei~e~~~ei~~l~~k~~~l~~El~~~~ 91 (99)
.-.|++-|-..+++|...+.+|......|..|..-.+
T Consensus 23 s~aK~dqlss~vq~LnAkv~qLe~dv~a~~~~~qAAk 59 (78)
T COG4238 23 SNAKIDQLSSDVQTLNAKVDQLENDVNAMRSDVQAAK 59 (78)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 3456666666777787778777777777776665433
No 313
>PRK04023 DNA polymerase II large subunit; Validated
Probab=38.36 E-value=23 Score=33.41 Aligned_cols=14 Identities=36% Similarity=0.444 Sum_probs=8.2
Q ss_pred HHHHHHHHHHhhcC
Q 041503 85 KELEHTQLRSKYGL 98 (99)
Q Consensus 85 ~El~~~~~~~~~~~ 98 (99)
+=|||--||.|.|+
T Consensus 717 EPlEKGiLRAk~~v 730 (1121)
T PRK04023 717 EPLEKGILRAKHDV 730 (1121)
T ss_pred cchHhhhhhhhcCe
Confidence 34566666666654
No 314
>COG4985 ABC-type phosphate transport system, auxiliary component [Inorganic ion transport and metabolism]
Probab=38.35 E-value=66 Score=25.94 Aligned_cols=31 Identities=26% Similarity=0.365 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 60 DLLVEEVRKLTLEIERLSDKFRLLHKELEHT 90 (99)
Q Consensus 60 ~~l~~ei~e~~~ei~~l~~k~~~l~~El~~~ 90 (99)
+-+.+|..++...+..|.++.+.|+.|+++.
T Consensus 217 ~~~~ae~seLq~r~~~l~~~L~~L~~e~~r~ 247 (289)
T COG4985 217 QHYVAEKSELQKRLAQLQTELDALRAELERQ 247 (289)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhhhc
Confidence 3445566777778888888888888888765
No 315
>PF01486 K-box: K-box region; InterPro: IPR002487 MADS genes in plants encode key developmental regulators of vegetative and reproductive development. The majority of the plant MADS proteins share a stereotypical MIKC structure. It comprises (from N- to C-terminal) an N-terminal domain, which is, however, present only in a minority of proteins; a MADS domain (see PDOC00302 from PROSITEDOC, IPR002100 from INTERPRO), which is the major determinant of DNA-binding but which also performs dimerisation and accessory factor binding functions; a weakly conserved intervening (I) domain, which constitutes a key molecular determinant for the selective formation of DNA-binding dimers; a keratin-like (K-box) domain, which promotes protein dimerisation; and a C-terminal (C) domain, which is involved in transcriptional activation or in the formation of ternary or quaternary protein complexes. The 80-amino acid K-box domain was originally identified as a region with low but significant similarity to a region of keratin, which is part of the coiled-coil sequence constituting the central rod-shaped domain of keratin [, , ]. The K-box protein-protein interaction domain which mediates heterodimerization of MIKC-type MADS proteins contains several heptad repeats in which the first and the fourth positions are occupied by hydrophobic amino acids suggesting that the K-box domain forms three amphipathic alpha-helices referred to as K1, K2, and K3 [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=38.34 E-value=78 Score=20.72 Aligned_cols=18 Identities=11% Similarity=0.134 Sum_probs=8.0
Q ss_pred eeEeccCCccchhhHHHH
Q 041503 45 NFQWAEDRKFSNEKIDLL 62 (99)
Q Consensus 45 fF~W~De~~~~~~k~~~l 62 (99)
++...|-...+.+....|
T Consensus 37 ~~~GedL~~Ls~~eL~~L 54 (100)
T PF01486_consen 37 HLMGEDLESLSLKELQQL 54 (100)
T ss_pred ccccccccccchHHHHHH
Confidence 444555444444443333
No 316
>COG0576 GrpE Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]
Probab=38.32 E-value=1.5e+02 Score=22.19 Aligned_cols=36 Identities=22% Similarity=0.256 Sum_probs=24.9
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 57 EKIDLLVEEVRKLTLEIERLSDKFRLLHKELEHTQL 92 (99)
Q Consensus 57 ~k~~~l~~ei~e~~~ei~~l~~k~~~l~~El~~~~~ 92 (99)
.+++.|++++.++.....++.+.++.+++.++++.-
T Consensus 43 ~~i~~Le~q~~e~~~~~lr~~Ae~eN~rkR~~re~e 78 (193)
T COG0576 43 QEIAELEAQLEELKDKYLRAQAEFENLRKRTERERE 78 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456667777777766777777777777777766543
No 317
>PF07407 Seadorna_VP6: Seadornavirus VP6 protein; InterPro: IPR009982 This family consists of several VP6 proteins from the Banna virus as well as a related protein VP5 from the Kadipiro virus. Members of this family are typically of around 420 residues in length. The function of this family is unknown.
Probab=38.25 E-value=63 Score=27.24 Aligned_cols=32 Identities=22% Similarity=0.101 Sum_probs=21.8
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 57 EKIDLLVEEVRKLTLEIERLSDKFRLLHKELE 88 (99)
Q Consensus 57 ~k~~~l~~ei~e~~~ei~~l~~k~~~l~~El~ 88 (99)
.-..+|+.|-..|+.|+++|+.+...|+.|..
T Consensus 32 ~e~~aLr~EN~~LKkEN~~Lk~eVerLE~e~l 63 (420)
T PF07407_consen 32 DENFALRMENHSLKKENNDLKIEVERLENEML 63 (420)
T ss_pred hhhhhHHHHhHHHHHHHHHHHHHHHHHHHHhh
Confidence 33456677777777777777777777766555
No 318
>KOG3335 consensus Predicted coiled-coil protein [General function prediction only]
Probab=38.10 E-value=99 Score=23.57 Aligned_cols=29 Identities=24% Similarity=0.359 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 62 LVEEVRKLTLEIERLSDKFRLLHKELEHT 90 (99)
Q Consensus 62 l~~ei~e~~~ei~~l~~k~~~l~~El~~~ 90 (99)
-.+|+.|+...++.|+.+++.|++++..-
T Consensus 104 ~~~e~~elr~~~~~l~~~i~~~~~~~~~L 132 (181)
T KOG3335|consen 104 RKQEIMELRLKVEKLENAIAELTKFFSQL 132 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34466677777777766676666666543
No 319
>PRK12495 hypothetical protein; Provisional
Probab=38.04 E-value=20 Score=28.16 Aligned_cols=28 Identities=29% Similarity=0.738 Sum_probs=19.6
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCeeEec
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQWA 49 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~W~ 49 (99)
.+|+.||.++. .=||-.| |+.|+-..=.
T Consensus 43 ~hC~~CG~PIp-------a~pG~~~--Cp~CQ~~~~~ 70 (226)
T PRK12495 43 AHCDECGDPIF-------RHDGQEF--CPTCQQPVTE 70 (226)
T ss_pred hhcccccCccc-------CCCCeeE--CCCCCCcccc
Confidence 78999999887 2266554 8988844333
No 320
>PF11365 DUF3166: Protein of unknown function (DUF3166); InterPro: IPR021507 This eukaryotic family of proteins has no known function.
Probab=37.95 E-value=1.3e+02 Score=20.62 Aligned_cols=24 Identities=38% Similarity=0.684 Sum_probs=17.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhc
Q 041503 72 EIERLSDKFRLLHKELEHTQLRSKYG 97 (99)
Q Consensus 72 ei~~l~~k~~~l~~El~~~~~~~~~~ 97 (99)
.|.++.++++.|..||.+ ++++||
T Consensus 23 kl~ele~eN~~l~~EL~k--yk~~~g 46 (96)
T PF11365_consen 23 KLSELEDENKQLTEELNK--YKSKYG 46 (96)
T ss_pred HHHHHHHHHHHHHHHHHH--HHHhcC
Confidence 456667777888889887 666775
No 321
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=37.94 E-value=13 Score=19.22 Aligned_cols=30 Identities=23% Similarity=0.547 Sum_probs=14.6
Q ss_pred cccCccccceeeeecCCCCCCcce----eeCCCCC
Q 041503 14 VCNECGGQIELFTSHTTKNPNRKF----WKCRVCK 44 (99)
Q Consensus 14 ~Cp~Cg~~~~~~tS~t~~NPgR~F----y~C~~C~ 44 (99)
.|+.|+.++... .....-+|+.| |+|..|+
T Consensus 1 ~C~~C~~~i~~~-~~~~~~~~~~~H~~Cf~C~~C~ 34 (39)
T smart00132 1 KCAGCGKPIRGG-ELVLRALGKVWHPECFKCSKCG 34 (39)
T ss_pred CccccCCcccCC-cEEEEeCCccccccCCCCcccC
Confidence 366777754331 00112245566 6666654
No 322
>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=37.85 E-value=33 Score=27.73 Aligned_cols=41 Identities=15% Similarity=0.301 Sum_probs=26.5
Q ss_pred cccccCcccccee--eeecCC-CCCCcceeeCCCCC-eeEeccCC
Q 041503 12 LQVCNECGGQIEL--FTSHTT-KNPNRKFWKCRVCK-NFQWAEDR 52 (99)
Q Consensus 12 ~~~Cp~Cg~~~~~--~tS~t~-~NPgR~Fy~C~~C~-fF~W~De~ 52 (99)
..+||.||..-.+ +..-++ ..++-+-+.|..|+ |++=.|..
T Consensus 224 R~~C~~Cg~~~~l~y~~~e~~~~~~~~r~e~C~~C~~YlK~~~~~ 268 (305)
T TIGR01562 224 RVKCSHCEESKHLAYLSLEHDAEKAVLKAETCDSCQGYLKILYQE 268 (305)
T ss_pred CccCCCCCCCCceeeEeecCCCCCcceEEeeccccccchhhhccc
Confidence 3899999974322 222222 46889999999998 55554443
No 323
>PLN00180 NDF6 (NDH-dependent flow 6); Provisional
Probab=37.46 E-value=39 Score=25.54 Aligned_cols=50 Identities=30% Similarity=0.460 Sum_probs=27.7
Q ss_pred eeCCCCCeeEeccCCcc--------------c--hhhHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 38 WKCRVCKNFQWAEDRKF--------------S--NEKIDLLVEEVR------KLTLEIERLSDKFRLLHKELEHTQ 91 (99)
Q Consensus 38 y~C~~C~fF~W~De~~~--------------~--~~k~~~l~~ei~------e~~~ei~~l~~k~~~l~~El~~~~ 91 (99)
|+|=+|-||-=.-++.| - ..+++.++++-| || |++..++.-.| -|||+.+
T Consensus 107 FT~WG~~fFgSmKDPfYDSe~YRgdGGDGT~hW~Yd~QEd~E~sAReeL~REEL---iEEIEQkVGGL-RELEEa~ 178 (180)
T PLN00180 107 FTCWGCLFFGSMKDPFYDSEEYRGDGGDGTGHWVYERQEDIEESARAELWREEL---IEEIEQKVGGL-RELEEAV 178 (180)
T ss_pred HHHHHHhheeccCCcccchHHhcccCCCCceeeEeehHHHHHHHHHHHHHHHHH---HHHHHHHhhhH-HHHHHhh
Confidence 45557777765444322 2 356666665433 44 44445566666 5777754
No 324
>COG1163 DRG Predicted GTPase [General function prediction only]
Probab=37.43 E-value=88 Score=26.24 Aligned_cols=34 Identities=38% Similarity=0.464 Sum_probs=25.4
Q ss_pred hhHHHHHHHHHH-----HH-HHHHHHHHHHHHHHHHHHHH
Q 041503 57 EKIDLLVEEVRK-----LT-LEIERLSDKFRLLHKELEHT 90 (99)
Q Consensus 57 ~k~~~l~~ei~e-----~~-~ei~~l~~k~~~l~~El~~~ 90 (99)
+|+.+++.||.. -+ .-|..|++++-+|+.||++.
T Consensus 6 EkIk~iEeeia~tpknKaTe~hig~lKaklA~Lr~El~~~ 45 (365)
T COG1163 6 EKIKAIEEEIARTPKNKATEHHIGLLKAKLAELREELEKR 45 (365)
T ss_pred HHHHHHHHHHHhcccchhhHHHHHHHHHHHHHHHHHHhhh
Confidence 466777777752 11 35677899999999999986
No 325
>PRK14011 prefoldin subunit alpha; Provisional
Probab=37.35 E-value=1.5e+02 Score=21.36 Aligned_cols=33 Identities=27% Similarity=0.359 Sum_probs=22.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 58 KIDLLVEEVRKLTLEIERLSDKFRLLHKELEHT 90 (99)
Q Consensus 58 k~~~l~~ei~e~~~ei~~l~~k~~~l~~El~~~ 90 (99)
|+..|..-++++...|+++++.+..+..+|+..
T Consensus 96 ri~~l~~~~~~l~~~i~~~~~~~~~l~~~L~~k 128 (144)
T PRK14011 96 SVEELDKTKKEGNKKIEELNKEITKLRKELEKR 128 (144)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555556677777778887888887776654
No 326
>PRK05771 V-type ATP synthase subunit I; Validated
Probab=37.29 E-value=1e+02 Score=26.60 Aligned_cols=32 Identities=25% Similarity=0.454 Sum_probs=17.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 62 LVEEVRKLTLEIERLSDKFRLLHKELEHTQLR 93 (99)
Q Consensus 62 l~~ei~e~~~ei~~l~~k~~~l~~El~~~~~~ 93 (99)
+..++.++..++++|+++++.++.+++.-.-|
T Consensus 98 ~~~~i~~l~~~~~~L~~~~~~l~~~~~~l~~~ 129 (646)
T PRK05771 98 IEKEIKELEEEISELENEIKELEQEIERLEPW 129 (646)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 34455555556666666665555555544433
No 327
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=36.95 E-value=15 Score=23.00 Aligned_cols=11 Identities=36% Similarity=0.863 Sum_probs=8.6
Q ss_pred ccccCccccce
Q 041503 13 QVCNECGGQIE 23 (99)
Q Consensus 13 ~~Cp~Cg~~~~ 23 (99)
.+||.||.++.
T Consensus 4 kHC~~CG~~Ip 14 (59)
T PF09889_consen 4 KHCPVCGKPIP 14 (59)
T ss_pred CcCCcCCCcCC
Confidence 57899988765
No 328
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=36.82 E-value=1.1e+02 Score=24.17 Aligned_cols=24 Identities=38% Similarity=0.446 Sum_probs=11.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 65 EVRKLTLEIERLSDKFRLLHKELE 88 (99)
Q Consensus 65 ei~e~~~ei~~l~~k~~~l~~El~ 88 (99)
.++++..++..++.++..++++|+
T Consensus 14 ~~~~~~~~~~~~~~~~~~~~~~~~ 37 (364)
T TIGR01242 14 EKRSLEKEKIRLERELERLRSEIE 37 (364)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444444444544445544443
No 329
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=36.80 E-value=22 Score=24.56 Aligned_cols=25 Identities=32% Similarity=0.416 Sum_probs=19.1
Q ss_pred cccccCccc-cceeeeecCCCCCCcc
Q 041503 12 LQVCNECGG-QIELFTSHTTKNPNRK 36 (99)
Q Consensus 12 ~~~Cp~Cg~-~~~~~tS~t~~NPgR~ 36 (99)
++.||+||. +-..|+-..+.+.-|+
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 478999996 5667777777777776
No 330
>PF14265 DUF4355: Domain of unknown function (DUF4355)
Probab=36.68 E-value=1.3e+02 Score=20.19 Aligned_cols=23 Identities=35% Similarity=0.515 Sum_probs=12.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 041503 71 LEIERLSDKFRLLHKELEHTQLR 93 (99)
Q Consensus 71 ~ei~~l~~k~~~l~~El~~~~~~ 93 (99)
.++..+.+++..+..++....|.
T Consensus 49 ~e~~~~~~el~~~~~e~~~~e~~ 71 (125)
T PF14265_consen 49 EELEELEKELEELEAELARRELR 71 (125)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 44555555555555555554443
No 331
>PF11488 Lge1: Transcriptional regulatory protein LGE1
Probab=36.62 E-value=1.2e+02 Score=19.51 Aligned_cols=26 Identities=19% Similarity=0.181 Sum_probs=19.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 63 VEEVRKLTLEIERLSDKFRLLHKELE 88 (99)
Q Consensus 63 ~~ei~e~~~ei~~l~~k~~~l~~El~ 88 (99)
-.+|..++.+|+.++.++.+...+++
T Consensus 29 ~~ei~~~d~~le~l~~q~~k~~~~~~ 54 (80)
T PF11488_consen 29 FKEIDSKDKELEELYQQDCKTEMEVK 54 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34788888899988888777765554
No 332
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=36.55 E-value=23 Score=27.07 Aligned_cols=25 Identities=28% Similarity=0.850 Sum_probs=16.5
Q ss_pred CcccccCccccceeeeecCCCCCCcceeeCCCCCee
Q 041503 11 SLQVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNF 46 (99)
Q Consensus 11 ~~~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF 46 (99)
+...|..||..... .++.||+|+-|
T Consensus 353 p~~~c~~cg~~~~~-----------~~~~c~~c~~~ 377 (389)
T PRK11788 353 PRYRCRNCGFTART-----------LYWHCPSCKAW 377 (389)
T ss_pred CCEECCCCCCCCcc-----------ceeECcCCCCc
Confidence 34668678865544 45679988854
No 333
>PF05377 FlaC_arch: Flagella accessory protein C (FlaC); InterPro: IPR008039 Although archaeal flagella appear superficially similar to those of bacteria, they are quite distinct []. In several archaea, the flagellin genes are followed immediately by the flagellar accessory genes flaCDEFGHIJ. The gene products may have a role in translocation, secretion, or assembly of the flagellum. FlaC is a protein whose exact role is unknown but it has been shown to be membrane-associated (by immuno-blotting fractionated cells) [].
Probab=36.47 E-value=1.1e+02 Score=19.05 Aligned_cols=24 Identities=13% Similarity=0.357 Sum_probs=13.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 60 DLLVEEVRKLTLEIERLSDKFRLL 83 (99)
Q Consensus 60 ~~l~~ei~e~~~ei~~l~~k~~~l 83 (99)
+.++.|+.++..+++++++.++.|
T Consensus 17 ~tvk~en~~i~~~ve~i~envk~l 40 (55)
T PF05377_consen 17 NTVKKENEEISESVEKIEENVKDL 40 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344456666666666666666555
No 334
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=36.31 E-value=73 Score=21.54 Aligned_cols=23 Identities=17% Similarity=0.079 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 041503 66 VRKLTLEIERLSDKFRLLHKELE 88 (99)
Q Consensus 66 i~e~~~ei~~l~~k~~~l~~El~ 88 (99)
+.++..++++|++++..|+.|++
T Consensus 73 ~~~~~~ei~~L~~el~~L~~E~d 95 (121)
T PRK09413 73 LAAAMKQIKELQRLLGKKTMENE 95 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 45666778888877777776643
No 335
>COG2919 Septum formation initiator [Cell division and chromosome partitioning]
Probab=36.28 E-value=1.3e+02 Score=20.60 Aligned_cols=33 Identities=21% Similarity=0.312 Sum_probs=20.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 57 EKIDLLVEEVRKLTLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 57 ~k~~~l~~ei~e~~~ei~~l~~k~~~l~~El~~ 89 (99)
.+...+...+.++..+++.|.+....|..|++.
T Consensus 50 ~~~~~l~~qi~~~~~e~~~L~~~~~~l~~ei~~ 82 (117)
T COG2919 50 ADVLQLQRQIAAQQAELEKLSARNTALEAEIKD 82 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444555666677777777766666666553
No 336
>PRK02655 psbI photosystem II reaction center I protein I; Provisional
Probab=36.15 E-value=19 Score=20.90 Aligned_cols=12 Identities=50% Similarity=0.839 Sum_probs=8.1
Q ss_pred eeecCC-CCCCcc
Q 041503 25 FTSHTT-KNPNRK 36 (99)
Q Consensus 25 ~tS~t~-~NPgR~ 36 (99)
+.|+.+ +||||+
T Consensus 23 flsnDP~RnP~rk 35 (38)
T PRK02655 23 FLSSDPTRNPGRK 35 (38)
T ss_pred cCCCCCCCCCCcc
Confidence 345554 899986
No 337
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.80 E-value=19 Score=23.04 Aligned_cols=14 Identities=21% Similarity=0.468 Sum_probs=10.6
Q ss_pred CCCcccccCccccc
Q 041503 9 RNSLQVCNECGGQI 22 (99)
Q Consensus 9 ~~~~~~Cp~Cg~~~ 22 (99)
..+++.||.||..-
T Consensus 45 ~~gev~CPYC~t~y 58 (62)
T COG4391 45 DEGEVVCPYCSTRY 58 (62)
T ss_pred CCCcEecCccccEE
Confidence 45679999999753
No 338
>KOG2391 consensus Vacuolar sorting protein/ubiquitin receptor VPS23 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=35.80 E-value=1.1e+02 Score=25.58 Aligned_cols=28 Identities=14% Similarity=0.137 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 041503 68 KLTLEIERLSDKFRLLHKELEHTQLRSK 95 (99)
Q Consensus 68 e~~~ei~~l~~k~~~l~~El~~~~~~~~ 95 (99)
...++|+.-.++++.+++.||.+..-..
T Consensus 239 Rt~EeL~~G~~kL~~~~etLEqq~~~L~ 266 (365)
T KOG2391|consen 239 RTEEELNIGKQKLVAMKETLEQQLQSLQ 266 (365)
T ss_pred hhHHHHHhhHHHHHHHHHHHHHHHHHHH
Confidence 3334555556667777777766655443
No 339
>smart00746 TRASH metallochaperone-like domain.
Probab=35.75 E-value=9.7 Score=18.50 Aligned_cols=9 Identities=44% Similarity=1.025 Sum_probs=5.6
Q ss_pred ccCccccce
Q 041503 15 CNECGGQIE 23 (99)
Q Consensus 15 Cp~Cg~~~~ 23 (99)
||.||..+.
T Consensus 1 c~~C~~~~~ 9 (39)
T smart00746 1 CSFCGKDIY 9 (39)
T ss_pred CCCCCCCcc
Confidence 567776553
No 340
>PF08912 Rho_Binding: Rho Binding; InterPro: IPR015008 Rho is responsible for the recognition and binding of Rho binding domain-containing proteins (such as ROCK) to Rho, resulting in activation of the GTPase which in turn modulates the phosphorylation of various signalling proteins. This domain is within an amphipathic alpha-helical coiled-coil and interacts with Rho through predominantly hydrophobic interactions []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0000910 cytokinesis, 0006468 protein phosphorylation; PDB: 1UIX_A 1S1C_X.
Probab=35.57 E-value=1.2e+02 Score=19.58 Aligned_cols=25 Identities=16% Similarity=0.314 Sum_probs=11.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 60 DLLVEEVRKLTLEIERLSDKFRLLH 84 (99)
Q Consensus 60 ~~l~~ei~e~~~ei~~l~~k~~~l~ 84 (99)
+.+..|-+++...+..+...+..++
T Consensus 6 ~~l~~EkeeL~~klk~~qeel~~~k 30 (69)
T PF08912_consen 6 ANLAKEKEELNNKLKKQQEELQKLK 30 (69)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHhHHHHHHHHHHHHHHHHHHHH
Confidence 3444455555544444444444443
No 341
>COG3879 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.50 E-value=1.2e+02 Score=24.03 Aligned_cols=32 Identities=25% Similarity=0.362 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 60 DLLVEEVRKLTLEIERLSDKFRLLHKELEHTQ 91 (99)
Q Consensus 60 ~~l~~ei~e~~~ei~~l~~k~~~l~~El~~~~ 91 (99)
..|+.|++.+.++..+|+++++.++..+...+
T Consensus 53 ~~L~~e~~s~Q~~~~~L~~ev~~~~~~~~s~~ 84 (247)
T COG3879 53 LDLVKELRSLQKKVNTLAAEVEDLENKLDSVR 84 (247)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35566777666666777767666666665544
No 342
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=35.40 E-value=17 Score=18.44 Aligned_cols=9 Identities=44% Similarity=1.283 Sum_probs=6.2
Q ss_pred cccCccccc
Q 041503 14 VCNECGGQI 22 (99)
Q Consensus 14 ~Cp~Cg~~~ 22 (99)
.||.||..+
T Consensus 1 ~Cp~CG~~~ 9 (23)
T PF13240_consen 1 YCPNCGAEI 9 (23)
T ss_pred CCcccCCCC
Confidence 478888654
No 343
>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=35.27 E-value=22 Score=25.66 Aligned_cols=14 Identities=21% Similarity=0.325 Sum_probs=10.5
Q ss_pred CCCCcceeeCCCCC
Q 041503 31 KNPNRKFWKCRVCK 44 (99)
Q Consensus 31 ~NPgR~Fy~C~~C~ 44 (99)
..-+..||.||.|+
T Consensus 103 ~e~~~~~Y~Cp~c~ 116 (158)
T TIGR00373 103 FETNNMFFICPNMC 116 (158)
T ss_pred hccCCCeEECCCCC
Confidence 34467899999887
No 344
>PF03112 DUF244: Uncharacterized protein family (ORF7) DUF; InterPro: IPR004335 Many of the proteins in this entry are Borrelia burgdorferi plasmid proteins of unknown function.
Probab=35.27 E-value=40 Score=25.14 Aligned_cols=8 Identities=25% Similarity=1.032 Sum_probs=4.7
Q ss_pred eeEeccCC
Q 041503 45 NFQWAEDR 52 (99)
Q Consensus 45 fF~W~De~ 52 (99)
-|-|.||-
T Consensus 45 Efdw~~eF 52 (158)
T PF03112_consen 45 EFDWKDEF 52 (158)
T ss_pred hhhHHHHH
Confidence 35666664
No 345
>PF11336 DUF3138: Protein of unknown function (DUF3138); InterPro: IPR021485 This family of proteins with unknown function appear to be restricted to Proteobacteria.
Probab=35.18 E-value=61 Score=28.16 Aligned_cols=25 Identities=20% Similarity=0.476 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 64 EEVRKLTLEIERLSDKFRLLHKELE 88 (99)
Q Consensus 64 ~ei~e~~~ei~~l~~k~~~l~~El~ 88 (99)
++|+.|..++..|++++.+|+..|.
T Consensus 25 ~~i~~L~~ql~aLq~~v~eL~~~la 49 (514)
T PF11336_consen 25 DQIKALQAQLQALQDQVNELRAKLA 49 (514)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3677777777777777777776664
No 346
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=35.13 E-value=38 Score=26.76 Aligned_cols=31 Identities=26% Similarity=0.529 Sum_probs=18.5
Q ss_pred CCcccccCccccceeeeecCCCCCCcceeeCCCCCee
Q 041503 10 NSLQVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNF 46 (99)
Q Consensus 10 ~~~~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF 46 (99)
.....||.||..-++. +..+--+-|..|++.
T Consensus 9 ~~~~~Cp~Cg~~~iv~------d~~~Ge~vC~~CG~V 39 (310)
T PRK00423 9 EEKLVCPECGSDKLIY------DYERGEIVCADCGLV 39 (310)
T ss_pred ccCCcCcCCCCCCeeE------ECCCCeEeecccCCc
Confidence 3447788888632211 134667778888753
No 347
>PF15269 zf-C2H2_7: Zinc-finger
Probab=35.13 E-value=22 Score=21.83 Aligned_cols=17 Identities=29% Similarity=0.759 Sum_probs=11.1
Q ss_pred CCCCCcce-eeCCCCCee
Q 041503 30 TKNPNRKF-WKCRVCKNF 46 (99)
Q Consensus 30 ~~NPgR~F-y~C~~C~fF 46 (99)
+.-||.+| |+|-+|-|-
T Consensus 12 prp~gkp~~ykcfqcpft 29 (54)
T PF15269_consen 12 PRPPGKPFKYKCFQCPFT 29 (54)
T ss_pred CCCCCCCccceeecCCcc
Confidence 34578887 777766553
No 348
>PHA01750 hypothetical protein
Probab=34.95 E-value=1.3e+02 Score=19.68 Aligned_cols=20 Identities=40% Similarity=0.366 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 041503 65 EVRKLTLEIERLSDKFRLLH 84 (99)
Q Consensus 65 ei~e~~~ei~~l~~k~~~l~ 84 (99)
|+.-+..||+.++.+.+.++
T Consensus 43 ELdNL~~ei~~~kikqDnl~ 62 (75)
T PHA01750 43 ELDNLKTEIEELKIKQDELS 62 (75)
T ss_pred HHHHHHHHHHHHHHhHHHHH
Confidence 55566667776665555543
No 349
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=34.91 E-value=18 Score=31.02 Aligned_cols=24 Identities=33% Similarity=0.807 Sum_probs=15.8
Q ss_pred CCcccccCccccceeeeecCCCCCCcceeeCCCCC
Q 041503 10 NSLQVCNECGGQIELFTSHTTKNPNRKFWKCRVCK 44 (99)
Q Consensus 10 ~~~~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~ 44 (99)
++...|+.||...+ +..++||.|+
T Consensus 516 ~p~~~C~~CG~~~~-----------~~~~~CP~CG 539 (555)
T cd01675 516 TPIDICNDCGYIGE-----------GEGFKCPKCG 539 (555)
T ss_pred cCCccCCCCCCCCc-----------CCCCCCcCCC
Confidence 33458888887443 3347899887
No 350
>TIGR00467 lysS_arch lysyl-tRNA synthetase, archaeal and spirochete. This model represents the lysyl-tRNA synthetases that are class I amino-acyl tRNA synthetases. It includes archaeal and spirochete examples of the enzyme. All other known examples are class IIc amino-acyl tRNA synthetases and seem to form a separate orthologous set.
Probab=34.84 E-value=36 Score=29.26 Aligned_cols=35 Identities=17% Similarity=0.479 Sum_probs=22.9
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCeeEecc
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQWAE 50 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~W~D 50 (99)
+.||.||+.....++..... .-.|.|. |++=-+.|
T Consensus 169 pic~~cGrv~~~~~~~~~~~--~v~Y~c~-cG~~g~~~ 203 (515)
T TIGR00467 169 VFCENCGRDTTTVNNYDNEY--SIEYSCE-CGNQESVD 203 (515)
T ss_pred eecCCcCccCceEEEecCCc--eEEEEcC-CCCEEEEe
Confidence 99999999765445443333 5889995 55444443
No 351
>PF01807 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0003896 DNA primase activity, 0008270 zinc ion binding, 0006260 DNA replication; PDB: 1D0Q_B 2AU3_A.
Probab=34.68 E-value=31 Score=22.76 Aligned_cols=28 Identities=25% Similarity=0.549 Sum_probs=14.0
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCK 44 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~ 44 (99)
..||.|+..-.-+.. ||.+..|.|-+|+
T Consensus 34 ~~CPfH~d~~pS~~i----~~~k~~~~Cf~Cg 61 (97)
T PF01807_consen 34 CLCPFHDDKTPSFSI----NPDKNRFKCFGCG 61 (97)
T ss_dssp E--SSS--SS--EEE----ETTTTEEEETTT-
T ss_pred EECcCCCCCCCceEE----ECCCCeEEECCCC
Confidence 679999864332322 3455689999998
No 352
>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=34.65 E-value=25 Score=24.74 Aligned_cols=13 Identities=38% Similarity=0.915 Sum_probs=10.7
Q ss_pred cceeeCCCCCeeE
Q 041503 35 RKFWKCRVCKNFQ 47 (99)
Q Consensus 35 R~Fy~C~~C~fF~ 47 (99)
-.||+|+.|+.+.
T Consensus 5 ~~fYkC~~CGniv 17 (125)
T TIGR00320 5 LQVYKCEVCGNIV 17 (125)
T ss_pred CcEEECCCCCcEE
Confidence 4699999999665
No 353
>PRK09343 prefoldin subunit beta; Provisional
Probab=34.62 E-value=1.4e+02 Score=20.52 Aligned_cols=24 Identities=21% Similarity=0.263 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 66 VRKLTLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 66 i~e~~~ei~~l~~k~~~l~~El~~ 89 (99)
++.+..+|+.|..+...+++.+++
T Consensus 80 ~E~ie~~ik~lekq~~~l~~~l~e 103 (121)
T PRK09343 80 KELLELRSRTLEKQEKKLREKLKE 103 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334445555555555555555544
No 354
>PF08606 Prp19: Prp19/Pso4-like; InterPro: IPR013915 This region is found specifically in PRP19-like protein. The region represented by this protein covers the sequence implicated in self-interaction and a coiled-coiled motif []. PRP19-like proteins form an oligomer that is necessary for spliceosome assembly [].
Probab=34.62 E-value=1.3e+02 Score=19.55 Aligned_cols=31 Identities=29% Similarity=0.304 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 60 DLLVEEVRKLTLEIERLSDKFRLLHKELEHT 90 (99)
Q Consensus 60 ~~l~~ei~e~~~ei~~l~~k~~~l~~El~~~ 90 (99)
..|++|=+.+-.|.=.|+.++...++||.+.
T Consensus 11 ~~lQnEWDa~mLE~f~LRk~l~~~rqELs~a 41 (70)
T PF08606_consen 11 STLQNEWDALMLENFTLRKQLDQTRQELSHA 41 (70)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3457788888888888898999999998764
No 355
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=34.51 E-value=30 Score=31.44 Aligned_cols=22 Identities=32% Similarity=0.690 Sum_probs=14.7
Q ss_pred CCC-Cccee----eCCCCC---eeEeccCC
Q 041503 31 KNP-NRKFW----KCRVCK---NFQWAEDR 52 (99)
Q Consensus 31 ~NP-gR~Fy----~C~~C~---fF~W~De~ 52 (99)
.|| +|||+ .||.|+ +|.|.|..
T Consensus 162 ~dP~nRRfHAQp~aCp~CGP~~~l~~~~g~ 191 (750)
T COG0068 162 KDPLNRRFHAQPIACPKCGPHLFLVNHDGE 191 (750)
T ss_pred cCccccccccccccCcccCCCeEEEcCCCc
Confidence 566 59997 477887 44445554
No 356
>PF05557 MAD: Mitotic checkpoint protein; InterPro: IPR008672 This family consists of several eukaryotic mitotic checkpoint (Mitotic arrest deficient or MAD) proteins. The mitotic spindle checkpoint monitors proper attachment of the bipolar spindle to the kinetochores of aligned sister chromatids and causes a cell cycle arrest in prometaphase when failures occur. Multiple components of the mitotic spindle checkpoint have been identified in Saccharomyces cerevisiae and higher eukaryotes. In Saccharomyces cerevisiae, the existence of a Mad1-dependent complex containing Mad2, Mad3, Bub3 and Cdc20 has been demonstrated [].; PDB: 1GO4_F 4DZO_A.
Probab=34.38 E-value=65 Score=28.28 Aligned_cols=38 Identities=34% Similarity=0.494 Sum_probs=28.1
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 57 EKIDLLVEEVRKLTLEIERLSDKFRLLHKELEHTQLRS 94 (99)
Q Consensus 57 ~k~~~l~~ei~e~~~ei~~l~~k~~~l~~El~~~~~~~ 94 (99)
.+...|+.+|.++..++..|..++..|..+|++-.|++
T Consensus 503 e~~~~L~~~~~~Le~e~~~L~~~~~~Le~~l~~~~L~g 540 (722)
T PF05557_consen 503 EELNELQKEIEELERENERLRQELEELESELEKLTLQG 540 (722)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCT
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Confidence 34455677888888888888888888888888754443
No 357
>COG1382 GimC Prefoldin, chaperonin cofactor [Posttranslational modification, protein turnover, chaperones]
Probab=34.11 E-value=1.5e+02 Score=21.04 Aligned_cols=17 Identities=24% Similarity=0.473 Sum_probs=7.2
Q ss_pred HHHHHHHHHHHHHHHHH
Q 041503 71 LEIERLSDKFRLLHKEL 87 (99)
Q Consensus 71 ~ei~~l~~k~~~l~~El 87 (99)
...+.++.++.+|+.+|
T Consensus 91 kQe~~l~e~l~eLq~~i 107 (119)
T COG1382 91 KQEEKLQERLEELQSEI 107 (119)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 33344444444444443
No 358
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=33.98 E-value=12 Score=30.36 Aligned_cols=30 Identities=17% Similarity=0.533 Sum_probs=19.8
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCeeEe
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQW 48 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~W 48 (99)
.+||.|+..+ +.. .-.+.++.||.|+++.-
T Consensus 29 ~KCp~c~~~~--y~~----eL~~n~~vcp~c~~h~r 58 (294)
T COG0777 29 TKCPSCGEML--YRK----ELESNLKVCPKCGHHMR 58 (294)
T ss_pred eECCCcccee--eHH----HHHhhhhcccccCcccc
Confidence 8999999643 222 22445788999976543
No 359
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=33.90 E-value=26 Score=26.50 Aligned_cols=22 Identities=14% Similarity=0.413 Sum_probs=17.0
Q ss_pred ccccCccccceeeeecCCCCCC
Q 041503 13 QVCNECGGQIELFTSHTTKNPN 34 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPg 34 (99)
-.||.||.++.+....+.++-|
T Consensus 154 ~~Cp~CG~~~~~~~~~~~~~~~ 175 (177)
T COG1439 154 DFCPICGSPLKRKRVKSRSSKG 175 (177)
T ss_pred CcCCCCCCceEEeeechhhccc
Confidence 6799999998887777665544
No 360
>COG2740 Predicted nucleic-acid-binding protein implicated in transcription termination [Transcription]
Probab=33.86 E-value=31 Score=23.30 Aligned_cols=20 Identities=25% Similarity=0.326 Sum_probs=15.2
Q ss_pred eeeecCCCCCCcceeeCCCC
Q 041503 24 LFTSHTTKNPNRKFWKCRVC 43 (99)
Q Consensus 24 ~~tS~t~~NPgR~Fy~C~~C 43 (99)
+.+-.+.+.|||-+|-|+.+
T Consensus 34 v~~d~~~k~~GRGaYv~~~~ 53 (95)
T COG2740 34 VVIDPTGKLPGRGAYVCPDR 53 (95)
T ss_pred EEEccccCCCCceEEEeCCH
Confidence 34455668999999999944
No 361
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=33.85 E-value=19 Score=21.41 Aligned_cols=12 Identities=25% Similarity=0.847 Sum_probs=9.0
Q ss_pred CCcccccCcccc
Q 041503 10 NSLQVCNECGGQ 21 (99)
Q Consensus 10 ~~~~~Cp~Cg~~ 21 (99)
+..+.||.||+.
T Consensus 44 ~~i~~Cp~CgRi 55 (56)
T PF02591_consen 44 DEIVFCPNCGRI 55 (56)
T ss_pred CCeEECcCCCcc
Confidence 345899999963
No 362
>TIGR02231 conserved hypothetical protein. This family consists of proteins over 500 amino acids long in Caenorhabditis elegans and several bacteria (Pseudomonas aeruginosa, Nostoc sp. PCC 7120, Leptospira interrogans, etc.). The function is unknown.
Probab=33.76 E-value=1.1e+02 Score=25.73 Aligned_cols=22 Identities=27% Similarity=0.357 Sum_probs=10.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 041503 66 VRKLTLEIERLSDKFRLLHKEL 87 (99)
Q Consensus 66 i~e~~~ei~~l~~k~~~l~~El 87 (99)
++++..++++++.++.+++.+|
T Consensus 147 ~~~~~~~~~~~~~~l~~l~~~l 168 (525)
T TIGR02231 147 DREAERRIRELEKQLSELQNEL 168 (525)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444555554555554444
No 363
>COG3937 Uncharacterized conserved protein [Function unknown]
Probab=33.76 E-value=63 Score=22.73 Aligned_cols=23 Identities=26% Similarity=0.388 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 041503 65 EVRKLTLEIERLSDKFRLLHKEL 87 (99)
Q Consensus 65 ei~e~~~ei~~l~~k~~~l~~El 87 (99)
++.++.+++..|+.+++.|+-++
T Consensus 84 ~~~~l~~rvd~Lerqv~~Lenk~ 106 (108)
T COG3937 84 EMDELTERVDALERQVADLENKL 106 (108)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHh
Confidence 44566667777777777776555
No 364
>PRK05580 primosome assembly protein PriA; Validated
Probab=33.71 E-value=68 Score=28.18 Aligned_cols=37 Identities=14% Similarity=0.283 Sum_probs=18.1
Q ss_pred ccccCccccceeeeecCC------CCCCcceeeCCCCCeeEec
Q 041503 13 QVCNECGGQIELFTSHTT------KNPNRKFWKCRVCKNFQWA 49 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~------~NPgR~Fy~C~~C~fF~W~ 49 (99)
..||.|+.+......... .-.-....+||.|+-..+.
T Consensus 391 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~~Cp~Cg~~~l~ 433 (679)
T PRK05580 391 AECPHCDASLTLHRFQRRLRCHHCGYQEPIPKACPECGSTDLV 433 (679)
T ss_pred cCCCCCCCceeEECCCCeEECCCCcCCCCCCCCCCCCcCCeeE
Confidence 677777776554432110 0001124567777655444
No 365
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=33.68 E-value=14 Score=22.46 Aligned_cols=9 Identities=44% Similarity=1.095 Sum_probs=6.7
Q ss_pred cccccCccc
Q 041503 12 LQVCNECGG 20 (99)
Q Consensus 12 ~~~Cp~Cg~ 20 (99)
...||.||.
T Consensus 26 l~~c~~cg~ 34 (56)
T PF01783_consen 26 LVKCPNCGE 34 (56)
T ss_dssp EEESSSSSS
T ss_pred eeeeccCCC
Confidence 367888885
No 366
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=33.61 E-value=24 Score=24.44 Aligned_cols=24 Identities=17% Similarity=0.714 Sum_probs=14.1
Q ss_pred cccc--CccccceeeeecCCCCCCcceeeCCCCC
Q 041503 13 QVCN--ECGGQIELFTSHTTKNPNRKFWKCRVCK 44 (99)
Q Consensus 13 ~~Cp--~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~ 44 (99)
+-|| .|++.+..- .. |. |.|+.|+
T Consensus 19 ~aC~~~~C~kKv~~~-~~-----~~--y~C~~C~ 44 (146)
T PF08646_consen 19 PACPNEKCNKKVTEN-GD-----GS--YRCEKCN 44 (146)
T ss_dssp EE-TSTTTS-B-EEE-TT-----TE--EEETTTT
T ss_pred CCCCCccCCCEeecC-CC-----cE--EECCCCC
Confidence 6799 999875544 21 11 9999887
No 367
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=33.36 E-value=10 Score=30.29 Aligned_cols=27 Identities=19% Similarity=0.436 Sum_probs=17.1
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCe
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKN 45 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~f 45 (99)
.+||.|+...-..- -.+.++.||.|++
T Consensus 28 ~~c~~c~~~~~~~~------l~~~~~vc~~c~~ 54 (292)
T PRK05654 28 TKCPSCGQVLYRKE------LEANLNVCPKCGH 54 (292)
T ss_pred eECCCccchhhHHH------HHhcCCCCCCCCC
Confidence 89999997432221 1233688998874
No 368
>PRK12366 replication factor A; Reviewed
Probab=33.36 E-value=27 Score=30.62 Aligned_cols=23 Identities=22% Similarity=0.686 Sum_probs=16.9
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCK 44 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~ 44 (99)
+.||.|++.+. . +..-|.|+.|+
T Consensus 533 ~aCp~CnkKv~-------~--~~g~~~C~~c~ 555 (637)
T PRK12366 533 YLCPNCRKRVE-------E--VDGEYICEFCG 555 (637)
T ss_pred ecccccCeEeE-------c--CCCcEECCCCC
Confidence 78999988764 1 22578899886
No 369
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=33.07 E-value=15 Score=26.12 Aligned_cols=25 Identities=32% Similarity=0.704 Sum_probs=18.4
Q ss_pred cccccCccccceeeeecCCCCCCcceeeCCCCCe
Q 041503 12 LQVCNECGGQIELFTSHTTKNPNRKFWKCRVCKN 45 (99)
Q Consensus 12 ~~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~f 45 (99)
.+.||.||++.++. ||. ..|..|+-
T Consensus 69 ~V~CP~C~K~TKmL--------Gr~-D~CM~C~~ 93 (114)
T PF11023_consen 69 QVECPNCGKQTKML--------GRV-DACMHCKE 93 (114)
T ss_pred eeECCCCCChHhhh--------chh-hccCcCCC
Confidence 38899999987664 344 47998873
No 370
>PF04999 FtsL: Cell division protein FtsL; InterPro: IPR007082 In Escherichia coli, nine gene products are known to be essential for assembly of the division septum. One of these, FtsL, is a bitopic membrane protein whose precise function is not understood. It has been proposed that FtsL interacts with the DivIC protein IPR007060 from INTERPRO [], however this interaction may be indirect [].; GO: 0007049 cell cycle, 0016021 integral to membrane
Probab=32.88 E-value=1.3e+02 Score=19.28 Aligned_cols=24 Identities=29% Similarity=0.475 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 65 EVRKLTLEIERLSDKFRLLHKELE 88 (99)
Q Consensus 65 ei~e~~~ei~~l~~k~~~l~~El~ 88 (99)
++.++..++.+|+...+.|+-|+.
T Consensus 43 ~l~~l~~~~~~l~~e~~~L~lE~~ 66 (97)
T PF04999_consen 43 ELQQLEKEIDQLQEENERLRLEIA 66 (97)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455555566666666666655543
No 371
>PF08537 NBP1: Fungal Nap binding protein NBP1; InterPro: IPR013743 NBP1 is a nuclear protein which has been shown in Saccharomyces cerevisiae (Bakers yeast) to be essential for the G2/M transition of the cell cycle.
Probab=32.80 E-value=1.4e+02 Score=24.61 Aligned_cols=35 Identities=20% Similarity=0.398 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 59 IDLLVEEVRKLTLEIERLSDKFRLLHKELEHTQLR 93 (99)
Q Consensus 59 ~~~l~~ei~e~~~ei~~l~~k~~~l~~El~~~~~~ 93 (99)
.-+|+.+|+++..+|.++..+++..+++|+=++-.
T Consensus 177 v~LLqkk~~~l~~~l~~~~~eL~~~~k~L~faqek 211 (323)
T PF08537_consen 177 VILLQKKIDELEERLNDLEKELEITKKDLKFAQEK 211 (323)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34556678888888877777777777777655443
No 372
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=32.77 E-value=56 Score=17.98 Aligned_cols=26 Identities=27% Similarity=0.695 Sum_probs=17.5
Q ss_pred cccccCccccceeeeecCCCCCCcceeeCCCCC
Q 041503 12 LQVCNECGGQIELFTSHTTKNPNRKFWKCRVCK 44 (99)
Q Consensus 12 ~~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~ 44 (99)
..+|+.||...++.+ ..-++.|+.|+
T Consensus 3 ~~~C~~C~~~~i~~~-------~~~~~~C~~Cg 28 (33)
T PF08792_consen 3 LKKCSKCGGNGIVNK-------EDDYEVCIFCG 28 (33)
T ss_pred ceEcCCCCCCeEEEe-------cCCeEEcccCC
Confidence 367877998876652 23467788776
No 373
>KOG2264 consensus Exostosin EXT1L [Signal transduction mechanisms]
Probab=32.73 E-value=88 Score=28.47 Aligned_cols=16 Identities=25% Similarity=0.463 Sum_probs=7.2
Q ss_pred HHHHHHHHHHHHHHHH
Q 041503 65 EVRKLTLEIERLSDKF 80 (99)
Q Consensus 65 ei~e~~~ei~~l~~k~ 80 (99)
||.++...||+|+..+
T Consensus 108 eI~~~n~kiEelk~~i 123 (907)
T KOG2264|consen 108 EIEEINTKIEELKRLI 123 (907)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 4444444444444333
No 374
>PF13334 DUF4094: Domain of unknown function (DUF4094)
Probab=32.57 E-value=1.3e+02 Score=20.26 Aligned_cols=30 Identities=27% Similarity=0.339 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 62 LVEEVRKLTLEIERLSDKFRLLHKELEHTQ 91 (99)
Q Consensus 62 l~~ei~e~~~ei~~l~~k~~~l~~El~~~~ 91 (99)
+..||.+--..|..|..+|-.|+.||...+
T Consensus 64 i~~eV~kTh~aIq~LdKtIS~LEMELAaAR 93 (95)
T PF13334_consen 64 IMGEVSKTHEAIQSLDKTISSLEMELAAAR 93 (95)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 445666555678889999999999997654
No 375
>TIGR03847 conserved hypothetical protein. The conserved hypothetical protein described here occurs as part of the trio of uncharacterized proteins common in the Actinobacteria.
Probab=32.32 E-value=22 Score=26.95 Aligned_cols=12 Identities=33% Similarity=0.692 Sum_probs=9.9
Q ss_pred CcccccCccccc
Q 041503 11 SLQVCNECGGQI 22 (99)
Q Consensus 11 ~~~~Cp~Cg~~~ 22 (99)
|.+.||.||.+.
T Consensus 155 GRP~CPlCg~Pl 166 (177)
T TIGR03847 155 GRPPCPLCGRPI 166 (177)
T ss_pred CCCCCCCCCCCC
Confidence 458999999875
No 376
>PF07820 TraC: TraC-like protein; InterPro: IPR012930 The members of this family are sequences that are similar to TraC (Q84HT8 from SWISSPROT) from Rhizobium etli. The gene encoding this protein is one of a group of genes found on plasmid p42a of Rhizobium etli (strain CFN 42/ATCC 51251) that are thought to be involved in the process of plasmid self-transmission. Mobilisation of plasmid p42a is of importance as it is required for transfer of plasmid p42d, the symbiotic plasmid which carries most of the genes required for nodulation and nitrogen fixation by this symbiotic bacterium. The predicted protein products of p42a are similar to known transfer proteins of Agrobacterium tumefaciens plasmid pTiC58 []. ; GO: 0000746 conjugation
Probab=32.25 E-value=1.1e+02 Score=20.95 Aligned_cols=18 Identities=28% Similarity=0.508 Sum_probs=10.0
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 041503 67 RKLTLEIERLSDKFRLLH 84 (99)
Q Consensus 67 ~e~~~ei~~l~~k~~~l~ 84 (99)
.++..+|++|+++++.+.
T Consensus 5 s~I~~eIekLqe~lk~~e 22 (92)
T PF07820_consen 5 SKIREEIEKLQEQLKQAE 22 (92)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 455555666665555553
No 377
>TIGR02977 phageshock_pspA phage shock protein A. Members of this family are the phage shock protein PspA, from the phage shock operon. This is a narrower family than the set of PspA and its homologs, sometimes several in a genome, as described by PFAM model pfam04012. PspA appears to maintain the protonmotive force under stress conditions that include overexpression of certain phage secretins, heat shock, ethanol, and protein export defects.
Probab=32.19 E-value=1.9e+02 Score=21.59 Aligned_cols=32 Identities=16% Similarity=0.283 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 61 LLVEEVRKLTLEIERLSDKFRLLHKELEHTQL 92 (99)
Q Consensus 61 ~l~~ei~e~~~ei~~l~~k~~~l~~El~~~~~ 92 (99)
.|..++..+...+..|+.++..|+..+++...
T Consensus 103 ~l~~~~~~~~~~v~~l~~~l~~L~~ki~~~k~ 134 (219)
T TIGR02977 103 ALERELAAVEETLAKLQEDIAKLQAKLAEARA 134 (219)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33445556666677777777777776665543
No 378
>COG3599 DivIVA Cell division initiation protein [Cell division and chromosome partitioning]
Probab=32.19 E-value=1.4e+02 Score=22.84 Aligned_cols=32 Identities=25% Similarity=0.342 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 62 LVEEVRKLTLEIERLSDKFRLLHKELEHTQLR 93 (99)
Q Consensus 62 l~~ei~e~~~ei~~l~~k~~~l~~El~~~~~~ 93 (99)
+..++..+..++++|++++..|.++|++-...
T Consensus 35 V~~dye~~l~e~~~l~~~i~~L~~~l~~~~~~ 66 (212)
T COG3599 35 VIDDYEQLLDENEDLEDEIDELKEELKEAADA 66 (212)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 34455567778888888888998888876553
No 379
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=32.18 E-value=1.2e+02 Score=25.00 Aligned_cols=25 Identities=12% Similarity=0.157 Sum_probs=12.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 65 EVRKLTLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 65 ei~e~~~ei~~l~~k~~~l~~El~~ 89 (99)
+++.+..+++.++.+++.++.||++
T Consensus 37 ~~~~~~~~~~~~~~~~~~~~~~~~~ 61 (398)
T PTZ00454 37 QEEYIKEEQKNLKRELIRAKEEVKR 61 (398)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444455555555555555543
No 380
>PF07061 Swi5: Swi5; InterPro: IPR010760 This entry represents Swi5 and is involved in meiotic DNA repair synthesis and meiotic joint molecule formation []. It is known to interact with Swi2, Rhp51 and Swi6 [].
Probab=32.12 E-value=1.2e+02 Score=19.98 Aligned_cols=26 Identities=31% Similarity=0.424 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 61 LLVEEVRKLTLEIERLSDKFRLLHKE 86 (99)
Q Consensus 61 ~l~~ei~e~~~ei~~l~~k~~~l~~E 86 (99)
.+.+++.++..++..+.+++..+..+
T Consensus 4 ~l~~~~~~L~~~~~~l~~~i~~~~~~ 29 (83)
T PF07061_consen 4 SLEAEIQELKEQIEQLEKEISELEAE 29 (83)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 44555555555555555555555444
No 381
>PF11932 DUF3450: Protein of unknown function (DUF3450); InterPro: IPR016866 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, they are found in an operon along with components of a TonB transport system (typified by Vibrio cholerae TonB2 [], and are predicted to be localized to the periplasmic space. Caution: the low-complexity nature of these sequences produces spurious BLAST hits to chromosome segregation ATPases (which are much longer in length and contain canonical Walker motifs). Accordingly, some members are misidentified as such.
Probab=32.06 E-value=1.5e+02 Score=22.44 Aligned_cols=13 Identities=54% Similarity=0.669 Sum_probs=5.1
Q ss_pred HHHHHHHHHHHHH
Q 041503 65 EVRKLTLEIERLS 77 (99)
Q Consensus 65 ei~e~~~ei~~l~ 77 (99)
|++.+..+++.|+
T Consensus 57 e~~~l~~e~e~L~ 69 (251)
T PF11932_consen 57 EYRQLEREIENLE 69 (251)
T ss_pred HHHHHHHHHHHHH
Confidence 3333333443333
No 382
>PRK09973 putative outer membrane lipoprotein; Provisional
Probab=31.94 E-value=1.6e+02 Score=19.75 Aligned_cols=31 Identities=26% Similarity=0.530 Sum_probs=17.5
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 57 EKIDLLVEEVRKLTLEIERLSDKFRLLHKEL 87 (99)
Q Consensus 57 ~k~~~l~~ei~e~~~ei~~l~~k~~~l~~El 87 (99)
+|.+.|.++|..++..+.++...+..++.++
T Consensus 24 ~kvdqLss~V~~L~~kvdql~~dv~~a~aaa 54 (85)
T PRK09973 24 QKVNQLASNVQTLNAKIARLEQDMKALRPQI 54 (85)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555666666666655555555555555443
No 383
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=31.56 E-value=1.7e+02 Score=19.84 Aligned_cols=17 Identities=29% Similarity=0.669 Sum_probs=12.2
Q ss_pred HHHHHHHHHHHHHHHHH
Q 041503 77 SDKFRLLHKELEHTQLR 93 (99)
Q Consensus 77 ~~k~~~l~~El~~~~~~ 93 (99)
+..++.|+.||.++.++
T Consensus 26 ~~Ri~kLk~~L~~e~~r 42 (118)
T PF02318_consen 26 EERIRKLKQELQKEKMR 42 (118)
T ss_dssp HHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 45678999999665554
No 384
>CHL00024 psbI photosystem II protein I
Probab=31.54 E-value=26 Score=20.15 Aligned_cols=12 Identities=50% Similarity=0.877 Sum_probs=7.9
Q ss_pred eeecCC-CCCCcc
Q 041503 25 FTSHTT-KNPNRK 36 (99)
Q Consensus 25 ~tS~t~-~NPgR~ 36 (99)
+.|+.+ .||||+
T Consensus 23 FlsnDp~RnP~rk 35 (36)
T CHL00024 23 FLSNDPGRNPGRK 35 (36)
T ss_pred ccCCCCCCCCCCC
Confidence 345554 899885
No 385
>PF07412 Geminin: Geminin; InterPro: IPR022786 This family contains the eukaryotic protein geminin (approximately 200 residues long). Geminin inhibits DNA replication by preventing the incorporation of MCM complex into prereplication complex, and is degraded during the mitotic phase of the cell cycle. It has been proposed that geminin inhibits DNA replication during S, G2, and M phases and that geminin destruction at the metaphase-anaphase transition permits replication in the succeeding cell cycle []. ; GO: 0008156 negative regulation of DNA replication; PDB: 1T6F_B 2LP0_B 1UII_B 2WVR_B 2ZXX_B.
Probab=31.47 E-value=93 Score=23.96 Aligned_cols=18 Identities=22% Similarity=0.315 Sum_probs=9.2
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 041503 66 VRKLTLEIERLSDKFRLL 83 (99)
Q Consensus 66 i~e~~~ei~~l~~k~~~l 83 (99)
|.++++||..|+..+..|
T Consensus 134 ie~~~eEi~~lk~en~~L 151 (200)
T PF07412_consen 134 IEQKDEEIAKLKEENEEL 151 (200)
T ss_dssp HHHHHHHHHHHHHHHHCC
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 444455555555555544
No 386
>TIGR03545 conserved hypothetical protein TIGR03545. This model represents a relatively rare but broadly distributed uncharacterized protein family, distributed in 1-2 percent of bacterial genomes, all of which have outer membranes. In many of these genomes, it is part of a two-gene pair.
Probab=31.39 E-value=1.6e+02 Score=25.70 Aligned_cols=29 Identities=24% Similarity=0.265 Sum_probs=20.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 64 EEVRKLTLEIERLSDKFRLLHKELEHTQL 92 (99)
Q Consensus 64 ~ei~e~~~ei~~l~~k~~~l~~El~~~~~ 92 (99)
.|++++..+++..+++++.++.||+.+.-
T Consensus 219 ~e~d~lk~e~~~~~~~i~~~~~~l~~~~~ 247 (555)
T TIGR03545 219 EEFDKLKKEGKADKQKIKSAKNDLQNDKK 247 (555)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhHH
Confidence 36777777777777778877777776543
No 387
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.27 E-value=1.6e+02 Score=19.51 Aligned_cols=16 Identities=31% Similarity=0.364 Sum_probs=8.2
Q ss_pred HHHHHHHHHHHHHHHH
Q 041503 59 IDLLVEEVRKLTLEIE 74 (99)
Q Consensus 59 ~~~l~~ei~e~~~ei~ 74 (99)
+.+|+.||++++++-.
T Consensus 20 I~LLQmEieELKEknn 35 (79)
T COG3074 20 ITLLQMEIEELKEKNN 35 (79)
T ss_pred HHHHHHHHHHHHHHhh
Confidence 4455556655554433
No 388
>PF09726 Macoilin: Transmembrane protein; InterPro: IPR019130 This entry represents the multi-pass transmembrane protein Macoilin, which is highly conserved in eukaryotes. ; GO: 0016021 integral to membrane
Probab=31.23 E-value=1.4e+02 Score=26.82 Aligned_cols=31 Identities=29% Similarity=0.449 Sum_probs=23.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 58 KIDLLVEEVRKLTLEIERLSDKFRLLHKELE 88 (99)
Q Consensus 58 k~~~l~~ei~e~~~ei~~l~~k~~~l~~El~ 88 (99)
+...|++|++.|..|+....++++.|+.|+.
T Consensus 546 r~~~lE~E~~~lr~elk~kee~~~~~e~~~~ 576 (697)
T PF09726_consen 546 RRRQLESELKKLRRELKQKEEQIRELESELQ 576 (697)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4456677888888888888888888888774
No 389
>PF12548 DUF3740: Sulfatase protein; InterPro: IPR024609 This uncharacterised domain is found in the C-terminal region of extracellular sulphatase proteins.
Probab=31.16 E-value=88 Score=22.71 Aligned_cols=23 Identities=39% Similarity=0.522 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 68 KLTLEIERLSDKFRLLHKELEHTQ 91 (99)
Q Consensus 68 e~~~ei~~l~~k~~~l~~El~~~~ 91 (99)
+++.+|+.|+.||.+| +|+...-
T Consensus 110 ~ID~eIe~Lq~Ki~~L-KeiR~hL 132 (145)
T PF12548_consen 110 HIDHEIETLQDKIKNL-KEIRGHL 132 (145)
T ss_pred HHHHHHHHHHHHHHHH-HHHHHHH
Confidence 7788899999999999 7776543
No 390
>PF13935 Ead_Ea22: Ead/Ea22-like protein
Probab=31.11 E-value=1.6e+02 Score=20.59 Aligned_cols=20 Identities=25% Similarity=0.233 Sum_probs=14.1
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 041503 73 IERLSDKFRLLHKELEHTQL 92 (99)
Q Consensus 73 i~~l~~k~~~l~~El~~~~~ 92 (99)
...+..++.++.++|+...-
T Consensus 92 ~~~~a~~~~~l~~~Le~ae~ 111 (139)
T PF13935_consen 92 NEDIALDVQKLRVELEAAEK 111 (139)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 55556778888888886543
No 391
>PF10234 Cluap1: Clusterin-associated protein-1; InterPro: IPR019366 This protein of 413 amino acids contains a central coiled-coil domain, possibly the region that binds to clusterin. Cluap1 expression is highest in the nucleus and gradually increases during late S to G2/M phases of the cell cycle and returns to the basal level in the G0/G1 phases. In addition, it is upregulated in colon cancer tissues compared to corresponding non-cancerous mucosa. It thus plays a crucial role in the life of the cell [].
Probab=31.09 E-value=2e+02 Score=22.95 Aligned_cols=29 Identities=28% Similarity=0.319 Sum_probs=20.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 66 VRKLTLEIERLSDKFRLLHKELEHTQLRS 94 (99)
Q Consensus 66 i~e~~~ei~~l~~k~~~l~~El~~~~~~~ 94 (99)
+..+...-..|.+||++-+.||++.+=|+
T Consensus 185 l~~l~~de~~Le~KIekkk~ELER~qKRL 213 (267)
T PF10234_consen 185 LNNLASDEANLEAKIEKKKQELERNQKRL 213 (267)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44555566677888888888888876554
No 392
>PRK06260 threonine synthase; Validated
Probab=30.93 E-value=32 Score=27.84 Aligned_cols=8 Identities=63% Similarity=1.547 Sum_probs=4.0
Q ss_pred ccccCccc
Q 041503 13 QVCNECGG 20 (99)
Q Consensus 13 ~~Cp~Cg~ 20 (99)
..||.||.
T Consensus 20 ~~Cp~cg~ 27 (397)
T PRK06260 20 YTCPECGG 27 (397)
T ss_pred ccCCCCCC
Confidence 34555554
No 393
>COG5509 Uncharacterized small protein containing a coiled-coil domain [Function unknown]
Probab=30.91 E-value=1.2e+02 Score=19.51 Aligned_cols=24 Identities=29% Similarity=0.335 Sum_probs=14.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 66 VRKLTLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 66 i~e~~~ei~~l~~k~~~l~~El~~ 89 (99)
|.|+.+-|.-|++.|.-|+-|+.+
T Consensus 27 V~El~eRIalLq~EIeRlkAe~~k 50 (65)
T COG5509 27 VAELEERIALLQAEIERLKAELAK 50 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Confidence 344555566666666666666654
No 394
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=30.83 E-value=23 Score=18.15 Aligned_cols=9 Identities=33% Similarity=1.143 Sum_probs=6.9
Q ss_pred ccccCcccc
Q 041503 13 QVCNECGGQ 21 (99)
Q Consensus 13 ~~Cp~Cg~~ 21 (99)
..||.||..
T Consensus 3 ~~Cp~Cg~~ 11 (26)
T PF13248_consen 3 MFCPNCGAE 11 (26)
T ss_pred CCCcccCCc
Confidence 578899874
No 395
>PF10601 zf-LITAF-like: LITAF-like zinc ribbon domain; InterPro: IPR006629 Members of this family display a conserved zinc ribbon structure [] with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure [].
Probab=30.79 E-value=32 Score=21.35 Aligned_cols=18 Identities=17% Similarity=0.248 Sum_probs=13.7
Q ss_pred cccccCccccceeeeecC
Q 041503 12 LQVCNECGGQIELFTSHT 29 (99)
Q Consensus 12 ~~~Cp~Cg~~~~~~tS~t 29 (99)
.+.||.|+..+...|...
T Consensus 7 ~~~CP~C~~~~~T~v~~~ 24 (73)
T PF10601_consen 7 RIYCPYCQQQVQTRVEYK 24 (73)
T ss_pred eeECCCCCCEEEEEEEEE
Confidence 388999999877766543
No 396
>PF04576 Zein-binding: Zein-binding; InterPro: IPR007656 This is a family of uncharacterised proteins.
Probab=30.78 E-value=1.1e+02 Score=20.88 Aligned_cols=23 Identities=22% Similarity=0.189 Sum_probs=13.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 041503 71 LEIERLSDKFRLLHKELEHTQLR 93 (99)
Q Consensus 71 ~ei~~l~~k~~~l~~El~~~~~~ 93 (99)
..+..-+..+..|..||++++..
T Consensus 6 ~~v~~er~~~~~L~~ELEeER~A 28 (94)
T PF04576_consen 6 RAVEAERKALAALYAELEEERSA 28 (94)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444455555677777776543
No 397
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=30.77 E-value=31 Score=24.94 Aligned_cols=23 Identities=30% Similarity=0.810 Sum_probs=17.3
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCK 44 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~ 44 (99)
.+||.||.+... ++ |+-| ||.|+
T Consensus 29 ~hCp~Cg~PLF~---Kd----G~v~--CPvC~ 51 (131)
T COG1645 29 KHCPKCGTPLFR---KD----GEVF--CPVCG 51 (131)
T ss_pred hhCcccCCccee---eC----CeEE--CCCCC
Confidence 689999988777 22 4444 99998
No 398
>KOG3478 consensus Prefoldin subunit 6, KE2 family [Posttranslational modification, protein turnover, chaperones]
Probab=30.72 E-value=1.2e+02 Score=21.70 Aligned_cols=27 Identities=26% Similarity=0.409 Sum_probs=21.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 66 VRKLTLEIERLSDKFRLLHKELEHTQL 92 (99)
Q Consensus 66 i~e~~~ei~~l~~k~~~l~~El~~~~~ 92 (99)
|+-++.||.++.++++-+++|.++.+-
T Consensus 78 lefI~~Eikr~e~~i~d~q~e~~k~R~ 104 (120)
T KOG3478|consen 78 LEFISKEIKRLENQIRDSQEEFEKQRE 104 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456778899999999998888887653
No 399
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=30.68 E-value=1.4e+02 Score=23.65 Aligned_cols=32 Identities=31% Similarity=0.283 Sum_probs=24.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 60 DLLVEEVRKLTLEIERLSDKFRLLHKELEHTQ 91 (99)
Q Consensus 60 ~~l~~ei~e~~~ei~~l~~k~~~l~~El~~~~ 91 (99)
+.++.+++++..+++.++.++..+++|+++-+
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 33 (364)
T TIGR01242 2 SELDVRIRKLEDEKRSLEKEKIRLERELERLR 33 (364)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34556778888888888888888888877644
No 400
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=30.56 E-value=1.4e+02 Score=23.16 Aligned_cols=24 Identities=8% Similarity=0.050 Sum_probs=10.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 60 DLLVEEVRKLTLEIERLSDKFRLL 83 (99)
Q Consensus 60 ~~l~~ei~e~~~ei~~l~~k~~~l 83 (99)
+.|+.||++|...||+++-+++.|
T Consensus 64 ~~lq~ev~~LrG~~E~~~~~l~~~ 87 (263)
T PRK10803 64 SDNQSDIDSLRGQIQENQYQLNQV 87 (263)
T ss_pred HHHHHHHHHHhhHHHHHHHHHHHH
Confidence 344445544444444444444333
No 401
>PF00261 Tropomyosin: Tropomyosin; InterPro: IPR000533 Tropomyosins [], are a family of closely related proteins present in muscle and non-muscle cells. In striated muscle, tropomyosin mediate the interactions between the troponin complex and actin so as to regulate muscle contraction []. The role of tropomyosin in smooth muscle and non-muscle tissues is not clear. Tropomyosin is an alpha-helical protein that forms a coiled-coil structure of 2 parallel helices containing 2 sets of 7 alternating actin binding sites []. There are multiple cell-specific isoforms, created by differential splicing of the messenger RNA from one gene, but the proportions of the isoforms vary between different cell types. Muscle isoforms of tropomyosin are characterised by having 284 amino acid residues and a highly conserved N-terminal region, whereas non-muscle forms are generally smaller and are heterogeneous in their N-terminal region. This entry represents tropomyosin (Tmp) 1, 2 and 3. Within the yeast Tmp1 and Tmp2, biochemical and sequence analyses indicate that Tpm2 spans four actin monomers along a filament, whereas Tpm1 spans five. Despite its shorter length, Tpm2 can compete with Tpm1 for binding to F-actin. Over-expression of Tpm2 in vivo alters the axial budding of haploids to a bipolar pattern, and this can be partially suppressed by co-over-expression of Tpm1. This suggests distinct functions for the two tropomyosins, and indicates that the ratio between them is important for correct morphogenesis [].; PDB: 2EFR_A 2Z5H_C 2Z5I_D 2D3E_B 2EFS_D 3U59_B 1C1G_C 1IHQ_A 3AZD_B 1MV4_B ....
Probab=30.55 E-value=1.7e+02 Score=22.05 Aligned_cols=29 Identities=31% Similarity=0.599 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 62 LVEEVRKLTLEIERLSDKFRLLHKELEHT 90 (99)
Q Consensus 62 l~~ei~e~~~ei~~l~~k~~~l~~El~~~ 90 (99)
|+.+|..+..+|...+.++..++.||..+
T Consensus 202 Le~~id~le~eL~~~k~~~~~~~~eld~~ 230 (237)
T PF00261_consen 202 LEKEIDRLEDELEKEKEKYKKVQEELDQT 230 (237)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445555556666666666666666543
No 402
>KOG2077 consensus JNK/SAPK-associated protein-1 [Signal transduction mechanisms]
Probab=30.51 E-value=1.2e+02 Score=27.55 Aligned_cols=17 Identities=35% Similarity=0.560 Sum_probs=10.4
Q ss_pred HHHHHHHHHHHHHHHHH
Q 041503 74 ERLSDKFRLLHKELEHT 90 (99)
Q Consensus 74 ~~l~~k~~~l~~El~~~ 90 (99)
.+|+.+|++|.+||++.
T Consensus 353 ~Klee~i~elEEElk~~ 369 (832)
T KOG2077|consen 353 LKLEEKIRELEEELKKA 369 (832)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 34556666676666654
No 403
>smart00787 Spc7 Spc7 kinetochore protein. This domain is found in cell division proteins which are required for kinetochore-spindle association.
Probab=30.49 E-value=1.6e+02 Score=23.74 Aligned_cols=23 Identities=30% Similarity=0.452 Sum_probs=9.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 041503 66 VRKLTLEIERLSDKFRLLHKELE 88 (99)
Q Consensus 66 i~e~~~ei~~l~~k~~~l~~El~ 88 (99)
+.++...|+..++++.++..++.
T Consensus 234 l~~l~~~I~~~~~~k~e~~~~I~ 256 (312)
T smart00787 234 LQELESKIEDLTNKKSELNTEIA 256 (312)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 33334444444444444444443
No 404
>PF11544 Spc42p: Spindle pole body component Spc42p; InterPro: IPR021611 Spc42p is a 42kDa component of the S.cerevisiae spindle body that localises to the electron dense central region of the SPB. Spc42p is a phosphoprotein which forms a polymeric layer at the periphery of the SPB central plaque. This functions during SPB duplication and also facilitates the attachment of the SPB to the nuclear membrane. ; PDB: 2Q6Q_B.
Probab=30.46 E-value=1.6e+02 Score=19.40 Aligned_cols=24 Identities=21% Similarity=0.259 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 60 DLLVEEVRKLTLEIERLSDKFRLL 83 (99)
Q Consensus 60 ~~l~~ei~e~~~ei~~l~~k~~~l 83 (99)
..-++||+.+..-+..|+.+..+.
T Consensus 15 ~~K~eEI~rLn~lv~sLR~KLiKY 38 (76)
T PF11544_consen 15 NDKQEEIDRLNILVGSLRGKLIKY 38 (76)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445668988888888888877766
No 405
>KOG4010 consensus Coiled-coil protein TPD52 [General function prediction only]
Probab=30.45 E-value=1.9e+02 Score=22.42 Aligned_cols=37 Identities=27% Similarity=0.469 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHhhcCC
Q 041503 63 VEEVRKLTLEIERLSDKFRLLHKELEH-----TQLRSKYGLS 99 (99)
Q Consensus 63 ~~ei~e~~~ei~~l~~k~~~l~~El~~-----~~~~~~~~~~ 99 (99)
++|-+++..|+.++.+.|..|++=|.- .-+.+|.||+
T Consensus 43 e~Ekeelr~EL~kvEeEI~TLrqVLaAKerH~~ELKRKLGlt 84 (208)
T KOG4010|consen 43 EEEKEELRTELAKVEEEIVTLRQVLAAKERHAAELKRKLGLT 84 (208)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcc
Confidence 446667777888888888777765532 2356666663
No 406
>PF08826 DMPK_coil: DMPK coiled coil domain like; InterPro: IPR014930 This domain is found in the myotonic dystrophy protein kinase (DMPK) and adopts a coiled coil structure. It plays a role in dimerisation []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1WT6_D.
Probab=30.30 E-value=1.4e+02 Score=18.65 Aligned_cols=32 Identities=16% Similarity=0.266 Sum_probs=17.2
Q ss_pred HHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHH
Q 041503 59 IDLLVEEVR---KLTLEIERLSDKFRLLHKELEHT 90 (99)
Q Consensus 59 ~~~l~~ei~---e~~~ei~~l~~k~~~l~~El~~~ 90 (99)
+.+|++||+ .+..|+...+..+..+..-|.+.
T Consensus 3 QsaL~~EirakQ~~~eEL~kvk~~n~~~e~kLqea 37 (61)
T PF08826_consen 3 QSALEAEIRAKQAIQEELTKVKSANLAFESKLQEA 37 (61)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356777776 34445555555555555444443
No 407
>PHA02109 hypothetical protein
Probab=30.28 E-value=1.5e+02 Score=23.07 Aligned_cols=35 Identities=23% Similarity=0.358 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 041503 62 LVEEVRKLTLEIERLSDKFRLLHKELEHTQLRSKYG 97 (99)
Q Consensus 62 l~~ei~e~~~ei~~l~~k~~~l~~El~~~~~~~~~~ 97 (99)
|..-|+-+.-|+.++++|++.++.|+++ .+--++|
T Consensus 198 L~~ki~~LS~E~~Q~~~Ki~N~R~~Vk~-~LSE~F~ 232 (233)
T PHA02109 198 LTIKLEALSDEACQVKHKILNLRAEVKR-RLSEDFG 232 (233)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHhcC
Confidence 3333455666777888888888888764 3444444
No 408
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=29.99 E-value=22 Score=22.36 Aligned_cols=13 Identities=38% Similarity=0.917 Sum_probs=9.8
Q ss_pred ccccCccccceee
Q 041503 13 QVCNECGGQIELF 25 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~ 25 (99)
-.||+||...+.+
T Consensus 42 ~~CPNCgGelv~R 54 (57)
T PF06906_consen 42 GVCPNCGGELVRR 54 (57)
T ss_pred CcCcCCCCccccC
Confidence 6799999876543
No 409
>PF04201 TPD52: Tumour protein D52 family; InterPro: IPR007327 The hD52 gene was originally identified through its elevated expression level in human breast carcinoma. Cloning of D52 homologues from other species has indicated that D52 may play roles in calcium-mediated signal transduction and cell proliferation. Two human homologues of hD52, hD53 and hD54, have also been identified, demonstrating the existence of a novel gene/protein family []. These proteins have an N-terminal coiled-coil that allows members to form homo- and heterodimers with each other [].
Probab=29.98 E-value=2.3e+02 Score=21.21 Aligned_cols=36 Identities=25% Similarity=0.474 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHhhcC
Q 041503 63 VEEVRKLTLEIERLSDKFRLLHKELE-----HTQLRSKYGL 98 (99)
Q Consensus 63 ~~ei~e~~~ei~~l~~k~~~l~~El~-----~~~~~~~~~~ 98 (99)
++|-+++..||.++.+.|..|++-|- -.-++.|.|+
T Consensus 28 EeE~eeLr~EL~KvEeEI~TLrqvL~aKer~~~eLKrkLGi 68 (162)
T PF04201_consen 28 EEEREELRSELAKVEEEIQTLRQVLAAKERHCAELKRKLGI 68 (162)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHCC
Confidence 33445555556555555555554432 2235556665
No 410
>PF06156 DUF972: Protein of unknown function (DUF972); InterPro: IPR010377 FUNCTION: Involved in initiation control of chromosome replication. SUBUNIT: Interacts with both DnaA and DnaN, acting as a bridge between these two proteins. SIMILARITY: Belongs to the YabA family.
Probab=29.72 E-value=1.9e+02 Score=19.83 Aligned_cols=24 Identities=25% Similarity=0.310 Sum_probs=10.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 65 EVRKLTLEIERLSDKFRLLHKELE 88 (99)
Q Consensus 65 ei~e~~~ei~~l~~k~~~l~~El~ 88 (99)
+|.+++..+..|-..+..|+.|..
T Consensus 23 ~~~~LK~~~~~l~EEN~~L~~EN~ 46 (107)
T PF06156_consen 23 ELEELKKQLQELLEENARLRIENE 46 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444444444444444444443
No 411
>PRK11020 hypothetical protein; Provisional
Probab=29.65 E-value=1.9e+02 Score=20.59 Aligned_cols=20 Identities=35% Similarity=0.375 Sum_probs=13.8
Q ss_pred hHHHHHHHHHHHHHHHHHHH
Q 041503 58 KIDLLVEEVRKLTLEIERLS 77 (99)
Q Consensus 58 k~~~l~~ei~e~~~ei~~l~ 77 (99)
.++.+..||..+..+|++|+
T Consensus 32 ~i~qf~~E~~~l~k~I~~lk 51 (118)
T PRK11020 32 KYAQFEKEKATLEAEIARLK 51 (118)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 34555667777877887775
No 412
>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=29.57 E-value=34 Score=22.19 Aligned_cols=13 Identities=38% Similarity=0.621 Sum_probs=11.1
Q ss_pred CCCCCCcceeeCC
Q 041503 29 TTKNPNRKFWKCR 41 (99)
Q Consensus 29 t~~NPgR~Fy~C~ 41 (99)
+.+.|||-+|-|+
T Consensus 33 ~~k~~GRGaYvc~ 45 (79)
T cd00279 33 TGKLPGRGAYVCA 45 (79)
T ss_pred CCCCCCCeEEEcC
Confidence 5567999999998
No 413
>PF10211 Ax_dynein_light: Axonemal dynein light chain; InterPro: IPR019347 Axonemal dynein light chain proteins play a dynamic role in flagellar and cilial motility. Eukaryotic cilia and flagella are complex organelles consisting of a core structure, the axoneme, which is composed of nine microtubule doublets forming a cylinder that surrounds a pair of central singlet microtubules. This ultra-structural arrangement seems to be one of the most stable micro-tubular assemblies known and is responsible for the flagellar and ciliary movement of a large number of organisms ranging from protozoan to mammals. This light chain interacts directly with the N-terminal half of the heavy chains [].
Probab=29.46 E-value=1.9e+02 Score=21.38 Aligned_cols=16 Identities=31% Similarity=0.351 Sum_probs=6.0
Q ss_pred HHHHHHHHHHHHHHHH
Q 041503 68 KLTLEIERLSDKFRLL 83 (99)
Q Consensus 68 e~~~ei~~l~~k~~~l 83 (99)
++..+++.|..++..+
T Consensus 131 ~L~~e~~~L~~~~~~l 146 (189)
T PF10211_consen 131 ELEEEKEELEKQVQEL 146 (189)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3333333333333333
No 414
>PRK02195 V-type ATP synthase subunit D; Provisional
Probab=29.44 E-value=1.7e+02 Score=21.99 Aligned_cols=30 Identities=27% Similarity=0.409 Sum_probs=18.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 58 KIDLLVEEVRKLTLEIERLSDKFRLLHKEL 87 (99)
Q Consensus 58 k~~~l~~ei~e~~~ei~~l~~k~~~l~~El 87 (99)
|.+.|..|+.++..+..+++++++++..+.
T Consensus 32 KR~~Li~e~~~~~~~~~~lr~~~~~~~~~a 61 (201)
T PRK02195 32 KKAQLQAEVRRAKAEAAELEQEYQKLRQAI 61 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456666677777666666665555544443
No 415
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=29.42 E-value=25 Score=21.07 Aligned_cols=10 Identities=30% Similarity=1.059 Sum_probs=8.0
Q ss_pred CcccccCccc
Q 041503 11 SLQVCNECGG 20 (99)
Q Consensus 11 ~~~~Cp~Cg~ 20 (99)
|.-+||.||.
T Consensus 10 GirkCp~CGt 19 (44)
T PF14952_consen 10 GIRKCPKCGT 19 (44)
T ss_pred ccccCCcCcC
Confidence 4578999996
No 416
>PF14818 DUF4482: Domain of unknown function (DUF4482)
Probab=29.37 E-value=1.4e+02 Score=21.76 Aligned_cols=35 Identities=26% Similarity=0.399 Sum_probs=25.3
Q ss_pred hhHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 57 EKIDLLVE---EVRKLTLEIERLSDKFRLLHKELEHTQ 91 (99)
Q Consensus 57 ~k~~~l~~---ei~e~~~ei~~l~~k~~~l~~El~~~~ 91 (99)
+|..+|+. |-.+-....+.|+.+|+.|++|+.-.+
T Consensus 17 Ek~ELLdrfd~ER~eWE~Q~kemq~kieql~~e~~~~r 54 (141)
T PF14818_consen 17 EKMELLDRFDRERQEWEQQWKEMQRKIEQLQKEVKPRR 54 (141)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcchhh
Confidence 44455544 666666678889999999999987664
No 417
>PF04799 Fzo_mitofusin: fzo-like conserved region; InterPro: IPR006884 This entry represents the heptad repeat domain which is conserved at the C terminus of Fzo/mitofusion family of GTPases. Fzo is a mediator of mitochondrial fusion during spermatogenesis []. This conserved region is also found in the human mitofusin protein []. This domain forms a dimeric antiparallel coiled coil structure, which has been proposed to act as a mitochodrial tether before vesicle fusion [].; GO: 0003924 GTPase activity, 0006184 GTP catabolic process, 0008053 mitochondrial fusion, 0005741 mitochondrial outer membrane, 0016021 integral to membrane; PDB: 1T3J_A.
Probab=29.35 E-value=1.7e+02 Score=21.97 Aligned_cols=58 Identities=22% Similarity=0.211 Sum_probs=11.5
Q ss_pred ceeeeecCCCCCCcceee----CC-------------CCCeeEeccCCccchhhHHHHHHHH----HHHHHHHHHHHHHH
Q 041503 22 IELFTSHTTKNPNRKFWK----CR-------------VCKNFQWAEDRKFSNEKIDLLVEEV----RKLTLEIERLSDKF 80 (99)
Q Consensus 22 ~~~~tS~t~~NPgR~Fy~----C~-------------~C~fF~W~De~~~~~~k~~~l~~ei----~e~~~ei~~l~~k~ 80 (99)
+-.+.+||++-..|.|=+ =. +|..-.+.+-... + +.|.+.| ++++.||++|+.++
T Consensus 61 lYERLtWT~~AKER~fK~Qfv~hAt~KLr~iv~~tsancs~QVqqeL~~t-f---~rL~~~Vd~~~~eL~~eI~~L~~~i 136 (171)
T PF04799_consen 61 LYERLTWTNKAKERAFKRQFVDHATEKLRLIVSFTSANCSHQVQQELSST-F---ARLCQQVDQTKNELEDEIKQLEKEI 136 (171)
T ss_dssp -------------------------------------------------H-H---HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHhcCchHHHHHHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHH-H---HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445677777777666622 11 5776666655421 1 2222222 25555555555555
Q ss_pred HHH
Q 041503 81 RLL 83 (99)
Q Consensus 81 ~~l 83 (99)
+.|
T Consensus 137 ~~l 139 (171)
T PF04799_consen 137 QRL 139 (171)
T ss_dssp HHH
T ss_pred HHH
Confidence 555
No 418
>PF05103 DivIVA: DivIVA protein; InterPro: IPR007793 The Bacillus subtilis divIVA1 mutation causes misplacement of the septum during cell division, resulting in the formation of small, circular, anucleate minicells []. Inactivation of divIVA produces a minicell phenotype, whereas overproduction of DivIVA results in a filamentation phenotype []. These proteins appear to contain coiled-coils.; PDB: 2WUK_C 2WUJ_A.
Probab=29.31 E-value=31 Score=23.08 Aligned_cols=20 Identities=25% Similarity=0.390 Sum_probs=8.6
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 041503 65 EVRKLTLEIERLSDKFRLLH 84 (99)
Q Consensus 65 ei~e~~~ei~~l~~k~~~l~ 84 (99)
++..+..++..|+.++..|.
T Consensus 33 ~~~~l~~e~~~L~~~~~~l~ 52 (131)
T PF05103_consen 33 ELERLQRENAELKEEIEELQ 52 (131)
T ss_dssp HHHHHHHHHHHHHHHHHCCC
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 34444444444444444433
No 419
>PRK00295 hypothetical protein; Provisional
Probab=29.25 E-value=1.5e+02 Score=18.57 Aligned_cols=23 Identities=9% Similarity=0.111 Sum_probs=11.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 041503 66 VRKLTLEIERLSDKFRLLHKELE 88 (99)
Q Consensus 66 i~e~~~ei~~l~~k~~~l~~El~ 88 (99)
|++|+..+-++..+|..|+..|.
T Consensus 21 ie~Ln~~v~~Qq~~I~~L~~ql~ 43 (68)
T PRK00295 21 IQALNDVLVEQQRVIERLQLQMA 43 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 45555555555544544444443
No 420
>PF02050 FliJ: Flagellar FliJ protein; InterPro: IPR012823 Many flagellar proteins are exported by a flagellum-specific export pathway. Attempts have been made to characterise the apparatus responsible for this process, by designing assays to screen for mutants with export defects []. Experiments involving filament removal from temperature-sensitive flagellar mutants of Salmonella typhimurium have shown that, while most mutants were able to regrow filaments, flhA, fliH, fliI and fliN mutants showed no or greatly reduced regrowth. This suggests that the corresponding gene products are involved in the process of flagellum-specific export. The sequences of fliH, fliI and the adjacent gene, fliJ, have been deduced. FliJ was shown to encode a protein of molecular mass 17,302 Da []. It is a membrane-associated protein that affects chemotactic events, mutations in FliJ result in failure to respond to chemotactic stimuli.; GO: 0003774 motor activity, 0001539 ciliary or flagellar motility, 0006935 chemotaxis, 0009288 bacterial-type flagellum, 0016020 membrane, 0044461 bacterial-type flagellum part; PDB: 3AJW_A.
Probab=29.20 E-value=1.5e+02 Score=18.51 Aligned_cols=33 Identities=21% Similarity=0.365 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 61 LLVEEVRKLTLEIERLSDKFRLLHKELEHTQLR 93 (99)
Q Consensus 61 ~l~~ei~e~~~ei~~l~~k~~~l~~El~~~~~~ 93 (99)
.|...|..+..++..++..+...+.+|......
T Consensus 56 ~l~~~i~~~~~~~~~~~~~~~~~r~~l~~a~~~ 88 (123)
T PF02050_consen 56 ALEQAIQQQQQELERLEQEVEQAREELQEARRE 88 (123)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344456666666666666666666666554443
No 421
>PF07047 OPA3: Optic atrophy 3 protein (OPA3); InterPro: IPR010754 OPA3 deficiency causes type III 3-methylglutaconic aciduria (MGA) in humans. This disease manifests with early bilateral optic atrophy, spasticity, extrapyramidal dysfunction, ataxia, and cognitive deficits, but normal longevity []. This family consists of several optic atrophy 3 (OPA3) proteins and related proteins from other eukaryotic species, the function is unknown.
Probab=29.18 E-value=1.1e+02 Score=21.38 Aligned_cols=19 Identities=26% Similarity=0.417 Sum_probs=8.4
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 041503 64 EEVRKLTLEIERLSDKFRL 82 (99)
Q Consensus 64 ~ei~e~~~ei~~l~~k~~~ 82 (99)
.+++++..++++|+.+++.
T Consensus 112 ~~l~~L~~~i~~L~~~~~~ 130 (134)
T PF07047_consen 112 ERLEELEERIEELEEQVEK 130 (134)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3444444444444444433
No 422
>PF08657 DASH_Spc34: DASH complex subunit Spc34 ; InterPro: IPR013966 The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis []. In Saccharomyces cerevisiae (Baker's yeast) DASH forms both rings and spiral structures on microtubules in vitro [, ]. Components of the DASH complex, including Dam1, Duo1, Spc34, Dad1 and Ask1, are essential and connect the centromere to the plus end of spindle microtubules [].
Probab=28.89 E-value=1.7e+02 Score=23.12 Aligned_cols=33 Identities=27% Similarity=0.295 Sum_probs=19.1
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 57 EKIDLLVEEVRKLTLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 57 ~k~~~l~~ei~e~~~ei~~l~~k~~~l~~El~~ 89 (99)
.++..|+..-.++..+|+.|++++...+.+|+.
T Consensus 180 eki~~Lr~~y~~l~~~i~~lE~~VaeQ~~qL~~ 212 (259)
T PF08657_consen 180 EKIAALRQRYNQLSNSIAYLEAEVAEQEAQLER 212 (259)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555555556666666666666666555554
No 423
>PF07412 Geminin: Geminin; InterPro: IPR022786 This family contains the eukaryotic protein geminin (approximately 200 residues long). Geminin inhibits DNA replication by preventing the incorporation of MCM complex into prereplication complex, and is degraded during the mitotic phase of the cell cycle. It has been proposed that geminin inhibits DNA replication during S, G2, and M phases and that geminin destruction at the metaphase-anaphase transition permits replication in the succeeding cell cycle []. ; GO: 0008156 negative regulation of DNA replication; PDB: 1T6F_B 2LP0_B 1UII_B 2WVR_B 2ZXX_B.
Probab=28.88 E-value=1.4e+02 Score=23.05 Aligned_cols=24 Identities=38% Similarity=0.416 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 65 EVRKLTLEIERLSDKFRLLHKELE 88 (99)
Q Consensus 65 ei~e~~~ei~~l~~k~~~l~~El~ 88 (99)
|.++|-.+|+.++..|..|++|+.
T Consensus 126 ENe~Lh~~ie~~~eEi~~lk~en~ 149 (200)
T PF07412_consen 126 ENEKLHKEIEQKDEEIAKLKEENE 149 (200)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 677888888888888888887764
No 424
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=28.79 E-value=1.3e+02 Score=22.74 Aligned_cols=7 Identities=57% Similarity=0.705 Sum_probs=2.5
Q ss_pred HHHHHHH
Q 041503 71 LEIERLS 77 (99)
Q Consensus 71 ~ei~~l~ 77 (99)
.+|+.++
T Consensus 176 ~eIe~~~ 182 (262)
T PF14257_consen 176 SEIEQLE 182 (262)
T ss_pred HHHHHHH
Confidence 3333333
No 425
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=28.79 E-value=42 Score=32.50 Aligned_cols=29 Identities=24% Similarity=0.432 Sum_probs=23.7
Q ss_pred eeeecCCCCCCcceeeCCCCCeeEeccCC
Q 041503 24 LFTSHTTKNPNRKFWKCRVCKNFQWAEDR 52 (99)
Q Consensus 24 ~~tS~t~~NPgR~Fy~C~~C~fF~W~De~ 52 (99)
-.+-=|+-||==+-|.||.|++|...|+.
T Consensus 901 tm~gITEVNPL~PHY~Cp~Cky~Ef~~d~ 929 (1444)
T COG2176 901 TMIGITEVNPLPPHYLCPECKYSEFIDDG 929 (1444)
T ss_pred HhhcccccCCCCccccCCCCceeeeecCC
Confidence 34555788999999999999999998854
No 426
>KOG3335 consensus Predicted coiled-coil protein [General function prediction only]
Probab=28.75 E-value=1.2e+02 Score=23.15 Aligned_cols=30 Identities=33% Similarity=0.352 Sum_probs=17.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 60 DLLVEEVRKLTLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 60 ~~l~~ei~e~~~ei~~l~~k~~~l~~El~~ 89 (99)
..|+.++.++..+|++++..+..|.+.|++
T Consensus 109 ~elr~~~~~l~~~i~~~~~~~~~L~~~l~~ 138 (181)
T KOG3335|consen 109 MELRLKVEKLENAIAELTKFFSQLHSKLNK 138 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 334445566666666666666666555544
No 427
>TIGR02231 conserved hypothetical protein. This family consists of proteins over 500 amino acids long in Caenorhabditis elegans and several bacteria (Pseudomonas aeruginosa, Nostoc sp. PCC 7120, Leptospira interrogans, etc.). The function is unknown.
Probab=28.72 E-value=1.4e+02 Score=25.10 Aligned_cols=31 Identities=26% Similarity=0.369 Sum_probs=22.6
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 57 EKIDLLVEEVRKLTLEIERLSDKFRLLHKEL 87 (99)
Q Consensus 57 ~k~~~l~~ei~e~~~ei~~l~~k~~~l~~El 87 (99)
++...|+++|+++..+++++++++..+...+
T Consensus 71 ~~~~~l~~~l~~l~~~~~~~~~~~~~~~~~~ 101 (525)
T TIGR02231 71 ERLAELRKQIRELEAELRDLEDRGDALKALA 101 (525)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567777788888888888877777776655
No 428
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=28.66 E-value=25 Score=19.60 Aligned_cols=11 Identities=27% Similarity=0.851 Sum_probs=7.5
Q ss_pred cccccCccccc
Q 041503 12 LQVCNECGGQI 22 (99)
Q Consensus 12 ~~~Cp~Cg~~~ 22 (99)
.+.||.|++.+
T Consensus 4 ~~~C~nC~R~v 14 (33)
T PF08209_consen 4 YVECPNCGRPV 14 (33)
T ss_dssp EEE-TTTSSEE
T ss_pred eEECCCCcCCc
Confidence 47899999864
No 429
>KOG2041 consensus WD40 repeat protein [General function prediction only]
Probab=28.65 E-value=51 Score=30.79 Aligned_cols=35 Identities=23% Similarity=0.587 Sum_probs=26.7
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCeeE
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQ 47 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~ 47 (99)
+.||.|......-++....-..-.||-||.|+.-.
T Consensus 1132 ~~c~ec~~kfP~CiasG~pIt~~~fWlC~~CkH~a 1166 (1189)
T KOG2041|consen 1132 LQCSECQTKFPVCIASGRPITDNIFWLCPRCKHRA 1166 (1189)
T ss_pred CCChhhcCcCceeeccCCccccceEEEcccccccc
Confidence 88999998877777776655555699999887543
No 430
>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 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 probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.
Probab=28.59 E-value=20 Score=21.73 Aligned_cols=34 Identities=21% Similarity=0.502 Sum_probs=17.3
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCeeEec
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQWA 49 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~W~ 49 (99)
..| .||.. -.++...-.-+---..|++|.+++.+
T Consensus 19 y~C-RCG~~--f~i~e~~l~~~~~iv~C~sCSL~I~V 52 (55)
T PF05207_consen 19 YPC-RCGGE--FEISEEDLEEGEVIVQCDSCSLWIRV 52 (55)
T ss_dssp EEE-TTSSE--EEEEHHHHHCT--EEEETTTTEEEEE
T ss_pred EcC-CCCCE--EEEcchhccCcCEEEECCCCccEEEE
Confidence 567 77766 22232222222555667777776654
No 431
>PF05766 NinG: Bacteriophage Lambda NinG protein; InterPro: IPR008713 The ninR region of phage lambda contains two recombination genes, ninB (also known as orf) and ninG (also known as rap). These genes are involved in the RecF and RecBCD recombination pathways of Escherichia coli that operate on phage lambda [, ]. NinB and NinG participate in Red recombination, the primary pathway operating when wild-type lambda grows lytically in rec+ cells [].
Probab=28.45 E-value=80 Score=23.98 Aligned_cols=77 Identities=23% Similarity=0.463 Sum_probs=36.7
Q ss_pred ccccCcccc------ceeeeecCCCCCCccee------eCCCCCeeEeccCCcc--------chhhHHHHHH--HHHH-H
Q 041503 13 QVCNECGGQ------IELFTSHTTKNPNRKFW------KCRVCKNFQWAEDRKF--------SNEKIDLLVE--EVRK-L 69 (99)
Q Consensus 13 ~~Cp~Cg~~------~~~~tS~t~~NPgR~Fy------~C~~C~fF~W~De~~~--------~~~k~~~l~~--ei~e-~ 69 (99)
..|-.||.. +-=+.|. ..+|.=+|. .|..|+.|.=-+...| +-++.+.|+. +... -
T Consensus 88 ~~CiSCG~~~~~~~dagHy~s~-g~~~~lRF~~~N~~~qC~~CN~~~sgn~~~Yr~~Li~kiG~~~ve~Le~~~~~~k~~ 166 (189)
T PF05766_consen 88 KPCISCGRKHGGQWDAGHYRSR-GAAPELRFNEDNIHAQCKHCNRHLSGNIVEYRIGLIEKIGQERVEWLEGPHEPRKWT 166 (189)
T ss_pred CCcccCCCcCCCCccccccccc-ccCcccccChhhHhHcCCccccccccCHHHHHHHHHHHHhHHHHHHHhcCCCCCCCC
Confidence 557788871 1122222 134444553 4668887744333222 4444444443 1110 0
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 041503 70 TLEIERLSDKFRLLHKELEHT 90 (99)
Q Consensus 70 ~~ei~~l~~k~~~l~~El~~~ 90 (99)
..++.++.+.+++..++|+++
T Consensus 167 ~~el~~i~~~y~~~~k~L~k~ 187 (189)
T PF05766_consen 167 IEELKAIIAIYRAKLKELKKE 187 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHh
Confidence 134555555555666666654
No 432
>PLN03166 60S ribosomal protein L34; Provisional
Probab=28.45 E-value=35 Score=23.33 Aligned_cols=26 Identities=27% Similarity=0.387 Sum_probs=20.1
Q ss_pred ccccCccccc---------ee---eeecCCCCCCccee
Q 041503 13 QVCNECGGQI---------EL---FTSHTTKNPNRKFW 38 (99)
Q Consensus 13 ~~Cp~Cg~~~---------~~---~tS~t~~NPgR~Fy 38 (99)
++|+.||.+. .. ..|++.+-|.|.|-
T Consensus 42 pkC~~cg~~L~Gi~~~Rp~~~~~~~lsK~~K~vsRaYG 79 (96)
T PLN03166 42 PKCPVTGKRIQGIPHLRPAEYKRSRLSRNRRTVNRAYG 79 (96)
T ss_pred CcCCCCCCccCCccCCChhhhhhhhcccCcCccccCcC
Confidence 8999999632 22 56889999999983
No 433
>PRK07218 replication factor A; Provisional
Probab=28.32 E-value=30 Score=29.12 Aligned_cols=19 Identities=37% Similarity=0.761 Sum_probs=15.0
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCK 44 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~ 44 (99)
..||.|++.+.. |.||.|+
T Consensus 298 ~rCP~C~r~v~~-------------~~C~~hG 316 (423)
T PRK07218 298 ERCPECGRVIQK-------------GQCRSHG 316 (423)
T ss_pred ecCcCccccccC-------------CcCCCCC
Confidence 789999988721 7899776
No 434
>KOG4657 consensus Uncharacterized conserved protein [Function unknown]
Probab=28.26 E-value=1.3e+02 Score=23.88 Aligned_cols=29 Identities=24% Similarity=0.353 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 60 DLLVEEVRKLTLEIERLSDKFRLLHKELE 88 (99)
Q Consensus 60 ~~l~~ei~e~~~ei~~l~~k~~~l~~El~ 88 (99)
..++.||.....+++.|..-++.++.|+-
T Consensus 89 ~~ieqeik~~q~elEvl~~n~Q~lkeE~d 117 (246)
T KOG4657|consen 89 MGIEQEIKATQSELEVLRRNLQLLKEEKD 117 (246)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 34455677777788888777777766653
No 435
>COG1938 Archaeal enzymes of ATP-grasp superfamily [General function prediction only]
Probab=28.26 E-value=99 Score=24.43 Aligned_cols=24 Identities=29% Similarity=0.490 Sum_probs=12.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 68 KLTLEIERLSDKFRLLHKELEHTQ 91 (99)
Q Consensus 68 e~~~ei~~l~~k~~~l~~El~~~~ 91 (99)
+|-.+-++++.++++|.+.+++++
T Consensus 208 ~L~keAe~i~~~lekl~eq~~~~~ 231 (244)
T COG1938 208 KLEKEAEEIEEQLEKLAEQLEKEE 231 (244)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444444445555555555555544
No 436
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=28.25 E-value=42 Score=25.00 Aligned_cols=31 Identities=26% Similarity=0.552 Sum_probs=22.2
Q ss_pred cccCccc-cceeeeecCC--CCCCcceeeCCCCC
Q 041503 14 VCNECGG-QIELFTSHTT--KNPNRKFWKCRVCK 44 (99)
Q Consensus 14 ~Cp~Cg~-~~~~~tS~t~--~NPgR~Fy~C~~C~ 44 (99)
+||.|+- ...+.=|+.. .|.=|+=--|+.|+
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~ 35 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECG 35 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccc
Confidence 7999996 4555556655 33457778899887
No 437
>PRK14155 heat shock protein GrpE; Provisional
Probab=28.06 E-value=2.7e+02 Score=21.28 Aligned_cols=35 Identities=20% Similarity=0.202 Sum_probs=20.1
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 57 EKIDLLVEEVRKLTLEIERLSDKFRLLHKELEHTQ 91 (99)
Q Consensus 57 ~k~~~l~~ei~e~~~ei~~l~~k~~~l~~El~~~~ 91 (99)
.+++.++.++.++...+.++.+.++..++=.+++.
T Consensus 20 ~~l~~le~e~~elkd~~lR~~AefeN~RKR~~kE~ 54 (208)
T PRK14155 20 QEIEALKAEVAALKDQALRYAAEAENTKRRAEREM 54 (208)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445555666666666666666666655555544
No 438
>KOG0976 consensus Rho/Rac1-interacting serine/threonine kinase Citron [Signal transduction mechanisms]
Probab=27.94 E-value=1.2e+02 Score=28.67 Aligned_cols=32 Identities=28% Similarity=0.441 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 62 LVEEVRKLTLEIERLSDKFRLLHKELEHTQLR 93 (99)
Q Consensus 62 l~~ei~e~~~ei~~l~~k~~~l~~El~~~~~~ 93 (99)
+..|++.++++.++..+++..|++||.++.+-
T Consensus 481 Veqe~emlKaen~rqakkiefmkEeiQethld 512 (1265)
T KOG0976|consen 481 VEQEYEMLKAENERQAKKIEFMKEEIQETHLD 512 (1265)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34477889999999999999999999988764
No 439
>PF07926 TPR_MLP1_2: TPR/MLP1/MLP2-like protein; InterPro: IPR012929 This domain is found in a number of proteins, including TPR protein (P12270 from SWISSPROT) and yeast myosin-like proteins 1 (MLP1, Q02455 from SWISSPROT) and 2 (MLP2, P40457 from SWISSPROT). These proteins share a number of features; for example, they all have coiled-coil regions and all three are associated with nuclear pores [, , ]. TPR is thought to be a component of nuclear pore complex- attached intranuclear filaments [], and is implicated in nuclear protein import []. Moreover, its N-terminal region is involved in the activation of oncogenic kinases, possibly by mediating the dimerisation of kinase domains or by targeting these kinases to the nuclear pore complex []. MLP1 and MLP2 are involved in the process of telomere length regulation, where they are thought to interact with proteins such as Tel1p and modulate their activity []. ; GO: 0006606 protein import into nucleus, 0005643 nuclear pore
Probab=27.92 E-value=1.7e+02 Score=20.21 Aligned_cols=29 Identities=38% Similarity=0.613 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 60 DLLVEEVRKLTLEIERLSDKFRLLHKELE 88 (99)
Q Consensus 60 ~~l~~ei~e~~~ei~~l~~k~~~l~~El~ 88 (99)
..|..||.++...+..|+.++..|+.=|+
T Consensus 101 ~~le~e~~~~~~r~~dL~~QN~lLh~QlE 129 (132)
T PF07926_consen 101 EQLEKELSELEQRIEDLNEQNKLLHDQLE 129 (132)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45556777777777777777777755443
No 440
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=27.79 E-value=50 Score=27.37 Aligned_cols=32 Identities=25% Similarity=0.569 Sum_probs=21.6
Q ss_pred CcccccCccccceeeeecCCCCCCcceeeCCCCCeeEeccCC
Q 041503 11 SLQVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQWAEDR 52 (99)
Q Consensus 11 ~~~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~W~De~ 52 (99)
+...||.|+... +||.+ .+||.|+.-.+....
T Consensus 214 ~~~~C~~Cd~~~---------~~~~~-a~CpRC~~~L~~~~~ 245 (403)
T TIGR00155 214 KLRSCSACHTTI---------LPAQE-PVCPRCSTPLYVRRR 245 (403)
T ss_pred CCCcCCCCCCcc---------CCCCC-cCCcCCCCcccCCCC
Confidence 346699999843 24443 569999977765543
No 441
>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=27.78 E-value=46 Score=22.94 Aligned_cols=10 Identities=20% Similarity=0.508 Sum_probs=5.4
Q ss_pred cceeeCCCCC
Q 041503 35 RKFWKCRVCK 44 (99)
Q Consensus 35 R~Fy~C~~C~ 44 (99)
|..-.||.|+
T Consensus 24 k~PivCP~CG 33 (108)
T PF09538_consen 24 KDPIVCPKCG 33 (108)
T ss_pred CCCccCCCCC
Confidence 3445566665
No 442
>PF10482 CtIP_N: Tumour-suppressor protein CtIP N-terminal domain; InterPro: IPR019518 CtIP is predominantly a nuclear protein that complexes with both BRCA1 and the BRCA1-associated RING domain protein (BARD1). At the protein level, CtIP expression varies with cell cycle progression in a pattern identical to that of BRCA1. Thus, the steady-state levels of CtIP polypeptides, which remain low in resting cells and G1 cycling cells, increase dramatically as Dividing cells traverse the G1/S boundary. CtIP can potentially modulate the functions ascribed to BRCA1 in transcriptional regulation, DNA repair, and/or cell cycle checkpoint control []. This N-terminal domain carries a coiled-coil region and is essential for homodimerisation of the protein []. The C-terminal domain is family CtIP_C and carries functionally important CxxC and RHR motifs, absence of which lead cells to grow slowly and show hypersensitivity to genotoxins [].
Probab=27.77 E-value=74 Score=22.76 Aligned_cols=23 Identities=30% Similarity=0.458 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 041503 66 VRKLTLEIERLSDKFRLLHKELE 88 (99)
Q Consensus 66 i~e~~~ei~~l~~k~~~l~~El~ 88 (99)
|-.+..|...|++.+++|+.||+
T Consensus 98 i~~L~nE~n~L~eEN~~L~eElk 120 (120)
T PF10482_consen 98 IFELTNEMNTLKEENKKLKEELK 120 (120)
T ss_pred HHHHHHHHHhHHHHHHHHHHHhC
Confidence 56777888888888888888873
No 443
>PF04859 DUF641: Plant protein of unknown function (DUF641); InterPro: IPR006943 This conserved region is found in a number of plant proteins of unknown function.
Probab=27.71 E-value=1.2e+02 Score=21.74 Aligned_cols=13 Identities=46% Similarity=0.624 Sum_probs=5.2
Q ss_pred HHHHHHHHHHHHH
Q 041503 65 EVRKLTLEIERLS 77 (99)
Q Consensus 65 ei~e~~~ei~~l~ 77 (99)
|++..+.||..|+
T Consensus 102 e~~~Kdsei~~Lr 114 (131)
T PF04859_consen 102 ELRAKDSEIDRLR 114 (131)
T ss_pred HHHHHHHHHHHHH
Confidence 3333344444443
No 444
>COG0718 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.68 E-value=64 Score=22.36 Aligned_cols=32 Identities=22% Similarity=0.468 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 041503 66 VRKLTLEIERLSDKFRLLHKELEHTQLRSKYG 97 (99)
Q Consensus 66 i~e~~~ei~~l~~k~~~l~~El~~~~~~~~~~ 97 (99)
+.++..+...++.++.+++.||+....-.++|
T Consensus 7 ~~~l~kqaqqmQ~~~~~~Q~ela~~ev~g~ag 38 (105)
T COG0718 7 MQKLMKQAQQMQKKMQKMQEELAQKEVTGKAG 38 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcEEeeecC
Confidence 44555667778888999999998776555444
No 445
>PF10186 Atg14: UV radiation resistance protein and autophagy-related subunit 14; InterPro: IPR018791 Class III phosphatidylinositol 3-kinase (PI3-kinase) regulates multiple membrane trafficking. In yeast, two distinct PI3-kinase complexes are known: complex I (Vps34, Vps15, Vps30/Atg6, and Atg14) is involved in autophagy, and complex II (Vps34, Vps15, Vps30/Atg6, and Vps38) functions in the vacuolar protein sorting pathway. In mammals, the counterparts of Vps34, Vps15, and Vps30/Atg6 are Vps34, p150, and Beclin 1, respectively. Mammalian UV irradiation resistance-associated gene (UVRAG) has been identified as identical to yeast Vps38 []. The Atg14 (autophagy-related protein 14) proteins are hydrophilic proteins and have a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole []. This entry represents Atg14 and UVRAG, which bind Beclin 1 to forms two distinct PI3-kinase complexes. This entry also includes Bakor (beclin-1-associated autophagy-related key regulator), also known as autophagy-related protein 14-like protein, which share sequence similarity to the yeast Atg14 protein []. Barkor positively regulates autophagy through its interaction with Beclin-1, with decreased levels of autophagosome formation observed when Barkor expression is eliminated []. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. ; GO: 0010508 positive regulation of autophagy
Probab=27.68 E-value=2.5e+02 Score=20.89 Aligned_cols=17 Identities=24% Similarity=0.395 Sum_probs=6.4
Q ss_pred HHHHHHHHHHHHHHHHH
Q 041503 71 LEIERLSDKFRLLHKEL 87 (99)
Q Consensus 71 ~ei~~l~~k~~~l~~El 87 (99)
.+++..+.++.+++..|
T Consensus 84 ~~i~~~r~~l~~~~~~l 100 (302)
T PF10186_consen 84 KRIEQKRERLEELRESL 100 (302)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 33333333333333333
No 446
>PRK07737 fliD flagellar capping protein; Validated
Probab=27.57 E-value=1.5e+02 Score=25.22 Aligned_cols=26 Identities=12% Similarity=0.383 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 59 IDLLVEEVRKLTLEIERLSDKFRLLH 84 (99)
Q Consensus 59 ~~~l~~ei~e~~~ei~~l~~k~~~l~ 84 (99)
...|..+|+.++.+|+++++++..++
T Consensus 443 ~~~l~~~i~~l~~~i~~~~~rl~~~e 468 (501)
T PRK07737 443 QFAIGKDLNQIETQIDRFQDRLKQIE 468 (501)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34566677777777777776666653
No 447
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=27.56 E-value=32 Score=30.39 Aligned_cols=22 Identities=18% Similarity=0.484 Sum_probs=15.1
Q ss_pred CcccccCccccceeeeecCCCCCCcceeeCCCCC
Q 041503 11 SLQVCNECGGQIELFTSHTTKNPNRKFWKCRVCK 44 (99)
Q Consensus 11 ~~~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~ 44 (99)
..-.|+.||.. .| ..+.||.|+
T Consensus 625 ~~~~C~~CG~~-----------~g-~~~~CP~CG 646 (656)
T PRK08270 625 TFSICPKHGYL-----------SG-EHEFCPKCG 646 (656)
T ss_pred CCcccCCCCCc-----------CC-CCCCCcCCc
Confidence 34789999963 11 248899887
No 448
>PF07028 DUF1319: Protein of unknown function (DUF1319); InterPro: IPR010746 This entry is represented by Commelina yellow mottle virus, Orf1. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family contains a number of viral proteins of unknown function approximately 200 residues long. Family members seem to be restricted to badnaviruses.
Probab=27.29 E-value=1.7e+02 Score=21.08 Aligned_cols=16 Identities=38% Similarity=0.673 Sum_probs=7.1
Q ss_pred HHHHHHHHHHHHHHHH
Q 041503 72 EIERLSDKFRLLHKEL 87 (99)
Q Consensus 72 ei~~l~~k~~~l~~El 87 (99)
+|++++++++.+..||
T Consensus 61 ~l~~l~~~l~~l~~eL 76 (126)
T PF07028_consen 61 ELKELKQELDVLSKEL 76 (126)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3444444444444443
No 449
>PF00831 Ribosomal_L29: Ribosomal L29 protein; InterPro: IPR001854 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L29 is one of the proteins from the large ribosomal subunit. L29 belongs to a family of ribosomal proteins of 63 to 138 amino-acid residues which, on the basis of sequence similarities [], groups: Red algal L29. Bacterial L29. Mammalian L35 Caenorhabditis elegans L35 (ZK652.4). Yeast L35. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1VSP_W 3MS1_Y 3MRZ_Y 3F1H_2 3PYT_Y 3PYO_Y 3D5D_2 3D5B_2 3PYR_Y 1VSA_W ....
Probab=27.29 E-value=1.4e+02 Score=18.03 Aligned_cols=19 Identities=32% Similarity=0.461 Sum_probs=8.6
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 041503 76 LSDKFRLLHKELEHTQLRS 94 (99)
Q Consensus 76 l~~k~~~l~~El~~~~~~~ 94 (99)
|.+++.+++.||-.-+++.
T Consensus 12 L~~~l~elk~eL~~Lr~q~ 30 (58)
T PF00831_consen 12 LQEKLEELKKELFNLRFQK 30 (58)
T ss_dssp HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 4444444445554444433
No 450
>COG3416 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=27.26 E-value=1.2e+02 Score=24.01 Aligned_cols=30 Identities=13% Similarity=0.369 Sum_probs=21.4
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 57 EKIDLLVEEVRKLTLEIERLSDKFRLLHKE 86 (99)
Q Consensus 57 ~k~~~l~~ei~e~~~ei~~l~~k~~~l~~E 86 (99)
+.+..++.-|..++.+|++|++++..|+.+
T Consensus 48 Q~vliqE~ALk~a~~~i~eLe~ri~~lq~~ 77 (233)
T COG3416 48 QRVLIQEQALKKASTQIKELEKRIAILQAG 77 (233)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 333444445778888999999888888765
No 451
>PF14723 SSFA2_C: Sperm-specific antigen 2 C-terminus
Probab=27.21 E-value=2.2e+02 Score=21.63 Aligned_cols=32 Identities=16% Similarity=0.149 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Q 041503 66 VRKLTLEIERLSDKFRLLHKELEHTQLRSKYG 97 (99)
Q Consensus 66 i~e~~~ei~~l~~k~~~l~~El~~~~~~~~~~ 97 (99)
+++|...-+.++.+.++|+.-|++..+...=|
T Consensus 147 aeQLQsLR~avRqElqELE~QL~DRl~~l~e~ 178 (179)
T PF14723_consen 147 AEQLQSLRSAVRQELQELEFQLEDRLLQLREQ 178 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcc
Confidence 44444444555556666666666666555433
No 452
>COG5185 HEC1 Protein involved in chromosome segregation, interacts with SMC proteins [Cell division and chromosome partitioning]
Probab=27.21 E-value=98 Score=27.38 Aligned_cols=32 Identities=28% Similarity=0.351 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 60 DLLVEEVRKLTLEIERLSDKFRLLHKELEHTQ 91 (99)
Q Consensus 60 ~~l~~ei~e~~~ei~~l~~k~~~l~~El~~~~ 91 (99)
.-|..||.+..+||+.|++++..|+.-|.+++
T Consensus 333 ~kl~~eie~kEeei~~L~~~~d~L~~q~~kq~ 364 (622)
T COG5185 333 EKLKSEIELKEEEIKALQSNIDELHKQLRKQG 364 (622)
T ss_pred HHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcC
Confidence 34455788888888888888888877766543
No 453
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=27.20 E-value=1.9e+02 Score=19.12 Aligned_cols=6 Identities=0% Similarity=0.589 Sum_probs=3.4
Q ss_pred Ccceee
Q 041503 34 NRKFWK 39 (99)
Q Consensus 34 gR~Fy~ 39 (99)
|.|+|.
T Consensus 36 gyR~Y~ 41 (108)
T cd01107 36 GYRYYS 41 (108)
T ss_pred CccccC
Confidence 555554
No 454
>PF15188 CCDC-167: Coiled-coil domain-containing protein 167
Probab=27.18 E-value=1.3e+02 Score=20.10 Aligned_cols=32 Identities=25% Similarity=0.326 Sum_probs=20.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 58 KIDLLVEEVRKLTLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 58 k~~~l~~ei~e~~~ei~~l~~k~~~l~~El~~ 89 (99)
....++.|...+...+.....+...|++|=-+
T Consensus 37 ~R~~lE~E~~~l~~~l~~~E~eL~~LrkENrK 68 (85)
T PF15188_consen 37 ARRSLEKELNELKEKLENNEKELKLLRKENRK 68 (85)
T ss_pred HHHHHHHHHHHHHHHhhccHHHHHHHHHhhhh
Confidence 44566666777766666666666677666444
No 455
>PF11382 DUF3186: Protein of unknown function (DUF3186); InterPro: IPR021522 This bacterial family of proteins has no known function.
Probab=27.12 E-value=1.5e+02 Score=23.51 Aligned_cols=29 Identities=21% Similarity=0.289 Sum_probs=17.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 61 LLVEEVRKLTLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 61 ~l~~ei~e~~~ei~~l~~k~~~l~~El~~ 89 (99)
.|+.+++++..+..+|+++++.++.+++.
T Consensus 36 ~l~~~~~~lr~e~~~l~~~~~~~~~~~~~ 64 (308)
T PF11382_consen 36 SLEDQFDSLREENDELRAELDALQAQLNA 64 (308)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445566666666666666666666654
No 456
>PF13094 CENP-Q: CENP-Q, a CENPA-CAD centromere complex subunit
Probab=27.12 E-value=2.3e+02 Score=19.95 Aligned_cols=18 Identities=22% Similarity=0.361 Sum_probs=8.2
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 041503 72 EIERLSDKFRLLHKELEH 89 (99)
Q Consensus 72 ei~~l~~k~~~l~~El~~ 89 (99)
.|+.|+++++.+..|+++
T Consensus 63 ~L~~Le~~~~~~~~e~~~ 80 (160)
T PF13094_consen 63 YLQELEKNAKALEREREE 80 (160)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 344444444444444443
No 457
>PRK00736 hypothetical protein; Provisional
Probab=27.10 E-value=1.7e+02 Score=18.37 Aligned_cols=23 Identities=13% Similarity=0.294 Sum_probs=11.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 041503 66 VRKLTLEIERLSDKFRLLHKELE 88 (99)
Q Consensus 66 i~e~~~ei~~l~~k~~~l~~El~ 88 (99)
|++|+..+-++..+|..|+..|.
T Consensus 21 ie~Ln~~v~~Qq~~i~~L~~ql~ 43 (68)
T PRK00736 21 IEELSDQLAEQWKTVEQMRKKLD 43 (68)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 45555555555555555544443
No 458
>PRK02935 hypothetical protein; Provisional
Probab=27.05 E-value=23 Score=24.94 Aligned_cols=24 Identities=21% Similarity=0.609 Sum_probs=16.7
Q ss_pred cccccCccccceeeeecCCCCCCcceeeCCCCC
Q 041503 12 LQVCNECGGQIELFTSHTTKNPNRKFWKCRVCK 44 (99)
Q Consensus 12 ~~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~ 44 (99)
.+.||.|+++.+++= | =..|..|+
T Consensus 70 qV~CP~C~K~TKmLG--------r-vD~CM~C~ 93 (110)
T PRK02935 70 QVICPSCEKPTKMLG--------R-VDACMHCN 93 (110)
T ss_pred eeECCCCCchhhhcc--------c-eeecCcCC
Confidence 389999999877652 2 23577775
No 459
>KOG3156 consensus Uncharacterized membrane protein [Function unknown]
Probab=27.01 E-value=1e+02 Score=24.14 Aligned_cols=23 Identities=22% Similarity=0.247 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 041503 71 LEIERLSDKFRLLHKELEHTQLR 93 (99)
Q Consensus 71 ~ei~~l~~k~~~l~~El~~~~~~ 93 (99)
.|...|++++++|+-||++..-.
T Consensus 116 sEF~~lr~e~EklkndlEk~ks~ 138 (220)
T KOG3156|consen 116 SEFANLRAENEKLKNDLEKLKSS 138 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 46667777788888888776543
No 460
>PRK09239 chorismate mutase; Provisional
Probab=26.96 E-value=2e+02 Score=19.37 Aligned_cols=34 Identities=3% Similarity=0.041 Sum_probs=23.1
Q ss_pred cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 54 FSNEKIDLLVEEVRKLTLEIERLSDKFRLLHKEL 87 (99)
Q Consensus 54 ~~~~k~~~l~~ei~e~~~ei~~l~~k~~~l~~El 87 (99)
-.+...+.++.+|++++.+|-.|-++=..+..++
T Consensus 7 ~~~~~L~~lR~~ID~ID~eIv~LLa~R~~l~~~I 40 (104)
T PRK09239 7 RAPAELAALRQSIDNIDAALIHMLAERFKCTQAV 40 (104)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456677888899999988877755544444443
No 461
>COG4839 FtsL Protein required for the initiation of cell division [Cell division and chromosome partitioning]
Probab=26.84 E-value=1.7e+02 Score=20.91 Aligned_cols=27 Identities=19% Similarity=0.220 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 63 VEEVRKLTLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 63 ~~ei~e~~~ei~~l~~k~~~l~~El~~ 89 (99)
..||-++...|.+.+..+..+++|+.+
T Consensus 66 q~ei~~Le~kIs~q~~e~~dlkqeV~d 92 (120)
T COG4839 66 QGEITDLESKISEQKTENDDLKQEVKD 92 (120)
T ss_pred HhHHHHHHHHHHHHHhhhhhHHHHHHH
Confidence 336777777777777777777777765
No 462
>PRK02195 V-type ATP synthase subunit D; Provisional
Probab=26.82 E-value=2.7e+02 Score=20.80 Aligned_cols=29 Identities=38% Similarity=0.568 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 65 EVRKLTLEIERLSDKFRLLHKELEHTQLR 93 (99)
Q Consensus 65 ei~e~~~ei~~l~~k~~~l~~El~~~~~~ 93 (99)
++-++..++..++.++..|-.|+++|+=+
T Consensus 127 ~ll~~~i~lAe~E~~l~~L~~ei~kT~rR 155 (201)
T PRK02195 127 ELVQLKIEAEVLQERLLLLEEELRKTTQR 155 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56677788888888999999999888643
No 463
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=26.69 E-value=28 Score=22.02 Aligned_cols=12 Identities=33% Similarity=1.019 Sum_probs=8.0
Q ss_pred ccccCcccccee
Q 041503 13 QVCNECGGQIEL 24 (99)
Q Consensus 13 ~~Cp~Cg~~~~~ 24 (99)
-+||.||..+.+
T Consensus 18 e~Cp~CG~~t~~ 29 (59)
T COG2260 18 EKCPVCGGDTKV 29 (59)
T ss_pred ccCCCCCCcccc
Confidence 368888876543
No 464
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=26.69 E-value=30 Score=30.95 Aligned_cols=23 Identities=26% Similarity=0.479 Sum_probs=15.0
Q ss_pred CcccccCccccceeeeecCCCCCCcceeeCCCCCe
Q 041503 11 SLQVCNECGGQIELFTSHTTKNPNRKFWKCRVCKN 45 (99)
Q Consensus 11 ~~~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~f 45 (99)
..-.|+.||...... +.||.|+-
T Consensus 679 ~~~~C~~CG~~~~~~------------~~CP~CG~ 701 (735)
T PRK07111 679 PVDRCPVCGYLGVIE------------DKCPKCGS 701 (735)
T ss_pred CCeecCCCCCCCCcC------------ccCcCCCC
Confidence 347899999533321 78998873
No 465
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=26.69 E-value=46 Score=21.23 Aligned_cols=32 Identities=22% Similarity=0.437 Sum_probs=19.1
Q ss_pred CCCCCCCC---cccccCccccceeeeecCCCCCCcceeeCCCCCe
Q 041503 4 STNESRNS---LQVCNECGGQIELFTSHTTKNPNRKFWKCRVCKN 45 (99)
Q Consensus 4 Ss~~~~~~---~~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~f 45 (99)
+|++-+.. -..|..||..+--..-.+ |..|+|
T Consensus 6 ~SfGKr~~k~tHt~CrRCG~~syh~qK~~----------CasCGy 40 (62)
T PRK04179 6 PSMGKRNKGKTHIRCRRCGRHSYNVRKKY----------CAACGF 40 (62)
T ss_pred cccccccCCcccchhcccCcccccccccc----------hhhcCC
Confidence 45553332 388988887644333332 888887
No 466
>PF01813 ATP-synt_D: ATP synthase subunit D ; InterPro: IPR002699 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The V-ATPases (or V1V0-ATPase) and A-ATPases (or A1A0-ATPase) are each composed of two linked complexes: the V1 or A1 complex contains the catalytic core that hydrolyses/synthesizes ATP, and the V0 or A0 complex that forms the membrane-spanning pore. The V- and A-ATPases both contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, , ]. The V- and A-ATPases more closely resemble one another in subunit structure than they do the F-ATPases, although the function of A-ATPases is closer to that of F-ATPases. This entry represents the D subunit found in V1 and A1 complexes of V- and A-ATPases, respectively. Subunit D appears to be located in the central stalk, whereas subunits E and G form part of the peripheral stalk connecting V1 and V0. This subunit is the most likely homologue to the gamma subunit of the F1 complex in F-ATPases, which undergoes rotation during ATP hydrolysis and serves an essential function in rotary catalysis [, ]. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0042626 ATPase activity, coupled to transmembrane movement of substances, 0046961 proton-transporting ATPase activity, rotational mechanism, 0015991 ATP hydrolysis coupled proton transport, 0033178 proton-transporting two-sector ATPase complex, catalytic domain; PDB: 3A5C_G 3A5D_G 3J0J_G 3AON_A.
Probab=26.65 E-value=1.9e+02 Score=21.14 Aligned_cols=30 Identities=43% Similarity=0.517 Sum_probs=19.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 58 KIDLLVEEVRKLTLEIERLSDKFRLLHKEL 87 (99)
Q Consensus 58 k~~~l~~ei~e~~~ei~~l~~k~~~l~~El 87 (99)
|.++|..|++++..++++++.++...-.+.
T Consensus 23 Krd~L~~e~~~~~~~~~~~r~~~~~~~~~a 52 (196)
T PF01813_consen 23 KRDALIREFRKLIKEAEELREELEELLKEA 52 (196)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 556777777777777777665555544443
No 467
>PRK13848 conjugal transfer protein TraC; Provisional
Probab=26.62 E-value=2.1e+02 Score=19.76 Aligned_cols=16 Identities=25% Similarity=0.492 Sum_probs=8.5
Q ss_pred HHHHHHHHHHHHHHHH
Q 041503 68 KLTLEIERLSDKFRLL 83 (99)
Q Consensus 68 e~~~ei~~l~~k~~~l 83 (99)
+++.+|++|+++.+.+
T Consensus 7 ~I~~eI~kLqe~lk~~ 22 (98)
T PRK13848 7 KIREEIAKLQEQLKQA 22 (98)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 4455566665555444
No 468
>smart00400 ZnF_CHCC zinc finger.
Probab=26.60 E-value=49 Score=19.42 Aligned_cols=27 Identities=26% Similarity=0.744 Sum_probs=17.5
Q ss_pred cccCccccceeeeecCCCCCCcceeeCCCCC
Q 041503 14 VCNECGGQIELFTSHTTKNPNRKFWKCRVCK 44 (99)
Q Consensus 14 ~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~ 44 (99)
.||.++....-+.. ||.+..|.|-+|+
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 58888875444444 3455667787775
No 469
>PF09738 DUF2051: Double stranded RNA binding protein (DUF2051); InterPro: IPR019139 This entry represents transcriptional repressors which preferentially bind to the GC-rich consensus sequence (5'-AGCCCCCGGCG-3') and may regulate expression of TNF, EGFR and PDGFA. They may control smooth muscle cell proliferation following artery injury through PDGFA repression and may also bind double-stranded RNA. They interact with the leucine-rich repeat domain of human flightless-I (FliI) protein.
Probab=26.56 E-value=1.2e+02 Score=24.49 Aligned_cols=34 Identities=32% Similarity=0.354 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCC
Q 041503 66 VRKLTLEIERLSDKFRLLHKELEHTQLRSKYGLS 99 (99)
Q Consensus 66 i~e~~~ei~~l~~k~~~l~~El~~~~~~~~~~~~ 99 (99)
++++..|-+.|.+++++|+..|+..+...+...+
T Consensus 221 LkKl~~eke~L~~qv~klk~qLee~~~~~~~~~~ 254 (302)
T PF09738_consen 221 LKKLADEKEELLEQVRKLKLQLEERQSEGRRQKS 254 (302)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhccccccc
No 470
>PF00816 Histone_HNS: H-NS histone family Partial NMR structure.; InterPro: IPR001801 The histone-like nucleoid-structuring (H-NS) protein belongs to a family of bacterial proteins that play a role in the formation of nucleoid structure and affect gene expression under certain conditions [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2LEV_A 1HNS_A 1LR1_B 1HNR_A 1NI8_A 1OV9_A 2JR1_A 3NR7_A 2L93_A 2L92_A.
Probab=26.50 E-value=1.8e+02 Score=18.70 Aligned_cols=15 Identities=33% Similarity=0.490 Sum_probs=7.1
Q ss_pred HHHHHHHHHHHHHHH
Q 041503 62 LVEEVRKLTLEIERL 76 (99)
Q Consensus 62 l~~ei~e~~~ei~~l 76 (99)
|.+++.+++.+++..
T Consensus 3 L~~~~~~l~~~~~~~ 17 (93)
T PF00816_consen 3 LEAQIKELEKEIEER 17 (93)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHH
Confidence 344455555444443
No 471
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=26.50 E-value=26 Score=29.54 Aligned_cols=36 Identities=14% Similarity=0.280 Sum_probs=22.4
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCeeEeccC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQWAED 51 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~W~De 51 (99)
+.||.|+-|-.-++.+...+-+ +.|..|+|--=.|-
T Consensus 97 VlC~~C~NPETel~itk~q~i~---~~CkACG~r~~~d~ 132 (400)
T KOG2767|consen 97 VLCPSCENPETELIITKKQTIS---LKCKACGFRSDMDL 132 (400)
T ss_pred eeCcCCCCCceeEEecccchhh---hHHHHcCCcccccc
Confidence 8999999875544444333333 45888876554444
No 472
>PRK05771 V-type ATP synthase subunit I; Validated
Probab=26.39 E-value=2.3e+02 Score=24.48 Aligned_cols=21 Identities=29% Similarity=0.419 Sum_probs=8.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 041503 65 EVRKLTLEIERLSDKFRLLHK 85 (99)
Q Consensus 65 ei~e~~~ei~~l~~k~~~l~~ 85 (99)
++.++..++++++++++++..
T Consensus 223 ~l~~l~~~~~~~~~~l~~~~~ 243 (646)
T PRK05771 223 ELEEIEKERESLLEELKELAK 243 (646)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 344444444444444444433
No 473
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=26.22 E-value=32 Score=17.59 Aligned_cols=9 Identities=33% Similarity=0.859 Sum_probs=6.4
Q ss_pred ccccCcccc
Q 041503 13 QVCNECGGQ 21 (99)
Q Consensus 13 ~~Cp~Cg~~ 21 (99)
..||.||+.
T Consensus 3 ~~C~~CgR~ 11 (25)
T PF13913_consen 3 VPCPICGRK 11 (25)
T ss_pred CcCCCCCCE
Confidence 568888863
No 474
>PRK04860 hypothetical protein; Provisional
Probab=26.19 E-value=23 Score=25.90 Aligned_cols=38 Identities=16% Similarity=0.467 Sum_probs=19.9
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCC-eeEeccC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCK-NFQWAED 51 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~-fF~W~De 51 (99)
-.| .|+............--|...|+|..|+ -|.+.++
T Consensus 120 Y~C-~C~~~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~~ 158 (160)
T PRK04860 120 YRC-KCQEHQLTVRRHNRVVRGEAVYRCRRCGETLVFKGE 158 (160)
T ss_pred EEc-CCCCeeCHHHHHHHHhcCCccEECCCCCceeEEecc
Confidence 678 5877211111111122356678898886 5555544
No 475
>PF05600 DUF773: Protein of unknown function (DUF773); InterPro: IPR008491 This family contains several eukaryotic sequences which are thought to be CDK5 activator-binding proteins, however, the function of this family is unknown.
Probab=26.09 E-value=1.8e+02 Score=25.02 Aligned_cols=32 Identities=25% Similarity=0.344 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 59 IDLLVEEVRKLTLEIERLSDKFRLLHKELEHT 90 (99)
Q Consensus 59 ~~~l~~ei~e~~~ei~~l~~k~~~l~~El~~~ 90 (99)
+..++.++.++.-++..|.++-+.|++++|.+
T Consensus 462 r~e~~~e~~~l~pkL~~l~~~Tr~Lq~~iE~~ 493 (507)
T PF05600_consen 462 RQEAQEEQQELEPKLDALVERTRELQKQIEAD 493 (507)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Confidence 33444455666666777777777777777765
No 476
>PRK02119 hypothetical protein; Provisional
Probab=26.03 E-value=1.8e+02 Score=18.47 Aligned_cols=24 Identities=8% Similarity=0.058 Sum_probs=12.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 66 VRKLTLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 66 i~e~~~ei~~l~~k~~~l~~El~~ 89 (99)
|++|+..+-+...+|..|+..|..
T Consensus 25 ie~LN~~v~~Qq~~id~L~~ql~~ 48 (73)
T PRK02119 25 LEELNQALIEQQFVIDKMQVQLRY 48 (73)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455555555555555555544443
No 477
>PF12718 Tropomyosin_1: Tropomyosin like; InterPro: IPR000533 Tropomyosins [], are a family of closely related proteins present in muscle and non-muscle cells. In striated muscle, tropomyosin mediate the interactions between the troponin complex and actin so as to regulate muscle contraction []. The role of tropomyosin in smooth muscle and non-muscle tissues is not clear. Tropomyosin is an alpha-helical protein that forms a coiled-coil structure of 2 parallel helices containing 2 sets of 7 alternating actin binding sites []. There are multiple cell-specific isoforms, created by differential splicing of the messenger RNA from one gene, but the proportions of the isoforms vary between different cell types. Muscle isoforms of tropomyosin are characterised by having 284 amino acid residues and a highly conserved N-terminal region, whereas non-muscle forms are generally smaller and are heterogeneous in their N-terminal region. This entry represents tropomyosin (Tmp) 1, 2 and 3. Within the yeast Tmp1 and Tmp2, biochemical and sequence analyses indicate that Tpm2 spans four actin monomers along a filament, whereas Tpm1 spans five. Despite its shorter length, Tpm2 can compete with Tpm1 for binding to F-actin. Over-expression of Tpm2 in vivo alters the axial budding of haploids to a bipolar pattern, and this can be partially suppressed by co-over-expression of Tpm1. This suggests distinct functions for the two tropomyosins, and indicates that the ratio between them is important for correct morphogenesis [].
Probab=26.02 E-value=2.4e+02 Score=19.96 Aligned_cols=20 Identities=35% Similarity=0.448 Sum_probs=8.9
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 041503 70 TLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 70 ~~ei~~l~~k~~~l~~El~~ 89 (99)
..+|..|..++..+..||+.
T Consensus 34 E~EI~sL~~K~~~lE~eld~ 53 (143)
T PF12718_consen 34 EQEITSLQKKNQQLEEELDK 53 (143)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 33444444444444444443
No 478
>PF10825 DUF2752: Protein of unknown function (DUF2752); InterPro: IPR021215 This family is conserved in bacteria. Many members are annotated as being putative membrane proteins.
Probab=25.92 E-value=30 Score=20.67 Aligned_cols=8 Identities=38% Similarity=0.862 Sum_probs=6.3
Q ss_pred ccccCccc
Q 041503 13 QVCNECGG 20 (99)
Q Consensus 13 ~~Cp~Cg~ 20 (99)
..||.||.
T Consensus 10 ~~CPgCG~ 17 (52)
T PF10825_consen 10 IPCPGCGM 17 (52)
T ss_pred CCCCCCcH
Confidence 56888885
No 479
>PHA03162 hypothetical protein; Provisional
Probab=25.88 E-value=1.3e+02 Score=21.99 Aligned_cols=22 Identities=27% Similarity=0.422 Sum_probs=11.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 041503 66 VRKLTLEIERLSDKFRLLHKEL 87 (99)
Q Consensus 66 i~e~~~ei~~l~~k~~~l~~El 87 (99)
+++|..||.+|+-.+.+|++-|
T Consensus 15 mEeLaaeL~kLqmENK~LKkkl 36 (135)
T PHA03162 15 MEDLAAEIAKLQLENKALKKKI 36 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4555555555555555554443
No 480
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=25.86 E-value=1.7e+02 Score=22.91 Aligned_cols=18 Identities=28% Similarity=0.580 Sum_probs=7.4
Q ss_pred HHHHHHHHHHHHHHHHHH
Q 041503 71 LEIERLSDKFRLLHKELE 88 (99)
Q Consensus 71 ~ei~~l~~k~~~l~~El~ 88 (99)
.+++.++.++..++.||.
T Consensus 52 ~e~e~le~qv~~~e~ei~ 69 (239)
T COG1579 52 IELEDLENQVSQLESEIQ 69 (239)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 334444444444444443
No 481
>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=25.73 E-value=29 Score=24.42 Aligned_cols=30 Identities=20% Similarity=0.632 Sum_probs=16.2
Q ss_pred ccccCccccceeeeecCCCCCCcceeeCCCCCeeEeccC
Q 041503 13 QVCNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQWAED 51 (99)
Q Consensus 13 ~~Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~W~De 51 (99)
|.||.|+-.-.- +...-|-||.|.+ .|...
T Consensus 3 p~CP~C~seytY--------~dg~~~iCpeC~~-EW~~~ 32 (109)
T TIGR00686 3 PPCPKCNSEYTY--------HDGTQLICPSCLY-EWNEN 32 (109)
T ss_pred CcCCcCCCcceE--------ecCCeeECccccc-ccccc
Confidence 567777753221 1223477887764 55433
No 482
>PRK14140 heat shock protein GrpE; Provisional
Probab=25.71 E-value=3e+02 Score=20.81 Aligned_cols=26 Identities=15% Similarity=0.470 Sum_probs=11.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 63 VEEVRKLTLEIERLSDKFRLLHKELE 88 (99)
Q Consensus 63 ~~ei~e~~~ei~~l~~k~~~l~~El~ 88 (99)
..+|.++..++.+|++++.-+.-|++
T Consensus 43 ~~~i~~l~~ei~elkd~~lR~~Ae~e 68 (191)
T PRK14140 43 QAKIAELEAKLDELEERYLRLQADFE 68 (191)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444444444444444444444433
No 483
>PRK09039 hypothetical protein; Validated
Probab=25.66 E-value=1.9e+02 Score=23.41 Aligned_cols=19 Identities=26% Similarity=0.373 Sum_probs=7.4
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 041503 69 LTLEIERLSDKFRLLHKEL 87 (99)
Q Consensus 69 ~~~ei~~l~~k~~~l~~El 87 (99)
+..+|+.|+.++..++.+|
T Consensus 142 L~~qI~aLr~Qla~le~~L 160 (343)
T PRK09039 142 LNQQIAALRRQLAALEAAL 160 (343)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3334444444443333333
No 484
>PRK14143 heat shock protein GrpE; Provisional
Probab=25.64 E-value=3e+02 Score=21.44 Aligned_cols=29 Identities=21% Similarity=0.436 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 60 DLLVEEVRKLTLEIERLSDKFRLLHKELE 88 (99)
Q Consensus 60 ~~l~~ei~e~~~ei~~l~~k~~~l~~El~ 88 (99)
..|..+|.++..+++.+++++.-+.-|.+
T Consensus 70 ~~l~~el~~l~~e~~elkd~~lR~~Adfe 98 (238)
T PRK14143 70 AQLEQELESLKQELEELNSQYMRIAADFD 98 (238)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444555555555555555544444443
No 485
>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=25.64 E-value=28 Score=22.25 Aligned_cols=14 Identities=29% Similarity=0.477 Sum_probs=8.6
Q ss_pred CCCCCCcceeeCCC
Q 041503 29 TTKNPNRKFWKCRV 42 (99)
Q Consensus 29 t~~NPgR~Fy~C~~ 42 (99)
+.+-|||-+|-|+.
T Consensus 32 ~~k~~GRGaYvc~~ 45 (78)
T PF04296_consen 32 SGKLPGRGAYVCPD 45 (78)
T ss_dssp TS---SEEEEEES-
T ss_pred CCCCCCCeEEEcCC
Confidence 44689999999984
No 486
>PF08181 DegQ: DegQ (SacQ) family; InterPro: IPR012554 This family consists of the DegQ (formerly sacQ) regulatory peptides. The DegQ family of peptides control the rates of synthesis of a class of both secreted and intracellular degradative enzymes in Bacillus subtilis. DegQ is 46 amino acids long and activates the synthesis of degradative enzymes. The expression of this peptide was shown to be subjected both to catabolite repression and DegS-DegU-mediated control. Thus allowing an increase in the rate of synthesis of degQ under conditions of nitrogen starvation [].
Probab=25.53 E-value=1.4e+02 Score=17.77 Aligned_cols=14 Identities=21% Similarity=0.432 Sum_probs=6.4
Q ss_pred HHHHHHHHHHHHHH
Q 041503 64 EEVRKLTLEIERLS 77 (99)
Q Consensus 64 ~ei~e~~~ei~~l~ 77 (99)
+||+|-+..+...+
T Consensus 18 ~eirett~sl~nin 31 (46)
T PF08181_consen 18 NEIRETTDSLRNIN 31 (46)
T ss_pred HHHHHHHHHHHHHH
Confidence 34444444444444
No 487
>KOG0977 consensus Nuclear envelope protein lamin, intermediate filament superfamily [Cell cycle control, cell division, chromosome partitioning; Nuclear structure]
Probab=25.36 E-value=1.8e+02 Score=25.66 Aligned_cols=32 Identities=25% Similarity=0.435 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 60 DLLVEEVRKLTLEIERLSDKFRLLHKELEHTQ 91 (99)
Q Consensus 60 ~~l~~ei~e~~~ei~~l~~k~~~l~~El~~~~ 91 (99)
..++.|+..+..++.+|...+..++++|..+.
T Consensus 165 ~~le~e~~~Lk~en~rl~~~l~~~r~~ld~Et 196 (546)
T KOG0977|consen 165 KALEDELKRLKAENSRLREELARARKQLDDET 196 (546)
T ss_pred HHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHH
Confidence 34444555555566666666666655555443
No 488
>PF02388 FemAB: FemAB family; InterPro: IPR003447 The femAB operon codes for two nearly identical approximately 50kDa proteins involved in the formation of the Staphylococcal pentaglycine interpeptide bridge in peptidoglycan []. These proteins are also considered as a factor influencing the level of methicillin resistance [].; GO: 0016755 transferase activity, transferring amino-acyl groups; PDB: 1XE4_A 1NE9_A 3GKR_A 1XIX_A 1P4N_A 1XF8_A 1LRZ_A.
Probab=25.29 E-value=2.4e+02 Score=23.10 Aligned_cols=19 Identities=21% Similarity=0.513 Sum_probs=10.4
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 041503 73 IERLSDKFRLLHKELEHTQ 91 (99)
Q Consensus 73 i~~l~~k~~~l~~El~~~~ 91 (99)
++++++++..+.+++++..
T Consensus 275 ~~~~~~q~~~~~k~~~~~~ 293 (406)
T PF02388_consen 275 LKELEEQLASLEKRIEEAE 293 (406)
T ss_dssp HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 5555555556655555543
No 489
>PF01302 CAP_GLY: CAP-Gly domain; InterPro: IPR000938 Cytoskeleton-associated proteins (CAP) are made of three distinct parts, an N-terminal section that is most probably globular and contains the CAP-Gly domain, a large central region predicted to be in an alpha-helical coiled-coil conformation and, finally, a short C-terminal globular domain. The CAP-Gly domain is a conserved, glycine-rich domain of about 42 residues found in some CAPs []. Proteins known to contain this domain include restin (also known as cytoplasmic linker protein-170 or CLIP-170), a 160 kDa protein associated with intermediate filaments and that links endocytic vesicles to microtubules; vertebrate dynactin (150 kDa dynein-associated polypeptide; DAP) and Drosophila glued, a major component of activator I; yeast protein BIK1, which seems to be required for the formation or stabilisation of microtubules during mitosis and for spindle pole body fusion during conjugation; yeast protein NIP100 (NIP80); human protein CKAP1/TFCB; Schizosaccharomyces pombe protein alp11 and Caenorhabditis elegans hypothetical protein F53F4.3. The latter proteins contain a N-terminal ubiquitin domain and a C-terminal CAP-Gly domain. The crystal structure of the CAP-Gly domain of C. elegans F53F4.3 protein, solved by single wavelength sulphur-anomalous phasing, revealed a novel protein fold containing three beta-sheets. The most conserved sequence, GKNDG, is located in two consecutive sharp turns on the surface, forming the entrance to a groove. Residues in the groove are highly conserved as measured from the information content of the aligned sequences. The C-terminal tail of another molecule in the crystal is bound in this groove []. ; PDB: 2CP6_A 2E4H_A 2E3H_A 3E2U_B 2HL3_B 3TQ7_Q 2HKQ_B 2HQH_A 2HKN_B 2HL5_C ....
Probab=25.28 E-value=32 Score=21.54 Aligned_cols=15 Identities=13% Similarity=0.508 Sum_probs=10.8
Q ss_pred CcceeeCC-CCCeeEe
Q 041503 34 NRKFWKCR-VCKNFQW 48 (99)
Q Consensus 34 gR~Fy~C~-~C~fF~W 48 (99)
|++||.|+ .+..|.=
T Consensus 49 G~rYF~c~~~~G~Fv~ 64 (69)
T PF01302_consen 49 GKRYFECPPNHGIFVR 64 (69)
T ss_dssp TEESS-SSTTTEEEEE
T ss_pred CEEEeeeCCCCEEEec
Confidence 69999997 7777753
No 490
>PF04194 PDCD2_C: Programmed cell death protein 2, C-terminal putative domain ; InterPro: IPR007320 PDCD2 is localized predominantly in the cytosol of cells situated at the opposite pole of the germinal centre from the centroblasts as well as in cells in the mantle zone. It has been shown to interact with BCL6, an evolutionarily conserved Kruppel-type zinc finger protein that functions as a strong transcriptional repressor and is required for germinal centre development. The rat homologue, Rp8, is associated with programmed cell death in thymocytes.; GO: 0005737 cytoplasm
Probab=25.16 E-value=51 Score=23.76 Aligned_cols=19 Identities=21% Similarity=0.618 Sum_probs=11.5
Q ss_pred CCCCCCCCCcccccCcccc
Q 041503 3 SSTNESRNSLQVCNECGGQ 21 (99)
Q Consensus 3 SSs~~~~~~~~~Cp~Cg~~ 21 (99)
+.........+.|+.||.+
T Consensus 88 ~~~~~~~~~ip~C~~Cg~~ 106 (164)
T PF04194_consen 88 STPIPPESDIPKCENCGSP 106 (164)
T ss_pred CCCCCccccCCCCccCCCc
Confidence 3333333336899999963
No 491
>PRK02793 phi X174 lysis protein; Provisional
Probab=25.14 E-value=1.9e+02 Score=18.33 Aligned_cols=39 Identities=10% Similarity=0.152 Sum_probs=0.0
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 041503 57 EKIDLLVEEVRKLTLEIERLSDKFRLLHKELEHTQLRSK 95 (99)
Q Consensus 57 ~k~~~l~~ei~e~~~ei~~l~~k~~~l~~El~~~~~~~~ 95 (99)
.+.+-++.-|++|+..+-++..+|..|+..|..-.-+.+
T Consensus 15 ~~lafQe~tIe~Ln~~v~~Qq~~I~~L~~~l~~L~~rl~ 53 (72)
T PRK02793 15 SRLAFQEITIEELNVTVTAHEMEMAKLRDHLRLLTEKLK 53 (72)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 492
>PF10146 zf-C4H2: Zinc finger-containing protein ; InterPro: IPR018482 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 family of proteins which appears to have a highly conserved zinc finger domain at the C-terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members of this family are annotated as being tumour-associated antigen HCA127 in humans, but this could not be confirmed.
Probab=25.12 E-value=2.2e+02 Score=22.03 Aligned_cols=33 Identities=18% Similarity=0.274 Sum_probs=0.0
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 57 EKIDLLVEEVRKLTLEIERLSDKFRLLHKELEH 89 (99)
Q Consensus 57 ~k~~~l~~ei~e~~~ei~~l~~k~~~l~~El~~ 89 (99)
.++..|++.|.+...+.++..+.+..+..|+..
T Consensus 60 ~DIn~lE~iIkqa~~er~~~~~~i~r~~eey~~ 92 (230)
T PF10146_consen 60 QDINTLENIIKQAESERNKRQEKIQRLYEEYKP 92 (230)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 493
>KOG3277 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.09 E-value=39 Score=25.37 Aligned_cols=33 Identities=21% Similarity=0.415 Sum_probs=0.0
Q ss_pred ccCccccceeeeecCCCCCCcceeeCCCCCeeE
Q 041503 15 CNECGGQIELFTSHTTKNPNRKFWKCRVCKNFQ 47 (99)
Q Consensus 15 Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C~fF~ 47 (99)
|.-||..-...+|+..---|=-+..||+|+-+.
T Consensus 82 CkvCntRs~ktisk~AY~~GvVivqC~gC~~~H 114 (165)
T KOG3277|consen 82 CKVCNTRSTKTISKQAYEKGVVIVQCPGCKNHH 114 (165)
T ss_pred eeccCCccccccChhhhhCceEEEECCCCccce
No 494
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=25.04 E-value=50 Score=23.03 Aligned_cols=21 Identities=19% Similarity=0.509 Sum_probs=0.0
Q ss_pred CCCcccccCccc--cceeeeecC
Q 041503 9 RNSLQVCNECGG--QIELFTSHT 29 (99)
Q Consensus 9 ~~~~~~Cp~Cg~--~~~~~tS~t 29 (99)
..|...||.||. .....+.+|
T Consensus 44 evG~~~cP~Cge~~~~a~vva~t 66 (102)
T PF04475_consen 44 EVGDTICPKCGEELDSAFVVADT 66 (102)
T ss_pred ecCcccCCCCCCccCceEEEecc
No 495
>PF04111 APG6: Autophagy protein Apg6; InterPro: IPR007243 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway [].; GO: 0006914 autophagy; PDB: 3Q8T_A 3VP7_A 4DDP_A.
Probab=24.98 E-value=3.2e+02 Score=21.83 Aligned_cols=39 Identities=28% Similarity=0.358 Sum_probs=0.0
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 041503 57 EKIDLLVEEVRKLTLEIERLSDKFRLLHKELEHTQLRSK 95 (99)
Q Consensus 57 ~k~~~l~~ei~e~~~ei~~l~~k~~~l~~El~~~~~~~~ 95 (99)
.....+..|.+++..+++.|.++...+..|++.-.....
T Consensus 50 ~el~~le~Ee~~l~~eL~~LE~e~~~l~~el~~le~e~~ 88 (314)
T PF04111_consen 50 EELEKLEQEEEELLQELEELEKEREELDQELEELEEELE 88 (314)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 496
>TIGR01807 CM_P2 chorismate mutase domain of proteobacterial P-protein, clade 2. This model represents one of two separate clades of the chorismate mutase domain of the gamma and beta and epsilon proteobacterial "P-protein" which contains an N-terminal chorismate mutase domain and a C-terminal prephenate dehydratase domain. It is also found in Aquifex aolicus.
Probab=24.92 E-value=1.8e+02 Score=18.06 Aligned_cols=28 Identities=11% Similarity=0.092 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 041503 60 DLLVEEVRKLTLEIERLSDKFRLLHKEL 87 (99)
Q Consensus 60 ~~l~~ei~e~~~ei~~l~~k~~~l~~El 87 (99)
+.++++|++++.+|-.|=++=..+..++
T Consensus 2 ~~lR~~ID~iD~~iv~Ll~~R~~~~~~i 29 (76)
T TIGR01807 2 EELRNKIDAIDDRILDLLSERATYAQAV 29 (76)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 497
>PF04568 IATP: Mitochondrial ATPase inhibitor, IATP; InterPro: IPR007648 ATP synthase inhibitor prevents the enzyme from switching to ATP hydrolysis during collapse of the electrochemical gradient, for example during oxygen deprivation [] ATP synthase inhibitor forms a one to one complex with the F1 ATPase, possibly by binding at the alpha-beta interface. It is thought to inhibit ATP synthesis by preventing the release of ATP []. The minimum inhibitory region for bovine inhibitor (P01096 from SWISSPROT) is from residues 39 to 72 []. The inhibitor has two oligomeric states, dimer (the active state) and tetramer. At low pH , the inhibitor forms a dimer via antiparallel coiled coil interactions between the C-terminal regions of two monomers. At high pH, the inhibitor forms tetramers and higher oligomers by coiled coil interactions involving the N terminus and inhibitory region, thus preventing the inhibitory activity []. ; GO: 0004857 enzyme inhibitor activity, 0045980 negative regulation of nucleotide metabolic process, 0005739 mitochondrion; PDB: 1GMJ_B 1OHH_H 1HF9_B 2V7Q_J.
Probab=24.92 E-value=2.3e+02 Score=19.34 Aligned_cols=35 Identities=23% Similarity=0.331 Sum_probs=0.0
Q ss_pred chhhHHHHHHHH---HHHHHHHHHHHHHHHH----HHHHHHH
Q 041503 55 SNEKIDLLVEEV---RKLTLEIERLSDKFRL----LHKELEH 89 (99)
Q Consensus 55 ~~~k~~~l~~ei---~e~~~ei~~l~~k~~~----l~~El~~ 89 (99)
+|.+......+. ..-.++|+.|+.++.+ .+++|++
T Consensus 53 ~f~krE~A~E~~Y~r~~EkEqL~~Lk~kl~~e~~~~~k~i~~ 94 (100)
T PF04568_consen 53 AFGKREAAQEEQYFRKKEKEQLKKLKEKLKEEIEHHRKEIDE 94 (100)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ccchHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 498
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=24.88 E-value=54 Score=25.33 Aligned_cols=30 Identities=23% Similarity=0.347 Sum_probs=0.0
Q ss_pred ccCccccceeeeecCCCCCC-----cceeeCCCCCe
Q 041503 15 CNECGGQIELFTSHTTKNPN-----RKFWKCRVCKN 45 (99)
Q Consensus 15 Cp~Cg~~~~~~tS~t~~NPg-----R~Fy~C~~C~f 45 (99)
||-||. ....+....+-|- =..+.|..|+|
T Consensus 17 CPvCg~-~l~~~~~~~~IPyFG~V~i~t~~C~~CgY 51 (201)
T COG1779 17 CPVCGG-TLKAHMYLYDIPYFGEVLISTGVCERCGY 51 (201)
T ss_pred CCcccc-eeeEEEeeecCCccceEEEEEEEccccCC
No 499
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=24.71 E-value=26 Score=26.55 Aligned_cols=19 Identities=37% Similarity=0.938 Sum_probs=0.0
Q ss_pred ccCccccceeeeecCCCCCCcceeeCCCC
Q 041503 15 CNECGGQIELFTSHTTKNPNRKFWKCRVC 43 (99)
Q Consensus 15 Cp~Cg~~~~~~tS~t~~NPgR~Fy~C~~C 43 (99)
||.||.+....+.+- |+.|
T Consensus 1 C~~CG~~~~~~~~~l----------C~~C 19 (236)
T PF04981_consen 1 CPRCGREIEPLIDGL----------CPDC 19 (236)
T ss_pred CCCCCCCCCCccccc----------ChHH
No 500
>PF10211 Ax_dynein_light: Axonemal dynein light chain; InterPro: IPR019347 Axonemal dynein light chain proteins play a dynamic role in flagellar and cilial motility. Eukaryotic cilia and flagella are complex organelles consisting of a core structure, the axoneme, which is composed of nine microtubule doublets forming a cylinder that surrounds a pair of central singlet microtubules. This ultra-structural arrangement seems to be one of the most stable micro-tubular assemblies known and is responsible for the flagellar and ciliary movement of a large number of organisms ranging from protozoan to mammals. This light chain interacts directly with the N-terminal half of the heavy chains [].
Probab=24.66 E-value=2.9e+02 Score=20.40 Aligned_cols=36 Identities=28% Similarity=0.353 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 041503 60 DLLVEEVRKLTLEIERLSDKFRLLHKELEHTQLRSK 95 (99)
Q Consensus 60 ~~l~~ei~e~~~ei~~l~~k~~~l~~El~~~~~~~~ 95 (99)
..+..+|.++..+++.|..++..++..++...-+..
T Consensus 123 ~~l~~~i~~L~~e~~~L~~~~~~l~~~~e~~ek~~~ 158 (189)
T PF10211_consen 123 QELEEEIEELEEEKEELEKQVQELKNKCEQLEKREE 158 (189)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Done!