Query 010992
Match_columns 496
No_of_seqs 115 out of 177
Neff 2.5
Searched_HMMs 46136
Date Fri Mar 29 06:53:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/010992.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/010992hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1142 Transcription initiati 100.0 3.3E-47 7.2E-52 366.6 11.1 215 268-489 25-242 (258)
2 PF03847 TFIID_20kDa: Transcri 100.0 1.6E-30 3.5E-35 208.1 7.1 68 403-470 1-68 (68)
3 COG5624 TAF61 Transcription in 99.9 5.1E-29 1.1E-33 253.4 0.1 102 387-489 370-473 (505)
4 cd07981 TAF12 TATA Binding Pro 99.9 7.8E-26 1.7E-30 180.6 9.0 72 401-472 1-72 (72)
5 PLN00035 histone H4; Provision 98.8 1.3E-08 2.9E-13 88.5 8.9 74 402-477 30-103 (103)
6 cd00076 H4 Histone H4, one of 98.8 2.2E-08 4.8E-13 84.3 8.4 74 400-475 12-85 (85)
7 PTZ00015 histone H4; Provision 98.8 3E-08 6.5E-13 86.1 8.9 76 398-475 27-102 (102)
8 COG2036 HHT1 Histones H3 and H 98.6 8.6E-08 1.9E-12 81.8 6.0 71 396-467 14-84 (91)
9 PF00125 Histone: Core histone 98.4 5E-07 1.1E-11 70.8 5.5 68 399-466 3-74 (75)
10 smart00803 TAF TATA box bindin 98.3 2E-06 4.4E-11 68.8 7.8 64 401-465 2-65 (65)
11 cd07979 TAF9 TATA Binding Prot 98.3 3.5E-06 7.6E-11 73.9 8.2 68 405-473 5-72 (117)
12 smart00417 H4 Histone H4. 98.2 3E-06 6.5E-11 70.1 6.6 64 398-462 10-73 (74)
13 PF00808 CBFD_NFYB_HMF: Histon 98.1 7.8E-06 1.7E-10 63.5 7.0 63 402-464 3-65 (65)
14 KOG3467 Histone H4 [Chromatin 98.1 8.1E-06 1.8E-10 70.9 7.5 78 398-477 26-103 (103)
15 smart00428 H3 Histone H3. 98.1 8.5E-06 1.8E-10 71.3 7.0 69 396-464 24-98 (105)
16 PLN00161 histone H3; Provision 97.9 4.2E-05 9.2E-10 69.8 7.2 78 396-474 50-132 (135)
17 PLN00121 histone H3; Provision 97.7 7.2E-05 1.6E-09 68.3 6.4 69 396-464 57-129 (136)
18 PF02291 TFIID-31kDa: Transcri 97.7 0.00011 2.3E-09 66.3 7.3 73 400-473 9-83 (129)
19 smart00576 BTP Bromodomain tra 97.7 0.00028 6E-09 57.3 8.6 68 403-472 8-75 (77)
20 PTZ00018 histone H3; Provision 97.6 9.8E-05 2.1E-09 67.4 5.9 69 396-464 57-129 (136)
21 cd08050 TAF6 TATA Binding Prot 97.6 0.00041 8.8E-09 69.7 9.7 75 404-479 2-76 (343)
22 PLN00160 histone H3; Provision 97.5 0.00018 3.8E-09 62.6 6.0 69 396-464 16-89 (97)
23 PF02269 TFIID-18kDa: Transcri 97.4 0.00016 3.5E-09 61.2 4.2 61 407-467 7-67 (93)
24 PF15630 CENP-S: Kinetochore c 97.2 0.00072 1.6E-08 56.2 6.0 61 407-467 11-73 (76)
25 smart00427 H2B Histone H2B. 97.2 0.0016 3.4E-08 56.2 7.6 60 407-466 7-66 (89)
26 PF02969 TAF: TATA box binding 97.1 0.0028 6.1E-08 51.6 7.5 64 401-465 3-66 (66)
27 KOG0869 CCAAT-binding factor, 96.9 0.0034 7.3E-08 59.3 7.2 71 396-466 27-98 (168)
28 PF07524 Bromo_TP: Bromodomain 96.8 0.0088 1.9E-07 48.1 8.5 64 407-472 12-75 (77)
29 PLN00158 histone H2B; Provisio 96.8 0.0047 1E-07 55.6 7.6 59 407-465 33-91 (116)
30 PTZ00463 histone H2B; Provisio 96.7 0.0058 1.2E-07 55.1 7.5 65 407-475 34-98 (117)
31 KOG3334 Transcription initiati 96.6 0.01 2.2E-07 55.3 8.0 68 406-474 18-85 (148)
32 cd07978 TAF13 The TATA Binding 96.6 0.014 3E-07 49.9 8.2 62 405-467 6-67 (92)
33 cd08048 TAF11 TATA Binding Pro 96.5 0.014 3E-07 49.4 8.1 65 402-467 17-84 (85)
34 cd00074 H2A Histone 2A; H2A is 96.3 0.014 3.1E-07 51.9 7.0 69 398-466 17-85 (115)
35 KOG0871 Class 2 transcription 96.1 0.031 6.7E-07 52.6 8.3 74 394-467 5-79 (156)
36 KOG1744 Histone H2B [Chromatin 95.8 0.026 5.7E-07 51.6 6.8 60 407-466 43-102 (127)
37 KOG2549 Transcription initiati 95.7 0.052 1.1E-06 59.3 9.6 93 396-489 5-98 (576)
38 KOG3423 Transcription initiati 95.7 0.056 1.2E-06 51.7 8.5 69 403-472 69-169 (176)
39 PF09415 CENP-X: CENP-S associ 95.7 0.013 2.9E-07 48.2 3.9 60 405-464 3-65 (72)
40 PF04719 TAFII28: hTAFII28-lik 95.2 0.082 1.8E-06 45.6 7.1 60 402-461 24-84 (90)
41 PF15511 CENP-T: Centromere ki 94.7 0.057 1.2E-06 56.2 5.9 60 400-459 350-414 (414)
42 KOG0870 DNA polymerase epsilon 94.7 0.047 1E-06 52.1 4.7 85 400-484 9-95 (172)
43 PF03540 TFIID_30kDa: Transcri 94.1 0.23 5E-06 39.3 6.7 50 401-451 2-51 (51)
44 PF05236 TAF4: Transcription i 94.0 0.051 1.1E-06 52.7 3.7 59 396-454 38-99 (264)
45 KOG1745 Histones H3 and H4 [Ch 93.9 0.042 9E-07 50.8 2.6 69 397-465 59-131 (137)
46 cd08045 TAF4 TATA Binding Prot 93.8 0.17 3.7E-06 47.9 6.5 59 395-453 38-99 (212)
47 COG5094 TAF9 Transcription ini 92.8 0.36 7.7E-06 44.9 6.7 71 406-477 19-92 (145)
48 COG5162 Transcription initiati 92.6 0.41 8.8E-06 46.2 7.2 47 405-451 73-137 (197)
49 COG5248 TAF19 Transcription in 92.0 0.71 1.5E-05 42.2 7.5 59 407-467 15-73 (126)
50 COG5150 Class 2 transcription 91.8 0.76 1.6E-05 42.9 7.6 71 396-466 6-77 (148)
51 KOG3901 Transcription initiati 91.1 1.1 2.3E-05 40.5 7.6 64 400-467 9-72 (109)
52 smart00350 MCM minichromosome 88.9 1.6 3.5E-05 46.2 8.1 67 399-465 415-502 (509)
53 TIGR02902 spore_lonB ATP-depen 88.8 1.2 2.6E-05 47.6 7.2 66 401-466 262-331 (531)
54 PRK00411 cdc6 cell division co 88.7 2.1 4.5E-05 42.3 8.3 66 402-467 207-282 (394)
55 TIGR03015 pepcterm_ATPase puta 88.3 1.8 3.8E-05 40.2 7.1 67 400-466 190-265 (269)
56 smart00414 H2A Histone 2A. 88.2 1.5 3.3E-05 38.7 6.3 68 399-466 7-74 (106)
57 COG5095 TAF6 Transcription ini 87.6 2.1 4.6E-05 45.2 7.9 76 400-477 4-80 (450)
58 TIGR02928 orc1/cdc6 family rep 86.2 2.8 6.1E-05 40.9 7.5 66 402-467 199-274 (365)
59 COG5208 HAP5 CCAAT-binding fac 86.2 1.1 2.3E-05 45.2 4.6 65 403-467 111-175 (286)
60 KOG3219 Transcription initiati 85.5 1.2 2.6E-05 43.5 4.5 67 399-466 110-177 (195)
61 KOG4336 TBP-associated transcr 84.9 2.7 5.8E-05 43.7 6.9 70 406-477 10-79 (323)
62 KOG2680 DNA helicase TIP49, TB 84.1 2.7 5.8E-05 44.6 6.6 64 403-466 359-428 (454)
63 COG1224 TIP49 DNA helicase TIP 83.5 2 4.4E-05 46.1 5.5 63 403-465 362-430 (450)
64 PTZ00017 histone H2A; Provisio 81.2 3.7 8E-05 38.1 5.7 69 398-466 24-92 (134)
65 PTZ00171 acyl carrier protein; 80.2 0.46 9.9E-06 43.8 -0.5 45 440-484 90-134 (148)
66 TIGR00635 ruvB Holliday juncti 77.7 7.6 0.00017 37.1 6.9 74 402-476 159-237 (305)
67 KOG1748 Acyl carrier protein/N 77.6 2 4.3E-05 39.8 2.8 64 422-485 52-118 (131)
68 TIGR02639 ClpA ATP-dependent C 77.2 3.9 8.5E-05 45.2 5.4 79 403-481 346-443 (731)
69 PRK13407 bchI magnesium chelat 77.0 7.2 0.00016 40.0 6.8 73 399-472 232-311 (334)
70 KOG3489 Mitochondrial import i 74.5 11 0.00024 33.1 6.3 50 403-452 23-82 (86)
71 PRK12449 acyl carrier protein; 74.4 0.95 2.1E-05 36.0 -0.1 44 440-483 25-68 (80)
72 TIGR02030 BchI-ChlI magnesium 73.0 8.8 0.00019 39.4 6.3 70 402-472 238-314 (337)
73 TIGR02420 dksA RNA polymerase- 73.0 3.2 6.9E-05 35.9 2.8 30 455-496 63-92 (110)
74 TIGR00368 Mg chelatase-related 72.0 9.7 0.00021 41.0 6.6 48 418-465 444-497 (499)
75 CHL00124 acpP acyl carrier pro 71.8 3 6.4E-05 33.4 2.1 30 445-474 30-59 (82)
76 TIGR02442 Cob-chelat-sub cobal 71.7 9.6 0.00021 41.8 6.6 58 412-469 242-306 (633)
77 PTZ00183 centrin; Provisional 71.3 35 0.00075 28.8 8.5 73 395-470 27-121 (158)
78 PLN00154 histone H2A; Provisio 70.1 14 0.00031 34.5 6.4 68 399-466 36-104 (136)
79 PRK05350 acyl carrier protein; 69.9 3.1 6.7E-05 33.7 1.8 25 450-474 36-60 (82)
80 KOG1658 DNA polymerase epsilon 69.2 3.5 7.5E-05 39.5 2.3 67 405-472 63-130 (162)
81 PF13335 Mg_chelatase_2: Magne 69.1 20 0.00044 30.6 6.7 47 418-464 41-93 (96)
82 cd01145 TroA_c Periplasmic bin 68.6 6.4 0.00014 36.5 3.9 77 401-477 111-192 (203)
83 KOG1659 Class 2 transcription 68.6 13 0.00027 37.3 6.0 55 423-477 35-97 (224)
84 cd03565 VHS_Tom1 VHS domain fa 68.2 13 0.00028 33.6 5.6 46 426-474 73-119 (141)
85 PF00745 GlutR_dimer: Glutamyl 67.7 4.8 0.0001 32.9 2.6 62 404-470 39-100 (101)
86 PRK09184 acyl carrier protein; 67.7 4.1 8.8E-05 34.6 2.2 39 447-485 37-75 (89)
87 PLN00157 histone H2A; Provisio 67.4 12 0.00027 34.7 5.4 69 398-466 23-91 (132)
88 PTZ00361 26 proteosome regulat 65.9 8.8 0.00019 40.8 4.7 65 403-467 355-424 (438)
89 COG0593 DnaA ATPase involved i 65.0 9.4 0.0002 40.7 4.7 72 400-475 299-371 (408)
90 TIGR02031 BchD-ChlD magnesium 64.8 11 0.00024 41.2 5.3 72 400-472 185-263 (589)
91 PLN02641 anthranilate phosphor 63.7 13 0.00027 38.5 5.2 76 407-483 4-89 (343)
92 cd05022 S-100A13 S-100A13: S-1 63.6 24 0.00052 29.9 6.0 55 397-452 21-86 (89)
93 cd06845 Bcl-2_like Apoptosis r 63.6 16 0.00034 32.4 5.2 47 404-453 51-107 (144)
94 PRK08727 hypothetical protein; 63.4 27 0.00058 33.2 7.0 64 403-467 163-231 (233)
95 CHL00081 chlI Mg-protoporyphyr 63.3 22 0.00048 36.9 6.9 72 400-472 249-327 (350)
96 PLN00156 histone H2AX; Provisi 62.0 21 0.00046 33.5 5.9 68 399-466 27-94 (139)
97 PRK07639 acyl carrier protein; 62.0 3.3 7.2E-05 34.5 0.7 31 444-474 30-60 (86)
98 PF00616 RasGAP: GTPase-activa 61.4 13 0.00028 33.4 4.3 26 423-448 97-122 (197)
99 PRK07117 acyl carrier protein; 60.7 2.1 4.6E-05 35.5 -0.7 40 444-484 30-69 (79)
100 TIGR00362 DnaA chromosomal rep 60.7 14 0.0003 37.6 4.8 70 399-472 285-362 (405)
101 PRK00080 ruvB Holliday junctio 60.3 23 0.0005 35.0 6.2 80 401-481 179-263 (328)
102 PF08546 ApbA_C: Ketopantoate 60.1 9.9 0.00022 32.1 3.2 55 419-473 57-112 (125)
103 TIGR00764 lon_rel lon-related 59.7 34 0.00073 37.8 7.9 62 404-465 311-389 (608)
104 PF07261 DnaB_2: Replication i 58.7 43 0.00094 26.0 6.3 48 417-466 10-59 (77)
105 PRK07081 acyl carrier protein; 58.5 3.9 8.4E-05 33.8 0.5 24 451-474 32-55 (83)
106 PRK15380 pathogenicity island 58.4 13 0.00028 38.4 4.2 70 396-466 113-191 (319)
107 PF04867 DUF643: Protein of un 58.2 14 0.00029 33.7 3.8 35 422-456 55-89 (114)
108 PRK13406 bchD magnesium chelat 57.4 43 0.00093 37.1 8.2 70 402-472 179-255 (584)
109 PRK05828 acyl carrier protein; 57.0 2 4.4E-05 36.0 -1.4 36 449-484 34-69 (84)
110 TIGR02890 spore_yteA sporulati 56.3 17 0.00036 34.1 4.2 29 456-496 70-98 (159)
111 TIGR00517 acyl_carrier acyl ca 55.6 3.8 8.2E-05 32.4 -0.0 34 450-483 33-66 (77)
112 PF00493 MCM: MCM2/3/5 family 55.4 7.3 0.00016 39.2 1.9 64 400-465 240-324 (331)
113 PRK09862 putative ATP-dependen 55.1 35 0.00076 37.2 7.0 49 418-466 437-491 (506)
114 PF10789 Phage_RpbA: Phage RNA 54.9 5.5 0.00012 36.0 0.9 39 418-456 48-86 (108)
115 PRK06508 acyl carrier protein; 54.3 10 0.00022 32.6 2.3 34 443-476 26-59 (93)
116 PRK10778 dksA RNA polymerase-b 54.1 10 0.00022 35.3 2.4 29 456-496 95-123 (151)
117 COG1734 DksA DnaK suppressor p 54.0 12 0.00026 33.9 2.8 29 456-496 64-92 (120)
118 TIGR03772 anch_rpt_subst ancho 53.9 13 0.00028 40.3 3.5 76 401-476 314-396 (479)
119 cd00052 EH Eps15 homology doma 53.8 57 0.0012 23.9 6.0 20 395-414 9-28 (67)
120 PRK00149 dnaA chromosomal repl 53.7 21 0.00046 37.0 4.9 28 446-473 378-406 (450)
121 PF07030 DUF1320: Protein of u 53.7 36 0.00079 30.2 5.7 37 403-440 12-48 (130)
122 PRK07360 FO synthase subunit 2 53.5 20 0.00044 36.7 4.7 76 403-478 3-82 (371)
123 TIGR01765 tspaseT_teng_N trans 53.3 20 0.00043 28.9 3.7 47 419-470 7-53 (73)
124 PRK08172 putative acyl carrier 53.0 5.4 0.00012 33.1 0.5 43 443-485 27-69 (82)
125 PLN00153 histone H2A; Provisio 52.9 34 0.00074 31.8 5.6 68 399-466 22-89 (129)
126 cd06457 M3A_MIP Peptidase M3 m 52.7 21 0.00046 37.6 4.8 62 421-483 62-129 (458)
127 PRK12402 replication factor C 52.6 25 0.00054 33.7 4.9 63 402-466 184-248 (337)
128 PRK04195 replication factor C 52.2 30 0.00064 36.5 5.8 69 402-472 160-230 (482)
129 cd05030 calgranulins Calgranul 52.1 35 0.00075 28.2 5.0 45 396-440 21-78 (88)
130 PF06570 DUF1129: Protein of u 51.9 17 0.00037 34.2 3.6 35 404-438 7-41 (206)
131 cd01020 TroA_b Metal binding p 51.9 19 0.00041 34.8 4.0 73 401-473 98-175 (264)
132 PF01432 Peptidase_M3: Peptida 51.5 26 0.00057 36.1 5.1 67 416-483 62-133 (458)
133 PRK05087 D-alanine--poly(phosp 51.0 8.5 0.00019 31.9 1.3 23 452-474 34-56 (78)
134 KOG1657 CCAAT-binding factor, 50.6 29 0.00063 34.6 5.1 78 395-472 68-145 (236)
135 cd03569 VHS_Hrs_Vps27p VHS dom 50.4 60 0.0013 29.5 6.7 32 403-436 82-113 (142)
136 COG4286 Uncharacterized conser 49.9 7.9 0.00017 40.1 1.2 74 405-478 143-224 (306)
137 PF12767 SAGA-Tad1: Transcript 49.8 45 0.00097 32.5 6.2 50 399-448 200-252 (252)
138 cd00043 CYCLIN Cyclin box fold 49.7 61 0.0013 24.0 5.7 58 405-462 3-70 (88)
139 cd05135 RasGAP_RASAL Ras GTPas 49.6 44 0.00096 34.6 6.4 43 426-475 149-191 (333)
140 PRK08402 replication factor A; 49.3 16 0.00034 38.2 3.2 83 400-486 2-93 (355)
141 TIGR01688 dltC D-alanine--poly 48.7 8.9 0.00019 32.0 1.1 21 454-474 33-53 (73)
142 PRK14086 dnaA chromosomal repl 48.4 27 0.00058 39.2 4.9 27 447-473 546-573 (617)
143 COG1202 Superfamily II helicas 48.1 19 0.00041 41.1 3.7 68 406-474 710-787 (830)
144 PRK15379 pathogenicity island 47.9 19 0.00042 37.4 3.5 70 396-466 113-191 (317)
145 smart00324 RhoGAP GTPase-activ 47.9 95 0.0021 27.5 7.5 34 434-467 112-145 (174)
146 PRK07668 hypothetical protein; 47.9 20 0.00042 36.2 3.5 33 406-438 9-41 (254)
147 cd05137 RasGAP_CLA2_BUD2 CLA2/ 46.9 40 0.00087 35.7 5.7 43 426-475 199-241 (395)
148 cd03197 GST_C_mPGES2 GST_C fam 46.9 34 0.00074 32.1 4.7 54 406-463 62-115 (149)
149 PTZ00252 histone H2A; Provisio 46.8 62 0.0013 30.4 6.3 69 398-466 22-92 (134)
150 PRK11034 clpA ATP-dependent Cl 46.3 28 0.00062 39.6 4.8 78 403-480 350-446 (758)
151 PF02881 SRP54_N: SRP54-type p 46.1 1E+02 0.0022 24.2 6.7 36 400-445 16-57 (75)
152 PF13565 HTH_32: Homeodomain-l 46.0 24 0.00053 27.4 3.1 35 421-472 32-66 (77)
153 PRK14086 dnaA chromosomal repl 45.9 80 0.0017 35.6 8.1 65 416-485 462-549 (617)
154 cd01017 AdcA Metal binding pro 45.9 22 0.00048 34.5 3.5 74 402-475 117-195 (282)
155 PRK06620 hypothetical protein; 45.6 86 0.0019 29.8 7.3 47 417-464 164-213 (214)
156 PRK06249 2-dehydropantoate 2-r 45.5 19 0.00041 35.3 3.0 12 462-473 285-296 (313)
157 cd05395 RasGAP_RASA4 Ras GTPas 45.4 51 0.0011 34.4 6.1 44 426-476 148-191 (337)
158 PRK14622 hypothetical protein; 45.4 13 0.00028 32.7 1.6 9 469-477 95-103 (103)
159 cd05391 RasGAP_p120GAP p120GAP 45.4 55 0.0012 33.7 6.3 42 426-474 126-167 (315)
160 PRK00982 acpP acyl carrier pro 44.9 20 0.00044 28.1 2.6 30 445-474 28-57 (78)
161 TIGR01560 put_DNA_pack unchara 44.5 43 0.00093 27.9 4.5 35 405-442 3-37 (91)
162 COG0236 AcpP Acyl carrier prot 44.4 7.5 0.00016 31.3 0.0 35 450-484 35-69 (80)
163 KOG2114 Vacuolar assembly/sort 44.4 20 0.00043 41.9 3.3 63 403-472 446-510 (933)
164 COG1474 CDC6 Cdc6-related prot 44.3 60 0.0013 33.8 6.4 61 403-463 191-261 (366)
165 smart00760 Bac_DnaA_C Bacteria 43.9 12 0.00026 29.0 1.1 48 424-474 2-50 (60)
166 PF04983 RNA_pol_Rpb1_3: RNA p 43.8 11 0.00023 33.5 0.9 47 404-460 112-158 (158)
167 PF13654 AAA_32: AAA domain; P 43.3 71 0.0015 34.9 7.1 66 403-468 425-507 (509)
168 cd01018 ZntC Metal binding pro 43.2 34 0.00073 33.1 4.2 74 402-475 116-194 (266)
169 TIGR01241 FtsH_fam ATP-depende 43.2 68 0.0015 33.9 6.7 32 436-467 264-295 (495)
170 KOG1087 Cytosolic sorting prot 42.9 67 0.0015 35.2 6.8 69 403-474 36-116 (470)
171 PF08429 PLU-1: PLU-1-like pro 42.6 82 0.0018 31.2 6.8 74 397-475 78-154 (335)
172 PRK05883 acyl carrier protein; 42.3 9.8 0.00021 32.2 0.4 38 445-482 39-76 (91)
173 cd05132 RasGAP_GAPA GAPA is an 42.3 59 0.0013 33.1 6.0 21 426-446 123-143 (331)
174 PRK08136 glycosyl transferase 42.2 34 0.00074 35.2 4.3 50 407-456 3-57 (317)
175 PRK05574 holA DNA polymerase I 42.2 1E+02 0.0022 29.9 7.3 64 401-467 145-213 (340)
176 PTZ00454 26S protease regulato 42.2 37 0.00079 35.6 4.6 66 403-468 317-387 (398)
177 PHA02839 Il-24-like protein; P 42.2 64 0.0014 31.0 5.7 73 390-462 42-133 (156)
178 PF07516 SecA_SW: SecA Wing an 42.1 28 0.00062 32.8 3.5 48 423-472 55-102 (214)
179 TIGR00362 DnaA chromosomal rep 42.0 91 0.002 31.8 7.3 52 416-468 284-338 (405)
180 TIGR01128 holA DNA polymerase 42.0 1.1E+02 0.0023 29.1 7.3 65 401-468 110-179 (302)
181 PRK14087 dnaA chromosomal repl 41.9 39 0.00084 35.8 4.8 28 446-473 377-405 (450)
182 PF00452 Bcl-2: Apoptosis regu 41.6 66 0.0014 26.5 5.2 49 405-455 14-72 (101)
183 cd01019 ZnuA Zinc binding prot 41.5 41 0.00089 33.1 4.6 74 402-475 125-203 (286)
184 COG0542 clpA ATP-binding subun 41.5 26 0.00057 40.4 3.7 65 409-481 678-744 (786)
185 PRK00095 mutL DNA mismatch rep 41.4 46 0.00099 36.7 5.4 54 423-477 532-596 (617)
186 PF08157 NUC129: NUC129 domain 41.4 56 0.0012 27.4 4.6 46 421-469 8-63 (63)
187 PRK00149 dnaA chromosomal repl 41.3 73 0.0016 33.2 6.6 17 417-433 297-313 (450)
188 cd01137 PsaA Metal binding pro 41.3 30 0.00065 34.1 3.6 75 401-475 120-201 (287)
189 PF13551 HTH_29: Winged helix- 41.2 83 0.0018 25.4 5.6 41 420-472 58-99 (112)
190 PHA00440 host protein H-NS-int 41.1 62 0.0013 29.1 5.1 43 404-446 26-68 (98)
191 PRK09281 F0F1 ATP synthase sub 41.0 36 0.00077 37.2 4.4 34 405-438 466-499 (502)
192 PRK13531 regulatory ATPase Rav 41.0 1.2E+02 0.0026 33.6 8.3 70 399-469 204-286 (498)
193 COG5247 BUR6 Class 2 transcrip 41.0 65 0.0014 29.5 5.3 38 428-465 50-87 (113)
194 PRK14955 DNA polymerase III su 40.8 66 0.0014 33.2 6.1 63 402-464 186-254 (397)
195 PF09943 DUF2175: Uncharacteri 40.7 63 0.0014 29.1 5.1 57 408-466 29-85 (101)
196 cd08324 CARD_NOD1_CARD4 Caspas 40.7 32 0.00069 30.2 3.2 31 405-437 49-79 (85)
197 PRK13428 F0F1 ATP synthase sub 40.6 94 0.002 33.2 7.3 73 399-471 315-404 (445)
198 CHL00176 ftsH cell division pr 40.6 79 0.0017 35.4 7.0 65 403-467 354-423 (638)
199 TIGR00962 atpA proton transloc 40.4 37 0.00081 37.0 4.5 35 404-438 464-498 (501)
200 PRK08903 DnaA regulatory inact 40.3 1.2E+02 0.0026 28.0 7.2 62 403-465 158-224 (227)
201 cd05128 RasGAP_GAP1_like The G 40.3 81 0.0017 32.4 6.6 42 426-474 132-173 (315)
202 COG4585 Signal transduction hi 40.1 51 0.0011 32.7 5.0 34 417-457 269-302 (365)
203 TIGR01446 DnaD_dom DnaD and ph 40.1 1.2E+02 0.0027 23.7 6.2 46 419-466 12-59 (73)
204 cd05130 RasGAP_Neurofibromin N 39.9 57 0.0012 33.7 5.5 43 426-475 135-177 (329)
205 PRK07764 DNA polymerase III su 39.6 44 0.00096 38.5 5.1 60 401-460 178-239 (824)
206 PTZ00465 rhoptry-associated pr 39.5 10 0.00022 42.0 0.1 66 408-473 48-125 (565)
207 COG3935 DnaD Putative primosom 39.4 80 0.0017 32.0 6.2 35 419-453 141-177 (246)
208 PRK05342 clpX ATP-dependent pr 39.3 34 0.00074 36.1 3.9 69 408-480 297-367 (412)
209 PRK09545 znuA high-affinity zi 39.2 44 0.00096 33.5 4.5 73 402-474 149-226 (311)
210 PRK13342 recombination factor 39.2 71 0.0015 32.9 6.1 65 401-467 150-219 (413)
211 TIGR00382 clpX endopeptidase C 38.6 30 0.00064 36.8 3.3 45 409-453 304-348 (413)
212 cd05023 S-100A11 S-100A11: S-1 38.5 96 0.0021 26.0 5.7 45 399-443 25-82 (89)
213 COG1466 HolA DNA polymerase II 38.0 94 0.002 31.2 6.5 65 403-467 141-207 (334)
214 TIGR02999 Sig-70_X6 RNA polyme 37.7 1.4E+02 0.003 26.3 6.9 64 407-476 4-69 (183)
215 PF08367 M16C_assoc: Peptidase 37.6 81 0.0017 30.4 5.8 65 405-471 174-240 (248)
216 PRK14959 DNA polymerase III su 37.6 49 0.0011 37.3 4.9 61 402-463 178-240 (624)
217 cd05394 RasGAP_RASA2 RASA2 (or 37.5 56 0.0012 34.0 5.0 44 425-475 130-173 (313)
218 PRK10911 oligopeptidase A; Pro 37.4 54 0.0012 36.8 5.2 67 417-484 287-357 (680)
219 TIGR03420 DnaA_homol_Hda DnaA 37.4 1.4E+02 0.003 27.1 7.0 62 403-465 160-226 (226)
220 TIGR02881 spore_V_K stage V sp 36.9 1.3E+02 0.0028 28.9 7.0 59 402-460 178-253 (261)
221 KOG3705 Glycoprotein 6-alpha-L 36.3 38 0.00081 37.3 3.7 93 399-492 117-226 (580)
222 PHA03181 helicase-primase prim 36.3 56 0.0012 37.8 5.1 40 404-444 607-646 (764)
223 PF10018 Med4: Vitamin-D-recep 36.2 63 0.0014 30.4 4.7 55 404-463 28-89 (188)
224 cd05026 S-100Z S-100Z: S-100Z 36.2 1.3E+02 0.0028 25.1 6.1 46 397-442 23-82 (93)
225 PF08165 FerA: FerA (NUC095) d 36.0 44 0.00096 27.4 3.2 40 421-463 9-48 (66)
226 TIGR02923 AhaC ATP synthase A1 35.7 63 0.0014 31.7 4.8 81 398-482 234-340 (343)
227 PRK00423 tfb transcription ini 35.6 73 0.0016 32.2 5.4 30 408-437 220-249 (310)
228 PF03885 DUF327: Protein of un 35.6 37 0.00081 31.0 3.1 51 403-453 41-96 (147)
229 COG1067 LonB Predicted ATP-dep 35.5 97 0.0021 35.1 6.8 71 396-466 312-398 (647)
230 PRK09648 RNA polymerase sigma 35.3 1.5E+02 0.0032 26.6 6.7 52 403-460 7-58 (189)
231 PRK09111 DNA polymerase III su 35.3 79 0.0017 35.1 6.0 63 402-465 191-255 (598)
232 COG3900 Predicted periplasmic 35.3 16 0.00035 37.2 0.7 65 403-472 123-192 (262)
233 TIGR00524 eIF-2B_rel eIF-2B al 35.3 60 0.0013 33.1 4.8 40 408-448 71-110 (303)
234 PRK13765 ATP-dependent proteas 35.3 92 0.002 35.0 6.5 48 418-465 338-398 (637)
235 PRK10664 transcriptional regul 35.2 55 0.0012 27.6 3.8 16 466-481 38-53 (90)
236 PF02885 Glycos_trans_3N: Glyc 35.2 23 0.00049 28.0 1.4 47 407-453 2-49 (66)
237 PRK13430 F0F1 ATP synthase sub 35.0 1.2E+02 0.0026 30.3 6.7 73 399-472 143-231 (271)
238 PRK14700 recombination factor 34.9 99 0.0021 32.2 6.2 65 403-467 40-115 (300)
239 COG2083 Uncharacterized protei 34.9 16 0.00035 34.4 0.6 72 404-484 26-117 (140)
240 KOG3341 RNA polymerase II tran 34.7 1.1E+02 0.0025 31.2 6.4 63 404-469 63-131 (249)
241 cd06571 Bac_DnaA_C C-terminal 34.5 31 0.00067 28.6 2.2 46 425-473 2-48 (90)
242 COG5566 Uncharacterized conser 34.3 92 0.002 29.5 5.4 60 405-469 14-75 (137)
243 PF13499 EF-hand_7: EF-hand do 33.9 1.4E+02 0.003 22.2 5.4 52 397-461 12-63 (66)
244 PRK12921 2-dehydropantoate 2-r 33.9 45 0.00098 31.8 3.5 13 440-452 220-232 (305)
245 PLN02353 probable UDP-glucose 33.8 1.1E+02 0.0024 33.0 6.6 73 404-476 188-267 (473)
246 smart00544 MA3 Domain in DAP-5 33.8 56 0.0012 27.2 3.6 18 452-469 66-83 (113)
247 cd05136 RasGAP_DAB2IP The DAB2 33.4 1.1E+02 0.0024 31.4 6.3 25 424-448 125-149 (309)
248 PRK09087 hypothetical protein; 33.2 2E+02 0.0044 27.5 7.7 50 416-466 169-221 (226)
249 COG2256 MGS1 ATPase related to 33.1 1.1E+02 0.0024 33.5 6.5 66 402-469 163-240 (436)
250 PRK12422 chromosomal replicati 33.0 1.1E+02 0.0023 32.7 6.3 27 454-485 351-377 (445)
251 PF14842 FliG_N: FliG N-termin 32.9 94 0.002 26.8 4.9 33 402-437 30-62 (108)
252 PF15601 Imm42: Immunity prote 32.6 37 0.0008 31.6 2.5 27 428-454 98-131 (134)
253 KOG1087 Cytosolic sorting prot 32.4 73 0.0016 34.9 5.1 75 400-484 76-150 (470)
254 PF11247 DUF2675: Protein of u 32.3 95 0.0021 27.9 4.9 47 398-445 21-67 (98)
255 PF07253 Gypsy: Gypsy protein; 32.3 1.5E+02 0.0032 32.8 7.3 51 414-466 145-201 (472)
256 PF13690 CheX: Chemotaxis phos 32.3 1E+02 0.0022 25.4 4.9 56 403-478 20-75 (94)
257 PF09123 DUF1931: Domain of un 32.2 31 0.00066 32.5 2.0 55 407-462 1-55 (138)
258 PRK00188 trpD anthranilate pho 32.2 86 0.0019 32.0 5.3 48 407-454 3-51 (339)
259 KOG3902 Histone acetyltransfer 31.9 3E+02 0.0066 29.4 9.1 59 405-465 28-88 (352)
260 PRK10733 hflB ATP-dependent me 31.8 1E+02 0.0023 34.1 6.2 64 405-468 325-393 (644)
261 PRK13343 F0F1 ATP synthase sub 31.6 62 0.0013 35.6 4.4 30 408-437 469-498 (502)
262 PRK02079 pyrroloquinoline quin 31.6 82 0.0018 27.0 4.3 24 408-435 39-62 (88)
263 TIGR02397 dnaX_nterm DNA polym 31.6 86 0.0019 30.5 5.0 63 402-465 176-240 (355)
264 PRK12710 flgJ flagellar rod as 31.5 55 0.0012 33.8 3.8 43 430-473 128-170 (291)
265 PRK09103 ribonucleotide-diphos 31.3 1E+02 0.0023 35.4 6.3 33 421-453 530-562 (758)
266 PF09860 DUF2087: Uncharacteri 31.3 57 0.0012 27.1 3.2 30 407-436 17-47 (71)
267 PRK12422 chromosomal replicati 31.1 85 0.0018 33.4 5.2 30 446-475 373-403 (445)
268 cd07018 S49_SppA_67K_type Sign 31.1 1E+02 0.0023 29.2 5.3 50 401-453 116-183 (222)
269 COG0593 DnaA ATPase involved i 31.0 40 0.00086 36.2 2.8 29 455-488 320-348 (408)
270 PRK14607 bifunctional glutamin 31.0 83 0.0018 34.2 5.2 77 407-483 195-282 (534)
271 PF12536 DUF3734: Patatin phos 30.6 8.6 0.00019 33.6 -1.8 54 404-462 21-74 (108)
272 KOG2389 Predicted bromodomain 30.4 1.3E+02 0.0029 32.1 6.4 63 403-466 31-93 (353)
273 cd08790 DED_DEDD Death Effecto 30.2 1.1E+02 0.0024 27.5 4.9 50 406-467 4-53 (97)
274 PF02867 Ribonuc_red_lgC: Ribo 30.2 1.1E+02 0.0024 33.1 6.0 33 421-453 308-340 (538)
275 cd03567 VHS_GGA VHS domain fam 30.1 93 0.002 28.5 4.6 46 426-473 72-119 (139)
276 TIGR02903 spore_lon_C ATP-depe 29.8 59 0.0013 35.9 4.0 66 402-467 353-430 (615)
277 cd06456 M3A_DCP_Oligopeptidase 29.7 90 0.002 32.9 5.1 65 418-483 35-103 (422)
278 PF06576 DUF1133: Protein of u 29.6 98 0.0021 30.3 4.9 50 400-451 53-117 (176)
279 PRK06256 biotin synthase; Vali 29.5 83 0.0018 31.2 4.6 45 406-450 6-50 (336)
280 PRK10569 NAD(P)H-dependent FMN 29.4 48 0.0011 31.1 2.8 26 414-439 147-172 (191)
281 PRK00440 rfc replication facto 29.3 1.4E+02 0.003 28.5 5.8 62 402-465 161-224 (319)
282 cd01016 TroA Metal binding pro 29.3 66 0.0014 31.5 3.8 73 402-474 105-184 (276)
283 PRK08215 sporulation sigma fac 29.2 1.4E+02 0.0031 28.6 5.9 54 397-460 14-67 (258)
284 PF02965 Met_synt_B12: Vitamin 29.1 1.4E+02 0.003 28.7 5.9 25 424-448 96-121 (211)
285 PRK13940 glutamyl-tRNA reducta 29.0 1.3E+02 0.0028 31.9 6.1 63 404-472 350-412 (414)
286 PRK03992 proteasome-activating 29.0 1.5E+02 0.0033 30.6 6.5 65 403-467 303-372 (389)
287 PRK08699 DNA polymerase III su 28.9 1.9E+02 0.0041 29.6 7.0 68 400-467 91-184 (325)
288 PRK05708 2-dehydropantoate 2-r 28.8 1E+02 0.0022 30.6 5.0 50 424-473 235-284 (305)
289 PF01297 TroA: Periplasmic sol 28.8 32 0.00068 32.6 1.5 76 401-476 95-175 (256)
290 PRK14950 DNA polymerase III su 28.8 98 0.0021 33.8 5.3 64 402-466 179-244 (585)
291 CHL00059 atpA ATP synthase CF1 28.7 88 0.0019 34.4 5.0 31 408-438 448-478 (485)
292 smart00337 BCL BCL (B-Cell lym 28.6 1E+02 0.0022 26.2 4.4 43 406-451 15-67 (100)
293 cd03561 VHS VHS domain family; 28.5 1.2E+02 0.0026 26.8 4.9 47 426-476 71-118 (133)
294 cd04400 RhoGAP_fBEM3 RhoGAP_fB 28.4 2.2E+02 0.0047 26.4 6.9 34 435-468 136-169 (190)
295 smart00047 LYZ2 Lysozyme subfa 28.4 77 0.0017 29.0 3.8 40 432-472 8-47 (147)
296 TIGR00706 SppA_dom signal pept 28.3 1.5E+02 0.0032 27.9 5.8 58 402-465 101-174 (207)
297 PRK06585 holA DNA polymerase I 28.3 1.5E+02 0.0032 29.3 6.1 64 402-467 142-210 (343)
298 PRK14903 16S rRNA methyltransf 28.3 1.1E+02 0.0024 32.2 5.5 64 403-467 52-122 (431)
299 PRK12711 flgJ flagellar rod as 28.3 62 0.0013 34.9 3.6 42 432-474 215-256 (392)
300 cd01049 RNRR2 Ribonucleotide R 28.2 1.9E+02 0.0042 28.0 6.7 79 402-483 196-274 (288)
301 PF00237 Ribosomal_L22: Riboso 28.2 1.5E+02 0.0034 25.3 5.4 45 402-451 8-59 (105)
302 PRK00199 ihfB integration host 28.2 20 0.00043 29.8 0.1 20 463-482 36-55 (94)
303 PRK05720 mtnA methylthioribose 28.2 1.1E+02 0.0024 32.0 5.3 29 421-449 111-139 (344)
304 PHA02102 hypothetical protein 28.1 49 0.0011 28.1 2.3 35 436-476 4-38 (72)
305 COG4749 Uncharacterized protei 28.1 62 0.0013 31.8 3.3 77 402-480 9-87 (196)
306 PRK14963 DNA polymerase III su 28.1 1.1E+02 0.0023 33.3 5.4 67 401-469 174-242 (504)
307 KOG0406 Glutathione S-transfer 28.1 1.2E+02 0.0026 30.5 5.4 59 422-480 93-157 (231)
308 COG2766 PrkA Putative Ser prot 28.0 83 0.0018 35.8 4.7 55 395-456 524-578 (649)
309 KOG2005 26S proteasome regulat 28.0 33 0.00071 39.7 1.7 94 401-494 171-282 (878)
310 PF01385 OrfB_IS605: Probable 27.9 77 0.0017 28.5 3.7 35 426-460 189-223 (227)
311 PRK08084 DNA replication initi 27.8 2.6E+02 0.0057 26.6 7.4 48 416-464 183-233 (235)
312 KOG3598 Thyroid hormone recept 27.7 16 0.00035 45.0 -0.7 8 191-198 1994-2001(2220)
313 cd07176 terB tellurite resista 27.7 1.3E+02 0.0029 24.3 4.8 13 436-448 77-89 (111)
314 KOG1673 Ras GTPases [General f 27.7 87 0.0019 31.0 4.2 54 425-481 134-196 (205)
315 PF11047 SopD: Salmonella oute 27.6 97 0.0021 32.7 4.8 70 396-466 113-191 (319)
316 PRK00373 V-type ATP synthase s 27.5 17 0.00037 34.5 -0.5 73 404-477 31-108 (204)
317 PF01221 Dynein_light: Dynein 27.4 51 0.0011 27.4 2.3 19 419-437 12-30 (89)
318 PF14677 FANCI_S3: FANCI solen 27.4 1.8E+02 0.0039 28.5 6.4 54 404-462 114-170 (219)
319 PF12422 Condensin2nSMC: Conde 27.3 62 0.0013 29.6 3.1 41 402-443 91-131 (152)
320 smart00385 CYCLIN domain prese 27.3 1.6E+02 0.0034 21.6 4.7 28 411-438 3-30 (83)
321 PF04157 EAP30: EAP30/Vps36 fa 27.3 2.1E+02 0.0046 27.4 6.7 63 405-467 61-145 (223)
322 COG1705 FlgJ Muramidase (flage 27.3 71 0.0015 31.7 3.6 40 431-471 42-81 (201)
323 KOG0034 Ca2+/calmodulin-depend 27.2 2.1E+02 0.0046 27.6 6.7 62 396-467 115-176 (187)
324 PF13963 Transpos_assoc: Trans 27.1 63 0.0014 26.6 2.8 34 432-467 21-63 (77)
325 KOG2948 Predicted metal-bindin 27.0 1.1E+02 0.0023 32.5 5.0 69 405-473 148-243 (327)
326 PRK09522 bifunctional glutamin 27.0 95 0.0021 34.0 4.9 49 407-455 200-249 (531)
327 cd02191 FtsZ FtsZ is a GTPase 26.8 1.2E+02 0.0026 30.8 5.2 76 402-478 135-219 (303)
328 PF01343 Peptidase_S49: Peptid 26.6 80 0.0017 28.3 3.6 34 417-453 77-110 (154)
329 PRK06200 2,3-dihydroxy-2,3-dih 26.5 29 0.00064 31.9 0.8 40 403-442 39-87 (263)
330 COG5262 HTA1 Histone H2A [Chro 26.3 1.8E+02 0.0039 27.4 5.8 70 396-465 21-90 (132)
331 cd05030 calgranulins Calgranul 26.3 1E+02 0.0022 25.4 3.9 42 423-472 2-44 (88)
332 PF01857 RB_B: Retinoblastoma- 26.3 1.7E+02 0.0036 26.9 5.6 59 404-467 15-86 (135)
333 TIGR00745 apbA_panE 2-dehydrop 26.3 74 0.0016 29.9 3.4 11 463-473 268-278 (293)
334 PRK14961 DNA polymerase III su 26.0 91 0.002 31.7 4.2 62 402-464 178-241 (363)
335 PRK15182 Vi polysaccharide bio 25.7 1.9E+02 0.0042 30.5 6.7 74 404-480 180-262 (425)
336 PF14094 DUF4272: Domain of un 25.7 1E+02 0.0022 29.9 4.4 35 441-475 165-200 (209)
337 PRK14964 DNA polymerase III su 25.6 1.3E+02 0.0029 32.8 5.6 62 402-464 175-238 (491)
338 PRK11034 clpA ATP-dependent Cl 25.5 77 0.0017 36.3 4.0 66 408-481 638-705 (758)
339 cd00454 Trunc_globin Truncated 25.5 1.3E+02 0.0028 25.1 4.4 49 425-476 9-57 (116)
340 PF07105 DUF1367: Protein of u 25.3 88 0.0019 31.0 3.8 46 404-460 73-118 (196)
341 PF07766 LETM1: LETM1-like pro 25.3 66 0.0014 32.0 3.1 31 406-439 136-166 (268)
342 PF02854 MIF4G: MIF4G domain; 25.3 1.2E+02 0.0027 26.3 4.4 45 405-450 2-49 (209)
343 PRK06893 DNA replication initi 25.3 3E+02 0.0064 26.1 7.3 59 403-464 162-227 (229)
344 PRK00285 ihfA integration host 25.1 1E+02 0.0023 25.8 3.8 18 464-481 38-55 (99)
345 PLN02964 phosphatidylserine de 25.1 1.4E+02 0.003 34.0 5.7 60 407-466 181-243 (644)
346 PF01934 DUF86: Protein of unk 25.0 2.5E+02 0.0053 23.6 6.0 51 406-456 7-58 (119)
347 PF10273 WGG: Pre-rRNA-process 25.0 66 0.0014 27.1 2.6 38 403-440 29-71 (82)
348 PRK08691 DNA polymerase III su 25.0 1.6E+02 0.0035 34.0 6.3 62 402-464 178-241 (709)
349 PRK00045 hemA glutamyl-tRNA re 24.8 1.8E+02 0.004 30.3 6.3 62 404-471 357-418 (423)
350 TIGR02510 NrdE-prime ribonucle 24.6 1.2E+02 0.0027 33.6 5.2 35 421-455 355-389 (571)
351 PRK13341 recombination factor 24.6 2.1E+02 0.0044 32.8 7.0 64 403-466 169-246 (725)
352 PF09644 Mg296: Mg296 protein; 24.6 1.3E+02 0.0028 27.9 4.5 54 409-465 66-119 (121)
353 cd01679 RNR_I Class I ribonucl 24.5 99 0.0021 33.2 4.4 30 422-451 310-339 (460)
354 TIGR02541 flagell_FlgJ flagell 24.5 1.1E+02 0.0025 31.5 4.6 44 429-473 145-188 (294)
355 PF04129 Vps52: Vps52 / Sac2 f 24.4 91 0.002 33.6 4.1 88 401-488 65-161 (508)
356 PF12921 ATP13: Mitochondrial 24.4 1.3E+02 0.0029 26.8 4.5 22 457-478 18-39 (126)
357 PRK00771 signal recognition pa 24.3 1.6E+02 0.0034 31.7 5.8 38 405-442 3-54 (437)
358 cd08045 TAF4 TATA Binding Prot 24.3 94 0.002 29.7 3.8 19 450-468 184-202 (212)
359 PRK00117 recX recombination re 24.3 97 0.0021 27.7 3.7 31 419-450 39-71 (157)
360 cd00336 Ribosomal_L22 Ribosoma 24.3 1.5E+02 0.0032 25.4 4.6 51 402-453 10-62 (105)
361 cd05127 RasGAP_IQGAP_related T 24.2 2.1E+02 0.0046 28.8 6.4 21 427-447 123-143 (325)
362 PF07464 ApoLp-III: Apolipopho 24.2 1.3E+02 0.0029 28.3 4.7 24 418-441 120-143 (155)
363 TIGR02419 C4_traR_proteo phage 24.2 1.4E+02 0.003 24.1 4.2 10 486-495 33-42 (63)
364 cd01936 Ntn_CA Cephalosporin a 24.0 1.7E+02 0.0037 31.3 6.0 64 404-472 337-405 (469)
365 PRK11064 wecC UDP-N-acetyl-D-m 24.0 2.6E+02 0.0056 29.3 7.2 70 404-476 185-261 (415)
366 PRK15057 UDP-glucose 6-dehydro 24.0 2.8E+02 0.006 29.1 7.3 60 419-478 187-252 (388)
367 PRK09490 metH B12-dependent me 24.0 1.4E+02 0.003 36.3 5.8 49 427-478 1093-1148(1229)
368 TIGR00511 ribulose_e2b2 ribose 23.9 1.5E+02 0.0032 30.1 5.3 40 407-448 68-107 (301)
369 PF10431 ClpB_D2-small: C-term 23.9 1.2E+02 0.0026 24.2 3.8 27 406-432 13-42 (81)
370 PRK14962 DNA polymerase III su 23.9 1.8E+02 0.0039 31.4 6.1 66 402-468 176-243 (472)
371 PRK05629 hypothetical protein; 23.9 2.4E+02 0.0052 27.9 6.6 66 402-468 126-193 (318)
372 PF10127 Nuc-transf: Predicted 23.8 1.9E+02 0.0041 27.8 5.8 21 432-452 213-233 (247)
373 KOG2612 Predicted integral mem 23.7 1.3E+02 0.0027 27.2 4.1 74 418-491 6-81 (103)
374 PF08369 PCP_red: Proto-chloro 23.6 78 0.0017 24.2 2.5 40 421-461 2-42 (45)
375 COG1710 Uncharacterized protei 23.5 74 0.0016 30.0 2.8 16 402-417 8-23 (139)
376 PRK14958 DNA polymerase III su 23.5 2E+02 0.0043 31.3 6.4 62 402-464 178-241 (509)
377 PF00161 RIP: Ribosome inactiv 23.5 1.4E+02 0.0029 28.0 4.6 70 399-469 122-197 (206)
378 cd03568 VHS_STAM VHS domain fa 23.5 1.4E+02 0.0031 27.3 4.6 36 401-438 76-111 (144)
379 COG1223 Predicted ATPase (AAA+ 23.5 1.9E+02 0.0041 30.9 6.0 36 434-469 322-357 (368)
380 PF13877 RPAP3_C: Potential Mo 23.4 2.2E+02 0.0049 23.4 5.4 32 404-435 21-59 (94)
381 TIGR00563 rsmB ribosomal RNA s 23.4 2.1E+02 0.0045 29.8 6.3 64 403-466 46-119 (426)
382 cd00159 RhoGAP RhoGAP: GTPase- 23.4 4.8E+02 0.01 22.4 7.7 30 435-464 109-138 (169)
383 PRK06347 autolysin; Reviewed 23.4 86 0.0019 35.1 3.8 39 432-471 150-188 (592)
384 cd05392 RasGAP_Neurofibromin_l 23.4 2.3E+02 0.005 28.5 6.5 23 426-448 126-148 (323)
385 PF08299 Bac_DnaA_C: Bacterial 23.3 30 0.00066 27.9 0.3 47 424-473 2-49 (70)
386 PRK06645 DNA polymerase III su 23.3 1.7E+02 0.0036 32.1 5.8 66 401-466 186-255 (507)
387 PF07156 Prenylcys_lyase: Pren 23.2 1.1E+02 0.0024 32.0 4.4 62 416-478 45-110 (368)
388 COG1241 MCM2 Predicted ATPase 23.2 1.4E+02 0.0031 34.2 5.5 48 418-465 524-590 (682)
389 cd00051 EFh EF-hand, calcium b 23.2 1.2E+02 0.0026 20.4 3.2 17 398-414 13-29 (63)
390 PLN02162 triacylglycerol lipas 23.2 77 0.0017 34.9 3.3 62 406-477 113-174 (475)
391 KOG1662 Mitochondrial F1F0-ATP 23.2 1.3E+02 0.0027 30.3 4.5 60 398-457 76-140 (210)
392 PRK00979 tetrahydromethanopter 23.2 1.3E+02 0.0028 31.5 4.7 77 395-471 42-148 (308)
393 PRK06596 RNA polymerase factor 23.1 3E+02 0.0065 27.3 7.1 27 434-460 52-78 (284)
394 PF07697 7TMR-HDED: 7TM-HD ext 23.1 2.1E+02 0.0045 26.0 5.6 54 399-452 21-81 (222)
395 PHA02571 a-gt.4 hypothetical p 23.0 80 0.0017 28.9 2.9 48 417-467 8-56 (109)
396 PF13022 HTH_Tnp_1_2: Helix-tu 22.9 1.5E+02 0.0033 28.2 4.7 66 403-470 33-107 (142)
397 cd07023 S49_Sppa_N_C Signal pe 22.8 1.5E+02 0.0033 27.6 4.7 34 417-453 137-170 (208)
398 TIGR01242 26Sp45 26S proteasom 22.8 1.2E+02 0.0025 30.7 4.3 65 403-467 294-363 (364)
399 COG5304 Uncharacterized protei 22.8 1.7E+02 0.0038 26.1 4.8 54 402-456 2-57 (92)
400 TIGR03566 FMN_reduc_MsuE FMN r 22.6 1E+02 0.0022 27.8 3.5 25 415-439 147-171 (174)
401 COG4077 Uncharacterized protei 22.6 1.8E+02 0.004 27.9 5.2 45 419-466 70-114 (156)
402 PRK12681 cysB transcriptional 22.5 56 0.0012 32.0 2.0 45 417-462 277-321 (324)
403 cd05027 S-100B S-100B: S-100B 22.5 2.9E+02 0.0063 23.1 5.9 33 397-431 21-60 (88)
404 KOG0027 Calmodulin and related 22.5 4E+02 0.0087 23.5 7.1 28 439-466 86-113 (151)
405 PRK12712 flgJ flagellar rod as 22.4 97 0.0021 32.9 3.7 40 432-472 197-236 (344)
406 cd04378 RhoGAP_GMIP_PARG1 RhoG 22.4 2.9E+02 0.0062 26.1 6.5 31 435-465 139-169 (203)
407 KOG1756 Histone 2A [Chromatin 22.3 2.5E+02 0.0053 26.6 5.9 71 396-466 22-92 (131)
408 PF13743 Thioredoxin_5: Thiore 22.3 1.3E+02 0.0027 27.9 4.1 54 422-478 115-171 (176)
409 COG1893 ApbA Ketopantoate redu 22.3 1.4E+02 0.003 30.2 4.7 36 417-452 230-266 (307)
410 PF05016 Plasmid_stabil: Plasm 22.3 50 0.0011 25.5 1.3 41 431-474 24-64 (90)
411 COG0091 RplV Ribosomal protein 22.2 1.6E+02 0.0036 27.0 4.7 57 401-460 19-77 (120)
412 COG0776 HimA Bacterial nucleoi 22.2 2.7E+02 0.0058 24.6 5.8 18 464-481 37-54 (94)
413 PLN00203 glutamyl-tRNA reducta 22.2 2.6E+02 0.0056 30.8 7.0 66 404-471 446-514 (519)
414 PRK10061 DNA damage-inducible 22.1 93 0.002 27.9 3.0 21 420-440 23-43 (96)
415 PRK07003 DNA polymerase III su 22.0 1.2E+02 0.0027 35.6 4.7 46 400-445 176-223 (830)
416 PF02268 TFIIA_gamma_N: Transc 22.0 2.5E+02 0.0054 22.4 5.1 32 405-440 17-48 (49)
417 PF06122 TraH: Conjugative rel 21.9 1.2E+02 0.0025 31.4 4.2 60 394-453 60-131 (361)
418 cd02202 FtsZ_type2 FtsZ is a G 21.8 1.2E+02 0.0026 31.4 4.2 76 404-480 151-238 (349)
419 PF02399 Herpes_ori_bp: Origin 21.8 2E+02 0.0044 33.8 6.4 80 393-476 519-604 (824)
420 TIGR02639 ClpA ATP-dependent C 21.8 85 0.0019 35.1 3.4 66 409-481 635-701 (731)
421 PRK06246 fumarate hydratase; P 21.8 1.6E+02 0.0034 30.4 5.0 49 401-449 3-61 (280)
422 PF14513 DAG_kinase_N: Diacylg 21.7 78 0.0017 29.4 2.6 42 428-474 27-68 (138)
423 TIGR03346 chaperone_ClpB ATP-d 21.7 1E+02 0.0022 35.3 4.0 66 409-481 749-815 (852)
424 TIGR03345 VI_ClpV1 type VI sec 21.7 1.4E+02 0.003 34.5 5.1 59 403-461 351-425 (852)
425 PRK05684 flgJ flagellar rod as 21.7 99 0.0021 32.2 3.6 43 430-473 150-192 (312)
426 PF14357 DUF4404: Domain of un 21.6 1.8E+02 0.0038 24.8 4.5 34 404-437 3-36 (85)
427 TIGR02392 rpoH_proteo alternat 21.6 3E+02 0.0065 26.8 6.7 54 398-460 12-65 (270)
428 PF06545 DUF1116: Protein of u 21.4 28 0.0006 34.7 -0.3 79 398-477 98-185 (216)
429 cd03025 DsbA_FrnE_like DsbA fa 21.4 2.5E+02 0.0054 24.8 5.6 25 427-451 142-166 (193)
430 TIGR02849 spore_III_AD stage I 21.3 2.2E+02 0.0047 25.5 5.2 48 406-455 23-70 (101)
431 COG0140 HisI Phosphoribosyl-AT 21.2 2.9E+02 0.0064 24.5 5.9 15 455-469 75-89 (92)
432 KOG1766 Enhancer of rudimentar 21.2 1.5E+02 0.0033 27.0 4.1 41 407-452 36-77 (104)
433 KOG4317 Predicted Zn-finger pr 21.2 81 0.0018 33.7 2.9 73 407-480 294-382 (383)
434 CHL00095 clpC Clp protease ATP 21.2 1.9E+02 0.004 33.1 5.9 75 405-480 351-497 (821)
435 TIGR02850 spore_sigG RNA polym 21.1 2.3E+02 0.0051 27.2 5.8 55 396-460 10-64 (254)
436 PF14630 ORC5_C: Origin recogn 21.0 2.2E+02 0.0048 27.9 5.7 63 403-472 7-69 (271)
437 PF08601 PAP1: Transcription f 21.0 35 0.00076 35.6 0.3 32 436-467 315-347 (347)
438 COG5251 TAF40 Transcription in 21.0 75 0.0016 31.4 2.4 52 401-453 115-166 (199)
439 PRK06305 DNA polymerase III su 20.9 2.1E+02 0.0046 30.5 5.9 62 402-464 180-243 (451)
440 KOG0027 Calmodulin and related 20.9 1.7E+02 0.0037 25.8 4.5 82 395-481 18-108 (151)
441 PF10163 EnY2: Transcription f 20.9 94 0.002 26.1 2.7 34 434-467 31-64 (86)
442 PRK12713 flgJ flagellar rod as 20.8 1E+02 0.0023 32.6 3.6 39 433-472 182-220 (339)
443 PF10431 ClpB_D2-small: C-term 20.7 64 0.0014 25.8 1.6 49 425-481 3-53 (81)
444 PRK09897 hypothetical protein; 20.6 85 0.0018 34.3 3.0 47 449-495 341-391 (534)
445 KOG2304 3-hydroxyacyl-CoA dehy 20.6 1.3E+02 0.0028 31.3 4.1 40 396-441 41-82 (298)
446 PLN02690 Agmatine deiminase 20.5 48 0.001 34.9 1.1 40 439-479 174-218 (374)
447 TIGR01505 tartro_sem_red 2-hyd 20.5 1.1E+02 0.0024 29.6 3.5 51 404-454 142-197 (291)
448 PF08236 SRI: SRI (Set2 Rpb1 i 20.4 80 0.0017 26.8 2.2 22 417-438 58-79 (88)
449 PF08766 DEK_C: DEK C terminal 20.4 1.1E+02 0.0024 23.5 2.8 22 451-472 17-38 (54)
450 TIGR01035 hemA glutamyl-tRNA r 20.4 2.4E+02 0.0053 29.5 6.2 62 405-470 355-416 (417)
451 PRK05872 short chain dehydroge 20.4 52 0.0011 31.5 1.2 13 403-415 42-54 (296)
452 PLN02437 ribonucleoside--dipho 20.3 1.3E+02 0.0028 34.9 4.5 32 421-452 540-571 (813)
453 PRK08535 translation initiatio 20.2 1.9E+02 0.0042 29.4 5.2 28 422-449 86-113 (310)
454 PF12418 AcylCoA_DH_N: Acyl-Co 20.2 77 0.0017 22.7 1.8 23 454-476 4-31 (34)
455 cd05134 RasGAP_RASA3 RASA3 (or 20.2 2.1E+02 0.0046 29.7 5.6 21 426-446 131-151 (310)
456 COG3395 Uncharacterized protei 20.2 1.4E+02 0.003 32.5 4.4 48 400-451 256-303 (413)
457 cd04393 RhoGAP_FAM13A1a RhoGAP 20.2 3.6E+02 0.0078 25.0 6.6 27 438-464 133-159 (189)
458 PRK13386 fliH flagellar assemb 20.2 1.4E+02 0.0031 29.3 4.2 22 418-439 114-135 (236)
459 PRK06948 ribonucleotide reduct 20.1 2.4E+02 0.0051 31.6 6.3 31 422-452 386-416 (595)
460 PF10367 Vps39_2: Vacuolar sor 20.1 2.6E+02 0.0057 22.6 5.1 76 407-494 13-88 (109)
461 smart00323 RasGAP GTPase-activ 20.1 2.3E+02 0.005 28.7 5.7 22 426-447 150-171 (344)
462 PF08328 ASL_C: Adenylosuccina 20.1 1.3E+02 0.0027 27.8 3.5 30 399-432 81-110 (115)
463 PF07624 PSD2: Protein of unkn 20.1 2.7E+02 0.0059 22.8 5.2 42 424-465 12-53 (76)
464 PF08479 POTRA_2: POTRA domain 20.1 1E+02 0.0022 24.5 2.6 42 397-438 9-50 (76)
465 TIGR03380 agmatine_aguA agmati 20.1 49 0.0011 34.6 1.1 40 439-479 162-206 (357)
466 PF14841 FliG_M: FliG middle d 20.0 1.4E+02 0.003 24.6 3.5 48 419-469 23-71 (79)
No 1
>KOG1142 consensus Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=100.00 E-value=3.3e-47 Score=366.62 Aligned_cols=215 Identities=35% Similarity=0.479 Sum_probs=164.9
Q ss_pred cccCccccccCCCCCCCCCCCCCCCCCCCCcchhccccCcccCCCCcchhhhhhcccccCCCCCCCCCCccccccccCC-
Q 010992 268 QSFNQPWLSSGSQGKPPLAPPSTYRPQMNTPSMQQRSHIPQQHSPLSTNLQQQHLSSVQPQQSKPSHQLPDHYGQQFSS- 346 (496)
Q Consensus 268 Q~~~Q~WL~~~~q~~p~l~sp~s~r~q~~~~~~QQr~h~~qQ~~~~~t~lqqqqlsq~qqqq~~~~~qqq~h~~QQl~~- 346 (496)
|..+++||+.+..+.++...| ++|+|++.+.+.+|.++.+|+-+. +..+.+. ....+...+..++|+. ++..
T Consensus 25 q~~qq~~~~~~~~~~s~~~~~-s~~~q~~~~~~~~~~~~~qq~~s~--~~~~~~~---~n~~~~s~~~~~~~~~-~~~~~ 97 (258)
T KOG1142|consen 25 QARQQQWLRQIQGIPSPESYP-SQRQQRFSPTCSIRENPNQQWIST--GYPQPQV---SNGGPPSQALNQQDSQ-QSAIS 97 (258)
T ss_pred HHHHhhhhccccCCCCCCCCh-hhccccCCCcccccCCCCcccccc--ccCcccc---ccCCchHHhhhhhhHH-hhccc
Confidence 455889999999898888886 999999999999998887777533 2221111 1111111112222332 2222
Q ss_pred -CCCCCCCccccccCCCCCCCCCCcccccc-CCCCccccCCcccCCCCcCCCcCCccCCHHHHHHHHHhhCCCCCCCHHH
Q 010992 347 -PRVPQSSPHQQQITRPPGSATQKPSSLAL-VQPNAVQTGNQSKIAGTESDEFGNRILTKRSIQELVNQIDPSERLDPDV 424 (496)
Q Consensus 347 -~~~~~~~~~qqq~~r~~~~~~qk~~sl~~-sqp~~~~~g~~~~~~~~~~~e~~nrILtKrKLqELVrqIDPsesLDpDV 424 (496)
.+.++....+....++.....++...-.. ++......+++.++.....++++++||.|+||+|||++||++++||+||
T Consensus 98 ~~q~P~~~~~q~~~~~~~~~~~~~~~~P~~~~~g~~~g~~~sp~~s~s~~~~~~~~il~k~kl~dLvqqId~~~~LD~dV 177 (258)
T KOG1142|consen 98 QQQQPASSPSQGSSMSNQTSSVQKDPAPVIGSQGSVSGGGTSPAGSSSQDEPGNNPILSKRKLDDLVQQIDGTTKLDDDV 177 (258)
T ss_pred cCCCCccCCCCCCCccccCcccccCCCCCCCCCCccCCCCCCCCcccccccCCCCccccccchhHHHHhhcCcccccHHH
Confidence 34444455556666777777776654433 2233333455556777788999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCCCcccccccCCcccc
Q 010992 425 EDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGDEIKTFRKPVRI 489 (496)
Q Consensus 425 EELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGFssDEIr~~rk~~~~ 489 (496)
||+||||||||||+|++|||+||||||+++||+|||+|||||+|||+||||++||+|.|||++..
T Consensus 178 edlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr~~Nm~iPgf~sd~~~~~~k~~pT 242 (258)
T KOG1142|consen 178 EDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLERNFNMEIPGFSSDEKRSKKKALPT 242 (258)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeeccccccCCCccccccccccccCCc
Confidence 99999999999999999999999999999999999999999999999999999999999999864
No 2
>PF03847 TFIID_20kDa: Transcription initiation factor TFIID subunit A; InterPro: IPR003228 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription [].; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_B.
Probab=99.96 E-value=1.6e-30 Score=208.13 Aligned_cols=68 Identities=63% Similarity=1.135 Sum_probs=57.9
Q ss_pred CHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCc
Q 010992 403 TKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNM 470 (496)
Q Consensus 403 tKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI 470 (496)
+|++|++||++|||+++||+||||+|++||||||++|+++||+||||||+++||+|||+|||||+|||
T Consensus 1 ~K~~l~~Lv~~iDp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Ler~~ni 68 (68)
T PF03847_consen 1 SKRKLQELVKQIDPNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLERNWNI 68 (68)
T ss_dssp -HHHHHHHHHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHHHS--
T ss_pred ChHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHhhcCC
Confidence 69999999999999999999999999999999999999999999999999999999999999999997
No 3
>COG5624 TAF61 Transcription initiation factor TFIID, subunit TAF12 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=99.94 E-value=5.1e-29 Score=253.42 Aligned_cols=102 Identities=44% Similarity=0.670 Sum_probs=93.9
Q ss_pred ccCCCCcCCCcCCccCCHHHHHHHHHhh-CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992 387 SKIAGTESDEFGNRILTKRSIQELVNQI-DPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLE 465 (496)
Q Consensus 387 ~~~~~~~~~e~~nrILtKrKLqELVrqI-DPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE 465 (496)
.|++-++. ++..||+.|+||+||++.| |..++||.||||+||++|||||+.|.+|+|+||||||+|+||++||+||||
T Consensus 370 ~k~p~ye~-D~~~Rl~skrkL~el~~~~vd~eekie~eveelll~~ad~fve~vt~FsCrlakhrkSdtlevrD~qlhlE 448 (505)
T COG5624 370 DKGPLYER-DDLWRLDSKRKLEELQHGGVDEEEKIENEVEELLLSRADGFVEPVTEFSCRLAKHRKSDTLEVRDGQLHLE 448 (505)
T ss_pred cCCCchhc-chhhhhhhhhhHHHHHhhccCcceeccchHHHHHHhhhcccccccchheeEeeccCCCCceeeccceeeec
Confidence 34555542 4568999999999999999 999999999999999999999999999999999999999999999999999
Q ss_pred hhcCccccCCCccccc-ccCCcccc
Q 010992 466 RNWNMTLPGFSGDEIK-TFRKPVRI 489 (496)
Q Consensus 466 RnWNI~IPGFssDEIr-~~rk~~~~ 489 (496)
|+|||++|||.+|+|+ .|||....
T Consensus 449 rnwnIr~pGf~~d~I~~s~rk~~pt 473 (505)
T COG5624 449 RNWNIRCPGFVDDIIHMSYRKQKPT 473 (505)
T ss_pred cccceecCcchHHHHHHHHHhcCCC
Confidence 9999999999999998 99998754
No 4
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind
Probab=99.93 E-value=7.8e-26 Score=180.62 Aligned_cols=72 Identities=63% Similarity=1.080 Sum_probs=70.7
Q ss_pred cCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccc
Q 010992 401 ILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTL 472 (496)
Q Consensus 401 ILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~I 472 (496)
+++|++|++||++||++++||+||+++|+++|||||++|+++||+||||||++||+++||+|||||+|||+|
T Consensus 1 i~~k~~l~~lv~~id~~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r~~~~~~ 72 (72)
T cd07981 1 ILTKRKLQELLKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLERNWNISI 72 (72)
T ss_pred CCcHHHHHHHHHhhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhcCCCC
Confidence 689999999999999999999999999999999999999999999999999999999999999999999986
No 5
>PLN00035 histone H4; Provisional
Probab=98.85 E-value=1.3e-08 Score=88.55 Aligned_cols=74 Identities=24% Similarity=0.358 Sum_probs=69.1
Q ss_pred CCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCCCc
Q 010992 402 LTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSG 477 (496)
Q Consensus 402 LtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGFss 477 (496)
|+|..|.+|++.- .-+.|.+|+.|.|.++.++|+++|+..|+.+|+|.+-.||+++||.|.|+|.+. .+.||+.
T Consensus 30 ipk~~IrRLARr~-GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~-~lyGf~~ 103 (103)
T PLN00035 30 ITKPAIRRLARRG-GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGR-TLYGFGG 103 (103)
T ss_pred CCHHHHHHHHHHc-CcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCC-cCCCCCC
Confidence 8999999999986 578999999999999999999999999999999999999999999999999755 8999963
No 6
>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution
Probab=98.80 E-value=2.2e-08 Score=84.28 Aligned_cols=74 Identities=24% Similarity=0.384 Sum_probs=69.4
Q ss_pred ccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCC
Q 010992 400 RILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGF 475 (496)
Q Consensus 400 rILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGF 475 (496)
.-|+|..|.+|++.- +-..|.+|+.|.|.++.++|+++|+..|+.+|+|.+-.||+..||.+.|+|. |..+-||
T Consensus 12 ~gi~k~~I~RLarr~-GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~-g~~~ygf 85 (85)
T cd00076 12 KGITKPAIRRLARRG-GVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQ-GRTLYGY 85 (85)
T ss_pred ccCCHHHHHHHHHHc-CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHC-CCCccCC
Confidence 449999999999985 5789999999999999999999999999999999999999999999999995 8888887
No 7
>PTZ00015 histone H4; Provisional
Probab=98.78 E-value=3e-08 Score=86.14 Aligned_cols=76 Identities=24% Similarity=0.337 Sum_probs=69.3
Q ss_pred CCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCC
Q 010992 398 GNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGF 475 (496)
Q Consensus 398 ~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGF 475 (496)
.-+-|+|..|.+|++.- .-+.|.+|+.|.|.++.++|+++|+..|+.+|+|.+-.||+++||.|.|+|.+. .+-||
T Consensus 27 ~i~gI~k~~IrRLarr~-GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~-~~ygf 102 (102)
T PTZ00015 27 NIRGITKGAIRRLARRG-GVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGR-TLYGF 102 (102)
T ss_pred cccCCCHHHHHHHHHHc-CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCC-CCCCC
Confidence 34568999999999974 778999999999999999999999999999999999999999999999999755 77777
No 8
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=98.59 E-value=8.6e-08 Score=81.85 Aligned_cols=71 Identities=24% Similarity=0.386 Sum_probs=66.4
Q ss_pred CcCCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992 396 EFGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERN 467 (496)
Q Consensus 396 e~~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn 467 (496)
.+...+|++..+.+|+|++... ++..++.|.|.+.+++|+..|.+.||.+|+|.|..||+.+||++.|++.
T Consensus 14 ~~~~~~Lp~apv~Ri~r~~~~~-Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~ 84 (91)
T COG2036 14 RSTDLLLPKAPVRRILRKAGAE-RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRL 84 (91)
T ss_pred hhhhhhcCchHHHHHHHHHhHH-HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHh
Confidence 3566789999999999999665 9999999999999999999999999999999999999999999999885
No 9
>PF00125 Histone: Core histone H2A/H2B/H3/H4 histone h2a signature histone h2b signature histone h3 signature histone h4 signature; InterPro: IPR007125 The core histones together with some other DNA binding proteins appear to form a superfamily defined by a common fold and distant sequence similarities [, ]. Some proteins contain local homology domains related to the histone fold [].; GO: 0003677 DNA binding; PDB: 2YFW_D 2YFV_B 1U35_H 2F8N_D 2PYO_D 2NQB_D 3AN2_C 3AZJ_C 3AV1_G 3AZM_G ....
Probab=98.40 E-value=5e-07 Score=70.85 Aligned_cols=68 Identities=22% Similarity=0.317 Sum_probs=61.5
Q ss_pred CccCCHHHHHHHHHhhCCC----CCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992 399 NRILTKRSIQELVNQIDPS----ERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER 466 (496)
Q Consensus 399 nrILtKrKLqELVrqIDPs----esLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER 466 (496)
...+.|--+..|+++|..+ ..++.++.++|..++|+|+.+|++.|+.+|+|.|..+|..+||++++..
T Consensus 3 ~~~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r~ 74 (75)
T PF00125_consen 3 RRLIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVRI 74 (75)
T ss_dssp SHSSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHHH
T ss_pred ccccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHhc
Confidence 3456778888888888665 7999999999999999999999999999999999999999999998864
No 10
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=98.35 E-value=2e-06 Score=68.77 Aligned_cols=64 Identities=22% Similarity=0.308 Sum_probs=59.6
Q ss_pred cCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992 401 ILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLE 465 (496)
Q Consensus 401 ILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE 465 (496)
+|++..|.+|++.++- ..|.+|+.+.|.+.++.|+..|+..|+++++|-|..||...||.+.|+
T Consensus 2 ~~p~~~i~ria~~~Gi-~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 2 WLPKETIKDVAESLGI-GNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred CCCHHHHHHHHHHCCC-ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 5789999999999744 589999999999999999999999999999999999999999999885
No 11
>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi
Probab=98.27 E-value=3.5e-06 Score=73.86 Aligned_cols=68 Identities=13% Similarity=0.288 Sum_probs=60.3
Q ss_pred HHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCcccc
Q 010992 405 RSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLP 473 (496)
Q Consensus 405 rKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IP 473 (496)
+-+..+++.. +-+.++++|...|+|++..++.+|+..|..+|||-|.++|+++||+|.++...+..|-
T Consensus 5 ~~v~~iLk~~-Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~~~f~ 72 (117)
T cd07979 5 RVIAAILKSM-GITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVDYSFT 72 (117)
T ss_pred HHHHHHHHHC-CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccCCC
Confidence 3466777765 5578999999999999999999999999999999999999999999999998885553
No 12
>smart00417 H4 Histone H4.
Probab=98.23 E-value=3e-06 Score=70.12 Aligned_cols=64 Identities=19% Similarity=0.299 Sum_probs=59.2
Q ss_pred CCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHH
Q 010992 398 GNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILV 462 (496)
Q Consensus 398 ~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQL 462 (496)
..+-|+|..|.+|+++ .+-+.|..++.|.|.++.++|+++|+..|+.+|+|.+-.||++.||.|
T Consensus 10 ~i~gI~k~~IrRLaRr-~GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~ 73 (74)
T smart00417 10 NIQGITKPAIRRLARR-GGVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVY 73 (74)
T ss_pred hhcCCCHHHHHHHHHH-cCcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHhee
Confidence 3456999999999997 477899999999999999999999999999999999999999999975
No 13
>PF00808 CBFD_NFYB_HMF: Histone-like transcription factor (CBF/NF-Y) and archaeal histone; InterPro: IPR003958 The CCAAT-binding factor (CBF) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin. The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding [, ]. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The A subunit can be split into 3 domains on the basis of sequence similarity, a non-conserved N-terminal 'A domain'; a highly-conserved central 'B domain' involved in DNA-binding; and a C-terminal 'C domain', which contains a number of glutamine and acidic residues involved in protein-protein interactions []. The A subunit shows striking similarity to the HAP3 subunit of the yeast CCAAT-binding heterotrimeric transcription factor [, ]. The Kluyveromyces lactis HAP3 protein has been predicted to contain a 4-cysteine zinc finger, which is thought to be present in similar HAP3 and CBF subunit A proteins, in which the third cysteine is replaced by a serine []. This domain is found in the CCAAT transcription factor and archaeal histones.; GO: 0043565 sequence-specific DNA binding, 0005622 intracellular; PDB: 1F1E_A 2BYM_D 2BYK_D 1HTA_A 1B67_A 1JFI_B 1KU5_B 1N1J_A 1BFM_A 1B6W_A ....
Probab=98.15 E-value=7.8e-06 Score=63.49 Aligned_cols=63 Identities=14% Similarity=0.274 Sum_probs=55.6
Q ss_pred CCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHH
Q 010992 402 LTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHL 464 (496)
Q Consensus 402 LtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhL 464 (496)
|.+.++..+++.......+..|+.++|.+.++.||+.++..|...|++.+..||..+||...|
T Consensus 3 lP~a~vkri~k~~~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 3 LPLARVKRIMKSDPDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp S-HHHHHHHHHHTSTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred CChHHHHHHhccCCCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 678899999999855668999999999999999999999999999999999999999997664
No 14
>KOG3467 consensus Histone H4 [Chromatin structure and dynamics]
Probab=98.14 E-value=8.1e-06 Score=70.85 Aligned_cols=78 Identities=24% Similarity=0.333 Sum_probs=69.1
Q ss_pred CCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCCCc
Q 010992 398 GNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSG 477 (496)
Q Consensus 398 ~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGFss 477 (496)
.-+-|+|-.|.+|.+.- .-..+..-..|-.-..+.+||+||+..||-.+.|-|.+||...||.+.|+|. ++.+-||++
T Consensus 26 nIqgitKpaIRRlARr~-GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~-G~~~~g~~~ 103 (103)
T KOG3467|consen 26 NIQGITKPAIRRLARRG-GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQ-GRTLYGFGG 103 (103)
T ss_pred hccccchHHHHHHHHhc-CcchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHc-CceeeccCC
Confidence 34557899999999974 4567788888889999999999999999999999999999999999999996 999999974
No 15
>smart00428 H3 Histone H3.
Probab=98.10 E-value=8.5e-06 Score=71.28 Aligned_cols=69 Identities=25% Similarity=0.241 Sum_probs=63.0
Q ss_pred CcCCccCCHHHHHHHHHhhCC------CCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHH
Q 010992 396 EFGNRILTKRSIQELVNQIDP------SERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHL 464 (496)
Q Consensus 396 e~~nrILtKrKLqELVrqIDP------sesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhL 464 (496)
.+.+-+|.|.-+.+||++|.. +..+.+++.++|.+.+|+|+.++.+.+..+|+|.|-.||..|||+|+.
T Consensus 24 kst~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~ 98 (105)
T smart00428 24 KSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLAR 98 (105)
T ss_pred cCcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHH
Confidence 356678899999999999942 468999999999999999999999999999999999999999999986
No 16
>PLN00161 histone H3; Provisional
Probab=97.86 E-value=4.2e-05 Score=69.80 Aligned_cols=78 Identities=21% Similarity=0.125 Sum_probs=67.5
Q ss_pred CcCCccCCHHHHHHHHHhhC-----CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCc
Q 010992 396 EFGNRILTKRSIQELVNQID-----PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNM 470 (496)
Q Consensus 396 e~~nrILtKrKLqELVrqID-----PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI 470 (496)
.+.+-+|.|--++.||++|- .+..+..++.++|.|.+|+|+-++.+.+-..|.|+|--||..|||+|+. |--+.
T Consensus 50 kst~lLIpklPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~-rirg~ 128 (135)
T PLN00161 50 KSTELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLAR-RIRGP 128 (135)
T ss_pred cccccccccccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHH-Hhccc
Confidence 45677889999999999993 3478999999999999999999999999999999999999999999986 44455
Q ss_pred cccC
Q 010992 471 TLPG 474 (496)
Q Consensus 471 ~IPG 474 (496)
++.+
T Consensus 129 ~~~~ 132 (135)
T PLN00161 129 IYGI 132 (135)
T ss_pred cccc
Confidence 5543
No 17
>PLN00121 histone H3; Provisional
Probab=97.72 E-value=7.2e-05 Score=68.28 Aligned_cols=69 Identities=23% Similarity=0.201 Sum_probs=63.8
Q ss_pred CcCCccCCHHHHHHHHHhhC----CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHH
Q 010992 396 EFGNRILTKRSIQELVNQID----PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHL 464 (496)
Q Consensus 396 e~~nrILtKrKLqELVrqID----PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhL 464 (496)
.+.+-+|.|--+..||++|. .+..+..++.++|.|.+|+|+-++.+.+-..|.|.|--||..|||+|+.
T Consensus 57 kst~lLI~k~pF~RLVREI~~~~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ 129 (136)
T PLN00121 57 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
T ss_pred cccccccccccHHHHHHHHHHHhCccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHH
Confidence 45678899999999999994 4579999999999999999999999999999999999999999999986
No 18
>PF02291 TFIID-31kDa: Transcription initiation factor IID, 31kD subunit; InterPro: IPR003162 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []. TAFII-31 protein is a transcriptional coactivator of the p53 protein [].; GO: 0006352 transcription initiation, DNA-dependent; PDB: 1TAF_A.
Probab=97.71 E-value=0.00011 Score=66.25 Aligned_cols=73 Identities=16% Similarity=0.330 Sum_probs=52.5
Q ss_pred ccCCH--HHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCcccc
Q 010992 400 RILTK--RSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLP 473 (496)
Q Consensus 400 rILtK--rKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IP 473 (496)
..+.| +.|..|++.+ +-...|+.|.-.|||+|-.|+.+|+..|-.+|+|.+..++++.||+|.++-..+..|-
T Consensus 9 ~~~PrDa~~i~~iL~~~-Gv~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~~~f~ 83 (129)
T PF02291_consen 9 KSLPRDARVIHLILKSM-GVTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLDHSFT 83 (129)
T ss_dssp ----HHHHHHHHHHHHT-T---B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT------
T ss_pred ccCChHHHHHHHHHHHc-CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHhhhcc
Confidence 34444 4577888887 4456899999999999999999999999999999999999999999999977776663
No 19
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=97.68 E-value=0.00028 Score=57.26 Aligned_cols=68 Identities=12% Similarity=0.261 Sum_probs=58.3
Q ss_pred CHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccc
Q 010992 403 TKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTL 472 (496)
Q Consensus 403 tKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~I 472 (496)
-|..+..+++.. +-+.+++++.|.|.+|+++|+..+...+-++|+|-+..++.+.||.+.|++ .|+.+
T Consensus 8 l~~~Vaqil~~~-Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~-~gi~~ 75 (77)
T smart00576 8 LRIAVAQILESA-GFDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALEN-LGISV 75 (77)
T ss_pred HHHHHHHHHHHc-CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH-hCccc
Confidence 355566666654 457899999999999999999999999999999999999999999999987 47765
No 20
>PTZ00018 histone H3; Provisional
Probab=97.63 E-value=9.8e-05 Score=67.40 Aligned_cols=69 Identities=23% Similarity=0.201 Sum_probs=63.9
Q ss_pred CcCCccCCHHHHHHHHHhhC----CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHH
Q 010992 396 EFGNRILTKRSIQELVNQID----PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHL 464 (496)
Q Consensus 396 e~~nrILtKrKLqELVrqID----PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhL 464 (496)
...+-+|.|--+..||++|. .+..+..++.++|.|.+|+|+-++.+.+-..|.|.|--||..|||+|+.
T Consensus 57 kst~lLI~k~pF~RLVREI~~~~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ 129 (136)
T PTZ00018 57 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
T ss_pred ccchhccccccHHHHHHHHHHHcCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHH
Confidence 45678899999999999994 4679999999999999999999999999999999999999999999885
No 21
>cd08050 TAF6 TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as
Probab=97.56 E-value=0.00041 Score=69.72 Aligned_cols=75 Identities=23% Similarity=0.287 Sum_probs=63.5
Q ss_pred HHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCCCccc
Q 010992 404 KRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGDE 479 (496)
Q Consensus 404 KrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGFssDE 479 (496)
++.+.++++.+ +-+.+++|+.+.|.+.+++++..|+..|+++|||-|..+|.+.||.+.|+..=--.+-||..-+
T Consensus 2 ~~~i~~ia~~~-Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~eplyG~~~~~ 76 (343)
T cd08050 2 QESIKLIAESL-GIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNVEPLYGFSSSE 76 (343)
T ss_pred hhHHHHHHHHc-CCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCCCcccCCCCCc
Confidence 45677777776 4568999999999999999999999999999999999999999999999885334566776543
No 22
>PLN00160 histone H3; Provisional
Probab=97.54 E-value=0.00018 Score=62.56 Aligned_cols=69 Identities=19% Similarity=0.135 Sum_probs=62.5
Q ss_pred CcCCccCCHHHHHHHHHhhCC-----CCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHH
Q 010992 396 EFGNRILTKRSIQELVNQIDP-----SERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHL 464 (496)
Q Consensus 396 e~~nrILtKrKLqELVrqIDP-----sesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhL 464 (496)
.+.+-+|.|.-++.||++|.. +..+..++.++|.+.+|+|+-.+.+.+-..|.|.|--||..||++|+.
T Consensus 16 kst~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~ 89 (97)
T PLN00160 16 KSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLAR 89 (97)
T ss_pred cchhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHH
Confidence 345678899999999999942 368899999999999999999999999999999999999999999985
No 23
>PF02269 TFIID-18kDa: Transcription initiation factor IID, 18kD subunit; InterPro: IPR003195 This family includes the Spt3 yeast transcription factors and the 18 kDa subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histone fold [].; GO: 0006366 transcription from RNA polymerase II promoter; PDB: 1BH9_A 1BH8_A.
Probab=97.42 E-value=0.00016 Score=61.19 Aligned_cols=61 Identities=20% Similarity=0.405 Sum_probs=31.9
Q ss_pred HHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992 407 IQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERN 467 (496)
Q Consensus 407 LqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn 467 (496)
|..|+--.+-...-.+|..++|-+|+-+||-+++..|+++|.+||+..|.++|+.|.|.|+
T Consensus 7 I~~mMy~fGD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~D 67 (93)
T PF02269_consen 7 IRQMMYGFGDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRKD 67 (93)
T ss_dssp CHHHHHCTTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC----------------------
T ss_pred HHHHHHHcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhcC
Confidence 5667776666678889999999999999999999999999999999999999999999885
No 24
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=97.25 E-value=0.00072 Score=56.18 Aligned_cols=61 Identities=18% Similarity=0.282 Sum_probs=50.8
Q ss_pred HHHHHHhh--CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992 407 IQELVNQI--DPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERN 467 (496)
Q Consensus 407 LqELVrqI--DPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn 467 (496)
+..+++++ +.+..+.+++...|.||+-++++++...--.+|||.|.+||+.+||.|...||
T Consensus 11 v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~Rrn 73 (76)
T PF15630_consen 11 VGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLARRN 73 (76)
T ss_dssp HHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTTT-
T ss_pred HHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhhcC
Confidence 34566666 35668999999999999999999999999999999999999999999999887
No 25
>smart00427 H2B Histone H2B.
Probab=97.19 E-value=0.0016 Score=56.17 Aligned_cols=60 Identities=22% Similarity=0.372 Sum_probs=56.4
Q ss_pred HHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992 407 IQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER 466 (496)
Q Consensus 407 LqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER 466 (496)
|...+++|.|+..|...+..+|--+++|+.|.|...|++||+..|..||..+||+...+-
T Consensus 7 i~kvLKqVhpd~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl 66 (89)
T smart00427 7 IYKVLKQVHPDTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRL 66 (89)
T ss_pred HHHHHHHhCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHH
Confidence 678899999999999999999999999999999999999999999999999999877654
No 26
>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex. TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.
Probab=97.06 E-value=0.0028 Score=51.62 Aligned_cols=64 Identities=17% Similarity=0.297 Sum_probs=50.7
Q ss_pred cCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992 401 ILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLE 465 (496)
Q Consensus 401 ILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE 465 (496)
+++++.+......++ -..|++|+..+|.+-++-.|..|+..|+++++|-|..+|...||...|+
T Consensus 3 ~~~~esvk~iAes~G-i~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 3 VFSQESVKDIAESLG-ISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp ---HHHHHHHHHHTT----B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred cCCHHHHHHHHHHcC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 677888888888874 4679999999999999999999999999999999999999999998874
No 27
>KOG0869 consensus CCAAT-binding factor, subunit A (HAP3) [Transcription]
Probab=96.85 E-value=0.0034 Score=59.29 Aligned_cols=71 Identities=13% Similarity=0.298 Sum_probs=64.3
Q ss_pred CcCCccCCHHHHHHHHHhh-CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992 396 EFGNRILTKRSIQELVNQI-DPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER 466 (496)
Q Consensus 396 e~~nrILtKrKLqELVrqI-DPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER 466 (496)
-+..++|.=.++-+++|++ .++.+|.+|+.|.+.|++.|||.=|+..|...|-.-|.+||...||.+.|..
T Consensus 27 reqDr~LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~t 98 (168)
T KOG0869|consen 27 REQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMST 98 (168)
T ss_pred chhhhhccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHH
Confidence 4567889989999999886 6688999999999999999999999999999999999999999999877664
No 28
>PF07524 Bromo_TP: Bromodomain associated; InterPro: IPR006565 This bromodomain is found in eukaryotic transcription factors and PHD domain containing proteins (IPR001965 from INTERPRO). The tandem PHD finger-bromodomain is found in many chromatin-associated proteins. It is involved in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). The tandem PHD finger-bromodomain of KAP1 has a distinct structure that joins the two protein modules. The first helix, alpha(Z), of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD finger on the other []. The Rap1 GTPase-activating protein, Sipa1, is modulated by the cellular bromodomain protein, Brd4. Brd4 belongs to the BET family and is a multifunctional protein involved in transcription, replication, the signal transduction pathway, and cell cycle progression. All of these functions are linked to its association with acetylated chromatin. It has tandem bromodomains []. The dysregulation of the Brd4-associated pathways may play an important role in breast cancer progression []. Bovine papillomavirus type 1 E2 also binds to chromosomes in a complex with Brd4. Interaction with Brd4 is additionally important for E2-mediated transcriptional regulation [, ].
Probab=96.83 E-value=0.0088 Score=48.06 Aligned_cols=64 Identities=16% Similarity=0.297 Sum_probs=53.2
Q ss_pred HHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccc
Q 010992 407 IQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTL 472 (496)
Q Consensus 407 LqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~I 472 (496)
+..+++.+ +=+...+.+.|.|.+|+.+||.++...+-++|.|.+.....+.||.+.|+. .|+.+
T Consensus 12 va~il~~~-GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~-~gi~v 75 (77)
T PF07524_consen 12 VAQILKHA-GFDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEE-MGISV 75 (77)
T ss_pred HHHHHHHc-CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH-hCCCC
Confidence 33344432 346789999999999999999999999999999999999999999999976 46654
No 29
>PLN00158 histone H2B; Provisional
Probab=96.82 E-value=0.0047 Score=55.60 Aligned_cols=59 Identities=20% Similarity=0.355 Sum_probs=56.1
Q ss_pred HHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992 407 IQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLE 465 (496)
Q Consensus 407 LqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE 465 (496)
|...+++|.|...|...+..+|--+.+|+.|.|...|++||++.+..||..+||+-..+
T Consensus 33 I~kVLKQVhPd~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvr 91 (116)
T PLN00158 33 IYKVLKQVHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVR 91 (116)
T ss_pred HHHHHHHhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHH
Confidence 88899999999999999999999999999999999999999999999999999987654
No 30
>PTZ00463 histone H2B; Provisional
Probab=96.74 E-value=0.0058 Score=55.12 Aligned_cols=65 Identities=25% Similarity=0.410 Sum_probs=59.1
Q ss_pred HHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCC
Q 010992 407 IQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGF 475 (496)
Q Consensus 407 LqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGF 475 (496)
|...|++|.|...|...+..+|--+.+|..|.|...|++||+..+..||..+||+-.++ +.+||-
T Consensus 34 I~KVLKqVhPd~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvr----LlLpGE 98 (117)
T PTZ00463 34 IFKVLKQVHPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIR----LVLPGE 98 (117)
T ss_pred HHHHHHhhCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHh----hcccHH
Confidence 88999999999999999999999999999999999999999999999999999987754 445653
No 31
>KOG3334 consensus Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=96.55 E-value=0.01 Score=55.31 Aligned_cols=68 Identities=15% Similarity=0.289 Sum_probs=61.0
Q ss_pred HHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccC
Q 010992 406 SIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPG 474 (496)
Q Consensus 406 KLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPG 474 (496)
.|.-+++.+ +-...|+-|.-.|||+|-.++..|+..|--+++|-+..+|++.||.|.++..-|..|-+
T Consensus 18 ~i~~iL~s~-GI~eyEprVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~~sf~~ 85 (148)
T KOG3334|consen 18 VIASILKSL-GIQEYEPRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVDHSFTP 85 (148)
T ss_pred HHHHHHHHc-CccccChHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhccccCC
Confidence 345666665 66789999999999999999999999999999999999999999999999988888866
No 32
>cd07978 TAF13 The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Several hy
Probab=96.55 E-value=0.014 Score=49.94 Aligned_cols=62 Identities=16% Similarity=0.410 Sum_probs=52.6
Q ss_pred HHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992 405 RSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERN 467 (496)
Q Consensus 405 rKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn 467 (496)
+.|..|+--.+-...-.+|..++|-+|.-+||-+++..||.+|..|++. +.++|+.|.|.++
T Consensus 6 ~ei~~mmy~~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~~r~~k-~~~eD~~FliR~D 67 (92)
T cd07978 6 KEIRQMMYGFGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQRRRGK-VKVEDLIFLLRKD 67 (92)
T ss_pred HHHHHHHHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCC-CCHHHHHHHHhcC
Confidence 4488888877666677888999999999999999999999999955555 5999999999764
No 33
>cd08048 TAF11 TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypothes
Probab=96.53 E-value=0.014 Score=49.44 Aligned_cols=65 Identities=17% Similarity=0.244 Sum_probs=57.5
Q ss_pred CCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCC---CCcchhhHHHHHhhh
Q 010992 402 LTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKS---DTLEAKDILVHLERN 467 (496)
Q Consensus 402 LtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKS---dTLEvKDVQLhLERn 467 (496)
|+|.++..|+..+.. .++.++|..+|..||..||-++++.|..+.+.++. .-|..+.|.-.+.|.
T Consensus 17 f~k~~iKr~~~~~~~-~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~rrl 84 (85)
T cd08048 17 FPKAAIKRLIQSVTG-QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYRRL 84 (85)
T ss_pred ccHHHHHHHHHHHcC-CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHHHh
Confidence 899999999999866 89999999999999999999999999999999887 677777776666553
No 34
>cd00074 H2A Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins.
Probab=96.26 E-value=0.014 Score=51.88 Aligned_cols=69 Identities=10% Similarity=0.168 Sum_probs=63.5
Q ss_pred CCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992 398 GNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER 466 (496)
Q Consensus 398 ~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER 466 (496)
.+-+|.-.+++.++++-...++++.++-..|..+.|.|+.+|++.|..+|||.|...|..+||++.+..
T Consensus 17 agL~fPV~ri~R~Lk~~~~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~n 85 (115)
T cd00074 17 AGLQFPVGRIHRYLKKGRYAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRN 85 (115)
T ss_pred cCccCcHHHHHHHHHcCccccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhc
Confidence 456788999999999765678999999999999999999999999999999999999999999999876
No 35
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=96.05 E-value=0.031 Score=52.55 Aligned_cols=74 Identities=14% Similarity=0.338 Sum_probs=68.3
Q ss_pred CCCcCCccCCHHHHHHHHHhhCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992 394 SDEFGNRILTKRSIQELVNQIDP-SERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERN 467 (496)
Q Consensus 394 ~~e~~nrILtKrKLqELVrqIDP-sesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn 467 (496)
+.++++--|.|..++.+|++|=| +..+..|+.|+|.+.+-+||.-|...|-++|-.+...||-.+-|.-.||+.
T Consensus 5 ~~~dde~sLPkAtv~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~L 79 (156)
T KOG0871|consen 5 GKEDDELSLPKATVNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENL 79 (156)
T ss_pred ccccccccCcHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHc
Confidence 34566777999999999999977 889999999999999999999999999999999999999999999999874
No 36
>KOG1744 consensus Histone H2B [Chromatin structure and dynamics]
Probab=95.85 E-value=0.026 Score=51.55 Aligned_cols=60 Identities=17% Similarity=0.308 Sum_probs=54.9
Q ss_pred HHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992 407 IQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER 466 (496)
Q Consensus 407 LqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER 466 (496)
+...+++|++..-|..+...++--+.+||+|+|+..|-+||..+|..||..++|+..++-
T Consensus 43 v~kvlk~Vhpd~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rL 102 (127)
T KOG1744|consen 43 VYKVLKQVHPDLGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRL 102 (127)
T ss_pred hhhhhhcccCCCCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHH
Confidence 334889999999999999999999999999999999999999999999999999886554
No 37
>KOG2549 consensus Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=95.74 E-value=0.052 Score=59.28 Aligned_cols=93 Identities=20% Similarity=0.235 Sum_probs=78.2
Q ss_pred CcCCccCC-HHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccC
Q 010992 396 EFGNRILT-KRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPG 474 (496)
Q Consensus 396 e~~nrILt-KrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPG 474 (496)
+..+-|+. +..++.+++.| +-+.|++|+.++|.+-.+.-|.+|+..|.+.-+|-|..+|.+.||...|.-.-=--+-|
T Consensus 5 ~~~~~v~s~~Es~k~vAEsl-Gi~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~nVep~yg 83 (576)
T KOG2549|consen 5 KESPTVVSPKESVKVVAESL-GITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLNVEPLYG 83 (576)
T ss_pred cccccccCcHHHHHHHHHHh-CccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhcccccccC
Confidence 34455666 77777777776 66889999999999999999999999999999999999999999998776543366789
Q ss_pred CCcccccccCCcccc
Q 010992 475 FSGDEIKTFRKPVRI 489 (496)
Q Consensus 475 FssDEIr~~rk~~~~ 489 (496)
|++-|+-.||+....
T Consensus 84 ~~s~~~i~fr~a~~~ 98 (576)
T KOG2549|consen 84 FGAQEIIPFRKASGG 98 (576)
T ss_pred cccCceeeccccCCC
Confidence 999999999987655
No 38
>KOG3423 consensus Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=95.67 E-value=0.056 Score=51.67 Aligned_cols=69 Identities=23% Similarity=0.347 Sum_probs=58.0
Q ss_pred CHHHHHHHHHhhCC------------------CCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCC------------
Q 010992 403 TKRSIQELVNQIDP------------------SERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKS------------ 452 (496)
Q Consensus 403 tKrKLqELVrqIDP------------------sesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKS------------ 452 (496)
.-..|.||+.++|- -.+.|+-|..||.-.|-+||.||+..|.+.||-|..
T Consensus 69 ~d~~l~efl~qLddYtP~IPDavt~~yL~~aGf~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kd 148 (176)
T KOG3423|consen 69 KDTHLEEFLAQLDDYTPTIPDAVTDHYLKKAGFQTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKD 148 (176)
T ss_pred cchHHHHHHHHHhcCCCCCcHHHHHHHHHhcCCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccc
Confidence 34568889988863 357788899999999999999999999999999984
Q ss_pred --CCcchhhHHHHHhhhcCccc
Q 010992 453 --DTLEAKDILVHLERNWNMTL 472 (496)
Q Consensus 453 --dTLEvKDVQLhLERnWNI~I 472 (496)
-||.++|+.-+|+. |||.|
T Consensus 149 kK~tLtmeDL~~AL~E-yGinv 169 (176)
T KOG3423|consen 149 KKYTLTMEDLSPALAE-YGINV 169 (176)
T ss_pred cceeeeHHHHHHHHHH-hCccc
Confidence 27899999888875 89887
No 39
>PF09415 CENP-X: CENP-S associating Centromere protein X; InterPro: IPR018552 Centromere protein X (CENP-X) is a component of the CENP-S complex. The CENP-S complex is composed of at least of CENP-S and CENP-X and is essential for the stable assembly of the outer kinetchore []. CENP-X is also a DNA-binding component of the Fanconi anemia (FA) core complex involved in DNA damage repair and genome maintenance. The FA complex is composed of CENPS, FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL/PHF9, FANCM, FAAP24 and CENPX. Interacts with CENPS, FANCM and FAAP24 [, ].; PDB: 4DRB_L 4DRA_H 3V9R_D.
Probab=95.67 E-value=0.013 Score=48.24 Aligned_cols=60 Identities=17% Similarity=0.216 Sum_probs=47.3
Q ss_pred HHHHHHHHhh--CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCC-cchhhHHHHH
Q 010992 405 RSIQELVNQI--DPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDT-LEAKDILVHL 464 (496)
Q Consensus 405 rKLqELVrqI--DPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdT-LEvKDVQLhL 464 (496)
+-|.+|++.- |.+.+|.+|+-+++.++.|-||...+.+|+..|+-.+.+. ||+.|++-++
T Consensus 3 ~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki~ 65 (72)
T PF09415_consen 3 ELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKIL 65 (72)
T ss_dssp HHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHC
T ss_pred HHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHH
Confidence 3455666632 6778999999999999999999999999999999999999 9999986543
No 40
>PF04719 TAFII28: hTAFII28-like protein conserved region; InterPro: IPR006809 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C terminus of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3 [, ].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005634 nucleus; PDB: 1BH9_B 1BH8_B.
Probab=95.16 E-value=0.082 Score=45.55 Aligned_cols=60 Identities=20% Similarity=0.276 Sum_probs=44.7
Q ss_pred CCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCC-CcchhhHH
Q 010992 402 LTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSD-TLEAKDIL 461 (496)
Q Consensus 402 LtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSd-TLEvKDVQ 461 (496)
|+|..|..|++.+..+..+.+.|.-+|..||.-||-++|+.|..+.+.++.. .|..+.|.
T Consensus 24 ~~k~~ikkli~~~~~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~hlr 84 (90)
T PF04719_consen 24 FNKAAIKKLINQVLGNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDHLR 84 (90)
T ss_dssp --HHHHHHHHHHHHS-S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHHHH
T ss_pred CCHHHHHHHHHHHcCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHH
Confidence 7899999999999988999999999999999999999999999999976644 34444443
No 41
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=94.68 E-value=0.057 Score=56.18 Aligned_cols=60 Identities=18% Similarity=0.233 Sum_probs=43.1
Q ss_pred ccCCHHHHHHHHHhhC-----CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhh
Q 010992 400 RILTKRSIQELVNQID-----PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKD 459 (496)
Q Consensus 400 rILtKrKLqELVrqID-----PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKD 459 (496)
--|....++.|+..+. .+.+|.+|+.++|.++.|.|.+.+++.-+.+|||-|-+|||-.|
T Consensus 350 P~lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 350 PSLPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp --S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred CCCCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 3344444444444442 46799999999999999999999999999999999999999887
No 42
>KOG0870 consensus DNA polymerase epsilon, subunit D [Transcription]
Probab=94.67 E-value=0.047 Score=52.08 Aligned_cols=85 Identities=20% Similarity=0.246 Sum_probs=68.1
Q ss_pred ccCCHHHHHHHHHhhCC--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCCCc
Q 010992 400 RILTKRSIQELVNQIDP--SERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSG 477 (496)
Q Consensus 400 rILtKrKLqELVrqIDP--sesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGFss 477 (496)
-.|.+.-|.+||+++=+ +..|..|+..+|.+-|--||..++.+|-.+||.-+..||.+.||.-.|+.-=+-.|-+-..
T Consensus 9 l~lP~AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Eiefs~f~~plk 88 (172)
T KOG0870|consen 9 LNLPNAIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEIEFSSFVNPLK 88 (172)
T ss_pred hhccHHHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHhchHHHhhHHH
Confidence 45788999999999954 4689999999999999999999999999999999999999999998888643333333223
Q ss_pred ccccccC
Q 010992 478 DEIKTFR 484 (496)
Q Consensus 478 DEIr~~r 484 (496)
+.+--||
T Consensus 89 ~~Le~yk 95 (172)
T KOG0870|consen 89 SALEAYK 95 (172)
T ss_pred HHHHHHH
Confidence 3444444
No 43
>PF03540 TFIID_30kDa: Transcription initiation factor TFIID 23-30kDa subunit; InterPro: IPR003923 Transcription initiation factor TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. The complex includes TATA binding protein (TBP) and various TBP-associated factors (TAFS). TFIID a bona fide RNA polymerase II-specific TATA-binding protein-associated factor (TAF) and is essential for viability []. TFIID acts to nucleate the transcription complex, recruiting the rest of the factors through a direct interaction with TFIIB. The TBP subunit of TFIID is sufficient for TATA-element binding and TFIIB interaction, and can support basal transcription. The protein belongs to the TAF2H family.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus
Probab=94.10 E-value=0.23 Score=39.33 Aligned_cols=50 Identities=16% Similarity=0.213 Sum_probs=40.4
Q ss_pred cCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcC
Q 010992 401 ILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRK 451 (496)
Q Consensus 401 ILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRK 451 (496)
+|....++-.+++. +-..-|+-+..|+.-.|.+||.||++.|++.||.|.
T Consensus 2 ~IPD~v~~~yL~~~-G~~~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~r~ 51 (51)
T PF03540_consen 2 TIPDEVTDYYLERS-GFQTSDPRVKRLVSLAAQKFISDIANDAMQYCKIRT 51 (51)
T ss_pred CCCHHHHHHHHHHC-CCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 34455555566654 556789999999999999999999999999999883
No 44
>PF05236 TAF4: Transcription initiation factor TFIID component TAF4 family; InterPro: IPR007900 Accurate transcription initiation at protein-coding genes by RNA polymerase II requires the assembly of a multiprotein complex around the mRNA start site. Transcription factor TFIID is one of the general factors involved in this process. Yeast TFIID comprises the TATA binding protein and 14 TBP-associated factors (TAFIIs), nine of which contain histone-fold domains (IPR007124 from INTERPRO). The C-terminal region of the TFIID-specific yeast TAF4 (yTAF4) containing the HFD shares strong sequence similarity with Drosophila (d)TAF4 and human TAF4. A structure/function analysis of yTAF4 demonstrates that the HFD, a short conserved C-terminal domain (CCTD), and the region separating them are all required for yTAF4 function. This region of similarity is found in Transcription initiation factor TFIID component TAF4 []. ; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_C.
Probab=94.04 E-value=0.051 Score=52.75 Aligned_cols=59 Identities=20% Similarity=0.319 Sum_probs=36.9
Q ss_pred CcCCccCCHHHHHHHHHhhC---CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCC
Q 010992 396 EFGNRILTKRSIQELVNQID---PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDT 454 (496)
Q Consensus 396 e~~nrILtKrKLqELVrqID---PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdT 454 (496)
+....+|+...|...|++|. ....+|+||.++|..-+++++.+||+.+..+|+||....
T Consensus 38 ~~~~~fL~~~~L~~~i~~i~~~~g~~~~~~d~l~llS~A~e~rLr~lie~~~~~s~hR~~~~ 99 (264)
T PF05236_consen 38 EKEEPFLNPSPLQKRIQKIAKKHGLKSVDEDVLELLSLATEERLRNLIEKAIVLSRHRRDSS 99 (264)
T ss_dssp ------S-HHHHHHHHHHHHHCTT--EE-TCHHHHHHHHHHHHHHHHHHHHH----------
T ss_pred cccccccCHHHHHHHHHHHHHHcCCcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccc
Confidence 34556899999999999996 345699999999999999999999999999999998764
No 45
>KOG1745 consensus Histones H3 and H4 [Chromatin structure and dynamics]
Probab=93.90 E-value=0.042 Score=50.81 Aligned_cols=69 Identities=23% Similarity=0.218 Sum_probs=61.0
Q ss_pred cCCccCCHHHHHHHHHhhC----CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992 397 FGNRILTKRSIQELVNQID----PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLE 465 (496)
Q Consensus 397 ~~nrILtKrKLqELVrqID----PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE 465 (496)
..+-+|.|--.+.||++|. ++..+-.+++..|.|.+|.|+-...+.+-..|-|-|--||..|||+|++.
T Consensus 59 stdLlI~K~PFqRlvrei~q~f~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArr 131 (137)
T KOG1745|consen 59 STDLLIRKLPFQRLVREIAQDFKTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 131 (137)
T ss_pred hhHHHhhcCcHHHHhHHHHhcccccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhh
Confidence 4556777888899999884 45688899999999999999999999999999999999999999999764
No 46
>cd08045 TAF4 TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryote. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are
Probab=93.79 E-value=0.17 Score=47.92 Aligned_cols=59 Identities=15% Similarity=0.224 Sum_probs=50.9
Q ss_pred CCcCCccCCHHHHHHHHHhhCCCC---CCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCC
Q 010992 395 DEFGNRILTKRSIQELVNQIDPSE---RLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSD 453 (496)
Q Consensus 395 ~e~~nrILtKrKLqELVrqIDPse---sLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSd 453 (496)
......+|.+..|...|++|.... .+|+|+.++|...+++|+-+|++.+..+|+||...
T Consensus 38 ~~~~~~fl~~~~l~~~~~~i~~~~g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~ 99 (212)
T cd08045 38 SQKDPSFLNPSPLAKKIRKIAKKHGLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDS 99 (212)
T ss_pred ccchhhccCHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence 345567899999999999996543 67999999999999999999999999999999554
No 47
>COG5094 TAF9 Transcription initiation factor TFIID, subunit TAF9 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=92.77 E-value=0.36 Score=44.86 Aligned_cols=71 Identities=18% Similarity=0.221 Sum_probs=57.4
Q ss_pred HHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCC---CCcchhhHHHHHhhhcCccccCCCc
Q 010992 406 SIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKS---DTLEAKDILVHLERNWNMTLPGFSG 477 (496)
Q Consensus 406 KLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKS---dTLEvKDVQLhLERnWNI~IPGFss 477 (496)
-|+=+++.+ .-+..++.|.=-||++|-.|..+|++.|.-+|||-|+ .+|.++||.|.|.-.-|..|-+--.
T Consensus 19 lihliL~Sl-gi~~ye~~VplQLl~FAhRYTq~vl~Dalvya~htgrg~~a~l~veDvrLA~at~v~~~F~pppP 92 (145)
T COG5094 19 LIHLILRSL-GIEEYEPKVPLQLLEFAHRYTQDVLEDALVYAKHTGRGHIATLGVEDVRLALATKVGRHFVPPPP 92 (145)
T ss_pred HHHHHHHhc-CchhhCccchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccCcccHHHHHHHHHHHhcCCcCCCCh
Confidence 344455544 5567888899999999999999999999999999854 4678899999999888888755443
No 48
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=92.64 E-value=0.41 Score=46.21 Aligned_cols=47 Identities=23% Similarity=0.422 Sum_probs=38.5
Q ss_pred HHHHHHHHhhCC------------------CCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcC
Q 010992 405 RSIQELVNQIDP------------------SERLDPDVEDILVDIAEDFVESITMFGCSLAKHRK 451 (496)
Q Consensus 405 rKLqELVrqIDP------------------sesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRK 451 (496)
+.|.+|+..+|- -.+.|.-|..||.-+|-+||.||...|.++-|-|.
T Consensus 73 ktlee~l~~mDsy~PliPd~v~DYyl~k~Gf~~~D~rvKkLl~L~aqKFvsDiA~dayqYsrIr~ 137 (197)
T COG5162 73 KTLEELLQNMDSYTPLIPDSVTDYYLEKAGFVTSDQRVKKLLSLLAQKFVSDIAVDAYQYSRIRQ 137 (197)
T ss_pred HHHHHHHHhcccCCCCccHHHHHHHHHhcCceeccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 568899999984 24567888899999999999999998888776664
No 49
>COG5248 TAF19 Transcription initiation factor TFIID, subunit TAF13 [Transcription]
Probab=91.99 E-value=0.71 Score=42.15 Aligned_cols=59 Identities=17% Similarity=0.238 Sum_probs=49.0
Q ss_pred HHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992 407 IQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERN 467 (496)
Q Consensus 407 LqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn 467 (496)
|..|+=..+-...--.|..+.|-+++-|++.++|..|..+|-.|+. +.++|.+|+|.|.
T Consensus 15 ikslmYayGDvv~P~~dt~~~L~e~V~dY~~~~ctna~~~Aq~rnK--~k~eDfkfaLr~D 73 (126)
T COG5248 15 IKSLMYAYGDVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQVRNK--TKTEDFKFALRRD 73 (126)
T ss_pred HHHHHHHhCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHhccc--chHHHHHHHHhhC
Confidence 5566665555566667888999999999999999999999997765 5789999999874
No 50
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=91.82 E-value=0.76 Score=42.88 Aligned_cols=71 Identities=14% Similarity=0.284 Sum_probs=63.8
Q ss_pred CcCCccCCHHHHHHHHHhh-CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992 396 EFGNRILTKRSIQELVNQI-DPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER 466 (496)
Q Consensus 396 e~~nrILtKrKLqELVrqI-DPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER 466 (496)
.+++--|.|..++.+|..| +.+..+..|+.|++.+.+=+||.-+...|-.+|...+..||..+.|--.||.
T Consensus 6 ~dDe~sLPKATVqKMvS~iLp~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALen 77 (148)
T COG5150 6 NDDENSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALEN 77 (148)
T ss_pred ccccccCcHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHh
Confidence 4566779999999999998 5577999999999999999999999999999999999999999988777775
No 51
>KOG3901 consensus Transcription initiation factor IID subunit [Transcription]
Probab=91.13 E-value=1.1 Score=40.49 Aligned_cols=64 Identities=16% Similarity=0.360 Sum_probs=48.7
Q ss_pred ccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992 400 RILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERN 467 (496)
Q Consensus 400 rILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn 467 (496)
++++|. |.-|+=-.+-...-=+|..++|-+|+=|||.++++.|..++ +.+.|.++|++|.|.|.
T Consensus 9 ~lF~Kd-l~~mmYgfGDd~nP~~~tv~~Le~iV~~Yi~elt~~a~~~g---~rgk~~veD~~f~lRkD 72 (109)
T KOG3901|consen 9 HLFSKD-LRSMMYGFGDDVNPYPETVDLLEDIVLEYITELTHAAMEIG---KRGKVKVEDFKFLLRKD 72 (109)
T ss_pred HHHHHH-HHHHHHhcCCCCCccHhHHHHHHHHHHHHHHHHHHHHHHhc---ccCceeHHHHHHHHHhC
Confidence 344443 66666655555555667788999999999999999999888 34457899999999874
No 52
>smart00350 MCM minichromosome maintenance proteins.
Probab=88.86 E-value=1.6 Score=46.25 Aligned_cols=67 Identities=21% Similarity=0.282 Sum_probs=53.3
Q ss_pred CccCCHHHHHHHHHhhCC--CCCCCHHHHHHHHHHHHHH-------------------HHHHHHHHHHhhhhcCCCCcch
Q 010992 399 NRILTKRSIQELVNQIDP--SERLDPDVEDILVDIAEDF-------------------VESITMFGCSLAKHRKSDTLEA 457 (496)
Q Consensus 399 nrILtKrKLqELVrqIDP--sesLDpDVEELLLeIADDF-------------------VDsVvt~ACrLAKHRKSdTLEv 457 (496)
..+++...|.+.+..+-. .-.|+++++++|.+++.+. ++.++..|..+||.|.++.|+.
T Consensus 415 ~~~~~~~~l~~yi~~ar~~~~P~ls~~~~~~i~~~y~~~R~~~~~~~~~~~~~~t~R~l~sliRla~A~A~l~~r~~V~~ 494 (509)
T smart00350 415 EVPISQEFLRKYIAYAREKIKPKLSEEAAEKLVKAYVDLRKEDSQSEARSSIPITVRQLESIIRLSEAHAKMRLSDVVEE 494 (509)
T ss_pred cccCCHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHhcccccccccccccCcCHHHHHHHHHHHHHHHHHcCCCccCH
Confidence 357887777777655533 2358999999999887663 3788999999999999999999
Q ss_pred hhHHHHHh
Q 010992 458 KDILVHLE 465 (496)
Q Consensus 458 KDVQLhLE 465 (496)
+||+.+++
T Consensus 495 ~Dv~~ai~ 502 (509)
T smart00350 495 ADVEEAIR 502 (509)
T ss_pred HHHHHHHH
Confidence 99987765
No 53
>TIGR02902 spore_lonB ATP-dependent protease LonB. Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.
Probab=88.84 E-value=1.2 Score=47.60 Aligned_cols=66 Identities=18% Similarity=0.211 Sum_probs=51.9
Q ss_pred cCCHHHHHHHHHhhCC--CCCCCHHHHHHHHHHHHH--HHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992 401 ILTKRSIQELVNQIDP--SERLDPDVEDILVDIAED--FVESITMFGCSLAKHRKSDTLEAKDILVHLER 466 (496)
Q Consensus 401 ILtKrKLqELVrqIDP--sesLDpDVEELLLeIADD--FVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER 466 (496)
-|++..|.++++.+-. +..|++++.++|.+.+.+ .+.+++..||.+|..++...|+.+||..+|+.
T Consensus 262 pL~~eei~~Il~~~a~k~~i~is~~al~~I~~y~~n~Rel~nll~~Aa~~A~~~~~~~It~~dI~~vl~~ 331 (531)
T TIGR02902 262 PLLDEEIKEIAKNAAEKIGINLEKHALELIVKYASNGREAVNIVQLAAGIALGEGRKRILAEDIEWVAEN 331 (531)
T ss_pred CCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHhhhhHHHHHHHHHHHHHHHhhCCCcEEcHHHHHHHhCC
Confidence 4566777777776632 357899999988877653 35678899999999999999999999999874
No 54
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=88.67 E-value=2.1 Score=42.30 Aligned_cols=66 Identities=15% Similarity=0.211 Sum_probs=50.7
Q ss_pred CCHHHHHHHHHhhC----CCCCCCHHHHHHHHHHHHH------HHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992 402 LTKRSIQELVNQID----PSERLDPDVEDILVDIAED------FVESITMFGCSLAKHRKSDTLEAKDILVHLERN 467 (496)
Q Consensus 402 LtKrKLqELVrqID----PsesLDpDVEELLLeIADD------FVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn 467 (496)
++++.+.++++.-- ....+++++.+++.+++.. ++-+++..|+.+|+.|+.++|+.+||.-++++.
T Consensus 207 y~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~ 282 (394)
T PRK00411 207 YTADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKS 282 (394)
T ss_pred CCHHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH
Confidence 35666666655431 1346899999999998854 345788999999999999999999999888875
No 55
>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.
Probab=88.32 E-value=1.8 Score=40.19 Aligned_cols=67 Identities=6% Similarity=0.050 Sum_probs=54.0
Q ss_pred ccCCHHHHHHHHHhh----C--CCCCCCHHHHHHHHHHHHH---HHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992 400 RILTKRSIQELVNQI----D--PSERLDPDVEDILVDIAED---FVESITMFGCSLAKHRKSDTLEAKDILVHLER 466 (496)
Q Consensus 400 rILtKrKLqELVrqI----D--PsesLDpDVEELLLeIADD---FVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER 466 (496)
.-|+...+.++++.. . ....+++++.+.|.++++- +|+.++..+...|..++.+.|+..||...+..
T Consensus 190 ~~l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~ 265 (269)
T TIGR03015 190 GPLDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAE 265 (269)
T ss_pred CCCCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 345666777766543 2 2346999999999999997 89999999999999999999999999887765
No 56
>smart00414 H2A Histone 2A.
Probab=88.24 E-value=1.5 Score=38.70 Aligned_cols=68 Identities=10% Similarity=0.176 Sum_probs=60.8
Q ss_pred CccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992 399 NRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER 466 (496)
Q Consensus 399 nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER 466 (496)
+-.+.-.+++.++++-.-..+++..+--.|..+-|-++.+|++.|...||.-|...|..+||++.+..
T Consensus 7 gL~fPVgRi~r~Lk~~~~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~n 74 (106)
T smart00414 7 GLQFPVGRIHRLLRKGTYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIRN 74 (106)
T ss_pred CccCchHHHHHHHHcCccccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhccC
Confidence 34567788999999876678999999999999999999999999999999999999999999988765
No 57
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=87.56 E-value=2.1 Score=45.19 Aligned_cols=76 Identities=18% Similarity=0.249 Sum_probs=63.0
Q ss_pred ccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcC-ccccCCCc
Q 010992 400 RILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWN-MTLPGFSG 477 (496)
Q Consensus 400 rILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWN-I~IPGFss 477 (496)
-|.+|+.|.++...+ +-+.||||+-.+|..=.+--|..||..|.++-.|-|.++|.+.||-..|.- .| -.+-||..
T Consensus 4 t~ws~et~KdvAesl-Gi~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~-lNVePLyGyd~ 80 (450)
T COG5095 4 TLWSKETLKDVAESL-GISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRS-LNVEPLYGYDP 80 (450)
T ss_pred eeecHHHHHHHHHHc-CCcccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHh-cCCCcccCCCC
Confidence 356788888888765 567899999999988888899999999999999999999999999988865 35 33455554
No 58
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=86.24 E-value=2.8 Score=40.85 Aligned_cols=66 Identities=9% Similarity=0.127 Sum_probs=49.7
Q ss_pred CCHHHHHHHHHhhC----CCCCCCHHHHHHHHHHHH------HHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992 402 LTKRSIQELVNQID----PSERLDPDVEDILVDIAE------DFVESITMFGCSLAKHRKSDTLEAKDILVHLERN 467 (496)
Q Consensus 402 LtKrKLqELVrqID----PsesLDpDVEELLLeIAD------DFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn 467 (496)
+++..|.++++..- ....+|+|+.+++.++++ ..+.+++..|+.+|..++.+.|+.+||.-.++..
T Consensus 199 ~~~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~ 274 (365)
T TIGR02928 199 YDAEELRDILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKI 274 (365)
T ss_pred CCHHHHHHHHHHHHHhhccCCCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence 46677777776442 234699999999988885 3566788899999999999999999988665543
No 59
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=86.24 E-value=1.1 Score=45.18 Aligned_cols=65 Identities=20% Similarity=0.314 Sum_probs=49.3
Q ss_pred CHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992 403 TKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERN 467 (496)
Q Consensus 403 tKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn 467 (496)
.=.+|..++|-=|.-.-|..||--++.++.+.||+.++.+|.-.||..|..+|...||.-.+++.
T Consensus 111 PlARIkkvMKtdedVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~kS 175 (286)
T COG5208 111 PLARIKKVMKTDEDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKS 175 (286)
T ss_pred cHHHHHHHHhcccchhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHHH
Confidence 33445555543222234555666788999999999999999999999999999999998887763
No 60
>KOG3219 consensus Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=85.47 E-value=1.2 Score=43.53 Aligned_cols=67 Identities=19% Similarity=0.259 Sum_probs=56.1
Q ss_pred CccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCC-CCcchhhHHHHHhh
Q 010992 399 NRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKS-DTLEAKDILVHLER 466 (496)
Q Consensus 399 nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKS-dTLEvKDVQLhLER 466 (496)
...|.|..|..|+.+|-+.. |++.|.=++..||.-||-+||+.|..++..++. .-|-.+.|.-.+.|
T Consensus 110 rs~f~Ka~iKkL~~~itg~~-v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~rr 177 (195)
T KOG3219|consen 110 RSAFPKAQIKKLMSSITGQS-VSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAYRR 177 (195)
T ss_pred HhcCCHHHHHHHHHHHhCCc-cCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHH
Confidence 44679999999999998777 999999999999999999999999999877764 46667777555544
No 61
>KOG4336 consensus TBP-associated transcription factor Prodos [Transcription]
Probab=84.88 E-value=2.7 Score=43.75 Aligned_cols=70 Identities=10% Similarity=0.168 Sum_probs=56.7
Q ss_pred HHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCCCc
Q 010992 406 SIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSG 477 (496)
Q Consensus 406 KLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGFss 477 (496)
.+..|+.+. +-+.+++.++|-|++|.+.+|+.|...+--+|.|-|.......||.|.|-+ +||.|+-+..
T Consensus 10 VV~~Ll~~~-gfd~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~-mnI~v~sL~~ 79 (323)
T KOG4336|consen 10 VVSNLLKTK-GFDSISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIE-MNIKVSSLYA 79 (323)
T ss_pred HHHHHHHHh-CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHH-hCCChhhhHH
Confidence 355566654 335699999999999999999999988888888888888899999999976 7998876543
No 62
>KOG2680 consensus DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=84.14 E-value=2.7 Score=44.63 Aligned_cols=64 Identities=20% Similarity=0.331 Sum_probs=51.1
Q ss_pred CHHHHHHHHHhh--CCCCCCCHHHHHHHHHHHHH----HHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992 403 TKRSIQELVNQI--DPSERLDPDVEDILVDIAED----FVESITMFGCSLAKHRKSDTLEAKDILVHLER 466 (496)
Q Consensus 403 tKrKLqELVrqI--DPsesLDpDVEELLLeIADD----FVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER 466 (496)
+++.+.++++-= .....|++|+.|+|..|..+ |.-.+++.|...|..||..++++.||+.+++-
T Consensus 359 ~~~d~~~IL~iRc~EEdv~m~~~A~d~Lt~i~~~tsLRYai~Lit~a~~~~~krk~~~v~~~di~r~y~L 428 (454)
T KOG2680|consen 359 TEEDIKKILRIRCQEEDVEMNPDALDLLTKIGEATSLRYAIHLITAASLVCLKRKGKVVEVDDIERVYRL 428 (454)
T ss_pred cHHHHHHHHHhhhhhhccccCHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHhcCceeehhHHHHHHHH
Confidence 566666665522 23568999999999999876 77889999999999999999999999766543
No 63
>COG1224 TIP49 DNA helicase TIP49, TBP-interacting protein [Transcription]
Probab=83.48 E-value=2 Score=46.06 Aligned_cols=63 Identities=24% Similarity=0.363 Sum_probs=49.3
Q ss_pred CHHHHHHHHHhh--CCCCCCCHHHHHHHHHHHHH----HHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992 403 TKRSIQELVNQI--DPSERLDPDVEDILVDIAED----FVESITMFGCSLAKHRKSDTLEAKDILVHLE 465 (496)
Q Consensus 403 tKrKLqELVrqI--DPsesLDpDVEELLLeIADD----FVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE 465 (496)
+++.|+++++-= .-+..||+|+-|.|.+|-.+ |.-..++-|..+||.||+.+|+++||..+.|
T Consensus 362 ~~~EireIi~iRa~ee~i~l~~~Ale~L~~ig~etSLRYa~qLL~pa~iiA~~rg~~~V~~~dVe~a~~ 430 (450)
T COG1224 362 SREEIREIIRIRAKEEDIELSDDALEYLTDIGEETSLRYAVQLLTPASIIAKRRGSKRVEVEDVERAKE 430 (450)
T ss_pred CHHHHHHHHHHhhhhhccccCHHHHHHHHhhchhhhHHHHHHhccHHHHHHHHhCCCeeehhHHHHHHH
Confidence 566666666522 23457999999999998875 6777888888899999999999999976654
No 64
>PTZ00017 histone H2A; Provisional
Probab=81.22 E-value=3.7 Score=38.09 Aligned_cols=69 Identities=10% Similarity=0.165 Sum_probs=62.0
Q ss_pred CCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992 398 GNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER 466 (496)
Q Consensus 398 ~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER 466 (496)
.+-.+.-.+|+.|+++-.-..+|...+--.|.-+.|-++.+|++.|...|+.-+..-|..++|++.+..
T Consensus 24 agL~FPVgRi~R~Lk~g~~a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~n 92 (134)
T PTZ00017 24 AGLQFPVGRVHRYLKKGRYAKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIRN 92 (134)
T ss_pred CCcccchHHHHHHHhccchhccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhccC
Confidence 355678889999999876778999999999999999999999999999999999999999999998854
No 65
>PTZ00171 acyl carrier protein; Provisional
Probab=80.21 E-value=0.46 Score=43.81 Aligned_cols=45 Identities=24% Similarity=0.519 Sum_probs=34.1
Q ss_pred HHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCCCcccccccC
Q 010992 440 TMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGDEIKTFR 484 (496)
Q Consensus 440 vt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGFssDEIr~~r 484 (496)
++..+.+..--+-|.|+.-||.+.||++|||.||---.+++++++
T Consensus 90 I~~ds~~~~dLg~DSLd~veLv~~LEdeFgI~Ipded~~~i~TV~ 134 (148)
T PTZ00171 90 ITPESNFVKDLGADSLDVVELLIAIEQEFNLTIPDHDAEKIKTVQ 134 (148)
T ss_pred CCCCcchhhhcCCCHHHHHHHHHHHHHHHCCccCHHHHHHCCCHH
Confidence 444556667778999999999999999999999854444555443
No 66
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=77.74 E-value=7.6 Score=37.14 Aligned_cols=74 Identities=14% Similarity=0.155 Sum_probs=53.5
Q ss_pred CCHHHHHHHHHhhCC--CCCCCHHHHHHHHHHHHH---HHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCCC
Q 010992 402 LTKRSIQELVNQIDP--SERLDPDVEDILVDIAED---FVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFS 476 (496)
Q Consensus 402 LtKrKLqELVrqIDP--sesLDpDVEELLLeIADD---FVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGFs 476 (496)
++...+.++++++-. ...+|+|+.+.|.+.++. ++..++..++.+|..++...++.++|.-.|+. +++..-|..
T Consensus 159 l~~~e~~~il~~~~~~~~~~~~~~al~~ia~~~~G~pR~~~~ll~~~~~~a~~~~~~~it~~~v~~~l~~-l~~~~~~l~ 237 (305)
T TIGR00635 159 YTVEELAEIVSRSAGLLNVEIEPEAALEIARRSRGTPRIANRLLRRVRDFAQVRGQKIINRDIALKALEM-LMIDELGLD 237 (305)
T ss_pred CCHHHHHHHHHHHHHHhCCCcCHHHHHHHHHHhCCCcchHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHH-hCCCCCCCC
Confidence 566677777776632 457999999888887653 56778888888888777787888888888876 444443333
No 67
>KOG1748 consensus Acyl carrier protein/NADH-ubiquinone oxidoreductase, NDUFAB1/SDAP subunit [Energy production and conversion; Lipid transport and metabolism; Secondary metabolites biosynthesis, transport and catabolism]
Probab=77.64 E-value=2 Score=39.80 Aligned_cols=64 Identities=27% Similarity=0.429 Sum_probs=50.8
Q ss_pred HHHHHHHHHHHHHHH---HHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCCCcccccccCC
Q 010992 422 PDVEDILVDIAEDFV---ESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGDEIKTFRK 485 (496)
Q Consensus 422 pDVEELLLeIADDFV---DsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGFssDEIr~~rk 485 (496)
++++|-++++...|- .+.+.-+..+.|--|.|.||--.|.+.||.+|||.||---+|+|++.+.
T Consensus 52 ~~v~~RVl~VVk~~dki~~~k~~~~s~f~~DLGlDSLD~VEiVMAlEEEFgiEIpd~dAdki~t~~d 118 (131)
T KOG1748|consen 52 KEVVDRVLDVVKKFDKIDPSKLTTDSDFFKDLGLDSLDTVEIVMALEEEFGIEIPDEDADKIKTVRD 118 (131)
T ss_pred HHHHHHHHHHHHHhhcCCccccchhhHHHHhcCCcccccchhhhhhHHHhCCccCcchhhhhCCHHH
Confidence 446676776665554 3456666677788899999999999999999999999999999987553
No 68
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA.
Probab=77.16 E-value=3.9 Score=45.22 Aligned_cols=79 Identities=9% Similarity=0.158 Sum_probs=58.1
Q ss_pred CHHHHHHHHHhhC------CCCCCCHHHHHHHHHHHHHHHH---------HHHHHHHHhhhhcC----CCCcchhhHHHH
Q 010992 403 TKRSIQELVNQID------PSERLDPDVEDILVDIAEDFVE---------SITMFGCSLAKHRK----SDTLEAKDILVH 463 (496)
Q Consensus 403 tKrKLqELVrqID------PsesLDpDVEELLLeIADDFVD---------sVvt~ACrLAKHRK----SdTLEvKDVQLh 463 (496)
+...+.++++.+- -+..+++|+.+.+.++++.||. ++++.||..++-+. ...|+..||.-+
T Consensus 346 ~~~~~~~il~~~~~~~e~~~~v~i~~~al~~~~~ls~ryi~~r~~P~kai~lld~a~a~~~~~~~~~~~~~v~~~~i~~~ 425 (731)
T TIGR02639 346 SIEETVKILKGLKEKYEEFHHVKYSDEALEAAVELSARYINDRFLPDKAIDVIDEAGASFRLRPKAKKKANVSVKDIENV 425 (731)
T ss_pred CHHHHHHHHHHHHHHHHhccCcccCHHHHHHHHHhhhcccccccCCHHHHHHHHHhhhhhhcCcccccccccCHHHHHHH
Confidence 5555555555332 2357999999999999999984 46788888766543 346899999999
Q ss_pred HhhhcCccccCCCccccc
Q 010992 464 LERNWNMTLPGFSGDEIK 481 (496)
Q Consensus 464 LERnWNI~IPGFssDEIr 481 (496)
+++.-||.+-.+..||+.
T Consensus 426 i~~~tgiP~~~~~~~~~~ 443 (731)
T TIGR02639 426 VAKMAHIPVKTVSVDDRE 443 (731)
T ss_pred HHHHhCCChhhhhhHHHH
Confidence 999778887777766553
No 69
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=77.00 E-value=7.2 Score=39.97 Aligned_cols=73 Identities=8% Similarity=0.041 Sum_probs=58.6
Q ss_pred CccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHH-H------HHHHHHHhhhhcCCCCcchhhHHHHHhhhcCcc
Q 010992 399 NRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVE-S------ITMFGCSLAKHRKSDTLEAKDILVHLERNWNMT 471 (496)
Q Consensus 399 nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVD-s------Vvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~ 471 (496)
..++.+.+|.++-+.+ +...+++++.+.+.+|+..+=. + ++..|..+|-.+|.+.|+.+||+-...--+..+
T Consensus 232 ~~~~~~~~i~~a~~~~-~~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~~aA~a~A~l~Gr~~V~~~Di~~~~~~vl~hR 310 (334)
T PRK13407 232 EDMQLRGRILGARARL-PQLKTPNTVLHDCAALCIALGSDGLRGELTLLRAARALAAFEGAEAVGRSHLRSVATMALSHR 310 (334)
T ss_pred cccCCHHHHHHHHHhc-CCcccCHHHHHHHHHHHHHHCCCCchHHHHHHHHHHHHHHHcCCCeeCHHHHHHHHHHhhhhh
Confidence 4578888888886665 7788999999999999988753 2 778888999999999999999976655444444
Q ss_pred c
Q 010992 472 L 472 (496)
Q Consensus 472 I 472 (496)
+
T Consensus 311 ~ 311 (334)
T PRK13407 311 L 311 (334)
T ss_pred c
Confidence 4
No 70
>KOG3489 consensus Mitochondrial import inner membrane translocase, subunit TIM8 [Intracellular trafficking, secretion, and vesicular transport]
Probab=74.54 E-value=11 Score=33.07 Aligned_cols=50 Identities=26% Similarity=0.411 Sum_probs=42.9
Q ss_pred CHHHHHHHHHhh----------CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCC
Q 010992 403 TKRSIQELVNQI----------DPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKS 452 (496)
Q Consensus 403 tKrKLqELVrqI----------DPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKS 452 (496)
-|.++++.|.++ +++.+||.-.|.-|...+|.|||.-..-.-+||+-++.
T Consensus 23 qk~k~~~~VHqft~~CWdKCi~~~~sklds~~e~ClsnCV~RfiDts~~I~~r~~~~~~~ 82 (86)
T KOG3489|consen 23 QKQKFQEQVHQFTEICWDKCIEKPGSKLDSSEETCLSNCVNRFIDTSLFIVKRLAQMNQG 82 (86)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 488899999887 56899999999999999999999988777788876654
No 71
>PRK12449 acyl carrier protein; Provisional
Probab=74.42 E-value=0.95 Score=36.00 Aligned_cols=44 Identities=11% Similarity=0.317 Sum_probs=32.1
Q ss_pred HHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCCCccccccc
Q 010992 440 TMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGDEIKTF 483 (496)
Q Consensus 440 vt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGFssDEIr~~ 483 (496)
++....+-..-+-+.|+.-+|..+||..||+.||-.--.+++++
T Consensus 25 i~~~~~l~~dlg~DSl~~~~li~~lE~~f~i~i~~~~~~~~~ti 68 (80)
T PRK12449 25 ITEQTHLKDDLAVDSIELVEFIINVEDEFHIAIPDEDVEDMVSM 68 (80)
T ss_pred cCCCCcHHHHcCCcHHHHHHHHHHHHHHhCCCCCHHHHHhCCCH
Confidence 34445555666888899999999999999999976544444443
No 72
>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I. This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria.
Probab=73.03 E-value=8.8 Score=39.35 Aligned_cols=70 Identities=14% Similarity=0.074 Sum_probs=53.6
Q ss_pred CCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHH-------HHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccc
Q 010992 402 LTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVES-------ITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTL 472 (496)
Q Consensus 402 LtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDs-------Vvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~I 472 (496)
+.+++|...-+. -+...+++++.+.+.+|+..+=.+ .+..|..+|..++.+.|+.+||+...+--+..++
T Consensus 238 ~~~~~I~~a~~~-~~~V~v~d~~~~~i~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~~dDv~~~a~~vL~HR~ 314 (337)
T TIGR02030 238 ALQAKIVNAQNL-LPQVTIPYDVLVKVAELCAELDVDGLRGELTLNRAAKALAAFEGRTEVTVDDIRRVAVLALRHRL 314 (337)
T ss_pred cCHHHHHHHHHH-hccCcCCHHHHHHHHHHHHHHCCCCCcHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHhC
Confidence 455666665443 477899999999999999987642 6677888999999999999999866655555444
No 73
>TIGR02420 dksA RNA polymerase-binding protein DksA. The model that is the basis for this family describes a small, pleiotropic protein, DksA (DnaK suppressor A), originally named as a multicopy suppressor of temperature sensitivity of dnaKJ mutants. DksA mutants are defective in quorum sensing, virulence, etc. DksA is now understood to bind RNA polymerase directly and modulate its response to small molecules to control the level of transcription of rRNA. Nearly all members of this family are in the Proteobacteria. Whether the closest homologs outside the Proteobacteria function equivalently is unknown. The low value set for the noise cutoff allows identification of possible DksA proteins from outside the proteobacteria. TIGR02419 describes a closely related family of short sequences usually found in prophage regions of proteobacterial genomes or in known phage.
Probab=72.97 E-value=3.2 Score=35.92 Aligned_cols=30 Identities=20% Similarity=0.041 Sum_probs=21.3
Q ss_pred cchhhHHHHHhhhcCccccCCCcccccccCCcccccCCCCCC
Q 010992 455 LEAKDILVHLERNWNMTLPGFSGDEIKTFRKPVRIVTDPIPL 496 (496)
Q Consensus 455 LEvKDVQLhLERnWNI~IPGFssDEIr~~rk~~~~~~d~~~~ 496 (496)
-++++|...|+|- .-.+|| .|-+||+|||+
T Consensus 63 ~~l~~i~~AL~ri---~~g~yG---------~C~~Cge~I~~ 92 (110)
T TIGR02420 63 KLIKKIDEALKRI---EDGEYG---------YCEECGEEIGL 92 (110)
T ss_pred HHHHHHHHHHHHH---hCCCCC---------chhccCCcccH
Confidence 3578889999983 223333 68899999983
No 74
>TIGR00368 Mg chelatase-related protein. The N-terminal end matches very strongly a pfam Mg_chelatase domain.
Probab=72.05 E-value=9.7 Score=41.04 Aligned_cols=48 Identities=10% Similarity=0.137 Sum_probs=43.5
Q ss_pred CCCCHHHHHHHHHHHHHH------HHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992 418 ERLDPDVEDILVDIAEDF------VESITMFGCSLAKHRKSDTLEAKDILVHLE 465 (496)
Q Consensus 418 esLDpDVEELLLeIADDF------VDsVvt~ACrLAKHRKSdTLEvKDVQLhLE 465 (496)
..||++++++|.++++.| .+.|+.-|..+|..++++.++.+||.-.|.
T Consensus 444 ~~l~~~~~~~l~~a~~~~~lS~R~~~rilrvArTiAdL~g~~~i~~~hv~eA~~ 497 (499)
T TIGR00368 444 CKLSAIDANDLEGALNKLGLSSRATHRILKVARTIADLKEEKNISREHLAEAIE 497 (499)
T ss_pred cCCCHHHHHHHHHHHHhcCCCchHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHh
Confidence 468999999999999998 789999999999999999999999976653
No 75
>CHL00124 acpP acyl carrier protein; Validated
Probab=71.75 E-value=3 Score=33.35 Aligned_cols=30 Identities=13% Similarity=0.557 Sum_probs=24.6
Q ss_pred HhhhhcCCCCcchhhHHHHHhhhcCccccC
Q 010992 445 SLAKHRKSDTLEAKDILVHLERNWNMTLPG 474 (496)
Q Consensus 445 rLAKHRKSdTLEvKDVQLhLERnWNI~IPG 474 (496)
.+..--+-+.|++-+|...||+.||+.|+-
T Consensus 30 ~l~~dlg~DSl~~~eli~~le~~f~i~i~~ 59 (82)
T CHL00124 30 NFTRDLGADSLDVVELVMAIEEKFDIEIPD 59 (82)
T ss_pred chhhhcCCcHHHHHHHHHHHHHHHCCccCH
Confidence 444434778889999999999999999984
No 76
>TIGR02442 Cob-chelat-sub cobaltochelatase subunit. A number of genomes (actinobacteria, cyanobacteria, betaproteobacteria and pseudomonads) which apparently biosynthesize B12, encode a cobN gene but are demonstrably lacking cobS and cobT. These genomes do, however contain a homolog (modelled here) of the magnesium chelatase subunits BchI/BchD family. Aside from the cyanobacteria (which have a separate magnesium chelatase trimer), these species do not make chlorins, so do not have any use for a magnesium chelatase. Furthermore, in nearly all cases the members of this family are proximal to either CobN itself or other genes involved in cobalt transport or B12 biosynthesis.
Probab=71.66 E-value=9.6 Score=41.77 Aligned_cols=58 Identities=16% Similarity=0.161 Sum_probs=46.4
Q ss_pred HhhCCCCCCCHHHHHHHHHHHHHHH-------HHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcC
Q 010992 412 NQIDPSERLDPDVEDILVDIAEDFV-------ESITMFGCSLAKHRKSDTLEAKDILVHLERNWN 469 (496)
Q Consensus 412 rqIDPsesLDpDVEELLLeIADDFV-------DsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWN 469 (496)
+++-+...|++++.++|.+++.++- .-++..|..+|..++.+.|+.+||+..++--+.
T Consensus 242 r~~~~~V~is~~~~~~l~~~~~~~~i~s~Ra~i~~~r~Ara~AaL~gr~~V~~~Dv~~A~~lvL~ 306 (633)
T TIGR02442 242 RSLLPSVRISDSLIRFISELCIEFGVDGHRADIVMARAARALAALDGRRRVTAEDVREAAELVLP 306 (633)
T ss_pred HHhCCCCCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHHHhh
Confidence 4455778999999999999999873 346677778999999999999999765554443
No 77
>PTZ00183 centrin; Provisional
Probab=71.27 E-value=35 Score=28.79 Aligned_cols=73 Identities=10% Similarity=0.143 Sum_probs=44.1
Q ss_pred CCcCCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHH----------HHHHHH------------HHHHHHHhhhhcCC
Q 010992 395 DEFGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIA----------EDFVES------------ITMFGCSLAKHRKS 452 (496)
Q Consensus 395 ~e~~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIA----------DDFVDs------------Vvt~ACrLAKHRKS 452 (496)
+.+++..|++..|..+++.++ ..++.+..+.|.... ++|+.. .+..++++.-..+.
T Consensus 27 D~~~~G~i~~~e~~~~l~~~g--~~~~~~~~~~l~~~~d~~~~g~i~~~eF~~~~~~~~~~~~~~~~l~~~F~~~D~~~~ 104 (158)
T PTZ00183 27 DTDGSGTIDPKELKVAMRSLG--FEPKKEEIKQMIADVDKDGSGKIDFEEFLDIMTKKLGERDPREEILKAFRLFDDDKT 104 (158)
T ss_pred CCCCCCcccHHHHHHHHHHhC--CCCCHHHHHHHHHHhCCCCCCcEeHHHHHHHHHHHhcCCCcHHHHHHHHHHhCCCCC
Confidence 445666788888888887763 223443333333322 245443 34556666666777
Q ss_pred CCcchhhHHHHHhhhcCc
Q 010992 453 DTLEAKDILVHLERNWNM 470 (496)
Q Consensus 453 dTLEvKDVQLhLERnWNI 470 (496)
..|+..|+.-.|++ +|.
T Consensus 105 G~i~~~e~~~~l~~-~~~ 121 (158)
T PTZ00183 105 GKISLKNLKRVAKE-LGE 121 (158)
T ss_pred CcCcHHHHHHHHHH-hCC
Confidence 78899999877764 453
No 78
>PLN00154 histone H2A; Provisional
Probab=70.14 E-value=14 Score=34.51 Aligned_cols=68 Identities=10% Similarity=0.110 Sum_probs=60.0
Q ss_pred CccCCHHHHHHHHHhhC-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992 399 NRILTKRSIQELVNQID-PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER 466 (496)
Q Consensus 399 nrILtKrKLqELVrqID-PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER 466 (496)
+-.+.=.+|+.|+++-. -.++|+..+--.|..+.|-+.-+|++.|...|+.-|..-|..++|++.+..
T Consensus 36 gL~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIrn 104 (136)
T PLN00154 36 GLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG 104 (136)
T ss_pred CccCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhccC
Confidence 44567788999999865 357999999999999999999999999999999999999999999988754
No 79
>PRK05350 acyl carrier protein; Provisional
Probab=69.86 E-value=3.1 Score=33.72 Aligned_cols=25 Identities=24% Similarity=0.387 Sum_probs=22.3
Q ss_pred cCCCCcchhhHHHHHhhhcCccccC
Q 010992 450 RKSDTLEAKDILVHLERNWNMTLPG 474 (496)
Q Consensus 450 RKSdTLEvKDVQLhLERnWNI~IPG 474 (496)
=+-+.|++-++.+.||+.||+.|+.
T Consensus 36 lg~DSld~veli~~lE~~fgI~i~~ 60 (82)
T PRK05350 36 LDLDSIDAVDLVVHLQKLTGKKIKP 60 (82)
T ss_pred cCCCHHHHHHHHHHHHHHHCCccCH
Confidence 3778899999999999999999974
No 80
>KOG1658 consensus DNA polymerase epsilon, subunit C [Replication, recombination and repair]
Probab=69.17 E-value=3.5 Score=39.47 Aligned_cols=67 Identities=21% Similarity=0.354 Sum_probs=52.8
Q ss_pred HHHHHHHHhhCCCCC-CCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccc
Q 010992 405 RSIQELVNQIDPSER-LDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTL 472 (496)
Q Consensus 405 rKLqELVrqIDPses-LDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~I 472 (496)
.+++++|+ +|+... +.+|+.-++..-||.||..+-..+-..|-.|+..++..+|+--.+|..|-..|
T Consensus 63 ~rik~vvk-l~pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai~~~de~~f 130 (162)
T KOG1658|consen 63 ARIKQVVK-LDPDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAIEAVDEFAF 130 (162)
T ss_pred HHHHhhcc-CCcchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccccchHHHHH
Confidence 34445554 355554 45667888999999999999999999999999999999999888888776443
No 81
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=69.05 E-value=20 Score=30.63 Aligned_cols=47 Identities=19% Similarity=0.247 Sum_probs=42.2
Q ss_pred CCCCHHHHHHHHHHHHHH------HHHHHHHHHHhhhhcCCCCcchhhHHHHH
Q 010992 418 ERLDPDVEDILVDIAEDF------VESITMFGCSLAKHRKSDTLEAKDILVHL 464 (496)
Q Consensus 418 esLDpDVEELLLeIADDF------VDsVvt~ACrLAKHRKSdTLEvKDVQLhL 464 (496)
..||++++++|.++++.| ++.|+.-|-.+|-.-+++.|+..||.-.|
T Consensus 41 ~~l~~~~~~~l~~~~~~~~lS~R~~~rilrvARTIADL~~~~~I~~~hi~EAl 93 (96)
T PF13335_consen 41 CPLSSEAKKLLEQAAEKLNLSARGYHRILRVARTIADLEGSERITREHIAEAL 93 (96)
T ss_pred cCCCHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHhHcCCCCCCHHHHHHHH
Confidence 569999999999999998 67889999999999999999999997655
No 82
>cd01145 TroA_c Periplasmic binding protein TroA_c. These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains.
Probab=68.65 E-value=6.4 Score=36.55 Aligned_cols=77 Identities=9% Similarity=0.059 Sum_probs=52.9
Q ss_pred cCCHHHHHHHHHhhC-CCCCCCHHHHHHHHHHHHHHHHHHHHHH----HHhhhhcCCCCcchhhHHHHHhhhcCccccCC
Q 010992 401 ILTKRSIQELVNQID-PSERLDPDVEDILVDIAEDFVESITMFG----CSLAKHRKSDTLEAKDILVHLERNWNMTLPGF 475 (496)
Q Consensus 401 ILtKrKLqELVrqID-PsesLDpDVEELLLeIADDFVDsVvt~A----CrLAKHRKSdTLEvKDVQLhLERnWNI~IPGF 475 (496)
-|.-.+...+++.|. .-.++|++-++...+=+++|++.+-..- .++++..+...|..-|.--||.|.||+.+-|+
T Consensus 111 Wldp~~~~~~a~~I~~~L~~~dP~~~~~y~~N~~~~~~~l~~l~~~~~~~l~~~~~~~~v~~H~af~Y~~~~yGl~~~~~ 190 (203)
T cd01145 111 WLDPNNAPALAKALADALIELDPSEQEEYKENLRVFLAKLNKLLREWERQFEGLKGIQVVAYHPSYQYLADWLGIEVVAS 190 (203)
T ss_pred ecCHHHHHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCeEEEecccHHHHHHHcCCceeee
Confidence 456666777777763 3346778877788888888877765433 33444444456667899999999999998655
Q ss_pred Cc
Q 010992 476 SG 477 (496)
Q Consensus 476 ss 477 (496)
-.
T Consensus 191 ~~ 192 (203)
T cd01145 191 LE 192 (203)
T ss_pred ec
Confidence 43
No 83
>KOG1659 consensus Class 2 transcription repressor NC2, alpha subunit (DRAP1) [Transcription]
Probab=68.63 E-value=13 Score=37.33 Aligned_cols=55 Identities=18% Similarity=0.208 Sum_probs=41.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh--------cCccccCCCc
Q 010992 423 DVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERN--------WNMTLPGFSG 477 (496)
Q Consensus 423 DVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn--------WNI~IPGFss 477 (496)
.|=-++-+-.+=|++++|..+|+.++.|++++|...-|+-+++.. .=..||+...
T Consensus 35 avPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~~FdFLk~~v~~vpd~~~ 97 (224)
T KOG1659|consen 35 AVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDPKFDFLKEVVEKVPDRQQ 97 (224)
T ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccchhHHHHHHHHhcCCCcc
Confidence 334455667788999999999999999999999988776655543 2245676664
No 84
>cd03565 VHS_Tom1 VHS domain family, Tom1 subfamily; The VHS domain is an essential part of Tom1 (Target of myb1 - retroviral oncogene) protein. The VHS domain has a superhelical structure similar to the structure of the ARM repeats and is present at the very N-termini of proteins. It is a right-handed superhelix of eight alpha helices. The VHS domain has been found in a number of proteins, some of which have been implicated in intracellular trafficking and sorting. The VHS domain of the Tom1 protein is essential for the negative regulation of Interleukin-1 and Tumor Necrosis Factor-induced signaling pathways.
Probab=68.15 E-value=13 Score=33.65 Aligned_cols=46 Identities=17% Similarity=0.370 Sum_probs=23.0
Q ss_pred HHHHHHH-HHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccC
Q 010992 426 DILVDIA-EDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPG 474 (496)
Q Consensus 426 ELLLeIA-DDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPG 474 (496)
.+.++|| .+|+++++.. +.+.+..--.+||+-.+.|=++|...|.+
T Consensus 73 ~fh~eiask~Fl~e~L~~---~i~~~~~~~~~Vk~kil~li~~W~~~f~~ 119 (141)
T cd03565 73 RFHVLVAKKDFIKDVLVK---LINPKNNPPTIVQEKVLALIQAWADAFRG 119 (141)
T ss_pred HHHHHHHHHHhhhHHHHH---HHcccCCCcHHHHHHHHHHHHHHHHHhCC
Confidence 4455555 4566653222 22211111235666667777777766644
No 85
>PF00745 GlutR_dimer: Glutamyl-tRNAGlu reductase, dimerisation domain; InterPro: IPR015896 Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway []. The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including vitamin B12, haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin []. The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes: (1) condensation of succinyl CoA and glycine (C4 pathway) using ALA synthase (2.3.1.37 from EC), or (2) decarboxylation of glutamate (C5 pathway) via three different enzymes, glutamyl-tRNA synthetase (6.1.1.17 from EC) to charge a tRNA with glutamate, glutamyl-tRNA reductase (1.2.1.70 from EC) to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and GSA aminotransferase (5.4.3.8 from EC) to catalyse a transamination reaction to produce ALA. The second stage is to convert ALA to uroporphyrinogen III, the first macrocyclic tetrapyrrolic structure in the pathway. This is achieved by the action of three enzymes in one common pathway: porphobilinogen (PBG) synthase (or ALA dehydratase, 4.2.1.24 from EC) to condense two ALA molecules to generate porphobilinogen; hydroxymethylbilane synthase (or PBG deaminase, 2.5.1.61 from EC) to polymerise four PBG molecules into preuroporphyrinogen (tetrapyrrole structure); and uroporphyrinogen III synthase (4.2.1.75 from EC) to link two pyrrole units together (rings A and D) to yield uroporphyrinogen III. Uroporphyrinogen III is the first branch point of the pathway. To synthesise cobalamin (vitamin B12), sirohaem, and coenzyme F430, uroporphyrinogen III needs to be converted into precorrin-2 by the action of uroporphyrinogen III methyltransferase (2.1.1.107 from EC). To synthesise haem and chlorophyll, uroporphyrinogen III needs to be decarboxylated into coproporphyrinogen III by the action of uroporphyrinogen III decarboxylase (4.1.1.37 from EC) []. This entry represents the helical dimerisation domain of glutamyl-tRNA reductase (1.2.1.70 from EC) []. This enzyme reduces glutamyl-tRNA to glutamate-1-semialdehyde during the first stage of tetrapyrrole biosynthesis by the C5 pathway [, ]. The enzyme requires NADPH as a cofactor.; GO: 0008883 glutamyl-tRNA reductase activity, 0050661 NADP binding, 0033014 tetrapyrrole biosynthetic process, 0055114 oxidation-reduction process; PDB: 1GPJ_A.
Probab=67.72 E-value=4.8 Score=32.85 Aligned_cols=62 Identities=15% Similarity=0.332 Sum_probs=33.5
Q ss_pred HHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCc
Q 010992 404 KRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNM 470 (496)
Q Consensus 404 KrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI 470 (496)
+..|..++++++ ++++.++.|-.+++.+++.+++.-....|.-..+- +..|+.-.|++-|++
T Consensus 39 ~~el~~~~~~l~----~~~~~~~~i~~~~~~~~~Kllh~p~~~Lr~~a~~~-~~~~~~~~l~~lF~l 100 (101)
T PF00745_consen 39 DEELERALKKLD----LDEDDEEVIEKLTRSLVNKLLHPPISNLREAAEEG-DGDEYLEALRKLFGL 100 (101)
T ss_dssp HHHHHHHHS-S--------------TTHHHHHHHHHHHHHHHHHHSS-TTT-T-THHHHHHHHHHHH
T ss_pred HHHHHHHHhhcc----CCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC-CHHHHHHHHHHHhCC
Confidence 445556666543 88888888888888888888888888888754443 335565666666654
No 86
>PRK09184 acyl carrier protein; Provisional
Probab=67.68 E-value=4.1 Score=34.59 Aligned_cols=39 Identities=13% Similarity=0.273 Sum_probs=29.7
Q ss_pred hhhcCCCCcchhhHHHHHhhhcCccccCCCcccccccCC
Q 010992 447 AKHRKSDTLEAKDILVHLERNWNMTLPGFSGDEIKTFRK 485 (496)
Q Consensus 447 AKHRKSdTLEvKDVQLhLERnWNI~IPGFssDEIr~~rk 485 (496)
...-+-+.|++-+|...||++||+.|+.-..++++.++-
T Consensus 37 ~~dLglDSld~velv~~lE~~fgi~i~~~~~~~~~~~~T 75 (89)
T PRK09184 37 GEGLGLDSIDILEIALVISKRYGFQLRSDNPDNQRIFAS 75 (89)
T ss_pred cccCCCcHHHHHHHHHHHHHHHCCcCCCcchhhhhccCC
Confidence 334678889999999999999999998655455554543
No 87
>PLN00157 histone H2A; Provisional
Probab=67.43 E-value=12 Score=34.71 Aligned_cols=69 Identities=10% Similarity=0.137 Sum_probs=60.7
Q ss_pred CCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992 398 GNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER 466 (496)
Q Consensus 398 ~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER 466 (496)
.+-.+.=-+|+.++++-.-..+|...+--.|..+.|-++.+|++.|...|+.-|..-|..++|++.+..
T Consensus 23 agL~FPVgRi~R~Lk~g~~a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~n 91 (132)
T PLN00157 23 AGLQFPVGRIARYLKAGKYATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVRN 91 (132)
T ss_pred cCcccchHHHHHHHhcCchhhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhcccC
Confidence 345667788999999876778999999999999999999999999999999999999999999888744
No 88
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=65.93 E-value=8.8 Score=40.83 Aligned_cols=65 Identities=12% Similarity=0.155 Sum_probs=43.5
Q ss_pred CHHHHHHHHHhhCCCCCCCHHH-HHHHHHHHHHH----HHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992 403 TKRSIQELVNQIDPSERLDPDV-EDILVDIAEDF----VESITMFGCSLAKHRKSDTLEAKDILVHLERN 467 (496)
Q Consensus 403 tKrKLqELVrqIDPsesLDpDV-EELLLeIADDF----VDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn 467 (496)
+.....++++..-....++++| .+.|+...+.| |..|+..|+.+|-.++...|..+|+.-.+++.
T Consensus 355 d~~~R~~Il~~~~~k~~l~~dvdl~~la~~t~g~sgAdI~~i~~eA~~~Alr~~r~~Vt~~D~~~A~~~v 424 (438)
T PTZ00361 355 DEKTKRRIFEIHTSKMTLAEDVDLEEFIMAKDELSGADIKAICTEAGLLALRERRMKVTQADFRKAKEKV 424 (438)
T ss_pred CHHHHHHHHHHHHhcCCCCcCcCHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCccCHHHHHHHHHHH
Confidence 3444555555433334454443 23344343333 67899999999999999999999999999986
No 89
>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]
Probab=65.02 E-value=9.4 Score=40.68 Aligned_cols=72 Identities=24% Similarity=0.370 Sum_probs=42.9
Q ss_pred ccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhc-CccccCC
Q 010992 400 RILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNW-NMTLPGF 475 (496)
Q Consensus 400 rILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnW-NI~IPGF 475 (496)
+.|++.-+.++++.+...... -.+|+++.-+|+.|=-.+-+ -+.|.|+.+.+..|+|.+||-|++ ++.+|-.
T Consensus 299 ~~iTi~~v~e~L~~~~~~~~~-itie~I~~~Va~~y~v~~~d---l~s~~R~~~i~~~RqiamyL~r~lt~~Slp~I 371 (408)
T COG0593 299 RAITIDLVKEILKDLLRAGEK-ITIEDIQKIVAEYYNVKVSD---LLSKSRTRNIVRPRQIAMYLARELTNLSLPEI 371 (408)
T ss_pred ccCcHHHHHHHHHHhhccccc-CCHHHHHHHHHHHhCCCHHH---hhccccccccchHHHHHHHHHHHHccCcHHHH
Confidence 355666666666665443333 45555666666655333322 466778888888888877777764 4666543
No 90
>TIGR02031 BchD-ChlD magnesium chelatase ATPase subunit D. This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. Unlike subunit I (TIGR02030), this subunit is not found in archaea.
Probab=64.78 E-value=11 Score=41.15 Aligned_cols=72 Identities=13% Similarity=0.023 Sum_probs=54.3
Q ss_pred ccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHH-------HHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccc
Q 010992 400 RILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVE-------SITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTL 472 (496)
Q Consensus 400 rILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVD-------sVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~I 472 (496)
.++.+++|.+. +++-+...|++++.+.|++++-++=- .++..|..+|..++.+.|+.+||+..++=-+..++
T Consensus 185 ~~~~~~~i~~a-r~~~~~V~i~~~~~~~l~~~~~~~gv~s~Ra~i~~~r~ArA~Aal~gr~~V~~~Dv~~a~~lvl~hR~ 263 (589)
T TIGR02031 185 LELLRGQIEAA-RELLPQVTISAEQVKELVLTAASLGISGHRADLFAVRAAKAHAALHGRTEVTEEDLKLAVELVLLPRA 263 (589)
T ss_pred hHHHHHHHHHH-HHhcCCccCCHHHHHHHHHHHHHcCCCCccHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHhhhhc
Confidence 34555656543 44557789999999999999866532 24567778899999999999999988887776554
No 91
>PLN02641 anthranilate phosphoribosyltransferase
Probab=63.66 E-value=13 Score=38.53 Aligned_cols=76 Identities=16% Similarity=0.249 Sum_probs=49.7
Q ss_pred HHHHHHhhCCCCCCCHH-HHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcc-hhhHHHHHhhh---c-----CccccCCC
Q 010992 407 IQELVNQIDPSERLDPD-VEDILVDIAEDFVESITMFGCSLAKHRKSDTLE-AKDILVHLERN---W-----NMTLPGFS 476 (496)
Q Consensus 407 LqELVrqIDPsesLDpD-VEELLLeIADDFVDsVvt~ACrLAKHRKSdTLE-vKDVQLhLERn---W-----NI~IPGFs 476 (496)
+.++|++|..+..|+.| +++++-.|.|+ ++++--.|..+|-+=|.++.| +....-.+... + -+-++|+|
T Consensus 4 ~~~~l~~l~~g~~Lt~eEa~~~~~~il~~-~~~~qigAfL~alr~kget~eEiag~~~a~~~~~~~~~~~~~~~D~~gtG 82 (343)
T PLN02641 4 FRQLIESLIQGTDLTEEEAEAALDFLLDD-ADEAQISAFLVLLRAKGETFEEIAGLARAMIKRARKVDGLVDAVDIVGTG 82 (343)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHHHHHHcC-CCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCCCCCCCCCCceeCCC
Confidence 67788888777777765 88999999998 888887787777766666533 22221111111 1 25567888
Q ss_pred ccccccc
Q 010992 477 GDEIKTF 483 (496)
Q Consensus 477 sDEIr~~ 483 (496)
+|-.+++
T Consensus 83 Gdg~~t~ 89 (343)
T PLN02641 83 GDGANTV 89 (343)
T ss_pred CCCCCcc
Confidence 8766543
No 92
>cd05022 S-100A13 S-100A13: S-100A13 domain found in proteins similar to S100A13. S100A13 is a calcium-binding protein belonging to a large S100 vertebrate-specific protein family within the EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100A13 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100A13 is involved in the cellular export of interleukin-1 (IL-1) and of fibroblast growth factor-1 (FGF-1), which plays an important role in angiogenesis and tissue regeneration. Export is based on the CuII-dependent formation of multiprotein complexes containing the S100A13 protein. Assembly of these complexes occurs near the inner surface of the plasma membrane. Binding of two Ca(II) ions per monomer triggers key conformational changes leading to the creation of two identical and symmetrical Cu(II)-binding sites on the surface of the protein, close to the interface between the two monomers. These Cu
Probab=63.62 E-value=24 Score=29.86 Aligned_cols=55 Identities=24% Similarity=0.316 Sum_probs=38.8
Q ss_pred cCCccCCHHHHHHHHHh-hCCCCCCC-HHHHHHHHHH---------HHHHHHHHHHHHHHhhhhcCC
Q 010992 397 FGNRILTKRSIQELVNQ-IDPSERLD-PDVEDILVDI---------AEDFVESITMFGCSLAKHRKS 452 (496)
Q Consensus 397 ~~nrILtKrKLqELVrq-IDPsesLD-pDVEELLLeI---------ADDFVDsVvt~ACrLAKHRKS 452 (496)
+++..|++..|..|+++ +..... + ++|+++|.++ -+||+.-|..-++...+.|..
T Consensus 21 ~~~g~i~~~ELk~ll~~elg~~ls-~~~~v~~mi~~~D~d~DG~I~F~EF~~l~~~l~~~~~~~~~~ 86 (89)
T cd05022 21 GGKESLTASEFQELLTQQLPHLLK-DVEGLEEKMKNLDVNQDSKLSFEEFWELIGELAKAVKGEKHL 86 (89)
T ss_pred CCCCeECHHHHHHHHHHHhhhhcc-CHHHHHHHHHHhCCCCCCCCcHHHHHHHHHHHHHHHHHHhhc
Confidence 67779999999999998 643222 3 6788887655 357888777777666665543
No 93
>cd06845 Bcl-2_like Apoptosis regulator proteins of the Bcl-2 family, named after B-cell lymphoma 2. This alignment model spans what have been described as Bcl-2 homology regions BH1, BH2, BH3, and BH4. Many members of this family have an additional C-terminal transmembrane segment. Some homologous proteins, which are not included in this model, may miss either the BH4 (Bax, Bak) or the BH2 (Bcl-X(S)) region, and some appear to only share the BH3 region (Bik, Bim, Bad, Bid, Egl-1). This family is involved in the regulation of the outer mitochondrial membrane's permeability and in promoting or preventing the release of apoptogenic factors, which in turn may trigger apoptosis by activating caspases. Bcl-2 and the closely related Bcl-X(L) are anti-apoptotic key regulators of programmed cell death. They are assumed to function via heterodimeric protein-protein interactions, binding pro-apoptotic proteins such as Bad (BCL2-antagonist of cell death), Bid, and Bim, by specifically interacting
Probab=63.59 E-value=16 Score=32.43 Aligned_cols=47 Identities=17% Similarity=0.363 Sum_probs=34.6
Q ss_pred HHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHH----------HHHHHHHhhhhcCCC
Q 010992 404 KRSIQELVNQIDPSERLDPDVEDILVDIAEDFVES----------ITMFGCSLAKHRKSD 453 (496)
Q Consensus 404 KrKLqELVrqIDPsesLDpDVEELLLeIADDFVDs----------Vvt~ACrLAKHRKSd 453 (496)
++.+.+++++++ .-++.+.+.+.++|++..+| ++.|++.||+|-...
T Consensus 51 ~~~f~~~~~~l~---~~~~~~~~~f~~v~~~lf~dg~inWGRIval~~f~~~la~~~~~~ 107 (144)
T cd06845 51 RRLFENMCRQLN---ISPDNAYEVFQEVARELFEDGGINWGRIVALFAFGGRLAVKCVEQ 107 (144)
T ss_pred HHHHHHHHHHhC---CCcchHHHHHHHHHHHHhccCCCChHHHHHHHHHHHHHHHHHHHc
Confidence 344556666665 34667889999999999888 567999999976544
No 94
>PRK08727 hypothetical protein; Validated
Probab=63.42 E-value=27 Score=33.20 Aligned_cols=64 Identities=13% Similarity=-0.012 Sum_probs=42.4
Q ss_pred CHHHHHHHHHhh--CCCCCCCHHHHHHHHHHHH-H--HHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992 403 TKRSIQELVNQI--DPSERLDPDVEDILVDIAE-D--FVESITMFGCSLAKHRKSDTLEAKDILVHLERN 467 (496)
Q Consensus 403 tKrKLqELVrqI--DPsesLDpDVEELLLeIAD-D--FVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn 467 (496)
....+.++++++ +.+..+|+||.++|++.++ | .+.++++.....|+..+. .|++..|+-+|+++
T Consensus 163 ~~e~~~~iL~~~a~~~~l~l~~e~~~~La~~~~rd~r~~l~~L~~l~~~~~~~~~-~it~~~~~~~l~~~ 231 (233)
T PRK08727 163 DDVARAAVLRERAQRRGLALDEAAIDWLLTHGERELAGLVALLDRLDRESLAAKR-RVTVPFLRRVLEEG 231 (233)
T ss_pred CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHhCC-CCCHHHHHHHHhhc
Confidence 455666666653 2467899999999999887 3 233345544433443343 58899998888775
No 95
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=63.27 E-value=22 Score=36.94 Aligned_cols=72 Identities=17% Similarity=0.157 Sum_probs=58.1
Q ss_pred ccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHH-------HHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccc
Q 010992 400 RILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVE-------SITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTL 472 (496)
Q Consensus 400 rILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVD-------sVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~I 472 (496)
..+.+.+|.++-+.+ +...+++++.+.+++|+..+=. -.+..|..+|-.++.+.|+..||+...+--+..++
T Consensus 249 ~~~~~~~I~~ar~~~-~~V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~pdDv~~~a~~vL~HR~ 327 (350)
T CHL00081 249 QEELRSKIVAAQNLL-PKVEIDYDLRVKISQICSELDVDGLRGDIVTNRAAKALAAFEGRTEVTPKDIFKVITLCLRHRL 327 (350)
T ss_pred cccCHHHHHHHHHhc-CCCccCHHHHHHHHHHHHHHCCCCChHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHhC
Confidence 345788888866655 6789999999999999999753 35677778899999999999999888777776555
No 96
>PLN00156 histone H2AX; Provisional
Probab=62.04 E-value=21 Score=33.47 Aligned_cols=68 Identities=12% Similarity=0.167 Sum_probs=60.0
Q ss_pred CccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992 399 NRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER 466 (496)
Q Consensus 399 nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER 466 (496)
+-.+.=-+|+.++++-.-..+|...+--.|..+.|-.+.+|++.|...|+..|..-|..++|++.+..
T Consensus 27 gL~FPVgRi~R~Lk~g~ya~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIrn 94 (139)
T PLN00156 27 GLQFPVGRIARFLKAGKYAERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRN 94 (139)
T ss_pred CcccchHHHHHHHhcCChhhccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhccC
Confidence 44567788999999877778999999999999999999999999999999999999999999988743
No 97
>PRK07639 acyl carrier protein; Provisional
Probab=62.04 E-value=3.3 Score=34.54 Aligned_cols=31 Identities=16% Similarity=0.270 Sum_probs=25.1
Q ss_pred HHhhhhcCCCCcchhhHHHHHhhhcCccccC
Q 010992 444 CSLAKHRKSDTLEAKDILVHLERNWNMTLPG 474 (496)
Q Consensus 444 CrLAKHRKSdTLEvKDVQLhLERnWNI~IPG 474 (496)
..|-..-+-+.|++-++.++||.+||+.||-
T Consensus 30 ~~l~edL~lDSld~velv~~lE~~fgi~i~d 60 (86)
T PRK07639 30 MRLNEDLYIDSVMMLQLIVYIEMDVKLCVPE 60 (86)
T ss_pred CCcccccCCChHHHHHHHHHHHHHHCCccCH
Confidence 3444555788889999999999999999973
No 98
>PF00616 RasGAP: GTPase-activator protein for Ras-like GTPase; InterPro: IPR001936 Ras proteins are membrane-associated molecular switches that bind GTP and GDP and slowly hydrolyze GTP to GDP []. This intrinsic GTPase activity of ras is stimulated by a family of proteins collectively known as 'GAP' or GTPase-activating proteins [, ]. As it is the GTP bound form of ras which is active, these proteins are said to be down-regulators of ras. The Ras GTPase-activating proteins are quite large (from 765 residues for sar1 to 3079 residues for IRA2) but share only a limited (about 250 residues) region of sequence similarity, referred to as the 'catalytic domain' or rasGAP domain. Note: There are distinctly different GAPs for the rap and rho/rac subfamilies of ras-like proteins (reviewed in reference []) that do not share sequence similarity with ras GAPs.; GO: 0005096 GTPase activator activity, 0051056 regulation of small GTPase mediated signal transduction, 0005622 intracellular; PDB: 3BXJ_B 1WQ1_G 1WER_A 1NF1_A 3FAY_A.
Probab=61.38 E-value=13 Score=33.43 Aligned_cols=26 Identities=15% Similarity=0.190 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhh
Q 010992 423 DVEDILVDIAEDFVESITMFGCSLAK 448 (496)
Q Consensus 423 DVEELLLeIADDFVDsVvt~ACrLAK 448 (496)
+-.+.|.+++++|++.|+.....+..
T Consensus 97 ~n~~~L~~~~~~~~~~i~~s~~~~P~ 122 (197)
T PF00616_consen 97 ENLQNLRELCESFLDAIISSIDQIPP 122 (197)
T ss_dssp HHHHHHHHHHHHHHHHHHGGGGGS-H
T ss_pred HHHHHHHHHHHHHHHHHHHhHHHhhH
Confidence 45578899999999999886655544
No 99
>PRK07117 acyl carrier protein; Validated
Probab=60.74 E-value=2.1 Score=35.47 Aligned_cols=40 Identities=13% Similarity=0.179 Sum_probs=31.5
Q ss_pred HHhhhhcCCCCcchhhHHHHHhhhcCccccCCCcccccccC
Q 010992 444 CSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGDEIKTFR 484 (496)
Q Consensus 444 CrLAKHRKSdTLEvKDVQLhLERnWNI~IPGFssDEIr~~r 484 (496)
..| +.-|.+.|++-||...||..||+.||---.+++++.+
T Consensus 30 ~~l-~DLg~DSlD~veiv~~led~f~i~I~~~~~~~i~Tv~ 69 (79)
T PRK07117 30 DSL-VDLGANSMDRAEIVIMTLESLSLKIPLVEFAGAKNIG 69 (79)
T ss_pred CCh-hhcCCChHHHHHHHHHHHHHHCCccCHHHHHhcCCHH
Confidence 344 3468899999999999999999999866666666544
No 100
>TIGR00362 DnaA chromosomal replication initiator protein DnaA. DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).
Probab=60.69 E-value=14 Score=37.59 Aligned_cols=70 Identities=13% Similarity=0.199 Sum_probs=32.2
Q ss_pred CccCCHHHHHHHHHhhCCCCC-CCHHHHHHHH-------HHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCc
Q 010992 399 NRILTKRSIQELVNQIDPSER-LDPDVEDILV-------DIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNM 470 (496)
Q Consensus 399 nrILtKrKLqELVrqIDPses-LDpDVEELLL-------eIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI 470 (496)
+-.|..+.|.-|++.++.+.. |...+..+.. +|..+|+++++...+.. +...|++++|.-.+.+.||+
T Consensus 285 ~~~l~~e~l~~ia~~~~~~~r~l~~~l~~l~~~a~~~~~~it~~~~~~~L~~~~~~----~~~~it~~~I~~~Va~~~~v 360 (405)
T TIGR00362 285 GLELPDEVLEFIAKNIRSNVRELEGALNRLLAYASLTGKPITLELAKEALKDLLRA----KKKEITIENIQEVVAKYYNI 360 (405)
T ss_pred CCCCCHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccc----cCCCCCHHHHHHHHHHHcCC
Confidence 344566666666666655432 2222111110 11124555555443321 22235666666666666655
Q ss_pred cc
Q 010992 471 TL 472 (496)
Q Consensus 471 ~I 472 (496)
.+
T Consensus 361 ~~ 362 (405)
T TIGR00362 361 KV 362 (405)
T ss_pred CH
Confidence 43
No 101
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=60.25 E-value=23 Score=34.97 Aligned_cols=80 Identities=9% Similarity=0.063 Sum_probs=55.2
Q ss_pred cCCHHHHHHHHHhhC--CCCCCCHHHHHHHHHHHHH---HHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCC
Q 010992 401 ILTKRSIQELVNQID--PSERLDPDVEDILVDIAED---FVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGF 475 (496)
Q Consensus 401 ILtKrKLqELVrqID--PsesLDpDVEELLLeIADD---FVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGF 475 (496)
.++...+.++++++- -+..+|+|+.+.|.+.++- ++..++...+.+|.-++...++..+|+-.|+. +++..=|+
T Consensus 179 ~~~~~e~~~il~~~~~~~~~~~~~~~~~~ia~~~~G~pR~a~~~l~~~~~~a~~~~~~~I~~~~v~~~l~~-~~~~~~~l 257 (328)
T PRK00080 179 FYTVEELEKIVKRSARILGVEIDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDGVITKEIADKALDM-LGVDELGL 257 (328)
T ss_pred CCCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH-hCCCcCCC
Confidence 456777777777663 3567999998888877743 36677777777776666677899999888865 55555555
Q ss_pred Cccccc
Q 010992 476 SGDEIK 481 (496)
Q Consensus 476 ssDEIr 481 (496)
...+++
T Consensus 258 ~~~~~~ 263 (328)
T PRK00080 258 DEMDRK 263 (328)
T ss_pred CHHHHH
Confidence 544433
No 102
>PF08546 ApbA_C: Ketopantoate reductase PanE/ApbA C terminal; InterPro: IPR013752 This is the C-terminal domain of 2-dehydropantoate 2-reductases also known as ketopantoate reductases, 1.1.1.169 from EC. The reaction catalysed by this enzyme is: (R)-pantoate + NADP(+) = 2-dehydropantoate + NADPH. AbpA catalyses the NADPH reduction of ketopantoic acid to pantoic acid in the alternative pyrimidine biosynthetic (APB) pathway []. ApbA and PanE are allelic []. ApbA, the ketopantoate reductase enzyme is required for the synthesis of thiamine via the APB biosynthetic pathway []. ; GO: 0016491 oxidoreductase activity, 0050661 NADP binding, 0055114 oxidation-reduction process; PDB: 1YJQ_A 1KS9_A 2OFP_A 1YON_A 2EW2_B 3EGO_B 3HN2_D 3GHY_B 3G17_E 3HWR_B ....
Probab=60.07 E-value=9.9 Score=32.10 Aligned_cols=55 Identities=16% Similarity=0.279 Sum_probs=24.2
Q ss_pred CCCHH-HHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCcccc
Q 010992 419 RLDPD-VEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLP 473 (496)
Q Consensus 419 sLDpD-VEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IP 473 (496)
.|+++ +++.+.++.+..-+...+.--.+.++|..+.=.+--.-+-+-+.+|+..|
T Consensus 57 ~l~~~~~~~~~~~~~~~~~~~~~SM~~D~~~gr~tEid~i~G~vv~~a~~~gv~~P 112 (125)
T PF08546_consen 57 PLDPDDLEEAIERLIRSTPDNRSSMLQDIEAGRPTEIDYINGYVVRLAKKHGVPTP 112 (125)
T ss_dssp S--HHHHHHHHHHHHHCTTTT--HHHHHHHTTB--SHHHTHHHHHHHHHHTT---H
T ss_pred cCcHHHHHHHHHHHHHhcCCccccHHHHHHHcccccHHHHHHHHHHHHHHHCCCCc
Confidence 46666 66666666666666555555555555544421112223445556666655
No 103
>TIGR00764 lon_rel lon-related putative ATP-dependent protease. Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.
Probab=59.71 E-value=34 Score=37.79 Aligned_cols=62 Identities=16% Similarity=0.167 Sum_probs=44.4
Q ss_pred HHHHHHHHHhh---C-CCCCCCHHHHHHHHHHHH-------------HHHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992 404 KRSIQELVNQI---D-PSERLDPDVEDILVDIAE-------------DFVESITMFGCSLAKHRKSDTLEAKDILVHLE 465 (496)
Q Consensus 404 KrKLqELVrqI---D-PsesLDpDVEELLLeIAD-------------DFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE 465 (496)
++++.+++.+. + ....||+++.+.|++.+- .-+.+|+..|..+|+.++++.|+.+||+-.|+
T Consensus 311 ~~~~~~~i~~~~~r~G~l~~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~ 389 (608)
T TIGR00764 311 RDKLVQFVAQEVKKDGRIPHFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKK 389 (608)
T ss_pred HHHHHHHHHHHHHHhCCCCcCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHH
Confidence 44455555543 2 234788987777765333 56788999999999999999999999976443
No 104
>PF07261 DnaB_2: Replication initiation and membrane attachment; InterPro: IPR006343 This entry represents a domain found in several bacterial replication initiation and membrane attachment proteins, DnaB and DnaD. The DnaD protein is a component of the PriA primosome. The PriA primosome functions to recruit the replication fork helicase onto the DNA []. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria []. The DnaB protein is essential for both replication initiation and membrane attachment of the origin region of the chromosome and Plasmid pUB110 in Bacillus subtilis. It is known that there are two different classes (DnaBI and DnaBII) in the DnaB mutants; DnaBI is essential for both chromosome and pUB110 replication, whereas DnaBII is necessary only for chromosome replication []. This domain tends to be found towards the C terminus of DnaB and DnaD proteins and is alpha helical in nature.; PDB: 2I5U_A 2ZC2_A.
Probab=58.68 E-value=43 Score=25.99 Aligned_cols=48 Identities=13% Similarity=0.062 Sum_probs=34.8
Q ss_pred CCCCCHHHHHHHHHHHH--HHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992 417 SERLDPDVEDILVDIAE--DFVESITMFGCSLAKHRKSDTLEAKDILVHLER 466 (496)
Q Consensus 417 sesLDpDVEELLLeIAD--DFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER 466 (496)
+..+.+-..+.|.++.| +|=.+|+..||+.|.-++... ++-|.-+|++
T Consensus 10 ~~~~s~~e~~~l~~~~~~~~~~~~~v~~ai~~~~~~~~~~--~~Yi~~Il~~ 59 (77)
T PF07261_consen 10 GRPPSPSEIEKLEKWIDDYGFSPEVVNEAIEYALENNKRS--FNYIEKILNN 59 (77)
T ss_dssp TSS--HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCT--S--HHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCCC--HHHHHHHHHH
Confidence 45677888888899999 999999999999999554443 6666655554
No 105
>PRK07081 acyl carrier protein; Provisional
Probab=58.48 E-value=3.9 Score=33.77 Aligned_cols=24 Identities=13% Similarity=0.469 Sum_probs=21.4
Q ss_pred CCCCcchhhHHHHHhhhcCccccC
Q 010992 451 KSDTLEAKDILVHLERNWNMTLPG 474 (496)
Q Consensus 451 KSdTLEvKDVQLhLERnWNI~IPG 474 (496)
|-+.|++-++.++||+.|||.||-
T Consensus 32 GlDSl~~v~li~~lE~~f~I~i~~ 55 (83)
T PRK07081 32 GLSSLATVQLMLAIEDAFDIEIPD 55 (83)
T ss_pred CCCHHHHHHHHHHHHHHhCCcCCH
Confidence 678889999999999999999964
No 106
>PRK15380 pathogenicity island 1 protein SopD2; Provisional
Probab=58.44 E-value=13 Score=38.45 Aligned_cols=70 Identities=23% Similarity=0.386 Sum_probs=54.7
Q ss_pred CcCCccCCHHHHHHHHHhhCC--CCCCCHHHHHHHHHHHHHHHHHHH-------HHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992 396 EFGNRILTKRSIQELVNQIDP--SERLDPDVEDILVDIAEDFVESIT-------MFGCSLAKHRKSDTLEAKDILVHLER 466 (496)
Q Consensus 396 e~~nrILtKrKLqELVrqIDP--sesLDpDVEELLLeIADDFVDsVv-------t~ACrLAKHRKSdTLEvKDVQLhLER 466 (496)
+-+..||.|.+|+++++--|. -+.|+.|-+|++++|++.+=+.|+ .+|..|-|.-..+. ++||..+-|-|
T Consensus 113 ~i~~~vI~q~~i~~iLN~sdn~i~k~M~~~E~eLFlkiC~~~G~~i~~~peLLq~~as~Lrk~V~~~~-~IK~aVY~lmR 191 (319)
T PRK15380 113 EIDGKVIDKCNLHRLLNVSENCIFKVMEEDEEELFFKICIKYGEKIARYPELLEGFANKLKDAVNEDD-DIKDEVYKLMR 191 (319)
T ss_pred EeCCEEeehhhHHHHhccchhheeeccchhHHHHHHHHHHHhccccccCHHHHHHHHHHHHHHhcccc-HHHHHHHHhhC
Confidence 567899999999999985554 358999999999999998766554 45667777767774 78888777765
No 107
>PF04867 DUF643: Protein of unknown function (DUF643); InterPro: IPR006951 These are proteins of unknown function found in Borrelia burgdorferi (Lyme disease spirochete)
Probab=58.20 E-value=14 Score=33.73 Aligned_cols=35 Identities=14% Similarity=0.283 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcc
Q 010992 422 PDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLE 456 (496)
Q Consensus 422 pDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLE 456 (496)
+|+..-+++.|.+||++|+..---+-||+++..++
T Consensus 55 ~eiind~l~p~k~fIkdvLKdk~li~kykn~kn~k 89 (114)
T PF04867_consen 55 NEIINDILDPAKKFIKDVLKDKYLIKKYKNSKNMK 89 (114)
T ss_pred HHHHHHHhhHHHHHHHHHHhhhHHHHHHhccccce
Confidence 45666678899999999999999999999886443
No 108
>PRK13406 bchD magnesium chelatase subunit D; Provisional
Probab=57.38 E-value=43 Score=37.09 Aligned_cols=70 Identities=11% Similarity=0.051 Sum_probs=55.7
Q ss_pred CCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHH-------HHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccc
Q 010992 402 LTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFV-------ESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTL 472 (496)
Q Consensus 402 LtKrKLqELVrqIDPsesLDpDVEELLLeIADDFV-------DsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~I 472 (496)
.++.+|.+.-+.+ ++..|++++.+.+.+++++|- ..++..|..+|-.++.+.|+.+||+..++--+..++
T Consensus 179 ~~~~~I~~AR~rl-~~v~v~~~~l~~i~~~~~~~gv~S~Ra~i~llraARa~AaL~Gr~~V~~~dv~~Aa~lvL~hR~ 255 (584)
T PRK13406 179 IDADDIAAARARL-PAVGPPPEAIAALCAAAAALGIASLRAPLLALRAARAAAALAGRTAVEEEDLALAARLVLAPRA 255 (584)
T ss_pred CCHHHHHHHHHHH-ccCCCCHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhhc
Confidence 3344555555555 578999999999999999985 457888889999999999999999888877766554
No 109
>PRK05828 acyl carrier protein; Validated
Probab=57.04 E-value=2 Score=36.01 Aligned_cols=36 Identities=25% Similarity=0.349 Sum_probs=27.5
Q ss_pred hcCCCCcchhhHHHHHhhhcCccccCCCcccccccC
Q 010992 449 HRKSDTLEAKDILVHLERNWNMTLPGFSGDEIKTFR 484 (496)
Q Consensus 449 HRKSdTLEvKDVQLhLERnWNI~IPGFssDEIr~~r 484 (496)
.-|-+.|++-++...||++|||.||.--.+++++++
T Consensus 34 dLg~DSLd~velv~~lE~~f~I~i~~e~~~~i~Tv~ 69 (84)
T PRK05828 34 ELKIDSLDMFSIIVSLESEFNIEFSDEKLMKLKNLA 69 (84)
T ss_pred hcCCCHHHHHHHHHHHHHHHCCCcCHHHHHhCCCHH
Confidence 358888999999999999999999754334454443
No 110
>TIGR02890 spore_yteA sporulation protein, yteA family. Members of this predicted regulatory protein are found only in endospore-forming members of the Firmicutes group of bacteria, and in nearly every such species; Clostridium perfringens seems to be an exception. The member from Bacillus subtilis, the model system for the study of the sporulation program, has been designated both yteA and yzwB. Some (but not all) members of this family show a strong sequence match to PFAM family pfam01258 the C4-type zinc finger protein, DksA/TraR family, but only one of the four key Cys residues is conserved. All members of this protein family share an additional C-terminal domain. The function of proteins in this family is unknown. YteA was detected in mature spores of Bacillus subtilis by Kuwana, et al., and appears to be expressed under control of sigma-K.
Probab=56.32 E-value=17 Score=34.14 Aligned_cols=29 Identities=28% Similarity=0.418 Sum_probs=21.1
Q ss_pred chhhHHHHHhhhcCccccCCCcccccccCCcccccCCCCCC
Q 010992 456 EAKDILVHLERNWNMTLPGFSGDEIKTFRKPVRIVTDPIPL 496 (496)
Q Consensus 456 EvKDVQLhLERnWNI~IPGFssDEIr~~rk~~~~~~d~~~~ 496 (496)
++++|.-.|+|-=+ -.|. .|.+||++|++
T Consensus 70 ~L~~Ie~AL~Ri~~-----------G~YG-~Ce~CGe~I~~ 98 (159)
T TIGR02890 70 ELREIEHALQKIEN-----------GTYG-ICEVCGKPIPY 98 (159)
T ss_pred HHHHHHHHHHHHhC-----------CCCC-eecccCCcccH
Confidence 38899999999611 2343 68899999973
No 111
>TIGR00517 acyl_carrier acyl carrier protein. S (Ser) at position 37 in the seed alignment, in the motif DSLD, is the phosphopantetheine attachment site.
Probab=55.55 E-value=3.8 Score=32.37 Aligned_cols=34 Identities=21% Similarity=0.513 Sum_probs=25.5
Q ss_pred cCCCCcchhhHHHHHhhhcCccccCCCccccccc
Q 010992 450 RKSDTLEAKDILVHLERNWNMTLPGFSGDEIKTF 483 (496)
Q Consensus 450 RKSdTLEvKDVQLhLERnWNI~IPGFssDEIr~~ 483 (496)
-+-+.|++-++...||+.||+.||.--.++++++
T Consensus 33 lglDSl~~veli~~lE~~f~i~i~~~~~~~~~tv 66 (77)
T TIGR00517 33 LGADSLDTVELVMALEEEFDIEIPDEEAEKIATV 66 (77)
T ss_pred cCCcHHHHHHHHHHHHHHHCCCCCHHHHHHCCcH
Confidence 4667888899999999999999975433344433
No 112
>PF00493 MCM: MCM2/3/5 family This family extends the MCM domain of Prosite.; InterPro: IPR001208 MCM proteins are DNA-dependent ATPases required for the initiation of eukaryotic DNA replication [, , ]. In eukaryotes there is a family of six proteins, MCM2 to MCM7. They were first identified in yeast where most of them have a direct role in the initiation of chromosomal DNA replication by interacting directly with autonomously replicating sequences (ARS). They were thus called minichromosome maintenance proteins, MCM proteins []. This family is also present in the archebacteria in 1 to 4 copies. Methanocaldococcus jannaschii (Methanococcus jannaschii) has four members, MJ0363, MJ0961, MJ1489 and MJECL13. The "MCM motif" contains Walker-A and Walker-B type nucleotide binding motifs. The diagnostic sequence defining the MCMs is IDEFDKM. Only Mcm2 (aka Cdc19 or Nda1) has been subjected to mutational analysis in this region, and most mutations abolish its activity []. The presence of a putative ATP-binding domain implies that these proteins may be involved in an ATP-consuming step in the initiation of DNA replication in eukaryotes. The MCM proteins bind together in a large complex []. Within this complex, individual subunits associate with different affinities, and there is a tightly associated core of Mcm4 (Cdc21), Mcm6 (Mis5) and Mcm7 []. This core complex in human MCMs has been associated with helicase activity in vitro [], leading to the suggestion that the MCM proteins are the eukaryotic replicative helicase. Schizosaccharomyces pombe (Fission yeast) MCMs, like those in metazoans, are found in the nucleus throughout the cell cycle. This is in contrast to the Saccharomyces cerevisiae (Baker's yeast) in which MCM proteins move in and out of the nucleus during each cell cycle. The assembly of the MCM complex in S. pombe is required for MCM localisation, ensuring that only intact MCM complexes remain in the nucleus [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0006260 DNA replication; PDB: 3F8T_A 3F9V_A.
Probab=55.36 E-value=7.3 Score=39.20 Aligned_cols=64 Identities=16% Similarity=0.303 Sum_probs=45.4
Q ss_pred ccCCHHHH---HHHHH-hhCCCCCCCHHHHHHHHHHHHH-----------------HHHHHHHHHHHhhhhcCCCCcchh
Q 010992 400 RILTKRSI---QELVN-QIDPSERLDPDVEDILVDIAED-----------------FVESITMFGCSLAKHRKSDTLEAK 458 (496)
Q Consensus 400 rILtKrKL---qELVr-qIDPsesLDpDVEELLLeIADD-----------------FVDsVvt~ACrLAKHRKSdTLEvK 458 (496)
..++...| -.++| .+.| .|++|++++|.+.--+ .+|+++..|...||.|-+++|+.+
T Consensus 240 ~~~~~~~lr~yI~yar~~~~P--~ls~ea~~~I~~~Yv~lR~~~~~~~~~~~iT~R~LeSLIRLseA~AKl~lr~~V~~~ 317 (331)
T PF00493_consen 240 KPISEDLLRKYIAYARQNIHP--VLSEEAKELIINYYVELRKESKSNNKSIPITIRQLESLIRLSEAHAKLRLRDEVTEE 317 (331)
T ss_dssp -TT-HCCCHHHHHHHHHHC----EE-HHCHHHHHHHHCCCCHCHHCHSS-B-SSCCCCCHHHHHHHHHHHCTTSSECSHH
T ss_pred CccCHHHHHHHHHHHHhhccc--ccCHHHHHHHHHHHHHhcccccccccccccchhhHHHHHHHHHHHHHHhccCceeHH
Confidence 34554434 45556 5555 7999999999765321 458899999999999999999999
Q ss_pred hHHHHHh
Q 010992 459 DILVHLE 465 (496)
Q Consensus 459 DVQLhLE 465 (496)
||..+++
T Consensus 318 Dv~~Ai~ 324 (331)
T PF00493_consen 318 DVEEAIR 324 (331)
T ss_dssp HHHHHHH
T ss_pred HHHHHHH
Confidence 9987765
No 113
>PRK09862 putative ATP-dependent protease; Provisional
Probab=55.11 E-value=35 Score=37.24 Aligned_cols=49 Identities=10% Similarity=0.137 Sum_probs=42.3
Q ss_pred CCCCHHHHHHHHHHHHHH------HHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992 418 ERLDPDVEDILVDIAEDF------VESITMFGCSLAKHRKSDTLEAKDILVHLER 466 (496)
Q Consensus 418 esLDpDVEELLLeIADDF------VDsVvt~ACrLAKHRKSdTLEvKDVQLhLER 466 (496)
..+++++.++|.+.+++| .+.++.-|-.+|..++++.|+.+||...|+=
T Consensus 437 ~~l~~~~~~~l~~~~~~~~lS~Ra~~rlLrvARTiADL~g~~~V~~~hv~eAl~y 491 (506)
T PRK09862 437 CKLESEDARWLEETLIHLGLSIRAWQRLLKVARTIADIDQSDIITRQHLQEAVSY 491 (506)
T ss_pred hCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHh
Confidence 468889999888888877 6778888999999999999999999888763
No 114
>PF10789 Phage_RpbA: Phage RNA polymerase binding, RpbA; InterPro: IPR019725 Upon infection, the RpbA encoded phage protein binds to the ADP-ribosylated core RNA polymerase and modulates function to preferentially bind T4 promoters. This is a non-essential protein to the phage life cycle.
Probab=54.92 E-value=5.5 Score=35.95 Aligned_cols=39 Identities=21% Similarity=0.368 Sum_probs=33.5
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcc
Q 010992 418 ERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLE 456 (496)
Q Consensus 418 esLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLE 456 (496)
..||++|.|+-.+|..+|-++.+....++-+-++++.||
T Consensus 48 ~~iD~~V~~~wi~Lm~~~r~~sl~~Gak~V~~~g~~rle 86 (108)
T PF10789_consen 48 KEIDEDVSDKWIELMRKHREDSLAAGAKFVRVNGKERLE 86 (108)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHccCceeccCCceecc
Confidence 468999999999999999999999888888877777653
No 115
>PRK06508 acyl carrier protein; Provisional
Probab=54.34 E-value=10 Score=32.63 Aligned_cols=34 Identities=18% Similarity=0.287 Sum_probs=26.9
Q ss_pred HHHhhhhcCCCCcchhhHHHHHhhhcCccccCCC
Q 010992 443 GCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFS 476 (496)
Q Consensus 443 ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGFs 476 (496)
-..+-+--+-+.|++-||.+.||++||++||.--
T Consensus 26 ds~~~edL~~DSLd~veli~~lE~eFgI~i~~ee 59 (93)
T PRK06508 26 ESHTIDDLGIDSLDFLDIVFAIDKAFGIKLPLEQ 59 (93)
T ss_pred CCcchhccCCCHHHHHHHHHHHHHHHCCccCHHH
Confidence 3344555678889999999999999999997543
No 116
>PRK10778 dksA RNA polymerase-binding transcription factor; Provisional
Probab=54.09 E-value=10 Score=35.28 Aligned_cols=29 Identities=17% Similarity=0.093 Sum_probs=20.7
Q ss_pred chhhHHHHHhhhcCccccCCCcccccccCCcccccCCCCCC
Q 010992 456 EAKDILVHLERNWNMTLPGFSGDEIKTFRKPVRIVTDPIPL 496 (496)
Q Consensus 456 EvKDVQLhLERnWNI~IPGFssDEIr~~rk~~~~~~d~~~~ 496 (496)
+++.|.-+|+| |.-..|| .|-.||++||+
T Consensus 95 ~L~~I~~AL~R---i~~gtYG---------~Ce~CGe~I~~ 123 (151)
T PRK10778 95 LIKKIEKTLKK---VEDEDFG---------YCESCGVEIGI 123 (151)
T ss_pred HHHHHHHHHHH---HhCCCCc---------eeccCCCcccH
Confidence 57889999999 3333333 48889999974
No 117
>COG1734 DksA DnaK suppressor protein [Signal transduction mechanisms]
Probab=53.98 E-value=12 Score=33.94 Aligned_cols=29 Identities=21% Similarity=0.234 Sum_probs=17.6
Q ss_pred chhhHHHHHhhhcCccccCCCcccccccCCcccccCCCCCC
Q 010992 456 EAKDILVHLERNWNMTLPGFSGDEIKTFRKPVRIVTDPIPL 496 (496)
Q Consensus 456 EvKDVQLhLERnWNI~IPGFssDEIr~~rk~~~~~~d~~~~ 496 (496)
.+++|...|+|- .--.|| .|-.||+|||+
T Consensus 64 ~l~~i~~al~rI---e~gtYG---------~Ce~cG~~Ip~ 92 (120)
T COG1734 64 LLRKIESALDRI---EEGTYG---------ICEECGEPIPE 92 (120)
T ss_pred HHHHHHHHHHHH---HcCCcc---------chhccCCcCCH
Confidence 456666777662 111222 48889999984
No 118
>TIGR03772 anch_rpt_subst anchored repeat ABC transporter, substrate-binding protein. Members of this protein family are ABC transporter permease subunits as identified by pfam00950, but additionally contain the Actinobacterial insert domain described by TIGR03769. Some homologs (lacking the insert) have been described as transporters of manganese or of chelated iron. Members of this family typically are found along with an ATP-binding cassette protein, a permease, and an LPXTG-anchored protein with two or three copies of the TIGR03769 insert that occurs just once in this protein family.
Probab=53.94 E-value=13 Score=40.25 Aligned_cols=76 Identities=14% Similarity=0.272 Sum_probs=56.1
Q ss_pred cCCHHHHHHHHHhh-CCCCCCCHHHHHHHHHHHHHHHHHHHHHHH----Hhhh--hcCCCCcchhhHHHHHhhhcCcccc
Q 010992 401 ILTKRSIQELVNQI-DPSERLDPDVEDILVDIAEDFVESITMFGC----SLAK--HRKSDTLEAKDILVHLERNWNMTLP 473 (496)
Q Consensus 401 ILtKrKLqELVrqI-DPsesLDpDVEELLLeIADDFVDsVvt~AC----rLAK--HRKSdTLEvKDVQLhLERnWNI~IP 473 (496)
-|.-+....+++.| +.-.++|++-.+...+=++.|++.+-...- ++|+ .++...|...|.--||+|.||+.+-
T Consensus 314 WlDP~na~~~a~~Ia~~LselDP~na~~Y~~Na~ay~~eL~~Ld~~~~~~la~ip~k~r~vvt~H~af~YLa~~YGL~~~ 393 (479)
T TIGR03772 314 WHNVKNAIAYVEVIRDKLIEVDPRGAQAYRSNASAYIHRLERLDTYVRRTIATIPPSRRHLITTHDAYSYLGQAYGLNIA 393 (479)
T ss_pred CcCHHHHHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccCCEEEEECCcHHHHHHHCCCeEE
Confidence 45677777777777 344578888888888888888777655444 4443 2445678889999999999999998
Q ss_pred CCC
Q 010992 474 GFS 476 (496)
Q Consensus 474 GFs 476 (496)
||-
T Consensus 394 ~~~ 396 (479)
T TIGR03772 394 GFV 396 (479)
T ss_pred eee
Confidence 764
No 119
>cd00052 EH Eps15 homology domain; found in proteins implicated in endocytosis, vesicle transport, and signal transduction. The alignment contains a pair of EF-hand motifs, typically one of them is canonical and binds to Ca2+, while the other may not bind to Ca2+. A hydrophobic binding pocket is formed by residues from both EF-hand motifs. The EH domain binds to proteins containing NPF (class I), [WF]W or SWG (class II), or H[TS]F (class III) sequence motifs.
Probab=53.79 E-value=57 Score=23.88 Aligned_cols=20 Identities=10% Similarity=0.293 Sum_probs=14.1
Q ss_pred CCcCCccCCHHHHHHHHHhh
Q 010992 395 DEFGNRILTKRSIQELVNQI 414 (496)
Q Consensus 395 ~e~~nrILtKrKLqELVrqI 414 (496)
+.+++..|++..|.++++++
T Consensus 9 D~~~~G~i~~~el~~~l~~~ 28 (67)
T cd00052 9 DPDGDGLISGDEARPFLGKS 28 (67)
T ss_pred CCCCCCcCcHHHHHHHHHHc
Confidence 44566677888888777765
No 120
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=53.72 E-value=21 Score=37.04 Aligned_cols=28 Identities=21% Similarity=0.459 Sum_probs=19.6
Q ss_pred hhhhcCCCCcchhhHHHHHhhhc-Ccccc
Q 010992 446 LAKHRKSDTLEAKDILVHLERNW-NMTLP 473 (496)
Q Consensus 446 LAKHRKSdTLEvKDVQLhLERnW-NI~IP 473 (496)
+.|-|+.+.+.+|.|..||-|++ ++.++
T Consensus 378 ~~~~R~~~~~~aR~iamyl~~~~~~~s~~ 406 (450)
T PRK00149 378 KSKSRTRNIARPRQIAMYLAKELTDLSLP 406 (450)
T ss_pred hCCCCCcccChHHHHHHHHHHHhcCCCHH
Confidence 45567777778888888877774 45554
No 121
>PF07030 DUF1320: Protein of unknown function (DUF1320); InterPro: IPR009752 This entry is represented by the Bacteriophage Mu, Gp36. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=53.65 E-value=36 Score=30.17 Aligned_cols=37 Identities=16% Similarity=0.302 Sum_probs=27.0
Q ss_pred CHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 010992 403 TKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESIT 440 (496)
Q Consensus 403 tKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVv 440 (496)
+...|.+|... +....+|+++.+..++-|+.+||..+
T Consensus 12 ~~~el~~ltd~-~~~~~~d~~~v~~Al~dA~~~Id~yL 48 (130)
T PF07030_consen 12 GEQELIQLTDD-DADGTIDPAVVEAALADASAEIDGYL 48 (130)
T ss_pred CHHHHHHHhcc-cccCCcCHHHHHHHHHHHHHHHHHHH
Confidence 44445555332 25578999999999999999999855
No 122
>PRK07360 FO synthase subunit 2; Reviewed
Probab=53.46 E-value=20 Score=36.66 Aligned_cols=76 Identities=16% Similarity=0.146 Sum_probs=55.6
Q ss_pred CHHHHHHHHHhhCCCCCCCHHHHHHHHHHHH-HHHHHHHHHHHHhhhhcCCCCcchh-h--HHHHHhhhcCccccCCCcc
Q 010992 403 TKRSIQELVNQIDPSERLDPDVEDILVDIAE-DFVESITMFGCSLAKHRKSDTLEAK-D--ILVHLERNWNMTLPGFSGD 478 (496)
Q Consensus 403 tKrKLqELVrqIDPsesLDpDVEELLLeIAD-DFVDsVvt~ACrLAKHRKSdTLEvK-D--VQLhLERnWNI~IPGFssD 478 (496)
+.+.+.++++++-.++.|+.+=...|++..| +.++.+...|-++-++...+.|++. . |.+.-..++|+.+=+|+.+
T Consensus 3 ~~~~~~~~~~~~~~g~~ls~~e~~~Ll~~~~~~~l~~L~~~A~~ir~~~~G~~v~~~~~~~i~~Tn~C~~~C~fC~~~~~ 82 (371)
T PRK07360 3 TDQIFEDILERARKGKDLSKEDALELLETTEPRRIFEILELADRLRKEQVGDTVTYVVNRNINFTNICEGHCGFCAFRRD 82 (371)
T ss_pred chHHHHHHHHHHhcCCCCCHHHHHHHhcCCChHHHHHHHHHHHHHHHHhcCCeEEEEeccCcccchhhhcCCccCCcccC
Confidence 4566889999998888888875555666654 7899999999999888887777641 2 3334555677777777765
No 123
>TIGR01765 tspaseT_teng_N transposase, putative, N-terminal domain. This model represents the N-terminal region of a family of putative transposases found in the largest copy number in Thermoanaerobacter tengcongensis. The three homologs in Bacillus anthracis are each split into two ORFs and This model represents the upstream ORF.
Probab=53.33 E-value=20 Score=28.92 Aligned_cols=47 Identities=13% Similarity=0.237 Sum_probs=28.2
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCc
Q 010992 419 RLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNM 470 (496)
Q Consensus 419 sLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI 470 (496)
.+++|..++|+++++.|-+ .++.+...|- +.-..+|++..|.+.+..
T Consensus 7 ~~~~e~~~~L~~tm~~f~~-A~n~~~~~~~----e~~~~~~~k~~L~~l~y~ 53 (73)
T TIGR01765 7 NFEDKEKEYLLDLIRAFSS-AVNFVIKRLL----EGKSHSELKKELQRLYYL 53 (73)
T ss_pred ecChhhHHHHHHHHHHHHH-HHHHHHHHHH----CCCChhHHHHHHHHHHhh
Confidence 3567778999999999863 3344444442 222456666666665543
No 124
>PRK08172 putative acyl carrier protein IacP; Validated
Probab=52.96 E-value=5.4 Score=33.08 Aligned_cols=43 Identities=19% Similarity=0.302 Sum_probs=32.6
Q ss_pred HHHhhhhcCCCCcchhhHHHHHhhhcCccccCCCcccccccCC
Q 010992 443 GCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGDEIKTFRK 485 (496)
Q Consensus 443 ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGFssDEIr~~rk 485 (496)
...|..--+-+.|++-|+.+.||.+||+.|+.--..+++++..
T Consensus 27 d~~l~~dL~~DSld~v~lv~~lEe~F~I~i~~~d~~~i~Tv~d 69 (82)
T PRK08172 27 QTHLVEDLYADSLDLIDIVFGLSEEFDISCNENDLPDMTTFAD 69 (82)
T ss_pred CcchhhhcCCCHHHHHHHHHHHHHHHCCCcCHHHHHHCCCHHH
Confidence 4455555678889999999999999999997665556666543
No 125
>PLN00153 histone H2A; Provisional
Probab=52.91 E-value=34 Score=31.78 Aligned_cols=68 Identities=12% Similarity=0.180 Sum_probs=59.6
Q ss_pred CccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992 399 NRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER 466 (496)
Q Consensus 399 nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER 466 (496)
+-.+.=-+++.++++-.-.++|...+--.|..+.|-++.+|++.|...|+..|..-|..+.|++.+..
T Consensus 22 gL~FpVgRi~R~Lr~g~~a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~n 89 (129)
T PLN00153 22 GLQFPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIRN 89 (129)
T ss_pred CcccchHHHHHHHhcCchhhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhccC
Confidence 45567788999999866677899999999999999999999999999999999999999999988744
No 126
>cd06457 M3A_MIP Peptidase M3 mitochondrial intermediate peptidase (MIP; EC 3.4.24.59) belongs to the widespread subfamily M3A, that show similarity to the Thimet oligopeptidase (TOP). It is one of three peptidases responsible for the proteolytic processing of both, nuclear and mitochondrial encoded precursor polypeptides targeted to the various subcompartments of the mitochondria. It cleaves intermediate-size proteins initially processed by mitochondrial processing peptidase (MPP) to yield a processing intermediate with a typical N-terminal octapeptide that is sequentially cleaved by MIP to mature-size protein. MIP cleaves precursor proteins of respiratory components, including subunits of the electron transport chain and tri-carboxylic acid cycle enzymes, and components of the mitochondrial genetic machinery, including ribosomal proteins, translation factors, and proteins required for mitochondrial DNA metabolism. It has been suggested that the human MIP (HMIP polypeptide; gene symbo
Probab=52.67 E-value=21 Score=37.56 Aligned_cols=62 Identities=10% Similarity=0.083 Sum_probs=38.8
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHhhhhcC------CCCcchhhHHHHHhhhcCccccCCCccccccc
Q 010992 421 DPDVEDILVDIAEDFVESITMFGCSLAKHRK------SDTLEAKDILVHLERNWNMTLPGFSGDEIKTF 483 (496)
Q Consensus 421 DpDVEELLLeIADDFVDsVvt~ACrLAKHRK------SdTLEvKDVQLhLERnWNI~IPGFssDEIr~~ 483 (496)
.++|+++|.+|++.-..-+-...-.|++..+ .+.|+.=|+-|+.|+.-...+ .+..++++.|
T Consensus 62 pe~v~~fL~~l~~~~~p~~~~e~~~L~~~~~~~~~~~~~~L~pwD~~yy~~~~~~~~~-~~d~~~l~~Y 129 (458)
T cd06457 62 PENVMEFLTELSEKLRPRAEEELAVLRDMKRKVLGKPLSSLAPWDRDYYTGQYRQSRF-DSEPSNLSPY 129 (458)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCCCHHHHHHHHHHHHHhhc-CCChHHhccc
Confidence 4668888888877766555554444444333 236888899888887533333 4566677766
No 127
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=52.60 E-value=25 Score=33.72 Aligned_cols=63 Identities=11% Similarity=0.075 Sum_probs=42.6
Q ss_pred CCHHHHHHHHHhhC--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992 402 LTKRSIQELVNQID--PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER 466 (496)
Q Consensus 402 LtKrKLqELVrqID--PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER 466 (496)
+++..+.++++++. -+..+++++.+.|++.+..=+..++...-++|. +.++|+.+||..++.+
T Consensus 184 ~~~~~~~~~l~~~~~~~~~~~~~~al~~l~~~~~gdlr~l~~~l~~~~~--~~~~It~~~v~~~~~~ 248 (337)
T PRK12402 184 PTDDELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTLQTAAL--AAGEITMEAAYEALGD 248 (337)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHH--cCCCCCHHHHHHHhCC
Confidence 45667777777763 344689999999998886555555554444442 2346899999877765
No 128
>PRK04195 replication factor C large subunit; Provisional
Probab=52.22 E-value=30 Score=36.46 Aligned_cols=69 Identities=16% Similarity=0.121 Sum_probs=49.8
Q ss_pred CCHHHHHHHHHhhC--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccc
Q 010992 402 LTKRSIQELVNQID--PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTL 472 (496)
Q Consensus 402 LtKrKLqELVrqID--PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~I 472 (496)
++.+.|.++|++|. .+..+|+++.+.|.+.+.-=+..++.....+|. +...|+..||...+.|.|...|
T Consensus 160 ~~~~~i~~~L~~i~~~egi~i~~eaL~~Ia~~s~GDlR~ain~Lq~~a~--~~~~it~~~v~~~~~~d~~~~i 230 (482)
T PRK04195 160 LSTRSIVPVLKRICRKEGIECDDEALKEIAERSGGDLRSAINDLQAIAE--GYGKLTLEDVKTLGRRDREESI 230 (482)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHhc--CCCCCcHHHHHHhhcCCCCCCH
Confidence 45667777777774 345789999999998887777777777777665 3446788888777767765544
No 129
>cd05030 calgranulins Calgranulins: S-100 domain found in proteins belonging to the Calgranulin subgroup of the S100 family of EF-hand calcium-modulated proteins, including S100A8, S100A9, and S100A12 . Note that the S-100 hierarchy, to which this Calgranulin group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. These proteins are expressed mainly in granulocytes, and are involved in inflammation, allergy, and neuritogenesis, as well as in host-parasite response. Calgranulins are modulated not only by calcium, but also by other metals such as zinc and copper. Structural data suggested that calgranulins may exist in multiple structural forms, homodimers, as well as hetero-oligomers. For example, the S100A8/S100A9 complex called calprotectin plays important roles in the regulation of inflammatory processes, wound repair, and regulating zinc-dependent enzymes as well as microbial growth.
Probab=52.09 E-value=35 Score=28.16 Aligned_cols=45 Identities=22% Similarity=0.366 Sum_probs=27.2
Q ss_pred CcCCccCCHHHHHHHHHhhCCC----CCCCHHHHHHHHHH---------HHHHHHHHH
Q 010992 396 EFGNRILTKRSIQELVNQIDPS----ERLDPDVEDILVDI---------AEDFVESIT 440 (496)
Q Consensus 396 e~~nrILtKrKLqELVrqIDPs----esLDpDVEELLLeI---------ADDFVDsVv 440 (496)
++.+..|++..|..|++..-+. ...+.+++++|.++ -++|+.-+.
T Consensus 21 ~~~~~~Is~~El~~ll~~~~g~~~t~~~~~~~v~~i~~~~D~d~dG~I~f~eF~~~~~ 78 (88)
T cd05030 21 KGHPDTLYKKEFKQLVEKELPNFLKKEKNQKAIDKIFEDLDTNQDGQLSFEEFLVLVI 78 (88)
T ss_pred CCCcccCCHHHHHHHHHHHhhHhhccCCCHHHHHHHHHHcCCCCCCcCcHHHHHHHHH
Confidence 3456789999999999743221 12246677766654 256775444
No 130
>PF06570 DUF1129: Protein of unknown function (DUF1129); InterPro: IPR009214 There are currently no experimental data for members of this group or their homologues. However, these proteins contain predicted integral membrane proteins (with several transmembrane segments).
Probab=51.92 E-value=17 Score=34.24 Aligned_cols=35 Identities=20% Similarity=0.368 Sum_probs=27.7
Q ss_pred HHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHH
Q 010992 404 KRSIQELVNQIDPSERLDPDVEDILVDIAEDFVES 438 (496)
Q Consensus 404 KrKLqELVrqIDPsesLDpDVEELLLeIADDFVDs 438 (496)
++=+.+|.++++....=|.|+||+|.||.|+-||.
T Consensus 7 ~~y~~~l~~~L~~~~~~e~~~e~~L~eil~~Llea 41 (206)
T PF06570_consen 7 QEYIFDLRKYLRSSGVSEEEIEELLEEILPHLLEA 41 (206)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHH
Confidence 33466888888776677888999999999987774
No 131
>cd01020 TroA_b Metal binding protein TroA_b. These proteins are predicted to function as initial receptors in ABC transport of metal ions. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=51.87 E-value=19 Score=34.79 Aligned_cols=73 Identities=16% Similarity=0.207 Sum_probs=46.9
Q ss_pred cCCHHHHHHHHHhhC-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHH----hhhhcCCCCcchhhHHHHHhhhcCcccc
Q 010992 401 ILTKRSIQELVNQID-PSERLDPDVEDILVDIAEDFVESITMFGCS----LAKHRKSDTLEAKDILVHLERNWNMTLP 473 (496)
Q Consensus 401 ILtKrKLqELVrqID-PsesLDpDVEELLLeIADDFVDsVvt~ACr----LAKHRKSdTLEvKDVQLhLERnWNI~IP 473 (496)
-|...+...+++.|. .-.++|++-++...+=+++|++.+-...-+ +++.++...|...|.--||+|.||+.+-
T Consensus 98 Wldp~n~~~~a~~I~~~L~~~dP~~~~~y~~N~~~~~~~l~~l~~~~~~~~~~~~~~~~v~~H~af~Y~~~~yGl~~~ 175 (264)
T cd01020 98 WYDPETMSKVANALADALVKADPDNKKYYQANAKKFVASLKPLAAKIAELSAKYKGAPVAATEPVFDYLLDALGMKER 175 (264)
T ss_pred ecCHhHHHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHHHHHHHHHHHHhhCCCCeEEEeCchHHHHHHHCCCccc
Confidence 455666666666662 334566666666666666666665443322 2444455678888999999999999864
No 132
>PF01432 Peptidase_M3: Peptidase family M3 This Prosite motif covers only the active site. This family belongs to family M3 of the peptidase classification.; InterPro: IPR001567 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to MEROPS peptidase family M3 (clan MA(E)), subfamilies M3A and M3B. The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA. The Thimet oligopeptidase family, is a large family of archaeal, bacterial and eukaryotic oligopeptidases that cleave medium sized peptides. The group contains: mitochondrial intermediate peptidase (3.4.24.59 from EC) Neurolysin, mitochondrial precursor, (3.4.24.16 from EC) Thimet oligopeptidase (3.4.24.15 from EC) Dipeptidyl carboxypeptidase (3.4.15.5 from EC) Oligopeptidase A (3.4.24.70 from EC) Oligoendopeptidase F ; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 2QR4_B 3CE2_A 1Y79_1 2H1J_A 2H1N_A 2O36_A 1S4B_P 2O3E_A 1I1I_P.
Probab=51.50 E-value=26 Score=36.06 Aligned_cols=67 Identities=13% Similarity=0.139 Sum_probs=45.9
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhh----hcCCC-CcchhhHHHHHhhhcCccccCCCccccccc
Q 010992 416 PSERLDPDVEDILVDIAEDFVESITMFGCSLAK----HRKSD-TLEAKDILVHLERNWNMTLPGFSGDEIKTF 483 (496)
Q Consensus 416 PsesLDpDVEELLLeIADDFVDsVvt~ACrLAK----HRKSd-TLEvKDVQLhLERnWNI~IPGFssDEIr~~ 483 (496)
......++|.++|.+++++..+-+....-.++| ..|.+ +|+.=|+.|+.++.-...+ .+..++++.|
T Consensus 62 ~m~~~~~~v~~fL~~~~~~~~p~~~~~~~~l~~~~~~~~g~~~~l~~wD~~y~~~~~~~~~~-~~~~~~~~~~ 133 (458)
T PF01432_consen 62 KMAKNPENVLDFLDELVKKLKPLLERELELLKKLKKKRLGLEKKLRPWDVAYYMEQYRQERY-DLDEEELSPY 133 (458)
T ss_dssp STTTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSSBBGGGHHHHHHHHHHHHT-SSSHHHHGGG
T ss_pred hhcCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCccccccchhHHHhhHHHHHHh-ccchhhcCCc
Confidence 356778899999999999888877777767766 66776 8999999777665432222 2444445443
No 133
>PRK05087 D-alanine--poly(phosphoribitol) ligase subunit 2; Validated
Probab=51.03 E-value=8.5 Score=31.87 Aligned_cols=23 Identities=26% Similarity=0.592 Sum_probs=19.7
Q ss_pred CCCcchhhHHHHHhhhcCccccC
Q 010992 452 SDTLEAKDILVHLERNWNMTLPG 474 (496)
Q Consensus 452 SdTLEvKDVQLhLERnWNI~IPG 474 (496)
-+.+++-++.+.||++||+.||.
T Consensus 34 lDSl~~veli~~lE~~fgi~i~~ 56 (78)
T PRK05087 34 LDSMGTVELLVELENRFDIEVPV 56 (78)
T ss_pred cchHHHHHHHHHHHHHhCCccCh
Confidence 46678889999999999999953
No 134
>KOG1657 consensus CCAAT-binding factor, subunit C (HAP5) [Transcription]
Probab=50.55 E-value=29 Score=34.63 Aligned_cols=78 Identities=17% Similarity=0.278 Sum_probs=59.7
Q ss_pred CCcCCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccc
Q 010992 395 DEFGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTL 472 (496)
Q Consensus 395 ~e~~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~I 472 (496)
.+..+..|...+|..++|.=+-.-.|..|+--++...++-||..+..++-..+..-+..+|.-+||.=++.+.-...|
T Consensus 68 ~d~~~~~lPlaRiKkimK~dedv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av~~s~~fdF 145 (236)
T KOG1657|consen 68 LDFKNHILPLARIKKIMKSDEDVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAVTQSETFDF 145 (236)
T ss_pred cchhhccCcHhhccccccccccccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHhccCCCccc
Confidence 345566666666665555322223677888888899999999999999999999999999999999999988755443
No 135
>cd03569 VHS_Hrs_Vps27p VHS domain family, Hrs and Vps27p subfamily; composed of Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and its yeast homolog Vps27p (vacuolar protein sorting). The VHS domain, an essential part of Hrs/Vps27p, has a superhelical structure similar to the structure of ARM (Armadillo) repeats and is present at the N-termini of proteins. Hrs also contains a FYVE (Fab1p, YOTB, Vac1p, and EEA1) zinc finger domain C-terminal to VHS, as well as two coiled-coil domains. Hrs has been proposed to play a role in at least three vesicle trafficking events: exocytosis, endocytosis, and endosome to lysosome trafficking. Hrs is involved in promoting rapid recycling of endocytosed signaling receptors to the plasma membrane.
Probab=50.35 E-value=60 Score=29.47 Aligned_cols=32 Identities=13% Similarity=0.370 Sum_probs=13.5
Q ss_pred CHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHH
Q 010992 403 TKRSIQELVNQIDPSERLDPDVEDILVDIAEDFV 436 (496)
Q Consensus 403 tKrKLqELVrqIDPsesLDpDVEELLLeIADDFV 436 (496)
+|+=|++|++-+.. ..+.+|.+-+|+|...|-
T Consensus 82 s~~fl~~l~~l~~~--~~~~~Vk~kil~li~~W~ 113 (142)
T cd03569 82 SREFMDELKDLIKT--TKNEEVRQKILELIQAWA 113 (142)
T ss_pred hHHHHHHHHHHHcc--cCCHHHHHHHHHHHHHHH
Confidence 34444444444432 344444444444444433
No 136
>COG4286 Uncharacterized conserved protein related to MYG1 family [Function unknown]
Probab=49.88 E-value=7.9 Score=40.13 Aligned_cols=74 Identities=18% Similarity=0.235 Sum_probs=43.9
Q ss_pred HHHHHHHHhhCCC---CCCCHHHHHHHHHHHHHHHHHHHHHHH---HhhhhcCCCCcchhhHHHHHhhhc--CccccCCC
Q 010992 405 RSIQELVNQIDPS---ERLDPDVEDILVDIAEDFVESITMFGC---SLAKHRKSDTLEAKDILVHLERNW--NMTLPGFS 476 (496)
Q Consensus 405 rKLqELVrqIDPs---esLDpDVEELLLeIADDFVDsVvt~AC---rLAKHRKSdTLEvKDVQLhLERnW--NI~IPGFs 476 (496)
+.|-+||+-..+. +.-|++--..-|.+|+||++.+....| +..++-.....|.+|+-|+|.|-+ .-.|.-.+
T Consensus 143 ~sl~~iv~~~np~~~~e~~~d~~F~~al~~a~~~l~~~~~~~~~w~~a~~~v~k~I~e~~~~iL~ld~~~pw~~~i~eie 222 (306)
T COG4286 143 RSLPDIVESFNPDWSDEDADDEGFLEALAFASDFLDNLFKTIVSWLRAYALVVKAIAETEDVILVLDRFCPWKEHIFEIE 222 (306)
T ss_pred cchHHHHHhcCCCcCCCCcchHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHhhCCcEEEecCCCcHHHHHHHhc
Confidence 3488888877553 344555555567899999999988877 222232333455566656665542 33344444
Q ss_pred cc
Q 010992 477 GD 478 (496)
Q Consensus 477 sD 478 (496)
+|
T Consensus 223 ~e 224 (306)
T COG4286 223 AE 224 (306)
T ss_pred cc
Confidence 44
No 137
>PF12767 SAGA-Tad1: Transcriptional regulator of RNA polII, SAGA, subunit; InterPro: IPR024738 The yeast Spt-Ada-Gcn5-Acetyl (SAGA) transferase complex is a multifunctional coactivator involved in multiple cellular processes [], including regulation of transcription by RNA polymerase II [, ]. It is formed of five major modular subunits and shows a high degree of structural conservation to human TFTC and STAGA []. This entry represents Ada1 (known as Tada1 in higher eukaryotes), one of the subunits that constitute the SAGA core. It also functions as a component of the SALSA and SLIK complexes. ; GO: 0070461 SAGA-type complex
Probab=49.77 E-value=45 Score=32.52 Aligned_cols=50 Identities=14% Similarity=0.170 Sum_probs=36.3
Q ss_pred CccCCHHHHHHHHHhhC---CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 010992 399 NRILTKRSIQELVNQID---PSERLDPDVEDILVDIAEDFVESITMFGCSLAK 448 (496)
Q Consensus 399 nrILtKrKLqELVrqID---PsesLDpDVEELLLeIADDFVDsVvt~ACrLAK 448 (496)
..+-.-..|.+-+..|. +-+.+++|+.++|.--.|.|+.+|++..+.++|
T Consensus 200 ~~LPD~~~L~~Rm~~ia~e~GL~gvs~~~a~ll~~ale~~LK~lI~s~l~~~r 252 (252)
T PF12767_consen 200 GELPDTQSLRKRMEQIAWEHGLGGVSDDCANLLNLALEVHLKNLIKSCLDLVR 252 (252)
T ss_pred CcCCCHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 33334444443333332 335899999999999999999999999998875
No 138
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=49.74 E-value=61 Score=23.98 Aligned_cols=58 Identities=14% Similarity=0.213 Sum_probs=37.6
Q ss_pred HHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHH----------HHHHHHHhhhhcCCCCcchhhHHH
Q 010992 405 RSIQELVNQIDPSERLDPDVEDILVDIAEDFVES----------ITMFGCSLAKHRKSDTLEAKDILV 462 (496)
Q Consensus 405 rKLqELVrqIDPsesLDpDVEELLLeIADDFVDs----------Vvt~ACrLAKHRKSdTLEvKDVQL 462 (496)
..+.+++.++.....++.++..+=..++|.|+.. |...+.-||.+-....+..+|+.-
T Consensus 3 ~~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~ 70 (88)
T cd00043 3 PTPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVH 70 (88)
T ss_pred chHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHHhH
Confidence 3455556666666689999999999999999874 223333444444344566777643
No 139
>cd05135 RasGAP_RASAL Ras GTPase activating-like protein (RASAL) or RASAL1 is a member of the GAP1 family, and a Ca2+ sensor responding in-phase to repetitive Ca2+ signals by associating with the plasma membrane and deactivating Ras. It contains a conserved domain structure comprising N-terminal tandem C2 domains, a highly conserved central RasGAP domain, and a C-terminal pleckstrin-homology domain that is associated with a Bruton's tyrosine kinase motif. RASAL, like Ca2+ -promoted Ras inactivator (CAPRI, or RASAL4), is a cytosolic protein that undergoes a rapid translocation to the plasma membrane in response to receptor-mediated elevation in the concentration of intracellular free Ca2+, a translocation that activates its ability to function as a RasGAP. However, unlike RASAL4, RASAL undergoes an oscillatory translocation to the plasma membrane that occurs in synchrony with repetitive Ca2+ spikes.
Probab=49.63 E-value=44 Score=34.59 Aligned_cols=43 Identities=9% Similarity=0.090 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCC
Q 010992 426 DILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGF 475 (496)
Q Consensus 426 ELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGF 475 (496)
+.|.+++++|+|.|++..+++-. +++.|--+|.+.-.-.+|+.
T Consensus 149 ~~L~~~~~~~~~~I~~S~~~~P~-------~lR~i~~~l~~~v~~kFp~~ 191 (333)
T cd05135 149 EMLQGYLSSITDAIVGSVSQCPP-------VMRLTFKQLHKRVEERFPEA 191 (333)
T ss_pred HHHHHHHHHHHHHHHhhHHhCCH-------HHHHHHHHHHHHHHHHCCCC
Confidence 56788899999998876655543 45555444444444444543
No 140
>PRK08402 replication factor A; Reviewed
Probab=49.34 E-value=16 Score=38.22 Aligned_cols=83 Identities=17% Similarity=0.189 Sum_probs=51.7
Q ss_pred ccCCHHHHHHHHHhhCCCCCCCHH-HHHHHHHHHHHHHHHHHHHHHHhhhhcCCC--------CcchhhHHHHHhhhcCc
Q 010992 400 RILTKRSIQELVNQIDPSERLDPD-VEDILVDIAEDFVESITMFGCSLAKHRKSD--------TLEAKDILVHLERNWNM 470 (496)
Q Consensus 400 rILtKrKLqELVrqIDPsesLDpD-VEELLLeIADDFVDsVvt~ACrLAKHRKSd--------TLEvKDVQLhLERnWNI 470 (496)
-+|+|..|.|++.+.. .||.+ +++.|-++.++|=-+.-+++..+|+.-|.+ .+.++||.--. ++|++
T Consensus 2 ~~~~~~~i~e~~~~~~---~vs~eei~~~l~~lv~~~~~~e~~A~~~ia~e~G~~~~~~~~~~~~kI~dl~~g~-~~V~v 77 (355)
T PRK08402 2 TVLTKEEIIERIERKT---GMSREEIEEKIREIMKEEGISEHAAALLLAEELGVNLEGEEEAPLMHISDLVPGM-RGVNI 77 (355)
T ss_pred ccccHHHHHHHHHHhh---CCCHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhCCCccCCCccCccCHHHccCCC-ceeeE
Confidence 4799999999999872 36654 778888888887533333667777765553 35677774222 44554
Q ss_pred cccCCCcccccccCCc
Q 010992 471 TLPGFSGDEIKTFRKP 486 (496)
Q Consensus 471 ~IPGFssDEIr~~rk~ 486 (496)
..-=....+.|.|.|.
T Consensus 78 ~~rVl~~~~~r~f~rr 93 (355)
T PRK08402 78 VGRVLRKYPPREYTKK 93 (355)
T ss_pred EEEEEEccCCceeecc
Confidence 4433344456666543
No 141
>TIGR01688 dltC D-alanine--poly(phosphoribitol) ligase, subunit 2. This protein is part of the teichoic acid operon in gram-positive organisms. Gram positive organisms incorporate teichoic acid in their cell walls, and in the fatty acid residues of the glycolipid component of the outer layer of the cytoplasmic membrane. This gene, dltC, encodes the alanyl carrier protein.
Probab=48.72 E-value=8.9 Score=32.02 Aligned_cols=21 Identities=10% Similarity=0.480 Sum_probs=16.9
Q ss_pred CcchhhHHHHHhhhcCccccC
Q 010992 454 TLEAKDILVHLERNWNMTLPG 474 (496)
Q Consensus 454 TLEvKDVQLhLERnWNI~IPG 474 (496)
.+.+-++.+.||.+|||.||-
T Consensus 33 S~~~v~Li~~lE~ef~I~i~~ 53 (73)
T TIGR01688 33 SFGTVQLLLEIQNQFDIDVPI 53 (73)
T ss_pred HHHHHHHHHHHHHHhCCccCH
Confidence 345667889999999999973
No 142
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=48.43 E-value=27 Score=39.25 Aligned_cols=27 Identities=26% Similarity=0.395 Sum_probs=17.9
Q ss_pred hhhcCCCCcchhhHHHHHhhh-cCcccc
Q 010992 447 AKHRKSDTLEAKDILVHLERN-WNMTLP 473 (496)
Q Consensus 447 AKHRKSdTLEvKDVQLhLERn-WNI~IP 473 (496)
.|.|+.+.+.+|.|.+||-|+ +++.++
T Consensus 546 s~~R~~~i~~aRqiAMYL~r~lt~~Sl~ 573 (617)
T PRK14086 546 GTSRSRVLVTARQIAMYLCRELTDLSLP 573 (617)
T ss_pred CCCCCcccchHHHHHHHHHHHHcCCCHH
Confidence 345666777788887777776 345554
No 143
>COG1202 Superfamily II helicase, archaea-specific [General function prediction only]
Probab=48.06 E-value=19 Score=41.11 Aligned_cols=68 Identities=24% Similarity=0.393 Sum_probs=47.8
Q ss_pred HHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhh---------hhcCCCCcchhhHHHHHhhhcCccc-cC
Q 010992 406 SIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLA---------KHRKSDTLEAKDILVHLERNWNMTL-PG 474 (496)
Q Consensus 406 KLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLA---------KHRKSdTLEvKDVQLhLERnWNI~I-PG 474 (496)
.+.+++.+.|.-..||+...|.|+.|+-||..--+...|..| +.|-+- .+.--|-.+|++.|+|.. ||
T Consensus 710 a~~~I~~e~d~ii~ld~k~~e~l~~i~~df~~c~c~d~ce~~~~~lse~ii~lR~~g-k~p~~Isr~l~~~Ygi~aYpg 787 (830)
T COG1202 710 ALLDILEEGDKIIELDPKLKEKLLLIYMDFLNCTCRDCCECAEQRLSEKIIELRIEG-KDPSQISRILEKRYGIQAYPG 787 (830)
T ss_pred HHHHHHhchhhhhcCCHHHHHHHHHHHHHHhcCchhhhHHHHHHHHHHHHHHHHhcC-CCHHHHHHHHHHhhCeeecCh
Confidence 345566666666789999999999999999764344334433 344433 366678899999999865 55
No 144
>PRK15379 pathogenicity island 1 effector protein SopD; Provisional
Probab=47.91 E-value=19 Score=37.42 Aligned_cols=70 Identities=17% Similarity=0.311 Sum_probs=54.9
Q ss_pred CcCCccCCHHHHHHHHHhhCC--CCCCCHHHHHHHHHHHHHHHHHHH-------HHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992 396 EFGNRILTKRSIQELVNQIDP--SERLDPDVEDILVDIAEDFVESIT-------MFGCSLAKHRKSDTLEAKDILVHLER 466 (496)
Q Consensus 396 e~~nrILtKrKLqELVrqIDP--sesLDpDVEELLLeIADDFVDsVv-------t~ACrLAKHRKSdTLEvKDVQLhLER 466 (496)
+-|+.||.+.+|+++++--|. -+.|+.|-+|++++|++.+=+.|. .+|..|-|.-..+. ++||..+-|-|
T Consensus 113 ~IG~~VI~qsni~~iln~s~n~i~~~m~~~e~elflkic~~~g~~i~~~pellq~~~~~lr~~v~~~~-~ik~~vy~~mr 191 (317)
T PRK15379 113 MVGDTVISQSNIKDILNISDDAVIESMSREERQLFLQICEVIGAKMTWHPELLQESISTLRKEVTGNA-QIKAAVYEMMR 191 (317)
T ss_pred EECCEEEeeccHHHHhccchhheeeccchhHHHHHHHHHHHhccccccCHHHHHHHHHHHHHHhcccc-HHHHHHHHhhC
Confidence 568899999999999985443 358999999999999998766654 46667777767764 78888777665
No 145
>smart00324 RhoGAP GTPase-activator protein for Rho-like GTPases. GTPase activator proteins towards Rho/Rac/Cdc42-like small GTPases. etter domain limits and outliers.
Probab=47.90 E-value=95 Score=27.48 Aligned_cols=34 Identities=9% Similarity=0.203 Sum_probs=27.0
Q ss_pred HHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992 434 DFVESITMFGCSLAKHRKSDTLEAKDILVHLERN 467 (496)
Q Consensus 434 DFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn 467 (496)
+++.-++.+-.++++|...+..+++.|..++-.+
T Consensus 112 ~~L~~l~~~l~~i~~~~~~n~M~~~nLa~~f~P~ 145 (174)
T smart00324 112 ATLRYLLAHLNRVAEHSEENKMTARNLAIVFGPT 145 (174)
T ss_pred HHHHHHHHHHHHHHhccccCCCCHHHHHHHHhcc
Confidence 5666778888889999888888999887776554
No 146
>PRK07668 hypothetical protein; Validated
Probab=47.90 E-value=20 Score=36.20 Aligned_cols=33 Identities=15% Similarity=0.187 Sum_probs=26.5
Q ss_pred HHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHH
Q 010992 406 SIQELVNQIDPSERLDPDVEDILVDIAEDFVES 438 (496)
Q Consensus 406 KLqELVrqIDPsesLDpDVEELLLeIADDFVDs 438 (496)
=+.+|.+.+.....-|+|+||+|.|+.|+|+|.
T Consensus 9 fl~~L~~yL~~~glseeeieeiL~Ei~~hLlEg 41 (254)
T PRK07668 9 FLDDTRVYLIAKGIKEEDIESFLEDAELHLIEG 41 (254)
T ss_pred HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH
Confidence 356888888555556889999999999999974
No 147
>cd05137 RasGAP_CLA2_BUD2 CLA2/BUD2 functions as a GTPase-activating protein (GAP) for BUD1/RSR1 and is necessary for proper bud-site selection in yeast. BUD2 has sequence similarity to the catalytic domain of RasGAPs, and stimulates the hydrolysis of BUD1-GTP to BUD1-GDP. Elimination of Bud2p activity by mutation causes a random budding pattern with no growth defect. Overproduction of Bud2p also alters the budding pattern.
Probab=46.91 E-value=40 Score=35.73 Aligned_cols=43 Identities=19% Similarity=0.296 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCC
Q 010992 426 DILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGF 475 (496)
Q Consensus 426 ELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGF 475 (496)
+.|.+++++|++.|+...+++-. ++|.|--+|.+.-...+|+.
T Consensus 199 ~~L~~~~~~~~~~I~~S~~~~P~-------~lR~i~~~lr~~v~~kfpd~ 241 (395)
T cd05137 199 ERLISLTEEIWKRIANTSNDLPQ-------EIRHILKYIRAKLEDRYGDF 241 (395)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCH-------HHHHHHHHHHHHHHHHCCCc
Confidence 56899999999999998877654 56666556655544555544
No 148
>cd03197 GST_C_mPGES2 GST_C family; microsomal Prostaglandin E synthase Type 2 (mPGES2) subfamily; mPGES2 is a membrane-anchored dimeric protein containing a CXXC motif which catalyzes the isomerization of PGH2 to PGE2. Unlike cytosolic PGE synthase (cPGES) and microsomal PGES Type 1 (mPGES1), mPGES2 does not require glutathione (GSH) for its activity, although its catalytic rate is increased two- to four-fold in the presence of DTT, GSH, or other thiol compounds. PGE2 is widely distributed in various tissues and is implicated in the sleep/wake cycle, relaxation/contraction of smooth muscle, excretion of sodium ions, maintenance of body temperature, and mediation of inflammation. mPGES2 contains an N-terminal hydrophobic domain which is membrane associated and a C-terminal soluble domain with a GST-like structure. The C-terminus contains two structural domains a N-terminal thioredoxin-fold domain and a C-terminal alpha helical domain. The GST active site is located in a cleft between t
Probab=46.90 E-value=34 Score=32.05 Aligned_cols=54 Identities=15% Similarity=0.194 Sum_probs=38.0
Q ss_pred HHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHH
Q 010992 406 SIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVH 463 (496)
Q Consensus 406 KLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLh 463 (496)
.|--+-+.+-...-|++|+.+.|.+-+|+|++.+... -+.=+.+.+++-||.++
T Consensus 62 aM~~isk~lkk~~~i~~D~r~~L~~a~~~w~~~~~~~----~~FlaGd~ptIADisvy 115 (149)
T cd03197 62 AMYLISKYLKKPRLLQDDVREWLYDALNTWVAALGKD----RQFHGGSKPNLADLAVY 115 (149)
T ss_pred HHHHHHHHhccccCCCchHHHHHHHHHHHHHHHhcCC----CCccCCCCCCHHHHHHH
Confidence 3444445555567788999999999999999875442 12334577999999654
No 149
>PTZ00252 histone H2A; Provisional
Probab=46.85 E-value=62 Score=30.38 Aligned_cols=69 Identities=10% Similarity=0.183 Sum_probs=57.7
Q ss_pred CCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhc--CCCCcchhhHHHHHhh
Q 010992 398 GNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHR--KSDTLEAKDILVHLER 466 (496)
Q Consensus 398 ~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHR--KSdTLEvKDVQLhLER 466 (496)
.+-.+.=-+|+.++++-.-.++|...+--.|..+-|-.+.+|++.|...|+.+ |..-|..++|++.+..
T Consensus 22 AGL~FPVgRi~R~Lr~g~ya~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIrN 92 (134)
T PTZ00252 22 AGLIFPVGRVGSLLRRGQYARRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVRH 92 (134)
T ss_pred cCccCchHHHHHHHHcCCcccccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhccC
Confidence 34567778899999987777899999999999999999999999999999763 4567889999888754
No 150
>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional
Probab=46.34 E-value=28 Score=39.57 Aligned_cols=78 Identities=13% Similarity=0.181 Sum_probs=55.1
Q ss_pred CHHHHHHHHHhh------CCCCCCCHHHHHHHHHHHHHHHH---------HHHHHHHHhhhh----cCCCCcchhhHHHH
Q 010992 403 TKRSIQELVNQI------DPSERLDPDVEDILVDIAEDFVE---------SITMFGCSLAKH----RKSDTLEAKDILVH 463 (496)
Q Consensus 403 tKrKLqELVrqI------DPsesLDpDVEELLLeIADDFVD---------sVvt~ACrLAKH----RKSdTLEvKDVQLh 463 (496)
+.....++++.+ ..+..+++++.+..+++++.||. ++++.||..++. ++..+|+..||.-+
T Consensus 350 s~~~~~~IL~~~~~~ye~~h~v~i~~~al~~a~~ls~ryi~~r~lPdKaidlldea~a~~~~~~~~~~~~~v~~~~i~~v 429 (758)
T PRK11034 350 SIEETVQIINGLKPKYEAHHDVRYTAKAVRAAVELAVKYINDRHLPDKAIDVIDEAGARARLMPVSKRKKTVNVADIESV 429 (758)
T ss_pred CHHHHHHHHHHHHHHhhhccCCCcCHHHHHHHHHHhhccccCccChHHHHHHHHHHHHhhccCcccccccccChhhHHHH
Confidence 344444455543 34678999999999999999876 478888865432 33456889999999
Q ss_pred HhhhcCccccCCCcccc
Q 010992 464 LERNWNMTLPGFSGDEI 480 (496)
Q Consensus 464 LERnWNI~IPGFssDEI 480 (496)
+++.-||.+--+..+|.
T Consensus 430 ~~~~tgip~~~~~~~~~ 446 (758)
T PRK11034 430 VARIARIPEKSVSQSDR 446 (758)
T ss_pred HHHHhCCChhhhhhhHH
Confidence 99988877655555553
No 151
>PF02881 SRP54_N: SRP54-type protein, helical bundle domain; InterPro: IPR013822 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the N-terminal helical bundle domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 1J8M_F 1J8Y_F 2J37_W 2OG2_A 3B9Q_A 2V3C_C 3NDB_B 1ZU5_B 1ZU4_A 1WGW_A ....
Probab=46.14 E-value=1e+02 Score=24.16 Aligned_cols=36 Identities=28% Similarity=0.505 Sum_probs=22.1
Q ss_pred ccCCHHHHHHHHHhhCCCCCCCHHHHHHHH------HHHHHHHHHHHHHHHH
Q 010992 400 RILTKRSIQELVNQIDPSERLDPDVEDILV------DIAEDFVESITMFGCS 445 (496)
Q Consensus 400 rILtKrKLqELVrqIDPsesLDpDVEELLL------eIADDFVDsVvt~ACr 445 (496)
.+++++.|.+++.+ +|++|+ ++|++||++|-...+.
T Consensus 16 ~~~~~~~i~~~l~e----------le~~Li~aDVg~~~a~~i~~~ik~~~~~ 57 (75)
T PF02881_consen 16 IFLTEKDIEEFLEE----------LEEALIEADVGVEVAEKIIENIKKKLIK 57 (75)
T ss_dssp SSCTHHHHHHHHHH----------HHHHHHHTTTSHHHHHHHHHHHHHHHHC
T ss_pred ccccHHhHHHHHHH----------HHHHHHHcCcCHHHHHHHHHHHHHHHhc
Confidence 44567777666664 356665 5677777777664443
No 152
>PF13565 HTH_32: Homeodomain-like domain
Probab=45.98 E-value=24 Score=27.38 Aligned_cols=35 Identities=17% Similarity=0.461 Sum_probs=27.1
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccc
Q 010992 421 DPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTL 472 (496)
Q Consensus 421 DpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~I 472 (496)
|+|+++.|++++++.- ....+.|.-+|+++||+.+
T Consensus 32 ~~e~~~~i~~~~~~~p-----------------~wt~~~i~~~L~~~~g~~~ 66 (77)
T PF13565_consen 32 DPEQRERIIALIEEHP-----------------RWTPREIAEYLEEEFGISV 66 (77)
T ss_pred cHHHHHHHHHHHHhCC-----------------CCCHHHHHHHHHHHhCCCC
Confidence 7788777777765322 5788999999999999876
No 153
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=45.94 E-value=80 Score=35.64 Aligned_cols=65 Identities=11% Similarity=0.153 Sum_probs=35.0
Q ss_pred CCCCCCHHHHHHHHHHHH---HHHHHHHHHHHHhhhhcCC--------------------CCcchhhHHHHHhhhcCccc
Q 010992 416 PSERLDPDVEDILVDIAE---DFVESITMFGCSLAKHRKS--------------------DTLEAKDILVHLERNWNMTL 472 (496)
Q Consensus 416 PsesLDpDVEELLLeIAD---DFVDsVvt~ACrLAKHRKS--------------------dTLEvKDVQLhLERnWNI~I 472 (496)
-+..|++||.++|++=.+ ..++.++..-+.+|+.++. ..|.+++|+-+..+.||+.
T Consensus 462 r~l~l~~eVi~yLa~r~~rnvR~LegaL~rL~a~a~~~~~~itl~la~~vL~~~~~~~~~~~it~d~I~~~Va~~f~v~- 540 (617)
T PRK14086 462 EQLNAPPEVLEFIASRISRNIRELEGALIRVTAFASLNRQPVDLGLTEIVLRDLIPEDSAPEITAAAIMAATADYFGLT- 540 (617)
T ss_pred cCCCCCHHHHHHHHHhccCCHHHHHHHHHHHHHHHHhhCCCCCHHHHHHHHHHhhccccCCcCCHHHHHHHHHHHhCCC-
Confidence 357888999988876544 2333333333333332221 2355566666666666554
Q ss_pred cCCCcccccccCC
Q 010992 473 PGFSGDEIKTFRK 485 (496)
Q Consensus 473 PGFssDEIr~~rk 485 (496)
.+||+.-+|
T Consensus 541 ----~~dl~s~~R 549 (617)
T PRK14086 541 ----VEDLCGTSR 549 (617)
T ss_pred ----HHHHhCCCC
Confidence 466655444
No 154
>cd01017 AdcA Metal binding protein AcdA. These proteins have been shown to function in the ABC uptake of Zn2+ and Mn2+ and in competence for genetic transformation and adhesion. The AcdA proteins belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a long alpha helix and they bind their ligand in the cleft between these domains. In addition, many of these proteins have a low complexity region containing metal binding histidine-rich motif (repetitive HDH sequence).
Probab=45.87 E-value=22 Score=34.49 Aligned_cols=74 Identities=18% Similarity=0.252 Sum_probs=48.9
Q ss_pred CCHHHHHHHHHhhCC-CCCCCHHHHHHHHHHHHHHHHHHHHHH----HHhhhhcCCCCcchhhHHHHHhhhcCccccCC
Q 010992 402 LTKRSIQELVNQIDP-SERLDPDVEDILVDIAEDFVESITMFG----CSLAKHRKSDTLEAKDILVHLERNWNMTLPGF 475 (496)
Q Consensus 402 LtKrKLqELVrqIDP-sesLDpDVEELLLeIADDFVDsVvt~A----CrLAKHRKSdTLEvKDVQLhLERnWNI~IPGF 475 (496)
|.-.....+++.|.. -.++|++-.+...+=++.|+..+-..- .++++.++...|..-|.--||.+.||+.+-|.
T Consensus 117 ldp~~~~~~a~~Ia~~L~~~dP~~~~~y~~N~~~~~~~L~~l~~~~~~~~~~~~~~~~v~~H~af~Y~~~~~gl~~~~~ 195 (282)
T cd01017 117 LSPVLAIQQVENIKDALIKLDPDNKEYYEKNAAAYAKKLEALDQEYRAKLAKAKGKTFVTQHAAFGYLARRYGLKQIAI 195 (282)
T ss_pred cCHHHHHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCeEEEecccHHHHHHHCCCeEEec
Confidence 455555566665532 235666666777777777766654332 33455556667889999999999999997653
No 155
>PRK06620 hypothetical protein; Validated
Probab=45.61 E-value=86 Score=29.80 Aligned_cols=47 Identities=15% Similarity=-0.017 Sum_probs=27.2
Q ss_pred CCCCCHHHHHHHHHHHH---HHHHHHHHHHHHhhhhcCCCCcchhhHHHHH
Q 010992 417 SERLDPDVEDILVDIAE---DFVESITMFGCSLAKHRKSDTLEAKDILVHL 464 (496)
Q Consensus 417 sesLDpDVEELLLeIAD---DFVDsVvt~ACrLAKHRKSdTLEvKDVQLhL 464 (496)
...|++||.+.|++-++ ..++++++....+|+.++. .|++..|+-+|
T Consensus 164 ~l~l~~ev~~~L~~~~~~d~r~l~~~l~~l~~~~~~~~~-~it~~~~~~~l 213 (214)
T PRK06620 164 SVTISRQIIDFLLVNLPREYSKIIEILENINYFALISKR-KITISLVKEVL 213 (214)
T ss_pred CCCCCHHHHHHHHHHccCCHHHHHHHHHHHHHHHHHcCC-CCCHHHHHHHh
Confidence 46789999999887665 2344444443344444443 35665554443
No 156
>PRK06249 2-dehydropantoate 2-reductase; Provisional
Probab=45.54 E-value=19 Score=35.32 Aligned_cols=12 Identities=17% Similarity=0.310 Sum_probs=6.5
Q ss_pred HHHhhhcCcccc
Q 010992 462 VHLERNWNMTLP 473 (496)
Q Consensus 462 LhLERnWNI~IP 473 (496)
+.+-|.+|+..|
T Consensus 285 v~~a~~~Gi~~P 296 (313)
T PRK06249 285 LAAARAAGCAMP 296 (313)
T ss_pred HHHHHHhCCCCc
Confidence 444555666555
No 157
>cd05395 RasGAP_RASA4 Ras GTPase activating-like 4 protein (RASAL4), also known as Ca2+ -promoted Ras inactivator (CAPRI), is a member of the GAP1 family. Members of the GAP1 family are characterized by a conserved domain structure comprising N-terminal tandem C2 domains, a highly conserved central RasGAP domain, and a C-terminal pleckstrin-homology domain that is associated with a Bruton's tyrosine kinase motif. RASAL4, like RASAL, is a cytosolic protein that undergoes a rapid translocation to the plasma membrane in response to a receptor-mediated elevation in the concentration of intracellular free Ca2+ ([Ca2+]i). However, unlike RASAL, RASAL4 does not sense oscillations in [Ca2+]i.
Probab=45.37 E-value=51 Score=34.39 Aligned_cols=44 Identities=9% Similarity=0.078 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCCC
Q 010992 426 DILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFS 476 (496)
Q Consensus 426 ELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGFs 476 (496)
+.|.++++.|++.|++...++-. .+|.|--+|.+...-.+|+-.
T Consensus 148 ~~L~~~~~~~l~~I~~S~~~~P~-------~iR~i~~~l~~~v~~rFp~~~ 191 (337)
T cd05395 148 QLLQSYLGELLTAILQSASYCPL-------VIRAVFRQLFLRVQERFPDPQ 191 (337)
T ss_pred HHHHHHHHHHHHHHHHHHHhCcH-------HHHHHHHHHHHHHHHHCCCcc
Confidence 56889999999999987665543 455555555444444555443
No 158
>PRK14622 hypothetical protein; Provisional
Probab=45.35 E-value=13 Score=32.67 Aligned_cols=9 Identities=33% Similarity=1.062 Sum_probs=7.2
Q ss_pred CccccCCCc
Q 010992 469 NMTLPGFSG 477 (496)
Q Consensus 469 NI~IPGFss 477 (496)
+|.||||++
T Consensus 95 g~~lPG~~~ 103 (103)
T PRK14622 95 GIKIPGIAG 103 (103)
T ss_pred CCCCCCCCC
Confidence 678999974
No 159
>cd05391 RasGAP_p120GAP p120GAP is a negative regulator of Ras that stimulates hydrolysis of bound GTP to GDP. Once the Ras regulator p120GAP, a member of the GAP protein family, is recruited to the membrane, it is transiently immobilized to interact with Ras-GTP. The down regulation of Ras by p120GAP is a critical step in the regulation of many cellular processes, which is disrupted in approximately 30% of human cancers. p120GAP contains SH2, SH3, PH, calcium- and lipid-binding domains, suggesting its involvement in a complex network of cellular interactions in vivo.
Probab=45.35 E-value=55 Score=33.68 Aligned_cols=42 Identities=24% Similarity=0.296 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccC
Q 010992 426 DILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPG 474 (496)
Q Consensus 426 ELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPG 474 (496)
+.|+.++++|++.|+...+.+-. ++|.|--+|.+.-.-.+|+
T Consensus 126 ~~L~~~~~~~~~~I~~S~~~~P~-------~lr~i~~~l~~~v~~kfp~ 167 (315)
T cd05391 126 EHLLNILSELVEKIFMAAEILPP-------TLRYIYGCLQKSVQAKWPT 167 (315)
T ss_pred HHHHHHHHHHHHHHHHhHHhCCH-------HHHHHHHHHHHHHHHHCCC
Confidence 56899999999999998776544 5666655555554444454
No 160
>PRK00982 acpP acyl carrier protein; Provisional
Probab=44.93 E-value=20 Score=28.14 Aligned_cols=30 Identities=20% Similarity=0.542 Sum_probs=23.5
Q ss_pred HhhhhcCCCCcchhhHHHHHhhhcCccccC
Q 010992 445 SLAKHRKSDTLEAKDILVHLERNWNMTLPG 474 (496)
Q Consensus 445 rLAKHRKSdTLEvKDVQLhLERnWNI~IPG 474 (496)
.|-.--|-|.|..-+|...||+.||+.|+-
T Consensus 28 ~l~~dlglDSl~~~~li~~le~~f~i~i~~ 57 (78)
T PRK00982 28 SFVDDLGADSLDTVELVMALEEEFGIEIPD 57 (78)
T ss_pred chHhhcCCCHHHHHHHHHHHHHHHCCCcCH
Confidence 342334778888899999999999999964
No 161
>TIGR01560 put_DNA_pack uncharacterized phage protein (possible DNA packaging). This model describes a small (~ 100 amino acids) protein found in phage and in putative prophage regions of a number of bacterial genomes. Members have been annotated in some cases as a possible DNA packaging protein, but the source of this annotation was not traced during construction of this model.
Probab=44.55 E-value=43 Score=27.86 Aligned_cols=35 Identities=17% Similarity=0.396 Sum_probs=27.0
Q ss_pred HHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q 010992 405 RSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMF 442 (496)
Q Consensus 405 rKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ 442 (496)
..|+.-+ +||..+ |++..+.+++-|.++|++.+..
T Consensus 3 ~~vK~~L-rId~d~--dD~li~~~i~aA~~~i~~~ig~ 37 (91)
T TIGR01560 3 DEVKLSL-RIDHDD--DDELIKLMIAAAQDYIQSAIGT 37 (91)
T ss_pred HHHHhHh-cCCCCc--cHHHHHHHHHHHHHHHHHHhCC
Confidence 3455556 588775 8999999999999999887643
No 162
>COG0236 AcpP Acyl carrier protein [Lipid metabolism / Secondary metabolites biosynthesis, transport, and catabolism]
Probab=44.45 E-value=7.5 Score=31.34 Aligned_cols=35 Identities=23% Similarity=0.409 Sum_probs=27.4
Q ss_pred cCCCCcchhhHHHHHhhhcCccccCCCcccccccC
Q 010992 450 RKSDTLEAKDILVHLERNWNMTLPGFSGDEIKTFR 484 (496)
Q Consensus 450 RKSdTLEvKDVQLhLERnWNI~IPGFssDEIr~~r 484 (496)
-+-+.|++-+|-+.||+.||+.||.--.+.+++.+
T Consensus 35 lg~DSld~veLi~~lE~~f~i~i~~e~~~~~~tv~ 69 (80)
T COG0236 35 LGLDSLDLVELVMALEEEFGIEIPDEELENIKTVG 69 (80)
T ss_pred cCccHHHHHHHHHHHHHHHCCcCCHHHHHHHHhHH
Confidence 47778899999999999999999866555555443
No 163
>KOG2114 consensus Vacuolar assembly/sorting protein PEP5/VPS11 [Intracellular trafficking, secretion, and vesicular transport]
Probab=44.42 E-value=20 Score=41.89 Aligned_cols=63 Identities=22% Similarity=0.195 Sum_probs=45.6
Q ss_pred CHHHHHHHHHhhCCCCCC-CHH-HHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccc
Q 010992 403 TKRSIQELVNQIDPSERL-DPD-VEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTL 472 (496)
Q Consensus 403 tKrKLqELVrqIDPsesL-DpD-VEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~I 472 (496)
-++||.++|+..|.++.+ |-| +.++|.+- +....|..|||.++.. ..+.||+++.+.||..-|
T Consensus 446 d~~kL~efI~~~~~g~~~fd~e~al~Ilr~s------nyl~~a~~LA~k~~~h-e~vl~ille~~~ny~eAl 510 (933)
T KOG2114|consen 446 DVEKLTEFISKCDKGEWFFDVETALEILRKS------NYLDEAELLATKFKKH-EWVLDILLEDLHNYEEAL 510 (933)
T ss_pred chHHHHHHHhcCCCcceeeeHHHHHHHHHHh------ChHHHHHHHHHHhccC-HHHHHHHHHHhcCHHHHH
Confidence 467899999998866654 322 44444432 5667788999988884 579999999999887654
No 164
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=44.29 E-value=60 Score=33.79 Aligned_cols=61 Identities=11% Similarity=0.165 Sum_probs=47.7
Q ss_pred CHHHHHHHHHh-h---CCCCCCCHHHHHHHHHHHHHHH------HHHHHHHHHhhhhcCCCCcchhhHHHH
Q 010992 403 TKRSIQELVNQ-I---DPSERLDPDVEDILVDIAEDFV------ESITMFGCSLAKHRKSDTLEAKDILVH 463 (496)
Q Consensus 403 tKrKLqELVrq-I---DPsesLDpDVEELLLeIADDFV------DsVvt~ACrLAKHRKSdTLEvKDVQLh 463 (496)
+...|.+.|++ + -....+|++|.++...++...- -+++..|+.+|..+++.++...||...
T Consensus 191 ~a~el~~Il~~R~~~~~~~~~~~~~vl~lia~~~a~~~GDAR~aidilr~A~eiAe~~~~~~v~~~~v~~a 261 (366)
T COG1474 191 TAEELYDILRERVEEGFSAGVIDDDVLKLIAALVAAESGDARKAIDILRRAGEIAEREGSRKVSEDHVREA 261 (366)
T ss_pred CHHHHHHHHHHHHHhhccCCCcCccHHHHHHHHHHHcCccHHHHHHHHHHHHHHHHhhCCCCcCHHHHHHH
Confidence 44555555442 2 2346899999999998887644 689999999999999999999999777
No 165
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=43.93 E-value=12 Score=28.99 Aligned_cols=48 Identities=29% Similarity=0.427 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh-cCccccC
Q 010992 424 VEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERN-WNMTLPG 474 (496)
Q Consensus 424 VEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn-WNI~IPG 474 (496)
+++++-.+|+.|= |-... -+.|-|+.+.++++.|..+|-|+ +|+.+..
T Consensus 2 ~~~I~~~Va~~~~--i~~~~-i~s~~R~~~~~~aR~iamyla~~~~~~sl~~ 50 (60)
T smart00760 2 IEEIIEAVAEYFG--VKPED-LKSKSRKREIVLARQIAMYLARELTDLSLPE 50 (60)
T ss_pred HHHHHHHHHHHhC--CCHHH-HhcCCCCcchhHHHHHHHHHHHHHHCCCHHH
Confidence 5677777888883 22222 46777888899999999999887 6666543
No 166
>PF04983 RNA_pol_Rpb1_3: RNA polymerase Rpb1, domain 3; InterPro: IPR007066 RNA polymerases catalyse the DNA dependent polymerisation of RNA. Prokaryotes contain a single RNA polymerase compared to three in eukaryotes (not including mitochondrial and chloroplast polymerases). This domain, domain 3, represents the pore domain. The 3' end of RNA is positioned close to this domain. The pore delimited by this domain is thought to act as a channel through which nucleotides enter the active site and/or where the 3' end of the RNA may be extruded during back-tracking [, ].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 1ZYR_D 1SMY_D 2A68_N 2O5J_D 3AOH_N 2O5I_D 2CW0_N 2A6H_N 2A69_D 3EQL_D ....
Probab=43.82 E-value=11 Score=33.47 Aligned_cols=47 Identities=19% Similarity=0.342 Sum_probs=33.9
Q ss_pred HHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhH
Q 010992 404 KRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDI 460 (496)
Q Consensus 404 KrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDV 460 (496)
|+.+.+|++.| .++.=.+.|-+|+|++-..+++.|.+++-. |-++||
T Consensus 112 k~~~~~li~~i---------~~~yG~~~~~~~ld~i~~lg~~~~t~~GfS-vgi~D~ 158 (158)
T PF04983_consen 112 KKSLGSLIHQI---------YREYGPEATVQFLDAIKRLGFRYLTRSGFS-VGIDDM 158 (158)
T ss_dssp CSHTTCHHHHH---------HHHSHHHHHHHHHHHHHHHHHHHHHHHTBB--SGGGC
T ss_pred ccchhhHHHHH---------HHHHCHHHHHHHHHHHHHHHHHHHHHcCee-EecccC
Confidence 44444555544 333335678899999999999999999976 688885
No 167
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=43.33 E-value=71 Score=34.86 Aligned_cols=66 Identities=12% Similarity=0.183 Sum_probs=45.7
Q ss_pred CHHHHHHHHHhhC------CCCCCCHHHHHHHHHHHH-----------HHHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992 403 TKRSIQELVNQID------PSERLDPDVEDILVDIAE-----------DFVESITMFGCSLAKHRKSDTLEAKDILVHLE 465 (496)
Q Consensus 403 tKrKLqELVrqID------PsesLDpDVEELLLeIAD-----------DFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE 465 (496)
+..++..+++-|. ....||.++...|++.+- ..|.+++..|.-+|+..+.+.|+..||+-+|+
T Consensus 425 ~~e~~~~~~~~i~~~~~~~~L~~~~~~Av~~li~~~~R~~q~kLsl~~~~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~ 504 (509)
T PF13654_consen 425 TEENIRQYARFIASICQKEGLPPFDRSAVARLIEYSARLDQDKLSLRFSWLADLLREANYWARKEGAKVITAEHVEQAIE 504 (509)
T ss_dssp -HHHHHHHHHHHHHHHHHHSS--BBHHHHHHHHHHHHHCC-SEEE--HHHHHHHHHHHHHHHHHCT-SSB-HHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHhCCEeCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHH
Confidence 4555554444442 234788888888877664 47889999999999999999999999999998
Q ss_pred hhc
Q 010992 466 RNW 468 (496)
Q Consensus 466 RnW 468 (496)
..+
T Consensus 505 ~r~ 507 (509)
T PF13654_consen 505 ERR 507 (509)
T ss_dssp H--
T ss_pred ccc
Confidence 754
No 168
>cd01018 ZntC Metal binding protein ZntC. These proteins are predicted to function as initial receptors in ABC transport of metal ions. They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a long alpha helix and bind their specific ligands in the cleft between these domains. In addition, many of these proteins possess a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=43.25 E-value=34 Score=33.08 Aligned_cols=74 Identities=12% Similarity=0.183 Sum_probs=49.9
Q ss_pred CCHHHHHHHHHhhC-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHH----hhhhcCCCCcchhhHHHHHhhhcCccccCC
Q 010992 402 LTKRSIQELVNQID-PSERLDPDVEDILVDIAEDFVESITMFGCS----LAKHRKSDTLEAKDILVHLERNWNMTLPGF 475 (496)
Q Consensus 402 LtKrKLqELVrqID-PsesLDpDVEELLLeIADDFVDsVvt~ACr----LAKHRKSdTLEvKDVQLhLERnWNI~IPGF 475 (496)
|.-.+...+++.|. .-.++|++-++...+=+++|++.+-...-. +++.++...+...|.--||.|.||+.+-|+
T Consensus 116 ldp~~~~~~a~~I~~~L~~~dP~~~~~y~~N~~~~~~~L~~l~~~~~~~~~~~~~~~~v~~H~af~Y~~~~ygl~~~~~ 194 (266)
T cd01018 116 LSPANAKIMAENIYEALAELDPQNATYYQANLDALLAELDALDSEIRTILSKLKQRAFMVYHPAWGYFARDYGLTQIPI 194 (266)
T ss_pred cCHHHHHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCeEEEECchhHHHHHHcCCEEEec
Confidence 56666666766663 334677777777777777777665544333 333344456788899999999999998765
No 169
>TIGR01241 FtsH_fam ATP-dependent metalloprotease FtsH. HflB(FtsH) is a pleiotropic protein required for correct cell division in bacteria. It has ATP-dependent zinc metalloprotease activity. It was formerly designated cell division protein FtsH.
Probab=43.24 E-value=68 Score=33.90 Aligned_cols=32 Identities=16% Similarity=0.222 Sum_probs=26.5
Q ss_pred HHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992 436 VESITMFGCSLAKHRKSDTLEAKDILVHLERN 467 (496)
Q Consensus 436 VDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn 467 (496)
|+.++..|+.+|..++...|+.+|+.-.|++.
T Consensus 264 l~~l~~eA~~~a~~~~~~~i~~~~l~~a~~~~ 295 (495)
T TIGR01241 264 LANLLNEAALLAARKNKTEITMNDIEEAIDRV 295 (495)
T ss_pred HHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHH
Confidence 67777778777777777889999999999975
No 170
>KOG1087 consensus Cytosolic sorting protein GGA2/TOM1 [Intracellular trafficking, secretion, and vesicular transport]
Probab=42.86 E-value=67 Score=35.15 Aligned_cols=69 Identities=13% Similarity=0.250 Sum_probs=45.0
Q ss_pred CHHHHHHHHHhhCCCCCCCHHHH------HHH-HHHHHHHH-----HHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCc
Q 010992 403 TKRSIQELVNQIDPSERLDPDVE------DIL-VDIAEDFV-----ESITMFGCSLAKHRKSDTLEAKDILVHLERNWNM 470 (496)
Q Consensus 403 tKrKLqELVrqIDPsesLDpDVE------ELL-LeIADDFV-----DsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI 470 (496)
.|..+..|.|+|-.+.. .++. |++ ..+-+-|- ++|+...+++.|....+ ++||+-.|+|=+.|+.
T Consensus 36 ~~eAvralkKRi~~k~s--~vq~lALtlLE~cvkNCG~~fh~~Va~k~fL~emVk~~k~~~~~-~~Vr~kiL~LI~~W~~ 112 (470)
T KOG1087|consen 36 PKEAVRALKKRLNSKNS--KVQLLALTLLETCVKNCGYSFHLQVASKEFLNEMVKRPKNKPRD-LKVREKILELIDTWQQ 112 (470)
T ss_pred cHHHHHHHHHHhccCCc--HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHhccccCCcc-hhHHHHHHHHHHHHHH
Confidence 56788888888864433 2211 111 11112222 24555588999988744 6899999999999999
Q ss_pred cccC
Q 010992 471 TLPG 474 (496)
Q Consensus 471 ~IPG 474 (496)
.|+|
T Consensus 113 af~~ 116 (470)
T KOG1087|consen 113 AFCG 116 (470)
T ss_pred HccC
Confidence 9998
No 171
>PF08429 PLU-1: PLU-1-like protein; InterPro: IPR013637 This domain is found in the central region of lysine-specific demethylases, which are nuclear proteins that may have a role in DNA-binding and transcription, and are associated with malignant cancer phenotypes []. The domain is also found in various other Jumonji/ARID domain-containing proteins (see IPR013129 from INTERPRO, IPR001606 from INTERPRO). ; GO: 0016706 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors, 0055114 oxidation-reduction process
Probab=42.59 E-value=82 Score=31.24 Aligned_cols=74 Identities=19% Similarity=0.287 Sum_probs=41.8
Q ss_pred cCCccCCHHHHHHHHHhhCCCCCCCHHHHHHHH---HHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCcccc
Q 010992 397 FGNRILTKRSIQELVNQIDPSERLDPDVEDILV---DIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLP 473 (496)
Q Consensus 397 ~~nrILtKrKLqELVrqIDPsesLDpDVEELLL---eIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IP 473 (496)
.....++=..|..||++++.-...-+|+ +.|. +-+++|.+.+-.. |.+....+.-++++ .+.....||+.||
T Consensus 78 ~~~~~~~l~~l~~Ll~e~~~L~~~~pEi-~~L~~l~~~ve~f~~~a~~~---L~~~~~~~~~~le~-Ll~~g~s~~v~lp 152 (335)
T PF08429_consen 78 KSRNKLTLEELEALLEEIESLPFDCPEI-DQLKELLEEVEEFQSRAQEA---LSDPESPSLEELEE-LLEEGESFGVDLP 152 (335)
T ss_pred cccccCCHHHHHHHHHHHhcCCeeCchH-HHHHHHHHHHHHHHHHHHHH---HhccccCCHHHHHH-HHHhcccCceeCh
Confidence 3455678888999999998655555663 3344 4455565554442 22211222122233 3566667777777
Q ss_pred CC
Q 010992 474 GF 475 (496)
Q Consensus 474 GF 475 (496)
.+
T Consensus 153 el 154 (335)
T PF08429_consen 153 EL 154 (335)
T ss_pred hH
Confidence 55
No 172
>PRK05883 acyl carrier protein; Validated
Probab=42.30 E-value=9.8 Score=32.15 Aligned_cols=38 Identities=16% Similarity=0.053 Sum_probs=25.8
Q ss_pred HhhhhcCCCCcchhhHHHHHhhhcCccccCCCcccccc
Q 010992 445 SLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGDEIKT 482 (496)
Q Consensus 445 rLAKHRKSdTLEvKDVQLhLERnWNI~IPGFssDEIr~ 482 (496)
.|..--+-+.|+.-++.+.||+.|||.|+.--..++++
T Consensus 39 ~l~~dlg~DSL~~v~lv~~lE~~fgI~i~~ee~~~~~T 76 (91)
T PRK05883 39 RLVDDVGLDSVAFAVGMVAIEERLGVALSEEDLLSCDT 76 (91)
T ss_pred chhhccCCChHHHHHHHHHHHHHHCCCcCHHHHHhCCC
Confidence 34344466777778888899999999996443333433
No 173
>cd05132 RasGAP_GAPA GAPA is an IQGAP-related protein and is predicted to bind to small GTPases, which are yet to be identified. IQGAP proteins are integral components of cytoskeletal regulation. Results from truncated GAPAs indicated that almost the entire region of GAPA homologous to IQGAP is required for cytokinesis in Dictyostelium. More members of the IQGAP family are emerging, and evidence suggests that there are both similarities and differences in their function.
Probab=42.25 E-value=59 Score=33.12 Aligned_cols=21 Identities=24% Similarity=0.363 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHh
Q 010992 426 DILVDIAEDFVESITMFGCSL 446 (496)
Q Consensus 426 ELLLeIADDFVDsVvt~ACrL 446 (496)
+.|.++++.|++.|+....++
T Consensus 123 ~~L~~~~~~fl~~I~~s~~~~ 143 (331)
T cd05132 123 TQLIEICNRFLDTIISSLNRL 143 (331)
T ss_pred HHHHHHHHHHHHHHHHHHHhC
Confidence 377899999999987765543
No 174
>PRK08136 glycosyl transferase family protein; Provisional
Probab=42.24 E-value=34 Score=35.15 Aligned_cols=50 Identities=14% Similarity=0.219 Sum_probs=37.3
Q ss_pred HHHHHHhhCCC----CCCCHH-HHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcc
Q 010992 407 IQELVNQIDPS----ERLDPD-VEDILVDIAEDFVESITMFGCSLAKHRKSDTLE 456 (496)
Q Consensus 407 LqELVrqIDPs----esLDpD-VEELLLeIADDFVDsVvt~ACrLAKHRKSdTLE 456 (496)
|.++|++|..+ ..|+.| +++++..|.|.-++++--.|..+|-+-|.+|.|
T Consensus 3 ~~~~i~~l~~G~~~~~~Lt~eEA~~~~~~il~g~~~~~qi~AfL~alr~KgET~e 57 (317)
T PRK08136 3 YAKIIKEIGRGKNGARDLDRDTARALYGAMLDGRVPDLELGAILIALRIKGESEA 57 (317)
T ss_pred HHHHHHHHHCCCCCCCCcCHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCCCHH
Confidence 45566666555 667654 888999999888888888888888777777654
No 175
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=42.23 E-value=1e+02 Score=29.88 Aligned_cols=64 Identities=9% Similarity=0.040 Sum_probs=43.1
Q ss_pred cCCHHHHHHHHHhhC--CCCCCCHHHHHHHHHHHHH---HHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992 401 ILTKRSIQELVNQID--PSERLDPDVEDILVDIAED---FVESITMFGCSLAKHRKSDTLEAKDILVHLERN 467 (496)
Q Consensus 401 ILtKrKLqELVrqID--PsesLDpDVEELLLeIADD---FVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn 467 (496)
-+.++.+.++|+++- -+..|++++.++|++.... ++.+-++.-|.++..+ .|+.+||.-.+-..
T Consensus 145 ~~~~~~~~~~i~~~~~~~g~~i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~---~It~~~I~~~i~~~ 213 (340)
T PRK05574 145 PPKEAELPQWIQQRLKQQGLQIDAAALQLLAERVEGNLLALAQELEKLALLYPDG---KITLEDVEEAVPDS 213 (340)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCC---CCCHHHHHHHHhhh
Confidence 356777777776663 4568999999999998864 4444555555454332 28999997665543
No 176
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=42.20 E-value=37 Score=35.63 Aligned_cols=66 Identities=15% Similarity=0.158 Sum_probs=42.6
Q ss_pred CHHHHHHHHHhhCCCCCCCHHHH-HHHHHHHHHH----HHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhc
Q 010992 403 TKRSIQELVNQIDPSERLDPDVE-DILVDIAEDF----VESITMFGCSLAKHRKSDTLEAKDILVHLERNW 468 (496)
Q Consensus 403 tKrKLqELVrqIDPsesLDpDVE-ELLLeIADDF----VDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnW 468 (496)
+++.-.++++.+.....+++|+. +.|.+..+.| |..||..|+..|-.|+...|+.+|+.-.+++..
T Consensus 317 ~~~~R~~Il~~~~~~~~l~~dvd~~~la~~t~g~sgaDI~~l~~eA~~~A~r~~~~~i~~~df~~A~~~v~ 387 (398)
T PTZ00454 317 DRRQKRLIFQTITSKMNLSEEVDLEDFVSRPEKISAADIAAICQEAGMQAVRKNRYVILPKDFEKGYKTVV 387 (398)
T ss_pred CHHHHHHHHHHHHhcCCCCcccCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHHHHHH
Confidence 34444455555544444554422 2233333333 778888888888888888999999999998863
No 177
>PHA02839 Il-24-like protein; Provisional
Probab=42.18 E-value=64 Score=30.99 Aligned_cols=73 Identities=18% Similarity=0.286 Sum_probs=50.1
Q ss_pred CCCcCCCcCCccCCHHHHHHH--------HH--------hhC---CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhc
Q 010992 390 AGTESDEFGNRILTKRSIQEL--------VN--------QID---PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHR 450 (496)
Q Consensus 390 ~~~~~~e~~nrILtKrKLqEL--------Vr--------qID---PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHR 450 (496)
.-++++.-+-++|+|+.|++. ++ +|= -+..+|..+..-+--||+.|+--+-.---+-.|..
T Consensus 42 VQAkD~~~~VRILr~evLqnIq~aE~CCflr~LLrFYLDrVFKnYqs~~~~~~ilRsiSSLANSFL~I~K~lq~~~~~~~ 121 (156)
T PHA02839 42 VQADDVDHNLRILTPALLNNITVSETCFFIYDMFELYLNDVFVKYTNTALKLNILKSLSSVANNFLAIFNKVKKRRVKKN 121 (156)
T ss_pred hcccCcccceEEcCHHHHhcCCccceeHHHHHHHHHHHHHHHHhccCCccchHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 445667778899998555431 11 110 13456788999999999999976665555666777
Q ss_pred CCCCcchhhHHH
Q 010992 451 KSDTLEAKDILV 462 (496)
Q Consensus 451 KSdTLEvKDVQL 462 (496)
+-++||+|.+.+
T Consensus 122 ~~~~~~~~~~~~ 133 (156)
T PHA02839 122 NVNVLEIKKLLL 133 (156)
T ss_pred Ccceeeehhhhe
Confidence 788899988754
No 178
>PF07516 SecA_SW: SecA Wing and Scaffold domain; InterPro: IPR011116 SecA protein binds to the plasma membrane where it interacts with proOmpA to support translocation of proOmpA through the membrane. SecA protein achieves this translocation, in association with SecY protein, in an ATP-dependent manner. This domain is composed of two C-terminal alpha helical subdomains: the wing and scaffold subdomains.; GO: 0017038 protein import, 0016020 membrane; PDB: 1NL3_B 1NKT_B 2FSG_B 2VDA_A 2FSH_A 2FSF_A 2FSI_A 2IPC_D 3JUX_A 3DIN_B ....
Probab=42.07 E-value=28 Score=32.76 Aligned_cols=48 Identities=19% Similarity=0.378 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccc
Q 010992 423 DVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTL 472 (496)
Q Consensus 423 DVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~I 472 (496)
++++.++++++++|++++..-|.--.+. +..+++.+.-.|.+.|++.+
T Consensus 55 ~~~~~i~~~~~~~i~~~v~~~~~~~~~~--~~~~~~~l~~~l~~~~~~~~ 102 (214)
T PF07516_consen 55 DLEEIILEMIEDVIDDIVDEYIPEKDSP--EEWDIEGLKDFLNQNFNLDF 102 (214)
T ss_dssp CCHHHHHHHHHHHHHHHHHHHSSSSSSS--TSSCHHHHHHHHHHCSSSSS
T ss_pred ChHHHHHHHHHHHHHHHHHHHcccccCc--ccccHHHHHHHHHHHcCCCc
Confidence 3677777777777777777655433222 45678889889999998744
No 179
>TIGR00362 DnaA chromosomal replication initiator protein DnaA. DnaA is involved in DNA biosynthesis; initiation of chromosome replication and can also be transcription regulator. The C-terminal of the family hits the pfam bacterial DnaA (bac_dnaA) domain family. For a review, see Kaguni (2006).
Probab=41.98 E-value=91 Score=31.81 Aligned_cols=52 Identities=10% Similarity=-0.059 Sum_probs=38.0
Q ss_pred CCCCCCHHHHHHHHHHHHH---HHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhc
Q 010992 416 PSERLDPDVEDILVDIAED---FVESITMFGCSLAKHRKSDTLEAKDILVHLERNW 468 (496)
Q Consensus 416 PsesLDpDVEELLLeIADD---FVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnW 468 (496)
.+..|++||.++|.+-.+. -++.++...|..|+..+.. |++..++-+|+..+
T Consensus 284 ~~~~l~~e~l~~ia~~~~~~~r~l~~~l~~l~~~a~~~~~~-it~~~~~~~L~~~~ 338 (405)
T TIGR00362 284 EGLELPDEVLEFIAKNIRSNVRELEGALNRLLAYASLTGKP-ITLELAKEALKDLL 338 (405)
T ss_pred cCCCCCHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHHhCCC-CCHHHHHHHHHHhc
Confidence 3578999998888877652 3566778888888776655 78878877777543
No 180
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=41.97 E-value=1.1e+02 Score=29.09 Aligned_cols=65 Identities=12% Similarity=0.157 Sum_probs=44.0
Q ss_pred cCCHHHHHHHHHhh--CCCCCCCHHHHHHHHHHHHH---HHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhc
Q 010992 401 ILTKRSIQELVNQI--DPSERLDPDVEDILVDIAED---FVESITMFGCSLAKHRKSDTLEAKDILVHLERNW 468 (496)
Q Consensus 401 ILtKrKLqELVrqI--DPsesLDpDVEELLLeIADD---FVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnW 468 (496)
.++.+.+.++|+++ .-+..|++++.+.|++.++. .+.+-++.-|.+++.+ .|+.+||.-++...-
T Consensus 110 ~~~~~~~~~~i~~~~~~~g~~i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~---~It~e~I~~~~~~~~ 179 (302)
T TIGR01128 110 TPKEQELPRWIQARLKKLGLRIDPDAVQLLAELVEGNLLAIAQELEKLALYAPDG---KITLEDVEEAVSDSA 179 (302)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCC---CCCHHHHHHHHhhhh
Confidence 35677777777766 34568999999999988864 3444455555555433 589999976665443
No 181
>PRK14087 dnaA chromosomal replication initiation protein; Provisional
Probab=41.90 E-value=39 Score=35.81 Aligned_cols=28 Identities=25% Similarity=0.255 Sum_probs=19.5
Q ss_pred hhhhcCCCCcchhhHHHHHhhhcC-cccc
Q 010992 446 LAKHRKSDTLEAKDILVHLERNWN-MTLP 473 (496)
Q Consensus 446 LAKHRKSdTLEvKDVQLhLERnWN-I~IP 473 (496)
+-|-|+.+.+.+|.|.+||-|++- +.++
T Consensus 377 ~s~~R~~~i~~~RqiamyL~r~~t~~sl~ 405 (450)
T PRK14087 377 DGKARSKSIVTARHIAMYLTKEILNHTLA 405 (450)
T ss_pred hCCCCCccccHHHHHHHHHHHHHcCCCHH
Confidence 456677788888888888877643 4444
No 182
>PF00452 Bcl-2: Apoptosis regulator proteins, Bcl-2 family; InterPro: IPR000712 Apoptosis, or programmed cell death (PCD), is a common and evolutionarily conserved property of all metazoans []. In many biological processes, apoptosis is required to eliminate supernumerary or dangerous (such as pre-cancerous) cells and to promote normal development. Dysregulation of apoptosis can, therefore, contribute to the development of many major diseases including cancer, autoimmunity and neurodegenerative disorders. In most cases, proteins of the caspase family execute the genetic programme that leads to cell death. Bcl-2 proteins are central regulators of caspase activation, and play a key role in cell death by regulating the integrity of the mitochondrial and endoplasmic reticulum (ER) membranes []. At least 20 Bcl-2 proteins have been reported in mammals, and several others have been identified in viruses. Bcl-2 family proteins fall roughly into three subtypes, which either promote cell survival (anti-apoptotic) or trigger cell death (pro-apoptotic). All members contain at least one of four conserved motifs, termed Bcl-2 Homology (BH) domains. Bcl-2 subfamily proteins, which contain at least BH1 and BH2, promote cell survival by inhibiting the adapters needed for the activation of caspases. Pro-apoptotic members potentially exert their effects by displacing the adapters from the pro-survival proteins; these proteins belong either to the Bax subfamily, which contain BH1-BH3, or to the BH3 subfamily, which mostly only feature BH3 []. Thus, the balance between antagonistic family members is believed to play a role in determining cell fate. Members of the wider Bcl-2 family, which also includes Bcl-x, Bcl-w and Mcl-1, are described by their similarity to Bcl-2 protein, a member of the pro-survival Bcl-2 subfamily []. Full-length Bcl-2 proteins feature all four BH domains, seven alpha-helices, and a C-terminal hydrophobic motif that targets the protein to the outer mitochondrial membrane, ER and nuclear envelope. Active cell suicide (apoptosis) is induced by events such as growth factor withdrawal and toxins. It is controlled by regulators, which have either an inhibitory effect on programmed cell death (anti-apoptotic) or block the protective effect of inhibitors (pro-apoptotic) [, ]. Many viruses have found a way of countering defensive apoptosis by encoding their own anti-apoptosis genes preventing their target-cells from dying too soon. All proteins belonging to the Bcl-2 family [] contain either a BH1, BH2, BH3, or BH4 domain. All anti-apoptotic proteins contain BH1 and BH2 domains, some of them contain an additional N-terminal BH4 domain (Bcl-2, Bcl-x(L), Bcl-w), which is never seen in pro-apoptotic proteins, except for Bcl-x(S). On the other hand, all pro-apoptotic proteins contain a BH3 domain (except for Bad) necessary for dimerisation with other proteins of Bcl-2 family and crucial for their killing activity, some of them also contain BH1 and BH2 domains (Bax, Bak). The BH3 domain is also present in some anti-apoptotic protein, such as Bcl-2 or Bcl-x(L). Proteins that are known to contain these domains include vertebrate Bcl-2 (alpha and beta isoforms) and Bcl-x (isoforms (Bcl-x(L) and Bcl-x(S)); mammalian proteins Bax and Bak; mouse protein Bid; Xenopus laevis proteins Xr1 and Xr11; human induced myeloid leukemia cell differentiation protein MCL1 and Caenorhabditis elegans protein ced-9.; GO: 0042981 regulation of apoptosis; PDB: 2WH6_A 1K3K_A 1AF3_A 3PK1_B 2K7W_A 1F16_A 3PL7_C 2VM6_A 3I1H_A 3MQP_A ....
Probab=41.55 E-value=66 Score=26.49 Aligned_cols=49 Identities=18% Similarity=0.298 Sum_probs=35.7
Q ss_pred HHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHH----------HHHHHHHhhhhcCCCCc
Q 010992 405 RSIQELVNQIDPSERLDPDVEDILVDIAEDFVES----------ITMFGCSLAKHRKSDTL 455 (496)
Q Consensus 405 rKLqELVrqIDPsesLDpDVEELLLeIADDFVDs----------Vvt~ACrLAKHRKSdTL 455 (496)
+.+.+++++++-. -++++.+.+.+++++..++ ++.|++.||++-..+..
T Consensus 14 ~~f~~~~~~l~~~--~~~~~~~~f~~v~~~lf~d~~inWGRIval~~f~~~l~~~~~~~~~ 72 (101)
T PF00452_consen 14 DFFENMLNQLNIN--TPDNAYETFNEVAEELFEDGGINWGRIVALFAFAGALAVECKERGR 72 (101)
T ss_dssp HHHHHHHHHHCSS--STTTHHHHHHHHHHHHTTTSSTCHHHHHHHHHHHHHHHHHHHHTTT
T ss_pred HHHHHHHHHhCCC--CcchHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHHHHcCC
Confidence 3477777777531 2233888888999888887 78899999998777654
No 183
>cd01019 ZnuA Zinc binding protein ZnuA. These proteins have been shown to function as initial receptors in the ABC uptake of Zn2+. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. They are comprised of two globular subdomains connected by a single helix and bind their specific ligands in the cleft between these domains. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=41.52 E-value=41 Score=33.07 Aligned_cols=74 Identities=16% Similarity=0.275 Sum_probs=55.7
Q ss_pred CCHHHHHHHHHhhCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHhh----hhcCCCCcchhhHHHHHhhhcCccccCC
Q 010992 402 LTKRSIQELVNQIDPS-ERLDPDVEDILVDIAEDFVESITMFGCSLA----KHRKSDTLEAKDILVHLERNWNMTLPGF 475 (496)
Q Consensus 402 LtKrKLqELVrqIDPs-esLDpDVEELLLeIADDFVDsVvt~ACrLA----KHRKSdTLEvKDVQLhLERnWNI~IPGF 475 (496)
|.-+++..+++.|... .++|++-++...+=+++|++.+-..--++. ..++...|..-|.--||.|.||+.+-++
T Consensus 125 ldp~n~~~~a~~I~~~L~~~dP~~~~~y~~N~~~~~~~L~~l~~~~~~~~~~~~~~~~v~~H~af~Yl~~~~gl~~~~~ 203 (286)
T cd01019 125 LSPENAAEVAQAVAEKLSALDPDNAATYAANLEAFNARLAELDATIKERLAPVKTKPFFVFHDAYGYFEKRYGLTQAGV 203 (286)
T ss_pred CCHHHHHHHHHHHHHHHHHHCchhHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCeEEEecccHHHHHHHcCCceeee
Confidence 7788888888887443 578899888888888888888765544333 3344456778888899999999987654
No 184
>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]
Probab=41.51 E-value=26 Score=40.43 Aligned_cols=65 Identities=23% Similarity=0.395 Sum_probs=49.0
Q ss_pred HHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhh--HHHHHhhhcCccccCCCccccc
Q 010992 409 ELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKD--ILVHLERNWNMTLPGFSGDEIK 481 (496)
Q Consensus 409 ELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKD--VQLhLERnWNI~IPGFssDEIr 481 (496)
||+++||.-..+.+--+|.|.+|+|.+++.+.. +|+ +|+-. |++.| +.+.+|+.|+ |.||+..+|
T Consensus 678 EFLNRid~II~F~~L~~~~l~~Iv~~~L~~l~~---~L~-~~~i~-l~~s~~a~~~l~~~gyd---~~~GARpL~ 744 (786)
T COG0542 678 EFLNRIDEIIPFNPLSKEVLERIVDLQLNRLAK---RLA-ERGIT-LELSDEAKDFLAEKGYD---PEYGARPLR 744 (786)
T ss_pred HHHhhcccEEeccCCCHHHHHHHHHHHHHHHHH---HHH-hCCce-EEECHHHHHHHHHhccC---CCcCchHHH
Confidence 677888877777777778899999999999988 566 33333 45544 4788899988 888887665
No 185
>PRK00095 mutL DNA mismatch repair protein; Reviewed
Probab=41.38 E-value=46 Score=36.70 Aligned_cols=54 Identities=17% Similarity=0.308 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHHHH-----------HHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCCCc
Q 010992 423 DVEDILVDIAEDFVE-----------SITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSG 477 (496)
Q Consensus 423 DVEELLLeIADDFVD-----------sVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGFss 477 (496)
+.+++|.+|.|+..+ -+.+.||+.|...|. .|+.+.+.--|++-..+..|-...
T Consensus 532 ~~~~~l~ell~~l~~~~~~~~~~~~~~las~ACr~AIk~g~-~Ls~~E~~~Ll~~L~~~~~P~~CP 596 (617)
T PRK00095 532 ELEELIRDLLDELAEEGDSDTLKERELLATMACHGAIRAGR-RLTLEEMNALLRQLEATENPGTCP 596 (617)
T ss_pred CHHHHHHHHHHHHHhcCCcchHHHHHHHHHHHHHHhhhccC-CCCHHHHHHHHHHHHhcccccCCC
Confidence 356666666655433 478999999987665 488888888888877788876553
No 186
>PF08157 NUC129: NUC129 domain; InterPro: IPR012579 This C-terminal domain is found in a novel family of hypothetical nucleolar proteins [].; GO: 0005634 nucleus
Probab=41.37 E-value=56 Score=27.42 Aligned_cols=46 Identities=24% Similarity=0.341 Sum_probs=32.9
Q ss_pred CHHHHHHHHHHHHHHHHHH----------HHHHHHhhhhcCCCCcchhhHHHHHhhhcC
Q 010992 421 DPDVEDILVDIAEDFVESI----------TMFGCSLAKHRKSDTLEAKDILVHLERNWN 469 (496)
Q Consensus 421 DpDVEELLLeIADDFVDsV----------vt~ACrLAKHRKSdTLEvKDVQLhLERnWN 469 (496)
|.++.++..+.|+|||.+. ++.-..|+..|... +---|+| +++.|+
T Consensus 8 d~~l~~~~QqaAk~Fi~~~LYGpgsnRTT~N~flSL~NKr~~v--KkAAvQF-v~k~Wg 63 (63)
T PF08157_consen 8 DQSLRDSQQQAAKDFIQSRLYGPGSNRTTVNEFLSLANKRLPV--KKAAVQF-VNKSWG 63 (63)
T ss_pred cchhhhHHHHHHHHHHHHhccCCCCCcccHHHHhhhhhccccc--HHHHHHH-HhhccC
Confidence 6788999999999999874 45667777777655 2334444 566675
No 187
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=41.29 E-value=73 Score=33.16 Aligned_cols=17 Identities=12% Similarity=0.134 Sum_probs=12.8
Q ss_pred CCCCCHHHHHHHHHHHH
Q 010992 417 SERLDPDVEDILVDIAE 433 (496)
Q Consensus 417 sesLDpDVEELLLeIAD 433 (496)
...|++||.|+|++-++
T Consensus 297 ~~~l~~e~l~~ia~~~~ 313 (450)
T PRK00149 297 GIDLPDEVLEFIAKNIT 313 (450)
T ss_pred CCCCCHHHHHHHHcCcC
Confidence 56789999888876544
No 188
>cd01137 PsaA Metal binding protein PsaA. These proteins have been shown to function as initial receptors in ABC transport of Mn2+ and as surface adhesins in some eubacterial species. They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=41.27 E-value=30 Score=34.11 Aligned_cols=75 Identities=9% Similarity=0.163 Sum_probs=52.2
Q ss_pred cCCHHHHHHHHHhhCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHH----Hhhh--hcCCCCcchhhHHHHHhhhcCcccc
Q 010992 401 ILTKRSIQELVNQIDP-SERLDPDVEDILVDIAEDFVESITMFGC----SLAK--HRKSDTLEAKDILVHLERNWNMTLP 473 (496)
Q Consensus 401 ILtKrKLqELVrqIDP-sesLDpDVEELLLeIADDFVDsVvt~AC----rLAK--HRKSdTLEvKDVQLhLERnWNI~IP 473 (496)
-|.-.....+++.|.. -.++|++-++...+=++.|++.+-...- +|+. .++...|..-|.--||.|.||+.+-
T Consensus 120 Wldp~~~~~~a~~Ia~~L~~~dP~~~~~y~~N~~~~~~~L~~l~~~~~~~l~~~~~~~~~~v~~H~af~Y~~~~yGl~~~ 199 (287)
T cd01137 120 WMSPKNAIIYVKNIAKALSEADPANAETYQKNAAAYKAKLKALDEWAKAKFATIPAEKRKLVTSEGAFSYFAKAYGLKEA 199 (287)
T ss_pred CcCHHHHHHHHHHHHHHHHHHCcccHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCcccCEEEEecccHHHHHHHcCCeEe
Confidence 3566777777777743 3467787777777777888777654443 3443 2445577888998899999999976
Q ss_pred CC
Q 010992 474 GF 475 (496)
Q Consensus 474 GF 475 (496)
|.
T Consensus 200 ~~ 201 (287)
T cd01137 200 YL 201 (287)
T ss_pred ec
Confidence 54
No 189
>PF13551 HTH_29: Winged helix-turn helix
Probab=41.16 E-value=83 Score=25.39 Aligned_cols=41 Identities=10% Similarity=0.261 Sum_probs=24.8
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHH-hhhcCccc
Q 010992 420 LDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHL-ERNWNMTL 472 (496)
Q Consensus 420 LDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhL-ERnWNI~I 472 (496)
|+++.++.|++++++. ... +...+..+.|..+| |+.|++.|
T Consensus 58 l~~~~~~~l~~~~~~~-----------p~~-g~~~~t~~~l~~~l~~~~~~~~~ 99 (112)
T PF13551_consen 58 LSEEQRAQLIELLREN-----------PPE-GRSRWTLEELAEWLIEEEFGIDV 99 (112)
T ss_pred CCHHHHHHHHHHHHHC-----------CCC-CCCcccHHHHHHHHHHhccCccC
Confidence 7777777776666532 222 22345667776665 77777665
No 190
>PHA00440 host protein H-NS-interacting protein
Probab=41.09 E-value=62 Score=29.14 Aligned_cols=43 Identities=21% Similarity=0.336 Sum_probs=35.8
Q ss_pred HHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHh
Q 010992 404 KRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSL 446 (496)
Q Consensus 404 KrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrL 446 (496)
++.|.+|.++++.++.+|+--.++|.+-.-.=.|-++.|+++-
T Consensus 26 ~e~l~~Lak~v~~GE~~~~~~re~lvqaLT~G~egai~F~~k~ 68 (98)
T PHA00440 26 EEDILDLAKQAGAGEEVNPKDKELLVQALTHGPEGAAAFAVRQ 68 (98)
T ss_pred HHHHHHHHhhcCCcccCChHHHHHHHHHHhhChHHHHHHHHHH
Confidence 5669999999999999999999999887777777777777653
No 191
>PRK09281 F0F1 ATP synthase subunit alpha; Validated
Probab=40.98 E-value=36 Score=37.20 Aligned_cols=34 Identities=21% Similarity=0.398 Sum_probs=23.0
Q ss_pred HHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHH
Q 010992 405 RSIQELVNQIDPSERLDPDVEDILVDIAEDFVES 438 (496)
Q Consensus 405 rKLqELVrqIDPsesLDpDVEELLLeIADDFVDs 438 (496)
.+..++++.||.+..||+++++.|.++..+|++.
T Consensus 466 ~~~~~~~~~I~~~~~l~~~~~~~L~~~i~~~~~~ 499 (502)
T PRK09281 466 SNHADLLEEIRETKDLSDEIEAKLKAAIEEFKKT 499 (502)
T ss_pred HhhHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHH
Confidence 3445666666666677777777777777777654
No 192
>PRK13531 regulatory ATPase RavA; Provisional
Probab=40.97 E-value=1.2e+02 Score=33.57 Aligned_cols=70 Identities=13% Similarity=0.200 Sum_probs=53.3
Q ss_pred CccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHH-------------HHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992 399 NRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDF-------------VESITMFGCSLAKHRKSDTLEAKDILVHLE 465 (496)
Q Consensus 399 nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDF-------------VDsVvt~ACrLAKHRKSdTLEvKDVQLhLE 465 (496)
..+|+...|.+|-++|+ ...++++|.|.+++|++.- .-.++..+-..|-..|.+.|...||++...
T Consensus 204 ~~vis~eel~~lq~~v~-~V~v~d~v~eyI~~L~~~lr~~r~~~~~SpR~~~~l~~~akA~A~l~GR~~V~p~Dv~ll~~ 282 (498)
T PRK13531 204 SLQITDEEYQQWQKEIG-KITLPDHVFELIFQLRQQLDALPNAPYVSDRRWKKAIRLLQASAFFSGRDAIAPIDLILLKD 282 (498)
T ss_pred cCCCCHHHHHHHHHHhc-ceeCCHHHHHHHHHHHHHHhcCCCCCCcCcHHHHHHHHHHHHHHHHCCCCCCCHHHHHHhHH
Confidence 45799999999988885 5789999999999998631 123455566677788999999999995444
Q ss_pred hhcC
Q 010992 466 RNWN 469 (496)
Q Consensus 466 RnWN 469 (496)
--|+
T Consensus 283 vL~H 286 (498)
T PRK13531 283 CLWH 286 (498)
T ss_pred Hhcc
Confidence 4454
No 193
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=40.96 E-value=65 Score=29.53 Aligned_cols=38 Identities=16% Similarity=0.144 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992 428 LVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLE 465 (496)
Q Consensus 428 LLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE 465 (496)
.-+-.+=|+..|+..+|+.|+...+..+.++-|+-..+
T Consensus 50 askalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~ 87 (113)
T COG5247 50 ASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATE 87 (113)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHh
Confidence 34455679999999999999999998877765544443
No 194
>PRK14955 DNA polymerase III subunits gamma and tau; Provisional
Probab=40.78 E-value=66 Score=33.16 Aligned_cols=63 Identities=14% Similarity=0.113 Sum_probs=39.1
Q ss_pred CCHHHHHHHHHhhC--CCCCCCHHHHHHHHHHHHH---HHHHHHHHHHHhhh-hcCCCCcchhhHHHHH
Q 010992 402 LTKRSIQELVNQID--PSERLDPDVEDILVDIAED---FVESITMFGCSLAK-HRKSDTLEAKDILVHL 464 (496)
Q Consensus 402 LtKrKLqELVrqID--PsesLDpDVEELLLeIADD---FVDsVvt~ACrLAK-HRKSdTLEvKDVQLhL 464 (496)
+....|.+.++++- .+..||+++.++|.++++. .+.+.++..|.++. +-...+|+.+||.-.+
T Consensus 186 l~~~ei~~~l~~~~~~~g~~i~~~al~~l~~~s~g~lr~a~~~L~kl~~~~~~~~~~~~It~~~v~~~v 254 (397)
T PRK14955 186 IPLEEIQQQLQGICEAEGISVDADALQLIGRKAQGSMRDAQSILDQVIAFSVESEGEGSIRYDKVAELL 254 (397)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhccccCCCCccCHHHHHHHH
Confidence 34555555555442 2456999999999999987 44455556666664 1223467777775443
No 195
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=40.65 E-value=63 Score=29.08 Aligned_cols=57 Identities=14% Similarity=0.152 Sum_probs=43.7
Q ss_pred HHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992 408 QELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER 466 (496)
Q Consensus 408 qELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER 466 (496)
.=|.+++-+....|.....+.|...+|++.+.+-.+=+|.+...++ |+|++....++
T Consensus 29 ~C~~~~~~~k~~~~~~~~~~aL~~l~~~l~~~iV~~kel~~~~~~e--e~k~~~~q~rK 85 (101)
T PF09943_consen 29 ECFREKASKKLYGDVPEDLAALLSLEDYLHEGIVYKKELERLAESE--EVKKVLRQVRK 85 (101)
T ss_pred HHHHHHHhhhcccChhhHHHHHHHHHHHHHHHHHHHHHhccccccH--HHHHHHHHHHH
Confidence 3466777777888888888899999999999998887777766666 67777655444
No 196
>cd08324 CARD_NOD1_CARD4 Caspase activation and recruitment domain similar to that found in NOD1. Caspase activation and recruitment domain (CARD) found in human NOD1 (CARD4) and similar proteins. NOD1 is a member of the Nod-like receptor (NLR) family, which plays a central role in the innate immune response. NLRs typically contain an N-terminal effector domain, a central nucleotide-binding domain and a C-terminal ligand-binding region of several leucine-rich repeats (LRRs). In NOD1, as well as NOD2, the N-terminal effector domain is a CARD. Nod1-CARD has been shown to interact with the CARD domain of the downstream effector RICK (RIP2, CARDIAK), a serine/threonine kinase. In general, CARDs are death domains (DDs) found associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation, and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form hom
Probab=40.65 E-value=32 Score=30.19 Aligned_cols=31 Identities=26% Similarity=0.440 Sum_probs=22.3
Q ss_pred HHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHH
Q 010992 405 RSIQELVNQIDPSERLDPDVEDILVDIAEDFVE 437 (496)
Q Consensus 405 rKLqELVrqIDPsesLDpDVEELLLeIADDFVD 437 (496)
|+|-+||+ .+++..-+--.++|.+++|+|||
T Consensus 49 RkLld~v~--akG~~~k~~F~~iL~e~~~~y~~ 79 (85)
T cd08324 49 RKILDLVQ--SKGEEVSEYFLYLLQQLADAYVD 79 (85)
T ss_pred HHHHHHHH--hcCchHHHHHHHHHHHHHHhhhh
Confidence 45555555 25556666678899999999997
No 197
>PRK13428 F0F1 ATP synthase subunit delta; Provisional
Probab=40.64 E-value=94 Score=33.16 Aligned_cols=73 Identities=11% Similarity=0.121 Sum_probs=47.1
Q ss_pred CccCCHHHHHHHHHhhCCCC-CCCHHHHHHHHHHHH-----HHHHHHHHHHHHhhhhcCCCCcc-----------hhhHH
Q 010992 399 NRILTKRSIQELVNQIDPSE-RLDPDVEDILVDIAE-----DFVESITMFGCSLAKHRKSDTLE-----------AKDIL 461 (496)
Q Consensus 399 nrILtKrKLqELVrqIDPse-sLDpDVEELLLeIAD-----DFVDsVvt~ACrLAKHRKSdTLE-----------vKDVQ 461 (496)
+..+++.+-.+|+.+|-.+. .+++.+..+|..++| .+.+-+-.+.-.+++|||--..+ .+.|.
T Consensus 315 ~p~i~~~~K~~ll~~l~~~~~~~~~~~~nfl~~lv~~~R~~~l~~i~~~~~~l~~~~~g~~~a~VtsA~pLs~~q~~~L~ 394 (445)
T PRK13428 315 DYTVPADGRVALLRKVLGGASTVNPVTVALLSQTVELLRGQPAEEAVLFLAELAVARRGEVVAQVSAAAELSDAQRTRLT 394 (445)
T ss_pred CCCCCHHHHHHHHHHHHhccccCCHHHHHHHHHHHHCCchhhHHHHHHHHHHHHHHHCCeeEEEEEeecCCCHHHHHHHH
Confidence 45677777778888875543 688888888888777 23333444444555666654332 34566
Q ss_pred HHHhhhcCcc
Q 010992 462 VHLERNWNMT 471 (496)
Q Consensus 462 LhLERnWNI~ 471 (496)
=.|++.||-.
T Consensus 395 ~~L~k~~g~~ 404 (445)
T PRK13428 395 EVLSRIYGRP 404 (445)
T ss_pred HHHHHHHCCc
Confidence 7788887743
No 198
>CHL00176 ftsH cell division protein; Validated
Probab=40.61 E-value=79 Score=35.42 Aligned_cols=65 Identities=17% Similarity=0.277 Sum_probs=43.7
Q ss_pred CHHHHHHHHHhhCCCCCCCHHH-HHHHHHHHHH----HHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992 403 TKRSIQELVNQIDPSERLDPDV-EDILVDIAED----FVESITMFGCSLAKHRKSDTLEAKDILVHLERN 467 (496)
Q Consensus 403 tKrKLqELVrqIDPsesLDpDV-EELLLeIADD----FVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn 467 (496)
+.+...++++..-....+++++ .+.|.+.++- -|.++++.|+.+|..|+...|+.+||...++|.
T Consensus 354 d~~~R~~IL~~~l~~~~~~~d~~l~~lA~~t~G~sgaDL~~lvneAal~a~r~~~~~It~~dl~~Ai~rv 423 (638)
T CHL00176 354 DREGRLDILKVHARNKKLSPDVSLELIARRTPGFSGADLANLLNEAAILTARRKKATITMKEIDTAIDRV 423 (638)
T ss_pred CHHHHHHHHHHHHhhcccchhHHHHHHHhcCCCCCHHHHHHHHHHHHHHHHHhCCCCcCHHHHHHHHHHH
Confidence 4555555666554445555543 2233332222 478899999999888888899999999999985
No 199
>TIGR00962 atpA proton translocating ATP synthase, F1 alpha subunit. The sequences of ATP synthase F1 alpha and beta subunits are related and both contain a nucleotide-binding site for ATP and ADP. They have a common amino terminal domain but vary at the C-terminus. The beta chain has catalytic activity, while the alpha chain is a regulatory subunit. The alpha-subunit contains a highly conserved adenine-specific noncatalytic nucleotide-binding domain. The conserved amino acid sequence is Gly-X-X-X-X-Gly-Lys. Proton translocating ATP synthase F1, alpha subunit is homologous to proton translocating ATP synthase archaeal/vacuolar(V1), B subunit.
Probab=40.38 E-value=37 Score=37.04 Aligned_cols=35 Identities=17% Similarity=0.451 Sum_probs=25.9
Q ss_pred HHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHH
Q 010992 404 KRSIQELVNQIDPSERLDPDVEDILVDIAEDFVES 438 (496)
Q Consensus 404 KrKLqELVrqIDPsesLDpDVEELLLeIADDFVDs 438 (496)
|.+..+++++|+.+..||+++++.|.++..+|++.
T Consensus 464 ~~~~~~~~~~i~~~~~l~~~~~~~L~~~i~~~~~~ 498 (501)
T TIGR00962 464 DANHPDILEEINTKKKLTEELEDKLKEALKNFKKT 498 (501)
T ss_pred HHhhHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHh
Confidence 33455677777777788888888888888888764
No 200
>PRK08903 DnaA regulatory inactivator Hda; Validated
Probab=40.33 E-value=1.2e+02 Score=28.01 Aligned_cols=62 Identities=10% Similarity=-0.011 Sum_probs=40.4
Q ss_pred CHHHHHHHHHhhC--CCCCCCHHHHHHHHHHHH---HHHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992 403 TKRSIQELVNQID--PSERLDPDVEDILVDIAE---DFVESITMFGCSLAKHRKSDTLEAKDILVHLE 465 (496)
Q Consensus 403 tKrKLqELVrqID--PsesLDpDVEELLLeIAD---DFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE 465 (496)
+.+.+.++++++. -+..|++++.++|++-.+ ..+.+|++.--..|+..| ..|++..|+-+|+
T Consensus 158 ~~~~~~~~l~~~~~~~~v~l~~~al~~L~~~~~gn~~~l~~~l~~l~~~~~~~~-~~i~~~~~~~~l~ 224 (227)
T PRK08903 158 SDADKIAALKAAAAERGLQLADEVPDYLLTHFRRDMPSLMALLDALDRYSLEQK-RPVTLPLLREMLA 224 (227)
T ss_pred CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHhC-CCCCHHHHHHHHh
Confidence 4445556666653 357899999999988655 234445555445666666 4578888877765
No 201
>cd05128 RasGAP_GAP1_like The GAP1 family of Ras GTPase-activating proteins includes GAP1(m) (or RASA2), GAP1_IP4BP (or RASA3), Ca2+ -promoted Ras inactivator (CAPRI, or RASAL4), and Ras GTPase activating-like proteins (RASAL) or RASAL1. The members are characterized by a conserved domain structure comprising N-terminal tandem C2 domains, a highly conserved central RasGAP domain, and a C-terminal pleckstrin homology domain that is associated with a Bruton's tyrosine kinase motif. While this domain structure is conserved, a small change in the function of each individual domain and the interaction between domains has a marked effect on the regulation of each protein.
Probab=40.29 E-value=81 Score=32.42 Aligned_cols=42 Identities=24% Similarity=0.260 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccC
Q 010992 426 DILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPG 474 (496)
Q Consensus 426 ELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPG 474 (496)
+.|.+++++|++.|++..+++-. +++.|--+|.+.-.-.+|+
T Consensus 132 ~~L~~~~~~~~~~I~~S~~~~P~-------~lr~i~~~l~~~v~~kFp~ 173 (315)
T cd05128 132 ENLRYYLDRLFEAITKSSVSCPT-------VMCDIFYQLRERVGERFPG 173 (315)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCH-------HHHHHHHHHHHHHHHHCCC
Confidence 67899999999999987665543 3444444444433333443
No 202
>COG4585 Signal transduction histidine kinase [Signal transduction mechanisms]
Probab=40.13 E-value=51 Score=32.72 Aligned_cols=34 Identities=26% Similarity=0.506 Sum_probs=27.6
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcch
Q 010992 417 SERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEA 457 (496)
Q Consensus 417 sesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEv 457 (496)
..+|++++|+.|..|+-|.|.||+ ||=+.+++++
T Consensus 269 ~~~L~~~~e~~l~rivQEaltN~~-------rHa~A~~v~V 302 (365)
T COG4585 269 LERLPPEAEDALFRIVQEALTNAI-------RHAQATEVRV 302 (365)
T ss_pred cccCChhHHHHHHHHHHHHHHHHH-------hccCCceEEE
Confidence 356899999999999999999886 6777776543
No 203
>TIGR01446 DnaD_dom DnaD and phage-associated domain. This model represents the conserved domain of DnaD, part of Bacillus subtilis replication restart primosome, and of a number of phage-associated proteins. Members, both chromosomal or phage-associated, are found in the Bacillus/Clostridium group of Gram-positive bacteria.
Probab=40.06 E-value=1.2e+02 Score=23.68 Aligned_cols=46 Identities=17% Similarity=0.018 Sum_probs=32.9
Q ss_pred CCCHHHHHHHHHHHHHHH--HHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992 419 RLDPDVEDILVDIAEDFV--ESITMFGCSLAKHRKSDTLEAKDILVHLER 466 (496)
Q Consensus 419 sLDpDVEELLLeIADDFV--DsVvt~ACrLAKHRKSdTLEvKDVQLhLER 466 (496)
.+.+--.+.|.++.|+|- .+|+..||+.|..++. ..++=|.-+|++
T Consensus 12 ~ls~~e~~~i~~~~~~~~~~~evI~~ai~~a~~~~~--~~~~Yi~~Il~~ 59 (73)
T TIGR01446 12 MLSPFEMEDLKYWLDEFGNSPELIKEALKEAVSNNK--ANYKYIDAILNN 59 (73)
T ss_pred CCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHcCC--CCHHHHHHHHHH
Confidence 577778888889999966 6999999999986533 345545444443
No 204
>cd05130 RasGAP_Neurofibromin Neurofibromin is the product of the neurofibromatosis type 1 gene (NF1) and shares a region of similarity with catalytic domain of the mammalian p120RasGAP protein and an extended similarity with the Saccharomyces cerevisiae RasGAP proteins Ira1 and Ira2. Neurofibromin has been shown to function as a GAP (GTPase-activating protein) which inhibits low molecular weight G proteins such as Ras by stimulating their intrinsic GTPase activity. NF1 is a common genetic disorder characterized by various symptoms ranging from predisposition for the development of tumors to learning disability or mental retardation. Loss of neurofibromin activity can be correlated to the increase in Ras-GTP concentration in neurofibromas of NF1 of patients, supporting the notion that unregulated Ras signaling may contribute to their development.
Probab=39.90 E-value=57 Score=33.73 Aligned_cols=43 Identities=14% Similarity=0.210 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCC
Q 010992 426 DILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGF 475 (496)
Q Consensus 426 ELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGF 475 (496)
+.|.+++|+|++.|++...++-. ++|.|--+|.+.-.-++|+.
T Consensus 135 ~~L~~~~~~fl~~I~~S~~~~P~-------~lR~i~~~l~~~v~~kFP~~ 177 (329)
T cd05130 135 RNLLQLTEKFFHAIINSSSEFPP-------QLRSVCHCLYQVVSQRFPNK 177 (329)
T ss_pred HHHHHHHHHHHHHHHHhHHhCCH-------HHHHHHHHHHHHHHHHCCCc
Confidence 56899999999999998766654 55666555555545555553
No 205
>PRK07764 DNA polymerase III subunits gamma and tau; Validated
Probab=39.65 E-value=44 Score=38.49 Aligned_cols=60 Identities=8% Similarity=0.106 Sum_probs=33.4
Q ss_pred cCCHHHHHHHHHhhCC--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhH
Q 010992 401 ILTKRSIQELVNQIDP--SERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDI 460 (496)
Q Consensus 401 ILtKrKLqELVrqIDP--sesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDV 460 (496)
.|+.+.|.++|++|.. +..+|+++.++|+++++.=+.++++..=+|+.+-+.+.|+.+||
T Consensus 178 ~l~~~~l~~~L~~il~~EGv~id~eal~lLa~~sgGdlR~Al~eLEKLia~~~~~~IT~e~V 239 (824)
T PRK07764 178 LVPPEVMRGYLERICAQEGVPVEPGVLPLVIRAGGGSVRDSLSVLDQLLAGAGPEGVTYERA 239 (824)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhhcCCCCCCHHHH
Confidence 3567777777777643 45678888888877766533333333323333222333544444
No 206
>PTZ00465 rhoptry-associated protein 1 (RAP-1); Provisional
Probab=39.46 E-value=10 Score=41.96 Aligned_cols=66 Identities=14% Similarity=0.248 Sum_probs=47.0
Q ss_pred HHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH-----------hhhhcCCCCcchhhHHHHHhhhcC-cccc
Q 010992 408 QELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCS-----------LAKHRKSDTLEAKDILVHLERNWN-MTLP 473 (496)
Q Consensus 408 qELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACr-----------LAKHRKSdTLEvKDVQLhLERnWN-I~IP 473 (496)
++++..++-.+.|.+|..+.|..+-|+|+|+||..+-. +++=...+.|.+.-|.+-+++.|- +.+|
T Consensus 48 D~~i~a~~~~~~i~~dM~~~l~~~~e~~vD~VC~~~~E~s~Cr~~V~~YV~RCk~gDCLTID~VkyP~n~eyqpL~LP 125 (565)
T PTZ00465 48 DTLMTLRDHMHNITKDMKHVLSNGREQIVNDVCSNAPEDSNCREVVNNYADRCEMYGCFTIDNVKYPLYQEYQPLSLP 125 (565)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhCchHHHHHHHhCCCchhhHHHHHHHHHHHhccCCceeeehhhccccCCCCCCCCC
Confidence 35555556667899999999999999999999987533 334456666767667777776654 5555
No 207
>COG3935 DnaD Putative primosome component and related proteins [DNA replication, recombination, and repair]
Probab=39.39 E-value=80 Score=32.01 Aligned_cols=35 Identities=11% Similarity=-0.083 Sum_probs=30.1
Q ss_pred CCCHHHHHHHHHHHHHHH--HHHHHHHHHhhhhcCCC
Q 010992 419 RLDPDVEDILVDIAEDFV--ESITMFGCSLAKHRKSD 453 (496)
Q Consensus 419 sLDpDVEELLLeIADDFV--DsVvt~ACrLAKHRKSd 453 (496)
-|.+==+|.|....|+|= .+||..||+.|..++..
T Consensus 141 ~lsP~e~E~L~~wld~d~~~~elI~~ALkeAv~~gK~ 177 (246)
T COG3935 141 MLSPFEIEDLQKWLDEDSHDPELIKAALKEAVENGKL 177 (246)
T ss_pred cCCchhHHHHHHHHHhcCCCHHHHHHHHHHHHHcCCc
Confidence 577776778889999999 99999999999988765
No 208
>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional
Probab=39.31 E-value=34 Score=36.12 Aligned_cols=69 Identities=14% Similarity=0.105 Sum_probs=46.3
Q ss_pred HHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhh-H-HHHHhhhcCccccCCCcccc
Q 010992 408 QELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKD-I-LVHLERNWNMTLPGFSGDEI 480 (496)
Q Consensus 408 qELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKD-V-QLhLERnWNI~IPGFssDEI 480 (496)
=||+.+||--..|++--+|.|.+|+++-.+.++....++.++++-+ |++.| + .+..++-|+. ++|+..+
T Consensus 297 PEflgRld~iv~f~~L~~~~L~~Il~~~~~~l~~q~~~~l~~~~i~-L~~t~~al~~Ia~~~~~~---~~GAR~L 367 (412)
T PRK05342 297 PEFIGRLPVVATLEELDEEALVRILTEPKNALVKQYQKLFEMDGVE-LEFTDEALEAIAKKAIER---KTGARGL 367 (412)
T ss_pred HHHhCCCCeeeecCCCCHHHHHHHHHHHHHHHHHHHHHHHHhCCcE-EEECHHHHHHHHHhCCCC---CCCCchH
Confidence 4778888887788888888899999988888888777777777766 44443 3 3334444553 3454443
No 209
>PRK09545 znuA high-affinity zinc transporter periplasmic component; Reviewed
Probab=39.23 E-value=44 Score=33.53 Aligned_cols=73 Identities=16% Similarity=0.159 Sum_probs=52.7
Q ss_pred CCHHHHHHHHHhhC-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHh----hhhcCCCCcchhhHHHHHhhhcCccccC
Q 010992 402 LTKRSIQELVNQID-PSERLDPDVEDILVDIAEDFVESITMFGCSL----AKHRKSDTLEAKDILVHLERNWNMTLPG 474 (496)
Q Consensus 402 LtKrKLqELVrqID-PsesLDpDVEELLLeIADDFVDsVvt~ACrL----AKHRKSdTLEvKDVQLhLERnWNI~IPG 474 (496)
|.-.....+++.|. .-.++|++-++...+=+++|++.+-..--.+ +..++...+..-|.--||.|.||+.+-|
T Consensus 149 ldp~~~~~~a~~I~~~L~~~dP~~~~~y~~N~~~~~~~L~~l~~~~~~~l~~~~~~~~i~~H~af~Yf~~~ygl~~~~ 226 (311)
T PRK09545 149 LSPEIARATAVAIHDKLVELMPQSKAKLDANLKDFEAQLAQTDKQIGNQLAPVKGKGYFVFHDAYGYFEKHYGLTPLG 226 (311)
T ss_pred CCHHHHHHHHHHHHHHHHHhChhhHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCcEEEECchHHHHHHhCCCceee
Confidence 46666667777763 3357888888888888888888765443333 3344555778889989999999999754
No 210
>PRK13342 recombination factor protein RarA; Reviewed
Probab=39.20 E-value=71 Score=32.95 Aligned_cols=65 Identities=17% Similarity=0.171 Sum_probs=41.5
Q ss_pred cCCHHHHHHHHHhh----CCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992 401 ILTKRSIQELVNQI----DPSE-RLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERN 467 (496)
Q Consensus 401 ILtKrKLqELVrqI----DPse-sLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn 467 (496)
-+++..+.++++++ +.+. .+++++.+.|+++++.-+..+++..-.++.. .+.|+.+||+-.+++.
T Consensus 150 ~ls~e~i~~lL~~~l~~~~~~~i~i~~~al~~l~~~s~Gd~R~aln~Le~~~~~--~~~It~~~v~~~~~~~ 219 (413)
T PRK13342 150 PLSEEDIEQLLKRALEDKERGLVELDDEALDALARLANGDARRALNLLELAALG--VDSITLELLEEALQKR 219 (413)
T ss_pred CCCHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHc--cCCCCHHHHHHHHhhh
Confidence 34566777777765 2233 7999999999998865444333333333332 4468999998888764
No 211
>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX). A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.
Probab=38.63 E-value=30 Score=36.83 Aligned_cols=45 Identities=16% Similarity=0.146 Sum_probs=31.2
Q ss_pred HHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCC
Q 010992 409 ELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSD 453 (496)
Q Consensus 409 ELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSd 453 (496)
||+.+||--..|++--+|.|.+|++...+.++..-.++-+.++-+
T Consensus 304 EflgRld~Iv~f~pL~~~~L~~Il~~~~n~l~kq~~~~l~~~gi~ 348 (413)
T TIGR00382 304 EFIGRLPVIATLEKLDEEALIAILTKPKNALVKQYQALFKMDNVE 348 (413)
T ss_pred HHhCCCCeEeecCCCCHHHHHHHHHHHHHHHHHHHHHHhccCCeE
Confidence 677778877777777777788888887777766555554444444
No 212
>cd05023 S-100A11 S-100A11: S-100A11 domain found in proteins similar to S100A11. S100A11 is a member of the S-100 domain family within EF-hand Ca2+-binding proteins superfamily. Note that the S-100 hierarchy, to which this S-100A11 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins exhibit unique patterns of tissue- and cell type-specific expression and have been implicated in the Ca2+-dependent regulation of diverse physiological processes, including cell cycle regulation, differentiation, growth, and metabolic control . S100 proteins have also been associated with a variety of pathological events, including neoplastic transformation and neurodegenerative diseases such as Alzheimer's, usually via over expression of the protein. S100A11 is expressed in smooth muscle and other tissues and involves in calcium-dependent membrane aggregation, which is important for cell vesiculation . As is the case for many other S100 proteins, S
Probab=38.55 E-value=96 Score=26.03 Aligned_cols=45 Identities=13% Similarity=0.223 Sum_probs=30.5
Q ss_pred CccCCHHHHHHHHHhhCC---CCCCC-HHHHHHHHHH---------HHHHHHHHHHHH
Q 010992 399 NRILTKRSIQELVNQIDP---SERLD-PDVEDILVDI---------AEDFVESITMFG 443 (496)
Q Consensus 399 nrILtKrKLqELVrqIDP---sesLD-pDVEELLLeI---------ADDFVDsVvt~A 443 (496)
+..|+|..|..|++.--+ ...++ .+++++|.++ -++||.-|..-|
T Consensus 25 ~~~Ls~~Elk~ll~~e~~~~~~~~~~~~~~~~ll~~~D~d~DG~I~f~EF~~l~~~l~ 82 (89)
T cd05023 25 SYQLSKTEFLSFMNTELASFTKNQKDPGVLDRMMKKLDLNSDGQLDFQEFLNLIGGLA 82 (89)
T ss_pred cCeECHHHHHHHHHHhhhHhhcCCCCHHHHHHHHHHcCCCCCCcCcHHHHHHHHHHHH
Confidence 458999999999988644 23455 5677777765 457776555443
No 213
>COG1466 HolA DNA polymerase III, delta subunit [DNA replication, recombination, and repair]
Probab=37.97 E-value=94 Score=31.24 Aligned_cols=65 Identities=9% Similarity=0.084 Sum_probs=45.3
Q ss_pred CHHHHHHHHHhhC--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992 403 TKRSIQELVNQID--PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERN 467 (496)
Q Consensus 403 tKrKLqELVrqID--PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn 467 (496)
..++|.++|++.- -+.+||+|+.++|++..+.=+..+...--+|+-..+...|+..||+-.+.+.
T Consensus 141 ~~~~l~~~i~~~~~~~~l~i~~~a~~~L~~~~~~nl~~i~~Ei~KL~l~~~~~~I~~~~V~~~v~~~ 207 (334)
T COG1466 141 DEAELPQWIKKRAKELGLKIDQEAIQLLLEALGGNLLAIAQEIEKLALYAGDKEITLEDVEEVVSDV 207 (334)
T ss_pred CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCCcHHHHHHHHHHHHHhCCCCcCCHHHHHHHHhcc
Confidence 4556666666552 4679999999999988875444444444455555555589999998887764
No 214
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=37.66 E-value=1.4e+02 Score=26.34 Aligned_cols=64 Identities=11% Similarity=0.130 Sum_probs=39.6
Q ss_pred HHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCC-cchhhH-HHHHhhhcCccccCCC
Q 010992 407 IQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDT-LEAKDI-LVHLERNWNMTLPGFS 476 (496)
Q Consensus 407 LqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdT-LEvKDV-QLhLERnWNI~IPGFs 476 (496)
+.+|+..+..+ | ++.+-+|.+.|...|..++.++.+.+..+. .+++|| +=++-|-|...++.|.
T Consensus 4 ~~~li~~~~~g---d---~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~~AeDlvQevfl~~~~~~~~~~~ 69 (183)
T TIGR02999 4 VTELLQQWQNG---D---AAARDQLFPQLYQELRRIARRQLRRERSGQTLQTTALVHEAYLRLSDQDEQKWD 69 (183)
T ss_pred HHHHHHHHHcC---C---HHHHHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHhhcccCCCC
Confidence 45566655333 2 456777777777788777777777665332 268886 5566677753445453
No 215
>PF08367 M16C_assoc: Peptidase M16C associated; InterPro: IPR013578 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This domain appears in eukaryotes as well as bacteria and tends to be found near the C terminus of metalloproteases and related sequences belonging to MEROPS peptidase family M16 (subfamily M16C, clan ME). These include: eupitrilysin, falcilysin, PreP peptidase, CYM1 peptidase and subfamily M16C non-peptidase homologues.; GO: 0008237 metallopeptidase activity, 0008270 zinc ion binding, 0006508 proteolysis; PDB: 2FGE_B 3S5I_A 3S5H_A 3S5M_A 3S5K_A.
Probab=37.64 E-value=81 Score=30.38 Aligned_cols=65 Identities=23% Similarity=0.213 Sum_probs=46.9
Q ss_pred HHHHHHHHhhCCCCCCCHH--HHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCcc
Q 010992 405 RSIQELVNQIDPSERLDPD--VEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMT 471 (496)
Q Consensus 405 rKLqELVrqIDPsesLDpD--VEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~ 471 (496)
.++-+|+++|=-+..+|+. ..++|.++..++..+|+..+-.+|..|-...+.. ...+-|.-+||.
T Consensus 174 ~~~~~ll~eil~~~~f~d~~rl~~ll~~~~s~~~~~i~~~Gh~~A~~ra~s~~s~--~~~~~e~~~Gl~ 240 (248)
T PF08367_consen 174 DEAFELLSEILTETDFDDKERLKELLKELKSDMESSIISSGHSYAMSRASSYLSR--SGALDELWSGLS 240 (248)
T ss_dssp HHHHHHHHHHHHCB-TT-HHHHHHHHHHHHHHHHHHHHH-HHHHHHHHCCCTT-H--HHHHHHHHHSHH
T ss_pred HHHHHHHHHHHhccCCCcHHHHHHHHHHHHHHHHHhhhhhHHHHHHHHHHhcCCH--HHHHHHHHcCHH
Confidence 4577788887556667766 7899999999999999999999999999997643 333445444453
No 216
>PRK14959 DNA polymerase III subunits gamma and tau; Provisional
Probab=37.58 E-value=49 Score=37.26 Aligned_cols=61 Identities=10% Similarity=0.060 Sum_probs=40.1
Q ss_pred CCHHHHHHHHHhhCC--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHH
Q 010992 402 LTKRSIQELVNQIDP--SERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVH 463 (496)
Q Consensus 402 LtKrKLqELVrqIDP--sesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLh 463 (496)
|+...|.+.|++|.. +..+|+++.++|.++++-=+.++++..-+++.+ +.++|+.+||.-.
T Consensus 178 Ls~~eL~~~L~~il~~egi~id~eal~lIA~~s~GdlR~Al~lLeqll~~-g~~~It~d~V~~~ 240 (624)
T PRK14959 178 LSEAGLEAHLTKVLGREGVDYDPAAVRLIARRAAGSVRDSMSLLGQVLAL-GESRLTIDGARGV 240 (624)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHh-cCCCcCHHHHHHH
Confidence 456666666666533 345999999999999886566666555555533 4456777776433
No 217
>cd05394 RasGAP_RASA2 RASA2 (or GAP1(m)) is a member of the GAP1 family of Ras GTPase-activating proteins that includes GAP1_IP4BP (or RASA3), CAPRI, and RASAL. In vitro, RASA2 has been shown to bind inositol 1,3,4,5-tetrakisphosphate (IP4), the water soluble inositol head group of the lipid second messenger phosphatidylinositol 3,4,5-trisphosphate (PIP3). In vivo studies also demonstrated that RASA2 binds PIP3, and it is recruited to the plasma membrane following agonist stimulation of PI 3-kinase. Furthermore, the membrane translocation is a consequence of the ability of its pleckstrin homology (PH) domain to bind PIP3.
Probab=37.49 E-value=56 Score=34.00 Aligned_cols=44 Identities=16% Similarity=0.037 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCC
Q 010992 425 EDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGF 475 (496)
Q Consensus 425 EELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGF 475 (496)
.+.|.+++++|++.|++.++.+-. ++++|--+|.+.-.-++|+.
T Consensus 130 ~~~L~~~~~~~~~~I~~S~~~~P~-------~lr~i~~~lr~~v~~rFp~~ 173 (313)
T cd05394 130 KENLRYYVDKVFFCIVKSSMSCPT-------VMCDIFYSLRHMAVKRFPND 173 (313)
T ss_pred HHHHHHHHHHHHHHHHhCcccCcH-------HHHHHHHHHHHHHHHHCCCh
Confidence 377889999999999988776653 47777666655555555553
No 218
>PRK10911 oligopeptidase A; Provisional
Probab=37.44 E-value=54 Score=36.75 Aligned_cols=67 Identities=21% Similarity=0.175 Sum_probs=42.6
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHH---Hhhh-hcCCCCcchhhHHHHHhhhcCccccCCCcccccccC
Q 010992 417 SERLDPDVEDILVDIAEDFVESITMFGC---SLAK-HRKSDTLEAKDILVHLERNWNMTLPGFSGDEIKTFR 484 (496)
Q Consensus 417 sesLDpDVEELLLeIADDFVDsVvt~AC---rLAK-HRKSdTLEvKDVQLhLERnWNI~IPGFssDEIr~~r 484 (496)
...-.++|+++|.+|++..+..+-...- .++| .-+.+.|+.=|+.|+.|+. .-.--.+..+++++|-
T Consensus 287 ma~spe~V~~fL~~l~~~~~p~a~~El~~L~~~~k~~~g~~~L~pWD~~yy~~~~-~~~~~~~d~~~l~~YF 357 (680)
T PRK10911 287 MAENPQQVLDFLTDLAKRARPQGEKELAQLRAFAKAEFGVDELQPWDIAYYSEKQ-KQHLYSISDEQLRPYF 357 (680)
T ss_pred hCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCChhhHHHHhhHH-HHhhcCCCHHHhcccC
Confidence 4556778899999888888776654442 3333 2355567778988888873 2222344566777763
No 219
>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda. Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.
Probab=37.42 E-value=1.4e+02 Score=27.11 Aligned_cols=62 Identities=10% Similarity=-0.017 Sum_probs=35.5
Q ss_pred CHHHHHHHHHhhC--CCCCCCHHHHHHHHHHHH---HHHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992 403 TKRSIQELVNQID--PSERLDPDVEDILVDIAE---DFVESITMFGCSLAKHRKSDTLEAKDILVHLE 465 (496)
Q Consensus 403 tKrKLqELVrqID--PsesLDpDVEELLLeIAD---DFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE 465 (496)
++..+.++++.+- ....+++++.++|.+... ..+.+|++.+-.+|..++. +|+++.|+=+||
T Consensus 160 ~~~e~~~~l~~~~~~~~~~~~~~~l~~L~~~~~gn~r~L~~~l~~~~~~~~~~~~-~i~~~~~~~~~~ 226 (226)
T TIGR03420 160 SDEEKIAALQSRAARRGLQLPDEVADYLLRHGSRDMGSLMALLDALDRASLAAKR-KITIPFVKEVLA 226 (226)
T ss_pred CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhccCCHHHHHHHHHHHHHHHHHhCC-CCCHHHHHHHhC
Confidence 4555556665542 245789998888876543 1233444444433433443 588888876654
No 220
>TIGR02881 spore_V_K stage V sporulation protein K. Members of this protein family are the stage V sporulation protein K (SpoVK), a close homolog of the Rubisco expression protein CbbX (TIGR02880) and a members of the ATPase family associated with various cellular activities (pfam00004). Members are strictly limited to bacterial endospore-forming species, but are not universal in this group and are missing from the Clostridium group.
Probab=36.92 E-value=1.3e+02 Score=28.87 Aligned_cols=59 Identities=14% Similarity=0.156 Sum_probs=35.2
Q ss_pred CCHHHHHHHHHhhCC--CCCCCHHHHHHHHHHHHH-------------HHHHHHHHHHHhhhhc--CCCCcchhhH
Q 010992 402 LTKRSIQELVNQIDP--SERLDPDVEDILVDIAED-------------FVESITMFGCSLAKHR--KSDTLEAKDI 460 (496)
Q Consensus 402 LtKrKLqELVrqIDP--sesLDpDVEELLLeIADD-------------FVDsVvt~ACrLAKHR--KSdTLEvKDV 460 (496)
++...|.++++.+-. ...+++++.+.|++.++. +|.++++.|++-...| +.+.++..|+
T Consensus 178 ~~~~el~~Il~~~~~~~~~~l~~~a~~~l~~~~~~~~~~~~~~~gn~R~~~n~~e~a~~~~~~r~~~~~~~~~~~~ 253 (261)
T TIGR02881 178 YTVEELMEIAERMVKEREYKLTEEAKWKLREHLYKVDQLSSREFSNARYVRNIIEKAIRRQAVRLLDKSDYSKEDL 253 (261)
T ss_pred CCHHHHHHHHHHHHHHcCCccCHHHHHHHHHHHHHHHhccCCCCchHHHHHHHHHHHHHHHHHHHhccCCCCHHHH
Confidence 356667777766633 457999999888776542 4556666665554444 2233444454
No 221
>KOG3705 consensus Glycoprotein 6-alpha-L-fucosyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=36.33 E-value=38 Score=37.31 Aligned_cols=93 Identities=18% Similarity=0.182 Sum_probs=65.9
Q ss_pred CccCCHHHHHHHHHhh-------------CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCC---cchhhH-H
Q 010992 399 NRILTKRSIQELVNQI-------------DPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDT---LEAKDI-L 461 (496)
Q Consensus 399 nrILtKrKLqELVrqI-------------DPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdT---LEvKDV-Q 461 (496)
.+-+.||+|++=+++| ..+..|.+...++||+.|+-- .++...+.+|-+..|++. -|++|| +
T Consensus 117 dhE~~rRri~~~i~E~w~fl~Sel~kvr~~~~~dl~e~~~~~LL~~~~h~-rSlm~d~~~l~q~dG~e~wR~Kea~dlt~ 195 (580)
T KOG3705|consen 117 DHEVQRRRIDDRIREMWYFLHSELGKVRKAASADLIENSTKILLETAEHM-RSLMGDSAQLEQLDGSEEWRFKEATDLTQ 195 (580)
T ss_pred cHHHHHHHHHhhHHHHHHHHHHHHHHHhhhhhhhHHhhHHHHHHhhHHHH-HHHHhHHHHHHhccCcHHHHHhHHhHHHH
Confidence 3467788888877776 134567778889999998754 467777777877777763 367787 6
Q ss_pred HHHhhhcCccccCCCcccccccCCcccccCC
Q 010992 462 VHLERNWNMTLPGFSGDEIKTFRKPVRIVTD 492 (496)
Q Consensus 462 LhLERnWNI~IPGFssDEIr~~rk~~~~~~d 492 (496)
|+.+|--.+.=|...++..|.+=+-+.-||-
T Consensus 196 lvqrri~~LQNPkdCs~AkkLVCnlnKgCGy 226 (580)
T KOG3705|consen 196 LVQRRIEKLQNPKDCSEAKKLVCNLNKGCGY 226 (580)
T ss_pred HHHHHHHHhcChHhhHHHhhheeeccCCccc
Confidence 6767666677777777777777777777763
No 222
>PHA03181 helicase-primase primase subunit; Provisional
Probab=36.26 E-value=56 Score=37.83 Aligned_cols=40 Identities=13% Similarity=0.238 Sum_probs=32.7
Q ss_pred HHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q 010992 404 KRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGC 444 (496)
Q Consensus 404 KrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~AC 444 (496)
|+.|.+|+++|......++++|+ +++.+.|++|.++..|.
T Consensus 607 k~~Ls~lL~~i~~~~~~~~~l~~-~~~~a~~~cd~Lv~~AF 646 (764)
T PHA03181 607 KEALSTLLEEICLCNDTDESLLT-IQEKVQKVFEELLYMAF 646 (764)
T ss_pred HHHHHHHHHHHHhccCCcccHHH-HHHHHHHHHHHHHHHHH
Confidence 88999999999888777776666 66777888888888765
No 223
>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=36.19 E-value=63 Score=30.41 Aligned_cols=55 Identities=24% Similarity=0.291 Sum_probs=35.8
Q ss_pred HHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhh-------hhcCCCCcchhhHHHH
Q 010992 404 KRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLA-------KHRKSDTLEAKDILVH 463 (496)
Q Consensus 404 KrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLA-------KHRKSdTLEvKDVQLh 463 (496)
-.+|..|-++| ..+|..+.++|.+|.+ +.+.+..+|..+ +......|+++||.=|
T Consensus 28 ~~~I~~L~~e~---~~ld~~i~~~~~~L~~--~~~~L~~~~~~~~~~~~~~~~~~~~~v~~~eLL~Y 89 (188)
T PF10018_consen 28 QARIQQLRAEI---EELDEQIRDILKQLKE--ARKELRTLPDQADEKLKSIPKAEKRPVDYEELLSY 89 (188)
T ss_pred HHHHHHHHHHH---HHHHHHHHHHHHHHHH--HHHHHHHHHHHhhhccccccccccCCCCHHHHHHH
Confidence 34566666665 5688888888888876 556666676333 3334456788888443
No 224
>cd05026 S-100Z S-100Z: S-100Z domain found in proteins similar to S100Z. S100Z is a member of the S100 domain family within the EF-hand Ca2+-binding proteins superfamily. Note that the S-100 hierarchy, to which this S-100Z group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately.S100 proteins exhibit unique patterns of tissue- and cell type-specific expression and have been implicated in the Ca2+-dependent regulation of diverse physiological processes, including cell cycle regulation, differentiation, growth, and metabolic control. S100Z is normally expressed in various tissues, with its highest level of expression being in spleen and leukocytes. The function of S100Z remains unclear. Preliminary structural data suggests that S100Z is homodimer, however a heterodimer with S100P has been reported. S100Z is capable of binding calcium ions. When calcium binds to S110Z, the protein experiences a conformational change, which exposes hydrophobic surfac
Probab=36.18 E-value=1.3e+02 Score=25.11 Aligned_cols=46 Identities=26% Similarity=0.375 Sum_probs=28.7
Q ss_pred cCCc-cCCHHHHHHHHHhhCC----CCCCCHHHHHHHHHH---------HHHHHHHHHHH
Q 010992 397 FGNR-ILTKRSIQELVNQIDP----SERLDPDVEDILVDI---------AEDFVESITMF 442 (496)
Q Consensus 397 ~~nr-ILtKrKLqELVrqIDP----sesLDpDVEELLLeI---------ADDFVDsVvt~ 442 (496)
+++. .|++..|.+|++..-+ ...-+.+|+++|.++ -+||+.-+...
T Consensus 23 dgdg~~Is~~EL~~ll~~~~~~~~~~~~~~~~v~~i~~elD~n~dG~Idf~EF~~l~~~l 82 (93)
T cd05026 23 EGDRYKLSKGELKELLQRELTDFLSSQKDPMLVDKIMNDLDSNKDNEVDFNEFVVLVAAL 82 (93)
T ss_pred CCCCCEECHHHHHHHHHHHhHHhcccccCHHHHHHHHHHhCCCCCCCCCHHHHHHHHHHH
Confidence 4444 5999999999977422 112345677777776 35666655444
No 225
>PF08165 FerA: FerA (NUC095) domain; InterPro: IPR012560 The ferlin gene family are characterised by multiple tandem C2 domains and a C-terminal transmembrane domain. They are found in a wide range of species and their function remains unknown, however, mutations in its two most well-characterised members, dysferlin and otoferlin, have been implicated in human disease []. This is central domain A in proteins of the Ferlin family [].; GO: 0016021 integral to membrane
Probab=35.97 E-value=44 Score=27.38 Aligned_cols=40 Identities=8% Similarity=0.243 Sum_probs=29.0
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHH
Q 010992 421 DPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVH 463 (496)
Q Consensus 421 DpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLh 463 (496)
+.++.++.+++-|++|+|+-. .|-.-++...+...|.+++
T Consensus 9 ~~~l~~~~~~lLdqlIeD~~~---pLP~~~~~~~~t~LD~~l~ 48 (66)
T PF08165_consen 9 EEELAELWLKLLDQLIEDCSK---PLPSLEGKPNATELDRQLR 48 (66)
T ss_pred HHHHHHHHHHHHHHHHHHhcC---CCCCCCCCCCCCHHHHHHH
Confidence 456889999999999999766 5555555555666676543
No 226
>TIGR02923 AhaC ATP synthase A1, C subunit. The A1/A0 ATP synthase is homologous to the V-type (V1/V0, vacuolar) ATPase, but functions in the ATP synthetic direction as does the F1/F0 ATPase of bacteria. The C subunit is part of the hydrophilic A1 "stalk" complex (AhaABCDEFG) which is the site of ATP generation and is coupled to the membrane-embedded proton translocating A0 complex.
Probab=35.69 E-value=63 Score=31.65 Aligned_cols=81 Identities=16% Similarity=0.238 Sum_probs=44.5
Q ss_pred CCccCCHHHHHHHHHhhC--------CCCCCCHHHHHHH------HHHHHHHHHHHHHHHHH-hhhhcCC----------
Q 010992 398 GNRILTKRSIQELVNQID--------PSERLDPDVEDIL------VDIAEDFVESITMFGCS-LAKHRKS---------- 452 (496)
Q Consensus 398 ~nrILtKrKLqELVrqID--------PsesLDpDVEELL------LeIADDFVDsVvt~ACr-LAKHRKS---------- 452 (496)
++..|.+.+|.+|+..-| ......+.+.+.+ +...|.++|+++...++ ++|+.-.
T Consensus 234 ~g~~l~~~~l~~l~~~~~~~~~~~~l~~t~y~~~l~~~~~~~~~~~~~~E~~~d~~~~~~~~~~~~~~~~~~~~~~~yl~ 313 (343)
T TIGR02923 234 GGYELDEEKLAPLAHIESIDEVVSALDGTKYGEDISEVLSEEEKSVAVFERALDEYLIKMATKLSLRYPLSVGPVLGYIL 313 (343)
T ss_pred cccccCHHHHHHHHcCCCHHHHHHHHhcCcchHHHHHHHhhccCcHHHHHHHHHHHHHHHHHHHhccCCCchHHHHHHHH
Confidence 445667777777765211 1122222233222 33445556666665553 3554443
Q ss_pred -CCcchhhHHHHHhhhcCccccCCCcccccc
Q 010992 453 -DTLEAKDILVHLERNWNMTLPGFSGDEIKT 482 (496)
Q Consensus 453 -dTLEvKDVQLhLERnWNI~IPGFssDEIr~ 482 (496)
..+|+++|..+++-..+ |++.|+||.
T Consensus 314 ~ke~Ei~nlr~I~~gk~~----~l~~e~I~~ 340 (343)
T TIGR02923 314 KKEREVRNLRAIARGKEE----GLPPEEIKE 340 (343)
T ss_pred HHHHHHHHHHHHHHHHHc----CCCHHHHHH
Confidence 34688888888776543 777888774
No 227
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=35.64 E-value=73 Score=32.15 Aligned_cols=30 Identities=17% Similarity=0.231 Sum_probs=19.3
Q ss_pred HHHHHhhCCCCCCCHHHHHHHHHHHHHHHH
Q 010992 408 QELVNQIDPSERLDPDVEDILVDIAEDFVE 437 (496)
Q Consensus 408 qELVrqIDPsesLDpDVEELLLeIADDFVD 437 (496)
.+||.++.....|+++|.+.-.+|+++..+
T Consensus 220 ~~~i~r~~~~L~L~~~v~~~A~~i~~~a~~ 249 (310)
T PRK00423 220 IDYVPRFASELGLSGEVQKKAIEILQKAKE 249 (310)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHHh
Confidence 455555555566777777777777766654
No 228
>PF03885 DUF327: Protein of unknown function (DUF327); InterPro: IPR005585 The proteins in this family are around 140-170 residues in length. The proteins contain many conserved residues, with the most conserved motifs found in the central and C-terminal region. The function of these proteins is unknown. ; PDB: 2P61_A 2QUP_A.
Probab=35.58 E-value=37 Score=30.96 Aligned_cols=51 Identities=20% Similarity=0.348 Sum_probs=33.2
Q ss_pred CHHHHHHHHHhhCCC-----CCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCC
Q 010992 403 TKRSIQELVNQIDPS-----ERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSD 453 (496)
Q Consensus 403 tKrKLqELVrqIDPs-----esLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSd 453 (496)
....|++|+.+||.. ...+-+-...-.++.-+|++.|+..+.++-++++-+
T Consensus 41 ~~e~L~~Ll~~I~~~G~~L~~~~t~~~l~~YK~~Vk~Fl~~~v~~~~~l~~~~~~~ 96 (147)
T PF03885_consen 41 SEEELQELLDEIDEQGERLAESPTLENLKRYKELVKQFLKEVVKNGYKLEEESSWD 96 (147)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHT-----
T ss_pred HHHHHHHHHHHHHHHHHHHhhCCCHHHHHHHHHHHHHHHHHHHHHHheeehcccCC
Confidence 347889999998642 233333344456899999999999999999888775
No 229
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=35.51 E-value=97 Score=35.12 Aligned_cols=71 Identities=15% Similarity=0.119 Sum_probs=53.7
Q ss_pred CcCCccCCHHHHHHHHHhhCC---CCCCCHHHHHHHHHHHHHH-------------HHHHHHHHHHhhhhcCCCCcchhh
Q 010992 396 EFGNRILTKRSIQELVNQIDP---SERLDPDVEDILVDIAEDF-------------VESITMFGCSLAKHRKSDTLEAKD 459 (496)
Q Consensus 396 e~~nrILtKrKLqELVrqIDP---sesLDpDVEELLLeIADDF-------------VDsVvt~ACrLAKHRKSdTLEvKD 459 (496)
...+.....+-++-++++|.. .-.||.++.+.|...|... +-+++..|+-+|+-.+.+.|+.+|
T Consensus 312 m~~~~~nr~k~~~~~~q~v~~d~~ip~~~~~Av~~li~~a~R~Ag~~~~Ltl~~rdl~~lv~~A~~ia~~~~~~~I~ae~ 391 (647)
T COG1067 312 MPITDANRSKLVQFYVQELARDGNIPHLDKDAVEELIREAARRAGDQNKLTLRLRDLGNLVREAGDIAVSEGRKLITAED 391 (647)
T ss_pred CCCChHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHHHhccccceeccCHHHHHHHHHHhhHHHhcCCcccCcHHH
Confidence 344444455556667777743 3578999887777777654 456888999999999999999999
Q ss_pred HHHHHhh
Q 010992 460 ILVHLER 466 (496)
Q Consensus 460 VQLhLER 466 (496)
|.-+|++
T Consensus 392 Ve~a~~~ 398 (647)
T COG1067 392 VEEALQK 398 (647)
T ss_pred HHHHHHh
Confidence 9998887
No 230
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=35.33 E-value=1.5e+02 Score=26.58 Aligned_cols=52 Identities=17% Similarity=0.181 Sum_probs=29.3
Q ss_pred CHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhH
Q 010992 403 TKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDI 460 (496)
Q Consensus 403 tKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDV 460 (496)
+-..+.+|+..+..+ | ++.+-+|.+.|-..|..++.++.+.+..+..+++||
T Consensus 7 ~~~~~~~l~~~~~~g---d---~~a~~~l~~~~~~~l~~~~~~~~~~~~~~~~~aeDl 58 (189)
T PRK09648 7 TGEELDALVAEAVAG---D---RRALREVLEIIRPLVVRYCRARLGGVERPGLSADDV 58 (189)
T ss_pred CchHHHHHHHHHHcC---C---HHHHHHHHHHHHHHHHHHHHHHhcccccCCCCHHHH
Confidence 344566666666433 2 345555566666666666666655544334466666
No 231
>PRK09111 DNA polymerase III subunits gamma and tau; Validated
Probab=35.33 E-value=79 Score=35.14 Aligned_cols=63 Identities=11% Similarity=0.106 Sum_probs=44.0
Q ss_pred CCHHHHHHHHHhhC--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992 402 LTKRSIQELVNQID--PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLE 465 (496)
Q Consensus 402 LtKrKLqELVrqID--PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE 465 (496)
+....|.+.|++|- .+..+|+++.++|+++++--+.+++...=+++.| +...|+.+||.-.|.
T Consensus 191 l~~~el~~~L~~i~~kegi~i~~eAl~lIa~~a~Gdlr~al~~Ldkli~~-g~g~It~e~V~~llg 255 (598)
T PRK09111 191 IEADVLAAHLSRIAAKEGVEVEDEALALIARAAEGSVRDGLSLLDQAIAH-GAGEVTAEAVRDMLG 255 (598)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhh-cCCCcCHHHHHHHhC
Confidence 45667777777763 3568999999999999887666666555444444 334688888876654
No 232
>COG3900 Predicted periplasmic protein [Function unknown]
Probab=35.32 E-value=16 Score=37.19 Aligned_cols=65 Identities=17% Similarity=0.322 Sum_probs=45.6
Q ss_pred CHHHHHHHHHhhCCCCCCCHHHHHHHH-HHHHHHHHHHHHHHHHhhhhcCCCCcchhhH-HHHH---hhhcCccc
Q 010992 403 TKRSIQELVNQIDPSERLDPDVEDILV-DIAEDFVESITMFGCSLAKHRKSDTLEAKDI-LVHL---ERNWNMTL 472 (496)
Q Consensus 403 tKrKLqELVrqIDPsesLDpDVEELLL-eIADDFVDsVvt~ACrLAKHRKSdTLEvKDV-QLhL---ERnWNI~I 472 (496)
-+..|++||.+||...-|+--..|+|+ +..|+.|+.|.. +||-+...|.-.+- +|.+ ++.|-|||
T Consensus 123 apgTiD~lvdei~~kyG~~lp~adllsadpyd~L~~gv~s-----s~~vg~~vVgg~ecd~lafr~ddvDfqIWI 192 (262)
T COG3900 123 APGTIDELVDEIDDKYGITLPGADLLSADPYDDLIAGVES-----SKFVGNAVVGGEECDQLAFRKDDVDFQIWI 192 (262)
T ss_pred CCCcHHHHHHHHHhhcCCCccchhhhccChHHHHHhhhhh-----hhhhhhhccCceeehhhhccCCCCceEEEe
Confidence 456799999999998888888888776 788888877765 56666665544443 2333 23577777
No 233
>TIGR00524 eIF-2B_rel eIF-2B alpha/beta/delta-related uncharacterized proteins. This model, eIF-2B_rel, describes half of a superfamily, where the other half consists of eukaryotic translation initiation factor 2B (eIF-2B) subunits alpha, beta, and delta. It is unclear whether the eIF-2B_rel set is monophyletic, or whether they are all more closely related to each other than to any eIF-2B subunit because the eIF-2B clade is highly derived. Members of this branch of the family are all uncharacterized with respect to function and are found in the Archaea, Bacteria, and Eukarya, although a number are described as putative translation intiation factor components. Proteins found by eIF-2B_rel include at least three clades, including a set of uncharacterized eukaryotic proteins, a set found in some but not all Archaea, and a set universal so far among the Archaea and closely related to several uncharacterized bacterial proteins.
Probab=35.32 E-value=60 Score=33.05 Aligned_cols=40 Identities=13% Similarity=0.175 Sum_probs=24.4
Q ss_pred HHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 010992 408 QELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAK 448 (496)
Q Consensus 408 qELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAK 448 (496)
+.|++.|.... =.+++.+.|++-+|+|+++.+...-++|+
T Consensus 71 ~~~~~~i~~~~-~~~~~k~~l~~~~~~~~~e~~~~~~~Ia~ 110 (303)
T TIGR00524 71 ERVLNSAENGE-SVEEAKESLLREAIEIIEEDLETNRKIGE 110 (303)
T ss_pred HHHHHHHhccC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444443221 23567889999999999877654333333
No 234
>PRK13765 ATP-dependent protease Lon; Provisional
Probab=35.29 E-value=92 Score=35.05 Aligned_cols=48 Identities=13% Similarity=0.194 Sum_probs=36.3
Q ss_pred CCCCHHHHHHHHHHHH-------------HHHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992 418 ERLDPDVEDILVDIAE-------------DFVESITMFGCSLAKHRKSDTLEAKDILVHLE 465 (496)
Q Consensus 418 esLDpDVEELLLeIAD-------------DFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE 465 (496)
..||+++.+.|++.+- .-|.+++..|..+|+.++.+.++.+||...++
T Consensus 338 ~~f~~eAVa~LI~~~~R~ag~r~~lsl~~~~l~~l~r~a~~~a~~~~~~~i~~~~v~~a~~ 398 (637)
T PRK13765 338 PHFDRDAVEEIIREAKRRAGRKGHLTLKLRDLGGLVRVAGDIARSEGAELTTAEHVLEAKK 398 (637)
T ss_pred CCCCHHHHHHHHHHHHHHhCCccccccCHHHHHHHHHHHHHHHHhhccceecHHHHHHHHH
Confidence 4789987777776443 24566888899999999999999888865544
No 235
>PRK10664 transcriptional regulator HU subunit beta; Provisional
Probab=35.21 E-value=55 Score=27.63 Aligned_cols=16 Identities=25% Similarity=0.354 Sum_probs=11.1
Q ss_pred hhcCccccCCCccccc
Q 010992 466 RNWNMTLPGFSGDEIK 481 (496)
Q Consensus 466 RnWNI~IPGFssDEIr 481 (496)
++=.+.|+|||.=+++
T Consensus 38 ~~~~v~l~gfG~F~v~ 53 (90)
T PRK10664 38 EGDDVALVGFGTFAVK 53 (90)
T ss_pred CCCEEEECCcEEEEEE
Confidence 3334778888887776
No 236
>PF02885 Glycos_trans_3N: Glycosyl transferase family, helical bundle domain Prosite entry for Thymidine and pyrimidine-nucleoside phosphorylases; InterPro: IPR017459 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. The glycosyl transferase family includes anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase (2.4.2.2 from EC) catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism. This N-terminal domain is found in various family 3 glycosyl transferases, including anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism.; PDB: 2DSJ_B 2ELC_B 2BPQ_A 1ZVW_B 3QR9_B 1V8G_B 2WK5_C 2J0F_C 2WK6_B 1UOU_A ....
Probab=35.18 E-value=23 Score=28.00 Aligned_cols=47 Identities=17% Similarity=0.270 Sum_probs=30.9
Q ss_pred HHHHHHhhCCCCCCCHH-HHHHHHHHHHHHHHHHHHHHHHhhhhcCCC
Q 010992 407 IQELVNQIDPSERLDPD-VEDILVDIAEDFVESITMFGCSLAKHRKSD 453 (496)
Q Consensus 407 LqELVrqIDPsesLDpD-VEELLLeIADDFVDsVvt~ACrLAKHRKSd 453 (496)
|.++|+++-.+..|+.| +++++-.|.|+=++++--.|...|-+-|.+
T Consensus 2 ~~~~l~~l~~g~~Ls~~e~~~~~~~i~~g~~s~~qiaAfL~al~~kge 49 (66)
T PF02885_consen 2 IKEILKKLRDGEDLSREEAKAAFDAILDGEVSDAQIAAFLMALRMKGE 49 (66)
T ss_dssp HHHHHHHHHTT----HHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH--
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCc
Confidence 56778777666777765 888888899888888888887777664444
No 237
>PRK13430 F0F1 ATP synthase subunit delta; Provisional
Probab=35.03 E-value=1.2e+02 Score=30.34 Aligned_cols=73 Identities=14% Similarity=0.151 Sum_probs=41.8
Q ss_pred CccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHH----HHHHHHH-HHHHhhhhcCCCCcc-----------hhhHHH
Q 010992 399 NRILTKRSIQELVNQIDPSERLDPDVEDILVDIAED----FVESITM-FGCSLAKHRKSDTLE-----------AKDILV 462 (496)
Q Consensus 399 nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADD----FVDsVvt-~ACrLAKHRKSdTLE-----------vKDVQL 462 (496)
+..+++.+-.+|+.++-. .++++.+..+|.-+++. .+.+|+. |.-.+++||+-...+ .+.|.=
T Consensus 143 ~p~i~~e~K~~ll~~l~~-~~~~~~~~nfl~~lv~~~R~~~l~~i~~~f~~l~~~~~~~~~a~VtSA~pLs~~q~~~L~~ 221 (271)
T PRK13430 143 DRAAPAEAKRELLARLLY-GKVTPVTERLAEQAVGRPRGRSIEEGLDELSNLAAARRGRSVATVTTAVPLSDEQKQRLAA 221 (271)
T ss_pred CCCCCHHHHHHHHHHHHh-ccCCHHHHHHHHHHHhCCChhhHHHHHHHHHHHHHHHcCeeEEEEEecCCCCHHHHHHHHH
Confidence 455677777777777633 24788888777777765 3434443 444445555544222 234555
Q ss_pred HHhhhcCccc
Q 010992 463 HLERNWNMTL 472 (496)
Q Consensus 463 hLERnWNI~I 472 (496)
.|++.||-.|
T Consensus 222 ~L~k~~g~~V 231 (271)
T PRK13430 222 ALSRIYGRPV 231 (271)
T ss_pred HHHHHHCCce
Confidence 6777776433
No 238
>PRK14700 recombination factor protein RarA; Provisional
Probab=34.91 E-value=99 Score=32.18 Aligned_cols=65 Identities=8% Similarity=0.021 Sum_probs=42.3
Q ss_pred CHHHHHHHHHhhCC--------CCCCCHHHHHHHHHHHHH---HHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992 403 TKRSIQELVNQIDP--------SERLDPDVEDILVDIAED---FVESITMFGCSLAKHRKSDTLEAKDILVHLERN 467 (496)
Q Consensus 403 tKrKLqELVrqIDP--------sesLDpDVEELLLeIADD---FVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn 467 (496)
++..|..+|++.-. ...||+|+.+.|.+++|- +.=++++.+|.++...+...|+.++|+-.+.+.
T Consensus 40 ~~~di~~il~ral~~~~~~~~~~~~i~~~al~~ia~~a~GDaR~aLN~LE~a~~~~~~~~~~~it~~~~~~~~~~~ 115 (300)
T PRK14700 40 SLVATQKLIEKALSQDEVLAKHKFKIDDGLYNAMHNYNEGDCRKILNLLERMFLISTRGDEIYLNKELFDQAVGET 115 (300)
T ss_pred CHHHHHHHHHHHHHhhhccCCcCCCcCHHHHHHHHHhcCCHHHHHHHHHHHHHhhccccCCCccCHHHHHHHHhHH
Confidence 66667766665521 247999999999999873 333566666754432222247888887777654
No 239
>COG2083 Uncharacterized protein conserved in archaea [Function unknown]
Probab=34.91 E-value=16 Score=34.39 Aligned_cols=72 Identities=18% Similarity=0.187 Sum_probs=48.7
Q ss_pred HHHHHHHHHhhCCCC--------CCCHHHHHHHHHHHHHH------------HHHHHHHHHHhhhhcCCCCcchhhHHHH
Q 010992 404 KRSIQELVNQIDPSE--------RLDPDVEDILVDIAEDF------------VESITMFGCSLAKHRKSDTLEAKDILVH 463 (496)
Q Consensus 404 KrKLqELVrqIDPse--------sLDpDVEELLLeIADDF------------VDsVvt~ACrLAKHRKSdTLEvKDVQLh 463 (496)
++.|.||+++=+|.. -++.+--|+|.+|+|+. |+++-. ..++-| ..+|+|=|.-+
T Consensus 26 rktL~ELL~ee~P~V~~rDG~~hyfkr~ELE~La~~ldE~e~~rlrlPivlEi~s~~~---~~i~Ir--gk~evkvI~kv 100 (140)
T COG2083 26 RKTLEELLREERPHVTLRDGTEHYFKRRELEFLAQILDEDEIPRLRLPIVLEISSGER---GAIYIR--GKVEVKVIKKV 100 (140)
T ss_pred hhHHHHHHhccCCeEEccCCceeeeeHHHHHHHHhhcchhhhhhccccEEEEeccCCC---ceEEEe--cchhhhhHHHH
Confidence 677999999987754 46677778999999986 222222 223333 35789999999
Q ss_pred HhhhcCccccCCCcccccccC
Q 010992 464 LERNWNMTLPGFSGDEIKTFR 484 (496)
Q Consensus 464 LERnWNI~IPGFssDEIr~~r 484 (496)
|.++|.|. ..|.+.-||
T Consensus 101 lG~e~~~~----e~dil~ly~ 117 (140)
T COG2083 101 LGFEEVIF----EEDILYLYR 117 (140)
T ss_pred hcchhhhc----ccCeEEEeh
Confidence 99999764 444444443
No 240
>KOG3341 consensus RNA polymerase II transcription factor complex subunit [Transcription]
Probab=34.67 E-value=1.1e+02 Score=31.20 Aligned_cols=63 Identities=21% Similarity=0.324 Sum_probs=39.3
Q ss_pred HHHHHHHHHhh--CCCCCCCHHHHHHHHHHHHHHHH----HHHHHHHHhhhhcCCCCcchhhHHHHHhhhcC
Q 010992 404 KRSIQELVNQI--DPSERLDPDVEDILVDIAEDFVE----SITMFGCSLAKHRKSDTLEAKDILVHLERNWN 469 (496)
Q Consensus 404 KrKLqELVrqI--DPsesLDpDVEELLLeIADDFVD----sVvt~ACrLAKHRKSdTLEvKDVQLhLERnWN 469 (496)
|+++++|+..| ||...-+..-.++| .+ .||.= .|+ ..|.++||++.-.+++.+|.-||-+.-+
T Consensus 63 R~~Fq~Mca~IGvDPlas~kgfw~~~l-gv-gdFYYelgVqvi-EvC~at~~~nGGlislqel~~~l~~~R~ 131 (249)
T KOG3341|consen 63 RNQFQEMCASIGVDPLASGKGFWAELL-GV-GDFYYELGVQVI-EVCLATKHTNGGLISLQELCNHLLQRRK 131 (249)
T ss_pred HHHHHHHHHHcCCCccccCcchHHHHh-hh-HHHHHHHhhHHH-HHHHHhhcccCCeeeHHHHHHHHHHHhc
Confidence 56778888876 66665543333222 22 22322 333 4799999999999999999776654433
No 241
>cd06571 Bac_DnaA_C C-terminal domain of bacterial DnaA proteins. The DNA-binding C-terminal domain of DnaA contains a helix-turn-helix motif that specifically interacts with the DnaA box, a 9-mer motif that occurs repetitively in the replication origin oriC. Multiple copies of DnaA, which is an ATPase, bind to 9-mers at the origin and form an initial complex in which the DNA strands are being separated in an ATP-dependent step.
Probab=34.54 E-value=31 Score=28.65 Aligned_cols=46 Identities=33% Similarity=0.427 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhc-Ccccc
Q 010992 425 EDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNW-NMTLP 473 (496)
Q Consensus 425 EELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnW-NI~IP 473 (496)
++++..+|+.| .|. ..--+.+-|+.+.+.++.|.+||-+++ |+.+.
T Consensus 2 ~~Ii~~Va~~~--~v~-~~~i~~~~R~~~~~~aR~ia~yl~~~~~~~s~~ 48 (90)
T cd06571 2 ELIIEAVAEYF--GIS-VEDLRSKSRKKEIALARQIAMYLARELTGLSLP 48 (90)
T ss_pred HHHHHHHHHHh--CCC-HHHHhcCCCCcCcchHHHHHHHHHHHHhCCCHH
Confidence 56677778888 333 333467778889999999999998885 66664
No 242
>COG5566 Uncharacterized conserved protein [Function unknown]
Probab=34.33 E-value=92 Score=29.47 Aligned_cols=60 Identities=17% Similarity=0.194 Sum_probs=39.6
Q ss_pred HHHHHHHHhhC--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcC
Q 010992 405 RSIQELVNQID--PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWN 469 (496)
Q Consensus 405 rKLqELVrqID--PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWN 469 (496)
.++..|+..+| |+..+...+-++|.+++|.|.-.+.....+-++ .. .++-|.+.|-++||
T Consensus 14 ~~~~aLfd~lD~ip~d~l~klwps~Lsev~eV~~ael~~a~ie~~g----k~-~alk~v~~l~~y~G 75 (137)
T COG5566 14 SKDSALFDFLDLIPGDNLRKLWPSLLSEVHEVFLAELEDAGIEDNG----KP-LALKLVFKLMEYGG 75 (137)
T ss_pred hhhhhhhhhhccCCchhHHHhhHHHHHHHHHHHHHHHHHHhhhhcc----Cc-hHHHHHHHHHHHcC
Confidence 34556666555 566666778888888888887777666655554 11 35556677777777
No 243
>PF13499 EF-hand_7: EF-hand domain pair; PDB: 1TCF_A 2TN4_A 1TN4_A 1A2X_A 2CT9_B 2OTG_B 2OS8_B 1SNL_A 3O4Y_A 3J04_E ....
Probab=33.86 E-value=1.4e+02 Score=22.24 Aligned_cols=52 Identities=6% Similarity=0.102 Sum_probs=29.7
Q ss_pred cCCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHH
Q 010992 397 FGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDIL 461 (496)
Q Consensus 397 ~~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQ 461 (496)
+++..|++..|..+++.+..... ++.++.++....+.+--.+...|+..+..
T Consensus 12 d~~G~i~~~el~~~~~~~~~~~~-------------~~~~~~~~~~~~~~~D~d~dG~i~~~Ef~ 63 (66)
T PF13499_consen 12 DGDGYISKEELRRALKHLGRDMS-------------DEESDEMIDQIFREFDTDGDGRISFDEFL 63 (66)
T ss_dssp TSSSEEEHHHHHHHHHHTTSHST-------------HHHHHHHHHHHHHHHTTTSSSSEEHHHHH
T ss_pred CccCCCCHHHHHHHHHHhccccc-------------HHHHHHHHHHHHHHhCCCCcCCCcHHHHh
Confidence 44445555555555554432211 55566666666666666677778777763
No 244
>PRK12921 2-dehydropantoate 2-reductase; Provisional
Probab=33.85 E-value=45 Score=31.80 Aligned_cols=13 Identities=8% Similarity=-0.069 Sum_probs=5.2
Q ss_pred HHHHHHhhhhcCC
Q 010992 440 TMFGCSLAKHRKS 452 (496)
Q Consensus 440 vt~ACrLAKHRKS 452 (496)
+...+++|+..|.
T Consensus 220 ~~E~~~v~~a~G~ 232 (305)
T PRK12921 220 LRECLAVARAEGA 232 (305)
T ss_pred HHHHHHHHHHcCC
Confidence 3333444444443
No 245
>PLN02353 probable UDP-glucose 6-dehydrogenase
Probab=33.85 E-value=1.1e+02 Score=33.02 Aligned_cols=73 Identities=3% Similarity=-0.039 Sum_probs=50.4
Q ss_pred HHHHHHHHHhhC---CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh----cCccccCCC
Q 010992 404 KRSIQELVNQID---PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERN----WNMTLPGFS 476 (496)
Q Consensus 404 KrKLqELVrqID---PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn----WNI~IPGFs 476 (496)
.++|.+|.+.+- .-...+.++-|+..=+.+-|.+--+.|+..||+.=..--+++.||.-.+... |++--||+|
T Consensus 188 ~~~~~~lY~~~~~~~~i~~~s~~~AE~~K~~eN~~ra~~Iaf~NEla~lce~~giD~~eV~~~~~~d~rig~~~l~PG~G 267 (473)
T PLN02353 188 VQALKDVYAHWVPEERIITTNLWSAELSKLAANAFLAQRISSVNAMSALCEATGADVSQVSHAVGKDSRIGPKFLNASVG 267 (473)
T ss_pred HHHHHHHHHHhhcCCCEEecCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHhCCCCcCCCCCCCCCCC
Confidence 456778887774 3346788999999999999988877777766655544456677775555544 455556654
No 246
>smart00544 MA3 Domain in DAP-5, eIF4G, MA-3 and other proteins. Highly alpha-helical. May contain repeats and/or regions similar to MIF4G domains Ponting (TIBS) "Novel eIF4G domain homologues" in press
Probab=33.84 E-value=56 Score=27.21 Aligned_cols=18 Identities=11% Similarity=0.108 Sum_probs=10.7
Q ss_pred CCCcchhhHHHHHhhhcC
Q 010992 452 SDTLEAKDILVHLERNWN 469 (496)
Q Consensus 452 SdTLEvKDVQLhLERnWN 469 (496)
.+.+...+++..+++-++
T Consensus 66 ~~~~~~~~~~~~f~~~~~ 83 (113)
T smart00544 66 ANVISTKQFEKGFWRLLE 83 (113)
T ss_pred cCCcCHHHHHHHHHHHHh
Confidence 345666666666666544
No 247
>cd05136 RasGAP_DAB2IP The DAB2IP family of Ras GTPase-activating proteins includes DAB2IP, nGAP, and Syn GAP. Disabled 2 interactive protein, (DAB2IP; also known as ASK-interacting protein 1 (AIP1)), is a member of the GTPase-activating proteins, down-regulates Ras-mediated signal pathways, and mediates TNF-induced activation of ASK1-JNK signaling pathways. The mechanism by which TNF signaling is coupled to DAB2IP is not known.
Probab=33.39 E-value=1.1e+02 Score=31.40 Aligned_cols=25 Identities=16% Similarity=-0.048 Sum_probs=20.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhh
Q 010992 424 VEDILVDIAEDFVESITMFGCSLAK 448 (496)
Q Consensus 424 VEELLLeIADDFVDsVvt~ACrLAK 448 (496)
..+.|.+++|.|++.|++..+++-.
T Consensus 125 n~~~L~~~~~~~~~~I~~S~~~~P~ 149 (309)
T cd05136 125 HQANLRMCCELAWCKIINSHCVFPA 149 (309)
T ss_pred HHHHHHHHHHHHHHHHHHhHHhCCH
Confidence 4578999999999999988776554
No 248
>PRK09087 hypothetical protein; Validated
Probab=33.15 E-value=2e+02 Score=27.55 Aligned_cols=50 Identities=24% Similarity=0.074 Sum_probs=32.5
Q ss_pred CCCCCCHHHHHHHHHHHHHHHHHHHH---HHHHhhhhcCCCCcchhhHHHHHhh
Q 010992 416 PSERLDPDVEDILVDIAEDFVESITM---FGCSLAKHRKSDTLEAKDILVHLER 466 (496)
Q Consensus 416 PsesLDpDVEELLLeIADDFVDsVvt---~ACrLAKHRKSdTLEvKDVQLhLER 466 (496)
-+..|++||.+.|++-++.=+..+.. .--+.|+.++. .|++..|+-+|+.
T Consensus 169 ~~~~l~~ev~~~La~~~~r~~~~l~~~l~~L~~~~~~~~~-~it~~~~~~~l~~ 221 (226)
T PRK09087 169 RQLYVDPHVVYYLVSRMERSLFAAQTIVDRLDRLALERKS-RITRALAAEVLNE 221 (226)
T ss_pred cCCCCCHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHhCC-CCCHHHHHHHHHh
Confidence 35789999999999877654444443 22233433343 3788888888864
No 249
>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]
Probab=33.06 E-value=1.1e+02 Score=33.49 Aligned_cols=66 Identities=20% Similarity=0.223 Sum_probs=46.1
Q ss_pred CCHHHHHHHHHh--hCCC-------CCCCHHHHHHHHHHHHHHH---HHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcC
Q 010992 402 LTKRSIQELVNQ--IDPS-------ERLDPDVEDILVDIAEDFV---ESITMFGCSLAKHRKSDTLEAKDILVHLERNWN 469 (496)
Q Consensus 402 LtKrKLqELVrq--IDPs-------esLDpDVEELLLeIADDFV---DsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWN 469 (496)
|+...|..+|++ .|.. ..||+++.++|++++|-=+ =+.++.+..++|..+ .+.+++++-+|.|...
T Consensus 163 L~~~di~~~l~ra~~~~~rgl~~~~~~i~~~a~~~l~~~s~GD~R~aLN~LE~~~~~~~~~~--~~~~~~l~~~l~~~~~ 240 (436)
T COG2256 163 LSSEDIKKLLKRALLDEERGLGGQIIVLDEEALDYLVRLSNGDARRALNLLELAALSAEPDE--VLILELLEEILQRRSA 240 (436)
T ss_pred CCHHHHHHHHHHHHhhhhcCCCcccccCCHHHHHHHHHhcCchHHHHHHHHHHHHHhcCCCc--ccCHHHHHHHHhhhhh
Confidence 367777777777 3332 2477999999999977433 356677888887666 5557788777777543
No 250
>PRK12422 chromosomal replication initiation protein; Provisional
Probab=33.03 E-value=1.1e+02 Score=32.70 Aligned_cols=27 Identities=11% Similarity=0.219 Sum_probs=16.5
Q ss_pred CcchhhHHHHHhhhcCccccCCCcccccccCC
Q 010992 454 TLEAKDILVHLERNWNMTLPGFSGDEIKTFRK 485 (496)
Q Consensus 454 TLEvKDVQLhLERnWNI~IPGFssDEIr~~rk 485 (496)
.+++++|+-...+.||+.+ +||+.-+|
T Consensus 351 ~~t~~~I~~~Va~~~~v~~-----~dl~s~~R 377 (445)
T PRK12422 351 RLTPSKIIRAVAQYYGVSP-----ESILGRSQ 377 (445)
T ss_pred CCCHHHHHHHHHHHhCCCH-----HHHhcCCC
Confidence 3666777777777776654 55554444
No 251
>PF14842 FliG_N: FliG N-terminal domain; PDB: 3HJL_A 3AJC_A 3USY_B.
Probab=32.93 E-value=94 Score=26.84 Aligned_cols=33 Identities=15% Similarity=0.458 Sum_probs=16.5
Q ss_pred CCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHH
Q 010992 402 LTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVE 437 (496)
Q Consensus 402 LtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVD 437 (496)
|+.+.+++|.++|.....+|.+..+ ++.+||.+
T Consensus 30 l~~~ei~~i~~~ma~l~~v~~~~~~---~Vl~EF~~ 62 (108)
T PF14842_consen 30 LDEEEIERISREMAKLGSVSPEEVE---EVLEEFYD 62 (108)
T ss_dssp S-HHHHHHHHHHHHT-----HHHHH---HHHHHHHH
T ss_pred CCHHHHHHHHHHHHccCCCCHHHHH---HHHHHHHH
Confidence 4667777888877666667766433 33445555
No 252
>PF15601 Imm42: Immunity protein 42
Probab=32.56 E-value=37 Score=31.56 Aligned_cols=27 Identities=15% Similarity=0.218 Sum_probs=21.5
Q ss_pred HHHHHHHH-------HHHHHHHHHHhhhhcCCCC
Q 010992 428 LVDIAEDF-------VESITMFGCSLAKHRKSDT 454 (496)
Q Consensus 428 LLeIADDF-------VDsVvt~ACrLAKHRKSdT 454 (496)
+..|+|-| +-+|+..||..|+..+.+.
T Consensus 98 i~~L~~yFvt~dG~~~f~~l~~a~~~a~~~~~~v 131 (134)
T PF15601_consen 98 ITSLSDYFVTSDGKDLFEVLFRALESAIEEKVDV 131 (134)
T ss_pred CCcHHHHhcCcchhhHHHHHHHHHHHHHhcCCCe
Confidence 55788888 5678999999998887763
No 253
>KOG1087 consensus Cytosolic sorting protein GGA2/TOM1 [Intracellular trafficking, secretion, and vesicular transport]
Probab=32.42 E-value=73 Score=34.87 Aligned_cols=75 Identities=12% Similarity=0.211 Sum_probs=50.7
Q ss_pred ccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCCCccc
Q 010992 400 RILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGDE 479 (496)
Q Consensus 400 rILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGFssDE 479 (496)
+|..|+-|.|||+.+..+. .|-.|.+.+|.|-|.|=+....-. +|++. +.-+-.-|+| -|+.||.-+.|.
T Consensus 76 ~Va~k~fL~emVk~~k~~~-~~~~Vr~kiL~LI~~W~~af~~~~---~~~~~-----~~~~y~~l~~-~G~~FP~r~~~s 145 (470)
T KOG1087|consen 76 QVASKEFLNEMVKRPKNKP-RDLKVREKILELIDTWQQAFCGPD---GYLPD-----YYQIYDELRR-KGVEFPQRDEES 145 (470)
T ss_pred HHHHHHHHHHHHhccccCC-cchhHHHHHHHHHHHHHHHccCCC---Ccchh-----HHHHHHHHHH-cCCcCCCCcccc
Confidence 4667999999999886666 999999999999999987654322 22221 2222222333 489999988776
Q ss_pred ccccC
Q 010992 480 IKTFR 484 (496)
Q Consensus 480 Ir~~r 484 (496)
+-..+
T Consensus 146 l~~~~ 150 (470)
T KOG1087|consen 146 LAVLT 150 (470)
T ss_pred ccccC
Confidence 55443
No 254
>PF11247 DUF2675: Protein of unknown function (DUF2675) ; InterPro: IPR022611 Members in this family of proteins include Bacteriophage T7 gene 5.5; they have no known function.
Probab=32.31 E-value=95 Score=27.91 Aligned_cols=47 Identities=15% Similarity=0.210 Sum_probs=36.0
Q ss_pred CCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 010992 398 GNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCS 445 (496)
Q Consensus 398 ~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACr 445 (496)
...+| .+.|-+|++.++.++.+|.--.++|..-..+=.|-++.|..+
T Consensus 21 ~e~~~-~e~ll~Lak~v~~GE~~~~~~re~l~qaLT~G~egav~f~~k 67 (98)
T PF11247_consen 21 QEEEF-EEDLLELAKKVGAGEKVSGFQREMLVQALTHGPEGAVAFVVK 67 (98)
T ss_pred HHHHH-HHHHHHHHhhcCCccccCHHHHHHHHHHHhcChHHHHHHHHH
Confidence 33444 455889999999999999998888887777666777766654
No 255
>PF07253 Gypsy: Gypsy protein; InterPro: IPR009882 This family consists of several Gypsy/Env proteins from Drosophila and Ceratitis fruit fly species. Gypsy is an endogenous retrovirus of Drosophila melanogaster. Phylogenetic studies suggest that occasional horizontal transfer events of gypsy occur between Drosophila species. Gypsy possesses infective properties associated with the products of the envelope gene that might be at the origin of these interspecies transfers [].
Probab=32.31 E-value=1.5e+02 Score=32.76 Aligned_cols=51 Identities=20% Similarity=0.249 Sum_probs=34.2
Q ss_pred hCCCCCCCHHHHHHHHH----HHHHHHHHHHHHHHHhhhhc--CCCCcchhhHHHHHhh
Q 010992 414 IDPSERLDPDVEDILVD----IAEDFVESITMFGCSLAKHR--KSDTLEAKDILVHLER 466 (496)
Q Consensus 414 IDPsesLDpDVEELLLe----IADDFVDsVvt~ACrLAKHR--KSdTLEvKDVQLhLER 466 (496)
++.....++...+.||. |.+++.+ +.+||.|||.- ++.-|+-+||+-.|+.
T Consensus 145 ~~~~~~~~~h~~~~ll~r~~ii~~~i~~--i~~ai~lAk~~ivn~~iLd~~el~~i~~~ 201 (472)
T PF07253_consen 145 IKGDSVDTDHLATTLLHRNRIIKEEIQN--IIRAIQLAKLNIVNSNILDHEELKSILSE 201 (472)
T ss_pred hcccccCchHHHHHHHHHHHHHHHHHHH--HHHHHHHHhcCCCChhhcChHHHHHHHHh
Confidence 34445555667777764 3333333 77999999974 4667888888887777
No 256
>PF13690 CheX: Chemotaxis phosphatase CheX; PDB: 3HM4_B 3H4Y_A 3H2D_A 3IIC_B.
Probab=32.25 E-value=1e+02 Score=25.42 Aligned_cols=56 Identities=9% Similarity=0.179 Sum_probs=29.9
Q ss_pred CHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCCCcc
Q 010992 403 TKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGD 478 (496)
Q Consensus 403 tKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGFssD 478 (496)
.|+-..+|++.+ ..+ ++|.+|++.+.+-||.+-|+-.+. ++. +..+++.+|-+-.+
T Consensus 20 ~~~~a~~la~~m-g~~--~~~~~e~~~da~~El~NiI~G~~~--~~l---------------~~~~~ls~P~v~~g 75 (94)
T PF13690_consen 20 DEELAKKLASAM-GEE--EEEDDEMVQDALGELANIIAGNAK--SEL---------------GEPIDLSPPSVIEG 75 (94)
T ss_dssp -HHHHHHHHHHH-SSS---SSHHHHHHHHHHHHHHHHHHHHH--HHH---------------T--EEE---EEEEE
T ss_pred CHHHHHHHHHHh-CCC--CcchhHHHHHHHHHHHHHHHHHHH--HHc---------------CCceeecCCEEEcC
Confidence 688888999988 322 444666666666666665555444 111 44667777766544
No 257
>PF09123 DUF1931: Domain of unknown function (DUF1931); InterPro: IPR015207 This entry represents a set of hypothetical bacterial proteins containing a core of six alpha-helices, where one central helix is surrounded by the other five. The exact function of this family has not, as yet, been determined []. ; PDB: 1WWS_A 1WWI_A 1R4V_A.
Probab=32.23 E-value=31 Score=32.49 Aligned_cols=55 Identities=16% Similarity=0.245 Sum_probs=38.4
Q ss_pred HHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHH
Q 010992 407 IQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILV 462 (496)
Q Consensus 407 LqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQL 462 (496)
|++|.|+. .+.-+|++=.+-+.+++++=+.|++..|-+-||..+.++|+..|+=+
T Consensus 1 fe~lFR~a-a~LdvdK~d~~r~~d~V~~Kl~DLl~va~~~Ak~ngRdvI~~~DLPI 55 (138)
T PF09123_consen 1 FERLFRKA-AGLDVDKNDAKRYSDFVEKKLYDLLLVAQENAKANGRDVIEPRDLPI 55 (138)
T ss_dssp HHHHHHHH-HS----HHHHHHHHHHHHHHHHHCCCCHHHHHHHTT-SEE-GGGS--
T ss_pred ChHHHHHH-hccCccHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeeccccCCc
Confidence 34566654 34557777777788999999999999999999999999999888743
No 258
>PRK00188 trpD anthranilate phosphoribosyltransferase; Provisional
Probab=32.20 E-value=86 Score=32.02 Aligned_cols=48 Identities=19% Similarity=0.265 Sum_probs=37.1
Q ss_pred HHHHHHhhCCCCCCCHH-HHHHHHHHHHHHHHHHHHHHHHhhhhcCCCC
Q 010992 407 IQELVNQIDPSERLDPD-VEDILVDIAEDFVESITMFGCSLAKHRKSDT 454 (496)
Q Consensus 407 LqELVrqIDPsesLDpD-VEELLLeIADDFVDsVvt~ACrLAKHRKSdT 454 (496)
|.++|++|-.+..|+.| +++++..|.|.-++++-..|..+|-+=|.++
T Consensus 3 ~~~~i~~l~~g~~Lt~~Ea~~~~~~il~g~~~~~q~~AfL~alr~kget 51 (339)
T PRK00188 3 MKELLEKLVEGEDLSEEEAEELMDAIMSGEATPAQIAAFLTALRVKGET 51 (339)
T ss_pred HHHHHHHHhCCCCCCHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCCC
Confidence 56777877666777754 8999999999988888888888777666664
No 259
>KOG3902 consensus Histone acetyltransferase PCAF/SAGA, subunit SUPT3H/SPT3 [Transcription]
Probab=31.89 E-value=3e+02 Score=29.41 Aligned_cols=59 Identities=22% Similarity=0.257 Sum_probs=38.5
Q ss_pred HHHHHHHHhhCCCCCCCHHHH--HHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992 405 RSIQELVNQIDPSERLDPDVE--DILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLE 465 (496)
Q Consensus 405 rKLqELVrqIDPsesLDpDVE--ELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE 465 (496)
-.|+.++-..+ +.-|+-+| .|+-+++--=|-.++-.+..+|-.|++..|..+|+.|-+.
T Consensus 28 veiQqmmf~sG--ei~~P~pett~Lved~V~gqvie~l~qa~eia~lrgsr~Itpedliflir 88 (352)
T KOG3902|consen 28 VEIQQMMFQSG--EIPDPLPETTNLVEDNVRGQVIESLVQANEIADLRGSRSITPEDLIFLIR 88 (352)
T ss_pred HHHHHHHHHhC--CCCCCcHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCccccChHHHHHHhh
Confidence 34555555432 33334333 4444555555566777889999999999999999976543
No 260
>PRK10733 hflB ATP-dependent metalloprotease; Reviewed
Probab=31.82 E-value=1e+02 Score=34.13 Aligned_cols=64 Identities=9% Similarity=0.107 Sum_probs=40.8
Q ss_pred HHHHHHHHhhCCCCCCCHHHH-HHHHHHHHH----HHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhc
Q 010992 405 RSIQELVNQIDPSERLDPDVE-DILVDIAED----FVESITMFGCSLAKHRKSDTLEAKDILVHLERNW 468 (496)
Q Consensus 405 rKLqELVrqIDPsesLDpDVE-ELLLeIADD----FVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnW 468 (496)
+...++++..-....+++++. +.|.+..+- =|++++..|..+|..++.+.|+..|+.-.++|-|
T Consensus 325 ~~R~~Il~~~~~~~~l~~~~d~~~la~~t~G~sgadl~~l~~eAa~~a~r~~~~~i~~~d~~~a~~~v~ 393 (644)
T PRK10733 325 RGREQILKVHMRRVPLAPDIDAAIIARGTPGFSGADLANLVNEAALFAARGNKRVVSMVEFEKAKDKIM 393 (644)
T ss_pred HHHHHHHHHHhhcCCCCCcCCHHHHHhhCCCCCHHHHHHHHHHHHHHHHHcCCCcccHHHHHHHHHHHh
Confidence 334444444433344444432 223333322 5778899999999999999999999988887754
No 261
>PRK13343 F0F1 ATP synthase subunit alpha; Provisional
Probab=31.63 E-value=62 Score=35.56 Aligned_cols=30 Identities=20% Similarity=0.189 Sum_probs=17.7
Q ss_pred HHHHHhhCCCCCCCHHHHHHHHHHHHHHHH
Q 010992 408 QELVNQIDPSERLDPDVEDILVDIAEDFVE 437 (496)
Q Consensus 408 qELVrqIDPsesLDpDVEELLLeIADDFVD 437 (496)
.++++.|+....|+++.++.|.++..+|.+
T Consensus 469 ~~~~~~i~~~~~l~~~~~~~l~~~~~~~~~ 498 (502)
T PRK13343 469 AALSLALESPRELDEAWLAALEEILREAGE 498 (502)
T ss_pred HHHHHHHHhcCCCCHHHHHHHHHHHHHHHH
Confidence 344555555556666666666666666654
No 262
>PRK02079 pyrroloquinoline quinone biosynthesis protein PqqD; Provisional
Probab=31.60 E-value=82 Score=26.99 Aligned_cols=24 Identities=25% Similarity=0.536 Sum_probs=15.6
Q ss_pred HHHHHhhCCCCCCCHHHHHHHHHHHHHH
Q 010992 408 QELVNQIDPSERLDPDVEDILVDIAEDF 435 (496)
Q Consensus 408 qELVrqIDPsesLDpDVEELLLeIADDF 435 (496)
.++++.||+.. .|+|++..|+++|
T Consensus 39 ~~Iw~~~DG~~----tv~eIi~~L~~~y 62 (88)
T PRK02079 39 GEILGLIDGKR----TVAAIIAELQQQF 62 (88)
T ss_pred HHHHHHccCCC----CHHHHHHHHHHHc
Confidence 35677777744 5666666666666
No 263
>TIGR02397 dnaX_nterm DNA polymerase III, subunit gamma and tau. This model represents the well-conserved first ~ 365 amino acids of the translation of the dnaX gene. The full-length product of the dnaX gene in the model bacterium E. coli is the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the exterme thermophile Thermus thermophilis.
Probab=31.58 E-value=86 Score=30.54 Aligned_cols=63 Identities=11% Similarity=0.147 Sum_probs=35.7
Q ss_pred CCHHHHHHHHHhhC--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992 402 LTKRSIQELVNQID--PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLE 465 (496)
Q Consensus 402 LtKrKLqELVrqID--PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE 465 (496)
++...|.++|+++- .+..+|+++.++|++.++.-+..+....=+++.+-+ ..|+.+||+-.+.
T Consensus 176 ~~~~~l~~~l~~~~~~~g~~i~~~a~~~l~~~~~g~~~~a~~~lekl~~~~~-~~it~~~v~~~~~ 240 (355)
T TIGR02397 176 IPLEDIVERLKKILDKEGIKIEDEALELIARAADGSLRDALSLLDQLISFGN-GNITYEDVNELLG 240 (355)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCChHHHHHHHHHHHhhcC-CCCCHHHHHHHhC
Confidence 35566666665542 245789999888888876434433333323333222 3477777765544
No 264
>PRK12710 flgJ flagellar rod assembly protein/muramidase FlgJ; Provisional
Probab=31.49 E-value=55 Score=33.83 Aligned_cols=43 Identities=21% Similarity=0.227 Sum_probs=35.7
Q ss_pred HHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCcccc
Q 010992 430 DIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLP 473 (496)
Q Consensus 430 eIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IP 473 (496)
+..++||+.|.-.|.++||.-|-.. .|.=-|-+||-.||-.+.
T Consensus 128 ~~~~~FI~~i~p~A~~~a~~~Gv~p-Sv~iAQAaLESGWGks~l 170 (291)
T PRK12710 128 SVVDDFVKSVWPTAKQAASLIGLDP-KLLVAQAALETGWGKFVT 170 (291)
T ss_pred ccHHHHHHHHHHHHHHHHHHhCcCh-HHHHHHHHHHccCCcccc
Confidence 6679999999999999999888764 455558899999997653
No 265
>PRK09103 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=31.30 E-value=1e+02 Score=35.39 Aligned_cols=33 Identities=15% Similarity=0.073 Sum_probs=26.4
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCC
Q 010992 421 DPDVEDILVDIAEDFVESITMFGCSLAKHRKSD 453 (496)
Q Consensus 421 DpDVEELLLeIADDFVDsVvt~ACrLAKHRKSd 453 (496)
++|+.++.-+|++..-...+..+|+|||.||.-
T Consensus 530 S~eA~~l~~~i~e~i~~~A~~aS~eLAkErG~f 562 (758)
T PRK09103 530 DGSANNLTHKTFEAIQYYLLKASNELAKEQGAC 562 (758)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCC
Confidence 456677777777777778889999999999864
No 266
>PF09860 DUF2087: Uncharacterized protein conserved in bacteria (DUF2087); InterPro: IPR018656 This domain, found in various hypothetical prokaryotic proteins and transcriptional activators, has no known function.
Probab=31.25 E-value=57 Score=27.06 Aligned_cols=30 Identities=20% Similarity=0.532 Sum_probs=24.3
Q ss_pred HHHHHHhhCCCCCCCH-HHHHHHHHHHHHHH
Q 010992 407 IQELVNQIDPSERLDP-DVEDILVDIAEDFV 436 (496)
Q Consensus 407 LqELVrqIDPsesLDp-DVEELLLeIADDFV 436 (496)
|..|+..++++..+++ ||-++|..+.|||+
T Consensus 17 L~~l~~~f~~g~~y~E~EVN~~L~~~~~D~a 47 (71)
T PF09860_consen 17 LEYLASRFEPGREYSEKEVNEILKRFFDDYA 47 (71)
T ss_pred HHHHHHhCCCCCccCHHHHHHHHHHHcccHH
Confidence 5677788888887765 59999999988886
No 267
>PRK12422 chromosomal replication initiation protein; Provisional
Probab=31.09 E-value=85 Score=33.41 Aligned_cols=30 Identities=10% Similarity=0.220 Sum_probs=23.8
Q ss_pred hhhhcCCCCcchhhHHHHHhhhc-CccccCC
Q 010992 446 LAKHRKSDTLEAKDILVHLERNW-NMTLPGF 475 (496)
Q Consensus 446 LAKHRKSdTLEvKDVQLhLERnW-NI~IPGF 475 (496)
+-|.|+.+.+.+|.|.+||-|++ |+.+|-.
T Consensus 373 ~s~~R~~~i~~~Rqiamyl~r~~t~~s~~~I 403 (445)
T PRK12422 373 LGRSQSREYVLPRQVAMYLCRQKLSLSYVKI 403 (445)
T ss_pred hcCCCCcccccHHHHHHHHHHHhcCCCHHHH
Confidence 56789999999999999998875 3665543
No 268
>cd07018 S49_SppA_67K_type Signal peptide peptidase A (SppA) 67K type, a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV) 67K type: SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. Members in this subfamily contain an amino-terminal domain in addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members (sometimes referred to as 67K type), similar to E. coli and Arabidopsis thaliana SppA peptidases. Unlike the eukaryotic functional homologs that are proposed to be aspartic proteases, site-directed mutagenesis and sequence analysis have shown that members in this subfamily, mostly bacterial, are serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys
Probab=31.08 E-value=1e+02 Score=29.22 Aligned_cols=50 Identities=8% Similarity=0.194 Sum_probs=34.7
Q ss_pred cCCHHHHHHHHHhhCC------------------CCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCC
Q 010992 401 ILTKRSIQELVNQIDP------------------SERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSD 453 (496)
Q Consensus 401 ILtKrKLqELVrqIDP------------------sesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSd 453 (496)
+..+-.+.+|+.++.- ...++++..|.+.++.|+.-+..+. .+|+.|+-+
T Consensus 116 ~~~~~~~~~ll~klGv~~~~~~~G~~K~~~~~~~~~~~s~~~r~~~~~~l~~~~~~f~~---~Va~~R~~~ 183 (222)
T cd07018 116 SAETLFFKGLLDKLGVEVQVFRVGEYKSAVEPFTRDDMSPEAREQTQALLDSLWDQYLA---DVAASRGLS 183 (222)
T ss_pred chhhhhHHHHHHHcCCcEEEEEEeccccccchhhcccCCHHHHHHHHHHHHHHHHHHHH---HHHHHcCCC
Confidence 3456677888887732 1257888888888777777666665 667788843
No 269
>COG0593 DnaA ATPase involved in DNA replication initiation [DNA replication, recombination, and repair]
Probab=31.03 E-value=40 Score=36.15 Aligned_cols=29 Identities=10% Similarity=0.249 Sum_probs=22.8
Q ss_pred cchhhHHHHHhhhcCccccCCCcccccccCCccc
Q 010992 455 LEAKDILVHLERNWNMTLPGFSGDEIKTFRKPVR 488 (496)
Q Consensus 455 LEvKDVQLhLERnWNI~IPGFssDEIr~~rk~~~ 488 (496)
++++||+-+..+.||+.+ +|++.-||...
T Consensus 320 itie~I~~~Va~~y~v~~-----~dl~s~~R~~~ 348 (408)
T COG0593 320 ITIEDIQKIVAEYYNVKV-----SDLLSKSRTRN 348 (408)
T ss_pred CCHHHHHHHHHHHhCCCH-----HHhhccccccc
Confidence 889999999999999977 66666555443
No 270
>PRK14607 bifunctional glutamine amidotransferase/anthranilate phosphoribosyltransferase; Provisional
Probab=31.01 E-value=83 Score=34.15 Aligned_cols=77 Identities=22% Similarity=0.300 Sum_probs=49.3
Q ss_pred HHHHHHhhCCCCCCCHH-HHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCc-chhhHHHHHhhhcC---------ccccCC
Q 010992 407 IQELVNQIDPSERLDPD-VEDILVDIAEDFVESITMFGCSLAKHRKSDTL-EAKDILVHLERNWN---------MTLPGF 475 (496)
Q Consensus 407 LqELVrqIDPsesLDpD-VEELLLeIADDFVDsVvt~ACrLAKHRKSdTL-EvKDVQLhLERnWN---------I~IPGF 475 (496)
+.+++++|..+..|+.| +++++..|.|.-++++--.|..+|-+-|.++. |+....-+|..... +-|-|.
T Consensus 195 ~~~~i~~l~~g~~Lt~~ea~~~~~~il~g~~~~~q~~AfL~alr~kget~~El~g~~~a~~~~~~~~~~~~~~~~D~~gt 274 (534)
T PRK14607 195 IKSYLKKLVEGEDLSFEEAEDVMEDITDGNATDAQIAGFLTALRMKGETADELAGFASVMREKSRHIPAPSPRTVDTCGT 274 (534)
T ss_pred HHHHHHHhccCCCCCHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHhCCcCCCCCCCceEEccC
Confidence 56778888777777765 88999999999888888888877776666643 23333333322211 334466
Q ss_pred Cccccccc
Q 010992 476 SGDEIKTF 483 (496)
Q Consensus 476 ssDEIr~~ 483 (496)
|+|-.+++
T Consensus 275 ggdg~~t~ 282 (534)
T PRK14607 275 GGDGFGTF 282 (534)
T ss_pred CCCCCCcc
Confidence 66655543
No 271
>PF12536 DUF3734: Patatin phospholipase ; InterPro: IPR021095 This entry represents bacterial proteins of approximately 110 amino acids in length. These proteins are found in association with PF01734 from PFAM. There are two completely conserved residues (F and G) that may be functionally important. The proteins in this family are frequently annotated as patatin family phospholipases however there is little accompanying literature to confirm this.
Probab=30.55 E-value=8.6 Score=33.55 Aligned_cols=54 Identities=28% Similarity=0.321 Sum_probs=34.6
Q ss_pred HHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHH
Q 010992 404 KRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILV 462 (496)
Q Consensus 404 KrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQL 462 (496)
|+.|.+|+++|.+..+-|+++. .|.++++...-+||. |.-.++......||..|
T Consensus 21 r~~i~~Ll~~lP~~~r~dp~~~-~l~~~~~~~~~~Ivh----Liy~~~~~e~~sKDyeF 74 (108)
T PF12536_consen 21 RHAIRELLERLPEELRDDPDVR-ELAELGCGKRVNIVH----LIYRRKPYEGHSKDYEF 74 (108)
T ss_pred HHHHHHHHHcCCHHHhCCHHHH-HHHHhcCCCceEEEE----eecCCCCccccccCccC
Confidence 5567788888877666666664 455666655555554 44455555567788876
No 272
>KOG2389 consensus Predicted bromodomain transcription factor [Transcription]
Probab=30.43 E-value=1.3e+02 Score=32.15 Aligned_cols=63 Identities=10% Similarity=0.218 Sum_probs=50.1
Q ss_pred CHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992 403 TKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER 466 (496)
Q Consensus 403 tKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER 466 (496)
.|-.....+..| +...++.-+.|.|-+++-.||-++...|-+++-|-|.--..+.||.+.|+-
T Consensus 31 a~~avaQIcqsl-g~~~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~d 93 (353)
T KOG2389|consen 31 ARVAVAQICQSL-GYSSTQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQD 93 (353)
T ss_pred HHHHHHHHHHhc-CCcccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHH
Confidence 344444444444 334566668999999999999999999999999999888889999998875
No 273
>cd08790 DED_DEDD Death Effector Domain of DEDD. Death Effector Domain (DED) found in DEDD. DEDD has been shown to block mitotic progression by inhibiting Cdk1 and to be involved in regulating the insulin signaling cascade. DEDD can bind to itself, to DEDD2, and to the two tandem DED-containing caspases, caspase-8 and -10. In general, DEDs comprise a subfamily of the Death Domain (DD) superfamily. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including PYRIN and CARD (Caspase activation and recruitment domain). They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=30.24 E-value=1.1e+02 Score=27.46 Aligned_cols=50 Identities=18% Similarity=0.294 Sum_probs=38.0
Q ss_pred HHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992 406 SIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERN 467 (496)
Q Consensus 406 KLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn 467 (496)
.|++++..|| +.||.+=.|+|.-+..|||.. .+..+.=+.+|+-+.||+.
T Consensus 4 ~lh~~l~~I~--e~L~~~DveaLkFLc~D~i~~----------~~~e~i~s~~~Lf~~Lee~ 53 (97)
T cd08790 4 SLHRMFDIVG--THLTHRDVRVLSFLFVDVIDD----------YERGLIRSGRDFLLALERQ 53 (97)
T ss_pred hHHHHHHHHH--HhcCHHHHHHHHHHhHHHhhh----------hhccCcCcHHHHHHHHHHc
Confidence 4889999885 678999899999999999963 1222223578888888886
No 274
>PF02867 Ribonuc_red_lgC: Ribonucleotide reductase, barrel domain; InterPro: IPR000788 Ribonucleotide reductase (1.17.4.1 from EC) [, ] catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs divide into three classes on the basis of their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, bacteriophage and viruses, 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 anaerobic bacteria and bacteriophage, 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. Ribonucleotide reductase is an oligomeric enzyme composed of a large subunit (700 to 1000 residues) and a small subunit (300 to 400 residues) - class II RNRs are less complex, using the small molecule B12 in place of the small chain []. The reduction of ribonucleotides to deoxyribonucleotides involves the transfer of free radicals, the function of each metallocofactor is to generate an active site thiyl radical. This thiyl radical then initiates the nucleotide reduction process by hydrogen atom abstraction from the ribonucleotide []. The radical-based reaction involves five cysteines: two of these are located at adjacent anti-parallel strands in a new type of ten-stranded alpha/beta-barrel; two others reside at the carboxyl end in a flexible arm; and the fifth, in a loop in the centre of the barrel, is positioned to initiate the radical reaction []. There are several regions of similarity in the sequence of the large chain of prokaryotes, eukaryotes and viruses spread across 3 domains: an N-terminal domain common to the mammalian and bacterial enzymes; a C-terminal domain common to the mammalian and viral ribonucleotide reductases; and a central domain common to all three [].; GO: 0004748 ribonucleoside-diphosphate reductase activity, 0006260 DNA replication, 0055114 oxidation-reduction process, 0005971 ribonucleoside-diphosphate reductase complex; PDB: 1DQ3_A 1XJN_A 1XJK_A 3O0O_B 1XJF_A 3O0Q_A 1XJJ_A 1XJG_A 1XJM_B 3O0N_B ....
Probab=30.18 E-value=1.1e+02 Score=33.11 Aligned_cols=33 Identities=18% Similarity=0.151 Sum_probs=29.1
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCC
Q 010992 421 DPDVEDILVDIAEDFVESITMFGCSLAKHRKSD 453 (496)
Q Consensus 421 DpDVEELLLeIADDFVDsVvt~ACrLAKHRKSd 453 (496)
++|+.++..+|++..-...+..+++|||+|+.=
T Consensus 308 S~ea~~~~~~i~e~i~~~a~~aS~~LA~e~G~~ 340 (538)
T PF02867_consen 308 SEEARELADEIFEHIYYAAYRASVELAKERGPF 340 (538)
T ss_dssp SHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-SS
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHhccCCcC
Confidence 478999999999999999999999999999864
No 275
>cd03567 VHS_GGA VHS domain family, GGA subfamily; GGA (Golgi-localized, Gamma-ear-containing, Arf-binding) comprise a subfamily of ubiquitously expressed, monomeric, motif-binding cargo/clathrin adaptor proteins. The VHS domain has a superhelical structure similar to the structure of the ARM (Armadillo) repeats and is present at the N-termini of proteins. GGA proteins have a multidomain structure consisting of an N-terminal VHS domain linked by a short proline-rich linker to a GAT (GGA and TOM) domain, which is followed by a long flexible linker to the C-terminal appendage, GAE (gamma-adaptin ear) domain. The VHS domain of GGA proteins binds to the acidic-cluster dileucine (DxxLL) motif found on the cytoplasmic tails of cargo proteins trafficked between the trans-Golgi network and the endosomal system.
Probab=30.08 E-value=93 Score=28.49 Aligned_cols=46 Identities=15% Similarity=0.320 Sum_probs=21.2
Q ss_pred HHHHHHH-HHHHHHHHHHHHHhhhhcC-CCCcchhhHHHHHhhhcCcccc
Q 010992 426 DILVDIA-EDFVESITMFGCSLAKHRK-SDTLEAKDILVHLERNWNMTLP 473 (496)
Q Consensus 426 ELLLeIA-DDFVDsVvt~ACrLAKHRK-SdTLEvKDVQLhLERnWNI~IP 473 (496)
.+.++|| ++|+++++...- .|+.+ ....+||+=.+.|=+.|...|+
T Consensus 72 ~fh~evas~~Fl~el~kl~~--~k~~~~~~~~~Vk~kil~li~~W~~~f~ 119 (139)
T cd03567 72 RFHSEVGKFRFLNELIKLVS--PKYLGSRTSEKVKTKIIELLYSWTLELP 119 (139)
T ss_pred HHHHHHHhHHHHHHHHHHhc--cccCCCCCCHHHHHHHHHHHHHHHHHhc
Confidence 4455555 555555443220 11111 1123555555666666665553
No 276
>TIGR02903 spore_lon_C ATP-dependent protease, Lon family. Members of this protein family resemble the widely distributed ATP-dependent protease La, also called Lon and LonA. It resembles even more closely LonB, which is a LonA paralog found in genomes if and only if the species is capable of endospore formation (as in Bacillus subtilis, Clostridium tetani, and select other members of the Firmicutes) and expressed specifically in the forespore compartment. Members of this family are restricted to a subset of spore-forming species, and are very likely to participate in the program of endospore formation. We propose the designation LonC.
Probab=29.85 E-value=59 Score=35.90 Aligned_cols=66 Identities=18% Similarity=0.152 Sum_probs=43.8
Q ss_pred CCHHHHHHHHHhhCC--CCCCCHHHHHHHHHHHHHH--HHHHHHHHHHhhhhc--------CCCCcchhhHHHHHhhh
Q 010992 402 LTKRSIQELVNQIDP--SERLDPDVEDILVDIAEDF--VESITMFGCSLAKHR--------KSDTLEAKDILVHLERN 467 (496)
Q Consensus 402 LtKrKLqELVrqIDP--sesLDpDVEELLLeIADDF--VDsVvt~ACrLAKHR--------KSdTLEvKDVQLhLERn 467 (496)
+++..+.++++++-. +..|++++.++|.+.+.+- ..+++..+|.++.+| +...|+.+||.-+|++.
T Consensus 353 ls~edi~~Il~~~a~~~~v~ls~eal~~L~~ys~~gRraln~L~~~~~~~~~~~~~~~~~~~~~~I~~edv~~~l~~~ 430 (615)
T TIGR02903 353 LTPEDIALIVLNAAEKINVHLAAGVEELIARYTIEGRKAVNILADVYGYALYRAAEAGKENDKVTITQDDVYEVIQIS 430 (615)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHCCCcHHHHHHHHHHHHHHHHHHHHHhccCCCCeeECHHHHHHHhCCC
Confidence 567778888887633 2468999999999876443 113555555555333 33368889998888864
No 277
>cd06456 M3A_DCP_Oligopeptidase_A Peptidase family M3 dipeptidyl carboxypeptidase (DCP; Dcp II; peptidyl dipeptidase; EC 3.4.15.5). This metal-binding M3A family also includes oligopeptidase A (OpdA; EC 3.4.24.70) enzyme. DCP cleaves dipeptides off the C-termini of various peptides and proteins, the smallest substrate being N-blocked tripeptides and unblocked tetrapeptides. DCP from E. coli is inhibited by the anti-hypertensive drug captopril, an inhibitor of the mammalian angiotensin converting enzyme (ACE, also called peptidyl dipeptidase A). Oligopeptidase A (OpdA) may play a specific role in the degradation of signal peptides after they are released from precursor forms of secreted proteins. It can also cleave N-acetyl-L-Ala.
Probab=29.71 E-value=90 Score=32.88 Aligned_cols=65 Identities=18% Similarity=0.136 Sum_probs=35.4
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHH---HHHHhhhhcCC-CCcchhhHHHHHhhhcCccccCCCccccccc
Q 010992 418 ERLDPDVEDILVDIAEDFVESITM---FGCSLAKHRKS-DTLEAKDILVHLERNWNMTLPGFSGDEIKTF 483 (496)
Q Consensus 418 esLDpDVEELLLeIADDFVDsVvt---~ACrLAKHRKS-dTLEvKDVQLhLERnWNI~IPGFssDEIr~~ 483 (496)
.+=.++|+++|-+|++.-+.-+-. .--.++|.+.. +.|+.=|+.++.++.= -....+..++++.|
T Consensus 35 a~sp~~v~~Fl~~l~~~~~p~~~~e~~~L~~~~~~~~~~~~l~~wD~~yy~~~~~-~~~~~~d~~~l~~Y 103 (422)
T cd06456 35 AKSPEAVLEFLEDLAPKAKPQAKKELAELQAFAKEEGGEDELEPWDWAYYSEKLR-KEKYDLDEEELRPY 103 (422)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCHHHHHHHHHHHH-HHhcCCCHHHHhcc
Confidence 344455777777777765544433 12334443333 3588889988877532 12233455555555
No 278
>PF06576 DUF1133: Protein of unknown function (DUF1133); InterPro: IPR010557 This family consists of a number of hypothetical proteins from Escherichia coli O157:H7 and Salmonella typhi. The function of this family is unknown.
Probab=29.56 E-value=98 Score=30.34 Aligned_cols=50 Identities=26% Similarity=0.383 Sum_probs=37.8
Q ss_pred ccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHH---------------HHHHHHHHHHHHhhhhcC
Q 010992 400 RILTKRSIQELVNQIDPSERLDPDVEDILVDIAE---------------DFVESITMFGCSLAKHRK 451 (496)
Q Consensus 400 rILtKrKLqELVrqIDPsesLDpDVEELLLeIAD---------------DFVDsVvt~ACrLAKHRK 451 (496)
.-|+|.+|.+.++++-...--.+|.|.+|.||-+ -|||.||... |++|.+
T Consensus 53 ~kitKtaI~~aLr~mkKsGi~k~EL~~~~~eil~gK~kS~La~ctD~Eal~iDrVI~~v--L~~~~g 117 (176)
T PF06576_consen 53 KKITKTAINEALRRMKKSGISKPELEAFLREILNGKQKSWLAFCTDDEALFIDRVIGEV--LAEHPG 117 (176)
T ss_pred ccccHHHHHHHHHHHHHhcCCcHHHHHHHHHHhCcccccccceecchHHHHHHHHHHHH--HHhCcc
Confidence 3468999999999998888888888888888754 3888888764 344444
No 279
>PRK06256 biotin synthase; Validated
Probab=29.48 E-value=83 Score=31.21 Aligned_cols=45 Identities=20% Similarity=0.235 Sum_probs=18.5
Q ss_pred HHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhc
Q 010992 406 SIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHR 450 (496)
Q Consensus 406 KLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHR 450 (496)
.|.+|++++-.++.|+.|-...|++..++-++++...|-++-++.
T Consensus 6 ~~~~~~~~~~~g~~~~~~e~~~ll~~~~~~~~~L~~~A~~~r~~~ 50 (336)
T PRK06256 6 DILKLARKLLEGEGLTKEEALALLEIPDDDLLELLAAAYEVRKHF 50 (336)
T ss_pred HHHHHHHHHHcCCCCCHHHHHHHHcCChHHHHHHHHHHHHHHHHh
Confidence 344555555444444444222233332333444444444443333
No 280
>PRK10569 NAD(P)H-dependent FMN reductase; Provisional
Probab=29.45 E-value=48 Score=31.14 Aligned_cols=26 Identities=15% Similarity=0.362 Sum_probs=21.0
Q ss_pred hCCCCCCCHHHHHHHHHHHHHHHHHH
Q 010992 414 IDPSERLDPDVEDILVDIAEDFVESI 439 (496)
Q Consensus 414 IDPsesLDpDVEELLLeIADDFVDsV 439 (496)
.|.+..+|+++++.|-+++|+|++-+
T Consensus 147 ~d~~~~~d~~~~~rl~~~~~~~~~~~ 172 (191)
T PRK10569 147 YHHQPQFTPNLQTRLDEALETFWQAL 172 (191)
T ss_pred cccccccCHHHHHHHHHHHHHHHHHH
Confidence 45556779999999999999998643
No 281
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=29.34 E-value=1.4e+02 Score=28.46 Aligned_cols=62 Identities=11% Similarity=0.081 Sum_probs=33.8
Q ss_pred CCHHHHHHHHHhhC--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992 402 LTKRSIQELVNQID--PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLE 465 (496)
Q Consensus 402 LtKrKLqELVrqID--PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE 465 (496)
++...|.+.++.+- .+..+++++.+.|++.++--+..+++..-+++.. .+.|+.+||...+.
T Consensus 161 l~~~ei~~~l~~~~~~~~~~i~~~al~~l~~~~~gd~r~~~~~l~~~~~~--~~~it~~~v~~~~~ 224 (319)
T PRK00440 161 LKKEAVAERLRYIAENEGIEITDDALEAIYYVSEGDMRKAINALQAAAAT--GKEVTEEAVYKITG 224 (319)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHc--CCCCCHHHHHHHhC
Confidence 44555555555442 3456888888888887764444433333333332 24566666654443
No 282
>cd01016 TroA Metal binding protein TroA. These proteins have been shown to function as initial receptors in ABC transport of Zn2+ and possibly Fe3+ in many eubacterial species. The TroA proteins belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=29.34 E-value=66 Score=31.52 Aligned_cols=73 Identities=15% Similarity=0.247 Sum_probs=43.9
Q ss_pred CCHHHHHHHHHhhC-CCCCCCHHHHHHHHHHHHHHHHHHHHHHH----Hhhh--hcCCCCcchhhHHHHHhhhcCccccC
Q 010992 402 LTKRSIQELVNQID-PSERLDPDVEDILVDIAEDFVESITMFGC----SLAK--HRKSDTLEAKDILVHLERNWNMTLPG 474 (496)
Q Consensus 402 LtKrKLqELVrqID-PsesLDpDVEELLLeIADDFVDsVvt~AC----rLAK--HRKSdTLEvKDVQLhLERnWNI~IPG 474 (496)
|.-.....+++.|. .-.++|++-.+...+=++.|++.+-..-- ++++ .++...+..-|.--||.|.||+.+-|
T Consensus 105 ldp~~~~~~a~~I~~~L~~~dP~~~~~y~~N~~~~~~~L~~l~~~~~~~l~~~~~~~~~~~t~H~af~Y~~~~ygl~~~~ 184 (276)
T cd01016 105 FDVKLWKYAVKAVAEVLSEKLPEHKDEFQANSEAYVEELDSLDAYAKKKIAEIPEQQRVLVTAHDAFGYFGRAYGFEVKG 184 (276)
T ss_pred cCHHHHHHHHHHHHHHHHHHCcccHHHHHHHHHHHHHHHHHHHHHHHHHHhhCchhcCeEEEecCcHHHHHHHcCCeEec
Confidence 34555555555552 22356666666666666666666544333 3333 23344556678889999999998744
No 283
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=29.15 E-value=1.4e+02 Score=28.62 Aligned_cols=54 Identities=9% Similarity=0.132 Sum_probs=33.5
Q ss_pred cCCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhH
Q 010992 397 FGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDI 460 (496)
Q Consensus 397 ~~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDV 460 (496)
....+|++..+.+|+.++..+ |.+ .+-+|.+.|..-|...|.++. .+..++.||
T Consensus 14 ~~~~~l~~~~~~~l~~~~~~g---d~~---a~~~l~~~~~~~v~~~a~~~~----~~~~~aeDl 67 (258)
T PRK08215 14 SKLPVLKNEEMRELFERMQNG---DKE---AREKLINGNLRLVLSVIQRFN----NRGENVDDL 67 (258)
T ss_pred CCCCCCCHHHHHHHHHHHHcC---CHH---HHHHHHHHHHHHHHHHHHHHh----CCCCCHHHH
Confidence 344688999999999987522 333 344555555555555555543 344678888
No 284
>PF02965 Met_synt_B12: Vitamin B12 dependent methionine synthase, activation domain; InterPro: IPR004223 Vitamin B12 dependent methionine synthase 2.1.1.13 from EC (5-methyltetrahydrofolate--homocysteine S-methyltransferase) catalyses the conversion of 5-methyltetrahydrofolate and L-homocysteine to tetrahydrofolate and L-methionine as the final step in de novo methionine biosynthesis. The enzyme requires methylcobalamin as a cofactor. In humans, defects in this enzyme are the cause of autosomal recessive inherited methylcobalamin deficiency (CBLG), which causes mental retardation, macrocytic anemia and homocystinuria. Mild deficiencies in activity may result in mild hyperhomocysteinemia, and mutations in the enzyme may be involved in tumorigenesis. Vitamin B12 dependent methionine synthase is found in prokaryotes and eukaryotes, but in prokaryotes the cofactor is cobalamin. In Escherichia coli, methionine synthase is a large enzyme composed of four structurally and functionally distinct modules: the first two modules bind homocysteine and tetrahydrofolate, the third module binds the B12 cofactor (IPR003759 from INTERPRO, IPR006158 from INTERPRO), and the C-terminal module (activation domain) binds S-adenosylmethionine. The activation domain is essential for the reductive activation of the enzyme. During the catalytic cycle, the highly reactive cob(I)alamin intermediate can be oxidised to produce an inactive cob(II)alamin enzyme; the enzyme is then reactivated via reductive methylation by the activation domain []. The activation domain adopts an unusual alpha/beta fold.; GO: 0008705 methionine synthase activity, 0009086 methionine biosynthetic process, 0005622 intracellular; PDB: 1J6R_A 2O2K_B 3BUL_A 1K7Y_A 1MSK_A 3IV9_A 1K98_A 3IVA_A.
Probab=29.14 E-value=1.4e+02 Score=28.66 Aligned_cols=25 Identities=16% Similarity=0.312 Sum_probs=12.5
Q ss_pred HHHHHHH-HHHHHHHHHHHHHHHhhh
Q 010992 424 VEDILVD-IAEDFVESITMFGCSLAK 448 (496)
Q Consensus 424 VEELLLe-IADDFVDsVvt~ACrLAK 448 (496)
.+.+|++ |||.++|.+++...+.-+
T Consensus 96 ~~~~~ldala~~~~Ea~~e~~~~~ir 121 (211)
T PF02965_consen 96 YKAFLLDALASRLAEALAEYLHEEIR 121 (211)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444444 555555555555444443
No 285
>PRK13940 glutamyl-tRNA reductase; Provisional
Probab=29.02 E-value=1.3e+02 Score=31.93 Aligned_cols=63 Identities=17% Similarity=0.292 Sum_probs=33.9
Q ss_pred HHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccc
Q 010992 404 KRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTL 472 (496)
Q Consensus 404 KrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~I 472 (496)
++.|..++++++ .+++.++.|-+++..+++.+++.-....|.-..+- +. ++.-.|++-||+.|
T Consensus 350 ~~el~r~~~~l~----~~~~~~~~i~~~~~~~~~kllh~P~~~lk~~~~~~-~~-~~~~~~~~lf~l~~ 412 (414)
T PRK13940 350 DLSLEKSLAKIR----NGKDAEEIIKRFAYEIKKKVLHYPVVGMKEASKQG-RS-DCLVCMKRMFGLNV 412 (414)
T ss_pred HHHHHHHHhhcC----CCccHHHHHHHHHHHHHHHHHHHHHHHHHHhhccC-hH-HHHHHHHHHhCCCC
Confidence 334555555543 24555555555666666666666555555422221 12 33357888888766
No 286
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=29.00 E-value=1.5e+02 Score=30.64 Aligned_cols=65 Identities=15% Similarity=0.173 Sum_probs=42.0
Q ss_pred CHHHHHHHHHhhCCCCCCCHH-HHHHHHHHHHHH----HHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992 403 TKRSIQELVNQIDPSERLDPD-VEDILVDIAEDF----VESITMFGCSLAKHRKSDTLEAKDILVHLERN 467 (496)
Q Consensus 403 tKrKLqELVrqIDPsesLDpD-VEELLLeIADDF----VDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn 467 (496)
+.....++++..-....++++ ..+.|.++++.| |..++..|+.+|-.++.+.|+.+|+.-.+++.
T Consensus 303 ~~~~R~~Il~~~~~~~~~~~~~~~~~la~~t~g~sgadl~~l~~eA~~~a~~~~~~~i~~~d~~~A~~~~ 372 (389)
T PRK03992 303 DEEGRLEILKIHTRKMNLADDVDLEELAELTEGASGADLKAICTEAGMFAIRDDRTEVTMEDFLKAIEKV 372 (389)
T ss_pred CHHHHHHHHHHHhccCCCCCcCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH
Confidence 444455555555444445432 223344444433 66788888888888888899999998888874
No 287
>PRK08699 DNA polymerase III subunit delta'; Validated
Probab=28.92 E-value=1.9e+02 Score=29.59 Aligned_cols=68 Identities=12% Similarity=0.204 Sum_probs=46.5
Q ss_pred ccCCHHHHHHHHHhh--------------CCCCCCCHHHHHHHHHHHHHHH------------HHHHHHHHHhhhhcCCC
Q 010992 400 RILTKRSIQELVNQI--------------DPSERLDPDVEDILVDIAEDFV------------ESITMFGCSLAKHRKSD 453 (496)
Q Consensus 400 rILtKrKLqELVrqI--------------DPsesLDpDVEELLLeIADDFV------------DsVvt~ACrLAKHRKSd 453 (496)
..|..+.+++|++.+ |+-+.||.+....|+++.+++. +.|...-..-|.+=.-.
T Consensus 91 ~~I~id~iR~l~~~~~~~p~~~~~kV~iiEp~~~Ld~~a~naLLk~LEep~~~~~~Ilvth~~~~ll~ti~SRc~~~~~~ 170 (325)
T PRK08699 91 LQIKIDAVREIIDNVYLTSVRGGLRVILIHPAESMNLQAANSLLKVLEEPPPQVVFLLVSHAADKVLPTIKSRCRKMVLP 170 (325)
T ss_pred CCcCHHHHHHHHHHHhhCcccCCceEEEEechhhCCHHHHHHHHHHHHhCcCCCEEEEEeCChHhChHHHHHHhhhhcCC
Confidence 458888888888776 4567899999999999999873 23332222233333445
Q ss_pred CcchhhHHHHHhhh
Q 010992 454 TLEAKDILVHLERN 467 (496)
Q Consensus 454 TLEvKDVQLhLERn 467 (496)
.++..|+.-.|+++
T Consensus 171 ~~~~~~~~~~L~~~ 184 (325)
T PRK08699 171 APSHEEALAYLRER 184 (325)
T ss_pred CCCHHHHHHHHHhc
Confidence 56777777777764
No 288
>PRK05708 2-dehydropantoate 2-reductase; Provisional
Probab=28.85 E-value=1e+02 Score=30.60 Aligned_cols=50 Identities=6% Similarity=0.094 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCcccc
Q 010992 424 VEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLP 473 (496)
Q Consensus 424 VEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IP 473 (496)
+++.+.++.+.+-+.-.++.-.+.|.|+.|.=.+--..+.+-|++|+.+|
T Consensus 235 ~~~~~~~~~~~~~~~~sSM~qD~~~gR~tEid~i~G~vvr~a~~~Gv~~P 284 (305)
T PRK05708 235 LHEEVQRVIQATAANYSSMYQDVRAGRRTEISYLLGYACRAADRHGLPLP 284 (305)
T ss_pred HHHHHHHHHHhccCCCcHHHHHHHcCCceeehhhhhHHHHHHHHcCCCCc
Confidence 44444444443333333444445555554422222334555666777665
No 289
>PF01297 TroA: Periplasmic solute binding protein family; InterPro: IPR006127 This is a family of ABC transporter metal-binding lipoproteins. An example is the periplasmic zinc-binding protein TroA P96116 from SWISSPROT that interacts with an ATP-binding cassette transport system in Treponema pallidum and plays a role in the transport of zinc across the cytoplasmic membrane. Related proteins are found in both Gram-positive and Gram-negative bacteria. ; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2PS9_A 2PS0_A 2OSV_A 2OGW_A 2PS3_A 2PRS_B 3MFQ_C 3GI1_B 2OV3_A 1PQ4_A ....
Probab=28.81 E-value=32 Score=32.61 Aligned_cols=76 Identities=17% Similarity=0.286 Sum_probs=52.0
Q ss_pred cCCHHHHHHHHHhhCC-CCCCCHHHHHHHHHHHHHHHHHHHHHHH----HhhhhcCCCCcchhhHHHHHhhhcCccccCC
Q 010992 401 ILTKRSIQELVNQIDP-SERLDPDVEDILVDIAEDFVESITMFGC----SLAKHRKSDTLEAKDILVHLERNWNMTLPGF 475 (496)
Q Consensus 401 ILtKrKLqELVrqIDP-sesLDpDVEELLLeIADDFVDsVvt~AC----rLAKHRKSdTLEvKDVQLhLERnWNI~IPGF 475 (496)
-|.-..+..+++.|.. -.++|++-++...+=++.|++.+-...- .+++.++...|..-|.--||.+.||+.+-|+
T Consensus 95 Wldp~~~~~~~~~Ia~~L~~~~P~~~~~y~~N~~~~~~~L~~l~~~~~~~~~~~~~~~~v~~h~~~~Y~~~~~gl~~~~~ 174 (256)
T PF01297_consen 95 WLDPENAKKMAEAIADALSELDPANKDYYEKNAEKYLKELDELDAEIKEKLAKLPGRPVVVYHDAFQYFAKRYGLKVIGV 174 (256)
T ss_dssp GGSHHHHHHHHHHHHHHHHHHTGGGHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSGGEEEEEESTTHHHHHHTT-EEEEE
T ss_pred HHHHHHHHHHHHHHHHHHHHhCccchHHHHHHHHHHHHHHHHHHHHHHHHhhcccCCeEEEEChHHHHHHHhcCCceeee
Confidence 3466666666666633 2357777777777777777766654443 4566666677889999999999999987654
Q ss_pred C
Q 010992 476 S 476 (496)
Q Consensus 476 s 476 (496)
-
T Consensus 175 ~ 175 (256)
T PF01297_consen 175 I 175 (256)
T ss_dssp E
T ss_pred e
Confidence 4
No 290
>PRK14950 DNA polymerase III subunits gamma and tau; Provisional
Probab=28.79 E-value=98 Score=33.84 Aligned_cols=64 Identities=11% Similarity=0.105 Sum_probs=40.0
Q ss_pred CCHHHHHHHHHhhC--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992 402 LTKRSIQELVNQID--PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER 466 (496)
Q Consensus 402 LtKrKLqELVrqID--PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER 466 (496)
++...|.+.++++- -+..||+++.++|+++++.=+..++...-+|+.+. .+.|+.+||+-.+.+
T Consensus 179 l~~~el~~~L~~~a~~egl~i~~eal~~La~~s~Gdlr~al~~LekL~~y~-~~~It~e~V~~ll~~ 244 (585)
T PRK14950 179 HSVADMAAHLRKIAAAEGINLEPGALEAIARAATGSMRDAENLLQQLATTY-GGEISLSQVQSLLGI 244 (585)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhc-CCCCCHHHHHHHhcC
Confidence 34555666666552 24568999988888888754445555544555543 345788887655544
No 291
>CHL00059 atpA ATP synthase CF1 alpha subunit
Probab=28.72 E-value=88 Score=34.40 Aligned_cols=31 Identities=13% Similarity=0.295 Sum_probs=21.8
Q ss_pred HHHHHhhCCCCCCCHHHHHHHHHHHHHHHHH
Q 010992 408 QELVNQIDPSERLDPDVEDILVDIAEDFVES 438 (496)
Q Consensus 408 qELVrqIDPsesLDpDVEELLLeIADDFVDs 438 (496)
.+++++|+....|+++.++.|.++..+|++.
T Consensus 448 ~~~~~~i~~~~~~~~~~~~~l~~~~~~~~~~ 478 (485)
T CHL00059 448 PQFQEIISSTKTFTEEAEALLKEAIQEQLEL 478 (485)
T ss_pred HHHHHHHHhcCCCCHHHHHHHHHHHHHHHHH
Confidence 3555666666777777777777777777665
No 292
>smart00337 BCL BCL (B-Cell lymphoma); contains BH1, BH2 regions. (BH1, BH2, (BH3 (one helix only)) and not BH4(one helix only)). Involved in apoptosis regulation
Probab=28.63 E-value=1e+02 Score=26.25 Aligned_cols=43 Identities=14% Similarity=0.258 Sum_probs=29.6
Q ss_pred HHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHH----------HHHHHHHhhhhcC
Q 010992 406 SIQELVNQIDPSERLDPDVEDILVDIAEDFVES----------ITMFGCSLAKHRK 451 (496)
Q Consensus 406 KLqELVrqIDPsesLDpDVEELLLeIADDFVDs----------Vvt~ACrLAKHRK 451 (496)
.+.+|+++++- =++++.+.+.++|++..+| ++.|+..||+|-.
T Consensus 15 ~f~~~~~~l~~---~~~~~~~~f~~Va~~lf~dg~inWGRIval~~F~~~la~~~~ 67 (100)
T smart00337 15 AFSSFSAQLHV---TPGTAIELFGEVATELFSDGNINWGRVVALLSFGGALAVKLV 67 (100)
T ss_pred HHHHHHHHhCC---CcccHHHHHHHHHHHHHccCCCCHHHHHHHHHHHHHHHHHHH
Confidence 34455555443 2456788899999887765 5788999998754
No 293
>cd03561 VHS VHS domain family; The VHS domain is present in Vps27 (Vacuolar Protein Sorting), Hrs (Hepatocyte growth factor-regulated tyrosine kinase substrate) and STAM (Signal Transducing Adaptor Molecule). It has a superhelical structure similar to that of the ARM (Armadillo) repeats and is present at the N-termini of proteins involved in intracellular membrane trafficking. There are four general groups of VHS domain containing proteins based on their association with other domains. The first group consists of proteins of the STAM/EAST/Hbp family which has the domain composition VHS-SH3-ITAM. The second consists of proteins with a FYVE domain C-terminal to VHS. The third consists of GGA proteins with a domain composition VHS-GAT (GGA and TOM)-GAE (gamma-adaptin ear) domain. The fourth consists of proteins with a VHS domain alone or with domains other than those mentioned above. In GGA proteins, VHS domains are involved in cargo recognition in trans-Golgi, thereby having a general me
Probab=28.49 E-value=1.2e+02 Score=26.81 Aligned_cols=47 Identities=17% Similarity=0.377 Sum_probs=32.5
Q ss_pred HHHHHHHH-HHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCCC
Q 010992 426 DILVDIAE-DFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFS 476 (496)
Q Consensus 426 ELLLeIAD-DFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGFs 476 (496)
.+..+||+ +|+++++ ++++.+...-.++|+-.+.|=.+|...|++..
T Consensus 71 ~f~~~i~s~~fl~~l~----~l~~~~~~~~~~Vk~kil~ll~~W~~~f~~~~ 118 (133)
T cd03561 71 PFHLQVADKEFLLELV----KIAKNSPKYDPKVREKALELILAWSESFGGHS 118 (133)
T ss_pred HHHHHHhhHHHHHHHH----HHhCCCCCCCHHHHHHHHHHHHHHHHHhcCCC
Confidence 36788888 8888854 34443323335788888888889998887653
No 294
>cd04400 RhoGAP_fBEM3 RhoGAP_fBEM3: RhoGAP (GTPase-activator [GAP] protein for Rho-like small GTPases) domain of fungal BEM3-like proteins. Bem3 is a GAP protein of Cdc42, and is specifically involved in the control of the initial assembly of the septin ring in yeast bud formation. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=28.44 E-value=2.2e+02 Score=26.45 Aligned_cols=34 Identities=6% Similarity=0.216 Sum_probs=24.8
Q ss_pred HHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhc
Q 010992 435 FVESITMFGCSLAKHRKSDTLEAKDILVHLERNW 468 (496)
Q Consensus 435 FVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnW 468 (496)
.+.-++.+-.++|+|.+.+..+++.+..++--+.
T Consensus 136 ~L~~L~~~L~~V~~~s~~NkM~~~NLa~vf~P~L 169 (190)
T cd04400 136 LLYVLFSFLRKIIEHSDVNKMNLRNVCIVFSPTL 169 (190)
T ss_pred HHHHHHHHHHHHHHhccccCCChHHhhhhcCCCC
Confidence 4455777888888888888888888776655443
No 295
>smart00047 LYZ2 Lysozyme subfamily 2. Eubacterial enzymes distantly related to eukaryotic lysozymes.
Probab=28.38 E-value=77 Score=28.97 Aligned_cols=40 Identities=15% Similarity=0.062 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccc
Q 010992 432 AEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTL 472 (496)
Q Consensus 432 ADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~I 472 (496)
.++||+.|+..|.++++.-+--. .+-=-|.+||-.||-..
T Consensus 8 ~~~fi~~~~~~A~~~~~~~gi~~-Sv~iAQAiLESgwG~S~ 47 (147)
T smart00047 8 TLEFVGKIFNEAQKAYQINGVYP-SILIAQAALESGWGTSK 47 (147)
T ss_pred HHHHHHHHHHHHHHHHHHcCCCH-HHHHHHHHHHcCCCCCC
Confidence 46899999999999998766431 23334889999999654
No 296
>TIGR00706 SppA_dom signal peptide peptidase SppA, 36K type. The member of this family from Bacillus subtilis was shown to have properties consistent with a role in degrading signal peptides after cleavage from precursor proteins, although it was not demonstrated conclusively.
Probab=28.35 E-value=1.5e+02 Score=27.88 Aligned_cols=58 Identities=24% Similarity=0.464 Sum_probs=36.0
Q ss_pred CCHHHHHHHHHhhC----------------CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992 402 LTKRSIQELVNQID----------------PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLE 465 (496)
Q Consensus 402 LtKrKLqELVrqID----------------PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE 465 (496)
+..-.+.+|+.+++ +...++++..|.+..+.|+.-+..+. .+|++|| ++.+++.-.++
T Consensus 101 ~~~~~~~~~l~k~Gv~~~~~~~g~~K~~~~~~~~~s~~~~e~~~~~l~~~~~~f~~---~va~~R~---~~~~~~~~~~~ 174 (207)
T TIGR00706 101 LQGANVEKLYEKLGIEFEVIKSGEYKDIGSPTRELTPEERDILQNLVNESYEQFVQ---VVAKGRN---LPVEDVKKFAD 174 (207)
T ss_pred EecCCHHHHHHhCCceEEEEEcCCCcCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH---HHHhcCC---CCHHHHHHHhc
Confidence 33444777777663 22357888777777777766666554 5689998 44555543343
No 297
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=28.33 E-value=1.5e+02 Score=29.30 Aligned_cols=64 Identities=14% Similarity=0.188 Sum_probs=43.2
Q ss_pred CCHHHHHHHHHhh--CCCCCCCHHHHHHHHHHHHH---HHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992 402 LTKRSIQELVNQI--DPSERLDPDVEDILVDIAED---FVESITMFGCSLAKHRKSDTLEAKDILVHLERN 467 (496)
Q Consensus 402 LtKrKLqELVrqI--DPsesLDpDVEELLLeIADD---FVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn 467 (496)
+..+.|.++|++. .-+.+||+++.++|++.+.. -+.+-++.-|.++. +..+|+.+||.-.+...
T Consensus 142 ~~~~~l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~--~~~~It~edV~~lv~~~ 210 (343)
T PRK06585 142 DDERDLARLIDDELAEAGLRITPDARALLVALLGGDRLASRNEIEKLALYAH--GKGEITLDDVRAVVGDA 210 (343)
T ss_pred CCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcC--CCCCCCHHHHHHHhCCc
Confidence 4566677777766 34678999999999998886 44444554444432 23469999997665543
No 298
>PRK14903 16S rRNA methyltransferase B; Provisional
Probab=28.31 E-value=1.1e+02 Score=32.23 Aligned_cols=64 Identities=20% Similarity=0.194 Sum_probs=38.6
Q ss_pred CHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHH--HHHH-----HHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992 403 TKRSIQELVNQIDPSERLDPDVEDILVDIAED--FVES-----ITMFGCSLAKHRKSDTLEAKDILVHLERN 467 (496)
Q Consensus 403 tKrKLqELVrqIDPsesLDpDVEELLLeIADD--FVDs-----Vvt~ACrLAKHRKSdTLEvKDVQLhLERn 467 (496)
.+..|+.+|+++-.+.+||+.+..+|.-=+.+ |.++ |++.++.|||.++...+ |.-|...+.|+
T Consensus 52 ~~~~lD~~i~~~~~~~~l~~~~r~iLr~~~yel~~~~~~p~~aavneaV~lak~~~~~~f-VNaVLr~~~r~ 122 (431)
T PRK14903 52 KEELLDWYINQLLKKKDIPPAVRVALRMGAYQLLFMNSVPDYAAVSETVKLVKNENFKKL-VNAVLRRLRTV 122 (431)
T ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHhccCCCcceeHHHHHHHHhccchHHH-HHHHHHHHHHh
Confidence 35566777777644447888887766543443 3344 88889999987643322 44444444443
No 299
>PRK12711 flgJ flagellar rod assembly protein/muramidase FlgJ; Reviewed
Probab=28.26 E-value=62 Score=34.94 Aligned_cols=42 Identities=26% Similarity=0.257 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccC
Q 010992 432 AEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPG 474 (496)
Q Consensus 432 ADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPG 474 (496)
-++||++|...|.+++|.-+-.. ++-=-|-+||-.||-..-+
T Consensus 215 ~~~FI~~Iap~Aqkvak~yGI~P-SV~IAQAALESGWG~S~LA 256 (392)
T PRK12711 215 PEGFVAKIWTHAQKAARELGVDP-RALVAQAALETGWGRRGIG 256 (392)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCH-HHHHHHHHHHccCCccccc
Confidence 38999999999999999888663 3333589999999976643
No 300
>cd01049 RNRR2 Ribonucleotide Reductase, R2/beta subunit, ferritin-like diiron-binding domain. Ribonucleotide Reductase, R2/beta subunit (RNRR2) is a member of a broad superfamily of ferritin-like diiron-carboxylate proteins. The RNR protein catalyzes the conversion of ribonucleotides to deoxyribonucleotides and is found in all eukaryotes, many prokaryotes, several viruses, and few archaea. The catalytically active form of RNR is a proposed alpha2-beta2 tetramer. The homodimeric alpha subunit (R1) contains the active site and redox active cysteines as well as the allosteric binding sites. The beta subunit (R2) contains a diiron cluster that, in its reduced state, reacts with dioxygen to form a stable tyrosyl radical and a diiron(III) cluster. This essential tyrosyl radical is proposed to generate a thiyl radical, located on a cysteine residue in the R1 active site that initiates ribonucleotide reduction. The beta subunit is composed of 10-13 helices, the 8 longest helices form an alpha-
Probab=28.22 E-value=1.9e+02 Score=27.98 Aligned_cols=79 Identities=18% Similarity=0.171 Sum_probs=52.7
Q ss_pred CCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCCCccccc
Q 010992 402 LTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGDEIK 481 (496)
Q Consensus 402 LtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGFssDEIr 481 (496)
+.-..+++|+++.+ +...+++.+.+.+|+++-|+....++-.+-+ -+-..++.++|.=+++-.-|.++=.+|-+.+-
T Consensus 196 ~~~~~~~~l~~~~~--~~~~~~~~~~v~~l~~~av~~E~~~~~~~~~-~~~~g~~~~~~~~yi~y~an~~l~~lG~~~~f 272 (288)
T cd01049 196 FACLLIRELLNENP--ELFTEEFKEEVYELIKEAVELEKEFARDLLP-DGILGLNKEDMKQYIEYVANRRLENLGLEKLF 272 (288)
T ss_pred HHHHHHHHHHHhCc--cccchhHHHHHHHHHHHHHHHHHHHHHHhcC-CCCCCcCHHHHHHHHHHHHHHHHHHCCCCCCC
Confidence 34566777777643 3445566777777777777666655544443 23566889999989988888888777776554
Q ss_pred cc
Q 010992 482 TF 483 (496)
Q Consensus 482 ~~ 483 (496)
..
T Consensus 273 ~~ 274 (288)
T cd01049 273 NV 274 (288)
T ss_pred CC
Confidence 43
No 301
>PF00237 Ribosomal_L22: Ribosomal protein L22p/L17e; InterPro: IPR001063 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 L22 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L22 is known to bind 23S rRNA. It belongs to a family of ribosomal proteins which includes: bacterial L22; algal and plant chloroplast L22 (in legumes L22 is encoded in the nucleus instead of the chloroplast); cyanelle L22; archaebacterial L22; mammalian L17; plant L17 and yeast YL17.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3CD6_R 1Q7Y_S 1VQ6_R 1YI2_R 1QVF_Q 3CCR_R 3CCU_R 3CCL_R 1YJ9_R 3CCQ_R ....
Probab=28.18 E-value=1.5e+02 Score=25.27 Aligned_cols=45 Identities=13% Similarity=0.305 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHhhCCCCCCCHHHHHHHHHH------HHHHHHHHHHHHHHhhh-hcC
Q 010992 402 LTKRSIQELVNQIDPSERLDPDVEDILVDI------AEDFVESITMFGCSLAK-HRK 451 (496)
Q Consensus 402 LtKrKLqELVrqIDPsesLDpDVEELLLeI------ADDFVDsVvt~ACrLAK-HRK 451 (496)
++-+|+.++++.|-+ .. |+|++..| +-.||.+++..|...|+ +.+
T Consensus 8 ~S~kk~~~v~~~Irg-~~----v~~A~~~L~~~~~k~a~~i~k~L~~a~~nA~~~~g 59 (105)
T PF00237_consen 8 ISPKKLREVARLIRG-MS----VDEAIAQLKFVPKKAAKFILKLLKSAIANAENNKG 59 (105)
T ss_dssp S-HHHHHHHHHHHTT-SB----HHHHHHHHHHHSSHHHHHHHHHHHHHHHHHHHHCT
T ss_pred CCHHHHHHHHHHHcC-CC----HHHHHHHHHhCcHHHHHHHHhhHHHHHhhcccccc
Confidence 567889999999843 22 33333333 45899999999999999 444
No 302
>PRK00199 ihfB integration host factor subunit beta; Reviewed
Probab=28.16 E-value=20 Score=29.82 Aligned_cols=20 Identities=20% Similarity=0.323 Sum_probs=13.4
Q ss_pred HHhhhcCccccCCCcccccc
Q 010992 463 HLERNWNMTLPGFSGDEIKT 482 (496)
Q Consensus 463 hLERnWNI~IPGFssDEIr~ 482 (496)
+|++.+.+.|+|||.=+++.
T Consensus 36 ~L~~g~~V~l~gfG~F~~~~ 55 (94)
T PRK00199 36 ALARGDRIEIRGFGSFSLHY 55 (94)
T ss_pred HHHcCCeEEEcCCEEEEEEE
Confidence 34666677888888766654
No 303
>PRK05720 mtnA methylthioribose-1-phosphate isomerase; Reviewed
Probab=28.16 E-value=1.1e+02 Score=32.00 Aligned_cols=29 Identities=14% Similarity=0.157 Sum_probs=24.0
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 010992 421 DPDVEDILVDIAEDFVESITMFGCSLAKH 449 (496)
Q Consensus 421 DpDVEELLLeIADDFVDsVvt~ACrLAKH 449 (496)
.+++.+.|++-|++|+++.+...-++++|
T Consensus 111 ~~~~~~~l~~~a~~~~~e~~~~~~~I~~~ 139 (344)
T PRK05720 111 GAERKAALEEEAIEIHEEDVEINRAIGEH 139 (344)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46788999999999999998766666665
No 304
>PHA02102 hypothetical protein
Probab=28.11 E-value=49 Score=28.15 Aligned_cols=35 Identities=17% Similarity=0.200 Sum_probs=26.4
Q ss_pred HHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCCC
Q 010992 436 VESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFS 476 (496)
Q Consensus 436 VDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGFs 476 (496)
++.+++.|..|+|.- +|+||+ .-|.+||+.|-+++
T Consensus 4 sneLvekA~eLqkLl----~eV~dl--Ase~~yGvein~~n 38 (72)
T PHA02102 4 SNELVEKALELQKLL----KEVKDL--ASEQDYGVEINDDN 38 (72)
T ss_pred hHHHHHHHHHHHHHH----HHHHHH--hhhhccceeeCCCC
Confidence 456677788888865 367775 67899999998874
No 305
>COG4749 Uncharacterized protein conserved in archaea [Function unknown]
Probab=28.10 E-value=62 Score=31.85 Aligned_cols=77 Identities=16% Similarity=0.340 Sum_probs=47.6
Q ss_pred CCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccc--cCCCccc
Q 010992 402 LTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTL--PGFSGDE 479 (496)
Q Consensus 402 LtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~I--PGFssDE 479 (496)
-+.++...-|.+|-- ..||++-||... +.+..+|||+-.+.++-+.-++..|.-.|..-.||+--++.+ +.|+.++
T Consensus 9 Ysq~Rw~NWl~r~rE-~elde~~ee~~~-vf~nm~dDViiAclki~~a~~~~~isk~~Av~ele~Ird~vlae~df~dEd 86 (196)
T COG4749 9 YSQSRWSNWLNRIRE-TELDEDNEETFA-VFDNMLDDVIIACLKIIRAVKEREISKADAVKELEKIRDLVLAEHDFGDED 86 (196)
T ss_pred HHHHHHHHHHHHHHH-hhcCCcchHHHH-HHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHhhhccCCCCchHH
Confidence 345556666666633 367777666554 666667777776666655555555555566666777666665 5666554
Q ss_pred c
Q 010992 480 I 480 (496)
Q Consensus 480 I 480 (496)
+
T Consensus 87 k 87 (196)
T COG4749 87 K 87 (196)
T ss_pred H
Confidence 3
No 306
>PRK14963 DNA polymerase III subunits gamma and tau; Provisional
Probab=28.07 E-value=1.1e+02 Score=33.35 Aligned_cols=67 Identities=12% Similarity=0.123 Sum_probs=47.4
Q ss_pred cCCHHHHHHHHHhhC--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcC
Q 010992 401 ILTKRSIQELVNQID--PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWN 469 (496)
Q Consensus 401 ILtKrKLqELVrqID--PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWN 469 (496)
-|+...|.++|++|- .+..+|+++.++|.++++.-+.++++..=+++.. .+.|+..||.-.+...|.
T Consensus 174 ~ls~~el~~~L~~i~~~egi~i~~~Al~~ia~~s~GdlR~aln~Lekl~~~--~~~It~~~V~~~l~~~~~ 242 (504)
T PRK14963 174 RLTEEEIAGKLRRLLEAEGREAEPEALQLVARLADGAMRDAESLLERLLAL--GTPVTRKQVEEALGLPPQ 242 (504)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhc--CCCCCHHHHHHHHCCCcH
Confidence 467888888887763 3567899999999999987776666544444333 236888888777666654
No 307
>KOG0406 consensus Glutathione S-transferase [Posttranslational modification, protein turnover, chaperones]
Probab=28.07 E-value=1.2e+02 Score=30.50 Aligned_cols=59 Identities=15% Similarity=0.222 Sum_probs=35.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhh-cCCCCc-----chhhHHHHHhhhcCccccCCCcccc
Q 010992 422 PDVEDILVDIAEDFVESITMFGCSLAKH-RKSDTL-----EAKDILVHLERNWNMTLPGFSGDEI 480 (496)
Q Consensus 422 pDVEELLLeIADDFVDsVvt~ACrLAKH-RKSdTL-----EvKDVQLhLERnWNI~IPGFssDEI 480 (496)
|--+.+..++--+|||+++..++....- ++.+.. |+..+.-+||++++-.=+.|+++.+
T Consensus 93 DPy~Ra~arfwa~~id~~~~~~~~~~~~~~~~e~~~~~~~e~~e~l~~lE~el~k~k~~fgG~~~ 157 (231)
T KOG0406|consen 93 DPYERAQARFWAEYIDKKVFFVGRFVVAAKGGEEQEAAKEELREALKVLEEELGKGKDFFGGETI 157 (231)
T ss_pred CHHHHHHHHHHHHHHHhHHHHHHHHHHhhcCchHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCCc
Confidence 3356666667777777666544443332 222222 3677788899998866667777543
No 308
>COG2766 PrkA Putative Ser protein kinase [Signal transduction mechanisms]
Probab=27.98 E-value=83 Score=35.84 Aligned_cols=55 Identities=16% Similarity=0.258 Sum_probs=42.7
Q ss_pred CCcCCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcc
Q 010992 395 DEFGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLE 456 (496)
Q Consensus 395 ~e~~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLE 456 (496)
+..++++++++.|..++++|..-.-|+.+ -.+||-++|+.++.+.=.||+...++
T Consensus 524 D~~TGee~~pd~le~~L~~iEe~~Gis~d-------a~kdFR~eiv~~~~~A~a~r~G~~~d 578 (649)
T COG2766 524 DPATGEELNPDALEKELRSIEEQAGISND-------APKDFRNEIVNFVLRARARRNGKNPD 578 (649)
T ss_pred CcccccccCccHHHHHHHHHHHhcCCCcc-------chHHHHHHHHHHHHHHHHHhcCCCCC
Confidence 34788899999999999999887778877 57899999999999744455344333
No 309
>KOG2005 consensus 26S proteasome regulatory complex, subunit RPN1/PSMD2 [Posttranslational modification, protein turnover, chaperones]
Probab=27.96 E-value=33 Score=39.66 Aligned_cols=94 Identities=19% Similarity=0.300 Sum_probs=47.9
Q ss_pred cCCHHHHHHHHHhhCC---CCCCCHHHHHHHHHHH-----HHHHHHHH-HHHHHhh----hhc-CCCCcchhhHHHHHhh
Q 010992 401 ILTKRSIQELVNQIDP---SERLDPDVEDILVDIA-----EDFVESIT-MFGCSLA----KHR-KSDTLEAKDILVHLER 466 (496)
Q Consensus 401 ILtKrKLqELVrqIDP---sesLDpDVEELLLeIA-----DDFVDsVv-t~ACrLA----KHR-KSdTLEvKDVQLhLER 466 (496)
.-+|.+|.+|+++|=+ +-.-+-|+.|+|+||- -+|||..- .+-|.+- +.- +-+.+-+.|+.+-+=+
T Consensus 171 ~~~~~dl~~l~~~iV~f~mkHNAE~eAiDlL~Eve~id~l~~~Vd~~n~~RvclYl~sc~~~lP~Pdd~~ll~~a~~IYl 250 (878)
T KOG2005|consen 171 APSKADLLDLVQEIVPFHMKHNAEFEAIDLLMEVEGIDLLLDYVDEHNYQRVCLYLTSCVPLLPGPDDVALLRTALKIYL 250 (878)
T ss_pred ccchHHHHHHHHHHHHHHHhccchhHHHHHHHHhhhHhHHHHHhhhhhHHHHHHHHHHHhhcCCCchhhHHHHHHHHHHH
Confidence 3478999999999954 2345667777777653 35555432 2223221 111 1122224444333333
Q ss_pred hcCcc---c-cCCCcccccccCCcccccCCCC
Q 010992 467 NWNMT---L-PGFSGDEIKTFRKPVRIVTDPI 494 (496)
Q Consensus 467 nWNI~---I-PGFssDEIr~~rk~~~~~~d~~ 494 (496)
.||-. | -.+--|+.+-.|..+..|.||.
T Consensus 251 Kf~~~~~al~~ai~l~~~~~v~~vf~s~~D~~ 282 (878)
T KOG2005|consen 251 KFNEYPRALVGAIRLDDMKEVKEVFTSCTDPL 282 (878)
T ss_pred HHHHhHHHHHHHHhcCcHHHHHHHHHhccCHH
Confidence 33311 0 1112356666677777777763
No 310
>PF01385 OrfB_IS605: Probable transposase; InterPro: IPR001959 This entry represents a conserved region of a probable transposase family, which is found in a number of uncharacterised bacterial proteins. A novel insertion sequence (IS)-like element of the Bacillus PS3 (Thermophilic bacterium PS-3) that promotes expression of the alanine carrier protein-encoding gene belongs to this entry, including IS891 [], IS1136 [], and IS1341 []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=27.86 E-value=77 Score=28.47 Aligned_cols=35 Identities=14% Similarity=0.172 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhH
Q 010992 426 DILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDI 460 (496)
Q Consensus 426 ELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDV 460 (496)
+=+..+.+||+..|+..-+..|...+-++|.++|+
T Consensus 189 ~k~~~~~~d~~hk~s~~iV~~~~~~~ve~l~~~~l 223 (227)
T PF01385_consen 189 RKIRNRRKDFLHKVSKKIVKEADEIGVEDLVVEDL 223 (227)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCeEeeCccEeCCC
Confidence 34457789999999999999999999999999987
No 311
>PRK08084 DNA replication initiation factor; Provisional
Probab=27.83 E-value=2.6e+02 Score=26.65 Aligned_cols=48 Identities=13% Similarity=-0.059 Sum_probs=26.9
Q ss_pred CCCCCCHHHHHHHHHHHH-H--HHHHHHHHHHHhhhhcCCCCcchhhHHHHH
Q 010992 416 PSERLDPDVEDILVDIAE-D--FVESITMFGCSLAKHRKSDTLEAKDILVHL 464 (496)
Q Consensus 416 PsesLDpDVEELLLeIAD-D--FVDsVvt~ACrLAKHRKSdTLEvKDVQLhL 464 (496)
-+..|++||.+.|++-++ | -+..+++..-+.+..+|. .|++..|+-+|
T Consensus 183 ~~~~l~~~v~~~L~~~~~~d~r~l~~~l~~l~~~~l~~~~-~it~~~~k~~l 233 (235)
T PRK08084 183 RGFELPEDVGRFLLKRLDREMRTLFMTLDQLDRASITAQR-KLTIPFVKEIL 233 (235)
T ss_pred cCCCCCHHHHHHHHHhhcCCHHHHHHHHHHHHHHHHhcCC-CCCHHHHHHHH
Confidence 357899999999998877 2 233444432222222222 26666655444
No 312
>KOG3598 consensus Thyroid hormone receptor-associated protein complex, subunit TRAP230 [Transcription]
Probab=27.73 E-value=16 Score=44.99 Aligned_cols=8 Identities=50% Similarity=0.580 Sum_probs=6.5
Q ss_pred cccccccc
Q 010992 191 QGMGVMGS 198 (496)
Q Consensus 191 Q~mG~mGs 198 (496)
|.||+-|+
T Consensus 1994 qa~g~~~~ 2001 (2220)
T KOG3598|consen 1994 QAMGNTSS 2001 (2220)
T ss_pred hccCCCCC
Confidence 78888777
No 313
>cd07176 terB tellurite resistance protein terB. This family contains uncharacterized bacterial proteins involved in tellurium resistance. The prototype of this CD is the Kp-terB protein from Klebsiella pneumoniae, whose 3D structure was recently determined. The biological function of terB and the mechanism responsible for tellurium resistance are unknown.
Probab=27.72 E-value=1.3e+02 Score=24.32 Aligned_cols=13 Identities=15% Similarity=0.138 Sum_probs=5.3
Q ss_pred HHHHHHHHHHhhh
Q 010992 436 VESITMFGCSLAK 448 (496)
Q Consensus 436 VDsVvt~ACrLAK 448 (496)
...++.+++.+|.
T Consensus 77 r~~~~~~~~~ia~ 89 (111)
T cd07176 77 RETAFAVAVDIAA 89 (111)
T ss_pred HHHHHHHHHHHHH
Confidence 3334444444443
No 314
>KOG1673 consensus Ras GTPases [General function prediction only]
Probab=27.71 E-value=87 Score=30.99 Aligned_cols=54 Identities=20% Similarity=0.340 Sum_probs=40.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhcCCC--------CcchhhH-HHHHhhhcCccccCCCccccc
Q 010992 425 EDILVDIAEDFVESITMFGCSLAKHRKSD--------TLEAKDI-LVHLERNWNMTLPGFSGDEIK 481 (496)
Q Consensus 425 EELLLeIADDFVDsVvt~ACrLAKHRKSd--------TLEvKDV-QLhLERnWNI~IPGFssDEIr 481 (496)
.|.+.+|--|.-+.|+..|.++||--+.. .+.+..| +++|.|-||+.. --+|+.
T Consensus 134 yD~fi~lp~e~Q~~I~~qar~YAk~mnAsL~F~Sts~sINv~KIFK~vlAklFnL~~---ti~~~~ 196 (205)
T KOG1673|consen 134 YDLFIDLPPELQETISRQARKYAKVMNASLFFCSTSHSINVQKIFKIVLAKLFNLPW---TIPEIL 196 (205)
T ss_pred hHhhhcCCHHHHHHHHHHHHHHHHHhCCcEEEeeccccccHHHHHHHHHHHHhCCce---eccccc
Confidence 46677777777889999999999988765 4556555 899999999754 344554
No 315
>PF11047 SopD: Salmonella outer protein D; InterPro: IPR022747 The proteins in this entry are also known as secreted effector proteins. Effector proteins function to alter host cell physiology and promote bacterial survival in host tissues. They contribute to the formation of Salmonella-induced filaments (Sifs) in infected epithelial cells and to replication in macrophages []. SopD is a type III virulence effector protein whose structure consists of 38% alpha-helix and 26% beta-strand [].; GO: 0009405 pathogenesis, 0033644 host cell membrane
Probab=27.56 E-value=97 Score=32.65 Aligned_cols=70 Identities=23% Similarity=0.400 Sum_probs=52.3
Q ss_pred CcCCccCCHHHHHHHHHhhCCC--CCCCHHHHHHHHHHHHHHHHHHH-------HHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992 396 EFGNRILTKRSIQELVNQIDPS--ERLDPDVEDILVDIAEDFVESIT-------MFGCSLAKHRKSDTLEAKDILVHLER 466 (496)
Q Consensus 396 e~~nrILtKrKLqELVrqIDPs--esLDpDVEELLLeIADDFVDsVv-------t~ACrLAKHRKSdTLEvKDVQLhLER 466 (496)
.-|+.||.+-+|+++++--|.. +.+++|-++++++|++-+=+.|. .+|..|-|.-..+ -++||-.+-|-|
T Consensus 113 ~Ig~~VI~q~~i~diln~sd~~v~~~m~~~E~~lFlkic~~~g~~i~~~pellq~~~~~lr~~v~~~-~~ik~~vy~~mr 191 (319)
T PF11047_consen 113 MIGDTVISQSNIQDILNVSDNCVVKSMSREERELFLKICEYYGSKITWHPELLQNSASTLRKEVNED-DQIKDAVYKLMR 191 (319)
T ss_pred EECCEEEeeccHHHHHhhhhhhhhhhccHHHHHHHHHHHHHHhhhhccCHHHHHHHHHHHHHHhccc-hHHHHHHHHhhC
Confidence 4578899999999999866543 58999999999999988766654 3455555555555 378887766655
No 316
>PRK00373 V-type ATP synthase subunit D; Reviewed
Probab=27.46 E-value=17 Score=34.52 Aligned_cols=73 Identities=21% Similarity=0.277 Sum_probs=38.7
Q ss_pred HHHHHHHHHhh----CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH-hhhhcCCCCcchhhHHHHHhhhcCccccCCCc
Q 010992 404 KRSIQELVNQI----DPSERLDPDVEDILVDIAEDFVESITMFGCS-LAKHRKSDTLEAKDILVHLERNWNMTLPGFSG 477 (496)
Q Consensus 404 KrKLqELVrqI----DPsesLDpDVEELLLeIADDFVDsVvt~ACr-LAKHRKSdTLEvKDVQLhLERnWNI~IPGFss 477 (496)
|+|.+.|+.++ +.-..+..++++.+.+..+.|..-....+-. +.....+ +....+|....+.-+|..||-|..
T Consensus 31 k~Krd~L~~e~~~~~~~~~~~r~~~~~~~~~a~~~l~~a~~~~G~~~~~~~~~~-~~~~~~v~~~~~ni~GV~vP~~~~ 108 (204)
T PRK00373 31 KDKRDELIMEFFDILDEAKKLREEVEEELEEAYKDFLMARAVEGSLAVEEAAAS-PKESLEVDVSSKNIMGVVVPVIEL 108 (204)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCHHHHHHHHhC-CCCCceEEEEeEEEEEEEeceEEe
Confidence 45555555554 1122344444444444444444333333221 1111112 345677778888999999999987
No 317
>PF01221 Dynein_light: Dynein light chain type 1 ; InterPro: IPR001372 Dynein is a multisubunit microtubule-dependent motor enzyme that acts as the force generating protein of eukaryotic cilia and flagella. The cytoplasmic isoform of dynein acts as a motor for the intracellular retrograde motility of vesicles and organelles along microtubules. Dynein is composed of a number of ATP-binding large subunits (see IPR004273 from INTERPRO), intermediate size subunits and small subunits. Among the small subunits, there is a family of highly conserved proteins which make up this family [, ]. Both type 1 (DLC1) and 2 (DLC2) dynein light chains have a similar two-layer alpha-beta core structure consisting of beta-alpha(2)-beta-X-beta(2) [, ].; GO: 0007017 microtubule-based process, 0005875 microtubule associated complex; PDB: 1F95_A 1F96_A 1F3C_A 3P8M_B 2XQQ_C 1RE6_A 1CMI_A 1PWK_A 1PWJ_A 4DS1_C ....
Probab=27.40 E-value=51 Score=27.38 Aligned_cols=19 Identities=5% Similarity=0.382 Sum_probs=13.2
Q ss_pred CCCHHHHHHHHHHHHHHHH
Q 010992 419 RLDPDVEDILVDIAEDFVE 437 (496)
Q Consensus 419 sLDpDVEELLLeIADDFVD 437 (496)
-|++|.++.++++|.+-++
T Consensus 12 dM~~~~~~~~~~~~~~a~~ 30 (89)
T PF01221_consen 12 DMPEEMQEEAIELAKEALK 30 (89)
T ss_dssp ES-HHHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHH
Confidence 4777877777777777665
No 318
>PF14677 FANCI_S3: FANCI solenoid 3; PDB: 3S51_A 3S4Z_A 3S4W_A.
Probab=27.40 E-value=1.8e+02 Score=28.54 Aligned_cols=54 Identities=11% Similarity=0.287 Sum_probs=34.3
Q ss_pred HHHHHHHHHhhCCCC-CCC--HHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHH
Q 010992 404 KRSIQELVNQIDPSE-RLD--PDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILV 462 (496)
Q Consensus 404 KrKLqELVrqIDPse-sLD--pDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQL 462 (496)
.+|+.++++.||... .-+ .|+.+.+.++-+.|-+.+.++-- ...+....|++.+
T Consensus 114 ~~k~~~FL~~i~~~~~~~~~~~d~~~~i~~~I~~f~r~~~~~~s-----~~~e~~~~K~~~~ 170 (219)
T PF14677_consen 114 PDKFSQFLSAIDMTDDNAEEEKDLTERIQFQIRQFQRELENFLS-----SEEEDFNSKEAVL 170 (219)
T ss_dssp GGGHHHHHHHTS----STTTT-HHHHHHHHHHHHHHHHHHHHHH-----S--SS--SHHHHH
T ss_pred hHHHHHHHHHhccccCCccccccHHHHHHHHHHHHHHHHhhccc-----cccccccchhHHH
Confidence 578999999998642 222 68999999999999999887543 3334344555543
No 319
>PF12422 Condensin2nSMC: Condensin II non structural maintenance of chromosomes subunit; InterPro: IPR024741 Subunit G2 is a non-SMC subunit of condensin II, which is involved in maintenance of the structural integrity of chromosomes. Condensin II is made up of SMC (structural maintenance of chromosomes) and non-SMC subunits. The non-SMC subunits bind to the catalytic ends of the SMC subunit dimer. The condensin holocomplex is able to introduce superhelical tension into DNA in an ATP hydrolysis- dependent manner, resulting in the formation of positive supercoils in the presence of topoisomerase I and of positive knots in the presence of topoisomerase II [].; GO: 0005634 nucleus
Probab=27.34 E-value=62 Score=29.64 Aligned_cols=41 Identities=10% Similarity=0.171 Sum_probs=29.7
Q ss_pred CCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q 010992 402 LTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFG 443 (496)
Q Consensus 402 LtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~A 443 (496)
+.-.++++++..+-. .+.+.+|+++|+++.+-++...+..+
T Consensus 91 ~~~~~~R~~L~~f~~-~k~~~~v~~mL~rl~~PiL~r~L~~~ 131 (152)
T PF12422_consen 91 PLHSKFREVLLSFHS-QKKRKGVDEMLLRLYEPILWRALQAA 131 (152)
T ss_pred HhHHHHHHHHHHHHh-cccccchHHHHHHHHHHHHHHHHcCC
Confidence 334556666666633 34899999999999998888777643
No 320
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=27.32 E-value=1.6e+02 Score=21.58 Aligned_cols=28 Identities=18% Similarity=0.484 Sum_probs=21.0
Q ss_pred HHhhCCCCCCCHHHHHHHHHHHHHHHHH
Q 010992 411 VNQIDPSERLDPDVEDILVDIAEDFVES 438 (496)
Q Consensus 411 VrqIDPsesLDpDVEELLLeIADDFVDs 438 (496)
+.++-....++.++..+-..|.|.|+.+
T Consensus 3 l~~~~~~~~~~~~~~~~a~~~~~~~l~~ 30 (83)
T smart00385 3 LRRVCKALNLDPETLNLAVNLLDRFLSD 30 (83)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHHHHHHH
Confidence 3334444678999999999999999874
No 321
>PF04157 EAP30: EAP30/Vps36 family; InterPro: IPR007286 EAP30 is a subunit of the ELL complex. The ELL is an 80kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 2ZME_A 3CUQ_A 1W7P_D 1U5T_B.
Probab=27.28 E-value=2.1e+02 Score=27.39 Aligned_cols=63 Identities=17% Similarity=0.254 Sum_probs=39.5
Q ss_pred HHHHHHHHhhC--CCCCCC------HHHHHHHHHHHHHHHHHHH-------------HHHHHhhhhc-CCCCcchhhHHH
Q 010992 405 RSIQELVNQID--PSERLD------PDVEDILVDIAEDFVESIT-------------MFGCSLAKHR-KSDTLEAKDILV 462 (496)
Q Consensus 405 rKLqELVrqID--PsesLD------pDVEELLLeIADDFVDsVv-------------t~ACrLAKHR-KSdTLEvKDVQL 462 (496)
.++++++..|+ +-..-+ ..+.++..|||-..+|-+. +.-|.+-|-| +.+.|..+||.-
T Consensus 61 ~~f~~~~~~lGvdp~~s~~~~s~~l~~~~~f~~ELa~qi~e~c~~~~~~~GGii~L~dl~~~~nr~R~g~~lISp~Di~~ 140 (223)
T PF04157_consen 61 SQFQSMCASLGVDPLASSKFWSESLKGSGDFYYELAVQIAEVCLATRSKNGGIISLSDLYCRYNRARGGSELISPEDILR 140 (223)
T ss_dssp HHHHHHHHHHT--CHCCTTCCCCCCSCHHHHHHHHHHHHHHHHHHHCCTTTSEEEHHHHHHHHHHCTTTSST--HHHHHH
T ss_pred HHHHHHHHHcCCCcccchhhhhhccccchhHHHHHHHHHHHHHHHHHhcCCCEEEHHHHHHHHHHhcccCCCcCHHHHHH
Confidence 47788888773 222222 4677888888887776543 3456667777 777777777777
Q ss_pred HHhhh
Q 010992 463 HLERN 467 (496)
Q Consensus 463 hLERn 467 (496)
.+++-
T Consensus 141 A~~~l 145 (223)
T PF04157_consen 141 ACKLL 145 (223)
T ss_dssp HHHHH
T ss_pred HHHHH
Confidence 76663
No 322
>COG1705 FlgJ Muramidase (flagellum-specific) [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=27.25 E-value=71 Score=31.69 Aligned_cols=40 Identities=18% Similarity=0.203 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCcc
Q 010992 431 IAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMT 471 (496)
Q Consensus 431 IADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~ 471 (496)
-.+.||+.+...|..+++..+-.. .+.=.|-+||-+||-+
T Consensus 42 ~~~~Fi~~i~~~A~~~~~~~gi~~-Si~iAQAiLESgwGks 81 (201)
T COG1705 42 SQQAFIDKIAPAAQPLAQEYGILP-SITIAQAILESGWGKS 81 (201)
T ss_pred hHHHHHHHHHHHHHHHHHHhCCCH-HHHHHHHHHHcCCcch
Confidence 556799999999999999888774 4555688999999966
No 323
>KOG0034 consensus Ca2+/calmodulin-dependent protein phosphatase (calcineurin subunit B), EF-Hand superfamily protein [Signal transduction mechanisms]
Probab=27.15 E-value=2.1e+02 Score=27.60 Aligned_cols=62 Identities=11% Similarity=0.194 Sum_probs=40.6
Q ss_pred CcCCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992 396 EFGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERN 467 (496)
Q Consensus 396 e~~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn 467 (496)
-++...|+|..|..+|+.+=... .|. ++|.+.+|+| +...-|-+-+...|...|-.=++++.
T Consensus 115 ~~~~G~I~reel~~iv~~~~~~~-~~~-~~e~~~~i~d--------~t~~e~D~d~DG~IsfeEf~~~v~~~ 176 (187)
T KOG0034|consen 115 LDGDGFISREELKQILRMMVGEN-DDM-SDEQLEDIVD--------KTFEEADTDGDGKISFEEFCKVVEKQ 176 (187)
T ss_pred CCCCCcCcHHHHHHHHHHHHccC-Ccc-hHHHHHHHHH--------HHHHHhCCCCCCcCcHHHHHHHHHcC
Confidence 34555688888888888773322 222 5566555554 55667778888888888876666654
No 324
>PF13963 Transpos_assoc: Transposase-associated domain
Probab=27.05 E-value=63 Score=26.58 Aligned_cols=34 Identities=24% Similarity=0.330 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHH---------HHhhhhcCCCCcchhhHHHHHhhh
Q 010992 432 AEDFVESITMFG---------CSLAKHRKSDTLEAKDILVHLERN 467 (496)
Q Consensus 432 ADDFVDsVvt~A---------CrLAKHRKSdTLEvKDVQLhLERn 467 (496)
+++||+-+...+ |.-+|.++. ++.+||..||-++
T Consensus 21 v~~Fi~~A~~~~~~~~~i~CPC~~C~N~~~--~~~~~V~~HL~~~ 63 (77)
T PF13963_consen 21 VEEFIDFAFSNPSNDNMIRCPCRKCKNEKR--QSRDDVHEHLVCR 63 (77)
T ss_pred HHHHHHHHHhcccCCCceECCchhhccCcc--CCHHHHHHHHHHh
Confidence 456666655544 555676666 6899999999874
No 325
>KOG2948 consensus Predicted metal-binding protein [General function prediction only]
Probab=27.04 E-value=1.1e+02 Score=32.48 Aligned_cols=69 Identities=23% Similarity=0.401 Sum_probs=41.0
Q ss_pred HHHHHHHHhh--CCCCCCCHHHH----HHHHHHHHHHHHHHHHHHHH-----------hhhhcCCC---Ccch-------
Q 010992 405 RSIQELVNQI--DPSERLDPDVE----DILVDIAEDFVESITMFGCS-----------LAKHRKSD---TLEA------- 457 (496)
Q Consensus 405 rKLqELVrqI--DPsesLDpDVE----ELLLeIADDFVDsVvt~ACr-----------LAKHRKSd---TLEv------- 457 (496)
-.|-.+|.++ |+++.=|++.+ +++--+-.||++.|-.-+|. |||.-+.+ .|.+
T Consensus 148 ~~l~~rv~~~N~~w~e~~~~~~~e~F~~Am~~vg~ef~~~v~~~~~sWlPar~~v~~ai~er~~~d~sG~i~v~~~~cPW 227 (327)
T KOG2948|consen 148 TSLSHRVGRFNPDWNEDSDDDEDERFQRAMDLVGKEFVNSVKFYANSWLPARELVEEAIAERFDVDPSGIILVLKQFCPW 227 (327)
T ss_pred cchHHHHhhcCCCcccCcchhHHHHHHHHHHHHHHHHHHHHHHHHHccccHHHHHHHHHHHhcCCCCCceEEEecCCCch
Confidence 3455666655 44543222333 44555667888888877753 33322221 2222
Q ss_pred hhHHHHHhhhcCcccc
Q 010992 458 KDILVHLERNWNMTLP 473 (496)
Q Consensus 458 KDVQLhLERnWNI~IP 473 (496)
||..|.||+++|+.+.
T Consensus 228 k~hlfelE~e~~ie~~ 243 (327)
T KOG2948|consen 228 KEHLFELEKEYKIEVK 243 (327)
T ss_pred HHHHHHHHHHhCCCcc
Confidence 8999999999998876
No 326
>PRK09522 bifunctional glutamine amidotransferase/anthranilate phosphoribosyltransferase; Provisional
Probab=27.03 E-value=95 Score=34.01 Aligned_cols=49 Identities=4% Similarity=0.180 Sum_probs=39.0
Q ss_pred HHHHHHhhCCCCCCCHH-HHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCc
Q 010992 407 IQELVNQIDPSERLDPD-VEDILVDIAEDFVESITMFGCSLAKHRKSDTL 455 (496)
Q Consensus 407 LqELVrqIDPsesLDpD-VEELLLeIADDFVDsVvt~ACrLAKHRKSdTL 455 (496)
|.+++++|-.+..|+.| +++++..|.|.-++++--.|..+|-+-|.+|.
T Consensus 200 ~~~~l~~~~~~~~Lt~eea~~~~~~il~g~~~~~qi~AfL~alr~kget~ 249 (531)
T PRK09522 200 LQPILEKLYQAQTLSQQESHQLFSAVVRGELKPEQLAAALVSMKIRGEHP 249 (531)
T ss_pred HHHHHHHhhcCCCCCHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCCCH
Confidence 56788887777777755 99999999999999988888888877666654
No 327
>cd02191 FtsZ FtsZ is a GTPase that is similar to the eukaryotic tubulins and is essential for cell division in prokaryotes. FtsZ is capable of polymerizing in a GTP-driven process into structures similar to those formed by tubulin. FtsZ forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells.
Probab=26.85 E-value=1.2e+02 Score=30.76 Aligned_cols=76 Identities=11% Similarity=0.088 Sum_probs=52.9
Q ss_pred CCHHHHHHHHHhhCCCCCCCHHHHHH---------HHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccc
Q 010992 402 LTKRSIQELVNQIDPSERLDPDVEDI---------LVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTL 472 (496)
Q Consensus 402 LtKrKLqELVrqIDPsesLDpDVEEL---------LLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~I 472 (496)
....-|++|.+.+|--..+|.|..-- -.+.+|+.|-..+..-..+-++.+.-.++++||.-.|+. =|+.+
T Consensus 135 NA~~~l~~L~~~~D~~iv~dN~~L~~~~~~~~~~~af~~~N~~ia~~i~~it~~i~~~g~invD~~dv~~~l~~-~G~a~ 213 (303)
T cd02191 135 NAAEGFQTLVREVDNLMVIPNEKLRQIGEKASLEGAFDHADEVLVRAVGGLFGAIEIEGEINVDFADVKNVMDG-GGVAM 213 (303)
T ss_pred hHHHHHHHHHHhCCEEEEEehHHHHHHhhcCChHHHHHHHHHHHHHHHHHHHHhhccCCcccCCHHHHHHHhcc-CCeEE
Confidence 34556888888888766666653211 234566666666666666777888889999999999965 58888
Q ss_pred cCCCcc
Q 010992 473 PGFSGD 478 (496)
Q Consensus 473 PGFssD 478 (496)
=||+..
T Consensus 214 ig~g~~ 219 (303)
T cd02191 214 VGYGSE 219 (303)
T ss_pred EEEEEe
Confidence 888743
No 328
>PF01343 Peptidase_S49: Peptidase family S49 peptidase classification.; InterPro: IPR002142 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This group of serine peptidases belong to MEROPS peptidase family S49 (protease IV family, clan S-). The predicted active site serine for members of this family occurs in a transmembrane domain. The domain defines sequences in viruses, archaea, bacteria and plants. These sequences are variously annotated in the different taxonomic groups, examples are: Viruses: capsid protein Archaea: proteinase IV homolog Bacteria: proteinase IV, sohB, SppA, pfaP, putative protease Plants: SppA, protease IV This group also contains proteins classified as non-peptidase homologues that either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of peptidases. Related proteins, non-peptidase homologs and unclassified S49 members are also to be found in IPR002810 from INTERPRO.; GO: 0008233 peptidase activity, 0006508 proteolysis; PDB: 3RST_B 3BEZ_D 3BF0_A.
Probab=26.64 E-value=80 Score=28.32 Aligned_cols=34 Identities=9% Similarity=0.264 Sum_probs=19.6
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCC
Q 010992 417 SERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSD 453 (496)
Q Consensus 417 sesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSd 453 (496)
...++++..|.+.++.|++-+..+. .+|+.|+-+
T Consensus 77 ~~~~s~~~r~~~~~~l~~~~~~f~~---~Va~~R~~~ 110 (154)
T PF01343_consen 77 RDPMSEEERENLQELLDELYDQFVN---DVAEGRGLS 110 (154)
T ss_dssp TSS--HHHHHHHHHHHHHHHHHHHH---HHHHHHTS-
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHH---HHHHccCCC
Confidence 4567777777776666665555544 446788754
No 329
>PRK06200 2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase; Provisional
Probab=26.48 E-value=29 Score=31.93 Aligned_cols=40 Identities=8% Similarity=0.110 Sum_probs=19.4
Q ss_pred CHHHHHHHHHhhCCCC-------CCCHHHHHHHHHHHHHH--HHHHHHH
Q 010992 403 TKRSIQELVNQIDPSE-------RLDPDVEDILVDIAEDF--VESITMF 442 (496)
Q Consensus 403 tKrKLqELVrqIDPse-------sLDpDVEELLLeIADDF--VDsVvt~ 442 (496)
++.++.+|..+++... .-++++++++.++.++| ||-|++.
T Consensus 39 ~~~~~~~~~~~~~~~~~~~~~D~~~~~~~~~~~~~~~~~~g~id~li~~ 87 (263)
T PRK06200 39 SAEKLASLRQRFGDHVLVVEGDVTSYADNQRAVDQTVDAFGKLDCFVGN 87 (263)
T ss_pred CHHHHHHHHHHhCCcceEEEccCCCHHHHHHHHHHHHHhcCCCCEEEEC
Confidence 4566777776654311 11233555555555554 4444443
No 330
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=26.35 E-value=1.8e+02 Score=27.37 Aligned_cols=70 Identities=11% Similarity=0.174 Sum_probs=58.4
Q ss_pred CcCCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992 396 EFGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLE 465 (496)
Q Consensus 396 e~~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE 465 (496)
+...-++.-.++++|+++-.-..++..++--.|.-+.+-.+..|++.|-..||--|...|..|.|++.+.
T Consensus 21 a~agl~fpvgrvkr~lk~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIr 90 (132)
T COG5262 21 AKAGLIFPVGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIR 90 (132)
T ss_pred hhcCccccHHHHHHHHHcCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhc
Confidence 3445566778899999965566788888888888888888999999999999999999999999988764
No 331
>cd05030 calgranulins Calgranulins: S-100 domain found in proteins belonging to the Calgranulin subgroup of the S100 family of EF-hand calcium-modulated proteins, including S100A8, S100A9, and S100A12 . Note that the S-100 hierarchy, to which this Calgranulin group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. These proteins are expressed mainly in granulocytes, and are involved in inflammation, allergy, and neuritogenesis, as well as in host-parasite response. Calgranulins are modulated not only by calcium, but also by other metals such as zinc and copper. Structural data suggested that calgranulins may exist in multiple structural forms, homodimers, as well as hetero-oligomers. For example, the S100A8/S100A9 complex called calprotectin plays important roles in the regulation of inflammatory processes, wound repair, and regulating zinc-dependent enzymes as well as microbial growth.
Probab=26.32 E-value=1e+02 Score=25.41 Aligned_cols=42 Identities=21% Similarity=0.282 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhc-CCCCcchhhHHHHHhhhcCccc
Q 010992 423 DVEDILVDIAEDFVESITMFGCSLAKHR-KSDTLEAKDILVHLERNWNMTL 472 (496)
Q Consensus 423 DVEELLLeIADDFVDsVvt~ACrLAKHR-KSdTLEvKDVQLhLERnWNI~I 472 (496)
++|+.+..|.+.|- ++|+.+ +...|+..|+.-.|+++++-.+
T Consensus 2 ~~e~~i~~~~~~f~--------~y~~~~~~~~~Is~~El~~ll~~~~g~~~ 44 (88)
T cd05030 2 ELEKAIETIINVFH--------QYSVRKGHPDTLYKKEFKQLVEKELPNFL 44 (88)
T ss_pred hHHHHHHHHHHHHH--------HHhccCCCcccCCHHHHHHHHHHHhhHhh
Confidence 56777777777774 566544 4678999999888887766554
No 332
>PF01857 RB_B: Retinoblastoma-associated protein B domain; InterPro: IPR002719 Retinoblastoma-like and retinoblastoma-associated proteins may have a function in cell cycle regulation. They form a complex with adenovirus E1A and SV40 large T antigen, and may bind and modulate the function of certain cellular proteins with which T and E1A compete for pocket binding. The proteins may act as tumor suppressors, and are potent inhibitors of E2F-mediated trans-activation. This domain has the cyclin fold []. The crystal structure of the Rb pocket bound to a nine-residue E7 peptide containing the LxCxE motif, shared by other Rb-binding viral and cellular proteins, shows that the LxCxE peptide binds a highly conserved groove on the B-box portion of the pocket; the A-box portion (see IPR002720 from INTERPRO) appears to be required for the stable folding of the B box. Also highly conserved is the extensive A-B interface, suggesting that it may be an additional protein-binding site. The A and B boxes each contain the cyclin-fold structural motif, with the LxCxE-binding site on the B-box cyclin fold being similar to a Cdk2-binding site of cyclin A and to a TBP-binding site of TFIIB []. The A and B boxes are found at the C-terminal end of the protein; the B-box is on C-terminal side of the A-box.; GO: 0051726 regulation of cell cycle, 0005634 nucleus; PDB: 1GUX_B 3POM_A 1GH6_B 1N4M_A 1O9K_H 4ELL_B 2R7G_C 4ELJ_A.
Probab=26.30 E-value=1.7e+02 Score=26.92 Aligned_cols=59 Identities=22% Similarity=0.335 Sum_probs=32.8
Q ss_pred HHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHH------------HHHH-HHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992 404 KRSIQELVNQIDPSERLDPDVEDILVDIAEDFVE------------SITM-FGCSLAKHRKSDTLEAKDILVHLERN 467 (496)
Q Consensus 404 KrKLqELVrqIDPsesLDpDVEELLLeIADDFVD------------sVvt-~ACrLAKHRKSdTLEvKDVQLhLERn 467 (496)
-.+|++|+.+++ |+++..+-+..+.|.-|. .++. .---+||.-+ ..+.++||..+.++.
T Consensus 15 ~~Rl~~LC~~L~----l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~-~~~sF~~Ii~~Yr~q 86 (135)
T PF01857_consen 15 AVRLQDLCERLD----LSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSK-EELSFKDIIKAYRKQ 86 (135)
T ss_dssp HHHHHHHHHHHT----TSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT--S--HHHHHHHHTTS
T ss_pred HHHHHHHHHHcC----CcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhc-CCCCHHHHHHHHHhc
Confidence 457899999986 555555555555443332 2222 1122344434 678999998888764
No 333
>TIGR00745 apbA_panE 2-dehydropantoate 2-reductase. This model describes enzymes that perform as 2-dehydropantoate 2-reductase, one of four enzymes required for the de novo biosynthesis of pantothenate (vitamin B5) from Asp and 2-oxoisovalerate. Although few members of the seed alignment are characterized experimentally, nearly all from complete genomes are found in a genome-wide (but not local) context of all three other pantothenate-biosynthetic enzymes (TIGR00222, TIGR00018, TIGR00223). The gene encoding this enzyme is designated apbA in Salmonella typhimurium and panE in Escherichia coli; this protein functions as a monomer and functions in the alternative pyrimidine biosynthetic, or APB, pathway, used to synthesize the pyrimidine moiety of thiamine. Note, synthesis of the pyrimidine moiety of thiamine occurs either via the first five steps in de novo purine biosynthesis, which uses the pur gene products, or through the APB pathway. Note that this family includes both NADH and NADPH
Probab=26.28 E-value=74 Score=29.94 Aligned_cols=11 Identities=18% Similarity=0.437 Sum_probs=5.3
Q ss_pred HHhhhcCcccc
Q 010992 463 HLERNWNMTLP 473 (496)
Q Consensus 463 hLERnWNI~IP 473 (496)
.+.|.+|+..|
T Consensus 268 ~~a~~~gv~~P 278 (293)
T TIGR00745 268 RLAEKLGIDAP 278 (293)
T ss_pred HHHHHcCCCCC
Confidence 34445555544
No 334
>PRK14961 DNA polymerase III subunits gamma and tau; Provisional
Probab=25.98 E-value=91 Score=31.71 Aligned_cols=62 Identities=11% Similarity=0.032 Sum_probs=35.7
Q ss_pred CCHHHHHHHHHhhCC--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHH
Q 010992 402 LTKRSIQELVNQIDP--SERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHL 464 (496)
Q Consensus 402 LtKrKLqELVrqIDP--sesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhL 464 (496)
+++..+.+.|+++-. +..+|+++.++|.+.++.=+.+++...-+++.. +.+.++.+||.-.|
T Consensus 178 l~~~el~~~L~~~~~~~g~~i~~~al~~ia~~s~G~~R~al~~l~~~~~~-~~~~It~~~v~~~l 241 (363)
T PRK14961 178 ISEEKIFNFLKYILIKESIDTDEYALKLIAYHAHGSMRDALNLLEHAINL-GKGNINIKNVTDML 241 (363)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHh-cCCCCCHHHHHHHH
Confidence 456667766666532 346899999988888765333333332222222 34557777774433
No 335
>PRK15182 Vi polysaccharide biosynthesis protein TviB; Provisional
Probab=25.72 E-value=1.9e+02 Score=30.51 Aligned_cols=74 Identities=18% Similarity=0.198 Sum_probs=45.7
Q ss_pred HHHHHHHHHhhC-CC--CCCCHHHHHHHHHHHHHHHHHHHHHHH---HhhhhcCCCCcchhhHHHHHhhhcCcc--ccC-
Q 010992 404 KRSIQELVNQID-PS--ERLDPDVEDILVDIAEDFVESITMFGC---SLAKHRKSDTLEAKDILVHLERNWNMT--LPG- 474 (496)
Q Consensus 404 KrKLqELVrqID-Ps--esLDpDVEELLLeIADDFVDsVvt~AC---rLAKHRKSdTLEvKDVQLhLERnWNI~--IPG- 474 (496)
.+.+.+|.+.|- .+ ...+.+.-|++.-+.+-|+.--+.++. .||+..|- ++.+|.-.....|++. -||
T Consensus 180 ~~~~~~ly~~~~~~~~~~~~~~~~AE~~Kl~~N~~~av~Ia~~NE~a~lae~~Gi---D~~~v~~a~~~~~~~~~~~pG~ 256 (425)
T PRK15182 180 AELIDEVYQQIISAGTYKAESIKVAEAAKVIENTQRDLNIALVNELAIIFNRLNI---DTEAVLRAAGSKWNFLPFRPGL 256 (425)
T ss_pred HHHHHHHHHHHhhcCcEEecCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCc---CHHHHHHHhcCCCCcccCCCCc
Confidence 457888888874 22 234566777777777777766555554 55565554 5555544456666644 678
Q ss_pred CCcccc
Q 010992 475 FSGDEI 480 (496)
Q Consensus 475 FssDEI 480 (496)
||+-=|
T Consensus 257 vGG~Cl 262 (425)
T PRK15182 257 VGGHCI 262 (425)
T ss_pred cccccc
Confidence 777544
No 336
>PF14094 DUF4272: Domain of unknown function (DUF4272)
Probab=25.71 E-value=1e+02 Score=29.86 Aligned_cols=35 Identities=23% Similarity=0.309 Sum_probs=24.2
Q ss_pred HHHHHhhhhcCCCCcchhhHHHHHhhhcCc-cccCC
Q 010992 441 MFGCSLAKHRKSDTLEAKDILVHLERNWNM-TLPGF 475 (496)
Q Consensus 441 t~ACrLAKHRKSdTLEvKDVQLhLERnWNI-~IPGF 475 (496)
+=+|.-|+.++.+.-.--|.-.++||.|.+ |+=|+
T Consensus 165 hWa~vdari~g~~~p~~ld~~vV~ERh~ALnWL~~~ 200 (209)
T PF14094_consen 165 HWACVDARINGQPAPAGLDEGVVYERHYALNWLIGY 200 (209)
T ss_pred HHHHHHHHhcCCCCCCCCCchHHHHHHHHHHHHhcC
Confidence 667888888777655556777788888774 44554
No 337
>PRK14964 DNA polymerase III subunits gamma and tau; Provisional
Probab=25.62 E-value=1.3e+02 Score=32.80 Aligned_cols=62 Identities=10% Similarity=0.098 Sum_probs=38.6
Q ss_pred CCHHHHHHHHHhhC--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHH
Q 010992 402 LTKRSIQELVNQID--PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHL 464 (496)
Q Consensus 402 LtKrKLqELVrqID--PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhL 464 (496)
++...|.+.+++|- -+..+|+++.++|++.++.=+.+++...-+++-+-+ +.|+.+||.-.|
T Consensus 175 l~~~el~~~L~~ia~~Egi~i~~eAL~lIa~~s~GslR~alslLdqli~y~~-~~It~e~V~~ll 238 (491)
T PRK14964 175 IPTDKLVEHLVDIAKKENIEHDEESLKLIAENSSGSMRNALFLLEQAAIYSN-NKISEKSVRDLL 238 (491)
T ss_pred ccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcC-CCCCHHHHHHHH
Confidence 35555666666663 345799999999998886544444443333333333 368888886543
No 338
>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional
Probab=25.54 E-value=77 Score=36.27 Aligned_cols=66 Identities=15% Similarity=0.284 Sum_probs=44.0
Q ss_pred HHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhH--HHHHhhhcCccccCCCccccc
Q 010992 408 QELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDI--LVHLERNWNMTLPGFSGDEIK 481 (496)
Q Consensus 408 qELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDV--QLhLERnWNI~IPGFssDEIr 481 (496)
-||+.+||.-..+.+--++.|.+|++.|++.+.. +| ++++-+ |++.|= .+..++.|+ +.||+..+|
T Consensus 638 pefl~Rid~ii~f~~L~~~~l~~I~~~~l~~~~~---~l-~~~~i~-l~~~~~~~~~l~~~~~~---~~~GAR~l~ 705 (758)
T PRK11034 638 PEFRNRLDNIIWFDHLSTDVIHQVVDKFIVELQA---QL-DQKGVS-LEVSQEARDWLAEKGYD---RAMGARPMA 705 (758)
T ss_pred HHHHccCCEEEEcCCCCHHHHHHHHHHHHHHHHH---HH-HHCCCC-ceECHHHHHHHHHhCCC---CCCCCchHH
Confidence 4888888877777777777789999999988865 34 344544 444443 344445554 567776665
No 339
>cd00454 Trunc_globin Truncated hemoglobins (trHbs) are a family of oxygen-binding heme proteins found in cyanobacteria, eubacteria, unicellular eukaryotes, and plants. The truncated hemoglobins have a characteristic two-over-two alpha helical folding pattern that is distinct from the three-over-three pattern found in other globins. A subset of these have been demonstrated to form homodimers.
Probab=25.48 E-value=1.3e+02 Score=25.11 Aligned_cols=49 Identities=12% Similarity=0.097 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCCC
Q 010992 425 EDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFS 476 (496)
Q Consensus 425 EELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGFs 476 (496)
++.|..|+|+|.+.|... ..++..-.. ++..++...|.+-|-..+-|-.
T Consensus 9 ~~~i~~lv~~FY~~i~~d-p~i~~~F~~--~~~~~~~~~~~~fl~~~~gg~~ 57 (116)
T cd00454 9 EEAIRALVDRFYARVAAD-PRLGPIFPA--DDLEEHRAKLADFLTQVLGGPG 57 (116)
T ss_pred HHHHHHHHHHHHHHHhcC-hHHHHhcCC--cchHHHHHHHHHHHHHHcCCCC
Confidence 467888888888887654 445554432 2466777777777766665433
No 340
>PF07105 DUF1367: Protein of unknown function (DUF1367); InterPro: IPR009797 This entry is represented by Bacteriophage VT2phi_272, P37. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several highly conserved, hypothetical bacterial and phage proteins of around 200 resides in length. The function of this family is unknown.
Probab=25.35 E-value=88 Score=30.98 Aligned_cols=46 Identities=22% Similarity=0.401 Sum_probs=27.4
Q ss_pred HHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhH
Q 010992 404 KRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDI 460 (496)
Q Consensus 404 KrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDV 460 (496)
|+-++.+|+.+.-.. + -+++|.++||+|++.| |++|..+.-..|+.
T Consensus 73 ~~lv~g~v~~la~~~--g--~~~~l~~~A~~yL~~v-------a~~R~~~~~~~k~f 118 (196)
T PF07105_consen 73 RKLVRGFVKFLASYA--G--SEDALQEAADQYLAKV-------AKKRARDIEAEKSF 118 (196)
T ss_pred HHHHHHHHHHHHHHh--C--CHHHHHHHHHHHHHHH-------HHHhhccchhhhCH
Confidence 445566666663110 1 1288999999999865 55664443334554
No 341
>PF07766 LETM1: LETM1-like protein; InterPro: IPR011685 This is a group of mainly hypothetical eukaryotic proteins. Putative features found in LETM1, such as a transmembrane domain and a CK2 and PKC phosphorylation site [], are relatively conserved throughout the family. Deletion of LETM1 is thought to be involved in the development of Wolf-Hirschhorn syndrome in humans []. A member of this family, P91927 from SWISSPROT, is known to be expressed in the mitochondria of Drosophila melanogaster [], suggesting that this may be a group of mitochondrial proteins.; PDB: 3SKQ_A.
Probab=25.33 E-value=66 Score=32.00 Aligned_cols=31 Identities=23% Similarity=0.527 Sum_probs=18.5
Q ss_pred HHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHH
Q 010992 406 SIQELVNQIDPSERLDPDVEDILVDIAEDFVESI 439 (496)
Q Consensus 406 KLqELVrqIDPsesLDpDVEELLLeIADDFVDsV 439 (496)
++.+++++|..+.. +.+||+| ++++-|.|+.
T Consensus 136 ~~~~~~~kv~~~~~--~s~~eil-~~~~lF~d~~ 166 (268)
T PF07766_consen 136 KLSEFFKKVRSGGH--PSNEEIL-KVAKLFKDEL 166 (268)
T ss_dssp HHHHHHHHHHT-BT--B-HHHHH-HHHTTS-HHH
T ss_pred HHHHHHHHhccCCC--CCHHHHH-HHHHhcCCCc
Confidence 77788887755555 3455544 7777777654
No 342
>PF02854 MIF4G: MIF4G domain; InterPro: IPR003890 This entry represents an MIF4G-like domain. MIF4G domains share a common structure but can differ in sequence. This entry is designated "type 3", and is found in nuclear cap-binding proteins, eIF4G, and UPF2. The MIF4G domain is a structural motif with an ARM (Armadillo) repeat-type fold, consisting of a 2-layer alpha/alpha right-handed superhelix. Proteins usually contain two or more structurally similar MIF4G domains connected by unstructured linkers. MIF4G domains are found in several proteins involved in RNA metabolism, including eIF4G (eukaryotic initiation factor 4-gamma), eIF-2b (translation initiation factor), UPF2 (regulator of nonsense transcripts 2), and nuclear cap-binding proteins (CBP80, CBC1, NCBP1), although the sequence identity between them may be low []. The nuclear cap-binding complex (CBC) is a heterodimer. Human CBC consists of a large CBP80 subunit and a small CBP20 subunit, the latter being critical for cap binding. CBP80 contains three MIF4G domains connected with long linkers, while CBP20 has an RNP (ribonucleoprotein)-type domain that associates with domains 2 and 3 of CBP80 []. The complex binds to 5'-cap of eukaryotic RNA polymerase II transcripts, such as mRNA and U snRNA. The binding is important for several mRNA nuclear maturation steps and for nonsense-mediated decay. It is also essential for nuclear export of U snRNAs in metazoans []. Eukaryotic translation initiation factor 4 gamma (eIF4G) plays a critical role in protein expression, and is at the centre of a complex regulatory network. Together with the cap-binding protein eIF4E, it recruits the small ribosomal subunit to the 5'-end of mRNA and promotes the assembly of a functional translation initiation complex, which scans along the mRNA to the translation start codon. The activity of eIF4G in translation initiation could be regulated through intra- and inter-protein interactions involving the ARM repeats []. In eIF4G, the MIF4G domain binds eIF4A, eIF3, RNA and DNA. Nonsense-mediated mRNA decay (NMD) in eukaryotes involves UPF1, UPF2 and UPF3 to accelerate the decay rate of two unique classes of transcripts: (1) nonsense mRNAs that arise through errors in gene expression, and (2) naturally occurring transcripts that lack coding errors but have built-in features that target them for accelerated decay (error-free mRNAs). NMD can trigger decay during any round of translation and can target CBC-bound or eIF-4E-bound transcripts []. UPF2 contains MIF4G domains, while UPF3 contains an RNP domain []. ; GO: 0005515 protein binding, 0016070 RNA metabolic process; PDB: 3FEY_A 3FEX_A 1H6K_C 1H2V_C 1H2U_A 1H2T_C 1N54_A 1N52_A 1HU3_A 3RK6_A ....
Probab=25.33 E-value=1.2e+02 Score=26.25 Aligned_cols=45 Identities=11% Similarity=0.226 Sum_probs=27.0
Q ss_pred HHHHHHHHhhCCCCCCCHHHHHHHHHHHHH---HHHHHHHHHHHhhhhc
Q 010992 405 RSIQELVNQIDPSERLDPDVEDILVDIAED---FVESITMFGCSLAKHR 450 (496)
Q Consensus 405 rKLqELVrqIDPsesLDpDVEELLLeIADD---FVDsVvt~ACrLAKHR 450 (496)
|++..+++++. ...+|..+++++-..-++ .++.|+..-+.-|...
T Consensus 2 r~v~~~lnklt-~~n~~~~~~~l~~~~~~~~~~~~~~i~~~i~~~a~~~ 49 (209)
T PF02854_consen 2 RKVRGILNKLT-PSNFESIIDELIKLNWSDDPETLKEIVKLIFEKAVEE 49 (209)
T ss_dssp HHHHHHHHHCS-STTHHHHHHHHHHHHHHSCHHHHHHHHHHHHHHHHHS
T ss_pred chHHHHHHHCC-HHHHHHHHHHHHHHHhhccHHHHHHHHHHHhhhhhcC
Confidence 56788888886 455666666555544443 5555555555555544
No 343
>PRK06893 DNA replication initiation factor; Validated
Probab=25.25 E-value=3e+02 Score=26.13 Aligned_cols=59 Identities=17% Similarity=0.142 Sum_probs=32.4
Q ss_pred CHHHHHHHHHhh--CCCCCCCHHHHHHHHHHHH-HH--HHHHHHHH--HHhhhhcCCCCcchhhHHHHH
Q 010992 403 TKRSIQELVNQI--DPSERLDPDVEDILVDIAE-DF--VESITMFG--CSLAKHRKSDTLEAKDILVHL 464 (496)
Q Consensus 403 tKrKLqELVrqI--DPsesLDpDVEELLLeIAD-DF--VDsVvt~A--CrLAKHRKSdTLEvKDVQLhL 464 (496)
....+.+++++. +.+..|++||.+.|++-.+ |+ +..+++.- ..+++.| .|++..|+-+|
T Consensus 162 d~e~~~~iL~~~a~~~~l~l~~~v~~~L~~~~~~d~r~l~~~l~~l~~~~~~~~~---~it~~~v~~~L 227 (229)
T PRK06893 162 TDEQKIIVLQRNAYQRGIELSDEVANFLLKRLDRDMHTLFDALDLLDKASLQAQR---KLTIPFVKEIL 227 (229)
T ss_pred CHHHHHHHHHHHHHHcCCCCCHHHHHHHHHhccCCHHHHHHHHHHHHHHHHhcCC---CCCHHHHHHHh
Confidence 344444444433 3467899999999998776 22 23333322 2223233 36777766554
No 344
>PRK00285 ihfA integration host factor subunit alpha; Reviewed
Probab=25.13 E-value=1e+02 Score=25.83 Aligned_cols=18 Identities=28% Similarity=0.518 Sum_probs=10.2
Q ss_pred HhhhcCccccCCCccccc
Q 010992 464 LERNWNMTLPGFSGDEIK 481 (496)
Q Consensus 464 LERnWNI~IPGFssDEIr 481 (496)
|.+.+.+.|+|||.=+++
T Consensus 38 L~~g~~V~l~gfG~F~~~ 55 (99)
T PRK00285 38 LENGEQVKLSGFGNFQLR 55 (99)
T ss_pred HHcCCeEEEcCCEEEEEE
Confidence 444445666676665544
No 345
>PLN02964 phosphatidylserine decarboxylase
Probab=25.08 E-value=1.4e+02 Score=34.01 Aligned_cols=60 Identities=10% Similarity=0.123 Sum_probs=41.4
Q ss_pred HHHHHHhhCCCC--CCC-HHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992 407 IQELVNQIDPSE--RLD-PDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER 466 (496)
Q Consensus 407 LqELVrqIDPse--sLD-pDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER 466 (496)
++++++.+|.+. .|| +|-.++|..+.+.+-++-+..+.++.-.-+...|+..|+.-+|++
T Consensus 181 i~~mf~~~D~DgdG~IdfdEFl~lL~~lg~~~seEEL~eaFk~fDkDgdG~Is~dEL~~vL~~ 243 (644)
T PLN02964 181 ARRILAIVDYDEDGQLSFSEFSDLIKAFGNLVAANKKEELFKAADLNGDGVVTIDELAALLAL 243 (644)
T ss_pred HHHHHHHhCCCCCCeEcHHHHHHHHHHhccCCCHHHHHHHHHHhCCCCCCcCCHHHHHHHHHh
Confidence 677777776543 444 234445555555556677888888888778888999999877766
No 346
>PF01934 DUF86: Protein of unknown function DUF86; InterPro: IPR008201 This entry describes prokaryotic proteins of unknown function.; PDB: 1YLM_A.
Probab=25.05 E-value=2.5e+02 Score=23.62 Aligned_cols=51 Identities=18% Similarity=0.165 Sum_probs=22.5
Q ss_pred HHHHHHHhhCCCCCC-CHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcc
Q 010992 406 SIQELVNQIDPSERL-DPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLE 456 (496)
Q Consensus 406 KLqELVrqIDPsesL-DpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLE 456 (496)
+|.+++..++..+-+ |....+++......-++.++.-++.+++.++-...+
T Consensus 7 ~i~~~~~~~~~eef~~d~~~~~av~~~l~~~~e~~~di~~~i~~~~~~~~p~ 58 (119)
T PF01934_consen 7 RIKEFTEGISREEFLSDRMLQDAVERNLQLIIEAIIDIAKHIISEEGLGKPG 58 (119)
T ss_dssp -------------TT-SHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT----S
T ss_pred chhhhhccccHHHHhcCHHHHHHHHHHHHHHHHHHhhhHHHHHHHhCCCCCc
Confidence 345555455543322 556667777666666777777777777766665443
No 347
>PF10273 WGG: Pre-rRNA-processing protein TSR2; InterPro: IPR019398 The pre-rRNA-processing protein TSR2 is required for 20S pre-rRNA processing []. This family contains a distinctive WGG motif.
Probab=25.00 E-value=66 Score=27.05 Aligned_cols=38 Identities=24% Similarity=0.357 Sum_probs=20.1
Q ss_pred CHHHHHHHHHhh-----CCCCCCCHHHHHHHHHHHHHHHHHHH
Q 010992 403 TKRSIQELVNQI-----DPSERLDPDVEDILVDIAEDFVESIT 440 (496)
Q Consensus 403 tKrKLqELVrqI-----DPsesLDpDVEELLLeIADDFVDsVv 440 (496)
++.|.+.|+..| +.+...-+|+||+|.++.|+-.+-++
T Consensus 29 s~~K~~~l~~~i~~~f~~~~~~~~~~le~~L~~~m~~eF~~~~ 71 (82)
T PF10273_consen 29 SQEKADWLAEVIVDWFTENKDPDADDLEDFLEDIMDDEFNTVV 71 (82)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHhHcCcee
Confidence 455555555554 22233355577777777655444444
No 348
>PRK08691 DNA polymerase III subunits gamma and tau; Validated
Probab=24.95 E-value=1.6e+02 Score=33.97 Aligned_cols=62 Identities=10% Similarity=0.093 Sum_probs=38.3
Q ss_pred CCHHHHHHHHHhhCC--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHH
Q 010992 402 LTKRSIQELVNQIDP--SERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHL 464 (496)
Q Consensus 402 LtKrKLqELVrqIDP--sesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhL 464 (496)
|+...|.+.|++|-. +..+|+++.++|.+.++-=+.++++..-+++.+ +...|+.+||.-.|
T Consensus 178 Ls~eeI~~~L~~Il~kEgi~id~eAL~~Ia~~A~GslRdAlnLLDqaia~-g~g~It~e~V~~lL 241 (709)
T PRK08691 178 MTAQQVADHLAHVLDSEKIAYEPPALQLLGRAAAGSMRDALSLLDQAIAL-GSGKVAENDVRQMI 241 (709)
T ss_pred CCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHHHHHHHHHh-cCCCcCHHHHHHHH
Confidence 456667766766644 457899999999999885444444444333333 33456666665443
No 349
>PRK00045 hemA glutamyl-tRNA reductase; Reviewed
Probab=24.82 E-value=1.8e+02 Score=30.33 Aligned_cols=62 Identities=15% Similarity=0.277 Sum_probs=33.7
Q ss_pred HHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCcc
Q 010992 404 KRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMT 471 (496)
Q Consensus 404 KrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~ 471 (496)
++.|..++++++. +++.+|.|-+++..+++.+++.-....|. ...-+..++.-.|++.||+.
T Consensus 357 ~~el~~~~~~l~~----~~~~~~~~~~~~~~~~~k~lh~p~~~lr~--~~~~~~~~~~~~~~~~f~~~ 418 (423)
T PRK00045 357 EEELERALKKLGP----GEDEEEVLEKLARSLVNKLLHAPTVRLKE--AAEEGDDEYLEALRELFGLD 418 (423)
T ss_pred HHHHHHHHHhccC----CccHHHHHHHHHHHHHHHHHHHHHHHHHh--hcccChHHHHHHHHHHhCCC
Confidence 4445555555532 33445555555666666666666666665 21123335556777778753
No 350
>TIGR02510 NrdE-prime ribonucleoside-diphosphate reductase, alpha chain. This model represents a small clade of ribonucleoside-diphosphate reductase, alpha chains which are sufficiently divergent from the usual Class I RNR alpha chains (NrdE or NrdA, TIGR02506) as to warrant their own model. The genes from Thermus thermophilus, Dichelobacter and Salinibacter are adjacent to the usual RNR beta chain.
Probab=24.61 E-value=1.2e+02 Score=33.59 Aligned_cols=35 Identities=17% Similarity=0.112 Sum_probs=27.6
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCc
Q 010992 421 DPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTL 455 (496)
Q Consensus 421 DpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTL 455 (496)
++|+.++.-+|.+..-+..+..+|+|||.||...|
T Consensus 355 S~ea~~~~~~i~e~i~~~A~~aS~eLA~ErG~~~l 389 (571)
T TIGR02510 355 SGAAFILNAEIFAEIKEAAEEASRELAEEHGEDEL 389 (571)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCcchh
Confidence 34677777777777777778899999999998643
No 351
>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed
Probab=24.61 E-value=2.1e+02 Score=32.82 Aligned_cols=64 Identities=13% Similarity=0.198 Sum_probs=39.7
Q ss_pred CHHHHHHHHHhhC---------CCCCCCHHHHHHHHHHHH---HHHHHHHHHHHHhhhhcCCC--CcchhhHHHHHhh
Q 010992 403 TKRSIQELVNQID---------PSERLDPDVEDILVDIAE---DFVESITMFGCSLAKHRKSD--TLEAKDILVHLER 466 (496)
Q Consensus 403 tKrKLqELVrqID---------PsesLDpDVEELLLeIAD---DFVDsVvt~ACrLAKHRKSd--TLEvKDVQLhLER 466 (496)
+...|.++++++- ....||+|+.++|.+.++ .-+.++++.+|..+...+.+ .|++.+++-++.+
T Consensus 169 s~edi~~IL~~~l~~~~~~~g~~~v~I~deaL~~La~~s~GD~R~lln~Le~a~~~~~~~~~~~i~It~~~~~e~l~~ 246 (725)
T PRK13341 169 SDEDLHQLLKRALQDKERGYGDRKVDLEPEAEKHLVDVANGDARSLLNALELAVESTPPDEDGLIDITLAIAEESIQQ 246 (725)
T ss_pred CHHHHHHHHHHHHHHHHhhcCCcccCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHhcccCCCCceeccHHHHHHHHHH
Confidence 4555666665542 246899999999999987 34556777777555432222 3566666555544
No 352
>PF09644 Mg296: Mg296 protein; InterPro: IPR019097 This protein of 129 residues is expressed in bacteria. It consists of three identical chains of five alpha helices. Two copies of each chain associate into a complex of six units of possible biological significance but of unknown function. ; PDB: 2I15_A.
Probab=24.60 E-value=1.3e+02 Score=27.91 Aligned_cols=54 Identities=24% Similarity=0.282 Sum_probs=26.8
Q ss_pred HHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992 409 ELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLE 465 (496)
Q Consensus 409 ELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE 465 (496)
++|+++|--+.|=+.-.+-...+||.|-|.++-+...||--.|-+ ++...--|+
T Consensus 66 evikqlD~la~lv~n~~dddk~~~q~FYeal~~fisAlAiTK~i~---~~R~hq~L~ 119 (121)
T PF09644_consen 66 EVIKQLDHLADLVKNPKDDDKKCCQQFYEALIVFISALAITKGIS---IKRLHQLLE 119 (121)
T ss_dssp HHH----------------HHHHHHHHHHHSHHHHHHHHHHTT-----TTHHHHHHH
T ss_pred HHHHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHHHHHHHHcCCC---HHHHHHHHc
Confidence 678999988888888888889999999998887777777766644 555544444
No 353
>cd01679 RNR_I Class I 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 many viruses, 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 anaerobic bacteria, bacteriophages, 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). Class I RNR is oxygen-dependent and can be subdivided into classes Ia (eukaryotes, prokaryotes, viruses and phages) and Ib (
Probab=24.55 E-value=99 Score=33.23 Aligned_cols=30 Identities=27% Similarity=0.226 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhcC
Q 010992 422 PDVEDILVDIAEDFVESITMFGCSLAKHRK 451 (496)
Q Consensus 422 pDVEELLLeIADDFVDsVvt~ACrLAKHRK 451 (496)
+|+.+++-+|++..-...+..+|+|||.||
T Consensus 310 ~ea~~~~~~i~e~i~~~a~~aS~~LA~e~G 339 (460)
T cd01679 310 EEALDLNDRIFETINYYALKASCELAKERG 339 (460)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 667778888888888889999999999977
No 354
>TIGR02541 flagell_FlgJ flagellar rod assembly protein/muramidase FlgJ. The N-terminal region of this protein acts directly in flagellar rod assembly. The C-terminal region is a flagellum-specific muramidase (peptidoglycan hydrolase) required for formation of the outer membrane L ring.
Probab=24.48 E-value=1.1e+02 Score=31.47 Aligned_cols=44 Identities=16% Similarity=0.114 Sum_probs=35.7
Q ss_pred HHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCcccc
Q 010992 429 VDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLP 473 (496)
Q Consensus 429 LeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IP 473 (496)
...-++||+.+...|.++||.-+-.. ++-=-|-+||-.||-...
T Consensus 145 ~~~~~~Fi~~i~p~A~~~a~~~Gip~-sv~iAQAaLESGWG~s~l 188 (294)
T TIGR02541 145 PGHPKSFVNSMLPHARKAAQQLGVPP-HLILAQAALESGWGQRQI 188 (294)
T ss_pred cCCHHHHHHHHHHHHHHHHHHhCCCH-HHHHHHHHHHccCCcccc
Confidence 35568999999999999999888663 455558899999996664
No 355
>PF04129 Vps52: Vps52 / Sac2 family ; InterPro: IPR007258 Vps52 complexes with Vps53 and Vps54 to form a multi-subunit complex involved in regulating membrane trafficking events [].
Probab=24.45 E-value=91 Score=33.64 Aligned_cols=88 Identities=19% Similarity=0.271 Sum_probs=56.4
Q ss_pred cCCHHHHHHHHHhhCCCCCCCHHHHHHHH--HHHHHHHHHHHHHHHHhhhhc----CCCCcchhhHHHHHhhhcC---cc
Q 010992 401 ILTKRSIQELVNQIDPSERLDPDVEDILV--DIAEDFVESITMFGCSLAKHR----KSDTLEAKDILVHLERNWN---MT 471 (496)
Q Consensus 401 ILtKrKLqELVrqIDPsesLDpDVEELLL--eIADDFVDsVvt~ACrLAKHR----KSdTLEvKDVQLhLERnWN---I~ 471 (496)
+=+|+++.+.+..+=....|.+++.+.+. ++-|+||+++++.-.++.... ..+.--++|+.-.||+--. -+
T Consensus 65 L~Nrk~~~~~L~~~i~~i~ipP~lI~~I~~~~v~e~~~~~~~~~~~k~~~~~~~~~~~~~~a~~d~~~~Le~L~~ka~~r 144 (508)
T PF04129_consen 65 LKNRKAVEEKLSPFIDDIVIPPDLIRSICEGPVNEQYIEELLELLKKKIFFSKDQSFKDSKAIKDVKPELEKLKNKAVER 144 (508)
T ss_pred HHhHHHHHHHHHHHHHHHcCCHHHHHhHhcCCCCHHHHHHHHHHHHHHHHHHhhcccccccchHHHHHHHHHHHHHHHHH
Confidence 33566666666655445678888877777 466778888777666544332 2344468888888886544 23
Q ss_pred ccCCCcccccccCCccc
Q 010992 472 LPGFSGDEIKTFRKPVR 488 (496)
Q Consensus 472 IPGFssDEIr~~rk~~~ 488 (496)
|--|-.+.|+..|++.+
T Consensus 145 ir~fl~~kI~~lr~~~t 161 (508)
T PF04129_consen 145 IRDFLLKKIKSLRKPKT 161 (508)
T ss_pred HHHHHHHHHHHHcCCCC
Confidence 45556667777777763
No 356
>PF12921 ATP13: Mitochondrial ATPase expression; InterPro: IPR024319 ATPase expression protein 2 (also known as ATP13 in some species) is necessary for the expression of subunit 9 of mitochondrial ATPase. The protein has a basic amino terminal signal sequence that is cleaved upon import into mitochondria [].
Probab=24.40 E-value=1.3e+02 Score=26.81 Aligned_cols=22 Identities=14% Similarity=0.351 Sum_probs=17.7
Q ss_pred hhhHHHHHhhhcCccccCCCcc
Q 010992 457 AKDILVHLERNWNMTLPGFSGD 478 (496)
Q Consensus 457 vKDVQLhLERnWNI~IPGFssD 478 (496)
+.+|+=+|++.|||.+-|...+
T Consensus 18 ~~~i~~~i~~~WgI~~~~~~~~ 39 (126)
T PF12921_consen 18 LDSIKSYIKSVWGIDVNGKKKE 39 (126)
T ss_pred HHHHHHHHHHhcCCCCCCcccc
Confidence 6677778899999999886554
No 357
>PRK00771 signal recognition particle protein Srp54; Provisional
Probab=24.35 E-value=1.6e+02 Score=31.74 Aligned_cols=38 Identities=16% Similarity=0.405 Sum_probs=24.4
Q ss_pred HHHHHHHHhhCCCCCCCHH--------HHHHHH------HHHHHHHHHHHHH
Q 010992 405 RSIQELVNQIDPSERLDPD--------VEDILV------DIAEDFVESITMF 442 (496)
Q Consensus 405 rKLqELVrqIDPsesLDpD--------VEELLL------eIADDFVDsVvt~ 442 (496)
++|...++.|-....||++ ++++|| +++++||+.|-..
T Consensus 3 ~~l~~~~~~l~~~~~l~e~~i~~~l~ei~~aLl~adV~~~~~~~~~~~v~~~ 54 (437)
T PRK00771 3 ESLRDALKKLAGKSRIDEKTVKEVVKDIQRALLQADVNVKLVKELSKSIKER 54 (437)
T ss_pred hHHHHHHHHHhCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHH
Confidence 3566777777767777776 455554 4667777766654
No 358
>cd08045 TAF4 TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryote. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are
Probab=24.34 E-value=94 Score=29.71 Aligned_cols=19 Identities=32% Similarity=0.497 Sum_probs=15.4
Q ss_pred cCCCCcchhhHHHHHhhhc
Q 010992 450 RKSDTLEAKDILVHLERNW 468 (496)
Q Consensus 450 RKSdTLEvKDVQLhLERnW 468 (496)
+.+..|.+|||.++||++=
T Consensus 184 k~~~~i~~rD~l~~LE~e~ 202 (212)
T cd08045 184 KKKRRITMRDVLFVLEREP 202 (212)
T ss_pred cccceeeHHHHHHHHHhCc
Confidence 3337789999999999873
No 359
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=24.28 E-value=97 Score=27.67 Aligned_cols=31 Identities=19% Similarity=0.417 Sum_probs=18.0
Q ss_pred CCCHH-HHHHHHHHH-HHHHHHHHHHHHHhhhhc
Q 010992 419 RLDPD-VEDILVDIA-EDFVESITMFGCSLAKHR 450 (496)
Q Consensus 419 sLDpD-VEELLLeIA-DDFVDsVvt~ACrLAKHR 450 (496)
-++++ ++++|-+|. .+||||. .+|..+++.+
T Consensus 39 g~~~~~i~~vl~~l~~~~~ldD~-~~a~~~~~~~ 71 (157)
T PRK00117 39 GFSEEVIEAVLDRLKEEGLLDDE-RFAESFVRSR 71 (157)
T ss_pred CCCHHHHHHHHHHHHHcCCCCHH-HHHHHHHHHH
Confidence 34555 444444443 4567776 7777777665
No 360
>cd00336 Ribosomal_L22 Ribosomal protein L22/L17e. L22 (L17 in eukaryotes) is a core protein of the large ribosomal subunit. It is the only ribosomal protein that interacts with all six domains of 23S rRNA, and is one of the proteins important for directing the proper folding and stabilizing the conformation of 23S rRNA. L22 is the largest protein contributor to the surface of the polypeptide exit channel, the tunnel through which the polypeptide product passes. L22 is also one of six proteins located at the putative translocon binding site on the exterior surface of the ribosome.
Probab=24.26 E-value=1.5e+02 Score=25.37 Aligned_cols=51 Identities=10% Similarity=0.107 Sum_probs=36.4
Q ss_pred CCHHHHHHHHHhhCCCCCCCHHH--HHHHHHHHHHHHHHHHHHHHHhhhhcCCC
Q 010992 402 LTKRSIQELVNQIDPSERLDPDV--EDILVDIAEDFVESITMFGCSLAKHRKSD 453 (496)
Q Consensus 402 LtKrKLqELVrqIDPsesLDpDV--EELLLeIADDFVDsVvt~ACrLAKHRKSd 453 (496)
++-+|+.++++.|.+. .+|+.. -+++.+=+-.+|.+++..|...|++.+.+
T Consensus 10 ~S~kK~~~v~~~Irg~-~v~~A~~~L~~~~kk~a~~i~k~l~sa~~nA~~~~~~ 62 (105)
T cd00336 10 ISPKKARLVARLIRGM-SVDEALAQLEFVPKKAAKIILKLLKSAEANAENNGLD 62 (105)
T ss_pred cCHHHHHHHHHHHcCC-cHHHHHHHHHhCCHHHHHHHHHHHHHHHHhHHHcCCC
Confidence 5678999999999553 344332 23333445688999999999999987765
No 361
>cd05127 RasGAP_IQGAP_related This family represents IQ motif containing GTPase activating protein (IQGAP) which associated with the Ras GTP-binding protein. A primary function of IQGAP proteins is to modulate cytoskeletal architecture. There are three known IQGAP family members: IQGAP1, IQGAP2 and IQGAP3. Human IQGAP1 and IQGAP2 share 62% indentity. IQGAPs are multi-domain molecules having a calponin-homology (CH) domain which binds F-actin, IQGAP-specific repeats, a single WW domain, four IQ motifs that mediate interactions with calmodulin, and a RasGAP related domain that binds active Rho family GTPases. IQGAP is an essential regulator of cytoskeletal function. IQGAP1 negatively regulates Ras family GTPases by stimulating their intrinsic GTPase activity, the protein actually lacks GAP activity. Both IQGAP1 and IQGAP2 specifically bind to Cdc42 and Rac1, but not to RhoA. Despite of their similarities to part of the sequence of RasGAP, neither IQGAP1 nor IQGAP2 interacts with Ras. IQGA
Probab=24.19 E-value=2.1e+02 Score=28.83 Aligned_cols=21 Identities=19% Similarity=0.290 Sum_probs=17.0
Q ss_pred HHHHHHHHHHHHHHHHHHHhh
Q 010992 427 ILVDIAEDFVESITMFGCSLA 447 (496)
Q Consensus 427 LLLeIADDFVDsVvt~ACrLA 447 (496)
.|.+++++|++.|+...+++-
T Consensus 123 ~L~~~~~~fl~~I~~s~~~~P 143 (325)
T cd05127 123 SLRELTEQFLDAIISSLDKIP 143 (325)
T ss_pred HHHHHHHHHHHHHHHHHHHCC
Confidence 588999999999988765543
No 362
>PF07464 ApoLp-III: Apolipophorin-III precursor (apoLp-III); InterPro: IPR010009 This family consists of several insect apolipoprotein-III sequences. Exchangeable apolipoproteins constitute a functionally important family of proteins that play critical roles in lipid transport and lipoprotein metabolism. Apolipophorin III (apoLp-III) is a prototypical exchangeable apolipoprotein found in many insect species that functions in transport of diacylglycerol (DAG) from the fat body lipid storage depot to flight muscles in the adult life stage [].; GO: 0008289 lipid binding, 0006869 lipid transport, 0005576 extracellular region; PDB: 1EQ1_A.
Probab=24.18 E-value=1.3e+02 Score=28.35 Aligned_cols=24 Identities=13% Similarity=0.185 Sum_probs=15.7
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHH
Q 010992 418 ERLDPDVEDILVDIAEDFVESITM 441 (496)
Q Consensus 418 esLDpDVEELLLeIADDFVDsVvt 441 (496)
....++++++|.++.|+|++..-.
T Consensus 120 ~~~~e~l~~~~K~~~D~~~k~~~~ 143 (155)
T PF07464_consen 120 EGANEKLQPAIKQAYDDAVKAAQK 143 (155)
T ss_dssp -SS-GGGHHHHHHHHHHHHHHHHH
T ss_pred HhhhHHHHHHHHHHHHHHHHHHHH
Confidence 567777777777777777766544
No 363
>TIGR02419 C4_traR_proteo phage/conjugal plasmid C-4 type zinc finger protein, TraR family. Members of this family are putative C4-type zinc finger proteins found almost exclusively in prophage regions, actual phage, or conjugal transfer regions of the Proteobactia. This small protein (about 70 amino acids) appears homologous to but is smaller than DksA (DnaK suppressor protein), found to be critical for regulating transcription of ribosomal RNA.
Probab=24.16 E-value=1.4e+02 Score=24.14 Aligned_cols=10 Identities=30% Similarity=0.564 Sum_probs=8.2
Q ss_pred cccccCCCCC
Q 010992 486 PVRIVTDPIP 495 (496)
Q Consensus 486 ~~~~~~d~~~ 495 (496)
.|.+||++||
T Consensus 33 ~C~~Cg~~Ip 42 (63)
T TIGR02419 33 ECEDCGEPIP 42 (63)
T ss_pred eeccCCCcCh
Confidence 6788888887
No 364
>cd01936 Ntn_CA Cephalosporin acylase (CA) belongs to a family of beta-lactam acylases that includes penicillin G acylase (PGA) and aculeacin A acylase. PGA and CA are crucial for the production of backbone chemicals like 6-aminopenicillanic acid and 7-aminocephalosporanic acid (7-ACA), which can be used to synthesize semi-synthetic penicillins and cephalosporins, respectively. While both PGA and CA have a conserved Ntn (N-terminal nucleophile) hydrolase fold and the structural similarity at their active sites is very high, their sequence similarity to other Ntn's is low.
Probab=24.04 E-value=1.7e+02 Score=31.34 Aligned_cols=64 Identities=13% Similarity=0.312 Sum_probs=32.3
Q ss_pred HHHHHHHHHhhCCCCCCCHH-HHHHHHH----HHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccc
Q 010992 404 KRSIQELVNQIDPSERLDPD-VEDILVD----IAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTL 472 (496)
Q Consensus 404 KrKLqELVrqIDPsesLDpD-VEELLLe----IADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~I 472 (496)
-.++.+|+.++....+++.+ ++++.++ +|+.|++.++. +|.. ......++++. +.+=++||...
T Consensus 337 ~~Ri~~ll~~~~~~~~~t~~d~~~~q~D~~~~~a~~l~~~L~~-~~~~---~~~~~~~~~~a-~~~L~~WD~~~ 405 (469)
T cd01936 337 SLRTRMGLEELQPGGRFTLEELQALKFDNRLYLAERVLPDLLA-ACAA---SDDAAADLAAA-CAVLAAWDRTA 405 (469)
T ss_pred HHHHHHHHhhcccCCCCCHHHHHHHhhCccchhHHHHHHHHHH-HHhh---cCCCCHHHHHH-HHHHHHhcCCC
Confidence 34677788765333456544 5666655 45566655543 3432 11222234444 33344687554
No 365
>PRK11064 wecC UDP-N-acetyl-D-mannosamine dehydrogenase; Provisional
Probab=24.04 E-value=2.6e+02 Score=29.31 Aligned_cols=70 Identities=11% Similarity=0.144 Sum_probs=41.0
Q ss_pred HHHHHHHHHhhCCCC--CCCHHHHHHHHHHHHHHHHHHHHHHHH---hhhhcCCCCcchhhHHHHHhhhcCc--cccCCC
Q 010992 404 KRSIQELVNQIDPSE--RLDPDVEDILVDIAEDFVESITMFGCS---LAKHRKSDTLEAKDILVHLERNWNM--TLPGFS 476 (496)
Q Consensus 404 KrKLqELVrqIDPse--sLDpDVEELLLeIADDFVDsVvt~ACr---LAKHRKSdTLEvKDVQLhLERnWNI--~IPGFs 476 (496)
.+++.+|.+.+.... ..+...-|+..-+.+-|+.--+.++.. ||++-+ |++.+|.-.+...|.+ --||+|
T Consensus 185 ~~~~~~ly~~~~~~~~~~~~~~~Ae~~Kl~~N~~~a~~ia~~nE~~~lae~~G---iD~~~v~~~~~~~~ri~~l~pG~G 261 (415)
T PRK11064 185 SARASELYKIFLEGECVVTNSRTAEMCKLTENSFRDVNIAFANELSLICADQG---INVWELIRLANRHPRVNILQPGPG 261 (415)
T ss_pred HHHHHHHHHHhcCCCeeeCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC---CCHHHHHHHhccCCCcccCCCCCC
Confidence 356778888775432 345566677766666677665555554 555555 5566665555555443 335543
No 366
>PRK15057 UDP-glucose 6-dehydrogenase; Provisional
Probab=23.99 E-value=2.8e+02 Score=29.06 Aligned_cols=60 Identities=13% Similarity=0.151 Sum_probs=38.0
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh--cCccc--cC--CCcc
Q 010992 419 RLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERN--WNMTL--PG--FSGD 478 (496)
Q Consensus 419 sLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn--WNI~I--PG--FssD 478 (496)
..+...-|+..-+.+-|+.--+.++..+|..=+.--+++.+|.-.+... +|..+ || ||+-
T Consensus 187 ~~~~~~AE~~Kl~~N~~~a~~Ia~~NE~a~lae~~GiD~~eV~~a~~~d~ri~~~~l~pG~G~GG~ 252 (388)
T PRK15057 187 FTDSTEAEAIKLFANTYLAMRVAYFNELDSYAESLGLNTRQIIEGVCLDPRIGNHYNNPSFGYGGY 252 (388)
T ss_pred eCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCcCHHHHHHHhcCCCCCCCccCCCCCCCCCc
Confidence 4677888888888888988877777665544333335566665555444 45444 54 4454
No 367
>PRK09490 metH B12-dependent methionine synthase; Provisional
Probab=23.98 E-value=1.4e+02 Score=36.35 Aligned_cols=49 Identities=10% Similarity=0.390 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhc-----CCCCcchhhHHHHHhhhc-Cccc-cCCCcc
Q 010992 427 ILVDIAEDFVESITMFGCSLAKHR-----KSDTLEAKDILVHLERNW-NMTL-PGFSGD 478 (496)
Q Consensus 427 LLLeIADDFVDsVvt~ACrLAKHR-----KSdTLEvKDVQLhLERnW-NI~I-PGFssD 478 (496)
+|--|||.++|.+++..++.-|+. ..+.++.+|+ ++..| |++. |||.+=
T Consensus 1093 ~~~ala~~laEa~aE~~h~~iR~~~wg~~~~e~~~~~~l---~~~~Y~G~R~spGYpac 1148 (1229)
T PRK09490 1093 MVKALADRLAEAFAEYLHERVRKEFWGYAPDENLSNEEL---IREKYQGIRPAPGYPAC 1148 (1229)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCCCCccccCHHHH---HhccCCCcCCCCCCCCC
Confidence 444678888888888888877655 3455666665 55666 7887 899863
No 368
>TIGR00511 ribulose_e2b2 ribose-1,5-bisphosphate isomerase, e2b2 family. The delineation of this family was based originally, in part, on a discussion and neighbor-joining phylogenetic study by Kyrpides and Woese of archaeal and other proteins homologous to the alpha, beta, and delta subunits of eukaryotic initiation factor 2B (eIF-2B), a five-subunit molecule that catalyzes GTP recycling for eIF-2. Recently, Sato, et al. assigned the function ribulose-1,5 bisphosphate isomerase.
Probab=23.94 E-value=1.5e+02 Score=30.08 Aligned_cols=40 Identities=5% Similarity=0.163 Sum_probs=24.6
Q ss_pred HHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 010992 407 IQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAK 448 (496)
Q Consensus 407 LqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAK 448 (496)
++.+++.|+. .-.+++.+.|++-+++|++.+...--++|+
T Consensus 68 i~~~~~~i~~--~~~~~~k~~l~~~~~~~~~e~~~a~~~I~~ 107 (301)
T TIGR00511 68 VRYVLKYMSG--EDVETLRETVIERADAFINQSDKAQERIGE 107 (301)
T ss_pred HHHHHHHhcc--CCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455555532 112557788999999999886554444443
No 369
>PF10431 ClpB_D2-small: C-terminal, D2-small domain, of ClpB protein ; InterPro: IPR019489 Most Clp ATPases form complexes with peptidase subunits and are involved in protein degradation, though some, such as ClpB, do not associate with peptidases and are involved in protein disaggregation []. This entry represents the C-terminal domain of Clp ATPases, often referred to as the D2-small domain, which forms a mixed alpha-beta structure. Compared with the adjacent AAA D1-small domain (IPR003959 from INTERPRO) it lacks the long coiled-coil insertion, and instead of helix C4 contains a beta-strand (e3) that is part of a three stranded beta-pleated sheet. In Thermophilus the whole protein forms a hexamer with the D1-small and D2-small domains located on the outside of the hexamer, with the long coiled-coil being exposed on the surface. The D2-small domain is essential for oligomerisation, forming a tight interface with the D2-large domain of a neighbouring subunit, thereby providing enough binding energy to stabilise the functional assembly [].; PDB: 3HWS_A 3HTE_F 1KYI_T 1G3I_S 1OFH_B 1OFI_A 1G41_A 1IM2_A 3PXI_A 1R6B_X ....
Probab=23.92 E-value=1.2e+02 Score=24.20 Aligned_cols=27 Identities=19% Similarity=0.308 Sum_probs=14.7
Q ss_pred HHHHHHHhhC---CCCCCCHHHHHHHHHHH
Q 010992 406 SIQELVNQID---PSERLDPDVEDILVDIA 432 (496)
Q Consensus 406 KLqELVrqID---PsesLDpDVEELLLeIA 432 (496)
.|.+|.+++. -...+|++|.+.|.+.+
T Consensus 13 ~l~~l~~~l~~~~i~l~~~~~~~~~l~~~~ 42 (81)
T PF10431_consen 13 QLKKLNERLKEKGIELEFDDAVVDYLAEKG 42 (81)
T ss_dssp HHHHHHHHHHHTTEEEEE-HHHHHHHHHHH
T ss_pred HHHHHHHHHHHCCCeEEecHHHHHHHHHhC
Confidence 4555554442 23467777777776654
No 370
>PRK14962 DNA polymerase III subunits gamma and tau; Provisional
Probab=23.90 E-value=1.8e+02 Score=31.42 Aligned_cols=66 Identities=8% Similarity=0.036 Sum_probs=41.6
Q ss_pred CCHHHHHHHHHhhC--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhc
Q 010992 402 LTKRSIQELVNQID--PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNW 468 (496)
Q Consensus 402 LtKrKLqELVrqID--PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnW 468 (496)
++...|.++++++. -+..+|+++.++|.+.++-=+..+++.-.+++...+ +.|+.+||.-.|.+..
T Consensus 176 l~~~el~~~L~~i~~~egi~i~~eal~~Ia~~s~GdlR~aln~Le~l~~~~~-~~It~e~V~~~l~~~~ 243 (472)
T PRK14962 176 ISDELIIKRLQEVAEAEGIEIDREALSFIAKRASGGLRDALTMLEQVWKFSE-GKITLETVHEALGLIP 243 (472)
T ss_pred ccHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcC-CCCCHHHHHHHHcCCC
Confidence 45666777777763 356899999999999776323334443334433322 2488999987776543
No 371
>PRK05629 hypothetical protein; Validated
Probab=23.89 E-value=2.4e+02 Score=27.93 Aligned_cols=66 Identities=15% Similarity=0.113 Sum_probs=41.8
Q ss_pred CCHHHHHHHHHhh--CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhc
Q 010992 402 LTKRSIQELVNQI--DPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNW 468 (496)
Q Consensus 402 LtKrKLqELVrqI--DPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnW 468 (496)
+..+.|.+.|++. ..+.+|++++.++|++....=...+...--+|+.+-+ ..|+.+||.-.+.++-
T Consensus 126 ~~~~~l~~wi~~~~~~~g~~i~~~A~~~L~~~~g~dl~~l~~EleKL~~~~~-~~It~e~V~~~v~~~~ 193 (318)
T PRK05629 126 LKPRERPGWVTQEFKNHGVRPTPDVVHALLEGVGSDLRELASAISQLVEDTQ-GNVTVEKVRAYYVGVA 193 (318)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHCccHHHHHHHHHHHHhcCC-CCcCHHHHHHHhCCCc
Confidence 3455555555554 3467899999999998775433334443445554433 4699999987766653
No 372
>PF10127 Nuc-transf: Predicted nucleotidyltransferase; InterPro: IPR018775 Proteins in this entry are predicted to catalyse the transfer of nucleotide residues from nucleoside diphosphates or triphosphates into dimer or polymer forms.
Probab=23.83 E-value=1.9e+02 Score=27.78 Aligned_cols=21 Identities=24% Similarity=0.196 Sum_probs=9.9
Q ss_pred HHHHHHHHHHHHHHhhhhcCC
Q 010992 432 AEDFVESITMFGCSLAKHRKS 452 (496)
Q Consensus 432 ADDFVDsVvt~ACrLAKHRKS 452 (496)
.++||++.+..+-..++....
T Consensus 213 l~~~i~~~l~~~~~~~~~~~~ 233 (247)
T PF10127_consen 213 LDDFIESELERAEEASKLPEK 233 (247)
T ss_pred HHHHHHHHHHHHHHhcCCCCC
Confidence 344555555554444444333
No 373
>KOG2612 consensus Predicted integral membrane protein [Function unknown]
Probab=23.71 E-value=1.3e+02 Score=27.20 Aligned_cols=74 Identities=18% Similarity=0.155 Sum_probs=52.8
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCc--chhhHHHHHhhhcCccccCCCcccccccCCcccccC
Q 010992 418 ERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTL--EAKDILVHLERNWNMTLPGFSGDEIKTFRKPVRIVT 491 (496)
Q Consensus 418 esLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTL--EvKDVQLhLERnWNI~IPGFssDEIr~~rk~~~~~~ 491 (496)
..||+.+--+|-.|.||.|.+|+..--.+-|.-|-.-+ ..+|--+++..+-|+.|-|+....-|+.---|..|+
T Consensus 6 iniDe~aNgilnnLL~~~iqdI~a~e~~~qkl~k~~~~D~rpedssY~f~~~gnLDI~Giqkqaek~~~~hCeNC~ 81 (103)
T KOG2612|consen 6 INIDEAANGILNNLLDDAIQDIFAEEHHLQKLGKLAALDGRPEDSSYRFCEMGNLDIFGIQKQAEKPMDCHCENCD 81 (103)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCccccceeecCCCCcchhhhhhhccCCccccCCCCc
Confidence 45777788888899999999998776555444333333 355878899988899999988655555555566665
No 374
>PF08369 PCP_red: Proto-chlorophyllide reductase 57 kD subunit; InterPro: IPR013580 This domain is found in bacteria and plant chloroplast proteins. It often appears at the C-terminal of nitrogenase component 1 type oxidoreductases (IPR000510 from INTERPRO) and sometimes independently in bacterial proteins such as the proto-chlorophyllide reductase subunit B of the cyanobacterium Synechocystis. This domain is also associated with chlorophyllide reductase subunit Z, converts chlorophylls (Chl) into bacteriochlorophylls (BChl) by reducing ring B of the tetrapyrrole.; GO: 0016491 oxidoreductase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process, 0055114 oxidation-reduction process; PDB: 2KRU_A 2L09_A.
Probab=23.62 E-value=78 Score=24.18 Aligned_cols=40 Identities=20% Similarity=0.116 Sum_probs=25.8
Q ss_pred CHHHHHHHHHHHHHHHHHHHHH-HHHhhhhcCCCCcchhhHH
Q 010992 421 DPDVEDILVDIAEDFVESITMF-GCSLAKHRKSDTLEAKDIL 461 (496)
Q Consensus 421 DpDVEELLLeIADDFVDsVvt~-ACrLAKHRKSdTLEvKDVQ 461 (496)
|+|+++.|-+| =-||...+.. +=++|+.+|.+.|++.+|.
T Consensus 2 ~~eA~~~L~~i-P~fvR~~~r~~~E~~Ar~~G~~~IT~e~v~ 42 (45)
T PF08369_consen 2 TDEAEARLDRI-PFFVRKKLRDAAEKYARERGYDEITVEVVD 42 (45)
T ss_dssp -HHHHHHHCTS--HHHHHHHHHHHHHHHHHCT-SEE-HHHHH
T ss_pred CHHHHHHHHHC-CHHHHHHHHHHHHHHHHHcCCCeECHHHHH
Confidence 56777777665 4576655544 4479999999999887763
No 375
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=23.52 E-value=74 Score=29.97 Aligned_cols=16 Identities=50% Similarity=0.785 Sum_probs=13.7
Q ss_pred CCHHHHHHHHHhhCCC
Q 010992 402 LTKRSIQELVNQIDPS 417 (496)
Q Consensus 402 LtKrKLqELVrqIDPs 417 (496)
|+-+++.||+++||..
T Consensus 8 l~ar~i~ELleki~e~ 23 (139)
T COG1710 8 LTARNIRELLEKIDED 23 (139)
T ss_pred hhhhhHHHHHHHcchh
Confidence 6778899999999864
No 376
>PRK14958 DNA polymerase III subunits gamma and tau; Provisional
Probab=23.52 E-value=2e+02 Score=31.35 Aligned_cols=62 Identities=13% Similarity=0.061 Sum_probs=35.7
Q ss_pred CCHHHHHHHHHhhC--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHH
Q 010992 402 LTKRSIQELVNQID--PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHL 464 (496)
Q Consensus 402 LtKrKLqELVrqID--PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhL 464 (496)
|+...|.+.|+.|- .+..+|+++.++|.+.++.=+.++++..=+++-+ +...|+.+||.-.|
T Consensus 178 l~~~~i~~~l~~il~~egi~~~~~al~~ia~~s~GslR~al~lLdq~ia~-~~~~It~~~V~~~l 241 (509)
T PRK14958 178 LPPLQIAAHCQHLLKEENVEFENAALDLLARAANGSVRDALSLLDQSIAY-GNGKVLIADVKTML 241 (509)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCcHHHHHHHHHHHHhc-CCCCcCHHHHHHHH
Confidence 45566666555552 3457889998888888775444443333222222 34457777775443
No 377
>PF00161 RIP: Ribosome inactivating protein; InterPro: IPR001574 A number of bacterial and plant toxins act by inhibiting protein synthesis in eukaryotic cells. The toxins of the shiga and ricin family inactivate 60S ribosomal subunits by an N-glycosidic cleavage which releases a specific adenine base from the sugar-phosphate backbone of 28S rRNA [, , ]. Members of the family include shiga and shiga-like toxins, and type I (e.g. trichosanthin and luffin) and type II (e.g. ricin, agglutinin and abrin) ribosome inactivating proteins (RIPs). All these toxins are structurally related. RIPs have been of considerable interest because of their potential use, conjugated with monoclonal antibodies, as immunotoxins to treat cancers. Further, trichosanthin has been shown to have potent activity against HIV-1-infected T cells and macrophages []. Elucidation of the structure-function relationships of RIPs has therefore become a major research effort. It is now known that RIPs are structurally related. A conserved glutamic residue has been implicated in the catalytic mechanism []; this lies near a conserved arginine, which also plays a role in catalysis [].; GO: 0030598 rRNA N-glycosylase activity, 0017148 negative regulation of translation; PDB: 3KU0_A 3KTZ_B 4EMF_A 3U6T_A 3QJI_A 3SJ6_A 3U6Z_A 3S9Q_A 4EMR_A 3U8F_A ....
Probab=23.51 E-value=1.4e+02 Score=28.01 Aligned_cols=70 Identities=16% Similarity=0.245 Sum_probs=42.0
Q ss_pred CccCCHHHHHHHHHhhCCCCC--CCHHHHHHHHHHHHHHHHHH----HHHHHHhhhhcCCCCcchhhHHHHHhhhcC
Q 010992 399 NRILTKRSIQELVNQIDPSER--LDPDVEDILVDIAEDFVESI----TMFGCSLAKHRKSDTLEAKDILVHLERNWN 469 (496)
Q Consensus 399 nrILtKrKLqELVrqIDPses--LDpDVEELLLeIADDFVDsV----vt~ACrLAKHRKSdTLEvKDVQLhLERnWN 469 (496)
+=-|+|..|.+.|+.+..... .+.++.+.|+-++--|.|-+ |+..+.-.-++. +...+.+-...||++|+
T Consensus 122 ~v~lG~~~L~~ai~~L~~~~~~~~~~~~araL~~~i~mvsEAaRF~~I~~~v~~~~~~~-~~~~~~~~~~~l~~nW~ 197 (206)
T PF00161_consen 122 NVPLGRQSLDDAIRTLARYDPNTDEADLARALLVLIQMVSEAARFRYIERRVSNNFDDN-RGFKPDPKMISLENNWG 197 (206)
T ss_dssp GSEBSHHHHHHHHHHHHTTSSTSTHHHHHHHHHHHHHHTHHHHHBHHHHHHHHHTTHCT-SEBESHHHHHHHHHTHH
T ss_pred cceEcHHHHHHHHHHHHhcCCccchHHHHHHHHHHeEeeecccccHHHHHHHHHhhccC-CCcCCCHHHHHHHhhHH
Confidence 346799999999999855433 55666677766655444422 111111111333 33566677788999997
No 378
>cd03568 VHS_STAM VHS domain family, STAM subfamily; members include STAM (Signal Transducing Adaptor Molecule), EAST (EGFR-associated protein with SH3 and TAM domains) and Hbp (Hrs-binding protein). Collectively, they are referred to as STAM. All STAMs have at their N-termini a VHS domain, which is involved in cytokine-mediated intracellular signal transduction and has a superhelical structure similar to the structure of ARM (Armadillo) repeats, followed by a SH3 (Src homology 3) domain, a well-established protein-protein interaction domain. At the C-termini of most vertebrate STAMS, an ITAM (Immunoreceptor Tyrosine-based Activation) motif is present, which mediates the binding of HRS (hepatocyte growth factor-regulated tyrosine kinase substrate) in endocytic and exocytic machineries.
Probab=23.51 E-value=1.4e+02 Score=27.32 Aligned_cols=36 Identities=19% Similarity=0.437 Sum_probs=24.0
Q ss_pred cCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHH
Q 010992 401 ILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVES 438 (496)
Q Consensus 401 ILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDs 438 (496)
|-+|+-|.+|++-|+.. .+.+|.+-+|+|.+.|-+.
T Consensus 76 vask~Fl~eL~kl~~~~--~~~~Vk~kil~li~~W~~~ 111 (144)
T cd03568 76 VASRDFTQELKKLINDR--VHPTVKEKLREVVKQWADE 111 (144)
T ss_pred HhhHHHHHHHHHHhccc--CCHHHHHHHHHHHHHHHHH
Confidence 44667777777777665 6777777777776665543
No 379
>COG1223 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=23.48 E-value=1.9e+02 Score=30.89 Aligned_cols=36 Identities=19% Similarity=0.214 Sum_probs=30.3
Q ss_pred HHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcC
Q 010992 434 DFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWN 469 (496)
Q Consensus 434 DFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWN 469 (496)
|.+|.|+..|.--|..-+.+.|+.+||+.+|++.-.
T Consensus 322 dikekvlK~aLh~Ai~ed~e~v~~edie~al~k~r~ 357 (368)
T COG1223 322 DIKEKVLKTALHRAIAEDREKVEREDIEKALKKERK 357 (368)
T ss_pred hHHHHHHHHHHHHHHHhchhhhhHHHHHHHHHhhcc
Confidence 567788888888888889999999999999998543
No 380
>PF13877 RPAP3_C: Potential Monad-binding region of RPAP3
Probab=23.44 E-value=2.2e+02 Score=23.44 Aligned_cols=32 Identities=16% Similarity=0.365 Sum_probs=22.9
Q ss_pred HHHHHHHHHhhCC-------CCCCCHHHHHHHHHHHHHH
Q 010992 404 KRSIQELVNQIDP-------SERLDPDVEDILVDIAEDF 435 (496)
Q Consensus 404 KrKLqELVrqIDP-------sesLDpDVEELLLeIADDF 435 (496)
.....++++.|++ +..||.|+-.-|+++.+++
T Consensus 21 ~~~~~~yL~~i~p~~l~~if~~~l~~~~L~~il~~l~~~ 59 (94)
T PF13877_consen 21 PEERYEYLKSIPPDSLPKIFKNSLEPEFLSEILEALNEH 59 (94)
T ss_pred HHHHHHHHHhCChHHHHHHHHccCCHHHHHHHHHHHHHH
Confidence 3456677888876 4689999877777776663
No 381
>TIGR00563 rsmB ribosomal RNA small subunit methyltransferase RsmB. The seed alignment is built from bacterial sequences only. Eukaryotic homologs include Nop2, a protein required for processing pre-rRNA, that is likely also a rRNA methyltransferase, although the fine specificity may differ. Cutoff scores are set to avoid treating archaeal and eukaroytic homologs automatically as functionally equivalent, although they may have very similar roles.
Probab=23.43 E-value=2.1e+02 Score=29.84 Aligned_cols=64 Identities=14% Similarity=0.067 Sum_probs=37.3
Q ss_pred CHHHHHHHHHhhCC--CCCCCHHHHHHHHHHHHH-HHHH-----HHHHHHHhhhhcCCCCc--chhhHHHHHhh
Q 010992 403 TKRSIQELVNQIDP--SERLDPDVEDILVDIAED-FVES-----ITMFGCSLAKHRKSDTL--EAKDILVHLER 466 (496)
Q Consensus 403 tKrKLqELVrqIDP--sesLDpDVEELLLeIADD-FVDs-----Vvt~ACrLAKHRKSdTL--EvKDVQLhLER 466 (496)
.+..|+++|+++-. ...++..+.-+++-.++. |-++ |++.|+.|||..+.+.. =|--|...+.|
T Consensus 46 ~~~~lD~~i~~~~~~~~~~l~~~~~~L~~~~~e~l~~~~~p~~aainEaVelaK~~~~~~~~~fVNgVLr~i~r 119 (426)
T TIGR00563 46 TLSQLDWLIKKLMDRPMKGKPRTVHYLILVGLYQLLYTRIPAHAAVAETVEGAKAIKRKGLKGLVNGVLRRFQR 119 (426)
T ss_pred hHHHHHHHHHHHhCCCccccCHHHHHHHHHHHHHHhcCCCCCEehHHHHHHHHHhcCCccchhhHHHHHHHHhh
Confidence 46667777777632 245666555444445555 3334 78999999997665421 13444555544
No 382
>cd00159 RhoGAP RhoGAP: GTPase-activator protein (GAP) for Rho-like GTPases; GAPs towards Rho/Rac/Cdc42-like small GTPases. Small GTPases (G proteins) cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when bound to GDP. The Rho family of small G proteins, which includes Cdc42Hs, activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. G proteins generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude. The RhoGAPs are one of the major classes of regulators of Rho G proteins.
Probab=23.42 E-value=4.8e+02 Score=22.43 Aligned_cols=30 Identities=3% Similarity=0.231 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHhhhhcCCCCcchhhHHHHH
Q 010992 435 FVESITMFGCSLAKHRKSDTLEAKDILVHL 464 (496)
Q Consensus 435 FVDsVvt~ACrLAKHRKSdTLEvKDVQLhL 464 (496)
.+..++.+-+++++|...+.+.++.|..++
T Consensus 109 ~L~~l~~~l~~v~~~~~~n~M~~~nLa~~f 138 (169)
T cd00159 109 LLKYLLKLLHKISQNSEVNKMTASNLAIVF 138 (169)
T ss_pred HHHHHHHHHHHHHhhccCCCCCHHHHHHHH
Confidence 455567788888888877777777765544
No 383
>PRK06347 autolysin; Reviewed
Probab=23.39 E-value=86 Score=35.10 Aligned_cols=39 Identities=13% Similarity=0.187 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCcc
Q 010992 432 AEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMT 471 (496)
Q Consensus 432 ADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~ 471 (496)
.++||+.|...|.++||..+--- .|.=-|-+||-.||-.
T Consensus 150 ~~~FI~~i~~~A~~~~~~~gi~a-Sv~iAQAiLESgwG~S 188 (592)
T PRK06347 150 VQSFIQTIQASSSQIAAENDLYA-SVMIAQAILESAYGTS 188 (592)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCh-HHHHHHHHHHccCCcc
Confidence 47999999999999999887552 4455588999999853
No 384
>cd05392 RasGAP_Neurofibromin_like Neurofibromin-like proteins include the Saccharomyces cerevisiae RasGAP proteins Ira1 and Ira2, the closest homolog of neurofibromin, which is responsible for the human autosomal dominant disease neurofibromatosis type I (NF1). The RasGAP Ira1/2 proteins are negative regulators of the Ras-cAMP signaling pathway and conserved from yeast to human. In yeast Ras proteins are activated by GEFs, and inhibited by two GAPs, Ira1 and Ira2. Ras proteins activate the cAMP/protein kinase A (PKA) pathway, which controls metabolism, stress resistance, growth, and meiosis. Recent studies showed that the kelch proteins Gpb1 and Gpb2 inhibit Ras activity via association with Ira1 and Ira2. Gpb1/2 bind to a conserved C-terminal domain of Ira1/2, and loss of Gpb1/2 results in a destabilization of Ira1 and Ira2, leading to elevated levels of Ras2-GTP and uninhibited cAMP-PKA signaling. Since the Gpb1/2 binding domain on Ira1/2 is conserved in the human neurofibromin prote
Probab=23.39 E-value=2.3e+02 Score=28.50 Aligned_cols=23 Identities=17% Similarity=0.278 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhh
Q 010992 426 DILVDIAEDFVESITMFGCSLAK 448 (496)
Q Consensus 426 ELLLeIADDFVDsVvt~ACrLAK 448 (496)
+.|.+++++|++.|+....++-.
T Consensus 126 ~~L~~~~~~~l~~I~~s~~~~P~ 148 (323)
T cd05392 126 DLLEKYCQKFIDAIISSLDRFPP 148 (323)
T ss_pred HHHHHHHHHHHHHHHHhHHhCCH
Confidence 56889999999999986655443
No 385
>PF08299 Bac_DnaA_C: Bacterial dnaA protein helix-turn-helix; InterPro: IPR013159 This entry represents the C-terminal domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; GO: 0005524 ATP binding, 0043565 sequence-specific DNA binding, 0006270 DNA-dependent DNA replication initiation, 0006275 regulation of DNA replication; PDB: 2HCB_B 3R8F_C 1L8Q_A 3PVP_B 3PVV_A 1J1V_A.
Probab=23.31 E-value=30 Score=27.86 Aligned_cols=47 Identities=32% Similarity=0.453 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhc-Ccccc
Q 010992 424 VEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNW-NMTLP 473 (496)
Q Consensus 424 VEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnW-NI~IP 473 (496)
+|+++-.+|+.|=-++ .--+.|-|+.+.+++++|..||-|++ ++.++
T Consensus 2 ~~~Ii~~Va~~~~v~~---~~i~s~~R~~~i~~aR~va~yL~r~~~~~sl~ 49 (70)
T PF08299_consen 2 IEDIIEAVAEYFGVSV---EDIRSKSRKRKIVEARQVAMYLARELTGLSLS 49 (70)
T ss_dssp HHHHHHHHHHHTT--H---HHHHSS---HHHHHHHHHHHHHHHHHS---HH
T ss_pred HHHHHHHHHHHHCCCH---HHHhCCCCChhhcchHHHHHHHHHHHhCCCHH
Confidence 4666777777773222 22345667777889999999998884 66554
No 386
>PRK06645 DNA polymerase III subunits gamma and tau; Validated
Probab=23.25 E-value=1.7e+02 Score=32.11 Aligned_cols=66 Identities=15% Similarity=0.061 Sum_probs=43.3
Q ss_pred cCCHHHHHHHHHhhCC--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcC--CCCcchhhHHHHHhh
Q 010992 401 ILTKRSIQELVNQIDP--SERLDPDVEDILVDIAEDFVESITMFGCSLAKHRK--SDTLEAKDILVHLER 466 (496)
Q Consensus 401 ILtKrKLqELVrqIDP--sesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRK--SdTLEvKDVQLhLER 466 (496)
-++...|.+.++++-. +..+|+++.++|.+.++--+.+++..-.+++.+-+ ...|+.+||.-.|.+
T Consensus 186 ~ls~~el~~~L~~i~~~egi~ie~eAL~~Ia~~s~GslR~al~~Ldkai~~~~~~~~~It~~~V~~llg~ 255 (507)
T PRK06645 186 RLSFEEIFKLLEYITKQENLKTDIEALRIIAYKSEGSARDAVSILDQAASMSAKSDNIISPQVINQMLGL 255 (507)
T ss_pred CCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhhccCCCCcCHHHHHHHHCC
Confidence 3567777777776643 45789999999999888766666555444433321 235788888655443
No 387
>PF07156 Prenylcys_lyase: Prenylcysteine lyase; InterPro: IPR010795 This entry represents a conserved region found in a group of prenylcysteine lyases (1.8.3.5 from EC) that are approximately 500 residues long. Prenylcysteine lyase is a FAD-dependent thioether oxidase that degrades a variety of prenylcysteines, producing free cysteine, an isoprenoid aldehyde and hydrogen peroxide as products of the reaction []. It has been noted that this enzyme has considerable homology with ClP55, a 55 kDa protein that is associated with chloride ion pumps [].; GO: 0016670 oxidoreductase activity, acting on a sulfur group of donors, oxygen as acceptor, 0030328 prenylcysteine catabolic process, 0055114 oxidation-reduction process
Probab=23.24 E-value=1.1e+02 Score=31.95 Aligned_cols=62 Identities=18% Similarity=0.310 Sum_probs=45.2
Q ss_pred CCCCCCHHHHHHHHHHH-HHHHHHHHHHHHHhhhhcCCCCcchhhH-HHHHhhhcCc--cccCCCcc
Q 010992 416 PSERLDPDVEDILVDIA-EDFVESITMFGCSLAKHRKSDTLEAKDI-LVHLERNWNM--TLPGFSGD 478 (496)
Q Consensus 416 PsesLDpDVEELLLeIA-DDFVDsVvt~ACrLAKHRKSdTLEvKDV-QLhLERnWNI--~IPGFssD 478 (496)
+...++. |+|++..|- |||++-.-...+..-|+.+-+..=++|| +-.+.-|||- .|.||.+-
T Consensus 45 ~~~~F~s-v~~l~~~lg~~~~~~~t~~t~~e~L~~~gi~~~fi~Elv~a~tRvNYgQ~~~i~a~~G~ 110 (368)
T PF07156_consen 45 PGFPFSS-VEELLSALGGDDFLNLTKVTGEEYLKENGISERFINELVQAATRVNYGQNVNIHAFAGL 110 (368)
T ss_pred CCCCcCC-HHHHHHHhCChHHHHHHHHHHHHHHHHCCCCHHHHHHHHHhheEeecccccchhhhhhh
Confidence 4455555 889888888 8899888877777777777666667777 4556778886 77777653
No 388
>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]
Probab=23.22 E-value=1.4e+02 Score=34.17 Aligned_cols=48 Identities=27% Similarity=0.275 Sum_probs=38.4
Q ss_pred CCCCHHHHHHHHHHHHHHH-------------------HHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992 418 ERLDPDVEDILVDIAEDFV-------------------ESITMFGCSLAKHRKSDTLEAKDILVHLE 465 (496)
Q Consensus 418 esLDpDVEELLLeIADDFV-------------------DsVvt~ACrLAKHRKSdTLEvKDVQLhLE 465 (496)
-.|.+|+.|.|.+.-.+-- |+|+..|-.+||-|=|+.|+.+||..+++
T Consensus 524 P~lt~ea~e~l~~~Yv~~Rk~~~~~~~~~~~piT~RqLEsiiRLaeA~Ak~rLS~~V~~eD~~eAi~ 590 (682)
T COG1241 524 PVLTEEAREELEDYYVEMRKKSALVEEKRTIPITARQLESIIRLAEAHAKMRLSDVVEEEDVDEAIR 590 (682)
T ss_pred cccCHHHHHHHHHHHHHhhhccccccccCcccccHHHHHHHHHHHHHHHhhhccCCCCHHHHHHHHH
Confidence 3688888888876654444 55899999999999999999999976654
No 389
>cd00051 EFh EF-hand, calcium binding motif; A diverse superfamily of calcium sensors and calcium signal modulators; most examples in this alignment model have 2 active canonical EF hands. Ca2+ binding induces a conformational change in the EF-hand motif, leading to the activation or inactivation of target proteins. EF-hands tend to occur in pairs or higher copy numbers.
Probab=23.20 E-value=1.2e+02 Score=20.44 Aligned_cols=17 Identities=6% Similarity=0.388 Sum_probs=8.7
Q ss_pred CCccCCHHHHHHHHHhh
Q 010992 398 GNRILTKRSIQELVNQI 414 (496)
Q Consensus 398 ~nrILtKrKLqELVrqI 414 (496)
.+..|++..+..+++.+
T Consensus 13 ~~g~l~~~e~~~~l~~~ 29 (63)
T cd00051 13 GDGTISADELKAALKSL 29 (63)
T ss_pred CCCcCcHHHHHHHHHHh
Confidence 33445555555555544
No 390
>PLN02162 triacylglycerol lipase
Probab=23.18 E-value=77 Score=34.94 Aligned_cols=62 Identities=15% Similarity=0.258 Sum_probs=41.6
Q ss_pred HHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCCCc
Q 010992 406 SIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSG 477 (496)
Q Consensus 406 KLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGFss 477 (496)
+...++-.+|....||+...-. | ..+.-+++-+||+||-+.+ +.|+-+.++.|+|.+-||=.
T Consensus 113 ~~~s~ig~~d~r~~l~~~~~~~--~--~~~~~~l~ima~klayen~------~~i~~~v~~~w~m~~v~~y~ 174 (475)
T PLN02162 113 TYTSFIGCSDRRIELDEKIDVG--S--IEYKSMLSIMASKISYESK------PFINSVVKNTWKMDLVGNYD 174 (475)
T ss_pred cHHhHhhcccccccccccCCcc--c--chhHHHHHHHHHHHhhcCH------HHHHHHHHHhcCccccchhh
Confidence 3455666667776666553100 0 1677788999999998643 44566689999999976643
No 391
>KOG1662 consensus Mitochondrial F1F0-ATP synthase, subunit OSCP/ATP5 [Energy production and conversion]
Probab=23.17 E-value=1.3e+02 Score=30.32 Aligned_cols=60 Identities=23% Similarity=0.321 Sum_probs=47.8
Q ss_pred CCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHH-----HHHHHHHHHHHhhhhcCCCCcch
Q 010992 398 GNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAED-----FVESITMFGCSLAKHRKSDTLEA 457 (496)
Q Consensus 398 ~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADD-----FVDsVvt~ACrLAKHRKSdTLEv 457 (496)
.+..|+|++-...|+.|....++++....+|--|||. |-+-|-.|...+.+|||.-.+++
T Consensus 76 ~nP~l~~~~k~~~i~di~~~~~~~~~t~NflnlLaeNgRL~~l~~Ivk~F~~lm~ahrGev~~~V 140 (210)
T KOG1662|consen 76 LNPTLTREKKKTAIDDIVEKLKLAPLTKNFLNLLAENGRLNNLTEIVKAFETLMNAHRGEVKVEV 140 (210)
T ss_pred cCCccchHHHHHHHHHHHHHhcccHhHHHHHHHHHHcCchhhHHHHHHHHHHHHHHhCCceEEEE
Confidence 4566788888888888888889999999999988884 45556678999999999764443
No 392
>PRK00979 tetrahydromethanopterin S-methyltransferase subunit H; Provisional
Probab=23.17 E-value=1.3e+02 Score=31.48 Aligned_cols=77 Identities=9% Similarity=0.073 Sum_probs=52.7
Q ss_pred CCcCCccCCHHHHHHHHHhhCCC---------CCCCHHHHHHHHHHHHHHHH-------------HHHHHHHHhhhhcC-
Q 010992 395 DEFGNRILTKRSIQELVNQIDPS---------ERLDPDVEDILVDIAEDFVE-------------SITMFGCSLAKHRK- 451 (496)
Q Consensus 395 ~e~~nrILtKrKLqELVrqIDPs---------esLDpDVEELLLeIADDFVD-------------sVvt~ACrLAKHRK- 451 (496)
+++...++.|.+=.+|+++.+.. ..+=-|-+|+|.++.|.+.+ +|++.|+++|+.-+
T Consensus 42 ~D~~~G~FDk~~Ae~Li~~~~elsd~tg~p~~~~v~~~~~eam~k~I~~v~~~~d~Pl~IDSt~p~a~eaaLk~~~e~G~ 121 (308)
T PRK00979 42 SDEKKGIFDKEKAEALINRQEELSDKTGNPALLDVVGESPEAMEKYIDFVSEITDLPFLIDSTSPEARIAAAKYATELGL 121 (308)
T ss_pred eccccCccCHHHHHHHHHHHHHHHHHhCCCeEEEEecChHHHHHHHHHHHHhcCCCCEEEeCCCHHHHHHHHHHhhhcCC
Confidence 35667789999999999987421 11222334445555555544 68899999998633
Q ss_pred -------CCCcchhhHHHHHhhhcCcc
Q 010992 452 -------SDTLEAKDILVHLERNWNMT 471 (496)
Q Consensus 452 -------SdTLEvKDVQLhLERnWNI~ 471 (496)
|=.+|.+|-.|-|-|+|++.
T Consensus 122 ~gR~IiNSIn~e~~~eel~llk~yg~a 148 (308)
T PRK00979 122 ADRAIYNSINPSIEEEEIEALKESDIK 148 (308)
T ss_pred CCceEEEeccCCCCHHHHHHHHHhCCc
Confidence 56677777778899999944
No 393
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=23.10 E-value=3e+02 Score=27.26 Aligned_cols=27 Identities=22% Similarity=0.228 Sum_probs=14.5
Q ss_pred HHHHHHHHHHHHhhhhcCCCCcchhhH
Q 010992 434 DFVESITMFGCSLAKHRKSDTLEAKDI 460 (496)
Q Consensus 434 DFVDsVvt~ACrLAKHRKSdTLEvKDV 460 (496)
++|+.-......+|++...+.+++.|+
T Consensus 52 ~Lv~~~~~lV~~ia~~~~~~~~~~eDL 78 (284)
T PRK06596 52 QLVLSHLRFVVHIARGYRGYGLPQADL 78 (284)
T ss_pred HHHHHhHHHHHHHHHHhcCCCCCHHHH
Confidence 334444444444454444456788887
No 394
>PF07697 7TMR-HDED: 7TM-HD extracellular; InterPro: IPR011624 This entry represents the extracellular domain of the 7TM-HD (7TM Receptors with HD hydrolase) protein family []. These proteins are known or predicted, to posses metal-dependent phospohydrolase activity.
Probab=23.08 E-value=2.1e+02 Score=26.04 Aligned_cols=54 Identities=26% Similarity=0.402 Sum_probs=42.6
Q ss_pred CccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHH-------HHhhhhcCC
Q 010992 399 NRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFG-------CSLAKHRKS 452 (496)
Q Consensus 399 nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~A-------CrLAKHRKS 452 (496)
....++++-++.++.|.+-..+|+++.+-+.+-.++|++.+.... -.|.+++.+
T Consensus 21 D~~~t~~~r~~a~~~v~pvy~~d~~~~~~~~~~~~~~f~~i~~~~~~~~~~~~~l~~~~~~ 81 (222)
T PF07697_consen 21 DEEATEQRRQEAAESVPPVYDFDPEVAEEVINRLEEFFEEIREIRQDSESEKDQLEKIKQS 81 (222)
T ss_pred CHHHHHHHHHHHHhcCCcceecCcHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHhhch
Confidence 456688888999999999999999999888888888887776665 455555444
No 395
>PHA02571 a-gt.4 hypothetical protein; Provisional
Probab=22.97 E-value=80 Score=28.89 Aligned_cols=48 Identities=25% Similarity=0.259 Sum_probs=33.6
Q ss_pred CCCCCHH-HHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992 417 SERLDPD-VEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERN 467 (496)
Q Consensus 417 sesLDpD-VEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn 467 (496)
...++++ |||++.+|=+.-.-.+...| +||-+.+.-|++.+..|-|+.
T Consensus 8 ~~~~~d~~~ee~~~~~q~~~e~eA~kkA---~K~lkKN~rEIkRL~~HAe~a 56 (109)
T PHA02571 8 VEELTDEEVEELLSELQARNEAEAEKKA---AKILKKNRREIKRLKKHAEEA 56 (109)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHhHHHHHHHHHHHHHH
Confidence 3456666 89999888887666666654 455555556899998887764
No 396
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=22.85 E-value=1.5e+02 Score=28.17 Aligned_cols=66 Identities=18% Similarity=0.231 Sum_probs=39.9
Q ss_pred CHHHHHHHHHhhCCCCC------C-CHHHHHHHHHHHHHHHHHHHHHH--HHhhhhcCCCCcchhhHHHHHhhhcCc
Q 010992 403 TKRSIQELVNQIDPSER------L-DPDVEDILVDIAEDFVESITMFG--CSLAKHRKSDTLEAKDILVHLERNWNM 470 (496)
Q Consensus 403 tKrKLqELVrqIDPses------L-DpDVEELLLeIADDFVDsVvt~A--CrLAKHRKSdTLEvKDVQLhLERnWNI 470 (496)
.|+.+.+++++|.-+.. - +.+-.+.+-++||+|+++-.... ..+=+-++.+ -.+|-|.|+|+|. |+
T Consensus 33 ~r~T~~eiAee~Gis~~tLYrWr~~~~~Fiey~n~la~~~~~~~~~eVy~~L~~~i~~~~-~svKaieLflk~~-GL 107 (142)
T PF13022_consen 33 ERRTQAEIAEEVGISRSTLYRWRQQNKAFIEYKNELADRFLSSHREEVYTQLMKKIRGGQ-PSVKAIELFLKRH-GL 107 (142)
T ss_dssp --S-HHHHHHHHTS-HHHHHHHHHH-HHHHHHHHHHHHHHHHTTHHHHHHHHHHHHHSSS---HHHHHHHHHHT-T-
T ss_pred ccchHHHHHHHhCCCHHHHHHHHhcCHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhCCC-ccHHHHHHHHHHc-Cc
Confidence 46667788888764431 1 33477888888888887755544 3333444666 4799999999984 54
No 397
>cd07023 S49_Sppa_N_C Signal peptide peptidase A (SppA), a serine protease, has catalytic Ser-Lys dyad. Signal peptide peptidase A (SppA; Peptidase S49; Protease IV): SppA is found in all three domains of life and is involved in the cleavage of signal peptides after their removal from the precursor proteins by signal peptidases. This subfamily contains members with either a single domain (sometimes referred to as 36K type), such as sohB peptidase, protein C and archaeal signal peptide peptidase, or an amino-terminal domain in addition to the carboxyl-terminal protease domain that is conserved in all the S49 family members (sometimes referred to as 67K type), similar to E. coli and Arabidopsis thaliana SppA peptidases. Site-directed mutagenesis and sequence analysis have shown these SppAs to be serine proteases. The predicted active site serine for members in this family occurs in a transmembrane domain. Mutagenesis studies also suggest that the catalytic center comprises a Ser-Lys dyad
Probab=22.81 E-value=1.5e+02 Score=27.59 Aligned_cols=34 Identities=18% Similarity=0.270 Sum_probs=19.7
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCC
Q 010992 417 SERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSD 453 (496)
Q Consensus 417 sesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSd 453 (496)
...++++..|.+.++.|+.-+..+. .+|+.||-+
T Consensus 137 ~~~~s~~~~e~~~~~l~~~~~~f~~---~Va~~R~~~ 170 (208)
T cd07023 137 DRPLTEEERAILQALVDDIYDQFVD---VVAEGRGMS 170 (208)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHH---HHHhcCCCC
Confidence 3557777666555555554443333 347888854
No 398
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=22.79 E-value=1.2e+02 Score=30.65 Aligned_cols=65 Identities=14% Similarity=0.161 Sum_probs=40.9
Q ss_pred CHHHHHHHHHhhCCCCCCCHH-HHHHHHHHHHHH----HHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992 403 TKRSIQELVNQIDPSERLDPD-VEDILVDIAEDF----VESITMFGCSLAKHRKSDTLEAKDILVHLERN 467 (496)
Q Consensus 403 tKrKLqELVrqIDPsesLDpD-VEELLLeIADDF----VDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn 467 (496)
+.....++++.......++++ -.+.|.++++.| |..++..|...|-.++...|+.+|+.-.+++.
T Consensus 294 ~~~~r~~Il~~~~~~~~l~~~~~~~~la~~t~g~sg~dl~~l~~~A~~~a~~~~~~~i~~~d~~~a~~~~ 363 (364)
T TIGR01242 294 DFEGRLEILKIHTRKMKLAEDVDLEAIAKMTEGASGADLKAICTEAGMFAIREERDYVTMDDFIKAVEKV 363 (364)
T ss_pred CHHHHHHHHHHHHhcCCCCccCCHHHHHHHcCCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHHh
Confidence 344444554444333334332 234555666554 45677777777777888999999999988863
No 399
>COG5304 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.77 E-value=1.7e+02 Score=26.15 Aligned_cols=54 Identities=17% Similarity=0.254 Sum_probs=37.4
Q ss_pred CCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHH--HHHHHHHhhhhcCCCCcc
Q 010992 402 LTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVES--ITMFGCSLAKHRKSDTLE 456 (496)
Q Consensus 402 LtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDs--Vvt~ACrLAKHRKSdTLE 456 (496)
-.|.++..+.+.++ ...+|+|+|..|-+=-+||-.. .-.++..++|..++=+|.
T Consensus 2 ~~ke~~~nM~k~lp-k~~~d~Eae~~l~Qdi~D~~~~~~fqk~afe~lkkd~riniR 57 (92)
T COG5304 2 RNKENISNMIKDLP-KNALDEEAENDLWQDIKDFEQEKHFQKAAFEYLKKDTRINIR 57 (92)
T ss_pred cchHHHHhhhhccc-hhccchhhHHHHHHhhHHHHHHHHHHHHHHHHhcccceeeEe
Confidence 36888999998884 4667888888888777777654 355666666655554443
No 400
>TIGR03566 FMN_reduc_MsuE FMN reductase, MsuE subfamily. Members of this protein family use NAD(P)H to reduce FMN and regenerate FMNH2. Members include the NADH-dependent enzyme MsuE from Pseudomonas aeruginosa, which serves as a partner to an FMNH2-dependent alkanesulfonate monooxygenase. The NADP-dependent enzyme from E. coli is outside the scope of this model.
Probab=22.61 E-value=1e+02 Score=27.80 Aligned_cols=25 Identities=0% Similarity=-0.105 Sum_probs=19.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHHHHHH
Q 010992 415 DPSERLDPDVEDILVDIAEDFVESI 439 (496)
Q Consensus 415 DPsesLDpDVEELLLeIADDFVDsV 439 (496)
|.++..|+++.+.|.+++|+|++-+
T Consensus 147 ~~g~l~d~~~~~~l~~~~~~~~~~~ 171 (174)
T TIGR03566 147 ADYRLASEALRARIALAVDRAAPLL 171 (174)
T ss_pred ccccccCHHHHHHHHHHHHHHHHHh
Confidence 4455678899999999999998765
No 401
>COG4077 Uncharacterized protein conserved in archaea [Function unknown]
Probab=22.56 E-value=1.8e+02 Score=27.87 Aligned_cols=45 Identities=18% Similarity=0.200 Sum_probs=26.1
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992 419 RLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER 466 (496)
Q Consensus 419 sLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER 466 (496)
....|..|++.+| |+||..+++---.--. .-+++-+..++-.||.
T Consensus 70 ~es~Eg~elI~e~-De~vr~~vei~te~~i--~~d~~GfeRlKeslE~ 114 (156)
T COG4077 70 KESFEGVELIKEI-DEFVRRIVEILTENPI--YPDTFGFERLKESLEM 114 (156)
T ss_pred ccCHHHHHHHHHH-HHHHHHHHHhhhcCCC--ccCcchHHHHHHHHHH
Confidence 3455666666666 9998877664332211 3345556666666654
No 402
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=22.53 E-value=56 Score=31.98 Aligned_cols=45 Identities=16% Similarity=0.212 Sum_probs=28.9
Q ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHH
Q 010992 417 SERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILV 462 (496)
Q Consensus 417 sesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQL 462 (496)
+..+++.+++++--|.+.+.+||++.|+.|-.+..-+.+ +|||+|
T Consensus 277 ~~~~~~~~~~fi~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~ 321 (324)
T PRK12681 277 GTFLRSYMYDFIERFAPHLTRDVVEKAVALRSNEEIEEM-FKDIKL 321 (324)
T ss_pred CchhhHHHHHHHHHHHHHHHHHHHHHHHHhhchHHHHHH-HhhcCC
Confidence 345666777777777777799999988877544333321 556544
No 403
>cd05027 S-100B S-100B: S-100B domain found in proteins similar to S100B. S100B is a calcium-binding protein belonging to a large S100 vertebrate-specific protein family within the EF-hand superfamily of calcium-binding proteins. Note that the S-100 hierarchy, to which this S-100B group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100B is most abundant in glial cells of the central nervous system, predominately in astrocytes. S100B is involved in signal transduction via the inhibition of protein phoshorylation, regulation of enzyme activity and by affecting the calcium homeostasis. Upon calcium binding the S100B homodimer changes conformation to expose a hydrophobic cleft, which represents the interaction site of S100B with its more than 20 known target proteins. These target proteins include several cellular architecture proteins such as tubulin and GFAP; S100B can inhibit polymerization of these oligomeric molecules. Furthermore, S100B i
Probab=22.51 E-value=2.9e+02 Score=23.07 Aligned_cols=33 Identities=21% Similarity=0.461 Sum_probs=22.0
Q ss_pred cCCc-cCCHHHHHHHHHh-----hCCCCCCC-HHHHHHHHHH
Q 010992 397 FGNR-ILTKRSIQELVNQ-----IDPSERLD-PDVEDILVDI 431 (496)
Q Consensus 397 ~~nr-ILtKrKLqELVrq-----IDPsesLD-pDVEELLLeI 431 (496)
+++. .|++..|..|++. ++. ..+ ++|+++|.++
T Consensus 21 dgdG~~I~~~eL~~ll~~~~~~~lg~--~~~~~~v~~~i~~~ 60 (88)
T cd05027 21 EGDKHKLKKSELKELINNELSHFLEE--IKEQEVVDKVMETL 60 (88)
T ss_pred CCCcCEECHHHHHHHHHHHhHHHhcC--CCCHHHHHHHHHHh
Confidence 4555 5899999999987 432 344 3477766655
No 404
>KOG0027 consensus Calmodulin and related proteins (EF-Hand superfamily) [Signal transduction mechanisms]
Probab=22.48 E-value=4e+02 Score=23.49 Aligned_cols=28 Identities=7% Similarity=-0.037 Sum_probs=15.2
Q ss_pred HHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992 439 ITMFGCSLAKHRKSDTLEAKDILVHLER 466 (496)
Q Consensus 439 Vvt~ACrLAKHRKSdTLEvKDVQLhLER 466 (496)
-+..|.++--.-+...|++.+++.+|.+
T Consensus 86 el~eaF~~fD~d~~G~Is~~el~~~l~~ 113 (151)
T KOG0027|consen 86 ELKEAFRVFDKDGDGFISASELKKVLTS 113 (151)
T ss_pred HHHHHHHHHccCCCCcCcHHHHHHHHHH
Confidence 4444555555555555666666555544
No 405
>PRK12712 flgJ flagellar rod assembly protein/muramidase FlgJ; Provisional
Probab=22.41 E-value=97 Score=32.86 Aligned_cols=40 Identities=13% Similarity=0.078 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccc
Q 010992 432 AEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTL 472 (496)
Q Consensus 432 ADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~I 472 (496)
.++||+.|...|.++||.-|-.. .+-=-|-+||-.||-++
T Consensus 197 ~~~FI~~l~p~A~~aa~~~Gi~p-sv~lAQAaLESGWGks~ 236 (344)
T PRK12712 197 VSAFVARMAGPAEAASRASGVPA-RLIVGQAALESGWGRRE 236 (344)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCh-HHHHHHHHHHccCCccc
Confidence 39999999999999999888663 45555889999999665
No 406
>cd04378 RhoGAP_GMIP_PARG1 RhoGAP_GMIP_PARG1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of GMIP (Gem interacting protein) and PARG1 (PTPL1-associated RhoGAP1). GMIP plays important roles in neurite growth and axonal guidance, and interacts with Gem, a member of the RGK subfamily of the Ras small GTPase superfamily, through the N-terminal half of the protein. GMIP contains a C-terminal RhoGAP domain. GMIP inhibits RhoA function, but is inactive towards Rac1 and Cdc41. PARG1 interacts with Rap2, also a member of the Ras small GTPase superfamily whose exact function is unknown, and shows strong preference for Rho. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases ge
Probab=22.36 E-value=2.9e+02 Score=26.08 Aligned_cols=31 Identities=3% Similarity=0.126 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992 435 FVESITMFGCSLAKHRKSDTLEAKDILVHLE 465 (496)
Q Consensus 435 FVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE 465 (496)
.+.-++.+-+++++|...+..+++.+..++-
T Consensus 139 ~L~~L~~~L~~V~~~s~~NkM~~~NLaivf~ 169 (203)
T cd04378 139 TLQHLIAHLYRVAEQFEENKMSPNNLGIVFG 169 (203)
T ss_pred HHHHHHHHHHHHHHHHHhhCCCHHHhhhhhc
Confidence 4455677778889888888888888776654
No 407
>KOG1756 consensus Histone 2A [Chromatin structure and dynamics]
Probab=22.30 E-value=2.5e+02 Score=26.58 Aligned_cols=71 Identities=11% Similarity=0.163 Sum_probs=56.8
Q ss_pred CcCCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh
Q 010992 396 EFGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLER 466 (496)
Q Consensus 396 e~~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER 466 (496)
+..+-++.--.|..++|+-.....|..++--+|.-+.+-..-+|++.+-..|+.-+...|..|-|++.+..
T Consensus 22 ~~agl~fPvgri~r~Lr~~~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~N 92 (131)
T KOG1756|consen 22 SRAGLQFPVGRIHRLLRKGRYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIRN 92 (131)
T ss_pred hhcccccCHHHHHHHHHccchhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHhC
Confidence 33445666778999999855666777777777777778888889999999999988888999999988863
No 408
>PF13743 Thioredoxin_5: Thioredoxin; PDB: 3KZQ_C.
Probab=22.27 E-value=1.3e+02 Score=27.85 Aligned_cols=54 Identities=19% Similarity=0.158 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCC---CcchhhHHHHHhhhcCccccCCCcc
Q 010992 422 PDVEDILVDIAEDFVESITMFGCSLAKHRKSD---TLEAKDILVHLERNWNMTLPGFSGD 478 (496)
Q Consensus 422 pDVEELLLeIADDFVDsVvt~ACrLAKHRKSd---TLEvKDVQLhLERnWNI~IPGFssD 478 (496)
=|+++++-++-++++...+..-.++|+.-+-+ +|=+-| .-+.+.|+.|-|+-..
T Consensus 115 LD~~~F~~d~~S~~~~~~~~~D~~la~~m~I~~~Ptlvi~~---~~~~~~g~~i~g~~~~ 171 (176)
T PF13743_consen 115 LDVEMFKEDLHSDEAKQAFQEDQQLAREMGITGFPTLVIFN---ENNEEYGILIEGYYSY 171 (176)
T ss_dssp --HHHHHHHHTSHHHHHHHHHHHHHHHHTT-SSSSEEEEE--------------------
T ss_pred CCHHHHHHHHhChHHHHHHHHHHHHHHHcCCCCCCEEEEEe---cccccccccccccccc
Confidence 34556666666666666666666777665544 222222 2345566666666543
No 409
>COG1893 ApbA Ketopantoate reductase [Coenzyme metabolism]
Probab=22.26 E-value=1.4e+02 Score=30.20 Aligned_cols=36 Identities=17% Similarity=0.191 Sum_probs=23.7
Q ss_pred CCCCCHHHHHHHHHHHHHH-HHHHHHHHHHhhhhcCC
Q 010992 417 SERLDPDVEDILVDIAEDF-VESITMFGCSLAKHRKS 452 (496)
Q Consensus 417 sesLDpDVEELLLeIADDF-VDsVvt~ACrLAKHRKS 452 (496)
+..+|+++.|.++.+.++. =+...++.-.++|+|.-
T Consensus 230 g~~~~~~~~~~v~~~~~~~~~~~~sSM~qDl~~gr~t 266 (307)
T COG1893 230 GVELPEEVVERVLAVIRATDAENYSSMLQDLEKGRPT 266 (307)
T ss_pred cCCCCHHHHHHHHHHHHhcccccCchHHHHHHcCCcc
Confidence 4689999999999999988 34444444444444433
No 410
>PF05016 Plasmid_stabil: Plasmid stabilisation system protein; InterPro: IPR007712 Members of this family are involved in plasmid stabilisation. The exact molecular function of this protein is not known.; PDB: 3KXE_A 1WMI_A 3KIQ_y 3KIX_y 2KC9_A 3KHA_B 3KIS_y 3KIU_y 2KC8_A 1Z8M_A ....
Probab=22.26 E-value=50 Score=25.51 Aligned_cols=41 Identities=15% Similarity=0.208 Sum_probs=27.6
Q ss_pred HHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccC
Q 010992 431 IAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPG 474 (496)
Q Consensus 431 IADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPG 474 (496)
.|+.|++.|....-+|+.+...-.. .+++. ++..|-+.+.+
T Consensus 24 ~a~~~~~~i~~~i~~l~~~P~~~~~-~~~~~--~~~~~~~~~~~ 64 (90)
T PF05016_consen 24 AAERFIDAIEKAIERLSENPEMGRP-SRELG--LKGYRRIRIGD 64 (90)
T ss_dssp HHHHHHHHHHHHHHHHHCCCCTTEE-EEETT--CTTEEEEEETT
T ss_pred HHHHHHHHHHHHHHhcccccccccc-ccccc--ccCcccccCce
Confidence 3889999999988889888777654 22222 44555565553
No 411
>COG0091 RplV Ribosomal protein L22 [Translation, ribosomal structure and biogenesis]
Probab=22.21 E-value=1.6e+02 Score=26.96 Aligned_cols=57 Identities=11% Similarity=0.204 Sum_probs=40.1
Q ss_pred cCCHHHHHHHHHhhCCCCCCCHH--HHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhH
Q 010992 401 ILTKRSIQELVNQIDPSERLDPD--VEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDI 460 (496)
Q Consensus 401 ILtKrKLqELVrqIDPsesLDpD--VEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDV 460 (496)
-++.+|..+.+..|-+. .+++. ..+..-.-|..+|..|++.|..-|.|++ -||..++
T Consensus 19 riSpkk~r~Va~~IrG~-~v~~A~~~L~~~pkKaa~~v~KvL~sA~aNAe~n~--gLd~d~L 77 (120)
T COG0091 19 RISPKKARLVADLIRGK-KVAEALAILEFVPKKAAKLVKKVLESAIANAENNK--GLDPDKL 77 (120)
T ss_pred cCChHHHHHHHHHHcCC-cHHHHHHHHHhChHHHHHHHHHHHHHHHhhHHhcc--CCChHHE
Confidence 45778888888888543 33332 2333456789999999999999999973 3555554
No 412
>COG0776 HimA Bacterial nucleoid DNA-binding protein [DNA replication, recombination, and repair]
Probab=22.21 E-value=2.7e+02 Score=24.57 Aligned_cols=18 Identities=28% Similarity=0.473 Sum_probs=11.9
Q ss_pred HhhhcCccccCCCccccc
Q 010992 464 LERNWNMTLPGFSGDEIK 481 (496)
Q Consensus 464 LERnWNI~IPGFssDEIr 481 (496)
|++-=.+.|.|||.=|++
T Consensus 37 L~~G~~V~l~gFG~F~v~ 54 (94)
T COG0776 37 LAKGERVELRGFGTFEVR 54 (94)
T ss_pred HHcCCeEEEeeeeeeEee
Confidence 344445677888887776
No 413
>PLN00203 glutamyl-tRNA reductase
Probab=22.19 E-value=2.6e+02 Score=30.81 Aligned_cols=66 Identities=11% Similarity=0.200 Sum_probs=38.8
Q ss_pred HHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCC--CCcch-hhHHHHHhhhcCcc
Q 010992 404 KRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKS--DTLEA-KDILVHLERNWNMT 471 (496)
Q Consensus 404 KrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKS--dTLEv-KDVQLhLERnWNI~ 471 (496)
++.|..+++++. ..++++-++.|-+++..+|+.+++.-....|.... +..+- .+..-.|++-||+.
T Consensus 446 ~~Eler~~~kl~--~~~~~~~~~~ie~~~~~ivnkllh~P~~~Lr~~a~~~~~~~~~~~~~~~l~~lF~l~ 514 (519)
T PLN00203 446 AAELEKCLSKMG--DDLTKKQRKAVEDLSRGIVNKLLHGPMQHLRCDGSDSRTVSETLENMHALNRMFDLE 514 (519)
T ss_pred HHHHHHHHHhcc--ccCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccCcccHHHHHHHHHHHhCCC
Confidence 344445555542 12677777777777777777777776666665431 11122 24556688888764
No 414
>PRK10061 DNA damage-inducible protein YebG; Provisional
Probab=22.07 E-value=93 Score=27.94 Aligned_cols=21 Identities=24% Similarity=0.262 Sum_probs=15.7
Q ss_pred CCHHHHHHHHHHHHHHHHHHH
Q 010992 420 LDPDVEDILVDIAEDFVESIT 440 (496)
Q Consensus 420 LDpDVEELLLeIADDFVDsVv 440 (496)
=+-|+.|=||||||.|.+=+.
T Consensus 23 KEADAyDKMLD~Ad~L~~~L~ 43 (96)
T PRK10061 23 KEADAYDKMLDTADLLDTWLT 43 (96)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 356788889999998876543
No 415
>PRK07003 DNA polymerase III subunits gamma and tau; Validated
Probab=22.01 E-value=1.2e+02 Score=35.55 Aligned_cols=46 Identities=11% Similarity=0.123 Sum_probs=32.0
Q ss_pred ccCCHHHHHHHHHhhCCC--CCCCHHHHHHHHHHHHHHHHHHHHHHHH
Q 010992 400 RILTKRSIQELVNQIDPS--ERLDPDVEDILVDIAEDFVESITMFGCS 445 (496)
Q Consensus 400 rILtKrKLqELVrqIDPs--esLDpDVEELLLeIADDFVDsVvt~ACr 445 (496)
+-|++..|.+.|++|-.. ..+|+++.++|.+++|-=+.+.++..-+
T Consensus 176 k~Ls~eeIv~~L~~Il~~EgI~id~eAL~lIA~~A~GsmRdALsLLdQ 223 (830)
T PRK07003 176 KQMPAGHIVSHLERILGEERIAFEPQALRLLARAAQGSMRDALSLTDQ 223 (830)
T ss_pred CCcCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 345677888888887543 4688999999999887655555554333
No 416
>PF02268 TFIIA_gamma_N: Transcription initiation factor IIA, gamma subunit, helical domain; InterPro: IPR015872 Transcription factor IIA (TFIIA) is one of several factors that form part of a transcription pre-initiation complex along with RNA polymerase II, the TATA-box-binding protein (TBP) and TBP-associated factors, on the TATA-box sequence upstream of the initiation start site. After initiation, some components of the pre-initiation complex (including TFIIA) remain attached and re-initiate a subsequent round of transcription. TFIIA binds to TBP to stabilise TBP binding to the TATA element. TFIIA also inhibits the cytokine HMGB1 (high mobility group 1 protein) binding to TBP [], and can dissociate HMGB1 already bound to TBP/TATA-box. Human and Drosophila TFIIA have three subunits: two large subunits, LN/alpha and LC/beta, derived from the same gene, and a small subunit, S/gamma. Yeast TFIIA has two subunits: a large TOA1 subunit that shows sequence similarity to the N-terminal of LN/alpha and the C-terminal of LC/beta, and a small subunit, TOA2 that is highly homologous with S/gamma. The conserved regions of the large and small subunits of TFIIA combine to form two domains: a four-helix bundle (helical domain) composed of two helices from each of the N-terminal regions of TOA1 and TOA2 in yeast; and a beta-barrel (beta-barrel domain) composed of beta-sheets from the C-terminal regions of TOA1 and TOA2 []. This entry represents the alpha-helical domain found at the N-terminal of the gamma subunit of transcription factor TFIIA.; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005672 transcription factor TFIIA complex; PDB: 1NVP_D 1RM1_B 1YTF_D 1NH2_D.
Probab=21.99 E-value=2.5e+02 Score=22.35 Aligned_cols=32 Identities=9% Similarity=0.324 Sum_probs=23.6
Q ss_pred HHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHH
Q 010992 405 RSIQELVNQIDPSERLDPDVEDILVDIAEDFVESIT 440 (496)
Q Consensus 405 rKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVv 440 (496)
+.|+|||. ...|+++....+|+-.|.-|++.+
T Consensus 17 dtLDeli~----~~~I~p~La~kVL~~FDksi~~~L 48 (49)
T PF02268_consen 17 DTLDELIQ----EGKITPQLAMKVLEQFDKSINEAL 48 (49)
T ss_dssp HHHHHHHH----TTSS-HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHH----cCCCCHHHHHHHHHHHHHHHHHHh
Confidence 34666666 478999999999988888777654
No 417
>PF06122 TraH: Conjugative relaxosome accessory transposon protein; InterPro: IPR010927 Six Tra proteins encoded by the F plasmid and required by F(+) cells to elaborate F pili. The six proteins are TraH, TraF, TraW, TraU, TrbI, and TrbB. Except for TrbI, these proteins were all identified as hallmarks of F-like type IV secretion systems (TFSSs), with no homologues among TFSS genes of P-type or I-type systems. With the exception of TrbI, which is an inner membrane protein, the remaining proteins are or are predicted to be periplasmic. TrbI consists of one membrane-spanning segment near its N terminus and an 88-residue, hydrophilic domain that extends into the periplasm []. It has been proposed that the TraH interaction group is to control F-pilus extension and retraction during conjugation [, , ].
Probab=21.89 E-value=1.2e+02 Score=31.40 Aligned_cols=60 Identities=10% Similarity=0.202 Sum_probs=42.4
Q ss_pred CCCcCCccCCHHHHHHHHHhhCCC----------CCCCHHHHHHHHHHHH--HHHHHHHHHHHHhhhhcCCC
Q 010992 394 SDEFGNRILTKRSIQELVNQIDPS----------ERLDPDVEDILVDIAE--DFVESITMFGCSLAKHRKSD 453 (496)
Q Consensus 394 ~~e~~nrILtKrKLqELVrqIDPs----------esLDpDVEELLLeIAD--DFVDsVvt~ACrLAKHRKSd 453 (496)
.-..+=.+|+++.|.+|+|.|-.+ ..|.++..+++-+|-+ +.+++....+|++||-=-..
T Consensus 60 ~f~GsFSfIn~dqlVq~lr~Ia~nA~gyAF~LAL~t~~p~~~~~~~~lq~~~~~lN~~~~nsCq~aq~lv~~ 131 (361)
T PF06122_consen 60 LFMGSFSFINSDQLVQMLRNIASNAPGYAFQLALQTLCPQCGNIMDKLQKIAQALNQMNINSCQAAQGLVNG 131 (361)
T ss_pred ccccccccCCHHHHHHHHHHHHHhhHHHHHHHHHHHhCHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHh
Confidence 335667789999999999999543 3577776665554432 35677788899999864444
No 418
>cd02202 FtsZ_type2 FtsZ is a GTPase that is similar to the eukaryotic tubulins and is essential for cell division in prokaryotes. FtsZ is capable of polymerizing in a GTP-driven process into structures similar to those formed by tubulin. FtsZ forms a ring-shaped septum at the site of bacterial cell division, which is required for constriction of cell membrane and cell envelope to yield two daughter cells.
Probab=21.80 E-value=1.2e+02 Score=31.36 Aligned_cols=76 Identities=14% Similarity=0.170 Sum_probs=47.2
Q ss_pred HHHHHHHHHhhCCCCCCCHHHH-H------HHHHHHHHHHHHHHHHHHHhh-----hhcCCCCcchhhHHHHHhhhcCcc
Q 010992 404 KRSIQELVNQIDPSERLDPDVE-D------ILVDIAEDFVESITMFGCSLA-----KHRKSDTLEAKDILVHLERNWNMT 471 (496)
Q Consensus 404 KrKLqELVrqIDPsesLDpDVE-E------LLLeIADDFVDsVvt~ACrLA-----KHRKSdTLEvKDVQLhLERnWNI~ 471 (496)
..-|++|.+.+|--..||.|.. + --.+.+|+-|-.++..-...- +..+.-.+++.||.-.|+. +|+.
T Consensus 151 ~~~l~~L~~~~D~viv~dNd~L~~~~~~~~~~f~~~N~~Ia~~i~~l~~~~r~~~~~~~g~invD~~dv~~~L~~-~G~~ 229 (349)
T cd02202 151 ARSLDALSEEADAIILFDNDAWKRKGESVEEAYDRINEEIARRIGLLLRAGEANAGDSVGESVLDASEVINTLSG-GGFA 229 (349)
T ss_pred HHHHHHHHHhCCEEEEEehHHHhhhccchHHHHHHHHHHHHHHHHHHHHhhhcccCCCCCeEeccHHHHHHHhcc-CCeE
Confidence 4568888888887767776642 1 112333333333333222222 2255667999999999965 7999
Q ss_pred ccCCCcccc
Q 010992 472 LPGFSGDEI 480 (496)
Q Consensus 472 IPGFssDEI 480 (496)
+-||+..+.
T Consensus 230 ~iG~g~~~~ 238 (349)
T cd02202 230 TIGYAREDL 238 (349)
T ss_pred EEEEEEEcc
Confidence 999986654
No 419
>PF02399 Herpes_ori_bp: Origin of replication binding protein; InterPro: IPR003450 This entry represents replication origin binding protein. It functions as a docking protein to recruit essential components of the viral replication machinery to viral DNA origins. In the presence of the major DNA-binding protein, it opens dsDNA which leads to a conformational change in the origin that facilitates DNA unwinding and subsequent replication [].; GO: 0003688 DNA replication origin binding, 0005524 ATP binding, 0006260 DNA replication
Probab=21.79 E-value=2e+02 Score=33.81 Aligned_cols=80 Identities=16% Similarity=0.289 Sum_probs=54.9
Q ss_pred cCCCcCCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHH-----HHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992 393 ESDEFGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAE-----DFVESITMFGCSLAKHRKSDTLEAKDILVHLERN 467 (496)
Q Consensus 393 ~~~e~~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIAD-----DFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn 467 (496)
...+-+..++.++.+..++++.=-...-+++.+++|..|++ .||+-++-.|| +|-.+-|+.++|-.-+-..
T Consensus 519 ~~~~~~~~~~~~~~v~~F~~kyL~~~~~~~~~~~ll~~L~~p~~r~~FvN~~~l~aC----~~~p~a~~s~~vf~~~y~~ 594 (824)
T PF02399_consen 519 PAIPPGADLADSDEVGAFVEKYLRPDVPIEDITELLKALASPIVRERFVNAAMLEAC----LRVPAALESEEVFRRIYDH 594 (824)
T ss_pred CCcCcchhhhccHHHHHHHHHHhcCCCChHHHHHHHHHhhCcHHHHHHHHHHHHHHH----hhcchhcccHHHHHHHHHH
Confidence 34556677777777887877763333334778999999885 58888888888 6666777888886555555
Q ss_pred cC-ccccCCC
Q 010992 468 WN-MTLPGFS 476 (496)
Q Consensus 468 WN-I~IPGFs 476 (496)
|. -+||=.+
T Consensus 595 y~sg~vPvv~ 604 (824)
T PF02399_consen 595 YASGVVPVVS 604 (824)
T ss_pred HhcCCcceec
Confidence 54 4566333
No 420
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA.
Probab=21.77 E-value=85 Score=35.10 Aligned_cols=66 Identities=20% Similarity=0.391 Sum_probs=42.9
Q ss_pred HHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCC-CcchhhHHHHHhhhcCccccCCCccccc
Q 010992 409 ELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSD-TLEAKDILVHLERNWNMTLPGFSGDEIK 481 (496)
Q Consensus 409 ELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSd-TLEvKDVQLhLERnWNI~IPGFssDEIr 481 (496)
+|+.+||--..|.+--+|.|.+|++.+++++.. +|. +++-+ .++-+-+.+.+++.|+ +.||+..++
T Consensus 635 ef~~Rid~Vi~F~pLs~e~l~~Iv~~~L~~l~~---~l~-~~~~~l~i~~~a~~~La~~~~~---~~~GaR~l~ 701 (731)
T TIGR02639 635 EFRNRLDAIIHFNPLSEEVLEKIVQKFVDELSK---QLN-EKNIKLELTDDAKKYLAEKGYD---EEFGARPLA 701 (731)
T ss_pred HHHhcCCeEEEcCCCCHHHHHHHHHHHHHHHHH---HHH-hCCCeEEeCHHHHHHHHHhCCC---cccCchHHH
Confidence 788888876666676678889999999988754 443 33332 2333334555666666 556777665
No 421
>PRK06246 fumarate hydratase; Provisional
Probab=21.75 E-value=1.6e+02 Score=30.41 Aligned_cols=49 Identities=18% Similarity=0.232 Sum_probs=33.0
Q ss_pred cCCHHHHHHHHHhh--CCCCCCCHHHHHHHHH--------HHHHHHHHHHHHHHHhhhh
Q 010992 401 ILTKRSIQELVNQI--DPSERLDPDVEDILVD--------IAEDFVESITMFGCSLAKH 449 (496)
Q Consensus 401 ILtKrKLqELVrqI--DPsesLDpDVEELLLe--------IADDFVDsVvt~ACrLAKH 449 (496)
.|...+|.+.|+++ +.+..|.+||.+.|.+ +|..+++.+++.+.--+|.
T Consensus 3 ~i~~~~i~~~v~~~~~~a~~~lp~Dv~~~l~~a~~~E~s~~ak~~l~~ileN~~iA~~~ 61 (280)
T PRK06246 3 EIHVEDIIEAVAELCIEANYYLPDDVKEALKKAYEKEESPIGKEILKAILENAEIAKEE 61 (280)
T ss_pred cccHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHhccChhHHHHHHHHHHHHHHHhcC
Confidence 34455566655554 4567899999999988 7777777777766544443
No 422
>PF14513 DAG_kinase_N: Diacylglycerol kinase N-terminus; PDB: 1TUZ_A.
Probab=21.74 E-value=78 Score=29.38 Aligned_cols=42 Identities=21% Similarity=0.379 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccC
Q 010992 428 LVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPG 474 (496)
Q Consensus 428 LLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPG 474 (496)
|.|+-.||-+ ...||||+..++|+.+-.++.|+-.+...||-
T Consensus 27 lkdvl~eF~~-----~g~~~~~~~~~~Id~egF~~Fm~~yLe~d~P~ 68 (138)
T PF14513_consen 27 LKDVLKEFHG-----DGSLAKYNPEEPIDYEGFKLFMKTYLEVDLPE 68 (138)
T ss_dssp HHHHHHHH-H-----TSGGGGGEETTEE-HHHHHHHHHHHTT-S--H
T ss_pred HHHHHHHHhc-----CCcccccCCCCCcCHHHHHHHHHHHHcCCCCH
Confidence 4444455543 45799999999999999999998888887774
No 423
>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB. Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.
Probab=21.72 E-value=1e+02 Score=35.31 Aligned_cols=66 Identities=21% Similarity=0.284 Sum_probs=40.0
Q ss_pred HHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCC-CcchhhHHHHHhhhcCccccCCCccccc
Q 010992 409 ELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSD-TLEAKDILVHLERNWNMTLPGFSGDEIK 481 (496)
Q Consensus 409 ELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSd-TLEvKDVQLhLERnWNI~IPGFssDEIr 481 (496)
||+.+||.-..+.+--+|.+.+|++-|++.+..+ + +.++-. .++-.-+.+.+++.|+ +-+|..+++
T Consensus 749 el~~Rid~IivF~PL~~e~l~~I~~l~L~~l~~~---l-~~~~~~l~i~~~a~~~L~~~~~~---~~~gaR~L~ 815 (852)
T TIGR03346 749 EFLNRIDEIVVFHPLGREQIARIVEIQLGRLRKR---L-AERKITLELSDAALDFLAEAGYD---PVYGARPLK 815 (852)
T ss_pred HHhcCcCeEEecCCcCHHHHHHHHHHHHHHHHHH---H-HHCCCeecCCHHHHHHHHHhCCC---CCCCchhHH
Confidence 6777888766666666666777777777766553 2 233332 3444445566666676 446777665
No 424
>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family. Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.
Probab=21.72 E-value=1.4e+02 Score=34.51 Aligned_cols=59 Identities=7% Similarity=0.157 Sum_probs=40.0
Q ss_pred CHHHHHHHHHhhC------CCCCCCHHHHHHHHHHHHHHHH---------HHHHHHHHhhhhc-CCCCcchhhHH
Q 010992 403 TKRSIQELVNQID------PSERLDPDVEDILVDIAEDFVE---------SITMFGCSLAKHR-KSDTLEAKDIL 461 (496)
Q Consensus 403 tKrKLqELVrqID------PsesLDpDVEELLLeIADDFVD---------sVvt~ACrLAKHR-KSdTLEvKDVQ 461 (496)
+...+.++++.+. -+..+++++.+.+.++++.||. |+++.||..+|-. .+...++.|+.
T Consensus 351 s~~~~~~iL~~~~~~~e~~~~v~i~d~al~~~~~ls~ryi~~r~LPDKAIdlldea~a~~~~~~~~~p~~~~~~~ 425 (852)
T TIGR03345 351 DEETAIRMLRGLAPVLEKHHGVLILDEAVVAAVELSHRYIPGRQLPDKAVSLLDTACARVALSQNATPAALEDLR 425 (852)
T ss_pred CHHHHHHHHHHHHHhhhhcCCCeeCHHHHHHHHHHcccccccccCccHHHHHHHHHHHHHHHhccCCchhHHHHH
Confidence 4444445544332 3467999999999999998875 4778888766653 45555666664
No 425
>PRK05684 flgJ flagellar rod assembly protein/muramidase FlgJ; Validated
Probab=21.67 E-value=99 Score=32.21 Aligned_cols=43 Identities=16% Similarity=0.155 Sum_probs=33.7
Q ss_pred HHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCcccc
Q 010992 430 DIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLP 473 (496)
Q Consensus 430 eIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IP 473 (496)
.-.++||+.|...|.++||.-|-.. .+-=-|-+||--||-...
T Consensus 150 ~s~~~FI~~i~p~A~~~a~~~GIp~-svilAQAaLESGWG~s~l 192 (312)
T PRK05684 150 GSSDDFVARLSPPAQKAAQQSGVPH-HLLLAQAALESGWGQREI 192 (312)
T ss_pred CCHHHHHHHHHHHHHHHHHHhCcCH-HHHHHHHHHhccCCcccc
Confidence 4458999999999999999877653 444448899999986653
No 426
>PF14357 DUF4404: Domain of unknown function (DUF4404)
Probab=21.65 E-value=1.8e+02 Score=24.79 Aligned_cols=34 Identities=15% Similarity=0.349 Sum_probs=27.1
Q ss_pred HHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHH
Q 010992 404 KRSIQELVNQIDPSERLDPDVEDILVDIAEDFVE 437 (496)
Q Consensus 404 KrKLqELVrqIDPsesLDpDVEELLLeIADDFVD 437 (496)
|..|..|=.+++....+|++-.+.|..+.||.=.
T Consensus 3 ~~~L~~L~~eL~~~~~ld~~~~~~L~~l~~dIe~ 36 (85)
T PF14357_consen 3 QELLEKLHQELEQNPPLDEETRAELSSLDDDIEA 36 (85)
T ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHHHH
Confidence 4567788888888889999999888888887543
No 427
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=21.62 E-value=3e+02 Score=26.82 Aligned_cols=54 Identities=13% Similarity=0.097 Sum_probs=30.1
Q ss_pred CCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhH
Q 010992 398 GNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDI 460 (496)
Q Consensus 398 ~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDV 460 (496)
...++++....+|++++-.. =|.+ ++-+|.+.|..-|...|.++.+ +.+++.||
T Consensus 12 ~~~~l~~~~e~~l~~~~~~~--gd~~---a~~~Lv~~~~~lV~~~a~~~~~----~~~~~eDL 65 (270)
T TIGR02392 12 RIPMLTPEEEYQLAKRLREH--GDLD---AAKKLVLSHLRFVVKIARGYRG----YGLPQADL 65 (270)
T ss_pred cCCCCCHHHHHHHHHHHHHC--CCHH---HHHHHHHHhHHHHHHHHHHHcC----CCCCHHHH
Confidence 44556777777777763100 0222 3345556666666666665543 34678887
No 428
>PF06545 DUF1116: Protein of unknown function (DUF1116); InterPro: IPR009499 This family contains hypothetical bacterial proteins of unknown function.; PDB: 3CLQ_A.
Probab=21.45 E-value=28 Score=34.73 Aligned_cols=79 Identities=14% Similarity=0.311 Sum_probs=44.4
Q ss_pred CCccCCHHHHHHHHHhhCC----CCCCCHHHHHHHHHHH--HHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhh---hc
Q 010992 398 GNRILTKRSIQELVNQIDP----SERLDPDVEDILVDIA--EDFVESITMFGCSLAKHRKSDTLEAKDILVHLER---NW 468 (496)
Q Consensus 398 ~nrILtKrKLqELVrqIDP----sesLDpDVEELLLeIA--DDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLER---nW 468 (496)
+.+--++..=.-|+++|.| ...-.++.+|++.-|+ |-|.=++...+||++-.-... ++-..|...+-| +|
T Consensus 98 E~H~Rn~Aat~ll~~~L~P~l~~~~~~~~~~~~v~~fl~~nd~FFLnl~MAa~K~~~daa~~-i~~stiVtaMarNG~~F 176 (216)
T PF06545_consen 98 ECHNRNIAATSLLLRELAPALVDTDFPKDDKAEVLEFLASNDHFFLNLSMAACKAMMDAARG-IPGSTIVTAMARNGVEF 176 (216)
T ss_dssp -SSS--HHHHHHHHHHHHHHHHTSSS-HHHHHHHHHHHTS-TTTTHHHHHHHHHHHHHHTSS--TT--BEEEEEEESSEE
T ss_pred hhhhHhHHHHHHHHHHHHHHHhccCCChHHHHHHHHHHhcCCceeehHHHHHHHHHHHHhcC-CCCCcEEEeeccCCcEE
Confidence 3344444444444554433 2233445666666665 668889999999987665443 455555566655 47
Q ss_pred CccccCCCc
Q 010992 469 NMTLPGFSG 477 (496)
Q Consensus 469 NI~IPGFss 477 (496)
||+|-|.+.
T Consensus 177 GIrvsG~gd 185 (216)
T PF06545_consen 177 GIRVSGLGD 185 (216)
T ss_dssp EEEETTTTT
T ss_pred EEEecCCCC
Confidence 788877753
No 429
>cd03025 DsbA_FrnE_like DsbA family, FrnE-like subfamily; composed of uncharacterized proteins containing a CXXC motif with similarity to DsbA and FrnE. FrnE is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the aromatic antibiotics frenolicin and nanaomycins.
Probab=21.41 E-value=2.5e+02 Score=24.79 Aligned_cols=25 Identities=20% Similarity=0.119 Sum_probs=10.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhcC
Q 010992 427 ILVDIAEDFVESITMFGCSLAKHRK 451 (496)
Q Consensus 427 LLLeIADDFVDsVvt~ACrLAKHRK 451 (496)
++..+.++-+++.+....++|+.++
T Consensus 142 ~~~~~~s~~~~~~l~~~~~~a~~~g 166 (193)
T cd03025 142 FLEDFQSDEAKQAIQEDQKLARELG 166 (193)
T ss_pred HHHHHcChHHHHHHHHHHHHHHHcC
Confidence 3333444444444444444444433
No 430
>TIGR02849 spore_III_AD stage III sporulation protein AD. Members of this family are the uncharacterized protein SpoIIIAD, part of the spoIIIA operon that acts at sporulation stage III as part of a cascade of events leading to endospore formation. Note that the start sites of members of this family as annotated tend to be variable; quite a few members have apparent homologous protein-coding regions continuing upstream of the first available start codon. The length of the alignment has been set to try to detect all valid members of the family, even if annotation of the start site begins too far downstream.
Probab=21.34 E-value=2.2e+02 Score=25.53 Aligned_cols=48 Identities=17% Similarity=0.325 Sum_probs=38.2
Q ss_pred HHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCc
Q 010992 406 SIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTL 455 (496)
Q Consensus 406 KLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTL 455 (496)
.+-++++++.....+|..-.+.|+++.- |-=|.+|+..+||.-|.+.+
T Consensus 23 ~ii~~l~~l~~~a~i~~~Yi~~llKiiG--IaYIaef~s~iCkDAG~~ai 70 (101)
T TIGR02849 23 AVVEVIQSLARKAGLDSLYLATVLKIIG--IAYIAEFGSQICKDAGEKAI 70 (101)
T ss_pred HHHHHHHHHHHHcCCChHHHHHHHHHHH--HHHHHHHHHHHHHHcChHHH
Confidence 4557778888888999998888888765 55678888888888887765
No 431
>COG0140 HisI Phosphoribosyl-ATP pyrophosphohydrolase [Amino acid transport and metabolism]
Probab=21.21 E-value=2.9e+02 Score=24.52 Aligned_cols=15 Identities=40% Similarity=0.592 Sum_probs=12.3
Q ss_pred cchhhHHHHHhhhcC
Q 010992 455 LEAKDILVHLERNWN 469 (496)
Q Consensus 455 LEvKDVQLhLERnWN 469 (496)
|+++||.-.|+|..+
T Consensus 75 v~l~dV~~eL~~R~~ 89 (92)
T COG0140 75 LSLEDVLRELERRHG 89 (92)
T ss_pred CCHHHHHHHHHHHhh
Confidence 789999999988643
No 432
>KOG1766 consensus Enhancer of rudimentary [General function prediction only]
Probab=21.19 E-value=1.5e+02 Score=26.95 Aligned_cols=41 Identities=12% Similarity=0.382 Sum_probs=30.1
Q ss_pred HHHHHHhhCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCC
Q 010992 407 IQELVNQIDPSE-RLDPDVEDILVDIAEDFVESITMFGCSLAKHRKS 452 (496)
Q Consensus 407 LqELVrqIDPse-sLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKS 452 (496)
..|.++++.|+. .|.-|+.++. ||||+..+.+|.+-.|--.
T Consensus 36 yEe~Lkk~nPs~~~ITYDIsqlf-----eFiD~L~DlS~lVy~~~t~ 77 (104)
T KOG1766|consen 36 YEEHLKKKNPSAPPITYDISQLF-----EFIDDLADLSMLVYNRETG 77 (104)
T ss_pred HHHHHHhcCCCCCCcceeHHHHH-----HHHHHHhhhhhhheecccc
Confidence 567888887764 6777766654 8999999999987655433
No 433
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=21.19 E-value=81 Score=33.71 Aligned_cols=73 Identities=19% Similarity=0.102 Sum_probs=44.3
Q ss_pred HHHHHHhhCCC--CCCCHHHHHHHHHHHHHHHH-----------HHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCcccc
Q 010992 407 IQELVNQIDPS--ERLDPDVEDILVDIAEDFVE-----------SITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLP 473 (496)
Q Consensus 407 LqELVrqIDPs--esLDpDVEELLLeIADDFVD-----------sVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IP 473 (496)
|.+|.+-|... +...++..|+ |.+|+.||- .|...+.--++-.+...+|+.|..+.+||.|+-.|+
T Consensus 294 lgdl~~~i~ga~k~~v~~e~rd~-l~~a~~k~~f~~~w~ne~~~~v~~~~~~~~ra~~~~~ve~~~~~g~~e~~~~~~v~ 372 (383)
T KOG4317|consen 294 LGDLQRLILGAIKEVKSSSGRDL-LKLAERKVFYMMCWVNEQNSEVWEALEPSVRAEKNSVVELNDYRGFPEMKKKDQFR 372 (383)
T ss_pred cccHHHHHhhhhhhhhchhHHHH-HHHhhhhheeeehhcccchhhhHHHhhhhhhcChhhheeHhhhcCchhhhcCCccc
Confidence 44555555443 2344444444 788888863 233333333444456678999999999999997664
Q ss_pred ---CCCcccc
Q 010992 474 ---GFSGDEI 480 (496)
Q Consensus 474 ---GFssDEI 480 (496)
|.-.+||
T Consensus 373 ~~~~v~ieei 382 (383)
T KOG4317|consen 373 KGGGVVIEEI 382 (383)
T ss_pred CCCcceeecc
Confidence 3334454
No 434
>CHL00095 clpC Clp protease ATP binding subunit
Probab=21.18 E-value=1.9e+02 Score=33.05 Aligned_cols=75 Identities=5% Similarity=0.060 Sum_probs=0.0
Q ss_pred HHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHH---------HHHHHHHHhhhhcC------------------------
Q 010992 405 RSIQELVNQIDPSERLDPDVEDILVDIAEDFVE---------SITMFGCSLAKHRK------------------------ 451 (496)
Q Consensus 405 rKLqELVrqIDPsesLDpDVEELLLeIADDFVD---------sVvt~ACrLAKHRK------------------------ 451 (496)
+.|.+...+.-... +++|+.+.+.++++.||. ++++.||..+|-..
T Consensus 351 r~l~~~~e~~~~v~-i~deal~~i~~ls~~yi~~r~lPdkaidlld~a~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 429 (821)
T CHL00095 351 FGLRSRYEKHHNLS-ISDKALEAAAKLSDQYIADRFLPDKAIDLLDEAGSRVRLINSRLPPAARELDKELREILKDKDEA 429 (821)
T ss_pred HHHHHHHHHHcCCC-CCHHHHHHHHHHhhccCccccCchHHHHHHHHHHHHHHhhccCCchhHHHHHHHHHHHHHHHHHH
Q ss_pred ---------------------------------------CCCcchhhHHHHHhhhcCccccCCCcccc
Q 010992 452 ---------------------------------------SDTLEAKDILVHLERNWNMTLPGFSGDEI 480 (496)
Q Consensus 452 ---------------------------------------SdTLEvKDVQLhLERnWNI~IPGFssDEI 480 (496)
...|+.+||.-++.+.-||.+--+..||.
T Consensus 430 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~i~~~~~~~tgip~~~~~~~~~ 497 (821)
T CHL00095 430 IREQDFETAKQLRDREMEVRAQIAAIIQSKKTEEEKRLEVPVVTEEDIAEIVSAWTGIPVNKLTKSES 497 (821)
T ss_pred HhCcchHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccccCCccCHHHHHHHHHHHHCCCchhhchhHH
No 435
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=21.06 E-value=2.3e+02 Score=27.18 Aligned_cols=55 Identities=9% Similarity=0.087 Sum_probs=34.1
Q ss_pred CcCCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhH
Q 010992 396 EFGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDI 460 (496)
Q Consensus 396 e~~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDV 460 (496)
.....+|+++...+|+.++-.+ |. +.+-+|.+.|..-|...|.++. .+..++.||
T Consensus 10 ~~~~~~l~~~~~~~li~~~~~g---d~---~a~~~L~~~~~~~v~~~a~~~~----~~~~~aeDl 64 (254)
T TIGR02850 10 TSKLPVLKNQEMRELFIRMQSG---DT---TAREKLINGNLRLVLSVIQRFN----NRGEYVDDL 64 (254)
T ss_pred ccCCCCCCHHHHHHHHHHHHcC---CH---HHHHHHHHHhHHHHHHHHHHHh----CCCCCHHHH
Confidence 3456788999999999877322 32 3455555566655555555443 334578888
No 436
>PF14630 ORC5_C: Origin recognition complex (ORC) subunit 5 C-terminus
Probab=21.01 E-value=2.2e+02 Score=27.92 Aligned_cols=63 Identities=17% Similarity=0.211 Sum_probs=40.5
Q ss_pred CHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccc
Q 010992 403 TKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTL 472 (496)
Q Consensus 403 tKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~I 472 (496)
+|..|.++|..-.+ ..+.....|...+|...||+-|++--+..+. + ++.++....++.|...+
T Consensus 7 s~~e~~~IL~~~~~-~~~~~~~~~~~~~ly~~f~~~i~~~~~~~~~---r---dl~eL~~i~~~lwp~y~ 69 (271)
T PF14630_consen 7 SKDELLEILSLDQP-SELPDLPDDIDRELYNQFVNLILDSFYSYTG---R---DLNELRHIAAKLWPKYV 69 (271)
T ss_pred CHHHHHHHHhhCCC-cccccccchHHHHHHHHHHHHHHHHHhhhcC---C---CHHHHHHHHHHHHHHHH
Confidence 56677777765333 3344556777888888888888887666662 2 35555555666666444
No 437
>PF08601 PAP1: Transcription factor PAP1; InterPro: IPR013910 The transcription factor Pap1 regulates antioxidant-gene transcription in response to H2O2 []. This region is cysteine rich. Alkylation of cysteine residues following treatment with a cysteine alkylating agent can mask the accessibility of the nuclear exporter Crm1, triggering nuclear accumulation and Pap1 dependent transcriptional expression []. ; PDB: 1SSE_B.
Probab=21.01 E-value=35 Score=35.64 Aligned_cols=32 Identities=22% Similarity=0.211 Sum_probs=21.0
Q ss_pred HHHHHHHHHHhhhhcCC-CCcchhhHHHHHhhh
Q 010992 436 VESITMFGCSLAKHRKS-DTLEAKDILVHLERN 467 (496)
Q Consensus 436 VDsVvt~ACrLAKHRKS-dTLEvKDVQLhLERn 467 (496)
||++|..-.+-||=-+. -+|+-+||+-+|+|.
T Consensus 315 id~lc~el~~kakcs~~g~vv~~~dv~~~l~kh 347 (347)
T PF08601_consen 315 IDGLCSELKKKAKCSESGVVVDEKDVQKILEKH 347 (347)
T ss_dssp HHHHHHHHTTT--EETTEE-EEHHHHHHHHHSS
T ss_pred hHHHHHHHHHhCccCCCCceecHHHHHHHHhcC
Confidence 67777766666664433 378999999999983
No 438
>COG5251 TAF40 Transcription initiation factor TFIID, subunit TAF11 [Transcription]
Probab=20.99 E-value=75 Score=31.40 Aligned_cols=52 Identities=15% Similarity=0.335 Sum_probs=39.8
Q ss_pred cCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCC
Q 010992 401 ILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSD 453 (496)
Q Consensus 401 ILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSd 453 (496)
-|+|..+..|+..| .+..+.+.+.=+|..++..||-.||+.|..+-..|+.+
T Consensus 115 ~lnKt~VKKlastV-~nQtVspNi~I~l~g~~KVfvGEiIElA~~Vq~~w~~s 166 (199)
T COG5251 115 SLNKTQVKKLASTV-ANQTVSPNIRIFLQGVGKVFVGEIIELAMIVQNKWLTS 166 (199)
T ss_pred CCCHHHHHHHHHHH-hccccCCCeeeeeechhHHHHHHHHHHHHHHHHHhccc
Confidence 35677777777776 45678888888899999999999999888876655544
No 439
>PRK06305 DNA polymerase III subunits gamma and tau; Validated
Probab=20.90 E-value=2.1e+02 Score=30.51 Aligned_cols=62 Identities=8% Similarity=0.038 Sum_probs=35.7
Q ss_pred CCHHHHHHHHHhhC--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHH
Q 010992 402 LTKRSIQELVNQID--PSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHL 464 (496)
Q Consensus 402 LtKrKLqELVrqID--PsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhL 464 (496)
++...|.+.++++- -+..+|+++.++|.+.++.=+.+++...-+++-.-+ +.|+.+||.-.+
T Consensus 180 l~~~el~~~L~~~~~~eg~~i~~~al~~L~~~s~gdlr~a~~~Lekl~~~~~-~~It~~~V~~l~ 243 (451)
T PRK06305 180 IPEETIIDKLALIAKQEGIETSREALLPIARAAQGSLRDAESLYDYVVGLFP-KSLDPDSVAKAL 243 (451)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhcc-CCcCHHHHHHHH
Confidence 45566666666552 245789999999888886544444444333332212 336776665433
No 440
>KOG0027 consensus Calmodulin and related proteins (EF-Hand superfamily) [Signal transduction mechanisms]
Probab=20.89 E-value=1.7e+02 Score=25.81 Aligned_cols=82 Identities=15% Similarity=0.251 Sum_probs=45.9
Q ss_pred CCcCCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHH---HHHHHHHHHHHHhhhhcCCCCc------chhhHHHHHh
Q 010992 395 DEFGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAE---DFVESITMFGCSLAKHRKSDTL------EAKDILVHLE 465 (496)
Q Consensus 395 ~e~~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIAD---DFVDsVvt~ACrLAKHRKSdTL------EvKDVQLhLE 465 (496)
+.++...|+++.|..+++.+..+ .-+.++.+++-++-- -.| +.-+|...++++-...+. +++++-..+.
T Consensus 18 D~d~~G~i~~~el~~~lr~lg~~-~t~~el~~~~~~~D~dg~g~I-~~~eF~~l~~~~~~~~~~~~~~~~el~eaF~~fD 95 (151)
T KOG0027|consen 18 DKDGDGKISVEELGAVLRSLGQN-PTEEELRDLIKEIDLDGDGTI-DFEEFLDLMEKLGEEKTDEEASSEELKEAFRVFD 95 (151)
T ss_pred CCCCCCcccHHHHHHHHHHcCCC-CCHHHHHHHHHHhCCCCCCeE-cHHHHHHHHHhhhcccccccccHHHHHHHHHHHc
Confidence 45667888888899999987554 333444454444431 111 233344444444444333 6777767777
Q ss_pred hhcCccccCCCccccc
Q 010992 466 RNWNMTLPGFSGDEIK 481 (496)
Q Consensus 466 RnWNI~IPGFssDEIr 481 (496)
++-+-.| +.+|++
T Consensus 96 ~d~~G~I---s~~el~ 108 (151)
T KOG0027|consen 96 KDGDGFI---SASELK 108 (151)
T ss_pred cCCCCcC---cHHHHH
Confidence 7655444 344554
No 441
>PF10163 EnY2: Transcription factor e(y)2; InterPro: IPR018783 Enhancer of yellow 2 (EnY2) is a small transcription factor which is combined in a complex with the TAFII40 protein []. This protein is conserved from protozoa to humans.; PDB: 4DHX_C 3FWC_P 3M99_C 3KIK_A 3KJL_C 3FWB_C 3MHS_B 3MHH_B.
Probab=20.86 E-value=94 Score=26.12 Aligned_cols=34 Identities=15% Similarity=0.315 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhh
Q 010992 434 DFVESITMFGCSLAKHRKSDTLEAKDILVHLERN 467 (496)
Q Consensus 434 DFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERn 467 (496)
.|.|+|-..+-...+.|+.+.+++.||.-.++-.
T Consensus 31 GW~d~vr~~~re~i~~~g~~~~~~~~l~~~i~P~ 64 (86)
T PF10163_consen 31 GWRDEVRQLCREIIRERGIDNLTFEDLLEEITPK 64 (86)
T ss_dssp THHHHHHHHHHHHHHHH-TTTSBHHHHHHHHHHH
T ss_pred ChHHHHHHHHHHHHHhhCCCCCCHHHHHHHHHHH
Confidence 6777777777777777999999999996665543
No 442
>PRK12713 flgJ flagellar rod assembly protein/muramidase FlgJ; Provisional
Probab=20.77 E-value=1e+02 Score=32.55 Aligned_cols=39 Identities=18% Similarity=0.142 Sum_probs=33.1
Q ss_pred HHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccc
Q 010992 433 EDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTL 472 (496)
Q Consensus 433 DDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~I 472 (496)
++||+.|...|.++||.-|-.. ++-=-|-+||-.||-++
T Consensus 182 ~~FI~~i~p~A~~~ak~~Gi~a-sviiAQAaLESGWG~s~ 220 (339)
T PRK12713 182 VDFVSRMSRAANVAAQQSGVPA-RLILGQAALESGWGRRE 220 (339)
T ss_pred HHHHHHHHHHHHHHHHHhCcCH-HHHHHHHHHHccCCccc
Confidence 8999999999999999888773 45555889999998665
No 443
>PF10431 ClpB_D2-small: C-terminal, D2-small domain, of ClpB protein ; InterPro: IPR019489 Most Clp ATPases form complexes with peptidase subunits and are involved in protein degradation, though some, such as ClpB, do not associate with peptidases and are involved in protein disaggregation []. This entry represents the C-terminal domain of Clp ATPases, often referred to as the D2-small domain, which forms a mixed alpha-beta structure. Compared with the adjacent AAA D1-small domain (IPR003959 from INTERPRO) it lacks the long coiled-coil insertion, and instead of helix C4 contains a beta-strand (e3) that is part of a three stranded beta-pleated sheet. In Thermophilus the whole protein forms a hexamer with the D1-small and D2-small domains located on the outside of the hexamer, with the long coiled-coil being exposed on the surface. The D2-small domain is essential for oligomerisation, forming a tight interface with the D2-large domain of a neighbouring subunit, thereby providing enough binding energy to stabilise the functional assembly [].; PDB: 3HWS_A 3HTE_F 1KYI_T 1G3I_S 1OFH_B 1OFI_A 1G41_A 1IM2_A 3PXI_A 1R6B_X ....
Probab=20.68 E-value=64 Score=25.78 Aligned_cols=49 Identities=20% Similarity=0.349 Sum_probs=26.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhH--HHHHhhhcCccccCCCccccc
Q 010992 425 EDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDI--LVHLERNWNMTLPGFSGDEIK 481 (496)
Q Consensus 425 EELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDV--QLhLERnWNI~IPGFssDEIr 481 (496)
+|.|.+|++..++.+.. +|++ ++-+ |++.|- .+..++.|+ ++||+-.|+
T Consensus 3 ~~~l~~I~~~~l~~l~~---~l~~-~~i~-l~~~~~~~~~l~~~~~~---~~~GAR~l~ 53 (81)
T PF10431_consen 3 EEDLEKIADLQLKKLNE---RLKE-KGIE-LEFDDAVVDYLAEKGYD---PEYGARPLR 53 (81)
T ss_dssp HHHHHHHHHSHHHHHHH---HHHH-TTEE-EEE-HHHHHHHHHHHHH---TTTTTTCHH
T ss_pred HHHHHHHHHHHHHHHHH---HHHH-CCCe-EEecHHHHHHHHHhCcc---cCCCHHHHH
Confidence 45667777777777766 4444 4433 444442 444455444 456666554
No 444
>PRK09897 hypothetical protein; Provisional
Probab=20.63 E-value=85 Score=34.33 Aligned_cols=47 Identities=17% Similarity=0.275 Sum_probs=32.9
Q ss_pred hcCCCCcchhhHHHHHhhhcCccccCCCcccccccC----CcccccCCCCC
Q 010992 449 HRKSDTLEAKDILVHLERNWNMTLPGFSGDEIKTFR----KPVRIVTDPIP 495 (496)
Q Consensus 449 HRKSdTLEvKDVQLhLERnWNI~IPGFssDEIr~~r----k~~~~~~d~~~ 495 (496)
.+...++--++|...|..+.+.-.+.++.+|.+.|. +.--++..+||
T Consensus 341 ~~~~~~~~w~~~i~~l~~~~~~iw~~l~~~d~~rf~~~l~~~~~~~~~~mP 391 (534)
T PRK09897 341 KREKHTVPWRYVILRLHEAVQEIVPHLNEHDHKRFSKGLARVFIDNYAAIP 391 (534)
T ss_pred hccccCccHHHHHHHHHHHHHHHHHhCCHHHHHHHHHhhhHHHHHhccCCC
Confidence 344455778999999998888888999988876544 44344455554
No 445
>KOG2304 consensus 3-hydroxyacyl-CoA dehydrogenase [Lipid transport and metabolism]
Probab=20.60 E-value=1.3e+02 Score=31.34 Aligned_cols=40 Identities=18% Similarity=0.351 Sum_probs=24.9
Q ss_pred CcCCccCC--HHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q 010992 396 EFGNRILT--KRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITM 441 (496)
Q Consensus 396 e~~nrILt--KrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt 441 (496)
+.+...|. ++.|.+=|++|..+...|+.++ -||||++.++
T Consensus 41 d~~~~aL~~A~~~I~~sl~rvakKk~~~~~~~------~~e~v~~~l~ 82 (298)
T KOG2304|consen 41 DANEDALSRATKAISSSLKRVAKKKKADDPVA------LEEFVDDTLD 82 (298)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHhhcccCChhh------HHHHHHHHHH
Confidence 33444443 4556777788877788888776 3555555544
No 446
>PLN02690 Agmatine deiminase
Probab=20.54 E-value=48 Score=34.91 Aligned_cols=40 Identities=30% Similarity=0.520 Sum_probs=34.1
Q ss_pred HHHHHHHhhhhcCCCCcchhhHHHHHhhhcC----cccc-CCCccc
Q 010992 439 ITMFGCSLAKHRKSDTLEAKDILVHLERNWN----MTLP-GFSGDE 479 (496)
Q Consensus 439 Vvt~ACrLAKHRKSdTLEvKDVQLhLERnWN----I~IP-GFssDE 479 (496)
+++..|.|-++|+-+ +.-.+|.-.|++.+| |||| |+..|+
T Consensus 174 ltTe~clln~nRNP~-lsk~~ie~~Lk~~LGv~kvIWL~~g~~~Dd 218 (374)
T PLN02690 174 LTTEECLLNPNRNPH-LTKEEIEEELKEYLGVEKVIWLPRGLYGDD 218 (374)
T ss_pred EEehhhhcCCCCCCC-CCHHHHHHHHHHHhCCCEEEEeCCCcCCCC
Confidence 788899999999988 789999999999998 6788 455553
No 447
>TIGR01505 tartro_sem_red 2-hydroxy-3-oxopropionate reductase. This model represents 2-hydroxy-3-oxopropionate reductase (EC 1.1.1.60), also called tartronate semialdehyde reductase. It follows glyoxylate carboligase and precedes glycerate kinase in D-glycerate pathway of glyoxylate degradation. The eventual product, 3-phosphoglycerate, is an intermediate of glycolysis and is readily metabolized. Tartronic semialdehyde, the substrate of this enzyme, may also come from other pathways, such as D-glucarate catabolism.
Probab=20.46 E-value=1.1e+02 Score=29.57 Aligned_cols=51 Identities=8% Similarity=0.107 Sum_probs=32.6
Q ss_pred HHHHHHHHHhhCCCC-CCCHHHHHHHHHHHHHHHHHH----HHHHHHhhhhcCCCC
Q 010992 404 KRSIQELVNQIDPSE-RLDPDVEDILVDIAEDFVESI----TMFGCSLAKHRKSDT 454 (496)
Q Consensus 404 KrKLqELVrqIDPse-sLDpDVEELLLeIADDFVDsV----vt~ACrLAKHRKSdT 454 (496)
.+++.+|++.+.... .+.++..-.+.+|++.++.-+ +..+..||+.-+-+.
T Consensus 142 ~~~~~~ll~~lg~~~~~~g~~g~a~~~Kl~~n~~~~~~~~~~~Ea~~l~~~~Gid~ 197 (291)
T TIGR01505 142 FDRVKPLFEALGKNIVLVGGNGDGQTCKVANQIIVALNIEAVSEALVFASKAGVDP 197 (291)
T ss_pred HHHHHHHHHHhcCCeEEeCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCH
Confidence 456888998887543 344434444666776666654 777888888765543
No 448
>PF08236 SRI: SRI (Set2 Rpb1 interacting) domain; InterPro: IPR013257 The SRI (Set2 Rpb1 interacting) domain mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation []. This domain is conserved from yeast to humans. Members of this family form a compact, closed three-helix bundle, with an up-down-up topology. The first and second helices are antiparallel to each other and are of similar length; the third helix, which is packed across helices alpha1 and alpha2 is slightly shorter, consisting of only 15 amino acids. Most conserved hydrophobic residues are largely buried in the interior of the structure and form an extensive and contiguous hydrophobic core that stabilises the packing of the three-helix bundle. This domain mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation []. ; GO: 0018024 histone-lysine N-methyltransferase activity, 0006355 regulation of transcription, DNA-dependent, 0034968 histone lysine methylation, 0005694 chromosome; PDB: 2A7O_A 2C5Z_A.
Probab=20.44 E-value=80 Score=26.77 Aligned_cols=22 Identities=9% Similarity=0.267 Sum_probs=11.2
Q ss_pred CCCCCHHHHHHHHHHHHHHHHH
Q 010992 417 SERLDPDVEDILVDIAEDFVES 438 (496)
Q Consensus 417 sesLDpDVEELLLeIADDFVDs 438 (496)
...|+++++.=+-+++++|++.
T Consensus 58 ~~~l~~~~~~Kik~fvk~Ym~K 79 (88)
T PF08236_consen 58 PLELSDSKRKKIKKFVKDYMDK 79 (88)
T ss_dssp GSS--HHHHHHHHHHHHHHHCC
T ss_pred ccccCHHHHHHHHHHHHHHHHH
Confidence 3555566655555555555554
No 449
>PF08766 DEK_C: DEK C terminal domain; InterPro: IPR014876 DEK is a chromatin associated protein that is linked with cancers and autoimmune disease. This domain is found at the C-terminal of DEK and is of clinical importance since it can reverse the characteristic abnormal DNA-mutagen sensitivity in fibroblasts from ataxia-telangiectasia (A-T) patients []. The structure of this domain shows it to be homologous to the E2F/DP transcription factor family []. This domain is also found in chitin synthase proteins like Q8TF96 from SWISSPROT, and in protein phosphatases such as Q6NN85 from SWISSPROT. ; PDB: 1Q1V_A.
Probab=20.44 E-value=1.1e+02 Score=23.52 Aligned_cols=22 Identities=27% Similarity=0.442 Sum_probs=14.4
Q ss_pred CCCCcchhhHHHHHhhhcCccc
Q 010992 451 KSDTLEAKDILVHLERNWNMTL 472 (496)
Q Consensus 451 KSdTLEvKDVQLhLERnWNI~I 472 (496)
.-+++..|+|.-.||..||+.+
T Consensus 17 dl~~vT~k~vr~~Le~~~~~dL 38 (54)
T PF08766_consen 17 DLDTVTKKQVREQLEERFGVDL 38 (54)
T ss_dssp -GGG--HHHHHHHHHHH-SS--
T ss_pred CHhHhhHHHHHHHHHHHHCCCc
Confidence 5667899999999999998876
No 450
>TIGR01035 hemA glutamyl-tRNA reductase. This enzyme, together with glutamate-1-semialdehyde-2,1-aminomutase (TIGR00713), leads to the production of delta-amino-levulinic acid from Glu-tRNA.
Probab=20.42 E-value=2.4e+02 Score=29.49 Aligned_cols=62 Identities=18% Similarity=0.307 Sum_probs=26.9
Q ss_pred HHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCc
Q 010992 405 RSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNM 470 (496)
Q Consensus 405 rKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI 470 (496)
+.|..++++++ .++++.++.|-+++...++.+++.-....|.-..+ =+..++.-.|++-||+
T Consensus 355 ~el~~~~~~l~---~~~~~~~~~~~~~~~~~~~k~lh~p~~~lk~~~~~-~~~~~~~~~~~~lf~l 416 (417)
T TIGR01035 355 KELEKALKKLP---GLSKDVEEVLEDLARKLINKLLHAPTVRLKQLADK-EESEVCLEALKNLFGL 416 (417)
T ss_pred HHHHHHHHhcc---cCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC-CChHHHHHHHHHHhCc
Confidence 33444444442 23444444444444444445544444444432211 1222344556666664
No 451
>PRK05872 short chain dehydrogenase; Provisional
Probab=20.37 E-value=52 Score=31.52 Aligned_cols=13 Identities=8% Similarity=0.302 Sum_probs=9.1
Q ss_pred CHHHHHHHHHhhC
Q 010992 403 TKRSIQELVNQID 415 (496)
Q Consensus 403 tKrKLqELVrqID 415 (496)
+..+|+++++++.
T Consensus 42 ~~~~l~~~~~~l~ 54 (296)
T PRK05872 42 EEAELAALAAELG 54 (296)
T ss_pred CHHHHHHHHHHhc
Confidence 4567778877764
No 452
>PLN02437 ribonucleoside--diphosphate reductase large subunit
Probab=20.32 E-value=1.3e+02 Score=34.89 Aligned_cols=32 Identities=19% Similarity=0.208 Sum_probs=26.8
Q ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCC
Q 010992 421 DPDVEDILVDIAEDFVESITMFGCSLAKHRKS 452 (496)
Q Consensus 421 DpDVEELLLeIADDFVDsVvt~ACrLAKHRKS 452 (496)
++|+.++.-+|++..-...+..+|+|||+||.
T Consensus 540 S~ea~~l~~~I~e~i~~~A~~aS~eLAke~G~ 571 (813)
T PLN02437 540 SPEAQQLNKDIFETIYYHALKASSELAAREGP 571 (813)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 35677888888888888889999999999984
No 453
>PRK08535 translation initiation factor IF-2B subunit delta; Provisional
Probab=20.22 E-value=1.9e+02 Score=29.39 Aligned_cols=28 Identities=18% Similarity=0.277 Sum_probs=21.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 010992 422 PDVEDILVDIAEDFVESITMFGCSLAKH 449 (496)
Q Consensus 422 pDVEELLLeIADDFVDsVvt~ACrLAKH 449 (496)
+++.+.|++-+++|++.+....-++|+|
T Consensus 86 ~~~k~~l~e~~~~~~~e~~~~~~~I~~~ 113 (310)
T PRK08535 86 EEARESVIERAEEFIESSENAVEKIGEI 113 (310)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6788899999999999876655555543
No 454
>PF12418 AcylCoA_DH_N: Acyl-CoA dehydrogenase N terminal ; InterPro: IPR020953 This entry represents the N-terminal domain of Acyl-CoA dehydrogenase, which is one of the enzymes involved in AcylCoA interaction in beta-oxidation []. The protein is found in association with PF02770 from PFAM, PF00441 from PFAM, PF02771 from PFAM.
Probab=20.20 E-value=77 Score=22.73 Aligned_cols=23 Identities=26% Similarity=0.430 Sum_probs=17.8
Q ss_pred CcchhhHHHHHhhhcCcc-----ccCCC
Q 010992 454 TLEAKDILVHLERNWNMT-----LPGFS 476 (496)
Q Consensus 454 TLEvKDVQLhLERnWNI~-----IPGFs 476 (496)
+..+||++|.|..-+|+. +|||.
T Consensus 4 ~ap~rD~~F~L~Evl~~~~~~~~~p~~~ 31 (34)
T PF12418_consen 4 KAPLRDMRFVLYEVLDADQHLQALPGFA 31 (34)
T ss_pred CCcHHHHHHHHHHHHCcHHHHhcCCCcc
Confidence 356899999999988864 56665
No 455
>cd05134 RasGAP_RASA3 RASA3 (or GAP1_IP4BP) is a member of the GAP1 family and has been shown to specifically bind 1,3,4,5-tetrakisphosphate (IP4). Thus, RASA3 may function as an IP4 receptor. The members of GAP1 family are characterized by a conserved domain structure comprising N-terminal tandem C2 domains, a highly conserved central RasGAP domain, and a C-terminal pleckstrin-homology domain that is associated with a Bruton's tyrosine kinase motif. Purified RASA3 stimulates GAP activity on Ras with about a five-fold lower potency than p120RasGAP, but shows no GAP-stimulating activity at all against Rac or Rab3A.
Probab=20.18 E-value=2.1e+02 Score=29.74 Aligned_cols=21 Identities=24% Similarity=0.235 Sum_probs=15.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHh
Q 010992 426 DILVDIAEDFVESITMFGCSL 446 (496)
Q Consensus 426 ELLLeIADDFVDsVvt~ACrL 446 (496)
+.|..++|.+++.|+..++++
T Consensus 131 ~~L~~~~~~i~~~I~~S~~~~ 151 (310)
T cd05134 131 ENLRQYVDRIFRVITKSGVSC 151 (310)
T ss_pred HHHHHHHHHHHHHHHhchhcC
Confidence 577788888888887655543
No 456
>COG3395 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.17 E-value=1.4e+02 Score=32.52 Aligned_cols=48 Identities=23% Similarity=0.378 Sum_probs=37.8
Q ss_pred ccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcC
Q 010992 400 RILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRK 451 (496)
Q Consensus 400 rILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRK 451 (496)
..+|++.|..++++.+-. +=|||.+|.+ +++.||.+++..|..=-|-+
T Consensus 256 s~~T~~Qv~~~~~~~~~~---~ldv~~~~~~-~~~~ie~~~~~v~a~~~~~~ 303 (413)
T COG3395 256 SPMTNKQVDALLQHAPVF---ELDVERLLSD-AEAYIERAVAWVLASLSHGR 303 (413)
T ss_pred cHHHHHHHHHHHHhCCcc---cccHHHHhhh-hHHHHHHHHHHHHhhcccCC
Confidence 345899999999976543 7789999998 99999999998887554433
No 457
>cd04393 RhoGAP_FAM13A1a RhoGAP_FAM13A1a: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of FAM13A1, isoform a-like proteins. The function of FAM13A1a is unknown. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by up several orders of magnitude.
Probab=20.16 E-value=3.6e+02 Score=25.02 Aligned_cols=27 Identities=11% Similarity=0.260 Sum_probs=18.9
Q ss_pred HHHHHHHHhhhhcCCCCcchhhHHHHH
Q 010992 438 SITMFGCSLAKHRKSDTLEAKDILVHL 464 (496)
Q Consensus 438 sVvt~ACrLAKHRKSdTLEvKDVQLhL 464 (496)
-++.+-.++|+|...+..+++.+..++
T Consensus 133 ~l~~~l~~V~~~s~~NkMt~~nLA~vf 159 (189)
T cd04393 133 FLCHFLSNVASQHHENRMTAENLAAVF 159 (189)
T ss_pred HHHHHHHHHHHcccccCCCHHHhhhhc
Confidence 355666777888888878877776544
No 458
>PRK13386 fliH flagellar assembly protein H; Provisional
Probab=20.15 E-value=1.4e+02 Score=29.26 Aligned_cols=22 Identities=18% Similarity=0.395 Sum_probs=11.9
Q ss_pred CCCCHHHHHHHHHHHHHHHHHH
Q 010992 418 ERLDPDVEDILVDIAEDFVESI 439 (496)
Q Consensus 418 esLDpDVEELLLeIADDFVDsV 439 (496)
..++.++++.|++||-+..+.|
T Consensus 114 ~~~~~~~~~~ll~La~~iA~~v 135 (236)
T PRK13386 114 AEYEQQQRDELLDLVEKVTRQV 135 (236)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3455556666666655554443
No 459
>PRK06948 ribonucleotide reductase-like protein; Provisional
Probab=20.14 E-value=2.4e+02 Score=31.57 Aligned_cols=31 Identities=23% Similarity=0.280 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhcCC
Q 010992 422 PDVEDILVDIAEDFVESITMFGCSLAKHRKS 452 (496)
Q Consensus 422 pDVEELLLeIADDFVDsVvt~ACrLAKHRKS 452 (496)
+|+.++.-+|.+..-+..+..+|+|||.||.
T Consensus 386 ~ea~~~~~~i~~~i~~~A~~aS~eLA~ErG~ 416 (595)
T PRK06948 386 PAAREMARYIASDLRHHAYAASAALAAERGA 416 (595)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 4556666666666666778899999999995
No 460
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=20.13 E-value=2.6e+02 Score=22.62 Aligned_cols=76 Identities=11% Similarity=0.094 Sum_probs=35.6
Q ss_pred HHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcCccccCCCcccccccCCc
Q 010992 407 IQELVNQIDPSERLDPDVEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWNMTLPGFSGDEIKTFRKP 486 (496)
Q Consensus 407 LqELVrqIDPsesLDpDVEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWNI~IPGFssDEIr~~rk~ 486 (496)
+.++++-|-.+..|++ +.++|.+..++..+.+-+..+..+.. + .+..+++..|.+.=+..| .|.. .+.
T Consensus 13 ~~~vL~~LP~~~~l~~-l~~fl~~~l~~~~~~~~~~~i~~~l~-~---~~~~~~~~~l~~~~~~~v------~i~~-~~~ 80 (109)
T PF10367_consen 13 PIDVLKLLPDDWPLSD-LSDFLCKSLRKYSNRKRESQIEKNLL-K---SENLQLKYELVKLRSRSV------VITE-STK 80 (109)
T ss_pred HHHHHHhCcCCCCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHH-H---hHHHHHHHHHHhhcCceE------EECC-CCC
Confidence 5566666655445443 55555555555555444433333222 1 233344444433222221 2222 345
Q ss_pred ccccCCCC
Q 010992 487 VRIVTDPI 494 (496)
Q Consensus 487 ~~~~~d~~ 494 (496)
|..|+.+|
T Consensus 81 C~vC~k~l 88 (109)
T PF10367_consen 81 CSVCGKPL 88 (109)
T ss_pred ccCcCCcC
Confidence 88888776
No 461
>smart00323 RasGAP GTPase-activator protein for Ras-like GTPases. All alpha-helical domain that accelerates the GTPase activity of Ras, thereby "switching" it into an "off" position. Improved domain limits from structure.
Probab=20.11 E-value=2.3e+02 Score=28.67 Aligned_cols=22 Identities=18% Similarity=0.228 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhh
Q 010992 426 DILVDIAEDFVESITMFGCSLA 447 (496)
Q Consensus 426 ELLLeIADDFVDsVvt~ACrLA 447 (496)
+.|.+++++|++.|+.....+-
T Consensus 150 ~~L~~~~~~~~~~I~~s~~~~P 171 (344)
T smart00323 150 ENLLQYVERLFDAIINSSDRLP 171 (344)
T ss_pred HHHHHHHHHHHHHHHHhHHhCc
Confidence 5788999999999988655443
No 462
>PF08328 ASL_C: Adenylosuccinate lyase C-terminal; InterPro: IPR013539 This domain is found at the C terminus of adenylosuccinate lyase(ASL; PurB in Escherichia coli). It has been identified in bacteria, eukaryotes and archaea and is found together with the lyase domain IPR000362 from INTERPRO. ASL catalyses the cleavage of succinylaminoimidazole carboxamide ribotide to aminoimidazole carboxamide ribotide and fumarate and the cleavage of adenylosuccinate to adenylate and fumarate []. ; GO: 0004018 N6-(1,2-dicarboxyethyl)AMP AMP-lyase (fumarate-forming) activity, 0006188 IMP biosynthetic process; PDB: 2HVG_A 2QGA_C 2PTS_A 2PTR_A 2PTQ_B 3BHG_A 3GZH_A.
Probab=20.10 E-value=1.3e+02 Score=27.78 Aligned_cols=30 Identities=17% Similarity=0.488 Sum_probs=20.7
Q ss_pred CccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHH
Q 010992 399 NRILTKRSIQELVNQIDPSERLDPDVEDILVDIA 432 (496)
Q Consensus 399 nrILtKrKLqELVrqIDPsesLDpDVEELLLeIA 432 (496)
++-|+|..|++||..+| |++++.+-|+.|.
T Consensus 81 g~~it~~~l~~fI~~L~----ip~~~k~~L~~lt 110 (115)
T PF08328_consen 81 GKKITKEDLREFIESLD----IPEEAKARLLALT 110 (115)
T ss_dssp TS---HHHHHHHHHTSS----S-HHHHHHHHH--
T ss_pred CCCCCHHHHHHHHHhCC----CCHHHHHHHHhcC
Confidence 45789999999999876 9999999888774
No 463
>PF07624 PSD2: Protein of unknown function (DUF1585); InterPro: IPR011478 This entry represents a conserved region at the C terminus of a family of cytochrome-like proteins found in bacteria such as Rhodopirellula baltica and Solibacter usitatus. These proteins also contain IPR013036 from INTERPRO, IPR013039 from INTERPRO, IPR013042 from INTERPRO and IPR013043 from INTERPRO.
Probab=20.08 E-value=2.7e+02 Score=22.77 Aligned_cols=42 Identities=14% Similarity=0.104 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHh
Q 010992 424 VEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLE 465 (496)
Q Consensus 424 VEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLE 465 (496)
..++|++=-|+|...+++..+.+|--|.-+--|-..|.-.++
T Consensus 12 Lk~~L~~~~~~~~~~~~~kl~~YAlGR~~~~~D~~~i~~i~~ 53 (76)
T PF07624_consen 12 LKQYLAERKDQFARCFAEKLLTYALGRPLEFSDRCEIDRIVE 53 (76)
T ss_pred HHHHHHHCHHHHHHHHHHHHHHHHcCCCCCcchHHHHHHHHH
Confidence 345566667899999999999999999877655555544444
No 464
>PF08479 POTRA_2: POTRA domain, ShlB-type; InterPro: IPR013686 The POTRA domain (for polypeptide-transport-associated domain) is found towards the N terminus of ShlB family proteins (IPR005565 from INTERPRO). ShlB is important in the secretion and activation of the haemolysin ShlA. It has been postulated that the POTRA domain has a chaperone-like function over ShlA; it may fold back into the C-terminal beta-barrel channel []. ; PDB: 2X8X_X 2QDZ_A 3NJT_A 3MC8_A 3MC9_B.
Probab=20.07 E-value=1e+02 Score=24.49 Aligned_cols=42 Identities=14% Similarity=0.192 Sum_probs=28.0
Q ss_pred cCCccCCHHHHHHHHHhhCCCCCCCHHHHHHHHHHHHHHHHH
Q 010992 397 FGNRILTKRSIQELVNQIDPSERLDPDVEDILVDIAEDFVES 438 (496)
Q Consensus 397 ~~nrILtKrKLqELVrqIDPsesLDpDVEELLLeIADDFVDs 438 (496)
+++.+|+...|.++++..-..+.=..++.+++-+|.+-|+++
T Consensus 9 ~G~~~~~~~~l~~~~~~~~g~~l~~~~l~~~~~~l~~~y~~~ 50 (76)
T PF08479_consen 9 EGNTLLPEEELQAILAPYIGRCLTLADLQQLADALTNYYREK 50 (76)
T ss_dssp ES-TSSSCCHHHHHHGGGTTSBB-HHHHHHHHHHHHHHHHHT
T ss_pred ECCCcCCHHHHHHHHHHhcCCCcCHHHHHHHHHHHHHHHHHc
Confidence 457788888999999987655444455666666666666553
No 465
>TIGR03380 agmatine_aguA agmatine deiminase. Members of this family are agmatine deiminase (3.5.3.12), as characterized in Pseudomonas aeruginosa and plants. Related deiminases include the peptidyl-arginine deiminase (3.5.3.15) as found in Porphyromonas gingivalis.
Probab=20.06 E-value=49 Score=34.61 Aligned_cols=40 Identities=30% Similarity=0.462 Sum_probs=34.2
Q ss_pred HHHHHHHhhhhcCCCCcchhhHHHHHhhhcC----cccc-CCCccc
Q 010992 439 ITMFGCSLAKHRKSDTLEAKDILVHLERNWN----MTLP-GFSGDE 479 (496)
Q Consensus 439 Vvt~ACrLAKHRKSdTLEvKDVQLhLERnWN----I~IP-GFssDE 479 (496)
+++..|.|-.+|+-+ +.-.+|.-.|++.+| |||| |+..||
T Consensus 162 ltTe~clln~nRNP~-ls~~eIe~~Lk~~LGv~kviWL~~g~~~Dd 206 (357)
T TIGR03380 162 LTTEECLLSEGRNPH-LTKEQIEEKLKDYLGVEKVIWLPDGLYNDE 206 (357)
T ss_pred EEEhhhhcCCCCCCC-CCHHHHHHHHHHHHCCCEEEEECCCCCCCC
Confidence 678899999999987 789999999999998 6787 666665
No 466
>PF14841 FliG_M: FliG middle domain; PDB: 3HJL_A 3AJC_A 1LKV_X 3SOH_D 3USY_B 3USW_A.
Probab=20.03 E-value=1.4e+02 Score=24.57 Aligned_cols=48 Identities=17% Similarity=0.302 Sum_probs=32.2
Q ss_pred CCCHH-HHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcchhhHHHHHhhhcC
Q 010992 419 RLDPD-VEDILVDIAEDFVESITMFGCSLAKHRKSDTLEAKDILVHLERNWN 469 (496)
Q Consensus 419 sLDpD-VEELLLeIADDFVDsVvt~ACrLAKHRKSdTLEvKDVQLhLERnWN 469 (496)
.||++ +-++|..|-+++-.+|+. ++|+-++-+.=-+++|.-.|++.+.
T Consensus 23 ~L~~~~AA~VL~~lp~e~r~~v~~---Ria~~~~v~~~~i~~ie~~L~~~l~ 71 (79)
T PF14841_consen 23 YLPPEQAAEVLSQLPEELRAEVVR---RIARLESVSPEVIEEIEEVLEEKLE 71 (79)
T ss_dssp TS-HHHHHHHHHTS-HHHHHHHHH---HHHTCCCCSHHHHHHHHHHHHHHCH
T ss_pred cCCHHHHHHHHHHCCHHHHHHHHH---HHHccCCCCHHHHHHHHHHHHHHHH
Confidence 46666 567777788888888877 5666666665567777777777653
Done!