Query 020150
Match_columns 330
No_of_seqs 21 out of 23
Neff 2.3
Searched_HMMs 46136
Date Fri Mar 29 07:25:28 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020150.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020150hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0154 RNA-binding protein RB 98.5 6.6E-09 1.4E-13 102.8 -3.1 221 66-287 235-457 (573)
2 KOG4509 Uncharacterized conser 86.9 1.2 2.6E-05 42.1 5.1 79 118-196 41-120 (247)
3 TIGR02395 rpoN_sigma RNA polym 80.2 5.4 0.00012 39.8 6.9 89 148-236 300-418 (429)
4 PF14297 DUF4373: Domain of un 79.9 8.6 0.00019 29.9 6.6 70 156-226 1-70 (87)
5 PLN02777 photosystem I P subun 79.4 1.5 3.2E-05 40.0 2.5 27 1-27 1-41 (167)
6 PF04552 Sigma54_DBD: Sigma-54 77.6 1.2 2.6E-05 39.3 1.3 88 148-235 31-147 (160)
7 PRK05932 RNA polymerase factor 72.2 12 0.00026 37.8 6.9 89 148-236 325-442 (455)
8 smart00657 RPOL4c DNA-directed 67.6 15 0.00032 30.4 5.5 45 180-224 34-79 (118)
9 PF03874 RNA_pol_Rpb4: RNA pol 67.3 17 0.00036 29.2 5.5 58 171-228 27-85 (117)
10 COG1508 RpoN DNA-directed RNA 65.9 17 0.00037 37.4 6.5 99 138-236 301-430 (444)
11 PRK12469 RNA polymerase factor 62.1 19 0.00041 37.0 6.1 89 148-236 351-468 (481)
12 KOG2499 Beta-N-acetylhexosamin 61.6 8.1 0.00018 40.6 3.4 51 142-192 306-373 (542)
13 cd04780 HTH_MerR-like_sg5 Heli 55.2 40 0.00086 27.0 5.7 56 169-225 3-70 (95)
14 PF01402 RHH_1: Ribbon-helix-h 54.4 24 0.00051 23.2 3.6 27 167-193 12-38 (39)
15 PF06570 DUF1129: Protein of u 54.0 20 0.00044 31.8 4.3 49 198-247 6-56 (206)
16 PF06798 PrkA: PrkA serine pro 52.8 84 0.0018 29.7 8.3 76 167-250 151-249 (254)
17 TIGR03252 uncharacterized HhH- 52.6 70 0.0015 29.3 7.4 73 197-291 58-146 (177)
18 PRK00440 rfc replication facto 52.1 74 0.0016 28.3 7.5 73 146-226 163-238 (319)
19 PHA01748 hypothetical protein 51.4 16 0.00036 27.5 2.8 29 168-196 16-44 (60)
20 COG4915 XpaC 5-bromo-4-chloroi 51.3 55 0.0012 31.0 6.7 53 171-232 58-115 (204)
21 TIGR01856 hisJ_fam histidinol 51.0 66 0.0014 29.1 7.0 81 166-246 122-210 (253)
22 TIGR00865 bcl-2 Apoptosis regu 50.9 22 0.00048 33.0 4.1 61 178-238 3-86 (213)
23 PF11166 DUF2951: Protein of u 50.8 11 0.00023 32.1 1.9 21 108-129 75-95 (98)
24 COG2137 OraA Uncharacterized p 49.9 37 0.00081 30.6 5.3 80 168-256 26-106 (174)
25 TIGR01359 UMP_CMP_kin_fam UMP- 48.0 52 0.0011 27.2 5.5 54 168-227 15-71 (183)
26 PF02847 MA3: MA3 domain; Int 47.2 21 0.00045 27.7 2.9 78 151-230 7-85 (113)
27 PRK12402 replication factor C 47.0 76 0.0017 28.6 6.8 75 147-227 187-263 (337)
28 smart00352 POU Found in Pit-Oc 46.2 24 0.00051 28.6 3.1 24 201-224 12-35 (75)
29 COG1713 Predicted HD superfami 45.9 9.5 0.0002 35.2 0.9 113 186-316 8-127 (187)
30 cd01104 HTH_MlrA-CarA Helix-Tu 45.8 80 0.0017 22.4 5.5 54 169-223 3-67 (68)
31 smart00265 BH4 BH4 Bcl-2 homol 43.6 24 0.00053 23.8 2.4 23 177-199 2-24 (27)
32 cd04764 HTH_MlrA-like_sg1 Heli 43.5 72 0.0016 23.0 5.0 53 170-224 4-67 (67)
33 PF08542 Rep_fac_C: Replicatio 43.0 67 0.0014 24.1 5.0 56 149-206 7-62 (89)
34 PF07568 HisKA_2: Histidine ki 41.8 42 0.00091 25.7 3.8 33 198-231 9-41 (76)
35 PF02417 Chromate_transp: Chro 41.6 18 0.00039 31.1 1.9 63 70-135 30-103 (169)
36 PRK03987 translation initiatio 40.5 96 0.0021 29.4 6.7 85 166-251 101-192 (262)
37 smart00544 MA3 Domain in DAP-5 40.3 92 0.002 24.3 5.6 76 151-228 7-83 (113)
38 PRK06585 holA DNA polymerase I 39.9 1.1E+02 0.0023 28.5 6.8 64 145-208 143-209 (343)
39 PTZ00111 DNA replication licen 39.8 2.1E+02 0.0046 32.2 9.9 30 180-210 698-734 (915)
40 KOG0488 Transcription factor B 39.7 31 0.00068 33.4 3.4 48 160-225 175-222 (309)
41 PF00046 Homeobox: Homeobox do 39.5 51 0.0011 22.9 3.6 40 143-183 5-44 (57)
42 TIGR01128 holA DNA polymerase 39.3 1.1E+02 0.0023 27.3 6.4 65 146-211 113-180 (302)
43 smart00845 GatB_Yqey GatB doma 38.8 68 0.0015 27.1 4.9 45 195-239 37-87 (147)
44 PF13560 HTH_31: Helix-turn-he 38.3 93 0.002 22.3 4.9 53 168-221 5-63 (64)
45 PF02885 Glycos_trans_3N: Glyc 38.1 83 0.0018 23.3 4.8 52 169-222 6-57 (66)
46 cd00592 HTH_MerR-like Helix-Tu 38.1 1.3E+02 0.0028 23.2 6.0 54 169-224 3-67 (100)
47 PF07766 LETM1: LETM1-like pro 37.1 69 0.0015 30.0 5.1 37 204-251 210-246 (268)
48 PF15176 LRR19-TM: Leucine-ric 36.6 34 0.00074 29.3 2.8 48 95-142 6-57 (102)
49 PHA00739 V3 structural protein 36.4 24 0.00051 29.8 1.8 35 88-122 42-79 (92)
50 PF00286 Flexi_CP: Viral coat 36.3 94 0.002 27.5 5.5 72 198-272 6-79 (140)
51 TIGR00270 conserved hypothetic 36.0 70 0.0015 28.2 4.7 79 132-219 49-128 (154)
52 PRK07452 DNA polymerase III su 36.0 1.3E+02 0.0028 27.6 6.6 59 149-207 135-197 (326)
53 PF02797 Chal_sti_synt_C: Chal 35.9 24 0.00053 30.6 1.9 34 198-236 66-99 (151)
54 PF01381 HTH_3: Helix-turn-hel 35.5 27 0.00058 23.9 1.7 28 206-234 2-29 (55)
55 PF06281 DUF1035: Protein of u 35.1 29 0.00063 28.2 2.0 42 89-130 24-68 (73)
56 PF02631 RecX: RecX family; I 34.9 47 0.001 26.8 3.2 65 192-258 1-66 (121)
57 PF04510 DUF577: Family of unk 34.7 81 0.0018 29.1 5.0 84 92-194 89-174 (174)
58 PRK05574 holA DNA polymerase I 34.7 1.4E+02 0.003 27.2 6.5 64 146-210 148-214 (340)
59 PRK09111 DNA polymerase III su 34.4 2.2E+02 0.0049 30.0 8.8 60 146-207 193-255 (598)
60 PRK00117 recX recombination re 34.2 95 0.002 26.0 5.1 62 168-237 17-79 (157)
61 KOG2286 Exocyst complex subuni 33.5 69 0.0015 34.7 5.0 94 118-236 481-582 (667)
62 PRK14530 adenylate kinase; Pro 32.8 1.5E+02 0.0033 25.8 6.2 64 161-226 12-78 (215)
63 PRK06266 transcription initiat 32.8 66 0.0014 28.8 4.1 43 178-223 4-46 (178)
64 PF02180 BH4: Bcl-2 homology r 32.7 22 0.00048 24.1 0.8 23 178-200 3-25 (27)
65 COG0283 Cmk Cytidylate kinase 32.4 71 0.0015 30.4 4.4 29 216-244 102-130 (222)
66 KOG2510 SWI-SNF chromatin-remo 32.1 30 0.00065 36.5 2.1 73 101-205 310-383 (532)
67 PRK04195 replication factor C 31.8 2.4E+02 0.0051 28.1 8.1 54 168-224 351-404 (482)
68 PRK10072 putative transcriptio 31.4 35 0.00076 28.0 2.0 33 201-234 34-66 (96)
69 PF12324 HTH_15: Helix-turn-he 31.2 86 0.0019 25.6 4.1 54 179-238 21-74 (77)
70 cd00056 ENDO3c endonuclease II 31.1 1.2E+02 0.0025 25.1 5.0 104 160-285 13-124 (158)
71 PHA01976 helix-turn-helix prot 30.6 33 0.00072 24.4 1.6 28 204-232 6-33 (67)
72 cd04411 Ribosomal_P1_P2_L12p R 30.6 21 0.00046 29.8 0.6 10 68-77 93-102 (105)
73 COG4174 ABC-type uncharacteriz 30.2 68 0.0015 32.4 4.0 52 159-210 75-132 (364)
74 PRK14137 recX recombination re 29.9 68 0.0015 29.2 3.7 71 177-258 54-125 (195)
75 PF10746 Phage_holin_6: Phage 29.8 33 0.0007 27.5 1.5 46 87-132 4-60 (66)
76 TIGR01360 aden_kin_iso1 adenyl 29.6 3.1E+02 0.0068 22.4 8.6 73 162-240 13-88 (188)
77 PF12446 DUF3682: Protein of u 29.0 29 0.00064 30.9 1.2 16 61-76 93-108 (133)
78 COG2704 DcuB Anaerobic C4-dica 28.8 41 0.0009 34.8 2.4 38 68-123 311-348 (436)
79 PF09840 DUF2067: Uncharacteri 28.8 1.1E+02 0.0023 28.1 4.8 67 176-257 71-149 (190)
80 KOG1869 Splicing coactivator S 28.7 1E+02 0.0022 32.0 5.0 53 168-220 72-145 (425)
81 cd04765 HTH_MlrA-like_sg2 Heli 28.6 2E+02 0.0043 23.1 5.8 31 195-225 37-70 (99)
82 PRK00117 recX recombination re 28.1 3.6E+02 0.0078 22.6 8.2 120 130-270 23-148 (157)
83 PF08069 Ribosomal_S13_N: Ribo 27.7 60 0.0013 25.3 2.6 29 197-225 28-56 (60)
84 PF11169 DUF2956: Protein of u 27.6 46 0.001 28.6 2.1 22 96-118 75-96 (103)
85 PF00428 Ribosomal_60s: 60s Ac 27.2 5.1 0.00011 31.6 -3.4 7 70-76 78-84 (88)
86 KOG4718 Non-SMC (structural ma 27.0 1.3E+02 0.0028 29.2 5.1 57 171-227 86-147 (235)
87 PF11836 DUF3356: Protein of u 26.8 1.6E+02 0.0035 24.2 5.1 40 164-208 18-58 (101)
88 KOG1577 Aldo/keto reductase fa 26.8 1.7E+02 0.0038 28.8 6.1 64 162-229 218-288 (300)
89 PRK02998 prsA peptidylprolyl i 26.7 1.3E+02 0.0029 28.0 5.2 98 211-312 66-168 (283)
90 PRK03892 ribonuclease P protei 25.9 1.6E+02 0.0034 28.2 5.4 65 169-233 137-215 (216)
91 PRK11677 hypothetical protein; 25.9 54 0.0012 28.7 2.3 29 106-138 1-29 (134)
92 PF13443 HTH_26: Cro/C1-type H 25.9 1.9E+02 0.0042 20.2 4.8 44 170-219 14-57 (63)
93 PF10771 DUF2582: Protein of u 25.6 82 0.0018 24.6 3.0 35 187-227 12-47 (65)
94 KOG2629 Peroxisomal membrane a 25.6 46 0.001 33.0 2.0 56 100-158 77-132 (300)
95 KOG0774 Transcription factor P 25.3 76 0.0017 31.7 3.4 82 130-216 183-270 (334)
96 TIGR02384 RelB_DinJ addiction 25.2 1.3E+02 0.0027 24.0 4.1 33 168-200 16-50 (83)
97 TIGR00017 cmk cytidylate kinas 24.9 3.1E+02 0.0068 24.7 7.0 80 163-244 13-130 (217)
98 PF10389 CoatB: Bacteriophage 24.7 59 0.0013 24.3 2.0 24 109-132 22-45 (46)
99 PHA02591 hypothetical protein; 24.7 58 0.0012 27.2 2.1 36 198-234 44-79 (83)
100 COG4860 Uncharacterized protei 24.5 1.3E+02 0.0027 27.9 4.4 40 202-242 96-135 (170)
101 cd00086 homeodomain Homeodomai 24.5 1.5E+02 0.0031 20.2 3.8 37 146-183 8-44 (59)
102 COG2761 FrnE Predicted dithiol 24.2 1.1E+02 0.0024 29.0 4.2 40 145-184 119-158 (225)
103 TIGR01167 LPXTG_anchor LPXTG-m 24.1 81 0.0018 20.3 2.4 21 99-119 3-23 (34)
104 cd07321 Extradiol_Dioxygenase_ 23.9 59 0.0013 25.6 2.0 54 185-238 6-59 (77)
105 PRK00118 putative DNA-binding 23.9 48 0.001 27.7 1.6 69 199-267 19-89 (104)
106 PF04840 Vps16_C: Vps16, C-ter 23.8 63 0.0014 31.1 2.6 36 278-313 197-232 (319)
107 cd04765 HTH_MlrA-like_sg2 Heli 23.7 1E+02 0.0022 24.8 3.4 53 178-230 39-92 (99)
108 PRK09726 antitoxin HipB; Provi 23.5 94 0.002 24.0 3.0 38 195-233 6-44 (88)
109 COG2059 ChrA Chromate transpor 23.5 68 0.0015 29.5 2.6 28 68-99 33-61 (195)
110 PRK14135 recX recombination re 23.4 3.2E+02 0.0069 24.8 6.8 64 185-261 125-188 (263)
111 PF08784 RPA_C: Replication pr 23.4 1.6E+02 0.0034 23.1 4.3 43 151-195 50-93 (102)
112 PRK07668 hypothetical protein; 23.3 1.1E+02 0.0025 29.2 4.1 34 198-232 6-40 (254)
113 PLN00138 large subunit ribosom 23.2 29 0.00063 29.5 0.2 12 66-77 98-109 (113)
114 PF13154 DUF3991: Protein of u 23.0 49 0.0011 25.3 1.4 19 189-207 1-19 (77)
115 PRK11448 hsdR type I restricti 23.0 3.2E+02 0.007 31.1 8.0 78 142-226 967-1053(1123)
116 PRK09459 pspG phage shock prot 22.9 42 0.00091 27.5 1.0 17 123-139 58-74 (76)
117 PRK06645 DNA polymerase III su 22.9 4.2E+02 0.009 27.5 8.2 61 146-206 189-253 (507)
118 TIGR02147 Fsuc_second hypothet 22.8 1.2E+02 0.0026 29.0 4.1 109 180-296 115-237 (271)
119 PF12651 RHH_3: Ribbon-helix-h 22.4 1.3E+02 0.0029 21.3 3.4 27 168-194 16-42 (44)
120 PF01026 TatD_DNase: TatD rela 22.3 1.3E+02 0.0028 27.1 4.1 36 197-232 219-255 (255)
121 cd01310 TatD_DNAse TatD like p 22.2 1.4E+02 0.003 25.5 4.0 32 200-231 218-250 (251)
122 cd04770 HTH_HMRTR Helix-Turn-H 22.1 4.1E+02 0.0089 21.4 6.6 30 195-224 37-68 (123)
123 COG2212 MnhF Multisubunit Na+/ 21.9 70 0.0015 26.5 2.1 39 106-148 3-41 (89)
124 PF05598 DUF772: Transposase d 21.7 1.2E+02 0.0027 22.2 3.2 32 196-227 4-36 (77)
125 PF00248 Aldo_ket_red: Aldo/ke 21.7 1.5E+02 0.0033 26.1 4.3 55 164-222 216-278 (283)
126 PTZ00373 60S Acidic ribosomal 21.6 33 0.00073 29.3 0.2 9 69-77 100-108 (112)
127 PF14163 SieB: Superinfection 21.5 1.2E+02 0.0025 25.7 3.4 12 196-207 101-112 (151)
128 PF13934 ELYS: Nuclear pore co 21.5 4.6E+02 0.01 23.9 7.5 101 96-218 101-204 (226)
129 PHA03211 serine/threonine kina 21.4 40 0.00087 33.4 0.7 36 64-99 92-127 (461)
130 PRK06361 hypothetical protein; 21.2 1.2E+02 0.0026 26.3 3.6 40 196-235 173-212 (212)
131 cd08315 Death_TRAILR_DR4_DR5 D 21.2 2.6E+02 0.0056 22.8 5.2 42 179-225 1-42 (96)
132 TIGR00694 thiM hydroxyethylthi 20.9 3.5E+02 0.0076 24.7 6.6 63 197-260 38-104 (249)
133 cd07922 CarBa CarBa is the A s 20.5 87 0.0019 25.4 2.4 46 185-230 7-52 (81)
134 cd08801 Death_UNC5D Death doma 20.5 2.5E+02 0.0054 24.2 5.1 67 149-228 9-75 (98)
135 PF11377 DUF3180: Protein of u 20.4 54 0.0012 28.3 1.2 38 105-144 28-65 (138)
136 PRK13890 conjugal transfer pro 20.4 4E+02 0.0086 22.2 6.3 49 169-219 10-64 (120)
137 cd04784 HTH_CadR-PbrR Helix-Tu 20.4 4.5E+02 0.0097 21.5 6.5 29 196-224 38-68 (127)
138 cd01049 RNRR2 Ribonucleotide R 20.3 6.6E+02 0.014 22.8 9.9 138 73-235 118-267 (288)
139 PF13744 HTH_37: Helix-turn-he 20.3 1.1E+02 0.0024 23.4 2.8 22 202-223 20-41 (80)
140 PRK00236 xerC site-specific ty 20.1 5.4E+02 0.012 21.7 8.3 30 197-226 53-82 (297)
141 PTZ00072 40S ribosomal protein 20.1 1.2E+02 0.0026 27.5 3.3 31 196-226 24-54 (148)
142 PRK14038 ADP-dependent glucoki 20.1 1.4E+02 0.0031 30.9 4.3 102 131-232 188-313 (453)
143 PRK08561 rps15p 30S ribosomal 20.0 1.5E+02 0.0031 27.0 3.9 31 196-226 27-57 (151)
144 PRK00283 xerD site-specific ty 20.0 5.6E+02 0.012 22.0 8.1 44 183-226 33-80 (299)
No 1
>KOG0154 consensus RNA-binding protein RBM5 and related proteins, contain G-patch and RRM domains [General function prediction only]
Probab=98.51 E-value=6.6e-09 Score=102.79 Aligned_cols=221 Identities=16% Similarity=0.062 Sum_probs=193.9
Q ss_pred hhhHHHHhcchhhHHhhhhhhhhccccccccCCCCCCCCCchhHHHhhhHhhhhhhhhhhhhhhhhcCChhhhhhhhhcc
Q 020150 66 EVEVEVEEELPWIQEKALDLVEFTGSVTQAIPGPRVGQSKLPWILAVPLAYVGVSFVIAFVKTVKKFNSPKFKRKKLVNK 145 (330)
Q Consensus 66 ~~e~e~e~e~~wiqekaldlve~tG~vtQaIPGPRvg~s~lPwllAlPLAylG~TFviA~vRtvrK~~SPraKRkR~VnK 145 (330)
+.++..+...+|+++++.+-++|+....|.+.+++...+-++|-++-.+++.|++.+..++....+....|.+.+-...=
T Consensus 235 ~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~l~~d~~~s~~~~~~~~~~~~~~~~~~~~q~~~~~~~~~i~q~~~~~~~~~ 314 (573)
T KOG0154|consen 235 ETDEYYEDPETSVYYDTDSGLYFNDASSQYLYGDDEQSDYFYAKLSPSLPEFGVPNALQKKKKKEKPKIAQVKTKDMEKW 314 (573)
T ss_pred cccCceecCCccceeeccccceeccccccccccCCCcceeeecccccccccccccHHHhhhcccccccchhhhhhhHHhh
Confidence 55666778899999999999999999999999999999999999999999999999999999999999999999988888
Q ss_pred hhhHHhhHHHHHhcCCCCCCchHHHHHHHhhCCChHHHHHHHHHHHhccCCCChHHHHHHHHHHhhc--CCCcHHHHHHH
Q 020150 146 NAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKAS--MLDDSQVAEIL 223 (330)
Q Consensus 146 Na~LvkSLdeyfp~gRda~~~~vLk~L~~KTGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as--~L~d~evaeiL 223 (330)
++++++..++|.-... ..+.....++....|+....|-.+|..|..+|+.++|+.+...+|.+... +|.+..++..-
T Consensus 315 ~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 393 (573)
T KOG0154|consen 315 AKYLSKEKDSYLLSST-PAHEGVHTGVNTSKGAEPGPVKKEKKLYKKKEKFVNPELSKRGSHVSPSKNLKLIDVSTGLSD 393 (573)
T ss_pred hhhhhccccccccccc-ccceecccccccccccCchhhhhhccccccchhccCccccccccccCccccccccccccCCCc
Confidence 8999988888765544 47788888999999999999999999999999999999999999998853 56666666666
Q ss_pred HHHHHhhhhccCCeeeecccccchhhhhHHHHHHHHHhHhhhccchhhhccCCCccchhhcccc
Q 020150 224 NEISRRFVREKGPVVMNMSGYSEKGFKRKLAVQALFGKVFYLSELPEFCSRDSSLIVKEIFGVT 287 (330)
Q Consensus 224 ~E~s~Ri~~~~G~vmmn~~G~Te~G~kRK~a~~aLF~KllyLsEl~ef~s~dssL~vkeiFGvT 287 (330)
++.....-.+++.....+.++.+.+|..+.+++.-|....+..|..+++.+...+..+.++|++
T Consensus 394 ~~~~~~~~~~~~~~~~~~~~l~r~~~~~~~~~~~~~~~s~~h~~n~~~~~~~~~~~~~~~~~~~ 457 (573)
T KOG0154|consen 394 SELEQEKSLKLVDKLKLMCLLCRRQFPSKGSLQKHLTPSDLHKENLDKHRRPSTLEEASAEGPL 457 (573)
T ss_pred hHhhhhhhhhccccchhhhhhhhccCCchHHHhhhcccccchhhhHHhhccchhhhhhcccccc
Confidence 6666666668888889999999999999999999999999999999999888655455555544
No 2
>KOG4509 consensus Uncharacterized conserved protein [Function unknown]
Probab=86.86 E-value=1.2 Score=42.07 Aligned_cols=79 Identities=16% Similarity=0.191 Sum_probs=62.6
Q ss_pred hhhhhhhhhhhhhhcCChhhhhhhhhcchhhHHhhHHHHHhcCCCCCCch-HHHHHHHhhCCChHHHHHHHHHHHhccCC
Q 020150 118 GVSFVIAFVKTVKKFNSPKFKRKKLVNKNAMVCKTIDELFQKGGDAVNPP-ALKGLVQKTGFSMEDVLRKYIRYALNEKP 196 (330)
Q Consensus 118 G~TFviA~vRtvrK~~SPraKRkR~VnKNa~LvkSLdeyfp~gRda~~~~-vLk~L~~KTGFs~~Ei~RKYirY~LnEr~ 196 (330)
||-++.-..|+.+-=|.-|-|=+--+.+-..-++-|.+|+.+..+...+- -.|--++.||||-+-||++|+.-.|+|--
T Consensus 41 GIdLi~e~lk~~~ldna~R~~i~~k~s~Ym~ka~diekYLdqekEdgk~~eQ~KI~~NaTG~SY~~iF~e~~dd~l~~V~ 120 (247)
T KOG4509|consen 41 GIDLIAEALKGMKLDNADRCKIMAKFSDYMDKAADIEKYLDQEKEDGKTHEQIKIAANATGFSYARIFGECCDDRLREVH 120 (247)
T ss_pred hHHHHHHHHccCCCcchHHHHHHHHHHHHHHHHHHHHHHhhhhccccchhhhhhhhhccCcccHHHHHHHHHhhhhheee
Confidence 88888888888776666666666667777777888999999777665554 55556789999999999999998888753
No 3
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. 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 sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=80.21 E-value=5.4 Score=39.82 Aligned_cols=89 Identities=26% Similarity=0.465 Sum_probs=68.4
Q ss_pred hHHhhHHHHHhcCCCCCCchHHHHHHHhhCCChHHHHH----HHH---------HHHhcc--------CCCChHHHHHHH
Q 020150 148 MVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLR----KYI---------RYALNE--------KPFNPDLVVNLI 206 (330)
Q Consensus 148 ~LvkSLdeyfp~gRda~~~~vLk~L~~KTGFs~~Ei~R----KYi---------rY~LnE--------r~F~~d~VaDLi 206 (330)
.||+.=.+||..|..++..=.||.+..++|.+-.-|=| ||+ +|.... ...+.+.|-+.|
T Consensus 300 ~Iv~~Q~~Ff~~G~~~LkPLtlkdiA~~lglheSTVSRav~~Kyi~tp~Gi~~lk~FFs~~~~~~~~g~~~S~~~Ik~~I 379 (429)
T TIGR02395 300 AIVEHQKDFFLGGPAALKPLTLREVAEELGLHESTISRAINNKYLQTPRGVFELKYFFSRGVQTDSGEGEVSSTAIKALI 379 (429)
T ss_pred HHHHHHHHHHhcCcccCcCCcHHHHHHHhCCCccchhhhhcCceEecCCceEEHHHhcCCccCCCCCCCccCHHHHHHHH
Confidence 45555578999998887777999999999999998887 774 566653 236777776665
Q ss_pred HH-----HhhcCCCcHHHHHHHHH----HHHhhhhccCC
Q 020150 207 QL-----RKASMLDDSQVAEILNE----ISRRFVREKGP 236 (330)
Q Consensus 207 ~L-----r~as~L~d~evaeiL~E----~s~Ri~~~~G~ 236 (330)
+- -+.--|||.+++++|.+ +|||-|-||=.
T Consensus 380 ~~lI~~E~~~~PlSD~~I~~~L~~~Gi~IaRRTVaKYRe 418 (429)
T TIGR02395 380 KELIAAEDKRKPLSDQKIAELLKEKGIKIARRTVAKYRE 418 (429)
T ss_pred HHHHHhcCCCCCCCHHHHHHHHHhcCCCeehHHHHHHHH
Confidence 52 23355999999999985 79999999843
No 4
>PF14297 DUF4373: Domain of unknown function (DUF4373)
Probab=79.93 E-value=8.6 Score=29.88 Aligned_cols=70 Identities=17% Similarity=0.238 Sum_probs=55.3
Q ss_pred HHhcCCCCCCchHHHHHHHhhCCChHHHHHHHHHHHhccCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHH
Q 020150 156 LFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEI 226 (330)
Q Consensus 156 yfp~gRda~~~~vLk~L~~KTGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~ 226 (330)
|||-.-++++-+.++.|+++.|-...-|+-+=|.++-.+.-+-...= ++..+-.-.+.+.+.|.+|+++.
T Consensus 1 YFp~dv~~~~D~ki~~l~~~~G~~G~~~y~~ll~~iy~~~~y~~~~~-~~~~~a~~~~~~~~~v~~II~~~ 70 (87)
T PF14297_consen 1 YFPLDVDFFSDPKIRRLMAEYGCEGYGIYWYLLEYIYKQGGYYLWWD-KLFLIARKLGVSEEYVEEIINEY 70 (87)
T ss_pred CcccccccccCHHHHHHHHHcCCchHHHHHHHHHHHHcCCCeEeeHH-HHHHHHHHHCcCHHHHHHHHHHh
Confidence 68888899999999999999999999999988888887776622111 14444455699999999999944
No 5
>PLN02777 photosystem I P subunit (PSI-P)
Probab=79.37 E-value=1.5 Score=39.97 Aligned_cols=27 Identities=44% Similarity=0.699 Sum_probs=16.3
Q ss_pred Cccccccccccc--------------cccCCCCCCCCCCCC
Q 020150 1 MASLATSSFSSL--------------QFLPRPKIPQPPFSS 27 (330)
Q Consensus 1 ~~~~~~~~~~~~--------------q~~~~p~~p~~~~~~ 27 (330)
|+.|.++|++|+ |.+.-|.+|||+-.+
T Consensus 1 ~~~l~~~~~~~~~~~~~~~~~~a~~~~~~~lp~lppp~~~~ 41 (167)
T PLN02777 1 MTPLSISSSSTLIDSKAPRSSAAASPQCVSLPTLPPPPVQS 41 (167)
T ss_pred CCccccccccccccCCCCCcCcccCCccccCCCCCCCCccc
Confidence 677777776653 555556666555433
No 6
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=77.57 E-value=1.2 Score=39.29 Aligned_cols=88 Identities=27% Similarity=0.454 Sum_probs=20.5
Q ss_pred hHHhhHHHHHhcCCCCCCchHHHHHHHhhCCChHHHHH----HHHHH---------HhccC-------CCChHHHHHHH-
Q 020150 148 MVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLR----KYIRY---------ALNEK-------PFNPDLVVNLI- 206 (330)
Q Consensus 148 ~LvkSLdeyfp~gRda~~~~vLk~L~~KTGFs~~Ei~R----KYirY---------~LnEr-------~F~~d~VaDLi- 206 (330)
+||+.=.+||..|...+..=-++.+...+|++..-|-| ||+.+ .+.-. .++.+.|-+.|
T Consensus 31 ~iv~~Q~~ff~~g~~~l~PLt~~~iA~~lgl~~STVSRav~~Ky~~t~~Gi~plk~fF~~~~~~~~~~~~S~~~ik~~i~ 110 (160)
T PF04552_consen 31 AIVERQKDFFLGGPGALKPLTMKDIADELGLHESTVSRAVKNKYIQTPRGIFPLKDFFSRSVSSGSGEEFSSEAIKARIK 110 (160)
T ss_dssp ------------------------------------------------------S-----SS--SS-SS---TTH-HHHH
T ss_pred HHHHHHHHHHhcCcccCcCCCHHHHHHHhCCCHhHHHHHHcCceeecCCeeeeHHHhccccccCCCCcccHHHHHHHHHH
Confidence 56777788999888777777999999999999988887 88753 22211 13344444333
Q ss_pred ---HH-HhhcCCCcHHHHHHHH----HHHHhhhhccC
Q 020150 207 ---QL-RKASMLDDSQVAEILN----EISRRFVREKG 235 (330)
Q Consensus 207 ---~L-r~as~L~d~evaeiL~----E~s~Ri~~~~G 235 (330)
+= -+.-.|||++++++|+ .+|||-|-||=
T Consensus 111 ~lI~~Ed~~~PlSD~~i~~~L~~~gi~isRRTVaKYR 147 (160)
T PF04552_consen 111 ELIEEEDKKKPLSDQEIAELLKEEGIKISRRTVAKYR 147 (160)
T ss_dssp HHHTTS-TTS---HHHHHHHHTTTTS---HHHHHHHH
T ss_pred HHHHhcCCCCCCCHHHHHHHHHHcCCCccHHHHHHHH
Confidence 32 2346899999999997 58999999884
No 7
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=72.17 E-value=12 Score=37.81 Aligned_cols=89 Identities=26% Similarity=0.477 Sum_probs=66.4
Q ss_pred hHHhhHHHHHhcCCCCCCchHHHHHHHhhCCChHHHHH----HHH---------HHHhccC-------CCChHHHHHHHH
Q 020150 148 MVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLR----KYI---------RYALNEK-------PFNPDLVVNLIQ 207 (330)
Q Consensus 148 ~LvkSLdeyfp~gRda~~~~vLk~L~~KTGFs~~Ei~R----KYi---------rY~LnEr-------~F~~d~VaDLi~ 207 (330)
.||+.=.+||..|..++..=.||.+..++|+.-.-|=| ||+ +|..... ..+.+.|-+.|+
T Consensus 325 ~Iv~~Q~~Ff~~G~~~LkPLtlkdvAe~lglheSTVSRav~~Kyv~tp~Gi~~lk~FFs~~~~~~~g~~~S~~~Ik~~Ik 404 (455)
T PRK05932 325 CIVEQQRDFFEHGEEALKPLVLKDIAEELGMHESTISRATTNKYMATPRGIFELKYFFSSAVSTDGGGEASSTAIRALIK 404 (455)
T ss_pred HHHHHHHHHHhCCcccCcCccHHHHHHHhCCCccchhhhhcCceeecCCceEEHHHhcccccCCCCCccccHHHHHHHHH
Confidence 34555578999998877777999999999999998887 774 5665422 245556665554
Q ss_pred HH-----hhcCCCcHHHHHHHHH----HHHhhhhccCC
Q 020150 208 LR-----KASMLDDSQVAEILNE----ISRRFVREKGP 236 (330)
Q Consensus 208 Lr-----~as~L~d~evaeiL~E----~s~Ri~~~~G~ 236 (330)
-= +.--|||.+++++|.+ ||||-|-||=.
T Consensus 405 ~lI~~Ed~~~PlSD~~I~~~L~~~Gi~IaRRTVaKYRe 442 (455)
T PRK05932 405 KLIAAENPKKPLSDSKIAELLKEQGIDVARRTVAKYRE 442 (455)
T ss_pred HHHHhcCCCCCCCHHHHHHHHHHcCCCeehHHHHHHHH
Confidence 21 2246999999999986 89999999954
No 8
>smart00657 RPOL4c DNA-directed RNA-polymerase II subunit.
Probab=67.63 E-value=15 Score=30.45 Aligned_cols=45 Identities=24% Similarity=0.392 Sum_probs=30.4
Q ss_pred hHHHHHHHHHHHhccCCC-ChHHHHHHHHHHhhcCCCcHHHHHHHH
Q 020150 180 MEDVLRKYIRYALNEKPF-NPDLVVNLIQLRKASMLDDSQVAEILN 224 (330)
Q Consensus 180 ~~Ei~RKYirY~LnEr~F-~~d~VaDLi~Lr~as~L~d~evaeiL~ 224 (330)
+..|++|.+.|+-+=..| |++.+..+..+=+..+|+..|++-|.|
T Consensus 34 l~~v~~~tl~Yl~~~~~~~~~e~i~~~~~~L~~~~L~k~E~~~i~N 79 (118)
T smart00657 34 LSTVMKKTLKYLSKFARFKNREIVRAVRTLLKSKKLHKFEIAQLGN 79 (118)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHhcCCCHHHHHHHhC
Confidence 355777777777554445 677777777665667777777776655
No 9
>PF03874 RNA_pol_Rpb4: RNA polymerase Rpb4; InterPro: IPR005574 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core. Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable [].; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3AYH_A 3H3V_E 4A3C_D 3PO3_D 3HOX_D 2R92_D 3HOU_D 1Y77_D 2R7Z_D 3QT1_D ....
Probab=67.30 E-value=17 Score=29.17 Aligned_cols=58 Identities=16% Similarity=0.162 Sum_probs=42.3
Q ss_pred HHHHhhCCChHHHHHHHHHHHhccCCCC-hHHHHHHHHHHhhcCCCcHHHHHHHHHHHH
Q 020150 171 GLVQKTGFSMEDVLRKYIRYALNEKPFN-PDLVVNLIQLRKASMLDDSQVAEILNEISR 228 (330)
Q Consensus 171 ~L~~KTGFs~~Ei~RKYirY~LnEr~F~-~d~VaDLi~Lr~as~L~d~evaeiL~E~s~ 228 (330)
...+.....+..+++|-+.|+-+=..+. ++.+..++..=+..||++.|+.-|+|-.=+
T Consensus 27 ~~~~~~~~~~~~~~~~~~~Yl~~~~~~~~~e~~~~l~~~L~~~~L~~~E~~qi~Nl~P~ 85 (117)
T PF03874_consen 27 KNKEDPPENLNTIQYKTLEYLEKFSKFQNPESIKELREELKKFGLTEFEILQIINLRPT 85 (117)
T ss_dssp HHHHHCSSCHCHHHHHHHHHHHHH-SSSSHHHHHHHHHHHTTSTS-HHHHHHHHHH--S
T ss_pred ccccccccchHHHHHHHHHHHHccccCCCHHHHHHHHHHHhcccCCHHHHHHHhcCCCC
Confidence 4556677788888888888888877776 788888887777888888888888875533
No 10
>COG1508 RpoN DNA-directed RNA polymerase specialized sigma subunit, sigma54 homolog [Transcription]
Probab=65.91 E-value=17 Score=37.39 Aligned_cols=99 Identities=26% Similarity=0.458 Sum_probs=77.4
Q ss_pred hhhhhhcch-hhHHhhHHHHHhcCCCCCCchHHHHHHHhhCCChHHHHH----HHH---------HHH----hccC----
Q 020150 138 KRKKLVNKN-AMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLR----KYI---------RYA----LNEK---- 195 (330)
Q Consensus 138 KRkR~VnKN-a~LvkSLdeyfp~gRda~~~~vLk~L~~KTGFs~~Ei~R----KYi---------rY~----LnEr---- 195 (330)
+|++++=|= .++|+-=+.||..|..++..=+||.+..+.|..-.-|.| ||+ +|. +...
T Consensus 301 qR~~TLlkV~~~Iv~~Q~~Ff~~g~~~l~PL~LrdvA~~i~~HESTISRai~nKy~~tprG~feLK~FFs~~i~s~~gg~ 380 (444)
T COG1508 301 QREETLLKVAEEIVEYQKAFFEGGEEALKPLVLRDVADEIGMHESTISRAITNKYLATPRGLFELKYFFSSSLASSEGGE 380 (444)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCcccCCcccHHHHHHHhCccHHHHHHHHhcccccCCcceeeHHHHHHHhccCCCCCc
Confidence 455554442 367777789999999999999999999999999999988 774 443 3344
Q ss_pred CCChHHHHHHHH-----HHhhcCCCcHHHHHHHHH----HHHhhhhccCC
Q 020150 196 PFNPDLVVNLIQ-----LRKASMLDDSQVAEILNE----ISRRFVREKGP 236 (330)
Q Consensus 196 ~F~~d~VaDLi~-----Lr~as~L~d~evaeiL~E----~s~Ri~~~~G~ 236 (330)
.++-+.|-.+|+ =++..-|||+.++++|-| +|||-|-||=-
T Consensus 381 ~~S~~~Ik~~Ik~lI~~E~~~~pLSD~kIa~lLkekGi~iARRTVAKYRe 430 (444)
T COG1508 381 ASSTEAIKALIKKLIEAEDKKKPLSDSKIAELLKEKGIDVARRTVAKYRE 430 (444)
T ss_pred cccHHHHHHHHHHHHhhccCCCCCCHHHHHHHHHHcCCchhHHhHHHHHH
Confidence 577878877764 245558999999999997 79999999954
No 11
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=62.12 E-value=19 Score=37.01 Aligned_cols=89 Identities=25% Similarity=0.382 Sum_probs=67.3
Q ss_pred hHHhhHHHHHhcCCCCCCchHHHHHHHhhCCChHHHHH----HHH---------HHHhccC-------CCChHHHHHHHH
Q 020150 148 MVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLR----KYI---------RYALNEK-------PFNPDLVVNLIQ 207 (330)
Q Consensus 148 ~LvkSLdeyfp~gRda~~~~vLk~L~~KTGFs~~Ei~R----KYi---------rY~LnEr-------~F~~d~VaDLi~ 207 (330)
.+|+.=.+||..|..++..=.||.+..+.|..-.-|=| ||+ +|...-. ....+.|-.+|+
T Consensus 351 ~Iv~~Q~~Ff~~G~~~LkPLtlkdVAe~lglHeSTVSRa~~~KY~~tp~GifeLK~FFs~~v~~~~g~~~Ss~~Ik~~Ik 430 (481)
T PRK12469 351 CIVARQRDFFRYGEIALKPLVLRDVAEELGLHESTISRATGNKYMATPRGTFEFKHFFPRKLEAAGGGECSAAAVRALIK 430 (481)
T ss_pred HHHHHHHHHHhCCcccCcCCcHHHHHHHhCCCcchhhHHhcCceeecCCceEeHHHhhccccCCCCCccccHHHHHHHHH
Confidence 34555568999998888888999999999999888877 784 5666422 244555666554
Q ss_pred H-----HhhcCCCcHHHHHHHHH----HHHhhhhccCC
Q 020150 208 L-----RKASMLDDSQVAEILNE----ISRRFVREKGP 236 (330)
Q Consensus 208 L-----r~as~L~d~evaeiL~E----~s~Ri~~~~G~ 236 (330)
- -+.--|||.+++++|++ ||||-|-||=.
T Consensus 431 ~lI~~Ed~~kPLSD~~I~~~L~~~GI~IARRTVAKYRe 468 (481)
T PRK12469 431 EMIAAEQAGDPLSDVALAEMLAGRGVLIARRTVAKYRE 468 (481)
T ss_pred HHHHhcCCCCCCCHHHHHHHHHhcCCCeechhHHHHHH
Confidence 3 12356999999999986 89999999954
No 12
>KOG2499 consensus Beta-N-acetylhexosaminidase [Carbohydrate transport and metabolism]
Probab=61.59 E-value=8.1 Score=40.62 Aligned_cols=51 Identities=35% Similarity=0.677 Sum_probs=42.6
Q ss_pred hhcchhhHHhhH---------HHHHhcCCCCCCc------hHHHHHHHhhCCChHH--HHHHHHHHHh
Q 020150 142 LVNKNAMVCKTI---------DELFQKGGDAVNP------PALKGLVQKTGFSMED--VLRKYIRYAL 192 (330)
Q Consensus 142 ~VnKNa~LvkSL---------deyfp~gRda~~~------~vLk~L~~KTGFs~~E--i~RKYirY~L 192 (330)
+.|++-.+++.| |+||+-|+|+++. +..|..|+|-||..++ ..|+|+.+++
T Consensus 306 ~~n~tydvls~i~~dv~evFp~~~~HlGGDEV~~~CW~s~~~Iq~fM~~kGfg~~~~~~~~~~~~~~~ 373 (542)
T KOG2499|consen 306 TNNHTYDVLSEIFEDVSEVFPDEFFHLGGDEVSTPCWKSNPEIQDFMRKKGFGLDTKSLERLYIQFLL 373 (542)
T ss_pred CchhHHHHHHHHHHHHHHhCcHHHeecCCceeecccccCChHHHHHHHhCCCCchHHHHHHHHHHHHH
Confidence 456666666665 7899999999975 4899999999999998 8999998875
No 13
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=55.19 E-value=40 Score=26.97 Aligned_cols=56 Identities=27% Similarity=0.450 Sum_probs=43.6
Q ss_pred HHHHHHhhCCChHHHHHHHHHHHh---------ccCCCChHHHHHHHH---HHhhcCCCcHHHHHHHHH
Q 020150 169 LKGLVQKTGFSMEDVLRKYIRYAL---------NEKPFNPDLVVNLIQ---LRKASMLDDSQVAEILNE 225 (330)
Q Consensus 169 Lk~L~~KTGFs~~Ei~RKYirY~L---------nEr~F~~d~VaDLi~---Lr~as~L~d~evaeiL~E 225 (330)
+.++..+||-+.. -+|-|.+.-| +.+-|+++.|..|-. ||+.+|++=++|+++|+.
T Consensus 3 I~eva~~~gvs~~-tlR~Ye~~GLl~p~~r~~~g~r~Y~~~dv~~l~~I~~L~~~~G~~l~~I~~~l~~ 70 (95)
T cd04780 3 MSELSKRSGVSVA-TIKYYLREGLLPEGRRLAPNQAEYSEAHVERLRLIRALQQEGGLPISQIKEVLDA 70 (95)
T ss_pred HHHHHHHHCcCHH-HHHHHHHCCCCCCCcCCCCCCeecCHHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 4678889999876 5677777655 346799999988765 555689999999999986
No 14
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=54.35 E-value=24 Score=23.24 Aligned_cols=27 Identities=30% Similarity=0.395 Sum_probs=23.7
Q ss_pred hHHHHHHHhhCCChHHHHHHHHHHHhc
Q 020150 167 PALKGLVQKTGFSMEDVLRKYIRYALN 193 (330)
Q Consensus 167 ~vLk~L~~KTGFs~~Ei~RKYirY~Ln 193 (330)
..|+.+..+.|-|..+++|..|+..|+
T Consensus 12 ~~l~~~a~~~g~s~s~~ir~ai~~~l~ 38 (39)
T PF01402_consen 12 ERLDELAKELGRSRSELIREAIREYLE 38 (39)
T ss_dssp HHHHHHHHHHTSSHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHCcCHHHHHHHHHHHHHh
Confidence 367899999999999999999988764
No 15
>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=54.00 E-value=20 Score=31.78 Aligned_cols=49 Identities=22% Similarity=0.444 Sum_probs=38.1
Q ss_pred ChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhh--ccCCeeeecccccch
Q 020150 198 NPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVR--EKGPVVMNMSGYSEK 247 (330)
Q Consensus 198 ~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~~--~~G~vmmn~~G~Te~ 247 (330)
|+|.+.||-+-=++.+++|+|+.|+|+|+-..+.+ +.|.--.++=| |.+
T Consensus 6 N~~y~~~l~~~L~~~~~~e~~~e~~L~eil~~LleaQk~G~tA~~lfG-~P~ 56 (206)
T PF06570_consen 6 NQEYIFDLRKYLRSSGVSEEEIEELLEEILPHLLEAQKKGKTARQLFG-DPK 56 (206)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHhCCCcHHHHcC-CHH
Confidence 56777777644488899999999999999999986 56766666666 543
No 16
>PF06798 PrkA: PrkA serine protein kinase C-terminal domain; InterPro: IPR010650 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. This entry is found at the C terminus of PrkA proteins - bacterial and archaeal serine kinases approximately 630 residues in length. PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases []. Note that many of these are hypothetical.
Probab=52.85 E-value=84 Score=29.70 Aligned_cols=76 Identities=20% Similarity=0.359 Sum_probs=51.7
Q ss_pred hHHHHHHHhhCCCh-------HHHHHHHHHHHhccCCCChH---------------HHHHHHHHHh-hcCCCcHHHHHHH
Q 020150 167 PALKGLVQKTGFSM-------EDVLRKYIRYALNEKPFNPD---------------LVVNLIQLRK-ASMLDDSQVAEIL 223 (330)
Q Consensus 167 ~vLk~L~~KTGFs~-------~Ei~RKYirY~LnEr~F~~d---------------~VaDLi~Lr~-as~L~d~evaeiL 223 (330)
.-|+.++.+-|.+- .||...|-+++-+-+.|+.+ .|.|++.+=. .+.-.|.+..+-.
T Consensus 151 ~~mrsIEe~igi~~~~~~~FR~ei~~~~~~~~~~g~~~~~~~~e~Lr~~iEkkL~~d~~~~~~~~t~~~k~~d~e~~~~~ 230 (254)
T PF06798_consen 151 RFMRSIEERIGISEEAKKDFRREIIKYISALAREGKKFDYTSYERLREAIEKKLFSDVKDLIKIITESSKTPDKEQQRKI 230 (254)
T ss_pred HHHHHHHHhcCCCcccHHHHHHHHHHHHHHHHcCCCCCChhhhHHHHHHHHHHHHHHHHHHHHhcchhccCCCHHHHHHH
Confidence 37788888777765 46666664444555788875 3455555444 3444688888888
Q ss_pred HHHHHhhhhccCCeeeecccccchhhh
Q 020150 224 NEISRRFVREKGPVVMNMSGYSEKGFK 250 (330)
Q Consensus 224 ~E~s~Ri~~~~G~vmmn~~G~Te~G~k 250 (330)
++.-.|+.++| |||+.|.+
T Consensus 231 ~~~i~rL~~~~--------GY~~~~A~ 249 (254)
T PF06798_consen 231 DEVIERLIKKY--------GYCEACAR 249 (254)
T ss_pred HHHHHHHHHcC--------CCCHHHHH
Confidence 88888888887 47777764
No 17
>TIGR03252 uncharacterized HhH-GPD family protein. This model describes a small, well-conserved bacterial protein family. Its sequence largely consists of a domain, HhH-GPD, found in a variety of related base excision DNA repair enzymes (see pfam00730).
Probab=52.58 E-value=70 Score=29.25 Aligned_cols=73 Identities=25% Similarity=0.294 Sum_probs=47.4
Q ss_pred CChHHHHHHHHHHhhc-CCCcHHHHHHHHHHHHhhhhccCCeeeecc-------------cccchhhhhHHHH--HHHHH
Q 020150 197 FNPDLVVNLIQLRKAS-MLDDSQVAEILNEISRRFVREKGPVVMNMS-------------GYSEKGFKRKLAV--QALFG 260 (330)
Q Consensus 197 F~~d~VaDLi~Lr~as-~L~d~evaeiL~E~s~Ri~~~~G~vmmn~~-------------G~Te~G~kRK~a~--~aLF~ 260 (330)
-+++.++++|.=+-|+ |+ ..+-|.-|.+.++.|.++||--+-++. =++..|+-||-|- -+.++
T Consensus 58 a~~eeL~~lI~~~pal~Gf-y~~KAk~Lk~~a~~iie~y~G~v~~L~~~~~p~t~~lre~Ll~LpGVG~KTAnvVL~~l~ 136 (177)
T TIGR03252 58 YDPQAFVALFSERPAVHRF-PGSMAKRVQALAQYVVDTYDGDATAVWTEGDPDGKELLRRLKALPGFGKQKAKIFLALLG 136 (177)
T ss_pred CCHHHHHHHHhcCccccCc-hHHHHHHHHHHHHHHHHHhCCChhhhhcccCCCcHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 4566666666433221 33 456778888999999999998663332 2456788888652 34445
Q ss_pred hHhhhccchhhhccCCCccchhhcccchhhh
Q 020150 261 KVFYLSELPEFCSRDSSLIVKEIFGVTDEDA 291 (330)
Q Consensus 261 KllyLsEl~ef~s~dssL~vkeiFGvTdeDa 291 (330)
+ -|||||+-.
T Consensus 137 ~---------------------~~~~~~~~~ 146 (177)
T TIGR03252 137 K---------------------QLGVTPEGW 146 (177)
T ss_pred H---------------------HhCCCCcch
Confidence 4 899999754
No 18
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=52.14 E-value=74 Score=28.31 Aligned_cols=73 Identities=12% Similarity=0.168 Sum_probs=50.8
Q ss_pred hhhHHhhHHHHHhcCCCCCCchHHHHHHHhhCCChHHH---HHHHHHHHhccCCCChHHHHHHHHHHhhcCCCcHHHHHH
Q 020150 146 NAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDV---LRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEI 222 (330)
Q Consensus 146 Na~LvkSLdeyfp~gRda~~~~vLk~L~~KTGFs~~Ei---~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaei 222 (330)
...+.+-|..++.+.+-.++..++..|...+|-++-.+ ++++..| .++.+.+.|.+++ .......|-++
T Consensus 163 ~~ei~~~l~~~~~~~~~~i~~~al~~l~~~~~gd~r~~~~~l~~~~~~---~~~it~~~v~~~~-----~~~~~~~i~~l 234 (319)
T PRK00440 163 KEAVAERLRYIAENEGIEITDDALEAIYYVSEGDMRKAINALQAAAAT---GKEVTEEAVYKIT-----GTARPEEIREM 234 (319)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHc---CCCCCHHHHHHHh-----CCCCHHHHHHH
Confidence 34567778888888777789999999999999887764 4555544 4678888887665 22334455555
Q ss_pred HHHH
Q 020150 223 LNEI 226 (330)
Q Consensus 223 L~E~ 226 (330)
++.+
T Consensus 235 ~~~~ 238 (319)
T PRK00440 235 IELA 238 (319)
T ss_pred HHHH
Confidence 5544
No 19
>PHA01748 hypothetical protein
Probab=51.40 E-value=16 Score=27.47 Aligned_cols=29 Identities=21% Similarity=0.329 Sum_probs=24.0
Q ss_pred HHHHHHHhhCCChHHHHHHHHHHHhccCC
Q 020150 168 ALKGLVQKTGFSMEDVLRKYIRYALNEKP 196 (330)
Q Consensus 168 vLk~L~~KTGFs~~Ei~RKYirY~LnEr~ 196 (330)
.|..+..+.|++..|++|+.|+..+.|+.
T Consensus 16 eld~~a~~~g~~RSE~Ir~Ai~~~~~~~~ 44 (60)
T PHA01748 16 LLDRYAIKHGLNRSEAIRKAIEKMVKDEL 44 (60)
T ss_pred HHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 35567888999999999999998887654
No 20
>COG4915 XpaC 5-bromo-4-chloroindolyl phosphate hydrolysis protein [General function prediction only]
Probab=51.33 E-value=55 Score=30.99 Aligned_cols=53 Identities=32% Similarity=0.417 Sum_probs=40.4
Q ss_pred HHHHhhCCChHHHHHHHHHHHhccCCCChHHHHHHHHHHhhcCCCc-----HHHHHHHHHHHHhhhh
Q 020150 171 GLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDD-----SQVAEILNEISRRFVR 232 (330)
Q Consensus 171 ~L~~KTGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d-----~evaeiL~E~s~Ri~~ 232 (330)
+-..++|-+-.|+ ||||=-|+| +=..++.|+|++-=.+ .|++++| ++++|||.
T Consensus 58 ~~l~e~gLT~kdy--kyiR~nLee------arqki~~l~K~l~q~kslq~f~q~n~~l-~iskriy~ 115 (204)
T COG4915 58 ERLHEAGLTDKDY--KYIRENLEE------ARQKIKRLEKLLKQEKSLQVFEQVNGGL-EISKRIYK 115 (204)
T ss_pred HHHHHccCccchH--HHHHHhHHH------HHHHHHHHHHHHHhhhHHHHHHHHhhHH-HHHHHHHH
Confidence 3346889998887 899999986 5577888888876554 4677776 68999983
No 21
>TIGR01856 hisJ_fam histidinol phosphate phosphatase HisJ family. This model represents the histidinol phosphate phosphatase HisJ of Bacillus subtilis, and related proteins from a number of species within a larger family of phosphatases in the PHP hydrolase family. HisJ catalyzes the penultimate step of histidine biosynthesis but shows no homology to the functionally equivalent sequence in E. coli, a domain of the bifunctional HisB protein. Note, however, that many species have two members and that Clostridium perfringens, predicted not to make histidine, has five members of this family; this family is designated subfamily rather than equivalog to indicate that members may not all act as HisJ.
Probab=50.96 E-value=66 Score=29.13 Aligned_cols=81 Identities=17% Similarity=0.188 Sum_probs=50.0
Q ss_pred chHHHHHHHhhCCChHHHHHHHHHHH--hccCCCChHHHHHHHHHHhhcCC------CcHHHHHHHHHHHHhhhhccCCe
Q 020150 166 PPALKGLVQKTGFSMEDVLRKYIRYA--LNEKPFNPDLVVNLIQLRKASML------DDSQVAEILNEISRRFVREKGPV 237 (330)
Q Consensus 166 ~~vLk~L~~KTGFs~~Ei~RKYirY~--LnEr~F~~d~VaDLi~Lr~as~L------~d~evaeiL~E~s~Ri~~~~G~v 237 (330)
.+.+.....+.|-+..++++.|.... +-+..|++|.++-+=-.|+-... .+..+-+.+.++.+.+-+.-..+
T Consensus 122 ~~~~~~~~~~~~~~~~~~~~~Y~~~~~~~i~~~~~~dvlgH~Dli~~~~~~~~~~~~~~~~~~~~~~~il~~~~~~g~~l 201 (253)
T TIGR01856 122 AEEFNEGLVSFYGNLEQAQRDYFESVYDSIQALFKPLVIGHIDLVQKFGPLFTDVSSFSDEVYELLQRILKLVASQGKAL 201 (253)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCCCCCCcccHhHHHHhCccccccccccHHHHHHHHHHHHHHHHcCCEE
Confidence 34454444466778999999997763 34556778888743222322222 44556667766666665554555
Q ss_pred eeecccccc
Q 020150 238 VMNMSGYSE 246 (330)
Q Consensus 238 mmn~~G~Te 246 (330)
=+|++|+..
T Consensus 202 EiNt~g~r~ 210 (253)
T TIGR01856 202 EFNTSGLRK 210 (253)
T ss_pred EEEcHhhcC
Confidence 589998754
No 22
>TIGR00865 bcl-2 Apoptosis regulator. in artificial membranes at acidic pH, proapoptotic Bcl-2 family proteins (including Bax and Bak) probably induce the mitochondrial permeability transition and cytochrome c release by interacting with permeability transition pores, the most important component for pore fomation of which is VDAC.
Probab=50.87 E-value=22 Score=33.04 Aligned_cols=61 Identities=21% Similarity=0.189 Sum_probs=42.8
Q ss_pred CChHHHHHHHHHHHhccCCCChHHHHHH-----------HHHHhh------------cCCCcHHHHHHHHHHHHhhhhcc
Q 020150 178 FSMEDVLRKYIRYALNEKPFNPDLVVNL-----------IQLRKA------------SMLDDSQVAEILNEISRRFVREK 234 (330)
Q Consensus 178 Fs~~Ei~RKYirY~LnEr~F~~d~VaDL-----------i~Lr~a------------s~L~d~evaeiL~E~s~Ri~~~~ 234 (330)
+|.-|++-|||-|.|.-+.+.++.-.++ ++=|.. .+-..++|++.|+.++.-+=++|
T Consensus 3 ~~~r~~v~~~~~yklsq~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~ps~v~~~Lr~igdEle~~~ 82 (213)
T TIGR00865 3 GSNRELVMKFISYKLSQRGGSWTAGEQIMKNGAPLLHGFIQHRAGPMTGETPSEGPPQDPPPSAVHQALRRAGDEFERRY 82 (213)
T ss_pred CchHHHHHHHHHHhhcccCCCCcchhhHHhhhhhhhccccccccccccccccccCCCCCCChHHHHHHHHHHHHHHHHHH
Confidence 4567999999999999999887654432 221211 22445679999999998887766
Q ss_pred CCee
Q 020150 235 GPVV 238 (330)
Q Consensus 235 G~vm 238 (330)
-...
T Consensus 83 ~~~f 86 (213)
T TIGR00865 83 RRAF 86 (213)
T ss_pred HHHH
Confidence 5543
No 23
>PF11166 DUF2951: Protein of unknown function (DUF2951); InterPro: IPR021337 This family of proteins has no known function. It has a highly conserved sequence.
Probab=50.78 E-value=11 Score=32.13 Aligned_cols=21 Identities=38% Similarity=0.804 Sum_probs=18.0
Q ss_pred hHHHhhhHhhhhhhhhhhhhhh
Q 020150 108 WILAVPLAYVGVSFVIAFVKTV 129 (330)
Q Consensus 108 wllAlPLAylG~TFviA~vRtv 129 (330)
||+.+--..+| ||+||+.||+
T Consensus 75 wilGlvgTi~g-sliia~lr~~ 95 (98)
T PF11166_consen 75 WILGLVGTIFG-SLIIALLRTI 95 (98)
T ss_pred HHHHHHHHHHH-HHHHHHHHHH
Confidence 88888777777 9999999996
No 24
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=49.88 E-value=37 Score=30.61 Aligned_cols=80 Identities=28% Similarity=0.427 Sum_probs=55.2
Q ss_pred HHHHHHHhhCCChHHHHHHHHHHHhccCCCChHHHHHHHHHHhhc-CCCcHHHHHHHHHHHHhhhhccCCeeeecccccc
Q 020150 168 ALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKAS-MLDDSQVAEILNEISRRFVREKGPVVMNMSGYSE 246 (330)
Q Consensus 168 vLk~L~~KTGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as-~L~d~evaeiL~E~s~Ri~~~~G~vmmn~~G~Te 246 (330)
+|+-|.. -+-.+|=||-.|.++.|+++.|+++|+-=... =|+|.+.||.. +..|+-+-|||..+- ..+-+
T Consensus 26 Al~~Ls~------R~rse~ELr~kL~k~~~~~~~Ie~Vi~~l~~~~~ldD~~fAe~~--i~~r~~~g~G~~rl~-qeL~q 96 (174)
T COG2137 26 ALRLLSR------RDRSEKELRRKLAKKEFSEEIIEEVIDRLAEEGYLDDTRFAEAY--IRSRSRKGKGPARLK-QELKQ 96 (174)
T ss_pred HHHHHHH------HHHHHHHHHHHHHhccCCHHHHHHHHHHHHHcCcccHHHHHHHH--HHHHHhcccChHHHH-HHHHH
Confidence 4555544 35567778888999999999999999855554 47999999975 345555559998763 34555
Q ss_pred hhhhhHHHHH
Q 020150 247 KGFKRKLAVQ 256 (330)
Q Consensus 247 ~G~kRK~a~~ 256 (330)
+|+-+-+.-+
T Consensus 97 kGi~~~~Ie~ 106 (174)
T COG2137 97 KGIDDEIIEE 106 (174)
T ss_pred cCCCHHHHHH
Confidence 6655444433
No 25
>TIGR01359 UMP_CMP_kin_fam UMP-CMP kinase family. This subfamily of the adenylate kinase superfamily contains examples of UMP-CMP kinase, as well as others proteins with unknown specificity, some currently designated adenylate kinase. All known members are eukaryotic.
Probab=48.01 E-value=52 Score=27.18 Aligned_cols=54 Identities=22% Similarity=0.396 Sum_probs=36.4
Q ss_pred HHHHHHHhhCC---ChHHHHHHHHHHHhccCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHH
Q 020150 168 ALKGLVQKTGF---SMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEIS 227 (330)
Q Consensus 168 vLk~L~~KTGF---s~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s 227 (330)
.-+.|.++.|| |+.+++|++++ +..-....+.+++ ..+.-.+|+-+.+.|.+.-
T Consensus 15 ~a~~la~~~~~~~is~~d~lr~~~~----~~~~~~~~~~~~~--~~g~~~~~~~~~~ll~~~~ 71 (183)
T TIGR01359 15 QCAKIVENFGFTHLSAGDLLRAEIK----SGSENGELIESMI--KNGKIVPSEVTVKLLKNAI 71 (183)
T ss_pred HHHHHHHHcCCeEEECChHHHHHHh----cCChHHHHHHHHH--HCCCcCCHHHHHHHHHHHH
Confidence 44789999998 68899999997 2222233455553 4566677777777776543
No 26
>PF02847 MA3: MA3 domain; InterPro: IPR003891 This entry represents the MI domain (after MA-3 and eIF4G), it is a protein-protein interaction module of ~130 amino acids [, , ]. It appears in several translation factors and is found in: One copy in plant and animal eIF4G 1 and 2 (DAP-5/NAT1/p97) Two copies in the animal programmed cell death protein 4 (PDCD4) or MA-3 that is induced during programmed cell death and inhibits neoplastic transformation Four tandem-repeated copies in a group of uncharacterised plant proteins The MI domain consists of seven alpha-helices, which pack into a globular form. The packing arrangement consists of repeating pairs of antiparallel helices packed one upon the other such that a superhelical axis is generated perpendicular to the alpha-helical axes []. The MI domain has also been named MA3 domain.; PDB: 2ION_A 2IOL_B 2NSZ_A 3EIQ_C 2HM8_A 2KZT_B 2IOS_A 2RG8_B 2ZU6_E 3EIJ_A ....
Probab=47.24 E-value=21 Score=27.74 Aligned_cols=78 Identities=21% Similarity=0.255 Sum_probs=53.0
Q ss_pred hhHHHHHhcCCCCCCchHHHHHHHhhCCChHHHHHHHHHHHhcc-CCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHh
Q 020150 151 KTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNE-KPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRR 229 (330)
Q Consensus 151 kSLdeyfp~gRda~~~~vLk~L~~KTGFs~~Ei~RKYirY~LnE-r~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~R 229 (330)
..|.+||-++...--.-.+++|..+ .-..+|++.=|..+|.+ +.+++-...=|.+|.+.--++.+++.+.+.+.-..
T Consensus 7 ~~l~ey~~~~d~~ea~~~l~el~~~--~~~~~vv~~~l~~~le~~~~~r~~~~~Ll~~L~~~~~~~~~~~~~gf~~~l~~ 84 (113)
T PF02847_consen 7 SILMEYFSSGDVDEAVECLKELKLP--SQHHEVVKVILECALEEKKSYREYYSKLLSHLCKRKLISKEQFQEGFEDLLES 84 (113)
T ss_dssp HHHHHHHHHT-HHHHHHHHHHTT-G--GGHHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH
T ss_pred HHHHHHhcCCCHHHHHHHHHHhCCC--ccHHHHHHHHHHHHhhccHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHhH
Confidence 4678888886443333355555444 66789999999999999 44544444445568888889999999988876554
Q ss_pred h
Q 020150 230 F 230 (330)
Q Consensus 230 i 230 (330)
+
T Consensus 85 l 85 (113)
T PF02847_consen 85 L 85 (113)
T ss_dssp H
T ss_pred h
Confidence 3
No 27
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=47.03 E-value=76 Score=28.55 Aligned_cols=75 Identities=9% Similarity=0.123 Sum_probs=53.9
Q ss_pred hhHHhhHHHHHhcCCCCCCchHHHHHHHhhCCChHHHHHHHHHHHhccCCCChHHHHHHHHHHhhcCC-C-cHHHHHHHH
Q 020150 147 AMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASML-D-DSQVAEILN 224 (330)
Q Consensus 147 a~LvkSLdeyfp~gRda~~~~vLk~L~~KTGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L-~-d~evaeiL~ 224 (330)
..+++-|.+.+.+.+-.++..+++.|...+|-++.+++.---.|+...+..|.+.|.+++ +- + ++.|-++++
T Consensus 187 ~~~~~~l~~~~~~~~~~~~~~al~~l~~~~~gdlr~l~~~l~~~~~~~~~It~~~v~~~~------~~~~~~~~i~~l~~ 260 (337)
T PRK12402 187 DELVDVLESIAEAEGVDYDDDGLELIAYYAGGDLRKAILTLQTAALAAGEITMEAAYEAL------GDVGTDEVIESLLD 260 (337)
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHcCCCCCHHHHHHHh------CCCCCHHHHHHHHH
Confidence 456778888888888789999999999999999999875444455555677777765533 32 2 456766666
Q ss_pred HHH
Q 020150 225 EIS 227 (330)
Q Consensus 225 E~s 227 (330)
.++
T Consensus 261 ai~ 263 (337)
T PRK12402 261 AAE 263 (337)
T ss_pred HHH
Confidence 554
No 28
>smart00352 POU Found in Pit-Oct-Unc transcription factors.
Probab=46.16 E-value=24 Score=28.56 Aligned_cols=24 Identities=17% Similarity=0.106 Sum_probs=20.9
Q ss_pred HHHHHHHHHhhcCCCcHHHHHHHH
Q 020150 201 LVVNLIQLRKASMLDDSQVAEILN 224 (330)
Q Consensus 201 ~VaDLi~Lr~as~L~d~evaeiL~ 224 (330)
+...+.+.|+.+|||-.|||+.++
T Consensus 12 ~~~~lk~~R~~lGLTQ~dvA~~lg 35 (75)
T smart00352 12 FAKTFKQRRIKLGFTQADVGLALG 35 (75)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHhc
Confidence 456688999999999999999876
No 29
>COG1713 Predicted HD superfamily hydrolase involved in NAD metabolism [Coenzyme metabolism]
Probab=45.92 E-value=9.5 Score=35.18 Aligned_cols=113 Identities=27% Similarity=0.411 Sum_probs=64.9
Q ss_pred HHHHHHhccCCCC--hHHHHHHHHHHhhcCCCc--HHHHHHHHHHHHhhhhccCCeeeecccccchhhhhHHHHHHHHHh
Q 020150 186 KYIRYALNEKPFN--PDLVVNLIQLRKASMLDD--SQVAEILNEISRRFVREKGPVVMNMSGYSEKGFKRKLAVQALFGK 261 (330)
Q Consensus 186 KYirY~LnEr~F~--~d~VaDLi~Lr~as~L~d--~evaeiL~E~s~Ri~~~~G~vmmn~~G~Te~G~kRK~a~~aLF~K 261 (330)
.++.-.|.++-|+ ..+..--+.|=.+.+++- ..+|.||-++++-.= +.=+ ++++-. |+.
T Consensus 8 ~~~~~~l~~kR~~H~l~V~~~A~~LA~~y~~d~~kA~~AgilHD~aK~~p--------------~~~~-~~~~~~--~~~ 70 (187)
T COG1713 8 AIVKELLSEKRFEHCLGVAETAIELAEAYGLDPEKAYLAGILHDIAKELP--------------EQKL-LKIAKK--YGL 70 (187)
T ss_pred HHHHHhcCHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHHHhhCC--------------HHHH-HHHHHH--hCC
Confidence 3455555666554 233333345555555553 456777777765321 1111 111111 333
Q ss_pred Hhh-hccchhhhcc-CCCccchhhcccchhhh-hhhhhhhccccCChhhHHhhhcCCC
Q 020150 262 VFY-LSELPEFCSR-DSSLIVKEIFGVTDEDA-DKLRQHTLSEAGDMDSLEKMVNDSD 316 (330)
Q Consensus 262 lly-LsEl~ef~s~-dssL~vkeiFGvTdeDa-~kLRi~~Lse~~d~~sLe~Mv~~s~ 316 (330)
..- +.+.+.+.-+ -|.-.+++-||++|||. +-+|.||... +++..|+|.|=-.|
T Consensus 71 ~~~~~~~~~~llH~~vgay~~~~~fGi~De~VL~AI~~HTtg~-~~mt~ldkIiyiAD 127 (187)
T COG1713 71 ELDLERESPLLLHGKVGAYLLKEEFGIKDEEVLSAIEYHTTGR-KQMTLLDKILYVAD 127 (187)
T ss_pred CchhhccChHHHHHHHHHHHHHHHhCCCcHHHHHHHHHhccCC-Cccchhhheeeeec
Confidence 222 2333444433 25668999999999996 5699999877 58999999875444
No 30
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=45.79 E-value=80 Score=22.44 Aligned_cols=54 Identities=26% Similarity=0.395 Sum_probs=35.9
Q ss_pred HHHHHHhhCCChHHHHHHHHH-HHhc-----c---CCCChHHHHHHHHHHh--hcCCCcHHHHHHH
Q 020150 169 LKGLVQKTGFSMEDVLRKYIR-YALN-----E---KPFNPDLVVNLIQLRK--ASMLDDSQVAEIL 223 (330)
Q Consensus 169 Lk~L~~KTGFs~~Ei~RKYir-Y~Ln-----E---r~F~~d~VaDLi~Lr~--as~L~d~evaeiL 223 (330)
++++.+.+|.+.. .+|+|.. +-+. + +.|+++.|.-|..++. ..|++=+|+++.|
T Consensus 3 ~~eva~~~gvs~~-tlr~w~~~~g~~~~~r~~~~~r~yt~~~v~~l~~i~~l~~~g~~l~~i~~~~ 67 (68)
T cd01104 3 IGAVARLTGVSPD-TLRAWERRYGLPAPQRTDGGHRLYSEADVARLRLIRRLTSEGVRISQAAALA 67 (68)
T ss_pred HHHHHHHHCcCHH-HHHHHHHhCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHCCCCHHHHHHHh
Confidence 4567788887754 5677775 4331 1 5788887765544332 3899999998876
No 31
>smart00265 BH4 BH4 Bcl-2 homology region 4.
Probab=43.64 E-value=24 Score=23.81 Aligned_cols=23 Identities=13% Similarity=0.427 Sum_probs=19.4
Q ss_pred CCChHHHHHHHHHHHhccCCCCh
Q 020150 177 GFSMEDVLRKYIRYALNEKPFNP 199 (330)
Q Consensus 177 GFs~~Ei~RKYirY~LnEr~F~~ 199 (330)
+++..|++-+||.|.|..+-+..
T Consensus 2 ~~~nRelV~~yv~yKLsQrgy~w 24 (27)
T smart00265 2 RLDNRELVVDYVTYKLSQNGYEW 24 (27)
T ss_pred CcchHHHHHHHHHHHHhhcCCCC
Confidence 67889999999999998876543
No 32
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=43.47 E-value=72 Score=23.01 Aligned_cols=53 Identities=25% Similarity=0.353 Sum_probs=35.7
Q ss_pred HHHHHhhCCChHHHHHHHHH-HHh-------ccCCCChHHHHHHHH---HHhhcCCCcHHHHHHHH
Q 020150 170 KGLVQKTGFSMEDVLRKYIR-YAL-------NEKPFNPDLVVNLIQ---LRKASMLDDSQVAEILN 224 (330)
Q Consensus 170 k~L~~KTGFs~~Ei~RKYir-Y~L-------nEr~F~~d~VaDLi~---Lr~as~L~d~evaeiL~ 224 (330)
.++.+.+|-+.. -+|.|-. +.| +-|-|+++.|.-|.. ||. .|++=+||+++||
T Consensus 4 ~evA~~~gvs~~-tlR~~~~~g~l~~~~~~~g~R~y~~~~l~~l~~i~~l~~-~g~~l~~i~~~l~ 67 (67)
T cd04764 4 KEVSEIIGVKPH-TLRYYEKEFNLYIPRTENGRRYYTDEDIELLKKIKTLLE-KGLSIKEIKEILN 67 (67)
T ss_pred HHHHHHHCcCHH-HHHHHHHhcCCCCCCCCCCceeeCHHHHHHHHHHHHHHH-CCCCHHHHHHHhC
Confidence 456667777665 4566654 233 335588888876654 455 8999999999885
No 33
>PF08542 Rep_fac_C: Replication factor C C-terminal domain; InterPro: IPR013748 Replication factor C (RFC) is a multimeric AAA+ protein complex that loads the DNA polymerase processivity clamp PCNA (Proliferating Cell Nuclear Antigen) onto DNA using ATP to drive the reaction []. PCNA functions at multiple levels in directing DNA metabolic pathways []. When bound to DNA, PCNA organises various proteins involved in DNA replication, DNA repair, DNA modification, and chromatin modelling. Replication factor C consists of five subunits in a spiral arrangement: Rfc1, Rfc2, Rfc3, Rfc4, and Rfc5 subunits. Rfc1 and Rfc2 load the PCNA sliding clamp onto DNA, while Rfc3 binds ATP and also acts as a checkpoint sensor. The RFC complex contains four ATP sites (sites A, B, C, and D) located at subunit interfaces. In each ATP site, an arginine residue from one subunit is located near the gamma-phosphate of ATP bound in the adjacent subunit. These arginine residues act as "arginine fingers" that can potentially perform two functions: sensing that ATP is bound and catalyzing ATP hydrolysis []. This entry represents the core domain found in Rfc1-5.; GO: 0003689 DNA clamp loader activity, 0005524 ATP binding, 0006260 DNA replication, 0005663 DNA replication factor C complex; PDB: 1SXJ_B 2CHG_B 2CHV_F 2CHQ_C 1IQP_A.
Probab=43.00 E-value=67 Score=24.13 Aligned_cols=56 Identities=18% Similarity=0.230 Sum_probs=34.7
Q ss_pred HHhhHHHHHhcCCCCCCchHHHHHHHhhCCChHHHHHHHHHHHhccCCCChHHHHHHH
Q 020150 149 VCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLI 206 (330)
Q Consensus 149 LvkSLdeyfp~gRda~~~~vLk~L~~KTGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi 206 (330)
.++.|=+...++.=.--...+..|... ||+..+|++.-.+++++- .+++.....++
T Consensus 7 ~i~~i~~~~~~~~~~~~~~~~~~l~~~-G~s~~~Il~~l~~~l~~~-~~~~~~k~~i~ 62 (89)
T PF08542_consen 7 VIEEILESCLNGDFKEARKKLYELLVE-GYSASDILKQLHEVLVES-DIPDSQKAEIL 62 (89)
T ss_dssp HHHHHHHHHHHTCHHHHHHHHHHHHHT-T--HHHHHHHHHHHHHTS-TSSHHHHHHHH
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHHc-CCCHHHHHHHHHHHHHHh-hccHHHHHHHH
Confidence 344444444444222223367788888 999999999999998887 66666555544
No 34
>PF07568 HisKA_2: Histidine kinase; InterPro: IPR011495 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Signal transducing histidine kinases are the key elements in two-component signal transduction systems, which control complex processes such as the initiation of development in microorganisms [, ]. Examples of histidine kinases are EnvZ, which plays a central role in osmoregulation [], and CheA, which plays a central role in the chemotaxis system []. Histidine kinases usually have an N-terminal ligand-binding domain and a C-terminal kinase domain, but other domains may also be present. The kinase domain is responsible for the autophosphorylation of the histidine with ATP, the phosphotransfer from the kinase to an aspartate of the response regulator, and (with bifunctional enzymes) the phosphotransfer from aspartyl phosphate back to ADP or to water []. The kinase core has a unique fold, distinct from that of the Ser/Thr/Tyr kinase superfamily. HKs can be roughly divided into two classes: orthodox and hybrid kinases [, ]. Most orthodox HKs, typified by the Escherichia coli EnvZ protein, function as periplasmic membrane receptors and have a signal peptide and transmembrane segment(s) that separate the protein into a periplasmic N-terminal sensing domain and a highly conserved cytoplasmic C-terminal kinase core. Members of this family, however, have an integral membrane sensor domain. Not all orthodox kinases are membrane bound, e.g., the nitrogen regulatory kinase NtrB (GlnL) is a soluble cytoplasmic HK []. Hybrid kinases contain multiple phosphodonor and phosphoacceptor sites and use multi-step phospho-relay schemes instead of promoting a single phosphoryl transfer. In addition to the sensor domain and kinase core, they contain a CheY-like receiver domain and a His-containing phosphotransfer (HPt) domain. This is the dimerisation and phosphoacceptor domain of a subfamily of histidine kinases. It shares sequence similarity with IPR003661 from INTERPRO and IPR011102 from INTERPRO. It is usually found adjacent to a C-terminal ATPase domain (IPR003594 from INTERPRO). This domain is found in a wide range of bacteria and also several archaea.
Probab=41.78 E-value=42 Score=25.72 Aligned_cols=33 Identities=24% Similarity=0.443 Sum_probs=27.3
Q ss_pred ChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhh
Q 020150 198 NPDLVVNLIQLRKASMLDDSQVAEILNEISRRFV 231 (330)
Q Consensus 198 ~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~ 231 (330)
|.-.|..||.|. +....|.++.++|.+...||.
T Consensus 9 nLq~i~sll~lq-~~~~~~~e~~~~L~~~~~RI~ 41 (76)
T PF07568_consen 9 NLQIISSLLRLQ-ARRSEDPEAREALEDAQNRIQ 41 (76)
T ss_pred HHHHHHHHHHHH-HhcCCCHHHHHHHHHHHHHHH
Confidence 445788999998 456799999999999999874
No 35
>PF02417 Chromate_transp: Chromate transporter; InterPro: IPR003370 This entry represents chromate transporters (CHR) [, ]. These proteins reduce chromate accumulation and are essential for chromate resistance. They are composed of one or two copies of this region. The short-chain CHR proteins form heterodimer transporters which efflux chromate ions from the cytoplasm, while the long chain CHR proteins appear to have arisen from a gene fusion event of two short chain transporters[].; GO: 0015109 chromate transmembrane transporter activity, 0015703 chromate transport
Probab=41.62 E-value=18 Score=31.12 Aligned_cols=63 Identities=21% Similarity=0.382 Sum_probs=37.3
Q ss_pred HHHhcchhhHHhhhhhhhhccccccccCCCC-------CCCCCchhHHHhhhHhh----hhhhhhhhhhhhhhcCCh
Q 020150 70 EVEEELPWIQEKALDLVEFTGSVTQAIPGPR-------VGQSKLPWILAVPLAYV----GVSFVIAFVKTVKKFNSP 135 (330)
Q Consensus 70 e~e~e~~wiqekaldlve~tG~vtQaIPGPR-------vg~s~lPwllAlPLAyl----G~TFviA~vRtvrK~~SP 135 (330)
|.-++..||-|+-. .+.. .+.|.+|||- +|-.--.|++|+-.... +..+++.+...++++.+.
T Consensus 30 ~~V~~~~wlt~~~f--~~~~-al~q~~PGP~~~n~a~~iG~~~~G~~Gai~a~~~~~lP~~l~~~~~~~~~~~~~~~ 103 (169)
T PF02417_consen 30 EFVERRGWLTEEEF--LEGL-ALAQALPGPIAINLATFIGYRLAGFLGAIVATIGFILPSFLLILLLSPLYSRFREN 103 (169)
T ss_pred HHhHccCCCCHHHH--HHHH-HHHHcCCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccc
Confidence 34455788876532 2222 4689999994 33344556666533222 445667777888888653
No 36
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=40.53 E-value=96 Score=29.40 Aligned_cols=85 Identities=16% Similarity=0.030 Sum_probs=51.9
Q ss_pred chHHHHHHHhhCCChHHHHHHHHHHHhccCCCChHHHHHHHH----HHhhcCCCcHHHHHHHHHHHHhhhh-ccCC--ee
Q 020150 166 PPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQ----LRKASMLDDSQVAEILNEISRRFVR-EKGP--VV 238 (330)
Q Consensus 166 ~~vLk~L~~KTGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~----Lr~as~L~d~evaeiL~E~s~Ri~~-~~G~--vm 238 (330)
..-|+-..+++|.+.+|.+++.-|.+.++-.=--|+..+.+. .=..++++ +++++.|.++++|=++ .+=. -.
T Consensus 101 ~~il~~~a~~~~~~~e~~~~~~~~~l~~~yg~~y~af~~~~~~~~~~l~~~~~~-~~~~~~l~~~~~~~~~~~~vki~~~ 179 (262)
T PRK03987 101 DKWLELAAEKLGKSLEEAWEEVGYKLEDEFGDLYDAFEEAAIEGEEALDDLGVP-EEWADALVEIARENIEVPKVKISGY 179 (262)
T ss_pred hhHHHHHHHHcCCCHHHHHHHHHHHHHHHhCcHHHHHHHHHhcChhhhccCCCC-HHHHHHHHHHHHHhCCCCcEEEEEE
Confidence 367889999999999999999999887772211112222111 11223455 5667777666666332 2211 24
Q ss_pred eecccccchhhhh
Q 020150 239 MNMSGYSEKGFKR 251 (330)
Q Consensus 239 mn~~G~Te~G~kR 251 (330)
+++.-++-.|+++
T Consensus 180 ie~~~~~~dGi~~ 192 (262)
T PRK03987 180 VDLTSPEPDGVEI 192 (262)
T ss_pred EEEEeCCCChHHH
Confidence 5666678889885
No 37
>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=40.30 E-value=92 Score=24.31 Aligned_cols=76 Identities=20% Similarity=0.219 Sum_probs=54.6
Q ss_pred hhHHHHHhcCCCCCCchHHHHHHHhhCCChHHHHHHHHHHHhccC-CCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHH
Q 020150 151 KTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEK-PFNPDLVVNLIQLRKASMLDDSQVAEILNEISR 228 (330)
Q Consensus 151 kSLdeyfp~gRda~~~~vLk~L~~KTGFs~~Ei~RKYirY~LnEr-~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~ 228 (330)
..|++||..+.-.--...|++|..+ .-.-|+++.-|-.+|.++ .+++-...=|-+|.+.--++.+++.+.+.++-.
T Consensus 7 ~~l~ey~~~~D~~ea~~~l~~L~~~--~~~~~vv~~~i~~~le~~~~~~~~~~~Ll~~L~~~~~~~~~~~~~~f~~~~~ 83 (113)
T smart00544 7 LIIEEYLSSGDTDEAVHCLLELKLP--EQHHEVVKVLLTCALEEKRTYREMYSVLLSRLCQANVISTKQFEKGFWRLLE 83 (113)
T ss_pred HHHHHHHHcCCHHHHHHHHHHhCCC--cchHHHHHHHHHHHHcCCccHHHHHHHHHHHHHHcCCcCHHHHHHHHHHHHh
Confidence 3688899776443333355555444 357899999999999996 576666666667888888999999888876443
No 38
>PRK06585 holA DNA polymerase III subunit delta; Reviewed
Probab=39.86 E-value=1.1e+02 Score=28.45 Aligned_cols=64 Identities=20% Similarity=0.179 Sum_probs=54.4
Q ss_pred chhhHHhhHHHHHhcCCCCCCchHHHHHHHhhCCChHHH---HHHHHHHHhccCCCChHHHHHHHHH
Q 020150 145 KNAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDV---LRKYIRYALNEKPFNPDLVVNLIQL 208 (330)
Q Consensus 145 KNa~LvkSLdeyfp~gRda~~~~vLk~L~~KTGFs~~Ei---~RKYirY~LnEr~F~~d~VaDLi~L 208 (330)
+...+..-|.+.+.+.+-.++..+++.|...+|-++..+ +.|-.-|+-..++-|.+.|.+++.-
T Consensus 143 ~~~~l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~It~edV~~lv~~ 209 (343)
T PRK06585 143 DERDLARLIDDELAEAGLRITPDARALLVALLGGDRLASRNEIEKLALYAHGKGEITLDDVRAVVGD 209 (343)
T ss_pred CHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHHHhcCCCCCCCHHHHHHHhCC
Confidence 356678889999999999999999999999999988665 6788888776678999999888653
No 39
>PTZ00111 DNA replication licensing factor MCM4; Provisional
Probab=39.79 E-value=2.1e+02 Score=32.23 Aligned_cols=30 Identities=27% Similarity=0.487 Sum_probs=20.6
Q ss_pred hHHHHHHHHHHHhc-cCC-CChHHHHHHH-----HHHh
Q 020150 180 MEDVLRKYIRYALN-EKP-FNPDLVVNLI-----QLRK 210 (330)
Q Consensus 180 ~~Ei~RKYirY~Ln-Er~-F~~d~VaDLi-----~Lr~ 210 (330)
..+++||||.|+=+ =.| +++++ .++| .||+
T Consensus 698 ~~~lLrkYI~YAR~~~~P~Ls~eA-~~~i~~~Yv~mR~ 734 (915)
T PTZ00111 698 DLDMLRMYIKFSKLHCFPKLSDEA-KKVITREYVKMRQ 734 (915)
T ss_pred CHHHHHHHHHHHhccCCCCCCHHH-HHHHHHHHHHHhh
Confidence 46899999999953 123 56665 5555 5886
No 40
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=39.67 E-value=31 Score=33.44 Aligned_cols=48 Identities=25% Similarity=0.279 Sum_probs=37.9
Q ss_pred CCCCCCchHHHHHHHhhCCChHHHHHHHHHHHhccCCCChHHHHHHHHHHhhcCCCcHHHHHHHHH
Q 020150 160 GGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNE 225 (330)
Q Consensus 160 gRda~~~~vLk~L~~KTGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~E 225 (330)
-|.+++---|++|++.+- .-||| .|+|=+.|=..+||||.||+---.-
T Consensus 175 sRTaFT~~Ql~~LEkrF~------~QKYL------------S~~DR~~LA~~LgLTdaQVKtWfQN 222 (309)
T KOG0488|consen 175 SRTAFSDHQLFELEKRFE------KQKYL------------SVADRIELAASLGLTDAQVKTWFQN 222 (309)
T ss_pred chhhhhHHHHHHHHHHHH------Hhhcc------------cHHHHHHHHHHcCCchhhHHHHHhh
Confidence 355677677888888763 46887 5889999999999999999977654
No 41
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=39.50 E-value=51 Score=22.90 Aligned_cols=40 Identities=18% Similarity=0.229 Sum_probs=31.8
Q ss_pred hcchhhHHhhHHHHHhcCCCCCCchHHHHHHHhhCCChHHH
Q 020150 143 VNKNAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDV 183 (330)
Q Consensus 143 VnKNa~LvkSLdeyfp~gRda~~~~vLk~L~~KTGFs~~Ei 183 (330)
..-+..-++-|.++|.. ..-.+......|..++|-+...|
T Consensus 5 ~~~t~~q~~~L~~~f~~-~~~p~~~~~~~la~~l~l~~~~V 44 (57)
T PF00046_consen 5 TRFTKEQLKVLEEYFQE-NPYPSKEEREELAKELGLTERQV 44 (57)
T ss_dssp SSSSHHHHHHHHHHHHH-SSSCHHHHHHHHHHHHTSSHHHH
T ss_pred CCCCHHHHHHHHHHHHH-hcccccccccccccccccccccc
Confidence 34566778888999997 44577778899999999998888
No 42
>TIGR01128 holA DNA polymerase III, delta subunit. subunit around DNA forming a DNA sliding clamp.
Probab=39.30 E-value=1.1e+02 Score=27.27 Aligned_cols=65 Identities=17% Similarity=0.151 Sum_probs=54.3
Q ss_pred hhhHHhhHHHHHhcCCCCCCchHHHHHHHhhCCChHHH---HHHHHHHHhccCCCChHHHHHHHHHHhh
Q 020150 146 NAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDV---LRKYIRYALNEKPFNPDLVVNLIQLRKA 211 (330)
Q Consensus 146 Na~LvkSLdeyfp~gRda~~~~vLk~L~~KTGFs~~Ei---~RKYirY~LnEr~F~~d~VaDLi~Lr~a 211 (330)
...+.+-|.++|.+.+-.++..+++.|...+|.++..+ +.|-.-|+-++ +.|.+.|.+++.-...
T Consensus 113 ~~~~~~~i~~~~~~~g~~i~~~a~~~l~~~~~~d~~~l~~el~KL~~~~~~~-~It~e~I~~~~~~~~~ 180 (302)
T TIGR01128 113 EQELPRWIQARLKKLGLRIDPDAVQLLAELVEGNLLAIAQELEKLALYAPDG-KITLEDVEEAVSDSAR 180 (302)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCcHHHHHHHHHHHHHhhCCCC-CCCHHHHHHHHhhhhc
Confidence 34566778999999999999999999999999998866 78888887666 7999999998875543
No 43
>smart00845 GatB_Yqey GatB domain. This domain is found in GatB and proteins related to bacterial Yqey. It is about 140 amino acid residues long. This domain is found at the C terminus of GatB which transamidates Glu-tRNA to Gln-tRNA. The function of this domain is uncertain. It does however suggest that Yqey and its relatives have a role in tRNA metabolism.
Probab=38.79 E-value=68 Score=27.15 Aligned_cols=45 Identities=24% Similarity=0.476 Sum_probs=29.1
Q ss_pred CCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHH------HhhhhccCCeee
Q 020150 195 KPFNPDLVVNLIQLRKASMLDDSQVAEILNEIS------RRFVREKGPVVM 239 (330)
Q Consensus 195 r~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s------~Ri~~~~G~vmm 239 (330)
-+++|+.+++|+.|=..=.+|...+.++|.... ..|+++||+..+
T Consensus 37 ~~i~~~~l~~li~lv~~g~It~~~ak~vl~~~~~~~~~~~~ii~~~~l~~i 87 (147)
T smart00845 37 SPITPEHLAELLKLIEDGTISGKIAKEVLEELLESGKSPEEIVEEKGLKQI 87 (147)
T ss_pred CCCCHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHcCCCHHHHHHHcCCccC
Confidence 356677777777777777777777777776553 356666665544
No 44
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=38.25 E-value=93 Score=22.31 Aligned_cols=53 Identities=19% Similarity=0.197 Sum_probs=34.9
Q ss_pred HHHHHHHhhCCChHHHHH------HHHHHHhccCCCChHHHHHHHHHHhhcCCCcHHHHH
Q 020150 168 ALKGLVQKTGFSMEDVLR------KYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAE 221 (330)
Q Consensus 168 vLk~L~~KTGFs~~Ei~R------KYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evae 221 (330)
.|+.+..+.|+|..++=+ .||+..-+-+...| ....+.+|=.++|++++++++
T Consensus 5 ~lr~~R~~~gls~~~lA~~~g~s~s~v~~iE~G~~~~p-~~~~l~~l~~~l~~~~~~~~~ 63 (64)
T PF13560_consen 5 RLRRLRERAGLSQAQLADRLGVSQSTVSRIERGRRPRP-SPDTLQRLARALGVPPDERAE 63 (64)
T ss_dssp HHHHHHHCHTS-HHHHHHHHTS-HHHHHHHHTTSSSS--BHHHHHHHHHHTT--HHHHHC
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHCCCCCCC-CHHHHHHHHHHHCcCHHHHcc
Confidence 467777777777777654 58888888887644 234566677889999888764
No 45
>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=38.10 E-value=83 Score=23.35 Aligned_cols=52 Identities=13% Similarity=0.155 Sum_probs=19.4
Q ss_pred HHHHHHhhCCChHHHHHHHHHHHhccCCCChHHHHHHHHHHhhcCCCcHHHHHH
Q 020150 169 LKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEI 222 (330)
Q Consensus 169 Lk~L~~KTGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaei 222 (330)
|+.|.+...++.+|+ +.-++..++. ..+|..++-++..=+.-|.|.+|++..
T Consensus 6 l~~l~~g~~Ls~~e~-~~~~~~i~~g-~~s~~qiaAfL~al~~kget~~Eiag~ 57 (66)
T PF02885_consen 6 LKKLRDGEDLSREEA-KAAFDAILDG-EVSDAQIAAFLMALRMKGETPEEIAGF 57 (66)
T ss_dssp HHHHHTT----HHHH-HHHHHHHHTT-SS-HHHHHHHHHHHHHH---HHHHHHH
T ss_pred HHHHHcCCCCCHHHH-HHHHHHHHcC-CCCHHHHHHHHHHHHHhCcCHHHHHHH
Confidence 333444444444443 2223333332 445555555554444555666665543
No 46
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=38.09 E-value=1.3e+02 Score=23.23 Aligned_cols=54 Identities=22% Similarity=0.332 Sum_probs=37.3
Q ss_pred HHHHHHhhCCChHHHHHHHHHHHh--------ccCCCChHHHHHHH---HHHhhcCCCcHHHHHHHH
Q 020150 169 LKGLVQKTGFSMEDVLRKYIRYAL--------NEKPFNPDLVVNLI---QLRKASMLDDSQVAEILN 224 (330)
Q Consensus 169 Lk~L~~KTGFs~~Ei~RKYirY~L--------nEr~F~~d~VaDLi---~Lr~as~L~d~evaeiL~ 224 (330)
++++..++|-+.. -+|.|.+.-+ +.+-|+++.|..+- .||. .|++-.+|+.+|.
T Consensus 3 ~~eva~~~gi~~~-tlr~~~~~Gll~~~~~~~g~r~y~~~dv~~l~~i~~l~~-~g~~~~~i~~~l~ 67 (100)
T cd00592 3 IGEVAKLLGVSVR-TLRYYEEKGLLPPERSENGYRLYSEEDLERLRLIRRLRE-LGLSLKEIRELLD 67 (100)
T ss_pred HHHHHHHHCcCHH-HHHHHHHCCCcCCCcCCCCCcccCHHHHHHHHHHHHHHH-cCCCHHHHHHHHh
Confidence 3567777887764 4566766544 44568887777654 4555 8999999998885
No 47
>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=37.11 E-value=69 Score=30.02 Aligned_cols=37 Identities=19% Similarity=0.348 Sum_probs=20.2
Q ss_pred HHHHHHhhcCCCcHHHHHHHHHHHHhhhhccCCeeeecccccchhhhh
Q 020150 204 NLIQLRKASMLDDSQVAEILNEISRRFVREKGPVVMNMSGYSEKGFKR 251 (330)
Q Consensus 204 DLi~Lr~as~L~d~evaeiL~E~s~Ri~~~~G~vmmn~~G~Te~G~kR 251 (330)
.+|.--..-.||++|+.++..+|+ ||..|+|..-+++
T Consensus 210 ~~i~~eGv~~Ls~~EL~~Ac~~RG-----------l~~~~~s~~~lr~ 246 (268)
T PF07766_consen 210 RLIKREGVDSLSEEELQDACYERG-----------LRSTGLSEEELRE 246 (268)
T ss_dssp HHHHHH-GGGS-HHHHHHHHHHTT--------------TT--HHHHHH
T ss_pred HHHHHhccccCCHHHHHHHHHHhC-----------CCcCCCCHHHHHH
Confidence 344434456789999999988887 5566776654443
No 48
>PF15176 LRR19-TM: Leucine-rich repeat family 19 TM domain
Probab=36.61 E-value=34 Score=29.33 Aligned_cols=48 Identities=25% Similarity=0.382 Sum_probs=36.6
Q ss_pred ccCCCCCCCCCchhHHHhhhHhhhhhhhhhhh---hhhhh-cCChhhhhhhh
Q 020150 95 AIPGPRVGQSKLPWILAVPLAYVGVSFVIAFV---KTVKK-FNSPKFKRKKL 142 (330)
Q Consensus 95 aIPGPRvg~s~lPwllAlPLAylG~TFviA~v---RtvrK-~~SPraKRkR~ 142 (330)
..|+|.-|+-+.|.|..+-++-+.++++|++. .+|+| +.|=|++|-..
T Consensus 6 ~~~~~~~~g~sW~~LVGVv~~al~~SlLIalaaKC~~~~k~~~SY~H~rL~e 57 (102)
T PF15176_consen 6 NAPGPGEGGRSWPFLVGVVVTALVTSLLIALAAKCPVWYKYLASYRHHRLPE 57 (102)
T ss_pred cCCCCCCCCcccHhHHHHHHHHHHHHHHHHHHHHhHHHHHHHhccccccCCc
Confidence 46899999999999999999999999999864 23333 45666665443
No 49
>PHA00739 V3 structural protein VP3
Probab=36.37 E-value=24 Score=29.76 Aligned_cols=35 Identities=34% Similarity=0.580 Sum_probs=27.6
Q ss_pred hccccccc--cCCC-CCCCCCchhHHHhhhHhhhhhhh
Q 020150 88 FTGSVTQA--IPGP-RVGQSKLPWILAVPLAYVGVSFV 122 (330)
Q Consensus 88 ~tG~vtQa--IPGP-Rvg~s~lPwllAlPLAylG~TFv 122 (330)
.+|++||. +|-| -||+|..|.+--+|++|+=+-.+
T Consensus 42 vsgt~ttssfv~np~Yvgssnat~~sLVPlFYllVlIi 79 (92)
T PHA00739 42 VSGTVTTSSFVSNPQYVGSSNATLVSLVPLFYLLVLII 79 (92)
T ss_pred EeeeEEeeccccCcceecCCCCchHhHHHHHHHHHHHH
Confidence 45777765 4888 69999999999999999864443
No 50
>PF00286 Flexi_CP: Viral coat protein; InterPro: IPR000052 Potexviruses and Carlaviruses are plant-infecting viruses whose genome consist of a single-stranded RNA molecule encapsided in a coat protein. The genome of many Potexviruses is known and their coat protein sequence has been shown to be rather well conserved []. The same observation applies to the coat protein of a variety of Carlaviruses whose sequences are related to those of Potexviruses [, ]. The coat proteins of Potexviruses and of Carlaviruses contain from 190 to 300 amino acid residues. The best conserved region of these coat proteins is located in the central part.; GO: 0005198 structural molecule activity, 0019028 viral capsid; PDB: 4DOX_B.
Probab=36.29 E-value=94 Score=27.50 Aligned_cols=72 Identities=17% Similarity=0.249 Sum_probs=47.4
Q ss_pred ChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhccCCeeeeccccc--chhhhhHHHHHHHHHhHhhhccchhhh
Q 020150 198 NPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKGPVVMNMSGYS--EKGFKRKLAVQALFGKVFYLSELPEFC 272 (330)
Q Consensus 198 ~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~~~~G~vmmn~~G~T--e~G~kRK~a~~aLF~KllyLsEl~ef~ 272 (330)
|++.++-+.++=.++|...+.+++++-++++--+..=----+++.|-+ ..|+-|...+.++-.+ -.-|+.||
T Consensus 6 t~e~i~~I~~~~~~lgvp~~~~~~~~~~la~~C~d~gSS~~~~~~G~~~~~~g~~~~~la~aiik~---~~tLRqfC 79 (140)
T PF00286_consen 6 TPEEIAAISAALQGLGVPTESVAKVAWDLARYCADNGSSRYTDPKGTSPFPGGVIRADLAAAIIKE---HCTLRQFC 79 (140)
T ss_dssp -HHHHHHHHHHHHHTT--GGGHHHHHHHHHHHHHHH---TT----SB--SSTT-BHHHHH-HHHHH---TTSHHHHH
T ss_pred CHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHhcCCCCCcccccCCcccCCCCccHHHHHHHHHHc---cCCHHHHH
Confidence 456666677766779999999999999999988887667889999999 5899999888776554 34578888
No 51
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=36.05 E-value=70 Score=28.16 Aligned_cols=79 Identities=10% Similarity=0.111 Sum_probs=49.8
Q ss_pred cCChhhhhhhhhcchhhHHhhHHHHHhcCCCCCCchHHHHHHHhhCCChHHHHHHHHHHHhcc-CCCChHHHHHHHHHHh
Q 020150 132 FNSPKFKRKKLVNKNAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNE-KPFNPDLVVNLIQLRK 210 (330)
Q Consensus 132 ~~SPraKRkR~VnKNa~LvkSLdeyfp~gRda~~~~vLk~L~~KTGFs~~Ei~RKYirY~LnE-r~F~~d~VaDLi~Lr~ 210 (330)
.+.++.+|++.......|++.+.+.+..-|.+..-. .++|.++.|.+ +.||+-.-|. ...+.+ -+.+|=+
T Consensus 49 ~~~~~~~~~~~~d~~~~l~~~~g~~Ir~~Re~~glS-qeeLA~~lgvs-----~s~IsriE~G~~~Ps~~---~l~kLa~ 119 (154)
T TIGR00270 49 ARKPVKRKRRKIDTTEELVEDYGIIIRREREKRGWS-QEQLAKKIQEK-----ESLIKKIENAEIEPEPK---VVEKLEK 119 (154)
T ss_pred CCCCCCCCCCccchHHHHHHHHHHHHHHHHHHcCCC-HHHHHHHhCCC-----HHHHHHHHCCCCCCCHH---HHHHHHH
Confidence 344455555556666778888888777777654443 66777777776 4566655553 344444 4566667
Q ss_pred hcCCCcHHH
Q 020150 211 ASMLDDSQV 219 (330)
Q Consensus 211 as~L~d~ev 219 (330)
++|.+=.+.
T Consensus 120 ~Lgvsl~el 128 (154)
T TIGR00270 120 LLKIKLREQ 128 (154)
T ss_pred HhCCCHHHH
Confidence 888876663
No 52
>PRK07452 DNA polymerase III subunit delta; Validated
Probab=36.04 E-value=1.3e+02 Score=27.64 Aligned_cols=59 Identities=24% Similarity=0.320 Sum_probs=51.6
Q ss_pred HHhhHHHHHhcCCCCCCchHHHHHHHhhCCChHHH---HHHHHHHHh-ccCCCChHHHHHHHH
Q 020150 149 VCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDV---LRKYIRYAL-NEKPFNPDLVVNLIQ 207 (330)
Q Consensus 149 LvkSLdeyfp~gRda~~~~vLk~L~~KTGFs~~Ei---~RKYirY~L-nEr~F~~d~VaDLi~ 207 (330)
+.+-|.+.+.+.+-.++..+++.|...+|.++..+ +.|-+-|+. ..++-|++.|..++.
T Consensus 135 l~~~i~~~~~~~g~~i~~~a~~~L~~~~g~dl~~l~~EleKL~ly~~~~~~~It~~~V~~~v~ 197 (326)
T PRK07452 135 LKQLVERTAQELGVKLTPEAAELLAEAVGNDSRRLYNELEKLALYAENSTKPISAEEVKALVS 197 (326)
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHHHHhCccHHHHHHHHHHHHHhccCCCCccCHHHHHHHhc
Confidence 77889999999999999999999999999999888 678777764 466799999999875
No 53
>PF02797 Chal_sti_synt_C: Chalcone and stilbene synthases, C-terminal domain; InterPro: IPR012328 Synonym(s): Chalcone synthase, Flavonone synthase, 6'-deoxychalcone synthase Naringenin-chalcone synthases (2.3.1.74 from EC) and stilbene synthases (STS) (formerly known as resveratrol synthases) are related plant enzymes. CHS is an important enzyme in flavanoid biosynthesis and STS is a key enzyme in stilbene-type phyloalexin biosynthesis. Both enzymes catalyze the addition of three molecules of malonyl-CoA to a starter CoA ester (a typical example is 4-coumaroyl-CoA), producing either a chalcone (with CHS) or stilbene (with STS) []. These enzymes have a conserved cysteine residue, located in the central section of the protein sequence, which is essential for the catalytic activity of both enzymes and probably represents the binding site for the 4-coumaryl-CoA group []. This domain of chalcone synthase is reported to be structurally similar to domains in thiolase and beta-ketoacyl synthase. The differences in activity are accounted for by differences in the N-terminal domain. ; GO: 0016746 transferase activity, transferring acyl groups; PDB: 3OV2_A 3OV3_B 1Z1F_A 1Z1E_A 3ALE_C 3OIT_A 2H84_A 1TEE_D 1TED_A 2P0U_A ....
Probab=35.93 E-value=24 Score=30.62 Aligned_cols=34 Identities=29% Similarity=0.261 Sum_probs=24.0
Q ss_pred ChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhccCC
Q 020150 198 NPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKGP 236 (330)
Q Consensus 198 ~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~~~~G~ 236 (330)
-|+=-+=|-++.++++|++++++ -|+.++++|||
T Consensus 66 HPGG~~ILd~v~~~L~L~~~~l~-----~Sr~vLr~yGN 99 (151)
T PF02797_consen 66 HPGGRKILDAVEEALGLSPEQLR-----ASREVLREYGN 99 (151)
T ss_dssp E-SSHHHHHHHHHHHTS-GGGGH-----HHHHHHHHH-B
T ss_pred cCChHHHHHHHHHHcCCCHHHHH-----HHHHHHHhcCC
Confidence 34444556678899999999864 68999999996
No 54
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=35.53 E-value=27 Score=23.88 Aligned_cols=28 Identities=36% Similarity=0.419 Sum_probs=20.3
Q ss_pred HHHHhhcCCCcHHHHHHHHHHHHhhhhcc
Q 020150 206 IQLRKASMLDDSQVAEILNEISRRFVREK 234 (330)
Q Consensus 206 i~Lr~as~L~d~evaeiL~E~s~Ri~~~~ 234 (330)
-++|+..|+|-.|+|+.++ +++..+.+|
T Consensus 2 k~~r~~~gls~~~la~~~g-is~~~i~~~ 29 (55)
T PF01381_consen 2 KELRKEKGLSQKELAEKLG-ISRSTISRI 29 (55)
T ss_dssp HHHHHHTTS-HHHHHHHHT-S-HHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHhC-CCcchhHHH
Confidence 3678899999999999887 666666554
No 55
>PF06281 DUF1035: Protein of unknown function (DUF1035); InterPro: IPR009379 Sulfolobus virus-like particle SSV1 and its fusellovirus homologues can be found in many acidic (pH less than 4.0) hot springs (greater than 70 degrees C) around the world. SSV1 contains a 15.5-kb double-stranded DNA genome that encodes 34 proteins with greater than 50 amino acids []. A site-specific integrase and a DnaA-like protein have been previously identified by sequence homology, and three structural proteins have been isolated from purified virus and identified by N-terminal sequencing (VP1, VP2, and VP3).; GO: 0005198 structural molecule activity, 0016021 integral to membrane
Probab=35.13 E-value=29 Score=28.24 Aligned_cols=42 Identities=33% Similarity=0.515 Sum_probs=30.0
Q ss_pred ccccccc--cCCC-CCCCCCchhHHHhhhHhhhhhhhhhhhhhhh
Q 020150 89 TGSVTQA--IPGP-RVGQSKLPWILAVPLAYVGVSFVIAFVKTVK 130 (330)
Q Consensus 89 tG~vtQa--IPGP-Rvg~s~lPwllAlPLAylG~TFviA~vRtvr 130 (330)
.|.+||. ++-| -+|+|..|.+--+|++|+=+..+.-.|-.||
T Consensus 24 sgt~t~ssfv~nP~yvGSsnA~iv~LVplFylLvlIiVPAvi~Yk 68 (73)
T PF06281_consen 24 SGTVTTSSFVSNPQYVGSSNATIVSLVPLFYLLVLIIVPAVIAYK 68 (73)
T ss_pred ecceeeccccCCcceecCCCccHHHHHHHHHHHHHHHhhhheeee
Confidence 5778664 4888 6888899999999999996554443333333
No 56
>PF02631 RecX: RecX family; InterPro: IPR003783 RecX is a putative bacterial regulatory protein []. The gene encoding RecX is found downstream of recA, and it is suggested that the RecX protein might be regulator of RecA activity by interaction with the RecA protein or filament [].; GO: 0006282 regulation of DNA repair; PDB: 3DFG_A 3D5L_B 3C1D_B 3E3V_A.
Probab=34.90 E-value=47 Score=26.77 Aligned_cols=65 Identities=28% Similarity=0.380 Sum_probs=0.0
Q ss_pred hccCCCChHHHHHHHHHHhhcC-CCcHHHHHHHHHHHHhhhhccCCeeeecccccchhhhhHHHHHHH
Q 020150 192 LNEKPFNPDLVVNLIQLRKASM-LDDSQVAEILNEISRRFVREKGPVVMNMSGYSEKGFKRKLAVQAL 258 (330)
Q Consensus 192 LnEr~F~~d~VaDLi~Lr~as~-L~d~evaeiL~E~s~Ri~~~~G~vmmn~~G~Te~G~kRK~a~~aL 258 (330)
|.++-|+++.++.+|+-=+..| |+|...|+..-+.-.+ .+.|||..+ ..-+.++|+.....-++|
T Consensus 1 L~~kg~~~e~I~~vi~~l~~~gyidD~~ya~~~v~~~~~-~~~~G~~~I-~~~L~~kGi~~~~i~~~l 66 (121)
T PF02631_consen 1 LKRKGFSEEAIEEVIDRLKELGYIDDERYAESYVRSRLR-RKGKGPRRI-RQKLKQKGIDREIIEEAL 66 (121)
T ss_dssp HHHTT--HHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHH-HTT--HHHH-HHHHHHTT--HHHHHHHH
T ss_pred CcccCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHhcc-cccccHHHH-HHHHHHHCCChHHHHHHH
No 57
>PF04510 DUF577: Family of unknown function (DUF577); InterPro: IPR007598 This is a family of Arabidopsis thaliana (Mouse-ear cress) proteins. Many of these members contain a repeated region.
Probab=34.71 E-value=81 Score=29.08 Aligned_cols=84 Identities=20% Similarity=0.319 Sum_probs=51.4
Q ss_pred cccccCCCCCCCCCchhHHHhhhHhh-hhhhhhhhhhhhhhcCChhhhhhhhhcchhhHHhhHHHHHhcCCC-CCCchHH
Q 020150 92 VTQAIPGPRVGQSKLPWILAVPLAYV-GVSFVIAFVKTVKKFNSPKFKRKKLVNKNAMVCKTIDELFQKGGD-AVNPPAL 169 (330)
Q Consensus 92 vtQaIPGPRvg~s~lPwllAlPLAyl-G~TFviA~vRtvrK~~SPraKRkR~VnKNa~LvkSLdeyfp~gRd-a~~~~vL 169 (330)
+.+.+=.|+- ...==|+||+--||- ||- +.-+ .++...-+.++++ +++|+.++..+|.+ ++-..+|
T Consensus 89 ~~~~L~~p~~-~d~~~W~LAl~~a~~~~Iq----l~e~----~~~~~~vk~L~~~---mv~Sv~elV~~g~E~~~l~rgl 156 (174)
T PF04510_consen 89 ISKVLLPPEE-VDVEDWVLALTGAVCMAIQ----LLES----SMRVDLVKELLPK---MVKSVKELVERGMEVGFLRRGL 156 (174)
T ss_pred HHHHcCCchh-ccHHHHHHHHHHHHHHHHH----Hhcc----ccHHHHHHHHHHH---HHHHHHHHHHcccHHHHHHHHH
Confidence 3444555543 222349998865554 322 2211 2223444556665 89999999999999 7766677
Q ss_pred HHHHHhhCCChHHHHHHHHHHHhcc
Q 020150 170 KGLVQKTGFSMEDVLRKYIRYALNE 194 (330)
Q Consensus 170 k~L~~KTGFs~~Ei~RKYirY~LnE 194 (330)
+.++.. |-|.+-||.-||
T Consensus 157 ~~~e~~-------v~~~~~~y~~~~ 174 (174)
T PF04510_consen 157 RDFESF-------VSRQMNWYKTSE 174 (174)
T ss_pred HHHHHH-------HHHHHHHhhccC
Confidence 777653 456677876554
No 58
>PRK05574 holA DNA polymerase III subunit delta; Reviewed
Probab=34.66 E-value=1.4e+02 Score=27.16 Aligned_cols=64 Identities=14% Similarity=0.112 Sum_probs=52.3
Q ss_pred hhhHHhhHHHHHhcCCCCCCchHHHHHHHhhCCChHHHHH---HHHHHHhccCCCChHHHHHHHHHHh
Q 020150 146 NAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLR---KYIRYALNEKPFNPDLVVNLIQLRK 210 (330)
Q Consensus 146 Na~LvkSLdeyfp~gRda~~~~vLk~L~~KTGFs~~Ei~R---KYirY~LnEr~F~~d~VaDLi~Lr~ 210 (330)
...+..-|.++|.+.+-.++..+++.|...+|-++..+-. |..-|+-+.+ .|.+.|..++.-..
T Consensus 148 ~~~~~~~i~~~~~~~g~~i~~~a~~~L~~~~~~d~~~l~~El~KL~l~~~~~~-It~~~I~~~i~~~~ 214 (340)
T PRK05574 148 EAELPQWIQQRLKQQGLQIDAAALQLLAERVEGNLLALAQELEKLALLYPDGK-ITLEDVEEAVPDSA 214 (340)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhCchHHHHHHHHHHHHhhcCCCC-CCHHHHHHHHhhhh
Confidence 4457788999999999999999999999999999887654 7777765544 99999998876533
No 59
>PRK09111 DNA polymerase III subunits gamma and tau; Validated
Probab=34.43 E-value=2.2e+02 Score=29.98 Aligned_cols=60 Identities=17% Similarity=0.198 Sum_probs=49.4
Q ss_pred hhhHHhhHHHHHhcCCCCCCchHHHHHHHhhCCChHHH---HHHHHHHHhccCCCChHHHHHHHH
Q 020150 146 NAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDV---LRKYIRYALNEKPFNPDLVVNLIQ 207 (330)
Q Consensus 146 Na~LvkSLdeyfp~gRda~~~~vLk~L~~KTGFs~~Ei---~RKYirY~LnEr~F~~d~VaDLi~ 207 (330)
...+.+.|.+.+.+.+-.++..++..|.+.+|-++-++ +.|.+-|. .+..+.+.|.+++.
T Consensus 193 ~~el~~~L~~i~~kegi~i~~eAl~lIa~~a~Gdlr~al~~Ldkli~~g--~g~It~e~V~~llg 255 (598)
T PRK09111 193 ADVLAAHLSRIAAKEGVEVEDEALALIARAAEGSVRDGLSLLDQAIAHG--AGEVTAEAVRDMLG 255 (598)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHhhc--CCCcCHHHHHHHhC
Confidence 45788888899998998899999999999999998766 45778774 45788888887764
No 60
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=34.24 E-value=95 Score=26.04 Aligned_cols=62 Identities=27% Similarity=0.390 Sum_probs=41.7
Q ss_pred HHHHHHHhhCCChHHHHHHHHHHHhccCCCChHHHHHHHHHHhhcC-CCcHHHHHHHHHHHHhhhhccCCe
Q 020150 168 ALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASM-LDDSQVAEILNEISRRFVREKGPV 237 (330)
Q Consensus 168 vLk~L~~KTGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~-L~d~evaeiL~E~s~Ri~~~~G~v 237 (330)
+|+-|..+ .+|..|| +-.|.++-|+++.+++.|+-=+..| |+|...|+..-..-.+ +.+|+-
T Consensus 17 al~~L~~r-~~s~~el-----~~kL~~kg~~~~~i~~vl~~l~~~~~ldD~~~a~~~~~~~~~--~~~g~~ 79 (157)
T PRK00117 17 ALRLLARR-EHSRAEL-----RRKLAAKGFSEEVIEAVLDRLKEEGLLDDERFAESFVRSRAR--KGYGPR 79 (157)
T ss_pred HHHHHccc-hhHHHHH-----HHHHHhcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHh--CCchHH
Confidence 44444443 5666665 4457788999999999988666666 7888888876554322 556653
No 61
>KOG2286 consensus Exocyst complex subunit SEC6 [Intracellular trafficking, secretion, and vesicular transport]
Probab=33.47 E-value=69 Score=34.66 Aligned_cols=94 Identities=14% Similarity=0.222 Sum_probs=55.3
Q ss_pred hhhhhhhh-----hhhhhhcCChhhhhhhhhcchhhHHhhHHHHHhcCCCCCCchHHHHHHHhhCCChHHHHHHHHHHHh
Q 020150 118 GVSFVIAF-----VKTVKKFNSPKFKRKKLVNKNAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYAL 192 (330)
Q Consensus 118 G~TFviA~-----vRtvrK~~SPraKRkR~VnKNa~LvkSLdeyfp~gRda~~~~vLk~L~~KTGFs~~Ei~RKYirY~L 192 (330)
|+++++.. =..+.|+.+++===- +-=.-+|.++|+||+-=..-+... +..+.... +.+++-+|||-++
T Consensus 481 ~~~~l~e~~~~d~~~~~~~lf~~~W~~g---~~~~~Iv~T~~dy~~D~~~~~~~~-f~~fi~e~---~~~~v~~Yl~~l~ 553 (667)
T KOG2286|consen 481 GVSGLLEEIFLDLQPLLNKLFTKEWCAG---SVTENIVATLDDYLPDFKELMGEY-FVRFIEEA---SLELVIEYLRALS 553 (667)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhhhhch---hhHHHHHHHHHHHHHHHHHHhhhH-HHHHHHHH---HHHHHHHHHHHHH
Confidence 66666554 234444444332111 112348999999998544433333 33333322 4688999999999
Q ss_pred ccCCCChHHHHHHHHHHhhcCCCcHHHHHHHH---HHHHhhhhccCC
Q 020150 193 NEKPFNPDLVVNLIQLRKASMLDDSQVAEILN---EISRRFVREKGP 236 (330)
Q Consensus 193 nEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~---E~s~Ri~~~~G~ 236 (330)
++|.|+. +.++.++ |+..++|++||.
T Consensus 554 ~kr~~~~------------------~~~~~i~~d~~~~~~~f~~~~~ 582 (667)
T KOG2286|consen 554 KKRASIQ------------------ELIEKIKSDAETLYHFFRKYGS 582 (667)
T ss_pred hhhhhHH------------------HHHHHHHhhHHHHHHHHHHhCc
Confidence 9999822 2222222 456788999998
No 62
>PRK14530 adenylate kinase; Provisional
Probab=32.84 E-value=1.5e+02 Score=25.75 Aligned_cols=64 Identities=19% Similarity=0.229 Sum_probs=40.3
Q ss_pred CCCCCchHHHHHHHhhCC---ChHHHHHHHHHHHhccCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHH
Q 020150 161 GDAVNPPALKGLVQKTGF---SMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEI 226 (330)
Q Consensus 161 Rda~~~~vLk~L~~KTGF---s~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~ 226 (330)
-.+..+-.-+.|.++.|| ++.+++|+++..-.++..-.-+...+. ++.+....|+.+.++|.+.
T Consensus 12 pGsGKsT~~~~La~~~~~~~i~~g~~lr~~~~~~~~~~~~~~~~~~~~--~~~g~~~~d~~~~~~l~~~ 78 (215)
T PRK14530 12 PGAGKGTQSSNLAEEFGVEHVTTGDALRANKQMDISDMDTEYDTPGEY--MDAGELVPDAVVNEIVEEA 78 (215)
T ss_pred CCCCHHHHHHHHHHHhCCeEEeccHHHHHhccCCcccccchHHHHHHH--HHcCCCCCHHHHHHHHHHH
Confidence 334455577899999999 999999998754443332222333442 3455556776666666554
No 63
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=32.84 E-value=66 Score=28.77 Aligned_cols=43 Identities=16% Similarity=0.145 Sum_probs=30.6
Q ss_pred CChHHHHHHHHHHHhccCCCChHHHHHHHHHHhhcCCCcHHHHHHH
Q 020150 178 FSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEIL 223 (330)
Q Consensus 178 Fs~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL 223 (330)
+....++++||+..... +...+.=|-+|..-.-+||+|+|+.|
T Consensus 4 ~~~~~~v~~~l~~~~~~---~~~~~~Vl~~L~~~g~~tdeeLA~~L 46 (178)
T PRK06266 4 MLNNPLVQKVLFEIMEG---DEEGFEVLKALIKKGEVTDEEIAEQT 46 (178)
T ss_pred hhcCHHHHHHHHHHhcC---CccHhHHHHHHHHcCCcCHHHHHHHH
Confidence 44567899999998874 33334334456665679999999987
No 64
>PF02180 BH4: Bcl-2 homology region 4; InterPro: IPR003093 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: 1AF3_A 2PON_B 1YSN_A 3PL7_B 3R85_A 2O2N_A 2P1L_C 1R2G_A 2O1Y_A 1BXL_A ....
Probab=32.74 E-value=22 Score=24.13 Aligned_cols=23 Identities=17% Similarity=0.556 Sum_probs=18.8
Q ss_pred CChHHHHHHHHHHHhccCCCChH
Q 020150 178 FSMEDVLRKYIRYALNEKPFNPD 200 (330)
Q Consensus 178 Fs~~Ei~RKYirY~LnEr~F~~d 200 (330)
++..|++-+||.|.|..|-+..+
T Consensus 3 ~~nR~lV~~yi~yKLsQrgy~w~ 25 (27)
T PF02180_consen 3 YDNRELVEDYISYKLSQRGYVWE 25 (27)
T ss_dssp HHHHHHHHHHHHHHHHHTTSTST
T ss_pred ccHHHHHHHHHHHHhhhcCCCCC
Confidence 56779999999999998876543
No 65
>COG0283 Cmk Cytidylate kinase [Nucleotide transport and metabolism]
Probab=32.41 E-value=71 Score=30.40 Aligned_cols=29 Identities=21% Similarity=0.279 Sum_probs=24.0
Q ss_pred cHHHHHHHHHHHHhhhhccCCeeeecccc
Q 020150 216 DSQVAEILNEISRRFVREKGPVVMNMSGY 244 (330)
Q Consensus 216 d~evaeiL~E~s~Ri~~~~G~vmmn~~G~ 244 (330)
-.+|-++|+++=|++.+..|.+|||-.-+
T Consensus 102 ~p~VR~~l~~~Qr~~a~~~~~~V~dGRDi 130 (222)
T COG0283 102 IPEVREALVKLQRAFAKNGPGIVADGRDI 130 (222)
T ss_pred cHHHHHHHHHHHHHHHhcCCCEEEecCCC
Confidence 35788999999999999988899986554
No 66
>KOG2510 consensus SWI-SNF chromatin-remodeling complex protein [Chromatin structure and dynamics]
Probab=32.08 E-value=30 Score=36.51 Aligned_cols=73 Identities=25% Similarity=0.270 Sum_probs=45.1
Q ss_pred CCCCCchhHHHhhhHhhhhhhhhhhhhhhhhcCChhhhhhhhhcchhhHHhhHHHHHhcCCCCCCchHHHHHHHhhCCCh
Q 020150 101 VGQSKLPWILAVPLAYVGVSFVIAFVKTVKKFNSPKFKRKKLVNKNAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSM 180 (330)
Q Consensus 101 vg~s~lPwllAlPLAylG~TFviA~vRtvrK~~SPraKRkR~VnKNa~LvkSLdeyfp~gRda~~~~vLk~L~~KTGFs~ 180 (330)
-+-+.+|.+.|-||-+++ .++.++++. -+ -+||||+ .++|-+.+ ......|
T Consensus 310 Sp~t~~p~~gakPldl~r-lYvsvke~g--g~--------~~v~knk------rd~a~~lg-ssaa~~l----------- 360 (532)
T KOG2510|consen 310 SPMTNLPAVGAKPLDLYR-LYVSVKEIG--GL--------TQVNKNK------RDLATNLG-SSAASSL----------- 360 (532)
T ss_pred CcccccccccccchhHHH-HHHHHHHhc--cc--------eeeccch------hhhhhccc-hHHHHHH-----------
Confidence 456778899999999988 444444443 22 3577777 56666655 1222222
Q ss_pred HHHHHHHHHHHhc-cCCCChHHHHHH
Q 020150 181 EDVLRKYIRYALN-EKPFNPDLVVNL 205 (330)
Q Consensus 181 ~Ei~RKYirY~Ln-Er~F~~d~VaDL 205 (330)
..-||||+++ |-.|+-+.-.|+
T Consensus 361 ---~k~y~~~lf~fec~f~Rg~e~p~ 383 (532)
T KOG2510|consen 361 ---KKQYIQYLFAFECKFERGEEPPP 383 (532)
T ss_pred ---HHHHHHHHHhhceeeeccCCCCH
Confidence 2359999996 556665554454
No 67
>PRK04195 replication factor C large subunit; Provisional
Probab=31.83 E-value=2.4e+02 Score=28.15 Aligned_cols=54 Identities=15% Similarity=0.050 Sum_probs=40.4
Q ss_pred HHHHHHHhhCCChHHHHHHHHHHHhccCCCChHHHHHHHHHHhhcCCCcHHHHHHHH
Q 020150 168 ALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILN 224 (330)
Q Consensus 168 vLk~L~~KTGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~ 224 (330)
.+..|.++++-|...+-.-|+.|+.-=-.=| ...-++|-..++|+++||.-++.
T Consensus 351 ~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~l~~~~~~~~~~ 404 (482)
T PRK04195 351 IAKKIAEKLHTSKRKVRREVLPFLSIIFKHN---PELAARLAAFLELTEEEIEFLTG 404 (482)
T ss_pred HHHHHHHHhCCCHHHHHHHHHHHHHHHHhcC---HHHHHHHHHHcCCCHHHHHHHhC
Confidence 4568999999999999998888764211112 45566777899999999987764
No 68
>PRK10072 putative transcriptional regulator; Provisional
Probab=31.35 E-value=35 Score=28.01 Aligned_cols=33 Identities=30% Similarity=0.348 Sum_probs=24.9
Q ss_pred HHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhcc
Q 020150 201 LVVNLIQLRKASMLDDSQVAEILNEISRRFVREK 234 (330)
Q Consensus 201 ~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~~~~ 234 (330)
...|+-+||+..|+|-.|+|+.|. ++.+-|.+|
T Consensus 34 ~~~eik~LR~~~glTQ~elA~~lG-vS~~TVs~W 66 (96)
T PRK10072 34 SFTEFEQLRKGTGLKIDDFARVLG-VSVAMVKEW 66 (96)
T ss_pred ChHHHHHHHHHcCCCHHHHHHHhC-CCHHHHHHH
Confidence 356778888888888888888887 666666655
No 69
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=31.20 E-value=86 Score=25.58 Aligned_cols=54 Identities=17% Similarity=0.223 Sum_probs=41.0
Q ss_pred ChHHHHHHHHHHHhccCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhccCCee
Q 020150 179 SMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKGPVV 238 (330)
Q Consensus 179 s~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~~~~G~vm 238 (330)
....+||--+|.+-.=+|-+.+.+| .|+|.+-++|+.+|....---|++-|.||
T Consensus 21 ~~~~L~r~LLr~LA~G~PVt~~~LA------~a~g~~~e~v~~~L~~~p~tEyD~~GrIV 74 (77)
T PF12324_consen 21 GFAWLLRPLLRLLAKGQPVTVEQLA------AALGWPVEEVRAALAAMPDTEYDDQGRIV 74 (77)
T ss_dssp THHHHHHHHHHHHTTTS-B-HHHHH------HHHT--HHHHHHHHHH-TTSEEETTSEEE
T ss_pred ccHHHHHHHHHHHHcCCCcCHHHHH------HHHCCCHHHHHHHHHhCCCceEcCCCCee
Confidence 4677899999999888888877655 58999999999999998877788888876
No 70
>cd00056 ENDO3c endonuclease III; includes endonuclease III (DNA-(apurinic or apyrimidinic site) lyase), alkylbase DNA glycosidases (Alka-family) and other DNA glycosidases
Probab=31.12 E-value=1.2e+02 Score=25.07 Aligned_cols=104 Identities=23% Similarity=0.239 Sum_probs=59.8
Q ss_pred CCCCCCchHHHHHHHhhCCChHHHHHHHHHHHhccCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhccCCeee
Q 020150 160 GGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKGPVVM 239 (330)
Q Consensus 160 gRda~~~~vLk~L~~KTGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~~~~G~vmm 239 (330)
-..+.-..+++.|..+.|.|.++|.+ -++ ++|-.+-..+| ...-|+.|.++++.+.++|+....
T Consensus 13 ~s~~~a~~~~~~l~~~~gpt~~~l~~-----------~~~---~~l~~~~~~~G--~~~kA~~i~~~a~~~~~~~~~~~~ 76 (158)
T cd00056 13 TTDKAVNKAYERLFERYGPTPEALAA-----------ADE---EELRELIRSLG--YRRKAKYLKELARAIVEGFGGLVL 76 (158)
T ss_pred ccHHHHHHHHHHHHHHhCCCHHHHHC-----------CCH---HHHHHHHHhcC--hHHHHHHHHHHHHHHHHHcCCccC
Confidence 33333445666777777644444332 122 44556666667 567899999999999999998763
Q ss_pred eccc-----ccchhhhhHHHHH-HHHHhHhhhccchhhhccCCCc--cchhhcc
Q 020150 240 NMSG-----YSEKGFKRKLAVQ-ALFGKVFYLSELPEFCSRDSSL--IVKEIFG 285 (330)
Q Consensus 240 n~~G-----~Te~G~kRK~a~~-aLF~KllyLsEl~ef~s~dssL--~vkeiFG 285 (330)
+.+- .+.+|+-+|.|-- .+| -+. .+.|.- |..+ .++.+++
T Consensus 77 ~~~~~~~~L~~l~GIG~~tA~~~l~~----~~~-~~~~pv-D~~v~r~~~~~~~ 124 (158)
T cd00056 77 DDPDAREELLALPGVGRKTANVVLLF----ALG-PDAFPV-DTHVRRVLKRLGL 124 (158)
T ss_pred CCcccHHHHHcCCCCCHHHHHHHHHH----HCC-CCCCcc-chhHHHHHHHhCC
Confidence 2221 2456776764432 222 222 555655 6443 4455554
No 71
>PHA01976 helix-turn-helix protein
Probab=30.58 E-value=33 Score=24.43 Aligned_cols=28 Identities=14% Similarity=0.291 Sum_probs=20.4
Q ss_pred HHHHHHhhcCCCcHHHHHHHHHHHHhhhh
Q 020150 204 NLIQLRKASMLDDSQVAEILNEISRRFVR 232 (330)
Q Consensus 204 DLi~Lr~as~L~d~evaeiL~E~s~Ri~~ 232 (330)
-|.++|+..|||-.|+|+.+. +++.-+.
T Consensus 6 rl~~~R~~~glt~~~lA~~~g-vs~~~v~ 33 (67)
T PHA01976 6 QLIKARNARAWSAPELSRRAG-VRHSLIY 33 (67)
T ss_pred HHHHHHHHcCCCHHHHHHHhC-CCHHHHH
Confidence 467889999999999998875 4433333
No 72
>cd04411 Ribosomal_P1_P2_L12p Ribosomal protein P1, P2, and L12p. Ribosomal proteins P1 and P2 are the eukaryotic proteins that are functionally equivalent to bacterial L7/L12. L12p is the archaeal homolog. Unlike other ribosomal proteins, the archaeal L12p and eukaryotic P1 and P2 do not share sequence similarity with their bacterial counterparts. They are part of the ribosomal stalk (called the L7/L12 stalk in bacteria), along with 28S rRNA and the proteins L11 and P0 in eukaryotes (23S rRNA, L11, and L10e in archaea). In bacterial ribosomes, L7/L12 homodimers bind the extended C-terminal helix of L10 to anchor the L7/L12 molecules to the ribosome. Eukaryotic P1/P2 heterodimers and archaeal L12p homodimers are believed to bind the L10 equivalent proteins, eukaryotic P0 and archaeal L10e, in a similar fashion. P1 and P2 (L12p, L7/L12) are the only proteins in the ribosome to occur as multimers, always appearing as sets of dimers. Recent data indicate that most archaeal species contain
Probab=30.56 E-value=21 Score=29.79 Aligned_cols=10 Identities=30% Similarity=0.547 Sum_probs=5.5
Q ss_pred hHHHHhcchh
Q 020150 68 EVEVEEELPW 77 (330)
Q Consensus 68 e~e~e~e~~w 77 (330)
|||+|++|.|
T Consensus 93 ~eE~dddmgf 102 (105)
T cd04411 93 EEEEDEDFGF 102 (105)
T ss_pred ccccccccCc
Confidence 3444556765
No 73
>COG4174 ABC-type uncharacterized transport system, permease component [General function prediction only]
Probab=30.21 E-value=68 Score=32.35 Aligned_cols=52 Identities=23% Similarity=0.469 Sum_probs=44.3
Q ss_pred cCCCCCCchHHHHHHHhhCCCh------HHHHHHHHHHHhccCCCChHHHHHHHHHHh
Q 020150 159 KGGDAVNPPALKGLVQKTGFSM------EDVLRKYIRYALNEKPFNPDLVVNLIQLRK 210 (330)
Q Consensus 159 ~gRda~~~~vLk~L~~KTGFs~------~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~ 210 (330)
.|...++...+++|++..||+- -..+-+|+|+-.-|--|-..-|-|||.=|-
T Consensus 75 rg~~GlDpe~i~~i~~~~GFDKp~~eR~~~Ml~~y~rfDfGeS~fr~~~VidLI~ekl 132 (364)
T COG4174 75 RGAQGLDPELIAEIEKQYGFDKPPLERYFLMLWDYARFDFGESFFRDASVIDLIKEKL 132 (364)
T ss_pred ccccCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHHhccccHHhhcCChHHHHHHHhC
Confidence 3556688889999999999995 356789999999999999999999997553
No 74
>PRK14137 recX recombination regulator RecX; Provisional
Probab=29.86 E-value=68 Score=29.19 Aligned_cols=71 Identities=20% Similarity=0.322 Sum_probs=49.0
Q ss_pred CCChHHHHHHHHHHHhccCCCChHHHHHHHH-HHhhcCCCcHHHHHHHHHHHHhhhhccCCeeeecccccchhhhhHHHH
Q 020150 177 GFSMEDVLRKYIRYALNEKPFNPDLVVNLIQ-LRKASMLDDSQVAEILNEISRRFVREKGPVVMNMSGYSEKGFKRKLAV 255 (330)
Q Consensus 177 GFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~-Lr~as~L~d~evaeiL~E~s~Ri~~~~G~vmmn~~G~Te~G~kRK~a~ 255 (330)
-+|..||-+ .|.++.|+++.|+.+|+ |+.-==|+|...|+..+ .-+.|||..+ ..-+.++|+...+.-
T Consensus 54 ~rS~~ELr~-----KL~~kg~~~e~Ie~vI~rL~e~gyLDD~rfAe~~~-----~~k~~Gp~rI-~~eL~qKGI~~~lI~ 122 (195)
T PRK14137 54 AMTAAELRA-----KLERRSEDEALVTEVLERVQELGYQDDAQVARAEN-----SRRGVGALRV-RQTLRRRGVEETLIE 122 (195)
T ss_pred hhhHHHHHH-----HHHhcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHH-----HhcCchHHHH-HHHHHHcCCCHHHHH
Confidence 455555444 57788999999999886 45545579999998742 1266888555 345668888877766
Q ss_pred HHH
Q 020150 256 QAL 258 (330)
Q Consensus 256 ~aL 258 (330)
++|
T Consensus 123 ~al 125 (195)
T PRK14137 123 ETL 125 (195)
T ss_pred HHH
Confidence 655
No 75
>PF10746 Phage_holin_6: Phage holin family 6; InterPro: IPR019682 This entry represents a protein conserved in Caudovirales (known as tailed bacteriophages). Holins are a diverse family of proteins that cause bacterial membrane lysis during late-protein synthesis.
Probab=29.78 E-value=33 Score=27.48 Aligned_cols=46 Identities=26% Similarity=0.453 Sum_probs=35.3
Q ss_pred hhccccccccC---CC------CC--CCCCchhHHHhhhHhhhhhhhhhhhhhhhhc
Q 020150 87 EFTGSVTQAIP---GP------RV--GQSKLPWILAVPLAYVGVSFVIAFVKTVKKF 132 (330)
Q Consensus 87 e~tG~vtQaIP---GP------Rv--g~s~lPwllAlPLAylG~TFviA~vRtvrK~ 132 (330)
.|+-.|.||.| ++ |. |-|---|....-++|.-+-...-+|++++|+
T Consensus 4 df~n~vvkaaPi~~~a~A~~~a~~f~GLslneWfyiati~YtvlQig~~v~k~v~~~ 60 (66)
T PF10746_consen 4 DFNNEVVKAAPIVGTAGADVVARYFWGLSLNEWFYIATIAYTVLQIGYLVWKKVRDW 60 (66)
T ss_pred ccccchheecCCccchhHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46777889998 33 33 6666679999999998777777788887765
No 76
>TIGR01360 aden_kin_iso1 adenylate kinase, isozyme 1 subfamily. Members of this family are adenylate kinase, EC 2.7.4.3. This clade is found only in eukaryotes and includes human adenylate kinase isozyme 1 (myokinase). Within the adenylate kinase superfamily, this set appears specifically closely related to a subfamily of eukaryotic UMP-CMP kinases (TIGR01359), rather than to the large clade of bacterial, archaeal, and eukaryotic adenylate kinase family members in TIGR01351.
Probab=29.62 E-value=3.1e+02 Score=22.38 Aligned_cols=73 Identities=12% Similarity=0.222 Sum_probs=45.1
Q ss_pred CCCCchHHHHHHHhhCCC---hHHHHHHHHHHHhccCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhccCCee
Q 020150 162 DAVNPPALKGLVQKTGFS---MEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKGPVV 238 (330)
Q Consensus 162 da~~~~vLk~L~~KTGFs---~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~~~~G~vm 238 (330)
.+..+-..+.|..+.||. +.+|+|+++. .+.+. -..+.++++ ....+.+..+.+.|.+.......+.+.++
T Consensus 13 GsGKsTl~~~l~~~~g~~~~~~g~~~~~~~~---~~~~~-~~~~~~~~~--~~~~~~~~~~~~~l~~~~~~~~~~~~~~i 86 (188)
T TIGR01360 13 GSGKGTQCEKIVEKYGFTHLSTGDLLRAEVA---SGSER-GKQLQAIME--SGDLVPLDTVLDLLKDAMVAALGTSKGFL 86 (188)
T ss_pred CCCHHHHHHHHHHHhCCcEEeHHHHHHHHHh---cCCHH-HHHHHHHHH--CCCCCCHHHHHHHHHHHHHcccCcCCeEE
Confidence 345555778888888865 7788998753 12221 123444432 33455667777777776666556666788
Q ss_pred ee
Q 020150 239 MN 240 (330)
Q Consensus 239 mn 240 (330)
+|
T Consensus 87 ~d 88 (188)
T TIGR01360 87 ID 88 (188)
T ss_pred Ee
Confidence 87
No 77
>PF12446 DUF3682: Protein of unknown function (DUF3682); InterPro: IPR022152 This domain family is found in eukaryotes, and is typically between 125 and 136 amino acids in length.
Probab=28.97 E-value=29 Score=30.89 Aligned_cols=16 Identities=38% Similarity=0.370 Sum_probs=8.4
Q ss_pred hchhhhhhHHHHhcch
Q 020150 61 KKKAEEVEVEVEEELP 76 (330)
Q Consensus 61 ~~~~~~~e~e~e~e~~ 76 (330)
-+++||+|||+|.|+.
T Consensus 93 h~rqEeeEEeEe~Ekq 108 (133)
T PF12446_consen 93 HTRQEEEEEEEENEKQ 108 (133)
T ss_pred ccchhhhhhhhhhhhh
Confidence 3445555555565553
No 78
>COG2704 DcuB Anaerobic C4-dicarboxylate transporter [General function prediction only]
Probab=28.84 E-value=41 Score=34.75 Aligned_cols=38 Identities=34% Similarity=0.556 Sum_probs=30.4
Q ss_pred hHHHHhcchhhHHhhhhhhhhccccccccCCCCCCCCCchhHHHhhhHhhhhhhhh
Q 020150 68 EVEVEEELPWIQEKALDLVEFTGSVTQAIPGPRVGQSKLPWILAVPLAYVGVSFVI 123 (330)
Q Consensus 68 e~e~e~e~~wiqekaldlve~tG~vtQaIPGPRvg~s~lPwllAlPLAylG~TFvi 123 (330)
+-=+...++||++-+.+||+ .-||++|+.+++++ -++.
T Consensus 311 dTf~~~h~~~iK~~~~~lv~-----------------~~PW~~AvalF~vS-~lv~ 348 (436)
T COG2704 311 DTFVSAHIDEIKAVAGELVQ-----------------TYPWLLAVALFFVS-ALVN 348 (436)
T ss_pred HHHHHhhHHHHHHHHHHHHH-----------------cCcHHHHHHHHHHH-HHHh
Confidence 34466789999999999986 35999999999997 4443
No 79
>PF09840 DUF2067: Uncharacterized protein conserved in archaea (DUF2067); InterPro: IPR019202 This family of archaeal proteins, have no known function.
Probab=28.77 E-value=1.1e+02 Score=28.08 Aligned_cols=67 Identities=24% Similarity=0.336 Sum_probs=42.3
Q ss_pred hCCChHHHHHHHHHHHhccCCCChHHHHHHHHHHhh----------cCCCcHHHHHHHHHHHHhhhhccCCeeeecccc-
Q 020150 176 TGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKA----------SMLDDSQVAEILNEISRRFVREKGPVVMNMSGY- 244 (330)
Q Consensus 176 TGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~a----------s~L~d~evaeiL~E~s~Ri~~~~G~vmmn~~G~- 244 (330)
..|+..+|||+ -++||+||.+.|.+.++.. +.++=+++-+++ +|+.+-|- .++++
T Consensus 71 ~~y~l~~i~r~------a~~~vp~d~L~~~L~~~G~~ae~~~~~i~T~a~~eev~~l~----~~Lse~~~----e~~~~~ 136 (190)
T PF09840_consen 71 YRYSLDDIFRE------AGYPVPPDLLVDALKLLGYKAEYREDVIKTDAPLEEVVELA----ERLSEIYK----ELRFQP 136 (190)
T ss_pred eEEcHHHHHHH------cCCCCCHHHHHHHHHhCCCeeEEeCCeEEecCCHHHHHHHH----HHHHHHHH----HHhcCc
Confidence 45788888885 4599999999999998643 233444444444 44444333 45666
Q ss_pred -cchhhhhHHHHHH
Q 020150 245 -SEKGFKRKLAVQA 257 (330)
Q Consensus 245 -Te~G~kRK~a~~a 257 (330)
|.+ .||=+++-+
T Consensus 137 ~~~~-aK~vi~~~s 149 (190)
T PF09840_consen 137 LGTK-AKRVIAAVS 149 (190)
T ss_pred cCHH-HHHHHHHHH
Confidence 666 666555443
No 80
>KOG1869 consensus Splicing coactivator SRm160/300, subunit SRm300 [RNA processing and modification]
Probab=28.74 E-value=1e+02 Score=32.02 Aligned_cols=53 Identities=23% Similarity=0.093 Sum_probs=38.0
Q ss_pred HHHHHHHhhCCChHHHHHHHHHHHhccCCCCh---------------------HHHHHHHHHHhhcCCCcHHHH
Q 020150 168 ALKGLVQKTGFSMEDVLRKYIRYALNEKPFNP---------------------DLVVNLIQLRKASMLDDSQVA 220 (330)
Q Consensus 168 vLk~L~~KTGFs~~Ei~RKYirY~LnEr~F~~---------------------d~VaDLi~Lr~as~L~d~eva 220 (330)
.|+.+...-|++-.||.+|---|-+|+-.=++ -.+..+.|+|.|+||.|.+|.
T Consensus 72 e~ee~lleqg~seeei~~k~~e~rknl~~~a~~~nE~~~~qe~S~teThqlara~eeq~e~~raAlgL~e~qv~ 145 (425)
T KOG1869|consen 72 ELEESLLEQGLSEEEILSKVQEDRKNLLLRAKLTNEEQEDQEMSSTETHQLARATEEQHEHERAALGLKELQVQ 145 (425)
T ss_pred HHHHHHHHhhhhHHHHHHHHHHHHHhHHhhccCCccccccchhhhhhhHHHHHHHHHHHHHHHHHhCcchhhcc
Confidence 34566677799999999987776655432222 245678899999999998874
No 81
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=28.62 E-value=2e+02 Score=23.15 Aligned_cols=31 Identities=16% Similarity=0.216 Sum_probs=19.7
Q ss_pred CCCChHHHHHHHHHHh---hcCCCcHHHHHHHHH
Q 020150 195 KPFNPDLVVNLIQLRK---ASMLDDSQVAEILNE 225 (330)
Q Consensus 195 r~F~~d~VaDLi~Lr~---as~L~d~evaeiL~E 225 (330)
|-|+++.|.-|..++. ..|++=++|+++|++
T Consensus 37 R~Yt~~di~~l~~I~~llr~~G~~l~~i~~~l~~ 70 (99)
T cd04765 37 RYYRPKDVELLLLIKHLLYEKGYTIEGAKQALKE 70 (99)
T ss_pred eeeCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 3467777766665553 467777777776664
No 82
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=28.08 E-value=3.6e+02 Score=22.59 Aligned_cols=120 Identities=17% Similarity=0.221 Sum_probs=68.9
Q ss_pred hhcCChhhhhhhhhcc--hhhHHhhHHHHHhcCCCCCCch-HHHH-HHH--hhCCChHHHHHHHHHHHhccCCCChHHHH
Q 020150 130 KKFNSPKFKRKKLVNK--NAMVCKTIDELFQKGGDAVNPP-ALKG-LVQ--KTGFSMEDVLRKYIRYALNEKPFNPDLVV 203 (330)
Q Consensus 130 rK~~SPraKRkR~VnK--Na~LvkSLdeyfp~gRda~~~~-vLk~-L~~--KTGFs~~Ei~RKYirY~LnEr~F~~d~Va 203 (330)
++..|-+-=|.++..| +..+++.+=+.|...+= ++-. --+. +.. ..|++ +..|++.|..+-|+.+.+.
T Consensus 23 ~r~~s~~el~~kL~~kg~~~~~i~~vl~~l~~~~~-ldD~~~a~~~~~~~~~~~~g-----~~~I~~~L~~kGi~~~~I~ 96 (157)
T PRK00117 23 RREHSRAELRRKLAAKGFSEEVIEAVLDRLKEEGL-LDDERFAESFVRSRARKGYG-----PRRIRQELRQKGVDREIIE 96 (157)
T ss_pred cchhHHHHHHHHHHhcCCCHHHHHHHHHHHHHcCC-CCHHHHHHHHHHHHHhCCch-----HHHHHHHHHHcCCCHHHHH
Confidence 4445555555566555 55666666555554433 2222 1111 111 13333 7789999999999999999
Q ss_pred HHHHHHhhcCCCcHHHHHHHHHHHHhhhhccCCeeeecccccchhhhhHHHHHHHHHhHhhhccchh
Q 020150 204 NLIQLRKASMLDDSQVAEILNEISRRFVREKGPVVMNMSGYSEKGFKRKLAVQALFGKVFYLSELPE 270 (330)
Q Consensus 204 DLi~Lr~as~L~d~evaeiL~E~s~Ri~~~~G~vmmn~~G~Te~G~kRK~a~~aLF~KllyLsEl~e 270 (330)
+.+.-- . .|++ +++.+.+++.|+++- +... ..+.-..+.|++|=|-.+....
T Consensus 97 ~~l~~~---~-~d~~--e~a~~~~~k~~~~~~-------~~~~--~~k~Ki~~~L~rkGF~~~~I~~ 148 (157)
T PRK00117 97 EALAEL---D-IDWE--ELARELARKKFRRPL-------PDDA--KEKAKLVRFLARRGFSMDVIQR 148 (157)
T ss_pred HHHHHc---C-ccHH--HHHHHHHHHHcCCCC-------CCCH--HHHHHHHHHHHHCCCCHHHHHH
Confidence 988742 2 3333 677777777766542 2222 2334457788888555544433
No 83
>PF08069 Ribosomal_S13_N: Ribosomal S13/S15 N-terminal domain; InterPro: IPR012606 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This domain is found at the N terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3U5C_N 3O30_G 3IZB_O 3O2Z_G 3U5G_N 2XZN_O 2XZM_O 3IZ6_O.
Probab=27.74 E-value=60 Score=25.31 Aligned_cols=29 Identities=31% Similarity=0.401 Sum_probs=22.1
Q ss_pred CChHHHHHHHHHHhhcCCCcHHHHHHHHH
Q 020150 197 FNPDLVVNLIQLRKASMLDDSQVAEILNE 225 (330)
Q Consensus 197 F~~d~VaDLi~Lr~as~L~d~evaeiL~E 225 (330)
.+++.|.|+|-==.--|++.+||.-|||+
T Consensus 28 ~~~~eVe~~I~klakkG~tpSqIG~iLRD 56 (60)
T PF08069_consen 28 YSPEEVEELIVKLAKKGLTPSQIGVILRD 56 (60)
T ss_dssp S-HHHHHHHHHHHCCTTHCHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHcCCCHHHhhhhhhh
Confidence 57788888764333389999999999997
No 84
>PF11169 DUF2956: Protein of unknown function (DUF2956); InterPro: IPR021339 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=27.57 E-value=46 Score=28.60 Aligned_cols=22 Identities=32% Similarity=0.578 Sum_probs=16.2
Q ss_pred cCCCCCCCCCchhHHHhhhHhhh
Q 020150 96 IPGPRVGQSKLPWILAVPLAYVG 118 (330)
Q Consensus 96 IPGPRvg~s~lPwllAlPLAylG 118 (330)
...+...++.|||+| |-|-++|
T Consensus 75 ~~~~~~~~~~LPW~L-L~lSW~g 96 (103)
T PF11169_consen 75 EISSQSRSSWLPWGL-LVLSWIG 96 (103)
T ss_pred cccccccccchhHHH-HHHHHHH
Confidence 345677889999986 5566777
No 85
>PF00428 Ribosomal_60s: 60s Acidic ribosomal protein; InterPro: IPR001813 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 [, ]. The 60S acidic ribosomal protein plays an important role in the elongation step of protein synthesis. This family includes archaebacterial L12, eukaryotic P0, P1 and P2 []. Some of the proteins in this family are allergens. Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Alt a 6, Alt a 12, Cla h 3, Cla h 4 and Cla h 12.; GO: 0003735 structural constituent of ribosome, 0006414 translational elongation, 0005622 intracellular, 0005840 ribosome; PDB: 3A1Y_C 3N2D_B 2LBF_A 3IZS_t 3IZR_t 1S4J_A 2JDL_C 2W1O_B 1S4H_A 2ZKR_g.
Probab=27.25 E-value=5.1 Score=31.60 Aligned_cols=7 Identities=14% Similarity=0.525 Sum_probs=2.7
Q ss_pred HHHhcch
Q 020150 70 EVEEELP 76 (330)
Q Consensus 70 e~e~e~~ 76 (330)
|+|++|.
T Consensus 78 Eed~dmG 84 (88)
T PF00428_consen 78 EEDDDMG 84 (88)
T ss_dssp S-SSSSS
T ss_pred ccccccC
Confidence 4444443
No 86
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=27.01 E-value=1.3e+02 Score=29.16 Aligned_cols=57 Identities=18% Similarity=0.312 Sum_probs=45.8
Q ss_pred HHHHhhCCChHHH--HHHHHHHHhccC---CCChHHHHHHHHHHhhcCCCcHHHHHHHHHHH
Q 020150 171 GLVQKTGFSMEDV--LRKYIRYALNEK---PFNPDLVVNLIQLRKASMLDDSQVAEILNEIS 227 (330)
Q Consensus 171 ~L~~KTGFs~~Ei--~RKYirY~LnEr---~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s 227 (330)
.=++.|||...|| |||-|...+-++ ...-++..|++-+++.-+|..+++.+.|..--
T Consensus 86 ~SkmaT~f~~nEielfrkalE~im~sed~~~asst~~~~~vlq~k~k~L~ks~iE~lLqkf~ 147 (235)
T KOG4718|consen 86 DSKMATGFTANEIELFRKALEKIMSSEDCHIASSTAYNDIVLQAKSKPLKKSRIEELLQKFI 147 (235)
T ss_pred hHHhcCCCCHHHHHHHHHHHHHHHhhhHhhhHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHH
Confidence 3478999999975 999998888771 12346778999999999999999999997543
No 87
>PF11836 DUF3356: Protein of unknown function (DUF3356); InterPro: IPR021791 This entry consists of bacterial and phage proteins whose function is not currently known. Many of the bacterial sequences are found within known or suspected prophages or gene transfer agents (GTA). Gene transfer agents are related to bacteriophages, but are distinguished by cellular regulatory mechanisms that strongly suggest they are more than just defective prophages [, ].
Probab=26.85 E-value=1.6e+02 Score=24.23 Aligned_cols=40 Identities=18% Similarity=0.216 Sum_probs=33.4
Q ss_pred CCchHHHHHHHhhCC-ChHHHHHHHHHHHhccCCCChHHHHHHHHH
Q 020150 164 VNPPALKGLVQKTGF-SMEDVLRKYIRYALNEKPFNPDLVVNLIQL 208 (330)
Q Consensus 164 ~~~~vLk~L~~KTGF-s~~Ei~RKYirY~LnEr~F~~d~VaDLi~L 208 (330)
++.++|.+|+.+||= +..+++.+ +....|.-..|..+|.+
T Consensus 18 LtlgaLaeLE~~~g~~~l~aL~~R-----f~~g~~s~~Dv~~vi~~ 58 (101)
T PF11836_consen 18 LTLGALAELEAALGAGGLFALVER-----FETGRFSARDVRAVIRA 58 (101)
T ss_pred CCHHHHHHHHHHcCCCCHHHHHHH-----HhcCCCCHHHHHHHHHH
Confidence 567899999999999 89999887 56778888888888753
No 88
>KOG1577 consensus Aldo/keto reductase family proteins [General function prediction only]
Probab=26.84 E-value=1.7e+02 Score=28.81 Aligned_cols=64 Identities=22% Similarity=0.358 Sum_probs=52.5
Q ss_pred CCCCchHHHHHHHhhCCChHHHHHHHHHHHhcc------CCCChHHHHHHHHHHhhcCCCcHHHHHHH-HHHHHh
Q 020150 162 DAVNPPALKGLVQKTGFSMEDVLRKYIRYALNE------KPFNPDLVVNLIQLRKASMLDDSQVAEIL-NEISRR 229 (330)
Q Consensus 162 da~~~~vLk~L~~KTGFs~~Ei~RKYirY~LnE------r~F~~d~VaDLi~Lr~as~L~d~evaeiL-~E~s~R 229 (330)
+-+..+.++.|.+|.|=|-..|+ |||++.- |-+||+-+.+=++.-. ..||++|++.+- ...-.|
T Consensus 218 ~ll~~~~l~~iA~K~~kt~aQIl---Lrw~~q~g~~vipKS~~~~Ri~eN~~vfd-f~Lt~ed~~~i~~~~~~~r 288 (300)
T KOG1577|consen 218 DLLEDPVLKEIAKKYNKTPAQIL---LRWALQRGVSVIPKSSNPERIKENFKVFD-FELTEEDMKKLDSLNSNER 288 (300)
T ss_pred ccccCHHHHHHHHHhCCCHHHHH---HHHHHhCCcEEEeccCCHHHHHHHHhhcc-ccCCHHHHHHHhhccccce
Confidence 44778899999999999999998 7788876 6899998888888655 789999999987 333343
No 89
>PRK02998 prsA peptidylprolyl isomerase; Reviewed
Probab=26.68 E-value=1.3e+02 Score=27.96 Aligned_cols=98 Identities=15% Similarity=0.271 Sum_probs=58.6
Q ss_pred hcCCCcHHHHHHHHHHHHhhhhccCCeeeecccc-cchhhhhHHHHHHHHHhHh--hhcc--chhhhccCCCccchhhcc
Q 020150 211 ASMLDDSQVAEILNEISRRFVREKGPVVMNMSGY-SEKGFKRKLAVQALFGKVF--YLSE--LPEFCSRDSSLIVKEIFG 285 (330)
Q Consensus 211 as~L~d~evaeiL~E~s~Ri~~~~G~vmmn~~G~-Te~G~kRK~a~~aLF~Kll--yLsE--l~ef~s~dssL~vkeiFG 285 (330)
....||+||.+.++++.++.-..|... +.-.|+ ++..+++.+--+-+..+++ +++| +.+|-. ..+.+..|+=
T Consensus 66 ~i~vsd~ev~~~i~~~~~~~~~~f~~~-L~~~G~~~~~~~r~~i~~~l~~~~~~~~~Vtd~ei~~~y~--~~~~v~~Ilv 142 (283)
T PRK02998 66 KYKVSDEEAKKQVEEAKDKMGDNFKST-LEQVGLKNEDELKEKMKPEIAFEKAIKATVTEKDVKDNYK--PEMKVSHILV 142 (283)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHH-HHHcCCCcHHHHHHHHHHHHHHHHHhcCCCCHHHHHHhcc--cceEEEEEEe
Confidence 357799999999999988754444433 455699 4788988888888887775 2332 122221 2355555553
Q ss_pred cchhhhhhhhhhhccccCChhhHHhhh
Q 020150 286 VTDEDADKLRQHTLSEAGDMDSLEKMV 312 (330)
Q Consensus 286 vTdeDa~kLRi~~Lse~~d~~sLe~Mv 312 (330)
-+.+.++.++=.. -.-.|.+.|-+..
T Consensus 143 ~~e~~A~~i~~~l-~~G~~F~~lA~~~ 168 (283)
T PRK02998 143 KDEKTAKEVKEKV-NNGEDFAALAKQY 168 (283)
T ss_pred CCHHHHHHHHHHH-HCCCCHHHHHHHh
Confidence 3455566654332 2223555554443
No 90
>PRK03892 ribonuclease P protein component 3; Provisional
Probab=25.94 E-value=1.6e+02 Score=28.23 Aligned_cols=65 Identities=14% Similarity=0.133 Sum_probs=51.1
Q ss_pred HHHHHHhhCCChHHHHHHHHHHHhccCC--------------CChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhc
Q 020150 169 LKGLVQKTGFSMEDVLRKYIRYALNEKP--------------FNPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVRE 233 (330)
Q Consensus 169 Lk~L~~KTGFs~~Ei~RKYirY~LnEr~--------------F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~~~ 233 (330)
|+.|-+..|+...-+++.|-...-=-++ |+.-..-||++|=...|++.+|+.+.|.+..+.|.++
T Consensus 137 L~plL~~~G~~Rar~L~~~r~~l~L~rKYd~P~VISS~A~s~~~lRsPRdl~aL~~~iGme~~ea~~~Ls~~p~~i~~~ 215 (216)
T PRK03892 137 LSPLLRANPYERANILRFMMKAWQLVNKYKVPRFITSSAESKWEVRGPRDLMSLGINIGMEIPQAKASLSFYPRIILKR 215 (216)
T ss_pred cHHHHhhCchhHHHHHHHHHHHHHHHHHcCCCEEEecCcchhccCCCHHHHHHHHHHhCCCHHHHHHHHHHhHHHHhhc
Confidence 4556667888888888877665544444 4456778999999999999999999999999888764
No 91
>PRK11677 hypothetical protein; Provisional
Probab=25.91 E-value=54 Score=28.71 Aligned_cols=29 Identities=21% Similarity=0.402 Sum_probs=18.8
Q ss_pred chhHHHhhhHhhhhhhhhhhhhhhhhcCChhhh
Q 020150 106 LPWILAVPLAYVGVSFVIAFVKTVKKFNSPKFK 138 (330)
Q Consensus 106 lPwllAlPLAylG~TFviA~vRtvrK~~SPraK 138 (330)
|+|+.|+-.+.+|+.+.+.+.| |++++.|
T Consensus 1 M~W~~a~i~livG~iiG~~~~R----~~~~~~~ 29 (134)
T PRK11677 1 MTWEYALIGLVVGIIIGAVAMR----FGNRKLR 29 (134)
T ss_pred CcHHHHHHHHHHHHHHHHHHHh----hccchhh
Confidence 5799999888888555444444 4555443
No 92
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=25.88 E-value=1.9e+02 Score=20.24 Aligned_cols=44 Identities=32% Similarity=0.340 Sum_probs=20.4
Q ss_pred HHHHHhhCCChHHHHHHHHHHHhccCCCChHHHHHHHHHHhhcCCCcHHH
Q 020150 170 KGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQV 219 (330)
Q Consensus 170 k~L~~KTGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~ev 219 (330)
+.|.+++|.+.. .+.-.++.+.-+ =-+..|.+|=++++.+-+|+
T Consensus 14 ~~La~~~gis~~-----tl~~~~~~~~~~-~~~~~l~~ia~~l~~~~~el 57 (63)
T PF13443_consen 14 KDLARKTGISRS-----TLSRILNGKPSN-PSLDTLEKIAKALNCSPEEL 57 (63)
T ss_dssp HHHHHHHT--HH-----HHHHHHTTT------HHHHHHHHHHHT--HHHC
T ss_pred HHHHHHHCcCHH-----HHHHHHhccccc-ccHHHHHHHHHHcCCCHHHH
Confidence 455555555543 445555655222 23356667777888775553
No 93
>PF10771 DUF2582: Protein of unknown function (DUF2582); InterPro: IPR019707 This entry represents conserved proteins found in bacteria and archaea. The function is not known. ; PDB: 2L02_B 2L01_A.
Probab=25.60 E-value=82 Score=24.57 Aligned_cols=35 Identities=26% Similarity=0.327 Sum_probs=19.2
Q ss_pred HHHHHhcc-CCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHH
Q 020150 187 YIRYALNE-KPFNPDLVVNLIQLRKASMLDDSQVAEILNEIS 227 (330)
Q Consensus 187 YirY~LnE-r~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s 227 (330)
.||.+|+| ++.+ +-.|+++++|+|.++.-+|-=.+
T Consensus 12 ~Vw~~L~~~~~~s------~~el~k~~~l~~~~~~~AiGWLa 47 (65)
T PF10771_consen 12 KVWQLLNENGEWS------VSELKKATGLSDKEVYLAIGWLA 47 (65)
T ss_dssp HHHHHHCCSSSEE------HHHHHHHCT-SCHHHHHHHHHHH
T ss_pred HHHHHHhhCCCcC------HHHHHHHhCcCHHHHHHHHHHHh
Confidence 35666776 3332 22345777777777766654333
No 94
>KOG2629 consensus Peroxisomal membrane anchor protein (peroxin) [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=25.55 E-value=46 Score=33.02 Aligned_cols=56 Identities=16% Similarity=0.223 Sum_probs=36.1
Q ss_pred CCCCCCchhHHHhhhHhhhhhhhhhhhhhhhhcCChhhhhhhhhcchhhHHhhHHHHHh
Q 020150 100 RVGQSKLPWILAVPLAYVGVSFVIAFVKTVKKFNSPKFKRKKLVNKNAMVCKTIDELFQ 158 (330)
Q Consensus 100 Rvg~s~lPwllAlPLAylG~TFviA~vRtvrK~~SPraKRkR~VnKNa~LvkSLdeyfp 158 (330)
-.+.+++-|.+++.+...| |++++|+.||+|==|..--... +|=...-+.||+.|-
T Consensus 77 ~~~~~rwrdy~vmAvi~aG--i~y~~y~~~K~YV~P~~l~~~~-~k~e~~k~~Ld~~~~ 132 (300)
T KOG2629|consen 77 QNVLRRWRDYFVMAVILAG--IAYAAYRFVKSYVLPRFLGESK-DKLEADKRQLDDQFD 132 (300)
T ss_pred ccchhhHHHHHHHHHHHhh--HHHHHHHHHHHHHHHHhhCccc-hhHHHHHHHHHHHHH
Confidence 4455667788888777777 8999999999998775322111 022344455665554
No 95
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=25.29 E-value=76 Score=31.69 Aligned_cols=82 Identities=24% Similarity=0.299 Sum_probs=61.8
Q ss_pred hhcCChhhhhhhhhcchhhHHhhHHHHHhcCCCCCCch--HHHHHHHhhCCChHHHH----HHHHHHHhccCCCChHHHH
Q 020150 130 KKFNSPKFKRKKLVNKNAMVCKTIDELFQKGGDAVNPP--ALKGLVQKTGFSMEDVL----RKYIRYALNEKPFNPDLVV 203 (330)
Q Consensus 130 rK~~SPraKRkR~VnKNa~LvkSLdeyfp~gRda~~~~--vLk~L~~KTGFs~~Ei~----RKYirY~LnEr~F~~d~Va 203 (330)
++|-..|.|| |-.+||+. +-|++||...+.---.+ +=.+|.+|||.+...|- +|-|||.=|=-+|-++ +
T Consensus 183 ~r~ldarRKR-RNFsK~aT--eiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k~~ee--~ 257 (334)
T KOG0774|consen 183 SRFLDARRKR-RNFSKQAT--EILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGKNQEE--A 257 (334)
T ss_pred HHHHHHHHhh-cccchhHH--HHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhhhhhh--h
Confidence 4566655554 44677764 77999999877644333 77899999999998885 5889999888877654 7
Q ss_pred HHHHHHhhcCCCc
Q 020150 204 NLIQLRKASMLDD 216 (330)
Q Consensus 204 DLi~Lr~as~L~d 216 (330)
||-++|+|-.-+.
T Consensus 258 ~l~~~kk~~~~~~ 270 (334)
T KOG0774|consen 258 NLYAAKKAVDATP 270 (334)
T ss_pred hhHhhcccccCCC
Confidence 9999999876654
No 96
>TIGR02384 RelB_DinJ addiction module antitoxin, RelB/DinJ family. Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the seed for this alignment all were found adjacent to toxin genes. The resulting model appears to describe a narrower set of proteins than Pfam model pfam04221, although many in the scope of this model are not obviously paired with toxin proteins. Several toxin/antitoxin pairs may occur in a single species.
Probab=25.19 E-value=1.3e+02 Score=23.98 Aligned_cols=33 Identities=12% Similarity=0.375 Sum_probs=26.9
Q ss_pred HHHHHHHhhCCChHHHHHHHHHHHhccCC--CChH
Q 020150 168 ALKGLVQKTGFSMEDVLRKYIRYALNEKP--FNPD 200 (330)
Q Consensus 168 vLk~L~~KTGFs~~Ei~RKYirY~LnEr~--F~~d 200 (330)
....+-.+.|.++.+.+|-+++|..+++. |++.
T Consensus 16 ~a~~i~~~lGl~~s~ai~~fl~qvv~~~~lPF~~~ 50 (83)
T TIGR02384 16 EAYAVFEELGLTPSTAIRMFLKQVIREQGLPFDLR 50 (83)
T ss_pred HHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCCcC
Confidence 34556688999999999999999999975 5443
No 97
>TIGR00017 cmk cytidylate kinase. This family consists of cytidylate kinase, which catalyzes the phosphorylation of cytidine 5-monophosphate (dCMP) to cytidine 5 -diphosphate (dCDP) in the presence of ATP or GTP. UMP and dCMP can also act as acceptors.
Probab=24.89 E-value=3.1e+02 Score=24.70 Aligned_cols=80 Identities=15% Similarity=0.130 Sum_probs=46.9
Q ss_pred CCCchHHHHHHHhhC---CChHHHHHHHHHHHhccCCCChHHHHHHHHHHhhcCC-------------------------
Q 020150 163 AVNPPALKGLVQKTG---FSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASML------------------------- 214 (330)
Q Consensus 163 a~~~~vLk~L~~KTG---Fs~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L------------------------- 214 (330)
+..+..++.|..+.| ++..+++|..-+++|... ++.+--..++.++...++
T Consensus 13 sGKst~~~~la~~~~~~~~~~g~~~r~~~~~~l~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~v~~~ir~~ 91 (217)
T TIGR00017 13 AGKSTVAKAVAEKLGYAYLDSGAMYRAIALAALQNR-VDLTSEDALAELISHLDIRFIPTNGEVEVFLNGEDVSEAIRTQ 91 (217)
T ss_pred CCHHHHHHHHHHHhCCceeeCchHHHHHHHHHHHcC-CCCCCHHHHHHHHHhCCCEEecCCCceeEEEcCcchHHHhcCH
Confidence 445557788888888 677888887766665543 333322333444444443
Q ss_pred ----------CcHHHHHHHHHHHHhhhhccCCeeeecccc
Q 020150 215 ----------DDSQVAEILNEISRRFVREKGPVVMNMSGY 244 (330)
Q Consensus 215 ----------~d~evaeiL~E~s~Ri~~~~G~vmmn~~G~ 244 (330)
..-.|.+.|.+.-+++.+ .|++||+=..+
T Consensus 92 ~v~~~~s~~a~~p~VR~~l~~~qr~~a~-~~~~Vi~Gr~~ 130 (217)
T TIGR00017 92 EVANAASKVAVFPKVREALLKRQQALAK-NDGIIADGRDI 130 (217)
T ss_pred HHHHHHHHHcCCHHHHHHHHHHHHHHhh-cCCEEEEEcCc
Confidence 223455667777777664 46788776543
No 98
>PF10389 CoatB: Bacteriophage coat protein B ; InterPro: IPR008020 The major coat protein in the capsid of filamentous bacteriophage forms a helical assembly of about 7000 identical protomers, with each protomer comprised of 46 amino acids, after the cleavage of the signal peptide. Each protomer forms a slightly curved helix that combines to form a tubular structure that encapsulates the viral DNA [].; PDB: 2IFO_A.
Probab=24.72 E-value=59 Score=24.31 Aligned_cols=24 Identities=29% Similarity=0.278 Sum_probs=21.5
Q ss_pred HHHhhhHhhhhhhhhhhhhhhhhc
Q 020150 109 ILAVPLAYVGVSFVIAFVKTVKKF 132 (330)
Q Consensus 109 llAlPLAylG~TFviA~vRtvrK~ 132 (330)
+.++..+.+|+...|+.||-+||.
T Consensus 22 i~~ig~avL~v~V~i~v~kwiRra 45 (46)
T PF10389_consen 22 IATIGGAVLGVIVGIAVYKWIRRA 45 (46)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhh
Confidence 678889999999999999999873
No 99
>PHA02591 hypothetical protein; Provisional
Probab=24.72 E-value=58 Score=27.17 Aligned_cols=36 Identities=19% Similarity=0.230 Sum_probs=26.9
Q ss_pred ChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhcc
Q 020150 198 NPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREK 234 (330)
Q Consensus 198 ~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~~~~ 234 (330)
+.|.+..|.+-=...|||-++||+.|. ++++.|++|
T Consensus 44 ~~dd~~~vA~eL~eqGlSqeqIA~~LG-VsqetVrKY 79 (83)
T PHA02591 44 SEDDLISVTHELARKGFTVEKIASLLG-VSVRKVRRY 79 (83)
T ss_pred ccchHHHHHHHHHHcCCCHHHHHHHhC-CCHHHHHHH
Confidence 456666777766778999999998874 666677666
No 100
>COG4860 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.52 E-value=1.3e+02 Score=27.87 Aligned_cols=40 Identities=23% Similarity=0.424 Sum_probs=31.3
Q ss_pred HHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhccCCeeeecc
Q 020150 202 VVNLIQLRKASMLDDSQVAEILNEISRRFVREKGPVVMNMS 242 (330)
Q Consensus 202 VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~~~~G~vmmn~~ 242 (330)
+.||-..=-|.-|+|+||.|...|+ .+++++=+++|.|+.
T Consensus 96 l~dL~dii~~~f~sdeev~ey~~ei-~~l~e~g~ts~~~vt 135 (170)
T COG4860 96 LSDLADIIYAAFLSDEEVKEYEDEI-KALMEEGNTSFLDVT 135 (170)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHH-HHHHHcCCceEeehh
Confidence 4455444456779999999999998 567888899998875
No 101
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=24.50 E-value=1.5e+02 Score=20.19 Aligned_cols=37 Identities=14% Similarity=0.214 Sum_probs=22.2
Q ss_pred hhhHHhhHHHHHhcCCCCCCchHHHHHHHhhCCChHHH
Q 020150 146 NAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDV 183 (330)
Q Consensus 146 Na~LvkSLdeyfp~gRda~~~~vLk~L~~KTGFs~~Ei 183 (330)
...-..-|.++|..+. -.+...+..|...+|-+...|
T Consensus 8 ~~~~~~~Le~~f~~~~-~P~~~~~~~la~~~~l~~~qV 44 (59)
T cd00086 8 TPEQLEELEKEFEKNP-YPSREEREELAKELGLTERQV 44 (59)
T ss_pred CHHHHHHHHHHHHhCC-CCCHHHHHHHHHHHCcCHHHH
Confidence 3444555666666633 455556667777777666555
No 102
>COG2761 FrnE Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=24.25 E-value=1.1e+02 Score=28.99 Aligned_cols=40 Identities=13% Similarity=0.346 Sum_probs=36.0
Q ss_pred chhhHHhhHHHHHhcCCCCCCchHHHHHHHhhCCChHHHH
Q 020150 145 KNAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVL 184 (330)
Q Consensus 145 KNa~LvkSLdeyfp~gRda~~~~vLk~L~~KTGFs~~Ei~ 184 (330)
.+.++-+--..||..|++=.+..+|-.|....|.+.+++-
T Consensus 119 ~~~~~~~lf~AyF~eg~nI~D~dVL~diA~~~GLD~~~~~ 158 (225)
T COG2761 119 QDRFLEALFEAYFEEGRNIGDEDVLADIAEEVGLDREEFK 158 (225)
T ss_pred HHHHHHHHHHHHhccCCCCCcHHHHHHHHHHhCCCHHHHH
Confidence 4677888889999999999999999999999999988764
No 103
>TIGR01167 LPXTG_anchor LPXTG-motif cell wall anchor domain. A common feature of this proteins containing this domain appears to be a high proportion of charged and zwitterionic residues immediatedly upstream of the LPXTG motif. This model differs from other descriptions of the LPXTG region by including a portion of that upstream charged region.
Probab=24.15 E-value=81 Score=20.28 Aligned_cols=21 Identities=29% Similarity=0.559 Sum_probs=16.1
Q ss_pred CCCCCCCchhHHHhhhHhhhh
Q 020150 99 PRVGQSKLPWILAVPLAYVGV 119 (330)
Q Consensus 99 PRvg~s~lPwllAlPLAylG~ 119 (330)
|.-|....+|+..+.++.++.
T Consensus 3 P~TG~~~~~~~~~~G~~l~~~ 23 (34)
T TIGR01167 3 PKTGESGNSLLLLLGLLLLGL 23 (34)
T ss_pred CCCCCcccHHHHHHHHHHHHH
Confidence 667888888888888866664
No 104
>cd07321 Extradiol_Dioxygenase_3A_like Subunit A of Class III extradiol dioxygenases. Extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. There are two major groups of dioxygenases according to the cleavage site of the aromatic ring. Intradiol enzymes cleave the aromatic ring between two hydroxyl groups, whereas extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes are evolutionary related and show sequence similarity, with the two domain class II enzymes evolving from the class I enzyme through gene duplication. Class III enzymes are different in sequence and structure and usually have two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents subunit A of c
Probab=23.92 E-value=59 Score=25.57 Aligned_cols=54 Identities=9% Similarity=-0.034 Sum_probs=42.8
Q ss_pred HHHHHHHhccCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhccCCee
Q 020150 185 RKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKGPVV 238 (330)
Q Consensus 185 RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~~~~G~vm 238 (330)
.|-++.++++..+=..+.+|=-++=...|||++|...++.---.+++.-=|+.+
T Consensus 6 ~~~~~~~~~~~~~re~f~~dp~a~~~~~~Lt~eE~~al~~rD~~~L~~lG~~~~ 59 (77)
T cd07321 6 EKLLEQLLVKPEVKERFKADPEAVLAEYGLTPEEKAALLARDVGALYVLGVNPM 59 (77)
T ss_pred HHHHHHHhcCHHHHHHHHhCHHHHHHHcCCCHHHHHHHHcCCHHHHHHcCCCHH
Confidence 677888888888888888888888888999999999888776666665544443
No 105
>PRK00118 putative DNA-binding protein; Validated
Probab=23.87 E-value=48 Score=27.74 Aligned_cols=69 Identities=17% Similarity=0.199 Sum_probs=39.9
Q ss_pred hHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhccCCeeeecccc--cchhhhhHHHHHHHHHhHhhhcc
Q 020150 199 PDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKGPVVMNMSGY--SEKGFKRKLAVQALFGKVFYLSE 267 (330)
Q Consensus 199 ~d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~~~~G~vmmn~~G~--Te~G~kRK~a~~aLF~KllyLsE 267 (330)
|+--..++.|+-..|+|..|||++++-.-..|++...-..-.+.-+ -..+++|-+.-+++|.++.|+-|
T Consensus 19 ~ekqRevl~L~y~eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~~~~~~~~~~~~~~~~~~~~~ 89 (104)
T PRK00118 19 TEKQRNYMELYYLDDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHLYEKFIERNELFDKIAYLKE 89 (104)
T ss_pred CHHHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHChHHHHHHHHHHHHHHHHHHH
Confidence 3345667777777788888888776532222222211111111100 01367888889999999998855
No 106
>PF04840 Vps16_C: Vps16, C-terminal region; InterPro: IPR006925 This protein forms part of the Class C vacuolar protein sorting (Vps) complex. Vps16 is essential for vacuolar protein sorting, which is essential for viability in plants, but not yeast []. The Class C Vps complex is required for SNARE-mediated membrane fusion at the lysosome-like yeast vacuole. It is thought to play essential roles in membrane docking and fusion at the Golgi-to-endosome and endosome-to-vacuole stages of transport []. The role of VPS16 in this complex is not known.; GO: 0006886 intracellular protein transport, 0005737 cytoplasm
Probab=23.85 E-value=63 Score=31.12 Aligned_cols=36 Identities=33% Similarity=0.352 Sum_probs=33.3
Q ss_pred ccchhhcccchhhhhhhhhhhccccCChhhHHhhhc
Q 020150 278 LIVKEIFGVTDEDADKLRQHTLSEAGDMDSLEKMVN 313 (330)
Q Consensus 278 L~vkeiFGvTdeDa~kLRi~~Lse~~d~~sLe~Mv~ 313 (330)
-.++.-|.|+|.-.--++|.+|.+.++.+.||++..
T Consensus 197 ~kl~k~Fkv~dkrfw~lki~aLa~~~~w~eL~~fa~ 232 (319)
T PF04840_consen 197 EKLKKEFKVPDKRFWWLKIKALAENKDWDELEKFAK 232 (319)
T ss_pred HHHHHHcCCcHHHHHHHHHHHHHhcCCHHHHHHHHh
Confidence 467889999999999999999999999999999864
No 107
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=23.69 E-value=1e+02 Score=24.80 Aligned_cols=53 Identities=19% Similarity=0.223 Sum_probs=40.3
Q ss_pred CChHHHHHH-HHHHHhccCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhh
Q 020150 178 FSMEDVLRK-YIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRF 230 (330)
Q Consensus 178 Fs~~Ei~RK-YirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri 230 (330)
|+.++|.+= .|+.+|++.-|+.+.+..++.........-+++-..|+++-.-+
T Consensus 39 Yt~~di~~l~~I~~llr~~G~~l~~i~~~l~~~~~~~~~~~~~~~~~~~~~~~~ 92 (99)
T cd04765 39 YRPKDVELLLLIKHLLYEKGYTIEGAKQALKEDGAAAIREEEAEERLPSIRAEL 92 (99)
T ss_pred eCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHhccccccchhhHHHHHHHHHHHH
Confidence 777777653 46667788889999999999887777777778888887765544
No 108
>PRK09726 antitoxin HipB; Provisional
Probab=23.50 E-value=94 Score=24.04 Aligned_cols=38 Identities=16% Similarity=0.315 Sum_probs=27.8
Q ss_pred CCCChHHHH-HHHHHHhhcCCCcHHHHHHHHHHHHhhhhc
Q 020150 195 KPFNPDLVV-NLIQLRKASMLDDSQVAEILNEISRRFVRE 233 (330)
Q Consensus 195 r~F~~d~Va-DLi~Lr~as~L~d~evaeiL~E~s~Ri~~~ 233 (330)
..+++..+. -|-.+|+..|+|.+|+|+.+. +++.-+.+
T Consensus 6 ~~~~~~~l~~~lk~~R~~~gltq~elA~~~g-vs~~tis~ 44 (88)
T PRK09726 6 KIYSPTQLANAMKLVRQQNGWTQSELAKKIG-IKQATISN 44 (88)
T ss_pred cccCHHHHHHHHHHHHHHcCCCHHHHHHHHC-cCHHHHHH
Confidence 567777775 456789999999999999876 55444443
No 109
>COG2059 ChrA Chromate transport protein ChrA [Inorganic ion transport and metabolism]
Probab=23.49 E-value=68 Score=29.48 Aligned_cols=28 Identities=39% Similarity=0.732 Sum_probs=18.9
Q ss_pred hHHHHhcchhhHHh-hhhhhhhccccccccCCC
Q 020150 68 EVEVEEELPWIQEK-ALDLVEFTGSVTQAIPGP 99 (330)
Q Consensus 68 e~e~e~e~~wiqek-aldlve~tG~vtQaIPGP 99 (330)
++|.-++-.||-|+ =.|++ ..+|.+|||
T Consensus 33 ~~e~V~~r~Wis~~ef~~~l----aisq~lPGP 61 (195)
T COG2059 33 RREVVERRKWISEEEFADAL----AISQLLPGP 61 (195)
T ss_pred HHHHHHhccCCCHHHHHHHH----HHHhcCCCH
Confidence 44555566999665 34444 367999999
No 110
>PRK14135 recX recombination regulator RecX; Provisional
Probab=23.43 E-value=3.2e+02 Score=24.79 Aligned_cols=64 Identities=16% Similarity=0.343 Sum_probs=0.0
Q ss_pred HHHHHHHhccCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhccCCeeeecccccchhhhhHHHHHHHHHh
Q 020150 185 RKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKGPVVMNMSGYSEKGFKRKLAVQALFGK 261 (330)
Q Consensus 185 RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~~~~G~vmmn~~G~Te~G~kRK~a~~aLF~K 261 (330)
++-|++.|..+.|+++.+...+. .+++.+--+.++..+++.++.+. ..+..-.++|+ .+.|..|
T Consensus 125 ~~~I~~kL~~kGi~~~~Ie~~l~-----~l~~~~~~d~a~~~~~k~~~~~~-------~~~~~~~k~Ki-~~~L~rk 188 (263)
T PRK14135 125 PRVIKQKLLQKGIEDEIIEEALS-----EYTEEDQIEVAQKLAEKLLKKYQ-------KLPFKALKQKI-IQSLLTK 188 (263)
T ss_pred hHHHHHHHHHcCCCHHHHHHHHH-----hCChhhHHHHHHHHHHHHHHHhc-------CCCHHHHHHHH-HHHHHhC
No 111
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=23.35 E-value=1.6e+02 Score=23.09 Aligned_cols=43 Identities=16% Similarity=0.304 Sum_probs=24.3
Q ss_pred hhHHHHHhcCCCCCCch-HHHHHHHhhCCChHHHHHHHHHHHhccC
Q 020150 151 KTIDELFQKGGDAVNPP-ALKGLVQKTGFSMEDVLRKYIRYALNEK 195 (330)
Q Consensus 151 kSLdeyfp~gRda~~~~-vLk~L~~KTGFs~~Ei~RKYirY~LnEr 195 (330)
+.|=+||.. ......| -+..|.++.|++..+ +|+-|.++.+|-
T Consensus 50 ~~Vl~~i~~-~~~~~~Gv~v~~I~~~l~~~~~~-v~~al~~L~~eG 93 (102)
T PF08784_consen 50 DKVLNFIKQ-QPNSEEGVHVDEIAQQLGMSENE-VRKALDFLSNEG 93 (102)
T ss_dssp HHHHHHHHC-----TTTEEHHHHHHHSTS-HHH-HHHHHHHHHHTT
T ss_pred HHHHHHHHh-cCCCCCcccHHHHHHHhCcCHHH-HHHHHHHHHhCC
Confidence 334455555 2223334 566777777887555 588888888763
No 112
>PRK07668 hypothetical protein; Validated
Probab=23.34 E-value=1.1e+02 Score=29.24 Aligned_cols=34 Identities=9% Similarity=0.260 Sum_probs=27.9
Q ss_pred ChHHHHHH-HHHHhhcCCCcHHHHHHHHHHHHhhhh
Q 020150 198 NPDLVVNL-IQLRKASMLDDSQVAEILNEISRRFVR 232 (330)
Q Consensus 198 ~~d~VaDL-i~Lr~as~L~d~evaeiL~E~s~Ri~~ 232 (330)
|++.+.|| .+| ...|++++|+.|+|+|.-..+.+
T Consensus 6 Neefl~~L~~yL-~~~glseeeieeiL~Ei~~hLlE 40 (254)
T PRK07668 6 GRKFLDDTRVYL-IAKGIKEEDIESFLEDAELHLIE 40 (254)
T ss_pred HHHHHHHHHHHH-HHCCCCHHHHHHHHHHHHHHHHH
Confidence 56777787 456 45689999999999999998875
No 113
>PLN00138 large subunit ribosomal protein LP2; Provisional
Probab=23.19 E-value=29 Score=29.51 Aligned_cols=12 Identities=17% Similarity=0.459 Sum_probs=6.8
Q ss_pred hhhHHHHhcchh
Q 020150 66 EVEVEVEEELPW 77 (330)
Q Consensus 66 ~~e~e~e~e~~w 77 (330)
|+|||+|++|.|
T Consensus 98 e~eeE~ddDmGf 109 (113)
T PLN00138 98 EEKEESDDDMGF 109 (113)
T ss_pred cccccccccccc
Confidence 334455667765
No 114
>PF13154 DUF3991: Protein of unknown function (DUF3991)
Probab=23.03 E-value=49 Score=25.26 Aligned_cols=19 Identities=26% Similarity=0.588 Sum_probs=17.6
Q ss_pred HHHhccCCCChHHHHHHHH
Q 020150 189 RYALNEKPFNPDLVVNLIQ 207 (330)
Q Consensus 189 rY~LnEr~F~~d~VaDLi~ 207 (330)
+|+.++|..+++.|..++.
T Consensus 1 ~YL~~~RgI~~~~v~~~~~ 19 (77)
T PF13154_consen 1 AYLTEERGIDPEIVDAFIN 19 (77)
T ss_pred CchhhhcCcCHHHHHHHHH
Confidence 4899999999999999987
No 115
>PRK11448 hsdR type I restriction enzyme EcoKI subunit R; Provisional
Probab=22.98 E-value=3.2e+02 Score=31.11 Aligned_cols=78 Identities=22% Similarity=0.356 Sum_probs=52.2
Q ss_pred hhcchhhHHhhHHHHHhcCCCCCCchHHHHHHHh---hCCChHHHHHHHHHHHhccCCCChHHHHHHHH-HHhhcCCC--
Q 020150 142 LVNKNAMVCKTIDELFQKGGDAVNPPALKGLVQK---TGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQ-LRKASMLD-- 215 (330)
Q Consensus 142 ~VnKNa~LvkSLdeyfp~gRda~~~~vLk~L~~K---TGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~-Lr~as~L~-- 215 (330)
.|..|..=..-|..+..++ ..++...|++|+.+ -||+-..+-+-|= ... |.+..||||. .|.|.|++
T Consensus 967 ~i~~~~~~i~al~~~~~~p-~~lt~~~l~~l~~~l~~~~~~~~~l~~a~~-----~~~-~~~~~a~ii~~iR~~~~~~~l 1039 (1123)
T PRK11448 967 FVRENINQIPALQVVVNRP-RDLTRKELKELRLLLDQQGFSEASLRSAWK-----ETK-NEDIAASIIGFIRQAALGDAL 1039 (1123)
T ss_pred HHHhcccccHHHHHHHhCC-ccCCHHHHHHHHHHhhhCCCCHHHHHHHHH-----hch-hhhHHHHHHHHHHHHhcCCcC
Confidence 3444444445555566666 44888888888733 4888776655443 222 8888999996 59999998
Q ss_pred ---cHHHHHHHHHH
Q 020150 216 ---DSQVAEILNEI 226 (330)
Q Consensus 216 ---d~evaeiL~E~ 226 (330)
++-|..+++.+
T Consensus 1040 ~~~~~~v~~a~~~~ 1053 (1123)
T PRK11448 1040 VPFEERVDHAMQKI 1053 (1123)
T ss_pred CCHHHHHHHHHHHH
Confidence 67777776663
No 116
>PRK09459 pspG phage shock protein G; Reviewed
Probab=22.87 E-value=42 Score=27.53 Aligned_cols=17 Identities=18% Similarity=0.579 Sum_probs=8.7
Q ss_pred hhhhhhhhhcCChhhhh
Q 020150 123 IAFVKTVKKFNSPKFKR 139 (330)
Q Consensus 123 iA~vRtvrK~~SPraKR 139 (330)
+-+||.++|-.+||.||
T Consensus 58 vW~~r~~~~~~~~~y~~ 74 (76)
T PRK09459 58 VWVIRAIKAPKVPRYQR 74 (76)
T ss_pred HHHHHHhhccccccccc
Confidence 34556655555555443
No 117
>PRK06645 DNA polymerase III subunits gamma and tau; Validated
Probab=22.87 E-value=4.2e+02 Score=27.53 Aligned_cols=61 Identities=13% Similarity=0.187 Sum_probs=47.9
Q ss_pred hhhHHhhHHHHHhcCCCCCCchHHHHHHHhhCCChHHH---HHHHHHHHhc-cCCCChHHHHHHH
Q 020150 146 NAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDV---LRKYIRYALN-EKPFNPDLVVNLI 206 (330)
Q Consensus 146 Na~LvkSLdeyfp~gRda~~~~vLk~L~~KTGFs~~Ei---~RKYirY~Ln-Er~F~~d~VaDLi 206 (330)
...+.+.|...+.+.+-.++..++..|.+.++-|+-++ +.|.+-|.-. .+.-+.+.|.+++
T Consensus 189 ~~el~~~L~~i~~~egi~ie~eAL~~Ia~~s~GslR~al~~Ldkai~~~~~~~~~It~~~V~~ll 253 (507)
T PRK06645 189 FEEIFKLLEYITKQENLKTDIEALRIIAYKSEGSARDAVSILDQAASMSAKSDNIISPQVINQML 253 (507)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHhhccCCCCcCHHHHHHHH
Confidence 45678888888888888889999999999999998877 5677777653 3357777776664
No 118
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=22.81 E-value=1.2e+02 Score=28.96 Aligned_cols=109 Identities=24% Similarity=0.298 Sum_probs=68.4
Q ss_pred hHHHHHHHHHHHhcc----CCCChHHHHHHHHHHhhcC--CCcHHHHHHHH--HHHHhhhh-ccCCeeeecccccchhhh
Q 020150 180 MEDVLRKYIRYALNE----KPFNPDLVVNLIQLRKASM--LDDSQVAEILN--EISRRFVR-EKGPVVMNMSGYSEKGFK 250 (330)
Q Consensus 180 ~~Ei~RKYirY~LnE----r~F~~d~VaDLi~Lr~as~--L~d~evaeiL~--E~s~Ri~~-~~G~vmmn~~G~Te~G~k 250 (330)
.-+.|......+++| .+|+.+ .-.|=+.++ +|-+||.++|. +..-=|-+ .-|+..-.-..+|-.+--
T Consensus 115 ~~~y~~~W~~~virel~~~~~~~~~----~~~ia~~l~p~is~~ev~~sL~~L~~~glikk~~~g~y~~t~~~l~~~~~~ 190 (271)
T TIGR02147 115 QFEYYRHWYNSVIRELLGVMPFADD----PEELAKRCFPKISAEQVKESLDLLERLGLIKKNEDGFYKQTDKAVSTGDEV 190 (271)
T ss_pred HHHHHHHHHHHHHHHHhhcCCCCCC----HHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeECCCCcEEeecceeecCCcc
Confidence 345666766667776 456544 112334455 89999999987 33322222 134445444456656666
Q ss_pred hHHHHHHHHHhHhhhcc--chhhh--ccC-CCccchhhcccchhhhhhhhh
Q 020150 251 RKLAVQALFGKVFYLSE--LPEFC--SRD-SSLIVKEIFGVTDEDADKLRQ 296 (330)
Q Consensus 251 RK~a~~aLF~KllyLsE--l~ef~--s~d-ssL~vkeiFGvTdeDa~kLRi 296 (330)
...+++......+.|+- ++.+- .|| |++ +||++++++++++=
T Consensus 191 ~~~avr~~h~q~l~lA~~al~~~p~~eR~~S~l----T~~i~~~~~~~i~~ 237 (271)
T TIGR02147 191 IPLAVRQYQKQMIDLAKEALDALPPSERDVSTV----TFGISEEAYKEIVK 237 (271)
T ss_pred chHHHHHHHHHHHHHHHHHHHhCCcccccccee----eEecCHHHHHHHHH
Confidence 78899999999998874 33332 223 445 79999999998853
No 119
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=22.37 E-value=1.3e+02 Score=21.30 Aligned_cols=27 Identities=30% Similarity=0.439 Sum_probs=23.3
Q ss_pred HHHHHHHhhCCChHHHHHHHHHHHhcc
Q 020150 168 ALKGLVQKTGFSMEDVLRKYIRYALNE 194 (330)
Q Consensus 168 vLk~L~~KTGFs~~Ei~RKYirY~LnE 194 (330)
.|+.|..+||-...+++|+=|...|.+
T Consensus 16 ~L~~ls~~t~i~~S~Ll~eAle~~l~k 42 (44)
T PF12651_consen 16 KLKELSEETGIPKSKLLREALEDYLEK 42 (44)
T ss_pred HHHHHHHHHCCCHHHHHHHHHHHHHHh
Confidence 578899999999999999988777754
No 120
>PF01026 TatD_DNase: TatD related DNase The Pfam entry finds members not in the Prosite definition.; InterPro: IPR001130 This family of proteins are related to a large superfamily of metalloenzymes []. TatD, a member of this family has been shown experimentally to be a DNase enzyme []. Allantoinase 3.5.2.5 from EC, N-isopropylammelide isopropyl amidohydrolase 3.5.1 from EC and the SCN1 protein from fission yeast belong to this family.; GO: 0016888 endodeoxyribonuclease activity, producing 5'-phosphomonoesters; PDB: 3E2V_B 1XWY_A 3GUW_D 3RCM_A 1ZZM_A 2XIO_A 1J6O_A 2GZX_A 3IPW_A 2Y1H_A ....
Probab=22.32 E-value=1.3e+02 Score=27.09 Aligned_cols=36 Identities=19% Similarity=0.298 Sum_probs=28.7
Q ss_pred CChHHHHHHHH-HHhhcCCCcHHHHHHHHHHHHhhhh
Q 020150 197 FNPDLVVNLIQ-LRKASMLDDSQVAEILNEISRRFVR 232 (330)
Q Consensus 197 F~~d~VaDLi~-Lr~as~L~d~evaeiL~E~s~Ri~~ 232 (330)
-.|..+.+.++ |-+.-+++.+++++++.+-++|+|.
T Consensus 219 ~~p~~i~~~~~~la~~~~~~~e~~~~~~~~N~~r~f~ 255 (255)
T PF01026_consen 219 NEPSNIPKVAQALAEIKGISLEELAQIIYENAKRLFG 255 (255)
T ss_dssp --GGGHHHHHHHHHHHHTSTHHHHHHHHHHHHHHHHT
T ss_pred CChHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhC
Confidence 36777777665 6667789999999999999999984
No 121
>cd01310 TatD_DNAse TatD like proteins; E.coli TatD is a cytoplasmic protein, shown to have magnesium dependent DNase activity.
Probab=22.17 E-value=1.4e+02 Score=25.48 Aligned_cols=32 Identities=19% Similarity=0.309 Sum_probs=25.2
Q ss_pred HHHHHHHH-HHhhcCCCcHHHHHHHHHHHHhhh
Q 020150 200 DLVVNLIQ-LRKASMLDDSQVAEILNEISRRFV 231 (330)
Q Consensus 200 d~VaDLi~-Lr~as~L~d~evaeiL~E~s~Ri~ 231 (330)
..+..++. |....||+.+++..++.+-++|+|
T Consensus 218 ~~~~~~~~~la~~~gl~~e~~~~~~~~N~~~ll 250 (251)
T cd01310 218 AYVKHVAEKIAELKGISVEEVAEVTTENAKRLF 250 (251)
T ss_pred hhHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHh
Confidence 34444444 556799999999999999999987
No 122
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=22.10 E-value=4.1e+02 Score=21.41 Aligned_cols=30 Identities=13% Similarity=0.201 Sum_probs=15.4
Q ss_pred CCCChHHHHHHHHH--HhhcCCCcHHHHHHHH
Q 020150 195 KPFNPDLVVNLIQL--RKASMLDDSQVAEILN 224 (330)
Q Consensus 195 r~F~~d~VaDLi~L--r~as~L~d~evaeiL~ 224 (330)
|-|+++.|..|-.+ =+.+|++=+||+++|+
T Consensus 37 R~Y~~~~i~~l~~I~~lr~~G~sl~eI~~~l~ 68 (123)
T cd04770 37 RLYGEADLARLRFIRRAQALGFSLAEIRELLS 68 (123)
T ss_pred ccCCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence 34555555543222 1345666666666664
No 123
>COG2212 MnhF Multisubunit Na+/H+ antiporter, MnhF subunit [Inorganic ion transport and metabolism]
Probab=21.86 E-value=70 Score=26.53 Aligned_cols=39 Identities=18% Similarity=0.473 Sum_probs=30.2
Q ss_pred chhHHHhhhHhhhhhhhhhhhhhhhhcCChhhhhhhhhcchhh
Q 020150 106 LPWILAVPLAYVGVSFVIAFVKTVKKFNSPKFKRKKLVNKNAM 148 (330)
Q Consensus 106 lPwllAlPLAylG~TFviA~vRtvrK~~SPraKRkR~VnKNa~ 148 (330)
+.|++-+.+..+++++.+++||+++-=|.| .|.|.-|..
T Consensus 3 ~~~~~~ial~i~~la~~l~~yRvi~GPt~~----DRvvalD~l 41 (89)
T COG2212 3 LEIMLLIALIILGLALLLALYRVIRGPTLP----DRVVALDTL 41 (89)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhCCCcc----chhhhHhHH
Confidence 578899999999999999999997765554 466655543
No 124
>PF05598 DUF772: Transposase domain (DUF772); InterPro: IPR008490 This presumed domain is found at the N terminus of transposase insH and other related transposases.
Probab=21.73 E-value=1.2e+02 Score=22.22 Aligned_cols=32 Identities=19% Similarity=0.332 Sum_probs=28.0
Q ss_pred CCChHHHHHHHHHHhhcCC-CcHHHHHHHHHHH
Q 020150 196 PFNPDLVVNLIQLRKASML-DDSQVAEILNEIS 227 (330)
Q Consensus 196 ~F~~d~VaDLi~Lr~as~L-~d~evaeiL~E~s 227 (330)
+++|....-++=++...|+ ||.++.+.|++--
T Consensus 4 ~~~~~~ml~~ll~~~~~~~~S~r~l~~~l~~~~ 36 (77)
T PF05598_consen 4 AYPPRMMLKALLLKYLFGLRSDRELEERLRDNL 36 (77)
T ss_pred CCCHHHHHHHHHHHHHHhcchHHHHHhhHhhhh
Confidence 6889999999999999999 9999999988753
No 125
>PF00248 Aldo_ket_red: Aldo/keto reductase family; InterPro: IPR023210 The aldo-keto reductase family includes a number of related monomeric NADPH-dependent oxidoreductases, such as aldehyde reductase, aldose reductase, prostaglandin F synthase, xylose reductase, rho crystallin, and many others []. All possess a similar structure, with a beta-alpha-beta fold characteristic of nucleotide binding proteins []. The fold comprises a parallel beta-8/alpha-8-barrel, which contains a novel NADP-binding motif. The binding site is located in a large, deep, elliptical pocket in the C-terminal end of the beta sheet, the substrate being bound in an extended conformation. The hydrophobic nature of the pocket favours aromatic and apolar substrates over highly polar ones []. Binding of the NADPH coenzyme causes a massive conformational change, reorienting a loop, effectively locking the coenzyme in place. This binding is more similar to FAD- than to NAD(P)-binding oxidoreductases []. Some proteins of this entry contain a K+ ion channel beta chain regulatory domain; these are reported to have oxidoreductase activity []. This entry represents the NADP-dependent oxidoreductase domain found in these proteins.; PDB: 1C9W_A 4F40_B 1VBJ_A 1XGD_A 1X97_A 2ACS_A 1EF3_A 2ACU_A 1PWM_A 2NVD_A ....
Probab=21.69 E-value=1.5e+02 Score=26.15 Aligned_cols=55 Identities=22% Similarity=0.329 Sum_probs=40.2
Q ss_pred CCchHHHHHHHhhCCChHHHHHHHHHHHhccC--------CCChHHHHHHHHHHhhcCCCcHHHHHH
Q 020150 164 VNPPALKGLVQKTGFSMEDVLRKYIRYALNEK--------PFNPDLVVNLIQLRKASMLDDSQVAEI 222 (330)
Q Consensus 164 ~~~~vLk~L~~KTGFs~~Ei~RKYirY~LnEr--------~F~~d~VaDLi~Lr~as~L~d~evaei 222 (330)
...+.++.+..+.|.+..++. |+|+|... .-+++-|.+.++--.. -|+++|+++|
T Consensus 216 ~~~~~l~~~a~~~g~s~~q~a---l~~~l~~~~~~~~i~g~~~~~~l~en~~a~~~-~L~~~~~~~i 278 (283)
T PF00248_consen 216 ELADALRELAEEHGVSPAQLA---LRWVLSHPGVASVIVGASSPEHLEENLAALDF-PLTEEELAEI 278 (283)
T ss_dssp GGHHHHHHHHHHHTSSHHHHH---HHHHHTSHTTEEEEEB-SSHHHHHHHHGGSSS-G--HHHHHHH
T ss_pred hhhhhhhhhhhhcccccchhh---hhhhhhccccccccCCCCCHHHHHHHHHHhCC-CCCHHHHHHH
Confidence 344589999999999999987 66777432 2578888888876644 8999999876
No 126
>PTZ00373 60S Acidic ribosomal protein P2; Provisional
Probab=21.61 E-value=33 Score=29.31 Aligned_cols=9 Identities=33% Similarity=0.549 Sum_probs=5.3
Q ss_pred HHHHhcchh
Q 020150 69 VEVEEELPW 77 (330)
Q Consensus 69 ~e~e~e~~w 77 (330)
||+|.+|.|
T Consensus 100 ee~ddDmgf 108 (112)
T PTZ00373 100 EEEEDDLGF 108 (112)
T ss_pred ccccccccc
Confidence 445556776
No 127
>PF14163 SieB: Superinfection exclusion protein B
Probab=21.52 E-value=1.2e+02 Score=25.70 Aligned_cols=12 Identities=42% Similarity=0.717 Sum_probs=6.1
Q ss_pred CCChHHHHHHHH
Q 020150 196 PFNPDLVVNLIQ 207 (330)
Q Consensus 196 ~F~~d~VaDLi~ 207 (330)
|.|..+|..|++
T Consensus 101 p~~~~~v~~L~~ 112 (151)
T PF14163_consen 101 PYNNPAVKSLLQ 112 (151)
T ss_pred cCCCHHHHHHHH
Confidence 445555555554
No 128
>PF13934 ELYS: Nuclear pore complex assembly
Probab=21.48 E-value=4.6e+02 Score=23.95 Aligned_cols=101 Identities=14% Similarity=0.121 Sum_probs=62.9
Q ss_pred cCCCCCCCCCchhHHHhhhHhhhhhhhhhhhhhhhhcCChhhhhhhhhcchhhHHhhHHHHHhcCCCCCCchHHHHHHHh
Q 020150 96 IPGPRVGQSKLPWILAVPLAYVGVSFVIAFVKTVKKFNSPKFKRKKLVNKNAMVCKTIDELFQKGGDAVNPPALKGLVQK 175 (330)
Q Consensus 96 IPGPRvg~s~lPwllAlPLAylG~TFviA~vRtvrK~~SPraKRkR~VnKNa~LvkSLdeyfp~gRda~~~~vLk~L~~K 175 (330)
++.|++.+.--+||+.+=+..-.-...++++|+++-.-+....-.- =..+.-+.++-| .+.-.
T Consensus 101 L~~ps~~~~~~~~Il~~L~~~~~~~lAL~y~~~~~p~l~s~~~~~~--~~~~La~~~v~E---------------Af~~~ 163 (226)
T PF13934_consen 101 LSHPSLIPWFPDKILQALLRRGDPKLALRYLRAVGPPLSSPEALTL--YFVALANGLVTE---------------AFSFQ 163 (226)
T ss_pred hCCCCCCcccHHHHHHHHHHCCChhHHHHHHHhcCCCCCCHHHHHH--HHHHHHcCCHHH---------------HHHHH
Confidence 4889888776779999888887888999999998776554411110 011111222222 22222
Q ss_pred hCCCh---HHHHHHHHHHHhccCCCChHHHHHHHHHHhhcCCCcHH
Q 020150 176 TGFSM---EDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQ 218 (330)
Q Consensus 176 TGFs~---~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~e 218 (330)
..|.. .+.+.+-+.+.+++.+ ..+.+.+|+.| =|+++|
T Consensus 164 R~~~~~~~~~l~e~l~~~~~~~~~-~~~~~~~Ll~L----Pl~~~E 204 (226)
T PF13934_consen 164 RSYPDELRRRLFEQLLEHCLEECA-RSGRLDELLSL----PLDEEE 204 (226)
T ss_pred HhCchhhhHHHHHHHHHHHHHHhh-hhhHHHHHHhC----CCChHH
Confidence 22333 4588899999998887 56667777654 455544
No 129
>PHA03211 serine/threonine kinase US3; Provisional
Probab=21.39 E-value=40 Score=33.36 Aligned_cols=36 Identities=14% Similarity=0.200 Sum_probs=22.1
Q ss_pred hhhhhHHHHhcchhhHHhhhhhhhhccccccccCCC
Q 020150 64 AEEVEVEVEEELPWIQEKALDLVEFTGSVTQAIPGP 99 (330)
Q Consensus 64 ~~~~e~e~e~e~~wiqekaldlve~tG~vtQaIPGP 99 (330)
+.+..+..+.++.|-.+.+.+.-.-.+.+...+|.+
T Consensus 92 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 127 (461)
T PHA03211 92 EDDDDDDAPDDVAYPDEYAEDDFLPGDGAPDHDPAP 127 (461)
T ss_pred hccCCCCCccccCCCCCCCCcceecCCCCCCCCCCC
Confidence 334445555666777777777666666666666554
No 130
>PRK06361 hypothetical protein; Provisional
Probab=21.24 E-value=1.2e+02 Score=26.25 Aligned_cols=40 Identities=13% Similarity=0.144 Sum_probs=33.9
Q ss_pred CCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhhhhccC
Q 020150 196 PFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRFVREKG 235 (330)
Q Consensus 196 ~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri~~~~G 235 (330)
+-+.+....+.++.+-.|+++++|-.++.+.-+|+.+.-|
T Consensus 173 ~~d~~~~~~~~~i~~~~gl~~~~v~~~~~~~~~~~~~~~~ 212 (212)
T PRK06361 173 PSDLITYEFARKVALGAGLTEKELEEALENNPKLLLKRLG 212 (212)
T ss_pred HHHHHHHHHHHHHHcCCCCCHHHHHHHHHHhHHHHHHhcC
Confidence 4455667788999999999999999999999999887654
No 131
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. 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 CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=21.22 E-value=2.6e+02 Score=22.76 Aligned_cols=42 Identities=14% Similarity=0.200 Sum_probs=0.0
Q ss_pred ChHHHHHHHHHHHhccCCCChHHHHHHHHHHhhcCCCcHHHHHHHHH
Q 020150 179 SMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNE 225 (330)
Q Consensus 179 s~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~E 225 (330)
...|.||+|+-|...+=+ ..+.-.|=+-+|||+.+|..|-.+
T Consensus 1 ~~~~~l~~~f~~i~~~V~-----~~~Wk~laR~LGLse~~I~~i~~~ 42 (96)
T cd08315 1 DPQETLRRSFDHFIKEVP-----FDSWNRLMRQLGLSENEIDVAKAN 42 (96)
T ss_pred CcHhHHHHHHHHHHHHCC-----HHHHHHHHHHcCCCHHHHHHHHHH
No 132
>TIGR00694 thiM hydroxyethylthiazole kinase. This model represents the hydoxyethylthiazole kinase, ThiM, of a number of bacteria, and C-terminal domains of bifunctional thiamine biosynthesis proteins of Saccharomyces cerevisiae and Schizosaccharomyces pombe, in which the N-terminal domain corresponds to the bacterial thiamine-phosphate pyrophosphorylase (EC 2.5.1.3), ThiE.
Probab=20.88 E-value=3.5e+02 Score=24.66 Aligned_cols=63 Identities=17% Similarity=0.153 Sum_probs=42.5
Q ss_pred CChHHHHHHHHHHhh----cCCCcHHHHHHHHHHHHhhhhccCCeeeecccccchhhhhHHHHHHHHH
Q 020150 197 FNPDLVVNLIQLRKA----SMLDDSQVAEILNEISRRFVREKGPVVMNMSGYSEKGFKRKLAVQALFG 260 (330)
Q Consensus 197 F~~d~VaDLi~Lr~a----s~L~d~evaeiL~E~s~Ri~~~~G~vmmn~~G~Te~G~kRK~a~~aLF~ 260 (330)
-+|+.|.|++..-.| .|+-.++..+.+....+..-+..-|||+|--|..-.|... .....|+.
T Consensus 38 ~~~~e~~~~~~~~~al~ik~G~l~~~~~~~i~~~~~~~~~~~~pvVlDPV~~~~s~~r~-~~~~~Ll~ 104 (249)
T TIGR00694 38 EAEEEVAELAKIAGALVINIGTLDKESIEAMIAAGKSANELGVPVVLDPVGVGATKFRT-ETALELLS 104 (249)
T ss_pred CCHHHHHHHHHHcCceEEeCCCCCHHHHHHHHHHHHHHHhcCCCEEEcccccccchhHH-HHHHHHHh
Confidence 367788888755444 3544557778777777655444568999999999998744 33444554
No 133
>cd07922 CarBa CarBa is the A subunit of 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. CarBa is the A subunit of 2-aminophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-aminophenyl-2,3-diol. 2-aminophenol 1,6-dioxygenase is a key enzyme in the carbazole degradation pathway isolated from bacterial strains with carbazole degradation ability. The enzyme is a heterotetramer composed of two A and two B subunits. CarB belongs to the class III extradiol dioxygenase family, composed of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Although the enzyme was originally isolated as a meta-cleavage enzyme for 2'-aminobiphenyl-2,3-diol involved in carbazole degradation, the enzyme has also shown high specificity for 2,3-dihydroxybiphenyl.
Probab=20.51 E-value=87 Score=25.42 Aligned_cols=46 Identities=7% Similarity=0.005 Sum_probs=33.3
Q ss_pred HHHHHHHhccCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHHhh
Q 020150 185 RKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISRRF 230 (330)
Q Consensus 185 RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~Ri 230 (330)
.|.||=+-.+..+-..+.+|=-++=++.|||++|.+-+++---+.+
T Consensus 7 nrli~~L~~dp~~rerF~~DPea~~~~~gLt~eE~~aL~~~D~~~L 52 (81)
T cd07922 7 NRLIQELFKDPGLIERFQDDPSAVFEEYGLTPAERAALREGTFGAL 52 (81)
T ss_pred HHHHHHHhcCHHHHHHHHHCHHHHHHHcCCCHHHHHHHHccCHHHH
Confidence 5666665555557777778888888899999999987765443333
No 134
>cd08801 Death_UNC5D Death domain found in Uncoordinated-5D. Death Domain (DD) found in Uncoordinated-5D (UNC5D). UNC5D is part of the UNC-5 homolog family. It is a receptor for the secreted netrin-1 and plays a role in axonal guidance, angiogenesis, and apoptosis. UNC5 proteins are transmembrane proteins with an extracellular domain consisting of two immunoglobulin repeats, two thrombospondin type-I modules and an intracellular region containing a ZU-5 domain, UPA domain and a DD. In general, 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 CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=20.46 E-value=2.5e+02 Score=24.16 Aligned_cols=67 Identities=27% Similarity=0.349 Sum_probs=43.7
Q ss_pred HHhhHHHHHhcCCCCCCchHHHHHHHhhCCChHHHHHHHHHHHhccCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHHHH
Q 020150 149 VCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVAEILNEISR 228 (330)
Q Consensus 149 LvkSLdeyfp~gRda~~~~vLk~L~~KTGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~s~ 228 (330)
||.+||.=-.+|+| -|.|.+|-+.+. ||-|.-+- +=--+.+-||-.-|.-.+=+=.+++-+|.|++|
T Consensus 9 lC~~LD~p~~kg~D------WR~LA~kL~iDR------yl~yFatk-~SPT~viLdLWEa~~~~~g~L~~La~aleeiGr 75 (98)
T cd08801 9 ICATFDTPNAKGKD------WQMLAQKNSIDR------NLSYFATQ-SSPSAVILSLWEARHQHDGDLDSLACALEEIGR 75 (98)
T ss_pred HHHHcCCCCCCCcc------HHHHHHHhcchh------HHHHHhcC-CChHHHHHHHHHHhcCCCCCHHHHHHHHHHhCc
Confidence 68899877777766 899999999763 99997654 222334444444444444444556667777665
No 135
>PF11377 DUF3180: Protein of unknown function (DUF3180); InterPro: IPR021517 Some members in this family of proteins are annotated as membrane proteins however this cannot be confirmed. Currently there is no known function.
Probab=20.42 E-value=54 Score=28.26 Aligned_cols=38 Identities=16% Similarity=0.196 Sum_probs=23.2
Q ss_pred CchhHHHhhhHhhhhhhhhhhhhhhhhcCChhhhhhhhhc
Q 020150 105 KLPWILAVPLAYVGVSFVIAFVKTVKKFNSPKFKRKKLVN 144 (330)
Q Consensus 105 ~lPwllAlPLAylG~TFviA~vRtvrK~~SPraKRkR~Vn 144 (330)
++||...+.+..+++--+..-+ .+|++. .+..+++++|
T Consensus 28 ~~p~~~~~~l~~la~~~~~~a~-~vr~~~-~~~~~~~~~~ 65 (138)
T PF11377_consen 28 PIPWTAGVTLLVLAAVELWLAW-QVRRRI-EIGPGRRQLN 65 (138)
T ss_pred CCchHHHHHHHHHHHHHHHHHH-HHHHHH-hcCCCCCCcC
Confidence 5689999999988854444444 456665 3334444443
No 136
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=20.41 E-value=4e+02 Score=22.20 Aligned_cols=49 Identities=10% Similarity=0.132 Sum_probs=31.6
Q ss_pred HHHHHHhhCCChHHHHH------HHHHHHhccCCCChHHHHHHHHHHhhcCCCcHHH
Q 020150 169 LKGLVQKTGFSMEDVLR------KYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQV 219 (330)
Q Consensus 169 Lk~L~~KTGFs~~Ei~R------KYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~ev 219 (330)
++.+..+.|.+..|+-+ .||.-..|.+. +| -...|..|=.+++++-+++
T Consensus 10 l~~ll~~~Glsq~eLA~~~Gis~~~is~iE~g~~-~p-s~~~l~kIa~aL~v~~~~L 64 (120)
T PRK13890 10 VLRLLDERHMTKKELSERSGVSISFLSDLTTGKA-NP-SLKVMEAIADALETPLPLL 64 (120)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHcCCC-CC-CHHHHHHHHHHHCCCHHHH
Confidence 34444444555554443 48888888776 66 4577888888999965554
No 137
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=20.38 E-value=4.5e+02 Score=21.50 Aligned_cols=29 Identities=10% Similarity=0.315 Sum_probs=13.1
Q ss_pred CCChHHHHHHHHHH--hhcCCCcHHHHHHHH
Q 020150 196 PFNPDLVVNLIQLR--KASMLDDSQVAEILN 224 (330)
Q Consensus 196 ~F~~d~VaDLi~Lr--~as~L~d~evaeiL~ 224 (330)
-|+++.|..|-.++ +.+|++=+||+++|.
T Consensus 38 ~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~ 68 (127)
T cd04784 38 LYDEEHLERLLFIRRCRSLDMSLDEIRTLLQ 68 (127)
T ss_pred ecCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 34555554332221 234555555555554
No 138
>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=20.29 E-value=6.6e+02 Score=22.85 Aligned_cols=138 Identities=14% Similarity=0.178 Sum_probs=68.3
Q ss_pred hcchhhHHhhhhhhhhccccccccCCCCCCCCCchhHHHhhhHhh--hhhhhhhhhhhhhhc-CChhhhhhhhhcchh--
Q 020150 73 EELPWIQEKALDLVEFTGSVTQAIPGPRVGQSKLPWILAVPLAYV--GVSFVIAFVKTVKKF-NSPKFKRKKLVNKNA-- 147 (330)
Q Consensus 73 ~e~~wiqekaldlve~tG~vtQaIPGPRvg~s~lPwllAlPLAyl--G~TFviA~vRtvrK~-~SPraKRkR~VnKNa-- 147 (330)
.+.|=|++|+..+........+. ++-.+..++...++ |+-|.-+|+=+ ..+ ..++.+..-.+++.+
T Consensus 118 ~~~~~l~~k~~~~~~~~~~~~~~--------~~~~~~~~lv~~~~lEgi~f~s~F~~~-~~l~~~g~m~g~~~~i~~I~R 188 (288)
T cd01049 118 ETDPALKKKADWILRWYDNLDDN--------TKESFAERLVAFAILEGIFFYSGFAAI-FWLARRGKMPGLAEIIELISR 188 (288)
T ss_pred hcCHHHHHHHHHHHHHHHhhhhc--------hHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHCCCccchHHHhHHHHc
Confidence 45688999998888777765432 55556666654322 64443333322 222 111222222222221
Q ss_pred -------hHHhhHHHHHhcCCCCCCchHHHHHHHhhCCChHHHHHHHHHHHhccCCCChHHHHHHHHHHhhcCCCcHHHH
Q 020150 148 -------MVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALNEKPFNPDLVVNLIQLRKASMLDDSQVA 220 (330)
Q Consensus 148 -------~LvkSLdeyfp~gRda~~~~vLk~L~~KTGFs~~Ei~RKYirY~LnEr~F~~d~VaDLi~Lr~as~L~d~eva 220 (330)
+-+.-+..++.+..+ .....+++.....-=...++-.+|++|++.+. ..|++.+++.
T Consensus 189 DE~~H~~~~~~~~~~l~~~~~~-~~~~~~~~~v~~l~~~av~~E~~~~~~~~~~~---------------~~g~~~~~~~ 252 (288)
T cd01049 189 DESLHGDFACLLIRELLNENPE-LFTEEFKEEVYELIKEAVELEKEFARDLLPDG---------------ILGLNKEDMK 252 (288)
T ss_pred cHHHHHHHHHHHHHHHHHhCcc-ccchhHHHHHHHHHHHHHHHHHHHHHHhcCCC---------------CCCcCHHHHH
Confidence 222333333333221 11111121111111124455556666665443 6788999988
Q ss_pred HHHHHHHHhhhhccC
Q 020150 221 EILNEISRRFVREKG 235 (330)
Q Consensus 221 eiL~E~s~Ri~~~~G 235 (330)
.-+.-++.|....-|
T Consensus 253 ~yi~y~an~~l~~lG 267 (288)
T cd01049 253 QYIEYVANRRLENLG 267 (288)
T ss_pred HHHHHHHHHHHHHCC
Confidence 888888888776544
No 139
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=20.28 E-value=1.1e+02 Score=23.36 Aligned_cols=22 Identities=27% Similarity=0.407 Sum_probs=13.0
Q ss_pred HHHHHHHHhhcCCCcHHHHHHH
Q 020150 202 VVNLIQLRKASMLDDSQVAEIL 223 (330)
Q Consensus 202 VaDLi~Lr~as~L~d~evaeiL 223 (330)
+.-|.+++++.|||..|+|+.|
T Consensus 20 ~~~i~~~~~~~~ltQ~e~A~~l 41 (80)
T PF13744_consen 20 MAAIRELREERGLTQAELAERL 41 (80)
T ss_dssp HHHHHHHHHCCT--HHHHHHHH
T ss_pred HHHHHHHHHHcCCCHHHHHHHH
Confidence 3446667777777777777665
No 140
>PRK00236 xerC site-specific tyrosine recombinase XerC; Reviewed
Probab=20.11 E-value=5.4e+02 Score=21.75 Aligned_cols=30 Identities=13% Similarity=0.234 Sum_probs=18.5
Q ss_pred CChHHHHHHHHHHhhcCCCcHHHHHHHHHH
Q 020150 197 FNPDLVVNLIQLRKASMLDDSQVAEILNEI 226 (330)
Q Consensus 197 F~~d~VaDLi~Lr~as~L~d~evaeiL~E~ 226 (330)
++++.+.+.+.-...-|++..-+...+.-+
T Consensus 53 i~~~~i~~~~~~~~~~~~~~~t~~~~~~~l 82 (297)
T PRK00236 53 LDAADLRSFLARRRRQGLSARSLARRLSAL 82 (297)
T ss_pred CCHHHHHHHHHHHHhcccChhHHHHHHHHH
Confidence 566667776665555566666666555543
No 141
>PTZ00072 40S ribosomal protein S13; Provisional
Probab=20.08 E-value=1.2e+02 Score=27.53 Aligned_cols=31 Identities=23% Similarity=0.160 Sum_probs=25.9
Q ss_pred CCChHHHHHHHHHHhhcCCCcHHHHHHHHHH
Q 020150 196 PFNPDLVVNLIQLRKASMLDDSQVAEILNEI 226 (330)
Q Consensus 196 ~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~ 226 (330)
.++++.|.|+|-==.--|++.+||+-+|++.
T Consensus 24 ~~~~eeVe~~I~klaKkG~~pSqIG~iLRD~ 54 (148)
T PTZ00072 24 KLSSSEVEDQICKLAKKGLTPSQIGVILRDS 54 (148)
T ss_pred cCCHHHHHHHHHHHHHCCCCHhHhhhhhhhc
Confidence 4688888888866666799999999999975
No 142
>PRK14038 ADP-dependent glucokinase; Provisional
Probab=20.05 E-value=1.4e+02 Score=30.94 Aligned_cols=102 Identities=16% Similarity=0.244 Sum_probs=63.1
Q ss_pred hcCChhhhh----hhhhcchhhHHhhHHHHHhcCCCCCCchHHHHHHHhhCCChHHHHHHHHHHHhc--cC--------C
Q 020150 131 KFNSPKFKR----KKLVNKNAMVCKTIDELFQKGGDAVNPPALKGLVQKTGFSMEDVLRKYIRYALN--EK--------P 196 (330)
Q Consensus 131 K~~SPraKR----kR~VnKNa~LvkSLdeyfp~gRda~~~~vLk~L~~KTGFs~~Ei~RKYirY~Ln--Er--------~ 196 (330)
.|++||+-| .+..|-..++.+.+.++|+.-....+--+|-|++.=.+++..+.|++=.+.+.. ++ +
T Consensus 188 ~~~aPRaNRfI~s~D~~N~~l~~~eef~~~l~ei~~~~Dl~vlSG~q~l~~~~~~~~l~~~~~~l~~l~~~~i~iH~EfA 267 (453)
T PRK14038 188 DFEAPRENRFIGAADDYNPNLYIRPEFRERFEEIAKKAELAIISGLQALTEENYREPFETVREHLKVLNERGIPAHLEFA 267 (453)
T ss_pred eeEcCCCceEEEecCCCCcceeecHHHHHHHHhhccCCCEEEEEchhhhccccHHHHHHHHHHHHHhcCcCCceEEEEee
Confidence 799999988 466777777888888888875445555566666655566666666655544433 22 2
Q ss_pred CC--hHHHHHHHHHHhh---cCCCcHHHHHHHH-----HHHHhhhh
Q 020150 197 FN--PDLVVNLIQLRKA---SMLDDSQVAEILN-----EISRRFVR 232 (330)
Q Consensus 197 F~--~d~VaDLi~Lr~a---s~L~d~evaeiL~-----E~s~Ri~~ 232 (330)
|. .+...+++.+=.- .||+..|++-+++ +.|+||++
T Consensus 268 s~~d~~~r~~i~~ilp~vDSlGmNE~ELa~ll~~lg~~~l~~~i~~ 313 (453)
T PRK14038 268 FTPDETVREEILGLLGKFYSVGLNEVELASIMEVMGEKTLAEKLLA 313 (453)
T ss_pred ccchHHHHHHHHhhCccccccccCHHHHHHHHHHhccchhhhhhhh
Confidence 22 2222333322112 7888889999887 44555544
No 143
>PRK08561 rps15p 30S ribosomal protein S15P; Reviewed
Probab=20.02 E-value=1.5e+02 Score=26.99 Aligned_cols=31 Identities=16% Similarity=0.243 Sum_probs=26.3
Q ss_pred CCChHHHHHHHHHHhhcCCCcHHHHHHHHHH
Q 020150 196 PFNPDLVVNLIQLRKASMLDDSQVAEILNEI 226 (330)
Q Consensus 196 ~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~ 226 (330)
.+++|.|.++|-==.--|++.+||+-+|++.
T Consensus 27 ~~~~eeve~~I~~lakkG~~pSqIG~~LRD~ 57 (151)
T PRK08561 27 DYSPEEIEELVVELAKQGYSPSMIGIILRDQ 57 (151)
T ss_pred cCCHHHHHHHHHHHHHCCCCHHHhhhhHhhc
Confidence 3788999988876666899999999999985
No 144
>PRK00283 xerD site-specific tyrosine recombinase XerD; Reviewed
Probab=20.01 E-value=5.6e+02 Score=21.96 Aligned_cols=44 Identities=9% Similarity=0.039 Sum_probs=28.3
Q ss_pred HHHHHHHHHhc----cCCCChHHHHHHHHHHhhcCCCcHHHHHHHHHH
Q 020150 183 VLRKYIRYALN----EKPFNPDLVVNLIQLRKASMLDDSQVAEILNEI 226 (330)
Q Consensus 183 i~RKYirY~Ln----Er~F~~d~VaDLi~Lr~as~L~d~evaeiL~E~ 226 (330)
.+++|++|+-. =..++++.|.+.+.-...-+++.+.+...+.-+
T Consensus 33 ~~~~~~~~~~~~~~~~~~l~~~~i~~~~~~~~~~~~~~~t~~~~~~~l 80 (299)
T PRK00283 33 DLELFAEWLAARGLSLAEATRDDLQAFLAELAEGGYKATSSARRLSAL 80 (299)
T ss_pred HHHHHHHHHHhcCCChHHCCHHHHHHHHHHHHhCCCCHHHHHHHHHHH
Confidence 45556665432 245788888888877666677777776655443
Done!