Query 024891
Match_columns 261
No_of_seqs 254 out of 1119
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 08:13:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024891.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024891hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01476 LysM: LysM domain; I 99.3 9.2E-13 2E-17 88.2 4.3 43 119-162 1-44 (44)
2 PRK06347 autolysin; Reviewed 99.3 1.7E-11 3.8E-16 123.5 9.7 109 44-162 482-592 (592)
3 PRK10783 mltD membrane-bound l 99.2 4.8E-11 1E-15 117.1 8.4 104 43-165 345-450 (456)
4 PRK06347 autolysin; Reviewed 99.1 2.6E-10 5.5E-15 115.1 10.1 114 43-164 407-526 (592)
5 PRK14125 cell division suppres 99.1 2.2E-10 4.8E-15 91.9 6.6 52 115-167 35-94 (103)
6 TIGR02899 spore_safA spore coa 99.0 5.3E-10 1.1E-14 73.5 5.1 43 121-163 1-44 (44)
7 cd00118 LysM Lysin domain, fou 99.0 1.3E-09 2.9E-14 69.7 5.7 45 118-162 2-46 (46)
8 PF12937 F-box-like: F-box-lik 98.9 1.4E-09 3.1E-14 74.2 3.2 44 44-88 2-45 (47)
9 TIGR02907 spore_VI_D stage VI 98.9 2.7E-09 5.9E-14 100.8 6.1 47 115-162 292-338 (338)
10 PRK10871 nlpD lipoprotein NlpD 98.8 4.8E-09 1E-13 99.0 5.7 48 118-165 62-109 (319)
11 COG1388 LytE FOG: LysM repeat 98.7 3.4E-08 7.4E-13 79.6 6.8 48 116-164 66-113 (124)
12 smart00257 LysM Lysin motif. 98.6 7.8E-08 1.7E-12 60.6 5.4 43 119-161 2-44 (44)
13 PRK13914 invasion associated s 98.6 5.9E-08 1.3E-12 95.8 6.6 47 117-164 28-74 (481)
14 smart00256 FBOX A Receptor for 98.6 4.6E-08 9.9E-13 63.5 3.2 40 46-86 1-40 (41)
15 PRK11198 LysM domain/BON super 98.5 2.5E-07 5.3E-12 78.2 7.1 47 116-162 95-146 (147)
16 PRK13914 invasion associated s 98.5 2.6E-07 5.6E-12 91.3 7.4 49 115-164 198-246 (481)
17 PF00646 F-box: F-box domain; 98.5 7.8E-08 1.7E-12 65.2 2.5 45 43-88 3-47 (48)
18 PRK10783 mltD membrane-bound l 98.3 1.2E-06 2.6E-11 86.3 6.2 48 116-164 343-390 (456)
19 KOG2997 F-box protein FBX9 [Ge 98.1 1.2E-06 2.6E-11 82.9 1.4 60 38-98 102-166 (366)
20 KOG2850 Predicted peptidoglyca 97.9 3.3E-06 7.2E-11 74.4 0.6 138 116-253 9-185 (186)
21 PF14555 UBA_4: UBA-like domai 97.7 5.3E-05 1.2E-09 51.3 4.1 35 217-251 5-39 (43)
22 PF04225 OapA: Opacity-associa 97.0 0.00077 1.7E-08 52.2 3.6 49 116-164 2-54 (85)
23 KOG2850 Predicted peptidoglyca 96.9 0.0005 1.1E-08 60.8 2.1 101 71-173 1-104 (186)
24 TIGR03505 FimV_core FimV N-ter 96.8 0.0015 3.3E-08 49.6 4.1 40 125-164 1-52 (74)
25 COG1652 XkdP Uncharacterized p 96.6 0.00071 1.5E-08 61.8 1.0 48 117-164 211-264 (269)
26 PRK10190 L,D-transpeptidase; P 96.6 0.0058 1.3E-07 58.0 6.7 49 115-163 36-86 (310)
27 PRK10260 L,D-transpeptidase; P 96.5 0.0064 1.4E-07 57.5 6.5 49 115-163 39-89 (306)
28 COG3858 Predicted glycosyl hyd 96.1 0.0064 1.4E-07 59.6 4.6 63 117-179 50-113 (423)
29 KOG2120 SCF ubiquitin ligase, 96.0 0.0053 1.2E-07 58.8 3.3 43 43-86 98-140 (419)
30 COG3858 Predicted glycosyl hyd 96.0 0.0026 5.7E-08 62.2 1.3 48 116-164 1-48 (423)
31 PLN03215 ascorbic acid mannose 95.9 0.005 1.1E-07 59.7 2.5 37 43-80 4-41 (373)
32 PF05489 Phage_tail_X: Phage T 94.6 0.078 1.7E-06 38.7 4.8 47 117-164 2-54 (60)
33 PRK11649 putative peptidase; P 93.9 0.099 2.1E-06 51.7 5.5 50 115-164 94-144 (439)
34 COG1388 LytE FOG: LysM repeat 93.1 0.064 1.4E-06 43.0 2.3 35 130-164 1-36 (124)
35 PF03943 TAP_C: TAP C-terminal 90.8 0.22 4.8E-06 35.1 2.5 35 217-251 5-39 (51)
36 COG0739 NlpD Membrane proteins 87.5 0.94 2E-05 40.3 4.7 49 117-165 2-50 (277)
37 smart00804 TAP_C C-terminal do 85.4 2.5 5.4E-05 31.2 5.2 37 214-250 14-50 (63)
38 KOG4341 F-box protein containi 84.1 0.72 1.6E-05 46.0 2.4 43 43-86 72-114 (483)
39 KOG4408 Putative Mg2+ and Co2+ 81.7 1.1 2.5E-05 43.3 2.7 139 43-189 8-169 (386)
40 COG3170 FimV Tfp pilus assembl 78.9 1.6 3.5E-05 45.8 3.0 48 117-164 189-248 (755)
41 KOG0274 Cdc4 and related F-box 77.3 1.1 2.5E-05 45.4 1.3 46 43-89 108-153 (537)
42 COG4784 Putative Zn-dependent 75.0 4 8.6E-05 40.1 4.2 44 118-161 430-476 (479)
43 PF00627 UBA: UBA/TS-N domain; 73.6 5.4 0.00012 25.7 3.4 25 223-247 12-36 (37)
44 COG3061 OapA Cell envelope opa 73.1 10 0.00022 34.9 6.1 51 115-165 158-212 (242)
45 PF13518 HTH_28: Helix-turn-he 69.4 5.3 0.00011 26.7 2.7 27 121-147 9-35 (52)
46 PF01527 HTH_Tnp_1: Transposas 66.8 3 6.5E-05 30.2 1.1 25 121-145 20-44 (76)
47 KOG0281 Beta-TrCP (transducin 66.6 5.1 0.00011 39.4 2.9 41 49-89 84-124 (499)
48 PF02796 HTH_7: Helix-turn-hel 66.5 6.4 0.00014 26.5 2.6 24 121-144 18-41 (45)
49 smart00165 UBA Ubiquitin assoc 64.4 12 0.00027 23.6 3.6 26 222-247 10-35 (37)
50 PF01476 LysM: LysM domain; I 60.0 5.1 0.00011 26.0 1.2 27 48-81 5-34 (44)
51 KOG3926 F-box proteins [Amino 59.3 7.3 0.00016 37.0 2.5 60 32-93 191-252 (332)
52 KOG3763 mRNA export factor TAP 57.9 25 0.00054 36.4 6.1 32 219-250 542-573 (585)
53 TIGR00264 alpha-NAC-related pr 55.5 22 0.00048 29.5 4.4 35 215-249 81-115 (116)
54 PF05225 HTH_psq: helix-turn-h 54.1 13 0.00029 25.2 2.5 24 121-144 12-36 (45)
55 PRK06369 nac nascent polypepti 52.9 27 0.00058 28.9 4.5 35 215-249 79-113 (115)
56 COG4254 Uncharacterized protei 52.7 11 0.00025 36.0 2.6 49 117-165 6-57 (339)
57 COG2963 Transposase and inacti 52.6 14 0.0003 29.2 2.7 27 118-144 18-45 (116)
58 PF02845 CUE: CUE domain; Int 51.1 51 0.0011 21.6 4.9 31 220-250 10-40 (42)
59 cd00194 UBA Ubiquitin Associat 50.5 31 0.00067 21.8 3.7 26 223-248 11-36 (38)
60 PF13384 HTH_23: Homeodomain-l 48.8 21 0.00045 23.8 2.8 27 121-147 14-40 (50)
61 smart00546 CUE Domain that may 46.3 56 0.0012 21.5 4.5 31 221-251 12-42 (43)
62 PRK05441 murQ N-acetylmuramic 45.8 35 0.00077 32.0 4.8 45 208-252 231-275 (299)
63 PF08765 Mor: Mor transcriptio 45.5 21 0.00045 28.4 2.8 21 124-144 72-92 (108)
64 PF14148 YhdB: YhdB-like prote 45.3 25 0.00053 27.0 2.9 33 225-257 4-49 (77)
65 PF04545 Sigma70_r4: Sigma-70, 45.2 30 0.00066 23.2 3.2 23 122-144 18-40 (50)
66 PRK09413 IS2 repressor TnpA; R 45.1 25 0.00053 28.4 3.2 29 117-145 22-50 (121)
67 PHA00675 hypothetical protein 44.4 25 0.00054 27.2 2.9 29 118-146 32-61 (78)
68 cd05007 SIS_Etherase N-acetylm 43.4 20 0.00044 32.7 2.7 38 208-245 218-255 (257)
69 PF04218 CENP-B_N: CENP-B N-te 40.9 14 0.0003 25.9 1.0 25 120-144 18-42 (53)
70 PF00392 GntR: Bacterial regul 40.0 25 0.00055 24.8 2.2 25 121-145 18-45 (64)
71 cd00569 HTH_Hin_like Helix-tur 39.7 46 0.00099 18.7 3.1 24 121-144 18-41 (42)
72 PF13936 HTH_38: Helix-turn-he 36.8 42 0.00092 22.4 2.8 24 121-144 17-40 (44)
73 PF11268 DUF3071: Protein of u 36.5 29 0.00063 30.4 2.4 30 116-145 61-90 (170)
74 PF01371 Trp_repressor: Trp re 34.1 35 0.00077 26.7 2.4 27 121-147 46-72 (87)
75 KOG2502 Tub family proteins [G 33.8 42 0.00091 32.8 3.3 45 35-80 36-89 (355)
76 smart00345 HTH_GNTR helix_turn 33.5 53 0.0011 21.8 2.9 23 126-148 22-45 (60)
77 smart00421 HTH_LUXR helix_turn 33.2 60 0.0013 21.0 3.2 25 121-145 15-39 (58)
78 COG1308 EGD2 Transcription fac 32.7 76 0.0016 26.6 4.2 33 217-249 89-121 (122)
79 TIGR00274 N-acetylmuramic acid 32.0 75 0.0016 29.8 4.6 44 207-250 225-268 (291)
80 PF12471 GTP_CH_N: GTP cyclohy 31.8 31 0.00068 30.9 1.9 27 118-144 164-190 (194)
81 PRK12570 N-acetylmuramic acid- 31.8 70 0.0015 30.0 4.4 45 206-250 225-269 (296)
82 PRK07993 DNA polymerase III su 31.8 3.1E+02 0.0067 26.1 8.8 37 219-256 176-212 (334)
83 TIGR01764 excise DNA binding d 31.7 98 0.0021 19.6 3.9 20 126-145 3-22 (49)
84 PF08220 HTH_DeoR: DeoR-like h 31.5 47 0.001 23.3 2.5 20 125-144 15-34 (57)
85 PF13808 DDE_Tnp_1_assoc: DDE_ 31.0 51 0.0011 25.4 2.8 23 45-67 62-84 (90)
86 PF00376 MerR: MerR family reg 30.5 58 0.0012 21.3 2.6 21 126-146 1-21 (38)
87 PHA01976 helix-turn-helix prot 29.8 36 0.00079 23.8 1.7 20 123-142 43-62 (67)
88 PF13542 HTH_Tnp_ISL3: Helix-t 29.8 63 0.0014 21.5 2.8 28 117-144 20-47 (52)
89 PF04255 DUF433: Protein of un 29.7 49 0.0011 23.3 2.3 24 121-144 28-52 (56)
90 PRK12845 3-ketosteroid-delta-1 29.4 44 0.00096 34.0 2.8 26 121-146 421-450 (564)
91 KOG1470 Phosphatidylinositol t 29.1 84 0.0018 30.4 4.4 35 225-259 47-81 (324)
92 cd04762 HTH_MerR-trunc Helix-T 28.9 69 0.0015 20.2 2.8 20 126-145 2-21 (49)
93 cd01104 HTH_MlrA-CarA Helix-Tu 28.5 63 0.0014 22.6 2.7 20 126-145 2-21 (68)
94 PF01381 HTH_3: Helix-turn-hel 28.5 30 0.00065 23.2 1.0 19 123-141 37-55 (55)
95 PRK12837 3-ketosteroid-delta-1 28.4 49 0.0011 32.9 2.9 27 121-147 372-402 (513)
96 PF10668 Phage_terminase: Phag 28.2 65 0.0014 23.6 2.8 23 124-146 22-44 (60)
97 PF04760 IF2_N: Translation in 28.1 42 0.00091 23.1 1.7 19 126-144 5-23 (54)
98 PF13693 HTH_35: Winged helix- 27.9 60 0.0013 25.0 2.6 23 122-144 13-35 (78)
99 PF01710 HTH_Tnp_IS630: Transp 27.7 70 0.0015 25.7 3.2 24 122-145 69-92 (119)
100 TIGR02531 yecD_yerC TrpR-relat 27.3 59 0.0013 25.4 2.6 27 120-146 46-72 (88)
101 COG4387 Mu-like prophage prote 26.8 76 0.0017 26.9 3.3 30 227-257 70-99 (139)
102 PF12637 TSCPD: TSCPD domain; 26.7 59 0.0013 25.4 2.5 19 126-144 45-63 (95)
103 PF04921 XAP5: XAP5, circadian 26.6 60 0.0013 30.0 2.9 46 118-163 114-160 (239)
104 TIGR02937 sigma70-ECF RNA poly 26.6 73 0.0016 24.4 3.0 23 122-144 124-146 (158)
105 COG3721 HugX Putative heme iro 26.4 73 0.0016 28.0 3.2 24 121-144 24-47 (176)
106 PF13411 MerR_1: MerR HTH fami 26.3 72 0.0016 22.3 2.7 21 126-146 2-22 (69)
107 cd04761 HTH_MerR-SF Helix-Turn 25.1 86 0.0019 20.3 2.8 20 126-145 2-21 (49)
108 smart00422 HTH_MERR helix_turn 24.9 81 0.0018 22.0 2.8 20 126-145 2-21 (70)
109 cd06170 LuxR_C_like C-terminal 23.8 1.1E+02 0.0024 19.9 3.2 25 121-145 12-36 (57)
110 PRK07843 3-ketosteroid-delta-1 23.4 68 0.0015 32.4 2.9 27 121-147 413-443 (557)
111 PRK12839 hypothetical protein; 23.3 66 0.0014 32.8 2.8 27 121-147 424-454 (572)
112 PF08299 Bac_DnaA_C: Bacterial 23.1 72 0.0015 23.4 2.2 22 125-146 4-25 (70)
113 PF13443 HTH_26: Cro/C1-type H 22.7 35 0.00076 23.6 0.5 20 124-143 40-59 (63)
114 COG5484 Uncharacterized conser 22.1 74 0.0016 30.0 2.6 23 124-146 19-41 (279)
115 cd04767 HTH_HspR-like_MBC Heli 22.1 2.2E+02 0.0048 23.5 5.2 21 126-146 3-23 (120)
116 PF03540 TFIID_30kDa: Transcri 21.8 1.6E+02 0.0035 20.9 3.7 28 225-252 3-39 (51)
117 PF13613 HTH_Tnp_4: Helix-turn 21.7 72 0.0016 22.0 1.9 25 120-144 15-39 (53)
118 COG1004 Ugd Predicted UDP-gluc 21.3 1.5E+02 0.0033 29.6 4.7 83 127-224 223-307 (414)
119 smart00760 Bac_DnaA_C Bacteria 20.7 71 0.0015 22.5 1.7 22 125-146 4-25 (60)
No 1
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=99.35 E-value=9.2e-13 Score=88.22 Aligned_cols=43 Identities=35% Similarity=0.569 Sum_probs=36.9
Q ss_pred EEccCCCcHHHHHHHhCCCHHHHHHHh-CCCCCcCccCCCEEEec
Q 024891 119 HRLARGDTVASLAVKYSVQVMDIKRLN-NMMSDHGIYSRERLLIP 162 (261)
Q Consensus 119 h~V~~GDTL~~IA~rYgvsv~~I~~~N-~L~s~~~i~~gq~L~IP 162 (261)
|+|++||||++||.+||+++++|+++| ++..+. |++||+|.||
T Consensus 1 y~V~~gDtl~~IA~~~~~~~~~l~~~N~~~~~~~-l~~G~~l~iP 44 (44)
T PF01476_consen 1 YTVQPGDTLWSIAKRYGISVDELMELNPNIDSDN-LQPGQKLCIP 44 (44)
T ss_dssp EEE-TT--HHHHHHHTTS-HHHHHHHCCTTHGGC-GGTTEEEEEC
T ss_pred CEECcCCcHHHHHhhhhhhHhHHHHhcCCCCccc-CCCCCEEEeC
Confidence 899999999999999999999999999 887765 9999999998
No 2
>PRK06347 autolysin; Reviewed
Probab=99.26 E-value=1.7e-11 Score=123.49 Aligned_cols=109 Identities=18% Similarity=0.226 Sum_probs=77.9
Q ss_pred cCCCcccHHHHHHhc--CCHHHHHHhhhhhhhhhhhccchhhHHHhhcCccccccccccCCCCCccccCCCCcceEEEEc
Q 024891 44 SALACPDTLRLILSN--LSVTDLARASCVCRAWSSVASDNNMIVLAFMAPWKLKEVVGMPLNGSFWRDNGIGKFAISHRL 121 (261)
Q Consensus 44 ~~lp~~D~L~~Il~r--L~p~~Lara~cVCk~W~~~~~~~~l~~aAF~aPWkl~~vvgsP~~~s~~~~~~~~~~~~~h~V 121 (261)
-.+..||+|+.|.++ +++.+| +.||.+.++....++.+..|-..... ..+..... ...+.......|+|
T Consensus 482 YtVk~GDTL~sIAkkygVSv~~L-------~~~N~l~s~~L~~GQ~L~Ip~~~~~s-~~~t~~~s-~~~~~~~~~~~Y~V 552 (592)
T PRK06347 482 YTVAKGDSLWRIANNNKVTIANL-------KSWNNLKSDFIYPGQKLKVSAGSTTN-NTNTAKPS-TNKPSNSTVKTYTV 552 (592)
T ss_pred eeecCCCCHHHHHHHHCCCHHHH-------HHhcCCCcccccCCcEEEEecCcccc-cccccCCc-cCCccCccceeeec
Confidence 456669999999995 589999 89999877665556665554321110 00000000 01111123568999
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHHhCCCCCcCccCCCEEEec
Q 024891 122 ARGDTVASLAVKYSVQVMDIKRLNNMMSDHGIYSRERLLIP 162 (261)
Q Consensus 122 ~~GDTL~~IA~rYgvsv~~I~~~N~L~s~~~i~~gq~L~IP 162 (261)
++||||++||+||||++++|+++|+|.+ +.|++||+|.|+
T Consensus 553 k~GDTL~sIA~KygvSv~~L~~~N~L~~-~~L~~GQ~L~I~ 592 (592)
T PRK06347 553 KKGDSLWAISRQYKTTVDNIKAWNKLTS-NMIHVGQKLTIK 592 (592)
T ss_pred CCCCcHHHHHHHhCCCHHHHHHhcCCCc-ccCCCCCEEecC
Confidence 9999999999999999999999999986 579999999986
No 3
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional
Probab=99.19 E-value=4.8e-11 Score=117.07 Aligned_cols=104 Identities=19% Similarity=0.272 Sum_probs=75.1
Q ss_pred ccCCCcccHHHHHHhc--CCHHHHHHhhhhhhhhhhhccchhhHHHhhcCccccccccccCCCCCccccCCCCcceEEEE
Q 024891 43 FSALACPDTLRLILSN--LSVTDLARASCVCRAWSSVASDNNMIVLAFMAPWKLKEVVGMPLNGSFWRDNGIGKFAISHR 120 (261)
Q Consensus 43 ~~~lp~~D~L~~Il~r--L~p~~Lara~cVCk~W~~~~~~~~l~~aAF~aPWkl~~vvgsP~~~s~~~~~~~~~~~~~h~ 120 (261)
.-.+.+||+|+.|+++ +++.+| +.||.+.++....++.+..|-. .... ........+.|+
T Consensus 345 ~y~Vk~GDTL~sIA~r~gvs~~~L-------~~~N~l~~~~L~~Gq~L~Ip~~--------~~~~---~~~~~~~~~~Y~ 406 (456)
T PRK10783 345 SYKVRSGDTLSGIASRLNVSTKDL-------QQWNNLRGSKLKVGQTLTIGAG--------SSAQ---RLANNSDSITYR 406 (456)
T ss_pred EEEECCCCcHHHHHHHHCcCHHHH-------HHHcCCCcccCCCCCEEEecCC--------cccc---cccccccceeEE
Confidence 3455669999999995 578888 8899986633333333333211 0000 001112346899
Q ss_pred ccCCCcHHHHHHHhCCCHHHHHHHhCCCCCcCccCCCEEEecCCC
Q 024891 121 LARGDTVASLAVKYSVQVMDIKRLNNMMSDHGIYSRERLLIPISS 165 (261)
Q Consensus 121 V~~GDTL~~IA~rYgvsv~~I~~~N~L~s~~~i~~gq~L~IP~~~ 165 (261)
|++||||++||+||||++++|+++|++.++ .|++||+|.|++..
T Consensus 407 Vr~GDTL~sIA~kygVtv~~L~~~N~l~~~-~L~pGq~L~l~v~~ 450 (456)
T PRK10783 407 VRKGDSLSSIAKRHGVNIKDVMRWNSDTAK-NLQPGDKLTLFVKN 450 (456)
T ss_pred eCCCCCHHHHHHHhCCCHHHHHHhcCCCCC-cCCCCCEEEEecCC
Confidence 999999999999999999999999998776 89999999999864
No 4
>PRK06347 autolysin; Reviewed
Probab=99.11 E-value=2.6e-10 Score=115.15 Aligned_cols=114 Identities=19% Similarity=0.250 Sum_probs=79.0
Q ss_pred ccCCCcccHHHHHHhc--CCHHHHHHhhhhhhhhhhhccchhhHHHhhcCcccccc--ccccCCCCC--ccccCCCCcce
Q 024891 43 FSALACPDTLRLILSN--LSVTDLARASCVCRAWSSVASDNNMIVLAFMAPWKLKE--VVGMPLNGS--FWRDNGIGKFA 116 (261)
Q Consensus 43 ~~~lp~~D~L~~Il~r--L~p~~Lara~cVCk~W~~~~~~~~l~~aAF~aPWkl~~--vvgsP~~~s--~~~~~~~~~~~ 116 (261)
+-.+..||+|+.|.++ +++.+| +.||.+.++....++.+..|-.... ....|.... ...........
T Consensus 407 ~ytVk~GDTL~sIA~kygVSv~~L-------~~~N~l~s~~L~~Gq~L~IP~~~~~~~~t~~~s~~~~~~k~~s~~~~~~ 479 (592)
T PRK06347 407 VYTVVKGDSLWRIANNNKVTIANL-------KSWNNLKSDFIYPGQKLKVSAGSTSNTNTSKPSTNTNTSKPSTNTNTNA 479 (592)
T ss_pred eEEecCCCCHHHHHHHhCCCHHHH-------HHHhCCCcceeccCcEEEEecCCcccccccccccccccccccccccccc
Confidence 5567779999999994 689999 8999887665444555555432110 000010000 00000111234
Q ss_pred EEEEccCCCcHHHHHHHhCCCHHHHHHHhCCCCCcCccCCCEEEecCC
Q 024891 117 ISHRLARGDTVASLAVKYSVQVMDIKRLNNMMSDHGIYSRERLLIPIS 164 (261)
Q Consensus 117 ~~h~V~~GDTL~~IA~rYgvsv~~I~~~N~L~s~~~i~~gq~L~IP~~ 164 (261)
..|+|++||||++||++|||++++|+++|+|.+ +.|++||+|.||..
T Consensus 480 ~~YtVk~GDTL~sIAkkygVSv~~L~~~N~l~s-~~L~~GQ~L~Ip~~ 526 (592)
T PRK06347 480 KVYTVAKGDSLWRIANNNKVTIANLKSWNNLKS-DFIYPGQKLKVSAG 526 (592)
T ss_pred eeeeecCCCCHHHHHHHHCCCHHHHHHhcCCCc-ccccCCcEEEEecC
Confidence 579999999999999999999999999999986 57999999999975
No 5
>PRK14125 cell division suppressor protein YneA; Provisional
Probab=99.09 E-value=2.2e-10 Score=91.87 Aligned_cols=52 Identities=25% Similarity=0.395 Sum_probs=45.6
Q ss_pred ceEEEEccCCCcHHHHHHHhCCC--------HHHHHHHhCCCCCcCccCCCEEEecCCCCc
Q 024891 115 FAISHRLARGDTVASLAVKYSVQ--------VMDIKRLNNMMSDHGIYSRERLLIPISSPE 167 (261)
Q Consensus 115 ~~~~h~V~~GDTL~~IA~rYgvs--------v~~I~~~N~L~s~~~i~~gq~L~IP~~~~~ 167 (261)
.+..|+|++|||||+||++|+++ ++.|++.|++.++ .|++||+|+||.....
T Consensus 35 ~~~~~tV~~GDTLW~IA~~y~~~~~l~~~~~v~~I~~~N~l~~~-~I~~Gq~L~IP~~~~~ 94 (103)
T PRK14125 35 QYVEITVQEGDTLWALADQYAGKHHMAKNEFIEWVEDVNNLPSG-HIKAGDKLVIPVLKSK 94 (103)
T ss_pred CcEEEEECCCCCHHHHHHHhCCCcCCCHHHHHHHHHHhcCCCCC-cCCCCCEEEEecCCCC
Confidence 46789999999999999999876 6889999999875 6999999999986543
No 6
>TIGR02899 spore_safA spore coat assembly protein SafA. in which one of which is found in most examples of endospore-forming bacteria. Lysin motifs are repeated in many proteins.
Probab=99.02 E-value=5.3e-10 Score=73.51 Aligned_cols=43 Identities=28% Similarity=0.467 Sum_probs=38.6
Q ss_pred ccCCCcHHHHHHHhCCCHHHHHHHhC-CCCCcCccCCCEEEecC
Q 024891 121 LARGDTVASLAVKYSVQVMDIKRLNN-MMSDHGIYSRERLLIPI 163 (261)
Q Consensus 121 V~~GDTL~~IA~rYgvsv~~I~~~N~-L~s~~~i~~gq~L~IP~ 163 (261)
|++||||++||.+||+++++|+++|. +...+.+++|++|+||.
T Consensus 1 v~~gdtl~~IA~~~~~~~~~l~~~N~~~~~~~~~~~g~~l~ip~ 44 (44)
T TIGR02899 1 VQKGDTLWKIAKKYGVDFDELIQANPQLSNPNLIYPGMKIKIPS 44 (44)
T ss_pred CCCCCCHHHHHHHHCcCHHHHHHHhhcCCCCCCcCCCCEEecCC
Confidence 68999999999999999999999997 54556799999999983
No 7
>cd00118 LysM Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function.
Probab=98.98 E-value=1.3e-09 Score=69.71 Aligned_cols=45 Identities=27% Similarity=0.554 Sum_probs=42.1
Q ss_pred EEEccCCCcHHHHHHHhCCCHHHHHHHhCCCCCcCccCCCEEEec
Q 024891 118 SHRLARGDTVASLAVKYSVQVMDIKRLNNMMSDHGIYSRERLLIP 162 (261)
Q Consensus 118 ~h~V~~GDTL~~IA~rYgvsv~~I~~~N~L~s~~~i~~gq~L~IP 162 (261)
.|+|++|||+++||.+||++..+|+++|.+.....+.+|+.|.||
T Consensus 2 ~~~v~~gdt~~~ia~~~~~~~~~~~~~N~~~~~~~~~~g~~l~ip 46 (46)
T cd00118 2 TYTVKKGDTLSSIAQRYGISVEELLKLNGLSDPDNLQVGQKLKIP 46 (46)
T ss_pred EEEECCCCCHHHHHHHHCcCHHHHHHHcCCCCccccCCCCEEecC
Confidence 589999999999999999999999999998666789999999998
No 8
>PF12937 F-box-like: F-box-like; PDB: 1P22_A 2OVP_B 2OVR_B 2OVQ_B 1FS1_A 1FS2_C 1FQV_I 1LDK_E 2AST_B 2ASS_B.
Probab=98.88 E-value=1.4e-09 Score=74.20 Aligned_cols=44 Identities=39% Similarity=0.549 Sum_probs=39.4
Q ss_pred cCCCcccHHHHHHhcCCHHHHHHhhhhhhhhhhhccchhhHHHhh
Q 024891 44 SALACPDTLRLILSNLSVTDLARASCVCRAWSSVASDNNMIVLAF 88 (261)
Q Consensus 44 ~~lp~~D~L~~Il~rL~p~~Lara~cVCk~W~~~~~~~~l~~aAF 88 (261)
..|| .|+|.+||+.|++.||+++++|||.|+.++.++.+|+..+
T Consensus 2 ~~LP-~Eil~~If~~L~~~dl~~~~~vcr~w~~~~~~~~lW~~~~ 45 (47)
T PF12937_consen 2 SSLP-DEILLEIFSYLDPRDLLRLSLVCRRWRRIANDNSLWRRLC 45 (47)
T ss_dssp CCS--HHHHHHHHTTS-HHHHHHHTTSSHHHHHHHTCCCHHHHHC
T ss_pred hHhH-HHHHHHHHhcCCHHHHHHHHHHHHHHHHHHCChhhhhhhc
Confidence 5799 9999999999999999999999999999998889999864
No 9
>TIGR02907 spore_VI_D stage VI sporulation protein D. SpoVID, the stage VI sporulation protein D, is restricted to endospore-forming members of the bacteria, all of which are found among the Firmicutes. It is widely distributed but not quite universal in this group. Between well-conserved N-terminal and C-terminal domains is a poorly conserved, low-complexity region of variable length, rich enough in glutamic acid to cause spurious BLAST search results unless a filter is used. The seed alignment for this model was trimmed, in effect, by choosing member sequences in which these regions are relatively short. SpoVID is involved in spore coat assembly by the mother cell compartment late in the process of sporulation.
Probab=98.87 E-value=2.7e-09 Score=100.77 Aligned_cols=47 Identities=26% Similarity=0.405 Sum_probs=44.6
Q ss_pred ceEEEEccCCCcHHHHHHHhCCCHHHHHHHhCCCCCcCccCCCEEEec
Q 024891 115 FAISHRLARGDTVASLAVKYSVQVMDIKRLNNMMSDHGIYSRERLLIP 162 (261)
Q Consensus 115 ~~~~h~V~~GDTL~~IA~rYgvsv~~I~~~N~L~s~~~i~~gq~L~IP 162 (261)
.|..|+|++||||++||+||||++..|+++|++. ++.|++||+|+||
T Consensus 292 ~~~~YiVq~GDTL~sIAkRYGVSV~~L~r~N~L~-~~~L~~GQ~L~IP 338 (338)
T TIGR02907 292 KLRMCIVQEGDTIETIAERYEISVSQLIRHNQLE-DFEVNEGQILYIP 338 (338)
T ss_pred ccEEEEECCCCCHHHHHHHHCcCHHHHHHHhCCC-ccccCCCCEEEeC
Confidence 5789999999999999999999999999999997 5789999999998
No 10
>PRK10871 nlpD lipoprotein NlpD; Provisional
Probab=98.82 E-value=4.8e-09 Score=98.98 Aligned_cols=48 Identities=19% Similarity=0.211 Sum_probs=45.6
Q ss_pred EEEccCCCcHHHHHHHhCCCHHHHHHHhCCCCCcCccCCCEEEecCCC
Q 024891 118 SHRLARGDTVASLAVKYSVQVMDIKRLNNMMSDHGIYSRERLLIPISS 165 (261)
Q Consensus 118 ~h~V~~GDTL~~IA~rYgvsv~~I~~~N~L~s~~~i~~gq~L~IP~~~ 165 (261)
.|+|++||||++||.+||+++.+|.++|+|..++.|++||+|.||...
T Consensus 62 ~y~Vk~GDTL~~IA~~~g~~~~~La~~N~l~~p~~I~~GQ~L~i~~~~ 109 (319)
T PRK10871 62 TYTVKKGDTLFYIAWITGNDFRDLAQRNNIQAPYSLNVGQTLQVGNAS 109 (319)
T ss_pred ceEECCCCHHHHHHHHHCcCHHHHHHhcCCCCCccccCCCEEEeCCCC
Confidence 699999999999999999999999999999988999999999998653
No 11
>COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane]
Probab=98.71 E-value=3.4e-08 Score=79.59 Aligned_cols=48 Identities=38% Similarity=0.659 Sum_probs=44.7
Q ss_pred eEEEEccCCCcHHHHHHHhCCCHHHHHHHhCCCCCcCccCCCEEEecCC
Q 024891 116 AISHRLARGDTVASLAVKYSVQVMDIKRLNNMMSDHGIYSRERLLIPIS 164 (261)
Q Consensus 116 ~~~h~V~~GDTL~~IA~rYgvsv~~I~~~N~L~s~~~i~~gq~L~IP~~ 164 (261)
...|+|++||||++||++||+++.+|+++|++.++ .|++||.|.+|..
T Consensus 66 ~~~~~V~~gdtL~~Ia~~~~~tv~~l~~~n~l~~~-~i~~gq~l~~~~~ 113 (124)
T COG1388 66 VVTYTVKKGDTLSKIARKYGVTVAELKQLNNLSSD-KIKVGQKLKLPVS 113 (124)
T ss_pred CceEEEecCCCHHHHHHHhCCCHHHHHHHhccCCC-ceecCcEEEEecc
Confidence 35799999999999999999999999999999886 8999999999973
No 12
>smart00257 LysM Lysin motif.
Probab=98.63 E-value=7.8e-08 Score=60.58 Aligned_cols=43 Identities=30% Similarity=0.564 Sum_probs=38.8
Q ss_pred EEccCCCcHHHHHHHhCCCHHHHHHHhCCCCCcCccCCCEEEe
Q 024891 119 HRLARGDTVASLAVKYSVQVMDIKRLNNMMSDHGIYSRERLLI 161 (261)
Q Consensus 119 h~V~~GDTL~~IA~rYgvsv~~I~~~N~L~s~~~i~~gq~L~I 161 (261)
|+|++|||+++||.+||++..+|+++|.......+.+|+.|.|
T Consensus 2 ~~v~~gdt~~~ia~~~~~~~~~~~~~N~~~~~~~~~~g~~l~i 44 (44)
T smart00257 2 YTVKKGDTLSSIARRYGISVSDLLELNNILDPDNLQVGQKLKI 44 (44)
T ss_pred eEeCCCCCHHHHHHHhCCCHHHHHHHcCCCCccccCCCCEEeC
Confidence 8899999999999999999999999999655567899998875
No 13
>PRK13914 invasion associated secreted endopeptidase; Provisional
Probab=98.61 E-value=5.9e-08 Score=95.85 Aligned_cols=47 Identities=23% Similarity=0.274 Sum_probs=43.4
Q ss_pred EEEEccCCCcHHHHHHHhCCCHHHHHHHhCCCCCcCccCCCEEEecCC
Q 024891 117 ISHRLARGDTVASLAVKYSVQVMDIKRLNNMMSDHGIYSRERLLIPIS 164 (261)
Q Consensus 117 ~~h~V~~GDTL~~IA~rYgvsv~~I~~~N~L~s~~~i~~gq~L~IP~~ 164 (261)
..|+|++||||++||++||+++++|+++|+|.. +.|++||.|+||..
T Consensus 28 ~tytVq~GDTLw~IA~~ygvtv~~I~~~N~l~~-~~I~~Gq~L~Ip~~ 74 (481)
T PRK13914 28 STVVVEAGDTLWGIAQSKGTTVDAIKKANNLTT-DKIVPGQKLQVNEV 74 (481)
T ss_pred ceEEECCCCCHHHHHHHHCCCHHHHHHHhCCCc-ccccCCCEEEeCCC
Confidence 469999999999999999999999999999975 57999999999954
No 14
>smart00256 FBOX A Receptor for Ubiquitination Targets.
Probab=98.58 E-value=4.6e-08 Score=63.48 Aligned_cols=40 Identities=33% Similarity=0.468 Sum_probs=37.7
Q ss_pred CCcccHHHHHHhcCCHHHHHHhhhhhhhhhhhccchhhHHH
Q 024891 46 LACPDTLRLILSNLSVTDLARASCVCRAWSSVASDNNMIVL 86 (261)
Q Consensus 46 lp~~D~L~~Il~rL~p~~Lara~cVCk~W~~~~~~~~l~~a 86 (261)
|| .|++.+|+.+|++.++.++++|||.|+.++.++.+|..
T Consensus 1 lP-~~ll~~I~~~l~~~d~~~~~~vc~~~~~~~~~~~~~~~ 40 (41)
T smart00256 1 LP-DEILEEILSKLPPKDLLRLRKVSRRWRSLIDSHDFWFK 40 (41)
T ss_pred CC-HHHHHHHHHcCCHHHHHHHHHHHHHHHHHhcChhhhhc
Confidence 67 99999999999999999999999999999999998864
No 15
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=98.53 E-value=2.5e-07 Score=78.17 Aligned_cols=47 Identities=28% Similarity=0.315 Sum_probs=41.9
Q ss_pred eEEEEccCCCcHHHHHHHhC---CCHHHHHHHhC--CCCCcCccCCCEEEec
Q 024891 116 AISHRLARGDTVASLAVKYS---VQVMDIKRLNN--MMSDHGIYSRERLLIP 162 (261)
Q Consensus 116 ~~~h~V~~GDTL~~IA~rYg---vsv~~I~~~N~--L~s~~~i~~gq~L~IP 162 (261)
...|+|++||||++||.+|+ .....|.++|+ +.+++.|++||+|.||
T Consensus 95 ~~~y~Vk~GDTL~~IA~~~~g~~~~~~~I~~~N~~~l~~~~~I~pGq~L~IP 146 (147)
T PRK11198 95 SQFYTVKSGDTLSAIAKKVYGNANKYNKIFEANKPMLKSPDKIYPGQVLRIP 146 (147)
T ss_pred CeEEEECCCCCHHHHHHHHcCChhhHHHHHHhhhhcCCCcCCcCcCCEEecC
Confidence 45799999999999999985 45779999998 7777889999999998
No 16
>PRK13914 invasion associated secreted endopeptidase; Provisional
Probab=98.49 E-value=2.6e-07 Score=91.35 Aligned_cols=49 Identities=41% Similarity=0.578 Sum_probs=45.3
Q ss_pred ceEEEEccCCCcHHHHHHHhCCCHHHHHHHhCCCCCcCccCCCEEEecCC
Q 024891 115 FAISHRLARGDTVASLAVKYSVQVMDIKRLNNMMSDHGIYSRERLLIPIS 164 (261)
Q Consensus 115 ~~~~h~V~~GDTL~~IA~rYgvsv~~I~~~N~L~s~~~i~~gq~L~IP~~ 164 (261)
.+..|+|++||||++||++||+++++|+++|+|.+ ..|++||+|.||..
T Consensus 198 ~a~tytVq~GDTL~sIAkrYgVtv~eI~~~N~l~s-~~L~pGQ~L~Ip~s 246 (481)
T PRK13914 198 NATTHAVKSGDTIWALSVKYGVSVQDIMSWNNLSS-SSIYVGQKLAIKQT 246 (481)
T ss_pred CCeEEEECCCCCHHHHHHHHCCCHHHHHHhcCCCc-cccCCCCEEEecCC
Confidence 46789999999999999999999999999999976 57999999999964
No 17
>PF00646 F-box: F-box domain; InterPro: IPR001810 The F-box domain was first described as a sequence motif found in cyclin-F that interacts with the protein SKP1 [, ]. This relatively conserved structural motif is present in numerous proteins and serves as a link between a target protein and a ubiquitin-conjugating enzyme. The SCF complex (e.g., Skp1-Cullin-F-box) plays a similar role as an E3 ligase in the ubiquitin protein degradation pathway [, ]. Different F-box proteins as a part of SCF complex recruit particular substrates for ubiquitination through specific protein-protein interaction domains. Many mammalian F-box domains contain leucine-rich or WD-40 repeats (IPR001680 from INTERPRO). However, several F-box proteins either have other previously described domains such as Sec7 domain found in FBS protein or do not contain defined protein-protein interaction domains or motifs.; GO: 0005515 protein binding; PDB: 2E32_A 2E31_A 3V7D_B 1NEX_B 3MKS_D 3L2O_B.
Probab=98.48 E-value=7.8e-08 Score=65.18 Aligned_cols=45 Identities=31% Similarity=0.424 Sum_probs=39.0
Q ss_pred ccCCCcccHHHHHHhcCCHHHHHHhhhhhhhhhhhccchhhHHHhh
Q 024891 43 FSALACPDTLRLILSNLSVTDLARASCVCRAWSSVASDNNMIVLAF 88 (261)
Q Consensus 43 ~~~lp~~D~L~~Il~rL~p~~Lara~cVCk~W~~~~~~~~l~~aAF 88 (261)
+..|| .|++.+|+.+|++.++.++++|||.|+.++++..+|...+
T Consensus 3 ~~~LP-~~il~~Il~~l~~~~~~~l~~vsk~~~~~~~~~~~~~~~~ 47 (48)
T PF00646_consen 3 LSDLP-DEILQEILSYLDPKDLLRLSLVSKRWRSLVDSPRLWKKII 47 (48)
T ss_dssp HHHS--HHHHHHHHHTS-HHHHHHHCTT-HHHHHHHTTHHHHHHHH
T ss_pred HHHCC-HHHHHHHHHHCcHHHHHHHHHHhhHHHHHHcCCCccHHHh
Confidence 45789 9999999999999999999999999999999999998765
No 18
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional
Probab=98.28 E-value=1.2e-06 Score=86.34 Aligned_cols=48 Identities=23% Similarity=0.362 Sum_probs=44.9
Q ss_pred eEEEEccCCCcHHHHHHHhCCCHHHHHHHhCCCCCcCccCCCEEEecCC
Q 024891 116 AISHRLARGDTVASLAVKYSVQVMDIKRLNNMMSDHGIYSRERLLIPIS 164 (261)
Q Consensus 116 ~~~h~V~~GDTL~~IA~rYgvsv~~I~~~N~L~s~~~i~~gq~L~IP~~ 164 (261)
...|+|++||||++||.+|||++.+|+++|++.+ +.|.+||+|.||.+
T Consensus 343 ~~~y~Vk~GDTL~sIA~r~gvs~~~L~~~N~l~~-~~L~~Gq~L~Ip~~ 390 (456)
T PRK10783 343 SRSYKVRSGDTLSGIASRLNVSTKDLQQWNNLRG-SKLKVGQTLTIGAG 390 (456)
T ss_pred ceEEEECCCCcHHHHHHHHCcCHHHHHHHcCCCc-ccCCCCCEEEecCC
Confidence 5689999999999999999999999999999976 68999999999975
No 19
>KOG2997 consensus F-box protein FBX9 [General function prediction only]
Probab=98.07 E-value=1.2e-06 Score=82.90 Aligned_cols=60 Identities=25% Similarity=0.378 Sum_probs=51.5
Q ss_pred CCCCcccCCCcccHHHHHHhcC-----CHHHHHHhhhhhhhhhhhccchhhHHHhhcCcccccccc
Q 024891 38 PMNSHFSALACPDTLRLILSNL-----SVTDLARASCVCRAWSSVASDNNMIVLAFMAPWKLKEVV 98 (261)
Q Consensus 38 ~~~~~~~~lp~~D~L~~Il~rL-----~p~~Lara~cVCk~W~~~~~~~~l~~aAF~aPWkl~~vv 98 (261)
|.=-++..|| +|+|..||+++ +.++|.+++||||.|...+.|+.+||.+|..-|+...+.
T Consensus 102 p~~~~~~~LP-dEvLm~I~~~vv~~~~d~rsL~~~s~vCr~F~~~~R~~~lwR~aC~KvW~~s~~~ 166 (366)
T KOG2997|consen 102 PELISISVLP-DEVLMRIFRWVVSSLLDLRSLEQLSLVCRGFYKCARDPELWRLACLKVWQRSCIK 166 (366)
T ss_pred hhhhhhhhCC-HHHHHHHHHHHHhhhcchhhHHHhHhhHHHHHHHHcChHHHHHHHHHHHHHhhhc
Confidence 4334478999 99999999954 569999999999999999999999999999999854433
No 20
>KOG2850 consensus Predicted peptidoglycan-binding protein, contains LysM domain [General function prediction only]
Probab=97.88 E-value=3.3e-06 Score=74.39 Aligned_cols=138 Identities=20% Similarity=0.168 Sum_probs=92.5
Q ss_pred eEEEEccCCCcHHHHHHHhCCCHHHHHHHhCCCCCcCccCCCEEEecCCCCccccc------------------------
Q 024891 116 AISHRLARGDTVASLAVKYSVQVMDIKRLNNMMSDHGIYSRERLLIPISSPELLID------------------------ 171 (261)
Q Consensus 116 ~~~h~V~~GDTL~~IA~rYgvsv~~I~~~N~L~s~~~i~~gq~L~IP~~~~~~~~~------------------------ 171 (261)
.++-+||.||||+.||++|.+.+.+|++.|++.+...+.+-+.+.||+.+...+++
T Consensus 9 ~l~~~iq~~dt~~a~al~~~~~va~i~RvN~~~r~q~f~a~~~i~~pv~~~~~~~g~~~~~~~~~~~~s~~~s~~r~sil 88 (186)
T KOG2850|consen 9 ELEVTIQEGDTLQAIALNYESDVADIKRVNNDDREQRFNALRSISIPVTRASSATGYQVQEDQDIRERSPMRSECRHSIL 88 (186)
T ss_pred heeeeeccCchhhhHHhhcccchhhheeeccchhhhhhccccceecccchhhhhhhhccccccchhhhcccccccchhhc
Confidence 45678899999999999999999999999998888888888999999765333221
Q ss_pred ----cccccc--------cchhHHHHHhhhccCCCCCCCCcccc---chhhhhhhhHHHHHHHhhhhccCHHHHHHHHHh
Q 024891 172 ----GICYIE--------FDTYAKREVAVLYLEGAPEKKPSCLL---NRVTSVHGRRRIINSLRRSMQVDDETAQYYLSI 236 (261)
Q Consensus 172 ----~~~~~~--------~d~~~~re~~v~~~~~~~~~~~~~~~---~~~~~E~~k~kl~~~~~r~m~~D~~~A~~YL~~ 236 (261)
.+..|. .+.++....++.|.+...-+..+... .....+.......+.+++.+.+..++..+||+.
T Consensus 89 r~~~p~~~P~~~~~~~~~~~~~~~~~~a~~~~eh~v~~~~~~tg~~~~~~~ga~~d~~~~e~v~k~~~vl~~~~~f~l~~ 168 (186)
T KOG2850|consen 89 REDTPTRSPLKLDSSTKRVCNLAAVVQAVGYQEHRVKPFDPNTGFQIAPAYGAESDESPVESVRKMNPVLPDHQVFYLAP 168 (186)
T ss_pred ccCCcccCchhhhcchhhhhhhhhhhhhhhhhhcCCCCCCccccceecccccCcccchhHHHHHHHhhccchhHHHhhcc
Confidence 111111 01122334456666665444433111 111223333446788999999999999999999
Q ss_pred cCCCHHHHHHHHHhhHH
Q 024891 237 SNGNLRAALSEFSADLE 253 (261)
Q Consensus 237 a~~d~~~Av~~~~~D~~ 253 (261)
....+.-|...+..+..
T Consensus 169 ~e~p~~~~~~h~~~~~~ 185 (186)
T KOG2850|consen 169 LEIPLPGADDHASVITD 185 (186)
T ss_pred ccCCCCCcccccccccc
Confidence 99888777666655543
No 21
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=97.70 E-value=5.3e-05 Score=51.34 Aligned_cols=35 Identities=26% Similarity=0.366 Sum_probs=27.9
Q ss_pred HHHhhhhccCHHHHHHHHHhcCCCHHHHHHHHHhh
Q 024891 217 NSLRRSMQVDDETAQYYLSISNGNLRAALSEFSAD 251 (261)
Q Consensus 217 ~~~~r~m~~D~~~A~~YL~~a~~d~~~Av~~~~~D 251 (261)
+.+....+++.++|+.||+.++||++.||..|.++
T Consensus 5 ~~F~~iTg~~~~~A~~~L~~~~wdle~Av~~y~~~ 39 (43)
T PF14555_consen 5 AQFMSITGADEDVAIQYLEANNWDLEAAVNAYFDD 39 (43)
T ss_dssp HHHHHHH-SSHHHHHHHHHHTTT-HHHHHHHHHHS
T ss_pred HHHHHHHCcCHHHHHHHHHHcCCCHHHHHHHHHhC
Confidence 33444445999999999999999999999999876
No 22
>PF04225 OapA: Opacity-associated protein A LysM-like domain; InterPro: IPR007340 This entry includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [].; PDB: 2GU1_A.
Probab=96.98 E-value=0.00077 Score=52.24 Aligned_cols=49 Identities=10% Similarity=0.102 Sum_probs=28.7
Q ss_pred eEEEEccCCCcHHHHHHHhCCCHHHHHHHhCCC----CCcCccCCCEEEecCC
Q 024891 116 AISHRLARGDTVASLAVKYSVQVMDIKRLNNMM----SDHGIYSRERLLIPIS 164 (261)
Q Consensus 116 ~~~h~V~~GDTL~~IA~rYgvsv~~I~~~N~L~----s~~~i~~gq~L~IP~~ 164 (261)
|..|+|++||||+.|=.++|++..+|.++=+.. .=..|+|||+|.+=..
T Consensus 2 W~~~~V~~GDtLs~iF~~~gls~~dl~~v~~~~~~~k~L~~L~pGq~l~f~~d 54 (85)
T PF04225_consen 2 WQEYTVKSGDTLSTIFRRAGLSASDLYAVLEADGEAKPLTRLKPGQTLEFQLD 54 (85)
T ss_dssp --EEE--TT--HHHHHHHTT--HHHHHHHHHHGGGT--GGG--TT-EEEEEE-
T ss_pred CcEEEECCCCcHHHHHHHcCCCHHHHHHHHhccCccchHhhCCCCCEEEEEEC
Confidence 568999999999999999999999987763211 1136999999998654
No 23
>KOG2850 consensus Predicted peptidoglycan-binding protein, contains LysM domain [General function prediction only]
Probab=96.90 E-value=0.0005 Score=60.76 Aligned_cols=101 Identities=20% Similarity=0.088 Sum_probs=77.2
Q ss_pred hhhhhhhccchhhHHHhhcCccccccccccCCCCCccccC---CCCcceEEEEccCCCcHHHHHHHhCCCHHHHHHHhCC
Q 024891 71 CRAWSSVASDNNMIVLAFMAPWKLKEVVGMPLNGSFWRDN---GIGKFAISHRLARGDTVASLAVKYSVQVMDIKRLNNM 147 (261)
Q Consensus 71 Ck~W~~~~~~~~l~~aAF~aPWkl~~vvgsP~~~s~~~~~---~~~~~~~~h~V~~GDTL~~IA~rYgvsv~~I~~~N~L 147 (261)
||.||.+ +..+.--.+-.+|+.....+-+.....++-+ ....+...+.++.++|-.+.+..|.+.+++..+.+..
T Consensus 1 ~~~~~~~--~~l~~~iq~~dt~~a~al~~~~~va~i~RvN~~~r~q~f~a~~~i~~pv~~~~~~~g~~~~~~~~~~~~s~ 78 (186)
T KOG2850|consen 1 CKVWRDA--HELEVTIQEGDTLQAIALNYESDVADIKRVNNDDREQRFNALRSISIPVTRASSATGYQVQEDQDIRERSP 78 (186)
T ss_pred Cchhhhh--hheeeeeccCchhhhHHhhcccchhhheeeccchhhhhhccccceecccchhhhhhhhccccccchhhhcc
Confidence 8999955 3334444667889988888877777777655 3446788899999999999999999999888888887
Q ss_pred CCCcCccCCCEEEecCCCCccccccc
Q 024891 148 MSDHGIYSRERLLIPISSPELLIDGI 173 (261)
Q Consensus 148 ~s~~~i~~gq~L~IP~~~~~~~~~~~ 173 (261)
...+..+.--.+-.|...+..+...+
T Consensus 79 ~~s~~r~silr~~~p~~~P~~~~~~~ 104 (186)
T KOG2850|consen 79 MRSECRHSILREDTPTRSPLKLDSST 104 (186)
T ss_pred cccccchhhcccCCcccCchhhhcch
Confidence 77667777777777777777654433
No 24
>TIGR03505 FimV_core FimV N-terminal domain. This region is found at, or about 200 amino acids from, the N-terminus of FimV from Pseudomonas aeruginosa, TspA of Neisseria meningitidis, and related proteins. Disruption of FimV blocks twitching motility from type IV pili; Semmler, et al. suggest a role for this family in peptidoglycan layer remodelling required by type IV fimbrial systems. Most but not all members of this protein family have a C-terminal region recognized by TIGR03504. In between is a highly variable, often repeat-filled region rich in the negatively charged amino acids Asp and Glu.
Probab=96.85 E-value=0.0015 Score=49.59 Aligned_cols=40 Identities=23% Similarity=0.203 Sum_probs=31.7
Q ss_pred CcHHHHHHHh---C-CCHH----HHHHHhC----CCCCcCccCCCEEEecCC
Q 024891 125 DTVASLAVKY---S-VQVM----DIKRLNN----MMSDHGIYSRERLLIPIS 164 (261)
Q Consensus 125 DTL~~IA~rY---g-vsv~----~I~~~N~----L~s~~~i~~gq~L~IP~~ 164 (261)
|||++||.+| + +++. .|.+.|. -.+.+.|++|++|.||..
T Consensus 1 DTLw~IA~~~~~~~~~s~~q~m~ai~~aNp~AF~~~nin~L~~G~~L~iP~~ 52 (74)
T TIGR03505 1 DTLWGIAQRVRPDNSVSLYQMMLALYRANPDAFIGGNINRLKVGQILRIPSE 52 (74)
T ss_pred CcHHHHHHHHccCCCCCHHHHHHHHHHHCHHhHhcCChhhcCCCCEEeCCCH
Confidence 8999999999 4 8888 6777773 113367999999999964
No 25
>COG1652 XkdP Uncharacterized protein containing LysM domain [Function unknown]
Probab=96.61 E-value=0.00071 Score=61.81 Aligned_cols=48 Identities=23% Similarity=0.253 Sum_probs=41.2
Q ss_pred EEEEccCCCcHHHHHHHh-CCC--HHHHHHHhC---CCCCcCccCCCEEEecCC
Q 024891 117 ISHRLARGDTVASLAVKY-SVQ--VMDIKRLNN---MMSDHGIYSRERLLIPIS 164 (261)
Q Consensus 117 ~~h~V~~GDTL~~IA~rY-gvs--v~~I~~~N~---L~s~~~i~~gq~L~IP~~ 164 (261)
..|+|++||||+.||+++ |.. -..|-.+|+ +...+.|++||+|.||..
T Consensus 211 ~~~~v~rgDTl~~is~~~Yg~~~~y~~I~~aNk~~~~~~p~~I~pGq~l~iP~~ 264 (269)
T COG1652 211 TTNTVKRGDTLWQISKKVYGDGVEYRKIAEANKALVLDNPDKIKPGQVLRIPDQ 264 (269)
T ss_pred eEEEeccCCcccccchhhcCcceEEEeHhhhhhhhccCCCCcCCCcceeeCCCc
Confidence 479999999999999986 444 467889999 778899999999999964
No 26
>PRK10190 L,D-transpeptidase; Provisional
Probab=96.56 E-value=0.0058 Score=57.95 Aligned_cols=49 Identities=14% Similarity=0.158 Sum_probs=42.3
Q ss_pred ceEEEEccCCC--cHHHHHHHhCCCHHHHHHHhCCCCCcCccCCCEEEecC
Q 024891 115 FAISHRLARGD--TVASLAVKYSVQVMDIKRLNNMMSDHGIYSRERLLIPI 163 (261)
Q Consensus 115 ~~~~h~V~~GD--TL~~IA~rYgvsv~~I~~~N~L~s~~~i~~gq~L~IP~ 163 (261)
....|+|+++| +|..||.+|++...+|+.+|.-.......+|++|+||.
T Consensus 36 ~~~~~~v~~~~~~~le~iA~~f~~g~~~l~~aNPgvd~~~p~~G~~i~iP~ 86 (310)
T PRK10190 36 QSLTVTVPDHNTQPLETFAAQYGQGLSNMLEANPGADVFLPKSGSQLTIPQ 86 (310)
T ss_pred ceEEEEecCCCCccHHHHHHHhCCCHHHHHHhCCCCCCCCCCCCCEEEecC
Confidence 45689999966 59999999999999999999866555678999999996
No 27
>PRK10260 L,D-transpeptidase; Provisional
Probab=96.50 E-value=0.0064 Score=57.55 Aligned_cols=49 Identities=14% Similarity=0.149 Sum_probs=42.2
Q ss_pred ceEEEEccCCC--cHHHHHHHhCCCHHHHHHHhCCCCCcCccCCCEEEecC
Q 024891 115 FAISHRLARGD--TVASLAVKYSVQVMDIKRLNNMMSDHGIYSRERLLIPI 163 (261)
Q Consensus 115 ~~~~h~V~~GD--TL~~IA~rYgvsv~~I~~~N~L~s~~~i~~gq~L~IP~ 163 (261)
....|+|++|| +|..||.||++...+|+++|.-.......+|++|+||.
T Consensus 39 ~~~~~~v~~~~~~~le~iA~~f~~g~~~l~~aNPgvdp~lp~~G~~i~iP~ 89 (306)
T PRK10260 39 QNQVITIPEGNTQPLEYFAAEYQMGLSNMMEANPGVDTFLPKGGTVLNIPQ 89 (306)
T ss_pred ccEEEEeCCCCCchHHHHHHHhCCCHHHHHHhCcCCCCCcCCCCCEEEeCC
Confidence 45689999966 59999999999999999999865555667999999996
No 28
>COG3858 Predicted glycosyl hydrolase [General function prediction only]
Probab=96.14 E-value=0.0064 Score=59.59 Aligned_cols=63 Identities=16% Similarity=0.027 Sum_probs=52.0
Q ss_pred EEEEccCCCcHHHHHHHhCCCHHHHHHHhCCCCCcCccCCCEEEecCCCCc-cccccccccccc
Q 024891 117 ISHRLARGDTVASLAVKYSVQVMDIKRLNNMMSDHGIYSRERLLIPISSPE-LLIDGICYIEFD 179 (261)
Q Consensus 117 ~~h~V~~GDTL~~IA~rYgvsv~~I~~~N~L~s~~~i~~gq~L~IP~~~~~-~~~~~~~~~~~d 179 (261)
..|.|++||||++||.++||+.+.+..+|.+..+..+..|-.|.||..+.. ..+++|..+..+
T Consensus 50 ~~y~~~~~d~~~Sia~~~~vt~~~~~~m~~~~~~~~l~~~~~l~~P~~~~~~~~t~~~~~~~~~ 113 (423)
T COG3858 50 HFYDVGPGDTLTSIARTVGVTQDSAAIMNFVICPGYLQYGLNLYIPSARKTDGETTAYYAPRPP 113 (423)
T ss_pred eEEEecCCcchhhhhhhhcCCHHHHHhhcccccccceeeeeEEeccCCCCCcceeEEEecCCCc
Confidence 469999999999999999999999999998887778899999999975433 456666554433
No 29
>KOG2120 consensus SCF ubiquitin ligase, Skp2 component [Posttranslational modification, protein turnover, chaperones]
Probab=96.03 E-value=0.0053 Score=58.78 Aligned_cols=43 Identities=28% Similarity=0.430 Sum_probs=41.3
Q ss_pred ccCCCcccHHHHHHhcCCHHHHHHhhhhhhhhhhhccchhhHHH
Q 024891 43 FSALACPDTLRLILSNLSVTDLARASCVCRAWSSVASDNNMIVL 86 (261)
Q Consensus 43 ~~~lp~~D~L~~Il~rL~p~~Lara~cVCk~W~~~~~~~~l~~a 86 (261)
|..|| +++|..||+.|.-++|-+++-|||.|.-+++|..+|..
T Consensus 98 ~~slp-DEill~IFs~L~kk~LL~~~~VC~Rfyr~~~de~lW~~ 140 (419)
T KOG2120|consen 98 WDSLP-DEILLGIFSCLCKKELLKVSGVCKRFYRLASDESLWQT 140 (419)
T ss_pred cccCC-HHHHHHHHHhccHHHHHHHHHHHHHHhhccccccceee
Confidence 78999 99999999999999999999999999999999999964
No 30
>COG3858 Predicted glycosyl hydrolase [General function prediction only]
Probab=96.02 E-value=0.0026 Score=62.24 Aligned_cols=48 Identities=19% Similarity=0.255 Sum_probs=44.0
Q ss_pred eEEEEccCCCcHHHHHHHhCCCHHHHHHHhCCCCCcCccCCCEEEecCC
Q 024891 116 AISHRLARGDTVASLAVKYSVQVMDIKRLNNMMSDHGIYSRERLLIPIS 164 (261)
Q Consensus 116 ~~~h~V~~GDTL~~IA~rYgvsv~~I~~~N~L~s~~~i~~gq~L~IP~~ 164 (261)
+.+|.|++||++..|+.+|+++..+|...|.+.+ +.|.+||+++||..
T Consensus 1 ~~i~~~~pg~~~~~i~~~~~~~~~~i~~~~~~~~-d~~~~~q~~~v~~~ 48 (423)
T COG3858 1 MSIHLVGPGDSRLIIAVYFPYTNNRIVNGNDYTN-DDLVDGQTFVVPPS 48 (423)
T ss_pred CEEEEccCCceeeeehhhcccccccccccccccc-ccccCceeEEECCc
Confidence 4579999999999999999999999988888888 68999999999963
No 31
>PLN03215 ascorbic acid mannose pathway regulator 1; Provisional
Probab=95.88 E-value=0.005 Score=59.73 Aligned_cols=37 Identities=35% Similarity=0.659 Sum_probs=33.6
Q ss_pred ccCCCcccHHHHHHhcC-CHHHHHHhhhhhhhhhhhccc
Q 024891 43 FSALACPDTLRLILSNL-SVTDLARASCVCRAWSSVASD 80 (261)
Q Consensus 43 ~~~lp~~D~L~~Il~rL-~p~~Lara~cVCk~W~~~~~~ 80 (261)
++.|| +|+|..|..|| ..-|+.|.++||++||+.+.-
T Consensus 4 Ws~Lp-~dll~~i~~~l~~~~d~~~~~~vC~sWr~a~~~ 41 (373)
T PLN03215 4 WSTLP-EELLHMIAGRLFSNVELKRFRSICRSWRSSVSG 41 (373)
T ss_pred hhhCC-HHHHHHHHhhCCcHHHHHHHHhhhhhHHHhccc
Confidence 67899 99999999999 778999999999999987664
No 32
>PF05489 Phage_tail_X: Phage Tail Protein X; InterPro: IPR008861 This entry is represented by Bacteriophage P2, GpX. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family is found in a family of phage tail proteins. Sequence analysis suggests that they are related to IPR002482 from INTERPRO which suggests a general peptidoglycan binding function.
Probab=94.57 E-value=0.078 Score=38.67 Aligned_cols=47 Identities=15% Similarity=0.174 Sum_probs=35.6
Q ss_pred EEEEccCCCcHHHHHHHh-CCC---HHHHHHHhC-CCCC-cCccCCCEEEecCC
Q 024891 117 ISHRLARGDTVASLAVKY-SVQ---VMDIKRLNN-MMSD-HGIYSRERLLIPIS 164 (261)
Q Consensus 117 ~~h~V~~GDTL~~IA~rY-gvs---v~~I~~~N~-L~s~-~~i~~gq~L~IP~~ 164 (261)
..++. .||||..||.|| |-. ++.|.++|. |..- ..+..|..|.||.-
T Consensus 2 ~v~t~-~GDtlD~I~~r~yG~~~~~~e~ll~aNp~La~~~~~lpaG~~I~lP~i 54 (60)
T PF05489_consen 2 TVYTT-QGDTLDLIAYRHYGREDGAVEALLEANPGLADTGPVLPAGTVIILPDI 54 (60)
T ss_pred EEEEe-CcCcHHHHHHHHhCcHHHHHHHHHHHChhhhhcCCcCCCCCEEECCCC
Confidence 34555 999999999987 554 478899995 4332 47899999999964
No 33
>PRK11649 putative peptidase; Provisional
Probab=93.91 E-value=0.099 Score=51.71 Aligned_cols=50 Identities=18% Similarity=0.246 Sum_probs=40.2
Q ss_pred ceEEEEccCCCcHHHHHHHhCCCHHHHHHHh-CCCCCcCccCCCEEEecCC
Q 024891 115 FAISHRLARGDTVASLAVKYSVQVMDIKRLN-NMMSDHGIYSRERLLIPIS 164 (261)
Q Consensus 115 ~~~~h~V~~GDTL~~IA~rYgvsv~~I~~~N-~L~s~~~i~~gq~L~IP~~ 164 (261)
.+..|+|++||||.+|=.+||++..++.++- ....-..|++||.|.+=..
T Consensus 94 ~~~~~~Vk~GDTl~~iL~r~Gi~~~di~~l~~~~~~L~~Lr~Gq~l~~~~d 144 (439)
T PRK11649 94 GVHEYVVSTGDTLSSILNQYGIDMSDISQLAAQDKELRNLKIGQQLSWTLT 144 (439)
T ss_pred ceEEEEeCCCCCHHHHHHHcCCCHHHHHHHHHcChHhhcCCCCCEEEEEEC
Confidence 4678999999999999999999999988772 2222246999999998643
No 34
>COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane]
Probab=93.12 E-value=0.064 Score=42.98 Aligned_cols=35 Identities=31% Similarity=0.443 Sum_probs=31.2
Q ss_pred HHHHhCCCHHHHHHHhCCCC-CcCccCCCEEEecCC
Q 024891 130 LAVKYSVQVMDIKRLNNMMS-DHGIYSRERLLIPIS 164 (261)
Q Consensus 130 IA~rYgvsv~~I~~~N~L~s-~~~i~~gq~L~IP~~ 164 (261)
||.+|++++++|+++|.+.. .+.+++|++|.+|..
T Consensus 1 ia~~~~~~v~~l~~~n~~~~~s~~i~~gq~l~~~~~ 36 (124)
T COG1388 1 IASKYGVSVKALKKANALTGKSDAIKPGQVLKIPGD 36 (124)
T ss_pred CcccccccHHHHHHHhcccCCCCccccCceEEccCC
Confidence 68899999999999999983 468999999999974
No 35
>PF03943 TAP_C: TAP C-terminal domain; InterPro: IPR005637 This entry contains the NXF family of shuttling transport receptors for nuclear export of mRNA, which include: vertebrate mRNA export factor TAP or nuclear RNA export factor 1 (NXF1). Caenorhabditis elegans nuclear RNA export factor 1 (nxf-1). yeast mRNA export factor MEX67. Members of the NXF family have a modular structure. A nuclear localization sequence and a noncanonical RNA recognition motif (RRM) (see PDOC00030 from PROSITEDOC) followed by four LRR repeats are located in its N-terminal half. The C-terminal half contains a NTF2 domain (see PDOC50177 from PROSITEDOC) followed by a second domain, TAP-C. The TAP-C domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate nuclear shuttling [,]. The Tap-C domain is made of four alpha helices packed against each other. The arrangement of helices 1, 2 and 3 is similar to that seen in a UBA fold. and is joined to the next module by flexible 12-residue Pro-rich linker [, ].; GO: 0051028 mRNA transport, 0005634 nucleus; PDB: 1OAI_A 1GO5_A 2KHH_A 2JP7_A.
Probab=90.77 E-value=0.22 Score=35.14 Aligned_cols=35 Identities=20% Similarity=0.181 Sum_probs=25.8
Q ss_pred HHHhhhhccCHHHHHHHHHhcCCCHHHHHHHHHhh
Q 024891 217 NSLRRSMQVDDETAQYYLSISNGNLRAALSEFSAD 251 (261)
Q Consensus 217 ~~~~r~m~~D~~~A~~YL~~a~~d~~~Av~~~~~D 251 (261)
..+..--++..+=++-+|+.++||+++|+..|.+.
T Consensus 5 ~~~s~~Tgmn~~~s~~CL~~n~Wd~~~A~~~F~~l 39 (51)
T PF03943_consen 5 QQFSQQTGMNLEWSQKCLEENNWDYERALQNFEEL 39 (51)
T ss_dssp HHHHHHCSS-CCHHHHHHHHTTT-CCHHHHHHHHC
T ss_pred HHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 33444444777788999999999999999999753
No 36
>COG0739 NlpD Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]
Probab=87.50 E-value=0.94 Score=40.26 Aligned_cols=49 Identities=22% Similarity=0.409 Sum_probs=43.5
Q ss_pred EEEEccCCCcHHHHHHHhCCCHHHHHHHhCCCCCcCccCCCEEEecCCC
Q 024891 117 ISHRLARGDTVASLAVKYSVQVMDIKRLNNMMSDHGIYSRERLLIPISS 165 (261)
Q Consensus 117 ~~h~V~~GDTL~~IA~rYgvsv~~I~~~N~L~s~~~i~~gq~L~IP~~~ 165 (261)
..|.|+.++||..|+.+++++...+...|++.....+..++.+.+|...
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 50 (277)
T COG0739 2 SLYVVKKGDTLSAIAARLGISAKDLARLNNLLKKRLLRIGQLLRVPRAA 50 (277)
T ss_pred ceEEecCCCHHHHHHHHcCCCHHHHHHHHhhccccccCccceeeecccc
Confidence 3588999999999999999999999999998765578889999999763
No 37
>smart00804 TAP_C C-terminal domain of vertebrate Tap protein. The vertebrate Tap protein is a member of the NXF family of shuttling transport receptors for the nuclear export of mRNA. Its most C-terminal domain is important for binding to FG repeat-containing nuclear pore proteins (FG-nucleoporins) and is sufficient to mediate shuttling. This domain forms a compact four-helix fold related to that of a UBA domain.
Probab=85.39 E-value=2.5 Score=31.21 Aligned_cols=37 Identities=19% Similarity=0.316 Sum_probs=28.2
Q ss_pred HHHHHHhhhhccCHHHHHHHHHhcCCCHHHHHHHHHh
Q 024891 214 RIINSLRRSMQVDDETAQYYLSISNGNLRAALSEFSA 250 (261)
Q Consensus 214 kl~~~~~r~m~~D~~~A~~YL~~a~~d~~~Av~~~~~ 250 (261)
.++..+..--++-.+=++--|+.+|||++.|+..|.+
T Consensus 14 ~~v~~~~~~Tgmn~~~s~~cLe~~~Wd~~~Al~~F~~ 50 (63)
T smart00804 14 EMVQAFSAQTGMNAEYSQMCLEDNNWDYERALKNFTE 50 (63)
T ss_pred HHHHHHHHHHCCCHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 3444444444566777888999999999999999976
No 38
>KOG4341 consensus F-box protein containing LRR [General function prediction only]
Probab=84.11 E-value=0.72 Score=45.96 Aligned_cols=43 Identities=28% Similarity=0.461 Sum_probs=39.2
Q ss_pred ccCCCcccHHHHHHhcCCHHHHHHhhhhhhhhhhhccchhhHHH
Q 024891 43 FSALACPDTLRLILSNLSVTDLARASCVCRAWSSVASDNNMIVL 86 (261)
Q Consensus 43 ~~~lp~~D~L~~Il~rL~p~~Lara~cVCk~W~~~~~~~~l~~a 86 (261)
-..|| -+++..||+.|....|-+++-||+.||.++.|..=|-.
T Consensus 72 ~~~LP-pEl~lkvFS~LDtksl~r~a~~c~~~n~~AlD~~~~q~ 114 (483)
T KOG4341|consen 72 SRSLP-PELLLKVFSMLDTKSLCRAAQCCTMWNKLALDGSCWQH 114 (483)
T ss_pred cccCC-HHHHHHHHHHHhHHHHHHHHHHHHHhhhhhhcccccee
Confidence 57899 99999999999999999999999999999999876644
No 39
>KOG4408 consensus Putative Mg2+ and Co2+ transporter CorD [Inorganic ion transport and metabolism]
Probab=81.66 E-value=1.1 Score=43.33 Aligned_cols=139 Identities=19% Similarity=0.148 Sum_probs=87.4
Q ss_pred ccCCCcccHHHHHHhcCCHHHHHHhhhhhhhhhhhccchhhHHHhhcCccccccccccCCCC------Ccc-ccCCCCcc
Q 024891 43 FSALACPDTLRLILSNLSVTDLARASCVCRAWSSVASDNNMIVLAFMAPWKLKEVVGMPLNG------SFW-RDNGIGKF 115 (261)
Q Consensus 43 ~~~lp~~D~L~~Il~rL~p~~Lara~cVCk~W~~~~~~~~l~~aAF~aPWkl~~vvgsP~~~------s~~-~~~~~~~~ 115 (261)
+..++ .++|-.|+.++.+++|++.+||-+....+.+...+|+..+..-|-... .+.+. +|- .+.+..+.
T Consensus 8 le~~~-~~~l~~vls~~~~~~~~~~a~vs~rLk~~~s~~~lw~r~c~k~l~is~---e~~~~~~etgqsF~h~~f~yvgv 83 (386)
T KOG4408|consen 8 LEWLP-RDPLHLVLSFLLYRDLINCAYVSRRLKELGSHLPLWNRPCKKYLLISE---EEKTQKYETGQSFLHDTFGYVGV 83 (386)
T ss_pred hhhcc-cccceeeecccchhhhhcceeechHHhhhhhccccccccccccccccc---cccCCcccccceeeeeecccceE
Confidence 45788 999999999999999999999999999999999999998866664332 12221 111 11111111
Q ss_pred eEEE---EccCCCcHH----HHHHHhCCCHHHHHHHhC-----CCC----CcCccCCCEEEecCCCCccccccccccccc
Q 024891 116 AISH---RLARGDTVA----SLAVKYSVQVMDIKRLNN-----MMS----DHGIYSRERLLIPISSPELLIDGICYIEFD 179 (261)
Q Consensus 116 ~~~h---~V~~GDTL~----~IA~rYgvsv~~I~~~N~-----L~s----~~~i~~gq~L~IP~~~~~~~~~~~~~~~~d 179 (261)
++-| +++.-|++. ..|++-|+..++|-..-. |.. ...+.-||++..|. .+..-+-++.+-
T Consensus 84 v~~~w~arlk~wd~ln~~~~~aal~ega~e~dl~a~e~s~~~kLp~~~r~~yrev~Gq~l~~yq----vLi~~~d~sH~~ 159 (386)
T KOG4408|consen 84 VLFPWAARLKDWDDLNKYLEPAALKEGAREPDLDAVEASIGCKLPDDYRCSYREVKGQTLTFYQ----VLIDMRDCSHIR 159 (386)
T ss_pred EEEechHhhhhhhhcccccccchhhccCcccchhhhhhcccccCCCccccchhhcCCeEEeehh----eeeecccCcccc
Confidence 1211 145556655 578888888887766542 222 23567899999883 233333333344
Q ss_pred hhHHHHHhhh
Q 024891 180 TYAKREVAVL 189 (261)
Q Consensus 180 ~~~~re~~v~ 189 (261)
..+.+|...+
T Consensus 160 ~ev~~e~~t~ 169 (386)
T KOG4408|consen 160 SEVQTEAVTF 169 (386)
T ss_pred chhhhhhhhh
Confidence 4455555444
No 40
>COG3170 FimV Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=78.94 E-value=1.6 Score=45.77 Aligned_cols=48 Identities=23% Similarity=0.299 Sum_probs=36.4
Q ss_pred EEEEccCCCcHHHHHHHh----CCCHHH----HHHHhC--CC--CCcCccCCCEEEecCC
Q 024891 117 ISHRLARGDTVASLAVKY----SVQVMD----IKRLNN--MM--SDHGIYSRERLLIPIS 164 (261)
Q Consensus 117 ~~h~V~~GDTL~~IA~rY----gvsv~~----I~~~N~--L~--s~~~i~~gq~L~IP~~ 164 (261)
..|+|++|||||.||-+- ++|+++ |.+.|- +. +-|++++|.+|.||.-
T Consensus 189 ~tyt~~~~Dtl~dIAs~~rp~~~vt~~Q~~lAly~lNP~af~~gni~RLr~GSvLriP~~ 248 (755)
T COG3170 189 DTYTVRSGDTLWDIASRLRPQDHVTVEQMLLALYQLNPQAFVNGNINRLRAGSVLRIPSA 248 (755)
T ss_pred cccccCCcchHHHHHHhhcCcccccHHHHHHHHHhhChhhhcccchhhccccceeeccch
Confidence 479999999999999985 455554 567773 11 2368999999999964
No 41
>KOG0274 consensus Cdc4 and related F-box and WD-40 proteins [General function prediction only]
Probab=77.26 E-value=1.1 Score=45.38 Aligned_cols=46 Identities=28% Similarity=0.367 Sum_probs=40.3
Q ss_pred ccCCCcccHHHHHHhcCCHHHHHHhhhhhhhhhhhccchhhHHHhhc
Q 024891 43 FSALACPDTLRLILSNLSVTDLARASCVCRAWSSVASDNNMIVLAFM 89 (261)
Q Consensus 43 ~~~lp~~D~L~~Il~rL~p~~Lara~cVCk~W~~~~~~~~l~~aAF~ 89 (261)
...|| -++...||..|++++|..++-||+.|+.+.+++..|...+.
T Consensus 108 i~~lp-~el~~~il~~Ld~~~l~~~~~v~~~w~~~~~~~~~~~~~~~ 153 (537)
T KOG0274|consen 108 LSLLP-SELSLHILSFLDGRDLLAVRQVCRNWNKLLDDDKVWWRMCR 153 (537)
T ss_pred hhccc-chhcccccccCCHHHhhhhhhhcchhhhhhhccchhhhhhh
Confidence 36788 78888899999999999999999999999999988876544
No 42
>COG4784 Putative Zn-dependent protease [General function prediction only]
Probab=74.99 E-value=4 Score=40.06 Aligned_cols=44 Identities=23% Similarity=0.301 Sum_probs=36.8
Q ss_pred EEEccCCCcHHHHHHHh-CC--CHHHHHHHhCCCCCcCccCCCEEEe
Q 024891 118 SHRLARGDTVASLAVKY-SV--QVMDIKRLNNMMSDHGIYSRERLLI 161 (261)
Q Consensus 118 ~h~V~~GDTL~~IA~rY-gv--sv~~I~~~N~L~s~~~i~~gq~L~I 161 (261)
.-+|++|||+.++|-+. |+ .++.++-+|.|.......+|+.++|
T Consensus 430 vvtVk~GqT~~~lAA~m~G~~rkldlfRllNam~~~a~~~pGd~vKi 476 (479)
T COG4784 430 VVTVKPGQTMASLAARMMGTDRKLDLFRLLNAMSPGATVRPGDKVKI 476 (479)
T ss_pred EEEecCCccHHHHHhhccCchhHHHHHHHHhccCCCCcCCCCCeeee
Confidence 44579999999999886 54 4677888999987788999999998
No 43
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=73.65 E-value=5.4 Score=25.67 Aligned_cols=25 Identities=32% Similarity=0.341 Sum_probs=21.7
Q ss_pred hccCHHHHHHHHHhcCCCHHHHHHH
Q 024891 223 MQVDDETAQYYLSISNGNLRAALSE 247 (261)
Q Consensus 223 m~~D~~~A~~YL~~a~~d~~~Av~~ 247 (261)
|+.+.+.|+..|..+++|+++|+..
T Consensus 12 mGf~~~~~~~AL~~~~~nve~A~~~ 36 (37)
T PF00627_consen 12 MGFSREQAREALRACNGNVERAVDW 36 (37)
T ss_dssp HTS-HHHHHHHHHHTTTSHHHHHHH
T ss_pred cCCCHHHHHHHHHHcCCCHHHHHHh
Confidence 4789999999999999999999863
No 44
>COG3061 OapA Cell envelope opacity-associated protein A [Cell envelope biogenesis, outer membrane]
Probab=73.12 E-value=10 Score=34.87 Aligned_cols=51 Identities=14% Similarity=0.249 Sum_probs=41.6
Q ss_pred ceEEEEccCCCcHHHHHHHhCCCHHHHHHHhCCCCC----cCccCCCEEEecCCC
Q 024891 115 FAISHRLARGDTVASLAVKYSVQVMDIKRLNNMMSD----HGIYSRERLLIPISS 165 (261)
Q Consensus 115 ~~~~h~V~~GDTL~~IA~rYgvsv~~I~~~N~L~s~----~~i~~gq~L~IP~~~ 165 (261)
.|.+|+|+.|+||..+=+-++.++.|+-..=+..+. ..|..||.+.|-...
T Consensus 158 ~wqsy~V~~G~TLaQlFRdn~LpitDVnAMakveGagkpLSnlkaGq~Vki~~na 212 (242)
T COG3061 158 NWQSYTVPQGKTLAQLFRDNNLPITDVNAMAKVEGAGKPLSNLKAGQKVKISLNA 212 (242)
T ss_pred cceeEEecCCccHHHHHhccCCChHHhHHHHhhccCCCchhhccCCCEEEEEEcC
Confidence 689999999999999999999999998766543221 258999999998653
No 45
>PF13518 HTH_28: Helix-turn-helix domain
Probab=69.38 E-value=5.3 Score=26.65 Aligned_cols=27 Identities=15% Similarity=0.299 Sum_probs=22.8
Q ss_pred ccCCCcHHHHHHHhCCCHHHHHHHhCC
Q 024891 121 LARGDTVASLAVKYSVQVMDIKRLNNM 147 (261)
Q Consensus 121 V~~GDTL~~IA~rYgvsv~~I~~~N~L 147 (261)
+..|.|+..||.+|||+...|.++-+.
T Consensus 9 ~~~g~s~~~~a~~~gis~~tv~~w~~~ 35 (52)
T PF13518_consen 9 YLEGESVREIAREFGISRSTVYRWIKR 35 (52)
T ss_pred HHcCCCHHHHHHHHCCCHhHHHHHHHH
Confidence 346889999999999999999887543
No 46
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=66.79 E-value=3 Score=30.19 Aligned_cols=25 Identities=20% Similarity=0.423 Sum_probs=22.0
Q ss_pred ccCCCcHHHHHHHhCCCHHHHHHHh
Q 024891 121 LARGDTVASLAVKYSVQVMDIKRLN 145 (261)
Q Consensus 121 V~~GDTL~~IA~rYgvsv~~I~~~N 145 (261)
.+.|.|+..||.+|||+...|.++=
T Consensus 20 ~~~g~sv~~va~~~gi~~~~l~~W~ 44 (76)
T PF01527_consen 20 LESGESVSEVAREYGISPSTLYNWR 44 (76)
T ss_dssp HHHHCHHHHHHHHHTS-HHHHHHHH
T ss_pred HHCCCceEeeecccccccccccHHH
Confidence 5899999999999999999999884
No 47
>KOG0281 consensus Beta-TrCP (transducin repeats containing)/Slimb proteins [Function unknown]
Probab=66.63 E-value=5.1 Score=39.39 Aligned_cols=41 Identities=27% Similarity=0.367 Sum_probs=35.8
Q ss_pred ccHHHHHHhcCCHHHHHHhhhhhhhhhhhccchhhHHHhhc
Q 024891 49 PDTLRLILSNLSVTDLARASCVCRAWSSVASDNNMIVLAFM 89 (261)
Q Consensus 49 ~D~L~~Il~rL~p~~Lara~cVCk~W~~~~~~~~l~~aAF~ 89 (261)
+.+-..||.-|...+|..+-.|||.|+.+.++..+|..-.+
T Consensus 84 ~hi~e~ilsyld~~sLc~celv~k~W~r~l~dg~~WKkLie 124 (499)
T KOG0281|consen 84 DHIAENILSYLDALSLCACELVCKEWKRVLSDGMLWKKLIE 124 (499)
T ss_pred HHHHHHHHHhcchhhhhHHHHHHHHHHHHhccchHHHHHHH
Confidence 56677788999999999999999999999999999976544
No 48
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=66.50 E-value=6.4 Score=26.46 Aligned_cols=24 Identities=25% Similarity=0.418 Sum_probs=19.0
Q ss_pred ccCCCcHHHHHHHhCCCHHHHHHH
Q 024891 121 LARGDTVASLAVKYSVQVMDIKRL 144 (261)
Q Consensus 121 V~~GDTL~~IA~rYgvsv~~I~~~ 144 (261)
...|-|+..||..+||+...|.++
T Consensus 18 ~~~G~si~~IA~~~gvsr~TvyR~ 41 (45)
T PF02796_consen 18 YAEGMSIAEIAKQFGVSRSTVYRY 41 (45)
T ss_dssp HHTT--HHHHHHHTTS-HHHHHHH
T ss_pred HHCCCCHHHHHHHHCcCHHHHHHH
Confidence 378899999999999999999886
No 49
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=64.44 E-value=12 Score=23.58 Aligned_cols=26 Identities=31% Similarity=0.289 Sum_probs=22.9
Q ss_pred hhccCHHHHHHHHHhcCCCHHHHHHH
Q 024891 222 SMQVDDETAQYYLSISNGNLRAALSE 247 (261)
Q Consensus 222 ~m~~D~~~A~~YL~~a~~d~~~Av~~ 247 (261)
.|+.+.+.|+.-|..++||+.+|+..
T Consensus 10 ~mGf~~~~a~~aL~~~~~d~~~A~~~ 35 (37)
T smart00165 10 EMGFSREEALKALRAANGNVERAAEY 35 (37)
T ss_pred HcCCCHHHHHHHHHHhCCCHHHHHHH
Confidence 45789999999999999999999764
No 50
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=60.01 E-value=5.1 Score=25.97 Aligned_cols=27 Identities=37% Similarity=0.422 Sum_probs=18.4
Q ss_pred cccHHHHHHh--cCCHHHHHHhhhhhhhhh-hhccch
Q 024891 48 CPDTLRLILS--NLSVTDLARASCVCRAWS-SVASDN 81 (261)
Q Consensus 48 ~~D~L~~Il~--rL~p~~Lara~cVCk~W~-~~~~~~ 81 (261)
.||+|+.|++ .+++.+| +.|| .+..+.
T Consensus 5 ~gDtl~~IA~~~~~~~~~l-------~~~N~~~~~~~ 34 (44)
T PF01476_consen 5 PGDTLWSIAKRYGISVDEL-------MELNPNIDSDN 34 (44)
T ss_dssp TT--HHHHHHHTTS-HHHH-------HHHCCTTHGGC
T ss_pred cCCcHHHHHhhhhhhHhHH-------HHhcCCCCccc
Confidence 4999999999 4588889 7788 665554
No 51
>KOG3926 consensus F-box proteins [Amino acid transport and metabolism]
Probab=59.27 E-value=7.3 Score=37.04 Aligned_cols=60 Identities=13% Similarity=0.119 Sum_probs=46.9
Q ss_pred CCcccCCCCCc-ccCCCcccHHHHHHhcC-CHHHHHHhhhhhhhhhhhccchhhHHHhhcCccc
Q 024891 32 PSTVISPMNSH-FSALACPDTLRLILSNL-SVTDLARASCVCRAWSSVASDNNMIVLAFMAPWK 93 (261)
Q Consensus 32 ~~~~~~~~~~~-~~~lp~~D~L~~Il~rL-~p~~Lara~cVCk~W~~~~~~~~l~~aAF~aPWk 93 (261)
.-++|+| +|- |..|| -+++..|+.|| .-+||--++-|=-....++.++.+|..-|..++.
T Consensus 191 qi~~~~~-~~ltl~dLP-~e~vl~Il~rlsDh~dL~s~aqa~etl~~l~~e~~iWkkLcqfHF~ 252 (332)
T KOG3926|consen 191 QITEPDP-AGLTLHDLP-LECVLNILLRLSDHRDLESLAQAWETLAKLSEERRIWKKLCQFHFN 252 (332)
T ss_pred cccCCCc-CCCCcccch-HHHHHHHHHHccCcchHHHHHHhhHHHHHHHHHHHHHHHHHHHHhh
Confidence 3456777 455 89999 99999999999 5677666666666667788999999998887664
No 52
>KOG3763 consensus mRNA export factor TAP/MEX67 [RNA processing and modification]
Probab=57.87 E-value=25 Score=36.35 Aligned_cols=32 Identities=19% Similarity=0.225 Sum_probs=25.9
Q ss_pred HhhhhccCHHHHHHHHHhcCCCHHHHHHHHHh
Q 024891 219 LRRSMQVDDETAQYYLSISNGNLRAALSEFSA 250 (261)
Q Consensus 219 ~~r~m~~D~~~A~~YL~~a~~d~~~Av~~~~~ 250 (261)
|.-.-++-..=+.--|++++|||+.|++.|.+
T Consensus 542 ~~~~tGln~~~s~~c~e~~nWdy~~A~k~F~~ 573 (585)
T KOG3763|consen 542 FQEETGLNSEWSTMCLEQNNWDYERALKLFIE 573 (585)
T ss_pred HHHHhcCChHHHHHHHHHccCCHHHHHHHHHH
Confidence 44444477777888999999999999999975
No 53
>TIGR00264 alpha-NAC-related protein. This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator.
Probab=55.51 E-value=22 Score=29.47 Aligned_cols=35 Identities=23% Similarity=0.297 Sum_probs=30.1
Q ss_pred HHHHHhhhhccCHHHHHHHHHhcCCCHHHHHHHHH
Q 024891 215 IINSLRRSMQVDDETAQYYLSISNGNLRAALSEFS 249 (261)
Q Consensus 215 l~~~~~r~m~~D~~~A~~YL~~a~~d~~~Av~~~~ 249 (261)
-++++..--++++++|+-=|+.++||+..|+....
T Consensus 81 DI~lV~eq~gvs~e~A~~AL~~~~gDl~~AI~~L~ 115 (116)
T TIGR00264 81 DIELVMKQCNVSKEEARRALEECGGDLAEAIMKLE 115 (116)
T ss_pred HHHHHHHHhCcCHHHHHHHHHHcCCCHHHHHHHhh
Confidence 35667777789999999999999999999998654
No 54
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=54.05 E-value=13 Score=25.23 Aligned_cols=24 Identities=25% Similarity=0.392 Sum_probs=17.9
Q ss_pred ccCC-CcHHHHHHHhCCCHHHHHHH
Q 024891 121 LARG-DTVASLAVKYSVQVMDIKRL 144 (261)
Q Consensus 121 V~~G-DTL~~IA~rYgvsv~~I~~~ 144 (261)
|+.| -++...|++||||...|.+.
T Consensus 12 v~~g~~S~r~AA~~ygVp~sTL~~r 36 (45)
T PF05225_consen 12 VKNGKMSIRKAAKKYGVPRSTLRRR 36 (45)
T ss_dssp HHTTSS-HHHHHHHHT--HHHHHHH
T ss_pred HHhCCCCHHHHHHHHCcCHHHHHHH
Confidence 5566 89999999999999999865
No 55
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=52.92 E-value=27 Score=28.90 Aligned_cols=35 Identities=29% Similarity=0.344 Sum_probs=30.3
Q ss_pred HHHHHhhhhccCHHHHHHHHHhcCCCHHHHHHHHH
Q 024891 215 IINSLRRSMQVDDETAQYYLSISNGNLRAALSEFS 249 (261)
Q Consensus 215 l~~~~~r~m~~D~~~A~~YL~~a~~d~~~Av~~~~ 249 (261)
-++++..--++++++|+-=|+.+++|+..|+....
T Consensus 79 dI~lv~~q~gvs~~~A~~AL~~~~gDl~~AI~~L~ 113 (115)
T PRK06369 79 DIELVAEQTGVSEEEARKALEEANGDLAEAILKLS 113 (115)
T ss_pred HHHHHHHHHCcCHHHHHHHHHHcCCcHHHHHHHHh
Confidence 35667777789999999999999999999998764
No 56
>COG4254 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=52.69 E-value=11 Score=36.03 Aligned_cols=49 Identities=20% Similarity=0.217 Sum_probs=41.8
Q ss_pred EEEEccCCCcHHHHHHHhCCCHHH---HHHHhCCCCCcCccCCCEEEecCCC
Q 024891 117 ISHRLARGDTVASLAVKYSVQVMD---IKRLNNMMSDHGIYSRERLLIPISS 165 (261)
Q Consensus 117 ~~h~V~~GDTL~~IA~rYgvsv~~---I~~~N~L~s~~~i~~gq~L~IP~~~ 165 (261)
+.|.|+.||||..++..|=.-.+. +...|....+..+.+|..|-||.+.
T Consensus 6 ~~yrv~~gdtli~l~~~yl~~~~g~r~~q~an~~~~P~~l~pgs~l~ip~~~ 57 (339)
T COG4254 6 LTYRVLFGDTLILLLGGYLTLLAGSRAAQPANTKRPPFILQPGSCLPIPLPA 57 (339)
T ss_pred ceeeeccccHHHHHHHHhhhccchhhhhcccccCCCCcccCCCccccCCCcc
Confidence 579999999999999999666554 5567888888999999999999764
No 57
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=52.55 E-value=14 Score=29.21 Aligned_cols=27 Identities=22% Similarity=0.416 Sum_probs=22.8
Q ss_pred EEEccCCCcHHHHHHHhCC-CHHHHHHH
Q 024891 118 SHRLARGDTVASLAVKYSV-QVMDIKRL 144 (261)
Q Consensus 118 ~h~V~~GDTL~~IA~rYgv-sv~~I~~~ 144 (261)
...+++|.|+..||++||| +...|.++
T Consensus 18 ~~~~~~g~sv~~vAr~~gv~~~~~l~~W 45 (116)
T COG2963 18 ALYLRGGDTVSEVAREFGIVSATQLYKW 45 (116)
T ss_pred HHHHhcCccHHHHHHHhCCCChHHHHHH
Confidence 3456899999999999995 99998864
No 58
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=51.10 E-value=51 Score=21.64 Aligned_cols=31 Identities=23% Similarity=0.312 Sum_probs=25.5
Q ss_pred hhhhccCHHHHHHHHHhcCCCHHHHHHHHHh
Q 024891 220 RRSMQVDDETAQYYLSISNGNLRAALSEFSA 250 (261)
Q Consensus 220 ~r~m~~D~~~A~~YL~~a~~d~~~Av~~~~~ 250 (261)
--|-.+|.++.+.-|..+++|++.|+....+
T Consensus 10 ~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL~ 40 (42)
T PF02845_consen 10 EMFPDLDREVIEAVLQANNGDVEAAIDALLE 40 (42)
T ss_dssp HHSSSS-HHHHHHHHHHTTTTHHHHHHHHHH
T ss_pred HHCCCCCHHHHHHHHHHcCCCHHHHHHHHHc
Confidence 3455699999999999999999999988754
No 59
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=50.49 E-value=31 Score=21.78 Aligned_cols=26 Identities=27% Similarity=0.295 Sum_probs=23.0
Q ss_pred hccCHHHHHHHHHhcCCCHHHHHHHH
Q 024891 223 MQVDDETAQYYLSISNGNLRAALSEF 248 (261)
Q Consensus 223 m~~D~~~A~~YL~~a~~d~~~Av~~~ 248 (261)
|+.+.+.|+.=|..++||+.+|+...
T Consensus 11 mGf~~~~~~~AL~~~~~d~~~A~~~L 36 (38)
T cd00194 11 MGFSREEARKALRATNNNVERAVEWL 36 (38)
T ss_pred cCCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 67889999999999999999998654
No 60
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=48.82 E-value=21 Score=23.77 Aligned_cols=27 Identities=19% Similarity=0.218 Sum_probs=19.6
Q ss_pred ccCCCcHHHHHHHhCCCHHHHHHHhCC
Q 024891 121 LARGDTVASLAVKYSVQVMDIKRLNNM 147 (261)
Q Consensus 121 V~~GDTL~~IA~rYgvsv~~I~~~N~L 147 (261)
+..|-|...||..+|||...+.++=+-
T Consensus 14 ~~~G~s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 14 LREGWSIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp HHHT--HHHHHHHHTS-HHHHHHHHT-
T ss_pred HHCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 345999999999999999999887443
No 61
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=46.34 E-value=56 Score=21.48 Aligned_cols=31 Identities=23% Similarity=0.349 Sum_probs=27.0
Q ss_pred hhhccCHHHHHHHHHhcCCCHHHHHHHHHhh
Q 024891 221 RSMQVDDETAQYYLSISNGNLRAALSEFSAD 251 (261)
Q Consensus 221 r~m~~D~~~A~~YL~~a~~d~~~Av~~~~~D 251 (261)
-|-.+|.+++++=|..+++|++.|+....++
T Consensus 12 mFP~l~~~~I~~~L~~~~g~ve~~i~~LL~~ 42 (43)
T smart00546 12 MFPNLDEEVIKAVLEANNGNVEATINNLLEG 42 (43)
T ss_pred HCCCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence 3667999999999999999999999887653
No 62
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=45.76 E-value=35 Score=31.96 Aligned_cols=45 Identities=18% Similarity=0.213 Sum_probs=36.4
Q ss_pred hhhhhHHHHHHHhhhhccCHHHHHHHHHhcCCCHHHHHHHHHhhH
Q 024891 208 SVHGRRRIINSLRRSMQVDDETAQYYLSISNGNLRAALSEFSADL 252 (261)
Q Consensus 208 ~E~~k~kl~~~~~r~m~~D~~~A~~YL~~a~~d~~~Av~~~~~D~ 252 (261)
.++.+.|-.+.+.+..++|+++|+..|+.++|+...|+-......
T Consensus 231 n~kl~~ra~~i~~~~~~~~~~~a~~~l~~~~~~vk~a~~~~~~~~ 275 (299)
T PRK05441 231 NEKLVDRAVRIVMEATGVSREEAEAALEAADGSVKLAIVMILTGL 275 (299)
T ss_pred HHHHHHHHHHHHHHHHCcCHHHHHHHHHHhCCCcHHHHHHHHhCC
Confidence 455556666778888889999999999999999999988765543
No 63
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=45.50 E-value=21 Score=28.36 Aligned_cols=21 Identities=38% Similarity=0.502 Sum_probs=16.5
Q ss_pred CCcHHHHHHHhCCCHHHHHHH
Q 024891 124 GDTVASLAVKYSVQVMDIKRL 144 (261)
Q Consensus 124 GDTL~~IA~rYgvsv~~I~~~ 144 (261)
|.++..||.+||+|...|.+.
T Consensus 72 G~n~~eLA~kyglS~r~I~~I 92 (108)
T PF08765_consen 72 GMNVRELARKYGLSERQIYRI 92 (108)
T ss_dssp SS-HHHHHHHHT--HHHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHHH
Confidence 999999999999999988775
No 64
>PF14148 YhdB: YhdB-like protein
Probab=45.33 E-value=25 Score=26.98 Aligned_cols=33 Identities=24% Similarity=0.403 Sum_probs=27.7
Q ss_pred cCHHHHHHHHHhcCCC-------------HHHHHHHHHhhHHHHhh
Q 024891 225 VDDETAQYYLSISNGN-------------LRAALSEFSADLEWERQ 257 (261)
Q Consensus 225 ~D~~~A~~YL~~a~~d-------------~~~Av~~~~~D~~WE~~ 257 (261)
+|||.|.||-.-+.|| |.|-|+.|.....+|++
T Consensus 4 ~DYDkALyYthrsqWDnLLiLMVrT~Dd~lSKkIEhFLHAy~f~~d 49 (77)
T PF14148_consen 4 ADYDKALYYTHRSQWDNLLILMVRTKDDLLSKKIEHFLHAYHFEKD 49 (77)
T ss_pred chhhHHHHHHHHhhhcceeeeeeechhHHHHHHHHHHHHHhhcccc
Confidence 8999999999999998 46888888877777654
No 65
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=45.23 E-value=30 Score=23.18 Aligned_cols=23 Identities=17% Similarity=0.361 Sum_probs=19.9
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHH
Q 024891 122 ARGDTVASLAVKYSVQVMDIKRL 144 (261)
Q Consensus 122 ~~GDTL~~IA~rYgvsv~~I~~~ 144 (261)
..|-|+..||..+|+|...+++.
T Consensus 18 ~~~~t~~eIa~~lg~s~~~V~~~ 40 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISRSTVRRI 40 (50)
T ss_dssp TST-SHHHHHHHHTSCHHHHHHH
T ss_pred cCCCCHHHHHHHHCCcHHHHHHH
Confidence 57889999999999999998875
No 66
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=45.08 E-value=25 Score=28.38 Aligned_cols=29 Identities=17% Similarity=0.180 Sum_probs=25.0
Q ss_pred EEEEccCCCcHHHHHHHhCCCHHHHHHHh
Q 024891 117 ISHRLARGDTVASLAVKYSVQVMDIKRLN 145 (261)
Q Consensus 117 ~~h~V~~GDTL~~IA~rYgvsv~~I~~~N 145 (261)
+...+..|-|+..||.+|||+...|.++=
T Consensus 22 V~~~~~~g~sv~evA~e~gIs~~tl~~W~ 50 (121)
T PRK09413 22 VQQSFEPGMTVSLVARQHGVAASQLFLWR 50 (121)
T ss_pred HHHHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence 34456789999999999999999999983
No 67
>PHA00675 hypothetical protein
Probab=44.42 E-value=25 Score=27.24 Aligned_cols=29 Identities=21% Similarity=0.184 Sum_probs=24.1
Q ss_pred EEEc-cCCCcHHHHHHHhCCCHHHHHHHhC
Q 024891 118 SHRL-ARGDTVASLAVKYSVQVMDIKRLNN 146 (261)
Q Consensus 118 ~h~V-~~GDTL~~IA~rYgvsv~~I~~~N~ 146 (261)
.+.. +.|.+.+.||++|||+...|..+=+
T Consensus 32 R~l~~r~G~s~~~IA~~fGVsrstV~~I~~ 61 (78)
T PHA00675 32 RELHEVEGMSYAVLAEKFEQSKGAIAKICR 61 (78)
T ss_pred HHHHHhcCccHHHHHHHhCCCHHHHHHHHc
Confidence 3444 8999999999999999999887643
No 68
>cd05007 SIS_Etherase N-acetylmuramic acid 6-phosphate etherase. Members of this family contain the SIS (Sugar ISomerase) domain. The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. The bacterial cell wall sugar N-acetylmuramic acid carries a unique D-lactyl ether substituent at the C3 position. The etherase catalyzes the cleavage of the lactyl ether bond of N-acetylmuramic acid 6-phosphate.
Probab=43.45 E-value=20 Score=32.74 Aligned_cols=38 Identities=21% Similarity=0.313 Sum_probs=31.6
Q ss_pred hhhhhHHHHHHHhhhhccCHHHHHHHHHhcCCCHHHHH
Q 024891 208 SVHGRRRIINSLRRSMQVDDETAQYYLSISNGNLRAAL 245 (261)
Q Consensus 208 ~E~~k~kl~~~~~r~m~~D~~~A~~YL~~a~~d~~~Av 245 (261)
-++.+.|-.+.+.+..++++++|+.+|+.++|+.+.|+
T Consensus 218 n~kl~~ra~~i~~~~~~~~~~~a~~~l~~~~~~~k~a~ 255 (257)
T cd05007 218 NEKLRERAIRIVMEATGVSRDEAEAALEQAGGDVKTAI 255 (257)
T ss_pred HHHHHHHHHHHHHHHHCcCHHHHHHHHHHhCCCceeee
Confidence 44555566677888888999999999999999998876
No 69
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=40.89 E-value=14 Score=25.89 Aligned_cols=25 Identities=20% Similarity=0.454 Sum_probs=18.5
Q ss_pred EccCCCcHHHHHHHhCCCHHHHHHH
Q 024891 120 RLARGDTVASLAVKYSVQVMDIKRL 144 (261)
Q Consensus 120 ~V~~GDTL~~IA~rYgvsv~~I~~~ 144 (261)
.+..|.+...||.+|||+...|..+
T Consensus 18 ~~e~g~s~~~ia~~fgv~~sTv~~I 42 (53)
T PF04218_consen 18 RLEEGESKRDIAREFGVSRSTVSTI 42 (53)
T ss_dssp HHHCTT-HHHHHHHHT--CCHHHHH
T ss_pred HHHcCCCHHHHHHHhCCCHHHHHHH
Confidence 3678999999999999998888765
No 70
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=39.97 E-value=25 Score=24.84 Aligned_cols=25 Identities=28% Similarity=0.458 Sum_probs=18.9
Q ss_pred ccCCCcH---HHHHHHhCCCHHHHHHHh
Q 024891 121 LARGDTV---ASLAVKYSVQVMDIKRLN 145 (261)
Q Consensus 121 V~~GDTL---~~IA~rYgvsv~~I~~~N 145 (261)
.++||.| ..||.+||||..-++++=
T Consensus 18 ~~~g~~lps~~~la~~~~vsr~tvr~al 45 (64)
T PF00392_consen 18 LPPGDRLPSERELAERYGVSRTTVREAL 45 (64)
T ss_dssp S-TTSBE--HHHHHHHHTS-HHHHHHHH
T ss_pred CCCCCEeCCHHHHHHHhccCCcHHHHHH
Confidence 4677755 899999999999998764
No 71
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=39.68 E-value=46 Score=18.65 Aligned_cols=24 Identities=33% Similarity=0.480 Sum_probs=19.9
Q ss_pred ccCCCcHHHHHHHhCCCHHHHHHH
Q 024891 121 LARGDTVASLAVKYSVQVMDIKRL 144 (261)
Q Consensus 121 V~~GDTL~~IA~rYgvsv~~I~~~ 144 (261)
...|.++..||..+|++...+.++
T Consensus 18 ~~~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 18 LAAGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHh
Confidence 457889999999999998887653
No 72
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=36.80 E-value=42 Score=22.41 Aligned_cols=24 Identities=17% Similarity=0.277 Sum_probs=16.3
Q ss_pred ccCCCcHHHHHHHhCCCHHHHHHH
Q 024891 121 LARGDTVASLAVKYSVQVMDIKRL 144 (261)
Q Consensus 121 V~~GDTL~~IA~rYgvsv~~I~~~ 144 (261)
...|-|+..||.++|++...|.+.
T Consensus 17 ~~~G~s~~~IA~~lg~s~sTV~re 40 (44)
T PF13936_consen 17 LEQGMSIREIAKRLGRSRSTVSRE 40 (44)
T ss_dssp HCS---HHHHHHHTT--HHHHHHH
T ss_pred HHcCCCHHHHHHHHCcCcHHHHHH
Confidence 578999999999999999988664
No 73
>PF11268 DUF3071: Protein of unknown function (DUF3071); InterPro: IPR021421 Some members in this family of proteins are annotated as DNA-binding proteins however this cannot be confirmed. Currently no function is known.
Probab=36.54 E-value=29 Score=30.42 Aligned_cols=30 Identities=23% Similarity=0.401 Sum_probs=26.4
Q ss_pred eEEEEccCCCcHHHHHHHhCCCHHHHHHHh
Q 024891 116 AISHRLARGDTVASLAVKYSVQVMDIKRLN 145 (261)
Q Consensus 116 ~~~h~V~~GDTL~~IA~rYgvsv~~I~~~N 145 (261)
-|.-.|+.|-|...||..||++++.|+++=
T Consensus 61 eIQarIRaGas~eeVA~~~G~~~~rV~rfa 90 (170)
T PF11268_consen 61 EIQARIRAGASAEEVAEEAGVPVERVRRFA 90 (170)
T ss_pred HHHHHHHCCCCHHHHHHHhCCCHHHhhhcc
Confidence 345668999999999999999999999874
No 74
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=34.14 E-value=35 Score=26.69 Aligned_cols=27 Identities=22% Similarity=0.385 Sum_probs=24.4
Q ss_pred ccCCCcHHHHHHHhCCCHHHHHHHhCC
Q 024891 121 LARGDTVASLAVKYSVQVMDIKRLNNM 147 (261)
Q Consensus 121 V~~GDTL~~IA~rYgvsv~~I~~~N~L 147 (261)
++.|-|-..||.++|+|+..|-|.|+.
T Consensus 46 L~~g~syreIa~~tgvS~aTItRvsr~ 72 (87)
T PF01371_consen 46 LDEGKSYREIAEETGVSIATITRVSRC 72 (87)
T ss_dssp HHTTSSHHHHHHHHTSTHHHHHHHHHH
T ss_pred HHCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 458999999999999999999999873
No 75
>KOG2502 consensus Tub family proteins [General function prediction only]
Probab=33.80 E-value=42 Score=32.77 Aligned_cols=45 Identities=24% Similarity=0.513 Sum_probs=34.7
Q ss_pred ccCCCC-CcccCCCcccHHHHHHhcCCH--------HHHHHhhhhhhhhhhhccc
Q 024891 35 VISPMN-SHFSALACPDTLRLILSNLSV--------TDLARASCVCRAWSSVASD 80 (261)
Q Consensus 35 ~~~~~~-~~~~~lp~~D~L~~Il~rL~p--------~~Lara~cVCk~W~~~~~~ 80 (261)
.++|.+ +.+..|| ...|.+|+.+.+- +..+.+++||+.|+..+.+
T Consensus 36 ~~s~~~~~~~~~l~-~~~L~d~~~r~eese~~wp~r~~vvs~~~~~~~~r~~~~~ 89 (355)
T KOG2502|consen 36 FPSPSDQSLWAALP-PELLSDVLKRDEESEDTWPSRRNVVSCAGVCDKWREISKE 89 (355)
T ss_pred CccccccchhhcCC-HhHHHHHhhhccccccccccccccccccchhhhhhhhccc
Confidence 344444 6689999 9999999998832 2478889999999987554
No 76
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=33.47 E-value=53 Score=21.81 Aligned_cols=23 Identities=13% Similarity=0.228 Sum_probs=18.9
Q ss_pred cHHHHHHHhCCCHHHHHHH-hCCC
Q 024891 126 TVASLAVKYSVQVMDIKRL-NNMM 148 (261)
Q Consensus 126 TL~~IA~rYgvsv~~I~~~-N~L~ 148 (261)
|...||.+||+|...+.++ +.|.
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~ 45 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLE 45 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 7889999999999998885 3443
No 77
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=33.23 E-value=60 Score=21.00 Aligned_cols=25 Identities=24% Similarity=0.230 Sum_probs=22.1
Q ss_pred ccCCCcHHHHHHHhCCCHHHHHHHh
Q 024891 121 LARGDTVASLAVKYSVQVMDIKRLN 145 (261)
Q Consensus 121 V~~GDTL~~IA~rYgvsv~~I~~~N 145 (261)
+..|-+...||.++|++...+.+.-
T Consensus 15 ~~~g~s~~eia~~l~is~~tv~~~~ 39 (58)
T smart00421 15 LAEGLTNKEIAERLGISEKTVKTHL 39 (58)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 4678999999999999999998764
No 78
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=32.71 E-value=76 Score=26.57 Aligned_cols=33 Identities=21% Similarity=0.251 Sum_probs=27.0
Q ss_pred HHHhhhhccCHHHHHHHHHhcCCCHHHHHHHHH
Q 024891 217 NSLRRSMQVDDETAQYYLSISNGNLRAALSEFS 249 (261)
Q Consensus 217 ~~~~r~m~~D~~~A~~YL~~a~~d~~~Av~~~~ 249 (261)
+++-.--.++.++|+-=|+.+|||+..|+....
T Consensus 89 kLV~eQa~VsreeA~kAL~e~~GDlaeAIm~L~ 121 (122)
T COG1308 89 KLVMEQAGVSREEAIKALEEAGGDLAEAIMKLT 121 (122)
T ss_pred HHHHHHhCCCHHHHHHHHHHcCCcHHHHHHHhc
Confidence 345444559999999999999999999998653
No 79
>TIGR00274 N-acetylmuramic acid 6-phosphate etherase. This protein, MurQ, is involved in recycling components of the bacterial murein sacculus turned over during cell growth. The cell wall metabolite anhydro-N-acetylmuramic acid (anhMurNAc) is converted by a kinase, AnmK, to MurNAc-phosphate, then converted to N-acetylglucosamine-phosphate by this etherase, called MurQ. This family of proteins is similar to the C-terminal half of a number of vertebrate glucokinase regulator proteins and contains a Prosite pattern which is shared by this group of proteins in a region of local similarity.
Probab=31.96 E-value=75 Score=29.80 Aligned_cols=44 Identities=16% Similarity=0.243 Sum_probs=35.5
Q ss_pred hhhhhhHHHHHHHhhhhccCHHHHHHHHHhcCCCHHHHHHHHHh
Q 024891 207 TSVHGRRRIINSLRRSMQVDDETAQYYLSISNGNLRAALSEFSA 250 (261)
Q Consensus 207 ~~E~~k~kl~~~~~r~m~~D~~~A~~YL~~a~~d~~~Av~~~~~ 250 (261)
+-++.+.|-.+.+.+..+++.++|+.+|+.++|+..-|+-....
T Consensus 225 ~N~kl~~Ra~~i~~~~~~~~~~~a~~~l~~~~~~vk~Ai~~~~~ 268 (291)
T TIGR00274 225 SNEKLKARAVRIVRQATDCNKELAEQTLLAADQNVKLAIVMILS 268 (291)
T ss_pred ccHHHHHHHHHHHHHHhCcCHHHHHHHHHHhCCCcHHHHHHHHh
Confidence 34555556567788888899999999999999999999886544
No 80
>PF12471 GTP_CH_N: GTP cyclohydrolase N terminal ; InterPro: IPR022163 This domain family is found in bacteria and eukaryotes, and is approximately 190 amino acids in length. This family is the N-terminal of GTP cyclohydrolase, the rate limiting enzyme in the synthesis of tetrahydrobiopterin.
Probab=31.81 E-value=31 Score=30.88 Aligned_cols=27 Identities=7% Similarity=0.148 Sum_probs=21.9
Q ss_pred EEEccCCCcHHHHHHHhCCCHHHHHHH
Q 024891 118 SHRLARGDTVASLAVKYSVQVMDIKRL 144 (261)
Q Consensus 118 ~h~V~~GDTL~~IA~rYgvsv~~I~~~ 144 (261)
.--|.|==-|-+||.||||+..+|+|.
T Consensus 164 K~AvEPVWyLPGVA~RFGi~E~~LRR~ 190 (194)
T PF12471_consen 164 KAAVEPVWYLPGVAERFGISEGELRRA 190 (194)
T ss_pred EEEecccccchhhHHHcCCCHHHHHHH
Confidence 344555566889999999999999986
No 81
>PRK12570 N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=31.77 E-value=70 Score=30.03 Aligned_cols=45 Identities=13% Similarity=0.158 Sum_probs=35.4
Q ss_pred hhhhhhhHHHHHHHhhhhccCHHHHHHHHHhcCCCHHHHHHHHHh
Q 024891 206 VTSVHGRRRIINSLRRSMQVDDETAQYYLSISNGNLRAALSEFSA 250 (261)
Q Consensus 206 ~~~E~~k~kl~~~~~r~m~~D~~~A~~YL~~a~~d~~~Av~~~~~ 250 (261)
.+-++.+.|-.+.+.+..++|+++|+..|+.++|+..-|+-....
T Consensus 225 ~~n~kl~~Ra~~i~~~~~~~~~~~a~~~l~~~~~~vk~ai~~~~~ 269 (296)
T PRK12570 225 ATNEKLVARAVRIVMQATGCSEDEAKELLKESDNDVKLAILMILT 269 (296)
T ss_pred cchHHHHHHHHHHHHHHHCcCHHHHHHHHHHhCCccHHHHHHHHh
Confidence 344555566667788888999999999999999999988875443
No 82
>PRK07993 DNA polymerase III subunit delta'; Validated
Probab=31.77 E-value=3.1e+02 Score=26.09 Aligned_cols=37 Identities=24% Similarity=0.402 Sum_probs=26.2
Q ss_pred HhhhhccCHHHHHHHHHhcCCCHHHHHHHHHhhHHHHh
Q 024891 219 LRRSMQVDDETAQYYLSISNGNLRAALSEFSADLEWER 256 (261)
Q Consensus 219 ~~r~m~~D~~~A~~YL~~a~~d~~~Av~~~~~D~~WE~ 256 (261)
+.+-..+|.+.|..=+.++++++.+|++... |..|+.
T Consensus 176 L~~~~~~~~~~a~~~~~la~G~~~~Al~l~~-~~~~~~ 212 (334)
T PRK07993 176 LSREVTMSQDALLAALRLSAGAPGAALALLQ-PERWQQ 212 (334)
T ss_pred HHHccCCCHHHHHHHHHHcCCCHHHHHHHhc-CchHHH
Confidence 4333458888888888999999999985554 445543
No 83
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=31.67 E-value=98 Score=19.63 Aligned_cols=20 Identities=30% Similarity=0.160 Sum_probs=17.8
Q ss_pred cHHHHHHHhCCCHHHHHHHh
Q 024891 126 TVASLAVKYSVQVMDIKRLN 145 (261)
Q Consensus 126 TL~~IA~rYgvsv~~I~~~N 145 (261)
|+..+|..+||+...|.++-
T Consensus 3 t~~e~a~~lgis~~ti~~~~ 22 (49)
T TIGR01764 3 TVEEAAEYLGVSKDTVYRLI 22 (49)
T ss_pred CHHHHHHHHCCCHHHHHHHH
Confidence 67899999999999999874
No 84
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=31.54 E-value=47 Score=23.31 Aligned_cols=20 Identities=35% Similarity=0.441 Sum_probs=17.9
Q ss_pred CcHHHHHHHhCCCHHHHHHH
Q 024891 125 DTVASLAVKYSVQVMDIKRL 144 (261)
Q Consensus 125 DTL~~IA~rYgvsv~~I~~~ 144 (261)
=|+..||..||||...|++.
T Consensus 15 ~s~~ela~~~~VS~~TiRRD 34 (57)
T PF08220_consen 15 VSVKELAEEFGVSEMTIRRD 34 (57)
T ss_pred EEHHHHHHHHCcCHHHHHHH
Confidence 47889999999999999885
No 85
>PF13808 DDE_Tnp_1_assoc: DDE_Tnp_1-associated
Probab=31.04 E-value=51 Score=25.37 Aligned_cols=23 Identities=35% Similarity=0.476 Sum_probs=20.5
Q ss_pred CCCcccHHHHHHhcCCHHHHHHh
Q 024891 45 ALACPDTLRLILSNLSVTDLARA 67 (261)
Q Consensus 45 ~lp~~D~L~~Il~rL~p~~Lara 67 (261)
.+||.|++..||+.|+|.+|.++
T Consensus 62 ~~PS~~Ti~rvl~~ld~~~l~~~ 84 (90)
T PF13808_consen 62 GVPSHDTIRRVLSRLDPEALEEA 84 (90)
T ss_pred CCCcHHHHHHHHHHCCHHHHHHH
Confidence 48899999999999999999655
No 86
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=30.50 E-value=58 Score=21.34 Aligned_cols=21 Identities=14% Similarity=0.194 Sum_probs=17.4
Q ss_pred cHHHHHHHhCCCHHHHHHHhC
Q 024891 126 TVASLAVKYSVQVMDIKRLNN 146 (261)
Q Consensus 126 TL~~IA~rYgvsv~~I~~~N~ 146 (261)
|+..+|...||++..|+.+=.
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~ 21 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYER 21 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHH
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 567899999999999999864
No 87
>PHA01976 helix-turn-helix protein
Probab=29.84 E-value=36 Score=23.85 Aligned_cols=20 Identities=20% Similarity=-0.001 Sum_probs=17.5
Q ss_pred CCCcHHHHHHHhCCCHHHHH
Q 024891 123 RGDTVASLAVKYSVQVMDIK 142 (261)
Q Consensus 123 ~GDTL~~IA~rYgvsv~~I~ 142 (261)
+-++|..||..|||+++.|.
T Consensus 43 ~~~~l~~ia~~l~v~~~~l~ 62 (67)
T PHA01976 43 NLKTLLRLADALGVTLDWLC 62 (67)
T ss_pred CHHHHHHHHHHHCcCHHHHh
Confidence 34889999999999999884
No 88
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=29.76 E-value=63 Score=21.53 Aligned_cols=28 Identities=18% Similarity=0.271 Sum_probs=21.7
Q ss_pred EEEEccCCCcHHHHHHHhCCCHHHHHHH
Q 024891 117 ISHRLARGDTVASLAVKYSVQVMDIKRL 144 (261)
Q Consensus 117 ~~h~V~~GDTL~~IA~rYgvsv~~I~~~ 144 (261)
+.+.+...=|+..||+.+||+...+++.
T Consensus 20 i~~~~~~~~s~~~vA~~~~vs~~TV~ri 47 (52)
T PF13542_consen 20 ILKLLRESRSFKDVARELGVSWSTVRRI 47 (52)
T ss_pred HHHHHhhcCCHHHHHHHHCCCHHHHHHH
Confidence 3344444459999999999999998875
No 89
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=29.72 E-value=49 Score=23.28 Aligned_cols=24 Identities=29% Similarity=0.531 Sum_probs=17.6
Q ss_pred ccCCCcHHHHHHHhC-CCHHHHHHH
Q 024891 121 LARGDTVASLAVKYS-VQVMDIKRL 144 (261)
Q Consensus 121 V~~GDTL~~IA~rYg-vsv~~I~~~ 144 (261)
+..|.|...|+..|. ++.++|..+
T Consensus 28 ~~~G~s~eeI~~~yp~Lt~~~i~aA 52 (56)
T PF04255_consen 28 LAAGESPEEIAEDYPSLTLEDIRAA 52 (56)
T ss_dssp HHTT--HHHHHHHSTT--HHHHHHH
T ss_pred HHcCCCHHHHHHHCCCCCHHHHHHH
Confidence 489999999999997 999999865
No 90
>PRK12845 3-ketosteroid-delta-1-dehydrogenase; Reviewed
Probab=29.37 E-value=44 Score=33.98 Aligned_cols=26 Identities=38% Similarity=0.459 Sum_probs=21.8
Q ss_pred ccCCCcHHHHHHHhCCCHHHHH----HHhC
Q 024891 121 LARGDTVASLAVKYSVQVMDIK----RLNN 146 (261)
Q Consensus 121 V~~GDTL~~IA~rYgvsv~~I~----~~N~ 146 (261)
+.++|||..||.+.||+++.|+ ++|.
T Consensus 421 ~~kadTleELA~k~gid~~~L~~TV~~yN~ 450 (564)
T PRK12845 421 AHRADSLADLARKIGVPVDTFVATMRRFNE 450 (564)
T ss_pred eEecCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 4589999999999999987765 6675
No 91
>KOG1470 consensus Phosphatidylinositol transfer protein PDR16 and related proteins [Lipid transport and metabolism]
Probab=29.07 E-value=84 Score=30.37 Aligned_cols=35 Identities=23% Similarity=0.335 Sum_probs=31.7
Q ss_pred cCHHHHHHHHHhcCCCHHHHHHHHHhhHHHHhhcc
Q 024891 225 VDDETAQYYLSISNGNLRAALSEFSADLEWERQGA 259 (261)
Q Consensus 225 ~D~~~A~~YL~~a~~d~~~Av~~~~~D~~WE~~~~ 259 (261)
.....-..||..-+||..+|.+.+.+.+.|-++-+
T Consensus 47 ~~d~cllRfLrAr~wnv~kA~kml~~tL~WR~~~~ 81 (324)
T KOG1470|consen 47 CSDACLLRFLRARKWNVKKASKMLSNTLKWRRSFG 81 (324)
T ss_pred CcHHHHHHHHHHcCCcHHHHHHHHHHHhHHHHhcC
Confidence 46778899999999999999999999999998754
No 92
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=28.85 E-value=69 Score=20.16 Aligned_cols=20 Identities=20% Similarity=0.129 Sum_probs=17.8
Q ss_pred cHHHHHHHhCCCHHHHHHHh
Q 024891 126 TVASLAVKYSVQVMDIKRLN 145 (261)
Q Consensus 126 TL~~IA~rYgvsv~~I~~~N 145 (261)
|+..+|..+||+...|.++=
T Consensus 2 s~~e~a~~lgvs~~tl~~~~ 21 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWV 21 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 57889999999999999883
No 93
>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=28.51 E-value=63 Score=22.60 Aligned_cols=20 Identities=15% Similarity=0.164 Sum_probs=17.8
Q ss_pred cHHHHHHHhCCCHHHHHHHh
Q 024891 126 TVASLAVKYSVQVMDIKRLN 145 (261)
Q Consensus 126 TL~~IA~rYgvsv~~I~~~N 145 (261)
|+..+|.++||+...|+++=
T Consensus 2 s~~eva~~~gvs~~tlr~w~ 21 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWE 21 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 57789999999999999873
No 94
>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=28.49 E-value=30 Score=23.22 Aligned_cols=19 Identities=21% Similarity=0.132 Sum_probs=16.3
Q ss_pred CCCcHHHHHHHhCCCHHHH
Q 024891 123 RGDTVASLAVKYSVQVMDI 141 (261)
Q Consensus 123 ~GDTL~~IA~rYgvsv~~I 141 (261)
.-|++..||..|||+++.|
T Consensus 37 ~~~~~~~ia~~l~~~~~~l 55 (55)
T PF01381_consen 37 SLDTLKKIAKALGVSPEYL 55 (55)
T ss_dssp BHHHHHHHHHHHTSEHHHH
T ss_pred CHHHHHHHHHHHCCCHHHC
Confidence 3488999999999999875
No 95
>PRK12837 3-ketosteroid-delta-1-dehydrogenase; Provisional
Probab=28.41 E-value=49 Score=32.95 Aligned_cols=27 Identities=30% Similarity=0.409 Sum_probs=22.0
Q ss_pred ccCCCcHHHHHHHhCCCHHHHH----HHhCC
Q 024891 121 LARGDTVASLAVKYSVQVMDIK----RLNNM 147 (261)
Q Consensus 121 V~~GDTL~~IA~rYgvsv~~I~----~~N~L 147 (261)
+.+.|||..||.+.|++++.|+ ++|.+
T Consensus 372 ~~kaDTleELA~k~gid~~~L~~Tv~~yN~~ 402 (513)
T PRK12837 372 WRTADTLEELAAKIGVPADALTATVARFNGF 402 (513)
T ss_pred eeecCCHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 3478999999999999987765 66743
No 96
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=28.17 E-value=65 Score=23.63 Aligned_cols=23 Identities=17% Similarity=0.215 Sum_probs=19.8
Q ss_pred CCcHHHHHHHhCCCHHHHHHHhC
Q 024891 124 GDTVASLAVKYSVQVMDIKRLNN 146 (261)
Q Consensus 124 GDTL~~IA~rYgvsv~~I~~~N~ 146 (261)
+=+|-.||.++||+...|+++=.
T Consensus 22 ~i~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 22 KIKLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred CccHHHHHHHHCCCHHHHHHHhh
Confidence 34899999999999999998743
No 97
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=28.12 E-value=42 Score=23.11 Aligned_cols=19 Identities=26% Similarity=0.296 Sum_probs=16.2
Q ss_pred cHHHHHHHhCCCHHHHHHH
Q 024891 126 TVASLAVKYSVQVMDIKRL 144 (261)
Q Consensus 126 TL~~IA~rYgvsv~~I~~~ 144 (261)
++..||..+|+++.+|.+.
T Consensus 5 ~V~elAk~l~v~~~~ii~~ 23 (54)
T PF04760_consen 5 RVSELAKELGVPSKEIIKK 23 (54)
T ss_dssp -TTHHHHHHSSSHHHHHHH
T ss_pred EHHHHHHHHCcCHHHHHHH
Confidence 5678999999999998876
No 98
>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A.
Probab=27.86 E-value=60 Score=25.01 Aligned_cols=23 Identities=17% Similarity=0.355 Sum_probs=17.3
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHH
Q 024891 122 ARGDTVASLAVKYSVQVMDIKRL 144 (261)
Q Consensus 122 ~~GDTL~~IA~rYgvsv~~I~~~ 144 (261)
+.|=||.+||..+|++...+..+
T Consensus 13 krG~sL~~lsr~~Gl~~~tl~na 35 (78)
T PF13693_consen 13 KRGTSLAALSREAGLSSSTLRNA 35 (78)
T ss_dssp TTS--HHHHHHHHSS-HHHHHHT
T ss_pred HcCCCHHHHHHHcCCCHHHHHHH
Confidence 58999999999999999887655
No 99
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=27.71 E-value=70 Score=25.70 Aligned_cols=24 Identities=25% Similarity=0.162 Sum_probs=21.5
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHHh
Q 024891 122 ARGDTVASLAVKYSVQVMDIKRLN 145 (261)
Q Consensus 122 ~~GDTL~~IA~rYgvsv~~I~~~N 145 (261)
.|+-||..||.+|||+...|-++=
T Consensus 69 ~pd~tl~Ela~~l~Vs~~ti~~~L 92 (119)
T PF01710_consen 69 NPDATLRELAERLGVSPSTIWRAL 92 (119)
T ss_pred CCCcCHHHHHHHcCCCHHHHHHHH
Confidence 689999999999999999987763
No 100
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=27.25 E-value=59 Score=25.39 Aligned_cols=27 Identities=19% Similarity=0.340 Sum_probs=24.0
Q ss_pred EccCCCcHHHHHHHhCCCHHHHHHHhC
Q 024891 120 RLARGDTVASLAVKYSVQVMDIKRLNN 146 (261)
Q Consensus 120 ~V~~GDTL~~IA~rYgvsv~~I~~~N~ 146 (261)
.+..|.|...||.++|+|...|.++.+
T Consensus 46 ll~~G~S~~eIA~~LgISrsTIyRi~R 72 (88)
T TIGR02531 46 MLKQGKTYSDIEAETGASTATISRVKR 72 (88)
T ss_pred HHHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 367899999999999999999998764
No 101
>COG4387 Mu-like prophage protein gp36 [Function unknown]
Probab=26.82 E-value=76 Score=26.86 Aligned_cols=30 Identities=13% Similarity=0.227 Sum_probs=24.4
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHhhHHHHhh
Q 024891 227 DETAQYYLSISNGNLRAALSEFSADLEWERQ 257 (261)
Q Consensus 227 ~~~A~~YL~~a~~d~~~Av~~~~~D~~WE~~ 257 (261)
-+.|+|||.-+- --++|...|+++.+|=+.
T Consensus 70 C~IA~Y~L~~~r-~Tdq~r~rYe~av~~L~~ 99 (139)
T COG4387 70 CDIARYRLCKNR-ATDQARQRYEDAVRFLEK 99 (139)
T ss_pred HHHHHHHHhhhh-hhHHHHHHHHHHHHHHHH
Confidence 468999999555 667899999999999653
No 102
>PF12637 TSCPD: TSCPD domain; InterPro: IPR024434 The domain is found in isolation in many proteins where it has a conserved C-terminal motif TSCPD, after which the domain is named. Most copies of the domain possess 4 conserved cysteines that may be part of an Iron-sulphur cluster. This domain is found at the C terminus of some ribonucleoside-diphosphate reductase enzymes.
Probab=26.72 E-value=59 Score=25.40 Aligned_cols=19 Identities=26% Similarity=0.256 Sum_probs=16.6
Q ss_pred cHHHHHHHhCCCHHHHHHH
Q 024891 126 TVASLAVKYSVQVMDIKRL 144 (261)
Q Consensus 126 TL~~IA~rYgvsv~~I~~~ 144 (261)
.|-++|+|+|+++++|.+.
T Consensus 45 rliS~~Lr~G~~~~~ii~~ 63 (95)
T PF12637_consen 45 RLISLALRSGVPPEEIIDQ 63 (95)
T ss_pred HHHHHHHHcCCCHHHHHHH
Confidence 3778999999999998876
No 103
>PF04921 XAP5: XAP5, circadian clock regulator; InterPro: IPR007005 These proteins are found in a wide range of eukaryotes. Their function is uncertain though they are nuclear proteins, possibly with DNA-binding activity.; GO: 0005634 nucleus
Probab=26.60 E-value=60 Score=30.03 Aligned_cols=46 Identities=28% Similarity=0.477 Sum_probs=31.0
Q ss_pred EEEccCCCcHHHHHHHhCCC-HHHHHHHhCCCCCcCccCCCEEEecC
Q 024891 118 SHRLARGDTVASLAVKYSVQ-VMDIKRLNNMMSDHGIYSRERLLIPI 163 (261)
Q Consensus 118 ~h~V~~GDTL~~IA~rYgvs-v~~I~~~N~L~s~~~i~~gq~L~IP~ 163 (261)
.-+|++|||++.+=.+---- ..+.+.+=....++++++..-|+||-
T Consensus 114 ~v~vKKGdtI~~FL~~~r~~l~~~f~el~~vsvd~LM~VkedlIiPH 160 (239)
T PF04921_consen 114 TVRVKKGDTIWQFLEKCRKQLAKEFRELRRVSVDDLMYVKEDLIIPH 160 (239)
T ss_pred eEEEcCCCCHHHHHHHHHHHHHHHhHHHHhcCHhheeeeccceeccC
Confidence 45689999999875443111 12233344456778999999999995
No 104
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=26.58 E-value=73 Score=24.42 Aligned_cols=23 Identities=22% Similarity=0.228 Sum_probs=20.8
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHH
Q 024891 122 ARGDTVASLAVKYSVQVMDIKRL 144 (261)
Q Consensus 122 ~~GDTL~~IA~rYgvsv~~I~~~ 144 (261)
..|-++..||..+|+|...|++.
T Consensus 124 ~~g~s~~eIA~~l~~s~~~v~~~ 146 (158)
T TIGR02937 124 LEGLSYKEIAEILGISVGTVKRR 146 (158)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHH
Confidence 47999999999999999999875
No 105
>COG3721 HugX Putative heme iron utilization protein [Inorganic ion transport and metabolism]
Probab=26.36 E-value=73 Score=27.99 Aligned_cols=24 Identities=25% Similarity=0.411 Sum_probs=22.1
Q ss_pred ccCCCcHHHHHHHhCCCHHHHHHH
Q 024891 121 LARGDTVASLAVKYSVQVMDIKRL 144 (261)
Q Consensus 121 V~~GDTL~~IA~rYgvsv~~I~~~ 144 (261)
-||.-||..||.+|+|++-+|.++
T Consensus 24 ~qPdg~~eamA~~~~v~~~eIv~a 47 (176)
T COG3721 24 TQPDGTLEAMAEQYNVTELEIVRA 47 (176)
T ss_pred hCCCCcHHHHHHHhCCCHHHHHHh
Confidence 378889999999999999999987
No 106
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=26.27 E-value=72 Score=22.34 Aligned_cols=21 Identities=14% Similarity=0.184 Sum_probs=18.5
Q ss_pred cHHHHHHHhCCCHHHHHHHhC
Q 024891 126 TVASLAVKYSVQVMDIKRLNN 146 (261)
Q Consensus 126 TL~~IA~rYgvsv~~I~~~N~ 146 (261)
|+..+|..+|||...|+.+=+
T Consensus 2 ti~eva~~~gvs~~tlr~y~~ 22 (69)
T PF13411_consen 2 TIKEVAKLLGVSPSTLRYYER 22 (69)
T ss_dssp EHHHHHHHTTTTHHHHHHHHH
T ss_pred cHHHHHHHHCcCHHHHHHHHH
Confidence 578899999999999999843
No 107
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, 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=25.14 E-value=86 Score=20.29 Aligned_cols=20 Identities=20% Similarity=0.209 Sum_probs=17.9
Q ss_pred cHHHHHHHhCCCHHHHHHHh
Q 024891 126 TVASLAVKYSVQVMDIKRLN 145 (261)
Q Consensus 126 TL~~IA~rYgvsv~~I~~~N 145 (261)
|+..+|...||++..|+.+-
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~ 21 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYE 21 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHH
Confidence 57889999999999999883
No 108
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=24.87 E-value=81 Score=22.03 Aligned_cols=20 Identities=20% Similarity=0.248 Sum_probs=18.0
Q ss_pred cHHHHHHHhCCCHHHHHHHh
Q 024891 126 TVASLAVKYSVQVMDIKRLN 145 (261)
Q Consensus 126 TL~~IA~rYgvsv~~I~~~N 145 (261)
|+..+|.++||+...|+.+=
T Consensus 2 s~~eva~~~gvs~~tlr~~~ 21 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYYE 21 (70)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 57889999999999999983
No 109
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=23.84 E-value=1.1e+02 Score=19.85 Aligned_cols=25 Identities=24% Similarity=0.212 Sum_probs=21.5
Q ss_pred ccCCCcHHHHHHHhCCCHHHHHHHh
Q 024891 121 LARGDTVASLAVKYSVQVMDIKRLN 145 (261)
Q Consensus 121 V~~GDTL~~IA~rYgvsv~~I~~~N 145 (261)
+..|-|...||..+|++...+.+.-
T Consensus 12 ~~~~~s~~eia~~l~~s~~tv~~~~ 36 (57)
T cd06170 12 LAEGKTNKEIADILGISEKTVKTHL 36 (57)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 3478899999999999999988774
No 110
>PRK07843 3-ketosteroid-delta-1-dehydrogenase; Reviewed
Probab=23.44 E-value=68 Score=32.39 Aligned_cols=27 Identities=33% Similarity=0.525 Sum_probs=22.1
Q ss_pred ccCCCcHHHHHHHhCCCHHHHH----HHhCC
Q 024891 121 LARGDTVASLAVKYSVQVMDIK----RLNNM 147 (261)
Q Consensus 121 V~~GDTL~~IA~rYgvsv~~I~----~~N~L 147 (261)
+.+.|||..||.+.|++.+.|+ ++|..
T Consensus 413 ~~kadTleELA~~~gid~~~L~aTV~~yN~~ 443 (557)
T PRK07843 413 IVKADTLAELAAKIGVPADALTATVQRFNGF 443 (557)
T ss_pred eeecCCHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 4578999999999999987665 67753
No 111
>PRK12839 hypothetical protein; Provisional
Probab=23.35 E-value=66 Score=32.79 Aligned_cols=27 Identities=30% Similarity=0.469 Sum_probs=21.9
Q ss_pred ccCCCcHHHHHHHhCCCHHHH----HHHhCC
Q 024891 121 LARGDTVASLAVKYSVQVMDI----KRLNNM 147 (261)
Q Consensus 121 V~~GDTL~~IA~rYgvsv~~I----~~~N~L 147 (261)
+.+.|||..||.+.|++++.| .++|..
T Consensus 424 ~~kadTleELA~k~gid~~~L~~TV~~yN~~ 454 (572)
T PRK12839 424 LTRGRTIEELAEKCGIDPAGLEATVAEFNEN 454 (572)
T ss_pred EEECCCHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 347899999999999997765 567854
No 112
>PF08299 Bac_DnaA_C: Bacterial dnaA protein helix-turn-helix; InterPro: IPR013159 This entry represents the C-terminal domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; GO: 0005524 ATP binding, 0043565 sequence-specific DNA binding, 0006270 DNA-dependent DNA replication initiation, 0006275 regulation of DNA replication; PDB: 2HCB_B 3R8F_C 1L8Q_A 3PVP_B 3PVV_A 1J1V_A.
Probab=23.14 E-value=72 Score=23.43 Aligned_cols=22 Identities=27% Similarity=0.445 Sum_probs=14.6
Q ss_pred CcHHHHHHHhCCCHHHHHHHhC
Q 024891 125 DTVASLAVKYSVQVMDIKRLNN 146 (261)
Q Consensus 125 DTL~~IA~rYgvsv~~I~~~N~ 146 (261)
+-+..+|..|||++++|..-.+
T Consensus 4 ~Ii~~Va~~~~v~~~~i~s~~R 25 (70)
T PF08299_consen 4 DIIEAVAEYFGVSVEDIRSKSR 25 (70)
T ss_dssp HHHHHHHHHTT--HHHHHSS--
T ss_pred HHHHHHHHHHCCCHHHHhCCCC
Confidence 3467899999999999985433
No 113
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=22.68 E-value=35 Score=23.60 Aligned_cols=20 Identities=15% Similarity=0.130 Sum_probs=15.7
Q ss_pred CCcHHHHHHHhCCCHHHHHH
Q 024891 124 GDTVASLAVKYSVQVMDIKR 143 (261)
Q Consensus 124 GDTL~~IA~rYgvsv~~I~~ 143 (261)
-++|..||.-+||++++|..
T Consensus 40 ~~~l~~ia~~l~~~~~el~~ 59 (63)
T PF13443_consen 40 LDTLEKIAKALNCSPEELFE 59 (63)
T ss_dssp HHHHHHHHHHHT--HHHCTE
T ss_pred HHHHHHHHHHcCCCHHHHhh
Confidence 38999999999999999864
No 114
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=22.14 E-value=74 Score=30.01 Aligned_cols=23 Identities=26% Similarity=0.284 Sum_probs=19.3
Q ss_pred CCcHHHHHHHhCCCHHHHHHHhC
Q 024891 124 GDTVASLAVKYSVQVMDIKRLNN 146 (261)
Q Consensus 124 GDTL~~IA~rYgvsv~~I~~~N~ 146 (261)
|=-|-.||.+|||++..|+.+=+
T Consensus 19 gmk~~dIAeklGvspntiksWKr 41 (279)
T COG5484 19 GMKLKDIAEKLGVSPNTIKSWKR 41 (279)
T ss_pred hccHHHHHHHhCCChHHHHHHHH
Confidence 34577899999999999998853
No 115
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. 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. A typical MerR regulator is 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 dissimilar C-terminal domains bind spe
Probab=22.11 E-value=2.2e+02 Score=23.46 Aligned_cols=21 Identities=5% Similarity=0.128 Sum_probs=18.1
Q ss_pred cHHHHHHHhCCCHHHHHHHhC
Q 024891 126 TVASLAVKYSVQVMDIKRLNN 146 (261)
Q Consensus 126 TL~~IA~rYgvsv~~I~~~N~ 146 (261)
|+..+|.+.||++..|+.+=+
T Consensus 3 sI~eVA~~~GVs~~TLR~wE~ 23 (120)
T cd04767 3 PIGVVAELLNIHPETLRIWER 23 (120)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 678999999999999997643
No 116
>PF03540 TFIID_30kDa: Transcription initiation factor TFIID 23-30kDa subunit; InterPro: IPR003923 Transcription initiation factor TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. The complex includes TATA binding protein (TBP) and various TBP-associated factors (TAFS). TFIID a bona fide RNA polymerase II-specific TATA-binding protein-associated factor (TAF) and is essential for viability []. TFIID acts to nucleate the transcription complex, recruiting the rest of the factors through a direct interaction with TFIIB. The TBP subunit of TFIID is sufficient for TATA-element binding and TFIIB interaction, and can support basal transcription. The protein belongs to the TAF2H family.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus
Probab=21.78 E-value=1.6e+02 Score=20.94 Aligned_cols=28 Identities=32% Similarity=0.494 Sum_probs=20.1
Q ss_pred cCHHHHHHHHHhcCCCH---------HHHHHHHHhhH
Q 024891 225 VDDETAQYYLSISNGNL---------RAALSEFSADL 252 (261)
Q Consensus 225 ~D~~~A~~YL~~a~~d~---------~~Av~~~~~D~ 252 (261)
+-+.+..|||+.+|++- .-|-+.|..|.
T Consensus 3 IPD~v~~~yL~~~G~~~~D~rv~RLvSLaaQKFisdI 39 (51)
T PF03540_consen 3 IPDEVTDYYLERSGFQTSDPRVKRLVSLAAQKFISDI 39 (51)
T ss_pred CCHHHHHHHHHHCCCCCCCHhHHHHHHHHHHHHHHHH
Confidence 34678899999999963 35666666654
No 117
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=21.71 E-value=72 Score=21.96 Aligned_cols=25 Identities=20% Similarity=0.312 Sum_probs=21.5
Q ss_pred EccCCCcHHHHHHHhCCCHHHHHHH
Q 024891 120 RLARGDTVASLAVKYSVQVMDIKRL 144 (261)
Q Consensus 120 ~V~~GDTL~~IA~rYgvsv~~I~~~ 144 (261)
..+.|.|...||.+|||+.....++
T Consensus 15 ~LR~~~~~~~La~~FgIs~stvsri 39 (53)
T PF13613_consen 15 YLRLNLTFQDLAYRFGISQSTVSRI 39 (53)
T ss_pred HHHcCCcHhHHhhheeecHHHHHHH
Confidence 3678999999999999999887765
No 118
>COG1004 Ugd Predicted UDP-glucose 6-dehydrogenase [Cell envelope biogenesis, outer membrane]
Probab=21.30 E-value=1.5e+02 Score=29.58 Aligned_cols=83 Identities=18% Similarity=0.230 Sum_probs=48.9
Q ss_pred HHHHHHHhCCCHHHHHHHhCCCCCcCccCCCEEEecCCCCccccccccccccchhHHHHHhhhccCCCCCCCCccccchh
Q 024891 127 VASLAVKYSVQVMDIKRLNNMMSDHGIYSRERLLIPISSPELLIDGICYIEFDTYAKREVAVLYLEGAPEKKPSCLLNRV 206 (261)
Q Consensus 127 L~~IA~rYgvsv~~I~~~N~L~s~~~i~~gq~L~IP~~~~~~~~~~~~~~~~d~~~~re~~v~~~~~~~~~~~~~~~~~~ 206 (261)
|..||.+.|+.+.++.+.=++ |++| |..-+ ++....||+|+|. |..++-..+.-+ +. .+.+.+..
T Consensus 223 ia~ice~~g~D~~~V~~gIGl--D~RI--G~~fl----~aG~GyGGsCfPK-D~~AL~~~a~~~----~~--~~~ll~av 287 (414)
T COG1004 223 IANICEKVGADVKQVAEGIGL--DPRI--GNHFL----NAGFGYGGSCFPK-DTKALIANAEEL----GY--DPNLLEAV 287 (414)
T ss_pred HHHHHHHhCCCHHHHHHHcCC--Cchh--hHhhC----CCCCCCCCcCCcH-hHHHHHHHHHhc----CC--chHHHHHH
Confidence 678999999999999998444 4554 33322 3445679999985 443333222211 11 11132222
Q ss_pred h--hhhhhHHHHHHHhhhhc
Q 024891 207 T--SVHGRRRIINSLRRSMQ 224 (261)
Q Consensus 207 ~--~E~~k~kl~~~~~r~m~ 224 (261)
. -++||.+|++++...+.
T Consensus 288 v~vN~~qk~~~~~~i~~~~~ 307 (414)
T COG1004 288 VEVNERRKDKLAEKILNHLG 307 (414)
T ss_pred HHHHHHHHHHHHHHHHHhcC
Confidence 2 34577778888877664
No 119
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=20.70 E-value=71 Score=22.50 Aligned_cols=22 Identities=18% Similarity=0.345 Sum_probs=18.2
Q ss_pred CcHHHHHHHhCCCHHHHHHHhC
Q 024891 125 DTVASLAVKYSVQVMDIKRLNN 146 (261)
Q Consensus 125 DTL~~IA~rYgvsv~~I~~~N~ 146 (261)
+-+..+|..|||++++|..-.+
T Consensus 4 ~I~~~Va~~~~i~~~~i~s~~R 25 (60)
T smart00760 4 EIIEAVAEYFGVKPEDLKSKSR 25 (60)
T ss_pred HHHHHHHHHhCCCHHHHhcCCC
Confidence 4567899999999999977665
Done!