Query 014940
Match_columns 415
No_of_seqs 314 out of 1957
Neff 6.0
Searched_HMMs 46136
Date Fri Mar 29 01:33:41 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014940.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014940hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK06347 autolysin; Reviewed 99.9 1.4E-25 2.9E-30 239.2 19.2 205 37-252 329-563 (592)
2 PRK06347 autolysin; Reviewed 99.9 2.4E-25 5.2E-30 237.3 18.9 167 38-215 405-592 (592)
3 PRK10783 mltD membrane-bound l 99.9 2.9E-22 6.3E-27 209.1 21.3 171 37-219 262-451 (456)
4 PRK10783 mltD membrane-bound l 99.6 5.5E-15 1.2E-19 154.7 13.0 108 38-156 343-450 (456)
5 PRK13914 invasion associated s 99.6 6.8E-15 1.5E-19 152.9 13.3 170 40-218 29-247 (481)
6 PF01476 LysM: LysM domain; I 99.2 1.3E-11 2.7E-16 87.9 3.9 43 173-215 1-44 (44)
7 COG1388 LytE FOG: LysM repeat 99.2 1.2E-10 2.5E-15 100.9 8.3 98 118-218 1-114 (124)
8 PF01476 LysM: LysM domain; I 99.0 4.3E-10 9.4E-15 79.9 4.2 44 107-153 1-44 (44)
9 PRK14125 cell division suppres 98.9 4.5E-09 9.7E-14 89.2 6.6 51 169-219 35-93 (103)
10 COG1388 LytE FOG: LysM repeat 98.8 1E-08 2.2E-13 88.7 7.5 95 52-155 1-113 (124)
11 cd00118 LysM Lysin domain, fou 98.7 3.2E-08 7E-13 68.0 5.7 44 172-215 2-46 (46)
12 TIGR02899 spore_safA spore coa 98.7 3.5E-08 7.7E-13 69.1 4.9 42 175-216 1-44 (44)
13 PRK14125 cell division suppres 98.6 1.5E-07 3.3E-12 79.9 6.5 50 103-156 35-92 (103)
14 cd00118 LysM Lysin domain, fou 98.5 1.7E-07 3.6E-12 64.4 5.6 45 106-153 2-46 (46)
15 TIGR02907 spore_VI_D stage VI 98.5 1.1E-07 2.4E-12 95.0 6.4 48 168-215 291-338 (338)
16 COG3858 Predicted glycosyl hyd 98.5 9.9E-08 2.1E-12 97.7 5.9 98 105-220 2-100 (423)
17 TIGR02899 spore_safA spore coa 98.5 1.5E-07 3.3E-12 65.9 4.8 43 109-154 1-44 (44)
18 PRK10871 nlpD lipoprotein NlpD 98.5 1.7E-07 3.6E-12 94.0 5.9 48 171-218 61-109 (319)
19 PRK13914 invasion associated s 98.4 4.1E-07 8.9E-12 95.4 7.2 48 171-218 28-75 (481)
20 PRK10871 nlpD lipoprotein NlpD 98.4 4.1E-07 8.9E-12 91.3 5.6 49 105-156 61-109 (319)
21 smart00257 LysM Lysin motif. 98.4 8.7E-07 1.9E-11 60.0 5.3 43 172-214 1-44 (44)
22 TIGR02907 spore_VI_D stage VI 98.3 1.2E-06 2.6E-11 87.6 6.2 49 101-153 290-338 (338)
23 smart00257 LysM Lysin motif. 98.2 4.1E-06 8.9E-11 56.6 5.4 44 106-152 1-44 (44)
24 PRK11198 LysM domain/BON super 98.1 3.8E-06 8.3E-11 75.6 5.6 50 104-153 95-146 (147)
25 COG3858 Predicted glycosyl hyd 98.1 3.8E-06 8.3E-11 86.2 5.6 97 39-156 2-98 (423)
26 PRK11198 LysM domain/BON super 98.0 1.1E-05 2.5E-10 72.5 5.3 46 170-215 95-146 (147)
27 PRK10260 L,D-transpeptidase; P 97.3 0.001 2.2E-08 66.6 8.9 67 20-92 22-90 (306)
28 PRK10190 L,D-transpeptidase; P 97.3 0.0011 2.4E-08 66.5 8.9 84 1-91 1-86 (310)
29 COG1652 XkdP Uncharacterized p 97.2 0.00014 3.1E-09 71.4 1.7 51 105-155 211-264 (269)
30 PRK10190 L,D-transpeptidase; P 96.4 0.0062 1.3E-07 61.2 6.3 51 103-156 36-88 (310)
31 PF04225 OapA: Opacity-associa 96.4 0.0043 9.4E-08 50.9 4.3 48 171-218 3-55 (85)
32 PRK10260 L,D-transpeptidase; P 96.4 0.0069 1.5E-07 60.7 6.3 51 103-156 39-91 (306)
33 PF04225 OapA: Opacity-associa 96.2 0.0031 6.7E-08 51.8 2.4 49 104-155 2-54 (85)
34 TIGR03505 FimV_core FimV N-ter 96.1 0.0062 1.3E-07 48.8 3.7 43 113-155 1-52 (74)
35 PF05489 Phage_tail_X: Phage T 96.1 0.009 1.9E-07 45.9 4.2 48 107-155 4-54 (60)
36 TIGR03505 FimV_core FimV N-ter 95.9 0.0083 1.8E-07 48.1 3.5 40 179-218 1-53 (74)
37 COG1652 XkdP Uncharacterized p 95.9 0.003 6.6E-08 62.0 0.9 48 171-218 211-265 (269)
38 PRK11649 putative peptidase; P 94.9 0.15 3.2E-06 53.9 9.8 114 102-218 93-237 (439)
39 PF05489 Phage_tail_X: Phage T 92.9 0.2 4.4E-06 38.5 4.6 43 175-217 5-54 (60)
40 COG3170 FimV Tfp pilus assembl 89.9 0.24 5.2E-06 54.6 3.0 51 169-219 187-250 (755)
41 COG3170 FimV Tfp pilus assembl 89.4 0.27 5.9E-06 54.2 3.1 53 103-155 187-248 (755)
42 PRK11649 putative peptidase; P 89.3 0.56 1.2E-05 49.6 5.2 49 170-218 95-145 (439)
43 COG3061 OapA Cell envelope opa 86.1 1.5 3.2E-05 42.2 5.4 74 143-219 134-213 (242)
44 COG3061 OapA Cell envelope opa 86.1 1.6 3.4E-05 42.0 5.6 71 82-155 136-211 (242)
45 COG4784 Putative Zn-dependent 76.4 4.9 0.00011 41.3 5.4 45 170-214 428-476 (479)
46 COG4254 Uncharacterized protei 75.8 2.5 5.4E-05 42.4 3.2 52 105-156 6-57 (339)
47 COG0739 NlpD Membrane proteins 74.7 4.8 0.0001 38.7 4.8 48 171-218 2-50 (277)
48 COG5004 P2-like prophage tail 74.5 5.6 0.00012 31.1 4.1 52 105-156 3-57 (70)
49 PF13518 HTH_28: Helix-turn-he 72.7 3.6 7.9E-05 29.3 2.7 24 176-199 10-33 (52)
50 COG4784 Putative Zn-dependent 71.8 4.9 0.00011 41.3 4.1 47 105-152 429-476 (479)
51 TIGR00247 conserved hypothetic 71.4 34 0.00073 35.0 10.3 55 38-121 39-101 (342)
52 KOG2850 Predicted peptidoglyca 65.2 3.5 7.6E-05 38.8 1.5 50 103-155 8-57 (186)
53 PF02796 HTH_7: Helix-turn-hel 63.4 7.5 0.00016 27.7 2.6 24 175-198 18-41 (45)
54 COG4254 Uncharacterized protei 62.4 6.2 0.00013 39.7 2.7 49 170-218 5-57 (339)
55 PF01527 HTH_Tnp_1: Transposas 56.6 6.2 0.00013 30.5 1.3 25 175-199 20-44 (76)
56 KOG1187 Serine/threonine prote 56.3 7.7 0.00017 39.9 2.3 31 284-314 72-107 (361)
57 KOG2850 Predicted peptidoglyca 56.3 7.4 0.00016 36.6 2.0 49 170-218 9-58 (186)
58 COG0739 NlpD Membrane proteins 55.7 16 0.00035 35.0 4.4 47 106-155 3-49 (277)
59 PF02796 HTH_7: Helix-turn-hel 54.0 14 0.00031 26.2 2.8 23 44-66 19-41 (45)
60 PF13518 HTH_28: Helix-turn-he 48.1 21 0.00045 25.3 2.9 24 45-68 11-34 (52)
61 PF13384 HTH_23: Homeodomain-l 47.1 21 0.00045 25.3 2.8 25 175-199 14-38 (50)
62 COG5004 P2-like prophage tail 45.2 43 0.00093 26.3 4.2 47 171-217 3-56 (70)
63 COG2963 Transposase and inacti 45.0 20 0.00044 30.2 2.8 25 175-199 21-46 (116)
64 PRK09413 IS2 repressor TnpA; R 44.5 22 0.00048 30.6 3.0 27 173-199 24-50 (121)
65 PF04218 CENP-B_N: CENP-B N-te 44.3 12 0.00027 27.7 1.2 24 175-198 19-42 (53)
66 cd00569 HTH_Hin_like Helix-tur 41.8 34 0.00073 20.8 2.9 23 176-198 19-41 (42)
67 PRK10270 putative aminodeoxych 41.5 2.6E+02 0.0056 28.7 10.7 19 38-56 39-57 (340)
68 KOG1924 RhoA GTPase effector D 40.6 96 0.0021 35.5 7.7 7 349-355 565-571 (1102)
69 PF04967 HTH_10: HTH DNA bindi 37.1 33 0.00072 25.7 2.5 24 41-64 18-41 (53)
70 PF13936 HTH_38: Helix-turn-he 34.3 43 0.00093 23.7 2.6 23 175-197 17-39 (44)
71 PF04545 Sigma70_r4: Sigma-70, 34.3 46 0.00099 23.7 2.9 22 44-65 18-39 (50)
72 PF00376 MerR: MerR family reg 32.3 38 0.00082 23.4 2.0 22 48-69 1-22 (38)
73 PF13384 HTH_23: Homeodomain-l 31.9 46 0.00099 23.5 2.5 22 45-66 16-37 (50)
74 PHA00675 hypothetical protein 31.5 46 0.00099 27.0 2.6 25 176-200 37-61 (78)
75 PF04545 Sigma70_r4: Sigma-70, 29.3 71 0.0015 22.7 3.2 23 176-198 18-40 (50)
76 PF05225 HTH_psq: helix-turn-h 29.0 54 0.0012 23.5 2.4 24 175-198 12-36 (45)
77 cd04761 HTH_MerR-SF Helix-Turn 28.8 59 0.0013 22.5 2.7 23 47-69 1-23 (49)
78 PF04255 DUF433: Protein of un 28.8 52 0.0011 24.5 2.4 24 175-198 28-52 (56)
79 PHA01976 helix-turn-helix prot 28.5 95 0.0021 23.1 3.9 51 43-133 12-62 (67)
80 cd04762 HTH_MerR-trunc Helix-T 28.3 64 0.0014 21.8 2.7 21 48-68 2-22 (49)
81 PF10668 Phage_terminase: Phag 28.2 69 0.0015 24.7 3.0 25 45-69 21-45 (60)
82 PF14451 Ub-Mut7C: Mut7-C ubiq 27.8 54 0.0012 26.7 2.5 45 170-214 24-73 (81)
83 PF12471 GTP_CH_N: GTP cyclohy 27.2 39 0.00086 31.8 1.8 59 127-198 132-190 (194)
84 PF10668 Phage_terminase: Phag 27.1 66 0.0014 24.8 2.7 23 179-201 23-45 (60)
85 PF01527 HTH_Tnp_1: Transposas 26.4 38 0.00083 26.0 1.4 25 44-68 21-45 (76)
86 PF13411 MerR_1: MerR HTH fami 25.0 61 0.0013 24.3 2.3 22 48-69 2-23 (69)
87 PF01710 HTH_Tnp_IS630: Transp 24.6 51 0.0011 28.3 2.0 26 175-200 15-40 (119)
88 TIGR01764 excise DNA binding d 23.8 1.3E+02 0.0028 20.4 3.7 36 180-215 3-39 (49)
89 PF08281 Sigma70_r4_2: Sigma-7 23.8 79 0.0017 22.6 2.6 22 44-65 24-45 (54)
90 cd01104 HTH_MlrA-CarA Helix-Tu 23.0 84 0.0018 23.5 2.7 20 180-199 2-21 (68)
91 PF08139 LPAM_1: Prokaryotic m 22.6 57 0.0012 20.9 1.3 13 2-14 8-20 (25)
92 smart00421 HTH_LUXR helix_turn 22.2 1.1E+02 0.0024 21.2 3.1 25 175-199 15-39 (58)
93 smart00351 PAX Paired Box doma 21.4 85 0.0019 27.2 2.8 24 176-199 31-54 (125)
94 PHA02591 hypothetical protein; 21.0 1.1E+02 0.0023 25.1 2.9 21 46-66 59-79 (83)
95 PRK09413 IS2 repressor TnpA; R 20.7 94 0.002 26.7 2.8 26 43-68 26-51 (121)
96 PF02618 YceG: YceG-like famil 20.7 1.2E+02 0.0026 30.3 4.0 19 103-121 44-62 (297)
97 PF13011 LZ_Tnp_IS481: leucine 20.6 83 0.0018 26.0 2.3 26 174-199 21-46 (85)
98 PF08765 Mor: Mor transcriptio 20.6 93 0.002 26.3 2.7 20 178-197 72-91 (108)
99 cd04764 HTH_MlrA-like_sg1 Heli 20.4 96 0.0021 23.3 2.6 20 48-67 2-21 (67)
100 PF13613 HTH_Tnp_4: Helix-turn 20.2 81 0.0017 23.0 2.0 24 175-198 16-39 (53)
101 PF13411 MerR_1: MerR HTH fami 20.1 97 0.0021 23.2 2.5 21 180-200 2-22 (69)
No 1
>PRK06347 autolysin; Reviewed
Probab=99.93 E-value=1.4e-25 Score=239.21 Aligned_cols=205 Identities=17% Similarity=0.180 Sum_probs=154.4
Q ss_pred ccEEEEeCCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCccCCCceEEeeccccccC------------Cc----c
Q 014940 37 ALLGYTLYTDLKVSEVGSLFNVDPVSILTANAIDISYSDVENHILPSQLFVRIPVTCACVD------------GI----R 100 (415)
Q Consensus 37 a~~~Ytv~~gdtL~~IA~~fgvs~~~L~~~N~l~~t~P~~~~~~L~~Gq~l~IP~~csc~~------------g~----~ 100 (415)
.+..|+|++||+|+.||++||++.++|+++|++ ..+.|.+||.|+||..-.-.. .. .
T Consensus 329 ~~~~Y~V~sGDTL~~IA~rygvSv~eL~~~N~l-------~~d~L~~Gq~L~VP~~~~~~~~~t~~~~~~~~~~~~~~~~ 401 (592)
T PRK06347 329 NAKIYTVVKGDSLWRIANNHKVTVANLKAWNNL-------KSDFIYPGQKLKVSAGSTTSDTNTSKPSTGTSTSKPSTGT 401 (592)
T ss_pred CceEEEeCCCCCHHHHHHHhCCCHHHHHHHhCC-------CccccccCcEEEEecccccccccccccccccccccccccc
Confidence 577899999999999999999999999999997 235789999999996311000 00 0
Q ss_pred cccceeEEeCCCCCHHHHHHHHhCCCCCHHHHHhhcCCCCCCCccCCcEEEecCCCcCCCCC------------cCCCCc
Q 014940 101 KSVSTHYKTRPSDTLTSIANQVYAGLVSADQLREANDIQDPDVLDVGVNLLVPLPCTCFNGT------------DNSLPA 168 (415)
Q Consensus 101 ~~~~~~YtV~~GDTL~~IA~~~fggLvs~~~L~~~N~l~~~~~L~~Gq~L~IP~~c~c~~~~------------~~~~~~ 168 (415)
...+..|+|++||||+.||++ |+ +++.+|++||++. .+.|.+||.|.||....-.... ......
T Consensus 402 ~~~~~~ytVk~GDTL~sIA~k-yg--VSv~~L~~~N~l~-s~~L~~Gq~L~IP~~~~~~~~t~~~s~~~~~~k~~s~~~~ 477 (592)
T PRK06347 402 STNAKVYTVVKGDSLWRIANN-NK--VTIANLKSWNNLK-SDFIYPGQKLKVSAGSTSNTNTSKPSTNTNTSKPSTNTNT 477 (592)
T ss_pred ccCceeEEecCCCCHHHHHHH-hC--CCHHHHHHHhCCC-cceeccCcEEEEecCCcccccccccccccccccccccccc
Confidence 124568999999999999999 99 9999999999975 4679999999999753210000 000112
Q ss_pred eeeeEEecCCCCHHHHHHHhCCCHHHHHHhcCCCCCCcCCCCEEEECCCCCCCCCC--CccCCCceeeccceeEEecCce
Q 014940 169 VYLSYVVKDVDTLAGIAARYRTTLTDLMNANAMGSTAVKAGDILAVPLPACATNFP--RYALDHGLIVPNGSYAITASHC 246 (415)
Q Consensus 169 ~~~tY~Vq~GDTL~sIA~rfgvt~~~L~~~N~l~~~~I~pGq~L~IPl~~~~ss~~--~~s~~~~l~v~~gsY~~~AG~~ 246 (415)
....|+|++|||||+||++||+++++|++||++..+.|++||.|.||.....+... ..+...........|.|..||.
T Consensus 478 ~~~~YtVk~GDTL~sIAkkygVSv~~L~~~N~l~s~~L~~GQ~L~Ip~~~~~s~~~t~~~s~~~~~~~~~~~Y~Vk~GDT 557 (592)
T PRK06347 478 NAKVYTVAKGDSLWRIANNNKVTIANLKSWNNLKSDFIYPGQKLKVSAGSTTNNTNTAKPSTNKPSNSTVKTYTVKKGDS 557 (592)
T ss_pred cceeeeecCCCCHHHHHHHHCCCHHHHHHhcCCCcccccCCcEEEEecCcccccccccCCccCCccCccceeeecCCCCc
Confidence 34689999999999999999999999999999987899999999999865332111 0000111111234699999999
Q ss_pred eEEeec
Q 014940 247 VQCSCG 252 (415)
Q Consensus 247 v~~~~~ 252 (415)
+.-|+.
T Consensus 558 L~sIA~ 563 (592)
T PRK06347 558 LWAISR 563 (592)
T ss_pred HHHHHH
Confidence 998883
No 2
>PRK06347 autolysin; Reviewed
Probab=99.93 E-value=2.4e-25 Score=237.30 Aligned_cols=167 Identities=19% Similarity=0.251 Sum_probs=134.6
Q ss_pred cEEEEeCCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCccCCCceEEeeccccccCC---------------cccc
Q 014940 38 LLGYTLYTDLKVSEVGSLFNVDPVSILTANAIDISYSDVENHILPSQLFVRIPVTCACVDG---------------IRKS 102 (415)
Q Consensus 38 ~~~Ytv~~gdtL~~IA~~fgvs~~~L~~~N~l~~t~P~~~~~~L~~Gq~l~IP~~csc~~g---------------~~~~ 102 (415)
...|+|+.||+|+.||++|||+.++|+++|++. ...|.+||.|+||..-.-... ....
T Consensus 405 ~~~ytVk~GDTL~sIA~kygVSv~~L~~~N~l~-------s~~L~~Gq~L~IP~~~~~~~~t~~~s~~~~~~k~~s~~~~ 477 (592)
T PRK06347 405 AKVYTVVKGDSLWRIANNNKVTIANLKSWNNLK-------SDFIYPGQKLKVSAGSTSNTNTSKPSTNTNTSKPSTNTNT 477 (592)
T ss_pred ceeEEecCCCCHHHHHHHhCCCHHHHHHHhCCC-------cceeccCcEEEEecCCcccccccccccccccccccccccc
Confidence 457999999999999999999999999999872 346899999999963210000 0011
Q ss_pred cceeEEeCCCCCHHHHHHHHhCCCCCHHHHHhhcCCCCCCCccCCcEEEecCCCcCCCCC------cCCCCceeeeEEec
Q 014940 103 VSTHYKTRPSDTLTSIANQVYAGLVSADQLREANDIQDPDVLDVGVNLLVPLPCTCFNGT------DNSLPAVYLSYVVK 176 (415)
Q Consensus 103 ~~~~YtV~~GDTL~~IA~~~fggLvs~~~L~~~N~l~~~~~L~~Gq~L~IP~~c~c~~~~------~~~~~~~~~tY~Vq 176 (415)
....|+|++|||||.||++ |+ +++++|++||++. .+.|++||+|.||....-.... .........+|+|+
T Consensus 478 ~~~~YtVk~GDTL~sIAkk-yg--VSv~~L~~~N~l~-s~~L~~GQ~L~Ip~~~~~s~~~t~~~s~~~~~~~~~~~Y~Vk 553 (592)
T PRK06347 478 NAKVYTVAKGDSLWRIANN-NK--VTIANLKSWNNLK-SDFIYPGQKLKVSAGSTTNNTNTAKPSTNKPSNSTVKTYTVK 553 (592)
T ss_pred cceeeeecCCCCHHHHHHH-HC--CCHHHHHHhcCCC-cccccCCcEEEEecCcccccccccCCccCCccCccceeeecC
Confidence 3457999999999999999 99 9999999999985 4689999999999864321110 00111235789999
Q ss_pred CCCCHHHHHHHhCCCHHHHHHhcCCCCCCcCCCCEEEEC
Q 014940 177 DVDTLAGIAARYRTTLTDLMNANAMGSTAVKAGDILAVP 215 (415)
Q Consensus 177 ~GDTL~sIA~rfgvt~~~L~~~N~l~~~~I~pGq~L~IP 215 (415)
+|||||+||+|||+++++|++||+|..+.|++||+|.|+
T Consensus 554 ~GDTL~sIA~KygvSv~~L~~~N~L~~~~L~~GQ~L~I~ 592 (592)
T PRK06347 554 KGDSLWAISRQYKTTVDNIKAWNKLTSNMIHVGQKLTIK 592 (592)
T ss_pred CCCcHHHHHHHhCCCHHHHHHhcCCCcccCCCCCEEecC
Confidence 999999999999999999999999988889999999985
No 3
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional
Probab=99.90 E-value=2.9e-22 Score=209.08 Aligned_cols=171 Identities=24% Similarity=0.311 Sum_probs=132.9
Q ss_pred ccEEEEeCCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCccCCC-ceEEeeccccc------cCCc----------
Q 014940 37 ALLGYTLYTDLKVSEVGSLFNVDPVSILTANAIDISYSDVENHILPSQ-LFVRIPVTCAC------VDGI---------- 99 (415)
Q Consensus 37 a~~~Ytv~~gdtL~~IA~~fgvs~~~L~~~N~l~~t~P~~~~~~L~~G-q~l~IP~~csc------~~g~---------- 99 (415)
.+..+.+..+++|..||+++|++.++|+++||. +. .....+.| +.++||....- ..+.
T Consensus 262 ~~~~V~v~~~i~L~~iA~~~gvs~~eL~~LNP~-~k----r~~t~p~g~~~llvP~~~~~~f~~~l~~~~~~~~~p~~~~ 336 (456)
T PRK10783 262 ALARVDLGQQIELAQAAEMAGMSLTKLKTFNAG-YK----RSTTAPSGPHYIMVPKKHADQLRESLASGEIAAVQSTLVA 336 (456)
T ss_pred ceEEEecCCCcCHHHHHHHcCCCHHHHHHhCcc-cc----CCCcCCCCCeEEEecCchhhHHHHhhhhhhhhhccccccc
Confidence 566677778889999999999999999999997 11 11112233 56777763210 0000
Q ss_pred --ccccceeEEeCCCCCHHHHHHHHhCCCCCHHHHHhhcCCCCCCCccCCcEEEecCCCcCCCCCcCCCCceeeeEEecC
Q 014940 100 --RKSVSTHYKTRPSDTLTSIANQVYAGLVSADQLREANDIQDPDVLDVGVNLLVPLPCTCFNGTDNSLPAVYLSYVVKD 177 (415)
Q Consensus 100 --~~~~~~~YtV~~GDTL~~IA~~~fggLvs~~~L~~~N~l~~~~~L~~Gq~L~IP~~c~c~~~~~~~~~~~~~tY~Vq~ 177 (415)
.......|+|++||||+.||++ |+ ++.++|++||++.+ +.|.+||+|.||..+.+... .......+|+|++
T Consensus 337 ~~~~~~~~~y~Vk~GDTL~sIA~r-~g--vs~~~L~~~N~l~~-~~L~~Gq~L~Ip~~~~~~~~---~~~~~~~~Y~Vr~ 409 (456)
T PRK10783 337 DNTPLNSRSYKVRSGDTLSGIASR-LN--VSTKDLQQWNNLRG-SKLKVGQTLTIGAGSSAQRL---ANNSDSITYRVRK 409 (456)
T ss_pred ccCcCCceEEEECCCCcHHHHHHH-HC--cCHHHHHHHcCCCc-ccCCCCCEEEecCCcccccc---cccccceeEEeCC
Confidence 0113568999999999999999 99 99999999999865 78999999999987654321 1123357899999
Q ss_pred CCCHHHHHHHhCCCHHHHHHhcCCCCCCcCCCCEEEECCCCC
Q 014940 178 VDTLAGIAARYRTTLTDLMNANAMGSTAVKAGDILAVPLPAC 219 (415)
Q Consensus 178 GDTL~sIA~rfgvt~~~L~~~N~l~~~~I~pGq~L~IPl~~~ 219 (415)
||||++||+||||++++|++||++..+.|++||+|.|++...
T Consensus 410 GDTL~sIA~kygVtv~~L~~~N~l~~~~L~pGq~L~l~v~~~ 451 (456)
T PRK10783 410 GDSLSSIAKRHGVNIKDVMRWNSDTAKNLQPGDKLTLFVKNN 451 (456)
T ss_pred CCCHHHHHHHhCCCHHHHHHhcCCCCCcCCCCCEEEEecCCC
Confidence 999999999999999999999998655999999999998763
No 4
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional
Probab=99.60 E-value=5.5e-15 Score=154.67 Aligned_cols=108 Identities=20% Similarity=0.183 Sum_probs=92.7
Q ss_pred cEEEEeCCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCccCCCceEEeeccccccCCcccccceeEEeCCCCCHHH
Q 014940 38 LLGYTLYTDLKVSEVGSLFNVDPVSILTANAIDISYSDVENHILPSQLFVRIPVTCACVDGIRKSVSTHYKTRPSDTLTS 117 (415)
Q Consensus 38 ~~~Ytv~~gdtL~~IA~~fgvs~~~L~~~N~l~~t~P~~~~~~L~~Gq~l~IP~~csc~~g~~~~~~~~YtV~~GDTL~~ 117 (415)
...|+|++||||+.||++||++.++|+++|++. ...|.+||.|.||.++.+...........|+|++||||+.
T Consensus 343 ~~~y~Vk~GDTL~sIA~r~gvs~~~L~~~N~l~-------~~~L~~Gq~L~Ip~~~~~~~~~~~~~~~~Y~Vr~GDTL~s 415 (456)
T PRK10783 343 SRSYKVRSGDTLSGIASRLNVSTKDLQQWNNLR-------GSKLKVGQTLTIGAGSSAQRLANNSDSITYRVRKGDSLSS 415 (456)
T ss_pred ceEEEECCCCcHHHHHHHHCcCHHHHHHHcCCC-------cccCCCCCEEEecCCcccccccccccceeEEeCCCCCHHH
Confidence 567999999999999999999999999999982 2568899999999876653222233457899999999999
Q ss_pred HHHHHhCCCCCHHHHHhhcCCCCCCCccCCcEEEecCCC
Q 014940 118 IANQVYAGLVSADQLREANDIQDPDVLDVGVNLLVPLPC 156 (415)
Q Consensus 118 IA~~~fggLvs~~~L~~~N~l~~~~~L~~Gq~L~IP~~c 156 (415)
||++ |+ +++++|++||++... .|++||+|.|++..
T Consensus 416 IA~k-yg--Vtv~~L~~~N~l~~~-~L~pGq~L~l~v~~ 450 (456)
T PRK10783 416 IAKR-HG--VNIKDVMRWNSDTAK-NLQPGDKLTLFVKN 450 (456)
T ss_pred HHHH-hC--CCHHHHHHhcCCCCC-cCCCCCEEEEecCC
Confidence 9999 99 999999999998655 89999999998864
No 5
>PRK13914 invasion associated secreted endopeptidase; Provisional
Probab=99.60 E-value=6.8e-15 Score=152.94 Aligned_cols=170 Identities=14% Similarity=0.126 Sum_probs=100.5
Q ss_pred EEEeCCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCccCCCceEEeecccccc-C-------------Ccccccce
Q 014940 40 GYTLYTDLKVSEVGSLFNVDPVSILTANAIDISYSDVENHILPSQLFVRIPVTCACV-D-------------GIRKSVST 105 (415)
Q Consensus 40 ~Ytv~~gdtL~~IA~~fgvs~~~L~~~N~l~~t~P~~~~~~L~~Gq~l~IP~~csc~-~-------------g~~~~~~~ 105 (415)
.|+|++||+|+.||++|+++.++|+++|.+ ..+.|.+||.|+||....-. . +.......
T Consensus 29 tytVq~GDTLw~IA~~ygvtv~~I~~~N~l-------~~~~I~~Gq~L~Ip~~~~~~~~~~~Vta~~LNVRsgps~s~~I 101 (481)
T PRK13914 29 TVVVEAGDTLWGIAQSKGTTVDAIKKANNL-------TTDKIVPGQKLQVNEVAAAEKTEKSVSATWLNVRSGAGVDNSI 101 (481)
T ss_pred eEEECCCCCHHHHHHHHCCCHHHHHHHhCC-------CcccccCCCEEEeCCCCcccccceeEecceEEEecCCCCCcce
Confidence 499999999999999999999999999987 23568899999999643100 0 11111223
Q ss_pred eEEeCCCCCHHHHH-HH--HhCCCCCHHH-HHhh-cC--CCCC---CCccCCcEEEe--------cC-------------
Q 014940 106 HYKTRPSDTLTSIA-NQ--VYAGLVSADQ-LREA-ND--IQDP---DVLDVGVNLLV--------PL------------- 154 (415)
Q Consensus 106 ~YtV~~GDTL~~IA-~~--~fggLvs~~~-L~~~-N~--l~~~---~~L~~Gq~L~I--------P~------------- 154 (415)
.-.+..||.+..+. +. ||. +.+.+ ..-| +. +.+. ..+..-|+++- |.
T Consensus 102 Igsl~~G~~V~Vl~~~~ngW~k--I~~~~GktGwV~~~YLs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 179 (481)
T PRK13914 102 ITSIKGGTKVTVETTESNGWHK--ITYNDGKTGFVNGKYLTDKVTSTPVAPTQEVKKETTTQQAAPAAETKTEVKQTTQA 179 (481)
T ss_pred eeeecCCCEEEEeecccCCeEE--EEcCCCCEEEEecccccCCCccCccccchhhhhccccccccchhcccchhccCCcc
Confidence 33445555544332 11 122 11100 0000 00 0000 00000011100 00
Q ss_pred ----CCcCCCCCcCCCCceeeeEEecCCCCHHHHHHHhCCCHHHHHHhcCCCCCCcCCCCEEEECCCC
Q 014940 155 ----PCTCFNGTDNSLPAVYLSYVVKDVDTLAGIAARYRTTLTDLMNANAMGSTAVKAGDILAVPLPA 218 (415)
Q Consensus 155 ----~c~c~~~~~~~~~~~~~tY~Vq~GDTL~sIA~rfgvt~~~L~~~N~l~~~~I~pGq~L~IPl~~ 218 (415)
+.................|+|++|||||.||++|++++++|++||++..+.|++||+|.||..+
T Consensus 180 ~~~~~~~~~~~~~~~~~~~a~tytVq~GDTL~sIAkrYgVtv~eI~~~N~l~s~~L~pGQ~L~Ip~sa 247 (481)
T PRK13914 180 TTPAPKVAETKETPVVDQNATTHAVKSGDTIWALSVKYGVSVQDIMSWNNLSSSSIYVGQKLAIKQTA 247 (481)
T ss_pred cCCcccccccccCccccCCCeEEEECCCCCHHHHHHHHCCCHHHHHHhcCCCccccCCCCEEEecCCC
Confidence 0000000000011234689999999999999999999999999999988899999999999764
No 6
>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=99.20 E-value=1.3e-11 Score=87.91 Aligned_cols=43 Identities=37% Similarity=0.619 Sum_probs=36.7
Q ss_pred EEecCCCCHHHHHHHhCCCHHHHHHhc-CCCCCCcCCCCEEEEC
Q 014940 173 YVVKDVDTLAGIAARYRTTLTDLMNAN-AMGSTAVKAGDILAVP 215 (415)
Q Consensus 173 Y~Vq~GDTL~sIA~rfgvt~~~L~~~N-~l~~~~I~pGq~L~IP 215 (415)
|+|++|||+++||++|+++.++|++|| ++..+.|++||+|.||
T Consensus 1 y~V~~gDtl~~IA~~~~~~~~~l~~~N~~~~~~~l~~G~~l~iP 44 (44)
T PF01476_consen 1 YTVQPGDTLWSIAKRYGISVDELMELNPNIDSDNLQPGQKLCIP 44 (44)
T ss_dssp EEE-TT--HHHHHHHTTS-HHHHHHHCCTTHGGCGGTTEEEEEC
T ss_pred CEECcCCcHHHHHhhhhhhHhHHHHhcCCCCcccCCCCCEEEeC
Confidence 899999999999999999999999999 7776669999999998
No 7
>COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane]
Probab=99.15 E-value=1.2e-10 Score=100.90 Aligned_cols=98 Identities=32% Similarity=0.484 Sum_probs=77.3
Q ss_pred HHHHHhCCCCCHHHHHhhcCCCC-CCCccCCcEEEecCCCcCCCC--C-cCCCC------------ceeeeEEecCCCCH
Q 014940 118 IANQVYAGLVSADQLREANDIQD-PDVLDVGVNLLVPLPCTCFNG--T-DNSLP------------AVYLSYVVKDVDTL 181 (415)
Q Consensus 118 IA~~~fggLvs~~~L~~~N~l~~-~~~L~~Gq~L~IP~~c~c~~~--~-~~~~~------------~~~~tY~Vq~GDTL 181 (415)
||.+ |+ +++++|+++|.+.. .+.+.+||+|.++..-.-... . ..... ....+|+|+.||+|
T Consensus 1 ia~~-~~--~~v~~l~~~n~~~~~s~~i~~gq~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~gdtL 77 (124)
T COG1388 1 IASK-YG--VSVKALKKANALTGKSDAIKPGQVLKIPGDISSTVNAGQTLSSLSNKVSDSSSASKAPPVVTYTVKKGDTL 77 (124)
T ss_pred Cccc-cc--ccHHHHHHHhcccCCCCccccCceEEccCCcccccccccccccccceeeccccccccCCCceEEEecCCCH
Confidence 4666 88 99999999999753 678999999999964111111 0 01111 11368999999999
Q ss_pred HHHHHHhCCCHHHHHHhcCCCCCCcCCCCEEEECCCC
Q 014940 182 AGIAARYRTTLTDLMNANAMGSTAVKAGDILAVPLPA 218 (415)
Q Consensus 182 ~sIA~rfgvt~~~L~~~N~l~~~~I~pGq~L~IPl~~ 218 (415)
+.||++|++++.+|+++|++.++.+++||.|.++...
T Consensus 78 ~~Ia~~~~~tv~~l~~~n~l~~~~i~~gq~l~~~~~~ 114 (124)
T COG1388 78 SKIARKYGVTVAELKQLNNLSSDKIKVGQKLKLPVSS 114 (124)
T ss_pred HHHHHHhCCCHHHHHHHhccCCCceecCcEEEEeccc
Confidence 9999999999999999999998899999999999743
No 8
>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=98.99 E-value=4.3e-10 Score=79.91 Aligned_cols=44 Identities=45% Similarity=0.675 Sum_probs=35.7
Q ss_pred EEeCCCCCHHHHHHHHhCCCCCHHHHHhhcCCCCCCCccCCcEEEec
Q 014940 107 YKTRPSDTLTSIANQVYAGLVSADQLREANDIQDPDVLDVGVNLLVP 153 (415)
Q Consensus 107 YtV~~GDTL~~IA~~~fggLvs~~~L~~~N~l~~~~~L~~Gq~L~IP 153 (415)
|+|++|||++.||++ |+ +++++|+++|+..+.+.|.+||+|.||
T Consensus 1 y~V~~gDtl~~IA~~-~~--~~~~~l~~~N~~~~~~~l~~G~~l~iP 44 (44)
T PF01476_consen 1 YTVQPGDTLWSIAKR-YG--ISVDELMELNPNIDSDNLQPGQKLCIP 44 (44)
T ss_dssp EEE-TT--HHHHHHH-TT--S-HHHHHHHCCTTHGGCGGTTEEEEEC
T ss_pred CEECcCCcHHHHHhh-hh--hhHhHHHHhcCCCCcccCCCCCEEEeC
Confidence 899999999999999 99 999999999944444559999999998
No 9
>PRK14125 cell division suppressor protein YneA; Provisional
Probab=98.86 E-value=4.5e-09 Score=89.19 Aligned_cols=51 Identities=29% Similarity=0.453 Sum_probs=45.0
Q ss_pred eeeeEEecCCCCHHHHHHHhCCC--------HHHHHHhcCCCCCCcCCCCEEEECCCCC
Q 014940 169 VYLSYVVKDVDTLAGIAARYRTT--------LTDLMNANAMGSTAVKAGDILAVPLPAC 219 (415)
Q Consensus 169 ~~~tY~Vq~GDTL~sIA~rfgvt--------~~~L~~~N~l~~~~I~pGq~L~IPl~~~ 219 (415)
.+.+|+|++|||||+||++|+++ +++|++.|++.++.|++||+|.||....
T Consensus 35 ~~~~~tV~~GDTLW~IA~~y~~~~~l~~~~~v~~I~~~N~l~~~~I~~Gq~L~IP~~~~ 93 (103)
T PRK14125 35 QYVEITVQEGDTLWALADQYAGKHHMAKNEFIEWVEDVNNLPSGHIKAGDKLVIPVLKS 93 (103)
T ss_pred CcEEEEECCCCCHHHHHHHhCCCcCCCHHHHHHHHHHhcCCCCCcCCCCCEEEEecCCC
Confidence 46789999999999999999865 5678888999888999999999998763
No 10
>COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane]
Probab=98.82 E-value=1e-08 Score=88.68 Aligned_cols=95 Identities=24% Similarity=0.429 Sum_probs=74.5
Q ss_pred HHHHcCCCHHHHHHhCCCCCCCCCCCCCccCCCceEEeecccccc--CCccc---c-------------cceeEEeCCCC
Q 014940 52 VGSLFNVDPVSILTANAIDISYSDVENHILPSQLFVRIPVTCACV--DGIRK---S-------------VSTHYKTRPSD 113 (415)
Q Consensus 52 IA~~fgvs~~~L~~~N~l~~t~P~~~~~~L~~Gq~l~IP~~csc~--~g~~~---~-------------~~~~YtV~~GD 113 (415)
||.+|+++.++|+++|.+. ...+.+..|+++.++..-.-. .+... . ....|+|++||
T Consensus 1 ia~~~~~~v~~l~~~n~~~-----~~s~~i~~gq~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~gd 75 (124)
T COG1388 1 IASKYGVSVKALKKANALT-----GKSDAIKPGQVLKIPGDISSTVNAGQTLSSLSNKVSDSSSASKAPPVVTYTVKKGD 75 (124)
T ss_pred CcccccccHHHHHHHhccc-----CCCCccccCceEEccCCcccccccccccccccceeeccccccccCCCceEEEecCC
Confidence 5789999999999999982 125677899999998531111 11100 0 13579999999
Q ss_pred CHHHHHHHHhCCCCCHHHHHhhcCCCCCCCccCCcEEEecCC
Q 014940 114 TLTSIANQVYAGLVSADQLREANDIQDPDVLDVGVNLLVPLP 155 (415)
Q Consensus 114 TL~~IA~~~fggLvs~~~L~~~N~l~~~~~L~~Gq~L~IP~~ 155 (415)
||+.||++ |+ +++.+|+++|++.+. .+++||.|.++..
T Consensus 76 tL~~Ia~~-~~--~tv~~l~~~n~l~~~-~i~~gq~l~~~~~ 113 (124)
T COG1388 76 TLSKIARK-YG--VTVAELKQLNNLSSD-KIKVGQKLKLPVS 113 (124)
T ss_pred CHHHHHHH-hC--CCHHHHHHHhccCCC-ceecCcEEEEecc
Confidence 99999999 99 999999999998654 9999999999873
No 11
>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=98.71 E-value=3.2e-08 Score=68.01 Aligned_cols=44 Identities=34% Similarity=0.651 Sum_probs=41.1
Q ss_pred eEEecCCCCHHHHHHHhCCCHHHHHHhcCCC-CCCcCCCCEEEEC
Q 014940 172 SYVVKDVDTLAGIAARYRTTLTDLMNANAMG-STAVKAGDILAVP 215 (415)
Q Consensus 172 tY~Vq~GDTL~sIA~rfgvt~~~L~~~N~l~-~~~I~pGq~L~IP 215 (415)
+|+|++|||+++||++|+++..+|+++|+.. ...+.+|+.|.||
T Consensus 2 ~~~v~~gdt~~~ia~~~~~~~~~~~~~N~~~~~~~~~~g~~l~ip 46 (46)
T cd00118 2 TYTVKKGDTLSSIAQRYGISVEELLKLNGLSDPDNLQVGQKLKIP 46 (46)
T ss_pred EEEECCCCCHHHHHHHHCcCHHHHHHHcCCCCccccCCCCEEecC
Confidence 6999999999999999999999999999984 5789999999987
No 12
>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=98.66 E-value=3.5e-08 Score=69.13 Aligned_cols=42 Identities=29% Similarity=0.475 Sum_probs=37.7
Q ss_pred ecCCCCHHHHHHHhCCCHHHHHHhcC-CCC-CCcCCCCEEEECC
Q 014940 175 VKDVDTLAGIAARYRTTLTDLMNANA-MGS-TAVKAGDILAVPL 216 (415)
Q Consensus 175 Vq~GDTL~sIA~rfgvt~~~L~~~N~-l~~-~~I~pGq~L~IPl 216 (415)
|++|||+|+||++|+++.++|.++|+ +.+ ..+.+||.|.||.
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 443 5799999999983
No 13
>PRK14125 cell division suppressor protein YneA; Provisional
Probab=98.55 E-value=1.5e-07 Score=79.87 Aligned_cols=50 Identities=22% Similarity=0.376 Sum_probs=42.3
Q ss_pred cceeEEeCCCCCHHHHHHHHhCCCCC--------HHHHHhhcCCCCCCCccCCcEEEecCCC
Q 014940 103 VSTHYKTRPSDTLTSIANQVYAGLVS--------ADQLREANDIQDPDVLDVGVNLLVPLPC 156 (415)
Q Consensus 103 ~~~~YtV~~GDTL~~IA~~~fggLvs--------~~~L~~~N~l~~~~~L~~Gq~L~IP~~c 156 (415)
.+..|+|++|||||+||++ |+ ++ +++|++.|++.+ +.|++||+|.||...
T Consensus 35 ~~~~~tV~~GDTLW~IA~~-y~--~~~~l~~~~~v~~I~~~N~l~~-~~I~~Gq~L~IP~~~ 92 (103)
T PRK14125 35 QYVEITVQEGDTLWALADQ-YA--GKHHMAKNEFIEWVEDVNNLPS-GHIKAGDKLVIPVLK 92 (103)
T ss_pred CcEEEEECCCCCHHHHHHH-hC--CCcCCCHHHHHHHHHHhcCCCC-CcCCCCCEEEEecCC
Confidence 4578999999999999999 87 43 577888899854 579999999999864
No 14
>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=98.55 E-value=1.7e-07 Score=64.37 Aligned_cols=45 Identities=42% Similarity=0.756 Sum_probs=41.6
Q ss_pred eEEeCCCCCHHHHHHHHhCCCCCHHHHHhhcCCCCCCCccCCcEEEec
Q 014940 106 HYKTRPSDTLTSIANQVYAGLVSADQLREANDIQDPDVLDVGVNLLVP 153 (415)
Q Consensus 106 ~YtV~~GDTL~~IA~~~fggLvs~~~L~~~N~l~~~~~L~~Gq~L~IP 153 (415)
.|+|++|||++.||++ |+ ++.++|+++|+..+...+.+|+.|.||
T Consensus 2 ~~~v~~gdt~~~ia~~-~~--~~~~~~~~~N~~~~~~~~~~g~~l~ip 46 (46)
T cd00118 2 TYTVKKGDTLSSIAQR-YG--ISVEELLKLNGLSDPDNLQVGQKLKIP 46 (46)
T ss_pred EEEECCCCCHHHHHHH-HC--cCHHHHHHHcCCCCccccCCCCEEecC
Confidence 5999999999999999 89 999999999998666789999999987
No 15
>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=98.54 E-value=1.1e-07 Score=94.98 Aligned_cols=48 Identities=29% Similarity=0.512 Sum_probs=45.0
Q ss_pred ceeeeEEecCCCCHHHHHHHhCCCHHHHHHhcCCCCCCcCCCCEEEEC
Q 014940 168 AVYLSYVVKDVDTLAGIAARYRTTLTDLMNANAMGSTAVKAGDILAVP 215 (415)
Q Consensus 168 ~~~~tY~Vq~GDTL~sIA~rfgvt~~~L~~~N~l~~~~I~pGq~L~IP 215 (415)
.....|+|++|||||+||+|||+++++|++||++..+.|++||+|.||
T Consensus 291 ~~~~~YiVq~GDTL~sIAkRYGVSV~~L~r~N~L~~~~L~~GQ~L~IP 338 (338)
T TIGR02907 291 TKLRMCIVQEGDTIETIAERYEISVSQLIRHNQLEDFEVNEGQILYIP 338 (338)
T ss_pred cccEEEEECCCCCHHHHHHHHCcCHHHHHHHhCCCccccCCCCEEEeC
Confidence 445789999999999999999999999999999987899999999998
No 16
>COG3858 Predicted glycosyl hydrolase [General function prediction only]
Probab=98.54 E-value=9.9e-08 Score=97.65 Aligned_cols=98 Identities=23% Similarity=0.192 Sum_probs=87.4
Q ss_pred eeEEeCCCCCHHHHHHHHhCCCCCHHHHHhhcCCCCCCCccCCcEEEecCCCcCCCCCcCCCCceeeeEEecCCCCHHHH
Q 014940 105 THYKTRPSDTLTSIANQVYAGLVSADQLREANDIQDPDVLDVGVNLLVPLPCTCFNGTDNSLPAVYLSYVVKDVDTLAGI 184 (415)
Q Consensus 105 ~~YtV~~GDTL~~IA~~~fggLvs~~~L~~~N~l~~~~~L~~Gq~L~IP~~c~c~~~~~~~~~~~~~tY~Vq~GDTL~sI 184 (415)
..|.|++||++..|+++ |+ .+..+|...|.... +.|.+||.+.||.. ...|.|++|||+++|
T Consensus 2 ~i~~~~pg~~~~~i~~~-~~--~~~~~i~~~~~~~~-d~~~~~q~~~v~~~--------------~~~y~~~~~d~~~Si 63 (423)
T COG3858 2 SIHLVGPGDSRLIIAVY-FP--YTNNRIVNGNDYTN-DDLVDGQTFVVPPS--------------GHFYDVGPGDTLTSI 63 (423)
T ss_pred EEEEccCCceeeeehhh-cc--cccccccccccccc-ccccCceeEEECCc--------------ceEEEecCCcchhhh
Confidence 35899999999999999 99 99999988888766 78999999999975 378999999999999
Q ss_pred HHHhCCCHHHHHHhcCCC-CCCcCCCCEEEECCCCCC
Q 014940 185 AARYRTTLTDLMNANAMG-STAVKAGDILAVPLPACA 220 (415)
Q Consensus 185 A~rfgvt~~~L~~~N~l~-~~~I~pGq~L~IPl~~~~ 220 (415)
|++|+++.+.+..+|... ...+++|-.|.+|-..-+
T Consensus 64 a~~~~vt~~~~~~m~~~~~~~~l~~~~~l~~P~~~~~ 100 (423)
T COG3858 64 ARTVGVTQDSAAIMNFVICPGYLQYGLNLYIPSARKT 100 (423)
T ss_pred hhhhcCCHHHHHhhcccccccceeeeeEEeccCCCCC
Confidence 999999999999999765 578999999999977644
No 17
>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=98.52 E-value=1.5e-07 Score=65.86 Aligned_cols=43 Identities=33% Similarity=0.555 Sum_probs=38.1
Q ss_pred eCCCCCHHHHHHHHhCCCCCHHHHHhhcCC-CCCCCccCCcEEEecC
Q 014940 109 TRPSDTLTSIANQVYAGLVSADQLREANDI-QDPDVLDVGVNLLVPL 154 (415)
Q Consensus 109 V~~GDTL~~IA~~~fggLvs~~~L~~~N~l-~~~~~L~~Gq~L~IP~ 154 (415)
|++|||||+||++ |+ +++++|+++|+. .+++.+.+||+|.||.
T Consensus 1 v~~gdtl~~IA~~-~~--~~~~~l~~~N~~~~~~~~~~~g~~l~ip~ 44 (44)
T TIGR02899 1 VQKGDTLWKIAKK-YG--VDFDELIQANPQLSNPNLIYPGMKIKIPS 44 (44)
T ss_pred CCCCCCHHHHHHH-HC--cCHHHHHHHhhcCCCCCCcCCCCEEecCC
Confidence 6899999999999 99 999999999984 4556799999999983
No 18
>PRK10871 nlpD lipoprotein NlpD; Provisional
Probab=98.48 E-value=1.7e-07 Score=94.04 Aligned_cols=48 Identities=29% Similarity=0.298 Sum_probs=44.5
Q ss_pred eeEEecCCCCHHHHHHHhCCCHHHHHHhcCCCC-CCcCCCCEEEECCCC
Q 014940 171 LSYVVKDVDTLAGIAARYRTTLTDLMNANAMGS-TAVKAGDILAVPLPA 218 (415)
Q Consensus 171 ~tY~Vq~GDTL~sIA~rfgvt~~~L~~~N~l~~-~~I~pGq~L~IPl~~ 218 (415)
.+|+|++|||||.||++||+++.+|.+||+|.+ ..|++||+|.||...
T Consensus 61 ~~y~Vk~GDTL~~IA~~~g~~~~~La~~N~l~~p~~I~~GQ~L~i~~~~ 109 (319)
T PRK10871 61 STYTVKKGDTLFYIAWITGNDFRDLAQRNNIQAPYSLNVGQTLQVGNAS 109 (319)
T ss_pred CceEECCCCHHHHHHHHHCcCHHHHHHhcCCCCCccccCCCEEEeCCCC
Confidence 579999999999999999999999999999975 799999999998654
No 19
>PRK13914 invasion associated secreted endopeptidase; Provisional
Probab=98.42 E-value=4.1e-07 Score=95.36 Aligned_cols=48 Identities=33% Similarity=0.338 Sum_probs=45.1
Q ss_pred eeEEecCCCCHHHHHHHhCCCHHHHHHhcCCCCCCcCCCCEEEECCCC
Q 014940 171 LSYVVKDVDTLAGIAARYRTTLTDLMNANAMGSTAVKAGDILAVPLPA 218 (415)
Q Consensus 171 ~tY~Vq~GDTL~sIA~rfgvt~~~L~~~N~l~~~~I~pGq~L~IPl~~ 218 (415)
.+|+|++|||||+||++|++++++|+++|++..+.|++||.|.||..+
T Consensus 28 ~tytVq~GDTLw~IA~~ygvtv~~I~~~N~l~~~~I~~Gq~L~Ip~~~ 75 (481)
T PRK13914 28 STVVVEAGDTLWGIAQSKGTTVDAIKKANNLTTDKIVPGQKLQVNEVA 75 (481)
T ss_pred ceEEECCCCCHHHHHHHHCCCHHHHHHHhCCCcccccCCCEEEeCCCC
Confidence 569999999999999999999999999999988899999999999654
No 20
>PRK10871 nlpD lipoprotein NlpD; Provisional
Probab=98.37 E-value=4.1e-07 Score=91.27 Aligned_cols=49 Identities=33% Similarity=0.357 Sum_probs=45.6
Q ss_pred eeEEeCCCCCHHHHHHHHhCCCCCHHHHHhhcCCCCCCCccCCcEEEecCCC
Q 014940 105 THYKTRPSDTLTSIANQVYAGLVSADQLREANDIQDPDVLDVGVNLLVPLPC 156 (415)
Q Consensus 105 ~~YtV~~GDTL~~IA~~~fggLvs~~~L~~~N~l~~~~~L~~Gq~L~IP~~c 156 (415)
..|+|++|||||.||++ |+ +++++|++||++.+++.|++||+|.||...
T Consensus 61 ~~y~Vk~GDTL~~IA~~-~g--~~~~~La~~N~l~~p~~I~~GQ~L~i~~~~ 109 (319)
T PRK10871 61 STYTVKKGDTLFYIAWI-TG--NDFRDLAQRNNIQAPYSLNVGQTLQVGNAS 109 (319)
T ss_pred CceEECCCCHHHHHHHH-HC--cCHHHHHHhcCCCCCccccCCCEEEeCCCC
Confidence 57999999999999998 99 999999999999999999999999998653
No 21
>smart00257 LysM Lysin motif.
Probab=98.36 E-value=8.7e-07 Score=59.99 Aligned_cols=43 Identities=35% Similarity=0.622 Sum_probs=38.5
Q ss_pred eEEecCCCCHHHHHHHhCCCHHHHHHhcCC-CCCCcCCCCEEEE
Q 014940 172 SYVVKDVDTLAGIAARYRTTLTDLMNANAM-GSTAVKAGDILAV 214 (415)
Q Consensus 172 tY~Vq~GDTL~sIA~rfgvt~~~L~~~N~l-~~~~I~pGq~L~I 214 (415)
+|+|++|||+++||++|+++.+++.++|+. ....+++|+.|.|
T Consensus 1 ~~~v~~gdt~~~ia~~~~~~~~~~~~~N~~~~~~~~~~g~~l~i 44 (44)
T smart00257 1 TYTVKKGDTLSSIARRYGISVSDLLELNNILDPDNLQVGQKLKI 44 (44)
T ss_pred CeEeCCCCCHHHHHHHhCCCHHHHHHHcCCCCccccCCCCEEeC
Confidence 489999999999999999999999999984 3578999998864
No 22
>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=98.27 E-value=1.2e-06 Score=87.61 Aligned_cols=49 Identities=24% Similarity=0.346 Sum_probs=45.1
Q ss_pred cccceeEEeCCCCCHHHHHHHHhCCCCCHHHHHhhcCCCCCCCccCCcEEEec
Q 014940 101 KSVSTHYKTRPSDTLTSIANQVYAGLVSADQLREANDIQDPDVLDVGVNLLVP 153 (415)
Q Consensus 101 ~~~~~~YtV~~GDTL~~IA~~~fggLvs~~~L~~~N~l~~~~~L~~Gq~L~IP 153 (415)
...+..|+|++|||||.||++ |+ +++++|+++|++. ++.|++||.|.||
T Consensus 290 ~~~~~~YiVq~GDTL~sIAkR-YG--VSV~~L~r~N~L~-~~~L~~GQ~L~IP 338 (338)
T TIGR02907 290 FTKLRMCIVQEGDTIETIAER-YE--ISVSQLIRHNQLE-DFEVNEGQILYIP 338 (338)
T ss_pred ccccEEEEECCCCCHHHHHHH-HC--cCHHHHHHHhCCC-ccccCCCCEEEeC
Confidence 346789999999999999999 99 9999999999986 6789999999998
No 23
>smart00257 LysM Lysin motif.
Probab=98.17 E-value=4.1e-06 Score=56.59 Aligned_cols=44 Identities=45% Similarity=0.719 Sum_probs=39.0
Q ss_pred eEEeCCCCCHHHHHHHHhCCCCCHHHHHhhcCCCCCCCccCCcEEEe
Q 014940 106 HYKTRPSDTLTSIANQVYAGLVSADQLREANDIQDPDVLDVGVNLLV 152 (415)
Q Consensus 106 ~YtV~~GDTL~~IA~~~fggLvs~~~L~~~N~l~~~~~L~~Gq~L~I 152 (415)
.|+|++|||++.||++ |+ ++.++|+++|+..+...+.+|+.|.|
T Consensus 1 ~~~v~~gdt~~~ia~~-~~--~~~~~~~~~N~~~~~~~~~~g~~l~i 44 (44)
T smart00257 1 TYTVKKGDTLSSIARR-YG--ISVSDLLELNNILDPDNLQVGQKLKI 44 (44)
T ss_pred CeEeCCCCCHHHHHHH-hC--CCHHHHHHHcCCCCccccCCCCEEeC
Confidence 4899999999999998 99 99999999999656667999998864
No 24
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=98.12 E-value=3.8e-06 Score=75.59 Aligned_cols=50 Identities=34% Similarity=0.569 Sum_probs=43.4
Q ss_pred ceeEEeCCCCCHHHHHHHHhCCCCCHHHHHhhcC--CCCCCCccCCcEEEec
Q 014940 104 STHYKTRPSDTLTSIANQVYAGLVSADQLREAND--IQDPDVLDVGVNLLVP 153 (415)
Q Consensus 104 ~~~YtV~~GDTL~~IA~~~fggLvs~~~L~~~N~--l~~~~~L~~Gq~L~IP 153 (415)
...|+|++|||||.||+++|+....+.+|.++|+ +.+++.|.+||+|.||
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 4579999999999999995564456899999998 6778889999999998
No 25
>COG3858 Predicted glycosyl hydrolase [General function prediction only]
Probab=98.09 E-value=3.8e-06 Score=86.19 Aligned_cols=97 Identities=25% Similarity=0.234 Sum_probs=84.6
Q ss_pred EEEEeCCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCccCCCceEEeeccccccCCcccccceeEEeCCCCCHHHH
Q 014940 39 LGYTLYTDLKVSEVGSLFNVDPVSILTANAIDISYSDVENHILPSQLFVRIPVTCACVDGIRKSVSTHYKTRPSDTLTSI 118 (415)
Q Consensus 39 ~~Ytv~~gdtL~~IA~~fgvs~~~L~~~N~l~~t~P~~~~~~L~~Gq~l~IP~~csc~~g~~~~~~~~YtV~~GDTL~~I 118 (415)
..|-+++|+++..|+.+|+.+..+|...|.. .++.++.||.+.||. ....|.|++|||+++|
T Consensus 2 ~i~~~~pg~~~~~i~~~~~~~~~~i~~~~~~-------~~d~~~~~q~~~v~~-----------~~~~y~~~~~d~~~Si 63 (423)
T COG3858 2 SIHLVGPGDSRLIIAVYFPYTNNRIVNGNDY-------TNDDLVDGQTFVVPP-----------SGHFYDVGPGDTLTSI 63 (423)
T ss_pred EEEEccCCceeeeehhhcccccccccccccc-------ccccccCceeEEECC-----------cceEEEecCCcchhhh
Confidence 3578899999999999999999999666555 226788999999997 3457999999999999
Q ss_pred HHHHhCCCCCHHHHHhhcCCCCCCCccCCcEEEecCCC
Q 014940 119 ANQVYAGLVSADQLREANDIQDPDVLDVGVNLLVPLPC 156 (415)
Q Consensus 119 A~~~fggLvs~~~L~~~N~l~~~~~L~~Gq~L~IP~~c 156 (415)
|++ |+ ++.+.++.+|....+..+..|-.+.+|...
T Consensus 64 a~~-~~--vt~~~~~~m~~~~~~~~l~~~~~l~~P~~~ 98 (423)
T COG3858 64 ART-VG--VTQDSAAIMNFVICPGYLQYGLNLYIPSAR 98 (423)
T ss_pred hhh-hc--CCHHHHHhhcccccccceeeeeEEeccCCC
Confidence 999 99 999999999998777889999999999754
No 26
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=97.96 E-value=1.1e-05 Score=72.54 Aligned_cols=46 Identities=30% Similarity=0.480 Sum_probs=39.8
Q ss_pred eeeEEecCCCCHHHHHHHhC---CCHHHHHHhcC--CCC-CCcCCCCEEEEC
Q 014940 170 YLSYVVKDVDTLAGIAARYR---TTLTDLMNANA--MGS-TAVKAGDILAVP 215 (415)
Q Consensus 170 ~~tY~Vq~GDTL~sIA~rfg---vt~~~L~~~N~--l~~-~~I~pGq~L~IP 215 (415)
..+|+|++|||||+||++|. .....|.++|+ +.+ +.|++||+|.||
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 36799999999999999985 35778999997 654 689999999998
No 27
>PRK10260 L,D-transpeptidase; Provisional
Probab=97.31 E-value=0.001 Score=66.60 Aligned_cols=67 Identities=10% Similarity=0.069 Sum_probs=49.6
Q ss_pred ccCCcccccCCCCCCCCccEEEEeCCCC--CHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCccCCCceEEeecc
Q 014940 20 VTPKSTIEPCSNSDSCSALLGYTLYTDL--KVSEVGSLFNVDPVSILTANAIDISYSDVENHILPSQLFVRIPVT 92 (415)
Q Consensus 20 ~~~~~~~~~C~~s~~C~a~~~Ytv~~gd--tL~~IA~~fgvs~~~L~~~N~l~~t~P~~~~~~L~~Gq~l~IP~~ 92 (415)
+.|..+-.+=.++.--.....|+++.++ +|..||++|++...+|+++||.- +.....+|+++.||..
T Consensus 22 ~~A~~y~lp~~~~~lvG~~~~~~v~~~~~~~le~iA~~f~~g~~~l~~aNPgv------dp~lp~~G~~i~iP~~ 90 (306)
T PRK10260 22 ASAVTYPLPTDGSRLVGQNQVITIPEGNTQPLEYFAAEYQMGLSNMMEANPGV------DTFLPKGGTVLNIPQQ 90 (306)
T ss_pred hhheeecCCCCCCceEcccEEEEeCCCCCchHHHHHHHhCCCHHHHHHhCcCC------CCCcCCCCCEEEeCCc
Confidence 4445555544455556677889998855 59999999999999999999971 1123368999999873
No 28
>PRK10190 L,D-transpeptidase; Provisional
Probab=97.28 E-value=0.0011 Score=66.45 Aligned_cols=84 Identities=14% Similarity=0.057 Sum_probs=57.0
Q ss_pred CchHHHHHHHHHHHhhhhhccCCcccccCCCCCCCCccEEEEeCCCC--CHHHHHHHcCCCHHHHHHhCCCCCCCCCCCC
Q 014940 1 MPKTLLYLLLLFSNAAMVLVTPKSTIEPCSNSDSCSALLGYTLYTDL--KVSEVGSLFNVDPVSILTANAIDISYSDVEN 78 (415)
Q Consensus 1 m~~~l~~~~~l~~~~~~~~~~~~~~~~~C~~s~~C~a~~~Ytv~~gd--tL~~IA~~fgvs~~~L~~~N~l~~t~P~~~~ 78 (415)
|.++..+++++++... ..+.|..+-.+=.++.--.....|+++.+| +|..||++|++...+|+++||.- +.
T Consensus 1 ~~~~~~~~~~~~~~~~-~~~~A~~y~lp~~~~~lvG~~~~~~v~~~~~~~le~iA~~f~~g~~~l~~aNPgv------d~ 73 (310)
T PRK10190 1 MRRVNILCSFALLFAS-HTSLAVTYPLPPEGSRLVGQSLTVTVPDHNTQPLETFAAQYGQGLSNMLEANPGA------DV 73 (310)
T ss_pred CcchhhHHHHHHHHhh-ccccceeeccCCCCCceecceEEEEecCCCCccHHHHHHHhCCCHHHHHHhCCCC------CC
Confidence 6666554444443321 223345554444555556678889998855 69999999999999999999971 12
Q ss_pred CccCCCceEEeec
Q 014940 79 HILPSQLFVRIPV 91 (415)
Q Consensus 79 ~~L~~Gq~l~IP~ 91 (415)
....+|++|.||.
T Consensus 74 ~~p~~G~~i~iP~ 86 (310)
T PRK10190 74 FLPKSGSQLTIPQ 86 (310)
T ss_pred CCCCCCCEEEecC
Confidence 2336899999986
No 29
>COG1652 XkdP Uncharacterized protein containing LysM domain [Function unknown]
Probab=97.20 E-value=0.00014 Score=71.37 Aligned_cols=51 Identities=31% Similarity=0.459 Sum_probs=47.2
Q ss_pred eeEEeCCCCCHHHHHHHHhCCCCCHHHHHhhcC---CCCCCCccCCcEEEecCC
Q 014940 105 THYKTRPSDTLTSIANQVYAGLVSADQLREAND---IQDPDVLDVGVNLLVPLP 155 (415)
Q Consensus 105 ~~YtV~~GDTL~~IA~~~fggLvs~~~L~~~N~---l~~~~~L~~Gq~L~IP~~ 155 (415)
.+|+|++|||||.|++++|++-+.+..|..+|+ +.+++.|.+||+|.||-.
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 489999999999999999998888999999999 678889999999999964
No 30
>PRK10190 L,D-transpeptidase; Provisional
Probab=96.42 E-value=0.0062 Score=61.19 Aligned_cols=51 Identities=24% Similarity=0.236 Sum_probs=44.9
Q ss_pred cceeEEeCCCC--CHHHHHHHHhCCCCCHHHHHhhcCCCCCCCccCCcEEEecCCC
Q 014940 103 VSTHYKTRPSD--TLTSIANQVYAGLVSADQLREANDIQDPDVLDVGVNLLVPLPC 156 (415)
Q Consensus 103 ~~~~YtV~~GD--TL~~IA~~~fggLvs~~~L~~~N~l~~~~~L~~Gq~L~IP~~c 156 (415)
....|+|+++| +|..||++ |+ +.+.+|+++|+..|+...++|++|.||..-
T Consensus 36 ~~~~~~v~~~~~~~le~iA~~-f~--~g~~~l~~aNPgvd~~~p~~G~~i~iP~~~ 88 (310)
T PRK10190 36 QSLTVTVPDHNTQPLETFAAQ-YG--QGLSNMLEANPGADVFLPKSGSQLTIPQQL 88 (310)
T ss_pred ceEEEEecCCCCccHHHHHHH-hC--CCHHHHHHhCCCCCCCCCCCCCEEEecCcc
Confidence 45679999866 59999999 99 999999999999888778899999999753
No 31
>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=96.41 E-value=0.0043 Score=50.89 Aligned_cols=48 Identities=31% Similarity=0.388 Sum_probs=29.0
Q ss_pred eeEEecCCCCHHHHHHHhCCCHHHHHHh---cCCC-C-CCcCCCCEEEECCCC
Q 014940 171 LSYVVKDVDTLAGIAARYRTTLTDLMNA---NAMG-S-TAVKAGDILAVPLPA 218 (415)
Q Consensus 171 ~tY~Vq~GDTL~sIA~rfgvt~~~L~~~---N~l~-~-~~I~pGq~L~IPl~~ 218 (415)
..|+|++||||+.|=+++|++..+|.++ +.-. . ..|+|||.|.+-+..
T Consensus 3 ~~~~V~~GDtLs~iF~~~gls~~dl~~v~~~~~~~k~L~~L~pGq~l~f~~d~ 55 (85)
T PF04225_consen 3 QEYTVKSGDTLSTIFRRAGLSASDLYAVLEADGEAKPLTRLKPGQTLEFQLDE 55 (85)
T ss_dssp -EEE--TT--HHHHHHHTT--HHHHHHHHHHGGGT--GGG--TT-EEEEEE-T
T ss_pred cEEEECCCCcHHHHHHHcCCCHHHHHHHHhccCccchHhhCCCCCEEEEEECC
Confidence 5799999999999999999998887554 3222 2 689999999988865
No 32
>PRK10260 L,D-transpeptidase; Provisional
Probab=96.37 E-value=0.0069 Score=60.72 Aligned_cols=51 Identities=20% Similarity=0.184 Sum_probs=44.5
Q ss_pred cceeEEeCCCC--CHHHHHHHHhCCCCCHHHHHhhcCCCCCCCccCCcEEEecCCC
Q 014940 103 VSTHYKTRPSD--TLTSIANQVYAGLVSADQLREANDIQDPDVLDVGVNLLVPLPC 156 (415)
Q Consensus 103 ~~~~YtV~~GD--TL~~IA~~~fggLvs~~~L~~~N~l~~~~~L~~Gq~L~IP~~c 156 (415)
....|+|++|| +|..||++ |+ +.+.+|+++|+..|+...++|++|.||..-
T Consensus 39 ~~~~~~v~~~~~~~le~iA~~-f~--~g~~~l~~aNPgvdp~lp~~G~~i~iP~~~ 91 (306)
T PRK10260 39 QNQVITIPEGNTQPLEYFAAE-YQ--MGLSNMMEANPGVDTFLPKGGTVLNIPQQL 91 (306)
T ss_pred ccEEEEeCCCCCchHHHHHHH-hC--CCHHHHHHhCcCCCCCcCCCCCEEEeCCcc
Confidence 44679999966 59999999 99 999999999998887778899999999753
No 33
>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=96.21 E-value=0.0031 Score=51.77 Aligned_cols=49 Identities=24% Similarity=0.297 Sum_probs=27.7
Q ss_pred ceeEEeCCCCCHHHHHHHHhCCCCCHHHHHhh---cCC-CCCCCccCCcEEEecCC
Q 014940 104 STHYKTRPSDTLTSIANQVYAGLVSADQLREA---NDI-QDPDVLDVGVNLLVPLP 155 (415)
Q Consensus 104 ~~~YtV~~GDTL~~IA~~~fggLvs~~~L~~~---N~l-~~~~~L~~Gq~L~IP~~ 155 (415)
|..|+|++||||..|-++ +| ++..+|.+. +.. ..-..|+|||+|.+-+.
T Consensus 2 W~~~~V~~GDtLs~iF~~-~g--ls~~dl~~v~~~~~~~k~L~~L~pGq~l~f~~d 54 (85)
T PF04225_consen 2 WQEYTVKSGDTLSTIFRR-AG--LSASDLYAVLEADGEAKPLTRLKPGQTLEFQLD 54 (85)
T ss_dssp --EEE--TT--HHHHHHH-TT----HHHHHHHHHHGGGT--GGG--TT-EEEEEE-
T ss_pred CcEEEECCCCcHHHHHHH-cC--CCHHHHHHHHhccCccchHhhCCCCCEEEEEEC
Confidence 678999999999999999 88 888776554 321 23357999999998764
No 34
>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=96.13 E-value=0.0062 Score=48.81 Aligned_cols=43 Identities=37% Similarity=0.321 Sum_probs=33.3
Q ss_pred CCHHHHHHHHhCC-CCCHH----HHHhhcCC----CCCCCccCCcEEEecCC
Q 014940 113 DTLTSIANQVYAG-LVSAD----QLREANDI----QDPDVLDVGVNLLVPLP 155 (415)
Q Consensus 113 DTL~~IA~~~fgg-Lvs~~----~L~~~N~l----~~~~~L~~Gq~L~IP~~ 155 (415)
||||.||+++..+ -+++. .|.+.||. .+.+.|++|+.|.||..
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 8999999994333 26766 67788985 35678999999999964
No 35
>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=96.07 E-value=0.009 Score=45.94 Aligned_cols=48 Identities=38% Similarity=0.415 Sum_probs=38.3
Q ss_pred EEeCCCCCHHHHHHHHhCCCCCH-HHHHhhcCCC-CC-CCccCCcEEEecCC
Q 014940 107 YKTRPSDTLTSIANQVYAGLVSA-DQLREANDIQ-DP-DVLDVGVNLLVPLP 155 (415)
Q Consensus 107 YtV~~GDTL~~IA~~~fggLvs~-~~L~~~N~l~-~~-~~L~~Gq~L~IP~~ 155 (415)
|+. .||||+.|+.|+||..--+ +.|.++|+.. +. ..|..|..|.+|.-
T Consensus 4 ~t~-~GDtlD~I~~r~yG~~~~~~e~ll~aNp~La~~~~~lpaG~~I~lP~i 54 (60)
T PF05489_consen 4 YTT-QGDTLDLIAYRHYGREDGAVEALLEANPGLADTGPVLPAGTVIILPDI 54 (60)
T ss_pred EEe-CcCcHHHHHHHHhCcHHHHHHHHHHHChhhhhcCCcCCCCCEEECCCC
Confidence 444 9999999999999955334 7899999973 33 46899999999964
No 36
>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=95.90 E-value=0.0083 Score=48.07 Aligned_cols=40 Identities=43% Similarity=0.590 Sum_probs=32.0
Q ss_pred CCHHHHHHHh---C-CCHH----HHHHhcCC---C-C-CCcCCCCEEEECCCC
Q 014940 179 DTLAGIAARY---R-TTLT----DLMNANAM---G-S-TAVKAGDILAVPLPA 218 (415)
Q Consensus 179 DTL~sIA~rf---g-vt~~----~L~~~N~l---~-~-~~I~pGq~L~IPl~~ 218 (415)
||||+||++| + +++. .|.+.|+- . + +.|++|++|.||-..
T Consensus 1 DTLw~IA~~~~~~~~~s~~q~m~ai~~aNp~AF~~~nin~L~~G~~L~iP~~~ 53 (74)
T TIGR03505 1 DTLWGIAQRVRPDNSVSLYQMMLALYRANPDAFIGGNINRLKVGQILRIPSEE 53 (74)
T ss_pred CcHHHHHHHHccCCCCCHHHHHHHHHHHCHHhHhcCChhhcCCCCEEeCCCHH
Confidence 8999999999 4 6776 57788852 2 2 689999999999754
No 37
>COG1652 XkdP Uncharacterized protein containing LysM domain [Function unknown]
Probab=95.85 E-value=0.003 Score=61.99 Aligned_cols=48 Identities=25% Similarity=0.362 Sum_probs=39.9
Q ss_pred eeEEecCCCCHHHHHHHh-C--CCHHHHHHhcC---CCC-CCcCCCCEEEECCCC
Q 014940 171 LSYVVKDVDTLAGIAARY-R--TTLTDLMNANA---MGS-TAVKAGDILAVPLPA 218 (415)
Q Consensus 171 ~tY~Vq~GDTL~sIA~rf-g--vt~~~L~~~N~---l~~-~~I~pGq~L~IPl~~ 218 (415)
.+|+|++|||||.||+++ | +....|..+|+ +.+ +.|++||+|.||-..
T Consensus 211 ~~~~v~rgDTl~~is~~~Yg~~~~y~~I~~aNk~~~~~~p~~I~pGq~l~iP~~~ 265 (269)
T COG1652 211 TTNTVKRGDTLWQISKKVYGDGVEYRKIAEANKALVLDNPDKIKPGQVLRIPDQL 265 (269)
T ss_pred eEEEeccCCcccccchhhcCcceEEEeHhhhhhhhccCCCCcCCCcceeeCCCcc
Confidence 389999999999999664 5 45577999998 554 799999999999754
No 38
>PRK11649 putative peptidase; Provisional
Probab=94.90 E-value=0.15 Score=53.95 Aligned_cols=114 Identities=18% Similarity=0.137 Sum_probs=73.7
Q ss_pred ccceeEEeCCCCCHHHHHHHHhCCCCCHHHHHhhcC-CCCCCCccCCcEEEecCCCcCC--------CCC-------cCC
Q 014940 102 SVSTHYKTRPSDTLTSIANQVYAGLVSADQLREAND-IQDPDVLDVGVNLLVPLPCTCF--------NGT-------DNS 165 (415)
Q Consensus 102 ~~~~~YtV~~GDTL~~IA~~~fggLvs~~~L~~~N~-l~~~~~L~~Gq~L~IP~~c~c~--------~~~-------~~~ 165 (415)
..+..|+|++||||..|=++ +| ++..++.+.-. ..+...|++||.|.+-+...-. +.. .++
T Consensus 93 ~~~~~~~Vk~GDTl~~iL~r-~G--i~~~di~~l~~~~~~L~~Lr~Gq~l~~~~d~dG~L~~l~~~~s~~~~~v~~R~dg 169 (439)
T PRK11649 93 AGVHEYVVSTGDTLSSILNQ-YG--IDMSDISQLAAQDKELRNLKIGQQLSWTLTADGDLQRLTWEVSRRETRTYDRTGN 169 (439)
T ss_pred CceEEEEeCCCCCHHHHHHH-cC--CCHHHHHHHHHcChHhhcCCCCCEEEEEECCCCCeEEEEEEeCCCeEEEEEecCC
Confidence 35678999999999999999 89 99888877622 2344579999999986432100 000 000
Q ss_pred CCc----------eeeeEEecCCCCHHHHHHHhCCCHHHHHHhcCCC----C-CCcCCCCEEEECCCC
Q 014940 166 LPA----------VYLSYVVKDVDTLAGIAARYRTTLTDLMNANAMG----S-TAVKAGDILAVPLPA 218 (415)
Q Consensus 166 ~~~----------~~~tY~Vq~GDTL~sIA~rfgvt~~~L~~~N~l~----~-~~I~pGq~L~IPl~~ 218 (415)
... ........-..+|+.-|.+-|++...++++..+- + ..|++|+.+.|=...
T Consensus 170 ~F~~~~~~~~~~~~~~~~~g~I~~Sl~~sa~~agl~~~~i~~~~~~~~~~idf~~lr~GD~f~v~~~~ 237 (439)
T PRK11649 170 GFKETSEMQQGEWVNSVLKGTVGGSFVASAKNAGLTSAEISAVIKALQWQMDFRKLKKGDEFSVLMSR 237 (439)
T ss_pred cEEEEEeecccEEEEEEEEEEEeccHHHHHHHcCCCHHHHHHHHHHhccCcChhhCCCCCEEEEEEEE
Confidence 000 0000111223589999999999988887776531 1 369999998876543
No 39
>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=92.91 E-value=0.2 Score=38.46 Aligned_cols=43 Identities=28% Similarity=0.425 Sum_probs=33.6
Q ss_pred ecCCCCHHHHH-HHhCCC---HHHHHHhcC-CC--CCCcCCCCEEEECCC
Q 014940 175 VKDVDTLAGIA-ARYRTT---LTDLMNANA-MG--STAVKAGDILAVPLP 217 (415)
Q Consensus 175 Vq~GDTL~sIA-~rfgvt---~~~L~~~N~-l~--~~~I~pGq~L~IPl~ 217 (415)
-++|||+..|+ +.||-. ++.++++|. +. ...+..|..|.+|--
T Consensus 5 t~~GDtlD~I~~r~yG~~~~~~e~ll~aNp~La~~~~~lpaG~~I~lP~i 54 (60)
T PF05489_consen 5 TTQGDTLDLIAYRHYGREDGAVEALLEANPGLADTGPVLPAGTVIILPDI 54 (60)
T ss_pred EeCcCcHHHHHHHHhCcHHHHHHHHHHHChhhhhcCCcCCCCCEEECCCC
Confidence 34999999999 456764 368899995 43 368999999999953
No 40
>COG3170 FimV Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=89.86 E-value=0.24 Score=54.61 Aligned_cols=51 Identities=31% Similarity=0.404 Sum_probs=39.9
Q ss_pred eeeeEEecCCCCHHHHHHHh----CCCHHH----HHHhcCC--C--C-CCcCCCCEEEECCCCC
Q 014940 169 VYLSYVVKDVDTLAGIAARY----RTTLTD----LMNANAM--G--S-TAVKAGDILAVPLPAC 219 (415)
Q Consensus 169 ~~~tY~Vq~GDTL~sIA~rf----gvt~~~----L~~~N~l--~--~-~~I~pGq~L~IPl~~~ 219 (415)
...+|+|++|||||+||.+- ++|+++ |.++|.- . + +.+++|.+|.||.-..
T Consensus 187 ~g~tyt~~~~Dtl~dIAs~~rp~~~vt~~Q~~lAly~lNP~af~~gni~RLr~GSvLriP~~~q 250 (755)
T COG3170 187 PGDTYTVRSGDTLWDIASRLRPQDHVTVEQMLLALYQLNPQAFVNGNINRLRAGSVLRIPSAAQ 250 (755)
T ss_pred CCcccccCCcchHHHHHHhhcCcccccHHHHHHHHHhhChhhhcccchhhccccceeeccchhh
Confidence 45799999999999999876 356654 6777853 1 2 6999999999997653
No 41
>COG3170 FimV Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=89.44 E-value=0.27 Score=54.17 Aligned_cols=53 Identities=26% Similarity=0.349 Sum_probs=39.5
Q ss_pred cceeEEeCCCCCHHHHHHHHhC-CCCCHH----HHHhhcCC----CCCCCccCCcEEEecCC
Q 014940 103 VSTHYKTRPSDTLTSIANQVYA-GLVSAD----QLREANDI----QDPDVLDVGVNLLVPLP 155 (415)
Q Consensus 103 ~~~~YtV~~GDTL~~IA~~~fg-gLvs~~----~L~~~N~l----~~~~~L~~Gq~L~IP~~ 155 (415)
...+|+|++|||||.||.+.=+ +-+|.+ .|.+.|+. .+-++|++|++|.||.-
T Consensus 187 ~g~tyt~~~~Dtl~dIAs~~rp~~~vt~~Q~~lAly~lNP~af~~gni~RLr~GSvLriP~~ 248 (755)
T COG3170 187 PGDTYTVRSGDTLWDIASRLRPQDHVTVEQMLLALYQLNPQAFVNGNINRLRAGSVLRIPSA 248 (755)
T ss_pred CCcccccCCcchHHHHHHhhcCcccccHHHHHHHHHhhChhhhcccchhhccccceeeccch
Confidence 3468999999999999988422 235554 46677886 23458999999999963
No 42
>PRK11649 putative peptidase; Provisional
Probab=89.31 E-value=0.56 Score=49.64 Aligned_cols=49 Identities=31% Similarity=0.394 Sum_probs=40.8
Q ss_pred eeeEEecCCCCHHHHHHHhCCCHHHHHHhcCC-C-CCCcCCCCEEEECCCC
Q 014940 170 YLSYVVKDVDTLAGIAARYRTTLTDLMNANAM-G-STAVKAGDILAVPLPA 218 (415)
Q Consensus 170 ~~tY~Vq~GDTL~sIA~rfgvt~~~L~~~N~l-~-~~~I~pGq~L~IPl~~ 218 (415)
...|+|++||||.+|=+++|++..++.++-.- . -..|++||.|.+-+..
T Consensus 95 ~~~~~Vk~GDTl~~iL~r~Gi~~~di~~l~~~~~~L~~Lr~Gq~l~~~~d~ 145 (439)
T PRK11649 95 VHEYVVSTGDTLSSILNQYGIDMSDISQLAAQDKELRNLKIGQQLSWTLTA 145 (439)
T ss_pred eEEEEeCCCCCHHHHHHHcCCCHHHHHHHHHcChHhhcCCCCCEEEEEECC
Confidence 46899999999999999999999998877322 2 2589999999997665
No 43
>COG3061 OapA Cell envelope opacity-associated protein A [Cell envelope biogenesis, outer membrane]
Probab=86.10 E-value=1.5 Score=42.19 Aligned_cols=74 Identities=20% Similarity=0.188 Sum_probs=53.2
Q ss_pred CccCCcEEEecCC-CcCCCCCcCCCCceeeeEEecCCCCHHHHHHHhCCCHHHHHHhcCCC---C--CCcCCCCEEEECC
Q 014940 143 VLDVGVNLLVPLP-CTCFNGTDNSLPAVYLSYVVKDVDTLAGIAARYRTTLTDLMNANAMG---S--TAVKAGDILAVPL 216 (415)
Q Consensus 143 ~L~~Gq~L~IP~~-c~c~~~~~~~~~~~~~tY~Vq~GDTL~sIA~rfgvt~~~L~~~N~l~---~--~~I~pGq~L~IPl 216 (415)
.+..+|...+|.. ...+..... +...+|+|+.|+||..+=|..+..+.|+.++-... . .+|+.||.++|-+
T Consensus 134 p~q~~q~~~v~~~~~~~P~~~s~---g~wqsy~V~~G~TLaQlFRdn~LpitDVnAMakveGagkpLSnlkaGq~Vki~~ 210 (242)
T COG3061 134 PIQAKQEKKVPRTVDAQPFKPSS---GNWQSYTVPQGKTLAQLFRDNNLPITDVNAMAKVEGAGKPLSNLKAGQKVKISL 210 (242)
T ss_pred hhhccCccccCCccccCccccCc---ccceeEEecCCccHHHHHhccCCChHHhHHHHhhccCCCchhhccCCCEEEEEE
Confidence 3556777777732 222222121 25689999999999999999999999987776432 2 5899999999999
Q ss_pred CCC
Q 014940 217 PAC 219 (415)
Q Consensus 217 ~~~ 219 (415)
.+.
T Consensus 211 naq 213 (242)
T COG3061 211 NAQ 213 (242)
T ss_pred cCc
Confidence 863
No 44
>COG3061 OapA Cell envelope opacity-associated protein A [Cell envelope biogenesis, outer membrane]
Probab=86.09 E-value=1.6 Score=42.02 Aligned_cols=71 Identities=11% Similarity=0.147 Sum_probs=46.5
Q ss_pred CCCceEEeeccccc-cCCcccccceeEEeCCCCCHHHHHHHHhCCCCCHHHHHhhcCCC---C-CCCccCCcEEEecCC
Q 014940 82 PSQLFVRIPVTCAC-VDGIRKSVSTHYKTRPSDTLTSIANQVYAGLVSADQLREANDIQ---D-PDVLDVGVNLLVPLP 155 (415)
Q Consensus 82 ~~Gq~l~IP~~csc-~~g~~~~~~~~YtV~~GDTL~~IA~~~fggLvs~~~L~~~N~l~---~-~~~L~~Gq~L~IP~~ 155 (415)
..++...+|..-.. .-......|.+|+|+.|+||..+=|. .+ ..+.++-++-... + -..|+.||+|+|-+.
T Consensus 136 q~~q~~~v~~~~~~~P~~~s~g~wqsy~V~~G~TLaQlFRd-n~--LpitDVnAMakveGagkpLSnlkaGq~Vki~~n 211 (242)
T COG3061 136 QAKQEKKVPRTVDAQPFKPSSGNWQSYTVPQGKTLAQLFRD-NN--LPITDVNAMAKVEGAGKPLSNLKAGQKVKISLN 211 (242)
T ss_pred hccCccccCCccccCccccCcccceeEEecCCccHHHHHhc-cC--CChHHhHHHHhhccCCCchhhccCCCEEEEEEc
Confidence 45666666632111 11122337899999999999999988 56 7766665553332 1 136999999999875
No 45
>COG4784 Putative Zn-dependent protease [General function prediction only]
Probab=76.36 E-value=4.9 Score=41.34 Aligned_cols=45 Identities=33% Similarity=0.364 Sum_probs=36.6
Q ss_pred eeeEEecCCCCHHHHHHHh-CC--CHHHHHHhcCCC-CCCcCCCCEEEE
Q 014940 170 YLSYVVKDVDTLAGIAARY-RT--TLTDLMNANAMG-STAVKAGDILAV 214 (415)
Q Consensus 170 ~~tY~Vq~GDTL~sIA~rf-gv--t~~~L~~~N~l~-~~~I~pGq~L~I 214 (415)
..--+||+|||+.++|.+- |+ +++-++-+|.|. ...++||+.++|
T Consensus 428 irvvtVk~GqT~~~lAA~m~G~~rkldlfRllNam~~~a~~~pGd~vKi 476 (479)
T COG4784 428 IRVVTVKPGQTMASLAARMMGTDRKLDLFRLLNAMSPGATVRPGDKVKI 476 (479)
T ss_pred EEEEEecCCccHHHHHhhccCchhHHHHHHHHhccCCCCcCCCCCeeee
Confidence 3456799999999999876 54 456778889987 479999999987
No 46
>COG4254 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=75.79 E-value=2.5 Score=42.39 Aligned_cols=52 Identities=27% Similarity=0.356 Sum_probs=45.6
Q ss_pred eeEEeCCCCCHHHHHHHHhCCCCCHHHHHhhcCCCCCCCccCCcEEEecCCC
Q 014940 105 THYKTRPSDTLTSIANQVYAGLVSADQLREANDIQDPDVLDVGVNLLVPLPC 156 (415)
Q Consensus 105 ~~YtV~~GDTL~~IA~~~fggLvs~~~L~~~N~l~~~~~L~~Gq~L~IP~~c 156 (415)
..|.|+.||||-.++..+..-+..+..++.+|...++-.+++|..|.||++.
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 5799999999999999965655667888999999888899999999999874
No 47
>COG0739 NlpD Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]
Probab=74.66 E-value=4.8 Score=38.67 Aligned_cols=48 Identities=40% Similarity=0.506 Sum_probs=43.2
Q ss_pred eeEEecCCCCHHHHHHHhCCCHHHHHHhcCCCCC-CcCCCCEEEECCCC
Q 014940 171 LSYVVKDVDTLAGIAARYRTTLTDLMNANAMGST-AVKAGDILAVPLPA 218 (415)
Q Consensus 171 ~tY~Vq~GDTL~sIA~rfgvt~~~L~~~N~l~~~-~I~pGq~L~IPl~~ 218 (415)
..|.++.++++..|+++++....++...|++... .+..|+.+.+|...
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 50 (277)
T COG0739 2 SLYVVKKGDTLSAIAARLGISAKDLARLNNLLKKRLLRIGQLLRVPRAA 50 (277)
T ss_pred ceEEecCCCHHHHHHHHcCCCHHHHHHHHhhccccccCccceeeecccc
Confidence 3589999999999999999999999999987654 89999999999874
No 48
>COG5004 P2-like prophage tail protein X [General function prediction only]
Probab=74.55 E-value=5.6 Score=31.13 Aligned_cols=52 Identities=27% Similarity=0.319 Sum_probs=39.0
Q ss_pred eeEEeCCCCCHHHHHHHHhCCCCC-HHHHHhhcCCC-CC-CCccCCcEEEecCCC
Q 014940 105 THYKTRPSDTLTSIANQVYAGLVS-ADQLREANDIQ-DP-DVLDVGVNLLVPLPC 156 (415)
Q Consensus 105 ~~YtV~~GDTL~~IA~~~fggLvs-~~~L~~~N~l~-~~-~~L~~Gq~L~IP~~c 156 (415)
..|+.+.|||++.++.++|+.... .+++.++|+-. +. ..|..|-.|.+|-..
T Consensus 3 ~~~Rt~~gDtvDalc~~~Ygrt~~v~eavl~ANpGlAd~gp~lp~gl~i~lPD~~ 57 (70)
T COG5004 3 MIVRTRQGDTVDALCWRVYGRTTGVTEAVLEANPGLADWGPVLPHGLAITLPDIA 57 (70)
T ss_pred eEEEeccCchHHHHHHHHHhhHHHHHHHHHhcCCChhhcCCCCccceeEecCCCC
Confidence 357778999999999999995443 36788899963 22 247789888888654
No 49
>PF13518 HTH_28: Helix-turn-helix domain
Probab=72.71 E-value=3.6 Score=29.34 Aligned_cols=24 Identities=8% Similarity=0.112 Sum_probs=21.4
Q ss_pred cCCCCHHHHHHHhCCCHHHHHHhc
Q 014940 176 KDVDTLAGIAARYRTTLTDLMNAN 199 (415)
Q Consensus 176 q~GDTL~sIA~rfgvt~~~L~~~N 199 (415)
..|+++..||++||++...|..|-
T Consensus 10 ~~g~s~~~~a~~~gis~~tv~~w~ 33 (52)
T PF13518_consen 10 LEGESVREIAREFGISRSTVYRWI 33 (52)
T ss_pred HcCCCHHHHHHHHCCCHhHHHHHH
Confidence 368899999999999999998885
No 50
>COG4784 Putative Zn-dependent protease [General function prediction only]
Probab=71.80 E-value=4.9 Score=41.31 Aligned_cols=47 Identities=19% Similarity=0.290 Sum_probs=37.5
Q ss_pred eeEEeCCCCCHHHHHHHHhCCC-CCHHHHHhhcCCCCCCCccCCcEEEe
Q 014940 105 THYKTRPSDTLTSIANQVYAGL-VSADQLREANDIQDPDVLDVGVNLLV 152 (415)
Q Consensus 105 ~~YtV~~GDTL~~IA~~~fggL-vs~~~L~~~N~l~~~~~L~~Gq~L~I 152 (415)
..-+||+|||+..+|.+ -.|. -+++-++-.|.+.....+++|++|+|
T Consensus 429 rvvtVk~GqT~~~lAA~-m~G~~rkldlfRllNam~~~a~~~pGd~vKi 476 (479)
T COG4784 429 RVVTVKPGQTMASLAAR-MMGTDRKLDLFRLLNAMSPGATVRPGDKVKI 476 (479)
T ss_pred EEEEecCCccHHHHHhh-ccCchhHHHHHHHHhccCCCCcCCCCCeeee
Confidence 35689999999999999 4543 23566777899877778999999987
No 51
>TIGR00247 conserved hypothetical protein, YceG family. This uncharacterized protein family, found in three of four microbial genomes, virtually always once per genome, includes YceG from Escherichia coli. This protein is encoded next to PabC, 4-amino-4-deoxychorismate lyase, in E. coli and numerous other proteobacteria, but that proximity is not conserved in other lineages. Numerous members of this family have been misannotated as aminodeoxychorismate lyase, apparently because of promiximty to PabC.
Probab=71.37 E-value=34 Score=34.98 Aligned_cols=55 Identities=11% Similarity=0.120 Sum_probs=35.6
Q ss_pred cEEEEeCCCCCHHHHHHHcC---C-C-HH---HHHHhCCCCCCCCCCCCCccCCCceEEeeccccccCCcccccceeEEe
Q 014940 38 LLGYTLYTDLKVSEVGSLFN---V-D-PV---SILTANAIDISYSDVENHILPSQLFVRIPVTCACVDGIRKSVSTHYKT 109 (415)
Q Consensus 38 ~~~Ytv~~gdtL~~IA~~fg---v-s-~~---~L~~~N~l~~t~P~~~~~~L~~Gq~l~IP~~csc~~g~~~~~~~~YtV 109 (415)
-+.++|+.|++..+|++.+. + . .. .+.++++. ...| ...+|.+
T Consensus 39 ~v~v~Ip~G~s~~~Ia~~L~~~GvI~s~~~F~~~ak~~~~--------~~~l---------------------kaG~Y~l 89 (342)
T TIGR00247 39 VYEFNIEKGTGVSKIAKELKKQKLIKSEKLLQYLLKIKGS--------LKQF---------------------KAGTYLL 89 (342)
T ss_pred cEEEEECCCCCHHHHHHHHHHCCCCCCHHHHHHHHHhcCC--------cCcc---------------------cceEEEE
Confidence 35689999999999998663 2 2 12 22222322 1112 2346999
Q ss_pred CCCCCHHHHHHH
Q 014940 110 RPSDTLTSIANQ 121 (415)
Q Consensus 110 ~~GDTL~~IA~~ 121 (415)
+++.+...|-+.
T Consensus 90 ~~~ms~~~il~~ 101 (342)
T TIGR00247 90 NGDMTVFEILKL 101 (342)
T ss_pred CCCCCHHHHHHH
Confidence 999999998877
No 52
>KOG2850 consensus Predicted peptidoglycan-binding protein, contains LysM domain [General function prediction only]
Probab=65.25 E-value=3.5 Score=38.76 Aligned_cols=50 Identities=16% Similarity=0.274 Sum_probs=38.3
Q ss_pred cceeEEeCCCCCHHHHHHHHhCCCCCHHHHHhhcCCCCCCCccCCcEEEecCC
Q 014940 103 VSTHYKTRPSDTLTSIANQVYAGLVSADQLREANDIQDPDVLDVGVNLLVPLP 155 (415)
Q Consensus 103 ~~~~YtV~~GDTL~~IA~~~fggLvs~~~L~~~N~l~~~~~L~~Gq~L~IP~~ 155 (415)
+...-+||.||||..||-+ |. ..+.+|.+.|++..-....+=+.+.+|..
T Consensus 8 ~~l~~~iq~~dt~~a~al~-~~--~~va~i~RvN~~~r~q~f~a~~~i~~pv~ 57 (186)
T KOG2850|consen 8 HELEVTIQEGDTLQAIALN-YE--SDVADIKRVNNDDREQRFNALRSISIPVT 57 (186)
T ss_pred hheeeeeccCchhhhHHhh-cc--cchhhheeeccchhhhhhccccceecccc
Confidence 3456789999999999988 88 99999999998744445555556666554
No 53
>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=63.45 E-value=7.5 Score=27.66 Aligned_cols=24 Identities=13% Similarity=0.181 Sum_probs=18.4
Q ss_pred ecCCCCHHHHHHHhCCCHHHHHHh
Q 014940 175 VKDVDTLAGIAARYRTTLTDLMNA 198 (415)
Q Consensus 175 Vq~GDTL~sIA~rfgvt~~~L~~~ 198 (415)
.+.|-++..||++||++...|.++
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 367899999999999999998775
No 54
>COG4254 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=62.36 E-value=6.2 Score=39.70 Aligned_cols=49 Identities=35% Similarity=0.391 Sum_probs=40.7
Q ss_pred eeeEEecCCCCHHHHHHHhCCCH---HHHHHhcCCCC-CCcCCCCEEEECCCC
Q 014940 170 YLSYVVKDVDTLAGIAARYRTTL---TDLMNANAMGS-TAVKAGDILAVPLPA 218 (415)
Q Consensus 170 ~~tY~Vq~GDTL~sIA~rfgvt~---~~L~~~N~l~~-~~I~pGq~L~IPl~~ 218 (415)
.++|+|+.||||-.++..|-... ..++.+|...+ ..+++|..|.||++.
T Consensus 5 ~~~yrv~~gdtli~l~~~yl~~~~g~r~~q~an~~~~P~~l~pgs~l~ip~~~ 57 (339)
T COG4254 5 ALTYRVLFGDTLILLLGGYLTLLAGSRAAQPANTKRPPFILQPGSCLPIPLPA 57 (339)
T ss_pred cceeeeccccHHHHHHHHhhhccchhhhhcccccCCCCcccCCCccccCCCcc
Confidence 37899999999999999996544 44677787765 699999999999877
No 55
>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=56.61 E-value=6.2 Score=30.50 Aligned_cols=25 Identities=16% Similarity=0.308 Sum_probs=21.7
Q ss_pred ecCCCCHHHHHHHhCCCHHHHHHhc
Q 014940 175 VKDVDTLAGIAARYRTTLTDLMNAN 199 (415)
Q Consensus 175 Vq~GDTL~sIA~rfgvt~~~L~~~N 199 (415)
...|.++..||++||++...|..|=
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 4789999999999999999999884
No 56
>KOG1187 consensus Serine/threonine protein kinase [Signal transduction mechanisms]
Probab=56.30 E-value=7.7 Score=39.88 Aligned_cols=31 Identities=19% Similarity=0.239 Sum_probs=27.1
Q ss_pred cccccCCCCCccc----ceeeeeeeCC-EEEEeecc
Q 014940 284 VTTQRSSAGCNVT----SCSYGGFVNG-TIVTMLST 314 (415)
Q Consensus 284 ~aT~~~s~~c~i~----~~vY~g~~ng-~i~a~~~~ 314 (415)
+||++|++++.|+ ++||+|.+++ +.+|+...
T Consensus 72 ~AT~~Fs~~~~ig~Ggfg~VYkG~l~~~~~vAVK~~ 107 (361)
T KOG1187|consen 72 KATNNFSESNLIGEGGFGTVYKGVLSDGTVVAVKRL 107 (361)
T ss_pred HHHhCCchhcceecCCCeEEEEEEECCCCEEEEEEe
Confidence 8999999999996 7799999976 88999844
No 57
>KOG2850 consensus Predicted peptidoglycan-binding protein, contains LysM domain [General function prediction only]
Probab=56.25 E-value=7.4 Score=36.62 Aligned_cols=49 Identities=22% Similarity=0.358 Sum_probs=41.1
Q ss_pred eeeEEecCCCCHHHHHHHhCCCHHHHHHhcCCCC-CCcCCCCEEEECCCC
Q 014940 170 YLSYVVKDVDTLAGIAARYRTTLTDLMNANAMGS-TAVKAGDILAVPLPA 218 (415)
Q Consensus 170 ~~tY~Vq~GDTL~sIA~rfgvt~~~L~~~N~l~~-~~I~pGq~L~IPl~~ 218 (415)
...-++|.|||+..||=+|..++.++.+.|++.. .....-..+.+|+..
T Consensus 9 ~l~~~iq~~dt~~a~al~~~~~va~i~RvN~~~r~q~f~a~~~i~~pv~~ 58 (186)
T KOG2850|consen 9 ELEVTIQEGDTLQAIALNYESDVADIKRVNNDDREQRFNALRSISIPVTR 58 (186)
T ss_pred heeeeeccCchhhhHHhhcccchhhheeeccchhhhhhccccceecccch
Confidence 4567899999999999999999999999998764 466666777888765
No 58
>COG0739 NlpD Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]
Probab=55.70 E-value=16 Score=34.95 Aligned_cols=47 Identities=32% Similarity=0.488 Sum_probs=41.6
Q ss_pred eEEeCCCCCHHHHHHHHhCCCCCHHHHHhhcCCCCCCCccCCcEEEecCC
Q 014940 106 HYKTRPSDTLTSIANQVYAGLVSADQLREANDIQDPDVLDVGVNLLVPLP 155 (415)
Q Consensus 106 ~YtV~~GDTL~~IA~~~fggLvs~~~L~~~N~l~~~~~L~~Gq~L~IP~~ 155 (415)
.|.++.++++..|+++ ++ ....++.+.|.......+..|+.+.++..
T Consensus 3 ~~~~~~~~~l~~~~~~-~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 49 (277)
T COG0739 3 LYVVKKGDTLSAIAAR-LG--ISAKDLARLNNLLKKRLLRIGQLLRVPRA 49 (277)
T ss_pred eEEecCCCHHHHHHHH-cC--CCHHHHHHHHhhccccccCccceeeeccc
Confidence 5899999999999999 89 99999999999855557889999999875
No 59
>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=54.02 E-value=14 Score=26.19 Aligned_cols=23 Identities=13% Similarity=0.323 Sum_probs=17.2
Q ss_pred CCCCCHHHHHHHcCCCHHHHHHh
Q 014940 44 YTDLKVSEVGSLFNVDPVSILTA 66 (415)
Q Consensus 44 ~~gdtL~~IA~~fgvs~~~L~~~ 66 (415)
..|.++.+||+.|||+...|.++
T Consensus 19 ~~G~si~~IA~~~gvsr~TvyR~ 41 (45)
T PF02796_consen 19 AEGMSIAEIAKQFGVSRSTVYRY 41 (45)
T ss_dssp HTT--HHHHHHHTTS-HHHHHHH
T ss_pred HCCCCHHHHHHHHCcCHHHHHHH
Confidence 36899999999999999888765
No 60
>PF13518 HTH_28: Helix-turn-helix domain
Probab=48.07 E-value=21 Score=25.27 Aligned_cols=24 Identities=13% Similarity=0.160 Sum_probs=20.5
Q ss_pred CCCCHHHHHHHcCCCHHHHHHhCC
Q 014940 45 TDLKVSEVGSLFNVDPVSILTANA 68 (415)
Q Consensus 45 ~gdtL~~IA~~fgvs~~~L~~~N~ 68 (415)
.|.++.+||+.|||+...|..|-.
T Consensus 11 ~g~s~~~~a~~~gis~~tv~~w~~ 34 (52)
T PF13518_consen 11 EGESVREIAREFGISRSTVYRWIK 34 (52)
T ss_pred cCCCHHHHHHHHCCCHhHHHHHHH
Confidence 578999999999999988877644
No 61
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=47.09 E-value=21 Score=25.32 Aligned_cols=25 Identities=12% Similarity=0.104 Sum_probs=18.8
Q ss_pred ecCCCCHHHHHHHhCCCHHHHHHhc
Q 014940 175 VKDVDTLAGIAARYRTTLTDLMNAN 199 (415)
Q Consensus 175 Vq~GDTL~sIA~rfgvt~~~L~~~N 199 (415)
+..|.+...||+.+|++...+.+|=
T Consensus 14 ~~~G~s~~~ia~~lgvs~~Tv~~w~ 38 (50)
T PF13384_consen 14 LREGWSIREIAKRLGVSRSTVYRWI 38 (50)
T ss_dssp HHHT--HHHHHHHHTS-HHHHHHHH
T ss_pred HHCCCCHHHHHHHHCcCHHHHHHHH
Confidence 3459999999999999999988874
No 62
>COG5004 P2-like prophage tail protein X [General function prediction only]
Probab=45.22 E-value=43 Score=26.34 Aligned_cols=47 Identities=19% Similarity=0.310 Sum_probs=34.2
Q ss_pred eeEEecCCCCHHHHHHH-hCCC---HHHHHHhcC-CC--CCCcCCCCEEEECCC
Q 014940 171 LSYVVKDVDTLAGIAAR-YRTT---LTDLMNANA-MG--STAVKAGDILAVPLP 217 (415)
Q Consensus 171 ~tY~Vq~GDTL~sIA~r-fgvt---~~~L~~~N~-l~--~~~I~pGq~L~IPl~ 217 (415)
..|.-+.|||+..++.| ||-+ .+.+.++|. +. ...+..|-.|.+|--
T Consensus 3 ~~~Rt~~gDtvDalc~~~Ygrt~~v~eavl~ANpGlAd~gp~lp~gl~i~lPD~ 56 (70)
T COG5004 3 MIVRTRQGDTVDALCWRVYGRTTGVTEAVLEANPGLADWGPVLPHGLAITLPDI 56 (70)
T ss_pred eEEEeccCchHHHHHHHHHhhHHHHHHHHHhcCCChhhcCCCCccceeEecCCC
Confidence 56777899999999966 5644 367889995 54 367888877776643
No 63
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=44.98 E-value=20 Score=30.22 Aligned_cols=25 Identities=20% Similarity=0.327 Sum_probs=21.3
Q ss_pred ecCCCCHHHHHHHhCC-CHHHHHHhc
Q 014940 175 VKDVDTLAGIAARYRT-TLTDLMNAN 199 (415)
Q Consensus 175 Vq~GDTL~sIA~rfgv-t~~~L~~~N 199 (415)
.+.|+|+..||++||+ +...|..|=
T Consensus 21 ~~~g~sv~~vAr~~gv~~~~~l~~W~ 46 (116)
T COG2963 21 LRGGDTVSEVAREFGIVSATQLYKWR 46 (116)
T ss_pred HhcCccHHHHHHHhCCCChHHHHHHH
Confidence 4689999999999995 888888763
No 64
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=44.52 E-value=22 Score=30.60 Aligned_cols=27 Identities=11% Similarity=-0.036 Sum_probs=24.0
Q ss_pred EEecCCCCHHHHHHHhCCCHHHHHHhc
Q 014940 173 YVVKDVDTLAGIAARYRTTLTDLMNAN 199 (415)
Q Consensus 173 Y~Vq~GDTL~sIA~rfgvt~~~L~~~N 199 (415)
..+..|.++..||++||++...|..|=
T Consensus 24 ~~~~~g~sv~evA~e~gIs~~tl~~W~ 50 (121)
T PRK09413 24 QSFEPGMTVSLVARQHGVAASQLFLWR 50 (121)
T ss_pred HHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence 346689999999999999999999994
No 65
>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=44.31 E-value=12 Score=27.70 Aligned_cols=24 Identities=8% Similarity=0.213 Sum_probs=17.3
Q ss_pred ecCCCCHHHHHHHhCCCHHHHHHh
Q 014940 175 VKDVDTLAGIAARYRTTLTDLMNA 198 (415)
Q Consensus 175 Vq~GDTL~sIA~rfgvt~~~L~~~ 198 (415)
+..|.+..+||++||++..++..+
T Consensus 19 ~e~g~s~~~ia~~fgv~~sTv~~I 42 (53)
T PF04218_consen 19 LEEGESKRDIAREFGVSRSTVSTI 42 (53)
T ss_dssp HHCTT-HHHHHHHHT--CCHHHHH
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHH
Confidence 468999999999999987777654
No 66
>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=41.76 E-value=34 Score=20.82 Aligned_cols=23 Identities=22% Similarity=0.231 Sum_probs=19.8
Q ss_pred cCCCCHHHHHHHhCCCHHHHHHh
Q 014940 176 KDVDTLAGIAARYRTTLTDLMNA 198 (415)
Q Consensus 176 q~GDTL~sIA~rfgvt~~~L~~~ 198 (415)
..|.+...||+.|+++...+.+|
T Consensus 19 ~~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 19 AAGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHh
Confidence 56889999999999999888764
No 67
>PRK10270 putative aminodeoxychorismate lyase; Provisional
Probab=41.50 E-value=2.6e+02 Score=28.70 Aligned_cols=19 Identities=16% Similarity=0.065 Sum_probs=16.1
Q ss_pred cEEEEeCCCCCHHHHHHHc
Q 014940 38 LLGYTLYTDLKVSEVGSLF 56 (415)
Q Consensus 38 ~~~Ytv~~gdtL~~IA~~f 56 (415)
-..++|+.|++..+||+.+
T Consensus 39 ~v~v~I~~G~t~~~Ia~~L 57 (340)
T PRK10270 39 ETIFTLKPGTGRLALGEQL 57 (340)
T ss_pred CEEEEECCCCCHHHHHHHH
Confidence 3568999999999999854
No 68
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=40.62 E-value=96 Score=35.46 Aligned_cols=7 Identities=29% Similarity=0.477 Sum_probs=3.5
Q ss_pred CCCCCCC
Q 014940 349 QSDGAGP 355 (415)
Q Consensus 349 ~~~~~~~ 355 (415)
+.+||-.
T Consensus 565 g~aG~PP 571 (1102)
T KOG1924|consen 565 GIAGGPP 571 (1102)
T ss_pred cccCCCC
Confidence 4555544
No 69
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=37.09 E-value=33 Score=25.68 Aligned_cols=24 Identities=4% Similarity=0.257 Sum_probs=21.1
Q ss_pred EEeCCCCCHHHHHHHcCCCHHHHH
Q 014940 41 YTLYTDLKVSEVGSLFNVDPVSIL 64 (415)
Q Consensus 41 Ytv~~gdtL~~IA~~fgvs~~~L~ 64 (415)
|..+...++.+||+.+|++...+.
T Consensus 18 fd~PR~~tl~elA~~lgis~st~~ 41 (53)
T PF04967_consen 18 FDVPRRITLEELAEELGISKSTVS 41 (53)
T ss_pred CCCCCcCCHHHHHHHhCCCHHHHH
Confidence 788999999999999999986553
No 70
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=34.32 E-value=43 Score=23.69 Aligned_cols=23 Identities=13% Similarity=0.169 Sum_probs=15.3
Q ss_pred ecCCCCHHHHHHHhCCCHHHHHH
Q 014940 175 VKDVDTLAGIAARYRTTLTDLMN 197 (415)
Q Consensus 175 Vq~GDTL~sIA~rfgvt~~~L~~ 197 (415)
.+.|.+...||+++|.+...+.+
T Consensus 17 ~~~G~s~~~IA~~lg~s~sTV~r 39 (44)
T PF13936_consen 17 LEQGMSIREIAKRLGRSRSTVSR 39 (44)
T ss_dssp HCS---HHHHHHHTT--HHHHHH
T ss_pred HHcCCCHHHHHHHHCcCcHHHHH
Confidence 46899999999999999888754
No 71
>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=34.28 E-value=46 Score=23.70 Aligned_cols=22 Identities=9% Similarity=0.345 Sum_probs=18.2
Q ss_pred CCCCCHHHHHHHcCCCHHHHHH
Q 014940 44 YTDLKVSEVGSLFNVDPVSILT 65 (415)
Q Consensus 44 ~~gdtL~~IA~~fgvs~~~L~~ 65 (415)
..+.|+.+||+.+|++.+.+..
T Consensus 18 ~~~~t~~eIa~~lg~s~~~V~~ 39 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISRSTVRR 39 (50)
T ss_dssp TST-SHHHHHHHHTSCHHHHHH
T ss_pred cCCCCHHHHHHHHCCcHHHHHH
Confidence 5688999999999999977664
No 72
>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=32.31 E-value=38 Score=23.41 Aligned_cols=22 Identities=23% Similarity=0.345 Sum_probs=18.3
Q ss_pred CHHHHHHHcCCCHHHHHHhCCC
Q 014940 48 KVSEVGSLFNVDPVSILTANAI 69 (415)
Q Consensus 48 tL~~IA~~fgvs~~~L~~~N~l 69 (415)
|..++|+++|++.+.|+.+=..
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~ 22 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYERE 22 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHT
T ss_pred CHHHHHHHHCCCHHHHHHHHHC
Confidence 4679999999999999998665
No 73
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=31.85 E-value=46 Score=23.50 Aligned_cols=22 Identities=9% Similarity=0.193 Sum_probs=16.7
Q ss_pred CCCCHHHHHHHcCCCHHHHHHh
Q 014940 45 TDLKVSEVGSLFNVDPVSILTA 66 (415)
Q Consensus 45 ~gdtL~~IA~~fgvs~~~L~~~ 66 (415)
.|.+..+||+.+|++...+..+
T Consensus 16 ~G~s~~~ia~~lgvs~~Tv~~w 37 (50)
T PF13384_consen 16 EGWSIREIAKRLGVSRSTVYRW 37 (50)
T ss_dssp HT--HHHHHHHHTS-HHHHHHH
T ss_pred CCCCHHHHHHHHCcCHHHHHHH
Confidence 3889999999999999888776
No 74
>PHA00675 hypothetical protein
Probab=31.52 E-value=46 Score=27.04 Aligned_cols=25 Identities=8% Similarity=0.088 Sum_probs=21.7
Q ss_pred cCCCCHHHHHHHhCCCHHHHHHhcC
Q 014940 176 KDVDTLAGIAARYRTTLTDLMNANA 200 (415)
Q Consensus 176 q~GDTL~sIA~rfgvt~~~L~~~N~ 200 (415)
+.|.+...||++||++...+...=+
T Consensus 37 r~G~s~~~IA~~fGVsrstV~~I~~ 61 (78)
T PHA00675 37 VEGMSYAVLAEKFEQSKGAIAKICR 61 (78)
T ss_pred hcCccHHHHHHHhCCCHHHHHHHHc
Confidence 7899999999999999988876543
No 75
>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=29.33 E-value=71 Score=22.69 Aligned_cols=23 Identities=22% Similarity=0.114 Sum_probs=19.1
Q ss_pred cCCCCHHHHHHHhCCCHHHHHHh
Q 014940 176 KDVDTLAGIAARYRTTLTDLMNA 198 (415)
Q Consensus 176 q~GDTL~sIA~rfgvt~~~L~~~ 198 (415)
..|-|+..||+++|++.+.+...
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 57889999999999999887654
No 76
>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=29.02 E-value=54 Score=23.47 Aligned_cols=24 Identities=21% Similarity=0.241 Sum_probs=17.0
Q ss_pred ecCC-CCHHHHHHHhCCCHHHHHHh
Q 014940 175 VKDV-DTLAGIAARYRTTLTDLMNA 198 (415)
Q Consensus 175 Vq~G-DTL~sIA~rfgvt~~~L~~~ 198 (415)
|+.| -++...|++|||+...|...
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 3455 78999999999999998754
No 77
>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=28.84 E-value=59 Score=22.52 Aligned_cols=23 Identities=22% Similarity=0.358 Sum_probs=19.6
Q ss_pred CCHHHHHHHcCCCHHHHHHhCCC
Q 014940 47 LKVSEVGSLFNVDPVSILTANAI 69 (415)
Q Consensus 47 dtL~~IA~~fgvs~~~L~~~N~l 69 (415)
.++.++|+++|++...|..+-..
T Consensus 1 ~~~~e~a~~~gv~~~tlr~~~~~ 23 (49)
T cd04761 1 YTIGELAKLTGVSPSTLRYYERI 23 (49)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHC
Confidence 36889999999999999988543
No 78
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=28.84 E-value=52 Score=24.54 Aligned_cols=24 Identities=29% Similarity=0.347 Sum_probs=17.4
Q ss_pred ecCCCCHHHHHHHhC-CCHHHHHHh
Q 014940 175 VKDVDTLAGIAARYR-TTLTDLMNA 198 (415)
Q Consensus 175 Vq~GDTL~sIA~rfg-vt~~~L~~~ 198 (415)
++.|++...|++.|. ++.+++.++
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 389999999999997 899998764
No 79
>PHA01976 helix-turn-helix protein
Probab=28.53 E-value=95 Score=23.15 Aligned_cols=51 Identities=20% Similarity=0.097 Sum_probs=36.2
Q ss_pred eCCCCCHHHHHHHcCCCHHHHHHhCCCCCCCCCCCCCccCCCceEEeeccccccCCcccccceeEEeCCCCCHHHHHHHH
Q 014940 43 LYTDLKVSEVGSLFNVDPVSILTANAIDISYSDVENHILPSQLFVRIPVTCACVDGIRKSVSTHYKTRPSDTLTSIANQV 122 (415)
Q Consensus 43 v~~gdtL~~IA~~fgvs~~~L~~~N~l~~t~P~~~~~~L~~Gq~l~IP~~csc~~g~~~~~~~~YtV~~GDTL~~IA~~~ 122 (415)
-..|.|..++|++.|++...+.++=... ....-+++..||+.
T Consensus 12 ~~~glt~~~lA~~~gvs~~~v~~~e~g~-------------------------------------~~p~~~~l~~ia~~- 53 (67)
T PHA01976 12 NARAWSAPELSRRAGVRHSLIYDFEADK-------------------------------------RLPNLKTLLRLADA- 53 (67)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHcCC-------------------------------------CCCCHHHHHHHHHH-
Confidence 3467888888998888888887763320 00123678899988
Q ss_pred hCCCCCHHHHH
Q 014940 123 YAGLVSADQLR 133 (415)
Q Consensus 123 fggLvs~~~L~ 133 (415)
|+ +++++|.
T Consensus 54 l~--v~~~~l~ 62 (67)
T PHA01976 54 LG--VTLDWLC 62 (67)
T ss_pred HC--cCHHHHh
Confidence 89 9988874
No 80
>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=28.29 E-value=64 Score=21.82 Aligned_cols=21 Identities=19% Similarity=0.275 Sum_probs=18.4
Q ss_pred CHHHHHHHcCCCHHHHHHhCC
Q 014940 48 KVSEVGSLFNVDPVSILTANA 68 (415)
Q Consensus 48 tL~~IA~~fgvs~~~L~~~N~ 68 (415)
++.++|+++|++...|..+=.
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~ 22 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVK 22 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 688999999999999998843
No 81
>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=28.20 E-value=69 Score=24.72 Aligned_cols=25 Identities=12% Similarity=0.213 Sum_probs=22.1
Q ss_pred CCCCHHHHHHHcCCCHHHHHHhCCC
Q 014940 45 TDLKVSEVGSLFNVDPVSILTANAI 69 (415)
Q Consensus 45 ~gdtL~~IA~~fgvs~~~L~~~N~l 69 (415)
...+|.+||+.+||+...|..+=..
T Consensus 21 g~i~lkdIA~~Lgvs~~tIr~WK~~ 45 (60)
T PF10668_consen 21 GKIKLKDIAEKLGVSESTIRKWKSR 45 (60)
T ss_pred CCccHHHHHHHHCCCHHHHHHHhhh
Confidence 4679999999999999999998665
No 82
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=27.82 E-value=54 Score=26.66 Aligned_cols=45 Identities=18% Similarity=0.177 Sum_probs=36.9
Q ss_pred eeeEEecCCCCHHHHHHHhCCCHHHH--HHhcCCC---CCCcCCCCEEEE
Q 014940 170 YLSYVVKDVDTLAGIAARYRTTLTDL--MNANAMG---STAVKAGDILAV 214 (415)
Q Consensus 170 ~~tY~Vq~GDTL~sIA~rfgvt~~~L--~~~N~l~---~~~I~pGq~L~I 214 (415)
...|....+.|+..+.+.+|+...++ .-.|+.. +..++.|+.|.|
T Consensus 24 ~~~~~~~~~~tvkd~IEsLGVP~tEV~~i~vNG~~v~~~~~~~~Gd~v~V 73 (81)
T PF14451_consen 24 PFTHPFDGGATVKDVIESLGVPHTEVGLILVNGRPVDFDYRLKDGDRVAV 73 (81)
T ss_pred ceEEecCCCCcHHHHHHHcCCChHHeEEEEECCEECCCcccCCCCCEEEE
Confidence 36788899999999999999988885 5567653 468999999876
No 83
>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=27.18 E-value=39 Score=31.78 Aligned_cols=59 Identities=20% Similarity=0.179 Sum_probs=33.8
Q ss_pred CCHHHHHhhcCCCCCCCccCCcEEEecCCCcCCCCCcCCCCceeeeEEecCCCCHHHHHHHhCCCHHHHHHh
Q 014940 127 VSADQLREANDIQDPDVLDVGVNLLVPLPCTCFNGTDNSLPAVYLSYVVKDVDTLAGIAARYRTTLTDLMNA 198 (415)
Q Consensus 127 vs~~~L~~~N~l~~~~~L~~Gq~L~IP~~c~c~~~~~~~~~~~~~tY~Vq~GDTL~sIA~rfgvt~~~L~~~ 198 (415)
+.+.||.++=. ..+|.+.-++++.... .....-.-|.+-=-|..||+|||+++.+|++.
T Consensus 132 ~~lpEi~eav~---~GrL~~DGki~~~~~g----------~~~VTK~AvEPVWyLPGVA~RFGi~E~~LRR~ 190 (194)
T PF12471_consen 132 MKLPEIREAVR---KGRLVPDGKIVLNSNG----------DLAVTKAAVEPVWYLPGVAERFGISEGELRRA 190 (194)
T ss_pred cCcHHHHHHHH---hCCCCCCCeEEecCCC----------cEEEEEEEecccccchhhHHHcCCCHHHHHHH
Confidence 45555555422 2356666666554211 11111223444446779999999999999874
No 84
>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=27.12 E-value=66 Score=24.84 Aligned_cols=23 Identities=13% Similarity=0.101 Sum_probs=20.2
Q ss_pred CCHHHHHHHhCCCHHHHHHhcCC
Q 014940 179 DTLAGIAARYRTTLTDLMNANAM 201 (415)
Q Consensus 179 DTL~sIA~rfgvt~~~L~~~N~l 201 (415)
=++-+||+++|++..+|..|=..
T Consensus 23 i~lkdIA~~Lgvs~~tIr~WK~~ 45 (60)
T PF10668_consen 23 IKLKDIAEKLGVSESTIRKWKSR 45 (60)
T ss_pred ccHHHHHHHHCCCHHHHHHHhhh
Confidence 37889999999999999999654
No 85
>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=26.40 E-value=38 Score=25.97 Aligned_cols=25 Identities=20% Similarity=0.310 Sum_probs=20.4
Q ss_pred CCCCCHHHHHHHcCCCHHHHHHhCC
Q 014940 44 YTDLKVSEVGSLFNVDPVSILTANA 68 (415)
Q Consensus 44 ~~gdtL~~IA~~fgvs~~~L~~~N~ 68 (415)
..|.++.+||+.|||++..|..|=.
T Consensus 21 ~~g~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 21 ESGESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp HHHCHHHHHHHHHTS-HHHHHHHHH
T ss_pred HCCCceEeeecccccccccccHHHH
Confidence 4588999999999999999888743
No 86
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=24.98 E-value=61 Score=24.33 Aligned_cols=22 Identities=23% Similarity=0.356 Sum_probs=19.4
Q ss_pred CHHHHHHHcCCCHHHHHHhCCC
Q 014940 48 KVSEVGSLFNVDPVSILTANAI 69 (415)
Q Consensus 48 tL~~IA~~fgvs~~~L~~~N~l 69 (415)
++.++|+++|++.+.|+.|=..
T Consensus 2 ti~eva~~~gvs~~tlr~y~~~ 23 (69)
T PF13411_consen 2 TIKEVAKLLGVSPSTLRYYERE 23 (69)
T ss_dssp EHHHHHHHTTTTHHHHHHHHHT
T ss_pred cHHHHHHHHCcCHHHHHHHHHh
Confidence 5789999999999999999554
No 87
>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=24.58 E-value=51 Score=28.28 Aligned_cols=26 Identities=8% Similarity=0.125 Sum_probs=22.8
Q ss_pred ecCCCCHHHHHHHhCCCHHHHHHhcC
Q 014940 175 VKDVDTLAGIAARYRTTLTDLMNANA 200 (415)
Q Consensus 175 Vq~GDTL~sIA~rfgvt~~~L~~~N~ 200 (415)
+..|.+...+|++|+|+...+..|=.
T Consensus 15 ~~~g~s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 15 IEKGKSIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred HHccchHHHHHHHhCcHHHHHHHHHH
Confidence 45789999999999999999999953
No 88
>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=23.76 E-value=1.3e+02 Score=20.38 Aligned_cols=36 Identities=17% Similarity=0.206 Sum_probs=24.3
Q ss_pred CHHHHHHHhCCCHHHHHHhcCCCC-CCcCCCCEEEEC
Q 014940 180 TLAGIAARYRTTLTDLMNANAMGS-TAVKAGDILAVP 215 (415)
Q Consensus 180 TL~sIA~rfgvt~~~L~~~N~l~~-~~I~pGq~L~IP 215 (415)
|+..+|+.+|++...|.+|=+-.. +..+.|....++
T Consensus 3 t~~e~a~~lgis~~ti~~~~~~g~i~~~~~g~~~~~~ 39 (49)
T TIGR01764 3 TVEEAAEYLGVSKDTVYRLIHEGELPAYRVGRHYRIP 39 (49)
T ss_pred CHHHHHHHHCCCHHHHHHHHHcCCCCeEEeCCeEEEe
Confidence 577899999999999988864321 223335555554
No 89
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 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 are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; 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: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=23.75 E-value=79 Score=22.64 Aligned_cols=22 Identities=5% Similarity=0.382 Sum_probs=15.2
Q ss_pred CCCCCHHHHHHHcCCCHHHHHH
Q 014940 44 YTDLKVSEVGSLFNVDPVSILT 65 (415)
Q Consensus 44 ~~gdtL~~IA~~fgvs~~~L~~ 65 (415)
-.|.+..+||+.+|++...+..
T Consensus 24 ~~g~s~~eIa~~l~~s~~~v~~ 45 (54)
T PF08281_consen 24 FQGMSYAEIAEILGISESTVKR 45 (54)
T ss_dssp TS---HHHHHHHCTS-HHHHHH
T ss_pred HHCcCHHHHHHHHCcCHHHHHH
Confidence 3688999999999999987764
No 90
>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=22.95 E-value=84 Score=23.46 Aligned_cols=20 Identities=15% Similarity=0.079 Sum_probs=17.9
Q ss_pred CHHHHHHHhCCCHHHHHHhc
Q 014940 180 TLAGIAARYRTTLTDLMNAN 199 (415)
Q Consensus 180 TL~sIA~rfgvt~~~L~~~N 199 (415)
++.++|+++|++...|..|=
T Consensus 2 s~~eva~~~gvs~~tlr~w~ 21 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWE 21 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 56789999999999999885
No 91
>PF08139 LPAM_1: Prokaryotic membrane lipoprotein lipid attachment site; InterPro: IPR012640 In prokaryotes, membrane lipoproteins are synthesized with a precursor signal peptide, which is cleaved by a specific lipoprotein signal peptidase (signal peptidase II). The peptidase recognises a conserved sequence and cuts upstream of a cysteine residue to which a glyceride-fatty acid lipid is attached [,]. This lipid attachment site is found in homologues of the VirB proteins of type IV secretion systems (T4SS). Conjugal transfer across the cell envelope of Gram-negative bacteria is mediated by a supramolecular structure termed mating pair formation (Mpf) complex. Collectively, secretion pathways ancestrally related to bacterial conjugation systems are now known as T4SS. T4SS are involved in the delivery of effector molecules to eukaryotic target cells; each of these systems exports distinct DNA or protein substrates to effect a myriad of changes in host cell physiology during infection [].
Probab=22.60 E-value=57 Score=20.89 Aligned_cols=13 Identities=46% Similarity=0.470 Sum_probs=7.8
Q ss_pred chHHHHHHHHHHH
Q 014940 2 PKTLLYLLLLFSN 14 (415)
Q Consensus 2 ~~~l~~~~~l~~~ 14 (415)
+|+|+.++.+|..
T Consensus 8 Kkil~~l~a~~~L 20 (25)
T PF08139_consen 8 KKILFPLLALFML 20 (25)
T ss_pred HHHHHHHHHHHHH
Confidence 6666666666643
No 92
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=22.22 E-value=1.1e+02 Score=21.16 Aligned_cols=25 Identities=16% Similarity=0.009 Sum_probs=21.3
Q ss_pred ecCCCCHHHHHHHhCCCHHHHHHhc
Q 014940 175 VKDVDTLAGIAARYRTTLTDLMNAN 199 (415)
Q Consensus 175 Vq~GDTL~sIA~rfgvt~~~L~~~N 199 (415)
+..|.+...||++++++...+..+-
T Consensus 15 ~~~g~s~~eia~~l~is~~tv~~~~ 39 (58)
T smart00421 15 LAEGLTNKEIAERLGISEKTVKTHL 39 (58)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 3578999999999999999887663
No 93
>smart00351 PAX Paired Box domain.
Probab=21.42 E-value=85 Score=27.20 Aligned_cols=24 Identities=4% Similarity=-0.107 Sum_probs=21.3
Q ss_pred cCCCCHHHHHHHhCCCHHHHHHhc
Q 014940 176 KDVDTLAGIAARYRTTLTDLMNAN 199 (415)
Q Consensus 176 q~GDTL~sIA~rfgvt~~~L~~~N 199 (415)
..|.+...||++||++...+.+|=
T Consensus 31 ~~G~s~~~iA~~~gvs~~tV~kwi 54 (125)
T smart00351 31 QNGVRPCDISRQLCVSHGCVSKIL 54 (125)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHH
Confidence 589999999999999999887774
No 94
>PHA02591 hypothetical protein; Provisional
Probab=20.97 E-value=1.1e+02 Score=25.10 Aligned_cols=21 Identities=19% Similarity=0.286 Sum_probs=14.3
Q ss_pred CCCHHHHHHHcCCCHHHHHHh
Q 014940 46 DLKVSEVGSLFNVDPVSILTA 66 (415)
Q Consensus 46 gdtL~~IA~~fgvs~~~L~~~ 66 (415)
|.|..+||+++|++.+.++++
T Consensus 59 GlSqeqIA~~LGVsqetVrKY 79 (83)
T PHA02591 59 GFTVEKIASLLGVSVRKVRRY 79 (83)
T ss_pred CCCHHHHHHHhCCCHHHHHHH
Confidence 666777777777777666554
No 95
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=20.66 E-value=94 Score=26.67 Aligned_cols=26 Identities=15% Similarity=0.130 Sum_probs=22.9
Q ss_pred eCCCCCHHHHHHHcCCCHHHHHHhCC
Q 014940 43 LYTDLKVSEVGSLFNVDPVSILTANA 68 (415)
Q Consensus 43 v~~gdtL~~IA~~fgvs~~~L~~~N~ 68 (415)
+..|.++.+||+.|||+...|..|=.
T Consensus 26 ~~~g~sv~evA~e~gIs~~tl~~W~r 51 (121)
T PRK09413 26 FEPGMTVSLVARQHGVAASQLFLWRK 51 (121)
T ss_pred HcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 45799999999999999999999843
No 96
>PF02618 YceG: YceG-like family; InterPro: IPR003770 This uncharacterised protein family, found in three of four microbial genomes, virtually always once per genome, includes YceG from Escherichia coli. Proteins in this family are typically between 332 and 389 amino acids in length. This protein is encoded next to PabC, 4-amino-4-deoxychorismate lyase, in Escherichia coli and numerous other proteobacteria, but that proximity is not conserved in other lineages. Numerous members of this family have been misannotated as aminodeoxychorismate lyase, apparently because of promiximty to PabC. The structure of Swiss:P28306 was solved by X-ray crystallography. This group represents an uncharacterised protein family UPF0755.; PDB: 2R1F_B.
Probab=20.65 E-value=1.2e+02 Score=30.31 Aligned_cols=19 Identities=16% Similarity=0.258 Sum_probs=12.6
Q ss_pred cceeEEeCCCCCHHHHHHH
Q 014940 103 VSTHYKTRPSDTLTSIANQ 121 (415)
Q Consensus 103 ~~~~YtV~~GDTL~~IA~~ 121 (415)
....|.++++.++..|.+.
T Consensus 44 kaG~Y~l~~~mS~~eil~~ 62 (297)
T PF02618_consen 44 KAGTYELNPGMSYKEILSI 62 (297)
T ss_dssp --EEEEE-TT--HHHHHHH
T ss_pred eeeEEEeCCCCCHHHHHHH
Confidence 4567999999999999988
No 97
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=20.60 E-value=83 Score=26.00 Aligned_cols=26 Identities=19% Similarity=0.050 Sum_probs=23.0
Q ss_pred EecCCCCHHHHHHHhCCCHHHHHHhc
Q 014940 174 VVKDVDTLAGIAARYRTTLTDLMNAN 199 (415)
Q Consensus 174 ~Vq~GDTL~sIA~rfgvt~~~L~~~N 199 (415)
+|..|-++..+|++|||+.....+|=
T Consensus 21 vv~~g~~~a~aA~~~gVS~~Ta~kW~ 46 (85)
T PF13011_consen 21 VVEQGWPVAHAAAEFGVSRRTAYKWL 46 (85)
T ss_pred HHHcCCcHHHHHHHhCCCHHHHHHHH
Confidence 56788999999999999999888885
No 98
>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=20.55 E-value=93 Score=26.26 Aligned_cols=20 Identities=10% Similarity=0.164 Sum_probs=15.2
Q ss_pred CCCHHHHHHHhCCCHHHHHH
Q 014940 178 VDTLAGIAARYRTTLTDLMN 197 (415)
Q Consensus 178 GDTL~sIA~rfgvt~~~L~~ 197 (415)
|.++..+|++||+|...+.+
T Consensus 72 G~n~~eLA~kyglS~r~I~~ 91 (108)
T PF08765_consen 72 GMNVRELARKYGLSERQIYR 91 (108)
T ss_dssp SS-HHHHHHHHT--HHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHH
Confidence 99999999999999988754
No 99
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=20.44 E-value=96 Score=23.33 Aligned_cols=20 Identities=20% Similarity=0.393 Sum_probs=18.2
Q ss_pred CHHHHHHHcCCCHHHHHHhC
Q 014940 48 KVSEVGSLFNVDPVSILTAN 67 (415)
Q Consensus 48 tL~~IA~~fgvs~~~L~~~N 67 (415)
++.++|+++||+...|+.|=
T Consensus 2 ~i~evA~~~gvs~~tlR~~~ 21 (67)
T cd04764 2 TIKEVSEIIGVKPHTLRYYE 21 (67)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 67899999999999999993
No 100
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=20.23 E-value=81 Score=23.04 Aligned_cols=24 Identities=13% Similarity=0.158 Sum_probs=19.7
Q ss_pred ecCCCCHHHHHHHhCCCHHHHHHh
Q 014940 175 VKDVDTLAGIAARYRTTLTDLMNA 198 (415)
Q Consensus 175 Vq~GDTL~sIA~rfgvt~~~L~~~ 198 (415)
.+.|.+...||.+||++...+.++
T Consensus 16 LR~~~~~~~La~~FgIs~stvsri 39 (53)
T PF13613_consen 16 LRLNLTFQDLAYRFGISQSTVSRI 39 (53)
T ss_pred HHcCCcHhHHhhheeecHHHHHHH
Confidence 467889999999999998776543
No 101
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=20.07 E-value=97 Score=23.19 Aligned_cols=21 Identities=14% Similarity=0.093 Sum_probs=18.5
Q ss_pred CHHHHHHHhCCCHHHHHHhcC
Q 014940 180 TLAGIAARYRTTLTDLMNANA 200 (415)
Q Consensus 180 TL~sIA~rfgvt~~~L~~~N~ 200 (415)
|+..+|+.+|++...|+.|=.
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 467899999999999999964
Done!