Query 018429
Match_columns 356
No_of_seqs 164 out of 829
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 08:56:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018429.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018429hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK06347 autolysin; Reviewed 99.6 2E-15 4.4E-20 157.6 9.5 113 17-153 478-591 (592)
2 PRK10783 mltD membrane-bound l 99.5 2.4E-14 5.3E-19 145.4 10.4 109 17-158 342-451 (456)
3 PRK06347 autolysin; Reviewed 99.5 2E-13 4.4E-18 142.8 11.1 124 16-157 403-527 (592)
4 PF01476 LysM: LysM domain; I 99.3 2.2E-12 4.8E-17 89.8 4.1 43 21-64 1-44 (44)
5 PRK13914 invasion associated s 99.2 5.5E-11 1.2E-15 122.1 10.4 50 17-67 26-75 (481)
6 PRK14125 cell division suppres 99.1 2.1E-10 4.6E-15 96.2 7.4 55 15-70 33-95 (103)
7 cd00118 LysM Lysin domain, fou 99.0 1.1E-09 2.4E-14 72.0 5.9 45 20-64 2-46 (46)
8 TIGR02899 spore_safA spore coa 99.0 1.2E-09 2.5E-14 74.4 5.2 43 23-65 1-44 (44)
9 TIGR02907 spore_VI_D stage VI 98.8 4E-09 8.6E-14 104.3 6.5 51 13-64 288-338 (338)
10 COG1388 LytE FOG: LysM repeat 98.8 1.6E-08 3.4E-13 84.4 6.5 50 18-68 66-115 (124)
11 PRK10871 nlpD lipoprotein NlpD 98.8 9.1E-09 2E-13 101.3 5.9 48 20-67 62-109 (319)
12 PRK10783 mltD membrane-bound l 98.7 6.2E-08 1.4E-12 99.0 8.9 130 14-157 259-391 (456)
13 smart00257 LysM Lysin motif. 98.7 6.6E-08 1.4E-12 62.7 5.6 43 21-63 2-44 (44)
14 COG1388 LytE FOG: LysM repeat 98.5 1.2E-07 2.6E-12 79.2 5.6 108 32-155 1-112 (124)
15 PRK13914 invasion associated s 98.5 3E-07 6.5E-12 94.9 7.4 52 17-69 198-249 (481)
16 PRK11198 LysM domain/BON super 98.4 5.4E-07 1.2E-11 79.2 5.8 48 17-64 94-146 (147)
17 PF01476 LysM: LysM domain; I 97.4 2.9E-05 6.2E-10 53.8 -0.1 41 106-153 1-43 (44)
18 PF04225 OapA: Opacity-associa 97.1 0.00046 1E-08 56.1 3.1 51 17-67 1-55 (85)
19 COG3858 Predicted glycosyl hyd 96.9 0.0007 1.5E-08 69.4 3.2 77 18-135 1-78 (423)
20 TIGR03505 FimV_core FimV N-ter 96.8 0.0017 3.6E-08 52.0 4.2 41 27-67 1-53 (74)
21 KOG2850 Predicted peptidoglyca 96.4 0.0017 3.8E-08 60.3 2.3 54 16-69 7-60 (186)
22 PRK10190 L,D-transpeptidase; P 96.4 0.0096 2.1E-07 59.2 7.6 56 17-72 36-93 (310)
23 PRK10260 L,D-transpeptidase; P 96.3 0.013 2.8E-07 58.2 7.6 56 17-72 39-96 (306)
24 PRK14125 cell division suppres 96.2 0.004 8.6E-08 52.6 3.1 51 104-159 37-94 (103)
25 COG1652 XkdP Uncharacterized p 96.1 0.0022 4.9E-08 60.8 1.2 49 19-67 211-265 (269)
26 TIGR02899 spore_safA spore coa 95.9 0.0057 1.2E-07 41.3 2.1 40 108-153 1-42 (44)
27 PRK10871 nlpD lipoprotein NlpD 95.6 0.006 1.3E-07 60.7 2.0 46 105-156 62-108 (319)
28 cd00118 LysM Lysin domain, fou 95.6 0.0077 1.7E-07 39.1 1.8 42 106-153 3-45 (46)
29 TIGR02907 spore_VI_D stage VI 95.1 0.012 2.5E-07 59.2 2.1 43 104-153 294-337 (338)
30 smart00257 LysM Lysin motif. 94.8 0.019 4.2E-07 36.6 1.8 42 106-153 2-44 (44)
31 PRK11649 putative peptidase; P 94.5 0.071 1.5E-06 55.0 6.0 52 16-67 93-145 (439)
32 COG3858 Predicted glycosyl hyd 94.4 0.053 1.2E-06 56.0 4.8 52 18-69 49-100 (423)
33 PF05489 Phage_tail_X: Phage T 90.7 0.85 1.8E-05 35.2 5.9 48 19-67 2-55 (60)
34 PRK11198 LysM domain/BON super 89.8 0.2 4.4E-06 44.2 2.1 45 105-153 97-145 (147)
35 COG0739 NlpD Membrane proteins 89.6 0.59 1.3E-05 43.0 5.0 49 19-67 2-50 (277)
36 COG3170 FimV Tfp pilus assembl 78.0 1.7 3.7E-05 47.9 2.9 51 18-68 188-250 (755)
37 PF02796 HTH_7: Helix-turn-hel 67.9 5.6 0.00012 28.3 2.7 24 23-46 18-41 (45)
38 PF13518 HTH_28: Helix-turn-he 67.8 5.6 0.00012 27.9 2.7 27 23-49 9-35 (52)
39 COG3061 OapA Cell envelope opa 67.7 8.8 0.00019 37.3 4.7 51 17-67 158-212 (242)
40 KOG2850 Predicted peptidoglyca 67.1 2.4 5.3E-05 39.7 0.8 54 15-68 116-176 (186)
41 COG4784 Putative Zn-dependent 54.8 25 0.00055 36.6 5.6 49 16-64 426-477 (479)
42 PF01527 HTH_Tnp_1: Transposas 52.4 10 0.00022 28.6 1.9 24 23-46 20-43 (76)
43 COG4254 Uncharacterized protei 43.7 21 0.00046 36.2 3.0 50 19-68 6-58 (339)
44 PF13384 HTH_23: Homeodomain-l 42.8 28 0.00061 24.4 2.8 27 23-49 14-40 (50)
45 PF05225 HTH_psq: helix-turn-h 41.0 26 0.00057 25.3 2.4 24 23-46 12-36 (45)
46 cd00569 HTH_Hin_like Helix-tur 40.2 35 0.00076 20.1 2.6 24 23-46 18-41 (42)
47 PF11268 DUF3071: Protein of u 39.7 23 0.00049 32.8 2.4 51 18-68 61-112 (170)
48 PF04545 Sigma70_r4: Sigma-70, 39.3 41 0.00089 23.8 3.2 23 24-46 18-40 (50)
49 PF08765 Mor: Mor transcriptio 37.1 33 0.00071 28.7 2.8 21 26-46 72-92 (108)
50 PRK09413 IS2 repressor TnpA; R 36.6 37 0.00081 28.7 3.1 28 21-48 24-51 (121)
51 COG2963 Transposase and inacti 34.6 36 0.00078 28.1 2.6 26 21-46 19-45 (116)
52 PF04255 DUF433: Protein of un 34.2 35 0.00075 25.5 2.2 24 23-46 28-52 (56)
53 PF04218 CENP-B_N: CENP-B N-te 32.5 22 0.00047 26.4 0.9 23 23-45 19-41 (53)
54 PHA00675 hypothetical protein 32.2 47 0.001 27.5 2.8 24 24-47 37-60 (78)
55 PF13936 HTH_38: Helix-turn-he 30.8 57 0.0012 23.2 2.8 23 23-45 17-39 (44)
56 smart00421 HTH_LUXR helix_turn 27.9 82 0.0018 21.4 3.2 25 23-47 15-39 (58)
57 PRK07121 hypothetical protein; 27.3 48 0.001 34.0 2.6 28 23-50 358-389 (492)
58 smart00345 HTH_GNTR helix_turn 26.0 55 0.0012 22.8 2.1 28 23-50 14-45 (60)
59 PF00376 MerR: MerR family reg 25.9 70 0.0015 22.3 2.5 22 28-49 1-22 (38)
60 PF04760 IF2_N: Translation in 25.5 49 0.0011 24.1 1.7 18 28-45 5-22 (54)
61 cd01104 HTH_MlrA-CarA Helix-Tu 25.3 76 0.0016 23.4 2.8 20 28-47 2-21 (68)
62 PRK12845 3-ketosteroid-delta-1 25.3 57 0.0012 34.7 2.8 28 23-50 421-452 (564)
63 COG3721 HugX Putative heme iro 25.2 74 0.0016 29.7 3.2 23 24-46 25-47 (176)
64 PF11020 DUF2610: Domain of un 24.4 72 0.0016 26.6 2.6 20 27-46 55-74 (82)
65 cd04762 HTH_MerR-trunc Helix-T 24.4 92 0.002 20.7 2.8 20 28-47 2-21 (49)
66 PHA01976 helix-turn-helix prot 24.0 49 0.0011 24.4 1.5 20 25-44 43-62 (67)
67 PRK12837 3-ketosteroid-delta-1 23.7 66 0.0014 33.5 2.9 28 23-50 372-403 (513)
68 TIGR02937 sigma70-ECF RNA poly 23.1 92 0.002 24.8 3.1 23 24-46 124-146 (158)
69 PF01381 HTH_3: Helix-turn-hel 22.6 42 0.00091 23.7 0.9 18 26-43 38-55 (55)
70 PF01710 HTH_Tnp_IS630: Transp 22.5 93 0.002 26.3 3.1 23 24-46 69-91 (119)
71 TIGR01764 excise DNA binding d 22.5 1.8E+02 0.0039 19.4 4.0 37 28-64 3-39 (49)
72 PF10668 Phage_terminase: Phag 22.4 92 0.002 24.4 2.8 20 28-47 24-43 (60)
73 PF13411 MerR_1: MerR HTH fami 22.1 91 0.002 23.0 2.6 20 28-47 2-21 (69)
74 PF08220 HTH_DeoR: DeoR-like h 22.0 84 0.0018 23.4 2.4 23 28-50 16-39 (57)
75 cd04761 HTH_MerR-SF Helix-Turn 21.1 1.1E+02 0.0024 20.9 2.8 20 28-47 2-21 (49)
76 TIGR02531 yecD_yerC TrpR-relat 20.9 94 0.002 25.7 2.7 26 23-48 47-72 (88)
77 PF01371 Trp_repressor: Trp re 20.8 87 0.0019 26.0 2.5 26 24-49 47-72 (87)
78 COG1652 XkdP Uncharacterized p 20.7 52 0.0011 31.4 1.3 45 105-153 212-261 (269)
79 PF13542 HTH_Tnp_ISL3: Helix-t 20.4 1.2E+02 0.0025 21.4 2.8 26 21-46 22-47 (52)
80 cd06170 LuxR_C_like C-terminal 20.3 1.4E+02 0.0031 20.4 3.2 23 24-46 13-35 (57)
81 PF00392 GntR: Bacterial regul 20.1 1.1E+02 0.0023 22.8 2.7 24 23-46 18-44 (64)
82 PF08299 Bac_DnaA_C: Bacterial 20.0 87 0.0019 24.3 2.2 18 28-45 5-22 (70)
No 1
>PRK06347 autolysin; Reviewed
Probab=99.60 E-value=2e-15 Score=157.62 Aligned_cols=113 Identities=19% Similarity=0.248 Sum_probs=87.7
Q ss_pred CeEEEEecCCCCHHHHHHHhCCCHHHHHHHhCCCCCCcccCCCEEEeCCCCCCCCCCCCCCCCCCCCCCCcccCCCCCCc
Q 018429 17 NYIEHQVSKMDTLAGVAIKYGVEVADIKRLNGLATDLQMFALKTLHIPLPGRHPPSPSLSDGSSSSGENSMERTPPRLGY 96 (356)
Q Consensus 17 ~~i~H~VkkGDTL~~IA~KYgVsV~dIKraNnL~sd~~L~~GQ~L~IPv~~~~~~s~~~s~~s~~~~e~k~~~aq~~~~~ 96 (356)
....|+|++||||++||++|||++++|+++|+|.. +.|++||.|.||............. + . ..+..
T Consensus 478 ~~~~YtVk~GDTL~sIAkkygVSv~~L~~~N~l~s-~~L~~GQ~L~Ip~~~~~s~~~t~~~-s-~-------~~~~~--- 544 (592)
T PRK06347 478 NAKVYTVAKGDSLWRIANNNKVTIANLKSWNNLKS-DFIYPGQKLKVSAGSTTNNTNTAKP-S-T-------NKPSN--- 544 (592)
T ss_pred cceeeeecCCCCHHHHHHHHCCCHHHHHHhcCCCc-ccccCCcEEEEecCcccccccccCC-c-c-------CCccC---
Confidence 45679999999999999999999999999999985 5799999999998643322110000 0 0 00000
Q ss_pred chhhhhcccccccCCCCCCCcc-ccccccChhHHHHHHHhCCCCCCCCCCCCCceEEE
Q 018429 97 SNILQSLESLRTESSKKGSLAT-GTSQKVSSAMSNLQKYYGLRSPNGKGKDEGTEMAV 153 (356)
Q Consensus 97 ~~~le~~~s~~vKsg~~dsLw~-gq~~kVSpaM~~L~~wnGL~p~~~~~l~~GqeLvv 153 (356)
.....|+|++| |+||. +++++|++ ..|..||+|.+ +.|++||.|.|
T Consensus 545 ----~~~~~Y~Vk~G--DTL~sIA~KygvSv--~~L~~~N~L~~---~~L~~GQ~L~I 591 (592)
T PRK06347 545 ----STVKTYTVKKG--DSLWAISRQYKTTV--DNIKAWNKLTS---NMIHVGQKLTI 591 (592)
T ss_pred ----ccceeeecCCC--CcHHHHHHHhCCCH--HHHHHhcCCCc---ccCCCCCEEec
Confidence 01123999999 99999 99999988 99999999985 66999999987
No 2
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional
Probab=99.54 E-value=2.4e-14 Score=145.40 Aligned_cols=109 Identities=18% Similarity=0.258 Sum_probs=89.8
Q ss_pred CeEEEEecCCCCHHHHHHHhCCCHHHHHHHhCCCCCCcccCCCEEEeCCCCCCCCCCCCCCCCCCCCCCCcccCCCCCCc
Q 018429 17 NYIEHQVSKMDTLAGVAIKYGVEVADIKRLNGLATDLQMFALKTLHIPLPGRHPPSPSLSDGSSSSGENSMERTPPRLGY 96 (356)
Q Consensus 17 ~~i~H~VkkGDTL~~IA~KYgVsV~dIKraNnL~sd~~L~~GQ~L~IPv~~~~~~s~~~s~~s~~~~e~k~~~aq~~~~~ 96 (356)
.+..|+|++||||+.||++|||++.+|+++|++.. +.|.+||.|.||....... .. . ....
T Consensus 342 ~~~~y~Vk~GDTL~sIA~r~gvs~~~L~~~N~l~~-~~L~~Gq~L~Ip~~~~~~~----~~---~---------~~~~-- 402 (456)
T PRK10783 342 NSRSYKVRSGDTLSGIASRLNVSTKDLQQWNNLRG-SKLKVGQTLTIGAGSSAQR----LA---N---------NSDS-- 402 (456)
T ss_pred CceEEEECCCCcHHHHHHHHCcCHHHHHHHcCCCc-ccCCCCCEEEecCCccccc----cc---c---------cccc--
Confidence 46789999999999999999999999999999986 6899999999997532211 00 0 0001
Q ss_pred chhhhhcccccccCCCCCCCcc-ccccccChhHHHHHHHhCCCCCCCCCCCCCceEEEeeCCC
Q 018429 97 SNILQSLESLRTESSKKGSLAT-GTSQKVSSAMSNLQKYYGLRSPNGKGKDEGTEMAVYRTGS 158 (356)
Q Consensus 97 ~~~le~~~s~~vKsg~~dsLw~-gq~~kVSpaM~~L~~wnGL~p~~~~~l~~GqeLvv~~~~~ 158 (356)
+ .|+|++| |+||. +++++|++ ..|.+||++.. . .|++||+|.||-...
T Consensus 403 --~-----~Y~Vr~G--DTL~sIA~kygVtv--~~L~~~N~l~~--~-~L~pGq~L~l~v~~~ 451 (456)
T PRK10783 403 --I-----TYRVRKG--DSLSSIAKRHGVNI--KDVMRWNSDTA--K-NLQPGDKLTLFVKNN 451 (456)
T ss_pred --e-----eEEeCCC--CCHHHHHHHhCCCH--HHHHHhcCCCC--C-cCCCCCEEEEecCCC
Confidence 1 2899999 99999 99999998 99999999986 4 899999999997653
No 3
>PRK06347 autolysin; Reviewed
Probab=99.47 E-value=2e-13 Score=142.82 Aligned_cols=124 Identities=19% Similarity=0.187 Sum_probs=91.2
Q ss_pred CCeEEEEecCCCCHHHHHHHhCCCHHHHHHHhCCCCCCcccCCCEEEeCCCCCCCCCCCCCCCCCCCCCCCcccCCCCCC
Q 018429 16 WNYIEHQVSKMDTLAGVAIKYGVEVADIKRLNGLATDLQMFALKTLHIPLPGRHPPSPSLSDGSSSSGENSMERTPPRLG 95 (356)
Q Consensus 16 ~~~i~H~VkkGDTL~~IA~KYgVsV~dIKraNnL~sd~~L~~GQ~L~IPv~~~~~~s~~~s~~s~~~~e~k~~~aq~~~~ 95 (356)
..+..|+|++||||+.||.+|||++++|+++|++.. +.|++||.|.||................... +- ..
T Consensus 403 ~~~~~ytVk~GDTL~sIA~kygVSv~~L~~~N~l~s-~~L~~Gq~L~IP~~~~~~~~t~~~s~~~~~~--k~--~s---- 473 (592)
T PRK06347 403 TNAKVYTVVKGDSLWRIANNNKVTIANLKSWNNLKS-DFIYPGQKLKVSAGSTSNTNTSKPSTNTNTS--KP--ST---- 473 (592)
T ss_pred cCceeEEecCCCCHHHHHHHhCCCHHHHHHHhCCCc-ceeccCcEEEEecCCcccccccccccccccc--cc--cc----
Confidence 356789999999999999999999999999999975 5799999999997643211100000000000 00 00
Q ss_pred cchhhhhcccccccCCCCCCCcc-ccccccChhHHHHHHHhCCCCCCCCCCCCCceEEEeeCC
Q 018429 96 YSNILQSLESLRTESSKKGSLAT-GTSQKVSSAMSNLQKYYGLRSPNGKGKDEGTEMAVYRTG 157 (356)
Q Consensus 96 ~~~~le~~~s~~vKsg~~dsLw~-gq~~kVSpaM~~L~~wnGL~p~~~~~l~~GqeLvv~~~~ 157 (356)
..-+....|+|++| |+||. +++++|++ +.|++||+|.. +.|++||.|.|+...
T Consensus 474 --~~~~~~~~YtVk~G--DTL~sIAkkygVSv--~~L~~~N~l~s---~~L~~GQ~L~Ip~~~ 527 (592)
T PRK06347 474 --NTNTNAKVYTVAKG--DSLWRIANNNKVTI--ANLKSWNNLKS---DFIYPGQKLKVSAGS 527 (592)
T ss_pred --cccccceeeeecCC--CCHHHHHHHHCCCH--HHHHHhcCCCc---ccccCCcEEEEecCc
Confidence 00011234999999 99999 99999988 99999999984 579999999998654
No 4
>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=99.30 E-value=2.2e-12 Score=89.75 Aligned_cols=43 Identities=33% Similarity=0.486 Sum_probs=36.8
Q ss_pred EEecCCCCHHHHHHHhCCCHHHHHHHh-CCCCCCcccCCCEEEeC
Q 018429 21 HQVSKMDTLAGVAIKYGVEVADIKRLN-GLATDLQMFALKTLHIP 64 (356)
Q Consensus 21 H~VkkGDTL~~IA~KYgVsV~dIKraN-nL~sd~~L~~GQ~L~IP 64 (356)
|+|++||||+.||.+|++++++|+++| ++..+. |++||.|.||
T Consensus 1 y~V~~gDtl~~IA~~~~~~~~~l~~~N~~~~~~~-l~~G~~l~iP 44 (44)
T PF01476_consen 1 YTVQPGDTLWSIAKRYGISVDELMELNPNIDSDN-LQPGQKLCIP 44 (44)
T ss_dssp EEE-TT--HHHHHHHTTS-HHHHHHHCCTTHGGC-GGTTEEEEEC
T ss_pred CEECcCCcHHHHHhhhhhhHhHHHHhcCCCCccc-CCCCCEEEeC
Confidence 899999999999999999999999999 887654 9999999998
No 5
>PRK13914 invasion associated secreted endopeptidase; Provisional
Probab=99.21 E-value=5.5e-11 Score=122.05 Aligned_cols=50 Identities=26% Similarity=0.245 Sum_probs=45.1
Q ss_pred CeEEEEecCCCCHHHHHHHhCCCHHHHHHHhCCCCCCcccCCCEEEeCCCC
Q 018429 17 NYIEHQVSKMDTLAGVAIKYGVEVADIKRLNGLATDLQMFALKTLHIPLPG 67 (356)
Q Consensus 17 ~~i~H~VkkGDTL~~IA~KYgVsV~dIKraNnL~sd~~L~~GQ~L~IPv~~ 67 (356)
....|+|++|||||.||++||+++++|+++|+|. ++.|++||.|+||...
T Consensus 26 sa~tytVq~GDTLw~IA~~ygvtv~~I~~~N~l~-~~~I~~Gq~L~Ip~~~ 75 (481)
T PRK13914 26 SASTVVVEAGDTLWGIAQSKGTTVDAIKKANNLT-TDKIVPGQKLQVNEVA 75 (481)
T ss_pred cCceEEECCCCCHHHHHHHHCCCHHHHHHHhCCC-cccccCCCEEEeCCCC
Confidence 4457999999999999999999999999999997 4579999999999653
No 6
>PRK14125 cell division suppressor protein YneA; Provisional
Probab=99.10 E-value=2.1e-10 Score=96.17 Aligned_cols=55 Identities=25% Similarity=0.313 Sum_probs=49.1
Q ss_pred CCCeEEEEecCCCCHHHHHHHhCCC--------HHHHHHHhCCCCCCcccCCCEEEeCCCCCCC
Q 018429 15 GWNYIEHQVSKMDTLAGVAIKYGVE--------VADIKRLNGLATDLQMFALKTLHIPLPGRHP 70 (356)
Q Consensus 15 ~~~~i~H~VkkGDTL~~IA~KYgVs--------V~dIKraNnL~sd~~L~~GQ~L~IPv~~~~~ 70 (356)
...|..|+|++|||||+||++|+++ +..|++.|++.++ .|++||+|+||+...+.
T Consensus 33 ~~~~~~~tV~~GDTLW~IA~~y~~~~~l~~~~~v~~I~~~N~l~~~-~I~~Gq~L~IP~~~~~~ 95 (103)
T PRK14125 33 KNQYVEITVQEGDTLWALADQYAGKHHMAKNEFIEWVEDVNNLPSG-HIKAGDKLVIPVLKSKS 95 (103)
T ss_pred CCCcEEEEECCCCCHHHHHHHhCCCcCCCHHHHHHHHHHhcCCCCC-cCCCCCEEEEecCCCCc
Confidence 4578999999999999999999887 7889999999865 79999999999987763
No 7
>cd00118 LysM Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function.
Probab=98.99 E-value=1.1e-09 Score=72.04 Aligned_cols=45 Identities=36% Similarity=0.566 Sum_probs=42.5
Q ss_pred EEEecCCCCHHHHHHHhCCCHHHHHHHhCCCCCCcccCCCEEEeC
Q 018429 20 EHQVSKMDTLAGVAIKYGVEVADIKRLNGLATDLQMFALKTLHIP 64 (356)
Q Consensus 20 ~H~VkkGDTL~~IA~KYgVsV~dIKraNnL~sd~~L~~GQ~L~IP 64 (356)
.|+|++||||+.||.+|+++..+|+++|.+.....|.+|+.|.||
T Consensus 2 ~~~v~~gdt~~~ia~~~~~~~~~~~~~N~~~~~~~~~~g~~l~ip 46 (46)
T cd00118 2 TYTVKKGDTLSSIAQRYGISVEELLKLNGLSDPDNLQVGQKLKIP 46 (46)
T ss_pred EEEECCCCCHHHHHHHHCcCHHHHHHHcCCCCccccCCCCEEecC
Confidence 599999999999999999999999999999667789999999998
No 8
>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=98.96 E-value=1.2e-09 Score=74.44 Aligned_cols=43 Identities=33% Similarity=0.451 Sum_probs=38.6
Q ss_pred ecCCCCHHHHHHHhCCCHHHHHHHhC-CCCCCcccCCCEEEeCC
Q 018429 23 VSKMDTLAGVAIKYGVEVADIKRLNG-LATDLQMFALKTLHIPL 65 (356)
Q Consensus 23 VkkGDTL~~IA~KYgVsV~dIKraNn-L~sd~~L~~GQ~L~IPv 65 (356)
|++||||+.||++|++++++|.++|. +.....|++||.|+||.
T Consensus 1 v~~gdtl~~IA~~~~~~~~~l~~~N~~~~~~~~~~~g~~l~ip~ 44 (44)
T TIGR02899 1 VQKGDTLWKIAKKYGVDFDELIQANPQLSNPNLIYPGMKIKIPS 44 (44)
T ss_pred CCCCCCHHHHHHHHCcCHHHHHHHhhcCCCCCCcCCCCEEecCC
Confidence 78999999999999999999999997 54456799999999984
No 9
>TIGR02907 spore_VI_D stage VI sporulation protein D. SpoVID, the stage VI sporulation protein D, is restricted to endospore-forming members of the bacteria, all of which are found among the Firmicutes. It is widely distributed but not quite universal in this group. Between well-conserved N-terminal and C-terminal domains is a poorly conserved, low-complexity region of variable length, rich enough in glutamic acid to cause spurious BLAST search results unless a filter is used. The seed alignment for this model was trimmed, in effect, by choosing member sequences in which these regions are relatively short. SpoVID is involved in spore coat assembly by the mother cell compartment late in the process of sporulation.
Probab=98.85 E-value=4e-09 Score=104.28 Aligned_cols=51 Identities=25% Similarity=0.287 Sum_probs=47.4
Q ss_pred CCCCCeEEEEecCCCCHHHHHHHhCCCHHHHHHHhCCCCCCcccCCCEEEeC
Q 018429 13 ANGWNYIEHQVSKMDTLAGVAIKYGVEVADIKRLNGLATDLQMFALKTLHIP 64 (356)
Q Consensus 13 ~~~~~~i~H~VkkGDTL~~IA~KYgVsV~dIKraNnL~sd~~L~~GQ~L~IP 64 (356)
.....|..|+|++||||+.||+||||++.+|+++|+|. ++.|++||.|+||
T Consensus 288 e~~~~~~~YiVq~GDTL~sIAkRYGVSV~~L~r~N~L~-~~~L~~GQ~L~IP 338 (338)
T TIGR02907 288 EQFTKLRMCIVQEGDTIETIAERYEISVSQLIRHNQLE-DFEVNEGQILYIP 338 (338)
T ss_pred ccccccEEEEECCCCCHHHHHHHHCcCHHHHHHHhCCC-ccccCCCCEEEeC
Confidence 45567899999999999999999999999999999998 6789999999998
No 10
>COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane]
Probab=98.76 E-value=1.6e-08 Score=84.40 Aligned_cols=50 Identities=38% Similarity=0.594 Sum_probs=45.9
Q ss_pred eEEEEecCCCCHHHHHHHhCCCHHHHHHHhCCCCCCcccCCCEEEeCCCCC
Q 018429 18 YIEHQVSKMDTLAGVAIKYGVEVADIKRLNGLATDLQMFALKTLHIPLPGR 68 (356)
Q Consensus 18 ~i~H~VkkGDTL~~IA~KYgVsV~dIKraNnL~sd~~L~~GQ~L~IPv~~~ 68 (356)
+..|+|++||||+.||++|++++.+|+++|++.++ .+++||.|.||....
T Consensus 66 ~~~~~V~~gdtL~~Ia~~~~~tv~~l~~~n~l~~~-~i~~gq~l~~~~~~~ 115 (124)
T COG1388 66 VVTYTVKKGDTLSKIARKYGVTVAELKQLNNLSSD-KIKVGQKLKLPVSSS 115 (124)
T ss_pred CceEEEecCCCHHHHHHHhCCCHHHHHHHhccCCC-ceecCcEEEEecccc
Confidence 46899999999999999999999999999999876 899999999998433
No 11
>PRK10871 nlpD lipoprotein NlpD; Provisional
Probab=98.76 E-value=9.1e-09 Score=101.33 Aligned_cols=48 Identities=23% Similarity=0.205 Sum_probs=45.7
Q ss_pred EEEecCCCCHHHHHHHhCCCHHHHHHHhCCCCCCcccCCCEEEeCCCC
Q 018429 20 EHQVSKMDTLAGVAIKYGVEVADIKRLNGLATDLQMFALKTLHIPLPG 67 (356)
Q Consensus 20 ~H~VkkGDTL~~IA~KYgVsV~dIKraNnL~sd~~L~~GQ~L~IPv~~ 67 (356)
.|+|++|||||.||.+||+++.+|.++|+|...+.|++||.|+||...
T Consensus 62 ~y~Vk~GDTL~~IA~~~g~~~~~La~~N~l~~p~~I~~GQ~L~i~~~~ 109 (319)
T PRK10871 62 TYTVKKGDTLFYIAWITGNDFRDLAQRNNIQAPYSLNVGQTLQVGNAS 109 (319)
T ss_pred ceEECCCCHHHHHHHHHCcCHHHHHHhcCCCCCccccCCCEEEeCCCC
Confidence 699999999999999999999999999999988999999999998764
No 12
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional
Probab=98.67 E-value=6.2e-08 Score=99.03 Aligned_cols=130 Identities=16% Similarity=0.160 Sum_probs=83.4
Q ss_pred CCCCeEEEEecCCCCHHHHHHHhCCCHHHHHHHhCCCCCCccc-CC-CEEEeCCCCCCCCCCCCCCCCCCCCCCCcccCC
Q 018429 14 NGWNYIEHQVSKMDTLAGVAIKYGVEVADIKRLNGLATDLQMF-AL-KTLHIPLPGRHPPSPSLSDGSSSSGENSMERTP 91 (356)
Q Consensus 14 ~~~~~i~H~VkkGDTL~~IA~KYgVsV~dIKraNnL~sd~~L~-~G-Q~L~IPv~~~~~~s~~~s~~s~~~~e~k~~~aq 91 (356)
....+....|..+.+|..||++|||++++|+++|.-.....+. .| +.|+||......-...+......... ......
T Consensus 259 ~~~~~~~V~v~~~i~L~~iA~~~gvs~~eL~~LNP~~kr~~t~p~g~~~llvP~~~~~~f~~~l~~~~~~~~~-p~~~~~ 337 (456)
T PRK10783 259 ESRALARVDLGQQIELAQAAEMAGMSLTKLKTFNAGYKRSTTAPSGPHYIMVPKKHADQLRESLASGEIAAVQ-STLVAD 337 (456)
T ss_pred CCCceEEEecCCCcCHHHHHHHcCCCHHHHHHhCccccCCCcCCCCCeEEEecCchhhHHHHhhhhhhhhhcc-cccccc
Confidence 3344555566666699999999999999999999643232232 23 78889986432110000000000000 000000
Q ss_pred CCCCcchhhhhcccccccCCCCCCCcc-ccccccChhHHHHHHHhCCCCCCCCCCCCCceEEEeeCC
Q 018429 92 PRLGYSNILQSLESLRTESSKKGSLAT-GTSQKVSSAMSNLQKYYGLRSPNGKGKDEGTEMAVYRTG 157 (356)
Q Consensus 92 ~~~~~~~~le~~~s~~vKsg~~dsLw~-gq~~kVSpaM~~L~~wnGL~p~~~~~l~~GqeLvv~~~~ 157 (356)
.. ......|+|++| |+||. +++++|++ ..|++||++.. +.+.+||.|.|+...
T Consensus 338 ~~------~~~~~~y~Vk~G--DTL~sIA~r~gvs~--~~L~~~N~l~~---~~L~~Gq~L~Ip~~~ 391 (456)
T PRK10783 338 NT------PLNSRSYKVRSG--DTLSGIASRLNVST--KDLQQWNNLRG---SKLKVGQTLTIGAGS 391 (456)
T ss_pred cC------cCCceEEEECCC--CcHHHHHHHHCcCH--HHHHHHcCCCc---ccCCCCCEEEecCCc
Confidence 00 011234899999 99999 99999988 99999999975 679999999998643
No 13
>smart00257 LysM Lysin motif.
Probab=98.65 E-value=6.6e-08 Score=62.73 Aligned_cols=43 Identities=33% Similarity=0.461 Sum_probs=39.6
Q ss_pred EEecCCCCHHHHHHHhCCCHHHHHHHhCCCCCCcccCCCEEEe
Q 018429 21 HQVSKMDTLAGVAIKYGVEVADIKRLNGLATDLQMFALKTLHI 63 (356)
Q Consensus 21 H~VkkGDTL~~IA~KYgVsV~dIKraNnL~sd~~L~~GQ~L~I 63 (356)
|+|++|||++.||.+|+++..+|+++|.......+++|+.|.|
T Consensus 2 ~~v~~gdt~~~ia~~~~~~~~~~~~~N~~~~~~~~~~g~~l~i 44 (44)
T smart00257 2 YTVKKGDTLSSIARRYGISVSDLLELNNILDPDNLQVGQKLKI 44 (44)
T ss_pred eEeCCCCCHHHHHHHhCCCHHHHHHHcCCCCccccCCCCEEeC
Confidence 8999999999999999999999999999666678999999875
No 14
>COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane]
Probab=98.54 E-value=1.2e-07 Score=79.15 Aligned_cols=108 Identities=19% Similarity=0.238 Sum_probs=75.5
Q ss_pred HHHHhCCCHHHHHHHhCCCC-CCcccCCCEEEeCCCCCCCCC--CCCCCCCCCCCCCCcccCCCCCCcchhhhhcccccc
Q 018429 32 VAIKYGVEVADIKRLNGLAT-DLQMFALKTLHIPLPGRHPPS--PSLSDGSSSSGENSMERTPPRLGYSNILQSLESLRT 108 (356)
Q Consensus 32 IA~KYgVsV~dIKraNnL~s-d~~L~~GQ~L~IPv~~~~~~s--~~~s~~s~~~~e~k~~~aq~~~~~~~~le~~~s~~v 108 (356)
||.+|++++++|+++|.+.. .+.+++||.|.||........ ....... . +....+. . .....+.-|+|
T Consensus 1 ia~~~~~~v~~l~~~n~~~~~s~~i~~gq~l~~~~~~~~~~~~~~~~~~~~-~----~~~~~~~-~---~~~~~~~~~~V 71 (124)
T COG1388 1 IASKYGVSVKALKKANALTGKSDAIKPGQVLKIPGDISSTVNAGQTLSSLS-N----KVSDSSS-A---SKAPPVVTYTV 71 (124)
T ss_pred CcccccccHHHHHHHhcccCCCCccccCceEEccCCccccccccccccccc-c----eeecccc-c---cccCCCceEEE
Confidence 68999999999999999982 457999999999975222111 1111100 0 0000000 0 11111234889
Q ss_pred cCCCCCCCcc-ccccccChhHHHHHHHhCCCCCCCCCCCCCceEEEee
Q 018429 109 ESSKKGSLAT-GTSQKVSSAMSNLQKYYGLRSPNGKGKDEGTEMAVYR 155 (356)
Q Consensus 109 Ksg~~dsLw~-gq~~kVSpaM~~L~~wnGL~p~~~~~l~~GqeLvv~~ 155 (356)
+.| |+||. ++++.|+. ..|..||+|.. +.+..||+|.+=.
T Consensus 72 ~~g--dtL~~Ia~~~~~tv--~~l~~~n~l~~---~~i~~gq~l~~~~ 112 (124)
T COG1388 72 KKG--DTLSKIARKYGVTV--AELKQLNNLSS---DKIKVGQKLKLPV 112 (124)
T ss_pred ecC--CCHHHHHHHhCCCH--HHHHHHhccCC---CceecCcEEEEec
Confidence 999 99999 99999977 99999999996 5999999999854
No 15
>PRK13914 invasion associated secreted endopeptidase; Provisional
Probab=98.47 E-value=3e-07 Score=94.94 Aligned_cols=52 Identities=31% Similarity=0.449 Sum_probs=47.1
Q ss_pred CeEEEEecCCCCHHHHHHHhCCCHHHHHHHhCCCCCCcccCCCEEEeCCCCCC
Q 018429 17 NYIEHQVSKMDTLAGVAIKYGVEVADIKRLNGLATDLQMFALKTLHIPLPGRH 69 (356)
Q Consensus 17 ~~i~H~VkkGDTL~~IA~KYgVsV~dIKraNnL~sd~~L~~GQ~L~IPv~~~~ 69 (356)
.+..|+|++|||||.||++|||++++|+++|+|.. ..|++||.|.||.....
T Consensus 198 ~a~tytVq~GDTL~sIAkrYgVtv~eI~~~N~l~s-~~L~pGQ~L~Ip~sa~~ 249 (481)
T PRK13914 198 NATTHAVKSGDTIWALSVKYGVSVQDIMSWNNLSS-SSIYVGQKLAIKQTANT 249 (481)
T ss_pred CCeEEEECCCCCHHHHHHHHCCCHHHHHHhcCCCc-cccCCCCEEEecCCCCc
Confidence 56789999999999999999999999999999985 57999999999986543
No 16
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=98.38 E-value=5.4e-07 Score=79.24 Aligned_cols=48 Identities=25% Similarity=0.205 Sum_probs=42.6
Q ss_pred CeEEEEecCCCCHHHHHHHhC---CCHHHHHHHhC--CCCCCcccCCCEEEeC
Q 018429 17 NYIEHQVSKMDTLAGVAIKYG---VEVADIKRLNG--LATDLQMFALKTLHIP 64 (356)
Q Consensus 17 ~~i~H~VkkGDTL~~IA~KYg---VsV~dIKraNn--L~sd~~L~~GQ~L~IP 64 (356)
....|+|++|||||.||.+|+ .....|.++|+ +.+.+.|++||+|.||
T Consensus 94 ~~~~y~Vk~GDTL~~IA~~~~g~~~~~~~I~~~N~~~l~~~~~I~pGq~L~IP 146 (147)
T PRK11198 94 ESQFYTVKSGDTLSAIAKKVYGNANKYNKIFEANKPMLKSPDKIYPGQVLRIP 146 (147)
T ss_pred CCeEEEECCCCCHHHHHHHHcCChhhHHHHHHhhhhcCCCcCCcCcCCEEecC
Confidence 456799999999999999985 45779999998 7777889999999998
No 17
>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=97.44 E-value=2.9e-05 Score=53.85 Aligned_cols=41 Identities=12% Similarity=0.249 Sum_probs=33.4
Q ss_pred ccccCCCCCCCcc-ccccccChhHHHHHHHh-CCCCCCCCCCCCCceEEE
Q 018429 106 LRTESSKKGSLAT-GTSQKVSSAMSNLQKYY-GLRSPNGKGKDEGTEMAV 153 (356)
Q Consensus 106 ~~vKsg~~dsLw~-gq~~kVSpaM~~L~~wn-GL~p~~~~~l~~GqeLvv 153 (356)
|+|++| |+||. ++++.++. ..|+.|| ++.. .. +.+||+|.|
T Consensus 1 y~V~~g--Dtl~~IA~~~~~~~--~~l~~~N~~~~~--~~-l~~G~~l~i 43 (44)
T PF01476_consen 1 YTVQPG--DTLWSIAKRYGISV--DELMELNPNIDS--DN-LQPGQKLCI 43 (44)
T ss_dssp EEE-TT----HHHHHHHTTS-H--HHHHHHCCTTHG--GC-GGTTEEEEE
T ss_pred CEECcC--CcHHHHHhhhhhhH--hHHHHhcCCCCc--cc-CCCCCEEEe
Confidence 789999 99999 99999998 9999999 8887 33 999999976
No 18
>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=97.07 E-value=0.00046 Score=56.07 Aligned_cols=51 Identities=20% Similarity=0.226 Sum_probs=28.6
Q ss_pred CeEEEEecCCCCHHHHHHHhCCCHHHHHHH---h-CCCCCCcccCCCEEEeCCCC
Q 018429 17 NYIEHQVSKMDTLAGVAIKYGVEVADIKRL---N-GLATDLQMFALKTLHIPLPG 67 (356)
Q Consensus 17 ~~i~H~VkkGDTL~~IA~KYgVsV~dIKra---N-nL~sd~~L~~GQ~L~IPv~~ 67 (356)
.|..|+|++||||+.|=.++|++..+|.++ + .-..=..|++||+|.+=+..
T Consensus 1 ~W~~~~V~~GDtLs~iF~~~gls~~dl~~v~~~~~~~k~L~~L~pGq~l~f~~d~ 55 (85)
T PF04225_consen 1 EWQEYTVKSGDTLSTIFRRAGLSASDLYAVLEADGEAKPLTRLKPGQTLEFQLDE 55 (85)
T ss_dssp ---EEE--TT--HHHHHHHTT--HHHHHHHHHHGGGT--GGG--TT-EEEEEE-T
T ss_pred CCcEEEECCCCcHHHHHHHcCCCHHHHHHHHhccCccchHhhCCCCCEEEEEECC
Confidence 478999999999999999999999988773 2 11123479999999886643
No 19
>COG3858 Predicted glycosyl hydrolase [General function prediction only]
Probab=96.87 E-value=0.0007 Score=69.36 Aligned_cols=77 Identities=14% Similarity=0.141 Sum_probs=64.0
Q ss_pred eEEEEecCCCCHHHHHHHhCCCHHHHHHHhCCCCCCcccCCCEEEeCCCCCCCCCCCCCCCCCCCCCCCcccCCCCCCcc
Q 018429 18 YIEHQVSKMDTLAGVAIKYGVEVADIKRLNGLATDLQMFALKTLHIPLPGRHPPSPSLSDGSSSSGENSMERTPPRLGYS 97 (356)
Q Consensus 18 ~i~H~VkkGDTL~~IA~KYgVsV~dIKraNnL~sd~~L~~GQ~L~IPv~~~~~~s~~~s~~s~~~~e~k~~~aq~~~~~~ 97 (356)
+.+|.|++||++..||.+|+++..+|...|.+.. +.|..||++.||....
T Consensus 1 ~~i~~~~pg~~~~~i~~~~~~~~~~i~~~~~~~~-d~~~~~q~~~v~~~~~----------------------------- 50 (423)
T COG3858 1 MSIHLVGPGDSRLIIAVYFPYTNNRIVNGNDYTN-DDLVDGQTFVVPPSGH----------------------------- 50 (423)
T ss_pred CEEEEccCCceeeeehhhcccccccccccccccc-ccccCceeEEECCcce-----------------------------
Confidence 4679999999999999999999999988999987 6899999999995321
Q ss_pred hhhhhcccccccCCCCCCCcc-ccccccChhHHHHHHHh
Q 018429 98 NILQSLESLRTESSKKGSLAT-GTSQKVSSAMSNLQKYY 135 (356)
Q Consensus 98 ~~le~~~s~~vKsg~~dsLw~-gq~~kVSpaM~~L~~wn 135 (356)
+ |+|.++ |+||. +++..|+. ..++.-+
T Consensus 51 --~-----y~~~~~--d~~~Sia~~~~vt~--~~~~~m~ 78 (423)
T COG3858 51 --F-----YDVGPG--DTLTSIARTVGVTQ--DSAAIMN 78 (423)
T ss_pred --E-----EEecCC--cchhhhhhhhcCCH--HHHHhhc
Confidence 1 778888 99998 88888865 6665544
No 20
>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=96.80 E-value=0.0017 Score=51.98 Aligned_cols=41 Identities=27% Similarity=0.240 Sum_probs=31.7
Q ss_pred CCHHHHHHHh---C-CCHH----HHHHHhC----CCCCCcccCCCEEEeCCCC
Q 018429 27 DTLAGVAIKY---G-VEVA----DIKRLNG----LATDLQMFALKTLHIPLPG 67 (356)
Q Consensus 27 DTL~~IA~KY---g-VsV~----dIKraNn----L~sd~~L~~GQ~L~IPv~~ 67 (356)
||||+||.+| + +++. .|.++|. --.-+.|++|+.|.||...
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 8887 6777772 1123579999999999743
No 21
>KOG2850 consensus Predicted peptidoglycan-binding protein, contains LysM domain [General function prediction only]
Probab=96.43 E-value=0.0017 Score=60.26 Aligned_cols=54 Identities=31% Similarity=0.492 Sum_probs=49.3
Q ss_pred CCeEEEEecCCCCHHHHHHHhCCCHHHHHHHhCCCCCCcccCCCEEEeCCCCCC
Q 018429 16 WNYIEHQVSKMDTLAGVAIKYGVEVADIKRLNGLATDLQMFALKTLHIPLPGRH 69 (356)
Q Consensus 16 ~~~i~H~VkkGDTL~~IA~KYgVsV~dIKraNnL~sd~~L~~GQ~L~IPv~~~~ 69 (356)
...++-+|+.||||.-||.+|.+++.+|+|.|++.......+-+.+.||+....
T Consensus 7 ~~~l~~~iq~~dt~~a~al~~~~~va~i~RvN~~~r~q~f~a~~~i~~pv~~~~ 60 (186)
T KOG2850|consen 7 AHELEVTIQEGDTLQAIALNYESDVADIKRVNNDDREQRFNALRSISIPVTRAS 60 (186)
T ss_pred hhheeeeeccCchhhhHHhhcccchhhheeeccchhhhhhccccceecccchhh
Confidence 456778999999999999999999999999999998889999999999997643
No 22
>PRK10190 L,D-transpeptidase; Provisional
Probab=96.43 E-value=0.0096 Score=59.17 Aligned_cols=56 Identities=20% Similarity=0.179 Sum_probs=46.5
Q ss_pred CeEEEEecCCC--CHHHHHHHhCCCHHHHHHHhCCCCCCcccCCCEEEeCCCCCCCCC
Q 018429 17 NYIEHQVSKMD--TLAGVAIKYGVEVADIKRLNGLATDLQMFALKTLHIPLPGRHPPS 72 (356)
Q Consensus 17 ~~i~H~VkkGD--TL~~IA~KYgVsV~dIKraNnL~sd~~L~~GQ~L~IPv~~~~~~s 72 (356)
....|+|+++| +|..||.+|++....|+.+|.-.......+|+.|+||....-++.
T Consensus 36 ~~~~~~v~~~~~~~le~iA~~f~~g~~~l~~aNPgvd~~~p~~G~~i~iP~~~ilP~~ 93 (310)
T PRK10190 36 QSLTVTVPDHNTQPLETFAAQYGQGLSNMLEANPGADVFLPKSGSQLTIPQQLILPDT 93 (310)
T ss_pred ceEEEEecCCCCccHHHHHHHhCCCHHHHHHhCCCCCCCCCCCCCEEEecCcccCCCC
Confidence 45679999977 599999999999999999998765555689999999987655544
No 23
>PRK10260 L,D-transpeptidase; Provisional
Probab=96.30 E-value=0.013 Score=58.24 Aligned_cols=56 Identities=16% Similarity=0.113 Sum_probs=46.2
Q ss_pred CeEEEEecCCCC--HHHHHHHhCCCHHHHHHHhCCCCCCcccCCCEEEeCCCCCCCCC
Q 018429 17 NYIEHQVSKMDT--LAGVAIKYGVEVADIKRLNGLATDLQMFALKTLHIPLPGRHPPS 72 (356)
Q Consensus 17 ~~i~H~VkkGDT--L~~IA~KYgVsV~dIKraNnL~sd~~L~~GQ~L~IPv~~~~~~s 72 (356)
....|+|++||| |..||.+|++....|+++|.-.......+|+.|+||...--++.
T Consensus 39 ~~~~~~v~~~~~~~le~iA~~f~~g~~~l~~aNPgvdp~lp~~G~~i~iP~~~ilP~~ 96 (306)
T PRK10260 39 QNQVITIPEGNTQPLEYFAAEYQMGLSNMMEANPGVDTFLPKGGTVLNIPQQLILPDT 96 (306)
T ss_pred ccEEEEeCCCCCchHHHHHHHhCCCHHHHHHhCcCCCCCcCCCCCEEEeCCccCCCCC
Confidence 456799999765 99999999999999999998765545679999999986655543
No 24
>PRK14125 cell division suppressor protein YneA; Provisional
Probab=96.20 E-value=0.004 Score=52.57 Aligned_cols=51 Identities=10% Similarity=0.064 Sum_probs=41.0
Q ss_pred ccccccCCCCCCCcc-ccccccCh------hHHHHHHHhCCCCCCCCCCCCCceEEEeeCCCC
Q 018429 104 ESLRTESSKKGSLAT-GTSQKVSS------AMSNLQKYYGLRSPNGKGKDEGTEMAVYRTGSS 159 (356)
Q Consensus 104 ~s~~vKsg~~dsLw~-gq~~kVSp------aM~~L~~wnGL~p~~~~~l~~GqeLvv~~~~~~ 159 (356)
..|+|++| |+||. ++++.++. .+..|+..|+|.+ +.+.+||.|.|-...+.
T Consensus 37 ~~~tV~~G--DTLW~IA~~y~~~~~l~~~~~v~~I~~~N~l~~---~~I~~Gq~L~IP~~~~~ 94 (103)
T PRK14125 37 VEITVQEG--DTLWALADQYAGKHHMAKNEFIEWVEDVNNLPS---GHIKAGDKLVIPVLKSK 94 (103)
T ss_pred EEEEECCC--CCHHHHHHHhCCCcCCCHHHHHHHHHHhcCCCC---CcCCCCCEEEEecCCCC
Confidence 45899999 99999 99997642 2578889999996 46999999999655443
No 25
>COG1652 XkdP Uncharacterized protein containing LysM domain [Function unknown]
Probab=96.09 E-value=0.0022 Score=60.79 Aligned_cols=49 Identities=27% Similarity=0.242 Sum_probs=41.8
Q ss_pred EEEEecCCCCHHHHHHH-hCCC--HHHHHHHhC---CCCCCcccCCCEEEeCCCC
Q 018429 19 IEHQVSKMDTLAGVAIK-YGVE--VADIKRLNG---LATDLQMFALKTLHIPLPG 67 (356)
Q Consensus 19 i~H~VkkGDTL~~IA~K-YgVs--V~dIKraNn---L~sd~~L~~GQ~L~IPv~~ 67 (356)
..|+|++|||||.||.+ ||.. -..|-.+|+ +...+.|++||.|.||-..
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 47999999999999987 4544 457888999 8889999999999999754
No 26
>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=95.87 E-value=0.0057 Score=41.26 Aligned_cols=40 Identities=13% Similarity=0.082 Sum_probs=33.5
Q ss_pred ccCCCCCCCcc-ccccccChhHHHHHHHhC-CCCCCCCCCCCCceEEE
Q 018429 108 TESSKKGSLAT-GTSQKVSSAMSNLQKYYG-LRSPNGKGKDEGTEMAV 153 (356)
Q Consensus 108 vKsg~~dsLw~-gq~~kVSpaM~~L~~wnG-L~p~~~~~l~~GqeLvv 153 (356)
|++| |+||. ++++.++. ..|+.+|+ +.. .+.+.+||.|.|
T Consensus 1 v~~g--dtl~~IA~~~~~~~--~~l~~~N~~~~~--~~~~~~g~~l~i 42 (44)
T TIGR02899 1 VQKG--DTLWKIAKKYGVDF--DELIQANPQLSN--PNLIYPGMKIKI 42 (44)
T ss_pred CCCC--CCHHHHHHHHCcCH--HHHHHHhhcCCC--CCCcCCCCEEec
Confidence 4677 99999 99999987 99999997 443 467999999876
No 27
>PRK10871 nlpD lipoprotein NlpD; Provisional
Probab=95.62 E-value=0.006 Score=60.73 Aligned_cols=46 Identities=9% Similarity=0.062 Sum_probs=41.4
Q ss_pred cccccCCCCCCCcc-ccccccChhHHHHHHHhCCCCCCCCCCCCCceEEEeeC
Q 018429 105 SLRTESSKKGSLAT-GTSQKVSSAMSNLQKYYGLRSPNGKGKDEGTEMAVYRT 156 (356)
Q Consensus 105 s~~vKsg~~dsLw~-gq~~kVSpaM~~L~~wnGL~p~~~~~l~~GqeLvv~~~ 156 (356)
.|+|++| |+||. ++.+.++. ..|+.||+|.. -..+.+||.|.|...
T Consensus 62 ~y~Vk~G--DTL~~IA~~~g~~~--~~La~~N~l~~--p~~I~~GQ~L~i~~~ 108 (319)
T PRK10871 62 TYTVKKG--DTLFYIAWITGNDF--RDLAQRNNIQA--PYSLNVGQTLQVGNA 108 (319)
T ss_pred ceEECCC--CHHHHHHHHHCcCH--HHHHHhcCCCC--CccccCCCEEEeCCC
Confidence 3999999 99999 99999988 99999999976 577999999999643
No 28
>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=95.61 E-value=0.0077 Score=39.06 Aligned_cols=42 Identities=17% Similarity=0.297 Sum_probs=36.7
Q ss_pred ccccCCCCCCCcc-ccccccChhHHHHHHHhCCCCCCCCCCCCCceEEE
Q 018429 106 LRTESSKKGSLAT-GTSQKVSSAMSNLQKYYGLRSPNGKGKDEGTEMAV 153 (356)
Q Consensus 106 ~~vKsg~~dsLw~-gq~~kVSpaM~~L~~wnGL~p~~~~~l~~GqeLvv 153 (356)
|+|+.| |+||. ++++.++. ..|..+|++.. ...+.+|+.+.|
T Consensus 3 ~~v~~g--dt~~~ia~~~~~~~--~~~~~~N~~~~--~~~~~~g~~l~i 45 (46)
T cd00118 3 YTVKKG--DTLSSIAQRYGISV--EELLKLNGLSD--PDNLQVGQKLKI 45 (46)
T ss_pred EEECCC--CCHHHHHHHHCcCH--HHHHHHcCCCC--ccccCCCCEEec
Confidence 778999 99999 99999987 99999999954 578899998865
No 29
>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=95.12 E-value=0.012 Score=59.20 Aligned_cols=43 Identities=16% Similarity=0.187 Sum_probs=39.2
Q ss_pred ccccccCCCCCCCcc-ccccccChhHHHHHHHhCCCCCCCCCCCCCceEEE
Q 018429 104 ESLRTESSKKGSLAT-GTSQKVSSAMSNLQKYYGLRSPNGKGKDEGTEMAV 153 (356)
Q Consensus 104 ~s~~vKsg~~dsLw~-gq~~kVSpaM~~L~~wnGL~p~~~~~l~~GqeLvv 153 (356)
.-|+|++| |+||. |++++|++ ..|++||+|.+ ..|++||.|.|
T Consensus 294 ~~YiVq~G--DTL~sIAkRYGVSV--~~L~r~N~L~~---~~L~~GQ~L~I 337 (338)
T TIGR02907 294 RMCIVQEG--DTIETIAERYEISV--SQLIRHNQLED---FEVNEGQILYI 337 (338)
T ss_pred EEEEECCC--CCHHHHHHHHCcCH--HHHHHHhCCCc---cccCCCCEEEe
Confidence 45899999 99999 99999998 99999999984 68999999986
No 30
>smart00257 LysM Lysin motif.
Probab=94.75 E-value=0.019 Score=36.65 Aligned_cols=42 Identities=12% Similarity=0.231 Sum_probs=35.0
Q ss_pred ccccCCCCCCCcc-ccccccChhHHHHHHHhCCCCCCCCCCCCCceEEE
Q 018429 106 LRTESSKKGSLAT-GTSQKVSSAMSNLQKYYGLRSPNGKGKDEGTEMAV 153 (356)
Q Consensus 106 ~~vKsg~~dsLw~-gq~~kVSpaM~~L~~wnGL~p~~~~~l~~GqeLvv 153 (356)
|+|++| |++|. ++++.+++ ..|..+|.... ...+.+|+.+.|
T Consensus 2 ~~v~~g--dt~~~ia~~~~~~~--~~~~~~N~~~~--~~~~~~g~~l~i 44 (44)
T smart00257 2 YTVKKG--DTLSSIARRYGISV--SDLLELNNILD--PDNLQVGQKLKI 44 (44)
T ss_pred eEeCCC--CCHHHHHHHhCCCH--HHHHHHcCCCC--ccccCCCCEEeC
Confidence 678999 99999 99999977 99999999544 567888987753
No 31
>PRK11649 putative peptidase; Provisional
Probab=94.50 E-value=0.071 Score=55.01 Aligned_cols=52 Identities=25% Similarity=0.241 Sum_probs=41.8
Q ss_pred CCeEEEEecCCCCHHHHHHHhCCCHHHHHHH-hCCCCCCcccCCCEEEeCCCC
Q 018429 16 WNYIEHQVSKMDTLAGVAIKYGVEVADIKRL-NGLATDLQMFALKTLHIPLPG 67 (356)
Q Consensus 16 ~~~i~H~VkkGDTL~~IA~KYgVsV~dIKra-NnL~sd~~L~~GQ~L~IPv~~ 67 (356)
..|..|+|++||||..|=.+||++..++.++ .....-..|++||.|.|-+..
T Consensus 93 ~~~~~~~Vk~GDTl~~iL~r~Gi~~~di~~l~~~~~~L~~Lr~Gq~l~~~~d~ 145 (439)
T PRK11649 93 AGVHEYVVSTGDTLSSILNQYGIDMSDISQLAAQDKELRNLKIGQQLSWTLTA 145 (439)
T ss_pred CceEEEEeCCCCCHHHHHHHcCCCHHHHHHHHHcChHhhcCCCCCEEEEEECC
Confidence 4578999999999999999999999998876 222223479999999996543
No 32
>COG3858 Predicted glycosyl hydrolase [General function prediction only]
Probab=94.41 E-value=0.053 Score=55.95 Aligned_cols=52 Identities=21% Similarity=0.052 Sum_probs=47.1
Q ss_pred eEEEEecCCCCHHHHHHHhCCCHHHHHHHhCCCCCCcccCCCEEEeCCCCCC
Q 018429 18 YIEHQVSKMDTLAGVAIKYGVEVADIKRLNGLATDLQMFALKTLHIPLPGRH 69 (356)
Q Consensus 18 ~i~H~VkkGDTL~~IA~KYgVsV~dIKraNnL~sd~~L~~GQ~L~IPv~~~~ 69 (356)
...|.|++||||++||++++|+.+.+..+|.......+.+|=.|.||-..+.
T Consensus 49 ~~~y~~~~~d~~~Sia~~~~vt~~~~~~m~~~~~~~~l~~~~~l~~P~~~~~ 100 (423)
T COG3858 49 GHFYDVGPGDTLTSIARTVGVTQDSAAIMNFVICPGYLQYGLNLYIPSARKT 100 (423)
T ss_pred ceEEEecCCcchhhhhhhhcCCHHHHHhhcccccccceeeeeEEeccCCCCC
Confidence 4569999999999999999999999999998877788999999999987665
No 33
>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=90.75 E-value=0.85 Score=35.17 Aligned_cols=48 Identities=25% Similarity=0.148 Sum_probs=35.4
Q ss_pred EEEEecCCCCHHHHHHHh-CCC---HHHHHHHhC-CCCC-CcccCCCEEEeCCCC
Q 018429 19 IEHQVSKMDTLAGVAIKY-GVE---VADIKRLNG-LATD-LQMFALKTLHIPLPG 67 (356)
Q Consensus 19 i~H~VkkGDTL~~IA~KY-gVs---V~dIKraNn-L~sd-~~L~~GQ~L~IPv~~ 67 (356)
.+|+. .||||..||.|| |-+ ++.|.++|. |..- ..|-+|..|.||.-.
T Consensus 2 ~v~t~-~GDtlD~I~~r~yG~~~~~~e~ll~aNp~La~~~~~lpaG~~I~lP~i~ 55 (60)
T PF05489_consen 2 TVYTT-QGDTLDLIAYRHYGREDGAVEALLEANPGLADTGPVLPAGTVIILPDIP 55 (60)
T ss_pred EEEEe-CcCcHHHHHHHHhCcHHHHHHHHHHHChhhhhcCCcCCCCCEEECCCCC
Confidence 34555 899999999875 554 478899995 4322 478889999999643
No 34
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=89.85 E-value=0.2 Score=44.23 Aligned_cols=45 Identities=11% Similarity=0.097 Sum_probs=36.6
Q ss_pred cccccCCCCCCCcc-ccccccC-hhHHHHHHHhC--CCCCCCCCCCCCceEEE
Q 018429 105 SLRTESSKKGSLAT-GTSQKVS-SAMSNLQKYYG--LRSPNGKGKDEGTEMAV 153 (356)
Q Consensus 105 s~~vKsg~~dsLw~-gq~~kVS-paM~~L~~wnG--L~p~~~~~l~~GqeLvv 153 (356)
.|+|++| |+||. ++++..+ ..+..|..+|+ +.. .+.+.+||+|.|
T Consensus 97 ~y~Vk~G--DTL~~IA~~~~g~~~~~~~I~~~N~~~l~~--~~~I~pGq~L~I 145 (147)
T PRK11198 97 FYTVKSG--DTLSAIAKKVYGNANKYNKIFEANKPMLKS--PDKIYPGQVLRI 145 (147)
T ss_pred EEEECCC--CCHHHHHHHHcCChhhHHHHHHhhhhcCCC--cCCcCcCCEEec
Confidence 4899999 99999 8887443 34688999998 664 577999999976
No 35
>COG0739 NlpD Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]
Probab=89.60 E-value=0.59 Score=43.00 Aligned_cols=49 Identities=29% Similarity=0.360 Sum_probs=44.7
Q ss_pred EEEEecCCCCHHHHHHHhCCCHHHHHHHhCCCCCCcccCCCEEEeCCCC
Q 018429 19 IEHQVSKMDTLAGVAIKYGVEVADIKRLNGLATDLQMFALKTLHIPLPG 67 (356)
Q Consensus 19 i~H~VkkGDTL~~IA~KYgVsV~dIKraNnL~sd~~L~~GQ~L~IPv~~ 67 (356)
..|.|+.+++|..|+.++++.+.++.+.|++.....+..++.+.+|...
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 50 (277)
T COG0739 2 SLYVVKKGDTLSAIAARLGISAKDLARLNNLLKKRLLRIGQLLRVPRAA 50 (277)
T ss_pred ceEEecCCCHHHHHHHHcCCCHHHHHHHHhhccccccCccceeeecccc
Confidence 4689999999999999999999999999998866578999999999875
No 36
>COG3170 FimV Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=77.97 E-value=1.7 Score=47.95 Aligned_cols=51 Identities=25% Similarity=0.199 Sum_probs=37.3
Q ss_pred eEEEEecCCCCHHHHHHHhC----CCHHH----HHHHhC--CC--CCCcccCCCEEEeCCCCC
Q 018429 18 YIEHQVSKMDTLAGVAIKYG----VEVAD----IKRLNG--LA--TDLQMFALKTLHIPLPGR 68 (356)
Q Consensus 18 ~i~H~VkkGDTL~~IA~KYg----VsV~d----IKraNn--L~--sd~~L~~GQ~L~IPv~~~ 68 (356)
-..|+|++|||||.||.+-- ||+.+ |.++|- +. +=+.|+.|.+|.||.-..
T Consensus 188 g~tyt~~~~Dtl~dIAs~~rp~~~vt~~Q~~lAly~lNP~af~~gni~RLr~GSvLriP~~~q 250 (755)
T COG3170 188 GDTYTVRSGDTLWDIASRLRPQDHVTVEQMLLALYQLNPQAFVNGNINRLRAGSVLRIPSAAQ 250 (755)
T ss_pred CcccccCCcchHHHHHHhhcCcccccHHHHHHHHHhhChhhhcccchhhccccceeeccchhh
Confidence 34599999999999999854 45554 666772 11 224799999999998543
No 37
>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=67.88 E-value=5.6 Score=28.32 Aligned_cols=24 Identities=21% Similarity=0.357 Sum_probs=18.7
Q ss_pred ecCCCCHHHHHHHhCCCHHHHHHH
Q 018429 23 VSKMDTLAGVAIKYGVEVADIKRL 46 (356)
Q Consensus 23 VkkGDTL~~IA~KYgVsV~dIKra 46 (356)
...|-|+..||+.+||+...|.|+
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 357899999999999999999886
No 38
>PF13518 HTH_28: Helix-turn-helix domain
Probab=67.83 E-value=5.6 Score=27.89 Aligned_cols=27 Identities=11% Similarity=0.204 Sum_probs=22.5
Q ss_pred ecCCCCHHHHHHHhCCCHHHHHHHhCC
Q 018429 23 VSKMDTLAGVAIKYGVEVADIKRLNGL 49 (356)
Q Consensus 23 VkkGDTL~~IA~KYgVsV~dIKraNnL 49 (356)
+..|.|+..||.+|||+...|.++=..
T Consensus 9 ~~~g~s~~~~a~~~gis~~tv~~w~~~ 35 (52)
T PF13518_consen 9 YLEGESVREIAREFGISRSTVYRWIKR 35 (52)
T ss_pred HHcCCCHHHHHHHHCCCHhHHHHHHHH
Confidence 346889999999999999999886543
No 39
>COG3061 OapA Cell envelope opacity-associated protein A [Cell envelope biogenesis, outer membrane]
Probab=67.65 E-value=8.8 Score=37.31 Aligned_cols=51 Identities=18% Similarity=0.198 Sum_probs=41.4
Q ss_pred CeEEEEecCCCCHHHHHHHhCCCHHHHHHHhCCCC----CCcccCCCEEEeCCCC
Q 018429 17 NYIEHQVSKMDTLAGVAIKYGVEVADIKRLNGLAT----DLQMFALKTLHIPLPG 67 (356)
Q Consensus 17 ~~i~H~VkkGDTL~~IA~KYgVsV~dIKraNnL~s----d~~L~~GQ~L~IPv~~ 67 (356)
.|..|+|..|+||..+=+-+++.+.|+-.+=+... -..|.+||.++|-+..
T Consensus 158 ~wqsy~V~~G~TLaQlFRdn~LpitDVnAMakveGagkpLSnlkaGq~Vki~~na 212 (242)
T COG3061 158 NWQSYTVPQGKTLAQLFRDNNLPITDVNAMAKVEGAGKPLSNLKAGQKVKISLNA 212 (242)
T ss_pred cceeEEecCCccHHHHHhccCCChHHhHHHHhhccCCCchhhccCCCEEEEEEcC
Confidence 89999999999999999999999999876543221 1258999999997754
No 40
>KOG2850 consensus Predicted peptidoglycan-binding protein, contains LysM domain [General function prediction only]
Probab=67.06 E-value=2.4 Score=39.73 Aligned_cols=54 Identities=41% Similarity=0.720 Sum_probs=49.9
Q ss_pred CCCeEEEEecCCCCHHH--HHHHhCCC-----HHHHHHHhCCCCCCcccCCCEEEeCCCCC
Q 018429 15 GWNYIEHQVSKMDTLAG--VAIKYGVE-----VADIKRLNGLATDLQMFALKTLHIPLPGR 68 (356)
Q Consensus 15 ~~~~i~H~VkkGDTL~~--IA~KYgVs-----V~dIKraNnL~sd~~L~~GQ~L~IPv~~~ 68 (356)
...++.|.|++-+++.+ ++-+||.. ++++++.|....+..++.-..+-||.+..
T Consensus 116 a~~~~eh~v~~~~~~tg~~~~~~~ga~~d~~~~e~v~k~~~vl~~~~~f~l~~~e~p~~~~ 176 (186)
T KOG2850|consen 116 AVGYQEHRVKPFDPNTGFQIAPAYGAESDESPVESVRKMNPVLPDHQVFYLAPLEIPLPGA 176 (186)
T ss_pred hhhhhhcCCCCCCccccceecccccCcccchhHHHHHHHhhccchhHHHhhccccCCCCCc
Confidence 44688999999999999 99999999 99999999988899999999999998876
No 41
>COG4784 Putative Zn-dependent protease [General function prediction only]
Probab=54.84 E-value=25 Score=36.62 Aligned_cols=49 Identities=16% Similarity=0.163 Sum_probs=39.7
Q ss_pred CCeEEEEecCCCCHHHHHHHh-CC--CHHHHHHHhCCCCCCcccCCCEEEeC
Q 018429 16 WNYIEHQVSKMDTLAGVAIKY-GV--EVADIKRLNGLATDLQMFALKTLHIP 64 (356)
Q Consensus 16 ~~~i~H~VkkGDTL~~IA~KY-gV--sV~dIKraNnL~sd~~L~~GQ~L~IP 64 (356)
.....-+||+|||+..+|-+- |+ .++-++-+|-|...-.+++|+.++|=
T Consensus 426 lrirvvtVk~GqT~~~lAA~m~G~~rkldlfRllNam~~~a~~~pGd~vKii 477 (479)
T COG4784 426 LRIRVVTVKPGQTMASLAARMMGTDRKLDLFRLLNAMSPGATVRPGDKVKII 477 (479)
T ss_pred eEEEEEEecCCccHHHHHhhccCchhHHHHHHHHhccCCCCcCCCCCeeeec
Confidence 345567899999999999875 33 46677789999988899999999883
No 42
>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=52.37 E-value=10 Score=28.64 Aligned_cols=24 Identities=17% Similarity=0.374 Sum_probs=20.7
Q ss_pred ecCCCCHHHHHHHhCCCHHHHHHH
Q 018429 23 VSKMDTLAGVAIKYGVEVADIKRL 46 (356)
Q Consensus 23 VkkGDTL~~IA~KYgVsV~dIKra 46 (356)
...|.|+..||.+|||+...|.++
T Consensus 20 ~~~g~sv~~va~~~gi~~~~l~~W 43 (76)
T PF01527_consen 20 LESGESVSEVAREYGISPSTLYNW 43 (76)
T ss_dssp HHHHCHHHHHHHHHTS-HHHHHHH
T ss_pred HHCCCceEeeecccccccccccHH
Confidence 367999999999999999999876
No 43
>COG4254 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.66 E-value=21 Score=36.20 Aligned_cols=50 Identities=24% Similarity=0.153 Sum_probs=43.4
Q ss_pred EEEEecCCCCHHHHHHHhCCCHHH---HHHHhCCCCCCcccCCCEEEeCCCCC
Q 018429 19 IEHQVSKMDTLAGVAIKYGVEVAD---IKRLNGLATDLQMFALKTLHIPLPGR 68 (356)
Q Consensus 19 i~H~VkkGDTL~~IA~KYgVsV~d---IKraNnL~sd~~L~~GQ~L~IPv~~~ 68 (356)
+.|.|+.||||..++..|=.-.+. ++.+|.+.....+..|..|-||.+..
T Consensus 6 ~~yrv~~gdtli~l~~~yl~~~~g~r~~q~an~~~~P~~l~pgs~l~ip~~~~ 58 (339)
T COG4254 6 LTYRVLFGDTLILLLGGYLTLLAGSRAAQPANTKRPPFILQPGSCLPIPLPAS 58 (339)
T ss_pred ceeeeccccHHHHHHHHhhhccchhhhhcccccCCCCcccCCCccccCCCccc
Confidence 569999999999999999876654 56689999999999999999998654
No 44
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=42.82 E-value=28 Score=24.42 Aligned_cols=27 Identities=15% Similarity=0.142 Sum_probs=19.2
Q ss_pred ecCCCCHHHHHHHhCCCHHHHHHHhCC
Q 018429 23 VSKMDTLAGVAIKYGVEVADIKRLNGL 49 (356)
Q Consensus 23 VkkGDTL~~IA~KYgVsV~dIKraNnL 49 (356)
+..|.|...||+.+||+...+.++=+-
T Consensus 14 ~~~G~s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 14 LREGWSIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp HHHT--HHHHHHHHTS-HHHHHHHHT-
T ss_pred HHCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 345999999999999999999886443
No 45
>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=40.99 E-value=26 Score=25.28 Aligned_cols=24 Identities=29% Similarity=0.396 Sum_probs=17.8
Q ss_pred ecCC-CCHHHHHHHhCCCHHHHHHH
Q 018429 23 VSKM-DTLAGVAIKYGVEVADIKRL 46 (356)
Q Consensus 23 VkkG-DTL~~IA~KYgVsV~dIKra 46 (356)
|+.| -++...|++|||+...|.+.
T Consensus 12 v~~g~~S~r~AA~~ygVp~sTL~~r 36 (45)
T PF05225_consen 12 VKNGKMSIRKAAKKYGVPRSTLRRR 36 (45)
T ss_dssp HHTTSS-HHHHHHHHT--HHHHHHH
T ss_pred HHhCCCCHHHHHHHHCcCHHHHHHH
Confidence 5566 89999999999999999864
No 46
>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=40.15 E-value=35 Score=20.09 Aligned_cols=24 Identities=21% Similarity=0.378 Sum_probs=20.0
Q ss_pred ecCCCCHHHHHHHhCCCHHHHHHH
Q 018429 23 VSKMDTLAGVAIKYGVEVADIKRL 46 (356)
Q Consensus 23 VkkGDTL~~IA~KYgVsV~dIKra 46 (356)
+..|.++..||..+|++...|.++
T Consensus 18 ~~~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 18 LAAGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHh
Confidence 456889999999999998887653
No 47
>PF11268 DUF3071: Protein of unknown function (DUF3071); InterPro: IPR021421 Some members in this family of proteins are annotated as DNA-binding proteins however this cannot be confirmed. Currently no function is known.
Probab=39.71 E-value=23 Score=32.78 Aligned_cols=51 Identities=18% Similarity=0.216 Sum_probs=35.1
Q ss_pred eEEEEecCCCCHHHHHHHhCCCHHHHHHHhC-CCCCCcccCCCEEEeCCCCC
Q 018429 18 YIEHQVSKMDTLAGVAIKYGVEVADIKRLNG-LATDLQMFALKTLHIPLPGR 68 (356)
Q Consensus 18 ~i~H~VkkGDTL~~IA~KYgVsV~dIKraNn-L~sd~~L~~GQ~L~IPv~~~ 68 (356)
-|.-.|+.|-|...||..||++++.|.+|=. ......-.+.+.+..|+...
T Consensus 61 eIQarIRaGas~eeVA~~~G~~~~rV~rfa~PVlaER~~~ae~A~~~~~~~~ 112 (170)
T PF11268_consen 61 EIQARIRAGASAEEVAEEAGVPVERVRRFAGPVLAERERAAEQARQVHPVRE 112 (170)
T ss_pred HHHHHHHCCCCHHHHHHHhCCCHHHhhhcccHHHHHHHHHHHHHhhCCCCCC
Confidence 3445688999999999999999999999764 22223334455555555443
No 48
>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=39.34 E-value=41 Score=23.83 Aligned_cols=23 Identities=22% Similarity=0.355 Sum_probs=19.4
Q ss_pred cCCCCHHHHHHHhCCCHHHHHHH
Q 018429 24 SKMDTLAGVAIKYGVEVADIKRL 46 (356)
Q Consensus 24 kkGDTL~~IA~KYgVsV~dIKra 46 (356)
-.|-|+..||..+|++...+++.
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 46889999999999999998864
No 49
>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=37.05 E-value=33 Score=28.70 Aligned_cols=21 Identities=29% Similarity=0.376 Sum_probs=15.9
Q ss_pred CCCHHHHHHHhCCCHHHHHHH
Q 018429 26 MDTLAGVAIKYGVEVADIKRL 46 (356)
Q Consensus 26 GDTL~~IA~KYgVsV~dIKra 46 (356)
|.++..||.+||+|...|.++
T Consensus 72 G~n~~eLA~kyglS~r~I~~I 92 (108)
T PF08765_consen 72 GMNVRELARKYGLSERQIYRI 92 (108)
T ss_dssp SS-HHHHHHHHT--HHHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHHH
Confidence 889999999999999888763
No 50
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=36.63 E-value=37 Score=28.74 Aligned_cols=28 Identities=18% Similarity=0.076 Sum_probs=24.0
Q ss_pred EEecCCCCHHHHHHHhCCCHHHHHHHhC
Q 018429 21 HQVSKMDTLAGVAIKYGVEVADIKRLNG 48 (356)
Q Consensus 21 H~VkkGDTL~~IA~KYgVsV~dIKraNn 48 (356)
..+..|-|+..||.+|||+...|.+|=+
T Consensus 24 ~~~~~g~sv~evA~e~gIs~~tl~~W~r 51 (121)
T PRK09413 24 QSFEPGMTVSLVARQHGVAASQLFLWRK 51 (121)
T ss_pred HHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3466799999999999999999999843
No 51
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=34.59 E-value=36 Score=28.10 Aligned_cols=26 Identities=19% Similarity=0.342 Sum_probs=21.5
Q ss_pred EEecCCCCHHHHHHHhCC-CHHHHHHH
Q 018429 21 HQVSKMDTLAGVAIKYGV-EVADIKRL 46 (356)
Q Consensus 21 H~VkkGDTL~~IA~KYgV-sV~dIKra 46 (356)
..+..|.|+..||++||| ....|.++
T Consensus 19 ~~~~~g~sv~~vAr~~gv~~~~~l~~W 45 (116)
T COG2963 19 LYLRGGDTVSEVAREFGIVSATQLYKW 45 (116)
T ss_pred HHHhcCccHHHHHHHhCCCChHHHHHH
Confidence 345689999999999996 98888863
No 52
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=34.22 E-value=35 Score=25.51 Aligned_cols=24 Identities=17% Similarity=0.317 Sum_probs=17.6
Q ss_pred ecCCCCHHHHHHHhC-CCHHHHHHH
Q 018429 23 VSKMDTLAGVAIKYG-VEVADIKRL 46 (356)
Q Consensus 23 VkkGDTL~~IA~KYg-VsV~dIKra 46 (356)
+..|.++..|+..|. ++.++|+.+
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 478999999999998 999999864
No 53
>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=32.55 E-value=22 Score=26.41 Aligned_cols=23 Identities=13% Similarity=0.335 Sum_probs=16.5
Q ss_pred ecCCCCHHHHHHHhCCCHHHHHH
Q 018429 23 VSKMDTLAGVAIKYGVEVADIKR 45 (356)
Q Consensus 23 VkkGDTL~~IA~KYgVsV~dIKr 45 (356)
+..|.+...||++|||+...|..
T Consensus 19 ~e~g~s~~~ia~~fgv~~sTv~~ 41 (53)
T PF04218_consen 19 LEEGESKRDIAREFGVSRSTVST 41 (53)
T ss_dssp HHCTT-HHHHHHHHT--CCHHHH
T ss_pred HHcCCCHHHHHHHhCCCHHHHHH
Confidence 56789999999999997776654
No 54
>PHA00675 hypothetical protein
Probab=32.23 E-value=47 Score=27.51 Aligned_cols=24 Identities=17% Similarity=0.111 Sum_probs=21.0
Q ss_pred cCCCCHHHHHHHhCCCHHHHHHHh
Q 018429 24 SKMDTLAGVAIKYGVEVADIKRLN 47 (356)
Q Consensus 24 kkGDTL~~IA~KYgVsV~dIKraN 47 (356)
+.|.+.+.||++|||+-..|..+=
T Consensus 37 r~G~s~~~IA~~fGVsrstV~~I~ 60 (78)
T PHA00675 37 VEGMSYAVLAEKFEQSKGAIAKIC 60 (78)
T ss_pred hcCccHHHHHHHhCCCHHHHHHHH
Confidence 789999999999999988887653
No 55
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=30.82 E-value=57 Score=23.16 Aligned_cols=23 Identities=13% Similarity=0.260 Sum_probs=15.7
Q ss_pred ecCCCCHHHHHHHhCCCHHHHHH
Q 018429 23 VSKMDTLAGVAIKYGVEVADIKR 45 (356)
Q Consensus 23 VkkGDTL~~IA~KYgVsV~dIKr 45 (356)
...|-++..||.++|++...|.+
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 56899999999999999988865
No 56
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=27.94 E-value=82 Score=21.39 Aligned_cols=25 Identities=16% Similarity=0.125 Sum_probs=21.7
Q ss_pred ecCCCCHHHHHHHhCCCHHHHHHHh
Q 018429 23 VSKMDTLAGVAIKYGVEVADIKRLN 47 (356)
Q Consensus 23 VkkGDTL~~IA~KYgVsV~dIKraN 47 (356)
+..|.+...||..+||+...+.++-
T Consensus 15 ~~~g~s~~eia~~l~is~~tv~~~~ 39 (58)
T smart00421 15 LAEGLTNKEIAERLGISEKTVKTHL 39 (58)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 4578999999999999999998753
No 57
>PRK07121 hypothetical protein; Validated
Probab=27.27 E-value=48 Score=34.00 Aligned_cols=28 Identities=25% Similarity=0.304 Sum_probs=23.3
Q ss_pred ecCCCCHHHHHHHhCCCHH----HHHHHhCCC
Q 018429 23 VSKMDTLAGVAIKYGVEVA----DIKRLNGLA 50 (356)
Q Consensus 23 VkkGDTL~~IA~KYgVsV~----dIKraNnL~ 50 (356)
+.+.|||..||.+.|+..+ .|.++|.+-
T Consensus 358 ~~kadtleeLA~~~gid~~~l~~tv~~yN~~~ 389 (492)
T PRK07121 358 AWKAETVEELARKLGIPPGGLQATVDAYNRAA 389 (492)
T ss_pred ccccCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 4578999999999999988 566799653
No 58
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=26.03 E-value=55 Score=22.83 Aligned_cols=28 Identities=21% Similarity=0.326 Sum_probs=21.4
Q ss_pred ecCCC---CHHHHHHHhCCCHHHHHH-HhCCC
Q 018429 23 VSKMD---TLAGVAIKYGVEVADIKR-LNGLA 50 (356)
Q Consensus 23 VkkGD---TL~~IA~KYgVsV~dIKr-aNnL~ 50 (356)
+.+|+ |...||.+|||+...+.+ ++.|.
T Consensus 14 ~~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~ 45 (60)
T smart00345 14 LRPGDKLPSERELAAQLGVSRTTVREALSRLE 45 (60)
T ss_pred CCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 44454 788999999999988887 45554
No 59
>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=25.95 E-value=70 Score=22.35 Aligned_cols=22 Identities=23% Similarity=0.232 Sum_probs=17.7
Q ss_pred CHHHHHHHhCCCHHHHHHHhCC
Q 018429 28 TLAGVAIKYGVEVADIKRLNGL 49 (356)
Q Consensus 28 TL~~IA~KYgVsV~dIKraNnL 49 (356)
|+..+|+..||++..|+.+=..
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 5678999999999999987643
No 60
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=25.46 E-value=49 Score=24.14 Aligned_cols=18 Identities=22% Similarity=0.383 Sum_probs=15.2
Q ss_pred CHHHHHHHhCCCHHHHHH
Q 018429 28 TLAGVAIKYGVEVADIKR 45 (356)
Q Consensus 28 TL~~IA~KYgVsV~dIKr 45 (356)
++..||+++|+++.+|.+
T Consensus 5 ~V~elAk~l~v~~~~ii~ 22 (54)
T PF04760_consen 5 RVSELAKELGVPSKEIIK 22 (54)
T ss_dssp -TTHHHHHHSSSHHHHHH
T ss_pred EHHHHHHHHCcCHHHHHH
Confidence 577899999999999876
No 61
>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=25.30 E-value=76 Score=23.37 Aligned_cols=20 Identities=25% Similarity=0.317 Sum_probs=17.9
Q ss_pred CHHHHHHHhCCCHHHHHHHh
Q 018429 28 TLAGVAIKYGVEVADIKRLN 47 (356)
Q Consensus 28 TL~~IA~KYgVsV~dIKraN 47 (356)
|+..+|+++||+...|+++=
T Consensus 2 s~~eva~~~gvs~~tlr~w~ 21 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWE 21 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 57889999999999999874
No 62
>PRK12845 3-ketosteroid-delta-1-dehydrogenase; Reviewed
Probab=25.28 E-value=57 Score=34.73 Aligned_cols=28 Identities=39% Similarity=0.545 Sum_probs=22.8
Q ss_pred ecCCCCHHHHHHHhCCCHHHHH----HHhCCC
Q 018429 23 VSKMDTLAGVAIKYGVEVADIK----RLNGLA 50 (356)
Q Consensus 23 VkkGDTL~~IA~KYgVsV~dIK----raNnL~ 50 (356)
|.+.|||..||.+.||.++.|+ ++|.+-
T Consensus 421 ~~kadTleELA~k~gid~~~L~~TV~~yN~~~ 452 (564)
T PRK12845 421 AHRADSLADLARKIGVPVDTFVATMRRFNEMA 452 (564)
T ss_pred eEecCCHHHHHHHcCCCHHHHHHHHHHHHHHH
Confidence 4589999999999999987655 688654
No 63
>COG3721 HugX Putative heme iron utilization protein [Inorganic ion transport and metabolism]
Probab=25.23 E-value=74 Score=29.71 Aligned_cols=23 Identities=30% Similarity=0.341 Sum_probs=20.9
Q ss_pred cCCCCHHHHHHHhCCCHHHHHHH
Q 018429 24 SKMDTLAGVAIKYGVEVADIKRL 46 (356)
Q Consensus 24 kkGDTL~~IA~KYgVsV~dIKra 46 (356)
++.-||..||.+|+|++.+|.++
T Consensus 25 qPdg~~eamA~~~~v~~~eIv~a 47 (176)
T COG3721 25 QPDGTLEAMAEQYNVTELEIVRA 47 (176)
T ss_pred CCCCcHHHHHHHhCCCHHHHHHh
Confidence 57779999999999999999886
No 64
>PF11020 DUF2610: Domain of unknown function (DUF2610); InterPro: IPR021277 This family is conserved in Proteobacteria. One member is annotated as being elongation factor P but this could not be confirmed.
Probab=24.40 E-value=72 Score=26.64 Aligned_cols=20 Identities=15% Similarity=0.135 Sum_probs=17.6
Q ss_pred CCHHHHHHHhCCCHHHHHHH
Q 018429 27 DTLAGVAIKYGVEVADIKRL 46 (356)
Q Consensus 27 DTL~~IA~KYgVsV~dIKra 46 (356)
..|+.||+++||+.++|.-|
T Consensus 55 ~kL~~La~~N~v~feeLc~Y 74 (82)
T PF11020_consen 55 SKLYKLAKENNVSFEELCVY 74 (82)
T ss_pred HHHHHHHHHcCCCHHHHHHH
Confidence 46899999999999999865
No 65
>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=24.37 E-value=92 Score=20.65 Aligned_cols=20 Identities=25% Similarity=0.243 Sum_probs=17.7
Q ss_pred CHHHHHHHhCCCHHHHHHHh
Q 018429 28 TLAGVAIKYGVEVADIKRLN 47 (356)
Q Consensus 28 TL~~IA~KYgVsV~dIKraN 47 (356)
|+..+|..+||+...|.++=
T Consensus 2 s~~e~a~~lgvs~~tl~~~~ 21 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWV 21 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 57889999999999999873
No 66
>PHA01976 helix-turn-helix protein
Probab=24.03 E-value=49 Score=24.39 Aligned_cols=20 Identities=25% Similarity=0.245 Sum_probs=17.1
Q ss_pred CCCCHHHHHHHhCCCHHHHH
Q 018429 25 KMDTLAGVAIKYGVEVADIK 44 (356)
Q Consensus 25 kGDTL~~IA~KYgVsV~dIK 44 (356)
.-++|..||..|||+++.|.
T Consensus 43 ~~~~l~~ia~~l~v~~~~l~ 62 (67)
T PHA01976 43 NLKTLLRLADALGVTLDWLC 62 (67)
T ss_pred CHHHHHHHHHHHCcCHHHHh
Confidence 34789999999999999883
No 67
>PRK12837 3-ketosteroid-delta-1-dehydrogenase; Provisional
Probab=23.70 E-value=66 Score=33.48 Aligned_cols=28 Identities=39% Similarity=0.552 Sum_probs=22.5
Q ss_pred ecCCCCHHHHHHHhCCCHHHHH----HHhCCC
Q 018429 23 VSKMDTLAGVAIKYGVEVADIK----RLNGLA 50 (356)
Q Consensus 23 VkkGDTL~~IA~KYgVsV~dIK----raNnL~ 50 (356)
+.+.|||..||.+.||..+.|+ +||.+-
T Consensus 372 ~~kaDTleELA~k~gid~~~L~~Tv~~yN~~~ 403 (513)
T PRK12837 372 WRTADTLEELAAKIGVPADALTATVARFNGFA 403 (513)
T ss_pred eeecCCHHHHHHHcCCCHHHHHHHHHHHHHHH
Confidence 4478999999999999977655 688653
No 68
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=23.06 E-value=92 Score=24.80 Aligned_cols=23 Identities=22% Similarity=0.222 Sum_probs=20.6
Q ss_pred cCCCCHHHHHHHhCCCHHHHHHH
Q 018429 24 SKMDTLAGVAIKYGVEVADIKRL 46 (356)
Q Consensus 24 kkGDTL~~IA~KYgVsV~dIKra 46 (356)
-.|-++..||..+||+...|.+.
T Consensus 124 ~~g~s~~eIA~~l~~s~~~v~~~ 146 (158)
T TIGR02937 124 LEGLSYKEIAEILGISVGTVKRR 146 (158)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHH
Confidence 46999999999999999999864
No 69
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=22.57 E-value=42 Score=23.70 Aligned_cols=18 Identities=33% Similarity=0.444 Sum_probs=14.6
Q ss_pred CCCHHHHHHHhCCCHHHH
Q 018429 26 MDTLAGVAIKYGVEVADI 43 (356)
Q Consensus 26 GDTL~~IA~KYgVsV~dI 43 (356)
-|++..||.-|||+++.|
T Consensus 38 ~~~~~~ia~~l~~~~~~l 55 (55)
T PF01381_consen 38 LDTLKKIAKALGVSPEYL 55 (55)
T ss_dssp HHHHHHHHHHHTSEHHHH
T ss_pred HHHHHHHHHHHCCCHHHC
Confidence 467888999999988765
No 70
>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=22.53 E-value=93 Score=26.32 Aligned_cols=23 Identities=30% Similarity=0.289 Sum_probs=20.0
Q ss_pred cCCCCHHHHHHHhCCCHHHHHHH
Q 018429 24 SKMDTLAGVAIKYGVEVADIKRL 46 (356)
Q Consensus 24 kkGDTL~~IA~KYgVsV~dIKra 46 (356)
.++-||..||.+|||+...|-++
T Consensus 69 ~pd~tl~Ela~~l~Vs~~ti~~~ 91 (119)
T PF01710_consen 69 NPDATLRELAERLGVSPSTIWRA 91 (119)
T ss_pred CCCcCHHHHHHHcCCCHHHHHHH
Confidence 46889999999999999988764
No 71
>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=22.52 E-value=1.8e+02 Score=19.40 Aligned_cols=37 Identities=22% Similarity=0.118 Sum_probs=23.6
Q ss_pred CHHHHHHHhCCCHHHHHHHhCCCCCCcccCCCEEEeC
Q 018429 28 TLAGVAIKYGVEVADIKRLNGLATDLQMFALKTLHIP 64 (356)
Q Consensus 28 TL~~IA~KYgVsV~dIKraNnL~sd~~L~~GQ~L~IP 64 (356)
|+..+|..+||+...|.++=+-..-...+.|...+|+
T Consensus 3 t~~e~a~~lgis~~ti~~~~~~g~i~~~~~g~~~~~~ 39 (49)
T TIGR01764 3 TVEEAAEYLGVSKDTVYRLIHEGELPAYRVGRHYRIP 39 (49)
T ss_pred CHHHHHHHHCCCHHHHHHHHHcCCCCeEEeCCeEEEe
Confidence 6789999999999999886422110112335555554
No 72
>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=22.41 E-value=92 Score=24.39 Aligned_cols=20 Identities=30% Similarity=0.479 Sum_probs=18.3
Q ss_pred CHHHHHHHhCCCHHHHHHHh
Q 018429 28 TLAGVAIKYGVEVADIKRLN 47 (356)
Q Consensus 28 TL~~IA~KYgVsV~dIKraN 47 (356)
+|-.||.++||+...|+++=
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 78899999999999999864
No 73
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=22.10 E-value=91 Score=23.03 Aligned_cols=20 Identities=25% Similarity=0.331 Sum_probs=18.0
Q ss_pred CHHHHHHHhCCCHHHHHHHh
Q 018429 28 TLAGVAIKYGVEVADIKRLN 47 (356)
Q Consensus 28 TL~~IA~KYgVsV~dIKraN 47 (356)
|+..+|+.+||+...|+.|=
T Consensus 2 ti~eva~~~gvs~~tlr~y~ 21 (69)
T PF13411_consen 2 TIKEVAKLLGVSPSTLRYYE 21 (69)
T ss_dssp EHHHHHHHTTTTHHHHHHHH
T ss_pred cHHHHHHHHCcCHHHHHHHH
Confidence 57889999999999999984
No 74
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=21.95 E-value=84 Score=23.36 Aligned_cols=23 Identities=35% Similarity=0.575 Sum_probs=19.4
Q ss_pred CHHHHHHHhCCCHHHHHH-HhCCC
Q 018429 28 TLAGVAIKYGVEVADIKR-LNGLA 50 (356)
Q Consensus 28 TL~~IA~KYgVsV~dIKr-aNnL~ 50 (356)
|+..||..||||...|++ +|.|.
T Consensus 16 s~~ela~~~~VS~~TiRRDl~~L~ 39 (57)
T PF08220_consen 16 SVKELAEEFGVSEMTIRRDLNKLE 39 (57)
T ss_pred EHHHHHHHHCcCHHHHHHHHHHHH
Confidence 688999999999999998 55554
No 75
>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=21.12 E-value=1.1e+02 Score=20.88 Aligned_cols=20 Identities=20% Similarity=0.288 Sum_probs=17.9
Q ss_pred CHHHHHHHhCCCHHHHHHHh
Q 018429 28 TLAGVAIKYGVEVADIKRLN 47 (356)
Q Consensus 28 TL~~IA~KYgVsV~dIKraN 47 (356)
|+..+|...||++..|+.+=
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~ 21 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYE 21 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHH
Confidence 57889999999999999983
No 76
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=20.89 E-value=94 Score=25.73 Aligned_cols=26 Identities=19% Similarity=0.327 Sum_probs=23.3
Q ss_pred ecCCCCHHHHHHHhCCCHHHHHHHhC
Q 018429 23 VSKMDTLAGVAIKYGVEVADIKRLNG 48 (356)
Q Consensus 23 VkkGDTL~~IA~KYgVsV~dIKraNn 48 (356)
+..|.|...||.++||+...|.++.+
T Consensus 47 l~~G~S~~eIA~~LgISrsTIyRi~R 72 (88)
T TIGR02531 47 LKQGKTYSDIEAETGASTATISRVKR 72 (88)
T ss_pred HHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 57899999999999999999998764
No 77
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=20.80 E-value=87 Score=26.04 Aligned_cols=26 Identities=23% Similarity=0.330 Sum_probs=23.2
Q ss_pred cCCCCHHHHHHHhCCCHHHHHHHhCC
Q 018429 24 SKMDTLAGVAIKYGVEVADIKRLNGL 49 (356)
Q Consensus 24 kkGDTL~~IA~KYgVsV~dIKraNnL 49 (356)
+.|-|=-.||.++||+++.|-|.|+.
T Consensus 47 ~~g~syreIa~~tgvS~aTItRvsr~ 72 (87)
T PF01371_consen 47 DEGKSYREIAEETGVSIATITRVSRC 72 (87)
T ss_dssp HTTSSHHHHHHHHTSTHHHHHHHHHH
T ss_pred HCCCCHHHHHHHhCCCHHHHHHHHHH
Confidence 47888899999999999999998864
No 78
>COG1652 XkdP Uncharacterized protein containing LysM domain [Function unknown]
Probab=20.69 E-value=52 Score=31.36 Aligned_cols=45 Identities=7% Similarity=0.026 Sum_probs=33.5
Q ss_pred cccccCCCCCCCcc--ccccccChhHHHHHHHhC---CCCCCCCCCCCCceEEE
Q 018429 105 SLRTESSKKGSLAT--GTSQKVSSAMSNLQKYYG---LRSPNGKGKDEGTEMAV 153 (356)
Q Consensus 105 s~~vKsg~~dsLw~--gq~~kVSpaM~~L~~wnG---L~p~~~~~l~~GqeLvv 153 (356)
+|+|+.| |+||. -+.|+...--..+...|+ +.. .+.+.+||.|.|
T Consensus 212 ~~~v~rg--DTl~~is~~~Yg~~~~y~~I~~aNk~~~~~~--p~~I~pGq~l~i 261 (269)
T COG1652 212 TNTVKRG--DTLWQISKKVYGDGVEYRKIAEANKALVLDN--PDKIKPGQVLRI 261 (269)
T ss_pred EEEeccC--CcccccchhhcCcceEEEeHhhhhhhhccCC--CCcCCCcceeeC
Confidence 5899999 99999 445565444455777777 444 788999999876
No 79
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=20.44 E-value=1.2e+02 Score=21.37 Aligned_cols=26 Identities=19% Similarity=0.385 Sum_probs=20.3
Q ss_pred EEecCCCCHHHHHHHhCCCHHHHHHH
Q 018429 21 HQVSKMDTLAGVAIKYGVEVADIKRL 46 (356)
Q Consensus 21 H~VkkGDTL~~IA~KYgVsV~dIKra 46 (356)
+.+...-|+..||+.+||+...++++
T Consensus 22 ~~~~~~~s~~~vA~~~~vs~~TV~ri 47 (52)
T PF13542_consen 22 KLLRESRSFKDVARELGVSWSTVRRI 47 (52)
T ss_pred HHHhhcCCHHHHHHHHCCCHHHHHHH
Confidence 33444459999999999999988874
No 80
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=20.26 E-value=1.4e+02 Score=20.39 Aligned_cols=23 Identities=17% Similarity=0.133 Sum_probs=20.3
Q ss_pred cCCCCHHHHHHHhCCCHHHHHHH
Q 018429 24 SKMDTLAGVAIKYGVEVADIKRL 46 (356)
Q Consensus 24 kkGDTL~~IA~KYgVsV~dIKra 46 (356)
..|-+...||..+++++..++.+
T Consensus 13 ~~~~s~~eia~~l~~s~~tv~~~ 35 (57)
T cd06170 13 AEGKTNKEIADILGISEKTVKTH 35 (57)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHH
Confidence 46889999999999999998875
No 81
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=20.14 E-value=1.1e+02 Score=22.81 Aligned_cols=24 Identities=25% Similarity=0.432 Sum_probs=17.7
Q ss_pred ecCCCCH---HHHHHHhCCCHHHHHHH
Q 018429 23 VSKMDTL---AGVAIKYGVEVADIKRL 46 (356)
Q Consensus 23 VkkGDTL---~~IA~KYgVsV~dIKra 46 (356)
.++||.| ..||++|+|+...++++
T Consensus 18 ~~~g~~lps~~~la~~~~vsr~tvr~a 44 (64)
T PF00392_consen 18 LPPGDRLPSERELAERYGVSRTTVREA 44 (64)
T ss_dssp S-TTSBE--HHHHHHHHTS-HHHHHHH
T ss_pred CCCCCEeCCHHHHHHHhccCCcHHHHH
Confidence 4556655 88999999999988874
No 82
>PF08299 Bac_DnaA_C: Bacterial dnaA protein helix-turn-helix; InterPro: IPR013159 This entry represents the C-terminal domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; GO: 0005524 ATP binding, 0043565 sequence-specific DNA binding, 0006270 DNA-dependent DNA replication initiation, 0006275 regulation of DNA replication; PDB: 2HCB_B 3R8F_C 1L8Q_A 3PVP_B 3PVV_A 1J1V_A.
Probab=20.02 E-value=87 Score=24.34 Aligned_cols=18 Identities=39% Similarity=0.623 Sum_probs=13.3
Q ss_pred CHHHHHHHhCCCHHHHHH
Q 018429 28 TLAGVAIKYGVEVADIKR 45 (356)
Q Consensus 28 TL~~IA~KYgVsV~dIKr 45 (356)
-+..+|..|||++++|..
T Consensus 5 Ii~~Va~~~~v~~~~i~s 22 (70)
T PF08299_consen 5 IIEAVAEYFGVSVEDIRS 22 (70)
T ss_dssp HHHHHHHHTT--HHHHHS
T ss_pred HHHHHHHHHCCCHHHHhC
Confidence 467899999999999973
Done!