Query 038519
Match_columns 324
No_of_seqs 275 out of 1370
Neff 4.3
Searched_HMMs 46136
Date Fri Mar 29 11:54:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038519.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038519hhsearch_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 1.6E-15 3.4E-20 157.0 9.4 113 29-157 478-591 (592)
2 PRK10783 mltD membrane-bound l 99.5 1.6E-14 3.5E-19 145.4 9.7 110 29-162 342-451 (456)
3 PRK06347 autolysin; Reviewed 99.5 1.4E-13 3.1E-18 142.6 9.7 124 28-161 403-527 (592)
4 PF01476 LysM: LysM domain; I 99.4 6E-13 1.3E-17 91.8 3.9 43 33-76 1-44 (44)
5 PRK13914 invasion associated s 99.3 1.8E-11 3.9E-16 124.2 10.2 51 28-79 25-75 (481)
6 PRK14125 cell division suppres 99.2 6.7E-11 1.5E-15 98.1 7.4 55 26-81 32-94 (103)
7 TIGR02899 spore_safA spore coa 99.1 1.7E-10 3.8E-15 77.9 5.2 43 35-77 1-44 (44)
8 cd00118 LysM Lysin domain, fou 99.1 3.9E-10 8.5E-15 73.8 6.1 45 32-76 2-46 (46)
9 PRK10871 nlpD lipoprotein NlpD 98.9 1.3E-09 2.7E-14 106.2 6.6 50 30-79 60-109 (319)
10 TIGR02907 spore_VI_D stage VI 98.9 1.3E-09 2.9E-14 106.4 6.6 48 28-76 291-338 (338)
11 PRK10783 mltD membrane-bound l 98.8 6.1E-09 1.3E-13 105.4 7.3 53 29-82 401-453 (456)
12 COG1388 LytE FOG: LysM repeat 98.8 1.1E-08 2.3E-13 84.8 6.4 51 30-81 66-116 (124)
13 smart00257 LysM Lysin motif. 98.8 1.7E-08 3.7E-13 65.2 5.5 44 32-75 1-44 (44)
14 PRK13914 invasion associated s 98.6 7.8E-08 1.7E-12 98.1 7.6 52 28-80 197-248 (481)
15 PRK11198 LysM domain/BON super 98.6 8.1E-08 1.7E-12 83.6 5.9 49 29-77 94-147 (147)
16 COG1388 LytE FOG: LysM repeat 98.3 6.6E-07 1.4E-11 74.1 4.9 109 44-159 1-112 (124)
17 PF04225 OapA: Opacity-associa 97.4 0.0001 2.2E-09 59.2 2.7 51 29-79 1-55 (85)
18 PRK10190 L,D-transpeptidase; P 97.3 0.00081 1.8E-08 65.9 7.9 54 30-83 37-92 (310)
19 PRK10260 L,D-transpeptidase; P 97.3 0.00093 2E-08 65.4 8.1 54 30-83 40-95 (306)
20 TIGR03505 FimV_core FimV N-ter 97.2 0.0003 6.6E-09 55.5 3.6 41 39-79 1-53 (74)
21 COG1652 XkdP Uncharacterized p 97.2 0.00011 2.5E-09 68.9 1.2 49 31-79 211-265 (269)
22 PF01476 LysM: LysM domain; I 96.9 0.00018 4E-09 49.3 -0.8 42 110-157 1-43 (44)
23 COG3858 Predicted glycosyl hyd 96.7 0.00081 1.8E-08 68.1 2.5 78 30-139 1-78 (423)
24 COG3858 Predicted glycosyl hyd 95.9 0.0093 2E-07 60.6 4.6 54 28-81 47-100 (423)
25 KOG2850 Predicted peptidoglyca 95.3 0.01 2.2E-07 54.5 2.3 53 28-80 7-59 (186)
26 PRK11649 putative peptidase; P 95.3 0.031 6.8E-07 57.0 5.9 52 28-79 93-145 (439)
27 TIGR02899 spore_safA spore coa 95.2 0.0085 1.8E-07 40.0 1.2 41 112-157 1-42 (44)
28 PRK10871 nlpD lipoprotein NlpD 94.7 0.015 3.2E-07 57.4 1.7 49 107-160 60-108 (319)
29 cd00118 LysM Lysin domain, fou 94.7 0.014 3.1E-07 37.4 1.1 43 110-157 3-45 (46)
30 PRK14125 cell division suppres 93.7 0.045 9.7E-07 45.7 2.3 51 109-163 38-94 (103)
31 TIGR02907 spore_VI_D stage VI 93.5 0.032 6.9E-07 55.4 1.2 46 106-157 292-337 (338)
32 PF05489 Phage_tail_X: Phage T 92.8 0.32 6.9E-06 36.9 5.5 48 31-79 2-55 (60)
33 smart00257 LysM Lysin motif. 92.2 0.068 1.5E-06 33.7 1.0 41 111-156 3-43 (44)
34 COG3061 OapA Cell envelope opa 90.7 0.39 8.5E-06 45.6 4.8 53 29-81 158-214 (242)
35 COG0739 NlpD Membrane proteins 90.0 0.54 1.2E-05 42.9 5.1 49 31-79 2-50 (277)
36 PRK11198 LysM domain/BON super 87.2 0.28 6.1E-06 42.8 1.2 48 107-157 95-145 (147)
37 COG3170 FimV Tfp pilus assembl 86.9 0.46 1E-05 51.5 2.8 52 28-79 186-249 (755)
38 PF13518 HTH_28: Helix-turn-he 76.3 2.6 5.6E-05 29.3 2.5 25 36-60 10-34 (52)
39 COG4784 Putative Zn-dependent 72.1 6.2 0.00013 40.3 4.9 47 30-76 428-477 (479)
40 PF01527 HTH_Tnp_1: Transposas 67.1 4.2 9E-05 30.5 2.0 25 35-59 20-44 (76)
41 COG4254 Uncharacterized protei 66.7 4.9 0.00011 40.0 2.8 50 31-80 6-58 (339)
42 PF02796 HTH_7: Helix-turn-hel 65.8 6.5 0.00014 27.6 2.6 24 35-58 18-41 (45)
43 PF13384 HTH_23: Homeodomain-l 56.8 13 0.00027 25.8 2.8 25 36-60 15-39 (50)
44 PRK09413 IS2 repressor TnpA; R 53.3 14 0.00031 30.9 3.0 28 32-59 23-50 (121)
45 PF04921 XAP5: XAP5, circadian 47.2 22 0.00047 34.2 3.6 60 19-79 102-162 (239)
46 PF04218 CENP-B_N: CENP-B N-te 46.7 9.1 0.0002 28.0 0.8 24 35-58 19-42 (53)
47 COG2963 Transposase and inacti 44.7 22 0.00048 29.0 2.9 26 33-58 19-45 (116)
48 PHA00675 hypothetical protein 44.2 23 0.0005 28.8 2.7 25 36-60 37-61 (78)
49 cd00569 HTH_Hin_like Helix-tur 43.8 36 0.00077 19.8 3.1 24 35-58 18-41 (42)
50 PF04545 Sigma70_r4: Sigma-70, 42.8 34 0.00073 23.9 3.2 23 36-58 18-40 (50)
51 PF05225 HTH_psq: helix-turn-h 41.4 23 0.0005 25.2 2.1 24 35-58 12-36 (45)
52 PF13936 HTH_38: Helix-turn-he 40.7 32 0.0007 24.0 2.8 24 35-58 17-40 (44)
53 PF08765 Mor: Mor transcriptio 38.9 30 0.00065 28.5 2.8 21 38-58 72-92 (108)
54 PF10668 Phage_terminase: Phag 36.7 37 0.00081 26.1 2.8 22 39-60 23-44 (60)
55 COG1652 XkdP Uncharacterized p 35.4 15 0.00033 34.6 0.6 47 109-157 212-261 (269)
56 cd04762 HTH_MerR-trunc Helix-T 33.9 50 0.0011 21.7 2.8 20 40-59 2-21 (49)
57 cd01104 HTH_MlrA-CarA Helix-Tu 31.8 50 0.0011 24.0 2.8 20 40-59 2-21 (68)
58 PHA01976 helix-turn-helix prot 31.2 32 0.0007 25.0 1.7 20 37-56 43-62 (67)
59 PF12471 GTP_CH_N: GTP cyclohy 30.1 69 0.0015 30.0 3.9 43 16-58 148-190 (194)
60 TIGR01764 excise DNA binding d 29.5 1E+02 0.0022 20.4 3.8 21 40-60 3-23 (49)
61 PF01381 HTH_3: Helix-turn-hel 29.0 28 0.00061 24.3 1.0 19 37-55 37-55 (55)
62 cd04761 HTH_MerR-SF Helix-Turn 28.3 68 0.0015 21.7 2.8 20 40-59 2-21 (49)
63 smart00421 HTH_LUXR helix_turn 28.3 81 0.0017 21.1 3.2 25 35-59 15-39 (58)
64 PF01710 HTH_Tnp_IS630: Transp 28.1 66 0.0014 26.9 3.2 24 36-59 69-92 (119)
65 PF01371 Trp_repressor: Trp re 28.1 63 0.0014 26.4 2.9 25 36-60 47-71 (87)
66 PF04255 DUF433: Protein of un 27.8 57 0.0012 24.0 2.4 24 35-58 28-52 (56)
67 PF00376 MerR: MerR family reg 27.7 66 0.0014 22.1 2.6 22 40-61 1-22 (38)
68 PF04760 IF2_N: Translation in 27.6 43 0.00093 24.1 1.7 19 40-58 5-23 (54)
69 PF01710 HTH_Tnp_IS630: Transp 26.4 44 0.00096 27.9 1.9 26 35-60 15-40 (119)
70 PF13411 MerR_1: MerR HTH fami 25.9 71 0.0015 23.3 2.7 21 40-60 2-22 (69)
71 PF11020 DUF2610: Domain of un 25.9 66 0.0014 26.4 2.6 22 37-58 53-74 (82)
72 KOG2850 Predicted peptidoglyca 25.8 23 0.00051 32.8 0.1 55 27-81 116-177 (186)
73 smart00422 HTH_MERR helix_turn 24.7 80 0.0017 22.9 2.8 20 40-59 2-21 (70)
74 COG5484 Uncharacterized conser 24.7 60 0.0013 31.9 2.6 23 38-60 19-41 (279)
75 PF13551 HTH_29: Winged helix- 24.5 71 0.0015 25.0 2.6 26 35-60 8-34 (112)
76 TIGR02937 sigma70-ECF RNA poly 23.3 91 0.002 24.6 3.1 23 36-58 124-146 (158)
77 TIGR02531 yecD_yerC TrpR-relat 22.9 77 0.0017 25.8 2.6 26 35-60 47-72 (88)
78 PF11268 DUF3071: Protein of u 22.8 64 0.0014 29.4 2.3 49 32-80 63-112 (170)
79 PF13542 HTH_Tnp_ISL3: Helix-t 22.8 99 0.0022 21.4 2.8 24 35-58 24-47 (52)
80 PF13443 HTH_26: Cro/C1-type H 21.3 38 0.00083 24.3 0.5 22 37-58 39-60 (63)
81 PF12964 DUF3853: Protein of u 21.3 66 0.0014 27.1 1.9 36 41-76 48-85 (96)
82 PF13693 HTH_35: Winged helix- 20.7 96 0.0021 25.0 2.6 23 36-58 13-35 (78)
83 cd04764 HTH_MlrA-like_sg1 Heli 20.3 1.1E+02 0.0024 22.4 2.8 20 40-59 2-21 (67)
No 1
>PRK06347 autolysin; Reviewed
Probab=99.61 E-value=1.6e-15 Score=157.05 Aligned_cols=113 Identities=19% Similarity=0.224 Sum_probs=87.8
Q ss_pred ceEEEEecCCCcHHHHHHHhCCCHHHHHHHcCCCCCCCCCCCCEEEeCCCCCCCCCCCCCCCcccccccccccCC-CCcc
Q 038519 29 GIIEHQVSKLDTLAGIAIKYGVDVADIRKLNGLSTDLQMFALKTLQIPLPGKHPPSPCLSNGYETRGQANHERTP-DHHV 107 (324)
Q Consensus 29 ~~~~h~Vq~GDTL~~IA~KYgVsV~eI~~~N~L~~~~~L~~GQ~L~IP~~~~~~~s~~~sngs~~r~~~~~~~ap-~~~~ 107 (324)
....|+|++|||||.||++|||++++|++||+|.. +.|++||.|.||............ .... .+ ....
T Consensus 478 ~~~~YtVk~GDTL~sIAkkygVSv~~L~~~N~l~s-~~L~~GQ~L~Ip~~~~~s~~~t~~--~s~~-------~~~~~~~ 547 (592)
T PRK06347 478 NAKVYTVAKGDSLWRIANNNKVTIANLKSWNNLKS-DFIYPGQKLKVSAGSTTNNTNTAK--PSTN-------KPSNSTV 547 (592)
T ss_pred cceeeeecCCCCHHHHHHHHCCCHHHHHHhcCCCc-ccccCCcEEEEecCcccccccccC--CccC-------CccCccc
Confidence 35689999999999999999999999999999975 589999999999864322111000 0000 00 1123
Q ss_pred cccccccccccccCCCCCcccChhHHHHhhhhCCCCCCCCCCCCCceeEE
Q 038519 108 QHDLFDSFRSLRLKSKPQWKVSPAMNSLQGYYGLKPTGQRPPSEGCEMAV 157 (324)
Q Consensus 108 ~~~vv~sgdSl~~~s~~~~~vS~Am~~Lq~wyGL~P~~~~~l~~G~elvv 157 (324)
..+.|++||+||.|++ +++|+ +..|..||+|.+ +.|++||.|.|
T Consensus 548 ~~Y~Vk~GDTL~sIA~-KygvS--v~~L~~~N~L~~---~~L~~GQ~L~I 591 (592)
T PRK06347 548 KTYTVKKGDSLWAISR-QYKTT--VDNIKAWNKLTS---NMIHVGQKLTI 591 (592)
T ss_pred eeeecCCCCcHHHHHH-HhCCC--HHHHHHhcCCCc---ccCCCCCEEec
Confidence 4567799999999999 99999 999999999984 45999999976
No 2
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional
Probab=99.54 E-value=1.6e-14 Score=145.44 Aligned_cols=110 Identities=19% Similarity=0.176 Sum_probs=90.8
Q ss_pred ceEEEEecCCCcHHHHHHHhCCCHHHHHHHcCCCCCCCCCCCCEEEeCCCCCCCCCCCCCCCcccccccccccCCCCccc
Q 038519 29 GIIEHQVSKLDTLAGIAIKYGVDVADIRKLNGLSTDLQMFALKTLQIPLPGKHPPSPCLSNGYETRGQANHERTPDHHVQ 108 (324)
Q Consensus 29 ~~~~h~Vq~GDTL~~IA~KYgVsV~eI~~~N~L~~~~~L~~GQ~L~IP~~~~~~~s~~~sngs~~r~~~~~~~ap~~~~~ 108 (324)
.+..|+|++|||||.||++|||++.+|++||++.. +.|.+||.|.||........ .+.....
T Consensus 342 ~~~~y~Vk~GDTL~sIA~r~gvs~~~L~~~N~l~~-~~L~~Gq~L~Ip~~~~~~~~-----------------~~~~~~~ 403 (456)
T PRK10783 342 NSRSYKVRSGDTLSGIASRLNVSTKDLQQWNNLRG-SKLKVGQTLTIGAGSSAQRL-----------------ANNSDSI 403 (456)
T ss_pred CceEEEECCCCcHHHHHHHHCcCHHHHHHHcCCCc-ccCCCCCEEEecCCcccccc-----------------cccccce
Confidence 46789999999999999999999999999999977 78999999999975322110 0011223
Q ss_pred ccccccccccccCCCCCcccChhHHHHhhhhCCCCCCCCCCCCCceeEEEecCc
Q 038519 109 HDLFDSFRSLRLKSKPQWKVSPAMNSLQGYYGLKPTGQRPPSEGCEMAVFRKRE 162 (324)
Q Consensus 109 ~~vv~sgdSl~~~s~~~~~vS~Am~~Lq~wyGL~P~~~~~l~~G~elvv~~k~~ 162 (324)
.++|++|||||.|+. +++|+ +..|.+||++... .|.+|++|.||.+..
T Consensus 404 ~Y~Vr~GDTL~sIA~-kygVt--v~~L~~~N~l~~~---~L~pGq~L~l~v~~~ 451 (456)
T PRK10783 404 TYRVRKGDSLSSIAK-RHGVN--IKDVMRWNSDTAK---NLQPGDKLTLFVKNN 451 (456)
T ss_pred eEEeCCCCCHHHHHH-HhCCC--HHHHHHhcCCCCC---cCCCCCEEEEecCCC
Confidence 567799999999999 99999 9999999998732 799999999998763
No 3
>PRK06347 autolysin; Reviewed
Probab=99.46 E-value=1.4e-13 Score=142.64 Aligned_cols=124 Identities=18% Similarity=0.144 Sum_probs=91.0
Q ss_pred cceEEEEecCCCcHHHHHHHhCCCHHHHHHHcCCCCCCCCCCCCEEEeCCCCCCCCCCC-CCCCcccccccccccCCCCc
Q 038519 28 RGIIEHQVSKLDTLAGIAIKYGVDVADIRKLNGLSTDLQMFALKTLQIPLPGKHPPSPC-LSNGYETRGQANHERTPDHH 106 (324)
Q Consensus 28 ~~~~~h~Vq~GDTL~~IA~KYgVsV~eI~~~N~L~~~~~L~~GQ~L~IP~~~~~~~s~~-~sngs~~r~~~~~~~ap~~~ 106 (324)
..+..|+|++|||||.||++|||++++|++||+|.. +.|++||.|.||.......... ........ .........
T Consensus 403 ~~~~~ytVk~GDTL~sIA~kygVSv~~L~~~N~l~s-~~L~~Gq~L~IP~~~~~~~~t~~~s~~~~~~---k~~s~~~~~ 478 (592)
T PRK06347 403 TNAKVYTVVKGDSLWRIANNNKVTIANLKSWNNLKS-DFIYPGQKLKVSAGSTSNTNTSKPSTNTNTS---KPSTNTNTN 478 (592)
T ss_pred cCceeEEecCCCCHHHHHHHhCCCHHHHHHHhCCCc-ceeccCcEEEEecCCcccccccccccccccc---ccccccccc
Confidence 346789999999999999999999999999999976 5799999999997643211100 00000000 000001112
Q ss_pred ccccccccccccccCCCCCcccChhHHHHhhhhCCCCCCCCCCCCCceeEEEecC
Q 038519 107 VQHDLFDSFRSLRLKSKPQWKVSPAMNSLQGYYGLKPTGQRPPSEGCEMAVFRKR 161 (324)
Q Consensus 107 ~~~~vv~sgdSl~~~s~~~~~vS~Am~~Lq~wyGL~P~~~~~l~~G~elvv~~k~ 161 (324)
...+.|+.||+||.|++ +++|+ |..|+.||+|.. +.|++|+.|.|+...
T Consensus 479 ~~~YtVk~GDTL~sIAk-kygVS--v~~L~~~N~l~s---~~L~~GQ~L~Ip~~~ 527 (592)
T PRK06347 479 AKVYTVAKGDSLWRIAN-NNKVT--IANLKSWNNLKS---DFIYPGQKLKVSAGS 527 (592)
T ss_pred ceeeeecCCCCHHHHHH-HHCCC--HHHHHHhcCCCc---ccccCCcEEEEecCc
Confidence 23456699999999999 99999 999999999973 469999999998754
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=99.36 E-value=6e-13 Score=91.78 Aligned_cols=43 Identities=35% Similarity=0.490 Sum_probs=36.5
Q ss_pred EEecCCCcHHHHHHHhCCCHHHHHHHc-CCCCCCCCCCCCEEEeC
Q 038519 33 HQVSKLDTLAGIAIKYGVDVADIRKLN-GLSTDLQMFALKTLQIP 76 (324)
Q Consensus 33 h~Vq~GDTL~~IA~KYgVsV~eI~~~N-~L~~~~~L~~GQ~L~IP 76 (324)
|+|++|||||.||++|++++++|+++| ++..+. |++||.|.||
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 776655 9999999998
No 5
>PRK13914 invasion associated secreted endopeptidase; Provisional
Probab=99.26 E-value=1.8e-11 Score=124.24 Aligned_cols=51 Identities=31% Similarity=0.275 Sum_probs=46.2
Q ss_pred cceEEEEecCCCcHHHHHHHhCCCHHHHHHHcCCCCCCCCCCCCEEEeCCCC
Q 038519 28 RGIIEHQVSKLDTLAGIAIKYGVDVADIRKLNGLSTDLQMFALKTLQIPLPG 79 (324)
Q Consensus 28 ~~~~~h~Vq~GDTL~~IA~KYgVsV~eI~~~N~L~~~~~L~~GQ~L~IP~~~ 79 (324)
..+..|+|++|||||.||++||+++++|+++|+|.. +.|++||.|+||...
T Consensus 25 asa~tytVq~GDTLw~IA~~ygvtv~~I~~~N~l~~-~~I~~Gq~L~Ip~~~ 75 (481)
T PRK13914 25 ASASTVVVEAGDTLWGIAQSKGTTVDAIKKANNLTT-DKIVPGQKLQVNEVA 75 (481)
T ss_pred ccCceEEECCCCCHHHHHHHHCCCHHHHHHHhCCCc-ccccCCCEEEeCCCC
Confidence 456789999999999999999999999999999965 689999999999653
No 6
>PRK14125 cell division suppressor protein YneA; Provisional
Probab=99.17 E-value=6.7e-11 Score=98.08 Aligned_cols=55 Identities=24% Similarity=0.298 Sum_probs=48.9
Q ss_pred CCcceEEEEecCCCcHHHHHHHhCCC--------HHHHHHHcCCCCCCCCCCCCEEEeCCCCCC
Q 038519 26 GRRGIIEHQVSKLDTLAGIAIKYGVD--------VADIRKLNGLSTDLQMFALKTLQIPLPGKH 81 (324)
Q Consensus 26 ~~~~~~~h~Vq~GDTL~~IA~KYgVs--------V~eI~~~N~L~~~~~L~~GQ~L~IP~~~~~ 81 (324)
....|..|+|++|||||+||++|+++ +.+|++.|++.++ .|++||+|+||....+
T Consensus 32 ~~~~~~~~tV~~GDTLW~IA~~y~~~~~l~~~~~v~~I~~~N~l~~~-~I~~Gq~L~IP~~~~~ 94 (103)
T PRK14125 32 DKNQYVEITVQEGDTLWALADQYAGKHHMAKNEFIEWVEDVNNLPSG-HIKAGDKLVIPVLKSK 94 (103)
T ss_pred CCCCcEEEEECCCCCHHHHHHHhCCCcCCCHHHHHHHHHHhcCCCCC-cCCCCCEEEEecCCCC
Confidence 34678999999999999999999876 6888999999775 7999999999988776
No 7
>TIGR02899 spore_safA spore coat assembly protein SafA. in which one of which is found in most examples of endospore-forming bacteria. Lysin motifs are repeated in many proteins.
Probab=99.09 E-value=1.7e-10 Score=77.91 Aligned_cols=43 Identities=40% Similarity=0.479 Sum_probs=38.9
Q ss_pred ecCCCcHHHHHHHhCCCHHHHHHHcC-CCCCCCCCCCCEEEeCC
Q 038519 35 VSKLDTLAGIAIKYGVDVADIRKLNG-LSTDLQMFALKTLQIPL 77 (324)
Q Consensus 35 Vq~GDTL~~IA~KYgVsV~eI~~~N~-L~~~~~L~~GQ~L~IP~ 77 (324)
|++|||||.||++|++++++|.++|+ +..+..|++||.|.||.
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 44557899999999984
No 8
>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=99.07 E-value=3.9e-10 Score=73.83 Aligned_cols=45 Identities=42% Similarity=0.586 Sum_probs=42.6
Q ss_pred EEEecCCCcHHHHHHHhCCCHHHHHHHcCCCCCCCCCCCCEEEeC
Q 038519 32 EHQVSKLDTLAGIAIKYGVDVADIRKLNGLSTDLQMFALKTLQIP 76 (324)
Q Consensus 32 ~h~Vq~GDTL~~IA~KYgVsV~eI~~~N~L~~~~~L~~GQ~L~IP 76 (324)
.|+|++|||+|.||.+|++++.+|.++|++.....|.+|+.|.||
T Consensus 2 ~~~v~~gdt~~~ia~~~~~~~~~~~~~N~~~~~~~~~~g~~l~ip 46 (46)
T cd00118 2 TYTVKKGDTLSSIAQRYGISVEELLKLNGLSDPDNLQVGQKLKIP 46 (46)
T ss_pred EEEECCCCCHHHHHHHHCcCHHHHHHHcCCCCccccCCCCEEecC
Confidence 689999999999999999999999999999667899999999997
No 9
>PRK10871 nlpD lipoprotein NlpD; Provisional
Probab=98.94 E-value=1.3e-09 Score=106.23 Aligned_cols=50 Identities=28% Similarity=0.179 Sum_probs=47.0
Q ss_pred eEEEEecCCCcHHHHHHHhCCCHHHHHHHcCCCCCCCCCCCCEEEeCCCC
Q 038519 30 IIEHQVSKLDTLAGIAIKYGVDVADIRKLNGLSTDLQMFALKTLQIPLPG 79 (324)
Q Consensus 30 ~~~h~Vq~GDTL~~IA~KYgVsV~eI~~~N~L~~~~~L~~GQ~L~IP~~~ 79 (324)
...|+|++|||||.||.+||+++.+|.+||+|.+++.|++||+|+||...
T Consensus 60 ~~~y~Vk~GDTL~~IA~~~g~~~~~La~~N~l~~p~~I~~GQ~L~i~~~~ 109 (319)
T PRK10871 60 GSTYTVKKGDTLFYIAWITGNDFRDLAQRNNIQAPYSLNVGQTLQVGNAS 109 (319)
T ss_pred CCceEECCCCHHHHHHHHHCcCHHHHHHhcCCCCCccccCCCEEEeCCCC
Confidence 45799999999999999999999999999999999999999999998764
No 10
>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=98.93 E-value=1.3e-09 Score=106.36 Aligned_cols=48 Identities=27% Similarity=0.356 Sum_probs=45.8
Q ss_pred cceEEEEecCCCcHHHHHHHhCCCHHHHHHHcCCCCCCCCCCCCEEEeC
Q 038519 28 RGIIEHQVSKLDTLAGIAIKYGVDVADIRKLNGLSTDLQMFALKTLQIP 76 (324)
Q Consensus 28 ~~~~~h~Vq~GDTL~~IA~KYgVsV~eI~~~N~L~~~~~L~~GQ~L~IP 76 (324)
+.|..|+|++|||||.||++|||++.+|+++|+|. ++.|++||+|+||
T Consensus 291 ~~~~~YiVq~GDTL~sIAkRYGVSV~~L~r~N~L~-~~~L~~GQ~L~IP 338 (338)
T TIGR02907 291 TKLRMCIVQEGDTIETIAERYEISVSQLIRHNQLE-DFEVNEGQILYIP 338 (338)
T ss_pred cccEEEEECCCCCHHHHHHHHCcCHHHHHHHhCCC-ccccCCCCEEEeC
Confidence 57899999999999999999999999999999997 6899999999998
No 11
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional
Probab=98.83 E-value=6.1e-09 Score=105.41 Aligned_cols=53 Identities=23% Similarity=0.307 Sum_probs=47.9
Q ss_pred ceEEEEecCCCcHHHHHHHhCCCHHHHHHHcCCCCCCCCCCCCEEEeCCCCCCC
Q 038519 29 GIIEHQVSKLDTLAGIAIKYGVDVADIRKLNGLSTDLQMFALKTLQIPLPGKHP 82 (324)
Q Consensus 29 ~~~~h~Vq~GDTL~~IA~KYgVsV~eI~~~N~L~~~~~L~~GQ~L~IP~~~~~~ 82 (324)
....|+|++|||||+||++|||++++|++||++... .|++||+|.|++.....
T Consensus 401 ~~~~Y~Vr~GDTL~sIA~kygVtv~~L~~~N~l~~~-~L~pGq~L~l~v~~~~~ 453 (456)
T PRK10783 401 DSITYRVRKGDSLSSIAKRHGVNIKDVMRWNSDTAK-NLQPGDKLTLFVKNNST 453 (456)
T ss_pred cceeEEeCCCCCHHHHHHHhCCCHHHHHHhcCCCCC-cCCCCCEEEEecCCCCC
Confidence 457899999999999999999999999999998776 89999999999876543
No 12
>COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane]
Probab=98.79 E-value=1.1e-08 Score=84.80 Aligned_cols=51 Identities=39% Similarity=0.617 Sum_probs=46.4
Q ss_pred eEEEEecCCCcHHHHHHHhCCCHHHHHHHcCCCCCCCCCCCCEEEeCCCCCC
Q 038519 30 IIEHQVSKLDTLAGIAIKYGVDVADIRKLNGLSTDLQMFALKTLQIPLPGKH 81 (324)
Q Consensus 30 ~~~h~Vq~GDTL~~IA~KYgVsV~eI~~~N~L~~~~~L~~GQ~L~IP~~~~~ 81 (324)
...|+|++||||+.||++|++++.+|+++|++.++ .|++||.|.||.....
T Consensus 66 ~~~~~V~~gdtL~~Ia~~~~~tv~~l~~~n~l~~~-~i~~gq~l~~~~~~~~ 116 (124)
T COG1388 66 VVTYTVKKGDTLSKIARKYGVTVAELKQLNNLSSD-KIKVGQKLKLPVSSSA 116 (124)
T ss_pred CceEEEecCCCHHHHHHHhCCCHHHHHHHhccCCC-ceecCcEEEEeccccc
Confidence 46899999999999999999999999999999886 9999999999984433
No 13
>smart00257 LysM Lysin motif.
Probab=98.77 E-value=1.7e-08 Score=65.18 Aligned_cols=44 Identities=34% Similarity=0.458 Sum_probs=40.0
Q ss_pred EEEecCCCcHHHHHHHhCCCHHHHHHHcCCCCCCCCCCCCEEEe
Q 038519 32 EHQVSKLDTLAGIAIKYGVDVADIRKLNGLSTDLQMFALKTLQI 75 (324)
Q Consensus 32 ~h~Vq~GDTL~~IA~KYgVsV~eI~~~N~L~~~~~L~~GQ~L~I 75 (324)
.|+|++|||+|.||.+|+++..+|.++|+......+.+|+.|.|
T Consensus 1 ~~~v~~gdt~~~ia~~~~~~~~~~~~~N~~~~~~~~~~g~~l~i 44 (44)
T smart00257 1 TYTVKKGDTLSSIARRYGISVSDLLELNNILDPDNLQVGQKLKI 44 (44)
T ss_pred CeEeCCCCCHHHHHHHhCCCHHHHHHHcCCCCccccCCCCEEeC
Confidence 38999999999999999999999999999666678999999875
No 14
>PRK13914 invasion associated secreted endopeptidase; Provisional
Probab=98.61 E-value=7.8e-08 Score=98.13 Aligned_cols=52 Identities=31% Similarity=0.464 Sum_probs=47.3
Q ss_pred cceEEEEecCCCcHHHHHHHhCCCHHHHHHHcCCCCCCCCCCCCEEEeCCCCC
Q 038519 28 RGIIEHQVSKLDTLAGIAIKYGVDVADIRKLNGLSTDLQMFALKTLQIPLPGK 80 (324)
Q Consensus 28 ~~~~~h~Vq~GDTL~~IA~KYgVsV~eI~~~N~L~~~~~L~~GQ~L~IP~~~~ 80 (324)
..+..|+|++|||||.||++|||++++|++||+|.. ..|++||.|.||....
T Consensus 197 ~~a~tytVq~GDTL~sIAkrYgVtv~eI~~~N~l~s-~~L~pGQ~L~Ip~sa~ 248 (481)
T PRK13914 197 QNATTHAVKSGDTIWALSVKYGVSVQDIMSWNNLSS-SSIYVGQKLAIKQTAN 248 (481)
T ss_pred CCCeEEEECCCCCHHHHHHHHCCCHHHHHHhcCCCc-cccCCCCEEEecCCCC
Confidence 457899999999999999999999999999999976 5799999999997643
No 15
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=98.58 E-value=8.1e-08 Score=83.62 Aligned_cols=49 Identities=27% Similarity=0.181 Sum_probs=43.5
Q ss_pred ceEEEEecCCCcHHHHHHHhC---CCHHHHHHHcC--CCCCCCCCCCCEEEeCC
Q 038519 29 GIIEHQVSKLDTLAGIAIKYG---VDVADIRKLNG--LSTDLQMFALKTLQIPL 77 (324)
Q Consensus 29 ~~~~h~Vq~GDTL~~IA~KYg---VsV~eI~~~N~--L~~~~~L~~GQ~L~IP~ 77 (324)
....|+|++|||||.||++|+ ..+.+|.++|+ +.+++.|++||+|.||.
T Consensus 94 ~~~~y~Vk~GDTL~~IA~~~~g~~~~~~~I~~~N~~~l~~~~~I~pGq~L~IP~ 147 (147)
T PRK11198 94 ESQFYTVKSGDTLSAIAKKVYGNANKYNKIFEANKPMLKSPDKIYPGQVLRIPE 147 (147)
T ss_pred CCeEEEECCCCCHHHHHHHHcCChhhHHHHHHhhhhcCCCcCCcCcCCEEecCC
Confidence 557899999999999999985 45789999998 88888999999999983
No 16
>COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane]
Probab=98.33 E-value=6.6e-07 Score=74.07 Aligned_cols=109 Identities=19% Similarity=0.179 Sum_probs=75.8
Q ss_pred HHHHhCCCHHHHHHHcCCCC-CCCCCCCCEEEeCCCCCCCC--CCCCCCCcccccccccccCCCCccccccccccccccc
Q 038519 44 IAIKYGVDVADIRKLNGLST-DLQMFALKTLQIPLPGKHPP--SPCLSNGYETRGQANHERTPDHHVQHDLFDSFRSLRL 120 (324)
Q Consensus 44 IA~KYgVsV~eI~~~N~L~~-~~~L~~GQ~L~IP~~~~~~~--s~~~sngs~~r~~~~~~~ap~~~~~~~vv~sgdSl~~ 120 (324)
||.+|++++++|+++|.+.. .+.+++||.|.+|....... .......+.......... .......+.+..||+||-
T Consensus 1 ia~~~~~~v~~l~~~n~~~~~s~~i~~gq~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~V~~gdtL~~ 79 (124)
T COG1388 1 IASKYGVSVKALKKANALTGKSDAIKPGQVLKIPGDISSTVNAGQTLSSLSNKVSDSSSAS-KAPPVVTYTVKKGDTLSK 79 (124)
T ss_pred CcccccccHHHHHHHhcccCCCCccccCceEEccCCcccccccccccccccceeecccccc-ccCCCceEEEecCCCHHH
Confidence 68999999999999999873 57899999999997522221 111111111110000000 001123456799999999
Q ss_pred CCCCCcccChhHHHHhhhhCCCCCCCCCCCCCceeEEEe
Q 038519 121 KSKPQWKVSPAMNSLQGYYGLKPTGQRPPSEGCEMAVFR 159 (324)
Q Consensus 121 ~s~~~~~vS~Am~~Lq~wyGL~P~~~~~l~~G~elvv~~ 159 (324)
+++ ++.++ +..|..||.+.. +.+..|+.+.+-.
T Consensus 80 Ia~-~~~~t--v~~l~~~n~l~~---~~i~~gq~l~~~~ 112 (124)
T COG1388 80 IAR-KYGVT--VAELKQLNNLSS---DKIKVGQKLKLPV 112 (124)
T ss_pred HHH-HhCCC--HHHHHHHhccCC---CceecCcEEEEec
Confidence 999 99999 999999999994 3689999998765
No 17
>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=97.41 E-value=0.0001 Score=59.24 Aligned_cols=51 Identities=22% Similarity=0.162 Sum_probs=29.8
Q ss_pred ceEEEEecCCCcHHHHHHHhCCCHHHHHHHcCCC----CCCCCCCCCEEEeCCCC
Q 038519 29 GIIEHQVSKLDTLAGIAIKYGVDVADIRKLNGLS----TDLQMFALKTLQIPLPG 79 (324)
Q Consensus 29 ~~~~h~Vq~GDTL~~IA~KYgVsV~eI~~~N~L~----~~~~L~~GQ~L~IP~~~ 79 (324)
.|..|+|++||||..|=.++|++..+|.++=... .-..|+|||+|.+-...
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 3789999999999999999999999887763321 22579999999986654
No 18
>PRK10190 L,D-transpeptidase; Provisional
Probab=97.29 E-value=0.00081 Score=65.88 Aligned_cols=54 Identities=19% Similarity=0.180 Sum_probs=46.3
Q ss_pred eEEEEecCCC--cHHHHHHHhCCCHHHHHHHcCCCCCCCCCCCCEEEeCCCCCCCC
Q 038519 30 IIEHQVSKLD--TLAGIAIKYGVDVADIRKLNGLSTDLQMFALKTLQIPLPGKHPP 83 (324)
Q Consensus 30 ~~~h~Vq~GD--TL~~IA~KYgVsV~eI~~~N~L~~~~~L~~GQ~L~IP~~~~~~~ 83 (324)
...|+|+++| +|..||++|++...+|+++|+-.+....++|+.|.||....-++
T Consensus 37 ~~~~~v~~~~~~~le~iA~~f~~g~~~l~~aNPgvd~~~p~~G~~i~iP~~~ilP~ 92 (310)
T PRK10190 37 SLTVTVPDHNTQPLETFAAQYGQGLSNMLEANPGADVFLPKSGSQLTIPQQLILPD 92 (310)
T ss_pred eEEEEecCCCCccHHHHHHHhCCCHHHHHHhCCCCCCCCCCCCCEEEecCcccCCC
Confidence 4679999966 59999999999999999999987776778999999998655443
No 19
>PRK10260 L,D-transpeptidase; Provisional
Probab=97.27 E-value=0.00093 Score=65.37 Aligned_cols=54 Identities=17% Similarity=0.095 Sum_probs=46.1
Q ss_pred eEEEEecCCCc--HHHHHHHhCCCHHHHHHHcCCCCCCCCCCCCEEEeCCCCCCCC
Q 038519 30 IIEHQVSKLDT--LAGIAIKYGVDVADIRKLNGLSTDLQMFALKTLQIPLPGKHPP 83 (324)
Q Consensus 30 ~~~h~Vq~GDT--L~~IA~KYgVsV~eI~~~N~L~~~~~L~~GQ~L~IP~~~~~~~ 83 (324)
...|+|++||| |..||++|++...+|+++|+-.++....+|++|.||...--++
T Consensus 40 ~~~~~v~~~~~~~le~iA~~f~~g~~~l~~aNPgvdp~lp~~G~~i~iP~~~ilP~ 95 (306)
T PRK10260 40 NQVITIPEGNTQPLEYFAAEYQMGLSNMMEANPGVDTFLPKGGTVLNIPQQLILPD 95 (306)
T ss_pred cEEEEeCCCCCchHHHHHHHhCCCHHHHHHhCcCCCCCcCCCCCEEEeCCccCCCC
Confidence 46899999664 9999999999999999999987766778999999998655443
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=97.24 E-value=0.0003 Score=55.47 Aligned_cols=41 Identities=27% Similarity=0.246 Sum_probs=33.3
Q ss_pred CcHHHHHHHh---C-CCHH----HHHHHcCC----CCCCCCCCCCEEEeCCCC
Q 038519 39 DTLAGIAIKY---G-VDVA----DIRKLNGL----STDLQMFALKTLQIPLPG 79 (324)
Q Consensus 39 DTL~~IA~KY---g-VsV~----eI~~~N~L----~~~~~L~~GQ~L~IP~~~ 79 (324)
||||+||.+| + +++. .|.+.|+- .+.+.|++|++|+||...
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 67788852 234789999999999753
No 21
>COG1652 XkdP Uncharacterized protein containing LysM domain [Function unknown]
Probab=97.22 E-value=0.00011 Score=68.92 Aligned_cols=49 Identities=29% Similarity=0.264 Sum_probs=43.2
Q ss_pred EEEEecCCCcHHHHHHHh---CCCHHHHHHHcC---CCCCCCCCCCCEEEeCCCC
Q 038519 31 IEHQVSKLDTLAGIAIKY---GVDVADIRKLNG---LSTDLQMFALKTLQIPLPG 79 (324)
Q Consensus 31 ~~h~Vq~GDTL~~IA~KY---gVsV~eI~~~N~---L~~~~~L~~GQ~L~IP~~~ 79 (324)
..|+|++|||||.||+++ ++....|..+|+ +.+++.|++||+|+||...
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 389999999999999986 366678999999 8888999999999999764
No 22
>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=96.85 E-value=0.00018 Score=49.26 Aligned_cols=42 Identities=12% Similarity=0.192 Sum_probs=33.3
Q ss_pred cccccccccccCCCCCcccChhHHHHhhhh-CCCCCCCCCCCCCceeEE
Q 038519 110 DLFDSFRSLRLKSKPQWKVSPAMNSLQGYY-GLKPTGQRPPSEGCEMAV 157 (324)
Q Consensus 110 ~vv~sgdSl~~~s~~~~~vS~Am~~Lq~wy-GL~P~~~~~l~~G~elvv 157 (324)
++|+.||++|.++. ++.++ ...|+.|| ++.+. . +.+|++|.|
T Consensus 1 y~V~~gDtl~~IA~-~~~~~--~~~l~~~N~~~~~~--~-l~~G~~l~i 43 (44)
T PF01476_consen 1 YTVQPGDTLWSIAK-RYGIS--VDELMELNPNIDSD--N-LQPGQKLCI 43 (44)
T ss_dssp EEE-TT--HHHHHH-HTTS---HHHHHHHCCTTHGG--C-GGTTEEEEE
T ss_pred CEECcCCcHHHHHh-hhhhh--HhHHHHhcCCCCcc--c-CCCCCEEEe
Confidence 35689999999999 99999 99999999 88865 4 999999876
No 23
>COG3858 Predicted glycosyl hydrolase [General function prediction only]
Probab=96.75 E-value=0.00081 Score=68.06 Aligned_cols=78 Identities=17% Similarity=0.073 Sum_probs=64.4
Q ss_pred eEEEEecCCCcHHHHHHHhCCCHHHHHHHcCCCCCCCCCCCCEEEeCCCCCCCCCCCCCCCcccccccccccCCCCcccc
Q 038519 30 IIEHQVSKLDTLAGIAIKYGVDVADIRKLNGLSTDLQMFALKTLQIPLPGKHPPSPCLSNGYETRGQANHERTPDHHVQH 109 (324)
Q Consensus 30 ~~~h~Vq~GDTL~~IA~KYgVsV~eI~~~N~L~~~~~L~~GQ~L~IP~~~~~~~s~~~sngs~~r~~~~~~~ap~~~~~~ 109 (324)
+..|.|++||++..||+.|+++..+|...|.+.+ +.|-+||++.||.... -
T Consensus 1 ~~i~~~~pg~~~~~i~~~~~~~~~~i~~~~~~~~-d~~~~~q~~~v~~~~~----------------------------~ 51 (423)
T COG3858 1 MSIHLVGPGDSRLIIAVYFPYTNNRIVNGNDYTN-DDLVDGQTFVVPPSGH----------------------------F 51 (423)
T ss_pred CEEEEccCCceeeeehhhcccccccccccccccc-ccccCceeEEECCcce----------------------------E
Confidence 3579999999999999999999999988889888 7899999999987542 1
Q ss_pred cccccccccccCCCCCcccChhHHHHhhhh
Q 038519 110 DLFDSFRSLRLKSKPQWKVSPAMNSLQGYY 139 (324)
Q Consensus 110 ~vv~sgdSl~~~s~~~~~vS~Am~~Lq~wy 139 (324)
+-+.++|++|.+.+ +-.|+ |..++.-+
T Consensus 52 y~~~~~d~~~Sia~-~~~vt--~~~~~~m~ 78 (423)
T COG3858 52 YDVGPGDTLTSIAR-TVGVT--QDSAAIMN 78 (423)
T ss_pred EEecCCcchhhhhh-hhcCC--HHHHHhhc
Confidence 22366888888888 78887 77766655
No 24
>COG3858 Predicted glycosyl hydrolase [General function prediction only]
Probab=95.89 E-value=0.0093 Score=60.59 Aligned_cols=54 Identities=24% Similarity=0.045 Sum_probs=49.2
Q ss_pred cceEEEEecCCCcHHHHHHHhCCCHHHHHHHcCCCCCCCCCCCCEEEeCCCCCC
Q 038519 28 RGIIEHQVSKLDTLAGIAIKYGVDVADIRKLNGLSTDLQMFALKTLQIPLPGKH 81 (324)
Q Consensus 28 ~~~~~h~Vq~GDTL~~IA~KYgVsV~eI~~~N~L~~~~~L~~GQ~L~IP~~~~~ 81 (324)
.....|.|++||||++||++++|+.+.+..+|.+..+..+.+|=.|.||...+.
T Consensus 47 ~~~~~y~~~~~d~~~Sia~~~~vt~~~~~~m~~~~~~~~l~~~~~l~~P~~~~~ 100 (423)
T COG3858 47 PSGHFYDVGPGDTLTSIARTVGVTQDSAAIMNFVICPGYLQYGLNLYIPSARKT 100 (423)
T ss_pred CcceEEEecCCcchhhhhhhhcCCHHHHHhhcccccccceeeeeEEeccCCCCC
Confidence 345789999999999999999999999999999888889999999999987766
No 25
>KOG2850 consensus Predicted peptidoglycan-binding protein, contains LysM domain [General function prediction only]
Probab=95.32 E-value=0.01 Score=54.50 Aligned_cols=53 Identities=32% Similarity=0.510 Sum_probs=48.5
Q ss_pred cceEEEEecCCCcHHHHHHHhCCCHHHHHHHcCCCCCCCCCCCCEEEeCCCCC
Q 038519 28 RGIIEHQVSKLDTLAGIAIKYGVDVADIRKLNGLSTDLQMFALKTLQIPLPGK 80 (324)
Q Consensus 28 ~~~~~h~Vq~GDTL~~IA~KYgVsV~eI~~~N~L~~~~~L~~GQ~L~IP~~~~ 80 (324)
....+-+||.||||..||.+|..++.+|+++|++.....+.+-+.+.||+...
T Consensus 7 ~~~l~~~iq~~dt~~a~al~~~~~va~i~RvN~~~r~q~f~a~~~i~~pv~~~ 59 (186)
T KOG2850|consen 7 AHELEVTIQEGDTLQAIALNYESDVADIKRVNNDDREQRFNALRSISIPVTRA 59 (186)
T ss_pred hhheeeeeccCchhhhHHhhcccchhhheeeccchhhhhhccccceecccchh
Confidence 44577899999999999999999999999999999889999999999998763
No 26
>PRK11649 putative peptidase; Provisional
Probab=95.29 E-value=0.031 Score=56.96 Aligned_cols=52 Identities=31% Similarity=0.343 Sum_probs=43.0
Q ss_pred cceEEEEecCCCcHHHHHHHhCCCHHHHHHHc-CCCCCCCCCCCCEEEeCCCC
Q 038519 28 RGIIEHQVSKLDTLAGIAIKYGVDVADIRKLN-GLSTDLQMFALKTLQIPLPG 79 (324)
Q Consensus 28 ~~~~~h~Vq~GDTL~~IA~KYgVsV~eI~~~N-~L~~~~~L~~GQ~L~IP~~~ 79 (324)
..|..|+|++||||..|=.+||++..++.++- ....-..|++||.|.+-...
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 45789999999999999999999999998772 22233579999999997554
No 27
>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=95.25 E-value=0.0085 Score=39.97 Aligned_cols=41 Identities=15% Similarity=0.135 Sum_probs=33.7
Q ss_pred cccccccccCCCCCcccChhHHHHhhhhC-CCCCCCCCCCCCceeEE
Q 038519 112 FDSFRSLRLKSKPQWKVSPAMNSLQGYYG-LKPTGQRPPSEGCEMAV 157 (324)
Q Consensus 112 v~sgdSl~~~s~~~~~vS~Am~~Lq~wyG-L~P~~~~~l~~G~elvv 157 (324)
++.||+||.++. ++.++ +..|+.+|+ +... ..+.+|+.|.|
T Consensus 1 v~~gdtl~~IA~-~~~~~--~~~l~~~N~~~~~~--~~~~~g~~l~i 42 (44)
T TIGR02899 1 VQKGDTLWKIAK-KYGVD--FDELIQANPQLSNP--NLIYPGMKIKI 42 (44)
T ss_pred CCCCCCHHHHHH-HHCcC--HHHHHHHhhcCCCC--CCcCCCCEEec
Confidence 367899999999 99998 999999997 4422 55899998876
No 28
>PRK10871 nlpD lipoprotein NlpD; Provisional
Probab=94.75 E-value=0.015 Score=57.36 Aligned_cols=49 Identities=8% Similarity=-0.103 Sum_probs=42.7
Q ss_pred ccccccccccccccCCCCCcccChhHHHHhhhhCCCCCCCCCCCCCceeEEEec
Q 038519 107 VQHDLFDSFRSLRLKSKPQWKVSPAMNSLQGYYGLKPTGQRPPSEGCEMAVFRK 160 (324)
Q Consensus 107 ~~~~vv~sgdSl~~~s~~~~~vS~Am~~Lq~wyGL~P~~~~~l~~G~elvv~~k 160 (324)
...+.|+.||+||.|+. ++.++ ++.|+.||+|... ..+.+||.|.|...
T Consensus 60 ~~~y~Vk~GDTL~~IA~-~~g~~--~~~La~~N~l~~p--~~I~~GQ~L~i~~~ 108 (319)
T PRK10871 60 GSTYTVKKGDTLFYIAW-ITGND--FRDLAQRNNIQAP--YSLNVGQTLQVGNA 108 (319)
T ss_pred CCceEECCCCHHHHHHH-HHCcC--HHHHHHhcCCCCC--ccccCCCEEEeCCC
Confidence 34566799999999999 99999 9999999999754 67999999999754
No 29
>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=94.72 E-value=0.014 Score=37.43 Aligned_cols=43 Identities=14% Similarity=0.180 Sum_probs=35.7
Q ss_pred cccccccccccCCCCCcccChhHHHHhhhhCCCCCCCCCCCCCceeEE
Q 038519 110 DLFDSFRSLRLKSKPQWKVSPAMNSLQGYYGLKPTGQRPPSEGCEMAV 157 (324)
Q Consensus 110 ~vv~sgdSl~~~s~~~~~vS~Am~~Lq~wyGL~P~~~~~l~~G~elvv 157 (324)
+.++.||++|.++. ++.++ +..|+.+|.+... ..+.+|+.+.|
T Consensus 3 ~~v~~gdt~~~ia~-~~~~~--~~~~~~~N~~~~~--~~~~~g~~l~i 45 (46)
T cd00118 3 YTVKKGDTLSSIAQ-RYGIS--VEELLKLNGLSDP--DNLQVGQKLKI 45 (46)
T ss_pred EEECCCCCHHHHHH-HHCcC--HHHHHHHcCCCCc--cccCCCCEEec
Confidence 34578999999998 89898 8999999999533 66899988765
No 30
>PRK14125 cell division suppressor protein YneA; Provisional
Probab=93.73 E-value=0.045 Score=45.66 Aligned_cols=51 Identities=8% Similarity=-0.001 Sum_probs=40.3
Q ss_pred ccccccccccccCCCCCcccC----h--hHHHHhhhhCCCCCCCCCCCCCceeEEEecCcc
Q 038519 109 HDLFDSFRSLRLKSKPQWKVS----P--AMNSLQGYYGLKPTGQRPPSEGCEMAVFRKREA 163 (324)
Q Consensus 109 ~~vv~sgdSl~~~s~~~~~vS----~--Am~~Lq~wyGL~P~~~~~l~~G~elvv~~k~~~ 163 (324)
.+.|++|||||.++. ++..+ + .+..|+..|+|.+. .+.+|+.|.|-.+.+.
T Consensus 38 ~~tV~~GDTLW~IA~-~y~~~~~l~~~~~v~~I~~~N~l~~~---~I~~Gq~L~IP~~~~~ 94 (103)
T PRK14125 38 EITVQEGDTLWALAD-QYAGKHHMAKNEFIEWVEDVNNLPSG---HIKAGDKLVIPVLKSK 94 (103)
T ss_pred EEEECCCCCHHHHHH-HhCCCcCCCHHHHHHHHHHhcCCCCC---cCCCCCEEEEecCCCC
Confidence 445799999999999 88654 2 26788899999853 4999999999876653
No 31
>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=93.48 E-value=0.032 Score=55.42 Aligned_cols=46 Identities=11% Similarity=0.158 Sum_probs=40.1
Q ss_pred cccccccccccccccCCCCCcccChhHHHHhhhhCCCCCCCCCCCCCceeEE
Q 038519 106 HVQHDLFDSFRSLRLKSKPQWKVSPAMNSLQGYYGLKPTGQRPPSEGCEMAV 157 (324)
Q Consensus 106 ~~~~~vv~sgdSl~~~s~~~~~vS~Am~~Lq~wyGL~P~~~~~l~~G~elvv 157 (324)
....++|+.||+||.++. ++.++ ++.|++||+|.+ ..+.+|+.|.|
T Consensus 292 ~~~~YiVq~GDTL~sIAk-RYGVS--V~~L~r~N~L~~---~~L~~GQ~L~I 337 (338)
T TIGR02907 292 KLRMCIVQEGDTIETIAE-RYEIS--VSQLIRHNQLED---FEVNEGQILYI 337 (338)
T ss_pred ccEEEEECCCCCHHHHHH-HHCcC--HHHHHHHhCCCc---cccCCCCEEEe
Confidence 345667899999999999 99999 999999999973 57999999876
No 32
>PF05489 Phage_tail_X: Phage Tail Protein X; InterPro: IPR008861 This entry is represented by Bacteriophage P2, GpX. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family is found in a family of phage tail proteins. Sequence analysis suggests that they are related to IPR002482 from INTERPRO which suggests a general peptidoglycan binding function.
Probab=92.81 E-value=0.32 Score=36.93 Aligned_cols=48 Identities=23% Similarity=0.140 Sum_probs=36.6
Q ss_pred EEEEecCCCcHHHHHHHh-CCC---HHHHHHHcC-CCCC-CCCCCCCEEEeCCCC
Q 038519 31 IEHQVSKLDTLAGIAIKY-GVD---VADIRKLNG-LSTD-LQMFALKTLQIPLPG 79 (324)
Q Consensus 31 ~~h~Vq~GDTL~~IA~KY-gVs---V~eI~~~N~-L~~~-~~L~~GQ~L~IP~~~ 79 (324)
..|+. .||||-.||.|| |-. ++.|.++|+ |..- ..|.+|..|.||...
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 999999999885 543 478899996 4333 589999999999654
No 33
>smart00257 LysM Lysin motif.
Probab=92.19 E-value=0.068 Score=33.74 Aligned_cols=41 Identities=10% Similarity=0.123 Sum_probs=33.1
Q ss_pred ccccccccccCCCCCcccChhHHHHhhhhCCCCCCCCCCCCCceeE
Q 038519 111 LFDSFRSLRLKSKPQWKVSPAMNSLQGYYGLKPTGQRPPSEGCEMA 156 (324)
Q Consensus 111 vv~sgdSl~~~s~~~~~vS~Am~~Lq~wyGL~P~~~~~l~~G~elv 156 (324)
.++.||++|.++. ++.++ +..|+.+|.+... ..+.+|+.+.
T Consensus 3 ~v~~gdt~~~ia~-~~~~~--~~~~~~~N~~~~~--~~~~~g~~l~ 43 (44)
T smart00257 3 TVKKGDTLSSIAR-RYGIS--VSDLLELNNILDP--DNLQVGQKLK 43 (44)
T ss_pred EeCCCCCHHHHHH-HhCCC--HHHHHHHcCCCCc--cccCCCCEEe
Confidence 3578999999998 89998 6999999996533 5688888765
No 34
>COG3061 OapA Cell envelope opacity-associated protein A [Cell envelope biogenesis, outer membrane]
Probab=90.74 E-value=0.39 Score=45.63 Aligned_cols=53 Identities=15% Similarity=0.158 Sum_probs=43.8
Q ss_pred ceEEEEecCCCcHHHHHHHhCCCHHHHHHHcCCCC---C-CCCCCCCEEEeCCCCCC
Q 038519 29 GIIEHQVSKLDTLAGIAIKYGVDVADIRKLNGLST---D-LQMFALKTLQIPLPGKH 81 (324)
Q Consensus 29 ~~~~h~Vq~GDTL~~IA~KYgVsV~eI~~~N~L~~---~-~~L~~GQ~L~IP~~~~~ 81 (324)
.|..|+|..|+||..+=+.+++.+.|+-.+=.... + ..|++||.|+|-+....
T Consensus 158 ~wqsy~V~~G~TLaQlFRdn~LpitDVnAMakveGagkpLSnlkaGq~Vki~~naqG 214 (242)
T COG3061 158 NWQSYTVPQGKTLAQLFRDNNLPITDVNAMAKVEGAGKPLSNLKAGQKVKISLNAQG 214 (242)
T ss_pred cceeEEecCCccHHHHHhccCCChHHhHHHHhhccCCCchhhccCCCEEEEEEcCcc
Confidence 79999999999999999999999999876654322 1 57999999999776543
No 35
>COG0739 NlpD Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]
Probab=90.01 E-value=0.54 Score=42.92 Aligned_cols=49 Identities=29% Similarity=0.348 Sum_probs=44.7
Q ss_pred EEEEecCCCcHHHHHHHhCCCHHHHHHHcCCCCCCCCCCCCEEEeCCCC
Q 038519 31 IEHQVSKLDTLAGIAIKYGVDVADIRKLNGLSTDLQMFALKTLQIPLPG 79 (324)
Q Consensus 31 ~~h~Vq~GDTL~~IA~KYgVsV~eI~~~N~L~~~~~L~~GQ~L~IP~~~ 79 (324)
..|.|+.+++|..|+.++++...++...|.+.....+..|+.+.+|...
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 50 (277)
T COG0739 2 SLYVVKKGDTLSAIAARLGISAKDLARLNNLLKKRLLRIGQLLRVPRAA 50 (277)
T ss_pred ceEEecCCCHHHHHHHHcCCCHHHHHHHHhhccccccCccceeeecccc
Confidence 4689999999999999999999999999998776688999999999875
No 36
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=87.24 E-value=0.28 Score=42.81 Aligned_cols=48 Identities=17% Similarity=0.014 Sum_probs=37.2
Q ss_pred ccccccccccccccCCCCCcccC-hhHHHHhhhhC--CCCCCCCCCCCCceeEE
Q 038519 107 VQHDLFDSFRSLRLKSKPQWKVS-PAMNSLQGYYG--LKPTGQRPPSEGCEMAV 157 (324)
Q Consensus 107 ~~~~vv~sgdSl~~~s~~~~~vS-~Am~~Lq~wyG--L~P~~~~~l~~G~elvv 157 (324)
...++++.||+||.++. ++... -.+..|..+|+ +. ..+.+.||++|.|
T Consensus 95 ~~~y~Vk~GDTL~~IA~-~~~g~~~~~~~I~~~N~~~l~--~~~~I~pGq~L~I 145 (147)
T PRK11198 95 SQFYTVKSGDTLSAIAK-KVYGNANKYNKIFEANKPMLK--SPDKIYPGQVLRI 145 (147)
T ss_pred CeEEEECCCCCHHHHHH-HHcCChhhHHHHHHhhhhcCC--CcCCcCcCCEEec
Confidence 34567899999999999 77543 34789999998 65 3367999999875
No 37
>COG3170 FimV Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=86.87 E-value=0.46 Score=51.48 Aligned_cols=52 Identities=27% Similarity=0.137 Sum_probs=39.8
Q ss_pred cceEEEEecCCCcHHHHHHHh----CCCHH----HHHHHcCC--C--CCCCCCCCCEEEeCCCC
Q 038519 28 RGIIEHQVSKLDTLAGIAIKY----GVDVA----DIRKLNGL--S--TDLQMFALKTLQIPLPG 79 (324)
Q Consensus 28 ~~~~~h~Vq~GDTL~~IA~KY----gVsV~----eI~~~N~L--~--~~~~L~~GQ~L~IP~~~ 79 (324)
..-..|+|++|||||.||.+- ++|++ .|.++|+- . +-+.|++|++|+||...
T Consensus 186 a~g~tyt~~~~Dtl~dIAs~~rp~~~vt~~Q~~lAly~lNP~af~~gni~RLr~GSvLriP~~~ 249 (755)
T COG3170 186 APGDTYTVRSGDTLWDIASRLRPQDHVTVEQMLLALYQLNPQAFVNGNINRLRAGSVLRIPSAA 249 (755)
T ss_pred CCCcccccCCcchHHHHHHhhcCcccccHHHHHHHHHhhChhhhcccchhhccccceeeccchh
Confidence 345689999999999999986 45655 46778862 2 22689999999999654
No 38
>PF13518 HTH_28: Helix-turn-helix domain
Probab=76.33 E-value=2.6 Score=29.27 Aligned_cols=25 Identities=12% Similarity=0.246 Sum_probs=22.3
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHHcC
Q 038519 36 SKLDTLAGIAIKYGVDVADIRKLNG 60 (324)
Q Consensus 36 q~GDTL~~IA~KYgVsV~eI~~~N~ 60 (324)
..|.|+..||++|||+...|.+|-.
T Consensus 10 ~~g~s~~~~a~~~gis~~tv~~w~~ 34 (52)
T PF13518_consen 10 LEGESVREIAREFGISRSTVYRWIK 34 (52)
T ss_pred HcCCCHHHHHHHHCCCHhHHHHHHH
Confidence 4688999999999999999998864
No 39
>COG4784 Putative Zn-dependent protease [General function prediction only]
Probab=72.09 E-value=6.2 Score=40.32 Aligned_cols=47 Identities=23% Similarity=0.216 Sum_probs=39.3
Q ss_pred eEEEEecCCCcHHHHHHHh-C--CCHHHHHHHcCCCCCCCCCCCCEEEeC
Q 038519 30 IIEHQVSKLDTLAGIAIKY-G--VDVADIRKLNGLSTDLQMFALKTLQIP 76 (324)
Q Consensus 30 ~~~h~Vq~GDTL~~IA~KY-g--VsV~eI~~~N~L~~~~~L~~GQ~L~IP 76 (324)
....+|++|||+..+|.+- | -.++-++-+|.|.....+.+|+.|+|-
T Consensus 428 irvvtVk~GqT~~~lAA~m~G~~rkldlfRllNam~~~a~~~pGd~vKii 477 (479)
T COG4784 428 IRVVTVKPGQTMASLAARMMGTDRKLDLFRLLNAMSPGATVRPGDKVKII 477 (479)
T ss_pred EEEEEecCCccHHHHHhhccCchhHHHHHHHHhccCCCCcCCCCCeeeec
Confidence 4557899999999999885 3 356778889999888899999999983
No 40
>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=67.08 E-value=4.2 Score=30.45 Aligned_cols=25 Identities=12% Similarity=0.361 Sum_probs=21.8
Q ss_pred ecCCCcHHHHHHHhCCCHHHHHHHc
Q 038519 35 VSKLDTLAGIAIKYGVDVADIRKLN 59 (324)
Q Consensus 35 Vq~GDTL~~IA~KYgVsV~eI~~~N 59 (324)
...|.|+..||++|||+...|.+|=
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 41
>COG4254 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=66.71 E-value=4.9 Score=40.02 Aligned_cols=50 Identities=24% Similarity=0.155 Sum_probs=43.3
Q ss_pred EEEEecCCCcHHHHHHHhCCCHH---HHHHHcCCCCCCCCCCCCEEEeCCCCC
Q 038519 31 IEHQVSKLDTLAGIAIKYGVDVA---DIRKLNGLSTDLQMFALKTLQIPLPGK 80 (324)
Q Consensus 31 ~~h~Vq~GDTL~~IA~KYgVsV~---eI~~~N~L~~~~~L~~GQ~L~IP~~~~ 80 (324)
..|.|+.||||..++..|=.-.+ .++..|.+..+..+++|..|.||.+..
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 68999999999999999965544 467789999999999999999998754
No 42
>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=65.83 E-value=6.5 Score=27.57 Aligned_cols=24 Identities=21% Similarity=0.337 Sum_probs=18.5
Q ss_pred ecCCCcHHHHHHHhCCCHHHHHHH
Q 038519 35 VSKLDTLAGIAIKYGVDVADIRKL 58 (324)
Q Consensus 35 Vq~GDTL~~IA~KYgVsV~eI~~~ 58 (324)
.+.|-|+..||+.|||+...|.++
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 357899999999999999999875
No 43
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=56.80 E-value=13 Score=25.85 Aligned_cols=25 Identities=16% Similarity=0.139 Sum_probs=19.0
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHHcC
Q 038519 36 SKLDTLAGIAIKYGVDVADIRKLNG 60 (324)
Q Consensus 36 q~GDTL~~IA~KYgVsV~eI~~~N~ 60 (324)
..|.|...||+.+||+...+.+|=.
T Consensus 15 ~~G~s~~~ia~~lgvs~~Tv~~w~k 39 (50)
T PF13384_consen 15 REGWSIREIAKRLGVSRSTVYRWIK 39 (50)
T ss_dssp HHT--HHHHHHHHTS-HHHHHHHHT
T ss_pred HCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3499999999999999999998843
No 44
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=53.32 E-value=14 Score=30.91 Aligned_cols=28 Identities=14% Similarity=0.094 Sum_probs=24.7
Q ss_pred EEEecCCCcHHHHHHHhCCCHHHHHHHc
Q 038519 32 EHQVSKLDTLAGIAIKYGVDVADIRKLN 59 (324)
Q Consensus 32 ~h~Vq~GDTL~~IA~KYgVsV~eI~~~N 59 (324)
...+..|-|+..||++|||+...|.+|=
T Consensus 23 ~~~~~~g~sv~evA~e~gIs~~tl~~W~ 50 (121)
T PRK09413 23 QQSFEPGMTVSLVARQHGVAASQLFLWR 50 (121)
T ss_pred HHHHcCCCCHHHHHHHHCcCHHHHHHHH
Confidence 3456789999999999999999999994
No 45
>PF04921 XAP5: XAP5, circadian clock regulator; InterPro: IPR007005 These proteins are found in a wide range of eukaryotes. Their function is uncertain though they are nuclear proteins, possibly with DNA-binding activity.; GO: 0005634 nucleus
Probab=47.18 E-value=22 Score=34.22 Aligned_cols=60 Identities=27% Similarity=0.206 Sum_probs=40.4
Q ss_pred ceeeecCCCcceEEEEecCCCcHHHHHHHhC-CCHHHHHHHcCCCCCCCCCCCCEEEeCCCC
Q 038519 19 HFVYEDLGRRGIIEHQVSKLDTLAGIAIKYG-VDVADIRKLNGLSTDLQMFALKTLQIPLPG 79 (324)
Q Consensus 19 sfv~~~~~~~~~~~h~Vq~GDTL~~IA~KYg-VsV~eI~~~N~L~~~~~L~~GQ~L~IP~~~ 79 (324)
+|+.+...+... .-+|++|||+|..=.+.- +-..+...|=.+..++.|++-..|+||-.-
T Consensus 102 ~fsywDGs~hrr-~v~vKKGdtI~~FL~~~r~~l~~~f~el~~vsvd~LM~VkedlIiPHhy 162 (239)
T PF04921_consen 102 PFSYWDGSGHRR-TVRVKKGDTIWQFLEKCRKQLAKEFRELRRVSVDDLMYVKEDLIIPHHY 162 (239)
T ss_pred EEEEECCCCCcc-eEEEcCCCCHHHHHHHHHHHHHHHhHHHHhcCHhheeeeccceeccCCc
Confidence 456665444443 778999999998755542 212345555556667889999999999653
No 46
>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=46.69 E-value=9.1 Score=28.01 Aligned_cols=24 Identities=17% Similarity=0.364 Sum_probs=17.8
Q ss_pred ecCCCcHHHHHHHhCCCHHHHHHH
Q 038519 35 VSKLDTLAGIAIKYGVDVADIRKL 58 (324)
Q Consensus 35 Vq~GDTL~~IA~KYgVsV~eI~~~ 58 (324)
+..|.+...||++|||+...|..+
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 568999999999999988887654
No 47
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=44.67 E-value=22 Score=29.01 Aligned_cols=26 Identities=19% Similarity=0.341 Sum_probs=22.1
Q ss_pred EEecCCCcHHHHHHHhCC-CHHHHHHH
Q 038519 33 HQVSKLDTLAGIAIKYGV-DVADIRKL 58 (324)
Q Consensus 33 h~Vq~GDTL~~IA~KYgV-sV~eI~~~ 58 (324)
...+.|.|+..||++||| ....|.+|
T Consensus 19 ~~~~~g~sv~~vAr~~gv~~~~~l~~W 45 (116)
T COG2963 19 LYLRGGDTVSEVAREFGIVSATQLYKW 45 (116)
T ss_pred HHHhcCccHHHHHHHhCCCChHHHHHH
Confidence 446789999999999995 99988865
No 48
>PHA00675 hypothetical protein
Probab=44.24 E-value=23 Score=28.75 Aligned_cols=25 Identities=20% Similarity=0.102 Sum_probs=22.2
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHHcC
Q 038519 36 SKLDTLAGIAIKYGVDVADIRKLNG 60 (324)
Q Consensus 36 q~GDTL~~IA~KYgVsV~eI~~~N~ 60 (324)
+.|.+.+.||++|||+-..|...=.
T Consensus 37 r~G~s~~~IA~~fGVsrstV~~I~~ 61 (78)
T PHA00675 37 VEGMSYAVLAEKFEQSKGAIAKICR 61 (78)
T ss_pred hcCccHHHHHHHhCCCHHHHHHHHc
Confidence 8999999999999999998887643
No 49
>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=43.80 E-value=36 Score=19.82 Aligned_cols=24 Identities=21% Similarity=0.358 Sum_probs=20.3
Q ss_pred ecCCCcHHHHHHHhCCCHHHHHHH
Q 038519 35 VSKLDTLAGIAIKYGVDVADIRKL 58 (324)
Q Consensus 35 Vq~GDTL~~IA~KYgVsV~eI~~~ 58 (324)
...|.++..||..+|++...|.++
T Consensus 18 ~~~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 18 LAAGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHh
Confidence 357889999999999999888764
No 50
>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=42.84 E-value=34 Score=23.90 Aligned_cols=23 Identities=26% Similarity=0.359 Sum_probs=19.6
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHH
Q 038519 36 SKLDTLAGIAIKYGVDVADIRKL 58 (324)
Q Consensus 36 q~GDTL~~IA~KYgVsV~eI~~~ 58 (324)
-.|-|+.+||..+|++...+.+.
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 57889999999999999998764
No 51
>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=41.35 E-value=23 Score=25.17 Aligned_cols=24 Identities=29% Similarity=0.368 Sum_probs=17.7
Q ss_pred ecCC-CcHHHHHHHhCCCHHHHHHH
Q 038519 35 VSKL-DTLAGIAIKYGVDVADIRKL 58 (324)
Q Consensus 35 Vq~G-DTL~~IA~KYgVsV~eI~~~ 58 (324)
|+.| -++...|++|||+...|.+.
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 4566 89999999999999999754
No 52
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=40.66 E-value=32 Score=24.03 Aligned_cols=24 Identities=13% Similarity=0.182 Sum_probs=16.1
Q ss_pred ecCCCcHHHHHHHhCCCHHHHHHH
Q 038519 35 VSKLDTLAGIAIKYGVDVADIRKL 58 (324)
Q Consensus 35 Vq~GDTL~~IA~KYgVsV~eI~~~ 58 (324)
.+.|-++..||+.+|++...|.+.
T Consensus 17 ~~~G~s~~~IA~~lg~s~sTV~re 40 (44)
T PF13936_consen 17 LEQGMSIREIAKRLGRSRSTVSRE 40 (44)
T ss_dssp HCS---HHHHHHHTT--HHHHHHH
T ss_pred HHcCCCHHHHHHHHCcCcHHHHHH
Confidence 468999999999999999988653
No 53
>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=38.88 E-value=30 Score=28.54 Aligned_cols=21 Identities=24% Similarity=0.355 Sum_probs=16.0
Q ss_pred CCcHHHHHHHhCCCHHHHHHH
Q 038519 38 LDTLAGIAIKYGVDVADIRKL 58 (324)
Q Consensus 38 GDTL~~IA~KYgVsV~eI~~~ 58 (324)
|.++..||++||+|...|.+.
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 999999999999999888654
No 54
>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=36.73 E-value=37 Score=26.09 Aligned_cols=22 Identities=41% Similarity=0.441 Sum_probs=19.6
Q ss_pred CcHHHHHHHhCCCHHHHHHHcC
Q 038519 39 DTLAGIAIKYGVDVADIRKLNG 60 (324)
Q Consensus 39 DTL~~IA~KYgVsV~eI~~~N~ 60 (324)
=+|-.||.++||+...|..|=.
T Consensus 23 i~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 23 IKLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred ccHHHHHHHHCCCHHHHHHHhh
Confidence 3789999999999999999854
No 55
>COG1652 XkdP Uncharacterized protein containing LysM domain [Function unknown]
Probab=35.39 E-value=15 Score=34.62 Aligned_cols=47 Identities=11% Similarity=0.020 Sum_probs=33.1
Q ss_pred ccccccccccccCCCCCcccChhHHHHhhhhC---CCCCCCCCCCCCceeEE
Q 038519 109 HDLFDSFRSLRLKSKPQWKVSPAMNSLQGYYG---LKPTGQRPPSEGCEMAV 157 (324)
Q Consensus 109 ~~vv~sgdSl~~~s~~~~~vS~Am~~Lq~wyG---L~P~~~~~l~~G~elvv 157 (324)
.++++.||+||.++..-|+..---..+..-|. +.+. +.+.+|+.+.|
T Consensus 212 ~~~v~rgDTl~~is~~~Yg~~~~y~~I~~aNk~~~~~~p--~~I~pGq~l~i 261 (269)
T COG1652 212 TNTVKRGDTLWQISKKVYGDGVEYRKIAEANKALVLDNP--DKIKPGQVLRI 261 (269)
T ss_pred EEEeccCCcccccchhhcCcceEEEeHhhhhhhhccCCC--CcCCCcceeeC
Confidence 67789999999999955666543445555566 4544 67888887654
No 56
>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=33.87 E-value=50 Score=21.68 Aligned_cols=20 Identities=25% Similarity=0.233 Sum_probs=18.0
Q ss_pred cHHHHHHHhCCCHHHHHHHc
Q 038519 40 TLAGIAIKYGVDVADIRKLN 59 (324)
Q Consensus 40 TL~~IA~KYgVsV~eI~~~N 59 (324)
|+.++|+.+||+...|.+|=
T Consensus 2 s~~e~a~~lgvs~~tl~~~~ 21 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWV 21 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 57899999999999999884
No 57
>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=31.84 E-value=50 Score=24.03 Aligned_cols=20 Identities=25% Similarity=0.353 Sum_probs=18.0
Q ss_pred cHHHHHHHhCCCHHHHHHHc
Q 038519 40 TLAGIAIKYGVDVADIRKLN 59 (324)
Q Consensus 40 TL~~IA~KYgVsV~eI~~~N 59 (324)
|+.++|+.+||+...|..|=
T Consensus 2 s~~eva~~~gvs~~tlr~w~ 21 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWE 21 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 57789999999999999884
No 58
>PHA01976 helix-turn-helix protein
Probab=31.23 E-value=32 Score=25.05 Aligned_cols=20 Identities=30% Similarity=0.293 Sum_probs=17.5
Q ss_pred CCCcHHHHHHHhCCCHHHHH
Q 038519 37 KLDTLAGIAIKYGVDVADIR 56 (324)
Q Consensus 37 ~GDTL~~IA~KYgVsV~eI~ 56 (324)
.-++|..||..|||++++|.
T Consensus 43 ~~~~l~~ia~~l~v~~~~l~ 62 (67)
T PHA01976 43 NLKTLLRLADALGVTLDWLC 62 (67)
T ss_pred CHHHHHHHHHHHCcCHHHHh
Confidence 44789999999999999984
No 59
>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=30.13 E-value=69 Score=29.99 Aligned_cols=43 Identities=21% Similarity=0.450 Sum_probs=32.2
Q ss_pred CccceeeecCCCcceEEEEecCCCcHHHHHHHhCCCHHHHHHH
Q 038519 16 SKGHFVYEDLGRRGIIEHQVSKLDTLAGIAIKYGVDVADIRKL 58 (324)
Q Consensus 16 s~Gsfv~~~~~~~~~~~h~Vq~GDTL~~IA~KYgVsV~eI~~~ 58 (324)
.-|..+.+..+.......-|.+==-|-+||+||||+..+|++.
T Consensus 148 ~DGki~~~~~g~~~VTK~AvEPVWyLPGVA~RFGi~E~~LRR~ 190 (194)
T PF12471_consen 148 PDGKIVLNSNGDLAVTKAAVEPVWYLPGVAERFGISEGELRRA 190 (194)
T ss_pred CCCeEEecCCCcEEEEEEEecccccchhhHHHcCCCHHHHHHH
Confidence 3455565545555566667777777889999999999999985
No 60
>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=29.50 E-value=1e+02 Score=20.38 Aligned_cols=21 Identities=24% Similarity=0.202 Sum_probs=18.3
Q ss_pred cHHHHHHHhCCCHHHHHHHcC
Q 038519 40 TLAGIAIKYGVDVADIRKLNG 60 (324)
Q Consensus 40 TL~~IA~KYgVsV~eI~~~N~ 60 (324)
|+.++|..+||+...|.++=.
T Consensus 3 t~~e~a~~lgis~~ti~~~~~ 23 (49)
T TIGR01764 3 TVEEAAEYLGVSKDTVYRLIH 23 (49)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 678899999999999998853
No 61
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=28.98 E-value=28 Score=24.27 Aligned_cols=19 Identities=42% Similarity=0.464 Sum_probs=15.5
Q ss_pred CCCcHHHHHHHhCCCHHHH
Q 038519 37 KLDTLAGIAIKYGVDVADI 55 (324)
Q Consensus 37 ~GDTL~~IA~KYgVsV~eI 55 (324)
.-|++..||..|||++++|
T Consensus 37 ~~~~~~~ia~~l~~~~~~l 55 (55)
T PF01381_consen 37 SLDTLKKIAKALGVSPEYL 55 (55)
T ss_dssp BHHHHHHHHHHHTSEHHHH
T ss_pred CHHHHHHHHHHHCCCHHHC
Confidence 3467899999999998875
No 62
>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=28.32 E-value=68 Score=21.66 Aligned_cols=20 Identities=25% Similarity=0.338 Sum_probs=18.1
Q ss_pred cHHHHHHHhCCCHHHHHHHc
Q 038519 40 TLAGIAIKYGVDVADIRKLN 59 (324)
Q Consensus 40 TL~~IA~KYgVsV~eI~~~N 59 (324)
|+.++|+..||+...|..|-
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~ 21 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYE 21 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHH
Confidence 57889999999999999994
No 63
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=28.26 E-value=81 Score=21.14 Aligned_cols=25 Identities=16% Similarity=0.126 Sum_probs=21.5
Q ss_pred ecCCCcHHHHHHHhCCCHHHHHHHc
Q 038519 35 VSKLDTLAGIAIKYGVDVADIRKLN 59 (324)
Q Consensus 35 Vq~GDTL~~IA~KYgVsV~eI~~~N 59 (324)
+..|.+...||..+|++...+...-
T Consensus 15 ~~~g~s~~eia~~l~is~~tv~~~~ 39 (58)
T smart00421 15 LAEGLTNKEIAERLGISEKTVKTHL 39 (58)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHH
Confidence 3578999999999999999987753
No 64
>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=28.14 E-value=66 Score=26.87 Aligned_cols=24 Identities=25% Similarity=0.238 Sum_probs=20.9
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHHc
Q 038519 36 SKLDTLAGIAIKYGVDVADIRKLN 59 (324)
Q Consensus 36 q~GDTL~~IA~KYgVsV~eI~~~N 59 (324)
.++-||.+||.+|||+...|..+=
T Consensus 69 ~pd~tl~Ela~~l~Vs~~ti~~~L 92 (119)
T PF01710_consen 69 NPDATLRELAERLGVSPSTIWRAL 92 (119)
T ss_pred CCCcCHHHHHHHcCCCHHHHHHHH
Confidence 588899999999999999987653
No 65
>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=28.06 E-value=63 Score=26.43 Aligned_cols=25 Identities=24% Similarity=0.336 Sum_probs=23.0
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHHcC
Q 038519 36 SKLDTLAGIAIKYGVDVADIRKLNG 60 (324)
Q Consensus 36 q~GDTL~~IA~KYgVsV~eI~~~N~ 60 (324)
+.|-|--+||.++|++++.|-+.|+
T Consensus 47 ~~g~syreIa~~tgvS~aTItRvsr 71 (87)
T PF01371_consen 47 DEGKSYREIAEETGVSIATITRVSR 71 (87)
T ss_dssp HTTSSHHHHHHHHTSTHHHHHHHHH
T ss_pred HCCCCHHHHHHHhCCCHHHHHHHHH
Confidence 4789999999999999999999885
No 66
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=27.76 E-value=57 Score=23.96 Aligned_cols=24 Identities=25% Similarity=0.349 Sum_probs=17.6
Q ss_pred ecCCCcHHHHHHHhC-CCHHHHHHH
Q 038519 35 VSKLDTLAGIAIKYG-VDVADIRKL 58 (324)
Q Consensus 35 Vq~GDTL~~IA~KYg-VsV~eI~~~ 58 (324)
+..|.+...|+..|. ++.++|..+
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 489999999999998 999999864
No 67
>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=27.68 E-value=66 Score=22.09 Aligned_cols=22 Identities=23% Similarity=0.258 Sum_probs=17.8
Q ss_pred cHHHHHHHhCCCHHHHHHHcCC
Q 038519 40 TLAGIAIKYGVDVADIRKLNGL 61 (324)
Q Consensus 40 TL~~IA~KYgVsV~eI~~~N~L 61 (324)
|+.++|+.+||++..|+.|=..
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 4678999999999999998643
No 68
>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=27.57 E-value=43 Score=24.06 Aligned_cols=19 Identities=26% Similarity=0.343 Sum_probs=15.8
Q ss_pred cHHHHHHHhCCCHHHHHHH
Q 038519 40 TLAGIAIKYGVDVADIRKL 58 (324)
Q Consensus 40 TL~~IA~KYgVsV~eI~~~ 58 (324)
++..||+.+|+++.+|.+.
T Consensus 5 ~V~elAk~l~v~~~~ii~~ 23 (54)
T PF04760_consen 5 RVSELAKELGVPSKEIIKK 23 (54)
T ss_dssp -TTHHHHHHSSSHHHHHHH
T ss_pred EHHHHHHHHCcCHHHHHHH
Confidence 5688999999999998764
No 69
>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=26.45 E-value=44 Score=27.90 Aligned_cols=26 Identities=15% Similarity=0.261 Sum_probs=23.3
Q ss_pred ecCCCcHHHHHHHhCCCHHHHHHHcC
Q 038519 35 VSKLDTLAGIAIKYGVDVADIRKLNG 60 (324)
Q Consensus 35 Vq~GDTL~~IA~KYgVsV~eI~~~N~ 60 (324)
+..|.+...+|+.|+|+...|.+|=.
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 56799999999999999999999944
No 70
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=25.93 E-value=71 Score=23.29 Aligned_cols=21 Identities=24% Similarity=0.327 Sum_probs=18.5
Q ss_pred cHHHHHHHhCCCHHHHHHHcC
Q 038519 40 TLAGIAIKYGVDVADIRKLNG 60 (324)
Q Consensus 40 TL~~IA~KYgVsV~eI~~~N~ 60 (324)
|+..+|+.+||+...|+.|=.
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 567899999999999999953
No 71
>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=25.90 E-value=66 Score=26.38 Aligned_cols=22 Identities=18% Similarity=0.218 Sum_probs=18.7
Q ss_pred CCCcHHHHHHHhCCCHHHHHHH
Q 038519 37 KLDTLAGIAIKYGVDVADIRKL 58 (324)
Q Consensus 37 ~GDTL~~IA~KYgVsV~eI~~~ 58 (324)
.=..|+.||+++||+.+||+.+
T Consensus 53 sl~kL~~La~~N~v~feeLc~Y 74 (82)
T PF11020_consen 53 SLSKLYKLAKENNVSFEELCVY 74 (82)
T ss_pred HHHHHHHHHHHcCCCHHHHHHH
Confidence 3457999999999999999864
No 72
>KOG2850 consensus Predicted peptidoglycan-binding protein, contains LysM domain [General function prediction only]
Probab=25.81 E-value=23 Score=32.82 Aligned_cols=55 Identities=44% Similarity=0.714 Sum_probs=49.0
Q ss_pred CcceEEEEecCCCcHHH--HHHHhCCC-----HHHHHHHcCCCCCCCCCCCCEEEeCCCCCC
Q 038519 27 RRGIIEHQVSKLDTLAG--IAIKYGVD-----VADIRKLNGLSTDLQMFALKTLQIPLPGKH 81 (324)
Q Consensus 27 ~~~~~~h~Vq~GDTL~~--IA~KYgVs-----V~eI~~~N~L~~~~~L~~GQ~L~IP~~~~~ 81 (324)
...++.|.|++-+++.+ |+-.||.. ++.+++.|....+..++.-..+-+|.+...
T Consensus 116 a~~~~eh~v~~~~~~tg~~~~~~~ga~~d~~~~e~v~k~~~vl~~~~~f~l~~~e~p~~~~~ 177 (186)
T KOG2850|consen 116 AVGYQEHRVKPFDPNTGFQIAPAYGAESDESPVESVRKMNPVLPDHQVFYLAPLEIPLPGAD 177 (186)
T ss_pred hhhhhhcCCCCCCccccceecccccCcccchhHHHHHHHhhccchhHHHhhccccCCCCCcc
Confidence 35688999999999999 99999999 999999999888888998889988887763
No 73
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=24.73 E-value=80 Score=22.92 Aligned_cols=20 Identities=30% Similarity=0.396 Sum_probs=18.1
Q ss_pred cHHHHHHHhCCCHHHHHHHc
Q 038519 40 TLAGIAIKYGVDVADIRKLN 59 (324)
Q Consensus 40 TL~~IA~KYgVsV~eI~~~N 59 (324)
|+..+|+.+||+...|+.|=
T Consensus 2 s~~eva~~~gvs~~tlr~~~ 21 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYYE 21 (70)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 57889999999999999994
No 74
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=24.69 E-value=60 Score=31.89 Aligned_cols=23 Identities=30% Similarity=0.257 Sum_probs=19.7
Q ss_pred CCcHHHHHHHhCCCHHHHHHHcC
Q 038519 38 LDTLAGIAIKYGVDVADIRKLNG 60 (324)
Q Consensus 38 GDTL~~IA~KYgVsV~eI~~~N~ 60 (324)
|=-|-.||.+|||++..|+.|=.
T Consensus 19 gmk~~dIAeklGvspntiksWKr 41 (279)
T COG5484 19 GMKLKDIAEKLGVSPNTIKSWKR 41 (279)
T ss_pred hccHHHHHHHhCCChHHHHHHHH
Confidence 34577899999999999999974
No 75
>PF13551 HTH_29: Winged helix-turn helix
Probab=24.48 E-value=71 Score=24.98 Aligned_cols=26 Identities=19% Similarity=0.222 Sum_probs=21.9
Q ss_pred ecCCC-cHHHHHHHhCCCHHHHHHHcC
Q 038519 35 VSKLD-TLAGIAIKYGVDVADIRKLNG 60 (324)
Q Consensus 35 Vq~GD-TL~~IA~KYgVsV~eI~~~N~ 60 (324)
+..|. |...||+.+||+...+.+|=.
T Consensus 8 ~~~g~~~~~~ia~~lg~s~~Tv~r~~~ 34 (112)
T PF13551_consen 8 LAEGVSTIAEIARRLGISRRTVYRWLK 34 (112)
T ss_pred HHcCCCcHHHHHHHHCcCHHHHHHHHH
Confidence 45677 699999999999999988753
No 76
>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=23.29 E-value=91 Score=24.61 Aligned_cols=23 Identities=17% Similarity=0.190 Sum_probs=20.5
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHH
Q 038519 36 SKLDTLAGIAIKYGVDVADIRKL 58 (324)
Q Consensus 36 q~GDTL~~IA~KYgVsV~eI~~~ 58 (324)
-.|-++..||..+||+...|.+.
T Consensus 124 ~~g~s~~eIA~~l~~s~~~v~~~ 146 (158)
T TIGR02937 124 LEGLSYKEIAEILGISVGTVKRR 146 (158)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHH
Confidence 46999999999999999998764
No 77
>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=22.95 E-value=77 Score=25.81 Aligned_cols=26 Identities=19% Similarity=0.302 Sum_probs=23.5
Q ss_pred ecCCCcHHHHHHHhCCCHHHHHHHcC
Q 038519 35 VSKLDTLAGIAIKYGVDVADIRKLNG 60 (324)
Q Consensus 35 Vq~GDTL~~IA~KYgVsV~eI~~~N~ 60 (324)
+..|.|..+||+.+||+...|.++..
T Consensus 47 l~~G~S~~eIA~~LgISrsTIyRi~R 72 (88)
T TIGR02531 47 LKQGKTYSDIEAETGASTATISRVKR 72 (88)
T ss_pred HHCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 57899999999999999999998764
No 78
>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=22.78 E-value=64 Score=29.42 Aligned_cols=49 Identities=16% Similarity=0.216 Sum_probs=33.3
Q ss_pred EEEecCCCcHHHHHHHhCCCHHHHHHHcC-CCCCCCCCCCCEEEeCCCCC
Q 038519 32 EHQVSKLDTLAGIAIKYGVDVADIRKLNG-LSTDLQMFALKTLQIPLPGK 80 (324)
Q Consensus 32 ~h~Vq~GDTL~~IA~KYgVsV~eI~~~N~-L~~~~~L~~GQ~L~IP~~~~ 80 (324)
.-.|+.|.|...||..||++++.|.++=. +.-...-.+.+...++....
T Consensus 63 QarIRaGas~eeVA~~~G~~~~rV~rfa~PVlaER~~~ae~A~~~~~~~~ 112 (170)
T PF11268_consen 63 QARIRAGASAEEVAEEAGVPVERVRRFAGPVLAERERAAEQARQVHPVRE 112 (170)
T ss_pred HHHHHCCCCHHHHHHHhCCCHHHhhhcccHHHHHHHHHHHHHhhCCCCCC
Confidence 34588999999999999999999998764 22222223445555555443
No 79
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=22.78 E-value=99 Score=21.42 Aligned_cols=24 Identities=17% Similarity=0.421 Sum_probs=19.5
Q ss_pred ecCCCcHHHHHHHhCCCHHHHHHH
Q 038519 35 VSKLDTLAGIAIKYGVDVADIRKL 58 (324)
Q Consensus 35 Vq~GDTL~~IA~KYgVsV~eI~~~ 58 (324)
+...-|+-.||+.+||+...+.++
T Consensus 24 ~~~~~s~~~vA~~~~vs~~TV~ri 47 (52)
T PF13542_consen 24 LRESRSFKDVARELGVSWSTVRRI 47 (52)
T ss_pred HhhcCCHHHHHHHHCCCHHHHHHH
Confidence 344459999999999999998764
No 80
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=21.33 E-value=38 Score=24.34 Aligned_cols=22 Identities=27% Similarity=0.315 Sum_probs=16.2
Q ss_pred CCCcHHHHHHHhCCCHHHHHHH
Q 038519 37 KLDTLAGIAIKYGVDVADIRKL 58 (324)
Q Consensus 37 ~GDTL~~IA~KYgVsV~eI~~~ 58 (324)
.-++|..||.-+||++++|..+
T Consensus 39 ~~~~l~~ia~~l~~~~~el~~~ 60 (63)
T PF13443_consen 39 SLDTLEKIAKALNCSPEELFEY 60 (63)
T ss_dssp -HHHHHHHHHHHT--HHHCTEC
T ss_pred cHHHHHHHHHHcCCCHHHHhhc
Confidence 3478999999999999998654
No 81
>PF12964 DUF3853: Protein of unknown function (DUF3853); InterPro: IPR024363 This entry represents a family of uncharacterised proteins that were found by clustering human gut metagenomic sequences [].
Probab=21.30 E-value=66 Score=27.08 Aligned_cols=36 Identities=17% Similarity=0.275 Sum_probs=29.0
Q ss_pred HHHHHHHhCCCHHHHHHHc--CCCCCCCCCCCCEEEeC
Q 038519 41 LAGIAIKYGVDVADIRKLN--GLSTDLQMFALKTLQIP 76 (324)
Q Consensus 41 L~~IA~KYgVsV~eI~~~N--~L~~~~~L~~GQ~L~IP 76 (324)
|.+||+-|||++..-.++= ++.++...+.|.+|+|-
T Consensus 48 ~~GlAklfgcSv~Ta~RiK~sG~id~AI~Q~Gr~IivD 85 (96)
T PF12964_consen 48 LKGLAKLFGCSVPTANRIKKSGKIDPAITQIGRKIIVD 85 (96)
T ss_pred HHHHHHHhCCCchhHHHHHhcCCccHHHHHcCCEEEEe
Confidence 6799999999998776665 56666778889998873
No 82
>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A.
Probab=20.73 E-value=96 Score=24.98 Aligned_cols=23 Identities=17% Similarity=0.341 Sum_probs=16.9
Q ss_pred cCCCcHHHHHHHhCCCHHHHHHH
Q 038519 36 SKLDTLAGIAIKYGVDVADIRKL 58 (324)
Q Consensus 36 q~GDTL~~IA~KYgVsV~eI~~~ 58 (324)
++|=||..||+.+|++...+..+
T Consensus 13 krG~sL~~lsr~~Gl~~~tl~na 35 (78)
T PF13693_consen 13 KRGTSLAALSREAGLSSSTLRNA 35 (78)
T ss_dssp TTS--HHHHHHHHSS-HHHHHHT
T ss_pred HcCCCHHHHHHHcCCCHHHHHHH
Confidence 58999999999999999887643
No 83
>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=20.30 E-value=1.1e+02 Score=22.39 Aligned_cols=20 Identities=20% Similarity=0.285 Sum_probs=18.0
Q ss_pred cHHHHHHHhCCCHHHHHHHc
Q 038519 40 TLAGIAIKYGVDVADIRKLN 59 (324)
Q Consensus 40 TL~~IA~KYgVsV~eI~~~N 59 (324)
++..+|+..||+...|+.|=
T Consensus 2 ~i~evA~~~gvs~~tlR~~~ 21 (67)
T cd04764 2 TIKEVSEIIGVKPHTLRYYE 21 (67)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 57889999999999999983
Done!