Query 043749
Match_columns 125
No_of_seqs 134 out of 1150
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 07:59:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043749.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043749hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK06347 autolysin; Reviewed 99.8 1.5E-18 3.2E-23 146.0 9.5 116 6-123 437-592 (592)
2 PRK06347 autolysin; Reviewed 99.7 5.8E-17 1.3E-21 136.5 9.1 118 5-124 361-525 (592)
3 PRK10783 mltD membrane-bound l 99.7 5.8E-16 1.3E-20 127.4 12.9 90 33-124 343-448 (456)
4 PRK13914 invasion associated s 99.4 1.1E-12 2.3E-17 108.1 9.5 44 32-77 26-74 (481)
5 PRK10783 mltD membrane-bound l 99.3 6.9E-12 1.5E-16 103.4 8.7 69 8-78 377-450 (456)
6 PF01476 LysM: LysM domain; I 99.3 1.6E-12 3.4E-17 74.1 3.4 38 36-75 1-44 (44)
7 PRK14125 cell division suppres 99.2 7.2E-11 1.6E-15 79.5 6.3 48 31-78 34-92 (103)
8 TIGR02899 spore_safA spore coa 99.0 7.6E-10 1.6E-14 62.1 3.9 36 38-75 1-43 (44)
9 cd00118 LysM Lysin domain, fou 98.9 3.4E-09 7.4E-14 58.4 4.6 39 35-75 2-46 (46)
10 TIGR02907 spore_VI_D stage VI 98.8 4E-09 8.6E-14 83.5 5.2 43 31-75 291-338 (338)
11 PRK10871 nlpD lipoprotein NlpD 98.8 5.5E-09 1.2E-13 82.7 4.5 42 34-77 61-108 (319)
12 COG1388 LytE FOG: LysM repeat 98.8 2.1E-08 4.6E-13 68.6 6.7 69 7-77 22-113 (124)
13 smart00257 LysM Lysin motif. 98.5 1.6E-07 3.6E-12 50.9 4.4 38 35-74 1-44 (44)
14 PRK11198 LysM domain/BON super 98.5 1.3E-07 2.8E-12 67.3 4.8 43 33-75 95-146 (147)
15 PRK13914 invasion associated s 98.5 1.4E-07 3E-12 78.2 5.4 43 33-77 199-246 (481)
16 PF04225 OapA: Opacity-associa 98.3 8.7E-07 1.9E-11 57.7 3.4 43 33-77 2-54 (85)
17 COG1388 LytE FOG: LysM repeat 98.3 1.9E-06 4.1E-11 58.9 5.1 76 47-124 1-112 (124)
18 PF01476 LysM: LysM domain; I 98.0 2.3E-06 4.9E-11 48.2 1.5 28 96-123 16-44 (44)
19 COG3858 Predicted glycosyl hyd 97.9 6E-06 1.3E-10 67.3 2.8 87 34-123 2-95 (423)
20 COG3858 Predicted glycosyl hyd 97.8 3.6E-05 7.7E-10 62.8 5.0 61 4-77 31-97 (423)
21 TIGR03505 FimV_core FimV N-ter 97.7 4.6E-05 1E-09 48.4 3.2 36 42-77 1-52 (74)
22 COG1652 XkdP Uncharacterized p 97.6 1.9E-05 4E-10 61.0 1.0 44 34-77 211-264 (269)
23 PRK10871 nlpD lipoprotein NlpD 97.1 0.00017 3.7E-09 57.3 1.1 41 84-124 65-107 (319)
24 TIGR02899 spore_safA spore coa 97.1 0.00058 1.3E-08 37.6 3.0 29 96-124 14-44 (44)
25 cd00118 LysM Lysin domain, fou 97.0 0.00091 2E-08 36.0 3.0 28 96-123 18-46 (46)
26 TIGR02907 spore_VI_D stage VI 96.8 0.0013 2.7E-08 52.6 3.2 28 96-123 311-338 (338)
27 PRK10190 L,D-transpeptidase; P 96.8 0.0029 6.3E-08 50.2 5.2 42 34-77 38-87 (310)
28 PRK10260 L,D-transpeptidase; P 96.7 0.0032 6.9E-08 49.9 5.2 41 34-76 41-89 (306)
29 PRK11649 putative peptidase; P 96.7 0.0029 6.3E-08 52.4 5.1 44 32-77 94-144 (439)
30 COG3170 FimV Tfp pilus assembl 96.7 0.0012 2.7E-08 57.1 2.6 45 33-77 188-248 (755)
31 PRK14125 cell division suppres 96.6 0.0027 5.8E-08 42.7 3.6 25 100-124 66-90 (103)
32 COG3061 OapA Cell envelope opa 96.5 0.0061 1.3E-07 46.2 5.3 67 10-78 135-212 (242)
33 PF05489 Phage_tail_X: Phage T 95.2 0.062 1.3E-06 32.6 4.6 43 35-78 3-55 (60)
34 smart00257 LysM Lysin motif. 95.0 0.036 7.7E-07 29.0 2.9 27 96-122 17-44 (44)
35 PRK11198 LysM domain/BON super 92.2 0.071 1.5E-06 37.8 1.2 26 98-123 118-146 (147)
36 COG4784 Putative Zn-dependent 89.7 0.47 1E-05 38.7 3.8 41 34-74 429-476 (479)
37 COG0739 NlpD Membrane proteins 81.0 2.6 5.7E-05 31.6 4.0 42 34-77 2-49 (277)
38 PRK10190 L,D-transpeptidase; P 80.4 2.2 4.7E-05 34.1 3.5 29 96-124 57-86 (310)
39 COG4254 Uncharacterized protei 80.3 1.7 3.6E-05 34.6 2.7 47 33-79 5-58 (339)
40 PRK10260 L,D-transpeptidase; P 78.8 2.6 5.7E-05 33.5 3.5 29 96-124 60-89 (306)
41 PF13518 HTH_28: Helix-turn-he 72.1 3 6.4E-05 23.3 1.7 22 39-62 10-31 (52)
42 PF02796 HTH_7: Helix-turn-hel 67.9 4.8 0.0001 22.4 1.9 21 39-61 19-39 (45)
43 COG5004 P2-like prophage tail 62.1 21 0.00046 22.1 4.0 46 34-79 3-58 (70)
44 COG1652 XkdP Uncharacterized p 59.7 6.3 0.00014 30.2 1.8 27 98-124 233-263 (269)
45 PHA00675 hypothetical protein 59.6 7.9 0.00017 24.7 1.9 22 39-62 37-58 (78)
46 TIGR03028 EpsE polysaccharide 58.9 34 0.00075 25.8 5.7 70 6-76 147-236 (239)
47 PF04218 CENP-B_N: CENP-B N-te 57.6 4.1 8.8E-05 23.8 0.3 21 38-60 19-39 (53)
48 PF13936 HTH_38: Helix-turn-he 55.7 12 0.00025 20.8 2.0 20 39-60 18-37 (44)
49 COG2963 Transposase and inacti 53.1 13 0.00028 24.6 2.2 24 37-62 20-44 (116)
50 PF05225 HTH_psq: helix-turn-h 51.2 10 0.00022 21.3 1.3 23 38-62 12-35 (45)
51 PF13384 HTH_23: Homeodomain-l 50.5 16 0.00034 20.2 2.1 22 39-62 15-36 (50)
52 PF01527 HTH_Tnp_1: Transposas 50.4 6.2 0.00014 23.8 0.3 23 38-62 20-42 (76)
53 PF08765 Mor: Mor transcriptio 50.4 13 0.00029 24.6 2.0 46 12-62 45-91 (108)
54 PF04545 Sigma70_r4: Sigma-70, 49.4 20 0.00044 20.0 2.4 22 39-62 18-39 (50)
55 PF14451 Ub-Mut7C: Mut7-C ubiq 48.2 51 0.0011 21.0 4.4 42 32-75 23-74 (81)
56 TIGR00370 conserved hypothetic 47.8 80 0.0017 23.5 6.0 80 40-121 89-200 (202)
57 PF13693 HTH_35: Winged helix- 47.2 19 0.00041 23.0 2.2 22 39-62 13-34 (78)
58 PF11112 PyocinActivator: Pyoc 47.0 20 0.00044 22.6 2.3 50 43-106 16-67 (76)
59 cd00569 HTH_Hin_like Helix-tur 46.9 24 0.00053 16.7 2.3 20 39-60 19-38 (42)
60 PRK09413 IS2 repressor TnpA; R 40.4 26 0.00056 23.6 2.2 26 35-62 23-48 (121)
61 KOG2850 Predicted peptidoglyca 39.8 21 0.00046 26.5 1.8 43 33-77 9-57 (186)
62 TIGR03027 pepcterm_export puta 38.9 28 0.00061 24.6 2.3 28 96-123 133-161 (165)
63 PF13542 HTH_Tnp_ISL3: Helix-t 37.9 33 0.00071 19.0 2.1 20 41-62 27-46 (52)
64 cd06919 Asp_decarbox Aspartate 36.6 17 0.00036 24.8 0.8 64 50-122 20-86 (111)
65 PHA01976 helix-turn-helix prot 35.4 24 0.00051 20.7 1.2 21 40-62 43-63 (67)
66 PRK10344 DNA-binding transcrip 35.2 36 0.00078 22.4 2.1 22 39-62 19-40 (92)
67 PF01381 HTH_3: Helix-turn-hel 34.3 19 0.0004 20.2 0.6 18 41-60 38-55 (55)
68 PF04255 DUF433: Protein of un 32.9 37 0.0008 19.8 1.8 22 39-61 29-50 (56)
69 smart00421 HTH_LUXR helix_turn 32.6 53 0.0012 17.7 2.4 23 38-62 15-37 (58)
70 cd04493 BRCA2DBD_OB1 BRCA2DBD_ 32.5 7.2 0.00016 26.1 -1.5 34 41-76 28-61 (100)
71 PRK05449 aspartate alpha-decar 31.8 22 0.00049 24.7 0.8 27 50-76 21-48 (126)
72 PF09012 FeoC: FeoC like trans 31.6 35 0.00075 20.5 1.6 32 43-76 16-49 (69)
73 PF13613 HTH_Tnp_4: Helix-turn 31.0 33 0.00073 19.6 1.4 21 38-60 16-36 (53)
74 PF13510 Fer2_4: 2Fe-2S iron-s 29.1 50 0.0011 20.7 2.0 19 34-52 11-29 (82)
75 PF08281 Sigma70_r4_2: Sigma-7 28.1 54 0.0012 18.3 1.9 21 39-61 24-44 (54)
76 PF11268 DUF3071: Protein of u 27.6 50 0.0011 24.1 2.0 25 36-62 64-88 (170)
77 PF07610 DUF1573: Protein of u 27.3 34 0.00074 19.0 0.9 22 18-43 17-38 (45)
78 PF00392 GntR: Bacterial regul 26.7 48 0.001 19.4 1.6 23 38-62 18-43 (64)
79 KOG1468 Predicted translation 26.3 1.2E+02 0.0026 24.4 4.0 42 35-78 242-295 (354)
80 TIGR02937 sigma70-ECF RNA poly 25.2 69 0.0015 20.8 2.3 22 39-62 124-145 (158)
81 PF11242 DUF2774: Protein of u 24.3 95 0.0021 19.0 2.5 21 40-62 12-32 (63)
82 PF13443 HTH_26: Cro/C1-type H 24.1 32 0.0007 19.8 0.5 20 41-62 40-59 (63)
83 PF01371 Trp_repressor: Trp re 24.0 77 0.0017 20.5 2.2 22 39-62 47-68 (87)
84 PF07836 DmpG_comm: DmpG-like 24.0 75 0.0016 19.6 2.1 25 45-71 26-53 (66)
85 PF08220 HTH_DeoR: DeoR-like h 23.9 65 0.0014 18.7 1.7 18 43-62 16-33 (57)
86 PRK12845 3-ketosteroid-delta-1 23.6 64 0.0014 27.6 2.3 23 38-62 421-443 (564)
87 TIGR02531 yecD_yerC TrpR-relat 23.2 62 0.0014 20.9 1.7 23 38-62 47-69 (88)
88 PF08356 EF_assoc_2: EF hand a 23.0 36 0.00077 22.2 0.5 15 38-52 42-58 (89)
89 smart00760 Bac_DnaA_C Bacteria 23.0 65 0.0014 18.8 1.7 14 40-53 44-57 (60)
90 TIGR00223 panD L-aspartate-alp 22.9 41 0.00088 23.5 0.8 27 50-76 21-48 (126)
91 PF04921 XAP5: XAP5, circadian 22.7 1.4E+02 0.003 23.1 3.7 62 12-77 95-161 (239)
92 COG2442 Uncharacterized conser 22.7 31 0.00066 22.0 0.1 43 19-62 17-63 (79)
93 cd06170 LuxR_C_like C-terminal 22.3 1.1E+02 0.0023 16.6 2.4 22 39-62 13-34 (57)
94 PF01710 HTH_Tnp_IS630: Transp 22.1 47 0.001 22.3 1.0 23 38-62 15-37 (119)
95 PRK12837 3-ketosteroid-delta-1 21.7 76 0.0016 26.6 2.3 23 38-62 372-394 (513)
96 PF13621 Cupin_8: Cupin-like d 21.3 41 0.0009 24.5 0.6 12 113-124 212-223 (251)
97 COG2739 Uncharacterized protei 21.0 86 0.0019 21.1 2.0 16 43-60 35-50 (105)
98 PF10668 Phage_terminase: Phag 20.9 1E+02 0.0022 18.6 2.2 18 43-62 24-41 (60)
99 smart00345 HTH_GNTR helix_turn 20.7 94 0.002 17.1 2.0 23 38-62 14-39 (60)
100 PF15608 PELOTA_1: PELOTA RNA 20.6 74 0.0016 21.2 1.7 12 41-52 22-33 (100)
101 PF12844 HTH_19: Helix-turn-he 20.4 54 0.0012 18.9 0.9 19 42-62 42-60 (64)
102 PF04760 IF2_N: Translation in 20.3 76 0.0016 18.0 1.5 18 43-62 5-22 (54)
103 PF00376 MerR: MerR family reg 20.2 92 0.002 16.7 1.7 18 43-62 1-18 (38)
104 PRK15483 type III restriction- 20.1 66 0.0014 29.8 1.7 27 33-60 308-334 (986)
No 1
>PRK06347 autolysin; Reviewed
Probab=99.77 E-value=1.5e-18 Score=146.03 Aligned_cols=116 Identities=16% Similarity=0.160 Sum_probs=82.4
Q ss_pred CCcccCCCCEEEEcccccCCCC---------------CcccCceeeEEcCCCCHHHHHHHhCCCCCHHHhhc-----cCC
Q 043749 6 GNQILGTKSLVKVPISCPCIDG---------------IKRSESTTNNVWPADTIDSILNEFGGLVSAEQINS-----TNG 65 (125)
Q Consensus 6 ~~~~l~~g~~l~IP~~c~c~~~---------------~~~~~~~~y~V~~GDTl~~IA~~y~~~vs~~~i~~-----~~~ 65 (125)
.+..|.+||.|.||..-.-... ........|+|++|||||+||++|| +++++|++ .+.
T Consensus 437 ~s~~L~~Gq~L~IP~~~~~~~~t~~~s~~~~~~k~~s~~~~~~~~YtVk~GDTL~sIAkkyg--VSv~~L~~~N~l~s~~ 514 (592)
T PRK06347 437 KSDFIYPGQKLKVSAGSTSNTNTSKPSTNTNTSKPSTNTNTNAKVYTVAKGDSLWRIANNNK--VTIANLKSWNNLKSDF 514 (592)
T ss_pred CcceeccCcEEEEecCCcccccccccccccccccccccccccceeeeecCCCCHHHHHHHHC--CCHHHHHHhcCCCccc
Confidence 3457999999999965210000 0011235799999999999999999 89999988 467
Q ss_pred CCCCCEEEEecCccccCCC------C---CCcceeeEe----------e-eCCcHHHHHHhcCCCCCCCCCCCEEEEc
Q 043749 66 SNYPTSLMIMLSCTCFNNG------N---NGVTSVYKS----------K-FWVMMAELVATNGLSQSVVDPIDILAIP 123 (125)
Q Consensus 66 i~~Gq~L~IP~~~~~~~~~------~---~~~~~~~~~----------y-~gvs~~~L~~~N~l~~~~l~~Gq~L~IP 123 (125)
|++||.|.||......... . ......|.. . ||+++++|++||+|....|++||+|.|+
T Consensus 515 L~~GQ~L~Ip~~~~~s~~~t~~~s~~~~~~~~~~~Y~Vk~GDTL~sIA~KygvSv~~L~~~N~L~~~~L~~GQ~L~I~ 592 (592)
T PRK06347 515 IYPGQKLKVSAGSTTNNTNTAKPSTNKPSNSTVKTYTVKKGDSLWAISRQYKTTVDNIKAWNKLTSNMIHVGQKLTIK 592 (592)
T ss_pred ccCCcEEEEecCcccccccccCCccCCccCccceeeecCCCCcHHHHHHHhCCCHHHHHHhcCCCcccCCCCCEEecC
Confidence 9999999999754321100 0 000011111 1 9999999999999987779999999986
No 2
>PRK06347 autolysin; Reviewed
Probab=99.70 E-value=5.8e-17 Score=136.48 Aligned_cols=118 Identities=19% Similarity=0.165 Sum_probs=83.4
Q ss_pred CCCcccCCCCEEEEcccccCCCC----------------CcccCceeeEEcCCCCHHHHHHHhCCCCCHHHhhc-----c
Q 043749 5 LGNQILGTKSLVKVPISCPCIDG----------------IKRSESTTNNVWPADTIDSILNEFGGLVSAEQINS-----T 63 (125)
Q Consensus 5 ~~~~~l~~g~~l~IP~~c~c~~~----------------~~~~~~~~y~V~~GDTl~~IA~~y~~~vs~~~i~~-----~ 63 (125)
+.+..|.+||.|.||..-.-... .....+..|+|++|||||+||++|| +++.+|+. .
T Consensus 361 l~~d~L~~Gq~L~VP~~~~~~~~~t~~~~~~~~~~~~~~~~~~~~~~ytVk~GDTL~sIA~kyg--VSv~~L~~~N~l~s 438 (592)
T PRK06347 361 LKSDFIYPGQKLKVSAGSTTSDTNTSKPSTGTSTSKPSTGTSTNAKVYTVVKGDSLWRIANNNK--VTIANLKSWNNLKS 438 (592)
T ss_pred CCccccccCcEEEEeccccccccccccccccccccccccccccCceeEEecCCCCHHHHHHHhC--CCHHHHHHHhCCCc
Confidence 34567999999999974211000 0012346899999999999999999 89999987 4
Q ss_pred CCCCCCCEEEEecCccccCC----C-----C------CCcceeeEee-----------eCCcHHHHHHhcCCCCCCCCCC
Q 043749 64 NGSNYPTSLMIMLSCTCFNN----G-----N------NGVTSVYKSK-----------FWVMMAELVATNGLSQSVVDPI 117 (125)
Q Consensus 64 ~~i~~Gq~L~IP~~~~~~~~----~-----~------~~~~~~~~~y-----------~gvs~~~L~~~N~l~~~~l~~G 117 (125)
+.|++||.|.||........ . . ......|... ||+++++|++||++.++.|++|
T Consensus 439 ~~L~~Gq~L~IP~~~~~~~~t~~~s~~~~~~k~~s~~~~~~~~YtVk~GDTL~sIAkkygVSv~~L~~~N~l~s~~L~~G 518 (592)
T PRK06347 439 DFIYPGQKLKVSAGSTSNTNTSKPSTNTNTSKPSTNTNTNAKVYTVAKGDSLWRIANNNKVTIANLKSWNNLKSDFIYPG 518 (592)
T ss_pred ceeccCcEEEEecCCcccccccccccccccccccccccccceeeeecCCCCHHHHHHHHCCCHHHHHHhcCCCcccccCC
Confidence 67999999999964321000 0 0 0000111110 9999999999999987789999
Q ss_pred CEEEEcC
Q 043749 118 DILAIPI 124 (125)
Q Consensus 118 q~L~IP~ 124 (125)
|+|.||.
T Consensus 519 Q~L~Ip~ 525 (592)
T PRK06347 519 QKLKVSA 525 (592)
T ss_pred cEEEEec
Confidence 9999984
No 3
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional
Probab=99.68 E-value=5.8e-16 Score=127.36 Aligned_cols=90 Identities=20% Similarity=0.242 Sum_probs=69.2
Q ss_pred ceeeEEcCCCCHHHHHHHhCCCCCHHHhhc-----cCCCCCCCEEEEecCccccCCCCCCcceeeEe----------e-e
Q 043749 33 STTNNVWPADTIDSILNEFGGLVSAEQINS-----TNGSNYPTSLMIMLSCTCFNNGNNGVTSVYKS----------K-F 96 (125)
Q Consensus 33 ~~~y~V~~GDTl~~IA~~y~~~vs~~~i~~-----~~~i~~Gq~L~IP~~~~~~~~~~~~~~~~~~~----------y-~ 96 (125)
..+|+|++||||++||++|| ++..+|++ .+.|++||.|.||.++.+...........|.. . |
T Consensus 343 ~~~y~Vk~GDTL~sIA~r~g--vs~~~L~~~N~l~~~~L~~Gq~L~Ip~~~~~~~~~~~~~~~~Y~Vr~GDTL~sIA~ky 420 (456)
T PRK10783 343 SRSYKVRSGDTLSGIASRLN--VSTKDLQQWNNLRGSKLKVGQTLTIGAGSSAQRLANNSDSITYRVRKGDSLSSIAKRH 420 (456)
T ss_pred ceEEEECCCCcHHHHHHHHC--cCHHHHHHHcCCCcccCCCCCEEEecCCcccccccccccceeEEeCCCCCHHHHHHHh
Confidence 46899999999999999999 88888887 45799999999998655421111111111211 1 9
Q ss_pred CCcHHHHHHhcCCCCCCCCCCCEEEEcC
Q 043749 97 WVMMAELVATNGLSQSVVDPIDILAIPI 124 (125)
Q Consensus 97 gvs~~~L~~~N~l~~~~l~~Gq~L~IP~ 124 (125)
|||+++|++||++..+.|+|||+|.|++
T Consensus 421 gVtv~~L~~~N~l~~~~L~pGq~L~l~v 448 (456)
T PRK10783 421 GVNIKDVMRWNSDTAKNLQPGDKLTLFV 448 (456)
T ss_pred CCCHHHHHHhcCCCCCcCCCCCEEEEec
Confidence 9999999999998755899999999975
No 4
>PRK13914 invasion associated secreted endopeptidase; Provisional
Probab=99.42 E-value=1.1e-12 Score=108.10 Aligned_cols=44 Identities=20% Similarity=0.132 Sum_probs=39.3
Q ss_pred CceeeEEcCCCCHHHHHHHhCCCCCHHHhhc-----cCCCCCCCEEEEecC
Q 043749 32 ESTTNNVWPADTIDSILNEFGGLVSAEQINS-----TNGSNYPTSLMIMLS 77 (125)
Q Consensus 32 ~~~~y~V~~GDTl~~IA~~y~~~vs~~~i~~-----~~~i~~Gq~L~IP~~ 77 (125)
.+.+|+|++|||||+||++|| +++++|++ ++.|++||+|.||..
T Consensus 26 sa~tytVq~GDTLw~IA~~yg--vtv~~I~~~N~l~~~~I~~Gq~L~Ip~~ 74 (481)
T PRK13914 26 SASTVVVEAGDTLWGIAQSKG--TTVDAIKKANNLTTDKIVPGQKLQVNEV 74 (481)
T ss_pred cCceEEECCCCCHHHHHHHHC--CCHHHHHHHhCCCcccccCCCEEEeCCC
Confidence 357899999999999999999 88999987 567999999999954
No 5
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional
Probab=99.32 E-value=6.9e-12 Score=103.36 Aligned_cols=69 Identities=16% Similarity=0.187 Sum_probs=56.9
Q ss_pred cccCCCCEEEEcccccCCCCCcccCceeeEEcCCCCHHHHHHHhCCCCCHHHhhc-----cCCCCCCCEEEEecCc
Q 043749 8 QILGTKSLVKVPISCPCIDGIKRSESTTNNVWPADTIDSILNEFGGLVSAEQINS-----TNGSNYPTSLMIMLSC 78 (125)
Q Consensus 8 ~~l~~g~~l~IP~~c~c~~~~~~~~~~~y~V~~GDTl~~IA~~y~~~vs~~~i~~-----~~~i~~Gq~L~IP~~~ 78 (125)
..|.+||.|.||..|.|..........+|+|++|||||+||++|| |++.+|++ .+.|++||+|.|++..
T Consensus 377 ~~L~~Gq~L~Ip~~~~~~~~~~~~~~~~Y~Vr~GDTL~sIA~kyg--Vtv~~L~~~N~l~~~~L~pGq~L~l~v~~ 450 (456)
T PRK10783 377 SKLKVGQTLTIGAGSSAQRLANNSDSITYRVRKGDSLSSIAKRHG--VNIKDVMRWNSDTAKNLQPGDKLTLFVKN 450 (456)
T ss_pred ccCCCCCEEEecCCcccccccccccceeEEeCCCCCHHHHHHHhC--CCHHHHHHhcCCCCCcCCCCCEEEEecCC
Confidence 569999999999988764322223347899999999999999999 89999987 2379999999999764
No 6
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=99.32 E-value=1.6e-12 Score=74.07 Aligned_cols=38 Identities=26% Similarity=0.387 Sum_probs=30.9
Q ss_pred eEEcCCCCHHHHHHHhCCCCCHHHhhc------cCCCCCCCEEEEe
Q 043749 36 NNVWPADTIDSILNEFGGLVSAEQINS------TNGSNYPTSLMIM 75 (125)
Q Consensus 36 y~V~~GDTl~~IA~~y~~~vs~~~i~~------~~~i~~Gq~L~IP 75 (125)
|+|++|||+|+||++|+ ++.++|++ .+.|.+||+|.||
T Consensus 1 y~V~~gDtl~~IA~~~~--~~~~~l~~~N~~~~~~~l~~G~~l~iP 44 (44)
T PF01476_consen 1 YTVQPGDTLWSIAKRYG--ISVDELMELNPNIDSDNLQPGQKLCIP 44 (44)
T ss_dssp EEE-TT--HHHHHHHTT--S-HHHHHHHCCTTHGGCGGTTEEEEEC
T ss_pred CEECcCCcHHHHHhhhh--hhHhHHHHhcCCCCcccCCCCCEEEeC
Confidence 89999999999999999 88998888 3459999999998
No 7
>PRK14125 cell division suppressor protein YneA; Provisional
Probab=99.18 E-value=7.2e-11 Score=79.54 Aligned_cols=48 Identities=15% Similarity=0.194 Sum_probs=37.0
Q ss_pred cCceeeEEcCCCCHHHHHHHhCCC--CC----HHHhhc-----cCCCCCCCEEEEecCc
Q 043749 31 SESTTNNVWPADTIDSILNEFGGL--VS----AEQINS-----TNGSNYPTSLMIMLSC 78 (125)
Q Consensus 31 ~~~~~y~V~~GDTl~~IA~~y~~~--vs----~~~i~~-----~~~i~~Gq~L~IP~~~ 78 (125)
..+.+|+|++|||||+||++|++. ++ +++|++ ++.|++||+|.||...
T Consensus 34 ~~~~~~tV~~GDTLW~IA~~y~~~~~l~~~~~v~~I~~~N~l~~~~I~~Gq~L~IP~~~ 92 (103)
T PRK14125 34 NQYVEITVQEGDTLWALADQYAGKHHMAKNEFIEWVEDVNNLPSGHIKAGDKLVIPVLK 92 (103)
T ss_pred CCcEEEEECCCCCHHHHHHHhCCCcCCCHHHHHHHHHHhcCCCCCcCCCCCEEEEecCC
Confidence 346889999999999999999842 22 234433 5679999999999754
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=98.97 E-value=7.6e-10 Score=62.11 Aligned_cols=36 Identities=22% Similarity=0.208 Sum_probs=31.6
Q ss_pred EcCCCCHHHHHHHhCCCCCHHHhhc-------cCCCCCCCEEEEe
Q 043749 38 VWPADTIDSILNEFGGLVSAEQINS-------TNGSNYPTSLMIM 75 (125)
Q Consensus 38 V~~GDTl~~IA~~y~~~vs~~~i~~-------~~~i~~Gq~L~IP 75 (125)
|++|||||+||++|+ ++.++|++ ++.+++||+|.||
T Consensus 1 v~~gdtl~~IA~~~~--~~~~~l~~~N~~~~~~~~~~~g~~l~ip 43 (44)
T TIGR02899 1 VQKGDTLWKIAKKYG--VDFDELIQANPQLSNPNLIYPGMKIKIP 43 (44)
T ss_pred CCCCCCHHHHHHHHC--cCHHHHHHHhhcCCCCCCcCCCCEEecC
Confidence 689999999999999 78888876 2469999999998
No 9
>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=98.89 E-value=3.4e-09 Score=58.41 Aligned_cols=39 Identities=28% Similarity=0.371 Sum_probs=34.4
Q ss_pred eeEEcCCCCHHHHHHHhCCCCCHHHhhc------cCCCCCCCEEEEe
Q 043749 35 TNNVWPADTIDSILNEFGGLVSAEQINS------TNGSNYPTSLMIM 75 (125)
Q Consensus 35 ~y~V~~GDTl~~IA~~y~~~vs~~~i~~------~~~i~~Gq~L~IP 75 (125)
.|+|++|||+|+||++|+ ++..+++. ...+.+|+.|.||
T Consensus 2 ~~~v~~gdt~~~ia~~~~--~~~~~~~~~N~~~~~~~~~~g~~l~ip 46 (46)
T cd00118 2 TYTVKKGDTLSSIAQRYG--ISVEELLKLNGLSDPDNLQVGQKLKIP 46 (46)
T ss_pred EEEECCCCCHHHHHHHHC--cCHHHHHHHcCCCCccccCCCCEEecC
Confidence 699999999999999999 78888877 3468999999987
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=98.85 E-value=4e-09 Score=83.46 Aligned_cols=43 Identities=23% Similarity=0.203 Sum_probs=38.8
Q ss_pred cCceeeEEcCCCCHHHHHHHhCCCCCHHHhhc-----cCCCCCCCEEEEe
Q 043749 31 SESTTNNVWPADTIDSILNEFGGLVSAEQINS-----TNGSNYPTSLMIM 75 (125)
Q Consensus 31 ~~~~~y~V~~GDTl~~IA~~y~~~vs~~~i~~-----~~~i~~Gq~L~IP 75 (125)
..+.+|+|++|||||+||++|| +++..|++ ++.|++||.|.||
T Consensus 291 ~~~~~YiVq~GDTL~sIAkRYG--VSV~~L~r~N~L~~~~L~~GQ~L~IP 338 (338)
T TIGR02907 291 TKLRMCIVQEGDTIETIAERYE--ISVSQLIRHNQLEDFEVNEGQILYIP 338 (338)
T ss_pred cccEEEEECCCCCHHHHHHHHC--cCHHHHHHHhCCCccccCCCCEEEeC
Confidence 4468999999999999999999 88888887 4689999999998
No 11
>PRK10871 nlpD lipoprotein NlpD; Provisional
Probab=98.79 E-value=5.5e-09 Score=82.68 Aligned_cols=42 Identities=19% Similarity=0.063 Sum_probs=37.9
Q ss_pred eeeEEcCCCCHHHHHHHhCCCCCHHHhhc------cCCCCCCCEEEEecC
Q 043749 34 TTNNVWPADTIDSILNEFGGLVSAEQINS------TNGSNYPTSLMIMLS 77 (125)
Q Consensus 34 ~~y~V~~GDTl~~IA~~y~~~vs~~~i~~------~~~i~~Gq~L~IP~~ 77 (125)
.+|+||+|||||+||++|| +++.+|++ ++.|++||+|.||..
T Consensus 61 ~~y~Vk~GDTL~~IA~~~g--~~~~~La~~N~l~~p~~I~~GQ~L~i~~~ 108 (319)
T PRK10871 61 STYTVKKGDTLFYIAWITG--NDFRDLAQRNNIQAPYSLNVGQTLQVGNA 108 (319)
T ss_pred CceEECCCCHHHHHHHHHC--cCHHHHHHhcCCCCCccccCCCEEEeCCC
Confidence 5799999999999999999 88888877 578999999999754
No 12
>COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane]
Probab=98.79 E-value=2.1e-08 Score=68.62 Aligned_cols=69 Identities=19% Similarity=0.300 Sum_probs=52.1
Q ss_pred CcccCCCCEEEEccc--ccCCCCC---cccC-------------ceeeEEcCCCCHHHHHHHhCCCCCHHHhhc-----c
Q 043749 7 NQILGTKSLVKVPIS--CPCIDGI---KRSE-------------STTNNVWPADTIDSILNEFGGLVSAEQINS-----T 63 (125)
Q Consensus 7 ~~~l~~g~~l~IP~~--c~c~~~~---~~~~-------------~~~y~V~~GDTl~~IA~~y~~~vs~~~i~~-----~ 63 (125)
...+.+||.|.+|.. -.-..+. .... ..+|+|++||||+.||++|+ +++.+|+. .
T Consensus 22 s~~i~~gq~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~gdtL~~Ia~~~~--~tv~~l~~~n~l~~ 99 (124)
T COG1388 22 SDAIKPGQVLKIPGDISSTVNAGQTLSSLSNKVSDSSSASKAPPVVTYTVKKGDTLSKIARKYG--VTVAELKQLNNLSS 99 (124)
T ss_pred CCccccCceEEccCCcccccccccccccccceeeccccccccCCCceEEEecCCCHHHHHHHhC--CCHHHHHHHhccCC
Confidence 567899999999963 1111110 0000 14799999999999999999 88888888 5
Q ss_pred CCCCCCCEEEEecC
Q 043749 64 NGSNYPTSLMIMLS 77 (125)
Q Consensus 64 ~~i~~Gq~L~IP~~ 77 (125)
+.+++||.|.++..
T Consensus 100 ~~i~~gq~l~~~~~ 113 (124)
T COG1388 100 DKIKVGQKLKLPVS 113 (124)
T ss_pred CceecCcEEEEecc
Confidence 78999999999963
No 13
>smart00257 LysM Lysin motif.
Probab=98.54 E-value=1.6e-07 Score=50.87 Aligned_cols=38 Identities=26% Similarity=0.362 Sum_probs=31.1
Q ss_pred eeEEcCCCCHHHHHHHhCCCCCHHHhhc------cCCCCCCCEEEE
Q 043749 35 TNNVWPADTIDSILNEFGGLVSAEQINS------TNGSNYPTSLMI 74 (125)
Q Consensus 35 ~y~V~~GDTl~~IA~~y~~~vs~~~i~~------~~~i~~Gq~L~I 74 (125)
.|+|++|||+|+||++|+ ++..++.. ...+++|+.|.|
T Consensus 1 ~~~v~~gdt~~~ia~~~~--~~~~~~~~~N~~~~~~~~~~g~~l~i 44 (44)
T smart00257 1 TYTVKKGDTLSSIARRYG--ISVSDLLELNNILDPDNLQVGQKLKI 44 (44)
T ss_pred CeEeCCCCCHHHHHHHhC--CCHHHHHHHcCCCCccccCCCCEEeC
Confidence 489999999999999999 67777766 246888887764
No 14
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=98.54 E-value=1.3e-07 Score=67.28 Aligned_cols=43 Identities=21% Similarity=0.091 Sum_probs=33.4
Q ss_pred ceeeEEcCCCCHHHHHHHhCCC-CCHHHhhc--------cCCCCCCCEEEEe
Q 043749 33 STTNNVWPADTIDSILNEFGGL-VSAEQINS--------TNGSNYPTSLMIM 75 (125)
Q Consensus 33 ~~~y~V~~GDTl~~IA~~y~~~-vs~~~i~~--------~~~i~~Gq~L~IP 75 (125)
..+|+|++|||||+||++|++. .....|.+ ++.|++||+|.||
T Consensus 95 ~~~y~Vk~GDTL~~IA~~~~g~~~~~~~I~~~N~~~l~~~~~I~pGq~L~IP 146 (147)
T PRK11198 95 SQFYTVKSGDTLSAIAKKVYGNANKYNKIFEANKPMLKSPDKIYPGQVLRIP 146 (147)
T ss_pred CeEEEECCCCCHHHHHHHHcCChhhHHHHHHhhhhcCCCcCCcCcCCEEecC
Confidence 4689999999999999998532 33444433 4679999999998
No 15
>PRK13914 invasion associated secreted endopeptidase; Provisional
Probab=98.53 E-value=1.4e-07 Score=78.16 Aligned_cols=43 Identities=30% Similarity=0.323 Sum_probs=39.2
Q ss_pred ceeeEEcCCCCHHHHHHHhCCCCCHHHhhc-----cCCCCCCCEEEEecC
Q 043749 33 STTNNVWPADTIDSILNEFGGLVSAEQINS-----TNGSNYPTSLMIMLS 77 (125)
Q Consensus 33 ~~~y~V~~GDTl~~IA~~y~~~vs~~~i~~-----~~~i~~Gq~L~IP~~ 77 (125)
..+|+|++|||||+||++|| +++++|++ .+.|++||+|.||..
T Consensus 199 a~tytVq~GDTL~sIAkrYg--Vtv~eI~~~N~l~s~~L~pGQ~L~Ip~s 246 (481)
T PRK13914 199 ATTHAVKSGDTIWALSVKYG--VSVQDIMSWNNLSSSSIYVGQKLAIKQT 246 (481)
T ss_pred CeEEEECCCCCHHHHHHHHC--CCHHHHHHhcCCCccccCCCCEEEecCC
Confidence 47899999999999999999 89999988 467999999999964
No 16
>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=98.27 E-value=8.7e-07 Score=57.69 Aligned_cols=43 Identities=21% Similarity=0.232 Sum_probs=27.1
Q ss_pred ceeeEEcCCCCHHHHHHHhCCCCCHHHhhc----------cCCCCCCCEEEEecC
Q 043749 33 STTNNVWPADTIDSILNEFGGLVSAEQINS----------TNGSNYPTSLMIMLS 77 (125)
Q Consensus 33 ~~~y~V~~GDTl~~IA~~y~~~vs~~~i~~----------~~~i~~Gq~L~IP~~ 77 (125)
|..|+|++||||+.|-+++| ++..++.+ -..|+|||.|.+-..
T Consensus 2 W~~~~V~~GDtLs~iF~~~g--ls~~dl~~v~~~~~~~k~L~~L~pGq~l~f~~d 54 (85)
T PF04225_consen 2 WQEYTVKSGDTLSTIFRRAG--LSASDLYAVLEADGEAKPLTRLKPGQTLEFQLD 54 (85)
T ss_dssp --EEE--TT--HHHHHHHTT----HHHHHHHHHHGGGT--GGG--TT-EEEEEE-
T ss_pred CcEEEECCCCcHHHHHHHcC--CCHHHHHHHHhccCccchHhhCCCCCEEEEEEC
Confidence 67899999999999999999 78877776 257999999999864
No 17
>COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane]
Probab=98.26 E-value=1.9e-06 Score=58.91 Aligned_cols=76 Identities=21% Similarity=0.216 Sum_probs=52.3
Q ss_pred HHHHhCCCCCHHHhhc-------cCCCCCCCEEEEecCccccC----CCCCCccee-----------eEee---------
Q 043749 47 ILNEFGGLVSAEQINS-------TNGSNYPTSLMIMLSCTCFN----NGNNGVTSV-----------YKSK--------- 95 (125)
Q Consensus 47 IA~~y~~~vs~~~i~~-------~~~i~~Gq~L~IP~~~~~~~----~~~~~~~~~-----------~~~y--------- 95 (125)
||.+|+ +++.+++. .+.+++||+|.++....... ......... +..|
T Consensus 1 ia~~~~--~~v~~l~~~n~~~~~s~~i~~gq~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~gdtL~ 78 (124)
T COG1388 1 IASKYG--VSVKALKKANALTGKSDAIKPGQVLKIPGDISSTVNAGQTLSSLSNKVSDSSSASKAPPVVTYTVKKGDTLS 78 (124)
T ss_pred Cccccc--ccHHHHHHHhcccCCCCccccCceEEccCCcccccccccccccccceeeccccccccCCCceEEEecCCCHH
Confidence 577888 67777766 45899999999996311100 000111000 1122
Q ss_pred -----eCCcHHHHHHhcCCCCCCCCCCCEEEEcC
Q 043749 96 -----FWVMMAELVATNGLSQSVVDPIDILAIPI 124 (125)
Q Consensus 96 -----~gvs~~~L~~~N~l~~~~l~~Gq~L~IP~ 124 (125)
|++++.+|++||++.++.+++||.|.+|.
T Consensus 79 ~Ia~~~~~tv~~l~~~n~l~~~~i~~gq~l~~~~ 112 (124)
T COG1388 79 KIARKYGVTVAELKQLNNLSSDKIKVGQKLKLPV 112 (124)
T ss_pred HHHHHhCCCHHHHHHHhccCCCceecCcEEEEec
Confidence 99999999999999988999999999973
No 18
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=98.03 E-value=2.3e-06 Score=48.24 Aligned_cols=28 Identities=25% Similarity=0.462 Sum_probs=24.8
Q ss_pred eCCcHHHHHHhc-CCCCCCCCCCCEEEEc
Q 043749 96 FWVMMAELVATN-GLSQSVVDPIDILAIP 123 (125)
Q Consensus 96 ~gvs~~~L~~~N-~l~~~~l~~Gq~L~IP 123 (125)
||++.++|++|| ++..+.|++||+|.||
T Consensus 16 ~~~~~~~l~~~N~~~~~~~l~~G~~l~iP 44 (44)
T PF01476_consen 16 YGISVDELMELNPNIDSDNLQPGQKLCIP 44 (44)
T ss_dssp TTS-HHHHHHHCCTTHGGCGGTTEEEEEC
T ss_pred hhhhHhHHHHhcCCCCcccCCCCCEEEeC
Confidence 999999999999 7876569999999998
No 19
>COG3858 Predicted glycosyl hydrolase [General function prediction only]
Probab=97.93 E-value=6e-06 Score=67.25 Aligned_cols=87 Identities=17% Similarity=0.043 Sum_probs=65.9
Q ss_pred eeeEEcCCCCHHHHHHHhCCCCCHHHhhc-----cCCCCCCCEEEEecCccccCCCCCCcceeeEe-eeCCcHHHHHHhc
Q 043749 34 TTNNVWPADTIDSILNEFGGLVSAEQINS-----TNGSNYPTSLMIMLSCTCFNNGNNGVTSVYKS-KFWVMMAELVATN 107 (125)
Q Consensus 34 ~~y~V~~GDTl~~IA~~y~~~vs~~~i~~-----~~~i~~Gq~L~IP~~~~~~~~~~~~~~~~~~~-y~gvs~~~L~~~N 107 (125)
..|.|++||++..||++|+ ++..+|.+ .+.|.+||.+.||.... ...+..++....++ .|||+++.+..+|
T Consensus 2 ~i~~~~pg~~~~~i~~~~~--~~~~~i~~~~~~~~d~~~~~q~~~v~~~~~-~y~~~~~d~~~Sia~~~~vt~~~~~~m~ 78 (423)
T COG3858 2 SIHLVGPGDSRLIIAVYFP--YTNNRIVNGNDYTNDDLVDGQTFVVPPSGH-FYDVGPGDTLTSIARTVGVTQDSAAIMN 78 (423)
T ss_pred EEEEccCCceeeeehhhcc--ccccccccccccccccccCceeEEECCcce-EEEecCCcchhhhhhhhcCCHHHHHhhc
Confidence 4699999999999999999 77777776 46799999999996422 22233443222222 2999999999999
Q ss_pred CCC-CCCCCCCCEEEEc
Q 043749 108 GLS-QSVVDPIDILAIP 123 (125)
Q Consensus 108 ~l~-~~~l~~Gq~L~IP 123 (125)
.+. ..-+.+|=.|.+|
T Consensus 79 ~~~~~~~l~~~~~l~~P 95 (423)
T COG3858 79 FVICPGYLQYGLNLYIP 95 (423)
T ss_pred ccccccceeeeeEEecc
Confidence 876 4468899888887
No 20
>COG3858 Predicted glycosyl hydrolase [General function prediction only]
Probab=97.79 E-value=3.6e-05 Score=62.82 Aligned_cols=61 Identities=26% Similarity=0.239 Sum_probs=50.3
Q ss_pred CCCCcccCCCCEEEEcccccCCCCCcccCceeeEEcCCCCHHHHHHHhCCCCCHHHhhc------cCCCCCCCEEEEecC
Q 043749 4 SLGNQILGTKSLVKVPISCPCIDGIKRSESTTNNVWPADTIDSILNEFGGLVSAEQINS------TNGSNYPTSLMIMLS 77 (125)
Q Consensus 4 ~~~~~~l~~g~~l~IP~~c~c~~~~~~~~~~~y~V~~GDTl~~IA~~y~~~vs~~~i~~------~~~i~~Gq~L~IP~~ 77 (125)
+..++.|.+||.+.||... ..|.|++|||+++||++|+ |+.++++. +..+.+|=.|.+|..
T Consensus 31 ~~~~d~~~~~q~~~v~~~~-----------~~y~~~~~d~~~Sia~~~~--vt~~~~~~m~~~~~~~~l~~~~~l~~P~~ 97 (423)
T COG3858 31 DYTNDDLVDGQTFVVPPSG-----------HFYDVGPGDTLTSIARTVG--VTQDSAAIMNFVICPGYLQYGLNLYIPSA 97 (423)
T ss_pred ccccccccCceeEEECCcc-----------eEEEecCCcchhhhhhhhc--CCHHHHHhhcccccccceeeeeEEeccCC
Confidence 4455778999999998753 6799999999999999999 88877766 457788888888854
No 21
>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=97.67 E-value=4.6e-05 Score=48.40 Aligned_cols=36 Identities=25% Similarity=0.072 Sum_probs=28.4
Q ss_pred CCHHHHHHHhC--CCCCHHHhhc--------------cCCCCCCCEEEEecC
Q 043749 42 DTIDSILNEFG--GLVSAEQINS--------------TNGSNYPTSLMIMLS 77 (125)
Q Consensus 42 DTl~~IA~~y~--~~vs~~~i~~--------------~~~i~~Gq~L~IP~~ 77 (125)
||||+||++|. +.+++.+.+. .+.|++|+.|.||..
T Consensus 1 DTLw~IA~~~~~~~~~s~~q~m~ai~~aNp~AF~~~nin~L~~G~~L~iP~~ 52 (74)
T TIGR03505 1 DTLWGIAQRVRPDNSVSLYQMMLALYRANPDAFIGGNINRLKVGQILRIPSE 52 (74)
T ss_pred CcHHHHHHHHccCCCCCHHHHHHHHHHHCHHhHhcCChhhcCCCCEEeCCCH
Confidence 89999999885 3367765543 367999999999964
No 22
>COG1652 XkdP Uncharacterized protein containing LysM domain [Function unknown]
Probab=97.62 E-value=1.9e-05 Score=60.96 Aligned_cols=44 Identities=25% Similarity=0.201 Sum_probs=33.6
Q ss_pred eeeEEcCCCCHHHHHH-HhCCCCCH------HH---hhccCCCCCCCEEEEecC
Q 043749 34 TTNNVWPADTIDSILN-EFGGLVSA------EQ---INSTNGSNYPTSLMIMLS 77 (125)
Q Consensus 34 ~~y~V~~GDTl~~IA~-~y~~~vs~------~~---i~~~~~i~~Gq~L~IP~~ 77 (125)
.+|+|++|||||.||+ .||..+.. +. +.+++.|++||+|.||-.
T Consensus 211 ~~~~v~rgDTl~~is~~~Yg~~~~y~~I~~aNk~~~~~~p~~I~pGq~l~iP~~ 264 (269)
T COG1652 211 TTNTVKRGDTLWQISKKVYGDGVEYRKIAEANKALVLDNPDKIKPGQVLRIPDQ 264 (269)
T ss_pred eEEEeccCCcccccchhhcCcceEEEeHhhhhhhhccCCCCcCCCcceeeCCCc
Confidence 3899999999999999 66632211 22 444789999999999954
No 23
>PRK10871 nlpD lipoprotein NlpD; Provisional
Probab=97.13 E-value=0.00017 Score=57.32 Aligned_cols=41 Identities=15% Similarity=0.054 Sum_probs=31.7
Q ss_pred CCCCcceeeEee-eCCcHHHHHHhcCCCC-CCCCCCCEEEEcC
Q 043749 84 GNNGVTSVYKSK-FWVMMAELVATNGLSQ-SVVDPIDILAIPI 124 (125)
Q Consensus 84 ~~~~~~~~~~~y-~gvs~~~L~~~N~l~~-~~l~~Gq~L~IP~ 124 (125)
+++|++.+.+++ ||+++++|++||+|.+ ..|++||+|.||.
T Consensus 65 Vk~GDTL~~IA~~~g~~~~~La~~N~l~~p~~I~~GQ~L~i~~ 107 (319)
T PRK10871 65 VKKGDTLFYIAWITGNDFRDLAQRNNIQAPYSLNVGQTLQVGN 107 (319)
T ss_pred ECCCCHHHHHHHHHCcCHHHHHHhcCCCCCccccCCCEEEeCC
Confidence 445554333444 9999999999999986 4699999999973
No 24
>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=97.11 E-value=0.00058 Score=37.59 Aligned_cols=29 Identities=31% Similarity=0.417 Sum_probs=25.1
Q ss_pred eCCcHHHHHHhcC-CCC-CCCCCCCEEEEcC
Q 043749 96 FWVMMAELVATNG-LSQ-SVVDPIDILAIPI 124 (125)
Q Consensus 96 ~gvs~~~L~~~N~-l~~-~~l~~Gq~L~IP~ 124 (125)
||++.++|+++|+ +.+ ..+++||+|.||.
T Consensus 14 ~~~~~~~l~~~N~~~~~~~~~~~g~~l~ip~ 44 (44)
T TIGR02899 14 YGVDFDELIQANPQLSNPNLIYPGMKIKIPS 44 (44)
T ss_pred HCcCHHHHHHHhhcCCCCCCcCCCCEEecCC
Confidence 9999999999997 444 4699999999984
No 25
>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=96.99 E-value=0.00091 Score=35.97 Aligned_cols=28 Identities=32% Similarity=0.444 Sum_probs=25.5
Q ss_pred eCCcHHHHHHhcCCC-CCCCCCCCEEEEc
Q 043749 96 FWVMMAELVATNGLS-QSVVDPIDILAIP 123 (125)
Q Consensus 96 ~gvs~~~L~~~N~l~-~~~l~~Gq~L~IP 123 (125)
|+++.++|+++|+.. ...+.+|+.|.||
T Consensus 18 ~~~~~~~~~~~N~~~~~~~~~~g~~l~ip 46 (46)
T cd00118 18 YGISVEELLKLNGLSDPDNLQVGQKLKIP 46 (46)
T ss_pred HCcCHHHHHHHcCCCCccccCCCCEEecC
Confidence 899999999999984 5679999999998
No 26
>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=96.77 E-value=0.0013 Score=52.60 Aligned_cols=28 Identities=29% Similarity=0.420 Sum_probs=26.7
Q ss_pred eCCcHHHHHHhcCCCCCCCCCCCEEEEc
Q 043749 96 FWVMMAELVATNGLSQSVVDPIDILAIP 123 (125)
Q Consensus 96 ~gvs~~~L~~~N~l~~~~l~~Gq~L~IP 123 (125)
||+++++|++||++....|++||+|.||
T Consensus 311 YGVSV~~L~r~N~L~~~~L~~GQ~L~IP 338 (338)
T TIGR02907 311 YEISVSQLIRHNQLEDFEVNEGQILYIP 338 (338)
T ss_pred HCcCHHHHHHHhCCCccccCCCCEEEeC
Confidence 9999999999999987789999999998
No 27
>PRK10190 L,D-transpeptidase; Provisional
Probab=96.77 E-value=0.0029 Score=50.20 Aligned_cols=42 Identities=12% Similarity=0.101 Sum_probs=35.1
Q ss_pred eeeEEcCCC--CHHHHHHHhCCCCCHHHhhc------cCCCCCCCEEEEecC
Q 043749 34 TTNNVWPAD--TIDSILNEFGGLVSAEQINS------TNGSNYPTSLMIMLS 77 (125)
Q Consensus 34 ~~y~V~~GD--Tl~~IA~~y~~~vs~~~i~~------~~~i~~Gq~L~IP~~ 77 (125)
..|+|+++| +|..||++|+ +..++|.+ +...++|++|.||..
T Consensus 38 ~~~~v~~~~~~~le~iA~~f~--~g~~~l~~aNPgvd~~~p~~G~~i~iP~~ 87 (310)
T PRK10190 38 LTVTVPDHNTQPLETFAAQYG--QGLSNMLEANPGADVFLPKSGSQLTIPQQ 87 (310)
T ss_pred EEEEecCCCCccHHHHHHHhC--CCHHHHHHhCCCCCCCCCCCCCEEEecCc
Confidence 679999976 5999999999 88888887 223689999999963
No 28
>PRK10260 L,D-transpeptidase; Provisional
Probab=96.74 E-value=0.0032 Score=49.87 Aligned_cols=41 Identities=12% Similarity=0.086 Sum_probs=34.7
Q ss_pred eeeEEcCCCC--HHHHHHHhCCCCCHHHhhc--c--C--CCCCCCEEEEec
Q 043749 34 TTNNVWPADT--IDSILNEFGGLVSAEQINS--T--N--GSNYPTSLMIML 76 (125)
Q Consensus 34 ~~y~V~~GDT--l~~IA~~y~~~vs~~~i~~--~--~--~i~~Gq~L~IP~ 76 (125)
..|+|++||| |..||++|+ +...+|++ + + ..++|++|.||.
T Consensus 41 ~~~~v~~~~~~~le~iA~~f~--~g~~~l~~aNPgvdp~lp~~G~~i~iP~ 89 (306)
T PRK10260 41 QVITIPEGNTQPLEYFAAEYQ--MGLSNMMEANPGVDTFLPKGGTVLNIPQ 89 (306)
T ss_pred EEEEeCCCCCchHHHHHHHhC--CCHHHHHHhCcCCCCCcCCCCCEEEeCC
Confidence 6799999764 999999999 88888887 2 2 567999999996
No 29
>PRK11649 putative peptidase; Provisional
Probab=96.72 E-value=0.0029 Score=52.39 Aligned_cols=44 Identities=25% Similarity=0.332 Sum_probs=37.3
Q ss_pred CceeeEEcCCCCHHHHHHHhCCCCCHHHhhc-------cCCCCCCCEEEEecC
Q 043749 32 ESTTNNVWPADTIDSILNEFGGLVSAEQINS-------TNGSNYPTSLMIMLS 77 (125)
Q Consensus 32 ~~~~y~V~~GDTl~~IA~~y~~~vs~~~i~~-------~~~i~~Gq~L~IP~~ 77 (125)
.|..|+|++||||.+|=+++| ++..++.+ ...|++||.+.+-..
T Consensus 94 ~~~~~~Vk~GDTl~~iL~r~G--i~~~di~~l~~~~~~L~~Lr~Gq~l~~~~d 144 (439)
T PRK11649 94 GVHEYVVSTGDTLSSILNQYG--IDMSDISQLAAQDKELRNLKIGQQLSWTLT 144 (439)
T ss_pred ceEEEEeCCCCCHHHHHHHcC--CCHHHHHHHHHcChHhhcCCCCCEEEEEEC
Confidence 356899999999999999999 78777765 357999999999753
No 30
>COG3170 FimV Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=96.65 E-value=0.0012 Score=57.09 Aligned_cols=45 Identities=24% Similarity=0.165 Sum_probs=36.5
Q ss_pred ceeeEEcCCCCHHHHHHHhC--CCCCHHHhhc--------------cCCCCCCCEEEEecC
Q 043749 33 STTNNVWPADTIDSILNEFG--GLVSAEQINS--------------TNGSNYPTSLMIMLS 77 (125)
Q Consensus 33 ~~~y~V~~GDTl~~IA~~y~--~~vs~~~i~~--------------~~~i~~Gq~L~IP~~ 77 (125)
..+|+|++|||||+||.+-- ..++.++++. -+++++|++|.||.-
T Consensus 188 g~tyt~~~~Dtl~dIAs~~rp~~~vt~~Q~~lAly~lNP~af~~gni~RLr~GSvLriP~~ 248 (755)
T COG3170 188 GDTYTVRSGDTLWDIASRLRPQDHVTVEQMLLALYQLNPQAFVNGNINRLRAGSVLRIPSA 248 (755)
T ss_pred CcccccCCcchHHHHHHhhcCcccccHHHHHHHHHhhChhhhcccchhhccccceeeccch
Confidence 47899999999999999543 3577777765 258999999999953
No 31
>PRK14125 cell division suppressor protein YneA; Provisional
Probab=96.63 E-value=0.0027 Score=42.70 Aligned_cols=25 Identities=24% Similarity=0.345 Sum_probs=21.6
Q ss_pred HHHHHHhcCCCCCCCCCCCEEEEcC
Q 043749 100 MAELVATNGLSQSVVDPIDILAIPI 124 (125)
Q Consensus 100 ~~~L~~~N~l~~~~l~~Gq~L~IP~ 124 (125)
++.|++.|++.++.|+|||+|.||.
T Consensus 66 v~~I~~~N~l~~~~I~~Gq~L~IP~ 90 (103)
T PRK14125 66 IEWVEDVNNLPSGHIKAGDKLVIPV 90 (103)
T ss_pred HHHHHHhcCCCCCcCCCCCEEEEec
Confidence 4667778999887899999999996
No 32
>COG3061 OapA Cell envelope opacity-associated protein A [Cell envelope biogenesis, outer membrane]
Probab=96.54 E-value=0.0061 Score=46.18 Aligned_cols=67 Identities=13% Similarity=0.113 Sum_probs=47.3
Q ss_pred cCCCCEEEEccccc-CCCCCcccCceeeEEcCCCCHHHHHHHhCCCCCHHHhhc----------cCCCCCCCEEEEecCc
Q 043749 10 LGTKSLVKVPISCP-CIDGIKRSESTTNNVWPADTIDSILNEFGGLVSAEQINS----------TNGSNYPTSLMIMLSC 78 (125)
Q Consensus 10 l~~g~~l~IP~~c~-c~~~~~~~~~~~y~V~~GDTl~~IA~~y~~~vs~~~i~~----------~~~i~~Gq~L~IP~~~ 78 (125)
++.++...+|..-. -+.......|.+|+|++|+||..+=|-++ ..+.++.. -+.+++||.+.|-+..
T Consensus 135 ~q~~q~~~v~~~~~~~P~~~s~g~wqsy~V~~G~TLaQlFRdn~--LpitDVnAMakveGagkpLSnlkaGq~Vki~~na 212 (242)
T COG3061 135 IQAKQEKKVPRTVDAQPFKPSSGNWQSYTVPQGKTLAQLFRDNN--LPITDVNAMAKVEGAGKPLSNLKAGQKVKISLNA 212 (242)
T ss_pred hhccCccccCCccccCccccCcccceeEEecCCccHHHHHhccC--CChHHhHHHHhhccCCCchhhccCCCEEEEEEcC
Confidence 45677777773321 12222233789999999999999999888 55555544 2679999999998753
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=95.15 E-value=0.062 Score=32.64 Aligned_cols=43 Identities=19% Similarity=0.089 Sum_probs=29.1
Q ss_pred eeEEcCCCCHHHHHH-HhCCCCCH-HHhhc--------cCCCCCCCEEEEecCc
Q 043749 35 TNNVWPADTIDSILN-EFGGLVSA-EQINS--------TNGSNYPTSLMIMLSC 78 (125)
Q Consensus 35 ~y~V~~GDTl~~IA~-~y~~~vs~-~~i~~--------~~~i~~Gq~L~IP~~~ 78 (125)
.|+. .|||++.||. .||..--. +.+.+ +..+.+|..|.+|...
T Consensus 3 v~t~-~GDtlD~I~~r~yG~~~~~~e~ll~aNp~La~~~~~lpaG~~I~lP~i~ 55 (60)
T PF05489_consen 3 VYTT-QGDTLDLIAYRHYGREDGAVEALLEANPGLADTGPVLPAGTVIILPDIP 55 (60)
T ss_pred EEEe-CcCcHHHHHHHHhCcHHHHHHHHHHHChhhhhcCCcCCCCCEEECCCCC
Confidence 3554 9999999999 56632111 23333 3579999999999653
No 34
>smart00257 LysM Lysin motif.
Probab=94.95 E-value=0.036 Score=29.01 Aligned_cols=27 Identities=15% Similarity=0.230 Sum_probs=23.3
Q ss_pred eCCcHHHHHHhcCCC-CCCCCCCCEEEE
Q 043749 96 FWVMMAELVATNGLS-QSVVDPIDILAI 122 (125)
Q Consensus 96 ~gvs~~~L~~~N~l~-~~~l~~Gq~L~I 122 (125)
|+++.++|+++|+.. ...+++|+.|.|
T Consensus 17 ~~~~~~~~~~~N~~~~~~~~~~g~~l~i 44 (44)
T smart00257 17 YGISVSDLLELNNILDPDNLQVGQKLKI 44 (44)
T ss_pred hCCCHHHHHHHcCCCCccccCCCCEEeC
Confidence 899999999999954 467999999874
No 35
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=92.17 E-value=0.071 Score=37.76 Aligned_cols=26 Identities=23% Similarity=0.370 Sum_probs=22.0
Q ss_pred CcHHHHHHhcC--CCC-CCCCCCCEEEEc
Q 043749 98 VMMAELVATNG--LSQ-SVVDPIDILAIP 123 (125)
Q Consensus 98 vs~~~L~~~N~--l~~-~~l~~Gq~L~IP 123 (125)
....+|+++|+ +.+ ..|+|||+|.||
T Consensus 118 ~~~~~I~~~N~~~l~~~~~I~pGq~L~IP 146 (147)
T PRK11198 118 NKYNKIFEANKPMLKSPDKIYPGQVLRIP 146 (147)
T ss_pred hhHHHHHHhhhhcCCCcCCcCcCCEEecC
Confidence 45789999998 665 469999999998
No 36
>COG4784 Putative Zn-dependent protease [General function prediction only]
Probab=89.74 E-value=0.47 Score=38.72 Aligned_cols=41 Identities=15% Similarity=0.081 Sum_probs=28.9
Q ss_pred eeeEEcCCCCHHHHHHHhCCCCCHHHhhc-------cCCCCCCCEEEE
Q 043749 34 TTNNVWPADTIDSILNEFGGLVSAEQINS-------TNGSNYPTSLMI 74 (125)
Q Consensus 34 ~~y~V~~GDTl~~IA~~y~~~vs~~~i~~-------~~~i~~Gq~L~I 74 (125)
..-+||+|||+.++|.+.-++..-.++-+ ...+++|+.++|
T Consensus 429 rvvtVk~GqT~~~lAA~m~G~~rkldlfRllNam~~~a~~~pGd~vKi 476 (479)
T COG4784 429 RVVTVKPGQTMASLAARMMGTDRKLDLFRLLNAMSPGATVRPGDKVKI 476 (479)
T ss_pred EEEEecCCccHHHHHhhccCchhHHHHHHHHhccCCCCcCCCCCeeee
Confidence 34679999999999996665222222222 567999999988
No 37
>COG0739 NlpD Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]
Probab=80.95 E-value=2.6 Score=31.65 Aligned_cols=42 Identities=19% Similarity=0.187 Sum_probs=34.2
Q ss_pred eeeEEcCCCCHHHHHHHhCCCCCHHHhhc------cCCCCCCCEEEEecC
Q 043749 34 TTNNVWPADTIDSILNEFGGLVSAEQINS------TNGSNYPTSLMIMLS 77 (125)
Q Consensus 34 ~~y~V~~GDTl~~IA~~y~~~vs~~~i~~------~~~i~~Gq~L~IP~~ 77 (125)
..|.++.||+|..|+++++ .....+.. ...++.|+.+.+|..
T Consensus 2 ~~~~~~~~~~l~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 49 (277)
T COG0739 2 SLYVVKKGDTLSAIAARLG--ISAKDLARLNNLLKKRLLRIGQLLRVPRA 49 (277)
T ss_pred ceEEecCCCHHHHHHHHcC--CCHHHHHHHHhhccccccCccceeeeccc
Confidence 3589999999999999999 56655555 227899999999975
No 38
>PRK10190 L,D-transpeptidase; Provisional
Probab=80.44 E-value=2.2 Score=34.07 Aligned_cols=29 Identities=14% Similarity=0.146 Sum_probs=25.7
Q ss_pred eCCcHHHHHHhcCCCCCC-CCCCCEEEEcC
Q 043749 96 FWVMMAELVATNGLSQSV-VDPIDILAIPI 124 (125)
Q Consensus 96 ~gvs~~~L~~~N~l~~~~-l~~Gq~L~IP~ 124 (125)
|+++..+|+++|.-.+.- .++|++|.||.
T Consensus 57 f~~g~~~l~~aNPgvd~~~p~~G~~i~iP~ 86 (310)
T PRK10190 57 YGQGLSNMLEANPGADVFLPKSGSQLTIPQ 86 (310)
T ss_pred hCCCHHHHHHhCCCCCCCCCCCCCEEEecC
Confidence 999999999999977664 48999999995
No 39
>COG4254 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=80.34 E-value=1.7 Score=34.65 Aligned_cols=47 Identities=19% Similarity=0.119 Sum_probs=35.0
Q ss_pred ceeeEEcCCCCHHHHHHHhCCCCCHHHhhc-------cCCCCCCCEEEEecCcc
Q 043749 33 STTNNVWPADTIDSILNEFGGLVSAEQINS-------TNGSNYPTSLMIMLSCT 79 (125)
Q Consensus 33 ~~~y~V~~GDTl~~IA~~y~~~vs~~~i~~-------~~~i~~Gq~L~IP~~~~ 79 (125)
..+|.|+.||||--++..|=++.+-....+ +..+++|.-|.||.+..
T Consensus 5 ~~~yrv~~gdtli~l~~~yl~~~~g~r~~q~an~~~~P~~l~pgs~l~ip~~~~ 58 (339)
T COG4254 5 ALTYRVLFGDTLILLLGGYLTLLAGSRAAQPANTKRPPFILQPGSCLPIPLPAS 58 (339)
T ss_pred cceeeeccccHHHHHHHHhhhccchhhhhcccccCCCCcccCCCccccCCCccc
Confidence 478999999999999998864322222221 67899999999998643
No 40
>PRK10260 L,D-transpeptidase; Provisional
Probab=78.81 E-value=2.6 Score=33.54 Aligned_cols=29 Identities=14% Similarity=0.258 Sum_probs=25.5
Q ss_pred eCCcHHHHHHhcCCCCCCC-CCCCEEEEcC
Q 043749 96 FWVMMAELVATNGLSQSVV-DPIDILAIPI 124 (125)
Q Consensus 96 ~gvs~~~L~~~N~l~~~~l-~~Gq~L~IP~ 124 (125)
|++...+|+++|.-.++.+ ++|++|.||.
T Consensus 60 f~~g~~~l~~aNPgvdp~lp~~G~~i~iP~ 89 (306)
T PRK10260 60 YQMGLSNMMEANPGVDTFLPKGGTVLNIPQ 89 (306)
T ss_pred hCCCHHHHHHhCcCCCCCcCCCCCEEEeCC
Confidence 9999999999999766544 8999999985
No 41
>PF13518 HTH_28: Helix-turn-helix domain
Probab=72.08 E-value=3 Score=23.34 Aligned_cols=22 Identities=23% Similarity=0.504 Sum_probs=18.2
Q ss_pred cCCCCHHHHHHHhCCCCCHHHhhc
Q 043749 39 WPADTIDSILNEFGGLVSAEQINS 62 (125)
Q Consensus 39 ~~GDTl~~IA~~y~~~vs~~~i~~ 62 (125)
..|.|+.+||++|| ++...+.+
T Consensus 10 ~~g~s~~~~a~~~g--is~~tv~~ 31 (52)
T PF13518_consen 10 LEGESVREIAREFG--ISRSTVYR 31 (52)
T ss_pred HcCCCHHHHHHHHC--CCHhHHHH
Confidence 36889999999999 77776655
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=67.88 E-value=4.8 Score=22.43 Aligned_cols=21 Identities=29% Similarity=0.392 Sum_probs=14.8
Q ss_pred cCCCCHHHHHHHhCCCCCHHHhh
Q 043749 39 WPADTIDSILNEFGGLVSAEQIN 61 (125)
Q Consensus 39 ~~GDTl~~IA~~y~~~vs~~~i~ 61 (125)
+.|-|..+||+.|| ++...+.
T Consensus 19 ~~G~si~~IA~~~g--vsr~Tvy 39 (45)
T PF02796_consen 19 AEGMSIAEIAKQFG--VSRSTVY 39 (45)
T ss_dssp HTT--HHHHHHHTT--S-HHHHH
T ss_pred HCCCCHHHHHHHHC--cCHHHHH
Confidence 57899999999999 7776654
No 43
>COG5004 P2-like prophage tail protein X [General function prediction only]
Probab=62.08 E-value=21 Score=22.08 Aligned_cols=46 Identities=9% Similarity=0.069 Sum_probs=30.0
Q ss_pred eeeEEcCCCCHHHHHH-HhCCCCCHHH--hh-c------cCCCCCCCEEEEecCcc
Q 043749 34 TTNNVWPADTIDSILN-EFGGLVSAEQ--IN-S------TNGSNYPTSLMIMLSCT 79 (125)
Q Consensus 34 ~~y~V~~GDTl~~IA~-~y~~~vs~~~--i~-~------~~~i~~Gq~L~IP~~~~ 79 (125)
.+|.-+.|||+..++. .||-+..+.+ +. | ...+..|-.+..|-...
T Consensus 3 ~~~Rt~~gDtvDalc~~~Ygrt~~v~eavl~ANpGlAd~gp~lp~gl~i~lPD~~~ 58 (70)
T COG5004 3 MIVRTRQGDTVDALCWRVYGRTTGVTEAVLEANPGLADWGPVLPHGLAITLPDIAA 58 (70)
T ss_pred eEEEeccCchHHHHHHHHHhhHHHHHHHHHhcCCChhhcCCCCccceeEecCCCCC
Confidence 3566779999999999 5552222211 11 1 35788888888887654
No 44
>COG1652 XkdP Uncharacterized protein containing LysM domain [Function unknown]
Probab=59.71 E-value=6.3 Score=30.23 Aligned_cols=27 Identities=26% Similarity=0.418 Sum_probs=20.5
Q ss_pred CcHHHHHHhcC---CCCC-CCCCCCEEEEcC
Q 043749 98 VMMAELVATNG---LSQS-VVDPIDILAIPI 124 (125)
Q Consensus 98 vs~~~L~~~N~---l~~~-~l~~Gq~L~IP~ 124 (125)
+--..|..+|+ +.++ .|+|||+|.||-
T Consensus 233 ~~y~~I~~aNk~~~~~~p~~I~pGq~l~iP~ 263 (269)
T COG1652 233 VEYRKIAEANKALVLDNPDKIKPGQVLRIPD 263 (269)
T ss_pred eEEEeHhhhhhhhccCCCCcCCCcceeeCCC
Confidence 34456788998 4454 599999999994
No 45
>PHA00675 hypothetical protein
Probab=59.63 E-value=7.9 Score=24.72 Aligned_cols=22 Identities=14% Similarity=0.107 Sum_probs=18.5
Q ss_pred cCCCCHHHHHHHhCCCCCHHHhhc
Q 043749 39 WPADTIDSILNEFGGLVSAEQINS 62 (125)
Q Consensus 39 ~~GDTl~~IA~~y~~~vs~~~i~~ 62 (125)
+.|.|+..||++|| ++-..+.+
T Consensus 37 r~G~s~~~IA~~fG--VsrstV~~ 58 (78)
T PHA00675 37 VEGMSYAVLAEKFE--QSKGAIAK 58 (78)
T ss_pred hcCccHHHHHHHhC--CCHHHHHH
Confidence 79999999999999 77665544
No 46
>TIGR03028 EpsE polysaccharide export protein EpsE. Sequences in this family of proteins are members of a polysaccharide export protein family (pfam02563) which includes the wza protein from E.coli. This family of proteins are homologous to the EpsE protein of the methanolan biosynthesis operon of Methylobacillus species strain 12S. The distribution of this protein appears to be restricted to a subset of exopolysaccharide operons containing a syntenic grouping of genes including a variant of the EpsH exosortase protein. Exosortase has been proposed to be involved in the targetting and processing of proteins containing the PEP-CTERM domain to the exopolysaccharide layer.
Probab=58.87 E-value=34 Score=25.75 Aligned_cols=70 Identities=13% Similarity=0.064 Sum_probs=42.3
Q ss_pred CCcccCCCCEEEEcccccC-CCCCcccCceeeEEcCCCCHHHHHHHhCCCCCHHHhhc-------------------cCC
Q 043749 6 GNQILGTKSLVKVPISCPC-IDGIKRSESTTNNVWPADTIDSILNEFGGLVSAEQINS-------------------TNG 65 (125)
Q Consensus 6 ~~~~l~~g~~l~IP~~c~c-~~~~~~~~~~~y~V~~GDTl~~IA~~y~~~vs~~~i~~-------------------~~~ 65 (125)
.|-.|++|+.+.||....- ..| .-..-..|..++|-|+.+.-.+-|++...-.... .+.
T Consensus 147 ~ni~L~~GD~I~V~~~~~v~v~G-~V~~pg~~~~~~~~tl~~al~~aGG~~~~a~~~~v~i~R~~~~g~~~~~~~~~~~~ 225 (239)
T TIGR03028 147 ENILVAGGDIIYVDRAPVFYIYG-EVQRPGAYRLERNMTVMQALAQGGGLTPRGTERGIRVMRRDDKGAVEEVSGELGDL 225 (239)
T ss_pred CCcEEcCCCEEEEcCCccEEEEe-EccCCeEEEeCCCCCHHHHHHhcCCCCcccCcceEEEEEECCCCcEEEEecCCCcc
Confidence 3578999999999965421 111 0011256888999998777666665433211111 234
Q ss_pred CCCCCEEEEec
Q 043749 66 SNYPTSLMIML 76 (125)
Q Consensus 66 i~~Gq~L~IP~ 76 (125)
|++|+.+.||.
T Consensus 226 l~~gDii~V~~ 236 (239)
T TIGR03028 226 VQPDDVIYVRE 236 (239)
T ss_pred cCCCCEEEEeC
Confidence 77888888874
No 47
>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=57.58 E-value=4.1 Score=23.75 Aligned_cols=21 Identities=29% Similarity=0.452 Sum_probs=14.4
Q ss_pred EcCCCCHHHHHHHhCCCCCHHHh
Q 043749 38 VWPADTIDSILNEFGGLVSAEQI 60 (125)
Q Consensus 38 V~~GDTl~~IA~~y~~~vs~~~i 60 (125)
+..|.+..+||+.|| ++...+
T Consensus 19 ~e~g~s~~~ia~~fg--v~~sTv 39 (53)
T PF04218_consen 19 LEEGESKRDIAREFG--VSRSTV 39 (53)
T ss_dssp HHCTT-HHHHHHHHT----CCHH
T ss_pred HHcCCCHHHHHHHhC--CCHHHH
Confidence 468999999999999 544444
No 48
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=55.66 E-value=12 Score=20.83 Aligned_cols=20 Identities=20% Similarity=0.234 Sum_probs=12.4
Q ss_pred cCCCCHHHHHHHhCCCCCHHHh
Q 043749 39 WPADTIDSILNEFGGLVSAEQI 60 (125)
Q Consensus 39 ~~GDTl~~IA~~y~~~vs~~~i 60 (125)
+.|-|+.+||+++| .+...+
T Consensus 18 ~~G~s~~~IA~~lg--~s~sTV 37 (44)
T PF13936_consen 18 EQGMSIREIAKRLG--RSRSTV 37 (44)
T ss_dssp CS---HHHHHHHTT----HHHH
T ss_pred HcCCCHHHHHHHHC--cCcHHH
Confidence 68999999999999 666544
No 49
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=53.07 E-value=13 Score=24.64 Aligned_cols=24 Identities=33% Similarity=0.555 Sum_probs=18.5
Q ss_pred EEcCCCCHHHHHHHhCCCC-CHHHhhc
Q 043749 37 NVWPADTIDSILNEFGGLV-SAEQINS 62 (125)
Q Consensus 37 ~V~~GDTl~~IA~~y~~~v-s~~~i~~ 62 (125)
..++|+|+.+||++|| + ....+..
T Consensus 20 ~~~~g~sv~~vAr~~g--v~~~~~l~~ 44 (116)
T COG2963 20 YLRGGDTVSEVAREFG--IVSATQLYK 44 (116)
T ss_pred HHhcCccHHHHHHHhC--CCChHHHHH
Confidence 3468999999999999 5 5555553
No 50
>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=51.24 E-value=10 Score=21.28 Aligned_cols=23 Identities=17% Similarity=0.289 Sum_probs=15.6
Q ss_pred EcCC-CCHHHHHHHhCCCCCHHHhhc
Q 043749 38 VWPA-DTIDSILNEFGGLVSAEQINS 62 (125)
Q Consensus 38 V~~G-DTl~~IA~~y~~~vs~~~i~~ 62 (125)
|+.| -|+.+.|++|| |+-..|.+
T Consensus 12 v~~g~~S~r~AA~~yg--Vp~sTL~~ 35 (45)
T PF05225_consen 12 VKNGKMSIRKAAKKYG--VPRSTLRR 35 (45)
T ss_dssp HHTTSS-HHHHHHHHT----HHHHHH
T ss_pred HHhCCCCHHHHHHHHC--cCHHHHHH
Confidence 4566 89999999999 77766654
No 51
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=50.52 E-value=16 Score=20.24 Aligned_cols=22 Identities=23% Similarity=0.273 Sum_probs=15.6
Q ss_pred cCCCCHHHHHHHhCCCCCHHHhhc
Q 043749 39 WPADTIDSILNEFGGLVSAEQINS 62 (125)
Q Consensus 39 ~~GDTl~~IA~~y~~~vs~~~i~~ 62 (125)
..|.|..+||+.+| ++...+.+
T Consensus 15 ~~G~s~~~ia~~lg--vs~~Tv~~ 36 (50)
T PF13384_consen 15 REGWSIREIAKRLG--VSRSTVYR 36 (50)
T ss_dssp HHT--HHHHHHHHT--S-HHHHHH
T ss_pred HCCCCHHHHHHHHC--cCHHHHHH
Confidence 44999999999999 88776655
No 52
>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=50.38 E-value=6.2 Score=23.85 Aligned_cols=23 Identities=13% Similarity=0.465 Sum_probs=19.0
Q ss_pred EcCCCCHHHHHHHhCCCCCHHHhhc
Q 043749 38 VWPADTIDSILNEFGGLVSAEQINS 62 (125)
Q Consensus 38 V~~GDTl~~IA~~y~~~vs~~~i~~ 62 (125)
...|.|+.++|++|| ++...|.+
T Consensus 20 ~~~g~sv~~va~~~g--i~~~~l~~ 42 (76)
T PF01527_consen 20 LESGESVSEVAREYG--ISPSTLYN 42 (76)
T ss_dssp HHHHCHHHHHHHHHT--S-HHHHHH
T ss_pred HHCCCceEeeecccc--cccccccH
Confidence 368999999999999 78887766
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=50.36 E-value=13 Score=24.59 Aligned_cols=46 Identities=13% Similarity=0.236 Sum_probs=19.5
Q ss_pred CCCEEEEcccccCCCCCcc-cCceeeEEcCCCCHHHHHHHhCCCCCHHHhhc
Q 043749 12 TKSLVKVPISCPCIDGIKR-SESTTNNVWPADTIDSILNEFGGLVSAEQINS 62 (125)
Q Consensus 12 ~g~~l~IP~~c~c~~~~~~-~~~~~y~V~~GDTl~~IA~~y~~~vs~~~i~~ 62 (125)
-|+.+.||-...-....+. .-..-|. |.+..++|++|| +|..++.+
T Consensus 45 gG~~iyiP~~~~~~~~~R~~~I~~~f~---G~n~~eLA~kyg--lS~r~I~~ 91 (108)
T PF08765_consen 45 GGQQIYIPKCDRLLRALRNREIRREFN---GMNVRELARKYG--LSERQIYR 91 (108)
T ss_dssp -SS------SHHHHHHHHHHHHHHH-----SS-HHHHHHHHT----HHHHHH
T ss_pred CCEeEEeeCccHHHHHHHHHHHHHHhC---CCCHHHHHHHHC--cCHHHHHH
Confidence 4788888864310000010 1112344 999999999999 88887766
No 54
>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=49.42 E-value=20 Score=19.95 Aligned_cols=22 Identities=18% Similarity=0.434 Sum_probs=17.0
Q ss_pred cCCCCHHHHHHHhCCCCCHHHhhc
Q 043749 39 WPADTIDSILNEFGGLVSAEQINS 62 (125)
Q Consensus 39 ~~GDTl~~IA~~y~~~vs~~~i~~ 62 (125)
-.|-|+.+||+.+| +|...+.+
T Consensus 18 ~~~~t~~eIa~~lg--~s~~~V~~ 39 (50)
T PF04545_consen 18 FEGLTLEEIAERLG--ISRSTVRR 39 (50)
T ss_dssp TST-SHHHHHHHHT--SCHHHHHH
T ss_pred cCCCCHHHHHHHHC--CcHHHHHH
Confidence 67889999999999 77766543
No 55
>PF14451 Ub-Mut7C: Mut7-C ubiquitin
Probab=48.21 E-value=51 Score=20.95 Aligned_cols=42 Identities=10% Similarity=0.142 Sum_probs=34.8
Q ss_pred CceeeEEcCCCCHHHHHHHhCCCCCHHHhhc----------cCCCCCCCEEEEe
Q 043749 32 ESTTNNVWPADTIDSILNEFGGLVSAEQINS----------TNGSNYPTSLMIM 75 (125)
Q Consensus 32 ~~~~y~V~~GDTl~~IA~~y~~~vs~~~i~~----------~~~i~~Gq~L~IP 75 (125)
....|....+-|+..+.+.+| +...++.. ...++.|+.+.|-
T Consensus 23 ~~~~~~~~~~~tvkd~IEsLG--VP~tEV~~i~vNG~~v~~~~~~~~Gd~v~V~ 74 (81)
T PF14451_consen 23 GPFTHPFDGGATVKDVIESLG--VPHTEVGLILVNGRPVDFDYRLKDGDRVAVY 74 (81)
T ss_pred CceEEecCCCCcHHHHHHHcC--CChHHeEEEEECCEECCCcccCCCCCEEEEE
Confidence 347788999999999999999 88887755 4678899988873
No 56
>TIGR00370 conserved hypothetical protein TIGR00370.
Probab=47.85 E-value=80 Score=23.50 Aligned_cols=80 Identities=10% Similarity=-0.030 Sum_probs=45.7
Q ss_pred CCCCHHHHHHHhCCCCCHHHhhc--c--------CCCCCC--------CEEEEecCccccCCCCCCc----ceeeEee--
Q 043749 40 PADTIDSILNEFGGLVSAEQINS--T--------NGSNYP--------TSLMIMLSCTCFNNGNNGV----TSVYKSK-- 95 (125)
Q Consensus 40 ~GDTl~~IA~~y~~~vs~~~i~~--~--------~~i~~G--------q~L~IP~~~~~~~~~~~~~----~~~~~~y-- 95 (125)
.|.-|..+|+..| .|.+++.+ . -...|| ..|.+|-.......+..|. ....-.|
T Consensus 89 ~g~DL~~vA~~~g--Ls~eevi~~Hs~~~y~V~~iGF~PGf~YL~~ld~~l~~PR~~~PR~~vPaGSVgIag~qt~IYp~ 166 (202)
T TIGR00370 89 FGPDLEEVAKINQ--LSPEEVIDIHSNGEYVVYMLGFQPGFPYLGGLPERLHTPRRASPRPSVPAGSVGIGGLQTGVYPI 166 (202)
T ss_pred CCCCHHHHHHHhC--cCHHHHHHHHhCCceEEEEEcCCCCchhccCCccccCCCCCCCCccccCCceeEEcccceEEEcc
Confidence 5678999999998 78888887 1 123344 4555554332222222221 0011123
Q ss_pred --------eCCcHHHHHHhcCCCCCCCCCCCEEE
Q 043749 96 --------FWVMMAELVATNGLSQSVVDPIDILA 121 (125)
Q Consensus 96 --------~gvs~~~L~~~N~l~~~~l~~Gq~L~ 121 (125)
.|-|.-.|-+.|.-.-..+++|+.++
T Consensus 167 ~sPGGW~iIGrTp~~lfd~~~~~p~ll~~GD~Vr 200 (202)
T TIGR00370 167 STPGGWQLIGKTPLALFDPQENPPTLLRAGDIVK 200 (202)
T ss_pred CCCCcceEeeecchhhhCCCCCCCcccCCCCEEE
Confidence 67788888555543334579999986
No 57
>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A.
Probab=47.16 E-value=19 Score=22.95 Aligned_cols=22 Identities=14% Similarity=0.296 Sum_probs=15.7
Q ss_pred cCCCCHHHHHHHhCCCCCHHHhhc
Q 043749 39 WPADTIDSILNEFGGLVSAEQINS 62 (125)
Q Consensus 39 ~~GDTl~~IA~~y~~~vs~~~i~~ 62 (125)
+.|=||.+||+.+| ++...+.+
T Consensus 13 krG~sL~~lsr~~G--l~~~tl~n 34 (78)
T PF13693_consen 13 KRGTSLAALSREAG--LSSSTLRN 34 (78)
T ss_dssp TTS--HHHHHHHHS--S-HHHHHH
T ss_pred HcCCCHHHHHHHcC--CCHHHHHH
Confidence 47999999999999 77766655
No 58
>PF11112 PyocinActivator: Pyocin activator protein PrtN
Probab=46.98 E-value=20 Score=22.63 Aligned_cols=50 Identities=12% Similarity=0.260 Sum_probs=28.4
Q ss_pred CHHHHHHHh--CCCCCHHHhhccCCCCCCCEEEEecCccccCCCCCCcceeeEeeeCCcHHHHHHh
Q 043749 43 TIDSILNEF--GGLVSAEQINSTNGSNYPTSLMIMLSCTCFNNGNNGVTSVYKSKFWVMMAELVAT 106 (125)
Q Consensus 43 Tl~~IA~~y--~~~vs~~~i~~~~~i~~Gq~L~IP~~~~~~~~~~~~~~~~~~~y~gvs~~~L~~~ 106 (125)
.|..|++.| | ++.....+ .+..|+ | |++.-....++++. ++|.+.||++|
T Consensus 16 pL~~v~~~yf~~--lt~~~a~r--k~~~g~-l--plPv~rl~~SqKs~-------~~V~v~dLA~y 67 (76)
T PF11112_consen 16 PLEEVCEDYFPH--LTPKTAKR--KANAGE-L--PLPVFRLDDSQKSP-------KFVHVQDLAAY 67 (76)
T ss_pred cHHHHHHHHHcc--CCHHHHHH--HHHCCC-C--CCceeecCCcccCC-------ceeeHHHHHHH
Confidence 477788755 6 56665544 344443 2 44332222223332 88999999886
No 59
>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=46.86 E-value=24 Score=16.65 Aligned_cols=20 Identities=20% Similarity=0.410 Sum_probs=15.8
Q ss_pred cCCCCHHHHHHHhCCCCCHHHh
Q 043749 39 WPADTIDSILNEFGGLVSAEQI 60 (125)
Q Consensus 39 ~~GDTl~~IA~~y~~~vs~~~i 60 (125)
..|.+...||+.|| ++...+
T Consensus 19 ~~~~s~~~ia~~~~--is~~tv 38 (42)
T cd00569 19 AAGESVAEIARRLG--VSRSTL 38 (42)
T ss_pred HcCCCHHHHHHHHC--CCHHHH
Confidence 57889999999999 665543
No 60
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=40.35 E-value=26 Score=23.58 Aligned_cols=26 Identities=23% Similarity=0.313 Sum_probs=21.9
Q ss_pred eeEEcCCCCHHHHHHHhCCCCCHHHhhc
Q 043749 35 TNNVWPADTIDSILNEFGGLVSAEQINS 62 (125)
Q Consensus 35 ~y~V~~GDTl~~IA~~y~~~vs~~~i~~ 62 (125)
...+..|.|+.+||++|| ++...|.+
T Consensus 23 ~~~~~~g~sv~evA~e~g--Is~~tl~~ 48 (121)
T PRK09413 23 QQSFEPGMTVSLVARQHG--VAASQLFL 48 (121)
T ss_pred HHHHcCCCCHHHHHHHHC--cCHHHHHH
Confidence 345678999999999999 88888877
No 61
>KOG2850 consensus Predicted peptidoglycan-binding protein, contains LysM domain [General function prediction only]
Probab=39.79 E-value=21 Score=26.48 Aligned_cols=43 Identities=16% Similarity=0.193 Sum_probs=30.3
Q ss_pred ceeeEEcCCCCHHHHHHHhCCCCCHHHhhc-c-----CCCCCCCEEEEecC
Q 043749 33 STTNNVWPADTIDSILNEFGGLVSAEQINS-T-----NGSNYPTSLMIMLS 77 (125)
Q Consensus 33 ~~~y~V~~GDTl~~IA~~y~~~vs~~~i~~-~-----~~i~~Gq~L~IP~~ 77 (125)
...-+||.||||..||-+|. ..+-++++ + ....+=+.+.+|..
T Consensus 9 ~l~~~iq~~dt~~a~al~~~--~~va~i~RvN~~~r~q~f~a~~~i~~pv~ 57 (186)
T KOG2850|consen 9 ELEVTIQEGDTLQAIALNYE--SDVADIKRVNNDDREQRFNALRSISIPVT 57 (186)
T ss_pred heeeeeccCchhhhHHhhcc--cchhhheeeccchhhhhhccccceecccc
Confidence 35678999999999999999 56666766 2 23444455666643
No 62
>TIGR03027 pepcterm_export putative polysaccharide export protein, PEP-CTERM sytem-associated. This protein family belongs to the larger set of polysaccharide biosynthesis/export proteins described by Pfam model pfam02563. Members of this family are variable in either containing of lacking a 78-residue insert, but appear to fall within a single clade, nevertheless, where the regions in which the gene is found encode components of the PEP-CTERM/EpsH proposed exosortase protein sorting system.
Probab=38.90 E-value=28 Score=24.64 Aligned_cols=28 Identities=25% Similarity=0.487 Sum_probs=20.9
Q ss_pred eCCcHHHHHHhcCCC-CCCCCCCCEEEEc
Q 043749 96 FWVMMAELVATNGLS-QSVVDPIDILAIP 123 (125)
Q Consensus 96 ~gvs~~~L~~~N~l~-~~~l~~Gq~L~IP 123 (125)
+.+...+|.+-..+. +..|+||++++||
T Consensus 133 ~~idl~~l~~~g~~~~n~~L~~gD~I~Vp 161 (165)
T TIGR03027 133 ISVRLKDLIKDGDVTANVELKPGDVLIIP 161 (165)
T ss_pred EEEEHHHHhhcCCccCCceeCCCCEEEEe
Confidence 667788887643343 4469999999998
No 63
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=37.87 E-value=33 Score=19.05 Aligned_cols=20 Identities=20% Similarity=0.403 Sum_probs=16.2
Q ss_pred CCCHHHHHHHhCCCCCHHHhhc
Q 043749 41 ADTIDSILNEFGGLVSAEQINS 62 (125)
Q Consensus 41 GDTl~~IA~~y~~~vs~~~i~~ 62 (125)
.-|+-.||+.+| ++...+.+
T Consensus 27 ~~s~~~vA~~~~--vs~~TV~r 46 (52)
T PF13542_consen 27 SRSFKDVARELG--VSWSTVRR 46 (52)
T ss_pred cCCHHHHHHHHC--CCHHHHHH
Confidence 349999999999 88877654
No 64
>cd06919 Asp_decarbox Aspartate alpha-decarboxylase or L-aspartate 1-decarboxylase, a pyruvoyl group-dependent decarboxylase in beta-alanine production. Decarboxylation of aspartate is the major route of beta-alanine production in bacteria, and is catalyzed by the enzyme L-aspartate decarboxylase (ADC), EC:4.1.1.11 which requires a pyruvoyl group for its activity. The pyruvoyl cofactor is covalently bound to the enzyme. The protein is synthesized as a proenzyme and cleaved via self-processing at Gly23-Ser24 to yield an alpha chain (C-terminal fragment) and beta chain (N-terminal fragment), and the pyruvoyl group. Beta-alanine is required for the biosynthesis of pantothenate, in which the enzyme plays a critical regulatory role. The active site of the tetrameric enzyme is located at the interface of two subunits, with a Lysine and a Histidine from the beta chain of one subunit forming the active site with residues from the alpha chain of the adjacent subunit. This alignment
Probab=36.60 E-value=17 Score=24.82 Aligned_cols=64 Identities=16% Similarity=0.239 Sum_probs=36.5
Q ss_pred HhCCCCCHH-HhhccCCCCCCCEEEEecCccccCCCCCCcceeeEee--eCCcHHHHHHhcCCCCCCCCCCCEEEE
Q 043749 50 EFGGLVSAE-QINSTNGSNYPTSLMIMLSCTCFNNGNNGVTSVYKSK--FWVMMAELVATNGLSQSVVDPIDILAI 122 (125)
Q Consensus 50 ~y~~~vs~~-~i~~~~~i~~Gq~L~IP~~~~~~~~~~~~~~~~~~~y--~gvs~~~L~~~N~l~~~~l~~Gq~L~I 122 (125)
.|.++++++ +|++...|.+++++.|-.. .+|. .+.+| .|-.=+-...+|+-..+..++|+.+.|
T Consensus 20 ~YeGSitID~~Ll~aagi~~~E~V~I~Nv-------~NG~--Rf~TYvI~g~~gSg~I~lNGAAAr~~~~GD~vII 86 (111)
T cd06919 20 NYEGSITIDEDLLEAAGILPYEKVLVVNV-------NNGA--RFETYVIPGERGSGVICLNGAAARLGQPGDRVII 86 (111)
T ss_pred ccceeEEECHHHHHhcCCCCCCEEEEEEC-------CCCc--EEEEEEEEcCCCCCEEEeCCHHHhcCCCCCEEEE
Confidence 455555543 5555667999999999742 2332 23344 333223334556655566777777766
No 65
>PHA01976 helix-turn-helix protein
Probab=35.36 E-value=24 Score=20.70 Aligned_cols=21 Identities=14% Similarity=0.272 Sum_probs=16.8
Q ss_pred CCCCHHHHHHHhCCCCCHHHhhc
Q 043749 40 PADTIDSILNEFGGLVSAEQINS 62 (125)
Q Consensus 40 ~GDTl~~IA~~y~~~vs~~~i~~ 62 (125)
+-|++..||+.|| ++.+++..
T Consensus 43 ~~~~l~~ia~~l~--v~~~~l~~ 63 (67)
T PHA01976 43 NLKTLLRLADALG--VTLDWLCG 63 (67)
T ss_pred CHHHHHHHHHHHC--cCHHHHhc
Confidence 3467999999999 88888754
No 66
>PRK10344 DNA-binding transcriptional regulator Nlp; Provisional
Probab=35.17 E-value=36 Score=22.40 Aligned_cols=22 Identities=9% Similarity=0.143 Sum_probs=18.5
Q ss_pred cCCCCHHHHHHHhCCCCCHHHhhc
Q 043749 39 WPADTIDSILNEFGGLVSAEQINS 62 (125)
Q Consensus 39 ~~GDTl~~IA~~y~~~vs~~~i~~ 62 (125)
+.|-||.+||+.+| ++...+.+
T Consensus 19 KrG~sLa~lsr~~G--ls~~TL~n 40 (92)
T PRK10344 19 KKGTSMAAESRRNG--LSSSTLAN 40 (92)
T ss_pred HcCCcHHHHHHHcC--CChHHHHH
Confidence 47999999999999 77777766
No 67
>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=34.30 E-value=19 Score=20.20 Aligned_cols=18 Identities=39% Similarity=0.597 Sum_probs=12.7
Q ss_pred CCCHHHHHHHhCCCCCHHHh
Q 043749 41 ADTIDSILNEFGGLVSAEQI 60 (125)
Q Consensus 41 GDTl~~IA~~y~~~vs~~~i 60 (125)
-|++..||+.|| ++.+++
T Consensus 38 ~~~~~~ia~~l~--~~~~~l 55 (55)
T PF01381_consen 38 LDTLKKIAKALG--VSPEYL 55 (55)
T ss_dssp HHHHHHHHHHHT--SEHHHH
T ss_pred HHHHHHHHHHHC--CCHHHC
Confidence 456888888888 666543
No 68
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=32.94 E-value=37 Score=19.76 Aligned_cols=22 Identities=14% Similarity=0.348 Sum_probs=14.9
Q ss_pred cCCCCHHHHHHHhCCCCCHHHhh
Q 043749 39 WPADTIDSILNEFGGLVSAEQIN 61 (125)
Q Consensus 39 ~~GDTl~~IA~~y~~~vs~~~i~ 61 (125)
+.|.|..+|++.|.. ++..++.
T Consensus 29 ~~G~s~eeI~~~yp~-Lt~~~i~ 50 (56)
T PF04255_consen 29 AAGESPEEIAEDYPS-LTLEDIR 50 (56)
T ss_dssp HTT--HHHHHHHSTT---HHHHH
T ss_pred HcCCCHHHHHHHCCC-CCHHHHH
Confidence 899999999999985 4666654
No 69
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=32.57 E-value=53 Score=17.74 Aligned_cols=23 Identities=17% Similarity=0.280 Sum_probs=18.7
Q ss_pred EcCCCCHHHHHHHhCCCCCHHHhhc
Q 043749 38 VWPADTIDSILNEFGGLVSAEQINS 62 (125)
Q Consensus 38 V~~GDTl~~IA~~y~~~vs~~~i~~ 62 (125)
+..|.+..+||+.+| ++...+..
T Consensus 15 ~~~g~s~~eia~~l~--is~~tv~~ 37 (58)
T smart00421 15 LAEGLTNKEIAERLG--ISEKTVKT 37 (58)
T ss_pred HHcCCCHHHHHHHHC--CCHHHHHH
Confidence 357999999999999 77766654
No 70
>cd04493 BRCA2DBD_OB1 BRCA2DBD_OB1: A subfamily of OB folds corresponding to the first OB fold (OB1) of the 800-amino acid C-terminal ssDNA binding domain (DBD) of BRCA2 (breast cancer susceptibility gene 2) protein, called BRCA2DBD. BRCA2 participates in homologous recombination-mediated repair of double-strand DNA breaks. It stimulates the displacement of Replication protein A (RPA), the most abundant eukaryotic ssDNA binding protein. It also facilitates filament formation. Mutations that map throughout the BRCA2 protein are associated with breast cancer susceptibility. BRCA2 is a large nuclear protein and its most conserved region is the C-terminal BRCA2DBD. BRCA2DBD binds ssDNA in vitro, and is composed of five structural domains, three of which are OB folds (OB1, OB2, and OB3). BRCA2DBD OB2 and OB3 are arranged in tandem, and their mode of binding can be considered qualitatively similar to two OB folds of RPA1, DBD-A and DBD-B (the major DBDs of RPA). BRCA2DBD OB1 binds DNA weakly.
Probab=32.45 E-value=7.2 Score=26.10 Aligned_cols=34 Identities=15% Similarity=0.017 Sum_probs=21.2
Q ss_pred CCCHHHHHHHhCCCCCHHHhhccCCCCCCCEEEEec
Q 043749 41 ADTIDSILNEFGGLVSAEQINSTNGSNYPTSLMIML 76 (125)
Q Consensus 41 GDTl~~IA~~y~~~vs~~~i~~~~~i~~Gq~L~IP~ 76 (125)
=|-.|+|-.... ....++.+...|++||+|.|-.
T Consensus 28 tDGWYsi~a~lD--~~L~~~l~~gkl~vGqKL~i~G 61 (100)
T cd04493 28 TDGWYSIRAQLD--PPLTNLVRKGKLRVGQKLRICG 61 (100)
T ss_pred ecCeEEEEEEeC--HHHHHHHHcCCeecccEEEEEC
Confidence 344444444444 3344444467899999999975
No 71
>PRK05449 aspartate alpha-decarboxylase; Provisional
Probab=31.75 E-value=22 Score=24.73 Aligned_cols=27 Identities=11% Similarity=0.240 Sum_probs=18.0
Q ss_pred HhCCCCCHH-HhhccCCCCCCCEEEEec
Q 043749 50 EFGGLVSAE-QINSTNGSNYPTSLMIML 76 (125)
Q Consensus 50 ~y~~~vs~~-~i~~~~~i~~Gq~L~IP~ 76 (125)
.|.++++++ +|.+...|.+++++.|-.
T Consensus 21 ~Y~GSitID~~Ll~aagi~p~E~V~V~N 48 (126)
T PRK05449 21 NYEGSITIDEDLLDAAGILENEKVQIVN 48 (126)
T ss_pred ccceeEEECHHHHHhcCCCCCCEEEEEE
Confidence 455555543 455566799999998874
No 72
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=31.60 E-value=35 Score=20.51 Aligned_cols=32 Identities=16% Similarity=0.252 Sum_probs=20.3
Q ss_pred CHHHHHHHhCCCCCHHHhhc--cCCCCCCCEEEEec
Q 043749 43 TIDSILNEFGGLVSAEQINS--TNGSNYPTSLMIML 76 (125)
Q Consensus 43 Tl~~IA~~y~~~vs~~~i~~--~~~i~~Gq~L~IP~ 76 (125)
|+.+||++|+ ++...+.. ...++-|..-.+..
T Consensus 16 S~~eLa~~~~--~s~~~ve~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 16 SLAELAREFG--ISPEAVEAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp EHHHHHHHTT----HHHHHHHHHHHHCCTSCEEEEE
T ss_pred CHHHHHHHHC--cCHHHHHHHHHHHHHCCcEEEecC
Confidence 6899999999 78877776 33444555555543
No 73
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=30.96 E-value=33 Score=19.57 Aligned_cols=21 Identities=19% Similarity=0.336 Sum_probs=16.8
Q ss_pred EcCCCCHHHHHHHhCCCCCHHHh
Q 043749 38 VWPADTIDSILNEFGGLVSAEQI 60 (125)
Q Consensus 38 V~~GDTl~~IA~~y~~~vs~~~i 60 (125)
.+.|.+...+|..|| ++....
T Consensus 16 LR~~~~~~~La~~Fg--Is~stv 36 (53)
T PF13613_consen 16 LRLNLTFQDLAYRFG--ISQSTV 36 (53)
T ss_pred HHcCCcHhHHhhhee--ecHHHH
Confidence 478999999999999 665544
No 74
>PF13510 Fer2_4: 2Fe-2S iron-sulfur cluster binding domain; PDB: 1Y56_A 3ADA_A 1VRQ_A 1X31_A 3AD9_A 3AD8_A 3AD7_A 2GAG_A 2GAH_A.
Probab=29.09 E-value=50 Score=20.71 Aligned_cols=19 Identities=32% Similarity=0.270 Sum_probs=16.7
Q ss_pred eeeEEcCCCCHHHHHHHhC
Q 043749 34 TTNNVWPADTIDSILNEFG 52 (125)
Q Consensus 34 ~~y~V~~GDTl~~IA~~y~ 52 (125)
..|.+.+|+||.+.+.+.|
T Consensus 11 ~~v~~~~G~til~al~~~g 29 (82)
T PF13510_consen 11 KPVEVPPGETILEALLAAG 29 (82)
T ss_dssp EEEEEEET-BHHHHHHHTT
T ss_pred EEEEEcCCCHHHHHHHHCC
Confidence 6799999999999999988
No 75
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=28.14 E-value=54 Score=18.30 Aligned_cols=21 Identities=14% Similarity=0.328 Sum_probs=13.7
Q ss_pred cCCCCHHHHHHHhCCCCCHHHhh
Q 043749 39 WPADTIDSILNEFGGLVSAEQIN 61 (125)
Q Consensus 39 ~~GDTl~~IA~~y~~~vs~~~i~ 61 (125)
-.|-|+.+||+.+| ++...+.
T Consensus 24 ~~g~s~~eIa~~l~--~s~~~v~ 44 (54)
T PF08281_consen 24 FQGMSYAEIAEILG--ISESTVK 44 (54)
T ss_dssp TS---HHHHHHHCT--S-HHHHH
T ss_pred HHCcCHHHHHHHHC--cCHHHHH
Confidence 46889999999999 7776654
No 76
>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=27.63 E-value=50 Score=24.10 Aligned_cols=25 Identities=16% Similarity=0.381 Sum_probs=21.8
Q ss_pred eEEcCCCCHHHHHHHhCCCCCHHHhhc
Q 043749 36 NNVWPADTIDSILNEFGGLVSAEQINS 62 (125)
Q Consensus 36 y~V~~GDTl~~IA~~y~~~vs~~~i~~ 62 (125)
=.++.|-|..+||..+| +++..+..
T Consensus 64 arIRaGas~eeVA~~~G--~~~~rV~r 88 (170)
T PF11268_consen 64 ARIRAGASAEEVAEEAG--VPVERVRR 88 (170)
T ss_pred HHHHCCCCHHHHHHHhC--CCHHHhhh
Confidence 34789999999999999 88888876
No 77
>PF07610 DUF1573: Protein of unknown function (DUF1573); InterPro: IPR011467 These hypothetical proteins from bacteria, such as Rhodopirellula baltica, Bacteroides thetaiotaomicron and Porphyromonas gingivalis, share a region of conserved sequence towards their N termini.
Probab=27.29 E-value=34 Score=18.95 Aligned_cols=22 Identities=27% Similarity=0.623 Sum_probs=13.3
Q ss_pred EcccccCCCCCcccCceeeEEcCCCC
Q 043749 18 VPISCPCIDGIKRSESTTNNVWPADT 43 (125)
Q Consensus 18 IP~~c~c~~~~~~~~~~~y~V~~GDT 43 (125)
|=.+|+|... .+....+++||+
T Consensus 17 v~tsCgCt~~----~~~~~~i~PGes 38 (45)
T PF07610_consen 17 VQTSCGCTTA----EYSKKPIAPGES 38 (45)
T ss_pred eeEccCCEEe----eCCcceECCCCE
Confidence 3467888533 223355888886
No 78
>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=26.70 E-value=48 Score=19.41 Aligned_cols=23 Identities=22% Similarity=0.511 Sum_probs=15.6
Q ss_pred EcCCCCH---HHHHHHhCCCCCHHHhhc
Q 043749 38 VWPADTI---DSILNEFGGLVSAEQINS 62 (125)
Q Consensus 38 V~~GDTl---~~IA~~y~~~vs~~~i~~ 62 (125)
.++||.| .+||++|+ ++-..+++
T Consensus 18 ~~~g~~lps~~~la~~~~--vsr~tvr~ 43 (64)
T PF00392_consen 18 LPPGDRLPSERELAERYG--VSRTTVRE 43 (64)
T ss_dssp S-TTSBE--HHHHHHHHT--S-HHHHHH
T ss_pred CCCCCEeCCHHHHHHHhc--cCCcHHHH
Confidence 3567755 78999999 77766655
No 79
>KOG1468 consensus Predicted translation initiation factor related to eIF-2B alpha/beta/delta subunits (CIG2/IDI2) [Translation, ribosomal structure and biogenesis]
Probab=26.34 E-value=1.2e+02 Score=24.37 Aligned_cols=42 Identities=10% Similarity=-0.031 Sum_probs=25.4
Q ss_pred eeEEcCCCC--------HHHHHHHhCCCCCHHHhhc----cCCCCCCCEEEEecCc
Q 043749 35 TNNVWPADT--------IDSILNEFGGLVSAEQINS----TNGSNYPTSLMIMLSC 78 (125)
Q Consensus 35 ~y~V~~GDT--------l~~IA~~y~~~vs~~~i~~----~~~i~~Gq~L~IP~~~ 78 (125)
--+++.||| |.-+|+.||. ..--.+- ...+.-|+.+.|-.+.
T Consensus 242 DrVarNGDTANKIGTy~LAv~aKhhgi--pFyvaaP~tsid~~l~tG~eIiIEERp 295 (354)
T KOG1468|consen 242 DRVARNGDTANKIGTYQLAVLAKHHGI--PFYVAAPFTSIDLSLATGDEIIIEERP 295 (354)
T ss_pred cceeccCcchhhhhhhHHHHHHHhcCC--ceEEeccccccccccCCCCeeEEeecC
Confidence 356788999 4445667772 2111111 3468899999997543
No 80
>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=25.17 E-value=69 Score=20.77 Aligned_cols=22 Identities=14% Similarity=0.225 Sum_probs=18.4
Q ss_pred cCCCCHHHHHHHhCCCCCHHHhhc
Q 043749 39 WPADTIDSILNEFGGLVSAEQINS 62 (125)
Q Consensus 39 ~~GDTl~~IA~~y~~~vs~~~i~~ 62 (125)
..|-++.+||+.+| ++...+.+
T Consensus 124 ~~g~s~~eIA~~l~--~s~~~v~~ 145 (158)
T TIGR02937 124 LEGLSYKEIAEILG--ISVGTVKR 145 (158)
T ss_pred hcCCCHHHHHHHHC--CCHHHHHH
Confidence 46999999999999 77776654
No 81
>PF11242 DUF2774: Protein of unknown function (DUF2774); InterPro: IPR021404 This entry is represented by Bacteriophage T4, Gp24.3; it is a family of uncharacterised viral proteins.
Probab=24.35 E-value=95 Score=18.99 Aligned_cols=21 Identities=14% Similarity=0.341 Sum_probs=16.8
Q ss_pred CCCCHHHHHHHhCCCCCHHHhhc
Q 043749 40 PADTIDSILNEFGGLVSAEQINS 62 (125)
Q Consensus 40 ~GDTl~~IA~~y~~~vs~~~i~~ 62 (125)
.|-++-+||+.+| .+..+...
T Consensus 12 ~g~~FveIAr~~~--i~a~e~a~ 32 (63)
T PF11242_consen 12 SGLSFVEIARKIG--ITAKEVAK 32 (63)
T ss_pred cCCcHHHHHHHhC--CCHHHHHH
Confidence 6889999999999 66666544
No 82
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=24.09 E-value=32 Score=19.81 Aligned_cols=20 Identities=25% Similarity=0.423 Sum_probs=13.8
Q ss_pred CCCHHHHHHHhCCCCCHHHhhc
Q 043749 41 ADTIDSILNEFGGLVSAEQINS 62 (125)
Q Consensus 41 GDTl~~IA~~y~~~vs~~~i~~ 62 (125)
-|++..||..|| ++..+|..
T Consensus 40 ~~~l~~ia~~l~--~~~~el~~ 59 (63)
T PF13443_consen 40 LDTLEKIAKALN--CSPEELFE 59 (63)
T ss_dssp HHHHHHHHHHHT----HHHCTE
T ss_pred HHHHHHHHHHcC--CCHHHHhh
Confidence 367888999999 78877753
No 83
>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=24.05 E-value=77 Score=20.50 Aligned_cols=22 Identities=27% Similarity=0.256 Sum_probs=18.5
Q ss_pred cCCCCHHHHHHHhCCCCCHHHhhc
Q 043749 39 WPADTIDSILNEFGGLVSAEQINS 62 (125)
Q Consensus 39 ~~GDTl~~IA~~y~~~vs~~~i~~ 62 (125)
+.|-|..+||+.+| +|...|-+
T Consensus 47 ~~g~syreIa~~tg--vS~aTItR 68 (87)
T PF01371_consen 47 DEGKSYREIAEETG--VSIATITR 68 (87)
T ss_dssp HTTSSHHHHHHHHT--STHHHHHH
T ss_pred HCCCCHHHHHHHhC--CCHHHHHH
Confidence 37999999999999 77777655
No 84
>PF07836 DmpG_comm: DmpG-like communication domain; InterPro: IPR012425 This domain is found towards the C-terminal region of various aldolase enzymes. It consists of five alpha-helices, four of which form an antiparallel helical bundle that plugs the C terminus of the N-terminal TIM barrel domain []. The communication domain is thought to play an important role in the heterodimerisation of the enzyme []. Members of this entry heterodimerise with members of IPR003361 from INTERPRO to form a bifunctional aldolase-dehydrogenase [].; GO: 0016833 oxo-acid-lyase activity, 0019439 aromatic compound catabolic process; PDB: 1NVM_E.
Probab=24.03 E-value=75 Score=19.63 Aligned_cols=25 Identities=12% Similarity=0.113 Sum_probs=14.2
Q ss_pred HHHHHHhCCCCCHHHhhc---cCCCCCCCE
Q 043749 45 DSILNEFGGLVSAEQINS---TNGSNYPTS 71 (125)
Q Consensus 45 ~~IA~~y~~~vs~~~i~~---~~~i~~Gq~ 71 (125)
..+|++|| |+..+|-- ...+..||+
T Consensus 26 ~raa~~yg--Vd~r~il~elgrR~~VgGQE 53 (66)
T PF07836_consen 26 ERAAERYG--VDPRDILVELGRRKLVGGQE 53 (66)
T ss_dssp HHHHHHHT----HHHHHHHHHHCT--TT-T
T ss_pred HHHHHHhC--cCHHHHHHHHhcccccCchH
Confidence 46788999 77777655 466777774
No 85
>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=23.88 E-value=65 Score=18.67 Aligned_cols=18 Identities=33% Similarity=0.606 Sum_probs=15.2
Q ss_pred CHHHHHHHhCCCCCHHHhhc
Q 043749 43 TIDSILNEFGGLVSAEQINS 62 (125)
Q Consensus 43 Tl~~IA~~y~~~vs~~~i~~ 62 (125)
|+.++|+.|| ||...+++
T Consensus 16 s~~ela~~~~--VS~~TiRR 33 (57)
T PF08220_consen 16 SVKELAEEFG--VSEMTIRR 33 (57)
T ss_pred EHHHHHHHHC--cCHHHHHH
Confidence 5789999999 88887776
No 86
>PRK12845 3-ketosteroid-delta-1-dehydrogenase; Reviewed
Probab=23.60 E-value=64 Score=27.60 Aligned_cols=23 Identities=17% Similarity=0.396 Sum_probs=19.5
Q ss_pred EcCCCCHHHHHHHhCCCCCHHHhhc
Q 043749 38 VWPADTIDSILNEFGGLVSAEQINS 62 (125)
Q Consensus 38 V~~GDTl~~IA~~y~~~vs~~~i~~ 62 (125)
+.++|||.++|++.| +..+.|+.
T Consensus 421 ~~kadTleELA~k~g--id~~~L~~ 443 (564)
T PRK12845 421 AHRADSLADLARKIG--VPVDTFVA 443 (564)
T ss_pred eEecCCHHHHHHHcC--CCHHHHHH
Confidence 458999999999999 78777776
No 87
>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=23.19 E-value=62 Score=20.89 Aligned_cols=23 Identities=26% Similarity=0.268 Sum_probs=19.1
Q ss_pred EcCCCCHHHHHHHhCCCCCHHHhhc
Q 043749 38 VWPADTIDSILNEFGGLVSAEQINS 62 (125)
Q Consensus 38 V~~GDTl~~IA~~y~~~vs~~~i~~ 62 (125)
+..|.|..+||+.+| ++...+.+
T Consensus 47 l~~G~S~~eIA~~Lg--ISrsTIyR 69 (88)
T TIGR02531 47 LKQGKTYSDIEAETG--ASTATISR 69 (88)
T ss_pred HHCCCCHHHHHHHHC--cCHHHHHH
Confidence 468999999999999 77776654
No 88
>PF08356 EF_assoc_2: EF hand associated; InterPro: IPR013567 This region predominantly appears near EF-hands (IPR002048 from INTERPRO) in GTP-binding proteins. It is found in all three eukaryotic kingdoms.
Probab=23.03 E-value=36 Score=22.23 Aligned_cols=15 Identities=27% Similarity=0.479 Sum_probs=12.9
Q ss_pred EcCC--CCHHHHHHHhC
Q 043749 38 VWPA--DTIDSILNEFG 52 (125)
Q Consensus 38 V~~G--DTl~~IA~~y~ 52 (125)
+++| ||.|.|=|+||
T Consensus 42 ierGR~ETtW~vLR~Fg 58 (89)
T PF08356_consen 42 IERGRHETTWTVLRKFG 58 (89)
T ss_pred HHhCcchHHHHHHHHcC
Confidence 4665 99999999999
No 89
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=23.00 E-value=65 Score=18.76 Aligned_cols=14 Identities=29% Similarity=0.418 Sum_probs=12.3
Q ss_pred CCCCHHHHHHHhCC
Q 043749 40 PADTIDSILNEFGG 53 (125)
Q Consensus 40 ~GDTl~~IA~~y~~ 53 (125)
-|.||.+||+.||+
T Consensus 44 ~~~sl~~Ig~~fg~ 57 (60)
T smart00760 44 TDLSLPEIGKIFGG 57 (60)
T ss_pred HCCCHHHHHHHhCC
Confidence 59999999999983
No 90
>TIGR00223 panD L-aspartate-alpha-decarboxylase. Members of this family are aspartate 1-decarboxylase, the enzyme that makes beta-alanine and C02 from aspartate. Beta-alanine is then used to make the vitamin pantothenate, from which coenzyme A is made. Aspartate 1-decarboxylase is synthesized as a proenzyme, then cleaved to an alpha (C-terminal) and beta (N-terminal) subunit with a pyruvoyl group.
Probab=22.93 E-value=41 Score=23.45 Aligned_cols=27 Identities=11% Similarity=0.215 Sum_probs=18.0
Q ss_pred HhCCCCCHH-HhhccCCCCCCCEEEEec
Q 043749 50 EFGGLVSAE-QINSTNGSNYPTSLMIML 76 (125)
Q Consensus 50 ~y~~~vs~~-~i~~~~~i~~Gq~L~IP~ 76 (125)
.|.++++.+ +|.+...|.+++++.|-.
T Consensus 21 ~Y~GSItID~~Lm~aagi~p~E~V~V~N 48 (126)
T TIGR00223 21 NYEGSITIDEDLLDAAGILENEKVDIVN 48 (126)
T ss_pred ccceeEEECHHHHHhcCCCCCCEEEEEE
Confidence 455555543 555566799999998863
No 91
>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=22.71 E-value=1.4e+02 Score=23.08 Aligned_cols=62 Identities=18% Similarity=0.117 Sum_probs=34.2
Q ss_pred CCCEEEEcccccCCCCCcccCceeeEEcCCCCHHHHHHHhCCC-C-CHHHhhc---cCCCCCCCEEEEecC
Q 043749 12 TKSLVKVPISCPCIDGIKRSESTTNNVWPADTIDSILNEFGGL-V-SAEQINS---TNGSNYPTSLMIMLS 77 (125)
Q Consensus 12 ~g~~l~IP~~c~c~~~~~~~~~~~y~V~~GDTl~~IA~~y~~~-v-s~~~i~~---~~~i~~Gq~L~IP~~ 77 (125)
..+.+.||+.==--++.+ .+-+|++|||+|..=.+.--. . ...+++. .+.+.+-.-|.||-.
T Consensus 95 K~eeI~I~fsywDGs~hr----r~v~vKKGdtI~~FL~~~r~~l~~~f~el~~vsvd~LM~VkedlIiPHh 161 (239)
T PF04921_consen 95 KAEEIEIPFSYWDGSGHR----RTVRVKKGDTIWQFLEKCRKQLAKEFRELRRVSVDDLMYVKEDLIIPHH 161 (239)
T ss_pred hCCeeEEEEEEECCCCCc----ceEEEcCCCCHHHHHHHHHHHHHHHhHHHHhcCHhheeeeccceeccCC
Confidence 456788887532111112 357899999999865543200 0 0112222 345777778888853
No 92
>COG2442 Uncharacterized conserved protein [Function unknown]
Probab=22.65 E-value=31 Score=21.97 Aligned_cols=43 Identities=23% Similarity=0.472 Sum_probs=29.2
Q ss_pred ccccc---CCCCCcccCc-eeeEEcCCCCHHHHHHHhCCCCCHHHhhc
Q 043749 19 PISCP---CIDGIKRSES-TTNNVWPADTIDSILNEFGGLVSAEQINS 62 (125)
Q Consensus 19 P~~c~---c~~~~~~~~~-~~y~V~~GDTl~~IA~~y~~~vs~~~i~~ 62 (125)
|--|+ |..|.+-..+ .-.-.+.|.|..+|+.-|.. ++.++|.+
T Consensus 17 P~i~gGkP~I~GtRI~V~~Il~~l~~G~s~eeil~dyp~-Lt~~dI~a 63 (79)
T COG2442 17 PGICGGKPCIRGTRIPVWDILEMLAAGESIEEILADYPD-LTLEDIRA 63 (79)
T ss_pred CcccCCcceEeCceecHHHHHHHHHCCCCHHHHHHhCCC-CCHHHHHH
Confidence 76675 4555433332 33556799999999999997 46677765
No 93
>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=22.33 E-value=1.1e+02 Score=16.57 Aligned_cols=22 Identities=18% Similarity=0.306 Sum_probs=17.8
Q ss_pred cCCCCHHHHHHHhCCCCCHHHhhc
Q 043749 39 WPADTIDSILNEFGGLVSAEQINS 62 (125)
Q Consensus 39 ~~GDTl~~IA~~y~~~vs~~~i~~ 62 (125)
..|-+..+||+.++ ++...+..
T Consensus 13 ~~~~s~~eia~~l~--~s~~tv~~ 34 (57)
T cd06170 13 AEGKTNKEIADILG--ISEKTVKT 34 (57)
T ss_pred HcCCCHHHHHHHHC--CCHHHHHH
Confidence 47889999999999 77766654
No 94
>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=22.13 E-value=47 Score=22.26 Aligned_cols=23 Identities=22% Similarity=0.361 Sum_probs=18.9
Q ss_pred EcCCCCHHHHHHHhCCCCCHHHhhc
Q 043749 38 VWPADTIDSILNEFGGLVSAEQINS 62 (125)
Q Consensus 38 V~~GDTl~~IA~~y~~~vs~~~i~~ 62 (125)
+..|.|..++|++|+ |+...+.+
T Consensus 15 ~~~g~s~~eaa~~F~--VS~~Tv~~ 37 (119)
T PF01710_consen 15 IEKGKSIREAAKRFG--VSRNTVYR 37 (119)
T ss_pred HHccchHHHHHHHhC--cHHHHHHH
Confidence 467999999999999 77766665
No 95
>PRK12837 3-ketosteroid-delta-1-dehydrogenase; Provisional
Probab=21.70 E-value=76 Score=26.60 Aligned_cols=23 Identities=26% Similarity=0.500 Sum_probs=19.1
Q ss_pred EcCCCCHHHHHHHhCCCCCHHHhhc
Q 043749 38 VWPADTIDSILNEFGGLVSAEQINS 62 (125)
Q Consensus 38 V~~GDTl~~IA~~y~~~vs~~~i~~ 62 (125)
+.++|||.++|++.| +..+.|+.
T Consensus 372 ~~kaDTleELA~k~g--id~~~L~~ 394 (513)
T PRK12837 372 WRTADTLEELAAKIG--VPADALTA 394 (513)
T ss_pred eeecCCHHHHHHHcC--CCHHHHHH
Confidence 347899999999999 77777765
No 96
>PF13621 Cupin_8: Cupin-like domain; PDB: 3AL6_C 3AL5_C 2XUM_A 2Y0I_A 1MZE_A 3KCY_A 1MZF_A 1YCI_A 2ILM_A 1H2L_A ....
Probab=21.29 E-value=41 Score=24.45 Aligned_cols=12 Identities=50% Similarity=0.819 Sum_probs=8.5
Q ss_pred CCCCCCEEEEcC
Q 043749 113 VVDPIDILAIPI 124 (125)
Q Consensus 113 ~l~~Gq~L~IP~ 124 (125)
.|.||+.|+||.
T Consensus 212 ~l~pGD~LfiP~ 223 (251)
T PF13621_consen 212 VLEPGDVLFIPP 223 (251)
T ss_dssp EEETT-EEEE-T
T ss_pred EECCCeEEEECC
Confidence 478999999995
No 97
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.03 E-value=86 Score=21.11 Aligned_cols=16 Identities=38% Similarity=0.630 Sum_probs=12.7
Q ss_pred CHHHHHHHhCCCCCHHHh
Q 043749 43 TIDSILNEFGGLVSAEQI 60 (125)
Q Consensus 43 Tl~~IA~~y~~~vs~~~i 60 (125)
|+.+||..|+ ||-+.+
T Consensus 35 Sl~EIAee~~--VSRqAI 50 (105)
T COG2739 35 SLSEIAEEFN--VSRQAI 50 (105)
T ss_pred cHHHHHHHhC--ccHHHH
Confidence 6899999999 775544
No 98
>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=20.87 E-value=1e+02 Score=18.56 Aligned_cols=18 Identities=28% Similarity=0.512 Sum_probs=15.9
Q ss_pred CHHHHHHHhCCCCCHHHhhc
Q 043749 43 TIDSILNEFGGLVSAEQINS 62 (125)
Q Consensus 43 Tl~~IA~~y~~~vs~~~i~~ 62 (125)
+|-+||.++| |+..+|..
T Consensus 24 ~lkdIA~~Lg--vs~~tIr~ 41 (60)
T PF10668_consen 24 KLKDIAEKLG--VSESTIRK 41 (60)
T ss_pred cHHHHHHHHC--CCHHHHHH
Confidence 6899999999 88888876
No 99
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=20.72 E-value=94 Score=17.06 Aligned_cols=23 Identities=22% Similarity=0.462 Sum_probs=16.6
Q ss_pred EcCCC---CHHHHHHHhCCCCCHHHhhc
Q 043749 38 VWPAD---TIDSILNEFGGLVSAEQINS 62 (125)
Q Consensus 38 V~~GD---Tl~~IA~~y~~~vs~~~i~~ 62 (125)
..+|+ |..+||++|+ ++...+.+
T Consensus 14 ~~~~~~l~s~~~la~~~~--vs~~tv~~ 39 (60)
T smart00345 14 LRPGDKLPSERELAAQLG--VSRTTVRE 39 (60)
T ss_pred CCCCCcCcCHHHHHHHHC--CCHHHHHH
Confidence 34454 7889999999 77666655
No 100
>PF15608 PELOTA_1: PELOTA RNA binding domain
Probab=20.61 E-value=74 Score=21.23 Aligned_cols=12 Identities=17% Similarity=0.484 Sum_probs=9.8
Q ss_pred CCCHHHHHHHhC
Q 043749 41 ADTIDSILNEFG 52 (125)
Q Consensus 41 GDTl~~IA~~y~ 52 (125)
=+.+..||++||
T Consensus 22 ~~~v~~i~~~~g 33 (100)
T PF15608_consen 22 WAEVERIAERYG 33 (100)
T ss_pred HHHHHHHHHHhC
Confidence 355788999999
No 101
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=20.40 E-value=54 Score=18.89 Aligned_cols=19 Identities=26% Similarity=0.487 Sum_probs=14.2
Q ss_pred CCHHHHHHHhCCCCCHHHhhc
Q 043749 42 DTIDSILNEFGGLVSAEQINS 62 (125)
Q Consensus 42 DTl~~IA~~y~~~vs~~~i~~ 62 (125)
+++..||..|| ++.+++..
T Consensus 42 ~~l~~i~~~~~--v~~~~l~~ 60 (64)
T PF12844_consen 42 STLKKIAEALG--VSLDELFD 60 (64)
T ss_dssp HHHHHHHHHHT--S-HHHHCC
T ss_pred HHHHHHHHHhC--CCHHHHhc
Confidence 56889999999 88887643
No 102
>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=20.34 E-value=76 Score=17.99 Aligned_cols=18 Identities=22% Similarity=0.506 Sum_probs=13.8
Q ss_pred CHHHHHHHhCCCCCHHHhhc
Q 043749 43 TIDSILNEFGGLVSAEQINS 62 (125)
Q Consensus 43 Tl~~IA~~y~~~vs~~~i~~ 62 (125)
++.++|+.+| ++..++..
T Consensus 5 ~V~elAk~l~--v~~~~ii~ 22 (54)
T PF04760_consen 5 RVSELAKELG--VPSKEIIK 22 (54)
T ss_dssp -TTHHHHHHS--SSHHHHHH
T ss_pred EHHHHHHHHC--cCHHHHHH
Confidence 4678999999 88877755
No 103
>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=20.21 E-value=92 Score=16.66 Aligned_cols=18 Identities=28% Similarity=0.423 Sum_probs=13.9
Q ss_pred CHHHHHHHhCCCCCHHHhhc
Q 043749 43 TIDSILNEFGGLVSAEQINS 62 (125)
Q Consensus 43 Tl~~IA~~y~~~vs~~~i~~ 62 (125)
|..++|+.+| ++...|+.
T Consensus 1 ti~e~A~~~g--vs~~tlR~ 18 (38)
T PF00376_consen 1 TIGEVAKLLG--VSPRTLRY 18 (38)
T ss_dssp EHHHHHHHHT--S-HHHHHH
T ss_pred CHHHHHHHHC--CCHHHHHH
Confidence 4578899999 88888876
No 104
>PRK15483 type III restriction-modification system StyLTI enzyme res; Provisional
Probab=20.06 E-value=66 Score=29.79 Aligned_cols=27 Identities=19% Similarity=0.228 Sum_probs=21.5
Q ss_pred ceeeEEcCCCCHHHHHHHhCCCCCHHHh
Q 043749 33 STTNNVWPADTIDSILNEFGGLVSAEQI 60 (125)
Q Consensus 33 ~~~y~V~~GDTl~~IA~~y~~~vs~~~i 60 (125)
..+++|+.||+|+.|+..|.+ ..+.+|
T Consensus 308 ~k~~~v~~GddL~~~s~~y~g-~~I~~i 334 (986)
T PRK15483 308 KKTFELAVGENLADIDPGFEG-LTIEYA 334 (986)
T ss_pred cEEEEECCCCchHHhhHHhCC-cEeeec
Confidence 378999999999999999986 234444
Done!