Query 024853
Match_columns 261
No_of_seqs 219 out of 1322
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 07:54:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024853.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024853hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01476 LysM: LysM domain; I 99.4 6.6E-14 1.4E-18 93.8 3.9 44 2-46 1-44 (44)
2 PRK06347 autolysin; Reviewed 99.3 3.4E-12 7.5E-17 128.6 5.8 96 1-98 481-579 (592)
3 TIGR02899 spore_safA spore coa 99.2 2.7E-11 5.8E-16 79.5 5.2 44 4-47 1-44 (44)
4 PRK10783 mltD membrane-bound l 99.1 1.1E-10 2.4E-15 114.4 5.8 89 2-98 346-434 (456)
5 PRK06347 autolysin; Reviewed 99.1 1.2E-10 2.6E-15 117.5 5.3 93 2-98 333-437 (592)
6 cd00118 LysM Lysin domain, fou 99.0 4.6E-10 1E-14 71.3 5.6 45 1-46 2-46 (46)
7 PRK14125 cell division suppres 99.0 4E-10 8.8E-15 90.7 6.2 48 2-51 39-94 (103)
8 PRK10871 nlpD lipoprotein NlpD 98.9 1.4E-09 3E-14 102.9 5.7 46 2-48 63-108 (319)
9 smart00257 LysM Lysin motif. 98.8 2.3E-08 4.9E-13 62.6 5.5 44 1-45 1-44 (44)
10 PRK13914 invasion associated s 98.6 4.5E-08 9.9E-13 96.9 5.8 45 2-48 30-74 (481)
11 PRK13914 invasion associated s 98.5 1.7E-07 3.6E-12 93.0 5.8 45 2-48 202-246 (481)
12 COG1388 LytE FOG: LysM repeat 98.5 1.9E-07 4.1E-12 74.9 4.9 45 2-48 69-113 (124)
13 TIGR03505 FimV_core FimV N-ter 97.8 2.8E-05 6E-10 59.5 3.7 41 8-48 1-52 (74)
14 COG3858 Predicted glycosyl hyd 97.6 4.5E-05 9.7E-10 74.7 3.4 135 2-142 4-146 (423)
15 COG1388 LytE FOG: LysM repeat 97.5 4.2E-05 9.1E-10 61.4 1.7 86 13-99 1-99 (124)
16 PF04225 OapA: Opacity-associa 97.5 8.6E-05 1.9E-09 57.8 3.3 47 1-47 4-53 (85)
17 PRK10783 mltD membrane-bound l 97.5 0.00017 3.6E-09 71.3 6.0 94 4-98 268-375 (456)
18 PRK10190 L,D-transpeptidase; P 97.3 0.00041 8.8E-09 65.9 6.0 46 2-48 40-87 (310)
19 PRK10260 L,D-transpeptidase; P 97.3 0.00046 1E-08 65.4 6.1 46 2-48 43-90 (306)
20 PF05489 Phage_tail_X: Phage T 96.8 0.0022 4.9E-08 47.2 4.6 45 5-49 6-55 (60)
21 COG3858 Predicted glycosyl hyd 95.6 0.011 2.4E-07 58.3 3.7 47 2-49 52-98 (423)
22 PRK11649 putative peptidase; P 95.4 0.016 3.5E-07 57.3 4.2 46 1-46 97-142 (439)
23 COG3170 FimV Tfp pilus assembl 94.9 0.023 4.9E-07 59.4 3.5 48 1-48 190-248 (755)
24 PRK11198 LysM domain/BON super 94.4 0.037 8.1E-07 46.8 3.2 20 1-20 97-116 (147)
25 COG0739 NlpD Membrane proteins 87.6 0.75 1.6E-05 40.6 4.1 47 1-48 3-49 (277)
26 COG5004 P2-like prophage tail 83.0 2.5 5.3E-05 32.4 4.4 48 2-49 5-57 (70)
27 COG3061 OapA Cell envelope opa 77.0 3.6 7.8E-05 38.2 4.3 48 1-48 161-211 (242)
28 PF13518 HTH_28: Helix-turn-he 73.3 3.6 7.8E-05 27.6 2.6 24 5-28 10-33 (52)
29 COG4254 Uncharacterized protei 70.7 3.4 7.4E-05 39.9 2.6 46 2-48 8-56 (339)
30 KOG2850 Predicted peptidoglyca 70.0 3 6.6E-05 37.4 2.0 47 2-49 12-58 (186)
31 PF01527 HTH_Tnp_1: Transposas 69.3 2.6 5.5E-05 30.6 1.2 24 5-28 21-44 (76)
32 PF01476 LysM: LysM domain; I 63.2 3.3 7.2E-05 27.0 0.7 24 72-95 4-27 (44)
33 PF02796 HTH_7: Helix-turn-hel 58.9 10 0.00022 25.7 2.6 23 5-27 19-41 (45)
34 PRK09413 IS2 repressor TnpA; R 51.7 16 0.00034 29.6 3.0 25 4-28 26-50 (121)
35 PF13384 HTH_23: Homeodomain-l 50.7 18 0.00038 24.2 2.7 23 6-28 16-38 (50)
36 COG2963 Transposase and inacti 49.8 17 0.00036 28.8 2.8 24 4-27 21-45 (116)
37 cd00569 HTH_Hin_like Helix-tur 47.0 27 0.00058 19.7 2.8 22 5-26 19-40 (42)
38 PF05225 HTH_psq: helix-turn-h 47.0 18 0.00039 24.9 2.2 24 4-27 12-36 (45)
39 PF04218 CENP-B_N: CENP-B N-te 43.3 13 0.00027 26.4 1.1 23 4-26 19-41 (53)
40 PHA00675 hypothetical protein 39.4 31 0.00066 27.2 2.7 24 5-28 37-60 (78)
41 PF13936 HTH_38: Helix-turn-he 39.0 35 0.00076 23.1 2.7 22 5-26 18-39 (44)
42 PF02183 HALZ: Homeobox associ 32.7 46 0.00099 23.2 2.5 23 224-246 5-27 (45)
43 PF08765 Mor: Mor transcriptio 30.1 49 0.0011 26.3 2.7 20 7-26 72-91 (108)
44 PF04545 Sigma70_r4: Sigma-70, 28.9 77 0.0017 21.3 3.1 22 5-26 18-39 (50)
45 PF10668 Phage_terminase: Phag 28.3 62 0.0013 24.1 2.7 20 9-28 24-43 (60)
46 PF01710 HTH_Tnp_IS630: Transp 28.2 41 0.00089 27.2 1.9 25 4-28 15-39 (119)
47 PF01381 HTH_3: Helix-turn-hel 25.6 34 0.00073 23.0 0.8 17 8-24 39-55 (55)
48 cd04762 HTH_MerR-trunc Helix-T 25.2 86 0.0019 19.8 2.7 20 9-28 2-21 (49)
49 PF07709 SRR: Seven Residue Re 24.7 45 0.00097 17.8 1.0 13 225-237 2-14 (14)
50 PHA01976 helix-turn-helix prot 24.5 49 0.0011 23.2 1.6 18 8-25 45-62 (67)
51 PLN00218 predicted protein; Pr 24.3 38 0.00083 28.6 1.1 29 139-167 61-100 (151)
52 PF04760 IF2_N: Translation in 24.1 50 0.0011 22.9 1.5 18 9-26 5-22 (54)
53 PF13693 HTH_35: Winged helix- 23.8 82 0.0018 24.5 2.7 21 5-25 13-33 (78)
54 PF01710 HTH_Tnp_IS630: Transp 23.8 88 0.0019 25.2 3.1 22 5-26 69-90 (119)
55 PRK10871 nlpD lipoprotein NlpD 22.7 30 0.00065 33.4 0.2 31 68-98 62-92 (319)
56 smart00421 HTH_LUXR helix_turn 22.1 1.2E+02 0.0027 19.5 3.1 23 5-27 16-38 (58)
57 cd01093 CRIB_PAK_like PAK (p21 22.1 50 0.0011 22.8 1.1 21 232-252 23-43 (46)
58 PF04255 DUF433: Protein of un 21.9 87 0.0019 22.2 2.4 23 5-27 29-52 (56)
59 PF13443 HTH_26: Cro/C1-type H 21.8 22 0.00048 24.8 -0.7 21 8-28 41-61 (63)
60 cd01104 HTH_MlrA-CarA Helix-Tu 21.6 98 0.0021 21.7 2.7 20 9-28 2-21 (68)
61 PF00392 GntR: Bacterial regul 21.6 75 0.0016 22.5 2.0 23 4-26 18-43 (64)
62 PF12116 SpoIIID: Stage III sp 21.4 43 0.00093 26.6 0.8 23 2-24 14-36 (82)
63 PF10810 DUF2545: Protein of u 21.1 20 0.00044 28.0 -1.1 23 139-161 55-77 (80)
64 PF13551 HTH_29: Winged helix- 20.8 96 0.0021 23.4 2.6 24 4-27 8-32 (112)
65 smart00345 HTH_GNTR helix_turn 20.7 1.4E+02 0.003 19.7 3.2 23 4-26 14-39 (60)
66 PF13542 HTH_Tnp_ISL3: Helix-t 20.6 1.2E+02 0.0025 20.3 2.7 19 8-26 28-46 (52)
67 PF12652 CotJB: CotJB protein; 20.2 1.3E+02 0.0028 23.4 3.2 44 202-256 22-69 (78)
68 TIGR02907 spore_VI_D stage VI 20.0 39 0.00085 33.0 0.4 29 70-98 297-325 (338)
No 1
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=99.45 E-value=6.6e-14 Score=93.76 Aligned_cols=44 Identities=41% Similarity=0.545 Sum_probs=37.4
Q ss_pred eeecCCCCHHHHHHHhCCCHHHHHHhcCCCCCCCCcCCCCEEEeC
Q 024853 2 TFGGRGETLTSISKQYGVSVYSIAAVNKNIVDVDLVFEGQRLNIP 46 (261)
Q Consensus 2 YtVq~GDTL~sIAkrYgVSv~~I~~~NP~I~~~d~L~pGQ~L~IP 46 (261)
|+|++|||||+||++||+++++|+++||++...+ |.+||+|+||
T Consensus 1 y~V~~gDtl~~IA~~~~~~~~~l~~~N~~~~~~~-l~~G~~l~iP 44 (44)
T PF01476_consen 1 YTVQPGDTLWSIAKRYGISVDELMELNPNIDSDN-LQPGQKLCIP 44 (44)
T ss_dssp EEE-TT--HHHHHHHTTS-HHHHHHHCCTTHGGC-GGTTEEEEEC
T ss_pred CEECcCCcHHHHHhhhhhhHhHHHHhcCCCCccc-CCCCCEEEeC
Confidence 8999999999999999999999999999886544 9999999998
No 2
>PRK06347 autolysin; Reviewed
Probab=99.28 E-value=3.4e-12 Score=128.57 Aligned_cols=96 Identities=15% Similarity=0.227 Sum_probs=72.7
Q ss_pred CeeecCCCCHHHHHHHhCCCHHHHHHhcCCCCCCCCcCCCCEEEeCCCcchhhhhhh---hhccccchhhHHhhhhhhhH
Q 024853 1 MTFGGRGETLTSISKQYGVSVYSIAAVNKNIVDVDLVFEGQRLNIPSSVREELQATV---KNVISSFDLKEIHRRSLNVF 77 (261)
Q Consensus 1 mYtVq~GDTL~sIAkrYgVSv~~I~~~NP~I~~~d~L~pGQ~L~IP~~~~~~~q~t~---~~~~s~y~i~~~~~~s~~tl 77 (261)
.|+|++|||||+||++|||++++|++|| ++. .+.|++||.|.||.........+. ....+.-....+...+++++
T Consensus 481 ~YtVk~GDTL~sIAkkygVSv~~L~~~N-~l~-s~~L~~GQ~L~Ip~~~~~s~~~t~~~s~~~~~~~~~~~Y~Vk~GDTL 558 (592)
T PRK06347 481 VYTVAKGDSLWRIANNNKVTIANLKSWN-NLK-SDFIYPGQKLKVSAGSTTNNTNTAKPSTNKPSNSTVKTYTVKKGDSL 558 (592)
T ss_pred eeeecCCCCHHHHHHHHCCCHHHHHHhc-CCC-cccccCCcEEEEecCcccccccccCCccCCccCccceeeecCCCCcH
Confidence 4899999999999999999999999999 575 578999999999975332211110 01111111223455789999
Q ss_pred HhhhhhcccchhhhccCCccc
Q 024853 78 YGRLDKRHISMQITHRLPHIW 98 (261)
Q Consensus 78 y~~~~k~gism~~l~~lp~i~ 98 (261)
+++++++|+++..|..+|.+.
T Consensus 559 ~sIA~KygvSv~~L~~~N~L~ 579 (592)
T PRK06347 559 WAISRQYKTTVDNIKAWNKLT 579 (592)
T ss_pred HHHHHHhCCCHHHHHHhcCCC
Confidence 999999999999999998765
No 3
>TIGR02899 spore_safA spore coat assembly protein SafA. in which one of which is found in most examples of endospore-forming bacteria. Lysin motifs are repeated in many proteins.
Probab=99.20 E-value=2.7e-11 Score=79.52 Aligned_cols=44 Identities=32% Similarity=0.637 Sum_probs=40.1
Q ss_pred ecCCCCHHHHHHHhCCCHHHHHHhcCCCCCCCCcCCCCEEEeCC
Q 024853 4 GGRGETLTSISKQYGVSVYSIAAVNKNIVDVDLVFEGQRLNIPS 47 (261)
Q Consensus 4 Vq~GDTL~sIAkrYgVSv~~I~~~NP~I~~~d~L~pGQ~L~IP~ 47 (261)
|++|||||+||++||+++++|.++||.+.+++.+.+||.|.||.
T Consensus 1 v~~gdtl~~IA~~~~~~~~~l~~~N~~~~~~~~~~~g~~l~ip~ 44 (44)
T TIGR02899 1 VQKGDTLWKIAKKYGVDFDELIQANPQLSNPNLIYPGMKIKIPS 44 (44)
T ss_pred CCCCCCHHHHHHHHCcCHHHHHHHhhcCCCCCCcCCCCEEecCC
Confidence 68999999999999999999999997665667899999999983
No 4
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional
Probab=99.09 E-value=1.1e-10 Score=114.43 Aligned_cols=89 Identities=18% Similarity=0.122 Sum_probs=69.9
Q ss_pred eeecCCCCHHHHHHHhCCCHHHHHHhcCCCCCCCCcCCCCEEEeCCCcchhhhhhhhhccccchhhHHhhhhhhhHHhhh
Q 024853 2 TFGGRGETLTSISKQYGVSVYSIAAVNKNIVDVDLVFEGQRLNIPSSVREELQATVKNVISSFDLKEIHRRSLNVFYGRL 81 (261)
Q Consensus 2 YtVq~GDTL~sIAkrYgVSv~~I~~~NP~I~~~d~L~pGQ~L~IP~~~~~~~q~t~~~~~s~y~i~~~~~~s~~tly~~~ 81 (261)
|+|++|||||+||++||+++.+|.++| ++.. +.|.+||.|.||......... .. -....+....++||++++
T Consensus 346 y~Vk~GDTL~sIA~r~gvs~~~L~~~N-~l~~-~~L~~Gq~L~Ip~~~~~~~~~-----~~-~~~~~Y~Vr~GDTL~sIA 417 (456)
T PRK10783 346 YKVRSGDTLSGIASRLNVSTKDLQQWN-NLRG-SKLKVGQTLTIGAGSSAQRLA-----NN-SDSITYRVRKGDSLSSIA 417 (456)
T ss_pred EEECCCCcHHHHHHHHCcCHHHHHHHc-CCCc-ccCCCCCEEEecCCccccccc-----cc-ccceeEEeCCCCCHHHHH
Confidence 899999999999999999999999999 5754 789999999999753321100 00 001123457899999999
Q ss_pred hhcccchhhhccCCccc
Q 024853 82 DKRHISMQITHRLPHIW 98 (261)
Q Consensus 82 ~k~gism~~l~~lp~i~ 98 (261)
+++|++++.+.++|.+.
T Consensus 418 ~kygVtv~~L~~~N~l~ 434 (456)
T PRK10783 418 KRHGVNIKDVMRWNSDT 434 (456)
T ss_pred HHhCCCHHHHHHhcCCC
Confidence 99999999999998543
No 5
>PRK06347 autolysin; Reviewed
Probab=99.07 E-value=1.2e-10 Score=117.49 Aligned_cols=93 Identities=16% Similarity=0.210 Sum_probs=70.2
Q ss_pred eeecCCCCHHHHHHHhCCCHHHHHHhcCCCCCCCCcCCCCEEEeCCCcchhhhhhhh------------hccccchhhHH
Q 024853 2 TFGGRGETLTSISKQYGVSVYSIAAVNKNIVDVDLVFEGQRLNIPSSVREELQATVK------------NVISSFDLKEI 69 (261)
Q Consensus 2 YtVq~GDTL~sIAkrYgVSv~~I~~~NP~I~~~d~L~pGQ~L~IP~~~~~~~q~t~~------------~~~s~y~i~~~ 69 (261)
|+|++|||||.||++||+++++|+++| ++. .+.|++||.|+||.........+.. .....+ ..+
T Consensus 333 Y~V~sGDTL~~IA~rygvSv~eL~~~N-~l~-~d~L~~Gq~L~VP~~~~~~~~~t~~~~~~~~~~~~~~~~~~~~--~~y 408 (592)
T PRK06347 333 YTVVKGDSLWRIANNHKVTVANLKAWN-NLK-SDFIYPGQKLKVSAGSTTSDTNTSKPSTGTSTSKPSTGTSTNA--KVY 408 (592)
T ss_pred EEeCCCCCHHHHHHHhCCCHHHHHHHh-CCC-ccccccCcEEEEeccccccccccccccccccccccccccccCc--eeE
Confidence 899999999999999999999999999 685 5899999999999642211100000 001111 123
Q ss_pred hhhhhhhHHhhhhhcccchhhhccCCccc
Q 024853 70 HRRSLNVFYGRLDKRHISMQITHRLPHIW 98 (261)
Q Consensus 70 ~~~s~~tly~~~~k~gism~~l~~lp~i~ 98 (261)
....+++|+++++++|+++..+..++.+.
T Consensus 409 tVk~GDTL~sIA~kygVSv~~L~~~N~l~ 437 (592)
T PRK06347 409 TVVKGDSLWRIANNNKVTIANLKSWNNLK 437 (592)
T ss_pred EecCCCCHHHHHHHhCCCHHHHHHHhCCC
Confidence 45779999999999999999999988654
No 6
>cd00118 LysM Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function.
Probab=99.05 E-value=4.6e-10 Score=71.28 Aligned_cols=45 Identities=38% Similarity=0.590 Sum_probs=41.1
Q ss_pred CeeecCCCCHHHHHHHhCCCHHHHHHhcCCCCCCCCcCCCCEEEeC
Q 024853 1 MTFGGRGETLTSISKQYGVSVYSIAAVNKNIVDVDLVFEGQRLNIP 46 (261)
Q Consensus 1 mYtVq~GDTL~sIAkrYgVSv~~I~~~NP~I~~~d~L~pGQ~L~IP 46 (261)
.|+|++|||+|+||++|+++..+|.++|+ +.+...+.+|+.|.||
T Consensus 2 ~~~v~~gdt~~~ia~~~~~~~~~~~~~N~-~~~~~~~~~g~~l~ip 46 (46)
T cd00118 2 TYTVKKGDTLSSIAQRYGISVEELLKLNG-LSDPDNLQVGQKLKIP 46 (46)
T ss_pred EEEECCCCCHHHHHHHHCcCHHHHHHHcC-CCCccccCCCCEEecC
Confidence 48999999999999999999999999995 5456889999999997
No 7
>PRK14125 cell division suppressor protein YneA; Provisional
Probab=99.04 E-value=4e-10 Score=90.73 Aligned_cols=48 Identities=25% Similarity=0.332 Sum_probs=41.0
Q ss_pred eeecCCCCHHHHHHHhCCC--------HHHHHHhcCCCCCCCCcCCCCEEEeCCCcch
Q 024853 2 TFGGRGETLTSISKQYGVS--------VYSIAAVNKNIVDVDLVFEGQRLNIPSSVRE 51 (261)
Q Consensus 2 YtVq~GDTL~sIAkrYgVS--------v~~I~~~NP~I~~~d~L~pGQ~L~IP~~~~~ 51 (261)
|+|++|||||+||++|+.+ ++.|.+.| ++. ++.|+|||+|.||.....
T Consensus 39 ~tV~~GDTLW~IA~~y~~~~~l~~~~~v~~I~~~N-~l~-~~~I~~Gq~L~IP~~~~~ 94 (103)
T PRK14125 39 ITVQEGDTLWALADQYAGKHHMAKNEFIEWVEDVN-NLP-SGHIKAGDKLVIPVLKSK 94 (103)
T ss_pred EEECCCCCHHHHHHHhCCCcCCCHHHHHHHHHHhc-CCC-CCcCCCCCEEEEecCCCC
Confidence 8999999999999999865 56788889 885 568999999999976543
No 8
>PRK10871 nlpD lipoprotein NlpD; Provisional
Probab=98.91 E-value=1.4e-09 Score=102.86 Aligned_cols=46 Identities=26% Similarity=0.202 Sum_probs=44.1
Q ss_pred eeecCCCCHHHHHHHhCCCHHHHHHhcCCCCCCCCcCCCCEEEeCCC
Q 024853 2 TFGGRGETLTSISKQYGVSVYSIAAVNKNIVDVDLVFEGQRLNIPSS 48 (261)
Q Consensus 2 YtVq~GDTL~sIAkrYgVSv~~I~~~NP~I~~~d~L~pGQ~L~IP~~ 48 (261)
|+||+|||||.||++||+++.+|+++| +|.+++.|++||+|.||..
T Consensus 63 y~Vk~GDTL~~IA~~~g~~~~~La~~N-~l~~p~~I~~GQ~L~i~~~ 108 (319)
T PRK10871 63 YTVKKGDTLFYIAWITGNDFRDLAQRN-NIQAPYSLNVGQTLQVGNA 108 (319)
T ss_pred eEECCCCHHHHHHHHHCcCHHHHHHhc-CCCCCccccCCCEEEeCCC
Confidence 899999999999999999999999999 8999999999999999854
No 9
>smart00257 LysM Lysin motif.
Probab=98.75 E-value=2.3e-08 Score=62.61 Aligned_cols=44 Identities=39% Similarity=0.611 Sum_probs=39.2
Q ss_pred CeeecCCCCHHHHHHHhCCCHHHHHHhcCCCCCCCCcCCCCEEEe
Q 024853 1 MTFGGRGETLTSISKQYGVSVYSIAAVNKNIVDVDLVFEGQRLNI 45 (261)
Q Consensus 1 mYtVq~GDTL~sIAkrYgVSv~~I~~~NP~I~~~d~L~pGQ~L~I 45 (261)
.|+|++|||+|+||++|+++..+|.++|| ..+...+.+|+.|.|
T Consensus 1 ~~~v~~gdt~~~ia~~~~~~~~~~~~~N~-~~~~~~~~~g~~l~i 44 (44)
T smart00257 1 TYTVKKGDTLSSIARRYGISVSDLLELNN-ILDPDNLQVGQKLKI 44 (44)
T ss_pred CeEeCCCCCHHHHHHHhCCCHHHHHHHcC-CCCccccCCCCEEeC
Confidence 48999999999999999999999999996 335678999999875
No 10
>PRK13914 invasion associated secreted endopeptidase; Provisional
Probab=98.61 E-value=4.5e-08 Score=96.93 Aligned_cols=45 Identities=29% Similarity=0.443 Sum_probs=42.0
Q ss_pred eeecCCCCHHHHHHHhCCCHHHHHHhcCCCCCCCCcCCCCEEEeCCC
Q 024853 2 TFGGRGETLTSISKQYGVSVYSIAAVNKNIVDVDLVFEGQRLNIPSS 48 (261)
Q Consensus 2 YtVq~GDTL~sIAkrYgVSv~~I~~~NP~I~~~d~L~pGQ~L~IP~~ 48 (261)
|+|++|||||.||++||+++++|+++| +|. ++.|++||.|.||..
T Consensus 30 ytVq~GDTLw~IA~~ygvtv~~I~~~N-~l~-~~~I~~Gq~L~Ip~~ 74 (481)
T PRK13914 30 VVVEAGDTLWGIAQSKGTTVDAIKKAN-NLT-TDKIVPGQKLQVNEV 74 (481)
T ss_pred EEECCCCCHHHHHHHHCCCHHHHHHHh-CCC-cccccCCCEEEeCCC
Confidence 899999999999999999999999999 784 688999999999953
No 11
>PRK13914 invasion associated secreted endopeptidase; Provisional
Probab=98.48 E-value=1.7e-07 Score=92.96 Aligned_cols=45 Identities=33% Similarity=0.502 Sum_probs=42.0
Q ss_pred eeecCCCCHHHHHHHhCCCHHHHHHhcCCCCCCCCcCCCCEEEeCCC
Q 024853 2 TFGGRGETLTSISKQYGVSVYSIAAVNKNIVDVDLVFEGQRLNIPSS 48 (261)
Q Consensus 2 YtVq~GDTL~sIAkrYgVSv~~I~~~NP~I~~~d~L~pGQ~L~IP~~ 48 (261)
|+|++|||||.||++||+++++|+++| ++. .+.|++||+|.||..
T Consensus 202 ytVq~GDTL~sIAkrYgVtv~eI~~~N-~l~-s~~L~pGQ~L~Ip~s 246 (481)
T PRK13914 202 HAVKSGDTIWALSVKYGVSVQDIMSWN-NLS-SSSIYVGQKLAIKQT 246 (481)
T ss_pred EEECCCCCHHHHHHHHCCCHHHHHHhc-CCC-ccccCCCCEEEecCC
Confidence 899999999999999999999999999 785 468999999999975
No 12
>COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane]
Probab=98.48 E-value=1.9e-07 Score=74.95 Aligned_cols=45 Identities=36% Similarity=0.626 Sum_probs=41.4
Q ss_pred eeecCCCCHHHHHHHhCCCHHHHHHhcCCCCCCCCcCCCCEEEeCCC
Q 024853 2 TFGGRGETLTSISKQYGVSVYSIAAVNKNIVDVDLVFEGQRLNIPSS 48 (261)
Q Consensus 2 YtVq~GDTL~sIAkrYgVSv~~I~~~NP~I~~~d~L~pGQ~L~IP~~ 48 (261)
|+|++||||+.||++|++++.+|+++| ++.+ +.+++||.|.+|..
T Consensus 69 ~~V~~gdtL~~Ia~~~~~tv~~l~~~n-~l~~-~~i~~gq~l~~~~~ 113 (124)
T COG1388 69 YTVKKGDTLSKIARKYGVTVAELKQLN-NLSS-DKIKVGQKLKLPVS 113 (124)
T ss_pred EEEecCCCHHHHHHHhCCCHHHHHHHh-ccCC-CceecCcEEEEecc
Confidence 899999999999999999999999999 6754 59999999999863
No 13
>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=97.76 E-value=2.8e-05 Score=59.50 Aligned_cols=41 Identities=32% Similarity=0.475 Sum_probs=34.4
Q ss_pred CCHHHHHHHh---C-CCHH----HHHHhcCCC---CCCCCcCCCCEEEeCCC
Q 024853 8 ETLTSISKQY---G-VSVY----SIAAVNKNI---VDVDLVFEGQRLNIPSS 48 (261)
Q Consensus 8 DTL~sIAkrY---g-VSv~----~I~~~NP~I---~~~d~L~pGQ~L~IP~~ 48 (261)
||||+||++| + +++. .|.++||+. .+.+.|++|++|.||..
T Consensus 1 DTLw~IA~~~~~~~~~s~~q~m~ai~~aNp~AF~~~nin~L~~G~~L~iP~~ 52 (74)
T TIGR03505 1 DTLWGIAQRVRPDNSVSLYQMMLALYRANPDAFIGGNINRLKVGQILRIPSE 52 (74)
T ss_pred CcHHHHHHHHccCCCCCHHHHHHHHHHHCHHhHhcCChhhcCCCCEEeCCCH
Confidence 8999999999 4 7877 688899854 24589999999999974
No 14
>COG3858 Predicted glycosyl hydrolase [General function prediction only]
Probab=97.59 E-value=4.5e-05 Score=74.74 Aligned_cols=135 Identities=12% Similarity=0.026 Sum_probs=90.5
Q ss_pred eeecCCCCHHHHHHHhCCCHHHHHHhcCCCCCCCCcCCCCEEEeCCCcchhhhhhhhhccccchhhHHhhhhhhhHHhhh
Q 024853 2 TFGGRGETLTSISKQYGVSVYSIAAVNKNIVDVDLVFEGQRLNIPSSVREELQATVKNVISSFDLKEIHRRSLNVFYGRL 81 (261)
Q Consensus 2 YtVq~GDTL~sIAkrYgVSv~~I~~~NP~I~~~d~L~pGQ~L~IP~~~~~~~q~t~~~~~s~y~i~~~~~~s~~tly~~~ 81 (261)
|.|++||++..|+++|+.+..+|...| .+.+ +.|.+||.+.||....- ..+..-.+.+++.....++.+.+..++
T Consensus 4 ~~~~pg~~~~~i~~~~~~~~~~i~~~~-~~~~-d~~~~~q~~~v~~~~~~---y~~~~~d~~~Sia~~~~vt~~~~~~m~ 78 (423)
T COG3858 4 HLVGPGDSRLIIAVYFPYTNNRIVNGN-DYTN-DDLVDGQTFVVPPSGHF---YDVGPGDTLTSIARTVGVTQDSAAIMN 78 (423)
T ss_pred EEccCCceeeeehhhcccccccccccc-cccc-ccccCceeEEECCcceE---EEecCCcchhhhhhhhcCCHHHHHhhc
Confidence 789999999999999999999999999 7877 99999999999974210 000011122333332233232222222
Q ss_pred --hhcccchhh--hccCCccccC--CCCCcccccch-hhhhccccCccC-CccceeeeecCCCCccccc
Q 024853 82 --DKRHISMQI--THRLPHIWRN--RLPSFDLKETL-QHSLNIFYGPLD-KKYFVMEITHGLPQAKTTG 142 (261)
Q Consensus 82 --~k~gism~~--l~~lp~i~~~--~~~~fd~~~~~-~~~~~il~g~l~-~~~~~~~~~~~l~~~~~~~ 142 (261)
...+. ++. ...+|..++. +...|++++.+ .+...+++.+.| .++.-.|.+|.-|.+..++
T Consensus 79 ~~~~~~~-l~~~~~l~~P~~~~~~~~t~~~~~~~~~~~~~~~~~~~~~p~~t~~~~F~~~~~~~g~l~~ 146 (423)
T COG3858 79 FVICPGY-LQYGLNLYIPSARKTDGETTAYYAPRPPTETGELVRRHAGPYLTYVDLFSYHAQENGNLTE 146 (423)
T ss_pred ccccccc-eeeeeEEeccCCCCCcceeEEEecCCCchhhhhhhhccCCcceeeeccchhcccccccccc
Confidence 11111 111 3457777776 88899999887 788888888888 7788889999977765544
No 15
>COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane]
Probab=97.51 E-value=4.2e-05 Score=61.36 Aligned_cols=86 Identities=20% Similarity=0.304 Sum_probs=60.0
Q ss_pred HHHHhCCCHHHHHHhcCCCCC-CCCcCCCCEEEeCCCcchhhhh--hhhhccccc----------hhhHHhhhhhhhHHh
Q 024853 13 ISKQYGVSVYSIAAVNKNIVD-VDLVFEGQRLNIPSSVREELQA--TVKNVISSF----------DLKEIHRRSLNVFYG 79 (261)
Q Consensus 13 IAkrYgVSv~~I~~~NP~I~~-~d~L~pGQ~L~IP~~~~~~~q~--t~~~~~s~y----------~i~~~~~~s~~tly~ 79 (261)
||.+|++++.+|..+| .+.. .+.+.+||+|.+|......... +.......+ ....+....+++|+.
T Consensus 1 ia~~~~~~v~~l~~~n-~~~~~s~~i~~gq~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~gdtL~~ 79 (124)
T COG1388 1 IASKYGVSVKALKKAN-ALTGKSDAIKPGQVLKIPGDISSTVNAGQTLSSLSNKVSDSSSASKAPPVVTYTVKKGDTLSK 79 (124)
T ss_pred CcccccccHHHHHHHh-cccCCCCccccCceEEccCCcccccccccccccccceeeccccccccCCCceEEEecCCCHHH
Confidence 6889999999999999 6643 7899999999999742111110 000000000 012344577999999
Q ss_pred hhhhcccchhhhccCCcccc
Q 024853 80 RLDKRHISMQITHRLPHIWR 99 (261)
Q Consensus 80 ~~~k~gism~~l~~lp~i~~ 99 (261)
+++++++++..+..++++..
T Consensus 80 Ia~~~~~tv~~l~~~n~l~~ 99 (124)
T COG1388 80 IARKYGVTVAELKQLNNLSS 99 (124)
T ss_pred HHHHhCCCHHHHHHHhccCC
Confidence 99999999999999876653
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=97.50 E-value=8.6e-05 Score=57.81 Aligned_cols=47 Identities=19% Similarity=0.227 Sum_probs=27.5
Q ss_pred CeeecCCCCHHHHHHHhCCCHHH---HHHhcCCCCCCCCcCCCCEEEeCC
Q 024853 1 MTFGGRGETLTSISKQYGVSVYS---IAAVNKNIVDVDLVFEGQRLNIPS 47 (261)
Q Consensus 1 mYtVq~GDTL~sIAkrYgVSv~~---I~~~NP~I~~~d~L~pGQ~L~IP~ 47 (261)
.|+|++||||..|-+++|++..+ |+++++.-..-..|+|||.|.+-.
T Consensus 4 ~~~V~~GDtLs~iF~~~gls~~dl~~v~~~~~~~k~L~~L~pGq~l~f~~ 53 (85)
T PF04225_consen 4 EYTVKSGDTLSTIFRRAGLSASDLYAVLEADGEAKPLTRLKPGQTLEFQL 53 (85)
T ss_dssp EEE--TT--HHHHHHHTT--HHHHHHHHHHGGGT--GGG--TT-EEEEEE
T ss_pred EEEECCCCcHHHHHHHcCCCHHHHHHHHhccCccchHhhCCCCCEEEEEE
Confidence 48999999999999999999876 455552222347899999998853
No 17
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional
Probab=97.49 E-value=0.00017 Score=71.29 Aligned_cols=94 Identities=13% Similarity=0.193 Sum_probs=62.5
Q ss_pred ecCCCCHHHHHHHhCCCHHHHHHhcCCCCCCCCcC-CC-CEEEeCCCcchhhhhhh------hhcccc------chhhHH
Q 024853 4 GGRGETLTSISKQYGVSVYSIAAVNKNIVDVDLVF-EG-QRLNIPSSVREELQATV------KNVISS------FDLKEI 69 (261)
Q Consensus 4 Vq~GDTL~sIAkrYgVSv~~I~~~NP~I~~~d~L~-pG-Q~L~IP~~~~~~~q~t~------~~~~s~------y~i~~~ 69 (261)
|..+.+|..||+++|+++++|.++||++.. +.+. .| +.|.||......-.... ...... -....+
T Consensus 268 v~~~i~L~~iA~~~gvs~~eL~~LNP~~kr-~~t~p~g~~~llvP~~~~~~f~~~l~~~~~~~~~p~~~~~~~~~~~~~y 346 (456)
T PRK10783 268 LGQQIELAQAAEMAGMSLTKLKTFNAGYKR-STTAPSGPHYIMVPKKHADQLRESLASGEIAAVQSTLVADNTPLNSRSY 346 (456)
T ss_pred cCCCcCHHHHHHHcCCCHHHHHHhCccccC-CCcCCCCCeEEEecCchhhHHHHhhhhhhhhhcccccccccCcCCceEE
Confidence 445568999999999999999999998854 3333 34 78889975332110000 000000 001123
Q ss_pred hhhhhhhHHhhhhhcccchhhhccCCccc
Q 024853 70 HRRSLNVFYGRLDKRHISMQITHRLPHIW 98 (261)
Q Consensus 70 ~~~s~~tly~~~~k~gism~~l~~lp~i~ 98 (261)
...+++|++++++++|+++..+.+++.+.
T Consensus 347 ~Vk~GDTL~sIA~r~gvs~~~L~~~N~l~ 375 (456)
T PRK10783 347 KVRSGDTLSGIASRLNVSTKDLQQWNNLR 375 (456)
T ss_pred EECCCCcHHHHHHHHCcCHHHHHHHcCCC
Confidence 44779999999999999999998887654
No 18
>PRK10190 L,D-transpeptidase; Provisional
Probab=97.32 E-value=0.00041 Score=65.92 Aligned_cols=46 Identities=26% Similarity=0.348 Sum_probs=41.2
Q ss_pred eeecCCC--CHHHHHHHhCCCHHHHHHhcCCCCCCCCcCCCCEEEeCCC
Q 024853 2 TFGGRGE--TLTSISKQYGVSVYSIAAVNKNIVDVDLVFEGQRLNIPSS 48 (261)
Q Consensus 2 YtVq~GD--TL~sIAkrYgVSv~~I~~~NP~I~~~d~L~pGQ~L~IP~~ 48 (261)
|+|+++| +|-.||++|++....|.++||++ ++...++|++|.||..
T Consensus 40 ~~v~~~~~~~le~iA~~f~~g~~~l~~aNPgv-d~~~p~~G~~i~iP~~ 87 (310)
T PRK10190 40 VTVPDHNTQPLETFAAQYGQGLSNMLEANPGA-DVFLPKSGSQLTIPQQ 87 (310)
T ss_pred EEecCCCCccHHHHHHHhCCCHHHHHHhCCCC-CCCCCCCCCEEEecCc
Confidence 7899966 59999999999999999999988 5667789999999974
No 19
>PRK10260 L,D-transpeptidase; Provisional
Probab=97.29 E-value=0.00046 Score=65.45 Aligned_cols=46 Identities=26% Similarity=0.348 Sum_probs=41.1
Q ss_pred eeecCCCC--HHHHHHHhCCCHHHHHHhcCCCCCCCCcCCCCEEEeCCC
Q 024853 2 TFGGRGET--LTSISKQYGVSVYSIAAVNKNIVDVDLVFEGQRLNIPSS 48 (261)
Q Consensus 2 YtVq~GDT--L~sIAkrYgVSv~~I~~~NP~I~~~d~L~pGQ~L~IP~~ 48 (261)
|+|++||| |..||++|++....|+++||++ ++....+|++|.||..
T Consensus 43 ~~v~~~~~~~le~iA~~f~~g~~~l~~aNPgv-dp~lp~~G~~i~iP~~ 90 (306)
T PRK10260 43 ITIPEGNTQPLEYFAAEYQMGLSNMMEANPGV-DTFLPKGGTVLNIPQQ 90 (306)
T ss_pred EEeCCCCCchHHHHHHHhCCCHHHHHHhCcCC-CCCcCCCCCEEEeCCc
Confidence 78999665 9999999999999999999988 5667789999999974
No 20
>PF05489 Phage_tail_X: Phage Tail Protein X; InterPro: IPR008861 This entry is represented by Bacteriophage P2, GpX. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family is found in a family of phage tail proteins. Sequence analysis suggests that they are related to IPR002482 from INTERPRO which suggests a general peptidoglycan binding function.
Probab=96.80 E-value=0.0022 Score=47.17 Aligned_cols=45 Identities=24% Similarity=0.423 Sum_probs=37.8
Q ss_pred cCCCCHHHHHHH-hCCC---HHHHHHhcCCCCCC-CCcCCCCEEEeCCCc
Q 024853 5 GRGETLTSISKQ-YGVS---VYSIAAVNKNIVDV-DLVFEGQRLNIPSSV 49 (261)
Q Consensus 5 q~GDTL~sIAkr-YgVS---v~~I~~~NP~I~~~-d~L~pGQ~L~IP~~~ 49 (261)
+.||||-.||.| ||-. ++.++++||++.+. ..+..|..|.||.-.
T Consensus 6 ~~GDtlD~I~~r~yG~~~~~~e~ll~aNp~La~~~~~lpaG~~I~lP~i~ 55 (60)
T PF05489_consen 6 TQGDTLDLIAYRHYGREDGAVEALLEANPGLADTGPVLPAGTVIILPDIP 55 (60)
T ss_pred eCcCcHHHHHHHHhCcHHHHHHHHHHHChhhhhcCCcCCCCCEEECCCCC
Confidence 489999999998 5654 46899999999776 788999999999643
No 21
>COG3858 Predicted glycosyl hydrolase [General function prediction only]
Probab=95.60 E-value=0.011 Score=58.33 Aligned_cols=47 Identities=36% Similarity=0.385 Sum_probs=42.3
Q ss_pred eeecCCCCHHHHHHHhCCCHHHHHHhcCCCCCCCCcCCCCEEEeCCCc
Q 024853 2 TFGGRGETLTSISKQYGVSVYSIAAVNKNIVDVDLVFEGQRLNIPSSV 49 (261)
Q Consensus 2 YtVq~GDTL~sIAkrYgVSv~~I~~~NP~I~~~d~L~pGQ~L~IP~~~ 49 (261)
|.|++||||++||.+++|+.+++..+|. +..+..+.+|=.|.||...
T Consensus 52 y~~~~~d~~~Sia~~~~vt~~~~~~m~~-~~~~~~l~~~~~l~~P~~~ 98 (423)
T COG3858 52 YDVGPGDTLTSIARTVGVTQDSAAIMNF-VICPGYLQYGLNLYIPSAR 98 (423)
T ss_pred EEecCCcchhhhhhhhcCCHHHHHhhcc-cccccceeeeeEEeccCCC
Confidence 8999999999999999999999999995 4457889999999999653
No 22
>PRK11649 putative peptidase; Provisional
Probab=95.43 E-value=0.016 Score=57.26 Aligned_cols=46 Identities=26% Similarity=0.352 Sum_probs=37.3
Q ss_pred CeeecCCCCHHHHHHHhCCCHHHHHHhcCCCCCCCCcCCCCEEEeC
Q 024853 1 MTFGGRGETLTSISKQYGVSVYSIAAVNKNIVDVDLVFEGQRLNIP 46 (261)
Q Consensus 1 mYtVq~GDTL~sIAkrYgVSv~~I~~~NP~I~~~d~L~pGQ~L~IP 46 (261)
.|+|++||||.+|-+++|++..++.+.-....+...|+|||.+.+-
T Consensus 97 ~~~Vk~GDTl~~iL~r~Gi~~~di~~l~~~~~~L~~Lr~Gq~l~~~ 142 (439)
T PRK11649 97 EYVVSTGDTLSSILNQYGIDMSDISQLAAQDKELRNLKIGQQLSWT 142 (439)
T ss_pred EEEeCCCCCHHHHHHHcCCCHHHHHHHHHcChHhhcCCCCCEEEEE
Confidence 4899999999999999999998877662222334689999999885
No 23
>COG3170 FimV Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=94.88 E-value=0.023 Score=59.40 Aligned_cols=48 Identities=25% Similarity=0.341 Sum_probs=38.3
Q ss_pred CeeecCCCCHHHHHHHh----CCCHH----HHHHhcCCCC---CCCCcCCCCEEEeCCC
Q 024853 1 MTFGGRGETLTSISKQY----GVSVY----SIAAVNKNIV---DVDLVFEGQRLNIPSS 48 (261)
Q Consensus 1 mYtVq~GDTL~sIAkrY----gVSv~----~I~~~NP~I~---~~d~L~pGQ~L~IP~~ 48 (261)
.|+|++|||||+||.+- +++++ .|.+.||+-- +.+.|++|++|.||..
T Consensus 190 tyt~~~~Dtl~dIAs~~rp~~~vt~~Q~~lAly~lNP~af~~gni~RLr~GSvLriP~~ 248 (755)
T COG3170 190 TYTVRSGDTLWDIASRLRPQDHVTVEQMLLALYQLNPQAFVNGNINRLRAGSVLRIPSA 248 (755)
T ss_pred ccccCCcchHHHHHHhhcCcccccHHHHHHHHHhhChhhhcccchhhccccceeeccch
Confidence 38999999999999985 45665 4788999542 2368999999999963
No 24
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=94.43 E-value=0.037 Score=46.80 Aligned_cols=20 Identities=25% Similarity=0.228 Sum_probs=17.5
Q ss_pred CeeecCCCCHHHHHHHhCCC
Q 024853 1 MTFGGRGETLTSISKQYGVS 20 (261)
Q Consensus 1 mYtVq~GDTL~sIAkrYgVS 20 (261)
.|+|++|||||+||++|..+
T Consensus 97 ~y~Vk~GDTL~~IA~~~~g~ 116 (147)
T PRK11198 97 FYTVKSGDTLSAIAKKVYGN 116 (147)
T ss_pred EEEECCCCCHHHHHHHHcCC
Confidence 38999999999999998543
No 25
>COG0739 NlpD Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]
Probab=87.59 E-value=0.75 Score=40.63 Aligned_cols=47 Identities=30% Similarity=0.528 Sum_probs=41.2
Q ss_pred CeeecCCCCHHHHHHHhCCCHHHHHHhcCCCCCCCCcCCCCEEEeCCC
Q 024853 1 MTFGGRGETLTSISKQYGVSVYSIAAVNKNIVDVDLVFEGQRLNIPSS 48 (261)
Q Consensus 1 mYtVq~GDTL~sIAkrYgVSv~~I~~~NP~I~~~d~L~pGQ~L~IP~~ 48 (261)
+|.++.|++|..|+.+++++...+...| ++.....+.+|+.+.+|..
T Consensus 3 ~~~~~~~~~l~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~ 49 (277)
T COG0739 3 LYVVKKGDTLSAIAARLGISAKDLARLN-NLLKKRLLRIGQLLRVPRA 49 (277)
T ss_pred eEEecCCCHHHHHHHHcCCCHHHHHHHH-hhccccccCccceeeeccc
Confidence 4789999999999999999999999999 5544448899999999976
No 26
>COG5004 P2-like prophage tail protein X [General function prediction only]
Probab=83.02 E-value=2.5 Score=32.36 Aligned_cols=48 Identities=17% Similarity=0.356 Sum_probs=36.7
Q ss_pred eeecCCCCHHHHHHH-hCCC---HHHHHHhcCCCCCC-CCcCCCCEEEeCCCc
Q 024853 2 TFGGRGETLTSISKQ-YGVS---VYSIAAVNKNIVDV-DLVFEGQRLNIPSSV 49 (261)
Q Consensus 2 YtVq~GDTL~sIAkr-YgVS---v~~I~~~NP~I~~~-d~L~pGQ~L~IP~~~ 49 (261)
|....|||+-.|+.+ ||-+ .+.++++||++.+- -.+..|-.|.+|...
T Consensus 5 ~Rt~~gDtvDalc~~~Ygrt~~v~eavl~ANpGlAd~gp~lp~gl~i~lPD~~ 57 (70)
T COG5004 5 VRTRQGDTVDALCWRVYGRTTGVTEAVLEANPGLADWGPVLPHGLAITLPDIA 57 (70)
T ss_pred EEeccCchHHHHHHHHHhhHHHHHHHHHhcCCChhhcCCCCccceeEecCCCC
Confidence 455689999999998 5544 45788899999766 456678888888654
No 27
>COG3061 OapA Cell envelope opacity-associated protein A [Cell envelope biogenesis, outer membrane]
Probab=77.02 E-value=3.6 Score=38.16 Aligned_cols=48 Identities=17% Similarity=0.219 Sum_probs=37.8
Q ss_pred CeeecCCCCHHHHHHHhCCCHHHHHHhcC--CCCCC-CCcCCCCEEEeCCC
Q 024853 1 MTFGGRGETLTSISKQYGVSVYSIAAVNK--NIVDV-DLVFEGQRLNIPSS 48 (261)
Q Consensus 1 mYtVq~GDTL~sIAkrYgVSv~~I~~~NP--~I~~~-d~L~pGQ~L~IP~~ 48 (261)
+|+|+.|+||..+=+-.++++.|+-++-. |-.++ +.|+.||.+.|-..
T Consensus 161 sy~V~~G~TLaQlFRdn~LpitDVnAMakveGagkpLSnlkaGq~Vki~~n 211 (242)
T COG3061 161 SYTVPQGKTLAQLFRDNNLPITDVNAMAKVEGAGKPLSNLKAGQKVKISLN 211 (242)
T ss_pred eEEecCCccHHHHHhccCCChHHhHHHHhhccCCCchhhccCCCEEEEEEc
Confidence 59999999999999999999888765531 22222 67999999999643
No 28
>PF13518 HTH_28: Helix-turn-helix domain
Probab=73.28 E-value=3.6 Score=27.56 Aligned_cols=24 Identities=21% Similarity=0.397 Sum_probs=20.8
Q ss_pred cCCCCHHHHHHHhCCCHHHHHHhc
Q 024853 5 GRGETLTSISKQYGVSVYSIAAVN 28 (261)
Q Consensus 5 q~GDTL~sIAkrYgVSv~~I~~~N 28 (261)
..|.|+..||++|||+...|..|-
T Consensus 10 ~~g~s~~~~a~~~gis~~tv~~w~ 33 (52)
T PF13518_consen 10 LEGESVREIAREFGISRSTVYRWI 33 (52)
T ss_pred HcCCCHHHHHHHHCCCHhHHHHHH
Confidence 368899999999999999887664
No 29
>COG4254 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=70.72 E-value=3.4 Score=39.88 Aligned_cols=46 Identities=20% Similarity=0.070 Sum_probs=40.6
Q ss_pred eeecCCCCHHHHHHHhCCCHH---HHHHhcCCCCCCCCcCCCCEEEeCCC
Q 024853 2 TFGGRGETLTSISKQYGVSVY---SIAAVNKNIVDVDLVFEGQRLNIPSS 48 (261)
Q Consensus 2 YtVq~GDTL~sIAkrYgVSv~---~I~~~NP~I~~~d~L~pGQ~L~IP~~ 48 (261)
|.|+.||||-.++..|-...+ .+..+| .+.++..++||..|.||..
T Consensus 8 yrv~~gdtli~l~~~yl~~~~g~r~~q~an-~~~~P~~l~pgs~l~ip~~ 56 (339)
T COG4254 8 YRVLFGDTLILLLGGYLTLLAGSRAAQPAN-TKRPPFILQPGSCLPIPLP 56 (339)
T ss_pred eeeccccHHHHHHHHhhhccchhhhhcccc-cCCCCcccCCCccccCCCc
Confidence 899999999999999976554 477889 8888999999999999965
No 30
>KOG2850 consensus Predicted peptidoglycan-binding protein, contains LysM domain [General function prediction only]
Probab=70.04 E-value=3 Score=37.38 Aligned_cols=47 Identities=26% Similarity=0.236 Sum_probs=40.9
Q ss_pred eeecCCCCHHHHHHHhCCCHHHHHHhcCCCCCCCCcCCCCEEEeCCCc
Q 024853 2 TFGGRGETLTSISKQYGVSVYSIAAVNKNIVDVDLVFEGQRLNIPSSV 49 (261)
Q Consensus 2 YtVq~GDTL~sIAkrYgVSv~~I~~~NP~I~~~d~L~pGQ~L~IP~~~ 49 (261)
-+||+||||..||-+|..++.+|...| ++........=+.+.||...
T Consensus 12 ~~iq~~dt~~a~al~~~~~va~i~RvN-~~~r~q~f~a~~~i~~pv~~ 58 (186)
T KOG2850|consen 12 VTIQEGDTLQAIALNYESDVADIKRVN-NDDREQRFNALRSISIPVTR 58 (186)
T ss_pred eeeccCchhhhHHhhcccchhhheeec-cchhhhhhccccceecccch
Confidence 378999999999999999999999999 67555777888889998764
No 31
>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=69.34 E-value=2.6 Score=30.58 Aligned_cols=24 Identities=21% Similarity=0.533 Sum_probs=20.9
Q ss_pred cCCCCHHHHHHHhCCCHHHHHHhc
Q 024853 5 GRGETLTSISKQYGVSVYSIAAVN 28 (261)
Q Consensus 5 q~GDTL~sIAkrYgVSv~~I~~~N 28 (261)
..|.|+..||++|||++..|..|=
T Consensus 21 ~~g~sv~~va~~~gi~~~~l~~W~ 44 (76)
T PF01527_consen 21 ESGESVSEVAREYGISPSTLYNWR 44 (76)
T ss_dssp HHHCHHHHHHHHHTS-HHHHHHHH
T ss_pred HCCCceEeeecccccccccccHHH
Confidence 579999999999999999998875
No 32
>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=63.18 E-value=3.3 Score=26.98 Aligned_cols=24 Identities=13% Similarity=0.134 Sum_probs=18.6
Q ss_pred hhhhhHHhhhhhcccchhhhccCC
Q 024853 72 RSLNVFYGRLDKRHISMQITHRLP 95 (261)
Q Consensus 72 ~s~~tly~~~~k~gism~~l~~lp 95 (261)
..++|+++++++++++...+.+++
T Consensus 4 ~~gDtl~~IA~~~~~~~~~l~~~N 27 (44)
T PF01476_consen 4 QPGDTLWSIAKRYGISVDELMELN 27 (44)
T ss_dssp -TT--HHHHHHHTTS-HHHHHHHC
T ss_pred CcCCcHHHHHhhhhhhHhHHHHhc
Confidence 568999999999999999999887
No 33
>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=58.92 E-value=10 Score=25.67 Aligned_cols=23 Identities=30% Similarity=0.518 Sum_probs=17.2
Q ss_pred cCCCCHHHHHHHhCCCHHHHHHh
Q 024853 5 GRGETLTSISKQYGVSVYSIAAV 27 (261)
Q Consensus 5 q~GDTL~sIAkrYgVSv~~I~~~ 27 (261)
+.|-|+..||+.+|||...|...
T Consensus 19 ~~G~si~~IA~~~gvsr~TvyR~ 41 (45)
T PF02796_consen 19 AEGMSIAEIAKQFGVSRSTVYRY 41 (45)
T ss_dssp HTT--HHHHHHHTTS-HHHHHHH
T ss_pred HCCCCHHHHHHHHCcCHHHHHHH
Confidence 46889999999999999988753
No 34
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=51.73 E-value=16 Score=29.62 Aligned_cols=25 Identities=20% Similarity=0.206 Sum_probs=22.6
Q ss_pred ecCCCCHHHHHHHhCCCHHHHHHhc
Q 024853 4 GGRGETLTSISKQYGVSVYSIAAVN 28 (261)
Q Consensus 4 Vq~GDTL~sIAkrYgVSv~~I~~~N 28 (261)
+..|-|+..||++|||+...|..|=
T Consensus 26 ~~~g~sv~evA~e~gIs~~tl~~W~ 50 (121)
T PRK09413 26 FEPGMTVSLVARQHGVAASQLFLWR 50 (121)
T ss_pred HcCCCCHHHHHHHHCcCHHHHHHHH
Confidence 4679999999999999999999884
No 35
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=50.67 E-value=18 Score=24.24 Aligned_cols=23 Identities=26% Similarity=0.313 Sum_probs=17.4
Q ss_pred CCCCHHHHHHHhCCCHHHHHHhc
Q 024853 6 RGETLTSISKQYGVSVYSIAAVN 28 (261)
Q Consensus 6 ~GDTL~sIAkrYgVSv~~I~~~N 28 (261)
.|-|...||+.+|+|...+..|=
T Consensus 16 ~G~s~~~ia~~lgvs~~Tv~~w~ 38 (50)
T PF13384_consen 16 EGWSIREIAKRLGVSRSTVYRWI 38 (50)
T ss_dssp HT--HHHHHHHHTS-HHHHHHHH
T ss_pred CCCCHHHHHHHHCcCHHHHHHHH
Confidence 49999999999999999887763
No 36
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=49.76 E-value=17 Score=28.77 Aligned_cols=24 Identities=17% Similarity=0.425 Sum_probs=20.2
Q ss_pred ecCCCCHHHHHHHhCC-CHHHHHHh
Q 024853 4 GGRGETLTSISKQYGV-SVYSIAAV 27 (261)
Q Consensus 4 Vq~GDTL~sIAkrYgV-Sv~~I~~~ 27 (261)
.++|.|+..||++||| +...|..|
T Consensus 21 ~~~g~sv~~vAr~~gv~~~~~l~~W 45 (116)
T COG2963 21 LRGGDTVSEVAREFGIVSATQLYKW 45 (116)
T ss_pred HhcCccHHHHHHHhCCCChHHHHHH
Confidence 4589999999999996 88887754
No 37
>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=47.01 E-value=27 Score=19.66 Aligned_cols=22 Identities=27% Similarity=0.505 Sum_probs=18.7
Q ss_pred cCCCCHHHHHHHhCCCHHHHHH
Q 024853 5 GRGETLTSISKQYGVSVYSIAA 26 (261)
Q Consensus 5 q~GDTL~sIAkrYgVSv~~I~~ 26 (261)
..|.++..||+.+|++...+..
T Consensus 19 ~~~~s~~~ia~~~~is~~tv~~ 40 (42)
T cd00569 19 AAGESVAEIARRLGVSRSTLYR 40 (42)
T ss_pred HcCCCHHHHHHHHCCCHHHHHH
Confidence 4688999999999999888764
No 38
>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=46.98 E-value=18 Score=24.89 Aligned_cols=24 Identities=21% Similarity=0.350 Sum_probs=17.4
Q ss_pred ecCC-CCHHHHHHHhCCCHHHHHHh
Q 024853 4 GGRG-ETLTSISKQYGVSVYSIAAV 27 (261)
Q Consensus 4 Vq~G-DTL~sIAkrYgVSv~~I~~~ 27 (261)
|+.| -++...|++|||+...|...
T Consensus 12 v~~g~~S~r~AA~~ygVp~sTL~~r 36 (45)
T PF05225_consen 12 VKNGKMSIRKAAKKYGVPRSTLRRR 36 (45)
T ss_dssp HHTTSS-HHHHHHHHT--HHHHHHH
T ss_pred HHhCCCCHHHHHHHHCcCHHHHHHH
Confidence 4556 89999999999999998754
No 39
>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=43.32 E-value=13 Score=26.36 Aligned_cols=23 Identities=26% Similarity=0.498 Sum_probs=16.1
Q ss_pred ecCCCCHHHHHHHhCCCHHHHHH
Q 024853 4 GGRGETLTSISKQYGVSVYSIAA 26 (261)
Q Consensus 4 Vq~GDTL~sIAkrYgVSv~~I~~ 26 (261)
+..|.+...||+.|||+...|..
T Consensus 19 ~e~g~s~~~ia~~fgv~~sTv~~ 41 (53)
T PF04218_consen 19 LEEGESKRDIAREFGVSRSTVST 41 (53)
T ss_dssp HHCTT-HHHHHHHHT--CCHHHH
T ss_pred HHcCCCHHHHHHHhCCCHHHHHH
Confidence 45788999999999998776653
No 40
>PHA00675 hypothetical protein
Probab=39.42 E-value=31 Score=27.15 Aligned_cols=24 Identities=17% Similarity=0.239 Sum_probs=20.9
Q ss_pred cCCCCHHHHHHHhCCCHHHHHHhc
Q 024853 5 GRGETLTSISKQYGVSVYSIAAVN 28 (261)
Q Consensus 5 q~GDTL~sIAkrYgVSv~~I~~~N 28 (261)
+.|.+...||++|||+...|.+.=
T Consensus 37 r~G~s~~~IA~~fGVsrstV~~I~ 60 (78)
T PHA00675 37 VEGMSYAVLAEKFEQSKGAIAKIC 60 (78)
T ss_pred hcCccHHHHHHHhCCCHHHHHHHH
Confidence 689999999999999999887543
No 41
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=39.04 E-value=35 Score=23.06 Aligned_cols=22 Identities=23% Similarity=0.416 Sum_probs=14.7
Q ss_pred cCCCCHHHHHHHhCCCHHHHHH
Q 024853 5 GRGETLTSISKQYGVSVYSIAA 26 (261)
Q Consensus 5 q~GDTL~sIAkrYgVSv~~I~~ 26 (261)
+.|-++..||+++|++...|..
T Consensus 18 ~~G~s~~~IA~~lg~s~sTV~r 39 (44)
T PF13936_consen 18 EQGMSIREIAKRLGRSRSTVSR 39 (44)
T ss_dssp CS---HHHHHHHTT--HHHHHH
T ss_pred HcCCCHHHHHHHHCcCcHHHHH
Confidence 5799999999999999988764
No 42
>PF02183 HALZ: Homeobox associated leucine zipper; InterPro: IPR003106 This region is a plant specific leucine zipper that is always found associated with a homeobox []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=32.74 E-value=46 Score=23.24 Aligned_cols=23 Identities=17% Similarity=0.488 Sum_probs=20.1
Q ss_pred CCHHHHHHHHhhhHHHHHHHHHH
Q 024853 224 ISFEESSHAYRKLEDDYEKFLSE 246 (261)
Q Consensus 224 ~~~ee~~~~y~~le~~y~~fl~~ 246 (261)
+||+-+++.|..|-.+|...+.|
T Consensus 5 ~Dy~~LK~~yd~Lk~~~~~L~~E 27 (45)
T PF02183_consen 5 RDYDALKASYDSLKAEYDSLKKE 27 (45)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 48999999999999999987765
No 43
>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=30.13 E-value=49 Score=26.34 Aligned_cols=20 Identities=25% Similarity=0.519 Sum_probs=14.8
Q ss_pred CCCHHHHHHHhCCCHHHHHH
Q 024853 7 GETLTSISKQYGVSVYSIAA 26 (261)
Q Consensus 7 GDTL~sIAkrYgVSv~~I~~ 26 (261)
|.++..||++||+|...|.+
T Consensus 72 G~n~~eLA~kyglS~r~I~~ 91 (108)
T PF08765_consen 72 GMNVRELARKYGLSERQIYR 91 (108)
T ss_dssp SS-HHHHHHHHT--HHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHH
Confidence 88999999999999887664
No 44
>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=28.85 E-value=77 Score=21.30 Aligned_cols=22 Identities=27% Similarity=0.377 Sum_probs=17.9
Q ss_pred cCCCCHHHHHHHhCCCHHHHHH
Q 024853 5 GRGETLTSISKQYGVSVYSIAA 26 (261)
Q Consensus 5 q~GDTL~sIAkrYgVSv~~I~~ 26 (261)
-.|-|+..||+.+|+|...+..
T Consensus 18 ~~~~t~~eIa~~lg~s~~~V~~ 39 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISRSTVRR 39 (50)
T ss_dssp TST-SHHHHHHHHTSCHHHHHH
T ss_pred cCCCCHHHHHHHHCCcHHHHHH
Confidence 3588999999999999987764
No 45
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=28.30 E-value=62 Score=24.07 Aligned_cols=20 Identities=30% Similarity=0.394 Sum_probs=18.5
Q ss_pred CHHHHHHHhCCCHHHHHHhc
Q 024853 9 TLTSISKQYGVSVYSIAAVN 28 (261)
Q Consensus 9 TL~sIAkrYgVSv~~I~~~N 28 (261)
+|-.||.++||+...|..|-
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 78899999999999999885
No 46
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=28.24 E-value=41 Score=27.17 Aligned_cols=25 Identities=20% Similarity=0.329 Sum_probs=21.8
Q ss_pred ecCCCCHHHHHHHhCCCHHHHHHhc
Q 024853 4 GGRGETLTSISKQYGVSVYSIAAVN 28 (261)
Q Consensus 4 Vq~GDTL~sIAkrYgVSv~~I~~~N 28 (261)
++.|.+...+|++|+|+...+..|=
T Consensus 15 ~~~g~s~~eaa~~F~VS~~Tv~~W~ 39 (119)
T PF01710_consen 15 IEKGKSIREAAKRFGVSRNTVYRWL 39 (119)
T ss_pred HHccchHHHHHHHhCcHHHHHHHHH
Confidence 4578999999999999999988773
No 47
>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=25.63 E-value=34 Score=23.05 Aligned_cols=17 Identities=41% Similarity=0.513 Sum_probs=11.8
Q ss_pred CCHHHHHHHhCCCHHHH
Q 024853 8 ETLTSISKQYGVSVYSI 24 (261)
Q Consensus 8 DTL~sIAkrYgVSv~~I 24 (261)
|++..||+.||++++.|
T Consensus 39 ~~~~~ia~~l~~~~~~l 55 (55)
T PF01381_consen 39 DTLKKIAKALGVSPEYL 55 (55)
T ss_dssp HHHHHHHHHHTSEHHHH
T ss_pred HHHHHHHHHHCCCHHHC
Confidence 56777777777777654
No 48
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=25.20 E-value=86 Score=19.78 Aligned_cols=20 Identities=20% Similarity=0.139 Sum_probs=17.3
Q ss_pred CHHHHHHHhCCCHHHHHHhc
Q 024853 9 TLTSISKQYGVSVYSIAAVN 28 (261)
Q Consensus 9 TL~sIAkrYgVSv~~I~~~N 28 (261)
|+..+|+.+||+...|..+=
T Consensus 2 s~~e~a~~lgvs~~tl~~~~ 21 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWV 21 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 56789999999999998774
No 49
>PF07709 SRR: Seven Residue Repeat; InterPro: IPR011714 This repeat is found in some Plasmodium and Theileria proteins.
Probab=24.73 E-value=45 Score=17.77 Aligned_cols=13 Identities=38% Similarity=0.731 Sum_probs=10.1
Q ss_pred CHHHHHHHHhhhH
Q 024853 225 SFEESSHAYRKLE 237 (261)
Q Consensus 225 ~~ee~~~~y~~le 237 (261)
.||.|+-+|..|+
T Consensus 2 ~~~~V~~aY~~l~ 14 (14)
T PF07709_consen 2 KFEKVKNAYEQLS 14 (14)
T ss_pred cHHHHHHHHHhcC
Confidence 3688888888774
No 50
>PHA01976 helix-turn-helix protein
Probab=24.53 E-value=49 Score=23.24 Aligned_cols=18 Identities=22% Similarity=0.388 Sum_probs=15.6
Q ss_pred CCHHHHHHHhCCCHHHHH
Q 024853 8 ETLTSISKQYGVSVYSIA 25 (261)
Q Consensus 8 DTL~sIAkrYgVSv~~I~ 25 (261)
+++..||+.|||+++.|.
T Consensus 45 ~~l~~ia~~l~v~~~~l~ 62 (67)
T PHA01976 45 KTLLRLADALGVTLDWLC 62 (67)
T ss_pred HHHHHHHHHHCcCHHHHh
Confidence 678899999999999885
No 51
>PLN00218 predicted protein; Provisional
Probab=24.30 E-value=38 Score=28.56 Aligned_cols=29 Identities=28% Similarity=0.625 Sum_probs=22.5
Q ss_pred ccccchhhhhhhhhHh-----------HHHhhhhhhhhhc
Q 024853 139 KTTGYFLVVVPLIAFC-----------IRCMIGAFHTRIA 167 (261)
Q Consensus 139 ~~~~~~~~~~p~~~f~-----------~~~~i~~~~~~i~ 167 (261)
+....+.+++|.++|| .||+|.-|--...
T Consensus 61 sislilnvllpalgfcgfqrggsswvvercvisffflils 100 (151)
T PLN00218 61 SISLILNVLLPALGFCGFQRGGSSWVVERCVISFFFLILS 100 (151)
T ss_pred hHHHHHHHHHHhhcccccccCCcceehhHHHHHHHHHHHH
Confidence 3445677899999999 5999998876554
No 52
>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=24.08 E-value=50 Score=22.89 Aligned_cols=18 Identities=22% Similarity=0.416 Sum_probs=14.7
Q ss_pred CHHHHHHHhCCCHHHHHH
Q 024853 9 TLTSISKQYGVSVYSIAA 26 (261)
Q Consensus 9 TL~sIAkrYgVSv~~I~~ 26 (261)
++..+|+.+|++..+|++
T Consensus 5 ~V~elAk~l~v~~~~ii~ 22 (54)
T PF04760_consen 5 RVSELAKELGVPSKEIIK 22 (54)
T ss_dssp -TTHHHHHHSSSHHHHHH
T ss_pred EHHHHHHHHCcCHHHHHH
Confidence 577899999999998654
No 53
>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A.
Probab=23.78 E-value=82 Score=24.54 Aligned_cols=21 Identities=29% Similarity=0.570 Sum_probs=16.2
Q ss_pred cCCCCHHHHHHHhCCCHHHHH
Q 024853 5 GRGETLTSISKQYGVSVYSIA 25 (261)
Q Consensus 5 q~GDTL~sIAkrYgVSv~~I~ 25 (261)
++|=||..||+.+|++...+.
T Consensus 13 krG~sL~~lsr~~Gl~~~tl~ 33 (78)
T PF13693_consen 13 KRGTSLAALSREAGLSSSTLR 33 (78)
T ss_dssp TTS--HHHHHHHHSS-HHHHH
T ss_pred HcCCCHHHHHHHcCCCHHHHH
Confidence 579999999999999998876
No 54
>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=23.78 E-value=88 Score=25.22 Aligned_cols=22 Identities=27% Similarity=0.342 Sum_probs=18.6
Q ss_pred cCCCCHHHHHHHhCCCHHHHHH
Q 024853 5 GRGETLTSISKQYGVSVYSIAA 26 (261)
Q Consensus 5 q~GDTL~sIAkrYgVSv~~I~~ 26 (261)
.+.-||..||++|||+...|..
T Consensus 69 ~pd~tl~Ela~~l~Vs~~ti~~ 90 (119)
T PF01710_consen 69 NPDATLRELAERLGVSPSTIWR 90 (119)
T ss_pred CCCcCHHHHHHHcCCCHHHHHH
Confidence 4778999999999999887764
No 55
>PRK10871 nlpD lipoprotein NlpD; Provisional
Probab=22.65 E-value=30 Score=33.40 Aligned_cols=31 Identities=3% Similarity=-0.170 Sum_probs=26.3
Q ss_pred HHhhhhhhhHHhhhhhcccchhhhccCCccc
Q 024853 68 EIHRRSLNVFYGRLDKRHISMQITHRLPHIW 98 (261)
Q Consensus 68 ~~~~~s~~tly~~~~k~gism~~l~~lp~i~ 98 (261)
.+....+||||.|+.++|.++..|-++|.|.
T Consensus 62 ~y~Vk~GDTL~~IA~~~g~~~~~La~~N~l~ 92 (319)
T PRK10871 62 TYTVKKGDTLFYIAWITGNDFRDLAQRNNIQ 92 (319)
T ss_pred ceEECCCCHHHHHHHHHCcCHHHHHHhcCCC
Confidence 3456789999999999999999998887774
No 56
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=22.07 E-value=1.2e+02 Score=19.50 Aligned_cols=23 Identities=22% Similarity=0.335 Sum_probs=19.6
Q ss_pred cCCCCHHHHHHHhCCCHHHHHHh
Q 024853 5 GRGETLTSISKQYGVSVYSIAAV 27 (261)
Q Consensus 5 q~GDTL~sIAkrYgVSv~~I~~~ 27 (261)
..|.+.-.||+.+|++...+...
T Consensus 16 ~~g~s~~eia~~l~is~~tv~~~ 38 (58)
T smart00421 16 AEGLTNKEIAERLGISEKTVKTH 38 (58)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHH
Confidence 46889999999999999887654
No 57
>cd01093 CRIB_PAK_like PAK (p21 activated kinase) Binding Domain (PBD), binds Cdc42p- and/or Rho-like small GTPases; also known as the Cdc42/Rac interactive binding (CRIB) motif; has been shown to inhibit transcriptional activation and cell transformation mediated by the Ras-Rac pathway. This subgroup of CRIB/PBD-domains is found N-terminal of Serine/Threonine kinase domains in PAK and PAK-like proteins.
Probab=22.06 E-value=50 Score=22.83 Aligned_cols=21 Identities=19% Similarity=0.590 Sum_probs=18.3
Q ss_pred HHhhhHHHHHHHHHHhCCCCc
Q 024853 232 AYRKLEDDYEKFLSECGMSKW 252 (261)
Q Consensus 232 ~y~~le~~y~~fl~~~g~s~~ 252 (261)
-|.-|..+.+++|..+|||+-
T Consensus 23 ~f~glP~eW~~ll~~sgis~~ 43 (46)
T cd01093 23 EFTGLPEEWQRLLKSSGITKE 43 (46)
T ss_pred cccCCCHHHHHHHHHcCCCHH
Confidence 368899999999999999973
No 58
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=21.86 E-value=87 Score=22.20 Aligned_cols=23 Identities=26% Similarity=0.459 Sum_probs=14.9
Q ss_pred cCCCCHHHHHHHhC-CCHHHHHHh
Q 024853 5 GRGETLTSISKQYG-VSVYSIAAV 27 (261)
Q Consensus 5 q~GDTL~sIAkrYg-VSv~~I~~~ 27 (261)
..|.+.-.|++.|. ++.++|.++
T Consensus 29 ~~G~s~eeI~~~yp~Lt~~~i~aA 52 (56)
T PF04255_consen 29 AAGESPEEIAEDYPSLTLEDIRAA 52 (56)
T ss_dssp HTT--HHHHHHHSTT--HHHHHHH
T ss_pred HcCCCHHHHHHHCCCCCHHHHHHH
Confidence 57888888888887 888887653
No 59
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=21.79 E-value=22 Score=24.75 Aligned_cols=21 Identities=24% Similarity=0.254 Sum_probs=12.0
Q ss_pred CCHHHHHHHhCCCHHHHHHhc
Q 024853 8 ETLTSISKQYGVSVYSIAAVN 28 (261)
Q Consensus 8 DTL~sIAkrYgVSv~~I~~~N 28 (261)
++|..||.-+|+++++|....
T Consensus 41 ~~l~~ia~~l~~~~~el~~~~ 61 (63)
T PF13443_consen 41 DTLEKIAKALNCSPEELFEYE 61 (63)
T ss_dssp HHHHHHHHHHT--HHHCTECC
T ss_pred HHHHHHHHHcCCCHHHHhhcC
Confidence 456667777777777665443
No 60
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=21.62 E-value=98 Score=21.66 Aligned_cols=20 Identities=25% Similarity=0.346 Sum_probs=17.5
Q ss_pred CHHHHHHHhCCCHHHHHHhc
Q 024853 9 TLTSISKQYGVSVYSIAAVN 28 (261)
Q Consensus 9 TL~sIAkrYgVSv~~I~~~N 28 (261)
|+..+|+.+||+...|..|=
T Consensus 2 s~~eva~~~gvs~~tlr~w~ 21 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWE 21 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 56789999999999999764
No 61
>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=21.61 E-value=75 Score=22.51 Aligned_cols=23 Identities=26% Similarity=0.478 Sum_probs=15.9
Q ss_pred ecCCCCH---HHHHHHhCCCHHHHHH
Q 024853 4 GGRGETL---TSISKQYGVSVYSIAA 26 (261)
Q Consensus 4 Vq~GDTL---~sIAkrYgVSv~~I~~ 26 (261)
.++||.| ..||++||||...+.+
T Consensus 18 ~~~g~~lps~~~la~~~~vsr~tvr~ 43 (64)
T PF00392_consen 18 LPPGDRLPSERELAERYGVSRTTVRE 43 (64)
T ss_dssp S-TTSBE--HHHHHHHHTS-HHHHHH
T ss_pred CCCCCEeCCHHHHHHHhccCCcHHHH
Confidence 3567755 7899999999886554
No 62
>PF12116 SpoIIID: Stage III sporulation protein D; InterPro: IPR014208 Members of this entry represent the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if, and only if, the species is capable of endospore formation. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation [].; PDB: 2L0K_A.
Probab=21.38 E-value=43 Score=26.59 Aligned_cols=23 Identities=22% Similarity=0.249 Sum_probs=16.1
Q ss_pred eeecCCCCHHHHHHHhCCCHHHH
Q 024853 2 TFGGRGETLTSISKQYGVSVYSI 24 (261)
Q Consensus 2 YtVq~GDTL~sIAkrYgVSv~~I 24 (261)
|.+..+.|+-..|+.||||-+.+
T Consensus 14 yIi~~~aTVR~~Ak~FGvSKSTV 36 (82)
T PF12116_consen 14 YIIETKATVRQAAKVFGVSKSTV 36 (82)
T ss_dssp HHHHH---HHHHHHHHTS-HHHH
T ss_pred HHHHcccHHHHHHHHHCCcHHHH
Confidence 67788999999999999997753
No 63
>PF10810 DUF2545: Protein of unknown function (DUF2545) ; InterPro: IPR024470 This family of proteins with unknown function appear to be restricted to Enterobacteriaceae. Their sequences are highly conserved.
Probab=21.11 E-value=20 Score=27.97 Aligned_cols=23 Identities=39% Similarity=0.673 Sum_probs=20.3
Q ss_pred ccccchhhhhhhhhHhHHHhhhh
Q 024853 139 KTTGYFLVVVPLIAFCIRCMIGA 161 (261)
Q Consensus 139 ~~~~~~~~~~p~~~f~~~~~i~~ 161 (261)
-+++.|+.++|.-+.-||-|+|+
T Consensus 55 ~vtglflflapacgliirfmvg~ 77 (80)
T PF10810_consen 55 IVTGLFLFLAPACGLIIRFMVGY 77 (80)
T ss_pred HHHHHHHHHhccccceeeeeecc
Confidence 35889999999999999999885
No 64
>PF13551 HTH_29: Winged helix-turn helix
Probab=20.81 E-value=96 Score=23.36 Aligned_cols=24 Identities=21% Similarity=0.333 Sum_probs=19.8
Q ss_pred ecCCC-CHHHHHHHhCCCHHHHHHh
Q 024853 4 GGRGE-TLTSISKQYGVSVYSIAAV 27 (261)
Q Consensus 4 Vq~GD-TL~sIAkrYgVSv~~I~~~ 27 (261)
+..|. |...||+.+|++...+..|
T Consensus 8 ~~~g~~~~~~ia~~lg~s~~Tv~r~ 32 (112)
T PF13551_consen 8 LAEGVSTIAEIARRLGISRRTVYRW 32 (112)
T ss_pred HHcCCCcHHHHHHHHCcCHHHHHHH
Confidence 35688 6999999999999987654
No 65
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=20.72 E-value=1.4e+02 Score=19.74 Aligned_cols=23 Identities=22% Similarity=0.294 Sum_probs=17.3
Q ss_pred ecCCC---CHHHHHHHhCCCHHHHHH
Q 024853 4 GGRGE---TLTSISKQYGVSVYSIAA 26 (261)
Q Consensus 4 Vq~GD---TL~sIAkrYgVSv~~I~~ 26 (261)
+.+|+ |.-.||++||+|...+.+
T Consensus 14 ~~~~~~l~s~~~la~~~~vs~~tv~~ 39 (60)
T smart00345 14 LRPGDKLPSERELAAQLGVSRTTVRE 39 (60)
T ss_pred CCCCCcCcCHHHHHHHHCCCHHHHHH
Confidence 34555 788999999999876654
No 66
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=20.58 E-value=1.2e+02 Score=20.34 Aligned_cols=19 Identities=16% Similarity=0.426 Sum_probs=16.3
Q ss_pred CCHHHHHHHhCCCHHHHHH
Q 024853 8 ETLTSISKQYGVSVYSIAA 26 (261)
Q Consensus 8 DTL~sIAkrYgVSv~~I~~ 26 (261)
-|+-.||+.+|++...+..
T Consensus 28 ~s~~~vA~~~~vs~~TV~r 46 (52)
T PF13542_consen 28 RSFKDVARELGVSWSTVRR 46 (52)
T ss_pred CCHHHHHHHHCCCHHHHHH
Confidence 3889999999999988764
No 67
>PF12652 CotJB: CotJB protein; InterPro: IPR024207 The cotJ operon proteins affect spore coat composition, and is controlled by sigma E. The genes, which include CotJB, are either required for the normal formation of the inner layers of the coat or are themselves structural components of the coat []. CotJB has been identified as a spore coat protein [].
Probab=20.17 E-value=1.3e+02 Score=23.37 Aligned_cols=44 Identities=30% Similarity=0.541 Sum_probs=33.1
Q ss_pred CCCCCCCCCCCCchhhhhcCCCCCHHHHHHHHhhhHHHHHHH---HHHhCCCCc-cccc
Q 024853 202 LDSGSRPRTNDPVEEQDQAQPLISFEESSHAYRKLEDDYEKF---LSECGMSKW-GYWR 256 (261)
Q Consensus 202 ~d~~~~~~~~~~s~~q~~~~~~~~~ee~~~~y~~le~~y~~f---l~~~g~s~~-gywr 256 (261)
||+|+ .+|++. -.|.++++-..+|..+|++. |.--|.+.+ .+|.
T Consensus 22 LDTHP--------~d~~Al---~~y~~~~~~~~~l~~~Ye~~yGPLt~~~~~~~~~~w~ 69 (78)
T PF12652_consen 22 LDTHP--------DDQEAL---EYYNEYSKQRKQLKKEYEKRYGPLTNFGVSPSRDPWQ 69 (78)
T ss_pred hcCCC--------CcHHHH---HHHHHHHHHHHHHHHHHHHHhCCCcCCCcCCCCCCcc
Confidence 77775 355555 68899999999999999986 556667766 5663
No 68
>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=20.01 E-value=39 Score=33.03 Aligned_cols=29 Identities=10% Similarity=-0.031 Sum_probs=25.6
Q ss_pred hhhhhhhHHhhhhhcccchhhhccCCccc
Q 024853 70 HRRSLNVFYGRLDKRHISMQITHRLPHIW 98 (261)
Q Consensus 70 ~~~s~~tly~~~~k~gism~~l~~lp~i~ 98 (261)
....++||+.+++++|++++.+.++|.+.
T Consensus 297 iVq~GDTL~sIAkRYGVSV~~L~r~N~L~ 325 (338)
T TIGR02907 297 IVQEGDTIETIAERYEISVSQLIRHNQLE 325 (338)
T ss_pred EECCCCCHHHHHHHHCcCHHHHHHHhCCC
Confidence 44789999999999999999999998664
Done!