Query 018290
Match_columns 358
No_of_seqs 330 out of 2130
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 07:44:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018290.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018290hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK06347 autolysin; Reviewed 99.9 6.7E-27 1.5E-31 241.7 18.3 167 40-217 404-592 (592)
2 PRK06347 autolysin; Reviewed 99.9 3.2E-26 6.9E-31 236.7 20.5 171 40-221 329-528 (592)
3 PRK10783 mltD membrane-bound l 99.9 1.9E-22 4.1E-27 204.4 20.2 172 40-221 262-451 (456)
4 PRK13914 invasion associated s 99.8 2.8E-20 6.1E-25 186.6 10.7 244 43-297 29-433 (481)
5 PRK10783 mltD membrane-bound l 99.6 1.5E-15 3.3E-20 154.1 13.2 109 40-159 342-450 (456)
6 PF01476 LysM: LysM domain; I 99.3 4.7E-12 1E-16 87.2 3.6 43 174-217 1-44 (44)
7 COG1388 LytE FOG: LysM repeat 99.2 5.3E-11 1.1E-15 100.2 8.0 95 121-219 1-113 (124)
8 PF01476 LysM: LysM domain; I 99.0 3.3E-10 7.1E-15 77.9 4.2 43 110-156 1-44 (44)
9 COG1388 LytE FOG: LysM repeat 98.9 3.1E-09 6.7E-14 89.4 8.0 95 55-157 1-112 (124)
10 TIGR02899 spore_safA spore coa 98.9 1.9E-09 4.1E-14 73.4 4.7 43 176-218 1-44 (44)
11 PRK14125 cell division suppres 98.9 3.1E-09 6.8E-14 87.0 6.4 51 171-222 36-94 (103)
12 cd00118 LysM Lysin domain, fou 98.9 3.6E-09 7.8E-14 71.0 5.4 45 173-217 2-46 (46)
13 PRK14125 cell division suppres 98.9 8.8E-09 1.9E-13 84.3 8.2 54 38-96 33-93 (103)
14 COG3858 Predicted glycosyl hyd 98.8 5.6E-09 1.2E-13 103.1 5.6 99 108-222 2-100 (423)
15 PRK10871 nlpD lipoprotein NlpD 98.7 1.3E-08 2.8E-13 98.7 5.7 49 172-220 61-109 (319)
16 TIGR02907 spore_VI_D stage VI 98.6 5.5E-08 1.2E-12 93.8 5.8 46 171-217 293-338 (338)
17 cd00118 LysM Lysin domain, fou 98.6 1.8E-07 4E-12 62.5 5.8 45 109-156 2-46 (46)
18 smart00257 LysM Lysin motif. 98.5 1.4E-07 3.1E-12 62.3 5.0 44 173-216 1-44 (44)
19 TIGR02899 spore_safA spore coa 98.5 1.2E-07 2.7E-12 64.3 4.7 43 112-157 1-44 (44)
20 PRK13914 invasion associated s 98.5 2E-07 4.4E-12 94.5 6.7 48 172-220 28-75 (481)
21 COG3858 Predicted glycosyl hyd 98.4 2.9E-07 6.3E-12 91.1 6.0 97 42-159 2-98 (423)
22 PRK10871 nlpD lipoprotein NlpD 98.4 3.2E-07 6.9E-12 89.0 5.9 49 108-159 61-109 (319)
23 PRK11198 LysM domain/BON super 98.3 8.1E-07 1.8E-11 77.4 5.2 47 172-218 96-147 (147)
24 TIGR02907 spore_VI_D stage VI 98.2 1.9E-06 4.1E-11 83.3 6.1 48 105-156 291-338 (338)
25 PRK11198 LysM domain/BON super 98.2 2.6E-06 5.6E-11 74.2 5.7 51 107-157 95-147 (147)
26 smart00257 LysM Lysin motif. 98.1 5.3E-06 1.2E-10 54.6 5.3 44 109-155 1-44 (44)
27 COG1652 XkdP Uncharacterized p 97.3 8.4E-05 1.8E-09 70.9 1.7 50 109-158 212-264 (269)
28 PRK10190 L,D-transpeptidase; P 97.1 0.00091 2E-08 64.8 6.3 50 171-220 37-88 (310)
29 PRK10260 L,D-transpeptidase; P 97.1 0.00094 2E-08 64.5 6.2 50 171-220 40-91 (306)
30 PRK10260 L,D-transpeptidase; P 97.0 0.0028 6E-08 61.3 8.7 50 40-94 39-90 (306)
31 TIGR03505 FimV_core FimV N-ter 97.0 0.00058 1.3E-08 52.6 3.1 41 180-220 1-53 (74)
32 COG1652 XkdP Uncharacterized p 96.9 0.00032 6.9E-09 66.9 1.4 49 172-220 211-265 (269)
33 PF04225 OapA: Opacity-associa 96.8 0.00079 1.7E-08 53.2 2.5 49 172-220 3-55 (85)
34 PRK10190 L,D-transpeptidase; P 96.7 0.0078 1.7E-07 58.4 8.8 50 40-94 36-87 (310)
35 PF04225 OapA: Opacity-associa 96.3 0.0025 5.4E-08 50.4 2.2 53 41-94 2-54 (85)
36 TIGR03505 FimV_core FimV N-ter 96.3 0.0059 1.3E-07 47.0 4.0 42 116-157 1-51 (74)
37 PF05489 Phage_tail_X: Phage T 96.2 0.0083 1.8E-07 44.3 4.4 49 109-158 3-54 (60)
38 PF05489 Phage_tail_X: Phage T 94.9 0.046 1E-06 40.3 4.4 44 177-220 6-55 (60)
39 PRK11649 putative peptidase; P 94.6 0.19 4.2E-06 51.4 9.5 108 106-216 94-233 (439)
40 PRK11649 putative peptidase; P 93.7 0.086 1.9E-06 53.9 4.9 48 172-219 96-144 (439)
41 COG3061 OapA Cell envelope opa 92.0 0.42 9E-06 44.1 6.2 76 81-159 133-212 (242)
42 COG3061 OapA Cell envelope opa 91.9 0.45 9.8E-06 43.9 6.3 75 146-220 134-212 (242)
43 COG3170 FimV Tfp pilus assembl 91.6 0.13 2.8E-06 54.8 2.8 51 170-220 187-249 (755)
44 COG3170 FimV Tfp pilus assembl 89.1 0.36 7.9E-06 51.5 3.6 52 106-157 187-247 (755)
45 COG4784 Putative Zn-dependent 89.0 0.52 1.1E-05 46.4 4.3 45 172-216 429-476 (479)
46 KOG2850 Predicted peptidoglyca 87.3 0.3 6.5E-06 44.1 1.4 154 42-220 10-175 (186)
47 PRK10838 spr outer membrane li 87.1 0.076 1.6E-06 48.3 -2.5 60 234-297 75-135 (190)
48 COG4254 Uncharacterized protei 82.4 1.2 2.7E-05 42.8 3.2 52 108-159 6-57 (339)
49 COG0739 NlpD Membrane proteins 82.4 2.2 4.7E-05 40.0 4.9 49 172-220 2-50 (277)
50 TIGR00247 conserved hypothetic 82.3 14 0.0003 36.6 10.8 19 41-59 39-57 (342)
51 COG0791 Spr Cell wall-associat 79.6 0.55 1.2E-05 42.3 -0.2 59 235-297 84-145 (197)
52 COG5004 P2-like prophage tail 76.3 4.9 0.00011 30.0 4.0 51 109-159 4-57 (70)
53 COG4784 Putative Zn-dependent 75.6 3.9 8.6E-05 40.4 4.4 48 108-155 429-476 (479)
54 COG4254 Uncharacterized protei 75.1 2.7 5.8E-05 40.6 3.0 49 172-220 6-57 (339)
55 KOG2850 Predicted peptidoglyca 71.3 2.3 4.9E-05 38.5 1.5 49 107-158 9-57 (186)
56 PF13518 HTH_28: Helix-turn-he 71.3 3.5 7.7E-05 28.3 2.3 24 177-200 10-33 (52)
57 PF01527 HTH_Tnp_1: Transposas 61.7 5.2 0.00011 29.9 1.6 25 176-200 20-44 (76)
58 PF02796 HTH_7: Helix-turn-hel 60.6 8.3 0.00018 26.3 2.4 23 177-199 19-41 (45)
59 PRK10270 putative aminodeoxych 57.9 92 0.002 30.9 10.1 17 42-58 40-56 (340)
60 PF07172 GRP: Glycine rich pro 56.9 7 0.00015 31.5 1.7 12 1-12 1-12 (95)
61 COG0739 NlpD Membrane proteins 55.1 20 0.00043 33.4 4.8 48 108-158 2-49 (277)
62 smart00004 NL Domain found in 55.0 5 0.00011 26.8 0.5 33 276-312 4-36 (38)
63 COG5004 P2-like prophage tail 53.9 32 0.0007 25.8 4.5 52 41-94 2-56 (70)
64 smart00796 AHS1 Allophanate hy 51.6 1.4E+02 0.0031 27.1 9.6 99 147-262 83-185 (201)
65 TIGR00370 conserved hypothetic 49.4 98 0.0021 28.3 8.2 90 148-262 74-175 (202)
66 PF00877 NLPC_P60: NlpC/P60 fa 49.1 0.28 6.1E-06 39.5 -7.7 58 238-297 1-58 (105)
67 PF13518 HTH_28: Helix-turn-he 47.4 20 0.00043 24.4 2.6 23 48-71 11-33 (52)
68 PF13384 HTH_23: Homeodomain-l 47.3 20 0.00043 24.4 2.6 24 177-200 15-38 (50)
69 PF04218 CENP-B_N: CENP-B N-te 45.9 11 0.00024 26.8 1.1 24 176-199 19-42 (53)
70 TIGR02219 phage_NlpC_fam putat 45.2 2.5 5.4E-05 36.0 -2.8 34 234-268 6-40 (134)
71 PRK09413 IS2 repressor TnpA; R 42.5 22 0.00048 29.5 2.6 28 174-201 24-51 (121)
72 PF02796 HTH_7: Helix-turn-hel 42.3 25 0.00053 23.9 2.4 23 47-70 19-41 (45)
73 COG2963 Transposase and inacti 40.8 24 0.00052 28.8 2.5 26 175-200 20-46 (116)
74 PF01710 HTH_Tnp_IS630: Transp 39.3 24 0.00053 29.2 2.4 75 112-199 15-91 (119)
75 PF04967 HTH_10: HTH DNA bindi 39.3 31 0.00068 24.7 2.6 24 43-67 17-40 (53)
76 cd00569 HTH_Hin_like Helix-tur 37.1 42 0.00091 19.7 2.8 23 177-199 19-41 (42)
77 PF14453 ThiS-like: ThiS-like 37.0 46 0.00099 24.3 3.1 44 43-90 9-52 (57)
78 PHA00675 hypothetical protein 37.0 32 0.00069 26.7 2.4 26 177-202 37-62 (78)
79 PF05393 Hum_adeno_E3A: Human 36.4 51 0.0011 26.2 3.5 39 318-356 11-52 (94)
80 PF05225 HTH_psq: helix-turn-h 36.2 30 0.00065 23.7 2.0 24 176-199 12-36 (45)
81 PF10668 Phage_terminase: Phag 35.6 37 0.0008 25.1 2.5 23 180-202 23-45 (60)
82 PF04255 DUF433: Protein of un 35.3 32 0.0007 24.6 2.2 24 176-199 28-52 (56)
83 PRK13733 conjugal transfer pro 33.8 42 0.00091 30.0 3.0 38 1-41 1-39 (171)
84 PF04545 Sigma70_r4: Sigma-70, 32.9 49 0.0011 22.6 2.8 23 177-199 18-40 (50)
85 PF13936 HTH_38: Helix-turn-he 32.7 44 0.00095 22.6 2.4 23 176-198 17-39 (44)
86 TIGR01764 excise DNA binding d 31.2 80 0.0017 20.7 3.6 37 181-217 3-39 (49)
87 PRK09570 rpoH DNA-directed RNA 25.7 64 0.0014 25.2 2.5 48 173-220 14-64 (79)
88 TIGR03028 EpsE polysaccharide 25.3 1.3E+02 0.0028 28.0 5.0 74 145-219 149-237 (239)
89 PF08765 Mor: Mor transcriptio 25.2 65 0.0014 26.2 2.6 20 179-198 72-91 (108)
90 PF13693 HTH_35: Winged helix- 24.5 66 0.0014 25.0 2.3 22 177-198 13-34 (78)
91 cd04762 HTH_MerR-trunc Helix-T 24.2 79 0.0017 20.5 2.5 21 181-201 2-22 (49)
92 PF13443 HTH_26: Cro/C1-type H 24.1 28 0.0006 24.9 0.2 53 114-200 9-61 (63)
93 PF00376 MerR: MerR family reg 23.6 81 0.0018 20.7 2.3 22 181-202 1-22 (38)
94 PF02618 YceG: YceG-like famil 23.1 83 0.0018 30.4 3.3 18 107-124 45-62 (297)
95 cd01104 HTH_MlrA-CarA Helix-Tu 22.7 79 0.0017 22.7 2.5 21 181-201 2-22 (68)
96 PF01527 HTH_Tnp_1: Transposas 22.5 49 0.0011 24.4 1.3 26 112-140 20-45 (76)
97 PF12471 GTP_CH_N: GTP cyclohy 22.4 55 0.0012 29.6 1.8 59 130-199 132-190 (194)
98 PRK09413 IS2 repressor TnpA; R 20.9 88 0.0019 25.9 2.6 25 46-71 26-50 (121)
99 smart00421 HTH_LUXR helix_turn 20.8 1.1E+02 0.0024 20.4 2.8 24 176-199 15-38 (58)
100 cd04761 HTH_MerR-SF Helix-Turn 20.7 1E+02 0.0022 20.5 2.5 21 181-201 2-22 (49)
101 PF13693 HTH_35: Winged helix- 20.6 96 0.0021 24.1 2.5 23 47-70 13-35 (78)
102 PF13542 HTH_Tnp_ISL3: Helix-t 20.5 1E+02 0.0022 21.0 2.5 21 179-199 27-47 (52)
No 1
>PRK06347 autolysin; Reviewed
Probab=99.95 E-value=6.7e-27 Score=241.73 Aligned_cols=167 Identities=20% Similarity=0.246 Sum_probs=135.1
Q ss_pred ccEEEECCCCCCHHHHHHHhCCCcHHHHHhcCCCCCCCCCCCcCCCCCeEEecccccCCCC--------------CccCC
Q 018290 40 ALVGYLPPNKTTISEIQSLFTVKNLRSILGANNFPPGTPRNFSVPAQKPIKVPIHCICSNG--------------TGVSD 105 (358)
Q Consensus 40 a~~~YtV~~GdTL~~IA~~fgvs~l~~L~~~N~L~~~~~~~~~L~~Gq~L~IP~~~~c~~~--------------~~~s~ 105 (358)
.+..|+|++||||+.||++|||+ +++|+++|++.. +.|.+||.|+||........ .....
T Consensus 404 ~~~~ytVk~GDTL~sIA~kygVS-v~~L~~~N~l~s-----~~L~~Gq~L~IP~~~~~~~~t~~~s~~~~~~k~~s~~~~ 477 (592)
T PRK06347 404 NAKVYTVVKGDSLWRIANNNKVT-IANLKSWNNLKS-----DFIYPGQKLKVSAGSTSNTNTSKPSTNTNTSKPSTNTNT 477 (592)
T ss_pred CceeEEecCCCCHHHHHHHhCCC-HHHHHHHhCCCc-----ceeccCcEEEEecCCcccccccccccccccccccccccc
Confidence 35689999999999999999999 699999998752 57999999999964221000 00112
Q ss_pred CcceEEEcCCCcHHHHHHHHhCCCccHHHHHHhcCCCCCCccCCCcEEEECCCCCcCCC--------Cccccceeeeeee
Q 018290 106 KVPVYTVKKDDGLDFIARTIFGQLLKYQKIVEANNISNPDLIQIGQNLTIPLPCSCDDV--------DNAKVVHYAHVVE 177 (358)
Q Consensus 106 ~~~~YtV~~GDTL~~IA~~~ygglvs~~~L~~~N~l~~~~~L~~Gq~L~IP~~~~~~~~--------~~~~~~~~~Y~V~ 177 (358)
....|+|++||||+.||++ |+ +++++|++||++.+ +.|++||+|.||........ .........|+|+
T Consensus 478 ~~~~YtVk~GDTL~sIAkk-yg--VSv~~L~~~N~l~s-~~L~~GQ~L~Ip~~~~~s~~~t~~~s~~~~~~~~~~~Y~Vk 553 (592)
T PRK06347 478 NAKVYTVAKGDSLWRIANN-NK--VTIANLKSWNNLKS-DFIYPGQKLKVSAGSTTNNTNTAKPSTNKPSNSTVKTYTVK 553 (592)
T ss_pred cceeeeecCCCCHHHHHHH-HC--CCHHHHHHhcCCCc-ccccCCcEEEEecCcccccccccCCccCCccCccceeeecC
Confidence 3458999999999999999 99 99999999999875 68999999999975432110 0111234689999
Q ss_pred cCChHHHHHHHhCCCHHHHhhhhCCCCCCCcCCCCeEEEC
Q 018290 178 EGSSFALIAQKFGTDRDTLMKLNGIHDDSKLIAGEPLDVP 217 (358)
Q Consensus 178 ~GDTL~~IA~kygvt~~~L~~~N~l~~~~~l~~Gq~L~IP 217 (358)
+|||||+||++||+++++|++||++.. +.|++||+|.|+
T Consensus 554 ~GDTL~sIA~KygvSv~~L~~~N~L~~-~~L~~GQ~L~I~ 592 (592)
T PRK06347 554 KGDSLWAISRQYKTTVDNIKAWNKLTS-NMIHVGQKLTIK 592 (592)
T ss_pred CCCcHHHHHHHhCCCHHHHHHhcCCCc-ccCCCCCEEecC
Confidence 999999999999999999999999975 789999999985
No 2
>PRK06347 autolysin; Reviewed
Probab=99.94 E-value=3.2e-26 Score=236.71 Aligned_cols=171 Identities=22% Similarity=0.229 Sum_probs=138.1
Q ss_pred ccEEEECCCCCCHHHHHHHhCCCcHHHHHhcCCCCCCCCCCCcCCCCCeEEecccccCCC---------------CCccC
Q 018290 40 ALVGYLPPNKTTISEIQSLFTVKNLRSILGANNFPPGTPRNFSVPAQKPIKVPIHCICSN---------------GTGVS 104 (358)
Q Consensus 40 a~~~YtV~~GdTL~~IA~~fgvs~l~~L~~~N~L~~~~~~~~~L~~Gq~L~IP~~~~c~~---------------~~~~s 104 (358)
.+..|+|++||||+.||++|+++ +++|++||+|.. +.|.+||.|+||....... .....
T Consensus 329 ~~~~Y~V~sGDTL~~IA~rygvS-v~eL~~~N~l~~-----d~L~~Gq~L~VP~~~~~~~~~t~~~~~~~~~~~~~~~~~ 402 (592)
T PRK06347 329 NAKIYTVVKGDSLWRIANNHKVT-VANLKAWNNLKS-----DFIYPGQKLKVSAGSTTSDTNTSKPSTGTSTSKPSTGTS 402 (592)
T ss_pred CceEEEeCCCCCHHHHHHHhCCC-HHHHHHHhCCCc-----cccccCcEEEEeccccccccccccccccccccccccccc
Confidence 67789999999999999999999 699999998753 6899999999996421100 00011
Q ss_pred CCcceEEEcCCCcHHHHHHHHhCCCccHHHHHHhcCCCCCCccCCCcEEEECCCCCcCC----C----------Cccccc
Q 018290 105 DKVPVYTVKKDDGLDFIARTIFGQLLKYQKIVEANNISNPDLIQIGQNLTIPLPCSCDD----V----------DNAKVV 170 (358)
Q Consensus 105 ~~~~~YtV~~GDTL~~IA~~~ygglvs~~~L~~~N~l~~~~~L~~Gq~L~IP~~~~~~~----~----------~~~~~~ 170 (358)
.....|+|++||+|+.||++ |+ +++++|++||++.. +.|.+||.|.||....... . ......
T Consensus 403 ~~~~~ytVk~GDTL~sIA~k-yg--VSv~~L~~~N~l~s-~~L~~Gq~L~IP~~~~~~~~t~~~s~~~~~~k~~s~~~~~ 478 (592)
T PRK06347 403 TNAKVYTVVKGDSLWRIANN-NK--VTIANLKSWNNLKS-DFIYPGQKLKVSAGSTSNTNTSKPSTNTNTSKPSTNTNTN 478 (592)
T ss_pred cCceeEEecCCCCHHHHHHH-hC--CCHHHHHHHhCCCc-ceeccCcEEEEecCCccccccccccccccccccccccccc
Confidence 23468999999999999999 99 99999999999875 6899999999996432100 0 001122
Q ss_pred eeeeeeecCChHHHHHHHhCCCHHHHhhhhCCCCCCCcCCCCeEEECCCCC
Q 018290 171 HYAHVVEEGSSFALIAQKFGTDRDTLMKLNGIHDDSKLIAGEPLDVPLKAC 221 (358)
Q Consensus 171 ~~~Y~V~~GDTL~~IA~kygvt~~~L~~~N~l~~~~~l~~Gq~L~IP~~~~ 221 (358)
...|+|++|||||+||++||+++++|++||++.+ +.|++||+|.||....
T Consensus 479 ~~~YtVk~GDTL~sIAkkygVSv~~L~~~N~l~s-~~L~~GQ~L~Ip~~~~ 528 (592)
T PRK06347 479 AKVYTVAKGDSLWRIANNNKVTIANLKSWNNLKS-DFIYPGQKLKVSAGST 528 (592)
T ss_pred ceeeeecCCCCHHHHHHHHCCCHHHHHHhcCCCc-ccccCCcEEEEecCcc
Confidence 4579999999999999999999999999999875 6899999999998654
No 3
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional
Probab=99.90 E-value=1.9e-22 Score=204.37 Aligned_cols=172 Identities=21% Similarity=0.260 Sum_probs=133.5
Q ss_pred ccEEEECCCCCCHHHHHHHhCCCcHHHHHhcCCCCCCCCCCCcCCCC-CeEEecccccCC------CC-----------C
Q 018290 40 ALVGYLPPNKTTISEIQSLFTVKNLRSILGANNFPPGTPRNFSVPAQ-KPIKVPIHCICS------NG-----------T 101 (358)
Q Consensus 40 a~~~YtV~~GdTL~~IA~~fgvs~l~~L~~~N~L~~~~~~~~~L~~G-q~L~IP~~~~c~------~~-----------~ 101 (358)
.+....+..+++|..||+++|++ +++|+++|+.- ......+.| +.|.||...... .+ .
T Consensus 262 ~~~~V~v~~~i~L~~iA~~~gvs-~~eL~~LNP~~---kr~~t~p~g~~~llvP~~~~~~f~~~l~~~~~~~~~p~~~~~ 337 (456)
T PRK10783 262 ALARVDLGQQIELAQAAEMAGMS-LTKLKTFNAGY---KRSTTAPSGPHYIMVPKKHADQLRESLASGEIAAVQSTLVAD 337 (456)
T ss_pred ceEEEecCCCcCHHHHHHHcCCC-HHHHHHhCccc---cCCCcCCCCCeEEEecCchhhHHHHhhhhhhhhhcccccccc
Confidence 55667778888999999999999 59999999621 122233334 678899753210 00 0
Q ss_pred ccCCCcceEEEcCCCcHHHHHHHHhCCCccHHHHHHhcCCCCCCccCCCcEEEECCCCCcCCCCccccceeeeeeecCCh
Q 018290 102 GVSDKVPVYTVKKDDGLDFIARTIFGQLLKYQKIVEANNISNPDLIQIGQNLTIPLPCSCDDVDNAKVVHYAHVVEEGSS 181 (358)
Q Consensus 102 ~~s~~~~~YtV~~GDTL~~IA~~~ygglvs~~~L~~~N~l~~~~~L~~Gq~L~IP~~~~~~~~~~~~~~~~~Y~V~~GDT 181 (358)
.......+|+|++||||+.||++ || ++.++|++||++.+ +.|.+||+|.||.++.+... .......+|+|++|||
T Consensus 338 ~~~~~~~~y~Vk~GDTL~sIA~r-~g--vs~~~L~~~N~l~~-~~L~~Gq~L~Ip~~~~~~~~-~~~~~~~~Y~Vr~GDT 412 (456)
T PRK10783 338 NTPLNSRSYKVRSGDTLSGIASR-LN--VSTKDLQQWNNLRG-SKLKVGQTLTIGAGSSAQRL-ANNSDSITYRVRKGDS 412 (456)
T ss_pred cCcCCceEEEECCCCcHHHHHHH-HC--cCHHHHHHHcCCCc-ccCCCCCEEEecCCcccccc-cccccceeEEeCCCCC
Confidence 00123458999999999999999 99 99999999999877 78999999999986544211 1122346899999999
Q ss_pred HHHHHHHhCCCHHHHhhhhCCCCCCCcCCCCeEEECCCCC
Q 018290 182 FALIAQKFGTDRDTLMKLNGIHDDSKLIAGEPLDVPLKAC 221 (358)
Q Consensus 182 L~~IA~kygvt~~~L~~~N~l~~~~~l~~Gq~L~IP~~~~ 221 (358)
|++||++||+++++|++||++... .|++||+|.|++...
T Consensus 413 L~sIA~kygVtv~~L~~~N~l~~~-~L~pGq~L~l~v~~~ 451 (456)
T PRK10783 413 LSSIAKRHGVNIKDVMRWNSDTAK-NLQPGDKLTLFVKNN 451 (456)
T ss_pred HHHHHHHhCCCHHHHHHhcCCCCC-cCCCCCEEEEecCCC
Confidence 999999999999999999998765 899999999998763
No 4
>PRK13914 invasion associated secreted endopeptidase; Provisional
Probab=99.82 E-value=2.8e-20 Score=186.62 Aligned_cols=244 Identities=11% Similarity=0.168 Sum_probs=147.2
Q ss_pred EEECCCCCCHHHHHHHhCCCcHHHHHhcCCCCCCCCCCCcCCCCCeEEecccccCCC--C--------Cc---cCCCcce
Q 018290 43 GYLPPNKTTISEIQSLFTVKNLRSILGANNFPPGTPRNFSVPAQKPIKVPIHCICSN--G--------TG---VSDKVPV 109 (358)
Q Consensus 43 ~YtV~~GdTL~~IA~~fgvs~l~~L~~~N~L~~~~~~~~~L~~Gq~L~IP~~~~c~~--~--------~~---~s~~~~~ 109 (358)
.|+|++|||||.||++|+++ +++|+++|+|.. +.|.+||.|+||....-.. . .+ .......
T Consensus 29 tytVq~GDTLw~IA~~ygvt-v~~I~~~N~l~~-----~~I~~Gq~L~Ip~~~~~~~~~~~Vta~~LNVRsgps~s~~II 102 (481)
T PRK13914 29 TVVVEAGDTLWGIAQSKGTT-VDAIKKANNLTT-----DKIVPGQKLQVNEVAAAEKTEKSVSATWLNVRSGAGVDNSII 102 (481)
T ss_pred eEEECCCCCHHHHHHHHCCC-HHHHHHHhCCCc-----ccccCCCEEEeCCCCcccccceeEecceEEEecCCCCCccee
Confidence 69999999999999999999 599999998753 6799999999997542100 0 00 0011122
Q ss_pred EEEcCCCcHHHHH-HH--HhC--------CCccHHHHHHh---cCCCCCCc---------cCCCc----EEE------EC
Q 018290 110 YTVKKDDGLDFIA-RT--IFG--------QLLKYQKIVEA---NNISNPDL---------IQIGQ----NLT------IP 156 (358)
Q Consensus 110 YtV~~GDTL~~IA-~~--~yg--------glvs~~~L~~~---N~l~~~~~---------L~~Gq----~L~------IP 156 (358)
-.+..|+.+..+. +. +|. |.|.-+-|.+- -++..+.. -.|.+ +++ .|
T Consensus 103 gsl~~G~~V~Vl~~~~ngW~kI~~~~GktGwV~~~YLs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 182 (481)
T PRK13914 103 TSIKGGTKVTVETTESNGWHKITYNDGKTGFVNGKYLTDKVTSTPVAPTQEVKKETTTQQAAPAAETKTEVKQTTQATTP 182 (481)
T ss_pred eeecCCCEEEEeecccCCeEEEEcCCCCEEEEecccccCCCccCccccchhhhhccccccccchhcccchhccCCcccCC
Confidence 2344444433321 10 111 00000000000 00000000 00000 000 01
Q ss_pred CCCCcCC--CCccccceeeeeeecCChHHHHHHHhCCCHHHHhhhhCCCCCCCcCCCCeEEECCCCCCCCC---------
Q 018290 157 LPCSCDD--VDNAKVVHYAHVVEEGSSFALIAQKFGTDRDTLMKLNGIHDDSKLIAGEPLDVPLKACNSSI--------- 225 (358)
Q Consensus 157 ~~~~~~~--~~~~~~~~~~Y~V~~GDTL~~IA~kygvt~~~L~~~N~l~~~~~l~~Gq~L~IP~~~~~s~~--------- 225 (358)
.+..... ..........|+|++|||||.||++|++++++|++||++.+ ..|++||+|.||..+.....
T Consensus 183 ~~~~~~~~~~~~~~~~a~tytVq~GDTL~sIAkrYgVtv~eI~~~N~l~s-~~L~pGQ~L~Ip~sa~~~~p~~~~~~~ap 261 (481)
T PRK13914 183 APKVAETKETPVVDQNATTHAVKSGDTIWALSVKYGVSVQDIMSWNNLSS-SSIYVGQKLAIKQTANTATPKAEVKTEAP 261 (481)
T ss_pred cccccccccCccccCCCeEEEECCCCCHHHHHHHHCCCHHHHHHhcCCCc-cccCCCCEEEecCCCCcCCcCccccccCC
Confidence 1100000 00111224689999999999999999999999999999976 58999999999984210000
Q ss_pred ------------------------------------C------------C-----------------------------C
Q 018290 226 ------------------------------------K------------A-----------------------------D 228 (358)
Q Consensus 226 ------------------------------------~------------~-----------------------------~ 228 (358)
| + .
T Consensus 262 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 341 (481)
T PRK13914 262 AAEKQAAPVVKENTNTNTATTEKKETTTQQQTAPKAPTEAAKPAPAPSTNTNANKTNTNTNTNTNNTNTSTPSKNTNTNT 341 (481)
T ss_pred chhhccCcchhcccccccceeecccccccccccccCchhhcCCCCCCcccccccccCCCcccccccccccCccccccCCC
Confidence 0 0 0
Q ss_pred c---------------------------cccceeecCceEEEeeCCceeeeeCCCCceeEEeccCCcCCCCCCcCccccC
Q 018290 229 S---------------------------FDNYLRVANGTYTFTANSCVKCQCDATNNWTLQCKPSQFQPSSPNSRWKTCP 281 (358)
Q Consensus 229 ~---------------------------~d~~l~v~~g~Y~~~a~~~~~~~c~~~~~~~l~~~~~~~~~~~~~~~~~~~~ 281 (358)
. ........+-+|.|++..+.+||||| +.+++|-..+...++++.+||....
T Consensus 342 ~~~~~~~~~~~~~~~~~~~~~~a~~~~iv~~A~~~lG~PY~wGG~sp~gfDCSG-lV~~vy~~~GI~LPR~s~~Q~~~G~ 420 (481)
T PRK13914 342 NSNTNTNSNTNANQGSSNNNSNSSASAIIAEAQKHLGKAYSWGGNGPTTFDCSG-YTKYVFAKAGISLPRTSGAQYASTT 420 (481)
T ss_pred CcccccCCCccCCCCccccCcchhHHHHHHHHHHHcCCcccCCCCCCCCcccHH-HHHHHHHHcCCCCCCChHHHHhcCc
Confidence 0 00012456779999999999999998 9999998887777888888886554
Q ss_pred ccccCCCCcceeeccc
Q 018290 282 SMLCGDSESLSIGNTT 297 (358)
Q Consensus 282 ~~~c~~~~~~~~g~~~ 297 (358)
... -++++.||+.
T Consensus 421 ~Vs---~selqpGDLV 433 (481)
T PRK13914 421 RIS---ESQAKPGDLV 433 (481)
T ss_pred ccc---cccCCCCCEE
Confidence 432 3579999986
No 5
>PRK10783 mltD membrane-bound lytic murein transglycosylase D; Provisional
Probab=99.64 E-value=1.5e-15 Score=154.15 Aligned_cols=109 Identities=19% Similarity=0.225 Sum_probs=92.2
Q ss_pred ccEEEECCCCCCHHHHHHHhCCCcHHHHHhcCCCCCCCCCCCcCCCCCeEEecccccCCCCCccCCCcceEEEcCCCcHH
Q 018290 40 ALVGYLPPNKTTISEIQSLFTVKNLRSILGANNFPPGTPRNFSVPAQKPIKVPIHCICSNGTGVSDKVPVYTVKKDDGLD 119 (358)
Q Consensus 40 a~~~YtV~~GdTL~~IA~~fgvs~l~~L~~~N~L~~~~~~~~~L~~Gq~L~IP~~~~c~~~~~~s~~~~~YtV~~GDTL~ 119 (358)
....|+|++||||+.||++||++ .++|+++|++.. +.|.+||.|+||..+.+.... .......|+|++||||+
T Consensus 342 ~~~~y~Vk~GDTL~sIA~r~gvs-~~~L~~~N~l~~-----~~L~~Gq~L~Ip~~~~~~~~~-~~~~~~~Y~Vr~GDTL~ 414 (456)
T PRK10783 342 NSRSYKVRSGDTLSGIASRLNVS-TKDLQQWNNLRG-----SKLKVGQTLTIGAGSSAQRLA-NNSDSITYRVRKGDSLS 414 (456)
T ss_pred CceEEEECCCCcHHHHHHHHCcC-HHHHHHHcCCCc-----ccCCCCCEEEecCCccccccc-ccccceeEEeCCCCCHH
Confidence 45689999999999999999999 599999998752 679999999999865543211 11234689999999999
Q ss_pred HHHHHHhCCCccHHHHHHhcCCCCCCccCCCcEEEECCCC
Q 018290 120 FIARTIFGQLLKYQKIVEANNISNPDLIQIGQNLTIPLPC 159 (358)
Q Consensus 120 ~IA~~~ygglvs~~~L~~~N~l~~~~~L~~Gq~L~IP~~~ 159 (358)
+||++ |+ |++++|++||++... .|++||+|.|+.+.
T Consensus 415 sIA~k-yg--Vtv~~L~~~N~l~~~-~L~pGq~L~l~v~~ 450 (456)
T PRK10783 415 SIAKR-HG--VNIKDVMRWNSDTAK-NLQPGDKLTLFVKN 450 (456)
T ss_pred HHHHH-hC--CCHHHHHHhcCCCCC-cCCCCCEEEEecCC
Confidence 99999 99 999999999998765 89999999998754
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=99.25 E-value=4.7e-12 Score=87.24 Aligned_cols=43 Identities=35% Similarity=0.602 Sum_probs=35.7
Q ss_pred eeeecCChHHHHHHHhCCCHHHHhhhh-CCCCCCCcCCCCeEEEC
Q 018290 174 HVVEEGSSFALIAQKFGTDRDTLMKLN-GIHDDSKLIAGEPLDVP 217 (358)
Q Consensus 174 Y~V~~GDTL~~IA~kygvt~~~L~~~N-~l~~~~~l~~Gq~L~IP 217 (358)
|+|++|||+++||++|++++++|+++| ++.. +.|++||+|.||
T Consensus 1 y~V~~gDtl~~IA~~~~~~~~~l~~~N~~~~~-~~l~~G~~l~iP 44 (44)
T PF01476_consen 1 YTVQPGDTLWSIAKRYGISVDELMELNPNIDS-DNLQPGQKLCIP 44 (44)
T ss_dssp EEE-TT--HHHHHHHTTS-HHHHHHHCCTTHG-GCGGTTEEEEEC
T ss_pred CEECcCCcHHHHHhhhhhhHhHHHHhcCCCCc-ccCCCCCEEEeC
Confidence 899999999999999999999999999 5554 459999999998
No 7
>COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane]
Probab=99.19 E-value=5.3e-11 Score=100.15 Aligned_cols=95 Identities=28% Similarity=0.450 Sum_probs=76.1
Q ss_pred HHHHHhCCCccHHHHHHhcCCCC-CCccCCCcEEEECCCCCcCCC------Cccc-----------cceeeeeeecCChH
Q 018290 121 IARTIFGQLLKYQKIVEANNISN-PDLIQIGQNLTIPLPCSCDDV------DNAK-----------VVHYAHVVEEGSSF 182 (358)
Q Consensus 121 IA~~~ygglvs~~~L~~~N~l~~-~~~L~~Gq~L~IP~~~~~~~~------~~~~-----------~~~~~Y~V~~GDTL 182 (358)
||.+ |+ +++++|+++|.+.. .+.+.+||+|.+|....-... .... .....|+|++||||
T Consensus 1 ia~~-~~--~~v~~l~~~n~~~~~s~~i~~gq~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~gdtL 77 (124)
T COG1388 1 IASK-YG--VSVKALKKANALTGKSDAIKPGQVLKIPGDISSTVNAGQTLSSLSNKVSDSSSASKAPPVVTYTVKKGDTL 77 (124)
T ss_pred Cccc-cc--ccHHHHHHHhcccCCCCccccCceEEccCCcccccccccccccccceeeccccccccCCCceEEEecCCCH
Confidence 4566 88 99999999998874 589999999999964211110 0010 11358999999999
Q ss_pred HHHHHHhCCCHHHHhhhhCCCCCCCcCCCCeEEECCC
Q 018290 183 ALIAQKFGTDRDTLMKLNGIHDDSKLIAGEPLDVPLK 219 (358)
Q Consensus 183 ~~IA~kygvt~~~L~~~N~l~~~~~l~~Gq~L~IP~~ 219 (358)
+.||++|++++.+|+++|.+.++ .+++||+|.+|..
T Consensus 78 ~~Ia~~~~~tv~~l~~~n~l~~~-~i~~gq~l~~~~~ 113 (124)
T COG1388 78 SKIARKYGVTVAELKQLNNLSSD-KIKVGQKLKLPVS 113 (124)
T ss_pred HHHHHHhCCCHHHHHHHhccCCC-ceecCcEEEEecc
Confidence 99999999999999999999885 9999999999984
No 8
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=99.01 E-value=3.3e-10 Score=77.92 Aligned_cols=43 Identities=44% Similarity=0.686 Sum_probs=35.4
Q ss_pred EEEcCCCcHHHHHHHHhCCCccHHHHHHhc-CCCCCCccCCCcEEEEC
Q 018290 110 YTVKKDDGLDFIARTIFGQLLKYQKIVEAN-NISNPDLIQIGQNLTIP 156 (358)
Q Consensus 110 YtV~~GDTL~~IA~~~ygglvs~~~L~~~N-~l~~~~~L~~Gq~L~IP 156 (358)
|+|++|||++.||++ |+ ++.++|+++| ++.. +.|.+||+|.||
T Consensus 1 y~V~~gDtl~~IA~~-~~--~~~~~l~~~N~~~~~-~~l~~G~~l~iP 44 (44)
T PF01476_consen 1 YTVQPGDTLWSIAKR-YG--ISVDELMELNPNIDS-DNLQPGQKLCIP 44 (44)
T ss_dssp EEE-TT--HHHHHHH-TT--S-HHHHHHHCCTTHG-GCGGTTEEEEEC
T ss_pred CEECcCCcHHHHHhh-hh--hhHhHHHHhcCCCCc-ccCCCCCEEEeC
Confidence 899999999999999 99 9999999999 5554 459999999998
No 9
>COG1388 LytE FOG: LysM repeat [Cell envelope biogenesis, outer membrane]
Probab=98.93 E-value=3.1e-09 Score=89.36 Aligned_cols=95 Identities=32% Similarity=0.515 Sum_probs=75.6
Q ss_pred HHHHhCCCcHHHHHhcCCCCCCCCCCCcCCCCCeEEecccccCC-C-CCcc-C--------------CCcceEEEcCCCc
Q 018290 55 IQSLFTVKNLRSILGANNFPPGTPRNFSVPAQKPIKVPIHCICS-N-GTGV-S--------------DKVPVYTVKKDDG 117 (358)
Q Consensus 55 IA~~fgvs~l~~L~~~N~L~~~~~~~~~L~~Gq~L~IP~~~~c~-~-~~~~-s--------------~~~~~YtV~~GDT 117 (358)
||.+|+++ +++|+++|.+.. ..+.+.+||.|.+|..-.-. . +... . .....|+|++||+
T Consensus 1 ia~~~~~~-v~~l~~~n~~~~---~s~~i~~gq~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~V~~gdt 76 (124)
T COG1388 1 IASKYGVS-VKALKKANALTG---KSDAIKPGQVLKIPGDISSTVNAGQTLSSLSNKVSDSSSASKAPPVVTYTVKKGDT 76 (124)
T ss_pred Cccccccc-HHHHHHHhcccC---CCCccccCceEEccCCcccccccccccccccceeeccccccccCCCceEEEecCCC
Confidence 57899999 699999998763 35789999999999631111 1 1000 0 0125899999999
Q ss_pred HHHHHHHHhCCCccHHHHHHhcCCCCCCccCCCcEEEECC
Q 018290 118 LDFIARTIFGQLLKYQKIVEANNISNPDLIQIGQNLTIPL 157 (358)
Q Consensus 118 L~~IA~~~ygglvs~~~L~~~N~l~~~~~L~~Gq~L~IP~ 157 (358)
|+.||++ |+ +++.+|+++|.+.++ .+++||.|.+|.
T Consensus 77 L~~Ia~~-~~--~tv~~l~~~n~l~~~-~i~~gq~l~~~~ 112 (124)
T COG1388 77 LSKIARK-YG--VTVAELKQLNNLSSD-KIKVGQKLKLPV 112 (124)
T ss_pred HHHHHHH-hC--CCHHHHHHHhccCCC-ceecCcEEEEec
Confidence 9999999 89 999999999999885 999999999986
No 10
>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=98.91 E-value=1.9e-09 Score=73.39 Aligned_cols=43 Identities=28% Similarity=0.546 Sum_probs=38.7
Q ss_pred eecCChHHHHHHHhCCCHHHHhhhhC-CCCCCCcCCCCeEEECC
Q 018290 176 VEEGSSFALIAQKFGTDRDTLMKLNG-IHDDSKLIAGEPLDVPL 218 (358)
Q Consensus 176 V~~GDTL~~IA~kygvt~~~L~~~N~-l~~~~~l~~Gq~L~IP~ 218 (358)
|++|||||+||++|++++++|.++|+ +.++..+.+||+|.||.
T Consensus 1 v~~gdtl~~IA~~~~~~~~~l~~~N~~~~~~~~~~~g~~l~ip~ 44 (44)
T TIGR02899 1 VQKGDTLWKIAKKYGVDFDELIQANPQLSNPNLIYPGMKIKIPS 44 (44)
T ss_pred CCCCCCHHHHHHHHCcCHHHHHHHhhcCCCCCCcCCCCEEecCC
Confidence 68999999999999999999999997 44557899999999984
No 11
>PRK14125 cell division suppressor protein YneA; Provisional
Probab=98.89 E-value=3.1e-09 Score=86.98 Aligned_cols=51 Identities=18% Similarity=0.339 Sum_probs=43.9
Q ss_pred eeeeeeecCChHHHHHHHhCCC--------HHHHhhhhCCCCCCCcCCCCeEEECCCCCC
Q 018290 171 HYAHVVEEGSSFALIAQKFGTD--------RDTLMKLNGIHDDSKLIAGEPLDVPLKACN 222 (358)
Q Consensus 171 ~~~Y~V~~GDTL~~IA~kygvt--------~~~L~~~N~l~~~~~l~~Gq~L~IP~~~~~ 222 (358)
+..|+|++|||||+||++|+.+ ++.|++.|++.+ +.|+|||+|.||.....
T Consensus 36 ~~~~tV~~GDTLW~IA~~y~~~~~l~~~~~v~~I~~~N~l~~-~~I~~Gq~L~IP~~~~~ 94 (103)
T PRK14125 36 YVEITVQEGDTLWALADQYAGKHHMAKNEFIEWVEDVNNLPS-GHIKAGDKLVIPVLKSK 94 (103)
T ss_pred cEEEEECCCCCHHHHHHHhCCCcCCCHHHHHHHHHHhcCCCC-CcCCCCCEEEEecCCCC
Confidence 4789999999999999999875 567788899876 57999999999987643
No 12
>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=98.88 E-value=3.6e-09 Score=71.03 Aligned_cols=45 Identities=36% Similarity=0.705 Sum_probs=42.4
Q ss_pred eeeeecCChHHHHHHHhCCCHHHHhhhhCCCCCCCcCCCCeEEEC
Q 018290 173 AHVVEEGSSFALIAQKFGTDRDTLMKLNGIHDDSKLIAGEPLDVP 217 (358)
Q Consensus 173 ~Y~V~~GDTL~~IA~kygvt~~~L~~~N~l~~~~~l~~Gq~L~IP 217 (358)
.|+|++|||+++||++|+++..+|.++|+..+...+.+|++|.||
T Consensus 2 ~~~v~~gdt~~~ia~~~~~~~~~~~~~N~~~~~~~~~~g~~l~ip 46 (46)
T cd00118 2 TYTVKKGDTLSSIAQRYGISVEELLKLNGLSDPDNLQVGQKLKIP 46 (46)
T ss_pred EEEECCCCCHHHHHHHHCcCHHHHHHHcCCCCccccCCCCEEecC
Confidence 689999999999999999999999999998666899999999987
No 13
>PRK14125 cell division suppressor protein YneA; Provisional
Probab=98.87 E-value=8.8e-09 Score=84.34 Aligned_cols=54 Identities=15% Similarity=0.192 Sum_probs=44.5
Q ss_pred cCccEEEECCCCCCHHHHHHHhCCC----c---HHHHHhcCCCCCCCCCCCcCCCCCeEEeccccc
Q 018290 38 CQALVGYLPPNKTTISEIQSLFTVK----N---LRSILGANNFPPGTPRNFSVPAQKPIKVPIHCI 96 (358)
Q Consensus 38 C~a~~~YtV~~GdTL~~IA~~fgvs----~---l~~L~~~N~L~~~~~~~~~L~~Gq~L~IP~~~~ 96 (358)
...+..|+|++|||||+||++|+.+ . +++|++.|+++. +.|++||.|+||...+
T Consensus 33 ~~~~~~~tV~~GDTLW~IA~~y~~~~~l~~~~~v~~I~~~N~l~~-----~~I~~Gq~L~IP~~~~ 93 (103)
T PRK14125 33 KNQYVEITVQEGDTLWALADQYAGKHHMAKNEFIEWVEDVNNLPS-----GHIKAGDKLVIPVLKS 93 (103)
T ss_pred CCCcEEEEECCCCCHHHHHHHhCCCcCCCHHHHHHHHHHhcCCCC-----CcCCCCCEEEEecCCC
Confidence 3577899999999999999999765 1 367888898863 4699999999997644
No 14
>COG3858 Predicted glycosyl hydrolase [General function prediction only]
Probab=98.80 E-value=5.6e-09 Score=103.06 Aligned_cols=99 Identities=24% Similarity=0.252 Sum_probs=91.3
Q ss_pred ceEEEcCCCcHHHHHHHHhCCCccHHHHHHhcCCCCCCccCCCcEEEECCCCCcCCCCccccceeeeeeecCChHHHHHH
Q 018290 108 PVYTVKKDDGLDFIARTIFGQLLKYQKIVEANNISNPDLIQIGQNLTIPLPCSCDDVDNAKVVHYAHVVEEGSSFALIAQ 187 (358)
Q Consensus 108 ~~YtV~~GDTL~~IA~~~ygglvs~~~L~~~N~l~~~~~L~~Gq~L~IP~~~~~~~~~~~~~~~~~Y~V~~GDTL~~IA~ 187 (358)
..|.|++||++..|+++ |+ .+..+|...|.+.. +.|.+||.+.||.. ...|.|++|||+++||+
T Consensus 2 ~i~~~~pg~~~~~i~~~-~~--~~~~~i~~~~~~~~-d~~~~~q~~~v~~~------------~~~y~~~~~d~~~Sia~ 65 (423)
T COG3858 2 SIHLVGPGDSRLIIAVY-FP--YTNNRIVNGNDYTN-DDLVDGQTFVVPPS------------GHFYDVGPGDTLTSIAR 65 (423)
T ss_pred EEEEccCCceeeeehhh-cc--cccccccccccccc-ccccCceeEEECCc------------ceEEEecCCcchhhhhh
Confidence 47999999999999999 99 99999988888888 89999999999964 37899999999999999
Q ss_pred HhCCCHHHHhhhhCCCCCCCcCCCCeEEECCCCCC
Q 018290 188 KFGTDRDTLMKLNGIHDDSKLIAGEPLDVPLKACN 222 (358)
Q Consensus 188 kygvt~~~L~~~N~l~~~~~l~~Gq~L~IP~~~~~ 222 (358)
+++++++.+..+|....+..+++|-.|.+|....+
T Consensus 66 ~~~vt~~~~~~m~~~~~~~~l~~~~~l~~P~~~~~ 100 (423)
T COG3858 66 TVGVTQDSAAIMNFVICPGYLQYGLNLYIPSARKT 100 (423)
T ss_pred hhcCCHHHHHhhcccccccceeeeeEEeccCCCCC
Confidence 99999999999998888889999999999988655
No 15
>PRK10871 nlpD lipoprotein NlpD; Provisional
Probab=98.73 E-value=1.3e-08 Score=98.66 Aligned_cols=49 Identities=27% Similarity=0.285 Sum_probs=46.2
Q ss_pred eeeeeecCChHHHHHHHhCCCHHHHhhhhCCCCCCCcCCCCeEEECCCC
Q 018290 172 YAHVVEEGSSFALIAQKFGTDRDTLMKLNGIHDDSKLIAGEPLDVPLKA 220 (358)
Q Consensus 172 ~~Y~V~~GDTL~~IA~kygvt~~~L~~~N~l~~~~~l~~Gq~L~IP~~~ 220 (358)
.+|+||+|||||.||.+||+++.+|.+||++.++..|++||+|+||...
T Consensus 61 ~~y~Vk~GDTL~~IA~~~g~~~~~La~~N~l~~p~~I~~GQ~L~i~~~~ 109 (319)
T PRK10871 61 STYTVKKGDTLFYIAWITGNDFRDLAQRNNIQAPYSLNVGQTLQVGNAS 109 (319)
T ss_pred CceEECCCCHHHHHHHHHCcCHHHHHHhcCCCCCccccCCCEEEeCCCC
Confidence 5799999999999999999999999999999999999999999998653
No 16
>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=98.60 E-value=5.5e-08 Score=93.76 Aligned_cols=46 Identities=24% Similarity=0.442 Sum_probs=43.4
Q ss_pred eeeeeeecCChHHHHHHHhCCCHHHHhhhhCCCCCCCcCCCCeEEEC
Q 018290 171 HYAHVVEEGSSFALIAQKFGTDRDTLMKLNGIHDDSKLIAGEPLDVP 217 (358)
Q Consensus 171 ~~~Y~V~~GDTL~~IA~kygvt~~~L~~~N~l~~~~~l~~Gq~L~IP 217 (358)
...|+|++||||++||+|||+++++|+++|++. ++.|++||+|.||
T Consensus 293 ~~~YiVq~GDTL~sIAkRYGVSV~~L~r~N~L~-~~~L~~GQ~L~IP 338 (338)
T TIGR02907 293 LRMCIVQEGDTIETIAERYEISVSQLIRHNQLE-DFEVNEGQILYIP 338 (338)
T ss_pred cEEEEECCCCCHHHHHHHHCcCHHHHHHHhCCC-ccccCCCCEEEeC
Confidence 468999999999999999999999999999987 5899999999998
No 17
>cd00118 LysM Lysin domain, found in a variety of enzymes involved in bacterial cell wall degradation. This domain may have a general peptidoglycan binding function.
Probab=98.55 E-value=1.8e-07 Score=62.52 Aligned_cols=45 Identities=44% Similarity=0.809 Sum_probs=41.9
Q ss_pred eEEEcCCCcHHHHHHHHhCCCccHHHHHHhcCCCCCCccCCCcEEEEC
Q 018290 109 VYTVKKDDGLDFIARTIFGQLLKYQKIVEANNISNPDLIQIGQNLTIP 156 (358)
Q Consensus 109 ~YtV~~GDTL~~IA~~~ygglvs~~~L~~~N~l~~~~~L~~Gq~L~IP 156 (358)
.|+|++|||++.||++ |+ ++.++|+++|+..+...+.+|+.|.||
T Consensus 2 ~~~v~~gdt~~~ia~~-~~--~~~~~~~~~N~~~~~~~~~~g~~l~ip 46 (46)
T cd00118 2 TYTVKKGDTLSSIAQR-YG--ISVEELLKLNGLSDPDNLQVGQKLKIP 46 (46)
T ss_pred EEEECCCCCHHHHHHH-HC--cCHHHHHHHcCCCCccccCCCCEEecC
Confidence 6999999999999999 88 999999999998666789999999987
No 18
>smart00257 LysM Lysin motif.
Probab=98.55 E-value=1.4e-07 Score=62.34 Aligned_cols=44 Identities=30% Similarity=0.573 Sum_probs=39.8
Q ss_pred eeeeecCChHHHHHHHhCCCHHHHhhhhCCCCCCCcCCCCeEEE
Q 018290 173 AHVVEEGSSFALIAQKFGTDRDTLMKLNGIHDDSKLIAGEPLDV 216 (358)
Q Consensus 173 ~Y~V~~GDTL~~IA~kygvt~~~L~~~N~l~~~~~l~~Gq~L~I 216 (358)
+|+|++|||+++||++|+++.++|.++|+..+...+.+|++|.|
T Consensus 1 ~~~v~~gdt~~~ia~~~~~~~~~~~~~N~~~~~~~~~~g~~l~i 44 (44)
T smart00257 1 TYTVKKGDTLSSIARRYGISVSDLLELNNILDPDNLQVGQKLKI 44 (44)
T ss_pred CeEeCCCCCHHHHHHHhCCCHHHHHHHcCCCCccccCCCCEEeC
Confidence 48899999999999999999999999999666678999998864
No 19
>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=98.54 E-value=1.2e-07 Score=64.28 Aligned_cols=43 Identities=40% Similarity=0.711 Sum_probs=38.3
Q ss_pred EcCCCcHHHHHHHHhCCCccHHHHHHhcC-CCCCCccCCCcEEEECC
Q 018290 112 VKKDDGLDFIARTIFGQLLKYQKIVEANN-ISNPDLIQIGQNLTIPL 157 (358)
Q Consensus 112 V~~GDTL~~IA~~~ygglvs~~~L~~~N~-l~~~~~L~~Gq~L~IP~ 157 (358)
|++||||++||++ |+ +++++|.++|+ +.+++.+.+||+|.||.
T Consensus 1 v~~gdtl~~IA~~-~~--~~~~~l~~~N~~~~~~~~~~~g~~l~ip~ 44 (44)
T TIGR02899 1 VQKGDTLWKIAKK-YG--VDFDELIQANPQLSNPNLIYPGMKIKIPS 44 (44)
T ss_pred CCCCCCHHHHHHH-HC--cCHHHHHHHhhcCCCCCCcCCCCEEecCC
Confidence 5889999999999 88 99999999997 44567899999999983
No 20
>PRK13914 invasion associated secreted endopeptidase; Provisional
Probab=98.49 E-value=2e-07 Score=94.47 Aligned_cols=48 Identities=35% Similarity=0.425 Sum_probs=44.3
Q ss_pred eeeeeecCChHHHHHHHhCCCHHHHhhhhCCCCCCCcCCCCeEEECCCC
Q 018290 172 YAHVVEEGSSFALIAQKFGTDRDTLMKLNGIHDDSKLIAGEPLDVPLKA 220 (358)
Q Consensus 172 ~~Y~V~~GDTL~~IA~kygvt~~~L~~~N~l~~~~~l~~Gq~L~IP~~~ 220 (358)
..|+|++|||||+||++||+++++|+++|++.+ +.|++||+|.||..+
T Consensus 28 ~tytVq~GDTLw~IA~~ygvtv~~I~~~N~l~~-~~I~~Gq~L~Ip~~~ 75 (481)
T PRK13914 28 STVVVEAGDTLWGIAQSKGTTVDAIKKANNLTT-DKIVPGQKLQVNEVA 75 (481)
T ss_pred ceEEECCCCCHHHHHHHHCCCHHHHHHHhCCCc-ccccCCCEEEeCCCC
Confidence 479999999999999999999999999999864 789999999999764
No 21
>COG3858 Predicted glycosyl hydrolase [General function prediction only]
Probab=98.43 E-value=2.9e-07 Score=91.09 Aligned_cols=97 Identities=26% Similarity=0.272 Sum_probs=86.3
Q ss_pred EEEECCCCCCHHHHHHHhCCCcHHHHHhcCCCCCCCCCCCcCCCCCeEEecccccCCCCCccCCCcceEEEcCCCcHHHH
Q 018290 42 VGYLPPNKTTISEIQSLFTVKNLRSILGANNFPPGTPRNFSVPAQKPIKVPIHCICSNGTGVSDKVPVYTVKKDDGLDFI 121 (358)
Q Consensus 42 ~~YtV~~GdTL~~IA~~fgvs~l~~L~~~N~L~~~~~~~~~L~~Gq~L~IP~~~~c~~~~~~s~~~~~YtV~~GDTL~~I 121 (358)
..|.|++||++..|+.+|+.+. .+|...|.++ . +.+.+||.+.||.. ..+|.|++||++++|
T Consensus 2 ~i~~~~pg~~~~~i~~~~~~~~-~~i~~~~~~~----~-d~~~~~q~~~v~~~------------~~~y~~~~~d~~~Si 63 (423)
T COG3858 2 SIHLVGPGDSRLIIAVYFPYTN-NRIVNGNDYT----N-DDLVDGQTFVVPPS------------GHFYDVGPGDTLTSI 63 (423)
T ss_pred EEEEccCCceeeeehhhccccc-cccccccccc----c-ccccCceeEEECCc------------ceEEEecCCcchhhh
Confidence 4689999999999999999996 9997777654 3 88999999999963 359999999999999
Q ss_pred HHHHhCCCccHHHHHHhcCCCCCCccCCCcEEEECCCC
Q 018290 122 ARTIFGQLLKYQKIVEANNISNPDLIQIGQNLTIPLPC 159 (358)
Q Consensus 122 A~~~ygglvs~~~L~~~N~l~~~~~L~~Gq~L~IP~~~ 159 (358)
|++ |+ ++.++++.+|.+..+..+++|-.+.+|...
T Consensus 64 a~~-~~--vt~~~~~~m~~~~~~~~l~~~~~l~~P~~~ 98 (423)
T COG3858 64 ART-VG--VTQDSAAIMNFVICPGYLQYGLNLYIPSAR 98 (423)
T ss_pred hhh-hc--CCHHHHHhhcccccccceeeeeEEeccCCC
Confidence 999 89 999999999998888899999999999644
No 22
>PRK10871 nlpD lipoprotein NlpD; Provisional
Probab=98.42 E-value=3.2e-07 Score=89.03 Aligned_cols=49 Identities=35% Similarity=0.542 Sum_probs=45.8
Q ss_pred ceEEEcCCCcHHHHHHHHhCCCccHHHHHHhcCCCCCCccCCCcEEEECCCC
Q 018290 108 PVYTVKKDDGLDFIARTIFGQLLKYQKIVEANNISNPDLIQIGQNLTIPLPC 159 (358)
Q Consensus 108 ~~YtV~~GDTL~~IA~~~ygglvs~~~L~~~N~l~~~~~L~~Gq~L~IP~~~ 159 (358)
.+|+|++||||+.||++ |+ +++.+|++||++.++..|++||+|.||.+.
T Consensus 61 ~~y~Vk~GDTL~~IA~~-~g--~~~~~La~~N~l~~p~~I~~GQ~L~i~~~~ 109 (319)
T PRK10871 61 STYTVKKGDTLFYIAWI-TG--NDFRDLAQRNNIQAPYSLNVGQTLQVGNAS 109 (319)
T ss_pred CceEECCCCHHHHHHHH-HC--cCHHHHHHhcCCCCCccccCCCEEEeCCCC
Confidence 58999999999999998 89 999999999999999999999999998643
No 23
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=98.31 E-value=8.1e-07 Score=77.38 Aligned_cols=47 Identities=21% Similarity=0.361 Sum_probs=41.8
Q ss_pred eeeeeecCChHHHHHHHhCC---CHHHHhhhhC--CCCCCCcCCCCeEEECC
Q 018290 172 YAHVVEEGSSFALIAQKFGT---DRDTLMKLNG--IHDDSKLIAGEPLDVPL 218 (358)
Q Consensus 172 ~~Y~V~~GDTL~~IA~kygv---t~~~L~~~N~--l~~~~~l~~Gq~L~IP~ 218 (358)
.+|+|++|||||+||++|+. .+.+|.++|+ +.+++.|+|||+|.||.
T Consensus 96 ~~y~Vk~GDTL~~IA~~~~g~~~~~~~I~~~N~~~l~~~~~I~pGq~L~IP~ 147 (147)
T PRK11198 96 QFYTVKSGDTLSAIAKKVYGNANKYNKIFEANKPMLKSPDKIYPGQVLRIPE 147 (147)
T ss_pred eEEEECCCCCHHHHHHHHcCChhhHHHHHHhhhhcCCCcCCcCcCCEEecCC
Confidence 67999999999999999853 4778999998 77888999999999984
No 24
>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=98.22 E-value=1.9e-06 Score=83.30 Aligned_cols=48 Identities=23% Similarity=0.407 Sum_probs=44.5
Q ss_pred CCcceEEEcCCCcHHHHHHHHhCCCccHHHHHHhcCCCCCCccCCCcEEEEC
Q 018290 105 DKVPVYTVKKDDGLDFIARTIFGQLLKYQKIVEANNISNPDLIQIGQNLTIP 156 (358)
Q Consensus 105 ~~~~~YtV~~GDTL~~IA~~~ygglvs~~~L~~~N~l~~~~~L~~Gq~L~IP 156 (358)
..+..|+|++||||+.||++ |+ +++++|+++|++. ++.|++||.|.||
T Consensus 291 ~~~~~YiVq~GDTL~sIAkR-YG--VSV~~L~r~N~L~-~~~L~~GQ~L~IP 338 (338)
T TIGR02907 291 TKLRMCIVQEGDTIETIAER-YE--ISVSQLIRHNQLE-DFEVNEGQILYIP 338 (338)
T ss_pred cccEEEEECCCCCHHHHHHH-HC--cCHHHHHHHhCCC-ccccCCCCEEEeC
Confidence 45679999999999999999 99 9999999999987 5899999999998
No 25
>PRK11198 LysM domain/BON superfamily protein; Provisional
Probab=98.19 E-value=2.6e-06 Score=74.23 Aligned_cols=51 Identities=47% Similarity=0.688 Sum_probs=44.4
Q ss_pred cceEEEcCCCcHHHHHHHHhCCCccHHHHHHhcC--CCCCCccCCCcEEEECC
Q 018290 107 VPVYTVKKDDGLDFIARTIFGQLLKYQKIVEANN--ISNPDLIQIGQNLTIPL 157 (358)
Q Consensus 107 ~~~YtV~~GDTL~~IA~~~ygglvs~~~L~~~N~--l~~~~~L~~Gq~L~IP~ 157 (358)
...|+|++|||||.||+++|+....+.+|.++|+ +.+++.|++||+|.||.
T Consensus 95 ~~~y~Vk~GDTL~~IA~~~~g~~~~~~~I~~~N~~~l~~~~~I~pGq~L~IP~ 147 (147)
T PRK11198 95 SQFYTVKSGDTLSAIAKKVYGNANKYNKIFEANKPMLKSPDKIYPGQVLRIPE 147 (147)
T ss_pred CeEEEECCCCCHHHHHHHHcCChhhHHHHHHhhhhcCCCcCCcCcCCEEecCC
Confidence 3589999999999999995565467889999998 77888999999999983
No 26
>smart00257 LysM Lysin motif.
Probab=98.14 E-value=5.3e-06 Score=54.55 Aligned_cols=44 Identities=50% Similarity=0.798 Sum_probs=38.9
Q ss_pred eEEEcCCCcHHHHHHHHhCCCccHHHHHHhcCCCCCCccCCCcEEEE
Q 018290 109 VYTVKKDDGLDFIARTIFGQLLKYQKIVEANNISNPDLIQIGQNLTI 155 (358)
Q Consensus 109 ~YtV~~GDTL~~IA~~~ygglvs~~~L~~~N~l~~~~~L~~Gq~L~I 155 (358)
.|+|++|||++.||++ |+ ++.+++.++|+..+...+.+|+.+.|
T Consensus 1 ~~~v~~gdt~~~ia~~-~~--~~~~~~~~~N~~~~~~~~~~g~~l~i 44 (44)
T smart00257 1 TYTVKKGDTLSSIARR-YG--ISVSDLLELNNILDPDNLQVGQKLKI 44 (44)
T ss_pred CeEeCCCCCHHHHHHH-hC--CCHHHHHHHcCCCCccccCCCCEEeC
Confidence 4899999999999999 89 99999999999656678999998864
No 27
>COG1652 XkdP Uncharacterized protein containing LysM domain [Function unknown]
Probab=97.34 E-value=8.4e-05 Score=70.88 Aligned_cols=50 Identities=44% Similarity=0.655 Sum_probs=47.0
Q ss_pred eEEEcCCCcHHHHHHHHhCCCccHHHHHHhcC---CCCCCccCCCcEEEECCC
Q 018290 109 VYTVKKDDGLDFIARTIFGQLLKYQKIVEANN---ISNPDLIQIGQNLTIPLP 158 (358)
Q Consensus 109 ~YtV~~GDTL~~IA~~~ygglvs~~~L~~~N~---l~~~~~L~~Gq~L~IP~~ 158 (358)
+|+|++|||||.|++++||+.+.+..|..+|+ +.+++.|++||+|.||..
T Consensus 212 ~~~v~rgDTl~~is~~~Yg~~~~y~~I~~aNk~~~~~~p~~I~pGq~l~iP~~ 264 (269)
T COG1652 212 TNTVKRGDTLWQISKKVYGDGVEYRKIAEANKALVLDNPDKIKPGQVLRIPDQ 264 (269)
T ss_pred EEEeccCCcccccchhhcCcceEEEeHhhhhhhhccCCCCcCCCcceeeCCCc
Confidence 89999999999999999998888999999999 778899999999999964
No 28
>PRK10190 L,D-transpeptidase; Provisional
Probab=97.12 E-value=0.00091 Score=64.79 Aligned_cols=50 Identities=16% Similarity=0.242 Sum_probs=44.8
Q ss_pred eeeeeeecCC--hHHHHHHHhCCCHHHHhhhhCCCCCCCcCCCCeEEECCCC
Q 018290 171 HYAHVVEEGS--SFALIAQKFGTDRDTLMKLNGIHDDSKLIAGEPLDVPLKA 220 (358)
Q Consensus 171 ~~~Y~V~~GD--TL~~IA~kygvt~~~L~~~N~l~~~~~l~~Gq~L~IP~~~ 220 (358)
...|+|+++| +|..||++|++....|+++|+..|+-..++|++|.||.+.
T Consensus 37 ~~~~~v~~~~~~~le~iA~~f~~g~~~l~~aNPgvd~~~p~~G~~i~iP~~~ 88 (310)
T PRK10190 37 SLTVTVPDHNTQPLETFAAQYGQGLSNMLEANPGADVFLPKSGSQLTIPQQL 88 (310)
T ss_pred eEEEEecCCCCccHHHHHHHhCCCHHHHHHhCCCCCCCCCCCCCEEEecCcc
Confidence 4689999966 5999999999999999999999888778999999999864
No 29
>PRK10260 L,D-transpeptidase; Provisional
Probab=97.11 E-value=0.00094 Score=64.52 Aligned_cols=50 Identities=18% Similarity=0.264 Sum_probs=44.8
Q ss_pred eeeeeeecCC--hHHHHHHHhCCCHHHHhhhhCCCCCCCcCCCCeEEECCCC
Q 018290 171 HYAHVVEEGS--SFALIAQKFGTDRDTLMKLNGIHDDSKLIAGEPLDVPLKA 220 (358)
Q Consensus 171 ~~~Y~V~~GD--TL~~IA~kygvt~~~L~~~N~l~~~~~l~~Gq~L~IP~~~ 220 (358)
...|+|++|| +|..||++|++....|+++|+..++-..++|++|.||.+.
T Consensus 40 ~~~~~v~~~~~~~le~iA~~f~~g~~~l~~aNPgvdp~lp~~G~~i~iP~~~ 91 (306)
T PRK10260 40 NQVITIPEGNTQPLEYFAAEYQMGLSNMMEANPGVDTFLPKGGTVLNIPQQL 91 (306)
T ss_pred cEEEEeCCCCCchHHHHHHHhCCCHHHHHHhCcCCCCCcCCCCCEEEeCCcc
Confidence 4689999966 5999999999999999999999887778999999999864
No 30
>PRK10260 L,D-transpeptidase; Provisional
Probab=97.04 E-value=0.0028 Score=61.34 Aligned_cols=50 Identities=12% Similarity=0.149 Sum_probs=39.5
Q ss_pred ccEEEECCCCC--CHHHHHHHhCCCcHHHHHhcCCCCCCCCCCCcCCCCCeEEeccc
Q 018290 40 ALVGYLPPNKT--TISEIQSLFTVKNLRSILGANNFPPGTPRNFSVPAQKPIKVPIH 94 (358)
Q Consensus 40 a~~~YtV~~Gd--TL~~IA~~fgvs~l~~L~~~N~L~~~~~~~~~L~~Gq~L~IP~~ 94 (358)
....|+|++|+ +|..||++|+++ +.+|+++|+-- +....++|+.|.||..
T Consensus 39 ~~~~~~v~~~~~~~le~iA~~f~~g-~~~l~~aNPgv----dp~lp~~G~~i~iP~~ 90 (306)
T PRK10260 39 QNQVITIPEGNTQPLEYFAAEYQMG-LSNMMEANPGV----DTFLPKGGTVLNIPQQ 90 (306)
T ss_pred ccEEEEeCCCCCchHHHHHHHhCCC-HHHHHHhCcCC----CCCcCCCCCEEEeCCc
Confidence 55679999865 599999999999 69999999521 2234579999999963
No 31
>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=97.01 E-value=0.00058 Score=52.58 Aligned_cols=41 Identities=22% Similarity=0.245 Sum_probs=33.3
Q ss_pred ChHHHHHHHh---C-CCHH----HHhhhhCC----CCCCCcCCCCeEEECCCC
Q 018290 180 SSFALIAQKF---G-TDRD----TLMKLNGI----HDDSKLIAGEPLDVPLKA 220 (358)
Q Consensus 180 DTL~~IA~ky---g-vt~~----~L~~~N~l----~~~~~l~~Gq~L~IP~~~ 220 (358)
||||+||++| + +++. .|.+.|+- .+.+.|++|++|.||...
T Consensus 1 DTLw~IA~~~~~~~~~s~~q~m~ai~~aNp~AF~~~nin~L~~G~~L~iP~~~ 53 (74)
T TIGR03505 1 DTLWGIAQRVRPDNSVSLYQMMLALYRANPDAFIGGNINRLKVGQILRIPSEE 53 (74)
T ss_pred CcHHHHHHHHccCCCCCHHHHHHHHHHHCHHhHhcCChhhcCCCCEEeCCCHH
Confidence 8999999999 3 6766 57788862 356789999999999864
No 32
>COG1652 XkdP Uncharacterized protein containing LysM domain [Function unknown]
Probab=96.94 E-value=0.00032 Score=66.90 Aligned_cols=49 Identities=20% Similarity=0.402 Sum_probs=42.1
Q ss_pred eeeeeecCChHHHHHHHh-CC--CHHHHhhhhC---CCCCCCcCCCCeEEECCCC
Q 018290 172 YAHVVEEGSSFALIAQKF-GT--DRDTLMKLNG---IHDDSKLIAGEPLDVPLKA 220 (358)
Q Consensus 172 ~~Y~V~~GDTL~~IA~ky-gv--t~~~L~~~N~---l~~~~~l~~Gq~L~IP~~~ 220 (358)
.+|+|++|||||.||+++ |. ....|..+|+ +.+++.|++||+|.||...
T Consensus 211 ~~~~v~rgDTl~~is~~~Yg~~~~y~~I~~aNk~~~~~~p~~I~pGq~l~iP~~~ 265 (269)
T COG1652 211 TTNTVKRGDTLWQISKKVYGDGVEYRKIAEANKALVLDNPDKIKPGQVLRIPDQL 265 (269)
T ss_pred eEEEeccCCcccccchhhcCcceEEEeHhhhhhhhccCCCCcCCCcceeeCCCcc
Confidence 389999999999999774 54 4567889998 7899999999999999764
No 33
>PF04225 OapA: Opacity-associated protein A LysM-like domain; InterPro: IPR007340 This entry includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [].; PDB: 2GU1_A.
Probab=96.82 E-value=0.00079 Score=53.24 Aligned_cols=49 Identities=20% Similarity=0.359 Sum_probs=28.0
Q ss_pred eeeeeecCChHHHHHHHhCCCHHHHhh---hhC-CCCCCCcCCCCeEEECCCC
Q 018290 172 YAHVVEEGSSFALIAQKFGTDRDTLMK---LNG-IHDDSKLIAGEPLDVPLKA 220 (358)
Q Consensus 172 ~~Y~V~~GDTL~~IA~kygvt~~~L~~---~N~-l~~~~~l~~Gq~L~IP~~~ 220 (358)
..|+|++||||..|=+++|++..+|.+ .++ ...-..|+|||.|.+-...
T Consensus 3 ~~~~V~~GDtLs~iF~~~gls~~dl~~v~~~~~~~k~L~~L~pGq~l~f~~d~ 55 (85)
T PF04225_consen 3 QEYTVKSGDTLSTIFRRAGLSASDLYAVLEADGEAKPLTRLKPGQTLEFQLDE 55 (85)
T ss_dssp -EEE--TT--HHHHHHHTT--HHHHHHHHHHGGGT--GGG--TT-EEEEEE-T
T ss_pred cEEEECCCCcHHHHHHHcCCCHHHHHHHHhccCccchHhhCCCCCEEEEEECC
Confidence 479999999999999999998877653 331 1233579999999987654
No 34
>PRK10190 L,D-transpeptidase; Provisional
Probab=96.69 E-value=0.0078 Score=58.39 Aligned_cols=50 Identities=14% Similarity=0.225 Sum_probs=39.4
Q ss_pred ccEEEECCCCC--CHHHHHHHhCCCcHHHHHhcCCCCCCCCCCCcCCCCCeEEeccc
Q 018290 40 ALVGYLPPNKT--TISEIQSLFTVKNLRSILGANNFPPGTPRNFSVPAQKPIKVPIH 94 (358)
Q Consensus 40 a~~~YtV~~Gd--TL~~IA~~fgvs~l~~L~~~N~L~~~~~~~~~L~~Gq~L~IP~~ 94 (358)
....|+|+++| +|.+||++|+++ +.+|+++|+-- +....++|+.|.||..
T Consensus 36 ~~~~~~v~~~~~~~le~iA~~f~~g-~~~l~~aNPgv----d~~~p~~G~~i~iP~~ 87 (310)
T PRK10190 36 QSLTVTVPDHNTQPLETFAAQYGQG-LSNMLEANPGA----DVFLPKSGSQLTIPQQ 87 (310)
T ss_pred ceEEEEecCCCCccHHHHHHHhCCC-HHHHHHhCCCC----CCCCCCCCCEEEecCc
Confidence 55679998865 699999999999 69999999521 2233679999999963
No 35
>PF04225 OapA: Opacity-associated protein A LysM-like domain; InterPro: IPR007340 This entry includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonization, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [].; PDB: 2GU1_A.
Probab=96.28 E-value=0.0025 Score=50.37 Aligned_cols=53 Identities=8% Similarity=0.031 Sum_probs=27.5
Q ss_pred cEEEECCCCCCHHHHHHHhCCCcHHHHHhcCCCCCCCCCCCcCCCCCeEEeccc
Q 018290 41 LVGYLPPNKTTISEIQSLFTVKNLRSILGANNFPPGTPRNFSVPAQKPIKVPIH 94 (358)
Q Consensus 41 ~~~YtV~~GdTL~~IA~~fgvs~l~~L~~~N~L~~~~~~~~~L~~Gq~L~IP~~ 94 (358)
|..|+|++||||+.|=+++|++. .+|.++=..+...+.-..|+|||.|.+-.+
T Consensus 2 W~~~~V~~GDtLs~iF~~~gls~-~dl~~v~~~~~~~k~L~~L~pGq~l~f~~d 54 (85)
T PF04225_consen 2 WQEYTVKSGDTLSTIFRRAGLSA-SDLYAVLEADGEAKPLTRLKPGQTLEFQLD 54 (85)
T ss_dssp --EEE--TT--HHHHHHHTT--H-HHHHHHHHHGGGT--GGG--TT-EEEEEE-
T ss_pred CcEEEECCCCcHHHHHHHcCCCH-HHHHHHHhccCccchHhhCCCCCEEEEEEC
Confidence 67899999999999999999994 665443221111123467999999988764
No 36
>TIGR03505 FimV_core FimV N-terminal domain. This region is found at, or about 200 amino acids from, the N-terminus of FimV from Pseudomonas aeruginosa, TspA of Neisseria meningitidis, and related proteins. Disruption of FimV blocks twitching motility from type IV pili; Semmler, et al. suggest a role for this family in peptidoglycan layer remodelling required by type IV fimbrial systems. Most but not all members of this protein family have a C-terminal region recognized by TIGR03504. In between is a highly variable, often repeat-filled region rich in the negatively charged amino acids Asp and Glu.
Probab=96.25 E-value=0.0059 Score=47.01 Aligned_cols=42 Identities=29% Similarity=0.266 Sum_probs=32.6
Q ss_pred CcHHHHHHHHhCCC-ccHH----HHHHhcCC----CCCCccCCCcEEEECC
Q 018290 116 DGLDFIARTIFGQL-LKYQ----KIVEANNI----SNPDLIQIGQNLTIPL 157 (358)
Q Consensus 116 DTL~~IA~~~yggl-vs~~----~L~~~N~l----~~~~~L~~Gq~L~IP~ 157 (358)
||||.||+++..+. +++. .|.+.|+- .+.+.|++|+.|.||.
T Consensus 1 DTLw~IA~~~~~~~~~s~~q~m~ai~~aNp~AF~~~nin~L~~G~~L~iP~ 51 (74)
T TIGR03505 1 DTLWGIAQRVRPDNSVSLYQMMLALYRANPDAFIGGNINRLKVGQILRIPS 51 (74)
T ss_pred CcHHHHHHHHccCCCCCHHHHHHHHHHHCHHhHhcCChhhcCCCCEEeCCC
Confidence 89999999943333 6655 67888973 2567899999999996
No 37
>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=96.21 E-value=0.0083 Score=44.31 Aligned_cols=49 Identities=29% Similarity=0.422 Sum_probs=38.1
Q ss_pred eEEEcCCCcHHHHHHHHhCCCccH-HHHHHhcCC-CCC-CccCCCcEEEECCC
Q 018290 109 VYTVKKDDGLDFIARTIFGQLLKY-QKIVEANNI-SNP-DLIQIGQNLTIPLP 158 (358)
Q Consensus 109 ~YtV~~GDTL~~IA~~~ygglvs~-~~L~~~N~l-~~~-~~L~~Gq~L~IP~~ 158 (358)
.|+. .|||++.|+.++||..--. +.+.++|+- .+. ..+..|..|.+|..
T Consensus 3 v~t~-~GDtlD~I~~r~yG~~~~~~e~ll~aNp~La~~~~~lpaG~~I~lP~i 54 (60)
T PF05489_consen 3 VYTT-QGDTLDLIAYRHYGREDGAVEALLEANPGLADTGPVLPAGTVIILPDI 54 (60)
T ss_pred EEEe-CcCcHHHHHHHHhCcHHHHHHHHHHHChhhhhcCCcCCCCCEEECCCC
Confidence 3444 9999999999999954333 789999984 343 57899999999964
No 38
>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=94.95 E-value=0.046 Score=40.32 Aligned_cols=44 Identities=27% Similarity=0.433 Sum_probs=34.0
Q ss_pred ecCChHHHHHHH-hCCC---HHHHhhhhCC-CCC-CCcCCCCeEEECCCC
Q 018290 177 EEGSSFALIAQK-FGTD---RDTLMKLNGI-HDD-SKLIAGEPLDVPLKA 220 (358)
Q Consensus 177 ~~GDTL~~IA~k-ygvt---~~~L~~~N~l-~~~-~~l~~Gq~L~IP~~~ 220 (358)
+.|||+..|+-| ||-. ++.++++|+. .+. ..+..|.+|.+|.-.
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 499999999955 5654 3788999974 333 478999999999643
No 39
>PRK11649 putative peptidase; Provisional
Probab=94.60 E-value=0.19 Score=51.37 Aligned_cols=108 Identities=22% Similarity=0.231 Sum_probs=68.0
Q ss_pred CcceEEEcCCCcHHHHHHHHhCCCccHHHHHHhcC-CCCCCccCCCcEEEECCCCCcCCC------Cc--------cccc
Q 018290 106 KVPVYTVKKDDGLDFIARTIFGQLLKYQKIVEANN-ISNPDLIQIGQNLTIPLPCSCDDV------DN--------AKVV 170 (358)
Q Consensus 106 ~~~~YtV~~GDTL~~IA~~~ygglvs~~~L~~~N~-l~~~~~L~~Gq~L~IP~~~~~~~~------~~--------~~~~ 170 (358)
.+..|+|++||||..|=++ +| ++..++.+.-. ..+...|++||.+.+-......-. +. ....
T Consensus 94 ~~~~~~Vk~GDTl~~iL~r-~G--i~~~di~~l~~~~~~L~~Lr~Gq~l~~~~d~dG~L~~l~~~~s~~~~~v~~R~dg~ 170 (439)
T PRK11649 94 GVHEYVVSTGDTLSSILNQ-YG--IDMSDISQLAAQDKELRNLKIGQQLSWTLTADGDLQRLTWEVSRRETRTYDRTGNG 170 (439)
T ss_pred ceEEEEeCCCCCHHHHHHH-cC--CCHHHHHHHHHcChHhhcCCCCCEEEEEECCCCCeEEEEEEeCCCeEEEEEecCCc
Confidence 3468999999999999999 88 99888876622 233458999999988532210000 00 0000
Q ss_pred e-------------eeeeeecCChHHHHHHHhCCCHHHHhhhhCC----CCCCCcCCCCeEEE
Q 018290 171 H-------------YAHVVEEGSSFALIAQKFGTDRDTLMKLNGI----HDDSKLIAGEPLDV 216 (358)
Q Consensus 171 ~-------------~~Y~V~~GDTL~~IA~kygvt~~~L~~~N~l----~~~~~l~~Gq~L~I 216 (358)
+ ......-..+|+.-|++.|++...++++-.+ .|-..|++|+.+.|
T Consensus 171 F~~~~~~~~~~~~~~~~~g~I~~Sl~~sa~~agl~~~~i~~~~~~~~~~idf~~lr~GD~f~v 233 (439)
T PRK11649 171 FKETSEMQQGEWVNSVLKGTVGGSFVASAKNAGLTSAEISAVIKALQWQMDFRKLKKGDEFSV 233 (439)
T ss_pred EEEEEeecccEEEEEEEEEEEeccHHHHHHHcCCCHHHHHHHHHHhccCcChhhCCCCCEEEE
Confidence 0 0011122468999999999988777655532 12245888886655
No 40
>PRK11649 putative peptidase; Provisional
Probab=93.72 E-value=0.086 Score=53.92 Aligned_cols=48 Identities=23% Similarity=0.340 Sum_probs=39.5
Q ss_pred eeeeeecCChHHHHHHHhCCCHHHHhhh-hCCCCCCCcCCCCeEEECCC
Q 018290 172 YAHVVEEGSSFALIAQKFGTDRDTLMKL-NGIHDDSKLIAGEPLDVPLK 219 (358)
Q Consensus 172 ~~Y~V~~GDTL~~IA~kygvt~~~L~~~-N~l~~~~~l~~Gq~L~IP~~ 219 (358)
..|+|++||||.+|-+++|++..++.++ ....+...|++||.|.+-..
T Consensus 96 ~~~~Vk~GDTl~~iL~r~Gi~~~di~~l~~~~~~L~~Lr~Gq~l~~~~d 144 (439)
T PRK11649 96 HEYVVSTGDTLSSILNQYGIDMSDISQLAAQDKELRNLKIGQQLSWTLT 144 (439)
T ss_pred EEEEeCCCCCHHHHHHHcCCCHHHHHHHHHcChHhhcCCCCCEEEEEEC
Confidence 5899999999999999999999888766 23334468999999988654
No 41
>COG3061 OapA Cell envelope opacity-associated protein A [Cell envelope biogenesis, outer membrane]
Probab=92.04 E-value=0.42 Score=44.09 Aligned_cols=76 Identities=20% Similarity=0.212 Sum_probs=52.1
Q ss_pred CcCCCCCeEEecccccCCCCCccCCCcceEEEcCCCcHHHHHHHHhCCCccHHHHHHhcCCCCC----CccCCCcEEEEC
Q 018290 81 FSVPAQKPIKVPIHCICSNGTGVSDKVPVYTVKKDDGLDFIARTIFGQLLKYQKIVEANNISNP----DLIQIGQNLTIP 156 (358)
Q Consensus 81 ~~L~~Gq~L~IP~~~~c~~~~~~s~~~~~YtV~~GDTL~~IA~~~ygglvs~~~L~~~N~l~~~----~~L~~Gq~L~IP 156 (358)
..+..++...+|..-....-...+..+.+|+|+.|+||..+=|. .+ ..+.++.++-+.... ..|+.||+++|-
T Consensus 133 ~p~q~~q~~~v~~~~~~~P~~~s~g~wqsy~V~~G~TLaQlFRd-n~--LpitDVnAMakveGagkpLSnlkaGq~Vki~ 209 (242)
T COG3061 133 EPIQAKQEKKVPRTVDAQPFKPSSGNWQSYTVPQGKTLAQLFRD-NN--LPITDVNAMAKVEGAGKPLSNLKAGQKVKIS 209 (242)
T ss_pred chhhccCccccCCccccCccccCcccceeEEecCCccHHHHHhc-cC--CChHHhHHHHhhccCCCchhhccCCCEEEEE
Confidence 34556777777743222111111236789999999999999988 56 888888777665432 269999999998
Q ss_pred CCC
Q 018290 157 LPC 159 (358)
Q Consensus 157 ~~~ 159 (358)
...
T Consensus 210 ~na 212 (242)
T COG3061 210 LNA 212 (242)
T ss_pred EcC
Confidence 754
No 42
>COG3061 OapA Cell envelope opacity-associated protein A [Cell envelope biogenesis, outer membrane]
Probab=91.87 E-value=0.45 Score=43.86 Aligned_cols=75 Identities=17% Similarity=0.178 Sum_probs=50.7
Q ss_pred ccCCCcEEEECCCCCcCCCCccccceeeeeeecCChHHHHHHHhCCCHHHHhhhhC---CCC-CCCcCCCCeEEECCCC
Q 018290 146 LIQIGQNLTIPLPCSCDDVDNAKVVHYAHVVEEGSSFALIAQKFGTDRDTLMKLNG---IHD-DSKLIAGEPLDVPLKA 220 (358)
Q Consensus 146 ~L~~Gq~L~IP~~~~~~~~~~~~~~~~~Y~V~~GDTL~~IA~kygvt~~~L~~~N~---l~~-~~~l~~Gq~L~IP~~~ 220 (358)
.++.++...+|..........+.+-..+|+|+.|+||..+=|.+++.+.|+.++=+ -.+ -..|+.||+++|-+.+
T Consensus 134 p~q~~q~~~v~~~~~~~P~~~s~g~wqsy~V~~G~TLaQlFRdn~LpitDVnAMakveGagkpLSnlkaGq~Vki~~na 212 (242)
T COG3061 134 PIQAKQEKKVPRTVDAQPFKPSSGNWQSYTVPQGKTLAQLFRDNNLPITDVNAMAKVEGAGKPLSNLKAGQKVKISLNA 212 (242)
T ss_pred hhhccCccccCCccccCccccCcccceeEEecCCccHHHHHhccCCChHHhHHHHhhccCCCchhhccCCCEEEEEEcC
Confidence 45667777776322111111122245789999999999999999998888765542 222 2469999999998764
No 43
>COG3170 FimV Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=91.59 E-value=0.13 Score=54.78 Aligned_cols=51 Identities=25% Similarity=0.286 Sum_probs=39.8
Q ss_pred ceeeeeeecCChHHHHHHHh----CCCHHH----HhhhhCC----CCCCCcCCCCeEEECCCC
Q 018290 170 VHYAHVVEEGSSFALIAQKF----GTDRDT----LMKLNGI----HDDSKLIAGEPLDVPLKA 220 (358)
Q Consensus 170 ~~~~Y~V~~GDTL~~IA~ky----gvt~~~----L~~~N~l----~~~~~l~~Gq~L~IP~~~ 220 (358)
...+|+|++|||||+||.+. ++|+++ |.++|+- .+-+.+++|++|.||.-.
T Consensus 187 ~g~tyt~~~~Dtl~dIAs~~rp~~~vt~~Q~~lAly~lNP~af~~gni~RLr~GSvLriP~~~ 249 (755)
T COG3170 187 PGDTYTVRSGDTLWDIASRLRPQDHVTVEQMLLALYQLNPQAFVNGNINRLRAGSVLRIPSAA 249 (755)
T ss_pred CCcccccCCcchHHHHHHhhcCcccccHHHHHHHHHhhChhhhcccchhhccccceeeccchh
Confidence 34789999999999999886 356554 6688863 244579999999999854
No 44
>COG3170 FimV Tfp pilus assembly protein FimV [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=89.15 E-value=0.36 Score=51.46 Aligned_cols=52 Identities=25% Similarity=0.270 Sum_probs=39.1
Q ss_pred CcceEEEcCCCcHHHHHHHHhC-CCccHH----HHHHhcCCC----CCCccCCCcEEEECC
Q 018290 106 KVPVYTVKKDDGLDFIARTIFG-QLLKYQ----KIVEANNIS----NPDLIQIGQNLTIPL 157 (358)
Q Consensus 106 ~~~~YtV~~GDTL~~IA~~~yg-glvs~~----~L~~~N~l~----~~~~L~~Gq~L~IP~ 157 (358)
...+|+|++|||||.||.+--+ +.++.+ .|.+.|+-. +-+++++|++|.||.
T Consensus 187 ~g~tyt~~~~Dtl~dIAs~~rp~~~vt~~Q~~lAly~lNP~af~~gni~RLr~GSvLriP~ 247 (755)
T COG3170 187 PGDTYTVRSGDTLWDIASRLRPQDHVTVEQMLLALYQLNPQAFVNGNINRLRAGSVLRIPS 247 (755)
T ss_pred CCcccccCCcchHHHHHHhhcCcccccHHHHHHHHHhhChhhhcccchhhccccceeeccc
Confidence 3469999999999999988433 345554 467788722 335899999999995
No 45
>COG4784 Putative Zn-dependent protease [General function prediction only]
Probab=89.01 E-value=0.52 Score=46.41 Aligned_cols=45 Identities=22% Similarity=0.400 Sum_probs=37.9
Q ss_pred eeeeeecCChHHHHHHHh-CC--CHHHHhhhhCCCCCCCcCCCCeEEE
Q 018290 172 YAHVVEEGSSFALIAQKF-GT--DRDTLMKLNGIHDDSKLIAGEPLDV 216 (358)
Q Consensus 172 ~~Y~V~~GDTL~~IA~ky-gv--t~~~L~~~N~l~~~~~l~~Gq~L~I 216 (358)
.--+||+|||+.++|.+. |+ +++-++-+|.+.....++||++++|
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 346799999999999764 65 4677889999988889999999998
No 46
>KOG2850 consensus Predicted peptidoglycan-binding protein, contains LysM domain [General function prediction only]
Probab=87.29 E-value=0.3 Score=44.12 Aligned_cols=154 Identities=19% Similarity=0.202 Sum_probs=87.9
Q ss_pred EEEECCCCCCHHHHHHHhCCCcHHHHHhcCCCCCCCCCCCcCCCCCeEEecccccCCCCCccCCCcceEEEcC-CCcHHH
Q 018290 42 VGYLPPNKTTISEIQSLFTVKNLRSILGANNFPPGTPRNFSVPAQKPIKVPIHCICSNGTGVSDKVPVYTVKK-DDGLDF 120 (358)
Q Consensus 42 ~~YtV~~GdTL~~IA~~fgvs~l~~L~~~N~L~~~~~~~~~L~~Gq~L~IP~~~~c~~~~~~s~~~~~YtV~~-GDTL~~ 120 (358)
+.-++++||||..||-.|..+ +.++.+.|++.. ....-+-..+++|....+. ...|.++. -++...
T Consensus 10 l~~~iq~~dt~~a~al~~~~~-va~i~RvN~~~r----~q~f~a~~~i~~pv~~~~~--------~~g~~~~~~~~~~~~ 76 (186)
T KOG2850|consen 10 LEVTIQEGDTLQAIALNYESD-VADIKRVNNDDR----EQRFNALRSISIPVTRASS--------ATGYQVQEDQDIRER 76 (186)
T ss_pred eeeeeccCchhhhHHhhcccc-hhhheeeccchh----hhhhccccceecccchhhh--------hhhhccccccchhhh
Confidence 356789999999999999999 599999998763 3555566788888753221 12333443 333333
Q ss_pred HHHHHhCCCccHHHHHHhcCCCCCCccCCCc----EEEECCCCCcCCCCccccceeeeeeecCChHHH--HHHHhCCC--
Q 018290 121 IARTIFGQLLKYQKIVEANNISNPDLIQIGQ----NLTIPLPCSCDDVDNAKVVHYAHVVEEGSSFAL--IAQKFGTD-- 192 (358)
Q Consensus 121 IA~~~ygglvs~~~L~~~N~l~~~~~L~~Gq----~L~IP~~~~~~~~~~~~~~~~~Y~V~~GDTL~~--IA~kygvt-- 192 (358)
+..+ -. -..+-++..+++.+|..+..-+ .+..+ ........|.|++-+.... ++-.||..
T Consensus 77 s~~~-s~--~r~silr~~~p~~~P~~~~~~~~~~~~~~~~---------~~a~~~~eh~v~~~~~~tg~~~~~~~ga~~d 144 (186)
T KOG2850|consen 77 SPMR-SE--CRHSILREDTPTRSPLKLDSSTKRVCNLAAV---------VQAVGYQEHRVKPFDPNTGFQIAPAYGAESD 144 (186)
T ss_pred cccc-cc--cchhhcccCCcccCchhhhcchhhhhhhhhh---------hhhhhhhhcCCCCCCccccceecccccCccc
Confidence 3332 11 1122223333333221110000 00011 0111234566777777777 77778776
Q ss_pred ---HHHHhhhhCCCCCCCcCCCCeEEECCCC
Q 018290 193 ---RDTLMKLNGIHDDSKLIAGEPLDVPLKA 220 (358)
Q Consensus 193 ---~~~L~~~N~l~~~~~l~~Gq~L~IP~~~ 220 (358)
++++++.|.......++-=..+.+|.+.
T Consensus 145 ~~~~e~v~k~~~vl~~~~~f~l~~~e~p~~~ 175 (186)
T KOG2850|consen 145 ESPVESVRKMNPVLPDHQVFYLAPLEIPLPG 175 (186)
T ss_pred chhHHHHHHHhhccchhHHHhhccccCCCCC
Confidence 7889999987655566666666677664
No 47
>PRK10838 spr outer membrane lipoprotein; Provisional
Probab=87.08 E-value=0.076 Score=48.28 Aligned_cols=60 Identities=13% Similarity=0.039 Sum_probs=46.3
Q ss_pred eeecCceEEEeeCCceeeeeCCCCceeEEec-cCCcCCCCCCcCccccCccccCCCCcceeeccc
Q 018290 234 LRVANGTYTFTANSCVKCQCDATNNWTLQCK-PSQFQPSSPNSRWKTCPSMLCGDSESLSIGNTT 297 (358)
Q Consensus 234 l~v~~g~Y~~~a~~~~~~~c~~~~~~~l~~~-~~~~~~~~~~~~~~~~~~~~c~~~~~~~~g~~~ 297 (358)
....+.+|.|++....+||||| +...+|-+ .....|+++.+||...-... -++++.||+.
T Consensus 75 ~~~~G~pY~~GG~s~~G~DCSG-fv~~vy~~~~Gi~LPr~t~~Q~~~g~~V~---~~~lqpGDLV 135 (190)
T PRK10838 75 ADWKGVRYRLGGSTKKGIDCSA-FVQRTFREQFGLELPRSTYEQQEMGKSVS---RSKLRTGDLV 135 (190)
T ss_pred HHHCCCCccCCCCCCCCeEcHH-HHHHHHHHhCCCCCCCCHHHHHhcCcCcc---cCCCCCCcEE
Confidence 3467789999999999999998 99989875 45566788777775544433 3579999986
No 48
>COG4254 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=82.44 E-value=1.2 Score=42.82 Aligned_cols=52 Identities=29% Similarity=0.325 Sum_probs=44.9
Q ss_pred ceEEEcCCCcHHHHHHHHhCCCccHHHHHHhcCCCCCCccCCCcEEEECCCC
Q 018290 108 PVYTVKKDDGLDFIARTIFGQLLKYQKIVEANNISNPDLIQIGQNLTIPLPC 159 (358)
Q Consensus 108 ~~YtV~~GDTL~~IA~~~ygglvs~~~L~~~N~l~~~~~L~~Gq~L~IP~~~ 159 (358)
..|.|+.||||..+...+...+-.+..++.+|.+.+|-.+++|..|.||.+-
T Consensus 6 ~~yrv~~gdtli~l~~~yl~~~~g~r~~q~an~~~~P~~l~pgs~l~ip~~~ 57 (339)
T COG4254 6 LTYRVLFGDTLILLLGGYLTLLAGSRAAQPANTKRPPFILQPGSCLPIPLPA 57 (339)
T ss_pred ceeeeccccHHHHHHHHhhhccchhhhhcccccCCCCcccCCCccccCCCcc
Confidence 6899999999999999965544456778899999999999999999999864
No 49
>COG0739 NlpD Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]
Probab=82.40 E-value=2.2 Score=39.98 Aligned_cols=49 Identities=31% Similarity=0.455 Sum_probs=43.9
Q ss_pred eeeeeecCChHHHHHHHhCCCHHHHhhhhCCCCCCCcCCCCeEEECCCC
Q 018290 172 YAHVVEEGSSFALIAQKFGTDRDTLMKLNGIHDDSKLIAGEPLDVPLKA 220 (358)
Q Consensus 172 ~~Y~V~~GDTL~~IA~kygvt~~~L~~~N~l~~~~~l~~Gq~L~IP~~~ 220 (358)
..|.|+.++++..|+++++....++.+.|.......+.+|+.+.+|...
T Consensus 2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 50 (277)
T COG0739 2 SLYVVKKGDTLSAIAARLGISAKDLARLNNLLKKRLLRIGQLLRVPRAA 50 (277)
T ss_pred ceEEecCCCHHHHHHHHcCCCHHHHHHHHhhccccccCccceeeecccc
Confidence 3689999999999999999999999999988765589999999999873
No 50
>TIGR00247 conserved hypothetical protein, YceG family. This uncharacterized protein family, found in three of four microbial genomes, virtually always once per genome, includes YceG from Escherichia coli. This protein is encoded next to PabC, 4-amino-4-deoxychorismate lyase, in E. coli and numerous other proteobacteria, but that proximity is not conserved in other lineages. Numerous members of this family have been misannotated as aminodeoxychorismate lyase, apparently because of promiximty to PabC.
Probab=82.31 E-value=14 Score=36.57 Aligned_cols=19 Identities=16% Similarity=0.170 Sum_probs=15.7
Q ss_pred cEEEECCCCCCHHHHHHHh
Q 018290 41 LVGYLPPNKTTISEIQSLF 59 (358)
Q Consensus 41 ~~~YtV~~GdTL~~IA~~f 59 (358)
-...+|++|+|..+|++..
T Consensus 39 ~v~v~Ip~G~s~~~Ia~~L 57 (342)
T TIGR00247 39 VYEFNIEKGTGVSKIAKEL 57 (342)
T ss_pred cEEEEECCCCCHHHHHHHH
Confidence 3567899999999999754
No 51
>COG0791 Spr Cell wall-associated hydrolases (invasion-associated proteins) [Cell envelope biogenesis, outer membrane]
Probab=79.64 E-value=0.55 Score=42.32 Aligned_cols=59 Identities=10% Similarity=0.150 Sum_probs=45.1
Q ss_pred eecCceEEEeeCCc-eeeeeCCCCceeEEeccCCc-CCCCC-CcCccccCccccCCCCcceeeccc
Q 018290 235 RVANGTYTFTANSC-VKCQCDATNNWTLQCKPSQF-QPSSP-NSRWKTCPSMLCGDSESLSIGNTT 297 (358)
Q Consensus 235 ~v~~g~Y~~~a~~~-~~~~c~~~~~~~l~~~~~~~-~~~~~-~~~~~~~~~~~c~~~~~~~~g~~~ 297 (358)
...+.+|.|++..+ .+|||+| +.++.|-...++ .|+++ ..||.......- +.+..||+.
T Consensus 84 ~~~g~pY~~gG~~~~~g~DCSg-lv~~~~~~~~gi~lpr~~~~~q~~~g~~v~~---~~~~~GDlv 145 (197)
T COG0791 84 SLLGTPYRWGGSTPRNGFDCSG-LVQYAYRLLVGIQLPRTTRADQWNVGTAVDD---SDLQPGDLV 145 (197)
T ss_pred hcCCCCeEeCCCCCCCcccCCc-chHHHHHHhcCccCCCCccHHHHhccCccCh---hhCCCCCEE
Confidence 56678999999976 4999998 999999885544 67888 888866333322 458999987
No 52
>COG5004 P2-like prophage tail protein X [General function prediction only]
Probab=76.29 E-value=4.9 Score=30.00 Aligned_cols=51 Identities=18% Similarity=0.339 Sum_probs=38.0
Q ss_pred eEEEcCCCcHHHHHHHHhCCCcc-HHHHHHhcCC-CCCC-ccCCCcEEEECCCC
Q 018290 109 VYTVKKDDGLDFIARTIFGQLLK-YQKIVEANNI-SNPD-LIQIGQNLTIPLPC 159 (358)
Q Consensus 109 ~YtV~~GDTL~~IA~~~ygglvs-~~~L~~~N~l-~~~~-~L~~Gq~L~IP~~~ 159 (358)
.++...|||+..++.++||.... .+.+.++|+- .+.. .+..|-.|.+|-..
T Consensus 4 ~~Rt~~gDtvDalc~~~Ygrt~~v~eavl~ANpGlAd~gp~lp~gl~i~lPD~~ 57 (70)
T COG5004 4 IVRTRQGDTVDALCWRVYGRTTGVTEAVLEANPGLADWGPVLPHGLAITLPDIA 57 (70)
T ss_pred EEEeccCchHHHHHHHHHhhHHHHHHHHHhcCCChhhcCCCCccceeEecCCCC
Confidence 57778999999999999984333 3678889984 3322 67788888888643
No 53
>COG4784 Putative Zn-dependent protease [General function prediction only]
Probab=75.65 E-value=3.9 Score=40.42 Aligned_cols=48 Identities=23% Similarity=0.250 Sum_probs=37.9
Q ss_pred ceEEEcCCCcHHHHHHHHhCCCccHHHHHHhcCCCCCCccCCCcEEEE
Q 018290 108 PVYTVKKDDGLDFIARTIFGQLLKYQKIVEANNISNPDLIQIGQNLTI 155 (358)
Q Consensus 108 ~~YtV~~GDTL~~IA~~~ygglvs~~~L~~~N~l~~~~~L~~Gq~L~I 155 (358)
...+||+|||+..+|.+.-|---+++-++-.|.+.....+.||++++|
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 356899999999999985441113667788899887779999999987
No 54
>COG4254 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=75.06 E-value=2.7 Score=40.64 Aligned_cols=49 Identities=22% Similarity=0.141 Sum_probs=42.7
Q ss_pred eeeeeecCChHHHHHHHhCCCH---HHHhhhhCCCCCCCcCCCCeEEECCCC
Q 018290 172 YAHVVEEGSSFALIAQKFGTDR---DTLMKLNGIHDDSKLIAGEPLDVPLKA 220 (358)
Q Consensus 172 ~~Y~V~~GDTL~~IA~kygvt~---~~L~~~N~l~~~~~l~~Gq~L~IP~~~ 220 (358)
.+|.|+.||||-.++..|=... ..+...|...+|..++||..|.||.+.
T Consensus 6 ~~yrv~~gdtli~l~~~yl~~~~g~r~~q~an~~~~P~~l~pgs~l~ip~~~ 57 (339)
T COG4254 6 LTYRVLFGDTLILLLGGYLTLLAGSRAAQPANTKRPPFILQPGSCLPIPLPA 57 (339)
T ss_pred ceeeeccccHHHHHHHHhhhccchhhhhcccccCCCCcccCCCccccCCCcc
Confidence 6899999999999999985543 456789999999999999999999875
No 55
>KOG2850 consensus Predicted peptidoglycan-binding protein, contains LysM domain [General function prediction only]
Probab=71.31 E-value=2.3 Score=38.53 Aligned_cols=49 Identities=20% Similarity=0.249 Sum_probs=40.1
Q ss_pred cceEEEcCCCcHHHHHHHHhCCCccHHHHHHhcCCCCCCccCCCcEEEECCC
Q 018290 107 VPVYTVKKDDGLDFIARTIFGQLLKYQKIVEANNISNPDLIQIGQNLTIPLP 158 (358)
Q Consensus 107 ~~~YtV~~GDTL~~IA~~~ygglvs~~~L~~~N~l~~~~~L~~Gq~L~IP~~ 158 (358)
...-++++|||+..||-+ |. ..+.++...|++........-+.+.+|..
T Consensus 9 ~l~~~iq~~dt~~a~al~-~~--~~va~i~RvN~~~r~q~f~a~~~i~~pv~ 57 (186)
T KOG2850|consen 9 ELEVTIQEGDTLQAIALN-YE--SDVADIKRVNNDDREQRFNALRSISIPVT 57 (186)
T ss_pred heeeeeccCchhhhHHhh-cc--cchhhheeeccchhhhhhccccceecccc
Confidence 346689999999999999 88 99999999998766566667777777763
No 56
>PF13518 HTH_28: Helix-turn-helix domain
Probab=71.30 E-value=3.5 Score=28.33 Aligned_cols=24 Identities=38% Similarity=0.523 Sum_probs=21.0
Q ss_pred ecCChHHHHHHHhCCCHHHHhhhh
Q 018290 177 EEGSSFALIAQKFGTDRDTLMKLN 200 (358)
Q Consensus 177 ~~GDTL~~IA~kygvt~~~L~~~N 200 (358)
..|.++..||++||++...+..|-
T Consensus 10 ~~g~s~~~~a~~~gis~~tv~~w~ 33 (52)
T PF13518_consen 10 LEGESVREIAREFGISRSTVYRWI 33 (52)
T ss_pred HcCCCHHHHHHHHCCCHhHHHHHH
Confidence 468899999999999999887765
No 57
>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=61.69 E-value=5.2 Score=29.88 Aligned_cols=25 Identities=28% Similarity=0.522 Sum_probs=21.6
Q ss_pred eecCChHHHHHHHhCCCHHHHhhhh
Q 018290 176 VEEGSSFALIAQKFGTDRDTLMKLN 200 (358)
Q Consensus 176 V~~GDTL~~IA~kygvt~~~L~~~N 200 (358)
...|.|+..||++|||+...|.+|=
T Consensus 20 ~~~g~sv~~va~~~gi~~~~l~~W~ 44 (76)
T PF01527_consen 20 LESGESVSEVAREYGISPSTLYNWR 44 (76)
T ss_dssp HHHHCHHHHHHHHHTS-HHHHHHHH
T ss_pred HHCCCceEeeecccccccccccHHH
Confidence 4789999999999999999998875
No 58
>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=60.56 E-value=8.3 Score=26.28 Aligned_cols=23 Identities=43% Similarity=0.683 Sum_probs=17.7
Q ss_pred ecCChHHHHHHHhCCCHHHHhhh
Q 018290 177 EEGSSFALIAQKFGTDRDTLMKL 199 (358)
Q Consensus 177 ~~GDTL~~IA~kygvt~~~L~~~ 199 (358)
+.|-+...||+.||++...|.++
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 57899999999999999998764
No 59
>PRK10270 putative aminodeoxychorismate lyase; Provisional
Probab=57.91 E-value=92 Score=30.88 Aligned_cols=17 Identities=6% Similarity=-0.160 Sum_probs=14.8
Q ss_pred EEEECCCCCCHHHHHHH
Q 018290 42 VGYLPPNKTTISEIQSL 58 (358)
Q Consensus 42 ~~YtV~~GdTL~~IA~~ 58 (358)
...+|++|+|..+||+.
T Consensus 40 v~v~I~~G~t~~~Ia~~ 56 (340)
T PRK10270 40 TIFTLKPGTGRLALGEQ 56 (340)
T ss_pred EEEEECCCCCHHHHHHH
Confidence 56889999999999964
No 60
>PF07172 GRP: Glycine rich protein family; InterPro: IPR010800 This family consists of glycine rich proteins. Some of them may be involved in resistance to environmental stress [].
Probab=56.90 E-value=7 Score=31.53 Aligned_cols=12 Identities=33% Similarity=0.321 Sum_probs=7.7
Q ss_pred CCchhHHHHHHH
Q 018290 1 MGNFQLKLVLLL 12 (358)
Q Consensus 1 m~~~~~ll~lll 12 (358)
|.|..|||+.||
T Consensus 1 MaSK~~llL~l~ 12 (95)
T PF07172_consen 1 MASKAFLLLGLL 12 (95)
T ss_pred CchhHHHHHHHH
Confidence 887776665443
No 61
>COG0739 NlpD Membrane proteins related to metalloendopeptidases [Cell envelope biogenesis, outer membrane]
Probab=55.11 E-value=20 Score=33.38 Aligned_cols=48 Identities=35% Similarity=0.585 Sum_probs=42.0
Q ss_pred ceEEEcCCCcHHHHHHHHhCCCccHHHHHHhcCCCCCCccCCCcEEEECCC
Q 018290 108 PVYTVKKDDGLDFIARTIFGQLLKYQKIVEANNISNPDLIQIGQNLTIPLP 158 (358)
Q Consensus 108 ~~YtV~~GDTL~~IA~~~ygglvs~~~L~~~N~l~~~~~L~~Gq~L~IP~~ 158 (358)
..|.++.++++..|+++ ++ ....++.+.|.......+..|+.+.+|..
T Consensus 2 ~~~~~~~~~~l~~~~~~-~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 49 (277)
T COG0739 2 SLYVVKKGDTLSAIAAR-LG--ISAKDLARLNNLLKKRLLRIGQLLRVPRA 49 (277)
T ss_pred ceEEecCCCHHHHHHHH-cC--CCHHHHHHHHhhccccccCccceeeeccc
Confidence 36899999999999999 88 99999999998776458899999999875
No 62
>smart00004 NL Domain found in Notch and Lin-12. The Notch protein is essential for the proper differentiation of the Drosophila ectoderm. This protein contains 3 NL domains.
Probab=55.00 E-value=5 Score=26.85 Aligned_cols=33 Identities=24% Similarity=0.677 Sum_probs=26.5
Q ss_pred CccccCccccCCCCcceeeccccCCCCcceeeecccc
Q 018290 276 RWKTCPSMLCGDSESLSIGNTTTSNNCNRTTCEYAGY 312 (358)
Q Consensus 276 ~~~~~~~~~c~~~~~~~~g~~~~~~~c~~~~c~y~g~ 312 (358)
.|..|+..+|. -+.||=.=-..||...|.|+|+
T Consensus 4 ~~~~C~~~~C~----~~~~dg~CD~~CN~~~C~~DG~ 36 (38)
T smart00004 4 PWPRCEDAQCW----DKFGDGVCDEECNNAECLWDGG 36 (38)
T ss_pred cccCCChhhCh----hhhCCCccchhhCcccCCCCCC
Confidence 47899988996 5677744457899999999996
No 63
>COG5004 P2-like prophage tail protein X [General function prediction only]
Probab=53.86 E-value=32 Score=25.76 Aligned_cols=52 Identities=15% Similarity=0.070 Sum_probs=36.5
Q ss_pred cEEEECCCCCCHHHHHHH-hCCC--cHHHHHhcCCCCCCCCCCCcCCCCCeEEeccc
Q 018290 41 LVGYLPPNKTTISEIQSL-FTVK--NLRSILGANNFPPGTPRNFSVPAQKPIKVPIH 94 (358)
Q Consensus 41 ~~~YtV~~GdTL~~IA~~-fgvs--~l~~L~~~N~L~~~~~~~~~L~~Gq~L~IP~~ 94 (358)
+..|+...|||+..++.+ ||-+ ..+.++++|+ +.......++.|..|.+|..
T Consensus 2 ~~~~Rt~~gDtvDalc~~~Ygrt~~v~eavl~ANp--GlAd~gp~lp~gl~i~lPD~ 56 (70)
T COG5004 2 LMIVRTRQGDTVDALCWRVYGRTTGVTEAVLEANP--GLADWGPVLPHGLAITLPDI 56 (70)
T ss_pred ceEEEeccCchHHHHHHHHHhhHHHHHHHHHhcCC--ChhhcCCCCccceeEecCCC
Confidence 346788999999999854 4422 1489999994 21123456888999988864
No 64
>smart00796 AHS1 Allophanate hydrolase subunit 1. This domain represents subunit 1 of allophanate hydrolase (AHS1).
Probab=51.56 E-value=1.4e+02 Score=27.13 Aligned_cols=99 Identities=17% Similarity=0.223 Sum_probs=58.8
Q ss_pred cCCCcEEEECCCCCcCCCCccccceeeeeeecCChHHHHHHHhCCCHHHHhhhhCCCCCC----CcCCCCeEEECCCCCC
Q 018290 147 IQIGQNLTIPLPCSCDDVDNAKVVHYAHVVEEGSSFALIAQKFGTDRDTLMKLNGIHDDS----KLIAGEPLDVPLKACN 222 (358)
Q Consensus 147 L~~Gq~L~IP~~~~~~~~~~~~~~~~~Y~V~~GDTL~~IA~kygvt~~~L~~~N~l~~~~----~l~~Gq~L~IP~~~~~ 222 (358)
..++..+.||. .|--.-|--|..+|+..|++.+++.++---..-. ...||.-...++...=
T Consensus 83 ~~~~r~~~IPV---------------~Y~~~~gpDL~~vA~~~gLs~~evi~~Hs~~~y~V~~iGF~PGf~YL~~ld~~l 147 (201)
T smart00796 83 EVPGRIIEIPV---------------CYGGEFGPDLEFVARHNGLSVDEVIRLHSAAEYRVYMLGFAPGFPYLGGLDPRL 147 (201)
T ss_pred CCCCcEEEEee---------------EeCCCCCCCHHHHHHHhCcCHHHHHHHHhCCCeEEEEEeccCCCchhcCCCccc
Confidence 34566778884 3433446689999999999999999887543321 1345543333322110
Q ss_pred CCCCCCccccceeecCceEEEeeCCceeeeeCCCCceeEE
Q 018290 223 SSIKADSFDNYLRVANGTYTFTANSCVKCQCDATNNWTLQ 262 (358)
Q Consensus 223 s~~~~~~~d~~l~v~~g~Y~~~a~~~~~~~c~~~~~~~l~ 262 (358)
.. |+. ..--..+|.|+-++++..+.=.--.+++-|++.
T Consensus 148 ~~-PR~-~~PR~~vPaGSVgIag~qt~IYp~~SPGGW~iI 185 (201)
T smart00796 148 AT-PRR-STPRTRVPAGSVGIAGAQTGIYPLESPGGWQLI 185 (201)
T ss_pred cC-CCC-CCCccccCCCeEEEccceeEEECCCCCCcceEe
Confidence 00 100 011246788888887777665555667778774
No 65
>TIGR00370 conserved hypothetical protein TIGR00370.
Probab=49.42 E-value=98 Score=28.32 Aligned_cols=90 Identities=14% Similarity=0.159 Sum_probs=59.7
Q ss_pred CCCcEEEECCCCCcCCCCccccceeeeeeecCChHHHHHHHhCCCHHHHhhhhCCCCCC----CcCCCC--------eEE
Q 018290 148 QIGQNLTIPLPCSCDDVDNAKVVHYAHVVEEGSSFALIAQKFGTDRDTLMKLNGIHDDS----KLIAGE--------PLD 215 (358)
Q Consensus 148 ~~Gq~L~IP~~~~~~~~~~~~~~~~~Y~V~~GDTL~~IA~kygvt~~~L~~~N~l~~~~----~l~~Gq--------~L~ 215 (358)
..+..+.||. .|--..|.-|..+|+..|++++++++.=--..-. ...||. .|.
T Consensus 74 ~~~r~~~iPV---------------~Y~~~~g~DL~~vA~~~gLs~eevi~~Hs~~~y~V~~iGF~PGf~YL~~ld~~l~ 138 (202)
T TIGR00370 74 VNRRIIEIPV---------------CYGGEFGPDLEEVAKINQLSPEEVIDIHSNGEYVVYMLGFQPGFPYLGGLPERLH 138 (202)
T ss_pred CCCeEEEEee---------------EeCCCCCCCHHHHHHHhCcCHHHHHHHHhCCceEEEEEcCCCCchhccCCccccC
Confidence 4556777884 4555678899999999999999998876433211 234553 333
Q ss_pred ECCCCCCCCCCCCccccceeecCceEEEeeCCceeeeeCCCCceeEE
Q 018290 216 VPLKACNSSIKADSFDNYLRVANGTYTFTANSCVKCQCDATNNWTLQ 262 (358)
Q Consensus 216 IP~~~~~s~~~~~~~d~~l~v~~g~Y~~~a~~~~~~~c~~~~~~~l~ 262 (358)
+|... .--..+|.|+-++++..+.=.--.+++-|++.
T Consensus 139 ~PR~~----------~PR~~vPaGSVgIag~qt~IYp~~sPGGW~iI 175 (202)
T TIGR00370 139 TPRRA----------SPRPSVPAGSVGIGGLQTGVYPISTPGGWQLI 175 (202)
T ss_pred CCCCC----------CCccccCCceeEEcccceEEEccCCCCcceEe
Confidence 33321 11247888888888887765555567889884
No 66
>PF00877 NLPC_P60: NlpC/P60 family; InterPro: IPR000064 The Escherichia coli NLPC/Listeria P60 domain occurs at the C terminus of a number of different bacterial and viral proteins. The viral proteins are either described as tail assembly proteins or Gp19. In bacteria, the proteins are variously described as being putative tail component of prophage, invasin, invasion associated protein, putative lipoprotein, cell wall hydrolase, or putative endopeptidase. The E. coli NLPC/Listeria P60 domain is contained within the boundaries of the cysteine peptidase domain that defines the MEROPS peptidase family C40 (clan C-). A type example being dipeptidyl-peptidase VI from Bacillus sphaericus and gamma-glutamyl-diamino acid-endopeptidase precursor from Lactococcus lactis 3.4.19.11 from EC. This group also contains proteins classified as non-peptidase homologues in that they either have been found experimentally to be without peptidase activity, or lack amino acid residues that are believed to be essential for the catalytic activity of peptidases in the C40 family. ; PDB: 3PVQ_B 3GT2_A 3NPF_B 2K1G_A 3I86_A 3S0Q_A 2XIV_A 3PBC_A 3NE0_A 3M1U_B ....
Probab=49.06 E-value=0.28 Score=39.54 Aligned_cols=58 Identities=10% Similarity=0.068 Sum_probs=33.8
Q ss_pred CceEEEeeCCceeeeeCCCCceeEEeccCCcCCCCCCcCccccCccccCCCCcceeeccc
Q 018290 238 NGTYTFTANSCVKCQCDATNNWTLQCKPSQFQPSSPNSRWKTCPSMLCGDSESLSIGNTT 297 (358)
Q Consensus 238 ~g~Y~~~a~~~~~~~c~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~c~~~~~~~~g~~~ 297 (358)
+.+|.|++.++.++||++ ..+.+|.+.....++.+..++ ..........+.++.||+.
T Consensus 1 G~pY~~Gg~~~~g~DCsg-lV~~~~~~~Gi~l~~~~~~~~-~~~~~~~~~~~~~~pGDli 58 (105)
T PF00877_consen 1 GTPYVWGGRSPDGFDCSG-LVRWVYRQAGINLPRTSADQY-SVGFQKRVPISELQPGDLI 58 (105)
T ss_dssp T-BB-TTGEETTEB-HHH-HHHHHHHTTTEE--SSHHHHT-TSSEEEHEEGGG-TTTEEE
T ss_pred CCeecCCCCCCCCcCcHH-HHHHHHHHhCCCCCccccccc-ccccccccchhcCCcccEE
Confidence 357999999999999998 999999888444444433321 2222212334567888875
No 67
>PF13518 HTH_28: Helix-turn-helix domain
Probab=47.39 E-value=20 Score=24.40 Aligned_cols=23 Identities=13% Similarity=0.218 Sum_probs=19.4
Q ss_pred CCCCHHHHHHHhCCCcHHHHHhcC
Q 018290 48 NKTTISEIQSLFTVKNLRSILGAN 71 (358)
Q Consensus 48 ~GdTL~~IA~~fgvs~l~~L~~~N 71 (358)
.|.|+.+||+.|||+. ..|..|-
T Consensus 11 ~g~s~~~~a~~~gis~-~tv~~w~ 33 (52)
T PF13518_consen 11 EGESVREIAREFGISR-STVYRWI 33 (52)
T ss_pred cCCCHHHHHHHHCCCH-hHHHHHH
Confidence 6889999999999995 7777664
No 68
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=47.29 E-value=20 Score=24.44 Aligned_cols=24 Identities=33% Similarity=0.491 Sum_probs=18.0
Q ss_pred ecCChHHHHHHHhCCCHHHHhhhh
Q 018290 177 EEGSSFALIAQKFGTDRDTLMKLN 200 (358)
Q Consensus 177 ~~GDTL~~IA~kygvt~~~L~~~N 200 (358)
..|.|...||+.+|++...+.+|=
T Consensus 15 ~~G~s~~~ia~~lgvs~~Tv~~w~ 38 (50)
T PF13384_consen 15 REGWSIREIAKRLGVSRSTVYRWI 38 (50)
T ss_dssp HHT--HHHHHHHHTS-HHHHHHHH
T ss_pred HCCCCHHHHHHHHCcCHHHHHHHH
Confidence 459999999999999999887764
No 69
>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=45.85 E-value=11 Score=26.78 Aligned_cols=24 Identities=42% Similarity=0.616 Sum_probs=17.0
Q ss_pred eecCChHHHHHHHhCCCHHHHhhh
Q 018290 176 VEEGSSFALIAQKFGTDRDTLMKL 199 (358)
Q Consensus 176 V~~GDTL~~IA~kygvt~~~L~~~ 199 (358)
+..|.+..+||++||++...+..+
T Consensus 19 ~e~g~s~~~ia~~fgv~~sTv~~I 42 (53)
T PF04218_consen 19 LEEGESKRDIAREFGVSRSTVSTI 42 (53)
T ss_dssp HHCTT-HHHHHHHHT--CCHHHHH
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHH
Confidence 467899999999999987776544
No 70
>TIGR02219 phage_NlpC_fam putative phage cell wall peptidase, NlpC/P60 family. Members of this family show sequence similarity to members of the NlpC/P60 family described by Pfam model pfam00877 and by Anantharaman and Aravind (PubMed:12620121). The NlpC/P60 family includes a number of characterized bacterial cell wall hydrolases. Members of this related family are all found in prophage regions of bacterial genomes.
Probab=45.15 E-value=2.5 Score=35.99 Aligned_cols=34 Identities=15% Similarity=0.067 Sum_probs=27.1
Q ss_pred eeecCceEEEeeCCc-eeeeeCCCCceeEEeccCCc
Q 018290 234 LRVANGTYTFTANSC-VKCQCDATNNWTLQCKPSQF 268 (358)
Q Consensus 234 l~v~~g~Y~~~a~~~-~~~~c~~~~~~~l~~~~~~~ 268 (358)
....+.+|.++++++ .+||||| +++.+|-+..++
T Consensus 6 ~~~lG~pY~~Gg~~~~~GfDCSG-lv~~~y~~~~Gi 40 (134)
T TIGR02219 6 RSWIGTPYRHQASTLGVGCDCLG-LVRGVWRALYGE 40 (134)
T ss_pred HHhCCCCeecCCCCCCCCcccHH-HHHHHHHHhcCC
Confidence 355778999999987 5999998 888888765444
No 71
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=42.54 E-value=22 Score=29.49 Aligned_cols=28 Identities=21% Similarity=0.381 Sum_probs=24.1
Q ss_pred eeeecCChHHHHHHHhCCCHHHHhhhhC
Q 018290 174 HVVEEGSSFALIAQKFGTDRDTLMKLNG 201 (358)
Q Consensus 174 Y~V~~GDTL~~IA~kygvt~~~L~~~N~ 201 (358)
..+..|.++..||++||++...|.+|=.
T Consensus 24 ~~~~~g~sv~evA~e~gIs~~tl~~W~r 51 (121)
T PRK09413 24 QSFEPGMTVSLVARQHGVAASQLFLWRK 51 (121)
T ss_pred HHHcCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 3456799999999999999999999853
No 72
>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=42.26 E-value=25 Score=23.89 Aligned_cols=23 Identities=22% Similarity=0.333 Sum_probs=16.3
Q ss_pred CCCCCHHHHHHHhCCCcHHHHHhc
Q 018290 47 PNKTTISEIQSLFTVKNLRSILGA 70 (358)
Q Consensus 47 ~~GdTL~~IA~~fgvs~l~~L~~~ 70 (358)
..|.++.+||+.|||+. ..|.++
T Consensus 19 ~~G~si~~IA~~~gvsr-~TvyR~ 41 (45)
T PF02796_consen 19 AEGMSIAEIAKQFGVSR-STVYRY 41 (45)
T ss_dssp HTT--HHHHHHHTTS-H-HHHHHH
T ss_pred HCCCCHHHHHHHHCcCH-HHHHHH
Confidence 57899999999999994 777653
No 73
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=40.80 E-value=24 Score=28.78 Aligned_cols=26 Identities=23% Similarity=0.450 Sum_probs=21.6
Q ss_pred eeecCChHHHHHHHhCC-CHHHHhhhh
Q 018290 175 VVEEGSSFALIAQKFGT-DRDTLMKLN 200 (358)
Q Consensus 175 ~V~~GDTL~~IA~kygv-t~~~L~~~N 200 (358)
..+.|+|+..||++||+ ....|.+|=
T Consensus 20 ~~~~g~sv~~vAr~~gv~~~~~l~~W~ 46 (116)
T COG2963 20 YLRGGDTVSEVAREFGIVSATQLYKWR 46 (116)
T ss_pred HHhcCccHHHHHHHhCCCChHHHHHHH
Confidence 35689999999999996 988888654
No 74
>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=39.33 E-value=24 Score=29.19 Aligned_cols=75 Identities=11% Similarity=0.146 Sum_probs=0.0
Q ss_pred EcCCCcHHHHHHHHhCCCccHHHHHHhcCCCCCCccCCCcEE--EECCCCCcCCCCccccceeeeeeecCChHHHHHHHh
Q 018290 112 VKKDDGLDFIARTIFGQLLKYQKIVEANNISNPDLIQIGQNL--TIPLPCSCDDVDNAKVVHYAHVVEEGSSFALIAQKF 189 (358)
Q Consensus 112 V~~GDTL~~IA~~~ygglvs~~~L~~~N~l~~~~~L~~Gq~L--~IP~~~~~~~~~~~~~~~~~Y~V~~GDTL~~IA~ky 189 (358)
+..|.+...+|+. |+ |+...+..|=.-.....+.+...- .|.. ......-.-.++-|+.+||++|
T Consensus 15 ~~~g~s~~eaa~~-F~--VS~~Tv~~W~k~~~~G~~~~k~r~~~Kid~----------~~L~~~v~~~pd~tl~Ela~~l 81 (119)
T PF01710_consen 15 IEKGKSIREAAKR-FG--VSRNTVYRWLKRKETGDLEPKPRGRKKIDR----------DELKALVEENPDATLRELAERL 81 (119)
T ss_pred HHccchHHHHHHH-hC--cHHHHHHHHHHhcccccccccccccccccH----------HHHHHHHHHCCCcCHHHHHHHc
Q ss_pred CCCHHHHhhh
Q 018290 190 GTDRDTLMKL 199 (358)
Q Consensus 190 gvt~~~L~~~ 199 (358)
|++...|..+
T Consensus 82 ~Vs~~ti~~~ 91 (119)
T PF01710_consen 82 GVSPSTIWRA 91 (119)
T ss_pred CCCHHHHHHH
No 75
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=39.26 E-value=31 Score=24.70 Aligned_cols=24 Identities=13% Similarity=0.331 Sum_probs=20.4
Q ss_pred EEECCCCCCHHHHHHHhCCCcHHHH
Q 018290 43 GYLPPNKTTISEIQSLFTVKNLRSI 67 (358)
Q Consensus 43 ~YtV~~GdTL~~IA~~fgvs~l~~L 67 (358)
.|.++++.|+.+||+.+||+. ..+
T Consensus 17 Yfd~PR~~tl~elA~~lgis~-st~ 40 (53)
T PF04967_consen 17 YFDVPRRITLEELAEELGISK-STV 40 (53)
T ss_pred CCCCCCcCCHHHHHHHhCCCH-HHH
Confidence 367899999999999999995 544
No 76
>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=37.10 E-value=42 Score=19.66 Aligned_cols=23 Identities=39% Similarity=0.618 Sum_probs=19.3
Q ss_pred ecCChHHHHHHHhCCCHHHHhhh
Q 018290 177 EEGSSFALIAQKFGTDRDTLMKL 199 (358)
Q Consensus 177 ~~GDTL~~IA~kygvt~~~L~~~ 199 (358)
..|.+...||+.+|++...+.++
T Consensus 19 ~~~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 19 AAGESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHh
Confidence 46889999999999998877654
No 77
>PF14453 ThiS-like: ThiS-like ubiquitin
Probab=36.96 E-value=46 Score=24.31 Aligned_cols=44 Identities=18% Similarity=0.212 Sum_probs=36.4
Q ss_pred EEECCCCCCHHHHHHHhCCCcHHHHHhcCCCCCCCCCCCcCCCCCeEE
Q 018290 43 GYLPPNKTTISEIQSLFTVKNLRSILGANNFPPGTPRNFSVPAQKPIK 90 (358)
Q Consensus 43 ~YtV~~GdTL~~IA~~fgvs~l~~L~~~N~L~~~~~~~~~L~~Gq~L~ 90 (358)
.+.++.+.||.++.+.+.-+ .|+.=+|+.+ +.++..|..|+.|.
T Consensus 9 ~~~~~~~~tl~~lr~~~k~~--~DI~I~NGF~--~~~d~~L~e~D~v~ 52 (57)
T PF14453_consen 9 EIETEENTTLFELRKESKPD--ADIVILNGFP--TKEDIELKEGDEVF 52 (57)
T ss_pred EEEcCCCcCHHHHHHhhCCC--CCEEEEcCcc--cCCccccCCCCEEE
Confidence 47788999999999999997 7899999876 34667788888764
No 78
>PHA00675 hypothetical protein
Probab=36.95 E-value=32 Score=26.68 Aligned_cols=26 Identities=31% Similarity=0.555 Sum_probs=22.1
Q ss_pred ecCChHHHHHHHhCCCHHHHhhhhCC
Q 018290 177 EEGSSFALIAQKFGTDRDTLMKLNGI 202 (358)
Q Consensus 177 ~~GDTL~~IA~kygvt~~~L~~~N~l 202 (358)
+.|.+...||++||++...+...=..
T Consensus 37 r~G~s~~~IA~~fGVsrstV~~I~~g 62 (78)
T PHA00675 37 VEGMSYAVLAEKFEQSKGAIAKICRY 62 (78)
T ss_pred hcCccHHHHHHHhCCCHHHHHHHHcc
Confidence 78999999999999999888765543
No 79
>PF05393 Hum_adeno_E3A: Human adenovirus early E3A glycoprotein; InterPro: IPR008652 This family consists of several early glycoproteins (E3A), from human adenovirus type 2.; GO: 0016021 integral to membrane
Probab=36.39 E-value=51 Score=26.24 Aligned_cols=39 Identities=33% Similarity=0.618 Sum_probs=21.2
Q ss_pred EEeecccccCCCC---CCCcccchhhHHHHHHHHHHHHHhhh
Q 018290 318 LTTLNSLSTCPSP---SNNASRIGSWNLLLISIFLVLLHFHL 356 (358)
Q Consensus 318 ~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~~ 356 (358)
.|+|++...-|.. .+.-.-+|+|.++++.+.++++++||
T Consensus 11 ~TsLtst~~~p~~~~~~n~~~~Lgm~~lvI~~iFil~Vilwf 52 (94)
T PF05393_consen 11 LTSLTSTTETPVVSMFVNNWPNLGMWFLVICGIFILLVILWF 52 (94)
T ss_pred eeeeeeecccceeEeecCCCCccchhHHHHHHHHHHHHHHHH
Confidence 6666553333432 23334567996666666555555554
No 80
>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=36.23 E-value=30 Score=23.69 Aligned_cols=24 Identities=38% Similarity=0.542 Sum_probs=17.0
Q ss_pred eecC-ChHHHHHHHhCCCHHHHhhh
Q 018290 176 VEEG-SSFALIAQKFGTDRDTLMKL 199 (358)
Q Consensus 176 V~~G-DTL~~IA~kygvt~~~L~~~ 199 (358)
|+.| -++...|++|||+...|.+.
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 78999999999999988743
No 81
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=35.60 E-value=37 Score=25.06 Aligned_cols=23 Identities=26% Similarity=0.322 Sum_probs=20.0
Q ss_pred ChHHHHHHHhCCCHHHHhhhhCC
Q 018290 180 SSFALIAQKFGTDRDTLMKLNGI 202 (358)
Q Consensus 180 DTL~~IA~kygvt~~~L~~~N~l 202 (358)
=++-+||+++|++...|..|-..
T Consensus 23 i~lkdIA~~Lgvs~~tIr~WK~~ 45 (60)
T PF10668_consen 23 IKLKDIAEKLGVSESTIRKWKSR 45 (60)
T ss_pred ccHHHHHHHHCCCHHHHHHHhhh
Confidence 36899999999999999988654
No 82
>PF04255 DUF433: Protein of unknown function (DUF433); InterPro: IPR007367 This is a family of uncharacterised proteins.; PDB: 2GA1_B.
Probab=35.32 E-value=32 Score=24.60 Aligned_cols=24 Identities=17% Similarity=0.210 Sum_probs=17.1
Q ss_pred eecCChHHHHHHHhC-CCHHHHhhh
Q 018290 176 VEEGSSFALIAQKFG-TDRDTLMKL 199 (358)
Q Consensus 176 V~~GDTL~~IA~kyg-vt~~~L~~~ 199 (358)
++.|.+...|++.|. ++.+++.++
T Consensus 28 ~~~G~s~eeI~~~yp~Lt~~~i~aA 52 (56)
T PF04255_consen 28 LAAGESPEEIAEDYPSLTLEDIRAA 52 (56)
T ss_dssp HHTT--HHHHHHHSTT--HHHHHHH
T ss_pred HHcCCCHHHHHHHCCCCCHHHHHHH
Confidence 389999999999997 899998764
No 83
>PRK13733 conjugal transfer protein TraV; Provisional
Probab=33.77 E-value=42 Score=29.99 Aligned_cols=38 Identities=26% Similarity=0.486 Sum_probs=22.0
Q ss_pred CCchhHHHHHHHHH-HHhhccccccccCcccccccccccCcc
Q 018290 1 MGNFQLKLVLLLFT-VCAALSTLSTAQDFKCSAQTAARCQAL 41 (358)
Q Consensus 1 m~~~~~ll~lll~l-~~~~~~~~~~~~~~~C~~~~~~~C~a~ 41 (358)
|+...+|++|+.+| ...+ +....+|.|+...++.|-+.
T Consensus 1 MK~~~~li~l~~~LlL~GC---Ag~~s~f~C~~t~sdqclsm 39 (171)
T PRK13733 1 MKQISLLIPLLGTLLLSGC---AGTNSEFECNATTSDTCMTM 39 (171)
T ss_pred CchhhHHHHHHHHHHhccc---cCCCCCCCCCCCCCcceeeH
Confidence 77655555544433 3335 33466789997656666543
No 84
>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=32.93 E-value=49 Score=22.58 Aligned_cols=23 Identities=30% Similarity=0.544 Sum_probs=18.7
Q ss_pred ecCChHHHHHHHhCCCHHHHhhh
Q 018290 177 EEGSSFALIAQKFGTDRDTLMKL 199 (358)
Q Consensus 177 ~~GDTL~~IA~kygvt~~~L~~~ 199 (358)
..|-|+..||+.+|++.+.+...
T Consensus 18 ~~~~t~~eIa~~lg~s~~~V~~~ 40 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISRSTVRRI 40 (50)
T ss_dssp TST-SHHHHHHHHTSCHHHHHHH
T ss_pred cCCCCHHHHHHHHCCcHHHHHHH
Confidence 56889999999999999887643
No 85
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=32.65 E-value=44 Score=22.60 Aligned_cols=23 Identities=35% Similarity=0.615 Sum_probs=14.9
Q ss_pred eecCChHHHHHHHhCCCHHHHhh
Q 018290 176 VEEGSSFALIAQKFGTDRDTLMK 198 (358)
Q Consensus 176 V~~GDTL~~IA~kygvt~~~L~~ 198 (358)
.+.|.+...||+++|.+...+.+
T Consensus 17 ~~~G~s~~~IA~~lg~s~sTV~r 39 (44)
T PF13936_consen 17 LEQGMSIREIAKRLGRSRSTVSR 39 (44)
T ss_dssp HCS---HHHHHHHTT--HHHHHH
T ss_pred HHcCCCHHHHHHHHCcCcHHHHH
Confidence 36899999999999999887754
No 86
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=31.24 E-value=80 Score=20.66 Aligned_cols=37 Identities=19% Similarity=0.287 Sum_probs=23.9
Q ss_pred hHHHHHHHhCCCHHHHhhhhCCCCCCCcCCCCeEEEC
Q 018290 181 SFALIAQKFGTDRDTLMKLNGIHDDSKLIAGEPLDVP 217 (358)
Q Consensus 181 TL~~IA~kygvt~~~L~~~N~l~~~~~l~~Gq~L~IP 217 (358)
|+..+|+.+|++...|.+|=.-..-...+.|....++
T Consensus 3 t~~e~a~~lgis~~ti~~~~~~g~i~~~~~g~~~~~~ 39 (49)
T TIGR01764 3 TVEEAAEYLGVSKDTVYRLIHEGELPAYRVGRHYRIP 39 (49)
T ss_pred CHHHHHHHHCCCHHHHHHHHHcCCCCeEEeCCeEEEe
Confidence 5678999999999999877643221223335555554
No 87
>PRK09570 rpoH DNA-directed RNA polymerase subunit H; Reviewed
Probab=25.74 E-value=64 Score=25.16 Aligned_cols=48 Identities=13% Similarity=0.249 Sum_probs=35.8
Q ss_pred eeeeecCChHHHHHHHhCCCHHHHhhhhC---CCCCCCcCCCCeEEECCCC
Q 018290 173 AHVVEEGSSFALIAQKFGTDRDTLMKLNG---IHDDSKLIAGEPLDVPLKA 220 (358)
Q Consensus 173 ~Y~V~~GDTL~~IA~kygvt~~~L~~~N~---l~~~~~l~~Gq~L~IP~~~ 220 (358)
.|.+-.-|-...+-++|++..++|-+.-. +..--.+++||+++|--++
T Consensus 14 kH~iLs~eE~~~lL~~y~i~~~qLP~I~~~DPv~r~~g~k~GdVvkI~R~S 64 (79)
T PRK09570 14 EHEILSEEEAKKLLKEYGIKPEQLPKIKASDPVVKAIGAKPGDVIKIVRKS 64 (79)
T ss_pred CeEECCHHHHHHHHHHcCCCHHHCCceeccChhhhhcCCCCCCEEEEEECC
Confidence 36677777788999999999999866553 2222368999999996553
No 88
>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=25.25 E-value=1.3e+02 Score=27.98 Aligned_cols=74 Identities=12% Similarity=-0.038 Sum_probs=41.1
Q ss_pred CccCCCcEEEECCCCCcCCCCccccceeeeeeecCChHHH-HHHHhCCCHHH------HhhhhC--------CCCCCCcC
Q 018290 145 DLIQIGQNLTIPLPCSCDDVDNAKVVHYAHVVEEGSSFAL-IAQKFGTDRDT------LMKLNG--------IHDDSKLI 209 (358)
Q Consensus 145 ~~L~~Gq~L~IP~~~~~~~~~~~~~~~~~Y~V~~GDTL~~-IA~kygvt~~~------L~~~N~--------l~~~~~l~ 209 (358)
-.|++|+.|.||.... ...-+.-.....|..+++.|+.+ |++.=|.+... |.+.|+ ..-.+.|+
T Consensus 149 i~L~~GD~I~V~~~~~-v~v~G~V~~pg~~~~~~~~tl~~al~~aGG~~~~a~~~~v~i~R~~~~g~~~~~~~~~~~~l~ 227 (239)
T TIGR03028 149 ILVAGGDIIYVDRAPV-FYIYGEVQRPGAYRLERNMTVMQALAQGGGLTPRGTERGIRVMRRDDKGAVEEVSGELGDLVQ 227 (239)
T ss_pred cEEcCCCEEEEcCCcc-EEEEeEccCCeEEEeCCCCCHHHHHHhcCCCCcccCcceEEEEEECCCCcEEEEecCCCcccC
Confidence 3799999999995321 00112222335677888888654 55554554321 112221 01113488
Q ss_pred CCCeEEECCC
Q 018290 210 AGEPLDVPLK 219 (358)
Q Consensus 210 ~Gq~L~IP~~ 219 (358)
+|++++||..
T Consensus 228 ~gDii~V~~s 237 (239)
T TIGR03028 228 PDDVIYVRES 237 (239)
T ss_pred CCCEEEEeCc
Confidence 9999998854
No 89
>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=25.16 E-value=65 Score=26.19 Aligned_cols=20 Identities=20% Similarity=0.484 Sum_probs=14.8
Q ss_pred CChHHHHHHHhCCCHHHHhh
Q 018290 179 GSSFALIAQKFGTDRDTLMK 198 (358)
Q Consensus 179 GDTL~~IA~kygvt~~~L~~ 198 (358)
|.+...+|++||+|...+.+
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 99999999999999887653
No 90
>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A.
Probab=24.47 E-value=66 Score=25.01 Aligned_cols=22 Identities=27% Similarity=0.472 Sum_probs=16.2
Q ss_pred ecCChHHHHHHHhCCCHHHHhh
Q 018290 177 EEGSSFALIAQKFGTDRDTLMK 198 (358)
Q Consensus 177 ~~GDTL~~IA~kygvt~~~L~~ 198 (358)
++|-||.+||+++|++...|..
T Consensus 13 krG~sL~~lsr~~Gl~~~tl~n 34 (78)
T PF13693_consen 13 KRGTSLAALSREAGLSSSTLRN 34 (78)
T ss_dssp TTS--HHHHHHHHSS-HHHHHH
T ss_pred HcCCCHHHHHHHcCCCHHHHHH
Confidence 5799999999999999887753
No 91
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=24.22 E-value=79 Score=20.52 Aligned_cols=21 Identities=19% Similarity=0.153 Sum_probs=17.9
Q ss_pred hHHHHHHHhCCCHHHHhhhhC
Q 018290 181 SFALIAQKFGTDRDTLMKLNG 201 (358)
Q Consensus 181 TL~~IA~kygvt~~~L~~~N~ 201 (358)
++..+|+.+|++...|.+|=.
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~ 22 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVK 22 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 467899999999999998853
No 92
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=24.15 E-value=28 Score=24.86 Aligned_cols=53 Identities=13% Similarity=0.142 Sum_probs=30.6
Q ss_pred CCCcHHHHHHHHhCCCccHHHHHHhcCCCCCCccCCCcEEEECCCCCcCCCCccccceeeeeeecCChHHHHHHHhCCCH
Q 018290 114 KDDGLDFIARTIFGQLLKYQKIVEANNISNPDLIQIGQNLTIPLPCSCDDVDNAKVVHYAHVVEEGSSFALIAQKFGTDR 193 (358)
Q Consensus 114 ~GDTL~~IA~~~ygglvs~~~L~~~N~l~~~~~L~~Gq~L~IP~~~~~~~~~~~~~~~~~Y~V~~GDTL~~IA~kygvt~ 193 (358)
.|=+...+|++ -| ++...+.++-+- .. . --.-|++..||+-+|+++
T Consensus 9 ~~it~~~La~~-~g--is~~tl~~~~~~---------~~-~---------------------~~~~~~l~~ia~~l~~~~ 54 (63)
T PF13443_consen 9 RGITQKDLARK-TG--ISRSTLSRILNG---------KP-S---------------------NPSLDTLEKIAKALNCSP 54 (63)
T ss_dssp TT--HHHHHHH-HT----HHHHHHHHTT---------T---------------------------HHHHHHHHHHHT--H
T ss_pred cCCCHHHHHHH-HC--cCHHHHHHHHhc---------cc-c---------------------cccHHHHHHHHHHcCCCH
Confidence 45577778877 56 777777665431 10 0 012378999999999999
Q ss_pred HHHhhhh
Q 018290 194 DTLMKLN 200 (358)
Q Consensus 194 ~~L~~~N 200 (358)
++|..+.
T Consensus 55 ~el~~~~ 61 (63)
T PF13443_consen 55 EELFEYE 61 (63)
T ss_dssp HHCTECC
T ss_pred HHHhhcC
Confidence 9998754
No 93
>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=23.58 E-value=81 Score=20.75 Aligned_cols=22 Identities=18% Similarity=0.197 Sum_probs=17.6
Q ss_pred hHHHHHHHhCCCHHHHhhhhCC
Q 018290 181 SFALIAQKFGTDRDTLMKLNGI 202 (358)
Q Consensus 181 TL~~IA~kygvt~~~L~~~N~l 202 (358)
|...+|+.+|+++..|+.|-..
T Consensus 1 ti~e~A~~~gvs~~tlR~ye~~ 22 (38)
T PF00376_consen 1 TIGEVAKLLGVSPRTLRYYERE 22 (38)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHT
T ss_pred CHHHHHHHHCCCHHHHHHHHHC
Confidence 4578999999999999988753
No 94
>PF02618 YceG: YceG-like family; InterPro: IPR003770 This uncharacterised protein family, found in three of four microbial genomes, virtually always once per genome, includes YceG from Escherichia coli. Proteins in this family are typically between 332 and 389 amino acids in length. This protein is encoded next to PabC, 4-amino-4-deoxychorismate lyase, in Escherichia coli and numerous other proteobacteria, but that proximity is not conserved in other lineages. Numerous members of this family have been misannotated as aminodeoxychorismate lyase, apparently because of promiximty to PabC. The structure of Swiss:P28306 was solved by X-ray crystallography. This group represents an uncharacterised protein family UPF0755.; PDB: 2R1F_B.
Probab=23.06 E-value=83 Score=30.43 Aligned_cols=18 Identities=11% Similarity=0.082 Sum_probs=12.2
Q ss_pred cceEEEcCCCcHHHHHHH
Q 018290 107 VPVYTVKKDDGLDFIART 124 (358)
Q Consensus 107 ~~~YtV~~GDTL~~IA~~ 124 (358)
...|.++++.++..|.+.
T Consensus 45 aG~Y~l~~~mS~~eil~~ 62 (297)
T PF02618_consen 45 AGTYELNPGMSYKEILSI 62 (297)
T ss_dssp -EEEEE-TT--HHHHHHH
T ss_pred eeEEEeCCCCCHHHHHHH
Confidence 358999999999988877
No 95
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=22.68 E-value=79 Score=22.72 Aligned_cols=21 Identities=24% Similarity=0.303 Sum_probs=18.2
Q ss_pred hHHHHHHHhCCCHHHHhhhhC
Q 018290 181 SFALIAQKFGTDRDTLMKLNG 201 (358)
Q Consensus 181 TL~~IA~kygvt~~~L~~~N~ 201 (358)
++..+|+++|++...|..|=.
T Consensus 2 s~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 467899999999999998864
No 96
>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=22.51 E-value=49 Score=24.41 Aligned_cols=26 Identities=12% Similarity=0.344 Sum_probs=21.3
Q ss_pred EcCCCcHHHHHHHHhCCCccHHHHHHhcC
Q 018290 112 VKKDDGLDFIARTIFGQLLKYQKIVEANN 140 (358)
Q Consensus 112 V~~GDTL~~IA~~~ygglvs~~~L~~~N~ 140 (358)
..+|.++..+|++ || |+...|..|=.
T Consensus 20 ~~~g~sv~~va~~-~g--i~~~~l~~W~~ 45 (76)
T PF01527_consen 20 LESGESVSEVARE-YG--ISPSTLYNWRK 45 (76)
T ss_dssp HHHHCHHHHHHHH-HT--S-HHHHHHHHH
T ss_pred HHCCCceEeeecc-cc--cccccccHHHH
Confidence 3678999999999 99 99999988854
No 97
>PF12471 GTP_CH_N: GTP cyclohydrolase N terminal ; InterPro: IPR022163 This domain family is found in bacteria and eukaryotes, and is approximately 190 amino acids in length. This family is the N-terminal of GTP cyclohydrolase, the rate limiting enzyme in the synthesis of tetrahydrobiopterin.
Probab=22.38 E-value=55 Score=29.59 Aligned_cols=59 Identities=17% Similarity=0.169 Sum_probs=33.3
Q ss_pred ccHHHHHHhcCCCCCCccCCCcEEEECCCCCcCCCCccccceeeeeeecCChHHHHHHHhCCCHHHHhhh
Q 018290 130 LKYQKIVEANNISNPDLIQIGQNLTIPLPCSCDDVDNAKVVHYAHVVEEGSSFALIAQKFGTDRDTLMKL 199 (358)
Q Consensus 130 vs~~~L~~~N~l~~~~~L~~Gq~L~IP~~~~~~~~~~~~~~~~~Y~V~~GDTL~~IA~kygvt~~~L~~~ 199 (358)
+.+.+|.++=. ...|.+.-++.++.... .....--|.+==-|-.||+|||+++.+|++.
T Consensus 132 ~~lpEi~eav~---~GrL~~DGki~~~~~g~--------~~VTK~AvEPVWyLPGVA~RFGi~E~~LRR~ 190 (194)
T PF12471_consen 132 MKLPEIREAVR---KGRLVPDGKIVLNSNGD--------LAVTKAAVEPVWYLPGVAERFGISEGELRRA 190 (194)
T ss_pred cCcHHHHHHHH---hCCCCCCCeEEecCCCc--------EEEEEEEecccccchhhHHHcCCCHHHHHHH
Confidence 55556655422 24677777777763210 0001112222223568999999999999863
No 98
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=20.92 E-value=88 Score=25.87 Aligned_cols=25 Identities=12% Similarity=-0.027 Sum_probs=21.9
Q ss_pred CCCCCCHHHHHHHhCCCcHHHHHhcC
Q 018290 46 PPNKTTISEIQSLFTVKNLRSILGAN 71 (358)
Q Consensus 46 V~~GdTL~~IA~~fgvs~l~~L~~~N 71 (358)
+..|.++.+||+.|||+. ..|..|=
T Consensus 26 ~~~g~sv~evA~e~gIs~-~tl~~W~ 50 (121)
T PRK09413 26 FEPGMTVSLVARQHGVAA-SQLFLWR 50 (121)
T ss_pred HcCCCCHHHHHHHHCcCH-HHHHHHH
Confidence 468999999999999995 8888884
No 99
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=20.81 E-value=1.1e+02 Score=20.37 Aligned_cols=24 Identities=25% Similarity=0.368 Sum_probs=20.2
Q ss_pred eecCChHHHHHHHhCCCHHHHhhh
Q 018290 176 VEEGSSFALIAQKFGTDRDTLMKL 199 (358)
Q Consensus 176 V~~GDTL~~IA~kygvt~~~L~~~ 199 (358)
+..|.+...||+.+|++...+...
T Consensus 15 ~~~g~s~~eia~~l~is~~tv~~~ 38 (58)
T smart00421 15 LAEGLTNKEIAERLGISEKTVKTH 38 (58)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHH
Confidence 357889999999999999887654
No 100
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.71 E-value=1e+02 Score=20.47 Aligned_cols=21 Identities=19% Similarity=0.191 Sum_probs=18.1
Q ss_pred hHHHHHHHhCCCHHHHhhhhC
Q 018290 181 SFALIAQKFGTDRDTLMKLNG 201 (358)
Q Consensus 181 TL~~IA~kygvt~~~L~~~N~ 201 (358)
++..+|+.+|++...|..|-.
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~~ 22 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYER 22 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHHH
Confidence 467899999999999998853
No 101
>PF13693 HTH_35: Winged helix-turn-helix DNA-binding; PDB: 1NEQ_A 1NER_A.
Probab=20.58 E-value=96 Score=24.10 Aligned_cols=23 Identities=9% Similarity=0.156 Sum_probs=16.0
Q ss_pred CCCCCHHHHHHHhCCCcHHHHHhc
Q 018290 47 PNKTTISEIQSLFTVKNLRSILGA 70 (358)
Q Consensus 47 ~~GdTL~~IA~~fgvs~l~~L~~~ 70 (358)
++|.||.+||..+|++. ..|..+
T Consensus 13 krG~sL~~lsr~~Gl~~-~tl~na 35 (78)
T PF13693_consen 13 KRGTSLAALSREAGLSS-STLRNA 35 (78)
T ss_dssp TTS--HHHHHHHHSS-H-HHHHHT
T ss_pred HcCCCHHHHHHHcCCCH-HHHHHH
Confidence 68999999999999995 665443
No 102
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=20.51 E-value=1e+02 Score=20.97 Aligned_cols=21 Identities=24% Similarity=0.466 Sum_probs=17.5
Q ss_pred CChHHHHHHHhCCCHHHHhhh
Q 018290 179 GSSFALIAQKFGTDRDTLMKL 199 (358)
Q Consensus 179 GDTL~~IA~kygvt~~~L~~~ 199 (358)
.-|+..||+.+|++.+.+.++
T Consensus 27 ~~s~~~vA~~~~vs~~TV~ri 47 (52)
T PF13542_consen 27 SRSFKDVARELGVSWSTVRRI 47 (52)
T ss_pred cCCHHHHHHHHCCCHHHHHHH
Confidence 348999999999999887653
Done!