Query gi|254781079|ref|YP_003065492.1| diguanylate cyclase [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 266
No_of_seqs 128 out of 12768
Neff 8.5
Searched_HMMs 39220
Date Tue May 31 16:01:14 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254781079.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10245 adrA diguanylate cycl 100.0 4.6E-39 1.2E-43 317.4 24.9 179 78-258 184-370 (371)
2 PRK09581 pleD response regulat 100.0 5E-40 1.3E-44 324.7 15.8 167 93-259 281-456 (457)
3 PRK09894 hypothetical protein; 100.0 2.7E-38 7E-43 311.5 17.0 165 97-262 123-292 (293)
4 PRK09966 hypothetical protein; 100.0 2.7E-37 6.9E-42 303.9 22.0 166 90-256 234-406 (407)
5 PRK13561 putative phosphodiest 100.0 1.2E-37 3E-42 306.6 19.1 175 87-263 214-392 (651)
6 PRK10060 RNase II stability mo 100.0 1.1E-38 2.8E-43 314.5 13.2 171 91-263 224-400 (663)
7 PRK11359 cAMP phosphodiesteras 100.0 1.5E-36 3.8E-41 298.3 14.4 169 92-263 364-535 (799)
8 PRK09776 putative sensor prote 100.0 2.3E-36 5.8E-41 296.8 14.0 168 92-260 676-851 (1116)
9 COG3706 PleD Response regulato 100.0 2.3E-33 5.8E-38 273.9 15.2 169 91-259 257-434 (435)
10 PRK11059 regulatory protein Cs 100.0 1.8E-31 4.5E-36 259.5 18.4 159 100-260 224-391 (642)
11 smart00267 GGDEF diguanylate c 100.0 1.3E-30 3.4E-35 252.8 13.3 155 102-258 1-163 (163)
12 COG2199 c-di-GMP synthetase (d 100.0 8E-30 2E-34 246.9 14.5 164 93-258 9-181 (181)
13 pfam00990 GGDEF GGDEF domain. 100.0 1.8E-29 4.6E-34 244.2 12.4 151 104-254 1-159 (159)
14 PRK11829 biofilm formation reg 100.0 1.7E-27 4.3E-32 229.2 16.1 184 79-264 272-466 (728)
15 cd01949 GGDEF Diguanylate-cycl 100.0 3.1E-28 7.8E-33 234.8 10.4 150 105-256 1-158 (158)
16 COG5001 Predicted signal trans 100.0 6.2E-26 1.6E-30 217.2 21.0 161 101-264 225-395 (663)
17 TIGR00254 GGDEF diguanylate cy 99.9 9.3E-23 2.4E-27 193.0 9.6 158 101-258 2-170 (171)
18 COG3887 Predicted signaling pr 98.3 0.00012 2.9E-09 55.0 16.1 133 126-264 172-305 (655)
19 cd07556 Nucleotidyl_cyc_III Cl 97.2 0.00041 1E-08 50.8 3.7 98 128-225 1-99 (133)
20 COG1353 Predicted CRISPR-assoc 96.5 0.023 5.8E-07 37.5 8.5 79 175-261 591-670 (799)
21 PRK02240 GTP cyclohydrolase II 96.1 0.025 6.5E-07 37.2 6.5 112 128-255 134-247 (254)
22 pfam05165 GGDN GGDN family. I 95.5 0.047 1.2E-06 35.1 6.0 114 127-256 126-241 (246)
23 TIGR02578 cas_TM1811_Csm1 CRIS 95.4 0.059 1.5E-06 34.4 6.3 123 125-251 289-450 (802)
24 TIGR02577 cas_TM1794_Crm2 CRIS 94.4 0.09 2.3E-06 32.9 5.1 79 171-249 566-665 (665)
25 TIGR02578 cas_TM1811_Csm1 CRIS 93.5 0.25 6.5E-06 29.5 5.8 116 126-249 651-802 (802)
26 cd07302 CHD cyclase homology d 92.5 0.2 5.1E-06 30.3 4.2 130 128-260 1-145 (177)
27 pfam00211 Guanylate_cyc Adenyl 92.3 0.18 4.6E-06 30.7 3.7 100 126-225 6-112 (186)
28 COG2429 Archaeal GTP cyclohydr 92.2 0.46 1.2E-05 27.5 5.7 84 157-256 162-245 (250)
29 PRK02240 GTP cyclohydrolase II 91.2 0.96 2.5E-05 25.1 6.5 115 131-262 4-126 (254)
30 PRK11477 carbohydrate diacid t 90.1 1.6 4E-05 23.5 15.0 132 116-262 147-290 (385)
31 smart00044 CYCc Adenylyl- / gu 89.2 0.35 8.9E-06 28.5 2.9 130 126-258 34-178 (194)
32 cd01700 Pol_V Pol V was discov 84.8 1.2 3.1E-05 24.4 3.6 24 229-252 310-333 (344)
33 PRK03352 DNA polymerase IV; Va 84.1 0.76 1.9E-05 25.9 2.3 18 229-246 308-325 (345)
34 cd03586 Pol_IV_kappa Pol_IV_ka 83.6 1.2 3E-05 24.4 3.1 24 229-252 302-325 (337)
35 PRK03609 umuC DNA polymerase V 81.4 2.3 6E-05 22.2 3.9 24 240-263 373-397 (422)
36 PRK03858 DNA polymerase IV; Va 80.2 1.7 4.4E-05 23.2 2.9 14 188-201 308-321 (398)
37 COG3835 CdaR Sugar diacid util 78.7 4.9 0.00012 19.7 15.1 141 105-262 133-281 (376)
38 PRK03103 DNA polymerase IV; Re 77.1 4.3 0.00011 20.2 4.2 15 241-255 371-386 (410)
39 PRK01810 DNA polymerase IV; Va 77.0 1.6 4.2E-05 23.3 2.0 29 144-172 252-285 (410)
40 cd01701 Pol_zeta Pol_zeta, a m 76.2 1.8 4.6E-05 23.1 2.0 15 231-245 372-386 (405)
41 PRK01216 DNA polymerase IV; Va 74.4 2.4 6.2E-05 22.0 2.3 21 230-250 304-324 (351)
42 PRK02406 DNA polymerase IV; Va 73.6 2.7 6.9E-05 21.7 2.4 16 231-246 311-326 (355)
43 cd00424 Pol_Y Y-family of DNA 73.2 2.1 5.2E-05 22.6 1.7 17 231-247 308-324 (341)
44 PRK02794 DNA polymerase IV; Pr 73.0 4 0.0001 20.4 3.2 19 239-257 393-412 (417)
45 COG2114 CyaA Adenylate cyclase 70.7 7.5 0.00019 18.3 5.6 132 127-261 45-182 (227)
46 pfam00817 IMS impB/mucB/samB f 61.6 5.4 0.00014 19.4 1.9 62 155-227 76-139 (148)
47 PRK08134 O-acetylhomoserine am 59.6 12 0.0003 16.8 7.4 94 126-251 339-432 (433)
48 TIGR00004 TIGR00004 endoribonu 55.5 2.4 6E-05 22.1 -0.7 47 105-151 33-97 (129)
49 PRK09509 fieF ferrous iron eff 52.6 9.6 0.00024 17.5 2.0 68 140-207 200-275 (300)
50 COG0053 MMT1 Predicted Co/Zn/C 49.3 17 0.00043 15.6 6.9 106 102-207 154-277 (304)
51 PRK05066 arginine repressor; P 48.6 15 0.00038 16.0 2.4 48 157-205 107-154 (156)
52 cd01703 Pol_iota Pol iota is m 48.0 11 0.00028 17.1 1.7 13 191-203 297-309 (394)
53 PTZ00205 DNA polymerase kappa; 45.4 11 0.00028 17.0 1.4 62 156-226 207-274 (571)
54 KOG2095 consensus 44.3 12 0.00031 16.7 1.5 18 144-162 294-311 (656)
55 COG1902 NemA NADH:flavin oxido 41.4 10 0.00025 17.4 0.6 59 143-202 188-249 (363)
56 PRK05506 bifunctional sulfate 40.2 20 0.00051 15.0 2.0 88 104-193 443-555 (613)
57 cd02930 DCR_FMN 2,4-dienoyl-Co 36.1 16 0.0004 15.9 1.0 56 143-200 176-234 (353)
58 cd01127 TrwB Bacterial conjuga 35.9 11 0.00028 17.1 0.1 12 136-147 306-317 (410)
59 KOG3330 consensus 35.4 22 0.00056 14.7 1.6 19 175-193 100-118 (183)
60 PRK07503 methionine gamma-lyas 35.0 27 0.00069 14.1 9.2 118 101-250 278-400 (403)
61 COG0404 GcvT Glycine cleavage 35.0 23 0.00059 14.6 1.7 59 130-189 47-121 (379)
62 COG0529 CysC Adenylylsulfate k 34.7 27 0.0007 14.0 2.6 87 105-193 24-135 (197)
63 cd01702 Pol_eta Pol eta is mem 33.3 11 0.00028 17.1 -0.2 22 230-251 320-341 (358)
64 PRK13665 hypothetical protein; 32.9 29 0.00074 13.8 2.5 91 167-262 167-263 (327)
65 cd03133 GATase1_ES1 Type 1 glu 32.5 30 0.00075 13.8 2.3 63 122-187 26-91 (213)
66 cd02803 OYE_like_FMN_family Ol 32.4 20 0.0005 15.1 1.0 56 143-200 180-238 (327)
67 PRK08249 cystathionine gamma-s 32.3 30 0.00076 13.8 8.9 118 101-250 275-397 (398)
68 PRK11780 isoprenoid biosynthes 31.8 30 0.00077 13.7 2.3 62 122-186 29-93 (217)
69 TIGR01078 arcA arginine deimin 31.5 31 0.00078 13.7 1.9 61 172-241 218-287 (421)
70 PRK08861 cystathionine gamma-s 30.6 32 0.00081 13.6 6.6 108 111-250 280-387 (388)
71 cd02932 OYE_YqiM_FMN Old yello 30.5 23 0.00059 14.6 1.1 55 143-200 193-251 (336)
72 pfam06675 DUF1177 Protein of u 30.4 32 0.00081 13.5 4.6 34 231-264 225-258 (276)
73 PRK05968 hypothetical protein; 29.1 33 0.00085 13.4 3.3 63 171-249 327-389 (389)
74 PRK08776 cystathionine gamma-s 28.9 34 0.00085 13.4 9.2 118 101-250 272-394 (405)
75 PRK08064 cystathionine beta-ly 28.7 34 0.00086 13.3 9.2 108 111-251 280-387 (390)
76 pfam12127 YdfA_immunity SigmaW 27.8 35 0.00089 13.2 3.0 91 167-262 166-262 (321)
77 PRK08248 O-acetylhomoserine am 27.4 35 0.0009 13.2 6.5 92 126-249 339-430 (431)
78 TIGR02630 xylose_isom_A xylose 27.4 36 0.00091 13.2 3.9 37 222-258 150-186 (437)
79 pfam01053 Cys_Met_Meta_PP Cys/ 27.1 36 0.00091 13.1 8.5 111 101-244 265-380 (381)
80 pfam10975 DUF2802 Protein of u 26.5 37 0.00094 13.0 4.0 35 84-118 5-39 (70)
81 cd04734 OYE_like_3_FMN Old yel 26.2 30 0.00078 13.7 1.1 56 143-200 180-238 (343)
82 PRK03341 arginine repressor; P 26.1 37 0.00095 13.0 2.4 46 157-204 121-166 (168)
83 PRK00441 argR arginine repress 25.7 38 0.00096 13.0 2.2 44 158-203 105-148 (149)
84 TIGR01522 ATPase-IIA2_Ca calci 25.2 30 0.00077 13.7 0.9 12 240-251 528-539 (856)
85 PRK13523 NADPH dehydrogenase N 25.2 33 0.00084 13.4 1.1 55 143-200 181-237 (337)
86 TIGR02854 spore_II_GA sigma-E 24.7 39 0.001 12.8 7.2 12 131-142 214-225 (320)
87 pfam08265 YL1_C YL1 nuclear pr 24.6 24 0.0006 14.5 0.3 15 104-118 11-27 (30)
88 PRK08133 O-succinylhomoserine 24.5 40 0.001 12.8 8.4 113 101-245 273-390 (391)
89 TIGR02823 oxido_YhdH putative 24.4 39 0.00099 12.9 1.3 44 149-193 79-123 (330)
90 PRK04280 arginine repressor; P 24.3 40 0.001 12.8 1.8 43 158-202 106-148 (149)
91 PRK12495 hypothetical protein; 24.1 22 0.00056 14.8 0.0 28 159-186 38-66 (221)
92 KOG4032 consensus 23.7 35 0.0009 13.2 1.0 35 169-203 67-101 (184)
93 TIGR01363 strep_his_triad stre 23.0 42 0.0011 12.6 4.4 141 96-253 33-195 (376)
94 smart00594 UAS UAS domain. 22.4 43 0.0011 12.5 2.2 29 172-200 55-83 (122)
95 cd02929 TMADH_HD_FMN Trimethyl 22.2 30 0.00078 13.7 0.4 39 143-181 189-230 (370)
96 PRK07360 FO synthase subunit 2 22.0 44 0.0011 12.4 1.7 29 229-261 343-371 (375)
97 PRK13700 conjugal transfer pro 22.0 19 0.00049 15.2 -0.6 14 190-203 331-344 (732)
98 cd03313 enolase Enolase: Enola 21.7 36 0.00092 13.1 0.7 23 231-257 340-362 (408)
99 pfam02863 Arg_repressor_C Argi 21.6 45 0.0011 12.4 1.9 44 156-201 26-69 (70)
100 PRK00077 eno phosphopyruvate h 21.5 30 0.00077 13.7 0.3 31 136-166 293-326 (427)
101 COG0841 AcrB Cation/multidrug 21.0 46 0.0012 12.3 6.2 23 229-251 666-688 (1009)
102 cd04733 OYE_like_2_FMN Old yel 20.7 37 0.00095 13.0 0.6 56 143-200 188-246 (338)
103 TIGR01017 rpsD_bact ribosomal 20.7 25 0.00064 14.3 -0.3 31 139-176 80-110 (217)
104 PRK10775 cell division protein 20.5 47 0.0012 12.2 1.6 57 123-179 80-136 (274)
105 PRK08045 cystathionine gamma-s 20.4 47 0.0012 12.2 8.9 107 111-249 279-385 (386)
106 PRK12677 xylose isomerase; Pro 20.3 47 0.0012 12.2 5.0 12 227-238 343-354 (389)
No 1
>PRK10245 adrA diguanylate cyclase AdrA; Provisional
Probab=100.00 E-value=4.6e-39 Score=317.35 Aligned_cols=179 Identities=31% Similarity=0.486 Sum_probs=160.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHCCCCHHHHHHHHH-------HCCCCEEEEEEECCCCCCCCCCCCCCC
Q ss_conf 9999999999999999999999999961040105020489998887-------708972575544221000114688654
Q gi|254781079|r 78 ISLLLGYISGSILKELFISYNRISQLSRIDCLSGLLNHSAFISSLG-------SYNEKLSIVFFDIDYFKQINDNFGHPV 150 (266)
Q Consensus 78 ~~~~~~~~~~~~~~~l~~~~~~l~~~a~~D~LTgL~NR~~f~~~l~-------~~~~~~~l~~idid~fk~iNd~~G~~~ 150 (266)
....++........++.+.+++|++++.+||||||+||++|+++++ ++++++++++||||+||.|||+|||++
T Consensus 184 y~l~~~~~~~~~a~~L~e~~r~Le~LA~tD~LTGL~NRR~f~~~L~~el~~a~R~~~~~aLllIDID~FK~INDtyGH~~ 263 (371)
T PRK10245 184 YPLLFGWVSYQTATKLAEHKRRLQVMSTRDGMTGVYNRRHWETMLRNEFDNCRRHNRDATLLIIDIDHFKSINDTWGHDV 263 (371)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEECCCCHHHHHCCCHHH
T ss_conf 99999999999999999999999999583600035459999999999999999649988999886335058886878489
Q ss_pred CCCCCCHHHCCCCCCCCCCHHHCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEECC-C
Q ss_conf 443110000000111110000001334303650168610123444589999986315406799568999999998779-9
Q gi|254781079|r 151 GDKVIAFLSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERC-H 229 (266)
Q Consensus 151 gD~~L~~va~~l~~~~~~~~~~~R~~gdeF~ill~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~t~s~Gia~~~-~ 229 (266)
||++|+++|++|+..++++|+++|+|||||+|++|+++.+++...++++++.+.... ...+..+.+|+|+|++.++ +
T Consensus 264 GD~vL~~vA~~L~~~lr~~DivaR~GGDEF~VLL~~~~~e~a~~~~~rl~~~l~~~~--~~~~~~i~lTiSiGIA~~~~~ 341 (371)
T PRK10245 264 GDEAIVALTRQLQITLRGSDVIGRFGGDEFAVIMSGTPAESAITAMLRVHEGLNTLR--LPNAPQVTLRISVGVAPLNPQ 341 (371)
T ss_pred HHHHHHHHHHHHHHHCCCCCEEEECCCCEEEEEECCCCHHHHHHHHHHHHHHHHCCC--CCCCCEEEEEEEEEEEECCCC
T ss_conf 999999999999986898788961588669999589996999999999999971636--689986999999999971699
Q ss_pred CCCHHHHHHHHHHHHHHHHHCCCCEEEEC
Q ss_conf 89989999999999999997099689994
Q gi|254781079|r 230 KEPISTIIYRADQALYVAKKSGRNRVVCF 258 (266)
Q Consensus 230 ~~~~~~ll~~Ad~Al~~AK~~gkn~~~~~ 258 (266)
+.+.++++++||.|||+||++|||||++-
T Consensus 342 ~~~~~eLL~~AD~ALY~AK~~GRNRVeVA 370 (371)
T PRK10245 342 MSHYREWLKSADLALYKAKKAGRNRTEVA 370 (371)
T ss_pred CCCHHHHHHHHHHHHHHHHHHCCCEEEEC
T ss_conf 99999999999999999998189969971
No 2
>PRK09581 pleD response regulator PleD; Reviewed
Probab=100.00 E-value=5e-40 Score=324.71 Aligned_cols=167 Identities=35% Similarity=0.545 Sum_probs=149.6
Q ss_pred HHHHHHHHHHHHHCCCHHCCCCHHHHHHHHH-------HCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCCC
Q ss_conf 9999999999961040105020489998887-------708972575544221000114688654443110000000111
Q gi|254781079|r 93 LFISYNRISQLSRIDCLSGLLNHSAFISSLG-------SYNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVV 165 (266)
Q Consensus 93 l~~~~~~l~~~a~~D~LTgL~NR~~f~~~l~-------~~~~~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~~~ 165 (266)
+....++..++|++|+|||||||++|.++++ +++++++++++|||+||.|||+|||.+||++|++||++|+.+
T Consensus 281 lr~~~~~~~~lA~~D~LTgL~NR~~f~~~L~~~~~~a~r~~~~~all~lDlD~FK~INDt~GH~~GD~lL~~vA~rL~~~ 360 (457)
T PRK09581 281 LRQNLEQSIEMAVTDGLTGLHNRRYFDMHLKQLIERANERGKPLSLMMLDIDHFKQVNDTYGHDAGDEVLREFAKRLRKN 360 (457)
T ss_pred HHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEECCCCCHHHHCCCCHHHHHHHHHHHHHHHHH
T ss_conf 99989999987365876671319999999999999999759938999998877428887669537799999999999987
Q ss_pred CCCCHHHCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCC-CEEEEEEEEEEEECC-CCCCHHHHHHHHHHH
Q ss_conf 110000001334303650168610123444589999986315406799-568999999998779-989989999999999
Q gi|254781079|r 166 FGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSG-PSIHITISAGIAERC-HKEPISTIIYRADQA 243 (266)
Q Consensus 166 ~~~~~~~~R~~gdeF~ill~~~~~~~~~~~~~~l~~~l~~~~~~~~~~-~~~~~t~s~Gia~~~-~~~~~~~ll~~Ad~A 243 (266)
+|+.|++||+|||||+|++|+++.+++..++++|+..+.+.++...++ ..+++|+|+||+.++ +++++++++++||.|
T Consensus 361 ~R~~D~vaR~GGDEF~ilL~~~~~~~a~~vaeri~~~i~~~pf~~~~~~~~i~vT~SiGia~~~~~~~~~~~Ll~~AD~A 440 (457)
T PRK09581 361 IRGTDLIARYGGEEFVVVMPDTDIEVAIAVAERIRRKIAEEPFAISDGKERLNVTVSIGVAELRPSGESIEALIKRADKA 440 (457)
T ss_pred CCCCCEEEEECCEEEEEEECCCCHHHHHHHHHHHHHHHHCCCCEECCCCEEEEEEEEEEEEECCCCCCCHHHHHHHHHHH
T ss_conf 69877999615706899978999999999999999999747945548988999999999997479989899999999999
Q ss_pred HHHHHHCCCCEEEECC
Q ss_conf 9999970996899940
Q gi|254781079|r 244 LYVAKKSGRNRVVCFS 259 (266)
Q Consensus 244 l~~AK~~gkn~~~~~~ 259 (266)
||+||++||||||.-+
T Consensus 441 mY~AK~~GRNrVv~~~ 456 (457)
T PRK09581 441 LYEAKNTGRNRVVALA 456 (457)
T ss_pred HHHHHHHCCCEEEECC
T ss_conf 9999962999699667
No 3
>PRK09894 hypothetical protein; Provisional
Probab=100.00 E-value=2.7e-38 Score=311.49 Aligned_cols=165 Identities=32% Similarity=0.480 Sum_probs=151.0
Q ss_pred HHHHHHHHHCCCHHCCCCHHHHHHHHHH-----CCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCHH
Q ss_conf 9999999610401050204899988877-----08972575544221000114688654443110000000111110000
Q gi|254781079|r 97 YNRISQLSRIDCLSGLLNHSAFISSLGS-----YNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFGTPMF 171 (266)
Q Consensus 97 ~~~l~~~a~~D~LTgL~NR~~f~~~l~~-----~~~~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~~~~~~~~~ 171 (266)
...++.+|.+|||||||||++|.+.+++ .+++++++++|||+||.|||+|||.+||++|+.+|++|+..+++++.
T Consensus 123 ~~~~~~~A~~D~LTGL~NRr~f~e~le~~l~~~~~~~~allliDiD~FK~IND~~GH~~GD~vL~~vA~~L~~~lr~~d~ 202 (293)
T PRK09894 123 IYLLTIRSNMDVLTGLPGRRVLDESFDHQLRNREPLNLYLALLDIDRFKLVNDTYGHLIGDVVLRTLATYLASWTRPYET 202 (293)
T ss_pred HHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCE
T ss_conf 99998870888534815489999999999985679977999997856637775878588999999999999985898788
Q ss_pred HCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHCC
Q ss_conf 00133430365016861012344458999998631540679956899999999877998998999999999999999709
Q gi|254781079|r 172 VGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERCHKEPISTIIYRADQALYVAKKSG 251 (266)
Q Consensus 172 ~~R~~gdeF~ill~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~t~s~Gia~~~~~~~~~~ll~~Ad~Al~~AK~~g 251 (266)
++|+|||||+|++|+.+.+++..++++++..+.+.++.. ++..+.+|+|+|++.++++.++++++++||.|||+||++|
T Consensus 203 vaR~GGDEF~ill~~~~~~~a~~~aeri~~~i~~~~~~~-~~~~i~it~SiGia~~~~~~~~e~Ll~~AD~ALY~AK~~G 281 (293)
T PRK09894 203 VYRYGGEEFIIILKAATDEEACRAGERIRQLIANQAITH-SEGRINITATFGVTRAFPEEPLDEVIGRADRAMYEGKQAG 281 (293)
T ss_pred EEEECCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCEEE-CCEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHCC
T ss_conf 997079658998489999999999999999997189556-8988999999999988999999999999999999999808
Q ss_pred CCEEEECCHHH
Q ss_conf 96899940210
Q gi|254781079|r 252 RNRVVCFSDIE 262 (266)
Q Consensus 252 kn~~~~~~~~~ 262 (266)
||+|++|++-+
T Consensus 282 RNrv~ffdee~ 292 (293)
T PRK09894 282 RNRVMFIDEQN 292 (293)
T ss_pred CCEEEEECCCC
T ss_conf 99899970896
No 4
>PRK09966 hypothetical protein; Provisional
Probab=100.00 E-value=2.7e-37 Score=303.89 Aligned_cols=166 Identities=28% Similarity=0.421 Sum_probs=148.9
Q ss_pred HHHHHHHHHHHHHHHHCCCHHCCCCHHHHHHHHHHC------CCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCC
Q ss_conf 999999999999996104010502048999888770------89725755442210001146886544431100000001
Q gi|254781079|r 90 LKELFISYNRISQLSRIDCLSGLLNHSAFISSLGSY------NEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLV 163 (266)
Q Consensus 90 ~~~l~~~~~~l~~~a~~D~LTgL~NR~~f~~~l~~~------~~~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~ 163 (266)
..+++..+++|.++|+||||||||||++|.+++++. .++.+++++|||+||.|||+|||.+||++|+.+|++|+
T Consensus 234 q~~L~~~n~qL~~~A~hD~LTGLpNR~~F~~~L~~~l~~~~~~~~~All~iDlD~FK~IND~~GH~~GD~vL~~vA~rL~ 313 (407)
T PRK09966 234 QLRLQAKNAQLLRTALHDPLTGLANRAAFRSGINTLMNNSDARKTSALLFLDGDNFKYINDTWGHATGDRVLIEIAKRLA 313 (407)
T ss_pred HHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf 99999999999886594003063679999999999998652389738999987246676767485689999999999999
Q ss_pred CCCCCCHHHCCCCCCEEEEECCCC-CHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEECCCCCCHHHHHHHHHH
Q ss_conf 111100000013343036501686-1012344458999998631540679956899999999877998998999999999
Q gi|254781079|r 164 VVFGTPMFVGRLGGEEFAAAALGS-SEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERCHKEPISTIIYRADQ 242 (266)
Q Consensus 164 ~~~~~~~~~~R~~gdeF~ill~~~-~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~t~s~Gia~~~~~~~~~~ll~~Ad~ 242 (266)
..+++.+.++|+|||||++++|+. ++.++..+++++.+.+.. ++...++..+.+|+|+|++.++++.++++++++||.
T Consensus 314 ~~~~~~d~vaR~GGDEF~ill~~~~~~~~~~~~~~~l~~~~~~-p~~~~~g~~i~it~SIGia~~~~~~~~~~Ll~~AD~ 392 (407)
T PRK09966 314 EFGGLRHKAYRLGGDEFAMVLYDVQSESEVQQICSALTQIFNL-PFDLHNGHQTTMTLSIGYAMTIEHASAEKLQELADH 392 (407)
T ss_pred HHCCCCCEEEEECHHHHHEEECCCCCHHHHHHHHHHHHHHHHC-CEECCCCCEEEEEEEEEEEECCCCCCHHHHHHHHHH
T ss_conf 8469879898531121412268999999999999999999716-856169958999999999978999799999999999
Q ss_pred HHHHHHHCCCCEEE
Q ss_conf 99999970996899
Q gi|254781079|r 243 ALYVAKKSGRNRVV 256 (266)
Q Consensus 243 Al~~AK~~gkn~~~ 256 (266)
|||+||++|+||++
T Consensus 393 AmY~AK~qr~~R~v 406 (407)
T PRK09966 393 NMYQAKHQRAEKLV 406 (407)
T ss_pred HHHHHHHCCCCCCC
T ss_conf 99999846898768
No 5
>PRK13561 putative phosphodiesterase; Provisional
Probab=100.00 E-value=1.2e-37 Score=306.64 Aligned_cols=175 Identities=17% Similarity=0.206 Sum_probs=157.8
Q ss_pred HHHHHHHHHHHHHHHHHHHCCCHHCCCCHHHHHHHHHHC---CCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCC
Q ss_conf 999999999999999996104010502048999888770---89725755442210001146886544431100000001
Q gi|254781079|r 87 GSILKELFISYNRISQLSRIDCLSGLLNHSAFISSLGSY---NEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLV 163 (266)
Q Consensus 87 ~~~~~~l~~~~~~l~~~a~~D~LTgL~NR~~f~~~l~~~---~~~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~ 163 (266)
+.+..++.+..+++++.+++|||||||||++|.++++++ +++++++++|+|+||.|||++||++||++|+++|++|+
T Consensus 214 N~~~~~l~~~~e~l~~~a~~DplTgLpNR~~f~~~L~~~l~~~~~~all~idld~fk~iNd~lGh~~GD~LL~~vA~rL~ 293 (651)
T PRK13561 214 NLNQQLLQRHYEEQNENAMRFPVSDLPNKALLMALLEQVVARKQTTALMIITCETLRDTAGVLKEAQREILLLTLVEKLK 293 (651)
T ss_pred HHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEEEHHHHHHHHHHHCHHHHHHHHHHHHHHHH
T ss_conf 99999999999999987310865699638999999999983688753999970457888763245779999999999999
Q ss_pred CCCCCCHHHCCCCCCEEEEECCCC-CHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEECCCCCCHHHHHHHHHH
Q ss_conf 111100000013343036501686-1012344458999998631540679956899999999877998998999999999
Q gi|254781079|r 164 VVFGTPMFVGRLGGEEFAAAALGS-SEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERCHKEPISTIIYRADQ 242 (266)
Q Consensus 164 ~~~~~~~~~~R~~gdeF~ill~~~-~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~t~s~Gia~~~~~~~~~~ll~~Ad~ 242 (266)
.++++++.+||+|||||++++|+. +++++..++++|...+.++ ...++..+.+++|+|++.++++.++++|+++||.
T Consensus 294 ~~l~~~~~lARlgGDEF~ill~~~~~~~~a~~la~~i~~~l~~p--~~~~~~~~~~~aSIGia~~~~~~~~~~LL~~AD~ 371 (651)
T PRK13561 294 SVLSPRMVLAQISGYDFAIIANGVKEPWHAITLGQQVLTIINER--LPIQRIQLRPSCSIGIAMFYGDLTAEQLYSRAVS 371 (651)
T ss_pred HHCCCCCEEEEECCCEEEEEECCCCCHHHHHHHHHHHHHHHHCC--EECCCEEEEEEEEEEEEECCCCCCHHHHHHHHHH
T ss_conf 63798878997258679999489998699999999999998275--3358805841478999967999899999999999
Q ss_pred HHHHHHHCCCCEEEECCHHHC
Q ss_conf 999999709968999402100
Q gi|254781079|r 243 ALYVAKKSGRNRVVCFSDIEN 263 (266)
Q Consensus 243 Al~~AK~~gkn~~~~~~~~~~ 263 (266)
|||+||++|||++++|+.-.+
T Consensus 372 Amy~AK~~G~n~~~~f~~~~~ 392 (651)
T PRK13561 372 AAFTARRKGKNQIQFFDPQQM 392 (651)
T ss_pred HHHHHHHCCCCEEEEECHHHH
T ss_conf 999999829973999783668
No 6
>PRK10060 RNase II stability modulator; Provisional
Probab=100.00 E-value=1.1e-38 Score=314.50 Aligned_cols=171 Identities=28% Similarity=0.405 Sum_probs=154.9
Q ss_pred HHHHHHHHHHHHHHHCCCHHCCCCHHHHHHHHHH-----CCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCCC
Q ss_conf 9999999999999610401050204899988877-----08972575544221000114688654443110000000111
Q gi|254781079|r 91 KELFISYNRISQLSRIDCLSGLLNHSAFISSLGS-----YNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVV 165 (266)
Q Consensus 91 ~~l~~~~~~l~~~a~~D~LTgL~NR~~f~~~l~~-----~~~~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~~~ 165 (266)
.+..+.+++++++|++|+|||||||.+|.+++++ .+++++|++||||+||.|||+|||++||++|++||++|+..
T Consensus 224 Te~k~~ee~l~~lA~~D~LTgLPNR~~~~~rL~~ai~~~~~~~~AvlfiDLD~FK~INDt~GH~~GD~lL~~vA~RL~~~ 303 (663)
T PRK10060 224 TEERRAQERLRILANTDSITGLPNRNAIQELIDHAIAQADNNQVGIVYLDLDNFKKVNDAYGHMFGDQLLQDVSLAILSC 303 (663)
T ss_pred CHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCHHHHCCCCHHHHHHHHHHHHHHHHH
T ss_conf 48999999999873677423866289999999999971769938999997867683446627088999999999999976
Q ss_pred CCCCHHHCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEECC-CCCCHHHHHHHHHHHH
Q ss_conf 110000001334303650168610123444589999986315406799568999999998779-9899899999999999
Q gi|254781079|r 166 FGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERC-HKEPISTIIYRADQAL 244 (266)
Q Consensus 166 ~~~~~~~~R~~gdeF~ill~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~t~s~Gia~~~-~~~~~~~ll~~Ad~Al 244 (266)
+++++.+||+|||||+|++|+.+.+++..++++|...+.. + ...++..+.+++|+||+.++ ++.++++|+++||.||
T Consensus 304 lr~~d~vARlGGDEFvvLl~~~~~~~~~~~a~ril~~l~~-P-~~i~~~~v~vsaSIGIa~~p~~~~~~~~Ll~~AD~Am 381 (663)
T PRK10060 304 LEEDQTLARLGGDEFLVLASHTSQAALEAMASRILTRLRL-P-FRIGLIEVYTGCSIGIALSPEHGDDSESLIRSADTAM 381 (663)
T ss_pred CCCCCEEEECCCCEEEEEECCCCHHHHHHHHHHHHHHHCC-C-EEECCEEEEEEEEEEEEECCCCCCCHHHHHHHHHHHH
T ss_conf 8998899854897899997789989999999999998506-8-7999999999889999980799999999999999999
Q ss_pred HHHHHCCCCEEEECCHHHC
Q ss_conf 9999709968999402100
Q gi|254781079|r 245 YVAKKSGRNRVVCFSDIEN 263 (266)
Q Consensus 245 ~~AK~~gkn~~~~~~~~~~ 263 (266)
|+||+.|||++++|++--+
T Consensus 382 y~AK~~Grn~~~~f~~~m~ 400 (663)
T PRK10060 382 YTAKEGGRGQFCVFSPEMN 400 (663)
T ss_pred HHHHHCCCCCCEEECHHHH
T ss_conf 9999708998166288999
No 7
>PRK11359 cAMP phosphodiesterase; Provisional
Probab=100.00 E-value=1.5e-36 Score=298.26 Aligned_cols=169 Identities=20% Similarity=0.278 Sum_probs=153.4
Q ss_pred HHHHHHHHHHHHHHCCCHHCCCCHHHHHHHHHH---CCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCC
Q ss_conf 999999999999610401050204899988877---08972575544221000114688654443110000000111110
Q gi|254781079|r 92 ELFISYNRISQLSRIDCLSGLLNHSAFISSLGS---YNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFGT 168 (266)
Q Consensus 92 ~l~~~~~~l~~~a~~D~LTgL~NR~~f~~~l~~---~~~~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~~~~~~ 168 (266)
+..+.+++++++|++|+|||||||++|.+++++ ...+.+++++|||+||.|||+|||.+||++|++||++|+.++|+
T Consensus 364 erk~~e~~L~~lA~~D~lTgl~nr~~~~~~l~~~~~~~~~~~~~~~d~d~fk~ind~~gh~~gd~~l~~~~~~l~~~~r~ 443 (799)
T PRK11359 364 EQEKSRQHIEQLIQFDPMTGLPNRNNLHNYLDDLVDKAVSPVVYLIGVDHIQDVIDSLGYAWADQALLEVVNRFREKLKP 443 (799)
T ss_pred HHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCHHHHCCCCHHHHHHHHHHHHHHHHHCCC
T ss_conf 99999999998747674248175999999999998358874899998757636776779737899999999999986799
Q ss_pred CHHHCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHH
Q ss_conf 00000133430365016861012344458999998631540679956899999999877998998999999999999999
Q gi|254781079|r 169 PMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERCHKEPISTIIYRADQALYVAK 248 (266)
Q Consensus 169 ~~~~~R~~gdeF~ill~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~t~s~Gia~~~~~~~~~~ll~~Ad~Al~~AK 248 (266)
+|+++|+|||||++++|+.+.+++..++++|+..+.. +...++..+.+|+|+||+. .++.+.++|+++||.|||+||
T Consensus 444 ~d~~~r~ggdeF~~~~~~~~~~~~~~~a~~i~~~~~~--~~~~~~~~~~~~~siGi~~-~~~~~~~~ll~~ad~A~~~ak 520 (799)
T PRK11359 444 DQYLCRIEGTQFVLVSLENDVSNITQIADELRNVVSK--PIMIDDKPFPLTLSIGISY-DVGKNRDYLLSTAHNAMDYIR 520 (799)
T ss_pred CCEEEEECCCEEEEEECCCCHHHHHHHHHHHHHHHCC--CEEECCEEEEEEEEEEEEC-CCCCCHHHHHHHHHHHHHHHH
T ss_conf 9889996487799996799989999999999997568--9999999999989999984-799999999999999999999
Q ss_pred HCCCCEEEECCHHHC
Q ss_conf 709968999402100
Q gi|254781079|r 249 KSGRNRVVCFSDIEN 263 (266)
Q Consensus 249 ~~gkn~~~~~~~~~~ 263 (266)
++|||++++|+...+
T Consensus 521 ~~g~~~~~~~~~~~~ 535 (799)
T PRK11359 521 KNGGNGWQFFSPAMN 535 (799)
T ss_pred HHCCCCEEECCHHHH
T ss_conf 808995686488899
No 8
>PRK09776 putative sensor protein; Provisional
Probab=100.00 E-value=2.3e-36 Score=296.84 Aligned_cols=168 Identities=28% Similarity=0.455 Sum_probs=152.7
Q ss_pred HHHHHHHHHHHHHHCCCHHCCCCHHHHHHHHHH-------CCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCC
Q ss_conf 999999999999610401050204899988877-------0897257554422100011468865444311000000011
Q gi|254781079|r 92 ELFISYNRISQLSRIDCLSGLLNHSAFISSLGS-------YNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVV 164 (266)
Q Consensus 92 ~l~~~~~~l~~~a~~D~LTgL~NR~~f~~~l~~-------~~~~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~~ 164 (266)
+.....++++++|+||+|||||||++|.+++++ .+++++++++|||+||.|||++||.+||++|+++|++|+.
T Consensus 676 ~~k~~~~~l~~~A~hD~LTgLpNR~~f~~~L~~~l~~~~~~~~~~al~~iDlD~Fk~iNd~~Gh~~GD~lL~~~a~rl~~ 755 (1116)
T PRK09776 676 ESRAMLRQLSYSASHDALTGLANRASFEKQLREALQTVNSTHQRHALVFIDLDRFKAVNDSAGHAAGDALLRELASLMLS 755 (1116)
T ss_pred HHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEEECHHHHHHHHHCCCCHHHHHHHHHHHHHHH
T ss_conf 99999999987544774348665999999999999999861992799999813213888702871678999999999997
Q ss_pred CCCCCHHHCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEECC-CCCCHHHHHHHHHHH
Q ss_conf 1110000001334303650168610123444589999986315406799568999999998779-989989999999999
Q gi|254781079|r 165 VFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERC-HKEPISTIIYRADQA 243 (266)
Q Consensus 165 ~~~~~~~~~R~~gdeF~ill~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~t~s~Gia~~~-~~~~~~~ll~~Ad~A 243 (266)
.++++|.++|+|||||++++++.+.+++..+++++.+.+.+.++. .++..+.+++|+||+.++ ++.++++++++||.|
T Consensus 756 ~~~~~d~~aR~ggdeF~ill~~~~~~~a~~ia~~i~~~i~~~~f~-~~~~~~~i~~SiGIa~~p~~~~~~~~Ll~~Ad~A 834 (1116)
T PRK09776 756 MLRSSDVLARLGGDEFGLLLPDCNVESARFIATRIISAINDYRFP-WEGRVYRVGASAGITAIDDNNHQASEVMSQADIA 834 (1116)
T ss_pred HCCCCCEEEEECCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCEE-ECCEEEEEEEEEEEEEECCCCCCHHHHHHHHHHH
T ss_conf 679898998315848999966999799999999999998578875-6898999899999998179999999999999999
Q ss_pred HHHHHHCCCCEEEECCH
Q ss_conf 99999709968999402
Q gi|254781079|r 244 LYVAKKSGRNRVVCFSD 260 (266)
Q Consensus 244 l~~AK~~gkn~~~~~~~ 260 (266)
||+||+.|||++.+|+.
T Consensus 835 my~AK~~Grn~~~~y~~ 851 (1116)
T PRK09776 835 CYAAKNAGRGRVTVYEP 851 (1116)
T ss_pred HHHHHHCCCCCEEEECC
T ss_conf 99998719994899672
No 9
>COG3706 PleD Response regulator containing a CheY-like receiver domain and a GGDEF domain [Signal transduction mechanisms]
Probab=100.00 E-value=2.3e-33 Score=273.93 Aligned_cols=169 Identities=37% Similarity=0.539 Sum_probs=155.3
Q ss_pred HHHHHHHHHHHHHHHCCCHHCCCCHHHHHHHHHH-------CCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCC
Q ss_conf 9999999999999610401050204899988877-------089725755442210001146886544431100000001
Q gi|254781079|r 91 KELFISYNRISQLSRIDCLSGLLNHSAFISSLGS-------YNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLV 163 (266)
Q Consensus 91 ~~l~~~~~~l~~~a~~D~LTgL~NR~~f~~~l~~-------~~~~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~ 163 (266)
+++....+++++++.+|+||||+||++|++++.. .+.|++++++|||+||.+||+|||.+||++|+.+|.+|+
T Consensus 257 ~~L~~~~~~~~~l~~~D~LTGL~NRR~~~~~L~~~~~ra~~~~~pls~~m~DID~FK~iNDt~GH~~GDevLr~vA~~L~ 336 (435)
T COG3706 257 RQLRESLERLQELALVDGLTGLFNRRYFDEHLADLWKRALREGRPLSLLMLDIDDFKEINDTYGHDVGDEVLRQVARRLR 336 (435)
T ss_pred HHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf 89999999998753244334766589999999999999985479716999713012413210188418899999999998
Q ss_pred CCCCCCHHHCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCC-EEEEEEEEEEEECCCCCC-HHHHHHHHH
Q ss_conf 111100000013343036501686101234445899999863154067995-689999999987799899-899999999
Q gi|254781079|r 164 VVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSGP-SIHITISAGIAERCHKEP-ISTIIYRAD 241 (266)
Q Consensus 164 ~~~~~~~~~~R~~gdeF~ill~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~-~~~~t~s~Gia~~~~~~~-~~~ll~~Ad 241 (266)
+.+++.|.++||||+||++++|+++.+.+..++++|+..+.+.++....+. ...+|+|+||+...++.+ +++++.+||
T Consensus 337 ~~vr~~Dl~aRyGGEEF~vvlp~t~~~~Ai~iaerIr~~i~~~~~~~~~~~~~~~~TiSiGVa~~~p~~~~~~~li~~AD 416 (435)
T COG3706 337 QTVRGLDLVARYGGEEFAVVLPDTDLEAAIAIAERIRQKINELPFVHELSREPLEVTISIGVAEGKPGEDSIEELLKRAD 416 (435)
T ss_pred HHCCCCCCCEECCCEEEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEEEEEEECCCCCCCHHHHHHHHH
T ss_conf 64323330001277269999448887899999999999974178301466543279999988745778876999999999
Q ss_pred HHHHHHHHCCCCEEEECC
Q ss_conf 999999970996899940
Q gi|254781079|r 242 QALYVAKKSGRNRVVCFS 259 (266)
Q Consensus 242 ~Al~~AK~~gkn~~~~~~ 259 (266)
.|||+||..|||+++.+.
T Consensus 417 ~aLy~AK~sGRnrv~~~~ 434 (435)
T COG3706 417 KALYKAKASGRNRVVVKR 434 (435)
T ss_pred HHHHHHHHCCCCEEEECC
T ss_conf 998677754964289616
No 10
>PRK11059 regulatory protein CsrD; Provisional
Probab=100.00 E-value=1.8e-31 Score=259.52 Aligned_cols=159 Identities=19% Similarity=0.221 Sum_probs=140.3
Q ss_pred HHHHHHCCCHHCCCCHHHHHHHHHHC-------CCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCC--CCH
Q ss_conf 99996104010502048999888770-------897257554422100011468865444311000000011111--000
Q gi|254781079|r 100 ISQLSRIDCLSGLLNHSAFISSLGSY-------NEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFG--TPM 170 (266)
Q Consensus 100 l~~~a~~D~LTgL~NR~~f~~~l~~~-------~~~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~~~~~--~~~ 170 (266)
++..|+.||+|||+||.+|+++++.. +.+.+|++||+|+||.|||++||++||++|+++|++|+..++ +++
T Consensus 224 IR~~Af~D~lTGL~NR~~F~~rL~s~L~~~~~~~~~GaVllIdld~fk~iNd~~G~~~gD~lL~~va~~L~~~l~r~~d~ 303 (642)
T PRK11059 224 IRSNAFLDAKTGLGNRLFFDNQLDTLLEDQEKVGAHGVVMLIRLPDFDLLQEELGESQVDELLFELINLLSTFVQRYPGA 303 (642)
T ss_pred HHHHHHCCCCCCCHHHHHHHHHHHHHHHCHHHCCCCEEEEEEECCHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf 98877507223850589999999999837454187559999987267699881095989999999999999997538987
Q ss_pred HHCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHC
Q ss_conf 00013343036501686101234445899999863154067995689999999987799899899999999999999970
Q gi|254781079|r 171 FVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERCHKEPISTIIYRADQALYVAKKS 250 (266)
Q Consensus 171 ~~~R~~gdeF~ill~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~t~s~Gia~~~~~~~~~~ll~~Ad~Al~~AK~~ 250 (266)
+++|+|||||+|++|+.+.+++..+++++...+.....+.... ....+|+|++.+++|++.++++++||.|||.||.+
T Consensus 304 ilARl~gdEFaILlP~~s~~ea~~lA~qLlk~l~~l~~~~~~d--~~~~~hIGia~y~~G~~~~~Ll~~AD~Al~~Ak~q 381 (642)
T PRK11059 304 LLARYSRSDFAVLLPHRSLKEADSLASQLLKAVDSLPPPKMLD--RDDFLHIGIAAYRSGQSTEQVMEEAEMALRSAQLQ 381 (642)
T ss_pred EEEEECCCEEEEEECCCCHHHHHHHHHHHHHHHHHCCCCCCCC--CCCEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHC
T ss_conf 7887158738999699985999999999999997136887677--77648999996889998999999999999999972
Q ss_pred CCCEEEECCH
Q ss_conf 9968999402
Q gi|254781079|r 251 GRNRVVCFSD 260 (266)
Q Consensus 251 gkn~~~~~~~ 260 (266)
|+|++.+|+.
T Consensus 382 g~n~w~~yd~ 391 (642)
T PRK11059 382 GGNSWFMYDK 391 (642)
T ss_pred CCCCCEEEEC
T ss_conf 8998377302
No 11
>smart00267 GGDEF diguanylate cyclase. Diguanylate cyclase, present in a variety of bacteria
Probab=99.97 E-value=1.3e-30 Score=252.85 Aligned_cols=155 Identities=35% Similarity=0.534 Sum_probs=142.5
Q ss_pred HHHHCCCHHCCCCHHHHHHHHHH-------CCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCHHHCC
Q ss_conf 99610401050204899988877-------08972575544221000114688654443110000000111110000001
Q gi|254781079|r 102 QLSRIDCLSGLLNHSAFISSLGS-------YNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFGTPMFVGR 174 (266)
Q Consensus 102 ~~a~~D~LTgL~NR~~f~~~l~~-------~~~~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~~~~~~~~~~~R 174 (266)
++|++|||||||||++|.+++++ .+.+++++++|||+|+.||+.||++.||++|+.+|++|+..+++++.++|
T Consensus 1 ~lA~~D~lTgL~Nr~~f~~~l~~~~~~~~~~~~~~~li~i~id~f~~in~~~G~~~gd~~l~~~a~~l~~~~~~~~~~~R 80 (163)
T smart00267 1 RLAFRDPLTGLPNRRYFEEELEQELQRAQRQGSPFALLLIDLDNFKDINDTYGHAVGDELLQEVAQRLSSCLRPGDLLAR 80 (163)
T ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCEEEEEEECCCHHHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCEEEE
T ss_conf 96888033485209999999999999888509958999998984578875338533566654201011025777778997
Q ss_pred CCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEECC-CCCCHHHHHHHHHHHHHHHHHCCCC
Q ss_conf 334303650168610123444589999986315406799568999999998779-9899899999999999999970996
Q gi|254781079|r 175 LGGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERC-HKEPISTIIYRADQALYVAKKSGRN 253 (266)
Q Consensus 175 ~~gdeF~ill~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~t~s~Gia~~~-~~~~~~~ll~~Ad~Al~~AK~~gkn 253 (266)
++||||++++|+.+.+++..++++|+..+.+. ...++..+.+++|+|+|.++ ++.++++++++|+.||++||++|+|
T Consensus 81 ~~~d~F~ill~~~~~~~~~~~~~~l~~~~~~~--~~~~~~~~~~t~siGia~~~~~~~~~~~ll~~A~~Al~~Ak~~G~n 158 (163)
T smart00267 81 LGGDEFALLLPETSLEEAIALAERILQQLREP--IIIHGIPLYLTISIGVAAYPNPGEDAEDLLKRADTALYQAKKAGRN 158 (163)
T ss_pred CCCCEEEEEECCCCHHHHHHHHHHHHHHHHHH--HHCCCCEEEEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCC
T ss_conf 27998999978999999999999999999634--3026954889888999982799999999999999999999985999
Q ss_pred EEEEC
Q ss_conf 89994
Q gi|254781079|r 254 RVVCF 258 (266)
Q Consensus 254 ~~~~~ 258 (266)
++++|
T Consensus 159 ~~~~y 163 (163)
T smart00267 159 QVAVY 163 (163)
T ss_pred EEEEC
T ss_conf 79969
No 12
>COG2199 c-di-GMP synthetase (diguanylate cyclase, GGDEF domain) [Signal transduction mechanisms]
Probab=99.97 E-value=8e-30 Score=246.92 Aligned_cols=164 Identities=39% Similarity=0.570 Sum_probs=144.7
Q ss_pred HHHHHHHHHHHHHCCCHHCCCCHHHHHHHHHHC-------CCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCCC
Q ss_conf 999999999996104010502048999888770-------8972575544221000114688654443110000000111
Q gi|254781079|r 93 LFISYNRISQLSRIDCLSGLLNHSAFISSLGSY-------NEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVV 165 (266)
Q Consensus 93 l~~~~~~l~~~a~~D~LTgL~NR~~f~~~l~~~-------~~~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~~~ 165 (266)
.....++++..+.+||||||+||+.|.+.++.. +.+++++++|||+||.|||+|||..||++|+.+|++|+..
T Consensus 9 ~~~~~~~l~~~a~~D~LTgl~NR~~~~~~l~~~~~~~~~~~~~~~l~liDiD~Fk~iND~~Gh~~GD~vL~~va~~L~~~ 88 (181)
T COG2199 9 LRKAEERLERLALHDPLTGLPNRRAFEERLERALARARRHGEPLALLLLDLDHFKQINDTYGHAAGDEVLREVARRLRSN 88 (181)
T ss_pred HHHHHHHHHHHHHHCHHCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCHHHHHHHHCHHHHHHHHHHHHHHHHHH
T ss_conf 99999999998625423187268999999999999734338856999996641025575457687999999999999986
Q ss_pred CCCCHHHCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEECCCC-CCH-HHHHHHHHHH
Q ss_conf 11000000133430365016861012344458999998631540679956899999999877998-998-9999999999
Q gi|254781079|r 166 FGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERCHK-EPI-STIIYRADQA 243 (266)
Q Consensus 166 ~~~~~~~~R~~gdeF~ill~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~t~s~Gia~~~~~-~~~-~~ll~~Ad~A 243 (266)
+++.+.++|+|||||++++|+.+.+++..++++|+..+..... ..+....+|+|+||+.++.+ .+. +.++.+||.|
T Consensus 89 ~~~~~~~~R~gGdEF~i~l~~~~~~~~~~~a~~i~~~i~~~~~--~~~~~~~~t~siGia~~~~~~~~~~~~l~~~Ad~a 166 (181)
T COG2199 89 LREGDLVARLGGDEFAVLLPGTSLEEAARLAERIRAALEEPFF--LGGEELRVTVSIGVALYPEDGSDDAELLLRRADLA 166 (181)
T ss_pred CCCCCEEEEECCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCC--CCCCCEEEEEEEEEEEECCCCCCHHHHHHHHHHHH
T ss_conf 4988789998775489997899989999999999999845344--57873368998999980688876099999999999
Q ss_pred HHHHHHCCCCEEEEC
Q ss_conf 999997099689994
Q gi|254781079|r 244 LYVAKKSGRNRVVCF 258 (266)
Q Consensus 244 l~~AK~~gkn~~~~~ 258 (266)
||.||+.|+|++.+|
T Consensus 167 l~~ak~~G~~~~~~~ 181 (181)
T COG2199 167 LYRAKRAGRNRVVVF 181 (181)
T ss_pred HHHHHHHCCCCEEEC
T ss_conf 999998389936649
No 13
>pfam00990 GGDEF GGDEF domain. This domain is found linked to a wide range of non-homologous domains in a variety of bacteria. It has been shown to be homologous to the adenylyl cyclase catalytic domain and has diguanylate cyclase activity. This observation correlates with the functional information available on two GGDEF-containing proteins, namely diguanylate cyclase and phosphodiesterase A of Acetobacter xylinum, both of which regulate the turnover of cyclic diguanosine monophosphate.
Probab=99.96 E-value=1.8e-29 Score=244.25 Aligned_cols=151 Identities=38% Similarity=0.562 Sum_probs=134.3
Q ss_pred HHCCCHHCCCCHHHHHHHHHH------CCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCHHHCCCCC
Q ss_conf 610401050204899988877------08972575544221000114688654443110000000111110000001334
Q gi|254781079|r 104 SRIDCLSGLLNHSAFISSLGS------YNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFGTPMFVGRLGG 177 (266)
Q Consensus 104 a~~D~LTgL~NR~~f~~~l~~------~~~~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~~~~~~~~~~~R~~g 177 (266)
|.||||||||||++|.+++++ .++++++++||||+||.||+.|||+.||++|+.+|++|+..+++++.++|++|
T Consensus 1 a~hD~lTgL~NR~~f~~~l~~~l~~~~~~~~~~l~~i~id~f~~in~~~G~~~gd~~L~~~a~~L~~~~~~~~~~~R~~~ 80 (159)
T pfam00990 1 AAHDPLTGLPNRRYFEEELEQELQRARRQSPLALLLLDLDNFKRINDTYGHAVGDEVLQEVAQRLSSSLRRSDLVARLGG 80 (159)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCHHHHHCCCCHHHHHHHHHHCCCCCCCCCCCCEEEECCC
T ss_conf 98861328121999999999999973159968999998975518675139678899998642333123368878996579
Q ss_pred CEEEEECCCCCHHHHHHHHHHHHHHHHHCC-CCCCCCCEEEEEEEEEEEECC-CCCCHHHHHHHHHHHHHHHHHCCCCE
Q ss_conf 303650168610123444589999986315-406799568999999998779-98998999999999999999709968
Q gi|254781079|r 178 EEFAAAALGSSEQEAAILANDLRKIIENSQ-INISSGPSIHITISAGIAERC-HKEPISTIIYRADQALYVAKKSGRNR 254 (266)
Q Consensus 178 deF~ill~~~~~~~~~~~~~~l~~~l~~~~-~~~~~~~~~~~t~s~Gia~~~-~~~~~~~ll~~Ad~Al~~AK~~gkn~ 254 (266)
|||++++|+.+.+++..+.+.+++.+.... +...++..+.+++|+|++.++ ++.++++++++||.||++||++||||
T Consensus 81 deF~vll~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~siGia~~~~~~~~~~~ll~~A~~Al~~AK~~G~Nr 159 (159)
T pfam00990 81 DEFAILLPDTSLEGAQELAERIRRLLAALKIPHTLSGLPLYVTISIGIAAYPNDGEDAEDLLKRADQALYQAKNQGRNR 159 (159)
T ss_pred CEEEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 9899997999979999999999999998407400258359999989999826999989999999999999999875999
No 14
>PRK11829 biofilm formation regulator HmsP; Provisional
Probab=99.96 E-value=1.7e-27 Score=229.16 Aligned_cols=184 Identities=17% Similarity=0.255 Sum_probs=158.3
Q ss_pred HHHHHHHHHHHHH---HHHHHHHHHHHHHHCCCHHCCCCHHHHHHHHHHC------CCCEEEEEEECCCCCCCCCCCCCC
Q ss_conf 9999999999999---9999999999996104010502048999888770------897257554422100011468865
Q gi|254781079|r 79 SLLLGYISGSILK---ELFISYNRISQLSRIDCLSGLLNHSAFISSLGSY------NEKLSIVFFDIDYFKQINDNFGHP 149 (266)
Q Consensus 79 ~~~~~~~~~~~~~---~l~~~~~~l~~~a~~D~LTgL~NR~~f~~~l~~~------~~~~~l~~idid~fk~iNd~~G~~ 149 (266)
-..++......++ .+.+..+++++.+.+-|+|+||||..|...+++. .+++++++++|+-++..|..++..
T Consensus 272 dde~g~l~~~ynrnqq~l~~~~~~~~~~~~r~p~t~lpn~~l~~~lleq~~~~~~~~~~~~l~~v~~~tl~~~~g~~~~~ 351 (728)
T PRK11829 272 DDELGVLVRNYNRNQQLLADAYADMGRISHRFPVTELPNRSLFISLLEKEIASSTRTDHFHLLVIGIETLQEVSGAMSEA 351 (728)
T ss_pred CCHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEEEHHHHHHHHCCCCHH
T ss_conf 42365888741534899999999987541148754687178999999999872146773279998546678764223156
Q ss_pred CCCCCCCHHHCCCCCCCCCCHHHCCCCCCEEEEECCC-CCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEECC
Q ss_conf 4443110000000111110000001334303650168-610123444589999986315406799568999999998779
Q gi|254781079|r 150 VGDKVIAFLSDQLVVVFGTPMFVGRLGGEEFAAAALG-SSEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERC 228 (266)
Q Consensus 150 ~gD~~L~~va~~l~~~~~~~~~~~R~~gdeF~ill~~-~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~t~s~Gia~~~ 228 (266)
..|++|..++++|+.+++++++++|+|||||+|+.++ ..+.+|..+++||...+.++ ...++..+..|+|||||.|+
T Consensus 352 q~~~Lllt~verl~~ci~~~~~laqls~~eFail~~~~~~P~~A~~lA~ril~~l~eP--~~~~~~~l~~sASIGIAlyP 429 (728)
T PRK11829 352 QHQQLLLTIVQRIEQCIDDSDLLAQLSKTEFAVLARGTRRSFPAMQLARRIMSQVTQP--LFFDEITLRPSASIGITRYQ 429 (728)
T ss_pred HHHHHHHHHHHHHHHHCCHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHHHHHCCC--CCCCCCCEEEEEEEEEECCC
T ss_conf 7888999999999852574555666267620220046798077999999999984588--43578734002689997589
Q ss_pred -CCCCHHHHHHHHHHHHHHHHHCCCCEEEECCHHHCC
Q ss_conf -989989999999999999997099689994021005
Q gi|254781079|r 229 -HKEPISTIIYRADQALYVAKKSGRNRVVCFSDIENN 264 (266)
Q Consensus 229 -~~~~~~~ll~~Ad~Al~~AK~~gkn~~~~~~~~~~~ 264 (266)
+|++.++|+++||.|||+||++|||++.||+.-=++
T Consensus 430 ~DG~taE~LLRnADtAMY~AK~~GRN~~~FF~p~m~~ 466 (728)
T PRK11829 430 AQQDTAESMMRNASTAMMAAHHEGRNQIMVFEPHLIE 466 (728)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHCCCEEEECCHHHHH
T ss_conf 9988999999979999999998389828976888999
No 15
>cd01949 GGDEF Diguanylate-cyclase (DGC) or GGDEF domain. Diguanylate-cyclase (DGC) or GGDEF domain: Originally named after a conserved residue pattern, and initially described as a domain of unknown function 1 (DUF1). This domain is widely present in bacteria, linked to a wide range of non-homologous domains in a variety of cell signaling proteins. The domain shows homology to the adenylyl cyclase catalytic domain. This correlates with the functional information available on two GGDEF-containing proteins, namely diguanylate cyclase and phosphodiesterase A of Acetobacter xylinum, both of which regulate the turnover of cyclic diguanosine monophosphate. Together with the EAL domain, GGDEF might be involved in regulating cell surface adhesion in bacteria.
Probab=99.95 E-value=3.1e-28 Score=234.84 Aligned_cols=150 Identities=43% Similarity=0.621 Sum_probs=136.7
Q ss_pred HCCCHHCCCCHHHHHHHHHH-------CCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCHHHCCCCC
Q ss_conf 10401050204899988877-------08972575544221000114688654443110000000111110000001334
Q gi|254781079|r 105 RIDCLSGLLNHSAFISSLGS-------YNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFGTPMFVGRLGG 177 (266)
Q Consensus 105 ~~D~LTgL~NR~~f~~~l~~-------~~~~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~~~~~~~~~~~R~~g 177 (266)
++|||||||||.+|.+++++ .++++++++++||+||.||+.|||+.||++|+.+|++|+..+++++.+||++|
T Consensus 1 ~~D~lTgL~Nr~~~~~~l~~~i~~~~~~~~~~~l~~i~id~f~~in~~~G~~~gD~~l~~~a~~l~~~~~~~~~~~R~~~ 80 (158)
T cd01949 1 YTDPLTGLPNRRAFEERLERLLARARRSGRPLALLLIDIDHFKQINDTYGHAAGDEVLKEVAERLRSSLRESDLVARLGG 80 (158)
T ss_pred CCCHHCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCHHHHHCCCCHHHHHHHHHHHHHHHCCCCCCCEEEEECC
T ss_conf 99810170149999999999999998619968999972886678887239646779999754464224789988999439
Q ss_pred CEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEECC-CCCCHHHHHHHHHHHHHHHHHCCCCEEE
Q ss_conf 303650168610123444589999986315406799568999999998779-9899899999999999999970996899
Q gi|254781079|r 178 EEFAAAALGSSEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERC-HKEPISTIIYRADQALYVAKKSGRNRVV 256 (266)
Q Consensus 178 deF~ill~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~t~s~Gia~~~-~~~~~~~ll~~Ad~Al~~AK~~gkn~~~ 256 (266)
|||++++|+.+.+++..++++|...+.... ...+..+.+++|+|++.++ ++.++++++++||.||++||++|||+++
T Consensus 81 d~F~vl~~~~~~~~~~~~~~~i~~~~~~~~--~~~~~~~~~~~siGia~~~~~~~~~~~ll~~A~~Al~~Ak~~G~~~~~ 158 (158)
T cd01949 81 DEFAILLPGTDLEEAEALAERLREAIEEPF--FIDGQEIRVTASIGIATYPEDGEDAEELLRRADEALYRAKRSGRNRVV 158 (158)
T ss_pred CEEEEEECCCCHHHHHHHHHHHHHHHHCHH--CCCCCCCCCEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf 899999689999999999999999981730--037876554279999980799998999999999999999988839699
No 16
>COG5001 Predicted signal transduction protein containing a membrane domain, an EAL and a GGDEF domain [Signal transduction mechanisms]
Probab=99.95 E-value=6.2e-26 Score=217.24 Aligned_cols=161 Identities=30% Similarity=0.497 Sum_probs=133.9
Q ss_pred HHHHHCCCHHCCCCHHHHHHHHHH-------CCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCHHHC
Q ss_conf 999610401050204899988877-------0897257554422100011468865444311000000011111000000
Q gi|254781079|r 101 SQLSRIDCLSGLLNHSAFISSLGS-------YNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFGTPMFVG 173 (266)
Q Consensus 101 ~~~a~~D~LTgL~NR~~f~~~l~~-------~~~~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~~~~~~~~~~~ 173 (266)
..+++.|.|||||||+.|..+++. .+..+++.+||+|+||.+||.|||..||.+|..|+++|+...+..-..+
T Consensus 225 ~~LAn~DsLTgLpNRr~ffa~Ldarlaaar~~g~rl~lgvIDLDgFKpvND~~GH~~GDrLLi~V~~RL~A~~~ap~~aa 304 (663)
T COG5001 225 DRLANLDSLTGLPNRRRFFAELDARLAAARQSGRRLVLGVIDLDGFKPVNDAFGHATGDRLLIEVGRRLKAFDGAPILAA 304 (663)
T ss_pred HHHHCCHHHCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCEECCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHH
T ss_conf 55534322128850667999877887421212871588998256770542001444125899999999876238737888
Q ss_pred CCCCCEEEEECCCCCHHHHH--HHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEECC-CCCCHHHHHHHHHHHHHHHHHC
Q ss_conf 13343036501686101234--44589999986315406799568999999998779-9899899999999999999970
Q gi|254781079|r 174 RLGGEEFAAAALGSSEQEAA--ILANDLRKIIENSQINISSGPSIHITISAGIAERC-HKEPISTIIYRADQALYVAKKS 250 (266)
Q Consensus 174 R~~gdeF~ill~~~~~~~~~--~~~~~l~~~l~~~~~~~~~~~~~~~t~s~Gia~~~-~~~~~~~ll~~Ad~Al~~AK~~ 250 (266)
|+|||||+++.|... .++. .-+..+.+.+.. ++. ..+...++++|+|+|..+ .+++.++|+.+||.|||+||+.
T Consensus 305 RLGGDEFa~i~p~~~-dDA~rva~a~al~e~L~A-pY~-l~~~~v~vgASiGia~fP~~a~t~EqLf~RADyALYhAK~~ 381 (663)
T COG5001 305 RLGGDEFALIIPALE-DDALRVAGARALCESLQA-PYD-LRGVRVQVGASIGIAPFPSGADTSEQLFERADYALYHAKQN 381 (663)
T ss_pred HHCCCEEEEECCCCC-CHHHHHCCHHHHHHHHCC-CCC-CCCCEEEEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHC
T ss_conf 706871489735789-678875046999998579-734-68862785112445326876652999997666899988752
Q ss_pred CCCEEEECCHHHCC
Q ss_conf 99689994021005
Q gi|254781079|r 251 GRNRVVCFSDIENN 264 (266)
Q Consensus 251 gkn~~~~~~~~~~~ 264 (266)
||+--+.|+.--++
T Consensus 382 gkG~AvlFda~hE~ 395 (663)
T COG5001 382 GKGAAVLFDARHEA 395 (663)
T ss_pred CCCCEEEECHHHHH
T ss_conf 89856874335788
No 17
>TIGR00254 GGDEF diguanylate cyclase (GGDEF) domain; InterPro: IPR000160 This domain appears to be ubiquitous in bacteria and is often linked to a regulatory domain, such as a phosphorylation receiver or oxygen sensing domain. Its function is to synthesize cyclic di-GMP, which is used as an intracellular signalling molecule in a wide variety of bacteria ,. Enzymatic activity can be strongly influenced by the adjacent domains. Processes regulated by this domain include exopolysaccharide synthesis, biofilm formation, motility and cell differentiation. Structural studies of PleD from Caulobacter crescentus show that this domain forms a five-stranded beta sheet surrounded by helices, similar to the catalytic core of adenylate cyclase ..
Probab=99.89 E-value=9.3e-23 Score=193.03 Aligned_cols=158 Identities=36% Similarity=0.556 Sum_probs=144.7
Q ss_pred HHHHHCCCHHCCCCHHHHHHHHHH-------CCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCCCC-CCCHHH
Q ss_conf 999610401050204899988877-------089725755442210001146886544431100000001111-100000
Q gi|254781079|r 101 SQLSRIDCLSGLLNHSAFISSLGS-------YNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVF-GTPMFV 172 (266)
Q Consensus 101 ~~~a~~D~LTgL~NR~~f~~~l~~-------~~~~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~~~~-~~~~~~ 172 (266)
+.++.+|++||++||+++.+.++. .+.+++++++|+|+||.+||++||+.||.+|+.++..++..+ +..|++
T Consensus 2 ~~~~~~d~ltg~~n~~~~~~~~~~~~~~~~~~~~~~~~~~~d~d~fk~~nd~~gh~~gd~~l~~~~~~~~~~~~r~~d~~ 81 (171)
T TIGR00254 2 ERLALRDPLTGLYNRRFLEELLDEELERAKRFGRSLSLLLIDLDNFKKINDTLGHDVGDEVLKEVARLLKSSLHRGSDLV 81 (171)
T ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCEEEEEEEHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCE
T ss_conf 64211134110010367999999888752024554134565300332210010301235899999999875310000100
Q ss_pred CCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCC-CCCEEEEEEEEEEEECC--CCCCHHHHHHHHHHHHHHHHH
Q ss_conf 013343036501686101234445899999863154067-99568999999998779--989989999999999999997
Q gi|254781079|r 173 GRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINIS-SGPSIHITISAGIAERC--HKEPISTIIYRADQALYVAKK 249 (266)
Q Consensus 173 ~R~~gdeF~ill~~~~~~~~~~~~~~l~~~l~~~~~~~~-~~~~~~~t~s~Gia~~~--~~~~~~~ll~~Ad~Al~~AK~ 249 (266)
+|+|||||++++|+++..++...+++++..+...+.... ....+.+++|+|++.++ ++.+.++++..||.+||.||+
T Consensus 82 ~r~gg~ef~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~ad~~~y~~k~ 161 (171)
T TIGR00254 82 GRYGGEEFAVILPGTPLEDALSKAERLRDALESKPIEVAHGSETLTLTVSIGVACYPGDHGLTLEELLKLADEALYKAKK 161 (171)
T ss_pred EECCCCEEEEEECCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf 11077515887317751578999999998764310012456512456665300103788731279999887788888875
Q ss_pred CCCCEEEEC
Q ss_conf 099689994
Q gi|254781079|r 250 SGRNRVVCF 258 (266)
Q Consensus 250 ~gkn~~~~~ 258 (266)
.|+|++...
T Consensus 162 ~g~~~~~~~ 170 (171)
T TIGR00254 162 AGRNRVFVA 170 (171)
T ss_pred HCCCCCCCC
T ss_conf 035531024
No 18
>COG3887 Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms]
Probab=98.33 E-value=0.00012 Score=55.03 Aligned_cols=133 Identities=14% Similarity=0.127 Sum_probs=97.2
Q ss_pred CCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCHHH-CCCCCCEEEEECCCCCHHHHHHHHHHHHHHHH
Q ss_conf 89725755442210001146886544431100000001111100000-01334303650168610123444589999986
Q gi|254781079|r 126 NEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFGTPMFV-GRLGGEEFAAAALGSSEQEAAILANDLRKIIE 204 (266)
Q Consensus 126 ~~~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~~~~~~~~~~-~R~~gdeF~ill~~~~~~~~~~~~~~l~~~l~ 204 (266)
..+.++..+-+||++.+-+...-+.--++=..|++.|.+-..++.+. -|+++|.|.+++.....++.+.-.=.+...+.
T Consensus 172 ~~k~vl~~i~vDNyDe~t~~~~d~~rs~inS~V~s~l~~~a~~~~if~rr~s~drf~~~~~~~~L~~l~~~kF~iLd~~R 251 (655)
T COG3887 172 NSKPVLGIISVDNYDEVTQGLSDSDRSQINSFVTSFLEEWATEYNIFLRRYSSDRFYAFTNYKILEKLEEDKFSILDEFR 251 (655)
T ss_pred CCCCEEEEEEECCHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHEEECCCEEEEEECHHHHHHHHHHHHHHHHHHH
T ss_conf 04736899984257777537873318999999999999999974465333037708999647999999873648999999
Q ss_pred HCCCCCCCCCEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEECCHHHCC
Q ss_conf 315406799568999999998779989989999999999999997099689994021005
Q gi|254781079|r 205 NSQINISSGPSIHITISAGIAERCHKEPISTIIYRADQALYVAKKSGRNRVVCFSDIENN 264 (266)
Q Consensus 205 ~~~~~~~~~~~~~~t~s~Gia~~~~~~~~~~ll~~Ad~Al~~AK~~gkn~~~~~~~~~~~ 264 (266)
+.. ....+++|+|+|++. ...++.++-..|-.+|..|--+|++||+...+.+.-
T Consensus 252 E~s----~~~~ipLTLSiGvg~--g~~~~~elg~vA~~~L~lAlgRGGDQVvIke~~~k~ 305 (655)
T COG3887 252 EES----SQKNIPLTLSIGVGY--GENNLIELGEVAQSNLDLALGRGGDQVVIKENNGKV 305 (655)
T ss_pred HHH----HCCCCCEEEEEEECC--CCCCHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCE
T ss_conf 874----034764699998536--766577899999875788742688669997379955
No 19
>cd07556 Nucleotidyl_cyc_III Class III nucleotidyl cyclases. Class III nucleotidyl cyclases are the largest, most diverse group of nucleotidyl cyclases (NC's) containing prokaryotic and eukaryotic proteins. They can be divided into two major groups; the mononucleotidyl cyclases (MNC's) and the diguanylate cyclases (DGC's). The MNC's, which include the adenylate cyclases (AC's) and the guanylate cyclases (GC's), have a conserved cyclase homology domain (CHD), while the DGC's have a conserved GGDEF domain, named after a conserved motif within this subgroup. Their products, cyclic guanylyl and adenylyl nucleotides, are second messengers that play important roles in eukaryotic signal transduction and prokaryotic sensory pathways.
Probab=97.17 E-value=0.00041 Score=50.81 Aligned_cols=98 Identities=20% Similarity=0.284 Sum_probs=77.6
Q ss_pred CEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCC-CHHHCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHC
Q ss_conf 72575544221000114688654443110000000111110-00000133430365016861012344458999998631
Q gi|254781079|r 128 KLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFGT-PMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENS 206 (266)
Q Consensus 128 ~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~~~~~~-~~~~~R~~gdeF~ill~~~~~~~~~~~~~~l~~~l~~~ 206 (266)
|.++++.||.+|..+.+.+|++...++|...-+.+...+.+ +..+-++-||.+..+++..+...+...+.++++.+.+.
T Consensus 1 pvtVlF~DI~gfT~l~e~~~~~~~~~~L~~~~~~~~~~v~~~~g~v~k~~GD~~~a~fg~~~~~~a~~~a~~~~~~~~~~ 80 (133)
T cd07556 1 PVTILFADIVGFTSLADALGPDEGDELLNELAGRFDSLIRRSGDLKIKTIGDEFMVVSGLDHPAAAVAFAEDMREAVSAL 80 (133)
T ss_pred CEEEEEEECCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCEEEEECCCEEEEEECCCCHHHHHHHHHHHHHHHHHH
T ss_conf 98999983146238888599999999999999998888874297589970656899637610556999999999999997
Q ss_pred CCCCCCCCEEEEEEEEEEE
Q ss_conf 5406799568999999998
Q gi|254781079|r 207 QINISSGPSIHITISAGIA 225 (266)
Q Consensus 207 ~~~~~~~~~~~~t~s~Gia 225 (266)
+........+++.++.|-+
T Consensus 81 ~~~~~~~l~iriGi~~G~v 99 (133)
T cd07556 81 NQSEGNPVRVRIGIHTGPV 99 (133)
T ss_pred HHCCCCCCCCCCEEEEEEE
T ss_conf 6301887664210263118
No 20
>COG1353 Predicted CRISPR-associated polymerase [Defense mechanisms]
Probab=96.55 E-value=0.023 Score=37.49 Aligned_cols=79 Identities=25% Similarity=0.315 Sum_probs=62.2
Q ss_pred CCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHC-CCC
Q ss_conf 3343036501686101234445899999863154067995689999999987799899899999999999999970-996
Q gi|254781079|r 175 LGGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERCHKEPISTIIYRADQALYVAKKS-GRN 253 (266)
Q Consensus 175 ~~gdeF~ill~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~t~s~Gia~~~~~~~~~~ll~~Ad~Al~~AK~~-gkn 253 (266)
=|||+..++.| ..++..++.++++.+.+.... ...+|+|+|++...+..+....+..|..+.-.||+. |||
T Consensus 591 sGGDDvla~g~---~d~vld~a~el~~~F~~~~~~-----~~~~t~SaGi~i~h~k~Pl~~~~~~~~~~e~~AK~~r~k~ 662 (799)
T COG1353 591 SGGDDVLAVGP---WDDVLDFAKELRELFSEFTGK-----NPKLTLSAGIVIVHHKFPLYFALREARELEEEAKENRGKN 662 (799)
T ss_pred ECCCCEEEECC---HHHHHHHHHHHHHHHHHHHCC-----CCCCCEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 66872478445---889999999999999998445-----8874157789980376809999999999999998740777
Q ss_pred EEEECCHH
Q ss_conf 89994021
Q gi|254781079|r 254 RVVCFSDI 261 (266)
Q Consensus 254 ~~~~~~~~ 261 (266)
.|.+|+.-
T Consensus 663 ~i~~~~r~ 670 (799)
T COG1353 663 AIGLFDRS 670 (799)
T ss_pred EEEEECCC
T ss_conf 07997268
No 21
>PRK02240 GTP cyclohydrolase III; Provisional
Probab=96.05 E-value=0.025 Score=37.15 Aligned_cols=112 Identities=20% Similarity=0.168 Sum_probs=70.5
Q ss_pred CEEEEEEECCCCCC-CCCCCC-CCCCCCCCCHHHCCCCCCCCCCHHHCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 72575544221000-114688-6544431100000001111100000013343036501686101234445899999863
Q gi|254781079|r 128 KLSIVFFDIDYFKQ-INDNFG-HPVGDKVIAFLSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIEN 205 (266)
Q Consensus 128 ~~~l~~idid~fk~-iNd~~G-~~~gD~~L~~va~~l~~~~~~~~~~~R~~gdeF~ill~~~~~~~~~~~~~~l~~~l~~ 205 (266)
...++=+||++... +-|..+ ++.-=++.+..+...+.....+.+.+=+|||.|.+++|+.+++......+.+....
T Consensus 134 ~V~iaH~Dvnd~T~~~Td~~s~~dt~~~I~~~y~~l~~~~~~~g~l~ff~GGDN~m~~~~~~~~~~~~~~i~~v~~~~-- 211 (254)
T PRK02240 134 YVQIAHFDINDITGTYTDIETAFDTYLSVQKVKLALMEELKKHDSLGFFIGGDNFMAPCNGLSEKDFLDAIEHVREEA-- 211 (254)
T ss_pred CEEEEEEEEECCCHHHCCCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEEECCCEEEEECCCCCHHHHHHHHHHHHHCC--
T ss_conf 259999854344112104777478999999999999999987498899845855998789877678999999987404--
Q ss_pred CCCCCCCCCEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEE
Q ss_conf 15406799568999999998779989989999999999999997099689
Q gi|254781079|r 206 SQINISSGPSIHITISAGIAERCHKEPISTIIYRADQALYVAKKSGRNRV 255 (266)
Q Consensus 206 ~~~~~~~~~~~~~t~s~Gia~~~~~~~~~~ll~~Ad~Al~~AK~~gkn~~ 255 (266)
.+.+-+.+|++ .++.+....|+.||..-+..|...+
T Consensus 212 ---------~i~lkvGIG~g-----~ta~~A~~~At~aLe~iR~~~~~~~ 247 (254)
T PRK02240 212 ---------GVELKAGIGIG-----KTAEDAGNLADHALEVIREGGTDVQ 247 (254)
T ss_pred ---------CCEEEEEECCC-----CCHHHHHHHHHHHHHHHHCCCCEEE
T ss_conf ---------94488644578-----8889999989989999964895479
No 22
>pfam05165 GGDN GGDN family. I have named this protein family of unknown function GGDN after the most conserved motif. The proteins are 200-270 amino acids in length.
Probab=95.50 E-value=0.047 Score=35.14 Aligned_cols=114 Identities=18% Similarity=0.204 Sum_probs=70.6
Q ss_pred CCEEEEEEECCCCCC-CCCCCC-CCCCCCCCCHHHCCCCCCCCCCHHHCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHH
Q ss_conf 972575544221000-114688-654443110000000111110000001334303650168610123444589999986
Q gi|254781079|r 127 EKLSIVFFDIDYFKQ-INDNFG-HPVGDKVIAFLSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIE 204 (266)
Q Consensus 127 ~~~~l~~idid~fk~-iNd~~G-~~~gD~~L~~va~~l~~~~~~~~~~~R~~gdeF~ill~~~~~~~~~~~~~~l~~~l~ 204 (266)
....++=+||++... .-|..+ ++.-=++.+..+...+.....+.+.+=+|||.|.+++|+.++.....+.+.++..+
T Consensus 126 ~~V~iaH~Dvnd~T~~~Td~~s~~dt~~~I~~~y~~l~~~~~~~g~l~ff~GGDN~m~~~~~~~~~~~~~~i~~i~~~~- 204 (246)
T pfam05165 126 GYVQIAHIDINNITGTITDIVSPVRTYYEVNDVMAKLMKVLEKIGALTQFIGGDNFMAPCNGIDAGIVLDINNSVKETV- 204 (246)
T ss_pred CCEEEEEEEEECCCHHHCCCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEEECCCEEEEECCCCCHHHHHHHHHHHHHHC-
T ss_conf 7349999855354122204676679999999999999999987498899845866999789865778999999988652-
Q ss_pred HCCCCCCCCCEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEE
Q ss_conf 3154067995689999999987799899899999999999999970996899
Q gi|254781079|r 205 NSQINISSGPSIHITISAGIAERCHKEPISTIIYRADQALYVAKKSGRNRVV 256 (266)
Q Consensus 205 ~~~~~~~~~~~~~~t~s~Gia~~~~~~~~~~ll~~Ad~Al~~AK~~gkn~~~ 256 (266)
.+.+-+.+|++ .++.+....|+.||..-+..+....+
T Consensus 205 ----------~i~lkvGIG~g-----~ta~~A~~~At~aLe~iR~~~~~~~~ 241 (246)
T pfam05165 205 ----------DVDLKAGIGIA-----PTAEDALALADEALEEIRGKIVPGPV 241 (246)
T ss_pred ----------CCEEEEEECCC-----CCHHHHHHHHHHHHHHHHHCCCCCCE
T ss_conf ----------95278514568-----88899999999899999726888876
No 23
>TIGR02578 cas_TM1811_Csm1 CRISPR-associated protein, Csm1 family; InterPro: IPR013408 CRISPR are Clustered Regularly Interspaced Short Palindromic Repeats. This family is encoded in a conserved gene cluster regularly found near CRISPR repeats and is designated Csm1, for CRISPR/Cas Subtype Mtube Protein 1. A typical example is TM1811 from Thermotoga maritima. .
Probab=95.44 E-value=0.059 Score=34.39 Aligned_cols=123 Identities=16% Similarity=0.196 Sum_probs=76.1
Q ss_pred CCCCEEEEEEECCCCCCC-CCCCCCCCCCC---------------CCCHHHCCCCCCCC---CCHHHCCC-----CCCEE
Q ss_conf 089725755442210001-14688654443---------------11000000011111---00000013-----34303
Q gi|254781079|r 125 YNEKLSIVFFDIDYFKQI-NDNFGHPVGDK---------------VIAFLSDQLVVVFG---TPMFVGRL-----GGEEF 180 (266)
Q Consensus 125 ~~~~~~l~~idid~fk~i-Nd~~G~~~gD~---------------~L~~va~~l~~~~~---~~~~~~R~-----~gdeF 180 (266)
..++|.|+..|+-+-... =..+|-+++++ +...+|..|-..+. .+|+++|. ||+.|
T Consensus 289 ~~~~FlLv~gD~sGIQ~FIf~~~~~~~t~~~A~k~LrGRSf~i~LL~e~~a~~il~~l~kalGGdvL~~~N~~~~~GG~F 368 (802)
T TIGR02578 289 NEEKFLLVSGDLSGIQDFIFRQAKAEITSKGALKSLRGRSFYIELLAEVIAKEILEELNKALGGDVLTRTNILFEGGGHF 368 (802)
T ss_pred CCCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHEECCCEE
T ss_conf 78740788625323468998655555433234564310458899999999999999841330432233222211147727
Q ss_pred EEECCCCCHHH--HHHHHHHHHHHHHHCCCCCCCC---CEEEEE----EEEEEEECC----CCCC--HHHHHHHHHHHHH
Q ss_conf 65016861012--3444589999986315406799---568999----999998779----9899--8999999999999
Q gi|254781079|r 181 AAAALGSSEQE--AAILANDLRKIIENSQINISSG---PSIHIT----ISAGIAERC----HKEP--ISTIIYRADQALY 245 (266)
Q Consensus 181 ~ill~~~~~~~--~~~~~~~l~~~l~~~~~~~~~~---~~~~~t----~s~Gia~~~----~~~~--~~~ll~~Ad~Al~ 245 (266)
.+|+|+++... ++.+.++|.+.+-+. ..+ ....++ .+.+++... +..+ +..+.+.--.++.
T Consensus 369 ~Ll~~nte~~~~~~~~~~~~i~~~l~~~----~~g~~~~~~~~~~~~~l~~~~~~~~~~~~d~~~D~f~~~~~~~~~kl~ 444 (802)
T TIGR02578 369 YLLLPNTEEAREALEKLREEIEEELLKE----FRGKIAIDLALSASLELSLGIASVAFSENDLENDRFAKKRKKLHEKLE 444 (802)
T ss_pred EEECCCCHHHHHHHHHHHHHHHHHHHHH----CCCCEEEEHHHHCCCCCCEEEEECCCHHHCCCCHHHHHHHHHHHHHHH
T ss_conf 9953788567999999999999999882----464101000110124451035430200110013168999999999999
Q ss_pred HHHHCC
Q ss_conf 999709
Q gi|254781079|r 246 VAKKSG 251 (266)
Q Consensus 246 ~AK~~g 251 (266)
.+|+..
T Consensus 445 ~~K~~~ 450 (802)
T TIGR02578 445 KKKKRR 450 (802)
T ss_pred HHHCCC
T ss_conf 986155
No 24
>TIGR02577 cas_TM1794_Crm2 CRISPR-associated protein, Crm2 family; InterPro: IPR013407 This entry is encoded within the CRISPR-associated RAMP module, a set of six genes found together in prokaryotic genomes . This gene cluster is found only in species with CRISPR repeats, usually near the repeats themselves. Because most of the six genes (but not those encoding this entry) contain RAMP domains, and because its appearance in a genome appears to depend on other CRISPR-associated Cas genes, the set is designated the CRISPR RAMP module. This entry, typified by TM1794 from Thermotoga maritima, is designated Crm2, for CRISPR RAMP Module protein 2..
Probab=94.44 E-value=0.09 Score=32.95 Aligned_cols=79 Identities=23% Similarity=0.189 Sum_probs=51.3
Q ss_pred HHCCCCCCEEEEECCC-C-CHHHHHHHHHHHHHHHHHCCCCCC-------------------CCCEEEEEEEEEEEECCC
Q ss_conf 0001334303650168-6-101234445899999863154067-------------------995689999999987799
Q gi|254781079|r 171 FVGRLGGEEFAAAALG-S-SEQEAAILANDLRKIIENSQINIS-------------------SGPSIHITISAGIAERCH 229 (266)
Q Consensus 171 ~~~R~~gdeF~ill~~-~-~~~~~~~~~~~l~~~l~~~~~~~~-------------------~~~~~~~t~s~Gia~~~~ 229 (266)
.+--.|||+-..++|- . -.+-|..+.+.....+........ ....-..|+|+||+...+
T Consensus 566 ~lvY~GGDDVLA~lP~~~naL~~A~~l~~~F~~~~~~~~~~~~~~~~e~E~~~~Y~~~KPs~~~~~~~~~~SaGl~I~H~ 645 (665)
T TIGR02577 566 VLVYAGGDDVLALLPVDTNALDVAKELRKEFSESLEKELGKERIKPYESEKVVRYQGEKPSEYTSLEEPTLSAGLVIVHH 645 (665)
T ss_pred EEEEECCCCEEEECCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCCEEEEEEEE
T ss_conf 78987355134552512568999999999999987530245677745775634426888876433567765267771111
Q ss_pred CCCHHHHHHHHHHHHHHHHH
Q ss_conf 89989999999999999997
Q gi|254781079|r 230 KEPISTIIYRADQALYVAKK 249 (266)
Q Consensus 230 ~~~~~~ll~~Ad~Al~~AK~ 249 (266)
..+..+.+..|..|+..||+
T Consensus 646 k~PL~~ale~a~~llk~AK~ 665 (665)
T TIGR02577 646 KEPLYDALELARELLKRAKE 665 (665)
T ss_pred CCCHHHHHHHHHHHHHHHCC
T ss_conf 05589999999999997359
No 25
>TIGR02578 cas_TM1811_Csm1 CRISPR-associated protein, Csm1 family; InterPro: IPR013408 CRISPR are Clustered Regularly Interspaced Short Palindromic Repeats. This family is encoded in a conserved gene cluster regularly found near CRISPR repeats and is designated Csm1, for CRISPR/Cas Subtype Mtube Protein 1. A typical example is TM1811 from Thermotoga maritima. .
Probab=93.45 E-value=0.25 Score=29.53 Aligned_cols=116 Identities=25% Similarity=0.276 Sum_probs=75.4
Q ss_pred CCCEEEEEEECCCCCCCCCCCCCCCCCC-----CCCHHHCCCCC--------C----------CCCCHH-----------
Q ss_conf 8972575544221000114688654443-----11000000011--------1----------110000-----------
Q gi|254781079|r 126 NEKLSIVFFDIDYFKQINDNFGHPVGDK-----VIAFLSDQLVV--------V----------FGTPMF----------- 171 (266)
Q Consensus 126 ~~~~~l~~idid~fk~iNd~~G~~~gD~-----~L~~va~~l~~--------~----------~~~~~~----------- 171 (266)
....+++.+|+||+-.|=-+=....... -+..+++.+.. . ++.+|+
T Consensus 651 ~k~l~~Lk~DvDnlG~iF~~g~~~~~~~~~~~sR~a~LS~~l~~FF~~~~~~l~~~~e~~~~~~GWddl~~~G~~~~~~~ 730 (802)
T TIGR02578 651 EKKLGVLKMDVDNLGEIFASGLKRETRSLLAISRLATLSRQLELFFKLELNHLAEDKEIEREDLGWDDLEERGKERRKRN 730 (802)
T ss_pred CCEEEEEECCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHCCCHHHHHHHHHHHCCCC
T ss_conf 81688864236677899985047643002579999899877878898747997447530121267278987404411685
Q ss_pred HCC--CCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 001--334303650168610123444589999986315406799568999999998779989989999999999999997
Q gi|254781079|r 172 VGR--LGGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERCHKEPISTIIYRADQALYVAKK 249 (266)
Q Consensus 172 ~~R--~~gdeF~ill~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~t~s~Gia~~~~~~~~~~ll~~Ad~Al~~AK~ 249 (266)
+|= =|||++.++ ..-.++..++.+|++.+..-.. ..-.+|+|+|+...++.-++..+...|+.++..||+
T Consensus 731 ~y~VYSGGDD~fl~---G~w~~~~~~a~~~~~~F~~ft~-----~~~~~T~S~G~~~~~~k~P~~~~a~~~Ee~l~~AK~ 802 (802)
T TIGR02578 731 IYVVYSGGDDLFLV---GAWDAVLELASDIREKFEKFTC-----RQDKLTLSAGVVVVSPKFPVRKAARIAEEALEAAKE 802 (802)
T ss_pred EEEEEECCCCCEEE---CCHHHHHHHHHHHHHHHHHHCC-----CCCCEEEEEEEEEECCCCCHHHHHHHHHHHHHHCCC
T ss_conf 37999856421032---6638999999999998887235-----786400034126627884689999998899985069
No 26
>cd07302 CHD cyclase homology domain. Catalytic domains of the mononucleotidyl cyclases (MNC's), also called cyclase homology domains (CHDs), are part of the class III nucleotidyl cyclases. This class includes eukaryotic and prokaryotic adenylate cyclases (AC's) and guanylate cyclases (GC's). They seem to share a common catalytic mechanism in their requirement for two magnesium ions to bind the polyphosphate moiety of the nucleotide.
Probab=92.54 E-value=0.2 Score=30.32 Aligned_cols=130 Identities=13% Similarity=0.100 Sum_probs=79.1
Q ss_pred CEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCC-CHHHCCCCCCEEEEECCC-----CCHHHHHHHHHHHHH
Q ss_conf 72575544221000114688654443110000000111110-000001334303650168-----610123444589999
Q gi|254781079|r 128 KLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFGT-PMFVGRLGGEEFAAAALG-----SSEQEAAILANDLRK 201 (266)
Q Consensus 128 ~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~~~~~~-~~~~~R~~gdeF~ill~~-----~~~~~~~~~~~~l~~ 201 (266)
..++++.||-+|..+-+.++.+.--++|..+-..+...+.. +..+-++-||.+.++++. ....++...+-.+.+
T Consensus 1 ~~~vlf~di~~ft~~~~~~~~~~~~~~l~~~~~~~~~~i~~~gg~~~k~~GD~~~~~f~~~~~~~~~~~~A~~~a~~i~~ 80 (177)
T cd07302 1 EVTVLFADIVGFTALSERLGPEELVELLNEYFSAFDEIIERHGGTVDKTIGDAVMAVFGLPGAHEDHAERAVRAALEMQE 80 (177)
T ss_pred CEEEEEEEECCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCEEEEEEECCEEEEEECCCCCCHHHHHHHHHHHHHHHH
T ss_conf 98999998357369887599999999999999999866764667999983581689955898863779999999999999
Q ss_pred HHHHCCCC--CCCCCEEEEEEEEEEEECC-C------CCCHHHHHHHHHHHHHHHHHCCCCEEEECCH
Q ss_conf 98631540--6799568999999998779-9------8998999999999999999709968999402
Q gi|254781079|r 202 IIENSQIN--ISSGPSIHITISAGIAERC-H------KEPISTIIYRADQALYVAKKSGRNRVVCFSD 260 (266)
Q Consensus 202 ~l~~~~~~--~~~~~~~~~t~s~Gia~~~-~------~~~~~~ll~~Ad~Al~~AK~~gkn~~~~~~~ 260 (266)
.+.+.... ......+++.++.|-+... - .+-..+-+..|..-+..++ .+++..=.+
T Consensus 81 ~~~~~~~~~~~~~~~~~riGih~G~v~~g~~G~~~~~~~~~G~~Vn~Aarl~~~a~---~~~Ilvs~~ 145 (177)
T cd07302 81 ALAELNAEREGGPPLRLRIGIHTGPVVAGVVGSERPEYTVIGDTVNLAARLESLAK---PGQILVSEA 145 (177)
T ss_pred HHHHHHHHCCCCCCCEEEEEEEECCCEEEECCCCCEEEEEECHHHHHHHHHHHCCC---CCEEEECHH
T ss_conf 99999985067898249999996274077747875134587608889999980489---997999989
No 27
>pfam00211 Guanylate_cyc Adenylate and Guanylate cyclase catalytic domain.
Probab=92.26 E-value=0.18 Score=30.69 Aligned_cols=100 Identities=19% Similarity=0.257 Sum_probs=60.3
Q ss_pred CCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCC-CCHHHCCCCCCEEEEECC--CCC-HHHH---HHHHHH
Q ss_conf 897257554422100011468865444311000000011111-000000133430365016--861-0123---444589
Q gi|254781079|r 126 NEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFG-TPMFVGRLGGEEFAAAAL--GSS-EQEA---AILAND 198 (266)
Q Consensus 126 ~~~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~~~~~-~~~~~~R~~gdeF~ill~--~~~-~~~~---~~~~~~ 198 (266)
-++.++++.||.+|..+-+.++.+.--.+|...-+.+...+. .+..+.++-||.+..++. ... ...+ ...+..
T Consensus 6 ~~~vtVlF~Di~gfT~l~e~~~~~~~~~~l~~~~~~~~~~v~~~gG~v~k~iGD~~ma~fg~~~~~~~~~~~~~~~~a~~ 85 (186)
T pfam00211 6 YDNVTILFADIVGFTALSSRHSPEELVRLLNDLYTRFDELLDKHGVYKVKTIGDAYMAASGLPPAASAHHAALLADMALD 85 (186)
T ss_pred CCCEEEEEEECCCHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCEEEEEECCCCCCHHHHHHHHHHHHHH
T ss_conf 79889999843674798885999999999999999999999966969999967858998589976528999999999999
Q ss_pred HHHHHHHCCCCCCCCCEEEEEEEEEEE
Q ss_conf 999986315406799568999999998
Q gi|254781079|r 199 LRKIIENSQINISSGPSIHITISAGIA 225 (266)
Q Consensus 199 l~~~l~~~~~~~~~~~~~~~t~s~Gia 225 (266)
+.+.+.+..........+++.++.|-+
T Consensus 86 ~~~~~~~~~~~~~~~l~~riGi~~G~v 112 (186)
T pfam00211 86 MVETIEEVNVGHLNGLRVRIGIHTGPV 112 (186)
T ss_pred HHHHHHHHHHCCCCCCCEEEEEEEEEE
T ss_conf 999999998544899736877677668
No 28
>COG2429 Archaeal GTP cyclohydrolase III [Nucleotide transport and metabolism]
Probab=92.19 E-value=0.46 Score=27.53 Aligned_cols=84 Identities=15% Similarity=0.143 Sum_probs=55.4
Q ss_pred HHHCCCCCCCCCCHHHCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEECCCCCCHHHH
Q ss_conf 00000011111000000133430365016861012344458999998631540679956899999999877998998999
Q gi|254781079|r 157 FLSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERCHKEPISTI 236 (266)
Q Consensus 157 ~va~~l~~~~~~~~~~~R~~gdeF~ill~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~t~s~Gia~~~~~~~~~~l 236 (266)
..+...+.....+.+..-+|||.|..++|+.+..+.......+.... .+.+-+.+|++ .++.+.
T Consensus 162 ~~~~L~~~l~k~gal~fflGGDN~ma~~p~~s~g~v~d~i~~v~~~~-----------~v~lkvGIGig-----~ta~~A 225 (250)
T COG2429 162 VYATLMRFLEKIGALLFFLGGDNIMAVCPGLSAGDVLDAIAEVLDDA-----------EVDLKVGIGIG-----KTARDA 225 (250)
T ss_pred HHHHHHHHHHHCCCEEEEECCCCEEEECCCCCCHHHHHHHHHHHHHH-----------CCCEEEEECCC-----CCHHHH
T ss_conf 99999999985495788735862587779987013999999998751-----------52257500558-----987788
Q ss_pred HHHHHHHHHHHHHCCCCEEE
Q ss_conf 99999999999970996899
Q gi|254781079|r 237 IYRADQALYVAKKSGRNRVV 256 (266)
Q Consensus 237 l~~Ad~Al~~AK~~gkn~~~ 256 (266)
...|+.||...+..|.-.++
T Consensus 226 ~~lA~~aLe~iR~~~~~~~~ 245 (250)
T COG2429 226 GALATHALEKIRGKGTKGWV 245 (250)
T ss_pred HHHHHHHHHHHHCCCCCCCE
T ss_conf 77788899998616970541
No 29
>PRK02240 GTP cyclohydrolase III; Provisional
Probab=91.21 E-value=0.96 Score=25.11 Aligned_cols=115 Identities=17% Similarity=0.159 Sum_probs=60.7
Q ss_pred EEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCCCC-----CCCHHHCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 755442210001146886544431100000001111-----100000013343036501686101234445899999863
Q gi|254781079|r 131 IVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVF-----GTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIEN 205 (266)
Q Consensus 131 l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~~~~-----~~~~~~~R~~gdeF~ill~~~~~~~~~~~~~~l~~~l~~ 205 (266)
+-+|.||+...=-.+.|...= --|+.+=.+|...+ ..+.++.-..-|+|..+.-+.+.++...+.+.|+...
T Consensus 4 vt~Iqi~~YgpWT~tlgprRE-~~lQ~lQarLya~l~~~f~~~~g~vf~~RfDn~iavtNGi~~~~h~~iq~~i~~~~-- 80 (254)
T PRK02240 4 ITLVQIDNYGPWTVTPNPRRE-SDLQALQSRLYADLNLQFGARDGYVFFTRFDNMIAVTNGIDLEAHARIQESIRNRY-- 80 (254)
T ss_pred EEEEEECCCCCCCCCCCCCCH-HHHHHHHHHHHHHHHHHHHHCCCEEEECCCCEEEEEECCCCHHHHHHHHHHHHHCC--
T ss_conf 899987587766577898718-89999999999999999850696872000111566415999899999999876239--
Q ss_pred CCCCCCCCCEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHH---HHCCCCEEEECCHHH
Q ss_conf 154067995689999999987799899899999999999999---970996899940210
Q gi|254781079|r 206 SQINISSGPSIHITISAGIAERCHKEPISTIIYRADQALYVA---KKSGRNRVVCFSDIE 262 (266)
Q Consensus 206 ~~~~~~~~~~~~~t~s~Gia~~~~~~~~~~ll~~Ad~Al~~A---K~~gkn~~~~~~~~~ 262 (266)
.+.+++|+|.+ +++-+....|-.+|..+ +...|+-+..++..+
T Consensus 81 ---------Pv~vs~~iG~g-----eTP~eA~~~A~~~lq~~g~aqd~~r~E~l~~~~~~ 126 (254)
T PRK02240 81 ---------PVTVSMGIGTA-----ETPYEAQKLATEALQEAGSAQDENRKEVLRIDSVA 126 (254)
T ss_pred ---------CCEEEEEEECC-----CCHHHHHHHHHHHHHHCCCCCCCCCEEEEECCCCC
T ss_conf ---------93599998526-----98799999999998743454334430354036766
No 30
>PRK11477 carbohydrate diacid transcriptional activator CdaR; Provisional
Probab=90.06 E-value=1.6 Score=23.48 Aligned_cols=132 Identities=11% Similarity=0.124 Sum_probs=74.4
Q ss_pred HHHHHHHHHC----CCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCHHHCCCCCCEEEEECCCCC---
Q ss_conf 8999888770----897257554422100011468865444311000000011111000000133430365016861---
Q gi|254781079|r 116 SAFISSLGSY----NEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFGTPMFVGRLGGEEFAAAALGSS--- 188 (266)
Q Consensus 116 ~~f~~~l~~~----~~~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~~~~~~~~~~~R~~gdeF~ill~~~~--- 188 (266)
..|.++.+.. ..|..+++++++..+ .|.+..-..+..+...+.. ..+++.++.++.++++++.|...
T Consensus 147 ~~l~~~a~~lgidl~~pr~~~ii~~~~~~-----~~~~~~~~~~~~~~~~l~~-~~~~~l~~~~~~~~~vvl~~~~~~~~ 220 (385)
T PRK11477 147 PALVEWAQRLGIDLNQPRVAAIVEVDSGQ-----LGVDSAMAELQQLQNALTT-PERNNLVAIVSLTEMVVLKPALNSFG 220 (385)
T ss_pred HHHHHHHHHCCCCCCCCEEEEEEEECCCC-----CCHHHHHHHHHHHHHHHCC-CCCCCEEEEECCCEEEEEEECCCCCC
T ss_conf 89999999849997897599999826643-----2224579999999998548-67577689940876999963544323
Q ss_pred ---HHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEECCC-CCCHHHHHHHHHHHHHHHHHC-CCCEEEECCHHH
Q ss_conf ---01234445899999863154067995689999999987799-899899999999999999970-996899940210
Q gi|254781079|r 189 ---EQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERCH-KEPISTIIYRADQALYVAKKS-GRNRVVCFSDIE 262 (266)
Q Consensus 189 ---~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~t~s~Gia~~~~-~~~~~~ll~~Ad~Al~~AK~~-gkn~~~~~~~~~ 262 (266)
.++.....+++...+.+. .... +.+|+..+-. -.+...-...|-.||..+|.. .+.++.+|+|..
T Consensus 221 ~~~~~~~~~~~~~l~~~l~~~-------~~~~--~~i~iG~~~~~~~~l~~Sy~~A~~al~~g~~~~~~~~i~~y~dl~ 290 (385)
T PRK11477 221 RWDAEDHRKRVEQLISRMKEY-------GQLR--FRVSLGNYFTGPGSIARSYRTAKTTMMVGKQRMPESRCYFYQDLM 290 (385)
T ss_pred CCCHHHHHHHHHHHHHHHHHH-------CCEE--EEEEECCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEHHCC
T ss_conf 246088999999999999862-------4820--899988765885799999999999999999738877689727447
No 31
>smart00044 CYCc Adenylyl- / guanylyl cyclase, catalytic domain. Present in two copies in mammalian adenylyl cyclases. Eubacterial homologues are known. Two residues (Asn, Arg) are thought to be involved in catalysis. These cyclases have important roles in a diverse range of cellular processes.
Probab=89.20 E-value=0.35 Score=28.47 Aligned_cols=130 Identities=12% Similarity=0.090 Sum_probs=64.0
Q ss_pred CCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCC-CCHHHCCCCCCEEEEECCC--CC-HHHHH---HHHHH
Q ss_conf 897257554422100011468865444311000000011111-0000001334303650168--61-01234---44589
Q gi|254781079|r 126 NEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFG-TPMFVGRLGGEEFAAAALG--SS-EQEAA---ILAND 198 (266)
Q Consensus 126 ~~~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~~~~~-~~~~~~R~~gdeF~ill~~--~~-~~~~~---~~~~~ 198 (266)
....++++.||-+|..+-+..+.+.-=.+|..+-+.+...+. .+..+-++-||.+.+++.. .+ ...+. ..+..
T Consensus 34 ~~~vtvlf~Di~gFT~l~e~~~p~~~~~~Ln~~f~~~~~~i~~~gg~~~k~iGD~~ma~fg~p~~~~~~~a~~a~~~al~ 113 (194)
T smart00044 34 YDNVTILFTDIVGFTTLSSEATPEQVVTLLNDLYSRFDRIIDRHGGYKVKTIGDAYMVVSGLPTEALVDHAELAADEALD 113 (194)
T ss_pred CCCEEEEEEECCCHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEEECCCEEEEEECCCCCCHHHHHHHHHHHHHH
T ss_conf 36489999872781454543999999999999999999999856849999738669998589997618999999999999
Q ss_pred HHHHHHHCCCCC-CCCCEEEEEEEEEEEECC-CC------CCHHHHHHHHHHHHHHHHHCCCCEEEEC
Q ss_conf 999986315406-799568999999998779-98------9989999999999999997099689994
Q gi|254781079|r 199 LRKIIENSQINI-SSGPSIHITISAGIAERC-HK------EPISTIIYRADQALYVAKKSGRNRVVCF 258 (266)
Q Consensus 199 l~~~l~~~~~~~-~~~~~~~~t~s~Gia~~~-~~------~~~~~ll~~Ad~Al~~AK~~gkn~~~~~ 258 (266)
+.+.+....... ..+..+++.++.|-+... -| +-..+.+..|..-...+| .++|..=
T Consensus 114 ~~~~~~~~~~~~~~~~l~~rIGIhtG~v~~G~iG~~~~~y~v~Gd~VN~AsRles~~~---~~~IlvS 178 (194)
T smart00044 114 MVESLKTVLSQHRGNGLRVRIGIHTGPVVAGVVGITMPRYCLFGDTVNLASRMESVGD---PGQILVS 178 (194)
T ss_pred HHHHHHHHHHHCCCCCCEEEEEEEEEEEEEEECCCCCCCCCEECHHHHHHHHHHCCCC---CCEEEEC
T ss_conf 9999999998646888517888973128999715777334534659999999972789---9989989
No 32
>cd01700 Pol_V Pol V was discovered in Escherichia coli as Umuc and UmuD proteins induced by UV. This branch of DNA polymerases is mostly found in bacteria. Pol V enables DNA replication to bypass covalently linked cys-sin T-T photo-dimers and 6-4 T-T or T-C photoproducts, which would otherwise stall the DNA replication fork.
Probab=84.81 E-value=1.2 Score=24.35 Aligned_cols=24 Identities=21% Similarity=0.148 Sum_probs=15.2
Q ss_pred CCCCHHHHHHHHHHHHHHHHHCCC
Q ss_conf 989989999999999999997099
Q gi|254781079|r 229 HKEPISTIIYRADQALYVAKKSGR 252 (266)
Q Consensus 229 ~~~~~~~ll~~Ad~Al~~AK~~gk 252 (266)
+-++.+++...|-..+...-+.|.
T Consensus 310 pT~~~~~I~~~a~~Ll~~~~~~~~ 333 (344)
T cd01700 310 PTSDTRDLIKAALRALEAIYRPGY 333 (344)
T ss_pred CCCCHHHHHHHHHHHHHHHHCCCC
T ss_conf 788999999999999999826999
No 33
>PRK03352 DNA polymerase IV; Validated
Probab=84.08 E-value=0.76 Score=25.91 Aligned_cols=18 Identities=17% Similarity=-0.014 Sum_probs=10.5
Q ss_pred CCCCHHHHHHHHHHHHHH
Q ss_conf 989989999999999999
Q gi|254781079|r 229 HKEPISTIIYRADQALYV 246 (266)
Q Consensus 229 ~~~~~~~ll~~Ad~Al~~ 246 (266)
+..+.+++...|-..+..
T Consensus 308 pT~~~~~i~~~a~~Ll~~ 325 (345)
T PRK03352 308 PTTDPDVITAAALDVLDL 325 (345)
T ss_pred CCCCHHHHHHHHHHHHHH
T ss_conf 559999999999999984
No 34
>cd03586 Pol_IV_kappa Pol_IV_kappa, a member of the Y-family of DNA polymerases. Pol_Y's can transverse replication-blocking DNA lesions, such as cyclobutane pyrimidine dimers resulting from UV damage, at the cost of an elevated error rate. The Y-family has no 3'-5' exonuclease activity. In addition to possessing a topology akin to a right hand, with "thumb", "fingers" and "palm" motifs, like polymerases from the A-, B-, C- and X-families, the Y-family has a unique "little finger" motif. Expression of Y-family polymerases is often induced by DNA damage. These polymerases are phylogenetically unrelated to classical DNA polymerases. Originally called the DinB family, they belong to the recently described Y-family of DNA polymerases. Pol IV is mostly found in bacteria and archaea. Although the structure of Pol IV is similar to that of Pol eta, it shows markedly differenct efficiencies and fidelities in bypassing various DNA lesions. All Pol IV-like polymerases studied to date are able to b
Probab=83.60 E-value=1.2 Score=24.45 Aligned_cols=24 Identities=17% Similarity=0.065 Sum_probs=15.0
Q ss_pred CCCCHHHHHHHHHHHHHHHHHCCC
Q ss_conf 989989999999999999997099
Q gi|254781079|r 229 HKEPISTIIYRADQALYVAKKSGR 252 (266)
Q Consensus 229 ~~~~~~~ll~~Ad~Al~~AK~~gk 252 (266)
+..+.+++...|-..+.+.-..|+
T Consensus 302 ~T~d~~~l~~~a~~ll~~~~~~~~ 325 (337)
T cd03586 302 PTNDTDDIYEAALELFEKLYDGGR 325 (337)
T ss_pred CCCCHHHHHHHHHHHHHHHHCCCC
T ss_conf 658999999999999999744899
No 35
>PRK03609 umuC DNA polymerase V subunit UmuC; Reviewed
Probab=81.44 E-value=2.3 Score=22.18 Aligned_cols=24 Identities=13% Similarity=0.034 Sum_probs=13.4
Q ss_pred HHHHHHHH-HHCCCCEEEECCHHHC
Q ss_conf 99999999-9709968999402100
Q gi|254781079|r 240 ADQALYVA-KKSGRNRVVCFSDIEN 263 (266)
Q Consensus 240 Ad~Al~~A-K~~gkn~~~~~~~~~~ 263 (266)
-+.+|..- ++-|++.+.+-+..-+
T Consensus 373 L~~~iD~In~rfG~~tI~~a~~~~~ 397 (422)
T PRK03609 373 LMKVLDTLNAKEGKGTLYFAGQGIQ 397 (422)
T ss_pred HHHHHHHHHHHHCCCEEEECCCCCC
T ss_conf 9999999998538995763137999
No 36
>PRK03858 DNA polymerase IV; Validated
Probab=80.20 E-value=1.7 Score=23.18 Aligned_cols=14 Identities=21% Similarity=0.117 Sum_probs=5.0
Q ss_pred CHHHHHHHHHHHHH
Q ss_conf 10123444589999
Q gi|254781079|r 188 SEQEAAILANDLRK 201 (266)
Q Consensus 188 ~~~~~~~~~~~l~~ 201 (266)
+.......+.++..
T Consensus 308 ~~~~i~~~a~~Ll~ 321 (398)
T PRK03858 308 STATILAAARELVA 321 (398)
T ss_pred CHHHHHHHHHHHHH
T ss_conf 99999999999999
No 37
>COG3835 CdaR Sugar diacid utilization regulator [Transcription / Signal transduction mechanisms]
Probab=78.70 E-value=4.9 Score=19.72 Aligned_cols=141 Identities=9% Similarity=0.037 Sum_probs=78.0
Q ss_pred HCCCHHCCCCHHHHHHHHHHC----CCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCCCC-CCCHHHCCCCCCE
Q ss_conf 104010502048999888770----89725755442210001146886544431100000001111-1000000133430
Q gi|254781079|r 105 RIDCLSGLLNHSAFISSLGSY----NEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVF-GTPMFVGRLGGEE 179 (266)
Q Consensus 105 ~~D~LTgL~NR~~f~~~l~~~----~~~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~~~~-~~~~~~~R~~gde 179 (266)
..|=+-.-.|-..|.+..+.. +.|-..+++...+ .+-..+...++.+...- ++++++-+.+++.
T Consensus 133 ~~~li~~~~~~~s~~~~Aq~lgiDLs~pR~ailv~~~~-----------~~~~~~~~~~~~~~~~~~~~~~~~i~~~~er 201 (376)
T COG3835 133 VSDLIQQKENTPSLAEWAQRLGIDLSKPRVAILVEGYN-----------EQLHNLQRMARLIQSSESRRNDVAILSLNER 201 (376)
T ss_pred HHHHHHCCCCCHHHHHHHHHHCCCCCCCCEEEEEECCC-----------CCCCCHHHHHHHHHHHCCCCCCEEEEECCCE
T ss_conf 99998565363889999998085557873799996467-----------7888089999999872355553367865726
Q ss_pred EEEECCCCC-HHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEECCCC-CCHHHHHHHHHHHHHHHHHCCC-CEEE
Q ss_conf 365016861-012344458999998631540679956899999999877998-9989999999999999997099-6899
Q gi|254781079|r 180 FAAAALGSS-EQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERCHK-EPISTIIYRADQALYVAKKSGR-NRVV 256 (266)
Q Consensus 180 F~ill~~~~-~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~t~s~Gia~~~~~-~~~~~ll~~Ad~Al~~AK~~gk-n~~~ 256 (266)
+++..+.+. ..+++....++...+...... .....++|+..+-.+ +....-...|..+|..++++.. .++.
T Consensus 202 vv~~~~~~~e~~~~~~~~~~i~~l~~~~~~~------~~~~~~ig~G~~~~~~~~l~~Sy~sA~~~l~~g~kr~p~~~i~ 275 (376)
T COG3835 202 VVLKPALSAERWDREVHSKRIEKLLARAKAY------GRLSLRIGAGNYFVGPDSLARSYESAKKTLEVGLKRKPESRIY 275 (376)
T ss_pred EEEECCCCCCCCHHHHHHHHHHHHHHHHHHC------CCCEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCE
T ss_conf 9995354432101667899999999998751------5410676447666784789999999999999987617888735
Q ss_pred ECCHHH
Q ss_conf 940210
Q gi|254781079|r 257 CFSDIE 262 (266)
Q Consensus 257 ~~~~~~ 262 (266)
+|+|..
T Consensus 276 fyedlr 281 (376)
T COG3835 276 FYEDLR 281 (376)
T ss_pred EECCCC
T ss_conf 541000
No 38
>PRK03103 DNA polymerase IV; Reviewed
Probab=77.07 E-value=4.3 Score=20.17 Aligned_cols=15 Identities=13% Similarity=0.140 Sum_probs=5.4
Q ss_pred HHHHHHH-HHCCCCEE
Q ss_conf 9999999-97099689
Q gi|254781079|r 241 DQALYVA-KKSGRNRV 255 (266)
Q Consensus 241 d~Al~~A-K~~gkn~~ 255 (266)
+.||..- ++-|++.+
T Consensus 371 ~~aiD~In~RfG~~~I 386 (410)
T PRK03103 371 GYVMDGIKEKYGDTAI 386 (410)
T ss_pred HHHHHHHHHHHCHHHH
T ss_conf 9999999986686389
No 39
>PRK01810 DNA polymerase IV; Validated
Probab=76.99 E-value=1.6 Score=23.34 Aligned_cols=29 Identities=14% Similarity=0.240 Sum_probs=11.4
Q ss_pred CCCCCCCCCC-----CCCHHHCCCCCCCCCCHHH
Q ss_conf 4688654443-----1100000001111100000
Q gi|254781079|r 144 DNFGHPVGDK-----VIAFLSDQLVVVFGTPMFV 172 (266)
Q Consensus 144 d~~G~~~gD~-----~L~~va~~l~~~~~~~~~~ 172 (266)
.++|++..|. .|...+....+-+|.....
T Consensus 252 ~tf~~~~~d~~~l~~~l~~l~~~va~rLR~~~~~ 285 (410)
T PRK01810 252 MTLSHDMDEEKELLDMLDRLSKSVSKRLQRKTLV 285 (410)
T ss_pred EECCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf 6679888999999999999999999999984982
No 40
>cd01701 Pol_zeta Pol_zeta, a member of the Y-family of DNA polymerases. Y-family polymerases can transverse normal replication-blocking DNA lesions, such as cyclobutane pyrimidine dimers resulting from UV damage, at higher error rate. The Y-family has no 3'-5' exonuclease activity. Pol zeta has also been named Rev1; this subfamily is mainly present in eukaryotes.
Probab=76.15 E-value=1.8 Score=23.06 Aligned_cols=15 Identities=13% Similarity=0.067 Sum_probs=6.6
Q ss_pred CCHHHHHHHHHHHHH
Q ss_conf 998999999999999
Q gi|254781079|r 231 EPISTIIYRADQALY 245 (266)
Q Consensus 231 ~~~~~ll~~Ad~Al~ 245 (266)
++.+++...|-.-+.
T Consensus 372 ~~~~~I~~~a~~Ll~ 386 (405)
T cd01701 372 DDFGVIGKEAKALFR 386 (405)
T ss_pred CCHHHHHHHHHHHHH
T ss_conf 999999999999999
No 41
>PRK01216 DNA polymerase IV; Validated
Probab=74.42 E-value=2.4 Score=22.04 Aligned_cols=21 Identities=10% Similarity=-0.154 Sum_probs=12.7
Q ss_pred CCCHHHHHHHHHHHHHHHHHC
Q ss_conf 899899999999999999970
Q gi|254781079|r 230 KEPISTIIYRADQALYVAKKS 250 (266)
Q Consensus 230 ~~~~~~ll~~Ad~Al~~AK~~ 250 (266)
..+.++++..|-..|.+.-..
T Consensus 304 ~t~~~~~~~~a~~lL~~~~~~ 324 (351)
T PRK01216 304 GISKDRAYSEALELLNKILEE 324 (351)
T ss_pred CCCHHHHHHHHHHHHHHHHHH
T ss_conf 878699999999999977752
No 42
>PRK02406 DNA polymerase IV; Validated
Probab=73.60 E-value=2.7 Score=21.69 Aligned_cols=16 Identities=19% Similarity=-0.068 Sum_probs=9.0
Q ss_pred CCHHHHHHHHHHHHHH
Q ss_conf 9989999999999999
Q gi|254781079|r 231 EPISTIIYRADQALYV 246 (266)
Q Consensus 231 ~~~~~ll~~Ad~Al~~ 246 (266)
.+.+++.+.|..-+..
T Consensus 311 ~~~~~i~~~a~~Ll~~ 326 (355)
T PRK02406 311 LSAEDLEQLARQLLAR 326 (355)
T ss_pred CCHHHHHHHHHHHHHH
T ss_conf 9999999999999974
No 43
>cd00424 Pol_Y Y-family of DNA polymerases. Pol_Y's can transverse replication-blocking DNA lesions, such as cyclobutane pyrimidine dimers resulting from UV damage, at the cost of an elevated error rate. The Y-family has no 3'-5' exonuclease activity. In addition to possessing a topology akin to a right hand, with "thumb", "fingers" and "palm" motifs, like polymerases from the A-, B-, C- and X-families, the Y-family has a unique "little finger" motif. Expression of Y-family polymerases is often induced by DNA damage. These polymerases are phylogenetically unrelated to classical DNA polymerases.
Probab=73.19 E-value=2.1 Score=22.60 Aligned_cols=17 Identities=12% Similarity=-0.037 Sum_probs=8.9
Q ss_pred CCHHHHHHHHHHHHHHH
Q ss_conf 99899999999999999
Q gi|254781079|r 231 EPISTIIYRADQALYVA 247 (266)
Q Consensus 231 ~~~~~ll~~Ad~Al~~A 247 (266)
.+...+.+.|..-+.+.
T Consensus 308 ~~~~~l~~~a~~Ll~~~ 324 (341)
T cd00424 308 SNNLLLLRVLDRLLRKL 324 (341)
T ss_pred CCHHHHHHHHHHHHHHH
T ss_conf 89999999999999997
No 44
>PRK02794 DNA polymerase IV; Provisional
Probab=73.05 E-value=4 Score=20.36 Aligned_cols=19 Identities=26% Similarity=0.207 Sum_probs=8.6
Q ss_pred HHHHHHHHH-HHCCCCEEEE
Q ss_conf 999999999-9709968999
Q gi|254781079|r 239 RADQALYVA-KKSGRNRVVC 257 (266)
Q Consensus 239 ~Ad~Al~~A-K~~gkn~~~~ 257 (266)
+.+.||..- ++=|++.+..
T Consensus 393 ~l~~aiD~In~RfG~~tI~~ 412 (417)
T PRK02794 393 AAERAIDALRAKFGAAAVER 412 (417)
T ss_pred HHHHHHHHHHHHHCCCCCCC
T ss_conf 99999999998647161021
No 45
>COG2114 CyaA Adenylate cyclase, family 3 (some proteins contain HAMP domain) [Signal transduction mechanisms]
Probab=70.70 E-value=7.5 Score=18.30 Aligned_cols=132 Identities=17% Similarity=0.202 Sum_probs=68.9
Q ss_pred CCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCC-CCHHHCCCCCCEEEEECCCCCH-HHHHHHHHHHHHHHH
Q ss_conf 97257554422100011468865444311000000011111-0000001334303650168610-123444589999986
Q gi|254781079|r 127 EKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFG-TPMFVGRLGGEEFAAAALGSSE-QEAAILANDLRKIIE 204 (266)
Q Consensus 127 ~~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~~~~~-~~~~~~R~~gdeF~ill~~~~~-~~~~~~~~~l~~~l~ 204 (266)
...++++.||-+|..+.+..|.+.--+++...-..+...+. .+..+-++-||-|...++.... +++...+........
T Consensus 45 ~~vtilfaDi~g~T~l~~~~~~~~~~~ll~~~~~~~~~~v~~~gG~v~k~iGD~~la~F~~p~~~~~A~~~a~~~~~~~~ 124 (227)
T COG2114 45 RRVTLLFADIVGSTELSESLGDEALVELLNLYFDAVAEVVARHGGRVVKFIGDGFLAVFGRPSPLEDAVACALDLQLALR 124 (227)
T ss_pred CEEEEEEEECCCCHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECEEEEEECCCCCCHHHHHHHHHHHHHHHH
T ss_conf 32899998720305566437868999999999999999999839779986531899972899975999999999889999
Q ss_pred HCCCCCCCC-CEEEEEEEEEEEECCCC---CCHHHHHHHHHHHHHHHHHCCCCEEEECCHH
Q ss_conf 315406799-56899999999877998---9989999999999999997099689994021
Q gi|254781079|r 205 NSQINISSG-PSIHITISAGIAERCHK---EPISTIIYRADQALYVAKKSGRNRVVCFSDI 261 (266)
Q Consensus 205 ~~~~~~~~~-~~~~~t~s~Gia~~~~~---~~~~~ll~~Ad~Al~~AK~~gkn~~~~~~~~ 261 (266)
......... ..+.+.+..|-+...+. +-.-+-...|-.--..|| ++++++-+++
T Consensus 125 ~~~~~~~~~~l~~riGi~~G~vv~~~~g~~~~~G~~VN~AaRLe~~a~---~g~i~iS~~~ 182 (227)
T COG2114 125 NPLARLRRESLRVRIGIHTGEVVVGNTGGYTVVGSAVNQAARLESLAK---PGQVLLSEAT 182 (227)
T ss_pred HHHHHCCCCCCEEEEEEECCCEEEECCCCCEEECHHHHHHHHHHHCCC---CCCEEEEHHH
T ss_conf 998643576614899971364388316774564589879999984168---9929960999
No 46
>pfam00817 IMS impB/mucB/samB family. These proteins are involved in UV protection.
Probab=61.62 E-value=5.4 Score=19.40 Aligned_cols=62 Identities=23% Similarity=0.101 Sum_probs=36.8
Q ss_pred CCHHHCCCCCCCCCCHHHCCCCCCEEEEECCCC--CHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEEC
Q ss_conf 100000001111100000013343036501686--1012344458999998631540679956899999999877
Q gi|254781079|r 155 IAFLSDQLVVVFGTPMFVGRLGGEEFAAAALGS--SEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAER 227 (266)
Q Consensus 155 L~~va~~l~~~~~~~~~~~R~~gdeF~ill~~~--~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~t~s~Gia~~ 227 (266)
...+.+.+..... +.+-.++-||+.+=+.+. .......++++|++.+.+. ..+++|+|++..
T Consensus 76 s~~i~~~l~~~~~--~~ve~~siDE~~ld~t~~~~~~~~~~~la~~ir~~i~~~---------~gl~~siGia~n 139 (148)
T pfam00817 76 SRRIAEILRRFSS--PKVEVYSIDEAFLDLTGLLRLFGGEEELAKRLRRAIAEE---------TGLTCSIGIAPN 139 (148)
T ss_pred HHHHHHHHHHHCC--CEEEECCCCEEEEECCCHHHHCCCHHHHHHHHHHHHHHH---------HCCEEEEEEECC
T ss_conf 9999999998699--869764777156864745542589999999999999998---------798289977168
No 47
>PRK08134 O-acetylhomoserine aminocarboxypropyltransferase; Validated
Probab=59.59 E-value=12 Score=16.80 Aligned_cols=94 Identities=19% Similarity=0.197 Sum_probs=52.6
Q ss_pred CCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCHHHCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 89725755442210001146886544431100000001111100000013343036501686101234445899999863
Q gi|254781079|r 126 NEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIEN 205 (266)
Q Consensus 126 ~~~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~~~~~~~~~~~R~~gdeF~ill~~~~~~~~~~~~~~l~~~l~~ 205 (266)
+...+++-+++++ |.+.+ ..+.+.++ --....-+||-|=.+..|....... +-..-+...
T Consensus 339 ~G~Gg~~sf~l~g--------~~~~~----~~f~~~l~----lf~~a~SlGg~eSLi~~Pa~~th~~--~~~e~~~~~-- 398 (433)
T PRK08134 339 RGAGSVFSFDLKG--------GRAAG----RKFIESLK----LFSHLANVGDARSLVIHPASTTHFR--MDAAALAAA-- 398 (433)
T ss_pred CCCEEEEEEEEEC--------CHHHH----HHHHHHCC----CCCCCCCCCCCCCEEECCCCCCCCC--CCHHHHHHC--
T ss_conf 9965899999969--------99999----99998388----1301226687530346763234635--899999866--
Q ss_pred CCCCCCCCCEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHCC
Q ss_conf 1540679956899999999877998998999999999999999709
Q gi|254781079|r 206 SQINISSGPSIHITISAGIAERCHKEPISTIIYRADQALYVAKKSG 251 (266)
Q Consensus 206 ~~~~~~~~~~~~~t~s~Gia~~~~~~~~~~ll~~Ad~Al~~AK~~g 251 (266)
.....-+ -+|+|+ +++++|+..-++||..||+.|
T Consensus 399 ----Gi~~~lv--RlSvGl------Ed~eDLi~DL~qAL~aa~~~~ 432 (433)
T PRK08134 399 ----GIGEGTI--RLSIGL------EDADDLIDDLKRALKAAEKAG 432 (433)
T ss_pred ----CCCCCEE--EEEECC------CCHHHHHHHHHHHHHHHHHCC
T ss_conf ----9893949--999411------999999999999999988745
No 48
>TIGR00004 TIGR00004 endoribonuclease L-PSP, putative; InterPro: IPR006056 This family includes proteins encoded by the yabJ gene from Bacillus subtilis that is required for adenine-mediated repression of purine biosynthetic genes in vivo and codes for an acid-soluble, 14-kDa protein. The structure of this protein has been solved and the protein is found to form a homotrimer. The trimer has a deep cleft that is a probably ligand binding site and possibly forms an enzymatic active site. However the ligand and reaction are unknown..
Probab=55.55 E-value=2.4 Score=22.15 Aligned_cols=47 Identities=15% Similarity=0.267 Sum_probs=34.0
Q ss_pred HCCCHHCCCCHHH-HHHHHHH-----------CCCC------EEEEEEECCCCCCCCCCCCCCCC
Q ss_conf 1040105020489-9988877-----------0897------25755442210001146886544
Q gi|254781079|r 105 RIDCLSGLLNHSA-FISSLGS-----------YNEK------LSIVFFDIDYFKQINDNFGHPVG 151 (266)
Q Consensus 105 ~~D~LTgL~NR~~-f~~~l~~-----------~~~~------~~l~~idid~fk~iNd~~G~~~g 151 (266)
=.||-||-.+.-. +.+|.++ .+.+ .++.+=||++|..+|+.||.=..
T Consensus 33 PldP~Tge~v~~g~~~eQa~Qvl~NlkAiL~aAG~~~~~vVK~TvfL~D~~dFA~vNevY~~YF~ 97 (129)
T TIGR00004 33 PLDPETGELVGGGDIAEQAEQVLENLKAILEAAGLSLDDVVKTTVFLTDLNDFAEVNEVYGQYFD 97 (129)
T ss_pred CCCCCCCEECCCCCHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCHHHHHHHHHHHHHHCC
T ss_conf 75898875727987888898999989999998279846668886630265668899989887548
No 49
>PRK09509 fieF ferrous iron efflux protein F; Reviewed
Probab=52.61 E-value=9.6 Score=17.49 Aligned_cols=68 Identities=12% Similarity=0.084 Sum_probs=47.4
Q ss_pred CCCCCCCCCCCCCCCCCHHHCCCCC---CCCCCHHHCCCCCCEEEE-----ECCCCCHHHHHHHHHHHHHHHHHCC
Q ss_conf 0011468865444311000000011---111000000133430365-----0168610123444589999986315
Q gi|254781079|r 140 KQINDNFGHPVGDKVIAFLSDQLVV---VFGTPMFVGRLGGEEFAA-----AALGSSEQEAAILANDLRKIIENSQ 207 (266)
Q Consensus 140 k~iNd~~G~~~gD~~L~~va~~l~~---~~~~~~~~~R~~gdeF~i-----ll~~~~~~~~~~~~~~l~~~l~~~~ 207 (266)
+.+++..|...-++.+.++.+.+.+ ..+-+++-.|..|+.+.+ +-|+.+..++..+++++++.+.+..
T Consensus 200 es~~~Lld~~~~~e~~~~I~~~i~~~~gV~~vh~lr~r~~G~~~~vd~hI~v~~~lsv~eaH~I~~~ve~~i~~~~ 275 (300)
T PRK09509 200 EAVQSLLDRALPDEERQEIIDIVTSWPGVSGAHDLRTRQSGPTRFIQLHLEMEDNLPLVQAHMVADQVEQALLRRF 275 (300)
T ss_pred HHHHHHHCCCCCHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHC
T ss_conf 9999985779998999999999972889877026898985892999999998979989999999999999999767
No 50
>COG0053 MMT1 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]
Probab=49.25 E-value=17 Score=15.62 Aligned_cols=106 Identities=20% Similarity=0.217 Sum_probs=61.8
Q ss_pred HHHHCCCHHCCCCHHHHHHHHH--HCCCCE-------EEEEEECCCCC-CCCCCCCCCCCCCCCCHHHCCCCC---CCCC
Q ss_conf 9961040105020489998887--708972-------57554422100-011468865444311000000011---1110
Q gi|254781079|r 102 QLSRIDCLSGLLNHSAFISSLG--SYNEKL-------SIVFFDIDYFK-QINDNFGHPVGDKVIAFLSDQLVV---VFGT 168 (266)
Q Consensus 102 ~~a~~D~LTgL~NR~~f~~~l~--~~~~~~-------~l~~idid~fk-~iNd~~G~~~gD~~L~~va~~l~~---~~~~ 168 (266)
.....|-+|.+.--..+.-..- .+-.+. .++....+-+| .++...|+..-++.+.++-+.+.. ..+-
T Consensus 154 ~h~~sD~~ts~~~lvgl~~~~~g~~~lD~i~a~~I~~~Il~~~~~~~~~s~~~L~d~~~~~~~~~~i~~~i~~~~~V~~v 233 (304)
T COG0053 154 LHHRSDVLTSLAVLVGLLGSLLGWPWLDPLAALLISLYILKTGFRLFKESVNELMDAALDPEDLEKIRAIILSVPGVKGV 233 (304)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCCCCCC
T ss_conf 88872999999999999999928398989999999999999999999999999847689989999999998466455230
Q ss_pred CHHHCCCCCCEEEE-----ECCCCCHHHHHHHHHHHHHHHHHCC
Q ss_conf 00000133430365-----0168610123444589999986315
Q gi|254781079|r 169 PMFVGRLGGEEFAA-----AALGSSEQEAAILANDLRKIIENSQ 207 (266)
Q Consensus 169 ~~~~~R~~gdeF~i-----ll~~~~~~~~~~~~~~l~~~l~~~~ 207 (266)
+++-.|+.|....+ +-|+.+.+++..+++++.+.+.+..
T Consensus 234 ~~lr~R~~G~~~~id~~i~v~~~ls~~eah~I~~~ie~~i~~~~ 277 (304)
T COG0053 234 HDLRTRKSGSRIFIDVHIEVDPDLSLEEAHEIADEVEKRIKKEF 277 (304)
T ss_pred HHEEEEEECCEEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHHC
T ss_conf 10156665887999999971999988889999999999999756
No 51
>PRK05066 arginine repressor; Provisional
Probab=48.58 E-value=15 Score=16.04 Aligned_cols=48 Identities=13% Similarity=0.158 Sum_probs=29.0
Q ss_pred HHHCCCCCCCCCCHHHCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 0000001111100000013343036501686101234445899999863
Q gi|254781079|r 157 FLSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIEN 205 (266)
Q Consensus 157 ~va~~l~~~~~~~~~~~R~~gdeF~ill~~~~~~~~~~~~~~l~~~l~~ 205 (266)
.+|..|-..-.+..+++=++||+=+++++ .+.+++..+.++|+..+++
T Consensus 107 ~vA~~iD~~~~~e~IlGTIAGDDTI~Vi~-~~~~~a~~l~~~l~~lle~ 154 (156)
T PRK05066 107 LIARLLDSLGKAEGILGTIAGDDTIFITP-ASGFTIEELLEAILELFEQ 154 (156)
T ss_pred HHHHHHHHCCCCCCEEEEECCCCEEEEEE-CCHHHHHHHHHHHHHHHHC
T ss_conf 99999982689766489971799899996-8867899999999999852
No 52
>cd01703 Pol_iota Pol iota is member of the DNA polymerase Y-family, and has also been called Rad30 homolog B. Unlike classic DNA polymerases,Y-family polymerases are induced by DNA damage. They can transverse normal replication-blocking DNA lesions. Unlike Pol eta, Pol iota is unable to replicate through a cis-syn T-T dimer. In human Pol iota, the base-pairing mode in the active site at the replicative end mat bee Hoogsteen instead of Watson-Click. Human Pol iota can incorporate the correct nucleotide opposite a purine much more efficiently than opposite a pyrimidine. Pol iota prefers to insert Guanosine instead of Adenosine opposite Thymidine.
Probab=48.03 E-value=11 Score=17.06 Aligned_cols=13 Identities=23% Similarity=0.174 Sum_probs=5.1
Q ss_pred HHHHHHHHHHHHH
Q ss_conf 2344458999998
Q gi|254781079|r 191 EAAILANDLRKII 203 (266)
Q Consensus 191 ~~~~~~~~l~~~l 203 (266)
+...++..|...+
T Consensus 297 ~l~~~~~~L~~Rl 309 (394)
T cd01703 297 ELEELLRSLLERL 309 (394)
T ss_pred HHHHHHHHHHHHH
T ss_conf 9999999999999
No 53
>PTZ00205 DNA polymerase kappa; Provisional
Probab=45.37 E-value=11 Score=17.02 Aligned_cols=62 Identities=19% Similarity=0.148 Sum_probs=32.3
Q ss_pred CHHHCCCCCCCCCC-HHHCCCCCCEEEEECCC-----CCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEE
Q ss_conf 00000001111100-00001334303650168-----6101234445899999863154067995689999999987
Q gi|254781079|r 156 AFLSDQLVVVFGTP-MFVGRLGGEEFAAAALG-----SSEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAE 226 (266)
Q Consensus 156 ~~va~~l~~~~~~~-~~~~R~~gdeF~ill~~-----~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~t~s~Gia~ 226 (266)
+++++.+++.+... ..+-.+|=||=.+=+.+ .....+..+++.|+..+.+. ..+|+|+||++
T Consensus 207 r~vS~~Ir~If~~Ytp~vE~lSLDEAYLDVT~~~~~~~g~~ta~~IA~eIR~~I~~e---------TgLT~SAGIAp 274 (571)
T PTZ00205 207 NEESNTVRRIVAEYDPNYISFGLDELTLEVSAYIERFEGTKTAEDVASELRVRVFGE---------TKLTASAGIGP 274 (571)
T ss_pred HHHHHHHHHHHHHHCCCCCCCCCCEEEEECCHHHHHCCCCCCHHHHHHHHHHHHHHH---------HCCCEEECCHH
T ss_conf 999999999999818303335524134644043442379998999999999999998---------69944655404
No 54
>KOG2095 consensus
Probab=44.30 E-value=12 Score=16.71 Aligned_cols=18 Identities=22% Similarity=0.414 Sum_probs=8.2
Q ss_pred CCCCCCCCCCCCCHHHCCC
Q ss_conf 4688654443110000000
Q gi|254781079|r 144 DNFGHPVGDKVIAFLSDQL 162 (266)
Q Consensus 144 d~~G~~~gD~~L~~va~~l 162 (266)
+.||...| ..|+.++.-+
T Consensus 294 ~~fg~~~g-~~l~~la~Gi 311 (656)
T KOG2095 294 KKFGEKNG-TWLRNLARGI 311 (656)
T ss_pred HHHCCCHH-HHHHHHHCCC
T ss_conf 86084101-8999886166
No 55
>COG1902 NemA NADH:flavin oxidoreductases, Old Yellow Enzyme family [Energy production and conversion]
Probab=41.42 E-value=10 Score=17.37 Aligned_cols=59 Identities=22% Similarity=0.321 Sum_probs=39.6
Q ss_pred CCCCCCCCC--CCCCCHHHCCCCCCCCCCH-HHCCCCCCEEEEECCCCCHHHHHHHHHHHHHH
Q ss_conf 146886544--4311000000011111000-00013343036501686101234445899999
Q gi|254781079|r 143 NDNFGHPVG--DKVIAFLSDQLVVVFGTPM-FVGRLGGEEFAAAALGSSEQEAAILANDLRKI 202 (266)
Q Consensus 143 Nd~~G~~~g--D~~L~~va~~l~~~~~~~~-~~~R~~gdeF~ill~~~~~~~~~~~~~~l~~~ 202 (266)
+|.||-..- =+++.+|.+.+++.++++- +.+|++.+|| -.-.+.+.++...+++.|...
T Consensus 188 tD~YGGSlENR~Rf~~EVv~aVr~~vg~~~~vg~Rls~~d~-~~~~g~~~~e~~~la~~L~~~ 249 (363)
T COG1902 188 TDEYGGSLENRARFLLEVVDAVREAVGADFPVGVRLSPDDF-FDGGGLTIEEAVELAKALEEA 249 (363)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCC-CCCCCCCHHHHHHHHHHHHHC
T ss_conf 77668858999889999999999972988669999774546-778888899999999999855
No 56
>PRK05506 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional
Probab=40.18 E-value=20 Score=15.05 Aligned_cols=88 Identities=15% Similarity=0.217 Sum_probs=44.2
Q ss_pred HHCCCHHCCCCH------HHHHHHHHHCCCCEEEEEEECCCCC-CCCCCCCCCCCCCC--CCHHHC---CCCC-------
Q ss_conf 610401050204------8999888770897257554422100-01146886544431--100000---0011-------
Q gi|254781079|r 104 SRIDCLSGLLNH------SAFISSLGSYNEKLSIVFFDIDYFK-QINDNFGHPVGDKV--IAFLSD---QLVV------- 164 (266)
Q Consensus 104 a~~D~LTgL~NR------~~f~~~l~~~~~~~~l~~idid~fk-~iNd~~G~~~gD~~--L~~va~---~l~~------- 164 (266)
...==+|||+.- ..+..+|.+.+. ...++|=|++. .+|.-+|+...|+. ++.++. .+..
T Consensus 443 ~~~iw~tGlsgsGKstiA~~le~~L~~~g~--~~~~LDGd~lR~gl~~dlgf~~~dR~enirR~~eva~l~~~aG~i~i~ 520 (613)
T PRK05506 443 PATVWFTGLSGSGKSTIANLVERRLHALGR--HTYVLDGDNVRHGLNRDLGFTDADRVENIRRVAEVARLMADAGLIVLV 520 (613)
T ss_pred CEEEEEECCCCCCHHHHHHHHHHHHHHCCC--CEEEECCHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEE
T ss_conf 769999778989747999999999997799--879988089874104577979899999999999999999868988999
Q ss_pred -CCC---CCHHHC--CCCCCEEEEECCCCCHHHHH
Q ss_conf -111---000000--13343036501686101234
Q gi|254781079|r 165 -VFG---TPMFVG--RLGGEEFAAAALGSSEQEAA 193 (266)
Q Consensus 165 -~~~---~~~~~~--R~~gdeF~ill~~~~~~~~~ 193 (266)
.+. ..--.+ .+++++|.-++-+++.+.++
T Consensus 521 a~iSp~~~~R~~~r~~~~~~~f~Ev~v~~~le~c~ 555 (613)
T PRK05506 521 SFISPFREERELARALIGEGEFVEVFVDTPLEVCE 555 (613)
T ss_pred ECCCCCHHHHHHHHHHCCCCCEEEEEEECCHHHHH
T ss_conf 75889989999999757888789999908999997
No 57
>cd02930 DCR_FMN 2,4-dienoyl-CoA reductase (DCR) FMN-binding domain. DCR in E. coli is an iron-sulfur flavoenzyme which contains FMN, FAD, and a 4Fe-4S cluster. It is also a monomer, unlike that of its eukaryotic counterparts which form homotetramers and lack the flavin and iron-sulfur cofactors. Metabolism of unsaturated fatty acids requires auxiliary enzymes in addition to those used in b-oxidation. After a given number of cycles through the b-oxidation pathway, those unsaturated fatty acyl-CoAs with double bonds at even-numbered carbon positions contain 2-trans, 4-cis double bonds that can not be modified by enoyl-CoA hydratase. DCR utilizes NADPH to remove the C4-C5 double bond. DCR can catalyze the reduction of both natural fatty acids with cis double bonds, as well as substrates containing trans double bonds. The reaction is initiated by hybrid transfer from NADPH to FAD, which in turn transfers electrons, one at a time, to FMN via the 4Fe-4S cluster. The fully reduced FMN provi
Probab=36.08 E-value=16 Score=15.85 Aligned_cols=56 Identities=20% Similarity=0.289 Sum_probs=36.6
Q ss_pred CCCCCCCCCC--CCCCHHHCCCCCCCCCC-HHHCCCCCCEEEEECCCCCHHHHHHHHHHHH
Q ss_conf 1468865444--31100000001111100-0000133430365016861012344458999
Q gi|254781079|r 143 NDNFGHPVGD--KVIAFLSDQLVVVFGTP-MFVGRLGGEEFAAAALGSSEQEAAILANDLR 200 (266)
Q Consensus 143 Nd~~G~~~gD--~~L~~va~~l~~~~~~~-~~~~R~~gdeF~ill~~~~~~~~~~~~~~l~ 200 (266)
.|.||-..-+ +++.+|.+.+++.++++ -+..|++++|+. --+.+.++...+++.|.
T Consensus 176 tDeYGGs~eNR~Rf~~Eiv~aVr~~vg~d~~v~~Ris~~d~~--~~G~~~~e~~~~~~~l~ 234 (353)
T cd02930 176 TDEWGGSFENRMRFPVEIVRAVRAAVGEDFIIIYRLSMLDLV--EGGSTWEEVVALAKALE 234 (353)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCC--CCCCCHHHHHHHHHHHH
T ss_conf 574579878887999999999999709987499973601268--99989999999999999
No 58
>cd01127 TrwB Bacterial conjugation protein TrwB, ATP binding domain. TrwB is a homohexamer encoded by conjugative plasmids in Gram-negative bacteria. TrwB also has an all alpha domain which has been hypothesized to be responsible for DNA binding. TrwB is a component of Type IV secretion and is responsible for the horizontal transfer of DNA between bacteria.
Probab=35.89 E-value=11 Score=17.06 Aligned_cols=12 Identities=33% Similarity=0.769 Sum_probs=4.0
Q ss_pred CCCCCCCCCCCC
Q ss_conf 221000114688
Q gi|254781079|r 136 IDYFKQINDNFG 147 (266)
Q Consensus 136 id~fk~iNd~~G 147 (266)
+.++.++.+.||
T Consensus 306 ~Q~~~Ql~~~YG 317 (410)
T cd01127 306 IQSYAQLEDIYG 317 (410)
T ss_pred ECCHHHHHHHHC
T ss_conf 178899999978
No 59
>KOG3330 consensus
Probab=35.36 E-value=22 Score=14.73 Aligned_cols=19 Identities=21% Similarity=0.172 Sum_probs=13.6
Q ss_pred CCCCEEEEECCCCCHHHHH
Q ss_conf 3343036501686101234
Q gi|254781079|r 175 LGGEEFAAAALGSSEQEAA 193 (266)
Q Consensus 175 ~~gdeF~ill~~~~~~~~~ 193 (266)
-+|+||.+++.+.+..+..
T Consensus 100 s~~~efsliLe~NPL~efV 118 (183)
T KOG3330 100 SDGNEFSLILEDNPLVEFV 118 (183)
T ss_pred CCCCEEEEEECCCCHHHHH
T ss_conf 9998899996678479998
No 60
>PRK07503 methionine gamma-lyase; Provisional
Probab=35.01 E-value=27 Score=14.07 Aligned_cols=118 Identities=19% Similarity=0.183 Sum_probs=61.5
Q ss_pred HHHHHCCCHH-----CCCCHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCHHHCCC
Q ss_conf 9996104010-----50204899988877089725755442210001146886544431100000001111100000013
Q gi|254781079|r 101 SQLSRIDCLS-----GLLNHSAFISSLGSYNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFGTPMFVGRL 175 (266)
Q Consensus 101 ~~~a~~D~LT-----gL~NR~~f~~~l~~~~~~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~~~~~~~~~~~R~ 175 (266)
+.+..+..+. ||++.-...-.-+......+++.+++++ |.+.+ +.+.+. ++--....-|
T Consensus 278 ~~L~~hp~V~~V~yPgL~shp~h~la~~q~~g~gg~~sf~l~g--------~~~~~----~~f~~~----L~lf~~a~Sl 341 (403)
T PRK07503 278 EFLARQPAVELVHYPGLPSFAQHALAQRQMRLPGGMIAFELKG--------GIEAG----RRFMNA----LQLFARAVSL 341 (403)
T ss_pred HHHHHCCCCCEEECCCCCCCCCHHHHHHHCCCCCCEEEEEECC--------CHHHH----HHHHHH----CCCCEEECCC
T ss_conf 9997489955898988889801899998678998368999669--------89999----999980----8946553166
Q ss_pred CCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHC
Q ss_conf 343036501686101234445899999863154067995689999999987799899899999999999999970
Q gi|254781079|r 176 GGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERCHKEPISTIIYRADQALYVAKKS 250 (266)
Q Consensus 176 ~gdeF~ill~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~t~s~Gia~~~~~~~~~~ll~~Ad~Al~~AK~~ 250 (266)
||-|=.+..|....... +...-+... - ..+ .- +-+|+|+ +++++|+.--++||..+|..
T Consensus 342 Gg~eSLi~~pa~~th~~--~~~e~r~~~---G--i~~-~l--iRlSVGl------Ed~~DLi~DL~qAL~a~k~~ 400 (403)
T PRK07503 342 GDAESLAQHPASMTHST--YTPEERAHH---G--ISE-GL--VRLSVGL------EDVEDLLADIAQALDACKVP 400 (403)
T ss_pred CCCCCEEECCCCCCCCC--CCHHHHHHC---C--CCC-CE--EEEEECC------CCHHHHHHHHHHHHHHHHHH
T ss_conf 77540324763346655--999999866---9--893-96--9998601------89999999999999973020
No 61
>COG0404 GcvT Glycine cleavage system T protein (aminomethyltransferase) [Amino acid transport and metabolism]
Probab=34.95 E-value=23 Score=14.57 Aligned_cols=59 Identities=15% Similarity=0.246 Sum_probs=29.4
Q ss_pred EEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCC----------------CCCCCHHHCCCCCCEEEEECCCCCH
Q ss_conf 57554422100011468865444311000000011----------------1110000001334303650168610
Q gi|254781079|r 130 SIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVV----------------VFGTPMFVGRLGGEEFAAAALGSSE 189 (266)
Q Consensus 130 ~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~~----------------~~~~~~~~~R~~gdeF~ill~~~~~ 189 (266)
.+-++|+.+|.+| +.-|.++..-+=+.+++.+.. .+.++-+++|++.|+|.++......
T Consensus 47 ~aGlfDvShmgk~-~V~GpdA~~~L~~l~~ndv~kl~~Gr~~Yt~~lne~G~v~dD~~v~rl~~d~f~lv~~a~~~ 121 (379)
T COG0404 47 AAGLFDVSHMGKV-EVSGPDAAAFLQRLLTNDVSKLKPGRARYTLMLNEDGGIIDDLIVYRLGEDRFFLVTNAATA 121 (379)
T ss_pred CCCEEECCCCEEE-EEECCCHHHHHHHHCCCCCCCCCCCCEEEEEEECCCCCEEEEEEEEEECCCEEEEEECCCCH
T ss_conf 5745864685699-99898999999977056667677774887245879998874179997269869999476662
No 62
>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]
Probab=34.66 E-value=27 Score=14.03 Aligned_cols=87 Identities=16% Similarity=0.250 Sum_probs=51.1
Q ss_pred HCCCHHCCCCH------HHHHHHHHHCCCCEEEEEEECCCCCC-CCCCCCCCCCCCC--CCHHHCCCCCCCCCC------
Q ss_conf 10401050204------89998887708972575544221000-1146886544431--100000001111100------
Q gi|254781079|r 105 RIDCLSGLLNH------SAFISSLGSYNEKLSIVFFDIDYFKQ-INDNFGHPVGDKV--IAFLSDQLVVVFGTP------ 169 (266)
Q Consensus 105 ~~D~LTgL~NR------~~f~~~l~~~~~~~~l~~idid~fk~-iNd~~G~~~gD~~--L~~va~~l~~~~~~~------ 169 (266)
..==+|||.-- .++.++|...+ ..+.++|=|+... .|.-+|+...|+. ++.+|..-+.....+
T Consensus 24 ~viW~TGLSGsGKSTiA~ale~~L~~~G--~~~y~LDGDnvR~gL~~dLgFs~edR~eniRRvaevAkll~daG~iviva 101 (197)
T COG0529 24 AVIWFTGLSGSGKSTIANALEEKLFAKG--YHVYLLDGDNVRHGLNRDLGFSREDRIENIRRVAEVAKLLADAGLIVIVA 101 (197)
T ss_pred EEEEEECCCCCCHHHHHHHHHHHHHHCC--CEEEEECCHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCEEEEEE
T ss_conf 5999646888878799999999999759--75898557467650057889786789999999999999998789089997
Q ss_pred ---------HH-HCCCCCCEEEEECCCCCHHHHH
Q ss_conf ---------00-0013343036501686101234
Q gi|254781079|r 170 ---------MF-VGRLGGEEFAAAALGSSEQEAA 193 (266)
Q Consensus 170 ---------~~-~~R~~gdeF~ill~~~~~~~~~ 193 (266)
+. -..++.++|.=++.+++.+.++
T Consensus 102 ~ISP~r~~R~~aR~~~~~~~FiEVyV~~pl~vce 135 (197)
T COG0529 102 FISPYREDRQMARELLGEGEFIEVYVDTPLEVCE 135 (197)
T ss_pred EECCCHHHHHHHHHHHCCCCEEEEEECCCHHHHH
T ss_conf 5173099999999972768628999579899998
No 63
>cd01702 Pol_eta Pol eta is member of the DNA polimerase Y-family. Unlike other Y-family members, Pol eta can efficiently and accurately replicate DNA past UV-induced cis-syn cyclobutane thymine-thumine (T-T) lesions. It synthesizes AA opposite a TT dimer. Pol eta is able to replicate through a variety of other distorting DNA lesion as well.
Probab=33.29 E-value=11 Score=17.06 Aligned_cols=22 Identities=14% Similarity=0.217 Sum_probs=13.0
Q ss_pred CCCHHHHHHHHHHHHHHHHHCC
Q ss_conf 8998999999999999999709
Q gi|254781079|r 230 KEPISTIIYRADQALYVAKKSG 251 (266)
Q Consensus 230 ~~~~~~ll~~Ad~Al~~AK~~g 251 (266)
..+.++++..|-..+.+--+.|
T Consensus 320 ~~d~~~i~~~A~~ll~~i~~~~ 341 (358)
T cd01702 320 YDDLEKLVKDAFKLLKQLNREG 341 (358)
T ss_pred CCCHHHHHHHHHHHHHHHHHHC
T ss_conf 9999999999999999998606
No 64
>PRK13665 hypothetical protein; Provisional
Probab=32.92 E-value=29 Score=13.83 Aligned_cols=91 Identities=23% Similarity=0.308 Sum_probs=48.4
Q ss_pred CCCHHHCCCCCCEEEEECCCC--CHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEECCCCCCH----HHHHHHH
Q ss_conf 100000013343036501686--1012344458999998631540679956899999999877998998----9999999
Q gi|254781079|r 167 GTPMFVGRLGGEEFAAAALGS--SEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERCHKEPI----STIIYRA 240 (266)
Q Consensus 167 ~~~~~~~R~~gdeF~ill~~~--~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~t~s~Gia~~~~~~~~----~~ll~~A 240 (266)
.+..+++|.|.- .+-.-+. +.++...--+.|.....+.. ...|...++ +|+-|+..+-|++. +.--..|
T Consensus 167 ~EeTIiARVGEg--IVs~IGSa~~hk~VLEnPd~ISk~VL~kg--LDagTAFeI-lSIDIADidVG~NIGA~Lq~dQAeA 241 (327)
T PRK13665 167 GEETIIARVGEG--IVSTIGSSESHKEVLENPDSISKTVLSKG--LDAGTAFEI-LSIDIADVDIGKNIGAKLQTDQAEA 241 (327)
T ss_pred CHHHHHHHHCCC--EEEEECCHHHHHHHHCCHHHHHHHHHHCC--CCCCCEEEE-EEEEEECCCCCCHHCHHHHHHHHHH
T ss_conf 412234333464--13000370258888629878799999636--786851699-9876534422400153440677767
Q ss_pred HHHHHHHHHCCCCEEEECCHHH
Q ss_conf 9999999970996899940210
Q gi|254781079|r 241 DQALYVAKKSGRNRVVCFSDIE 262 (266)
Q Consensus 241 d~Al~~AK~~gkn~~~~~~~~~ 262 (266)
|....+||.+.|.--....++|
T Consensus 242 Dk~vAqAkAE~RRA~AvA~EQE 263 (327)
T PRK13665 242 DKNIAQAKAEERRAMAVALEQE 263 (327)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
T ss_conf 7899998788899999999999
No 65
>cd03133 GATase1_ES1 Type 1 glutamine amidotransferase (GATase1)-like domain found in zebrafish ES1. Type 1 glutamine amidotransferase (GATase1)-like domain found in zebrafish ES1. This group includes, proteins similar to ES1, Escherichia coli enhancing lycopene biosynthesis protein 2, Azospirillum brasilense iaaC and, human HES1. The catalytic triad typical of GATase1domains is not conserved in this GATase1-like domain. However, in common with GATase1domains a reactive cys residue is found in the sharp turn between a beta strand and an alpha helix termed the nucleophile elbow. Zebrafish ES1 is expressed specifically in adult photoreceptor cells and appears to be a cytoplasmic protein. A. brasilense iaaC is involved in controlling IAA biosynthesis.
Probab=32.46 E-value=30 Score=13.77 Aligned_cols=63 Identities=17% Similarity=0.197 Sum_probs=38.0
Q ss_pred HHHCCCCEEEEEEECCCCCCCCCCCCCCCCCC--CCCHHHCCCCCCCCCCHHHCCCCCCEE-EEECCCC
Q ss_conf 87708972575544221000114688654443--110000000111110000001334303-6501686
Q gi|254781079|r 122 LGSYNEKLSIVFFDIDYFKQINDNFGHPVGDK--VIAFLSDQLVVVFGTPMFVGRLGGEEF-AAAALGS 187 (266)
Q Consensus 122 l~~~~~~~~l~~idid~fk~iNd~~G~~~gD~--~L~~va~~l~~~~~~~~~~~R~~gdeF-~ill~~~ 187 (266)
+.+.+-.+...--|++....||-.-|.+.++. +|.+-|+.-+..+.+ +..+..++| ++++|+.
T Consensus 26 L~~~g~~~~cfAPdi~Q~hVvnH~tge~~~e~RNVLvESARIaRG~I~~---l~~~~~~d~DaLiiPGG 91 (213)
T cd03133 26 LDRAGAEVQCFAPDIEQMHVVNHLTGEAEGESRNVLVESARIARGNIKD---LAKLKAADFDALIFPGG 91 (213)
T ss_pred HHHCCCEEEEECCCCCCCCCEECCCCCCCCCHHHHHHHHHHHHCCCCCC---HHHCCHHHCCEEEECCC
T ss_conf 9868987999669987121100368985760177898998876258556---45699867898997885
No 66
>cd02803 OYE_like_FMN_family Old yellow enzyme (OYE)-like FMN binding domain. OYE was the first flavin-dependent enzyme identified, however its true physiological role remains elusive to this day. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase.
Probab=32.40 E-value=20 Score=15.14 Aligned_cols=56 Identities=20% Similarity=0.314 Sum_probs=36.6
Q ss_pred CCCCCCCCCC--CCCCHHHCCCCCCCCCC-HHHCCCCCCEEEEECCCCCHHHHHHHHHHHH
Q ss_conf 1468865444--31100000001111100-0000133430365016861012344458999
Q gi|254781079|r 143 NDNFGHPVGD--KVIAFLSDQLVVVFGTP-MFVGRLGGEEFAAAALGSSEQEAAILANDLR 200 (266)
Q Consensus 143 Nd~~G~~~gD--~~L~~va~~l~~~~~~~-~~~~R~~gdeF~ill~~~~~~~~~~~~~~l~ 200 (266)
+|.||-..-+ +++.+|.+.+++.++++ -+-.|++++++.- .+.+.++...+++.+.
T Consensus 180 tD~YGGs~eNR~Rf~~eii~air~~vg~df~vgvRls~~d~~~--~g~~~~e~~~~~~~l~ 238 (327)
T cd02803 180 TDEYGGSLENRARFLLEIVAAVREAVGPDFPVGVRLSADDFVP--GGLTLEEAIEIAKALE 238 (327)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEECHHHCCC--CCCCHHHHHHHHHHHH
T ss_conf 7778889899989999999999997398876179977021268--9999899999999998
No 67
>PRK08249 cystathionine gamma-synthase; Provisional
Probab=32.32 E-value=30 Score=13.76 Aligned_cols=118 Identities=19% Similarity=0.201 Sum_probs=58.8
Q ss_pred HHHHHCCCHH-----CCCCHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCHHHCCC
Q ss_conf 9996104010-----50204899988877089725755442210001146886544431100000001111100000013
Q gi|254781079|r 101 SQLSRIDCLS-----GLLNHSAFISSLGSYNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFGTPMFVGRL 175 (266)
Q Consensus 101 ~~~a~~D~LT-----gL~NR~~f~~~l~~~~~~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~~~~~~~~~~~R~ 175 (266)
+.+..+..++ ||++.....-.-+......+++.+++++ |.+. .+.+-+.| +--....-+
T Consensus 275 ~~L~~hp~V~~V~yPgL~s~p~h~la~~~~~g~gg~~sf~l~g--------~~~~----~~~f~~~l----~l~~~a~Sl 338 (398)
T PRK08249 275 EYLQTEPLVEAVNYPGLPTHPNHAIAKAQMRGFGGMLSFALKG--------GMDT----VRRLLPRL----QYAHRAANL 338 (398)
T ss_pred HHHHHCCCCCEEECCCCCCCCCHHHHHHHCCCCCCCEEEEEEC--------CHHH----HHHHHHHC----CCCEECCCC
T ss_conf 9998399807798999999968899998679999711799818--------9999----99999718----805005563
Q ss_pred CCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHC
Q ss_conf 343036501686101234445899999863154067995689999999987799899899999999999999970
Q gi|254781079|r 176 GGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERCHKEPISTIIYRADQALYVAKKS 250 (266)
Q Consensus 176 ~gdeF~ill~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~t~s~Gia~~~~~~~~~~ll~~Ad~Al~~AK~~ 250 (266)
||-|=.+.-|...... . +...-++.. - ..++ - +-+|+|+ +++++|+..-++|+...|++
T Consensus 339 Gg~eSLi~~p~~~th~-~-~~~e~r~~~---G--i~~~-l--iRlSvGl------Ed~~DLi~DL~qAL~~ir~~ 397 (398)
T PRK08249 339 GAVETIVGPARTTSHV-E-NTPEERAAL---G--IPEG-L--VRISVGI------EDTEDLIADLAQAFASVREE 397 (398)
T ss_pred CCCCCEEECHHHCCCC-C-CCHHHHHHC---C--CCCC-E--EEEEEEC------CCHHHHHHHHHHHHHHHHHH
T ss_conf 8766120281324763-4-999999976---9--8939-4--9999600------99999999999999998855
No 68
>PRK11780 isoprenoid biosynthesis protein with amidotransferase-like domain; Provisional
Probab=31.80 E-value=30 Score=13.70 Aligned_cols=62 Identities=18% Similarity=0.152 Sum_probs=35.4
Q ss_pred HHHCCCCEEEEEEECCCCCCCCCCCCCCCCCC--CCCHHHCCCCCCCCCCHHHCCCCCCEE-EEECCC
Q ss_conf 87708972575544221000114688654443--110000000111110000001334303-650168
Q gi|254781079|r 122 LGSYNEKLSIVFFDIDYFKQINDNFGHPVGDK--VIAFLSDQLVVVFGTPMFVGRLGGEEF-AAAALG 186 (266)
Q Consensus 122 l~~~~~~~~l~~idid~fk~iNd~~G~~~gD~--~L~~va~~l~~~~~~~~~~~R~~gdeF-~ill~~ 186 (266)
+.+.+-.+...-=|++.+..||-.-|.+.++. +|.+-|+.-+..+.+ +..+..++| ++++|+
T Consensus 29 L~r~ga~~~cfAPd~~Q~hvvnH~tge~~~e~RNVLvESARIaRG~I~~---l~~~~~~d~DaLI~PG 93 (217)
T PRK11780 29 LDRAGAEAQCFAPDIPQLHVINHLTGEEMAETRNVLVESARIARGEIKD---LAEADAEDFDALIVPG 93 (217)
T ss_pred HHHCCCEEEEECCCCCCCCCEECCCCCCCCHHHHHHHHHHHHHCCCCCC---HHHCCHHHCCEEEECC
T ss_conf 9867986799769965201211258983732477899998876158667---4569975678799678
No 69
>TIGR01078 arcA arginine deiminase; InterPro: IPR003876 This is a family of arginine deiminases, 3.5.3.6 from EC. The aligned region corresponds to the C-terminal of the protein. These enzymes catalyse the conversion of arginine + H2O to citrulline + NH3. Also found in this family is the Streptococcus anti tumor glycoprotein .; GO: 0016990 arginine deiminase activity, 0006527 arginine catabolic process.
Probab=31.51 E-value=31 Score=13.66 Aligned_cols=61 Identities=21% Similarity=0.281 Sum_probs=31.5
Q ss_pred HCCC-CCCEEEE----ECCC----CCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEECCCCCCHHHHHHHHH
Q ss_conf 0013-3430365----0168----6101234445899999863154067995689999999987799899899999999
Q gi|254781079|r 172 VGRL-GGEEFAA----AALG----SSEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERCHKEPISTIIYRAD 241 (266)
Q Consensus 172 ~~R~-~gdeF~i----ll~~----~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~t~s~Gia~~~~~~~~~~ll~~Ad 241 (266)
-.++ |||+|++ |+-+ |+.+.++++|+.|-..- .+.--+| +.++++....-+..+.+++..|
T Consensus 218 ~~~~EGGDvl~l~~~vl~iG~SERT~~q~ve~LA~~LF~~k--------~~~f~~v-lA~~~Pk~ra~MHLDTVfTm~D 287 (421)
T TIGR01078 218 TASIEGGDVLVLGKDVLAIGISERTSAQSVEKLAKSLFANK--------EGGFKKV-LAIKIPKNRALMHLDTVFTMVD 287 (421)
T ss_pred CCCCCCCEEEEECCCEEEEEECCCCCHHHHHHHHHHHHHCC--------CCCCCEE-EEECCCCCCCCCCCCCCCCEEC
T ss_conf 76225504766448678996124488889999999998403--------3765558-9971755567864113142424
No 70
>PRK08861 cystathionine gamma-synthase; Provisional
Probab=30.55 E-value=32 Score=13.55 Aligned_cols=108 Identities=17% Similarity=0.126 Sum_probs=56.2
Q ss_pred CCCCHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCHHHCCCCCCEEEEECCCCCHH
Q ss_conf 50204899988877089725755442210001146886544431100000001111100000013343036501686101
Q gi|254781079|r 111 GLLNHSAFISSLGSYNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQ 190 (266)
Q Consensus 111 gL~NR~~f~~~l~~~~~~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~~~~~~~~~~~R~~gdeF~ill~~~~~~ 190 (266)
||++.-.+.-.-+......+++.+++++ |.+. ...+.+.++ --....-|||-|=.+..|.....
T Consensus 280 gL~shp~h~lak~~~~g~ggm~sf~l~~--------~~~~----~~~f~~~l~----lf~~a~SlGg~eSLi~~p~s~sh 343 (388)
T PRK08861 280 SLPEHPGHEIAKKQQSGFGSMLSFEFAG--------SFEQ----LKVFVKALK----LFSLAESLGGVESLICHPASMTH 343 (388)
T ss_pred CCCCCCCHHHHHHHCCCCCCEEEEEECC--------CHHH----HHHHHHHCC----CCEECCCCCCCCCEEECCCCCCC
T ss_conf 9999926999986456986269999779--------8999----999998388----05331166877502137754554
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHC
Q ss_conf 234445899999863154067995689999999987799899899999999999999970
Q gi|254781079|r 191 EAAILANDLRKIIENSQINISSGPSIHITISAGIAERCHKEPISTIIYRADQALYVAKKS 250 (266)
Q Consensus 191 ~~~~~~~~l~~~l~~~~~~~~~~~~~~~t~s~Gia~~~~~~~~~~ll~~Ad~Al~~AK~~ 250 (266)
. .+-++-+... .....-+ -+|+|+ +++++|+..-++||.+|++.
T Consensus 344 ~--~~~~~~~~~~------gi~~~li--RlsVGl------Ed~eDLi~Dl~qAL~~a~~~ 387 (388)
T PRK08861 344 R--AMGEEALAEA------GVSQQLL--RLSVGL------EDAQDLIADLKQAFAKAAEA 387 (388)
T ss_pred C--CCCHHHHHHC------CCCCCEE--EEEECC------CCHHHHHHHHHHHHHHHHHC
T ss_conf 1--1899999866------9894969--999421------99999999999999998756
No 71
>cd02932 OYE_YqiM_FMN Old yellow enzyme (OYE) YqjM-like FMN binding domain. YqjM is involved in the oxidative stress response of Bacillus subtilis. Like the other OYE members, each monomer of YqjM contains FMN as a non-covalently bound cofactor and uses NADPH as a reducing agent. The YqjM enzyme exists as a homotetramer that is assembled as a dimer of catalytically dependent dimers, while other OYE members exist only as monomers or dimers. Moreover, the protein displays a shared active site architecture where an arginine finger at the COOH terminus of one monomer extends into the active site of the adjacent monomer and is directly involved in substrate recognition. Another remarkable difference in the binding of the ligand in YqjM is represented by the contribution of the NH2-terminal tyrosine instead of a COOH-terminal tyrosine in OYE and its homologs.
Probab=30.47 E-value=23 Score=14.60 Aligned_cols=55 Identities=16% Similarity=0.347 Sum_probs=36.9
Q ss_pred CCCCCCCCCC--CCCCHHHCCCCCCCCCCH-HHCCCCCCEEEEECCC-CCHHHHHHHHHHHH
Q ss_conf 1468865444--311000000011111000-0001334303650168-61012344458999
Q gi|254781079|r 143 NDNFGHPVGD--KVIAFLSDQLVVVFGTPM-FVGRLGGEEFAAAALG-SSEQEAAILANDLR 200 (266)
Q Consensus 143 Nd~~G~~~gD--~~L~~va~~l~~~~~~~~-~~~R~~gdeF~ill~~-~~~~~~~~~~~~l~ 200 (266)
.|.||-..-+ +++.+|.+.+++.++++- +..|++++|+. ++ .+.++...+++.+.
T Consensus 193 tDeYGGs~enR~Rf~~Eii~aVr~~vg~d~~vgvRis~~d~~---~~g~~~~e~~~~a~~l~ 251 (336)
T cd02932 193 TDEYGGSLENRMRFLLEVVDAVRAVWPEDKPLFVRISATDWV---EGGWDLEDSVELAKALK 251 (336)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCC---CCCCCHHHHHHHHHHHH
T ss_conf 786799789998899999999999839988706896452357---89989999999999999
No 72
>pfam06675 DUF1177 Protein of unknown function (DUF1177). This family consists of several hypothetical archaeal and and bacterial proteins of around 300 residues in length. The function of this family is unknown.
Probab=30.43 E-value=32 Score=13.54 Aligned_cols=34 Identities=21% Similarity=0.097 Sum_probs=27.7
Q ss_pred CCHHHHHHHHHHHHHHHHHCCCCEEEECCHHHCC
Q ss_conf 9989999999999999997099689994021005
Q gi|254781079|r 231 EPISTIIYRADQALYVAKKSGRNRVVCFSDIENN 264 (266)
Q Consensus 231 ~~~~~ll~~Ad~Al~~AK~~gkn~~~~~~~~~~~ 264 (266)
....++-..+-.++.-||.-|++++.||++-|=+
T Consensus 225 sh~~di~~A~RF~vEvaK~fg~G~c~fyde~E~~ 258 (276)
T pfam06675 225 SHEVDIEHASRFCVEVAKYFGRGGCKFYDENEFA 258 (276)
T ss_pred CCHHHHHHHHHHHHHHHHHHCCCCCEEECHHHHH
T ss_conf 6588899999999999999737973353899999
No 73
>PRK05968 hypothetical protein; Provisional
Probab=29.06 E-value=33 Score=13.37 Aligned_cols=63 Identities=22% Similarity=0.162 Sum_probs=35.5
Q ss_pred HHCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 0001334303650168610123444589999986315406799568999999998779989989999999999999997
Q gi|254781079|r 171 FVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERCHKEPISTIIYRADQALYVAKK 249 (266)
Q Consensus 171 ~~~R~~gdeF~ill~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~t~s~Gia~~~~~~~~~~ll~~Ad~Al~~AK~ 249 (266)
...-|||-|=.+.-|.++......- ++ +.. .- ....-+ -+|+|+ +++++|+..-++||..|++
T Consensus 327 ~a~SlGg~eSLi~~~~~~~~~~~~~-~~-~~~---~G---i~~~li--RlSVGl------Ed~eDLi~Dl~qAL~~a~k 389 (389)
T PRK05968 327 LGVSWGGHESLVVPAEVVLQQKAQP-NS-AAR---FG---ISPRSV--RLHVGL------EGTEALWADLEQALAAASR 389 (389)
T ss_pred EECCCCCCCCCCCCCHHHCCCCCCH-HH-HHH---CC---CCCCEE--EEEEEE------CCHHHHHHHHHHHHHHHCC
T ss_conf 6316686430218706641677998-89-986---59---694969--999310------9999999999999998439
No 74
>PRK08776 cystathionine gamma-synthase; Provisional
Probab=28.90 E-value=34 Score=13.35 Aligned_cols=118 Identities=20% Similarity=0.241 Sum_probs=60.7
Q ss_pred HHHHHCCCHH-----CCCCHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCHHHCCC
Q ss_conf 9996104010-----50204899988877089725755442210001146886544431100000001111100000013
Q gi|254781079|r 101 SQLSRIDCLS-----GLLNHSAFISSLGSYNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFGTPMFVGRL 175 (266)
Q Consensus 101 ~~~a~~D~LT-----gL~NR~~f~~~l~~~~~~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~~~~~~~~~~~R~ 175 (266)
+.+..+..+. ||++.-...-.-+......+++.+++++ |.+. .+.+.+.++ --....-+
T Consensus 272 ~~L~~hp~V~~V~YPgL~shp~h~la~r~~~G~Ggm~Sf~l~~--------~~~~----~~~f~d~l~----lf~~a~Sl 335 (405)
T PRK08776 272 ALLDGHAAVNQVYFPGLASHPGHALAARQQKGFGAMLSFELEG--------GEAA----VRAFVDGLR----YFTLAESL 335 (405)
T ss_pred HHHHHCCCCCEEECCCCCCCCCHHHHHHCCCCCCCEEEEEECC--------HHHH----HHHHHHHCC----CCEEEECC
T ss_conf 9997098968688988889816789986489986526888457--------3999----999998088----36252153
Q ss_pred CCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHC
Q ss_conf 343036501686101234445899999863154067995689999999987799899899999999999999970
Q gi|254781079|r 176 GGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERCHKEPISTIIYRADQALYVAKKS 250 (266)
Q Consensus 176 ~gdeF~ill~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~t~s~Gia~~~~~~~~~~ll~~Ad~Al~~AK~~ 250 (266)
||-|=.+..|....... +-++-+... . . ...-+ -+|+|+ +++++|+..-++||.+|+.-
T Consensus 336 Gg~eSLi~~P~~~th~~--~~~e~r~~~---G--i-~~~li--RlSvGl------Ed~~DLi~DL~qAL~~a~a~ 394 (405)
T PRK08776 336 GGVESLIAHPASMTHAA--MTAEARAAA---G--I-SDGLL--RLSVGI------ESAEDLLIDLRAGLARAEAV 394 (405)
T ss_pred CCCCCEEECCCCCCCCC--CCHHHHHHC---C--C-CCCEE--EEEEEC------CCHHHHHHHHHHHHHHHHHH
T ss_conf 76541302775446645--899999866---9--8-93969--999500------99999999999999999988
No 75
>PRK08064 cystathionine beta-lyase; Provisional
Probab=28.74 E-value=34 Score=13.33 Aligned_cols=108 Identities=18% Similarity=0.228 Sum_probs=54.9
Q ss_pred CCCCHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCHHHCCCCCCEEEEECCCCCHH
Q ss_conf 50204899988877089725755442210001146886544431100000001111100000013343036501686101
Q gi|254781079|r 111 GLLNHSAFISSLGSYNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQ 190 (266)
Q Consensus 111 gL~NR~~f~~~l~~~~~~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~~~~~~~~~~~R~~gdeF~ill~~~~~~ 190 (266)
||++.....-.-+......+++-+++.+ . +....+-+.++ --....-+||-|=.+..|.....
T Consensus 280 gL~s~p~h~l~~~~~~g~Gg~~sf~l~~---------~----~~~~~f~~~l~----l~~~a~SlGg~eSLi~~p~~~th 342 (390)
T PRK08064 280 GLQTHLGFDIQQSQATSAGAVLSFTLQS---------E----EAVRQFVSKVK----LPVFAVSLGAVESILSYPAKMSH 342 (390)
T ss_pred CCCCCCCHHHHHHCCCCCCEEEEEEECC---------H----HHHHHHHHHCC----CCEEEECCCCCCCEEECCCCCCC
T ss_conf 9999914999996289971499999899---------9----99999998388----26221163774441047622466
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHHCC
Q ss_conf 2344458999998631540679956899999999877998998999999999999999709
Q gi|254781079|r 191 EAAILANDLRKIIENSQINISSGPSIHITISAGIAERCHKEPISTIIYRADQALYVAKKSG 251 (266)
Q Consensus 191 ~~~~~~~~l~~~l~~~~~~~~~~~~~~~t~s~Gia~~~~~~~~~~ll~~Ad~Al~~AK~~g 251 (266)
.. +.+.-+... .....- +-+|+|+ +++++|+..-++||.+.|+--
T Consensus 343 ~~--~~~e~~~~~------Gi~~~l--iRlSvGl------E~~~DLi~DL~qAL~~i~~~~ 387 (390)
T PRK08064 343 AA--MPKEERDER------GITDGL--LRLSVGL------ENVDDLIADFEQALSYVEEPV 387 (390)
T ss_pred CC--CCHHHHHHC------CCCCCE--EEEEECC------CCHHHHHHHHHHHHHHHHHHH
T ss_conf 34--899999975------989394--9999600------899999999999999733143
No 76
>pfam12127 YdfA_immunity SigmaW regulon antibacterial. This protein is found in bacteria. Proteins in this family are about 330 amino acids in length. The operon from which this protein is derived confers immunity for the host species to a broad range of antibacterial compounds, unlike the specific immunity proteins that are linked to and co-regulated with their antibiotic-synthesis proteins.
Probab=27.77 E-value=35 Score=13.21 Aligned_cols=91 Identities=22% Similarity=0.313 Sum_probs=49.0
Q ss_pred CCCHHHCCCCCCEEEEECCCC--CHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEECCCCCC----HHHHHHHH
Q ss_conf 100000013343036501686--101234445899999863154067995689999999987799899----89999999
Q gi|254781079|r 167 GTPMFVGRLGGEEFAAAALGS--SEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERCHKEP----ISTIIYRA 240 (266)
Q Consensus 167 ~~~~~~~R~~gdeF~ill~~~--~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~t~s~Gia~~~~~~~----~~~ll~~A 240 (266)
.+..+++|.|.- .+-.-+. +.++...--+.|.+...+.. ...|...++ +|+-|+..+-|++ .+.--..|
T Consensus 166 ~EeTIiARVGEg--IVs~IGSa~~hk~VLEnPd~ISk~VL~kg--LDagTAFeI-lSIDIADvdVG~NIGA~Lq~dQAeA 240 (321)
T pfam12127 166 GEETIIARVGEG--IVTTIGSADTHKEVLENPDSISKTVLEKG--LDAGTAFEI-LSIDIADIDVGENIGARLQTDQAEA 240 (321)
T ss_pred CHHHHHHHHCCC--EEEEECCCCHHHHHHCCHHHHHHHHHHCC--CCCCCEEEE-EEEEEECCCHHHHHCHHHHHHHHHH
T ss_conf 502344343474--24013262328799729878799998536--786851699-9875423412222254551778878
Q ss_pred HHHHHHHHHCCCCEEEECCHHH
Q ss_conf 9999999970996899940210
Q gi|254781079|r 241 DQALYVAKKSGRNRVVCFSDIE 262 (266)
Q Consensus 241 d~Al~~AK~~gkn~~~~~~~~~ 262 (266)
|....+||.+.|.-.....++|
T Consensus 241 Dk~vAqAkAE~RRA~AvA~EQE 262 (321)
T pfam12127 241 DKRIAQAKAEERRAMAVAREQE 262 (321)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
T ss_conf 7899987788899999999899
No 77
>PRK08248 O-acetylhomoserine aminocarboxypropyltransferase; Validated
Probab=27.42 E-value=35 Score=13.17 Aligned_cols=92 Identities=21% Similarity=0.266 Sum_probs=50.1
Q ss_pred CCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCHHHCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 89725755442210001146886544431100000001111100000013343036501686101234445899999863
Q gi|254781079|r 126 NEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIEN 205 (266)
Q Consensus 126 ~~~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~~~~~~~~~~~R~~gdeF~ill~~~~~~~~~~~~~~l~~~l~~ 205 (266)
+...+++.+++.+ |.+.+ ..+.+.|+ --....-+||-|=.+.-|....... +-+.-+...
T Consensus 339 ~g~G~~~sf~l~~--------~~~~~----~~f~~~L~----lf~~a~SlGg~eSLi~~pa~~th~~--~~~~~r~~~-- 398 (431)
T PRK08248 339 KGQGAILTFEIKG--------GVEAG----KKLIDSVK----LFSHLANVGDSKSLIIHPASTTHEQ--LSEEEQRAA-- 398 (431)
T ss_pred CCCEEEEEEEECC--------CHHHH----HHHHHHCC----CCEECCCCCCCCCEEECCCCCCCCC--CCHHHHHHC--
T ss_conf 9960699999728--------89999----99998378----3611326676571645764355210--899999866--
Q ss_pred CCCCCCCCCEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 15406799568999999998779989989999999999999997
Q gi|254781079|r 206 SQINISSGPSIHITISAGIAERCHKEPISTIIYRADQALYVAKK 249 (266)
Q Consensus 206 ~~~~~~~~~~~~~t~s~Gia~~~~~~~~~~ll~~Ad~Al~~AK~ 249 (266)
. ..+ .- +-+|+|+ +++++|+..-++||.+|+.
T Consensus 399 -G--i~~-~l--iRlSVGl------Ed~eDLi~DL~qAL~~a~~ 430 (431)
T PRK08248 399 -G--VTP-GL--VRLSVGT------ESIDDIIEDLRQAIEQSQA 430 (431)
T ss_pred -C--CCC-CE--EEEEECC------CCHHHHHHHHHHHHHHHCC
T ss_conf -9--794-95--9999410------9999999999999997237
No 78
>TIGR02630 xylose_isom_A xylose isomerase; InterPro: IPR013452 Xylose isomerase (5.3.1.5 from EC) is an enzyme which interconverts D-xylose and D-xylulose.; GO: 0009045 xylose isomerase activity.
Probab=27.36 E-value=36 Score=13.16 Aligned_cols=37 Identities=24% Similarity=0.261 Sum_probs=17.8
Q ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEC
Q ss_conf 9998779989989999999999999997099689994
Q gi|254781079|r 222 AGIAERCHKEPISTIIYRADQALYVAKKSGRNRVVCF 258 (266)
Q Consensus 222 ~Gia~~~~~~~~~~ll~~Ad~Al~~AK~~gkn~~~~~ 258 (266)
-|.|..++.+-+.--=.+...||-.+|+-|...+||+
T Consensus 150 ~GAATsp~adVFAyAAAQVKkaLe~Tk~LGGENYVFW 186 (437)
T TIGR02630 150 HGAATSPDADVFAYAAAQVKKALEVTKKLGGENYVFW 186 (437)
T ss_pred CCCCCCCCCCCEECHHHHHHHHHHHHHHHCCCCCEEC
T ss_conf 6566683801141138999999999998658862431
No 79
>pfam01053 Cys_Met_Meta_PP Cys/Met metabolism PLP-dependent enzyme. This family includes enzymes involved in cysteine and methionine metabolism. The following are members: Cystathionine gamma-lyase, Cystathionine gamma-synthase, Cystathionine beta-lyase, Methionine gamma-lyase, OAH/OAS sulfhydrylase, O-succinylhomoserine sulfhydrylase All of these members participate is slightly different reactions. All these enzymes use PLP (pyridoxal-5'-phosphate) as a cofactor.
Probab=27.13 E-value=36 Score=13.13 Aligned_cols=111 Identities=20% Similarity=0.207 Sum_probs=57.1
Q ss_pred HHHHHCCCHH-----CCCCHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCHHHCCC
Q ss_conf 9996104010-----50204899988877089725755442210001146886544431100000001111100000013
Q gi|254781079|r 101 SQLSRIDCLS-----GLLNHSAFISSLGSYNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFGTPMFVGRL 175 (266)
Q Consensus 101 ~~~a~~D~LT-----gL~NR~~f~~~l~~~~~~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~~~~~~~~~~~R~ 175 (266)
+.+..+..+. ||+....+.-.-+..+...+++-+++++ .+. ...+.+.| +--....-|
T Consensus 265 ~~L~~hp~V~~V~yPgL~s~p~~~~~~r~~~g~ggl~sf~l~~---------~~~----~~~f~d~l----~lf~~~~Sl 327 (381)
T pfam01053 265 EFLEEHPKVEKVYYPGLPSHPGHELAKKQMSGFGGMLSFELKG---------GEA----ASKFLDNL----KLFSLAESL 327 (381)
T ss_pred HHHHHCCCCCEEECCCCCCCCCHHHHHHHCCCCCCEEEEEECC---------HHH----HHHHHHHC----CCCEECCCC
T ss_conf 9997299977795758999804999997589999731898678---------999----99999847----713353565
Q ss_pred CCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEECCCCCCHHHHHHHHHHHH
Q ss_conf 343036501686101234445899999863154067995689999999987799899899999999999
Q gi|254781079|r 176 GGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERCHKEPISTIIYRADQAL 244 (266)
Q Consensus 176 ~gdeF~ill~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~t~s~Gia~~~~~~~~~~ll~~Ad~Al 244 (266)
||-|-.+..|...... .+-..-+... .. ...-+ -+|+|+ +++++|+..-++||
T Consensus 328 Gg~eSLi~~p~~~~h~--~~~~~~r~~~-----gi-~~~li--RlSvGl------Ed~~DLi~DL~qAL 380 (381)
T pfam01053 328 GGVESLISHPATMTHA--SIPPEEREAA-----GI-TDGLI--RLSVGI------EDVDDLIADLKQAL 380 (381)
T ss_pred CCCCCEEECCCCCCCC--CCCHHHHHHC-----CC-CCCEE--EEEEEE------CCHHHHHHHHHHHC
T ss_conf 8756065576413531--1899999866-----97-93959--999500------99999999999863
No 80
>pfam10975 DUF2802 Protein of unknown function (DUF2802). This bacterial family of proteins has no known function.
Probab=26.48 E-value=37 Score=13.05 Aligned_cols=35 Identities=20% Similarity=0.093 Sum_probs=26.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCHHCCCCHHHH
Q ss_conf 99999999999999999999610401050204899
Q gi|254781079|r 84 YISGSILKELFISYNRISQLSRIDCLSGLLNHSAF 118 (266)
Q Consensus 84 ~~~~~~~~~l~~~~~~l~~~a~~D~LTgL~NR~~f 118 (266)
.....+.+.+....+++.++...||-+.+|+|..=
T Consensus 5 q~l~~l~~~l~~l~~~~~el~~~dp~~~~Y~~A~k 39 (70)
T pfam10975 5 QRLAELEQQLKELQDRQEELEQQDPQSRLYSRAAK 39 (70)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHH
T ss_conf 99999999999999999999854975313999999
No 81
>cd04734 OYE_like_3_FMN Old yellow enzyme (OYE)-related FMN binding domain, group 3. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Other members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase. One member of this subgroup, the Sinorhizobium meliloti stachydrine utilization protein stcD, has been idenified as a putative N-methylproline demethylase.
Probab=26.24 E-value=30 Score=13.67 Aligned_cols=56 Identities=21% Similarity=0.296 Sum_probs=36.3
Q ss_pred CCCCCCCCCC--CCCCHHHCCCCCCCCCCH-HHCCCCCCEEEEECCCCCHHHHHHHHHHHH
Q ss_conf 1468865444--311000000011111000-000133430365016861012344458999
Q gi|254781079|r 143 NDNFGHPVGD--KVIAFLSDQLVVVFGTPM-FVGRLGGEEFAAAALGSSEQEAAILANDLR 200 (266)
Q Consensus 143 Nd~~G~~~gD--~~L~~va~~l~~~~~~~~-~~~R~~gdeF~ill~~~~~~~~~~~~~~l~ 200 (266)
+|.||-..-+ +++.+|.+.+++.++++- +..|++.+++.= .+.+.++...+++.+.
T Consensus 180 tDeYGGs~eNR~Rf~~EIi~~Ir~~vg~~f~i~~Ris~~~~~~--~g~~~~e~~~~~~~l~ 238 (343)
T cd04734 180 TDEYGGSLENRMRFLLEVLAAVRAAVGPDFIVGIRISGDEDTE--GGLSPDEALEIAARLA 238 (343)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCC--CCCCHHHHHHHHHHHH
T ss_conf 6767988899989999999999998198776158867623568--9899899999999999
No 82
>PRK03341 arginine repressor; Provisional
Probab=26.10 E-value=37 Score=13.00 Aligned_cols=46 Identities=20% Similarity=0.328 Sum_probs=25.3
Q ss_pred HHHCCCCCCCCCCHHHCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHH
Q ss_conf 000000111110000001334303650168610123444589999986
Q gi|254781079|r 157 FLSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIE 204 (266)
Q Consensus 157 ~va~~l~~~~~~~~~~~R~~gdeF~ill~~~~~~~~~~~~~~l~~~l~ 204 (266)
.+|..|.. ....++++=++||+=+++++ .+.+++..++++|....+
T Consensus 121 ~va~~iD~-~~~~eI~GTIAGdDTIlVi~-~~~~~a~~l~~~L~~l~~ 166 (168)
T PRK03341 121 YLASAIDR-AALPYVVGTIAGDDTVLVVA-REPMTGAELAARLENLAT 166 (168)
T ss_pred HHHHHHHH-CCCCCCEEEEECCCEEEEEE-CCHHHHHHHHHHHHHHHH
T ss_conf 99999984-79987379860499899997-888899999999999874
No 83
>PRK00441 argR arginine repressor; Provisional
Probab=25.71 E-value=38 Score=12.95 Aligned_cols=44 Identities=16% Similarity=0.277 Sum_probs=21.4
Q ss_pred HHCCCCCCCCCCHHHCCCCCCEEEEECCCCCHHHHHHHHHHHHHHH
Q ss_conf 0000011111000000133430365016861012344458999998
Q gi|254781079|r 158 LSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKII 203 (266)
Q Consensus 158 va~~l~~~~~~~~~~~R~~gdeF~ill~~~~~~~~~~~~~~l~~~l 203 (266)
+|..|-. .+..++++=++||+=+++++ .+.+++..+.++|...+
T Consensus 105 va~~iD~-~~~~~I~GTIAGdDTilvi~-~~~~~a~~l~~~i~~ll 148 (149)
T PRK00441 105 AAEAIDT-LNFDGIAGTIAGDNTIFILV-RSLEKAQEIVEKLKKLI 148 (149)
T ss_pred HHHHHHH-CCCCCCEEEEECCCEEEEEE-CCHHHHHHHHHHHHHHH
T ss_conf 9999983-79987279860599899997-88899999999999985
No 84
>TIGR01522 ATPase-IIA2_Ca calcium-transporting P-type ATPase, PMR1-type; InterPro: IPR006413 This family describes the P-type ATPase responsible for translocating calcium ions across the golgi membrane of fungi and animals , , and is of particular importance in the sarcoplasmic reticulum of skeletal and cardiac muscle in vertebrates . The calcium P-type ATPases have been characterised as Type IIA based on a phylogenetic analysis which distinguishes this group from the Type IIB PMCA calcium pump represented by IPR006408 from INTERPRO. ; GO: 0005388 calcium-transporting ATPase activity, 0006816 calcium ion transport, 0016021 integral to membrane.
Probab=25.22 E-value=30 Score=13.69 Aligned_cols=12 Identities=25% Similarity=0.567 Sum_probs=8.1
Q ss_pred HHHHHHHHHHCC
Q ss_conf 999999999709
Q gi|254781079|r 240 ADQALYVAKKSG 251 (266)
Q Consensus 240 Ad~Al~~AK~~g 251 (266)
+.+|+.-||+-|
T Consensus 528 ~~TAv~IA~~lG 539 (856)
T TIGR01522 528 EETAVSIARRLG 539 (856)
T ss_pred HHHHHHHHHHCC
T ss_conf 899999987728
No 85
>PRK13523 NADPH dehydrogenase NamA; Provisional
Probab=25.15 E-value=33 Score=13.42 Aligned_cols=55 Identities=15% Similarity=0.268 Sum_probs=35.4
Q ss_pred CCCCCCCCCC--CCCCHHHCCCCCCCCCCHHHCCCCCCEEEEECCCCCHHHHHHHHHHHH
Q ss_conf 1468865444--311000000011111000000133430365016861012344458999
Q gi|254781079|r 143 NDNFGHPVGD--KVIAFLSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLR 200 (266)
Q Consensus 143 Nd~~G~~~gD--~~L~~va~~l~~~~~~~~~~~R~~gdeF~ill~~~~~~~~~~~~~~l~ 200 (266)
+|.||-..-+ +++.+|.+.+++.. +..+..|++++||.- -+.+.++...+++.+.
T Consensus 181 tD~YGGs~eNR~Rf~lEii~aVr~~~-~~~v~vRis~~d~~~--gG~~~~d~~~~~~~l~ 237 (337)
T PRK13523 181 TDEYGGSPENRYRFLREIIDAVKEVW-DGPLFVRISASDYHP--DGLTVQDYVQYAKWMK 237 (337)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHC-CCCEEEEECCCCCCC--CCCCHHHHHHHHHHHH
T ss_conf 58558888999889999999999865-886399933655578--9989899999999999
No 86
>TIGR02854 spore_II_GA sigma-E processing peptidase SpoIIGA; InterPro: IPR005081 Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. The peptidases families associated with clan U- have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported. This group of peptidases belong to the MEROPS peptidase family U4 (SpoIIGA peptidase family, clan U-). Sporulation in bacteria such as Bacillus subtilis involves the formation of a polar septum, which divides the sporangium into a mother cell and a forespore. The sigma E factor, which is encoded within the spoIIG operon, is a cell-specific regulatory protein that directs gene transcription in the mother cell. Sigma E is synthesised as an inactive proprotein pro-sigma E, which is converted to the mature factor by the putative processing enzyme SpoIIGA . ; GO: 0004190 aspartic-type endopeptidase activity, 0006508 proteolysis, 0030436 sporulation (sensu Bacteria).
Probab=24.74 E-value=39 Score=12.82 Aligned_cols=12 Identities=17% Similarity=0.501 Sum_probs=6.0
Q ss_pred EEEEECCCCCCC
Q ss_conf 755442210001
Q gi|254781079|r 131 IVFFDIDYFKQI 142 (266)
Q Consensus 131 l~~idid~fk~i 142 (266)
|+.++-+-+|.+
T Consensus 214 V~vve~~~l~~~ 225 (320)
T TIGR02854 214 VIVVEKDSLKSL 225 (320)
T ss_pred CEEEEHHHHHCC
T ss_conf 113136777303
No 87
>pfam08265 YL1_C YL1 nuclear protein C-terminal domain. This domain is found in proteins of the YL1 family. These proteins have been shown to be DNA-binding and may be a transcription factor. This domain is found in proteins that are not YL1 proteins.
Probab=24.59 E-value=24 Score=14.51 Aligned_cols=15 Identities=40% Similarity=0.377 Sum_probs=9.8
Q ss_pred HHCCCHHCCC--CHHHH
Q ss_conf 6104010502--04899
Q gi|254781079|r 104 SRIDCLSGLL--NHSAF 118 (266)
Q Consensus 104 a~~D~LTgL~--NR~~f 118 (266)
.+.||.|||+ |..+|
T Consensus 11 ~Y~DP~T~l~Y~n~eaf 27 (30)
T pfam08265 11 KYKDPKTGLPYSNVEAF 27 (30)
T ss_pred CCCCCCCCCCCCCHHHH
T ss_conf 43488879811488886
No 88
>PRK08133 O-succinylhomoserine sulfhydrylase; Validated
Probab=24.51 E-value=40 Score=12.79 Aligned_cols=113 Identities=15% Similarity=0.174 Sum_probs=56.0
Q ss_pred HHHHHCCCHH-----CCCCHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCHHHCCC
Q ss_conf 9996104010-----50204899988877089725755442210001146886544431100000001111100000013
Q gi|254781079|r 101 SQLSRIDCLS-----GLLNHSAFISSLGSYNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFGTPMFVGRL 175 (266)
Q Consensus 101 ~~~a~~D~LT-----gL~NR~~f~~~l~~~~~~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~~~~~~~~~~~R~ 175 (266)
+.+..+..+. ||++.-...-.-+......+++.+++++ |.+.+. ++-..++--....-+
T Consensus 273 ~~L~~hp~V~~V~yPgL~shp~h~la~r~~~g~Gg~~sf~l~g--------~~~~~~--------~f~~~l~l~~~a~Sl 336 (391)
T PRK08133 273 EWLEAHPGVERVFYPGLPSHPQHELAKRQQKGGGAIVSFEVKG--------GREAAW--------RVIDATRLISITANL 336 (391)
T ss_pred HHHHCCCCCCEEECCCCCCCCCHHHHHHCCCCCCCEEEEEECC--------CHHHHH--------HHHHHCCCCEEECCC
T ss_conf 9997099914798999989977789997089997258999719--------999999--------999828846561352
Q ss_pred CCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEECCCCCCHHHHHHHHHHHHH
Q ss_conf 3430365016861012344458999998631540679956899999999877998998999999999999
Q gi|254781079|r 176 GGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERCHKEPISTIIYRADQALY 245 (266)
Q Consensus 176 ~gdeF~ill~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~t~s~Gia~~~~~~~~~~ll~~Ad~Al~ 245 (266)
||-|-.+..|....... +...-++.. - ..+ .-+ -+|+|+ +++++|+..-++||.
T Consensus 337 Gg~eSLi~~Pa~~th~~--~~~e~r~~~---G--I~~-~li--RlSVGl------Ed~~DLi~Dl~qAL~ 390 (391)
T PRK08133 337 GDTKTTITHPATTTHGR--LSPEARAAA---G--ITE-GLI--RVAVGL------EDVADLKADLARGLA 390 (391)
T ss_pred CCCCCEEECCCCCCCCC--CCHHHHHHC---C--CCC-CEE--EEEEEE------CCHHHHHHHHHHHHC
T ss_conf 77301226751134543--899999866---9--894-959--999610------999999999999867
No 89
>TIGR02823 oxido_YhdH putative quinone oxidoreductase, YhdH/YhfP family; InterPro: IPR014188 This entry represents a subfamily of the alcohol dehydrogenase, a superfamily in which some members are zinc-binding medium-chain alcohol dehydrogenases while others are quinone oxidoreductases with no bound zinc. This entry includes YhdH from Escherichia coli and YhfP from Bacillus subtilis both of which bind NADPH or NAD, but not zinc. Both proteins have been studied crystallographically for insight into function. .
Probab=24.44 E-value=39 Score=12.86 Aligned_cols=44 Identities=23% Similarity=0.058 Sum_probs=15.4
Q ss_pred CCCCCCCCHHHCCCCCCCCCCHHHCCCCCCEEEEECCC-CCHHHHH
Q ss_conf 54443110000000111110000001334303650168-6101234
Q gi|254781079|r 149 PVGDKVIAFLSDQLVVVFGTPMFVGRLGGEEFAAAALG-SSEQEAA 193 (266)
Q Consensus 149 ~~gD~~L~~va~~l~~~~~~~~~~~R~~gdeF~ill~~-~~~~~~~ 193 (266)
+.||++|..=-..=..+-+...-.+|+-+| .+|=+|. -+..||+
T Consensus 79 ~~GD~VivTGyglG~~H~GGysqyaRVp~d-WlVpLP~glsl~eAM 123 (330)
T TIGR02823 79 RPGDEVIVTGYGLGVSHDGGYSQYARVPAD-WLVPLPEGLSLREAM 123 (330)
T ss_pred CCCCEEEEEEECCCCCCCCCCEEEEEECHH-HEECCCCCCCHHHHH
T ss_conf 788718997402456515762235673323-101588988988999
No 90
>PRK04280 arginine repressor; Provisional
Probab=24.33 E-value=40 Score=12.77 Aligned_cols=43 Identities=7% Similarity=0.214 Sum_probs=22.3
Q ss_pred HHCCCCCCCCCCHHHCCCCCCEEEEECCCCCHHHHHHHHHHHHHH
Q ss_conf 000001111100000013343036501686101234445899999
Q gi|254781079|r 158 LSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKI 202 (266)
Q Consensus 158 va~~l~~~~~~~~~~~R~~gdeF~ill~~~~~~~~~~~~~~l~~~ 202 (266)
+|..|-.. ...++++=++||+=+++++ .+++++..+.+++...
T Consensus 106 va~~iD~~-~~~~I~GTiAGdDTilVi~-~s~~~a~~l~~~l~~l 148 (149)
T PRK04280 106 IGALLDNL-DWEEILGTICGDDTCLIIC-RTPEDTEVVKDRFLNM 148 (149)
T ss_pred HHHHHHHC-CCCCCEEEEECCCEEEEEE-CCHHHHHHHHHHHHHH
T ss_conf 99999847-9987189860499899998-9999999999999974
No 91
>PRK12495 hypothetical protein; Provisional
Probab=24.14 E-value=22 Score=14.77 Aligned_cols=28 Identities=14% Similarity=0.065 Sum_probs=17.2
Q ss_pred HCCCCCCCC-CCHHHCCCCCCEEEEECCC
Q ss_conf 000011111-0000001334303650168
Q gi|254781079|r 159 SDQLVVVFG-TPMFVGRLGGEEFAAAALG 186 (266)
Q Consensus 159 a~~l~~~~~-~~~~~~R~~gdeF~ill~~ 186 (266)
|.+-..++. -++.++|+.|-|||=-+..
T Consensus 38 ATMTN~HC~~CGdPIFR~dGqeFCPTCQ~ 66 (221)
T PRK12495 38 ATMTNAHCDECGSPIFRHDGQEFCPTCQH 66 (221)
T ss_pred CCCCCCCCCCCCCHHHHCCCCCCCCCCCC
T ss_conf 21021200223672340476614864235
No 92
>KOG4032 consensus
Probab=23.68 E-value=35 Score=13.18 Aligned_cols=35 Identities=29% Similarity=0.199 Sum_probs=18.4
Q ss_pred CHHHCCCCCCEEEEECCCCCHHHHHHHHHHHHHHH
Q ss_conf 00000133430365016861012344458999998
Q gi|254781079|r 169 PMFVGRLGGEEFAAAALGSSEQEAAILANDLRKII 203 (266)
Q Consensus 169 ~~~~~R~~gdeF~ill~~~~~~~~~~~~~~l~~~l 203 (266)
.+.+.+++++||.+.+.+.+..+....+.++...+
T Consensus 67 eE~L~~~l~~EFnt~~eDDS~~~ia~~L~n~f~~~ 101 (184)
T KOG4032 67 EELLLELLGDEFNTKVEDDSLPEIAQLLLNLFHDI 101 (184)
T ss_pred HHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHH
T ss_conf 99999998887631356787799999999999999
No 93
>TIGR01363 strep_his_triad streptococcal histidine triad protein; InterPro: IPR006270 The sequences represented in this group are identified by a domain which consists of the N-terminal half of a family of Streptococcal proteins that contain a signal peptide and then up to five repeats of a region that includes a His-X-X-His-X-His (histidine triad) motif. Additional copies of the repeats are found in more poorly conserved regions. Members of this family from Streptococcus pneumoniae are suggested to cleave human C3, and the member PhpA has been shown in vaccine studies to be a protective antigen in mice . .
Probab=22.96 E-value=42 Score=12.58 Aligned_cols=141 Identities=13% Similarity=0.164 Sum_probs=73.1
Q ss_pred HHHHHHHHHHCCCHHCCCCHHH----HHHHHHHCCCCEEEEEEEC----------CCCCCCCCCCCCCC--CCCCCCHHH
Q ss_conf 9999999961040105020489----9988877089725755442----------21000114688654--443110000
Q gi|254781079|r 96 SYNRISQLSRIDCLSGLLNHSA----FISSLGSYNEKLSIVFFDI----------DYFKQINDNFGHPV--GDKVIAFLS 159 (266)
Q Consensus 96 ~~~~l~~~a~~D~LTgL~NR~~----f~~~l~~~~~~~~l~~idi----------d~fk~iNd~~G~~~--gD~~L~~va 159 (266)
...+-.+.+++|.--|-..... .++-.++.+=..==++|.| |++.-.|-.--+++ .+++|..=-
T Consensus 33 ~~~~~N~vaYID~~~GkA~~~~~N~T~D~vS~~EGI~AEQIViKITDQGYVTSHGDHYHyYNGKVPYDAIISEELLM~DP 112 (376)
T TIGR01363 33 SAKEDNRVAYIDGSQGKAKQKKENLTPDEVSKREGINAEQIVIKITDQGYVTSHGDHYHYYNGKVPYDAIISEELLMKDP 112 (376)
T ss_pred CCCCCCCEEEEECCCCCCCCCCCCCCHHHHHHHHCCCCCEEEEEEECCCEECCCCCEEEEECCCCCCHHHHHHHHHCCCC
T ss_conf 40114735787577554567502577656767628871237899705760313686014327855631322136643788
Q ss_pred C-CCC-----CCCCCCHHHCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEECCCCCCH
Q ss_conf 0-001-----1111000000133430365016861012344458999998631540679956899999999877998998
Q gi|254781079|r 160 D-QLV-----VVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRKIIENSQINISSGPSIHITISAGIAERCHKEPI 233 (266)
Q Consensus 160 ~-~l~-----~~~~~~~~~~R~~gdeF~ill~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~t~s~Gia~~~~~~~~ 233 (266)
+ +|+ ..+ .+..|-.+.|. +-|.|......+-.+..++|.+...+..-...+ -|++. .
T Consensus 113 NY~lK~~DivNEi-~~GYVIKV~G~-YYVYLK~aa~~~NiRTK~~I~~Q~~~~~~~~~~---------~Glaq------v 175 (376)
T TIGR01363 113 NYRLKDSDIVNEI-KGGYVIKVNGK-YYVYLKDAAHADNIRTKEEIARQKQERSKEAKE---------KGLAQ------V 175 (376)
T ss_pred CCCCCCCCCEEEE-CCCEEEEECCE-EEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHC---------CCEEE------H
T ss_conf 7344643200220-38668988581-889617212210130178999998743343322---------54010------1
Q ss_pred HHHHHHHHHHHHHHHHCCCC
Q ss_conf 99999999999999970996
Q gi|254781079|r 234 STIIYRADQALYVAKKSGRN 253 (266)
Q Consensus 234 ~~ll~~Ad~Al~~AK~~gkn 253 (266)
..|-.++|.|...||.+||-
T Consensus 176 ahl~~~~~~AV~~A~~QGRY 195 (376)
T TIGR01363 176 AHLSKREDAAVAEARRQGRY 195 (376)
T ss_pred HHHCHHHHHHHHHHHHCCCC
T ss_conf 12032467899999847881
No 94
>smart00594 UAS UAS domain.
Probab=22.40 E-value=43 Score=12.50 Aligned_cols=29 Identities=17% Similarity=0.117 Sum_probs=18.1
Q ss_pred HCCCCCCEEEEECCCCCHHHHHHHHHHHH
Q ss_conf 00133430365016861012344458999
Q gi|254781079|r 172 VGRLGGEEFAAAALGSSEQEAAILANDLR 200 (266)
Q Consensus 172 ~~R~~gdeF~ill~~~~~~~~~~~~~~l~ 200 (266)
+-++=.+.|++.-.+.+..++..++..++
T Consensus 55 V~~~i~~nfVfw~~d~~~~eg~~~~~~y~ 83 (122)
T smart00594 55 VKSLIRENFIFWQVDVDTSEGQRVSQFYK 83 (122)
T ss_pred HHHHHHHCEEEEEECCCCHHHHHHHHHCC
T ss_conf 99999734889875168745999998628
No 95
>cd02929 TMADH_HD_FMN Trimethylamine dehydrogenase (TMADH) and histamine dehydrogenase (HD) FMN-binding domain. TMADH is an iron-sulfur flavoprotein that catalyzes the oxidative demethylation of trimethylamine to form dimethylamine and formaldehyde. The protein forms a symetrical dimer with each subunit containing one 4Fe-4S cluster and one FMN cofactor. It contains a unique flavin, in the form of a 6-S-cysteinyl FMN which is bent by ~25 degrees along the N5-N10 axis of the flavin isoalloxazine ring. This modification of the conformation of the flavin is thought to facilitate catalysis.The closely related histamine dehydrogenase catalyzes oxidative deamination of histamine.
Probab=22.17 E-value=30 Score=13.67 Aligned_cols=39 Identities=13% Similarity=0.229 Sum_probs=22.8
Q ss_pred CCCCCCCCCC--CCCCHHHCCCCCCCCCC-HHHCCCCCCEEE
Q ss_conf 1468865444--31100000001111100-000013343036
Q gi|254781079|r 143 NDNFGHPVGD--KVIAFLSDQLVVVFGTP-MFVGRLGGEEFA 181 (266)
Q Consensus 143 Nd~~G~~~gD--~~L~~va~~l~~~~~~~-~~~~R~~gdeF~ 181 (266)
+|.||-..-+ +++.+|.+.+++.++++ -+..|+++||+.
T Consensus 189 tDeYGGS~enR~Rf~~Eii~aVr~~vg~df~i~~R~s~~~~~ 230 (370)
T cd02929 189 TDEYGGSLENRARFWRETLEDTKDAVGDDCAVATRFSVDELI 230 (370)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCC
T ss_conf 774689889998999999999999719987599998941256
No 96
>PRK07360 FO synthase subunit 2; Reviewed
Probab=22.00 E-value=44 Score=12.45 Aligned_cols=29 Identities=10% Similarity=0.041 Sum_probs=14.6
Q ss_pred CCCCHHHHHHHHHHHHHHHHHCCCCEEEECCHH
Q ss_conf 989989999999999999997099689994021
Q gi|254781079|r 229 HKEPISTIIYRADQALYVAKKSGRNRVVCFSDI 261 (266)
Q Consensus 229 ~~~~~~~ll~~Ad~Al~~AK~~gkn~~~~~~~~ 261 (266)
...+.+++......|=...++ |-.+|+.+
T Consensus 343 ~~~~~~~l~~~i~~aG~~p~e----R~t~Y~~~ 371 (375)
T PRK07360 343 TCMSVEELENAIKSIGRIPKQ----RDTLYEII 371 (375)
T ss_pred CCCCHHHHHHHHHHCCCCCHH----CCCCCCEE
T ss_conf 889999999999984998311----17888657
No 97
>PRK13700 conjugal transfer protein TraD; Provisional
Probab=22.00 E-value=19 Score=15.17 Aligned_cols=14 Identities=14% Similarity=0.283 Sum_probs=5.9
Q ss_pred HHHHHHHHHHHHHH
Q ss_conf 12344458999998
Q gi|254781079|r 190 QEAAILANDLRKII 203 (266)
Q Consensus 190 ~~~~~~~~~l~~~l 203 (266)
+++++.+..|+..+
T Consensus 331 ~~aeKta~SIrsvL 344 (732)
T PRK13700 331 EKIEKTAISIRAVL 344 (732)
T ss_pred CCCHHHHHHHHHHH
T ss_conf 76088999999999
No 98
>cd03313 enolase Enolase: Enolases are homodimeric enzymes that catalyse the reversible dehydration of 2-phospho-D-glycerate to phosphoenolpyruvate as part of the glycolytic and gluconeogenesis pathways. The reaction is facilitated by the presence of metal ions.
Probab=21.74 E-value=36 Score=13.10 Aligned_cols=23 Identities=30% Similarity=0.325 Sum_probs=10.1
Q ss_pred CCHHHHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf 998999999999999999709968999
Q gi|254781079|r 231 EPISTIIYRADQALYVAKKSGRNRVVC 257 (266)
Q Consensus 231 ~~~~~ll~~Ad~Al~~AK~~gkn~~~~ 257 (266)
-+..+.+..+ ..||+.|-..++.
T Consensus 340 GTvset~ea~----~la~~~g~~~ivS 362 (408)
T cd03313 340 GTLTETIEAI----KLAKKNGYGVVVS 362 (408)
T ss_pred CCHHHHHHHH----HHHHHCCCEEEEE
T ss_conf 7299999999----9999869879997
No 99
>pfam02863 Arg_repressor_C Arginine repressor, C-terminal domain.
Probab=21.63 E-value=45 Score=12.39 Aligned_cols=44 Identities=20% Similarity=0.395 Sum_probs=27.3
Q ss_pred CHHHCCCCCCCCCCHHHCCCCCCEEEEECCCCCHHHHHHHHHHHHH
Q ss_conf 0000000111110000001334303650168610123444589999
Q gi|254781079|r 156 AFLSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQEAAILANDLRK 201 (266)
Q Consensus 156 ~~va~~l~~~~~~~~~~~R~~gdeF~ill~~~~~~~~~~~~~~l~~ 201 (266)
..+|..|.+ .+..++++=++||+=+++++ .+++++..+.+++++
T Consensus 26 ~~va~~iD~-~~~~~I~GTiAGdDTilii~-~~~~~a~~l~~~i~~ 69 (70)
T pfam02863 26 QLVASLIDS-LKLPEILGTIAGDDTILVIC-RSEEDAEELAEKIKK 69 (70)
T ss_pred HHHHHHHHH-CCCCCCEEEECCCCEEEEEE-CCHHHHHHHHHHHHH
T ss_conf 999999984-79985489945899899997-898999999999971
No 100
>PRK00077 eno phosphopyruvate hydratase; Provisional
Probab=21.51 E-value=30 Score=13.68 Aligned_cols=31 Identities=19% Similarity=0.273 Sum_probs=14.1
Q ss_pred CCCCCCCCCCCCCC---CCCCCCCHHHCCCCCCC
Q ss_conf 22100011468865---44431100000001111
Q gi|254781079|r 136 IDYFKQINDNFGHP---VGDKVIAFLSDQLVVVF 166 (266)
Q Consensus 136 id~fk~iNd~~G~~---~gD~~L~~va~~l~~~~ 166 (266)
-++|+.++..+|.. +||.+...-..+|++.+
T Consensus 293 ~~gw~~lt~~lg~k~~iVGDDL~vTn~~rl~kgi 326 (427)
T PRK00077 293 WDGWALLTERLGDKVQLVGDDLFVTNPKILKEGI 326 (427)
T ss_pred HHHHHHHHHHHCCCEEEECCCCCCCCHHHHHHHH
T ss_conf 8999999997099679988841346889997255
No 101
>COG0841 AcrB Cation/multidrug efflux pump [Defense mechanisms]
Probab=21.00 E-value=46 Score=12.30 Aligned_cols=23 Identities=22% Similarity=0.157 Sum_probs=15.2
Q ss_pred CCCCHHHHHHHHHHHHHHHHHCC
Q ss_conf 98998999999999999999709
Q gi|254781079|r 229 HKEPISTIIYRADQALYVAKKSG 251 (266)
Q Consensus 229 ~~~~~~~ll~~Ad~Al~~AK~~g 251 (266)
.+.+.+++-+.|++.+..+++..
T Consensus 666 ~g~d~~~l~~~a~~~~~~~~~~p 688 (1009)
T COG0841 666 RGGDLEALRQAANQLLEKANQSP 688 (1009)
T ss_pred ECCCHHHHHHHHHHHHHHHHHCC
T ss_conf 48999999999999999986089
No 102
>cd04733 OYE_like_2_FMN Old yellow enzyme (OYE)-related FMN binding domain, group 2. Each monomer of OYE contains FMN as a non-covalently bound cofactor, uses NADPH as a reducing agent with oxygens, quinones, and alpha,beta-unsaturated aldehydes and ketones, and can act as electron acceptors in the catalytic reaction. Other members of OYE family include trimethylamine dehydrogenase, 2,4-dienoyl-CoA reductase, enoate reductase, pentaerythriol tetranitrate reductase, xenobiotic reductase, and morphinone reductase.
Probab=20.70 E-value=37 Score=13.02 Aligned_cols=56 Identities=18% Similarity=0.310 Sum_probs=36.1
Q ss_pred CCCCCCCCC--CCCCCHHHCCCCCCCCCC-HHHCCCCCCEEEEECCCCCHHHHHHHHHHHH
Q ss_conf 146886544--431100000001111100-0000133430365016861012344458999
Q gi|254781079|r 143 NDNFGHPVG--DKVIAFLSDQLVVVFGTP-MFVGRLGGEEFAAAALGSSEQEAAILANDLR 200 (266)
Q Consensus 143 Nd~~G~~~g--D~~L~~va~~l~~~~~~~-~~~~R~~gdeF~ill~~~~~~~~~~~~~~l~ 200 (266)
.|.||-..- =+++.+|.+.+++.++++ -+..|++++||.- .+.+.++...+++.+.
T Consensus 188 tDeYGGS~ENR~Rf~lEii~avr~~vg~d~~v~~Ris~~d~~~--~G~~~~d~~~~~~~l~ 246 (338)
T cd04733 188 TDEYGGSLENRARLLLEIYDAIRAAVGPGFPVGIKLNSADFQR--GGFTEEDALEVVEALE 246 (338)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEECHHHHCC--CCCCHHHHHHHHHHHH
T ss_conf 6857989889988999999999997199886999845354247--9999899999999998
No 103
>TIGR01017 rpsD_bact ribosomal protein S4; InterPro: IPR005709 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , . The S4 domain is a small domain consisting of 60-65 amino acid residues that probably mediates binding to RNA. This family consists of organelle (chloroplast and mitochondrial) ribosomal protein S4 as well as bacterial ribosomal protein S4.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=20.68 E-value=25 Score=14.33 Aligned_cols=31 Identities=32% Similarity=0.545 Sum_probs=15.0
Q ss_pred CCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCHHHCCCC
Q ss_conf 00011468865444311000000011111000000133
Q gi|254781079|r 139 FKQINDNFGHPVGDKVIAFLSDQLVVVFGTPMFVGRLG 176 (266)
Q Consensus 139 fk~iNd~~G~~~gD~~L~~va~~l~~~~~~~~~~~R~~ 176 (266)
|+..+-..| ..|+.+|..+=.+| +.+|||+|
T Consensus 80 f~~A~~~~G-ntGe~LL~~LE~RL------DNvVYRlG 110 (217)
T TIGR01017 80 FKEAKKLKG-NTGENLLELLESRL------DNVVYRLG 110 (217)
T ss_pred HHHHHCCCC-HHHHHHHHHHHCCC------CCEEECCC
T ss_conf 999843787-27899999861100------10102127
No 104
>PRK10775 cell division protein FtsQ; Provisional
Probab=20.51 E-value=47 Score=12.23 Aligned_cols=57 Identities=11% Similarity=0.042 Sum_probs=25.9
Q ss_pred HHCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCHHHCCCCCCE
Q ss_conf 770897257554422100011468865444311000000011111000000133430
Q gi|254781079|r 123 GSYNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFGTPMFVGRLGGEE 179 (266)
Q Consensus 123 ~~~~~~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~~~~~~~~~~~R~~gde 179 (266)
.....+.+.+-+|++..+.-=+.+..-..=.+=+.=-+.|+-.+.++..+||||++.
T Consensus 80 ~~~~~~G~Fft~Dl~~iq~~le~lPWV~~asVRR~WPd~L~V~v~E~~PvArWn~~~ 136 (274)
T PRK10775 80 LALGAPGTFMTQDVNIIQQQIERLPWIKQVSVRKQWPDELKIHLVEYVPIARWNDQH 136 (274)
T ss_pred HHCCCCCCEEEECHHHHHHHHHHCCCEEEEEEEEECCCCEEEEEEEECCEEEECCCC
T ss_conf 844789975750699999999849993378899848996099999853489989987
No 105
>PRK08045 cystathionine gamma-synthase; Provisional
Probab=20.40 E-value=47 Score=12.21 Aligned_cols=107 Identities=19% Similarity=0.189 Sum_probs=56.1
Q ss_pred CCCCHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCCCCHHHCCCCCCEEEEECCCCCHH
Q ss_conf 50204899988877089725755442210001146886544431100000001111100000013343036501686101
Q gi|254781079|r 111 GLLNHSAFISSLGSYNEKLSIVFFDIDYFKQINDNFGHPVGDKVIAFLSDQLVVVFGTPMFVGRLGGEEFAAAALGSSEQ 190 (266)
Q Consensus 111 gL~NR~~f~~~l~~~~~~~~l~~idid~fk~iNd~~G~~~gD~~L~~va~~l~~~~~~~~~~~R~~gdeF~ill~~~~~~ 190 (266)
||++.....-..++.....+++.+++++ |. +....+.+.++ --....-+||-|=.+.-|.+...
T Consensus 279 gL~s~p~h~la~~q~~g~Ggm~sf~l~g--------~~----~~~~~f~~~l~----lf~~a~SlGg~eSLi~~pa~~th 342 (386)
T PRK08045 279 SLPENQGHEIAARQQKGFGAMLSFELDG--------DE----QTLRRFLGGLS----LFTLAESLGGVESLISHAATMTH 342 (386)
T ss_pred CCCCCCCHHHHHHCCCCCCCEEEEEECC--------CH----HHHHHHHHHCC----CCEECCCCCCCCCEEECCCCCCC
T ss_conf 9989957799997089997357999659--------79----99999997088----35560266886400037642356
Q ss_pred HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf 23444589999986315406799568999999998779989989999999999999997
Q gi|254781079|r 191 EAAILANDLRKIIENSQINISSGPSIHITISAGIAERCHKEPISTIIYRADQALYVAKK 249 (266)
Q Consensus 191 ~~~~~~~~l~~~l~~~~~~~~~~~~~~~t~s~Gia~~~~~~~~~~ll~~Ad~Al~~AK~ 249 (266)
. .+-..-+... -..+ .- +-+|+|+ +++++|+..-++||..|++
T Consensus 343 ~--~~~~e~r~~~-----Gi~~-~l--iRlSvGl------Ed~eDLi~DL~qAL~aa~~ 385 (386)
T PRK08045 343 A--GMAPEARAAA-----GISE-TL--LRISTGI------EDGEDLIADLENGFRAANK 385 (386)
T ss_pred C--CCCHHHHHHC-----CCCC-CE--EEEEEEE------CCHHHHHHHHHHHHHHHCC
T ss_conf 5--6899999866-----9895-96--9999600------9999999999999998506
No 106
>PRK12677 xylose isomerase; Provisional
Probab=20.31 E-value=47 Score=12.20 Aligned_cols=12 Identities=8% Similarity=0.216 Sum_probs=7.2
Q ss_pred CCCCCCHHHHHH
Q ss_conf 799899899999
Q gi|254781079|r 227 RCHKEPISTIIY 238 (266)
Q Consensus 227 ~~~~~~~~~ll~ 238 (266)
...+++.++++.
T Consensus 343 l~~~~s~~~l~a 354 (389)
T PRK12677 343 LAAGESLADLLA 354 (389)
T ss_pred CCCCCCHHHHHH
T ss_conf 578878999987
Done!