Query         gi|254780695|ref|YP_003065108.1| flagellar MS-ring protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 563
No_of_seqs    144 out of 1037
Neff          8.2 
Searched_HMMs 39220
Date          Sun May 29 20:20:18 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780695.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK06007 fliF flagellar MS-rin 100.0       0       0  948.7  59.6  532    1-554     3-540 (540)
  2 PRK12800 fliF flagellar MS-rin 100.0       0       0  948.9  58.3  540    5-553    15-571 (572)
  3 PRK07193 fliF flagellar MS-rin 100.0       0       0  913.6  56.1  535    2-555     8-549 (550)
  4 COG1766 fliF Flagellar basal b 100.0       0       0  861.4  46.7  534    1-553     3-545 (545)
  5 pfam01514 YscJ_FliF Secretory  100.0       0       0  411.7  23.9  201   18-224     2-205 (206)
  6 TIGR00206 fliF flagellar M-rin 100.0       0       0  388.9  33.5  538    9-554    11-610 (611)
  7 pfam08345 YscJ_FliF_C Flagella 100.0 7.7E-38   2E-42  270.8  16.7  162  249-413     1-162 (162)
  8 TIGR02544 III_secr_YscJ type I 100.0 4.4E-30 1.1E-34  219.2  19.7  179   34-213     5-197 (203)
  9 COG4669 EscJ Type III secretor 100.0 1.2E-26   3E-31  196.4  19.5  177   37-215    11-191 (246)
 10 PRK05934 type III secretion sy  98.5 5.4E-07 1.4E-11   65.6   6.8   97  118-221    59-157 (341)
 11 TIGR02830 spore_III_AG stage I  96.1   0.023 5.9E-07   34.8   6.6  100  189-296    12-115 (193)
 12 PRK06007 fliF flagellar MS-rin  94.1    0.45 1.1E-05   26.2  15.4   73    2-74      7-106 (540)
 13 pfam09413 DUF2007 Protein of u  92.5    0.65 1.6E-05   25.2   6.8   53   51-103     3-67  (68)
 14 PRK10629 hypothetical protein;  89.2     1.6 4.1E-05   22.5   6.5   55   48-103    40-98  (127)
 15 PRK11114 cellulose synthase re  85.4     2.6 6.7E-05   21.1   9.6   88  381-468   665-755 (759)
 16 pfam04612 GspM General secreti  84.6     2.4 6.2E-05   21.4   5.0   37    4-43      1-37  (159)
 17 COG3944 Capsular polysaccharid  84.1       2 5.1E-05   21.9   4.5   35  181-215   123-162 (226)
 18 pfam11294 DUF3095 Protein of u  82.9     2.5 6.5E-05   21.2   4.6   48   52-99     46-96  (373)
 19 pfam02706 Wzz Chain length det  82.3     3.5   9E-05   20.3   5.7   15  182-196   123-137 (139)
 20 PRK03427 cell division protein  77.2     2.6 6.7E-05   21.1   3.1   33   22-54      6-38  (331)
 21 PRK04335 cell division protein  77.0     2.4 6.2E-05   21.4   2.9   33   22-54      5-37  (319)
 22 PRK01741 cell division protein  74.1     2.2 5.5E-05   21.7   2.0   33   22-54      4-36  (342)
 23 PRK10949 protease 4; Provision  71.4     7.1 0.00018   18.3   5.6   39    3-41      4-43  (618)
 24 COG4535 CorC Putative Mg2+ and  69.2     4.2 0.00011   19.8   2.6   38  379-416   230-267 (293)
 25 PRK13254 cytochrome c-type bio  69.1     7.9  0.0002   17.9   4.0   40   18-60      4-43  (149)
 26 KOG1176 consensus               68.5     8.1 0.00021   17.9   6.8   16  187-202   236-251 (537)
 27 TIGR01074 rep ATP-dependent DN  68.3       5 0.00013   19.3   2.8   15   63-77    361-375 (677)
 28 pfam01910 DUF77 Domain of unkn  66.2       9 0.00023   17.6   4.6   48   58-105    17-68  (92)
 29 PRK13165 cytochrome c-type bio  65.5     9.3 0.00024   17.5   4.1   39   19-60      5-43  (161)
 30 PRK03598 hypothetical protein;  65.3     6.7 0.00017   18.5   3.0   30   20-49      2-31  (331)
 31 PRK13390 acyl-CoA synthetase;   64.0     9.9 0.00025   17.3   8.5   23   43-65     71-93  (501)
 32 COG3115 ZipA Cell division pro  62.7     9.1 0.00023   17.5   3.3   33   22-54      5-37  (324)
 33 PRK07867 acyl-CoA synthetase;   62.6      11 0.00027   17.1   8.0   29   43-74     76-104 (505)
 34 PRK13150 cytochrome c-type bio  62.2      11 0.00027   17.1   4.0   39   19-60      5-43  (159)
 35 pfam03180 Lipoprotein_9 NLPA l  62.1      11 0.00027   17.1   3.6  105   78-191    95-211 (236)
 36 PRK13159 cytochrome c-type bio  61.9      11 0.00028   17.1   4.4   39   19-60      5-43  (156)
 37 PRK09861 cytoplasmic membrane   60.9      11 0.00029   16.9   3.9   25   79-103   130-156 (272)
 38 PRK05605 acyl-CoA synthetase;   60.7      11 0.00029   16.9   9.7   14  525-538   555-568 (571)
 39 PTZ00233 variable surface prot  59.5     4.8 0.00012   19.4   1.4   18  454-471   451-468 (509)
 40 PRK09732 hypothetical protein;  58.8      12 0.00031   16.7   6.4   62  178-239     2-65  (134)
 41 PRK10270 hypothetical protein;  58.7      12 0.00031   16.7   5.0   24   50-73     40-63  (340)
 42 pfam04814 HNF-1_N Hepatocyte n  58.7      12 0.00031   16.7   5.0   37  516-552    90-126 (177)
 43 PRK13388 acyl-CoA synthetase;   58.0      13 0.00032   16.6   8.0   33   39-74     70-102 (544)
 44 PRK06219 consensus              57.2      13 0.00033   16.5   8.1   23   43-65     89-111 (547)
 45 pfam03100 CcmE CcmE. CcmE is t  56.4      11 0.00029   16.9   2.9   39   19-60      4-42  (130)
 46 PRK05696 fliL flagellar basal   56.0     9.3 0.00024   17.5   2.4   27  233-259   132-158 (168)
 47 COG3105 Uncharacterized protei  55.9      14 0.00035   16.4   6.9   27  438-464     7-33  (138)
 48 PRK11677 cytochrome d ubiquino  55.2      14 0.00036   16.3   5.8   18  531-548    48-65  (134)
 49 PRK03584 acetoacetyl-CoA synth  55.2      14 0.00036   16.3   7.9   27   59-88    125-151 (652)
 50 KOG4238 consensus               55.0     9.1 0.00023   17.5   2.2   35   60-94    211-246 (627)
 51 TIGR01006 polys_exp_MPA1 polys  54.6      14 0.00036   16.3   4.5   18  379-396   135-153 (235)
 52 PRK00174 acetyl-CoA synthetase  54.3      14 0.00037   16.2   8.1   40   59-101   116-156 (648)
 53 PRK05620 acyl-CoA synthetase;   53.8      15 0.00037   16.2   9.9   14  525-538   545-558 (571)
 54 pfam06898 YqfD Putative stage   53.0      15 0.00038   16.1   3.7   41   36-76     97-137 (383)
 55 PRK11480 tauA taurine transpor  51.8      16  0.0004   16.0   3.6   28  532-559   211-238 (320)
 56 PRK07021 fliL flagellar basal   50.6      16 0.00042   15.8   3.1   25  234-258   124-148 (159)
 57 TIGR01925 spIIAB anti-sigma F   50.4     9.4 0.00024   17.4   1.7   48  354-413    18-71  (137)
 58 TIGR03017 EpsF chain length de  49.5      17 0.00044   15.7   5.8   26  176-201   133-159 (444)
 59 PRK03739 2-isopropylmalate syn  49.5      17 0.00044   15.7   6.5   90   53-165    47-136 (552)
 60 PRK13628 serine/threonine tran  47.6      18 0.00046   15.5   4.4   32    4-35      1-32  (402)
 61 PRK11901 hypothetical protein;  47.6      18 0.00047   15.5   3.9   28   20-47     35-62  (329)
 62 pfam10969 DUF2771 Protein of u  47.3      12  0.0003   16.8   1.8   28   23-50      5-32  (161)
 63 pfam09919 DUF2149 Uncharacteri  47.1     7.9  0.0002   18.0   0.8   19   68-87     73-91  (91)
 64 PRK08008 caiC putative crotono  46.4      19 0.00048   15.4   7.8   26   41-66     82-107 (517)
 65 COG0011 Uncharacterized conser  46.4      19 0.00048   15.4   5.9   61   47-107     8-74  (100)
 66 PRK11063 metQ DL-methionine tr  45.7      19  0.0005   15.4   3.6   25   79-103   129-155 (271)
 67 PRK13391 acyl-CoA synthetase;   45.1      20 0.00051   15.3   8.2   70    3-76     30-101 (514)
 68 TIGR00970 leuA_yeast 2-isoprop  45.0      13 0.00033   16.5   1.7   95  137-252   109-205 (615)
 69 TIGR02554 PrgH type III secret  44.6      20 0.00052   15.2   5.0  128   56-217   197-330 (423)
 70 PRK00269 zipA cell division pr  44.4      20 0.00052   15.2   2.8   27   21-47      5-31  (295)
 71 COG2268 Uncharacterized protei  44.1      21 0.00052   15.2   4.5   19   68-86     55-73  (548)
 72 pfam09976 DUF2133 Uncharacteri  43.9      21 0.00053   15.2   4.9   33    4-43      3-35  (43)
 73 PRK13952 mscL large-conductanc  43.7      21 0.00053   15.2   7.1   30  435-464    83-112 (143)
 74 pfam06408 consensus             43.5     7.4 0.00019   18.2   0.2   29  169-197   143-172 (471)
 75 PRK08343 secD preprotein trans  43.3      21 0.00054   15.1   6.6   17  378-394   216-232 (414)
 76 TIGR00915 2A0602 RND transport  43.2      21 0.00054   15.1   6.0   89  166-260    82-178 (1058)
 77 PRK12933 secD preprotein trans  42.5      22 0.00056   15.0   4.9  195   44-263    39-266 (604)
 78 pfam09580 Spore_YhcN_YlaJ Spor  42.1      22 0.00056   15.0   8.9   73  129-214    61-135 (169)
 79 PRK10617 cytochrome c-type pro  41.3      23 0.00058   14.9   4.4  128    5-155     9-151 (200)
 80 PRK02220 4-oxalocrotonate taut  41.2      23 0.00058   14.9   4.5   37  175-211     4-43  (61)
 81 COG2332 CcmE Cytochrome c-type  40.6      23 0.00059   14.8   4.3   34   20-53      6-39  (153)
 82 PRK09731 putative general secr  40.1      24  0.0006   14.8   4.8   32   12-43     27-58  (178)
 83 PRK05677 acyl-CoA synthetase;   39.6      24 0.00061   14.7   7.9   18   44-61     98-115 (562)
 84 PRK06155 crotonobetaine/carnit  39.4      24 0.00062   14.7   7.9   23   43-65    105-127 (552)
 85 PRK12406 acyl-CoA synthetase;   39.4      24 0.00062   14.7   7.8   29   38-66     54-82  (510)
 86 PRK03592 haloalkane dehalogena  39.0      23 0.00059   14.9   2.2   19  534-552   269-287 (294)
 87 pfam04415 DUF515 Protein of un  38.9      25 0.00063   14.7   3.3   22   18-39     27-48  (416)
 88 TIGR00063 folE GTP cyclohydrol  38.8      25 0.00063   14.7   4.0   37  230-266   107-143 (183)
 89 PRK09841 cryptic autophosphory  38.0      25 0.00065   14.6   5.6   40    2-50     19-58  (726)
 90 PRK05529 cell division protein  37.4      26 0.00066   14.5   5.6  111    7-170    20-131 (255)
 91 PRK11556 multidrug efflux syst  37.4      26 0.00066   14.5   3.7   41  112-156   153-193 (415)
 92 COG3149 PulM Type II secretory  36.8      27 0.00068   14.5   5.2   31   13-43     27-57  (181)
 93 PRK08455 fliL flagellar basal   36.6      17 0.00043   15.8   1.2   17  234-250   149-165 (180)
 94 PRK08276 acyl-CoA synthetase;   36.3      27 0.00069   14.4   8.3   33   38-73     66-98  (507)
 95 COG0841 AcrB Cation/multidrug   36.1      27 0.00069   14.4   9.4   26  129-154   150-175 (1009)
 96 PRK07771 consensus              35.4      28 0.00071   14.3   8.0   10  200-209   215-224 (541)
 97 TIGR02742 TrbC_Ftype type-F co  35.0      18 0.00047   15.5   1.2   46  154-199     5-53  (139)
 98 COG3583 Uncharacterized protei  34.8      28 0.00073   14.3   5.0   60   18-77     10-72  (309)
 99 COG1464 NlpA ABC-type metal io  34.7      29 0.00073   14.2   2.9  102   79-189   127-241 (268)
100 TIGR00106 TIGR00106 conserved   34.1      29 0.00075   14.2   4.2   49   54-102    14-68  (103)
101 PRK06188 acyl-CoA synthetase;   33.9      29 0.00075   14.2   8.0   31   41-74     80-110 (522)
102 PRK10927 essential cell divisi  33.5      30 0.00076   14.1   2.8   80   18-98     30-123 (319)
103 PRK08316 acyl-CoA synthetase;   33.5      30 0.00076   14.1  10.0   29   38-66     78-106 (525)
104 PRK11033 zntA zinc/cadmium/mer  32.8      30 0.00078   14.1   2.0   26  235-260   217-244 (739)
105 COG4744 Uncharacterized conser  32.5      31 0.00079   14.0   2.8   18   69-87     97-114 (121)
106 TIGR01478 STEVOR variant surfa  32.5      31 0.00079   14.0   4.0   11  387-397   240-250 (315)
107 PRK06164 acyl-CoA synthetase;   31.6      32 0.00082   13.9  10.0   22   44-65     83-104 (541)
108 PRK00023 cmk cytidylate kinase  31.2      33 0.00083   13.9   3.4  136   51-197    47-221 (225)
109 TIGR02667 moaB_proteo molybden  31.1      19 0.00048   15.4   0.7   22  532-553    41-62  (163)
110 PRK06145 acyl-CoA synthetase;   30.6      33 0.00085   13.8   7.9   29   38-66     69-97  (497)
111 PRK11519 tyrosine kinase; Prov  30.1      34 0.00087   13.7   5.6   20   31-50     39-58  (720)
112 cd00371 HMA Heavy-metal-associ  29.8      34 0.00088   13.7   5.6   41  135-189    12-52  (63)
113 TIGR00418 thrS threonyl-tRNA s  29.6      35 0.00088   13.7   3.4   29  132-160    46-74  (595)
114 pfam10971 DUF2773 Protein of u  29.4      27 0.00068   14.4   1.2   22  532-553    21-42  (81)
115 pfam11576 DUF3236 Protein of u  28.9      36 0.00091   13.6   3.6   42  206-252   110-151 (154)
116 PRK13729 conjugal transfer pil  28.9      16 0.00042   15.9   0.1   35   13-47      3-37  (474)
117 PRK01710 murD UDP-N-acetylmura  28.5      25 0.00065   14.6   1.0   56   19-78     13-69  (458)
118 pfam08478 POTRA_1 POTRA domain  28.4      36 0.00092   13.6   3.1   26  136-161    34-59  (67)
119 PRK07798 acyl-CoA synthetase;   28.3      36 0.00093   13.5   7.9   31   41-74     73-103 (532)
120 TIGR01495 ETRAMP early transcr  28.0      37 0.00094   13.5   3.5   23   19-41     60-83  (99)
121 TIGR02004 PTS-IIBC-malX PTS sy  27.9      37 0.00094   13.5   3.5   27  440-466   388-414 (540)
122 TIGR00869 sec62 protein transl  27.9      37 0.00094   13.5   3.1   36  429-464   144-179 (259)
123 COG2098 Uncharacterized protei  27.8      37 0.00095   13.5   3.2   51   98-159    16-66  (116)
124 PRK10907 intramembrane serine   27.6      37 0.00095   13.5   6.2   45   55-99      8-54  (276)
125 PRK07008 acyl-CoA synthetase;   27.6      37 0.00096   13.5   9.6   22   44-65     87-108 (539)
126 PRK06178 acyl-CoA synthetase;   27.1      38 0.00097   13.4   7.6   14  524-537   552-565 (567)
127 PRK07768 acyl-CoA synthetase;   26.6      39 0.00099   13.3   8.6   15   59-73     38-52  (543)
128 TIGR00739 yajC preprotein tran  26.4      39   0.001   13.3   2.1   26  442-467     6-31  (86)
129 pfam11829 DUF3349 Protein of u  26.4      39   0.001   13.3   3.0   62   45-107    22-95  (97)
130 PRK07770 consensus              26.2      40   0.001   13.3   7.9   37   38-77     74-110 (508)
131 PRK06187 acyl-CoA synthetase;   26.2      40   0.001   13.3   8.0   34   40-76     75-108 (520)
132 pfam11823 DUF3343 Protein of u  26.1      40   0.001   13.3   6.9   58   47-106     3-68  (73)
133 PRK10673 hypothetical protein;  26.1      40   0.001   13.3   1.9   20  534-553   236-255 (255)
134 COG3603 Uncharacterized conser  26.1      40   0.001   13.3   5.1   40   62-101    82-123 (128)
135 pfam05663 DUF809 Protein of un  25.8      40   0.001   13.3   6.3   77    2-92      3-87  (138)
136 PRK10549 signal transduction h  25.7      33 0.00084   13.8   1.2   53   18-70      7-61  (467)
137 pfam01756 ACOX Acyl-CoA oxidas  25.4      20  0.0005   15.3  -0.0   34  182-215   104-137 (186)
138 PRK00745 4-oxalocrotonate taut  25.3      41   0.001   13.2   4.8   36  175-210     4-42  (62)
139 PRK06287 cobalt transport prot  25.2      29 0.00073   14.2   0.8   24  440-463    80-103 (105)
140 PRK08279 acyl-CoA synthetase;   24.8      42  0.0011   13.1   7.9   22   44-65    115-136 (602)
141 PRK04319 acetyl-CoA synthetase  24.8      42  0.0011   13.1   8.2   21   43-63    120-140 (570)
142 pfam00580 UvrD-helicase UvrD/R  24.5      43  0.0011   13.1   8.2   22   48-69     46-67  (494)
143 PRK12785 fliL flagellar basal   24.4      13 0.00033   16.5  -1.1   22  234-259   136-157 (167)
144 PRK08130 putative aldolase; Va  24.2      42  0.0011   13.1   1.5   21  199-219    48-68  (213)
145 PRK06839 acyl-CoA synthetase;   24.2      43  0.0011   13.1   8.9   23   42-64     74-96  (496)
146 TIGR00998 8a0101 efflux pump m  24.0      43  0.0011   13.0   3.0   58   21-89      2-61  (379)
147 TIGR02371 ala_DH_arch alanine   24.0      40   0.001   13.3   1.3   28  145-177    63-90  (327)
148 PRK13383 acyl-CoA synthetase;   23.9      44  0.0011   13.0   7.9   22   43-64    107-128 (516)
149 PTZ00042 stevor; Provisional    23.9      44  0.0011   13.0   4.0   27  440-466   267-293 (304)
150 pfam00403 HMA Heavy-metal-asso  23.8      44  0.0011   13.0   2.6   22  136-157    13-34  (62)
151 pfam06153 DUF970 Protein of un  23.8      44  0.0011   13.0   5.0   53   48-100     1-63  (109)
152 cd02192 PurM-like3 AIR synthas  23.8      44  0.0011   13.0   3.7   18  148-165    24-41  (283)
153 TIGR01005 eps_transp_fam exopo  23.5      44  0.0011   13.0   5.4   29   23-51     17-45  (778)
154 cd01324 cbb3_Oxidase_CcoQ Cyto  23.5      44  0.0011   13.0   4.7   39    1-52      1-39  (48)
155 PRK00915 2-isopropylmalate syn  23.4      45  0.0011   13.0   5.8   46   53-102    21-66  (511)
156 PRK07529 acyl-CoA synthetase;   23.4      45  0.0011   13.0  12.7   15  197-211   246-260 (632)
157 PRK07788 acyl-CoA synthetase;   23.2      45  0.0011   12.9   7.9   56   43-101    64-127 (552)
158 cd04389 RhoGAP_KIAA1688 RhoGAP  23.0      45  0.0012   12.9   2.1   23   51-73     43-66  (187)
159 PRK00870 haloalkane dehalogena  23.0      45  0.0012   12.9   2.1   20  534-553   282-301 (302)
160 PRK11760 putative RNA 2'-O-rib  22.7      46  0.0012   12.9   1.8   50  185-247    83-132 (356)
161 PRK10476 multidrug resistance   22.7      46  0.0012   12.9   1.6   19   55-73     53-71  (348)
162 smart00824 PKS_TE Thioesterase  22.7      46  0.0012   12.9   1.8   17  534-550   196-212 (212)
163 PRK06087 short chain acyl-CoA   22.0      47  0.0012   12.8  10.8   19   44-62     98-116 (548)
164 cd02847 Chitobiase_C_term Chit  22.0      41  0.0011   13.2   1.1   13   66-78      2-14  (78)
165 PRK11100 sensory histidine kin  22.0      48  0.0012   12.8   4.1   29  381-410   365-394 (475)
166 pfam01765 RRF Ribosome recycli  21.9      48  0.0012   12.8   4.1   34  377-413    49-84  (165)
167 COG2815 Uncharacterized protei  21.8      48  0.0012   12.8   1.8   37   35-75     13-51  (303)
168 PRK06531 yajC preprotein trans  21.6      48  0.0012   12.7   1.9   10  454-463    17-26  (120)
169 TIGR03056 bchO_mg_che_rel puta  21.6      48  0.0012   12.7   1.9   18  534-551   261-278 (278)
170 PRK09481 sspA stringent starva  21.4      49  0.0012   12.7   2.9   53   43-101     5-57  (211)
171 COG4674 Uncharacterized ABC-ty  21.3      36 0.00091   13.6   0.6   56   45-100   110-165 (249)
172 pfam09179 TilS TilS substrate   21.1      50  0.0013   12.7   2.8   21  532-552     4-24  (69)
173 TIGR02782 TrbB_P P-type conjug  20.9      50  0.0013   12.6   5.2   63  132-200     3-67  (315)
174 PRK06357 hypothetical protein;  20.8      50  0.0013   12.6   3.1   20  199-218    51-70  (211)
175 TIGR03261 phnS2 putative 2-ami  20.7      50  0.0013   12.6   6.3   43   38-80     13-57  (334)
176 cd04390 RhoGAP_ARHGAP22_24_25   20.6      51  0.0013   12.6   1.9   10  200-209   151-160 (199)
177 PRK11486 flagellar biosynthesi  20.3      51  0.0013   12.6   4.6   17  537-553   105-121 (124)
178 PRK00783 DNA-directed RNA poly  20.1      52  0.0013   12.5   3.3   38  181-218    18-55  (265)
179 TIGR01846 type_I_sec_HlyB type  20.0      52  0.0013   12.5   2.3  112    4-146   252-365 (703)

No 1  
>PRK06007 fliF flagellar MS-ring protein; Reviewed
Probab=100.00  E-value=0  Score=948.68  Aligned_cols=532  Identities=28%  Similarity=0.417  Sum_probs=443.4

Q ss_pred             CCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEECCCCCHHHHHHHHHHHHHCCCCEEECCCC
Q ss_conf             96789999999986406987889999999999999999999846998245038999899999999999779929991899
Q gi|254780695|r    1 MAILDQLLQFFKSGTSLGRTRILILASVILVPIMLFMAARFFVNSPHYDNLYVKLEVSDVNRISVALSEANIDFRISDNG   80 (563)
Q Consensus         1 m~~~~~l~~~~~~~~~l~~~~ki~~~~~~~~~i~~~~~~~~~~~~p~y~~L~~~l~~~d~~~i~~~L~~~gI~y~~~~~g   80 (563)
                      |.|.+.+.+|.++|++|+++|||++++++++++++++++++|.++|+|++||+||+++|+++|++.|+++||+|+++++|
T Consensus         3 ~~l~~~~~~~~~~~~~l~~~qki~l~~~~~~~i~~~~~l~~~~~~p~y~~L~~~l~~~da~~I~~~L~~~gI~Y~l~~~G   82 (540)
T PRK06007          3 MKLKELMEKLLEFLKKLSKLRKIALIGAAAAVIAAIVALVLWASRPDYRVLYSNLSDQDAGQIVAALDQAGIPYKVSSDG   82 (540)
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEECCCCCHHHHHHHHHHHHHCCCCEEECCCC
T ss_conf             68999999999999706988899999999999999999998416997277028999899999999999879975976999


Q ss_pred             CEEEECHHHHHHHHHHHHHCCCCCCCCCCHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEECC
Q ss_conf             77995189999999999976998877663256530588842599999999999999999999960576314899998336
Q gi|254780695|r   81 SSISVPSSMVGKARIHLAAQGLPSSSSNSGYELFDKVNSFGLTSFMQEITRVRALEGEIARTIQSISGIVAARVHIVMPD  160 (563)
Q Consensus        81 ~~I~Vp~~~~~~~r~~La~~glp~~~~~~g~el~d~~~~~g~T~~~~~~~~~ralegeL~rtI~~~~~V~~ArV~l~~p~  160 (563)
                      ++|+||+++++++||.||++|||+++ ..|||+||+.++||+|+|+|+++|+|||||||+|||++|++|++|||||++|+
T Consensus        83 ~~I~Vp~~~v~~~Rl~LA~~Glp~~~-~~G~elfd~~~~~g~T~f~~~~~~~ralegELartI~~l~~V~~ArVhl~~Pe  161 (540)
T PRK06007         83 GTILVPEDKVDELRLKLASEGLPKGG-SVGYELFDKSSGFGITQFEEQVNYQRALEGELARTIESLDGVKAARVHLALPK  161 (540)
T ss_pred             CEEEECHHHHHHHHHHHHHCCCCCCC-CCCHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCC
T ss_conf             77997677899999999976999999-97589873689877579999999999999999999971368114699996899


Q ss_pred             CCCCCCCCCCCCEEEEEECCCC--CCHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCEEECCCC--CCCCCHHHHHHHHH
Q ss_conf             6655555558715999706877--8988999999999865401883526998289835003676--53332479999999
Q gi|254780695|r  161 MGSFRKIGARPTASVMIRAINP--SVYKSAEAIRHLVAAAVPNLDMGDVTVLDSTGKLLTANEM--ERNILGKSLSIVQA  236 (563)
Q Consensus       161 ~~~f~~~~~~~sASV~l~~~~~--l~~~qv~~I~~lVa~sV~gL~~e~VtVvD~~G~~L~~~~~--~~~~~~~~~~~~~~  236 (563)
                      +++|.+++.+|||||+|+++++  |+++||+||+||||+|||||+|+||||+|++|++|++..+  .+..+++|++|+++
T Consensus       162 ~s~F~~~~~~~tASV~l~l~~g~~Ls~~qV~aI~~LVa~sV~gL~~enVtVvD~~G~lLs~~~~~~~~~~~~~q~~~~~~  241 (540)
T PRK06007        162 ESVFVREQQPPSASVVLTLKPGRTLDPEQVKAIVHLVASAVPGLKPENVTVVDQNGNLLSDGSDDSSSSLAAKQLKLKQQ  241 (540)
T ss_pred             CCCCCCCCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCHHHHHHHHH
T ss_conf             87552468887568999836998799999999999999746999811369987999852578887654220789999999


Q ss_pred             HHHHHHHHHHHHHHHHCCCCEEEEEEEEEEECCCEEEEEEEECCCCCCCCCEEEEEEECCC-CCCCCCCCCCCCCCCCCC
Q ss_conf             9999999999887754087806999884432230167888514787765421577630256-677777778777777876
Q gi|254780695|r  237 IQHEIEMNINKALAAFLGVDNFRSAVVAELNMDTQQIREIVYDPDSKVERSIRLSKDAQRS-ETSQPESAVTVEQNMPHV  315 (563)
Q Consensus       237 ~E~~~~~kI~~~L~~i~G~~~v~v~V~~~ldfd~~~~~~e~y~p~~~~~~s~~~~~~~~~s-~~~~~~G~pG~~sN~p~~  315 (563)
                      +|++|++||.++|+|++|+||++|+|+++||||++++++++|+|++++++|+++.++++.+ .+..++|+||+.+|.|+.
T Consensus       242 ~E~~l~~~i~~~L~~i~G~g~~~v~V~a~ldf~~~~~~~e~y~P~~~~v~s~~~~~~~~~~~~~~~~~GvpG~~sN~p~~  321 (540)
T PRK06007        242 VEKRLQQRIESILAPILGPGNVRAQVTADLDFDKVEQTEETYDPNGPVVRSEQTSEEESNGGGGAVTGGVPGALSNQPPN  321 (540)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCEEEEEEEEECCCCEEEEEEEECCCCCEEEEEEEEEEECCCCCCCCCCCCCCCCCCCCCC
T ss_conf             99999999999987300898369999888614755899999889996043478887630467787789998865788998


Q ss_pred             CCCC-CCCCCCCCCCCCCCEEEEECCCCEEEEEEECCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             6666-677766665544310342105617999970785100102565305432456665555334698999999998643
Q gi|254780695|r  316 SDRK-VPLPRSLENTDKKEEQSNYEINTKSIATTHDNYKLERLSIAVVVNKGRLTEVLGRSADQGKIDSYLAEINKIVSA  394 (563)
Q Consensus       316 ~~~~-~~~~~~~~~~~~~~~t~NYev~~t~~~~~~~~G~I~rlSVAV~Vn~~~~~~~~g~~~~~~~~~eel~~I~~lV~~  394 (563)
                      ++.. .+++.++++|+++++|+|||+||++++++++||.|+|+||||+||+.+..+++++..+.|++++++++|++||++
T Consensus       322 ~~~~~~~~~~~~~~~~~~~~t~NYev~~~~~~~~~~~G~i~rlSVaV~vd~~~~~~~~~~~~~~p~s~~el~~I~~lV~~  401 (540)
T PRK06007        322 QQAQGNGGNNSTSSSSRSEETTNYEVDKTISHTKKQPGTVKRLSVAVVVNKVVIADGDGDVEYQPLSAEELAQIEKLVRS  401 (540)
T ss_pred             CCCCCCCCCCCCCCCCCCCEEEECCCCCEEEEEECCCCEEEEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf             65567777778875410110573135708999975895488989999974642357776556787999999999999998


Q ss_pred             HCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             12566113876899850356654343444562045899999999999999999999999999997787520112210001
Q gi|254780695|r  395 ATGINSRRGDTITITSMDFLENQLFNSGTVQVSFMDILSRHFATVINALVFLVGTLLVTFLGLHALRRLHNIDDAKKGEV  474 (563)
Q Consensus       395 AiG~d~~RGD~VtV~~~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~lll~~~vl~~l~~~~~~~~~~~~~~  474 (563)
                      |+|||++|||+|+|+++||........+  ..++|.....+......++++++++++++|+++|++++............
T Consensus       402 AvG~d~~RGD~VtV~~~~F~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~l~ll~l~l~~~v~Rp~~~~~~~~~~~~~~~  479 (540)
T PRK06007        402 AVGFDAARGDSVNVVNVPFTRAAEEEEP--ELPLWEQPGFIDLLKLAALWILLVALVLIFKVVRPLLRRAEAEEEEAAEA  479 (540)
T ss_pred             HHCCCCCCCCEEEEEEECCCCCCCCCCC--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf             7276756798699997326775543345--65144427899999999999999999999999988765215566554433


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHH
Q ss_conf             12212334333210000012221000133433334444431010021100689999999988699989999999986378
Q gi|254780695|r  475 GGKSILSPPPISSAVTTGLMPNDNIALDSSNQDIFSHSRNLQSRINSYVSKQSDLRLLHMIEINEERFAKILRKWARSEI  554 (563)
Q Consensus       475 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~lv~e~Pe~vA~vLR~WL~ee~  554 (563)
                      .....   .   ...    ..+.      ..   .................+.+++|++|+++|||++|+|||+||+||+
T Consensus       480 ~~~~~---~---~~~----~~~~------~~---~~~~~~~~~~~~~~~~~~~~~~i~~lv~e~Pe~vA~lLR~Wl~ede  540 (540)
T PRK06007        480 EALEE---E---EEA----LLDE------LA---DDEVEELREEEDEHKYEDLLKRLRELAKEDPEEVAQVLRTWLNEDE  540 (540)
T ss_pred             CCCCC---C---CCC----CCCC------CC---CCCCCCCCCCCCCCCHHHHHHHHHHHHHHCHHHHHHHHHHHHHCCC
T ss_conf             33344---5---445----5666------55---4322223334333223899999999998799999999999864579


No 2  
>PRK12800 fliF flagellar MS-ring protein; Reviewed
Probab=100.00  E-value=0  Score=948.87  Aligned_cols=540  Identities=22%  Similarity=0.323  Sum_probs=445.4

Q ss_pred             HHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEECCCCCHHHHHHHHHHHHHCCCCEEECCCCCEEE
Q ss_conf             99999999864069878899999999999999999998469982450389998999999999997799299918997799
Q gi|254780695|r    5 DQLLQFFKSGTSLGRTRILILASVILVPIMLFMAARFFVNSPHYDNLYVKLEVSDVNRISVALSEANIDFRISDNGSSIS   84 (563)
Q Consensus         5 ~~l~~~~~~~~~l~~~~ki~~~~~~~~~i~~~~~~~~~~~~p~y~~L~~~l~~~d~~~i~~~L~~~gI~y~~~~~g~~I~   84 (563)
                      ++..||+++|++|+..|++.+++++++++++++++++|.++|+|++||++|++.|+++|++.|+++||||+++++|++|+
T Consensus        15 ~~~~~~~~~~~~l~~~r~~~l~~~la~~va~~~~~~~w~~~p~y~~Ly~~L~~~D~~~iv~~L~~~~IpY~l~~~g~~Il   94 (572)
T PRK12800         15 EKAGQWFDRVRSLQITRKLTMMAMIALAVAAGLAVFFWSQKPGYQSLYTGLDEKGNAEAADLLRTAQIPFKIDQGTGAIS   94 (572)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEECCCCCCHHHHHHHHHHHHHCCCCEEECCCCCEEE
T ss_conf             88999999875487344799999999999999999985169983542589997899999999997799779879997599


Q ss_pred             ECHHHHHHHHHHHHHCCCCCCCCCCHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCC
Q ss_conf             51899999999999769988776632565305888425999999999999999999999605763148999983366655
Q gi|254780695|r   85 VPSSMVGKARIHLAAQGLPSSSSNSGYELFDKVNSFGLTSFMQEITRVRALEGEIARTIQSISGIVAARVHIVMPDMGSF  164 (563)
Q Consensus        85 Vp~~~~~~~r~~La~~glp~~~~~~g~el~d~~~~~g~T~~~~~~~~~ralegeL~rtI~~~~~V~~ArV~l~~p~~~~f  164 (563)
                      ||+++++++||.||++|||.++...|||+||+.++||+|+|+|++||+|||||||+|||++|++|++|||||++||+++|
T Consensus        95 VP~~~v~~~Rl~LA~~Glp~~g~~~GfElld~~~~~G~Sqf~e~v~y~rAlEgELaRTI~~l~~V~~ARVHLalPk~s~F  174 (572)
T PRK12800         95 VPQDRLYDARLKLAGSGLTGKETGGGFELMEKDPGFGVSQFVENARYQHALETELSRTIGTLRPVREARVHLAIPKPSAF  174 (572)
T ss_pred             ECHHHHHHHHHHHHHCCCCCCCCCCCHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCCC
T ss_conf             24767899999999768998999876898766888874799999999999999999999843670224899967998764


Q ss_pred             CCCCCCCCEEEEEECCCC--CCHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCEEECCCCC--CCCCHHHHHHHHHHHHH
Q ss_conf             555558715999706877--89889999999998654018835269982898350036765--33324799999999999
Q gi|254780695|r  165 RKIGARPTASVMIRAINP--SVYKSAEAIRHLVAAAVPNLDMGDVTVLDSTGKLLTANEME--RNILGKSLSIVQAIQHE  240 (563)
Q Consensus       165 ~~~~~~~sASV~l~~~~~--l~~~qv~~I~~lVa~sV~gL~~e~VtVvD~~G~~L~~~~~~--~~~~~~~~~~~~~~E~~  240 (563)
                      +|++.+|||||+|++++|  |+++||.||+||||+|||||+|+||||+||+|++|+..+++  ...+..|++|++++|+.
T Consensus       175 ~r~~~~psASV~l~l~~G~~L~~~QV~aIv~LVAsSVpgL~p~~VtVvDq~G~LLs~~~~~~~~~~~~~q~~~~~~~E~~  254 (572)
T PRK12800        175 TRQRDVASASVVLELRGGQGLERNQVDAIVNLVASSIPDMTPERVTVVDQSGRMLSIADPNSDAAQHAAQFEQVRRQESS  254 (572)
T ss_pred             CCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCHHHEEEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf             24688997259996579997999999999999984279988423079858998625789875310027899999999999


Q ss_pred             HHHHHHHHHHHHCCCCEEEEEEEEEEECCCEEEEEEEECCCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCC--
Q ss_conf             999999887754087806999884432230167888514787765421577630256677777778777777876666--
Q gi|254780695|r  241 IEMNINKALAAFLGVDNFRSAVVAELNMDTQQIREIVYDPDSKVERSIRLSKDAQRSETSQPESAVTVEQNMPHVSDR--  318 (563)
Q Consensus       241 ~~~kI~~~L~~i~G~~~v~v~V~~~ldfd~~~~~~e~y~p~~~~~~s~~~~~~~~~s~~~~~~G~pG~~sN~p~~~~~--  318 (563)
                      |++||.++|.|++|+|||+|+|+++|||+++++++|+|||++++++|++.+++..  .+..++|+||+.+|.|+..+.  
T Consensus       255 ~~~rI~~~L~pivG~gn~~a~V~adlDF~~~e~t~e~ydp~~~~vrSeq~~e~~~--~~~~~~GvPGa~sN~P~~~~~~~  332 (572)
T PRK12800        255 YNQRIRELLEPMTGPGRVNPEVSVDMDFSVVEEARELYNGEPAKLRSEQVSDTST--SATGPQGPPGATSNSPGQPPAPA  332 (572)
T ss_pred             HHHHHHHHHHHHCCCCCEEEEEEEEECCCCEEEEEEEECCCCCCCCEEEEEECCC--CCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             9999999988662788259999888616753788887479876333047620135--67778899876478899888642


Q ss_pred             ----------CCCCCCCCCCCCCCCEEEEECCCCEEEEEEECCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCHHHHHHH
Q ss_conf             ----------6677766665544310342105617999970785100102565305432456665555334698999999
Q gi|254780695|r  319 ----------KVPLPRSLENTDKKEEQSNYEINTKSIATTHDNYKLERLSIAVVVNKGRLTEVLGRSADQGKIDSYLAEI  388 (563)
Q Consensus       319 ----------~~~~~~~~~~~~~~~~t~NYev~~t~~~~~~~~G~I~rlSVAV~Vn~~~~~~~~g~~~~~~~~~eel~~I  388 (563)
                                +..+.....+++++++|+|||+||+++|+++++|.|+|+||||+||+....+++|+.+++|++++|+++|
T Consensus       333 ~~~~~~~~~~~~~~~~~~~~~~~~~~TrNYEv~rti~~~~~~~G~I~RLSVAVvVd~~~~~~~~g~~~~~p~s~eel~~i  412 (572)
T PRK12800        333 AAGAPGTPAAGQAAAAAAPTESSKSATRNYELDRTLQHTRQPAGRIKRVSVAVLLDNVPRPGAKGKMVEQPLTAAELTRI  412 (572)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCEEECEECCEEEEEECCCCEEEEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHH
T ss_conf             24688876556666667776433331031211537999975886488999999972543457777757788899999999


Q ss_pred             HHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             99864312566113876899850356654343444562045899999999999999999999999999997787520112
Q gi|254780695|r  389 NKIVSAATGINSRRGDTITITSMDFLENQLFNSGTVQVSFMDILSRHFATVINALVFLVGTLLVTFLGLHALRRLHNIDD  468 (563)
Q Consensus       389 ~~lV~~AiG~d~~RGD~VtV~~~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~lll~~~vl~~l~~~~~~~~  468 (563)
                      ++||++|+|||.+|||+|+|+++||.....+..+.+  +||+.  .|+..++++++.++++++++|+++||+.+.+....
T Consensus       413 ~~LV~~AvG~d~~RGD~v~V~~~pF~~~~~~~~~~~--~~we~--p~~~~~~r~l~~alv~l~llf~VvRP~lk~l~~~~  488 (572)
T PRK12800        413 EGLVKQAVGFDAARGDTVSVMNAPFVREAVAGEEGP--KWWED--PRVQNGLRLLVGAVVVLALLFGVVRPTLRQLTGVT  488 (572)
T ss_pred             HHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCCCCC--CCCCC--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             999997518873569778998547777654334577--54325--89999999999999999999999999999741555


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCC-CCCHHHHHHHHHHHHHHCHHHHHHHHH
Q ss_conf             2100011221233433321000001222100013343333444443101002-110068999999998869998999999
Q gi|254780695|r  469 AKKGEVGGKSILSPPPISSAVTTGLMPNDNIALDSSNQDIFSHSRNLQSRIN-SYVSKQSDLRLLHMIEINEERFAKILR  547 (563)
Q Consensus       469 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~i~~lv~e~Pe~vA~vLR  547 (563)
                      +............ .+.  ........++...++....+......+...... ....++..+.+++||+++|++||+|||
T Consensus       489 ~~~~~~~~~~~~~-~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~e~~l~~iR~lv~~dP~rVA~ViK  565 (572)
T PRK12800        489 AVKEKQKKGGNDG-TPQ--SADVRMVDDDDDLLPRLGEDTASIGQDKKLAIALPDAYEERMRLAREAVKADSKRVAQVVK  565 (572)
T ss_pred             CCCHHHCCCCCCC-CCC--CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCHHHHHHHHH
T ss_conf             4210111244545-643--2100025664321001232100126653224667641999999999998749999999999


Q ss_pred             HHHHHH
Q ss_conf             998637
Q gi|254780695|r  548 KWARSE  553 (563)
Q Consensus       548 ~WL~ee  553 (563)
                      +||++|
T Consensus       566 ~Wi~~d  571 (572)
T PRK12800        566 GWVASE  571 (572)
T ss_pred             HHHHCC
T ss_conf             998646


No 3  
>PRK07193 fliF flagellar MS-ring protein; Reviewed
Probab=100.00  E-value=0  Score=913.62  Aligned_cols=535  Identities=24%  Similarity=0.308  Sum_probs=423.1

Q ss_pred             CHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEECCCCCHHHHHHHHHHHHHCCCCEEECCCCC
Q ss_conf             67899999999864069878899999999999999999998469982450389998999999999997799299918997
Q gi|254780695|r    2 AILDQLLQFFKSGTSLGRTRILILASVILVPIMLFMAARFFVNSPHYDNLYVKLEVSDVNRISVALSEANIDFRISDNGS   81 (563)
Q Consensus         2 ~~~~~l~~~~~~~~~l~~~~ki~~~~~~~~~i~~~~~~~~~~~~p~y~~L~~~l~~~d~~~i~~~L~~~gI~y~~~~~g~   81 (563)
                      ++|++|+++|++|.. +.+||+++++++++++++++++++|.++|+|++||+||+++|+++|+++|+++||||+++++|+
T Consensus         8 ~~~~~l~~~w~~~~~-~~~~k~~~i~~~a~~v~~~~~l~~~~~~p~y~~Ly~~L~~~da~~I~~~L~~~~i~y~~~~~g~   86 (550)
T PRK07193          8 AMLSKLKQKWSPFRL-RGNRKLILLALLALLVAAAIVLSLWRSSQGYRPLYGSQENVPTSQVVEVLEAEGISYRIEPDSG   86 (550)
T ss_pred             HHHHHHHHHHHHCCC-CCCCEEHHHHHHHHHHHHHHHHHHHHCCCCCEEECCCCCHHHHHHHHHHHHHCCCCEEECCCCC
T ss_conf             999999999985042-5672304799999999999999864179970773289998999999999998799879869997


Q ss_pred             EEEECHHHHHHHHHHHHHCCCCCCCCCCHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEECCC
Q ss_conf             79951899999999999769988776632565305888425999999999999999999999605763148999983366
Q gi|254780695|r   82 SISVPSSMVGKARIHLAAQGLPSSSSNSGYELFDKVNSFGLTSFMQEITRVRALEGEIARTIQSISGIVAARVHIVMPDM  161 (563)
Q Consensus        82 ~I~Vp~~~~~~~r~~La~~glp~~~~~~g~el~d~~~~~g~T~~~~~~~~~ralegeL~rtI~~~~~V~~ArV~l~~p~~  161 (563)
                      +|+||+++++++||.||++|||+++ +.|||+||+.++||+|+|+|+++|+|||||||+|||++|++|++|||||++|++
T Consensus        87 ~I~Vp~~~v~~~Rl~LA~~Glp~~~-~~G~elfd~~~~~g~t~f~q~v~y~rAlegELartI~~l~~V~~ArVhL~~P~~  165 (550)
T PRK07193         87 QVLVAEDQLGKARMLLAAKGVKAKL-PSGLELLDKDSPLGTSQFMQNVRYRRSLEGELAQSIMALDAVESARVHLAIPKS  165 (550)
T ss_pred             EEEECHHHHHHHHHHHHHCCCCCCC-CCCHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCC
T ss_conf             5993488899999999975799999-973788725888774699999999999999999999714780246999966998


Q ss_pred             CCCCC-CCCCCCEEEEEECCCC--CCHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCEEECCCCC----CCCCHHHHHHH
Q ss_conf             65555-5558715999706877--89889999999998654018835269982898350036765----33324799999
Q gi|254780695|r  162 GSFRK-IGARPTASVMIRAINP--SVYKSAEAIRHLVAAAVPNLDMGDVTVLDSTGKLLTANEME----RNILGKSLSIV  234 (563)
Q Consensus       162 ~~f~~-~~~~~sASV~l~~~~~--l~~~qv~~I~~lVa~sV~gL~~e~VtVvD~~G~~L~~~~~~----~~~~~~~~~~~  234 (563)
                      ++|++ ++.+|||||+|+++++  |+++||.||+||||+|||||+|+||||+|++|++|+.+.++    ...+..|++|+
T Consensus       166 s~F~~~~~~~~sASV~l~l~~g~~L~~~qV~aI~~LVa~sV~gL~penVtVvD~~G~lLs~~~~~~~~~~~~~~~ql~~~  245 (550)
T PRK07193        166 SSFVRQNPELPSASVMLRLKPGQKLSPEQVEAIVNLVAGSVPGLKPANVSVVDQHGNLLSAGIDANEDGTQSRKSQLEYA  245 (550)
T ss_pred             CCCCCCCCCCCCEEEEEEECCCCCCCHHHHHHHHHHHHHCCCCCCHHHEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHH
T ss_conf             76302568888359999806998689999999999998536999877838977899755577877642101038899999


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEECCCEEEEEEEECCCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCC
Q ss_conf             99999999999988775408780699988443223016788851478776542157763025667777777877777787
Q gi|254780695|r  235 QAIQHEIEMNINKALAAFLGVDNFRSAVVAELNMDTQQIREIVYDPDSKVERSIRLSKDAQRSETSQPESAVTVEQNMPH  314 (563)
Q Consensus       235 ~~~E~~~~~kI~~~L~~i~G~~~v~v~V~~~ldfd~~~~~~e~y~p~~~~~~s~~~~~~~~~s~~~~~~G~pG~~sN~p~  314 (563)
                      +++|++|++||+++|+|++|+|||+|+|+++||||+.++++++|+|++. .+++++.++.  +++..++|+||+.+|.|+
T Consensus       246 ~~~E~~l~~~i~~~L~~i~G~~n~~v~V~a~ldf~~~~~t~e~ydp~~~-v~se~~~~e~--~~~~~~~G~pG~~sN~pp  322 (550)
T PRK07193        246 QELEQSTIKNAASMLTPVLGAGNFRVSVAADVDFSRVEETRESYGPAPV-VTNENTSQEN--SNDDMALGIPGSLSNRPP  322 (550)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEECCCEEEEEEEECCCCC-EEEEEEEECC--CCCCCCCCCCCCCCCCCC
T ss_conf             9999999999999988534898469999999731535899998689873-0125675303--567788889886678899


Q ss_pred             CCCCCCCCCCCCCCCCCCCEEEEECCCCEEEEEEECCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             66666677766665544310342105617999970785100102565305432456665555334698999999998643
Q gi|254780695|r  315 VSDRKVPLPRSLENTDKKEEQSNYEINTKSIATTHDNYKLERLSIAVVVNKGRLTEVLGRSADQGKIDSYLAEINKIVSA  394 (563)
Q Consensus       315 ~~~~~~~~~~~~~~~~~~~~t~NYev~~t~~~~~~~~G~I~rlSVAV~Vn~~~~~~~~g~~~~~~~~~eel~~I~~lV~~  394 (563)
                      ..+....  +..+.++++++++|||+||+++|+++++|.|+|+||||+||+....       ..+++++++++|++||++
T Consensus       323 ~~~~~~~--~~~~~~~~~~~t~NYev~~t~~~~~~~~g~i~rlsVAVvVd~~~~~-------~~~~s~eel~~I~~LV~~  393 (550)
T PRK07193        323 QAGAGQT--PAAARNLRSEESRQYAYDRSVRHTRYQQGQLEKLSVAVVLNKAAAP-------LKGWTPEQLAQLKRMVED  393 (550)
T ss_pred             CCCCCCC--CCCCCCCCCEEEEEEECCEEEEEEECCCCEEEEEEEEEEECCCCCC-------CCCCCHHHHHHHHHHHHH
T ss_conf             8877788--8877753202566433260899998688469998999997576677-------889899999999999999


Q ss_pred             HCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             12566113876899850356654343444562045899999999999999999999999999997787520112210001
Q gi|254780695|r  395 ATGINSRRGDTITITSMDFLENQLFNSGTVQVSFMDILSRHFATVINALVFLVGTLLVTFLGLHALRRLHNIDDAKKGEV  474 (563)
Q Consensus       395 AiG~d~~RGD~VtV~~~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~lll~~~vl~~l~~~~~~~~~~~~~~  474 (563)
                      |+|||..|||+|+|.++||.......  .+..+||..  .++..+++++++++++++++||++|++.+............
T Consensus       394 AvG~d~~RGD~v~V~~~pF~~~~~~~--~~~~~~~~~--~~~~~~~~~~l~~ll~Llli~~vlRplvk~~~~~~~~~~~~  469 (550)
T PRK07193        394 AIGIDAARGDSLTINSFDFAPPTVAV--EPAMPWWQE--PSTQAWLRYIIGGLLGLLLLFFVLRPLVKHLTRTGSENLPA  469 (550)
T ss_pred             HHCCCCCCCCEEEEEECCCCCCCCCC--CCCCCHHCC--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf             73757456874799960467765444--567851106--89999999999999999999999999999973103333333


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHH
Q ss_conf             12212334333210000012221000133433334444431010021100689999999988699989999999986378
Q gi|254780695|r  475 GGKSILSPPPISSAVTTGLMPNDNIALDSSNQDIFSHSRNLQSRINSYVSKQSDLRLLHMIEINEERFAKILRKWARSEI  554 (563)
Q Consensus       475 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~lv~e~Pe~vA~vLR~WL~ee~  554 (563)
                      ...........................+............... ......+...++|++|+++||++||+|||+||+||+
T Consensus       470 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~L~-~~~~~~e~~i~~ir~la~e~Pe~VA~vlR~WL~eDe  548 (550)
T PRK07193        470 AISSASALEALEHVDTGVAGADSLPETANALSASSLLGSDDLP-EPGSGLEVKIEHLQLLANKEPERVAEVIKQWINSNE  548 (550)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCC-CCCCCHHHHHHHHHHHHHHCHHHHHHHHHHHHHCCC
T ss_conf             4453322123332100233222222221123444554300056-657758999999999997199999999999865217


Q ss_pred             H
Q ss_conf             6
Q gi|254780695|r  555 E  555 (563)
Q Consensus       555 ~  555 (563)
                      .
T Consensus       549 ~  549 (550)
T PRK07193        549 R  549 (550)
T ss_pred             C
T ss_conf             7


No 4  
>COG1766 fliF Flagellar basal body M-ring protein [Cell motility and secretion]
Probab=100.00  E-value=0  Score=861.39  Aligned_cols=534  Identities=29%  Similarity=0.428  Sum_probs=432.5

Q ss_pred             CCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEECCCCCHHHHHHHHHHHHHCCCCEEECCCC
Q ss_conf             96789999999986406987889999999999999999999846998245038999899999999999779929991899
Q gi|254780695|r    1 MAILDQLLQFFKSGTSLGRTRILILASVILVPIMLFMAARFFVNSPHYDNLYVKLEVSDVNRISVALSEANIDFRISDNG   80 (563)
Q Consensus         1 m~~~~~l~~~~~~~~~l~~~~ki~~~~~~~~~i~~~~~~~~~~~~p~y~~L~~~l~~~d~~~i~~~L~~~gI~y~~~~~g   80 (563)
                      |.|+..+..+.++|.+++++|||.+++++++++++++++.+|.++|+|++||++|+.+|+++|+.+|+++||||+++++|
T Consensus         3 ~~l~~~~~k~~~~~~~~~~~~ki~l~~~~~~~v~~~v~l~l~~~~p~y~~Ly~~l~~~d~~~Iv~~L~~~~I~y~v~~~G   82 (545)
T COG1766           3 ENLRQLLKKLKEFWGKLTKKQKIVLLGAGAALVAVLVALLLWSRQPKYRTLYSNLSEEDAGRIVQELDQMNIPYKVSSDG   82 (545)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEECCCCCEEEECCCCCHHHHHHHHHHHHHCCCCCEECCCC
T ss_conf             16899999989998665166789999999999999998723327996364036777777889999998638984637999


Q ss_pred             CEEEECHHHHHHHHHHHHHCCCCCCCCCCHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEECC
Q ss_conf             77995189999999999976998877663256530588842599999999999999999999960576314899998336
Q gi|254780695|r   81 SSISVPSSMVGKARIHLAAQGLPSSSSNSGYELFDKVNSFGLTSFMQEITRVRALEGEIARTIQSISGIVAARVHIVMPD  160 (563)
Q Consensus        81 ~~I~Vp~~~~~~~r~~La~~glp~~~~~~g~el~d~~~~~g~T~~~~~~~~~ralegeL~rtI~~~~~V~~ArV~l~~p~  160 (563)
                      ++|+||+++++++||.||++|||+++. .||||||+..+||+|+|+|+++|+|||||||+|||++|++|++|||||++||
T Consensus        83 ~~ilVP~~~v~~~Rl~lA~~GLp~~~~-~GyElfd~~~~fG~T~f~~~v~~~RAlegELartI~~l~~V~~ArVhl~lPk  161 (545)
T COG1766          83 GTILVPEDQVYELRLKLAAEGLPKSGN-VGYELFDDNSKFGLTDFMQQVNYQRALEGELARTIVAIDGVKAARVHLVLPK  161 (545)
T ss_pred             CEEECCHHHHHHHHHHHHHCCCCCCCC-CCHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCHHHEEEEEECCC
T ss_conf             769676889999999998747987788-6666642444326436777888999987999999997644223058884588


Q ss_pred             CCCCCCCCCCCCEEEEEECCCC--CCHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCEEECCCCC--CCCCHHHHHHHHH
Q ss_conf             6655555558715999706877--89889999999998654018835269982898350036765--3332479999999
Q gi|254780695|r  161 MGSFRKIGARPTASVMIRAINP--SVYKSAEAIRHLVAAAVPNLDMGDVTVLDSTGKLLTANEME--RNILGKSLSIVQA  236 (563)
Q Consensus       161 ~~~f~~~~~~~sASV~l~~~~~--l~~~qv~~I~~lVa~sV~gL~~e~VtVvD~~G~~L~~~~~~--~~~~~~~~~~~~~  236 (563)
                      +++|++++++|||||+|+++||  |+++||.||+||||+|||||+++||||+||+|++|+..+++  .....+|++++++
T Consensus       162 ~s~Fv~~q~~psASV~l~l~pG~~l~~~qV~aI~~LVs~aVpgL~~enVtVvDq~g~ll~~~~~~~~~~~~~~q~~~~~~  241 (545)
T COG1766         162 DSLFVRDQQPPSASVVLKLKPGRNLSREQVRAIVHLVSSAVPGLKPENVTVVDQSGRLLSQSDDDSGSDAALSQLKLKSD  241 (545)
T ss_pred             CCHHHCCCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf             21202136788438999706888789999999999998626999700347855887602445663104789999999999


Q ss_pred             HHHHHHHHHHHHHHHHCCCCEEEEEEEEEEECCCEEEEEEEECCCCC--CCCCEEEEEEECCCCCCCCCCCCCCC-CCCC
Q ss_conf             99999999998877540878069998844322301678885147877--65421577630256677777778777-7778
Q gi|254780695|r  237 IQHEIEMNINKALAAFLGVDNFRSAVVAELNMDTQQIREIVYDPDSK--VERSIRLSKDAQRSETSQPESAVTVE-QNMP  313 (563)
Q Consensus       237 ~E~~~~~kI~~~L~~i~G~~~v~v~V~~~ldfd~~~~~~e~y~p~~~--~~~s~~~~~~~~~s~~~~~~G~pG~~-sN~p  313 (563)
                      +|+.|++||.++|.|++|.||++|+|++++||++.++++|.|+|+++  +.+|++..++.+.+..+.++|+||+. +|+|
T Consensus       242 vE~~l~~kI~~~L~pv~G~~nv~~~Vta~lDfs~~e~~~e~y~P~~~~~~~rS~q~~~s~~~~~~~~~~g~pg~~~sN~P  321 (545)
T COG1766         242 VEKRLEKKIQNILEPVLGAGNVRASVTAELDFSAKESTEEKYDPNGREPAVRSEQTVTSLSQSGQGTQGGVPGALESNQP  321 (545)
T ss_pred             HHHHHHHHHHHHHHHHCCCCEEEEEEEEEECCCCCEECCEEECCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCC
T ss_conf             99999999998765431787069998642004633001235478876655301121001332268878997760457799


Q ss_pred             CCCCCCCCCCCCCCCCCCCCEEEEECCCCEEEEEEECCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf             76666667776666554431034210561799997078510010256530543245666555533469899999999864
Q gi|254780695|r  314 HVSDRKVPLPRSLENTDKKEEQSNYEINTKSIATTHDNYKLERLSIAVVVNKGRLTEVLGRSADQGKIDSYLAEINKIVS  393 (563)
Q Consensus       314 ~~~~~~~~~~~~~~~~~~~~~t~NYev~~t~~~~~~~~G~I~rlSVAV~Vn~~~~~~~~g~~~~~~~~~eel~~I~~lV~  393 (563)
                      +..+.....+..+ .+.++++|+|||+|++++||++++|+|+|+||||+||+.+. +..++..+.|++++++++|+++|+
T Consensus       322 ~~~~~~~~~~~~~-~~~~~e~ttNYEv~~~~~~t~~~~g~i~rlsVaVvVd~~~~-~~~~~~~~~p~s~~~~~~i~~lv~  399 (545)
T COG1766         322 PVAGNQNGKDTSN-YTEKKEETTNYEVDRTISHTKKEPGTIRRLSVAVVVDGKSL-AGTGEKEYTPLSDEELKEIEDLVR  399 (545)
T ss_pred             CCCCCCCCCCCCC-CCCCCCCCHHHHHHHHHHHHHHCCCEEEEEEEEEEECCCCC-CCCCCCCCCCCCHHHHHHHHHHHH
T ss_conf             8788655444010-01113320002023678876526650356789999816334-566766677777899999999999


Q ss_pred             HHCCCCCCCCCEEEEEECCCCCCCCCCCC--CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             31256611387689985035665434344--4562045899999999999999999999999999997787520112210
Q gi|254780695|r  394 AATGINSRRGDTITITSMDFLENQLFNSG--TVQVSFMDILSRHFATVINALVFLVGTLLVTFLGLHALRRLHNIDDAKK  471 (563)
Q Consensus       394 ~AiG~d~~RGD~VtV~~~~F~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~l~~lll~~~vl~~l~~~~~~~~~~~  471 (563)
                      +|+|||..|||+|+|.++||.+ ......  .+...+|.  ...+...+.+++..+++++++|+++|++.+......+..
T Consensus       400 ~a~G~d~~RGDsv~V~n~~F~~-~~~~~~~e~~~~~~~~--~~~~~~~~~~~~~~l~~~lv~~~~~r~~i~~~~~~~~e~  476 (545)
T COG1766         400 DAVGYDAKRGDSVTVVNIPFDR-SEDQEAEEGDGKPEWE--TQSFLDSLIPVALYLVVFLVLFIIVRPVIRPRRRRGAEA  476 (545)
T ss_pred             HHCCCCCCCCCEEEEECCCCCC-CCCCCCCCCCCCHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHH
T ss_conf             7348774568746883267763-1233211134314442--034687999999999999999999999999875155200


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCHHHHHHHHHHHHHHCHHHHHHHHHHHHH
Q ss_conf             00112212334333210000012221000133433334444431010021100689999999988699989999999986
Q gi|254780695|r  472 GEVGGKSILSPPPISSAVTTGLMPNDNIALDSSNQDIFSHSRNLQSRINSYVSKQSDLRLLHMIEINEERFAKILRKWAR  551 (563)
Q Consensus       472 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~lv~e~Pe~vA~vLR~WL~  551 (563)
                      ...............  ..    +      +.. .....+........+....+...++|++|++++||++|.|||+||.
T Consensus       477 ~~~~~~~~~~~~~~~--~~----~------~~~-~~~~~e~~~~~~~~~~~~~e~~~~~l~~ma~~~Pe~vA~vir~Wl~  543 (545)
T COG1766         477 LEAAEEERQGPEEED--VL----P------EEI-RDSNDEQLGLGDEEQRRGKEVLLERLREMAKEDPERVAKVIRQWLN  543 (545)
T ss_pred             HHHHCCCCCCCCCCC--CC----C------CCC-CCCCHHHCCCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH
T ss_conf             001102335632344--56----4------212-3552111154530111235899999999986198999999999862


Q ss_pred             HH
Q ss_conf             37
Q gi|254780695|r  552 SE  553 (563)
Q Consensus       552 ee  553 (563)
                      ++
T Consensus       544 e~  545 (545)
T COG1766         544 ED  545 (545)
T ss_pred             CC
T ss_conf             69


No 5  
>pfam01514 YscJ_FliF Secretory protein of YscJ/FliF family. This family includes proteins that are related to the YscJ lipoprotein, and the amino terminus of FliF, the flageller M-ring protein. The members of the YscJ family are thought to be involved in secretion of several proteins. The FliF protein ring is thought to be part of the export apparatus for flageller proteins, based on the similarity to YscJ proteins.
Probab=100.00  E-value=0  Score=411.74  Aligned_cols=201  Identities=34%  Similarity=0.512  Sum_probs=181.0

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEECCCCCHHHHHHHHHHHHHCCCCEEECCCC--CEEEECHHHHHHHHH
Q ss_conf             987889999999999999999999846998245038999899999999999779929991899--779951899999999
Q gi|254780695|r   18 GRTRILILASVILVPIMLFMAARFFVNSPHYDNLYVKLEVSDVNRISVALSEANIDFRISDNG--SSISVPSSMVGKARI   95 (563)
Q Consensus        18 ~~~~ki~~~~~~~~~i~~~~~~~~~~~~p~y~~L~~~l~~~d~~~i~~~L~~~gI~y~~~~~g--~~I~Vp~~~~~~~r~   95 (563)
                      .+.+|+.+     +++++++++++|.++|+|++||+||+++|+++|++.|+++||+|++.++|  ++|+||+++++++||
T Consensus         2 ~~~~~i~~-----~~i~~l~~l~~~~~~p~y~~Ly~~L~~~da~~i~~~L~~~gI~y~~~~~g~g~tI~Vp~~~~~~ar~   76 (206)
T pfam01514         2 KKLRKIAL-----AVVALLLLLLLLAGCPDYVTLYTGLSEKDANEVLAALLQAGIPAEKSPDGDGGTILVPEDDVARARE   76 (206)
T ss_pred             CCHHHHHH-----HHHHHHHHHHHHHCCCCCEECCCCCCHHHHHHHHHHHHHCCCCEEEEECCCCCEEEECCCHHHHHHH
T ss_conf             73001089-----9999999999984799856111599999999999999987997598548987289916014899999


Q ss_pred             HHHHCCCCCCCCCCHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCCEEE
Q ss_conf             99976998877663256530588842599999999999999999999960576314899998336665555555871599
Q gi|254780695|r   96 HLAAQGLPSSSSNSGYELFDKVNSFGLTSFMQEITRVRALEGEIARTIQSISGIVAARVHIVMPDMGSFRKIGARPTASV  175 (563)
Q Consensus        96 ~La~~glp~~~~~~g~el~d~~~~~g~T~~~~~~~~~ralegeL~rtI~~~~~V~~ArV~l~~p~~~~f~~~~~~~sASV  175 (563)
                      .||++|||+++. .||+.|++.++||+|+|+|+++|+|||||||+|||++|++|++|||||++|++++|.+++.+|||||
T Consensus        77 ~La~~GlP~~~~-~g~~~~f~~~~lg~T~~~~~~~~~rAle~eL~rtI~~i~gV~~ArVhl~lPe~s~f~~~~~~~sASV  155 (206)
T pfam01514        77 LLAAKGLPREGF-VGLEEIFPKDGLGSSPFEERARLIYALEQELSRTLSQIDGVISARVHIVLPERSLFGRESQPPSASV  155 (206)
T ss_pred             HHHHCCCCCCCC-CCHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEECCCCCCCCCCCCCCCEEE
T ss_conf             999759999999-8899982689876789999999999999999999972788306799996788776555678886689


Q ss_pred             EEECCCCCC-HHHHHHHHHHHHHHHHCCCCCCEEEEECCCCEEECCCCCC
Q ss_conf             970687789-8899999999986540188352699828983500367653
Q gi|254780695|r  176 MIRAINPSV-YKSAEAIRHLVAAAVPNLDMGDVTVLDSTGKLLTANEMER  224 (563)
Q Consensus       176 ~l~~~~~l~-~~qv~~I~~lVa~sV~gL~~e~VtVvD~~G~~L~~~~~~~  224 (563)
                      +|+++++.. ..||.||+||||+|||||+||||||+|++|++|++.++++
T Consensus       156 ~l~l~~g~~l~~qV~~I~~LVa~SV~gL~~enVtVvD~~G~~Ls~~~d~~  205 (206)
T pfam01514       156 FIKYSPGVNLDAQVPAIKNLVASSVPGLKYDNVSVVDQPGTLLSASSDQS  205 (206)
T ss_pred             EEEECCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCCCCCCCCCCC
T ss_conf             99837999819999999999997459988035599889998778888767


No 6  
>TIGR00206 fliF flagellar M-ring protein FliF; InterPro: IPR000067 This family corresponds to the FliF protein. FliF is the major protein of the M-ring in bacterial flagellar basal body . The basal body consists of four rings (L,P,S and M) surrounding the flagellar rod, which is believed to transmit motor rotation to the filament . The M ring is integral to the inner membrane of the cell, and may be connected to the rod via the S (supramembrane) ring, which lies just distal to it. The L and P rings reside in the outer membrane and periplasmic space, respectively. FliF lacks a signal peptide and is predicted to have considerable alpha-helical structure, including an N-terminal sequence that is likely to be membrane-spanning . Overall, however, FliF has a relatively hydrophilic sequence, with a high charge density, especially towards its C-terminus .; GO: 0003774 motor activity, 0001539 ciliary or flagellar motility, 0009431 flagellin-based flagellum basal body MS ring.
Probab=100.00  E-value=0  Score=388.92  Aligned_cols=538  Identities=26%  Similarity=0.342  Sum_probs=398.2

Q ss_pred             HHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCC------CCEEECCCCCHH-HHHHHHHHHHHCCCCEEECCCCC
Q ss_conf             99998640698788999999999999999999984699------824503899989-99999999997799299918997
Q gi|254780695|r    9 QFFKSGTSLGRTRILILASVILVPIMLFMAARFFVNSP------HYDNLYVKLEVS-DVNRISVALSEANIDFRISDNGS   81 (563)
Q Consensus         9 ~~~~~~~~l~~~~ki~~~~~~~~~i~~~~~~~~~~~~p------~y~~L~~~l~~~-d~~~i~~~L~~~gI~y~~~~~g~   81 (563)
                      .....|.++.+.+++.++.++.+++++++++..|...+      .|.++|.+++.. +.+.+...|+..++||+++.+|+
T Consensus        11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~   90 (611)
T TIGR00206        11 KALEFFKKLSKLQKIALILAGAAVIALLVFLLLFASKSKDYTQGGYALLFEGLSDEYDGGLILEELDQENVPYKLSEDGG   90 (611)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHCCCCEECCCCC
T ss_conf             67888876431114678999999999999987520343100134202222010124456788887765305510026872


Q ss_pred             EEEECHHHHHHHHHHHHHCCCCCCCCCCHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEECCC
Q ss_conf             79951899999999999769988776632565305888425999999999999999999999605763148999983366
Q gi|254780695|r   82 SISVPSSMVGKARIHLAAQGLPSSSSNSGYELFDKVNSFGLTSFMQEITRVRALEGEIARTIQSISGIVAARVHIVMPDM  161 (563)
Q Consensus        82 ~I~Vp~~~~~~~r~~La~~glp~~~~~~g~el~d~~~~~g~T~~~~~~~~~ralegeL~rtI~~~~~V~~ArV~l~~p~~  161 (563)
                      .+.+|++.+++.|+.|+.+|+|+.+. .||++||...+||.|+|++++++.|+++++|.++|..+++|..++||+++|++
T Consensus        91 ~~~~p~~~~~~~~~~~~~~g~p~~~~-~~~~~~~~~~g~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~  169 (611)
T TIGR00206        91 VILVPEDKVDELRLTLAAEGLPKTGS-VGFELFDQDKGFGLTDFEEDINLVRALEGELSRTIEALDPVKGAKVHLALPKD  169 (611)
T ss_pred             EEECCHHHHHHHHHHHHHHCCCCCCC-CCCHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCH
T ss_conf             34132666778888776522554444-54011024356632201345667777777888888751220002034423630


Q ss_pred             CCCCCC-CCCCCEEEEEECCCC--CCHHH--HHHHHHHHHHHHHCCCCCCEEEEECCCCEEEC-CCCC----CCCCHHHH
Q ss_conf             655555-558715999706877--89889--99999999865401883526998289835003-6765----33324799
Q gi|254780695|r  162 GSFRKI-GARPTASVMIRAINP--SVYKS--AEAIRHLVAAAVPNLDMGDVTVLDSTGKLLTA-NEME----RNILGKSL  231 (563)
Q Consensus       162 ~~f~~~-~~~~sASV~l~~~~~--l~~~q--v~~I~~lVa~sV~gL~~e~VtVvD~~G~~L~~-~~~~----~~~~~~~~  231 (563)
                      ++|... +.+++|+|++++.|+  +.+.+  +.|+.+|++.+||||.++||+++|+.|..+.. .+.+    ......++
T Consensus       170 ~~~~~~~~~~~~~~~~~~~~pg~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~  249 (611)
T TIGR00206       170 ALFVGEEQEPPSASVVLKLKPGSDLDPGQKKIEGLVHLVSAAVPGLPPDNVALVDENGTLLGEFSDLDGGDGKDLADKQL  249 (611)
T ss_pred             HHHHCCCCCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCHHCCCCCCCCCHHHHHHHHH
T ss_conf             22200000233220577415775211025788999999987622676454367506752000000100111134456666


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCE-EEEEEEEEEECCCEEEEEEEECCCCC-----------------CCCCEEEEEE
Q ss_conf             99999999999999988775408780-69998844322301678885147877-----------------6542157763
Q gi|254780695|r  232 SIVQAIQHEIEMNINKALAAFLGVDN-FRSAVVAELNMDTQQIREIVYDPDSK-----------------VERSIRLSKD  293 (563)
Q Consensus       232 ~~~~~~E~~~~~kI~~~L~~i~G~~~-v~v~V~~~ldfd~~~~~~e~y~p~~~-----------------~~~s~~~~~~  293 (563)
                      .++..+|..++.++..+|.+++|.++ +.+++++++||.+...+++.|+|.+.                 ..++.+..++
T Consensus       250 ~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~d~~~~~~~~~~~~p~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~  329 (611)
T TIGR00206       250 KYKSDVEGDLEGEIESLLSPILGGDNFVVARVNAELDFSKEETTEEEYEPNGLENQDPKASYNTRKVSDGVLRSAQLLEE  329 (611)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCCHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             66666777888889988776523673378875200012200000122034543344531000024555666665554323


Q ss_pred             ECCCCCCCC-CCCCCCCCCCCCCCC--CC-----CCCCCCC---------CCCCCCCEEEEECCCCEEEEEEECCCCCCC
Q ss_conf             025667777-777877777787666--66-----6777666---------655443103421056179999707851001
Q gi|254780695|r  294 AQRSETSQP-ESAVTVEQNMPHVSD--RK-----VPLPRSL---------ENTDKKEEQSNYEINTKSIATTHDNYKLER  356 (563)
Q Consensus       294 ~~~s~~~~~-~G~pG~~sN~p~~~~--~~-----~~~~~~~---------~~~~~~~~t~NYev~~t~~~~~~~~G~I~r  356 (563)
                      ...+.+..+ +|.||..+|.|...+  ..     ..+....         ......+++.||+++++..++...+|.+.+
T Consensus       330 ~~~g~g~~~~gg~pg~~~~~p~p~~~~~~~~~~~~~~~~~~~~~~~~~~gp~~~~~~~~~~~~~~~~~~~~~~~~g~~~~  409 (611)
T TIGR00206       330 EYEGDGYPPVGGPPGAGGNQPAPTPNPPVQGLKDNGGNKEPGKYEKNNSGPRSTQLNEKSNYEVGRTIREIKGSLGDLVD  409 (611)
T ss_pred             HHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHCCCCCCCHHHCCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             32156655467667655556677787655665433443331010003555310000110010001245665301233332


Q ss_pred             CEEEEECCCCCC-CCCCCC--CCCCCCCHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCCC--CCCCCCCCCCCCHHHH
Q ss_conf             025653054324-566655--55334698999999998643125661138768998503566--5434344456204589
Q gi|254780695|r  357 LSIAVVVNKGRL-TEVLGR--SADQGKIDSYLAEINKIVSAATGINSRRGDTITITSMDFLE--NQLFNSGTVQVSFMDI  431 (563)
Q Consensus       357 lSVAV~Vn~~~~-~~~~g~--~~~~~~~~eel~~I~~lV~~AiG~d~~RGD~VtV~~~~F~~--~~~~~~~~~~~~~~~~  431 (563)
                      +.+++++++... .-++|.  ..+.|+..+++.+++.+++.++||...|||.+++.+++|.+  +...........++..
T Consensus       410 ~~~~~~~~~~~~~~~~~g~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~gd~~~~~~~~~~~~~p~~~~~~~~~~~~~~~  489 (611)
T TIGR00206       410 LGWAVVVDGKGDFALPDGKNKLEYLPLSLEELKDIEDLLKEAVGYSPDRGDSLTVRNLSFNPLAPVINNETGGELPPFDG  489 (611)
T ss_pred             HHEEEEECCCCCCCCCCCCHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCEECCCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             00124551543302543200100011004567889999988751121245410001354211110010012221122223


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             99999999999999999999999999977875201122100011221233433321000001222100013343333444
Q gi|254780695|r  432 LSRHFATVINALVFLVGTLLVTFLGLHALRRLHNIDDAKKGEVGGKSILSPPPISSAVTTGLMPNDNIALDSSNQDIFSH  511 (563)
Q Consensus       432 ~~~~~~~~~~~~~~~l~~lll~~~vl~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~  511 (563)
                       ......+.....+..+.+++++++...+++..................      ..........+...++.........
T Consensus       490 -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~  562 (611)
T TIGR00206       490 -EKFLDSLTPASKWLLLLLLAFLLGGKLIRPLLERRLELVPELDKQADL------REEEEDEVEGELIKLPDLNKKVEDQ  562 (611)
T ss_pred             -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHCCCCCCCCHHHHHHHHHH
T ss_conf             -556666677889999999999998889999999999875677777888------7777653033113302466665444


Q ss_pred             C-CCCHHHCCCCCHHHHHHHHHHHHHHCH----HHHHHHHHHHHHHHH
Q ss_conf             4-431010021100689999999988699----989999999986378
Q gi|254780695|r  512 S-RNLQSRINSYVSKQSDLRLLHMIEINE----ERFAKILRKWARSEI  554 (563)
Q Consensus       512 ~-~~~~~~~~~~~~~~~~~~i~~lv~e~P----e~vA~vLR~WL~ee~  554 (563)
                      . .......+.........+++.+.+++|    +.++.++|.|+.++.
T Consensus       563 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~w~~~~~  610 (611)
T TIGR00206       563 GGLNEGLEEEEVRYEVSLEELRGLLKEKPDEIAEDFALLLRDWLLEDG  610 (611)
T ss_pred             HHHCCCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCC
T ss_conf             320033204678999999999875214615689999999999862048


No 7  
>pfam08345 YscJ_FliF_C Flagellar M-ring protein C-terminal. This domain is found in bacterial flagellar M-ring (FliF) proteins together with the YscJ/FliF domain (pfam01514).
Probab=100.00  E-value=7.7e-38  Score=270.77  Aligned_cols=162  Identities=30%  Similarity=0.440  Sum_probs=146.0

Q ss_pred             HHHHCCCCEEEEEEEEEEECCCEEEEEEEECCCCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             77540878069998844322301678885147877654215776302566777777787777778766666677766665
Q gi|254780695|r  249 LAAFLGVDNFRSAVVAELNMDTQQIREIVYDPDSKVERSIRLSKDAQRSETSQPESAVTVEQNMPHVSDRKVPLPRSLEN  328 (563)
Q Consensus       249 L~~i~G~~~v~v~V~~~ldfd~~~~~~e~y~p~~~~~~s~~~~~~~~~s~~~~~~G~pG~~sN~p~~~~~~~~~~~~~~~  328 (563)
                      |.|+||+||++|+|+++|||++.++++++|+|++++++|+++.++..++.. .++|+||+.+|+|+.++.. .++...+.
T Consensus         1 L~~i~G~gn~~v~V~~~ldf~~~e~t~e~ydP~~~~v~Se~~~~e~~~~~~-~~~G~pG~~sN~p~~~~~~-~~~~~~~~   78 (162)
T pfam08345         1 LEPVVGPGNVRVQVTADLDFDKVEQTEETYDPNGGVVRSEQTSEESSTGSG-AAGGVPGVLSNLPPAPATA-PGGNGSST   78 (162)
T ss_pred             CCCEECCCCEEEEEEEEEECCCEEEEEEEECCCCCEEEEEEEEEEECCCCC-CCCCCCCCCCCCCCCCCCC-CCCCCCCC
T ss_conf             974477996799999998526449999998999970400788876125777-8889987626779987767-77888865


Q ss_pred             CCCCCEEEEECCCCEEEEEEECCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCEEEE
Q ss_conf             54431034210561799997078510010256530543245666555533469899999999864312566113876899
Q gi|254780695|r  329 TDKKEEQSNYEINTKSIATTHDNYKLERLSIAVVVNKGRLTEVLGRSADQGKIDSYLAEINKIVSAATGINSRRGDTITI  408 (563)
Q Consensus       329 ~~~~~~t~NYev~~t~~~~~~~~G~I~rlSVAV~Vn~~~~~~~~g~~~~~~~~~eel~~I~~lV~~AiG~d~~RGD~VtV  408 (563)
                      |+++++++|||+||+++|++++||.|+||||||+||+.+.. ..+...+.|++++++++|++||++|+|||.+|||+|+|
T Consensus        79 ~~~~~~t~NYev~~~~~~~~~~~G~I~rlsvaV~vd~~~~~-~~~~~~~~~~s~ee~~~i~~lV~~AiG~d~~RGD~v~V  157 (162)
T pfam08345        79 SSRSEETRNYEVSRTVRHTVQAPGKIKRLSVAVVVDGVYVV-ADGKAAYVPRSPEELAQIEALVKSAVGFDAARGDSVTV  157 (162)
T ss_pred             CCCEEEEEECCCCCEEEEEECCCCEEEEEEEEEEECCCCCC-CCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCEEEE
T ss_conf             31101256312574899998189817778999998564236-77853346679999999999999960888778998999


Q ss_pred             EECCC
Q ss_conf             85035
Q gi|254780695|r  409 TSMDF  413 (563)
Q Consensus       409 ~~~~F  413 (563)
                      .++||
T Consensus       158 ~~~~F  162 (162)
T pfam08345       158 VSMPF  162 (162)
T ss_pred             EECCC
T ss_conf             94689


No 8  
>TIGR02544 III_secr_YscJ type III secretion apparatus lipoprotein, YscJ/HrcJ family; InterPro: IPR003282 Secretion of virulence factors in Gram-negative bacteria involves transportation of the protein across two membranes to reach the cell exterior. There have been four secretion systems described in animal enteropathogens such as Salmonella and Yersinia, with further sequence similarities in plant pathogens like Ralstonia and Erwinia.   The type III secretion system is of great interest as it is used to transport virulence factors from the pathogen directly into the host cell  and is only triggered when the bacterium comes into close contact with the host. The protein subunits of the system are very similar to those of bacterial flagellar biosynthesis . However, while the latter forms a ring structure to allow secretion of flagellin and is an integral part of the flagellum itself, type III subunits in the outer membrane translocate secreted proteins through a channel-like structure.    One of the outer membrane protein subunit families, termed "K" here for nomenclature purposes, aids in the structural assembly of the invasion complex . It is also described as a lipoprotein. Members of this family include the Salmonella PrgK and SsaJ genes, MxiJ from Shigella, YscJ from Yersinia, and from the plant enteropathogens NolT (Rhizobium) and HrcJ Erwinia). The flagellar M-ring protein FliF also shares a low level of similarity, presumably due to evolution of the type III secretion system from the flagellar biosynthetic pathway.; GO: 0009306 protein secretion.
Probab=99.97  E-value=4.4e-30  Score=219.18  Aligned_cols=179  Identities=27%  Similarity=0.357  Sum_probs=162.5

Q ss_pred             HHHHHHHHHHCCCCCE-EECCCCCHHHHHHHHHHHHHCCCCEEE------C--CCC--CEEEECHHHHHHHHHHHHHCCC
Q ss_conf             9999999984699824-503899989999999999977992999------1--899--7799518999999999997699
Q gi|254780695|r   34 MLFMAARFFVNSPHYD-NLYVKLEVSDVNRISVALSEANIDFRI------S--DNG--SSISVPSSMVGKARIHLAAQGL  102 (563)
Q Consensus        34 ~~~~~~~~~~~~p~y~-~L~~~l~~~d~~~i~~~L~~~gI~y~~------~--~~g--~~I~Vp~~~~~~~r~~La~~gl  102 (563)
                      ++++.+.++++..+.. .||+||+..||++|.+.|..+||.-+-      .  .+|  -+|.|++.|+.+|--.|...||
T Consensus         5 ~~~~~l~llL~GC~~~~~Ly~gL~e~eANe~lA~L~~~gI~A~K~~~~~~~~~k~Gv~~~~~Ve~~~~~~A~~lL~~~GL   84 (203)
T TIGR02544         5 LLLLLLLLLLTGCKVDLELYSGLSEREANEMLALLMRHGIDAEKVQAVSEKSGKGGVLYTISVEESDFARAVELLRQNGL   84 (203)
T ss_pred             HHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHHCCCCEEECHHHEECCCCCEEEEEEECCHHHHHHHHHHHHHCCC
T ss_conf             89999999971787405650478987899999999966983453122100378852588986187899999999986388


Q ss_pred             CCCCCCCHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEECCCC-CCCCCCCCCCEEEEEECCC
Q ss_conf             887766325653058884259999999999999999999996057631489999833666-5555555871599970687
Q gi|254780695|r  103 PSSSSNSGYELFDKVNSFGLTSFMQEITRVRALEGEIARTIQSISGIVAARVHIVMPDMG-SFRKIGARPTASVMIRAIN  181 (563)
Q Consensus       103 p~~~~~~g~el~d~~~~~g~T~~~~~~~~~ralegeL~rtI~~~~~V~~ArV~l~~p~~~-~f~~~~~~~sASV~l~~~~  181 (563)
                      |...+..--++|-+ ++|-+|-.+|++||..|+|.+|++||+.||||-+||||+++|++. ...+..+|+||||+|+..+
T Consensus        85 P~~~~~~~~~~Fp~-~gLvsSP~eEraR~~ya~eQ~Le~tLs~IdGV~~ArVhVvlP~~d~~~~~~~~P~sAsVfikY~~  163 (203)
T TIGR02544        85 PRQSFVNLGELFPK-DGLVSSPTEERARLLYAIEQELEQTLSQIDGVISARVHVVLPENDNENGRPKKPSSASVFIKYRP  163 (203)
T ss_pred             CCCCCCCHHHHCCC-CCEECCHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEECCCCCCCCCCCCCCEEEEEEEECC
T ss_conf             89532368875135-77034869999999999999999986017926866799972167887788988543889998668


Q ss_pred             CCCH-H-HHHHHHHHHHHHHHCCCCCCEEEEECC
Q ss_conf             7898-8-999999999865401883526998289
Q gi|254780695|r  182 PSVY-K-SAEAIRHLVAAAVPNLDMGDVTVLDST  213 (563)
Q Consensus       182 ~l~~-~-qv~~I~~lVa~sV~gL~~e~VtVvD~~  213 (563)
                      +.+. . .+--|+.||++|||||+-|||+|+=+-
T Consensus       164 ~~~~~~h~~~~IK~Lv~~Si~gL~Yd~vSVvl~p  197 (203)
T TIGR02544       164 GLNLDAHLIPKIKRLVANSIPGLAYDNVSVVLVP  197 (203)
T ss_pred             CCCCCCCCCCHHHHHHHHHCCCCCCCCEEEEEEC
T ss_conf             9782003365268999860378871656899860


No 9  
>COG4669 EscJ Type III secretory pathway, lipoprotein EscJ [Intracellular trafficking and secretion]
Probab=99.95  E-value=1.2e-26  Score=196.43  Aligned_cols=177  Identities=23%  Similarity=0.309  Sum_probs=156.4

Q ss_pred             HHHHHHHCCCCCEEECCCCCHHHHHHHHHHHHHCCCCEEE--CCCCC-EEEECHHHHHHHHHHHHHCCCCCCCCCCHHHH
Q ss_conf             9999984699824503899989999999999977992999--18997-79951899999999999769988776632565
Q gi|254780695|r   37 MAARFFVNSPHYDNLYVKLEVSDVNRISVALSEANIDFRI--SDNGS-SISVPSSMVGKARIHLAAQGLPSSSSNSGYEL  113 (563)
Q Consensus        37 ~~~~~~~~~p~y~~L~~~l~~~d~~~i~~~L~~~gI~y~~--~~~g~-~I~Vp~~~~~~~r~~La~~glp~~~~~~g~el  113 (563)
                      +.+.++.+..+ +-||++|+..||++|.+.|..+||..+-  +.+|+ +|+|++.|..+|--.|-.+|||......--++
T Consensus        11 l~l~l~L~gCk-~~Ly~gL~e~eANemlAlL~~~gI~A~K~~~~~g~~~l~Ve~~~fa~Av~iL~~~GlPr~~f~~l~d~   89 (246)
T COG4669          11 LLLILLLTGCK-VDLYTGLSEKEANEMLALLMSHGINAEKKADKDGGTSLLVEESDFAEAVEILNQNGLPRKKFTTLGDI   89 (246)
T ss_pred             HHHHHHHHCCH-HHHHCCCCHHHHHHHHHHHHHCCCCCEEECCCCCCEEEEECHHHHHHHHHHHHHCCCCCCCCCCHHHH
T ss_conf             99999983356-98870798767889999999859760110467785589976899999999998669998777749985


Q ss_pred             HCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCCEEEEEECCCCCCHH-HHHHHH
Q ss_conf             3058884259999999999999999999996057631489999833666555555587159997068778988-999999
Q gi|254780695|r  114 FDKVNSFGLTSFMQEITRVRALEGEIARTIQSISGIVAARVHIVMPDMGSFRKIGARPTASVMIRAINPSVYK-SAEAIR  192 (563)
Q Consensus       114 ~d~~~~~g~T~~~~~~~~~ralegeL~rtI~~~~~V~~ArV~l~~p~~~~f~~~~~~~sASV~l~~~~~l~~~-qv~~I~  192 (563)
                      |-+ +++-+|..+|++||..|++.+|++||+.||||-+||||+++|+++.--++..|.||||+++..++-..+ .+..|+
T Consensus        90 Fp~-dgLVsSP~eEkaR~~~~~eQ~le~tLs~mDGVi~ArV~I~lp~~~~~g~~~~P~saSVfIky~~~~nl~~~v~~IK  168 (246)
T COG4669          90 FPK-DGLVSSPTEEKARLNYAKEQQLEQTLSKMDGVISARVHISLPEDDDEGKNALPSSASVFIKYSPDVNLSIYVSQIK  168 (246)
T ss_pred             CCC-CCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEECCCCCCCCCCCCCCEEEEEEEECCCCCHHHHHHHHH
T ss_conf             876-5665782899999999999999999975676588889997577786678888740689999568898167689999


Q ss_pred             HHHHHHHHCCCCCCEEEEECCCC
Q ss_conf             99986540188352699828983
Q gi|254780695|r  193 HLVAAAVPNLDMGDVTVLDSTGK  215 (563)
Q Consensus       193 ~lVa~sV~gL~~e~VtVvD~~G~  215 (563)
                      +||++|||||.+|||+|+=+.+.
T Consensus       169 ~LV~nSv~gL~YenISVVl~~~~  191 (246)
T COG4669         169 RLVANSVPGLQYENISVVLVPAS  191 (246)
T ss_pred             HHHHHCCCCCCHHCEEEEEEECC
T ss_conf             99981567776000699982044


No 10 
>PRK05934 type III secretion system protein; Validated
Probab=98.46  E-value=5.4e-07  Score=65.62  Aligned_cols=97  Identities=15%  Similarity=0.271  Sum_probs=79.8

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCCEEEEEECCC--CCCHHHHHHHHHHH
Q ss_conf             8842599999999999999999999960576314899998336665555555871599970687--78988999999999
Q gi|254780695|r  118 NSFGLTSFMQEITRVRALEGEIARTIQSISGIVAARVHIVMPDMGSFRKIGARPTASVMIRAIN--PSVYKSAEAIRHLV  195 (563)
Q Consensus       118 ~~~g~T~~~~~~~~~ralegeL~rtI~~~~~V~~ArV~l~~p~~~~f~~~~~~~sASV~l~~~~--~l~~~qv~~I~~lV  195 (563)
                      +.+|--...+    -.|+...|+|.+..+..|-+|.|-|.+|...   +...++-.||+|.+..  .+++.-+.+|....
T Consensus        59 sq~gnpkl~E----slaKKEQlE~DLTmF~pva~AtVAlslpted---d~~~~~~iSVILs~~k~etls~sLl~SItDYL  131 (341)
T PRK05934         59 SQLGNPKLIE----SLAKKEQLEKDLTMFHPVASATVALSLPTED---DEDSPAEISVILSLRKAETLSPSLLHSITDYL  131 (341)
T ss_pred             HHCCCHHHHH----HHHHHHHHHHHHHHHHHHHHHEEEECCCCCC---CCCCCCEEEEEEECCCCCCCCHHHHHHHHHHH
T ss_conf             2127868899----8878998865444320553420333067656---78876226888862500123788999999998


Q ss_pred             HHHHHCCCCCCEEEEECCCCEEECCC
Q ss_conf             86540188352699828983500367
Q gi|254780695|r  196 AAAVPNLDMGDVTVLDSTGKLLTANE  221 (563)
Q Consensus       196 a~sV~gL~~e~VtVvD~~G~~L~~~~  221 (563)
                      ++|||||+.|.+|.-|+.||+.+-..
T Consensus       132 ~sSvPGLtkEhItLSDnlGNlYsP~~  157 (341)
T PRK05934        132 SSSVPGLTKEHITLSDNLGNLYSPLS  157 (341)
T ss_pred             HHCCCCCCHHHEECCCCCCCCCCCCH
T ss_conf             62188743321522015677248403


No 11 
>TIGR02830 spore_III_AG stage III sporulation protein AG; InterPro: IPR014195    This entry represents the stage III sporulation protein AG, which is encoded in a spore formation operon: spoIIIAABCDEFGH under the control of sigma G . A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species..
Probab=96.12  E-value=0.023  Score=34.80  Aligned_cols=100  Identities=12%  Similarity=0.113  Sum_probs=53.1

Q ss_pred             HHHHHHHHHHHHCCCCCCE--EEEEC-CCCEEECCC-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEE
Q ss_conf             9999999865401883526--99828-983500367-6533324799999999999999999887754087806999884
Q gi|254780695|r  189 EAIRHLVAAAVPNLDMGDV--TVLDS-TGKLLTANE-MERNILGKSLSIVQAIQHEIEMNINKALAAFLGVDNFRSAVVA  264 (563)
Q Consensus       189 ~~I~~lVa~sV~gL~~e~V--tVvD~-~G~~L~~~~-~~~~~~~~~~~~~~~~E~~~~~kI~~~L~~i~G~~~v~v~V~~  264 (563)
                      -||.-|+.++.=.-..+..  .++.+ ...-.-... .........-+.-.+||++|+++++.+|+.|-|.|+|.|-|++
T Consensus        12 iG~~ll~~s~~F~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~yE~~~e~~Lk~~Le~I~GVg~V~V~vnL   91 (193)
T TIGR02830        12 IGLLLLLVSSFFSSSEDIEITAVVKESDTPNNEKTEPEFVQGEKQKEDEISDYEKEYENELKEILEKIEGVGDVTVMVNL   91 (193)
T ss_pred             HHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEE
T ss_conf             99999999876178566332542223335654455532256655444237999999999999986420375614899996


Q ss_pred             EEECCCEEEEEEEECCCCCCCCCEEEEEEECC
Q ss_conf             43223016788851478776542157763025
Q gi|254780695|r  265 ELNMDTQQIREIVYDPDSKVERSIRLSKDAQR  296 (563)
Q Consensus       265 ~ldfd~~~~~~e~y~p~~~~~~s~~~~~~~~~  296 (563)
                      +      .+....|.-|.  ...++++.++.+
T Consensus        92 ~------~~e~~v~ekN~--~~~~~tT~EtD~  115 (193)
T TIGR02830        92 D------SSEEKVYEKNT--SKGQQTTEETDK  115 (193)
T ss_pred             C------CCCEEEEEECC--CCCCEEEEEEEC
T ss_conf             5------99616667815--567536544744


No 12 
>PRK06007 fliF flagellar MS-ring protein; Reviewed
Probab=94.14  E-value=0.45  Score=26.23  Aligned_cols=73  Identities=14%  Similarity=0.260  Sum_probs=49.4

Q ss_pred             CHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHH-------HH----------------CCCCCEEECCC----
Q ss_conf             6789999999986406987889999999999999999999-------84----------------69982450389----
Q gi|254780695|r    2 AILDQLLQFFKSGTSLGRTRILILASVILVPIMLFMAARF-------FV----------------NSPHYDNLYVK----   54 (563)
Q Consensus         2 ~~~~~l~~~~~~~~~l~~~~ki~~~~~~~~~i~~~~~~~~-------~~----------------~~p~y~~L~~~----   54 (563)
                      ++++++++||++|....+.-.++++++++++++++++..-       |.                ..=.|++==.|    
T Consensus         7 ~~~~~~~~~~~~l~~~qki~l~~~~~~~i~~~~~l~~~~~~p~y~~L~~~l~~~da~~I~~~L~~~gI~Y~l~~~G~~I~   86 (540)
T PRK06007          7 ELMEKLLEFLKKLSKLRKIALIGAAAAVIAAIVALVLWASRPDYRVLYSNLSDQDAGQIVAALDQAGIPYKVSSDGGTIL   86 (540)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEECCCCCHHHHHHHHHHHHHCCCCEEECCCCCEEE
T ss_conf             99999999997069888999999999999999999984169972770289998999999999998799759769997799


Q ss_pred             CCHHHHHHHHHHHHHCCCCE
Q ss_conf             99899999999999779929
Q gi|254780695|r   55 LEVSDVNRISVALSEANIDF   74 (563)
Q Consensus        55 l~~~d~~~i~~~L~~~gI~y   74 (563)
                      .+..+...+--.|-..|+|-
T Consensus        87 Vp~~~v~~~Rl~LA~~Glp~  106 (540)
T PRK06007         87 VPEDKVDELRLKLASEGLPK  106 (540)
T ss_pred             ECHHHHHHHHHHHHHCCCCC
T ss_conf             76778999999999769999


No 13 
>pfam09413 DUF2007 Protein of unknown function (DUF2007). This is a family of proteins with unknown function.
Probab=92.52  E-value=0.65  Score=25.19  Aligned_cols=53  Identities=23%  Similarity=0.216  Sum_probs=42.4

Q ss_pred             ECCCCCHHHHHHHHHHHHHCCCCEEECCCCC------------EEEECHHHHHHHHHHHHHCCCC
Q ss_conf             0389998999999999997799299918997------------7995189999999999976998
Q gi|254780695|r   51 LYVKLEVSDVNRISVALSEANIDFRISDNGS------------SISVPSSMVGKARIHLAAQGLP  103 (563)
Q Consensus        51 L~~~l~~~d~~~i~~~L~~~gI~y~~~~~g~------------~I~Vp~~~~~~~r~~La~~glp  103 (563)
                      |+.--++--.+.+.+.|+.+||+|-+-+...            +|+|+++++.+||-.|+.+|++
T Consensus         3 LlrTnD~v~is~~~aLL~~agI~~~v~D~~mS~lEGsig~~PRRlmV~~~d~~~Ar~iL~dag~~   67 (68)
T pfam09413         3 LLRTNDPVLISFAQALLKGAGIEAFVADQNMSILEGSIGILPRRLMVRDDDLDRARRLLADAGLG   67 (68)
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCEEEECCCCHHCCCCCCCEEEEEEECHHHHHHHHHHHHHCCCC
T ss_conf             43127762999999997127997799447522204654535679986576899999999975878


No 14 
>PRK10629 hypothetical protein; Provisional
Probab=89.24  E-value=1.6  Score=22.55  Aligned_cols=55  Identities=16%  Similarity=0.199  Sum_probs=38.4

Q ss_pred             CEEECCCCCHHHHHHHHHHHHHCCCCEEE-CCCCCEEEE--C-HHHHHHHHHHHHHCCCC
Q ss_conf             24503899989999999999977992999-189977995--1-89999999999976998
Q gi|254780695|r   48 YDNLYVKLEVSDVNRISVALSEANIDFRI-SDNGSSISV--P-SSMVGKARIHLAAQGLP  103 (563)
Q Consensus        48 y~~L~~~l~~~d~~~i~~~L~~~gI~y~~-~~~g~~I~V--p-~~~~~~~r~~La~~glp  103 (563)
                      -++...|++--|---|...|+++||.||- ..++.+++|  + .++--.||-.|... ||
T Consensus        40 ir~~~qg~~~pdgf~~~q~Lda~GI~~KSIt~en~~lLIRf~s~eqQl~AreVL~~~-Lg   98 (127)
T PRK10629         40 IRAVQQGASLPDGFSVYHHLDANGIHFKSITPENDSLLITFDSPEQSAAAKEVLDRT-LP   98 (127)
T ss_pred             EEECCCCCCCCCCCHHHHHHHHCCCCEEEECCCCCEEEEEECCHHHHHHHHHHHHHH-CC
T ss_conf             755468987998234899887669732565215980899979989999999999986-68


No 15 
>PRK11114 cellulose synthase regulator protein; Provisional
Probab=85.43  E-value=2.6  Score=21.12  Aligned_cols=88  Identities=14%  Similarity=0.052  Sum_probs=47.3

Q ss_pred             CHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCCCCC-CCCCCCCCCCHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHH
Q ss_conf             9899999999864312566113876899850356654-343444562045899999999--9999999999999999999
Q gi|254780695|r  381 IDSYLAEINKIVSAATGINSRRGDTITITSMDFLENQ-LFNSGTVQVSFMDILSRHFAT--VINALVFLVGTLLVTFLGL  457 (563)
Q Consensus       381 ~~eel~~I~~lV~~AiG~d~~RGD~VtV~~~~F~~~~-~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~l~~lll~~~vl  457 (563)
                      +++.+..+.+...+.--...-+||.+.+..-.+...- .+.-.....+||...++++..  ++..++.+++++++.+.++
T Consensus       665 ~~~~l~~l~~aL~~~~~~a~i~Gdlali~~~~v~S~rvg~~Y~vG~LPw~~~v~~~~s~hP~lLa~~~~l~~ll~a~~~~  744 (759)
T PRK11114        665 SPRGLALLNDALNDSGKRAQIFGSVAVIRESGVESLRVGDVYYVGHLPWYERVWYALSNHPVLLAVLAALSVLLLALVLW  744 (759)
T ss_pred             CHHHHHHHHHHHHCCCHHHHCCCCEEEEECCCEEEEECCCEEEECCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             86779999998738130523323689994891699974886563247799999999817869999999999999999999


Q ss_pred             HHHHHHHHCCC
Q ss_conf             97787520112
Q gi|254780695|r  458 HALRRLHNIDD  468 (563)
Q Consensus       458 ~~l~~~~~~~~  468 (563)
                      +.+|++..+..
T Consensus       745 ~~Lr~~a~rRL  755 (759)
T PRK11114        745 RLLRRIARRRL  755 (759)
T ss_pred             HHHHHHHHHHC
T ss_conf             99999998635


No 16 
>pfam04612 GspM General secretion pathway, M protein. This is a family of membrane proteins involved in the secretion of a number of molecules in Gram-negative bacteria. The precise function of these proteins is unknown, though in Vibrio cholerae, the EpsM protein interacts with the EpsL protein, and also forms homodimers.
Probab=84.57  E-value=2.4  Score=21.37  Aligned_cols=37  Identities=16%  Similarity=0.309  Sum_probs=26.5

Q ss_pred             HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             8999999998640698788999999999999999999984
Q gi|254780695|r    4 LDQLLQFFKSGTSLGRTRILILASVILVPIMLFMAARFFV   43 (563)
Q Consensus         4 ~~~l~~~~~~~~~l~~~~ki~~~~~~~~~i~~~~~~~~~~   43 (563)
                      |+++++||   .+++++=+.++++.++++++++++..+|.
T Consensus         1 ~~~l~~ww---~~ls~REq~ll~~~~~~l~~~l~y~~lw~   37 (159)
T pfam04612         1 MEQLRAWW---QQLSPREQRLLAVLGAVLLLVLLYLGLWQ   37 (159)
T ss_pred             CHHHHHHH---HHCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             92789998---71699899999999999999999999998


No 17 
>COG3944 Capsular polysaccharide biosynthesis protein [Cell envelope biogenesis, outer membrane]
Probab=84.06  E-value=2  Score=21.90  Aligned_cols=35  Identities=14%  Similarity=0.274  Sum_probs=25.7

Q ss_pred             CCCCHHHHHHHHHHHHHHHH-----CCCCCCEEEEECCCC
Q ss_conf             77898899999999986540-----188352699828983
Q gi|254780695|r  181 NPSVYKSAEAIRHLVAAAVP-----NLDMGDVTVLDSTGK  215 (563)
Q Consensus       181 ~~l~~~qv~~I~~lVa~sV~-----gL~~e~VtVvD~~G~  215 (563)
                      ..-+|++..-|+|-++.+..     =|+++||++++..--
T Consensus       123 ~~~~p~~Aa~IAN~~~~vf~~~i~~im~vd~v~Ils~A~~  162 (226)
T COG3944         123 NDGSPEEAAEIANSISEVFAKVIPEIMNVDNVSILSEAEA  162 (226)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCC
T ss_conf             7998679999999999999985176237676156111456


No 18 
>pfam11294 DUF3095 Protein of unknown function (DUF3095). Some members in this bacterial family of proteins are annotated as adenylyl cyclase however this cannot be confirmed. Currently no function is known.
Probab=82.88  E-value=2.5  Score=21.23  Aligned_cols=48  Identities=27%  Similarity=0.499  Sum_probs=33.8

Q ss_pred             CCCCCHHHHHHHH---HHHHHCCCCEEECCCCCEEEECHHHHHHHHHHHHH
Q ss_conf             3899989999999---99997799299918997799518999999999997
Q gi|254780695|r   52 YVKLEVSDVNRIS---VALSEANIDFRISDNGSSISVPSSMVGKARIHLAA   99 (563)
Q Consensus        52 ~~~l~~~d~~~i~---~~L~~~gI~y~~~~~g~~I~Vp~~~~~~~r~~La~   99 (563)
                      |+..+..-++.|.   +.|....+||-+..||.++.||.+.+..+|-.|+.
T Consensus        46 YK~VN~~Ga~~IaAv~Na~~~~~~PFvFGGDGA~favPp~~~~~ar~ALa~   96 (373)
T pfam11294        46 YKDVNMAGASVIAAVLNALGGRDFPFVFGGDGATFAVPPDLAERARQALAA   96 (373)
T ss_pred             CCCCHHHHHHHHHHHHHHCCCCCCCEEECCCCEEEECCHHHHHHHHHHHHH
T ss_conf             431408889999999971069987858468985786488889999999999


No 19 
>pfam02706 Wzz Chain length determinant protein. This family includes proteins involved in lipopolysaccharide (lps) biosynthesis. This family comprises the whole length of chain length determinant protein (or wzz protein) that confers a modal distribution of chain length on the O-antigen component of lps. This region is also found as part of bacterial tyrosine kinases.
Probab=82.32  E-value=3.5  Score=20.27  Aligned_cols=15  Identities=20%  Similarity=0.087  Sum_probs=11.6

Q ss_pred             CCCHHHHHHHHHHHH
Q ss_conf             789889999999998
Q gi|254780695|r  182 PSVYKSAEAIRHLVA  196 (563)
Q Consensus       182 ~l~~~qv~~I~~lVa  196 (563)
                      +-+|+....|+|-+|
T Consensus       123 ~~dP~~Aa~iaN~~a  137 (139)
T pfam02706       123 GEDPEEAARIANSIA  137 (139)
T ss_pred             CCCHHHHHHHHHHHH
T ss_conf             699999999988773


No 20 
>PRK03427 cell division protein ZipA; Provisional
Probab=77.17  E-value=2.6  Score=21.13  Aligned_cols=33  Identities=18%  Similarity=0.341  Sum_probs=26.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCEEECCC
Q ss_conf             899999999999999999998469982450389
Q gi|254780695|r   22 ILILASVILVPIMLFMAARFFVNSPHYDNLYVK   54 (563)
Q Consensus        22 ki~~~~~~~~~i~~~~~~~~~~~~p~y~~L~~~   54 (563)
                      |++|+++++++|+++++-.+|.+|..-.-+|.+
T Consensus         6 RliLIIvGaIAIiALL~HGlWtsRKErs~~f~d   38 (331)
T PRK03427          6 RLILIIVGAIAIIALLVHGFWTSRKERSSMFRD   38 (331)
T ss_pred             HHHHHHHHHHHHHHHHHHHCEECCCCCCCCCCC
T ss_conf             999999999999999985202234554410024


No 21 
>PRK04335 cell division protein ZipA; Provisional
Probab=77.04  E-value=2.4  Score=21.35  Aligned_cols=33  Identities=9%  Similarity=0.118  Sum_probs=26.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCEEECCC
Q ss_conf             899999999999999999998469982450389
Q gi|254780695|r   22 ILILASVILVPIMLFMAARFFVNSPHYDNLYVK   54 (563)
Q Consensus        22 ki~~~~~~~~~i~~~~~~~~~~~~p~y~~L~~~   54 (563)
                      +++++++++++|+++++-.+|.+|-.-.-+|.+
T Consensus         5 rlILIIvGaIAIiALL~HGlWtsRKErs~~f~d   37 (319)
T PRK04335          5 RFVLIVVGALAIAALLFHGLWTSKKEGKSKFGD   37 (319)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
T ss_conf             029999999999999984011004455543466


No 22 
>PRK01741 cell division protein ZipA; Provisional
Probab=74.11  E-value=2.2  Score=21.69  Aligned_cols=33  Identities=12%  Similarity=0.211  Sum_probs=25.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCEEECCC
Q ss_conf             899999999999999999998469982450389
Q gi|254780695|r   22 ILILASVILVPIMLFMAARFFVNSPHYDNLYVK   54 (563)
Q Consensus        22 ki~~~~~~~~~i~~~~~~~~~~~~p~y~~L~~~   54 (563)
                      +++|+++++++|+++++-.+|.+|-.---+|.+
T Consensus         4 rlILIIvGaIAI~ALL~HGLWTsRKErs~~F~~   36 (342)
T PRK01741          4 NTILIILGILALVALVAHGLWSNRREKSQYFDN   36 (342)
T ss_pred             EEHHHHHHHHHHHHHHHHCCCCCCCCCCHHCCC
T ss_conf             254999999999999985121134445311047


No 23 
>PRK10949 protease 4; Provisional
Probab=71.37  E-value=7.1  Score=18.27  Aligned_cols=39  Identities=18%  Similarity=0.217  Sum_probs=26.7

Q ss_pred             HHHHHHHHHHH-HHHCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             78999999998-6406987889999999999999999999
Q gi|254780695|r    3 ILDQLLQFFKS-GTSLGRTRILILASVILVPIMLFMAARF   41 (563)
Q Consensus         3 ~~~~l~~~~~~-~~~l~~~~ki~~~~~~~~~i~~~~~~~~   41 (563)
                      |+..+..||+. |+.|...|++++.++++++++++++++.
T Consensus         4 ~~~~i~~~f~~~w~~l~~~R~~i~nl~f~~~i~~~v~~~~   43 (618)
T PRK10949          4 LWRIIAGFFKWTWRLLNFVREMVLNLFFIFLILVGVGIWM   43 (618)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999999999999999999999999987


No 24 
>COG4535 CorC Putative Mg2+ and Co2+ transporter CorC [Inorganic ion transport and metabolism]
Probab=69.15  E-value=4.2  Score=19.78  Aligned_cols=38  Identities=26%  Similarity=0.275  Sum_probs=34.7

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCCCC
Q ss_conf             46989999999986431256611387689985035665
Q gi|254780695|r  379 GKIDSYLAEINKIVSAATGINSRRGDTITITSMDFLEN  416 (563)
Q Consensus       379 ~~~~eel~~I~~lV~~AiG~d~~RGD~VtV~~~~F~~~  416 (563)
                      .++++|.+-|--||.+|.|.-+.||+.|.+-.++|.-.
T Consensus       230 ~FsDeevDTIGGLVm~afGhLP~RGE~i~i~~~~FkV~  267 (293)
T COG4535         230 HFSDEEVDTIGGLVMQAFGHLPARGEKIDIGGYQFKVA  267 (293)
T ss_pred             CCCHHHHHHHHHHHHHHHCCCCCCCCEEEECCEEEEEE
T ss_conf             88722212166799998366877787788746378986


No 25 
>PRK13254 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=69.05  E-value=7.9  Score=17.94  Aligned_cols=40  Identities=20%  Similarity=0.228  Sum_probs=29.7

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEECCCCCHHHH
Q ss_conf             9878899999999999999999998469982450389998999
Q gi|254780695|r   18 GRTRILILASVILVPIMLFMAARFFVNSPHYDNLYVKLEVSDV   60 (563)
Q Consensus        18 ~~~~ki~~~~~~~~~i~~~~~~~~~~~~p~y~~L~~~l~~~d~   60 (563)
                      .++||+++++++++++++++++++++-+..-...|   +|+|.
T Consensus         4 ~rkkRl~~v~~~~~~l~~a~~Lil~al~~ni~yFy---TPsEi   43 (149)
T PRK13254          4 RKRRRLLIILGALAALGLAVALVLYALRQNIVFFY---TPSEV   43 (149)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHCEEEEE---CHHHH
T ss_conf             11224789999999999999999999862806997---88999


No 26 
>KOG1176 consensus
Probab=68.54  E-value=8.1  Score=17.88  Aligned_cols=16  Identities=6%  Similarity=-0.008  Sum_probs=8.1

Q ss_pred             HHHHHHHHHHHHHHCC
Q ss_conf             9999999998654018
Q gi|254780695|r  187 SAEAIRHLVAAAVPNL  202 (563)
Q Consensus       187 qv~~I~~lVa~sV~gL  202 (563)
                      -+.|+-.++.+++.+.
T Consensus       236 H~~Gl~~~~~~~~~~~  251 (537)
T KOG1176         236 HIYGLITLLLSLLAGG  251 (537)
T ss_pred             HHHHHHHHHHHHHHCC
T ss_conf             9968999999998468


No 27 
>TIGR01074 rep ATP-dependent DNA helicase Rep; InterPro: IPR005752    RepA hexameric DNA helicase contain ATP-binding domains similar to those seen in monomeric helicases but which are arranged in a ring. There is compelling evidence to suggest that a single ssDNA molecule passes through the centre of the hexameric ring. Activity of the enzyme is based upon two separate but coupled activities, ssDNA translocation and duplex destabilisation, and is driven by energy derived from the continuous ATP-binding and hydrolysis events that take place in the active-site cleft. The resulting conformational changes that accompany these events underpin the coupling process and allow the helicase to translocate along the DNA, destabilizing the duplex and separating the two strands in an active process  ; GO: 0004003 ATP-dependent DNA helicase activity, 0006268 DNA unwinding during replication, 0005737 cytoplasm.
Probab=68.34  E-value=5  Score=19.31  Aligned_cols=15  Identities=27%  Similarity=0.572  Sum_probs=6.4

Q ss_pred             HHHHHHHCCCCEEEC
Q ss_conf             999999779929991
Q gi|254780695|r   63 ISVALSEANIDFRIS   77 (563)
Q Consensus        63 i~~~L~~~gI~y~~~   77 (563)
                      +...|....|||+|+
T Consensus       361 lEk~L~~~rIPY~lS  375 (677)
T TIGR01074       361 LEKALQQNRIPYKLS  375 (677)
T ss_pred             HHHHHHHCCCCCEEC
T ss_conf             999986268982535


No 28 
>pfam01910 DUF77 Domain of unknown function DUF77. Domain of unknown function. The crystal structure of two of these members shows that this domain has a ferredoxin like fold and is likely to exists as at least homodimers. Sulphate ions are are located at the dimer interfaces, which are thought to confer additional stability. Although the function of this domain remains to be identified, its structure suggests a role in protein-protein interactions possibly regulated by the binding of small-molecule ligands.
Probab=66.23  E-value=9  Score=17.58  Aligned_cols=48  Identities=21%  Similarity=0.257  Sum_probs=36.9

Q ss_pred             HHHHHHHHHHHHCCCCEEECCCCCEEEECHHHHHH----HHHHHHHCCCCCC
Q ss_conf             99999999999779929991899779951899999----9999997699887
Q gi|254780695|r   58 SDVNRISVALSEANIDFRISDNGSSISVPSSMVGK----ARIHLAAQGLPSS  105 (563)
Q Consensus        58 ~d~~~i~~~L~~~gI~y~~~~~g~~I~Vp~~~~~~----~r~~La~~glp~~  105 (563)
                      .-.++++..|++.|++|++.+-|++|--+-+++-+    +.-.+...|.|.-
T Consensus        17 ~yVa~~i~vi~~sgl~y~l~pmgT~iEge~dev~~~v~~~~e~~~~~G~~RV   68 (92)
T pfam01910        17 KYVAAVIEVLKESGLKYELGPMGTTIEGEWDEVMEVVKKAHEALFEAGAPRV   68 (92)
T ss_pred             HHHHHHHHHHHHCCCCEEECCCEEEEECCHHHHHHHHHHHHHHHHHCCCCEE
T ss_conf             9999999999974997584487008877899999999999999997699879


No 29 
>PRK13165 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=65.55  E-value=9.3  Score=17.49  Aligned_cols=39  Identities=21%  Similarity=0.376  Sum_probs=27.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEECCCCCHHHH
Q ss_conf             878899999999999999999998469982450389998999
Q gi|254780695|r   19 RTRILILASVILVPIMLFMAARFFVNSPHYDNLYVKLEVSDV   60 (563)
Q Consensus        19 ~~~ki~~~~~~~~~i~~~~~~~~~~~~p~y~~L~~~l~~~d~   60 (563)
                      ++||+++++++++++++.+++++++-+..-...|   +|+|.
T Consensus         5 rkkRl~~i~~~~~~l~~a~~Lil~al~~ni~yF~---TPsEv   43 (161)
T PRK13165          5 RKKRLWLACAVLAGLALTIGLVLYALRSNIDLFY---TPGEI   43 (161)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEE---CHHHH
T ss_conf             8767999999999999999999999871731886---78998


No 30 
>PRK03598 hypothetical protein; Provisional
Probab=65.34  E-value=6.7  Score=18.45  Aligned_cols=30  Identities=3%  Similarity=0.174  Sum_probs=15.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCE
Q ss_conf             788999999999999999999984699824
Q gi|254780695|r   20 TRILILASVILVPIMLFMAARFFVNSPHYD   49 (563)
Q Consensus        20 ~~ki~~~~~~~~~i~~~~~~~~~~~~p~y~   49 (563)
                      ++++++++++++++++.++.+||.......
T Consensus         2 kk~~~~~~~~~~~~~~~~~~~~~~~~~~~~   31 (331)
T PRK03598          2 KKPVVIGLAVVALVAVGAGGWWWYQSRQDN   31 (331)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHEEECCCC
T ss_conf             833899999999999999976521405788


No 31 
>PRK13390 acyl-CoA synthetase; Provisional
Probab=63.99  E-value=9.9  Score=17.30  Aligned_cols=23  Identities=9%  Similarity=0.018  Sum_probs=16.0

Q ss_pred             HCCCCCEEECCCCCHHHHHHHHH
Q ss_conf             46998245038999899999999
Q gi|254780695|r   43 VNSPHYDNLYVKLEVSDVNRISV   65 (563)
Q Consensus        43 ~~~p~y~~L~~~l~~~d~~~i~~   65 (563)
                      ...-.+++|...+.+.+...++.
T Consensus        71 ~~Gav~vpl~~~~~~~~~~~il~   93 (501)
T PRK13390         71 RSGLYITAINHHLTAPEADYIVG   93 (501)
T ss_pred             HHCEEEEEECCCCCHHHHHHHHH
T ss_conf             85959980689899999999985


No 32 
>COG3115 ZipA Cell division protein [Cell division and chromosome partitioning]
Probab=62.71  E-value=9.1  Score=17.54  Aligned_cols=33  Identities=15%  Similarity=0.262  Sum_probs=22.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCEEECCC
Q ss_conf             899999999999999999998469982450389
Q gi|254780695|r   22 ILILASVILVPIMLFMAARFFVNSPHYDNLYVK   54 (563)
Q Consensus        22 ki~~~~~~~~~i~~~~~~~~~~~~p~y~~L~~~   54 (563)
                      +.++|++++++|+++++-.+|.||-.-...|..
T Consensus         5 r~ILIIvG~IAIiaLLvhGlWtsRkE~s~~F~~   37 (324)
T COG3115           5 RLILIIVGAIAIIALLVHGLWTSRKERSSYFRD   37 (324)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCHHHCCCCCC
T ss_conf             467999999999999986333110110210124


No 33 
>PRK07867 acyl-CoA synthetase; Validated
Probab=62.56  E-value=11  Score=17.13  Aligned_cols=29  Identities=10%  Similarity=0.011  Sum_probs=16.2

Q ss_pred             HCCCCCEEECCCCCHHHHHHHHHHHHHCCCCE
Q ss_conf             46998245038999899999999999779929
Q gi|254780695|r   43 VNSPHYDNLYVKLEVSDVNRISVALSEANIDF   74 (563)
Q Consensus        43 ~~~p~y~~L~~~l~~~d~~~i~~~L~~~gI~y   74 (563)
                      ...--+++|...+..++...+   |+..+...
T Consensus        76 ~~Gav~vplnp~~~~~~l~~~---l~~a~~~~  104 (505)
T PRK07867         76 LSGIVPVGLNPTRRGAALARD---IAHADCQV  104 (505)
T ss_pred             HHCEEEEEECCCCCHHHHHHH---HHHCCCCE
T ss_conf             869799950899999999999---98479959


No 34 
>PRK13150 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=62.25  E-value=11  Score=17.10  Aligned_cols=39  Identities=18%  Similarity=0.283  Sum_probs=27.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEECCCCCHHHH
Q ss_conf             878899999999999999999998469982450389998999
Q gi|254780695|r   19 RTRILILASVILVPIMLFMAARFFVNSPHYDNLYVKLEVSDV   60 (563)
Q Consensus        19 ~~~ki~~~~~~~~~i~~~~~~~~~~~~p~y~~L~~~l~~~d~   60 (563)
                      ++||+++++++++++.+++++++++-+-.....|   +|+|.
T Consensus         5 rk~RL~~v~~~~~~l~~a~~Lvl~al~~ni~yFy---tPsev   43 (159)
T PRK13150          5 RKNRLWVVCAVLAGLGLTTALVLYALRANIDLFY---TPGEI   43 (159)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEE---CHHHH
T ss_conf             8768999999999999999999999871744886---78998


No 35 
>pfam03180 Lipoprotein_9 NLPA lipoprotein. This family of bacterial lipoproteins contains several antigenic members, that may be involved in bacterial virulence. Their precise function is unknown. However they are probably distantly related to pfam00497 which are solute binding proteins.
Probab=62.10  E-value=11  Score=17.08  Aligned_cols=105  Identities=17%  Similarity=0.249  Sum_probs=54.0

Q ss_pred             CCCCEEEECHHHHHHHH--HHHHHCCCCCCCCCCHHHHHCCCCCCCCCH--HHHHHHHHHHHHHHHHHHHHHCCCCCEEE
Q ss_conf             89977995189999999--999976998877663256530588842599--99999999999999999996057631489
Q gi|254780695|r   78 DNGSSISVPSSMVGKAR--IHLAAQGLPSSSSNSGYELFDKVNSFGLTS--FMQEITRVRALEGEIARTIQSISGIVAAR  153 (563)
Q Consensus        78 ~~g~~I~Vp~~~~~~~r--~~La~~glp~~~~~~g~el~d~~~~~g~T~--~~~~~~~~ralegeL~rtI~~~~~V~~Ar  153 (563)
                      ++|.+|.||.+-...+|  ..|...||-+-..  |.       ++..|.  -.++-+-..-.|-+.+++-++++.|..|-
T Consensus        95 p~Ga~IaIpnD~sN~~RAL~lL~~aGLI~Lk~--~~-------~~~~t~~DI~~Npk~l~~~ev~a~ql~~~l~dvD~av  165 (236)
T pfam03180        95 PDGATIAVPNDPSNEGRALLLLEKAGLIKLKD--GA-------GLLATVKDITENPKNLKIKELEAAQLPRALDDVDAAV  165 (236)
T ss_pred             CCCCEEEECCCCCHHHHHHHHHHHCCCEEECC--CC-------CCCCCHHHHHHCCCCCEEEEECHHHHHHHCCCCCEEE
T ss_conf             79998981588442999999999889889768--99-------9878988897286776699916777554216657899


Q ss_pred             EEEEE-------CCCC-CCCCCCCCCCEEEEEECCCCCCHHHHHHH
Q ss_conf             99983-------3666-55555558715999706877898899999
Q gi|254780695|r  154 VHIVM-------PDMG-SFRKIGARPTASVMIRAINPSVYKSAEAI  191 (563)
Q Consensus       154 V~l~~-------p~~~-~f~~~~~~~sASV~l~~~~~l~~~qv~~I  191 (563)
                      ++=..       |.+. +|.+....+-+-++.......+...++.+
T Consensus       166 in~n~a~~agl~p~~~~l~~e~~~~~y~n~ivvr~~~~d~~~ik~l  211 (236)
T pfam03180       166 INTNYALQAGLDPKKDALFEEDKDSPYVNIIVVREDDKDDPAVKKL  211 (236)
T ss_pred             ECHHHHHHCCCCHHHHHHHCCCCCCCEEEEEEEECCCCCCHHHHHH
T ss_conf             8656798879492121331478899837999981777699999999


No 36 
>PRK13159 cytochrome c-type biogenesis protein CcmE; Reviewed
Probab=61.87  E-value=11  Score=17.05  Aligned_cols=39  Identities=23%  Similarity=0.246  Sum_probs=28.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEECCCCCHHHH
Q ss_conf             878899999999999999999998469982450389998999
Q gi|254780695|r   19 RTRILILASVILVPIMLFMAARFFVNSPHYDNLYVKLEVSDV   60 (563)
Q Consensus        19 ~~~ki~~~~~~~~~i~~~~~~~~~~~~p~y~~L~~~l~~~d~   60 (563)
                      ++||+++++.+++++++++++++|+-+......|   +|+|.
T Consensus         5 rk~Rl~~i~~~~~~~~~av~Lil~al~~ni~yF~---TPsEv   43 (156)
T PRK13159          5 RKQRLWLVIGVLTAAALAVTLIVFALQRNMSYLF---TPSQV   43 (156)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCEEEEE---CHHHH
T ss_conf             8889999999999999999999999861827997---89998


No 37 
>PRK09861 cytoplasmic membrane lipoprotein-28; Provisional
Probab=60.93  E-value=11  Score=16.94  Aligned_cols=25  Identities=20%  Similarity=0.452  Sum_probs=11.4

Q ss_pred             CCCEEEECHHHHHHHH--HHHHHCCCC
Q ss_conf             9977995189999999--999976998
Q gi|254780695|r   79 NGSSISVPSSMVGKAR--IHLAAQGLP  103 (563)
Q Consensus        79 ~g~~I~Vp~~~~~~~r--~~La~~glp  103 (563)
                      +|.+|.||.+-....|  ..|...||-
T Consensus       130 ~Ga~IaIPnDpsN~~RAL~lL~~aGLI  156 (272)
T PRK09861        130 EGATVAIPNDPTNLGRALLLLQKEKLI  156 (272)
T ss_pred             CCCEEEECCCHHHHHHHHHHHHHCCCE
T ss_conf             999898047812699999999988978


No 38 
>PRK05605 acyl-CoA synthetase; Validated
Probab=60.66  E-value=11  Score=16.91  Aligned_cols=14  Identities=7%  Similarity=-0.104  Sum_probs=8.3

Q ss_pred             HHHHHHHHHHHHHC
Q ss_conf             68999999998869
Q gi|254780695|r  525 KQSDLRLLHMIEIN  538 (563)
Q Consensus       525 ~~~~~~i~~lv~e~  538 (563)
                      +..|++||+++.++
T Consensus       555 KidR~~LR~~~~~~  568 (571)
T PRK05605        555 KVRRREVREELLEK  568 (571)
T ss_pred             CHHHHHHHHHHHHH
T ss_conf             26399999999997


No 39 
>PTZ00233 variable surface protein Vir18; Provisional
Probab=59.50  E-value=4.8  Score=19.39  Aligned_cols=18  Identities=22%  Similarity=0.313  Sum_probs=8.0

Q ss_pred             HHHHHHHHHHHHCCCCCC
Q ss_conf             999997787520112210
Q gi|254780695|r  454 FLGLHALRRLHNIDDAKK  471 (563)
Q Consensus       454 ~~vl~~l~~~~~~~~~~~  471 (563)
                      +|=+-||+|.+-...+..
T Consensus       451 LFKyTPLWrvLTKknRKk  468 (509)
T PTZ00233        451 LFKYTPLWRVLTKKNRKK  468 (509)
T ss_pred             HHCCCHHHHHHHHCCCCC
T ss_conf             862262366551114355


No 40 
>PRK09732 hypothetical protein; Provisional
Probab=58.80  E-value=12  Score=16.71  Aligned_cols=62  Identities=19%  Similarity=0.035  Sum_probs=45.0

Q ss_pred             ECCCCCCHHHHHHH-HHHHHHHHHCCCCCCEEEEECCCCEEECC-CCCCCCCHHHHHHHHHHHH
Q ss_conf             06877898899999-99998654018835269982898350036-7653332479999999999
Q gi|254780695|r  178 RAINPSVYKSAEAI-RHLVAAAVPNLDMGDVTVLDSTGKLLTAN-EMERNILGKSLSIVQAIQH  239 (563)
Q Consensus       178 ~~~~~l~~~qv~~I-~~lVa~sV~gL~~e~VtVvD~~G~~L~~~-~~~~~~~~~~~~~~~~~E~  239 (563)
                      +.++-|+.+.++.| ..-++.+-..=-+=+|.|+|..|+++.-. -|+....+-.+.+++.+..
T Consensus         2 ~tk~~Ltl~~A~~i~~aa~~~A~~~g~~v~IaVvD~~G~L~a~~RmDgA~~~S~~iA~~KA~TA   65 (134)
T PRK09732          2 KTKVILSQQMASAIIAAGQEEAQKNNWSVSIAVADDGGHLLALSRMDDCAPIAAYISQEKARTA   65 (134)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCEEEEEECCCCCCCCHHHHHHHHHHH
T ss_conf             8634236999999999999999983998799999899999888754999424099999999998


No 41 
>PRK10270 hypothetical protein; Provisional
Probab=58.75  E-value=12  Score=16.70  Aligned_cols=24  Identities=8%  Similarity=0.007  Sum_probs=13.4

Q ss_pred             EECCCCCHHHHHHHHHHHHHCCCC
Q ss_conf             503899989999999999977992
Q gi|254780695|r   50 NLYVKLEVSDVNRISVALSEANID   73 (563)
Q Consensus        50 ~L~~~l~~~d~~~i~~~L~~~gI~   73 (563)
                      +.|.=-......+|...|.++||=
T Consensus        40 vvv~I~~G~s~~~Ia~~L~~~gvI   63 (340)
T PRK10270         40 TIFTLKPGTGRLALGEQLYADKII   63 (340)
T ss_pred             EEEEECCCCCHHHHHHHHHHCCCC
T ss_conf             899989999999999999988683


No 42 
>pfam04814 HNF-1_N Hepatocyte nuclear factor 1 (HNF-1), N terminus. This family consists of the N terminus of homeobox-containing transcription factor HNF-1. This region contains a dimerization sequence and an acidic region that may be involved in transcription activation. Mutations and the common Ala/Val 98 polymorphism in HNF-1 cause the type 3 form of maturity-onset diabetes of the young (MODY3).
Probab=58.73  E-value=12  Score=16.70  Aligned_cols=37  Identities=11%  Similarity=0.241  Sum_probs=28.7

Q ss_pred             HHHCCCCCHHHHHHHHHHHHHHCHHHHHHHHHHHHHH
Q ss_conf             0100211006899999999886999899999999863
Q gi|254780695|r  516 QSRINSYVSKQSDLRLLHMIEINEERFAKILRKWARS  552 (563)
Q Consensus       516 ~~~~~~~~~~~~~~~i~~lv~e~Pe~vA~vLR~WL~e  552 (563)
                      .+.....+..+.+..+++|.++||=+||..||..|..
T Consensus        90 le~l~~EEaa~qra~Ve~ll~~d~~~v~~~Ik~~m~~  126 (177)
T pfam04814        90 LERLSPEEAAHQRAEVDRLLREDPWRVAKMIKSYMQQ  126 (177)
T ss_pred             HHCCCCHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHH
T ss_conf             2225825888889999999972849999999999987


No 43 
>PRK13388 acyl-CoA synthetase; Provisional
Probab=58.04  E-value=13  Score=16.62  Aligned_cols=33  Identities=9%  Similarity=-0.049  Sum_probs=20.4

Q ss_pred             HHHHHCCCCCEEECCCCCHHHHHHHHHHHHHCCCCE
Q ss_conf             999846998245038999899999999999779929
Q gi|254780695|r   39 ARFFVNSPHYDNLYVKLEVSDVNRISVALSEANIDF   74 (563)
Q Consensus        39 ~~~~~~~p~y~~L~~~l~~~d~~~i~~~L~~~gI~y   74 (563)
                      +..+...--|++|...+...+...+   |...+...
T Consensus        70 la~~~~Gav~vpln~~~~~~el~~~---l~~~~~~~  102 (544)
T PRK13388         70 AAAALGGYVLCGLNTTRRGEALAAD---IRRADCQI  102 (544)
T ss_pred             HHHHHHCEEEEEECCCCCHHHHHHH---HHHCCCCE
T ss_conf             9999859399987999999999999---98469809


No 44 
>PRK06219 consensus
Probab=57.18  E-value=13  Score=16.53  Aligned_cols=23  Identities=9%  Similarity=0.053  Sum_probs=13.8

Q ss_pred             HCCCCCEEECCCCCHHHHHHHHH
Q ss_conf             46998245038999899999999
Q gi|254780695|r   43 VNSPHYDNLYVKLEVSDVNRISV   65 (563)
Q Consensus        43 ~~~p~y~~L~~~l~~~d~~~i~~   65 (563)
                      ...--+++|+..+.+++...+++
T Consensus        89 ~~Gav~vpl~~~~~~~~l~~~l~  111 (547)
T PRK06219         89 MIGAVLHTINVRLSPEQILYTMN  111 (547)
T ss_pred             HHCEEEECCCCCCCHHHHHHHHH
T ss_conf             85979975499999999999997


No 45 
>pfam03100 CcmE CcmE. CcmE is the product of one of a cluster of Ccm genes that are necessary for cytochrome c biosynthesis in eubacteria. Expression of these proteins is induced when the organisms are grown under anaerobic conditions with nitrate or nitrite as the final electron acceptor.
Probab=56.37  E-value=11  Score=16.89  Aligned_cols=39  Identities=26%  Similarity=0.304  Sum_probs=27.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEECCCCCHHHH
Q ss_conf             878899999999999999999998469982450389998999
Q gi|254780695|r   19 RTRILILASVILVPIMLFMAARFFVNSPHYDNLYVKLEVSDV   60 (563)
Q Consensus        19 ~~~ki~~~~~~~~~i~~~~~~~~~~~~p~y~~L~~~l~~~d~   60 (563)
                      ++||+++++++++++++++++++++-+..-..-|   +|+|.
T Consensus         4 r~kRl~~i~~~~~~~~~~~~Lil~al~~n~~yf~---tPsEl   42 (130)
T pfam03100         4 RKRRLLLVLAALAALGLAVALVLYALRDNIVFFY---TPSEV   42 (130)
T ss_pred             CEEEHHHHHHHHHHHHHHHHHHHHHHHHCEEEEE---CHHHH
T ss_conf             3245478999999999999999998761812998---79998


No 46 
>PRK05696 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=55.96  E-value=9.3  Score=17.48  Aligned_cols=27  Identities=7%  Similarity=0.115  Sum_probs=20.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCEEE
Q ss_conf             999999999999998877540878069
Q gi|254780695|r  233 IVQAIQHEIEMNINKALAAFLGVDNFR  259 (563)
Q Consensus       233 ~~~~~E~~~~~kI~~~L~~i~G~~~v~  259 (563)
                      =|.++.+++...|++.|.+.-|.+.+.
T Consensus       132 Gk~~Lr~e~~~~in~~l~~~~g~~~V~  158 (168)
T PRK05696        132 GKEELRQKALASVQETLQKVTGKPVVE  158 (168)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCEE
T ss_conf             899999999999999976313887512


No 47 
>COG3105 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.85  E-value=14  Score=16.39  Aligned_cols=27  Identities=26%  Similarity=0.074  Sum_probs=14.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999778752
Q gi|254780695|r  438 TVINALVFLVGTLLVTFLGLHALRRLH  464 (563)
Q Consensus       438 ~~~~~~~~~l~~lll~~~vl~~l~~~~  464 (563)
                      .+..+++.+++++++.+++.|+..+..
T Consensus         7 ~W~~a~igLvvGi~IG~li~Rlt~~~~   33 (138)
T COG3105           7 TWEYALIGLVVGIIIGALIARLTNRKL   33 (138)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCHHH
T ss_conf             999999999999999999999823022


No 48 
>PRK11677 cytochrome d ubiquinol oxidase subunit III; Provisional
Probab=55.20  E-value=14  Score=16.32  Aligned_cols=18  Identities=17%  Similarity=0.067  Sum_probs=8.3

Q ss_pred             HHHHHHHCHHHHHHHHHH
Q ss_conf             999988699989999999
Q gi|254780695|r  531 LLHMIEINEERFAKILRK  548 (563)
Q Consensus       531 i~~lv~e~Pe~vA~vLR~  548 (563)
                      -+.-|.++=...|.++.+
T Consensus        48 Yr~ev~~HF~~tA~Ll~~   65 (134)
T PRK11677         48 YRQELVDHFARSAELLDT   65 (134)
T ss_pred             HHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999999


No 49 
>PRK03584 acetoacetyl-CoA synthetase; Provisional
Probab=55.16  E-value=14  Score=16.31  Aligned_cols=27  Identities=15%  Similarity=0.273  Sum_probs=12.9

Q ss_pred             HHHHHHHHHHHCCCCEEECCCCCEEEECHH
Q ss_conf             999999999977992999189977995189
Q gi|254780695|r   59 DVNRISVALSEANIDFRISDNGSSISVPSS   88 (563)
Q Consensus        59 d~~~i~~~L~~~gI~y~~~~~g~~I~Vp~~   88 (563)
                      .++++...|.+.||.   ..|--.|+.|..
T Consensus       125 ~v~rlA~~L~~~GV~---~GDrVai~lpn~  151 (652)
T PRK03584        125 QVAALAQALRALGVG---PGDRVAAYLPNI  151 (652)
T ss_pred             HHHHHHHHHHHCCCC---CCCEEEEECCCC
T ss_conf             999999999975989---999999987898


No 50 
>KOG4238 consensus
Probab=55.02  E-value=9.1  Score=17.54  Aligned_cols=35  Identities=26%  Similarity=0.418  Sum_probs=15.3

Q ss_pred             HHHHHHHHHHCCC-CEEECCCCCEEEECHHHHHHHH
Q ss_conf             9999999997799-2999189977995189999999
Q gi|254780695|r   60 VNRISVALSEANI-DFRISDNGSSISVPSSMVGKAR   94 (563)
Q Consensus        60 ~~~i~~~L~~~gI-~y~~~~~g~~I~Vp~~~~~~~r   94 (563)
                      .+++++.|++.+| ||++..+-.-++||++.++.++
T Consensus       211 vqqvve~lq~~~ivp~~~~~~v~elfv~e~~l~~~~  246 (627)
T KOG4238         211 VQQVVELLQEQNIVPYTIIKDVHELFVPENKLDHVR  246 (627)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHHCCCCCHHHHHH
T ss_conf             999999998669871554377887718822898998


No 51 
>TIGR01006 polys_exp_MPA1 polysaccharide export protein, MPA1 family; InterPro: IPR005701    The MPA1 proteins function in capsule polysaccharide and exopolysaccharide polymerization and/or export. They possess a characteristic carboxy-terminal ATP-binding domain and one or more regions which can form coiled-coils and are located in the periplasmic domain between the two transmembrane regions of the protein .; GO: 0015542 sugar efflux transmembrane transporter activity, 0006859 extracellular carbohydrate transport, 0016021 integral to membrane.
Probab=54.59  E-value=14  Score=16.26  Aligned_cols=18  Identities=11%  Similarity=0.145  Sum_probs=7.8

Q ss_pred             CCCHHHHHH-HHHHHHHHC
Q ss_conf             469899999-999864312
Q gi|254780695|r  379 GKIDSYLAE-INKIVSAAT  396 (563)
Q Consensus       379 ~~~~eel~~-I~~lV~~Ai  396 (563)
                      |..++.+++ +++..+.-+
T Consensus       135 ~~~a~~iAn~~~~V~s~~i  153 (235)
T TIGR01006       135 PQDAEKIANSLAEVASKKI  153 (235)
T ss_pred             CHHHHHHHHHHHHHHHHHH
T ss_conf             6148999999998878865


No 52 
>PRK00174 acetyl-CoA synthetase; Provisional
Probab=54.28  E-value=14  Score=16.22  Aligned_cols=40  Identities=23%  Similarity=0.282  Sum_probs=17.7

Q ss_pred             HHHHHHHHHHHCCCCEEECCCCCEEEECHH-HHHHHHHHHHHCC
Q ss_conf             999999999977992999189977995189-9999999999769
Q gi|254780695|r   59 DVNRISVALSEANIDFRISDNGSSISVPSS-MVGKARIHLAAQG  101 (563)
Q Consensus        59 d~~~i~~~L~~~gI~y~~~~~g~~I~Vp~~-~~~~~r~~La~~g  101 (563)
                      .++++...|.+.||.   ..|--.|+.|.. +.--+-+..+.-|
T Consensus       116 ~v~rlA~~L~~~GV~---~GDrVai~lpn~~E~vva~lA~~kiG  156 (648)
T PRK00174        116 EVCRFANALKKLGVK---KGDRVAIYMPMIPEAAVAMLACARIG  156 (648)
T ss_pred             HHHHHHHHHHHCCCC---CCCEEEEECCCCHHHHHHHHHHHHHC
T ss_conf             999999999973969---98999998799899999999999819


No 53 
>PRK05620 acyl-CoA synthetase; Validated
Probab=53.78  E-value=15  Score=16.17  Aligned_cols=14  Identities=14%  Similarity=0.043  Sum_probs=7.9

Q ss_pred             HHHHHHHHHHHHHC
Q ss_conf             68999999998869
Q gi|254780695|r  525 KQSDLRLLHMIEIN  538 (563)
Q Consensus       525 ~~~~~~i~~lv~e~  538 (563)
                      +..|++||++.++.
T Consensus       545 Ki~r~~LRe~~~~~  558 (571)
T PRK05620        545 KFDKKDLRQHLRNG  558 (571)
T ss_pred             CHHHHHHHHHHHCC
T ss_conf             35299999999869


No 54 
>pfam06898 YqfD Putative stage IV sporulation protein YqfD. This family consists of several putative bacterial stage IV sporulation (SpoIV) proteins. YqfD of Bacillus subtilis is known to be essential for efficient sporulation although its exact function is unknown.
Probab=53.05  E-value=15  Score=16.09  Aligned_cols=41  Identities=12%  Similarity=0.149  Sum_probs=26.0

Q ss_pred             HHHHHHHHCCCCCEEECCCCCHHHHHHHHHHHHHCCCCEEE
Q ss_conf             99999984699824503899989999999999977992999
Q gi|254780695|r   36 FMAARFFVNSPHYDNLYVKLEVSDVNRISVALSEANIDFRI   76 (563)
Q Consensus        36 ~~~~~~~~~~p~y~~L~~~l~~~d~~~i~~~L~~~gI~y~~   76 (563)
                      ++++++++|.=-|..=+.|.++..-.+|...|++.||..-.
T Consensus        97 f~~~l~~lS~fVW~I~i~G~~~~t~~~i~~~L~~~gi~~G~  137 (383)
T pfam06898        97 FVILLYFLSNFIWSIDIKTAKNIAEHEIRQQLNEIGVKSGV  137 (383)
T ss_pred             HHHHHHHHHHEEEEEEEECCCCCCHHHHHHHHHHCCCCCCE
T ss_conf             99999978406999999869989989999999986997780


No 55 
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=51.84  E-value=16  Score=15.97  Aligned_cols=28  Identities=7%  Similarity=-0.073  Sum_probs=20.9

Q ss_pred             HHHHHHCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9998869998999999998637863542
Q gi|254780695|r  532 LHMIEINEERFAKILRKWARSEIEDRYT  559 (563)
Q Consensus       532 ~~lv~e~Pe~vA~vLR~WL~ee~~~~~~  559 (563)
                      ++|+++|||.|...+|.|..-...-+.+
T Consensus       211 ~~Fa~e~Pe~V~~flkv~~~A~~~~~~n  238 (320)
T PRK11480        211 KDFAEKHPEVVKAFAKSAIDAQQPYIAN  238 (320)
T ss_pred             HHHHHHCHHHHHHHHHHHHHHHHHHHHC
T ss_conf             9999889899999999999999999959


No 56 
>PRK07021 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=50.59  E-value=16  Score=15.84  Aligned_cols=25  Identities=16%  Similarity=0.113  Sum_probs=14.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCEE
Q ss_conf             9999999999999887754087806
Q gi|254780695|r  234 VQAIQHEIEMNINKALAAFLGVDNF  258 (563)
Q Consensus       234 ~~~~E~~~~~kI~~~L~~i~G~~~v  258 (563)
                      ++++.+++.++|+..|.+--+.+.+
T Consensus       124 k~~L~~ei~~~vn~~l~~~~~~~~V  148 (159)
T PRK07021        124 KQKLAAEIKETLEQPLVPGQPKQVV  148 (159)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCE
T ss_conf             9999999999999987456888834


No 57 
>TIGR01925 spIIAB anti-sigma F factor; InterPro: IPR010194   This entry describes the SpoIIAB anti-sigma F factor. Sigma F regulates spore development in B subtilis. SpoIIAB binds to sigma F, preventing formation of the transcription complex at the promoter . SpoIIAA (anti-anti-sigma F factor) binds to SpoIIAB to inhibit association with sigma F, however SpoIIAB can phosphorylate SpoIIAA, causing disassociation of the SpoIIAA/B complex . The SpoIIE phosphatase dephosphorylates SpoIIAA.; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0016989 sigma factor antagonist activity, 0006468 protein amino acid phosphorylation, 0030435 sporulation, 0045892 negative regulation of transcription DNA-dependent.
Probab=50.41  E-value=9.4  Score=17.45  Aligned_cols=48  Identities=19%  Similarity=0.252  Sum_probs=35.3

Q ss_pred             CCCCEEEEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHC------CCCCCCCCEEEEEECCC
Q ss_conf             0010256530543245666555533469899999999864312------56611387689985035
Q gi|254780695|r  354 LERLSIAVVVNKGRLTEVLGRSADQGKIDSYLAEINKIVSAAT------GINSRRGDTITITSMDF  413 (563)
Q Consensus       354 I~rlSVAV~Vn~~~~~~~~g~~~~~~~~~eel~~I~~lV~~Ai------G~d~~RGD~VtV~~~~F  413 (563)
                      --|+|||-.+-+-.            -+=+|+.+|+..|+.||      ||..+.+..|.+...--
T Consensus        18 FARVtVasFia~LD------------PT~~El~diK~~VSEAVTNAIIHGYE~~~~~~V~I~~~~~   71 (137)
T TIGR01925        18 FARVTVASFIAQLD------------PTLEELTDIKTAVSEAVTNAIIHGYEENKEGVVIISATIE   71 (137)
T ss_pred             CHHHHHHHHHHHCC------------CCHHHHHHHHHHHHHHHHCCEEECEEECCCCEEEEEEEEE
T ss_conf             01344544675428------------7544455554333223212053145637997789999960


No 58 
>TIGR03017 EpsF chain length determinant protein EpsF. Sequences in this family of proteins are members of the chain length determinant family (pfam02706) which includes the wzc protein from E.coli. This family of proteins are homologous to the EpsF protein of the methanolan biosynthesis operon of Methylobacillus species strain 12S. The distribution of this protein appears to be restricted to a subset of exopolysaccharide operons containing a syntenic grouping of genes including a variant of the EpsH exosortase protein. Exosortase has been proposed to be involved in the targetting and processing of proteins containing the PEP-CTERM domain to the exopolysaccharide layer.
Probab=49.49  E-value=17  Score=15.73  Aligned_cols=26  Identities=15%  Similarity=0.038  Sum_probs=16.5

Q ss_pred             EEECC-CCCCHHHHHHHHHHHHHHHHC
Q ss_conf             97068-778988999999999865401
Q gi|254780695|r  176 MIRAI-NPSVYKSAEAIRHLVAAAVPN  201 (563)
Q Consensus       176 ~l~~~-~~l~~~qv~~I~~lVa~sV~g  201 (563)
                      +++.. .+-+|+.+..|.|.++...-.
T Consensus       133 vi~Is~~~~dP~~Aa~v~n~l~~~y~~  159 (444)
T TIGR03017       133 VISIEFSGVDPRFAATVANAFAQAYID  159 (444)
T ss_pred             EEEEEEEECCHHHHHHHHHHHHHHHHH
T ss_conf             899998609999999999999999999


No 59 
>PRK03739 2-isopropylmalate synthase; Validated
Probab=49.47  E-value=17  Score=15.73  Aligned_cols=90  Identities=19%  Similarity=0.156  Sum_probs=57.3

Q ss_pred             CCCCHHHHHHHHHHHHHCCCCEEECCCCCEEEECHHHHHHHHHHHHHCCCCCCCCCCHHHHHCCCCCCCCCHHHHHHHHH
Q ss_conf             89998999999999997799299918997799518999999999997699887766325653058884259999999999
Q gi|254780695|r   53 VKLEVSDVNRISVALSEANIDFRISDNGSSISVPSSMVGKARIHLAAQGLPSSSSNSGYELFDKVNSFGLTSFMQEITRV  132 (563)
Q Consensus        53 ~~l~~~d~~~i~~~L~~~gI~y~~~~~g~~I~Vp~~~~~~~r~~La~~glp~~~~~~g~el~d~~~~~g~T~~~~~~~~~  132 (563)
                      -.|+.+|--.|...|++.||+|= . .|--..=| .+..-.| .++..++......        ...|           -
T Consensus        47 vs~s~eeKl~IA~~Ld~lGVd~I-E-aGfP~ssp-~d~e~vr-~i~~~~~~p~d~~--------i~~l-----------~  103 (552)
T PRK03739         47 EPMSPERKLRMFDLLVKIGFKEI-E-VGFPSASQ-TDFDFVR-ELIEEGLIPDDVT--------IQVL-----------T  103 (552)
T ss_pred             CCCCHHHHHHHHHHHHHCCCCEE-E-EECCCCCH-HHHHHHH-HHHHHCCCCCCCE--------EEEE-----------H
T ss_conf             99899999999999997699989-9-60587897-8999999-9998278987741--------5311-----------3


Q ss_pred             HHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCC
Q ss_conf             999999999996057631489999833666555
Q gi|254780695|r  133 RALEGEIARTIQSISGIVAARVHIVMPDMGSFR  165 (563)
Q Consensus       133 ralegeL~rtI~~~~~V~~ArV~l~~p~~~~f~  165 (563)
                      ||.+..+.+++.++.+.+.++||+.+|-..++.
T Consensus       104 ~ar~~~i~~~~~al~~a~~~~vh~~~~tS~~h~  136 (552)
T PRK03739        104 QAREHLIERTFEALEGAKRAIVHLYNSTSPLQR  136 (552)
T ss_pred             HCCHHHHHHHHHHHCCCCCCEEEEECCCCHHHH
T ss_conf             206767889999855888635777625779999


No 60 
>PRK13628 serine/threonine transporter SstT; Provisional
Probab=47.61  E-value=18  Score=15.54  Aligned_cols=32  Identities=9%  Similarity=0.209  Sum_probs=24.6

Q ss_pred             HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHH
Q ss_conf             89999999986406987889999999999999
Q gi|254780695|r    4 LDQLLQFFKSGTSLGRTRILILASVILVPIML   35 (563)
Q Consensus         4 ~~~l~~~~~~~~~l~~~~ki~~~~~~~~~i~~   35 (563)
                      +++++.++++|++.+-..|++++.++-+++..
T Consensus         1 ~~~~~~~~~~~~k~sL~~~IligivlGi~~G~   32 (402)
T PRK13628          1 MQQMSSLLRRLARGSLVKQILIGLVLGILLAL   32 (402)
T ss_pred             CHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHH
T ss_conf             93689999999858879999999999999999


No 61 
>PRK11901 hypothetical protein; Reviewed
Probab=47.55  E-value=18  Score=15.54  Aligned_cols=28  Identities=21%  Similarity=0.374  Sum_probs=18.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             7889999999999999999999846998
Q gi|254780695|r   20 TRILILASVILVPIMLFMAARFFVNSPH   47 (563)
Q Consensus        20 ~~ki~~~~~~~~~i~~~~~~~~~~~~p~   47 (563)
                      +|-+.|++++++++++|+++.=-+..|+
T Consensus        35 RQh~MiGiGILVLLLLIIgIgSALKaPs   62 (329)
T PRK11901         35 RQHMMIGIGILVLLLLIIAIGSALKAPT   62 (329)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             8889999999999999998656432898


No 62 
>pfam10969 DUF2771 Protein of unknown function (DUF2771). This bacterial family of proteins has no known function.
Probab=47.31  E-value=12  Score=16.76  Aligned_cols=28  Identities=7%  Similarity=0.077  Sum_probs=17.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCEE
Q ss_conf             9999999999999999999846998245
Q gi|254780695|r   23 LILASVILVPIMLFMAARFFVNSPHYDN   50 (563)
Q Consensus        23 i~~~~~~~~~i~~~~~~~~~~~~p~y~~   50 (563)
                      .++++++++++++..++.+|.+++...+
T Consensus         5 ~~l~a~v~v~~~~~~gv~~W~~~~~~~P   32 (161)
T pfam10969         5 ALLLAGLVVVLAAVAGVGVWLLVRDHGP   32 (161)
T ss_pred             EHHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             0248889998888654237762789998


No 63 
>pfam09919 DUF2149 Uncharacterized conserved protein (DUF2149). This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=47.06  E-value=7.9  Score=17.96  Aligned_cols=19  Identities=26%  Similarity=0.557  Sum_probs=14.0

Q ss_pred             HHCCCCEEECCCCCEEEECH
Q ss_conf             97799299918997799518
Q gi|254780695|r   68 SEANIDFRISDNGSSISVPS   87 (563)
Q Consensus        68 ~~~gI~y~~~~~g~~I~Vp~   87 (563)
                      .+.|+.|++. +|..|+||+
T Consensus        73 ~r~G~aYrl~-~Gk~IyVpe   91 (91)
T pfam09919        73 ERLGTAYRLK-DGKLIYVPE   91 (91)
T ss_pred             EEEEEEEECC-CCCEEECCC
T ss_conf             6827888749-986895569


No 64 
>PRK08008 caiC putative crotonobetaine/carnitine-CoA ligase; Validated
Probab=46.43  E-value=19  Score=15.42  Aligned_cols=26  Identities=8%  Similarity=-0.084  Sum_probs=15.8

Q ss_pred             HHHCCCCCEEECCCCCHHHHHHHHHH
Q ss_conf             98469982450389998999999999
Q gi|254780695|r   41 FFVNSPHYDNLYVKLEVSDVNRISVA   66 (563)
Q Consensus        41 ~~~~~p~y~~L~~~l~~~d~~~i~~~   66 (563)
                      .+...-.|++|...+..++...++..
T Consensus        82 ~~~~Gav~vpl~~~~~~~~l~~il~~  107 (517)
T PRK08008         82 LAKIGAIMVPINARLLREESAWILQN  107 (517)
T ss_pred             HHHHCCEEEEECCCCCHHHHHHHHHH
T ss_conf             99869699977887999999999985


No 65 
>COG0011 Uncharacterized conserved protein [Function unknown]
Probab=46.39  E-value=19  Score=15.42  Aligned_cols=61  Identities=16%  Similarity=0.134  Sum_probs=42.3

Q ss_pred             CCEEECCC-CC-HHHHHHHHHHHHHCCCCEEECCCCCEEEECHHHHHHH----HHHHHHCCCCCCCC
Q ss_conf             82450389-99-8999999999997799299918997799518999999----99999769988776
Q gi|254780695|r   47 HYDNLYVK-LE-VSDVNRISVALSEANIDFRISDNGSSISVPSSMVGKA----RIHLAAQGLPSSSS  107 (563)
Q Consensus        47 ~y~~L~~~-l~-~~d~~~i~~~L~~~gI~y~~~~~g~~I~Vp~~~~~~~----r~~La~~glp~~~~  107 (563)
                      ++.|+-++ -+ .+-.++++..|++.|++|++.+-|+.|-.+=+++-++    .-.+...|.|.-..
T Consensus         8 sviP~gt~~~svs~yVa~~i~~lk~~glky~~~pm~T~iEg~~del~~~ik~~~Ea~~~~g~~Rv~t   74 (100)
T COG0011           8 SVIPLGTGGPSVSKYVAEAIEILKESGLKYQLGPMGTVIEGELDELMEAVKEAHEAVFEKGAPRVST   74 (100)
T ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHCCCCEEECCCCEEEEECHHHHHHHHHHHHHHHHHCCCCEEEE
T ss_conf             9984678998789999999999997499526067621898629999999999999998629964899


No 66 
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=45.69  E-value=19  Score=15.35  Aligned_cols=25  Identities=28%  Similarity=0.446  Sum_probs=9.4

Q ss_pred             CCCEEEECHHHHHH--HHHHHHHCCCC
Q ss_conf             99779951899999--99999976998
Q gi|254780695|r   79 NGSSISVPSSMVGK--ARIHLAAQGLP  103 (563)
Q Consensus        79 ~g~~I~Vp~~~~~~--~r~~La~~glp  103 (563)
                      +|.+|.+|.+-...  +-..|...||-
T Consensus       129 ~Ga~IaIPND~sN~~RAL~lL~~aGLI  155 (271)
T PRK11063        129 DGSQVAVPNDPTNLGRSLLLLQKVGLI  155 (271)
T ss_pred             CCCEEEECCCCCHHHHHHHHHHHCCCE
T ss_conf             999998048856099999999988988


No 67 
>PRK13391 acyl-CoA synthetase; Provisional
Probab=45.10  E-value=20  Score=15.29  Aligned_cols=70  Identities=10%  Similarity=-0.108  Sum_probs=32.1

Q ss_pred             HHHHHHHHHHHHHHC--CHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEECCCCCHHHHHHHHHHHHHCCCCEEE
Q ss_conf             789999999986406--98788999999999999999999984699824503899989999999999977992999
Q gi|254780695|r    3 ILDQLLQFFKSGTSL--GRTRILILASVILVPIMLFMAARFFVNSPHYDNLYVKLEVSDVNRISVALSEANIDFRI   76 (563)
Q Consensus         3 ~~~~l~~~~~~~~~l--~~~~ki~~~~~~~~~i~~~~~~~~~~~~p~y~~L~~~l~~~d~~~i~~~L~~~gI~y~~   76 (563)
                      |.++..++-..|..+  .+..++.+..-- ..=..+.++..+...-.+++|...+.+++...++   +..+..+=+
T Consensus        30 L~~~~~~~A~~L~~~Gv~~gd~V~i~~~n-~~e~~~~~lA~~~~Gav~vpl~~~~~~~~l~~~l---~~~~~~~li  101 (514)
T PRK13391         30 LEARSNRLAHLFRSHGLRRGDHVAIFMEN-NLRYLEACWAAERSGLYYTCVNSYLTPAEAAYIV---DDSGARALI  101 (514)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCEEEEEECC-CHHHHHHHHHHHHHCEEEEEECCCCCHHHHHHHH---HHCCCCEEE
T ss_conf             99999999999997595998999999489-7999999999998590999568999999999999---866996999


No 68 
>TIGR00970 leuA_yeast 2-isopropylmalate synthase; InterPro: IPR005668    Alpha-isopropylmalate synthase (2.3.3.13 from EC) catalyses the first step in the biosynthesis of leucine, the condensation of acetyl-CoA and alpha- ketoisovalerate to form 2-isopropylmalate synthase. This model describes a family of 2-isopropylmalate synthases as found in yeasts and in a minority of studied bacteria.; GO: 0003852 2-isopropylmalate synthase activity, 0009098 leucine biosynthetic process.
Probab=45.02  E-value=13  Score=16.52  Aligned_cols=95  Identities=20%  Similarity=0.210  Sum_probs=49.3

Q ss_pred             HHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCCEEEEEECCCCCCHHHHHHHH--HHHHHHHHCCCCCCEEEEECCC
Q ss_conf             99999996057631489999833666555555587159997068778988999999--9998654018835269982898
Q gi|254780695|r  137 GEIARTIQSISGIVAARVHIVMPDMGSFRKIGARPTASVMIRAINPSVYKSAEAIR--HLVAAAVPNLDMGDVTVLDSTG  214 (563)
Q Consensus       137 geL~rtI~~~~~V~~ArV~l~~p~~~~f~~~~~~~sASV~l~~~~~l~~~qv~~I~--~lVa~sV~gL~~e~VtVvD~~G  214 (563)
                      .=+.|||+++.|=+.|.||+-..-..+|-+        |+-+.  .+..-+-.||.  .||...+.+-..       +.+
T Consensus       109 ~LI~RT~eAl~GAk~A~vH~YnatS~lfRe--------vVFr~--sr~E~~~~A~~g~K~vrk~tk~a~~-------~~~  171 (615)
T TIGR00970       109 ELIKRTVEALSGAKKATVHLYNATSDLFRE--------VVFRA--SREEVLALAVEGSKLVRKLTKDAAK-------SKE  171 (615)
T ss_pred             HHHHHHHHHHHCCCCEEEEEHHHCCHHHHH--------HHHCC--CHHHHHHHHHHHHHHHHHHHHHHHH-------CCC
T ss_conf             789999998306862167540112425667--------86405--7689999864278999999873341-------577


Q ss_pred             CEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             35003676533324799999999999999999887754
Q gi|254780695|r  215 KLLTANEMERNILGKSLSIVQAIQHEIEMNINKALAAF  252 (563)
Q Consensus       215 ~~L~~~~~~~~~~~~~~~~~~~~E~~~~~kI~~~L~~i  252 (563)
                      .-..=.-+....+...++|-.++=.    =|..+..|.
T Consensus       172 T~W~fEySPE~fsdTe~efA~evCe----AVk~~w~Pt  205 (615)
T TIGR00970       172 TRWSFEYSPESFSDTELEFAVEVCE----AVKEVWKPT  205 (615)
T ss_pred             CCCCCEECCCCCCCCCHHHHHHHHH----HHHHHHCCC
T ss_conf             6453100677678885478999999----877761787


No 69 
>TIGR02554 PrgH type III secretion apparatues protein PrgH/EprH; InterPro: IPR013387    In Salmonella, the gene encoding this protein is part of a four-gene operon PrgHIJK, while in other organisms it is found in type III secretion operons. PrgH has been shown to be required for type III secretion  and is a structural component of the needle complex, which is the core component of type III secretion systems ..
Probab=44.63  E-value=20  Score=15.24  Aligned_cols=128  Identities=13%  Similarity=0.124  Sum_probs=79.9

Q ss_pred             CHHHHHHHHHHHHHCCCCEEEC--CCCCEEEECHHH---HHHHHHHHHHCCCCCCCCCCHHHHHCCCCCCCCCHHHHHHH
Q ss_conf             9899999999999779929991--899779951899---99999999976998877663256530588842599999999
Q gi|254780695|r   56 EVSDVNRISVALSEANIDFRIS--DNGSSISVPSSM---VGKARIHLAAQGLPSSSSNSGYELFDKVNSFGLTSFMQEIT  130 (563)
Q Consensus        56 ~~~d~~~i~~~L~~~gI~y~~~--~~g~~I~Vp~~~---~~~~r~~La~~glp~~~~~~g~el~d~~~~~g~T~~~~~~~  130 (563)
                      ....++++-..|-..+.++++=  +|| .|+|-..+   --.+|-.|+...+++.-     ++...   =+.+   +   
T Consensus       197 ~~r~~Ael~~lLg~~~~rf~vLPGrDg-~~YVaaa~~rd~~WaR~~Llra~~~~~~-----~v~~~---~~E~---~---  261 (423)
T TIGR02554       197 GQRQLAELNGLLGDEKERFAVLPGRDG-VLYVAAADERDAVWARQALLRAELDEKI-----EVVEI---GAER---K---  261 (423)
T ss_pred             HHHHHHHHHHHHCCCCCCCEECCCCCC-EEEEEECCCCCCHHHHHHHHHHCCCCCE-----EEEEC---CCCC---H---
T ss_conf             211210012332578888634368886-5899702778851178898740477870-----89742---7542---0---


Q ss_pred             HHHHHHHHHHHHHHH-CCCCCEEEEEEEECCCCCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCEEE
Q ss_conf             999999999999960-5763148999983366655555558715999706877898899999999986540188352699
Q gi|254780695|r  131 RVRALEGEIARTIQS-ISGIVAARVHIVMPDMGSFRKIGARPTASVMIRAINPSVYKSAEAIRHLVAAAVPNLDMGDVTV  209 (563)
Q Consensus       131 ~~ralegeL~rtI~~-~~~V~~ArV~l~~p~~~~f~~~~~~~sASV~l~~~~~l~~~qv~~I~~lVa~sV~gL~~e~VtV  209 (563)
                             .++|=+.. -+.|..-||||.-|++=.|+=.++          +..++...-+-...=++...|-  .++|.|
T Consensus       262 -------Rv~rwLde~~P~lafyrl~lD~Pr~P~l~lsrQ----------R~~~~~a~r~~l~~~Lr~l~PY--a~~V~i  322 (423)
T TIGR02554       262 -------RVSRWLDEARPELAFYRLRLDEPRKPELWLSRQ----------RSALDKAARERLIGELRRLMPY--AEDVRI  322 (423)
T ss_pred             -------HHHHHHHCCCCCEEEEEEEECCCCCCCEEEECC----------CCHHHHHHHHHHHHHHHHHCCC--CCCEEE
T ss_conf             -------356423006883468998607888970787158----------8841389999999987765672--220028


Q ss_pred             EECCCCEE
Q ss_conf             82898350
Q gi|254780695|r  210 LDSTGKLL  217 (563)
Q Consensus       210 vD~~G~~L  217 (563)
                      ||.+-...
T Consensus       323 ~~~dd~a~  330 (423)
T TIGR02554       323 IDVDDEAA  330 (423)
T ss_pred             EECCHHHH
T ss_conf             85365889


No 70 
>PRK00269 zipA cell division protein ZipA; Reviewed
Probab=44.42  E-value=20  Score=15.22  Aligned_cols=27  Identities=7%  Similarity=-0.148  Sum_probs=17.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             889999999999999999999846998
Q gi|254780695|r   21 RILILASVILVPIMLFMAARFFVNSPH   47 (563)
Q Consensus        21 ~ki~~~~~~~~~i~~~~~~~~~~~~p~   47 (563)
                      -|.++|++++++|+++++=.||..+-.
T Consensus         5 LR~~LIIVGalaI~AlLlHGw~r~Re~   31 (295)
T PRK00269          5 LREWLIVIGIIVIAGILFDGWRRMRGG   31 (295)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHEECCCC
T ss_conf             456999999999999998650211354


No 71 
>COG2268 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.10  E-value=21  Score=15.19  Aligned_cols=19  Identities=26%  Similarity=0.442  Sum_probs=11.0

Q ss_pred             HHCCCCEEECCCCCEEEEC
Q ss_conf             9779929991899779951
Q gi|254780695|r   68 SEANIDFRISDNGSSISVP   86 (563)
Q Consensus        68 ~~~gI~y~~~~~g~~I~Vp   86 (563)
                      ++.|-.|++-..|+.|..|
T Consensus        55 ~~~g~~~~vV~gGg~~v~P   73 (548)
T COG2268          55 DEAGGGQKVVRGGGAIVMP   73 (548)
T ss_pred             CCCCCCCCEEECCCEEEEC
T ss_conf             4345775378558648843


No 72 
>pfam09976 DUF2133 Uncharacterized protein conserved in bacteria (DUF2133). This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=43.85  E-value=21  Score=15.17  Aligned_cols=33  Identities=12%  Similarity=0.100  Sum_probs=18.1

Q ss_pred             HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             8999999998640698788999999999999999999984
Q gi|254780695|r    4 LDQLLQFFKSGTSLGRTRILILASVILVPIMLFMAARFFV   43 (563)
Q Consensus         4 ~~~l~~~~~~~~~l~~~~ki~~~~~~~~~i~~~~~~~~~~   43 (563)
                      .++++.||++..+       .++++++++++++++.-+|.
T Consensus         3 ~e~ik~wwk~~G~-------~ii~~vvl~~~g~~G~~~w~   35 (43)
T pfam09976         3 LERLKAWWKRYGK-------WIIVGAVLALAGVAGWRGWQ   35 (43)
T ss_pred             HHHHHHHHHHHCH-------HHHHHHHHHHHHHHHHHHHH
T ss_conf             8899999998179-------99999999999999999999


No 73 
>PRK13952 mscL large-conductance mechanosensitive channel; Provisional
Probab=43.74  E-value=21  Score=15.15  Aligned_cols=30  Identities=23%  Similarity=0.445  Sum_probs=17.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999999778752
Q gi|254780695|r  435 HFATVINALVFLVGTLLVTFLGLHALRRLH  464 (563)
Q Consensus       435 ~~~~~~~~~~~~l~~lll~~~vl~~l~~~~  464 (563)
                      .++.++..++-.++..+.+|++++++-+..
T Consensus        83 ~yG~fl~avInFlIiA~vvF~vVk~~nkl~  112 (143)
T PRK13952         83 AYGNFITVLINFLILAFIIFLMVKAINRLR  112 (143)
T ss_pred             EHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             099999999999999999999999999987


No 74 
>pfam06408 consensus
Probab=43.54  E-value=7.4  Score=18.16  Aligned_cols=29  Identities=28%  Similarity=0.132  Sum_probs=16.5

Q ss_pred             CCCCEEEEEECCCCCCH-HHHHHHHHHHHH
Q ss_conf             58715999706877898-899999999986
Q gi|254780695|r  169 ARPTASVMIRAINPSVY-KSAEAIRHLVAA  197 (563)
Q Consensus       169 ~~~sASV~l~~~~~l~~-~qv~~I~~lVa~  197 (563)
                      .-|||-|.--..||+-. --=+|+.++.+.
T Consensus       143 ~GpTAv~~hGANPGlVShfvKqaLldiA~~  172 (471)
T pfam06408       143 GGPTAVSTCGANPGMVSWFVKQALVDLAAD  172 (471)
T ss_pred             CCCEEEEECCCCCHHHHHHHHHHHHHHHHH
T ss_conf             998077746899518999999999999998


No 75 
>PRK08343 secD preprotein translocase subunit SecD; Reviewed
Probab=43.27  E-value=21  Score=15.11  Aligned_cols=17  Identities=12%  Similarity=0.059  Sum_probs=10.9

Q ss_pred             CCCCHHHHHHHHHHHHH
Q ss_conf             34698999999998643
Q gi|254780695|r  378 QGKIDSYLAEINKIVSA  394 (563)
Q Consensus       378 ~~~~~eel~~I~~lV~~  394 (563)
                      ...+.+|-+++..+.++
T Consensus       216 g~~~~~eA~~LA~~L~s  232 (414)
T PRK08343        216 TEEAEEEAKELYIHLRA  232 (414)
T ss_pred             CCCCHHHHHHHHHHHHC
T ss_conf             86549999999999865


No 76 
>TIGR00915 2A0602 RND transporter, hydrophobe/amphiphile efflux-1 (HAE1) family; InterPro: IPR004764   Hydrophobe/amphiphile efflux-1 HAE1 is involved in toxin production and resistance processes.; GO: 0005215 transporter activity, 0006810 transport, 0016021 integral to membrane.
Probab=43.18  E-value=21  Score=15.10  Aligned_cols=89  Identities=12%  Similarity=0.165  Sum_probs=66.0

Q ss_pred             CCCCCCCEEEEEECCCCCCHHHH-HHHHHHHHHHHHCCCC----CCEEEEECCCCEEEC-C--CCCCCCCHHHHHHHHHH
Q ss_conf             55558715999706877898899-9999999865401883----526998289835003-6--76533324799999999
Q gi|254780695|r  166 KIGARPTASVMIRAINPSVYKSA-EAIRHLVAAAVPNLDM----GDVTVLDSTGKLLTA-N--EMERNILGKSLSIVQAI  237 (563)
Q Consensus       166 ~~~~~~sASV~l~~~~~l~~~qv-~~I~~lVa~sV~gL~~----e~VtVvD~~G~~L~~-~--~~~~~~~~~~~~~~~~~  237 (563)
                      +....-++||+||-.++-+++-+ --++|=++.+-|.|..    ..|+|.=...+.|-- .  ++++..+      +..+
T Consensus        82 ~s~s~G~~~itlTF~~gtd~DiAqVqVQNkL~~A~~~LP~~Vq~~Gv~V~K~~~~fLlv~~l~s~dG~~~------~~dl  155 (1058)
T TIGR00915        82 ESDSDGSATITLTFEQGTDPDIAQVQVQNKLQLATPLLPQEVQRQGVRVEKASSNFLLVIGLVSDDGSMD------KEDL  155 (1058)
T ss_pred             CCCCCCEEEEEEEECCCCCCCHHHHHHHHHHHHHHHCCCHHHHHCCCEEEEECCCEEEEEEEECCCCCCC------HHHH
T ss_conf             2057612899998538989550365664469887310516773088169973253389999974887657------7899


Q ss_pred             HHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             99999999988775408780699
Q gi|254780695|r  238 QHEIEMNINKALAAFLGVDNFRS  260 (563)
Q Consensus       238 E~~~~~kI~~~L~~i~G~~~v~v  260 (563)
                      -.++.+++++-|+++-|.|+|++
T Consensus       156 ~dY~~s~~~d~~sR~~GVGdv~~  178 (1058)
T TIGR00915       156 SDYVASNLVDPISRLEGVGDVQL  178 (1058)
T ss_pred             HHHHHHHCCCCCCEECCCCEEEE
T ss_conf             99999636773211057630788


No 77 
>PRK12933 secD preprotein translocase subunit SecD; Reviewed
Probab=42.47  E-value=22  Score=15.03  Aligned_cols=195  Identities=14%  Similarity=0.165  Sum_probs=84.0

Q ss_pred             CCCCCEEECCCCCHHHHHHHHHHHHHCCCCEE-ECCCCCEEEEC--HH-HHHHHHHHHHHCCCCC---------CCCCCH
Q ss_conf             69982450389998999999999997799299-91899779951--89-9999999999769988---------776632
Q gi|254780695|r   44 NSPHYDNLYVKLEVSDVNRISVALSEANIDFR-ISDNGSSISVP--SS-MVGKARIHLAAQGLPS---------SSSNSG  110 (563)
Q Consensus        44 ~~p~y~~L~~~l~~~d~~~i~~~L~~~gI~y~-~~~~g~~I~Vp--~~-~~~~~r~~La~~glp~---------~~~~~g  110 (563)
                      ..|.-+.-...-...+..++.+.|+++||.|+ +..+++.|++-  .. +=-+||-.|... |..         ...|.|
T Consensus        39 ~~pAvQIs~~~~~~~~~~~~~~~L~~~~I~~~~~~~~~~~~~irf~~~~~Ql~Ak~~l~~~-l~~~~~VALnlap~tP~W  117 (604)
T PRK12933         39 EDAAVQVSAKAGLLLTPVALRQLLQAQGINVKRIDQKEGKTLIVLDDDSQQSQAKTLLSSM-VKEPKELTLSLASAAPSW  117 (604)
T ss_pred             CCCEEEEECCCCCCCCHHHHHHHHHHCCCCCCEEEECCCEEEEEECCHHHHHHHHHHHHHH-HCCCCEEEEECCCCCHHH
T ss_conf             9873898668777578999999999779986325751882899979888899999999987-288827998679998199


Q ss_pred             HHHHCCCCCC-------CCCHHHHHHHHHHH-------HHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCCEEEE
Q ss_conf             5653058884-------25999999999999-------999999999605763148999983366655555558715999
Q gi|254780695|r  111 YELFDKVNSF-------GLTSFMQEITRVRA-------LEGEIARTIQSISGIVAARVHIVMPDMGSFRKIGARPTASVM  176 (563)
Q Consensus       111 ~el~d~~~~~-------g~T~~~~~~~~~ra-------legeL~rtI~~~~~V~~ArV~l~~p~~~~f~~~~~~~sASV~  176 (563)
                      ..-+.- .++       |=+.|.-++....+       +..++.+.++. ..|+...+...             ....+.
T Consensus       118 L~~iGa-~Pm~LGLDLrGGvhfLLeVD~~~av~~rle~~~~dir~~LR~-~~Ir~~~i~~~-------------~~~~i~  182 (604)
T PRK12933        118 LQNMGF-SPIKLGLDLRGGVQFLLDVDVDPVYQEQRDALVDSLRQFLRE-QGIRGVSVRLD-------------DTDQLN  182 (604)
T ss_pred             HHHCCC-CCCCCCEECCCCEEEEEEECHHHHHHHHHHHHHHHHHHHHHH-CCCCCCEEEEC-------------CCCEEE
T ss_conf             996699-773134314784189999748999999999899999999997-59863114654-------------798699


Q ss_pred             EECCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCEEECC-CCCCCCCHHHHHHHHHHHHHHHHHHHHH--HHHH-
Q ss_conf             70687789889999999998654018835269982898350036-7653332479999999999999999988--7754-
Q gi|254780695|r  177 IRAINPSVYKSAEAIRHLVAAAVPNLDMGDVTVLDSTGKLLTAN-EMERNILGKSLSIVQAIQHEIEMNINKA--LAAF-  252 (563)
Q Consensus       177 l~~~~~l~~~qv~~I~~lVa~sV~gL~~e~VtVvD~~G~~L~~~-~~~~~~~~~~~~~~~~~E~~~~~kI~~~--L~~i-  252 (563)
                      +.+.   +.++...+..++....|++.     +....++.+.-. .+..-..-.....+|. -+-+++||..+  -+|. 
T Consensus       183 v~~~---~~~~~~~a~~~l~~~~~~~~-----~~~~~~~~l~l~~se~~~~~i~~~Av~Q~-ieilRnRVdeLGVsEP~I  253 (604)
T PRK12933        183 VTLP---DNDARSAVRQFIQQNYPNWQ-----VTNSDDRGLQLKLSQQEKTKLRNLTVQQN-LQIMRSRIEELGITEALV  253 (604)
T ss_pred             EEEC---CHHHHHHHHHHHHHHCCCEE-----EEECCCCEEEEEECHHHHHHHHHHHHHHH-HHHHHHHHHHCCCCCCEE
T ss_conf             9968---98899999999985099718-----97469966999989999999999999999-999997653006788717


Q ss_pred             --CCCCEEEEEEE
Q ss_conf             --08780699988
Q gi|254780695|r  253 --LGVDNFRSAVV  263 (563)
Q Consensus       253 --~G~~~v~v~V~  263 (563)
                        -|.+++.|+.-
T Consensus       254 QrQG~dRIvVqLP  266 (604)
T PRK12933        254 QRQGEHRIRIELP  266 (604)
T ss_pred             EEECCCEEEEECC
T ss_conf             9977957999889


No 78 
>pfam09580 Spore_YhcN_YlaJ Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ). This entry contains YhcN and YlaJ, which are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic, 40-residue C-terminal domain.
Probab=42.13  E-value=22  Score=14.99  Aligned_cols=73  Identities=22%  Similarity=0.186  Sum_probs=50.9

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCC--CC
Q ss_conf             9999999999999996057631489999833666555555587159997068778988999999999865401883--52
Q gi|254780695|r  129 ITRVRALEGEIARTIQSISGIVAARVHIVMPDMGSFRKIGARPTASVMIRAINPSVYKSAEAIRHLVAAAVPNLDM--GD  206 (563)
Q Consensus       129 ~~~~ralegeL~rtI~~~~~V~~ArV~l~~p~~~~f~~~~~~~sASV~l~~~~~l~~~qv~~I~~lVa~sV~gL~~--e~  206 (563)
                      ..+..-+-..|++-+.++++|++|+|-.+            .-.|-|-+++... ......-|+.=|+.+|....|  .+
T Consensus        61 ~~~~~~~A~~i~~~~~~~~~V~dA~vvVt------------~~~a~V~v~~~~~-~~~~~~~ik~~V~~~v~~~~p~~~~  127 (169)
T pfam09580        61 NIERGEVADKIARRVAKLPEVEDAAVVVT------------GEEALVAVDLDNG-ERSLTEEIKKQVKKAVKSVDPRIYN  127 (169)
T ss_pred             CCCHHHHHHHHHHHHHCCCCCCEEEEEEE------------CCEEEEEEECCCC-CHHHHHHHHHHHHHHHHHCCCCCCE
T ss_conf             72099999999999961788644689998------------9979999973886-4035899999999999840888656


Q ss_pred             EEEEECCC
Q ss_conf             69982898
Q gi|254780695|r  207 VTVLDSTG  214 (563)
Q Consensus       207 VtVvD~~G  214 (563)
                      |-|++...
T Consensus       128 VyVs~D~d  135 (169)
T pfam09580       128 VYVSADPD  135 (169)
T ss_pred             EEEECCHH
T ss_conf             99966989


No 79 
>PRK10617 cytochrome c-type protein NapC; Provisional
Probab=41.32  E-value=23  Score=14.91  Aligned_cols=128  Identities=14%  Similarity=0.143  Sum_probs=51.0

Q ss_pred             HHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHH---------CCCCCEEECCCCCHHHHHHHHHHHHHCCCCEE
Q ss_conf             999999998640698788999999999999999999984---------69982450389998999999999997799299
Q gi|254780695|r    5 DQLLQFFKSGTSLGRTRILILASVILVPIMLFMAARFFV---------NSPHYDNLYVKLEVSDVNRISVALSEANIDFR   75 (563)
Q Consensus         5 ~~l~~~~~~~~~l~~~~ki~~~~~~~~~i~~~~~~~~~~---------~~p~y~~L~~~l~~~d~~~i~~~L~~~gI~y~   75 (563)
                      ..++.+|..|+.=+   ++.++++  +++++++++++|.         ++..+=  .++=+-.+  .+.+.+++ -|-|.
T Consensus         9 ~~~~r~w~~~~~ps---~~~lg~l--~~iG~~~Gii~w~gf~~~me~Tnt~eFC--iSCH~M~~--~vy~Ey~~-siHy~   78 (200)
T PRK10617          9 GLIKRLWKWWRTPS---RLALGTL--LLIGFVGGIIFWGGFNTGMEKANTEEFC--ISCHEMRN--TVYQEYMD-TVHYN   78 (200)
T ss_pred             CHHHHHHHHHCCCH---HHHHHHH--HHHHHHHHHHHHHHHHHHHHHHCCCCHH--HHHHCCCH--HHHHHHHC-CCCCC
T ss_conf             59999999975815---7799999--9999999999999999999982884144--58864768--78999643-78877


Q ss_pred             ECCCCCE-----EEECHHHHHHHHHH-HHHCCCCCCCCCCHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             9189977-----99518999999999-99769988776632565305888425999999999999999999999605763
Q gi|254780695|r   76 ISDNGSS-----ISVPSSMVGKARIH-LAAQGLPSSSSNSGYELFDKVNSFGLTSFMQEITRVRALEGEIARTIQSISGI  149 (563)
Q Consensus        76 ~~~~g~~-----I~Vp~~~~~~~r~~-La~~glp~~~~~~g~el~d~~~~~g~T~~~~~~~~~ralegeL~rtI~~~~~V  149 (563)
                      -. .|-+     =-||.+-.+...-+ -|++.       +..+++.+   +.+-| -+..+..+.-+.+-+| .+.-|..
T Consensus        79 N~-sGVrA~C~DCHVPh~~~~k~~rKi~Aske-------v~~~~~g~---IdT~E-KFe~~R~~mA~~~W~r-mkandS~  145 (200)
T PRK10617         79 NR-SGVRATCPDCHVPHEWGPKMIRKIKASKE-------LYGKIFGL---IDTPQ-KFEAHRLTMAQNEWRR-MKDNNSQ  145 (200)
T ss_pred             CC-CCCCCCCCCCCCCCCCHHHHHHHHHHHHH-------HHHHHHCC---CCCHH-HHHHHHHHHHHHHHHH-HHCCCCH
T ss_conf             77-88611077767884319999999999999-------99998357---89878-9998599999999999-8627862


Q ss_pred             CEEEEE
Q ss_conf             148999
Q gi|254780695|r  150 VAARVH  155 (563)
Q Consensus       150 ~~ArV~  155 (563)
                      +--.-|
T Consensus       146 eCRnCH  151 (200)
T PRK10617        146 ECRNCH  151 (200)
T ss_pred             HHCCCC
T ss_conf             100416


No 80 
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=41.19  E-value=23  Score=14.90  Aligned_cols=37  Identities=24%  Similarity=0.201  Sum_probs=23.8

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHH---CCCCCCEEEEE
Q ss_conf             99706877898899999999986540---18835269982
Q gi|254780695|r  175 VMIRAINPSVYKSAEAIRHLVAAAVP---NLDMGDVTVLD  211 (563)
Q Consensus       175 V~l~~~~~l~~~qv~~I~~lVa~sV~---gL~~e~VtVvD  211 (563)
                      |-+++..|++.+|-+.+..=|..|+-   |-.+|+|.|+=
T Consensus         4 I~V~m~eGRt~EQK~~l~~~vT~a~~~~~g~p~e~V~Vii   43 (61)
T PRK02220          4 VHIELIEGRTEEQLKALVKDVTAAVSKNTGAPAEHIHVII   43 (61)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHHHHHCCCHHHEEEEE
T ss_conf             9999838999999999999999999998198956889999


No 81 
>COG2332 CcmE Cytochrome c-type biogenesis protein CcmE [Posttranslational modification, protein turnover, chaperones]
Probab=40.61  E-value=23  Score=14.84  Aligned_cols=34  Identities=15%  Similarity=0.208  Sum_probs=26.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEECC
Q ss_conf             7889999999999999999999846998245038
Q gi|254780695|r   20 TRILILASVILVPIMLFMAARFFVNSPHYDNLYV   53 (563)
Q Consensus        20 ~~ki~~~~~~~~~i~~~~~~~~~~~~p~y~~L~~   53 (563)
                      ++|+.+++++++++++.+.++++.-+..-..+|.
T Consensus         6 r~Rl~~il~~~a~l~~a~~l~Lyal~~ni~~fy~   39 (153)
T COG2332           6 RKRLWIILAGLAGLALAVGLVLYALRSNIDYFYT   39 (153)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEC
T ss_conf             3148999999999999999987642037508987


No 82 
>PRK09731 putative general secretion pathway protein YghD; Provisional
Probab=40.11  E-value=24  Score=14.79  Aligned_cols=32  Identities=3%  Similarity=-0.071  Sum_probs=21.4

Q ss_pred             HHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             98640698788999999999999999999984
Q gi|254780695|r   12 KSGTSLGRTRILILASVILVPIMLFMAARFFV   43 (563)
Q Consensus        12 ~~~~~l~~~~ki~~~~~~~~~i~~~~~~~~~~   43 (563)
                      ..|.+.+++-+.++++.++++++++++-.+|.
T Consensus        27 q~w~grspREqrLv~~~gavLll~i~YwgiWq   58 (178)
T PRK09731         27 QHLAGRSPREKGMLLAAVVFLFSVGYYVLIWQ   58 (178)
T ss_pred             HHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             98668988999999987999999999999883


No 83 
>PRK05677 acyl-CoA synthetase; Validated
Probab=39.59  E-value=24  Score=14.74  Aligned_cols=18  Identities=6%  Similarity=-0.112  Sum_probs=8.7

Q ss_pred             CCCCCEEECCCCCHHHHH
Q ss_conf             699824503899989999
Q gi|254780695|r   44 NSPHYDNLYVKLEVSDVN   61 (563)
Q Consensus        44 ~~p~y~~L~~~l~~~d~~   61 (563)
                      ..--++++...+...+..
T Consensus        98 ~Gav~vplnp~~~~~el~  115 (562)
T PRK05677         98 AGLIVVNTNPLYTAREME  115 (562)
T ss_pred             HCEEEEECCCCCCHHHHH
T ss_conf             495998229889999999


No 84 
>PRK06155 crotonobetaine/carnitine-CoA ligase; Provisional
Probab=39.40  E-value=24  Score=14.72  Aligned_cols=23  Identities=9%  Similarity=-0.091  Sum_probs=12.3

Q ss_pred             HCCCCCEEECCCCCHHHHHHHHH
Q ss_conf             46998245038999899999999
Q gi|254780695|r   43 VNSPHYDNLYVKLEVSDVNRISV   65 (563)
Q Consensus        43 ~~~p~y~~L~~~l~~~d~~~i~~   65 (563)
                      ...--|++|+..+...+...+..
T Consensus       105 ~~Gav~vpl~~~~~~~~l~~~l~  127 (552)
T PRK06155        105 WLGAIAVPINTALRGPQLSHILR  127 (552)
T ss_pred             HHCEEEEEECCCCCHHHHHHHHH
T ss_conf             84919996789899999999998


No 85 
>PRK12406 acyl-CoA synthetase; Provisional
Probab=39.35  E-value=24  Score=14.72  Aligned_cols=29  Identities=7%  Similarity=-0.114  Sum_probs=19.8

Q ss_pred             HHHHHHCCCCCEEECCCCCHHHHHHHHHH
Q ss_conf             99998469982450389998999999999
Q gi|254780695|r   38 AARFFVNSPHYDNLYVKLEVSDVNRISVA   66 (563)
Q Consensus        38 ~~~~~~~~p~y~~L~~~l~~~d~~~i~~~   66 (563)
                      ++..|...-.|++|...+.+.+...++..
T Consensus        54 ~lA~~~~Gav~vpl~~~~~~~~l~~~l~~   82 (510)
T PRK12406         54 AYAAMRLGAYAVPVNWHFKPEEIAYILED   82 (510)
T ss_pred             HHHHHHHCCEEEEECCCCCHHHHHHHHHH
T ss_conf             99999859299987999999999999997


No 86 
>PRK03592 haloalkane dehalogenase; Provisional
Probab=38.96  E-value=23  Score=14.85  Aligned_cols=19  Identities=16%  Similarity=0.419  Sum_probs=16.7

Q ss_pred             HHHHCHHHHHHHHHHHHHH
Q ss_conf             9886999899999999863
Q gi|254780695|r  534 MIEINEERFAKILRKWARS  552 (563)
Q Consensus       534 lv~e~Pe~vA~vLR~WL~e  552 (563)
                      .-.|+||+++++|+.||+.
T Consensus       269 ~~~E~Pe~v~~~i~~FL~~  287 (294)
T PRK03592        269 LQEDSPDEIGAAIAAWLRR  287 (294)
T ss_pred             HHHCCHHHHHHHHHHHHHH
T ss_conf             2752999999999999974


No 87 
>pfam04415 DUF515 Protein of unknown function (DUF515). Family of hypothetical Archaeal proteins.
Probab=38.94  E-value=25  Score=14.67  Aligned_cols=22  Identities=27%  Similarity=0.540  Sum_probs=12.0

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9878899999999999999999
Q gi|254780695|r   18 GRTRILILASVILVPIMLFMAA   39 (563)
Q Consensus        18 ~~~~ki~~~~~~~~~i~~~~~~   39 (563)
                      .+++||++|++++.++++++++
T Consensus        27 err~riiIga~il~iIIl~~~~   48 (416)
T pfam04415        27 ERRKRLIIGALVLSVIILLLVF   48 (416)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
T ss_conf             3344100689999999999999


No 88 
>TIGR00063 folE GTP cyclohydrolase I; InterPro: IPR001474   GTP cyclohydrolase I (3.5.4.16 from EC) catalyzes the biosynthesis of formic acid and dihydroneopterin triphosphate from GTP. This reaction is the first step in the biosynthesis of tetrahydrofolate in prokaryotes, of tetrahydrobiopterin in vertebrates, and of pteridine-containing pigments in insects. The comparison of the sequence of the enzyme from bacterial and eukaryotic sources shows that the structure of this enzyme has been extremely well conserved throughout evolution .; GO: 0003934 GTP cyclohydrolase I activity, 0019438 aromatic compound biosynthetic process, 0005737 cytoplasm.
Probab=38.81  E-value=25  Score=14.66  Aligned_cols=37  Identities=19%  Similarity=0.166  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEE
Q ss_conf             9999999999999999988775408780699988443
Q gi|254780695|r  230 SLSIVQAIQHEIEMNINKALAAFLGVDNFRSAVVAEL  266 (563)
Q Consensus       230 ~~~~~~~~E~~~~~kI~~~L~~i~G~~~v~v~V~~~l  266 (563)
                      -..-+-|+.+.|.++|...|.-|+++.+|.|.+.|.-
T Consensus       107 ~farRlQvQERLT~QIa~a~~eiL~p~gVaVv~eA~H  143 (183)
T TIGR00063       107 MFARRLQVQERLTKQIAEALQEILEPRGVAVVVEATH  143 (183)
T ss_pred             HHHCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEEEE
T ss_conf             9862651468899999999998737898289986567


No 89 
>PRK09841 cryptic autophosphorylating protein tyrosine kinase Etk; Provisional
Probab=37.96  E-value=25  Score=14.57  Aligned_cols=40  Identities=15%  Similarity=0.345  Sum_probs=18.1

Q ss_pred             CHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEE
Q ss_conf             6789999999986406987889999999999999999999846998245
Q gi|254780695|r    2 AILDQLLQFFKSGTSLGRTRILILASVILVPIMLFMAARFFVNSPHYDN   50 (563)
Q Consensus         2 ~~~~~l~~~~~~~~~l~~~~ki~~~~~~~~~i~~~~~~~~~~~~p~y~~   50 (563)
                      ||.+-+.-+|++|       ++++++.++++++  .+++.+...|.|..
T Consensus        19 DL~~ll~iL~r~~-------~~Ii~v~~~~~~l--a~~y~~~~tPiY~A   58 (726)
T PRK09841         19 DLLRLVGELWDHR-------KFIISVTALFTLI--AVAYSLLSTPIYQA   58 (726)
T ss_pred             CHHHHHHHHHHHH-------HHHHHHHHHHHHH--HHHHHHHCCCEEEE
T ss_conf             5999999999877-------9999999999999--99999756984788


No 90 
>PRK05529 cell division protein FtsQ; Provisional
Probab=37.38  E-value=26  Score=14.51  Aligned_cols=111  Identities=15%  Similarity=0.085  Sum_probs=61.0

Q ss_pred             HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEECCCCCHHHHHHHHHHHHHCCCCEEECCCCCEEEEC
Q ss_conf             99999986406987889999999999999999999846998245038999899999999999779929991899779951
Q gi|254780695|r    7 LLQFFKSGTSLGRTRILILASVILVPIMLFMAARFFVNSPHYDNLYVKLEVSDVNRISVALSEANIDFRISDNGSSISVP   86 (563)
Q Consensus         7 l~~~~~~~~~l~~~~ki~~~~~~~~~i~~~~~~~~~~~~p~y~~L~~~l~~~d~~~i~~~L~~~gI~y~~~~~g~~I~Vp   86 (563)
                      ..+-.++|+.-.++|++.+.+++..+++++++++..+.+|    ||.                  +. ++.-.| .=.++
T Consensus        20 ~~~~~~~~~~~~r~r~~~~~~~~g~v~~l~~~v~~~~fSp----ll~------------------v~-~I~V~G-~~~~~   75 (255)
T PRK05529         20 DYERVRRFTTRIRRRFILLACAVGAVLTLLLFVMLSAYSP----LLA------------------LR-SIEVAG-NMRVK   75 (255)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC----CEE------------------EE-EEEEEC-CCCCC
T ss_conf             8999999999888888989999999999999999854175----469------------------88-999989-83479


Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCC-C
Q ss_conf             899999999999769988776632565305888425999999999999999999999605763148999983366655-5
Q gi|254780695|r   87 SSMVGKARIHLAAQGLPSSSSNSGYELFDKVNSFGLTSFMQEITRVRALEGEIARTIQSISGIVAARVHIVMPDMGSF-R  165 (563)
Q Consensus        87 ~~~~~~~r~~La~~glp~~~~~~g~el~d~~~~~g~T~~~~~~~~~ralegeL~rtI~~~~~V~~ArV~l~~p~~~~f-~  165 (563)
                      .+++-+      ..+.|. |.+    |+ .   +  .            ..++++.|+.++.|++|+|.-..|..=.. +
T Consensus        76 ~~~V~~------a~~~~~-G~p----L~-~---v--d------------~~~v~~~l~~lp~V~sa~V~r~~P~~l~I~V  126 (255)
T PRK05529         76 PQDIVA------ALRDQF-GKP----LP-L---V--D------------PETVRKKLAAFPLIRSYSVESKPPGTIVVRV  126 (255)
T ss_pred             HHHHHH------HHCCCC-CCE----EE-E---E--C------------HHHHHHHHHCCCCEEEEEEEECCCCCEEEEE
T ss_conf             999999------865878-985----13-8---8--6------------9999998744998558999963979269999


Q ss_pred             CCCCC
Q ss_conf             55558
Q gi|254780695|r  166 KIGAR  170 (563)
Q Consensus       166 ~~~~~  170 (563)
                      .+++|
T Consensus       127 ~ER~P  131 (255)
T PRK05529        127 VERVP  131 (255)
T ss_pred             EEEEE
T ss_conf             95052


No 91 
>PRK11556 multidrug efflux system subunit MdtA; Provisional
Probab=37.36  E-value=26  Score=14.51  Aligned_cols=41  Identities=17%  Similarity=0.233  Sum_probs=19.7

Q ss_pred             HHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEE
Q ss_conf             653058884259999999999999999999996057631489999
Q gi|254780695|r  112 ELFDKVNSFGLTSFMQEITRVRALEGEIARTIQSISGIVAARVHI  156 (563)
Q Consensus       112 el~d~~~~~g~T~~~~~~~~~ralegeL~rtI~~~~~V~~ArV~l  156 (563)
                      .|+.+ ......+++......+.-+..|...-..+   +.|+.+|
T Consensus       153 ~L~~~-~~iS~~~ld~~~a~~~~A~A~l~~a~a~l---~~A~~~L  193 (415)
T PRK11556        153 QLAKT-NLVSRQELDAQQALVSETEGTIKADEAAV---ASAQLQL  193 (415)
T ss_pred             HHHHC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHH
T ss_conf             98765-99569999989999999999999999999---9998752


No 92 
>COG3149 PulM Type II secretory pathway, component PulM [Intracellular trafficking and secretion]
Probab=36.81  E-value=27  Score=14.46  Aligned_cols=31  Identities=6%  Similarity=-0.036  Sum_probs=20.9

Q ss_pred             HHHHCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             8640698788999999999999999999984
Q gi|254780695|r   13 SGTSLGRTRILILASVILVPIMLFMAARFFV   43 (563)
Q Consensus        13 ~~~~l~~~~ki~~~~~~~~~i~~~~~~~~~~   43 (563)
                      .|.+++++-|-++.+++++.++++.++.+|-
T Consensus        27 ~w~~~~PREr~mL~g~Ga~L~Lvi~Y~~~Wq   57 (181)
T COG3149          27 RWRGLPPRERKMLLGGGAFLLLVILYLLIWQ   57 (181)
T ss_pred             HHCCCCHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             9826991888899872699999999999836


No 93 
>PRK08455 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=36.59  E-value=17  Score=15.80  Aligned_cols=17  Identities=24%  Similarity=0.311  Sum_probs=10.3

Q ss_pred             HHHHHHHHHHHHHHHHH
Q ss_conf             99999999999998877
Q gi|254780695|r  234 VQAIQHEIEMNINKALA  250 (563)
Q Consensus       234 ~~~~E~~~~~kI~~~L~  250 (563)
                      +.++..++.++|..+|.
T Consensus       149 k~~Lr~ei~~~in~~l~  165 (180)
T PRK08455        149 KERLKDEIVGKLNEFLI  165 (180)
T ss_pred             HHHHHHHHHHHHHHHHC
T ss_conf             99999999999998736


No 94 
>PRK08276 acyl-CoA synthetase; Validated
Probab=36.26  E-value=27  Score=14.40  Aligned_cols=33  Identities=9%  Similarity=0.043  Sum_probs=20.0

Q ss_pred             HHHHHHCCCCCEEECCCCCHHHHHHHHHHHHHCCCC
Q ss_conf             999984699824503899989999999999977992
Q gi|254780695|r   38 AARFFVNSPHYDNLYVKLEVSDVNRISVALSEANID   73 (563)
Q Consensus        38 ~~~~~~~~p~y~~L~~~l~~~d~~~i~~~L~~~gI~   73 (563)
                      ++..|...-.|++|-..+...+...+.   +..+..
T Consensus        66 ~lA~~~~Ga~~vpl~~~~~~~~l~~il---~~~~~~   98 (507)
T PRK08276         66 MWAARRSGLYYVPINWHLTAAEIAYIV---DDSGAK   98 (507)
T ss_pred             HHHHHHHCCEEEEECCCCCHHHHHHHH---HHCCCC
T ss_conf             999998697999638889999999999---855997


No 95 
>COG0841 AcrB Cation/multidrug efflux pump [Defense mechanisms]
Probab=36.11  E-value=27  Score=14.38  Aligned_cols=26  Identities=4%  Similarity=0.167  Sum_probs=13.7

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEEE
Q ss_conf             99999999999999960576314899
Q gi|254780695|r  129 ITRVRALEGEIARTIQSISGIVAARV  154 (563)
Q Consensus       129 ~~~~ralegeL~rtI~~~~~V~~ArV  154 (563)
                      .......+..|.+-|.+++||.++.+
T Consensus       150 ~~l~~~~~~~l~~~L~~v~GV~~V~~  175 (1009)
T COG0841         150 SDLTDYAASNVRDELSRVPGVGSVQL  175 (1009)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCEEEEE
T ss_conf             99999999999998735999149997


No 96 
>PRK07771 consensus
Probab=35.40  E-value=28  Score=14.31  Aligned_cols=10  Identities=10%  Similarity=0.082  Sum_probs=5.1

Q ss_pred             HCCCCCCEEE
Q ss_conf             0188352699
Q gi|254780695|r  200 PNLDMGDVTV  209 (563)
Q Consensus       200 ~gL~~e~VtV  209 (563)
                      -+++++++..
T Consensus       215 ~~~~~~d~~l  224 (541)
T PRK07771        215 LGVSDADRVL  224 (541)
T ss_pred             CCCCCCCEEE
T ss_conf             4899887799


No 97 
>TIGR02742 TrbC_Ftype type-F conjugative transfer system pilin assembly protein TrbC; InterPro: IPR014113   This entry represents TrbC, a protein that is an essential component of the F-type conjugative pilus assembly system for the transfer of plasmid DNA , . The N-terminal portion of these proteins is heterogeneous. .
Probab=34.97  E-value=18  Score=15.51  Aligned_cols=46  Identities=17%  Similarity=0.225  Sum_probs=21.4

Q ss_pred             EEEEECCCCCC--CCCCCCCCEEEEEECC-CCCCHHHHHHHHHHHHHHH
Q ss_conf             99983366655--5555587159997068-7789889999999998654
Q gi|254780695|r  154 VHIVMPDMGSF--RKIGARPTASVMIRAI-NPSVYKSAEAIRHLVAAAV  199 (563)
Q Consensus       154 V~l~~p~~~~f--~~~~~~~sASV~l~~~-~~l~~~qv~~I~~lVa~sV  199 (563)
                      |.+.||++.++  ..+.....|+++|+-- ++--.+.++.|..|+....
T Consensus         5 vSfSMP~~~L~~l~~q~~~~g~p~VlRG~~~~~f~~T~~~i~~L~~~~~   53 (139)
T TIGR02742         5 VSFSMPEPLLKQLLDQAEKLGAPLVLRGLLDNGFKATVTAIQSLIKKGG   53 (139)
T ss_pred             EEEECCHHHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHHHCCC
T ss_conf             8630797899999999997189789706689888899999999973458


No 98 
>COG3583 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.84  E-value=28  Score=14.25  Aligned_cols=60  Identities=17%  Similarity=0.149  Sum_probs=32.8

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEECCC---CCHHHHHHHHHHHHHCCCCEEEC
Q ss_conf             9878899999999999999999998469982450389---99899999999999779929991
Q gi|254780695|r   18 GRTRILILASVILVPIMLFMAARFFVNSPHYDNLYVK---LEVSDVNRISVALSEANIDFRIS   77 (563)
Q Consensus        18 ~~~~ki~~~~~~~~~i~~~~~~~~~~~~p~y~~L~~~---l~~~d~~~i~~~L~~~gI~y~~~   77 (563)
                      ++..-++++..++.+.+++++.+.-.+..+-.+-+.|   +...-++.+.+.|.++|+.|.=.
T Consensus        10 s~s~~~~l~~g~~l~v~~~a~~~~~~tk~~vtv~v~Ge~~~v~T~a~tV~d~l~e~G~kv~d~   72 (309)
T COG3583          10 SKSKMLRLAAGLLLVVLLIAGGVAEATKKTVTVTVDGEKMLVKTHASTVIDLLEEAGIKVGDQ   72 (309)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHCEEEEEECCEEEEEEHHHHHHHHHHHHCCCCCCCC
T ss_conf             455037788889999999876788750203899987857232010446889998609663431


No 99 
>COG1464 NlpA ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]
Probab=34.73  E-value=29  Score=14.24  Aligned_cols=102  Identities=18%  Similarity=0.237  Sum_probs=44.9

Q ss_pred             CCCEEEECHHH--HHHHHHHHHHCCCCCCCCCCHHHHHCCCCCCCCCHHH--HHHHHHHHHHHHHHHHHHHCCCCCEEEE
Q ss_conf             99779951899--9999999997699887766325653058884259999--9999999999999999960576314899
Q gi|254780695|r   79 NGSSISVPSSM--VGKARIHLAAQGLPSSSSNSGYELFDKVNSFGLTSFM--QEITRVRALEGEIARTIQSISGIVAARV  154 (563)
Q Consensus        79 ~g~~I~Vp~~~--~~~~r~~La~~glp~~~~~~g~el~d~~~~~g~T~~~--~~~~~~ralegeL~rtI~~~~~V~~ArV  154 (563)
                      +|.+|.||.+-  -.|+-..|..+||-+-.  .|..       .-.|..+  ++-+-..-.|-|=+++=++++.|.-|-+
T Consensus       127 ~GatIaiPNDpsN~gRAL~lL~~aGLIkLk--~~~~-------~~aT~~DI~eNPK~lki~EldAaqlpRaLddvD~AvI  197 (268)
T COG1464         127 DGATIAIPNDPTNEGRALLLLQKAGLIKLK--DGVN-------LLATPKDITENPKNLKIKELEAAQLPRALDDVDAAVI  197 (268)
T ss_pred             CCCEEECCCCCCCHHHHHHHHHHCCCEEEC--CCCC-------CCCCHHHHHHCCCCCEEEECCHHHCCCCCCCCCEEEE
T ss_conf             999898878987356799999987967976--8876-------5588878861944575687056756532035677987


Q ss_pred             EEE-------ECC-CCCCCCC-CCCCCEEEEEECCCCCCHHHHH
Q ss_conf             998-------336-6655555-5587159997068778988999
Q gi|254780695|r  155 HIV-------MPD-MGSFRKI-GARPTASVMIRAINPSVYKSAE  189 (563)
Q Consensus       155 ~l~-------~p~-~~~f~~~-~~~~sASV~l~~~~~l~~~qv~  189 (563)
                      +=.       -|+ +.+|.+. ...|-+-+++.-...-+...++
T Consensus       198 N~nyA~~AgL~p~kdai~~e~~~~spY~Niivvr~~d~d~~~ik  241 (268)
T COG1464         198 NTNYALQAGLNPKKDALFEEDKDSSPYVNIIVVREEDKDDPAVK  241 (268)
T ss_pred             CCHHHHHCCCCCCCCCEECCCCCCCCCEEEEEECCCCCCCHHHH
T ss_conf             43079775999120421414666786247999715566888999


No 100
>TIGR00106 TIGR00106 conserved hypothetical protein TIGR00106; InterPro: IPR002767   This entry contains several hypothetical proteins of unknown function found in archaebacteria, eukaryotes and eubacteria. The structures of YBL001c from Saccharomyces cerevisiae and its homologue MTH1187 from the archaea Methanobacterium thermoautotrophicum have been determined . These proteins have a ferredoxin-like alpha/beta sandwich structure with anti-parallel beta-sheets. Generally, they have two domains that form a single beta-sheet dimer, where two dimers pack sheet-to-sheet into a tetramer, some proteins having an extra C-terminal helix. .
Probab=34.13  E-value=29  Score=14.18  Aligned_cols=49  Identities=16%  Similarity=0.146  Sum_probs=37.8

Q ss_pred             CCCHHH-HHHHHHHHH----HCCCCEEECCCCCEEEE-CHHHHHHHHHHHHHCCC
Q ss_conf             999899-999999999----77992999189977995-18999999999997699
Q gi|254780695|r   54 KLEVSD-VNRISVALS----EANIDFRISDNGSSISV-PSSMVGKARIHLAAQGL  102 (563)
Q Consensus        54 ~l~~~d-~~~i~~~L~----~~gI~y~~~~~g~~I~V-p~~~~~~~r~~La~~gl  102 (563)
                      +-|-++ .+.+...|.    +.+|.|++++=|+.|-. |=+++-.+--..-...+
T Consensus        14 g~SvS~YVA~~~k~L~Gyqae~~lk~~l~~mGT~iEgEdld~l~~~~~~~Hea~~   68 (103)
T TIGR00106        14 GASVSSYVAAVIKVLKGYQAEEGLKYELHAMGTLIEGEDLDELFEAIKAIHEAVF   68 (103)
T ss_pred             CCCHHHHHHHHHHHHHHHCCCCCCCEEECCCCCEEECCCHHHHHHHHHHHHHHHH
T ss_conf             8777789999999985103445774344257652304697899999999865475


No 101
>PRK06188 acyl-CoA synthetase; Validated
Probab=33.95  E-value=29  Score=14.16  Aligned_cols=31  Identities=19%  Similarity=0.040  Sum_probs=18.4

Q ss_pred             HHHCCCCCEEECCCCCHHHHHHHHHHHHHCCCCE
Q ss_conf             9846998245038999899999999999779929
Q gi|254780695|r   41 FFVNSPHYDNLYVKLEVSDVNRISVALSEANIDF   74 (563)
Q Consensus        41 ~~~~~p~y~~L~~~l~~~d~~~i~~~L~~~gI~y   74 (563)
                      .+...-.|++|...+..++...+   |+..+...
T Consensus        80 ~~~~Gav~vpl~~~~~~~~~~~~---l~~~~~~~  110 (522)
T PRK06188         80 AQLLGLRRTALHPLGSLDDHAYI---LEDAEISA  110 (522)
T ss_pred             HHHHCEEEEEECCCCCHHHHHHH---HHHCCCCE
T ss_conf             99859599976899999999999---97359989


No 102
>PRK10927 essential cell division protein; Provisional
Probab=33.49  E-value=30  Score=14.11  Aligned_cols=80  Identities=14%  Similarity=0.209  Sum_probs=38.4

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHH--CCCCCEEEC-------CCC--CHHHHHHHHHHHHHCCCCEEECC---CCCEE
Q ss_conf             98788999999999999999999984--699824503-------899--98999999999997799299918---99779
Q gi|254780695|r   18 GRTRILILASVILVPIMLFMAARFFV--NSPHYDNLY-------VKL--EVSDVNRISVALSEANIDFRISD---NGSSI   83 (563)
Q Consensus        18 ~~~~ki~~~~~~~~~i~~~~~~~~~~--~~p~y~~L~-------~~l--~~~d~~~i~~~L~~~gI~y~~~~---~g~~I   83 (563)
                      +..-++++.+ +++++++|++.+||.  ++|+-.++.       .+|  -|+|.=..+..|+...|.+..-.   .|+.+
T Consensus        30 p~~s~~~~al-a~avlv~FiGGLyFith~K~e~~~~l~~~~~~~ngLPPKPEErWrYIKELEnRq~gV~~Ptepsagg~v  108 (319)
T PRK10927         30 PAVSPAMVAI-AAAVLVTFIGGLYFITHHKKEESETLQSQKVTGNGLPPKPEERWRYIKELESRQPGVRAPTEPSAGGEV  108 (319)
T ss_pred             CCCCHHHHHH-HHHHHHHHHCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCC
T ss_conf             8766589999-999999975004788705876677575667777789998278889999986158898789888777877


Q ss_pred             EECHHHHHHHHHHHH
Q ss_conf             951899999999999
Q gi|254780695|r   84 SVPSSMVGKARIHLA   98 (563)
Q Consensus        84 ~Vp~~~~~~~r~~La   98 (563)
                      ..+..--++-|-+|.
T Consensus       109 ~~~~qLT~EQRQLLe  123 (319)
T PRK10927        109 KTPEQLTPEQRQLLE  123 (319)
T ss_pred             CCCCCCCHHHHHHHH
T ss_conf             770217999999999


No 103
>PRK08316 acyl-CoA synthetase; Validated
Probab=33.46  E-value=30  Score=14.11  Aligned_cols=29  Identities=7%  Similarity=-0.152  Sum_probs=19.6

Q ss_pred             HHHHHHCCCCCEEECCCCCHHHHHHHHHH
Q ss_conf             99998469982450389998999999999
Q gi|254780695|r   38 AARFFVNSPHYDNLYVKLEVSDVNRISVA   66 (563)
Q Consensus        38 ~~~~~~~~p~y~~L~~~l~~~d~~~i~~~   66 (563)
                      ++..|...-.|++|+..+.+++...++..
T Consensus        78 ~lA~~~~Gav~vpl~~~~~~~~l~~~l~~  106 (525)
T PRK08316         78 RFACARAGAVLVPVNFMLTGEELAYILDH  106 (525)
T ss_pred             HHHHHHHCEEEEEECCCCCHHHHHHHHHH
T ss_conf             99999859199977898999999999985


No 104
>PRK11033 zntA zinc/cadmium/mercury/lead-transporting ATPase; Provisional
Probab=32.82  E-value=30  Score=14.06  Aligned_cols=26  Identities=4%  Similarity=0.135  Sum_probs=10.5

Q ss_pred             HHHHHHHHHHHHHHHHHHCC--CCEEEE
Q ss_conf             99999999999988775408--780699
Q gi|254780695|r  235 QAIQHEIEMNINKALAAFLG--VDNFRS  260 (563)
Q Consensus       235 ~~~E~~~~~kI~~~L~~i~G--~~~v~v  260 (563)
                      +-+|...+.|-.+.+..+..  +..+++
T Consensus       217 ~~LE~~a~~ra~~ai~~L~~l~P~~A~v  244 (739)
T PRK11033        217 ERLEGYAASRARQGVSALMALVPETATR  244 (739)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCEEEE
T ss_conf             9999999999999999987369997899


No 105
>COG4744 Uncharacterized conserved protein [Function unknown]
Probab=32.55  E-value=31  Score=14.01  Aligned_cols=18  Identities=28%  Similarity=0.610  Sum_probs=10.7

Q ss_pred             HCCCCEEECCCCCEEEECH
Q ss_conf             7799299918997799518
Q gi|254780695|r   69 EANIDFRISDNGSSISVPS   87 (563)
Q Consensus        69 ~~gI~y~~~~~g~~I~Vp~   87 (563)
                      +.|..|++. +|.-|+||.
T Consensus        97 ~lGt~yrla-dgr~IyVpe  114 (121)
T COG4744          97 ALGTAYRLA-DGRVIYVPE  114 (121)
T ss_pred             EEEEEEECC-CCEEEEECC
T ss_conf             513677607-970899417


No 106
>TIGR01478 STEVOR variant surface antigen, stevor family; InterPro: IPR006374   Malaria is still a major cause of mortality in many areas of the world. Plasmodium falciparum causes the most severe human form of the disease and is responsible for most fatalities. Severe cases of malaria can occur when the parasite invades and then proliferates within red blood cell erythrocytes. The parasite produces many variant antigenic proteins, encoded by multigene families, which are present on the surface of the infected erythrocyte and play important roles in virulence. A crucial survival mechanism for the malaria parasite is its ability to evade the immune response by switching these variant surface antigens. The high virulence of P. falciparum relative to other malarial parasites is in large part due to the fact that in this organism many of these surface antigens mediate the binding of infected erythrocytes to the vascular endothelium (cytoadherence) and non-infected erythrocytes (rosetting). This can lead to the accumulation of infected cells in the vasculature of a variety of organs, blocking the blood flow and reducing the oxygen supply. Clinical symptoms of severe infection can include fever, progressive anaemia, multi-organ dysfunction and coma. For more information see .   This entry represents the stevor (short for "subtelomeric variable open reading frame") family of predicted variant surface antigens. This is the third largest variant surface antigen family in P. falciparum, with 33 genes identified in the genome of this parasite . The function of these proteins is not known, but they are expressed during several stages of the parasite life-cycle and may play a variety of roles in parasite survival and infection ..
Probab=32.49  E-value=31  Score=14.00  Aligned_cols=11  Identities=18%  Similarity=0.447  Sum_probs=5.1

Q ss_pred             HHHHHHHHHCC
Q ss_conf             99998643125
Q gi|254780695|r  387 EINKIVSAATG  397 (563)
Q Consensus       387 ~I~~lV~~AiG  397 (563)
                      .|+....+|+|
T Consensus       240 SlEsa~~t~~~  250 (315)
T TIGR01478       240 SLESALKTAVG  250 (315)
T ss_pred             HHHHHHHHHHH
T ss_conf             99999987345


No 107
>PRK06164 acyl-CoA synthetase; Validated
Probab=31.57  E-value=32  Score=13.91  Aligned_cols=22  Identities=9%  Similarity=-0.002  Sum_probs=13.2

Q ss_pred             CCCCCEEECCCCCHHHHHHHHH
Q ss_conf             6998245038999899999999
Q gi|254780695|r   44 NSPHYDNLYVKLEVSDVNRISV   65 (563)
Q Consensus        44 ~~p~y~~L~~~l~~~d~~~i~~   65 (563)
                      ..--+++|+..+.+++...++.
T Consensus        83 ~Gav~vpi~~~~~~~~l~~~l~  104 (541)
T PRK06164         83 LGATVLAVNTRYRSAEVADILG  104 (541)
T ss_pred             HCCEEEEECCCCCHHHHHHHHH
T ss_conf             5909997589899999999998


No 108
>PRK00023 cmk cytidylate kinase; Provisional
Probab=31.21  E-value=33  Score=13.87  Aligned_cols=136  Identities=17%  Similarity=0.197  Sum_probs=78.8

Q ss_pred             ECCCCCHHHHHHHHHHHHHCCCCEEECCCCCEEEECHHHHHH-H------------------HH-------HHH-HCCCC
Q ss_conf             038999899999999999779929991899779951899999-9------------------99-------999-76998
Q gi|254780695|r   51 LYVKLEVSDVNRISVALSEANIDFRISDNGSSISVPSSMVGK-A------------------RI-------HLA-AQGLP  103 (563)
Q Consensus        51 L~~~l~~~d~~~i~~~L~~~gI~y~~~~~g~~I~Vp~~~~~~-~------------------r~-------~La-~~glp  103 (563)
                      +-.+++..+...+...|....|.|....++..++++..++.. +                  |-       .++ ..|+.
T Consensus        47 ~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~v~l~~~dv~~~lrs~eI~~~vS~iA~~~~VR~~l~~~Qr~~~~~~g~V  126 (225)
T PRK00023         47 LQHGVDLEDEEALVALAAHLDISFENGPDGQEVFLNGEDVSDEIRTEEVGNAASKVAAIPEVREALVERQRAFAEAPGLV  126 (225)
T ss_pred             HHHCCCCCCHHHHHHHHHCCCCCCCCCCCCCEEEECCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCEE
T ss_conf             98485965799999998549820036887637986795127988227888889886387889999999999998536916


Q ss_pred             CCCCCCHHHHHCCC-CCCCCCHHHHHHHHHHHHHH----------HHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCC
Q ss_conf             87766325653058-88425999999999999999----------99999960576314899998336665555555871
Q gi|254780695|r  104 SSSSNSGYELFDKV-NSFGLTSFMQEITRVRALEG----------EIARTIQSISGIVAARVHIVMPDMGSFRKIGARPT  172 (563)
Q Consensus       104 ~~~~~~g~el~d~~-~~~g~T~~~~~~~~~raleg----------eL~rtI~~~~~V~~ArV~l~~p~~~~f~~~~~~~s  172 (563)
                      ..|..+|.-+|-+. =+|-.|-..+---.+|..|-          ++...|..=|....-|-|      ++.    .+|.
T Consensus       127 ~eGRDIGTvVfPdA~lK~fL~As~~~RA~RR~~el~~~g~~~~~~~v~~~i~~RD~~D~~R~~------sPL----~~a~  196 (225)
T PRK00023        127 MDGRDIGTVVFPDAELKIFLTASAEERAERRYKELQAKGISVNFEDLLAEIKERDERDSNRAV------APL----KPAE  196 (225)
T ss_pred             EECCCCCEEEECCCCEEEEEECCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCHHHCCCCC------CCC----CCCC
T ss_conf             742543138806887677786798999999999998758877799999999863420233776------787----5489


Q ss_pred             EEEEEECCCCCCHHH-HHHHHHHHHH
Q ss_conf             599970687789889-9999999986
Q gi|254780695|r  173 ASVMIRAINPSVYKS-AEAIRHLVAA  197 (563)
Q Consensus       173 ASV~l~~~~~l~~~q-v~~I~~lVa~  197 (563)
                      -++++. ...++.+| +.-|.++|-.
T Consensus       197 DAi~ID-ts~lti~evv~~i~~~i~~  221 (225)
T PRK00023        197 DALLLD-TSGLSIEEVVEKILALIEQ  221 (225)
T ss_pred             CEEEEE-CCCCCHHHHHHHHHHHHHH
T ss_conf             818998-9899999999999999999


No 109
>TIGR02667 moaB_proteo molybdenum cofactor biosynthesis protein B; InterPro: IPR013484    MoaB is thought to be involved in molybdopterin biosynthesis, though its exact role is not known. Structural studies of this polypeptide suggest that it may play a role in substrate-shuttling during biosynthesis . MoaB was capable of binding GTP, and it was suggested that the putative active site could also bind precursor Z and/or molybdenum. Potential protein interaction domains were also found, implying that MoaB may play a transport and/or storage role in molybdopterin biosynthesis. .
Probab=31.08  E-value=19  Score=15.43  Aligned_cols=22  Identities=5%  Similarity=0.184  Sum_probs=14.1

Q ss_pred             HHHHHHCHHHHHHHHHHHHHHH
Q ss_conf             9998869998999999998637
Q gi|254780695|r  532 LHMIEINEERFAKILRKWARSE  553 (563)
Q Consensus       532 ~~lv~e~Pe~vA~vLR~WL~ee  553 (563)
                      |.++++|-++...+++.|+.++
T Consensus        41 R~iv~DD~y~iRA~Vs~WIAd~   62 (163)
T TIGR02667        41 RAIVKDDIYQIRAQVSEWIADP   62 (163)
T ss_pred             CCCCHHHHHHHHHHHHHHCCCC
T ss_conf             4326744899999998734898


No 110
>PRK06145 acyl-CoA synthetase; Validated
Probab=30.57  E-value=33  Score=13.80  Aligned_cols=29  Identities=14%  Similarity=-0.008  Sum_probs=19.7

Q ss_pred             HHHHHHCCCCCEEECCCCCHHHHHHHHHH
Q ss_conf             99998469982450389998999999999
Q gi|254780695|r   38 AARFFVNSPHYDNLYVKLEVSDVNRISVA   66 (563)
Q Consensus        38 ~~~~~~~~p~y~~L~~~l~~~d~~~i~~~   66 (563)
                      ++..|...--|++|...+.+++...+...
T Consensus        69 ~lA~~~~Gav~vpl~~~~~~~~l~~il~~   97 (497)
T PRK06145         69 AFAASYLGAVFLPINYRLAADEVAYILGD   97 (497)
T ss_pred             HHHHHHHCCEEEEECCCCCHHHHHHHHHH
T ss_conf             99999859099944898999999999984


No 111
>PRK11519 tyrosine kinase; Provisional
Probab=30.11  E-value=34  Score=13.75  Aligned_cols=20  Identities=20%  Similarity=0.318  Sum_probs=10.8

Q ss_pred             HHHHHHHHHHHHHCCCCCEE
Q ss_conf             99999999999846998245
Q gi|254780695|r   31 VPIMLFMAARFFVNSPHYDN   50 (563)
Q Consensus        31 ~~i~~~~~~~~~~~~p~y~~   50 (563)
                      ++++++.+++.+...|.|+.
T Consensus        39 ~i~~~~a~~y~~~~tP~Y~A   58 (720)
T PRK11519         39 AVFALCAVVYTFFATPIYSA   58 (720)
T ss_pred             HHHHHHHHHHHHCCCCEEEE
T ss_conf             99999999999518984788


No 112
>cd00371 HMA Heavy-metal-associated domain (HMA) is a conserved domain of approximately 30 amino acid residues found in a number of proteins that transport or detoxify heavy metals, for example, the CPx-type heavy metal ATPases and copper chaperones. HMA domain contains two cysteine residues that are important in binding and transfer of metal ions, such as copper, cadmium, cobalt and zinc. In the case of copper, stoichiometry of binding is one Cu+ ion per binding domain. Repeats of the HMA domain in copper chaperone has been associated with Menkes/Wilson disease due to binding of multiple copper ions.
Probab=29.76  E-value=34  Score=13.71  Aligned_cols=41  Identities=7%  Similarity=0.110  Sum_probs=26.6

Q ss_pred             HHHHHHHHHHHCCCCCEEEEEEEECCCCCCCCCCCCCCEEEEEECCCCCCHHHHH
Q ss_conf             9999999996057631489999833666555555587159997068778988999
Q gi|254780695|r  135 LEGEIARTIQSISGIVAARVHIVMPDMGSFRKIGARPTASVMIRAINPSVYKSAE  189 (563)
Q Consensus       135 legeL~rtI~~~~~V~~ArV~l~~p~~~~f~~~~~~~sASV~l~~~~~l~~~qv~  189 (563)
                      =..-+++.+..++||.+++|.+.-.              +|.+...+.++.+++.
T Consensus        12 C~~~Ie~~l~~~~GV~~~~vn~~~~--------------~v~V~~~~~~~~~~i~   52 (63)
T cd00371          12 CVSKIEKALEKLPGVESVEVDLETG--------------KATVEYDPEVSPEELL   52 (63)
T ss_pred             HHHHHHHHHCCCCCCEEEEEECCCC--------------EEEEEECCCCCHHHHH
T ss_conf             9999999970799957999988899--------------9999989999999999


No 113
>TIGR00418 thrS threonyl-tRNA synthetase; InterPro: IPR002320   The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases .   Threonyl-tRNA synthetase (6.1.1.3 from EC) exists as a monomer and belongs to class IIa. The enzyme from Escherichia coli represses the translation of its own mRNA. The crystal structure of the complex between tRNA(Thr) and ThrRS show structural features that reveal novel strategies for providing specificity in tRNA selection. These include an amino-terminal domain containing a novel protein fold that makes minor groove contacts with the tRNA acceptor stem. The enzyme induces a large deformation of the anticodon loop, resulting in an interaction between two adjacent anticodon bases, which accounts for their prominent role in tRNA identity and translational regulation. A zinc ion found in the active site is implicated in amino acid recognition/discrimination . The zinc ion may act to ensure that only amino acids that possess a hydroxyl group attached to the beta-position are activated .; GO: 0004829 threonine-tRNA ligase activity, 0005524 ATP binding, 0006412 translation, 0006435 threonyl-tRNA aminoacylation, 0005737 cytoplasm.
Probab=29.61  E-value=35  Score=13.69  Aligned_cols=29  Identities=17%  Similarity=0.145  Sum_probs=13.9

Q ss_pred             HHHHHHHHHHHHHHCCCCCEEEEEEEECC
Q ss_conf             99999999999960576314899998336
Q gi|254780695|r  132 VRALEGEIARTIQSISGIVAARVHIVMPD  160 (563)
Q Consensus       132 ~ralegeL~rtI~~~~~V~~ArV~l~~p~  160 (563)
                      ..++|.++-..+.....|..-.|.+.-++
T Consensus        46 l~~ie~~m~~~~~~~~~~~~~~~s~~~A~   74 (595)
T TIGR00418        46 LEKIEKEMKEIIKKNYPIARLSVSLEEAL   74 (595)
T ss_pred             HHHHHHHHHHHHHHHCCEEEEEECHHHHH
T ss_conf             99999999999864057025772478999


No 114
>pfam10971 DUF2773 Protein of unknown function (DUF2773). This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=29.44  E-value=27  Score=14.44  Aligned_cols=22  Identities=14%  Similarity=0.262  Sum_probs=15.1

Q ss_pred             HHHHHHCHHHHHHHHHHHHHHH
Q ss_conf             9998869998999999998637
Q gi|254780695|r  532 LHMIEINEERFAKILRKWARSE  553 (563)
Q Consensus       532 ~~lv~e~Pe~vA~vLR~WL~ee  553 (563)
                      +.++-.||.-.|.|.+.||++|
T Consensus        21 r~lamNNpqlaaDVkt~wLK~d   42 (81)
T pfam10971        21 RSLAMNNPQLAADVKTAWLKED   42 (81)
T ss_pred             HHHHHCCCCCHHHHHHHHHCCC
T ss_conf             7877268421278889886058


No 115
>pfam11576 DUF3236 Protein of unknown function (DUF3236). This family of proteins with unknown function appears to be restricted to Methanobacteria.
Probab=28.92  E-value=36  Score=13.61  Aligned_cols=42  Identities=24%  Similarity=0.431  Sum_probs=26.6

Q ss_pred             CEEEEECCCCEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             26998289835003676533324799999999999999999887754
Q gi|254780695|r  206 DVTVLDSTGKLLTANEMERNILGKSLSIVQAIQHEIEMNINKALAAF  252 (563)
Q Consensus       206 ~VtVvD~~G~~L~~~~~~~~~~~~~~~~~~~~E~~~~~kI~~~L~~i  252 (563)
                      =-.++|..|++|+..-+.+     .+-++..+|...+......|..+
T Consensus       110 mLvimD~kgRiLTaslSPs-----~iiHk~~ie~~v~~E~~eAL~ri  151 (154)
T pfam11576       110 MLVIMDSKGRILTAALSPS-----HVIHKKSIEEAVELELEEALERI  151 (154)
T ss_pred             EEEEECCCCCEEEECCCCH-----HHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             7999838876875137912-----64300449999999999999983


No 116
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=28.91  E-value=16  Score=15.85  Aligned_cols=35  Identities=3%  Similarity=0.120  Sum_probs=21.6

Q ss_pred             HHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             86406987889999999999999999999846998
Q gi|254780695|r   13 SGTSLGRTRILILASVILVPIMLFMAARFFVNSPH   47 (563)
Q Consensus        13 ~~~~l~~~~ki~~~~~~~~~i~~~~~~~~~~~~p~   47 (563)
                      +++.+.+++++++.+++++.+++.++-.||++.-+
T Consensus         3 n~n~~~~r~q~~~~~~~~~~~~~~g~g~~y~~~~~   37 (474)
T PRK13729          3 NINTIVKRKQYLWLGIVVVGTASAGGGALYLSDVD   37 (474)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCC
T ss_conf             27888999999999999987650354158862110


No 117
>PRK01710 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=28.54  E-value=25  Score=14.59  Aligned_cols=56  Identities=14%  Similarity=0.268  Sum_probs=35.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH-CCCCCEEECCCCCHHHHHHHHHHHHHCCCCEEECC
Q ss_conf             8788999999999999999999984-69982450389998999999999997799299918
Q gi|254780695|r   19 RTRILILASVILVPIMLFMAARFFV-NSPHYDNLYVKLEVSDVNRISVALSEANIDFRISD   78 (563)
Q Consensus        19 ~~~ki~~~~~~~~~i~~~~~~~~~~-~~p~y~~L~~~l~~~d~~~i~~~L~~~gI~y~~~~   78 (563)
                      +.+|+.+++.+...+.++    .++ .+...+..|-.-+..+...+...|+..||++.+..
T Consensus        13 ~~kkv~i~GlG~sG~a~a----~~L~~~g~~v~~~D~~~~~~~~~~~~~l~~~gi~~~~g~   69 (458)
T PRK01710         13 KNKKVAVVGIGVSNIPLI----KFLVKLGAKVTAFDKKSEEELGEISLELKEKGVNLELGE   69 (458)
T ss_pred             CCCEEEEEEECHHHHHHH----HHHHHCCCEEEEEECCCCHHHHHHHHHHHHCCCEEEECC
T ss_conf             899699997878899999----999978897999989884314899999985799899578


No 118
>pfam08478 POTRA_1 POTRA domain, FtsQ-type. FtsQ/DivIB bacterial division proteins (pfam03799) contain an N-terminal POTRA domain (for polypeptide-transport-associated domain). This is found in different types of proteins, usually associated with a transmembrane beta-barrel. FtsQ/DivIB may have chaperone-like roles, which has also been postulated for the POTRA domain in other contexts.
Probab=28.40  E-value=36  Score=13.56  Aligned_cols=26  Identities=19%  Similarity=0.243  Sum_probs=22.3

Q ss_pred             HHHHHHHHHHCCCCCEEEEEEEECCC
Q ss_conf             99999999605763148999983366
Q gi|254780695|r  136 EGEIARTIQSISGIVAARVHIVMPDM  161 (563)
Q Consensus       136 egeL~rtI~~~~~V~~ArV~l~~p~~  161 (563)
                      ..++++.|++++-|++|+|+-..|..
T Consensus        34 ~~~i~~~l~~~p~I~~a~V~r~~P~~   59 (67)
T pfam08478        34 LNAIEDRLEKLPWIKSASVRRQWPNT   59 (67)
T ss_pred             HHHHHHHHHCCCCEEEEEEEEECCCE
T ss_conf             99999987478872699999977998


No 119
>PRK07798 acyl-CoA synthetase; Validated
Probab=28.32  E-value=36  Score=13.55  Aligned_cols=31  Identities=10%  Similarity=0.041  Sum_probs=17.5

Q ss_pred             HHHCCCCCEEECCCCCHHHHHHHHHHHHHCCCCE
Q ss_conf             9846998245038999899999999999779929
Q gi|254780695|r   41 FFVNSPHYDNLYVKLEVSDVNRISVALSEANIDF   74 (563)
Q Consensus        41 ~~~~~p~y~~L~~~l~~~d~~~i~~~L~~~gI~y   74 (563)
                      .|...-.+++|+..+.+++...   .|+..+...
T Consensus        73 ~~~~Gav~vpl~~~~~~~~l~~---~l~~~~~~~  103 (532)
T PRK07798         73 AFKARAVPVNVNYRYVEDELRY---LLDDSDAVA  103 (532)
T ss_pred             HHHHCCEEEECCCCCCHHHHHH---HHHHCCCCE
T ss_conf             9984919981287689999999---998539849


No 120
>TIGR01495 ETRAMP early transcribed membrane protein (ETRAMP) family; InterPro: IPR006389   These sequences represent a family of proteins from the malaria parasite Plasmodium falciparum, several of which have been shown to be expressed specifically in the ring stage as well as the rodent parasite Plasmodium yoelii . A homolog from Plasmodium chabaudi was localized to the parasitophorous vacuole membrane . Members have an initial hydrophobic, Phe/Tyr-rich stretch long enough to span the membrane, a highly charged region rich in Lys, a second putative transmembrane region, and a second highly charged, low complexity sequence region. Some members have up to 100 residues of additional C-terminal sequence. These genes have been shown to be found in the sub-telomeric regions of both Plasmodium falciparum and P. yoelii chromosomes..
Probab=28.00  E-value=37  Score=13.51  Aligned_cols=23  Identities=30%  Similarity=0.400  Sum_probs=15.0

Q ss_pred             HHHHHHHHH-HHHHHHHHHHHHHH
Q ss_conf             878899999-99999999999999
Q gi|254780695|r   19 RTRILILAS-VILVPIMLFMAARF   41 (563)
Q Consensus        19 ~~~ki~~~~-~~~~~i~~~~~~~~   41 (563)
                      ++|+++++. .++..++++++..+
T Consensus        60 r~~k~ilySl~~as~lAlL~g~~~   83 (99)
T TIGR01495        60 RNKKIILYSLSIASGLALLVGAGV   83 (99)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             752279998999999999999999


No 121
>TIGR02004 PTS-IIBC-malX PTS system, maltose and glucose-specific IIBC component; InterPro: IPR011301   This entry represents a family of PTS enzyme II fused B and C components including and most closely related to the MalX maltose and glucose-specific transporter of Escherichia coli ..
Probab=27.95  E-value=37  Score=13.50  Aligned_cols=27  Identities=4%  Similarity=-0.144  Sum_probs=12.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             999999999999999999977875201
Q gi|254780695|r  440 INALVFLVGTLLVTFLGLHALRRLHNI  466 (563)
Q Consensus       440 ~~~~~~~l~~lll~~~vl~~l~~~~~~  466 (563)
                      -||-+..+++.+.+..++++.|-.+.+
T Consensus       388 TKWylVp~vaAiWFvvYYfvFk~aIt~  414 (540)
T TIGR02004       388 TKWYLVPVVAAIWFVVYYFVFKFAITK  414 (540)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCEEEEE
T ss_conf             478899999999999998631134788


No 122
>TIGR00869 sec62 protein translocation protein, Sec62 family; InterPro: IPR011553   Members of the NSCC2 family have been sequenced from various fungal and animal species including Saccharomyces cerevisiae, Drosophila melanogaster and Homo sapiens. These proteins are the Sec62 proteins, believed to be associated with the Sec61 and Sec63 constituents of the general protein secretary systems of yeast microsomes. They are also the non-selective cation (NS) channels of the mammalian cytoplasmic membrane. The yeast Sec62 protein has been shown to be essential for cell growth. The mammalian NS channel proteins have been implicated in platelet derived growth factor(PGDF) dependent single channel current in fibroblasts. These channels are essentially closed in serum deprived tissue-culture cells and are specifically opened by exposure to PDGF. These channels are reported to exhibit equal selectivity for Na+, K+ and Cs+ with low permeability to Ca2+, and no permeability to anions.   This family of Sec62 proteins is restricted to the Ascomycota. ; GO: 0008565 protein transporter activity, 0015031 protein transport, 0030176 integral to endoplasmic reticulum membrane.
Probab=27.89  E-value=37  Score=13.50  Aligned_cols=36  Identities=8%  Similarity=-0.068  Sum_probs=17.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             589999999999999999999999999999778752
Q gi|254780695|r  429 MDILSRHFATVINALVFLVGTLLVTFLGLHALRRLH  464 (563)
Q Consensus       429 ~~~~~~~~~~~~~~~~~~l~~lll~~~vl~~l~~~~  464 (563)
                      |....+....++-.|.++++++++.+.++|++.-.+
T Consensus       144 WP~fmR~G~wYlS~G~lG~ig~FF~~ailRl~lfvl  179 (259)
T TIGR00869       144 WPIFMRRGSWYLSLGALGIIGVFFAVAILRLILFVL  179 (259)
T ss_pred             CHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             214563551200455788999999999999999997


No 123
>COG2098 Uncharacterized protein conserved in archaea [Function unknown]
Probab=27.77  E-value=37  Score=13.48  Aligned_cols=51  Identities=20%  Similarity=0.175  Sum_probs=34.0

Q ss_pred             HHCCCCCCCCCCHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEC
Q ss_conf             97699887766325653058884259999999999999999999996057631489999833
Q gi|254780695|r   98 AAQGLPSSSSNSGYELFDKVNSFGLTSFMQEITRVRALEGEIARTIQSISGIVAARVHIVMP  159 (563)
Q Consensus        98 a~~glp~~~~~~g~el~d~~~~~g~T~~~~~~~~~ralegeL~rtI~~~~~V~~ArV~l~~p  159 (563)
                      =..|+- -|  .-|..|-.. +..-.       -.-.||.-++++|+--+-|.+|+|||.-.
T Consensus        16 FEaGIk-lG--alyHqf~Gt-Pvs~~-------~a~~le~aI~esi~~QP~v~daeV~Id~~   66 (116)
T COG2098          16 FEAGIK-LG--ALYHQFVGT-PVSPG-------TAESLEKAIEESIKVQPFVEDAEVKIDRD   66 (116)
T ss_pred             HHCCCC-HH--HHHHHHCCC-CCCCC-------CHHHHHHHHHHHHHCCCCEEEEEEEECCC
T ss_conf             871520-33--122333077-67854-------36899999999872287455679996465


No 124
>PRK10907 intramembrane serine protease GlpG; Provisional
Probab=27.63  E-value=37  Score=13.47  Aligned_cols=45  Identities=13%  Similarity=0.119  Sum_probs=35.5

Q ss_pred             CCHHHHHHHHHHHHHCCCCEEECCCCC-EEEE-CHHHHHHHHHHHHH
Q ss_conf             998999999999997799299918997-7995-18999999999997
Q gi|254780695|r   55 LEVSDVNRISVALSEANIDFRISDNGS-SISV-PSSMVGKARIHLAA   99 (563)
Q Consensus        55 l~~~d~~~i~~~L~~~gI~y~~~~~g~-~I~V-p~~~~~~~r~~La~   99 (563)
                      -++..|.+-++.|..+||+.++..+++ .|.+ ++++..+++-.|..
T Consensus         8 ~n~r~Aq~f~dYl~~~gi~~~v~~~~~~~lwl~de~~~~~a~~~l~~   54 (276)
T PRK10907          8 SNPRLAQAFVDYMATQGVILTIQQHNQSDIWLADESQAERVRAELAR   54 (276)
T ss_pred             CCHHHHHHHHHHHHHCCCCEEEECCCCEEEEECCHHHHHHHHHHHHH
T ss_conf             99899999999998679907983089568995183679999999999


No 125
>PRK07008 acyl-CoA synthetase; Validated
Probab=27.57  E-value=37  Score=13.46  Aligned_cols=22  Identities=9%  Similarity=0.055  Sum_probs=11.4

Q ss_pred             CCCCCEEECCCCCHHHHHHHHH
Q ss_conf             6998245038999899999999
Q gi|254780695|r   44 NSPHYDNLYVKLEVSDVNRISV   65 (563)
Q Consensus        44 ~~p~y~~L~~~l~~~d~~~i~~   65 (563)
                      ..--+++|+..+.+++...+++
T Consensus        87 ~Gav~vpl~~~~~~~~l~~il~  108 (539)
T PRK07008         87 SGAVCHTINPRLFPEQIAYIVN  108 (539)
T ss_pred             HCEEEEEECCCCCHHHHHHHHH
T ss_conf             4969984489999999999997


No 126
>PRK06178 acyl-CoA synthetase; Validated
Probab=27.12  E-value=38  Score=13.41  Aligned_cols=14  Identities=21%  Similarity=0.230  Sum_probs=9.5

Q ss_pred             HHHHHHHHHHHHHH
Q ss_conf             06899999999886
Q gi|254780695|r  524 SKQSDLRLLHMIEI  537 (563)
Q Consensus       524 ~~~~~~~i~~lv~e  537 (563)
                      -+..|++++++++|
T Consensus       552 GKidR~~Lr~~~~e  565 (567)
T PRK06178        552 GKVKKQELQALLEE  565 (567)
T ss_pred             CCHHHHHHHHHHHH
T ss_conf             55639999999984


No 127
>PRK07768 acyl-CoA synthetase; Validated
Probab=26.58  E-value=39  Score=13.34  Aligned_cols=15  Identities=27%  Similarity=0.406  Sum_probs=9.4

Q ss_pred             HHHHHHHHHHHCCCC
Q ss_conf             999999999977992
Q gi|254780695|r   59 DVNRISVALSEANID   73 (563)
Q Consensus        59 d~~~i~~~L~~~gI~   73 (563)
                      .+.++...|.+.||.
T Consensus        38 ~~~rlA~~L~~~Gv~   52 (543)
T PRK07768         38 RARRIAGGLAAAGVG   52 (543)
T ss_pred             HHHHHHHHHHHCCCC
T ss_conf             999999999976969


No 128
>TIGR00739 yajC preprotein translocase, YajC subunit; InterPro: IPR003849   This entry describes proteins of unknown function..
Probab=26.41  E-value=39  Score=13.33  Aligned_cols=26  Identities=19%  Similarity=0.254  Sum_probs=13.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             99999999999999999778752011
Q gi|254780695|r  442 ALVFLVGTLLVTFLGLHALRRLHNID  467 (563)
Q Consensus       442 ~~~~~l~~lll~~~vl~~l~~~~~~~  467 (563)
                      .+.++++.++|.|+++||=++..+..
T Consensus         6 l~~lv~~~~~FYFl~~RPQ~K~~k~~   31 (86)
T TIGR00739         6 LLPLVLIFLIFYFLIIRPQRKRRKAH   31 (86)
T ss_pred             HHHHHHHHHHHHHHHCCHHHHHHHHH
T ss_conf             89999999999997049779888988


No 129
>pfam11829 DUF3349 Protein of unknown function (DUF3349). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 99 to 124 amino acids in length.
Probab=26.40  E-value=39  Score=13.32  Aligned_cols=62  Identities=24%  Similarity=0.349  Sum_probs=41.8

Q ss_pred             CCCCEEEC----CCCCHHHHHHHHHHHHHCCCCEEECCCC-------CEE-EECHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             99824503----8999899999999999779929991899-------779-951899999999999769988776
Q gi|254780695|r   45 SPHYDNLY----VKLEVSDVNRISVALSEANIDFRISDNG-------SSI-SVPSSMVGKARIHLAAQGLPSSSS  107 (563)
Q Consensus        45 ~p~y~~L~----~~l~~~d~~~i~~~L~~~gI~y~~~~~g-------~~I-~Vp~~~~~~~r~~La~~glp~~~~  107 (563)
                      .++|.+|+    .-|+.+|..+|...|...|... ++..-       -+= +=...++.+++..|++.|-|..+.
T Consensus        22 ~~Dy~pLLALL~r~Ltddev~~Va~~L~~~~~~~-i~~~dI~~~I~~vt~~~P~p~di~RV~arLaa~GwPl~~~   95 (97)
T pfam11829        22 GPDYVPLLALLRRRLTDDEVAEVAAELTRRGEPA-IDDDDIGVLITAVTDELPSPEDVERVRARLAAHGWPLADP   95 (97)
T ss_pred             CCCCHHHHHHHHCCCCHHHHHHHHHHHHHCCCCC-CCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCCC
T ss_conf             8870899999814288999999999998647899-9999999999998747989899999999998679998999


No 130
>PRK07770 consensus
Probab=26.17  E-value=40  Score=13.30  Aligned_cols=37  Identities=11%  Similarity=0.152  Sum_probs=23.1

Q ss_pred             HHHHHHCCCCCEEECCCCCHHHHHHHHHHHHHCCCCEEEC
Q ss_conf             9999846998245038999899999999999779929991
Q gi|254780695|r   38 AARFFVNSPHYDNLYVKLEVSDVNRISVALSEANIDFRIS   77 (563)
Q Consensus        38 ~~~~~~~~p~y~~L~~~l~~~d~~~i~~~L~~~gI~y~~~   77 (563)
                      ++..|...-.|++|+..+.+++...+   |+..+..+=+.
T Consensus        74 ~la~~~~Gav~vpl~~~~~~~~l~~~---l~~~~~~~ii~  110 (508)
T PRK07770         74 ALALHTAGAVLVPLNTRYKAEEAADI---LARSGAKLLFV  110 (508)
T ss_pred             HHHHHHHCCEEEEECCCCCHHHHHHH---HHHCCCCEEEE
T ss_conf             99999859599976999999999999---99629989998


No 131
>PRK06187 acyl-CoA synthetase; Validated
Probab=26.17  E-value=40  Score=13.30  Aligned_cols=34  Identities=12%  Similarity=0.078  Sum_probs=19.5

Q ss_pred             HHHHCCCCCEEECCCCCHHHHHHHHHHHHHCCCCEEE
Q ss_conf             9984699824503899989999999999977992999
Q gi|254780695|r   40 RFFVNSPHYDNLYVKLEVSDVNRISVALSEANIDFRI   76 (563)
Q Consensus        40 ~~~~~~p~y~~L~~~l~~~d~~~i~~~L~~~gI~y~~   76 (563)
                      ..|...-.|++|...+.+++...+   |+..+..+=+
T Consensus        75 A~~~~Gav~vpl~~~~~~~~l~~i---l~~~~~~~vi  108 (520)
T PRK06187         75 AVPKIGAVLHPVNWRLAPEEIAYI---LNDAEDRVVL  108 (520)
T ss_pred             HHHHHCCEEEEECCCCCHHHHHHH---HHHCCCCEEE
T ss_conf             999859399962888999999999---9854995999


No 132
>pfam11823 DUF3343 Protein of unknown function (DUF3343). This family of proteins are functionally uncharacterized. This protein is found in bacteria and archaea. Proteins in this family are typically between 78 to 102 amino acids in length.
Probab=26.14  E-value=40  Score=13.29  Aligned_cols=58  Identities=14%  Similarity=0.162  Sum_probs=47.1

Q ss_pred             CCEEECCCCCHHHHHHHHHHHHHCCCCEEECC--------CCCEEEECHHHHHHHHHHHHHCCCCCCC
Q ss_conf             82450389998999999999997799299918--------9977995189999999999976998877
Q gi|254780695|r   47 HYDNLYVKLEVSDVNRISVALSEANIDFRISD--------NGSSISVPSSMVGKARIHLAAQGLPSSS  106 (563)
Q Consensus        47 ~y~~L~~~l~~~d~~~i~~~L~~~gI~y~~~~--------~g~~I~Vp~~~~~~~r~~La~~glp~~~  106 (563)
                      .|..+|  -+..++-.....|+++||++++-+        =|-+|..+.++...+.-.|..+++...+
T Consensus         3 ~~ii~F--~st~~a~~~e~~lk~~~i~~~liP~Pr~is~~CGlai~~~~~~~e~i~~~l~~~~i~~~~   68 (73)
T pfam11823         3 YYLITF--PSTHHALKAEKLLKKAGIKVKLIPTPREISSGCGLAIKFDLEDLEAIKKILEENGIEPEG   68 (73)
T ss_pred             EEEEEE--CCHHHHHHHHHHHHHCCCCEEEECCCHHHCCCCCEEEEECHHHHHHHHHHHHHCCCCEEE
T ss_conf             699998--887999999999988899879957985554799639997888899999999987998048


No 133
>PRK10673 hypothetical protein; Provisional
Probab=26.12  E-value=40  Score=13.29  Aligned_cols=20  Identities=5%  Similarity=0.252  Sum_probs=17.3

Q ss_pred             HHHHCHHHHHHHHHHHHHHH
Q ss_conf             98869998999999998637
Q gi|254780695|r  534 MIEINEERFAKILRKWARSE  553 (563)
Q Consensus       534 lv~e~Pe~vA~vLR~WL~ee  553 (563)
                      .-.|+|++++..|+.||+|.
T Consensus       236 ~~~E~P~~~~~~i~~FL~~k  255 (255)
T PRK10673        236 VHAEKPDAVLRAIRRYLNDK  255 (255)
T ss_pred             CHHHCHHHHHHHHHHHHCCC
T ss_conf             27879999999999987769


No 134
>COG3603 Uncharacterized conserved protein [Function unknown]
Probab=26.08  E-value=40  Score=13.29  Aligned_cols=40  Identities=25%  Similarity=0.242  Sum_probs=17.1

Q ss_pred             HHHHHHHHCCCCEEECC--CCCEEEECHHHHHHHHHHHHHCC
Q ss_conf             99999997799299918--99779951899999999999769
Q gi|254780695|r   62 RISVALSEANIDFRISD--NGSSISVPSSMVGKARIHLAAQG  101 (563)
Q Consensus        62 ~i~~~L~~~gI~y~~~~--~g~~I~Vp~~~~~~~r~~La~~g  101 (563)
                      .|...|.++||+--.-+  +|.-|+|.+++...|+-.|...|
T Consensus        82 sV~~pLsd~gigIFavStydtDhiLVr~~dLekAv~~L~eaG  123 (128)
T COG3603          82 SVSQPLSDNGIGIFAVSTYDTDHILVREEDLEKAVKALEEAG  123 (128)
T ss_pred             HHHHHHHHCCCCEEEEEECCCCEEEEEHHHHHHHHHHHHHCC
T ss_conf             654457657952799971257469983455999999999708


No 135
>pfam05663 DUF809 Protein of unknown function (DUF809). This family consists of several proteins of unknown function Raphanus sativus (Radish) and Brassica napus (Rape).
Probab=25.81  E-value=40  Score=13.25  Aligned_cols=77  Identities=21%  Similarity=0.285  Sum_probs=40.1

Q ss_pred             CHHHHHHHHHHHHHHCCHHHHHHHHHHH--HHHHHHHHHHHHHHCCCCCEEECCCCCHHHHHHHHHHHHHCCCCEEECCC
Q ss_conf             6789999999986406987889999999--99999999999984699824503899989999999999977992999189
Q gi|254780695|r    2 AILDQLLQFFKSGTSLGRTRILILASVI--LVPIMLFMAARFFVNSPHYDNLYVKLEVSDVNRISVALSEANIDFRISDN   79 (563)
Q Consensus         2 ~~~~~l~~~~~~~~~l~~~~ki~~~~~~--~~~i~~~~~~~~~~~~p~y~~L~~~l~~~d~~~i~~~L~~~gI~y~~~~~   79 (563)
                      .|+++|+-|-.+++.-  --|..++..+  +.++.+-+-+.||.+..            .--.-+..|+..+|||++.-+
T Consensus         3 tffeklstfchnltpt--eckvsvisffllafllmahiwlswfsnnq------------hclrtmrhleklkipyefqyg   68 (138)
T pfam05663         3 TFFEKLSTFCHNLTPT--ECKVSVISFFLLAFLLMAHIWLSWFSNNQ------------HCLRTMRHLEKLKIPYEFQYG   68 (138)
T ss_pred             HHHHHHHHHHCCCCCC--CEEEEHHHHHHHHHHHHHHHHHHHHCCCH------------HHHHHHHHHHHCCCCEEEEEC
T ss_conf             0999998886159840--00420489999999999999999973758------------899999999861787034411


Q ss_pred             --CCEEE----ECHHHHHH
Q ss_conf             --97799----51899999
Q gi|254780695|r   80 --GSSIS----VPSSMVGK   92 (563)
Q Consensus        80 --g~~I~----Vp~~~~~~   92 (563)
                        |-.|.    ||.+.+..
T Consensus        69 wlgvkitiksnvpndevtk   87 (138)
T pfam05663        69 WLGVKITIKSNVPNDEVTK   87 (138)
T ss_pred             CEEEEEEEECCCCCHHHHH
T ss_conf             1568999845899467642


No 136
>PRK10549 signal transduction histidine-protein kinase BaeS; Provisional
Probab=25.73  E-value=33  Score=13.82  Aligned_cols=53  Identities=17%  Similarity=0.085  Sum_probs=28.9

Q ss_pred             CHHHH--HHHHHHHHHHHHHHHHHHHHHCCCCCEEECCCCCHHHHHHHHHHHHHC
Q ss_conf             98788--999999999999999999984699824503899989999999999977
Q gi|254780695|r   18 GRTRI--LILASVILVPIMLFMAARFFVNSPHYDNLYVKLEVSDVNRISVALSEA   70 (563)
Q Consensus        18 ~~~~k--i~~~~~~~~~i~~~~~~~~~~~~p~y~~L~~~l~~~d~~~i~~~L~~~   70 (563)
                      +-+.|  +.+.+..+++++++.+++.|+-.-.|.--+.....+....+...|.+.
T Consensus         7 ~i~~Klfl~~~~~~~~~~~~~~~~~~~~f~~~f~~y~~~~~~~~~~~~~~~l~~~   61 (467)
T PRK10549          7 GITGKLFLAIFATCIVLLITMHWAVRISFERGFIDYIKHGNEQRLQMLSDALGEQ   61 (467)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             6699999999999999999999999999999899999998999999999999999


No 137
>pfam01756 ACOX Acyl-CoA oxidase. This is a family of Acyl-CoA oxidases EC:1.3.3.6. Acyl-coA oxidase converts acyl-CoA into trans-2- enoyl-CoA.
Probab=25.36  E-value=20  Score=15.34  Aligned_cols=34  Identities=9%  Similarity=0.084  Sum_probs=31.3

Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCCCEEEEECCCC
Q ss_conf             7898899999999986540188352699828983
Q gi|254780695|r  182 PSVYKSAEAIRHLVAAAVPNLDMGDVTVLDSTGK  215 (563)
Q Consensus       182 ~l~~~qv~~I~~lVa~sV~gL~~e~VtVvD~~G~  215 (563)
                      -++++|+..|+..|-.....|.|+-|.+||..+-
T Consensus       104 ~ls~~q~~~i~~~i~~L~~~lRp~Av~LVDAF~~  137 (186)
T pfam01756       104 YLSPDQIDQVREQILKLLAEVRPNAVALTDAFDL  137 (186)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             9998999999999999999878889999611579


No 138
>PRK00745 4-oxalocrotonate tautomerase; Provisional
Probab=25.27  E-value=41  Score=13.19  Aligned_cols=36  Identities=6%  Similarity=0.042  Sum_probs=22.0

Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHH---HCCCCCCEEEE
Q ss_conf             9970687789889999999998654---01883526998
Q gi|254780695|r  175 VMIRAINPSVYKSAEAIRHLVAAAV---PNLDMGDVTVL  210 (563)
Q Consensus       175 V~l~~~~~l~~~qv~~I~~lVa~sV---~gL~~e~VtVv  210 (563)
                      |.+++..|+|.+|-+.+..=|..++   -|-.|+.|.|+
T Consensus         4 i~V~~~eGRt~EQK~~l~~~iT~a~~~~lg~~pe~V~Vi   42 (62)
T PRK00745          4 FHIELFEGRTVEQKRKFVEEITRVTVETLGCPPESVDII   42 (62)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHHHHHCCCCCCEEEE
T ss_conf             999983899999999999999999999839592039999


No 139
>PRK06287 cobalt transport protein CbiN; Validated
Probab=25.19  E-value=29  Score=14.25  Aligned_cols=24  Identities=8%  Similarity=0.023  Sum_probs=9.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999977875
Q gi|254780695|r  440 INALVFLVGTLLVTFLGLHALRRL  463 (563)
Q Consensus       440 ~~~~~~~l~~lll~~~vl~~l~~~  463 (563)
                      +..++..++.+++.|-+.+.++|+
T Consensus        80 ~a~iiG~l~t~aia~Gvg~ii~k~  103 (105)
T PRK06287         80 AAIIIGTLLVLAISFGVGSIFKKS  103 (105)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             999999999999998888752025


No 140
>PRK08279 acyl-CoA synthetase; Validated
Probab=24.80  E-value=42  Score=13.13  Aligned_cols=22  Identities=5%  Similarity=-0.263  Sum_probs=11.4

Q ss_pred             CCCCCEEECCCCCHHHHHHHHH
Q ss_conf             6998245038999899999999
Q gi|254780695|r   44 NSPHYDNLYVKLEVSDVNRISV   65 (563)
Q Consensus        44 ~~p~y~~L~~~l~~~d~~~i~~   65 (563)
                      ..--|++|...+..++...++.
T Consensus       115 aGav~vpln~~~~~~~l~~~l~  136 (602)
T PRK08279        115 LGVVVALLNTQQRGEVLAHSIN  136 (602)
T ss_pred             HCEEEEEECCCCCHHHHHHHHH
T ss_conf             5909973187789999999997


No 141
>PRK04319 acetyl-CoA synthetase; Provisional
Probab=24.77  E-value=42  Score=13.13  Aligned_cols=21  Identities=10%  Similarity=-0.031  Sum_probs=13.1

Q ss_pred             HCCCCCEEECCCCCHHHHHHH
Q ss_conf             469982450389998999999
Q gi|254780695|r   43 VNSPHYDNLYVKLEVSDVNRI   63 (563)
Q Consensus        43 ~~~p~y~~L~~~l~~~d~~~i   63 (563)
                      ...--|++||..+.+++...+
T Consensus       120 k~Gav~vpl~~~~~~~~l~~~  140 (570)
T PRK04319        120 KIGAIVGPLFEAFMEEAVRDR  140 (570)
T ss_pred             HHCCEEEEECCCCCHHHHHHH
T ss_conf             869499930888998999999


No 142
>pfam00580 UvrD-helicase UvrD/REP helicase. The Rep family helicases are composed of four structural domains. The Rep family function as dimers. REP helicases catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA. Bacillus subtilis addA and Escherichia coli exodeoxyribonuclease V beta have large insertions near to the carboxy-terminus relative to other members of the family.
Probab=24.48  E-value=43  Score=13.09  Aligned_cols=22  Identities=9%  Similarity=0.075  Sum_probs=13.6

Q ss_pred             CEEECCCCCHHHHHHHHHHHHH
Q ss_conf             2450389998999999999997
Q gi|254780695|r   48 YDNLYVKLEVSDVNRISVALSE   69 (563)
Q Consensus        48 y~~L~~~l~~~d~~~i~~~L~~   69 (563)
                      ...|.--.+.+.+.+|.+++..
T Consensus        46 ~~IL~lTFT~kAA~Em~~Ri~~   67 (494)
T pfam00580        46 EEILAVTFTNKAAREMKERILK   67 (494)
T ss_pred             HHEEEEECHHHHHHHHHHHHHH
T ss_conf             4787670289999999999998


No 143
>PRK12785 fliL flagellar basal body-associated protein FliL; Reviewed
Probab=24.41  E-value=13  Score=16.49  Aligned_cols=22  Identities=18%  Similarity=0.294  Sum_probs=12.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCEEE
Q ss_conf             99999999999998877540878069
Q gi|254780695|r  234 VQAIQHEIEMNINKALAAFLGVDNFR  259 (563)
Q Consensus       234 ~~~~E~~~~~kI~~~L~~i~G~~~v~  259 (563)
                      +.++..++.++|...|    |++.|+
T Consensus       136 k~~Lr~ell~rin~~l----~~~~V~  157 (167)
T PRK12785        136 LFRLKEELTRRVNVAL----APAQVN  157 (167)
T ss_pred             HHHHHHHHHHHHHHHC----CCCCEE
T ss_conf             9999999999998541----788235


No 144
>PRK08130 putative aldolase; Validated
Probab=24.24  E-value=42  Score=13.11  Aligned_cols=21  Identities=24%  Similarity=0.460  Sum_probs=15.9

Q ss_pred             HHCCCCCCEEEEECCCCEEEC
Q ss_conf             401883526998289835003
Q gi|254780695|r  199 VPNLDMGDVTVLDSTGKLLTA  219 (563)
Q Consensus       199 V~gL~~e~VtVvD~~G~~L~~  219 (563)
                      ...|+++++.++|.+|+++..
T Consensus        48 ~~~l~~~div~vd~dG~~~~G   68 (213)
T PRK08130         48 LGRLDPARLSKVDADGNWLSG   68 (213)
T ss_pred             HHHCCHHHHEEECCCCCCCCC
T ss_conf             123988890765567872589


No 145
>PRK06839 acyl-CoA synthetase; Validated
Probab=24.19  E-value=43  Score=13.06  Aligned_cols=23  Identities=9%  Similarity=-0.164  Sum_probs=12.1

Q ss_pred             HHCCCCCEEECCCCCHHHHHHHH
Q ss_conf             84699824503899989999999
Q gi|254780695|r   42 FVNSPHYDNLYVKLEVSDVNRIS   64 (563)
Q Consensus        42 ~~~~p~y~~L~~~l~~~d~~~i~   64 (563)
                      |...-.|++|-..+.+.+...+.
T Consensus        74 ~~~Gav~vpl~~~~~~~~l~~~l   96 (496)
T PRK06839         74 AKVECIAVPLNIRLTENELIFQL   96 (496)
T ss_pred             HHHCEEEEEECCCCCHHHHHHHH
T ss_conf             98492999658999999999999


No 146
>TIGR00998 8a0101 efflux pump membrane protein; InterPro: IPR005694    emrA and emrB confer resistance to carbonylcyanide m-chlorophenylhydrazone, nalidixic acid, and a number of other toxic compounds. EmrB encodes a highly hydrophobic 56.2-kDa peptide, with 14 potential alpha-helices to span the inner membrane. EmrA encodes a putative 42.7-kDa peptide containing a single hydrophobic domain and a large C-terminal hydrophilic domain.; GO: 0015238 drug transporter activity, 0006855 multidrug transport, 0009276 1-2nm peptidoglycan-based cell wall.
Probab=24.03  E-value=43  Score=13.04  Aligned_cols=58  Identities=22%  Similarity=0.397  Sum_probs=26.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH-CCCCCEEECCCCCHHHHHHHHHHHHHCCC-CEEECCCCCEEEECHHH
Q ss_conf             88999999999999999999984-69982450389998999999999997799-29991899779951899
Q gi|254780695|r   21 RILILASVILVPIMLFMAARFFV-NSPHYDNLYVKLEVSDVNRISVALSEANI-DFRISDNGSSISVPSSM   89 (563)
Q Consensus        21 ~ki~~~~~~~~~i~~~~~~~~~~-~~p~y~~L~~~l~~~d~~~i~~~L~~~gI-~y~~~~~g~~I~Vp~~~   89 (563)
                      +++....+++.+++++++.+||. ..-+|.      ++.|+   .-.=++..| ||+++  |..|-|-.++
T Consensus         2 k~~~~l~vv~Li~~a~a~~~y~~~~~~~~~------~T~dA---YV~a~~~~v~sF~Vs--G~v~~v~~~d   61 (379)
T TIGR00998         2 KKFLLLLVVLLIVVALAYAIYWFLVLRDYE------STDDA---YVKANQLQVSSFQVS--GSVIEVNVDD   61 (379)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHCC------CHHHH---HCCCCCEEEEEEEEE--EEEEEEEECC
T ss_conf             306799999999999999999998874011------21146---212773023246573--2489997437


No 147
>TIGR02371 ala_DH_arch alanine dehydrogenase; InterPro: IPR012742   This enzyme, a homologue of bacterial ornithine cyclodeaminases and marsupial mu-crystallins, is a homodimeric NAD-dependent alanine dehydrogenase found in Archaeoglobus fulgidus and several other archaea..
Probab=24.00  E-value=40  Score=13.27  Aligned_cols=28  Identities=29%  Similarity=0.445  Sum_probs=19.7

Q ss_pred             HCCCCCEEEEEEEECCCCCCCCCCCCCCEEEEE
Q ss_conf             057631489999833666555555587159997
Q gi|254780695|r  145 SISGIVAARVHIVMPDMGSFRKIGARPTASVMI  177 (563)
Q Consensus       145 ~~~~V~~ArV~l~~p~~~~f~~~~~~~sASV~l  177 (563)
                      .+.||+...||=..|.+...     |+=.++++
T Consensus        63 ~~aGvK~VNvHPgNPdr~sL-----PTVMAlii   90 (327)
T TIGR02371        63 EIAGVKIVNVHPGNPDRNSL-----PTVMALII   90 (327)
T ss_pred             CCCCEEEEECCCCCCCCCCC-----CCEEEEEE
T ss_conf             55623899417755778876-----30145666


No 148
>PRK13383 acyl-CoA synthetase; Provisional
Probab=23.92  E-value=44  Score=13.02  Aligned_cols=22  Identities=0%  Similarity=-0.047  Sum_probs=12.4

Q ss_pred             HCCCCCEEECCCCCHHHHHHHH
Q ss_conf             4699824503899989999999
Q gi|254780695|r   43 VNSPHYDNLYVKLEVSDVNRIS   64 (563)
Q Consensus        43 ~~~p~y~~L~~~l~~~d~~~i~   64 (563)
                      ...-.|++|...+..++...+.
T Consensus       107 k~Gav~vPl~~~~~~~~l~~~l  128 (516)
T PRK13383        107 LLGADVVPISTEFRSDALAAAL  128 (516)
T ss_pred             HHCCEEEEECCCCCHHHHHHHH
T ss_conf             8691999578889999999999


No 149
>PTZ00042 stevor; Provisional
Probab=23.89  E-value=44  Score=13.02  Aligned_cols=27  Identities=33%  Similarity=0.436  Sum_probs=11.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             999999999999999999977875201
Q gi|254780695|r  440 INALVFLVGTLLVTFLGLHALRRLHNI  466 (563)
Q Consensus       440 ~~~~~~~l~~lll~~~vl~~l~~~~~~  466 (563)
                      +.++++++++++|+++...+.||+.+.
T Consensus       267 IaalVLlilaVvLIILYIWLyrRRKnS  293 (304)
T PTZ00042        267 IAALVLLILAVVLIILYIWLYRRRKNS  293 (304)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             999999999999999999999841242


No 150
>pfam00403 HMA Heavy-metal-associated domain.
Probab=23.84  E-value=44  Score=13.01  Aligned_cols=22  Identities=9%  Similarity=0.413  Sum_probs=16.9

Q ss_pred             HHHHHHHHHHCCCCCEEEEEEE
Q ss_conf             9999999960576314899998
Q gi|254780695|r  136 EGEIARTIQSISGIVAARVHIV  157 (563)
Q Consensus       136 egeL~rtI~~~~~V~~ArV~l~  157 (563)
                      ..-+++++..++||.+++|.+.
T Consensus        13 ~~~Ie~~l~~~~GV~~v~v~~~   34 (62)
T pfam00403        13 AKKVEKALSKLPGVSSVSVDLE   34 (62)
T ss_pred             HHHHHHHHHCCCCCEEEEEECC
T ss_conf             9999999855999549999878


No 151
>pfam06153 DUF970 Protein of unknown function (DUF970). Family of uncharacterized bacterial proteins.
Probab=23.82  E-value=44  Score=13.01  Aligned_cols=53  Identities=21%  Similarity=0.268  Sum_probs=40.0

Q ss_pred             CEEECCCCCHHHHHHHHHHHHHCCCCE-EECCCCC---------EEEECHHHHHHHHHHHHHC
Q ss_conf             245038999899999999999779929-9918997---------7995189999999999976
Q gi|254780695|r   48 YDNLYVKLEVSDVNRISVALSEANIDF-RISDNGS---------SISVPSSMVGKARIHLAAQ  100 (563)
Q Consensus        48 y~~L~~~l~~~d~~~i~~~L~~~gI~y-~~~~~g~---------~I~Vp~~~~~~~r~~La~~  100 (563)
                      |+.++.=...+|+..+.+.|.++|+.. +|+..|+         -|-|.+++++++.-.+...
T Consensus         1 MKLiiAIVqd~Da~~l~~~L~~~~~~~TkLaStGGFLr~GNtTlliGvede~V~~vl~iIk~~   63 (109)
T pfam06153         1 MKLVIAIVQDQDANRLSDALTEKGFRATKLASTGGFLKAGNTTLLIGVEDERVDDVLSIIKEN   63 (109)
T ss_pred             CEEEEEEEECCCHHHHHHHHHHCCEEEEEEECCCCCCCCCCEEEEEEECHHHHHHHHHHHHHH
T ss_conf             908999973211799999999889549998746662226976999984288889999999986


No 152
>cd02192 PurM-like3 AIR synthase (PurM) related protein, subgroup 3 of unknown function. The family of PurM related proteins includes Hydrogen expression/formation protein HypE, AIR synthases, FGAM synthase and Selenophosphate synthetase (SelD). They all contain two conserved domains and seem to dimerize. The N-terminal domain forms the dimer interface and is a putative ATP binding domain.
Probab=23.77  E-value=44  Score=13.01  Aligned_cols=18  Identities=11%  Similarity=-0.106  Sum_probs=8.6

Q ss_pred             CCCEEEEEEEECCCCCCC
Q ss_conf             631489999833666555
Q gi|254780695|r  148 GIVAARVHIVMPDMGSFR  165 (563)
Q Consensus       148 ~V~~ArV~l~~p~~~~f~  165 (563)
                      +-....|-+-+.++.--+
T Consensus        24 ~~~~~~V~~giGDDaAVi   41 (283)
T cd02192          24 PFDSLGVAADLGDDAAAI   41 (283)
T ss_pred             CCCCCCCCCCCCCCEEEE
T ss_conf             998888575799765899


No 153
>TIGR01005 eps_transp_fam exopolysaccharide transport protein family; InterPro: IPR005700    The bacterial exopolysaccharide transport protein is part of a large genetic locus which is associated with exopolysaccharide (EPS) biosynthesis. Detailed molecular characterization and gene fusion analysis revealed at least seven gene products are involved in the overall regulation, which among other things, include exopolysaccharide biosynthesis, property of conferring virulence and exopolysaccharide export.; GO: 0015542 sugar efflux transmembrane transporter activity, 0006859 extracellular carbohydrate transport.
Probab=23.53  E-value=44  Score=12.97  Aligned_cols=29  Identities=21%  Similarity=0.297  Sum_probs=18.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCEEE
Q ss_conf             99999999999999999998469982450
Q gi|254780695|r   23 LILASVILVPIMLFMAARFFVNSPHYDNL   51 (563)
Q Consensus        23 i~~~~~~~~~i~~~~~~~~~~~~p~y~~L   51 (563)
                      ..+++.+++++.++++.+.++-+|.|..-
T Consensus        17 ~~lia~fv~~v~~LgaAya~fAtp~Y~a~   45 (778)
T TIGR01005        17 RLLIAAFVVVVIALGAAYALFATPYYKAD   45 (778)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCE
T ss_conf             99999999999999999998546434201


No 154
>cd01324 cbb3_Oxidase_CcoQ Cytochrome cbb oxidase CcoQ.  Cytochrome cbb3 oxidase, the terminal oxidase in the respiratory chains of proteobacteria, is a multi-chain transmembrane protein located in the cell membrane. Like other cytochrome oxidases, it catalyzes the reduction of O2 and simultaneously pumps protons across the membrane.  Found exclusively in proteobacteria, cbb3 is believed to be a modern enzyme that has evolved independently to perform a specialized function in microaerobic energy metabolism. The cbb3 operon contains four genes (ccoNOQP or fixNOQP), with ccoN coding for subunit I.  Instead of a CuA-containing subunit II analogous to other cytochrome oxidases, cbb3 utilizes subunits ccoO and ccoP, which contain one and two hemes, respectively, to transfer electrons to the binuclear center.  ccoQ, the fourth subunit, is a single transmembrane helix protein.  It has been shown to protect the core complex from proteolytic degradation by serine proteases.  See cd00919, cd01322
Probab=23.50  E-value=44  Score=12.97  Aligned_cols=39  Identities=18%  Similarity=0.242  Sum_probs=23.2

Q ss_pred             CCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEC
Q ss_conf             9678999999998640698788999999999999999999984699824503
Q gi|254780695|r    1 MAILDQLLQFFKSGTSLGRTRILILASVILVPIMLFMAARFFVNSPHYDNLY   52 (563)
Q Consensus         1 m~~~~~l~~~~~~~~~l~~~~ki~~~~~~~~~i~~~~~~~~~~~~p~y~~L~   52 (563)
                      |+.-+.+.+|-+.|             +++.++++++++++|.-+|..+-.|
T Consensus         1 Md~y~~lr~~AdsW-------------gLl~~~~~Figvv~wa~~Pg~k~~~   39 (48)
T cd01324           1 MDIGETLRGLADSW-------------GLLYLALFFLGVVVWAFRPGRKKAF   39 (48)
T ss_pred             CCHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHHCCCCCCHHH
T ss_conf             96789999999999-------------9999999999998750588762357


No 155
>PRK00915 2-isopropylmalate synthase; Validated
Probab=23.40  E-value=45  Score=12.96  Aligned_cols=46  Identities=17%  Similarity=0.198  Sum_probs=28.2

Q ss_pred             CCCCHHHHHHHHHHHHHCCCCEEECCCCCEEEECHHHHHHHHHHHHHCCC
Q ss_conf             89998999999999997799299918997799518999999999997699
Q gi|254780695|r   53 VKLEVSDVNRISVALSEANIDFRISDNGSSISVPSSMVGKARIHLAAQGL  102 (563)
Q Consensus        53 ~~l~~~d~~~i~~~L~~~gI~y~~~~~g~~I~Vp~~~~~~~r~~La~~gl  102 (563)
                      -.++.+|.-.|...|++.||+| +.. | -=.+-..+....| .++..++
T Consensus        21 v~fs~e~K~~Ia~~L~~~GV~~-IE~-G-~P~~s~~d~e~~~-~i~~~~~   66 (511)
T PRK00915         21 ASLTVEEKLQIAKQLERLGVDV-IEA-G-FPASSPGDFEAVK-RIARTVK   66 (511)
T ss_pred             CCCCHHHHHHHHHHHHHCCCCE-EEE-E-CCCCCHHHHHHHH-HHHHCCC
T ss_conf             9989999999999999769898-998-2-6778978999999-9986059


No 156
>PRK07529 acyl-CoA synthetase; Validated
Probab=23.37  E-value=45  Score=12.95  Aligned_cols=15  Identities=27%  Similarity=0.324  Sum_probs=8.6

Q ss_pred             HHHHCCCCCCEEEEE
Q ss_conf             654018835269982
Q gi|254780695|r  197 AAVPNLDMGDVTVLD  211 (563)
Q Consensus       197 ~sV~gL~~e~VtVvD  211 (563)
                      ...-++.++++...-
T Consensus       246 ~~~~~~~~~d~~l~~  260 (632)
T PRK07529        246 ALLLGLGPGDTVLCG  260 (632)
T ss_pred             HHHHCCCCCCEEEEC
T ss_conf             997389988579970


No 157
>PRK07788 acyl-CoA synthetase; Validated
Probab=23.17  E-value=45  Score=12.93  Aligned_cols=56  Identities=13%  Similarity=0.149  Sum_probs=29.2

Q ss_pred             HCCCCCEEECCC---CCHHH----HHHHHHHHHHCCCCEEECCCCCEEEECHH-HHHHHHHHHHHCC
Q ss_conf             469982450389---99899----99999999977992999189977995189-9999999999769
Q gi|254780695|r   43 VNSPHYDNLYVK---LEVSD----VNRISVALSEANIDFRISDNGSSISVPSS-MVGKARIHLAAQG  101 (563)
Q Consensus        43 ~~~p~y~~L~~~---l~~~d----~~~i~~~L~~~gI~y~~~~~g~~I~Vp~~-~~~~~r~~La~~g  101 (563)
                      ...|+-..|..+   ++..+    +.++...|.+.||.   ..|--.|+-|.. +.-.+-+.....|
T Consensus        64 ~r~Pd~~Alv~~~~~lTY~eL~~~a~~lA~~L~~~Gv~---~GdrVai~~~ns~e~v~a~lA~~k~G  127 (552)
T PRK07788         64 RRAPDRAALIDEEGELTYAELDEASHALARGLLAKGVR---AGDGVAVLARNHRGFVIALYAAGKLG  127 (552)
T ss_pred             HHCCCCEEEEECCEEEEHHHHHHHHHHHHHHHHHCCCC---CCCEEEEEECCCHHHHHHHHHHHHHC
T ss_conf             76899849996994570999999999999999976959---99999999088099999999999849


No 158
>cd04389 RhoGAP_KIAA1688 RhoGAP_KIAA1688: GTPase-activator protein (GAP) domain for Rho-like GTPases found in KIAA1688-like proteins; KIAA1688 is a protein of unknown function that contains a RhoGAP domain and a myosin tail homology 4 (MyTH4) domain. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=23.03  E-value=45  Score=12.91  Aligned_cols=23  Identities=9%  Similarity=0.332  Sum_probs=11.9

Q ss_pred             ECC-CCCHHHHHHHHHHHHHCCCC
Q ss_conf             038-99989999999999977992
Q gi|254780695|r   51 LYV-KLEVSDVNRISVALSEANID   73 (563)
Q Consensus        51 L~~-~l~~~d~~~i~~~L~~~gI~   73 (563)
                      +|- .=+..+..++...++...++
T Consensus        43 IFR~sGs~~~i~~l~~~~d~g~~~   66 (187)
T cd04389          43 IFRVPGDIDEVNELKLRVDQWDYP   66 (187)
T ss_pred             EEEECCCHHHHHHHHHHHHCCCCC
T ss_conf             246078699999999998368987


No 159
>PRK00870 haloalkane dehalogenase; Provisional
Probab=22.99  E-value=45  Score=12.91  Aligned_cols=20  Identities=20%  Similarity=0.335  Sum_probs=17.1

Q ss_pred             HHHHCHHHHHHHHHHHHHHH
Q ss_conf             98869998999999998637
Q gi|254780695|r  534 MIEINEERFAKILRKWARSE  553 (563)
Q Consensus       534 lv~e~Pe~vA~vLR~WL~ee  553 (563)
                      .-.|+||+++..|..||+..
T Consensus       282 ~~~E~Pe~~~~~i~~FLr~~  301 (302)
T PRK00870        282 LQEDSGEELAEAIVSFIRAN  301 (302)
T ss_pred             HHHCCHHHHHHHHHHHHHHC
T ss_conf             58759999999999999758


No 160
>PRK11760 putative RNA 2'-O-ribose methyltransferase; Provisional
Probab=22.75  E-value=46  Score=12.88  Aligned_cols=50  Identities=10%  Similarity=0.053  Sum_probs=21.5

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCEEEEECCCCEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             889999999998654018835269982898350036765333247999999999999999998
Q gi|254780695|r  185 YKSAEAIRHLVAAAVPNLDMGDVTVLDSTGKLLTANEMERNILGKSLSIVQAIQHEIEMNINK  247 (563)
Q Consensus       185 ~~qv~~I~~lVa~sV~gL~~e~VtVvD~~G~~L~~~~~~~~~~~~~~~~~~~~E~~~~~kI~~  247 (563)
                      .+.|..|...++..            -..|.+.-. -.+......-..+-+++..-+++..+.
T Consensus        83 ~DRispi~~~l~~~------------~~~~~L~vE-~pDTnegK~Ls~fcRkft~pLr~aLrk  132 (356)
T PRK11760         83 EDRISPILAALQGV------------PKFGELRVE-TPDTNEGKELSKFCRKFTVPLRQALRK  132 (356)
T ss_pred             CCCHHHHHHHHHHC------------CCCCEEEEE-CCCCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             66578999998627------------886437886-589734378999999878999999986


No 161
>PRK10476 multidrug resistance protein MdtN; Provisional
Probab=22.72  E-value=46  Score=12.87  Aligned_cols=19  Identities=16%  Similarity=-0.013  Sum_probs=8.2

Q ss_pred             CCHHHHHHHHHHHHHCCCC
Q ss_conf             9989999999999977992
Q gi|254780695|r   55 LEVSDVNRISVALSEANID   73 (563)
Q Consensus        55 l~~~d~~~i~~~L~~~gI~   73 (563)
                      ++++-.+.|...+=..|=.
T Consensus        53 Is~~VsG~V~~V~V~egq~   71 (348)
T PRK10476         53 VASEVGGRIVELAVTENQA   71 (348)
T ss_pred             EECCCCEEEEEEEECCCCE
T ss_conf             9343445999999469998


No 162
>smart00824 PKS_TE Thioesterase. Peptide synthetases are involved in the non-ribosomal synthesis of peptide antibiotics. Next to the operons encoding these enzymes, in almost all cases, are genes that encode proteins that have similarity to the type II fatty acid thioesterases of vertebrates. There are also modules within the peptide synthetases that also share this similarity. With respect to antibiotic production, thioesterases are required for the addition of the last amino acid to the peptide antibiotic, thereby forming a cyclic antibiotic. Thioesterases (non-integrated) have molecular masses of 25-29 kDa.
Probab=22.65  E-value=46  Score=12.86  Aligned_cols=17  Identities=24%  Similarity=0.517  Sum_probs=14.8

Q ss_pred             HHHHCHHHHHHHHHHHH
Q ss_conf             98869998999999998
Q gi|254780695|r  534 MIEINEERFAKILRKWA  550 (563)
Q Consensus       534 lv~e~Pe~vA~vLR~WL  550 (563)
                      |.+++...+|++|+.||
T Consensus       196 ml~e~~~~~A~~i~~wl  212 (212)
T smart00824      196 MMEEHAAATARAVHDWL  212 (212)
T ss_pred             HHHHHHHHHHHHHHHHC
T ss_conf             41430999999999769


No 163
>PRK06087 short chain acyl-CoA synthetase; Reviewed
Probab=22.04  E-value=47  Score=12.78  Aligned_cols=19  Identities=5%  Similarity=-0.078  Sum_probs=9.0

Q ss_pred             CCCCCEEECCCCCHHHHHH
Q ss_conf             6998245038999899999
Q gi|254780695|r   44 NSPHYDNLYVKLEVSDVNR   62 (563)
Q Consensus        44 ~~p~y~~L~~~l~~~d~~~   62 (563)
                      ..--|++|+..+...+...
T Consensus        98 ~Gav~vpl~~~~~~~el~~  116 (548)
T PRK06087         98 TGAVSVPLLPSWREAELVW  116 (548)
T ss_pred             HCEEEEEECCCCCHHHHHH
T ss_conf             3909996789999999999


No 164
>cd02847 Chitobiase_C_term Chitobiase C-terminus domain. Chitobiase (AKA N-acetylglucosaminidase) digests the beta, 1-4 glycosidic bonds of the N-acetylglucosamine (NAG) oligomers found in chitin, an important structural element of fungal cell wall and arthropod exoskeletons.  It is thought to proceed through an acid-base reaction mechanism, in which one protein carboxylate acts as catalytic acid, while the nucleophile is the polar acetamido group of the sugar in a substrate-assisted reaction with retention of the anomeric configuration. The C-terminus of chitobiase may be related to the immunoglobulin and/or fibronectin type III superfamilies.  These domains are associated with different types of catalytic domains at  either the N-terminal or C-terminal end and may be involved in homodimeric/tetrameric/dodecameric interactions.  Members of this family include members of the alpha amylase family, sialidase, galactose oxidase, cellulase, cellulose, hyaluronate lyase, chitobiase, and chit
Probab=21.96  E-value=41  Score=13.18  Aligned_cols=13  Identities=38%  Similarity=0.690  Sum_probs=5.3

Q ss_pred             HHHHCCCCEEECC
Q ss_conf             9997799299918
Q gi|254780695|r   66 ALSEANIDFRISD   78 (563)
Q Consensus        66 ~L~~~gI~y~~~~   78 (563)
                      +|+.+||.|++..
T Consensus         2 KLdkaGi~YRlP~   14 (78)
T cd02847           2 KLDKAGIDYRLPV   14 (78)
T ss_pred             CHHHCCCCEECCC
T ss_conf             4775797021699


No 165
>PRK11100 sensory histidine kinase CreC; Provisional
Probab=21.95  E-value=48  Score=12.77  Aligned_cols=29  Identities=21%  Similarity=0.355  Sum_probs=20.5

Q ss_pred             CHHHHHH-HHHHHHHHCCCCCCCCCEEEEEE
Q ss_conf             9899999-99986431256611387689985
Q gi|254780695|r  381 IDSYLAE-INKIVSAATGINSRRGDTITITS  410 (563)
Q Consensus       381 ~~eel~~-I~~lV~~AiG~d~~RGD~VtV~~  410 (563)
                      ++..+.+ +.+|+.||+-|..+.| .|.|..
T Consensus       365 D~~~L~qvl~NLl~NAikys~~~g-~I~I~~  394 (475)
T PRK11100        365 DPFLLRQALGNLLDNAIDFTPEGG-TITLSA  394 (475)
T ss_pred             CHHHHHHHHHHHHHHHHHHCCCCC-EEEEEE
T ss_conf             899999999999999997389997-799999


No 166
>pfam01765 RRF Ribosome recycling factor. The ribosome recycling factor (RRF / ribosome release factor) dissociates the ribosome from the mRNA after termination of translation, and is essential bacterial growth. Thus ribosomes are "recycled" and ready for another round of protein synthesis.
Probab=21.87  E-value=48  Score=12.76  Aligned_cols=34  Identities=21%  Similarity=0.274  Sum_probs=22.2

Q ss_pred             CCCCCHHHHHHHHHHHHHH-CCCCCCC-CCEEEEEECCC
Q ss_conf             3346989999999986431-2566113-87689985035
Q gi|254780695|r  377 DQGKIDSYLAEINKIVSAA-TGINSRR-GDTITITSMDF  413 (563)
Q Consensus       377 ~~~~~~eel~~I~~lV~~A-iG~d~~R-GD~VtV~~~~F  413 (563)
                      ..||++..+..|..-+.++ +|+++.+ |+.   .-++|
T Consensus        49 I~~~D~~~v~~I~kAI~~s~LglnP~~dg~~---Irv~i   84 (165)
T pfam01765        49 ITPWDKSLIKAIEKAILASDLGLNPQNDGQV---IRIPI   84 (165)
T ss_pred             EEECCHHHHHHHHHHHHHCCCCCCCCCCCCE---EEEEC
T ss_conf             8734244379999999857999787747877---89858


No 167
>COG2815 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.84  E-value=48  Score=12.76  Aligned_cols=37  Identities=24%  Similarity=0.317  Sum_probs=19.0

Q ss_pred             HHHHHHHHHCCCCCE--EECCCCCHHHHHHHHHHHHHCCCCEE
Q ss_conf             999999984699824--50389998999999999997799299
Q gi|254780695|r   35 LFMAARFFVNSPHYD--NLYVKLEVSDVNRISVALSEANIDFR   75 (563)
Q Consensus        35 ~~~~~~~~~~~p~y~--~L~~~l~~~d~~~i~~~L~~~gI~y~   75 (563)
                      .+++.++|. .|.++  +-..+++..+|   ...|+..|...+
T Consensus        13 v~~~~~~~~-~p~~v~vP~v~g~~~~~A---~~~l~~~~l~v~   51 (303)
T COG2815          13 VLLATFFPV-SPDKVKVPNVAGLDEEDA---KAELQKAGLEVG   51 (303)
T ss_pred             HHHHHEEEE-CCCEEECCCCCCCCHHHH---HHHHHHCCCEEE
T ss_conf             996412120-687146377677648999---999986475353


No 168
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=21.65  E-value=48  Score=12.73  Aligned_cols=10  Identities=10%  Similarity=0.218  Sum_probs=3.8

Q ss_pred             HHHHHHHHHH
Q ss_conf             9999977875
Q gi|254780695|r  454 FLGLHALRRL  463 (563)
Q Consensus       454 ~~vl~~l~~~  463 (563)
                      ||.+|+-++.
T Consensus        17 ffmiRpQkK~   26 (120)
T PRK06531         17 FFMQRQQKKQ   26 (120)
T ss_pred             HHEECHHHHH
T ss_conf             8603748899


No 169
>TIGR03056 bchO_mg_che_rel putative magnesium chelatase accessory protein. Members of this family belong to the alpha/beta fold family hydrolases (pfam00561). Members are found in bacterial genomes if and only if they encoded for anoxygenic photosynthetic systems similar to that of Rhodobacter capsulatus and other alpha-Proteobacteria. Members often are encoded in the same operon as subunits of the protoporphyrin IX magnesium chelatase, and were once designated BchO. No literature supports a role as an actual subunit of magnesium chelatase, but an accessory role is possible, as suggested by placement by its probable hydrolase activity.
Probab=21.59  E-value=48  Score=12.72  Aligned_cols=18  Identities=11%  Similarity=0.112  Sum_probs=15.9

Q ss_pred             HHHHCHHHHHHHHHHHHH
Q ss_conf             988699989999999986
Q gi|254780695|r  534 MIEINEERFAKILRKWAR  551 (563)
Q Consensus       534 lv~e~Pe~vA~vLR~WL~  551 (563)
                      .-.|+||+++++|+.||.
T Consensus       261 ~~~E~Pe~v~~~i~~fle  278 (278)
T TIGR03056       261 VHEEQADGVVGLILQAAE  278 (278)
T ss_pred             HHHHHHHHHHHHHHHHHC
T ss_conf             689759999999999859


No 170
>PRK09481 sspA stringent starvation protein A; Provisional
Probab=21.40  E-value=49  Score=12.70  Aligned_cols=53  Identities=15%  Similarity=0.157  Sum_probs=33.4

Q ss_pred             HCCCCCEEECCCCCHHHHHHHHHHHHHCCCCEEECCCCCEEEECHHHHHHHHHHHHHCC
Q ss_conf             46998245038999899999999999779929991899779951899999999999769
Q gi|254780695|r   43 VNSPHYDNLYVKLEVSDVNRISVALSEANIDFRISDNGSSISVPSSMVGKARIHLAAQG  101 (563)
Q Consensus        43 ~~~p~y~~L~~~l~~~d~~~i~~~L~~~gI~y~~~~~g~~I~Vp~~~~~~~r~~La~~g  101 (563)
                      .|+.++-.||+.--.-=+..|-=.|.+.||+|++      +.|+-.+....-+.+.-.|
T Consensus         5 ~~~~~mm~LY~~~~sp~s~rVri~L~EKgl~~e~------~~vd~~~~~~~~l~iNP~G   57 (211)
T PRK09481          5 ANKRSVMTLFSGPTDIYSHQVRIVLAEKGVSVEI------EQVEKDNLPQDLIDLNPYQ   57 (211)
T ss_pred             CCCCCEEEEECCCCCHHHHHHHHHHHHCCCCCEE------EEECCCCCCHHHHHHCCCC
T ss_conf             5777337776999984799999999966998669------8738664879999748899


No 171
>COG4674 Uncharacterized ABC-type transport system, ATPase component [General function prediction only]
Probab=21.34  E-value=36  Score=13.61  Aligned_cols=56  Identities=14%  Similarity=0.159  Sum_probs=25.3

Q ss_pred             CCCCEEECCCCCHHHHHHHHHHHHHCCCCEEECCCCCEEEECHHHHHHHHHHHHHC
Q ss_conf             99824503899989999999999977992999189977995189999999999976
Q gi|254780695|r   45 SPHYDNLYVKLEVSDVNRISVALSEANIDFRISDNGSSISVPSSMVGKARIHLAAQ  100 (563)
Q Consensus        45 ~p~y~~L~~~l~~~d~~~i~~~L~~~gI~y~~~~~g~~I~Vp~~~~~~~r~~La~~  100 (563)
                      ++-+..||..+..++...|-..|.--|..-+-..--+.+.--++|.-+.-|.|+..
T Consensus       110 k~v~a~L~~r~~~~e~~ride~La~igL~~~~~~~A~~LSHGqKQwLEIGMll~Q~  165 (249)
T COG4674         110 KSVFASLFARLRAEERRRIDELLATIGLGDERDRLAALLSHGQKQWLEIGMLLAQD  165 (249)
T ss_pred             CCHHHHHHHHCCHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCHHHHHHHHEEECCC
T ss_conf             55587864431745777798899880652443036666153246653001155058


No 172
>pfam09179 TilS TilS substrate binding domain. This domain is found in the tRNA(Ile) lysidine synthetase (TilS) protein.
Probab=21.06  E-value=50  Score=12.65  Aligned_cols=21  Identities=19%  Similarity=0.438  Sum_probs=10.9

Q ss_pred             HHHHHHCHHHHHHHHHHHHHH
Q ss_conf             999886999899999999863
Q gi|254780695|r  532 LHMIEINEERFAKILRKWARS  552 (563)
Q Consensus       532 ~~lv~e~Pe~vA~vLR~WL~e  552 (563)
                      ..|..-.|.+..+|||.||..
T Consensus         4 ~~l~~l~~~r~~~lLR~wL~~   24 (69)
T pfam09179         4 AALAALSPARQRNLLRYWLAQ   24 (69)
T ss_pred             HHHHHCCHHHHHHHHHHHHHH
T ss_conf             887759999999999999998


No 173
>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB; InterPro: IPR014149   This entry represents TrbB, a protein, which is encoded in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer . TrbB is a homologue of the vir system VirB11 ATPase , and the Flp pilus system ATPase TadA ..
Probab=20.93  E-value=50  Score=12.64  Aligned_cols=63  Identities=19%  Similarity=0.169  Sum_probs=32.3

Q ss_pred             HHHHHHHHHHHHHHC-CCCCEEEEEEEECCCCCCCCCCCCCCEEEEEECCCC-CCHHHHHHHHHHHHHHHH
Q ss_conf             999999999999605-763148999983366655555558715999706877-898899999999986540
Q gi|254780695|r  132 VRALEGEIARTIQSI-SGIVAARVHIVMPDMGSFRKIGARPTASVMIRAINP-SVYKSAEAIRHLVAAAVP  200 (563)
Q Consensus       132 ~ralegeL~rtI~~~-~~V~~ArV~l~~p~~~~f~~~~~~~sASV~l~~~~~-l~~~qv~~I~~lVa~sV~  200 (563)
                      .|.|+..|...|..+ |.=.=.=++| .|+-.+|++.=..+     +...+. +++.++++|.++||+.+.
T Consensus         3 ~r~l~~~lG~~i~~~LdD~~vvEIML-NpDG~Lwve~Lg~G-----~~~~G~t~~~~~a~~Ii~~vA~~l~   67 (315)
T TIGR02782         3 VRKLRRALGPEIAAALDDPKVVEIML-NPDGKLWVERLGEG-----MEPLGKTVSPADAERIIGLVADYLG   67 (315)
T ss_pred             HHHHHHHHHHHHHHHHCCCCEEEEEE-CCCCHHHHHHCCCC-----CCCCCCCCCHHHHHHHHHHHHHHHC
T ss_conf             67899998999999737988389986-69870105006797-----3001661178999999999987644


No 174
>PRK06357 hypothetical protein; Provisional
Probab=20.85  E-value=50  Score=12.62  Aligned_cols=20  Identities=15%  Similarity=0.333  Sum_probs=15.0

Q ss_pred             HHCCCCCCEEEEECCCCEEE
Q ss_conf             40188352699828983500
Q gi|254780695|r  199 VPNLDMGDVTVLDSTGKLLT  218 (563)
Q Consensus       199 V~gL~~e~VtVvD~~G~~L~  218 (563)
                      ...|+++++.++|.+|+.+.
T Consensus        51 ~~~l~~ediv~vD~~G~~i~   70 (211)
T PRK06357         51 LCDLSPYEILVVDNNNEVVE   70 (211)
T ss_pred             CCCCCHHHEEEECCCCCEEC
T ss_conf             35798889789869999836


No 175
>TIGR03261 phnS2 putative 2-aminoethylphosphonate ABC transport system, 1-aminoethylphosphonate-binding protein component. This ABC transporter extracellular solute-binding protein is found in a number of genomes in operon-like contexts strongly suggesting a substrate specificity for 2-aminoethylphosphonate (2-AEP). The characterized PhnSTUV system is absent in the genomes in which this system is found. These genomes encode systems for the catabolism of 2-AEP, making the need for a 2-AEP-specific transporter likely.
Probab=20.73  E-value=50  Score=12.61  Aligned_cols=43  Identities=9%  Similarity=0.096  Sum_probs=32.6

Q ss_pred             HHHHHHCCCCCEEECCCCCHHHHHHHHHHHHHC--CCCEEECCCC
Q ss_conf             999984699824503899989999999999977--9929991899
Q gi|254780695|r   38 AARFFVNSPHYDNLYVKLEVSDVNRISVALSEA--NIDFRISDNG   80 (563)
Q Consensus        38 ~~~~~~~~p~y~~L~~~l~~~d~~~i~~~L~~~--gI~y~~~~~g   80 (563)
                      +..--.....-.++|+..+..-...|+...++.  ||..++-..+
T Consensus        13 ~~a~aa~~~~~l~VYss~~~~~~~~i~~~Fek~~tgIkV~~v~~~   57 (334)
T TIGR03261        13 FSACNSKANTELTVYTAIEDELIAKYKDAFEKVNPDIKINWVRDS   57 (334)
T ss_pred             HHHHHHCCCCEEEEEECCCHHHHHHHHHHHHHHCCCCEEEEEECC
T ss_conf             983103029959999699888999999999977799489999897


No 176
>cd04390 RhoGAP_ARHGAP22_24_25 RhoGAP_ARHGAP22_24_25:  GTPase-activator protein (GAP) domain for Rho-like GTPases found in ARHGAP22, 24 and 25-like proteins; longer isoforms of these proteins contain an additional N-terminal pleckstrin homology (PH) domain. ARHGAP25 (KIA0053) has been identified as a GAP for Rac1 and Cdc42. Short isoforms (without the PH domain) of ARHGAP24, called RC-GAP72 and p73RhoGAP, and of ARHGAP22, called p68RacGAP, has been shown to be involved in angiogenesis and endothelial cell capillary formation. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the r
Probab=20.59  E-value=51  Score=12.59  Aligned_cols=10  Identities=0%  Similarity=0.282  Sum_probs=3.6

Q ss_pred             HCCCCCCEEE
Q ss_conf             0188352699
Q gi|254780695|r  200 PNLDMGDVTV  209 (563)
Q Consensus       200 ~gL~~e~VtV  209 (563)
                      -.|++.|..+
T Consensus       151 NkM~~~NLAi  160 (199)
T cd04390         151 NKMSVQNLAT  160 (199)
T ss_pred             CCCCHHHHHH
T ss_conf             4898388888


No 177
>PRK11486 flagellar biosynthesis protein FliO; Provisional
Probab=20.31  E-value=51  Score=12.55  Aligned_cols=17  Identities=12%  Similarity=0.425  Sum_probs=10.9

Q ss_pred             HCHHHHHHHHHHHHHHH
Q ss_conf             69998999999998637
Q gi|254780695|r  537 INEERFAKILRKWARSE  553 (563)
Q Consensus       537 e~Pe~vA~vLR~WL~ee  553 (563)
                      ..|..++++|++-|+..
T Consensus       105 ~~~~~F~~~L~~~lkr~  121 (124)
T PRK11486        105 IPQADFQSVMKNLLKRS  121 (124)
T ss_pred             CCCHHHHHHHHHHHCCC
T ss_conf             99655999999997024


No 178
>PRK00783 DNA-directed RNA polymerase subunit D; Provisional
Probab=20.06  E-value=52  Score=12.52  Aligned_cols=38  Identities=32%  Similarity=0.444  Sum_probs=33.4

Q ss_pred             CCCCHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCEEE
Q ss_conf             77898899999999986540188352699828983500
Q gi|254780695|r  181 NPSVYKSAEAIRHLVAAAVPNLDMGDVTVLDSTGKLLT  218 (563)
Q Consensus       181 ~~l~~~qv~~I~~lVa~sV~gL~~e~VtVvD~~G~~L~  218 (563)
                      .+.+..-+.||+..+=+-||.|.-+.|.|.++++.+-.
T Consensus        18 ~~~~~s~aNalRRillseVPt~AId~V~I~~NtS~l~D   55 (265)
T PRK00783         18 SGVTPAFANALRRAMIAEVPTLAIEDVNIYDNTSALFD   55 (265)
T ss_pred             ECCCHHHHHHHHHHHHHCCCEEEEEEEEEEECCCCCCC
T ss_conf             78988998899999987397027999999858731455


No 179
>TIGR01846 type_I_sec_HlyB type I secretion system ATPase; InterPro: IPR010132   Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This entry contains one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N terminus, but rather carry signals located toward the extreme C terminus to direct type I secretion.; GO: 0005524 ATP binding, 0008565 protein transporter activity, 0015031 protein transport, 0016021 integral to membrane.
Probab=20.03  E-value=52  Score=12.51  Aligned_cols=112  Identities=16%  Similarity=0.162  Sum_probs=64.4

Q ss_pred             HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEECCCCCHHHHHHHHHHHHHCCC--CEEECCCCC
Q ss_conf             899999999864069878899999999999999999998469982450389998999999999997799--299918997
Q gi|254780695|r    4 LDQLLQFFKSGTSLGRTRILILASVILVPIMLFMAARFFVNSPHYDNLYVKLEVSDVNRISVALSEANI--DFRISDNGS   81 (563)
Q Consensus         4 ~~~l~~~~~~~~~l~~~~ki~~~~~~~~~i~~~~~~~~~~~~p~y~~L~~~l~~~d~~~i~~~L~~~gI--~y~~~~~g~   81 (563)
                      |+++.+|.   ++    .-+.+.+=+..+++++.+|+||+.+=+|+++++=.-.-=-.-++.=+-...|  .|+-+.+.+
T Consensus       252 le~IR~FL---TG----saLT~~lDl~F~~vF~AVMf~YSp~LT~vV~~SL~~Y~~~s~~v~p~LRkRVe~kfe~~A~~~  324 (703)
T TIGR01846       252 LEQIRNFL---TG----SALTVVLDLLFVVVFLAVMFFYSPTLTGVVIGSLVCYALLSVFVSPILRKRVEDKFERSAEAT  324 (703)
T ss_pred             HHHHHHHH---HH----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             77786576---66----799999877788867878876401688789999999999999850011023577641340002


Q ss_pred             EEEECHHHHHHHHHHHHHCCCCCCCCCCHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             79951899999999999769988776632565305888425999999999999999999999605
Q gi|254780695|r   82 SISVPSSMVGKARIHLAAQGLPSSSSNSGYELFDKVNSFGLTSFMQEITRVRALEGEIARTIQSI  146 (563)
Q Consensus        82 ~I~Vp~~~~~~~r~~La~~glp~~~~~~g~el~d~~~~~g~T~~~~~~~~~ralegeL~rtI~~~  146 (563)
                      +.+|-+=-                    |-+-. |.+   ++|-..+-++.|-|=+.++++-...
T Consensus       325 sFLvEsVt--------------------Gi~TI-Ka~---A~Epq~~~rW~~~LA~Yv~~SF~~~  365 (703)
T TIGR01846       325 SFLVESVT--------------------GIETI-KAS---AVEPQFQRRWDRQLAAYVAASFRVT  365 (703)
T ss_pred             EEEEEEEE--------------------CCCCC-CCC---CCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             12122310--------------------25410-003---2176676589999999997567898


Done!