Query         gi|254780773|ref|YP_003065186.1| zinc metallopeptidase [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 349
No_of_seqs    200 out of 3136
Neff          8.3 
Searched_HMMs 39220
Date          Sun May 29 21:25:13 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780773.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK10779 zinc metallopeptidase 100.0       0       0  712.6  28.7  341    1-347     1-449 (449)
  2 TIGR00054 TIGR00054 membrane-a 100.0       0       0  661.1  25.6  341    1-348     1-462 (463)
  3 COG0750 Predicted membrane-ass 100.0       0       0  436.1  24.1  346    4-349     2-375 (375)
  4 cd06163 S2P-M50_PDZ_RseP-like  100.0       0       0  428.1  16.0  174    7-346     1-182 (182)
  5 pfam02163 Peptidase_M50 Peptid 100.0 4.3E-42       0  310.1  14.8  205    9-343     1-205 (205)
  6 cd05709 S2P-M50 Site-2 proteas 100.0 1.3E-33 3.2E-38  251.7   9.4  179    9-342     2-180 (180)
  7 cd06159 S2P-M50_PDZ_Arch Uncha  99.9 2.1E-26 5.4E-31  201.8  11.6  133    6-324   109-241 (263)
  8 LOAD_S2Pmetalloprt consensus    99.9 2.6E-24 6.7E-29  187.4   7.4  147   10-314     2-148 (148)
  9 cd06161 S2P-M50_SpoIVFB SpoIVF  99.8 1.6E-18   4E-23  147.5  14.1  151    7-342    30-180 (208)
 10 cd06164 S2P-M50_SpoIVFB_CBS Sp  99.8 4.6E-18 1.2E-22  144.3  15.1  148    8-337    46-193 (227)
 11 KOG2921 consensus               99.8   4E-18   1E-22  144.8  11.0  137    5-163   121-266 (484)
 12 cd06162 S2P-M50_PDZ_SREBP Ster  99.7 1.5E-15 3.8E-20  127.0  11.5   85    5-111   125-209 (277)
 13 cd06160 S2P-M50_like_2 Unchara  99.6 2.9E-14 7.5E-19  118.1  13.0   78    7-108    33-111 (183)
 14 cd06158 S2P-M50_like_1 Unchara  99.6 1.1E-14 2.8E-19  121.1   7.7   94    8-110     2-102 (181)
 15 cd00989 PDZ_metalloprotease PD  99.4 1.1E-13 2.8E-18  114.2   5.4   75  111-186     5-79  (79)
 16 TIGR02037 degP_htrA_DO proteas  99.3 8.1E-13 2.1E-17  108.1   4.5   66  121-187   296-362 (484)
 17 cd00991 PDZ_archaeal_metallopr  99.2   1E-11 2.6E-16  100.5   4.9   61  120-180    12-73  (79)
 18 PRK10139 serine endoprotease;   99.1 8.9E-11 2.3E-15   94.1   6.3   65  121-186   293-358 (455)
 19 PRK10942 serine endoprotease;   99.1 8.2E-11 2.1E-15   94.3   5.3   65  121-186   315-380 (474)
 20 PRK10898 serine endoprotease;   99.1 1.2E-10   3E-15   93.3   5.4   65  121-186   283-348 (355)
 21 cd00988 PDZ_CTP_protease PDZ d  99.1 2.3E-10 5.8E-15   91.2   5.3   68  119-186    14-83  (85)
 22 cd00986 PDZ_LON_protease PDZ d  99.0 4.3E-10 1.1E-14   89.3   4.8   64  120-185    10-74  (79)
 23 cd00987 PDZ_serine_protease PD  99.0 5.4E-10 1.4E-14   88.7   4.9   63  120-183    26-89  (90)
 24 cd00990 PDZ_glycyl_aminopeptid  99.0 5.3E-10 1.3E-14   88.7   4.7   63  120-185    14-76  (80)
 25 TIGR02860 spore_IV_B stage IV   99.0 8.4E-10 2.1E-14   87.3   5.1   78  128-206   141-222 (423)
 26 TIGR02038 protease_degS peripl  99.0 8.9E-10 2.3E-14   87.2   4.9   64  121-185   288-352 (358)
 27 TIGR02037 degP_htrA_DO proteas  98.7 1.7E-08 4.3E-13   78.4   4.6   60  121-180   419-481 (484)
 28 cd00136 PDZ PDZ domain, also c  98.6 3.2E-08 8.2E-13   76.4   4.1   54  119-172    14-69  (70)
 29 COG0793 Prc Periplasmic protea  98.6 2.7E-07 6.8E-12   70.1   8.4   69  118-186   112-183 (406)
 30 PRK10139 serine endoprotease;   98.6 7.6E-08 1.9E-12   73.8   4.7   59  120-179   392-450 (455)
 31 PRK10942 serine endoprotease;   98.6 8.8E-08 2.3E-12   73.4   4.9   59  120-179   411-469 (474)
 32 COG3480 SdrC Predicted secrete  98.6 2.3E-07 5.9E-12   70.5   6.9  153  121-277   133-294 (342)
 33 TIGR03279 cyano_FeS_chp putati  98.4 3.2E-07 8.2E-12   69.5   5.0   62  121-185     1-62  (433)
 34 COG1994 SpoIVFB Zn-dependent p  98.4 1.2E-06 3.1E-11   65.6   7.7   44  273-316   136-179 (230)
 35 PRK11186 carboxy-terminal prot  98.4 2.4E-06 6.1E-11   63.5   8.3   66  120-185   259-334 (673)
 36 smart00228 PDZ Domain present   98.4 4.2E-07 1.1E-11   68.7   4.4   57  119-176    27-85  (85)
 37 PRK10779 zinc metallopeptidase  98.2 1.6E-06 4.2E-11   64.6   4.9   59  120-178   128-187 (449)
 38 COG0265 DegQ Trypsin-like seri  98.2   2E-06 5.1E-11   64.1   5.1   66  120-186   272-338 (347)
 39 KOG3129 consensus               98.2 2.5E-06 6.5E-11   63.3   5.6   78  120-198   141-221 (231)
 40 pfam00595 PDZ PDZ domain (Also  98.2 1.5E-06 3.9E-11   64.8   3.4   52  120-172    26-79  (80)
 41 cd00992 PDZ_signaling PDZ doma  98.1 2.4E-06   6E-11   63.6   3.6   54  118-172    26-81  (82)
 42 TIGR00054 TIGR00054 membrane-a  97.8 1.6E-05 4.2E-10   57.8   3.4   83  120-202   137-229 (463)
 43 COG3975 Predicted protease wit  97.6 8.2E-05 2.1E-09   52.9   4.6   59  121-187   465-523 (558)
 44 KOG1320 consensus               97.6 7.7E-05   2E-09   53.1   4.2   95   94-189   369-469 (473)
 45 KOG1421 consensus               97.6 9.4E-05 2.4E-09   52.5   4.4   64  121-186   306-369 (955)
 46 KOG3209 consensus               97.5 0.00011 2.8E-09   52.1   3.7   62  115-177   775-839 (984)
 47 pfam04495 GRASP55_65 GRASP55/6  97.0  0.0014 3.5E-08   44.5   5.0   68  121-188    46-115 (280)
 48 PRK09681 putative type II secr  96.9  0.0011 2.8E-08   45.2   4.1   58  125-183   254-315 (319)
 49 TIGR01713 typeII_sec_gspC gene  96.9  0.0011 2.8E-08   45.1   3.7   54  125-178   220-274 (281)
 50 pfam01434 Peptidase_M41 Peptid  96.7  0.0017 4.3E-08   43.9   3.5   67   17-102    10-78  (192)
 51 KOG3532 consensus               96.6  0.0023 5.9E-08   42.9   3.5   47  121-167   401-447 (1051)
 52 TIGR00225 prc C-terminal proce  96.3   0.018 4.5E-07   36.8   6.7   58  119-176    67-131 (361)
 53 COG3031 PulC Type II secretory  96.3  0.0059 1.5E-07   40.1   4.0   54  125-178   214-268 (275)
 54 COG1994 SpoIVFB Zn-dependent p  96.2  0.0028 7.3E-08   42.3   2.1   72   14-107    51-123 (230)
 55 KOG3553 consensus               96.2  0.0028 7.1E-08   42.4   2.0   55  120-176    61-117 (124)
 56 KOG3580 consensus               96.0  0.0035 8.8E-08   41.7   1.9   53  121-173   432-487 (1027)
 57 KOG3834 consensus               95.9    0.01 2.6E-07   38.4   3.9   69  121-189   112-182 (462)
 58 KOG3552 consensus               95.9  0.0055 1.4E-07   40.3   2.4   55  119-175    75-132 (1298)
 59 PRK10733 hflB ATP-dependent me  95.8  0.0084 2.1E-07   39.1   3.3   39   23-65     34-72  (644)
 60 KOG3834 consensus               95.7   0.013 3.3E-07   37.8   3.7   71  118-189    15-88  (462)
 61 KOG3209 consensus               95.7  0.0092 2.3E-07   38.8   2.9   54  121-174   374-431 (984)
 62 KOG0606 consensus               94.7   0.014 3.6E-07   37.5   1.5   42  120-161   660-703 (1205)
 63 KOG3542 consensus               94.3   0.022 5.7E-07   36.1   1.8   34  121-154   565-598 (1283)
 64 KOG1421 consensus               94.3   0.062 1.6E-06   33.1   3.9   54  121-184   774-827 (955)
 65 KOG3651 consensus               93.8   0.042 1.1E-06   34.2   2.4   53  121-174    33-88  (429)
 66 KOG3580 consensus               93.5   0.056 1.4E-06   33.4   2.5   57  122-179   223-282 (1027)
 67 KOG3549 consensus               93.4   0.066 1.7E-06   32.9   2.8   55  119-174    81-138 (505)
 68 KOG3605 consensus               92.9    0.19 4.7E-06   29.8   4.5   67  110-176   663-735 (829)
 69 TIGR01241 FtsH_fam ATP-depende  92.6   0.041 1.1E-06   34.3   0.7   11  178-188   338-348 (505)
 70 KOG1892 consensus               92.4   0.076 1.9E-06   32.4   1.9   57  120-177   962-1021(1629)
 71 KOG3551 consensus               90.2    0.16 4.2E-06   30.2   1.8   55  119-174   111-168 (506)
 72 COG0465 HflB ATP-dependent Zn   89.3    0.29 7.3E-06   28.5   2.5   27   29-55     32-58  (596)
 73 KOG0609 consensus               88.3    0.32   8E-06   28.2   2.1   55  119-174   147-204 (542)
 74 KOG1738 consensus               87.6    0.61 1.6E-05   26.2   3.2   44  121-164   228-274 (638)
 75 KOG3550 consensus               86.4    0.38 9.8E-06   27.6   1.7   54  118-172   114-171 (207)
 76 KOG3606 consensus               86.4    0.73 1.8E-05   25.7   3.1   55  121-176   197-254 (358)
 77 KOG3571 consensus               86.1    0.61 1.6E-05   26.2   2.6   57  120-176   279-340 (626)
 78 pfam11874 DUF3394 Domain of un  85.7    0.56 1.4E-05   26.5   2.2   26  120-145   124-149 (183)
 79 KOG3605 consensus               83.0    0.67 1.7E-05   25.9   1.7   26  317-342   585-610 (829)
 80 pfam01079 Hint Hint module. Th  80.8     1.8 4.5E-05   23.0   3.1   58  128-187    24-82  (214)
 81 pfam07136 DUF1385 Protein of u  79.4     4.8 0.00012   20.0   5.6   16   95-110    43-58  (235)
 82 pfam02128 Peptidase_M36 Fungal  77.7    0.18 4.7E-06   29.8  -2.7   17  304-320   315-331 (368)
 83 cd04278 ZnMc_MMP Zinc-dependen  73.0     1.8 4.7E-05   22.9   1.4   12   53-64      4-15  (157)
 84 TIGR02289 M3_not_pepF oligoend  72.4       2 5.1E-05   22.7   1.5   25  136-160   253-278 (553)
 85 cd06457 M3A_MIP Peptidase M3 m  69.0     3.5 8.9E-05   21.0   2.1   17   23-39    138-154 (458)
 86 KOG4407 consensus               69.0     5.2 0.00013   19.8   3.0   45  121-165   146-192 (1973)
 87 COG5233 GRH1 Peripheral Golgi   68.2     3.3 8.4E-05   21.2   1.9   31  121-151    66-96  (417)
 88 cd06456 M3A_DCP_Oligopeptidase  66.9     4.4 0.00011   20.3   2.3   22  300-321   395-416 (422)
 89 pfam00413 Peptidase_M10 Matrix  66.2     2.1 5.2E-05   22.6   0.5   14   50-64      2-15  (158)
 90 TIGR01700 PNPH purine nucleosi  66.0     2.9 7.4E-05   21.5   1.2   15  132-146    96-110 (259)
 91 COG0339 Dcp Zn-dependent oligo  63.8     5.1 0.00013   19.8   2.2   32  225-257   462-493 (683)
 92 pfam01432 Peptidase_M3 Peptida  63.5     5.6 0.00014   19.6   2.3   20  300-319   421-440 (448)
 93 COG0260 PepB Leucyl aminopepti  62.1     3.4 8.8E-05   21.0   1.0   29  122-151   302-330 (485)
 94 cd06459 M3B_Oligoendopeptidase  61.8     4.2 0.00011   20.4   1.4   27  136-162   137-165 (427)
 95 TIGR00181 pepF oligoendopeptid  61.7     3.9 9.9E-05   20.6   1.2   19   15-33    389-410 (611)
 96 cd06455 M3A_TOP Peptidase M3 T  60.3       6 0.00015   19.3   2.0   22  299-320   446-467 (472)
 97 pfam00883 Peptidase_M17 Cytoso  59.0     4.2 0.00011   20.4   1.0   29  122-151   135-163 (312)
 98 PRK04860 hypothetical protein;  58.7       5 0.00013   19.9   1.4   18   18-36     66-83  (160)
 99 TIGR01697 PNPH-PUNA-XAPA inosi  57.8     6.2 0.00016   19.3   1.7   12  133-144   103-114 (266)
100 pfam06838 Alum_res Aluminium r  54.6     8.3 0.00021   18.4   1.9   42  129-170    87-128 (405)
101 cd06258 Peptidase_M3_like The   54.1     8.7 0.00022   18.3   2.0   21  300-320   340-360 (365)
102 PRK00913 leucyl aminopeptidase  51.7     6.2 0.00016   19.2   0.9   27  124-151   308-334 (491)
103 KOG3714 consensus               51.6     4.8 0.00012   20.0   0.3   14  134-147   141-155 (411)
104 cd00433 Peptidase_M17 Cytosol   50.1     6.4 0.00016   19.2   0.8   27  124-151   291-317 (468)
105 KOG1565 consensus               48.5     6.2 0.00016   19.3   0.5   12   15-26    211-222 (469)
106 TIGR02386 rpoC_TIGR DNA-direct  48.0     5.7 0.00014   19.5   0.2   10  136-145  1295-1304(1552)
107 PRK05113 electron transport co  43.4      22 0.00057   15.4   3.6   34    4-37      1-34  (184)
108 KOG2597 consensus               43.1      11 0.00029   17.4   1.2   25  126-151   328-352 (513)
109 pfam04298 Zn_peptidase_2 Putat  43.0      15 0.00039   16.6   1.8   32  277-308   143-176 (222)
110 cd04282 ZnMc_meprin Zinc-depen  42.7      12  0.0003   17.3   1.2   11  135-145   104-114 (230)
111 TIGR03296 M6dom_TIGR03296 M6 f  41.4     4.2 0.00011   20.5  -1.3   11  142-152   140-150 (286)
112 COG2317 Zn-dependent carboxype  40.8      16 0.00041   16.4   1.6   11  166-176   243-253 (497)
113 COG4307 Uncharacterized protei  40.6      15 0.00039   16.5   1.5   17   56-72     56-72  (349)
114 KOG3984 consensus               40.5     9.4 0.00024   18.0   0.4   28  130-157   118-145 (286)
115 TIGR02290 M3_fam_3 oligoendope  40.1      16 0.00041   16.4   1.6   16   87-102   219-234 (600)
116 COG4956 Integral membrane prot  40.0      19 0.00048   16.0   1.9   34  145-178   272-307 (356)
117 COG3091 SprT Zn-dependent meta  39.9      21 0.00052   15.7   2.1   23   13-36     59-81  (156)
118 cd06460 M32_Taq Peptidase fami  38.2      19 0.00049   15.9   1.7   16  305-320   371-386 (396)
119 COG4100 Cystathionine beta-lya  38.1      16  0.0004   16.4   1.3   40  131-170    99-138 (416)
120 pfam06167 MtfA Phosphoenolpyru  37.4      15 0.00039   16.5   1.1   18  145-162   128-145 (248)
121 PRK13267 archaemetzincin-like   36.8      14 0.00035   16.9   0.8   12  138-149    67-78  (177)
122 pfam08434 CLCA_N Calcium-activ  36.8      13 0.00033   17.0   0.6   16  129-144    91-106 (262)
123 pfam05547 Peptidase_M6 Immune   35.8     3.9  0.0001   20.6  -2.1   22  152-173   419-440 (646)
124 pfam02074 Peptidase_M32 Carbox  35.7      23 0.00058   15.4   1.7   16  305-320   470-485 (494)
125 COG3732 SrlE Phosphotransferas  34.2      31 0.00079   14.4   5.1   56  258-313   167-231 (328)
126 COG1164 Oligoendopeptidase F [  34.1      29 0.00073   14.7   2.0   31  131-161   286-322 (598)
127 TIGR01592 holin_SPP1 holin, SP  33.7      31  0.0008   14.4   2.3   24  274-297     8-31  (82)
128 COG4219 MecR1 Antirepressor re  33.0      20  0.0005   15.8   1.1   16  289-304   269-284 (337)
129 PRK07118 ferredoxin; Validated  31.1      35 0.00088   14.1   3.5   34    4-37      1-34  (276)
130 cd03506 Delta6-FADS-like The D  31.0      35 0.00089   14.1   2.5   32    5-38      3-34  (204)
131 pfam10462 Peptidase_M66 Peptid  30.5     7.7  0.0002   18.6  -1.4   15   55-69     46-60  (304)
132 pfam11667 DUF3267 Protein of u  30.5       9 0.00023   18.1  -1.0   21   15-35      4-24  (107)
133 pfam01435 Peptidase_M48 Peptid  29.9      26 0.00065   15.0   1.2   21  130-150    40-60  (222)
134 COG2707 Predicted membrane pro  29.6      37 0.00093   13.9   2.8   23  288-310   125-147 (151)
135 PRK05015 aminopeptidase B; Pro  29.6     7.9  0.0002   18.5  -1.4   27  124-151   242-268 (424)
136 PRK09194 prolyl-tRNA synthetas  29.1      34 0.00086   14.2   1.7   21   42-62     88-108 (570)
137 cd03507 Delta12-FADS-like The   29.1      37 0.00095   13.9   2.4   27    6-32     37-63  (222)
138 TIGR00819 ydaH AbgT transporte  28.6      31 0.00078   14.5   1.4   30  273-302   403-441 (527)
139 TIGR01393 lepA GTP-binding pro  28.5      20 0.00052   15.7   0.5   35   33-72     50-85  (598)
140 pfam00262 Calreticulin Calreti  27.4      32 0.00082   14.3   1.4   25   64-88     87-111 (359)
141 TIGR02149 glgA_Coryne glycogen  27.3      40   0.001   13.7   2.0   72  129-206   152-226 (416)
142 COG4043 Preprotein translocase  27.2      28 0.00072   14.7   1.1   37  131-168    29-72  (111)
143 PRK07740 hypothetical protein;  27.0      19 0.00048   15.9   0.1   21  132-152    65-87  (240)
144 TIGR01687 moaD_arch MoaD famil  26.7      37 0.00094   13.9   1.6   47  121-169    31-85  (93)
145 pfam09101 Exotox-A_bind Exotox  26.4      41  0.0011   13.6   2.4   13  138-150    31-43  (274)
146 COG0442 ProS Prolyl-tRNA synth  26.3      41   0.001   13.6   1.7   21   42-62     88-108 (500)
147 cd03510 Rhizobitoxine-FADS-lik  25.0      44  0.0011   13.4   2.8   25   12-38     31-55  (175)
148 PRK04897 heat shock protein Ht  24.9      35  0.0009   14.0   1.2   17  131-147   110-126 (298)
149 TIGR02737 caa3_CtaG cytochrome  24.5      45  0.0011   13.3   3.4   36  307-342   100-138 (286)
150 pfam02031 Peptidase_M7 Strepto  24.0      19  0.0005   15.8  -0.3   22  152-173    24-45  (132)
151 PRK01827 thyA thymidylate synt  23.8      46  0.0012   13.2   2.9   50  130-179   188-239 (264)
152 COG4273 Uncharacterized conser  23.6      47  0.0012   13.2   1.8   33  121-153    49-81  (135)
153 TIGR03284 thym_sym thymidylate  23.5      47  0.0012   13.2   3.1   50  130-179   220-271 (296)
154 PRK03982 heat shock protein Ht  23.4      39   0.001   13.7   1.2   31  131-161    98-130 (288)
155 pfam04228 Zn_peptidase Putativ  23.4      33 0.00084   14.3   0.8   14  164-177   113-126 (292)
156 KOG3638 consensus               23.1      48  0.0012   13.1   2.9   61  126-187   218-278 (414)
157 COG3127 Predicted ABC-type tra  22.9      47  0.0012   13.2   1.5   44  299-342   773-816 (829)
158 TIGR03616 RutG pyrimidine util  22.8      48  0.0012   13.1   4.1   84  252-335   307-396 (429)
159 KOG0662 consensus               22.1      38 0.00096   13.9   0.9   11  166-176   128-138 (292)
160 pfam00303 Thymidylat_synt Thym  22.1      50  0.0013   13.0   2.8   47  130-176   186-234 (262)
161 pfam03926 consensus             21.8      50  0.0013   13.0   1.9   16   17-32     59-74  (149)
162 COG2738 Predicted Zn-dependent  21.7      51  0.0013   13.0   1.7   35  276-310   144-180 (226)
163 KOG2090 consensus               21.6      48  0.0012   13.1   1.4   21  293-313   581-601 (704)
164 PRK02391 heat shock protein Ht  21.1      47  0.0012   13.2   1.2   31  131-161   107-139 (297)
165 PRK10720 uracil transporter; P  20.8      53  0.0013   12.8   3.9   83  251-333   287-375 (429)
166 PRK05973 replicative DNA helic  20.8      50  0.0013   13.0   1.3   22  123-144    46-69  (237)
167 PRK11067 outer membrane protei  20.8      53  0.0013   12.8   2.6   11   55-65    263-273 (801)
168 PHA01511 coat protein           20.6      53  0.0014   12.8   3.5   67  132-205   263-329 (430)
169 PRK05457 heat shock protein Ht  20.6      45  0.0012   13.3   1.0   31  131-161   107-139 (289)
170 TIGR02299 HpaE 5-carboxymethyl  20.2      28 0.00073   14.7  -0.0   18  250-267   445-462 (494)

No 1  
>PRK10779 zinc metallopeptidase; Provisional
Probab=100.00  E-value=0  Score=712.58  Aligned_cols=341  Identities=30%  Similarity=0.520  Sum_probs=306.2

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEEECCCHHEEEEECCCEEEEEEEEEECCEEECCCCC-----
Q ss_conf             936899999999999999997337799999849750045530683112786059807999977112111001244-----
Q gi|254780773|r    1 MFWLDCFLLYTVSLIIIVVIHEFGHYMVARLCNIRVLSFSVGFGPELIGITSRSGVRWKVSLIPLGGYVSFSEDE-----   75 (349)
Q Consensus         1 m~~~~~~~~~~~~l~~~v~iHE~GH~~~Ar~~gv~V~~FsiGfgp~l~~~~~k~~t~y~i~~~PlGgyV~~~~~e-----   75 (349)
                      |.+++++++|+++|+++|++||+|||++||+|||||++|||||||+||++++|+||||+++|||+||||||.||+     
T Consensus         1 m~~l~~i~~fi~~l~~~V~iHElGHfl~Ak~~gv~V~~FsIGfGp~l~~~~~k~gTey~i~~iPlGGYVkm~~e~~~~~~   80 (449)
T PRK10779          1 LSILWNLAAFIVALGVLITVHEFGHFWVARRCGVRVERFSIGFGKALWRRTDRLGTEYVIALIPLGGYVKMLDERAEPVA   80 (449)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEECEEEECCCCHHEEEECCCCEEEEEEEEECCCEEECCCCCCCCCC
T ss_conf             93799999999999999998857879999986985487975688152468367981999999503228835778866688


Q ss_pred             --CCHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCC-CC------------------------------------
Q ss_conf             --550665036842101342112333211221110111001-23------------------------------------
Q gi|254780773|r   76 --KDMRSFFCAAPWKKILTVLAGPLANCVMAILFFTFFFYN-TG------------------------------------  116 (349)
Q Consensus        76 --~~~~~f~~~~~~~R~~i~~AGp~~N~ilA~iif~~~~~~-~g------------------------------------  116 (349)
                        +++++|++||+|||+++++|||++||++|+++|++++.. .+                                    
T Consensus        81 ~~~~~~~f~~k~~~~R~~i~~aGp~~N~ila~iif~~if~~G~~~~~~~i~~v~~~s~a~~agl~~GD~i~~idg~~~~~  160 (449)
T PRK10779         81 PELRHHAFNNKTVGQRAAIIAAGPVANFIFAIFAYWLVFIIGVPGVRPVVGEIAPNSIAAQAQIAPGTELKAVDGIETPD  160 (449)
T ss_pred             CCHHHHHHCCCCCCEEEEEECCCHHHHHHHHHHHHHHEEECCCCCCCCEECCCCCCCHHHHCCCCCCCEEEEECCEECCC
T ss_conf             31223544138811389874276167778999986622441555545300431468888873888887899989998576


Q ss_pred             -----------------------------------------------------------CCCCCCCCCCCCCHHHHHHCC
Q ss_conf             -----------------------------------------------------------333200024567556530014
Q gi|254780773|r  117 -----------------------------------------------------------VMKPVVSNVSPASPAAIAGVK  137 (349)
Q Consensus       117 -----------------------------------------------------------~~~p~I~~V~~~spA~~AGL~  137 (349)
                                                                                 ..+|++++|.|+|||++||||
T Consensus       161 ~~~~~~~l~~~~g~~~~~i~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lgi~~~~p~~~~vi~~V~~~spA~~AGL~  240 (449)
T PRK10779        161 WDAVRLQLVSKIGDEQTTVTVAPFGSDQRRDKTLDLRHWAFEPDKQDPVSSLGIRPRGPQIEPVLEEVQPNSAASKAGLQ  240 (449)
T ss_pred             HHHHHHHHHHHCCCCCEEEEEECCCCCCEEEEEECCHHCCCCCCCCCCHHHCCCCCCCCCCCCEEEEECCCCHHHHCCCC
T ss_conf             89889999885057760699940786411333202011024654345112215333677777435420799989974898


Q ss_pred             CCCEEEEECCCCCCCCHHHHHHCCCCCCCCCEEEEEECCCCEEEECCCCCCCCCCCCCEEEEEEEECCCCCCC-----CC
Q ss_conf             5662888878304540011111014678863169996587313101121100565431000012203444432-----12
Q gi|254780773|r  138 KGDCIISLDGITVSAFEEVAPYVRENPLHEISLVLYREHVGVLHLKVMPRLQDTVDRFGIKRQVPSVGISFSY-----DE  212 (349)
Q Consensus       138 ~GD~Il~InG~~V~s~~dl~~~i~~~~g~~v~i~v~R~~~~~~~~~v~p~~~~~~~~~g~~~~~~~igi~~~~-----~~  212 (349)
                      +||+|++|||+++++|+|+...++++++++++++++|+++ ..+.+++|+.....+     ...+.+|+.+..     +.
T Consensus       241 ~GD~I~~Ing~~i~s~~~l~~~i~~~~~~~i~l~v~R~g~-~~~~~v~p~~~~~~~-----~~~g~~gi~~~~~~~~~~~  314 (449)
T PRK10779        241 AGDRIVKVDGQPLTQWVTFVMLVRDNPGKPLALEIERQGS-PLSLTLIPDTKPVNG-----KAEGFAGVVPKVIPLPDEY  314 (449)
T ss_pred             CCCEEEEECCEECCCHHHHHHHHHHCCCCEEEEEEEECCC-EEEEEEEEEEECCCC-----CEEEEEEECCCCCCCCCCC
T ss_conf             8877999999871659999999986899869999997895-899999640351588-----3367985224335676531


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             33345668887689888655422310000000255420022466730122333456530503478999999999999963
Q gi|254780773|r  213 TKLHSRTVLQSFSRGLDEISSITRGFLGVLSSAFGKDTRLNQISGPVGIARIAKNFFDHGFNAYIAFLAMFSWAIGFMNL  292 (349)
Q Consensus       213 ~~~~~~~~~~a~~~~~~~~~~~~~~~~~~l~~l~~g~~~~~~lsGPVgIa~~~~~~a~~G~~~~l~~~a~isi~Lg~~Nl  292 (349)
                      .....+++.+|+..+.+++++++..++..++++++|+.+.+++||||||++++++++++|+..+|+|+|+||+|||+|||
T Consensus       315 ~~~~~~~~~~a~~~~~~~t~~~~~~~~~~l~~l~tG~v~~~~lsGPVgIa~~~g~~a~~G~~~~l~~~A~iSi~Lgi~NL  394 (449)
T PRK10779        315 KTVRQYGPFSAIYEATDKTWQLMKLTVSMLGKLITGDVKLNNLSGPISIAQGAGMSAELGVVYYLMFLALISVNLGIINL  394 (449)
T ss_pred             EEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             37885178999999999999999999999999823865633357862332011167887599999999999999999985


Q ss_pred             HCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             0647224369999999888278699999999999999999999999999998887
Q gi|254780773|r  293 LPIPILDGGHLITFLLEMIRGKSLGVSVTRVITRMGLCIILFLFFLGIRNDIYGL  347 (349)
Q Consensus       293 LPip~LDGG~i~~~~~E~i~gr~i~~~~~~~~~~~g~~ll~~l~i~~~~nDi~rl  347 (349)
                      ||||+|||||+++.+||+|||||+|+|++++++++|++++++||++++||||.||
T Consensus       395 LPIP~LDGG~i~~~~iE~I~gr~l~~k~~~~~~~iG~~~li~Lmi~~~~nDi~RL  449 (449)
T PRK10779        395 FPLPVLDGGHLLFLAIEKLKGGPVSERVQDFSYRIGSILLVLLMGLALFNDFSRL  449 (449)
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             7876767069899999998489999899999999999999999999998887539


No 2  
>TIGR00054 TIGR00054 membrane-associated zinc metalloprotease, putative; InterPro: IPR004387   Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases .   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.    This family contains putative zinc metallopeptidases belonging to MEROPS peptidase family M50 (S2P protease family, clan MM). The N-terminal region of contains a perfectly conserved motif HEXGH, where the Glu is the active site and the His residues coordinate the metal cation. The family of bacterial and plant proteins also includes a region that hits the PDZ domain (IPR001478 from INTERPRO), found in a number of proteins targeted to the membrane by binding to a peptide ligand . The family includes EcfE, which is a homolog of human site-2 protease (S2P), a membrane-bound zinc metalloprotease involved in regulated intramembrane proteolysis. In Escherichia coli EcfE activates the sigma(E) pathway of stress response through a site-2 cleavage of anti-sigma(E), RseA.; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis, 0016021 integral to membrane.
Probab=100.00  E-value=0  Score=661.09  Aligned_cols=341  Identities=34%  Similarity=0.630  Sum_probs=311.6

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEEECCCHHEEEEECCCEEEEEEEEEECCEEECCC---CC--
Q ss_conf             9368999999999999999973377999998497500455306831127860598079999771121110012---44--
Q gi|254780773|r    1 MFWLDCFLLYTVSLIIIVVIHEFGHYMVARLCNIRVLSFSVGFGPELIGITSRSGVRWKVSLIPLGGYVSFSE---DE--   75 (349)
Q Consensus         1 m~~~~~~~~~~~~l~~~v~iHE~GH~~~Ar~~gv~V~~FsiGfgp~l~~~~~k~~t~y~i~~~PlGgyV~~~~---~e--   75 (349)
                      |.+|..+.+|+++|+++|++||||||++||+|||||++|||||||+||.+.|+.||||++|+|||||||||+|   +|  
T Consensus         1 ~~~l~~l~sFi~~La~Li~vHElGHF~~Ar~~GvkV~~FsiGFGp~lW~~~~~~~TeY~is~IPLGGYVk~~Gfd~lD~e   80 (463)
T TIGR00054         1 MSFLWILASFIIALAVLIFVHELGHFLAARLCGVKVERFSIGFGPKLWLKFKKNGTEYAISLIPLGGYVKMKGFDGLDKE   80 (463)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEECCCCHHHHHCCCCCCEEEEEEECCCCEEECCCCCCCCCC
T ss_conf             93788899999999999999988899999877946999742027056520013674589875326543623788997664


Q ss_pred             --------CCHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCC-CCCCCCC------------------------------
Q ss_conf             --------5506650368421013421123332112211101-1100123------------------------------
Q gi|254780773|r   76 --------KDMRSFFCAAPWKKILTVLAGPLANCVMAILFFT-FFFYNTG------------------------------  116 (349)
Q Consensus        76 --------~~~~~f~~~~~~~R~~i~~AGp~~N~ilA~iif~-~~~~~~g------------------------------  116 (349)
                              .++++|+++|..||++|++|||++|+++|++.++ ++.. .|                              
T Consensus        81 ~~~~~~~e~~~~~f~~~s~~~k~~i~~aG~~~N~iFa~~~~~~~~~~-~G~~~~~~~~vi~~~~~~S~a~~a~~~~Gd~i  159 (463)
T TIGR00054        81 EEEVKPPETDKDLFNNKSVLQKAIIIFAGPLANFIFAIFVYIDLVSL-IGVPGYEVGPVIEELDKNSIALEAGIEPGDEI  159 (463)
T ss_pred             CCCCCCCCCCHHHHHCCCHHHEEHEECCCHHHHHHHHHHHHHHHHHH-HCCCCCCCCCCCCCCCHHHHHHHHCCCCCCEE
T ss_conf             10367652101365268712310100144143599999999989998-04244213664565544579987116898478


Q ss_pred             ----------------------------------------------------------------------CCCCCCCCCC
Q ss_conf             ----------------------------------------------------------------------3332000245
Q gi|254780773|r  117 ----------------------------------------------------------------------VMKPVVSNVS  126 (349)
Q Consensus       117 ----------------------------------------------------------------------~~~p~I~~V~  126 (349)
                                                                                            ..++++.+|+
T Consensus       160 l~~~~~~~~~f~~~~~~~~~~~~g~~~~~I~~~PF~S~~e~~~~L~L~~~~~~~~~~~~~~~lgl~~~~P~ie~vl~~~~  239 (463)
T TIGR00054       160 LSVNGKKIPGFKDVRKQIADIVAGEPMVEILAAPFNSDIEREVKLDLRNWTFEVEKEDAVEQLGLKPRGPKIEPVLSDVT  239 (463)
T ss_pred             EEECCCCCCCCHHHHHHHHHHHCCCCCCEEEECCCCCCCHHHCCCCCEEEEEECCCCCHHHHCCCCCCCCCCEEEECCCC
T ss_conf             74077667880889999999751785415776577754112000033123862112552554144247872012331267


Q ss_pred             CCCHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCCCCCCCCEEEEEECCCCEEEECCCCCCCCCCCCCEEEEEEEECCC
Q ss_conf             67556530014566288887830454001111101467886316999658731310112110056543100001220344
Q gi|254780773|r  127 PASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRENPLHEISLVLYREHVGVLHLKVMPRLQDTVDRFGIKRQVPSVGI  206 (349)
Q Consensus       127 ~~spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~~~g~~v~i~v~R~~~~~~~~~v~p~~~~~~~~~g~~~~~~~igi  206 (349)
                      ++|||++||||+||+|+++||++..+|.|+...++++|++++++.++||| ++++.+++|+..++.++     ..+.+|+
T Consensus       240 ~N~~A~~AGLk~GD~I~~i~g~~l~~w~d~v~~v~~np~~~~~i~v~R~G-~~l~~~l~p~~~~~~gK-----aIg~ig~  313 (463)
T TIGR00054       240 PNSPAEKAGLKEGDKIISIDGEKLKSWRDFVSLVKENPGKSLEIKVERNG-ETLSISLTPEAKKDKGK-----AIGFIGI  313 (463)
T ss_pred             CCCHHHHCCCCCCCEEEEECCCCCCCHHHHHHHHHHCCCCEEEEEEEECC-CEEEEEEEEEEECCCCC-----EEEEEEE
T ss_conf             88537753465688898556812344245899998689956999997278-14634787530079973-----6898775


Q ss_pred             CCCCCCCC-----CCCCCHHHHHHHHHHHHHHHHHHHEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHH
Q ss_conf             44321233-----3456688876898886554223100000002554200224667301223334565305034789999
Q gi|254780773|r  207 SFSYDETK-----LHSRTVLQSFSRGLDEISSITRGFLGVLSSAFGKDTRLNQISGPVGIARIAKNFFDHGFNAYIAFLA  281 (349)
Q Consensus       207 ~~~~~~~~-----~~~~~~~~a~~~~~~~~~~~~~~~~~~l~~l~~g~~~~~~lsGPVgIa~~~~~~a~~G~~~~l~~~a  281 (349)
                      .|......     ...+++.+|+.++.+.+.++++.++..+.++++|+.+.++|||||||++.+++.|+.|..+++.|.|
T Consensus       314 ~P~~~~~~d~~~~v~~~~~l~a~~~~~~~~~~~~~li~~~l~~Li~g~~~l~~lSGPVgIv~~~~~~A~~G~~~ll~F~A  393 (463)
T TIGR00054       314 SPSLKKLEDEYKVVVSYGILEALAKAAEATKDIVKLILKLLGKLITGSLKLKNLSGPVGIVKGAGSSANLGIVYLLQFGA  393 (463)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             68753031132100244267899999999989999999988875400022200567421545512466764999998999


Q ss_pred             HHHHHHHHHHHHC--CCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999996306--472243699999998882786999999999999999999999999999988873
Q gi|254780773|r  282 MFSWAIGFMNLLP--IPILDGGHLITFLLEMIRGKSLGVSVTRVITRMGLCIILFLFFLGIRNDIYGLM  348 (349)
Q Consensus       282 ~isi~Lg~~NlLP--ip~LDGG~i~~~~~E~i~gr~i~~~~~~~~~~~g~~ll~~l~i~~~~nDi~rl~  348 (349)
                      +||+|||++||||  ||+|||||++|.++|.|+|||+|+|++..++.+|.+++++||++++|||+.||+
T Consensus       394 llSiNLgi~NLlPiviP~LDGG~llfl~iE~i~Gkp~~~~~q~~~~~~G~~lLl~L~~l~lfND~~rLl  462 (463)
T TIGR00054       394 LLSINLGIINLLPIVIPALDGGQLLFLFIEAIRGKPLPEKVQAFVYRIGVALLLLLMVLGLFNDLLRLL  462 (463)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             999999999888778624242578788998735897766899999999999999999999988876511


No 3  
>COG0750 Predicted membrane-associated Zn-dependent proteases 1 [Cell envelope biogenesis, outer membrane]
Probab=100.00  E-value=0  Score=436.10  Aligned_cols=346  Identities=33%  Similarity=0.613  Sum_probs=298.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEEECCCHHEEEEECCCEEEEEEEEEECCEEECCCCC--------
Q ss_conf             899999999999999997337799999849750045530683112786059807999977112111001244--------
Q gi|254780773|r    4 LDCFLLYTVSLIIIVVIHEFGHYMVARLCNIRVLSFSVGFGPELIGITSRSGVRWKVSLIPLGGYVSFSEDE--------   75 (349)
Q Consensus         4 ~~~~~~~~~~l~~~v~iHE~GH~~~Ar~~gv~V~~FsiGfgp~l~~~~~k~~t~y~i~~~PlGgyV~~~~~e--------   75 (349)
                      +..++.+++++.+++++||+|||+.||+|+++|++|++||||+++++++|.+|+|.++++|+||||+|.+++        
T Consensus         2 ~~~~i~~i~~~~~lv~~he~gh~~~a~~~~~~v~~f~ig~g~~l~~~~~~~~~~~~i~~~plggyv~~~~~~~~~~~~~~   81 (375)
T COG0750           2 MLTIIAFIIALGVLVFVHELGHFWVARRCGVKVERFSIGFGPKLFSRKDKGGTEYVLSAIPLGGYVKMLGEDAEEVVLKG   81 (375)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCEEEEEEECCCCEEEEEEECCCEEEEEEEECCCCCCCCCC
T ss_conf             07888898888899999998899999863752589786212016998426880899984261139999873554423354


Q ss_pred             --CCHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCC---CCCCCCCCCCCCCHHHHHHCCCCCEEEEECCCCC
Q ss_conf             --55066503684210134211233321122111011100123---3332000245675565300145662888878304
Q gi|254780773|r   76 --KDMRSFFCAAPWKKILTVLAGPLANCVMAILFFTFFFYNTG---VMKPVVSNVSPASPAAIAGVKKGDCIISLDGITV  150 (349)
Q Consensus        76 --~~~~~f~~~~~~~R~~i~~AGp~~N~ilA~iif~~~~~~~g---~~~p~I~~V~~~spA~~AGL~~GD~Il~InG~~V  150 (349)
                        +.++.|..++.|+|..+.+|||.+|++++.+.+.......|   ...|.++++.++|||+.||+++||+|+++|++++
T Consensus        82 ~~~~~~~f~~~~~~~~~~~~~~Gp~~n~i~~~~~~~~~~~~~G~~~~~~~~~~~v~~~s~a~~a~l~~Gd~iv~~~~~~i  161 (375)
T COG0750          82 PEPRPRAFNAKSVWQRIAIVFAGPLFNFILAIVLFVVLFFVIGLVPVASPVVGEVAPKSAAALAGLRPGDRIVAVDGEKV  161 (375)
T ss_pred             CCCCHHHHHCCCCCCCEEEEECCCCHHHHHHHHHHHHHHEEECEEECCCCCCCCCCCCCHHHHCCCCCCCEEEECCCEEC
T ss_conf             34440333034544141699806542788999999886605210212366543445476788757888978995085204


Q ss_pred             CCCHHHHHHCCCCCCCC---CEEEEEE-CCCCE-------EEECCCCCCCC-CCCCCEEEEEEEECCCCCCC---CCCCC
Q ss_conf             54001111101467886---3169996-58731-------31011211005-65431000012203444432---12333
Q gi|254780773|r  151 SAFEEVAPYVRENPLHE---ISLVLYR-EHVGV-------LHLKVMPRLQD-TVDRFGIKRQVPSVGISFSY---DETKL  215 (349)
Q Consensus       151 ~s~~dl~~~i~~~~g~~---v~i~v~R-~~~~~-------~~~~v~p~~~~-~~~~~g~~~~~~~igi~~~~---~~~~~  215 (349)
                      .+|++.+..+..+++..   +++.+.| ++...       ...++.|.... ..+........+.++..+..   .....
T Consensus       162 ~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~~~~~~~i~~~~i~~~p~~~~~~~~~~  241 (375)
T COG0750         162 ASWDDVRRLLVAAAGDVFNLLTILVIRLDGEAHAVAAEIIKSLGLTPVVIPLKPGDKIVAVDVGAIGLSPNGEPDVGKVL  241 (375)
T ss_pred             CCHHHHHHHHHHCCCCCCCEEEEEEEECCCEEECCCCCCCCEECCCCCCCCCCCCCEEEEEEEEEECCCCCCCCCCCCCC
T ss_conf             56667779987533565550799998326544201012222103667645447896246740004245577664323012


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             45668887689888655422310000000255420022466730122333456530503478999999999999963064
Q gi|254780773|r  216 HSRTVLQSFSRGLDEISSITRGFLGVLSSAFGKDTRLNQISGPVGIARIAKNFFDHGFNAYIAFLAMFSWAIGFMNLLPI  295 (349)
Q Consensus       216 ~~~~~~~a~~~~~~~~~~~~~~~~~~l~~l~~g~~~~~~lsGPVgIa~~~~~~a~~G~~~~l~~~a~isi~Lg~~NlLPi  295 (349)
                      .+.++.+++..+++++.+....+++.++++.++..+.++++||++|++..++.++.|+.++++|++|+|++||++||+|+
T Consensus       242 ~~~~~~~~i~~~v~~~~~~~~~~~~~l~~~~~~~~~~~~l~Gpi~i~~~~~~~~~~~~~~~l~~~~~lsi~lg~lNllP~  321 (375)
T COG0750         242 VKYGPLEAVGLAVEKTGRLVKLTLKMLKKLITGDLSLKNLSGPIGIAKIAGAAASLGLINLLFFLALLSINLGILNLLPI  321 (375)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHCEEEECCCCCCCCEEEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHCHH
T ss_conf             24461677888876556688888877641414521565355406888834466665699999999999999999996425


Q ss_pred             CCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             722436999999988827869999999999999999999999999999888739
Q gi|254780773|r  296 PILDGGHLITFLLEMIRGKSLGVSVTRVITRMGLCIILFLFFLGIRNDIYGLMQ  349 (349)
Q Consensus       296 p~LDGG~i~~~~~E~i~gr~i~~~~~~~~~~~g~~ll~~l~i~~~~nDi~rl~~  349 (349)
                      |+|||||+++.++|.++|||++++.+..++..|+++++.+|+++++||+.|++.
T Consensus       322 p~LDGG~i~~~~~e~~~g~~~~~~~~~~~~~~g~~ll~~~~~~~~~~di~~~~~  375 (375)
T COG0750         322 PPLDGGHLLFYLLEALRGKPLSERVEAALYRIGLALLLLLMLLATFNDLLRLFR  375 (375)
T ss_pred             HHCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             418888999999999808988823512588899999999999998852311259


No 4  
>cd06163 S2P-M50_PDZ_RseP-like RseP-like Site-2 proteases (S2P), zinc metalloproteases (MEROPS family M50A), cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. In Escherichia coli, the S2P homolog RseP is involved in the sigmaE pathway of extracytoplasmic stress responses. Also included in this group are such homologs as Bacillus subtilis YluC, Mycobacterium tuberculosis Rv2869c S2P, and Bordetella bronchiseptica HurP.  Rv2869c S2P appears to have a role in the regulation of prokaryotic lipid biosynthesis and membrane composition and YluC of Bacillus has a role in transducing membrane stress. This group includes bacterial and eukaryotic S2P/M50s homologs with either one or two PDZ domains present. PDZ domains are believed to have a regulatory role. The RseP PDZ domain is required for the inhibitory reaction that prevents cleavage of its substrate, RseA.
Probab=100.00  E-value=0  Score=428.08  Aligned_cols=174  Identities=43%  Similarity=0.841  Sum_probs=166.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEEECCCHHEEEEECCCEEEEEEEEEECCEEECCCCC--------CCH
Q ss_conf             999999999999997337799999849750045530683112786059807999977112111001244--------550
Q gi|254780773|r    7 FLLYTVSLIIIVVIHEFGHYMVARLCNIRVLSFSVGFGPELIGITSRSGVRWKVSLIPLGGYVSFSEDE--------KDM   78 (349)
Q Consensus         7 ~~~~~~~l~~~v~iHE~GH~~~Ar~~gv~V~~FsiGfgp~l~~~~~k~~t~y~i~~~PlGgyV~~~~~e--------~~~   78 (349)
                      ++.|+++++++|++||+|||++||+|||||++|||||||++++|+ |+||+|+++++|+||||||.||+        +++
T Consensus         1 il~fi~~l~vlV~vHElGH~~~Ar~~Gv~V~~FsIGfGp~l~~~~-~~~T~~~i~~iPlGGyV~~~g~~~~~~~~~~~~~   79 (182)
T cd06163           1 ILAFILVLGILIFVHELGHFLVAKLFGVKVEEFSIGFGPKLFSFK-KGETEYSISAIPLGGYVKMLGEDPEEEADPEDDP   79 (182)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEECCCCCEEEEE-CCCEEEEEEEEHHHHHHHHCCCCCCCCCCCCCCH
T ss_conf             964999999999999899899999949856698863785115677-0883698540144356654267765558864232


Q ss_pred             HHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCCHHHHH
Q ss_conf             66503684210134211233321122111011100123333200024567556530014566288887830454001111
Q gi|254780773|r   79 RSFFCAAPWKKILTVLAGPLANCVMAILFFTFFFYNTGVMKPVVSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEVAP  158 (349)
Q Consensus        79 ~~f~~~~~~~R~~i~~AGp~~N~ilA~iif~~~~~~~g~~~p~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~~dl~~  158 (349)
                      ++|++||+|||++|++|||++|+++|+++|+.+                                               
T Consensus        80 ~~f~~~~~~~R~~i~~AGp~~N~ilA~~i~~~l-----------------------------------------------  112 (182)
T cd06163          80 RSFNSKPVWQRILIVFAGPLANFLLAIVLFAVL-----------------------------------------------  112 (182)
T ss_pred             HHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHH-----------------------------------------------
T ss_conf             447439989999999858999999999999999-----------------------------------------------


Q ss_pred             HCCCCCCCCCEEEEEECCCCEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             10146788631699965873131011211005654310000122034444321233345668887689888655422310
Q gi|254780773|r  159 YVRENPLHEISLVLYREHVGVLHLKVMPRLQDTVDRFGIKRQVPSVGISFSYDETKLHSRTVLQSFSRGLDEISSITRGF  238 (349)
Q Consensus       159 ~i~~~~g~~v~i~v~R~~~~~~~~~v~p~~~~~~~~~g~~~~~~~igi~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~  238 (349)
                                                                                                      
T Consensus       113 --------------------------------------------------------------------------------  112 (182)
T cd06163         113 --------------------------------------------------------------------------------  112 (182)
T ss_pred             --------------------------------------------------------------------------------
T ss_conf             --------------------------------------------------------------------------------


Q ss_pred             EECCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCH
Q ss_conf             00000025542002246673012233345653050347899999999999996306472243699999998882786999
Q gi|254780773|r  239 LGVLSSAFGKDTRLNQISGPVGIARIAKNFFDHGFNAYIAFLAMFSWAIGFMNLLPIPILDGGHLITFLLEMIRGKSLGV  318 (349)
Q Consensus       239 ~~~l~~l~~g~~~~~~lsGPVgIa~~~~~~a~~G~~~~l~~~a~isi~Lg~~NlLPip~LDGG~i~~~~~E~i~gr~i~~  318 (349)
                                                            +.++|.+|+|||++||||+|||||||+++.+||+++|||+|+
T Consensus       113 --------------------------------------l~~~a~is~~L~i~NLLPip~LDGG~il~~~~E~i~gr~~~~  154 (182)
T cd06163         113 --------------------------------------LSFLALLSINLGILNLLPIPALDGGHLLFLLIEAIRGRPLSE  154 (182)
T ss_pred             --------------------------------------HHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHCCCCCH
T ss_conf             --------------------------------------999999999999997068876772375999999995899999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999999999888
Q gi|254780773|r  319 SVTRVITRMGLCIILFLFFLGIRNDIYG  346 (349)
Q Consensus       319 ~~~~~~~~~g~~ll~~l~i~~~~nDi~r  346 (349)
                      |+++.++.+|+++++.+|+++++|||.|
T Consensus       155 ~~~~~~~~~G~~~l~~lm~~~~~nDi~r  182 (182)
T cd06163         155 KVEEIIQTIGFALLLGLMLFVTFNDIVR  182 (182)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             9999999999999999999999875149


No 5  
>pfam02163 Peptidase_M50 Peptidase family M50.
Probab=100.00  E-value=4.3e-42  Score=310.07  Aligned_cols=205  Identities=35%  Similarity=0.609  Sum_probs=178.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEEECCCHHEEEEECCCEEEEEEEEEECCEEECCCCCCCHHHHCCCCCCC
Q ss_conf             99999999999973377999998497500455306831127860598079999771121110012445506650368421
Q gi|254780773|r    9 LYTVSLIIIVVIHEFGHYMVARLCNIRVLSFSVGFGPELIGITSRSGVRWKVSLIPLGGYVSFSEDEKDMRSFFCAAPWK   88 (349)
Q Consensus         9 ~~~~~l~~~v~iHE~GH~~~Ar~~gv~V~~FsiGfgp~l~~~~~k~~t~y~i~~~PlGgyV~~~~~e~~~~~f~~~~~~~   88 (349)
                      .+++++.+++++||+||+++||++|++|++|++||||.+++++ +++|+|.++++| |+++     ++++++++++++|+
T Consensus         1 ~~~~~l~i~i~~HE~gH~~~Ar~~G~~v~~~~~~~g~~~~~~~-~~~~~~~~~~~~-g~~~-----~~~~~~~~~~~~~~   73 (205)
T pfam02163         1 AFILALLISVVVHELGHALVARRFGVKVERFAIGFGPLLFLHL-DGATEYTIRLMF-GAFG-----APINREFKKKSRKQ   73 (205)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEECCCCCCHHEE-CCCEEEEEECCC-CCCC-----CCCCHHHCCCCHHH
T ss_conf             9079999999999999999999929997424234677421016-687259861146-7677-----76765543577656


Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCCCCCCCC
Q ss_conf             01342112333211221110111001233332000245675565300145662888878304540011111014678863
Q gi|254780773|r   89 KILTVLAGPLANCVMAILFFTFFFYNTGVMKPVVSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRENPLHEI  168 (349)
Q Consensus        89 R~~i~~AGp~~N~ilA~iif~~~~~~~g~~~p~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~~~g~~v  168 (349)
                      |+.|.+|||++|+++|++++.......+...+........++                                      
T Consensus        74 ~~~V~~AGP~~Nlila~i~~~~~~~~~~~~~~~~~~~~~~~~--------------------------------------  115 (205)
T pfam02163        74 RLKISLAGPLANFILALLLLALLLLLPGIPVPPVIGGVVVGS--------------------------------------  115 (205)
T ss_pred             HHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC--------------------------------------
T ss_conf             756533117888999999999999833666554433222331--------------------------------------


Q ss_pred             EEEEEECCCCEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHEECCCCCCCC
Q ss_conf             16999658731310112110056543100001220344443212333456688876898886554223100000002554
Q gi|254780773|r  169 SLVLYREHVGVLHLKVMPRLQDTVDRFGIKRQVPSVGISFSYDETKLHSRTVLQSFSRGLDEISSITRGFLGVLSSAFGK  248 (349)
Q Consensus       169 ~i~v~R~~~~~~~~~v~p~~~~~~~~~g~~~~~~~igi~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~l~~l~~g  248 (349)
                                                                                                      
T Consensus       116 --------------------------------------------------------------------------------  115 (205)
T pfam02163       116 --------------------------------------------------------------------------------  115 (205)
T ss_pred             --------------------------------------------------------------------------------
T ss_conf             --------------------------------------------------------------------------------


Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf             20022466730122333456530503478999999999999963064722436999999988827869999999999999
Q gi|254780773|r  249 DTRLNQISGPVGIARIAKNFFDHGFNAYIAFLAMFSWAIGFMNLLPIPILDGGHLITFLLEMIRGKSLGVSVTRVITRMG  328 (349)
Q Consensus       249 ~~~~~~lsGPVgIa~~~~~~a~~G~~~~l~~~a~isi~Lg~~NlLPip~LDGG~i~~~~~E~i~gr~i~~~~~~~~~~~g  328 (349)
                          .+++||+++.+..+++++.++..++.+++++|++||+|||||+|||||||+++.++ .+++|+.++|.+++.+.++
T Consensus       116 ----~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~inl~L~~fNLLPippLDGG~il~~ll-~~~~~~~~~~~~~~~~~~~  190 (205)
T pfam02163       116 ----SSLSGPVAIAKVGSTSALSGLIALLAFLALLNLNLGLFNLLPIPPLDGGHILRALL-AVRGRPLNERAENYIYLVG  190 (205)
T ss_pred             ----CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHH-HHHCCCCHHHHHHHHHHHH
T ss_conf             ----00253189998756667778999999999999999999648888878289999999-9846851799999999999


Q ss_pred             HHHHHHHHHHHHHHH
Q ss_conf             999999999999999
Q gi|254780773|r  329 LCIILFLFFLGIRND  343 (349)
Q Consensus       329 ~~ll~~l~i~~~~nD  343 (349)
                      +++++.+|+++++||
T Consensus       191 ~~ll~~l~~~~~~~d  205 (205)
T pfam02163       191 LALLLLLILLLLFND  205 (205)
T ss_pred             HHHHHHHHHHHHCCC
T ss_conf             999999999880159


No 6  
>cd05709 S2P-M50 Site-2 protease (S2P) class of zinc metalloproteases (MEROPS family M50) cleaves transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of this family use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. The domain core structure appears to contain at least three transmembrane helices with a catalytic zinc atom coordinated by three conserved residues contained within the consensus sequence HExxH, together with a conserved aspartate residue. The S2P/M50 family of RIP proteases is widely distributed; in eukaryotic cells, they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum (ER) stress responses. In sterol-depleted mammalian cells, a two-step proteolytic process releases the N-terminal domains of sterol regulatory element-bindin
Probab=100.00  E-value=1.3e-33  Score=251.66  Aligned_cols=179  Identities=36%  Similarity=0.637  Sum_probs=148.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEEECCCHHEEEEECCCEEEEEEEEEECCEEECCCCCCCHHHHCCCCCCC
Q ss_conf             99999999999973377999998497500455306831127860598079999771121110012445506650368421
Q gi|254780773|r    9 LYTVSLIIIVVIHEFGHYMVARLCNIRVLSFSVGFGPELIGITSRSGVRWKVSLIPLGGYVSFSEDEKDMRSFFCAAPWK   88 (349)
Q Consensus         9 ~~~~~l~~~v~iHE~GH~~~Ar~~gv~V~~FsiGfgp~l~~~~~k~~t~y~i~~~PlGgyV~~~~~e~~~~~f~~~~~~~   88 (349)
                      .+++++.+++++||+||+++||++|+++++|+.||   .++. +++++.|++.++|+|||+|+.+++++..   ++++|+
T Consensus         2 ~~~~~l~i~i~iHE~gH~~~A~~~G~~~~~~~~~~---~~~p-~~~~~~~~~~~ip~gG~~~~~~~~~~~~---~~~~~~   74 (180)
T cd05709           2 AFILALLISVTVHELGHALVARRLGVKVARFSGGF---TLNP-LKHGDPYGIILIPLGGYAKPVGENPRAF---KKPRWQ   74 (180)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHCCCC---CCCC-CCCCCCCCHHHHHCEEEEEEECCCHHHC---CCCCCC
T ss_conf             66999999999999999999999699768874753---3366-4699815086631327997755681420---488120


Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCCCCCCCC
Q ss_conf             01342112333211221110111001233332000245675565300145662888878304540011111014678863
Q gi|254780773|r   89 KILTVLAGPLANCVMAILFFTFFFYNTGVMKPVVSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRENPLHEI  168 (349)
Q Consensus        89 R~~i~~AGp~~N~ilA~iif~~~~~~~g~~~p~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~~~g~~v  168 (349)
                      |++|.+|||++|+++|++.+.......+...+..                                              
T Consensus        75 ~~~i~~AGP~~Nl~la~i~~~~~~~~~~~~~~~~----------------------------------------------  108 (180)
T cd05709          75 RLLVALAGPLANLLLALLLLLLLLLLGGLPPAPV----------------------------------------------  108 (180)
T ss_pred             EEEEEEEHHHHHHHHHHHHHHHHHHHCCCCCCCH----------------------------------------------
T ss_conf             1210200688999999999999999703544320----------------------------------------------


Q ss_pred             EEEEEECCCCEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHEECCCCCCCC
Q ss_conf             16999658731310112110056543100001220344443212333456688876898886554223100000002554
Q gi|254780773|r  169 SLVLYREHVGVLHLKVMPRLQDTVDRFGIKRQVPSVGISFSYDETKLHSRTVLQSFSRGLDEISSITRGFLGVLSSAFGK  248 (349)
Q Consensus       169 ~i~v~R~~~~~~~~~v~p~~~~~~~~~g~~~~~~~igi~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~l~~l~~g  248 (349)
                                                                                                      
T Consensus       109 --------------------------------------------------------------------------------  108 (180)
T cd05709         109 --------------------------------------------------------------------------------  108 (180)
T ss_pred             --------------------------------------------------------------------------------
T ss_conf             --------------------------------------------------------------------------------


Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHH
Q ss_conf             20022466730122333456530503478999999999999963064722436999999988827869999999999999
Q gi|254780773|r  249 DTRLNQISGPVGIARIAKNFFDHGFNAYIAFLAMFSWAIGFMNLLPIPILDGGHLITFLLEMIRGKSLGVSVTRVITRMG  328 (349)
Q Consensus       249 ~~~~~~lsGPVgIa~~~~~~a~~G~~~~l~~~a~isi~Lg~~NlLPip~LDGG~i~~~~~E~i~gr~i~~~~~~~~~~~g  328 (349)
                                       ++....++..++.+++++|+++++|||||+|||||||++..++|..++|     .++..+..+
T Consensus       109 -----------------~~~~~~~~~~~l~~~~~in~~l~~fNLlPippLDGg~il~~~l~~~~~~-----~~~~~~~~~  166 (180)
T cd05709         109 -----------------GQAASSGLANLLAFLALINLNLAVFNLLPIPPLDGGRILRALLEAIRGR-----VEERLEAYG  166 (180)
T ss_pred             -----------------HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHH-----HHHHHHHHH
T ss_conf             -----------------3667889999999999999999999808888888599999994799999-----999999999


Q ss_pred             HHHHHHHHHHHHHH
Q ss_conf             99999999999999
Q gi|254780773|r  329 LCIILFLFFLGIRN  342 (349)
Q Consensus       329 ~~ll~~l~i~~~~n  342 (349)
                      +.+++.+++..+++
T Consensus       167 ~~~ll~l~~~~~~~  180 (180)
T cd05709         167 FAILLGLLLLLLLN  180 (180)
T ss_pred             HHHHHHHHHHHHHC
T ss_conf             99999999999709


No 7  
>cd06159 S2P-M50_PDZ_Arch Uncharacterized Archaeal homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the S2P/M50 family of RIP proteases use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. In eukaryotic cells they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum stress responses. In prokaryotes they regulate such processes as sporulation, cell division, stress response, and cell differentiation. This group appears to be limited to Archaeal S2P/M50s homologs with additional putative N-terminal transmembrane spanning regions, relative to the core protein, and either one or two PDZ domains present.
Probab=99.94  E-value=2.1e-26  Score=201.85  Aligned_cols=133  Identities=32%  Similarity=0.510  Sum_probs=118.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEEECCCHHEEEEECCCEEEEEEEEEECCEEECCCCCCCHHHHCCCC
Q ss_conf             99999999999999973377999998497500455306831127860598079999771121110012445506650368
Q gi|254780773|r    6 CFLLYTVSLIIIVVIHEFGHYMVARLCNIRVLSFSVGFGPELIGITSRSGVRWKVSLIPLGGYVSFSEDEKDMRSFFCAA   85 (349)
Q Consensus         6 ~~~~~~~~l~~~v~iHE~GH~~~Ar~~gv~V~~FsiGfgp~l~~~~~k~~t~y~i~~~PlGgyV~~~~~e~~~~~f~~~~   85 (349)
                      .+.++++++.+.+++||+||.++||.+|+||+  |.|+   +            +..+|+|+||     |||++++++++
T Consensus       109 p~~~~~~al~v~~vvHE~~Hgi~ar~~~i~vk--S~G~---l------------l~~ip~GAFv-----Epdeee~~~a~  166 (263)
T cd06159         109 PLPYGIIALVVGVVVHELSHGILARVEGIKVK--SGGL---L------------LLIIPPGAFV-----EPDEEELNKAD  166 (263)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEC--CCHH---H------------HHHHCCCCCC-----CCCHHHHHCCC
T ss_conf             37899999999999998888999998186330--1156---7------------8661642235-----88979985288


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCCCCC
Q ss_conf             42101342112333211221110111001233332000245675565300145662888878304540011111014678
Q gi|254780773|r   86 PWKKILTVLAGPLANCVMAILFFTFFFYNTGVMKPVVSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRENPL  165 (349)
Q Consensus        86 ~~~R~~i~~AGp~~N~ilA~iif~~~~~~~g~~~p~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~~~g  165 (349)
                      +.+|+++++|||.+|+++|++.+..++                                                     
T Consensus       167 ~~~r~ri~aAG~~~N~v~~~i~~~l~f-----------------------------------------------------  193 (263)
T cd06159         167 RRIRLRIFAAGVTANFVVALIAFALFF-----------------------------------------------------  193 (263)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHH-----------------------------------------------------
T ss_conf             154533200360998999999999999-----------------------------------------------------


Q ss_pred             CCCEEEEEECCCCEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHEECCCCC
Q ss_conf             86316999658731310112110056543100001220344443212333456688876898886554223100000002
Q gi|254780773|r  166 HEISLVLYREHVGVLHLKVMPRLQDTVDRFGIKRQVPSVGISFSYDETKLHSRTVLQSFSRGLDEISSITRGFLGVLSSA  245 (349)
Q Consensus       166 ~~v~i~v~R~~~~~~~~~v~p~~~~~~~~~g~~~~~~~igi~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~l~~l  245 (349)
                                                                                                      
T Consensus       194 --------------------------------------------------------------------------------  193 (263)
T cd06159         194 --------------------------------------------------------------------------------  193 (263)
T ss_pred             --------------------------------------------------------------------------------
T ss_conf             --------------------------------------------------------------------------------


Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHH
Q ss_conf             5542002246673012233345653050347899999999999996306472243699999998882786999999999
Q gi|254780773|r  246 FGKDTRLNQISGPVGIARIAKNFFDHGFNAYIAFLAMFSWAIGFMNLLPIPILDGGHLITFLLEMIRGKSLGVSVTRVI  324 (349)
Q Consensus       246 ~~g~~~~~~lsGPVgIa~~~~~~a~~G~~~~l~~~a~isi~Lg~~NlLPip~LDGG~i~~~~~E~i~gr~i~~~~~~~~  324 (349)
                                                     ++|+.|+|++||+|||||.-||||||++..+.|.+.+|..+++.++..
T Consensus       194 -------------------------------l~W~~~iNf~lglfN~lPa~plDGg~v~~~~~~~~~~r~~~~~~~~~~  241 (263)
T cd06159         194 -------------------------------LYWIFWINFLLGLFNCLPAIPLDGGHVFRDLLEALLRRFPSEKAERVV  241 (263)
T ss_pred             -------------------------------HHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHH
T ss_conf             -------------------------------999999999999983576665760679999899998538751178899


No 8  
>LOAD_S2Pmetalloprt consensus
Probab=99.90  E-value=2.6e-24  Score=187.37  Aligned_cols=147  Identities=36%  Similarity=0.685  Sum_probs=113.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEEECCCHHEEEEECCCEEEEEEEEEECCEEECCCCCCCHHHHCCCCCCCC
Q ss_conf             99999999999733779999984975004553068311278605980799997711211100124455066503684210
Q gi|254780773|r   10 YTVSLIIIVVIHEFGHYMVARLCNIRVLSFSVGFGPELIGITSRSGVRWKVSLIPLGGYVSFSEDEKDMRSFFCAAPWKK   89 (349)
Q Consensus        10 ~~~~l~~~v~iHE~GH~~~Ar~~gv~V~~FsiGfgp~l~~~~~k~~t~y~i~~~PlGgyV~~~~~e~~~~~f~~~~~~~R   89 (349)
                      +++++.+.+++||+||+++||++|++++++++++++.+..             +|+|||++++++++   .++..++|+|
T Consensus         2 ~~v~l~i~v~vHElgH~~~A~~~G~~~~~~~~~~~~~~~~-------------~~~Gg~~~~~~~~~---~~~~~~~~~~   65 (148)
T LOAD_S2Pmetall    2 FLIALGVSVVVHELGHALVARRFGVKVESFAIGLGLNLFK-------------IPPGGFVELKGEDP---DLKKKSRKAR   65 (148)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCHHHH-------------HHCEEEEECCCCCC---HHCCCCHHHH
T ss_conf             6299999999999999999999699487787563026776-------------50315775687650---1014785666


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCCCCCCCCE
Q ss_conf             13421123332112211101110012333320002456755653001456628888783045400111110146788631
Q gi|254780773|r   90 ILTVLAGPLANCVMAILFFTFFFYNTGVMKPVVSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRENPLHEIS  169 (349)
Q Consensus        90 ~~i~~AGp~~N~ilA~iif~~~~~~~g~~~p~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~~~g~~v~  169 (349)
                      ++|.+|||++|+++|++.+...... +......   .+..+..                                     
T Consensus        66 ~~I~~AGP~~Nl~la~~~~~~~~~~-g~~~~~~---~~~~~~~-------------------------------------  104 (148)
T LOAD_S2Pmetall   66 LLVSAAGPLANLLLALLLLLLLFLL-GVPLLLP---VPVVSVV-------------------------------------  104 (148)
T ss_pred             HHHHHHCHHHHHHHHHHHHHHHHHH-CCCCCCC---CCCCCHH-------------------------------------
T ss_conf             0352313088899999999999995-2231012---2222116-------------------------------------


Q ss_pred             EEEEECCCCEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHEECCCCCCCCC
Q ss_conf             69996587313101121100565431000012203444432123334566888768988865542231000000025542
Q gi|254780773|r  170 LVLYREHVGVLHLKVMPRLQDTVDRFGIKRQVPSVGISFSYDETKLHSRTVLQSFSRGLDEISSITRGFLGVLSSAFGKD  249 (349)
Q Consensus       170 i~v~R~~~~~~~~~v~p~~~~~~~~~g~~~~~~~igi~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~l~~l~~g~  249 (349)
                                                                                                      
T Consensus       105 --------------------------------------------------------------------------------  104 (148)
T LOAD_S2Pmetall  105 --------------------------------------------------------------------------------  104 (148)
T ss_pred             --------------------------------------------------------------------------------
T ss_conf             --------------------------------------------------------------------------------


Q ss_pred             CCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCC
Q ss_conf             00224667301223334565305034789999999999999630647224369999999888278
Q gi|254780773|r  250 TRLNQISGPVGIARIAKNFFDHGFNAYIAFLAMFSWAIGFMNLLPIPILDGGHLITFLLEMIRGK  314 (349)
Q Consensus       250 ~~~~~lsGPVgIa~~~~~~a~~G~~~~l~~~a~isi~Lg~~NlLPip~LDGG~i~~~~~E~i~gr  314 (349)
                                           ..+..++.+.+++|+.+++|||+|+||||||||+..+.+..++|
T Consensus       105 ---------------------~~~~~~l~~~~~in~~l~~fNLlPi~pLDGg~Il~~ll~~~~~~  148 (148)
T LOAD_S2Pmetall  105 ---------------------AGLLSFLFFLALLNLNLALFNLLPIPPLDGGKILRALLEELRGR  148 (148)
T ss_pred             ---------------------HHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCC
T ss_conf             ---------------------79999999999999999999946887878499999999998388


No 9  
>cd06161 S2P-M50_SpoIVFB SpoIVFB Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50B), regulates intramembrane proteolysis (RIP), and is involved in the pro-sigmaK pathway of bacterial spore formation. SpoIVFB (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA (bypass-of-forespore A), and SpoIVB (sporulation protein, stage IV cell wall formation, B locus). SpoIVFB is negatively regulated by SpoIVFA and BofA and activated by SpoIVB. It is thought that SpoIVFB, SpoIVFA, and BofA are located in the mother-cell membrane that surrounds the forespore and that SpoIVB is secreted from the forespore into the space between the two where it activates SpoIVFB.
Probab=99.80  E-value=1.6e-18  Score=147.54  Aligned_cols=151  Identities=36%  Similarity=0.639  Sum_probs=110.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEEECCCHHEEEEECCCEEEEEEEEEECCEEECCCCCCCHHHHCCCCC
Q ss_conf             99999999999999733779999984975004553068311278605980799997711211100124455066503684
Q gi|254780773|r    7 FLLYTVSLIIIVVIHEFGHYMVARLCNIRVLSFSVGFGPELIGITSRSGVRWKVSLIPLGGYVSFSEDEKDMRSFFCAAP   86 (349)
Q Consensus         7 ~~~~~~~l~~~v~iHE~GH~~~Ar~~gv~V~~FsiGfgp~l~~~~~k~~t~y~i~~~PlGgyV~~~~~e~~~~~f~~~~~   86 (349)
                      -+...+.+..+|++||+||.++||++|++|++                     +...|+||.++++++.+        ++
T Consensus        30 ~~~~~l~lf~sVl~HElgH~l~A~~~G~~v~~---------------------I~L~pfGG~a~~~~~~~--------~~   80 (208)
T cd06161          30 GLLEALLLFLSVLLHELGHALVARRYGIRVRS---------------------ITLLPFGGVAELEEEPE--------TP   80 (208)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC---------------------EEEEEEEEEEECCCCCC--------CH
T ss_conf             99999999999999999999999994998886---------------------58885012566367775--------78


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCCCCCC
Q ss_conf             21013421123332112211101110012333320002456755653001456628888783045400111110146788
Q gi|254780773|r   87 WKKILTVLAGPLANCVMAILFFTFFFYNTGVMKPVVSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRENPLH  166 (349)
Q Consensus        87 ~~R~~i~~AGp~~N~ilA~iif~~~~~~~g~~~p~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~~~g~  166 (349)
                      +|++.|..|||++|+++|.+.+......                                                    
T Consensus        81 ~~e~~IalAGPl~nl~l~~~~~~l~~~~----------------------------------------------------  108 (208)
T cd06161          81 KEEFVIALAGPLVSLLLAGLFYLLYLLL----------------------------------------------------  108 (208)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHC----------------------------------------------------
T ss_conf             8888999833488999999999999975----------------------------------------------------


Q ss_pred             CCEEEEEECCCCEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHEECCCCCC
Q ss_conf             63169996587313101121100565431000012203444432123334566888768988865542231000000025
Q gi|254780773|r  167 EISLVLYREHVGVLHLKVMPRLQDTVDRFGIKRQVPSVGISFSYDETKLHSRTVLQSFSRGLDEISSITRGFLGVLSSAF  246 (349)
Q Consensus       167 ~v~i~v~R~~~~~~~~~v~p~~~~~~~~~g~~~~~~~igi~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~l~~l~  246 (349)
                                         +.                                                           
T Consensus       109 -------------------~~-----------------------------------------------------------  110 (208)
T cd06161         109 -------------------PG-----------------------------------------------------------  110 (208)
T ss_pred             -------------------CC-----------------------------------------------------------
T ss_conf             -------------------66-----------------------------------------------------------


Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHH
Q ss_conf             54200224667301223334565305034789999999999999630647224369999999888278699999999999
Q gi|254780773|r  247 GKDTRLNQISGPVGIARIAKNFFDHGFNAYIAFLAMFSWAIGFMNLLPIPILDGGHLITFLLEMIRGKSLGVSVTRVITR  326 (349)
Q Consensus       247 ~g~~~~~~lsGPVgIa~~~~~~a~~G~~~~l~~~a~isi~Lg~~NlLPip~LDGG~i~~~~~E~i~gr~i~~~~~~~~~~  326 (349)
                            .   ++              ...++.+++++|+.+++|||+|+.||||||++.++.-+.+++   .|.......
T Consensus       111 ------~---~~--------------~~~~~~~~~~~Nl~l~~FNLlP~~PLDGGrilrall~~~~~~---~~at~~a~~  164 (208)
T cd06161         111 ------G---GP--------------LSSLLEFLAQVNLILGLFNLLPALPLDGGRVLRALLWRRTGY---RRATRIAAR  164 (208)
T ss_pred             ------C---CH--------------HHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHCCH---HHHHHHHHH
T ss_conf             ------4---16--------------999999999999999999828787886699999999986178---999999999


Q ss_pred             HHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999
Q gi|254780773|r  327 MGLCIILFLFFLGIRN  342 (349)
Q Consensus       327 ~g~~ll~~l~i~~~~n  342 (349)
                      +|..+-..+++..++.
T Consensus       165 ~g~~~~~~l~~~g~~~  180 (208)
T cd06161         165 IGQLFAILLVVLGLFL  180 (208)
T ss_pred             HHHHHHHHHHHHHHHH
T ss_conf             9999999999999999


No 10 
>cd06164 S2P-M50_SpoIVFB_CBS SpoIVFB Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50B), regulates intramembrane proteolysis (RIP), and is involved in the pro-sigmaK pathway of bacterial spore formation. In this subgroup, SpoIVFB (sporulation protein, stage IV cell wall formation, F locus, promoter-distal B) contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domain. SpoIVFB is one of 4 proteins involved in endospore formation; the others are SpoIVFA (sporulation protein, stage IV cell wall formation, F locus, promoter-proximal A), BofA (bypass-of-forespore A), and SpoIVB (sporulation protein, stage IV cell wall formation, B locus). SpoIVFB is negatively regulated by SpoIVFA and BofA and activated by SpoIVB. It is thought that SpoIVFB, SpoIVFA, and BofA are located in the mother-cell membrane that surrounds the forespore and that SpoIVB is secreted from the forespore into the space between the two where it activates SpoIVFB. It has been proposed tha
Probab=99.80  E-value=4.6e-18  Score=144.31  Aligned_cols=148  Identities=31%  Similarity=0.560  Sum_probs=103.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEEECCCHHEEEEECCCEEEEEEEEEECCEEECCCCCCCHHHHCCCCCC
Q ss_conf             99999999999997337799999849750045530683112786059807999977112111001244550665036842
Q gi|254780773|r    8 LLYTVSLIIIVVIHEFGHYMVARLCNIRVLSFSVGFGPELIGITSRSGVRWKVSLIPLGGYVSFSEDEKDMRSFFCAAPW   87 (349)
Q Consensus         8 ~~~~~~l~~~v~iHE~GH~~~Ar~~gv~V~~FsiGfgp~l~~~~~k~~t~y~i~~~PlGgyV~~~~~e~~~~~f~~~~~~   87 (349)
                      +.+.+.+.++|++||+||.++||++|++|++                     +...|+||..+++++.+        +++
T Consensus        46 ~~~a~~lf~sVllHElgHal~Ar~~G~~v~~---------------------I~L~~fGG~a~~~~~~~--------~p~   96 (227)
T cd06164          46 LAAALLLFASVLLHELGHSLVARRYGIPVRS---------------------ITLFLFGGVARLEREPE--------TPG   96 (227)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC---------------------EEEEEEEEEEECCCCCC--------CHH
T ss_conf             9999999999999999999999992998471---------------------78896351465258999--------967


Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCCCCCCC
Q ss_conf             10134211233321122111011100123333200024567556530014566288887830454001111101467886
Q gi|254780773|r   88 KKILTVLAGPLANCVMAILFFTFFFYNTGVMKPVVSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRENPLHE  167 (349)
Q Consensus        88 ~R~~i~~AGp~~N~ilA~iif~~~~~~~g~~~p~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~~~g~~  167 (349)
                      +.+.|..|||++|++++.+.+.......+                                                   
T Consensus        97 ~e~~Ia~AGPl~n~~l~~~~~~l~~~~~~---------------------------------------------------  125 (227)
T cd06164          97 QEFVIAIAGPLVSLVLALLFLLLSLALPG---------------------------------------------------  125 (227)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCC---------------------------------------------------
T ss_conf             77266440178999999999999987455---------------------------------------------------


Q ss_pred             CEEEEEECCCCEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHEECCCCCCC
Q ss_conf             31699965873131011211005654310000122034444321233345668887689888655422310000000255
Q gi|254780773|r  168 ISLVLYREHVGVLHLKVMPRLQDTVDRFGIKRQVPSVGISFSYDETKLHSRTVLQSFSRGLDEISSITRGFLGVLSSAFG  247 (349)
Q Consensus       168 v~i~v~R~~~~~~~~~v~p~~~~~~~~~g~~~~~~~igi~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~l~~l~~  247 (349)
                               ..                                                                     
T Consensus       126 ---------~~---------------------------------------------------------------------  127 (227)
T cd06164         126 ---------SG---------------------------------------------------------------------  127 (227)
T ss_pred             ---------CC---------------------------------------------------------------------
T ss_conf             ---------64---------------------------------------------------------------------


Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHH
Q ss_conf             42002246673012233345653050347899999999999996306472243699999998882786999999999999
Q gi|254780773|r  248 KDTRLNQISGPVGIARIAKNFFDHGFNAYIAFLAMFSWAIGFMNLLPIPILDGGHLITFLLEMIRGKSLGVSVTRVITRM  327 (349)
Q Consensus       248 g~~~~~~lsGPVgIa~~~~~~a~~G~~~~l~~~a~isi~Lg~~NlLPip~LDGG~i~~~~~E~i~gr~i~~~~~~~~~~~  327 (349)
                              .++              ...++.+++++|+.+++|||||.+||||||++.+++-+.+|++  .|........
T Consensus       128 --------~~~--------------~~~~~~~l~~~Nl~l~~fNLLP~~PLDGGrilra~lw~~~g~~--~~at~~a~~~  183 (227)
T cd06164         128 --------AGP--------------LGVLLGYLALINLLLAVFNLLPAFPLDGGRVLRALLWRRTGDY--LKATRIAAWV  183 (227)
T ss_pred             --------CHH--------------HHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCH--HHHHHHHHHH
T ss_conf             --------407--------------9999999999999999997387888870799999999995779--8999999999


Q ss_pred             HHHHHHHHHH
Q ss_conf             9999999999
Q gi|254780773|r  328 GLCIILFLFF  337 (349)
Q Consensus       328 g~~ll~~l~i  337 (349)
                      |-++-+.+++
T Consensus       184 G~~~a~~l~~  193 (227)
T cd06164         184 GRGFAVLLII  193 (227)
T ss_pred             HHHHHHHHHH
T ss_conf             9999999999


No 11 
>KOG2921 consensus
Probab=99.77  E-value=4e-18  Score=144.76  Aligned_cols=137  Identities=27%  Similarity=0.438  Sum_probs=111.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEEECCCHHEEEEECCCEEEEEEEEEECCEEECCCCCCCHHHHCCC
Q ss_conf             99999999999999997337799999849750045530683112786059807999977112111001244550665036
Q gi|254780773|r    5 DCFLLYTVSLIIIVVIHEFGHYMVARLCNIRVLSFSVGFGPELIGITSRSGVRWKVSLIPLGGYVSFSEDEKDMRSFFCA   84 (349)
Q Consensus         5 ~~~~~~~~~l~~~v~iHE~GH~~~Ar~~gv~V~~FsiGfgp~l~~~~~k~~t~y~i~~~PlGgyV~~~~~e~~~~~f~~~   84 (349)
                      ..+=+|+.++.+.+++||+||.++|-..||+|+-|.|.+                +...| ||||     |-|.+..++.
T Consensus       121 ~~I~yf~t~lvi~~vvHElGHalAA~segV~vngfgIfi----------------~aiyP-gafv-----dl~~dhLqsl  178 (484)
T KOG2921         121 SGIAYFLTSLVITVVVHELGHALAAASEGVQVNGFGIFI----------------AAIYP-GAFV-----DLDNDHLQSL  178 (484)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEE----------------EEECC-CHHH-----HHHHHHHHHC
T ss_conf             222156656777787887657999875486130058999----------------88737-5121-----0016677615


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC--------CCCCCCCCCHHH-HHHCCCCCEEEEECCCCCCCCHH
Q ss_conf             842101342112333211221110111001233332--------000245675565-30014566288887830454001
Q gi|254780773|r   85 APWKKILTVLAGPLANCVMAILFFTFFFYNTGVMKP--------VVSNVSPASPAA-IAGVKKGDCIISLDGITVSAFEE  155 (349)
Q Consensus        85 ~~~~R~~i~~AGp~~N~ilA~iif~~~~~~~g~~~p--------~I~~V~~~spA~-~AGL~~GD~Il~InG~~V~s~~d  155 (349)
                      ++.+|++|+.||+.-||++|.+...+++...-...|        +|.+|...||+. .-||++||+|+++||.+|++.+|
T Consensus       179 ~~fr~LrIfcAGIWHNfvfallc~lal~~lpViLsPfya~g~gV~Vtev~~~Spl~gprGL~vgdvitsldgcpV~~v~d  258 (484)
T KOG2921         179 PSFRALRIFCAGIWHNFVFALLCVLALFLLPVILSPFYAHGEGVTVTEVPSVSPLFGPRGLSVGDVITSLDGCPVHKVSD  258 (484)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHCCCEEEEEECCCCCCCCCCCCCCCCCEEEECCCCCCCCHHH
T ss_conf             44777888765488889999999999986247423466638507999445557775765677665577537854588889


Q ss_pred             HHHHCCCC
Q ss_conf             11110146
Q gi|254780773|r  156 VAPYVREN  163 (349)
Q Consensus       156 l~~~i~~~  163 (349)
                      ..+-++.+
T Consensus       259 W~ecl~ts  266 (484)
T KOG2921         259 WLECLATS  266 (484)
T ss_pred             HHHHHHHH
T ss_conf             99999864


No 12 
>cd06162 S2P-M50_PDZ_SREBP Sterol regulatory element-binding protein (SREBP) Site-2 protease (S2P), a zinc metalloprotease (MEROPS family M50A), regulates intramembrane proteolysis (RIP) of SREBP and is part of a signal transduction mechanism involved in sterol and lipid metabolism. In sterol-depleted mammalian cells, a two-step proteolytic process releases the N-terminal domains of SREBPs from membranes of the endoplasmic reticulum (ER). These domains translocate into the nucleus, where they activate genes of cholesterol and fatty acid biosynthesis. The first cleavage occurs at Site-1 within the ER lumen to generate an intermediate that is subsequently released from the membrane by cleavage at Site-2, which lies within the first transmembrane domain. It is the second proteolytic step that is carried out by the SREBP Site-2 protease (S2P) which is present in this CD family.  This group appears to be limited to eumetazoan proteins and contains one PDZ domain.
Probab=99.66  E-value=1.5e-15  Score=126.99  Aligned_cols=85  Identities=25%  Similarity=0.378  Sum_probs=71.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEEECCCHHEEEEECCCEEEEEEEEEECCEEECCCCCCCHHHHCCC
Q ss_conf             99999999999999997337799999849750045530683112786059807999977112111001244550665036
Q gi|254780773|r    5 DCFLLYTVSLIIIVVIHEFGHYMVARLCNIRVLSFSVGFGPELIGITSRSGVRWKVSLIPLGGYVSFSEDEKDMRSFFCA   84 (349)
Q Consensus         5 ~~~~~~~~~l~~~v~iHE~GH~~~Ar~~gv~V~~FsiGfgp~l~~~~~k~~t~y~i~~~PlGgyV~~~~~e~~~~~f~~~   84 (349)
                      ...-++++++.+..++||+||.++|.+++|+|+.|.+.    +            .-.+| |+||     |-+.+..++.
T Consensus       125 s~l~Y~~~al~is~v~HElGHA~aA~~e~V~v~~~G~~----~------------~~i~P-gA~v-----~l~~~~L~~l  182 (277)
T cd06162         125 SQLGYYFTALLISGVVHEMGHGVAAVREQVRVNGFGIF----F------------FIIYP-GAYV-----DLFTDHLNLI  182 (277)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEE----E------------EEEEC-CCEE-----EECHHHHHCC
T ss_conf             89899999999999999998999998628715222499----9------------99802-4047-----7179998348


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             842101342112333211221110111
Q gi|254780773|r   85 APWKKILTVLAGPLANCVMAILFFTFF  111 (349)
Q Consensus        85 ~~~~R~~i~~AGp~~N~ilA~iif~~~  111 (349)
                      ++|||++|+.||+..|+++|.+.+..+
T Consensus       183 ~~~~~Lri~cAGiWHN~vl~~~a~lll  209 (277)
T cd06162         183 SPVQQLRIFCAGVWHNFVLGLVGYLLL  209 (277)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             888877864413698999999999999


No 13 
>cd06160 S2P-M50_like_2 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the S2P/M50 family of RIP proteases use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. In eukaryotic cells they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum stress responses. In prokaryotes they regulate such processes as sporulation, cell division, stress response, and cell differentiation. This group includes bacterial, eukaryotic, and Archaeal S2P/M50s homologs with additional putative N- and C-terminal transmembrane spanning regions, relative to the core protein, and no PDZ domains.
Probab=99.60  E-value=2.9e-14  Score=118.06  Aligned_cols=78  Identities=26%  Similarity=0.433  Sum_probs=58.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEE-EEEECCCHHEEEEECCCEEEEEEEEEECCEEECCCCCCCHHHHCCCC
Q ss_conf             99999999999999733779999984975004-55306831127860598079999771121110012445506650368
Q gi|254780773|r    7 FLLYTVSLIIIVVIHEFGHYMVARLCNIRVLS-FSVGFGPELIGITSRSGVRWKVSLIPLGGYVSFSEDEKDMRSFFCAA   85 (349)
Q Consensus         7 ~~~~~~~l~~~v~iHE~GH~~~Ar~~gv~V~~-FsiGfgp~l~~~~~k~~t~y~i~~~PlGgyV~~~~~e~~~~~f~~~~   85 (349)
                      -+.+.+++..++++||+||+++||++|+|+.. |.|=+..                .-.+||+.+++++.+        +
T Consensus        33 gl~~al~l~~il~~HElGH~l~a~~~gv~~~~p~fiP~~~----------------lg~fGav~~~~~~~~--------~   88 (183)
T cd06160          33 GLPFALALLAILGIHEMGHYLAARRHGVKASLPYFIPFPF----------------IGTFGAFIRMRSPIP--------N   88 (183)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEECCCC----------------HHHHHEEEECCCCCC--------C
T ss_conf             9999999999999999999999999399777603566620----------------231010234567898--------9


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             42101342112333211221110
Q gi|254780773|r   86 PWKKILTVLAGPLANCVMAILFF  108 (349)
Q Consensus        86 ~~~R~~i~~AGp~~N~ilA~iif  108 (349)
                      +++.+.+..|||+++++++..++
T Consensus        89 ~~~~~~ia~aGPl~g~~~~~~~~  111 (183)
T cd06160          89 RKALFDIALAGPLAGLLLALPVL  111 (183)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             89988998750888999999999


No 14 
>cd06158 S2P-M50_like_1 Uncharacterized homologs of Site-2 protease (S2P), zinc metalloproteases (MEROPS family M50) which cleave transmembrane domains of substrate proteins, regulating intramembrane proteolysis (RIP) of diverse signal transduction mechanisms. Members of the S2P/M50 family of RIP proteases use proteolytic activity within the membrane to transfer information across membranes to integrate gene expression with physiologic stresses occurring in another cellular compartment. In eukaryotic cells they regulate such processes as sterol and lipid metabolism, and endoplasmic reticulum stress responses. In prokaryotes they regulate such processes as sporulation, cell division, stress response, and cell differentiation. This group includes bacterial, eukaryotic, and Archaeal S2P/M50s homologs with a minimal core protein and no PDZ domains.
Probab=99.56  E-value=1.1e-14  Score=121.07  Aligned_cols=94  Identities=26%  Similarity=0.408  Sum_probs=55.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEE--EECCCHHEEEEECCCEEEEEEEEE-----ECCEEECCCCCCCHHH
Q ss_conf             999999999999973377999998497500455--306831127860598079999771-----1211100124455066
Q gi|254780773|r    8 LLYTVSLIIIVVIHEFGHYMVARLCNIRVLSFS--VGFGPELIGITSRSGVRWKVSLIP-----LGGYVSFSEDEKDMRS   80 (349)
Q Consensus         8 ~~~~~~l~~~v~iHE~GH~~~Ar~~gv~V~~Fs--iGfgp~l~~~~~k~~t~y~i~~~P-----lGgyV~~~~~e~~~~~   80 (349)
                      +..++++.+.+++||++|.++|+++|-+-.+..  +-..|.  ...|--||    -.+|     .+|+.|-  .+-+++.
T Consensus         2 l~~~~~~~~si~~HE~aHa~~A~~~GD~t~~~~GrltLnPl--~hid~~G~----i~l~~~~~~~~Gwakp--v~~~~~~   73 (181)
T cd06158           2 LIVIIAVLLAITLHEFAHAYVAYRLGDPTARRAGRLTLNPL--AHIDPIGT----IILPLLLPFLFGWAKP--VPVNPRN   73 (181)
T ss_pred             EEHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHCCCEECCCH--HHCCCHHH----HHHHHHHHHHCCCCCC--CCCCCCC
T ss_conf             22299999999999999999999849954887695435826--75050278----9999998763235677--4654001


Q ss_pred             HCCCCCCCCHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             503684210134211233321122111011
Q gi|254780773|r   81 FFCAAPWKKILTVLAGPLANCVMAILFFTF  110 (349)
Q Consensus        81 f~~~~~~~R~~i~~AGp~~N~ilA~iif~~  110 (349)
                      + +.++|++.+|.+|||++|+++|++....
T Consensus        74 ~-~~~r~~~~~valAGPl~Nl~la~~~~~~  102 (181)
T cd06158          74 F-KNPRRGMLLVSLAGPLSNLLLALLFALL  102 (181)
T ss_pred             C-CCCCCEEEEHHHHHHHHHHHHHHHHHHH
T ss_conf             2-5776635303363589999999999999


No 15 
>cd00989 PDZ_metalloprotease PDZ domain of bacterial and plant zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=99.45  E-value=1.1e-13  Score=114.16  Aligned_cols=75  Identities=33%  Similarity=0.606  Sum_probs=66.7

Q ss_pred             CCCCCCCCCCCCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCCCCCCCCEEEEEECCCCEEEECCCC
Q ss_conf             1001233332000245675565300145662888878304540011111014678863169996587313101121
Q gi|254780773|r  111 FFYNTGVMKPVVSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRENPLHEISLVLYREHVGVLHLKVMP  186 (349)
Q Consensus       111 ~~~~~g~~~p~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~~~g~~v~i~v~R~~~~~~~~~v~p  186 (349)
                      +....+...|+|++|.++|||++|||++||+|++|||+++.+|+|+...++.+++++++++++|+++ ..+++++|
T Consensus         5 ~~~~~p~~~~vV~~V~~~spA~~AGl~~GD~I~~ing~~v~~~~~~~~~i~~~~~~~i~l~v~R~g~-~~~~~vtP   79 (79)
T cd00989           5 FVPGGPPIEPVIGEVVPGSPAAKAGLKAGDRILAINGQKIKSWEDLVDAVQENPGKPLTLTVERNGE-TITLTLTP   79 (79)
T ss_pred             EEECCCCCCCEEEEECCCCHHHHCCCCCCCEEEEECCEECCCHHHHHHHHHHCCCCEEEEEEEECCE-EEEEEEEC
T ss_conf             9948999999999989999899859999999999999995899999999985899889999999999-98999879


No 16 
>TIGR02037 degP_htrA_DO protease Do; InterPro: IPR011782   Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases .   Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , .   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.    This family consists serine peptidases belonging to MEROPS peptidase family S1, subfamily S1C (protease Do, clan PA(S)). They are variously designated DegP, DegQ, heat shock protein HtrA, MucD and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in Escherichia coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens . The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures .; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis.
Probab=99.35  E-value=8.1e-13  Score=108.14  Aligned_cols=66  Identities=29%  Similarity=0.517  Sum_probs=59.7

Q ss_pred             CCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCC-CCCCCCEEEEEECCCCEEEECCCCC
Q ss_conf             000245675565300145662888878304540011111014-6788631699965873131011211
Q gi|254780773|r  121 VVSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRE-NPLHEISLVLYREHVGVLHLKVMPR  187 (349)
Q Consensus       121 ~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~-~~g~~v~i~v~R~~~~~~~~~v~p~  187 (349)
                      .|.+|.++|||++||||+||+|+++||++|+++.||+..|.. .||+++++++.|+|++ .+++++-.
T Consensus       296 LV~~V~~gSPA~kAGlk~GDvI~~~nGk~i~~~~~L~~~i~~~~pG~~~~L~i~R~Gk~-~~~~V~l~  362 (484)
T TIGR02037       296 LVAQVLPGSPAEKAGLKAGDVILSVNGKKIKSFADLRRAIGTLKPGKKVTLTILRKGKE-KTITVTLG  362 (484)
T ss_pred             EEEEECCCCCHHCCCCCCCCEEEEECCEEECCHHHHHHHHHCCCCCCEEEEEEEECCEE-EEEEEEEE
T ss_conf             88854489701006753266899858864058799989874058987799999978868-88999981


No 17 
>cd00991 PDZ_archaeal_metalloprotease PDZ domain of archaeal zinc metalloprotases, presumably membrane-associated or integral membrane proteases, which may be involved in signalling and regulatory mechanisms. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=99.23  E-value=1e-11  Score=100.51  Aligned_cols=61  Identities=23%  Similarity=0.370  Sum_probs=56.3

Q ss_pred             CCCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCC-CCCCCCEEEEEECCCCEE
Q ss_conf             2000245675565300145662888878304540011111014-678863169996587313
Q gi|254780773|r  120 PVVSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRE-NPLHEISLVLYREHVGVL  180 (349)
Q Consensus       120 p~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~-~~g~~v~i~v~R~~~~~~  180 (349)
                      -+|.+|.++|||++|||++||+|++|||++|++.+|+.+++.. +||+++++++.|++++..
T Consensus        12 v~V~~V~~gsPA~~AGL~~GDVI~~Ing~~I~~~~d~~~~l~~~~pG~~v~v~v~R~g~~lT   73 (79)
T cd00991          12 VVIVGVIVGSPAENAVLHTGDVIYSINGTPITTLEDFMEALKPTKPGEVITVTVLPSTTKLT   73 (79)
T ss_pred             EEEEEECCCCHHHHCCCCCCCEEEEECCEECCCHHHHHHHHHCCCCCCEEEEEEEECCEEEE
T ss_conf             79999678996998699988899998999987999999999618999989999998999977


No 18 
>PRK10139 serine endoprotease; Provisional
Probab=99.14  E-value=8.9e-11  Score=94.06  Aligned_cols=65  Identities=37%  Similarity=0.501  Sum_probs=58.1

Q ss_pred             CCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCC-CCCCCCEEEEEECCCCEEEECCCC
Q ss_conf             000245675565300145662888878304540011111014-678863169996587313101121
Q gi|254780773|r  121 VVSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRE-NPLHEISLVLYREHVGVLHLKVMP  186 (349)
Q Consensus       121 ~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~-~~g~~v~i~v~R~~~~~~~~~v~p  186 (349)
                      .|.+|.++|||++||||+||+|+++||++|++.+|+...+.. .||+++++++.|+++ ..+++++.
T Consensus       293 lV~~V~~~sPA~kAGLk~GDVI~~vnG~~V~~~~dL~~~v~~~~pG~~v~l~v~R~Gk-~~~~~vtl  358 (455)
T PRK10139        293 FVSEVLPNSGSAKAGVKSGDIITSLNGKPLNSFAELRSRIATTEPGTKVKLGLLRNGK-PLEVEVTL  358 (455)
T ss_pred             EEEEECCCCCHHHCCCCCCCEEEEECCEECCCHHHHHHHHHCCCCCCEEEEEEEECCE-EEEEEEEE
T ss_conf             5665447883687699999999998998968999999999608988889999999997-99999995


No 19 
>PRK10942 serine endoprotease; Provisional
Probab=99.12  E-value=8.2e-11  Score=94.30  Aligned_cols=65  Identities=34%  Similarity=0.445  Sum_probs=58.3

Q ss_pred             CCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCC-CCCCCCEEEEEECCCCEEEECCCC
Q ss_conf             000245675565300145662888878304540011111014-678863169996587313101121
Q gi|254780773|r  121 VVSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRE-NPLHEISLVLYREHVGVLHLKVMP  186 (349)
Q Consensus       121 ~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~-~~g~~v~i~v~R~~~~~~~~~v~p  186 (349)
                      .|.+|.++|||++|||++||+|+++||++|++.+|+...+.. .||+++++++.|+++ ..+++++.
T Consensus       315 lV~~V~~~sPA~kAGL~~GDVI~~vdG~~I~~~~dL~~~v~~~~pG~~V~l~v~R~Gk-~~~v~Vtl  380 (474)
T PRK10942        315 FVSQVLPNSSAAKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKMTLGLLRDGK-PVNVNLEL  380 (474)
T ss_pred             EEEECCCCCCHHHCCCCCCCEEEEECCEECCCHHHHHHHHHCCCCCCEEEEEEEECCE-EEEEEEEE
T ss_conf             6520177993677699989999998998968999999999618988889999999998-99999996


No 20 
>PRK10898 serine endoprotease; Provisional
Probab=99.10  E-value=1.2e-10  Score=93.26  Aligned_cols=65  Identities=37%  Similarity=0.449  Sum_probs=58.0

Q ss_pred             CCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCC-CCCCCCEEEEEECCCCEEEECCCC
Q ss_conf             000245675565300145662888878304540011111014-678863169996587313101121
Q gi|254780773|r  121 VVSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRE-NPLHEISLVLYREHVGVLHLKVMP  186 (349)
Q Consensus       121 ~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~-~~g~~v~i~v~R~~~~~~~~~v~p  186 (349)
                      .|.+|.|+|||++||||+||+|+++||+++.+.+|+.+.+.. +||+++++++.|+++ ..+++++.
T Consensus       283 ~V~~V~~~sPA~~AGL~~GDvI~~idg~~v~~~~~l~~~l~~~~pGd~v~l~v~R~G~-~~~~~VtL  348 (355)
T PRK10898        283 VVNEVSPDGPAANAGIQVNDLIISVNNKPAISALETMDQVAEIRPGSVIPVVVMRDDK-QLTLQVTI  348 (355)
T ss_pred             EEEEECCCCHHHHCCCCCCCEEEEECCEECCCHHHHHHHHHHCCCCCEEEEEEEECCE-EEEEEEEE
T ss_conf             8988799995898599989999998998938999999999718997989999999999-99999997


No 21 
>cd00988 PDZ_CTP_protease PDZ domain of C-terminal processing-, tail-specific-, and tricorn proteases, which function in posttranslational protein processing, maturation, and disassembly or degradation, in Bacteria, Archaea, and plant chloroplasts. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=99.06  E-value=2.3e-10  Score=91.25  Aligned_cols=68  Identities=32%  Similarity=0.485  Sum_probs=59.5

Q ss_pred             CCCCCCCCCCCHHHHHHCCCCCEEEEECCCCCCC--CHHHHHHCCCCCCCCCEEEEEECCCCEEEECCCC
Q ss_conf             3200024567556530014566288887830454--0011111014678863169996587313101121
Q gi|254780773|r  119 KPVVSNVSPASPAAIAGVKKGDCIISLDGITVSA--FEEVAPYVRENPLHEISLVLYREHVGVLHLKVMP  186 (349)
Q Consensus       119 ~p~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s--~~dl~~~i~~~~g~~v~i~v~R~~~~~~~~~v~p  186 (349)
                      ..+|.+|.++|||++|||++||+|++|||+++.+  ++++.+.++..+|+++++++.|.+.+..+++++.
T Consensus        14 ~~~V~~v~~gsPA~~aGl~~GD~I~~Vng~~v~~~~~~~~~~~lrg~~Gt~V~l~v~R~~~~~~~~~l~R   83 (85)
T cd00988          14 GLVITSVLPGSPAAKAGIKAGDIIVAIDGEPVDGLSLEDVVKLLRGKAGTKVRLTLKRGDGEPREVTLTR   83 (85)
T ss_pred             EEEEEEECCCCHHHHHCCCCCCEEEEECCEECCCCCHHHHHHHHCCCCCCEEEEEEECCCCCEEEEEEEE
T ss_conf             8999996899958980899999999999999789999999998659999889999990999899999998


No 22 
>cd00986 PDZ_LON_protease PDZ domain of ATP-dependent LON serine proteases. Most PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this bacterial subfamily of protease-associated PDZ domains a C-terminal beta-strand  is thought to form the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=99.00  E-value=4.3e-10  Score=89.32  Aligned_cols=64  Identities=30%  Similarity=0.401  Sum_probs=56.2

Q ss_pred             CCCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCC-CCCCCCEEEEEECCCCEEEECCC
Q ss_conf             2000245675565300145662888878304540011111014-67886316999658731310112
Q gi|254780773|r  120 PVVSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRE-NPLHEISLVLYREHVGVLHLKVM  185 (349)
Q Consensus       120 p~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~-~~g~~v~i~v~R~~~~~~~~~v~  185 (349)
                      -+|.+|.++|||+.+ |++||+|+++||+++++.+|+..+++. +||+++++++.|++++ .+++++
T Consensus        10 v~V~~V~~gsPA~~~-Lk~GDvI~~vdGk~v~~~~~l~~~i~~~~~Gd~V~l~v~R~gk~-~~~~vt   74 (79)
T cd00986          10 VYVTSVVEGMPAAGK-LKAGDHIIAVDGKPFKEAEELIDYIQSKKEGDTVKLKVKREEKE-LPEDLI   74 (79)
T ss_pred             EEEEEECCCCCHHHC-CCCCCEEEEECCEECCCHHHHHHHHHCCCCCCEEEEEEEECCEE-EEEEEE
T ss_conf             899996799973770-77899999999989579999999996599999899999999999-999999


No 23 
>cd00987 PDZ_serine_protease PDZ domain of tryspin-like serine proteases, such as DegP/HtrA, which are oligomeric proteins involved in heat-shock response, chaperone function, and apoptosis. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=98.99  E-value=5.4e-10  Score=88.68  Aligned_cols=63  Identities=32%  Similarity=0.526  Sum_probs=56.1

Q ss_pred             CCCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCCC-CCCCCEEEEEECCCCEEEEC
Q ss_conf             20002456755653001456628888783045400111110146-78863169996587313101
Q gi|254780773|r  120 PVVSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVREN-PLHEISLVLYREHVGVLHLK  183 (349)
Q Consensus       120 p~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~~-~g~~v~i~v~R~~~~~~~~~  183 (349)
                      -.|.+|.++|||++|||++||+|+++||++|.+.+|+.+.++.. +++++.+++.|+|+. .+++
T Consensus        26 v~V~~V~~~spA~~aGl~~GDiI~~ing~~i~~~~~~~~~l~~~~~g~~v~~~v~R~g~~-~~~~   89 (90)
T cd00987          26 VLVASVDPGSPAAKAGLKPGDVILAVNGKPVKSVADLRRALAELKPGDKVTLTVLRGGKE-LTVT   89 (90)
T ss_pred             EEEEEECCCCHHHHCCCCCCCEEEEECCEECCCHHHHHHHHHHCCCCCEEEEEEEECCEE-EEEE
T ss_conf             999998999959982999998999999999389999999998269998799999999999-9978


No 24 
>cd00990 PDZ_glycyl_aminopeptidase PDZ domain associated with archaeal and bacterial M61 glycyl-aminopeptidases. May be responsible for substrate recognition and/or binding, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of protease-associated PDZ domains a C-terminal beta-strand is presumed to form the peptide-binding groove base, a circular permutation with respect to PDZ domains found in Eumetazoan signaling proteins.
Probab=98.98  E-value=5.3e-10  Score=88.72  Aligned_cols=63  Identities=22%  Similarity=0.391  Sum_probs=54.8

Q ss_pred             CCCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCCCCCCCCEEEEEECCCCEEEECCC
Q ss_conf             200024567556530014566288887830454001111101467886316999658731310112
Q gi|254780773|r  120 PVVSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRENPLHEISLVLYREHVGVLHLKVM  185 (349)
Q Consensus       120 p~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~~~g~~v~i~v~R~~~~~~~~~v~  185 (349)
                      ..|..|.++|||++|||++||+|+++||.++++|++...  ..++|+++++++.|+++ ..+++++
T Consensus        14 ~~V~~V~~~sPA~~AGl~~GD~IvaidG~~v~~~~~~~~--~~~~G~~v~l~v~R~g~-l~~~~vt   76 (80)
T cd00990          14 GKVTFVRDDSPADKAGLVAGDELVAVNGWRVDALQDRLK--EYQAGDPVELTVFRDDR-LIEVPLT   76 (80)
T ss_pred             EEEEEECCCCHHHHCCCCCCCEEEEECCEEEHHHHHHHH--HCCCCCEEEEEEEECCE-EEEEEEE
T ss_conf             999998889969985999899999999999237899997--36998989999999999-9998999


No 25 
>TIGR02860 spore_IV_B stage IV sporulation protein B; InterPro: IPR014219   Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases .   Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , .   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.    SpoIVB, the stage IV sporulation protein B of endospore-forming bacteria such as Bacillus subtilis, is a serine proteinase expressed in the spore (rather than mother cell) compartment, that participates in a proteolytic activation cascade for Sigma-K. It appears to be universal among endospore-forming bacteria and occurs nowhere else. The members of this entry belong to MEROPS peptidase family S55 (SpoIVB peptidase, clan PA)..
Probab=98.96  E-value=8.4e-10  Score=87.35  Aligned_cols=78  Identities=23%  Similarity=0.443  Sum_probs=63.8

Q ss_pred             CCHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCCCC--CCCCEEEEEECCCCEEEECCCCCCCCCCCC--CEEEEEEEE
Q ss_conf             7556530014566288887830454001111101467--886316999658731310112110056543--100001220
Q gi|254780773|r  128 ASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRENP--LHEISLVLYREHVGVLHLKVMPRLQDTVDR--FGIKRQVPS  203 (349)
Q Consensus       128 ~spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~~~--g~~v~i~v~R~~~~~~~~~v~p~~~~~~~~--~g~~~~~~~  203 (349)
                      .|||++||||.||.|++|||++|++-+|+..++++..  +++++++++|+++ ..+.++.|...+..++  +|.......
T Consensus       141 ~sPg~~AGi~~GD~I~~iNg~~i~~~~d~~~~i~~~g~~g~~l~l~i~R~~~-~i~~~~~p~~~~~e~~YrIGLyiRDsa  219 (423)
T TIGR02860       141 ESPGEEAGIQIGDIILKINGEKIKNMEDIAKLINKAGKTGEKLKLTIKRGGK-IIETKIKPVKDKEEGRYRIGLYIRDSA  219 (423)
T ss_pred             ECCHHHCCEEEEEEEEEECCCHHCCHHHHHHHHHHHHHCCCEEEEEEEECCC-EEEEEEEEEEECCCCCEEEEEEEEECC
T ss_conf             4636547845610899988811035345688887543059548999985890-899866133337887538998994166


Q ss_pred             CCC
Q ss_conf             344
Q gi|254780773|r  204 VGI  206 (349)
Q Consensus       204 igi  206 (349)
                      .|+
T Consensus       220 AGi  222 (423)
T TIGR02860       220 AGI  222 (423)
T ss_pred             CCC
T ss_conf             433


No 26 
>TIGR02038 protease_degS periplasmic serine peptidase DegS; InterPro: IPR011783   Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases .   Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , .   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.    This family consists of the periplasmic serine protease DegS (HhoB). They belong to MEROPS peptidase family S1, subfamily S1C (protease Do, clan PA(S)). They are a shorter paralogs of protease Do (HtrA, DegP) and DegQ (HhoA). They are found in Escherichia coli and several of the gammaproteobacteria. DegS contains a trypsin domain and a single copy of PDZ domain (in contrast to DegP with two copies). A critical role of this DegS is to sense stress by detecting misfolded proteins in the periplasm. DegS then cleaves the periplasmic domain of RseA, a transmembrane protein and inhibitor of sigmaE, activating the sigmaE-driven expression of periplasmic proteases/chaperones , , .; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis.
Probab=98.95  E-value=8.9e-10  Score=87.17  Aligned_cols=64  Identities=36%  Similarity=0.488  Sum_probs=57.8

Q ss_pred             CCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCC-CCCCCCEEEEEECCCCEEEECCC
Q ss_conf             000245675565300145662888878304540011111014-67886316999658731310112
Q gi|254780773|r  121 VVSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRE-NPLHEISLVLYREHVGVLHLKVM  185 (349)
Q Consensus       121 ~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~-~~g~~v~i~v~R~~~~~~~~~v~  185 (349)
                      +|.+|.|++||++||+++.|.|+++||+++.+.+++.+.+.+ +||+.|.+|+.|+|++ +++.|+
T Consensus       288 vv~~vdPnGPAA~Ag~l~~Dvilk~dg~~~~g~~~~md~vA~~~PG~~v~~tvlR~Gk~-l~LpV~  352 (358)
T TIGR02038       288 VVTGVDPNGPAARAGILVRDVILKVDGKEVIGAEELMDRVAETRPGSKVLVTVLRKGKQ-LELPVT  352 (358)
T ss_pred             EEECCCCCCHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHCCCCCCEEEEEEECCCCE-EEEEEE
T ss_conf             88534898767650677155789867953675655455543179997789999706967-870078


No 27 
>TIGR02037 degP_htrA_DO protease Do; InterPro: IPR011782   Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases .   Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , .   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.    This family consists serine peptidases belonging to MEROPS peptidase family S1, subfamily S1C (protease Do, clan PA(S)). They are variously designated DegP, DegQ, heat shock protein HtrA, MucD and protease DO. The ortholog in Pseudomonas aeruginosa is designated MucD and is found in an operon that controls mucoid phenotype. This family also includes the DegQ (HhoA) paralog in Escherichia coli which can rescue a DegP mutant, but not the smaller DegS paralog, which cannot. Members of this family are located in the periplasm and have separable functions as both protease and chaperone. Members have a trypsin domain and two copies of a PDZ domain. This protein protects bacteria from thermal and other stresses and may be important for the survival of bacterial pathogens . The chaperone function is dominant at low temperatures, whereas the proteolytic activity is turned on at elevated temperatures .; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis.
Probab=98.71  E-value=1.7e-08  Score=78.35  Aligned_cols=60  Identities=30%  Similarity=0.466  Sum_probs=52.9

Q ss_pred             CCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCC--CCCCC-CCEEEEEECCCCEE
Q ss_conf             00024567556530014566288887830454001111101--46788-63169996587313
Q gi|254780773|r  121 VVSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVR--ENPLH-EISLVLYREHVGVL  180 (349)
Q Consensus       121 ~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~--~~~g~-~v~i~v~R~~~~~~  180 (349)
                      +|..|.++|||+++|||+||+|++||+++|+|..|+.+++.  ..++. ++.+.|+|++...+
T Consensus       419 ~V~~v~~~s~Aa~~Gl~~GDvI~~vN~~~V~s~~e~~~~l~~~~k~~~k~~~L~i~Rg~~~~~  481 (484)
T TIGR02037       419 VVTKVVSGSPAARAGLQPGDVILSVNQQPVSSVAELNKVLARAKKGGRKKVALLIERGGATIF  481 (484)
T ss_pred             EEEEECCCCHHHHCCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEEEEECCEEEE
T ss_conf             999733888899717876618995088014678999999997328870479999998780689


No 28 
>cd00136 PDZ PDZ domain, also called DHR (Dlg homologous region) or GLGF (after a conserved sequence motif). Many PDZ domains bind C-terminal polypeptides, though binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. Heterodimerization through PDZ-PDZ domain interactions adds to the domain's versatility, and PDZ domain-mediated interactions may be modulated dynamically through target phosphorylation. Some PDZ domains play a role in scaffolding supramolecular complexes. PDZ domains are found in diverse signaling proteins in bacteria, archebacteria, and eurkayotes. This CD contains two distinct structural subgroups with either a N- or C-terminal beta-strand forming the peptide-binding groove base. The circular permutation placing the strand on the N-terminus appears to be found in Eumetazoa only, while the C-terminal variant is found in all three kingdoms of life, and seems to co-occur with protease domains. PDZ domains have been named after PSD95(pos
Probab=98.63  E-value=3.2e-08  Score=76.42  Aligned_cols=54  Identities=33%  Similarity=0.584  Sum_probs=49.2

Q ss_pred             CCCCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCC--HHHHHHCCCCCCCCCEEEE
Q ss_conf             32000245675565300145662888878304540--0111110146788631699
Q gi|254780773|r  119 KPVVSNVSPASPAAIAGVKKGDCIISLDGITVSAF--EEVAPYVRENPLHEISLVL  172 (349)
Q Consensus       119 ~p~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~--~dl~~~i~~~~g~~v~i~v  172 (349)
                      ..+|.+|.++|||++|||++||+|++|||+++.++  +++.+.++..+++++++++
T Consensus        14 ~i~V~~v~~~spA~~aGL~~GD~I~~ing~~v~~~~~~~~~~~l~~~~g~~v~l~v   69 (70)
T cd00136          14 GVVVLSVEPGSPAERAGLQAGDVILAVNGTDVKNLTLEDVAELLKKEVGEKVTLTV   69 (70)
T ss_pred             CEEEEECCCCCHHHHCCCCCCCEEEEECCEECCCCCHHHHHHHHCCCCCCEEEEEE
T ss_conf             89999809989799879998999999999996899899999996289879799998


No 29 
>COG0793 Prc Periplasmic protease [Cell envelope biogenesis, outer membrane]
Probab=98.61  E-value=2.7e-07  Score=70.07  Aligned_cols=69  Identities=29%  Similarity=0.417  Sum_probs=57.2

Q ss_pred             CCCCCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCC--HHHHHHCCCCCCCCCEEEEEECC-CCEEEECCCC
Q ss_conf             332000245675565300145662888878304540--01111101467886316999658-7313101121
Q gi|254780773|r  118 MKPVVSNVSPASPAAIAGVKKGDCIISLDGITVSAF--EEVAPYVRENPLHEISLVLYREH-VGVLHLKVMP  186 (349)
Q Consensus       118 ~~p~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~--~dl~~~i~~~~g~~v~i~v~R~~-~~~~~~~v~p  186 (349)
                      -...|.++.+++||++||+++||+|++|||+++..-  ++..+.++..+|..+++++.|.+ .+..+++++.
T Consensus       112 ~~~~V~s~~~~~PA~kagi~~GD~I~~IdG~~~~~~~~~~av~~irG~~Gt~V~L~i~r~~~~k~~~v~l~R  183 (406)
T COG0793         112 GGVKVVSPIDGSPAAKAGIKPGDVIIKIDGKSVGGVSLDEAVKLIRGKPGTKVTLTILRAGGGKPFTVTLTR  183 (406)
T ss_pred             CCCEEECCCCCCCHHHHCCCCCCEEEEECCEECCCCCHHHHHHHHCCCCCCEEEEEEEECCCCCEEEEEEEE
T ss_conf             982695068899267608998888999899976677777899972689997568999966899536899998


No 30 
>PRK10139 serine endoprotease; Provisional
Probab=98.57  E-value=7.6e-08  Score=73.83  Aligned_cols=59  Identities=29%  Similarity=0.421  Sum_probs=52.8

Q ss_pred             CCCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCCCCCCCCEEEEEECCCCE
Q ss_conf             200024567556530014566288887830454001111101467886316999658731
Q gi|254780773|r  120 PVVSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRENPLHEISLVLYREHVGV  179 (349)
Q Consensus       120 p~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~~~g~~v~i~v~R~~~~~  179 (349)
                      -+|.+|.++|||+++||++||+|++||+++|+|.+|+.+++++.+ +.+.+.+.|++...
T Consensus       392 VvV~~V~~gS~Aa~aGLr~GDVI~~VN~~~V~sv~d~~~~l~~~~-~~v~L~V~Rgg~~~  450 (455)
T PRK10139        392 IKIDEVVKGSPAAQAGLQKDDVIIGVNRDRVNSIAEMRKVLAAKP-AIIALQIVRGNESI  450 (455)
T ss_pred             EEEEEECCCCHHHHCCCCCCCEEEEECCEECCCHHHHHHHHHCCC-CEEEEEEEECCEEE
T ss_conf             799984789989986999999999779987399999999985589-72899999899689


No 31 
>PRK10942 serine endoprotease; Provisional
Probab=98.56  E-value=8.8e-08  Score=73.38  Aligned_cols=59  Identities=34%  Similarity=0.532  Sum_probs=52.6

Q ss_pred             CCCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCCCCCCCCEEEEEECCCCE
Q ss_conf             200024567556530014566288887830454001111101467886316999658731
Q gi|254780773|r  120 PVVSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRENPLHEISLVLYREHVGV  179 (349)
Q Consensus       120 p~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~~~g~~v~i~v~R~~~~~  179 (349)
                      -+|.+|.++|||+++||++||+|++||+++|+|.+|+.+++++.+ +.+.+.+.|++...
T Consensus       411 VvV~~V~~~S~Aa~aGLr~GDVI~~VN~~~V~s~~dl~~~l~~~~-~~v~L~V~Rgg~~~  469 (474)
T PRK10942        411 VVVDNVKPGTPAAQIGLKKGDVIIGANQQPVKNIAELRKILDSKP-SVLALNIQRGDSSI  469 (474)
T ss_pred             EEEEEECCCCHHHHCCCCCCCEEEEECCEECCCHHHHHHHHHHCC-CEEEEEEEECCEEE
T ss_conf             699994799979985999998899779988499999999996089-83899999899579


No 32 
>COG3480 SdrC Predicted secreted protein containing a PDZ domain [Signal transduction mechanisms]
Probab=98.56  E-value=2.3e-07  Score=70.52  Aligned_cols=153  Identities=19%  Similarity=0.244  Sum_probs=87.1

Q ss_pred             CCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCC-CCCCCCEEEEEECCCCEEEECCCCCCCCCCCCCEEEE
Q ss_conf             000245675565300145662888878304540011111014-6788631699965873131011211005654310000
Q gi|254780773|r  121 VVSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRE-NPLHEISLVLYREHVGVLHLKVMPRLQDTVDRFGIKR  199 (349)
Q Consensus       121 ~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~-~~g~~v~i~v~R~~~~~~~~~v~p~~~~~~~~~g~~~  199 (349)
                      ++.+|.++|||..- |+.||.|+++||+++.+.+|+.+++++ .+|++++++++|.+......+.+-...+..++-|+..
T Consensus       133 yv~~v~~~~~~~gk-l~~gD~i~avdg~~f~s~~e~i~~v~~~k~Gd~VtI~~~r~~~~~~~~~~tl~~~~~~g~~giGI  211 (342)
T COG3480         133 YVLSVIDNSPFKGK-LEAGDTIIAVDGEPFTSSDELIDYVSSKKPGDEVTIDYERHNETPEIVTITLIKNDDNGKAGIGI  211 (342)
T ss_pred             EEEECCCCCCHHCE-ECCCCEEEEECCEECCCHHHHHHHHHCCCCCCEEEEEEEECCCCCCEEEEEEEEECCCCCCEEEE
T ss_conf             99971478631022-32687688558944578899999985468897699999951698726899999604688641215


Q ss_pred             EEEECC-----CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHEECCCCC--CCCCCCCCCCCCCCH-HHHHHHHHHHC
Q ss_conf             122034-----4443212333456688876898886554223100000002--554200224667301-22333456530
Q gi|254780773|r  200 QVPSVG-----ISFSYDETKLHSRTVLQSFSRGLDEISSITRGFLGVLSSA--FGKDTRLNQISGPVG-IARIAKNFFDH  271 (349)
Q Consensus       200 ~~~~ig-----i~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~l~~l--~~g~~~~~~lsGPVg-Ia~~~~~~a~~  271 (349)
                      ....-.     .....+.......+..-.++.++.  .+++..-+.. +..  -||....+.--|||| |.|-...+++.
T Consensus       212 sl~d~~~v~~~~~V~~~~~~IGGPSAGLMFSL~Iy--~qlt~~DL~~-g~~IAGTGTI~~DG~VG~IGGI~qKvvAA~~A  288 (342)
T COG3480         212 SLVDAPEVWAPPDVDFNTENIGGPSAGLMFSLAIY--DQLTKGDLTG-GRFIAGTGTIEVDGKVGPIGGIDQKVVAAAKA  288 (342)
T ss_pred             EEECCCCCCCCCCEEEECCCCCCCCHHHEEEHHHH--HHCCCCCCCC-CEEEECCEEECCCCCCCCCCCHHHHHHHHHHC
T ss_conf             86347654568726751244799754333529888--6405311358-66984111334688335745476776778765


Q ss_pred             CHHHHH
Q ss_conf             503478
Q gi|254780773|r  272 GFNAYI  277 (349)
Q Consensus       272 G~~~~l  277 (349)
                      |-..||
T Consensus       289 GA~vFf  294 (342)
T COG3480         289 GADVFF  294 (342)
T ss_pred             CCCEEE
T ss_conf             985998


No 33 
>TIGR03279 cyano_FeS_chp putative FeS-containing Cyanobacterial-specific oxidoreductase. Members of this protein family are predicted FeS-containing oxidoreductases of unknown function, apparently restricted to and universal across the Cyanobacteria. The high trusted cutoff score for this model, 700 bits, excludes homologs from other lineages. This exclusion seems justified because a significant number of sequence positions are simultaneously unique to and invariant across the Cyanobacteria, suggesting a specialized, conserved function, perhaps related to photosynthesis. A distantly related protein family, TIGR03278, in universal in and restricted to archaeal methanogens, and may be linked to methanogenesis.
Probab=98.43  E-value=3.2e-07  Score=69.53  Aligned_cols=62  Identities=19%  Similarity=0.313  Sum_probs=44.3

Q ss_pred             CCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCCCCCCCCEEEEEECCCCEEEECCC
Q ss_conf             00024567556530014566288887830454001111101467886316999658731310112
Q gi|254780773|r  121 VVSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRENPLHEISLVLYREHVGVLHLKVM  185 (349)
Q Consensus       121 ~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~~~g~~v~i~v~R~~~~~~~~~v~  185 (349)
                      +|.+|.|+|+|+++|+++||++++|||+++.+.-|.+-++.   .+.+++.+.+.+.+..++.+.
T Consensus         1 ~I~~V~pgSiA~e~Gie~GD~llsING~~i~DiiDy~f~~~---de~~~L~v~~~~Ge~~~ieie   62 (433)
T TIGR03279         1 LISAVLPGSIAEELGFEPGDALVSINGVAPRDLIDYQFLCA---DEELELEVLDANGESHQIEIE   62 (433)
T ss_pred             CEEEECCCCHHHHHCCCCCCEEEEECCCCCCCCEEEEECCC---CCEEEEEEECCCCCEEEEEEE
T ss_conf             94157799978983899998899889945555143411215---855999999589979999984


No 34 
>COG1994 SpoIVFB Zn-dependent proteases [General function prediction only]
Probab=98.42  E-value=1.2e-06  Score=65.57  Aligned_cols=44  Identities=39%  Similarity=0.686  Sum_probs=37.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCC
Q ss_conf             03478999999999999963064722436999999988827869
Q gi|254780773|r  273 FNAYIAFLAMFSWAIGFMNLLPIPILDGGHLITFLLEMIRGKSL  316 (349)
Q Consensus       273 ~~~~l~~~a~isi~Lg~~NlLPip~LDGG~i~~~~~E~i~gr~i  316 (349)
                      +..++...+.+|..|++|||+|+|||||||++....++-....+
T Consensus       136 ~~~~~~~la~~Nl~L~lFNLiPi~PLDGg~vlr~~~~~~~~~~~  179 (230)
T COG1994         136 LFAFLAALALVNLVLALFNLLPIPPLDGGRVLRALLPRRYGAAI  179 (230)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999973778876589999986389999999


No 35 
>PRK11186 carboxy-terminal protease; Provisional
Probab=98.37  E-value=2.4e-06  Score=63.52  Aligned_cols=66  Identities=18%  Similarity=0.351  Sum_probs=53.6

Q ss_pred             CCCCCCCCCCHHHHHH-CCCCCEEEEE--CCCCCCC-----CHHHHHHCCCCCCCCCEEEEEECCCC--EEEECCC
Q ss_conf             2000245675565300-1456628888--7830454-----00111110146788631699965873--1310112
Q gi|254780773|r  120 PVVSNVSPASPAAIAG-VKKGDCIISL--DGITVSA-----FEEVAPYVRENPLHEISLVLYREHVG--VLHLKVM  185 (349)
Q Consensus       120 p~I~~V~~~spA~~AG-L~~GD~Il~I--nG~~V~s-----~~dl~~~i~~~~g~~v~i~v~R~~~~--~~~~~v~  185 (349)
                      .+|.++.||+||+++| |++||+|++|  +|+++.+     .+|+++.|+..+|.+|++++.|.+.+  ...++++
T Consensus       259 ~~Iv~~i~GgPA~k~g~L~~gD~Ii~V~q~~~~~~dviG~~lddvV~lIRG~kGT~V~L~I~r~~~~~~~~~v~i~  334 (673)
T PRK11186        259 TVIKSLVAGGPAAKSKKLSVGDKIVGVGQDGKEIVDVIGWRLDDVVALIKGPKGSKVRLEILPAGKGTKTRIVTLT  334 (673)
T ss_pred             EEEEEECCCCHHHHHCCCCCCCEEEEECCCCCCCCCCCCCCHHHHHHHHCCCCCCEEEEEEEECCCCCCEEEEEEE
T ss_conf             9999706899588738999899999825789874202376599999985389988799999978888861699999


No 36 
>smart00228 PDZ Domain present in PSD-95, Dlg, and ZO-1/2. Also called DHR (Dlg homologous region) or GLGF (relatively well conserved tetrapeptide in these domains). Some PDZs have been shown to bind C-terminal polypeptides; others appear to bind internal (non-C-terminal) polypeptides. Different PDZs possess different binding specificities.
Probab=98.37  E-value=4.2e-07  Score=68.71  Aligned_cols=57  Identities=35%  Similarity=0.540  Sum_probs=47.8

Q ss_pred             CCCCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCC--HHHHHHCCCCCCCCCEEEEEECC
Q ss_conf             32000245675565300145662888878304540--01111101467886316999658
Q gi|254780773|r  119 KPVVSNVSPASPAAIAGVKKGDCIISLDGITVSAF--EEVAPYVRENPLHEISLVLYREH  176 (349)
Q Consensus       119 ~p~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~--~dl~~~i~~~~g~~v~i~v~R~~  176 (349)
                      ..+|.+|.++|||+++||++||+|++|||+++.+.  ++....++.. +.++++++.|++
T Consensus        27 gv~I~~v~~~s~A~~~Gl~~GD~I~~vng~~v~~~~~~~~~~~~~~~-~~~v~l~v~r~~   85 (85)
T smart00228       27 GVVVSSVVPGSPAAKAGLKVGDVILEVNGTSVEGLTHLEAVDLLKKA-GGKVTLTVLRGG   85 (85)
T ss_pred             CEEEEEECCCCHHHHCCCCCCCEEEEECCEECCCCCHHHHHHHHHCC-CCEEEEEEEECC
T ss_conf             89999987999478768989999999999998999899999998779-997999999496


No 37 
>PRK10779 zinc metallopeptidase; Provisional
Probab=98.24  E-value=1.6e-06  Score=64.62  Aligned_cols=59  Identities=22%  Similarity=0.303  Sum_probs=47.9

Q ss_pred             CCCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCCC-CCCCCEEEEEECCCC
Q ss_conf             20002456755653001456628888783045400111110146-788631699965873
Q gi|254780773|r  120 PVVSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVREN-PLHEISLVLYREHVG  178 (349)
Q Consensus       120 p~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~~-~g~~v~i~v~R~~~~  178 (349)
                      |++++|.++|||++||+++||+|+++||+++.+|+|....+..+ ..++.++.+.+.+.+
T Consensus       128 ~~i~~v~~~s~a~~agl~~GD~i~~idg~~~~~~~~~~~~l~~~~g~~~~~i~v~~~~~~  187 (449)
T PRK10779        128 PVVGEIAPNSIAAQAQIAPGTELKAVDGIETPDWDAVRLQLVSKIGDEQTTVTVAPFGSD  187 (449)
T ss_pred             CEECCCCCCCHHHHCCCCCCCEEEEECCEECCCHHHHHHHHHHHCCCCCEEEEEECCCCC
T ss_conf             300431468888873888887899989998576898899998850577606999407864


No 38 
>COG0265 DegQ Trypsin-like serine proteases, typically periplasmic, contain C-terminal PDZ domain [Posttranslational modification, protein turnover, chaperones]
Probab=98.22  E-value=2e-06  Score=64.06  Aligned_cols=66  Identities=36%  Similarity=0.497  Sum_probs=57.0

Q ss_pred             CCCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCC-CCCCCCEEEEEECCCCEEEECCCC
Q ss_conf             2000245675565300145662888878304540011111014-678863169996587313101121
Q gi|254780773|r  120 PVVSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRE-NPLHEISLVLYREHVGVLHLKVMP  186 (349)
Q Consensus       120 p~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~-~~g~~v~i~v~R~~~~~~~~~v~p  186 (349)
                      ..+.+|.++|||+++|+++||.|+++||+++.+..|+.+.+.. ++++++.+++.|+++ ..+.+++.
T Consensus       272 ~~V~~v~~~spa~~agi~~Gdii~~~ng~~v~~~~~l~~~v~~~~~g~~v~~~~~r~g~-~~~~~v~l  338 (347)
T COG0265         272 AVVLGVLPGSPAAKAGIKAGDIITAVNGKPVASLSDLVAAVASNRPGDEVALKLLRGGK-ERELAVTL  338 (347)
T ss_pred             CEEEEECCCCHHHHCCCCCCCEEEEECCEECCCHHHHHHHHHCCCCCCEEEEEEEECCE-EEEEEEEC
T ss_conf             68865179985787378778779978998855788888887326999768899997883-57776861


No 39 
>KOG3129 consensus
Probab=98.22  E-value=2.5e-06  Score=63.32  Aligned_cols=78  Identities=28%  Similarity=0.388  Sum_probs=63.8

Q ss_pred             CCCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCCHHH---HHHCCCCCCCCCEEEEEECCCCEEEECCCCCCCCCCCCCE
Q ss_conf             2000245675565300145662888878304540011---1110146788631699965873131011211005654310
Q gi|254780773|r  120 PVVSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEV---APYVRENPLHEISLVLYREHVGVLHLKVMPRLQDTVDRFG  196 (349)
Q Consensus       120 p~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~~dl---~~~i~~~~g~~v~i~v~R~~~~~~~~~v~p~~~~~~~~~g  196 (349)
                      .+|++|.|+|||++|||+.||.|+++.+..--++..+   ...++.+.++.+.+++.|++. ...+.++|+.....+..|
T Consensus       141 a~V~sV~~~SPA~~aGl~~gD~il~fGnV~sgn~~~lq~i~~~v~~~e~~~v~v~v~R~g~-~v~L~ltP~~W~GrGLLG  219 (231)
T KOG3129         141 AVVDSVVPGSPADEAGLCVGDEILKFGNVHSGNFLPLQNIAAVVQSNEDQIVSVTVIREGQ-KVVLSLTPKKWQGRGLLG  219 (231)
T ss_pred             EEEEECCCCCHHHHHCCCCCCEEEEECCCCCCCCHHHHHHHHHHHHCCCCCEEEEEECCCC-EEEEEECCCCCCCCCCEE
T ss_conf             8875227898345407543765788533246552258898999874437623579961797-788996764355886010


Q ss_pred             EE
Q ss_conf             00
Q gi|254780773|r  197 IK  198 (349)
Q Consensus       197 ~~  198 (349)
                      ..
T Consensus       220 C~  221 (231)
T KOG3129         220 CN  221 (231)
T ss_pred             EE
T ss_conf             01


No 40 
>pfam00595 PDZ PDZ domain (Also known as DHR or GLGF). PDZ domains are found in diverse signaling proteins.
Probab=98.16  E-value=1.5e-06  Score=64.82  Aligned_cols=52  Identities=27%  Similarity=0.458  Sum_probs=43.8

Q ss_pred             CCCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCC--HHHHHHCCCCCCCCCEEEE
Q ss_conf             2000245675565300145662888878304540--0111110146788631699
Q gi|254780773|r  120 PVVSNVSPASPAAIAGVKKGDCIISLDGITVSAF--EEVAPYVRENPLHEISLVL  172 (349)
Q Consensus       120 p~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~--~dl~~~i~~~~g~~v~i~v  172 (349)
                      -+|.+|.++|||+.+||++||+|++|||+++.++  ++..+.++.. ++++++++
T Consensus        26 ~~V~~V~~~~~A~~~gL~~GD~Il~VNg~~v~~~~~~~~~~~l~~~-~~~v~L~V   79 (80)
T pfam00595        26 IFVSEVLPGGAAEAGGLQVGDRILSINGQDLENMSHDEAVLALKGS-GGEVTLTI   79 (80)
T ss_pred             EEEEEECCCCCHHHCCCCCCCEEEEECCEECCCCCHHHHHHHHHCC-CCEEEEEE
T ss_conf             8999977898055487999999999999998999899999999749-99299998


No 41 
>cd00992 PDZ_signaling PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) polypeptides and even to lipids has been demonstrated. In this subfamily of PDZ domains an N-terminal beta-strand forms the peptide-binding groove base, a circular permutation with respect to PDZ domains found in proteases.
Probab=98.12  E-value=2.4e-06  Score=63.55  Aligned_cols=54  Identities=30%  Similarity=0.528  Sum_probs=46.1

Q ss_pred             CCCCCCCCCCCCHHHHHHCCCCCEEEEECCCCCC--CCHHHHHHCCCCCCCCCEEEE
Q ss_conf             3320002456755653001456628888783045--400111110146788631699
Q gi|254780773|r  118 MKPVVSNVSPASPAAIAGVKKGDCIISLDGITVS--AFEEVAPYVRENPLHEISLVL  172 (349)
Q Consensus       118 ~~p~I~~V~~~spA~~AGL~~GD~Il~InG~~V~--s~~dl~~~i~~~~g~~v~i~v  172 (349)
                      ...+|.+|.|+|||+.+||++||+|++|||+++.  +.+++.+.+++.+. .+++++
T Consensus        26 ~~~~I~~v~~~s~A~~~~L~~GD~Il~INg~~v~~~~~~~v~~~l~~~~~-~v~L~V   81 (82)
T cd00992          26 GGIFVSRVEPGGPAERGGLRVGDRILEVNGVSVEGLTHEEAVELLKNSGD-EVTLTV   81 (82)
T ss_pred             CCEEEEEECCCCCHHHCCCCCCCEEEEECCEECCCCCHHHHHHHHHCCCC-EEEEEE
T ss_conf             99999998689903434899999989899999999989999999984999-599998


No 42 
>TIGR00054 TIGR00054 membrane-associated zinc metalloprotease, putative; InterPro: IPR004387   Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases .   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.    This family contains putative zinc metallopeptidases belonging to MEROPS peptidase family M50 (S2P protease family, clan MM). The N-terminal region of contains a perfectly conserved motif HEXGH, where the Glu is the active site and the His residues coordinate the metal cation. The family of bacterial and plant proteins also includes a region that hits the PDZ domain (IPR001478 from INTERPRO), found in a number of proteins targeted to the membrane by binding to a peptide ligand . The family includes EcfE, which is a homolog of human site-2 protease (S2P), a membrane-bound zinc metalloprotease involved in regulated intramembrane proteolysis. In Escherichia coli EcfE activates the sigma(E) pathway of stress response through a site-2 cleavage of anti-sigma(E), RseA.; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis, 0016021 integral to membrane.
Probab=97.82  E-value=1.6e-05  Score=57.75  Aligned_cols=83  Identities=24%  Similarity=0.406  Sum_probs=57.0

Q ss_pred             CCCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCCCCCCCCEEEEEE---------CC-CCEEEECCCCCCC
Q ss_conf             2000245675565300145662888878304540011111014678863169996---------58-7313101121100
Q gi|254780773|r  120 PVVSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRENPLHEISLVLYR---------EH-VGVLHLKVMPRLQ  189 (349)
Q Consensus       120 p~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~~~g~~v~i~v~R---------~~-~~~~~~~v~p~~~  189 (349)
                      |+|+++.++|.|.+|++++||+|+++||+++.+|+|+...+.+....++.+++.+         +. -+..+.++.++..
T Consensus       137 ~vi~~~~~~S~a~~a~~~~Gd~il~~~~~~~~~f~~~~~~~~~~~~g~~~~~I~~~PF~S~~e~~~~L~L~~~~~~~~~~  216 (463)
T TIGR00054       137 PVIEELDKNSIALEAGIEPGDEILSVNGKKIPGFKDVRKQIADIVAGEPMVEILAAPFNSDIEREVKLDLRNWTFEVEKE  216 (463)
T ss_pred             CCCCCCCHHHHHHHHCCCCCCEEEEECCCCCCCCHHHHHHHHHHHCCCCCCEEEECCCCCCCHHHCCCCCEEEEEECCCC
T ss_conf             64565544579987116898478740776678808899999997517854157765777541120000331238621125


Q ss_pred             CCCCCCEEEEEEE
Q ss_conf             5654310000122
Q gi|254780773|r  190 DTVDRFGIKRQVP  202 (349)
Q Consensus       190 ~~~~~~g~~~~~~  202 (349)
                      +.....|+....|
T Consensus       217 ~~~~~lgl~~~~P  229 (463)
T TIGR00054       217 DAVEQLGLKPRGP  229 (463)
T ss_pred             CHHHHCCCCCCCC
T ss_conf             5255414424787


No 43 
>COG3975 Predicted protease with the C-terminal PDZ domain [General function prediction only]
Probab=97.62  E-value=8.2e-05  Score=52.91  Aligned_cols=59  Identities=27%  Similarity=0.397  Sum_probs=44.8

Q ss_pred             CCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCCCCCCCCEEEEEECCCCEEEECCCCC
Q ss_conf             0002456755653001456628888783045400111110146788631699965873131011211
Q gi|254780773|r  121 VVSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRENPLHEISLVLYREHVGVLHLKVMPR  187 (349)
Q Consensus       121 ~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~~~g~~v~i~v~R~~~~~~~~~v~p~  187 (349)
                      .|..|.++|||++|||.+||+|++|||.+ .      +.-+...++.+++++.|++. ..+..+++.
T Consensus       465 ~i~~V~~~gPA~~AGl~~Gd~ivai~G~s-~------~l~~~~~~d~i~v~~~~~~~-L~e~~v~~~  523 (558)
T COG3975         465 KITFVFPGGPAYKAGLSPGDKIVAINGIS-D------QLDRYKVNDKIQVHVFREGR-LREFLVKLG  523 (558)
T ss_pred             EEEECCCCCHHHHCCCCCCCEEEEECCCC-C------CCCCCCCCCCEEEEECCCCC-EEEEECCCC
T ss_conf             99844789816751588756799976735-5------52214426624899825782-388521368


No 44 
>KOG1320 consensus
Probab=97.60  E-value=7.7e-05  Score=53.09  Aligned_cols=95  Identities=22%  Similarity=0.321  Sum_probs=65.3

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCC----C-CCCCCCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCCC-CCCC
Q ss_conf             1123332112211101110012----3-33320002456755653001456628888783045400111110146-7886
Q gi|254780773|r   94 LAGPLANCVMAILFFTFFFYNT----G-VMKPVVSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVREN-PLHE  167 (349)
Q Consensus        94 ~AGp~~N~ilA~iif~~~~~~~----g-~~~p~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~~-~g~~  167 (349)
                      .-|.-|+.+++-+.|....-..    + ..--++.+|.|++||..+|+++||+|++|||++|.+..|+.+.++.. +.+.
T Consensus       369 ~~g~~s~~i~~g~vf~~~~~~~~~~~~~~q~v~is~Vlp~~~~~~~~~~~g~~V~~vng~~V~n~~~l~~~i~~~~~~~~  448 (473)
T KOG1320         369 YIGLPSYYIFAGLVFVPLTKSYIFPSGVVQLVLVSQVLPGSINGGYGLKPGDQVVKVNGKPVKNLKHLYELIEECSTEDK  448 (473)
T ss_pred             CCCCEEEEEECCEEEEECCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCEEEEECCEEEECHHHHHHHHHHCCCCCE
T ss_conf             67840499965378852577866655633589998864699761002367878998889885256879999875276766


Q ss_pred             CEEEEEECCCCEEEECCCCCCC
Q ss_conf             3169996587313101121100
Q gi|254780773|r  168 ISLVLYREHVGVLHLKVMPRLQ  189 (349)
Q Consensus       168 v~i~v~R~~~~~~~~~v~p~~~  189 (349)
                      +.+. .|.+.+..++.+.|+..
T Consensus       449 v~vl-~~~~~e~~tl~Il~~~~  469 (473)
T KOG1320         449 VAVL-DRRSAEDATLEILPEHK  469 (473)
T ss_pred             EEEE-EECCCCCEEEEEECCCC
T ss_conf             9999-71476302589502335


No 45 
>KOG1421 consensus
Probab=97.58  E-value=9.4e-05  Score=52.51  Aligned_cols=64  Identities=25%  Similarity=0.409  Sum_probs=57.2

Q ss_pred             CCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCCCCCCCCEEEEEECCCCEEEECCCC
Q ss_conf             000245675565300145662888878304540011111014678863169996587313101121
Q gi|254780773|r  121 VVSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRENPLHEISLVLYREHVGVLHLKVMP  186 (349)
Q Consensus       121 ~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~~~g~~v~i~v~R~~~~~~~~~v~p  186 (349)
                      ++..|.++|||++. |++||..+++|++-+.++.++-+.+.+.-|+.++++++|+++ ..+++++-
T Consensus       306 vV~~vL~~gpa~k~-Le~GDillavN~t~l~df~~l~~iLDegvgk~l~LtI~Rggq-elel~vtv  369 (955)
T KOG1421         306 VVETVLPEGPAEKK-LEPGDILLAVNSTCLNDFEALEQILDEGVGKNLELTIQRGGQ-ELELTVTV  369 (955)
T ss_pred             EEEEECCCCCHHHC-CCCCCEEEEECCEEHHHHHHHHHHHHHCCCCEEEEEEEECCE-EEEEEEEE
T ss_conf             99873369803302-577867999833316889999987752358508999984888-99999974


No 46 
>KOG3209 consensus
Probab=97.49  E-value=0.00011  Score=52.07  Aligned_cols=62  Identities=16%  Similarity=0.347  Sum_probs=50.1

Q ss_pred             CCCCCCCCCCCCCCCHHHHHH-CCCCCEEEEECCCCCCC--CHHHHHHCCCCCCCCCEEEEEECCC
Q ss_conf             233332000245675565300-14566288887830454--0011111014678863169996587
Q gi|254780773|r  115 TGVMKPVVSNVSPASPAAIAG-VKKGDCIISLDGITVSA--FEEVAPYVRENPLHEISLVLYREHV  177 (349)
Q Consensus       115 ~g~~~p~I~~V~~~spA~~AG-L~~GD~Il~InG~~V~s--~~dl~~~i~~~~g~~v~i~v~R~~~  177 (349)
                      ...+.+.|+.+.++|||+.-| |+.||+|++|||++|.+  ..|+++.|++ +|-+|++++.-.++
T Consensus       775 ~~kp~sgiGrIieGSPAdRCgkLkVGDrilAVNG~sI~~lsHadiv~LIKd-aGlsVtLtIip~ee  839 (984)
T KOG3209         775 QNKPESGIGRIIEGSPADRCGKLKVGDRILAVNGQSILNLSHADIVSLIKD-AGLSVTLTIIPPEE  839 (984)
T ss_pred             CCCCCCCCCCCCCCCHHHHHCCCCCCCEEEEECCEEEECCCCHHHHHHHHH-CCCEEEEEECCHHC
T ss_conf             668987743125698167505543265688754703303672568888873-68558999748010


No 47 
>pfam04495 GRASP55_65 GRASP55/65 family. GRASP55 (Golgi reassembly stacking protein of 55 kDa) and GRASP65 (a 65 kDa) protein are highly homologous. GRASP55 is a component of the Golgi stacking machinery. GRASP65, an N-ethylmaleimide- sensitive membrane protein required for the stacking of Golgi cisternae in a cell-free system.
Probab=97.00  E-value=0.0014  Score=44.49  Aligned_cols=68  Identities=28%  Similarity=0.391  Sum_probs=56.6

Q ss_pred             CCCCCCCCCHHHHHHCCC-CCEEEEECCCCCCCCHHHHHHCCCCCCCCCEEEEEE-CCCCEEEECCCCCC
Q ss_conf             000245675565300145-662888878304540011111014678863169996-58731310112110
Q gi|254780773|r  121 VVSNVSPASPAAIAGVKK-GDCIISLDGITVSAFEEVAPYVRENPLHEISLVLYR-EHVGVLHLKVMPRL  188 (349)
Q Consensus       121 ~I~~V~~~spA~~AGL~~-GD~Il~InG~~V~s~~dl~~~i~~~~g~~v~i~v~R-~~~~~~~~~v~p~~  188 (349)
                      -|-+|.++|||+.|||++ .|-|+.-+..-...-+|+.+.++.+.++++.+-|+- +.+.+..++++|+.
T Consensus        46 hvl~v~~~SPA~~AgL~~~~DYIiG~~~~~l~~~~~l~~~v~~~~~~~l~lyVYN~~~d~~R~V~i~p~~  115 (280)
T pfam04495        46 HVLDVHPNSPAALAGLQPYSDYIIGTDSGLLRGEDDLFELVESHEGRPLKLYVYNSETDVVREVTITPNR  115 (280)
T ss_pred             EEEECCCCCHHHHCCCCCCCCEEEECCCCCCCCHHHHHHHHHHHCCCCEEEEEECCCCCCEEEEEEECCC
T ss_conf             9984489997997488877786873684231456789999997369976999965788836789985277


No 48 
>PRK09681 putative type II secretion protein GspC; Provisional
Probab=96.94  E-value=0.0011  Score=45.17  Aligned_cols=58  Identities=21%  Similarity=0.377  Sum_probs=45.1

Q ss_pred             CCCCCH---HHHHHCCCCCEEEEECCCCCCCCHHHHHHCCC-CCCCCCEEEEEECCCCEEEEC
Q ss_conf             456755---65300145662888878304540011111014-678863169996587313101
Q gi|254780773|r  125 VSPASP---AAIAGVKKGDCIISLDGITVSAFEEVAPYVRE-NPLHEISLVLYREHVGVLHLK  183 (349)
Q Consensus       125 V~~~sp---A~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~-~~g~~v~i~v~R~~~~~~~~~  183 (349)
                      +.||..   .+++|||+||.+++|||.+.++.....+.++. +.-++++++|+|||+. .++.
T Consensus       254 l~PGkd~~lF~~~Glq~gDlavsiNG~dLtDp~~a~~~~~~l~~ate~~ltVeRdGq~-~~I~  315 (319)
T PRK09681        254 VKPGADRSLFDASGFKEGDIAIALNQQDFTDPRAMIALMRQLPSMDSIQLTVLRKGAR-YDIS  315 (319)
T ss_pred             ECCCCCHHHHHHCCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHCCEEEEEEEECCEE-EEEE
T ss_conf             2799888999972999888889826966789899999999600071558999979968-9999


No 49 
>TIGR01713 typeII_sec_gspC general secretion pathway protein C; InterPro: IPR001639   The general (type II) secretion pathway (GSP) within Gram-negative bacteria is a signal sequence-dependent process responsible for protein export , , . The process has two stages: exoproteins are first translocated across the inner membrane by the general signal-dependent export pathway (GEP), and then across the outer membrane by a species-specific accessory mechanism.   A number of molecules are involved in the GSP; one of these is known as the 'C' protein, the most probable location of which is the inner membrane . This suggests that protein C is part of the GEP apparatus, aiding trans-location of exoproteins from the cytoplasm to the periplasm, prior to transport across the outer membrane. The size of the 'C' protein is around 270 to 300 amino acids. It apparently contains a single transmembrane domain located in the N-terminal section. The short N-terminal domain is predicted to be cytoplasmic and the large C-terminal domain periplasmic.   The gene encoding the 'C' protein has been sequenced in a variety of bacteria such as Aeromonas (exeC); Erwinia (outC); Escherichia coli (yheE or gspC); Klebsiella pneumoniae (pulC); or Vibrio cholerae (epsC).; GO: 0008565 protein transporter activity, 0015628 protein secretion by the type II secretion system, 0015627 type II protein secretion system complex.
Probab=96.87  E-value=0.0011  Score=45.10  Aligned_cols=54  Identities=20%  Similarity=0.304  Sum_probs=46.8

Q ss_pred             CCCCCHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCC-CCCCCCEEEEEECCCC
Q ss_conf             45675565300145662888878304540011111014-6788631699965873
Q gi|254780773|r  125 VSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRE-NPLHEISLVLYREHVG  178 (349)
Q Consensus       125 V~~~spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~-~~g~~v~i~v~R~~~~  178 (349)
                      .-+.+..++.|||.||.-+++||..+++-++..++++. ...++.++||+|||+.
T Consensus       220 gK~~~lF~~~GLq~gD~AvalNgLdLrd~e~a~~~l~~l~~~~~~~ltv~RdG~~  274 (281)
T TIGR01713       220 GKDPSLFYKSGLQDGDIAVALNGLDLRDPEQAKQALQLLRELTELTLTVERDGQR  274 (281)
T ss_pred             CCCHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHCCCCCEEEEEEECCCC
T ss_conf             8985453411685673246536888779899999999730486608999977942


No 50 
>pfam01434 Peptidase_M41 Peptidase family M41.
Probab=96.69  E-value=0.0017  Score=43.86  Aligned_cols=67  Identities=27%  Similarity=0.325  Sum_probs=43.7

Q ss_pred             HHHHHHHHHHHHHHHHC--CEEEEEEEECCCHHEEEEECCCEEEEEEEEEECCEEECCCCCCCHHHHCCCCCCCCHHHHH
Q ss_conf             99997337799999849--7500455306831127860598079999771121110012445506650368421013421
Q gi|254780773|r   17 IVVIHEFGHYMVARLCN--IRVLSFSVGFGPELIGITSRSGVRWKVSLIPLGGYVSFSEDEKDMRSFFCAAPWKKILTVL   94 (349)
Q Consensus        17 ~v~iHE~GH~~~Ar~~g--v~V~~FsiGfgp~l~~~~~k~~t~y~i~~~PlGgyV~~~~~e~~~~~f~~~~~~~R~~i~~   94 (349)
                      .+.+||.||.++|.++.  -+|.+=+|         ..|++         -+||+.+.++| |...+.+....+|+.|++
T Consensus        10 ~vA~HEaGHAlva~~l~~~~~v~kvtI---------~prg~---------alG~t~~~p~e-d~~~~tk~~l~~~I~v~L   70 (192)
T pfam01434        10 LVAYHEAGHALVGLLLPGADPVHKVTI---------IPRGQ---------ALGYTQFLPEE-DKLLYTKSQLLARIDVAL   70 (192)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCEEEEE---------EECCC---------CCEEEEECCCC-CCCCCCHHHHHHHHHHHH
T ss_conf             999999999999998469998217998---------62788---------76357865730-112158999999999986


Q ss_pred             HHHHHHHH
Q ss_conf             12333211
Q gi|254780773|r   95 AGPLANCV  102 (349)
Q Consensus        95 AGp~~N~i  102 (349)
                      ||-.+--+
T Consensus        71 gGraAEei   78 (192)
T pfam01434        71 GGRAAEEL   78 (192)
T ss_pred             HHHHHHHH
T ss_conf             38999999


No 51 
>KOG3532 consensus
Probab=96.56  E-value=0.0023  Score=42.91  Aligned_cols=47  Identities=17%  Similarity=0.297  Sum_probs=41.8

Q ss_pred             CCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCCCCCCC
Q ss_conf             00024567556530014566288887830454001111101467886
Q gi|254780773|r  121 VVSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRENPLHE  167 (349)
Q Consensus       121 ~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~~~g~~  167 (349)
                      .|-.|.+++||.+|.+++||+.++|||.||.+-++...+++...++.
T Consensus       401 ~v~tv~~ns~a~k~~~~~gdvlvai~~~pi~s~~q~~~~~~s~~~~~  447 (1051)
T KOG3532         401 KVCTVEDNSLADKAAFKPGDVLVAINNVPIRSERQATRFLQSTTGDL  447 (1051)
T ss_pred             EEEEECCCCHHHHHCCCCCCEEEEECCCCCHHHHHHHHHHHHCCCCE
T ss_conf             99970689754675268655699855852315999999998614406


No 52 
>TIGR00225 prc C-terminal processing peptidase; InterPro: IPR004447   Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases .   Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , .   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.  This group of serine peptidases belong to MEROPS peptidase family S41 (clan SM), subfamily S41A (C-terminal processing peptidase). It is a family of C-terminal peptidases with different substrates in different species, including processing of D1 protein of the photosystem II reaction centre in higher plants, and cleavage of a peptide of 11 residues from the precursor form of penicillin-binding protein in Escherichia coli.; GO: 0008236 serine-type peptidase activity, 0006508 proteolysis.
Probab=96.30  E-value=0.018  Score=36.83  Aligned_cols=58  Identities=28%  Similarity=0.445  Sum_probs=51.1

Q ss_pred             CCCCCCCCCCCHHHHHHCCCCCEEEEECCC-----CCCCC--HHHHHHCCCCCCCCCEEEEEECC
Q ss_conf             320002456755653001456628888783-----04540--01111101467886316999658
Q gi|254780773|r  119 KPVVSNVSPASPAAIAGVKKGDCIISLDGI-----TVSAF--EEVAPYVRENPLHEISLVLYREH  176 (349)
Q Consensus       119 ~p~I~~V~~~spA~~AGL~~GD~Il~InG~-----~V~s~--~dl~~~i~~~~g~~v~i~v~R~~  176 (349)
                      ...+....+++||+++|+++||.|+++||+     ++..|  ++....++..++..+.+++.|.+
T Consensus        67 ~~~~~~~~~g~p~~~~g~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~g~~~~~~~~~~g  131 (361)
T TIGR00225        67 ELVIVSPLEGSPAEKAGLKPGDKILKVNGKGGPLESVLGLSLDDAVALIRGKKGTKVSLEILRAG  131 (361)
T ss_pred             EEEEEECCCCCCHHHCCCCCCCEEEEECCCCCCCHHHHHCCHHHHHHHHCCCCCCEEEEEEECCC
T ss_conf             37886214677311204666640686167666410222012578899750777861689984277


No 53 
>COG3031 PulC Type II secretory pathway, component PulC [Intracellular trafficking and secretion]
Probab=96.25  E-value=0.0059  Score=40.13  Aligned_cols=54  Identities=13%  Similarity=0.255  Sum_probs=46.8

Q ss_pred             CCCCCHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCC-CCCCCCEEEEEECCCC
Q ss_conf             45675565300145662888878304540011111014-6788631699965873
Q gi|254780773|r  125 VSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRE-NPLHEISLVLYREHVG  178 (349)
Q Consensus       125 V~~~spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~-~~g~~v~i~v~R~~~~  178 (349)
                      ..+.|..++.|||+||.-+++|+...++.+|+...++. ..-++..+|+.|+|..
T Consensus       214 gkd~slF~~sglq~GDIavaiNnldltdp~~m~~llq~l~~m~s~qlTv~R~G~r  268 (275)
T COG3031         214 GKDGSLFYKSGLQRGDIAVAINNLDLTDPEDMFRLLQMLRNMPSLQLTVIRRGKR  268 (275)
T ss_pred             CCCCCHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHHCCCCEEEEEEECCCC
T ss_conf             9983244550688765689965866689899999999611386507999945853


No 54 
>COG1994 SpoIVFB Zn-dependent proteases [General function prediction only]
Probab=96.17  E-value=0.0028  Score=42.29  Aligned_cols=72  Identities=28%  Similarity=0.341  Sum_probs=54.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCEEEEEEEECCCHHEEEEECCCEEEEEEEEEECCEEECCCCCCCHHHHCCCCCCCCHHHH
Q ss_conf             99999997337799999849750045530683112786059807999977112111001244550665036842101342
Q gi|254780773|r   14 LIIIVVIHEFGHYMVARLCNIRVLSFSVGFGPELIGITSRSGVRWKVSLIPLGGYVSFSEDEKDMRSFFCAAPWKKILTV   93 (349)
Q Consensus        14 l~~~v~iHE~GH~~~Ar~~gv~V~~FsiGfgp~l~~~~~k~~t~y~i~~~PlGgyV~~~~~e~~~~~f~~~~~~~R~~i~   93 (349)
                      +..-++.||+||...+|..++++.  ++-+                   .++||+..+++...+.+.++..+ +++.++.
T Consensus        51 l~~rl~l~~~gh~~~~~~~~~~l~--~~~i-------------------~~~~g~~~~~~~~v~~~~~~~~~-~~g~lvs  108 (230)
T COG1994          51 LAHRLVLHPLGHSDEAGRLGLKLL--LALL-------------------FGFGGFGFLKPVPVNPRGEFLIR-LAGPLVS  108 (230)
T ss_pred             HHHHHHHHHHCCHHHHHHHHHHHH--HHHH-------------------HHHHHHHEECCCCCCHHHHHHHC-CCCHHHH
T ss_conf             999999986013999998787799--9999-------------------98658841044661658864111-3314999


Q ss_pred             HH-HHHHHHHHHHHH
Q ss_conf             11-233321122111
Q gi|254780773|r   94 LA-GPLANCVMAILF  107 (349)
Q Consensus        94 ~A-Gp~~N~ilA~ii  107 (349)
                      .| ||+.|+.+|++.
T Consensus       109 ~algpl~ni~la~~~  123 (230)
T COG1994         109 LALGPLTNIALAVLG  123 (230)
T ss_pred             HHHHHHHHHHHHHHH
T ss_conf             988899888999999


No 55 
>KOG3553 consensus
Probab=96.16  E-value=0.0028  Score=42.36  Aligned_cols=55  Identities=24%  Similarity=0.436  Sum_probs=39.2

Q ss_pred             CCCCCCCCCCHHHHHHCCCCCEEEEECCCCCC--CCHHHHHHCCCCCCCCCEEEEEECC
Q ss_conf             20002456755653001456628888783045--4001111101467886316999658
Q gi|254780773|r  120 PVVSNVSPASPAAIAGVKKGDCIISLDGITVS--AFEEVAPYVRENPLHEISLVLYREH  176 (349)
Q Consensus       120 p~I~~V~~~spA~~AGL~~GD~Il~InG~~V~--s~~dl~~~i~~~~g~~v~i~v~R~~  176 (349)
                      -+|..|.++|||+.|||+.+|+|+.+||-..+  +-+.-+..++++  +.+.+.|.|.+
T Consensus        61 iYvT~V~eGsPA~~AGLrihDKIlQvNG~DfTMvTHd~Avk~i~k~--~vl~mLVaR~~  117 (124)
T KOG3553          61 IYVTRVSEGSPAEIAGLRIHDKILQVNGWDFTMVTHDQAVKRITKE--EVLRMLVARQS  117 (124)
T ss_pred             EEEEEECCCCHHHHHCCEECCEEEEECCCEEEEEEHHHHHHHHHHH--HHHHHHHHHHC
T ss_conf             7999704698366400220356888647405888768888786375--79999988603


No 56 
>KOG3580 consensus
Probab=96.02  E-value=0.0035  Score=41.69  Aligned_cols=53  Identities=23%  Similarity=0.425  Sum_probs=31.3

Q ss_pred             CCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCC--HHHHHH-CCCCCCCCCEEEEE
Q ss_conf             000245675565300145662888878304540--011111-01467886316999
Q gi|254780773|r  121 VVSNVSPASPAAIAGVKKGDCIISLDGITVSAF--EEVAPY-VRENPLHEISLVLY  173 (349)
Q Consensus       121 ~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~--~dl~~~-i~~~~g~~v~i~v~  173 (349)
                      .|.+|.++|||++-|||.||.|+.||..+..+.  +|-+.+ +.--+|+++++...
T Consensus       432 FVaGvqegspA~~eGlqEGDQIL~VN~vdF~nl~REeAVlfLL~lPkGEevtilaQ  487 (1027)
T KOG3580         432 FVAGVQEGSPAEQEGLQEGDQILKVNTVDFRNLVREEAVLFLLELPKGEEVTILAQ  487 (1027)
T ss_pred             EEEECCCCCCHHHCCCCCCCEEEEECCCCCHHHHHHHHHHHHHCCCCCCEEEEHHH
T ss_conf             87411268830111300036267753633010427888999862899767761343


No 57 
>KOG3834 consensus
Probab=95.89  E-value=0.01  Score=38.42  Aligned_cols=69  Identities=22%  Similarity=0.351  Sum_probs=54.9

Q ss_pred             CCCCCCCCCHHHHHHCC-CCCEEEEECCCCCCCCHHHHHHCCCCCCCCCEEEEEEC-CCCEEEECCCCCCC
Q ss_conf             00024567556530014-56628888783045400111110146788631699965-87313101121100
Q gi|254780773|r  121 VVSNVSPASPAAIAGVK-KGDCIISLDGITVSAFEEVAPYVRENPLHEISLVLYRE-HVGVLHLKVMPRLQ  189 (349)
Q Consensus       121 ~I~~V~~~spA~~AGL~-~GD~Il~InG~~V~s~~dl~~~i~~~~g~~v~i~v~R~-~~~~~~~~v~p~~~  189 (349)
                      -|-+|.++|||+.|||+ .+|-|+.+-+..-...+|+...|+.+.++...+-|+-- .+...+++++|+..
T Consensus       112 Hvl~V~p~SPaalAgl~~~~DYivG~~~~~~~~~eDl~~lIeshe~kpLklyVYN~D~d~~ReVti~pn~a  182 (462)
T KOG3834         112 HVLSVEPNSPAALAGLRPYTDYIVGIWDAVMHEEEDLFTLIESHEGKPLKLYVYNHDTDSCREVTITPNSA  182 (462)
T ss_pred             EEEECCCCCHHHHCCCCCCCCEEECCHHHHCCCHHHHHHHHHHCCCCCCCEEEEECCCCCCCEEEEECCCC
T ss_conf             44643899878850553365357435455234157899999860278741467644777520478611432


No 58 
>KOG3552 consensus
Probab=95.87  E-value=0.0055  Score=40.29  Aligned_cols=55  Identities=25%  Similarity=0.459  Sum_probs=43.9

Q ss_pred             CC-CCCCCCCCCHHHHHHCCCCCEEEEECCCCCCC--CHHHHHHCCCCCCCCCEEEEEEC
Q ss_conf             32-00024567556530014566288887830454--00111110146788631699965
Q gi|254780773|r  119 KP-VVSNVSPASPAAIAGVKKGDCIISLDGITVSA--FEEVAPYVRENPLHEISLVLYRE  175 (349)
Q Consensus       119 ~p-~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s--~~dl~~~i~~~~g~~v~i~v~R~  175 (349)
                      .| +|-.|++|+|+. --|+|||.|+.|||++|++  |+.+.+.++... +.++++|.+.
T Consensus        75 rPviVr~VT~GGps~-GKL~PGDQIl~vN~Epv~daprervIdlvRace-~sv~ltV~qP  132 (1298)
T KOG3552          75 RPVIVRFVTEGGPSI-GKLQPGDQILAVNGEPVKDAPRERVIDLVRACE-SSVNLTVCQP  132 (1298)
T ss_pred             CCEEEEEECCCCCCC-CCCCCCCEEEEECCCCCCCCCHHHHHHHHHHHH-HHCCEEEECC
T ss_conf             706999846898765-633677747874686321143889999999876-4103488604


No 59 
>PRK10733 hflB ATP-dependent metalloprotease; Reviewed
Probab=95.84  E-value=0.0084  Score=39.05  Aligned_cols=39  Identities=15%  Similarity=0.346  Sum_probs=18.6

Q ss_pred             HHHHHHHHHHCCEEEEEEEECCCHHEEEEECCCEEEEEEEEEE
Q ss_conf             3779999984975004553068311278605980799997711
Q gi|254780773|r   23 FGHYMVARLCNIRVLSFSVGFGPELIGITSRSGVRWKVSLIPL   65 (349)
Q Consensus        23 ~GH~~~Ar~~gv~V~~FsiGfgp~l~~~~~k~~t~y~i~~~Pl   65 (349)
                      +..|+.. +..=+|++-.|.  ..-...+++++++|... +|.
T Consensus        34 ys~f~~~-~~~~~v~~v~i~--~~~i~~~~~~~~~~~~~-~p~   72 (644)
T PRK10733         34 YSTFLQE-VNQDQVREARIN--GREINVTKKDSNRYTTY-IPV   72 (644)
T ss_pred             HHHHHHH-HHCCCEEEEEEE--CCEEEEEECCCCEEEEE-CCC
T ss_conf             9999999-984991599995--77999998689769985-788


No 60 
>KOG3834 consensus
Probab=95.67  E-value=0.013  Score=37.78  Aligned_cols=71  Identities=24%  Similarity=0.374  Sum_probs=50.2

Q ss_pred             CCCCCCCCCCCCHHHHHHCCC-CCEEEEECCCCCCCCHH-HHHHCCCCCCCCCEEEEEECCC-CEEEECCCCCCC
Q ss_conf             332000245675565300145-66288887830454001-1111014678863169996587-313101121100
Q gi|254780773|r  118 MKPVVSNVSPASPAAIAGVKK-GDCIISLDGITVSAFEE-VAPYVRENPLHEISLVLYREHV-GVLHLKVMPRLQ  189 (349)
Q Consensus       118 ~~p~I~~V~~~spA~~AGL~~-GD~Il~InG~~V~s~~d-l~~~i~~~~g~~v~i~v~R~~~-~~~~~~v~p~~~  189 (349)
                      ..-.+-.|++||||.+|||++ -|=|++|||..++.-+| +...++.+-.+ +++++.-... ++..+.+.|...
T Consensus        15 eg~hvlkVqedSpa~~aglepffdFIvSI~g~rL~~dnd~Lk~llk~~sek-Vkltv~n~kt~~~R~v~I~ps~~   88 (462)
T KOG3834          15 EGYHVLKVQEDSPAHKAGLEPFFDFIVSINGIRLNKDNDTLKALLKANSEK-VKLTVYNSKTQEVRIVEIVPSNN   88 (462)
T ss_pred             EEEEEEEEECCCHHHHCCCCHHHHHHHEECCCCCCCCHHHHHHHHHHCCCC-EEEEEEECCCCEEEEEEECCCCC
T ss_conf             047899863378677567503444410017400267658999988742412-17998855542367898424312


No 61 
>KOG3209 consensus
Probab=95.67  E-value=0.0092  Score=38.78  Aligned_cols=54  Identities=30%  Similarity=0.458  Sum_probs=32.3

Q ss_pred             CCCCCCCCCHHHHHH-CCCCCEEEEECCCCCC--CCHHHHHHCCCCC-CCCCEEEEEE
Q ss_conf             000245675565300-1456628888783045--4001111101467-8863169996
Q gi|254780773|r  121 VVSNVSPASPAAIAG-VKKGDCIISLDGITVS--AFEEVAPYVRENP-LHEISLVLYR  174 (349)
Q Consensus       121 ~I~~V~~~spA~~AG-L~~GD~Il~InG~~V~--s~~dl~~~i~~~~-g~~v~i~v~R  174 (349)
                      .|.+|.+++||++-| |++||+|+.|||+.+-  +-.|.++..+.-| |+.+++++-|
T Consensus       374 qVKsvl~DGPAa~dGkle~GDviV~INg~cvlGhTHAqaV~~fqaiPvg~~V~L~lcR  431 (984)
T KOG3209         374 QVKSVLKDGPAAQDGKLETGDVIVHINGECVLGHTHAQAVKRFQAIPVGQSVDLVLCR  431 (984)
T ss_pred             EEEECCCCCCHHHCCCCCCCCEEEEECCCEECCCCHHHHHHHHHCCCCCCEEEEEEEC
T ss_conf             3410035884664385335758999778264361079888774113568706689854


No 62 
>KOG0606 consensus
Probab=94.73  E-value=0.014  Score=37.53  Aligned_cols=42  Identities=33%  Similarity=0.445  Sum_probs=34.3

Q ss_pred             CCCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCC--HHHHHHCC
Q ss_conf             2000245675565300145662888878304540--01111101
Q gi|254780773|r  120 PVVSNVSPASPAAIAGVKKGDCIISLDGITVSAF--EEVAPYVR  161 (349)
Q Consensus       120 p~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~--~dl~~~i~  161 (349)
                      -.++.|.++|||..||++++|.|+.+||+++...  .++.+.+-
T Consensus       660 h~v~sv~egsPA~~agls~~DlIthvnge~v~gl~H~ev~~Lll  703 (1205)
T KOG0606         660 HSVGSVEEGSPAFEAGLSAGDLITHVNGEPVHGLVHTEVMELLL  703 (1205)
T ss_pred             EEEEEECCCCCCCCCCCCCCCEEEECCCCCCCHHHHHHHHHHHH
T ss_conf             24454237887334677723346741685430010899999997


No 63 
>KOG3542 consensus
Probab=94.33  E-value=0.022  Score=36.11  Aligned_cols=34  Identities=35%  Similarity=0.577  Sum_probs=30.4

Q ss_pred             CCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCCH
Q ss_conf             0002456755653001456628888783045400
Q gi|254780773|r  121 VVSNVSPASPAAIAGVKKGDCIISLDGITVSAFE  154 (349)
Q Consensus       121 ~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~~  154 (349)
                      .|.+|.|+|-|+.+|++.||.|+++||+.-.+.+
T Consensus       565 fV~~V~pgskAa~~GlKRgDqilEVNgQnfenis  598 (1283)
T KOG3542         565 FVAEVFPGSKAAREGLKRGDQILEVNGQNFENIS  598 (1283)
T ss_pred             EEEEECCCCHHHHHHHHHHHHHHHCCCCCHHHHH
T ss_conf             8863068846777654201143210452322202


No 64 
>KOG1421 consensus
Probab=94.25  E-value=0.062  Score=33.08  Aligned_cols=54  Identities=26%  Similarity=0.540  Sum_probs=37.4

Q ss_pred             CCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCCCCCCCCEEEEEECCCCEEEECC
Q ss_conf             0002456755653001456628888783045400111110146788631699965873131011
Q gi|254780773|r  121 VVSNVSPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRENPLHEISLVLYREHVGVLHLKV  184 (349)
Q Consensus       121 ~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~~~g~~v~i~v~R~~~~~~~~~v  184 (349)
                      +|+-|.+.-+--   |..||+|+++||+.|...+|+.++.      +++..+.|+|.+ .++++
T Consensus       774 ~ishv~~~~~ki---l~~gdiilsvngk~itr~~dl~d~~------eid~~ilrdg~~-~~iki  827 (955)
T KOG1421         774 VISHVRPLLHKI---LGVGDIILSVNGKMITRLSDLHDFE------EIDAVILRDGIE-MEIKI  827 (955)
T ss_pred             EEEEECCCCCCC---CCCCCEEEEECCEEEEEEHHHHHHH------HHHEEEEECCCE-EEEEE
T ss_conf             998422576501---1346489995676776502233455------312045415818-99982


No 65 
>KOG3651 consensus
Probab=93.84  E-value=0.042  Score=34.19  Aligned_cols=53  Identities=28%  Similarity=0.464  Sum_probs=41.9

Q ss_pred             CCCCCCCCCHHHHHH-CCCCCEEEEECCCCCCC--CHHHHHHCCCCCCCCCEEEEEE
Q ss_conf             000245675565300-14566288887830454--0011111014678863169996
Q gi|254780773|r  121 VVSNVSPASPAAIAG-VKKGDCIISLDGITVSA--FEEVAPYVRENPLHEISLVLYR  174 (349)
Q Consensus       121 ~I~~V~~~spA~~AG-L~~GD~Il~InG~~V~s--~~dl~~~i~~~~g~~v~i~v~R  174 (349)
                      +|..|..++||+.-| ++.||.|++|||.+|..  -.++...++.+. .++.+.+.+
T Consensus        33 YiVQvFD~tPAa~dG~i~~GDEi~avNg~svKGktKveVAkmIQ~~~-~eV~IhyNK   88 (429)
T KOG3651          33 YIVQVFDKTPAAKDGRIRCGDEIVAVNGISVKGKTKVEVAKMIQVSL-NEVKIHYNK   88 (429)
T ss_pred             EEEEECCCCCHHCCCCCCCCCEEEEECCEEECCCCHHHHHHHHHHHC-CCEEEEEHH
T ss_conf             99876169832104740237756876345652710799999999714-656998110


No 66 
>KOG3580 consensus
Probab=93.47  E-value=0.056  Score=33.37  Aligned_cols=57  Identities=19%  Similarity=0.406  Sum_probs=42.8

Q ss_pred             CCCCCCCCHHHHHH-CCCCCEEEEECCCCCCC--CHHHHHHCCCCCCCCCEEEEEECCCCE
Q ss_conf             00245675565300-14566288887830454--001111101467886316999658731
Q gi|254780773|r  122 VSNVSPASPAAIAG-VKKGDCIISLDGITVSA--FEEVAPYVRENPLHEISLVLYREHVGV  179 (349)
Q Consensus       122 I~~V~~~spA~~AG-L~~GD~Il~InG~~V~s--~~dl~~~i~~~~g~~v~i~v~R~~~~~  179 (349)
                      |..+...+-|+.-| ||.||.|++|||+...+  ..|-...|.++.|+ ..+.|.|+..++
T Consensus       223 vKeit~~gLAardgnlqEGDiiLkINGtvteNmSLtDar~LIEkS~GK-L~lvVlRD~~qt  282 (1027)
T KOG3580         223 VKEITRTGLAARDGNLQEGDIILKINGTVTENMSLTDARKLIEKSRGK-LQLVVLRDSQQT  282 (1027)
T ss_pred             HHHHCCCCHHHCCCCCCCCCEEEEECCEEECCCCCHHHHHHHHHCCCC-EEEEEEECCCCE
T ss_conf             433302311112488655637999776740344405678898743673-689999327851


No 67 
>KOG3549 consensus
Probab=93.38  E-value=0.066  Score=32.85  Aligned_cols=55  Identities=33%  Similarity=0.498  Sum_probs=45.5

Q ss_pred             CCCCCCCCCCCHHHHHH-CCCCCEEEEECCCCCCC--CHHHHHHCCCCCCCCCEEEEEE
Q ss_conf             32000245675565300-14566288887830454--0011111014678863169996
Q gi|254780773|r  119 KPVVSNVSPASPAAIAG-VKKGDCIISLDGITVSA--FEEVAPYVRENPLHEISLVLYR  174 (349)
Q Consensus       119 ~p~I~~V~~~spA~~AG-L~~GD~Il~InG~~V~s--~~dl~~~i~~~~g~~v~i~v~R  174 (349)
                      +-+|+.+.++..|+..| |=.||-|+.|||..|..  .+|+++.+++ +|+++++||..
T Consensus        81 PvviSkI~kdQaAd~tG~LFvGDAilqvNGi~v~~c~HeevV~iLRN-AGdeVtlTV~~  138 (505)
T KOG3549          81 PVVISKIYKDQAADITGQLFVGDAILQVNGIYVTACPHEEVVNILRN-AGDEVTLTVKH  138 (505)
T ss_pred             CEEEEHHHHHHHHHHCCCEEEEEEEEEECCEEEECCCHHHHHHHHHH-CCCEEEEEEHH
T ss_conf             47863032554420017467400557755577614880899999870-69879998276


No 68 
>KOG3605 consensus
Probab=92.95  E-value=0.19  Score=29.77  Aligned_cols=67  Identities=21%  Similarity=0.344  Sum_probs=47.5

Q ss_pred             CCCCCCCCCCC--CCCCCCCCCHHHHHH-CCCCCEEEEECCCCCCC--CHHHHHHCCCCCC-CCCEEEEEECC
Q ss_conf             11001233332--000245675565300-14566288887830454--0011111014678-86316999658
Q gi|254780773|r  110 FFFYNTGVMKP--VVSNVSPASPAAIAG-VKKGDCIISLDGITVSA--FEEVAPYVRENPL-HEISLVLYREH  176 (349)
Q Consensus       110 ~~~~~~g~~~p--~I~~V~~~spA~~AG-L~~GD~Il~InG~~V~s--~~dl~~~i~~~~g-~~v~i~v~R~~  176 (349)
                      ++-++||..-|  +|.....++||+..| |.-||+|++|||.+.-.  .+.-+.+|+..++ ..|+++|.+--
T Consensus       663 iVESGWGSmLPTVViAnmm~~GpAarsgkLnIGDQiiaING~SLVGLPLstcQs~Ik~~KnQT~VkltiV~cp  735 (829)
T KOG3605         663 IVESGWGSILPTVVIANMMHGGPAARSGKLNIGDQIMSINGTSLVGLPLSTCQSIIKGLKNQTAVKLNIVSCP  735 (829)
T ss_pred             EEECCCCCCCHHHHHHHCCCCCHHHHCCCCCCCCEEEEECCCEECCCCHHHHHHHHHCCCCCCEEEEEEECCC
T ss_conf             9834754311589987513677165438766322257644721106607999999861555405888776189


No 69 
>TIGR01241 FtsH_fam ATP-dependent metallopeptidase HflB; InterPro: IPR005936   Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases .   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.    This group of metallopeptidases belong to MEROPS peptidase family M41 (FtsH endopeptidase family, clan MA(E)). The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH.    FtsH is a membrane-anchored ATP-dependent protease that degrades misfolded or misassembled membrane proteins as well as a subset of cytoplasmic regulatory proteins. FtsH is a 647-residue protein of 70 kDa, with two putative transmembrane segments towards its N terminus which anchor the protein to the membrane, giving rise to a periplasmic domain of 70 residues and a cytoplasmic segment of 520 residues containing the ATPase and protease domains . ; GO: 0004222 metalloendopeptidase activity, 0030163 protein catabolic process, 0016020 membrane.
Probab=92.57  E-value=0.041  Score=34.28  Aligned_cols=11  Identities=27%  Similarity=0.483  Sum_probs=5.1

Q ss_pred             CEEEECCCCCC
Q ss_conf             31310112110
Q gi|254780773|r  178 GVLHLKVMPRL  188 (349)
Q Consensus       178 ~~~~~~v~p~~  188 (349)
                      .+..+|+.|+-
T Consensus       338 pV~KvTIIPRG  348 (505)
T TIGR01241       338 PVHKVTIIPRG  348 (505)
T ss_pred             CCCCEEECCCC
T ss_conf             52325631478


No 70 
>KOG1892 consensus
Probab=92.40  E-value=0.076  Score=32.43  Aligned_cols=57  Identities=19%  Similarity=0.301  Sum_probs=42.6

Q ss_pred             CCCCCCCCCCHHHHHH-CCCCCEEEEECCCCCCCCHH--HHHHCCCCCCCCCEEEEEECCC
Q ss_conf             2000245675565300-14566288887830454001--1111014678863169996587
Q gi|254780773|r  120 PVVSNVSPASPAAIAG-VKKGDCIISLDGITVSAFEE--VAPYVRENPLHEISLVLYREHV  177 (349)
Q Consensus       120 p~I~~V~~~spA~~AG-L~~GD~Il~InG~~V~s~~d--l~~~i~~~~g~~v~i~v~R~~~  177 (349)
                      -+|.+|++|+||+.-| |++||..++|||.+.-...+  -.+++ .+.|..|.++|.+.+.
T Consensus       962 IYvKsVV~GgaAd~DGRL~aGDQLLsVdG~SLiGisQErAA~lm-trtg~vV~leVaKqgA 1021 (1629)
T KOG1892         962 IYVKSVVEGGAADHDGRLEAGDQLLSVDGHSLIGISQERAARLM-TRTGNVVHLEVAKQGA 1021 (1629)
T ss_pred             EEEEEECCCCCCCCCCCCCCCCEEEEECCCCCCCCCHHHHHHHH-HCCCCEEEEEHHHHHH
T ss_conf             47987315875455564015763664558201142588899987-4248757875132356


No 71 
>KOG3551 consensus
Probab=90.23  E-value=0.16  Score=30.16  Aligned_cols=55  Identities=20%  Similarity=0.285  Sum_probs=42.3

Q ss_pred             CCCCCCCCCCCHHHHHH-CCCCCEEEEECCCCCCC--CHHHHHHCCCCCCCCCEEEEEE
Q ss_conf             32000245675565300-14566288887830454--0011111014678863169996
Q gi|254780773|r  119 KPVVSNVSPASPAAIAG-VKKGDCIISLDGITVSA--FEEVAPYVRENPLHEISLVLYR  174 (349)
Q Consensus       119 ~p~I~~V~~~spA~~AG-L~~GD~Il~InG~~V~s--~~dl~~~i~~~~g~~v~i~v~R  174 (349)
                      +-.|+.+.++-.|++++ |..||.|++|||+...+  .++-++.++ +.|++|.+.|..
T Consensus       111 PIlISKIFkGlAADQt~aL~~gDaIlSVNG~dL~~AtHdeAVqaLK-raGkeV~levKy  168 (506)
T KOG3551         111 PILISKIFKGLAADQTGALFLGDAILSVNGEDLRDATHDEAVQALK-RAGKEVLLEVKY  168 (506)
T ss_pred             CEEHHHHHCCCCCCCCCCEEECCEEEEECCHHHHHCCHHHHHHHHH-HHCCEEEEEEEH
T ss_conf             3566775152220323662314479973552333202699999998-617553213210


No 72 
>COG0465 HflB ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]
Probab=89.31  E-value=0.29  Score=28.47  Aligned_cols=27  Identities=15%  Similarity=0.190  Sum_probs=14.1

Q ss_pred             HHHHCCEEEEEEEECCCHHEEEEECCC
Q ss_conf             998497500455306831127860598
Q gi|254780773|r   29 ARLCNIRVLSFSVGFGPELIGITSRSG   55 (349)
Q Consensus        29 Ar~~gv~V~~FsiGfgp~l~~~~~k~~   55 (349)
                      ....+-+|++.++...-.....+.+++
T Consensus        32 ~~~~~~~v~~~~~~~~~~~v~~~~~~~   58 (596)
T COG0465          32 QLVSGGKVSSVSIKGDSKTVNLKLKDG   58 (596)
T ss_pred             HHHHCCCCEEEEECCCCEEEEEEECCC
T ss_conf             997267851899827732899886488


No 73 
>KOG0609 consensus
Probab=88.34  E-value=0.32  Score=28.18  Aligned_cols=55  Identities=27%  Similarity=0.418  Sum_probs=43.3

Q ss_pred             CCCCCCCCCCCHHHHHH-CCCCCEEEEECCCCCCC--CHHHHHHCCCCCCCCCEEEEEE
Q ss_conf             32000245675565300-14566288887830454--0011111014678863169996
Q gi|254780773|r  119 KPVVSNVSPASPAAIAG-VKKGDCIISLDGITVSA--FEEVAPYVRENPLHEISLVLYR  174 (349)
Q Consensus       119 ~p~I~~V~~~spA~~AG-L~~GD~Il~InG~~V~s--~~dl~~~i~~~~g~~v~i~v~R  174 (349)
                      ..+|..+..|+.|+..| |+.||+|+++||.++.+  .++++..+++.. ..+++.+.-
T Consensus       147 ~~~vARI~~GG~~~r~glL~~GD~i~EvNGi~v~~~~~~e~q~~l~~~~-G~itfkiiP  204 (542)
T KOG0609         147 KVVVARIMHGGMADRQGLLHVGDEILEVNGISVANKSPEELQELLRNSR-GSITFKIIP  204 (542)
T ss_pred             CCEEEEECCCCCCHHCCCEEECCCHHEECCEECCCCCHHHHHHHHHHCC-CCEEEEECC
T ss_conf             6078552027840003510206512103675215679799999998488-837999763


No 74 
>KOG1738 consensus
Probab=87.60  E-value=0.61  Score=26.22  Aligned_cols=44  Identities=30%  Similarity=0.470  Sum_probs=34.8

Q ss_pred             CCCCCCCCCHHHHHH-CCCCCEEEEECCCCCCCCHH--HHHHCCCCC
Q ss_conf             000245675565300-14566288887830454001--111101467
Q gi|254780773|r  121 VVSNVSPASPAAIAG-VKKGDCIISLDGITVSAFEE--VAPYVRENP  164 (349)
Q Consensus       121 ~I~~V~~~spA~~AG-L~~GD~Il~InG~~V~s~~d--l~~~i~~~~  164 (349)
                      ++.++.++|||..-+ +.+||.++.||++.+-.|+-  ++..++..+
T Consensus       228 ~~s~~~e~Spad~~~kI~dgdEv~qiN~qtvVgwqlk~vV~sL~~~~  274 (638)
T KOG1738         228 VTSKIFEQSPADYRQKILDGDEVLQINEQTVVGWQLKVVVSSLRETP  274 (638)
T ss_pred             ECCCCCCCCHHHHHHCCCCCCCEEEECCCCCCCCHHHHHHHHCCCCC
T ss_conf             44655658867775224673310342364214601576875024576


No 75 
>KOG3550 consensus
Probab=86.42  E-value=0.38  Score=27.60  Aligned_cols=54  Identities=26%  Similarity=0.525  Sum_probs=37.9

Q ss_pred             CCC-CCCCCCCCCHHHHHH-CCCCCEEEEECCCCCCCC--HHHHHHCCCCCCCCCEEEE
Q ss_conf             332-000245675565300-145662888878304540--0111110146788631699
Q gi|254780773|r  118 MKP-VVSNVSPASPAAIAG-VKKGDCIISLDGITVSAF--EEVAPYVRENPLHEISLVL  172 (349)
Q Consensus       118 ~~p-~I~~V~~~spA~~AG-L~~GD~Il~InG~~V~s~--~dl~~~i~~~~g~~v~i~v  172 (349)
                      .+| +|+.+.|++.|+.-| |+.||..+++||.+|..-  +.-++.+... ...+.+.+
T Consensus       114 nspiyisriipggvadrhgglkrgdqllsvngvsvege~hekavellkaa-~gsvklvv  171 (207)
T KOG3550         114 NSPIYISRIIPGGVADRHGGLKRGDQLLSVNGVSVEGEHHEKAVELLKAA-VGSVKLVV  171 (207)
T ss_pred             CCCEEEEEECCCCCCCCCCCCCCCCEEEEECCEEECCHHHHHHHHHHHHH-CCCEEEEE
T ss_conf             89647886247752001376445564676546420313169999999973-57678987


No 76 
>KOG3606 consensus
Probab=86.38  E-value=0.73  Score=25.69  Aligned_cols=55  Identities=20%  Similarity=0.427  Sum_probs=40.0

Q ss_pred             CCCCCCCCCHHHHHHCC-CCCEEEEECCCCCC--CCHHHHHHCCCCCCCCCEEEEEECC
Q ss_conf             00024567556530014-56628888783045--4001111101467886316999658
Q gi|254780773|r  121 VVSNVSPASPAAIAGVK-KGDCIISLDGITVS--AFEEVAPYVRENPLHEISLVLYREH  176 (349)
Q Consensus       121 ~I~~V~~~spA~~AGL~-~GD~Il~InG~~V~--s~~dl~~~i~~~~g~~v~i~v~R~~  176 (349)
                      -|+..+|++-|+.-||. ..|.+++|||.+|.  +.+++.+.+-.+. ...-+||...|
T Consensus       197 FISRlVpGGLAeSTGLLaVnDEVlEVNGIEVaGKTLDQVTDMMvANs-hNLIiTVkPAN  254 (358)
T KOG3606         197 FISRLVPGGLAESTGLLAVNDEVLEVNGIEVAGKTLDQVTDMMVANS-HNLIITVKPAN  254 (358)
T ss_pred             EEEEECCCCCCCCCCEEEECCEEEEECCEEECCCCHHHHHHHHHHCC-CCEEEEECCCC
T ss_conf             78850377520134405532416887577841523888788876344-64389961444


No 77 
>KOG3571 consensus
Probab=86.14  E-value=0.61  Score=26.20  Aligned_cols=57  Identities=18%  Similarity=0.355  Sum_probs=41.6

Q ss_pred             CCCCCCCCCCHHHHHH-CCCCCEEEEECCCCCCCC--HHHHHHCCC--CCCCCCEEEEEECC
Q ss_conf             2000245675565300-145662888878304540--011111014--67886316999658
Q gi|254780773|r  120 PVVSNVSPASPAAIAG-VKKGDCIISLDGITVSAF--EEVAPYVRE--NPLHEISLVLYREH  176 (349)
Q Consensus       120 p~I~~V~~~spA~~AG-L~~GD~Il~InG~~V~s~--~dl~~~i~~--~~g~~v~i~v~R~~  176 (349)
                      -+|+++.++++-+.-| +++||.|+.||..+..+.  +|-+..+++  +...++++++.+-.
T Consensus       279 IYVgsImkgGAVA~DGRIe~GDMiLQVNevsFENmSNd~AVrvLREaV~~~gPi~ltvAk~~  340 (626)
T KOG3571         279 IYVGSIMKGGAVALDGRIEPGDMILQVNEVSFENMSNDQAVRVLREAVSRPGPIKLTVAKCW  340 (626)
T ss_pred             EEEEEECCCCEEECCCCCCCCCEEEEEEECCHHHCCCHHHHHHHHHHHCCCCCEEEEEEECC
T ss_conf             58864136860311476575533787400123104764999999998636787378886022


No 78 
>pfam11874 DUF3394 Domain of unknown function (DUF3394). This domain is functionally uncharacterized. This domain is found in bacteria. This presumed domain is about 190 amino acids in length. This domain is found associated with pfam06808.
Probab=85.74  E-value=0.56  Score=26.47  Aligned_cols=26  Identities=31%  Similarity=0.345  Sum_probs=16.2

Q ss_pred             CCCCCCCCCCHHHHHHCCCCCEEEEE
Q ss_conf             20002456755653001456628888
Q gi|254780773|r  120 PVVSNVSPASPAAIAGVKKGDCIISL  145 (349)
Q Consensus       120 p~I~~V~~~spA~~AGL~~GD~Il~I  145 (349)
                      -.|+.+..+|||+++|++-||.|+++
T Consensus       124 ~~vd~~~f~s~Aek~G~d~d~~I~~v  149 (183)
T pfam11874       124 VIVDEVEFGSPAEKAGIDFDWEIVEV  149 (183)
T ss_pred             EEEEECCCCCHHHHHCCCCCCEEEEE
T ss_conf             89995488986888268778689999


No 79 
>KOG3605 consensus
Probab=83.02  E-value=0.67  Score=25.92  Aligned_cols=26  Identities=8%  Similarity=-0.005  Sum_probs=16.9

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999999
Q gi|254780773|r  317 GVSVTRVITRMGLCIILFLFFLGIRN  342 (349)
Q Consensus       317 ~~~~~~~~~~~g~~ll~~l~i~~~~n  342 (349)
                      ++..+-++|.+|=++-+..|=|.--|
T Consensus       585 SdeAQfIAQSIGQAFqVAY~EFLrAN  610 (829)
T KOG3605         585 SDEAQFIAQSIGQAFQVAYMEFLRAN  610 (829)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             32578999988899999999999872


No 80 
>pfam01079 Hint Hint module. This is an alignment of the Hint module in the Hedgehog proteins. It does not include any Inteins which also possess the Hint module.
Probab=80.80  E-value=1.8  Score=23.04  Aligned_cols=58  Identities=14%  Similarity=0.295  Sum_probs=36.8

Q ss_pred             CCHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCCCCCCCCEEE-EEECCCCEEEECCCCC
Q ss_conf             75565300145662888878304540011111014678863169-9965873131011211
Q gi|254780773|r  128 ASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRENPLHEISLV-LYREHVGVLHLKVMPR  187 (349)
Q Consensus       128 ~spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~~~g~~v~i~-v~R~~~~~~~~~v~p~  187 (349)
                      ++--...-|++||++++.|..---.++++..++...|.+.-.+. ++-++.+  .++++|.
T Consensus        24 G~~k~m~~L~~GD~Vla~d~~G~~~yS~Vi~Fldr~~~~~~~F~~I~T~~g~--~l~LT~~   82 (214)
T pfam01079        24 GGTKPMSDLRIGDRVLAADSDGKLVYSPVILFLDRDPEQRREFYVIETENGR--KLTLTPA   82 (214)
T ss_pred             CCEEEHHHCCCCCEEEEECCCCCEEEEEEEEEEEECCCCCEEEEEEEECCCC--EEEECHH
T ss_conf             9888937768888899865899998885799982176711899999958998--6997325


No 81 
>pfam07136 DUF1385 Protein of unknown function (DUF1385). This family contains a number of hypothetical bacterial proteins of unknown function approximately 300 residues in length. Some family members are predicted to be metal-dependent.
Probab=79.43  E-value=4.8  Score=20.02  Aligned_cols=16  Identities=19%  Similarity=0.158  Sum_probs=6.6

Q ss_pred             HHHHHHHHHHHHHCCC
Q ss_conf             1233321122111011
Q gi|254780773|r   95 AGPLANCVMAILFFTF  110 (349)
Q Consensus        95 AGp~~N~ilA~iif~~  110 (349)
                      ...+..+++|..+|..
T Consensus        43 ~t~~~s~~~ai~lF~~   58 (235)
T pfam07136        43 LTVILSLAFAIGLFFV   58 (235)
T ss_pred             HHHHHHHHHHHHHHHH
T ss_conf             9999999999999999


No 82 
>pfam02128 Peptidase_M36 Fungalysin metallopeptidase (M36).
Probab=77.74  E-value=0.18  Score=29.82  Aligned_cols=17  Identities=0%  Similarity=0.172  Sum_probs=8.1

Q ss_pred             HHHHHHHHHCCCCCHHH
Q ss_conf             99999888278699999
Q gi|254780773|r  304 ITFLLEMIRGKSLGVSV  320 (349)
Q Consensus       304 ~~~~~E~i~gr~i~~~~  320 (349)
                      +.+++++..=-|.++..
T Consensus       315 m~lv~dgmkLqPcnPtF  331 (368)
T pfam02128       315 MKLVMDGMKLQPCNPGF  331 (368)
T ss_pred             HHHHHHHHHCCCCCCCH
T ss_conf             99999887428999973


No 83 
>cd04278 ZnMc_MMP Zinc-dependent metalloprotease, matrix metalloproteinase (MMP) sub-family. MMPs are responsible for a great deal of pericellular proteolysis of extracellular matrix and cell surface molecules, playing crucial roles in morphogenesis, cell fate specification, cell migration, tissue repair, tumorigenesis, gain or loss of tissue-specific functions, and apoptosis. In many instances, they are anchored to cell membranes via trans-membrane domains, and their activity is controlled via TIMPs (tissue inhibitors of metalloproteinases).
Probab=73.00  E-value=1.8  Score=22.90  Aligned_cols=12  Identities=8%  Similarity=0.498  Sum_probs=5.8

Q ss_pred             CCCEEEEEEEEE
Q ss_conf             598079999771
Q gi|254780773|r   53 RSGVRWKVSLIP   64 (349)
Q Consensus        53 k~~t~y~i~~~P   64 (349)
                      |..-.|++.-.|
T Consensus         4 k~~lty~i~~~~   15 (157)
T cd04278           4 KTNLTYRILNYP   15 (157)
T ss_pred             CCCEEEEEECCC
T ss_conf             870589984279


No 84 
>TIGR02289 M3_not_pepF oligoendopeptidase, M3 family; InterPro: IPR011976   Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases .   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.    This family consists of probable oligoendopeptidases belonging to MEROPS peptidase family M3, subfamily M3B (clan MA(E)). The family is related to lactococcal PepF and group B streptococcal PepB (IPR004438 from INTERPRO) but in a distinct clade with considerable sequence differences not only to IPR004438 from INTERPRO but also to IPR011977 from INTERPRO. Likely substrates are small peptides and not whole proteins, as with PepF, but members are not characterised and the activity profile may differ. Several bacteria have both a member of this family and a member of the PepF family..
Probab=72.36  E-value=2  Score=22.67  Aligned_cols=25  Identities=24%  Similarity=0.321  Sum_probs=13.3

Q ss_pred             CCCCCE-EEEECCCCCCCCHHHHHHC
Q ss_conf             145662-8888783045400111110
Q gi|254780773|r  136 VKKGDC-IISLDGITVSAFEEVAPYV  160 (349)
Q Consensus       136 L~~GD~-Il~InG~~V~s~~dl~~~i  160 (349)
                      ++|+|. -.-.||++..-..+.-..+
T Consensus       253 l~pwD~s~~~~~gn~L~P~~~~~~~~  278 (553)
T TIGR02289       253 LRPWDESAVFLDGNVLKPFGNVDFLL  278 (553)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCHHHHH
T ss_conf             14201576788678668866778999


No 85 
>cd06457 M3A_MIP Peptidase M3 mitochondrial intermediate peptidase (MIP; EC 3.4.24.59) belongs to the widespread subfamily M3A, that show similarity to the Thimet oligopeptidase (TOP). It is one of three peptidases responsible for the proteolytic processing of both, nuclear and mitochondrial encoded precursor polypeptides targeted to the various subcompartments of the mitochondria. It cleaves intermediate-size proteins initially processed by mitochondrial processing peptidase (MPP) to yield a processing intermediate with a typical N-terminal octapeptide that is sequentially cleaved by MIP to mature-size protein.  MIP cleaves precursor proteins of respiratory components, including subunits of the electron transport chain and tri-carboxylic acid cycle enzymes, and components of the mitochondrial genetic machinery, including ribosomal proteins, translation factors, and proteins required for mitochondrial DNA metabolism. It has been suggested that the human MIP (HMIP polypeptide; gene symbo
Probab=69.00  E-value=3.5  Score=20.98  Aligned_cols=17  Identities=24%  Similarity=0.272  Sum_probs=10.1

Q ss_pred             HHHHHHHHHHCCEEEEE
Q ss_conf             37799999849750045
Q gi|254780773|r   23 FGHYMVARLCNIRVLSF   39 (349)
Q Consensus        23 ~GH~~~Ar~~gv~V~~F   39 (349)
                      .=..++.|++|++.++=
T Consensus       138 Glf~i~~~Lfgi~~~~~  154 (458)
T cd06457         138 GLSRLFSRLYGIRLVPV  154 (458)
T ss_pred             HHHHHHHHHHCEEEEEC
T ss_conf             99999999857456874


No 86 
>KOG4407 consensus
Probab=68.95  E-value=5.2  Score=19.78  Aligned_cols=45  Identities=16%  Similarity=0.496  Sum_probs=35.9

Q ss_pred             CCCCCCCCCHHHHHHCCCCCEEEEECCCCCCC--CHHHHHHCCCCCC
Q ss_conf             00024567556530014566288887830454--0011111014678
Q gi|254780773|r  121 VVSNVSPASPAAIAGVKKGDCIISLDGITVSA--FEEVAPYVRENPL  165 (349)
Q Consensus       121 ~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s--~~dl~~~i~~~~g  165 (349)
                      .+.+|.++.||--|-||.||+++.+|.+++..  ++++...+..+|.
T Consensus       146 f~~eV~~n~~a~~a~LQ~~d~V~mvn~q~~A~ia~sti~S~~kqt~~  192 (1973)
T KOG4407         146 FIKEVQANGPAHYANLQTGDRVLMVNNQPIAGIAYSTIVSMIKQTPA  192 (1973)
T ss_pred             HHHHHCCCCHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHCCCCC
T ss_conf             21123358745877652266157750675422103132220125888


No 87 
>COG5233 GRH1 Peripheral Golgi membrane protein [Intracellular trafficking and secretion]
Probab=68.23  E-value=3.3  Score=21.16  Aligned_cols=31  Identities=35%  Similarity=0.528  Sum_probs=23.7

Q ss_pred             CCCCCCCCCHHHHHHCCCCCEEEEECCCCCC
Q ss_conf             0002456755653001456628888783045
Q gi|254780773|r  121 VVSNVSPASPAAIAGVKKGDCIISLDGITVS  151 (349)
Q Consensus       121 ~I~~V~~~spA~~AGL~~GD~Il~InG~~V~  151 (349)
                      .+-.|.+.+||++||.-.||-|+.+|+.++.
T Consensus        66 ~~lrv~~~~~~e~~~~~~~dyilg~n~Dp~~   96 (417)
T COG5233          66 EVLRVNPESPAEKAGMVVGDYILGINEDPLR   96 (417)
T ss_pred             HHEECCCCCHHHHHCCCCCEEEEEECCCCHH
T ss_conf             2200365676675101000058763588279


No 88 
>cd06456 M3A_DCP_Oligopeptidase_A Peptidase family M3 dipeptidyl carboxypeptidase (DCP; Dcp II; peptidyl dipeptidase; EC 3.4.15.5). This metal-binding M3A family also includes oligopeptidase A (OpdA; EC 3.4.24.70) enzyme. DCP cleaves dipeptides off the C-termini of various peptides and proteins, the smallest substrate being N-blocked tripeptides and unblocked tetrapeptides. DCP from E. coli is inhibited by the anti-hypertensive drug captopril, an inhibitor of the mammalian angiotensin converting enzyme (ACE, also called  peptidyl dipeptidase A). Oligopeptidase A (OpdA) may play a specific role in the degradation of signal peptides after they are released from precursor forms of secreted proteins. It can also cleave N-acetyl-L-Ala.
Probab=66.90  E-value=4.4  Score=20.28  Aligned_cols=22  Identities=18%  Similarity=0.273  Sum_probs=15.2

Q ss_pred             HHHHHHHHHHHHHCCCCCHHHH
Q ss_conf             3699999998882786999999
Q gi|254780773|r  300 GGHLITFLLEMIRGKSLGVSVT  321 (349)
Q Consensus       300 GG~i~~~~~E~i~gr~i~~~~~  321 (349)
                      |++=...+++..+||+++.+..
T Consensus       395 Gs~~~~e~~~~FlGR~P~~~al  416 (422)
T cd06456         395 GSRDPMELFRAFRGRDPSIEAL  416 (422)
T ss_pred             CCCCHHHHHHHHCCCCCCHHHH
T ss_conf             9949999999856999984789


No 89 
>pfam00413 Peptidase_M10 Matrixin. The members of this family are enzymes that cleave peptides. These proteases require zinc for catalysis.
Probab=66.18  E-value=2.1  Score=22.57  Aligned_cols=14  Identities=0%  Similarity=0.202  Sum_probs=8.3

Q ss_pred             EEECCCEEEEEEEEE
Q ss_conf             860598079999771
Q gi|254780773|r   50 ITSRSGVRWKVSLIP   64 (349)
Q Consensus        50 ~~~k~~t~y~i~~~P   64 (349)
                      |+ |....|++.-.|
T Consensus         2 W~-k~~lTy~i~~~~   15 (158)
T pfam00413         2 WK-KKNLTYRIVNYT   15 (158)
T ss_pred             CC-CCCEEEEEECCC
T ss_conf             98-881579983579


No 90 
>TIGR01700 PNPH purine nucleoside phosphorylase I, inosine and guanosine-specific; InterPro: IPR011270   This entry represents a family of bacterial and metazoan purine phosphorylases acting primarily on inosine and guanosine and not acting on adenosine. PNP-I refers to the nomenclature from Bacillus stearothermophilus  where PHP-II refers to the nucleotidase acting on adenosine as the primary substrate. The bacterial enzymes (PUNA) are typified by the Bacillus PupG protein  which is involved in the metabolism of nucleosides as a carbon source. Several metazoan enzymes (PNPH) are well characterised including the human  and bovine  enzymes which have been crystallised. ; GO: 0004731 purine-nucleoside phosphorylase activity, 0006139 nucleobase nucleoside nucleotide and nucleic acid metabolic process.
Probab=66.01  E-value=2.9  Score=21.53  Aligned_cols=15  Identities=27%  Similarity=0.304  Sum_probs=10.1

Q ss_pred             HHHHCCCCCEEEEEC
Q ss_conf             530014566288887
Q gi|254780773|r  132 AIAGVKKGDCIISLD  146 (349)
Q Consensus       132 ~~AGL~~GD~Il~In  146 (349)
                      =++-+|+||.++==|
T Consensus        96 iN~~F~~GDlmlI~D  110 (259)
T TIGR01700        96 INTEFKVGDLMLIRD  110 (259)
T ss_pred             CCCCCCCCCEEEECC
T ss_conf             277766777789711


No 91 
>COG0339 Dcp Zn-dependent oligopeptidases [Amino acid transport and metabolism]
Probab=63.82  E-value=5.1  Score=19.83  Aligned_cols=32  Identities=19%  Similarity=0.268  Sum_probs=13.8

Q ss_pred             HHHHHHHHHHHHHHEECCCCCCCCCCCCCCCCC
Q ss_conf             898886554223100000002554200224667
Q gi|254780773|r  225 SRGLDEISSITRGFLGVLSSAFGKDTRLNQISG  257 (349)
Q Consensus       225 ~~~~~~~~~~~~~~~~~l~~l~~g~~~~~~lsG  257 (349)
                      -.+.+++.++.-.+-..+-.+++. +...++||
T Consensus       462 Lls~dEV~TLFHEfGHgLH~mlt~-v~~~~vsG  493 (683)
T COG0339         462 LLSHDEVTTLFHEFGHGLHHLLTR-VKYPGVSG  493 (683)
T ss_pred             EEEHHHHHHHHHHHHHHHHHHHHC-CCCCCCCC
T ss_conf             310788999998753688887633-87456678


No 92 
>pfam01432 Peptidase_M3 Peptidase family M3. This is the Thimet oligopeptidase family, large family of mammalian and bacterial oligopeptidases that cleave medium sized peptides. The group also contains mitochondrial intermediate peptidase which is encoded by nuclear DNA but functions within the mitochondria to remove the leader sequence.
Probab=63.54  E-value=5.6  Score=19.59  Aligned_cols=20  Identities=20%  Similarity=0.130  Sum_probs=9.4

Q ss_pred             HHHHHHHHHHHHHCCCCCHH
Q ss_conf             36999999988827869999
Q gi|254780773|r  300 GGHLITFLLEMIRGKSLGVS  319 (349)
Q Consensus       300 GG~i~~~~~E~i~gr~i~~~  319 (349)
                      |++=-..+++...||..+..
T Consensus       421 gs~~p~ell~~f~gr~~~~~  440 (448)
T pfam01432       421 GSLDPLELLKKFGGRMPSAD  440 (448)
T ss_pred             CCCCHHHHHHHHCCCCCCHH
T ss_conf             98269999998289999858


No 93 
>COG0260 PepB Leucyl aminopeptidase [Amino acid transport and metabolism]
Probab=62.08  E-value=3.4  Score=21.02  Aligned_cols=29  Identities=34%  Similarity=0.456  Sum_probs=22.7

Q ss_pred             CCCCCCCCHHHHHHCCCCCEEEEECCCCCC
Q ss_conf             002456755653001456628888783045
Q gi|254780773|r  122 VSNVSPASPAAIAGVKKGDCIISLDGITVS  151 (349)
Q Consensus       122 I~~V~~~spA~~AGL~~GD~Il~InG~~V~  151 (349)
                      |-...+|.|...| .+|||+|++-||+.|+
T Consensus       302 vl~~~ENm~~g~A-~rPGDVits~~GkTVE  330 (485)
T COG0260         302 VLPAVENMPSGNA-YRPGDVITSMNGKTVE  330 (485)
T ss_pred             EEEEECCCCCCCC-CCCCCEEEECCCEEEE
T ss_conf             9761315878789-9998767805970899


No 94 
>cd06459 M3B_Oligoendopeptidase_F Peptidase family M3B Oligopeptidase F (PepF; Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and includes oligoendopeptidase F from Lactococcus lactis. This enzyme hydrolyzes peptides containing between 7 and 17 amino acids with fairly broad specificity. The PepF gene is duplicated in L. lactis on the plasmid that bears it, while a shortened second copy is found in Bacillus subtilis. Most bacterial PepFs are cytoplasmic endopeptidases; however, the PepF Bacillus amyloliquefaciens oligopeptidase is a secreted protein and may facilitate the process of sporulation. Specifically, the yjbG gene encoding the homolog of the PepF1 and PepF2 oligoendopeptidases of Lactococcus lactis has been identified in Bacillus subtilis as an inhibitor of sporulation initiation when over expressed from a multicopy plasmid.
Probab=61.83  E-value=4.2  Score=20.43  Aligned_cols=27  Identities=22%  Similarity=0.155  Sum_probs=12.9

Q ss_pred             CCCCCEEEEECCC--CCCCCHHHHHHCCC
Q ss_conf             1456628888783--04540011111014
Q gi|254780773|r  136 VKKGDCIISLDGI--TVSAFEEVAPYVRE  162 (349)
Q Consensus       136 L~~GD~Il~InG~--~V~s~~dl~~~i~~  162 (349)
                      |++.|.=..+...  +.-+|+|..+.+.+
T Consensus       137 l~~~D~~~p~~~~~~~~~~~~ea~~~v~~  165 (427)
T cd06459         137 LRPYDLYAPLVSGNPPKYTYEEAKELVLE  165 (427)
T ss_pred             CHHHHHCCCCCCCCCCCCCHHHHHHHHHH
T ss_conf             15988148788888886899999999999


No 95 
>TIGR00181 pepF oligoendopeptidase F; InterPro: IPR004438   Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases .   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.    This group of metallopeptidases belong to MEROPS peptidase family M3 (clan MA(E)), the type example being oligoendopeptidase F from Lactococcus lactis. The enzyme hydrolyses peptides of 7 and 17 amino acids with fairly broad specificity. Differences in substrate specificity should be expected in other species. The gene is duplicated in L. lactis on the plasmid that bears it. A shortened second copy is found in Bacillus subtilis.; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis.
Probab=61.70  E-value=3.9  Score=20.65  Aligned_cols=19  Identities=21%  Similarity=0.417  Sum_probs=11.3

Q ss_pred             HHHHHHHHHHH---HHHHHHHC
Q ss_conf             99999973377---99999849
Q gi|254780773|r   15 IIIVVIHEFGH---YMVARLCN   33 (349)
Q Consensus        15 ~~~v~iHE~GH---~~~Ar~~g   33 (349)
                      ++...+||+||   ++.|....
T Consensus       389 ~~~TLaHE~GHS~Hs~~s~~~Q  410 (611)
T TIGR00181       389 SVFTLAHELGHSMHSYFSSKHQ  410 (611)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCC
T ss_conf             2579999855679998654117


No 96 
>cd06455 M3A_TOP Peptidase M3 Thimet oligopeptidase (TOP; PZ-peptidase; endo-oligopeptidase A; endopeptidase 24.15; soluble metallo-endopeptidase; EC 3.4.24.15) family also includes neurolysin (endopeptidase 24.16, microsomal endopeptidase, mitochondrial oligopeptidase M, neurotensin endopeptidase, soluble angiotensin II-binding protein, thimet oligopeptidase II) which hydrolyzes oligopeptides such as neurotensin, bradykinin and dynorphin A. TOP and neurolysin are neuropeptidases expressed abundantly in the testis, but also found in the liver, lung and kidney. They are involved in the metabolism of neuropeptides under 20 amino acid residues long and cleave most bioactive peptides at the same sites, but recognize different positions on some naturally occurring and synthetic peptides; they cleave at distinct sites on the 13-residue bioactive peptide neurotensin, which modulates central dopaminergic and cholinergic circuits.  TOP has been shown to degrade peptides released by the proteasom
Probab=60.28  E-value=6  Score=19.34  Aligned_cols=22  Identities=14%  Similarity=0.135  Sum_probs=15.5

Q ss_pred             CHHHHHHHHHHHHHCCCCCHHH
Q ss_conf             4369999999888278699999
Q gi|254780773|r  299 DGGHLITFLLEMIRGKSLGVSV  320 (349)
Q Consensus       299 DGG~i~~~~~E~i~gr~i~~~~  320 (349)
                      -|++=...+++..+||+++.+.
T Consensus       446 Ggs~~~~e~~~~F~GR~P~~~a  467 (472)
T cd06455         446 GGSKDAADMLKDFLGREPNNDA  467 (472)
T ss_pred             CCCCCHHHHHHHHCCCCCCCHH
T ss_conf             8991899999984699998157


No 97 
>pfam00883 Peptidase_M17 Cytosol aminopeptidase family, catalytic domain. The two associated zinc ions and the active site are entirely enclosed within the C-terminal catalytic domain in leucine aminopeptidase.
Probab=59.01  E-value=4.2  Score=20.42  Aligned_cols=29  Identities=28%  Similarity=0.425  Sum_probs=24.2

Q ss_pred             CCCCCCCCHHHHHHCCCCCEEEEECCCCCC
Q ss_conf             002456755653001456628888783045
Q gi|254780773|r  122 VSNVSPASPAAIAGVKKGDCIISLDGITVS  151 (349)
Q Consensus       122 I~~V~~~spA~~AGL~~GD~Il~InG~~V~  151 (349)
                      +-...+|+|...| .+|||+|.+-||+.|+
T Consensus       135 i~~l~EN~is~~A-~rPgDVi~s~~GkTVE  163 (312)
T pfam00883       135 VLALTENMISGTA-MRPGDIITAMNGKTVE  163 (312)
T ss_pred             EEEEECCCCCCCC-CCCCCEEEECCCCEEE
T ss_conf             9870103789988-9999778917997898


No 98 
>PRK04860 hypothetical protein; Provisional
Probab=58.73  E-value=5  Score=19.88  Aligned_cols=18  Identities=50%  Similarity=0.731  Sum_probs=8.8

Q ss_pred             HHHHHHHHHHHHHHHCCEE
Q ss_conf             9997337799999849750
Q gi|254780773|r   18 VVIHEFGHYMVARLCNIRV   36 (349)
Q Consensus        18 v~iHE~GH~~~Ar~~gv~V   36 (349)
                      |+-||+.|+++=+++| ||
T Consensus        66 vVpHEvAHllv~~lfG-rV   83 (160)
T PRK04860         66 VVPHELAHLLVYQLFG-RV   83 (160)
T ss_pred             CCHHHHHHHHHHHHHC-CC
T ss_conf             3358999999999808-87


No 99 
>TIGR01697 PNPH-PUNA-XAPA inosine guanosine and xanthosine phosphorylase family; InterPro: IPR011268   This entry describes a subset of the phosphorylase family. The entry excludes the methylthioadenosine phosphorylases (MTAP, IPR010044 from INTERPRO), which are believed to play a specific role in the recycling of methionine from methylthioadenosine.    This entry consists of three clades of purine phosphorylases based on a neighbour-joining tree using the MTAP family as an out group. The highest-branching clade (IPR011269 from INTERPRO) consists of a group of sequences from both Gram-positive and Gram-negative bacteria which have been shown to act as purine nucleotide phosphorylases but whose physiological substrate and role in vivo remain unknown . Of the two remaining clades, one is xanthosine phosphorylase (XAPA, IPR010943 from INTERPRO); it is limited to certain gammaproteobacteria and constitutes a special purine phosphorylase found in a specialised operon for xanthosine catabolism . The enzyme also acts on the same purines (inosine and guanosine) as the other characterised members of this subfamily, but is only induced when xanthosine must be degraded. The remaining and largest clade consists of purine nucleotide phosphorylases (PNPH, IPR011270 from INTERPRO) from metazoa  and bacteria  which act primarily on guanosine and inosine, and do not act on adenosine. Sequences from Clostridium and Thermotoga fall between these last two clades and are uncharacterised with respect to substrate range. ; GO: 0004731 purine-nucleoside phosphorylase activity, 0006139 nucleobase nucleoside nucleotide and nucleic acid metabolic process.
Probab=57.77  E-value=6.2  Score=19.27  Aligned_cols=12  Identities=42%  Similarity=0.470  Sum_probs=6.3

Q ss_pred             HHHCCCCCEEEE
Q ss_conf             300145662888
Q gi|254780773|r  133 IAGVKKGDCIIS  144 (349)
Q Consensus       133 ~AGL~~GD~Il~  144 (349)
                      ++.+++||.++=
T Consensus       103 n~~~~~GdLm~i  114 (266)
T TIGR01697       103 NADFKPGDLMII  114 (266)
T ss_pred             CCCCCCCCEEEE
T ss_conf             678898537997


No 100
>pfam06838 Alum_res Aluminium resistance protein. This family represents the aluminium resistance protein, which confers resistance to aluminium in bacteria.
Probab=54.59  E-value=8.3  Score=18.39  Aligned_cols=42  Identities=19%  Similarity=0.218  Sum_probs=29.2

Q ss_pred             CHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCCCCCCCCEE
Q ss_conf             556530014566288887830454001111101467886316
Q gi|254780773|r  129 SPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRENPLHEISL  170 (349)
Q Consensus       129 spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~~~g~~v~i  170 (349)
                      +-|--+=|+|||+++++-|+|-++.+++.-.-.+.+|.-.+.
T Consensus        87 ~~aLfg~LrPGD~ll~itG~PYDTL~eVIGi~g~~~GSL~e~  128 (405)
T pfam06838        87 ATALFGVLRPGDELLYITGKPYDTLEEVIGIRGEGQGSLKDF  128 (405)
T ss_pred             HHHHHHCCCCCCEEEECCCCCCHHHHHHHCCCCCCCCCHHHH
T ss_conf             999983678998787448997365898718588998888995


No 101
>cd06258 Peptidase_M3_like The peptidase M3-like family, also called neurolysin-like family, is part of the "zincins" metallopeptidases, and includes M3, M2 and M32 families of metallopeptidases.  The M3 family is subdivided into two subfamilies: the widespread M3A, which comprises a number of high-molecular mass endo- and exopeptidases from bacteria, archaea, protozoa, fungi, plants and animals, and the small M3B, whose members are enzymes primarily from bacteria. Well-known mammalian/eukaryotic M3A endopeptidases are the thimet oligopeptidase (TOP; endopeptidase 3.4.24.15), neurolysin (alias endopeptidase 3.4.24.16), and the mitochondrial intermediate peptidase. The first two are intracellular oligopeptidases, which act only on relatively short substrates of less than 20 amino acid residues, while the latter cleaves N-terminal octapeptides from proteins during their import into the mitochondria. The M3A subfamily also contains several bacterial endopeptidases, collectively called olig
Probab=54.11  E-value=8.7  Score=18.25  Aligned_cols=21  Identities=14%  Similarity=0.112  Sum_probs=13.5

Q ss_pred             HHHHHHHHHHHHHCCCCCHHH
Q ss_conf             369999999888278699999
Q gi|254780773|r  300 GGHLITFLLEMIRGKSLGVSV  320 (349)
Q Consensus       300 GG~i~~~~~E~i~gr~i~~~~  320 (349)
                      |++=...++|..+||+++.+.
T Consensus       340 ~s~~~~el~~~f~Gr~p~~~a  360 (365)
T cd06258         340 NSEPWKELLKRATGEDPNADA  360 (365)
T ss_pred             CCCCHHHHHHHHHCCCCCHHH
T ss_conf             899999999997785998078


No 102
>PRK00913 leucyl aminopeptidase; Provisional
Probab=51.70  E-value=6.2  Score=19.24  Aligned_cols=27  Identities=26%  Similarity=0.455  Sum_probs=20.2

Q ss_pred             CCCCCCHHHHHHCCCCCEEEEECCCCCC
Q ss_conf             2456755653001456628888783045
Q gi|254780773|r  124 NVSPASPAAIAGVKKGDCIISLDGITVS  151 (349)
Q Consensus       124 ~V~~~spA~~AGL~~GD~Il~InG~~V~  151 (349)
                      ...+|.|...| .+|||+|.+-||+.|+
T Consensus       308 ~~~ENm~~g~a-~~pgDvi~~~~GktvE  334 (491)
T PRK00913        308 AACENMPSGNA-YRPGDVLTSMSGKTIE  334 (491)
T ss_pred             EHHHCCCCCCC-CCCCCEEEECCCCEEE
T ss_conf             61213888889-9985557806994798


No 103
>KOG3714 consensus
Probab=51.58  E-value=4.8  Score=20.04  Aligned_cols=14  Identities=29%  Similarity=0.539  Sum_probs=5.9

Q ss_pred             HHCCCCC-EEEEECC
Q ss_conf             0014566-2888878
Q gi|254780773|r  134 AGVKKGD-CIISLDG  147 (349)
Q Consensus       134 AGL~~GD-~Il~InG  147 (349)
                      -|-+.|. ..++++.
T Consensus       141 VGr~gg~~q~~sl~~  155 (411)
T KOG3714         141 VGRRGGGQQLLSLGD  155 (411)
T ss_pred             CCCCCCCCCCCCCCC
T ss_conf             277788653211178


No 104
>cd00433 Peptidase_M17 Cytosol aminopeptidase family, N-terminal and catalytic domains.  Family M17 contains zinc- and manganese-dependent exopeptidases ( EC  3.4.11.1), including leucine aminopeptidase. They catalyze removal of amino acids from the N-terminus of a protein and play a key role in protein degradation and in the metabolism of biologically active peptides. They do not contain HEXXH motif (which is used as one of the signature patterns to group the peptidase families) in the metal-binding site. The two associated zinc ions and the active site are entirely enclosed within the C-terminal catalytic domain in leucine aminopeptidase. The enzyme is a hexamer, with the catalytic domains clustered around the three-fold axis, and the two trimers related to one another by a two-fold rotation. The N-terminal domain is structurally similar to the ADP-ribose binding Macro domain. This family includes proteins from bacteria, archaea, animals and plants.
Probab=50.13  E-value=6.4  Score=19.18  Aligned_cols=27  Identities=30%  Similarity=0.313  Sum_probs=20.0

Q ss_pred             CCCCCCHHHHHHCCCCCEEEEECCCCCC
Q ss_conf             2456755653001456628888783045
Q gi|254780773|r  124 NVSPASPAAIAGVKKGDCIISLDGITVS  151 (349)
Q Consensus       124 ~V~~~spA~~AGL~~GD~Il~InG~~V~  151 (349)
                      ...+|.|...| .+|||+|++-||+.|+
T Consensus       291 ~~~EN~~~~~a-~rpgDvi~~~~GktvE  317 (468)
T cd00433         291 PLAENMISGNA-YRPGDVITSRSGKTVE  317 (468)
T ss_pred             EHHHCCCCCCC-CCCCCEEECCCCCEEE
T ss_conf             62314878889-8984658827996899


No 105
>KOG1565 consensus
Probab=48.51  E-value=6.2  Score=19.25  Aligned_cols=12  Identities=42%  Similarity=0.841  Sum_probs=7.7

Q ss_pred             HHHHHHHHHHHH
Q ss_conf             999999733779
Q gi|254780773|r   15 IIIVVIHEFGHY   26 (349)
Q Consensus        15 ~~~v~iHE~GH~   26 (349)
                      ...|++||.||.
T Consensus       211 l~~Va~HEiGH~  222 (469)
T KOG1565         211 LFLVAAHEIGHA  222 (469)
T ss_pred             HHHHHHHHCCCC
T ss_conf             677754301100


No 106
>TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit; InterPro: IPR012754   DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.   RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:  RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors.  RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs.  Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits.   This entry represents the beta-prime subunit, RpoC, found in most bacteria. It excludes some, mainly cyanobacterial, species where RpoC is replaced by two homologous proteins that include an additional domain. One arm of the "claw" is predominantly formed by this subunit, the other being predominantly formed by the beta subunit. The active site of the enzyme is defined by three invariant aspartate residues within the beta-prime subunit .; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription.
Probab=47.96  E-value=5.7  Score=19.52  Aligned_cols=10  Identities=50%  Similarity=0.743  Sum_probs=5.1

Q ss_pred             CCCCCEEEEE
Q ss_conf             1456628888
Q gi|254780773|r  136 VKKGDCIISL  145 (349)
Q Consensus       136 L~~GD~Il~I  145 (349)
                      +++||.|-++
T Consensus      1295 v~~GDIlAkl 1304 (1552)
T TIGR02386      1295 VKPGDILAKL 1304 (1552)
T ss_pred             CCCCCEEEEC
T ss_conf             4747478860


No 107
>PRK05113 electron transport complex protein RnfB; Provisional
Probab=43.36  E-value=22  Score=15.40  Aligned_cols=34  Identities=6%  Similarity=0.103  Sum_probs=24.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEE
Q ss_conf             8999999999999999973377999998497500
Q gi|254780773|r    4 LDCFLLYTVSLIIIVVIHEFGHYMVARLCNIRVL   37 (349)
Q Consensus         4 ~~~~~~~~~~l~~~v~iHE~GH~~~Ar~~gv~V~   37 (349)
                      |.++++.++.++.+=++--+.-.+++|+|.|.++
T Consensus         1 m~~il~av~~l~~lGl~~g~~L~~Ask~f~Ve~D   34 (184)
T PRK05113          1 MNTIWIAVIALSLLALVFGAILGFASRRFKVEGD   34 (184)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             9159999999999999999999998762046799


No 108
>KOG2597 consensus
Probab=43.08  E-value=11  Score=17.42  Aligned_cols=25  Identities=36%  Similarity=0.434  Sum_probs=18.7

Q ss_pred             CCCCHHHHHHCCCCCEEEEECCCCCC
Q ss_conf             56755653001456628888783045
Q gi|254780773|r  126 SPASPAAIAGVKKGDCIISLDGITVS  151 (349)
Q Consensus       126 ~~~spA~~AGL~~GD~Il~InG~~V~  151 (349)
                      .+|+|...| -+|||+|++-||+.|.
T Consensus       328 cENm~sg~A-~kpgDVit~~nGKtve  352 (513)
T KOG2597         328 CENMPSGNA-TKPGDVITLRNGKTVE  352 (513)
T ss_pred             ECCCCCCCC-CCCCCEEEECCCCEEE
T ss_conf             005887557-8987478812786787


No 109
>pfam04298 Zn_peptidase_2 Putative neutral zinc metallopeptidase. Zinc metallopeptidase zinc binding regions have been predicted in some family members by a pattern match (Prosite:PS00142).
Probab=43.02  E-value=15  Score=16.58  Aligned_cols=32  Identities=13%  Similarity=0.468  Sum_probs=14.8

Q ss_pred             HHHHHHHHHHHH-HHHHHCCCC-CCHHHHHHHHH
Q ss_conf             899999999999-996306472-24369999999
Q gi|254780773|r  277 IAFLAMFSWAIG-FMNLLPIPI-LDGGHLITFLL  308 (349)
Q Consensus       277 l~~~a~isi~Lg-~~NlLPip~-LDGG~i~~~~~  308 (349)
                      +.+++++.+.++ +|.++-+|. +|-.+=.....
T Consensus       143 l~~igi~lf~~~vlf~lvTLPVEfDAS~RAl~~L  176 (222)
T pfam04298       143 LLLIGIILFSAAVLFQLVTLPVEFDASRRALAIL  176 (222)
T ss_pred             HHHHHHHHHHHHHHHHHEECCCEECCHHHHHHHH
T ss_conf             9999999999999997132230026256799999


No 110
>cd04282 ZnMc_meprin Zinc-dependent metalloprotease, meprin_like subfamily. Meprins are membrane-bound or secreted extracellular proteases, which cleave a variety of targets, including peptides such as parathyroid hormone, gastrin, and cholecystokinin, cytokines such as osteopontin, and proteins such as collagen IV, fibronectin, casein and gelatin. Meprins may also be able to release proteins from the cell surface. Closely related meprin alpha- and beta-subunits form homo- and hetero-oligomers; these complexes are found on epithelial cells of the intestine, for example, and are also expressed in certain cancer cells.
Probab=42.71  E-value=12  Score=17.30  Aligned_cols=11  Identities=27%  Similarity=0.486  Sum_probs=4.5

Q ss_pred             HCCCCCEEEEE
Q ss_conf             01456628888
Q gi|254780773|r  135 GVKKGDCIISL  145 (349)
Q Consensus       135 GL~~GD~Il~I  145 (349)
                      |-+.|-..+++
T Consensus       104 G~~gg~Q~vsl  114 (230)
T cd04282         104 GDQQGGQNLSI  114 (230)
T ss_pred             CCCCCEEEEEE
T ss_conf             65388056650


No 111
>TIGR03296 M6dom_TIGR03296 M6 family metalloprotease domain. This model describes a metalloproteinase domain, with a characteristic HExxH motif. Examples of this domain are found in proteins in the family of immune inhibitor A, which cleaves antibacterial peptides, and in other, only distantly related proteases. This model is built to be broader and more inclusive than pfam05547.
Probab=41.35  E-value=4.2  Score=20.45  Aligned_cols=11  Identities=27%  Similarity=0.685  Sum_probs=5.5

Q ss_pred             EEEECCCCCCC
Q ss_conf             88887830454
Q gi|254780773|r  142 IISLDGITVSA  152 (349)
Q Consensus       142 Il~InG~~V~s  152 (349)
                      ...+||+++.+
T Consensus       140 ~~~~~G~~i~~  150 (286)
T TIGR03296       140 TLPIDGTTIGG  150 (286)
T ss_pred             CCCCCCEEEEC
T ss_conf             41109978725


No 112
>COG2317 Zn-dependent carboxypeptidase [Amino acid transport and metabolism]
Probab=40.76  E-value=16  Score=16.40  Aligned_cols=11  Identities=0%  Similarity=0.184  Sum_probs=4.5

Q ss_pred             CCCEEEEEECC
Q ss_conf             86316999658
Q gi|254780773|r  166 HEISLVLYREH  176 (349)
Q Consensus       166 ~~v~i~v~R~~  176 (349)
                      ..|.+|..-++
T Consensus       243 ~DVRITTRy~~  253 (497)
T COG2317         243 NDVRITTRYNE  253 (497)
T ss_pred             CCEEEEEECCC
T ss_conf             75368740477


No 113
>COG4307 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=40.58  E-value=15  Score=16.53  Aligned_cols=17  Identities=29%  Similarity=0.507  Sum_probs=13.6

Q ss_pred             EEEEEEEEEECCEEECC
Q ss_conf             07999977112111001
Q gi|254780773|r   56 VRWKVSLIPLGGYVSFS   72 (349)
Q Consensus        56 t~y~i~~~PlGgyV~~~   72 (349)
                      +.|.+.+=+.||+|+-+
T Consensus        56 CNw~V~ad~~~~~C~aC   72 (349)
T COG4307          56 CNWLVPADQLGGLCRAC   72 (349)
T ss_pred             HCCCCCCCCCCCCCHHH
T ss_conf             34742146677612555


No 114
>KOG3984 consensus
Probab=40.54  E-value=9.4  Score=18.02  Aligned_cols=28  Identities=14%  Similarity=0.169  Sum_probs=16.4

Q ss_pred             HHHHHHCCCCCEEEEECCCCCCCCHHHH
Q ss_conf             5653001456628888783045400111
Q gi|254780773|r  130 PAAIAGVKKGDCIISLDGITVSAFEEVA  157 (349)
Q Consensus       130 pA~~AGL~~GD~Il~InG~~V~s~~dl~  157 (349)
                      .+-+++.+.||..+--|-..+..+.+..
T Consensus       118 ggin~~f~vgdiMli~DHin~~G~agq~  145 (286)
T KOG3984         118 GGINPKFAVGDIMLIKDHINLPGLAGQN  145 (286)
T ss_pred             CCCCCCCCCCCEEEEECCCCCCCCCCCC
T ss_conf             5768554224389970103774326899


No 115
>TIGR02290 M3_fam_3 oligoendopeptidase, pepF/M3 family; InterPro: IPR011977   Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases .   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.    This family consists of probable oligoendopeptidases belonging to MEROPS peptidase family M3, subfamily M3B (clan MA(E)). It is related to lactococcal PepF and group B streptococcal PepB (IPR004438 from INTERPRO) but in a distinct clade with considerable sequence differences not only to IPR004438 from INTERPRO but also to IPR011976 from INTERPRO. Members are not characterised with respect to their substrates and the activity profile may differ..
Probab=40.10  E-value=16  Score=16.37  Aligned_cols=16  Identities=31%  Similarity=0.441  Sum_probs=7.4

Q ss_pred             CCCHHHHHHHHHHHHH
Q ss_conf             2101342112333211
Q gi|254780773|r   87 WKKILTVLAGPLANCV  102 (349)
Q Consensus        87 ~~R~~i~~AGp~~N~i  102 (349)
                      |++-...+|=++.|+-
T Consensus       219 ~~~~~~~~a~~LN~l~  234 (600)
T TIGR02290       219 WEKEAPTLAAILNALA  234 (600)
T ss_pred             HHHHHHHHHHHHHHHH
T ss_conf             8750026999986555


No 116
>COG4956 Integral membrane protein (PIN domain superfamily) [General function prediction only]
Probab=40.01  E-value=19  Score=15.95  Aligned_cols=34  Identities=21%  Similarity=0.387  Sum_probs=18.9

Q ss_pred             ECCCCCCCCHHHHHHCCC--CCCCCCEEEEEECCCC
Q ss_conf             878304540011111014--6788631699965873
Q gi|254780773|r  145 LDGITVSAFEEVAPYVRE--NPLHEISLVLYREHVG  178 (349)
Q Consensus       145 InG~~V~s~~dl~~~i~~--~~g~~v~i~v~R~~~~  178 (349)
                      +-|.++-+.+|+.++++.  .||++.++.+.++|+|
T Consensus       272 ~qgV~vLNINDLAnAVkP~vlpGe~l~v~iiK~GkE  307 (356)
T COG4956         272 LQGVQVLNINDLANAVKPVVLPGEELTVQIIKDGKE  307 (356)
T ss_pred             HCCCCEECHHHHHHHHCCCCCCCCEEEEEEEECCCC
T ss_conf             448846308888887377315787168998506765


No 117
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=39.93  E-value=21  Score=15.67  Aligned_cols=23  Identities=30%  Similarity=0.355  Sum_probs=16.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCEE
Q ss_conf             999999997337799999849750
Q gi|254780773|r   13 SLIIIVVIHEFGHYMVARLCNIRV   36 (349)
Q Consensus        13 ~l~~~v~iHE~GH~~~Ar~~gv~V   36 (349)
                      .+..=|+-||+.|+++=+.+| ++
T Consensus        59 ~f~~~vV~HELaHl~ly~~~g-r~   81 (156)
T COG3091          59 DFIEQVVPHELAHLHLYQEFG-RY   81 (156)
T ss_pred             HHHHHHHHHHHHHHHHHHHCC-CC
T ss_conf             999998899999999999827-87


No 118
>cd06460 M32_Taq Peptidase family M32 is a subclass of metallocarboxypeptidases which are distributed mainly in bacteria and archaea, and contain a HEXXH motif that coordinates a divalent cation such as Zn2+ or Co2+, so far only observed in the active site of neutral metallopeptidases but not in carboxypeptidases. M32 includes the thermostable carboxypeptidases (E.C. 3.4.17.19) from Thermus aquaticus (TaqCP) and Pyrococcus furiosus (PfuCP), which have broad specificities toward a wide range of C-terminal substrates that include basic, aromatic, neutral and polar amino acids. These enzymes have a similar fold to the M3 peptidases such as neurolysin and the M2 angiotensin converting enzyme (ACE). Novel peptidases from protozoa Trypanosoma cruzi, a causative agent of Chagas' disease, and Leishmania major, a parasite that causes leishmaniasis, are the first eukaryotic M32 enzymes identified so far, thus making these enzymes an attractive potential target for drug development against these o
Probab=38.22  E-value=19  Score=15.90  Aligned_cols=16  Identities=25%  Similarity=0.268  Sum_probs=12.7

Q ss_pred             HHHHHHHHCCCCCHHH
Q ss_conf             9999888278699999
Q gi|254780773|r  305 TFLLEMIRGKSLGVSV  320 (349)
Q Consensus       305 ~~~~E~i~gr~i~~~~  320 (349)
                      -.+++.++|++++++.
T Consensus       371 ~eLl~~~TGe~l~~~~  386 (396)
T cd06460         371 DELLKKATGEPLNPEY  386 (396)
T ss_pred             HHHHHHHHCCCCCHHH
T ss_conf             9999998689998799


No 119
>COG4100 Cystathionine beta-lyase family protein involved in aluminum resistance [Inorganic ion transport and metabolism]
Probab=38.13  E-value=16  Score=16.44  Aligned_cols=40  Identities=20%  Similarity=0.217  Sum_probs=27.9

Q ss_pred             HHHHHCCCCCEEEEECCCCCCCCHHHHHHCCCCCCCCCEE
Q ss_conf             6530014566288887830454001111101467886316
Q gi|254780773|r  131 AAIAGVKKGDCIISLDGITVSAFEEVAPYVRENPLHEISL  170 (349)
Q Consensus       131 A~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~~~g~~v~i  170 (349)
                      |--.=|+|||..+.|-|.|-++.+|+.-.-.+..|.-.+.
T Consensus        99 aLfg~LRpgDell~i~G~PYDTLeevIG~rg~~~gSL~df  138 (416)
T COG4100          99 ALFGILRPGDELLYITGSPYDTLEEVIGLRGEGQGSLKDF  138 (416)
T ss_pred             HHHHCCCCCCEEEEECCCCCHHHHHHHCCCCCCCCCHHHH
T ss_conf             9984268887477752886056898756277785427873


No 120
>pfam06167 MtfA Phosphoenolpyruvate:glucose-phosphotransferase regulator. MtfA (earlier known as YeeI) is a transcription factor A that binds Mlc (make large colonies), itself a repressor of glucose and hence a protein important in regulation of the phosphoenolpyruvate:glucose-phosphotransferase (ptsG) system, the major glucose transporter in E.coli. Mlc is a repressor of ptsG, and MtfA is found to bind and inactivate Mlc with high affinity. The membrane-bound protein EIICBGlc encoded by the ptsG gene is the major glucose transporter in Escherichia coli.
Probab=37.44  E-value=15  Score=16.54  Aligned_cols=18  Identities=11%  Similarity=0.145  Sum_probs=12.1

Q ss_pred             ECCCCCCCCHHHHHHCCC
Q ss_conf             878304540011111014
Q gi|254780773|r  145 LDGITVSAFEEVAPYVRE  162 (349)
Q Consensus       145 InG~~V~s~~dl~~~i~~  162 (349)
                      -+|.-|-||+|+..-.+.
T Consensus       128 ~~G~vvLSW~dv~~g~~~  145 (248)
T pfam06167       128 EQGPVILSWQDVLAGGAN  145 (248)
T ss_pred             CCCCEEEEHHHHHHHCCC
T ss_conf             589579779999744427


No 121
>PRK13267 archaemetzincin-like protein; Reviewed
Probab=36.78  E-value=14  Score=16.88  Aligned_cols=12  Identities=25%  Similarity=0.507  Sum_probs=4.9

Q ss_pred             CCCEEEEECCCC
Q ss_conf             566288887830
Q gi|254780773|r  138 KGDCIISLDGIT  149 (349)
Q Consensus       138 ~GD~Il~InG~~  149 (349)
                      ++|.++.|-+..
T Consensus        67 ~~~~vlgvt~~D   78 (177)
T PRK13267         67 NGDATIGITDCD   78 (177)
T ss_pred             CCCEEEEEECCC
T ss_conf             997299995254


No 122
>pfam08434 CLCA_N Calcium-activated chloride channel. The CLCA family of calcium-activated chloride channels has been identified in many epithelial and endothelial cell types as well as in smooth muscle cells and has four or five putative transmembrane regions. Additionally to their role as chloride channels some CLCA proteins function as adhesion molecules and may also have roles as tumour suppressors. The domain described here is found at the N-terminus of CLCAs.
Probab=36.78  E-value=13  Score=17.03  Aligned_cols=16  Identities=25%  Similarity=0.295  Sum_probs=7.3

Q ss_pred             CHHHHHHCCCCCEEEE
Q ss_conf             5565300145662888
Q gi|254780773|r  129 SPAAIAGVKKGDCIIS  144 (349)
Q Consensus       129 spA~~AGL~~GD~Il~  144 (349)
                      .+|...-.+.-|++++
T Consensus        91 ~~a~~Ety~~ADV~Va  106 (262)
T pfam08434        91 LRPKQESYKKADVIVA  106 (262)
T ss_pred             CCCCHHHCCCCCEEEC
T ss_conf             4530101046677965


No 123
>pfam05547 Peptidase_M6 Immune inhibitor A peptidase M6. The insect pathogenic Gram-positive Bacillus thuringiensis secretes immune inhibitor A, a metallopeptidase, which specifically cleaves host antibacterial proteins. A homologue of immune inhibitor A, PrtV, has been identified in the Gram-negative human pathogen Vibrio cholerae.
Probab=35.85  E-value=3.9  Score=20.63  Aligned_cols=22  Identities=5%  Similarity=0.015  Sum_probs=13.7

Q ss_pred             CCHHHHHHCCCCCCCCCEEEEE
Q ss_conf             4001111101467886316999
Q gi|254780773|r  152 AFEEVAPYVRENPLHEISLVLY  173 (349)
Q Consensus       152 s~~dl~~~i~~~~g~~v~i~v~  173 (349)
                      .|-++.--++..+|++|++...
T Consensus       419 ~Wv~~~~dLsayaGk~V~l~f~  440 (646)
T pfam05547       419 KWIDASYDLSAYAGKKVKLRFD  440 (646)
T ss_pred             CEEEEEECCHHHCCCEEEEEEE
T ss_conf             5078775452426965799999


No 124
>pfam02074 Peptidase_M32 Carboxypeptidase Taq (M32) metallopeptidase.
Probab=35.66  E-value=23  Score=15.35  Aligned_cols=16  Identities=19%  Similarity=0.266  Sum_probs=11.0

Q ss_pred             HHHHHHHHCCCCCHHH
Q ss_conf             9999888278699999
Q gi|254780773|r  305 TFLLEMIRGKSLGVSV  320 (349)
Q Consensus       305 ~~~~E~i~gr~i~~~~  320 (349)
                      -.+++.++|+|++++.
T Consensus       470 ~eLi~~~TGe~l~~~~  485 (494)
T pfam02074       470 KELLKKATGEDVNAEY  485 (494)
T ss_pred             HHHHHHHHCCCCCHHH
T ss_conf             9999998689998799


No 125
>COG3732 SrlE Phosphotransferase system sorbitol-specific component IIBC [Carbohydrate transport and metabolism]
Probab=34.15  E-value=31  Score=14.44  Aligned_cols=56  Identities=20%  Similarity=0.268  Sum_probs=33.5

Q ss_pred             CCHH-HHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHH--------CCCCCCHHHHHHHHHHHHHC
Q ss_conf             3012-23334565305034789999999999999630--------64722436999999988827
Q gi|254780773|r  258 PVGI-ARIAKNFFDHGFNAYIAFLAMFSWAIGFMNLL--------PIPILDGGHLITFLLEMIRG  313 (349)
Q Consensus       258 PVgI-a~~~~~~a~~G~~~~l~~~a~isi~Lg~~NlL--------Pip~LDGG~i~~~~~E~i~g  313 (349)
                      .+++ .|...+..++-+.+.+-|+|++|..+|+++--        ++-||-+.-.=..++-.|-+
T Consensus       167 vv~vffqagR~tid~vlknilPFMAFvs~lIgii~~tglGd~iA~~l~PLA~~~~Gll~la~iC~  231 (328)
T COG3732         167 VVAVFFQAGRDTIDTVLKNILPFMAFVSALIGIILYTGLGDVIAHGLSPLANSIWGLLLLALICS  231 (328)
T ss_pred             HHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHC
T ss_conf             20345552346899999865679999999999998720677875346512257299999999966


No 126
>COG1164 Oligoendopeptidase F [Amino acid transport and metabolism]
Probab=34.13  E-value=29  Score=14.68  Aligned_cols=31  Identities=26%  Similarity=0.301  Sum_probs=14.4

Q ss_pred             HHHHH---CCCCCEEEE-EC--CCCCCCCHHHHHHCC
Q ss_conf             65300---145662888-87--830454001111101
Q gi|254780773|r  131 AAIAG---VKKGDCIIS-LD--GITVSAFEEVAPYVR  161 (349)
Q Consensus       131 A~~AG---L~~GD~Il~-In--G~~V~s~~dl~~~i~  161 (349)
                      |+.-|   +++.|+=.- .+  -.+-.+++|..+.+.
T Consensus       286 ~k~Lgl~~l~~yD~~~p~~~~~~~~~~s~~ea~~~v~  322 (598)
T COG1164         286 AKVLGLEKLRPYDLYAPLLDKDPSPEYSYEEAKELVL  322 (598)
T ss_pred             HHHCCCCCCCHHHCCCCCCCCCCCCCCCHHHHHHHHH
T ss_conf             9871998588655079844577775666999999999


No 127
>TIGR01592 holin_SPP1 holin, SPP1 family; InterPro: IPR006479   This group of sequences represent one of more than 30 families of phage proteins, all lacking detectable homology with each other, known or believed to act as holins. Holins act in cell lysis by bacteriophage. Members of this family are found in phage PBSX and phage SPP1, among others. .
Probab=33.68  E-value=31  Score=14.39  Aligned_cols=24  Identities=17%  Similarity=0.469  Sum_probs=21.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             347899999999999996306472
Q gi|254780773|r  274 NAYIAFLAMFSWAIGFMNLLPIPI  297 (349)
Q Consensus       274 ~~~l~~~a~isi~Lg~~NlLPip~  297 (349)
                      ...|..+||+|=.|.+.|.=|||.
T Consensus         8 RtiLL~iALvNQ~L~~~g~~~iPv   31 (82)
T TIGR01592         8 RTILLIIALVNQFLAMKGISPIPV   31 (82)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf             899999999999999758974430


No 128
>COG4219 MecR1 Antirepressor regulating drug resistance, predicted signal transduction N-terminal membrane component [Transcription / Signal transduction mechanisms]
Probab=32.98  E-value=20  Score=15.80  Aligned_cols=16  Identities=13%  Similarity=-0.195  Sum_probs=7.9

Q ss_pred             HHHHHCCCCCCHHHHH
Q ss_conf             9963064722436999
Q gi|254780773|r  289 FMNLLPIPILDGGHLI  304 (349)
Q Consensus       289 ~~NlLPip~LDGG~i~  304 (349)
                      ..|+.|=-+.-|-|-+
T Consensus       269 ~~~l~~~~~~g~nk~l  284 (337)
T COG4219         269 NPPLACHWPAGGNKPL  284 (337)
T ss_pred             CCCCCCCCCCCCCCHH
T ss_conf             8986544434566438


No 129
>PRK07118 ferredoxin; Validated
Probab=31.09  E-value=35  Score=14.11  Aligned_cols=34  Identities=9%  Similarity=0.070  Sum_probs=26.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEE
Q ss_conf             8999999999999999973377999998497500
Q gi|254780773|r    4 LDCFLLYTVSLIIIVVIHEFGHYMVARLCNIRVL   37 (349)
Q Consensus         4 ~~~~~~~~~~l~~~v~iHE~GH~~~Ar~~gv~V~   37 (349)
                      |..++..++.|+.+=++--+.-.+++|.|.|.++
T Consensus         1 m~~il~~~~~l~~lg~~~g~~L~~ask~f~Ve~D   34 (276)
T PRK07118          1 MNLILFAVLSLGALGLVFGILLAFASKKFAVEED   34 (276)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             9129999999999999999999998650036789


No 130
>cd03506 Delta6-FADS-like The Delta6 Fatty Acid Desaturase (Delta6-FADS)-like CD includes the integral-membrane enzymes: delta-4, delta-5, delta-6, delta-8, delta-8-sphingolipid, and delta-11 desaturases found in vertebrates, higher plants, fungi, and bacteria. These desaturases are required for the synthesis of highly unsaturated fatty acids (HUFAs), which are mainly esterified into phospholipids and contribute to maintaining membrane fluidity. While HUFAs may be required for cold tolerance in bacteria, plants and fish, the primary role of HUFAs in mammals is cell signaling. These enzymes are described as front-end desaturases because they introduce a double bond between the pre-exiting double bond and the carboxyl (front) end of the fatty acid. Various substrates are involved, with both acyl-coenzyme A (CoA) and acyl-lipid desaturases present in this CD. Acyl-lipid desaturases are localized in the membranes of cyanobacterial thylakoid, plant endoplasmic reticulum (ER), and plastid; an
Probab=31.01  E-value=35  Score=14.10  Aligned_cols=32  Identities=19%  Similarity=-0.040  Sum_probs=19.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEE
Q ss_conf             9999999999999999733779999984975004
Q gi|254780773|r    5 DCFLLYTVSLIIIVVIHEFGHYMVARLCNIRVLS   38 (349)
Q Consensus         5 ~~~~~~~~~l~~~v~iHE~GH~~~Ar~~gv~V~~   38 (349)
                      .++++....-......||.+|.-+.|.-  ++++
T Consensus         3 ~~~~~G~~~~~~~~l~Hea~H~~~~~~~--~~N~   34 (204)
T cd03506           3 LAILLGLFWAQGGFLAHDAGHGQVFKNR--WLNK   34 (204)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCC--HHHH
T ss_conf             9999999999999999973111302880--9999


No 131
>pfam10462 Peptidase_M66 Peptidase M66. This family of metallopeptidases contains StcE, a virulence factor found in Shiga toxigenic Escherichia coli organisms. StcE peptidase cleaves C1 esterase inhibitor.
Probab=30.54  E-value=7.7  Score=18.61  Aligned_cols=15  Identities=7%  Similarity=0.093  Sum_probs=11.7

Q ss_pred             CEEEEEEEEEECCEE
Q ss_conf             807999977112111
Q gi|254780773|r   55 GVRWKVSLIPLGGYV   69 (349)
Q Consensus        55 ~t~y~i~~~PlGgyV   69 (349)
                      .+|..+.-||+|=|.
T Consensus        46 p~~L~i~~i~~gmlt   60 (304)
T pfam10462        46 PYELLIQTLDFGMLT   60 (304)
T ss_pred             CCEEEEEEECEEEEC
T ss_conf             864588554448454


No 132
>pfam11667 DUF3267 Protein of unknown function (DUF3267). This family of proteins has no known function.
Probab=30.49  E-value=9  Score=18.15  Aligned_cols=21  Identities=19%  Similarity=0.471  Sum_probs=16.7

Q ss_pred             HHHHHHHHHHHHHHHHHHCCE
Q ss_conf             999999733779999984975
Q gi|254780773|r   15 IIIVVIHEFGHYMVARLCNIR   35 (349)
Q Consensus        15 ~~~v~iHE~GH~~~Ar~~gv~   35 (349)
                      .+++.+||+=|.+..|.++=+
T Consensus         4 ~~~~~iHE~iH~i~f~~f~~~   24 (107)
T pfam11667         4 LLLLILHELLHGIFFKLFGKS   24 (107)
T ss_pred             EEEHHHHHHHHHHHHHHCCCC
T ss_conf             984499999999688860156


No 133
>pfam01435 Peptidase_M48 Peptidase family M48.
Probab=29.88  E-value=26  Score=15.02  Aligned_cols=21  Identities=19%  Similarity=0.172  Sum_probs=11.1

Q ss_pred             HHHHHHCCCCCEEEEECCCCC
Q ss_conf             565300145662888878304
Q gi|254780773|r  130 PAAIAGVKKGDCIISLDGITV  150 (349)
Q Consensus       130 pA~~AGL~~GD~Il~InG~~V  150 (349)
                      -|+++|+....++.-+|+.++
T Consensus        40 l~~~~~~~~~~~v~v~~~~~~   60 (222)
T pfam01435        40 VADRLGLPAGPEVYVVDSPVR   60 (222)
T ss_pred             HHHHCCCCCCCEEEEECCCCC
T ss_conf             999769999987888748998


No 134
>COG2707 Predicted membrane protein [Function unknown]
Probab=29.57  E-value=37  Score=13.94  Aligned_cols=23  Identities=13%  Similarity=0.304  Sum_probs=12.8

Q ss_pred             HHHHHHCCCCCCHHHHHHHHHHH
Q ss_conf             99963064722436999999988
Q gi|254780773|r  288 GFMNLLPIPILDGGHLITFLLEM  310 (349)
Q Consensus       288 g~~NlLPip~LDGG~i~~~~~E~  310 (349)
                      |+|+=.|.=||++..++..+..+
T Consensus       125 a~fgGvpvGPlIaaGil~l~~~k  147 (151)
T COG2707         125 ALFGGVPVGPLIAAGILSLLVGK  147 (151)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHH
T ss_conf             33678324247888799999988


No 135
>PRK05015 aminopeptidase B; Provisional
Probab=29.56  E-value=7.9  Score=18.52  Aligned_cols=27  Identities=30%  Similarity=0.231  Sum_probs=22.5

Q ss_pred             CCCCCCHHHHHHCCCCCEEEEECCCCCC
Q ss_conf             2456755653001456628888783045
Q gi|254780773|r  124 NVSPASPAAIAGVKKGDCIISLDGITVS  151 (349)
Q Consensus       124 ~V~~~spA~~AGL~~GD~Il~InG~~V~  151 (349)
                      -..+|.|...| .+|||+|.+-||+.|+
T Consensus       242 ~~aENm~sg~A-~rPGDVit~~nGkTVE  268 (424)
T PRK05015        242 CCAENLISGNA-FKLGDIITYKNGKTVE  268 (424)
T ss_pred             EEECCCCCCCC-CCCHHHHHHCCCCEEE
T ss_conf             85505778778-8838889763997799


No 136
>PRK09194 prolyl-tRNA synthetase; Provisional
Probab=29.15  E-value=34  Score=14.17  Aligned_cols=21  Identities=29%  Similarity=0.661  Sum_probs=17.7

Q ss_pred             ECCCHHEEEEECCCEEEEEEE
Q ss_conf             068311278605980799997
Q gi|254780773|r   42 GFGPELIGITSRSGVRWKVSL   62 (349)
Q Consensus        42 Gfgp~l~~~~~k~~t~y~i~~   62 (349)
                      .+|+.+|++++|++.+|.+++
T Consensus        88 ~~g~el~r~kDR~~~~~~L~P  108 (570)
T PRK09194         88 KYGPELLRLKDRHGRDFVLGP  108 (570)
T ss_pred             HCCHHHEEEECCCCCEEEECC
T ss_conf             236134698527898565378


No 137
>cd03507 Delta12-FADS-like The Delta12 Fatty Acid Desaturase (Delta12-FADS)-like CD includes the integral-membrane enzymes, delta-12 acyl-lipid desaturases, oleate 12-hydroxylases, omega3 and omega6 fatty acid desaturases, and other related proteins, found in a wide range of organisms including higher plants, green algae, diatoms, nematodes, fungi, and bacteria. The expression of these proteins appears to be temperature dependent: decreases in temperature result in increased levels of fatty acid desaturation within membrane lipids subsequently altering cell membrane fluidity. An important enzyme for the production of polyunsaturates in plants is the oleate delta-12 desaturase (Arabidopsis FAD2) of the endoplasmic reticulum. This enzyme accepts l-acyl-2-oleoyl-sn-glycero-3-phosphocholine as substrate and requires NADH:cytochrome b oxidoreductase, cytochrome b, and oxygen for activity. FAD2 converts oleate(18:1) to linoleate (18:2) and is closely related to oleate 12-hydroxylase which cat
Probab=29.08  E-value=37  Score=13.88  Aligned_cols=27  Identities=15%  Similarity=0.032  Sum_probs=18.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999733779999984
Q gi|254780773|r    6 CFLLYTVSLIIIVVIHEFGHYMVARLC   32 (349)
Q Consensus         6 ~~~~~~~~l~~~v~iHE~GH~~~Ar~~   32 (349)
                      .++.+....++-+..||.||..+.|-.
T Consensus        37 ~~~~G~~~~~lfvl~HDa~H~s~~k~r   63 (222)
T cd03507          37 WIVQGLFLTGLFVLGHDCGHGSFSDNR   63 (222)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             999999999999999981323036881


No 138
>TIGR00819 ydaH AbgT transporter family; InterPro: IPR011540   The p-aminobenzoyl-glutamate transporter family includes two putative transporters, the AbgT protein of Escherichia coli and MtrF of Neisseria gonorrhoeae. AbgT expression is apparently cryptic in wild type cells, but when present on a high copy number plasmid, or when expressed at higher levels due to mutation, it allows utilization of p-aminobenzoyl-glutamate as a source of p-aminobenzoate for p-aminobenzoate auxotrophs . p-Aminobenzoate is a constituent of, and a precursor for, the biosynthesis of folic acid. It is not currently known if AbgT is naturally involved in transporting p-aminobenzoyl-glutamate, or if it only becomes involved when under altered regulation. MtrF is an inner membrane protein which, together with the MtrCDE efflux pump, is required for high-level resistance to hydrophobic antimicrobial agents in N. gonorrhoeae . Its role in this process is not known, but it has been suggested that it may be a component of the efflux pump which is dispensible for basal activity, but required for high-level activity ..
Probab=28.56  E-value=31  Score=14.48  Aligned_cols=30  Identities=23%  Similarity=0.331  Sum_probs=18.8

Q ss_pred             HHHHHHHHHHHHHHHHHHH---------HHCCCCCCHHH
Q ss_conf             0347899999999999996---------30647224369
Q gi|254780773|r  273 FNAYIAFLAMFSWAIGFMN---------LLPIPILDGGH  302 (349)
Q Consensus       273 ~~~~l~~~a~isi~Lg~~N---------lLPip~LDGG~  302 (349)
                      +..|..+.+++|+.+|=--         ..|+-.|-|-|
T Consensus       403 F~Gl~L~~~F~~l~I~S~SA~W~~~APIFVPMlML~Gy~  441 (527)
T TIGR00819       403 FVGLILLSAFLNLFIASASAIWAVLAPIFVPMLMLLGYA  441 (527)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             999999999999998615679988613788999860465


No 139
>TIGR01393 lepA GTP-binding protein LepA; InterPro: IPR006297   LepA (GUF1 in Saccaromyces) is a GTP-binding membrane protein related to EF-G and EF-Tu. Two types of phylogenetic tree, rooted by other GTP-binding proteins, suggest that eukaryotic homologs (including GUF1 of yeast) originated within the bacterial LepA family. The function of the proteins in this family are unknown. ; GO: 0005525 GTP binding.
Probab=28.51  E-value=20  Score=15.72  Aligned_cols=35  Identities=26%  Similarity=0.410  Sum_probs=23.1

Q ss_pred             CCEEEEEEEECCCHHEEEE-ECCCEEEEEEEEEECCEEECC
Q ss_conf             9750045530683112786-059807999977112111001
Q gi|254780773|r   33 NIRVLSFSVGFGPELIGIT-SRSGVRWKVSLIPLGGYVSFS   72 (349)
Q Consensus        33 gv~V~~FsiGfgp~l~~~~-~k~~t~y~i~~~PlGgyV~~~   72 (349)
                      |+.++.=|+     =+.|| .++|.+|.|.+|===|=|-|+
T Consensus        50 GITIK~qaV-----~l~Yk~~~DGe~Y~LNLIDTPGHVDFs   85 (598)
T TIGR01393        50 GITIKAQAV-----RLKYKVAKDGETYVLNLIDTPGHVDFS   85 (598)
T ss_pred             CCEEECCCE-----EEEEEEECCCCEEEEEEECCCCCCCCC
T ss_conf             820115634-----753375338878899645288972127


No 140
>pfam00262 Calreticulin Calreticulin family.
Probab=27.40  E-value=32  Score=14.34  Aligned_cols=25  Identities=20%  Similarity=0.424  Sum_probs=20.7

Q ss_pred             EECCEEECCCCCCCHHHHCCCCCCC
Q ss_conf             1121110012445506650368421
Q gi|254780773|r   64 PLGGYVSFSEDEKDMRSFFCAAPWK   88 (349)
Q Consensus        64 PlGgyV~~~~~e~~~~~f~~~~~~~   88 (349)
                      ==|||+|+-.++.|.+.|..++++.
T Consensus        87 CGGaYiKLl~~~~d~~~f~~~TpY~  111 (359)
T pfam00262        87 CGGAYIKLLSKDFDQKKFSGETPYT  111 (359)
T ss_pred             CCCEEEEECCCCCCHHHCCCCCCEE
T ss_conf             3530467525768987858998605


No 141
>TIGR02149 glgA_Coryne glycogen synthase, Corynebacterium family; InterPro: IPR011875    This entry describes Corynebacterium glutamicum GlgA and closely related proteins in other species. This enzyme is required for glycogen biosynthesis and appears to replace the distantly related IPR011835 from INTERPRO, family of ADP-glucose type glycogen synthase in Corynebacterium glutamicum, Mycobacterium tuberculosis, Bifidobacterium longum, and Streptomyces coelicolor ..
Probab=27.35  E-value=40  Score=13.68  Aligned_cols=72  Identities=21%  Similarity=0.265  Sum_probs=44.7

Q ss_pred             CHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCCCCC-CCCEEEEEECCCCEEEECC--CCCCCCCCCCCEEEEEEEECC
Q ss_conf             5565300145662888878304540011111014678-8631699965873131011--211005654310000122034
Q gi|254780773|r  129 SPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRENPL-HEISLVLYREHVGVLHLKV--MPRLQDTVDRFGIKRQVPSVG  205 (349)
Q Consensus       129 spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~~~g-~~v~i~v~R~~~~~~~~~v--~p~~~~~~~~~g~~~~~~~ig  205 (349)
                      |=+|+-+++.-|+|++|.+-.=   +|   +++..|+ ++-.+.|.|||.++.+..-  --...+..+++|+.++.|++=
T Consensus       152 sW~EktA~~aAd~vIAVS~amr---~D---iL~~YP~lD~~kv~Vv~NGId~~~y~~~~~~~~~~v~~~~Gid~~rP~~l  225 (416)
T TIGR02149       152 SWAEKTAIEAADRVIAVSGAMR---ED---ILKVYPDLDPEKVHVVYNGIDTKEYKPAADDDGNKVLDRYGIDRSRPYVL  225 (416)
T ss_pred             HHHHHHHHHHCCCEEEHHHHCH---HH---HHCCCCCCCCCCEEEEECCCCHHHHCCCCCCCHHHHHHHHCCCCCCCEEE
T ss_conf             4788889985040653111033---55---83158688846468886476457606888874113466326799888789


Q ss_pred             C
Q ss_conf             4
Q gi|254780773|r  206 I  206 (349)
Q Consensus       206 i  206 (349)
                      +
T Consensus       226 F  226 (416)
T TIGR02149       226 F  226 (416)
T ss_pred             E
T ss_conf             8


No 142
>COG4043 Preprotein translocase subunit Sec61beta [Intracellular    trafficking, secretion, and vesicular transport]
Probab=27.19  E-value=28  Score=14.70  Aligned_cols=37  Identities=30%  Similarity=0.623  Sum_probs=23.3

Q ss_pred             HHHHHCCCCCEEEEECC-------CCCCCCHHHHHHCCCCCCCCC
Q ss_conf             65300145662888878-------304540011111014678863
Q gi|254780773|r  131 AAIAGVKKGDCIISLDG-------ITVSAFEEVAPYVRENPLHEI  168 (349)
Q Consensus       131 A~~AGL~~GD~Il~InG-------~~V~s~~dl~~~i~~~~g~~v  168 (349)
                      ++..++++||+|+ .||       ..+.+++.+.+.+++-|-+.+
T Consensus        29 ~krr~ik~GD~Ii-F~~~~l~v~V~~vr~Y~tF~~mlreepiE~v   72 (111)
T COG4043          29 PKRRQIKPGDKII-FNGDKLKVEVIDVRVYDTFEEMLREEPIENV   72 (111)
T ss_pred             HHHCCCCCCCEEE-ECCCEEEEEEEEEEEHHHHHHHHHHCCHHHH
T ss_conf             7662789899899-8388467999987605689999985486651


No 143
>PRK07740 hypothetical protein; Provisional
Probab=27.01  E-value=19  Score=15.92  Aligned_cols=21  Identities=24%  Similarity=0.465  Sum_probs=13.5

Q ss_pred             HHHHCCC--CCEEEEECCCCCCC
Q ss_conf             5300145--66288887830454
Q gi|254780773|r  132 AIAGVKK--GDCIISLDGITVSA  152 (349)
Q Consensus       132 ~~AGL~~--GD~Il~InG~~V~s  152 (349)
                      |.-|+.|  ||+|++|-..++.+
T Consensus        65 ETTGl~p~~gD~IIeIgAVkv~~   87 (240)
T PRK07740         65 ETTGFSPDQGDEILSIAAVKTVG   87 (240)
T ss_pred             ECCCCCCCCCCEEEEEEEEEEEC
T ss_conf             58998988898789998999999


No 144
>TIGR01687 moaD_arch MoaD family protein; InterPro: IPR010038   Members of this family appear to be archaeal and bacterial (proteobacteria and Thermus) versions of MoaD, subunit 1 of molybdopterin converting factor..
Probab=26.71  E-value=37  Score=13.93  Aligned_cols=47  Identities=17%  Similarity=0.304  Sum_probs=26.9

Q ss_pred             CCCCCCCCCHHHHHHCCCC-------CEEEEECCC-CCCCCHHHHHHCCCCCCCCCE
Q ss_conf             0002456755653001456-------628888783-045400111110146788631
Q gi|254780773|r  121 VVSNVSPASPAAIAGVKKG-------DCIISLDGI-TVSAFEEVAPYVRENPLHEIS  169 (349)
Q Consensus       121 ~I~~V~~~spA~~AGL~~G-------D~Il~InG~-~V~s~~dl~~~i~~~~g~~v~  169 (349)
                      .+......+|-..+.+-..       +.++.+||+ .++..+++...+++  |++|.
T Consensus        31 ll~~l~~~Yp~~~~e~~~et~~~~~~~v~ilvNGran~~~l~GL~~~Lkd--GD~va   85 (93)
T TIGR01687        31 LLEELSSRYPKEFSELFKETGLGLVPNVIILVNGRANVDWLEGLETELKD--GDVVA   85 (93)
T ss_pred             HHHHHHHHCCHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCCCCCCCCCC--CCEEE
T ss_conf             89998861565566651477887646578985164143220365752327--87567


No 145
>pfam09101 Exotox-A_bind Exotoxin A binding. Members of this family are found in Pseudomonas aeruginosa exotoxin A, and are responsible for binding of the toxin to the alpha-2-macroglobulin receptor, with subsequent internalisation into endosomes. The domain adopts a thirteen-strand antiparallel beta jelly roll topology, which belongs to the Concanavalin A-like lectins/glucanases fold superfamily.
Probab=26.41  E-value=41  Score=13.57  Aligned_cols=13  Identities=31%  Similarity=0.399  Sum_probs=5.9

Q ss_pred             CCCEEEEECCCCC
Q ss_conf             5662888878304
Q gi|254780773|r  138 KGDCIISLDGITV  150 (349)
Q Consensus       138 ~GD~Il~InG~~V  150 (349)
                      |.|.|..-||+-|
T Consensus        31 p~~~i~dtngegv   43 (274)
T pfam09101        31 PDDAIADTNGEGV   43 (274)
T ss_pred             CCCCCCCCCCCCE
T ss_conf             9840007888737


No 146
>COG0442 ProS Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=26.26  E-value=41  Score=13.61  Aligned_cols=21  Identities=33%  Similarity=0.629  Sum_probs=18.2

Q ss_pred             ECCCHHEEEEECCCEEEEEEE
Q ss_conf             068311278605980799997
Q gi|254780773|r   42 GFGPELIGITSRSGVRWKVSL   62 (349)
Q Consensus        42 Gfgp~l~~~~~k~~t~y~i~~   62 (349)
                      ||||.+++.|++++-+|.+++
T Consensus        88 ~f~~El~~v~drg~~~l~L~P  108 (500)
T COG0442          88 GFGPELFRVKDRGDRPLALRP  108 (500)
T ss_pred             CCCHHHEEEECCCCCEEEECC
T ss_conf             036444899716996343578


No 147
>cd03510 Rhizobitoxine-FADS-like This CD includes the dihydrorhizobitoxine fatty acid desaturase (RtxC) characterized in Bradyrhizobium japonicum USDA110, and other related proteins. Dihydrorhizobitoxine desaturase is reported to be involved in the final step of rhizobitoxine biosynthesis. This domain family appears to be structurally related to the membrane fatty acid desaturases and the alkane hydroxylases. They all share in common extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. Comparison of sequences also reveals the existence of three regions of conserved histidine cluster motifs that contain eight histidine residues: HXXXH, HXX(X)HH, and HXXHH. These histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within homologs, stearoyl CoA desaturase and alkane hydroxylase.
Probab=24.96  E-value=44  Score=13.39  Aligned_cols=25  Identities=16%  Similarity=0.259  Sum_probs=17.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCEEEE
Q ss_conf             999999999733779999984975004
Q gi|254780773|r   12 VSLIIIVVIHEFGHYMVARLCNIRVLS   38 (349)
Q Consensus        12 ~~l~~~v~iHE~GH~~~Ar~~gv~V~~   38 (349)
                      ..-.+.+..||..|..+.|.-  +.++
T Consensus        31 ~~~~l~~~~Hea~H~~~~~~~--~~N~   55 (175)
T cd03510          31 RQRALAILMHDAAHGLLFRNR--RLND   55 (175)
T ss_pred             HHHHHHHHHHHHHHHHHCCCC--HHHH
T ss_conf             999999999999987204885--2999


No 148
>PRK04897 heat shock protein HtpX; Provisional
Probab=24.95  E-value=35  Score=14.04  Aligned_cols=17  Identities=12%  Similarity=0.219  Sum_probs=7.3

Q ss_pred             HHHHHCCCCCEEEEECC
Q ss_conf             65300145662888878
Q gi|254780773|r  131 AAIAGVKKGDCIISLDG  147 (349)
Q Consensus       131 A~~AGL~~GD~Il~InG  147 (349)
                      |...|..+.+..+.+..
T Consensus       110 AFatG~~~~~~~V~vt~  126 (298)
T PRK04897        110 AFATGSDPKNAAVAVTT  126 (298)
T ss_pred             EEEEECCCCCEEEEECH
T ss_conf             69950688887899617


No 149
>TIGR02737 caa3_CtaG cytochrome c oxidase assembly factor CtaG; InterPro: IPR014108   Members of this family are the CtaG protein required for assembly of active cytochrome c oxidase of the caa3 type, as found in Bacillus subtilis..
Probab=24.50  E-value=45  Score=13.33  Aligned_cols=36  Identities=19%  Similarity=0.296  Sum_probs=29.8

Q ss_pred             HHHHHHC---CCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9988827---86999999999999999999999999999
Q gi|254780773|r  307 LLEMIRG---KSLGVSVTRVITRMGLCIILFLFFLGIRN  342 (349)
Q Consensus       307 ~~E~i~g---r~i~~~~~~~~~~~g~~ll~~l~i~~~~n  342 (349)
                      +||++..   ||-.+++....+.==++|+++..+|.+|+
T Consensus       100 l~~~i~~klr~p~v~~v~k~~t~PliALLLFNGLFSlYH  138 (286)
T TIGR02737       100 LYEKIFEKLRRPFVKAVLKFLTKPLIALLLFNGLFSLYH  138 (286)
T ss_pred             HHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             899999885413899999997308999999845788754


No 150
>pfam02031 Peptidase_M7 Streptomyces extracellular neutral proteinase (M7) family.
Probab=24.01  E-value=19  Score=15.84  Aligned_cols=22  Identities=14%  Similarity=0.203  Sum_probs=8.4

Q ss_pred             CCHHHHHHCCCCCCCCCEEEEE
Q ss_conf             4001111101467886316999
Q gi|254780773|r  152 AFEEVAPYVRENPLHEISLVLY  173 (349)
Q Consensus       152 s~~dl~~~i~~~~g~~v~i~v~  173 (349)
                      .|++-+.-++-.++...++++.
T Consensus        24 iWN~sV~NV~L~~g~~a~~~~~   45 (132)
T pfam02031        24 IWNSSVSNVRLQEGSNADFTYY   45 (132)
T ss_pred             HHHCCCCCEEEECCCCCCEEEE
T ss_conf             8745577467504888777999


No 151
>PRK01827 thyA thymidylate synthase; Reviewed
Probab=23.83  E-value=46  Score=13.25  Aligned_cols=50  Identities=16%  Similarity=0.256  Sum_probs=34.2

Q ss_pred             HHHHHHCCCCCEEEEECCCCCCC--CHHHHHHCCCCCCCCCEEEEEECCCCE
Q ss_conf             56530014566288887830454--001111101467886316999658731
Q gi|254780773|r  130 PAAIAGVKKGDCIISLDGITVSA--FEEVAPYVRENPLHEISLVLYREHVGV  179 (349)
Q Consensus       130 pA~~AGL~~GD~Il~InG~~V~s--~~dl~~~i~~~~g~~v~i~v~R~~~~~  179 (349)
                      -|...|++||+-+-.+.+.-|..  .+.+.+.++..|-..-++.+.++-...
T Consensus       188 iA~~~gl~pg~l~~~~gD~HIY~nHie~vkeql~R~P~~~P~L~i~~~~~~i  239 (264)
T PRK01827        188 IAQQTGLKVGEFVHTIGDAHIYSNHLEQARLQLSREPRPLPKLVINPDIKSI  239 (264)
T ss_pred             HHHHHCCCCCEEEEEEEEEEEHHHHHHHHHHHHCCCCCCCCEEEECCCCCCC
T ss_conf             9998587477899992067865768999999856799999968968999971


No 152
>COG4273 Uncharacterized conserved protein [Function unknown]
Probab=23.60  E-value=47  Score=13.22  Aligned_cols=33  Identities=24%  Similarity=0.468  Sum_probs=25.6

Q ss_pred             CCCCCCCCCHHHHHHCCCCCEEEEECCCCCCCC
Q ss_conf             000245675565300145662888878304540
Q gi|254780773|r  121 VVSNVSPASPAAIAGVKKGDCIISLDGITVSAF  153 (349)
Q Consensus       121 ~I~~V~~~spA~~AGL~~GD~Il~InG~~V~s~  153 (349)
                      -+.+|-.++|+..--=+.|++|+.+||-|..-.
T Consensus        49 C~agvg~gv~~l~~~arsgrrIlalDGCp~~Ca   81 (135)
T COG4273          49 CTAGVGAGVPALVDAARSGRRILALDGCPLRCA   81 (135)
T ss_pred             EEECCCCCCHHHHHHHHCCCCEEEECCCHHHHH
T ss_conf             231015784889987643783697549737889


No 153
>TIGR03284 thym_sym thymidylate synthase. Members of this protein family are thymidylate synthase, an enzyme that produces dTMP from dUMP. In prokaryotes, its gene usually is found close to that for dihydrofolate reductase, and in some systems the two enzymes are found as a fusion protein. This model excludes a set of related proteins (TIGR03283) that appears to replace this family in archaeal methanogens, where tetrahydrofolate is replaced by tetrahydromethanopterin.
Probab=23.53  E-value=47  Score=13.21  Aligned_cols=50  Identities=18%  Similarity=0.235  Sum_probs=35.8

Q ss_pred             HHHHHHCCCCCEEEEECCCCCCC--CHHHHHHCCCCCCCCCEEEEEECCCCE
Q ss_conf             56530014566288887830454--001111101467886316999658731
Q gi|254780773|r  130 PAAIAGVKKGDCIISLDGITVSA--FEEVAPYVRENPLHEISLVLYREHVGV  179 (349)
Q Consensus       130 pA~~AGL~~GD~Il~InG~~V~s--~~dl~~~i~~~~g~~v~i~v~R~~~~~  179 (349)
                      -|...|++||+.|-.+.+.-|..  .+++.+.++..|-.--++.+.++-.++
T Consensus       220 iA~~~gl~pg~l~~~~gDaHIY~nHie~v~eql~R~P~~~P~L~i~~~~~~i  271 (296)
T TIGR03284       220 IAQETGLEVGEFVHTLGDAHLYSNHLEQAKLQLTREPRPLPKLKLNPEKKDI  271 (296)
T ss_pred             HHHHHCCCCCEEEEECCEEEEHHHHHHHHHHHHCCCCCCCCEEEECCCCCCC
T ss_conf             9998487577799991365767868999999966899999988967998863


No 154
>PRK03982 heat shock protein HtpX; Provisional
Probab=23.43  E-value=39  Score=13.72  Aligned_cols=31  Identities=10%  Similarity=0.118  Sum_probs=13.9

Q ss_pred             HHHHHCCCCCEEEEECCCCC--CCCHHHHHHCC
Q ss_conf             65300145662888878304--54001111101
Q gi|254780773|r  131 AAIAGVKKGDCIISLDGITV--SAFEEVAPYVR  161 (349)
Q Consensus       131 A~~AGL~~GD~Il~InG~~V--~s~~dl~~~i~  161 (349)
                      |...|..+.+..+.+..-=+  -+-+|+...+.
T Consensus        98 AFa~G~~~~~~~V~vt~GLL~~L~~dEl~aVlA  130 (288)
T PRK03982         98 AFATGRDPKHAVVAVTEGILNLLNEDELEGVIA  130 (288)
T ss_pred             EEEECCCCCCEEEEEEHHHHHHCCHHHHHHHHH
T ss_conf             687268999858996489987389999999999


No 155
>pfam04228 Zn_peptidase Putative neutral zinc metallopeptidase. Members of this family have a predicted zinc binding motif characteristic of neutral zinc metallopeptidases (Prosite:PDOC00129).
Probab=23.37  E-value=33  Score=14.25  Aligned_cols=14  Identities=29%  Similarity=0.380  Sum_probs=6.9

Q ss_pred             CCCCCEEEEEECCC
Q ss_conf             78863169996587
Q gi|254780773|r  164 PLHEISLVLYREHV  177 (349)
Q Consensus       164 ~g~~v~i~v~R~~~  177 (349)
                      +-++-++.+.++..
T Consensus       113 ~Y~~P~lvlf~~~~  126 (292)
T pfam04228       113 TYQPPTLVLYSGVT  126 (292)
T ss_pred             CCCCCEEEEECCCC
T ss_conf             88998589841886


No 156
>KOG3638 consensus
Probab=23.06  E-value=48  Score=13.15  Aligned_cols=61  Identities=16%  Similarity=0.337  Sum_probs=37.5

Q ss_pred             CCCCHHHHHHCCCCCEEEEECCCCCCCCHHHHHHCCCCCCCCCEEEEEECCCCEEEECCCCC
Q ss_conf             56755653001456628888783045400111110146788631699965873131011211
Q gi|254780773|r  126 SPASPAAIAGVKKGDCIISLDGITVSAFEEVAPYVRENPLHEISLVLYREHVGVLHLKVMPR  187 (349)
Q Consensus       126 ~~~spA~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~~~g~~v~i~v~R~~~~~~~~~v~p~  187 (349)
                      .++..-....|.+||.+++-|-.+-..++.+...+...|.+..++.+..-... .++.++|+
T Consensus       218 ~~~~~k~m~el~iGD~Vla~~~~~~~~~spv~~~lhR~pe~~~~F~~i~t~~g-~~l~lT~~  278 (414)
T KOG3638         218 EQGGRKRMDELSIGDYVLAADQGGQTTYSPVALFLHREPEARAEFVVIETEQG-ETLQLTPQ  278 (414)
T ss_pred             EECCEEECCCCCCCCEEECCCCCCCCCCCCHHHHHCCCCCCCCCCEEEECCCC-CCCCCCCC
T ss_conf             50642435778989847612668841137224221558544554168865777-64543420


No 157
>COG3127 Predicted ABC-type transport system involved in lysophospholipase L1 biosynthesis, permease component [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=22.90  E-value=47  Score=13.21  Aligned_cols=44  Identities=9%  Similarity=-0.145  Sum_probs=20.8

Q ss_pred             CHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             43699999998882786999999999999999999999999999
Q gi|254780773|r  299 DGGHLITFLLEMIRGKSLGVSVTRVITRMGLCIILFLFFLGIRN  342 (349)
Q Consensus       299 DGG~i~~~~~E~i~gr~i~~~~~~~~~~~g~~ll~~l~i~~~~n  342 (349)
                      -|+-....++-.++.=|..+.+.-..-.++++.-.++-+..+|.
T Consensus       773 ~~~aa~w~v~~~vf~lp~~pd~al~~~v~~l~~~~g~~l~G~w~  816 (829)
T COG3127         773 GAEAAAWVLVAKVFDLPWSPDWALWTIVLALVGAVGLGLAGGWL  816 (829)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             54589999999985588987568999999999999999877899


No 158
>TIGR03616 RutG pyrimidine utilization transport protein G. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the uracil-xanthine permease family defined by TIGR00801. As well as the The Nucleobase:Cation Symporter-2 (NCS2) Family (TC 2.A.40).
Probab=22.83  E-value=48  Score=13.12  Aligned_cols=84  Identities=10%  Similarity=0.227  Sum_probs=51.6

Q ss_pred             CCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHH------CCCCCHHHHHHHH
Q ss_conf             2246673012233345653050347899999999999996306472243699999998882------7869999999999
Q gi|254780773|r  252 LNQISGPVGIARIAKNFFDHGFNAYIAFLAMFSWAIGFMNLLPIPILDGGHLITFLLEMIR------GKSLGVSVTRVIT  325 (349)
Q Consensus       252 ~~~lsGPVgIa~~~~~~a~~G~~~~l~~~a~isi~Lg~~NlLPip~LDGG~i~~~~~E~i~------gr~i~~~~~~~~~  325 (349)
                      ..|=.|-+++-++.+.-.-+--..++-+++++.-.=+++..+|-|.|-|--++....=...      .++++.+..+.+.
T Consensus       307 fsqNiGvi~lT~V~SR~V~~~aa~ilillg~~pK~gal~~sIP~pVlGG~~lvmFGmIaa~Giril~~~~vd~~~~rNl~  386 (429)
T TIGR03616       307 YAENIGVMAVTKVYSTLVFVAAAVFAILLGFSPKFGALIHTIPVAVLGGASIVVFGLIAVAGARIWVQNKVDLTQNGNLI  386 (429)
T ss_pred             HHCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHH
T ss_conf             10122355422766409999999999999988999999985878788699999999999999999997046868875014


Q ss_pred             HHHHHHHHHH
Q ss_conf             9999999999
Q gi|254780773|r  326 RMGLCIILFL  335 (349)
Q Consensus       326 ~~g~~ll~~l  335 (349)
                      .+++.+.+++
T Consensus       387 iva~sl~~G~  396 (429)
T TIGR03616       387 MVAVTLVLGA  396 (429)
T ss_pred             HHHHHHHHHC
T ss_conf             6899999856


No 159
>KOG0662 consensus
Probab=22.13  E-value=38  Score=13.86  Aligned_cols=11  Identities=18%  Similarity=0.320  Sum_probs=5.2

Q ss_pred             CCCEEEEEECC
Q ss_conf             86316999658
Q gi|254780773|r  166 HEISLVLYREH  176 (349)
Q Consensus       166 ~~v~i~v~R~~  176 (349)
                      ++.++.+.|+|
T Consensus       128 kpqnllin~ng  138 (292)
T KOG0662         128 KPQNLLINRNG  138 (292)
T ss_pred             CCCEEEECCCC
T ss_conf             71107753688


No 160
>pfam00303 Thymidylat_synt Thymidylate synthase.
Probab=22.11  E-value=50  Score=13.02  Aligned_cols=47  Identities=17%  Similarity=0.269  Sum_probs=31.5

Q ss_pred             HHHHHHCCCCCEEEEECCCCCCC--CHHHHHHCCCCCCCCCEEEEEECC
Q ss_conf             56530014566288887830454--001111101467886316999658
Q gi|254780773|r  130 PAAIAGVKKGDCIISLDGITVSA--FEEVAPYVRENPLHEISLVLYREH  176 (349)
Q Consensus       130 pA~~AGL~~GD~Il~InG~~V~s--~~dl~~~i~~~~g~~v~i~v~R~~  176 (349)
                      -|...|+++|+.+..+++.-|..  .+.+.+.++..|...-++.+.++.
T Consensus       186 iA~~~gl~~G~~~~~~gd~HIY~~h~~~v~~ql~r~p~~~P~l~i~~~~  234 (262)
T pfam00303       186 IAQVTGLEPGEFIHTIGDAHIYENHVDQVKEQLSREPRPFPKLKINPEV  234 (262)
T ss_pred             HHHHHCCCCCEEEEEEEEEEEHHHHHHHHHHHHCCCCCCCCEEEECCCC
T ss_conf             9998578678899993355647869999999956799999978967998


No 161
>pfam03926 consensus
Probab=21.79  E-value=50  Score=12.98  Aligned_cols=16  Identities=38%  Similarity=0.488  Sum_probs=7.1

Q ss_pred             HHHHHHHHHHHHHHHH
Q ss_conf             9999733779999984
Q gi|254780773|r   17 IVVIHEFGHYMVARLC   32 (349)
Q Consensus        17 ~v~iHE~GH~~~Ar~~   32 (349)
                      -|+-||+-||.+=...
T Consensus        59 ~vI~HEL~Hy~lh~~~   74 (149)
T pfam03926        59 QVVPHELAHLHLYQLF   74 (149)
T ss_pred             HHHHHHHHHHHHHHHC
T ss_conf             3179999999999986


No 162
>COG2738 Predicted Zn-dependent protease [General function prediction only]
Probab=21.67  E-value=51  Score=12.96  Aligned_cols=35  Identities=17%  Similarity=0.378  Sum_probs=23.4

Q ss_pred             HHHHHHHHHHHHH-HHHHHCCCC-CCHHHHHHHHHHH
Q ss_conf             7899999999999-996306472-2436999999988
Q gi|254780773|r  276 YIAFLAMFSWAIG-FMNLLPIPI-LDGGHLITFLLEM  310 (349)
Q Consensus       276 ~l~~~a~isi~Lg-~~NlLPip~-LDGG~i~~~~~E~  310 (349)
                      .+.|++.+=++.+ +|+|.-+|. .|-.+=..-.+|.
T Consensus       144 ~ll~lGiiLfs~aVLF~lvTLPVEFDAS~RA~~~l~~  180 (226)
T COG2738         144 GLLWLGIILFSAAVLFQLVTLPVEFDASSRALKQLES  180 (226)
T ss_pred             HHHHHHHHHHHHHHHHHEEECCEEECCHHHHHHHHHH
T ss_conf             8999999999999998223123121511889999984


No 163
>KOG2090 consensus
Probab=21.58  E-value=48  Score=13.12  Aligned_cols=21  Identities=19%  Similarity=0.257  Sum_probs=8.3

Q ss_pred             HCCCCCCHHHHHHHHHHHHHC
Q ss_conf             064722436999999988827
Q gi|254780773|r  293 LPIPILDGGHLITFLLEMIRG  313 (349)
Q Consensus       293 LPip~LDGG~i~~~~~E~i~g  313 (349)
                      .|-+.-|--+++..+-++..|
T Consensus       581 ~p~~~~~~td~~~~v~rk~~~  601 (704)
T KOG2090         581 CPLIAEDTTDLLSEVKRKFSG  601 (704)
T ss_pred             CCCCCCCHHHHHHHHHHHCCC
T ss_conf             456554568999999986068


No 164
>PRK02391 heat shock protein HtpX; Provisional
Probab=21.11  E-value=47  Score=13.20  Aligned_cols=31  Identities=13%  Similarity=0.100  Sum_probs=14.5

Q ss_pred             HHHHHCCCCCEEEEECCC--CCCCCHHHHHHCC
Q ss_conf             653001456628888783--0454001111101
Q gi|254780773|r  131 AAIAGVKKGDCIISLDGI--TVSAFEEVAPYVR  161 (349)
Q Consensus       131 A~~AGL~~GD~Il~InG~--~V~s~~dl~~~i~  161 (349)
                      |-..|..+.+.++.+.--  +.-+-+|+..++.
T Consensus       107 AFAtG~~~~~a~V~vT~GLL~~L~~dEL~aVLA  139 (297)
T PRK02391        107 AFATGRSPKNAVVCVTTGLLRRLDPEELEAVLA  139 (297)
T ss_pred             EEEECCCCCCEEEEECHHHHHHCCHHHHHHHHH
T ss_conf             257458998769997579886399999999999


No 165
>PRK10720 uracil transporter; Provisional
Probab=20.82  E-value=53  Score=12.85  Aligned_cols=83  Identities=12%  Similarity=0.288  Sum_probs=50.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHH-H-----HHHHCCCCCHHHHHHH
Q ss_conf             022466730122333456530503478999999999999963064722436999999-9-----8882786999999999
Q gi|254780773|r  251 RLNQISGPVGIARIAKNFFDHGFNAYIAFLAMFSWAIGFMNLLPIPILDGGHLITFL-L-----EMIRGKSLGVSVTRVI  324 (349)
Q Consensus       251 ~~~~lsGPVgIa~~~~~~a~~G~~~~l~~~a~isi~Lg~~NlLPip~LDGG~i~~~~-~-----E~i~gr~i~~~~~~~~  324 (349)
                      +..|=.|-+++-++.+.-.-+.-..++-.++++.-.=+++..+|-|.+-|-.++..- +     ..+...+++....+..
T Consensus       287 TyseNiGvi~lT~V~SR~V~~~aavilIllg~~pK~galiasIP~pVlGG~~ivlFG~Iaa~Gir~L~~~~vd~~~~rNl  366 (429)
T PRK10720        287 TYGENIGVMAITRVYSTWVIGGAAIFAILLSCVGKLAAAIQSIPLPVMGGVSLLLYGVIGASGIRVLIESKVDYNKAQNL  366 (429)
T ss_pred             CCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCH
T ss_conf             43565121445045510879999999999986699999998687878869999999999999999999714776888601


Q ss_pred             HHHHHHHHH
Q ss_conf             999999999
Q gi|254780773|r  325 TRMGLCIIL  333 (349)
Q Consensus       325 ~~~g~~ll~  333 (349)
                      ..++..+.+
T Consensus       367 ~ivav~l~~  375 (429)
T PRK10720        367 ILTSVILII  375 (429)
T ss_pred             HHHHHHHHH
T ss_conf             453999996


No 166
>PRK05973 replicative DNA helicase; Provisional
Probab=20.81  E-value=50  Score=12.98  Aligned_cols=22  Identities=18%  Similarity=0.453  Sum_probs=12.0

Q ss_pred             CCCCCCCHHHH--HHCCCCCEEEE
Q ss_conf             02456755653--00145662888
Q gi|254780773|r  123 SNVSPASPAAI--AGVKKGDCIIS  144 (349)
Q Consensus       123 ~~V~~~spA~~--AGL~~GD~Il~  144 (349)
                      ......+||.+  .||+|||.|+=
T Consensus        46 ~~~~~~~pa~~l~~gLqPGDLIIl   69 (237)
T PRK05973         46 AKAAATTPAEELFGQLRPGDLVLL   69 (237)
T ss_pred             HHHCCCCCHHHHHCCCCCCCEEEE
T ss_conf             763036958998568998677999


No 167
>PRK11067 outer membrane protein assembly factor YaeT; Provisional
Probab=20.76  E-value=53  Score=12.84  Aligned_cols=11  Identities=27%  Similarity=0.510  Sum_probs=3.9

Q ss_pred             CEEEEEEEEEE
Q ss_conf             80799997711
Q gi|254780773|r   55 GVRWKVSLIPL   65 (349)
Q Consensus        55 ~t~y~i~~~Pl   65 (349)
                      |-.|.++-+=+
T Consensus       263 G~~Y~~g~i~~  273 (801)
T PRK11067        263 GDQYKLSGVQV  273 (801)
T ss_pred             CCEEEEEEEEE
T ss_conf             97498723799


No 168
>PHA01511 coat protein
Probab=20.62  E-value=53  Score=12.82  Aligned_cols=67  Identities=18%  Similarity=0.215  Sum_probs=37.5

Q ss_pred             HHHHCCCCCEEEEECCCCCCCCHHHHHHCCCCCCCCCEEEEEECCCCEEEECCCCCCCCCCCCCEEEEEEEECC
Q ss_conf             53001456628888783045400111110146788631699965873131011211005654310000122034
Q gi|254780773|r  132 AIAGVKKGDCIISLDGITVSAFEEVAPYVRENPLHEISLVLYREHVGVLHLKVMPRLQDTVDRFGIKRQVPSVG  205 (349)
Q Consensus       132 ~~AGL~~GD~Il~InG~~V~s~~dl~~~i~~~~g~~v~i~v~R~~~~~~~~~v~p~~~~~~~~~g~~~~~~~ig  205 (349)
                      +.+|++.||.+.      +.....+..+-++.-++..++.|.|--.. .++++.|+.....+......+.++-.
T Consensus       263 aTtg~~~Gd~ft------iaGV~~~h~itK~~tgq~~tFrVv~~~sg-tti~I~Pkpi~~d~~~~s~~~kaYaN  329 (430)
T PHA01511        263 ATTGLKRGDKIS------FTGVKFLGQMAKNVLAQDATFSVVRVVDG-THVEITPKPVALDDVSLSPEQRAYAN  329 (430)
T ss_pred             EECCCCCCCEEE------EECHHHHHHHHHHCCCCCCEEEEEEECCC-CEEEEECCCCCCCCCCCCHHHHCCCC
T ss_conf             404742144578------81136887753520488625899996158-66797024422666776612201244


No 169
>PRK05457 heat shock protein HtpX; Provisional
Probab=20.61  E-value=45  Score=13.31  Aligned_cols=31  Identities=16%  Similarity=0.210  Sum_probs=13.9

Q ss_pred             HHHHHCCCCCEEEEECCCC--CCCCHHHHHHCC
Q ss_conf             6530014566288887830--454001111101
Q gi|254780773|r  131 AAIAGVKKGDCIISLDGIT--VSAFEEVAPYVR  161 (349)
Q Consensus       131 A~~AGL~~GD~Il~InG~~--V~s~~dl~~~i~  161 (349)
                      |-.+|-.+.+-.+.+.---  .-|-+|+...+.
T Consensus       107 AFAtG~~p~~a~VaVT~GLL~~L~~dELegVlA  139 (289)
T PRK05457        107 AFATGASKNNSLVAVSTGLLQNMSRDEVEAVLA  139 (289)
T ss_pred             EEECCCCCCCEEEEECHHHHHHCCHHHHHHHHH
T ss_conf             014268988879998579997679999999999


No 170
>TIGR02299 HpaE 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase; InterPro: IPR011985    This entry represents the dehydrogenase responsible for the conversion of 5-carboxymethyl-2-hydroxymuconate semialdehyde to 5-carboxymethyl-2-hydroxymuconate (a tricarboxylic acid). This is the step in the degradation of 4-hydroxyphenylacetic acid via homoprotocatechuate following the oxidative opening of the aromatic ring ..
Probab=20.23  E-value=28  Score=14.69  Aligned_cols=18  Identities=11%  Similarity=0.268  Sum_probs=7.4

Q ss_pred             CCCCCCCCCCHHHHHHHH
Q ss_conf             002246673012233345
Q gi|254780773|r  250 TRLNQISGPVGIARIAKN  267 (349)
Q Consensus       250 ~~~~~lsGPVgIa~~~~~  267 (349)
                      .+..+|.-|=|=.+.+|.
T Consensus       445 ~NVR~Lp~PFGG~K~SG~  462 (494)
T TIGR02299       445 QNVRDLPTPFGGVKASGI  462 (494)
T ss_pred             CCCCCCCCCCCCCCCCCC
T ss_conf             455787357886178867


Done!