Query         gi|254781112|ref|YP_003065525.1| putative amino acid-binding periplasmic ABC transporter protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 274
No_of_seqs    120 out of 6677
Neff          9.2 
Searched_HMMs 39220
Date          Mon May 30 05:04:49 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781112.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK11260 cystine transporter s 100.0       0       0  340.4  21.1  257    5-266     1-263 (264)
  2 PRK10797 glutamate and asparta 100.0       0       0  329.7  19.6  258    8-269     3-278 (302)
  3 PRK09495 glnH glutamine ABC tr 100.0       0       0  320.9  20.0  220   39-264    23-245 (247)
  4 TIGR01096 3A0103s03R lysine-ar 100.0 2.9E-44       0  293.3  16.4  232   28-261    14-333 (333)
  5 PRK11917 bifunctional adhesin/ 100.0 7.4E-44       0  290.9  18.1  244    8-261     3-258 (259)
  6 pfam00497 SBP_bac_3 Bacterial  100.0 8.9E-42       0  278.1  16.6  216   43-263     1-224 (224)
  7 smart00062 PBPb Bacterial peri 100.0 3.9E-41 1.4E-45  274.1  16.6  216   42-261     1-219 (219)
  8 cd00134 PBPb Bacterial peripla 100.0   4E-41 1.4E-45  274.0  15.5  215   43-261     1-218 (218)
  9 TIGR02995 ectoine_ehuB ectoine 100.0 1.8E-34 4.6E-39  232.8  12.7  235   27-264    20-271 (285)
 10 PRK09959 hybrid sensory histid 100.0 5.7E-33 1.5E-37  223.6  14.3  223   36-264   297-522 (1197)
 11 COG0834 HisJ ABC-type amino ac 100.0 2.7E-31 6.9E-36  213.2  18.8  227   35-266    28-268 (275)
 12 PRK10859 putative transglycosy 100.0 4.2E-31 1.1E-35  212.0  12.4  222   35-264    37-269 (507)
 13 PRK09959 hybrid sensory histid  99.9 1.3E-25 3.3E-30  178.1  15.9  223   37-264    52-280 (1197)
 14 COG4623 Predicted soluble lyti  99.9 3.2E-23 8.2E-28  163.3  11.7  222   34-263    16-248 (473)
 15 KOG1052 consensus               99.6 8.1E-14 2.1E-18  105.1  13.2  226   40-273   215-581 (656)
 16 TIGR03431 PhnD phosphonate ABC  99.5 1.8E-13 4.5E-18  103.1  10.8  207   40-260    26-263 (288)
 17 KOG1053 consensus               99.5 2.9E-14 7.3E-19  107.9   6.0  196   66-262   466-806 (1258)
 18 TIGR01098 3A0109s03R phosphona  99.4 1.3E-12 3.2E-17   97.8   7.4  195   40-246    50-298 (299)
 19 TIGR02285 TIGR02285 conserved   99.4 1.2E-11 3.1E-16   91.7  11.4  222   40-264    18-288 (293)
 20 COG3221 PhnD ABC-type phosphat  99.4   7E-12 1.8E-16   93.2  10.2  211   36-258    30-269 (299)
 21 pfam00060 Lig_chan Ligand-gate  99.2 1.9E-10 4.7E-15   84.4   9.3  126  134-263    95-238 (270)
 22 PRK11553 alkanesulfonate trans  99.2 9.2E-10 2.3E-14   80.1  12.4  211   37-264    23-258 (314)
 23 smart00079 PBPe Eukaryotic hom  99.1 4.4E-10 1.1E-14   82.1   8.8  116  141-262     2-133 (134)
 24 KOG1054 consensus               99.1 1.5E-10 3.7E-15   85.0   5.7  218   40-261   416-790 (897)
 25 KOG4440 consensus               99.1 1.1E-10 2.7E-15   85.8   3.4  192   66-263   463-806 (993)
 26 TIGR03427 ABC_peri_uca ABC tra  98.9 7.1E-09 1.8E-13   74.6   8.5  209   40-264     1-239 (328)
 27 PRK11480 tauA taurine transpor  98.8 1.9E-08   5E-13   71.9   6.7  206   39-265    21-260 (320)
 28 pfam09084 NMT1 NMT1/THI5 like.  98.6 2.1E-08 5.4E-13   71.6   3.4  128   74-203    13-155 (216)
 29 COG0715 TauA ABC-type nitrate/  98.6 4.7E-07 1.2E-11   63.3  10.3  190   72-264    50-268 (335)
 30 PRK09861 cytoplasmic membrane   98.2   1E-05 2.6E-10   55.0   8.8  202   36-265    27-268 (272)
 31 PRK11063 metQ DL-methionine tr  98.2   2E-05 5.2E-10   53.2   9.8  199   37-263    27-265 (271)
 32 COG0725 ModA ABC-type molybdat  98.1 2.2E-05 5.7E-10   53.0   8.8  202   36-260    25-252 (258)
 33 COG4521 TauA ABC-type taurine   98.1 0.00022 5.5E-09   46.8  13.1  190   42-247    30-239 (334)
 34 PRK10677 modA molybdate transp  98.1 7.6E-05 1.9E-09   49.7  10.3  202   35-260    21-252 (257)
 35 COG2358 Imp TRAP-type uncharac  97.9 1.1E-05 2.7E-10   54.9   3.8  145   38-194    23-192 (321)
 36 COG1638 DctP TRAP-type C4-dica  97.8 0.00021 5.3E-09   47.0   8.6  173   70-247    47-265 (332)
 37 TIGR01729 taurine_ABC_bnd taur  97.7 0.00012   3E-09   48.5   7.0  174   73-249    21-215 (304)
 38 PRK09501 potD spermidine/putre  97.7  0.0006 1.5E-08   44.1   9.4  210   29-263    15-293 (348)
 39 COG1464 NlpA ABC-type metal io  97.6 0.00016 4.2E-09   47.6   5.7  198   41-266    29-266 (268)
 40 COG1732 OpuBC Periplasmic glyc  97.6 4.8E-05 1.2E-09   50.9   2.6  203   37-259    29-281 (300)
 41 COG4588 AcfC Accessory coloniz  97.5 0.00045 1.2E-08   44.9   7.6  180   68-260    34-248 (252)
 42 pfam03401 Bug Tripartite trica  97.3  0.0012 3.1E-08   42.2   7.3  141  123-265    73-246 (274)
 43 pfam03180 Lipoprotein_9 NLPA l  97.1 0.00065 1.7E-08   43.9   4.0  194   43-265     1-232 (236)
 44 CHL00180 rbcR LysR transcripti  97.1    0.02 5.1E-07   34.7  11.5  177   38-233    92-286 (307)
 45 PRK09791 putative DNA-binding   97.1  0.0073 1.9E-07   37.4   9.1  190   39-248    93-294 (302)
 46 pfam03466 LysR_substrate LysR   97.0  0.0024 6.2E-08   40.3   6.3  174   39-233     4-191 (209)
 47 COG4663 FcbT1 TRAP-type mannit  96.9   0.012 3.1E-07   36.0   9.5   72   30-108    24-101 (363)
 48 PRK11151 DNA-binding transcrip  96.8   0.014 3.7E-07   35.6   9.2  188   40-249    90-291 (305)
 49 PRK12684 transcriptional regul  96.8   0.021 5.3E-07   34.6  10.0  202   39-263    91-306 (313)
 50 PRK11242 DNA-binding transcrip  96.8  0.0094 2.4E-07   36.7   8.2  171   39-233    89-274 (292)
 51 PRK12683 transcriptional regul  96.8   0.044 1.1E-06   32.6  11.7  174   39-233    91-278 (308)
 52 PRK12679 cbl transcriptional r  96.8   0.045 1.1E-06   32.5  11.6  189   39-249    91-293 (316)
 53 pfam04069 OpuAC Substrate bind  96.7   0.004   1E-07   39.0   5.6  167   70-242    17-224 (256)
 54 pfam03480 SBP_bac_7 Bacterial   96.7  0.0012   3E-08   42.3   2.9  103  140-247   126-233 (285)
 55 PRK12682 transcriptional regul  96.2     0.1 2.6E-06   30.3  11.6  187   39-247    91-291 (309)
 56 PRK12681 cysB transcriptional   96.2   0.067 1.7E-06   31.4   9.1  174   39-233    91-278 (324)
 57 PRK10341 DNA-binding transcrip  96.0   0.056 1.4E-06   31.9   8.1  157   70-233   113-281 (312)
 58 COG3181 Uncharacterized protei  96.0   0.039   1E-06   32.9   7.2  133  125-259   119-284 (319)
 59 TIGR01728 SsuA_fam ABC transpo  95.9   0.024 6.2E-07   34.2   5.9  134   72-207    22-178 (311)
 60 PRK12680 transcriptional regul  95.8    0.15 3.8E-06   29.3   9.6  201   39-264    91-307 (327)
 61 TIGR03414 ABC_choline_bnd chol  95.7   0.036 9.3E-07   33.1   6.1  213   36-264     3-263 (290)
 62 PRK11074 putative DNA-binding   95.7     0.1 2.6E-06   30.3   8.2  199   39-261    90-299 (300)
 63 PRK04168 hypothetical protein;  95.6   0.043 1.1E-06   32.6   6.2  211   36-266    28-318 (336)
 64 PRK11062 nhaR transcriptional   95.6    0.13 3.3E-06   29.6   8.6  188   40-246    92-292 (296)
 65 PRK09755 putative binding prot  95.6    0.19 4.9E-06   28.6   9.9   82  171-265   244-330 (535)
 66 PRK10682 putrescine transporte  95.4    0.22 5.6E-06   28.2  11.0  208   34-263    23-314 (370)
 67 TIGR01256 modA molybdate ABC t  95.3   0.045 1.2E-06   32.5   5.4  183   71-260    10-224 (225)
 68 COG1910 Periplasmic molybdate-  95.0   0.051 1.3E-06   32.2   5.0  156   78-245    14-198 (223)
 69 PRK00489 hisG ATP phosphoribos  94.9   0.064 1.6E-06   31.6   5.3  170   85-266    47-223 (287)
 70 PRK11119 proX glycine betaine   94.5   0.096 2.4E-06   30.5   5.3  116   40-169    29-177 (332)
 71 PRK09986 DNA-binding transcrip  94.4    0.29 7.5E-06   27.5   7.6  184   39-247    79-276 (278)
 72 TIGR03061 pip_yhgE_Nterm YhgE/  94.3    0.19 4.9E-06   28.6   6.5   61   40-109    41-103 (164)
 73 TIGR00787 dctP TRAP transporte  94.3   0.045 1.1E-06   32.5   3.2  123  124-255   118-245 (267)
 74 COG4143 TbpA ABC-type thiamine  94.2    0.44 1.1E-05   26.4   8.2  216   40-271    25-300 (336)
 75 COG0687 PotD Spermidine/putres  94.1    0.46 1.2E-05   26.3  13.0  187   72-263    47-307 (363)
 76 PRK11205 tbpA thiamine transpo  93.9    0.51 1.3E-05   26.0   8.4  206   38-258    16-275 (326)
 77 PRK11013 DNA-binding transcrip  93.4    0.61 1.6E-05   25.5   9.6  173   39-233    92-277 (309)
 78 PRK11233 nitrogen assimilation  93.0    0.71 1.8E-05   25.1  10.8  193   39-250    89-293 (305)
 79 TIGR03339 phn_lysR aminoethylp  92.7    0.77   2E-05   24.9   8.6  175   40-240    86-276 (279)
 80 COG1511 Predicted membrane pro  92.7    0.78   2E-05   24.8   8.0   57   53-109    50-108 (780)
 81 COG2113 ProX ABC-type proline/  92.7    0.15 3.9E-06   29.2   3.8  131   36-179    26-181 (302)
 82 TIGR00212 hemC porphobilinogen  92.3    0.57 1.4E-05   25.7   6.3  132   93-242    62-218 (312)
 83 PRK03537 hypothetical protein;  92.2    0.47 1.2E-05   26.2   5.8  135  123-262    17-183 (188)
 84 PRK09508 leuO leucine transcri  91.6     1.1 2.7E-05   24.0   8.7  155   71-232   129-294 (314)
 85 PRK01066 porphobilinogen deami  91.6     1.1 2.7E-05   24.0   9.3  136   93-241    80-227 (234)
 86 pfam10613 Lig_chan-Glu_bd Liga  91.4   0.045 1.2E-06   32.5  -0.2   31   60-90     13-43  (65)
 87 PRK11716 DNA-binding transcrip  91.0     1.2 3.1E-05   23.6   7.4  175   39-233    65-253 (269)
 88 PRK09906 DNA-binding transcrip  90.7     1.3 3.3E-05   23.5   8.1  173   39-233    88-275 (296)
 89 TIGR03261 phnS2 putative 2-ami  89.7     1.6   4E-05   23.0   7.8  190   71-266    37-288 (334)
 90 TIGR02424 TF_pcaQ pca operon t  88.3     0.3 7.8E-06   27.4   2.0  192   37-247    89-297 (300)
 91 pfam00405 Transferrin Transfer  87.7     2.1 5.5E-05   22.1   6.3  113   88-202    34-212 (328)
 92 pfam01379 Porphobil_deam Porph  86.7     1.8 4.5E-05   22.6   5.2  138   93-240    61-212 (213)
 93 PRK00072 hemC porphobilinogen   86.3     2.6 6.5E-05   21.6   6.1  158   93-265    64-241 (300)
 94 COG0040 HisG ATP phosphoribosy  86.0     1.4 3.5E-05   23.4   4.3  149   91-249    52-211 (290)
 95 PRK10852 thiosulfate transport  85.6     2.8   7E-05   21.4   6.2  135  122-261   115-284 (338)
 96 PRK01686 hisG ATP phosphoribos  85.5    0.84 2.1E-05   24.7   3.0  152   85-248    48-205 (212)
 97 pfam01634 HisG ATP phosphoribo  84.9     1.3 3.4E-05   23.4   3.8  146   93-248     5-158 (161)
 98 PRK10752 sulfate transporter s  84.5     3.1 7.9E-05   21.1   6.5  182   71-261    42-278 (329)
 99 cd00494 HMBS Hydroxymethylbila  83.9     3.3 8.4E-05   21.0   6.7  159   92-265    59-237 (292)
100 PRK09474 malE maltose ABC tran  82.2     1.1 2.9E-05   23.8   2.6  108   28-148    16-157 (394)
101 COG2107 Predicted periplasmic   81.9     1.2 2.9E-05   23.8   2.5  100  145-246    91-198 (272)
102 PRK11482 putative DNA-binding   80.2     4.5 0.00011   20.1   7.0  152   71-232    83-248 (266)
103 PRK11466 hybrid sensory histid  79.0     4.9 0.00013   19.9   5.5   76  116-196   653-734 (912)
104 PRK10837 putative DNA-binding   78.4     5.1 0.00013   19.8   8.9  174   39-233    87-273 (291)
105 TIGR03227 PhnS 2-aminoethylpho  77.9     3.7 9.4E-05   20.7   4.0  136   71-206    56-244 (367)
106 PRK10216 DNA-binding transcrip  75.9       6 0.00015   19.3   8.1  135   71-206    83-236 (288)
107 PRK03601 transcriptional regul  69.0     8.7 0.00022   18.4   7.6  177   39-245    87-268 (275)
108 COG0181 HemC Porphobilinogen d  68.8     8.8 0.00023   18.3   6.3  156   93-264    63-239 (307)
109 PRK10094 DNA-binding transcrip  68.1     9.1 0.00023   18.2   8.1  183   40-241    91-287 (308)
110 PRK13583 hisG ATP phosphoribos  67.0     7.4 0.00019   18.8   3.5  121   85-208    48-190 (226)
111 PRK00178 tolB translocation pr  66.6     2.8 7.2E-05   21.4   1.3   40   41-90     34-73  (433)
112 PRK04281 consensus              65.5     5.7 0.00014   19.5   2.6   41   67-107    60-102 (254)
113 PRK00830 consensus              64.2     4.9 0.00013   19.9   2.1   41   67-107    64-106 (273)
114 TIGR02743 TraW type-F conjugat  62.7     8.8 0.00022   18.3   3.2   66   70-138    34-111 (217)
115 COG2998 TupB ABC-type tungstat  62.1     6.2 0.00016   19.3   2.3   93   37-143    26-125 (280)
116 PRK01033 imidazole glycerol ph  61.5     6.3 0.00016   19.2   2.3   41   67-107    60-102 (253)
117 PRK11091 aerobic respiration c  61.5      12 0.00031   17.5   5.5   52  145-196   521-577 (779)
118 TIGR02294 nickel_nikA nickel A  60.4     5.8 0.00015   19.4   1.9   78  170-247   201-287 (513)
119 PRK10693 response regulator of  58.2     9.6 0.00024   18.1   2.7   34   72-106    22-55  (337)
120 PRK02145 consensus              56.5     7.6 0.00019   18.7   2.0   42   67-108    61-104 (257)
121 PRK03629 tolB translocation pr  56.4     4.6 0.00012   20.1   0.8   36   42-87     34-69  (430)
122 PRK01742 tolB translocation pr  55.1     7.2 0.00018   18.9   1.7   20   70-89     54-73  (430)
123 PRK01659 consensus              55.1     9.6 0.00025   18.1   2.3   42   67-108    60-103 (252)
124 PRK10653 D-ribose transporter   53.5      11 0.00029   17.6   2.5   61   36-107    22-87  (295)
125 PRK13738 conjugal transfer pil  53.5      17 0.00042   16.6   4.0   55   26-101     7-62  (210)
126 PRK11899 prephenate dehydratas  53.5     9.6 0.00024   18.1   2.1  113   84-202    28-157 (284)
127 TIGR02144 LysX_arch Lysine bio  53.5     7.7  0.0002   18.7   1.6   34   68-101   110-145 (289)
128 pfam06510 DUF1102 Protein of u  53.2      16  0.0004   16.8   3.2   10   53-64     52-61  (183)
129 TIGR00070 hisG ATP phosphoribo  52.7     4.7 0.00012   20.0   0.4  147   96-250    58-239 (317)
130 TIGR03572 WbuZ glycosyl amidat  52.3      11 0.00027   17.8   2.2   41   67-107    60-102 (232)
131 PRK02621 consensus              52.1      12  0.0003   17.6   2.3   42   67-108    60-103 (254)
132 pfam00800 PDT Prephenate dehyd  51.6     8.9 0.00023   18.3   1.7  117   80-202    19-154 (181)
133 PRK11898 prephenate dehydratas  51.2      10 0.00027   17.9   2.0  113   83-202    26-158 (285)
134 PRK02083 imidazole glycerol ph  50.5      11 0.00029   17.7   2.1   42   67-108    60-103 (253)
135 PRK02747 consensus              49.9      13 0.00032   17.4   2.2   42   67-108    60-103 (257)
136 COG0107 HisF Imidazoleglycerol  49.8     9.8 0.00025   18.0   1.7   23  174-196   208-230 (256)
137 PRK07239 bifunctional uroporph  49.8      19 0.00048   16.3   4.3   59  145-203   138-216 (381)
138 TIGR03298 argP transcriptional  48.9      20  0.0005   16.2   8.6  189   40-249    89-290 (292)
139 COG1613 Sbp ABC-type sulfate t  48.6      20  0.0005   16.2   6.5  136  122-259   126-293 (348)
140 COG0583 LysR Transcriptional r  47.7      20 0.00052   16.1   8.4  154   71-232   109-273 (297)
141 PRK13684 Ycf48-like protein; P  46.7      17 0.00044   16.5   2.6   19    1-19      1-19  (333)
142 TIGR00631 uvrb excinuclease AB  46.6      13 0.00032   17.4   1.8   29   81-109   471-504 (667)
143 cd04731 HisF The cyclase subun  46.5      16  0.0004   16.8   2.3   42   67-108    57-100 (243)
144 pfam01715 IPPT IPP transferase  46.2      22 0.00055   15.9   5.4   44  223-266   153-199 (253)
145 pfam02621 DUF178 Putative peri  45.6      22 0.00056   15.9   4.7   26   81-106    24-49  (248)
146 PRK04792 tolB translocation pr  45.1     9.1 0.00023   18.2   0.9   40   42-91     35-74  (450)
147 TIGR00174 miaA tRNA delta(2)-i  44.6      23 0.00058   15.8   3.2   36  227-262   190-229 (307)
148 PRK05211 consensus              43.2      19 0.00048   16.3   2.3   41   67-107    51-93  (248)
149 PRK05137 tolB translocation pr  41.1      10 0.00027   17.9   0.7   23   67-89     54-76  (437)
150 PRK02515 psbU photosystem II c  39.2      28 0.00071   15.3   3.0   21    1-21      1-21  (144)
151 TIGR00971 3a0106s03 sulfate AB  38.8      28 0.00072   15.2   6.7  139  122-262   103-273 (320)
152 PRK10743 heat shock protein Ib  37.9      11 0.00027   17.8   0.3   34   48-85     31-64  (137)
153 TIGR02129 hisA_euk phosphoribo  37.4      13 0.00034   17.2   0.8   55  140-199   191-258 (274)
154 TIGR00735 hisF imidazoleglycer  37.0      11 0.00027   17.8   0.2   21  176-196   268-288 (312)
155 cd01424 MGS_CPS_II Methylglyox  36.8      22 0.00056   15.9   1.8   34   77-110    39-75  (110)
156 PRK11139 DNA-binding transcrip  35.6      32  0.0008   14.9   8.8  185   39-247    92-292 (295)
157 TIGR01980 sufB FeS assembly pr  35.1      25 0.00063   15.6   1.8   12  188-199   387-398 (469)
158 TIGR01054 rgy reverse gyrase;   34.3      11 0.00028   17.8  -0.1   18   91-108   401-418 (1843)
159 PRK04922 tolB translocation pr  34.2      26 0.00067   15.4   1.9   40   42-90     38-77  (439)
160 TIGR00623 sula cell division i  33.6      27 0.00068   15.3   1.8   61   91-152    99-162 (168)
161 pfam10991 DUF2815 Protein of u  33.6      34 0.00087   14.7   5.0   16   42-57      7-22  (181)
162 cd01423 MGS_CPS_I_III Methylgl  32.9      24 0.00061   15.6   1.5   34   77-110    39-79  (116)
163 PRK13357 branched-chain amino   32.8      17 0.00044   16.5   0.7   43  153-196   259-302 (357)
164 PRK00050 mraW S-adenosyl-methy  32.8      35 0.00089   14.6   3.7   41  223-263   206-255 (309)
165 COG2182 MalE Maltose-binding p  32.5      29 0.00074   15.1   1.9   24   71-94     58-81  (420)
166 pfam00072 Response_reg Respons  29.6      36 0.00091   14.6   1.9   33  163-195    17-49  (111)
167 COG2247 LytB Putative cell wal  29.5      40   0.001   14.3   3.1   81   72-162    43-145 (337)
168 PRK11597 heat shock chaperone   29.4      19 0.00048   16.3   0.5   34   48-85     29-62  (142)
169 TIGR00004 TIGR00004 endoribonu  29.2      30 0.00077   15.0   1.5   23  251-273    86-108 (129)
170 pfam01795 Methyltransf_5 MraW   29.1      32 0.00082   14.8   1.6   46   61-106    44-97  (310)
171 PRK13584 hisG ATP phosphoribos  29.0      36 0.00091   14.6   1.8  149   84-249    45-199 (204)
172 TIGR02122 TRAP_TAXI TRAP trans  28.7      25 0.00064   15.5   1.0  128   71-199    44-197 (319)
173 pfam02642 consensus             27.5      43  0.0011   14.1   2.1  149   88-247    34-196 (259)
174 cd00156 REC Signal receiver do  27.4      43  0.0011   14.1   2.0   34  163-196    16-49  (113)
175 COG4150 CysP ABC-type sulfate   27.3      18 0.00047   16.4   0.1   27  121-148   119-146 (341)
176 COG0275 Predicted S-adenosylme  26.9      44  0.0011   14.0   6.1   46  220-265   207-261 (314)
177 KOG0623 consensus               26.4      44  0.0011   14.0   1.9   18  252-269   378-395 (541)
178 PRK11289 ampC beta-lactamase;   26.3      45  0.0012   13.9   2.2   32    5-36      1-32  (387)
179 COG0077 PheA Prephenate dehydr  26.0      34 0.00087   14.7   1.3  117   79-202    22-158 (279)
180 TIGR01752 flav_long flavodoxin  25.5      47  0.0012   13.8   5.2  156   63-250     7-174 (176)
181 TIGR01132 pgm phosphoglucomuta  24.3      36 0.00092   14.5   1.2   34   39-87    229-262 (553)
182 PRK02889 tolB translocation pr  23.6      47  0.0012   13.8   1.6   16   68-83     53-68  (430)
183 PRK03147 thiol-disulfide oxido  23.6      48  0.0012   13.7   1.7   21   41-65     34-54  (176)
184 PRK12450 foldase protein PrsA;  23.5      51  0.0013   13.6   2.8   20    5-24      1-20  (309)
185 PRK00059 prsA peptidylprolyl i  23.3      35  0.0009   14.6   0.9   20    5-24      1-20  (336)
186 KOG4596 consensus               22.4      36 0.00093   14.5   0.9   38  234-272  1478-1517(1936)
187 PRK09590 celB cellobiose phosp  21.8      55  0.0014   13.4   1.8   33   74-106    22-54  (104)
188 pfam00496 SBP_bac_5 Bacterial   21.7      55  0.0014   13.4   5.0   70  171-245   150-224 (361)
189 TIGR02089 TTC tartrate dehydro  21.6      41   0.001   14.2   1.0   24   72-95     25-49  (355)
190 PRK13348 chromosome replicatio  21.4      56  0.0014   13.3   9.3  160   73-242   109-284 (294)
191 cd06155 eu_AANH_C_1 A group of  21.2      44  0.0011   14.0   1.1   14  252-265    64-77  (101)
192 COG1197 Mfd Transcription-repa  21.2      57  0.0014   13.3   1.9   10  181-190   690-699 (1139)

No 1  
>PRK11260 cystine transporter subunit; Provisional
Probab=100.00  E-value=0  Score=340.42  Aligned_cols=257  Identities=25%  Similarity=0.448  Sum_probs=219.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH--HHCHHHHHHCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCC
Q ss_conf             99999999999999999999999998--4178878858958999628998724870469984889885216789976299
Q gi|254781112|r    5 LRDLRKIFFSKYLFFAPFFILFSYYF--VIYPFRTEDQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNL   82 (274)
Q Consensus         5 ~~~mk~~~~~~~l~~~~~~~~~~~~~--~~~~~~~~~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~   82 (274)
                      |++|.|..+...+.++++..+.+.+.  .....+++++|+|+||++++||||+|.  |.+|+++||++|+++++++++|+
T Consensus         1 ~~~~~~~~~~~~l~~~~~~~~~~~~~a~~~~L~~I~~~G~L~Vg~~~~~pPf~~~--d~~G~~~GfdvDl~~~ia~~lg~   78 (264)
T PRK11260          1 LAHLGRQALMGVMAVALVAGMSVKSFADEGLLNKVKERGTLLVGLEGTYPPFSFQ--GEDGKLTGFEVEFAEALAKHLGV   78 (264)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHCCEEEEEECCCCCCCEEE--CCCCCEEEEEHHHHHHHHHHHCC
T ss_conf             9046799999999999999835765434243999986998999977898893689--99999888719999999998499


Q ss_pred             CCCCCCCCHHHHHHHHHCCCCCCCH-HCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCEEEECCCHH
Q ss_conf             8555668988988643103221100-00367567542002333222222222111222-211111233432023101012
Q gi|254781112|r   83 KVEFFETAVSGLITGLDTNRYDVLV-NVAITPERQKKYDFSIPYIAHRVLLVVRSDQQ-DIRSFKDLTDKTVAQILGTDL  160 (274)
Q Consensus        83 ~~~~~~~~~~~~~~~l~~g~~D~~~-~~~~t~eR~~~~~fs~p~~~~~~~~~~~~~~~-~~~~~~dL~g~~V~~~~g~~~  160 (274)
                      +++|++++|++++..|++|++|+++ ++++|+||++.+.||.||+.....+++++++. .+++++||+|++||+..|+.+
T Consensus        79 ~~e~~~~~~~~~i~~L~~g~~Di~~~~~t~T~eR~~~~~Fs~PY~~~~~~~~v~~~~~~~i~~~~dL~Gk~V~v~~gs~~  158 (264)
T PRK11260         79 KASLKPTKWDGMLASLDSKRIDVVINQVTISDERKKKYDFSTPYTVSGIQALVKKGNEGTIKTAADLKGKKVGVGLGTNY  158 (264)
T ss_pred             CEEEEECCHHHHHHHHHCCCCCEEECCCCCCHHHHHHCCCCCCEEEEEEEEEEECCCCCCCCCHHHHCCCEEEEECCCHH
T ss_conf             56999788899999986699466725753588888517767743774459999878976668978966871688569789


Q ss_pred             HHHHHCC--CCCCEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEEEECCCHHHHH
Q ss_conf             2332013--45421336855777755443210036655899999984587667326236776877079998189989999
Q gi|254781112|r  161 SRFAKEL--KSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKGNNKLTR  238 (274)
Q Consensus       161 ~~~l~~~--~~~~~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~L~~  238 (274)
                      ++++++.  +.++..+++..+++++|.+||+|+++.+...+.++.++.+..   ..+..++....+++++++|++++|++
T Consensus       159 ~~~l~~~~~~~~i~~~~~~~~~~~~l~~G~vDa~i~d~~~~~~~~~~~~~~---~~~~~~~~~~~~~~iav~k~~~~L~~  235 (264)
T PRK11260        159 EEWLRQNVQGVDVRTYDDDPTKYQDLRVGRIDAILVDRLAALDLVKKTNDT---LAVTGEAFSRQESGVALRKGNPDLLK  235 (264)
T ss_pred             HHHHHHHCCCCCEEEECCHHHHHHHHHCCCCCEEEECHHHHHHHHHHCCCC---EEECCCCCCCCEEEEEEECCCHHHHH
T ss_conf             999986088981686366189999987598679994599999999868997---89806876665089999899999999


Q ss_pred             HHHHHHHHHHHCCHHHHHHHHHCCCCCC
Q ss_conf             9999999999798599999876788877
Q gi|254781112|r  239 SINEILCAIHLDGTYKKIFDRYFDKNII  266 (274)
Q Consensus       239 ~in~~l~~l~~~G~~~~I~~kw~g~d~~  266 (274)
                      .+|++|.+|++||++++|++||||.|+.
T Consensus       236 ~in~~L~~l~~dG~~~~i~~KwfG~D~t  263 (264)
T PRK11260        236 AVNNAIAEMQKDGTLKALSEKWFGADVT  263 (264)
T ss_pred             HHHHHHHHHHHCCHHHHHHHHHCCCCCC
T ss_conf             9999999999677799999765799899


No 2  
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=100.00  E-value=0  Score=329.66  Aligned_cols=258  Identities=19%  Similarity=0.269  Sum_probs=213.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH----HHHHCHHHHHHCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHC---
Q ss_conf             999999999999999999999----9841788788589589996289987248704699848898852167899762---
Q gi|254781112|r    8 LRKIFFSKYLFFAPFFILFSY----YFVIYPFRTEDQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRL---   80 (274)
Q Consensus         8 mk~~~~~~~l~~~~~~~~~~~----~~~~~~~~~~~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~l---   80 (274)
                      |||++...+.+.++..+..+.    +......++.++|+|+||++.+||||+|.  |.+|++.||++|++++|++.+   
T Consensus         3 ~kk~~~~~l~~~l~~~~~~~~~~~~a~~~tL~~Ik~~G~l~vG~~~~~pPf~~~--d~~g~~vGfdvDla~~ia~~l~~~   80 (302)
T PRK10797          3 LRKLATALLALGLSAGLAQAEDAAPAAGSTLDKIAKNGVIVVGHRESSVPFSYY--DNQQKVVGYSQDYSNAIVEAVKKK   80 (302)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHCCEEEEEECCCCCCCEEE--CCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             589999999999999997456777532271999986998999989998997168--999985154179999999999877


Q ss_pred             ----CCCCCCCCCCHHHHHHHHHCCCCCCCH-HCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEE
Q ss_conf             ----998555668988988643103221100-003675675420023332222222221112222111112334320231
Q gi|254781112|r   81 ----NLKVEFFETAVSGLITGLDTNRYDVLV-NVAITPERQKKYDFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQI  155 (274)
Q Consensus        81 ----g~~~~~~~~~~~~~~~~l~~g~~D~~~-~~~~t~eR~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~dL~g~~V~~~  155 (274)
                          +++++|++++|+.++++|++|++|+++ ++++|+||++.++||.||+..+..+++++++ .+++++||+||+||++
T Consensus        81 l~~~~~~v~~v~~~~~~rip~L~~gk~Di~~~~~t~T~eR~k~vdFS~pY~~~~~~llv~k~s-~Iks~~DL~GK~V~V~  159 (302)
T PRK10797         81 LNKPDLQVKLIPITSQNRIPLLQNGTFDFECGSTTNNLERQKQAAFSDTIFVVGTRLLTKKGG-DIKDFADLKGKAVVVT  159 (302)
T ss_pred             HCCCCCEEEEEECCHHHHHHHHHCCCCCEEEECCCCCHHHHCCEEECCCCEECCEEEEEECCC-CCCCHHHHCCCEEEEE
T ss_conf             446773499997578887799978980889735756977741242146627714689997788-6667566089979996


Q ss_pred             CCCHHHHHHHC------CCCCCEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEEE
Q ss_conf             01012233201------345421336855777755443210036655899999984587667326236776877079998
Q gi|254781112|r  156 LGTDLSRFAKE------LKSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMM  229 (274)
Q Consensus       156 ~g~~~~~~l~~------~~~~~~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  229 (274)
                      .|++.+.++++      .+.+++.+++..++++.|.+||+|+++.|......+..+...... +.+...+....++++++
T Consensus       160 ~GTt~e~~~~~~~~~~~~~~~iv~~~~~~~a~~~L~~GrvDA~~~D~~~l~~~~~~~~~~~~-~~iv~~~~~~e~ygia~  238 (302)
T PRK10797        160 SGTTSEVLLNKLNEEQKMNMRIISAKDHGDSFRTLESGRAVAFMMDDALLAGERAKAKKPDN-WEIVGKPQSQEAYGCML  238 (302)
T ss_pred             CCCHHHHHHHHHHHHHCCCCEEEECCCHHHHHHHHHCCCCCEEEECHHHHHHHHHHCCCCCC-EEEECCCCCCCCEEEEE
T ss_conf             78739999998667506772378508889999999859950998122988899986369975-49937867776079999


Q ss_pred             ECCCHHHHHHHHHHHHHHHHCCHHHHHHHHHCCCCCCCCC
Q ss_conf             1899899999999999999798599999876788877568
Q gi|254781112|r  230 RKGNNKLTRSINEILCAIHLDGTYKKIFDRYFDKNIISSV  269 (274)
Q Consensus       230 ~k~~~~L~~~in~~l~~l~~~G~~~~I~~kw~g~d~~~~~  269 (274)
                      +|+|++|++.+|++|.+|++||+|++|++||||+++++..
T Consensus       239 rKgd~~L~~~Vn~aL~~l~~dGt~~~I~~KWF~~p~P~~~  278 (302)
T PRK10797        239 RKDDPQFKKLMDDTIAQAQTSGEAEKWFDKWFKNPIPPKN  278 (302)
T ss_pred             ECCCHHHHHHHHHHHHHHHHCCCHHHHHHHHCCCCCCCCC
T ss_conf             6899999999999999999778299999987599999998


No 3  
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=100.00  E-value=0  Score=320.90  Aligned_cols=220  Identities=29%  Similarity=0.453  Sum_probs=198.9

Q ss_pred             HCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCC-HHCCCCHHHHH
Q ss_conf             58958999628998724870469984889885216789976299855566898898864310322110-00036756754
Q gi|254781112|r   39 DQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVSGLITGLDTNRYDVL-VNVAITPERQK  117 (274)
Q Consensus        39 ~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~~~~~~~~~~~~~l~~g~~D~~-~~~~~t~eR~~  117 (274)
                      +.++|+||++++||||+|.  + .|++.||++|++++|++++|++++|++++|++++++|++|++|++ .++++|+||++
T Consensus        23 ~~~~l~Vg~~~~~pPf~f~--~-~g~~~GfdvDl~~~ia~~lg~~~e~~~~~~~~~i~~l~~g~~D~~~~~~~~T~eR~~   99 (247)
T PRK09495         23 ADKELVVATDTAFVPFEFK--Q-GDKYVGFDVDLWAAIAKELKLDYTLKPMDFSGIIPALQTKNIDLALAGITITDERKK   99 (247)
T ss_pred             CCCEEEEEECCCCCCEEEC--C-CCEEEEEHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCCCCCEEECCCCCCHHHHH
T ss_conf             4994999989987980576--7-992788299999999999699469997788999999976995636466014789984


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCHHHHHHHCC--CCCCEEECCHHHHHHHHHHHHHHCCCCC
Q ss_conf             20023332222222221112222111112334320231010122332013--4542133685577775544321003665
Q gi|254781112|r  118 KYDFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTDLSRFAKEL--KSHLVFSHNFEQSLQLLLSKRTDATMIP  195 (274)
Q Consensus       118 ~~~fs~p~~~~~~~~~~~~~~~~~~~~~dL~g~~V~~~~g~~~~~~l~~~--~~~~~~~~~~~~~~~~l~~grvD~~~~~  195 (274)
                      .++||.||+..+..+++++++..+++++||+|++||++.|+..++++++.  +.++..+++.++++++|.+||+|+++.+
T Consensus       100 ~~~FS~py~~~~~~i~v~~~~~~i~~~~dL~Gk~v~v~~Gs~~~~~~~~~~~~~~i~~~~~~~~~~~aL~~GrvDa~v~d  179 (247)
T PRK09495        100 AIDFSDGYYKSGLLVMVKANNNDIKSVKDLDGKVVAVKSGTGSVDYAKANIKTKDLRQFPNIDNAYLELGTGRADAVLHD  179 (247)
T ss_pred             HCCCCCCCEEEEEEEEEECCCCCCCCHHHCCCCEEEEECCCHHHHHHHHHCCCCCEEECCCHHHHHHHHHCCCEEEEEEC
T ss_conf             33347770772469999899977798245489889984695899999963889866965988999998765873499956


Q ss_pred             HHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEEEECCCHHHHHHHHHHHHHHHHCCHHHHHHHHHCCCC
Q ss_conf             589999998458766732623677687707999818998999999999999997985999998767888
Q gi|254781112|r  196 DIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYFDKN  264 (274)
Q Consensus       196 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~L~~~in~~l~~l~~~G~~~~I~~kw~g~d  264 (274)
                      ...+.+++++.+..  .+.+...+....+++++++|+++ |++.||++|.+|++||+|++|++||||.|
T Consensus       180 ~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~ia~~k~~~-L~~~in~aL~~l~~dG~~~~l~~kwfG~~  245 (247)
T PRK09495        180 TPNILYFIKTAGNG--QFKAVGDSLEAQQYGIAFPKGSD-LREKVNGALKTLKENGTYNEIYKKWFGTE  245 (247)
T ss_pred             HHHHHHHHHHCCCC--CEEEECCCCCCCEEEEEEECCHH-HHHHHHHHHHHHHHCCHHHHHHHHHCCCC
T ss_conf             89999999848999--78994677776459999928829-99999999999997886999999867999


No 4  
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein; InterPro: IPR005768   Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. The protein components of these traffic systems include one or two transmembrane protein components, one or two membrane-associated ATP-binding proteins (ABC transporters; see IPR003439 from INTERPRO) and a high affinity periplasmic solute-binding protein. The later are thought to bind the substrate in the vicinity of the inner membrane, and to transfer it to a complex of inner membrane proteins for concentration into the cytoplasm.     In Gram-positive bacteria which are surrounded by a single membrane and have therefore no periplasmic region the equivalent proteins are bound to the membrane via an N-terminal lipid anchor. These homolog proteins do not play an integral role in the transport process per se, but probably serve as receptors to trigger or initiate translocation of the solute through the membrane by binding to external sites of the integral membrane proteins of the efflux system. In addition at least some solute-binding proteins function in the initiation of sensory transduction pathways.    On the basis of sequence similarities, the vast majority of these solute-binding proteins can be grouped into eight families of clusters, which generally correlate with the nature of the solute bound. Family 3 groups together specific amino acids and opine-binding periplasmic proteins and a periplasmic homolog with catalytic activity. ; GO: 0005215 transporter activity, 0006810 transport, 0030288 outer membrane-bounded periplasmic space.
Probab=100.00  E-value=2.9e-44  Score=293.35  Aligned_cols=232  Identities=30%  Similarity=0.484  Sum_probs=208.3

Q ss_pred             HHHHHCHHHHHHCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCC-------CCCCCCCCCHHHHHHHHHC
Q ss_conf             998417887885895899962899872487046998488988521678997629-------9855566898898864310
Q gi|254781112|r   28 YYFVIYPFRTEDQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLN-------LKVEFFETAVSGLITGLDT  100 (274)
Q Consensus        28 ~~~~~~~~~~~~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg-------~~~~~~~~~~~~~~~~l~~  100 (274)
                      ++.++....+++++.|+||++++||||++.  |.+|++.||+|||+++|++++.       .+++|++.+|+++++.|+.
T Consensus        14 ~~~~a~~~a~~~~~~v~~gt~~~y~PF~~~--~a~G~~~GFDvDl~~alc~~~~gD~GWdh~~c~~~~~~~~~liPsL~~   91 (333)
T TIGR01096        14 ASSAATAAAAKEKGSVRIGTETAYPPFEFK--DADGKLVGFDVDLANALCKEMKGDPGWDHAKCKFVEQAFDGLIPSLKA   91 (333)
T ss_pred             HHHHCCHHHHHHCCCEEEEECCCCCCCCCC--CCCCCEEEHHHHHHHHHHHHHCCCCCCCCCEEEEECCCHHHHHHHHHC
T ss_conf             986215688852880799865787986551--889545632678999999984589996431488842756652025453


Q ss_pred             CCCCCC-H-HCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC-----------------------CC-CCCEEE
Q ss_conf             322110-0-003675675420023332222222221112222111112-----------------------33-432023
Q gi|254781112|r  101 NRYDVL-V-NVAITPERQKKYDFSIPYIAHRVLLVVRSDQQDIRSFKD-----------------------LT-DKTVAQ  154 (274)
Q Consensus       101 g~~D~~-~-~~~~t~eR~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~d-----------------------L~-g~~V~~  154 (274)
                      |++|++ + ++++|++|++.+.||.|||..+..|++++|++..++.+|                       |+ |++|||
T Consensus        92 k~~Dai~an~~~It~~R~~~i~F~~~yy~~~~~f~v~~~~~~~~~~~~~E~~~Ld~~A~~~K~~~d~~~~~L~nG~~~gV  171 (333)
T TIGR01096        92 KKVDAIMANAMSITDERQKQIDFSDPYYATGAGFVVKKDSDLAKTLEDGENYSLDNQADAAKKEIDDVTKFLKNGKKVGV  171 (333)
T ss_pred             CCEEEEEECCCCCCHHHHHHHCCCCCCCCCCCEEEEECCCCCCCCHHHHCCCCCCCCCHHHHHHHHHHHHHHHCCCEEEE
T ss_conf             80689972665546656632114430000443022224887543145330367200037989989989998527548986


Q ss_pred             ECCCHHHHHHHCC------CCCCEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEEC----CC-----C
Q ss_conf             1010122332013------4542133685577775544321003665589999998458766732623----67-----7
Q gi|254781112|r  155 ILGTDLSRFAKEL------KSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIA----DR-----M  219 (274)
Q Consensus       155 ~~g~~~~~~l~~~------~~~~~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~----~~-----~  219 (274)
                      +.||+.+.|+++.      ..+++.|++.+++...|.+||+|+++.|...+..+..+.+.......+.    ..     .
T Consensus       172 ~~GTT~~~~~~~~~~~~Nl~v~~~~Y~~~~~~~~dL~~GR~Da~~~D~~~l~~~~~~~~~gkd~~~~g~~~~~~PLGP~~  251 (333)
T TIGR01096       172 QSGTTHEQYLKDEFKPKNLGVDIVEYDSYDNANMDLKAGRIDAVLADASVLAEGFLKPPNGKDLKFVGPKVTDEPLGPVK  251 (333)
T ss_pred             CCCCCHHHHHHHHCCCCCCEEEEEEECCHHHHHHHHHCCCCEEEECCHHHHHHHHHCCCCCCCEEECCCCCCCCCCCCCC
T ss_conf             26884899998624433742666640886799999757962177436588888873789888637728322688989855


Q ss_pred             CCCCC------------------EEEEEEC-------------------CC---HHHHHHHHHHHHHHHHCCHHHHHHHH
Q ss_conf             68770------------------7999818-------------------99---89999999999999979859999987
Q gi|254781112|r  220 KDNSA------------------VAFMMRK-------------------GN---NKLTRSINEILCAIHLDGTYKKIFDR  259 (274)
Q Consensus       220 ~~~~~------------------~~~~~~k-------------------~~---~~L~~~in~~l~~l~~~G~~~~I~~k  259 (274)
                      ....+                  +|+++||                   +|   .+|...+|++|+.|++||+|++|++|
T Consensus       252 ~FG~g~W~DiV~W~~YAL~~A~E~Gig~rk~de~~~s~Np~i~r~lg~~~Dt~G~eL~~~~n~Al~~~~adGtY~~i~~k  331 (333)
T TIGR01096       252 YFGDGYWFDIVRWSAYALVAAEEVGIGLRKVDEVKASTNPEIKRLLGSEGDTIGKELKAKFNKALKAIRADGTYQKISKK  331 (333)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHCCCCCCHHHHHCCCCCCHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHH
T ss_conf             57888300121446677763443212534558885188830232204556512189999999999999865874688865


Q ss_pred             HC
Q ss_conf             67
Q gi|254781112|r  260 YF  261 (274)
Q Consensus       260 w~  261 (274)
                      ||
T Consensus       332 wf  333 (333)
T TIGR01096       332 WF  333 (333)
T ss_pred             CC
T ss_conf             19


No 5  
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=100.00  E-value=7.4e-44  Score=290.91  Aligned_cols=244  Identities=18%  Similarity=0.284  Sum_probs=199.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHH--HHCHHHHHHCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHC---CC
Q ss_conf             99999999999999999999998--41788788589589996289987248704699848898852167899762---99
Q gi|254781112|r    8 LRKIFFSKYLFFAPFFILFSYYF--VIYPFRTEDQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRL---NL   82 (274)
Q Consensus         8 mk~~~~~~~l~~~~~~~~~~~~~--~~~~~~~~~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~l---g~   82 (274)
                      +||.++...++.+..+...+.+.  ......++++|+|+||++++||||+|.+ +.+|++.||++|++++|++++   ++
T Consensus         3 ~~~~l~~~~~~~l~~~~~~~~~~a~~~~l~~I~~~G~L~vg~~~~~pPf~~~d-~~~g~~~GfDvDla~~iAk~llg~~~   81 (259)
T PRK11917          3 FRKSLLKLAVFALGACVAFSNANAAEGKLESIKSKGQLIVGVKNDVPHYALLD-QATGEIKGFEIDVAKLLAKSILGDDK   81 (259)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCHHHHCHHHHHHHCCEEEEEECCCCCCCCEEE-CCCCCEEEEEHHHHHHHHHHHCCCCC
T ss_conf             27999999999999998634521114419999859989999878978862056-79996788879999999999659985


Q ss_pred             CCCCCCCCHHHHHHHHHCCCCCCCH-HCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCHHH
Q ss_conf             8555668988988643103221100-003675675420023332222222221112222111112334320231010122
Q gi|254781112|r   83 KVEFFETAVSGLITGLDTNRYDVLV-NVAITPERQKKYDFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTDLS  161 (274)
Q Consensus        83 ~~~~~~~~~~~~~~~l~~g~~D~~~-~~~~t~eR~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~dL~g~~V~~~~g~~~~  161 (274)
                      +++|++++|+.+++.|++|++|+++ ++++|+||++.++||.||+.....+++++++ .+++++||+|++||+..|++.+
T Consensus        82 ~v~~v~~~~~~~~p~L~~gkvD~i~~~~tiT~eR~k~vdFS~PY~~~~~~ilv~k~~-~i~~~~DL~gk~Vgv~~gst~~  160 (259)
T PRK11917         82 KIKLVAVNAKTRGPLLDNGSVDAVIATFTITPERKRIYNFSEPYYQDAIGLLVLKEK-NYKSLADMKGANIGVAQAATTK  160 (259)
T ss_pred             EEEEEEECHHHHHHHHHCCCEEEEEECCCCCCCHHCCEEECCCEEEEEEEEEEECCC-CCCCHHHHCCCCEEEEECCCHH
T ss_conf             699997067877689877985599866476765430576224769965599998999-9999899589817999278469


Q ss_pred             HHHHC----CC--CCCEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEEEECCCHH
Q ss_conf             33201----34--5421336855777755443210036655899999984587667326236776877079998189989
Q gi|254781112|r  162 RFAKE----LK--SHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKGNNK  235 (274)
Q Consensus       162 ~~l~~----~~--~~~~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~  235 (274)
                      ..+.+    .+  .++..+++..++..+|.+||+|+++.+...+..+..+..      .+.+++..+.+++++++|++++
T Consensus       161 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~grvDa~~~d~~~~~~~~~~~~------~~~~~~~~~~~~giavrKgd~~  234 (259)
T PRK11917        161 KAIGEAAKKIGIDVKFSEFPDYPSIKAALDAKRVDAFSVDKSILLGYVDDKS------EILPDSFEPQSYGIVTKKDDPA  234 (259)
T ss_pred             HHHHHHHHHCCCCEEEEECCCHHHHHHHHHCCCEEEEECCHHHHHHHHHCCC------CCCCCCCCCCEEEEEEECCCHH
T ss_conf             9999988860885169964999999999984980299826999999986198------0168888752589999489989


Q ss_pred             HHHHHHHHHHHHHHCCHHHHHHHHHC
Q ss_conf             99999999999997985999998767
Q gi|254781112|r  236 LTRSINEILCAIHLDGTYKKIFDRYF  261 (274)
Q Consensus       236 L~~~in~~l~~l~~~G~~~~I~~kw~  261 (274)
                      |++.+|.+|++++  |++++|++||.
T Consensus       235 l~~~vn~~i~~~k--~~l~~i~~KWg  258 (259)
T PRK11917        235 FAKYVDDFVKEHK--NEIDALAKKWG  258 (259)
T ss_pred             HHHHHHHHHHHHH--HHHHHHHHHHC
T ss_conf             9999999999966--51999998649


No 6  
>pfam00497 SBP_bac_3 Bacterial extracellular solute-binding proteins, family 3.
Probab=100.00  E-value=8.9e-42  Score=278.07  Aligned_cols=216  Identities=37%  Similarity=0.600  Sum_probs=193.1

Q ss_pred             EEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCCH-HCCCCHHHHHHHCC
Q ss_conf             89996289987248704699848898852167899762998555668988988643103221100-00367567542002
Q gi|254781112|r   43 LRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVSGLITGLDTNRYDVLV-NVAITPERQKKYDF  121 (274)
Q Consensus        43 l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~~~~~~~~~~~~~l~~g~~D~~~-~~~~t~eR~~~~~f  121 (274)
                      ||||++++||||.|.  |++|++.|+++|+++++++++|++++++.+||.+++.+++.|++|+++ ++++|++|++.+.|
T Consensus         1 l~v~~~~~~pP~~~~--~~~G~~~G~~~dil~~i~~~lg~~~~~~~~p~~~~~~~l~~g~~D~~~~~~~~t~~R~~~~~~   78 (224)
T pfam00497         1 LRVGTDADYPPFSYL--DEDGKLVGFDVDLAKAIAKRLGVKVEFVPVSWDGLIPALQSGKIDVIIAGMTITPERKKKVDF   78 (224)
T ss_pred             CEEEECCCCCCCEEE--CCCCCEEEEHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCCCCCEEECCCCCCHHHHHHHCC
T ss_conf             989958998991599--999978882999999999997996799985889999999769987661367788555102125


Q ss_pred             CCCCCCCCCCCCCCCCCC----CCCCCCCCCCCCEEEECCCHHHHHHHCC---CCCCEEECCHHHHHHHHHHHHHHCCCC
Q ss_conf             333222222222111222----2111112334320231010122332013---454213368557777554432100366
Q gi|254781112|r  122 SIPYIAHRVLLVVRSDQQ----DIRSFKDLTDKTVAQILGTDLSRFAKEL---KSHLVFSHNFEQSLQLLLSKRTDATMI  194 (274)
Q Consensus       122 s~p~~~~~~~~~~~~~~~----~~~~~~dL~g~~V~~~~g~~~~~~l~~~---~~~~~~~~~~~~~~~~l~~grvD~~~~  194 (274)
                      |.||+..+..++++++..    .+++++||+|++||++.|+.+..++...   +.++..+.++++++++|.+||+|+++.
T Consensus        79 s~p~~~~~~~~~~~~~~~~~~~~~~~~~dL~~~~I~v~~g~~~~~~l~~~~~~~~~i~~~~~~~~~l~~L~~gr~D~~i~  158 (224)
T pfam00497        79 SDPYYYSGQVLVVRKDSPPKIKSIKDLADLKGKKVGVQKGTTQEDLLKELAPKGAEIVLYDDQAEALQALAAGRVDAVVA  158 (224)
T ss_pred             CCCEEECCEEEEEECCCCCCCCCCCCHHHHCCCEEEEECCCHHHHHHHHHCCCCCEEEEECCHHHHHHHHHCCCEEEEEE
T ss_conf             75344047179999898765456589899779779996897799999860624451699542788888987497689995


Q ss_pred             CHHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEEEECCCHHHHHHHHHHHHHHHHCCHHHHHHHHHCCC
Q ss_conf             558999999845876673262367768770799981899899999999999999798599999876788
Q gi|254781112|r  195 PDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYFDK  263 (274)
Q Consensus       195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~L~~~in~~l~~l~~~G~~~~I~~kw~g~  263 (274)
                      +...+.+++++.+..   ......+....+++++++|++++|++.+|++|.+|++||++++|++||||+
T Consensus       159 ~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~k~~~~l~~~~n~~l~~l~~~G~~~~I~~ky~g~  224 (224)
T pfam00497       159 DSPVAAYLIKKNPGL---NLVVGEPLSGEPYGIAVRKGDPELLAAVNKALAELKADGTLAKLYEKWFGK  224 (224)
T ss_pred             CHHHHHHHHHHCCCC---EEEECCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHCCHHHHHHHHHCCC
T ss_conf             799999999868997---299436777614999997999999999999999999684999999752899


No 7  
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=100.00  E-value=3.9e-41  Score=274.07  Aligned_cols=216  Identities=38%  Similarity=0.627  Sum_probs=195.9

Q ss_pred             CEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCCH-HCCCCHHHHHHHC
Q ss_conf             589996289987248704699848898852167899762998555668988988643103221100-0036756754200
Q gi|254781112|r   42 ALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVSGLITGLDTNRYDVLV-NVAITPERQKKYD  120 (274)
Q Consensus        42 ~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~~~~~~~~~~~~~l~~g~~D~~~-~~~~t~eR~~~~~  120 (274)
                      +||||++++||||.|.  |++|+++|+.+|+++++++++|++++++.+||.+++..+++|++|+++ +.+++++|++.+.
T Consensus         1 ~i~v~~~~~~pP~~~~--~~~G~~~G~~~Dil~~~~~~lg~~i~~~~~~~~r~~~~l~~g~~D~~~~~~~~~~~r~~~~~   78 (219)
T smart00062        1 TLRVGTNGDYPPFSFA--DEDGELTGFDVDLAKAIAKELGLKVEFVEVSFDNLLTALKSGKIDVVAAGMTITPERAKQVD   78 (219)
T ss_pred             CEEEEECCCCCCEEEE--CCCCCEEEEHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCCCCCEEEEECCCCHHHHHCCC
T ss_conf             9899978998992799--99997788299999999999799679998478999999975897705311357867750022


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCHHHHHHHCC--CCCCEEECCHHHHHHHHHHHHHHCCCCCHHH
Q ss_conf             23332222222221112222111112334320231010122332013--4542133685577775544321003665589
Q gi|254781112|r  121 FSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTDLSRFAKEL--KSHLVFSHNFEQSLQLLLSKRTDATMIPDIP  198 (274)
Q Consensus       121 fs~p~~~~~~~~~~~~~~~~~~~~~dL~g~~V~~~~g~~~~~~l~~~--~~~~~~~~~~~~~~~~l~~grvD~~~~~~~~  198 (274)
                      ||.||+.....++++++.+ +++++||+|++||++.|+.++.++.+.  +.+++.+.+.++++++|.+||+|+++.+...
T Consensus        79 ~s~p~~~~~~~~~~~~~~~-~~~~~dL~g~~i~~~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~l~~g~vD~~i~~~~~  157 (219)
T smart00062       79 FSDPYYKSGQVILVRKDSP-IKSLEDLKGKKVAVVAGTTGEELLKKLYPEAKIVSYDSQAEALAALKAGRADAAVADAPA  157 (219)
T ss_pred             CCCCEECCCEEEEEECCCC-CCCHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEEECCHHHHHHHHHCCCEEEEEECHHH
T ss_conf             2455002444799965899-799799679779995798799999972878528985999999999983987999977999


Q ss_pred             HHHHHHHCCCCCCCEEECCCCCCCCCEEEEEECCCHHHHHHHHHHHHHHHHCCHHHHHHHHHC
Q ss_conf             999998458766732623677687707999818998999999999999997985999998767
Q gi|254781112|r  199 FFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYF  261 (274)
Q Consensus       199 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~L~~~in~~l~~l~~~G~~~~I~~kw~  261 (274)
                      +.+++++.+.....+ +........+++++++|++++|++.+|++|++|++||++++|.+|||
T Consensus       158 ~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~l~~~~n~~l~~l~~~G~l~~I~~kyf  219 (219)
T smart00062      158 LAALVKQHGLPELKI-VGDPLDTPEGYAFAVRKGDPELLDKINKALKELKADGTLKKIYEKWF  219 (219)
T ss_pred             HHHHHHHCCCCCEEE-ECCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHCCHHHHHHHCCC
T ss_conf             999998489998378-34677776419999959999999999999999996809999984569


No 8  
>cd00134 PBPb Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of  substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD.
Probab=100.00  E-value=4e-41  Score=273.99  Aligned_cols=215  Identities=35%  Similarity=0.572  Sum_probs=190.7

Q ss_pred             EEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCCH-HCCCCHHHHHHHCC
Q ss_conf             89996289987248704699848898852167899762998555668988988643103221100-00367567542002
Q gi|254781112|r   43 LRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVSGLITGLDTNRYDVLV-NVAITPERQKKYDF  121 (274)
Q Consensus        43 l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~~~~~~~~~~~~~l~~g~~D~~~-~~~~t~eR~~~~~f  121 (274)
                      |+||++++||||+|.  |++|++.||++|+++++++++|++++|+.+||++++..|++|++|+++ +.++|++|++.+.|
T Consensus         1 l~Vg~~~~~pP~~~~--~~~G~~~G~~~dl~~~i~~~lg~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~~t~~R~~~~~f   78 (218)
T cd00134           1 LTVGTAGTYPPFSFR--DANGELTGFDVDLAKAIAKELGVKVKFVEVDWDGLITALKSGKVDLIAAGMTITPERAKQVDF   78 (218)
T ss_pred             CEEEECCCCCCCEEE--CCCCCEEEEHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCCCCCEEEEEECCCHHHHCCCCC
T ss_conf             989948998990689--999978883999999999996996699975889999998579977688850258566141455


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCHHHHHHHCC--CCCCEEECCHHHHHHHHHHHHHHCCCCCHHHH
Q ss_conf             3332222222221112222111112334320231010122332013--45421336855777755443210036655899
Q gi|254781112|r  122 SIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTDLSRFAKEL--KSHLVFSHNFEQSLQLLLSKRTDATMIPDIPF  199 (274)
Q Consensus       122 s~p~~~~~~~~~~~~~~~~~~~~~dL~g~~V~~~~g~~~~~~l~~~--~~~~~~~~~~~~~~~~l~~grvD~~~~~~~~~  199 (274)
                      |.||+..+..++++++. .+++++||+|++||++.|+.++.++++.  ..+++.+++.++++++|.+||+|+++.+...+
T Consensus        79 s~p~~~~~~~~~~~~~~-~~~~~~dl~g~~i~v~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~l~~G~vD~~v~~~~~~  157 (218)
T cd00134          79 SDPYYKSGQVILVKKGS-PIKSVKDLKGKKVAVQKGSTAEKYLKKALPEAKVVSYDDNAEALAALENGRADAVIVDEIAL  157 (218)
T ss_pred             CCCEECCCEEEEEECCC-CCCCHHHHCCCEEEEECCCHHHHHHHHHHCCCEEEEECCHHHHHHHHHCCCCEEEEECHHHH
T ss_conf             76444157079998689-99998997796267958988999999731575499969999999999859946999769999


Q ss_pred             HHHHHHCCCCCCCEEECCCCCCCCCEEEEEECCCHHHHHHHHHHHHHHHHCCHHHHHHHHHC
Q ss_conf             99998458766732623677687707999818998999999999999997985999998767
Q gi|254781112|r  200 FNFLERRPHDGNLFKIADRMKDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYF  261 (274)
Q Consensus       200 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~L~~~in~~l~~l~~~G~~~~I~~kw~  261 (274)
                      .+++++.+... ..........+.++++++++++++|++.||++|.+|++||++++|++|||
T Consensus       158 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~l~~~~n~~l~~l~~~G~~~~I~~kwf  218 (218)
T cd00134         158 AALLKKHPPEL-KIVGPSIDLEPLGFGVAVGKDNKELLDAVNKALKELRADGELKKISKKWF  218 (218)
T ss_pred             HHHHHHCCCCC-EEECCCCCCCCEEEEEEECCCCHHHHHHHHHHHHHHHHCHHHHHHHHCCC
T ss_conf             99998679981-99635667673489999749999999999999999986829999984569


No 9  
>TIGR02995 ectoine_ehuB ectoine/hydroxyectoine ABC transporter solute-binding protein; InterPro: IPR014337   Members of this entry are the extracellular solute-binding proteins of ABC transporters and they closely resemble amino acid transporters. The member from Sinorhizobium meliloti (Rhizobium meliloti) is involved in ectoine uptake, both for osmoprotection and for catabolism. All other members of the seed alignment are found associated with ectoine catabolic genes..
Probab=100.00  E-value=1.8e-34  Score=232.84  Aligned_cols=235  Identities=23%  Similarity=0.362  Sum_probs=198.7

Q ss_pred             HHHHHHCHHHHHHCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCC-CCCCCCCHHHHHHHHHCCCCCC
Q ss_conf             999841788788589589996289987248704699848898852167899762998-5556689889886431032211
Q gi|254781112|r   27 SYYFVIYPFRTEDQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLK-VEFFETAVSGLITGLDTNRYDV  105 (274)
Q Consensus        27 ~~~~~~~~~~~~~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~-~~~~~~~~~~~~~~l~~g~~D~  105 (274)
                      +........+.+++|.+|||+ .|-+||+|...|  |+.+|..+|++++|+++||++ |.+..++|..++++|+.|++|.
T Consensus        20 ~aa~a~~LeelKeQG~~Ria~-ANE~Pf~y~g~D--Gkv~G~~PdvA~aifK~lGi~dVn~~~te~G~lIPGL~AgRfDa   96 (285)
T TIGR02995        20 AAADALTLEELKEQGFVRIAI-ANEVPFAYVGAD--GKVAGAAPDVARAIFKRLGIKDVNASVTEYGALIPGLKAGRFDA   96 (285)
T ss_pred             HHHHHHHHHHHHCCCEEEEEE-CCCCCCCCCCCC--CCCCCCCHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCCHHHH
T ss_conf             547552157552353047740-067864002688--53136855789999985481100000356403145410102568


Q ss_pred             CH-HCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCC-CCCCCCCCC---CCCEEEECCCHHHHHHHCCCC---CCEEECCH
Q ss_conf             00-00367567542002333222222222111222-211111233---432023101012233201345---42133685
Q gi|254781112|r  106 LV-NVAITPERQKKYDFSIPYIAHRVLLVVRSDQQ-DIRSFKDLT---DKTVAQILGTDLSRFAKELKS---HLVFSHNF  177 (274)
Q Consensus       106 ~~-~~~~t~eR~~~~~fs~p~~~~~~~~~~~~~~~-~~~~~~dL~---g~~V~~~~g~~~~~~l~~~~~---~~~~~~~~  177 (274)
                      +. ++.++|||++.+.||+|.+.....|+++|+++ .+.+.+|+.   ..+|+++.|++..+|+++.+.   +++.+++.
T Consensus        97 iaAg~~i~PeRCkqVaft~P~~~~~eallvkKGNPk~L~sY~DiAknP~~K~a~~~G~~e~~~ar~~GVk~eqi~~vPd~  176 (285)
T TIGR02995        97 IAAGLFIKPERCKQVAFTEPILSLAEALLVKKGNPKELKSYKDIAKNPEVKVAVVAGAVEVKYAREAGVKEEQIVVVPDT  176 (285)
T ss_pred             HHHCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHCCCCCEEEECCCCHHHHHHHHCCCCCCEEEEECCC
T ss_conf             86115788566646440688644755211258788887752020068231276124723789998658986607882487


Q ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCC--CCEEECCC-----CCCCCCEEEEEECCCHHHHHHHHHHHHHHHHC
Q ss_conf             577775544321003665589999998458766--73262367-----76877079998189989999999999999979
Q gi|254781112|r  178 EQSLQLLLSKRTDATMIPDIPFFNFLERRPHDG--NLFKIADR-----MKDNSAVAFMMRKGNNKLTRSINEILCAIHLD  250 (274)
Q Consensus       178 ~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~--~~~~~~~~-----~~~~~~~~~~~~k~~~~L~~~in~~l~~l~~~  250 (274)
                      +..+++|.+||+|++....+++.....+....+  ......++     |..-..=+++||++|.+|++.||..|.++++|
T Consensus       177 ~~~l~~vq~~RaDay~~t~Lt~~~La~K~gd~nVE~~~pfvdPvvkdaPv~i~ygg~AFRpeDkeLRDafn~~L~k~~~s  256 (285)
T TIGR02995       177 ASALKAVQDKRADAYAATELTVKDLAKKAGDANVEVLAPFVDPVVKDAPVRINYGGLAFRPEDKELRDAFNVELAKLKES  256 (285)
T ss_pred             HHHHHHHHHHCCCEECCCCCCHHHHHHHCCCCCCEECCCCCCCCCCCCCCEECCCCCCCCCCCHHHHHHHHHHHHHHHCC
T ss_conf             16788877403422003323478898533897620004321531058873411672011666677787998999986246


Q ss_pred             CHHHHHHHHH-CCCC
Q ss_conf             8599999876-7888
Q gi|254781112|r  251 GTYKKIFDRY-FDKN  264 (274)
Q Consensus       251 G~~~~I~~kw-~g~d  264 (274)
                      ++|.+|+.+| |.+.
T Consensus       257 ~e~~Ki~apyGfs~~  271 (285)
T TIGR02995       257 DEFKKIVAPYGFSKK  271 (285)
T ss_pred             CCCHHHHCCCCCCHH
T ss_conf             540112213688888


No 10 
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=100.00  E-value=5.7e-33  Score=223.59  Aligned_cols=223  Identities=16%  Similarity=0.207  Sum_probs=192.0

Q ss_pred             HHHHCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCCCCC-CCHHHHHHHHHCCCCCCCHHCCCCHH
Q ss_conf             78858958999628998724870469984889885216789976299855566-89889886431032211000036756
Q gi|254781112|r   36 RTEDQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFE-TAVSGLITGLDTNRYDVLVNVAITPE  114 (274)
Q Consensus        36 ~~~~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~~~~-~~~~~~~~~l~~g~~D~~~~~~~t~e  114 (274)
                      ..+++++++|+++++||||+|.  |.+|++.|+.+|+++.|..++|+++++++ .+|.+....+++|++|++..+.++++
T Consensus       297 WL~~hP~irv~~~~~~aP~sf~--D~~G~~~Gi~aD~L~lIs~rtGL~Fe~v~~~~~~~~~~~l~~g~~D~l~~~~~s~~  374 (1197)
T PRK09959        297 WIKQHPDLKVLENPYSPPYSMT--DENGSVRGVMGDILNIITLQTGLNFSPITVSHNIHAGTQLNPGGWDILPGAIYSED  374 (1197)
T ss_pred             HHHHCCCEEEEECCCCCCEEEE--CCCCCCCCCHHHHHHHHHHHHCCEEEEEECCCHHHHHHHHHCCCCHHCCCCCCCCC
T ss_conf             9997897599717998994578--88997643279999999998796689983698799999987698122032357854


Q ss_pred             HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCHHHHHHHC--CCCCCEEECCHHHHHHHHHHHHHHCC
Q ss_conf             7542002333222222222111222211111233432023101012233201--34542133685577775544321003
Q gi|254781112|r  115 RQKKYDFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTDLSRFAKE--LKSHLVFSHNFEQSLQLLLSKRTDAT  192 (274)
Q Consensus       115 R~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~dL~g~~V~~~~g~~~~~~l~~--~~~~~~~~~~~~~~~~~l~~grvD~~  192 (274)
                      |++.+.||.||...+.++++|++.....+++  +|+||++..|+....++++  ++.+++.+++..+++++|.+|++|++
T Consensus       375 r~~~l~fT~py~~~p~ViV~r~~~~~~~~l~--~gkrvai~~~~~~~~~l~~~yP~i~~v~v~s~~~al~~v~~G~aDa~  452 (1197)
T PRK09959        375 RENNVLFAEAFITTPYVFVMQKAPDSEQTLK--KGMKVAIPYYYELHSQLKEMYPEVEWIKVDNASAAFHKVKEGELDAL  452 (1197)
T ss_pred             CCCCCEECCCCCCCCEEEEEECCCCCCCCHH--CCCEEEECCCCCHHHHHHHHCCCCEEEEECCHHHHHHHHHCCCCCEE
T ss_conf             4346554132356875999963786301142--19889991785068999986898349980999999999977887667


Q ss_pred             CCCHHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEEEECCCHHHHHHHHHHHHHHHHCCHHHHHHHHHCCCC
Q ss_conf             665589999998458766732623677687707999818998999999999999997985999998767888
Q gi|254781112|r  193 MIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYFDKN  264 (274)
Q Consensus       193 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~L~~~in~~l~~l~~~G~~~~I~~kw~g~d  264 (274)
                      +.+...+.+++.+....... ........+..++|++++++|+|+..+|++|..|... |+++|.+||.+..
T Consensus       453 v~~l~~a~y~i~~~~~~~L~-~~~~~~~~~~~lafaV~~d~peL~sILnKaL~sIpp~-E~~~I~~rW~~~~  522 (1197)
T PRK09959        453 VATQLNSRYMIDHYYPNELY-HFLIPGVPNASLSFAFPRGEPELKDIINKALNAIPPS-EVLRLTEKWIKMP  522 (1197)
T ss_pred             EEHHHHHHHHHHHHCCCCCE-EEECCCCCCCCEEEEECCCCHHHHHHHHHHHHHCCHH-HHHHHHHHHCCCC
T ss_conf             42447789999874566504-8741587763269998799889999999999839999-9999998530467


No 11 
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=100.00  E-value=2.7e-31  Score=213.21  Aligned_cols=227  Identities=33%  Similarity=0.524  Sum_probs=187.1

Q ss_pred             HHHHHCCCEEEEECCCC-CCEEEEEECCC-CCEEEEEEEEHHHHHHHCCCC--CCCCCCCHHHHHHHHHCCCCCCCH-HC
Q ss_conf             87885895899962899-87248704699-848898852167899762998--555668988988643103221100-00
Q gi|254781112|r   35 FRTEDQSALRVGTDGIY-PPHSFHAQDGR-GELTGFDIDLIKEVAHRLNLK--VEFFETAVSGLITGLDTNRYDVLV-NV  109 (274)
Q Consensus        35 ~~~~~~~~l~v~~~~~~-pP~~~~~~d~~-g~~~G~~~dl~~~i~~~lg~~--~~~~~~~~~~~~~~l~~g~~D~~~-~~  109 (274)
                      ..+...+.++|++...+ +||+|..  .. |++.||++|+++++++.++..  ++++..+|..+++.+++|++|+++ ++
T Consensus        28 ~~~~~~~~~~v~~~~~~~~p~~~~~--~~~~~~~G~dvdl~~~ia~~l~~~~~~~~~~~~~~~~~~~l~~g~~D~~~~~~  105 (275)
T COG0834          28 DKIKARGKLRVGTEATYAPPFEFLD--AKGGKLVGFDVDLAKAIAKRLGGDKKVEFVPVAWDGLIPALKAGKVDIIIAGM  105 (275)
T ss_pred             HHHHHCCEEEEEECCCCCCCCEEEC--CCCCEEEEEHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHCCCCCEEEECC
T ss_conf             6664477599997268889841023--88870676529999999998467742488506887763898779988898567


Q ss_pred             CCCHHHHHHHCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCEEEECCCH--HHHHHHCC--CCCCEEECCHHHHHHHH
Q ss_conf             3675675420023332222222221112222-1111123343202310101--22332013--45421336855777755
Q gi|254781112|r  110 AITPERQKKYDFSIPYIAHRVLLVVRSDQQD-IRSFKDLTDKTVAQILGTD--LSRFAKEL--KSHLVFSHNFEQSLQLL  184 (274)
Q Consensus       110 ~~t~eR~~~~~fs~p~~~~~~~~~~~~~~~~-~~~~~dL~g~~V~~~~g~~--~~~~l~~~--~~~~~~~~~~~~~~~~l  184 (274)
                      ++|++|.+.+.||.||+..+..++++++... +++++||+|++||+..|+.  ........  ..+++.+++..+++++|
T Consensus       106 ~~t~~r~~~~~fs~py~~~~~~~~~~~~~~~~~~~~~DL~gk~v~v~~gt~~~~~~~~~~~~~~~~~~~~~~~~~~~~al  185 (275)
T COG0834         106 TITPERKKKVDFSDPYYYSGQVLLVKKDSDIGIKSLEDLKGKKVGVQLGTTDEAEEKAKKPGPNAKIVAYDSNAEALLAL  185 (275)
T ss_pred             CCCHHHHHCCCCCCCEEECCEEEEEECCCCCCCCCHHHHCCCEEEEECCCHHHHHHHHHHCCCCCEEEECCCHHHHHHHH
T ss_conf             36877752005677736546589997688545589889589769996684588887764046774499818889999999


Q ss_pred             HHHHHHCCCCCHHHHHHH--HHHCCCCCCCEEECCCCCC-CCCEEEEEECC-CHHHHHHHHHHHHHHHHCCHHHHHHHHH
Q ss_conf             443210036655899999--9845876673262367768-77079998189-9899999999999999798599999876
Q gi|254781112|r  185 LSKRTDATMIPDIPFFNF--LERRPHDGNLFKIADRMKD-NSAVAFMMRKG-NNKLTRSINEILCAIHLDGTYKKIFDRY  260 (274)
Q Consensus       185 ~~grvD~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~-~~~~~~~~~k~-~~~L~~~in~~l~~l~~~G~~~~I~~kw  260 (274)
                      .+||+|+++.+...+.++  ..+.+..   ......... ..+++++++++ +.+|++.+|++|.+++++|++++|++||
T Consensus       186 ~~Gr~Da~~~d~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~n~~l~~l~~~G~~~~i~~kw  262 (275)
T COG0834         186 KNGRADAVVSDSAVLAGLKLLKKNPGL---YVLLVFPGLSVEYLGIALRKGDDPELLEAVNKALKELKADGTLQKISDKW  262 (275)
T ss_pred             HCCCCCEEEECHHHHHHHHHHHCCCCC---CCCCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHH
T ss_conf             849988997068887666653015565---32114556654320001246855999999999999998197099999986


Q ss_pred             CCCCCC
Q ss_conf             788877
Q gi|254781112|r  261 FDKNII  266 (274)
Q Consensus       261 ~g~d~~  266 (274)
                      |+.+..
T Consensus       263 ~~~~~~  268 (275)
T COG0834         263 FGPDDY  268 (275)
T ss_pred             CCCCCC
T ss_conf             685433


No 12 
>PRK10859 putative transglycosylase; Provisional
Probab=99.97  E-value=4.2e-31  Score=212.02  Aligned_cols=222  Identities=22%  Similarity=0.318  Sum_probs=190.5

Q ss_pred             HHHHHCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCCCCCC-CHHHHHHHHHCCCCCCC-HHCCCC
Q ss_conf             8788589589996289987248704699848898852167899762998555668-98898864310322110-000367
Q gi|254781112|r   35 FRTEDQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFET-AVSGLITGLDTNRYDVL-VNVAIT  112 (274)
Q Consensus        35 ~~~~~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~~~~~-~~~~~~~~l~~g~~D~~-~~~~~t  112 (274)
                      .+++++|+|||++..+  |-+|+..  .|++.||++||++..++.+|+++++++. +.+.+++.|++|+.|++ +|+++|
T Consensus        37 ~~I~~rG~LrV~T~~s--pttYy~~--~~~~~GFEYELak~FA~~LGV~L~i~~~~~~~el~~~L~~G~~DiaAAgLt~t  112 (507)
T PRK10859         37 AAIQARGELRVSTIHS--PLTYSTI--NGKPFGLDYELAKQFADYLGVKLKVTVRQNISQLFDDLDNGNADLLAAGLVYN  112 (507)
T ss_pred             HHHHHCCEEEEEEECC--CCEEEEC--CCCCCCHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHCCCCCEEECCCCCC
T ss_conf             9999789689999758--9659941--99647799999999999809917999749999999998679988895578778


Q ss_pred             HHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCHHHHHHHCCCC------C--CEEECCHHHHHHHH
Q ss_conf             567542002333222222222111222211111233432023101012233201345------4--21336855777755
Q gi|254781112|r  113 PERQKKYDFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTDLSRFAKELKS------H--LVFSHNFEQSLQLL  184 (274)
Q Consensus       113 ~eR~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~dL~g~~V~~~~g~~~~~~l~~~~~------~--~~~~~~~~~~~~~l  184 (274)
                      ++|.+.+.|+.||+..+..+|.|++..+.++++||.|++|.+..|+.+.+.+++.+.      .  ...-.+.++.++++
T Consensus       113 ~~R~~~~~~~p~Y~~v~q~LVyr~g~~rP~~l~DL~G~~I~V~~gSsy~e~L~~Lk~~~~P~L~w~~~~~~~teeLL~~V  192 (507)
T PRK10859        113 SERVKNYQPGPTYYSVSQQLVYRVGQYRPRTLGDLTGEQLTVAPGHVVVNDLQTLKETKFPELSWKVDDKKGSAELLEQV  192 (507)
T ss_pred             HHHHHCCCCCCCCCCEEEEEEEECCCCCCCCHHHCCCCEEEECCCCHHHHHHHHHHHCCCCCEEEEECCCCCHHHHHHHH
T ss_conf             53674043568650300399995899898897783798699817975999999988534897159955899999999999


Q ss_pred             HHHHHHCCCCCHHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEEEECCC-HHHHHHHHHHHHHHHHCCHHHHHHHHHCCC
Q ss_conf             4432100366558999999845876673262367768770799981899-899999999999999798599999876788
Q gi|254781112|r  185 LSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKGN-NKLTRSINEILCAIHLDGTYKKIFDRYFDK  263 (274)
Q Consensus       185 ~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~-~~L~~~in~~l~~l~~~G~~~~I~~kw~g~  263 (274)
                      .+|++|++++|...+.-...-.|..    .+......+.++++++++++ ..|...+++.+.+++++|++.+|.+||||.
T Consensus       193 ~~g~IdyTVaDS~~~~l~qr~~P~L----~vaf~l~~~~~iaWa~~k~~d~sL~~al~~ff~~~~~~g~l~~L~erYfgh  268 (507)
T PRK10859        193 IEGKLDYTIADSVAISLFQRVHPEL----AVALDVTDEQPVTWFSPLDDDNTLSAALLDFFNEMNEDGTLARLEEKYLGH  268 (507)
T ss_pred             HCCCCCEEEECCHHHHHHHHHCCCH----HCCCCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHCC
T ss_conf             7598776885548899877648440----122456887513788458997899999999999850484899999998455


Q ss_pred             C
Q ss_conf             8
Q gi|254781112|r  264 N  264 (274)
Q Consensus       264 d  264 (274)
                      -
T Consensus       269 ~  269 (507)
T PRK10859        269 G  269 (507)
T ss_pred             C
T ss_conf             2


No 13 
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=99.94  E-value=1.3e-25  Score=178.07  Aligned_cols=223  Identities=14%  Similarity=0.179  Sum_probs=178.9

Q ss_pred             HHHCCCEEEEE-CCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCCCCCC-CHHHHHHHHHCCCCCCCHH-CCCCH
Q ss_conf             88589589996-289987248704699848898852167899762998555668-9889886431032211000-03675
Q gi|254781112|r   37 TEDQSALRVGT-DGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFET-AVSGLITGLDTNRYDVLVN-VAITP  113 (274)
Q Consensus        37 ~~~~~~l~v~~-~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~~~~~-~~~~~~~~l~~g~~D~~~~-~~~t~  113 (274)
                      -.++++|+||+ .++||||.+.  ++.+.++|+.+|++..|++.+|++++++.. +++..+++|++|++|++.+ ...++
T Consensus        52 L~~~~~l~vgv~~pd~~Pf~~~--~~~~~yeGI~ADYl~li~~~L~~~i~v~~y~~r~~al~AL~~GeIDl~~~~~~~~~  129 (1197)
T PRK09959         52 LASKKNLVIAVHKSQTATLLHT--DSQQRVRGINADYLNLLKRALNIKLTLREYADHQKAMDALEEGEVDIVLSHLVASP  129 (1197)
T ss_pred             HHHCCEEEEEEECCCCCCEEEE--CCCCCCCCCCHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCCEECCCCCCCC
T ss_conf             9738858997106889996772--79986468479999999998689879995699999999997599756345444576


Q ss_pred             HHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCHHHHHHHC--CCCCCEEECCHHHHHHHHHHHHHHC
Q ss_conf             67542002333222222222111222211111233432023101012233201--3454213368557777554432100
Q gi|254781112|r  114 ERQKKYDFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTDLSRFAKE--LKSHLVFSHNFEQSLQLLLSKRTDA  191 (274)
Q Consensus       114 eR~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~dL~g~~V~~~~g~~~~~~l~~--~~~~~~~~~~~~~~~~~l~~grvD~  191 (274)
                      .++..+.+|.||..+..+++++.+.. .....+.++.+|+.+.++.....+++  +..+++.|++..+++.++..|++|+
T Consensus       130 ~~~~~~~~s~p~~~~~p~~v~~~~~~-~~~~~~~~~~~va~v~~y~~~~~i~~~yP~a~i~~~~s~~~Al~AVa~G~aD~  208 (1197)
T PRK09959        130 PLNDDIAATKPLIITFPALVTTLHDS-MRPLTSSKPVNIARVANYPPDEVIHQSFPKATIISFTNLYQALASVSAGQNDY  208 (1197)
T ss_pred             CCCCCCCCCCCCCCCCCEEEEECCCC-CCCCCCCCCEEEEEECCCCCHHHHHHHCCCCEEEECCCHHHHHHHHHCCCCCE
T ss_conf             42346533685323675589973333-58765677527999578898799998599666996689999999997799888


Q ss_pred             CCCCHHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEEEECCCHHHHHHHHHHHHHHHHCCHHHHHHHHHCC-CC
Q ss_conf             36655899999984587667326236776877079998189989999999999999979859999987678-88
Q gi|254781112|r  192 TMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYFD-KN  264 (274)
Q Consensus       192 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~L~~~in~~l~~l~~~G~~~~I~~kw~g-~d  264 (274)
                      ++++..++.+++.+.......+. ........+..|++++++..|.+.+|++|+.+... .-.+|.++|++ -+
T Consensus       209 ~igd~~s~~~li~~~~~~~l~~~-~~~~~~~~~~~f~~~~~~~~L~~~in~~L~~i~~~-~~~~i~~rW~~~~~  280 (1197)
T PRK09959        209 FIGSNIITSSMISRYFTHSLNVV-KYYNSPRQYNFFLTRKESVILNEVLNRFVDALTNE-VRYEVSQNWLDTGN  280 (1197)
T ss_pred             EEECHHHHHHHHHHHCCCCEEEE-ECCCCCCCCEEEEECCCCHHHHHHHHHHHHHCCHH-HHHHHHHHCCCCCC
T ss_conf             96029999999974402680352-12457764415787887578999999999837966-79999972367798


No 14 
>COG4623 Predicted soluble lytic transglycosylase fused to an ABC-type amino acid-binding protein [Cell envelope biogenesis, outer membrane]
Probab=99.90  E-value=3.2e-23  Score=163.28  Aligned_cols=222  Identities=22%  Similarity=0.315  Sum_probs=187.3

Q ss_pred             HHHHHHCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCCCCCCCH-HHHHHHHHCCCCCCCH-HCCC
Q ss_conf             8878858958999628998724870469984889885216789976299855566898-8988643103221100-0036
Q gi|254781112|r   34 PFRTEDQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAV-SGLITGLDTNRYDVLV-NVAI  111 (274)
Q Consensus        34 ~~~~~~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~~~~~~~-~~~~~~l~~g~~D~~~-~~~~  111 (274)
                      -+.++..|+|+|++..+  |.+|...  +|.+.|+++|++++.++.+|+++++++.+- ++++.+|++|+.|+++ |..+
T Consensus        16 l~~Iq~rGvLrV~tins--p~sy~~~--~~~p~G~eYelak~Fa~yLgV~Lki~~~~n~dqLf~aL~ng~~DL~Aagl~~   91 (473)
T COG4623          16 LAAIQARGVLRVSTINS--PLSYFED--KGGPTGLEYELAKAFADYLGVKLKIIPADNIDQLFDALDNGNADLAAAGLLY   91 (473)
T ss_pred             HHHHHHCCEEEEEEECC--CCCEECC--CCCCCCHHHHHHHHHHHHHCCEEEEEECCCHHHHHHHHHCCCCCEECCCCCC
T ss_conf             89998668079984058--6500003--7986535599999999985976899866778889999857993324265667


Q ss_pred             CHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCHHHHHHHCCC-----C---CCEEECCHHHHHHH
Q ss_conf             756754200233322222222211122221111123343202310101223320134-----5---42133685577775
Q gi|254781112|r  112 TPERQKKYDFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTDLSRFAKELK-----S---HLVFSHNFEQSLQL  183 (274)
Q Consensus       112 t~eR~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~dL~g~~V~~~~g~~~~~~l~~~~-----~---~~~~~~~~~~~~~~  183 (274)
                      .++|.+.+.....|+..++.++.|++..+.+++++|+|++|-+..|+...+-++..+     .   ++-.....++.+.+
T Consensus        92 ~~~~l~~~~~gP~y~svs~qlVyRkG~~Rp~~l~~L~g~~i~v~~gs~~~~~l~~lk~~kyP~l~~k~d~~~~~~dLle~  171 (473)
T COG4623          92 NSERLKNFQPGPTYYSVSQQLVYRKGQYRPRSLGQLKGRQITVAKGSAHVEDLKLLKETKYPELIWKVDDKLGVEDLLEM  171 (473)
T ss_pred             CHHHHCCCCCCCCEECCCHHHHHHCCCCCCCCHHHCCCCEEECCCCCHHHHHHHHHHHHHCCHHHHHHCCCCCHHHHHHH
T ss_conf             96674046788720022588876528878788887367556406996888999999873163443020221269999999


Q ss_pred             HHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEEEECC-CHHHHHHHHHHHHHHHHCCHHHHHHHHHCC
Q ss_conf             5443210036655899999984587667326236776877079998189-989999999999999979859999987678
Q gi|254781112|r  184 LLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKG-NNKLTRSINEILCAIHLDGTYKKIFDRYFD  262 (274)
Q Consensus       184 l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~-~~~L~~~in~~l~~l~~~G~~~~I~~kw~g  262 (274)
                      +..|++|+.+.+...+..+.+-.|...    +........+.++.++.+ +..|...++..+.+++++|-+++|.+||+|
T Consensus       172 v~~Gkldytiads~~is~~q~i~P~la----Vafd~tde~~v~Wy~~~~dd~tL~a~ll~F~~~~~e~g~larleeky~g  247 (473)
T COG4623         172 VAEGKLDYTIADSVEISLFQRVHPELA----VAFDLTDEQPVAWYLPRDDDSTLSAALLDFLNEAKEDGLLARLEEKYLG  247 (473)
T ss_pred             HHCCCCCEEEECCHHHHHHHHHCCCCE----EEEECCCCCCCEEECCCCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHC
T ss_conf             964776615516188898988572221----3220135667346605896688999999999873052078999999724


Q ss_pred             C
Q ss_conf             8
Q gi|254781112|r  263 K  263 (274)
Q Consensus       263 ~  263 (274)
                      +
T Consensus       248 H  248 (473)
T COG4623         248 H  248 (473)
T ss_pred             C
T ss_conf             4


No 15 
>KOG1052 consensus
Probab=99.57  E-value=8.1e-14  Score=105.14  Aligned_cols=226  Identities=25%  Similarity=0.358  Sum_probs=156.9

Q ss_pred             CCCEEEEECCCCCCEEEEEEC-----CCCCEEEEEEEEHHHHHHHCCCCCCCCCC-----------CHHHHHHHHHCCCC
Q ss_conf             895899962899872487046-----99848898852167899762998555668-----------98898864310322
Q gi|254781112|r   40 QSALRVGTDGIYPPHSFHAQD-----GRGELTGFDIDLIKEVAHRLNLKVEFFET-----------AVSGLITGLDTNRY  103 (274)
Q Consensus        40 ~~~l~v~~~~~~pP~~~~~~d-----~~g~~~G~~~dl~~~i~~~lg~~~~~~~~-----------~~~~~~~~l~~g~~  103 (274)
                      ..+++|++-.. +||.....+     ++....||++|+++++++.++++++++.+           .|++++..|.+|++
T Consensus       215 ~~~l~v~~~~~-~P~~~~~~~~~~~~~~~~~~G~~idll~~l~~~l~f~~~~~~~~~~~g~~~~~g~~~g~v~~l~~~~a  293 (656)
T KOG1052         215 GKPLRVGVVTE-PPFVDLVEDLAILNGNDRIEGFEIDLLQALAKRLNFSYEIIFVPDGSGSRDPNGNWDGLVGQLVDGEA  293 (656)
T ss_pred             CCEEEEEEECC-CCCEEEECCCCCCCCCCCCCEEEHHHHHHHHHHCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHCCCE
T ss_conf             95379987715-89525630433457776401260999999998769758999625788886888876789999971813


Q ss_pred             CCCHHCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCC-------------------------------------------
Q ss_conf             1100003675675420023332222222221112222-------------------------------------------
Q gi|254781112|r  104 DVLVNVAITPERQKKYDFSIPYIAHRVLLVVRSDQQD-------------------------------------------  140 (274)
Q Consensus       104 D~~~~~~~t~eR~~~~~fs~p~~~~~~~~~~~~~~~~-------------------------------------------  140 (274)
                      |+.++++++++|++.++||.||+.....+++++....                                           
T Consensus       294 dvg~~~tit~~R~~~vdfT~p~~~~~~~i~~~~~~~~~~~~~fl~Pf~~~vW~~i~~~~l~~~~~~~~~~~~~~~~~~~~  373 (656)
T KOG1052         294 DVGADITITPERSKYVDFTIPYLQFGIVIIVRKPDSRSKLWNFLAPFSPEVWLLILASLLLVGLLLWILERLSPYELPPR  373 (656)
T ss_pred             EEEECEEECCCHHHCEEECCEEEECCEEEEEEECCCCCHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf             00103176002030053213287545799998267420177874667189999999999999999987753044113543


Q ss_pred             --------------------------------------------------------------------CCCCCCCC---C
Q ss_conf             --------------------------------------------------------------------11111233---4
Q gi|254781112|r  141 --------------------------------------------------------------------IRSFKDLT---D  149 (274)
Q Consensus       141 --------------------------------------------------------------------~~~~~dL~---g  149 (274)
                                                                                          +++++||.   +
T Consensus       374 ~~~~~~~~~~~~~~~~~~~~~~q~~~~~p~~~~~Rll~~~w~~~~lil~ssYTa~L~a~Lt~~~~~~~i~~~~dL~~~~~  453 (656)
T KOG1052         374 QIVTSLFSLLNCLWLTVGSLLQQGSDEIPRSLSTRLLLGAWWLFVLILISSYTANLTAFLTVPRLRSPIDSLDDLADQSN  453 (656)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHEEEECCCCCCCCCCHHHHHHHCC
T ss_conf             23121123667789988765512565466307799999999999999998755732301451567887357999987508


Q ss_pred             CCEEEECCCHHHHHHHCC-------CC-CCEEECCHHHHHHHHHHHH---HHCCCCCHHHHHHHHHHCCCCCCCEEECCC
Q ss_conf             320231010122332013-------45-4213368557777554432---100366558999999845876673262367
Q gi|254781112|r  150 KTVAQILGTDLSRFAKEL-------KS-HLVFSHNFEQSLQLLLSKR---TDATMIPDIPFFNFLERRPHDGNLFKIADR  218 (274)
Q Consensus       150 ~~V~~~~g~~~~~~l~~~-------~~-~~~~~~~~~~~~~~l~~gr---vD~~~~~~~~~~~~~~~~~~~~~~~~~~~~  218 (274)
                      ..+|...|+....++++.       .. ..+.+.+.++....+.+|.   +. ++.+.....++.....  ...+.....
T Consensus       454 ~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~v~~~~~~~~~-~~~~~~~~~~~~~~~~--~c~~~~v~~  530 (656)
T KOG1052         454 IPYGTQRGSFTRIYLEESEDMWAFKVSQRSVPLASPEEGVERVRKGPSGGYA-FASDELYLAYLFLRDE--ICDLTEVGE  530 (656)
T ss_pred             CCCEEECCCHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHCCCCCCEE-EEECHHHHHHHHHHCC--CCCEEEECC
T ss_conf             7710233605678776527765332146554568999999999669987679-9941377999986236--862488066


Q ss_pred             CCCCCCEEEEEECCCHHHHHHHHHHHHHHHHCCHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf             7687707999818998999999999999997985999998767888775689877
Q gi|254781112|r  219 MKDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYFDKNIISSVPGCS  273 (274)
Q Consensus       219 ~~~~~~~~~~~~k~~~~L~~~in~~l~~l~~~G~~~~I~~kw~g~d~~~~~~~~~  273 (274)
                      .....+++ +++++++ |+..++.+|.++.+.|.++++.+||+-..--  .|.|+
T Consensus       531 ~~~~~~~~-~~~~~Sp-l~~~is~~Il~l~e~g~l~~~~~kw~~~~~~--~~~~~  581 (656)
T KOG1052         531 PFLYKGYG-AFPKGSP-LRSLISRAILKLQETGILQKLKRKWFSKKPC--LPKCS  581 (656)
T ss_pred             CCCCCCEE-EECCCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC--CCCCC
T ss_conf             45657645-7618983-4788749999856517999999998525776--76555


No 16 
>TIGR03431 PhnD phosphonate ABC transporter, periplasmic phosphonate binding protein. Note that this model does not identify all phnD-subfamily genes with evident phosphonate context, but all sequences above the trusted context may be inferred to bind phosphonate compounds even in the absence of such context. Furthermore, there is ample evidence to suggest that many other members of the TIGR01098 subfamily have a different primary function.
Probab=99.52  E-value=1.8e-13  Score=103.06  Aligned_cols=207  Identities=18%  Similarity=0.237  Sum_probs=132.5

Q ss_pred             CCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCCCCC-CCHHHHHHHHHCCCCCCCH-H-CCCCHHHH
Q ss_conf             8958999628998724870469984889885216789976299855566-8988988643103221100-0-03675675
Q gi|254781112|r   40 QSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFE-TAVSGLITGLDTNRYDVLV-N-VAITPERQ  116 (274)
Q Consensus        40 ~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~~~~-~~~~~~~~~l~~g~~D~~~-~-~~~t~eR~  116 (274)
                      ..+|++|+-+...|-....     ++    --+.+.+.+.+|.+++++. .++...++++.+|++|++. + .++-.-. 
T Consensus        26 p~~l~~gv~P~~~~~~~~~-----~~----~Pl~~yL~~~lg~~Ve~~~~~~y~~~~eal~~g~~Dia~~~p~~yv~a~-   95 (288)
T TIGR03431        26 PKELNFGIIPTENASDLKQ-----RW----EPLADYLSKKLGVKVKLFFATDYAGVIEGMRFGKVDIAWYGPSSYAEAY-   95 (288)
T ss_pred             CCEEEEEEECCCCHHHHHH-----HH----HHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCCEEEEECCHHHHHHH-
T ss_conf             8368999806999999999-----99----9999999998789789996899999999998598309998847889986-


Q ss_pred             HHHCCCCCCC---------CCCCCCCCCCCCCCCCCCCCCCCCCEEEEC-----CCHHH-HHH-HCCCC-------CCEE
Q ss_conf             4200233322---------222222211122221111123343202310-----10122-332-01345-------4213
Q gi|254781112|r  117 KKYDFSIPYI---------AHRVLLVVRSDQQDIRSFKDLTDKTVAQIL-----GTDLS-RFA-KELKS-------HLVF  173 (274)
Q Consensus       117 ~~~~fs~p~~---------~~~~~~~~~~~~~~~~~~~dL~g~~V~~~~-----g~~~~-~~l-~~~~~-------~~~~  173 (274)
                      +... ..|+.         .....+++|+|+ .+++++||+|++|+...     |+... ..+ ++.+.       ++..
T Consensus        96 ~~~~-~~~la~~~~~~g~~~y~s~iivr~Ds-~i~sl~DLkGk~iaf~~~~StSG~l~P~~~L~~~~g~~~~~~f~~v~~  173 (288)
T TIGR03431        96 QKAN-AEAFAIEVNADGSTGYYSVLIVKKDS-PIKSLEDLKGKTFGFVDPNSTSGFLVPSYYLFKKNGIKPKEYFKKVTF  173 (288)
T ss_pred             HCCC-CEEEEEEECCCCCCCEEEEEEEECCC-CCCCHHHHCCCEEEECCCCCCHHHHHHHHHHHHHCCCCHHHHHHHEEE
T ss_conf             5259-74889985158886457999998999-888778957987660287411113999999998659972545531331


Q ss_pred             ECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHC-CCCCCCEEECC--CCCCCCCEEEEEECC-CHHHHHHHHHHHHHHHH
Q ss_conf             368557777554432100366558999999845-87667326236--776877079998189-98999999999999997
Q gi|254781112|r  174 SHNFEQSLQLLLSKRTDATMIPDIPFFNFLERR-PHDGNLFKIAD--RMKDNSAVAFMMRKG-NNKLTRSINEILCAIHL  249 (274)
Q Consensus       174 ~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~-~~~~~~~~~~~--~~~~~~~~~~~~~k~-~~~L~~~in~~l~~l~~  249 (274)
                      ..+++.++..+.+|++|+..........+..+. +.....+++..  ++....  .++++++ ++++++.|-++|-.|.+
T Consensus       174 ~gshd~~~~aV~~G~~Dag~~~~~~~~~~~~~~~~~~~~~lrvi~~S~~iP~~--~~~v~~~l~~~~~~~i~~all~l~~  251 (288)
T TIGR03431       174 SGSHEAAILAVANGTVDAATTNDENLDRMIRKGQPDAMEDLRIIWKSPLIPNG--PIVYRKDLPADLKAKIRKAFLNYHK  251 (288)
T ss_pred             CCCHHHHHHHHHCCCCCEEEECHHHHHHHHHCCCCCHHHCEEEEEECCCCCCC--CEEEECCCCHHHHHHHHHHHHHCCC
T ss_conf             57878999999859932998338889999974796303136999867888877--1899699999999999999980786


Q ss_pred             CCHH-HHHHHHH
Q ss_conf             9859-9999876
Q gi|254781112|r  250 DGTY-KKIFDRY  260 (274)
Q Consensus       250 ~G~~-~~I~~kw  260 (274)
                      +.+- ..+.++|
T Consensus       252 ~d~~~~~~l~~~  263 (288)
T TIGR03431       252 TDKACFEKIAGG  263 (288)
T ss_pred             CCHHHHHHHHCC
T ss_conf             787689987425


No 17 
>KOG1053 consensus
Probab=99.50  E-value=2.9e-14  Score=107.91  Aligned_cols=196  Identities=18%  Similarity=0.228  Sum_probs=140.0

Q ss_pred             EEEEEEEHHHHHHHCCCCCCC-----------CCCCHHHHHHHHHCCCCCCCH-HCCCCHHHHHHHCCCCCCCCCCCCCC
Q ss_conf             898852167899762998555-----------668988988643103221100-00367567542002333222222222
Q gi|254781112|r   66 TGFDIDLIKEVAHRLNLKVEF-----------FETAVSGLITGLDTNRYDVLV-NVAITPERQKKYDFSIPYIAHRVLLV  133 (274)
Q Consensus        66 ~G~~~dl~~~i~~~lg~~~~~-----------~~~~~~~~~~~l~~g~~D~~~-~~~~t~eR~~~~~fs~p~~~~~~~~~  133 (274)
                      .||.+||++.+++.+|+.+..           +.--|++++.+|..+++|++. +.++++||.+.++||.|+..++..++
T Consensus       466 kGfCIDiLkKlA~~v~FtYDLYlVtnGKhGkk~ng~WnGmIGev~~~rA~MAVgSltINeeRSevVDFSvPFveTgIsVm  545 (1258)
T KOG1053         466 KGFCIDILKKLARDVKFTYDLYLVTNGKHGKKINGVWNGMIGEVVYQRADMAVGSLTINEERSEVVDFSVPFVETGISVM  545 (1258)
T ss_pred             HHHHHHHHHHHHHHCCCCEEEEEECCCCCCCEECCCCHHHHHHHHHHHHHEEEEEEEECHHHHCCCCCCCCCCCCCEEEE
T ss_conf             05569999998865386368999527754530057310268998752001366556753123120022244300461799


Q ss_pred             CCCCCCC----------------------------------CCCC-----CCCCCCC-----------------------
Q ss_conf             1112222----------------------------------1111-----1233432-----------------------
Q gi|254781112|r  134 VRSDQQD----------------------------------IRSF-----KDLTDKT-----------------------  151 (274)
Q Consensus       134 ~~~~~~~----------------------------------~~~~-----~dL~g~~-----------------------  151 (274)
                      ++..+..                                  +.+.     .--+|++                       
T Consensus       546 V~rsngtvspsAFLePfs~svWVmmFVm~livaai~vFlFEy~SPvgyn~~l~~gkkpggp~FtigkaiwllwaLvFnns  625 (1258)
T KOG1053         546 VARSNGTVSPSAFLEPFSPSVWVMMFVMCLIVAAITVFLFEYFSPVGYNRNLANGKKPGGPSFTIGKAIWLLWALVFNNS  625 (1258)
T ss_pred             EEECCCCCCCHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEHHHHHHHHHHHHHCCC
T ss_conf             98127865843530776457999999999999999998874207555364446777889863012067999999982787


Q ss_pred             EE--EECCCHH----------------------------HHHHHC-----------CCC---------------------
Q ss_conf             02--3101012----------------------------233201-----------345---------------------
Q gi|254781112|r  152 VA--QILGTDL----------------------------SRFAKE-----------LKS---------------------  169 (274)
Q Consensus       152 V~--~~~g~~~----------------------------~~~l~~-----------~~~---------------------  169 (274)
                      |.  ..+|++.                            +++..+           +..                     
T Consensus       626 Vpv~nPKgtTskiMv~VWAfFavifLAsYTANLAAfMIqE~~~d~vSGlsD~KfqrP~dq~PpFRFGTVpngSTE~niR~  705 (1258)
T KOG1053         626 VPVENPKGTTSKIMVLVWAFFAVIFLASYTANLAAFMIQEEYYDTVSGLSDPKFQRPHDQYPPFRFGTVPNGSTERNIRS  705 (1258)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHH
T ss_conf             68889973188999999999999999998877888876330121204667401268644589841004789844666775


Q ss_pred             ---------CCEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEEEECCCHHHHHHH
Q ss_conf             ---------42133685577775544321003665589999998458766732623677687707999818998999999
Q gi|254781112|r  170 ---------HLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKGNNKLTRSI  240 (274)
Q Consensus       170 ---------~~~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~L~~~i  240 (274)
                               ......+.++++..|++|+.||++.|..+..|..-+..+......-.+.+....+|+++++|+++ +...|
T Consensus       706 Nyp~MHeYM~kyNq~~v~dal~sLK~gKLDAFIyDaAVLnY~agkDegCKLvTIGsgKvFAttGYGIal~k~Sp-wkr~I  784 (1258)
T KOG1053         706 NYPEMHEYMVKYNQPGVEDALESLKNGKLDAFIYDAAVLNYMAGKDEGCKLVTIGSGKVFATTGYGIALPKNSP-WKRQI  784 (1258)
T ss_pred             CCHHHHHHHHHHCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCEEEEECCCCEEEECCEEEECCCCCC-CHHHH
T ss_conf             50999999998566760889998761660167788888777633577964898327735654020340389995-04467


Q ss_pred             HHHHHHHHHCCHHHHHHHHHCC
Q ss_conf             9999999979859999987678
Q gi|254781112|r  241 NEILCAIHLDGTYKKIFDRYFD  262 (274)
Q Consensus       241 n~~l~~l~~~G~~~~I~~kw~g  262 (274)
                      |.+|-+...+|+++++..+|+-
T Consensus       785 dlallQy~gdGeme~Le~~Wlt  806 (1258)
T KOG1053         785 DLALLQYLGDGEMEMLETLWLT  806 (1258)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHH
T ss_conf             8999987166569999877730


No 18 
>TIGR01098 3A0109s03R phosphonate ABC transporter, periplasmic phosphonate-binding protein; InterPro: IPR005770    Bacterial binding protein-dependent transport systems ,  are multicomponent systems typically composed of a periplasmic substrate-binding protein, one or two reciprocally homologous integral inner-membrane proteins and one or two peripheral membrane ATP-binding proteins that couple energy to the active transport system. The integral inner-membrane proteins translocate the substrate across the membrane. It has been shown ,  that most of these proteins contain a conserved region located about 80 to 100 residues from their C-terminal extremity. This region seems  to be located in a cytoplasmic loop between two transmembrane domains. Apart from the conserved region, the sequence of these proteins is quite divergent, and they have a variable number of transmembrane helices.    This is a family of periplasmic proteins which are part of the transport system for alkylphosphonate uptake. ; GO: 0015604 phosphonate transmembrane transporter activity, 0015716 phosphonate transport, 0030288 outer membrane-bounded periplasmic space.
Probab=99.38  E-value=1.3e-12  Score=97.76  Aligned_cols=195  Identities=22%  Similarity=0.238  Sum_probs=132.3

Q ss_pred             CCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCCCCC-CCHHHHHHHHHCCCCCCCH--HCCCC-H-H
Q ss_conf             8958999628998724870469984889885216789976299855566-8988988643103221100--00367-5-6
Q gi|254781112|r   40 QSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFE-TAVSGLITGLDTNRYDVLV--NVAIT-P-E  114 (274)
Q Consensus        40 ~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~~~~-~~~~~~~~~l~~g~~D~~~--~~~~t-~-e  114 (274)
                      .++|++|+-++--|-...   .+.+      -|...+-++||++|++.+ .++..++++++.|++|+.+  +.+|- . .
T Consensus        50 p~~l~~g~~P~e~~~~~~---~~~~------pL~~~Lek~Lg~kV~~~~~~dY~a~IEamr~g~~D~a~~g~~sY~~A~~  120 (299)
T TIGR01098        50 PKELNFGILPGENASNLA---RRWE------PLKDYLEKKLGIKVELFVATDYSAVIEAMRFGRVDIAWFGPSSYVLAHR  120 (299)
T ss_pred             CCEEEEEEECCCCHHHHH---HHHH------HHHHHHHHHCCCCEEEEEECCCCCEEEEECCCCEEEEEECCCHHHEEEE
T ss_conf             772689984488755777---7668------9999888755886799861683103342326807898347851232200


Q ss_pred             HHHHHCCC---------CCCCCCCCCCCCCCCCCCCCCCCC----CCCCCEEEEC-----CCHHH-HHHH-C----CC--
Q ss_conf             75420023---------332222222221112222111112----3343202310-----10122-3320-1----34--
Q gi|254781112|r  115 RQKKYDFS---------IPYIAHRVLLVVRSDQQDIRSFKD----LTDKTVAQIL-----GTDLS-RFAK-E----LK--  168 (274)
Q Consensus       115 R~~~~~fs---------~p~~~~~~~~~~~~~~~~~~~~~d----L~g~~V~~~~-----g~~~~-~~l~-~----~~--  168 (274)
                      |...-.|.         ++=-.+...++++++++ |++++|    |+||++|..-     |+... .++. +    ..  
T Consensus       121 ~~~~~~~a~~~~~~~~~~g~~~Y~S~~iv~~dS~-i~~~~DlL~~LKGK~~af~Dp~STSG~l~P~~~l~~~~~~~~~~~  199 (299)
T TIGR01098       121 RANAEAFALTAIRYVSTDGSPGYYSVIIVKADSP-IKSLKDLLKKLKGKTFAFGDPASTSGYLVPRYQLLKEGGLDADKD  199 (299)
T ss_pred             CCCCCHHHHHHHHHCCCCCCCCEEEEEEECCCCC-CCCHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHCCCCCCC
T ss_conf             1387012134433116888983489999838999-633899997507975985068875124778899876507898885


Q ss_pred             -----CCCEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC-------------CCCEEECC--CCCCCCCEEEE
Q ss_conf             -----54213368557777554432100366558999999845876-------------67326236--77687707999
Q gi|254781112|r  169 -----SHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHD-------------GNLFKIAD--RMKDNSAVAFM  228 (274)
Q Consensus       169 -----~~~~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~-------------~~~~~~~~--~~~~~~~~~~~  228 (274)
                           .+++...++++.+..+.+|++|+++.............+..             ...+++..  +++...+  ++
T Consensus       200 d~~~F~~~~~~G~Hd~~~~~V~nG~vDaA~~~~~~~~~~~~~~~~~~~~~~~~~g~~D~~~~~~vI~~S~~IPndp--~~  277 (299)
T TIGR01098       200 DDKFFSEVVFSGSHDASILAVANGKVDAATNNSSAIERLKKRGPSDKFKKKVAKGATDLMKKVRVIWKSPLIPNDP--IA  277 (299)
T ss_pred             CCCCCCEEEEECCHHHHHHHHHHCCCCEEEECHHHHHHHHHCCCCCCCCEEECCCCCCCHHCEEEEEECCCCCCCC--EE
T ss_conf             3452332688431589999988088545765304466565303235651552047767137017875237877875--46


Q ss_pred             EECC-CH--HHHHHHHHHHHH
Q ss_conf             8189-98--999999999999
Q gi|254781112|r  229 MRKG-NN--KLTRSINEILCA  246 (274)
Q Consensus       229 ~~k~-~~--~L~~~in~~l~~  246 (274)
                      +|++ ++  +|++.|-+++..
T Consensus       278 ~R~~L~~yP~~k~ki~~~F~~  298 (299)
T TIGR01098       278 VRSDLPPYPELKEKIRDAFLD  298 (299)
T ss_pred             EECCCCCCHHHHHHHHHHHHC
T ss_conf             525789667799999999851


No 19 
>TIGR02285 TIGR02285 conserved hypothetical protein; InterPro: IPR011972    Members of this family are found in several Proteobacteria, including Pseudomonas putida (strain KT2440), Bdellovibrio bacteriovorus HD100 (three members), Aeromonas hydrophila, and Chromobacterium violaceum ATCC 12472. The function is unknown..
Probab=99.36  E-value=1.2e-11  Score=91.70  Aligned_cols=222  Identities=21%  Similarity=0.275  Sum_probs=148.5

Q ss_pred             CCCEEEEECCCCCCEEEEEECCC------CCEEEEEEEEHHHHHHHC-CCCCCCCCCCHHHHHHHHHCCCCCCC-HHCCC
Q ss_conf             89589996289987248704699------848898852167899762-99855566898898864310322110-00036
Q gi|254781112|r   40 QSALRVGTDGIYPPHSFHAQDGR------GELTGFDIDLIKEVAHRL-NLKVEFFETAVSGLITGLDTNRYDVL-VNVAI  111 (274)
Q Consensus        40 ~~~l~v~~~~~~pP~~~~~~d~~------g~~~G~~~dl~~~i~~~l-g~~~~~~~~~~~~~~~~l~~g~~D~~-~~~~~  111 (274)
                      +..|.+.+ .|+|||...  |+.      -+-.|..-.+..+|-.++ .++.+++.++..|....+++|+--++ .++-.
T Consensus        18 ~e~I~W~~-~D~PPf~I~--~G~Gmmvdi~~grG~~D~~~~~i~r~lP~Y~H~~~~~~~aR~~~~~Q~~~~~~C~~~ll~   94 (293)
T TIGR02285        18 KEAITWIV-SDLPPFFIF--DGPGMMVDIKKGRGVLDVVLKLIRRKLPEYEHRIVRVSVARSLKMLQQGKAVVCDVNLLK   94 (293)
T ss_pred             CCCCEEEE-ECCCCEEEE--ECCCEEEEECCCCCCCHHHHHHHHHHCCCCCCEEEEEEHHHHHHHHHCCCCCCCCCCCCC
T ss_conf             72111511-147872687--088028973168872033679999836547513899866789999863886021551447


Q ss_pred             CHHHHHHHCCC--CCCC-CCCCCCCCCCCCC-CCCCCC-----CCC------CCCEEEECC----CHHHHHHHCCCC---
Q ss_conf             75675420023--3322-2222222111222-211111-----233------432023101----012233201345---
Q gi|254781112|r  112 TPERQKKYDFS--IPYI-AHRVLLVVRSDQQ-DIRSFK-----DLT------DKTVAQILG----TDLSRFAKELKS---  169 (274)
Q Consensus       112 t~eR~~~~~fs--~p~~-~~~~~~~~~~~~~-~~~~~~-----dL~------g~~V~~~~g----~~~~~~l~~~~~---  169 (274)
                      ||||++++.||  .|.. ..+..++.++... .+....     ||.      +++.+++.|    .-.+..+.+.+.   
T Consensus        95 TPEReK~~~Fstf~~~~~~~p~glv~~~~~~~~~~~~~~G~~VdL~~Ll~~~~~~~~~~a~RsYg~~ID~~L~~~~~~~~  174 (293)
T TIGR02285        95 TPEREKFLIFSTFDPTLVVLPVGLVLRKELAAEVRDLADGDDVDLKKLLASKKLRLGVIASRSYGAQIDDILKDKKDKKN  174 (293)
T ss_pred             CCCHHHHEECCHHHHHHHHCCCCEEECCCCCCCCCHHCCCCCHHHHHHHCCCCCCEEEEEEECCHHHHHHHHHHCCCCCC
T ss_conf             86154320001247898647842365222232351120676101788731888644788630115789999973689624


Q ss_pred             -CCEEECCHHH-HHHHHHHHHHHCCCCCHHHHHHHHH-------------HCCCCCCCEEECC--CCCCCCCEEEEEECC
Q ss_conf             -4213368557-7775544321003665589999998-------------4587667326236--776877079998189
Q gi|254781112|r  170 -HLVFSHNFEQ-SLQLLLSKRTDATMIPDIPFFNFLE-------------RRPHDGNLFKIAD--RMKDNSAVAFMMRKG  232 (274)
Q Consensus       170 -~~~~~~~~~~-~~~~l~~grvD~~~~~~~~~~~~~~-------------~~~~~~~~~~~~~--~~~~~~~~~~~~~k~  232 (274)
                       +.+.-....+ .++||..||+++++.=.....||.+             +.......+....  ........+++-+|.
T Consensus       175 ~~~~~n~~~~nGl~~mL~~~R~~~tL~Y~~E~~Yy~~skfGyGsstvsdl~~~~~~~~~~~lpv~g~~~~i~v~vaCpkt  254 (293)
T TIGR02285       175 SRVIGNAASGNGLFKMLEKGRVQYTLAYPPEVVYYEESKFGYGSSTVSDLQKKGALAPLKFLPVAGVAAEISVVVACPKT  254 (293)
T ss_pred             CCEECCCCCHHHHHHHHHCCCCCEEECCHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCEEEEEECCCCCEEEEEEEECCC
T ss_conf             22205553035799997524333031452332444431145551468888724577881264004777677899840888


Q ss_pred             --CHHHHHHHHHHHHHHHHCCHHHHHHHHHCCCC
Q ss_conf             --98999999999999997985999998767888
Q gi|254781112|r  233 --NNKLTRSINEILCAIHLDGTYKKIFDRYFDKN  264 (274)
Q Consensus       233 --~~~L~~~in~~l~~l~~~G~~~~I~~kw~g~d  264 (274)
                        ..+.+..||++|.+...++.|.+.+.+|+.-+
T Consensus       255 ~wG~~~~~dId~~L~~~~~~~~~~~~~~rWL~~~  288 (293)
T TIGR02285       255 EWGRKVVADIDQLLSELKVDPKYEKAVDRWLSLE  288 (293)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCHHHHHHHCCCCHH
T ss_conf             7789999999999886430411254442048915


No 20 
>COG3221 PhnD ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=99.36  E-value=7e-12  Score=93.18  Aligned_cols=211  Identities=18%  Similarity=0.179  Sum_probs=133.5

Q ss_pred             HHHHCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCCCCC-CCHHHHHHHHHCCCCCCCH--HCCCC
Q ss_conf             78858958999628998724870469984889885216789976299855566-8988988643103221100--00367
Q gi|254781112|r   36 RTEDQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFE-TAVSGLITGLDTNRYDVLV--NVAIT  112 (274)
Q Consensus        36 ~~~~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~~~~-~~~~~~~~~l~~g~~D~~~--~~~~t  112 (274)
                      .....++|++|+.+.--|         .+......-+.+.+.+.+|+++++.. .++...++++.+|++|+++  +.++.
T Consensus        30 ~~~~~~~l~~gi~p~e~~---------~~~~~~~~pl~~~L~~~lG~~V~~~~a~dy~~vieal~~g~~D~A~~~~~a~~  100 (299)
T COG3221          30 AAEDPKELRVGIVPTENP---------TNLIPAWAPLADYLEKELGIPVEFFVATDYAAVIEALRAGQVDIAWLGPSAYV  100 (299)
T ss_pred             CCCCCCCEEEEECCCCCH---------HHHHHHHHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCEEEEECCCHHHH
T ss_conf             226875359997688886---------87887656699898898699543572576899999985896107741857789


Q ss_pred             HHHHHH--H---CCC-CCCC--CCCCCCCCCCCCCCCCCCCCCCCCCEEEEC-----CCHHH-HHHHCCC-C------CC
Q ss_conf             567542--0---023-3322--222222211122221111123343202310-----10122-3320134-5------42
Q gi|254781112|r  113 PERQKK--Y---DFS-IPYI--AHRVLLVVRSDQQDIRSFKDLTDKTVAQIL-----GTDLS-RFAKELK-S------HL  171 (274)
Q Consensus       113 ~eR~~~--~---~fs-~p~~--~~~~~~~~~~~~~~~~~~~dL~g~~V~~~~-----g~~~~-~~l~~~~-~------~~  171 (274)
                      ....+.  .   ..+ .+..  .+...+++++|++ +++++||+|||++...     |+... .++...+ .      ..
T Consensus       101 ~a~~~~~~~e~~~~~~~~dg~~~Y~S~~i~~~ds~-i~sl~dlkgk~~af~d~~StSG~l~P~~~L~~~g~~d~~~~f~~  179 (299)
T COG3221         101 EAVDRALAGEPLAQTVQKDGSPGYYSVIIVRADSP-IKSLEDLKGKRFAFGDPDSTSGYLFPLYYLAKEGGIDPDKFFGE  179 (299)
T ss_pred             HHHHHCCCCCCEEEEECCCCCCCEEEEEEEECCCC-CCHHHHHCCCEEECCCCCCCCHHHHHHHHHHHHCCCCHHHHHCE
T ss_conf             98641245420133212589865178999927997-43378826996763699854124768999998438984654226


Q ss_pred             EEE-CCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCC-CCCCEEECC--CCCCCCCEEEEEECC-CHHHHHHHHHHHHH
Q ss_conf             133-6855777755443210036655899999984587-667326236--776877079998189-98999999999999
Q gi|254781112|r  172 VFS-HNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPH-DGNLFKIAD--RMKDNSAVAFMMRKG-NNKLTRSINEILCA  246 (274)
Q Consensus       172 ~~~-~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~-~~~~~~~~~--~~~~~~~~~~~~~k~-~~~L~~~in~~l~~  246 (274)
                      +.+ .+++.++.++.+|++|+...............+. ....+.+..  ++....  .++++++ ++++++.+-++|..
T Consensus       180 v~~~G~H~~a~~aV~nG~vDva~~~~~~~~~~~~~~~~~~~~~l~vi~~S~~iP~~--pi~vr~~L~~~~k~kl~~af~~  257 (299)
T COG3221         180 VIFSGGHDAAVLAVANGQVDVAAVNSSARGLLKKAAPEGVAEKLRVIWKSPLIPND--PIAVRSDLPADLKEKLRDAFLD  257 (299)
T ss_pred             EECCCHHHHHHHHHHCCCCEEEECCHHHHHHHHHHCCCCCHHHCEEEEECCCCCCC--CEEEECCCCHHHHHHHHHHHHH
T ss_conf             50357079999999748830885228888777640433453342699955898999--7888377999999999999984


Q ss_pred             HHHCCHHHHHHH
Q ss_conf             997985999998
Q gi|254781112|r  247 IHLDGTYKKIFD  258 (274)
Q Consensus       247 l~~~G~~~~I~~  258 (274)
                      +.++-....|.+
T Consensus       258 l~~~~~~~~l~~  269 (299)
T COG3221         258 LAKTEDKKILLD  269 (299)
T ss_pred             CCCCCCCHHHHH
T ss_conf             374311358897


No 21 
>pfam00060 Lig_chan Ligand-gated ion channel. This family includes the four transmembrane regions of the ionotropic glutamate receptors and NMDA receptors.
Probab=99.18  E-value=1.9e-10  Score=84.36  Aligned_cols=126  Identities=17%  Similarity=0.228  Sum_probs=94.8

Q ss_pred             CCCCCCCCCCCCCCCCC---CEEEECCCHHHHHHHCCCC--------------CCEEECCHHHHHHHHHHHH-HHCCCCC
Q ss_conf             11122221111123343---2023101012233201345--------------4213368557777554432-1003665
Q gi|254781112|r  134 VRSDQQDIRSFKDLTDK---TVAQILGTDLSRFAKELKS--------------HLVFSHNFEQSLQLLLSKR-TDATMIP  195 (274)
Q Consensus       134 ~~~~~~~~~~~~dL~g~---~V~~~~g~~~~~~l~~~~~--------------~~~~~~~~~~~~~~l~~gr-vD~~~~~  195 (274)
                      +.+-...+++++||...   ++|+..++....+.++...              ....+.+.+++++.+.+|+ ++|++.+
T Consensus        95 ~~~~~~~I~~i~dL~~~~~~~~g~~~~~~~~~~f~~s~~~~~~~~~~~~~~~~~~~~~~~~~egi~~v~~g~~~~A~i~e  174 (270)
T pfam00060        95 VERMQSPIQSLEDLAKQNKIGYGTLRGGSTFEFFKESKNPTYRRMWEYMISFKGEVNVESYEEGVQRVRKGNGLYAFLME  174 (270)
T ss_pred             CCCCCCCCCCHHHHHHCCCCCEEEECCCCHHHHHHHCCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCCEEEEEC
T ss_conf             13347775789999867987311140761677778614306889999987506667778999999998658862899952


Q ss_pred             HHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEEEECCCHHHHHHHHHHHHHHHHCCHHHHHHHHHCCC
Q ss_conf             58999999845876673262367768770799981899899999999999999798599999876788
Q gi|254781112|r  196 DIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYFDK  263 (274)
Q Consensus       196 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~L~~~in~~l~~l~~~G~~~~I~~kw~g~  263 (274)
                      .....++..+.+-   .....++.....+++++++|++| +++.+|.+|.+++++|.++++.+||+..
T Consensus       175 ~~~l~~~~~~~~c---~l~~vg~~f~~~~~g~a~~k~Sp-~~~~~s~~il~l~E~G~l~~l~~kW~~~  238 (270)
T pfam00060       175 SAYLEYEVARDCC---KLTTVGEVFGTKGYGIAFPKGSP-LRDKLSRAILELRESGELQKLENKWWKK  238 (270)
T ss_pred             HHHHHHHHHHCCC---CCEEECCCCCCCCEEEEECCCCC-HHHHHHHHHHHHHHCCHHHHHHHHHCCC
T ss_conf             5889999970487---62780531145754688518993-0999999999987267899999864589


No 22 
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=99.17  E-value=9.2e-10  Score=80.06  Aligned_cols=211  Identities=13%  Similarity=0.134  Sum_probs=115.9

Q ss_pred             HHHCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHH-CCCCCCCCCCC-HHHHHHHHHCCCCCCCHHCCCCH-
Q ss_conf             8858958999628998724870469984889885216789976-29985556689-88988643103221100003675-
Q gi|254781112|r   37 TEDQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHR-LNLKVEFFETA-VSGLITGLDTNRYDVLVNVAITP-  113 (274)
Q Consensus        37 ~~~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~-lg~~~~~~~~~-~~~~~~~l~~g~~D~~~~~~~t~-  113 (274)
                      .....+||||......|.... . ..    |    +.   .+. .+.+++|...+ -..++++|..|.+|+.. +..+| 
T Consensus        23 ~~~~~~lrIgyq~~~~~~~~~-~-~~----~----~~---ek~~~~~kV~w~~F~~G~~~~eAl~aG~iD~~~-~g~~p~   88 (314)
T PRK11553         23 ESSPEALRIGYQKGSIGLVLA-K-SH----Q----LL---EKRFPQTKISWVEFPAGPQMLEALNVGSIDLGS-TGDIPP   88 (314)
T ss_pred             HCCCCEEEEEECCCCHHHHHH-H-HC----C----HH---HHHCCCCCEEEEECCCCHHHHHHHHCCCCCEEE-ECCHHH
T ss_conf             348975999961774158999-8-52----8----67---661789835899789748999999769975451-158589


Q ss_pred             --HHHHHH--CC--CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCHHHHH----HHCCCCC---CEE-ECCHHH
Q ss_conf             --675420--02--333222222222111222211111233432023101012233----2013454---213-368557
Q gi|254781112|r  114 --ERQKKY--DF--SIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTDLSRF----AKELKSH---LVF-SHNFEQ  179 (274)
Q Consensus       114 --eR~~~~--~f--s~p~~~~~~~~~~~~~~~~~~~~~dL~g~~V~~~~g~~~~~~----l~~~~~~---~~~-~~~~~~  179 (274)
                        ......  .+  ..+.......+++++++ .|++++||+||||++..|+..+.+    +++.+..   +.. .-.+.+
T Consensus        89 i~a~a~G~~~~~va~~~~~~~~~~i~V~~~S-~I~s~aDLkGKkVa~~~Gs~~~~~l~~aL~~aGL~~~DV~~v~l~p~d  167 (314)
T PRK11553         89 IFAQAAGADLVYVGVEPPKPKAEVILVAENS-PIKTVADLKGHKVAFQKGSSSHNLLLRALRQAGLKFTDIQPTYLTPAD  167 (314)
T ss_pred             HHHHHCCCCEEEEEEECCCCCCEEEEEECCC-CCCCHHHHCCCEEEEECCCHHHHHHHHHHHHCCCCHHHEEEEECCCHH
T ss_conf             9998669986999986378864189984898-778888938998974179737999999999869988991898459388


Q ss_pred             HHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEEEE---CCCHHHHHHHHHHHHHH----HHC-C
Q ss_conf             777554432100366558999999845876673262367768770799981---89989999999999999----979-8
Q gi|254781112|r  180 SLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMR---KGNNKLTRSINEILCAI----HLD-G  251 (274)
Q Consensus       180 ~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---k~~~~L~~~in~~l~~l----~~~-G  251 (274)
                      +..+|.+|+||++...+........+ ... ..+.-.........+.++-+   +++|++...+-+++.+.    +++ -
T Consensus       168 ~~aAl~~G~VDA~~~w~P~~~~a~~~-~ga-Rvl~dg~~~~~~~~~~~~~~~fa~~~p~~v~~~l~~l~~a~~w~~~~p~  245 (314)
T PRK11553        168 ARAAFQQGNVDAWAIWDPYYSAALLQ-GGV-RVLKDGTDLNQTGSFYLAARPYAEKNGAFIQQVLATLSEADALTRSQRA  245 (314)
T ss_pred             HHHHHHCCCCCEEEECCHHHHHHHHC-CCC-EEEECCCCCCCCCCEEEECHHHHHHCHHHHHHHHHHHHHHHHHHHHCHH
T ss_conf             99999669978899756789999862-895-8985376667776168861898887999999999999999999997999


Q ss_pred             HHHHHHHHHCCCC
Q ss_conf             5999998767888
Q gi|254781112|r  252 TYKKIFDRYFDKN  264 (274)
Q Consensus       252 ~~~~I~~kw~g~d  264 (274)
                      +..+++.+..|.+
T Consensus       246 eaa~i~A~~~gl~  258 (314)
T PRK11553        246 QSIALLAKTMGLP  258 (314)
T ss_pred             HHHHHHHHHHCCC
T ss_conf             9999999987929


No 23 
>smart00079 PBPe Eukaryotic homologues of bacterial periplasmic substrate binding proteins. Prokaryotic homologues are represented by a separate alignment: PBPb
Probab=99.12  E-value=4.4e-10  Score=82.05  Aligned_cols=116  Identities=16%  Similarity=0.215  Sum_probs=91.9

Q ss_pred             CCCCCCCCC---CCEEEECCCHHHHHHHCCCC-------------CCEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHH
Q ss_conf             111112334---32023101012233201345-------------42133685577775544321003665589999998
Q gi|254781112|r  141 IRSFKDLTD---KTVAQILGTDLSRFAKELKS-------------HLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLE  204 (274)
Q Consensus       141 ~~~~~dL~g---~~V~~~~g~~~~~~l~~~~~-------------~~~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~  204 (274)
                      |++++||..   .+.|++.|+....+.+....             .-..+.+.+++++.+.+|+ .|++.+.....++..
T Consensus         2 I~s~~DL~~q~~i~yGtv~~ss~~~fF~~s~~~~y~~mw~~m~~~~~~~v~~~~eGv~rv~~g~-yAfi~e~~~l~y~~~   80 (134)
T smart00079        2 ITSVEDLAKQTKIEYGTIRGSSTLAFFKRSGNPEYSRMWNYMSASPSVFVKSYAEGVQRVRVSN-YAFLMESTYLDYELS   80 (134)
T ss_pred             CCCHHHHHCCCCCEEEEECCCHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHCC-CEEECCCHHHHHHHC
T ss_conf             7998998428872016878963899988778658999999986285556677899999998078-235505147899860


Q ss_pred             HCCCCCCCEEECCCCCCCCCEEEEEECCCHHHHHHHHHHHHHHHHCCHHHHHHHHHCC
Q ss_conf             4587667326236776877079998189989999999999999979859999987678
Q gi|254781112|r  205 RRPHDGNLFKIADRMKDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYFD  262 (274)
Q Consensus       205 ~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~L~~~in~~l~~l~~~G~~~~I~~kw~g  262 (274)
                      +   + ..+...+.+....+++++++|++| |++.||.+|.+|+++|.+++|.+|||.
T Consensus        81 ~---~-C~l~~vG~~f~~~~ygia~~kgSp-~~~~is~~Il~l~e~G~l~~l~~kW~~  133 (134)
T smart00079       81 Q---N-CDLMTVGENFGRKGYGIAFPKGSP-LRDDLSRAILKLSESGELQKLENKWWK  133 (134)
T ss_pred             C---C-CCEEEECEEEECCCEEEEECCCCH-HHHHHHHHHHHHHHCCHHHHHHHHHCC
T ss_conf             6---7-874895306641545788339981-499999999998857879999986169


No 24 
>KOG1054 consensus
Probab=99.10  E-value=1.5e-10  Score=85.02  Aligned_cols=218  Identities=20%  Similarity=0.343  Sum_probs=141.6

Q ss_pred             CCCEEEEECCCCCCEEEEEE-----CCCCCEEEEEEEEHHHHHHHCCCCCCCCCC------------C-HHHHHHHHHCC
Q ss_conf             89589996289987248704-----699848898852167899762998555668------------9-88988643103
Q gi|254781112|r   40 QSALRVGTDGIYPPHSFHAQ-----DGRGELTGFDIDLIKEVAHRLNLKVEFFET------------A-VSGLITGLDTN  101 (274)
Q Consensus        40 ~~~l~v~~~~~~pP~~~~~~-----d~~g~~~G~~~dl~~~i~~~lg~~~~~~~~------------~-~~~~~~~l~~g  101 (274)
                      ..++.|-+.-.- ||.....     .++.++.||.+|++.+|++..|+++++...            . |++++..|-.|
T Consensus       416 n~tvvvttiL~s-pyvm~kkn~~~~egn~ryEGyCvdLa~~iAkhi~~~Y~l~iv~dgkyGardaD~k~WnGMvGeLv~g  494 (897)
T KOG1054         416 NRTVVVTTILES-PYVMLKKNHEQLEGNERYEGYCVDLAAEIAKHIGIKYKLFIVGDGKYGARDADTKIWNGMVGELVYG  494 (897)
T ss_pred             CCEEEEEEECCC-CHHHHHHHHHHHCCCCCCCEEHHHHHHHHHHHCCCEEEEEEECCCCCCCCCCCCCCCCCHHHHHHCC
T ss_conf             652899971379-5457775477731776431338999999997507417899923776566688764113346787558


Q ss_pred             CCCCC-HHCCCCHHHHHHHCCCCCCCCCCCCCCCCC-CC--CCCCCCCC-------------------------------
Q ss_conf             22110-000367567542002333222222222111-22--22111112-------------------------------
Q gi|254781112|r  102 RYDVL-VNVAITPERQKKYDFSIPYIAHRVLLVVRS-DQ--QDIRSFKD-------------------------------  146 (274)
Q Consensus       102 ~~D~~-~~~~~t~eR~~~~~fs~p~~~~~~~~~~~~-~~--~~~~~~~d-------------------------------  146 (274)
                      +.|++ +..++|.+|++.++||.|++.....+..++ +.  +.+-++-|                               
T Consensus       495 rAdiavApLTIt~~REeviDFSKPfMslGISIMIKKPqKsk~gVFSFldPLa~eIWm~ivfaYiGVSvvlFLVSrFSPYE  574 (897)
T KOG1054         495 RADIAVAPLTITLVREEVIDFSKPFMSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYE  574 (897)
T ss_pred             CCCEEEEEEEEEHHHHHHHCCCCCHHHCCEEEEEECCCCCCCCEEEECCHHHHHHHHHHHHHHHCCEEEEEEEECCCCHH
T ss_conf             43347722364301244642466344427689980766578870562154577899999998735158899874257301


Q ss_pred             --------------------------------------------CCCCCEE---------EECCCHH--HHH--------
Q ss_conf             --------------------------------------------3343202---------3101012--233--------
Q gi|254781112|r  147 --------------------------------------------LTDKTVA---------QILGTDL--SRF--------  163 (274)
Q Consensus       147 --------------------------------------------L~g~~V~---------~~~g~~~--~~~--------  163 (274)
                                                                  |.|.-+|         ++..++.  ..+        
T Consensus       575 wh~Ee~~rg~~t~~~~~NeFgifNsLWFsLgAFMQQG~DI~PRslSGRIvggvWWFFTlIIiSSYTANLAAFLTvErMvs  654 (897)
T KOG1054         575 WHTEEFERGRFTPSDPPNEFGIFNSLWFSLGAFMQQGCDISPRSLSGRIVGGVWWFFTLIIISSYTANLAAFLTVERMVS  654 (897)
T ss_pred             EECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCEECCCHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             00221146887888998621136778999999996577878310366551020555456454450567888886986348


Q ss_pred             --------HHCCCC--------------------------------C-CEEECCHHHHHHHHHHHHHHCCCCCHHHHHHH
Q ss_conf             --------201345--------------------------------4-21336855777755443210036655899999
Q gi|254781112|r  164 --------AKELKS--------------------------------H-LVFSHNFEQSLQLLLSKRTDATMIPDIPFFNF  202 (274)
Q Consensus       164 --------l~~~~~--------------------------------~-~~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~  202 (274)
                              +++...                                + -+.+.+.++++..+...+..+++.-+.+...|
T Consensus       655 PIESaEDLAkQteIaYGt~~~GSTkeFFr~Skiavy~kMW~yM~SaepsVFv~t~aeGv~rVRksKGkyAfLLEsTmNey  734 (897)
T KOG1054         655 PIESAEDLAKQTEIAYGTLDSGSTKEFFRRSKIAVYEKMWTYMKSAEPSVFVRTTAEGVARVRKSKGKYAFLLESTMNEY  734 (897)
T ss_pred             CCHHHHHHHHCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEHHHHHHHHHHHCCCCEEEEHHHHHHHH
T ss_conf             41128887522114344047874688886526799999999975179603654156689998733771675317566566


Q ss_pred             HHHCCCCCCCEEECCCCCCCCCEEEEEECCCHHHHHHHHHHHHHHHHCCHHHHHHHHHC
Q ss_conf             98458766732623677687707999818998999999999999997985999998767
Q gi|254781112|r  203 LERRPHDGNLFKIADRMKDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYF  261 (274)
Q Consensus       203 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~L~~~in~~l~~l~~~G~~~~I~~kw~  261 (274)
                      ..+..... ..++. .-....+|++|-++++ .|+..+|-++-.+.+.|+++++-+||.
T Consensus       735 ~eqRkPCD-TMKVG-gNLds~GYGiATp~Gs-slr~~vNLAvLkL~E~G~LdKLkNKWW  790 (897)
T KOG1054         735 IEQRKPCD-TMKVG-GNLDSKGYGIATPKGS-SLRNAVNLAVLKLNEQGLLDKLKNKWW  790 (897)
T ss_pred             HHCCCCCC-CEECC-CCCCCCCEEECCCCCC-CCCCCHHHHHHHHCCCCHHHHHHHHHC
T ss_conf             64369863-10106-6557765010477773-010202124220110243777642002


No 25 
>KOG4440 consensus
Probab=99.05  E-value=1.1e-10  Score=85.82  Aligned_cols=192  Identities=15%  Similarity=0.240  Sum_probs=132.7

Q ss_pred             EEEEEEEHHHHHHHCCCCCCCC--------------------CCCHHHHHHHHHCCCCCCC-HHCCCCHHHHHHHCCCCC
Q ss_conf             8988521678997629985556--------------------6898898864310322110-000367567542002333
Q gi|254781112|r   66 TGFDIDLIKEVAHRLNLKVEFF--------------------ETAVSGLITGLDTNRYDVL-VNVAITPERQKKYDFSIP  124 (274)
Q Consensus        66 ~G~~~dl~~~i~~~lg~~~~~~--------------------~~~~~~~~~~l~~g~~D~~-~~~~~t~eR~~~~~fs~p  124 (274)
                      .||.+|++-.++..++..++..                    ...|++++..|.+|+.|++ .+++++|||++++.||.|
T Consensus       463 ~G~cIDLLi~Ls~~~Nftyd~~l~~dg~fg~~~~vnnsseT~~kew~G~iGEL~~~~ADMivaplTINpERa~yieFskP  542 (993)
T KOG4440         463 YGFCIDLLIKLSRTMNFTYDVHLVADGKFGTQERVNNSSETNKKEWNGMIGELLSGQADMIVAPLTINPERAQYIEFSKP  542 (993)
T ss_pred             HHHHHHHHHHHHHHHCCEEEEEEEECCCCCCEEEEECCCCCCCCEEHHHHHHHHCCCCCEEEECEEECHHHHHHEECCCC
T ss_conf             68899999999886256366888644656516764045532351411112444078555376110137224544222675


Q ss_pred             CCCCCCCCCCCCCCC----------------------------------------CCCCCCC------------------
Q ss_conf             222222222111222----------------------------------------2111112------------------
Q gi|254781112|r  125 YIAHRVLLVVRSDQQ----------------------------------------DIRSFKD------------------  146 (274)
Q Consensus       125 ~~~~~~~~~~~~~~~----------------------------------------~~~~~~d------------------  146 (274)
                      +...+.-++.++...                                        +++ .+|                  
T Consensus       543 fkYqGitILeKk~~r~Stl~SFlQPfqstLW~lv~~SVhvVal~lYlLDrfSPFgRFk-~~ds~~~ee~alnlssAmWF~  621 (993)
T KOG4440         543 FKYQGITILEKKEIRRSTLDSFLQPFQSTLWLLVGLSVHVVALMLYLLDRFSPFGRFK-VNDSEEEEEDALNLSSAMWFS  621 (993)
T ss_pred             CCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEE-ECCCCCCHHHHCCHHHHHHHH
T ss_conf             1015668985078987448888767777799999999999999999987148643244-156764255523524658887


Q ss_pred             ----CC-CC----------CE-E---------EECCCHH--HHH--HHCCCC----------------------------
Q ss_conf             ----33-43----------20-2---------3101012--233--201345----------------------------
Q gi|254781112|r  147 ----LT-DK----------TV-A---------QILGTDL--SRF--AKELKS----------------------------  169 (274)
Q Consensus       147 ----L~-g~----------~V-~---------~~~g~~~--~~~--l~~~~~----------------------------  169 (274)
                          |+ |.          || |         ++..|+.  ..+  +.++..                            
T Consensus       622 WGVLLNSGigEgtPRSfSARvLGmVWaGFaMIiVASYTANLAAFLVLdrPe~~ltGinDpRLRNps~nf~~aTVk~SsVd  701 (993)
T KOG4440         622 WGVLLNSGIGEGTPRSFSARVLGMVWAGFAMIIVASYTANLAAFLVLDRPEERLTGINDPRLRNPSDNFIYATVKQSSVD  701 (993)
T ss_pred             HHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHEEEHHHHHHHHHHEEECCCCCCCCCCCCCCCCCCCCCEEEEEECCCCHH
T ss_conf             67664366678997531377888887524202002523101431232472103667887111683113168873175088


Q ss_pred             ----------------CCEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEEEECCC
Q ss_conf             ----------------4213368557777554432100366558999999845876673262367768770799981899
Q gi|254781112|r  170 ----------------HLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKGN  233 (274)
Q Consensus       170 ----------------~~~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~  233 (274)
                                      +.-.|.+.+++++.+.+|+.+|++.|.....+-..+.    ......+....+.+|+++++|++
T Consensus       702 ~YFrRqVELS~MyR~ME~hNy~~A~eAiq~v~~gkL~AFIWDS~rLEfEAs~~----CeLvT~GeLFgRSgyGIGlqK~S  777 (993)
T KOG4440         702 IYFRRQVELSTMYRHMEKHNYESAAEAIQAVRDGKLHAFIWDSARLEFEASQK----CELVTTGELFGRSGYGIGLQKDS  777 (993)
T ss_pred             HHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCEEEEEEECCCEEEHHHCC----CEEEECCCCCCCCCCCCCCCCCC
T ss_conf             99888867888887632002455999999987496168985031033202046----40675112015344431035699


Q ss_pred             HHHHHHHHHHHHHHHHCCHHHHHHHHHCCC
Q ss_conf             899999999999999798599999876788
Q gi|254781112|r  234 NKLTRSINEILCAIHLDGTYKKIFDRYFDK  263 (274)
Q Consensus       234 ~~L~~~in~~l~~l~~~G~~~~I~~kw~g~  263 (274)
                      | +...+.-+|-++.++|.++++-++|...
T Consensus       778 P-Wt~~vtlaIL~~hEsGfMEkLDk~Wi~~  806 (993)
T KOG4440         778 P-WTQNVTLAILKSHESGFMEKLDKTWIRY  806 (993)
T ss_pred             C-CCHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             9-7303579998861310677777789871


No 26 
>TIGR03427 ABC_peri_uca ABC transporter periplasmic binding protein, urea carboxylase region. Members of this family are ABC transporter periplasmic binding proteins associated with the urea carboxylase/allophanate hydrolase pathway, an alternative to urease for urea degradation. The protein is restricted to bacteria with the pathway, with its gene close to the urea carboxylase and allophanate hydrolase genes. The substrate for this transporter therefore is likely to be urea or a compound from which urea is easily derived.
Probab=98.92  E-value=7.1e-09  Score=74.56  Aligned_cols=209  Identities=11%  Similarity=0.140  Sum_probs=130.8

Q ss_pred             CCCEEEEEC--CCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCCCCCC-CHHHHHHHHHCCCCCCCHHCC---CCH
Q ss_conf             895899962--89987248704699848898852167899762998555668-988988643103221100003---675
Q gi|254781112|r   40 QSALRVGTD--GIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFET-AVSGLITGLDTNRYDVLVNVA---ITP  113 (274)
Q Consensus        40 ~~~l~v~~~--~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~~~~~-~~~~~~~~l~~g~~D~~~~~~---~t~  113 (274)
                      +++++||.+  +.|.|+.+-  .++    |    +.+..+++.|++++++.. ++...+..+..|++|.++...   .+-
T Consensus         1 k~~~kig~S~w~Gw~Pw~~A--~e~----G----ifkKw~~k~Gi~Vel~~f~dy~~si~a~~AG~~Dg~~~Tn~Dal~i   70 (328)
T TIGR03427         1 KDKFKVCWSIYAGWMPWGYA--AQQ----G----IVDKWADKYGITIEVVQINDYVESINQYTAGKFDGCTMTNMDALTI   70 (328)
T ss_pred             CCCEEEEEECCCCHHHHHHH--HHC----C----CHHHHHHHCCCEEEEEECCCHHHHHHHHHCCCCCEEEEECCHHHHH
T ss_conf             99339997268538889999--974----9----2655588759737999828848889999758977477626156651


Q ss_pred             HHHHHHCC----CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCHHHHH----HHCCCC---CCEEE-CCHHHHH
Q ss_conf             67542002----333222222222111222211111233432023101012233----201345---42133-6855777
Q gi|254781112|r  114 ERQKKYDF----SIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTDLSRF----AKELKS---HLVFS-HNFEQSL  181 (274)
Q Consensus       114 eR~~~~~f----s~p~~~~~~~~~~~~~~~~~~~~~dL~g~~V~~~~g~~~~~~----l~~~~~---~~~~~-~~~~~~~  181 (274)
                      ....-+..    ..-|.....++++| +   +++++||+||+|++..++..+.+    |++.+.   .+..+ -+..+..
T Consensus        71 ~aa~Gvd~~~vlv~D~SnG~D~Ivak-~---~~slaDLKGKkVav~~~svshyLL~rALe~aGLs~~DV~vVn~~~~d~~  146 (328)
T TIGR03427        71 PAAGGVDTTALIVGDFSNGNDGIVLK-G---GKSLADLKGQKVNLVELSVSHYLLARALESVGLSEKDVKVVNTSDADIV  146 (328)
T ss_pred             HHCCCCCEEEEEEECCCCCCCEEEEC-C---CCCHHHHCCCEEECCCCCCHHHHHHHHHHHCCCCHHHEEEEECCCHHHH
T ss_conf             31179972899985257887479978-9---9887884898883247870799999999986998899078847954699


Q ss_pred             HHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEEEEC----CCHH----HHHHHHHHHHHHHHCCH-
Q ss_conf             75544321003665589999998458766732623677687707999818----9989----99999999999997985-
Q gi|254781112|r  182 QLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRK----GNNK----LTRSINEILCAIHLDGT-  252 (274)
Q Consensus       182 ~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k----~~~~----L~~~in~~l~~l~~~G~-  252 (274)
                      .++.+|++|+++.-++.... +.+.+....++.....|-.-... ++++.    +||+    |...+-++++-|..+.+ 
T Consensus       147 aAf~sg~VdA~vTWeP~ls~-i~~~~ga~~iF~Ss~iPGeI~D~-lvV~~~~L~~nP~~~kAlv~aW~e~~~~m~~~~~~  224 (328)
T TIGR03427       147 AAFITKDVTAVVTWNPQLSE-IKAQPGANEVFDSSQIPGEILDL-MVVNTQTLKANPNLGKALTGAWYETMALMSAGDAA  224 (328)
T ss_pred             HHHHCCCCCEEEEECHHHHH-HHHCCCCCEEEECCCCCCCEEEE-EEECHHHHHHCHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             99747998789997856899-97289982644257788840379-99858988879999999999999999998649812


Q ss_pred             ---HHHHHHHHCCCC
Q ss_conf             ---999998767888
Q gi|254781112|r  253 ---YKKIFDRYFDKN  264 (274)
Q Consensus       253 ---~~~I~~kw~g~d  264 (274)
                         .-+++.|=-|.|
T Consensus       225 ~~~a~~~ma~~~G~d  239 (328)
T TIGR03427       225 GKAALEAMAKASGTD  239 (328)
T ss_pred             HHHHHHHHHHHHCCC
T ss_conf             799999999874999


No 27 
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=98.77  E-value=1.9e-08  Score=71.86  Aligned_cols=206  Identities=10%  Similarity=0.073  Sum_probs=119.1

Q ss_pred             HCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCCCCCC-CHHHHHHHHHCCCCCCCHHCCCCHH---
Q ss_conf             589589996289987248704699848898852167899762998555668-9889886431032211000036756---
Q gi|254781112|r   39 DQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFET-AVSGLITGLDTNRYDVLVNVAITPE---  114 (274)
Q Consensus        39 ~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~~~~~-~~~~~~~~l~~g~~D~~~~~~~t~e---  114 (274)
                      +..+||||....--|+.+-..  +|.           +.+.+|++++|+.. ....+.+++.+|.+|+.. +..+|-   
T Consensus        21 ~~~~v~igYq~~~~p~~~aka--~g~-----------~ek~~G~kV~W~~F~sG~~~~eAlasG~vDig~-~G~~P~~~a   86 (320)
T PRK11480         21 QAVNVTVAYQTSAEPAKVAQA--DNT-----------FAKESGATVDWRKFDSGASIVRALASGDVQIGN-LGSSPLAVA   86 (320)
T ss_pred             CCCEEEEEEECCCCCHHHHHH--CCC-----------HHHHCCCCEEEEECCCHHHHHHHHHCCCCCEEC-CCCCHHHHH
T ss_conf             764599998069862899986--384-----------567519812799779759999999669975645-778479999


Q ss_pred             --HHHH--HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCHHHH----HHHCCCCC---CE-EECCHHHHHH
Q ss_conf             --7542--00233322222222211122221111123343202310101223----32013454---21-3368557777
Q gi|254781112|r  115 --RQKK--YDFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTDLSR----FAKELKSH---LV-FSHNFEQSLQ  182 (274)
Q Consensus       115 --R~~~--~~fs~p~~~~~~~~~~~~~~~~~~~~~dL~g~~V~~~~g~~~~~----~l~~~~~~---~~-~~~~~~~~~~  182 (274)
                        +...  +.+....+.....+++|+   .+++++||+||+|++..|+..+.    .+++.+..   +. ..-.+.++..
T Consensus        87 ~a~g~~ik~v~i~~~~~~~ealvv~~---~I~s~~DLkGKkVav~~gS~~hy~ll~aL~~~Gl~~~dV~iv~m~p~d~~a  163 (320)
T PRK11480         87 ASQQVPIEVFLLASKLGNSEALVVKK---TISKPEDLIGKRIAVPFISTTHYSLLAALKHWGIKPGQVEIVNLQPPAIIA  163 (320)
T ss_pred             HHCCCCEEEEEEECCCCCCEEEEECC---CCCCHHHCCCCEEECCCCCCHHHHHHHHHHHCCCCHHHEEEEECCCHHHHH
T ss_conf             86799859999854789743899568---999968849998960788731899999999859998990788449288999


Q ss_pred             HHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEECCCCC---CCCCEEEEEE----CCCHHHHHHHH----HHHHHHHHCC
Q ss_conf             55443210036655899999984587667326236776---8770799981----89989999999----9999999798
Q gi|254781112|r  183 LLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRMK---DNSAVAFMMR----KGNNKLTRSIN----EILCAIHLDG  251 (274)
Q Consensus       183 ~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~----k~~~~L~~~in----~~l~~l~~~G  251 (274)
                      ++.+|+||++........ -+++..   ..+.......   .+..-.+.++    +++|+++..+=    ++.+..+++.
T Consensus       164 A~~~G~vDa~~~W~P~l~-~l~~~G---~vL~~s~~~~~~G~pt~d~~vv~~~Fa~e~Pe~V~~flkv~~~A~~~~~~np  239 (320)
T PRK11480        164 AWQRGDIDGAYVWAPAVN-ALEKDG---KVLTDSEQVGQWGAPTLDVWVVRKDFAEKHPEVVKAFAKSAIDAQQPYIANP  239 (320)
T ss_pred             HHHCCCCCEEEECCHHHH-HHHHCC---CEEEECHHHHHCCCCCCCEEEECHHHHHHCHHHHHHHHHHHHHHHHHHHHCH
T ss_conf             997699787962677999-998439---7886416642048974556886399998898999999999999999999596


Q ss_pred             H-------HHHHHHHHCCCCC
Q ss_conf             5-------9999987678887
Q gi|254781112|r  252 T-------YKKIFDRYFDKNI  265 (274)
Q Consensus       252 ~-------~~~I~~kw~g~d~  265 (274)
                      .       --+.+.|+.|-+.
T Consensus       240 d~~~~~~~~~~~iAk~~G~~~  260 (320)
T PRK11480        240 DAWLKQPENISKLARLSGVPE  260 (320)
T ss_pred             HHHHCCCHHHHHHHHHHCCCH
T ss_conf             744048488999999959898


No 28 
>pfam09084 NMT1 NMT1/THI5 like. This family contains the NMT1 and THI5 proteins. These proteins are proposed to be required for the biosynthesis of the pyrimidine moiety of thiamine. They are regulated by thiamine.
Probab=98.64  E-value=2.1e-08  Score=71.62  Aligned_cols=128  Identities=19%  Similarity=0.079  Sum_probs=81.6

Q ss_pred             HHHHHHCCCCCCCCCC-CHHHHHHHHHCCCCCCCHHC--CCCHHHHHHHCCC--CC-CCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             7899762998555668-98898864310322110000--3675675420023--33-22222222211122221111123
Q gi|254781112|r   74 KEVAHRLNLKVEFFET-AVSGLITGLDTNRYDVLVNV--AITPERQKKYDFS--IP-YIAHRVLLVVRSDQQDIRSFKDL  147 (274)
Q Consensus        74 ~~i~~~lg~~~~~~~~-~~~~~~~~l~~g~~D~~~~~--~~t~eR~~~~~fs--~p-~~~~~~~~~~~~~~~~~~~~~dL  147 (274)
                      +-++++.|++++++.. ++...+..|.+|++|+....  ..-..+.+...+.  .. +-.....+++++++ .+++++||
T Consensus        13 ~G~f~~~GL~Ve~~~~~~~~~~~~al~sG~~D~a~~~~~~~~~~~~~g~~~~~i~~~~~~~~~~~~v~~~~-~i~s~~DL   91 (216)
T pfam09084        13 KGYFKEEGLDVEIVEPADPSDAVQLVAAGKADFGVSYQPSLLLARAKGLPVVSVAALIQHPPNGLISLKDS-GIKSPKDL   91 (216)
T ss_pred             CCCHHHCCCCEEEEECCCCHHHHHHHHCCCCCEEECCCHHHHHHHHCCCEEEEEEECCCCCCEEEEEECCC-CCCCHHHH
T ss_conf             79468849808999668827899999769867785371999999978984999996435897289997888-98997895


Q ss_pred             CCCCEEEECCCHHH----HHHHCCCC-----CCEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHH
Q ss_conf             34320231010122----33201345-----4213368557777554432100366558999999
Q gi|254781112|r  148 TDKTVAQILGTDLS----RFAKELKS-----HLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFL  203 (274)
Q Consensus       148 ~g~~V~~~~g~~~~----~~l~~~~~-----~~~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~  203 (274)
                      +||+|++..++...    .++++.+.     +++.. ++.+...+|.+|++|+++........+.
T Consensus        92 kGk~i~~~~~~~~~~~l~~~L~~~Gl~~~dv~~v~~-~~~~~~~al~~G~vDa~~~~~~~~~~~~  155 (216)
T pfam09084        92 KGKRIGYSGSPFEEALLKALLAKAGGDPSDVTLVNV-GGTSLSPALLTGKVDAAIGGYYNWEGVE  155 (216)
T ss_pred             CCCEEEEECCCHHHHHHHHHHHHCCCCHHHEEEEEC-CHHHHHHHHHCCCCCEEEECCCCHHHHH
T ss_conf             898899637972899999999985999899089967-8488888985699558996246757999


No 29 
>COG0715 TauA ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]
Probab=98.64  E-value=4.7e-07  Score=63.31  Aligned_cols=190  Identities=14%  Similarity=0.115  Sum_probs=110.5

Q ss_pred             EHHHHHHHCCC-CCCCCC-CCHHHHHHHHHCCCCCCCHHCCCCH----HHHH--HHCCCCCCCCC--CCCCCCCCCCCCC
Q ss_conf             16789976299-855566-8988988643103221100003675----6754--20023332222--2222211122221
Q gi|254781112|r   72 LIKEVAHRLNL-KVEFFE-TAVSGLITGLDTNRYDVLVNVAITP----ERQK--KYDFSIPYIAH--RVLLVVRSDQQDI  141 (274)
Q Consensus        72 l~~~i~~~lg~-~~~~~~-~~~~~~~~~l~~g~~D~~~~~~~t~----eR~~--~~~fs~p~~~~--~~~~~~~~~~~~~  141 (274)
                      ..+..+++.|+ +++++. .+|....+.+..|.+|+........    .+..  -+..-......  ...+++++++ .+
T Consensus        50 ~~kG~f~~~Gl~~V~~~~~~~~~~~~~~l~~G~~D~a~~~~~~~~~~~~~~~g~pv~~va~~~~~~~~~~i~~~~~~-~i  128 (335)
T COG0715          50 KEKGFFKKEGLDDVELVEFTGGAPVLEALAAGALDFAVYYTGDTPLIAAGAAGAPVKVVAALVQNGNGIALLVLKDS-GI  128 (335)
T ss_pred             HHCCHHHHCCCCEEEEEECCCCHHHHHHHHCCCCCEEEECCCCHHHHHHHCCCCCEEEEEEEEECCCCEEEEECCCC-CC
T ss_conf             97891777499758997079845799999769988874237855999963569997999987437973299973887-76


Q ss_pred             CCCCCCCCCCEEEECCCH-HHH----HHHCCCC---CC-EEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCC
Q ss_conf             111123343202310101-223----3201345---42-13368557777554432100366558999999845876673
Q gi|254781112|r  142 RSFKDLTDKTVAQILGTD-LSR----FAKELKS---HL-VFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNL  212 (274)
Q Consensus       142 ~~~~dL~g~~V~~~~g~~-~~~----~l~~~~~---~~-~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~  212 (274)
                      ++++||+||+||+..++. ...    ++.+.+.   ++ +..-.+.+...+|.+|++|+++..+...... ...+.... 
T Consensus       129 ~~~adlkGk~vg~~~~~~~~~~~l~~~L~~~Gl~~~dv~~v~~~~~~~~~al~~g~vda~~~~ep~~~~~-~~~~~~~~-  206 (335)
T COG0715         129 KSVADLKGKKVGVPFGGSTSDFLLRYALAKAGLDPDDVELVNLPPADAVAALAAGQVDAFVVWEPWNAAA-EGEGGGRV-  206 (335)
T ss_pred             CCHHHCCCCEEEEECCCCCHHHHHHHHHHHCCCCHHHCEEEECCHHHHHHHHHCCCCCEEEECCHHHHHH-HHCCCCEE-
T ss_conf             7713338998998189970799999999986999899468736929999999759868899666798997-31578579-


Q ss_pred             EEECCCCCC-CCCEEEEEEC----CCHH----HHHHHHHHHHHHHHCC-HHHHHHHHHCCCC
Q ss_conf             262367768-7707999818----9989----9999999999999798-5999998767888
Q gi|254781112|r  213 FKIADRMKD-NSAVAFMMRK----GNNK----LTRSINEILCAIHLDG-TYKKIFDRYFDKN  264 (274)
Q Consensus       213 ~~~~~~~~~-~~~~~~~~~k----~~~~----L~~~in~~l~~l~~~G-~~~~I~~kw~g~d  264 (274)
                      +........ .....+..++    .+|+    |...+-++..-+.++. +..+++.++.++.
T Consensus       207 ~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~v~a~~~a~~~~~~~p~~a~~~~~~~~~~~  268 (335)
T COG0715         207 LLDGADLWGNHPELVLVVRKEFIEANPEAVKAFLKALAKATAWANAHPDEAAEILAKAAGEL  268 (335)
T ss_pred             EEECCCCCCCCCEEEEEECHHHHHHCHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHCCCC
T ss_conf             86156667667426999558877669999999999999999999979899999999853655


No 30 
>PRK09861 cytoplasmic membrane lipoprotein-28; Provisional
Probab=98.23  E-value=1e-05  Score=55.00  Aligned_cols=202  Identities=14%  Similarity=0.124  Sum_probs=112.0

Q ss_pred             HHHHCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHH-HHCCCCCCCCC-CCHHHHHHHHHCCCCCCCH--HCC-
Q ss_conf             788589589996289987248704699848898852167899-76299855566-8988988643103221100--003-
Q gi|254781112|r   36 RTEDQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVA-HRLNLKVEFFE-TAVSGLITGLDTNRYDVLV--NVA-  110 (274)
Q Consensus        36 ~~~~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~-~~lg~~~~~~~-~~~~~~~~~l~~g~~D~~~--~~~-  110 (274)
                      ...+.++|+||+.+.  |+.-.            .+.+...+ ++-|++++++. .+|.+--.+|.+|++|+-.  -.. 
T Consensus        27 ~~~~~k~ikVG~~~~--p~~~i------------~e~~~~~~~ek~G~~leiv~FsDy~~PN~AL~~G~iDaN~fQH~py   92 (272)
T PRK09861         27 SSSDAKHIKVGVING--AEQDV------------AEVAKKVAKEKYGLDVELVGFSGSLLPNDATNHGELDANVFQHRPF   92 (272)
T ss_pred             CCCCCCEEEEEECCC--CHHHH------------HHHHHHHHHHHCCCEEEEEEECCCCCHHHHHHCCCCCCHHHHHHHH
T ss_conf             767897389996789--86999------------9999988876179768999946862262897679836024557999


Q ss_pred             ---CCHHHHHHHCCC--CCCCCCCCCCCCCCCCCCCCCCCCCC-CCCEEEECCCH-HHH---HHHCCCC-----------
Q ss_conf             ---675675420023--33222222222111222211111233-43202310101-223---3201345-----------
Q gi|254781112|r  111 ---ITPERQKKYDFS--IPYIAHRVLLVVRSDQQDIRSFKDLT-DKTVAQILGTD-LSR---FAKELKS-----------  169 (274)
Q Consensus       111 ---~t~eR~~~~~fs--~p~~~~~~~~~~~~~~~~~~~~~dL~-g~~V~~~~g~~-~~~---~l~~~~~-----------  169 (274)
                         +.+++  .+.+.  .+.+..+.+++.+    ++++++||+ |-+|++..+.+ ..+   ++++.+.           
T Consensus        93 L~~~n~~~--g~~L~~v~~~~~~P~glYS~----K~ksl~dlp~Ga~IaIPnDpsN~~RAL~lL~~aGLI~Lk~~~~~~~  166 (272)
T PRK09861         93 LEQDNQAH--GYKLVAVGNTFVFPMAGYSK----KIKTVAQIKEGATVAIPNDPTNLGRALLLLQKEKLITLKEGKGLLP  166 (272)
T ss_pred             HHHHHHHC--CCCEEEEEEEEEEEEEECCC----CCCCHHHCCCCCEEEECCCHHHHHHHHHHHHHCCCEEECCCCCCCC
T ss_conf             99999986--99579973167830140344----6598758479998980478126999999999889789779999777


Q ss_pred             ------------CCEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC--CCCEEECCCCCCCCCEEEEEECCCHH
Q ss_conf             ------------4213368557777554432100366558999999845876--67326236776877079998189989
Q gi|254781112|r  170 ------------HLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHD--GNLFKIADRMKDNSAVAFMMRKGNNK  235 (274)
Q Consensus       170 ------------~~~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~k~~~~  235 (274)
                                  ++++. +..+..+.|....+|++++....+    ...+..  ...+.. .....+..-.+++++++..
T Consensus       167 t~~DI~~NPk~lk~~e~-~aaql~rsl~Dp~vD~avin~n~a----~~agl~p~~dal~~-E~~~~py~niiavr~~~~d  240 (272)
T PRK09861        167 TALDITDNPRHLQIMEL-EGAQLPRVLDDPKVDVAIISTTYI----QQTGLSPVHDSVFI-EDKNSPYVNILVAREDNKN  240 (272)
T ss_pred             CHHHHHCCCCCCEEEEC-CHHHHHHHHCCCCCCEEEECHHHH----HHCCCCCCCCCEEE-CCCCCCEEEEEEECCCCCC
T ss_conf             74457608877679982-677746750577616899760579----88777944002036-6899983799998276769


Q ss_pred             HHHHHHHHHHHHHHCCHHHHHHHHHCCCCC
Q ss_conf             999999999999979859999987678887
Q gi|254781112|r  236 LTRSINEILCAIHLDGTYKKIFDRYFDKNI  265 (274)
Q Consensus       236 L~~~in~~l~~l~~~G~~~~I~~kw~g~d~  265 (274)
                      - ..+ +.|.+..+|.+.++.+++-|+-.+
T Consensus       241 ~-~~i-k~lv~a~~S~evk~~i~~~y~G~~  268 (272)
T PRK09861        241 A-ENV-KEFLQSYQSPEVAKAAETIFNGGA  268 (272)
T ss_pred             C-HHH-HHHHHHHCCHHHHHHHHHHCCCCE
T ss_conf             9-899-999999779999999998779963


No 31 
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=98.20  E-value=2e-05  Score=53.19  Aligned_cols=199  Identities=13%  Similarity=0.093  Sum_probs=107.6

Q ss_pred             HHHCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHH-HHCCCCCCCCC-CCHHHHHHHHHCCCCCCCH--HCC--
Q ss_conf             88589589996289987248704699848898852167899-76299855566-8988988643103221100--003--
Q gi|254781112|r   37 TEDQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVA-HRLNLKVEFFE-TAVSGLITGLDTNRYDVLV--NVA--  110 (274)
Q Consensus        37 ~~~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~-~~lg~~~~~~~-~~~~~~~~~l~~g~~D~~~--~~~--  110 (274)
                      ..+..+|+||+.+.  |+.-.            .+.+...+ ++.|++++++. .+|..--.+|.+|.+|+-.  ...  
T Consensus        27 ~~~~~~ikVG~~~g--p~~ei------------~e~~~~~~~ek~G~~veiv~FsDy~~pN~AL~~G~iDaN~fQH~~yL   92 (271)
T PRK11063         27 EKDPNHIKVGVIVG--AEQQV------------AEVAQKVAKEKYGLDVELVTFNDYVLPNEALSKGDIDANAFQHKPYL   92 (271)
T ss_pred             CCCCCEEEEEECCC--CHHHH------------HHHHHHHHHHHCCCEEEEEEECCCHHHHHHHHCCCCCHHHHHCHHHH
T ss_conf             56798189984689--87999------------99988888860797689999368321558986798442345579999


Q ss_pred             --CCHHHHHHHCCC--CCCCCCCCCCCCCCCCCCCCCCCCCC-CCCEEEECCCH-HHH---HHHCCCC------------
Q ss_conf             --675675420023--33222222222111222211111233-43202310101-223---3201345------------
Q gi|254781112|r  111 --ITPERQKKYDFS--IPYIAHRVLLVVRSDQQDIRSFKDLT-DKTVAQILGTD-LSR---FAKELKS------------  169 (274)
Q Consensus       111 --~t~eR~~~~~fs--~p~~~~~~~~~~~~~~~~~~~~~dL~-g~~V~~~~g~~-~~~---~l~~~~~------------  169 (274)
                        +.+++  .+.+.  .+.+..+..++.    ..+++++||. |-+|++..+.+ ..+   ++++.+.            
T Consensus        93 ~~~nk~~--g~~L~~v~~~~~~P~glYS----~K~ksl~elp~Ga~IaIPND~sN~~RAL~lL~~aGLIkLk~~~~~~~T  166 (271)
T PRK11063         93 DQQIKDR--GYKLVAVGNTFVYPIAGYS----KKIKSLDELQDGSQVAVPNDPTNLGRSLLLLQKVGLIKLKDGVGLLPT  166 (271)
T ss_pred             HHHHHHC--CCCEEEEEEEEEEEEEEEE----CCCCCHHHCCCCCEEEECCCCCHHHHHHHHHHHCCCEEECCCCCCCCC
T ss_conf             9999977--9957998667784158642----365886475699999804885609999999998898897799998789


Q ss_pred             -----------CCEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCC--CCEEECCCCCCCCCEEEEEECCCHHH
Q ss_conf             -----------42133685577775544321003665589999998458766--73262367768770799981899899
Q gi|254781112|r  170 -----------HLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDG--NLFKIADRMKDNSAVAFMMRKGNNKL  236 (274)
Q Consensus       170 -----------~~~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~k~~~~L  236 (274)
                                 ++++. +..+..+.|....+|+++++...    ....+...  ..+.. .....+..-.+++++++.. 
T Consensus       167 ~~DI~~Npk~l~~~e~-daaql~rsl~D~dv~~aviN~~~----a~~agl~p~kdal~~-E~~~~py~Nvivvr~~~kd-  239 (271)
T PRK11063        167 VLDIVENPKNLKIVEL-EAPQLPRSLDDAQIALAVINTTY----ASQIGLTPAKDGIFV-EDKDSPYVNLIVAREDNKD-  239 (271)
T ss_pred             HHHHHCCCCCCEEEEC-CHHHHHHHCCCCCEEEEEECHHH----HHHCCCCCCCCCEEE-CCCCCCEEEEEEECCCCCC-
T ss_conf             6688548877489990-37764431357651089814778----977798934250477-7899983899998277779-


Q ss_pred             HHHHHHHHHHHHHCCHHHHHHHHHCCC
Q ss_conf             999999999999798599999876788
Q gi|254781112|r  237 TRSINEILCAIHLDGTYKKIFDRYFDK  263 (274)
Q Consensus       237 ~~~in~~l~~l~~~G~~~~I~~kw~g~  263 (274)
                       +..=+.|.+..+|.+.++.+++-|+-
T Consensus       240 -~~~ik~lv~~~~S~evk~~I~~~~~G  265 (271)
T PRK11063        240 -AENVKKFVQAYQSDEVYEAANKVFNG  265 (271)
T ss_pred             -CHHHHHHHHHHCCHHHHHHHHHHCCC
T ss_conf             -98999999997799999999987799


No 32 
>COG0725 ModA ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=98.13  E-value=2.2e-05  Score=52.95  Aligned_cols=202  Identities=17%  Similarity=0.225  Sum_probs=121.4

Q ss_pred             HHHHCCCEEEEECCCC-CCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCCCCCCCHHHHHHHHHCCC-CCCCHHCCC-C
Q ss_conf             7885895899962899-872487046998488988521678997629985556689889886431032-211000036-7
Q gi|254781112|r   36 RTEDQSALRVGTDGIY-PPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVSGLITGLDTNR-YDVLVNVAI-T  112 (274)
Q Consensus        36 ~~~~~~~l~v~~~~~~-pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~~~~~~~~~~~~~l~~g~-~D~~~~~~~-t  112 (274)
                      .+++..+|+|...... .|++               ++..+..++.|.++++..-....+...+++|. +|+..+... .
T Consensus        25 ~~~~~~~i~VfAAaSL~~~l~---------------~i~~~F~~~~~~~V~~~f~gS~~l~~qIe~Ga~~D~fiSa~~~~   89 (258)
T COG0725          25 AAQEAATITVFAAASLTDALE---------------EIAKQFEKETGVKVEVEFGGSGALARQIEQGAPADLFISADDAY   89 (258)
T ss_pred             CCCCCCEEEEEEEHHHHHHHH---------------HHHHHHHHHHCCEEEEEECCHHHHHHHHHCCCCCCEEEECCHHH
T ss_conf             445674099998156689999---------------99999999879879999613899999997599868799888888


Q ss_pred             HH--HHHH-H--CCCCCCCCCCCCCCCCCCCC-CCCCCCCC---CCCCEEE------ECCCHHHHHHHCC------CCCC
Q ss_conf             56--7542-0--02333222222222111222-21111123---3432023------1010122332013------4542
Q gi|254781112|r  113 PE--RQKK-Y--DFSIPYIAHRVLLVVRSDQQ-DIRSFKDL---TDKTVAQ------ILGTDLSRFAKEL------KSHL  171 (274)
Q Consensus       113 ~e--R~~~-~--~fs~p~~~~~~~~~~~~~~~-~~~~~~dL---~g~~V~~------~~g~~~~~~l~~~------~~~~  171 (274)
                      ..  .++. +  .+..++.....++++++++. ....+.++   .+.|+++      +.|....+.++..      ..++
T Consensus        90 ~~~l~~~g~~~~~~~~~fa~n~lvl~~~~~~~~~~~~~~~l~~~~~~~lai~~p~~~P~G~ya~~~l~~~g~~~~~~~k~  169 (258)
T COG0725          90 MDKLEDKGLIYADSRIVFAGNRLVLAVPKGSKKKIESLEDLLERPDVRLAIGDPKTVPAGKYAKEALELLGLWYTLKDKL  169 (258)
T ss_pred             HHHHHHCCCCCCCCEEEEECCEEEEEEECCCCCCCCHHHHHHCCCCCEEEECCCCCCCCHHHHHHHHHHHCHHHHCCCCE
T ss_conf             99998668856671577425748999868874565129887308785799648876971499999999705145336754


Q ss_pred             EEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEEEECC--CHHHHHHHHHHHHHHHH
Q ss_conf             1336855777755443210036655899999984587667326236776877079998189--98999999999999997
Q gi|254781112|r  172 VFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKG--NNKLTRSINEILCAIHL  249 (274)
Q Consensus       172 ~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~--~~~L~~~in~~l~~l~~  249 (274)
                      +...+..+++..+.+|++|+.+.-...+...    ........+......+..+.+++.++  ++++...+-+.|..   
T Consensus       170 v~~~~v~~~l~~V~~G~ad~g~vy~sd~~~~----~~~~~~~~~~~~~~~Pi~y~iav~~~~~~~~~A~~f~~fl~s---  242 (258)
T COG0725         170 VLATNVRQALAYVETGEADAGFVYVSDALLS----KKVKIVGVFPEDLHSPIVYPIAVLKNAKNPELAKEFVDFLLS---  242 (258)
T ss_pred             EECCCHHHHHHHHHCCCCCEEEEEEEHHHHC----CCCEEEEECCCCCCCCEEEEEEEECCCCCHHHHHHHHHHHHC---
T ss_conf             6536579899998637877799997633406----776089973566689716789997388985999999999718---


Q ss_pred             CCHHHHHHHHH
Q ss_conf             98599999876
Q gi|254781112|r  250 DGTYKKIFDRY  260 (274)
Q Consensus       250 ~G~~~~I~~kw  260 (274)
                       .+-++|.++|
T Consensus       243 -~~a~~il~~~  252 (258)
T COG0725         243 -PEAQEILEKY  252 (258)
T ss_pred             -HHHHHHHHHC
T ss_conf             -7779999984


No 33 
>COG4521 TauA ABC-type taurine transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=98.08  E-value=0.00022  Score=46.83  Aligned_cols=190  Identities=13%  Similarity=0.124  Sum_probs=108.7

Q ss_pred             CEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCCCCCCCH-HHHHHHHHCCCCCCC-HHCCCCH---HHH
Q ss_conf             58999628998724870469984889885216789976299855566898-898864310322110-0003675---675
Q gi|254781112|r   42 ALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAV-SGLITGLDTNRYDVL-VNVAITP---ERQ  116 (274)
Q Consensus        42 ~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~~~~~~~-~~~~~~l~~g~~D~~-~~~~~t~---eR~  116 (274)
                      .++||....--|+---..|      |       ..++..|.++.|...+. .+.+.+|-+|.+++- .|-+...   .|.
T Consensus        30 ~vtVgYQt~~eP~kvaqAD------g-------~~aK~~gatiDWRkFdSG~~vv~AlASGdvqiG~iGSsplaaAaSr~   96 (334)
T COG4521          30 DVTVGYQTSAEPAKVAQAD------G-------AFAKESGATIDWRKFDSGASIVRALASGDVQIGNIGSSPLAAAASRQ   96 (334)
T ss_pred             EEEEEEEECCCCCCCCCCC------C-------HHHHHCCCCCCHHHCCCHHHHHHHHHCCCCCCCCCCCCHHHHHHHCC
T ss_conf             1688654035752021346------3-------56776078545110475368999986288610465785666776358


Q ss_pred             HH--HCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCH--HH--HHHHCCCCC---CEE-ECCHHHHHHHHHH
Q ss_conf             42--00233322222222211122221111123343202310101--22--332013454---213-3685577775544
Q gi|254781112|r  117 KK--YDFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTD--LS--RFAKELKSH---LVF-SHNFEQSLQLLLS  186 (274)
Q Consensus       117 ~~--~~fs~p~~~~~~~~~~~~~~~~~~~~~dL~g~~V~~~~g~~--~~--~~l~~~~~~---~~~-~~~~~~~~~~l~~  186 (274)
                      --  .-|-..-.-.+..+++|+++ .|.+++||.||+|++.-=++  |.  .-++.++.+   +.. --.+.+...+-..
T Consensus        97 vpie~f~~~~~ig~sEALVvr~gs-gI~kpeDL~GK~iavPFvSTtHysLLaaLkhw~idp~~V~IlNl~Pp~IaAAwqR  175 (334)
T COG4521          97 VPIEVFLLASQIGNSEALVVRKGS-GIEKPEDLIGKRIAVPFVSTTHYSLLAALKHWGIDPGQVEILNLQPPAIAAAWQR  175 (334)
T ss_pred             CCEEEEEHHHHCCCCCEEEEECCC-CCCCHHHHCCCEECCCEEEHHHHHHHHHHHHCCCCCCCEEEECCCCHHHHHHHHC
T ss_conf             865885301212863103552377-8698578646721042430008999999987187855246861597899999870


Q ss_pred             HHHHCCCCCHHHHHHHHHHCCC-CCCCEEECCCCCCCCCEEEEEECC----CHHHHHHHHHHHHHH
Q ss_conf             3210036655899999984587-667326236776877079998189----989999999999999
Q gi|254781112|r  187 KRTDATMIPDIPFFNFLERRPH-DGNLFKIADRMKDNSAVAFMMRKG----NNKLTRSINEILCAI  247 (274)
Q Consensus       187 grvD~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~k~----~~~L~~~in~~l~~l  247 (274)
                      |.+|++..-..-... +++.+. ..+.-. ...-..+..-.+.++|+    +|+.+..|-+....-
T Consensus       176 GDIDgAyVW~PAl~e-l~ksGkVltDs~q-vgqwgaPTfdvwVvrkdfAekhPe~v~aFakv~~da  239 (334)
T COG4521         176 GDIDGAYVWAPALSE-LKKSGKVLTDSEQ-VGQWGAPTFDVWVVRKDFAEKHPEVVAAFAKVALDA  239 (334)
T ss_pred             CCCCCEEECCHHHHH-HHHCCCEECCHHH-HHCCCCCCEEEEEEEHHHHHHCHHHHHHHHHHHHHH
T ss_conf             787722544676888-8625857526888-621479851368863176676969999999988876


No 34 
>PRK10677 modA molybdate transporter periplasmic protein; Provisional
Probab=98.05  E-value=7.6e-05  Score=49.65  Aligned_cols=202  Identities=12%  Similarity=0.133  Sum_probs=116.3

Q ss_pred             HHHHHCCCEEEEECCCC-CCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCCCCCCCHHHHHHHHHCCC-CCCCHHCCCC
Q ss_conf             87885895899962899-872487046998488988521678997629985556689889886431032-2110000367
Q gi|254781112|r   35 FRTEDQSALRVGTDGIY-PPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVSGLITGLDTNR-YDVLVNVAIT  112 (274)
Q Consensus        35 ~~~~~~~~l~v~~~~~~-pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~~~~~~~~~~~~~l~~g~-~D~~~~~~~t  112 (274)
                      ....+.++|+|....+. +|+.               ||....-+..|+++++..-....+...+++|. +|+..+....
T Consensus        21 ~~~a~~~~l~V~aAAsL~~~~~---------------ei~~~Fek~~g~~v~~~fgsSg~L~~QI~~GAp~DvF~sAd~~   85 (257)
T PRK10677         21 NALADEGKITVFAAASLTNAMQ---------------DIATQYKKEKGVDVVSSFASSSTLARQIEAGAPADLFISADQK   85 (257)
T ss_pred             CCCCCCCEEEEEEECCCHHHHH---------------HHHHHHHHHHCCEEEEEECCHHHHHHHHHCCCCCCEEEECCHH
T ss_conf             3325688599999257689999---------------9999998841984999966489999999828996589978757


Q ss_pred             -HHHH---HHHCCC--CCCCCCCCCCCCCCCCC----CCCCCCC----CCCCCEEEE------CCCHHHHHHHCC-----
Q ss_conf             -5675---420023--33222222222111222----2111112----334320231------010122332013-----
Q gi|254781112|r  113 -PERQ---KKYDFS--IPYIAHRVLLVVRSDQQ----DIRSFKD----LTDKTVAQI------LGTDLSRFAKEL-----  167 (274)
Q Consensus       113 -~eR~---~~~~fs--~p~~~~~~~~~~~~~~~----~~~~~~d----L~g~~V~~~------~g~~~~~~l~~~-----  167 (274)
                       .++.   ..+.-.  .++.....+++++++..    .+....|    +.+.||++.      .|-...+.+++.     
T Consensus        86 ~~~~l~~~~~i~~~~~~~~a~n~lvli~pk~~~~~~~~i~~~~d~~~ll~~~riaia~P~~aP~G~ya~~~L~~~gl~~~  165 (257)
T PRK10677         86 WMDYAVDKKAIDTATRQTLLGNSLVVVAPKASEQKDFTIDKKTDWTSLLNGGRLAVGDPDHVPAGIYAKEALQKLGAWDT  165 (257)
T ss_pred             HHHHHHHCCCCCCCCEEEEECCEEEEEEECCCCCCCCCCCCCCCHHHHCCCCCEEEECCCCCCCHHHHHHHHHHCCCHHH
T ss_conf             78999867785677645621474999984687778644343323777425880898588888657999999997676655


Q ss_pred             -CCCCEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEEEECC--CHHHHHHHHHHH
Q ss_conf             -45421336855777755443210036655899999984587667326236776877079998189--989999999999
Q gi|254781112|r  168 -KSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKG--NNKLTRSINEIL  244 (274)
Q Consensus       168 -~~~~~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~--~~~L~~~in~~l  244 (274)
                       ..+++..++..+.+..+.+|++|+.+.-...+..    .........++.....+..+.+++-++  ++..     +.+
T Consensus       166 l~~klv~~~nV~~~l~~v~~G~adaG~Vy~Sda~~----~~~~~~~~~~p~~~~~pi~y~~ai~~~~~~~~a-----~~F  236 (257)
T PRK10677        166 LSPKLAPAEDVRGALALVERNEAPLGIVYGSDAVA----SKGVKVVATFPEDSHKKVEYPMAIVEGHNNATV-----SAF  236 (257)
T ss_pred             HCCCEEECCCHHHHHHHHHCCCCCEEEEECCHHHC----CCCCEEEEECCHHHCCCCEEEEEEECCCCCHHH-----HHH
T ss_conf             06541325769999999982998789997000222----688649998774538961455899759999999-----999


Q ss_pred             HHHHHCCHHHHHHHHH
Q ss_conf             9999798599999876
Q gi|254781112|r  245 CAIHLDGTYKKIFDRY  260 (274)
Q Consensus       245 ~~l~~~G~~~~I~~kw  260 (274)
                      -+...|.+-++|++||
T Consensus       237 ~~fl~S~~a~~Il~~~  252 (257)
T PRK10677        237 YDYLKGPQAAEIFKRY  252 (257)
T ss_pred             HHHHCCHHHHHHHHHH
T ss_conf             9997799999999982


No 35 
>COG2358 Imp TRAP-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=97.91  E-value=1.1e-05  Score=54.91  Aligned_cols=145  Identities=14%  Similarity=0.099  Sum_probs=79.5

Q ss_pred             HHCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHH-HCCCCCCCCCCCH-HHHHHHHHCCCCCCCHHCC-----
Q ss_conf             85895899962899872487046998488988521678997-6299855566898-8988643103221100003-----
Q gi|254781112|r   38 EDQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAH-RLNLKVEFFETAV-SGLITGLDTNRYDVLVNVA-----  110 (274)
Q Consensus        38 ~~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~-~lg~~~~~~~~~~-~~~~~~l~~g~~D~~~~~~-----  110 (274)
                      .+...+++|+...-=.|  +         =+...|++.+.+ ..|++++.++..- -.-+..+.+|++|+....+     
T Consensus        23 ~~~~~itigTG~~~G~Y--Y---------~ig~~ia~~~~~~~~~i~~~v~~tggSv~Nl~~i~~Ge~d~alvq~d~a~~   91 (321)
T COG2358          23 AEPKFITIGTGSTGGVY--Y---------PIGGGLAQLLNKDEKGIECSVVPTGGSVENLKLLASGEADLALVQSDVAYE   91 (321)
T ss_pred             CCCEEEEEEECCCCCEE--E---------EHHHHHHHHHHCCCCCEEEEEEECCCHHHHHHHHHCCCCCHHHHHHHHHHH
T ss_conf             67637999606998622--3---------037899999851477818999606542999986753762535666789999


Q ss_pred             ------CCHH--HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEE-ECCCH----HHHHHHCCCCCCEE----
Q ss_conf             ------6756--7542002333222222222111222211111233432023-10101----22332013454213----
Q gi|254781112|r  111 ------ITPE--RQKKYDFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQ-ILGTD----LSRFAKELKSHLVF----  173 (274)
Q Consensus       111 ------~t~e--R~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~dL~g~~V~~-~~g~~----~~~~l~~~~~~~~~----  173 (274)
                            .-+.  ..+.+..--+++.....+++|+++. |++++||+||||++ ..||-    ....++..+....+    
T Consensus        92 ay~G~g~f~~~~~~~~lr~v~~lype~~~vv~r~d~~-Ikti~DL~GKrV~iG~~gSgt~~~a~~il~a~Gi~~~~~~~~  170 (321)
T COG2358          92 AYNGTGSFEGKGKDENLRAVAALYPEPFHVVTRKDAG-IKTIADLKGKRVAIGPPGSGTEATARQILEALGITYDDYELD  170 (321)
T ss_pred             HHHCCCCCCCCCCCCCHHHHEECCCCEEEEEEECCCC-CCEEHHCCCCEEEECCCCCCCHHHHHHHHHHCCCCCCCHHHH
T ss_conf             8718531145665514332213054208999966889-656010389888626999740889999999739997624566


Q ss_pred             -ECCHHHHHHHHHHHHHHCCCC
Q ss_conf             -368557777554432100366
Q gi|254781112|r  174 -SHNFEQSLQLLLSKRTDATMI  194 (274)
Q Consensus       174 -~~~~~~~~~~l~~grvD~~~~  194 (274)
                       .-...+...++.+|++|+++.
T Consensus       171 ~~~~~a~~~~~l~~g~iDA~~~  192 (321)
T COG2358         171 LGLGDAESADALKNGTIDAAFY  192 (321)
T ss_pred             HHCCCHHHHHHHHCCCCCEEEE
T ss_conf             6337306578763796328998


No 36 
>COG1638 DctP TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=97.78  E-value=0.00021  Score=46.96  Aligned_cols=173  Identities=13%  Similarity=0.080  Sum_probs=103.3

Q ss_pred             EEEHHHHHHHCCCCCCCCCCCH------HHHHHHHHCCCCCCCH-HCCCCHHHHH-HHCCCCCCCCCCC-----------
Q ss_conf             5216789976299855566898------8988643103221100-0036756754-2002333222222-----------
Q gi|254781112|r   70 IDLIKEVAHRLNLKVEFFETAV------SGLITGLDTNRYDVLV-NVAITPERQK-KYDFSIPYIAHRV-----------  130 (274)
Q Consensus        70 ~dl~~~i~~~lg~~~~~~~~~~------~~~~~~l~~g~~D~~~-~~~~t~eR~~-~~~fs~p~~~~~~-----------  130 (274)
                      ..+.+++.+++|=++++...|.      ..+++.|+.|.+|+.. +.+....+.. .-.|+.||+....           
T Consensus        47 ~~fa~~v~ekt~G~l~i~vfP~~qLG~~~~~ie~l~~G~id~~~~s~~~l~~~~P~~~v~~lPflf~d~~~~~~~~~~~~  126 (332)
T COG1638          47 KKFAELVEEKTGGRLKIEVFPNSQLGGEAEMIEQLRSGTLDIGVVSLGFLAGLVPEFGVFDLPFLFRDEEHARRVLDSEF  126 (332)
T ss_pred             HHHHHHHHHHCCCEEEEEECCCCCCCCHHHHHHHHHCCCCEEEECCCHHHCCCCCCCEEECCCEEECCHHHHHHHHHHHH
T ss_conf             99999999871993899976675668769999999659730785065232113875012248755189999999971388


Q ss_pred             -----------CCC--------CC--CC-CCCCCCCCCCCCCCEEEECCCHHHHHHHCCCCCCEEECCHHHHHHHHHHHH
Q ss_conf             -----------222--------11--12-222111112334320231010122332013454213368557777554432
Q gi|254781112|r  131 -----------LLV--------VR--SD-QQDIRSFKDLTDKTVAQILGTDLSRFAKELKSHLVFSHNFEQSLQLLLSKR  188 (274)
Q Consensus       131 -----------~~~--------~~--~~-~~~~~~~~dL~g~~V~~~~g~~~~~~l~~~~~~~~~~~~~~~~~~~l~~gr  188 (274)
                                 .+.        .|  .. ...+.+++||+|+++-++....+..+.+..+...+..+ ..+.+.+|.+|-
T Consensus       127 g~~l~~~~e~~g~~~l~~~~~G~R~~t~~k~PI~~peDlkGlkiRv~~s~~~~~~~~a~GA~P~pm~-f~Evy~aLqtGv  205 (332)
T COG1638         127 GEELLKSLEAKGLKGLAFWENGFRQFTSNKRPIKTPEDLKGLKIRVPQSPLLLAMFKALGANPTPMP-FAEVYTALQTGV  205 (332)
T ss_pred             HHHHHHHHHHCCCEEEEEECCCCEEEEECCCCCCCHHHHCCCEEECCCCHHHHHHHHHCCCCCCCCC-HHHHHHHHHCCC
T ss_conf             9999999997695799986275223334678778968967984635898899999998699897788-899999997497


Q ss_pred             HHCCCCCHHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEEEECC-----CHHHHHHHHHHHHHH
Q ss_conf             10036655899999984587667326236776877079998189-----989999999999999
Q gi|254781112|r  189 TDATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKG-----NNKLTRSINEILCAI  247 (274)
Q Consensus       189 vD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~-----~~~L~~~in~~l~~l  247 (274)
                      ||+.-.+....  +-.+.......  ....-....++.+.+++.     .++.+..|.++..+-
T Consensus       206 VDGqEnp~~~i--~~~k~~EVqky--~t~tnH~~~~~~~~~s~~~w~~L~~e~q~il~~aa~e~  265 (332)
T COG1638         206 VDGQENPLSNI--YSAKLYEVQKY--LTLTNHIYLPLAVLVSKAFWDSLPEEDQTILLEAAKEA  265 (332)
T ss_pred             CCCCCCCHHHH--HCCCHHHHHHH--HHHCCCCCCCEEEEECHHHHHCCCHHHHHHHHHHHHHH
T ss_conf             00441767666--10426567566--52156655542689738988309999999999999999


No 37 
>TIGR01729 taurine_ABC_bnd taurine ABC transporter, periplasmic binding protein; InterPro: IPR010068   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).    This entry identifies a cluster of ABC transporter periplasmic substrate binding proteins, apparently specific for taurine. Transport systems for taurine (NH2-CH2-CH2-SO3H), sulphonates, and sulphate esters import sulphur when sulphate levels are low. The most closely related proteins outside this family are putative aliphatic sulphonate binding proteins..
Probab=97.75  E-value=0.00012  Score=48.47  Aligned_cols=174  Identities=17%  Similarity=0.146  Sum_probs=107.8

Q ss_pred             HHHHHHHCCCCCCCCCCCH-HHHHHHHHCCCCCCC-HHCCC---CHHHHH--HHCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             6789976299855566898-898864310322110-00036---756754--2002333222222222111222211111
Q gi|254781112|r   73 IKEVAHRLNLKVEFFETAV-SGLITGLDTNRYDVL-VNVAI---TPERQK--KYDFSIPYIAHRVLLVVRSDQQDIRSFK  145 (274)
Q Consensus        73 ~~~i~~~lg~~~~~~~~~~-~~~~~~l~~g~~D~~-~~~~~---t~eR~~--~~~fs~p~~~~~~~~~~~~~~~~~~~~~  145 (274)
                      ....++..|.++.|+..+. ..++.+|-+|++|+- .|-+.   -..|+-  .+-|-.-.+-.+.+|++|+++ .|..++
T Consensus        21 fda~aKe~gaTiDWRkFdSGadi~~AlASG~V~IG~~GSsplaaAASr~vpie~f~~~~~iG~SEALVar~g~-GIeKpe   99 (304)
T TIGR01729        21 FDAYAKEAGATIDWRKFDSGADIVAALASGDVDIGVVGSSPLAAAASREVPIEVFLVVDKIGKSEALVAREGA-GIEKPE   99 (304)
T ss_pred             HHHHHHCCCCEEEEEEECCHHHHHHHHHCCCCCCCCCCCCHHHHHHHCCCCEEEEEEECCCCCCCEEEEECCC-CCCCHH
T ss_conf             2245430488020011044165555653386332222470789987268830020100102872002454367-887666


Q ss_pred             CCCCCCEEEECC--CHHHH--HHHC-CCCC--CEEEC--CHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC-CCCEEE
Q ss_conf             233432023101--01223--3201-3454--21336--8557777554432100366558999999845876-673262
Q gi|254781112|r  146 DLTDKTVAQILG--TDLSR--FAKE-LKSH--LVFSH--NFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHD-GNLFKI  215 (274)
Q Consensus       146 dL~g~~V~~~~g--~~~~~--~l~~-~~~~--~~~~~--~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~-~~~~~~  215 (274)
                      ||+||+|+|+-=  +.|.-  -|++ .+.+  -+..-  .+.+.+-+...|.+|++-.-..-+. .+.+.+.- .+.-.+
T Consensus       100 DL~GK~vaVPFvSTtHysLLaaLk~vw~~dp~~V~IlNl~PP~I~AAwqRGDIDaAYVW~PAl~-~l~k~GKV~~DSeqv  178 (304)
T TIGR01729       100 DLKGKKVAVPFVSTTHYSLLAALKHVWKVDPKEVEILNLKPPEIVAAWQRGDIDAAYVWDPALS-ELKKSGKVVSDSEQV  178 (304)
T ss_pred             HHCCCEEECCCCCHHHHHHHHHHHHHHCCCCCEEEEEECCCHHHHHHHHCCCCCCCCCCHHHHH-HHHHCCCEEECHHHH
T ss_conf             7178845027511345899998887626787605786179657998754388262103745688-775359668525787


Q ss_pred             CCCCCCCCCEEEEEECC----CHHHHHHHHHHHHHHHH
Q ss_conf             36776877079998189----98999999999999997
Q gi|254781112|r  216 ADRMKDNSAVAFMMRKG----NNKLTRSINEILCAIHL  249 (274)
Q Consensus       216 ~~~~~~~~~~~~~~~k~----~~~L~~~in~~l~~l~~  249 (274)
                       ..-..+..=++.++|+    ||+.+..|-+.+..-.+
T Consensus       179 -gawgaPTfD~wvvrkdfAeknPe~v~aF~Kv~~dAya  215 (304)
T TIGR01729       179 -GAWGAPTFDAWVVRKDFAEKNPEVVKAFVKVLADAYA  215 (304)
T ss_pred             -HHCCCCCCCEEEEECHHHHHCHHHHHHHHHHHHHHHH
T ss_conf             -4136873102465214543070789999988998501


No 38 
>PRK09501 potD spermidine/putrescine ABC transporter periplasmic substrate-binding protein; Reviewed
Probab=97.65  E-value=0.0006  Score=44.09  Aligned_cols=210  Identities=16%  Similarity=0.148  Sum_probs=108.4

Q ss_pred             HHHHCHHHHHHCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCCCCCCC-HHHHHHHHHC---CCCC
Q ss_conf             98417887885895899962899872487046998488988521678997629985556689-8898864310---3221
Q gi|254781112|r   29 YFVIYPFRTEDQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETA-VSGLITGLDT---NRYD  104 (274)
Q Consensus        29 ~~~~~~~~~~~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~~~~~~-~~~~~~~l~~---g~~D  104 (274)
                      +..+.++.+.+.++|+|-.   |.  .|.           +.|+++..-++.|++|++...+ -+.++..|+.   |.+|
T Consensus        15 ~l~~~~~~a~~~~~L~i~~---W~--~Yi-----------~~~~i~~Fe~etGikV~~~~~~s~ee~~akL~a~~~~~yD   78 (348)
T PRK09501         15 ALGMSAAHADDNNTLYFYN---WT--EYV-----------PPGLLEQFTKETGIKVIYSTYESNETMYAKLKTYKDGAYD   78 (348)
T ss_pred             HHHCCHHHHCCCCEEEEEC---CC--CCC-----------CHHHHHHHHHHHCCEEEEEECCCHHHHHHHHHCCCCCCCE
T ss_conf             9735033543389799987---10--018-----------9789999999989889999549999999999717999828


Q ss_pred             CCHHCCCCHHHH--------------------------H----HHCCCCCCCCCCCCCCCCCCC---CCCCCCCCC----
Q ss_conf             100003675675--------------------------4----200233322222222211122---221111123----
Q gi|254781112|r  105 VLVNVAITPERQ--------------------------K----KYDFSIPYIAHRVLLVVRSDQ---QDIRSFKDL----  147 (274)
Q Consensus       105 ~~~~~~~t~eR~--------------------------~----~~~fs~p~~~~~~~~~~~~~~---~~~~~~~dL----  147 (274)
                      ++..-.+..+|-                          .    .-.|+-||.....++..+++.   ..+++++||    
T Consensus        79 vv~ps~~~v~~l~~~gll~~LD~s~ipN~~nl~p~~~~~~~dp~~~y~vPy~wGt~Gi~yn~d~v~~~~~~SW~dL~dp~  158 (348)
T PRK09501         79 LVVPSTYYVDKMRKEGMIQKIDKSKLTNFSNLDPDMLNKPFDPNNDYSIPYIWGATAIGVNGDAVDPKSVTSWADLWKPE  158 (348)
T ss_pred             EEEECHHHHHHHHHCCCCCCCCHHHCCCHHHCCHHHHCCCCCCCCCEEEEEEEECCEEEEEECCCCCCCCCCHHHHCCHH
T ss_conf             99979689999997798454784228481226976744774899848988997511599850114788888789854966


Q ss_pred             -CCCCEEEEC-------------C----CHHH-------HHHHCCCCCCEEECCHHHHHHHHHHHHHHCCCCCHHHHHHH
Q ss_conf             -343202310-------------1----0122-------33201345421336855777755443210036655899999
Q gi|254781112|r  148 -TDKTVAQIL-------------G----TDLS-------RFAKELKSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNF  202 (274)
Q Consensus       148 -~g~~V~~~~-------------g----~~~~-------~~l~~~~~~~~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~  202 (274)
                       +|+ |++..             |    +...       +.+++...++..+.+ ++..+.+.+|++++.++-.-.+...
T Consensus       159 ~kGk-i~~~d~~~~~~~~al~~lG~~~n~~d~~~l~~a~~~L~~~~~~i~~~~s-d~~~~~l~~Gev~ia~~wsgda~~~  236 (348)
T PRK09501        159 YKGS-LLLTDDAREVFQMALRKLGYSGNTTDPKEIEAAYNELKKLMPNVAAFNS-DNPANPYMEGEVNLGMIWNGSAFVA  236 (348)
T ss_pred             HCCE-EEECCCHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCCEEEEEC-CCHHHHHHCCCCEEEEEECHHHHHH
T ss_conf             4790-7971667899999999827998889999999999999985110589817-7054698738832998740589999


Q ss_pred             HHHCCCCCCCEEECCCCCCCCCEEEEEECC--CHHHHH-HHHHHHHHHHHCCHHHHHHHHHCCC
Q ss_conf             984587667326236776877079998189--989999-9999999999798599999876788
Q gi|254781112|r  203 LERRPHDGNLFKIADRMKDNSAVAFMMRKG--NNKLTR-SINEILCAIHLDGTYKKIFDRYFDK  263 (274)
Q Consensus       203 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~--~~~L~~-~in~~l~~l~~~G~~~~I~~kw~g~  263 (274)
                      . +.. ....+.++.+-..---=+++++++  |+++.. .||-.+     +.+..+-...+.|.
T Consensus       237 ~-~~~-~~i~~v~PkEG~~~w~D~~~Ipk~A~n~e~A~~FInf~l-----~Pevaa~~a~~~~y  293 (348)
T PRK09501        237 R-QAG-TPIDVVWPKEGGIFWMDSLAIPANAKNKEGALKLINFLL-----RPDVAKQVAETIGY  293 (348)
T ss_pred             H-HCC-CCCCEEECCCCCEEEEEEEEEECCCCCHHHHHHHHHHHH-----CHHHHHHHHHHHCC
T ss_conf             9-708-997189757886699899889899989899999999861-----97999999997488


No 39 
>COG1464 NlpA ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]
Probab=97.58  E-value=0.00016  Score=47.60  Aligned_cols=198  Identities=14%  Similarity=0.128  Sum_probs=99.6

Q ss_pred             CCEEEEECCCCCCEEEEEECCCCCEEEEEEE-EHHHHHHHCCCCCCCCC-CCHHHHHHHHHCCCCCCC-H-HCCCCHH--
Q ss_conf             9589996289987248704699848898852-16789976299855566-898898864310322110-0-0036756--
Q gi|254781112|r   41 SALRVGTDGIYPPHSFHAQDGRGELTGFDID-LIKEVAHRLNLKVEFFE-TAVSGLITGLDTNRYDVL-V-NVAITPE--  114 (274)
Q Consensus        41 ~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~d-l~~~i~~~lg~~~~~~~-~~~~~~~~~l~~g~~D~~-~-~~~~t~e--  114 (274)
                      .+|+||+.+.  |+.        +.    .+ .++...++-|++++++. .+|..--.+|.+|++|+- + -..|-++  
T Consensus        29 ~~I~vg~~~~--p~a--------~i----le~~~k~~~~k~Gi~l~i~~FtDY~~PN~AL~~gdiDaN~FQH~pyL~~~~   94 (268)
T COG1464          29 KTIKVGATPG--PHA--------EI----LEVVVKPALKKKGLDLKIVEFTDYVQPNEALADGDIDANAFQHKPYLDQFN   94 (268)
T ss_pred             CCEEEEECCC--CHH--------HH----HHHHHHHHHHHCCCEEEEEEECCCCCHHHHHHCCCCCCHHHHCHHHHHHHH
T ss_conf             7179963689--659--------99----999987788855965999981487665578766884600121468899999


Q ss_pred             HHHHHCCC--CCCCCCCCCCCCCCCCCCCCCCCCCC-CCCEEEECCCH-HHH---HHHCCCC------------------
Q ss_conf             75420023--33222222222111222211111233-43202310101-223---3201345------------------
Q gi|254781112|r  115 RQKKYDFS--IPYIAHRVLLVVRSDQQDIRSFKDLT-DKTVAQILGTD-LSR---FAKELKS------------------  169 (274)
Q Consensus       115 R~~~~~fs--~p~~~~~~~~~~~~~~~~~~~~~dL~-g~~V~~~~g~~-~~~---~l~~~~~------------------  169 (274)
                      ++....+.  ..-+..+.+++.    .++++++||+ |-+|++..+-+ ..+   .+++.|.                  
T Consensus        95 k~~~~~Lv~vg~~~i~Pmg~YS----kk~ksl~el~~GatIaiPNDpsN~gRAL~lL~~aGLIkLk~~~~~~aT~~DI~e  170 (268)
T COG1464          95 KEHGGKLVAVGNTHIEPMGLYS----KKYKSLAELKDGATIAIPNDPTNEGRALLLLQKAGLIKLKDGVNLLATPKDITE  170 (268)
T ss_pred             HHCCCCEEEEEEEEECCCEECC----HHCCCHHHCCCCCEEECCCCCCCHHHHHHHHHHCCCEEECCCCCCCCCHHHHHH
T ss_conf             9739978987557761425012----200868467999989887898735679999998796797688765588878861


Q ss_pred             ---CCEEE-CCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEECCC--CCCCCCEEEEEECCCH--HHHHHHH
Q ss_conf             ---42133-68557777554432100366558999999845876673262367--7687707999818998--9999999
Q gi|254781112|r  170 ---HLVFS-HNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADR--MKDNSAVAFMMRKGNN--KLTRSIN  241 (274)
Q Consensus       170 ---~~~~~-~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~k~~~--~L~~~in  241 (274)
                         ++... -+..+..+.|..  +|+++++..    |..+.+.....-.+..+  ..+++.--+++|+++.  +....  
T Consensus       171 NPK~lki~EldAaqlpRaLdd--vD~AvIN~n----yA~~AgL~p~kdai~~e~~~~spY~Niivvr~~d~d~~~ik~--  242 (268)
T COG1464         171 NPKNLKIKELEAAQLPRALDD--VDAAVINTN----YALQAGLNPKKDALFEEDKDSSPYVNIIVVREEDKDDPAVKK--  242 (268)
T ss_pred             CCCCCEEEECCHHHCCCCCCC--CCEEEECCH----HHHHCCCCCCCCCEECCCCCCCCCEEEEEECCCCCCCHHHHH--
T ss_conf             944575687056756532035--677987430----797759991204214146667862479997155668889999--


Q ss_pred             HHHHHHHHCCHH-HHHHHHHCCCCCC
Q ss_conf             999999979859-9999876788877
Q gi|254781112|r  242 EILCAIHLDGTY-KKIFDRYFDKNII  266 (274)
Q Consensus       242 ~~l~~l~~~G~~-~~I~~kw~g~d~~  266 (274)
                        |.+..+|.+. .-|.++|=|.-++
T Consensus       243 --lv~a~qs~evk~~i~k~y~G~~vP  266 (268)
T COG1464         243 --LVEAYQSDEVKAFIEKKYKGAVVP  266 (268)
T ss_pred             --HHHHHCCHHHHHHHHHHHCCCCCC
T ss_conf             --999974999999999972887566


No 40 
>COG1732 OpuBC Periplasmic glycine betaine/choline-binding (lipo)protein of an ABC-type transport system (osmoprotectant binding protein) [Cell envelope biogenesis, outer membrane]
Probab=97.56  E-value=4.8e-05  Score=50.91  Aligned_cols=203  Identities=16%  Similarity=0.114  Sum_probs=108.3

Q ss_pred             HHHCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCCCCCCCHH--HHHHHHHCCCCCCC---HH---
Q ss_conf             88589589996289987248704699848898852167899762998555668988--98864310322110---00---
Q gi|254781112|r   37 TEDQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVS--GLITGLDTNRYDVL---VN---  108 (274)
Q Consensus        37 ~~~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~~~~~~~~--~~~~~l~~g~~D~~---~~---  108 (274)
                      +.++++|+||.-.    |+  +    +   .+..+|+.++.+.-|++++.+..-=.  =...++.+|++|+.   .|   
T Consensus        29 ~~~~~~I~VgsK~----~t--E----~---~IL~~m~~~lle~~~~kv~~~~~lG~t~v~~~Al~~G~IDiYpEYTGt~~   95 (300)
T COG1732          29 ASAAKTIVVGSKI----FT--E----Q---YILGNILKQLLEKNGIKVEDKTGLGGTAVVRNALKSGDIDIYPEYTGTAL   95 (300)
T ss_pred             CCCCCCEEEECCC----CC--H----H---HHHHHHHHHHHHHCCCCEEECCCCCCHHHHHHHHHCCCCCEEEEECCHHH
T ss_conf             2357887983477----83--8----8---99999999999865991454168885299999997598776854323145


Q ss_pred             --CCC-------CHHH---------HH--HHCCCCCC-CCCCCCCCCCCCC---CCCCCCCCCCC----CCEEEECCCH-
Q ss_conf             --036-------7567---------54--20023332-2222222211122---22111112334----3202310101-
Q gi|254781112|r  109 --VAI-------TPER---------QK--KYDFSIPY-IAHRVLLVVRSDQ---QDIRSFKDLTD----KTVAQILGTD-  159 (274)
Q Consensus       109 --~~~-------t~eR---------~~--~~~fs~p~-~~~~~~~~~~~~~---~~~~~~~dL~g----~~V~~~~g~~-  159 (274)
                        ...       +|+-         ++  .+.|-.|+ +..++++.+|++.   ..+++++||+.    .+.|....+. 
T Consensus        96 ~~~lk~~~~~~~dp~~~y~~vK~~~~k~~~l~wl~p~~~nNTyA~av~~~~A~~~~i~TiSDLak~~~~l~~g~~~eF~~  175 (300)
T COG1732          96 FSFLKKDPPASKDPKKVYETVKKLDAKQFKLVWLKPAGFNNTYALAVRKDVAEKYNLETISDLAKHSNQLKLGADSEFAE  175 (300)
T ss_pred             HHHCCCCCCCCCCHHHHHHHHHHHHHHCCCEEEECCCCCCCCEEEEECHHHHHHHCCCCHHHHHHHHHHCEECCCHHHHC
T ss_conf             66345676454798999999999888607978965468776058996198898819816999998665346227842313


Q ss_pred             ----HHHHHHCCCCCC---EEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCC--CCCEEECCCCCCCCCEEEEEE
Q ss_conf             ----223320134542---13368557777554432100366558999999845876--673262367768770799981
Q gi|254781112|r  160 ----LSRFAKELKSHL---VFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHD--GNLFKIADRMKDNSAVAFMMR  230 (274)
Q Consensus       160 ----~~~~l~~~~~~~---~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~  230 (274)
                          +..+.+.++.+.   +..-+.-..++++.+|.+|++.+-..-+  .+......  .+. .-..++...   +..++
T Consensus       176 R~DG~~~l~k~Yg~~~~~~~~~m~~gl~y~Al~~g~~d~~~~YsTDg--~I~~~~L~VLkDD-K~~fP~Y~~---apvvr  249 (300)
T COG1732         176 RADGLPALQKAYGFDFKPDLRTMDGGLTYQALKNGTVDAADAYSTDG--RIAAYGLKVLKDD-KGFFPPYQA---APVVR  249 (300)
T ss_pred             CCCCCHHHHHHHCCCCCCCCEECCCHHHHHHHHCCCCCEEEECCCCC--CCCCCCCEEEECC-CCCCCCCCC---CCEEC
T ss_conf             65122899998487668874433815899998749977676314552--2122685797068-767998765---64021


Q ss_pred             ----CCCHHHHHHHHHHHHHHHHCCHHHHHHHH
Q ss_conf             ----89989999999999999979859999987
Q gi|254781112|r  231 ----KGNNKLTRSINEILCAIHLDGTYKKIFDR  259 (274)
Q Consensus       231 ----k~~~~L~~~in~~l~~l~~~G~~~~I~~k  259 (274)
                          +++|+|...+|+-..++..+ +++++--+
T Consensus       250 e~vlk~~Pel~~~l~~l~~kid~~-tMq~LNy~  281 (300)
T COG1732         250 EEVLKKHPELKTILNKLSGKIDTE-TMQALNYR  281 (300)
T ss_pred             HHHHHHCHHHHHHHHHHHCCCCHH-HHHHHHHH
T ss_conf             877767988999998875458999-99998777


No 41 
>COG4588 AcfC Accessory colonization factor AcfC, contains ABC-type periplasmic domain [General function prediction only]
Probab=97.55  E-value=0.00045  Score=44.86  Aligned_cols=180  Identities=17%  Similarity=0.217  Sum_probs=116.0

Q ss_pred             EEEEEHHHHHHHCCCCCCCCC--C-CHHHHHHHHHCCCCCCCHHCCCCHHH---HH-HHCCC----CCCCCCCCCCCCCC
Q ss_conf             885216789976299855566--8-98898864310322110000367567---54-20023----33222222222111
Q gi|254781112|r   68 FDIDLIKEVAHRLNLKVEFFE--T-AVSGLITGLDTNRYDVLVNVAITPER---QK-KYDFS----IPYIAHRVLLVVRS  136 (274)
Q Consensus        68 ~~~dl~~~i~~~lg~~~~~~~--~-~~~~~~~~l~~g~~D~~~~~~~t~eR---~~-~~~fs----~p~~~~~~~~~~~~  136 (274)
                      -..|+++...++.|.+|.+..  . .|..--    .++.|+++|.+-..-.   +. .-.||    .|+|.-+..+++++
T Consensus        34 aL~~vA~~~~ektg~kVnvt~GPq~tW~~kA----kknADilfgaseqsalaia~~~~~~fs~~~i~ply~R~aiIlvkk  109 (252)
T COG4588          34 ALKDVAKKYEEKTGIKVNVTAGPQATWNEKA----KKNADILFGASEQSALAIAEDHKDSFSEKNIQPLYLRPAIILVKK  109 (252)
T ss_pred             HHHHHHHHHHHHHCEEEEEECCCCCHHHHHH----HCCCCEEECCCHHHHHHHHHHCCCCCCCCCCCEEEEECEEEEECC
T ss_conf             8999999987874807999418861044564----136745641648889999985633355202531354021799627


Q ss_pred             CCC-CCCCCCCCC--CCCEEEECC--------C-HHHHHHHC---------CCCCCEEE-CCHHHHHHHHHH-HHHHCCC
Q ss_conf             222-211111233--432023101--------0-12233201---------34542133-685577775544-3210036
Q gi|254781112|r  137 DQQ-DIRSFKDLT--DKTVAQILG--------T-DLSRFAKE---------LKSHLVFS-HNFEQSLQLLLS-KRTDATM  193 (274)
Q Consensus       137 ~~~-~~~~~~dL~--g~~V~~~~g--------~-~~~~~l~~---------~~~~~~~~-~~~~~~~~~l~~-grvD~~~  193 (274)
                      +++ .|+.++||-  |-+|.|..|        + .+|..+-+         ...+++.| ++.-.+.+++.+ -.+|+++
T Consensus       110 gNPknIk~~eDll~~gi~ivV~dGaG~sntsgtgvwED~agr~~~ie~v~afR~NI~~fapnSgaArkaf~~~~~aDawI  189 (252)
T COG4588         110 GNPKNIKGFEDLLKPGIGIVVNDGAGVSNTSGTGVWEDIAGRKGNIETVAAFRKNIVAFAPNSGAARKAFENQPDADAWI  189 (252)
T ss_pred             CCCCCCCCHHHHHCCCCEEEEECCCCCCCCCCCEEHHHHHCCCCCHHHHHHHHHCEEEECCCCCHHHHHHHCCCCCCEEE
T ss_conf             99544456888705786299837976447777220486541011488999988523897468704899985499985588


Q ss_pred             CCHHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEEEECC-CHHHHHHHHHHHHHHHHCCHHHHHHHHH
Q ss_conf             655899999984587667326236776877079998189-9899999999999999798599999876
Q gi|254781112|r  194 IPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKG-NNKLTRSINEILCAIHLDGTYKKIFDRY  260 (274)
Q Consensus       194 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~-~~~L~~~in~~l~~l~~~G~~~~I~~kw  260 (274)
                      .-.    .|...+|.....+.+.....-...+.++..++ +++-++.++-     ..|-+-++|++||
T Consensus       190 tW~----dWa~snpdig~~v~~~~d~vIyRd~nv~~~~~a~~ea~~F~dy-----l~S~EAq~ifkky  248 (252)
T COG4588         190 TWA----DWAKSNPDIGDAVEIEKDYVIYRDFNVALAKDANKEARDFADY-----LQSDEAQKIFKKY  248 (252)
T ss_pred             EEC----CHHHHCCCHHCEEECCCCEEEEEECCEEECCCCCHHHHHHHHH-----HHHHHHHHHHHHH
T ss_conf             701----3233098501004516661775402034368999789999999-----7217789999860


No 42 
>pfam03401 Bug Tripartite tricarboxylate transporter family receptor. These probable extra-cytoplasmic solute receptors are strongly overrepresented in several beta-proteobacteria. This family, formerly known as Bug - Bordetella uptake gene (bug) product - is a family of bacterial tripartite tricarboxylate receptors of the extracytoplasmic solute binding receptor-dependent transporter group of families, distinct from the ABC and TRAP-T families. The TctABC system has been characterized in S. typhimurium, and TctC is the extracytoplasmic tricarboxylate-binding receptor which binds the transporters TctA and TctB, two integral membrane proteins. Complete three-component systems are found only in bacteria.
Probab=97.31  E-value=0.0012  Score=42.19  Aligned_cols=141  Identities=15%  Similarity=0.138  Sum_probs=89.1

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCC-------C-CCEEEE-CCCHHH----HHHHCCCC--CCEEECCHHHHHHHHHHH
Q ss_conf             33222222222111222211111233-------4-320231-010122----33201345--421336855777755443
Q gi|254781112|r  123 IPYIAHRVLLVVRSDQQDIRSFKDLT-------D-KTVAQI-LGTDLS----RFAKELKS--HLVFSHNFEQSLQLLLSK  187 (274)
Q Consensus       123 ~p~~~~~~~~~~~~~~~~~~~~~dL~-------g-~~V~~~-~g~~~~----~~l~~~~~--~~~~~~~~~~~~~~l~~g  187 (274)
                      ..+...+.+++++++++ +++++||.       | .++|.. .|+..+    .+.+..+.  +.+.|+...+.+.+|..|
T Consensus        73 a~~~~~~~~l~v~~dsp-~~t~~dli~~ak~~Pg~~~~g~~G~gs~~hl~~~~l~~~~G~~~~~Vpy~G~~~~~~allgG  151 (274)
T pfam03401        73 SLLATSPMVLVVPADSP-FKTLQELVAYAKANPGKLTFASAGIGTSNHLAGELLASKAGVQLSHVPYKGSSPALQDLLGG  151 (274)
T ss_pred             HHHHCCCEEEEECCCCC-CCCHHHHHHHHHHCCCCEEEECCCCCCCCHHHHHHHHHHCCCCEEEECCCCCHHHHHHHHCC
T ss_conf             86501635889779997-56899999999848996587327888631899999999709964883467832668998678


Q ss_pred             HHHCCCCCHHHHHHHHHHCCCCCCC------------EEECCC-----CCCCCCEEEEEECC-CHHHHHHHHHHHHHHHH
Q ss_conf             2100366558999999845876673------------262367-----76877079998189-98999999999999997
Q gi|254781112|r  188 RTDATMIPDIPFFNFLERRPHDGNL------------FKIADR-----MKDNSAVAFMMRKG-NNKLTRSINEILCAIHL  249 (274)
Q Consensus       188 rvD~~~~~~~~~~~~~~~~~~~~~~------------~~~~~~-----~~~~~~~~~~~~k~-~~~L~~~in~~l~~l~~  249 (274)
                      ++|+.+........+++.-......            ++...+     ......+++..+++ .++.++.+++++.++.+
T Consensus       152 ~vd~~~~~~~~~~~~v~~G~lr~Lav~~~~R~~~~PdVPT~~E~G~~~~~~~~w~g~~ap~gtP~~~~~~l~~a~~~~~~  231 (274)
T pfam03401       152 RVDMMIDSLTSTAPYIKAGKLRALAVTSPKRSPQLPDVPTVAELGLKGFEAGVWFGLVAPKGTPPAVVEKLNDAIKKALK  231 (274)
T ss_pred             EEEEEEECCHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCHHHHCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHHHHC
T ss_conf             44599835132044541798259999757567544899976884878714788888763498899999999999999974


Q ss_pred             CCHHHHHHHHHCCCCC
Q ss_conf             9859999987678887
Q gi|254781112|r  250 DGTYKKIFDRYFDKNI  265 (274)
Q Consensus       250 ~G~~~~I~~kw~g~d~  265 (274)
                      |.++.+-+++ .|..+
T Consensus       232 dpe~~~~~~~-~g~~~  246 (274)
T pfam03401       232 DPEVVERLAN-LGMEP  246 (274)
T ss_pred             CHHHHHHHHH-CCCCC
T ss_conf             9999999997-78957


No 43 
>pfam03180 Lipoprotein_9 NLPA lipoprotein. This family of bacterial lipoproteins contains several antigenic members, that may be involved in bacterial virulence. Their precise function is unknown. However they are probably distantly related to pfam00497 which are solute binding proteins.
Probab=97.08  E-value=0.00065  Score=43.87  Aligned_cols=194  Identities=15%  Similarity=0.155  Sum_probs=103.0

Q ss_pred             EEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCCCCCC-CHHHHHHHHHCCCCCCCH--HCCC----CHHH
Q ss_conf             89996289987248704699848898852167899762998555668-988988643103221100--0036----7567
Q gi|254781112|r   43 LRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFET-AVSGLITGLDTNRYDVLV--NVAI----TPER  115 (274)
Q Consensus        43 l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~~~~~-~~~~~~~~l~~g~~D~~~--~~~~----t~eR  115 (274)
                      ||||+.+.  |+.        +.    .+.++..+++-|++++++.. +|..--.+|.+|++|+-.  -..+    ++++
T Consensus         1 lkvG~~~~--p~~--------~i----~~~v~~~~~~~Gi~veiv~F~Dy~~pN~AL~~GeIDaN~fQH~~yl~~~n~~~   66 (236)
T pfam03180         1 LKVGATPG--PHA--------EV----LEVAKPLAKKKGLDLEIVEFTDYVQPNTALADGEIDANAFQHLPYLDQFNKEG   66 (236)
T ss_pred             CEEEECCC--CHH--------HH----HHHHHHHHHHCCCEEEEEEECCCCCHHHHHHCCCCCHHHHCCHHHHHHHHHHC
T ss_conf             98964389--769--------99----99999999964987999981686455079778995524443899999999977


Q ss_pred             HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCEEEECCCH-HHH---HHHCCCC---------------------
Q ss_conf             542002333222222222111222211111233-43202310101-223---3201345---------------------
Q gi|254781112|r  116 QKKYDFSIPYIAHRVLLVVRSDQQDIRSFKDLT-DKTVAQILGTD-LSR---FAKELKS---------------------  169 (274)
Q Consensus       116 ~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~dL~-g~~V~~~~g~~-~~~---~l~~~~~---------------------  169 (274)
                      ...+.--.+.+..+.+++.+    .+++++||+ |-+|++..+.+ ..+   ++++.+.                     
T Consensus        67 g~~L~~v~~~~~~p~glYS~----k~ksl~~lp~Ga~IaIpnD~sN~~RAL~lL~~aGLI~Lk~~~~~~~t~~DI~~Npk  142 (236)
T pfam03180        67 GLDLVAVGNTHVEPIGLYSK----KYKSLSELPDGATIAVPNDPSNEGRALLLLEKAGLIKLKDGAGLLATVKDITENPK  142 (236)
T ss_pred             CCCEEEEEEEEECCEEEEEC----CCCCHHHCCCCCEEEECCCCCHHHHHHHHHHHCCCEEECCCCCCCCCHHHHHHCCC
T ss_conf             99679963046723795433----76887585799989815884429999999998898897689998789888972867


Q ss_pred             --CCEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCC-EEECCCCCCCCCEEEEEECCCH--HHHHHHHHHH
Q ss_conf             --4213368557777554432100366558999999845876673-2623677687707999818998--9999999999
Q gi|254781112|r  170 --HLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNL-FKIADRMKDNSAVAFMMRKGNN--KLTRSINEIL  244 (274)
Q Consensus       170 --~~~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~k~~~--~L~~~in~~l  244 (274)
                        ++++. +..+..+.|  ..+|++++...    |....+..... .........+....+++++++.  +...    .|
T Consensus       143 ~l~~~ev-~a~ql~~~l--~dvD~avin~n----~a~~agl~p~~~~l~~e~~~~~y~n~ivvr~~~~d~~~ik----~l  211 (236)
T pfam03180       143 NLKIKEL-EAAQLPRAL--DDVDAAVINTN----YALQAGLDPKKDALFEEDKDSPYVNIIVVREDDKDDPAVK----KL  211 (236)
T ss_pred             CCEEEEE-CHHHHHHHC--CCCCEEEECHH----HHHHCCCCHHHHHHHCCCCCCCEEEEEEEECCCCCCHHHH----HH
T ss_conf             7669991-677755421--66578998656----7988794921213314788998379999817776999999----99


Q ss_pred             HHHHHCCHHHHHHHHHCCCCC
Q ss_conf             999979859999987678887
Q gi|254781112|r  245 CAIHLDGTYKKIFDRYFDKNI  265 (274)
Q Consensus       245 ~~l~~~G~~~~I~~kw~g~d~  265 (274)
                      .+..+|.++++.+++-|+-.+
T Consensus       212 ~e~~~s~~vk~~i~~~y~G~~  232 (236)
T pfam03180       212 VKAYQSEEVKAFIEKKYGGAV  232 (236)
T ss_pred             HHHHCCHHHHHHHHHHCCCCE
T ss_conf             999879999999998869944


No 44 
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=97.07  E-value=0.02  Score=34.69  Aligned_cols=177  Identities=10%  Similarity=0.080  Sum_probs=104.7

Q ss_pred             HHCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHC-CCCCCCCCCCHHHHHHHHHCCCCCCCH-HCCCCHHH
Q ss_conf             8589589996289987248704699848898852167899762-998555668988988643103221100-00367567
Q gi|254781112|r   38 EDQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRL-NLKVEFFETAVSGLITGLDTNRYDVLV-NVAITPER  115 (274)
Q Consensus        38 ~~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~l-g~~~~~~~~~~~~~~~~l~~g~~D~~~-~~~~t~eR  115 (274)
                      .++|+|+||+.+...-             .+..+++....++. ++++++...+...+++.|.+|++|+.. +....++.
T Consensus        92 ~~~g~lrI~~~~s~~~-------------~~lp~~l~~f~~~~P~v~i~l~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~  158 (307)
T CHL00180         92 LQGGTLIIGASQTTGT-------------YLMPRLIGLFRQKYPQIAVQLQVHSTRRIAWSVANGQIDLAIIGGEVPTEL  158 (307)
T ss_pred             CCCCCCCCCCCCHHHH-------------HHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHCCCEEEEEECCCCCCCC
T ss_conf             1258601010406666-------------643588999999888997278977999999999879800999757788666


Q ss_pred             HHHHCCCCCCCCCCCCCCCCCCCCC----CCCCCCCCCCCEE-EECCCHHH----HHHHCCCCC------CEEECCHHHH
Q ss_conf             5420023332222222221112222----1111123343202-31010122----332013454------2133685577
Q gi|254781112|r  116 QKKYDFSIPYIAHRVLLVVRSDQQD----IRSFKDLTDKTVA-QILGTDLS----RFAKELKSH------LVFSHNFEQS  180 (274)
Q Consensus       116 ~~~~~fs~p~~~~~~~~~~~~~~~~----~~~~~dL~g~~V~-~~~g~~~~----~~l~~~~~~------~~~~~~~~~~  180 (274)
                      ...+. ..++.....++++.++.+.    .-+++||.+.+.. ...++...    .+++..+.+      ..++++.+..
T Consensus       159 ~~~l~-~~~l~~~~~~lv~~~~hpla~~~~v~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l  237 (307)
T CHL00180        159 KDNLQ-VTPYAEDELALILPKSHPFAKLKKIQKEDLYRLRFIALDSQSTIRKVIDNILIQNGIDSSRFKIEMELNSIEAI  237 (307)
T ss_pred             CCCEE-EEEEECCCEEEEECCCCHHHCCCCCCHHHHHCCCEEEECCCCCHHHHHHHHHHHCCCCCCCCEEEEEECCHHHH
T ss_conf             78549-99943242799973898022399999999817984871799968999999999769984554279997809999


Q ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEE-CCCCCCCCCEEEEEECCC
Q ss_conf             77554432100366558999999845876673262-367768770799981899
Q gi|254781112|r  181 LQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKI-ADRMKDNSAVAFMMRKGN  233 (274)
Q Consensus       181 ~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~k~~  233 (274)
                      .+++.+|-.= .+.+.......+..    +....+ ...+.....+++..+++.
T Consensus       238 ~~~v~~g~Gi-a~lP~~~v~~~~~~----g~l~~~~~~~~~~~r~i~lv~~~~r  286 (307)
T CHL00180        238 KNAVQSGLGA-AFVSVSAIEKELEL----GTLHWAKIENITIKRTLSIITNPNR  286 (307)
T ss_pred             HHHHHHCCEE-EECCHHHHHHHHHC----CCEEEEECCCCCCEEEEEEEEECCC
T ss_conf             9999939949-98259999989877----9889997899985049999997959


No 45 
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=97.05  E-value=0.0073  Score=37.40  Aligned_cols=190  Identities=14%  Similarity=0.198  Sum_probs=108.5

Q ss_pred             HCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHC-CCCCCCCCCCHHHHHHHHHCCCCCCCHHCCCCHHHHH
Q ss_conf             589589996289987248704699848898852167899762-9985556689889886431032211000036756754
Q gi|254781112|r   39 DQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRL-NLKVEFFETAVSGLITGLDTNRYDVLVNVAITPERQK  117 (274)
Q Consensus        39 ~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~l-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~t~eR~~  117 (274)
                      ..|+|+||+.+....             .+..+++....++- ++++++....+..+++.|.+|++|+..+..+......
T Consensus        93 ~~G~l~Ig~~~~~~~-------------~~lp~~l~~f~~~~P~v~i~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~  159 (302)
T PRK09791         93 LAGQINIGMGASISR-------------SLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTINTYYQGPYDH  159 (302)
T ss_pred             CCCEEEEEECHHHHH-------------HHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHCCCCCEEEECCCCCCCCC
T ss_conf             663399986268898-------------7119999999998879779999899999999998799778996567887887


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCC--CCCCCCCCCCCEEEEC--CCHH---HHHHHCCCC---CCEEECCHHHHHHHHHHH
Q ss_conf             20023332222222221112222--1111123343202310--1012---233201345---421336855777755443
Q gi|254781112|r  118 KYDFSIPYIAHRVLLVVRSDQQD--IRSFKDLTDKTVAQIL--GTDL---SRFAKELKS---HLVFSHNFEQSLQLLLSK  187 (274)
Q Consensus       118 ~~~fs~p~~~~~~~~~~~~~~~~--~~~~~dL~g~~V~~~~--g~~~---~~~l~~~~~---~~~~~~~~~~~~~~l~~g  187 (274)
                      .+. ..|++..+..++++++.+.  ..+++||.+.......  |...   .++..+.+.   ......+......++..|
T Consensus       160 ~l~-~~~l~~~~~~~v~~~~hpl~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~g~~p~~~~~~~~~~~~~~lv~~g  238 (302)
T PRK09791        160 EFT-FEKLLEKQFAIFCRPGHPAIGARSIKQLLDYSWTMPTPHGSYYKQLSELLDDQAQTPQVGVVCETFSACISLVAKS  238 (302)
T ss_pred             CEE-EEEEEEEEEEEEECCCCCCCCCCCHHHHHCCCEEEECCCCCHHHHHHHHHHHCCCCCCEEEEECCHHHHHHHHHHC
T ss_conf             647-9997740159998389843579899998479938757999799999999996799985699999299999999978


Q ss_pred             HHHCCCCCHHHHHHHHHHCCCCCCCEEE-CCCCCCCCCEEEEEECCCHHHHHHHHHHHHHHH
Q ss_conf             2100366558999999845876673262-367768770799981899899999999999999
Q gi|254781112|r  188 RTDATMIPDIPFFNFLERRPHDGNLFKI-ADRMKDNSAVAFMMRKGNNKLTRSINEILCAIH  248 (274)
Q Consensus       188 rvD~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~k~~~~L~~~in~~l~~l~  248 (274)
                      ..= .+.+...+...+....    ...+ ...+.....++++.+++.. +-...+..|..++
T Consensus       239 ~gv-~ilp~~~~~~~~~~~~----lv~lpl~~~~~~~~~~lv~r~~~~-~spa~~~fi~~lr  294 (302)
T PRK09791        239 DFL-SILPEEMGCDPLHGQG----LVMLPVSEILPKAAYYLIQRRDSR-QTPLTASLITQFR  294 (302)
T ss_pred             CEE-EEECHHHHHHHHHCCC----EEEEECCCCCCCEEEEEEEECCCC-CCHHHHHHHHHHH
T ss_conf             967-9631999987874899----999979998860089999989098-8999999999999


No 46 
>pfam03466 LysR_substrate LysR substrate binding domain. The structure of this domain is known and is similar to the periplasmic binding proteins.
Probab=96.99  E-value=0.0024  Score=40.32  Aligned_cols=174  Identities=17%  Similarity=0.237  Sum_probs=105.8

Q ss_pred             HCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHC-CCCCCCCCCCHHHHHHHHHCCCCCCCHHCCCCHHHHH
Q ss_conf             589589996289987248704699848898852167899762-9985556689889886431032211000036756754
Q gi|254781112|r   39 DQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRL-NLKVEFFETAVSGLITGLDTNRYDVLVNVAITPERQK  117 (274)
Q Consensus        39 ~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~l-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~t~eR~~  117 (274)
                      .+|+|+||+.+....             .+..+++....++. ++++++...+..++.+.+++|++|+.......+.  .
T Consensus         4 ~~G~i~I~~~~~~~~-------------~~lp~~l~~f~~~~P~i~i~i~~~~~~~i~~~l~~g~~Di~i~~~~~~~--~   68 (209)
T pfam03466         4 PRGRLRIGAPPTFAA-------------YLLPPLLARFRERYPDVELELREGDSEELLDLLAEGELDLAIRRGPPDD--P   68 (209)
T ss_pred             CCEEEEEEEEHHHHH-------------HHHHHHHHHHHHHCCCCEEEEEECCCHHHHHHHHCCCCEEEEECCCCCC--C
T ss_conf             878999993889999-------------9999999999998889289999898488999998698148873178999--9


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCC----CCCCCCCCCCCCEEEEC-CCHH----HHHHHCCCC---CCEEECCHHHHHHHHH
Q ss_conf             2002333222222222111222----21111123343202310-1012----233201345---4213368557777554
Q gi|254781112|r  118 KYDFSIPYIAHRVLLVVRSDQQ----DIRSFKDLTDKTVAQIL-GTDL----SRFAKELKS---HLVFSHNFEQSLQLLL  185 (274)
Q Consensus       118 ~~~fs~p~~~~~~~~~~~~~~~----~~~~~~dL~g~~V~~~~-g~~~----~~~l~~~~~---~~~~~~~~~~~~~~l~  185 (274)
                      .+ -+.+.+....++++.++.+    ..-+++||.+.+..... +...    +++.+..+.   ....+++...+..++.
T Consensus        69 ~~-~~~~l~~~~~~~~~s~~~~l~~~~~i~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lv~  147 (209)
T pfam03466        69 GL-EARPLFEEPLVLVAPPDHPLAAGEPVSLEDLADEPLILLEPGSGLRDLVDRALERAGLRPRVALEVNSLEALLAAVA  147 (209)
T ss_pred             CE-EEEEEEEEEEEEEECCCCHHHCCCCCCHHHHCCCCEEEECCCCCCHHHHHHHHHHCCCCCCEEEEECCHHHHHHHHH
T ss_conf             80-89997624136553367055428975435514665798569987137998778764876302467478799999999


Q ss_pred             HHHHHCCCCCHHHHHHHHHHCCCCCCCEEEC-CCCCCCCCEEEEEECCC
Q ss_conf             4321003665589999998458766732623-67768770799981899
Q gi|254781112|r  186 SKRTDATMIPDIPFFNFLERRPHDGNLFKIA-DRMKDNSAVAFMMRKGN  233 (274)
Q Consensus       186 ~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~k~~  233 (274)
                      +|..= .+.+...+..+...    .....+. ........+++..+++.
T Consensus       148 ~g~Gi-~~lp~~~~~~~~~~----~~L~~i~~~~~~~~~~~~li~~~~~  191 (209)
T pfam03466       148 AGLGI-ALLPRSAVARELAD----GRLVVLPLPDPPLPRPIYLVYRKGR  191 (209)
T ss_pred             HCCEE-EECCHHHHHHHHHC----CCEEEEECCCCCCCCEEEEEEECCC
T ss_conf             49999-99139999988758----9989995888887447999998949


No 47 
>COG4663 FcbT1 TRAP-type mannitol/chloroaromatic compound transport system, periplasmic component [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=96.94  E-value=0.012  Score=36.03  Aligned_cols=72  Identities=11%  Similarity=0.074  Sum_probs=52.7

Q ss_pred             HHHCHHHHHHCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCCCCC------CCHHHHHHHHHCCCC
Q ss_conf             84178878858958999628998724870469984889885216789976299855566------898898864310322
Q gi|254781112|r   30 FVIYPFRTEDQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFE------TAVSGLITGLDTNRY  103 (274)
Q Consensus        30 ~~~~~~~~~~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~~~~------~~~~~~~~~l~~g~~  103 (274)
                      ..+.++-++..+++|.-...+||+--       ...-|...++++.+++..|=++++++      +|--+.++++++|.+
T Consensus        24 ~~a~~~~a~~~p~~~wrltsswpksl-------dt~~g~a~~~Ak~v~~mT~G~fqIqvfaAgeivpglq~~DaV~aGtv   96 (363)
T COG4663          24 GLATPAIAQENPKVRWRLTSSWPKSL-------DTIYGGAEDMAKAVAEMTGGNFQIQVFAAGEIVPGLQALDAVKAGTV   96 (363)
T ss_pred             HHCCCHHHCCCCCEEEEEECCCCCCC-------CHHCCHHHHHHHHHHHHHCCCEEEEECCCCCCCCCHHHHHHHHCCCC
T ss_conf             31460233248835899832688875-------31214499999999985089448997357771666025768752863


Q ss_pred             CCCHH
Q ss_conf             11000
Q gi|254781112|r  104 DVLVN  108 (274)
Q Consensus       104 D~~~~  108 (274)
                      |+.-+
T Consensus        97 e~gHt  101 (363)
T COG4663          97 EMGHT  101 (363)
T ss_pred             CCCCE
T ss_conf             13440


No 48 
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=96.84  E-value=0.014  Score=35.56  Aligned_cols=188  Identities=16%  Similarity=0.239  Sum_probs=106.8

Q ss_pred             CCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHC-CCCCCCCCCCHHHHHHHHHCCCCCCCHHCCCCHHHHHH
Q ss_conf             89589996289987248704699848898852167899762-99855566898898864310322110000367567542
Q gi|254781112|r   40 QSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRL-NLKVEFFETAVSGLITGLDTNRYDVLVNVAITPERQKK  118 (274)
Q Consensus        40 ~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~l-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~t~eR~~~  118 (274)
                      .|.|+||+.+...++             +..+++..+.++. ++++++...+...+++.|.+|++|+...... ++. ..
T Consensus        90 ~G~lrig~~~~~~~~-------------llp~~l~~f~~~~P~v~i~l~~~~~~~l~~~l~~g~~D~~i~~~~-~~~-~~  154 (305)
T PRK11151         90 SGPLHIGLIPTVGPY-------------LLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALV-KES-EA  154 (305)
T ss_pred             CCEEEEEEHHHHHHH-------------CCCHHHHHHHHCCCCCEEEEEECCCHHHHHHHHCCCCCEEEEECC-CCC-CC
T ss_conf             641431102223332-------------382779998623898379999887577787865788537998458-899-87


Q ss_pred             HCCCCCCCCCCCCCCCCCCCCC----CCCCCCCCCCCEEEE-CCCHHH----HHHHCCC---CCCEEECCHHHHHHHHHH
Q ss_conf             0023332222222221112222----111112334320231-010122----3320134---542133685577775544
Q gi|254781112|r  119 YDFSIPYIAHRVLLVVRSDQQD----IRSFKDLTDKTVAQI-LGTDLS----RFAKELK---SHLVFSHNFEQSLQLLLS  186 (274)
Q Consensus       119 ~~fs~p~~~~~~~~~~~~~~~~----~~~~~dL~g~~V~~~-~g~~~~----~~l~~~~---~~~~~~~~~~~~~~~l~~  186 (274)
                      +. ..|++..+.+++++++.+.    --+++||.+..+... .|+...    .+....+   .......+.+....++..
T Consensus       155 ~~-~~~l~~e~l~lv~~~~hpla~~~~i~l~~L~~~~~i~~~~~~~~r~~~~~~~~~~g~~~~~~~~~~~~~~i~~lV~~  233 (305)
T PRK11151        155 FI-EVPLFDEPMLLAVYEDHPWANRDRVPMSDLAGEKLLMLEDGHCLRDQAMGFCFEAGADEDTHFRATSLETLRNMVAA  233 (305)
T ss_pred             CE-EEEECCCCEEEEEECCCCCCCCCCCCHHHHCCCCEEEECCCCCHHHHHHHHHHHCCCCCCEEEEEECHHHHHHHHHH
T ss_conf             26-87620462799995898433699989999769988996899859999999999779998738999447999999992


Q ss_pred             HHHHCCCCCHHHHHHHHHHCCCCCCCEEE-CCCCCCCCCEEEEEECCCHHHHHHHHHHHHHHHH
Q ss_conf             32100366558999999845876673262-3677687707999818998999999999999997
Q gi|254781112|r  187 KRTDATMIPDIPFFNFLERRPHDGNLFKI-ADRMKDNSAVAFMMRKGNNKLTRSINEILCAIHL  249 (274)
Q Consensus       187 grvD~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~k~~~~L~~~in~~l~~l~~  249 (274)
                      |..= .+.+.........    ......+ ...+.....++++.+++.+ |.......++.+++
T Consensus       234 G~Gv-~ilp~~~v~~~~~----~~~l~~~pl~~~~~~r~i~lv~r~~~~-ls~~~~~~~e~ir~  291 (305)
T PRK11151        234 GSGI-TLLPALAVPNERK----RDGVCYLPCIKPEPRRTIGLVYRPGSP-LRSRYEQLAEAIRA  291 (305)
T ss_pred             CCCE-EECCHHHHHHHCC----CCCEEEEECCCCCCEEEEEEEEECCCC-CCHHHHHHHHHHHH
T ss_conf             9968-9835999862212----698899988899973699999989098-78999999999999


No 49 
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=96.84  E-value=0.021  Score=34.56  Aligned_cols=202  Identities=13%  Similarity=0.121  Sum_probs=113.5

Q ss_pred             HCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHC-CCCCCCCCCCHHHHHHHHHCCCCCCCHHCCCCHHHHH
Q ss_conf             589589996289987248704699848898852167899762-9985556689889886431032211000036756754
Q gi|254781112|r   39 DQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRL-NLKVEFFETAVSGLITGLDTNRYDVLVNVAITPERQK  117 (274)
Q Consensus        39 ~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~l-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~t~eR~~  117 (274)
                      .+|.|+||+.+....             .+.++++....++. ++++++...+..++.+.|.+|++|+......-+. ..
T Consensus        91 ~~G~l~ig~~~s~~~-------------~~lp~~l~~f~~~~P~v~l~l~~~~~~~~~~~l~~g~~Dl~i~~~~~~~-~~  156 (313)
T PRK12684         91 DQGNLTIATTHTQAR-------------YALPAAIAEFKKRYPKVRLSILQGSPTQIAEMVIHDQADLAIATEAIAD-YK  156 (313)
T ss_pred             CCCEEECCHHHHHHH-------------HCCCHHHHHHHHHCCCEEEEEEECCHHHHHHHHHCCCCCEEECCCCCCC-CC
T ss_conf             775141102455575-------------1594999999844898089997178899999997799665504357777-78


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCC----CCCCCCCCCCCEEE-ECCCHH----HHHHHCCCC--C-CEEECCHHHHHHHHH
Q ss_conf             20023332222222221112222----11111233432023-101012----233201345--4-213368557777554
Q gi|254781112|r  118 KYDFSIPYIAHRVLLVVRSDQQD----IRSFKDLTDKTVAQ-ILGTDL----SRFAKELKS--H-LVFSHNFEQSLQLLL  185 (274)
Q Consensus       118 ~~~fs~p~~~~~~~~~~~~~~~~----~~~~~dL~g~~V~~-~~g~~~----~~~l~~~~~--~-~~~~~~~~~~~~~l~  185 (274)
                      .+ -+.|.+....++++..+.+.    .-+++||.+..+.. ..|+..    +......+.  + +.+..+.+....++.
T Consensus       157 ~l-~~~~l~~~~~~~v~~~~hpla~~~~v~l~dL~~~p~I~~~~~~~~r~~i~~~~~~~g~~p~~~~e~~~~~~i~~~V~  235 (313)
T PRK12684        157 EL-VSLPCYQWNHAVVVPPDHPLLERKPLTLEDLAQYPLITYDDAFAGRSKINKAFALRGLKPDIVLEAIDADVIKTYVE  235 (313)
T ss_pred             CE-EEEEEEECCEEEEECCCCCCCCCCCCCHHHHCCCCEEECCCCCCHHHHHHHHHHHCCCCCCEEEEECCHHHHHHHHH
T ss_conf             73-89980322168995389854469999999985999896289985899999999977998747999997999999999


Q ss_pred             HHHHHCCCCCHHHHHHHHHHCCCCCCCEEE-CCCCCCCCCEEEEEECCCHHHHHHHHHHHHHHHHCCHHHHHHHHHCCC
Q ss_conf             432100366558999999845876673262-367768770799981899899999999999999798599999876788
Q gi|254781112|r  186 SKRTDATMIPDIPFFNFLERRPHDGNLFKI-ADRMKDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYFDK  263 (274)
Q Consensus       186 ~grvD~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~k~~~~L~~~in~~l~~l~~~G~~~~I~~kw~g~  263 (274)
                      .|-.= .+.+.....    .. .+.....+ ...+.....++++.+|+.. |-......|+-+++. ==.++.++|+.-
T Consensus       236 ~GlGi-~ilP~~a~~----~~-~~~~L~~lp~~~~~~~~~~~v~~~k~~~-ls~~~r~FIe~l~e~-l~r~~~~~~~~~  306 (313)
T PRK12684        236 LGLGV-GIVADMAFD----PE-RDRNLRAIPAGHLFGSNVTRVALKQGAY-LRGYVYTFIELFSPT-LNRKLVEQALKG  306 (313)
T ss_pred             HCCCH-HHHHHHHHC----HH-HCCCEEEEECCCCCCCEEEEEEEECCCC-CCHHHHHHHHHHHHH-CCHHHHHHHHHC
T ss_conf             59857-255999846----76-3898799978467766059999979886-689999999998746-598999999837


No 50 
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=96.84  E-value=0.0094  Score=36.69  Aligned_cols=171  Identities=16%  Similarity=0.227  Sum_probs=102.9

Q ss_pred             HCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHC-CCCCCCCCCCHHHHHHHHHCCCCCCCHHCCCCHHHHH
Q ss_conf             589589996289987248704699848898852167899762-9985556689889886431032211000036756754
Q gi|254781112|r   39 DQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRL-NLKVEFFETAVSGLITGLDTNRYDVLVNVAITPERQK  117 (274)
Q Consensus        39 ~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~l-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~t~eR~~  117 (274)
                      .+|.|+||+.+.+.-             .+..+++..+.++. ++++++...+...+.+.|.+|++|+.....  +.+..
T Consensus        89 ~~G~l~ig~~~~~~~-------------~~l~~~l~~f~~~~P~i~i~l~~~~~~~~~~~l~~~~~D~~i~~~--~~~~~  153 (292)
T PRK11242         89 SRGSLRLAMTPTFTA-------------YLIGPLIDAFHARYPGITLTIREMPQERIEALLADDELDVGIAFA--PVHSP  153 (292)
T ss_pred             CCCEEEEECHHHHHH-------------HHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHCCCCCEEEEEC--CCCCC
T ss_conf             776586302457788-------------873899888886488973489976889999998679855799836--88887


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCC-----CCCCCCCCCCCEEEECC-CHH----HHHHHCCCCC---CEEECCHHHHHHHH
Q ss_conf             20023332222222221112222-----11111233432023101-012----2332013454---21336855777755
Q gi|254781112|r  118 KYDFSIPYIAHRVLLVVRSDQQD-----IRSFKDLTDKTVAQILG-TDL----SRFAKELKSH---LVFSHNFEQSLQLL  184 (274)
Q Consensus       118 ~~~fs~p~~~~~~~~~~~~~~~~-----~~~~~dL~g~~V~~~~g-~~~----~~~l~~~~~~---~~~~~~~~~~~~~l  184 (274)
                      .+ -+.|++....++++.++.+.     .-+++||.+........ +..    +.+.++.+.+   ...+++......++
T Consensus       154 ~l-~~~~l~~~~~~~v~~~~h~la~~~~~is~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~V  232 (292)
T PRK11242        154 EI-EAQPLFTETLALVVGRTHPLAARRKPLTLDELADEPLVLLSAEFATREQIDRYFRRHGITPRVAIEANSISAVLEIV  232 (292)
T ss_pred             CC-EEEEECCCEEEEEEECCCHHHHCCCCCCHHHHCCCCEEEECCCCCHHHHHHHHHHHCCCCCCEEEEECCHHHHHHHH
T ss_conf             72-56542045079999089804227999999998189989967998579999999997699985367538899999999


Q ss_pred             HHHHHHCCCCCHHHHHHHHHHCCCCCCCEEE-CCCCCCCCCEEEEEECCC
Q ss_conf             4432100366558999999845876673262-367768770799981899
Q gi|254781112|r  185 LSKRTDATMIPDIPFFNFLERRPHDGNLFKI-ADRMKDNSAVAFMMRKGN  233 (274)
Q Consensus       185 ~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~k~~  233 (274)
                      .+|..= .+.+...+    ...+   ....+ ...+.....++++.+|+.
T Consensus       233 ~~g~Gi-~ilP~~~~----~~~~---~l~~i~l~~~~~~r~i~lv~~k~~  274 (292)
T PRK11242        233 RRGRLA-TLLPAAIA----REHD---DLCAVALDPPLPQRTAALLRRKGA  274 (292)
T ss_pred             HHCCEE-EEEHHHHH----HHCC---CEEEEECCCCCCEEEEEEEEECCC
T ss_conf             979969-97028986----0089---989998989987039999998939


No 51 
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=96.79  E-value=0.044  Score=32.57  Aligned_cols=174  Identities=11%  Similarity=0.147  Sum_probs=101.7

Q ss_pred             HCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHC-CCCCCCCCCCHHHHHHHHHCCCCCCCHHCCCCHHHHH
Q ss_conf             589589996289987248704699848898852167899762-9985556689889886431032211000036756754
Q gi|254781112|r   39 DQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRL-NLKVEFFETAVSGLITGLDTNRYDVLVNVAITPERQK  117 (274)
Q Consensus        39 ~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~l-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~t~eR~~  117 (274)
                      ..|.|+||+......|             +.+.++....++. ++++++...+..++++.|.+|++|+...... ..+..
T Consensus        91 ~~G~l~Ig~~~~~~~~-------------~lp~~l~~f~~~~P~v~i~l~~~~~~~~~~~L~~g~~Dl~i~~~~-~~~~~  156 (308)
T PRK12683         91 DSGRLTVATTHTQARY-------------ALPKVVRQFTEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEA-LDREP  156 (308)
T ss_pred             CCCEEEECCCCHHHHH-------------CCCHHHHHHHHHCCCCEEEEEECCHHHHHHHHHCCCCCEEECCCC-CCCCC
T ss_conf             7762420013201120-------------168466899987899669996078699999997799778806667-78887


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCC----CCCCCCCCCCCEEEE-CCCHH----HHHHHCCCC---CCEEECCHHHHHHHHH
Q ss_conf             20023332222222221112222----111112334320231-01012----233201345---4213368557777554
Q gi|254781112|r  118 KYDFSIPYIAHRVLLVVRSDQQD----IRSFKDLTDKTVAQI-LGTDL----SRFAKELKS---HLVFSHNFEQSLQLLL  185 (274)
Q Consensus       118 ~~~fs~p~~~~~~~~~~~~~~~~----~~~~~dL~g~~V~~~-~g~~~----~~~l~~~~~---~~~~~~~~~~~~~~l~  185 (274)
                      .+ .+.|++....++++.++.+.    .-+++||.+..+... .|+..    +.+..+.+.   ...+..+.+....++.
T Consensus       157 ~l-~~~~l~~~~~~lv~~~~hpla~~~~v~l~dl~~~p~I~~~~~~~~r~~i~~~~~~~g~~p~~~~e~~~~~~i~~~V~  235 (308)
T PRK12683        157 DL-VSFPYYSWHHVVVVPKGHPLTGRENLTLEALAEYPIITYDQGFTGRSHIDQAFAEAGAVPDIVLTALDADVIKTYVE  235 (308)
T ss_pred             CC-EEEEECCCCEEEEECCCCCCCCCCCCCHHHHCCCCEEECCCCCCHHHHHHHHHHHCCCCCCEEEEECCHHHHHHHHH
T ss_conf             71-68761245158984699953369999999985999896189982999999999977999857999998999999999


Q ss_pred             HHHHHCCCCCHHHHHHHHHHCCCCCCCEEE-CCCCCCCCCEEEEEECCC
Q ss_conf             432100366558999999845876673262-367768770799981899
Q gi|254781112|r  186 SKRTDATMIPDIPFFNFLERRPHDGNLFKI-ADRMKDNSAVAFMMRKGN  233 (274)
Q Consensus       186 ~grvD~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~k~~  233 (274)
                      .|-.=+ +.+.......    .... .+.+ ..++.....++++.+|+.
T Consensus       236 ~g~Gi~-ilp~~~~~~~----~~~~-lv~l~~~~~~~~~~~~i~~rk~~  278 (308)
T PRK12683        236 LGMGVG-IVAAMAYDPQ----RDTG-LVALDTQHLFEANTTRVALRRGA  278 (308)
T ss_pred             HCCCHH-HHHHHHHHHH----HCCC-EEEEECCCCCCCCEEEEEECCCC
T ss_conf             798470-7899998788----6099-79998978876617999990968


No 52 
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=96.77  E-value=0.045  Score=32.52  Aligned_cols=189  Identities=10%  Similarity=0.095  Sum_probs=113.1

Q ss_pred             HCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHC-CCCCCCCCCCHHHHHHHHHCCCCCCCHHCCCCHHHHH
Q ss_conf             589589996289987248704699848898852167899762-9985556689889886431032211000036756754
Q gi|254781112|r   39 DQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRL-NLKVEFFETAVSGLITGLDTNRYDVLVNVAITPERQK  117 (274)
Q Consensus        39 ~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~l-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~t~eR~~  117 (274)
                      ..|.|+||+.....+|             +.++++....++. +++++++..+...+.+.|.+|++|+...... .....
T Consensus        91 ~~G~l~Ig~~~t~a~~-------------~LP~~l~~F~~~~P~v~l~l~~~~~~~i~~~l~~g~~Dl~i~~~~-~~~~p  156 (316)
T PRK12679         91 TSGVLTIATTHTQARY-------------SLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASER-LSNDP  156 (316)
T ss_pred             CCCEEEEEEEECCHHC-------------CCCHHHHHHHHHCCCCEEEEEECCHHHHHHHHHCCCCCEEECCCC-CCCCC
T ss_conf             7764999985032010-------------381999999986899538998478799999998799885222467-78997


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCCC----CCCCCCCCCCEEE-ECCCHH----HHHHHCCCC--C-CEEECCHHHHHHHHH
Q ss_conf             200233322222222211122221----1111233432023-101012----233201345--4-213368557777554
Q gi|254781112|r  118 KYDFSIPYIAHRVLLVVRSDQQDI----RSFKDLTDKTVAQ-ILGTDL----SRFAKELKS--H-LVFSHNFEQSLQLLL  185 (274)
Q Consensus       118 ~~~fs~p~~~~~~~~~~~~~~~~~----~~~~dL~g~~V~~-~~g~~~----~~~l~~~~~--~-~~~~~~~~~~~~~l~  185 (274)
                       -..+.|++.....++++.+++..    -+++||.+..+.. ..|+..    +++..+.+.  + +.+..+.+....++.
T Consensus       157 -~l~~~p~~~~~~~lvvp~~HpLa~~~~vsl~~L~~~plI~~~~g~~~R~~id~~f~~~G~~p~i~~e~~~~~~i~~~V~  235 (316)
T PRK12679        157 -QLVAFPWFRWHHSLLVPLDHPLTQITPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDVIKTYVA  235 (316)
T ss_pred             -CCEEEEEEECCEEEEECCCCCCCCCCCCCHHHHCCCCEEEECCCCHHHHHHHHHHHHCCCCCCEEEEECCHHHHHHHHH
T ss_conf             -6079980553413560189951248998999987999895089984999999999977999977999998999999999


Q ss_pred             HHHHHCCCCCHHHHHHHHHHCCCCCCCEEE-CCCCCCCCCEEEEEECCCHHHHHHHHHHHHHHHH
Q ss_conf             432100366558999999845876673262-3677687707999818998999999999999997
Q gi|254781112|r  186 SKRTDATMIPDIPFFNFLERRPHDGNLFKI-ADRMKDNSAVAFMMRKGNNKLTRSINEILCAIHL  249 (274)
Q Consensus       186 ~grvD~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~k~~~~L~~~in~~l~~l~~  249 (274)
                      .|-.=+ +.+....     ....+.....+ ..........+++++|+.. |....-..|.-...
T Consensus       236 ~GlGva-ilp~~a~-----~~~~~~~l~~~~~~~~~~~~~~~~~~~r~~~-l~~~~~~Fi~~~~~  293 (316)
T PRK12679        236 LGLGIG-LVAEQSS-----GEQEEKNLIRLDTRHLFDANTVWLGLKRGQL-QRNYVWRFLELCNA  293 (316)
T ss_pred             HCCCEE-ECHHHHC-----CCCCCCCEEEECCCCCCCCCEEEEEEECCCC-CHHHHHHHHHHHHC
T ss_conf             899099-7014450-----7546898899326346766538999967875-56999999997520


No 53 
>pfam04069 OpuAC Substrate binding domain of ABC-type glycine betaine transport system. Part of a high affinity multicomponent binding-protein-dependent transport system involved in bacterial osmoregulation. This domain is often fused to the permease component of the transporter complex. Family members are often integral membrane proteins or predicted to be attached to the membrane by a lipid anchor. Glycine betaine is involved in protection from high osmolarity environments for example in Bacillus subtilis. The family member OpuBC is closely related, and involved in choline transport. Choline is necessary for the biosynthesis of glycine betaine. L-carnitine is important for osmoregulation in Listeria monocytogenes. Family also contains proteins binding l-proline (ProX), histidine (HisX) and taurine (TauA).
Probab=96.73  E-value=0.004  Score=38.98  Aligned_cols=167  Identities=14%  Similarity=0.086  Sum_probs=91.1

Q ss_pred             EEEHHHHHHHCCCCCCCCCCCH-HHHHHHHHCCCCCCCHH-CCCCHH------HHH--HHCCCCCC-CCCCCCCCCCCCC
Q ss_conf             5216789976299855566898-89886431032211000-036756------754--20023332-2222222211122
Q gi|254781112|r   70 IDLIKEVAHRLNLKVEFFETAV-SGLITGLDTNRYDVLVN-VAITPE------RQK--KYDFSIPY-IAHRVLLVVRSDQ  138 (274)
Q Consensus        70 ~dl~~~i~~~lg~~~~~~~~~~-~~~~~~l~~g~~D~~~~-~~~t~e------R~~--~~~fs~p~-~~~~~~~~~~~~~  138 (274)
                      ..++..+.+.+|++++.+...- .-++.+|.+|++|+... ...+-.      -.+  ......|. ......+.+++..
T Consensus        17 a~i~~~~Le~~G~~V~~~~~~~~~~~~~al~~G~iDi~~~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~Vp~~~   96 (256)
T pfam04069        17 ANIAAQLLEALGYVVELVGLGSTAVLFAALASGDIDLYPEEWTGTTYEAYKKAVEEKLGLLVLGPLGAGNTYGLAVPKYV   96 (256)
T ss_pred             HHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCEEEHHCCCCHHHHHHHHHHCCCCEEECCCCCCCCEEEEEECHHH
T ss_conf             99999999976981698547870899999976997586333066257999987514687386135777875899985888


Q ss_pred             ---CCCCCCCCCCCC----------CEEEECCCHHH----HHHHCCCCCCE-EECC-----HHHHHHHHHHHHHHCCCCC
Q ss_conf             ---221111123343----------20231010122----33201345421-3368-----5577775544321003665
Q gi|254781112|r  139 ---QDIRSFKDLTDK----------TVAQILGTDLS----RFAKELKSHLV-FSHN-----FEQSLQLLLSKRTDATMIP  195 (274)
Q Consensus       139 ---~~~~~~~dL~g~----------~V~~~~g~~~~----~~l~~~~~~~~-~~~~-----~~~~~~~l~~grvD~~~~~  195 (274)
                         ..+++++||+..          -++...|+...    ..++.++.... ....     ..+..+++.+|+.+++..-
T Consensus        97 a~~~~i~si~dL~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~yGl~~~~~~~~s~~~~~a~~~~A~~~g~~~v~~~w  176 (256)
T pfam04069        97 AEKPGIKSISDLAKPADDELGFKGEFIGRPDGWGCTRSTEGLLKAYGLDKYELVEGSEAAMDALLYAAIKRGEPDVVYAW  176 (256)
T ss_pred             HHHCCCCCHHHHHCCCCCCCCCCCCEECCCCCCCCCHHHHHHHHHCCCCCEEECCCCHHHHHHHHHHHHHCCCCEEEEEC
T ss_conf             83569987999727421024888655327888540067899998639764012358555459999999984998899963


Q ss_pred             HHHHHHHHHHCCCCCCCEEECCC--CC-CCCCEEEEEEC----CCHHHHHHHHH
Q ss_conf             58999999845876673262367--76-87707999818----99899999999
Q gi|254781112|r  196 DIPFFNFLERRPHDGNLFKIADR--MK-DNSAVAFMMRK----GNNKLTRSINE  242 (274)
Q Consensus       196 ~~~~~~~~~~~~~~~~~~~~~~~--~~-~~~~~~~~~~k----~~~~L~~~in~  242 (274)
                      .......  +..    ...+.++  .. .....+..+++    ++|+....+++
T Consensus       177 ~p~~~~~--~~d----l~~L~Dp~~~~~~~~~v~~v~~~~~~~~~P~~~~~l~~  224 (256)
T pfam04069       177 TPDWMIK--KYD----LVVLEDPKGLFPPAYNVVPVVRKGFAEKHPEVAAFLNK  224 (256)
T ss_pred             CCCHHHH--HCC----EEECCCCCCCCCCCCEEEEEECHHHHHHCHHHHHHHHH
T ss_conf             7616554--279----69936886457976558752104677779899999986


No 54 
>pfam03480 SBP_bac_7 Bacterial extracellular solute-binding protein, family 7. This family of proteins are involved in binding extracellular solutes for transport across the bacterial cytoplasmic membrane. This family includes a C4-dicarboxylate-binding protein and the sialic acid-binding protein SiaP. The structure of the SiaP receptor has revealed an overall topology similar to ATP binding cassette ESR (extracytoplasmic solute receptors) proteins. Upon binding of sialic acid, SiaP undergoes domain closure about a hinge region and kinking of an alpha-helix hinge component.
Probab=96.73  E-value=0.0012  Score=42.28  Aligned_cols=103  Identities=14%  Similarity=0.020  Sum_probs=63.7

Q ss_pred             CCCCCCCCCCCCEEEECCCHHHHHHHCCCCCCEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEECCCC
Q ss_conf             21111123343202310101223320134542133685577775544321003665589999998458766732623677
Q gi|254781112|r  140 DIRSFKDLTDKTVAQILGTDLSRFAKELKSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRM  219 (274)
Q Consensus       140 ~~~~~~dL~g~~V~~~~g~~~~~~l~~~~~~~~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  219 (274)
                      .+++++||+|++|-+..+.....+++..+...+...-. +.+.+|.+|-+|++......... . +.......+  ....
T Consensus       126 pi~~~~DlkG~KiR~~~~~~~~~~~~alGa~pv~~~~~-evy~aLq~GvvDg~~~~~~~~~~-~-~~~ev~ky~--~~~~  200 (285)
T pfam03480       126 PINSPEDLKGLKLRVPPSPLLGEVFKALGANPTPMPFG-EVYTALQTGVVDGQENPLSNIYS-Q-KFYEVQKYL--TETN  200 (285)
T ss_pred             CCCCHHHHCCCEEEECCCHHHHHHHHHCCCCCCCCCHH-HHHHHHHHCCEEEEECCCHHHHH-H-CHHHHCCEE--EECC
T ss_conf             88997996798288358679999999859974015758-89999970846267537135654-0-412113367--2256


Q ss_pred             CCCCCEEEEEECC-----CHHHHHHHHHHHHHH
Q ss_conf             6877079998189-----989999999999999
Q gi|254781112|r  220 KDNSAVAFMMRKG-----NNKLTRSINEILCAI  247 (274)
Q Consensus       220 ~~~~~~~~~~~k~-----~~~L~~~in~~l~~l  247 (274)
                      .......+.++++     +++.+..|.++-.+.
T Consensus       201 ~~~~~~~~~~n~~~w~~L~~~~q~~i~~a~~~a  233 (285)
T pfam03480       201 HGYLDYLVVMNKDTWDSLPPDLQAILEEAAKEA  233 (285)
T ss_pred             CHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf             335678999249999649999999999999999


No 55 
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=96.18  E-value=0.1  Score=30.26  Aligned_cols=187  Identities=10%  Similarity=0.165  Sum_probs=104.8

Q ss_pred             HCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHC-CCCCCCCCCCHHHHHHHHHCCCCCCCHHCCCCHHHHH
Q ss_conf             589589996289987248704699848898852167899762-9985556689889886431032211000036756754
Q gi|254781112|r   39 DQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRL-NLKVEFFETAVSGLITGLDTNRYDVLVNVAITPERQK  117 (274)
Q Consensus        39 ~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~l-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~t~eR~~  117 (274)
                      ..|+|+||+.+....+             +.++++....++. ++++++...+...+.+.+.+|++|+..... ..+...
T Consensus        91 ~~G~lrIg~~~~~~~~-------------~lp~~l~~f~~~~P~v~l~l~~~~~~~~~~~l~~g~~Dl~i~~~-~~~~~~  156 (309)
T PRK12682         91 DSGTLTIATTHTQARY-------------VLPRVVAKFRKRYPKVNLSLHQGSPDEIAQMVISGEADIGIATE-SLDDDP  156 (309)
T ss_pred             CCCCCCCCCCHHHHHH-------------CCCHHHHHHHHHCCCCEEEEEECCHHHHHHHHHCCCCCHHHHHC-CCCCCC
T ss_conf             7774121243133320-------------38625399998789837999837829999999769976456507-777898


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCC----CCCCCCCCCCCCEEEE-CCCH----HHHHHHCCCC---CCEEECCHHHHHHHHH
Q ss_conf             2002333222222222111222----2111112334320231-0101----2233201345---4213368557777554
Q gi|254781112|r  118 KYDFSIPYIAHRVLLVVRSDQQ----DIRSFKDLTDKTVAQI-LGTD----LSRFAKELKS---HLVFSHNFEQSLQLLL  185 (274)
Q Consensus       118 ~~~fs~p~~~~~~~~~~~~~~~----~~~~~~dL~g~~V~~~-~g~~----~~~~l~~~~~---~~~~~~~~~~~~~~l~  185 (274)
                      .+. ..|++....+++++++.+    ..-+++||++..+... .|+.    .+.+....+.   ......+.+....++.
T Consensus       157 ~l~-~~~l~~~~~~~v~~~~h~la~~~~i~~~dL~~~p~I~~~~~~~~r~~~~~~~~~~g~~p~~~~~~~~~~~~~~~v~  235 (309)
T PRK12682        157 DLV-TLPCYDWTHAVIVPSDHPLAQKERITLEDLAEYPLITYHPGFTGRSAIDKAFAAAGLQPDIVLEAIDSDVIKTYVR  235 (309)
T ss_pred             CEE-EEEEECCCEEEEECCCCHHHCCCCCCHHHHCCCCEEEECCCCCHHHHHHHHHHHCCCCCCEEEEECCHHHHHHHHH
T ss_conf             808-9993315236761699721149999999982899797279986799999999977999626999998999999999


Q ss_pred             HHHHHCCCCCHHHHHHHHHHCCCCCCCEEE-CCCCCCCCCEEEEEECCCHHHHHHHHHHHHHH
Q ss_conf             432100366558999999845876673262-36776877079998189989999999999999
Q gi|254781112|r  186 SKRTDATMIPDIPFFNFLERRPHDGNLFKI-ADRMKDNSAVAFMMRKGNNKLTRSINEILCAI  247 (274)
Q Consensus       186 ~grvD~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~k~~~~L~~~in~~l~~l  247 (274)
                      .|-.=+ +.+.....    ... ....+.+ ......+..++++.+|+.. +-..+...|+-+
T Consensus       236 ~G~Gi~-~lp~~~~~----~~~-~~~Lv~v~~~~~~~~~~~~l~~rk~~~-l~~~~~~FId~l  291 (309)
T PRK12682        236 LGLGVG-IIAEMAYR----PDR-DGDLVALPAGHLFGPNTAWVAVKRGAY-LRNYVYDFIELL  291 (309)
T ss_pred             HCCEEE-HHHHHHHH----HHH-CCCEEEEECCCCCCCCEEEEEEECCCC-CCHHHHHHHHHH
T ss_conf             599424-22899833----764-799899979887776179999969661-189999999999


No 56 
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=96.16  E-value=0.067  Score=31.44  Aligned_cols=174  Identities=12%  Similarity=0.122  Sum_probs=103.7

Q ss_pred             HCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHC-CCCCCCCCCCHHHHHHHHHCCCCCCCHHCCCCHHHHH
Q ss_conf             589589996289987248704699848898852167899762-9985556689889886431032211000036756754
Q gi|254781112|r   39 DQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRL-NLKVEFFETAVSGLITGLDTNRYDVLVNVAITPERQK  117 (274)
Q Consensus        39 ~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~l-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~t~eR~~  117 (274)
                      ..|.|+||+......|             +.++++....++. ++++++...+..++.+.+.+|++|+..... ..+...
T Consensus        91 ~~G~L~Ia~~~t~a~~-------------~LP~~i~~F~~~~P~v~l~l~~~~~~~i~~~l~~g~~DlaI~~e-~~~~~~  156 (324)
T PRK12681         91 DKGSLYIATTHTQARY-------------ALPPVIKGFIKRYPRVSLHMHQGSPTQIAEAAAKGEADFAIATE-ALHLYD  156 (324)
T ss_pred             CCCEEEEEECHHHHHH-------------HHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHCCCCCCCCCCC-CCCCCC
T ss_conf             7634999853588887-------------72599999998789984465317879999999879987231246-666688


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCC----CCCCCCCCCCCEEE-ECCCHH----HHHHHCCCC--C-CEEECCHHHHHHHHH
Q ss_conf             20023332222222221112222----11111233432023-101012----233201345--4-213368557777554
Q gi|254781112|r  118 KYDFSIPYIAHRVLLVVRSDQQD----IRSFKDLTDKTVAQ-ILGTDL----SRFAKELKS--H-LVFSHNFEQSLQLLL  185 (274)
Q Consensus       118 ~~~fs~p~~~~~~~~~~~~~~~~----~~~~~dL~g~~V~~-~~g~~~----~~~l~~~~~--~-~~~~~~~~~~~~~l~  185 (274)
                      . ....|++....+++++++++.    --+++||.+..+.. ..|+..    ++...+.+.  + +.+..+.+....++.
T Consensus       157 d-l~~~P~~~~~~~vvvp~~HPLa~~~~itl~dL~~~plI~~~~g~~~R~~id~~f~~~g~~P~iv~e~~~~~~I~~~V~  235 (324)
T PRK12681        157 D-LIMLPCYHWNRSVVVPPDHPLAKKKKLTIEELAQYPLVTYVFGFTGRSELDTAFNRAGLTPRIVFTATDADVIKTYVR  235 (324)
T ss_pred             C-CEEEEEEECCCCCCCCCCCCCCCCCCCCHHHHCCCCEEEECCCCCHHHHHHHHHHHCCCCCEEEEEECCHHHHHHHHH
T ss_conf             7-468640003222457999965579999999986998596149982999999999988997607999898999999999


Q ss_pred             HHHHHCCCCCHHHHHHHHHHCCCCCCCEEE-CCCCCCCCCEEEEEECCC
Q ss_conf             432100366558999999845876673262-367768770799981899
Q gi|254781112|r  186 SKRTDATMIPDIPFFNFLERRPHDGNLFKI-ADRMKDNSAVAFMMRKGN  233 (274)
Q Consensus       186 ~grvD~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~k~~  233 (274)
                      .|-.=+ +.+....     ....+.....+ ...+......+++++|+.
T Consensus       236 ~GlGV~-ilp~mA~-----~~~~d~~l~~~~~~~~f~~~~t~i~~r~g~  278 (324)
T PRK12681        236 LGLGVG-VIASMAV-----DPVADPDLVAIDASHLFAHSTTKIGFRRGT  278 (324)
T ss_pred             HCCEEE-ECHHHHC-----CCCCCCCEEEEECCCCCCCCEEEEEEECCC
T ss_conf             599139-7035551-----965578817843655677764799997997


No 57 
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=96.01  E-value=0.056  Score=31.92  Aligned_cols=157  Identities=13%  Similarity=0.172  Sum_probs=91.4

Q ss_pred             EEEHHHHHHHC-CCCCCCCCCCHHHHHHHHHCCCCCCCHHCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCC--CCCCCCC
Q ss_conf             52167899762-99855566898898864310322110000367567542002333222222222111222--2111112
Q gi|254781112|r   70 IDLIKEVAHRL-NLKVEFFETAVSGLITGLDTNRYDVLVNVAITPERQKKYDFSIPYIAHRVLLVVRSDQQ--DIRSFKD  146 (274)
Q Consensus        70 ~dl~~~i~~~l-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~t~eR~~~~~fs~p~~~~~~~~~~~~~~~--~~~~~~d  146 (274)
                      .+++....+.. ++++++...+....++.+++|++|+..+....+.....+ ...|.+....++++.++.+  .-.+++|
T Consensus       113 p~~l~~f~~~~P~v~i~l~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~-~~~~l~~~~~~lv~~~~~p~~~~~~l~~  191 (312)
T PRK10341        113 SDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSNEMKLQDL-HVEPLFESEFVLVASKSRTCTGTTTLES  191 (312)
T ss_pred             HHHHHHHHHHCCCCEEEEEECCHHHHHHHHHCCCCEEEEEECCCCCCCCCE-EEEEEECCCEEEEECCCCCCCCCCCHHH
T ss_conf             999999999888977999989999999999669861999743687777874-9999512428999767542348979899


Q ss_pred             CCCCCEEEEC-CCHH----HHHHHCCCC---CCEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEEC-C
Q ss_conf             3343202310-1012----233201345---42133685577775544321003665589999998458766732623-6
Q gi|254781112|r  147 LTDKTVAQIL-GTDL----SRFAKELKS---HLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIA-D  217 (274)
Q Consensus       147 L~g~~V~~~~-g~~~----~~~l~~~~~---~~~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~-~  217 (274)
                      |.+....... ++.+    ..++++.+.   .....++......++.+|..= .+.+...+..+     .......+. .
T Consensus       192 L~~~~~il~~~~~~~~~~~~~~~~~~g~~~~~~~~~~s~~~i~~lv~~g~gi-~~lP~~~~~~~-----~~~~L~~lpl~  265 (312)
T PRK10341        192 LKNEQWVLPQTNMGYYSELLTTLQRNGISIENIVKTDSVVTIYNLVLNADFL-TVIPCDMTSPF-----GSNQFITIPIK  265 (312)
T ss_pred             HCCCCEEEECCCCCHHHHHHHHHHHCCCCCCCEEEECHHHHHHHHHHHCCEE-EEEHHHHHHHH-----CCCCEEEEECC
T ss_conf             8079868606998589999999997699988169989099999999979958-97269999663-----18989999899


Q ss_pred             CCCCCCCEEEEEECCC
Q ss_conf             7768770799981899
Q gi|254781112|r  218 RMKDNSAVAFMMRKGN  233 (274)
Q Consensus       218 ~~~~~~~~~~~~~k~~  233 (274)
                      .+.....++++.+|+.
T Consensus       266 ~~~~~~~~~lv~~k~~  281 (312)
T PRK10341        266 ETLPVARYAAVWSKNY  281 (312)
T ss_pred             CCCCEEEEEEEEECCC
T ss_conf             9885118999998939


No 58 
>COG3181 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=95.99  E-value=0.039  Score=32.88  Aligned_cols=133  Identities=17%  Similarity=0.140  Sum_probs=82.8

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCC-------CCCEEEECC--CHH----HHHHHCCC--CCCEEECCHHHHHHHHHHHHH
Q ss_conf             222222222111222211111233-------432023101--012----23320134--542133685577775544321
Q gi|254781112|r  125 YIAHRVLLVVRSDQQDIRSFKDLT-------DKTVAQILG--TDL----SRFAKELK--SHLVFSHNFEQSLQLLLSKRT  189 (274)
Q Consensus       125 ~~~~~~~~~~~~~~~~~~~~~dL~-------g~~V~~~~g--~~~----~~~l~~~~--~~~~~~~~~~~~~~~l~~grv  189 (274)
                      ....+..++++++++ +++++||.       |...+.-.|  +..    ..+.+..+  ...+.|+..-+++..|+.|++
T Consensus       119 v~~~p~~l~v~~~s~-~~t~~dlv~~~k~~p~~v~~~~~g~Gs~dhl~~~~~~k~~Gi~~~~Vpy~g~gea~taLlgg~v  197 (319)
T COG3181         119 LVSDPGVLVVRADSP-YKTLKDLVAYAKADPGSVIGGGSGLGSADHLAGALFAKAAGIKITYVPYKGGGEALTALLGGHV  197 (319)
T ss_pred             EECCCCEEEEECCCC-CCCHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHCCCE
T ss_conf             113661599817887-3669999999985998089547888958899999999973896257741686487899860866


Q ss_pred             HCCCCCHHHHHHHHHHCCCCCCC-------------EE----ECCCCCCCCCEEEEEECC-CHHHHHHHHHHHHHHHHCC
Q ss_conf             00366558999999845876673-------------26----236776877079998189-9899999999999999798
Q gi|254781112|r  190 DATMIPDIPFFNFLERRPHDGNL-------------FK----IADRMKDNSAVAFMMRKG-NNKLTRSINEILCAIHLDG  251 (274)
Q Consensus       190 D~~~~~~~~~~~~~~~~~~~~~~-------------~~----~~~~~~~~~~~~~~~~k~-~~~L~~~in~~l~~l~~~G  251 (274)
                      |+...+........+.- .....             ++    ...+.......++..+++ +.+....++++++++.+|.
T Consensus       198 ~a~~~~~se~~~~vksG-~lr~Lav~s~eRl~~~pdvPT~~E~G~~~~~~~wrgvfap~g~~~e~~~~~~~a~kk~l~s~  276 (319)
T COG3181         198 DAGSTNLSELLSQVKSG-TLRLLAVFSEERLPGLPDVPTLKEQGYDVVMSIWRGVFAPAGTPDEIIAKLSAALKKALASP  276 (319)
T ss_pred             EEEECCHHHHHHHHCCC-CEEEEEEECHHHCCCCCCCCCHHHCCCCEEEEEEEEEEECCCCCHHHHHHHHHHHHHHHCCH
T ss_conf             54436712435563057-46787753431067799999867638754664435898079999999999999999986398


Q ss_pred             HHHHHHHH
Q ss_conf             59999987
Q gi|254781112|r  252 TYKKIFDR  259 (274)
Q Consensus       252 ~~~~I~~k  259 (274)
                      ++++.+++
T Consensus       277 e~~~~~~~  284 (319)
T COG3181         277 EWQKRLKE  284 (319)
T ss_pred             HHHHHHHH
T ss_conf             89999985


No 59 
>TIGR01728 SsuA_fam ABC transporter, substrate-binding protein, aliphatic sulfonates family; InterPro: IPR010067   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).    Members of this family are substrate-binding periplasmic proteins of ABC transporters. This subfamily includes SsuA, a member of a transporter operon needed to obtain sulphur from aliphatic sulphonates. Related proteins include taurine (NH2-CH2-CH2-S03H) binding proteins, the probable sulphate ester binding protein AtsR, and the probable aromatic sulphonate binding protein AsfC. All these families make sulphur available when Cys and sulphate levels are low.; GO: 0006790 sulfur metabolic process, 0006810 transport, 0016020 membrane.
Probab=95.93  E-value=0.024  Score=34.17  Aligned_cols=134  Identities=19%  Similarity=0.107  Sum_probs=80.8

Q ss_pred             EHHHHHHHCCCCCCCCCCC-HHHHHHHHHCCCCCCCH-HC--CCCHHHHHH-HCCC----CCCCCCCCCCCCCCCCCCCC
Q ss_conf             1678997629985556689-88988643103221100-00--367567542-0023----33222222222111222211
Q gi|254781112|r   72 LIKEVAHRLNLKVEFFETA-VSGLITGLDTNRYDVLV-NV--AITPERQKK-YDFS----IPYIAHRVLLVVRSDQQDIR  142 (274)
Q Consensus        72 l~~~i~~~lg~~~~~~~~~-~~~~~~~l~~g~~D~~~-~~--~~t~eR~~~-~~fs----~p~~~~~~~~~~~~~~~~~~  142 (274)
                      +.+.-..+-|.+++|+..+ -...++.|..|.+|+-. +.  +.... ... ...-    .+.......+++.++ ..++
T Consensus        22 ~~~~~~~~~g~~~~~~~f~~g~~~~~~l~~g~~d~g~~g~~p~~~~~-~~g~~~~~~~~~~~~~~~~~~~~~~~~-~~i~   99 (311)
T TIGR01728        22 LLEKEGGKEGTKVEWVEFPGGPPELEALGAGSLDFGYIGPGPALNAY-AAGNADIKAVGLSSDGPSATALVVGKG-SGIR   99 (311)
T ss_pred             HHHHCCCCCCCEEEEEEECCCHHHHHHHCCCCCCCCCCCCCHHEEEC-CCCCCCEEEEEEECCCCCCEEEEECCC-CCCC
T ss_conf             13440365661247886267547777520565001433673120100-036764679985257764035663366-7730


Q ss_pred             CCCCCCCCCEEEECCCHHHHHH----HCCC------C----CCEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCC
Q ss_conf             1112334320231010122332----0134------5----42133685577775544321003665589999998458
Q gi|254781112|r  143 SFKDLTDKTVAQILGTDLSRFA----KELK------S----HLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRP  207 (274)
Q Consensus       143 ~~~dL~g~~V~~~~g~~~~~~l----~~~~------~----~~~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~  207 (274)
                      +++||+||+|++..|+....++    .+.+      .    ..+..-++.++..++.+|.+|++............+.+
T Consensus       100 ~~~dlkGk~~a~~~g~~~~~~~~~~l~~~ggl~~~~~~~~d~~~~~~~~~~~~~a~~~g~~da~~~~~P~~~~~~~~~~  178 (311)
T TIGR01728       100 SVKDLKGKRIAVPKGGSGHDLLLRALLKAGGLEDNLLSGDDVDILELGPSDARAALAAGQVDAWGIWEPWLSALVEEGG  178 (311)
T ss_pred             HHHHCCCCEEEEECCCCHHHHHHHHHHHHCCCCCCCCCCCCEEEEECCCHHHHHHHHCCCCCEEECCCCCHHHHHHHCC
T ss_conf             1433477456630666157899999997347200036876315540260456776540462212116871445432226


No 60 
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=95.81  E-value=0.15  Score=29.26  Aligned_cols=201  Identities=13%  Similarity=0.113  Sum_probs=120.3

Q ss_pred             HCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHC-CCCCCCCCCCHHHHHHHHHCCCCCCCH-HCCCCHHHH
Q ss_conf             589589996289987248704699848898852167899762-998555668988988643103221100-003675675
Q gi|254781112|r   39 DQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRL-NLKVEFFETAVSGLITGLDTNRYDVLV-NVAITPERQ  116 (274)
Q Consensus        39 ~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~l-g~~~~~~~~~~~~~~~~l~~g~~D~~~-~~~~t~eR~  116 (274)
                      ..|.|+||+..+-..|             +.+.++...-++- ++++++...+..++.+.+.+|++|+.. .......  
T Consensus        91 ~~G~L~Ig~~~t~a~~-------------~LP~vi~~f~~~yP~V~l~l~~~~~~~l~e~l~~g~~Diai~~~~~~~~--  155 (327)
T PRK12680         91 SQGQLTLTTTHTQARF-------------VLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAVVSTAGGEP--  155 (327)
T ss_pred             CCEEEEEEEECHHHHH-------------HHHHHHHHHHHHCCCCEEEEEECCCHHHHHHHHCCCCCEEEECCCCCCC--
T ss_conf             7337999984227777-------------5689999999868996799998982889999978994099944777799--


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCCC-----CCCCCCCCCCCEEE-ECCCHH----HHHHHCCCC--CC-EEECCHHHHHHH
Q ss_conf             420023332222222221112222-----11111233432023-101012----233201345--42-133685577775
Q gi|254781112|r  117 KKYDFSIPYIAHRVLLVVRSDQQD-----IRSFKDLTDKTVAQ-ILGTDL----SRFAKELKS--HL-VFSHNFEQSLQL  183 (274)
Q Consensus       117 ~~~~fs~p~~~~~~~~~~~~~~~~-----~~~~~dL~g~~V~~-~~g~~~----~~~l~~~~~--~~-~~~~~~~~~~~~  183 (274)
                       .-..+.|.+....+++++++.+.     .-+++||.+..+.. ..|+..    ++..++.+.  ++ .+..+.+....+
T Consensus       156 -~~~~~~pl~~~~~~vvvP~~HpL~~~~~~i~L~~La~~plI~~~~g~~~r~~id~af~~~Gl~P~iv~ea~~~d~Ik~~  234 (327)
T PRK12680        156 -SAGIAVPLYRWRRLVVVPRGHALDTPRTAPDMAALAEHPLISYDSSTRPGSSLQRAFAQVGLEPSIALTALDADLIKTY  234 (327)
T ss_pred             -CCCEEEEEEECCEEEEEECCCCCCCCCCCCCHHHHHCCCEEECCCCCCHHHHHHHHHHHCCCCCCEEEEECCHHHHHHH
T ss_conf             -7654767522357999978981005899999999808988963899867999999999779976479999959999999


Q ss_pred             HHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEE-CCCCCCCCCEEEEEECCCHHHHHHHHHHHHHHHHCCHHHHHHHHHCC
Q ss_conf             54432100366558999999845876673262-36776877079998189989999999999999979859999987678
Q gi|254781112|r  184 LLSKRTDATMIPDIPFFNFLERRPHDGNLFKI-ADRMKDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYFD  262 (274)
Q Consensus       184 l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~k~~~~L~~~in~~l~~l~~~G~~~~I~~kw~g  262 (274)
                      +..|-.= .+++..-.     . ..+.....+ ...+....-..++++++.- |+...-+.|..+-.. ==.+..++.+.
T Consensus       235 V~~GlGV-~Ivp~mA~-----~-~~d~~l~~~~~~~l~~~~~~~~~~~~~~~-lr~~~~~fi~~~~p~-l~~~~~~~~~~  305 (327)
T PRK12680        235 VRAGLGV-GLVAEMAV-----N-AFDEDLRAWPAPAPIAECIAWAVLPRDRV-LRDYALDLVHVLAPQ-IDKRDLRRVLD  305 (327)
T ss_pred             HHHCCEE-EECHHHHH-----C-CCCCCEEEEECCCCCCCCEEEEEEECCCH-HHHHHHHHHHHHCCC-CCHHHHHHHHC
T ss_conf             9949861-88164762-----8-76898389406457775605999978846-899999999986688-89999999826


Q ss_pred             CC
Q ss_conf             88
Q gi|254781112|r  263 KN  264 (274)
Q Consensus       263 ~d  264 (274)
                      -|
T Consensus       306 ~~  307 (327)
T PRK12680        306 GN  307 (327)
T ss_pred             CC
T ss_conf             88


No 61 
>TIGR03414 ABC_choline_bnd choline ABC transporter, periplasmic binding protein. Partial phylogenetic profiling (PMID:16930487) vs. the genome property of glycine betaine biosynthesis from choline consistently reveals a member of this ABC transporter periplasmic binding protein as the best match, save for the betaine biosynthesis enzymes themselves. Genomes often carry several paralogs, one encoded together with the permease and ATP-binding components and another encoded next to a choline-sulfatase gene, suggesting that different members of this protein family interact with shared components and give some flexibility in substrate. Of two members from Sinorhizobium meliloti 1021, one designated ChoX has been shown experimentally to bind choline (though not various related compounds such as betaine) and to be required for about 60 % of choline uptake. Members of this protein have an invariant Cys residue near the N-terminus and likely are lipoproteins.
Probab=95.72  E-value=0.036  Score=33.08  Aligned_cols=213  Identities=16%  Similarity=0.108  Sum_probs=103.1

Q ss_pred             HHHHCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCCHHC-CCCHH
Q ss_conf             78858958999628998724870469984889885216789976299855566898898864310322110000-36756
Q gi|254781112|r   36 RTEDQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVSGLITGLDTNRYDVLVNV-AITPE  114 (274)
Q Consensus        36 ~~~~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~~~~~~~~~~~~~l~~g~~D~~~~~-~~t~e  114 (274)
                      +..+.++|+||.. +|+-         +   -+...+++.|.+++|++|+++..+-.-++.++.+|++|+.... ..+.+
T Consensus         3 ~~a~~~~V~i~~~-~W~s---------~---~~~t~v~~~iLE~~GY~Ve~~~~~~~~~~~~la~GdiDv~~e~W~p~~~   69 (290)
T TIGR03414         3 EPASCKTVRFADV-GWTD---------I---TATTALASVLLEGLGYQPKVTLLSVPVTYAGLKDGDLDVFLGNWMPAME   69 (290)
T ss_pred             CHHCCCCEEEEEC-CCCH---------H---HHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHCCCCEEEEECCCCCCH
T ss_conf             7100996699606-8648---------9---9999999999997499648996774999999976997078711147857


Q ss_pred             --HHH-----HHC-CCCCCCCCCCCCCCCCCC--CCCCCCCCCC-------CCCEEEECCCHHHHH----HH--CCCC-C
Q ss_conf             --754-----200-233322222222211122--2211111233-------432023101012233----20--1345-4
Q gi|254781112|r  115 --RQK-----KYD-FSIPYIAHRVLLVVRSDQ--QDIRSFKDLT-------DKTVAQILGTDLSRF----AK--ELKS-H  170 (274)
Q Consensus       115 --R~~-----~~~-fs~p~~~~~~~~~~~~~~--~~~~~~~dL~-------g~~V~~~~g~~~~~~----l~--~~~~-~  170 (274)
                        ..+     .+. ....+-.....+++++--  ..+++++||+       |+-+|...|+.....    ++  .++. .
T Consensus        70 ~~~~~~~~~g~v~~lg~~~~~a~~g~~VP~Yv~d~~l~si~DL~~~~~~f~g~i~gi~~G~~~~~~~~~~i~~~~ygL~~  149 (290)
T TIGR03414        70 PDIKPYLESGSVEVLGPNLEGAKYTLAVPTYVADAGLKSFADIAKFKDKLDGKIYGIEPGNDGNRLIQKMIDKNAFGLGG  149 (290)
T ss_pred             HHHHHHHHCCCEEECCCCCCCCEEEEEECHHHHHCCCCCHHHHHHCHHHCCCCEECCCCCCCHHHHHHHHHHHHCCCCCC
T ss_conf             78998863696898356667863789854147765999999998586752997613679984778999998764079887


Q ss_pred             CEEEC-CHHHHH----HHHHHHHHHCCCC--CHHHHHHH-HHHCCCCCCCEEECCCCCCCCCEEEEEECC----CHHHH-
Q ss_conf             21336-855777----7554432100366--55899999-984587667326236776877079998189----98999-
Q gi|254781112|r  171 LVFSH-NFEQSL----QLLLSKRTDATMI--PDIPFFNF-LERRPHDGNLFKIADRMKDNSAVAFMMRKG----NNKLT-  237 (274)
Q Consensus       171 ~~~~~-~~~~~~----~~l~~grvD~~~~--~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~----~~~L~-  237 (274)
                      ..... +....+    .+..+|+-=++..  +......| ++.....   -....+......++..++++    +|+.. 
T Consensus       150 ~~l~~~S~aam~a~l~~A~~~~epiv~~~W~Phw~~~~~dl~~L~~~---~~~~g~~~~~~~v~~~~~~~f~~~~P~~~~  226 (290)
T TIGR03414       150 FKLVESSEAGMLAQVARAVKRKEWVVFLGWEPHPMNTNFKMTYLTGG---DDYFGPNYGGATVYTNTRKGYAAECPNVGK  226 (290)
T ss_pred             CEECCCCHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHCCEEEECCC---CCCCCCCCCHHHEEECCCHHHHHHCHHHHH
T ss_conf             02136888999999999998699989982377545551770670587---445789986220664147058787938999


Q ss_pred             ---------HHHHHHHHHHHHCC-HHHHHHHHHCCCC
Q ss_conf             ---------99999999999798-5999998767888
Q gi|254781112|r  238 ---------RSINEILCAIHLDG-TYKKIFDRYFDKN  264 (274)
Q Consensus       238 ---------~~in~~l~~l~~~G-~~~~I~~kw~g~d  264 (274)
                               +.+|..+..+.++| ..++..++|+..+
T Consensus       227 ~l~~~~~~~~~~~~~~~~i~~~g~~~~~aA~~Wi~~n  263 (290)
T TIGR03414       227 LLTNLTFTLDMENQIMGAILNDGKDPEAAARQWLKAN  263 (290)
T ss_pred             HHHCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHC
T ss_conf             9961589989999999999975999999999999979


No 62 
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=95.65  E-value=0.1  Score=30.31  Aligned_cols=199  Identities=14%  Similarity=0.129  Sum_probs=103.6

Q ss_pred             HCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHH-CCCCCCCCCCCHHHHHHHHHCCCCCCCHHCCCCHHHHH
Q ss_conf             58958999628998724870469984889885216789976-29985556689889886431032211000036756754
Q gi|254781112|r   39 DQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHR-LNLKVEFFETAVSGLITGLDTNRYDVLVNVAITPERQK  117 (274)
Q Consensus        39 ~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~-lg~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~t~eR~~  117 (274)
                      .+|+|+|++.....++ +            ...++....++ =++++++.....++..+.+.+|++|+..+.........
T Consensus        90 ~~G~lri~~~~~~~~~-~------------l~~~l~~f~~~~P~v~l~l~~~~~~~~~~~l~~g~~Dlai~~~~~~p~~~  156 (300)
T PRK11074         90 WRGQLSIALDNIVRPD-R------------TRQLIADFYRHFDDVELIIRQEVFNGVWDALADGRADIAIGATRAIPVGG  156 (300)
T ss_pred             CCCEEEEEECCHHHHH-H------------HHHHHHHHHHHCCCCEEEEEECCCHHHHHHHHCCCCCEEEECCCCCCCCC
T ss_conf             8425999865335789-9------------99999999998869579999766367999997699778994376778888


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCC-----CCCCCCCCCCCEEEECCCHHH--H-HHHCC-CCCCEEECCHHHHHHHHHHHH
Q ss_conf             20023332222222221112222-----111112334320231010122--3-32013-454213368557777554432
Q gi|254781112|r  118 KYDFSIPYIAHRVLLVVRSDQQD-----IRSFKDLTDKTVAQILGTDLS--R-FAKEL-KSHLVFSHNFEQSLQLLLSKR  188 (274)
Q Consensus       118 ~~~fs~p~~~~~~~~~~~~~~~~-----~~~~~dL~g~~V~~~~g~~~~--~-~l~~~-~~~~~~~~~~~~~~~~l~~gr  188 (274)
                      .+. ..++......+++..+.+.     ..+.++|......+..++...  . ..... ......+++....++++.+|-
T Consensus       157 ~~~-~~~l~~~~~~~v~~~~hpLa~~~~~l~~~~l~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~Gl  235 (300)
T PRK11074        157 RFA-FRDMGMLSWAFVVSSDHPLALMDGPLSDDELRPYPSICLEDTSRTLPKRITWLLDNQRRLVVPDWESAINCLSAGL  235 (300)
T ss_pred             CEE-EEECCCCEEEEEECCCCHHHCCCCCCCHHHHHHCCEEEECCCCCCCCCCCEEEECCCCEEEECCHHHHHHHHHHCC
T ss_conf             657-8881442056674589755408998999999619778862662223210003545764799898999999999699


Q ss_pred             HHCCCCCHHHHHHHHHHCCCCCCCEEE-CCCCCCCCCEEEEEECCCHHHHHHHHHHHHHHHHCCHHHHHHHHHC
Q ss_conf             100366558999999845876673262-3677687707999818998999999999999997985999998767
Q gi|254781112|r  189 TDATMIPDIPFFNFLERRPHDGNLFKI-ADRMKDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFDRYF  261 (274)
Q Consensus       189 vD~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~k~~~~L~~~in~~l~~l~~~G~~~~I~~kw~  261 (274)
                      .= .+.+...+..++..-    ..+.+ ...+....+++++.++++.  -..+-..++-+.++   .++.++|+
T Consensus       236 Gi-a~lP~~~~~~~l~~G----~Lv~l~~~~~~~~~~~~lv~~~~~~--sPa~r~fld~L~d~---~~~~~~~~  299 (300)
T PRK11074        236 GV-GMVPTHFAKPLIESG----KLVEKTLENPKPDSPCCLTWNQNDM--SPALAWLLDYLGDS---ETLNKEWL  299 (300)
T ss_pred             EE-EHHHHHHHHHHHHCC----CEEEECCCCCCCCEEEEEEECCCCC--CHHHHHHHHHHHCC---HHHHHHHH
T ss_conf             68-940699999996089----9999827888885389999889999--98999999998371---00224752


No 63 
>PRK04168 hypothetical protein; Provisional
Probab=95.63  E-value=0.043  Score=32.59  Aligned_cols=211  Identities=15%  Similarity=0.153  Sum_probs=100.1

Q ss_pred             HHHHCCCEEEEECCCC-CCEEEEEECCCCCEEEEEEEEHHHHHHH-CCCCCCCCCCCHHHHHHHHH--CCCCCCCHHCCC
Q ss_conf             7885895899962899-8724870469984889885216789976-29985556689889886431--032211000036
Q gi|254781112|r   36 RTEDQSALRVGTDGIY-PPHSFHAQDGRGELTGFDIDLIKEVAHR-LNLKVEFFETAVSGLITGLD--TNRYDVLVNVAI  111 (274)
Q Consensus        36 ~~~~~~~l~v~~~~~~-pP~~~~~~d~~g~~~G~~~dl~~~i~~~-lg~~~~~~~~~~~~~~~~l~--~g~~D~~~~~~~  111 (274)
                      .++++++|+|-..+.. .||.               ++.++..++ -|++++...--...+...+.  ...+|++.++.+
T Consensus        28 ~~~~~~~l~Vf~AGSL~~pf~---------------ei~~~Fe~~~p~v~v~~e~~GS~~~ar~Ite~g~~aDVfaSAD~   92 (336)
T PRK04168         28 EAEPPGKLKIFHAGSLSVPFE---------------EYEKEFEAYYPNVDVQREAGGSVACVRKITELGKPADILASADY   92 (336)
T ss_pred             CCCCCEEEEEEECCCCHHHHH---------------HHHHHHHHHCCCCEEEEEECCHHHHHHHHHHCCCCCCEEEECCH
T ss_conf             778861599997552589999---------------99999998789965999847389999999957999888998985


Q ss_pred             CHHHHH----HHCCCCCCCCCCCCCCCCCCCC---CC--CCCCC-C--CCCCEEE------ECCCH--------------
Q ss_conf             756754----2002333222222222111222---21--11112-3--3432023------10101--------------
Q gi|254781112|r  112 TPERQK----KYDFSIPYIAHRVLLVVRSDQQ---DI--RSFKD-L--TDKTVAQ------ILGTD--------------  159 (274)
Q Consensus       112 t~eR~~----~~~fs~p~~~~~~~~~~~~~~~---~~--~~~~d-L--~g~~V~~------~~g~~--------------  159 (274)
                      +.=+..    ..+|..++-....++....++.   .+  .+|-+ |  .|.++|.      ..|+.              
T Consensus        93 ~~i~~ll~p~~adw~v~FA~N~lViayt~~Sk~a~ei~~~nWyeiL~~~~Vk~g~sdP~~DP~Gyrt~~~~~LAe~~Y~~  172 (336)
T PRK04168         93 TLIPKMMIPEYADWYVMFATNEIVLAYTDKSKYADEINSDNWYEILQRPGVKWGFSDPNDDPCGYRSLMVLQLAELYYND  172 (336)
T ss_pred             HHHHHHHCCCCCCCEEEECCCEEEEEECCCCCCCCCCCCCCHHHHHCCCCCEEEECCCCCCCCHHHHHHHHHHHHHHCCC
T ss_conf             78788746443341012115538999768882110057331889857798579837998898608999999999986068


Q ss_pred             ---HHHHHHCC-------------------CCCCEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHH---CCCCCC---
Q ss_conf             ---22332013-------------------45421336855777755443210036655899999984---587667---
Q gi|254781112|r  160 ---LSRFAKEL-------------------KSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLER---RPHDGN---  211 (274)
Q Consensus       160 ---~~~~l~~~-------------------~~~~~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~---~~~~~~---  211 (274)
                         +++.+.+.                   ..++...+...+.+..|.+|++|+.+.-...+...-..   .|..-+   
T Consensus       173 pgl~~~l~~~~~n~~~~~~~i~~p~~~~~n~~k~~~rp~e~~Ll~~lesG~~Dy~f~Y~S~A~q~~L~yv~LP~eINL~~  252 (336)
T PRK04168        173 PTIYDKLVLKNTNFYVNGTYIRSPKEILVNRPKIFVRPKEVELLGLLETGAMDYLFIYKSVAVQHNLKYIELPDEINLGD  252 (336)
T ss_pred             CCHHHHHHHHCCCCCCCCCCCCCHHHHCCCCCCCEECCCHHHHHHHHHCCCCCEEEEEEEHHHHCCCCCCCCCHHHCCCC
T ss_conf             41788886403553345422356043114554311055267777787558864698762448676997003833314678


Q ss_pred             ----------CEEECCC----CCCCCCEEEEEECC--CHHHHHHHHHHHHHHHHCCHHHHHHHHHCCCCCC
Q ss_conf             ----------3262367----76877079998189--9899999999999999798599999876788877
Q gi|254781112|r  212 ----------LFKIADR----MKDNSAVAFMMRKG--NNKLTRSINEILCAIHLDGTYKKIFDRYFDKNII  266 (274)
Q Consensus       212 ----------~~~~~~~----~~~~~~~~~~~~k~--~~~L~~~in~~l~~l~~~G~~~~I~~kw~g~d~~  266 (274)
                                .+.+...    .-.+.-|++++.++  |+++...|=+.|.    +.+-++|+++ .|++.+
T Consensus       253 ~~~ad~Y~~vsv~v~~~~~t~~g~PIvY~iTV~~~A~n~e~A~~FV~fll----s~~Gq~il~~-~G~~p~  318 (336)
T PRK04168        253 YSYADFYKKVSVTLTGKKPTITAKPIVYGITVPKNAPNREAAIEFLKYLL----DEGGPKIFEN-NGQPPI  318 (336)
T ss_pred             CCCCCCCCEEEEEECCCCCCEECCCEEEEEECCCCCCCHHHHHHHHHHHH----CCHHHHHHHH-CCCCCC
T ss_conf             11002010589997178751214766898764689999899999999984----8025899997-599987


No 64 
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=95.61  E-value=0.13  Score=29.63  Aligned_cols=188  Identities=11%  Similarity=0.065  Sum_probs=101.6

Q ss_pred             CCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHH-CCCCCCCCCCCHHHHHHHHHCCCCCCCHH-CCCCHHHHH
Q ss_conf             8958999628998724870469984889885216789976-29985556689889886431032211000-036756754
Q gi|254781112|r   40 QSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHR-LNLKVEFFETAVSGLITGLDTNRYDVLVN-VAITPERQK  117 (274)
Q Consensus        40 ~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~-lg~~~~~~~~~~~~~~~~l~~g~~D~~~~-~~~t~eR~~  117 (274)
                      ...++||+.+..+++ +            ...++..+.+. -++++....-+.+.++..|..++.|++.. ...... ..
T Consensus        92 ~~~lrvGi~~tl~k~-~------------~~~lL~~~~~~~~~v~l~~~eg~~~~LL~~L~~~~LDlvLsd~p~~~~-~~  157 (296)
T PRK11062         92 NLLFDVGVADALSKR-L------------VSRVLLAAVPEDESIHLRCFESTHEMLLEQLSQHKLDMILSDCPVDST-QQ  157 (296)
T ss_pred             CCEEEEEEHHHHHHH-H------------HHHHHHHHHHCCCCEEEEEECCCHHHHHHHHHCCCCCEEEECCCCCCC-CC
T ss_conf             705999852464698-9------------999999997228977999934987999999983898757606888755-68


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEC-CCH----HHHHHHCCCCC--C-EEECCHHHHHHHHHHHHH
Q ss_conf             200233322222222211122221111123343202310-101----22332013454--2-133685577775544321
Q gi|254781112|r  118 KYDFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQIL-GTD----LSRFAKELKSH--L-VFSHNFEQSLQLLLSKRT  189 (274)
Q Consensus       118 ~~~fs~p~~~~~~~~~~~~~~~~~~~~~dL~g~~V~~~~-g~~----~~~~l~~~~~~--~-~~~~~~~~~~~~l~~grv  189 (274)
                      .-.|+.+....+..++..++......+++|.+..+-... ++.    .+.+..+.+.+  + .+++ ...+++.+...-.
T Consensus       158 ~~~~s~~L~~~~v~~~~~~~l~~~~fP~~L~~~plllp~~~S~lR~~ld~wf~~~gI~P~Iv~E~d-D~allk~~a~~G~  236 (296)
T PRK11062        158 EGLFSKKLGECGVSFFCTNPLPEKPFPACLEERRLLIPGRRTMLGRKLLNWFNSQGLNVEILGEFD-DAALMKAFGAYHD  236 (296)
T ss_pred             CCEEEEECCCCCEEEEECCCCCCCCCHHHHCCCCCCCCCCCCHHHHHHHHHHHHCCCCCEEEEEEC-CHHHHHHHHHHCC
T ss_conf             863898746684689845744458795775579840279987589999999996899844999859-8999999998199


Q ss_pred             HCCCCCHHHHHHHHHHCCCCCCCEEECCCC-CCCCCEEEEEEC--CCHHHHHHHHHHHHH
Q ss_conf             003665589999998458766732623677-687707999818--998999999999999
Q gi|254781112|r  190 DATMIPDIPFFNFLERRPHDGNLFKIADRM-KDNSAVAFMMRK--GNNKLTRSINEILCA  246 (274)
Q Consensus       190 D~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~k--~~~~L~~~in~~l~~  246 (274)
                      -.++.+..+......+...    ..+...+ .....|++...+  .+|.+....+.+-..
T Consensus       237 Gva~~P~~v~~d~~~~~~l----~~~g~~~~v~e~fyAIt~~R~~~hP~v~~i~~~~~~~  292 (296)
T PRK11062        237 AIFVAPSIYAQDIYADHSV----VEIGRVENVKEEYHVIFAERMIQHPAVQRICNTDFSA  292 (296)
T ss_pred             CEEECCHHHHHHHHHCCCC----EEECCCCCCEEEEEEEECCCCCCCHHHHHHHHHHHHH
T ss_conf             8898789999999857991----8944578842679998504468986999999999987


No 65 
>PRK09755 putative binding protein; Provisional
Probab=95.55  E-value=0.19  Score=28.62  Aligned_cols=82  Identities=10%  Similarity=0.092  Sum_probs=45.9

Q ss_pred             CEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEEEEC-----CCHHHHHHHHHHHH
Q ss_conf             2133685577775544321003665589999998458766732623677687707999818-----99899999999999
Q gi|254781112|r  171 LVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRK-----GNNKLTRSINEILC  245 (274)
Q Consensus       171 ~~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k-----~~~~L~~~in~~l~  245 (274)
                      ....++....+.+|.+|++|............ .+....  .+...+ .....  ++.++-     +|+.++.+|+.+|.
T Consensus       244 ~~~i~d~~t~~~~l~sGevD~~~~~~~~~~~~-~~~~~~--~~~~~p-~~~~~--y~~~N~~~~p~~D~~VRqAi~~AiD  317 (535)
T PRK09755        244 YLALDNSVTGYNRYRAGEVDLTWVPAQQIPAI-EKSLPG--ELRIIP-RLNSE--YYNFNLEKPPFNDVRVRRALYLTVD  317 (535)
T ss_pred             EEECCCHHHHHHHHHCCCCEEECCCHHHHHHH-HHCCCC--CEEEEE-CCCEE--EEEEECCCCCCCCHHHHHHHHHHHC
T ss_conf             99779689999998779823851898999999-745688--589983-25338--9976046576679999999997537


Q ss_pred             HHHHCCHHHHHHHHHCCCCC
Q ss_conf             99979859999987678887
Q gi|254781112|r  246 AIHLDGTYKKIFDRYFDKNI  265 (274)
Q Consensus       246 ~l~~~G~~~~I~~kw~g~d~  265 (274)
                      +       +.|.++-||...
T Consensus       318 r-------~~i~~~v~G~~~  330 (535)
T PRK09755        318 R-------QLIAQKVLGLRT  330 (535)
T ss_pred             H-------HHHHHHHCCCCC
T ss_conf             9-------999998537872


No 66 
>PRK10682 putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional
Probab=95.38  E-value=0.22  Score=28.24  Aligned_cols=208  Identities=15%  Similarity=0.110  Sum_probs=101.7

Q ss_pred             HHHHHHCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCCCCCC-CHHHHHHHHHCCC--CCCCHHCC
Q ss_conf             88788589589996289987248704699848898852167899762998555668-9889886431032--21100003
Q gi|254781112|r   34 PFRTEDQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFET-AVSGLITGLDTNR--YDVLVNVA  110 (274)
Q Consensus        34 ~~~~~~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~~~~~-~~~~~~~~l~~g~--~D~~~~~~  110 (274)
                      ...+++.++|+|-.   |.=  |.           +.|+++..-++.|++|++... +-++++..|+.|.  +|++..-.
T Consensus        23 ~~~aa~~~~Lnv~n---W~~--Yi-----------~p~~i~~FeketGikV~~~~~~snee~~akl~ag~~gyDvv~ps~   86 (370)
T PRK10682         23 GTLAAEQKTLHIYN---WSD--YI-----------APDTVANFEKETGIKVVYDVFDSNEVLEGKLMAGSTGFDLVVPSA   86 (370)
T ss_pred             CHHHHCCCEEEEEC---CCC--CC-----------CHHHHHHHHHHHCCEEEEEECCCHHHHHHHHHCCCCCCCEEEECH
T ss_conf             05664279799981---676--57-----------977999999997988999954998999999966999998899777


Q ss_pred             CCHHH-------------------------HH---H----HCCCCCCCCCCCCCCCCCCCC--------CCCCCCCC---
Q ss_conf             67567-------------------------54---2----002333222222222111222--------21111123---
Q gi|254781112|r  111 ITPER-------------------------QK---K----YDFSIPYIAHRVLLVVRSDQQ--------DIRSFKDL---  147 (274)
Q Consensus       111 ~t~eR-------------------------~~---~----~~fs~p~~~~~~~~~~~~~~~--------~~~~~~dL---  147 (274)
                      +.-+|                         .+   .    -.|+-||......+..+++.-        ...++++|   
T Consensus        87 ~~v~~~~~~gll~pLD~sklpN~~ni~p~~~~~~~~~dpg~~YsVPy~wGt~GI~Yn~d~v~~~~g~~~p~~sW~~l~~P  166 (370)
T PRK10682         87 SFLERQLTAGVFQPLDKSKLPNWKNLDPELLKLVAKHDPDNKYAMPYMWATTGIGYNVDKVKAVLGEDAPVDSWDLVLKP  166 (370)
T ss_pred             HHHHHHHHCCCCCCCCHHHCCCHHHCCHHHHHHHHCCCCCCEEEEEEEECCEEEEEECCCCCCCCCCCCCCCHHHHHHCH
T ss_conf             99999997698464770008674442999884100369997599888842259999765442234678884629986492


Q ss_pred             ------CCCCEEEEC-------------CCH-----HHH-------HHHCCCCCCEEECCHHHHHHHHHHHHHHCCCCCH
Q ss_conf             ------343202310-------------101-----223-------3201345421336855777755443210036655
Q gi|254781112|r  148 ------TDKTVAQIL-------------GTD-----LSR-------FAKELKSHLVFSHNFEQSLQLLLSKRTDATMIPD  196 (274)
Q Consensus       148 ------~g~~V~~~~-------------g~~-----~~~-------~l~~~~~~~~~~~~~~~~~~~l~~grvD~~~~~~  196 (274)
                            ++.+|++..             |..     .++       .+.+.+.++..+.+ .+....|.+|++.+.++-.
T Consensus       167 ~~~~k~k~~~v~~ld~~~~~~~~aL~~lG~~~n~~~~~d~~~aa~~~L~~~kp~v~~~~s-~~~~~~l~~Gei~~a~~ws  245 (370)
T PRK10682        167 ENLEKLKSCGVSFLDAPEEIFATVLNYLGKDPNSTKADDYTGPATDLLLKLRPNIRYFHS-SQYINDLANGDICVAIGWA  245 (370)
T ss_pred             HHHHHCCCCCEEEECCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHCHHCCEECC-CHHHHHHHCCCEEEEEEEC
T ss_conf             756530358558976888999999997699989999999999999999971222441037-2889998548679999740


Q ss_pred             HHHHHHH---HHCCCCCCCEEE-CCCCCCCCCEEEEEECC--CHHHHHH-HHHHHHHHHHCCHHHHHHHHHCCC
Q ss_conf             8999999---845876673262-36776877079998189--9899999-999999999798599999876788
Q gi|254781112|r  197 IPFFNFL---ERRPHDGNLFKI-ADRMKDNSAVAFMMRKG--NNKLTRS-INEILCAIHLDGTYKKIFDRYFDK  263 (274)
Q Consensus       197 ~~~~~~~---~~~~~~~~~~~~-~~~~~~~~~~~~~~~k~--~~~L~~~-in~~l~~l~~~G~~~~I~~kw~g~  263 (274)
                      -.+....   .......+...+ +.+-..---=+++++++  |+++... ||-.+     +.+..+....|.|.
T Consensus       246 Gd~~~~~~~~~~~~~~~~i~yv~PkEG~~~w~D~~~Ipk~A~n~~~A~~FInf~l-----~Pe~aa~~~~~~~y  314 (370)
T PRK10682        246 GDVWQASNRAKEAKNGVNVSFSIPKEGAMAFFDVFAMPADAKNKDEAYQFLNYLL-----RPDVIAHISDHVFY  314 (370)
T ss_pred             HHHHHHHHHHHHCCCCCEEEEEECCCCCEEEEEEEEEECCCCCHHHHHHHHHHHC-----CHHHHHHHHHHHCC
T ss_conf             8999999999863578706998158874588878888689999699999999850-----97999999986478


No 67 
>TIGR01256 modA molybdate ABC transporter, periplasmic molybdate-binding protein; InterPro: IPR005950   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).     This entry describes the molybdate ABC transporter periplasmic binding protein in bacteria and archae. Several of the periplasmic receptors constitute a diverse class of binding proteins that differ widely in size, sequence and ligand specificity. It has been shown experimentally by radioactive labeling that ModA represents a hydrophylioc periplasmic-binding protein in Gram-negative organisms and its counterpart in Gram-positive organisms is a lipoprotein. The other components of the system include ModB, an integral membrane protein and ModC, the ATP-binding subunit. Almost all of them display a common beta/alpha folding motif and have similar tertiary structures consisting of two globular domains.; GO: 0015412 molybdate transmembrane-transporting ATPase activity, 0015689 molybdate ion transport, 0030288 outer membrane-bounded periplasmic space.
Probab=95.31  E-value=0.045  Score=32.48  Aligned_cols=183  Identities=20%  Similarity=0.279  Sum_probs=114.9

Q ss_pred             EEHHHHHHHCC-CCCCCCCCCHHHHHHHHHCCC-CCCCHHCCC-CH----HHHHHHCCCC-CCCCCCCCCCCCCCCCCCC
Q ss_conf             21678997629-985556689889886431032-211000036-75----6754200233-3222222222111222211
Q gi|254781112|r   71 DLIKEVAHRLN-LKVEFFETAVSGLITGLDTNR-YDVLVNVAI-TP----ERQKKYDFSI-PYIAHRVLLVVRSDQQDIR  142 (274)
Q Consensus        71 dl~~~i~~~lg-~~~~~~~~~~~~~~~~l~~g~-~D~~~~~~~-t~----eR~~~~~fs~-p~~~~~~~~~~~~~~~~~~  142 (274)
                      ||.+...++.| .+|.+..-+...+...+++|= +|+..++.- .+    |+...+.++. -|.....++++.+.+...+
T Consensus        10 ~i~~~F~k~~g~~~Vv~sFgsSg~L~~QI~~GAP~D~F~SA~~~~~~~L~~~g~~v~~~~~~~~~n~LVL~~~~~~~~~~   89 (225)
T TIGR01256        10 EIAKQFEKRTGKNKVVFSFGSSGTLYTQIENGAPADVFISADEKRPKKLVDKGLVVKGSEFVYAGNKLVLISPKNSRVVD   89 (225)
T ss_pred             HHHHHHHCCCCCCEEEEEECCCHHHHHHHHCCCCEEEEECCCCCCCHHHHHCCCEECCCCEEEEEEEEEEEECCCCCCCC
T ss_conf             99988620089956999876817899999717978876614634540466378730254458986218998535542013


Q ss_pred             CCCCC---------CCCCEEE------ECCCHHHHHHHCCC------CCCEEEC-CHHHHHHHHHHHHHHCCCCCHHHHH
Q ss_conf             11123---------3432023------10101223320134------5421336-8557777554432100366558999
Q gi|254781112|r  143 SFKDL---------TDKTVAQ------ILGTDLSRFAKELK------SHLVFSH-NFEQSLQLLLSKRTDATMIPDIPFF  200 (274)
Q Consensus       143 ~~~dL---------~g~~V~~------~~g~~~~~~l~~~~------~~~~~~~-~~~~~~~~l~~grvD~~~~~~~~~~  200 (274)
                      +.+.|         +.++|++      +.|-...+.+++.+      .+++.-. |..++++.+..|+.|+.+.-...+.
T Consensus        90 ~~~~l~~p~~~~~l~~~~vaigdP~~~P~G~~A~E~L~~lgl~~~l~~kLV~g~P~vrQA~~~V~~~nA~~GiVa~Sdv~  169 (225)
T TIGR01256        90 SLDILKKPGWVIVLKDKTVAIGDPKHAPYGAAAKEVLQKLGLWEKLKKKLVYGEPDVRQALQFVETGNAPIGIVALSDVI  169 (225)
T ss_pred             CHHHHCCCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCHHHHCCEEECCCCHHHHHHHHHHCCCCEEEEEHHEEE
T ss_conf             02211389748998637023468244435799999997079762564486524888999988877258866687311022


Q ss_pred             HHHHHCCCCCCCEEECCCCCCCCCEEEEEECC--CHHHHHHHHHHHHHHHHCCHHHHHHHHH
Q ss_conf             99984587667326236776877079998189--9899999999999999798599999876
Q gi|254781112|r  201 NFLERRPHDGNLFKIADRMKDNSAVAFMMRKG--NNKLTRSINEILCAIHLDGTYKKIFDRY  260 (274)
Q Consensus       201 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~--~~~L~~~in~~l~~l~~~G~~~~I~~kw  260 (274)
                      ...+   .......++...+.+-.+-+++-++  |.+....+=+.|    ++.+=.+|++||
T Consensus       170 ~~~K---~~~~v~~~p~~ly~Pi~yp~~i~~~g~n~~~a~~f~dyL----~sp~A~~il~~Y  224 (225)
T TIGR01256       170 PSGK---KVGSVAVIPEDLYKPIKYPAVIVKGGKNNAAAKAFIDYL----KSPEAKEILRKY  224 (225)
T ss_pred             ECCC---CCCEEEEECHHHCCCEEEEEEEEECCCCHHHHHHHHHHH----CCHHHHHHHHCC
T ss_conf             0003---662799963312796021178871687608999999870----796476786305


No 68 
>COG1910 Periplasmic molybdate-binding protein/domain [Inorganic ion transport and metabolism]
Probab=95.02  E-value=0.051  Score=32.15  Aligned_cols=156  Identities=17%  Similarity=0.128  Sum_probs=85.3

Q ss_pred             HHCCCCCCCCCC-CHHHHHHHHHCCCCCCCH-HC------CCCHHHHHHHCCCC----CCCCCCCCCCCCCCCC-CCCCC
Q ss_conf             762998555668-988988643103221100-00------36756754200233----3222222222111222-21111
Q gi|254781112|r   78 HRLNLKVEFFET-AVSGLITGLDTNRYDVLV-NV------AITPERQKKYDFSI----PYIAHRVLLVVRSDQQ-DIRSF  144 (274)
Q Consensus        78 ~~lg~~~~~~~~-~~~~~~~~l~~g~~D~~~-~~------~~t~eR~~~~~fs~----p~~~~~~~~~~~~~~~-~~~~~  144 (274)
                      +..+...+.+.+ +|.. +..++.|++|+.. -+      .|+..--+.+.-..    --+.-.+.++++++.+ .++++
T Consensus        14 ~~~~~~~~~~~vGS~gG-~~~i~~G~adiag~hlld~~~g~ynip~v~~~~~~~~~LI~g~~Re~Gl~v~~gnpk~i~~~   92 (223)
T COG1910          14 KEAGETAKTVYVGSMGG-LLAIKRGEADIAGIHLLDNESGTYNIPYVKKYLPGEAVLIRGYLREQGLMVQKGNPKNISSL   92 (223)
T ss_pred             HHCCCCCCEEEECCCCC-HHHHHHCCCCEEEEEECCCCCCCEEHHHHHHCCCCCEEEEEEEEEEEEEEEECCCCCCCCCH
T ss_conf             41523450688604455-47666254514442132577874423004230788469985366510368864897766249


Q ss_pred             CCCCCCCEEE---ECCC----HHHHHHHCCCC---CCE----EECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCC
Q ss_conf             1233432023---1010----12233201345---421----33685577775544321003665589999998458766
Q gi|254781112|r  145 KDLTDKTVAQ---ILGT----DLSRFAKELKS---HLV----FSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDG  210 (274)
Q Consensus       145 ~dL~g~~V~~---~~g~----~~~~~l~~~~~---~~~----~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~  210 (274)
                      +||.++.+..   .+|+    ..++.+...+.   .+.    +..+......++.+|++|+-+.-..    +..++..+ 
T Consensus        93 edl~~~d~~fVNR~rGSGTR~LlD~~L~~~~~~~~~I~GY~~e~~th~avA~aVa~G~AD~GvGlr~----~A~~~gL~-  167 (223)
T COG1910          93 EDLLRKDLRFVNRNRGSGTRILLDELLGELNILPDSIKGYSDEATTHDAVASAVASGRADAGVGLRH----AAEKYGLD-  167 (223)
T ss_pred             HHHHHCCCEEEECCCCCCHHHHHHHHHHHCCCCCHHCCCCCCCCCCCHHHHHHHHCCCCCCCCCHHH----HHHHCCCC-
T ss_conf             9885267578715899658999999998737670105784323212089999997589872501799----99984985-


Q ss_pred             CCEEECCCCCCCCCEEEEEECCCH--HHHHHHHHHHH
Q ss_conf             732623677687707999818998--99999999999
Q gi|254781112|r  211 NLFKIADRMKDNSAVAFMMRKGNN--KLTRSINEILC  245 (274)
Q Consensus       211 ~~~~~~~~~~~~~~~~~~~~k~~~--~L~~~in~~l~  245 (274)
                            ..|...+.|-|+++|++-  .....|-++|+
T Consensus       168 ------Fipl~~E~YD~virke~~~~~~vr~fi~~L~  198 (223)
T COG1910         168 ------FIPLGDEEYDFVIRKERLDKPVVRAFIKALK  198 (223)
T ss_pred             ------EEECCCCEEEEEEEHHHCCCHHHHHHHHHHC
T ss_conf             ------1774562578998456705888999999861


No 69 
>PRK00489 hisG ATP phosphoribosyltransferase; Reviewed
Probab=94.93  E-value=0.064  Score=31.58  Aligned_cols=170  Identities=15%  Similarity=0.137  Sum_probs=93.5

Q ss_pred             CCCCCCHHHHHHHHHCCCCCC-CHHCCCCHHHHHHHC--CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCHHH
Q ss_conf             556689889886431032211-000036756754200--23332222222221112222111112334320231010122
Q gi|254781112|r   85 EFFETAVSGLITGLDTNRYDV-LVNVAITPERQKKYD--FSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTDLS  161 (274)
Q Consensus        85 ~~~~~~~~~~~~~l~~g~~D~-~~~~~~t~eR~~~~~--fs~p~~~~~~~~~~~~~~~~~~~~~dL~g~~V~~~~g~~~~  161 (274)
                      ++.......+-..+..|.+|+ +.|.-+-.|....+.  ....|.....++.++++. .+++++||.|+||+.-.-....
T Consensus        47 ~~~~~R~~DIp~yV~~G~~DlGI~G~D~l~E~~~~v~~~~~LgfG~crlvvAvP~~~-~~~~~~dl~~~rIATkyp~it~  125 (287)
T PRK00489         47 EVLFLRPDDIPGYVADGVVDLGITGEDLLEESDADVEELLDLGFGKCRLVLAVPEDS-DYTGPEDLAGKRIATSYPNLTR  125 (287)
T ss_pred             EEEEECHHHHHHHHHCCCCCEEEEEEEEHHHCCCCCEEEECCCCCCEEEEEEECCCC-CCCCHHHHCCCEEEECHHHHHH
T ss_conf             999988798999997699777551331212068981699706887489999951778-8899578278589730066999


Q ss_pred             HHHHCCCCC--CEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEEEECC--CHHHH
Q ss_conf             332013454--21336855777755443210036655899999984587667326236776877079998189--98999
Q gi|254781112|r  162 RFAKELKSH--LVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKG--NNKLT  237 (274)
Q Consensus       162 ~~l~~~~~~--~~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~--~~~L~  237 (274)
                      +|+.+.+.+  ++......+.  +-.-|-.|+ ++|-...-..++.+..     .+.......+. .+..++.  +++-.
T Consensus       126 ~yf~~~Gi~~~iv~l~GavE~--aP~lGlAD~-IvDivsTG~TL~~NgL-----k~ie~Il~S~A-~LI~n~~~~~~~k~  196 (287)
T PRK00489        126 RYLAEKGINARVVELSGAVEV--APRLGLADA-IVDLVSTGATLRANGL-----KEVEVILRSEA-VLIANKAWWDPEKR  196 (287)
T ss_pred             HHHHHCCCCEEEEECCCCEEC--CCCCCCCCE-EEEEECCCHHHHHCCC-----EEEEEEEECEE-EEEEECCCCCHHHH
T ss_conf             999986993799977672304--666681008-9997167487998799-----88357750235-99980776986799


Q ss_pred             HHHHHHHHHHHHCCHHHHHHHHHCCCCCC
Q ss_conf             99999999999798599999876788877
Q gi|254781112|r  238 RSINEILCAIHLDGTYKKIFDRYFDKNII  266 (274)
Q Consensus       238 ~~in~~l~~l~~~G~~~~I~~kw~g~d~~  266 (274)
                      +.++.-+..++.  .+.+=-.+|+-.|++
T Consensus       197 ~~i~~l~~ri~g--vl~A~~~~~i~~Nvp  223 (287)
T PRK00489        197 EKIDKLLTRIQG--VLRARESKYLMMNAP  223 (287)
T ss_pred             HHHHHHHHHHHH--HHHHHCEEEEEEECC
T ss_conf             999999999999--997731899999787


No 70 
>PRK11119 proX glycine betaine transporter periplasmic subunit; Provisional
Probab=94.50  E-value=0.096  Score=30.48  Aligned_cols=116  Identities=13%  Similarity=0.081  Sum_probs=65.5

Q ss_pred             CCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCC-CCCCCHHHHHHHHHCCCCCCCHHCCCCHHHHHH
Q ss_conf             8958999628998724870469984889885216789976299855-566898898864310322110000367567542
Q gi|254781112|r   40 QSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVE-FFETAVSGLITGLDTNRYDVLVNVAITPERQKK  118 (274)
Q Consensus        40 ~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~-~~~~~~~~~~~~l~~g~~D~~~~~~~t~eR~~~  118 (274)
                      -++++++.. +|.=         +   -+...+++.+.+++|++|+ ....+..-++.+|.+|++|+..+. +.|.....
T Consensus        29 g~tV~~a~~-~W~~---------~---~a~t~v~~~~Le~lGY~Ve~~~~~~~~~~~~ala~GdiD~~~~~-WlP~~~~~   94 (332)
T PRK11119         29 GITVQPAQS-TIAE---------E---TFQTLLVSRALEKLGYDVNKPKEVDYNVFYTSIASGDATFTAVN-WFPLHDDQ   94 (332)
T ss_pred             CCEEEEEEC-CCHH---------H---HHHHHHHHHHHHHCCCCCCCCEECCHHHHHHHHHCCCCEEEECC-CCCCCHHH
T ss_conf             977876016-8408---------9---99999999999986998542014446889999855884486556-17651799


Q ss_pred             H---------CCCCCCCCC-CCCCCCCC---CCCCCCCCCCCCC-------------C--CEEEECCCHHH----HHHHC
Q ss_conf             0---------023332222-22222111---2222111112334-------------3--20231010122----33201
Q gi|254781112|r  119 Y---------DFSIPYIAH-RVLLVVRS---DQQDIRSFKDLTD-------------K--TVAQILGTDLS----RFAKE  166 (274)
Q Consensus       119 ~---------~fs~p~~~~-~~~~~~~~---~~~~~~~~~dL~g-------------~--~V~~~~g~~~~----~~l~~  166 (274)
                      +         .-..++... ...+++.+   +...+++++||+.             |  -+|...|+...    ..++.
T Consensus        95 ~~~~~~~~~~~~~g~~~~ga~~G~~V~~~~~d~~~I~si~dLkdp~~a~~Fd~~~~GKg~i~g~~pGwg~~~~~~~~i~~  174 (332)
T PRK11119         95 YEAAGGDKKFYREGVIVGGAAQGYLIDKKTADKYNITNIAQLKDPKIAKLFDTNGDGKADLTGCNPGWGCEAVINHQLKA  174 (332)
T ss_pred             HHHHCCCCEEEECCCCCCCCCEEEEEECCCCCCCCCCCHHHHHCHHHHHHCCCCCCCCEEEEECCCCCCHHHHHHHHHHH
T ss_conf             99732776476424335665136895023321148578998628678986076778850288148872066899999986


Q ss_pred             CCC
Q ss_conf             345
Q gi|254781112|r  167 LKS  169 (274)
Q Consensus       167 ~~~  169 (274)
                      ++.
T Consensus       175 ygL  177 (332)
T PRK11119        175 YGL  177 (332)
T ss_pred             CCC
T ss_conf             799


No 71 
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=94.38  E-value=0.29  Score=27.47  Aligned_cols=184  Identities=13%  Similarity=0.125  Sum_probs=103.7

Q ss_pred             HCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHC-CCCCCCCCCCHHHHHHHHHCCCCCCCH-HCCCCHHHH
Q ss_conf             589589996289987248704699848898852167899762-998555668988988643103221100-003675675
Q gi|254781112|r   39 DQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRL-NLKVEFFETAVSGLITGLDTNRYDVLV-NVAITPERQ  116 (274)
Q Consensus        39 ~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~l-g~~~~~~~~~~~~~~~~l~~g~~D~~~-~~~~t~eR~  116 (274)
                      .++.|+||+.+....             ++..+++....++. ++++++......+..+.|.+|++|+.. .....+  .
T Consensus        79 ~~g~l~Ig~~~~~~~-------------~~l~~~l~~f~~~~P~i~v~i~~~~~~~~~~~l~~~~~D~a~~~~~~~~--~  143 (278)
T PRK09986         79 EAGRIELGVVGTALW-------------GRMRPAMRHFLKENPNVEVLFREKSPSMQMALLERRELDAGIWRMALEP--N  143 (278)
T ss_pred             CCCCEEEEECHHHHH-------------HHHHHHHHHHHHHCCCEEEEEEECCHHHHHHHHHCCCCCEEEECCCCCC--C
T ss_conf             777336874216888-------------7642899999987898399999788699999997799758996377778--8


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCCC----CCCCCCCCCCCEEEEC-CCHH----HHHHHCCCC---CCEEECCHHHHHHHH
Q ss_conf             420023332222222221112222----1111123343202310-1012----233201345---421336855777755
Q gi|254781112|r  117 KKYDFSIPYIAHRVLLVVRSDQQD----IRSFKDLTDKTVAQIL-GTDL----SRFAKELKS---HLVFSHNFEQSLQLL  184 (274)
Q Consensus       117 ~~~~fs~p~~~~~~~~~~~~~~~~----~~~~~dL~g~~V~~~~-g~~~----~~~l~~~~~---~~~~~~~~~~~~~~l  184 (274)
                      ..+. ..|......++++.++.+.    .-+++||.+.++.... +...    .......+.   ....+++....+.++
T Consensus       144 ~~~~-~~~l~~~~~~~~~~~~hpla~~~~i~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~V  222 (278)
T PRK09986        144 PGFT-SLRLHESAFAVAVPEEHLLASKSSVPLKALRNEYFVTLPSVHSDWGFLQRVCQQAGFSPQIIREVNEPQTVLAMV  222 (278)
T ss_pred             CCCE-EEEEEECCCEEEECCCCCCCCCCCCCHHHHCCCCEEEECCCCCHHHHHHHHHHHCCCCCCEEEEECCHHHHHHHH
T ss_conf             7742-688774163799659873336999999998599979867998669999999997799851799999899999999


Q ss_pred             HHHHHHCCCCCHHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEEEECCCHHHHHHHHHHHHHH
Q ss_conf             443210036655899999984587667326236776877079998189989999999999999
Q gi|254781112|r  185 LSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKGNNKLTRSINEILCAI  247 (274)
Q Consensus       185 ~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~L~~~in~~l~~l  247 (274)
                      .+|..=+ +.+....     +.... +....+..+..+..++++-++++.  -..+.+.++.+
T Consensus       223 ~~G~Gia-ilp~~~~-----~~~~~-~v~~~Pl~~~~~~~~~lv~~~~~~--~p~~~~fi~~l  276 (278)
T PRK09986        223 SMGIGIT-LVADSYA-----QMPWP-GVVFRPLKERIPADLYIVYHQQQA--TPALEKLLAAL  276 (278)
T ss_pred             HHCCEEE-EEHHHHH-----CCCCC-CEEEEECCCCCCEEEEEEECCCCC--CHHHHHHHHHH
T ss_conf             9799899-8417774-----23789-999998899980389999849999--99999999986


No 72 
>TIGR03061 pip_yhgE_Nterm YhgE/Pip N-terminal domain. This family contains the N-terminal domain of a family of multiple membrane-spanning proteins of Gram-positive bacteria. One member was shown to be a host protein essential for phage infection, so many members of this family are called "phage infection protein". A separate model, TIGR03062, represents the conserved C-terminal domain. The domains are separated by regions highly variable in both length and sequence, often containing extended heptad repeats as described in model TIGR03057.
Probab=94.33  E-value=0.19  Score=28.63  Aligned_cols=61  Identities=13%  Similarity=0.260  Sum_probs=40.5

Q ss_pred             CCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCC--CCCCCCCCCHHHHHHHHHCCCCCCCHHC
Q ss_conf             895899962899872487046998488988521678997629--9855566898898864310322110000
Q gi|254781112|r   40 QSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLN--LKVEFFETAVSGLITGLDTNRYDVLVNV  109 (274)
Q Consensus        40 ~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg--~~~~~~~~~~~~~~~~l~~g~~D~~~~~  109 (274)
                      -+.|.||+         ++.|...+..|=.+.+.+.+.+.|.  -++.|+.++-+...++|++|++.++.-+
T Consensus        41 ~~~lpvAV---------VN~D~g~~~~g~~~~~G~~lv~~L~~~~~~~w~~vs~~~A~~gl~~G~yy~~i~I  103 (164)
T TIGR03061        41 LDNLPVAV---------VNEDKGATYDGKTLNAGDDLVKELKKNDDLDWHFVSAKEAEKGLADGKYYMVITI  103 (164)
T ss_pred             CCCCEEEE---------EECCCCCCCCCCCCCHHHHHHHHHHCCCCCEEEECCHHHHHHHHHCCCEEEEEEE
T ss_conf             57871899---------9778786508815228999999873388861798489999988864956999997


No 73 
>TIGR00787 dctP TRAP transporter solute receptor, DctP family; InterPro: IPR004682   TRAP-T family proteins generally consist of three components, and these systems have so far been found in Gram-negative bacteria, Gram-positive bacteria and archaea. Only one member of the family has been both sequenced and functionally characterised. This system is the DctPQM system of Rhodobacter capsulatus. DctP is a periplasmic dicarboxylate (malate, fumarate, succinate) binding receptor that is biochemically well-characterised.; GO: 0006810 transport, 0030288 outer membrane-bounded periplasmic space.
Probab=94.28  E-value=0.045  Score=32.50  Aligned_cols=123  Identities=11%  Similarity=0.063  Sum_probs=79.7

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCHHHHHHHCCCCCCEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHH
Q ss_conf             32222222221112222111112334320231010122332013454213368557777554432100366558999999
Q gi|254781112|r  124 PYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTDLSRFAKELKSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFL  203 (274)
Q Consensus       124 p~~~~~~~~~~~~~~~~~~~~~dL~g~~V~~~~g~~~~~~l~~~~~~~~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~  203 (274)
                      .++..+.--++-.. ..+..++|++|.+|-+...-......+-.|....... ..+.+.+|.+|=||+  -...+...|-
T Consensus       118 ~~w~nG~R~~t~~~-~p~~~p~D~kGLKiRi~~s~~~~~~~~~lGA~P~~~~-F~EvY~ALq~gvVDg--qENP~s~~~s  193 (267)
T TIGR00787       118 AYWDNGFRQFTSSK-KPVTKPEDLKGLKIRIPASPVLEAQFKALGANPEPMA-FSEVYTALQTGVVDG--QENPLSNIYS  193 (267)
T ss_pred             HHHHCCHHHHHCCC-CCCCCCHHHCCCCCCCCCCHHHHHHHHHCCCCCCCCC-HHHHHHHHHCCCCCC--CCCCHHHHHH
T ss_conf             33233145422143-4124603325874025986899999997089984126-589999875481010--0467277621


Q ss_pred             HHCCCCCCCEEECCCCCCCCCEEEEEECC-----CHHHHHHHHHHHHHHHHCCHHHH
Q ss_conf             84587667326236776877079998189-----98999999999999997985999
Q gi|254781112|r  204 ERRPHDGNLFKIADRMKDNSAVAFMMRKG-----NNKLTRSINEILCAIHLDGTYKK  255 (274)
Q Consensus       204 ~~~~~~~~~~~~~~~~~~~~~~~~~~~k~-----~~~L~~~in~~l~~l~~~G~~~~  255 (274)
                      .+...-.+...+.  -..-.++.+.+++.     .++|+..|.++.   ++.|+|++
T Consensus       194 ~KlYEVqKyL~~t--nH~y~g~~v~~n~~~w~~L~~dl~~~~~~A~---~ea~~~~~  245 (267)
T TIGR00787       194 SKLYEVQKYLSLT--NHGYLGYLVVVNKAFWKSLPPDLQAVVKEAA---KEATEYQR  245 (267)
T ss_pred             HHHHHHHHHHHHH--HHHHCCCCEEEEHHHHHCCCHHHHHHHHHHH---HHHHHHHH
T ss_conf             0212364345331--0303262027503674318788999999999---99999888


No 74 
>COG4143 TbpA ABC-type thiamine transport system, periplasmic component [Coenzyme metabolism]
Probab=94.20  E-value=0.44  Score=26.37  Aligned_cols=216  Identities=13%  Similarity=0.133  Sum_probs=102.8

Q ss_pred             CCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCCCCCCC-H----HHHHHHHHCCCCCCCHHCC-CCH
Q ss_conf             895899962899872487046998488988521678997629985556689-8----8988643103221100003-675
Q gi|254781112|r   40 QSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETA-V----SGLITGLDTNRYDVLVNVA-ITP  113 (274)
Q Consensus        40 ~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~~~~~~-~----~~~~~~l~~g~~D~~~~~~-~t~  113 (274)
                      .++|+|.+...|     ...      -|-...+.++.-++.+++++|+... -    +|+...=.+-+.|++.|+. ..-
T Consensus        25 t~~LtVytydSF-----~~e------wg~Gp~vk~~FE~~~~~~v~fV~~~d~v~llnRl~leg~~~~ADvvvGldn~~l   93 (336)
T COG4143          25 TPTLTVYTYDSF-----ASE------WGPGPKVKKAFEAEYGCKVNFVALGDGVELLNRLILEGKNPKADVVVGLDNNLL   93 (336)
T ss_pred             CCEEEEEEEEEE-----ECC------CCCCHHHHHHHHHHHCCEEEEEECCCHHHHHHHHHHCCCCCCCCEEEECCHHHH
T ss_conf             853899997634-----225------688578999999985952899970758999999997078988858993472778


Q ss_pred             HHHHHHCCC----------------------CCCCCCCCCCCCCCCC--CCCCCCCCCCC----CCEEEEC------C--
Q ss_conf             675420023----------------------3322222222211122--22111112334----3202310------1--
Q gi|254781112|r  114 ERQKKYDFS----------------------IPYIAHRVLLVVRSDQ--QDIRSFKDLTD----KTVAQIL------G--  157 (274)
Q Consensus       114 eR~~~~~fs----------------------~p~~~~~~~~~~~~~~--~~~~~~~dL~g----~~V~~~~------g--  157 (274)
                      +|.+...+-                      .||-..-..++..++.  ..-++++||..    .+|.++.      |  
T Consensus        94 ~~A~~~~lf~~~~~d~~~~~vp~~~~~d~f~~P~DyGy~a~vYd~~~~~~ppksL~dL~~~~y~~~ii~qdPrtSspGl~  173 (336)
T COG4143          94 ARARETGLFAPYGVDASDVPVPEGWKIDTFALPYDYGYFAFVYDKTKLKNPPKSLKDLVEPEYAGKIIYQDPRTSSPGLG  173 (336)
T ss_pred             HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECHHHHCCCCCCHHHHCCCCCCCCEEECCCCCCCCCHH
T ss_conf             88885587666789855788876535675101245412899976577528762689863851269578069887884078


Q ss_pred             ---C---HH--H---HHHHCCCCC-CEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEE-CC--CCCCC
Q ss_conf             ---0---12--2---332013454-213368557777554432100366558999999845876673262-36--77687
Q gi|254781112|r  158 ---T---DL--S---RFAKELKSH-LVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKI-AD--RMKDN  222 (274)
Q Consensus       158 ---~---~~--~---~~l~~~~~~-~~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~-~~--~~~~~  222 (274)
                         +   .+  +   ++-++...+ +...++=.+++.++..|+.+.++.-...-.+.+.-.... ..... +.  ...+.
T Consensus       174 fLlW~~svyg~d~~~~~W~kL~~~~v~v~~gWSeaY~aFt~GEap~VLSYtTspay~~~~~~~~-~~~a~~f~eG~ylqi  252 (336)
T COG4143         174 FLLWTISVYGEDGAPEAWAKLADNGVTVTKGWSEAYGAFTKGEAPLVLSYTTSPAYHVYPEKKD-RYAAALFPEGHYLQV  252 (336)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHHHCCEEECCCHHHHHHHHHCCCCCEEEEECCCCCHHCCCCCCC-CCCHHCCCCCCEEEE
T ss_conf             8999987636231899999998588686586798898874786557998606822102532002-210011788853677


Q ss_pred             CCEEEEEECCCHHHHHHHHHHHHHHHHCCHHHHHHH--HHC-CCCCCCCCCC
Q ss_conf             707999818998999999999999997985999998--767-8887756898
Q gi|254781112|r  223 SAVAFMMRKGNNKLTRSINEILCAIHLDGTYKKIFD--RYF-DKNIISSVPG  271 (274)
Q Consensus       223 ~~~~~~~~k~~~~L~~~in~~l~~l~~~G~~~~I~~--kw~-g~d~~~~~~~  271 (274)
                      ++.+..-+..+++|.+.|=+.+    -|++.++++-  .|. =..-+.++|+
T Consensus       253 Egaa~~k~~knp~LA~~F~~Fm----lS~e~Q~~ip~~nwm~Pa~~~~~Lp~  300 (336)
T COG4143         253 EGAAVLKGAKNPELADKFLQFM----LSPEFQDAIPTTNWMYPAVKNVPLPA  300 (336)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH----HCHHHHHHCCCCCEEEECCCCCCCCH
T ss_conf             6653112799879999999997----09877840784543323478986877


No 75 
>COG0687 PotD Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]
Probab=94.11  E-value=0.46  Score=26.25  Aligned_cols=187  Identities=19%  Similarity=0.129  Sum_probs=94.0

Q ss_pred             EHHHHHHHCCCCCCCCCCC-HHHHHHHHHCCC--CCCCHHCCCCHH------------------------HHH-------
Q ss_conf             1678997629985556689-889886431032--211000036756------------------------754-------
Q gi|254781112|r   72 LIKEVAHRLNLKVEFFETA-VSGLITGLDTNR--YDVLVNVAITPE------------------------RQK-------  117 (274)
Q Consensus        72 l~~~i~~~lg~~~~~~~~~-~~~~~~~l~~g~--~D~~~~~~~t~e------------------------R~~-------  117 (274)
                      +++...+++|++|.+...+ ++.+...++.|.  +|++..-.....                        +-.       
T Consensus        47 ~~~~F~k~tGi~V~~~~~~sne~~~ak~~~g~~~~Dvv~~s~~~~~~~~~~gll~~lD~skl~n~~~l~~~~~~~~~~d~  126 (363)
T COG0687          47 LLKPFEKETGIKVVYDTFDSNEEMLAKLKAGGGGYDVVVPSGYFVARLIKEGLLQPLDKSKLPNWKNLDPEFLNPPKFDP  126 (363)
T ss_pred             HHHHHHHHHCCEEEEECCCCHHHHHHHHHHCCCCCCEEECCHHHHHHHHHCCCCCCCCHHHCCCHHHCCHHHHCCCCCCC
T ss_conf             89989999899799953898699999998089998879718889999986675675896666482116987835776788


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCC----CCCCCCCC---------CCCCEEEEC-------------C----CHHHH-----
Q ss_conf             2002333222222222111222----21111123---------343202310-------------1----01223-----
Q gi|254781112|r  118 KYDFSIPYIAHRVLLVVRSDQQ----DIRSFKDL---------TDKTVAQIL-------------G----TDLSR-----  162 (274)
Q Consensus       118 ~~~fs~p~~~~~~~~~~~~~~~----~~~~~~dL---------~g~~V~~~~-------------g----~~~~~-----  162 (274)
                      .-.|+-||+....++..+++.-    ..++++||         +|+++....             |    +..++     
T Consensus       127 g~~y~vPy~~g~t~i~Yn~~~~~~~~~~~sW~~l~d~~~~~~~k~~~~~~~d~~~~~~~~al~~lg~~~n~~~~~~~~~a  206 (363)
T COG0687         127 GNKYSVPYFWGTTGIAYNTDKVKDAPPPTSWADLFDPEKFPGLKGKGVALLDDDREVFGAALALLGKSPNTTDPEDLKKA  206 (363)
T ss_pred             CCEECEEEEEEEEEEEEECCCCCCCCCCCCHHHHHCCHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCHHHHHHH
T ss_conf             88603167886469999800058999998899983842002232575301366057899999971899788998899999


Q ss_pred             --HHHCCCCCCEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEEEECCC--HHHHH
Q ss_conf             --32013454213368557777554432100366558999999845876673262367768770799981899--89999
Q gi|254781112|r  163 --FAKELKSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKGN--NKLTR  238 (274)
Q Consensus       163 --~l~~~~~~~~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~--~~L~~  238 (274)
                        .+.+.+.-.+.+.+..+..+.|.+|++++.++-.-.+.............+..+.+-..--.-.++++|+.  ++...
T Consensus       207 ~~~L~~~kp~~~~~~~~~~~~~~l~~Gev~~a~~w~g~~~~~~~~~~~~~i~~~~p~eG~~~w~D~~~ipk~a~n~~~A~  286 (363)
T COG0687         207 FDLLDKLKPVNVYWFDGSQYVQLLANGEVVLAMGWSGDAAAAKAAKNGAPIEFVIPKEGSILWFDNLAIPKGAKNVDAAY  286 (363)
T ss_pred             HHHHHHHCCCEEEEECCHHHHHHHHCCCEEEEEEECHHHHHHHHCCCCCEEEEECCCCCCEEEEEEEEEECCCCCHHHHH
T ss_conf             99999727850899636278889866997899977778999862558980577347887347878899879999989999


Q ss_pred             -HHHHHHHHHHHCCHHHHHHHHHCCC
Q ss_conf             -9999999999798599999876788
Q gi|254781112|r  239 -SINEILCAIHLDGTYKKIFDRYFDK  263 (274)
Q Consensus       239 -~in~~l~~l~~~G~~~~I~~kw~g~  263 (274)
                       .||..+.     .+..+...++.+.
T Consensus       287 ~fInf~~~-----pe~~a~~~~~~~y  307 (363)
T COG0687         287 KFINFLLD-----PEVAAKLAEFVGY  307 (363)
T ss_pred             HHHHHHCC-----HHHHHHHHHHHCC
T ss_conf             99998519-----8999999873267


No 76 
>PRK11205 tbpA thiamine transporter substrate binding subunit; Provisional
Probab=93.89  E-value=0.51  Score=26.00  Aligned_cols=206  Identities=13%  Similarity=0.115  Sum_probs=92.4

Q ss_pred             HHCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCCCCCC-CHHHHHHHH----HCCCCCCCHHCCC-
Q ss_conf             8589589996289987248704699848898852167899762998555668-988988643----1032211000036-
Q gi|254781112|r   38 EDQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFET-AVSGLITGL----DTNRYDVLVNVAI-  111 (274)
Q Consensus        38 ~~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~~~~~-~~~~~~~~l----~~g~~D~~~~~~~-  111 (274)
                      .+.++|+|.+...|.      .| -    |-...|.++.-++.|++|+++.. +-..++.-|    .+...|++.++.. 
T Consensus        16 ~~~~~l~vyt~dsf~------~d-~----g~~~~l~~~Fek~tGikV~~v~~~dg~~ll~Rl~~Eg~np~ADVv~gvD~~   84 (326)
T PRK11205         16 FAKPVLTVYTYDSFA------AD-W----GPGPAVKKAFEAECGCELKFVALEDGVSLLNRLRLEGKNSKADVVLGLDNN   84 (326)
T ss_pred             CCCCEEEEEECCCCC------CC-C----CCCHHHHHHHHHHHCCEEEEEECCCHHHHHHHHHHCCCCCCCCEEEECCHH
T ss_conf             029879999665444------46-6----864799999989879689999679679999999973899976589981767


Q ss_pred             CHHHHHHHC-----------------CCCC----CCCCCCCCCCCCCC--CCCCCCCCCCC----CCEEEEC--CCH--H
Q ss_conf             756754200-----------------2333----22222222211122--22111112334----3202310--101--2
Q gi|254781112|r  112 TPERQKKYD-----------------FSIP----YIAHRVLLVVRSDQ--QDIRSFKDLTD----KTVAQIL--GTD--L  160 (274)
Q Consensus       112 t~eR~~~~~-----------------fs~p----~~~~~~~~~~~~~~--~~~~~~~dL~g----~~V~~~~--g~~--~  160 (274)
                      .-.|...-.                 |.++    |-....+++..++.  +..++++||..    .+|++..  .+.  .
T Consensus        85 ~l~~A~~~gl~~p~~s~~~~~~ip~~~~d~~~vp~d~g~~a~vYn~~~~~~~P~S~~DL~~p~~kgki~i~dP~tSs~g~  164 (326)
T PRK11205         85 LLAAAKKTGLFAPSGVDTSAVTVPGGWNDDTFVPYDYGYFAFVYDKEKLKNPPKSLKELVESDQNWKVIYQDPRTSTPGL  164 (326)
T ss_pred             HHHHHHHCCCCCCCCCCHHHCCCCCCCCCCCEECCCCCEEEEEEEHHHCCCCCCCHHHHHCCHHCCCEEECCCCCCCCHH
T ss_conf             89999986996525686110248600269852113476589998422237887698987273303886633888785279


Q ss_pred             H--------------HHHHCCCCCCE-EECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEECCCCCCCCCE
Q ss_conf             2--------------33201345421-33685577775544321003665589999998458766732623677687707
Q gi|254781112|r  161 S--------------RFAKELKSHLV-FSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAV  225 (274)
Q Consensus       161 ~--------------~~l~~~~~~~~-~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  225 (274)
                      .              ++-++...+.. ...+-.+++.++..|++|.++.-...-.+......................--
T Consensus       165 a~l~~~i~~~Ge~~~e~W~~L~~N~~~~~~gws~a~~~~~~Ge~~ivlsy~~spa~~~~~~~~~~~~~~~~~eG~~~~ie  244 (326)
T PRK11205        165 GLLLWMKKVYGDDAPQAWQKLAKKTVTVTKGWSEAYGLFLKGEADLVLSYTTSPAYHIIAEKKDNYAAANFSEGHYLQVE  244 (326)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCCCEEEEEECCHHHHHHHCCCCCCCEEECCCCCEEEEE
T ss_conf             99999999716328999999986384447883388887644767579985147787764136665422445887277766


Q ss_pred             EEEEECC--CHHHHHHHHHHHHHHHHCCHHHHHHH
Q ss_conf             9998189--98999999999999997985999998
Q gi|254781112|r  226 AFMMRKG--NNKLTRSINEILCAIHLDGTYKKIFD  258 (274)
Q Consensus       226 ~~~~~k~--~~~L~~~in~~l~~l~~~G~~~~I~~  258 (274)
                      +.++-|+  |++....|=..|.    |.+.++++.
T Consensus       245 gagI~k~akn~e~A~kFidfll----S~eaQ~~~~  275 (326)
T PRK11205        245 VAARTAASKQPELAQKFLQFMV----SPAFQNAIP  275 (326)
T ss_pred             EEEEECCCCCHHHHHHHHHHHC----CHHHHHHHH
T ss_conf             7898379999899999999975----899999864


No 77 
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=93.42  E-value=0.61  Score=25.49  Aligned_cols=173  Identities=9%  Similarity=0.080  Sum_probs=94.7

Q ss_pred             HCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHC-CCCCCCCCCCHHHHHHHHHCCCCCCCHHCCCCHHHHH
Q ss_conf             589589996289987248704699848898852167899762-9985556689889886431032211000036756754
Q gi|254781112|r   39 DQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRL-NLKVEFFETAVSGLITGLDTNRYDVLVNVAITPERQK  117 (274)
Q Consensus        39 ~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~l-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~t~eR~~  117 (274)
                      ..|.|+||+.+.+..             ++...++....++. ++++++...+...+.+.+.+|++|+.........  .
T Consensus        92 ~~G~lri~~~~~~~~-------------~~lp~~l~~f~~~~P~v~v~i~~~~~~~~~~~l~~~~~Dl~l~~~~~~~--~  156 (309)
T PRK11013         92 RQGQLSIACLPVFSQ-------------SLLPGLCQPFLARYPDVSLNIVPQESPLLEEWLSAQRHDLGLTETLHTP--A  156 (309)
T ss_pred             CCCCCCCCCCHHHHH-------------HHCCHHHHHHHHHCCCCEEEEEECCHHHHHHHHHCCCCCEEEEECCCCC--C
T ss_conf             367656530067898-------------8665231567843898079999898599999997599778996078899--8


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCC----CCCCCCCCCCCEEE-ECCCHHH----HHHHCCCC---CCEEECCHHHHHHHHH
Q ss_conf             20023332222222221112222----11111233432023-1010122----33201345---4213368557777554
Q gi|254781112|r  118 KYDFSIPYIAHRVLLVVRSDQQD----IRSFKDLTDKTVAQ-ILGTDLS----RFAKELKS---HLVFSHNFEQSLQLLL  185 (274)
Q Consensus       118 ~~~fs~p~~~~~~~~~~~~~~~~----~~~~~dL~g~~V~~-~~g~~~~----~~l~~~~~---~~~~~~~~~~~~~~l~  185 (274)
                      .. -..|.+.....+++.++.+.    .-+++||.+..... ..++.+.    .+..+.+.   ...+.++......++.
T Consensus       157 ~~-~~~~l~~~~~~~v~~~~hpla~~~~i~~~dL~~~~~i~~~~~~~~r~~~~~~~~~~g~~~~~~~e~~~~~~~~~lV~  235 (309)
T PRK11013        157 GT-ERTELLTLDEVCVLPDGHPLAAKKVLTPDDFQGENFISLSRTDSYRQLLDQLFAEHGVKRRMVVETHSAASVCAMVR  235 (309)
T ss_pred             CC-EEEEEEEEEEEEECCCCCCCCCCCCCCHHHHCCCCEEECCCCCCHHHHHHHHHHHCCCCCCEEEEECCHHHHHHHHH
T ss_conf             75-78886420146754789800049999999973898696389994999999999976999776999896999999999


Q ss_pred             HHHHHCCCCCHHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEEEECCC
Q ss_conf             432100366558999999845876673262367768770799981899
Q gi|254781112|r  186 SKRTDATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKGN  233 (274)
Q Consensus       186 ~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~  233 (274)
                      .|-.= .+.+...+..+...    ...+. +..+..+..+++..+++.
T Consensus       236 ~G~Gv-ail~~~~~~~~~~~----g~~~~-pl~~~~~~~~~lv~~~~r  277 (309)
T PRK11013        236 AGLGV-SIVNPLTALDYAGS----GLVVR-PFSISVPFTVSLIRPLHR  277 (309)
T ss_pred             HCCEE-EEECHHHHHHHHHC----CEEEE-ECCCCCCEEEEEEEECCC
T ss_conf             79969-99469999866219----90999-888899618999998999


No 78 
>PRK11233 nitrogen assimilation transcriptional regulator; Provisional
Probab=92.99  E-value=0.71  Score=25.09  Aligned_cols=193  Identities=11%  Similarity=0.091  Sum_probs=104.3

Q ss_pred             HCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHC-CCCCCCCCCCHHHHHHHHHCCCCCCCHHCCCCHHHHH
Q ss_conf             589589996289987248704699848898852167899762-9985556689889886431032211000036756754
Q gi|254781112|r   39 DQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRL-NLKVEFFETAVSGLITGLDTNRYDVLVNVAITPERQK  117 (274)
Q Consensus        39 ~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~l-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~t~eR~~  117 (274)
                      .+|.++||+.+.....            .+...++..+.++. ++++++...+...+.+.|.+|++|+.......+  ..
T Consensus        89 ~~G~l~ig~~p~~~~~------------~l~~p~l~~f~~~~P~v~v~l~~~~~~~l~~~l~~g~~Dlai~~~~~~--~~  154 (305)
T PRK11233         89 LSGQVSIGLAPGTAAS------------SITMPLLQAVRAEFPEIVIYLHENSGAVLNEKLINGQLDMAVIYEHSP--VA  154 (305)
T ss_pred             CCCEEEEEEECCHHHH------------HHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHCCCEEEEEEECCCC--CC
T ss_conf             7404999996215566------------536999999999789429997238879999998769847999827989--88


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCEEEEC-CCHHH----HHHHCCCC--C-CEEECCHHHHHHHHHHHH
Q ss_conf             2002333222222222111222-21111123343202310-10122----33201345--4-213368557777554432
Q gi|254781112|r  118 KYDFSIPYIAHRVLLVVRSDQQ-DIRSFKDLTDKTVAQIL-GTDLS----RFAKELKS--H-LVFSHNFEQSLQLLLSKR  188 (274)
Q Consensus       118 ~~~fs~p~~~~~~~~~~~~~~~-~~~~~~dL~g~~V~~~~-g~~~~----~~l~~~~~--~-~~~~~~~~~~~~~l~~gr  188 (274)
                      .+ -+.|+...+.+++.+.+.+ .--++.||.+..+.... ++...    ......+.  + ..++++......++..|-
T Consensus       155 ~l-~~~~l~~~~l~lv~~~~~p~~~i~l~~l~~~~~i~~~~~~~~r~~~~~~~~~~~~~~~~~~e~~~~~~i~~~V~~G~  233 (305)
T PRK11233        155 GV-SSQALLKEDLFLVGTQDCPGQSVDLNAIAQMNLFLPRDYSAVRLRVDEAFSLRRLTAKVIGEIESIATLTAAIASGM  233 (305)
T ss_pred             CC-EEEEEEECCEEEEECCCCCCCCCCHHHHCCCCEEECCCCCHHHHHHHHHHHHCCCCCCEEEEECCHHHHHHHHHHCC
T ss_conf             82-89999853589998477887878999980899898799984999999999977999847999996999999999799


Q ss_pred             HHCCCCCHHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEEEECCCH--HHHHHHHHHHHHHHHC
Q ss_conf             1003665589999998458766732623677687707999818998--9999999999999979
Q gi|254781112|r  189 TDATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKGNN--KLTRSINEILCAIHLD  250 (274)
Q Consensus       189 vD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~--~L~~~in~~l~~l~~~  250 (274)
                      .= .+.+...+..+....  ......+ ..+....++++..+++.+  .-...+-+.|.++..+
T Consensus       234 Gi-ailP~~~~~~~~~~~--~~~~~~~-~~p~~~~~~~l~~~~~r~lspaa~af~d~L~~~~~~  293 (305)
T PRK11233        234 GV-TVLPESAARSLCGAV--NGWMSRI-TTPSMSLSLSLNLSARANLSPQAQAVKEILLSLISS  293 (305)
T ss_pred             EE-EEEHHHHHHHHHHCC--CEEEEEC-CCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHHHC
T ss_conf             78-987199999875349--7699925-999866599999989098899999999999997747


No 79 
>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).
Probab=92.74  E-value=0.77  Score=24.87  Aligned_cols=175  Identities=12%  Similarity=0.131  Sum_probs=100.2

Q ss_pred             CCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHH-CCCCCCCCCCCHHHHHHHHHCCCCCCCHHCCCCHHHHHH
Q ss_conf             8958999628998724870469984889885216789976-299855566898898864310322110000367567542
Q gi|254781112|r   40 QSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHR-LNLKVEFFETAVSGLITGLDTNRYDVLVNVAITPERQKK  118 (274)
Q Consensus        40 ~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~-lg~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~t~eR~~~  118 (274)
                      .+.|+||+..   ++ +            ..+++..+.++ -++++++...+...+++.|.+|++|++......  ....
T Consensus        86 ~g~l~ig~~~---~~-~------------l~~~l~~f~~~~P~v~i~i~~~~~~~~~~~L~~~~~Di~i~~~~~--~~~~  147 (279)
T TIGR03339        86 EGSLRIAATA---PY-Y------------VLDLVARFRQRYPGIEVSVRIGNSQEVLQALQSYRVDVAVSSEVV--DDPR  147 (279)
T ss_pred             CCEEEECCCH---HH-H------------HHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHCCCEEEEEECCCC--CCCC
T ss_conf             4516861751---77-8------------999999999858986057895580877754025965899972788--9998


Q ss_pred             HCCCCCCCCCCCCCCCCCCCCC----CCCCCCCCCCCEEE-ECCCHHH----HHHHCCCC---CCEEECCHHHHHHHHHH
Q ss_conf             0023332222222221112222----11111233432023-1010122----33201345---42133685577775544
Q gi|254781112|r  119 YDFSIPYIAHRVLLVVRSDQQD----IRSFKDLTDKTVAQ-ILGTDLS----RFAKELKS---HLVFSHNFEQSLQLLLS  186 (274)
Q Consensus       119 ~~fs~p~~~~~~~~~~~~~~~~----~~~~~dL~g~~V~~-~~g~~~~----~~l~~~~~---~~~~~~~~~~~~~~l~~  186 (274)
                      + .+.|+...+.++++.++.+.    --+++||.+.+... ..|+...    ....+.+.   .....++......++.+
T Consensus       148 ~-~~~~l~~~~~~~~~~~~~~la~~~~i~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~  226 (279)
T TIGR03339       148 L-DRVVLGNDPLVAVVHRQHPLAERESVTLEELAGQPLLMREPGSVTRQTTEEALAAAGVAPRPALEIGSREAIREAVLA  226 (279)
T ss_pred             E-EEEEEECCCEEEEEECCCHHHCCCCCCHHHHCCCCEEEECCCCCHHHHHHHHHHHCCCCCCEEEEECCHHHHHHHHHH
T ss_conf             3-999940444899991886332399999999769998982899839999999999779987536778969999999997


Q ss_pred             HHHHCCCCCHHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEEEECC---CHHHHHHH
Q ss_conf             3210036655899999984587667326236776877079998189---98999999
Q gi|254781112|r  187 KRTDATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKG---NNKLTRSI  240 (274)
Q Consensus       187 grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~---~~~L~~~i  240 (274)
                      |..=+ +.+...+    ...+. -..++ ...+.....++++.+|+   +|.....+
T Consensus       227 G~Gia-ilP~~~v----~~~~~-l~~~p-l~~~~~~~~~~l~~~~~r~~sp~~~aFi  276 (279)
T TIGR03339       227 GLGVS-VVSAAEV----GRDPR-LRVLP-IVGAEPTMDEYLYCLKERRGARLIAAFL  276 (279)
T ss_pred             CCEEE-EEEHHHH----HHCCC-EEEEE-CCCCCCCCEEEEEEECCCCCCHHHHHHH
T ss_conf             99389-7148996----10989-89998-9888986279999989986899999999


No 80 
>COG1511 Predicted membrane protein [Function unknown]
Probab=92.70  E-value=0.78  Score=24.84  Aligned_cols=57  Identities=12%  Similarity=0.306  Sum_probs=39.7

Q ss_pred             CEEEEEECCCCCEEEEEEEEHHHHHHHCC--CCCCCCCCCHHHHHHHHHCCCCCCCHHC
Q ss_conf             72487046998488988521678997629--9855566898898864310322110000
Q gi|254781112|r   53 PHSFHAQDGRGELTGFDIDLIKEVAHRLN--LKVEFFETAVSGLITGLDTNRYDVLVNV  109 (274)
Q Consensus        53 P~~~~~~d~~g~~~G~~~dl~~~i~~~lg--~~~~~~~~~~~~~~~~l~~g~~D~~~~~  109 (274)
                      |-..++.|....+.|-.+++.+.+.+.+.  -+++|+.++-....++++.|+++++.-+
T Consensus        50 pVAVVNeDkg~t~~Gk~~~iG~~~V~~L~kn~~~~w~fVs~~~A~~gl~~g~Yya~i~I  108 (780)
T COG1511          50 PVAVVNEDKGATFNGKKVNIGDDLVKTLKKNKSLDWHFVSREEAEKGLKDGKYYAVIYI  108 (780)
T ss_pred             CEEEEECCCCCCCCCCEEEHHHHHHHHHCCCCCCCEEEECHHHHHHHHHHCCCEEEEEE
T ss_conf             46998577666647751107899999860688986289678989867760784399983


No 81 
>COG2113 ProX ABC-type proline/glycine betaine transport systems, periplasmic components [Amino acid transport and metabolism]
Probab=92.67  E-value=0.15  Score=29.22  Aligned_cols=131  Identities=17%  Similarity=0.136  Sum_probs=72.3

Q ss_pred             HHHHCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCCHHC--CCCH
Q ss_conf             78858958999628998724870469984889885216789976299855566898898864310322110000--3675
Q gi|254781112|r   36 RTEDQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVSGLITGLDTNRYDVLVNV--AITP  113 (274)
Q Consensus        36 ~~~~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~~~~~~~~~~~~~l~~g~~D~~~~~--~~t~  113 (274)
                      ....-++++++. .+|..       +.     +...+++.+.+.+|++++.++.+..-++..|.+|++|+..+.  ..++
T Consensus        26 ~~~~~~tV~~a~-~~W~s-------~~-----~~t~v~~~iLk~~Gy~v~~~~~~~~~~~~sla~gd~D~~~~~W~p~~~   92 (302)
T COG2113          26 AAEAGKTVRIAD-VGWTS-------GT-----ATTNVAKKILKGLGYTVELVTLDTAVMYQSLAKGDLDVFPEAWLPTTP   92 (302)
T ss_pred             CCCCCCEEEEEE-CCCCH-------HH-----HHHHHHHHHHHHCCCCCEEEECCHHHHHHHHHCCCCCCCCCEECCCCH
T ss_conf             345588258843-69617-------89-----999999999996799624665559999999973797532010268875


Q ss_pred             H-----HHHHHCCCCC-CC-CCCCCCCCCCCCC--CCCCCCCC-------CCCCEEEECCCHHH----HHHHCCCC---C
Q ss_conf             6-----7542002333-22-2222222111222--21111123-------34320231010122----33201345---4
Q gi|254781112|r  114 E-----RQKKYDFSIP-YI-AHRVLLVVRSDQQ--DIRSFKDL-------TDKTVAQILGTDLS----RFAKELKS---H  170 (274)
Q Consensus       114 e-----R~~~~~fs~p-~~-~~~~~~~~~~~~~--~~~~~~dL-------~g~~V~~~~g~~~~----~~l~~~~~---~  170 (274)
                      +     .++......+ .+ -....+.+++--.  .+++++|+       .|+-++...|+...    ..++..+.   .
T Consensus        93 ~~~~~~~~~~~v~~~~~~~~Ga~~g~~vp~y~~d~~iksi~D~~~~~d~~~g~i~g~~pG~g~~~~~~~~~k~y~~~~~~  172 (302)
T COG2113          93 DDYKKAVKDKKVELGGTNLEGAKQGWAVPKYVADAGIKSIADLAKFKDKFGGKIYGIEPGWGCMRVIEDAIKAYGLGLKG  172 (302)
T ss_pred             HHHHHHHCCCCEEECCCCCCCCEEEEEECEEHHHCCCCCHHHHHHCCCCCCCCEECCCCCCCHHHHHHHHHHHCCCCCCC
T ss_conf             88998742685441354667724789824003423556565698666877785781589973548999998643655364


Q ss_pred             CEEECCHHH
Q ss_conf             213368557
Q gi|254781112|r  171 LVFSHNFEQ  179 (274)
Q Consensus       171 ~~~~~~~~~  179 (274)
                      ...+++..+
T Consensus       173 ~~lv~~s~~  181 (302)
T COG2113         173 FELVESSEA  181 (302)
T ss_pred             EEEECCCHH
T ss_conf             488447478


No 82 
>TIGR00212 hemC porphobilinogen deaminase; InterPro: IPR000860   Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway . The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including vitamin B12, haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin .   The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes: (1) condensation of succinyl CoA and glycine (C4 pathway) using ALA synthase (2.3.1.37 from EC), or (2) decarboxylation of glutamate (C5 pathway) via three different enzymes, glutamyl-tRNA synthetase (6.1.1.17 from EC) to charge a tRNA with glutamate, glutamyl-tRNA reductase (1.2.1.70 from EC) to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and GSA aminotransferase (5.4.3.8 from EC) to catalyse a transamination reaction to produce ALA.   The second stage is to convert ALA to uroporphyrinogen III, the first macrocyclic tetrapyrrolic structure in the pathway. This is achieved by the action of three enzymes in one common pathway: porphobilinogen (PBG) synthase (or ALA dehydratase, 4.2.1.24 from EC) to condense two ALA molecules to generate porphobilinogen; hydroxymethylbilane synthase (or PBG deaminase, 2.5.1.61 from EC) to polymerise four PBG molecules into preuroporphyrinogen (tetrapyrrole structure); and uroporphyrinogen III synthase (4.2.1.75 from EC) to link two pyrrole units together (rings A and D) to yield uroporphyrinogen III.   Uroporphyrinogen III is the first branch point of the pathway. To synthesise cobalamin (vitamin B12), sirohaem, and coenzyme F430, uroporphyrinogen III needs to be converted into precorrin-2 by the action of uroporphyrinogen III methyltransferase (2.1.1.107 from EC). To synthesise haem and chlorophyll, uroporphyrinogen III needs to be decarboxylated into coproporphyrinogen III by the action of uroporphyrinogen III decarboxylase (4.1.1.37 from EC) .   This entry represents hydroxymethylbilane synthase (or porphobilinogen deaminase, 2.5.1.61 from EC), which functions during the second stage of tetrapyrrole biosynthesis. This enzyme catalyses the polymerisation of four PBG molecules into the tetrapyrrole structure, preuroporphyrinogen, with the concomitant release of four molecules of ammonia. This enzyme uses a unique dipyrro-methane cofactor made from two molecules of PBG, which is covalently attached to a cysteine side chain. The tetrapyrrole product is synthesized in an ordered, sequential fashion, by initial attachment of the first pyrrole unit (ring A) to the cofactor, followed by subsequent additions of the remaining pyrrole units (rings B, C, D) to the growing pyrrole chain . The link between the pyrrole ring and the cofactor is broken once all the pyrroles have been added. This enzyme is folded into three distinct domains that enclose a single, large active site that makes use of an aspartic acid as its one essential catalytic residue, acting as a general acid/base during catalysis , . A deficiency of hydroxymethylbilane synthase is implicated in the neuropathic disease, Acute Intermittent Porphyria (AIP) . ; GO: 0004418 hydroxymethylbilane synthase activity, 0033014 tetrapyrrole biosynthetic process.
Probab=92.34  E-value=0.57  Score=25.70  Aligned_cols=132  Identities=20%  Similarity=0.223  Sum_probs=75.2

Q ss_pred             HHHHHHHCCCCCCCH-HC----CCC-HHHHHHHCCCCCCCCCCCCCCCCCCC------CCCCCCCCCCCCCEEEECCCHH
Q ss_conf             988643103221100-00----367-56754200233322222222211122------2211111233432023101012
Q gi|254781112|r   93 GLITGLDTNRYDVLV-NV----AIT-PERQKKYDFSIPYIAHRVLLVVRSDQ------QDIRSFKDLTDKTVAQILGTDL  160 (274)
Q Consensus        93 ~~~~~l~~g~~D~~~-~~----~~t-~eR~~~~~fs~p~~~~~~~~~~~~~~------~~~~~~~dL~g~~V~~~~g~~~  160 (274)
                      ++.++|.+|++|++. |+    +.. ++.   .        .=.+|..|.+.      ..+.++++|-   =|...||+.
T Consensus        62 Ele~aLL~geiD~AVHSlKD~P~~~~~~g---L--------~~~a~~~RedP~D~l~s~~~~~l~~LP---~GA~vGTSS  127 (312)
T TIGR00212        62 ELEQALLDGEIDLAVHSLKDVPTVLSPEG---L--------EIAAVLKREDPRDVLVSRKYLSLEELP---QGAKVGTSS  127 (312)
T ss_pred             HHHHHHHCCCCCEEEECCCCCCCCCCCCC---C--------EEEEECCCCCCCCEEEECCCCCHHHCC---CCCEEECCH
T ss_conf             99999625984488843023576559888---2--------786355878864268862788851277---988897457


Q ss_pred             HH---HHHC--CCCCCEEEC-CHHHHHHHHHH-HHHHCCCCCHHHHHHHHHHCCCCC-CCEE-----ECCCCCCCCCEEE
Q ss_conf             23---3201--345421336-85577775544-321003665589999998458766-7326-----2367768770799
Q gi|254781112|r  161 SR---FAKE--LKSHLVFSH-NFEQSLQLLLS-KRTDATMIPDIPFFNFLERRPHDG-NLFK-----IADRMKDNSAVAF  227 (274)
Q Consensus       161 ~~---~l~~--~~~~~~~~~-~~~~~~~~l~~-grvD~~~~~~~~~~~~~~~~~~~~-~~~~-----~~~~~~~~~~~~~  227 (274)
                      -+   +++.  +..+++... |.+.-++.|.. |++||++....    .+.+....+ -+..     ...+...+.-+++
T Consensus       128 ~RR~aql~~~RPDl~~~~lRGNi~TRl~Kl~~Gg~~DAiiLA~A----GL~RLg~~~~~i~~~~~~~~~~PA~GQG~i~v  203 (312)
T TIGR00212       128 LRRKAQLKALRPDLEIEPLRGNIDTRLRKLDEGGEYDAIILAAA----GLKRLGLENDVITEVLDPEVMLPAVGQGAIAV  203 (312)
T ss_pred             HHHHHHHHHCCCCCEEEECCCCHHHHHHHHCCCCCCHHHHHHHH----HHHCCCCCCHHHHHCCCHHHCCCCCCCCEEEE
T ss_conf             99999998308994499746987999998518882048999888----75302541013431478114178866757999


Q ss_pred             EEECCCHHHHHHHHH
Q ss_conf             981899899999999
Q gi|254781112|r  228 MMRKGNNKLTRSINE  242 (274)
Q Consensus       228 ~~~k~~~~L~~~in~  242 (274)
                      .+|+++..+.+.+++
T Consensus       204 e~R~dD~~~~~il~~  218 (312)
T TIGR00212       204 ECRKDDTEIKEILKE  218 (312)
T ss_pred             EEECCCHHHHHHHHH
T ss_conf             984587799998620


No 83 
>PRK03537 hypothetical protein; Provisional
Probab=92.16  E-value=0.47  Score=26.17  Aligned_cols=135  Identities=13%  Similarity=0.144  Sum_probs=73.9

Q ss_pred             CCCCCCCCCCCCCCCCC-CCCCCCC-CC--CCCEEEE------CCCHHHHHHHCC-----C------C---------CCE
Q ss_conf             33222222222111222-2111112-33--4320231------010122332013-----4------5---------421
Q gi|254781112|r  123 IPYIAHRVLLVVRSDQQ-DIRSFKD-LT--DKTVAQI------LGTDLSRFAKEL-----K------S---------HLV  172 (274)
Q Consensus       123 ~p~~~~~~~~~~~~~~~-~~~~~~d-L~--g~~V~~~------~g~~~~~~l~~~-----~------~---------~~~  172 (274)
                      .+|-....++++|++.+ .+.++.| |.  +.|||+.      .|....+++.+.     +      .         +..
T Consensus        17 ~~Fa~N~Lvliv~~~~~~~~~~~ld~L~~p~~ri~~stP~~dP~G~Ya~~~l~~a~~~~~g~~~~l~~ka~~lvgg~~s~   96 (188)
T PRK03537         17 VMFARNRLCAIARADVMLTSENLLDLLLDPDIRLGTSTPGADPSGDYAWQLFDRAEALKAGAGEALRTKALQLVGGPNSA   96 (188)
T ss_pred             EEEECCCEEEEECCCCCCCCCCHHHHHCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCC
T ss_conf             45332868999728987674468888439974998269998972489999999887527761789999887741776566


Q ss_pred             EECCHHHHHH-HHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEEEECCCHHHHHHHHHHHHHHHHCC
Q ss_conf             3368557777-554432100366558999999845876673262367768770799981899899999999999999798
Q gi|254781112|r  173 FSHNFEQSLQ-LLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKGNNKLTRSINEILCAIHLDG  251 (274)
Q Consensus       173 ~~~~~~~~~~-~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~L~~~in~~l~~l~~~G  251 (274)
                      ...+...... .+..|++|+.+.-...+.....+.+. -..+.++.+......|++++.++..+-    -+.+.+..-|.
T Consensus        97 ~~p~gr~~~~~~~~~geaDa~ivY~TdA~~a~~~~~~-l~~v~iP~~~~~~~~Y~iav~~~a~~~----A~~f~~flls~  171 (188)
T PRK03537         97 PIPAGRNAYEWLIENKQADIFIGYCTSAALALKEVPD-LQIVDLPEPLAVGANYGLAVLKDASEA----ARPLAEFILSP  171 (188)
T ss_pred             CCCCCCHHHHHHHCCCCCCEEEEEECCHHHHHHCCCC-CEEEECCCCCCCCCCEEEEECCCCCHH----HHHHHHHHCCH
T ss_conf             6887520323331059745799985147878515898-549958800066632357873688099----99999997399


Q ss_pred             HHHHHHHHH-CC
Q ss_conf             599999876-78
Q gi|254781112|r  252 TYKKIFDRY-FD  262 (274)
Q Consensus       252 ~~~~I~~kw-~g  262 (274)
                      +-++|+++| |.
T Consensus       172 ~gQ~iL~~~GF~  183 (188)
T PRK03537        172 KGQAILAQYGFS  183 (188)
T ss_pred             HHHHHHHHCCCC
T ss_conf             999999980899


No 84 
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=91.59  E-value=1.1  Score=24.02  Aligned_cols=155  Identities=9%  Similarity=0.105  Sum_probs=86.0

Q ss_pred             EEHHHHHHHC-CCCCCCCCCCHHHHHHHHHCCCCCCCHHCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC---CCCC
Q ss_conf             2167899762-99855566898898864310322110000367567542002333222222222111222211---1112
Q gi|254781112|r   71 DLIKEVAHRL-NLKVEFFETAVSGLITGLDTNRYDVLVNVAITPERQKKYDFSIPYIAHRVLLVVRSDQQDIR---SFKD  146 (274)
Q Consensus        71 dl~~~i~~~l-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~t~eR~~~~~fs~p~~~~~~~~~~~~~~~~~~---~~~d  146 (274)
                      .++..+.+.. ++++++.........+.|.+|++|++.+.....  ...+ -+.|++.+..+++++++.+...   +.++
T Consensus       129 ~ll~~~~~~~P~v~l~~~~~~~~~~~~~L~~g~iDl~I~~~~~~--~~~~-~~~~L~~d~~v~v~~~~HP~~~~~lt~~~  205 (314)
T PRK09508        129 QIYNRIEQIAPNIHLVFKSSLNQNIEHQLRYQETEFVISYEEFD--RPEF-TSVPLFKDELVLVASKNHPRIKGPILEEQ  205 (314)
T ss_pred             HHHHHHHHHCCCCEEEEEECCCHHHHHHHHCCCCCEEEECCCCC--CCCC-EEEEEEECCEEEEECCCCCCCCCCCCHHH
T ss_conf             99999998689977999857706499999769952999678779--9873-48999724649998299976789999999


Q ss_pred             CCCCCEEEE--CCC--HHHHHHHCCCC--C-CEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEECCCC
Q ss_conf             334320231--010--12233201345--4-2133685577775544321003665589999998458766732623677
Q gi|254781112|r  147 LTDKTVAQI--LGT--DLSRFAKELKS--H-LVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRM  219 (274)
Q Consensus       147 L~g~~V~~~--~g~--~~~~~l~~~~~--~-~~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  219 (274)
                      +....-.+.  .|.  ..+.++.+.+.  + .....+.......+..+..= .+++...+..+..+.+..   ....+..
T Consensus       206 ~~~~~hv~~s~~~~~~~~~~~l~~~~~~r~i~~~~~s~~~~~~lv~~td~i-a~lP~~~a~~~~~~~~l~---~~~lP~~  281 (314)
T PRK09508        206 LYNEQHAVVSLDRFASFSQPWYDTVDKQASIAYQGMALSSVLNVVSQTHLV-AIAPRWLAEEFAESLELQ---ILPLPLK  281 (314)
T ss_pred             HHHCCCEEEECCCCCCHHHHHHHHCCCCCEEEEEECCHHHHHHHHHHCCEE-EHHHHHHHHHHHHCCCCE---EECCCCC
T ss_conf             961998899639988589999995798631899958899999999839977-589999999864429957---9789989


Q ss_pred             CCCCCEEEEEECC
Q ss_conf             6877079998189
Q gi|254781112|r  220 KDNSAVAFMMRKG  232 (274)
Q Consensus       220 ~~~~~~~~~~~k~  232 (274)
                      .....+++.-++.
T Consensus       282 ~~~~~~~l~WH~r  294 (314)
T PRK09508        282 NNSRTCYLSWHES  294 (314)
T ss_pred             CCCEEEEEEECCC
T ss_conf             8873699997899


No 85 
>PRK01066 porphobilinogen deaminase; Provisional
Probab=91.56  E-value=1.1  Score=24.00  Aligned_cols=136  Identities=13%  Similarity=0.044  Sum_probs=70.2

Q ss_pred             HHHHHHHCCCCCCCH-HCC--CCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCEEEECCCHHHH---HHH
Q ss_conf             988643103221100-003--6756754200233322222222211122221111123-343202310101223---320
Q gi|254781112|r   93 GLITGLDTNRYDVLV-NVA--ITPERQKKYDFSIPYIAHRVLLVVRSDQQDIRSFKDL-TDKTVAQILGTDLSR---FAK  165 (274)
Q Consensus        93 ~~~~~l~~g~~D~~~-~~~--~t~eR~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~dL-~g~~V~~~~g~~~~~---~l~  165 (274)
                      ++..+|.+|++|++. ++-  ++++......+ .+--...-+++.+++    .++++| +|-+||    |...+   .++
T Consensus        80 ele~aLl~g~iDiAVHSlKDlP~~~~l~i~av-~~R~d~rDvLv~~~~----~~l~~lp~~a~IG----TSS~RR~aql~  150 (234)
T PRK01066         80 DVDFLVLSGKCDLAIHSAKDLPEPPKLTVVAI-TAGLDPSDLLVYAEK----YLLQPLPKRPRIG----SSSLRREELLK  150 (234)
T ss_pred             HHHHHHHCCCCCEEEEECCCCCCCCCCEEEEE-ECCCCHHHHHHCCCC----CCCCCCCCCCEEE----CCCHHHHHHHH
T ss_conf             99999976987789871578899999768999-657898888760467----6412288668773----16661999999


Q ss_pred             C--CCCCCEEE-CCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEECCCCC--CCCCEEEEEECCCHHHHHHH
Q ss_conf             1--34542133-6855777755443210036655899999984587667326236776--87707999818998999999
Q gi|254781112|r  166 E--LKSHLVFS-HNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRMK--DNSAVAFMMRKGNNKLTRSI  240 (274)
Q Consensus       166 ~--~~~~~~~~-~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~k~~~~L~~~i  240 (274)
                      .  +..+++.. .|.+..++.|.+|++|+++...    ..+.+...........+++.  .+..+++-.++++.++.+.+
T Consensus       151 ~~~pdl~i~~iRGNI~TRl~Kl~~g~~DaiILA~----AGL~RLgl~~~~~~~lp~~~~pgQGalaIe~R~dD~~~~~ll  226 (234)
T PRK01066        151 LLFPSGIILDIRGTIEERLKLLERGKYDAIVVAK----AAVLRLGLRLPYTIELPPPYHPLQGRLAITAKKHIAKWKTLF  226 (234)
T ss_pred             HHCCCCCEEECCCCHHHHHHHHCCCCCCEEEHHH----HHHHHCCCCCCCEEECCCCCCCCCCCEEEEECCCCHHHHHHH
T ss_conf             8789997896408999999986178989533898----999875897754585589887886828899807979999999


Q ss_pred             H
Q ss_conf             9
Q gi|254781112|r  241 N  241 (274)
Q Consensus       241 n  241 (274)
                      +
T Consensus       227 ~  227 (234)
T PRK01066        227 L  227 (234)
T ss_pred             H
T ss_conf             9


No 86 
>pfam10613 Lig_chan-Glu_bd Ligated ion channel L-glutamate- and glycine-binding site. This region, sometimes called the S1 domain, is the luminal domain just upstream of the first, M1, transmembrane region of transmembrane ion-channel proteins, and it binds L-glutamate and glycine. It is found in association with Lig_chan, pfam00060.
Probab=91.40  E-value=0.045  Score=32.48  Aligned_cols=31  Identities=29%  Similarity=0.562  Sum_probs=26.0

Q ss_pred             CCCCCEEEEEEEEHHHHHHHCCCCCCCCCCC
Q ss_conf             6998488988521678997629985556689
Q gi|254781112|r   60 DGRGELTGFDIDLIKEVAHRLNLKVEFFETA   90 (274)
Q Consensus        60 d~~g~~~G~~~dl~~~i~~~lg~~~~~~~~~   90 (274)
                      .++.++.||.+||++++++.+|+++++..++
T Consensus        13 ~G~~~yeGyciDLl~~ls~~l~F~y~~~~v~   43 (65)
T pfam10613        13 TGNERFEGYCIDLLDELAKILGFNYEIYLVP   43 (65)
T ss_pred             CCCCCEEEHHHHHHHHHHHHCCCEEEEEECC
T ss_conf             8973240279999999999849749999778


No 87 
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=90.97  E-value=1.2  Score=23.64  Aligned_cols=175  Identities=6%  Similarity=0.052  Sum_probs=94.1

Q ss_pred             HCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHC-CCCCCCCCCCHHHHHHHHHCCCCCCCHHCCCCHHHHH
Q ss_conf             589589996289987248704699848898852167899762-9985556689889886431032211000036756754
Q gi|254781112|r   39 DQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRL-NLKVEFFETAVSGLITGLDTNRYDVLVNVAITPERQK  117 (274)
Q Consensus        39 ~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~l-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~t~eR~~  117 (274)
                      ..|+|+||......             ..+..+++....++- ++++++...+...+++.|.+|++|+...... .....
T Consensus        65 ~~G~lri~~~~t~~-------------~~~lp~~l~~f~~~~P~v~~~l~~~~~~~~~~~l~~g~~D~ai~~~p-~~~~~  130 (269)
T PRK11716         65 LSGELSLFCSVTAA-------------YSHLPPILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAAKP-ETLPS  130 (269)
T ss_pred             CCCCEEEEECHHHH-------------HHHCCHHHHHHHHHCCCCEEEEECCCHHHHHHHHHCCCCCEEEEECC-CCCCC
T ss_conf             76626998514887-------------77546789999998889448984289999999998699558999378-78999


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCCC-----CCCCCCCCCCEEEEC-CCH---HHHHHHCCCCC--C-EEECCHHHHHHHHH
Q ss_conf             200233322222222211122221-----111123343202310-101---22332013454--2-13368557777554
Q gi|254781112|r  118 KYDFSIPYIAHRVLLVVRSDQQDI-----RSFKDLTDKTVAQIL-GTD---LSRFAKELKSH--L-VFSHNFEQSLQLLL  185 (274)
Q Consensus       118 ~~~fs~p~~~~~~~~~~~~~~~~~-----~~~~dL~g~~V~~~~-g~~---~~~~l~~~~~~--~-~~~~~~~~~~~~l~  185 (274)
                      .+. ..|+...+.+++++++....     ....|+....+.... |..   .+.+.++.+..  + .++.+.+....++.
T Consensus       131 ~l~-~~~l~~~~l~~v~p~~~~~~~~~~~~~~~dl~~~p~il~~~~~~r~~~~~~~~~~~~~p~i~~e~~~~~~i~~~V~  209 (269)
T PRK11716        131 SLA-FSPIDEIPLVLIAPALPCPVRQQVSQEKPDWSRIPFILPEHGPARRRIDLWFRRHKIKPNIYAQVSGHEAIVSMVA  209 (269)
T ss_pred             CEE-EEEEEEEEEEEEEECCCCHHHCCCCCCHHHHHCCCEEECCCCCHHHHHHHHHHHCCCCCCEEEEECCHHHHHHHHH
T ss_conf             769-9996564189999788415436356884468338678158982799999999976999717999897999999999


Q ss_pred             HHHHHCCCCCHHHHHHHHHHCCCCCCCEEEC-CCCCCCCCEEEEEECCC
Q ss_conf             4321003665589999998458766732623-67768770799981899
Q gi|254781112|r  186 SKRTDATMIPDIPFFNFLERRPHDGNLFKIA-DRMKDNSAVAFMMRKGN  233 (274)
Q Consensus       186 ~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~k~~  233 (274)
                      .|-.= .+.+...+    ...+.......+. .++..+..++++.+|+.
T Consensus       210 ~G~Gi-ailP~~~~----~~~~~~~~l~~l~~~~~~~~~~i~l~~~~~r  253 (269)
T PRK11716        210 LGCGV-GILPEVVL----DNSPVRDRVQRLEVPPELTPFELGVCCQKKR  253 (269)
T ss_pred             HCCEE-EEHHHHHH----HCCCCCCCEEEEECCCCCCCEEEEEEEECCC
T ss_conf             79941-72059998----3275579889974899887369999997998


No 88 
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=90.74  E-value=1.3  Score=23.51  Aligned_cols=173  Identities=13%  Similarity=0.066  Sum_probs=93.9

Q ss_pred             HCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHC-CCCCCCCCCCHHHHHHHHHCCCCCCCHHCCCCHHHHH
Q ss_conf             589589996289987248704699848898852167899762-9985556689889886431032211000036756754
Q gi|254781112|r   39 DQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRL-NLKVEFFETAVSGLITGLDTNRYDVLVNVAITPERQK  117 (274)
Q Consensus        39 ~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~l-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~t~eR~~  117 (274)
                      .++.|+||+.+....             .+..+++....++. ++++++........++.+.+|++|+.......  ...
T Consensus        88 ~~~~l~ig~~~~~~~-------------~~lp~~l~~f~~~~P~v~v~l~~~~~~~~~~~l~~g~~D~~i~~~~~--~~~  152 (296)
T PRK09906         88 EDRQLTIGFVPSAEV-------------NLLPKVLPMFRLRHPDTLIELVSLINTQQEEKLRRGELDVGFMRHPV--YSD  152 (296)
T ss_pred             CCCEEEEEECHHHHH-------------HHHHHHHHHHHHHCCCCCEEEEECCCHHHHHHHHCCCCCEEEEECCC--CCC
T ss_conf             771388321225699-------------99999999987408986348997580899999986997679873688--998


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCC----CCCCCCCCCCCEEEEC---CCHH----HHHHHCCCC---CCEEECCHHHHHHH
Q ss_conf             20023332222222221112222----1111123343202310---1012----233201345---42133685577775
Q gi|254781112|r  118 KYDFSIPYIAHRVLLVVRSDQQD----IRSFKDLTDKTVAQIL---GTDL----SRFAKELKS---HLVFSHNFEQSLQL  183 (274)
Q Consensus       118 ~~~fs~p~~~~~~~~~~~~~~~~----~~~~~dL~g~~V~~~~---g~~~----~~~l~~~~~---~~~~~~~~~~~~~~  183 (274)
                      .+. +.|++..+.++++.++.+.    --+++||.+.......   +...    ..+..+.+.   .....++......+
T Consensus       153 ~l~-~~~l~~~~~~~~~~~~hpla~~~~i~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~g~~p~~~~~~~~~~~~~~~  231 (296)
T PRK09906        153 EID-YLELLDEPLVVVLPVDHPLAHEKEITAAQLDGVNFISPDPAQSGSLAPIIKAWFAQHNSQPNIVQVATNILVTMNL  231 (296)
T ss_pred             CEE-EEEEECCEEEEEEECCCCCCCCCCCCHHHHCCCCEEEECCCCCCCHHHHHHHHHHHCCCCCCEEEEECCHHHHHHH
T ss_conf             818-9985046079998289810059998999975998796366547609999999999779997469998989999999


Q ss_pred             HHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEEEECCC
Q ss_conf             54432100366558999999845876673262367768770799981899
Q gi|254781112|r  184 LLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKGN  233 (274)
Q Consensus       184 l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~  233 (274)
                      +..|-.= .+.+....     ....................++++-++++
T Consensus       232 v~~G~Gi-~~lP~~~~-----~~~~~~l~~~pl~~~~~~~~~~l~~r~~~  275 (296)
T PRK09906        232 VGMGLGC-TIIPGYMN-----NFNTGQVVFRPLAGNVPSIALLMAWKKGE  275 (296)
T ss_pred             HHHCCEE-EECHHHHH-----HHCCCCEEEEECCCCCCEEEEEEEECCCC
T ss_conf             9949899-98458773-----10689999998899987028999987999


No 89 
>TIGR03261 phnS2 putative 2-aminoethylphosphonate ABC transport system, 1-aminoethylphosphonate-binding protein component. This ABC transporter extracellular solute-binding protein is found in a number of genomes in operon-like contexts strongly suggesting a substrate specificity for 2-aminoethylphosphonate (2-AEP). The characterized PhnSTUV system is absent in the genomes in which this system is found. These genomes encode systems for the catabolism of 2-AEP, making the need for a 2-AEP-specific transporter likely.
Probab=89.73  E-value=1.6  Score=22.99  Aligned_cols=190  Identities=10%  Similarity=0.089  Sum_probs=85.9

Q ss_pred             EEHHHHHHH-CCCCCCCCCCCHHHHHH----HHHCCCCCCCHHCCCCH-HHHH--------------HH--CCCCC----
Q ss_conf             216789976-29985556689889886----43103221100003675-6754--------------20--02333----
Q gi|254781112|r   71 DLIKEVAHR-LNLKVEFFETAVSGLIT----GLDTNRYDVLVNVAITP-ERQK--------------KY--DFSIP----  124 (274)
Q Consensus        71 dl~~~i~~~-lg~~~~~~~~~~~~~~~----~l~~g~~D~~~~~~~t~-eR~~--------------~~--~fs~p----  124 (274)
                      .+++..-++ .|++|+++...-..++.    .-.+.++|++++...+. .+.+              .+  .|.++    
T Consensus        37 ~i~~~Fek~~tgIkV~~v~~~tgel~~rl~aEk~~p~aDV~~g~~~~~~~~~~~~gll~~y~~~~~~~l~~~~~d~~~~~  116 (334)
T TIGR03261        37 KYKDAFEKVNPDIKINWVRDSTGIITAKLLAEKNNPQADVVWGLAASSLALLDKEGMLKPYKPKGLDALNPKFRDAKNPP  116 (334)
T ss_pred             HHHHHHHHHCCCCEEEEEECCHHHHHHHHHHCCCCCCCEEEEECCHHHHHHHHHCCCCCCCCCCCHHHCCHHHCCCCCCC
T ss_conf             99999997779948999989729999999964579986599845657899988604315777530544788652978885


Q ss_pred             CCC----CCCCCCCCC------CCCCCCCCCCCCC----CCEEEE----CCCHHH---------------HHHHCCCCCC
Q ss_conf             222----222222111------2222111112334----320231----010122---------------3320134542
Q gi|254781112|r  125 YIA----HRVLLVVRS------DQQDIRSFKDLTD----KTVAQI----LGTDLS---------------RFAKELKSHL  171 (274)
Q Consensus       125 ~~~----~~~~~~~~~------~~~~~~~~~dL~g----~~V~~~----~g~~~~---------------~~l~~~~~~~  171 (274)
                      ++.    ....+...+      +-+..++++||-.    -+|++.    .|+.+.               ++++++..++
T Consensus       117 ~~~g~~~~~~~i~yN~~~~~~~~~p~P~sw~DL~dp~ykg~i~~~~p~~sg~~~~~l~~~~~~~G~d~g~~~l~~l~~N~  196 (334)
T TIGR03261       117 HWVGMDAWMAAICFNTVEAKKKGLPKPTSWEDLTKPEYKGHIVMPNPASSGTGFLDVSAWLQMMGEDKGWDYMDKLHKNI  196 (334)
T ss_pred             EEEEEEEEEEEEEEEHHHCCCCCCCCCCCHHHHCCHHHCCEEECCCCCCCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHH
T ss_conf             16887524678997444404258999999999709474895873488863389999999999735288999999998632


Q ss_pred             EEE-CCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEEEECC--CHHHHHHHHHHHHHHH
Q ss_conf             133-6855777755443210036655899999984587667326236776877079998189--9899999999999999
Q gi|254781112|r  172 VFS-HNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKG--NNKLTRSINEILCAIH  248 (274)
Q Consensus       172 ~~~-~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~--~~~L~~~in~~l~~l~  248 (274)
                      ..+ .+......++.+|++...+........... ... ...+..+.+-..-..-++++.|+  |++....|=..+    
T Consensus       197 ~~~~~~~~~~~~~v~~Ge~~ig~~~~~~~~~~~~-~g~-pv~~v~P~eG~~~~~~~~~Ivk~a~n~~~Ak~Fidfl----  270 (334)
T TIGR03261       197 AVYTHSGSKPCKLAGMGEFPIGISMAYRALKEKK-KGA-PIDVVFPKEGLGWDIEATAIIKGSKNNDAAKKLVDWS----  270 (334)
T ss_pred             CCCCCCCCHHHHHHHCCCEEEEEEECCHHHHHHH-CCC-CEEEEECCCCCEEEEEEEEEECCCCCHHHHHHHHHHH----
T ss_conf             4167776388899865985799973545788764-389-7338945898478773588887998989999999997----


Q ss_pred             HCCHHHHHHHHHCCCCCC
Q ss_conf             798599999876788877
Q gi|254781112|r  249 LDGTYKKIFDRYFDKNII  266 (274)
Q Consensus       249 ~~G~~~~I~~kw~g~d~~  266 (274)
                      -|-+.++++.+.+..-+.
T Consensus       271 lS~e~Q~~~a~~~~~p~~  288 (334)
T TIGR03261       271 ISDEAMELYAKNYAVVAT  288 (334)
T ss_pred             CCHHHHHHHHHCCEECCC
T ss_conf             699999999964903468


No 90 
>TIGR02424 TF_pcaQ pca operon transcription factor PcaQ; InterPro: IPR012787    Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate . Members occur only in proteobacteria.; GO: 0003677 DNA binding, 0016563 transcription activator activity, 0019619 protocatechuate catabolic process, 0045941 positive regulation of transcription.
Probab=88.31  E-value=0.3  Score=27.37  Aligned_cols=192  Identities=17%  Similarity=0.197  Sum_probs=107.7

Q ss_pred             HHHCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHH-HHHCCCCCCCCCCCHHHHHHHHHCCCCCCCHHCCCCHHH
Q ss_conf             8858958999628998724870469984889885216789-976299855566898898864310322110000367567
Q gi|254781112|r   37 TEDQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEV-AHRLNLKVEFFETAVSGLITGLDTNRYDVLVNVAITPER  115 (274)
Q Consensus        37 ~~~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i-~~~lg~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~t~eR  115 (274)
                      ..+..+++||.-++-+      .       =+.++.++.+ .+.....+.+..-+..-+++.|+.|..|++.|=---||+
T Consensus        89 ~~~~~~~~~GaLPTVa------A-------~L~P~~~~~f~~~~p~~~~~i~tG~n~~Lld~LR~G~LDlVvGRL~ape~  155 (300)
T TIGR02424        89 EGEGPTVRVGALPTVA------A-------RLMPEVVKRFLAEAPRLRLRIVTGENAYLLDQLRVGELDLVVGRLGAPET  155 (300)
T ss_pred             HCCCCEEEECCCHHHH------H-------HHHHHHHHHHHHHCCCCEEEEEECCCHHHHHHHCCCCCEEEEECCCCCHH
T ss_conf             1489648972646689------9-------99999999999616895589987785787987228980277606888321


Q ss_pred             HHHHCCCCCCCCCCCCCCCCCCCCCCC----CCCCCCCCCEEEE-CCCHHHHHHH----CCCC----CCEEECCHHHHHH
Q ss_conf             542002333222222222111222211----1112334320231-0101223320----1345----4213368557777
Q gi|254781112|r  116 QKKYDFSIPYIAHRVLLVVRSDQQDIR----SFKDLTDKTVAQI-LGTDLSRFAK----ELKS----HLVFSHNFEQSLQ  182 (274)
Q Consensus       116 ~~~~~fs~p~~~~~~~~~~~~~~~~~~----~~~dL~g~~V~~~-~g~~~~~~l~----~~~~----~~~~~~~~~~~~~  182 (274)
                      -+.+.| ++.|..+..+++|+|++...    +.+.|..+-|-.+ .|++.-.+++    +.|.    ..++.-|..=+=+
T Consensus       156 MqGl~F-e~LY~E~v~~VVragHPL~~~p~~~~~~L~~yPvl~P~~g~~IR~~~erll~a~G~~~l~~r~EtvS~~fgR~  234 (300)
T TIGR02424       156 MQGLSF-EHLYNERVVFVVRAGHPLLAAPSLSVASLADYPVLLPPEGSIIRPLVERLLIACGIPALPQRIETVSDSFGRR  234 (300)
T ss_pred             HCCCCC-CCCCCCCEEEEECCCCCCCCCCCCCHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHH
T ss_conf             158642-5144773378870857855788777788733881048622267999999998747655660134431578877


Q ss_pred             HHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEE-CCCCCCCCCEEEEEECCCH--HHHHHHHHHHHHH
Q ss_conf             554432100366558999999845876673262-3677687707999818998--9999999999999
Q gi|254781112|r  183 LLLSKRTDATMIPDIPFFNFLERRPHDGNLFKI-ADRMKDNSAVAFMMRKGNN--KLTRSINEILCAI  247 (274)
Q Consensus       183 ~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~k~~~--~L~~~in~~l~~l  247 (274)
                      -+..... .|+++.-.+..-+    .++..... .+.-....+.|+..|.+.+  .=+..+-++|...
T Consensus       235 y~~~sdA-~WiiS~gvv~~dl----~~G~L~~Lp~~~~~t~GPVGL~~R~d~~~s~aaq~f~~alr~~  297 (300)
T TIGR02424       235 YVRESDA-VWIISEGVVAKDL----ADGTLVELPVDTRETAGPVGLCTRPDEQLSRAAQLFVDALRSA  297 (300)
T ss_pred             HHHHCCC-EEECCHHHHHHHH----CCCCEEECCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf             7645472-5772667898875----2892776465757788770215488877898999999999998


No 91 
>pfam00405 Transferrin Transferrin.
Probab=87.68  E-value=2.1  Score=22.13  Aligned_cols=113  Identities=11%  Similarity=0.126  Sum_probs=63.3

Q ss_pred             CCCHHHHHHHHHCCCCCCCH---HCCCCHHHHHHHC---CC-------CCCCCCCCCCCCCCCCCCCCCCCCCCCCCEE-
Q ss_conf             68988988643103221100---0036756754200---23-------3322222222211122221111123343202-
Q gi|254781112|r   88 ETAVSGLITGLDTNRYDVLV---NVAITPERQKKYD---FS-------IPYIAHRVLLVVRSDQQDIRSFKDLTDKTVA-  153 (274)
Q Consensus        88 ~~~~~~~~~~l~~g~~D~~~---~~~~t~eR~~~~~---fs-------~p~~~~~~~~~~~~~~~~~~~~~dL~g~~V~-  153 (274)
                      ..+-..++..+++|++|++.   +-.++.-+.++-.   ..       .|-.....+.++|+++. + +++||+|++-+ 
T Consensus        34 ~~s~~~C~~~I~~~~AD~~~ldgg~vy~Ag~~~y~L~Pi~~E~y~~~~~~~~~Y~aVAVVkk~s~-~-~~~~LrGkkSCH  111 (328)
T pfam00405        34 KSSYLECIQAIAENEADAITLDGGLVYEAGLAPYKLKPVAAEVYGSKEEPQTHYYAVAVVKKGSN-F-QLNQLQGKKSCH  111 (328)
T ss_pred             CCCHHHHHHHHHCCCCCEEEECHHHHHHHHCCCCCCEEEEEECCCCCCCCCCEEEEEEEEECCCC-C-CHHHCCCCCCCC
T ss_conf             89999999999769998898686999986446589866897512577889854899999976887-6-675617986313


Q ss_pred             ----EECCCHHH-HHHHC------------------------CCC-----------------------CCEEECCHHHHH
Q ss_conf             ----31010122-33201------------------------345-----------------------421336855777
Q gi|254781112|r  154 ----QILGTDLS-RFAKE------------------------LKS-----------------------HLVFSHNFEQSL  181 (274)
Q Consensus       154 ----~~~g~~~~-~~l~~------------------------~~~-----------------------~~~~~~~~~~~~  181 (274)
                          -..|+... .++..                        ++.                       ....|..+.-++
T Consensus       112 tg~g~taGw~iPig~l~~~~~~~~~~~~~~~avs~FF~~SCvPGa~~~~~~~LC~lC~G~~~~~C~~~~~e~Y~Gy~GAf  191 (328)
T pfam00405       112 TGLGRSAGWNIPIGLLRPQLPWAIPREPLEKAVSKFFSASCVPGADEGAFPKLCQLCAGDGENKCACSNNEPYFGYSGAF  191 (328)
T ss_pred             CCCCCCCCCCCCHHHHHCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCHHHH
T ss_conf             67787433011289873126757899858899998606246689899878524654789986767899877665740099


Q ss_pred             HHHHHHHHHCCCCCHHHHHHH
Q ss_conf             755443210036655899999
Q gi|254781112|r  182 QLLLSKRTDATMIPDIPFFNF  202 (274)
Q Consensus       182 ~~l~~grvD~~~~~~~~~~~~  202 (274)
                      +-|..|..|++++...++...
T Consensus       192 rCL~eg~GDVAFvkh~tV~en  212 (328)
T pfam00405       192 KCLKDGAGDVAFVKHSTVFEN  212 (328)
T ss_pred             HHHHCCCCCEEEEECCCHHHH
T ss_conf             865318975698705436653


No 92 
>pfam01379 Porphobil_deam Porphobilinogen deaminase, dipyromethane cofactor binding domain.
Probab=86.71  E-value=1.8  Score=22.65  Aligned_cols=138  Identities=19%  Similarity=0.127  Sum_probs=68.6

Q ss_pred             HHHHHHHCCCCCCCH-HCC--CCHHHHHHHCCCC--CCCCCCCCCCCCCCCCCCCCCCCC-CCCCEEEECCCHHHHHHHC
Q ss_conf             988643103221100-003--6756754200233--322222222211122221111123-3432023101012233201
Q gi|254781112|r   93 GLITGLDTNRYDVLV-NVA--ITPERQKKYDFSI--PYIAHRVLLVVRSDQQDIRSFKDL-TDKTVAQILGTDLSRFAKE  166 (274)
Q Consensus        93 ~~~~~l~~g~~D~~~-~~~--~t~eR~~~~~fs~--p~~~~~~~~~~~~~~~~~~~~~dL-~g~~V~~~~g~~~~~~l~~  166 (274)
                      ++.++|.+|++|++. ++-  ++... +.+....  +--....+++.+.    ..++++| +|.+||...-== ...++.
T Consensus        61 ele~aLl~~~iDiAVHS~KDlP~~~~-~~l~i~avl~R~d~rD~Li~~~----~~~l~~lp~ga~IGTSS~RR-~aql~~  134 (213)
T pfam01379        61 ELEEALLNGEIDLAVHSLKDVPTELP-EGLVLGAIPKREDPRDALVSRN----GKSLEDLPEGSVVGTSSLRR-SAQLKR  134 (213)
T ss_pred             HHHHHHHCCCCCEEEEECCCCCCCCC-CCCEEEEEECCCCHHHHHHCCC----CCCHHHCCCCCEEECCCHHH-HHHHHH
T ss_conf             99999970987878760465776479-8746876644788666443026----76665677676553253779-999998


Q ss_pred             --CCCCCEEE-CCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEEC-----CCCCCCCCEEEEEECCCHHHHH
Q ss_conf             --34542133-685577775544321003665589999998458766732623-----6776877079998189989999
Q gi|254781112|r  167 --LKSHLVFS-HNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIA-----DRMKDNSAVAFMMRKGNNKLTR  238 (274)
Q Consensus       167 --~~~~~~~~-~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~k~~~~L~~  238 (274)
                        +..+++.. .|.+..++.|.+|++|+.+....-.    .+...........     .+...+..+++-.+++|.++.+
T Consensus       135 ~~pdl~~~~iRGNV~TRl~KL~~g~~DaiiLA~Agl----~RL~l~~~i~~~l~~~~~~PA~gQGaIaie~r~~d~~i~~  210 (213)
T pfam01379       135 KRPDLKFEPLRGNVDTRLRKLDEGEYDAIILAAAGL----KRLGLEDRITQSLPPEDMLPAVGQGALAIECRKGDEEILA  210 (213)
T ss_pred             HCCCCCEEECCCCHHHHHHHHHCCCCCEEEEHHHHH----HHCCCCCCCCEECCHHHCCCHHHHHHEEEEEECCCHHHHH
T ss_conf             689984677668889999997578987986367678----6668731140671877648837430369988169899999


Q ss_pred             HH
Q ss_conf             99
Q gi|254781112|r  239 SI  240 (274)
Q Consensus       239 ~i  240 (274)
                      .+
T Consensus       211 ll  212 (213)
T pfam01379       211 LL  212 (213)
T ss_pred             HH
T ss_conf             74


No 93 
>PRK00072 hemC porphobilinogen deaminase; Reviewed
Probab=86.25  E-value=2.6  Score=21.64  Aligned_cols=158  Identities=16%  Similarity=0.119  Sum_probs=77.7

Q ss_pred             HHHHHHHCCCCCCCH-HCC--CCHHHHHHHCCC--CCCCCCCCCCCCCCCCCCCCCCCCC-CCCCEEEECCCHHHH---H
Q ss_conf             988643103221100-003--675675420023--3322222222211122221111123-343202310101223---3
Q gi|254781112|r   93 GLITGLDTNRYDVLV-NVA--ITPERQKKYDFS--IPYIAHRVLLVVRSDQQDIRSFKDL-TDKTVAQILGTDLSR---F  163 (274)
Q Consensus        93 ~~~~~l~~g~~D~~~-~~~--~t~eR~~~~~fs--~p~~~~~~~~~~~~~~~~~~~~~dL-~g~~V~~~~g~~~~~---~  163 (274)
                      ++..+|.+|++|++. ++-  ++.. .+.+...  .+--....+++.++    ..++++| +|.+||.    ..-+   .
T Consensus        64 ele~aLl~g~iDiAVHSlKDlPt~~-~~~l~i~avl~R~d~rDvLv~~~----~~~l~~Lp~ga~IGT----SS~RR~aq  134 (300)
T PRK00072         64 ELEEALLDGEIDIAVHSLKDVPTEL-PEGLVLAAIPEREDPRDAFVSND----YASLDDLPEGAVVGT----SSLRRQAQ  134 (300)
T ss_pred             HHHHHHHHCCCCEEEEECCCCCCCC-CCCCEEEEEECCCCHHHHHHCCC----CCCCCCCCCCCEEEC----CCHHHHHH
T ss_conf             9999998287552554134578758-98855876554788678530146----675133899988850----46508999


Q ss_pred             HHC--CCCCCEEE-CCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEE-----CCCCCCCCCEEEEEECCCHH
Q ss_conf             201--34542133-68557777554432100366558999999845876673262-----36776877079998189989
Q gi|254781112|r  164 AKE--LKSHLVFS-HNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKI-----ADRMKDNSAVAFMMRKGNNK  235 (274)
Q Consensus       164 l~~--~~~~~~~~-~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~k~~~~  235 (274)
                      ++.  +..+++.. .|.+..++.|.+|++|+.+....    .+.+..........     ..+...+..+++-.++++.+
T Consensus       135 l~~~~pdl~~~~iRGNv~TRl~Kl~~g~~DaiiLA~A----gl~RL~l~~~i~~~l~~~~~~PA~gQGaiave~r~~d~~  210 (300)
T PRK00072        135 LLALRPDLEIKDLRGNVDTRLRKLDEGEYDAIILAAA----GLKRLGLEDRITELLDPDEMLPAVGQGALGIECRADDEE  210 (300)
T ss_pred             HHHHCCCCCEEECCCCHHHHHHHHHCCCCCEEEHHHH----HHHHCCCCCCEEEEECHHHCCCCCCCCEEEEEEECCCHH
T ss_conf             9986799956776688899999975678645420676----786657854216985533357854630389999449988


Q ss_pred             H---HHHHHHHHHHHHHCCHHHHHHHHHCCCCC
Q ss_conf             9---99999999999979859999987678887
Q gi|254781112|r  236 L---TRSINEILCAIHLDGTYKKIFDRYFDKNI  265 (274)
Q Consensus       236 L---~~~in~~l~~l~~~G~~~~I~~kw~g~d~  265 (274)
                      +   ...+|..-.....  ..|+-+-+-++-+-
T Consensus       211 ~~~~l~~in~~~t~~~~--~aER~~L~~L~ggC  241 (300)
T PRK00072        211 ILELLAPLNHAETRLCV--TAERAFLRALEGGC  241 (300)
T ss_pred             HHHHHHHHCCHHHHHHH--HHHHHHHHHCCCCC
T ss_conf             88776650898899999--99999998639999


No 94 
>COG0040 HisG ATP phosphoribosyltransferase [Amino acid transport and metabolism]
Probab=85.97  E-value=1.4  Score=23.36  Aligned_cols=149  Identities=13%  Similarity=0.122  Sum_probs=75.6

Q ss_pred             HHHHHHHHHCCCCCC-CHHCCCCHHHH---HHHCC--CCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CEEEECCCHHHHH
Q ss_conf             889886431032211-00003675675---42002--33322222222211122221111123343-2023101012233
Q gi|254781112|r   91 VSGLITGLDTNRYDV-LVNVAITPERQ---KKYDF--SIPYIAHRVLLVVRSDQQDIRSFKDLTDK-TVAQILGTDLSRF  163 (274)
Q Consensus        91 ~~~~~~~l~~g~~D~-~~~~~~t~eR~---~~~~f--s~p~~~~~~~~~~~~~~~~~~~~~dL~g~-~V~~~~g~~~~~~  163 (274)
                      ...+-..+..|.+|+ +.|--.-.|+.   ..+..  -.+|-....++-++.+. .+++.+|+.|+ ||+.-.-....+|
T Consensus        52 ~~DIP~yV~~G~~DlGItG~D~l~E~~~~~~~v~~l~dL~fG~crl~vAvp~~~-~~~~~~~l~~~~rIATkYp~l~~~y  130 (290)
T COG0040          52 AQDIPTYVEDGVADLGITGEDVLRESGLDDASVEELLDLGFGGCRLVVAVPEES-DYTSPEDLKGRLRIATKYPNLARKY  130 (290)
T ss_pred             HHHHHHHHHCCCEEEEEECHHHHHHCCCCCCCCEEHCCCCCCCEEEEEEECCCC-CCCCHHHHCCCCEEEECCHHHHHHH
T ss_conf             688448985685004132113133314676571001017877579999955776-7568457268846887368999999


Q ss_pred             HHCCCCC--CEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEEEE-CC-CHHHHHH
Q ss_conf             2013454--213368557777554432100366558999999845876673262367768770799981-89-9899999
Q gi|254781112|r  164 AKELKSH--LVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMR-KG-NNKLTRS  239 (274)
Q Consensus       164 l~~~~~~--~~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-k~-~~~L~~~  239 (274)
                      .++.+.+  ++......+.  +-..|-.|++ +|-.+.-..++.+..    ..+ ....... -++..+ +. ..+-.+.
T Consensus       131 f~~~g~~~~Ii~l~GsvE~--aP~~GlADaI-vDivsTG~TLkaNgL----~~i-d~i~~ss-a~LI~n~~~~~~~k~~~  201 (290)
T COG0040         131 FAEKGIDVEIIKLSGSVEL--APALGLADAI-VDIVSTGTTLKANGL----KEI-EVIYDSS-ARLIVNAKASLKDKQEL  201 (290)
T ss_pred             HHHCCCEEEEEECCCCEEE--CCCCCCCCEE-EEEECCCHHHHHCCC----EEE-EEEEEEE-EEEEECCCCCCCHHHHH
T ss_conf             9975966999975572763--0156853168-885067775897799----887-8898547-89996164232105799


Q ss_pred             HHHHHHHHHH
Q ss_conf             9999999997
Q gi|254781112|r  240 INEILCAIHL  249 (274)
Q Consensus       240 in~~l~~l~~  249 (274)
                      +++-+.+++.
T Consensus       202 i~~l~~rl~g  211 (290)
T COG0040         202 IDQLVTRLKG  211 (290)
T ss_pred             HHHHHHHHHH
T ss_conf             9999999999


No 95 
>PRK10852 thiosulfate transporter subunit; Provisional
Probab=85.60  E-value=2.8  Score=21.44  Aligned_cols=135  Identities=16%  Similarity=0.164  Sum_probs=67.0

Q ss_pred             CCCCCCCCCCCCCCCCCC-CCCCCCCCC--CCCEEEEC----C---CHH-H--HHH-HCCC--------------CCCEE
Q ss_conf             333222222222111222-211111233--43202310----1---012-2--332-0134--------------54213
Q gi|254781112|r  122 SIPYIAHRVLLVVRSDQQ-DIRSFKDLT--DKTVAQIL----G---TDL-S--RFA-KELK--------------SHLVF  173 (274)
Q Consensus       122 s~p~~~~~~~~~~~~~~~-~~~~~~dL~--g~~V~~~~----g---~~~-~--~~l-~~~~--------------~~~~~  173 (274)
                      |.||.. ..+|++|++++ .|++|+||.  |-.|....    |   +++ .  .+. +..+              .++..
T Consensus       115 s~pytS-tivFlVRkGNPK~IkdW~DL~k~gV~VItPNPKTSGgaRwnyLAAwg~a~~~~gg~e~~a~~fv~~l~~NVpV  193 (338)
T PRK10852        115 SSPFYS-TMGFLVRKGNPKNIHDWNDLVRSDVKLIFPNPKTSGNARYTYLAAWGAADKADGGDKAKTEQFMTQFLKNVEV  193 (338)
T ss_pred             CCCEEE-EEEEEEECCCCCCCCCHHHHCCCCCEEECCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCC
T ss_conf             964466-7999980799566877577464897897579988840769999999999986499989999999999836851


Q ss_pred             EC-CHHHHHHHH-HHHHHHCCCCCHHHHHHHHHHCCCCCCCEEECC-CCCCCCCEEEEE----ECCCHHHHHHHHHHHHH
Q ss_conf             36-855777755-443210036655899999984587667326236-776877079998----18998999999999999
Q gi|254781112|r  174 SH-NFEQSLQLL-LSKRTDATMIPDIPFFNFLERRPHDGNLFKIAD-RMKDNSAVAFMM----RKGNNKLTRSINEILCA  246 (274)
Q Consensus       174 ~~-~~~~~~~~l-~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~----~k~~~~L~~~in~~l~~  246 (274)
                      .+ +-..+...+ ..|..|+.+.-+..+....++...+...+.++. ......+.++.=    +++..+..+.    .-+
T Consensus       194 ld~gaR~AT~tF~~rg~GDVLl~~ENEa~l~~~~~g~~~~eiV~Ps~sIlae~pVAvVDk~vdk~GTr~vA~A----yL~  269 (338)
T PRK10852        194 FDTGGRGATTTFAERGLGDVLISFESEVNNIRKQYEAQGFEVVIPKTNILAEFPVAWVDKNVQANGTEKAAKA----YLN  269 (338)
T ss_pred             CCCCCHHHHHHHHHCCCCCEEEEHHHHHHHHHHHHCCCCCEEECCCCCEEECCCEEEEEECCCCCCCHHHHHH----HHH
T ss_conf             5897167889998738675675216789999996089971498899756606974898601234588999999----999


Q ss_pred             HHHCCHHHHHHHHHC
Q ss_conf             997985999998767
Q gi|254781112|r  247 IHLDGTYKKIFDRYF  261 (274)
Q Consensus       247 l~~~G~~~~I~~kw~  261 (274)
                      .--|.+-++|..|.+
T Consensus       270 yLyS~eaQ~i~Ak~~  284 (338)
T PRK10852        270 WLYSPQAQTIITDYY  284 (338)
T ss_pred             HHCCHHHHHHHHHHC
T ss_conf             865989999999808


No 96 
>PRK01686 hisG ATP phosphoribosyltransferase catalytic subunit; Reviewed
Probab=85.54  E-value=0.84  Score=24.65  Aligned_cols=152  Identities=13%  Similarity=0.073  Sum_probs=77.1

Q ss_pred             CCCCCCHHHHHHHHHCCCCCC-CHHCCCCHHHHHHHC--CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCHHH
Q ss_conf             556689889886431032211-000036756754200--23332222222221112222111112334320231010122
Q gi|254781112|r   85 EFFETAVSGLITGLDTNRYDV-LVNVAITPERQKKYD--FSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTDLS  161 (274)
Q Consensus        85 ~~~~~~~~~~~~~l~~g~~D~-~~~~~~t~eR~~~~~--fs~p~~~~~~~~~~~~~~~~~~~~~dL~g~~V~~~~g~~~~  161 (274)
                      ++..+....+-..+..|.+|+ +.|.-+-.|....+.  ....|.....++-++.+   ....++..++||+.-.-....
T Consensus        48 ~~~~~r~~DIp~~V~~G~~DlGI~G~D~l~E~~~~v~~l~dL~fG~c~l~vA~p~~---~~~~~~~~~~rIATkYp~it~  124 (212)
T PRK01686         48 RFLLVRATDVPTYVEHGAADLGIVGKDVLMEHGKDLYEPLDLGIGKCRLSVAVPPG---ASAPDLGARLRVATKYPNIAR  124 (212)
T ss_pred             EEEEECHHHHHHHHHCCCCCEEEEEHHHHHCCCCCCEEEECCCCCEEEEEEEECCC---CCCCCCCCCCEEEEEHHHHHH
T ss_conf             99998768889999779976886158877525899169962686118999995277---775200489899986288899


Q ss_pred             HHHHCCCCCC--EEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEEEECCCHHH-HH
Q ss_conf             3320134542--13368557777554432100366558999999845876673262367768770799981899899-99
Q gi|254781112|r  162 RFAKELKSHL--VFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKGNNKL-TR  238 (274)
Q Consensus       162 ~~l~~~~~~~--~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~L-~~  238 (274)
                      +|..+.+.++  +......+  -+-..|-.|+++ |-...-..++.+..     .+..... ...-.+..++..-.. .+
T Consensus       125 ~yf~~~gi~~~iv~l~GavE--~aP~~G~AD~Iv-Div~TG~TLk~NgL-----~~i~~Il-~s~A~LI~n~~s~~~k~~  195 (212)
T PRK01686        125 EYFAEKGVQVEIIKLYGSVE--LAPLVGLADAIV-DLVSTGNTLRANGL-----VEVEEIM-DISARLIVNKASLKLKRD  195 (212)
T ss_pred             HHHHHCCCCEEEEECCCCCC--CCCCCCCCCEEE-EEECCHHHHHHCCC-----EEEEEEE-EEEEEEEECHHHHHHHHH
T ss_conf             99997399614895415223--567788423899-98477688998799-----9805888-878999996899887699


Q ss_pred             HHHHHHHHHH
Q ss_conf             9999999999
Q gi|254781112|r  239 SINEILCAIH  248 (274)
Q Consensus       239 ~in~~l~~l~  248 (274)
                      .|+..+..++
T Consensus       196 ~I~~li~~l~  205 (212)
T PRK01686        196 EIQPLIEKLR  205 (212)
T ss_pred             HHHHHHHHHH
T ss_conf             9999999999


No 97 
>pfam01634 HisG ATP phosphoribosyltransferase.
Probab=84.94  E-value=1.3  Score=23.43  Aligned_cols=146  Identities=12%  Similarity=0.150  Sum_probs=76.6

Q ss_pred             HHHHHHHCCCCCC-CHHCCCCHHHH-HHH-CC-CCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCEEEECCCHHHHHHHCC
Q ss_conf             9886431032211-00003675675-420-02-333222222222111222211111233-4320231010122332013
Q gi|254781112|r   93 GLITGLDTNRYDV-LVNVAITPERQ-KKY-DF-SIPYIAHRVLLVVRSDQQDIRSFKDLT-DKTVAQILGTDLSRFAKEL  167 (274)
Q Consensus        93 ~~~~~l~~g~~D~-~~~~~~t~eR~-~~~-~f-s~p~~~~~~~~~~~~~~~~~~~~~dL~-g~~V~~~~g~~~~~~l~~~  167 (274)
                      .+-..+..|.+|+ +.|.-+-.|.. +.+ .. ..+|.....++.++++ ..+.+.+|+. ++||+.-.-....+|+.+.
T Consensus         5 DIp~yV~~G~~DlGI~G~D~l~E~~~~~v~~l~dL~fG~crl~vA~p~~-~~~~~~~dl~~~~rIATkYp~it~~~~~~~   83 (161)
T pfam01634         5 DIPVFVEDGVVDLGITGEDLVREEELADVEELLDLDFGSCKLVVAVPES-GPYRSPEDLAGGKRIATKYPNLARKYFRKN   83 (161)
T ss_pred             HHHHHHHCCCCCEEEEEHHHHHCCCCCCEEEEECCCCCCEEEEEEEECC-CCCCCHHHHCCCCEEEEECHHHHHHHHHHC
T ss_conf             8999982899768986722221479787688742687768999996277-775897795479799996539999999981


Q ss_pred             CCC--CEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEEEECCCH-HHHHHHHHHH
Q ss_conf             454--2133685577775544321003665589999998458766732623677687707999818998-9999999999
Q gi|254781112|r  168 KSH--LVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKGNN-KLTRSINEIL  244 (274)
Q Consensus       168 ~~~--~~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~-~L~~~in~~l  244 (274)
                      +.+  ++......++  +-..|-.|+++ |-...-..++.+...     +...... ..-.+..++... .-.+.+++.+
T Consensus        84 gi~~~ii~l~GavE~--aP~~g~AD~Iv-Div~TG~TLk~NgL~-----~i~~I~~-ssA~LI~n~~s~~~k~~~i~~l~  154 (161)
T pfam01634        84 GIDAEIIKLDGSVEA--APALGIADAIV-DLVSTGETLRANGLK-----EIETIMD-SSAVLIANKNSLEEKEQVIDELV  154 (161)
T ss_pred             CCEEEEEECCCCCCC--CCCCCCCCEEE-EEECCHHHHHHCCCE-----EEEEEEE-EEEEEEECCHHHHHHHHHHHHHH
T ss_conf             982689975573344--66667666899-997888999988999-----9179999-89999997246677799999999


Q ss_pred             HHHH
Q ss_conf             9999
Q gi|254781112|r  245 CAIH  248 (274)
Q Consensus       245 ~~l~  248 (274)
                      ..|+
T Consensus       155 ~~l~  158 (161)
T pfam01634       155 TRLQ  158 (161)
T ss_pred             HHHH
T ss_conf             9998


No 98 
>PRK10752 sulfate transporter subunit; Provisional
Probab=84.51  E-value=3.1  Score=21.13  Aligned_cols=182  Identities=14%  Similarity=0.150  Sum_probs=83.7

Q ss_pred             EEHHHHHHHCCCCCCCCCC---CH--HH-HHHHHHCCCCCCCH-HCCCCHHHH-----------HH-HCCCCCCCCCCCC
Q ss_conf             2167899762998555668---98--89-88643103221100-003675675-----------42-0023332222222
Q gi|254781112|r   71 DLIKEVAHRLNLKVEFFET---AV--SG-LITGLDTNRYDVLV-NVAITPERQ-----------KK-YDFSIPYIAHRVL  131 (274)
Q Consensus        71 dl~~~i~~~lg~~~~~~~~---~~--~~-~~~~l~~g~~D~~~-~~~~t~eR~-----------~~-~~fs~p~~~~~~~  131 (274)
                      ...+...++.|-++++...   +-  .| .+++|   +.|++. +....-++-           +. -.=|.||. +..+
T Consensus        42 ~F~~~wk~~tG~~V~i~qShGGSg~QARaVi~Gl---~ADVVtlal~~Did~l~~~GlI~~dW~~~~P~ns~pyt-Stiv  117 (329)
T PRK10752         42 AFSAHWKQQTGDNVVIRQSHGGSGKQATSVINGI---EADVVTLALAYDVDAIAERGRIDKNWIKRLPDNSAPYT-STIV  117 (329)
T ss_pred             HHHHHHHHHHCCCEEEEECCCCCHHHHHHHHCCC---CCCEEEECCHHHHHHHHHCCCCCCCHHHHCCCCCCCEE-EEEE
T ss_conf             9999998832990389855787627899984787---56778751421368998679999145654889996522-3799


Q ss_pred             CCCCCCCC-CCCCCCCCCC--CCEEEEC----CC---HH----HHHHHCCC--------------CCCEEEC-CHHHHHH
Q ss_conf             22111222-2111112334--3202310----10---12----23320134--------------5421336-8557777
Q gi|254781112|r  132 LVVRSDQQ-DIRSFKDLTD--KTVAQIL----GT---DL----SRFAKELK--------------SHLVFSH-NFEQSLQ  182 (274)
Q Consensus       132 ~~~~~~~~-~~~~~~dL~g--~~V~~~~----g~---~~----~~~l~~~~--------------~~~~~~~-~~~~~~~  182 (274)
                      |++|++++ .|++|+||..  -.|....    |.   ++    ...+++.+              .++...+ +-..+..
T Consensus       118 flVRkGNPK~IkdW~DL~k~gV~VItPNPKTSG~aRwn~LAawg~a~~~~gg~e~~a~~fv~~l~~NV~vld~gaR~AT~  197 (329)
T PRK10752        118 FLVRKGNPKQIHDWNDLIKPGVSVITPNPKSSGGARWNYLAAWGYALHHNNNDQAKAQDFVKALYKNVEVLDSGARGSTN  197 (329)
T ss_pred             EEECCCCCCCCCCHHHHCCCCCEEECCCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCCCCCHHHHH
T ss_conf             99718995668774674648978976899887317799999999999724999999999999998368525897346778


Q ss_pred             HH-HHHHHHCCCCCHHHHHHHHHHCCCCCCCEEECCC-CCCCCCEEEEEE-----CCCHHHHHHHHHHHHHHHHCCHHHH
Q ss_conf             55-4432100366558999999845876673262367-768770799981-----8998999999999999997985999
Q gi|254781112|r  183 LL-LSKRTDATMIPDIPFFNFLERRPHDGNLFKIADR-MKDNSAVAFMMR-----KGNNKLTRSINEILCAIHLDGTYKK  255 (274)
Q Consensus       183 ~l-~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~-----k~~~~L~~~in~~l~~l~~~G~~~~  255 (274)
                      .+ ..|..|+.+.-+..+....++...+...+.++.. .....+.++ +.     ++..+..+.    .-+.--+.+-++
T Consensus       198 tF~~rg~GDVLlt~ENEa~l~~~~~g~~~~eiV~P~~silae~pVAv-Vd~~vdk~GTr~~A~a----yl~fLys~eaQ~  272 (329)
T PRK10752        198 TFVERGIGDVLIAWENEALLAANELGKDKFEIVTPSESILAEPTVSV-VDKVVEKKGTREVAEA----YLKYLYSPEGQE  272 (329)
T ss_pred             HHHHCCCCCEEEEHHHHHHHHHHHCCCCCCEEECCCCCEECCCCEEE-EECCCCCCCCHHHHHH----HHHHHCCHHHHH
T ss_conf             99864867557634379999998608998628789963551597599-8344566688999999----999865979999


Q ss_pred             HHHHHC
Q ss_conf             998767
Q gi|254781112|r  256 IFDRYF  261 (274)
Q Consensus       256 I~~kw~  261 (274)
                      |..|.+
T Consensus       273 i~Ak~~  278 (329)
T PRK10752        273 IAAKNY  278 (329)
T ss_pred             HHHHHC
T ss_conf             999808


No 99 
>cd00494 HMBS Hydroxymethylbilane synthase (HMBS), also known as porphobilinogen deaminase (PBGD), is an intermediate enzyme in the biosynthetic pathway of tetrapyrrolic ring systems, such as heme, chlorophylls, and vitamin B12.  HMBS catalyzes the conversion of porphobilinogen (PBG) into hydroxymethylbilane (HMB).  HMBS consists of three domains, and is believed to bind substrate through a hinge-bending motion of domains I and II.  HMBS is found in all organisms except viruses.
Probab=83.92  E-value=3.3  Score=20.97  Aligned_cols=159  Identities=21%  Similarity=0.198  Sum_probs=78.8

Q ss_pred             HHHHHHHHCCCCCCCH-HCC--CCHHHHHHHCCC-C-CCCCCCCCCCCCCCCCCCCCCCCC-CCCCEEEECCCHHHH---
Q ss_conf             8988643103221100-003--675675420023-3-322222222211122221111123-343202310101223---
Q gi|254781112|r   92 SGLITGLDTNRYDVLV-NVA--ITPERQKKYDFS-I-PYIAHRVLLVVRSDQQDIRSFKDL-TDKTVAQILGTDLSR---  162 (274)
Q Consensus        92 ~~~~~~l~~g~~D~~~-~~~--~t~eR~~~~~fs-~-p~~~~~~~~~~~~~~~~~~~~~dL-~g~~V~~~~g~~~~~---  162 (274)
                      .++..+|.+|++|++. ++-  ++.. .+.+... . +--....+++.+++    .++++| +|.+||.    ..-+   
T Consensus        59 kele~aLl~g~iDiAVHSlKDlPt~~-~~gl~i~avl~R~dprDvlv~~~~----~~l~~lp~ga~IGT----SS~RR~a  129 (292)
T cd00494          59 KELEEALLNGEIDLAVHSLKDVPTEL-PEGLVLGAIPKREDPRDALVSRNG----SSLEDLPAGSVVGT----SSLRRQA  129 (292)
T ss_pred             HHHHHHHHCCCCCEEEEECCCCCCCC-CCCCEEEEEECCCCCCCHHHCCCC----HHHHCCCCCCEEEE----CCCCHHH
T ss_conf             99999997098787986046577747-987468766347882224440640----02212898987851----4743799


Q ss_pred             HHHC--CCCCCEEE-CCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEE-----ECCCCCCCCCEEEEEECCCH
Q ss_conf             3201--34542133-6855777755443210036655899999984587667326-----23677687707999818998
Q gi|254781112|r  163 FAKE--LKSHLVFS-HNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFK-----IADRMKDNSAVAFMMRKGNN  234 (274)
Q Consensus       163 ~l~~--~~~~~~~~-~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~~k~~~  234 (274)
                      .++.  +..+++.. .|.+..++.|.+|++|+.+....-    +.+.........     ...+...+..+++-.++++.
T Consensus       130 ql~~~~pdl~i~~iRGNV~TRl~KL~~g~~DaiILA~AG----L~RLgl~~~i~~~l~~~~~~PA~gQGaiave~r~~d~  205 (292)
T cd00494         130 QLKRKRPDLKFEPLRGNVDTRLRKLDEGEYDAIILAAAG----LKRLGLEDRITQYLSPEVMLPAVGQGALAIECRKGDE  205 (292)
T ss_pred             HHHHHCCCCCEEECCCCHHHHHHHHHCCCCCEEEEHHHH----HHHCCCCCCCCCCCCHHCCCCCCCCCEEEEEEECCCH
T ss_conf             999868999546765889999998516787477544656----7554784202300363107887665306888724898


Q ss_pred             H---HHHHHHHHHHHHHHCCHHHHHHHHHCCCCC
Q ss_conf             9---999999999999979859999987678887
Q gi|254781112|r  235 K---LTRSINEILCAIHLDGTYKKIFDRYFDKNI  265 (274)
Q Consensus       235 ~---L~~~in~~l~~l~~~G~~~~I~~kw~g~d~  265 (274)
                      +   +...+|..-.....  +.|+-+-+-+|-+-
T Consensus       206 ~~~~~l~~in~~~t~~~~--~aER~~l~~l~ggC  237 (292)
T cd00494         206 ELLALLKPLNHEETALCV--LAERAFLRELEGGC  237 (292)
T ss_pred             HHHHHHHHHCCHHHHHHH--HHHHHHHHHHCCCC
T ss_conf             888888775587889999--99999999848999


No 100
>PRK09474 malE maltose ABC transporter periplasmic protein; Reviewed
Probab=82.16  E-value=1.1  Score=23.82  Aligned_cols=108  Identities=13%  Similarity=0.158  Sum_probs=52.6

Q ss_pred             HHHHHCHHHHHHCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCCCCCCCH-H-HHHHHHHCCCC-C
Q ss_conf             9984178878858958999628998724870469984889885216789976299855566898-8-98864310322-1
Q gi|254781112|r   28 YYFVIYPFRTEDQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAV-S-GLITGLDTNRY-D  104 (274)
Q Consensus        28 ~~~~~~~~~~~~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~~~~~~~-~-~~~~~l~~g~~-D  104 (274)
                      ..+.+....+.+.++|+|=++.+           .+. .+ ..++++..-+..|++|+++..+. . .+..++..|+. |
T Consensus        16 ~~~~~~~~~~~~~~~ltvW~~~~-----------~~~-~~-l~~~~~~Fe~~~gi~V~v~~~~~~~~kl~~a~~~G~~PD   82 (394)
T PRK09474         16 LMLSASALAKIEEGKLVIWINGD-----------KGY-NG-LAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDGPD   82 (394)
T ss_pred             HHHHCCCCCCCCCCEEEEEECCC-----------HHH-HH-HHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHCCCCCCC
T ss_conf             99736432456678699995797-----------056-99-999999974540977999710268999997420799995


Q ss_pred             CCH----------------HCCCCHHH-HHH------------HCCCCCCCCCCCCCCCCCCC--CCCCCCCCCC
Q ss_conf             100----------------00367567-542------------00233322222222211122--2211111233
Q gi|254781112|r  105 VLV----------------NVAITPER-QKK------------YDFSIPYIAHRVLLVVRSDQ--QDIRSFKDLT  148 (274)
Q Consensus       105 ~~~----------------~~~~t~eR-~~~------------~~fs~p~~~~~~~~~~~~~~--~~~~~~~dL~  148 (274)
                      ++.                .+..+.+- ...            -.|.-|+...+.+++.+++-  ...++++||.
T Consensus        83 v~~~~~~~~~~~a~~G~l~pl~~~~~~~~~~~~~~~~a~tydGk~YgvP~~~~t~~L~YNKdl~~~pP~TwdEl~  157 (394)
T PRK09474         83 IIFWAHDRFGGYAQSGLLAEVTPSKAFQDKLVPFTWDAVRYNGKLIGYPIAVEALSLIYNKDLVPNPPKTWEEIP  157 (394)
T ss_pred             EEEECCHHHHHHHHCCCCCCCCCCHHHHHHCCHHHHHCEEECCEEEEECCCCCCEEEEEEHHHCCCCCCCHHHHH
T ss_conf             899884769999978986638856444530463345246889888886301223068874000368999999999


No 101
>COG2107 Predicted periplasmic solute-binding protein [General function prediction only]
Probab=81.90  E-value=1.2  Score=23.78  Aligned_cols=100  Identities=15%  Similarity=0.121  Sum_probs=51.0

Q ss_pred             CCCCCCCEEEECCCHHHHHHHC--CCCCCEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHH-CCCCC---CCEEECCC
Q ss_conf             1233432023101012233201--345421336855777755443210036655899999984-58766---73262367
Q gi|254781112|r  145 KDLTDKTVAQILGTDLSRFAKE--LKSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLER-RPHDG---NLFKIADR  218 (274)
Q Consensus       145 ~dL~g~~V~~~~g~~~~~~l~~--~~~~~~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~-~~~~~---~~~~~~~~  218 (274)
                      .||+++||++.--.+-...+-+  .+...+.+-..++...++.+|+||+-+.=...-..|.+. .....   ..+.-.  
T Consensus        91 ~~l~~~rvavpG~~TTA~lL~rl~~p~~~~V~m~fdeI~~Avl~G~VDaGvlIHE~~~ty~~~gL~~v~Dl~d~W~~~--  168 (272)
T COG2107          91 KDLKGKRVAVPGEMTTAALLFRLAYPKAEIVYMPFDEIIPAVLEGKVDAGVLIHEEQLTYALYGLKKVLDLGDWWKEK--  168 (272)
T ss_pred             CCCCCCEEECCCCCCHHHHHHHHHCCCCEEEEEEHHHHHHHHHCCCCCCCEEEEEHHCCHHHHCCEEEEEHHHHHHHH--
T ss_conf             655666575678531899999986787369971288878999728876535876010131030815763488999874--


Q ss_pred             CCCCCCEE-EEEECC-CHHHHHHHHHHHHH
Q ss_conf             76877079-998189-98999999999999
Q gi|254781112|r  219 MKDNSAVA-FMMRKG-NNKLTRSINEILCA  246 (274)
Q Consensus       219 ~~~~~~~~-~~~~k~-~~~L~~~in~~l~~  246 (274)
                      ..-+.|+| ++++|+ ..+....|..++.+
T Consensus       169 ~~LPlPLG~~~irk~l~~~~a~~~~~al~~  198 (272)
T COG2107         169 TGLPLPLGCIAIRKDLPKDTAEAIKDALRK  198 (272)
T ss_pred             CCCCCCCCHHHHHCCCCHHHHHHHHHHHHH
T ss_conf             299867513341101899999999999999


No 102
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=80.24  E-value=4.5  Score=20.14  Aligned_cols=152  Identities=13%  Similarity=0.117  Sum_probs=79.2

Q ss_pred             EEHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCCHHCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC---CCCCC
Q ss_conf             216789976299855566898898864310322110000367567542002333222222222111222211---11123
Q gi|254781112|r   71 DLIKEVAHRLNLKVEFFETAVSGLITGLDTNRYDVLVNVAITPERQKKYDFSIPYIAHRVLLVVRSDQQDIR---SFKDL  147 (274)
Q Consensus        71 dl~~~i~~~lg~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~t~eR~~~~~fs~p~~~~~~~~~~~~~~~~~~---~~~dL  147 (274)
                      .++..+.+... ++.+...+.....+.|..|++|++.+......  . -..+.+++....+++++++++...   +++++
T Consensus        83 ~l~~~l~~~aP-~i~l~~~~~~~~~~~L~~~~~Dl~i~~~~~~~--~-~~~~~~L~~d~~v~v~~~~HP~~~~~~t~e~~  158 (266)
T PRK11482         83 VIYQAIKPHYP-QLLLRNIPISDAENQLSQFQTDLIIDTHSCTN--R-TIQHHVLFTDNMVLVCRQGHPCLSLEDDEETL  158 (266)
T ss_pred             HHHHHHHHHCC-CEEEEECCCCCHHHHHHCCCCCEEEECCCCCC--C-CEEEEEEEECCEEEEEECCCCCCCCCCCHHHH
T ss_conf             99999997799-86999568657889985699888985688898--7-63899999428899998968556999999999


Q ss_pred             CCCCEE-E-ECC---CHHHHHHHCCCCC--C-EEECCHHHHHHHHHHHHHHCCC-CCHHHHHHHHHHCCCCCCCEEECCC
Q ss_conf             343202-3-101---0122332013454--2-1336855777755443210036-6558999999845876673262367
Q gi|254781112|r  148 TDKTVA-Q-ILG---TDLSRFAKELKSH--L-VFSHNFEQSLQLLLSKRTDATM-IPDIPFFNFLERRPHDGNLFKIADR  218 (274)
Q Consensus       148 ~g~~V~-~-~~g---~~~~~~l~~~~~~--~-~~~~~~~~~~~~l~~grvD~~~-~~~~~~~~~~~~~~~~~~~~~~~~~  218 (274)
                      ....-. + ..|   +..+..+++.+.+  + ....+...+...+.+  .|++. ++...+..+....+.    .....+
T Consensus       159 ~~~~Hv~~~~~~~~~~~~~~~l~~~~~~R~i~~~~~~~~~~~~lv~~--tdli~~~P~~la~~~~~~~~L----~~lp~p  232 (266)
T PRK11482        159 DNAAHTLLLPEGQNFSGLRQRLQEMFPDRQISFSSYNILTIAALIAS--SDMLGLMPSRFYNLFSRCWPL----EKLPFP  232 (266)
T ss_pred             HCCCCEEEECCCCCCCHHHHHHHHCCCCCEEEEEECCHHHHHHHHHH--CCEEEEHHHHHHHHHHHHCCC----EEECCC
T ss_conf             62999999769998779999999749998599997999999999984--999985899999998876798----794689


Q ss_pred             C--CCCCCEEEEEECC
Q ss_conf             7--6877079998189
Q gi|254781112|r  219 M--KDNSAVAFMMRKG  232 (274)
Q Consensus       219 ~--~~~~~~~~~~~k~  232 (274)
                      +  .....+++.-+|.
T Consensus       233 p~~~~~~~~~l~Wh~r  248 (266)
T PRK11482        233 SLNEEQIDFSLHYNKL  248 (266)
T ss_pred             CCCCCCEEEEEEECCC
T ss_conf             9889964699998855


No 103
>PRK11466 hybrid sensory histidine kinase TorS; Provisional
Probab=79.03  E-value=4.9  Score=19.90  Aligned_cols=76  Identities=12%  Similarity=0.089  Sum_probs=49.3

Q ss_pred             HHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCH-----HHHHHHCCCCCCEEECCHHHHHHHHHHHH-H
Q ss_conf             54200233322222222211122221111123343202310101-----22332013454213368557777554432-1
Q gi|254781112|r  116 QKKYDFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTD-----LSRFAKELKSHLVFSHNFEQSLQLLLSKR-T  189 (274)
Q Consensus       116 ~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~dL~g~~V~~~~g~~-----~~~~l~~~~~~~~~~~~~~~~~~~l~~gr-v  189 (274)
                      -..|.|+-|+-....     ...........+.|.+|-++.+..     ...+++..+.++....|-.+++..+..++ +
T Consensus       653 GS~F~~~LPl~~~~~-----~~~~~~~~~~~~~~lrVLvVEDn~~N~~v~~~~L~~lG~~v~~A~nG~eAle~l~~~~~f  727 (912)
T PRK11466        653 GSCFCLRLPLRHATA-----PVPKTVNQAVRLDGLRLLLIEDNPLTQRITVEMLNTSGAQVVAVGNAAQALETLQNSEPF  727 (912)
T ss_pred             CEEEEEEEECCCCCC-----CCCCCCCCCCCCCCCEEEEEECCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHCCCC
T ss_conf             728999997778887-----876433466577888699994878899999999998699899989999999999718998


Q ss_pred             HCCCCCH
Q ss_conf             0036655
Q gi|254781112|r  190 DATMIPD  196 (274)
Q Consensus       190 D~~~~~~  196 (274)
                      |.+++|-
T Consensus       728 DlVLmDi  734 (912)
T PRK11466        728 AAALVDF  734 (912)
T ss_pred             CEEEECC
T ss_conf             5898769


No 104
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=78.38  E-value=5.1  Score=19.78  Aligned_cols=174  Identities=11%  Similarity=0.054  Sum_probs=96.8

Q ss_pred             HCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHC-CCCCCCCCCCHHHHHHHHHCCCCCCCHHCCCCHHHHH
Q ss_conf             589589996289987248704699848898852167899762-9985556689889886431032211000036756754
Q gi|254781112|r   39 DQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRL-NLKVEFFETAVSGLITGLDTNRYDVLVNVAITPERQK  117 (274)
Q Consensus        39 ~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~l-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~t~eR~~  117 (274)
                      .+++|+||+......             .+..+++....++. ++++++...+..++++.+.+|++|+......  ....
T Consensus        87 ~~g~l~i~~~~~~~~-------------~~l~~~l~~f~~~~P~v~l~l~~~~~~~~~~~l~~~~~D~~i~~~~--~~~~  151 (291)
T PRK10837         87 DNGAIRIYASSTIGN-------------YILPAMIARYRHDYPQLPLELSVGNSQDVIQAVLDFRVDIGLIEGP--CHST  151 (291)
T ss_pred             CCCEEEEEEEHHHHH-------------HHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHCCCCEEEECCC--CCCC
T ss_conf             886299996179999-------------9999999999964899359999888899999998088416674178--8998


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCC---CCCCCCCCCCCEEE-ECCCHH----HHHHHCCCC--C-CEEECCHHHHHHHHHH
Q ss_conf             20023332222222221112222---11111233432023-101012----233201345--4-2133685577775544
Q gi|254781112|r  118 KYDFSIPYIAHRVLLVVRSDQQD---IRSFKDLTDKTVAQ-ILGTDL----SRFAKELKS--H-LVFSHNFEQSLQLLLS  186 (274)
Q Consensus       118 ~~~fs~p~~~~~~~~~~~~~~~~---~~~~~dL~g~~V~~-~~g~~~----~~~l~~~~~--~-~~~~~~~~~~~~~l~~  186 (274)
                      .+ -..|+.....++++..+.+.   --+++||.+..... ..|+..    +.++...+.  + ...+.+.+....++.+
T Consensus       152 ~l-~~~~l~~~~~~~v~~p~~~l~~~~i~~~~l~~~~~i~~~~~~~~r~~~~~~~~~~~~~~~~~~~~~~~~~i~~~v~~  230 (291)
T PRK10837        152 EI-ISEPWLEDELVVFAAPDSPLARGPVTLEQLAAAPWILRERGSGTREIVDYLLLSHLPRFEMAMELGNSEAIKHAVRH  230 (291)
T ss_pred             CE-EEEEEECCCEEEEECCCCHHHCCCCCHHHHHCCCEEEECCCCCHHHHHHHHHHHCCCCCCEEEECCCHHHHHHHHHH
T ss_conf             71-89994414189998788665379999899807987994499868999999998548865301312979999999995


Q ss_pred             HHHHCCCCCHHHHHHHHHHCCCCCCCEEE-CCCCCCCCCEEEEEECCC
Q ss_conf             32100366558999999845876673262-367768770799981899
Q gi|254781112|r  187 KRTDATMIPDIPFFNFLERRPHDGNLFKI-ADRMKDNSAVAFMMRKGN  233 (274)
Q Consensus       187 grvD~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~k~~  233 (274)
                      |.. ..+.+...+...+..-    ....+ .+.+....++++..+|+.
T Consensus       231 G~G-ia~lp~~~v~~~l~~g----~L~~l~~~~~~~~~~~~lv~~k~~  273 (291)
T PRK10837        231 GLG-ISCLSRRVIADQLQAG----TLVEVAVPLPRLMRTLWRIHHRQK  273 (291)
T ss_pred             CCC-EEECCHHHHHHHHHCC----CEEEEECCCCCCCCEEEEEEECCC
T ss_conf             991-8972499999998789----979970788886127999998978


No 105
>TIGR03227 PhnS 2-aminoethylphosphonate ABC transporter, periplasmic 2-aminoethylphosphonate binding protein. This ABC transporter periplasmic substrate binding protein component is found in a region of the salmonella typhimurium LT2 genome responsible for the catabolism of 2-aminoethylphosphonate via the phnWX pathway (GenProp0238). The protein contains a match to pfam01547 for the "Bacterial extracellular solute-binding protein" domain.
Probab=77.86  E-value=3.7  Score=20.68  Aligned_cols=136  Identities=15%  Similarity=0.127  Sum_probs=68.3

Q ss_pred             EEHHHHHHHCCCCCCCCCCCHHHHHHHHH----CCCCCCCHHCCCCHHHHHHHCC----------------------CCC
Q ss_conf             21678997629985556689889886431----0322110000367567542002----------------------333
Q gi|254781112|r   71 DLIKEVAHRLNLKVEFFETAVSGLITGLD----TNRYDVLVNVAITPERQKKYDF----------------------SIP  124 (274)
Q Consensus        71 dl~~~i~~~lg~~~~~~~~~~~~~~~~l~----~g~~D~~~~~~~t~eR~~~~~f----------------------s~p  124 (274)
                      +++.+.-++.|++|+++...-..++.-|+    +.++|++.+....-.|...-..                      -.|
T Consensus        56 ~~~~aFek~tGikV~~v~~~sge~laRl~aEk~nPqaDVv~~~d~~~~~A~~~GLl~py~~~~~~~ip~~~k~~dg~~~~  135 (367)
T TIGR03227        56 DQFDAFEKAEGIKVNIVEAGGGEVVERAAKEKGNPKADVIVTAPPFIQQAAAEGLLANFNSDAAKAIPAIAKAADGLWAP  135 (367)
T ss_pred             HHHHHHHHHHCCEEEEEECCHHHHHHHHHHCCCCCCCEEEEECCHHHHHHHHCCCCCCCCCCCHHHCCHHHHCCCCCEEE
T ss_conf             87688888669838999897799999999522799720999785799999978895627896645577766377983898


Q ss_pred             CCCCCCCCCCCCCC--CCCCCCCCCCC----CCEEEEC----CCHHH----------------HHHHCCCCCCEE-ECCH
Q ss_conf             22222222211122--22111112334----3202310----10122----------------332013454213-3685
Q gi|254781112|r  125 YIAHRVLLVVRSDQ--QDIRSFKDLTD----KTVAQIL----GTDLS----------------RFAKELKSHLVF-SHNF  177 (274)
Q Consensus       125 ~~~~~~~~~~~~~~--~~~~~~~dL~g----~~V~~~~----g~~~~----------------~~l~~~~~~~~~-~~~~  177 (274)
                      +.....++++.++.  ...++++||-.    -+|++..    ++.+.                +++++...+.+. ..+.
T Consensus       136 ~~~~~~~~~yN~~~~k~~PkSW~DL~dP~ykgkI~~~dP~tS~~g~~~l~~~~~~~G~eD~a~~~~~~L~~N~~~~~~s~  215 (367)
T TIGR03227       136 FVKNYFSFAINPKLLKSAPASFADLLDADFKGKLAYSNPAQAADGMAVIILAFALFGSEDAAFAYLAKLEANNKFHSAGT  215 (367)
T ss_pred             EECCEEEEEEEHHHHCCCCCCHHHHHCCCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCEECCCC
T ss_conf             85557999998577057998899872853378289528776617999999999970985388999998874486724781


Q ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHHHHC
Q ss_conf             57777554432100366558999999845
Q gi|254781112|r  178 EQSLQLLLSKRTDATMIPDIPFFNFLERR  206 (274)
Q Consensus       178 ~~~~~~l~~grvD~~~~~~~~~~~~~~~~  206 (274)
                      .....++.+|++.....+...........
T Consensus       216 ~~~~~~~~~GE~~va~g~~~~~~~~~~~~  244 (367)
T TIGR03227       216 GKLNALLNKGEIAVANGDLQMDLADAEHG  244 (367)
T ss_pred             HHHHHHHHCCCEEEEEEECCHHHHHHHHC
T ss_conf             79999985786789952020436777627


No 106
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=75.86  E-value=6  Score=19.34  Aligned_cols=135  Identities=10%  Similarity=0.086  Sum_probs=66.5

Q ss_pred             EEHHHHHHHC-CCCCCCCCCCHHHHHHHHHCCCCCCCHHCCCCHHHHHH-HC----C--CCCCCCCCCCCCCCCCCCCCC
Q ss_conf             2167899762-99855566898898864310322110000367567542-00----2--333222222222111222211
Q gi|254781112|r   71 DLIKEVAHRL-NLKVEFFETAVSGLITGLDTNRYDVLVNVAITPERQKK-YD----F--SIPYIAHRVLLVVRSDQQDIR  142 (274)
Q Consensus        71 dl~~~i~~~l-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~t~eR~~~-~~----f--s~p~~~~~~~~~~~~~~~~~~  142 (274)
                      .+++.+.+.. ++.+++.+.+.+. ++.|..|++|++.+......|... +.    +  ...++.+..+++++++++.++
T Consensus        83 ~l~~~i~~~AP~v~l~~~~~~~~~-~~~L~~g~iDl~i~~~~~~p~~~~~~~~~p~~~~~~~l~~d~~~v~~r~~HP~~~  161 (288)
T PRK10216         83 ALSQQIYQRYPQATIKLRNWDYDS-LDAITRGEVDIGFTGRESHPRSRELLSLLPLAIDFEVLFSDLPCVWLRKDHPALH  161 (288)
T ss_pred             HHHHHHHHHCCCCEEEEECCCCCH-HHHHHCCCCCEEEECCCCCCCCHHHHHCCCCCCCEEEEEEEEEEEEECCCCCCCC
T ss_conf             999999976999779962489355-9999759976898356568630455512764343179996006999808994346


Q ss_pred             ---CCCCCCCCC-EEEE-CC---CHHHHHHHCCCCC--C-EEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHC
Q ss_conf             ---111233432-0231-01---0122332013454--2-13368557777554432100366558999999845
Q gi|254781112|r  143 ---SFKDLTDKT-VAQI-LG---TDLSRFAKELKSH--L-VFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERR  206 (274)
Q Consensus       143 ---~~~dL~g~~-V~~~-~g---~~~~~~l~~~~~~--~-~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~  206 (274)
                         +++++-..+ |.+. .|   +..+..+.+.+.+  + ...++...+..++.....+.+......+..+..+.
T Consensus       162 ~~ltle~y~~~~Hv~v~~~~~~~~~~d~~L~~~g~~R~i~~~~~~f~~~~~~~~~~~~~li~t~p~~a~~~~~~~  236 (288)
T PRK10216        162 EEWNLDTFLRYPHISICWEQSDTWALDDVLQELGRERTIALSLPGFEQSLFMAAQPDHLLLATAPRYCQHYNQLH  236 (288)
T ss_pred             CCCCHHHHHHCCCEEEECCCCCCCHHHHHHHHCCCCCCEEEEECCHHHHHHHHHCCCCCEEEECHHHHHHHHHHC
T ss_conf             898999997589869844888876279999973986517999498898899995689849981099999998764


No 107
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=69.03  E-value=8.7  Score=18.35  Aligned_cols=177  Identities=13%  Similarity=0.146  Sum_probs=89.7

Q ss_pred             HCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHC-CCCCCCCCCCHHHHHHHHHCCCCCCCHHCCCCHHHHH
Q ss_conf             589589996289987248704699848898852167899762-9985556689889886431032211000036756754
Q gi|254781112|r   39 DQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRL-NLKVEFFETAVSGLITGLDTNRYDVLVNVAITPERQK  117 (274)
Q Consensus        39 ~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~l-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~t~eR~~  117 (274)
                      .++.++||+..+...             .+..+++..+.++. ++++++...+...++..|.+|++|+...... + ...
T Consensus        87 ~~~~l~ig~~~~~~~-------------~~l~~~l~~~~~~~P~v~l~l~~~~~~~~~~~L~~~~~Dl~i~~~~-p-~~~  151 (275)
T PRK03601         87 RHNEFSIGASASLWE-------------CMLNQWLGRLYQNQEELQFEARIAQRQSLVKQLHERQLDLLITTEA-P-KMD  151 (275)
T ss_pred             CCCCEEEEEEHHHHH-------------HHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHCCCCCEEEECCC-C-CCC
T ss_conf             776099997757789-------------9999999999997889679999889899999997799358997779-9-888


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCHHH----HHHHCCCCCCEEECCHHHHHHHHHHHHHHCCC
Q ss_conf             20023332222222221112222111112334320231010122----33201345421336855777755443210036
Q gi|254781112|r  118 KYDFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTDLS----RFAKELKSHLVFSHNFEQSLQLLLSKRTDATM  193 (274)
Q Consensus       118 ~~~fs~p~~~~~~~~~~~~~~~~~~~~~dL~g~~V~~~~g~~~~----~~l~~~~~~~~~~~~~~~~~~~l~~grvD~~~  193 (274)
                      .+ -+.+.......+++......-   +++.  -+....|....    ..............+.+...+++..|..=+ +
T Consensus       152 ~l-~~~~l~~~~l~l~~s~~~~~~---~~~~--~i~l~~~~~~~~~~~~~~~~~~~p~~~~~s~~~~~~~v~~g~Gia-~  224 (275)
T PRK03601        152 EF-SSQLLGHFTLALYTSAPSKNK---SELN--YLRLEWGPDFQQHEAGLIGADEVPILTTSSAELARQQLATLNGCA-W  224 (275)
T ss_pred             CE-EEEEECCEEEEEEECCCCCCC---CCCC--EEEEECCCCHHHHHHHHCCCCCCCEEEECHHHHHHHHHHHCCCEE-E
T ss_conf             84-799952356899977864334---6887--588206720679997523567798588578999999999789099-9


Q ss_pred             CCHHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEEEECCCHHHHHHHHHHHH
Q ss_conf             6558999999845876673262367768770799981899899999999999
Q gi|254781112|r  194 IPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKGNNKLTRSINEILC  245 (274)
Q Consensus       194 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~L~~~in~~l~  245 (274)
                      .+...    .+..+   ....+.+.+....+++.+-+|+++. ...|.+.|+
T Consensus       225 LP~~~----~~~~g---~L~~v~~~~~~~rp~y~v~~k~~~~-~~~ir~~l~  268 (275)
T PRK03601        225 LPVHW----AKEKG---GLHTVVDSTTLSRPLYAIWLQNSDK-QALIRDLLK  268 (275)
T ss_pred             CCHHH----HHHCC---CEEECCCCCCCCEEEEEEEECCCCC-HHHHHHHHH
T ss_conf             93788----71189---9899999997714799999688973-799999982


No 108
>COG0181 HemC Porphobilinogen deaminase [Coenzyme metabolism]
Probab=68.75  E-value=8.8  Score=18.32  Aligned_cols=156  Identities=21%  Similarity=0.205  Sum_probs=74.6

Q ss_pred             HHHHHHHCCCCCCCH-HCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCC------CCCCCCCCCCCCEEEECCCHHHH---
Q ss_conf             988643103221100-00367567542002333222222222111222------21111123343202310101223---
Q gi|254781112|r   93 GLITGLDTNRYDVLV-NVAITPERQKKYDFSIPYIAHRVLLVVRSDQQ------DIRSFKDLTDKTVAQILGTDLSR---  162 (274)
Q Consensus        93 ~~~~~l~~g~~D~~~-~~~~t~eR~~~~~fs~p~~~~~~~~~~~~~~~------~~~~~~dL~g~~V~~~~g~~~~~---  162 (274)
                      ++...|.+|++|++. ++---|     ..+..++  .-.++..|.+..      ...++++|   .-|...||+.-+   
T Consensus        63 Ele~all~g~~DiAVHSlKDvP-----~~~p~gL--~laai~~R~dprDalVs~~~~~l~~L---P~Ga~VGTSSlRR~a  132 (307)
T COG0181          63 ELEQALLEGEIDIAVHSLKDVP-----TELPEGL--VLAAIPEREDPRDALVSRDGYDLEEL---PEGAVVGTSSLRRQA  132 (307)
T ss_pred             HHHHHHHCCCCCEEEEECCCCC-----CCCCCCC--EEEEECCCCCHHHEEEECCCCCHHHC---CCCCCCCCCHHHHHH
T ss_conf             9999997699778976044487-----5689993--69996178995366888788856348---998831452687999


Q ss_pred             HHHC--CCCCCEEE-CCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEE-----CCCCCCCCCEEEEEECCCH
Q ss_conf             3201--34542133-68557777554432100366558999999845876673262-----3677687707999818998
Q gi|254781112|r  163 FAKE--LKSHLVFS-HNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKI-----ADRMKDNSAVAFMMRKGNN  234 (274)
Q Consensus       163 ~l~~--~~~~~~~~-~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~~~~~k~~~  234 (274)
                      .++.  +..++... .|.+..++.|.+|.+|+++...    ..+++....+.....     ..+...+..+++-.++++.
T Consensus       133 ql~~~rPdl~i~~lRGNVdTRL~KL~~g~yDAIILA~----AGL~RLgl~~~~~~~l~p~~~~PA~gQGal~ie~R~~d~  208 (307)
T COG0181         133 QLKALRPDLKIEPLRGNVDTRLRKLDEGEYDAIILAA----AGLKRLGLENRITEILDPEEFLPAPGQGALAIECRAGDE  208 (307)
T ss_pred             HHHHHCCCCEEEECCCCHHHHHHHHHCCCCCHHHHHH----HHHHHCCCCCCCEEECCHHHCCCCCCCCEEEEEEECCCH
T ss_conf             9998699976996657688899986167852999999----999862874222063475426898888669999963967


Q ss_pred             H---HHHHHHHHHHHHHHCCHHHHHHHHHCCCC
Q ss_conf             9---99999999999997985999998767888
Q gi|254781112|r  235 K---LTRSINEILCAIHLDGTYKKIFDRYFDKN  264 (274)
Q Consensus       235 ~---L~~~in~~l~~l~~~G~~~~I~~kw~g~d  264 (274)
                      +   +...+|..=..+.-  .-++-+-+.++-.
T Consensus       209 ~~~~ll~~i~~~~t~~~v--~aERa~l~~L~gg  239 (307)
T COG0181         209 KVLELLAELNDEDTRICV--TAERAFLRELEGG  239 (307)
T ss_pred             HHHHHHHHCCCCHHHHHH--HHHHHHHHHHCCC
T ss_conf             899999861582088999--9999999962899


No 109
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=68.07  E-value=9.1  Score=18.23  Aligned_cols=183  Identities=13%  Similarity=0.165  Sum_probs=92.1

Q ss_pred             CCCEEEEECCC-CCCEEEEEECCCCCEEEEEEEEHHHHHHHC-CCCCCCCCCCHHHHHHHHHCCCCCCCHHCCCCHHHHH
Q ss_conf             89589996289-987248704699848898852167899762-9985556689889886431032211000036756754
Q gi|254781112|r   40 QSALRVGTDGI-YPPHSFHAQDGRGELTGFDIDLIKEVAHRL-NLKVEFFETAVSGLITGLDTNRYDVLVNVAITPERQK  117 (274)
Q Consensus        40 ~~~l~v~~~~~-~pP~~~~~~d~~g~~~G~~~dl~~~i~~~l-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~t~eR~~  117 (274)
                      .+.+++++... +.|.             +..+++..+.++. ++++++....+...++.+.++.+|+..++..++....
T Consensus        91 ~g~l~i~~~~~~~~~~-------------~l~~ll~~~~~~~P~v~i~i~~~~~~~~~~~l~~~~~dl~i~~~~~~~~~~  157 (308)
T PRK10094         91 ERQVNIVINNLLYNPQ-------------AVASLLAWLNERYPFTQFHISRQIYMGVWDSLLYEGFSLAIGVTGTEALAN  157 (308)
T ss_pred             CCEEEEEECCHHHHHH-------------HHHHHHHHHHHHCCCCEEEEEECCCCCHHHHHHCCCCCEEEEECCCCCCCC
T ss_conf             5449999522011166-------------799999999997899889999602334799997499729999368877888


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCC-----CCCCCCCCCCCEEEECCCH---HHHHHHCC-CCCCEEECCHHHHHHHHHHHH
Q ss_conf             20023332222222221112222-----1111123343202310101---22332013-454213368557777554432
Q gi|254781112|r  118 KYDFSIPYIAHRVLLVVRSDQQD-----IRSFKDLTDKTVAQILGTD---LSRFAKEL-KSHLVFSHNFEQSLQLLLSKR  188 (274)
Q Consensus       118 ~~~fs~p~~~~~~~~~~~~~~~~-----~~~~~dL~g~~V~~~~g~~---~~~~l~~~-~~~~~~~~~~~~~~~~l~~gr  188 (274)
                      .+. ..|.......+++..+.+.     ..+.++|..........+.   ........ +.....+++.+..+.++.+|-
T Consensus       158 ~~~-~~~l~~~~~~~v~~~~hpla~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~aGl  236 (308)
T PRK10094        158 TFS-LDPLGSVQWRFVMAADHPLANVEEPLTEAQLRRFPAVNIEDSARTLTKRVAWRLPGQKEIIVPDMETKIAAHLAGV  236 (308)
T ss_pred             CEE-EEECCCCHHHHHHCCCCHHHCCCCCCCHHHHHHCCEEEECCCCCCHHHHHEEEECCCCEEEECCHHHHHHHHHHCC
T ss_conf             769-9993130233210789844528999999999619656730651100020125507875499898999999999799


Q ss_pred             HHCCCCCHHHHHHHHHHCCCCCCCE-EECCCCCCCCCEEEEEECCC--HHHHHHHH
Q ss_conf             1003665589999998458766732-62367768770799981899--89999999
Q gi|254781112|r  189 TDATMIPDIPFFNFLERRPHDGNLF-KIADRMKDNSAVAFMMRKGN--NKLTRSIN  241 (274)
Q Consensus       189 vD~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~k~~--~~L~~~in  241 (274)
                      .= .+.+...+..++..-    ..+ ...+....+.+++++-+|++  +.+...++
T Consensus       237 Gi-a~lP~~~v~~~l~~G----~LV~~~l~~~~~~~~l~l~wr~~~~~~~v~~~i~  287 (308)
T PRK10094        237 GI-GFLPKSLCQSMIDNQ----QLVSRVIPTMRPPSPLSLAWRKFGSGKAVEDIVT  287 (308)
T ss_pred             EE-ECCHHHHHHHHHHCC----CEEEEECCCCCCCEEEEEEEECCCCCHHHHHHHH
T ss_conf             88-923499999998789----8899968999998089999977999879999999


No 110
>PRK13583 hisG ATP phosphoribosyltransferase catalytic subunit; Provisional
Probab=67.02  E-value=7.4  Score=18.80  Aligned_cols=121  Identities=13%  Similarity=0.108  Sum_probs=58.5

Q ss_pred             CCCCCCHHHHHHHHHCCCCCC-CHHCCCCHHHHHH----HC--CCCCCCCCCCCCCCCCCCCCCCCCCCCC---------
Q ss_conf             556689889886431032211-0000367567542----00--2333222222222111222211111233---------
Q gi|254781112|r   85 EFFETAVSGLITGLDTNRYDV-LVNVAITPERQKK----YD--FSIPYIAHRVLLVVRSDQQDIRSFKDLT---------  148 (274)
Q Consensus        85 ~~~~~~~~~~~~~l~~g~~D~-~~~~~~t~eR~~~----~~--fs~p~~~~~~~~~~~~~~~~~~~~~dL~---------  148 (274)
                      ++..+....+-..+..|.+|+ +.|.-+-.|....    +.  ....|.....++-++..-..+.+.+||.         
T Consensus        48 ~i~~~r~~DIp~yV~~G~~DlGItG~D~l~E~~~~~~~~v~~~~~LgfG~c~LvvAvP~~w~dv~s~~dl~~~~~~~~~~  127 (226)
T PRK13583         48 ELLFLSASEIPRELGAGRVDLGVTGEDLVREKLADWDKRVEIVARLGFGHADLVVAVPEIWIDVDTMADLDDVAADFRAR  127 (226)
T ss_pred             EEEEECHHHHHHHHHCCCCCEEEEEHHHHHHCCCCCCCCEEEEECCCCCCEEEEEEECCCCCCCCCHHHHHHHHHHHHHC
T ss_conf             89997555689999769865665022555422446145277632178561669999444013554400055664554421


Q ss_pred             -CC--CEEEECCCHHHHHHHCCCCC---CEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCC
Q ss_conf             -43--20231010122332013454---21336855777755443210036655899999984587
Q gi|254781112|r  149 -DK--TVAQILGTDLSRFAKELKSH---LVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPH  208 (274)
Q Consensus       149 -g~--~V~~~~g~~~~~~l~~~~~~---~~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~  208 (274)
                       |+  ||+.-.-....+|..+.+.+   ++......|+  +-.-|-.|++ +|-...-..++.+..
T Consensus       128 ~~~~lrIATkyp~lt~~~f~~~gi~~~~ii~~~GavE~--aP~~GlaD~I-VDiv~TG~TLk~NgL  190 (226)
T PRK13583        128 HGRRLRIATKYWRLTQQFLSQKGVQDYRLVESLGATEG--APAAGSAEII-VDITSTGETLRANHL  190 (226)
T ss_pred             CCCCEEEEECCCHHHHHHHHHCCCCCCEEEECCCCCCC--CCCCCCCCEE-EEEECCHHHHHHCCC
T ss_conf             45414764047326578898669964059977770213--5667873489-998487588998799


No 111
>PRK00178 tolB translocation protein TolB; Provisional
Probab=66.62  E-value=2.8  Score=21.39  Aligned_cols=40  Identities=15%  Similarity=0.241  Sum_probs=19.9

Q ss_pred             CCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCCCCCCC
Q ss_conf             95899962899872487046998488988521678997629985556689
Q gi|254781112|r   41 SALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETA   90 (274)
Q Consensus        41 ~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~~~~~~   90 (274)
                      ..+.|++    +||..   ++.+.   ...++.+.|...|...=.|.+++
T Consensus        34 ~~ipIAI----~pF~~---~~~~~---~~~~i~~iI~~DL~~sG~F~~l~   73 (433)
T PRK00178         34 RAIPIAV----VPFGW---QGGSV---LPEDMAQIIGNDLRNSGYFEPIP   73 (433)
T ss_pred             CEEEEEE----CCCCC---CCCCC---HHHHHHHHHHHHHHCCCCCEECC
T ss_conf             6040698----57666---68762---24899999998886288855248


No 112
>PRK04281 consensus
Probab=65.53  E-value=5.7  Score=19.52  Aligned_cols=41  Identities=17%  Similarity=0.173  Sum_probs=23.4

Q ss_pred             EEEEEEHHHHHHHCCCCCCCCC--CCHHHHHHHHHCCCCCCCH
Q ss_conf             9885216789976299855566--8988988643103221100
Q gi|254781112|r   67 GFDIDLIKEVAHRLNLKVEFFE--TAVSGLITGLDTNRYDVLV  107 (274)
Q Consensus        67 G~~~dl~~~i~~~lg~~~~~~~--~~~~~~~~~l~~g~~D~~~  107 (274)
                      ....++++.+++...+++++=-  .+-+.+...+..|-=-++.
T Consensus        60 ~~~~~~I~~i~~~~~vpi~vGGGIrs~e~~~~ll~~GadkVii  102 (254)
T PRK04281         60 DTILHIIEEVAGQVFIPLTVGGGVRTVADIRRLLNAGADKVSI  102 (254)
T ss_pred             HHHHHHHHHHHHHCCCCEEEECCEEECHHHHHHHHCCCCEEEE
T ss_conf             3089999999850796289977754518899999769988997


No 113
>PRK00830 consensus
Probab=64.18  E-value=4.9  Score=19.89  Aligned_cols=41  Identities=17%  Similarity=0.148  Sum_probs=22.8

Q ss_pred             EEEEEEHHHHHHHCCCCCCCCC--CCHHHHHHHHHCCCCCCCH
Q ss_conf             9885216789976299855566--8988988643103221100
Q gi|254781112|r   67 GFDIDLIKEVAHRLNLKVEFFE--TAVSGLITGLDTNRYDVLV  107 (274)
Q Consensus        67 G~~~dl~~~i~~~lg~~~~~~~--~~~~~~~~~l~~g~~D~~~  107 (274)
                      ....++++.+++...+++++=-  .+-+.+...+..|-=-++.
T Consensus        64 ~~~~~~I~~i~~~~~~pi~vGGGIrs~e~~~~ll~~GadkVvI  106 (273)
T PRK00830         64 ATMIDVIERTAEEVFIPLTVGGGIRSIEDIRQILRAGADKVSV  106 (273)
T ss_pred             CCHHHHHHHHHHHCCCCEEEECCEEECCCHHHHHHCCCCEEEC
T ss_conf             4279999999986699589608843773289999769863983


No 114
>TIGR02743 TraW type-F conjugative transfer system protein TraW; InterPro: IPR014114   This entry represents TraW, an essential component of the F-type conjugative transfer system for plasmid DNA transfer that has been shown to be localized to the periplasm , ..
Probab=62.70  E-value=8.8  Score=18.34  Aligned_cols=66  Identities=8%  Similarity=0.189  Sum_probs=29.5

Q ss_pred             EEEHHHHHHHCC-CCCCCCCCCHHHHHHHHHCCCCC------CCHHCCCCHHHHH-H----HCCCCCCCCCCCCCCCCCC
Q ss_conf             521678997629-98555668988988643103221------1000036756754-2----0023332222222221112
Q gi|254781112|r   70 IDLIKEVAHRLN-LKVEFFETAVSGLITGLDTNRYD------VLVNVAITPERQK-K----YDFSIPYIAHRVLLVVRSD  137 (274)
Q Consensus        70 ~dl~~~i~~~lg-~~~~~~~~~~~~~~~~l~~g~~D------~~~~~~~t~eR~~-~----~~fs~p~~~~~~~~~~~~~  137 (274)
                      .|+++.|-++|. ++-   .-.++++...+++.-..      .+.+++.|.+-+- +    +.++..+.....-+++++|
T Consensus        34 ~D~L~~I~~rL~~l~~---sGe~~~~~q~~~~rv~e~v~rP~pv~~l~~t~~~~t~~~DPS~tl~~di~d~~G~v~~k~G  110 (217)
T TIGR02743        34 PDMLEVIEQRLKRLEQ---SGELKAMQQRFQERVLEHVKRPPPVPGLSTTETPKTFYFDPSITLARDILDEKGQVLAKKG  110 (217)
T ss_pred             HHHHHHHHHHHHHHHC---CCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEECCEEEECCCCCCCCCEEEECCC
T ss_conf             7799999999998612---4018999999999999860387876887665665168856727706476598851887068


Q ss_pred             C
Q ss_conf             2
Q gi|254781112|r  138 Q  138 (274)
Q Consensus       138 ~  138 (274)
                      .
T Consensus       111 t  111 (217)
T TIGR02743       111 T  111 (217)
T ss_pred             E
T ss_conf             0


No 115
>COG2998 TupB ABC-type tungstate transport system, permease component [Coenzyme metabolism]
Probab=62.15  E-value=6.2  Score=19.28  Aligned_cols=93  Identities=17%  Similarity=0.262  Sum_probs=54.4

Q ss_pred             HHHCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCCHHCCCCHHHH
Q ss_conf             88589589996289987248704699848898852167899762998555668988988643103221100003675675
Q gi|254781112|r   37 TEDQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVSGLITGLDTNRYDVLVNVAITPERQ  116 (274)
Q Consensus        37 ~~~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~t~eR~  116 (274)
                      ..+...||+++...        .+.+    |+.-++.-..-+..|++++++.+--...+++=+.|.+|++.--++  .++
T Consensus        26 sa~~~~LrmATTTS--------t~dt----GLLd~l~p~fE~~~g~~v~~vAvGTG~ALkmge~gdvDvv~vHap--k~E   91 (280)
T COG2998          26 SADAAELRMATTTS--------TEDT----GLLDVLLPKFEKYTGYDVQVVAVGTGKALKMGERGDVDVVIVHAP--KAE   91 (280)
T ss_pred             CCCCCEEEEEEECC--------CCCC----CCHHHHHHHHHHCCCCEEEEEEECCHHHHHHHCCCCCCEEEEECC--HHH
T ss_conf             75420378854302--------4556----318887776643369658999812358775112688678998370--778


Q ss_pred             HHHC---C---CCCCCCCCCCCCCCCCCC-CCCC
Q ss_conf             4200---2---333222222222111222-2111
Q gi|254781112|r  117 KKYD---F---SIPYIAHRVLLVVRSDQQ-DIRS  143 (274)
Q Consensus       117 ~~~~---f---s~p~~~~~~~~~~~~~~~-~~~~  143 (274)
                      +.|.   |   ..|+...-..++-+++.+ .+++
T Consensus        92 ~~fv~~G~gv~r~~vmYNdFiiVgp~~dpA~~k~  125 (280)
T COG2998          92 KEFVKDGFGVDRRPVMYNDFIIVGPADDPAGIKD  125 (280)
T ss_pred             HHHHHCCCCCCCCCEEEEEEEEECCCCCCHHCCC
T ss_conf             9998727886676101311799877666111122


No 116
>PRK01033 imidazole glycerol phosphate synthase subunit HisF; Provisional
Probab=61.49  E-value=6.3  Score=19.23  Aligned_cols=41  Identities=12%  Similarity=0.057  Sum_probs=24.9

Q ss_pred             EEEEEEHHHHHHHCCCCCCCCC--CCHHHHHHHHHCCCCCCCH
Q ss_conf             9885216789976299855566--8988988643103221100
Q gi|254781112|r   67 GFDIDLIKEVAHRLNLKVEFFE--TAVSGLITGLDTNRYDVLV  107 (274)
Q Consensus        67 G~~~dl~~~i~~~lg~~~~~~~--~~~~~~~~~l~~g~~D~~~  107 (274)
                      +...++++.+++...+++++--  .+-++....+..|-=-++.
T Consensus        60 ~~n~~~I~~I~~~~~ipi~vGGGIrs~e~~~~ll~~GadkVii  102 (253)
T PRK01033         60 EPNYELIENLASECFMPLCYGGGIKTVEQAKRIFSLGVEKVSI  102 (253)
T ss_pred             CCHHHHHHHHHHHCCCCEEEECCCCCHHHHHHHHHCCCCEEEE
T ss_conf             0169999999987699889868812168889998679866999


No 117
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=61.48  E-value=12  Score=17.46  Aligned_cols=52  Identities=8%  Similarity=0.106  Sum_probs=40.9

Q ss_pred             CCCCCCCEEEECCCH-----HHHHHHCCCCCCEEECCHHHHHHHHHHHHHHCCCCCH
Q ss_conf             123343202310101-----2233201345421336855777755443210036655
Q gi|254781112|r  145 KDLTDKTVAQILGTD-----LSRFAKELKSHLVFSHNFEQSLQLLLSKRTDATMIPD  196 (274)
Q Consensus       145 ~dL~g~~V~~~~g~~-----~~~~l~~~~~~~~~~~~~~~~~~~l~~grvD~~~~~~  196 (274)
                      ..+.+.+|-++-+..     ...++++.+.++..+.|-.+++.++..+++|.+++|-
T Consensus       521 ~~~~~lrILvVEDn~iN~~V~~~~L~~lG~~v~~A~nG~eALe~~~~~~fDLILMDi  577 (779)
T PRK11091        521 MPLPALNILLVEDIELNVIVARSLLEKLGNSVDVAMTGKDALEMFKPGEYDLVLLDI  577 (779)
T ss_pred             CCCCCCEEEEECCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHCCCCCCEEEEEC
T ss_conf             688888189986889999999999997599999989999999985069999899828


No 118
>TIGR02294 nickel_nikA nickel ABC transporter, periplasmic nickel-binding protein; InterPro: IPR011980    Members of this family are periplasmic nickel-binding proteins of nickel ABC transporters. Nickel is bound specifically, albeit weakly, through water molecules positioned in the binding site. The amino acids whose side chains line the binding site include Tyr-44, Met-49, Trp-122, Arg-159, Trp-420, and Tyr-424 (numbering based on the precursor sequence of Escherichia coli NikA) with the Arg contributing a hydrogen bond indirectly through a water molecule ..
Probab=60.39  E-value=5.8  Score=19.44  Aligned_cols=78  Identities=9%  Similarity=0.055  Sum_probs=53.0

Q ss_pred             CCEEECCHHHHHHHHHHHHHHCCCCC----HHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEEEEC-C----CHHHHHHH
Q ss_conf             42133685577775544321003665----589999998458766732623677687707999818-9----98999999
Q gi|254781112|r  170 HLVFSHNFEQSLQLLLSKRTDATMIP----DIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRK-G----NNKLTRSI  240 (274)
Q Consensus       170 ~~~~~~~~~~~~~~l~~grvD~~~~~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k-~----~~~L~~~i  240 (274)
                      .+...++.+..+.++.+|++|.+.++    ..+....+.+...+..+......|....-+.+=-.+ +    +...+.+|
T Consensus       201 ~vKVIPD~~TR~LAfe~Ge~dLi~G~~rGtG~i~~DtF~ql~~~~~Y~t~lS~P~~Tr~L~lNt~~kd~~~~Dl~VR~A~  280 (513)
T TIGR02294       201 TVKVIPDAETRALAFESGEVDLIFGNERGTGVIDLDTFAQLKEDGKYQTALSQPMETRMLLLNTGKKDEATSDLAVRQAL  280 (513)
T ss_pred             EEEEECCHHHHHHHHHCCCCCEEECCCCCCCCCCHHHHHHHHCCCCCCEECCCCHHHHHHHHHCCCCCCHHHHHHHHHHH
T ss_conf             78873673368887631861023236656740142257763128773201047511245433220102200026899997


Q ss_pred             HHHHHHH
Q ss_conf             9999999
Q gi|254781112|r  241 NEILCAI  247 (274)
Q Consensus       241 n~~l~~l  247 (274)
                      |.++.+-
T Consensus       281 nhavnK~  287 (513)
T TIGR02294       281 NHAVNKQ  287 (513)
T ss_pred             HHCCCHH
T ss_conf             4034768


No 119
>PRK10693 response regulator of RpoS; Provisional
Probab=58.24  E-value=9.6  Score=18.11  Aligned_cols=34  Identities=12%  Similarity=0.048  Sum_probs=16.1

Q ss_pred             EHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCC
Q ss_conf             16789976299855566898898864310322110
Q gi|254781112|r   72 LIKEVAHRLNLKVEFFETAVSGLITGLDTNRYDVL  106 (274)
Q Consensus        72 l~~~i~~~lg~~~~~~~~~~~~~~~~l~~g~~D~~  106 (274)
                      ++..+.++.|+++.. ..+-...++.++....|++
T Consensus        22 ~l~~~L~~~G~~V~~-A~nG~eAl~~l~~~~pDLI   55 (337)
T PRK10693         22 LLDSWFSSLGATTVL-AADGVDALELLGGFTPDLM   55 (337)
T ss_pred             HHHHHHHHCCCEEEE-ECCHHHHHHHHHCCCCCEE
T ss_conf             999999978999999-8999999999865899999


No 120
>PRK02145 consensus
Probab=56.50  E-value=7.6  Score=18.74  Aligned_cols=42  Identities=19%  Similarity=0.192  Sum_probs=25.9

Q ss_pred             EEEEEEHHHHHHHCCCCCCCCC--CCHHHHHHHHHCCCCCCCHH
Q ss_conf             9885216789976299855566--89889886431032211000
Q gi|254781112|r   67 GFDIDLIKEVAHRLNLKVEFFE--TAVSGLITGLDTNRYDVLVN  108 (274)
Q Consensus        67 G~~~dl~~~i~~~lg~~~~~~~--~~~~~~~~~l~~g~~D~~~~  108 (274)
                      +...++++.+++...+++++=-  .+-+++...+..|---++.+
T Consensus        61 ~~~~~~I~~i~~~~~iPi~vGGGIrs~e~~~~ll~~GadkVii~  104 (257)
T PRK02145         61 DLILPIIEAVASQVFIPLTVGGGVRAVEDVRRLLNAGADKVSMN  104 (257)
T ss_pred             HHHHHHHHHHHHHCCCCEEEECCCCCHHHHHHHHHCCCCEEEEH
T ss_conf             40899999999656874896277304688999998199889841


No 121
>PRK03629 tolB translocation protein TolB; Provisional
Probab=56.38  E-value=4.6  Score=20.08  Aligned_cols=36  Identities=25%  Similarity=0.240  Sum_probs=17.7

Q ss_pred             CEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCCCC
Q ss_conf             5899962899872487046998488988521678997629985556
Q gi|254781112|r   42 ALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFF   87 (274)
Q Consensus        42 ~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~~~   87 (274)
                      .+.|++    +||.+..   .+   ....|+.+.|...|...=.|.
T Consensus        34 ~~PIAV----~pF~~~g---~~---~~~~~i~~II~~DL~rSG~F~   69 (430)
T PRK03629         34 ARPIGV----VPFKWAG---PG---AAPEDIGGIVAADLRNSGKFN   69 (430)
T ss_pred             CCCEEE----ECCCCCC---CC---CCHHHHHHHHHHHHHHCCCCE
T ss_conf             325699----2864478---88---646789999987687577815


No 122
>PRK01742 tolB translocation protein TolB; Provisional
Probab=55.07  E-value=7.2  Score=18.86  Aligned_cols=20  Identities=25%  Similarity=0.185  Sum_probs=11.6

Q ss_pred             EEEHHHHHHHCCCCCCCCCC
Q ss_conf             52167899762998555668
Q gi|254781112|r   70 IDLIKEVAHRLNLKVEFFET   89 (274)
Q Consensus        70 ~dl~~~i~~~lg~~~~~~~~   89 (274)
                      .|+.+-|...|...=.|.+.
T Consensus        54 ~~i~~vI~~DL~~SG~F~~i   73 (430)
T PRK01742         54 EDIAKIIAADLRNSGKFNPI   73 (430)
T ss_pred             HHHHHHHHHHHHCCCCCCCC
T ss_conf             78999998777608472625


No 123
>PRK01659 consensus
Probab=55.05  E-value=9.6  Score=18.09  Aligned_cols=42  Identities=17%  Similarity=0.204  Sum_probs=24.9

Q ss_pred             EEEEEEHHHHHHHCCCCCCCCC--CCHHHHHHHHHCCCCCCCHH
Q ss_conf             9885216789976299855566--89889886431032211000
Q gi|254781112|r   67 GFDIDLIKEVAHRLNLKVEFFE--TAVSGLITGLDTNRYDVLVN  108 (274)
Q Consensus        67 G~~~dl~~~i~~~lg~~~~~~~--~~~~~~~~~l~~g~~D~~~~  108 (274)
                      +...++++.+++...+++++=-  .+-+.....+..|-=-++.+
T Consensus        60 ~~n~~~I~~i~~~~~ipi~vGGGIrs~e~~~~~l~~GadkViig  103 (252)
T PRK01659         60 KTMVDVVEKVAAKVFIPLTVGGGISSVKDMKRLLRAGADKVSIN  103 (252)
T ss_pred             HHHHHHHHHHHHHCCCCEEEECCEECHHHHHHHHHCCCCEEEEC
T ss_conf             64899999999756974799633200688889874488559831


No 124
>PRK10653 D-ribose transporter subunit RbsB; Provisional
Probab=53.55  E-value=11  Score=17.65  Aligned_cols=61  Identities=11%  Similarity=0.218  Sum_probs=32.6

Q ss_pred             HHHHCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCCCCCCC--HH---HHHHHHHCCCCCCCH
Q ss_conf             7885895899962899872487046998488988521678997629985556689--88---988643103221100
Q gi|254781112|r   36 RTEDQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETA--VS---GLITGLDTNRYDVLV  107 (274)
Q Consensus        36 ~~~~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~~~~~~--~~---~~~~~l~~g~~D~~~  107 (274)
                      .+..+++|=+.+..---|| |...          ++=++..+++.|+++-+....  .+   +.++.+...++|++.
T Consensus        22 ~a~a~~TIgvivp~i~npf-f~~v----------~~gie~~a~~~Gy~l~v~~s~~d~~~q~~~i~~li~~~vdgii   87 (295)
T PRK10653         22 NAMAKDTIALVVSTLNNPF-FVSL----------KDGAQKEADKLGYNLVVLDSQNNPAKELANVQDLTVRGTKILL   87 (295)
T ss_pred             HHHCCCEEEEEECCCCCHH-HHHH----------HHHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHHCCCCEEE
T ss_conf             7752997999948987979-9999----------9999999997699899983999999999999999976998899


No 125
>PRK13738 conjugal transfer pilus assembly protein TraW; Provisional
Probab=53.52  E-value=17  Score=16.64  Aligned_cols=55  Identities=11%  Similarity=0.239  Sum_probs=26.0

Q ss_pred             HHHHHHHCHHHHHHCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCC-CCCCCCCCCHHHHHHHHHCC
Q ss_conf             99998417887885895899962899872487046998488988521678997629-98555668988988643103
Q gi|254781112|r   26 FSYYFVIYPFRTEDQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLN-LKVEFFETAVSGLITGLDTN  101 (274)
Q Consensus        26 ~~~~~~~~~~~~~~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg-~~~~~~~~~~~~~~~~l~~g  101 (274)
                      ++.+..+.+.+|++-|++    ...| |.  .           +.|++..|-+++. ++   ..-.|+++.+.+++.
T Consensus         7 ~~~~~~~~~~~AkDlG~~----G~t~-pI--~-----------E~DlL~~I~~RL~~~e---~sGel~~~q~~~~~r   62 (210)
T PRK13738          7 IALLIWGQSVAAADLGTW----GDLW-PV--K-----------EPDMLTVIMQRLTALE---QSGEMGRKMDAFKER   62 (210)
T ss_pred             HHHHHHCCHHHHHHCCCC----CCCC-CC--C-----------CHHHHHHHHHHHHHHH---HCCHHHHHHHHHHHH
T ss_conf             999996743247645764----4542-63--5-----------2779999999999878---577499999999999


No 126
>PRK11899 prephenate dehydratase; Provisional
Probab=53.47  E-value=9.6  Score=18.11  Aligned_cols=113  Identities=7%  Similarity=0.087  Sum_probs=53.4

Q ss_pred             CCCCC-CCHHHHHHHHHCCCCCCC-HHC------CCCHHHHHHHCCCC------CCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             55566-898898864310322110-000------36756754200233------32222222221112222111112334
Q gi|254781112|r   84 VEFFE-TAVSGLITGLDTNRYDVL-VNV------AITPERQKKYDFSI------PYIAHRVLLVVRSDQQDIRSFKDLTD  149 (274)
Q Consensus        84 ~~~~~-~~~~~~~~~l~~g~~D~~-~~~------~~t~eR~~~~~fs~------p~~~~~~~~~~~~~~~~~~~~~dL~g  149 (274)
                      .+.++ .+++.+++++++|++|.. ..+      ++.+- .+-+.-+.      -++.....++.+++.. +.++..+..
T Consensus        28 ~~~v~~~s~~~vf~aV~~g~~d~gvvPiENS~eG~V~~~-~dll~~~~l~I~~E~~l~I~h~L~~~~~~~-l~~I~~VyS  105 (284)
T PRK11899         28 MEPLPCATFEDAFEAVESGEADLAMIPIENSLAGRVADI-HHLLPESGLHIVGEYFLPIHHQLMALPGAT-LEDIKTVHS  105 (284)
T ss_pred             CCEECCCCHHHHHHHHHCCCCCEEEEEECCCCEEEHHHH-HHHHCCCCCEEEEEEEEEEEEEEEECCCCC-HHHCEEEEE
T ss_conf             736606999999999977998879986416764756888-987573898799988650114564079998-541779997


Q ss_pred             CCEEEECCCH-HHHHHHCCCCCCEEECCHHHHHHHHHH--HHHHCCCCCHHHHHHH
Q ss_conf             3202310101-223320134542133685577775544--3210036655899999
Q gi|254781112|r  150 KTVAQILGTD-LSRFAKELKSHLVFSHNFEQSLQLLLS--KRTDATMIPDIPFFNF  202 (274)
Q Consensus       150 ~~V~~~~g~~-~~~~l~~~~~~~~~~~~~~~~~~~l~~--grvD~~~~~~~~~~~~  202 (274)
                      +    ..... ..+|+++++.+.+.+.+...+.+.+..  .+-.++++...-+..|
T Consensus       106 H----Pqal~QC~~~L~~~~~~~~~~~sta~Aa~~v~~~~~~~~AAI~s~~aa~~y  157 (284)
T PRK11899        106 H----PHALGQCRKIIRALGLKPVVAADTAGAAREVAERGDPSMAALASRLAAELY  157 (284)
T ss_pred             E----HHHHHHHHHHHHHCCCCEEEECCCHHHHHHHHHCCCCCEEECCHHHHHHHC
T ss_conf             5----489999999999769824994380999999996699870110608565224


No 127
>TIGR02144 LysX_arch Lysine biosynthesis enzyme LysX; InterPro: IPR011870    The family of proteins found in this family include the characterised LysX from Thermus thermophilus  which is part of a well-organised lysine biosynthesis gene cluster . LysX is believed to carry out an ATP-dependent acylation of the amino group of alpha-aminoadipate in the prokaryotic version of the fungal AAA lysine biosynthesis pathway. No species having a sequence in this family contains the elements of the more common diaminopimelate lysine biosythesis pathway, and none has been shown to be a lysine auxotroph. These sequences have mainly recieved the name of the related enzyme, "ribosomal protein S6 modification protein RimK". RimK has been characterised in Escherichia coli, and acts by ATP-dependent condensation of S6 with glutamate residues .; GO: 0003824 catalytic activity, 0005524 ATP binding, 0009085 lysine biosynthetic process.
Probab=53.46  E-value=7.7  Score=18.69  Aligned_cols=34  Identities=18%  Similarity=0.243  Sum_probs=28.0

Q ss_pred             EEEEEHHHHHHHCCCCCCCCCC--CHHHHHHHHHCC
Q ss_conf             8852167899762998555668--988988643103
Q gi|254781112|r   68 FDIDLIKEVAHRLNLKVEFFET--AVSGLITGLDTN  101 (274)
Q Consensus        68 ~~~dl~~~i~~~lg~~~~~~~~--~~~~~~~~l~~g  101 (274)
                      |+.+=+..++++||+++-++|+  +|.|++.-+++.
T Consensus       110 ~d~~~A~~~~e~lGYPvV~KP~~GSWGRlV~~~~d~  145 (289)
T TIGR02144       110 FDREAALKAAEELGYPVVLKPVIGSWGRLVSKIRDK  145 (289)
T ss_pred             ECHHHHHHHHHHCCCCEEEECCCCCHHHHHHHHCCH
T ss_conf             286899999997089889708888437887640378


No 128
>pfam06510 DUF1102 Protein of unknown function (DUF1102). This family consists of several hypothetical archaeal proteins of unknown function.
Probab=53.25  E-value=16  Score=16.79  Aligned_cols=10  Identities=20%  Similarity=0.527  Sum_probs=6.2

Q ss_pred             CEEEEEECCCCC
Q ss_conf             724870469984
Q gi|254781112|r   53 PHSFHAQDGRGE   64 (274)
Q Consensus        53 P~~~~~~d~~g~   64 (274)
                      ||.|.+  .+|+
T Consensus        52 PY~yi~--~~Gk   61 (183)
T pfam06510        52 PYVYLN--NNGK   61 (183)
T ss_pred             CEEEEC--CCCE
T ss_conf             458984--7984


No 129
>TIGR00070 hisG ATP phosphoribosyltransferase; InterPro: IPR001348   ATP phosphoribosyltransferase (2.4.2.17 from EC) is the enzyme that catalyzes the first step in the biosynthesis of histidine in bacteria, fungi and plants as shown below. It is a member of the larger phosphoribosyltransferase superfamily of enzymes which catalyse the condensation of 5-phospho-alpha-D-ribose 1-diphosphate with nitrogenous bases in the presence of divalent metal ions .  ATP + 5-phospho-alpha-D-ribose 1-diphosphate = 1-(5-phospho-D-ribosyl)-ATP + diphosphate  Histidine biosynthesis is an energetically expensive process and ATP phosphoribosyltransferase activity is subject to control at several levels. Transcriptional regulation is based primarily on nutrient conditions and determines the amount of enzyme present in the cell, while feedback inihibition rapidly modulates activity in response to cellular conditions. The enzyme has been shown to be inhibited by 1-(5-phospho-D-ribosyl)-ATP, histidine, ppGpp (a signal associated with adverse environmental conditions) and ADP and AMP (which reflect the overall energy status of the cell). As this pathway of histidine biosynthesis is present only in prokayrotes, plants and fungi, this enzyme is a promising target for the development of novel antimicrobial compounds and herbicides.   This entry represents the two forms of ATP phosphoribosyltransferase: a long form containing two catalytic domains and a C-terminal regulatory domain, and a short form in which the regulatory domain is missing. The long form is catalytically competent, but in organisms with the short form, a histidyl-tRNA synthetase paralogue, HisZ, is required for enzyme activity .   The structures of the long form enzymes from Escherichia coli (P60757 from SWISSPROT) and Mycobacterium tuberculosis (P60759 from SWISSPROT) have been determined , . The enzyme itself exists in equilibrium between an active dimeric form, an inactive hexameric form and higher aggregates. Interconversion between the various forms is largely reversible and is influenced by the binding of the natural substrates and inhibitors of the enzyme. The two catalytic domains are linked by a two-stranded beta-sheet and togther form a "periplamsic binding protein fold". A crevice between these domains contains the active site. The C-terminal domain is not directly involved in catalysis but appears to be involved the formation of hexamers, induced by the binding of inhibitors such as histidine to the enzyme, thus regulating activity.; GO: 0003879 ATP phosphoribosyltransferase activity, 0000105 histidine biosynthetic process.
Probab=52.66  E-value=4.7  Score=20.02  Aligned_cols=147  Identities=15%  Similarity=0.171  Sum_probs=85.6

Q ss_pred             HHHHCCCCCC-CHHCCCCHH----HHHH-----HCCC--CCCCCCCCCCCCCCCC-CCCCCCCCCC----CC--CEEEEC
Q ss_conf             6431032211-000036756----7542-----0023--3322222222211122-2211111233----43--202310
Q gi|254781112|r   96 TGLDTNRYDV-LVNVAITPE----RQKK-----YDFS--IPYIAHRVLLVVRSDQ-QDIRSFKDLT----DK--TVAQIL  156 (274)
Q Consensus        96 ~~l~~g~~D~-~~~~~~t~e----R~~~-----~~fs--~p~~~~~~~~~~~~~~-~~~~~~~dL~----g~--~V~~~~  156 (274)
                      ..+..|.+|+ +.|.-.-.|    |...     +..-  .+|-.....+-+..+. +.+++++||+    |+  +|+.-.
T Consensus        58 ~~V~~G~aDlGI~G~D~l~EE~L~~~~~~~~~~V~~l~dL~fG~c~L~vA~p~~~yP~~~~~~dl~~kvGg~ev~IAT~F  137 (317)
T TIGR00070        58 TYVEDGVADLGITGEDVLREELLNRNVDSELKNVEILEDLNFGGCKLVVAVPEDSYPDYRGPEDLKEKVGGKEVRIATEF  137 (317)
T ss_pred             HHHHCCCEEEEEECCEEEEECHHCCCCCCCCCHHHHHHHCCCCCCEEEEECCCCCCCCCCCCCCCHHCCCCCEEEEEECC
T ss_conf             13226625334861024431011131114652325553268997136887470137876873000121589648998267


Q ss_pred             CCHHHHHHHCCC------CC--CEEECCHHHHHHHHHHHH--HHCCCCCHHHHHHHHHHCCCCCCCEEECCCCCCCCCEE
Q ss_conf             101223320134------54--213368557777554432--10036655899999984587667326236776877079
Q gi|254781112|r  157 GTDLSRFAKELK------SH--LVFSHNFEQSLQLLLSKR--TDATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVA  226 (274)
Q Consensus       157 g~~~~~~l~~~~------~~--~~~~~~~~~~~~~l~~gr--vD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  226 (274)
                      =-...+|+++++      .+  +.......|+  +..-|-  .|+ ++|-...-..++.+..-     ..+.......-.
T Consensus       138 P~~a~~Yf~~~gGttvek~~~~i~~L~GSvE~--Ap~~G~PeAD~-I~DLvstG~TL~~NgL~-----~id~i~~ks~a~  209 (317)
T TIGR00070       138 PHLAKKYFRELGGTTVEKLSVEIIELNGSVEL--APLIGIPEADA-IVDLVSTGTTLRENGLR-----EIDVILDKSSAR  209 (317)
T ss_pred             HHHHHHHHHHCCCCEEEEEEEEEEECCCCEEE--ECCCCCCCCCE-EEEEECCHHHHHHCCCE-----EEEEEECCEEEE
T ss_conf             57999999861894466555799822263860--01278973000-25421112789753968-----898884240378


Q ss_pred             EEEECC------CHHHHHHHHHHHHHHHHC
Q ss_conf             998189------989999999999999979
Q gi|254781112|r  227 FMMRKG------NNKLTRSINEILCAIHLD  250 (274)
Q Consensus       227 ~~~~k~------~~~L~~~in~~l~~l~~~  250 (274)
                      +..+|.      +.++.+.+-..|+...+.
T Consensus       210 LI~N~~S~~~~~~~~~i~~l~~~i~~V~~a  239 (317)
T TIGR00070       210 LIANRESYKDKSKKQLIDELVTRIKGVIEA  239 (317)
T ss_pred             EEECCCCCCCCCCHHHHHHHHHHHHHHHCC
T ss_conf             843675568641079999999877776400


No 130
>TIGR03572 WbuZ glycosyl amidation-associated protein WbuZ. This clade of sequences is highly similar to the HisF protein, but generally represents the second HisF homolog in the genome where the other is an authentic HisF observed in the context of a complete histidine biosynthesis operon. The similarity between these WbuZ sequences and true HisFs is such that often the closest match by BLAST of a WbuZ is a HisF. Only by making a multiple sequence alignment is the homology relationship among the WbuZ sequences made apparent. WbuZ genes are invariably observed in the presence of a homolog of the HisH protein (designated WbuY) and a proposed N-acetyl sugar amidotransferase designated in WbuX in E. coli, IfnA in P. aeriginosa and PseA in C. jejuni. Similarly, this trio of genes is invariably found in the context of saccharide biosynthesis loci. It has been shown that the WbuYZ homologs are not essential components of the activity expressed by WbuX, leading to the proposal that these to pr
Probab=52.30  E-value=11  Score=17.83  Aligned_cols=41  Identities=12%  Similarity=0.027  Sum_probs=24.4

Q ss_pred             EEEEEEHHHHHHHCCCCCCCCC--CCHHHHHHHHHCCCCCCCH
Q ss_conf             9885216789976299855566--8988988643103221100
Q gi|254781112|r   67 GFDIDLIKEVAHRLNLKVEFFE--TAVSGLITGLDTNRYDVLV  107 (274)
Q Consensus        67 G~~~dl~~~i~~~lg~~~~~~~--~~~~~~~~~l~~g~~D~~~  107 (274)
                      +...++++.+++...+++++=-  .+-+++...+..|-=-++.
T Consensus        60 ~~n~~~I~~i~~~~~ipi~vGGGIrs~e~~~~ll~~GadkVii  102 (232)
T TIGR03572        60 EPLFELISNLAEECFMPLTVGGGIRSLEDAKKLLSLGADKVSI  102 (232)
T ss_pred             CCHHHHHHHHHHHCCCCEEEEECEEEHHHHHHHHHCCCCEEEE
T ss_conf             2179999999997298589971330389999999769968993


No 131
>PRK02621 consensus
Probab=52.10  E-value=12  Score=17.58  Aligned_cols=42  Identities=17%  Similarity=0.187  Sum_probs=25.0

Q ss_pred             EEEEEEHHHHHHHCCCCCCCCC--CCHHHHHHHHHCCCCCCCHH
Q ss_conf             9885216789976299855566--89889886431032211000
Q gi|254781112|r   67 GFDIDLIKEVAHRLNLKVEFFE--TAVSGLITGLDTNRYDVLVN  108 (274)
Q Consensus        67 G~~~dl~~~i~~~lg~~~~~~~--~~~~~~~~~l~~g~~D~~~~  108 (274)
                      ....++++.+++...+++++=-  .+-+.+...+..|---++.+
T Consensus        60 ~~~~~~I~~i~~~~~ipi~vGGGIrs~e~~~~ll~~GadkVii~  103 (254)
T PRK02621         60 ATLIDVVYRTAEQVFIPLTVGGGISSLEGIKELLRAGADKVSLN  103 (254)
T ss_pred             HHHHHHHHHHHHHCCCCEEEECCEEEHHHHHHHHHCCCCEEEEC
T ss_conf             42899999999867985899633535799999997499989998


No 132
>pfam00800 PDT Prephenate dehydratase. This protein is involved in Phenylalanine biosynthesis. This protein catalyses the decarboxylation of prephenate to phenylpyruvate.
Probab=51.55  E-value=8.9  Score=18.29  Aligned_cols=117  Identities=10%  Similarity=0.158  Sum_probs=60.0

Q ss_pred             CCCCCCCCCC-CHHHHHHHHHCCCCCCCH-HC------CCCHHHHHHHCC-----CCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             2998555668-988988643103221100-00------367567542002-----3332222222221112222111112
Q gi|254781112|r   80 LNLKVEFFET-AVSGLITGLDTNRYDVLV-NV------AITPERQKKYDF-----SIPYIAHRVLLVVRSDQQDIRSFKD  146 (274)
Q Consensus        80 lg~~~~~~~~-~~~~~~~~l~~g~~D~~~-~~------~~t~eR~~~~~f-----s~p~~~~~~~~~~~~~~~~~~~~~d  146 (274)
                      .+-..++++. ++..+++.+.+|++|... .+      ++.+--+--..+     ..-++.....++.+++.    +++|
T Consensus        19 ~~~~~~~~~~~s~~~v~~av~~g~~d~gvvPiENS~~G~V~~~~DlL~~~~l~I~~E~~l~I~~~L~~~~~~----~l~~   94 (181)
T pfam00800        19 FGQSVELVPCPSIEDVFEAVENGEADYAVVPIENSIEGSVNETLDLLLESDLKIVGEVVLPIHHCLLARPGT----DLED   94 (181)
T ss_pred             CCCCCCEEECCCHHHHHHHHHCCCCCEEEEECCCCCCCCHHHHHHHHHHCCCEEEEEEEEEEEEEEECCCCC----CCCC
T ss_conf             399883786699999999997799866776221245556789999998499879999986221001017998----6012


Q ss_pred             CCCCCEEEE-CCCH-HHHHHHCC--CCCCEEECCHHHHHHHHH--HHHHHCCCCCHHHHHHH
Q ss_conf             334320231-0101-22332013--454213368557777554--43210036655899999
Q gi|254781112|r  147 LTDKTVAQI-LGTD-LSRFAKEL--KSHLVFSHNFEQSLQLLL--SKRTDATMIPDIPFFNF  202 (274)
Q Consensus       147 L~g~~V~~~-~g~~-~~~~l~~~--~~~~~~~~~~~~~~~~l~--~grvD~~~~~~~~~~~~  202 (274)
                      ++  +|... ..-. ...|++++  +.+++.+.|...+.+.+.  +++-++++++..-+..|
T Consensus        95 I~--~V~SHpqal~QC~~~l~~~~p~~~~~~~~sTa~Aa~~v~~~~~~~~aAIas~~aa~~y  154 (181)
T pfam00800        95 IK--TVYSHPQALAQCREFLEKHLPGAERVPVSSTAAAAKIVAAEGDKGAAAIASELAAELY  154 (181)
T ss_pred             CE--EEEEEHHHHHHHHHHHHHHCCCCEEEECCCHHHHHHHHHHCCCCCEEEECHHHHHHHC
T ss_conf             11--7884279999999999984899889982765999999995699881340509899885


No 133
>PRK11898 prephenate dehydratase; Provisional
Probab=51.21  E-value=10  Score=17.86  Aligned_cols=113  Identities=13%  Similarity=0.122  Sum_probs=59.1

Q ss_pred             CCCCCC-CCHHHHHHHHHCCCCCCC-HH--------CCCCHHHH-HH--H-CCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             855566-898898864310322110-00--------03675675-42--0-02333222222222111222211111233
Q gi|254781112|r   83 KVEFFE-TAVSGLITGLDTNRYDVL-VN--------VAITPERQ-KK--Y-DFSIPYIAHRVLLVVRSDQQDIRSFKDLT  148 (274)
Q Consensus        83 ~~~~~~-~~~~~~~~~l~~g~~D~~-~~--------~~~t~eR~-~~--~-~fs~p~~~~~~~~~~~~~~~~~~~~~dL~  148 (274)
                      .+++++ .++...++++++|++|.. ..        +..|-+.- ..  + ..-.-++.....++.+.+     +++|++
T Consensus        26 ~~~~~~~~s~~~vf~aV~~g~~d~gvvPiENS~~G~V~~t~D~L~~~~~l~I~gE~~l~I~h~Ll~~~~-----~l~~I~  100 (285)
T PRK11898         26 EAELVPYDSIPDVLDAVEAGEVDYAVVPIENSIEGSVNPTLDYLAHGSPLQIVAEIVLPIAQHLLVRPG-----HLADIR  100 (285)
T ss_pred             CCEEEECCCHHHHHHHHHCCCCCEEEEEEECCCCEECHHHHHHHHCCCCCEEEEEEEEEEEEEEECCCC-----CHHHCE
T ss_conf             952786699999999997799877998780458467099899872059958999999877469862799-----865583


Q ss_pred             CCCEEE-ECCCH-HHHHHHCC--CCCCEEECCHHHHHHHHHHHHH--HCCCCCHHHHHHH
Q ss_conf             432023-10101-22332013--4542133685577775544321--0036655899999
Q gi|254781112|r  149 DKTVAQ-ILGTD-LSRFAKEL--KSHLVFSHNFEQSLQLLLSKRT--DATMIPDIPFFNF  202 (274)
Q Consensus       149 g~~V~~-~~g~~-~~~~l~~~--~~~~~~~~~~~~~~~~l~~grv--D~~~~~~~~~~~~  202 (274)
                        +|-. ...-. ...|++++  +.+++.+.|...+.+++..+.-  .++++...-+..|
T Consensus       101 --~V~SHpqal~QC~~~L~~~~p~~~~v~~~sTa~Aa~~v~~~~~~~~AAIas~~aa~~y  158 (285)
T PRK11898        101 --TVYSHPQALAQCRKWLAEHLPGAELEPANSTAAAAQYVAEHPAEPIAAIASERAAELY  158 (285)
T ss_pred             --EEEECHHHHHHHHHHHHHHCCCCEEEECCCHHHHHHHHHHCCCCCEEECCHHHHHHHC
T ss_conf             --7872347999999999973888689990758999999984899771440447662124


No 134
>PRK02083 imidazole glycerol phosphate synthase subunit HisF; Provisional
Probab=50.51  E-value=11  Score=17.65  Aligned_cols=42  Identities=17%  Similarity=0.120  Sum_probs=25.4

Q ss_pred             EEEEEEHHHHHHHCCCCCCCCC--CCHHHHHHHHHCCCCCCCHH
Q ss_conf             9885216789976299855566--89889886431032211000
Q gi|254781112|r   67 GFDIDLIKEVAHRLNLKVEFFE--TAVSGLITGLDTNRYDVLVN  108 (274)
Q Consensus        67 G~~~dl~~~i~~~lg~~~~~~~--~~~~~~~~~l~~g~~D~~~~  108 (274)
                      +...++++.+++...+++++=-  .+-+.+...+..|---++.+
T Consensus        60 ~~~~~~I~~i~~~~~~pi~vGGGIrs~e~~~~ll~~GadkVvig  103 (253)
T PRK02083         60 DTMKDVVERVAEQVFIPLTVGGGIRSVEDARRLLRAGADKVSIN  103 (253)
T ss_pred             HHHHHHHHHHHHHCCCCEEEECCCCCHHHHHHHHHCCCCEEEEC
T ss_conf             41799999999863987785176213898768987798789999


No 135
>PRK02747 consensus
Probab=49.86  E-value=13  Score=17.38  Aligned_cols=42  Identities=17%  Similarity=0.147  Sum_probs=24.8

Q ss_pred             EEEEEEHHHHHHHCCCCCCCCC--CCHHHHHHHHHCCCCCCCHH
Q ss_conf             9885216789976299855566--89889886431032211000
Q gi|254781112|r   67 GFDIDLIKEVAHRLNLKVEFFE--TAVSGLITGLDTNRYDVLVN  108 (274)
Q Consensus        67 G~~~dl~~~i~~~lg~~~~~~~--~~~~~~~~~l~~g~~D~~~~  108 (274)
                      +...++++.+++...+++++=-  .+-+.+...+..|-=-++.+
T Consensus        60 ~~~~~lI~~i~~~~~ipi~vGGGIrs~e~~~~ll~~GadkViig  103 (257)
T PRK02747         60 GTMLDVVARTAEQCFMPLTVGGGVRTVDDIRKLLLAGADKVSIN  103 (257)
T ss_pred             HHHHHHHHHHHHHCCCCEEEECCCCCHHHHHHHHHCCCCEEEEC
T ss_conf             52899999999866998898488207388789987699689834


No 136
>COG0107 HisF Imidazoleglycerol-phosphate synthase [Amino acid transport and metabolism]
Probab=49.83  E-value=9.8  Score=18.03  Aligned_cols=23  Identities=13%  Similarity=0.213  Sum_probs=16.1

Q ss_pred             ECCHHHHHHHHHHHHHHCCCCCH
Q ss_conf             36855777755443210036655
Q gi|254781112|r  174 SHNFEQSLQLLLSKRTDATMIPD  196 (274)
Q Consensus       174 ~~~~~~~~~~l~~grvD~~~~~~  196 (274)
                      ..+.+.....+..|++|+++...
T Consensus       208 aG~~ehf~eaf~~~~adAaLAAs  230 (256)
T COG0107         208 AGKPEHFVEAFTEGKADAALAAS  230 (256)
T ss_pred             CCCHHHHHHHHHHCCCHHHHHHH
T ss_conf             89688999999815700887644


No 137
>PRK07239 bifunctional uroporphyrinogen-III synthetase/response regulator domain protein; Validated
Probab=49.83  E-value=19  Score=16.27  Aligned_cols=59  Identities=17%  Similarity=0.243  Sum_probs=38.5

Q ss_pred             CCCCCCCEEEECCCH---------HHHHHHCCCCCCEEE-----------CCHHHHHHHHHHHHHHCCCCCHHHHHHHH
Q ss_conf             123343202310101---------223320134542133-----------68557777554432100366558999999
Q gi|254781112|r  145 KDLTDKTVAQILGTD---------LSRFAKELKSHLVFS-----------HNFEQSLQLLLSKRTDATMIPDIPFFNFL  203 (274)
Q Consensus       145 ~dL~g~~V~~~~g~~---------~~~~l~~~~~~~~~~-----------~~~~~~~~~l~~grvD~~~~~~~~~~~~~  203 (274)
                      .++.|++|+++..-.         ....++..+.+++.+           ...+.++.++.+|++|++..........+
T Consensus       138 ~gv~G~rIAVQlHGa~~~~eP~p~~~~~Lr~aGAeV~~V~vYRW~~p~d~~~l~~Lv~~i~~g~vDAVtFTSAPaa~al  216 (381)
T PRK07239        138 EGVAGKRIAVQLHGAADEWDPLPEFLEALRAAGAEVVPVPVYRWVPPPDGGPFDRLVDLIATRQLDAVTFTSAPAVAAL  216 (381)
T ss_pred             CCCCCCEEEEEECCCCCCCCCCHHHHHHHHHCCCEEEEECCEECCCCCCCCHHHHHHHHHHHCCCCEEEECCHHHHHHH
T ss_conf             7988888999814766666878899999997798688956543269998547999999997088888996578999999


No 138
>TIGR03298 argP transcriptional regulator, ArgP family. ArgP used to be known as IciA. ArgP is a positive regulator of argK. It is a negative autoregulator in presence of arginine. It competes with DnaA for oriC iteron (13-mer) binding. It activates dnaA and nrd transcription. It has been demonstrated to be part of the pho regulon (PMID:10589831). ArgP mutants convey canavanine (an L-arginine structural homolog) sensitivity (PMID: 15150242).
Probab=48.94  E-value=20  Score=16.19  Aligned_cols=189  Identities=13%  Similarity=0.080  Sum_probs=94.3

Q ss_pred             CCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCCHHCCCCHHHHHHH
Q ss_conf             89589996289987248704699848898852167899762998555668988988643103221100003675675420
Q gi|254781112|r   40 QSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAVSGLITGLDTNRYDVLVNVAITPERQKKY  119 (274)
Q Consensus        40 ~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~t~eR~~~~  119 (274)
                      .+.++|++..+..          +   .+..+.+..+.+.-++++++...+.++.++.++.|.+|++......+.  ..+
T Consensus        89 ~g~l~i~~~~~~~----------~---~~l~p~l~~f~~~~~v~l~l~~~~~~~~~d~l~~g~~~~ai~~~~~~~--~~~  153 (292)
T TIGR03298        89 PVTLSIAVNADSL----------A---TWFLPALAPVLAQEGVLLDLVVEDQDHTAELLRSGEVLGAVTTQAKPV--QGC  153 (292)
T ss_pred             CEEEEEEECHHHH----------H---HHHHHHHHHHHHCCCCEEEEEECCCHHHHHHHHCCCEEEEEECCCCCC--CCC
T ss_conf             4258887635778----------8---878999999998089879998545245899985697589997578889--886


Q ss_pred             CCCCCCCCCCCCCCCCCC-----CCCCCCCCCCCCCCEEE-ECCC-HHHHHHHCC---C--CCCEEECCHHHHHHHHHHH
Q ss_conf             023332222222221112-----22211111233432023-1010-122332013---4--5421336855777755443
Q gi|254781112|r  120 DFSIPYIAHRVLLVVRSD-----QQDIRSFKDLTDKTVAQ-ILGT-DLSRFAKEL---K--SHLVFSHNFEQSLQLLLSK  187 (274)
Q Consensus       120 ~fs~p~~~~~~~~~~~~~-----~~~~~~~~dL~g~~V~~-~~g~-~~~~~l~~~---~--~~~~~~~~~~~~~~~l~~g  187 (274)
                      . ..|+......++...+     .+...+.+||.+...-. ..+. ....+....   .  .....+++.+...+++.+|
T Consensus       154 ~-~~~L~~~~~~~vasP~~~~~~~~~~~~~~~L~~~p~l~~~~~~~~~~~~~~~~~~~~~~~~~~~v~s~~~~~~~v~aG  232 (292)
T TIGR03298       154 R-VVPLGAMRYLAVASPAFAARYFPDGVTAEALARAPVIVFNRKDDLQDRFLRRLFGLPVSPPRHYVPSSEGFVEAARAG  232 (292)
T ss_pred             E-EEECCCEEEEEEECHHHHHHCCCCCCCHHHHHCCCEEEECCCCCHHHHHHHHCCCCCCCCCEEEECCHHHHHHHHHHC
T ss_conf             7-999114018999888999862899999999936987996599647899998505777665168988899999999949


Q ss_pred             HHHCCCCCHHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEEEEC-CCHHHHHHHHHHHHHHHH
Q ss_conf             21003665589999998458766732623677687707999818-998999999999999997
Q gi|254781112|r  188 RTDATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRK-GNNKLTRSINEILCAIHL  249 (274)
Q Consensus       188 rvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k-~~~~L~~~in~~l~~l~~  249 (274)
                      ..= .+.+...+...+..-    ..+.+.+....+.++++..++ .++.++..++..++..++
T Consensus       233 lGi-a~lP~~~v~~~l~~G----~LV~llp~~~~~~~l~~~~~r~~s~~~r~f~d~l~~~ar~  290 (292)
T TIGR03298       233 LGW-GMVPELQAEPHLAAG----RLVDLAPGRALDVPLYWHHWRLESRVLERLTDAVVAAARR  290 (292)
T ss_pred             CEE-EECCHHHHHHHHHCC----CEEEECCCCCCCCCEECCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             988-969699999998589----8588499987982164806686788999999999999986


No 139
>COG1613 Sbp ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=48.60  E-value=20  Score=16.16  Aligned_cols=136  Identities=16%  Similarity=0.149  Sum_probs=62.0

Q ss_pred             CCCCCCCCCCCCCCCCCC-CCCCCCCCCC--CCEEEEC----CCHHHHHHH-------CCCC--------------CCEE
Q ss_conf             333222222222111222-2111112334--3202310----101223320-------1345--------------4213
Q gi|254781112|r  122 SIPYIAHRVLLVVRSDQQ-DIRSFKDLTD--KTVAQIL----GTDLSRFAK-------ELKS--------------HLVF  173 (274)
Q Consensus       122 s~p~~~~~~~~~~~~~~~-~~~~~~dL~g--~~V~~~~----g~~~~~~l~-------~~~~--------------~~~~  173 (274)
                      |.||. +..+|++|++++ .|++++||-.  -.|....    |..--.||-       ..+.              ++..
T Consensus       126 s~Pyt-StivFlVRkGNPK~I~DW~DL~k~gV~VItpNPKTSGgARWN~Laawa~a~~~~~gdeaka~~fV~~L~~nvpv  204 (348)
T COG1613         126 SAPYT-STIVFLVRKGNPKQIRDWDDLVKPGVQVITPNPKTSGGARWNYLAAWAYALKTNGGDEAKAKDFVGKLYKNVPV  204 (348)
T ss_pred             CCCCC-CEEEEEEECCCCCCCCCHHHHCCCCCEEECCCCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCCC
T ss_conf             87733-06999993699655675577465886797689988765227889998998714799889999999999846832


Q ss_pred             -ECCHHHHHHH-HHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEECC-CCCCCCCEEEEEECC-CHHHHHHHHHHHHHHHH
Q ss_conf             -3685577775-5443210036655899999984587667326236-776877079998189-98999999999999997
Q gi|254781112|r  174 -SHNFEQSLQL-LLSKRTDATMIPDIPFFNFLERRPHDGNLFKIAD-RMKDNSAVAFMMRKG-NNKLTRSINEILCAIHL  249 (274)
Q Consensus       174 -~~~~~~~~~~-l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~k~-~~~L~~~in~~l~~l~~  249 (274)
                       -.+-..+-.. ..+|-.|+.+.-+..+....++...+...+..+. ......+.+. +.++ +..=-..+-.+..+..-
T Consensus       205 ld~gaRgAT~tF~qrgiGDVLi~wENEA~la~~e~g~~~feiV~Ps~si~aEpPVAV-Vd~~vdkkgtr~vAeAyl~yLy  283 (348)
T COG1613         205 LDTGARGATTTFVQRGIGDVLIAWENEALLALNELGGDKFEIVTPSVSILAEPPVAV-VDKNVDKKGTRKVAEAYLKYLY  283 (348)
T ss_pred             CCCCCCHHHHHHHHCCCCCEEEEECHHHHHHHHHHCCCCCCEECCCEEEEECCCEEE-EECCCCCCCCHHHHHHHHHHHC
T ss_conf             458852125788863866478872418888799746887668768602660697478-7511233356899999998755


Q ss_pred             CCHHHHHHHH
Q ss_conf             9859999987
Q gi|254781112|r  250 DGTYKKIFDR  259 (274)
Q Consensus       250 ~G~~~~I~~k  259 (274)
                      |.+-++|..|
T Consensus       284 s~~gQ~i~Ak  293 (348)
T COG1613         284 SPEGQEIAAK  293 (348)
T ss_pred             CHHHHHHHHH
T ss_conf             8388899998


No 140
>COG0583 LysR Transcriptional regulator [Transcription]
Probab=47.74  E-value=20  Score=16.07  Aligned_cols=154  Identities=13%  Similarity=0.072  Sum_probs=77.6

Q ss_pred             EEHHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCCHHCCCCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC--CCCCC
Q ss_conf             2167899762998555668988988643103221100003675675420023332222222221112222111--11233
Q gi|254781112|r   71 DLIKEVAHRLNLKVEFFETAVSGLITGLDTNRYDVLVNVAITPERQKKYDFSIPYIAHRVLLVVRSDQQDIRS--FKDLT  148 (274)
Q Consensus        71 dl~~~i~~~lg~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~t~eR~~~~~fs~p~~~~~~~~~~~~~~~~~~~--~~dL~  148 (274)
                      .++....++.. ++.+...........+.+|++|++...... .... -....+.......+++..+.+....  ++++.
T Consensus       109 ~~l~~f~~~~P-~~~~~~~~~~~~~~~l~~~~~D~~i~~~~~-~~~~-~~~~~~l~~~~~~~v~~~~~~~~~~~~~~~~~  185 (297)
T COG0583         109 PLLARFRARYP-EIELELGTSDRLLEDLVEGELDLAIRAGPP-PPPD-GLVARPLFSEELVLVVPASHPLAARHGLPDLP  185 (297)
T ss_pred             HHHHHHHHHCC-CEEEEEECCHHHHHHHHCCCCEEEEEECCC-CCCC-CEEEEEEECCCEEEEEECCCHHHHCCCCCCCC
T ss_conf             99999999789-839998256649999877993499995886-6888-74688960364799995784665147864477


Q ss_pred             CCCEEEECCC-HH----HHHHHCCC---CCCEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEECC-CC
Q ss_conf             4320231010-12----23320134---5421336855777755443210036655899999984587667326236-77
Q gi|254781112|r  149 DKTVAQILGT-DL----SRFAKELK---SHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIAD-RM  219 (274)
Q Consensus       149 g~~V~~~~g~-~~----~~~l~~~~---~~~~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~  219 (274)
                      .......... ..    .......+   .......+......++.+|.. ..+.+...+..+..  +.  ....... .+
T Consensus       186 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~g-i~~~p~~~~~~~~~--~~--~~~~~~~~~~  260 (297)
T COG0583         186 GEPLILLEHGCILRRLLDQALALAGWRPRIRLEVNSAEALLQAVAAGLG-IALLPESLARPDLA--GR--LVRVLPLPPP  260 (297)
T ss_pred             CCHHHCCCCCCHHHHHHHHHHHHCCCCCCCEEEECCHHHHHHHHHHCCC-EEEECHHHHHHHHC--CC--CEEEECCCCC
T ss_conf             2412306765315776677888624666865999909999999996998-38641999988754--89--1899547778


Q ss_pred             CCCCCEEEEEECC
Q ss_conf             6877079998189
Q gi|254781112|r  220 KDNSAVAFMMRKG  232 (274)
Q Consensus       220 ~~~~~~~~~~~k~  232 (274)
                      .....+++..+++
T Consensus       261 ~~~~~~~~~~~~~  273 (297)
T COG0583         261 PLPRPLYLVWRKS  273 (297)
T ss_pred             CCCCEEEEEEECC
T ss_conf             8776399999588


No 141
>PRK13684 Ycf48-like protein; Provisional
Probab=46.72  E-value=17  Score=16.50  Aligned_cols=19  Identities=32%  Similarity=0.469  Sum_probs=13.2

Q ss_pred             CHHHHHHHHHHHHHHHHHH
Q ss_conf             9579999999999999999
Q gi|254781112|r    1 MRRLLRDLRKIFFSKYLFF   19 (274)
Q Consensus         1 m~~~~~~mk~~~~~~~l~~   19 (274)
                      |+++|++.++++...++.+
T Consensus         1 m~~~~~~~~~l~l~~~~~~   19 (333)
T PRK13684          1 MKRLLKSLLNLLLLLALGL   19 (333)
T ss_pred             CHHHHHHHHHHHHHHHHHH
T ss_conf             9268888999999999998


No 142
>TIGR00631 uvrb excinuclease ABC, B subunit; InterPro: IPR004807 All proteins in this family for which functions are known are DNA helicases that function in the nucleotide excision repair and are endonucleases that make the 3' incision next to DNA damage. They are part of a pathway requiring UvrA, UvrB, UvrC, and UvrD homologs.; GO: 0009381 excinuclease ABC activity, 0006289 nucleotide-excision repair, 0005737 cytoplasm, 0009380 excinuclease repair complex.
Probab=46.60  E-value=13  Score=17.38  Aligned_cols=29  Identities=28%  Similarity=0.641  Sum_probs=15.8

Q ss_pred             CCCCCCCCCCH---H--HHHHHHHCCCCCCCHHC
Q ss_conf             99855566898---8--98864310322110000
Q gi|254781112|r   81 NLKVEFFETAV---S--GLITGLDTNRYDVLVNV  109 (274)
Q Consensus        81 g~~~~~~~~~~---~--~~~~~l~~g~~D~~~~~  109 (274)
                      |++++|-..+=   .  .++.+|+.|++|++.|+
T Consensus       471 Gikv~YLHSeIdt~ER~eiirdLR~G~fDVLVGI  504 (667)
T TIGR00631       471 GIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGI  504 (667)
T ss_pred             CCEEEEECCHHHHHHHHHHHHHHCCCCCEEEEEC
T ss_conf             8379871455789999999998447884088600


No 143
>cd04731 HisF The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)-formimino-5-aminoimidazole-4-carboxamide ribonucleotide (PRFAR) to imidazole glycerol phosphate (ImGP) and 5'-(5-aminoimidazole-4-carboxamide) ribonucleotide (AICAR). This conversion involves two tightly coupled reactions in distinct active sites of IGPS. The two catalytic domains can be fused, like in fungi and plants, or peformed by a heterodimer (HisH-glutaminase and HisF-cyclase), like in bacteria.
Probab=46.54  E-value=16  Score=16.80  Aligned_cols=42  Identities=14%  Similarity=0.115  Sum_probs=24.8

Q ss_pred             EEEEEEHHHHHHHCCCCCCCC--CCCHHHHHHHHHCCCCCCCHH
Q ss_conf             988521678997629985556--689889886431032211000
Q gi|254781112|r   67 GFDIDLIKEVAHRLNLKVEFF--ETAVSGLITGLDTNRYDVLVN  108 (274)
Q Consensus        67 G~~~dl~~~i~~~lg~~~~~~--~~~~~~~~~~l~~g~~D~~~~  108 (274)
                      +...++++.+++...+++++=  ..+-+.....+..|---++.+
T Consensus        57 ~~n~~~i~~i~~~~~~pi~vGGGIrs~~~~~~~l~~GadkVvig  100 (243)
T cd04731          57 ETMLDVVERVAEEVFIPLTVGGGIRSLEDARRLLRAGADKVSIN  100 (243)
T ss_pred             CCHHHHHHHHHHHCCCCEEEEEEEEEHHHHHHHHHCCCCEEEEC
T ss_conf             00799999999867986899850664799999997799789989


No 144
>pfam01715 IPPT IPP transferase. This is a family of IPP transferases EC:2.5.1.8 also known as tRNA delta(2)-isopentenylpyrophosphate transferase. These enzymes modify both cytoplasmic and mitochondrial tRNAs at A(37) to give isopentenyl A(37).
Probab=46.19  E-value=22  Score=15.92  Aligned_cols=44  Identities=9%  Similarity=0.203  Sum_probs=32.7

Q ss_pred             CCEEEEEECCCHHHHHHHHHHHHHHHHCCHHHH---HHHHHCCCCCC
Q ss_conf             707999818998999999999999997985999---99876788877
Q gi|254781112|r  223 SAVAFMMRKGNNKLTRSINEILCAIHLDGTYKK---IFDRYFDKNII  266 (274)
Q Consensus       223 ~~~~~~~~k~~~~L~~~in~~l~~l~~~G~~~~---I~~kw~g~d~~  266 (274)
                      ..+.+.+..+.+.|.+.|++.+..|.++|-+++   |++++++.+..
T Consensus       153 ~~~~i~l~~~r~~L~~rI~~Rv~~Ml~~GlieEv~~L~~~~~~~~~~  199 (253)
T pfam01715       153 DIVQIGLARDREVLHERIARRVDDMLESGLVEEVKALYAQGLNEDLP  199 (253)
T ss_pred             CCEEEEECCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHCCCCCCHH
T ss_conf             77378837988999999999999998768999999999758996448


No 145
>pfam02621 DUF178 Putative periplasminc binding protein (DUF178). This family of proteins belong to the periplasmic binding protein clan.
Probab=45.62  E-value=22  Score=15.87  Aligned_cols=26  Identities=23%  Similarity=0.126  Sum_probs=21.2

Q ss_pred             CCCCCCCCCCHHHHHHHHHCCCCCCC
Q ss_conf             99855566898898864310322110
Q gi|254781112|r   81 NLKVEFFETAVSGLITGLDTNRYDVL  106 (274)
Q Consensus        81 g~~~~~~~~~~~~~~~~l~~g~~D~~  106 (274)
                      +.+++++.-+...+-..+.+|++|+.
T Consensus        24 ~~~~~~~~~~P~~Ln~~l~~g~lDv~   49 (248)
T pfam02621        24 GLDFELVLADPETLNRLLLEGELDVA   49 (248)
T ss_pred             CCCEEEEECCHHHHHHHHHCCCCCEE
T ss_conf             89759986899999999986999887


No 146
>PRK04792 tolB translocation protein TolB; Provisional
Probab=45.11  E-value=9.1  Score=18.23  Aligned_cols=40  Identities=20%  Similarity=0.339  Sum_probs=20.4

Q ss_pred             CEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCCCCCCCH
Q ss_conf             58999628998724870469984889885216789976299855566898
Q gi|254781112|r   42 ALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETAV   91 (274)
Q Consensus        42 ~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~~~~~~~   91 (274)
                      .+.||+    +||.+.   +.+.   +..|+.+-|...|...=.|.+++.
T Consensus        35 ~~PIAV----~pF~~~---g~~~---~~~~i~~II~~DL~rSG~F~~l~~   74 (450)
T PRK04792         35 ARPIAI----VPFKWE---GEGK---LPTDISAVIASDLQRSGKFSPVPT   74 (450)
T ss_pred             CCCEEE----ECCCCC---CCCC---HHHHHHHHHHHHHHHCCCCEECCH
T ss_conf             425499----375456---8743---257999999988760878552596


No 147
>TIGR00174 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; InterPro: IPR002627 tRNA isopentenyltransferases 2.5.1.8 from EC also known as tRNA delta(2)-isopentenylpyrophosphate transferases or IPP transferases. These enzymes modify both cytoplasmic and mitochondrial tRNAs at A(37) to give isopentenyl A(37) .; GO: 0004811 tRNA isopentenyltransferase activity, 0005524 ATP binding, 0008033 tRNA processing.
Probab=44.63  E-value=23  Score=15.78  Aligned_cols=36  Identities=14%  Similarity=0.243  Sum_probs=28.3

Q ss_pred             EEEE-CCCHHHHHHHHHHHHHHHHCC---HHHHHHHHHCC
Q ss_conf             9981-899899999999999999798---59999987678
Q gi|254781112|r  227 FMMR-KGNNKLTRSINEILCAIHLDG---TYKKIFDRYFD  262 (274)
Q Consensus       227 ~~~~-k~~~~L~~~in~~l~~l~~~G---~~~~I~~kw~g  262 (274)
                      +++. .+...|...|++.+.+|.++|   |+++||+||-.
T Consensus       190 ~~l~~~~~e~L~~RI~~R~~~Ml~sGl~~Evk~Ly~~~~~  229 (307)
T TIGR00174       190 IGLAPLEREALHERIEQRVHEMLESGLLAEVKGLYAKYDK  229 (307)
T ss_pred             HHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             7630058645677899999999986389999999851755


No 148
>PRK05211 consensus
Probab=43.23  E-value=19  Score=16.27  Aligned_cols=41  Identities=12%  Similarity=0.075  Sum_probs=24.9

Q ss_pred             EEEEEEHHHHHHHCCCCCCCCC--CCHHHHHHHHHCCCCCCCH
Q ss_conf             9885216789976299855566--8988988643103221100
Q gi|254781112|r   67 GFDIDLIKEVAHRLNLKVEFFE--TAVSGLITGLDTNRYDVLV  107 (274)
Q Consensus        67 G~~~dl~~~i~~~lg~~~~~~~--~~~~~~~~~l~~g~~D~~~  107 (274)
                      ..+.++++.+++...+++++=-  .+-+.+...+..|-=-++.
T Consensus        51 ~~n~~~I~~i~~~~~~Pl~vGGGIrs~~~i~~ll~~GadkVii   93 (248)
T PRK05211         51 VVDKSWVSRVAEVIDIPFCVAGGIKSVEDAREILSFGADKISI   93 (248)
T ss_pred             CCHHHHHHHHHHHCCCCEEEECCCCCHHHHHHHHHCCCCEEEE
T ss_conf             2149999999976798589627801389999999879988998


No 149
>PRK05137 tolB translocation protein TolB; Provisional
Probab=41.05  E-value=10  Score=17.88  Aligned_cols=23  Identities=17%  Similarity=0.167  Sum_probs=12.7

Q ss_pred             EEEEEEHHHHHHHCCCCCCCCCC
Q ss_conf             98852167899762998555668
Q gi|254781112|r   67 GFDIDLIKEVAHRLNLKVEFFET   89 (274)
Q Consensus        67 G~~~dl~~~i~~~lg~~~~~~~~   89 (274)
                      .+..|+.+.|...|...=.|.++
T Consensus        54 ~l~~~i~~II~~DL~~SG~F~~l   76 (437)
T PRK05137         54 ELGADIAQVIAADLKRSGLFAPI   76 (437)
T ss_pred             HHHHHHHHHHHHHHHHCCCCEEC
T ss_conf             35688999999778638895564


No 150
>PRK02515 psbU photosystem II complex extrinsic protein precursor U; Provisional
Probab=39.16  E-value=28  Score=15.25  Aligned_cols=21  Identities=29%  Similarity=0.400  Sum_probs=12.5

Q ss_pred             CHHHHHHHHHHHHHHHHHHHH
Q ss_conf             957999999999999999999
Q gi|254781112|r    1 MRRLLRDLRKIFFSKYLFFAP   21 (274)
Q Consensus         1 m~~~~~~mk~~~~~~~l~~~~   21 (274)
                      |||+|+.+-+.+....+++.+
T Consensus         1 mkrl~~~L~~ll~v~~L~lg~   21 (144)
T PRK02515          1 MKRLLSWLVRLLVVLSLLLGL   21 (144)
T ss_pred             CCHHHHHHHHHHHHHHHHHHH
T ss_conf             917999999999999999998


No 151
>TIGR00971 3a0106s03 sulfate ABC transporter, sulfate-binding protein; InterPro: IPR005669   Thiosulphate-binding proteins (gene cysP) specifically binds thiosulphate and are involved in the transport systems for this nutrients , . There are two conserved regions in the protein, one located in the N-terminal region and the other in the central part of these proteins. The second pattern includes two adjacent amino acids (Ser-Gly) that, in sbp, are known to be essential for sulphate binding . ; GO: 0015419 sulfate transmembrane-transporting ATPase activity, 0008272 sulfate transport, 0030288 outer membrane-bounded periplasmic space.
Probab=38.77  E-value=28  Score=15.21  Aligned_cols=139  Identities=14%  Similarity=0.154  Sum_probs=79.6

Q ss_pred             CCCCCCCCCCCCCCCCCC-CCCCCCCCC--CCCEEEEC----CCHHHHHHHCCC---------------------CCCEE
Q ss_conf             333222222222111222-211111233--43202310----101223320134---------------------54213
Q gi|254781112|r  122 SIPYIAHRVLLVVRSDQQ-DIRSFKDLT--DKTVAQIL----GTDLSRFAKELK---------------------SHLVF  173 (274)
Q Consensus       122 s~p~~~~~~~~~~~~~~~-~~~~~~dL~--g~~V~~~~----g~~~~~~l~~~~---------------------~~~~~  173 (274)
                      |.||+. +.+|++|+++| .|.+|+||-  |.+|..+.    |..=..||..++                     .++..
T Consensus       103 S~Py~S-T~~FLVRKGNPK~I~DWnDL~~~~v~~I~PNPK~SG~AR~~YLaAWG~A~~~~~~D~aK~~~F~~~l~KNvEV  181 (320)
T TIGR00971       103 SAPYTS-TIVFLVRKGNPKQIHDWNDLIKPGVSVITPNPKSSGGARYNYLAAWGYALHADNGDKAKAEQFVKALLKNVEV  181 (320)
T ss_pred             CCCCCE-EEEEEEECCCCCCCCCHHHHHHCCCEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCCEEE
T ss_conf             886201-3355675479896465134633587586078898641578999987667513787624589999998501033


Q ss_pred             ECCHHH--HHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEECCC-CCCCCCEEEEEECC-CHHHHHHHHHHHHHHHH
Q ss_conf             368557--777554432100366558999999845876673262367-76877079998189-98999999999999997
Q gi|254781112|r  174 SHNFEQ--SLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADR-MKDNSAVAFMMRKG-NNKLTRSINEILCAIHL  249 (274)
Q Consensus       174 ~~~~~~--~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~k~-~~~L~~~in~~l~~l~~  249 (274)
                      .++-..  .-.-+..|-.|+.+.-+..+....++...+...+.++.. ....-+.++ |-|. ...=.+.+-++--+.-=
T Consensus       182 lD~G~RGaT~TF~ERG~GDVLI~~E~E~~~~~~~~~~~~FE~V~P~~~ILAE~~V~~-VDK~V~~~~T~~~A~AYL~yLY  260 (320)
T TIGR00971       182 LDSGARGATNTFVERGLGDVLIAFENEALLIRKELEKDKFEIVIPSESILAEPTVSV-VDKVVEKKGTKKVAEAYLKYLY  260 (320)
T ss_pred             EECCCCCCCCCHHHCCCCHHHHHHHHHHHHHHHHHCCCCCEEECCCCCCCCCCCEEE-EECCCCCCCHHHHHHHHHHHHC
T ss_conf             206888652101110633001345788999999633487268647743213565035-7433032345899999997404


Q ss_pred             CCHHHHHHHHHCC
Q ss_conf             9859999987678
Q gi|254781112|r  250 DGTYKKIFDRYFD  262 (274)
Q Consensus       250 ~G~~~~I~~kw~g  262 (274)
                      |.+-+.|..+||=
T Consensus       261 SP~~Q~I~~~~yY  273 (320)
T TIGR00971       261 SPEGQEIIAKNYY  273 (320)
T ss_pred             CCCHHHHHHHCCC
T ss_conf             9413567654267


No 152
>PRK10743 heat shock protein IbpA; Provisional
Probab=37.90  E-value=11  Score=17.84  Aligned_cols=34  Identities=21%  Similarity=0.358  Sum_probs=20.2

Q ss_pred             CCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCC
Q ss_conf             28998724870469984889885216789976299855
Q gi|254781112|r   48 DGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVE   85 (274)
Q Consensus        48 ~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~   85 (274)
                      ..+||||+....|+.    .|.++++-+=+.+-.++++
T Consensus        31 ~~~YPpyNI~k~~e~----~y~Ie~AvAGf~k~di~I~   64 (137)
T PRK10743         31 NGGYPPYNVELVDEN----HYRIAIAVAGFAESELEIT   64 (137)
T ss_pred             CCCCCCCEEEEECCC----EEEEEEEECCCCHHHEEEE
T ss_conf             789999508990698----3999999778786893899


No 153
>TIGR02129 hisA_euk phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase; InterPro: IPR011858    This enzyme acts in the biosynthesis of histidine and has been characterised in Saccharomyces cerevisiae  and Arabidopsis  where it complements the Escherichia coli HisA gene. In eukaryotes the gene is known as HIS6. In bacteria, this gene is found in Fibrobacter succinogenes, presumably due to lateral gene transfer from plants in the rumen gut.; GO: 0003949 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino]imidazole-4-carboxamide isomerase activity, 0000105 histidine biosynthetic process.
Probab=37.39  E-value=13  Score=17.20  Aligned_cols=55  Identities=13%  Similarity=-0.002  Sum_probs=31.9

Q ss_pred             CCCCCCCCCCCCEEEECCCHHHHHHHCCC---C----CCEEEC------CHHHHHHHHHHHHHHCCCCCHHHH
Q ss_conf             21111123343202310101223320134---5----421336------855777755443210036655899
Q gi|254781112|r  140 DIRSFKDLTDKTVAQILGTDLSRFAKELK---S----HLVFSH------NFEQSLQLLLSKRTDATMIPDIPF  199 (274)
Q Consensus       140 ~~~~~~dL~g~~V~~~~g~~~~~~l~~~~---~----~~~~~~------~~~~~~~~l~~grvD~~~~~~~~~  199 (274)
                      ..=+-+|..|+.-|+     .|++...++   .    ..+.|.      +.-+.+..|.+||||..++..+-+
T Consensus       191 FLiHAADVEGl~~GI-----DE~LV~~LgEw~p~~~~ip~tYAGGakS~~DL~~v~~lSkGKVDLT~GSaLDI  258 (274)
T TIGR02129       191 FLIHAADVEGLCKGI-----DEELVKKLGEWSPVYDDIPVTYAGGAKSIDDLDLVKELSKGKVDLTIGSALDI  258 (274)
T ss_pred             CEEEEEEECCCCCCC-----CHHHHHHHCCCCCCCCCCCEEEECCCEEHHHHHHHHHHCCCCEEEEECCHHHH
T ss_conf             125544422334687-----57999984345888752431772786556568999985088088974331322


No 154
>TIGR00735 hisF imidazoleglycerol phosphate synthase, cyclase subunit; InterPro: IPR004651 Histidine is formed by several complex and distinct biochemical reactions catalysed by eight enzymes. Proteins involved in steps 4 and 6 of the histidine biosynthesis pathway are contained in one family. These enzymes are called His6 and His7 in eukaryotes and HisA and HisF in prokaryotes. HisA is a phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (), involved in the fourth step of histidine biosynthesis. The bacterial HisF protein is a cyclase which catalyzes the cyclization reaction that produces D-erythro-imidazole glycerol phosphate during the sixth step of histidine biosynthesis. The yeast His7 protein is a bifunctional protein which catalyzes an amido-transferase reaction that generates imidazole-glycerol phosphate and 5-aminoimidazol-4-carboxamide. The latter is the ribonucleotide used for purine biosynthesis. The enzyme also catalyzes the cyclization reaction that produces D-erythro-imidazole glycerol phosphate, and is involved in the fifth and sixth steps in histidine biosynthesis.    This family describes the histidine biosynthesis protein, HisF. ; GO: 0000107 imidazoleglycerol-phosphate synthase activity, 0000105 histidine biosynthetic process, 0005737 cytoplasm, 0009382 imidazoleglycerol-phosphate synthase complex.
Probab=36.96  E-value=11  Score=17.79  Aligned_cols=21  Identities=14%  Similarity=0.208  Sum_probs=10.7

Q ss_pred             CHHHHHHHHHHHHHHCCCCCH
Q ss_conf             855777755443210036655
Q gi|254781112|r  176 NFEQSLQLLLSKRTDATMIPD  196 (274)
Q Consensus       176 ~~~~~~~~l~~grvD~~~~~~  196 (274)
                      ..+....++..|++||++...
T Consensus       268 ~~eHf~EAF~~gkADAaLaAS  288 (312)
T TIGR00735       268 KPEHFYEAFTKGKADAALAAS  288 (312)
T ss_pred             CCCCHHHHHHCCCHHHHHHHH
T ss_conf             853003222100034534435


No 155
>cd01424 MGS_CPS_II Methylglyoxal synthase-like domain from type II glutamine-dependent carbamoyl phosphate synthetase (CSP). CSP, a CarA and CarB heterodimer, catalyzes the production of carbamoyl phosphate which is subsequently employed in the metabolic pathways responsible for the synthesis of pyrimidine nucleotides or arginine. The MGS-like domain is the C-terminal domain of CarB and appears to play a regulatory role in CPS function by binding allosteric effector molecules, including UMP and ornithine.
Probab=36.81  E-value=22  Score=15.86  Aligned_cols=34  Identities=9%  Similarity=0.260  Sum_probs=19.1

Q ss_pred             HHHCCCCCCCCCC---CHHHHHHHHHCCCCCCCHHCC
Q ss_conf             9762998555668---988988643103221100003
Q gi|254781112|r   77 AHRLNLKVEFFET---AVSGLITGLDTNRYDVLVNVA  110 (274)
Q Consensus        77 ~~~lg~~~~~~~~---~~~~~~~~l~~g~~D~~~~~~  110 (274)
                      .+..|++++.+.-   ....+++.+++|++|++.+.+
T Consensus        39 L~~~Gi~~~~v~k~~e~~p~i~d~i~~~~i~lVINt~   75 (110)
T cd01424          39 LQEAGIPVEVVNKVSEGRPNIVDLIKNGEIQLVINTP   75 (110)
T ss_pred             HHHCCCCCEEEECCCCCCCCHHHHHHCCCEEEEEECC
T ss_conf             9864986403300567997689999779358999778


No 156
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=35.58  E-value=32  Score=14.90  Aligned_cols=185  Identities=10%  Similarity=0.028  Sum_probs=94.4

Q ss_pred             HCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHC-CCCCCCCCCCHHHHHHHHHCCCCCCCHHCCCCHHHHH
Q ss_conf             589589996289987248704699848898852167899762-9985556689889886431032211000036756754
Q gi|254781112|r   39 DQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRL-NLKVEFFETAVSGLITGLDTNRYDVLVNVAITPERQK  117 (274)
Q Consensus        39 ~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~l-g~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~t~eR~~  117 (274)
                      ..+.|+|++...+.-. |            ....+....++. ++++++...+.   ..++..+++|++......+.  .
T Consensus        92 ~~g~l~I~~~~~~~~~-~------------l~p~l~~f~~~~P~i~v~l~~~~~---~~~l~~~~~Diai~~~~~~~--~  153 (295)
T PRK11139         92 AKGALTVSLLPSFAIK-W------------LVPRLSSFNEAHPDIDVRLQAVDR---LEDFLRDDVDVAIRYGRGNW--P  153 (295)
T ss_pred             CCCEEEEEEECCHHHH-H------------HHHHHHHHHHCCCCEEEEEEECCC---HHHHHCCCCEEEEEEECCCC--C
T ss_conf             7873999996322777-6------------334666666108858999996241---66663347438999723776--7


Q ss_pred             HHCCCCCCCCCCCCCCCCCCC----CCCCCCCCCCCCCEEE-ECCCHHHHHHHCCC-----C-CCEEECCHHHHHHHHHH
Q ss_conf             200233322222222211122----2211111233432023-10101223320134-----5-42133685577775544
Q gi|254781112|r  118 KYDFSIPYIAHRVLLVVRSDQ----QDIRSFKDLTDKTVAQ-ILGTDLSRFAKELK-----S-HLVFSHNFEQSLQLLLS  186 (274)
Q Consensus       118 ~~~fs~p~~~~~~~~~~~~~~----~~~~~~~dL~g~~V~~-~~g~~~~~~l~~~~-----~-~~~~~~~~~~~~~~l~~  186 (274)
                      . ..+.++......+++..+.    ....+++||++..+-. ..+..+..+.+..+     . ....+++....++++.+
T Consensus       154 ~-l~~~~l~~~~~~~vasp~~~~~~~~~~~~~dL~~~~li~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~  232 (295)
T PRK11139        154 G-LRVEKLLDEYLFPVCSPALLNGGKPLKTPEDLARHTLLHDDSREDWRAWFRAAGLNDINVQQGPIFSHSSMALQAAIH  232 (295)
T ss_pred             C-EEEEEEECCEEEEEECHHHHHHCCCCCCHHHHHCCCEEEECCCCHHHHHHHHCCCCCCCCCCCEEECCHHHHHHHHHH
T ss_conf             6-279994044699998879996479999999981898796369621588998569865467875288789999999995


Q ss_pred             HHHHCCCCCHHHHHHHHHHCCCCCCCEEEC-CCCCCCCCEEEEEECCC---HHHHHHHHHHHHHH
Q ss_conf             321003665589999998458766732623-67768770799981899---89999999999999
Q gi|254781112|r  187 KRTDATMIPDIPFFNFLERRPHDGNLFKIA-DRMKDNSAVAFMMRKGN---NKLTRSINEILCAI  247 (274)
Q Consensus       187 grvD~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~k~~---~~L~~~in~~l~~l  247 (274)
                      |.. ..+.+...+...+.+-    ..+.+. +....+.++++..+++.   +..+..++.-++++
T Consensus       233 G~G-ia~lp~~~v~~~l~~G----~Lv~~l~~~~~~~~~~~lv~~~~~~~~p~v~~F~~~L~~~~  292 (295)
T PRK11139        233 GQG-VALGRRVLAQPEIEAG----RLVCPFDIVLPSKNAFYLVCPPSQAELPKVAAFRQWLLAEA  292 (295)
T ss_pred             CCE-EEECCHHHHHHHHHCC----CEEEECCCCCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHH
T ss_conf             992-9977799999998789----97998986667887599998089878989999999999985


No 157
>TIGR01980 sufB FeS assembly protein SufB; InterPro: IPR010231   Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems.   The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly .   The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets.   In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen .   This entry represents SufB, which is part of the SUF system and forms a complex with SufBCD.; GO: 0005515 protein binding, 0016226 iron-sulfur cluster assembly.
Probab=35.08  E-value=25  Score=15.57  Aligned_cols=12  Identities=17%  Similarity=0.293  Sum_probs=5.1

Q ss_pred             HHHCCCCCHHHH
Q ss_conf             210036655899
Q gi|254781112|r  188 RTDATMIPDIPF  199 (274)
Q Consensus       188 rvD~~~~~~~~~  199 (274)
                      +||+.++|+...
T Consensus       387 ~CD~Ll~Dd~S~  398 (469)
T TIGR01980       387 QCDSLLLDDESA  398 (469)
T ss_pred             EEEEEEECCCCC
T ss_conf             566556578422


No 158
>TIGR01054 rgy reverse gyrase; InterPro: IPR005736   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA.    Reverse gyrase is a type IA topoisomerase that is unique among these enzymes in its requirement for ATP. Reverse gyrase is a hyperthermophile-specific enzyme that acts as a renaturase by positively supercoiling DNA, and by annealing complementary single-strand circles . Hyperthermophilic organisms must protect themselves against heat-induced degradation, and reverse gyrase acts to reduce the rate of double-strand DNA breakage, a function that does not require ATP hydrolysis and which is independent of its positive supercoiling abilities. Reverse gyrase achieves this by recognising nicked DNA and recruiting a protein coat to the site of damage .   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=34.31  E-value=11  Score=17.76  Aligned_cols=18  Identities=17%  Similarity=0.231  Sum_probs=7.1

Q ss_pred             HHHHHHHHHCCCCCCCHH
Q ss_conf             889886431032211000
Q gi|254781112|r   91 VSGLITGLDTNRYDVLVN  108 (274)
Q Consensus        91 ~~~~~~~l~~g~~D~~~~  108 (274)
                      ..+.++.+..|++|++.|
T Consensus       401 ~~~~~~~F~~GE~dVliG  418 (1843)
T TIGR01054       401 PKEDLEKFAEGEIDVLIG  418 (1843)
T ss_pred             CCCCHHHHHCCCEEEEEE
T ss_conf             732034663485136877


No 159
>PRK04922 tolB translocation protein TolB; Provisional
Probab=34.23  E-value=26  Score=15.40  Aligned_cols=40  Identities=15%  Similarity=0.176  Sum_probs=19.5

Q ss_pred             CEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCCCCCCC
Q ss_conf             5899962899872487046998488988521678997629985556689
Q gi|254781112|r   42 ALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFFETA   90 (274)
Q Consensus        42 ~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~~~~~~   90 (274)
                      .+.|++    +||.+.  +....   ...|+.+.|...|...=.|.+++
T Consensus        38 ~~pIAV----~pF~~~--~~~~~---~~~~i~~II~~DL~~SG~F~~l~   77 (439)
T PRK04922         38 ATPIAV----VPMPYQ--GSGTA---PQTDVSAVVSADLDRSGQFRTLP   77 (439)
T ss_pred             CEEEEE----ECCCCC--CCCCC---HHHHHHHHHHHHHHHCCCCCCCC
T ss_conf             050699----375657--87655---03649999986577272744159


No 160
>TIGR00623 sula cell division inhibitor SulA; InterPro: IPR004596   All proteins in this family for which the functions are known are cell division inhibitors. In Escherichia coli, SulA is one of the SOS regulated genes. Accumulation of SulA causes rapid cessation of cell division and the appearance of long, non-septate filaments. The expression of SulA is repressed by LexA. The N-terminus of SulA may be involved in recognising the cell division apparatus.; GO: 0009432 SOS response, 0009276 1-2nm peptidoglycan-based cell wall.
Probab=33.60  E-value=27  Score=15.35  Aligned_cols=61  Identities=18%  Similarity=0.260  Sum_probs=33.6

Q ss_pred             HHHHHHHHHCCCCCCCHHCC---CCHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCE
Q ss_conf             88988643103221100003---675675420023332222222221112222111112334320
Q gi|254781112|r   91 VSGLITGLDTNRYDVLVNVA---ITPERQKKYDFSIPYIAHRVLLVVRSDQQDIRSFKDLTDKTV  152 (274)
Q Consensus        91 ~~~~~~~l~~g~~D~~~~~~---~t~eR~~~~~fs~p~~~~~~~~~~~~~~~~~~~~~dL~g~~V  152 (274)
                      -+.++.+|++|++.++.|.-   -|+|-..... ...-.-...+|+.|.-...-..-..+.|.+|
T Consensus        99 ~E~M~rAL~TGNYsVViGWl~~eLTEee~~~L~-~AA~~G~a~GFIMRP~r~~s~~~r~~SgLKI  162 (168)
T TIGR00623        99 VESMIRALRTGNYSVVIGWLTDELTEEEHAKLV-EAAEEGNAMGFIMRPVRAISQPRRQLSGLKI  162 (168)
T ss_pred             HHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHH-HHHHCCCCCEEEECCCHHCCCCCCCCCCCEE
T ss_conf             999999971499348871466304767899999-9985389712533780210345556441021


No 161
>pfam10991 DUF2815 Protein of unknown function (DUF2815). This is a phage related family of proteins with unknown function.
Probab=33.55  E-value=34  Score=14.70  Aligned_cols=16  Identities=19%  Similarity=0.538  Sum_probs=7.9

Q ss_pred             CEEEEECCCCCCEEEE
Q ss_conf             5899962899872487
Q gi|254781112|r   42 ALRVGTDGIYPPHSFH   57 (274)
Q Consensus        42 ~l~v~~~~~~pP~~~~   57 (274)
                      .+|.+--.-|-|....
T Consensus         7 ~VRlSy~~l~ep~~~~   22 (181)
T pfam10991         7 NVRLSYANLFEPKSIE   22 (181)
T ss_pred             CEEEECCCCCCCCCCC
T ss_conf             4889843104664344


No 162
>cd01423 MGS_CPS_I_III Methylglyoxal synthase-like domain found in pyr1 and URA1-like carbamoyl phosphate synthetases (CPS), including ammonia-dependent CPS Type I, and glutamine-dependent CPS Type III. These are multidomain proteins, in which MGS is the C-terminal domain.
Probab=32.94  E-value=24  Score=15.62  Aligned_cols=34  Identities=15%  Similarity=0.128  Sum_probs=18.3

Q ss_pred             HHHCCCCCCCCCCC-------HHHHHHHHHCCCCCCCHHCC
Q ss_conf             97629985556689-------88988643103221100003
Q gi|254781112|r   77 AHRLNLKVEFFETA-------VSGLITGLDTNRYDVLVNVA  110 (274)
Q Consensus        77 ~~~lg~~~~~~~~~-------~~~~~~~l~~g~~D~~~~~~  110 (274)
                      .+..|++++.+...       -...++.+++|++|++.+++
T Consensus        39 l~~~Gi~~~~v~k~~e~~~~~~p~i~d~i~~g~i~lVINtp   79 (116)
T cd01423          39 LLENGIPVTPVAWPSEEPQNDKPSLRELLAEGKIDLVINLP   79 (116)
T ss_pred             HHHCCCCCEEEEEECCCCCCCCCCHHHHHHCCCEEEEEECC
T ss_conf             99869965798786246789996699999769868999888


No 163
>PRK13357 branched-chain amino acid aminotransferase; Provisional
Probab=32.80  E-value=17  Score=16.51  Aligned_cols=43  Identities=12%  Similarity=-0.020  Sum_probs=28.6

Q ss_pred             EEECCCHHHHHHHCCCCCCEEEC-CHHHHHHHHHHHHHHCCCCCH
Q ss_conf             23101012233201345421336-855777755443210036655
Q gi|254781112|r  153 AQILGTDLSRFAKELKSHLVFSH-NFEQSLQLLLSKRTDATMIPD  196 (274)
Q Consensus       153 ~~~~g~~~~~~l~~~~~~~~~~~-~~~~~~~~l~~grvD~~~~~~  196 (274)
                      |+.+.+..+ ++++.+.++.+-. +.++.+.+...|++|=+++..
T Consensus       259 GITR~svi~-la~~~G~~V~Er~i~~~el~~a~~~g~l~E~F~tG  302 (357)
T PRK13357        259 GITRDSLLQ-LAKDLGLTVEERDVSIDEWQADAASGEFTEAFACG  302 (357)
T ss_pred             CHHHHHHHH-HHHHCCCEEEEEECCHHHHHHHHHCCCEEEEEECC
T ss_conf             744999999-99986981799965999999775459737999635


No 164
>PRK00050 mraW S-adenosyl-methyltransferase MraW; Provisional
Probab=32.78  E-value=35  Score=14.62  Aligned_cols=41  Identities=17%  Similarity=0.381  Sum_probs=29.4

Q ss_pred             CCEEEEEECCCHHHHHHHHHHHHHHHHCCHH---------HHHHHHHCCC
Q ss_conf             7079998189989999999999999979859---------9999876788
Q gi|254781112|r  223 SAVAFMMRKGNNKLTRSINEILCAIHLDGTY---------KKIFDRYFDK  263 (274)
Q Consensus       223 ~~~~~~~~k~~~~L~~~in~~l~~l~~~G~~---------~~I~~kw~g~  263 (274)
                      +.+.+.|+.+=.+|...+.++..-++..|.+         ++|++++|-.
T Consensus       206 QALRI~VN~EL~~L~~~L~~~~~~L~~gGrl~vISfHSLEDRiVK~ff~~  255 (309)
T PRK00050        206 QAIRIEVNDELEELEEALEAALEVLAPGGRLSVISFHSLEDRIVKRFFKE  255 (309)
T ss_pred             HHHHHHHCCHHHHHHHHHHHHHHHHHCCCEEEEEEECCHHHHHHHHHHHH
T ss_conf             99999970269999999999999985075399998433257899999997


No 165
>COG2182 MalE Maltose-binding periplasmic proteins/domains [Carbohydrate transport and metabolism]
Probab=32.49  E-value=29  Score=15.12  Aligned_cols=24  Identities=17%  Similarity=0.281  Sum_probs=16.3

Q ss_pred             EEHHHHHHHCCCCCCCCCCCHHHH
Q ss_conf             216789976299855566898898
Q gi|254781112|r   71 DLIKEVAHRLNLKVEFFETAVSGL   94 (274)
Q Consensus        71 dl~~~i~~~lg~~~~~~~~~~~~~   94 (274)
                      +.+..+-++.|++|+++..+....
T Consensus        58 ~~~~kfek~~gi~V~i~~~~~~d~   81 (420)
T COG2182          58 EAAAKFEKETGIKVKIVEEDYDDL   81 (420)
T ss_pred             HHHHHHHHHHCCEEEEEECCCCCH
T ss_conf             999999998797589994675048


No 166
>pfam00072 Response_reg Response regulator receiver domain. This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain.
Probab=29.57  E-value=36  Score=14.57  Aligned_cols=33  Identities=21%  Similarity=0.263  Sum_probs=16.4

Q ss_pred             HHHCCCCCCEEECCHHHHHHHHHHHHHHCCCCC
Q ss_conf             320134542133685577775544321003665
Q gi|254781112|r  163 FAKELKSHLVFSHNFEQSLQLLLSKRTDATMIP  195 (274)
Q Consensus       163 ~l~~~~~~~~~~~~~~~~~~~l~~grvD~~~~~  195 (274)
                      +++..+.++..+.+.+++++.+...+.|.++.|
T Consensus        17 ~L~~~g~~v~~a~~g~~al~~~~~~~~dlvi~D   49 (111)
T pfam00072        17 LLEKEGYVVAEADDGEEALELLKEKRPDLILLD   49 (111)
T ss_pred             HHHHCCCEEEEECCHHHHHHHHHHCCCCEEEEE
T ss_conf             999889999998999999999984799899995


No 167
>COG2247 LytB Putative cell wall-binding domain [Cell envelope biogenesis, outer membrane]
Probab=29.45  E-value=40  Score=14.27  Aligned_cols=81  Identities=17%  Similarity=0.255  Sum_probs=39.4

Q ss_pred             EHHHHHHHCCCCCCCCCCCHH----HHHHHHHCCCCCC--CHH--CCCCHHHHHHHCCCCCCCCCCCCC-CCCC-CCCCC
Q ss_conf             167899762998555668988----9886431032211--000--036756754200233322222222-2111-22221
Q gi|254781112|r   72 LIKEVAHRLNLKVEFFETAVS----GLITGLDTNRYDV--LVN--VAITPERQKKYDFSIPYIAHRVLL-VVRS-DQQDI  141 (274)
Q Consensus        72 l~~~i~~~lg~~~~~~~~~~~----~~~~~l~~g~~D~--~~~--~~~t~eR~~~~~fs~p~~~~~~~~-~~~~-~~~~~  141 (274)
                      ++..+++.++-++-  .+||+    +....+.+-+-|.  +.|  .+.++.-++...        +..+ +.|. |++++
T Consensus        43 lA~~iaellNA~Vl--ttpwg~ynes~~~eI~~lnpd~VLIIGGp~AVs~~yE~~Lk--------s~GitV~RigG~nR~  112 (337)
T COG2247          43 LALPIAELLNAPVL--TTPWGIYNESVLDEIIELNPDLVLIIGGPIAVSPNYENALK--------SLGITVKRIGGANRY  112 (337)
T ss_pred             HHHHHHHHHCCEEE--ECCCCCCCHHHHHHHHHHCCCEEEEECCCCCCCHHHHHHHH--------HCCCEEEEECCCCHH
T ss_conf             75679997589057--26754213999999996198659997898757865899998--------579579993376268


Q ss_pred             CCC------------CCCCCCCEEEECCCHHHH
Q ss_conf             111------------123343202310101223
Q gi|254781112|r  142 RSF------------KDLTDKTVAQILGTDLSR  162 (274)
Q Consensus       142 ~~~------------~dL~g~~V~~~~g~~~~~  162 (274)
                      .+-            .-+++-+++++.|+.|..
T Consensus       113 ETa~~v~~~~~~~yp~af~n~kvvvv~GwDy~~  145 (337)
T COG2247         113 ETAEKVAKFFREDYPNAFKNVKVVVVYGWDYAD  145 (337)
T ss_pred             HHHHHHHHHHHHHCHHHHCCEEEEEEECCCCHH
T ss_conf             999999999976442331581799996602277


No 168
>PRK11597 heat shock chaperone IbpB; Provisional
Probab=29.35  E-value=19  Score=16.29  Aligned_cols=34  Identities=18%  Similarity=0.361  Sum_probs=19.4

Q ss_pred             CCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCC
Q ss_conf             28998724870469984889885216789976299855
Q gi|254781112|r   48 DGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVE   85 (274)
Q Consensus        48 ~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~   85 (274)
                      ..+||||+....|++    .|.++++-+=+.+-.++++
T Consensus        29 ~~~yPpYNI~k~~e~----~y~IeiAvaGf~k~di~I~   62 (142)
T PRK11597         29 SQSFPPYNIEKSDDN----HYRITLALAGFRQEDLDIQ   62 (142)
T ss_pred             CCCCCCCEEEEECCC----EEEEEEEECCCCHHHEEEE
T ss_conf             789999669991797----2999999688775778999


No 169
>TIGR00004 TIGR00004 endoribonuclease L-PSP, putative; InterPro: IPR006056   This family includes proteins encoded by the yabJ gene from Bacillus subtilis that is required for adenine-mediated repression of purine biosynthetic genes in vivo and codes for an acid-soluble, 14-kDa protein. The structure of this protein has been solved  and the protein is found to form a homotrimer. The trimer has a deep cleft that is a probably ligand binding site and possibly forms an enzymatic active site. However the ligand and reaction are unknown..
Probab=29.23  E-value=30  Score=15.01  Aligned_cols=23  Identities=22%  Similarity=0.608  Sum_probs=14.8

Q ss_pred             CHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf             85999998767888775689877
Q gi|254781112|r  251 GTYKKIFDRYFDKNIISSVPGCS  273 (274)
Q Consensus       251 G~~~~I~~kw~g~d~~~~~~~~~  273 (274)
                      .++++||.+||++.-+.+-||-|
T Consensus        86 A~vNevY~~YF~~~~V~~~PARs  108 (129)
T TIGR00004        86 AEVNEVYGQYFDEHSVEPYPARS  108 (129)
T ss_pred             HHHHHHHHHHCCCCCCCCCCCHH
T ss_conf             89998988754877778777311


No 170
>pfam01795 Methyltransf_5 MraW methylase family. Members of this family are probably SAM dependent methyltransferases based on Escherichia coli mraW. This family appears to be related to pfam01596.
Probab=29.09  E-value=32  Score=14.84  Aligned_cols=46  Identities=26%  Similarity=0.343  Sum_probs=27.7

Q ss_pred             CCCCEEEEEEEEHHH-HH-HHC---CCCCCCCCCCHHHHHHHH---HCCCCCCC
Q ss_conf             998488988521678-99-762---998555668988988643---10322110
Q gi|254781112|r   61 GRGELTGFDIDLIKE-VA-HRL---NLKVEFFETAVSGLITGL---DTNRYDVL  106 (274)
Q Consensus        61 ~~g~~~G~~~dl~~~-i~-~~l---g~~~~~~~~~~~~~~~~l---~~g~~D~~  106 (274)
                      ..|.+.|+|-|---. .+ +.+   +-.+.++...|..+-..+   .-+++|.+
T Consensus        44 ~~~~li~iDrD~~ai~~a~~~l~~~~~r~~~~~~nF~~l~~~l~~~~~~~vdGi   97 (310)
T pfam01795        44 EEGRLIGIDRDPQAIANAKERLKPFKGRVTLIHSNFANLFAYLKELGVGKVDGI   97 (310)
T ss_pred             CCCEEEEEECCHHHHHHHHHHCCCCCCCEEEEECCHHHHHHHHHHCCCCCCCEE
T ss_conf             999799998989999999985302588589992537579999987598766789


No 171
>PRK13584 hisG ATP phosphoribosyltransferase catalytic subunit; Provisional
Probab=29.01  E-value=36  Score=14.58  Aligned_cols=149  Identities=12%  Similarity=0.134  Sum_probs=70.9

Q ss_pred             CCCCCCCHHHHHHHHHCCCCCC-CHHCCCCHHHHHH-HCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCHH
Q ss_conf             5556689889886431032211-0000367567542-002-333222222222111222211111233432023101012
Q gi|254781112|r   84 VEFFETAVSGLITGLDTNRYDV-LVNVAITPERQKK-YDF-SIPYIAHRVLLVVRSDQQDIRSFKDLTDKTVAQILGTDL  160 (274)
Q Consensus        84 ~~~~~~~~~~~~~~l~~g~~D~-~~~~~~t~eR~~~-~~f-s~p~~~~~~~~~~~~~~~~~~~~~dL~g~~V~~~~g~~~  160 (274)
                      +++.......+-..+..|.+|+ +.|.-+-.|.... +.. ..+|......+.+++        ++..++||+.-.-...
T Consensus        45 i~~~~vR~~DIp~yV~~G~~DiGIvG~D~l~E~~~~v~~lldL~~G~crl~vA~~~--------~~~~~~rIATkYp~it  116 (204)
T PRK13584         45 IECILVKGSDVPIYVEQGMADIGIVGSDILDERQYNVNNLLNMPFGACHFAVAAKP--------ETTNYRKIATSYVHTA  116 (204)
T ss_pred             EEEEEECHHHHHHHHHCCCCCEEEECCHHHHCCCCCEEEEECCCCCCEEEEEEECC--------CCCCCCEEEEEHHHHH
T ss_conf             79999886888999974986577526420222689814765267674789999667--------7567878987257799


Q ss_pred             HHHHHCCCCC--CEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEEEECCCH-HHH
Q ss_conf             2332013454--2133685577775544321003665589999998458766732623677687707999818998-999
Q gi|254781112|r  161 SRFAKELKSH--LVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKGNN-KLT  237 (274)
Q Consensus       161 ~~~l~~~~~~--~~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~-~L~  237 (274)
                      .+|.++.+.+  ++......+.  +-..|-.|++ +|-...-..++.+..     .+..... ...-.+..++..- .=.
T Consensus       117 ~~~f~~~gi~~eii~l~GsvEl--AP~~GlAD~I-vDiveTG~TLk~NgL-----~~~e~I~-~s~a~LI~N~~s~~~k~  187 (204)
T PRK13584        117 ETYFKSKGIDVELIKLNGSVEL--ACVVDMVDGI-VDIVQTGTTLKANGL-----VEKQHIS-DINARLITNKAAYFKKS  187 (204)
T ss_pred             HHHHHHCCCCEEEEEEEEEEEE--CCCCCCCCEE-EEEECCCHHHHHCCC-----EEEEEEE-EEEEEEEECHHHHHHHH
T ss_conf             9999970995289997536853--6788875589-998377588998799-----8868998-65789999889999889


Q ss_pred             HHHHHHHHHHHH
Q ss_conf             999999999997
Q gi|254781112|r  238 RSINEILCAIHL  249 (274)
Q Consensus       238 ~~in~~l~~l~~  249 (274)
                      +.|++.+..++.
T Consensus       188 ~~I~~li~~l~~  199 (204)
T PRK13584        188 QLIEQFIRSLEV  199 (204)
T ss_pred             HHHHHHHHHHHH
T ss_conf             999999999999


No 172
>TIGR02122 TRAP_TAXI TRAP transporter solute receptor, TAXI family; InterPro: IPR011852    This family is one of at least three major families of extracytoplasmic solute receptor (ESR) for TRAP (Tripartite ATP-independent Periplasmic Transporter) transporters. The others are the DctP (IPR004682 from INTERPRO) and SmoM (IPR004682 from INTERPRO) families. These transporters are secondary (driven by an ion gradient) but composed of three polypeptides, although in some species the 4-TM and 12-TM integral membrane proteins are fused. Substrates for this transporter family are not fully characterised but, besides C4 dicarboxylates, may include mannitol and other compounds ..
Probab=28.68  E-value=25  Score=15.51  Aligned_cols=128  Identities=17%  Similarity=0.155  Sum_probs=64.9

Q ss_pred             EEHHHHHHHCC--CCCCCCCCC-HHHHHHHHHCCCCCCCHHC----CCCHHHHHHHCC---------CCCCCCCCCCCCC
Q ss_conf             21678997629--985556689-8898864310322110000----367567542002---------3332222222221
Q gi|254781112|r   71 DLIKEVAHRLN--LKVEFFETA-VSGLITGLDTNRYDVLVNV----AITPERQKKYDF---------SIPYIAHRVLLVV  134 (274)
Q Consensus        71 dl~~~i~~~lg--~~~~~~~~~-~~~~~~~l~~g~~D~~~~~----~~t~eR~~~~~f---------s~p~~~~~~~~~~  134 (274)
                      .+.+.+....+  ..+...... .......+..|+.+.....    .+..+....+.+         ....+.....+++
T Consensus        44 ~~~~~~~~~~~~~~~~~~~~~~~s~~n~~~~~~~~~~~~~~~~~~~~~a~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~  123 (319)
T TIGR02122        44 AIAQLINKALGKVLRVSAQSTGGSVENVNLLEAGEAELAIVQSDVAYYAYEGIGEFEFKGPVEKLRALASLYPEYIQIVV  123 (319)
T ss_pred             HHHHHHHHCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHCCCCCCCCEEEE
T ss_conf             45555421013220223211454112333333213455554433344432101110012333200000012454210232


Q ss_pred             CCCCCCCCCCCCCCCCCEEEECCCHHH-----HHHHCCC-----CCCEEECCHHHHHHHHHHHHHHCCCCCHHHH
Q ss_conf             112222111112334320231010122-----3320134-----5421336855777755443210036655899
Q gi|254781112|r  135 RSDQQDIRSFKDLTDKTVAQILGTDLS-----RFAKELK-----SHLVFSHNFEQSLQLLLSKRTDATMIPDIPF  199 (274)
Q Consensus       135 ~~~~~~~~~~~dL~g~~V~~~~g~~~~-----~~l~~~~-----~~~~~~~~~~~~~~~l~~grvD~~~~~~~~~  199 (274)
                      ++++ .++++.||+|+++.+.......     ..++..+     .....+....+....+.++..|+.+......
T Consensus       124 ~~~~-~~~~~~dl~gk~~~~~~~~sg~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~g~~  197 (319)
T TIGR02122       124 RKDS-GIKTVADLKGKRVAVGAPGSGTELNARAVLKAAGLTYDDIKEAEYLGYAEAADALKDGKIDAAFITAGLP  197 (319)
T ss_pred             ECCC-CCCCHHHHCCCEECCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHCCCCCCHHHHHCCCCCEEEECCCCC
T ss_conf             0113-4310122035300024666430134778876504651120011102310001343202310001013444


No 173
>pfam02642 consensus
Probab=27.46  E-value=43  Score=14.06  Aligned_cols=149  Identities=16%  Similarity=0.096  Sum_probs=69.3

Q ss_pred             CCCHHHHHHHHHCCCCCCCH-HCCCCHH-HHHHHCCC-C-CCCC-CCCCCCCCCCCCCCCCCCCCCCCCEEEECCCH-HH
Q ss_conf             68988988643103221100-0036756-75420023-3-3222-22222211122221111123343202310101-22
Q gi|254781112|r   88 ETAVSGLITGLDTNRYDVLV-NVAITPE-RQKKYDFS-I-PYIA-HRVLLVVRSDQQDIRSFKDLTDKTVAQILGTD-LS  161 (274)
Q Consensus        88 ~~~~~~~~~~l~~g~~D~~~-~~~~t~e-R~~~~~fs-~-p~~~-~~~~~~~~~~~~~~~~~~dL~g~~V~~~~g~~-~~  161 (274)
                      ..+=+.+-....+|++|+.. ++.--+. ++++...+ . .+-. .+..++.++       ..++++++|+++--.+ ..
T Consensus        34 l~DIetLN~~A~~g~~dvskiS~~ayp~i~d~Y~lL~~G~alG~G~GPlvva~~-------~~~l~~~~iAvPG~~TTA~  106 (259)
T pfam02642        34 IADIETLNREALKNRYEVSAISAHLYPLIADKYALLPVGTSLGYGYGPIVVSKK-------EVSLKLKRLATPGEHTTAH  106 (259)
T ss_pred             EECHHHHHHHHHCCCCCEEEECHHHHHHHHHCEEEEECHHHCCCCCCCEEEECC-------CCCCCCCEEECCCHHHHHH
T ss_conf             527999999998189997887597788686068875332230488687478547-------7777899897877367999


Q ss_pred             HHHHC--CCCCCEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEECC----CCCCCCCEE-EEEECC-C
Q ss_conf             33201--345421336855777755443210036655899999984587667326236----776877079-998189-9
Q gi|254781112|r  162 RFAKE--LKSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIAD----RMKDNSAVA-FMMRKG-N  233 (274)
Q Consensus       162 ~~l~~--~~~~~~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~~~~-~~~~k~-~  233 (274)
                      -..+-  ...+.+. -..++.+.++.+|++|+-+.=...-.-|. +  +.........    ...-+.|+| ++++|+ .
T Consensus       107 lL~~l~~~~~~~v~-~~FdeI~~aV~~G~vDaGviIHE~rftY~-~--gL~~~~DLG~wW~~~tglPlPLG~ivirr~Lg  182 (259)
T pfam02642       107 LLCKLYYPDAELVP-MPFDRIIQAVLEGKVDAGALIHEERFSYH-D--GLKVVKDLGDLWKEKVDLPLPLGCNAIRKDVP  182 (259)
T ss_pred             HHHHHHCCCCEEEE-EEHHHHHHHHHCCCCCCEEEEEHHHHHHH-C--CCEEEEEHHHHHHHHCCCCCCCHHHHHHHCCC
T ss_conf             99998558875999-56899899997599871079763142140-3--98787358899877409987634678661079


Q ss_pred             HHHHHHHHHHHHHH
Q ss_conf             89999999999999
Q gi|254781112|r  234 NKLTRSINEILCAI  247 (274)
Q Consensus       234 ~~L~~~in~~l~~l  247 (274)
                      .+.+..+++++.+=
T Consensus       183 ~~~~~~~~~~lr~S  196 (259)
T pfam02642       183 LEVVILLKRALRES  196 (259)
T ss_pred             HHHHHHHHHHHHHH
T ss_conf             99999999999999


No 174
>cd00156 REC Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; contains a phosphoacceptor site that is phosphorylated by histidine kinase homologs; usually found N-terminal to a DNA binding effector domain; forms homodimers
Probab=27.44  E-value=43  Score=14.06  Aligned_cols=34  Identities=18%  Similarity=0.225  Sum_probs=18.4

Q ss_pred             HHHCCCCCCEEECCHHHHHHHHHHHHHHCCCCCH
Q ss_conf             3201345421336855777755443210036655
Q gi|254781112|r  163 FAKELKSHLVFSHNFEQSLQLLLSKRTDATMIPD  196 (274)
Q Consensus       163 ~l~~~~~~~~~~~~~~~~~~~l~~grvD~~~~~~  196 (274)
                      .+++.+.++..+.+..++++.+.+++.|.++.|-
T Consensus        16 ~L~~~g~~v~~a~~g~~al~~~~~~~~dlvi~D~   49 (113)
T cd00156          16 LLEKEGYEVVEAEDGEEALALLAEEKPDLILLDI   49 (113)
T ss_pred             HHHHCCCEEEEECCHHHHHHHHHHCCCCEEEECC
T ss_conf             9998899999989999999998757999999779


No 175
>COG4150 CysP ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=27.30  E-value=18  Score=16.37  Aligned_cols=27  Identities=26%  Similarity=0.535  Sum_probs=20.2

Q ss_pred             CCCCCCCCCCCCCCCCCCC-CCCCCCCCC
Q ss_conf             2333222222222111222-211111233
Q gi|254781112|r  121 FSIPYIAHRVLLVVRSDQQ-DIRSFKDLT  148 (274)
Q Consensus       121 fs~p~~~~~~~~~~~~~~~-~~~~~~dL~  148 (274)
                      =|.|||.... +++|++++ .|++|+||.
T Consensus       119 nsSPfYS~~a-FLVR~GNPK~IkdW~DLv  146 (341)
T COG4150         119 NSSPFYSTMA-FLVRKGNPKNIKDWDDLV  146 (341)
T ss_pred             CCCCCCCCHH-HHHHCCCCCCCCCHHHHH
T ss_conf             8896432327-775368966676577775


No 176
>COG0275 Predicted S-adenosylmethionine-dependent methyltransferase involved in cell envelope biogenesis [Cell envelope biogenesis, outer membrane]
Probab=26.86  E-value=44  Score=13.99  Aligned_cols=46  Identities=13%  Similarity=0.283  Sum_probs=35.2

Q ss_pred             CCCCCEEEEEECCCHHHHHHHHHHHHHHHHCCHH---------HHHHHHHCCCCC
Q ss_conf             6877079998189989999999999999979859---------999987678887
Q gi|254781112|r  220 KDNSAVAFMMRKGNNKLTRSINEILCAIHLDGTY---------KKIFDRYFDKNI  265 (274)
Q Consensus       220 ~~~~~~~~~~~k~~~~L~~~in~~l~~l~~~G~~---------~~I~~kw~g~d~  265 (274)
                      ..-+.+.+.|+.+-.+|...+..++..++..|++         ++|.+++|-+..
T Consensus       207 r~FQAiRI~VNdEL~~L~~~L~~a~~~L~~~GRl~VIsFHSLEDRiVK~ff~~~s  261 (314)
T COG0275         207 RTFQAIRIYVNDELEELEEALEAALDLLKPGGRLAVISFHSLEDRIVKNFFKELS  261 (314)
T ss_pred             HHHHHHEEEEHHHHHHHHHHHHHHHHHHCCCCEEEEEEECCHHHHHHHHHHHHHC
T ss_conf             6563410000567999999999999961889679999953428999999999840


No 177
>KOG0623 consensus
Probab=26.37  E-value=44  Score=14.01  Aligned_cols=18  Identities=22%  Similarity=0.357  Sum_probs=11.7

Q ss_pred             HHHHHHHHHCCCCCCCCC
Q ss_conf             599999876788877568
Q gi|254781112|r  252 TYKKIFDRYFDKNIISSV  269 (274)
Q Consensus       252 ~~~~I~~kw~g~d~~~~~  269 (274)
                      .++.|.+-|=.+-|+.|+
T Consensus       378 ~iEtISkaYGnQAVViSv  395 (541)
T KOG0623         378 SIETISKAYGNQAVVISV  395 (541)
T ss_pred             HHHHHHHHHCCEEEEEEE
T ss_conf             189998872770499996


No 178
>PRK11289 ampC beta-lactamase; Provisional
Probab=26.35  E-value=45  Score=13.93  Aligned_cols=32  Identities=9%  Similarity=-0.001  Sum_probs=17.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHH
Q ss_conf             99999999999999999999999998417887
Q gi|254781112|r    5 LRDLRKIFFSKYLFFAPFFILFSYYFVIYPFR   36 (274)
Q Consensus         5 ~~~mk~~~~~~~l~~~~~~~~~~~~~~~~~~~   36 (274)
                      |+-|+|.++..+++...+++..+.+.++.+.+
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~a~~~~   32 (387)
T PRK11289          1 MSLMMKSLLAALLLTASISAFAAPAAAATSQQ   32 (387)
T ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHH
T ss_conf             91799999999999999986167655699799


No 179
>COG0077 PheA Prephenate dehydratase [Amino acid transport and metabolism]
Probab=26.02  E-value=34  Score=14.69  Aligned_cols=117  Identities=9%  Similarity=0.157  Sum_probs=62.8

Q ss_pred             HCCCCCCCCCC-CHHHHHHHHHCCCCCCCH-HC------CCCHHHHHHHCCC------CCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             62998555668-988988643103221100-00------3675675420023------3322222222211122221111
Q gi|254781112|r   79 RLNLKVEFFET-AVSGLITGLDTNRYDVLV-NV------AITPERQKKYDFS------IPYIAHRVLLVVRSDQQDIRSF  144 (274)
Q Consensus        79 ~lg~~~~~~~~-~~~~~~~~l~~g~~D~~~-~~------~~t~eR~~~~~fs------~p~~~~~~~~~~~~~~~~~~~~  144 (274)
                      ..+-..+..+. +...+++++.+|++|... .+      ++.+-- +....+      .-.+.....++++.+    .++
T Consensus        22 ~f~~~~~~~p~~ti~evf~ave~g~aD~gVVPIENS~eG~V~~tl-DlL~~~~l~IvgE~~lpI~h~L~~~~~----~~l   96 (279)
T COG0077          22 LFGSGAELLPCSTIEDVFKAVENGEADYGVVPIENSIEGSVNETL-DLLAETDLQIVGEIVLPIHHCLLVKGG----VDL   96 (279)
T ss_pred             HCCCCCEECCCCCHHHHHHHHHCCCCCEEEEEEEECCCCCHHHHH-HHHCCCCCEEEEEEEEEEEEEEEECCC----CCH
T ss_conf             610354012479999999999769986699976603884038878-754359868999999877999981688----886


Q ss_pred             CCCCCCCEEEE-CCCH-HHHHHHCC--CCCCEEECCHHHHHHHHHH--HHHHCCCCCHHHHHHH
Q ss_conf             12334320231-0101-22332013--4542133685577775544--3210036655899999
Q gi|254781112|r  145 KDLTDKTVAQI-LGTD-LSRFAKEL--KSHLVFSHNFEQSLQLLLS--KRTDATMIPDIPFFNF  202 (274)
Q Consensus       145 ~dL~g~~V~~~-~g~~-~~~~l~~~--~~~~~~~~~~~~~~~~l~~--grvD~~~~~~~~~~~~  202 (274)
                      ++++  +|-.. .... ..+|++++  +.+++...|..++.+++..  .+..|++++...+..|
T Consensus        97 ~~Ik--~vySHpqalaQc~~~L~~~~p~~~~~~~~STa~Aak~v~~~~~~~~AAIas~~aA~~y  158 (279)
T COG0077          97 EEIK--TVYSHPQALAQCRKFLRAHLPGVEIEYTSSTAEAAKLVAEGPDETVAAIASELAAELY  158 (279)
T ss_pred             HHCE--EEEECCHHHHHHHHHHHHCCCCCEEEECCCHHHHHHHHHHCCCCCEEEECCHHHHHHC
T ss_conf             6575--8874728999999999972888369981788999999972898673687698789773


No 180
>TIGR01752 flav_long flavodoxin; InterPro: IPR010086   Flavodoxins are small redox-active proteins with a flavin mononucleotide (FMN) prosthetic group. They function as electron transfer agents in a variety of microbial metabolic processes, including nitrogen fixation by nitrogenase , sulphite reduction , and light-dependent NADP+ reduction during photosynthesis . This entry describes the long chain type, typical for nitrogen fixation but associated with pyruvate formate-lyase activation and cobalamin-dependent methionine synthase activity in Escherichia coli .; GO: 0010181 FMN binding, 0006118 electron transport.
Probab=25.55  E-value=47  Score=13.84  Aligned_cols=156  Identities=23%  Similarity=0.300  Sum_probs=82.6

Q ss_pred             CCEEEEEEEEHHHHHHHCC-CC-CCCCCCCHHHHHHHHHCCCCCCC-HHCCCCHHHHHHHCCCCCCCCCCCCCC--CCCC
Q ss_conf             8488988521678997629-98-55566898898864310322110-000367567542002333222222222--1112
Q gi|254781112|r   63 GELTGFDIDLIKEVAHRLN-LK-VEFFETAVSGLITGLDTNRYDVL-VNVAITPERQKKYDFSIPYIAHRVLLV--VRSD  137 (274)
Q Consensus        63 g~~~G~~~dl~~~i~~~lg-~~-~~~~~~~~~~~~~~l~~g~~D~~-~~~~~t~eR~~~~~fs~p~~~~~~~~~--~~~~  137 (274)
                      |.-+|.+-.+++.|.+.+| .. +..+.+.-.+.. .  -..+|++ .++ +|..      +=+    -+ .+=  +...
T Consensus         7 Gt~TG~T~~iAe~I~~~lG~~~~~d~~ni~~~~~~-~--~~~Y~~LIlGt-PTw~------~Ge----Lq-GleaGCes~   71 (176)
T TIGR01752         7 GTDTGNTEGIAEKIAKELGKESDVDVFNIAKASLE-D--LEAYDILILGT-PTWG------VGE----LQ-GLEAGCESE   71 (176)
T ss_pred             ECCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCHH-H--HHCCCCEEEEC-CCCC------CCC----CC-CCCCCCCCC
T ss_conf             45876078999999998188866210132312468-6--63487058744-7666------776----66-654467742


Q ss_pred             --CCCCCCCC--CCCCCCEEEECCCHHHHHHHCCCCCCEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCE
Q ss_conf             --22211111--23343202310101223320134542133685577775544321003665589999998458766732
Q gi|254781112|r  138 --QQDIRSFK--DLTDKTVAQILGTDLSRFAKELKSHLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLF  213 (274)
Q Consensus       138 --~~~~~~~~--dL~g~~V~~~~g~~~~~~l~~~~~~~~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~  213 (274)
                        ...+.+++  ||+||+||..          -++.+..-.++..+++..|...=.+.  ....+.     .-|.+..-+
T Consensus        72 dW~~~~~~L~~~dl~GK~VAlf----------GlGDQ~~Ysd~F~dgmg~L~d~~~~~--Ga~~VG-----~wPtdGY~F  134 (176)
T TIGR01752        72 DWEEFLSDLEELDLKGKTVALF----------GLGDQEGYSDTFCDGMGILYDKIKAR--GAKVVG-----FWPTDGYEF  134 (176)
T ss_pred             CHHHHHHHHHHCCCCCCEEEEE----------ECCCCCCCHHHHHHHHHHHHHHHHHC--CCEEEE-----CCCCCCEEC
T ss_conf             1677765442023588768997----------25884611066787788999998515--880775-----146995001


Q ss_pred             EECCCCCCC-CCEEEEEECCCH-HH-HHHHHHHHHHHHHC
Q ss_conf             623677687-707999818998-99-99999999999979
Q gi|254781112|r  214 KIADRMKDN-SAVAFMMRKGNN-KL-TRSINEILCAIHLD  250 (274)
Q Consensus       214 ~~~~~~~~~-~~~~~~~~k~~~-~L-~~~in~~l~~l~~~  250 (274)
                      ..+...... ...++|+=.+|+ .| .++|.+++.+++..
T Consensus       135 ~aSkA~~~gd~FVGLAlDeDNQ~dLT~~RI~~Wv~qIk~~  174 (176)
T TIGR01752       135 EASKAVRDGDKFVGLALDEDNQPDLTEERIEKWVEQIKPE  174 (176)
T ss_pred             CCCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             5664300687158872154377423189999999998764


No 181
>TIGR01132 pgm phosphoglucomutase, alpha-D-glucose phosphate-specific; InterPro: IPR005852    Phosphoglucomutase, alpha-D-glucose phosphate-specific () links the anaerobic or aerobic glycolysis of glucose-6-phosphate and glucose-1-phosphate produced by various glycan phosphorylases by catalysing the transfer of a phosphate group between C-1 and C-6 of glucose .     Alpha-D-glucose 1-phosphate = alpha-D-glucose 6-phosphate.; GO: 0004614 phosphoglucomutase activity, 0005975 carbohydrate metabolic process.
Probab=24.33  E-value=36  Score=14.53  Aligned_cols=34  Identities=35%  Similarity=0.673  Sum_probs=26.3

Q ss_pred             HCCCEEEEECCCCCCEEEEEECCCCCEEEEEEEEHHHHHHHCCCCCCCC
Q ss_conf             5895899962899872487046998488988521678997629985556
Q gi|254781112|r   39 DQSALRVGTDGIYPPHSFHAQDGRGELTGFDIDLIKEVAHRLNLKVEFF   87 (274)
Q Consensus        39 ~~~~l~v~~~~~~pP~~~~~~d~~g~~~G~~~dl~~~i~~~lg~~~~~~   87 (274)
                      ++-.||+|++    |+.           |-.+|+++.|+++-++++.+|
T Consensus       229 ~~Agl~lGvD----PLG-----------Ga~v~YW~~Ia~~y~L~lt~V  262 (553)
T TIGR01132       229 RKAGLRLGVD----PLG-----------GAGVDYWKEIAEKYNLDLTLV  262 (553)
T ss_pred             HHCCCEECCC----CCC-----------CCCHHHHHHHHHHHCCCEEEE
T ss_conf             6589777234----677-----------787367899998757864765


No 182
>PRK02889 tolB translocation protein TolB; Provisional
Probab=23.59  E-value=47  Score=13.82  Aligned_cols=16  Identities=13%  Similarity=0.048  Sum_probs=9.8

Q ss_pred             EEEEEHHHHHHHCCCC
Q ss_conf             8852167899762998
Q gi|254781112|r   68 FDIDLIKEVAHRLNLK   83 (274)
Q Consensus        68 ~~~dl~~~i~~~lg~~   83 (274)
                      ..-|+.+-|...|...
T Consensus        53 ~~~~i~~II~~DL~~S   68 (430)
T PRK02889         53 LPQQVTSIVRADLARS   68 (430)
T ss_pred             CHHHHHHHHHHHHHHC
T ss_conf             5067999999888728


No 183
>PRK03147 thiol-disulfide oxidoreductase; Provisional
Probab=23.55  E-value=48  Score=13.74  Aligned_cols=21  Identities=24%  Similarity=0.347  Sum_probs=10.9

Q ss_pred             CCEEEEECCCCCCEEEEEECCCCCE
Q ss_conf             9589996289987248704699848
Q gi|254781112|r   41 SALRVGTDGIYPPHSFHAQDGRGEL   65 (274)
Q Consensus        41 ~~l~v~~~~~~pP~~~~~~d~~g~~   65 (274)
                      ..+.||  ..-|.|+..  |-+|+.
T Consensus        34 ~~~~iG--~~aP~f~l~--~l~G~~   54 (176)
T PRK03147         34 EKMQVG--KEAPNFVLT--DLEGKK   54 (176)
T ss_pred             CCCCCC--CCCCCCEEE--CCCCCE
T ss_conf             523379--908971627--899898


No 184
>PRK12450 foldase protein PrsA; Reviewed
Probab=23.46  E-value=51  Score=13.60  Aligned_cols=20  Identities=5%  Similarity=0.165  Sum_probs=12.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999
Q gi|254781112|r    5 LRDLRKIFFSKYLFFAPFFI   24 (274)
Q Consensus         5 ~~~mk~~~~~~~l~~~~~~~   24 (274)
                      |..|+|++.....+++.+.+
T Consensus         1 m~~mKK~~~~~~~~~svl~L   20 (309)
T PRK12450          1 MKQMNKLITGVVTLATVVTL   20 (309)
T ss_pred             CCHHHHHHHHHHHHHHHHHH
T ss_conf             91799999999999999999


No 185
>PRK00059 prsA peptidylprolyl isomerase; Provisional
Probab=23.33  E-value=35  Score=14.60  Aligned_cols=20  Identities=20%  Similarity=0.132  Sum_probs=12.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999
Q gi|254781112|r    5 LRDLRKIFFSKYLFFAPFFI   24 (274)
Q Consensus         5 ~~~mk~~~~~~~l~~~~~~~   24 (274)
                      |++|||+.+...+.+..++.
T Consensus         1 ~~~~~ki~~~~ii~~~~~~~   20 (336)
T PRK00059          1 MKSAKKIVASLLVGVFIFSA   20 (336)
T ss_pred             CCCHHHHHHHHHHHHHHHHH
T ss_conf             95079999999999999998


No 186
>KOG4596 consensus
Probab=22.39  E-value=36  Score=14.52  Aligned_cols=38  Identities=16%  Similarity=0.239  Sum_probs=26.2

Q ss_pred             HHHHHHHHHHHHHHHHCCHHHHHHHHHCCC--CCCCCCCCC
Q ss_conf             899999999999999798599999876788--877568987
Q gi|254781112|r  234 NKLTRSINEILCAIHLDGTYKKIFDRYFDK--NIISSVPGC  272 (274)
Q Consensus       234 ~~L~~~in~~l~~l~~~G~~~~I~~kw~g~--d~~~~~~~~  272 (274)
                      +.|...++.....++.. +++++..+||.+  |+..|.|+|
T Consensus      1478 ~~l~S~~~~~~~eit~e-rleell~~~f~~~~d~as~~~~~ 1517 (1936)
T KOG4596        1478 ASLQSVYSGENAEITAE-RLEELLNRWFAQLRDVASSTILE 1517 (1936)
T ss_pred             HHHHHHHCCCCHHHHHH-HHHHHHHHHHHHHHHHHCCHHHH
T ss_conf             88999980752134688-89999998889876550221666


No 187
>PRK09590 celB cellobiose phosphotransferase system IIB component; Reviewed
Probab=21.75  E-value=55  Score=13.39  Aligned_cols=33  Identities=9%  Similarity=0.083  Sum_probs=19.1

Q ss_pred             HHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCC
Q ss_conf             789976299855566898898864310322110
Q gi|254781112|r   74 KEVAHRLNLKVEFFETAVSGLITGLDTNRYDVL  106 (274)
Q Consensus        74 ~~i~~~lg~~~~~~~~~~~~~~~~l~~g~~D~~  106 (274)
                      +..++.-|+++++..++-.+..+.+++.++|++
T Consensus        22 ~~~A~~~G~dveI~Av~~~e~~~~i~~~~yDv~   54 (104)
T PRK09590         22 TEFLKGKGKDIEVDAISATEGGKAIAAAAFDLY   54 (104)
T ss_pred             HHHHHHCCCCEEEEEEEHHHHHHHHCCCCCCEE
T ss_conf             999997698369998488898876322688789


No 188
>pfam00496 SBP_bac_5 Bacterial extracellular solute-binding proteins, family 5 Middle. The borders of this family are based on the PDBSum definitions of the domain edges for the periplasmic oligopeptide-binding protein from Salmonella typhimurium.
Probab=21.75  E-value=55  Score=13.39  Aligned_cols=70  Identities=10%  Similarity=0.047  Sum_probs=35.4

Q ss_pred             CEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEEEECC-----CHHHHHHHHHHHH
Q ss_conf             21336855777755443210036655899999984587667326236776877079998189-----9899999999999
Q gi|254781112|r  171 LVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRMKDNSAVAFMMRKG-----NNKLTRSINEILC  245 (274)
Q Consensus       171 ~~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~-----~~~L~~~in~~l~  245 (274)
                      +..+.+......++.+|++|.+..............+..    .+...+ .....++.++..     |+.++.+|..+|.
T Consensus       150 ~~~~~~~~~~~~~l~~G~iD~~~~~~~~~~~~~~~~~~~----~~~~~~-~~~~~~l~~N~~~~~~~d~~vR~Ai~~aid  224 (361)
T pfam00496       150 FRVIPDDAARLAALQSGEVDDVAGLPPSDLAQLEKDPGL----DVLEGP-GGGTYYLAFNTKKPPFDDVRVRQALAYAID  224 (361)
T ss_pred             EEECCCCHHHHHHHHCCCEEEECCCCHHHHHHHHHCCCE----EEEECC-CCEEEEEECCCCCCCCCCHHHHHHHHHHCC
T ss_conf             998688389999987698008846998999999748973----899748-861798721468876699999999997339


No 189
>TIGR02089 TTC tartrate dehydrogenase; InterPro: IPR011829    Tartrate dehydrogenase catalyzes the oxidation of both meso- and (+)-tartrate as well as a D-malate . These enzymes are closely related to the 3-isopropylmalate and isohomocitrate dehydrogenases found in IPR004429 from INTERPRO and IPR011828 from INTERPRO, respectively.; GO: 0009027 tartrate dehydrogenase activity, 0051287 NAD binding.
Probab=21.58  E-value=41  Score=14.19  Aligned_cols=24  Identities=25%  Similarity=0.290  Sum_probs=12.2

Q ss_pred             EHHHHHHHCC-CCCCCCCCCHHHHH
Q ss_conf             1678997629-98555668988988
Q gi|254781112|r   72 LIKEVAHRLN-LKVEFFETAVSGLI   95 (274)
Q Consensus        72 l~~~i~~~lg-~~~~~~~~~~~~~~   95 (274)
                      +++++++..| +.+++...||.++-
T Consensus        25 VL~A~a~~hG~~~l~~~~FpWSs~d   49 (355)
T TIGR02089        25 VLEAAAKKHGGLSLEFTEFPWSSCD   49 (355)
T ss_pred             HHHHHHHHCCCEEEEECCCCCCCHH
T ss_conf             9999997419848740258986338


No 190
>PRK13348 chromosome replication initiation inhibitor protein; Provisional
Probab=21.36  E-value=56  Score=13.34  Aligned_cols=160  Identities=13%  Similarity=0.054  Sum_probs=80.9

Q ss_pred             HHHHHHHCCCCCCCCCCCHHHHHHHHHCCCCCCCHHCCCCHHHHHHHCCCCCCCCCCCCCCCCCC-----CCCCCCCCCC
Q ss_conf             67899762998555668988988643103221100003675675420023332222222221112-----2221111123
Q gi|254781112|r   73 IKEVAHRLNLKVEFFETAVSGLITGLDTNRYDVLVNVAITPERQKKYDFSIPYIAHRVLLVVRSD-----QQDIRSFKDL  147 (274)
Q Consensus        73 ~~~i~~~lg~~~~~~~~~~~~~~~~l~~g~~D~~~~~~~t~eR~~~~~fs~p~~~~~~~~~~~~~-----~~~~~~~~dL  147 (274)
                      +....++-++.+++...+.++.++.+..|.+|++......+..   -..+.|+......++...+     .....+.++|
T Consensus       109 l~~~~~~p~~~l~l~~~~~~~~~~~l~~g~~d~ai~~~~~~~~---~~~~~~l~~~~~~~vasp~~~~~~~~~~~~~~~l  185 (294)
T PRK13348        109 LASVLAGERILLELIVDDQDHTFALLERGEVVGCVSTQSKPMR---GCLAEPLGTMRYRCVAAPAFAARYFPQGLTRHSA  185 (294)
T ss_pred             HHHHHHCCCCEEEEEECCCHHHHHHHHCCCCEEEEECCCCCCC---CCEEEECCCEEEEEEECHHHHHHCCCCCCCHHHH
T ss_conf             9999856797788873451368999974941244533788888---8568982251599998778998607899998898


Q ss_pred             CCCCEEEE-CCCH-HHHHHHCC-----CC-CCEEECCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCEEECCCC
Q ss_conf             34320231-0101-22332013-----45-42133685577775544321003665589999998458766732623677
Q gi|254781112|r  148 TDKTVAQI-LGTD-LSRFAKEL-----KS-HLVFSHNFEQSLQLLLSKRTDATMIPDIPFFNFLERRPHDGNLFKIADRM  219 (274)
Q Consensus       148 ~g~~V~~~-~g~~-~~~~l~~~-----~~-~~~~~~~~~~~~~~l~~grvD~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  219 (274)
                      .+...... .++. ...+....     +. ....+++.+...+++.+|-. ..+.+...+...+.+-    ..+.+.+..
T Consensus       186 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~G~G-i~~lP~~~v~~~l~~G----~Lv~vlp~~  260 (294)
T PRK13348        186 LKAPAVAFNRKDTLQSSFLQRLFGLPVGAYPRHYVPSTHAHLAAIRHGLG-YGMVPELLIGPLLAAG----RLVDLAPAH  260 (294)
T ss_pred             HCCCEEEECCCCCHHHHHHHHCCCCCCCCCCEEEECCHHHHHHHHHHCCE-EEECCHHHHHHHHHCC----CEEECCCCC
T ss_conf             25988996599716689998646887676646898979999999997992-8966499999998489----878917999


Q ss_pred             CCCCCEEEEEECC---CHHHHHHHHH
Q ss_conf             6877079998189---9899999999
Q gi|254781112|r  220 KDNSAVAFMMRKG---NNKLTRSINE  242 (274)
Q Consensus       220 ~~~~~~~~~~~k~---~~~L~~~in~  242 (274)
                        +.+.++..+++   +|.....++.
T Consensus       261 --~~~v~l~~~~~~~~~p~~~af~d~  284 (294)
T PRK13348        261 --PVDVALYWHHWEVEPPTMEALSQR  284 (294)
T ss_pred             --CCCEEEEEECCCCCCHHHHHHHHH
T ss_conf             --771479800688689799999999


No 191
>cd06155 eu_AANH_C_1 A group of hypothetical eukaryotic proteins, characterized by the presence of an adenine nucleotide alpha hydrolase (AANH)-like domain located N-terminal to two distinctly different YjgF-YER057c-UK114-like domains. This CD contains the first of these domains. The YjgF-YER057c-UK114 protein family is a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function.  The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.
Probab=21.23  E-value=44  Score=14.03  Aligned_cols=14  Identities=21%  Similarity=0.574  Sum_probs=7.8

Q ss_pred             HHHHHHHHHCCCCC
Q ss_conf             59999987678887
Q gi|254781112|r  252 TYKKIFDRYFDKNI  265 (274)
Q Consensus       252 ~~~~I~~kw~g~d~  265 (274)
                      +++++|.+||+..-
T Consensus        64 ~~N~vY~~~F~~~~   77 (101)
T cd06155          64 EVNSVYGTFFDKPN   77 (101)
T ss_pred             HHHHHHHHHCCCCC
T ss_conf             99999999859999


No 192
>COG1197 Mfd Transcription-repair coupling factor (superfamily II helicase) [DNA replication, recombination, and repair / Transcription]
Probab=21.21  E-value=57  Score=13.32  Aligned_cols=10  Identities=30%  Similarity=0.348  Sum_probs=3.5

Q ss_pred             HHHHHHHHHH
Q ss_conf             7755443210
Q gi|254781112|r  181 LQLLLSKRTD  190 (274)
Q Consensus       181 ~~~l~~grvD  190 (274)
                      ++.|.+|++|
T Consensus       690 l~~la~G~vD  699 (1139)
T COG1197         690 LKGLAEGKVD  699 (1139)
T ss_pred             HHHHHCCCCC
T ss_conf             9998569845


Done!