Query         gi|254780563|ref|YP_003064976.1| extracellular solute-binding protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 195
No_of_seqs    106 out of 2115
Neff          9.0 
Searched_HMMs 39220
Date          Mon May 30 00:10:33 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780563.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR03261 phnS2 putative 2-ami 100.0 1.8E-38 4.7E-43  239.1  16.8  184    6-190     2-198 (334)
  2 TIGR03227 PhnS 2-aminoethylpho 100.0 2.3E-35 5.8E-40  221.4  15.5  186    2-190    12-210 (367)
  3 PRK11205 tbpA thiamine transpo 100.0 2.1E-33 5.4E-38  210.2  13.6  168   19-191    11-192 (326)
  4 COG4143 TbpA ABC-type thiamine 100.0 2.3E-28 5.9E-33  181.5  13.6  186    1-190     1-200 (336)
  5 COG1840 AfuA ABC-type Fe3+ tra  99.9 2.1E-23 5.3E-28  153.2  10.7  147   43-190     1-158 (299)
  6 PRK09501 potD spermidine/putre  99.9 1.7E-22 4.2E-27  148.1  12.0  183    2-188     1-206 (348)
  7 TIGR01254 sfuA ABC transporter  99.9 1.3E-22 3.4E-27  148.7   9.9  165   26-190     2-183 (324)
  8 PRK10682 putrescine transporte  99.8 6.9E-20 1.7E-24  133.2  11.7  183    2-188     4-221 (370)
  9 COG0687 PotD Spermidine/putres  99.8 4.5E-18 1.1E-22  122.8  11.5  185    1-186     1-215 (363)
 10 PRK09474 malE maltose ABC tran  99.5 2.1E-13 5.3E-18   96.2  10.0  189    2-192     1-230 (394)
 11 TIGR01276 thiB thiamin/thiamin  99.4   2E-13   5E-18   96.3   5.4  164   23-189    12-189 (326)
 12 PRK10677 modA molybdate transp  99.1 2.4E-09 6.2E-14   73.0  12.1   84    2-85      1-87  (257)
 13 PRK11622 putative ABC transpor  99.0 2.6E-08 6.6E-13   67.1  14.1  185    1-187     1-242 (401)
 14 COG2182 MalE Maltose-binding p  99.0 2.2E-09 5.5E-14   73.3   8.0  118   26-145    40-172 (420)
 15 PRK10974 glycerol-3-phosphate   98.9 1.6E-08   4E-13   68.4  10.3  143    1-145     1-176 (439)
 16 PRK10852 thiosulfate transport  98.9 1.5E-07 3.9E-12   62.7  14.3  155   19-189    18-192 (338)
 17 PRK04168 hypothetical protein;  98.8   2E-07 5.1E-12   62.1  13.2  139    2-159     5-152 (336)
 18 PRK10752 sulfate transporter s  98.8 5.3E-07 1.3E-11   59.7  13.6  154   20-189    15-186 (329)
 19 COG1653 UgpB ABC-type sugar tr  98.7 2.4E-07   6E-12   61.7  10.6  142    3-145     5-174 (433)
 20 COG0725 ModA ABC-type molybdat  98.7 3.5E-07 8.8E-12   60.7  11.0  117   23-158    26-144 (258)
 21 COG4134 ABC-type uncharacteriz  98.6 3.5E-07   9E-12   60.7   9.5  142   48-191    59-241 (384)
 22 TIGR03431 PhnD phosphonate ABC  98.4 1.7E-05 4.2E-10   51.1  13.0  152    1-175     1-163 (288)
 23 COG1613 Sbp ABC-type sulfate t  98.4 1.7E-05 4.4E-10   51.0  12.8  152   25-189    36-203 (348)
 24 COG4588 AcfC Accessory coloniz  98.4 3.1E-06 7.9E-11   55.3   8.6  161    2-189     1-166 (252)
 25 COG4150 CysP ABC-type sulfate   98.0 4.2E-05 1.1E-09   48.8   7.7  173    1-188     5-196 (341)
 26 COG3221 PhnD ABC-type phosphat  97.8  0.0016 4.1E-08   39.8  13.4  151    1-173     1-169 (299)
 27 TIGR01098 3A0109s03R phosphona  97.5  0.0031   8E-08   38.1  11.8  133   26-173    50-193 (299)
 28 COG2998 TupB ABC-type tungstat  97.5  0.0003 7.8E-09   43.9   5.8   71   14-84     17-90  (280)
 29 PRK10797 glutamate and asparta  97.0   0.026 6.7E-07   32.9  12.7   54   35-88     65-121 (302)
 30 PRK11260 cystine transporter s  97.0   0.013 3.3E-07   34.6   9.7   43   40-82     65-107 (264)
 31 PRK09495 glnH glutamine ABC tr  96.9  0.0038 9.7E-08   37.7   6.9   81    2-83      1-93  (247)
 32 PRK11553 alkanesulfonate trans  96.7   0.041 1.1E-06   31.7  12.5   86    2-87      1-91  (314)
 33 TIGR00971 3a0106s03 sulfate AB  96.7  0.0057 1.4E-07   36.7   6.1  140   36-188    24-179 (320)
 34 pfam01547 SBP_bac_1 Bacterial   96.6  0.0049 1.3E-07   37.0   5.1   65   37-101     7-79  (260)
 35 PRK10918 phosphate transporter  96.2   0.092 2.3E-06   29.8   9.9  146    7-172     7-177 (346)
 36 TIGR01256 modA molybdate ABC t  96.0  0.0065 1.7E-07   36.3   3.2  102   38-160     6-116 (225)
 37 COG1732 OpuBC Periplasmic glyc  95.8     0.1 2.7E-06   29.5   8.6  122   23-145    29-160 (300)
 38 COG1464 NlpA ABC-type metal io  95.4   0.065 1.7E-06   30.6   6.4   62    1-62      1-66  (268)
 39 PRK11480 tauA taurine transpor  95.1    0.24 6.2E-06   27.4  10.6   71   13-83      9-82  (320)
 40 COG2113 ProX ABC-type proline/  95.1    0.24 6.2E-06   27.4  11.6   80    1-80      1-86  (302)
 41 PRK11119 proX glycine betaine   94.8     0.3 7.7E-06   26.8  13.1  162    1-175     1-178 (332)
 42 PRK11063 metQ DL-methionine tr  94.6    0.11 2.8E-06   29.3   5.9   52  140-193   220-271 (271)
 43 COG0226 PstS ABC-type phosphat  93.8     0.5 1.3E-05   25.6   9.5  129   26-169    42-188 (318)
 44 PRK01326 prsA foldase protein   93.3    0.17 4.3E-06   28.3   4.6   13   44-56     63-75  (310)
 45 COG3019 Predicted metal-bindin  92.9    0.27 6.8E-06   27.1   5.2   64    2-66      1-64  (149)
 46 PRK09861 cytoplasmic membrane   92.7    0.37 9.5E-06   26.3   5.7   54    9-62     13-69  (272)
 47 PRK12679 cbl transcriptional r  92.3    0.82 2.1E-05   24.3   8.7  139   23-188    89-237 (316)
 48 PRK12450 foldase protein PrsA;  92.2    0.47 1.2E-05   25.7   5.8   56    1-56      3-77  (309)
 49 PRK10641 btuB vitamin B12/coba  91.3    0.31 7.8E-06   26.8   4.0   36    1-37      1-36  (615)
 50 PRK03002 prsA peptidylprolyl i  91.2    0.48 1.2E-05   25.7   4.9   34    1-34      1-35  (285)
 51 PRK11917 bifunctional adhesin/  90.3     1.3 3.4E-05   23.1  10.9   43   41-83     66-111 (259)
 52 PRK10598 hypothetical protein;  89.4    0.76 1.9E-05   24.5   4.7   48    2-55      1-50  (186)
 53 PRK04405 prsA peptidylprolyl i  88.5     1.6   4E-05   22.7   5.8   54    1-56      4-76  (298)
 54 PRK10662 beta-lactamase/D-alan  88.3     1.1 2.8E-05   23.6   4.9   56    1-61      1-59  (377)
 55 COG4521 TauA ABC-type taurine   87.6    0.99 2.5E-05   23.9   4.3   63    2-64      4-68  (334)
 56 PRK10002 outer membrane protei  86.0     0.7 1.8E-05   24.7   2.8   32    1-33      1-37  (362)
 57 PRK11289 ampC beta-lactamase;   85.5     1.3 3.3E-05   23.2   4.0   54    1-59      3-59  (387)
 58 PRK11627 hypothetical protein;  85.0     1.1 2.8E-05   23.7   3.4   28    1-32      1-28  (192)
 59 pfam03466 LysR_substrate LysR   84.4     3.1 7.9E-05   21.0   8.1   59   24-82      3-64  (209)
 60 PRK09701 D-allose transporter   83.7     3.3 8.5E-05   20.9   5.7   58    2-60      1-62  (311)
 61 PRK03095 prsA peptidylprolyl i  82.9     2.8 7.3E-05   21.3   4.8   31    2-33      1-31  (287)
 62 PRK02998 prsA peptidylprolyl i  82.6     2.9 7.3E-05   21.2   4.7   33    1-34      1-33  (283)
 63 pfam01514 YscJ_FliF Secretory   82.4     3.7 9.5E-05   20.6   5.3   37   22-59     21-57  (206)
 64 PRK06934 flavodoxin; Provision  82.3     3.8 9.7E-05   20.6   5.4   39    2-40      9-50  (221)
 65 PRK13791 lysozyme inhibitor; P  81.7    0.83 2.1E-05   24.3   1.7   36    1-36      1-38  (114)
 66 pfam04069 OpuAC Substrate bind  81.6       4  0.0001   20.4   9.1  136   28-175     2-145 (256)
 67 PRK12681 cysB transcriptional   80.2     4.5 0.00011   20.1   9.1   57   23-79     89-148 (324)
 68 PRK13861 type IV secretion sys  80.1     2.5 6.4E-05   21.6   3.7   19    1-19      1-19  (293)
 69 PRK12682 transcriptional regul  78.1     5.2 0.00013   19.7   6.2   52   25-76     91-145 (309)
 70 PRK10355 xylF D-xylose transpo  77.0     5.7 0.00014   19.6   5.5   57    2-60      1-63  (330)
 71 PRK09967 putative outer membra  76.0     2.8 7.1E-05   21.3   3.0   22    1-23      1-22  (160)
 72 PRK10523 lipoprotein involved   75.3     2.1 5.3E-05   22.0   2.2   56    1-58      1-62  (234)
 73 pfam07273 DUF1439 Protein of u  75.2     4.4 0.00011   20.2   3.8   46    2-55      1-49  (177)
 74 PRK13486 bifunctional enteroba  74.9     4.9 0.00012   19.9   4.0   37    2-38      1-37  (696)
 75 PRK12684 transcriptional regul  74.6     6.6 0.00017   19.2   7.6   57   23-79     89-148 (313)
 76 TIGR02036 dsdC D-serine deamin  74.6     1.7 4.2E-05   22.6   1.5   51   25-78     94-147 (302)
 77 TIGR03042 PS_II_psbQ_bact phot  73.2     4.9 0.00012   19.9   3.6   46    3-49      2-47  (142)
 78 PRK06760 hypothetical protein;  73.1     4.4 0.00011   20.2   3.4   65    2-68      1-84  (223)
 79 PRK13528 outer membrane recept  73.0     3.2 8.2E-05   21.0   2.7   35    1-35      3-42  (727)
 80 TIGR02747 TraV type IV conjuga  72.7     2.5 6.4E-05   21.6   2.1   22    1-22      1-22  (174)
 81 pfam05170 AsmA AsmA family. Th  72.4     7.1 0.00018   19.0   4.3   50    2-58      1-50  (537)
 82 PRK11242 DNA-binding transcrip  72.2     7.5 0.00019   18.9  10.5   55   25-79     89-146 (292)
 83 COG3017 LolB Outer membrane li  71.4     3.7 9.3E-05   20.6   2.7   30    1-30      3-32  (206)
 84 PRK13483 enterobactin receptor  71.1     7.7  0.0002   18.8   4.3   23    1-23      1-23  (663)
 85 TIGR03525 GldK gliding motilit  70.6     3.4 8.8E-05   20.8   2.4   27    2-31      1-27  (449)
 86 PRK02889 tolB translocation pr  69.8     3.9  0.0001   20.5   2.5   32    1-33      3-34  (430)
 87 PRK10653 D-ribose transporter   68.7     9.1 0.00023   18.4   5.9   59    2-61      3-65  (295)
 88 PRK10833 putative assembly pro  68.6     7.7  0.0002   18.8   3.8   50    2-58      1-50  (617)
 89 PRK13513 putative outer membra  68.1     9.3 0.00024   18.3   4.5   36    2-37      8-46  (660)
 90 PRK12696 flgH flagellar basal   66.6     4.8 0.00012   20.0   2.4   20    1-22      1-20  (238)
 91 TIGR02544 III_secr_YscJ type I  66.2      10 0.00026   18.1   5.3   43    9-57      6-48  (203)
 92 TIGR00439 ftsX putative protei  66.1      10 0.00026   18.1   4.4   78    5-82     35-141 (314)
 93 pfam10566 Glyco_hydro_97 Glyco  65.7     5.2 0.00013   19.8   2.5   22    2-23      1-22  (643)
 94 PRK02710 plastocyanin; Provisi  65.0      10 0.00026   18.1   3.9   34    1-34      1-36  (119)
 95 PRK12680 transcriptional regul  64.8      11 0.00028   18.0  10.6   57   23-79     89-148 (327)
 96 PRK04792 tolB translocation pr  64.4       6 0.00015   19.4   2.6   17    1-17      1-17  (450)
 97 PRK13697 cytochrome c6; Provis  63.8     5.2 0.00013   19.8   2.2   26    2-27      1-26  (111)
 98 pfam12262 Lipase_bact_N Bacter  63.5     5.6 0.00014   19.6   2.3   24    2-25      1-24  (269)
 99 PRK12473 hypothetical protein;  62.2      12 0.00031   17.7   6.4   43   24-68     28-84  (193)
100 TIGR03414 ABC_choline_bnd chol  61.7      12 0.00032   17.6  10.6  124   22-160     3-131 (290)
101 COG5510 Predicted small secret  61.6     7.3 0.00019   18.9   2.6   20    1-20      1-22  (44)
102 TIGR01902 dapE-lys-deAc N-acet  60.7     7.8  0.0002   18.8   2.6   45   28-72      6-51  (352)
103 PRK10859 putative transglycosy  60.4      13 0.00033   17.5  12.0   41   39-79     66-107 (507)
104 COG3015 CutF Uncharacterized l  59.9     8.8 0.00022   18.5   2.8   33    1-34      1-37  (178)
105 COG0715 TauA ABC-type nitrate/  58.9      14 0.00035   17.3  12.5   42   44-85     51-96  (335)
106 COG4594 FecB ABC-type Fe3+-cit  58.4      11 0.00028   17.9   3.1   25    1-25      3-27  (310)
107 PRK09791 putative DNA-binding   57.8      15 0.00037   17.2   9.4   57   23-79     91-150 (302)
108 cd01477 vWA_F09G8-8_type VWA F  57.6      11 0.00028   17.9   3.0   86   75-161    21-108 (193)
109 PRK09408 ompX outer membrane p  57.1      12  0.0003   17.7   3.1   53    2-61      1-55  (171)
110 PRK13618 psbV cytochrome c-550  57.1     8.8 0.00022   18.5   2.4   59    1-59      1-72  (163)
111 pfam01456 Mucin Mucin-like gly  56.4     8.3 0.00021   18.6   2.2   28    1-28      1-28  (143)
112 PRK13619 psbV cytochrome c-550  55.3     8.6 0.00022   18.5   2.1   59    1-59      1-72  (161)
113 PRK09810 entericidin A; Provis  54.9     7.3 0.00019   18.9   1.7   17    1-17      1-17  (41)
114 TIGR01368 CPSaseIIsmall carbam  53.9     4.1 0.00011   20.3   0.3   12   51-62    217-228 (383)
115 PRK09859 multidrug efflux syst  52.6      14 0.00036   17.3   2.8   24    1-24      1-25  (385)
116 cd00614 CGS_like CGS_like: Cys  52.3      18 0.00046   16.7   5.4   43   25-67     77-119 (369)
117 PRK06767 methionine gamma-lyas  51.0      19 0.00048   16.6   5.6   45   24-68     97-141 (386)
118 PRK11716 DNA-binding transcrip  50.7      19 0.00049   16.5   4.7   58   23-80     63-123 (269)
119 PRK10802 peptidoglycan-associa  50.6      19 0.00048   16.6   3.2   23    1-23      1-25  (173)
120 PRK08861 cystathionine gamma-s  50.5      19 0.00049   16.5   5.2   43   25-67     90-132 (388)
121 PRK13484 putative iron-regulat  50.3      19 0.00048   16.6   3.2   25  105-129   135-159 (682)
122 PRK10866 outer membrane protei  50.3      19 0.00048   16.6   3.2   25  164-188   218-242 (243)
123 PRK12683 transcriptional regul  50.0      20  0.0005   16.5   8.7   55   25-79     91-148 (308)
124 PRK10341 DNA-binding transcrip  49.2      20 0.00052   16.4   9.0   41   38-78    110-151 (312)
125 PRK03757 hypothetical protein;  48.9      13 0.00033   17.5   2.1   16    2-17      1-16  (191)
126 PRK08248 O-acetylhomoserine am  48.9      20 0.00052   16.4   4.1   44   25-68    101-144 (431)
127 PRK01742 tolB translocation pr  47.9      16  0.0004   17.0   2.5   17    1-17      3-19  (430)
128 PRK10959 outer membrane protei  47.3      18 0.00046   16.7   2.7   29    2-31      1-29  (212)
129 TIGR03502 lipase_Pla1_cef extr  47.0      16 0.00041   17.0   2.4   21    2-22      1-21  (792)
130 COG3338 Cah Carbonic anhydrase  47.0     7.7  0.0002   18.8   0.8   52    2-56      1-61  (250)
131 TIGR02740 TraF-like TraF-like   46.8      15 0.00037   17.2   2.2   29   34-62    207-235 (306)
132 CHL00133 psbV photosystem II c  46.3      17 0.00044   16.8   2.5   59    1-59      1-72  (163)
133 COG1638 DctP TRAP-type C4-dica  45.6      23 0.00059   16.1   6.3   60    1-61      1-69  (332)
134 PRK08474 F0F1 ATP synthase sub  44.7      24 0.00061   16.0   5.4   47   13-59     90-138 (176)
135 pfam02402 Lysis_col Lysis prot  44.5     9.6 0.00025   18.2   1.0   21    2-22      1-21  (46)
136 PRK09934 putative fimbrial pro  44.4      24 0.00061   16.0   3.3   29    2-31      1-29  (171)
137 PRK02944 OxaA-like protein pre  44.3      21 0.00054   16.3   2.7   23    2-24      1-25  (255)
138 PRK07504 O-succinylhomoserine   44.3      24 0.00062   16.0   5.8   43   25-67    102-144 (397)
139 PHA00019 phage assembly protei  43.1      25 0.00064   15.9   5.2   51    1-58      1-51  (428)
140 COG0505 CarA Carbamoylphosphat  42.7      22 0.00057   16.2   2.6   35   43-77     96-131 (368)
141 PRK12701 flgH flagellar basal   41.1      27 0.00069   15.7   2.8   22    2-23      1-22  (230)
142 TIGR03302 OM_YfiO outer membra  41.0      27  0.0007   15.7   4.0   24  164-187   209-232 (235)
143 PRK10554 outer membrane porin   41.0      25 0.00064   15.9   2.6   32    2-34      1-37  (373)
144 COG1512 Beta-propeller domains  40.9      27  0.0007   15.7   4.8   27   34-60     45-71  (271)
145 PRK11151 DNA-binding transcrip  40.7      28  0.0007   15.6   8.0   55   24-78     88-145 (305)
146 PRK07503 methionine gamma-lyas  40.7      28 0.00071   15.6   5.0   44   25-68    102-145 (403)
147 COG2854 Ttg2D ABC-type transpo  40.4      27 0.00068   15.7   2.7   23    1-23      2-24  (202)
148 PRK06460 hypothetical protein;  40.3      28 0.00071   15.6   4.9   55   25-79     82-136 (375)
149 pfam07901 DUF1672 Protein of u  40.3      28 0.00072   15.6   3.8   21    2-23      1-21  (304)
150 PRK10877 thiol:disulfide inter  40.2      28 0.00072   15.6   3.9   46    2-64      1-46  (232)
151 COG3417 FlgN Collagen-binding   39.8      27 0.00069   15.7   2.7   22    1-22      1-22  (200)
152 TIGR00631 uvrb excinuclease AB  39.6      29 0.00073   15.5   4.3  119   26-146   446-600 (667)
153 TIGR01420 pilT_fam twitching m  39.3      29 0.00074   15.5   3.5   40  135-175   113-154 (350)
154 PTZ00334 trans-sialidase; Prov  38.8      20 0.00051   16.4   1.9   21    2-22     39-60  (780)
155 PRK13731 conjugal transfer sur  38.6      20 0.00052   16.4   1.9   23    2-24      3-25  (243)
156 COG2980 RlpB Rare lipoprotein   37.6      31 0.00079   15.3   5.0   68    2-70      1-77  (178)
157 PRK08249 cystathionine gamma-s  37.5      31 0.00079   15.3   5.2   43   25-67    101-143 (398)
158 TIGR02086 IPMI_arch 3-isopropy  37.4      19 0.00047   16.6   1.5   47   37-83     76-125 (431)
159 pfam00988 CPSase_sm_chain Carb  36.9      30 0.00076   15.5   2.5   27  122-154    26-52  (131)
160 COG3065 Slp Starvation-inducib  36.7      26 0.00067   15.7   2.2   24    1-24      4-27  (191)
161 pfam06551 DUF1120 Protein of u  36.1      33 0.00084   15.2   3.0   31    2-32      1-33  (145)
162 TIGR03339 phn_lysR aminoethylp  35.7      33 0.00085   15.2  10.4   56   23-79     83-139 (279)
163 PRK12789 flgI flagellar basal   35.4      15 0.00038   17.2   0.8   16    1-16      1-16  (367)
164 TIGR02346 chap_CCT_theta T-com  34.5      31 0.00079   15.3   2.3   41   26-67    264-304 (554)
165 TIGR00232 tktlase_bact transke  34.3      14 0.00035   17.4   0.4   16   39-55    193-208 (675)
166 PRK08114 cystathionine beta-ly  33.8      36 0.00091   15.0   6.2   54   25-78     99-152 (395)
167 PRK07810 O-succinylhomoserine   33.7      36 0.00092   15.0   4.8   44   25-68    110-153 (406)
168 COG2247 LytB Putative cell wal  33.6      36 0.00092   15.0   4.2   36    2-37      1-38  (337)
169 PRK13703 conjugal pilus assemb  33.6      35 0.00089   15.1   2.4   12   22-33     17-28  (247)
170 PRK10808 outer membrane protei  33.5      36 0.00092   15.0   3.3   18    2-19      1-18  (347)
171 pfam01441 Lipoprotein_6 Lipopr  33.5      36 0.00092   15.0   2.6   24    2-25      1-24  (209)
172 PRK09733 putative fimbrial pro  33.3      36 0.00093   14.9   3.3   30    2-32      2-31  (181)
173 PRK10159 outer membrane phosph  33.1      24 0.00061   16.0   1.5   32    2-34      1-37  (351)
174 pfam03971 IDH Monomeric isocit  32.7      37 0.00095   14.9   3.6   32   30-61      2-39  (735)
175 COG4851 CamS Protein involved   32.2      38 0.00097   14.8   2.6   23  166-188   199-221 (382)
176 CHL00197 carA carbamoyl-phosph  31.8      24 0.00062   16.0   1.4   23  138-160   226-248 (383)
177 pfam08085 Entericidin Enterici  31.5      39   0.001   14.8   2.6   15    2-16      1-15  (42)
178 PRK00031 lolA outer-membrane l  31.4      26 0.00066   15.8   1.5   13    2-14      1-13  (201)
179 PRK10510 putative outer membra  31.4      39   0.001   14.8   2.9   22    2-23      1-22  (219)
180 COG3470 Tpd Uncharacterized pr  31.3      40   0.001   14.7   2.6   28    2-29      3-30  (179)
181 PRK11671 mltC murein transglyc  30.8      40   0.001   14.7   3.6   18    1-18      1-18  (360)
182 PRK06234 methionine gamma-lyas  30.1      41  0.0011   14.6   5.5   44   25-68    101-144 (399)
183 pfam01053 Cys_Met_Meta_PP Cys/  30.0      42  0.0011   14.6   5.7   44   25-68     89-132 (381)
184 PRK07811 cystathionine gamma-s  29.6      42  0.0011   14.6   5.6   54   25-78     95-148 (386)
185 PRK12564 carbamoyl phosphate s  29.3      30 0.00076   15.4   1.5   23  138-160   203-225 (355)
186 PRK13659 hypothetical protein;  28.9      43  0.0011   14.5   4.6   46    2-47      5-53  (112)
187 PRK08045 cystathionine gamma-s  28.9      43  0.0011   14.5   5.5   42   25-66     89-130 (386)
188 PRK05967 cystathionine beta-ly  28.9      43  0.0011   14.5   5.4   43   25-67    101-143 (392)
189 PRK07050 cystathionine beta-ly  28.7      44  0.0011   14.5   5.2   43   25-67    102-144 (394)
190 PRK09915 putative outer membra  28.6      41  0.0011   14.6   2.1   21    2-22      6-26  (488)
191 PRK08475 F0F1 ATP synthase sub  28.6      44  0.0011   14.5   2.5   22   37-58     43-65  (170)
192 COG5633 Predicted periplasmic   28.3      33 0.00083   15.2   1.5   21    2-24      1-21  (123)
193 pfam07424 TrbM TrbM. This fami  28.3      45  0.0011   14.4   2.8   12  139-150   149-160 (189)
194 pfam04076 BOF Bacterial OB fol  28.3      40   0.001   14.7   2.0   17    2-18      1-17  (126)
195 COG1204 Superfamily II helicas  28.2      45  0.0011   14.4   4.0   36   27-62     76-113 (766)
196 PRK13893 conjugal transfer pro  28.2      30 0.00077   15.4   1.3   16    1-16      1-16  (193)
197 pfam06510 DUF1102 Protein of u  27.7      46  0.0012   14.4   2.5   23    2-24      1-23  (183)
198 pfam08139 LPAM_1 Prokaryotic m  27.5      43  0.0011   14.5   2.0   20    2-23      1-20  (26)
199 PRK06084 O-acetylhomoserine am  27.2      47  0.0012   14.3   5.6   43   25-67     95-137 (424)
200 TIGR01729 taurine_ABC_bnd taur  26.8      45  0.0012   14.4   2.0   27   43-69     20-46  (304)
201 pfam09358 UBA_e1_C Ubiquitin-a  26.6      43  0.0011   14.5   1.9   35   28-62     30-67  (124)
202 PRK09973 putative outer membra  26.5      19 0.00048   16.6   0.0   28    1-28      1-28  (85)
203 PRK10449 heat-inducible protei  26.5      48  0.0012   14.3   2.6   21    2-24      1-21  (140)
204 PRK11624 cdsA CDP-diglyceride   25.9      49  0.0013   14.2   2.7   17    1-17      1-17  (285)
205 PRK08605 D-lactate dehydrogena  25.8      50  0.0013   14.2   4.4   32   28-61      3-34  (332)
206 COG5455 Predicted integral mem  25.7      49  0.0013   14.2   2.1   27    1-28      1-27  (129)
207 PRK12838 carbamoyl phosphate s  25.6      34 0.00087   15.1   1.2   23  138-160   199-221 (356)
208 PRK13524 outer membrane recept  25.4      50  0.0013   14.2   2.0   23    2-24      1-23  (742)
209 TIGR01088 aroQ 3-dehydroquinat  25.4      51  0.0013   14.1   3.3   41   26-66     15-58  (144)
210 PRK08133 O-succinylhomoserine   25.3      51  0.0013   14.1   5.2   43   25-67     98-140 (391)
211 PRK09028 cystathionine beta-ly  25.3      51  0.0013   14.1   4.7   42   25-66     98-139 (394)
212 PRK06007 fliF flagellar MS-rin  25.3      51  0.0013   14.1   6.2   47   12-59     34-80  (540)
213 pfam12354 Internalin_N Bacteri  25.3      41  0.0011   14.6   1.6   32    1-32      1-32  (57)
214 pfam11777 DUF3316 Protein of u  25.3      51  0.0013   14.1   5.6   19    2-20      1-19  (114)
215 pfam05079 DUF680 Protein of un  25.2      39 0.00099   14.8   1.4   24    2-25      1-24  (73)
216 TIGR01431 adm_rel adenosine de  25.0      51  0.0013   14.1   2.4  148   41-189   245-457 (486)
217 KOG0634 consensus               24.6      52  0.0013   14.1   4.1   34  152-185   322-355 (472)
218 PRK13680 hypothetical protein;  24.3      53  0.0014   14.0   4.4   49    1-49      4-56  (121)
219 PRK09578 periplasmic multidrug  24.1      53  0.0014   14.0   2.8   21    3-23      6-26  (385)
220 PRK10270 hypothetical protein;  24.0      54  0.0014   14.0   2.4   52  139-190   184-242 (340)
221 PRK10287 thiosulfate:cyanide s  23.5      54  0.0014   14.0   1.9   13    1-13      1-13  (104)
222 KOG0559 consensus               23.4      55  0.0014   13.9   4.6   19   41-59    270-288 (457)
223 TIGR01181 dTDP_gluc_dehyt dTDP  23.4      49  0.0013   14.2   1.7   28   35-62    163-190 (340)
224 PRK01622 OxaA-like protein pre  23.3      55  0.0014   13.9   3.3   21    1-21      1-24  (266)
225 TIGR01347 sucB 2-oxoglutarate   23.3      50  0.0013   14.2   1.7   23   37-59    240-263 (435)
226 COG3056 Uncharacterized lipopr  23.0      56  0.0014   13.9   3.2   26    6-31     15-40  (204)
227 PRK09906 DNA-binding transcrip  22.7      57  0.0015   13.8  11.5   55   26-80     89-146 (296)
228 COG2984 ABC-type uncharacteriz  22.6      57  0.0015   13.8   7.8  130    1-130     1-170 (322)
229 CHL00180 rbcR LysR transcripti  22.5      58  0.0015   13.8   9.8   54   25-78     93-149 (307)
230 PRK10903 peptidyl-prolyl cis-t  22.4      58  0.0015   13.8   3.0   34    1-34      1-36  (190)
231 cd00713 GltS Glutamine amidotr  22.0      21 0.00054   16.3  -0.4   69  114-183   166-245 (413)
232 PRK12700 flgH flagellar basal   22.0      59  0.0015   13.7   3.3   22    1-22      1-22  (230)
233 PTZ00203 cathepsin L protease;  21.9      59  0.0015   13.7   4.9   44    4-54      5-48  (348)
234 TIGR01626 ytfJ_HI0045 conserve  21.8      60  0.0015   13.7   2.3   21    2-22      1-21  (184)
235 PRK11548 hypothetical protein;  21.7      60  0.0015   13.7   2.4   23    1-23      1-23  (113)
236 PRK05968 hypothetical protein;  21.7      60  0.0015   13.7   4.9   44   25-68    100-143 (389)
237 pfam06291 Lambda_Bor Bor prote  21.7      57  0.0015   13.8   1.8   18    2-21      1-18  (97)
238 TIGR03519 Bac_Flav_fam_1 Bacte  21.1      62  0.0016   13.6   2.3   13    2-14      1-13  (292)
239 COG2913 OlmA Outer membrane li  21.1      62  0.0016   13.6   2.7   31    1-33      2-32  (147)
240 COG2838 Icd Monomeric isocitra  20.3      64  0.0016   13.5   3.0   32   29-60      7-44  (744)

No 1  
>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=100.00  E-value=1.8e-38  Score=239.07  Aligned_cols=184  Identities=15%  Similarity=0.144  Sum_probs=152.7

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHHH-CCCCCCCCCHHHHHH---HHHHHC-CCCCEEEEC
Q ss_conf             999999999999861244458808998189989999999999987-598621000013566---765210-666557504
Q gi|254780563|r    6 IYTYLLLLCGFTEAFSTENTTKYLTLYTDQNQSVMLPIIHSFEER-TGVKISPIYTSSIQR---PPITQG-SPVDVIITK   80 (195)
Q Consensus         6 ~~~~l~l~~~~~~~~~~~~~~~~lvVYs~~~~~~~~~~~~~Fek~-tgIkV~~~~~~~~~~---~~~~~~-~~~d~~~~~   80 (195)
                      ++..|++ ++++.+|+++.++++|||||+++++.+++++++|||+ |||+|+++++++.+.   +..+++ +++|++|+.
T Consensus         2 ~~~~~~~-~~~~~~a~aa~~~~~l~VYss~~~~~~~~i~~~Fek~~tgIkV~~v~~~tgel~~rl~aEk~~p~aDV~~g~   80 (334)
T TIGR03261         2 VVAGFIM-TSLFFSACNSKANTELTVYTAIEDELIAKYKDAFEKVNPDIKINWVRDSTGIITAKLLAEKNNPQADVVWGL   80 (334)
T ss_pred             HHHHHHH-HHHHHHHHHHCCCCEEEEEECCCHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHCCCCCCCEEEEEC
T ss_conf             8899999-999998310302995999969988899999999997779948999989729999999964579986599845


Q ss_pred             CHHHH--HHHHHHHCCCCCCCCCCCCCCCCCCCC--CCCCCCCCEEEEEEEHHHHCCC--CCCCCHHHHCCHHHCCEEEE
Q ss_conf             22332--343310000123422234720001222--2234434505888733440134--45578888408667685996
Q gi|254780563|r   81 DETSL--ALNEDLLHKLPAHLIKKNSFVLKNENK--KLMRISFDTQVLAYSTKRIKIA--DLPKSVFDLTNAQWKKRLSI  154 (195)
Q Consensus        81 d~~~l--~~~~~~l~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~n~~~~~~~--~~P~sw~DL~~p~~kG~i~~  154 (195)
                      +...+  ..++|+|++|.++..+++++.++++++  +|+++.....+++||++.++..  ++|+||+||+||+|||+|+|
T Consensus        81 ~~~~~~~~~~~gll~~y~~~~~~~l~~~~~d~~~~~~~~g~~~~~~~i~yN~~~~~~~~~p~P~sw~DL~dp~ykg~i~~  160 (334)
T TIGR03261        81 AASSLALLDKEGMLKPYKPKGLDALNPKFRDAKNPPHWVGMDAWMAAICFNTVEAKKKGLPKPTSWEDLTKPEYKGHIVM  160 (334)
T ss_pred             CHHHHHHHHHCCCCCCCCCCCHHHCCHHHCCCCCCCEEEEEEEEEEEEEEEHHHCCCCCCCCCCCHHHHCCHHHCCEEEC
T ss_conf             65789998860431577753054478865297888516887524678997444404258999999999709474895873


Q ss_pred             CCCCCCHH--HHHHHHHHHHCHHHHHHHHHHHHHCCCC
Q ss_conf             28983049--9999999960869999999998608870
Q gi|254780563|r  155 APNNISFH--RLLNTMEQTPNKTVVQDFIKNITANEIL  190 (195)
Q Consensus       155 ~~~~~s~~--~~~~a~~~~~G~~~~~~~l~~l~~N~~~  190 (195)
                      +++..++.  .++.++++.+|+|++|+|+++|++|...
T Consensus       161 ~~p~~sg~~~~~l~~~~~~~G~d~g~~~l~~l~~N~~~  198 (334)
T TIGR03261       161 PNPASSGTGFLDVSAWLQMMGEDKGWDYMDKLHKNIAV  198 (334)
T ss_pred             CCCCCCHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHCC
T ss_conf             48886338999999999973528899999999863241


No 2  
>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=100.00  E-value=2.3e-35  Score=221.44  Aligned_cols=186  Identities=17%  Similarity=0.180  Sum_probs=145.6

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCC-----HHHHHHHHHHHHHHCCCCCCCCCHHHHHH---HHHHHCCC
Q ss_conf             02599999999999998612444588089981899-----89999999999987598621000013566---76521066
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTENTTKYLTLYTDQN-----QSVMLPIIHSFEERTGVKISPIYTSSIQR---PPITQGSP   73 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~~~~~lvVYs~~~-----~~~~~~~~~~Fek~tgIkV~~~~~~~~~~---~~~~~~~~   73 (195)
                      |||..+.....+++... ...+.++..|+||++.+     ....+.++++|||+|||+|+++.+++.+.   +..++++|
T Consensus        12 ~~~~~~~~~~~~~~~~~-~~~a~a~~~~~vy~~~~~~~~~~~~~~~~~~aFek~tGikV~~v~~~sge~laRl~aEk~nP   90 (367)
T TIGR03227        12 LRRFALAAGAAALLQGA-AAPAQAAAVVLVYSADGLEDGDNSLYQDQFDAFEKAEGIKVNIVEAGGGEVVERAAKEKGNP   90 (367)
T ss_pred             HHHHHHHHHHHHHHHHC-CCCCCCCCEEEEEECCCCCCCCCCHHHHHHHHHHHHHCCEEEEEECCHHHHHHHHHHCCCCC
T ss_conf             99999999999998642-35554586599996466434443468887688888669838999897799999999522799


Q ss_pred             -CCEEEECCHHHH-HHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEHHHHCCCCCCCCHHHHCCHHHCCE
Q ss_conf             -655750422332-343310000123422234720001222223443450588873344013445578888408667685
Q gi|254780563|r   74 -VDVIITKDETSL-ALNEDLLHKLPAHLIKKNSFVLKNENKKLMRISFDTQVLAYSTKRIKIADLPKSVFDLTNAQWKKR  151 (195)
Q Consensus        74 -~d~~~~~d~~~l-~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~P~sw~DL~~p~~kG~  151 (195)
                       +||+++.|.... ..++|+|+||.++..+++++.+++.+++|+++...+.+++||++.++  .+|+||+||+||+|||+
T Consensus        91 qaDVv~~~d~~~~~A~~~GLl~py~~~~~~~ip~~~k~~dg~~~~~~~~~~~~~yN~~~~k--~~PkSW~DL~dP~ykgk  168 (367)
T TIGR03227        91 KADVIVTAPPFIQQAAAEGLLANFNSDAAKAIPAIAKAADGLWAPFVKNYFSFAINPKLLK--SAPASFADLLDADFKGK  168 (367)
T ss_pred             CCEEEEECCHHHHHHHHCCCCCCCCCCCHHHCCHHHHCCCCCEEEEECCEEEEEEEHHHHC--CCCCCHHHHHCCCCCCE
T ss_conf             7209997857999999788956278966455777663779838988555799999857705--79988998728533782


Q ss_pred             EEECCCC--CCHHHHHHHHHHHHC-HHHHHHHHHHHHHCCCC
Q ss_conf             9962898--304999999999608-69999999998608870
Q gi|254780563|r  152 LSIAPNN--ISFHRLLNTMEQTPN-KTVVQDFIKNITANEIL  190 (195)
Q Consensus       152 i~~~~~~--~s~~~~~~a~~~~~G-~~~~~~~l~~l~~N~~~  190 (195)
                      |+++++.  +++.+++.++.+.+| +|++|+|+++|++|.+.
T Consensus       169 I~~~dP~tS~~g~~~l~~~~~~~G~eD~a~~~~~~L~~N~~~  210 (367)
T TIGR03227       169 LAYSNPAQAADGMAVIILAFALFGSEDAAFAYLAKLEANNKF  210 (367)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCE
T ss_conf             895287766179999999999709853889999988744867


No 3  
>PRK11205 tbpA thiamine transporter substrate binding subunit; Provisional
Probab=100.00  E-value=2.1e-33  Score=210.23  Aligned_cols=168  Identities=14%  Similarity=0.160  Sum_probs=135.5

Q ss_pred             HHCCCCCCCCEEEECCCCHHHH----HHHHHHHHHHCCCCCCCCCHHHH-H---HHH-HHHCCCCCEEEECCHHHHH--H
Q ss_conf             6124445880899818998999----99999999875986210000135-6---676-5210666557504223323--4
Q gi|254780563|r   19 AFSTENTTKYLTLYTDQNQSVM----LPIIHSFEERTGVKISPIYTSSI-Q---RPP-ITQGSPVDVIITKDETSLA--L   87 (195)
Q Consensus        19 ~~~~~~~~~~lvVYs~~~~~~~----~~~~~~Fek~tgIkV~~~~~~~~-~---~~~-~~~~~~~d~~~~~d~~~l~--~   87 (195)
                      |.++..++++|+|||++++...    +.++++|||+|||+|+++..++. +   ++. +++++++|++++.|.+.+.  .
T Consensus        11 ~a~~~~~~~~l~vyt~dsf~~d~g~~~~l~~~Fek~tGikV~~v~~~dg~~ll~Rl~~Eg~np~ADVv~gvD~~~l~~A~   90 (326)
T PRK11205         11 CAAPAFAKPVLTVYTYDSFAADWGPGPAVKKAFEAECGCELKFVALEDGVSLLNRLRLEGKNSKADVVLGLDNNLLAAAK   90 (326)
T ss_pred             HCCCCCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHCCEEEEEECCCHHHHHHHHHHCCCCCCCCEEEECCHHHHHHHH
T ss_conf             63620029879999665444466864799999989879689999679679999999973899976589981767899999


Q ss_pred             HHHHHCCCCCCCCC-CCCCCCCCCCCCCCCCCCCEEEEEEEHHHHCCCCCCCCHHHHCCHHHCCEEEECCC--CCCHHHH
Q ss_conf             33100001234222-34720001222223443450588873344013445578888408667685996289--8304999
Q gi|254780563|r   88 NEDLLHKLPAHLIK-KNSFVLKNENKKLMRISFDTQVLAYSTKRIKIADLPKSVFDLTNAQWKKRLSIAPN--NISFHRL  164 (195)
Q Consensus        88 ~~~~l~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~P~sw~DL~~p~~kG~i~~~~~--~~s~~~~  164 (195)
                      ++|+|+|+.++... +++..++++  .|+++.....+++||+++++  ++|+||+||++|+|||+|++++|  |++++++
T Consensus        91 ~~gl~~p~~s~~~~~~ip~~~~d~--~~vp~d~g~~a~vYn~~~~~--~~P~S~~DL~~p~~kgki~i~dP~tSs~g~a~  166 (326)
T PRK11205         91 KTGLFAPSGVDTSAVTVPGGWNDD--TFVPYDYGYFAFVYDKEKLK--NPPKSLKELVESDQNWKVIYQDPRTSTPGLGL  166 (326)
T ss_pred             HCCCCCCCCCCHHHCCCCCCCCCC--CEECCCCCEEEEEEEHHHCC--CCCCCHHHHHCCHHCCCEEECCCCCCCCHHHH
T ss_conf             869965256861102486002698--52113476589998422237--88769898727330388663388878527999


Q ss_pred             HHHHHHHHCHHHHHHHHHHHHHCCCCC
Q ss_conf             999999608699999999986088705
Q gi|254780563|r  165 LNTMEQTPNKTVVQDFIKNITANEILT  191 (195)
Q Consensus       165 ~~a~~~~~G~~~~~~~l~~l~~N~~~~  191 (195)
                      +.++++.+|++. .++|++|++|++..
T Consensus       167 l~~~i~~~Ge~~-~e~W~~L~~N~~~~  192 (326)
T PRK11205        167 LLWMKKVYGDDA-PQAWQKLAKKTVTV  192 (326)
T ss_pred             HHHHHHHHCCCH-HHHHHHHHHCCCCC
T ss_conf             999999716328-99999998638444


No 4  
>COG4143 TbpA ABC-type thiamine transport system, periplasmic component [Coenzyme metabolism]
Probab=99.96  E-value=2.3e-28  Score=181.49  Aligned_cols=186  Identities=15%  Similarity=0.127  Sum_probs=141.2

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCH---HHH-HHHHHHHHHHCCCCCCCCCHHH-----HHHHHHHHC
Q ss_conf             9025999999999999986124445880899818998---999-9999999987598621000013-----566765210
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFSTENTTKYLTLYTDQNQ---SVM-LPIIHSFEERTGVKISPIYTSS-----IQRPPITQG   71 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~~~~~~~lvVYs~~~~---~~~-~~~~~~Fek~tgIkV~~~~~~~-----~~~~~~~~~   71 (195)
                      ||+ ++...++++++++.+++++++.++|+||++.+.   +.. ..++++||++|+++|+++...+     +.+++++.+
T Consensus         1 m~~-~l~~~~~~all~~~~~~a~~~t~~LtVytydSF~~ewg~Gp~vk~~FE~~~~~~v~fV~~~d~v~llnRl~leg~~   79 (336)
T COG4143           1 MRR-LLRALIGLALLVSAALGAQAATPTLTVYTYDSFASEWGPGPKVKKAFEAEYGCKVNFVALGDGVELLNRLILEGKN   79 (336)
T ss_pred             CHH-HHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEECCCCCCHHHHHHHHHHHCCEEEEEECCCHHHHHHHHHHCCCC
T ss_conf             902-4999999999999865776348538999976342256885789999999859528999707589999999970789


Q ss_pred             CCCCEEEECCHHHHH--HHHHHHCCCCCCCC-CCCCCCCCCCCCCCCCCCCCEEEEEEEHHHHCCCCCCCCHHHHCCHHH
Q ss_conf             666557504223323--43310000123422-234720001222223443450588873344013445578888408667
Q gi|254780563|r   72 SPVDVIITKDETSLA--LNEDLLHKLPAHLI-KKNSFVLKNENKKLMRISFDTQVLAYSTKRIKIADLPKSVFDLTNAQW  148 (195)
Q Consensus        72 ~~~d~~~~~d~~~l~--~~~~~l~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~P~sw~DL~~p~~  148 (195)
                      +.+|++++.|...+.  .+.++|.++..+.. .+++..+++..- .+++.+.+..++||++.++  ++|+|++||++|+|
T Consensus        80 ~~ADvvvGldn~~l~~A~~~~lf~~~~~d~~~~~vp~~~~~d~f-~~P~DyGy~a~vYd~~~~~--~ppksL~dL~~~~y  156 (336)
T COG4143          80 PKADVVVGLDNNLLARARETGLFAPYGVDASDVPVPEGWKIDTF-ALPYDYGYFAFVYDKTKLK--NPPKSLKDLVEPEY  156 (336)
T ss_pred             CCCCEEEECCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCEEEEEECHHHHC--CCCCCHHHHCCCCC
T ss_conf             88858993472778888855876667898557888765356751-0124541289997657752--87626898638512


Q ss_pred             CCEEEECCC--CCCHHHHHHHHHHHHCHHHHHHHHHHHHHCCCC
Q ss_conf             685996289--830499999999960869999999998608870
Q gi|254780563|r  149 KKRLSIAPN--NISFHRLLNTMEQTPNKTVVQDFIKNITANEIL  190 (195)
Q Consensus       149 kG~i~~~~~--~~s~~~~~~a~~~~~G~~~~~~~l~~l~~N~~~  190 (195)
                      +|+|.+++|  |++|.+|+.++++.+|+|.+++||++|++|++.
T Consensus       157 ~~~ii~qdPrtSspGl~fLlW~~svyg~d~~~~~W~kL~~~~v~  200 (336)
T COG4143         157 AGKIIYQDPRTSSPGLGFLLWTISVYGEDGAPEAWAKLADNGVT  200 (336)
T ss_pred             CCCEEECCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCEE
T ss_conf             69578069887884078899998763623189999999858868


No 5  
>COG1840 AfuA ABC-type Fe3+ transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=99.90  E-value=2.1e-23  Score=153.22  Aligned_cols=147  Identities=20%  Similarity=0.187  Sum_probs=118.8

Q ss_pred             HHHHHHHHCCCCCCCCCHHHH---HHHHHHHCC--CCCEEEECCHHHHH--HHHHHHCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             999999875986210000135---667652106--66557504223323--43310000123422234720001222223
Q gi|254780563|r   43 IIHSFEERTGVKISPIYTSSI---QRPPITQGS--PVDVIITKDETSLA--LNEDLLHKLPAHLIKKNSFVLKNENKKLM  115 (195)
Q Consensus        43 ~~~~Fek~tgIkV~~~~~~~~---~~~~~~~~~--~~d~~~~~d~~~l~--~~~~~l~~~~~~~~~~~~~~~~~~~~~~~  115 (195)
                      ++++|++++||+|+++..++.   ++++.++++  ++|++|+.+...+.  .++|++++|.++....+++.++++++.+.
T Consensus         1 ~~~~f~~~~gikv~~~~~~s~~~~~~~~~e~~~~~~aDv~~~~~~~~~~~l~~~gll~~y~~~~~~~i~~~~~~~~~~~~   80 (299)
T COG1840           1 LIKAFEKKPGIKVEFVDAGSGELLARIIAEKGNPQAADVLWGGAPVSLDQLKEAGLLQPYKSPELDEIPAWAPDPDGAYG   80 (299)
T ss_pred             CHHHHHHCCCCEEEEEECCCHHHHHHHHHHCCCCCCCCEEEECCHHHHHHHHHCCCCCCCCCCCHHHHHHCCCCCCCCCC
T ss_conf             95567337796689874884899999997224899881896068169999985797222698346565331346444665


Q ss_pred             CCCCCEEEEEEEHHHHCCCCC--CCCHHHHCCHHHCCEEEECCCCCCHHHHHHHHH--HHHCHHHHHHHHHHHHHCCCC
Q ss_conf             443450588873344013445--578888408667685996289830499999999--960869999999998608870
Q gi|254780563|r  116 RISFDTQVLAYSTKRIKIADL--PKSVFDLTNAQWKKRLSIAPNNISFHRLLNTME--QTPNKTVVQDFIKNITANEIL  190 (195)
Q Consensus       116 ~~~~~~~~~~~n~~~~~~~~~--P~sw~DL~~p~~kG~i~~~~~~~s~~~~~~a~~--~~~G~~~~~~~l~~l~~N~~~  190 (195)
                      ...+...+++||++..+....  |+||.||++|+|||+++++++++++.. +.++.  +.+|++.+|+|++.|++|...
T Consensus        81 ~~~~~~~~~~~n~~~~~~~~~~~P~~w~DL~~p~~kg~i~~~~p~~s~~~-~~~~~~~~~~G~~~~~~~l~~l~~n~~~  158 (299)
T COG1840          81 GGYVGPLVFAVNTDYNKDLLKPVPKSWADLAKPEYKGKVQMADPTSSGTA-YAALLALQAYGEEKGWAYLKGLAANLAT  158 (299)
T ss_pred             CCEEEEEEEEEEEECCCCCCCCCCCCHHHHHCHHHCCCEEEECCCCCHHH-HHHHHHHHHCCHHHHHHHHHHHHHHCCC
T ss_conf             64477899999611034456899867998709886698465478855899-9999999864879999999999985133


No 6  
>PRK09501 potD spermidine/putrescine ABC transporter periplasmic substrate-binding protein; Reviewed
Probab=99.89  E-value=1.7e-22  Score=148.07  Aligned_cols=183  Identities=13%  Similarity=0.118  Sum_probs=123.7

Q ss_pred             CHHHHHHHHHHH-HHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHH---HHH-HCCCCCE
Q ss_conf             025999999999-99998612444588089981899899999999999875986210000135667---652-1066655
Q gi|254780563|r    2 FKRTIYTYLLLL-CGFTEAFSTENTTKYLTLYTDQNQSVMLPIIHSFEERTGVKISPIYTSSIQRP---PIT-QGSPVDV   76 (195)
Q Consensus         2 mkk~~~~~l~l~-~~~~~~~~~~~~~~~lvVYs~~~~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~---~~~-~~~~~d~   76 (195)
                      |||...+.|.+. +++++++++++..++|+||++.++ +.+.++++||++|||+|++...++++.+   ++. .+.+-|+
T Consensus         1 ~~~~~~~ll~~~a~~l~~~~~~a~~~~~L~i~~W~~Y-i~~~~i~~Fe~etGikV~~~~~~s~ee~~akL~a~~~~~yDv   79 (348)
T PRK09501          1 MKKWSRHLLAAGALALGMSAAHADDNNTLYFYNWTEY-VPPGLLEQFTKETGIKVIYSTYESNETMYAKLKTYKDGAYDL   79 (348)
T ss_pred             CHHHHHHHHHHHHHHHHCCHHHHCCCCEEEEECCCCC-CCHHHHHHHHHHHCCEEEEEECCCHHHHHHHHHCCCCCCCEE
T ss_conf             9368999999999997350335433897999871001-897899999999898899995499999999997179998289


Q ss_pred             EEECCHH-HHHHHHHHHCCCCCCCC---CCCCCCCCC-----CCCCCCCCCCCEEEEEEEHHHHCCCCCCCCHHHHCCHH
Q ss_conf             7504223-32343310000123422---234720001-----22222344345058887334401344557888840866
Q gi|254780563|r   77 IITKDET-SLALNEDLLHKLPAHLI---KKNSFVLKN-----ENKKLMRISFDTQVLAYSTKRIKIADLPKSVFDLTNAQ  147 (195)
Q Consensus        77 ~~~~d~~-~l~~~~~~l~~~~~~~~---~~~~~~~~~-----~~~~~~~~~~~~~~~~~n~~~~~~~~~P~sw~DL~~p~  147 (195)
                      ++..+.. ....++|+++|++....   .++.+.+.+     ...+.+|+.....+++||++.++.. +|+||.||++|+
T Consensus        80 v~ps~~~v~~l~~~gll~~LD~s~ipN~~nl~p~~~~~~~dp~~~y~vPy~wGt~Gi~yn~d~v~~~-~~~SW~dL~dp~  158 (348)
T PRK09501         80 VVPSTYYVDKMRKEGMIQKIDKSKLTNFSNLDPDMLNKPFDPNNDYSIPYIWGATAIGVNGDAVDPK-SVTSWADLWKPE  158 (348)
T ss_pred             EEECHHHHHHHHHCCCCCCCCHHHCCCHHHCCHHHHCCCCCCCCCEEEEEEEECCEEEEEECCCCCC-CCCCHHHHCCHH
T ss_conf             9979689999997798454784228481226976744774899848988997511599850114788-888789854966


Q ss_pred             HCCEEEECCCCCCHHHHHHHHHHHH---------CHHHHHHHHHHHHHCC
Q ss_conf             7685996289830499999999960---------8699999999986088
Q gi|254780563|r  148 WKKRLSIAPNNISFHRLLNTMEQTP---------NKTVVQDFIKNITANE  188 (195)
Q Consensus       148 ~kG~i~~~~~~~s~~~~~~a~~~~~---------G~~~~~~~l~~l~~N~  188 (195)
                      |||+|++.+.....  +..++....         .-+++++.|++++.|-
T Consensus       159 ~kGki~~~d~~~~~--~~~al~~lG~~~n~~d~~~l~~a~~~L~~~~~~i  206 (348)
T PRK09501        159 YKGSLLLTDDAREV--FQMALRKLGYSGNTTDPKEIEAAYNELKKLMPNV  206 (348)
T ss_pred             HCCEEEECCCHHHH--HHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCCE
T ss_conf             47907971667899--9999998279988899999999999999851105


No 7  
>TIGR01254 sfuA ABC transporter periplasmic binding protein, thiB subfamily; InterPro: IPR005948   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 and a high affinity periplasmic solute-binding protein. In Gram-positive bacteria, which are surrounded by a single membrane and therefore have no periplasmic region, the equivalent proteins are bound to the membrane via an N-terminal lipid anchor. These homologue 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.    Thiamine pyrophosphate 1 is a required cofactor synthesized de novo in Salmonella typhimurium. The primary role for TPP is in central metabolism as an electron carrier and nucleophile for such enzymes as pyruvate dehydrogenase (1.2.4.1 from EC), acetolactate synthase (4.1.3.18 from EC), and alpha-ketoglutarate dehydrogenase (1.2.4.2 from EC). Despite its importance in cellular physiology, neither the de novo biosynthetic pathway nor the salvage systems for thiamine are fully understood in any organism.    The thiamine ABC transporter, periplasmic binding protein in bacteria is believed to be involved in the specific translocation of thiamine and its phosphoesters across the inner membrane. The protein belongs to the larger ABC transport system which consists of at least three components: the inner membrane permease; thiamine binding protein and an ATP-binding subunit. It has been experimentally demonstrated that mutants in the various steps in the de novo synthesis of thiamine and its biologically active form, namely thiamine pyrophosphate can be exogenously supplemented with thiamine, thiamine monophosphate (TMP) or thiamine pyrophosphate TPP. ; GO: 0005215 transporter activity, 0006810 transport, 0030288 outer membrane-bounded periplasmic space.
Probab=99.88  E-value=1.3e-22  Score=148.65  Aligned_cols=165  Identities=15%  Similarity=0.178  Sum_probs=139.6

Q ss_pred             CCCEEEECCCCHH----HHHHHHHHHH-HHCCCCCCCCCHHH-----HHHHHHHHCCCCCEEEECCHHHHH--HHHHHHC
Q ss_conf             8808998189989----9999999999-87598621000013-----566765210666557504223323--4331000
Q gi|254780563|r   26 TKYLTLYTDQNQS----VMLPIIHSFE-ERTGVKISPIYTSS-----IQRPPITQGSPVDVIITKDETSLA--LNEDLLH   93 (195)
Q Consensus        26 ~~~lvVYs~~~~~----~~~~~~~~Fe-k~tgIkV~~~~~~~-----~~~~~~~~~~~~d~~~~~d~~~l~--~~~~~l~   93 (195)
                      ..+|+|||+.|+.    .+..+.++|| .+++|+|+++..++     +.++++++++.+|++.|.|+..+.  .+.|+|+
T Consensus         2 ~~~l~v~tydSF~~~wG~~p~~e~~f~kA~~~C~~~fv~~~d~~~lLNrL~L~g~~~~ADvVlGLDN~ll~~A~~~Glla   81 (324)
T TIGR01254         2 QTTLTVYTYDSFAADWGLGPKVEKAFEKADAQCKVKFVALGDAGELLNRLRLEGKNPKADVVLGLDNNLLEKAEKTGLLA   81 (324)
T ss_pred             CCEEEEEEEECCCCCCCCCHHHHHHHHCCCCCCCEEEEECCCCEEEEEEEEECCCCCCCCEEECCCHHHHHHHHHCCCCC
T ss_conf             85588988632147876204788763005888627888438843321112313698843167652367899998717423


Q ss_pred             CCCCCCCCCCCCCCCCCCC-CCCCCCCCEEEEEEEHHHHCCC--CCCCCHHHHCCHHHCCEEEECC--CCCCHHHHHHHH
Q ss_conf             0123422234720001222-2234434505888733440134--4557888840866768599628--983049999999
Q gi|254780563|r   94 KLPAHLIKKNSFVLKNENK-KLMRISFDTQVLAYSTKRIKIA--DLPKSVFDLTNAQWKKRLSIAP--NNISFHRLLNTM  168 (195)
Q Consensus        94 ~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~n~~~~~~~--~~P~sw~DL~~p~~kG~i~~~~--~~~s~~~~~~a~  168 (195)
                      +..+.....+.-..+..+. ...++.+.+..++|++.++..+  .+|+|++||.+|+++-+++.++  +|++|++|+.+|
T Consensus        82 ~~~sv~~~~v~~p~~w~~~Gtf~p~DYGY~A~vYDk~~l~~~~L~LP~SL~eL~~~~~~~~viy~dPrTSsPG~GlLlw~  161 (324)
T TIGR01254        82 PAQSVDLAKVAVPTGWDDAGTFLPVDYGYVAFVYDKKKLQNPKLALPKSLKELVEPEYDLLVIYQDPRTSSPGLGLLLWM  161 (324)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCEEEECCCEEEEEECHHHHCCCCCCCCCCHHHHCCHHHCCEEEECCCCCCCHHHHHHHHH
T ss_conf             35787533247888657677460000121342431587548888888673663472152634653888672568999987


Q ss_pred             HHHHCHHHHHHHHHHHHHCCCC
Q ss_conf             9960869999999998608870
Q gi|254780563|r  169 EQTPNKTVVQDFIKNITANEIL  190 (195)
Q Consensus       169 ~~~~G~~~~~~~l~~l~~N~~~  190 (195)
                      ..++|+|.++.||+.|..+++.
T Consensus       162 ~~~Yg~d~a~~aW~~l~~~tv~  183 (324)
T TIGR01254       162 KSVYGEDKAPQAWKQLRKKTVT  183 (324)
T ss_pred             HHCCCHHHHHHHHHHHHHCCCE
T ss_conf             6237800379999999837947


No 8  
>PRK10682 putrescine transporter subunit: periplasmic-binding component of ABC superfamily; Provisional
Probab=99.83  E-value=6.9e-20  Score=133.16  Aligned_cols=183  Identities=14%  Similarity=0.150  Sum_probs=122.7

Q ss_pred             CHHHHHHHHHHHHHHHHHH-CCCCCCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHH---HHHCCCCCEE
Q ss_conf             0259999999999999861-24445880899818998999999999998759862100001356676---5210666557
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAF-STENTTKYLTLYTDQNQSVMLPIIHSFEERTGVKISPIYTSSIQRPP---ITQGSPVDVI   77 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~-~~~~~~~~lvVYs~~~~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~~---~~~~~~~d~~   77 (195)
                      ++|++++.|++++.++.++ ++++++++|+||++.++ +...++++|||+|||+|++...++.+.+.   +..+..-|++
T Consensus         4 ~~~~~~~~l~~~~~~~~~~~~~aa~~~~Lnv~nW~~Y-i~p~~i~~FeketGikV~~~~~~snee~~akl~ag~~gyDvv   82 (370)
T PRK10682          4 LNKKWLSGLVAGALMAVSVGTLAAEQKTLHIYNWSDY-IAPDTVANFEKETGIKVVYDVFDSNEVLEGKLMAGSTGFDLV   82 (370)
T ss_pred             HHHHHHHHHHHHHHHHHHCCHHHHCCCEEEEECCCCC-CCHHHHHHHHHHHCCEEEEEECCCHHHHHHHHHCCCCCCCEE
T ss_conf             7788999999999999852056642797999816765-797799999999798899995499899999996699999889


Q ss_pred             EECCH-HHHHHHHHHHCCCCCCCCC---CCCCCCCC-------CCCCCCCCCCCEEEEEEEHHHHCC----CCCCCCHHH
Q ss_conf             50422-3323433100001234222---34720001-------222223443450588873344013----445578888
Q gi|254780563|r   78 ITKDE-TSLALNEDLLHKLPAHLIK---KNSFVLKN-------ENKKLMRISFDTQVLAYSTKRIKI----ADLPKSVFD  142 (195)
Q Consensus        78 ~~~d~-~~l~~~~~~l~~~~~~~~~---~~~~~~~~-------~~~~~~~~~~~~~~~~~n~~~~~~----~~~P~sw~D  142 (195)
                      +..+. .....++|+++|++....+   ++.+.++.       ...+.+|+.....+|+||+++++.    ..+|+||.+
T Consensus        83 ~ps~~~v~~~~~~gll~pLD~sklpN~~ni~p~~~~~~~~~dpg~~YsVPy~wGt~GI~Yn~d~v~~~~g~~~p~~sW~~  162 (370)
T PRK10682         83 VPSASFLERQLTAGVFQPLDKSKLPNWKNLDPELLKLVAKHDPDNKYAMPYMWATTGIGYNVDKVKAVLGEDAPVDSWDL  162 (370)
T ss_pred             EECHHHHHHHHHCCCCCCCCHHHCCCHHHCCHHHHHHHHCCCCCCEEEEEEEECCEEEEEECCCCCCCCCCCCCCCHHHH
T ss_conf             97779999999769846477000867444299988410036999759988884225999976544223467888462998


Q ss_pred             HCCHHHCCE-----EEECCCCCCHHHHHHHHHHHHCH-----------HHHHHHHHHHHHCC
Q ss_conf             408667685-----99628983049999999996086-----------99999999986088
Q gi|254780563|r  143 LTNAQWKKR-----LSIAPNNISFHRLLNTMEQTPNK-----------TVVQDFIKNITANE  188 (195)
Q Consensus       143 L~~p~~kG~-----i~~~~~~~s~~~~~~a~~~~~G~-----------~~~~~~l~~l~~N~  188 (195)
                      |++|+++||     |++.+.....  +..++.. .|.           .++.++|.+++.|-
T Consensus       163 l~~P~~~~k~k~~~v~~ld~~~~~--~~~aL~~-lG~~~n~~~~~d~~~aa~~~L~~~kp~v  221 (370)
T PRK10682        163 VLKPENLEKLKSCGVSFLDAPEEI--FATVLNY-LGKDPNSTKADDYTGPATDLLLKLRPNI  221 (370)
T ss_pred             HHCHHHHHHCCCCCEEEECCHHHH--HHHHHHH-CCCCCCCCCHHHHHHHHHHHHHHHCHHC
T ss_conf             649275653035855897688899--9999997-6999899999999999999999712224


No 9  
>COG0687 PotD Spermidine/putrescine-binding periplasmic protein [Amino acid transport and metabolism]
Probab=99.77  E-value=4.5e-18  Score=122.82  Aligned_cols=185  Identities=19%  Similarity=0.175  Sum_probs=115.9

Q ss_pred             CCHHHHH---HHHHHHHHHHHHH--CCCCCCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHH---HHHHCC
Q ss_conf             9025999---9999999999861--2444588089981899899999999999875986210000135667---652106
Q gi|254780563|r    1 MFKRTIY---TYLLLLCGFTEAF--STENTTKYLTLYTDQNQSVMLPIIHSFEERTGVKISPIYTSSIQRP---PITQGS   72 (195)
Q Consensus         1 mmkk~~~---~~l~l~~~~~~~~--~~~~~~~~lvVYs~~~~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~---~~~~~~   72 (195)
                      |||+...   ..+..+++.+++.  ++.++.++|+||++..+... .++++|||+|||+|++...++.+.+   ++.+..
T Consensus         1 m~k~~~~~~~~~~~~~~~a~~~~~~~a~a~~~~l~v~~w~gy~~~-~~~~~F~k~tGi~V~~~~~~sne~~~ak~~~g~~   79 (363)
T COG0687           1 MMKKLSRRSFLALAALALAALAGAAAAAAEGKTLNVYNWGGYIDP-ALLKPFEKETGIKVVYDTFDSNEEMLAKLKAGGG   79 (363)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHCHHHHHHCCCEEEEECCCCCCCH-HHHHHHHHHHCCEEEEECCCCHHHHHHHHHHCCC
T ss_conf             941466667899999999986000456625785999647875577-8899899998997999538986999999980899


Q ss_pred             CCCEEEECC-HHHHHHHHHHHCCCCCCCCCC---CCCCCCCCC------CCCCCCCCCEEEEEEEHHHHCCCCCCCCHHH
Q ss_conf             665575042-233234331000012342223---472000122------2223443450588873344013445578888
Q gi|254780563|r   73 PVDVIITKD-ETSLALNEDLLHKLPAHLIKK---NSFVLKNEN------KKLMRISFDTQVLAYSTKRIKIADLPKSVFD  142 (195)
Q Consensus        73 ~~d~~~~~d-~~~l~~~~~~l~~~~~~~~~~---~~~~~~~~~------~~~~~~~~~~~~~~~n~~~~~~~~~P~sw~D  142 (195)
                      .-|++.... ......++|++++++.....+   +.+.+....      .+-+|+.....+++||+++++...+|+||.|
T Consensus        80 ~~Dvv~~s~~~~~~~~~~gll~~lD~skl~n~~~l~~~~~~~~~~d~g~~y~vPy~~g~t~i~Yn~~~~~~~~~~~sW~~  159 (363)
T COG0687          80 GYDVVVPSGYFVARLIKEGLLQPLDKSKLPNWKNLDPEFLNPPKFDPGNKYSVPYFWGTTGIAYNTDKVKDAPPPTSWAD  159 (363)
T ss_pred             CCCEEECCHHHHHHHHHCCCCCCCCHHHCCCHHHCCHHHHCCCCCCCCCEECEEEEEEEEEEEEECCCCCCCCCCCCHHH
T ss_conf             98879718889999986675675896666482116987835776788886031678864699998000589999988999


Q ss_pred             HCCHH----HCCE-EEECCCCCCHHHHHHHHHHHH-------CHHHHHHHHHHHHH
Q ss_conf             40866----7685-996289830499999999960-------86999999999860
Q gi|254780563|r  143 LTNAQ----WKKR-LSIAPNNISFHRLLNTMEQTP-------NKTVVQDFIKNITA  186 (195)
Q Consensus       143 L~~p~----~kG~-i~~~~~~~s~~~~~~a~~~~~-------G~~~~~~~l~~l~~  186 (195)
                      |++|+    +||+ +.+-+....-..+..+.+...       .-+++.+.|.+++.
T Consensus       160 l~d~~~~~~~k~~~~~~~d~~~~~~~~al~~lg~~~n~~~~~~~~~a~~~L~~~kp  215 (363)
T COG0687         160 LFDPEKFPGLKGKGVALLDDDREVFGAALALLGKSPNTTDPEDLKKAFDLLDKLKP  215 (363)
T ss_pred             HHCCHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCC
T ss_conf             83842002232575301366057899999971899788998899999999997278


No 10 
>PRK09474 malE maltose ABC transporter periplasmic protein; Reviewed
Probab=99.50  E-value=2.1e-13  Score=96.18  Aligned_cols=189  Identities=14%  Similarity=0.164  Sum_probs=107.8

Q ss_pred             CHHHH--HHHHHHHHHH-HHHHCCCCCCCCEEEECCCC--HHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHH---HHCCC
Q ss_conf             02599--9999999999-98612444588089981899--89999999999987598621000013566765---21066
Q gi|254780563|r    2 FKRTI--YTYLLLLCGF-TEAFSTENTTKYLTLYTDQN--QSVMLPIIHSFEERTGVKISPIYTSSIQRPPI---TQGSP   73 (195)
Q Consensus         2 mkk~~--~~~l~l~~~~-~~~~~~~~~~~~lvVYs~~~--~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~~~---~~~~~   73 (195)
                      |||.+  ++..++++++ +.+.++++.+.+|+|.....  .+.+++++++||+++||+|++...+..+..+.   ..++.
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ltvW~~~~~~~~~l~~~~~~Fe~~~gi~V~v~~~~~~~~kl~~a~~~G~~   80 (394)
T PRK09474          1 IKKGLRILALSALTTLMLSASALAKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVTVEHPDKLEEKFPQVAATGDG   80 (394)
T ss_pred             CCHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCHHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHCCCCC
T ss_conf             94158899999999999736432456678699995797056999999999745409779997102689999974207999


Q ss_pred             CCEEEE-CCHHHHHHHHHHHCCCCCCCC--CCCCCCC-----CCCCCCCCCCCCCEEEEEEEHHHHCCCCCCCCHHHHCC
Q ss_conf             655750-422332343310000123422--2347200-----01222223443450588873344013445578888408
Q gi|254780563|r   74 VDVIIT-KDETSLALNEDLLHKLPAHLI--KKNSFVL-----KNENKKLMRISFDTQVLAYSTKRIKIADLPKSVFDLTN  145 (195)
Q Consensus        74 ~d~~~~-~d~~~l~~~~~~l~~~~~~~~--~~~~~~~-----~~~~~~~~~~~~~~~~~~~n~~~~~~~~~P~sw~DL~~  145 (195)
                      .|+++. .+........|+|+++.....  +...+..     .+-.-|-+|+.....++.||++.++  ++|+||+||..
T Consensus        81 PDv~~~~~~~~~~~a~~G~l~pl~~~~~~~~~~~~~~~~a~tydGk~YgvP~~~~t~~L~YNKdl~~--~pP~TwdEl~~  158 (394)
T PRK09474         81 PDIIFWAHDRFGGYAQSGLLAEVTPSKAFQDKLVPFTWDAVRYNGKLIGYPIAVEALSLIYNKDLVP--NPPKTWEEIPA  158 (394)
T ss_pred             CCEEEECCHHHHHHHHCCCCCCCCCCHHHHHHCCHHHHHCEEECCEEEEECCCCCCEEEEEEHHHCC--CCCCCHHHHHH
T ss_conf             9589988476999997898663885644453046334524688988888630122306887400036--89999999999


Q ss_pred             --HHH--CCEEEEC-CCCCCHHH--HHHHH------------------HHHHCHHHHHHHHHHHHHCCCCCC
Q ss_conf             --667--6859962-89830499--99999------------------996086999999999860887056
Q gi|254780563|r  146 --AQW--KKRLSIA-PNNISFHR--LLNTM------------------EQTPNKTVVQDFIKNITANEILTK  192 (195)
Q Consensus       146 --p~~--kG~i~~~-~~~~s~~~--~~~a~------------------~~~~G~~~~~~~l~~l~~N~~~~~  192 (195)
                        .+.  +|+..+. +....+..  ++.+.                  +...+--++.+|++.|..++...+
T Consensus       159 ~ak~l~~~g~~~~~~~~~~~~~~~~~~~~~Gg~~f~~~~gg~d~~~~~~ns~~~v~al~~~~~l~~~g~~~~  230 (394)
T PRK09474        159 LDKELKKKGKSAIMWNLQEPYFTWPLIAADGGYAFKKENGGYDVKDVGVNNAGAKAGLQFLVDLIKNKHMNA  230 (394)
T ss_pred             HHHHHHHCCCCEEEECCCCHHHHHHHHHHCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCC
T ss_conf             999987538640452266418778999807884434378875554354489999999999999997599898


No 11 
>TIGR01276 thiB thiamin/thiamin pyrophosphate ABC transporter, thiamin/thiamin pyrophospate-binding protein; InterPro: IPR005967   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 and a high affinity periplasmic solute-binding protein. In Gram-positive bacteria, which are surrounded by a single membrane and therefore have no periplasmic region, the equivalent proteins are bound to the membrane via an N-terminal lipid anchor. These homologue 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.    Thiamine pyrophosphate (TPP) is a required cofactor synthesized de novo in Salmonella typhimurium . The primary role for TPP is in central metabolism as an electron carrier and nucleophile for such enzymes as pyruvate dehydrogenase (1.2.4.1 from EC), acetolactate synthase (4.1.3.18 from EC), and alpha-ketoglutarate dehydrogenase (1.2.4.2 from EC). Despite its importance in cellular physiology, neither the de novo biosynthetic pathway nor the salvage systems for thiamine are fully understood in any organism.    The thiamine ABC transporter, periplasmic binding protein in proteobacteria is believed to be involved in the specific translocation of thiamine and its phosphoesters across the inner membrane The protein belongs to the larger ABC transport system which consists of at least three components: the inner membrane permease; thiamine binding protein and an ATP-binding subunit. It has been experimentally demonstrated that mutants in the various steps in the de novo synthesis of thiamine and its biologically active form, namely thiamine pyrophosphate can be exogenously supplemented with thiamine, thiamine monophosphate or thiamine pyrophosphate.; GO: 0005524 ATP binding, 0042626 ATPase activity coupled to transmembrane movement of substances, 0006810 transport, 0030288 outer membrane-bounded periplasmic space.
Probab=99.42  E-value=2e-13  Score=96.34  Aligned_cols=164  Identities=17%  Similarity=0.170  Sum_probs=121.6

Q ss_pred             CCCCCCEEEECCCC---HHHHHH-HHHHHH-HHCCCCCCCCCHHH-----HHHHHHHHCCCCCEEEECCHHHHH--HHHH
Q ss_conf             44588089981899---899999-999999-87598621000013-----566765210666557504223323--4331
Q gi|254780563|r   23 ENTTKYLTLYTDQN---QSVMLP-IIHSFE-ERTGVKISPIYTSS-----IQRPPITQGSPVDVIITKDETSLA--LNED   90 (195)
Q Consensus        23 ~~~~~~lvVYs~~~---~~~~~~-~~~~Fe-k~tgIkV~~~~~~~-----~~~~~~~~~~~~d~~~~~d~~~l~--~~~~   90 (195)
                      ..+.+.|+|||+++   ++...| +.++|| ..+.+.++++...+     ++.+++++++.+|++.|.|+..|-  .+-|
T Consensus        12 ~~A~~~~~VY~YDSF~~~WG~GP~VK~~FEkA~~~C~~~l~~lE~~~~LLNR~RlEGK~~KAD~VLGLDN~lL~~A~KTG   91 (326)
T TIGR01276        12 VFAKQVLTVYSYDSFAADWGAGPKVKKDFEKADPNCELKLVALEDVVVLLNRLRLEGKKSKADVVLGLDNFLLDAAEKTG   91 (326)
T ss_pred             HHCCCEEEEEECCCCCCCCCCCCCCHHHHHCCCCCCCEEEEECCCCEEEEEEEEECCCCCCCCEEECCHHHHHHHHHHCC
T ss_conf             65054016850224332357758421144057876413656413330322122303666543367633056787664166


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEHHHHCCCCCCCCHHHHCCHHHCCEEEE--CCCCCCHHHHHHHH
Q ss_conf             0000123422234720001222223443450588873344013445578888408667685996--28983049999999
Q gi|254780563|r   91 LLHKLPAHLIKKNSFVLKNENKKLMRISFDTQVLAYSTKRIKIADLPKSVFDLTNAQWKKRLSI--APNNISFHRLLNTM  168 (195)
Q Consensus        91 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~P~sw~DL~~p~~kG~i~~--~~~~~s~~~~~~a~  168 (195)
                      +|++.-.+...-..| -+..+.++.|+.+..+.++|.+.+++  +||+|+++|...+=.-++..  |-+|+.|..++.+|
T Consensus        92 ~FA~~~V~~~~~~~P-~~W~N~TF~PFDyG~yAFVYDK~KL~--NPP~SLKELVEs~Q~~~VIYQDPRTS~~G~GLL~WM  168 (326)
T TIGR01276        92 LFAKSNVDLDALDLP-TKWANDTFLPFDYGYYAFVYDKTKLK--NPPKSLKELVESDQDLRVIYQDPRTSSVGLGLLLWM  168 (326)
T ss_pred             CCCCCCCCCEECCCC-CCCCCCCCCCCCCCCEEEEEECCCCC--CCCHHHHHHHCCCCCCEEEEECCCCCCCCCHHHHHH
T ss_conf             435565550000488-77467621564457535787210146--886445765203577268975687686443476655


Q ss_pred             HHHHCHHHHHHHHHHHHHCCC
Q ss_conf             996086999999999860887
Q gi|254780563|r  169 EQTPNKTVVQDFIKNITANEI  189 (195)
Q Consensus       169 ~~~~G~~~~~~~l~~l~~N~~  189 (195)
                      ...|-.|+...=|+.|...-+
T Consensus       169 ~~VYP~D~~~~AW~~L~K~TV  189 (326)
T TIGR01276       169 NKVYPADDIQSAWKKLDKKTV  189 (326)
T ss_pred             HHCCCCCCHHHHHHHHCCCEE
T ss_conf             440785544789997446436


No 12 
>PRK10677 modA molybdate transporter periplasmic protein; Provisional
Probab=99.10  E-value=2.4e-09  Score=73.00  Aligned_cols=84  Identities=18%  Similarity=0.288  Sum_probs=67.7

Q ss_pred             CHHHHH-HHHHHHHHHHHHHCCCCCCCCEEEECCCC-HHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHH-HCCCCCEEE
Q ss_conf             025999-99999999998612444588089981899-899999999999875986210000135667652-106665575
Q gi|254780563|r    2 FKRTIY-TYLLLLCGFTEAFSTENTTKYLTLYTDQN-QSVMLPIIHSFEERTGVKISPIYTSSIQRPPIT-QGSPVDVII   78 (195)
Q Consensus         2 mkk~~~-~~l~l~~~~~~~~~~~~~~~~lvVYs~~~-~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~~~~-~~~~~d~~~   78 (195)
                      |-|.|+ .++...+.++.+++..+++++|+||...+ ...++++.+.||+++|++|++..+++..+.... .+.|+|+|+
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~a~~~~l~V~aAAsL~~~~~ei~~~Fek~~g~~v~~~fgsSg~L~~QI~~GAp~DvF~   80 (257)
T PRK10677          1 MARKWLNLFAGAALSFAVAGNALADEGKITVFAAASLTNAMQDIATQYKKEKGVDVVSSFASSSTLARQIEAGAPADLFI   80 (257)
T ss_pred             CCHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCEEEEEECCHHHHHHHHHCCCCCCEEE
T ss_conf             91289999999999872355332568859999925768999999999988419849999664899999998289965899


Q ss_pred             ECCHHHH
Q ss_conf             0422332
Q gi|254780563|r   79 TKDETSL   85 (195)
Q Consensus        79 ~~d~~~l   85 (195)
                      ++|...+
T Consensus        81 sAd~~~~   87 (257)
T PRK10677         81 SADQKWM   87 (257)
T ss_pred             ECCHHHH
T ss_conf             7875778


No 13 
>PRK11622 putative ABC transporter solute-binding protein; Provisional
Probab=99.01  E-value=2.6e-08  Score=67.12  Aligned_cols=185  Identities=11%  Similarity=0.115  Sum_probs=106.2

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCC-----------CCCCCEEEECCCCHHHH----HHHHHHHHHHCCCCCCCCCH-HH--
Q ss_conf             90259999999999999861244-----------45880899818998999----99999999875986210000-13--
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFSTE-----------NTTKYLTLYTDQNQSVM----LPIIHSFEERTGVKISPIYT-SS--   62 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~~-----------~~~~~lvVYs~~~~~~~----~~~~~~Fek~tgIkV~~~~~-~~--   62 (195)
                      |||+.++...++++..+..+++.           +.-++|..|-+.....+    +-+.+++.++|||+++-+.. ++  
T Consensus         1 ~~r~~~~~~~~l~~~~~~~~~~~~~~~W~~i~~~A~GqtV~f~aWGGs~~iN~yi~w~~~~l~~~y~ItL~~Vk~~Dt~~   80 (401)
T PRK11622          1 MMRHLLALLGLLALLSLAAAASDAANTWQQILEEAKGQTVYFNAWGGSPAINRYLDWVAKELKERYGITLKHVKLADIAE   80 (401)
T ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHCCEEEEECCCCHHH
T ss_conf             95889999999998750145764448999999971698899997679577759999999999998596689952545899


Q ss_pred             -HHHHHHHH----C--CCCCEEEE-CCHHHHHHHHHHHC-CCC--CCCCCCCCC------CCCC-CCCCCCCCCCCEEEE
Q ss_conf             -56676521----0--66655750-42233234331000-012--342223472------0001-222223443450588
Q gi|254780563|r   63 -IQRPPITQ----G--SPVDVIIT-KDETSLALNEDLLH-KLP--AHLIKKNSF------VLKN-ENKKLMRISFDTQVL  124 (195)
Q Consensus        63 -~~~~~~~~----~--~~~d~~~~-~d~~~l~~~~~~l~-~~~--~~~~~~~~~------~~~~-~~~~~~~~~~~~~~~  124 (195)
                       ..+++.++    +  ...|++|. .++..-+++.++|. |..  -++...++.      +|-. -+|+=.|....-.++
T Consensus        81 av~rvlaEk~AG~~~~GsvDliWINGENF~~mK~~~LL~gp~~~~LPN~~~vd~~~~v~~DFg~PtdG~EaPWg~aQ~vf  160 (401)
T PRK11622         81 AVNRLLAEKQAGRDTGGSVDLVWINGENFRTLKEAGLLYGPFAETLPNWRYVDTQLPVREDFGVPTEGLEAPWGVAQLVF  160 (401)
T ss_pred             HHHHHHHHHHHCCCCCCCEEEEEECCHHHHHHHHCCCCCCCHHHHCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEE
T ss_conf             99999999860778898445899886128988867831387666594042058875535557873665516765531899


Q ss_pred             EEEHHHHCCCCCCCCHHHHCC--HHHCCEEEECC-CCCCHHHHH-HHHHHHHCHH-----------------HHHHHHHH
Q ss_conf             873344013445578888408--66768599628-983049999-9999960869-----------------99999999
Q gi|254780563|r  125 AYSTKRIKIADLPKSVFDLTN--AQWKKRLSIAP-NNISFHRLL-NTMEQTPNKT-----------------VVQDFIKN  183 (195)
Q Consensus       125 ~~n~~~~~~~~~P~sw~DL~~--p~~kG~i~~~~-~~~s~~~~~-~a~~~~~G~~-----------------~~~~~l~~  183 (195)
                      +|++.+++  ++|+|..+|+.  .+.-||+..|. |.-+|.+|+ +.++..-|..                 ..|+||+.
T Consensus       161 ~ydsa~v~--~pP~s~~eLl~wak~nPGrfTYP~PPdF~GstFlkq~L~~l~~~~~~l~~p~~~~~~~~~~~plW~yLd~  238 (401)
T PRK11622        161 IYDSARVP--QPPQSPAELLEWAKANPGRFTYPRPPDFTGTAFLKQLLIELTGDPAALKQPVDDATFARVTAPLWDYLDE  238 (401)
T ss_pred             EECHHHCC--CCCCCHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHCCCHHHHCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             98766559--9998999999999978997148999987537999999999739856751867889999873899999998


Q ss_pred             HHHC
Q ss_conf             8608
Q gi|254780563|r  184 ITAN  187 (195)
Q Consensus       184 l~~N  187 (195)
                      |..+
T Consensus       239 l~P~  242 (401)
T PRK11622        239 LHPY  242 (401)
T ss_pred             HCHH
T ss_conf             5778


No 14 
>COG2182 MalE Maltose-binding periplasmic proteins/domains [Carbohydrate transport and metabolism]
Probab=98.99  E-value=2.2e-09  Score=73.29  Aligned_cols=118  Identities=20%  Similarity=0.242  Sum_probs=76.8

Q ss_pred             CCCEEEECC--CCHHHHHHHHHHHHHHCCCCCCCCCHHH--HHHHHHHH---CCCCCEEE-ECCHHHHHHHHHHHCCCCC
Q ss_conf             880899818--9989999999999987598621000013--56676521---06665575-0422332343310000123
Q gi|254780563|r   26 TKYLTLYTD--QNQSVMLPIIHSFEERTGVKISPIYTSS--IQRPPITQ---GSPVDVII-TKDETSLALNEDLLHKLPA   97 (195)
Q Consensus        26 ~~~lvVYs~--~~~~~~~~~~~~Fek~tgIkV~~~~~~~--~~~~~~~~---~~~~d~~~-~~d~~~l~~~~~~l~~~~~   97 (195)
                      +++|+|+.+  ...+.+....++||+++||+|+++....  ........   +...|+|. ..|....+..+|++.+.+.
T Consensus        40 ~~~ltvW~~~~~~~~~i~~~~~kfek~~gi~V~i~~~~~~d~~~~~~~~~paGqgpDi~~~~hD~iG~~a~~G~l~~i~~  119 (420)
T COG2182          40 EKKLTVWVDGEKEVDGIKEAAAKFEKETGIKVKIVEEDYDDLLEKFLLAAPAGQGPDIFVWAHDRIGGLAEAGLLLEIDP  119 (420)
T ss_pred             CCEEEEEECCCHHHHHHHHHHHHHHHHHCCEEEEEECCCCCHHHHHHCCCCCCCCCCEEEECCHHHHHHHHCCCCCCCCC
T ss_conf             87489975783067999999999999879758999467504888860137778889779856136779986781011676


Q ss_pred             CCCCC---CCCCCCC--CCCCCC--CCCCCEEEEEEEHHHHCCCCCCCCHHHHCC
Q ss_conf             42223---4720001--222223--443450588873344013445578888408
Q gi|254780563|r   98 HLIKK---NSFVLKN--ENKKLM--RISFDTQVLAYSTKRIKIADLPKSVFDLTN  145 (195)
Q Consensus        98 ~~~~~---~~~~~~~--~~~~~~--~~~~~~~~~~~n~~~~~~~~~P~sw~DL~~  145 (195)
                      .....   .+.....  -+|..+  |.....+++.||++.++.  +|++|+||..
T Consensus       120 ~~~~~~~~~~~~~~a~~y~GkiYGlP~~~Et~~L~YNKdlv~~--~P~T~~el~~  172 (420)
T COG2182         120 YATKYTDFYPAALVAATYKGKLYGLPQAVETLALYYNKDLVPE--PPKTWEELEA  172 (420)
T ss_pred             CHHHHHCCCHHHHHHHHCCCEEEECCHHHHHHHHHEECCCCCC--CCCCHHHHHH
T ss_conf             3444404446666653238878725566645653010001478--8425999999


No 15 
>PRK10974 glycerol-3-phosphate transporter periplasmic binding protein; Provisional
Probab=98.92  E-value=1.6e-08  Score=68.37  Aligned_cols=143  Identities=16%  Similarity=0.217  Sum_probs=78.4

Q ss_pred             CCHHHH-HHHHHHHHHHHHHHCCCCCCCCEEEECC---CCHHHHHHHHHHHHHHC-CCCCCCCCHHH----HHHHHHH--
Q ss_conf             902599-9999999999986124445880899818---99899999999999875-98621000013----5667652--
Q gi|254780563|r    1 MFKRTI-YTYLLLLCGFTEAFSTENTTKYLTLYTD---QNQSVMLPIIHSFEERT-GVKISPIYTSS----IQRPPIT--   69 (195)
Q Consensus         1 mmkk~~-~~~l~l~~~~~~~~~~~~~~~~lvVYs~---~~~~~~~~~~~~Fek~t-gIkV~~~~~~~----~~~~~~~--   69 (195)
                      ||-|.+ .+.+.++++++.++ ++...-||+.+.+   ...+.++.++++|++++ +|+|+.+..+.    .+.....  
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~-~a~a~~eI~fWh~~~g~~~~~l~~lv~eFn~~~p~i~V~~~~~g~y~~~l~k~~aa~~   79 (439)
T PRK10974          1 MFMKSLRSTALGLALGLALSG-NAQAVTEIPFWHSMEGELGKEVDSLAQRFNASQPDYKIVPVYKGNYEQNLAAGIAAFR   79 (439)
T ss_pred             CCHHHHHHHHHHHHHHHHHCC-CCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCCHHHHHHHHHHHHH
T ss_conf             955789999999999998445-5679769999358998157999999999998785918999865899999999999872


Q ss_pred             -HCCCCCEEEECC-HHHHHHHHHHHCCCCCCCCC---C-----CCCC---C-CC-CCC--CCCCCCCCEEEEEEEHHHHC
Q ss_conf             -106665575042-23323433100001234222---3-----4720---0-01-222--22344345058887334401
Q gi|254780563|r   70 -QGSPVDVIITKD-ETSLALNEDLLHKLPAHLIK---K-----NSFV---L-KN-ENK--KLMRISFDTQVLAYSTKRIK  132 (195)
Q Consensus        70 -~~~~~d~~~~~d-~~~l~~~~~~l~~~~~~~~~---~-----~~~~---~-~~-~~~--~~~~~~~~~~~~~~n~~~~~  132 (195)
                       .+.| |++...+ ........+.+.|+..-..+   .     ..+.   + .+ .+|  +..|+.....++.||++.++
T Consensus        80 ag~~P-dv~~~~~~~~~~~~~~~~l~pl~~~~~~~~~~~d~~~~~p~~~~~~~~~~~Gk~yglP~~~s~~vlyYNkdlf~  158 (439)
T PRK10974         80 SGNAP-AILQVYEVGTATMMASKAIKPVYDVFKDAGIPFDESQFVPTVAGYYSDAKTGHLLSQPFNSSTPVLYYNKDAFK  158 (439)
T ss_pred             CCCCC-EEEEECCCCHHHHHHCCCCCCCHHHHHHCCCCCCHHHHHHHHHHHHCCCCCCEEEEEEECCCCEEEEEEHHHHH
T ss_conf             69998-29998743099999769977717989725878785653278887612577986999830377659998589999


Q ss_pred             CC-----CCCCCHHHHCC
Q ss_conf             34-----45578888408
Q gi|254780563|r  133 IA-----DLPKSVFDLTN  145 (195)
Q Consensus       133 ~~-----~~P~sw~DL~~  145 (195)
                      ..     .+|++|+||.+
T Consensus       159 kAGlDp~~pP~TWdEl~~  176 (439)
T PRK10974        159 KAGLDPEQPPKTWQDLAA  176 (439)
T ss_pred             HCCCCCCCCCCCHHHHHH
T ss_conf             769998899999999999


No 16 
>PRK10852 thiosulfate transporter subunit; Provisional
Probab=98.88  E-value=1.5e-07  Score=62.72  Aligned_cols=155  Identities=17%  Similarity=0.140  Sum_probs=85.8

Q ss_pred             HHCCCCCCCCEEEECCC-CHHHHHHHHHHHH----HHC-CCCCCCC--CH-HHHHHHHHHHCCCCCEEEECC---HHHHH
Q ss_conf             61244458808998189-9899999999999----875-9862100--00-135667652106665575042---23323
Q gi|254780563|r   19 AFSTENTTKYLTLYTDQ-NQSVMLPIIHSFE----ERT-GVKISPI--YT-SSIQRPPITQGSPVDVIITKD---ETSLA   86 (195)
Q Consensus        19 ~~~~~~~~~~lvVYs~~-~~~~~~~~~~~Fe----k~t-gIkV~~~--~~-~~~~~~~~~~~~~~d~~~~~d---~~~l~   86 (195)
                      ..++.+++.||.-.|.. ..++-+++..+|.    +++ |-+|++.  ++ ++.|.+....+-++||+...-   ...+ 
T Consensus        18 ~~~g~a~~~~LlnVSYd~tRely~~~n~~F~~~Wk~~~~g~~V~i~qShGGSg~QARaVi~GL~ADVVtlal~~Did~l-   96 (338)
T PRK10852         18 LLAGHAQATELLNSSYDVSRELFAALNPPFEQQWAKDNGGDKLTIKQSHAGSSKQALAILQGLKADVVTYNQVTDVQIL-   96 (338)
T ss_pred             HHCCCCCCCEEEECCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCHHHHHHHHCCCCCCEEEEECCCCHHHH-
T ss_conf             9737877726885130547999999989999999975689618998547876057899847875446875254324889-


Q ss_pred             HHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEHHHHCCCCCCCCHHHHCCHHHCCEEEECCCCCCHHH---
Q ss_conf             43310000123422234720001222223443450588873344013445578888408667685996289830499---
Q gi|254780563|r   87 LNEDLLHKLPAHLIKKNSFVLKNENKKLMRISFDTQVLAYSTKRIKIADLPKSVFDLTNAQWKKRLSIAPNNISFHR---  163 (195)
Q Consensus        87 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~P~sw~DL~~p~~kG~i~~~~~~~s~~~---  163 (195)
                      .+.|.|  .++.|....|.+       -.+++ ...++.+  ++-.++. .++|.||.+|-  =++..|+|.+|+.+   
T Consensus        97 ~~~g~L--I~~dW~~~lP~n-------s~pyt-StivFlV--RkGNPK~-IkdW~DL~k~g--V~VItPNPKTSGgaRwn  161 (338)
T PRK10852         97 HDKGKL--IPADWQSRLPNN-------SSPFY-STMGFLV--RKGNPKN-IHDWNDLVRSD--VKLIFPNPKTSGNARYT  161 (338)
T ss_pred             HHCCCC--CCCCHHHHCCCC-------CCCEE-EEEEEEE--ECCCCCC-CCCHHHHCCCC--CEEECCCCCCCCCHHHH
T ss_conf             862786--780546538999-------96446-6799998--0799566-87757746489--78975799888407699


Q ss_pred             HHHHH----HHHHC-HHHHHHHHHHHHHCCC
Q ss_conf             99999----99608-6999999999860887
Q gi|254780563|r  164 LLNTM----EQTPN-KTVVQDFIKNITANEI  189 (195)
Q Consensus       164 ~~~a~----~~~~G-~~~~~~~l~~l~~N~~  189 (195)
                      ++++.    ....| ++++.+|+++|..|-.
T Consensus       162 yLAAwg~a~~~~gg~e~~a~~fv~~l~~NVp  192 (338)
T PRK10852        162 YLAAWGAADKADGGDKAKTEQFMTQFLKNVE  192 (338)
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHHHHHHCCC
T ss_conf             9999999998649998999999999983685


No 17 
>PRK04168 hypothetical protein; Provisional
Probab=98.82  E-value=2e-07  Score=62.06  Aligned_cols=139  Identities=15%  Similarity=0.182  Sum_probs=88.3

Q ss_pred             CHHHHHHHHHHHHHHHHHHCC---CCCCCCEEEECCCC-HHHHHHHHHHHHHHC-CCCCCCCCHHHH--HHHHHHHCCCC
Q ss_conf             025999999999999986124---44588089981899-899999999999875-986210000135--66765210666
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFST---ENTTKYLTLYTDQN-QSVMLPIIHSFEERT-GVKISPIYTSSI--QRPPITQGSPV   74 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~---~~~~~~lvVYs~~~-~~~~~~~~~~Fek~t-gIkV~~~~~~~~--~~~~~~~~~~~   74 (195)
                      +++.++.++++++.+.++|.+   ...+++|+|+...| ....+++.++||+++ |++|+...+++.  .+++.+.+.++
T Consensus         5 ~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~l~Vf~AGSL~~pf~ei~~~Fe~~~p~v~v~~e~~GS~~~ar~Ite~g~~a   84 (336)
T PRK04168          5 RRKIVIVILLLLALVFLGCVNTSEAEPPGKLKIFHAGSLSVPFEEYEKEFEAYYPNVDVQREAGGSVACVRKITELGKPA   84 (336)
T ss_pred             CEEHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEEECCCCHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHCCCCC
T ss_conf             32203799999999970555777778861599997552589999999999987899659998473899999999579998


Q ss_pred             CEEEECCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEHHHHCCCC-CCCCHHHHC-CHHHCCEE
Q ss_conf             5575042233234331000012342223472000122222344345058887334401344-557888840-86676859
Q gi|254780563|r   75 DVIITKDETSLALNEDLLHKLPAHLIKKNSFVLKNENKKLMRISFDTQVLAYSTKRIKIAD-LPKSVFDLT-NAQWKKRL  152 (195)
Q Consensus        75 d~~~~~d~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~-~P~sw~DL~-~p~~kG~i  152 (195)
                      |+|.++|...+-   .++.           +.+.+   .+..+.....+++|+.+---.++ .+++|.+.+ +|.-  ++
T Consensus        85 DVfaSAD~~~i~---~ll~-----------p~~ad---w~v~FA~N~lViayt~~Sk~a~ei~~~nWyeiL~~~~V--k~  145 (336)
T PRK04168         85 DILASADYTLIP---KMMI-----------PEYAD---WYVMFATNEIVLAYTDKSKYADEINSDNWYEILQRPGV--KW  145 (336)
T ss_pred             CEEEECCHHHHH---HHHC-----------CCCCC---CEEEECCCEEEEEECCCCCCCCCCCCCCHHHHHCCCCC--EE
T ss_conf             889989857878---8746-----------44334---10121155389997688821100573318898577985--79


Q ss_pred             EECCCCC
Q ss_conf             9628983
Q gi|254780563|r  153 SIAPNNI  159 (195)
Q Consensus       153 ~~~~~~~  159 (195)
                      +..+|+.
T Consensus       146 g~sdP~~  152 (336)
T PRK04168        146 GFSDPND  152 (336)
T ss_pred             EECCCCC
T ss_conf             8379988


No 18 
>PRK10752 sulfate transporter subunit; Provisional
Probab=98.76  E-value=5.3e-07  Score=59.67  Aligned_cols=154  Identities=16%  Similarity=0.085  Sum_probs=86.8

Q ss_pred             HCCCCCCCCEEEECCC-CHHHHHHHHHHHHH----HCCCCCCCCC---HHHHHHHHHHHCCCCCEEEECCHHHH--HHHH
Q ss_conf             1244458808998189-98999999999998----7598621000---01356676521066655750422332--3433
Q gi|254780563|r   20 FSTENTTKYLTLYTDQ-NQSVMLPIIHSFEE----RTGVKISPIY---TSSIQRPPITQGSPVDVIITKDETSL--ALNE   89 (195)
Q Consensus        20 ~~~~~~~~~lvVYs~~-~~~~~~~~~~~Fek----~tgIkV~~~~---~~~~~~~~~~~~~~~d~~~~~d~~~l--~~~~   89 (195)
                      +++.+++-+|.-.|.. ..++-+.+..+|.+    +||-+|++..   +++.|.+....+-++||+...-..-+  ..+.
T Consensus        15 ~~~~~~~~~llnvSYd~tRely~~~n~~F~~~wk~~tG~~V~i~qShGGSg~QARaVi~Gl~ADVVtlal~~Did~l~~~   94 (329)
T PRK10752         15 TSVMAKDIQLLNVSYDPTRELYEQYNKAFSAHWKQQTGDNVVIRQSHGGSGKQATSVINGIEADVVTLALAYDVDAIAER   94 (329)
T ss_pred             HHHHHCCEEEEEECCHHHHHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCHHHHHHHHCCCCCCEEEECCHHHHHHHHHC
T ss_conf             46540552699614075899999998999999988329903898557876278999847875677875142136899867


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEHHHHCCCCCCCCHHHHCCHHHCCEEEECCCCCCHHH---HHH
Q ss_conf             10000123422234720001222223443450588873344013445578888408667685996289830499---999
Q gi|254780563|r   90 DLLHKLPAHLIKKNSFVLKNENKKLMRISFDTQVLAYSTKRIKIADLPKSVFDLTNAQWKKRLSIAPNNISFHR---LLN  166 (195)
Q Consensus        90 ~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~P~sw~DL~~p~~kG~i~~~~~~~s~~~---~~~  166 (195)
                      |+   .++++....|.+       -.+++ ...++.  .++-.++. .++|.||.+|-  =++..|+|.+|+.+   +++
T Consensus        95 Gl---I~~dW~~~~P~n-------s~pyt-Stivfl--VRkGNPK~-IkdW~DL~k~g--V~VItPNPKTSG~aRwn~LA  158 (329)
T PRK10752         95 GR---IDKNWIKRLPDN-------SAPYT-STIVFL--VRKGNPKQ-IHDWNDLIKPG--VSVITPNPKSSGGARWNYLA  158 (329)
T ss_pred             CC---CCCCHHHHCCCC-------CCCEE-EEEEEE--ECCCCCCC-CCCHHHHCCCC--CEEECCCCCCCCHHHHHHHH
T ss_conf             99---991456548899-------96522-379999--71899566-87746746489--78976899887317799999


Q ss_pred             HH----HHHHCH-HHHHHHHHHHHHCCC
Q ss_conf             99----996086-999999999860887
Q gi|254780563|r  167 TM----EQTPNK-TVVQDFIKNITANEI  189 (195)
Q Consensus       167 a~----~~~~G~-~~~~~~l~~l~~N~~  189 (195)
                      +.    .+..|. +++.+|+++|..|-.
T Consensus       159 awg~a~~~~gg~e~~a~~fv~~l~~NV~  186 (329)
T PRK10752        159 AWGYALHHNNNDQAKAQDFVKALYKNVE  186 (329)
T ss_pred             HHHHHHHHCCCCHHHHHHHHHHHHHCCC
T ss_conf             9999997249999999999999983685


No 19 
>COG1653 UgpB ABC-type sugar transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=98.71  E-value=2.4e-07  Score=61.65  Aligned_cols=142  Identities=17%  Similarity=0.201  Sum_probs=76.2

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCC-CC-CCEEEECCC---C-HHHHHHHHHHHHHHCC-CCCCCCCHHH---HHHHH---HH
Q ss_conf             2599999999999998612444-58-808998189---9-8999999999998759-8621000013---56676---52
Q gi|254780563|r    3 KRTIYTYLLLLCGFTEAFSTEN-TT-KYLTLYTDQ---N-QSVMLPIIHSFEERTG-VKISPIYTSS---IQRPP---IT   69 (195)
Q Consensus         3 kk~~~~~l~l~~~~~~~~~~~~-~~-~~lvVYs~~---~-~~~~~~~~~~Fek~tg-IkV~~~~~~~---~~~~~---~~   69 (195)
                      .++.+..+++++++++|+++.. ++ .+++++...   . ....+.++++|+++++ |+|+++....   .+.+.   ..
T Consensus         5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~i~~f~~~~p~ikV~~~~~~~~~~~~~l~~~~~a   84 (433)
T COG1653           5 SKLLLLLLAAALGLAACGSAAASAAGVTITFWHSWTGGEEADALEELIKEFEKENPGIKVKVVNVPGDDYLQKLLTALAS   84 (433)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHCCCEEEEEEECCHHHHHHHHHHHHHC
T ss_conf             99999999999999999743024557439999833787315899999999997779847999856758899999999857


Q ss_pred             HCCCCCEEEECC-HHHHHHHHHH-HCCCCCCC-----CCCCCC---CCCCCCCCC--CCCCCCEEEEEEEHHHHCCCC--
Q ss_conf             106665575042-2332343310-00012342-----223472---000122222--344345058887334401344--
Q gi|254780563|r   70 QGSPVDVIITKD-ETSLALNEDL-LHKLPAHL-----IKKNSF---VLKNENKKL--MRISFDTQVLAYSTKRIKIAD--  135 (195)
Q Consensus        70 ~~~~~d~~~~~d-~~~l~~~~~~-l~~~~~~~-----~~~~~~---~~~~~~~~~--~~~~~~~~~~~~n~~~~~~~~--  135 (195)
                      .+.| |++...+ ........+. +.++.+..     .....+   .....+|..  +|......++.||++.++...  
T Consensus        85 g~~p-Dv~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~dG~~y~~P~~~~~~~~~ynkd~~~~aG~~  163 (433)
T COG1653          85 GDAP-DVVQLDPEWLAAFAKAGGLLEDLTDLINPKLDLSDFPPALLDTTTYDGKLYGVPFNSSTPALFYNKDLFKKAGLK  163 (433)
T ss_pred             CCCC-EEEEECCHHHHHHHHHCCCCCCCCCCCCCCHHHHHCCHHHHHHEEECCEEEEEEEECCCCEEEEEHHHHHHCCCC
T ss_conf             9998-199977376899997267656664100123024430477674246898689998432475699878999976999


Q ss_pred             C-CCCHHHHCC
Q ss_conf             5-578888408
Q gi|254780563|r  136 L-PKSVFDLTN  145 (195)
Q Consensus       136 ~-P~sw~DL~~  145 (195)
                      . |++|+||..
T Consensus       164 ~pp~tw~e~~~  174 (433)
T COG1653         164 PPPKTWDELLA  174 (433)
T ss_pred             CCCCCHHHHHH
T ss_conf             99999899999


No 20 
>COG0725 ModA ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=98.70  E-value=3.5e-07  Score=60.71  Aligned_cols=117  Identities=24%  Similarity=0.287  Sum_probs=75.8

Q ss_pred             CCCCCCEEEECCCC-HHHHHHHHHHHHHHCCCCCCCCCHHHHHHHH-HHHCCCCCEEEECCHHHHHHHHHHHCCCCCCCC
Q ss_conf             44588089981899-8999999999998759862100001356676-521066655750422332343310000123422
Q gi|254780563|r   23 ENTTKYLTLYTDQN-QSVMLPIIHSFEERTGVKISPIYTSSIQRPP-ITQGSPVDVIITKDETSLALNEDLLHKLPAHLI  100 (195)
Q Consensus        23 ~~~~~~lvVYs~~~-~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~~-~~~~~~~d~~~~~d~~~l~~~~~~l~~~~~~~~  100 (195)
                      ...+++++|+...+ .+..+++.++|++++|++|++..+++.++.. .+.+.|+|+|++++...+..-...         
T Consensus        26 ~~~~~~i~VfAAaSL~~~l~~i~~~F~~~~~~~V~~~f~gS~~l~~qIe~Ga~~D~fiSa~~~~~~~l~~~---------   96 (258)
T COG0725          26 AQEAATITVFAAASLTDALEEIAKQFEKETGVKVEVEFGGSGALARQIEQGAPADLFISADDAYMDKLEDK---------   96 (258)
T ss_pred             CCCCCEEEEEEEHHHHHHHHHHHHHHHHHHCCEEEEEECCHHHHHHHHHCCCCCCEEEECCHHHHHHHHHC---------
T ss_conf             45674099998156689999999999998798799996138999999975998687998888889999866---------


Q ss_pred             CCCCCCCCCCCCCCCCCCCCEEEEEEEHHHHCCCCCCCCHHHHCCHHHCCEEEECCCC
Q ss_conf             2347200012222234434505888733440134455788884086676859962898
Q gi|254780563|r  101 KKNSFVLKNENKKLMRISFDTQVLAYSTKRIKIADLPKSVFDLTNAQWKKRLSIAPNN  158 (195)
Q Consensus       101 ~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~P~sw~DL~~p~~kG~i~~~~~~  158 (195)
                           .. ...+....+.....++++..+-.   ....+|.||.+++ -+++++.++.
T Consensus        97 -----g~-~~~~~~~~fa~n~lvl~~~~~~~---~~~~~~~~l~~~~-~~~lai~~p~  144 (258)
T COG0725          97 -----GL-IYADSRIVFAGNRLVLAVPKGSK---KKIESLEDLLERP-DVRLAIGDPK  144 (258)
T ss_pred             -----CC-CCCCCEEEEECCEEEEEEECCCC---CCCCHHHHHHCCC-CCEEEECCCC
T ss_conf             -----88-56671577425748999868874---5651298873087-8579964887


No 21 
>COG4134 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=98.63  E-value=3.5e-07  Score=60.66  Aligned_cols=142  Identities=13%  Similarity=0.108  Sum_probs=86.8

Q ss_pred             HHHCCCCCCCCCHHH---HHH----HHHHHCCC--CCEEEEC-CHHHHHHHHHHHCCC---CCCCCCCCCCC-----C-C
Q ss_conf             987598621000013---566----76521066--6557504-223323433100001---23422234720-----0-0
Q gi|254780563|r   48 EERTGVKISPIYTSS---IQR----PPITQGSP--VDVIITK-DETSLALNEDLLHKL---PAHLIKKNSFV-----L-K  108 (195)
Q Consensus        48 ek~tgIkV~~~~~~~---~~~----~~~~~~~~--~d~~~~~-d~~~l~~~~~~l~~~---~~~~~~~~~~~-----~-~  108 (195)
                      +.+|||+|.++..+.   ..+    +.++++++  .|++|.. .........+++...   +-+.-..+...     | .
T Consensus        59 ~~kYgi~v~~~~l~~~~a~~~~~a~~AAG~~e~g~VDl~~~~g~n~p~lk~~~~Ly~~~~~~LPnwr~~d~ql~~tdf~~  138 (384)
T COG4134          59 KAKYGIKVAIVRLDAADAVKRLIAELAAGRDEGGSVDLLWINGENFPTLKEAGLLYTPWAEDLPNWRYVDHQLPRTDFSV  138 (384)
T ss_pred             HCCCCEEEEEECCCHHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCHHHHHCCCCCCCHHHHCCCCHHHCHHCCCCCCCC
T ss_conf             20025178751241888888899998642556872689983575413343166202512321866012030035332578


Q ss_pred             CCCCCCCCCCCCEEEEEEEHHHHCCCCCCCCHHHHCC--HHHCCEEEECCC--CCCHHHHHHHHHH--------------
Q ss_conf             1222223443450588873344013445578888408--667685996289--8304999999999--------------
Q gi|254780563|r  109 NENKKLMRISFDTQVLAYSTKRIKIADLPKSVFDLTN--AQWKKRLSIAPN--NISFHRLLNTMEQ--------------  170 (195)
Q Consensus       109 ~~~~~~~~~~~~~~~~~~n~~~~~~~~~P~sw~DL~~--p~~kG~i~~~~~--~~s~~~~~~a~~~--------------  170 (195)
                      +-+|.-.++...-.++.|.  ..+.+++|+|++||+.  .+.-+|+..+.|  +.++.+|+..+.-              
T Consensus       139 pt~Gl~~~~~~~q~~f~yd--~~k~~~~P~s~eeLL~wA~aNP~rf~Y~~P~~gg~G~~Fl~~~~i~Lt~d~~~l~~avD  216 (384)
T COG4134         139 PTEGLESPWGGNQLVFIYD--RDKVPQVPQSFEELLVWAKANPKRFGYPRPPNGGTGTAFLKQLLIMLTGDAAALQQAVD  216 (384)
T ss_pred             CCCCCCCCCCCCCCEEEEC--CCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCHHHHCCCCC
T ss_conf             8776214402775238872--34478877399999999985967535689998886076999889985485576507888


Q ss_pred             ----HHCHHHHHHHHHHHHHCCCCC
Q ss_conf             ----608699999999986088705
Q gi|254780563|r  171 ----TPNKTVVQDFIKNITANEILT  191 (195)
Q Consensus       171 ----~~G~~~~~~~l~~l~~N~~~~  191 (195)
                          ..+++..|+|+..|.++.-++
T Consensus       217 pat~~k~~~p~WqYl~~Lh~~i~r~  241 (384)
T COG4134         217 PATFAKVWAPLWQYLDELHPYIWRT  241 (384)
T ss_pred             HHHHHHHCCHHHHHHHHHHHHHHHC
T ss_conf             0777762108999999861556013


No 22 
>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=98.40  E-value=1.7e-05  Score=51.12  Aligned_cols=152  Identities=16%  Similarity=0.134  Sum_probs=78.9

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCCCEEE-E-CCCCHH----HHHHHHHHHHHHCCCCCCCCCHHHHHH-HHHHHCCC
Q ss_conf             9025999999999999986124445880899-8-189989----999999999987598621000013566-76521066
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFSTENTTKYLTL-Y-TDQNQS----VMLPIIHSFEERTGVKISPIYTSSIQR-PPITQGSP   73 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~~~~~~~lvV-Y-s~~~~~----~~~~~~~~Fek~tgIkV~~~~~~~~~~-~~~~~~~~   73 (195)
                      ||||.++.++++++++++...+....++|++ + ...+..    .-+|+.+..++++|++|+++...+-.. ....++..
T Consensus         1 m~~r~l~~~~~~~~~~~~~a~a~~~p~~l~~gv~P~~~~~~~~~~~~Pl~~yL~~~lg~~Ve~~~~~~y~~~~eal~~g~   80 (288)
T TIGR03431         1 MLRRLILSLVAAFMLISSNAQAEDWPKELNFGIIPTENASDLKQRWEPLADYLSKKLGVKVKLFFATDYAGVIEGMRFGK   80 (288)
T ss_pred             CCHHHHHHHHHHHHHHCCHHHHCCCCCEEEEEEECCCCHHHHHHHHHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCC
T ss_conf             90889999999999974322430488368999806999999999999999999998789789996899999999998598


Q ss_pred             CCEEEECCHHHHHH-HHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEHHHHCCCCCCCCHHHHCCHHHCCE-
Q ss_conf             65575042233234-3310000123422234720001222223443450588873344013445578888408667685-
Q gi|254780563|r   74 VDVIITKDETSLAL-NEDLLHKLPAHLIKKNSFVLKNENKKLMRISFDTQVLAYSTKRIKIADLPKSVFDLTNAQWKKR-  151 (195)
Q Consensus        74 ~d~~~~~d~~~l~~-~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~P~sw~DL~~p~~kG~-  151 (195)
                      .|+.+......... +.....++-...         ..+|.    ..+..+++.+.|     ...+++.||     ||| 
T Consensus        81 ~Dia~~~p~~yv~a~~~~~~~~la~~~---------~~~g~----~~y~s~iivr~D-----s~i~sl~DL-----kGk~  137 (288)
T TIGR03431        81 VDIAWYGPSSYAEAYQKANAEAFAIEV---------NADGS----TGYYSVLIVKKD-----SPIKSLEDL-----KGKT  137 (288)
T ss_pred             CEEEEECCHHHHHHHHCCCCEEEEEEE---------CCCCC----CCEEEEEEEECC-----CCCCCHHHH-----CCCE
T ss_conf             309998847889986525974889985---------15888----645799999899-----988877895-----7987


Q ss_pred             EEECCCC-CCHHHHHHHHH-HHHCHH
Q ss_conf             9962898-30499999999-960869
Q gi|254780563|r  152 LSIAPNN-ISFHRLLNTME-QTPNKT  175 (195)
Q Consensus       152 i~~~~~~-~s~~~~~~a~~-~~~G~~  175 (195)
                      ++++++. .++.-+-..++ ...|.+
T Consensus       138 iaf~~~~StSG~l~P~~~L~~~~g~~  163 (288)
T TIGR03431       138 FGFVDPNSTSGFLVPSYYLFKKNGIK  163 (288)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHCCCC
T ss_conf             66028741111399999999865997


No 23 
>COG1613 Sbp ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=98.38  E-value=1.7e-05  Score=51.00  Aligned_cols=152  Identities=12%  Similarity=0.048  Sum_probs=81.4

Q ss_pred             CCCCEEEECCC-CHHHHHHHHHHHH----HHCCCCCCCCC--HH-HHHHHHHHHCCCCCEEEECCHHHHHHHHHHHCCCC
Q ss_conf             58808998189-9899999999999----87598621000--01-35667652106665575042233234331000012
Q gi|254780563|r   25 TTKYLTLYTDQ-NQSVMLPIIHSFE----ERTGVKISPIY--TS-SIQRPPITQGSPVDVIITKDETSLALNEDLLHKLP   96 (195)
Q Consensus        25 ~~~~lvVYs~~-~~~~~~~~~~~Fe----k~tgIkV~~~~--~~-~~~~~~~~~~~~~d~~~~~d~~~l~~~~~~l~~~~   96 (195)
                      .+-+|..-|.. ..+.-+++..+|.    .++|-.|.+..  ++ .-|.+....+-++|++-.+-..-+.+-...--..+
T Consensus        36 ~~~tLlnVSYd~tre~y~~~n~aF~~~WkaetG~~Vti~qShGGSgkQaRsViDGl~ADVVtlal~~Did~i~~~g~li~  115 (348)
T COG1613          36 KDTTLLNVSYDPTRELYKEYNPAFAKYWKAETGETVTIQQSHGGSGKQARSVIDGLEADVVTLALAYDIDAIAKAGGLID  115 (348)
T ss_pred             CCCEEEEEECCCCHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHCCCCCCCEEEEEHHHHHHHHHHHCCCCC
T ss_conf             67258885215658889998899999988731983599965787620357660675332466411311899997268789


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEHHHHCCCCCCCCHHHHCCHHHCCEEEECCCCCCHHH---HHH----HHH
Q ss_conf             3422234720001222223443450588873344013445578888408667685996289830499---999----999
Q gi|254780563|r   97 AHLIKKNSFVLKNENKKLMRISFDTQVLAYSTKRIKIADLPKSVFDLTNAQWKKRLSIAPNNISFHR---LLN----TME  169 (195)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~P~sw~DL~~p~~kG~i~~~~~~~s~~~---~~~----a~~  169 (195)
                      +.+....+.+       -.+++. ..++.+  ++-.++. .++|.||.+|.-  ++.+|+|.+|+-+   +++    ++.
T Consensus       116 ~dW~~rlp~n-------s~PytS-tivFlV--RkGNPK~-I~DW~DL~k~gV--~VItpNPKTSGgARWN~Laawa~a~~  182 (348)
T COG1613         116 KDWQKRLPNN-------SAPYTS-TIVFLV--RKGNPKQ-IRDWDDLVKPGV--QVITPNPKTSGGARWNYLAAWAYALK  182 (348)
T ss_pred             CCHHHHCCCC-------CCCCCC-EEEEEE--ECCCCCC-CCCHHHHCCCCC--EEECCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             4657648699-------877330-699999--3699655-675577465886--79768998876522788999899871


Q ss_pred             HHHCHHH-HHHHHHHHHHCCC
Q ss_conf             9608699-9999999860887
Q gi|254780563|r  170 QTPNKTV-VQDFIKNITANEI  189 (195)
Q Consensus       170 ~~~G~~~-~~~~l~~l~~N~~  189 (195)
                      ...|.++ +.+|+.+|..|-.
T Consensus       183 ~~~gdeaka~~fV~~L~~nvp  203 (348)
T COG1613         183 TNGGDEAKAKDFVGKLYKNVP  203 (348)
T ss_pred             CCCCCHHHHHHHHHHHHHCCC
T ss_conf             479988999999999984683


No 24 
>COG4588 AcfC Accessory colonization factor AcfC, contains ABC-type periplasmic domain [General function prediction only]
Probab=98.36  E-value=3.1e-06  Score=55.27  Aligned_cols=161  Identities=13%  Similarity=0.202  Sum_probs=92.2

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCC-HHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCEEEEC
Q ss_conf             02599999999999998612444588089981899-89999999999987598621000013566765210666557504
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTENTTKYLTLYTDQN-QSVMLPIIHSFEERTGVKISPIYTSSIQRPPITQGSPVDVIITK   80 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~~~~~lvVYs~~~-~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~~~~~~~~~d~~~~~   80 (195)
                      ||+.++.++++++++++     ....++.+|.... ......+.+.||++||++|++..+....=-...+ ..+|++++.
T Consensus         1 Mk~~~~i~~~~~La~s~-----~~~adinlYGpGGPhtaL~~vA~~~~ektg~kVnvt~GPq~tW~~kAk-knADilfga   74 (252)
T COG4588           1 MKKAVLILLIFLLAFSS-----AANADINLYGPGGPHTALKDVAKKYEEKTGIKVNVTAGPQATWNEKAK-KNADILFGA   74 (252)
T ss_pred             CCHHHHHHHHHHHHHHH-----HHCCEEEEECCCCCCHHHHHHHHHHHHHHCEEEEEECCCCCHHHHHHH-CCCCEEECC
T ss_conf             93368899999997246-----404517876699986789999999878748079994188610445641-367456416


Q ss_pred             CHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEHHHHCCCCCCCCHHHHCCHHHCCEEEECCC---
Q ss_conf             22332343310000123422234720001222223443450588873344013445578888408667685996289---
Q gi|254780563|r   81 DETSLALNEDLLHKLPAHLIKKNSFVLKNENKKLMRISFDTQVLAYSTKRIKIADLPKSVFDLTNAQWKKRLSIAPN---  157 (195)
Q Consensus        81 d~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~P~sw~DL~~p~~kG~i~~~~~---  157 (195)
                      ....+..-   ...++..        |  ......+..+++.++.+-+.  .++ -.++++||++|--+  |++.+.   
T Consensus        75 seqsalai---a~~~~~~--------f--s~~~i~ply~R~aiIlvkkg--NPk-nIk~~eDll~~gi~--ivV~dGaG~  136 (252)
T COG4588          75 SEQSALAI---AEDHKDS--------F--SEKNIQPLYLRPAIILVKKG--NPK-NIKGFEDLLKPGIG--IVVNDGAGV  136 (252)
T ss_pred             CHHHHHHH---HHHCCCC--------C--CCCCCCEEEEECEEEEECCC--CCC-CCCCHHHHHCCCCE--EEEECCCCC
T ss_conf             48889999---9856333--------5--52025313540217996279--954-44568887057862--998379764


Q ss_pred             -CCCHHHHHHHHHHHHCHHHHHHHHHHHHHCCC
Q ss_conf             -83049999999996086999999999860887
Q gi|254780563|r  158 -NISFHRLLNTMEQTPNKTVVQDFIKNITANEI  189 (195)
Q Consensus       158 -~~s~~~~~~a~~~~~G~~~~~~~l~~l~~N~~  189 (195)
                       +.|++..-.-   .-|.-...|-+.+++.|.+
T Consensus       137 sntsgtgvwED---~agr~~~ie~v~afR~NI~  166 (252)
T COG4588         137 SNTSGTGVWED---IAGRKGNIETVAAFRKNIV  166 (252)
T ss_pred             CCCCCCEEHHH---HHCCCCCHHHHHHHHHCEE
T ss_conf             47777220486---5410114889999885238


No 25 
>COG4150 CysP ABC-type sulfate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=97.97  E-value=4.2e-05  Score=48.81  Aligned_cols=173  Identities=16%  Similarity=0.123  Sum_probs=93.3

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEECC-CCHHHHHHHHHHHHH----HC-CCCCCCCC---HHHHHHHHHHHC
Q ss_conf             9025999999999999986124445880899818-998999999999998----75-98621000---013566765210
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFSTENTTKYLTLYTD-QNQSVMLPIIHSFEE----RT-GVKISPIY---TSSIQRPPITQG   71 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~~~~~~~lvVYs~-~~~~~~~~~~~~Fek----~t-gIkV~~~~---~~~~~~~~~~~~   71 (195)
                      .|||.++..+.++++++.+..+.+++.+|.=-|. -+.++-..+-++|++    ++ |-++++..   +++.+.+...++
T Consensus         5 ~mkk~~~~~~~~~~L~a~~~qa~as~~~lLNsSYDv~RElf~a~N~~F~~~w~~~~pG~~lti~QSHAGsSkQAraIlqG   84 (341)
T COG4150           5 LMKKNLLIGATILALFAALLQAGASATELLNSSYDVSRELFAALNPAFEAQWAKDNPGDKLTIKQSHAGSSKQARAILQG   84 (341)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHH
T ss_conf             78898876699999999987614670667630567899999983989998888608996468723456655889999854


Q ss_pred             CCCCEEEECCHH--HHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEHHHHCCCCCCCCHHHHCCHHHC
Q ss_conf             666557504223--323433100001234222347200012222234434505888733440134455788884086676
Q gi|254780563|r   72 SPVDVIITKDET--SLALNEDLLHKLPAHLIKKNSFVLKNENKKLMRISFDTQVLAYSTKRIKIADLPKSVFDLTNAQWK  149 (195)
Q Consensus        72 ~~~d~~~~~d~~--~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~P~sw~DL~~p~~k  149 (195)
                      -.+||+.-....  ....+.|.|.|.  +|....|.+.   ..+|...     .+.+  ++-.++ -.++|+||....- 
T Consensus        85 L~ADVVTfNQVtDVqiLhdkg~lipA--dWq~~lPnns---SPfYS~~-----aFLV--R~GNPK-~IkdW~DLvRdDV-  150 (341)
T COG4150          85 LKADVVTFNQVTDVQILHDKGKLIPA--DWQSRLPNNS---SPFYSTM-----AFLV--RKGNPK-NIKDWDDLVRDDV-  150 (341)
T ss_pred             CCCCEEEEECCEEEEEEHHCCCCCCH--HHHHHCCCCC---CCCCCCH-----HHHH--HCCCCC-CCCCHHHHHHHCC-
T ss_conf             24566774021024321104870462--4564099888---9643232-----7775--368966-6765777755034-


Q ss_pred             CEEEECCCCCCHHH---HHHHH----HHHHCH-HHHHHHHHHHHHCC
Q ss_conf             85996289830499---99999----996086-99999999986088
Q gi|254780563|r  150 KRLSIAPNNISFHR---LLNTM----EQTPNK-TVVQDFIKNITANE  188 (195)
Q Consensus       150 G~i~~~~~~~s~~~---~~~a~----~~~~G~-~~~~~~l~~l~~N~  188 (195)
                       |+..|+|..|+.+   +++++    .+..|+ .+..||++++-.|-
T Consensus       151 -k~iFPNPKTSGNaRYTYLAA~~~a~~af~gD~~k~~ef~~k~~~Nv  196 (341)
T COG4150         151 -KLIFPNPKTSGNARYTYLAAWGAADEAFGGDKAKTEEFMTKFLKNV  196 (341)
T ss_pred             -EEECCCCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHCCC
T ss_conf             -4766899888760015889878887652685889999999996188


No 26 
>COG3221 PhnD ABC-type phosphate/phosphonate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=97.80  E-value=0.0016  Score=39.81  Aligned_cols=151  Identities=11%  Similarity=0.039  Sum_probs=80.5

Q ss_pred             CCHHHHHHHHHHHHHHHHH-HCCCCCCC-------CEEE--ECCC-CHH---HHHHHHHHHHHHCCCCCCCCCHHHHHHH
Q ss_conf             9025999999999999986-12444588-------0899--8189-989---9999999999875986210000135667
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEA-FSTENTTK-------YLTL--YTDQ-NQS---VMLPIIHSFEERTGVKISPIYTSSIQRP   66 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~-~~~~~~~~-------~lvV--Ys~~-~~~---~~~~~~~~Fek~tgIkV~~~~~~~~~~~   66 (195)
                      ||||.++....+++..+.+ |+......       +|++  -.+. ..+   .-+++.+.++++.|++|+.....+-+..
T Consensus         1 m~~~~~~~~~~~a~~~l~~~~~~~~~~~~~~~~~~~l~~gi~p~e~~~~~~~~~~pl~~~L~~~lG~~V~~~~a~dy~~v   80 (299)
T COG3221           1 MKKKKLLLASAAAVLALAGCCGSSESDAPAAEDPKELRVGIVPTENPTNLIPAWAPLADYLEKELGIPVEFFVATDYAAV   80 (299)
T ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHHHCCCEEEEECCCHHHH
T ss_conf             94278899999999999863257745432226875359997688886878876566998988986995435725768999


Q ss_pred             HH-HHCCCCCEEEECCHHHHHHHHH--HHCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEHHHHCCCCCCCCHHHH
Q ss_conf             65-2106665575042233234331--00001234222347200012222234434505888733440134455788884
Q gi|254780563|r   67 PI-TQGSPVDVIITKDETSLALNED--LLHKLPAHLIKKNSFVLKNENKKLMRISFDTQVLAYSTKRIKIADLPKSVFDL  143 (195)
Q Consensus        67 ~~-~~~~~~d~~~~~d~~~l~~~~~--~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~P~sw~DL  143 (195)
                      .+ ..+...|+-|......+...+.  ..++....         ...+|.-    .+..+++.+++     .+.++..||
T Consensus        81 ieal~~g~~D~A~~~~~a~~~a~~~~~~~e~~~~~---------~~~dg~~----~Y~S~~i~~~d-----s~i~sl~dl  142 (299)
T COG3221          81 IEALRAGQVDIAWLGPSAYVEAVDRALAGEPLAQT---------VQKDGSP----GYYSVIIVRAD-----SPIKSLEDL  142 (299)
T ss_pred             HHHHHCCCEEEEECCCHHHHHHHHHCCCCCCEEEE---------ECCCCCC----CEEEEEEEECC-----CCCCHHHHH
T ss_conf             99985896107741857789986412454201332---------1258986----51789999279-----974337882


Q ss_pred             CCHHHCCEEEECCC-CCCHHHHHHHHHHHHC
Q ss_conf             08667685996289-8304999999999608
Q gi|254780563|r  144 TNAQWKKRLSIAPN-NISFHRLLNTMEQTPN  173 (195)
Q Consensus       144 ~~p~~kG~i~~~~~-~~s~~~~~~a~~~~~G  173 (195)
                      ..    .+++++++ |.|+.-+-..++...|
T Consensus       143 kg----k~~af~d~~StSG~l~P~~~L~~~g  169 (299)
T COG3221         143 KG----KRFAFGDPDSTSGYLFPLYYLAKEG  169 (299)
T ss_pred             CC----CEEECCCCCCCCHHHHHHHHHHHHC
T ss_conf             69----9676369985412476899999843


No 27 
>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=97.54  E-value=0.0031  Score=38.13  Aligned_cols=133  Identities=13%  Similarity=0.090  Sum_probs=71.3

Q ss_pred             CCCEEE-E-CCCC-HH---HHHHHHHHHHHHCCCCCCCCCHHHHHHHH-HHHCCCCCEEEECCHHHHHH-HHHHHCCCCC
Q ss_conf             880899-8-1899-89---99999999998759862100001356676-52106665575042233234-3310000123
Q gi|254780563|r   26 TKYLTL-Y-TDQN-QS---VMLPIIHSFEERTGVKISPIYTSSIQRPP-ITQGSPVDVIITKDETSLAL-NEDLLHKLPA   97 (195)
Q Consensus        26 ~~~lvV-Y-s~~~-~~---~~~~~~~~Fek~tgIkV~~~~~~~~~~~~-~~~~~~~d~~~~~d~~~l~~-~~~~l~~~~~   97 (195)
                      .+||++ + .+.+ .+   .-+|+.+..||+.|++|+++-...-..++ ..+..+.|+-|....+.+.+ .....++...
T Consensus        50 p~~l~~g~~P~e~~~~~~~~~~pL~~~Lek~Lg~kV~~~~~~dY~a~IEamr~g~~D~a~~g~~sY~~A~~~~~~~~~a~  129 (299)
T TIGR01098        50 PKELNFGILPGENASNLARRWEPLKDYLEKKLGIKVELFVATDYSAVIEAMRFGRVDIAWFGPSSYVLAHRRANAEAFAL  129 (299)
T ss_pred             CCEEEEEEECCCCHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCEEEEECCCCEEEEEECCCHHHEEEECCCCCHHHH
T ss_conf             77268998448875577776689999888755886799861683103342326807898347851232200138701213


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCEEEEEEEHHHHCCCCCCCCHHHHCCHHHCCE-EEECCC-CCCHHHH-HHHHHHHHC
Q ss_conf             422234720001222223443450588873344013445578888408667685-996289-8304999-999999608
Q gi|254780563|r   98 HLIKKNSFVLKNENKKLMRISFDTQVLAYSTKRIKIADLPKSVFDLTNAQWKKR-LSIAPN-NISFHRL-LNTMEQTPN  173 (195)
Q Consensus        98 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~P~sw~DL~~p~~kG~-i~~~~~-~~s~~~~-~~a~~~~~G  173 (195)
                      .-..     ....+    +-..+..+++.+.+     -+.++++||+ ...||| ++..++ |+||+-+ ...|....|
T Consensus       130 ~~~~-----~~~~~----g~~~Y~S~~iv~~d-----S~i~~~~DlL-~~LKGK~~af~Dp~STSG~l~P~~~l~~~~~  193 (299)
T TIGR01098       130 TAIR-----YVSTD----GSPGYYSVIIVKAD-----SPIKSLKDLL-KKLKGKTFAFGDPASTSGYLVPRYQLLKEGG  193 (299)
T ss_pred             HHHH-----HCCCC----CCCCEEEEEEECCC-----CCCCCHHHHH-HHCCCCEEEECCCCCCCHHHHHHHHHHHHHC
T ss_conf             4433-----11688----89834899998389-----9963389999-7507975985068875124778899876507


No 28 
>COG2998 TupB ABC-type tungstate transport system, permease component [Coenzyme metabolism]
Probab=97.47  E-value=0.0003  Score=43.91  Aligned_cols=71  Identities=14%  Similarity=0.234  Sum_probs=53.9

Q ss_pred             HHHHHHHCCCCCCCCEEEECC---CCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCEEEECCHHH
Q ss_conf             999986124445880899818---99899999999999875986210000135667652106665575042233
Q gi|254780563|r   14 CGFTEAFSTENTTKYLTLYTD---QNQSVMLPIIHSFEERTGVKISPIYTSSIQRPPITQGSPVDVIITKDETS   84 (195)
Q Consensus        14 ~~~~~~~~~~~~~~~lvVYs~---~~~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~~~~~~~~~d~~~~~d~~~   84 (195)
                      ++++..+++.+++.+|.+-|.   .+-.+.+.++..||+.+|++|+++..++.+.+..+++...|+++...+..
T Consensus        17 iala~~~a~sa~~~~LrmATTTSt~dtGLLd~l~p~fE~~~g~~v~~vAvGTG~ALkmge~gdvDvv~vHapk~   90 (280)
T COG2998          17 IALASYSASSADAAELRMATTTSTEDTGLLDVLLPKFEKYTGYDVQVVAVGTGKALKMGERGDVDVVIVHAPKA   90 (280)
T ss_pred             HHHHHHHCCCCCCCEEEEEEECCCCCCCCHHHHHHHHHHCCCCEEEEEEECCHHHHHHHCCCCCCEEEEECCHH
T ss_conf             99999860575420378854302455631888777664336965899981235877511268867899837077


No 29 
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=96.98  E-value=0.026  Score=32.87  Aligned_cols=54  Identities=17%  Similarity=0.221  Sum_probs=38.1

Q ss_pred             CCHHHHHHHHHHHHHHC---CCCCCCCCHHHHHHHHHHHCCCCCEEEECCHHHHHHH
Q ss_conf             99899999999999875---9862100001356676521066655750422332343
Q gi|254780563|r   35 QNQSVMLPIIHSFEERT---GVKISPIYTSSIQRPPITQGSPVDVIITKDETSLALN   88 (195)
Q Consensus        35 ~~~~~~~~~~~~Fek~t---gIkV~~~~~~~~~~~~~~~~~~~d~~~~~d~~~l~~~   88 (195)
                      .+-++...+.++..++-   |++|+++..+...+.....+...|+++........++
T Consensus        65 fdvDla~~ia~~l~~~l~~~~~~v~~v~~~~~~rip~L~~gk~Di~~~~~t~T~eR~  121 (302)
T PRK10797         65 YSQDYSNAIVEAVKKKLNKPDLQVKLIPITSQNRIPLLQNGTFDFECGSTTNNLERQ  121 (302)
T ss_pred             CHHHHHHHHHHHHHHHHCCCCCEEEEEECCHHHHHHHHHCCCCCEEEECCCCCHHHH
T ss_conf             417999999999987744677349999757888779997898088973575697774


No 30 
>PRK11260 cystine transporter subunit; Provisional
Probab=96.96  E-value=0.013  Score=34.64  Aligned_cols=43  Identities=19%  Similarity=0.127  Sum_probs=33.6

Q ss_pred             HHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCEEEECCH
Q ss_conf             9999999998759862100001356676521066655750422
Q gi|254780563|r   40 MLPIIHSFEERTGVKISPIYTSSIQRPPITQGSPVDVIITKDE   82 (195)
Q Consensus        40 ~~~~~~~Fek~tgIkV~~~~~~~~~~~~~~~~~~~d~~~~~d~   82 (195)
                      .-++.+++.++-|++++++..+-.+++...++...|++++...
T Consensus        65 dvDl~~~ia~~lg~~~e~~~~~~~~~i~~L~~g~~Di~~~~~t  107 (264)
T PRK11260         65 EVEFAEALAKHLGVKASLKPTKWDGMLASLDSKRIDVVINQVT  107 (264)
T ss_pred             EHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCCCCCEEECCCC
T ss_conf             1999999999849956999788899999986699466725753


No 31 
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=96.94  E-value=0.0038  Score=37.65  Aligned_cols=81  Identities=14%  Similarity=0.065  Sum_probs=54.4

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCC------------HHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHH
Q ss_conf             02599999999999998612444588089981899------------899999999999875986210000135667652
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTENTTKYLTLYTDQN------------QSVMLPIIHSFEERTGVKISPIYTSSIQRPPIT   69 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~~~~~lvVYs~~~------------~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~~~~   69 (195)
                      |||.+.. ++++++++.++++.+++++|+|=+..+            ....-++.+++.++.|++++++..+-.+++...
T Consensus         1 mk~~~~~-~~~~~~~~~~~~~~a~~~~l~Vg~~~~~pPf~f~~~g~~~GfdvDl~~~ia~~lg~~~e~~~~~~~~~i~~l   79 (247)
T PRK09495          1 MKSVLKV-SLAALTLAFAVSSHAADKELVVATDTAFVPFEFKQGDKYVGFDVDLWAAIAKELKLDYTLKPMDFSGIIPAL   79 (247)
T ss_pred             CHHHHHH-HHHHHHHHHHHHHHHCCCEEEEEECCCCCCEEECCCCEEEEEHHHHHHHHHHHHCCCEEEEECCHHHHHHHH
T ss_conf             9779999-999999999876651499499998998798057679927882999999999996994699977889999999


Q ss_pred             HCCCCCEEEECCHH
Q ss_conf             10666557504223
Q gi|254780563|r   70 QGSPVDVIITKDET   83 (195)
Q Consensus        70 ~~~~~d~~~~~d~~   83 (195)
                      ++...|++++.-..
T Consensus        80 ~~g~~D~~~~~~~~   93 (247)
T PRK09495         80 QTKNIDLALAGITI   93 (247)
T ss_pred             HCCCCCEEECCCCC
T ss_conf             76995636466014


No 32 
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=96.74  E-value=0.041  Score=31.74  Aligned_cols=86  Identities=17%  Similarity=0.112  Sum_probs=49.2

Q ss_pred             CHHHHHHHHHHHHHHHHH-HCCCCCCCCEEE-ECCCCH-HHHHHHHHHHHHHC-CCCCCCCCHHHHHHHH-HHHCCCCCE
Q ss_conf             025999999999999986-124445880899-818998-99999999999875-9862100001356676-521066655
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEA-FSTENTTKYLTL-YTDQNQ-SVMLPIIHSFEERT-GVKISPIYTSSIQRPP-ITQGSPVDV   76 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~-~~~~~~~~~lvV-Ys~~~~-~~~~~~~~~Fek~t-gIkV~~~~~~~~~~~~-~~~~~~~d~   76 (195)
                      |||.+...|..+++++++ +++.+..++|+| |..... ..+..-..-|||++ |.+|++....+...+. .......|+
T Consensus         1 ~~~~l~~~la~~~~~~~~~~~~~~~~~~lrIgyq~~~~~~~~~~~~~~~ek~~~~~kV~w~~F~~G~~~~eAl~aG~iD~   80 (314)
T PRK11553          1 MRNIIKLALAGLLSVSTLAVAAESSPEALRIGYQKGSIGLVLAKSHQLLEKRFPQTKISWVEFPAGPQMLEALNVGSIDL   80 (314)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCHHHHHHHHCCHHHHHCCCCCEEEEECCCCHHHHHHHHCCCCCE
T ss_conf             97799999999999987544433489759999617741589998528676617898358997897489999997699754


Q ss_pred             EEECCHHHHHH
Q ss_conf             75042233234
Q gi|254780563|r   77 IITKDETSLAL   87 (195)
Q Consensus        77 ~~~~d~~~l~~   87 (195)
                      -...+.+.+..
T Consensus        81 ~~~g~~p~i~a   91 (314)
T PRK11553         81 GSTGDIPPIFA   91 (314)
T ss_pred             EEECCHHHHHH
T ss_conf             51158589999


No 33 
>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=96.68  E-value=0.0057  Score=36.67  Aligned_cols=140  Identities=14%  Similarity=0.056  Sum_probs=80.3

Q ss_pred             CHHHHHHHHHHHHH----HCC-CCCCCCC--HHH-HHHHHHHHCCCCCEEEECCHHHHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf             98999999999998----759-8621000--013-566765210666557504223323433100001234222347200
Q gi|254780563|r   36 NQSVMLPIIHSFEE----RTG-VKISPIY--TSS-IQRPPITQGSPVDVIITKDETSLALNEDLLHKLPAHLIKKNSFVL  107 (195)
Q Consensus        36 ~~~~~~~~~~~Fek----~tg-IkV~~~~--~~~-~~~~~~~~~~~~d~~~~~d~~~l~~~~~~l~~~~~~~~~~~~~~~  107 (195)
                      +.++-+.+-++|++    ++| =+|.+..  +++ -|......+-.+|++......-...-.+.....+.++....|.+-
T Consensus        24 ~RELy~~~N~~F~~~W~~~~GGD~~~i~QSH~gs~KQA~~v~~G~~ADvVT~~~~~DV~~~~~~G~lI~~~W~~rLP~NS  103 (320)
T TIGR00971        24 TRELYEQYNKAFEAHWKKDTGGDKVVIKQSHGGSGKQALSVLNGLEADVVTLALAYDVQILAERGRLIDKDWIKRLPDNS  103 (320)
T ss_pred             HHHHHHHHCHHHHHHHHHHCCCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHCCCCC
T ss_conf             06999871815787566644895478974268860688998700125577888887689998438736546886287878


Q ss_pred             CCCCCCCCCCCCCEEEEEEEHHHHCCCCCCCCHHHHCCHHHCCEEEECCCCCCHHH-------HHHHHHHHHCHH-HHHH
Q ss_conf             01222223443450588873344013445578888408667685996289830499-------999999960869-9999
Q gi|254780563|r  108 KNENKKLMRISFDTQVLAYSTKRIKIADLPKSVFDLTNAQWKKRLSIAPNNISFHR-------LLNTMEQTPNKT-VVQD  179 (195)
Q Consensus       108 ~~~~~~~~~~~~~~~~~~~n~~~~~~~~~P~sw~DL~~p~~kG~i~~~~~~~s~~~-------~~~a~~~~~G~~-~~~~  179 (195)
                      .       | ....+++.+  ++-.+++ .++|.||.+|.-  ++..|+|.+||.+       |=.+..+..|+. ++.+
T Consensus       104 ~-------P-y~ST~~FLV--RKGNPK~-I~DWnDL~~~~v--~~I~PNPK~SG~AR~~YLaAWG~A~~~~~~D~aK~~~  170 (320)
T TIGR00971       104 A-------P-YTSTIVFLV--RKGNPKQ-IHDWNDLIKPGV--SVITPNPKSSGGARYNYLAAWGYALHADNGDKAKAEQ  170 (320)
T ss_pred             C-------C-CCEEEEEEE--ECCCCCC-CCCHHHHHHCCC--EEEECCCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHH
T ss_conf             8-------6-201335567--5479896-465134633587--5860788986415789999876675137876245899


Q ss_pred             HHHHHHHCC
Q ss_conf             999986088
Q gi|254780563|r  180 FIKNITANE  188 (195)
Q Consensus       180 ~l~~l~~N~  188 (195)
                      |+++|-.|.
T Consensus       171 F~~~l~KNv  179 (320)
T TIGR00971       171 FVKALLKNV  179 (320)
T ss_pred             HHHHHHCCE
T ss_conf             999985010


No 34 
>pfam01547 SBP_bac_1 Bacterial extracellular solute-binding protein. This family also includes the bacterial extracellular solute-binding protein family POTD/POTF.
Probab=96.55  E-value=0.0049  Score=37.01  Aligned_cols=65  Identities=18%  Similarity=0.270  Sum_probs=41.9

Q ss_pred             HHHHHHHHHHHHHH-CCCCCCCCCHHHHH---H---HHHHHCCCCCEEEECCHH-HHHHHHHHHCCCCCCCCC
Q ss_conf             89999999999987-59862100001356---6---765210666557504223-323433100001234222
Q gi|254780563|r   37 QSVMLPIIHSFEER-TGVKISPIYTSSIQ---R---PPITQGSPVDVIITKDET-SLALNEDLLHKLPAHLIK  101 (195)
Q Consensus        37 ~~~~~~~~~~Fek~-tgIkV~~~~~~~~~---~---~~~~~~~~~d~~~~~d~~-~l~~~~~~l~~~~~~~~~  101 (195)
                      ...+++++++||++ +||+|++...+..+   +   .+...+.+.|++...... ....+.|+++++......
T Consensus         7 ~~~~~~li~~Fe~~~p~IkV~~~~~~~~~~~~kl~~~~~ag~~~~Dv~~~~~~~~~~~~~~g~l~~l~~~~~~   79 (260)
T pfam01547         7 GAALQALVAEFEKEHPGIKVEVESVGSGSLAQKLTTAIAAGDGPADVFASADDWLAKLAKAGLLLPLDDYVKN   79 (260)
T ss_pred             HHHHHHHHHHHHHHCCCCEEEEEECCCHHHHHHHHHHHHCCCCCCEEEEECCHHHHHHHHCCCEEECCHHHCC
T ss_conf             9999999999998884908999978827999999999976999866999783658999876974507422102


No 35 
>PRK10918 phosphate transporter subunit; Provisional
Probab=96.18  E-value=0.092  Score=29.76  Aligned_cols=146  Identities=12%  Similarity=-0.009  Sum_probs=73.7

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCEEEEC-CCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCEEEECCHHHH
Q ss_conf             999999999998612444588089981-8998999999999998759862100001356676521066655750422332
Q gi|254780563|r    7 YTYLLLLCGFTEAFSTENTTKYLTLYT-DQNQSVMLPIIHSFEERTGVKISPIYTSSIQRPPITQGSPVDVIITKDETSL   85 (195)
Q Consensus         7 ~~~l~l~~~~~~~~~~~~~~~~lvVYs-~~~~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~~~~~~~~~d~~~~~d~~~l   85 (195)
                      +...++++.|++....+.++.+|+=-. +....+.+.+..+|.+++|++|+|...++..-+..-.+. .-.|.+.|...-
T Consensus         7 ~~~~~~~~~ls~~a~~a~aa~~l~GaGaTf~~p~~~~w~~~~~~~~g~~v~Y~~~GSG~G~~~f~~g-~vdFa~SD~pls   85 (346)
T PRK10918          7 TVATVVAATLSMSAFSAFAAASLTGAGATFPAPVYAKWADTYQKETGNKVNYQGIGSSGGVKQIIAN-TVDFGASDAPLS   85 (346)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHCCCEEEECCCCCHHHHHHHHCC-CCCEEECCCCCC
T ss_conf             9999999999887767876166124143349999999999999845986898266878999999738-985664588889


Q ss_pred             HHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEHHHHCCCC--------------CCCCHHH---------
Q ss_conf             34331000012342223472000122222344345058887334401344--------------5578888---------
Q gi|254780563|r   86 ALNEDLLHKLPAHLIKKNSFVLKNENKKLMRISFDTQVLAYSTKRIKIAD--------------LPKSVFD---------  142 (195)
Q Consensus        86 ~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~--------------~P~sw~D---------  142 (195)
                        .+. +..               ..-.-.|+...+.+++||-.-++..+              ..+.|+|         
T Consensus        86 --~~~-~~~---------------~~~~~~P~~~g~iav~yNlpgv~~~~L~L~~~~la~IF~G~It~WnDp~I~~lNPg  147 (346)
T PRK10918         86 --DEK-LAQ---------------EGLFQFPTVIGGVVLAVNIPGLKSGELVLDGKTLGDIYLGKIKKWDDEAIAKLNPG  147 (346)
T ss_pred             --HHH-HHH---------------CCCCCCCEEECCEEEEEECCCCCCCEEEECHHHHHHHHHCCCCCCCCHHHHHCCCC
T ss_conf             --788-833---------------68714885611279999778876750312899999998485676787656630889


Q ss_pred             HCCHHHCCEEEECCC-CCCHHHHHHHHHHHH
Q ss_conf             408667685996289-830499999999960
Q gi|254780563|r  143 LTNAQWKKRLSIAPN-NISFHRLLNTMEQTP  172 (195)
Q Consensus       143 L~~p~~kG~i~~~~~-~~s~~~~~~a~~~~~  172 (195)
                      +.-|.-+-.++.|+. |++ +..++..++..
T Consensus       148 ~~LP~~~I~vv~RsD~SGT-T~~FT~yLs~~  177 (346)
T PRK10918        148 LKLPSQNIAVVRRADGSGT-SFVFTSYLAKV  177 (346)
T ss_pred             CCCCCCCEEEEEECCCCCC-HHHHHHHHHHC
T ss_conf             9899986399970798602-99999999862


No 36 
>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=95.99  E-value=0.0065  Score=36.31  Aligned_cols=102  Identities=25%  Similarity=0.303  Sum_probs=63.7

Q ss_pred             HHHHHHHHHHHHHCC-CCCCCCCHHHHHHHHH-HHCCCCCEEEECCHHHHH--HHHHHHCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             999999999998759-8621000013566765-210666557504223323--433100001234222347200012222
Q gi|254780563|r   38 SVMLPIIHSFEERTG-VKISPIYTSSIQRPPI-TQGSPVDVIITKDETSLA--LNEDLLHKLPAHLIKKNSFVLKNENKK  113 (195)
Q Consensus        38 ~~~~~~~~~Fek~tg-IkV~~~~~~~~~~~~~-~~~~~~d~~~~~d~~~l~--~~~~~l~~~~~~~~~~~~~~~~~~~~~  113 (195)
                      +...++.+.|+|+|| .+|.+-.+++..+... +++.|.|+|+++|.-.+-  .+.++..+...                
T Consensus         6 ~Al~~i~~~F~k~~g~~~Vv~sFgsSg~L~~QI~~GAP~D~F~SA~~~~~~~L~~~g~~v~~~~----------------   69 (225)
T TIGR01256         6 DALKEIAKQFEKRTGKNKVVFSFGSSGTLYTQIENGAPADVFISADEKRPKKLVDKGLVVKGSE----------------   69 (225)
T ss_pred             HHHHHHHHHHHCCCCCCEEEEEECCCHHHHHHHHCCCCEEEEECCCCCCCHHHHHCCCEECCCC----------------
T ss_conf             8999999886200899569998768178999997179788766146345404663787302544----------------


Q ss_pred             CCCCCCCEEEEEEEHHHHCCCCCCCCHHHHCCHHHC-----CEEEECCCCCC
Q ss_conf             234434505888733440134455788884086676-----85996289830
Q gi|254780563|r  114 LMRISFDTQVLAYSTKRIKIADLPKSVFDLTNAQWK-----KRLSIAPNNIS  160 (195)
Q Consensus       114 ~~~~~~~~~~~~~n~~~~~~~~~P~sw~DL~~p~~k-----G~i~~~~~~~s  160 (195)
                       ..+...-.+++...+    .-.-++..+|.+|+|.     ++++|.+|.+.
T Consensus        70 -~~~~~n~LVL~~~~~----~~~~~~~~~l~~p~~~~~l~~~~vaigdP~~~  116 (225)
T TIGR01256        70 -FVYAGNKLVLISPKN----SRVVDSLDILKKPGWVIVLKDKTVAIGDPKHA  116 (225)
T ss_pred             -EEEEEEEEEEEECCC----CCCCCCHHHHCCCCEEEEEECCCCCCCCCCCC
T ss_conf             -589862189985355----42013022113897489986370234682444


No 37 
>COG1732 OpuBC Periplasmic glycine betaine/choline-binding (lipo)protein of an ABC-type transport system (osmoprotectant binding protein) [Cell envelope biogenesis, outer membrane]
Probab=95.77  E-value=0.1  Score=29.46  Aligned_cols=122  Identities=12%  Similarity=0.099  Sum_probs=60.5

Q ss_pred             CCCCCCEEEECC-CC-HHHHHHHHHHHHHHCCCCCCCCCHH--HHHHHHHHHCCCCCEEEEC---CHHHHHHHHHHHCCC
Q ss_conf             445880899818-99-8999999999998759862100001--3566765210666557504---223323433100001
Q gi|254780563|r   23 ENTTKYLTLYTD-QN-QSVMLPIIHSFEERTGVKISPIYTS--SIQRPPITQGSPVDVIITK---DETSLALNEDLLHKL   95 (195)
Q Consensus        23 ~~~~~~lvVYs~-~~-~~~~~~~~~~Fek~tgIkV~~~~~~--~~~~~~~~~~~~~d~~~~~---d~~~l~~~~~~l~~~   95 (195)
                      ..++++++|=|- .. ..++..|+...=+++|++|+...+-  +.-...+.++...|+++.=   ........+.-...-
T Consensus        29 ~~~~~~I~VgsK~~tE~~IL~~m~~~lle~~~~kv~~~~~lG~t~v~~~Al~~G~IDiYpEYTGt~~~~~lk~~~~~~~d  108 (300)
T COG1732          29 ASAAKTIVVGSKIFTEQYILGNILKQLLEKNGIKVEDKTGLGGTAVVRNALKSGDIDIYPEYTGTALFSFLKKDPPASKD  108 (300)
T ss_pred             CCCCCCEEEECCCCCHHHHHHHHHHHHHHHCCCCEEECCCCCCHHHHHHHHHCCCCCEEEEECCHHHHHHCCCCCCCCCC
T ss_conf             23578879834778388999999999998659914541688852999999975987768543231456634567645479


Q ss_pred             CCCCCCCCCCCCCCCC-CCCCCCC--CCEEEEEEEHHHHCCCCCCCCHHHHCC
Q ss_conf             2342223472000122-2223443--450588873344013445578888408
Q gi|254780563|r   96 PAHLIKKNSFVLKNEN-KKLMRIS--FDTQVLAYSTKRIKIADLPKSVFDLTN  145 (195)
Q Consensus        96 ~~~~~~~~~~~~~~~~-~~~~~~~--~~~~~~~~n~~~~~~~~~P~sw~DL~~  145 (195)
                      +....+.+...+.... -.|....  -..+.+++..+..+... .++..||..
T Consensus       109 p~~~y~~vK~~~~k~~~l~wl~p~~~nNTyA~av~~~~A~~~~-i~TiSDLak  160 (300)
T COG1732         109 PKKVYETVKKLDAKQFKLVWLKPAGFNNTYALAVRKDVAEKYN-LETISDLAK  160 (300)
T ss_pred             HHHHHHHHHHHHHHCCCEEEECCCCCCCCEEEEECHHHHHHHC-CCCHHHHHH
T ss_conf             8999999999888607978965468776058996198898819-816999998


No 38 
>COG1464 NlpA ABC-type metal ion transport system, periplasmic component/surface antigen [Inorganic ion transport and metabolism]
Probab=95.37  E-value=0.065  Score=30.63  Aligned_cols=62  Identities=10%  Similarity=0.095  Sum_probs=34.3

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCC--CCEEEECC-CCHH-HHHHHHHHHHHHCCCCCCCCCHHH
Q ss_conf             90259999999999999861244458--80899818-9989-999999999987598621000013
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFSTENTT--KYLTLYTD-QNQS-VMLPIIHSFEERTGVKISPIYTSS   62 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~~~~~--~~lvVYs~-~~~~-~~~~~~~~Fek~tgIkV~~~~~~~   62 (195)
                      ||++..+..++.+++++++|++....  ++++|-+. .+.. +.+.+.+.--++.||+++++..++
T Consensus         1 m~~~~~~~~~~~~~l~~~~~~~~~~~~~~~I~vg~~~~p~a~ile~~~k~~~~k~Gi~l~i~~FtD   66 (268)
T COG1464           1 MKKLKKLALALVALLALAACGAAAAKATKTIKVGATPGPHAEILEVVVKPALKKKGLDLKIVEFTD   66 (268)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCHHHHHHHHHHHHHHHCCCEEEEEEECC
T ss_conf             943889999999999997522311345771799636896599999998778885596599998148


No 39 
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=95.12  E-value=0.24  Score=27.37  Aligned_cols=71  Identities=11%  Similarity=0.039  Sum_probs=42.5

Q ss_pred             HHHHHHHHCCCCCCCCEEE-EC-CCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCC-CCCEEEECCHH
Q ss_conf             9999986124445880899-81-899899999999999875986210000135667652106-66557504223
Q gi|254780563|r   13 LCGFTEAFSTENTTKYLTL-YT-DQNQSVMLPIIHSFEERTGVKISPIYTSSIQRPPITQGS-PVDVIITKDET   83 (195)
Q Consensus        13 ~~~~~~~~~~~~~~~~lvV-Ys-~~~~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~~~~~~~-~~d~~~~~d~~   83 (195)
                      ++..++..+..+++.||+| |- .........--..|||+.|++|+++..++...+.+.-++ ..|+-...+.+
T Consensus         9 ~~~~~~~~~~~a~~~~v~igYq~~~~p~~~aka~g~~ek~~G~kV~W~~F~sG~~~~eAlasG~vDig~~G~~P   82 (320)
T PRK11480          9 LLAALAFIAFQAQAVNVTVAYQTSAEPAKVAQADNTFAKESGATVDWRKFDSGASIVRALASGDVQIGNLGSSP   82 (320)
T ss_pred             HHHHHHHHHHHCCCCEEEEEEECCCCCHHHHHHCCCHHHHCCCCEEEEECCCHHHHHHHHHCCCCCEECCCCCH
T ss_conf             99998631421576459999806986289998638456751981279977975999999966997564577847


No 40 
>COG2113 ProX ABC-type proline/glycine betaine transport systems, periplasmic components [Amino acid transport and metabolism]
Probab=95.11  E-value=0.24  Score=27.35  Aligned_cols=80  Identities=9%  Similarity=-0.017  Sum_probs=43.8

Q ss_pred             CCHHHHHHHHH-HHHHHHHHHC---CCCCCCCEEE-E-CCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCC
Q ss_conf             90259999999-9999998612---4445880899-8-189989999999999987598621000013566765210666
Q gi|254780563|r    1 MFKRTIYTYLL-LLCGFTEAFS---TENTTKYLTL-Y-TDQNQSVMLPIIHSFEERTGVKISPIYTSSIQRPPITQGSPV   74 (195)
Q Consensus         1 mmkk~~~~~l~-l~~~~~~~~~---~~~~~~~lvV-Y-s~~~~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~~~~~~~~~   74 (195)
                      |+++..+...+ ++++++++.+   .....++|++ + ++.+......+.+.-=|++|++|+++..++.-......+...
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~a~~a~~~~~~~tV~~a~~~W~s~~~~t~v~~~iLk~~Gy~v~~~~~~~~~~~~sla~gd~   80 (302)
T COG2113           1 MKKLLALLAAVAAAALLAAAAAAAAAAEAGKTVRIADVGWTSGTATTNVAKKILKGLGYTVELVTLDTAVMYQSLAKGDL   80 (302)
T ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEECCCCHHHHHHHHHHHHHHHCCCCCEEEECCHHHHHHHHHCCCC
T ss_conf             92389999999999998622001113455882588436961789999999999996799624665559999999973797


Q ss_pred             CEEEEC
Q ss_conf             557504
Q gi|254780563|r   75 DVIITK   80 (195)
Q Consensus        75 d~~~~~   80 (195)
                      |++.+.
T Consensus        81 D~~~~~   86 (302)
T COG2113          81 DVFPEA   86 (302)
T ss_pred             CCCCCE
T ss_conf             532010


No 41 
>PRK11119 proX glycine betaine transporter periplasmic subunit; Provisional
Probab=94.77  E-value=0.3  Score=26.81  Aligned_cols=162  Identities=7%  Similarity=-0.035  Sum_probs=67.7

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCC---CCCCEEE-ECCC-CHHHHHHHHHHHHHHCCCCCCCCCHHHHHHH-HHHHCCCC
Q ss_conf             902599999999999998612444---5880899-8189-9899999999999875986210000135667-65210666
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFSTEN---TTKYLTL-YTDQ-NQSVMLPIIHSFEERTGVKISPIYTSSIQRP-PITQGSPV   74 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~~~---~~~~lvV-Ys~~-~~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~-~~~~~~~~   74 (195)
                      +|++++++.+.+.++++....++.   +-.+|.+ |.+. +......+...-=++-|.+|+.+...+...+ ....+...
T Consensus         1 ~~~~~~l~~~a~~~~~~~~a~a~~~pg~g~tV~~a~~~W~~~~a~t~v~~~~Le~lGY~Ve~~~~~~~~~~~~ala~Gdi   80 (332)
T PRK11119          1 KMRHKVLLATALATLISTSAFAADLPGKGITVQPAQSTIAEETFQTLLVSRALEKLGYDVNKPKEVDYNVFYTSIASGDA   80 (332)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCHHHHHHHHHHHHHHHHCCCCCCCCEECCHHHHHHHHHCCCC
T ss_conf             91188899999999852276525589999778760168408999999999999986998542014446889999855884


Q ss_pred             CEEEECCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEHHHHCCCCCCCCHHHHCCHHH------
Q ss_conf             55750422332343310000123422234720001222223443450588873344013445578888408667------
Q gi|254780563|r   75 DVIITKDETSLALNEDLLHKLPAHLIKKNSFVLKNENKKLMRISFDTQVLAYSTKRIKIADLPKSVFDLTNAQW------  148 (195)
Q Consensus        75 d~~~~~d~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~P~sw~DL~~p~~------  148 (195)
                      |++...=.+   .....+.++......       ...+...+  ....++.+.+... ...-.+|++||.||++      
T Consensus        81 D~~~~~WlP---~~~~~~~~~~~~~~~-------~~~g~~~~--ga~~G~~V~~~~~-d~~~I~si~dLkdp~~a~~Fd~  147 (332)
T PRK11119         81 TFTAVNWFP---LHDDQYEAAGGDKKF-------YREGVIVG--GAAQGYLIDKKTA-DKYNITNIAQLKDPKIAKLFDT  147 (332)
T ss_pred             EEEECCCCC---CCHHHHHHHCCCCEE-------EECCCCCC--CCCEEEEEECCCC-CCCCCCCHHHHHCHHHHHHCCC
T ss_conf             486556176---517999973277647-------64243356--6513689502332-1148578998628678986076


Q ss_pred             ----CCEEEECCCCCCHHHHHHHHHHHHCHH
Q ss_conf             ----685996289830499999999960869
Q gi|254780563|r  149 ----KKRLSIAPNNISFHRLLNTMEQTPNKT  175 (195)
Q Consensus       149 ----kG~i~~~~~~~s~~~~~~a~~~~~G~~  175 (195)
                          ||+|..-+++..........+..+|-+
T Consensus       148 ~~~GKg~i~g~~pGwg~~~~~~~~i~~ygL~  178 (332)
T PRK11119        148 NGDGKADLTGCNPGWGCEAVINHQLKAYGLT  178 (332)
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHHCCCC
T ss_conf             7788502881488720668999999867996


No 42 
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=94.65  E-value=0.11  Score=29.31  Aligned_cols=52  Identities=10%  Similarity=0.094  Sum_probs=29.8

Q ss_pred             HHHHCCHHHCCEEEECCCCCCHHHHHHHHHHHHCHHHHHHHHHHHHHCCCCCCC
Q ss_conf             888408667685996289830499999999960869999999998608870567
Q gi|254780563|r  140 VFDLTNAQWKKRLSIAPNNISFHRLLNTMEQTPNKTVVQDFIKNITANEILTKY  193 (195)
Q Consensus       140 w~DL~~p~~kG~i~~~~~~~s~~~~~~a~~~~~G~~~~~~~l~~l~~N~~~~~~  193 (195)
                      ++|. +..|...++.+...-.. .++..+...+--+...+|++.-....++.+|
T Consensus       220 ~E~~-~~py~Nvivvr~~~kd~-~~ik~lv~~~~S~evk~~I~~~~~G~~ip~W  271 (271)
T PRK11063        220 VEDK-DSPYVNLIVAREDNKDA-ENVKKFVQAYQSDEVYEAANKVFNGGAVKGW  271 (271)
T ss_pred             ECCC-CCCEEEEEEECCCCCCC-HHHHHHHHHHCCHHHHHHHHHHCCCCEECCC
T ss_conf             7789-99838999982777799-8999999997799999999987799842389


No 43 
>COG0226 PstS ABC-type phosphate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=93.76  E-value=0.5  Score=25.56  Aligned_cols=129  Identities=11%  Similarity=0.071  Sum_probs=62.2

Q ss_pred             CCCEEEE-CCCCHHHHHHHHHHHHHHC-CCCCCCCCHHHHHHHH-HHHCCCCCEEEECCHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             8808998-1899899999999999875-9862100001356676-52106665575042233234331000012342223
Q gi|254780563|r   26 TKYLTLY-TDQNQSVMLPIIHSFEERT-GVKISPIYTSSIQRPP-ITQGSPVDVIITKDETSLALNEDLLHKLPAHLIKK  102 (195)
Q Consensus        26 ~~~lvVY-s~~~~~~~~~~~~~Fek~t-gIkV~~~~~~~~~~~~-~~~~~~~d~~~~~d~~~l~~~~~~l~~~~~~~~~~  102 (195)
                      ..+|++- |+...-+.+.+.++|.+++ +++|++...++..-.. ...+. .|+ -..|...-..+......        
T Consensus        42 ~~~l~~~GSttv~p~~~~~a~~~~~~~~~~~v~~q~~GSg~G~~~~~~~~-vDi-g~ss~p~~~~e~~~~~~--------  111 (318)
T COG0226          42 SGSLTIAGSTTVAPLMEAWAEEFQKAYPNVKVNVQAGGSGAGIKQALAGG-VDI-GASSRPLKDSEKEADAK--------  111 (318)
T ss_pred             CCEEEEECCCCHHHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHCCC-CCC-CCCCCCCCCCHHHHHHH--------
T ss_conf             43599836573899999999999987899478763686618899875267-703-13576666326799874--------


Q ss_pred             CCCCCCCCCCCCCCCCCCEEEEEEEHHHHCCCC------------CCCCHHHHCCHHHCCEEEE--CC-CCCCHHHHHHH
Q ss_conf             472000122222344345058887334401344------------5578888408667685996--28-98304999999
Q gi|254780563|r  103 NSFVLKNENKKLMRISFDTQVLAYSTKRIKIAD------------LPKSVFDLTNAQWKKRLSI--AP-NNISFHRLLNT  167 (195)
Q Consensus       103 ~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~------------~P~sw~DL~~p~~kG~i~~--~~-~~~s~~~~~~a  167 (195)
                         .  ...-.-+++...+.+++||.+-.....            ..+.|.|+.-+.-...|..  |+ .|++...|..-
T Consensus       112 ---~--~~~l~~~pva~d~i~vi~N~~~~~~~~Lt~~~l~~If~G~it~W~d~~~~~~n~~I~vv~R~~~SGT~~~F~~~  186 (318)
T COG0226         112 ---A--GKKLVEFPVAIDAIVVIVNLPNPDVLNLTKDQLADIFSGKITNWNDVGGQLLNPGITVVGRSDGSGTTETFTEY  186 (318)
T ss_pred             ---C--CCCCEEEEEEEEEEEEEECCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEECCCCCCHHHHHHHH
T ss_conf             ---0--79866977887779999758985413479999999970888755566865589985688478777769999999


Q ss_pred             HH
Q ss_conf             99
Q gi|254780563|r  168 ME  169 (195)
Q Consensus       168 ~~  169 (195)
                      +.
T Consensus       187 l~  188 (318)
T COG0226         187 LL  188 (318)
T ss_pred             HH
T ss_conf             87


No 44 
>PRK01326 prsA foldase protein PrsA; Reviewed
Probab=93.25  E-value=0.17  Score=28.28  Aligned_cols=13  Identities=38%  Similarity=0.549  Sum_probs=10.4

Q ss_pred             HHHHHHHCCCCCC
Q ss_conf             9999987598621
Q gi|254780563|r   44 IHSFEERTGVKIS   56 (195)
Q Consensus        44 ~~~Fek~tgIkV~   56 (195)
                      -+.|+++||.+|.
T Consensus        63 ~kvLe~~Yg~kVs   75 (310)
T PRK01326         63 SRVFEKQYGDKVS   75 (310)
T ss_pred             HHHHHHHHCCCCC
T ss_conf             9999998626178


No 45 
>COG3019 Predicted metal-binding protein [General function prediction only]
Probab=92.87  E-value=0.27  Score=27.14  Aligned_cols=64  Identities=11%  Similarity=0.166  Sum_probs=42.2

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHH
Q ss_conf             02599999999999998612444588089981899899999999999875986210000135667
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTENTTKYLTLYTDQNQSVMLPIIHSFEERTGVKISPIYTSSIQRP   66 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~~~~~lvVYs~~~~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~   66 (195)
                      |+|..+++.+.++++...+.+.+++.++++|-+-.=.-...+++..+ ..|++|.....+....+
T Consensus         1 Mrr~~~l~~l~a~~l~~~~~~~a~~~~~~vyksPnCGCC~~w~~~mk-~~Gf~Vk~~~~~d~~al   64 (149)
T COG3019           1 MRRRAFLRSLAALGLGSTGPAQAQATEMVVYKSPNCGCCDEWAQHMK-ANGFEVKVVETDDFLAL   64 (149)
T ss_pred             CCHHHHHHHHHHHHHHCCCCHHCCEEEEEEEECCCCCCHHHHHHHHH-HCCCEEEEEECCCHHHH
T ss_conf             91268999999998531440010103578873889861799999998-67957898525728999


No 46 
>PRK09861 cytoplasmic membrane lipoprotein-28; Provisional
Probab=92.67  E-value=0.37  Score=26.30  Aligned_cols=54  Identities=17%  Similarity=0.110  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHHHCCCC-CCCCEEEE-CCCC-HHHHHHHHHHHHHHCCCCCCCCCHHH
Q ss_conf             9999999998612444-58808998-1899-89999999999987598621000013
Q gi|254780563|r    9 YLLLLCGFTEAFSTEN-TTKYLTLY-TDQN-QSVMLPIIHSFEERTGVKISPIYTSS   62 (195)
Q Consensus         9 ~l~l~~~~~~~~~~~~-~~~~lvVY-s~~~-~~~~~~~~~~Fek~tgIkV~~~~~~~   62 (195)
                      .|+++++++++|++.+ ..++|+|= +..+ .++.+.+.+...++.|++|+++..++
T Consensus        13 ~ll~~~~~l~~C~~~~~~~k~ikVG~~~~p~~~i~e~~~~~~~ek~G~~leiv~FsD   69 (272)
T PRK09861         13 ALLLAGILLAGCDQSSSDAKHIKVGVINGAEQDVAEVAKKVAKEKYGLDVELVGFSG   69 (272)
T ss_pred             HHHHHHHHHHHCCCCCCCCCEEEEEECCCCHHHHHHHHHHHHHHHCCCEEEEEEECC
T ss_conf             999999998745897678973899967898699999999888761797689999468


No 47 
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=92.35  E-value=0.82  Score=24.33  Aligned_cols=139  Identities=14%  Similarity=0.079  Sum_probs=69.6

Q ss_pred             CCCCCCEEEECCC--CHHHHHHHHHHHHHHC-CCCCCCCCHHHHHHHHHHHCCCCCEEEECCHHHHHHHHHHHCCCCCCC
Q ss_conf             4458808998189--9899999999999875-986210000135667652106665575042233234331000012342
Q gi|254780563|r   23 ENTTKYLTLYTDQ--NQSVMLPIIHSFEERT-GVKISPIYTSSIQRPPITQGSPVDVIITKDETSLALNEDLLHKLPAHL   99 (195)
Q Consensus        23 ~~~~~~lvVYs~~--~~~~~~~~~~~Fek~t-gIkV~~~~~~~~~~~~~~~~~~~d~~~~~d~~~l~~~~~~l~~~~~~~   99 (195)
                      ....++|+|-+..  ......+++..|.+++ +|++++..+++.+......+...|+.+..+...               
T Consensus        89 ~~~~G~l~Ig~~~t~a~~~LP~~l~~F~~~~P~v~l~l~~~~~~~i~~~l~~g~~Dl~i~~~~~~---------------  153 (316)
T PRK12679         89 NDTSGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERLS---------------  153 (316)
T ss_pred             CCCCCEEEEEEEECCHHCCCCHHHHHHHHHCCCCEEEEEECCHHHHHHHHHCCCCCEEECCCCCC---------------
T ss_conf             88776499998503201038199999998689953899847879999999879988522246778---------------


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCEEEEEEEHHHHCCCCCCCCHHHHCCHHHCCEEEECCCCCCHHHHHHHHHHHHCHH----
Q ss_conf             2234720001222223443450588873344013445578888408667685996289830499999999960869----
Q gi|254780563|r  100 IKKNSFVLKNENKKLMRISFDTQVLAYSTKRIKIADLPKSVFDLTNAQWKKRLSIAPNNISFHRLLNTMEQTPNKT----  175 (195)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~P~sw~DL~~p~~kG~i~~~~~~~s~~~~~~a~~~~~G~~----  175 (195)
                              .+++-...+......++++..+.--....+-+|+||.+..|    .+.+.++.+...+.......|-.    
T Consensus       154 --------~~p~l~~~p~~~~~~~lvvp~~HpLa~~~~vsl~~L~~~pl----I~~~~g~~~R~~id~~f~~~G~~p~i~  221 (316)
T PRK12679        154 --------NDPQLVAFPWFRWHHSLLVPLDHPLTQITPLTLESIAKWPL----ITYRQGITGRSRIDDAFARKGLLADIV  221 (316)
T ss_pred             --------CCCCCEEEEEEECCEEEEECCCCCCCCCCCCCHHHHCCCCE----EEECCCCHHHHHHHHHHHHCCCCCCEE
T ss_conf             --------99760799805534135601899512489989999879998----950899849999999999779999779


Q ss_pred             ---HHHHHHHHHHHCC
Q ss_conf             ---9999999986088
Q gi|254780563|r  176 ---VVQDFIKNITANE  188 (195)
Q Consensus       176 ---~~~~~l~~l~~N~  188 (195)
                         ...+-++.+.+.|
T Consensus       222 ~e~~~~~~i~~~V~~G  237 (316)
T PRK12679        222 LSAQDSDVIKTYVALG  237 (316)
T ss_pred             EEECCHHHHHHHHHHC
T ss_conf             9999899999999989


No 48 
>PRK12450 foldase protein PrsA; Reviewed
Probab=92.19  E-value=0.47  Score=25.70  Aligned_cols=56  Identities=23%  Similarity=0.277  Sum_probs=27.5

Q ss_pred             CCHHHHHHHHHHHHHH-HHHHCCCCCCCCEEE-----------EC-----CCCHHHHHH--HHHHHHHHCCCCCC
Q ss_conf             9025999999999999-986124445880899-----------81-----899899999--99999987598621
Q gi|254780563|r    1 MFKRTIYTYLLLLCGF-TEAFSTENTTKYLTL-----------YT-----DQNQSVMLP--IIHSFEERTGVKIS   56 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~-~~~~~~~~~~~~lvV-----------Ys-----~~~~~~~~~--~~~~Fek~tgIkV~   56 (195)
                      +|||+++..+.++.++ +++|++.+....|+-           |.     .........  +-+.|+++||-+|.
T Consensus         3 ~mKK~~~~~~~~~svl~LaAC~s~~~~~~v~t~kgg~IT~~efy~~~K~t~~gq~~L~~mi~~KvLe~kYg~kVs   77 (309)
T PRK12450          3 QMNKLITGVVTLATVVTLSACQSSHNNTKLVSMKGDTITVSDFYNETKNTELAQKAMLSLVISRVFETQYANKVS   77 (309)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             799999999999999999860589998368983599240999999985341589999999999999998535178


No 49 
>PRK10641 btuB vitamin B12/cobalamin outer membrane transporter; Provisional
Probab=91.31  E-value=0.31  Score=26.79  Aligned_cols=36  Identities=19%  Similarity=0.324  Sum_probs=19.8

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCH
Q ss_conf             9025999999999999986124445880899818998
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFSTENTTKYLTLYTDQNQ   37 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~~~~~~~lvVYs~~~~   37 (195)
                      ||||+.+..++.+.++ ...+...+.+|+||-.++.+
T Consensus         1 ~~~~~~~~~~~~~~~~-~~~a~~~~~devvVTAtr~~   36 (615)
T PRK10641          1 MIKKASLLTALSVTAF-SAWAQDTSPDTLVVTANRFQ   36 (615)
T ss_pred             CCHHHHHHHHHHHHCC-HHHHCCCCCCEEEEECCCCC
T ss_conf             9448999999987513-35433589971999034851


No 50 
>PRK03002 prsA peptidylprolyl isomerase; Reviewed
Probab=91.16  E-value=0.48  Score=25.66  Aligned_cols=34  Identities=21%  Similarity=0.245  Sum_probs=18.3

Q ss_pred             CCHHHHHHHHHHHHHH-HHHHCCCCCCCCEEEECC
Q ss_conf             9025999999999999-986124445880899818
Q gi|254780563|r    1 MFKRTIYTYLLLLCGF-TEAFSTENTTKYLTLYTD   34 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~-~~~~~~~~~~~~lvVYs~   34 (195)
                      |+||+|+....+++.+ +++|++....+.|.-+.+
T Consensus         1 mkkK~i~~~~~~~svl~LaaC~~~~~~~~VAtv~g   35 (285)
T PRK03002          1 MRGKHIFIITALISILMLSACGQKNSSATVATATD   35 (285)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECC
T ss_conf             96018999999999999998457999977998689


No 51 
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=90.30  E-value=1.3  Score=23.11  Aligned_cols=43  Identities=16%  Similarity=0.270  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHC---CCCCCCCCHHHHHHHHHHHCCCCCEEEECCHH
Q ss_conf             99999999875---98621000013566765210666557504223
Q gi|254780563|r   41 LPIIHSFEERT---GVKISPIYTSSIQRPPITQGSPVDVIITKDET   83 (195)
Q Consensus        41 ~~~~~~Fek~t---gIkV~~~~~~~~~~~~~~~~~~~d~~~~~d~~   83 (195)
                      -.+.++..++-   +++|+++..+...+.....+...|++++....
T Consensus        66 vDla~~iAk~llg~~~~v~~v~~~~~~~~p~L~~gkvD~i~~~~ti  111 (259)
T PRK11917         66 IDVAKLLAKSILGDDKKIKLVAVNAKTRGPLLDNGSVDAVIATFTI  111 (259)
T ss_pred             HHHHHHHHHHHCCCCCEEEEEEECHHHHHHHHHCCCEEEEEECCCC
T ss_conf             9999999999659985699997067877689877985599866476


No 52 
>PRK10598 hypothetical protein; Provisional
Probab=89.37  E-value=0.76  Score=24.54  Aligned_cols=48  Identities=19%  Similarity=0.271  Sum_probs=30.5

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHH--HHHHCCCCC
Q ss_conf             025999999999999986124445880899818998999999999--998759862
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTENTTKYLTLYTDQNQSVMLPIIHS--FEERTGVKI   55 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~~~~~lvVYs~~~~~~~~~~~~~--Fek~tgIkV   55 (195)
                      |||.++.+.+++++++++|++-.+      ||-...++-+-+-+.  |+++.||.-
T Consensus         1 mkk~~l~~~l~l~~llsGC~~l~q------YsISEqEin~YL~~~~~~~k~iGi~g   50 (186)
T PRK10598          1 MKKFLLAAALLVSGLLVGCNQLTQ------YTISEQEINQYLAKHNNFSKDIGLPG   50 (186)
T ss_pred             CCHHHHHHHHHHHHHHHCCCCCCC------EEECHHHHHHHHHHHCCHHHHCCCCC
T ss_conf             912699999999999714353364------40079999999987433787718887


No 53 
>PRK04405 prsA peptidylprolyl isomerase; Provisional
Probab=88.49  E-value=1.6  Score=22.71  Aligned_cols=54  Identities=15%  Similarity=0.164  Sum_probs=26.8

Q ss_pred             CCHHHHHHHHHHHHHH-HHHHCCCCCCCCEEEECC----------------CCHHHHHHH--HHHHHHHCCCCCC
Q ss_conf             9025999999999999-986124445880899818----------------998999999--9999987598621
Q gi|254780563|r    1 MFKRTIYTYLLLLCGF-TEAFSTENTTKYLTLYTD----------------QNQSVMLPI--IHSFEERTGVKIS   56 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~-~~~~~~~~~~~~lvVYs~----------------~~~~~~~~~--~~~Fek~tgIkV~   56 (195)
                      +|||.++..+.+++++ +++|+  ...++|+-+.+                ........+  -+.|+++||-+|.
T Consensus         4 ~MKK~~l~~~~~~~~l~LaaCs--s~~~~Vat~kg~~IT~~e~y~~~k~~~~g~~~l~~mi~~kvl~~~yg~kVs   76 (298)
T PRK04405          4 KMKKWALAAASAGLLLSLAGCS--SNNKTVATYKGGKITESQYYKEMKQSSAGKQTLANMIIYRALEKQYGKKVS   76 (298)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCC--CCCCEEEEECCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             7899999999999999998717--999769986398725999999986442367999999999999998746067


No 54 
>PRK10662 beta-lactamase/D-alanine carboxypeptidase; Provisional
Probab=88.34  E-value=1.1  Score=23.62  Aligned_cols=56  Identities=13%  Similarity=0.109  Sum_probs=32.4

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHHHC---CCCCCCCCHH
Q ss_conf             902599999999999998612444588089981899899999999999875---9862100001
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFSTENTTKYLTLYTDQNQSVMLPIIHSFEERT---GVKISPIYTS   61 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~~~~~~~lvVYs~~~~~~~~~~~~~Fek~t---gIkV~~~~~~   61 (195)
                      |++|.++..+++++.+++.++.+..+.++.+     .+.++.+++..=+++   |.-|-++.++
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-----~d~iD~~~~~~m~~~~iPG~avavv~~~   59 (377)
T PRK10662          1 MKRALLLSAALLAASLTSVAAAQPIADPLLA-----SDIVDRYAQHIFYGSGATGMALVVIDGN   59 (377)
T ss_pred             CCHHHHHHHHHHHHHHHHHCCCCCCCCHHHH-----HHHHHHHHHHHHHHCCCCEEEEEEEECC
T ss_conf             9168999999999998850487655780257-----7889999999998579984899999899


No 55 
>COG4521 TauA ABC-type taurine transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=87.62  E-value=0.99  Score=23.88  Aligned_cols=63  Identities=14%  Similarity=0.050  Sum_probs=32.6

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCEEE-EC-CCCHHHHHHHHHHHHHHCCCCCCCCCHHHHH
Q ss_conf             025999999999999986124445880899-81-8998999999999998759862100001356
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTENTTKYLTL-YT-DQNQSVMLPIIHSFEERTGVKISPIYTSSIQ   64 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~~~~~lvV-Ys-~~~~~~~~~~~~~Fek~tgIkV~~~~~~~~~   64 (195)
                      |+|.....-+++++...+.+..+++.+++| |- +....-...-=-.|+|++|-++.++..++..
T Consensus         4 ~~r~~~l~~~~aa~a~~l~~~~Aqa~~vtVgYQt~~eP~kvaqADg~~aK~~gatiDWRkFdSG~   68 (334)
T COG4521           4 LRRISSLSSLLAALAFVLLAFAAQAVDVTVGYQTSAEPAKVAQADGAFAKESGATIDWRKFDSGA   68 (334)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCEEEEEEEECCCCCCCCCCCCHHHHHCCCCCCHHHCCCHH
T ss_conf             77788888899999988767664223168865403575202134635677607854511047536


No 56 
>PRK10002 outer membrane protein F; Provisional
Probab=86.01  E-value=0.7  Score=24.72  Aligned_cols=32  Identities=19%  Similarity=0.232  Sum_probs=18.0

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCC-----CCCCEEEEC
Q ss_conf             902599999999999998612444-----588089981
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFSTEN-----TTKYLTLYT   33 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~~~-----~~~~lvVYs   33 (195)
                      ||||+++..++.+++++. .+.++     .-.+|-||.
T Consensus         1 mMKK~~LA~ai~all~ag-~a~AAeVYn~DGn~Ldl~G   37 (362)
T PRK10002          1 MMKRNILAVIVPALLVAG-TANAAEIYNKDGNKVDLYG   37 (362)
T ss_pred             CCHHHHHHHHHHHHHHHC-CCCEEEEEECCCCEEEECC
T ss_conf             930879999999998606-4417899858998898738


No 57 
>PRK11289 ampC beta-lactamase; Provisional
Probab=85.54  E-value=1.3  Score=23.23  Aligned_cols=54  Identities=15%  Similarity=0.266  Sum_probs=35.2

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHHHC---CCCCCCCC
Q ss_conf             902599999999999998612444588089981899899999999999875---98621000
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFSTENTTKYLTLYTDQNQSVMLPIIHSFEERT---GVKISPIY   59 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~~~~~~~lvVYs~~~~~~~~~~~~~Fek~t---gIkV~~~~   59 (195)
                      ||+|.++..+++..+++++++++.++..     ..-.+.++.+++++-+++   |+-|-++.
T Consensus         3 ~~~~~~~~~~~~~~~~~~~~~~~~~a~~-----~~~~~~id~~i~~~m~~~~iPG~avaVv~   59 (387)
T PRK11289          3 LMMKSLLAALLLTASISAFAAPAAAATS-----QQLKDIVDRAIAPLMEEYDIPGMAVAVTY   59 (387)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCCH-----HHHHHHHHHHHHHHHHHCCCCEEEEEEEE
T ss_conf             7999999999999999861676556997-----99999999999999985799808999999


No 58 
>PRK11627 hypothetical protein; Provisional
Probab=85.00  E-value=1.1  Score=23.66  Aligned_cols=28  Identities=18%  Similarity=0.279  Sum_probs=16.4

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEE
Q ss_conf             90259999999999999861244458808998
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFSTENTTKYLTLY   32 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~~~~~~~lvVY   32 (195)
                      ||||.++.  ++.++++++|++  ++..|.+=
T Consensus         1 ~mkk~~~~--l~a~~lL~gCas--~p~~l~l~   28 (192)
T PRK11627          1 MLKKILFP--LVALFMLAGCAT--PPTTLEVS   28 (192)
T ss_pred             CHHHHHHH--HHHHHHHHHHCC--CCCEEEEC
T ss_conf             92879999--999999986069--97637867


No 59 
>pfam03466 LysR_substrate LysR substrate binding domain. The structure of this domain is known and is similar to the periplasmic binding proteins.
Probab=84.36  E-value=3.1  Score=21.04  Aligned_cols=59  Identities=15%  Similarity=0.188  Sum_probs=43.6

Q ss_pred             CCCCCEEEECC--CCHHHHHHHHHHHHHHC-CCCCCCCCHHHHHHHHHHHCCCCCEEEECCH
Q ss_conf             45880899818--99899999999999875-9862100001356676521066655750422
Q gi|254780563|r   24 NTTKYLTLYTD--QNQSVMLPIIHSFEERT-GVKISPIYTSSIQRPPITQGSPVDVIITKDE   82 (195)
Q Consensus        24 ~~~~~lvVYs~--~~~~~~~~~~~~Fek~t-gIkV~~~~~~~~~~~~~~~~~~~d~~~~~d~   82 (195)
                      ..+++|.|=+.  .......+++..|.+++ +|++++......+.....++...|+.+....
T Consensus         3 ~~~G~i~I~~~~~~~~~~lp~~l~~f~~~~P~i~i~i~~~~~~~i~~~l~~g~~Di~i~~~~   64 (209)
T pfam03466         3 GPRGRLRIGAPPTFAAYLLPPLLARFRERYPDVELELREGDSEELLDLLAEGELDLAIRRGP   64 (209)
T ss_pred             CCCEEEEEEEEHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCHHHHHHHHCCCCEEEEECCC
T ss_conf             98789999938899999999999999998889289999898488999998698148873178


No 60 
>PRK09701 D-allose transporter subunit; Provisional
Probab=83.71  E-value=3.3  Score=20.88  Aligned_cols=58  Identities=16%  Similarity=0.074  Sum_probs=27.4

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCE--EEECCCC-HH-HHHHHHHHHHHHCCCCCCCCCH
Q ss_conf             0259999999999999861244458808--9981899-89-9999999999875986210000
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTENTTKYL--TLYTDQN-QS-VMLPIIHSFEERTGVKISPIYT   60 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~~~~~l--vVYs~~~-~~-~~~~~~~~Fek~tgIkV~~~~~   60 (195)
                      |||.+..+..++++++.+ ++++.+.++  ++.+-.+ ++ .+..=+++.-++.|++|++...
T Consensus         1 m~k~~~~~~~~~~~~~~~-~~a~a~~~iavi~k~~~npf~~~~~~Ga~~aAk~~G~~v~v~~~   62 (311)
T PRK09701          1 MNKYLKYFSGTLVGLMLS-TSAFAAAEYAVVLKTLSNPFWVDMKKGIEDEAKTLGVSVDIFAS   62 (311)
T ss_pred             CCHHHHHHHHHHHHHHHH-HHHHHCCCEEEEECCCCCHHHHHHHHHHHHHHHHHCCEEEEEEC
T ss_conf             936999999999999988-87743684999968889989999999999999986997999927


No 61 
>PRK03095 prsA peptidylprolyl isomerase; Reviewed
Probab=82.94  E-value=2.8  Score=21.26  Aligned_cols=31  Identities=10%  Similarity=0.031  Sum_probs=15.8

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEC
Q ss_conf             02599999999999998612444588089981
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTENTTKYLTLYT   33 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~~~~~lvVYs   33 (195)
                      |||+++....+.++.+++|++.+ ++.|+-+.
T Consensus         1 MKK~~la~~~~svl~LaaC~~~~-~~~vat~k   31 (287)
T PRK03095          1 MKKAMLALAATSVIALSACGTSS-SDKIVTSK   31 (287)
T ss_pred             CCHHHHHHHHHHHHHHHHCCCCC-CCEEEEEC
T ss_conf             90789999999999998516899-87589846


No 62 
>PRK02998 prsA peptidylprolyl isomerase; Reviewed
Probab=82.55  E-value=2.9  Score=21.24  Aligned_cols=33  Identities=9%  Similarity=0.129  Sum_probs=18.4

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEECC
Q ss_conf             9025999999999999986124445880899818
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFSTENTTKYLTLYTD   34 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~~~~~~~lvVYs~   34 (195)
                      |-||+++..++++++++++++|.. +++|+-+.+
T Consensus         1 Mkkkk~~~~~~~~~~~l~LaaC~s-~~~vat~kg   33 (283)
T PRK02998          1 MKKKKLFIGTIISCVVLALSACGS-SDNVVTSKV   33 (283)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHCCC-CCCEEEECC
T ss_conf             935899999999999999986689-981798439


No 63 
>pfam01514 YscJ_FliF Secretory protein of YscJ/FliF family. This family includes proteins that are related to the YscJ lipoprotein, and the amino terminus of FliF, the flageller M-ring protein. The members of the YscJ family are thought to be involved in secretion of several proteins. The FliF protein ring is thought to be part of the export apparatus for flageller proteins, based on the similarity to YscJ proteins.
Probab=82.40  E-value=3.7  Score=20.59  Aligned_cols=37  Identities=16%  Similarity=0.275  Sum_probs=27.9

Q ss_pred             CCCCCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             44458808998189989999999999987598621000
Q gi|254780563|r   22 TENTTKYLTLYTDQNQSVMLPIIHSFEERTGVKISPIY   59 (195)
Q Consensus        22 ~~~~~~~lvVYs~~~~~~~~~~~~~Fek~tgIkV~~~~   59 (195)
                      -....+-.++|++.++.....+++..++ .||.-++..
T Consensus        21 ~~~~p~y~~Ly~~L~~~da~~i~~~L~~-~gI~y~~~~   57 (206)
T pfam01514        21 LAGCPDYVTLYTGLSEKDANEVLAALLQ-AGIPAEKSP   57 (206)
T ss_pred             HHCCCCCEECCCCCCHHHHHHHHHHHHH-CCCCEEEEE
T ss_conf             8479985611159999999999999998-799759854


No 64 
>PRK06934 flavodoxin; Provisional
Probab=82.29  E-value=3.8  Score=20.55  Aligned_cols=39  Identities=13%  Similarity=0.275  Sum_probs=20.9

Q ss_pred             CHHHHHHHHHHHHHHHHHHCC-CCC--CCCEEEECCCCHHHH
Q ss_conf             025999999999999986124-445--880899818998999
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFST-ENT--TKYLTLYTDQNQSVM   40 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~-~~~--~~~lvVYs~~~~~~~   40 (195)
                      |+|+++.++.++++..+.|++ .++  .+.|++|=+++++..
T Consensus         9 ~~~~~~~~~~~~~~~~~~~a~~~~q~~~k~LI~Yfs~~~~~~   50 (221)
T PRK06934          9 LTKHLILFLAVAVSSLSLIAEAADQNARRVLIVYFSQPEDVK   50 (221)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCCC
T ss_conf             478899999999998888750377677557999964755555


No 65 
>PRK13791 lysozyme inhibitor; Provisional
Probab=81.70  E-value=0.83  Score=24.31  Aligned_cols=36  Identities=19%  Similarity=0.476  Sum_probs=27.7

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCCCE--EEECCCC
Q ss_conf             90259999999999999861244458808--9981899
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFSTENTTKYL--TLYTDQN   36 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~~~~~~~l--vVYs~~~   36 (195)
                      |||++++.+.++++.+++....-++++|+  ++||+..
T Consensus         1 ~~~~~~~~~~~~l~als~~~~~m~~~~eitk~~YtC~~   38 (114)
T PRK13791          1 MMKRKLIPFTLFLAALSASTTSIAASQEISKSIYTCND   38 (114)
T ss_pred             CCCCCCCCHHHHHHHHHCCCCEEHHHHEEEEEEEEECC
T ss_conf             96431104899999872353201233201305898359


No 66 
>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=81.64  E-value=4  Score=20.41  Aligned_cols=136  Identities=14%  Similarity=0.022  Sum_probs=64.8

Q ss_pred             CEEEEC--CCCHHHHHHHHHHHHHHCCCCCCCCCHHHHH-HHHHHHCCCCCEEEECCHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             089981--8998999999999998759862100001356-6765210666557504223323433100001234222347
Q gi|254780563|r   28 YLTLYT--DQNQSVMLPIIHSFEERTGVKISPIYTSSIQ-RPPITQGSPVDVIITKDETSLALNEDLLHKLPAHLIKKNS  104 (195)
Q Consensus        28 ~lvVYs--~~~~~~~~~~~~~Fek~tgIkV~~~~~~~~~-~~~~~~~~~~d~~~~~d~~~l~~~~~~l~~~~~~~~~~~~  104 (195)
                      +|+|=+  +.+...+..+....-++.|++|+.+..++.. ......+...|++...=.+..  ...+...+.....    
T Consensus         2 tI~ig~~~w~e~~i~a~i~~~~Le~~G~~V~~~~~~~~~~~~~al~~G~iDi~~~~w~~~~--~~~~~~~~~~~~~----   75 (256)
T pfam04069         2 TIVIGSKNWTEQEILANIAAQLLEALGYVVELVGLGSTAVLFAALASGDIDLYPEEWTGTT--YEAYKKAVEEKLG----   75 (256)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHCCCCCEEEHHCCCCH--HHHHHHHHHCCCC----
T ss_conf             2999268862899999999999997698169854787089999997699758633306625--7999987514687----


Q ss_pred             CCCCCCCCCCCCCCCCEEEEEEEHHHHCCCCCCCCHHHHCCH-----HHCCEEEECCCCCCHHHHHHHHHHHHCHH
Q ss_conf             200012222234434505888733440134455788884086-----67685996289830499999999960869
Q gi|254780563|r  105 FVLKNENKKLMRISFDTQVLAYSTKRIKIADLPKSVFDLTNA-----QWKKRLSIAPNNISFHRLLNTMEQTPNKT  175 (195)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~P~sw~DL~~p-----~~kG~i~~~~~~~s~~~~~~a~~~~~G~~  175 (195)
                        .....   ........++++... +....-.+||.||.++     ..+|++.-.+++...+.....++..+|-+
T Consensus        76 --~~~~~---~~~~~~~~g~~Vp~~-~a~~~~i~si~dL~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~yGl~  145 (256)
T pfam04069        76 --LLVLG---PLGAGNTYGLAVPKY-VAEKPGIKSISDLAKPADDELGFKGEFIGRPDGWGCTRSTEGLLKAYGLD  145 (256)
T ss_pred             --EEECC---CCCCCCEEEEEECHH-HHHHCCCCCHHHHHCCCCCCCCCCCCEECCCCCCCCCHHHHHHHHHCCCC
T ss_conf             --38613---577787589998588-88356998799972742102488865532788854006789999863976


No 67 
>PRK12681 cysB transcriptional regulator CysB; Reviewed
Probab=80.22  E-value=4.5  Score=20.13  Aligned_cols=57  Identities=19%  Similarity=0.177  Sum_probs=38.6

Q ss_pred             CCCCCCEEEECCCC--HHHHHHHHHHHHHHC-CCCCCCCCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             44588089981899--899999999999875-9862100001356676521066655750
Q gi|254780563|r   23 ENTTKYLTLYTDQN--QSVMLPIIHSFEERT-GVKISPIYTSSIQRPPITQGSPVDVIIT   79 (195)
Q Consensus        23 ~~~~~~lvVYs~~~--~~~~~~~~~~Fek~t-gIkV~~~~~~~~~~~~~~~~~~~d~~~~   79 (195)
                      ....++|.|-+..+  .....+++..|.+++ +|++++..++..+......+...|+.+.
T Consensus        89 ~~~~G~L~Ia~~~t~a~~~LP~~i~~F~~~~P~v~l~l~~~~~~~i~~~l~~g~~DlaI~  148 (324)
T PRK12681         89 WPDKGSLYIATTHTQARYALPPVIKGFIKRYPRVSLHMHQGSPTQIAEAAAKGEADFAIA  148 (324)
T ss_pred             CCCCCEEEEEECHHHHHHHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHCCCCCCCCC
T ss_conf             887634999853588887725999999987899844653178799999998799872312


No 68 
>PRK13861 type IV secretion system protein VirB9; Provisional
Probab=80.09  E-value=2.5  Score=21.56  Aligned_cols=19  Identities=32%  Similarity=0.301  Sum_probs=11.1

Q ss_pred             CCHHHHHHHHHHHHHHHHH
Q ss_conf             9025999999999999986
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEA   19 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~   19 (195)
                      ||||.++.++++++..+.+
T Consensus         1 mmk~l~~~~~~~l~~~~~a   19 (293)
T PRK13861          1 MIKKLFLTLACLLFAAIGA   19 (293)
T ss_pred             CCHHHHHHHHHHHHHHHHH
T ss_conf             9089999999999861266


No 69 
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=78.13  E-value=5.2  Score=19.75  Aligned_cols=52  Identities=21%  Similarity=0.244  Sum_probs=27.3

Q ss_pred             CCCCEEEECC--CCHHHHHHHHHHHHHHC-CCCCCCCCHHHHHHHHHHHCCCCCE
Q ss_conf             5880899818--99899999999999875-9862100001356676521066655
Q gi|254780563|r   25 TTKYLTLYTD--QNQSVMLPIIHSFEERT-GVKISPIYTSSIQRPPITQGSPVDV   76 (195)
Q Consensus        25 ~~~~lvVYs~--~~~~~~~~~~~~Fek~t-gIkV~~~~~~~~~~~~~~~~~~~d~   76 (195)
                      ..++|.|-+.  .......+++.+|.+++ +|++++..+.+.+..........|+
T Consensus        91 ~~G~lrIg~~~~~~~~~lp~~l~~f~~~~P~v~l~l~~~~~~~~~~~l~~g~~Dl  145 (309)
T PRK12682         91 DSGTLTIATTHTQARYVLPRVVAKFRKRYPKVNLSLHQGSPDEIAQMVISGEADI  145 (309)
T ss_pred             CCCCCCCCCCHHHHHHCCCHHHHHHHHHCCCCEEEEEECCHHHHHHHHHCCCCCH
T ss_conf             7774121243133320386253999987898379998378299999997699764


No 70 
>PRK10355 xylF D-xylose transporter subunit XylF; Provisional
Probab=76.99  E-value=5.7  Score=19.56  Aligned_cols=57  Identities=14%  Similarity=0.024  Sum_probs=24.9

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCEEE---ECCCCHHHHHHHHHHHH---HHCCCCCCCCCH
Q ss_conf             025999999999999986124445880899---81899899999999999---875986210000
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTENTTKYLTL---YTDQNQSVMLPIIHSFE---ERTGVKISPIYT   60 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~~~~~lvV---Ys~~~~~~~~~~~~~Fe---k~tgIkV~~~~~   60 (195)
                      ||.+.++.+++++++++++++  .++++.|   ..+.+...-..+.+.|+   ++.|++|.+...
T Consensus         1 mk~k~~~~~~~~~~~~~~~~a--~a~~~~IGv~~~~~~~~~~~~~~~~~~~~Ake~G~~v~v~dA   63 (330)
T PRK10355          1 MKIKNILLTLCAALLLTSVAA--HAKEVKIGMAIDDLRLERWQKDRDIFVKKAESLGAKVFVQSA   63 (330)
T ss_pred             CCHHHHHHHHHHHHHHHCCHH--HHCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCCEEEEECC
T ss_conf             966899999999999844611--213867999906888868999999999999975998999718


No 71 
>PRK09967 putative outer membrane lipoprotein; Provisional
Probab=75.98  E-value=2.8  Score=21.31  Aligned_cols=22  Identities=14%  Similarity=0.184  Sum_probs=14.3

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             90259999999999999861244
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFSTE   23 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~~   23 (195)
                      |||+ +++.++++++++++|++.
T Consensus         1 m~k~-~~~~~l~~~l~lsgC~s~   22 (160)
T PRK09967          1 MIKH-LVAPLIFTSLILTGCQSP   22 (160)
T ss_pred             CHHH-HHHHHHHHHHHHHHCCCC
T ss_conf             9078-999999999999845899


No 72 
>PRK10523 lipoprotein involved with copper homeostasis and adhesion; Provisional
Probab=75.32  E-value=2.1  Score=22.04  Aligned_cols=56  Identities=23%  Similarity=0.307  Sum_probs=31.5

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHH-----H-CCCCCCCC
Q ss_conf             9025999999999999986124445880899818998999999999998-----7-59862100
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFSTENTTKYLTLYTDQNQSVMLPIIHSFEE-----R-TGVKISPI   58 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~~~~~~~lvVYs~~~~~~~~~~~~~Fek-----~-tgIkV~~~   58 (195)
                      ||||.++..++.+.+++.. +|.+..+.=.+ +...+...+++-+.|.-     . .||+..+.
T Consensus         1 ~mkk~~~~~~~a~g~~~l~-GC~~r~~~~~~-~~~~~~~lkpm~qsf~GvLPCADCsGI~ttL~   62 (234)
T PRK10523          1 MMKKAILTALAAVGLFALM-GCNNRAEVDTL-SPAQAAELKPMQQSWRGVLPCADCEGIDTSLF   62 (234)
T ss_pred             CHHHHHHHHHHHHHHHHHH-CCCCCCCCCCC-CCCHHHCCCCHHHHHCCEEECCCCCCCEEEEE
T ss_conf             9058999999999999876-34665434666-75322026703355346020346678435899


No 73 
>pfam07273 DUF1439 Protein of unknown function (DUF1439). This family consists of several hypothetical bacterial proteins of around 190 residues in length. Several members of this family are annotated as being putative lipoproteins and are often known as YceB. The function of this family is unknown.
Probab=75.18  E-value=4.4  Score=20.16  Aligned_cols=46  Identities=17%  Similarity=0.331  Sum_probs=24.1

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHH---HHHHHCCCCC
Q ss_conf             02599999999999998612444588089981899899999999---9998759862
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTENTTKYLTLYTDQNQSVMLPIIH---SFEERTGVKI   55 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~~~~~lvVYs~~~~~~~~~~~~---~Fek~tgIkV   55 (195)
                      ||+.++..+++ ++++++|.+      |+.||= ++..+...++   .|+++.||.-
T Consensus         1 Mk~~~~~~~~l-~~~LsgC~~------ls~ysI-SE~Ein~yL~k~~~~~k~~gi~g   49 (177)
T pfam07273         1 MKKLLLLILLL-VLLLSGCAS------LSQYSI-SEAEINQYLQKEVHLEKKVGIPG   49 (177)
T ss_pred             CCHHHHHHHHH-HHHHHCCCC------CCCEEE-CHHHHHHHHHHHCCHHHHHCCCC
T ss_conf             91489999999-999715575------662526-69999999987457778608877


No 74 
>PRK13486 bifunctional enterobactin receptor/adhesin protein; Provisional
Probab=74.90  E-value=4.9  Score=19.92  Aligned_cols=37  Identities=11%  Similarity=0.091  Sum_probs=26.0

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCHH
Q ss_conf             0259999999999999861244458808998189989
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTENTTKYLTLYTDQNQS   38 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~~~~~lvVYs~~~~~   38 (195)
                      |+-..+.++++.|+..++.+...+.++|||=..+.+.
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~d~vvVTatr~~~   37 (696)
T PRK13486          1 MRITTLASVVIPCLGFSASSIAAAEDVMIVSASGYEK   37 (696)
T ss_pred             CCHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCC
T ss_conf             9614789999987532034434568849990168616


No 75 
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=74.64  E-value=6.6  Score=19.19  Aligned_cols=57  Identities=21%  Similarity=0.255  Sum_probs=37.0

Q ss_pred             CCCCCCEEEECCC--CHHHHHHHHHHHHHHC-CCCCCCCCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             4458808998189--9899999999999875-9862100001356676521066655750
Q gi|254780563|r   23 ENTTKYLTLYTDQ--NQSVMLPIIHSFEERT-GVKISPIYTSSIQRPPITQGSPVDVIIT   79 (195)
Q Consensus        23 ~~~~~~lvVYs~~--~~~~~~~~~~~Fek~t-gIkV~~~~~~~~~~~~~~~~~~~d~~~~   79 (195)
                      ....+.|.|-+..  ......+++..|.++| +|++++..+++.+......+...|+.+.
T Consensus        89 ~~~~G~l~ig~~~s~~~~~lp~~l~~f~~~~P~v~l~l~~~~~~~~~~~l~~g~~Dl~i~  148 (313)
T PRK12684         89 AQDQGNLTIATTHTQARYALPAAIAEFKKRYPKVRLSILQGSPTQIAEMVIHDQADLAIA  148 (313)
T ss_pred             CCCCCEEECCHHHHHHHHCCCHHHHHHHHHCCCEEEEEEECCHHHHHHHHHCCCCCEEEC
T ss_conf             677751411024555751594999999844898089997178899999997799665504


No 76 
>TIGR02036 dsdC D-serine deaminase transcriptional activator; InterPro: IPR011781    This family, part of the LysR family of transcriptional regulators, activates transcription of the gene for D-serine deaminase, dsdA. Trusted members of this family so far are found adjacent to dsdA and only in Gammaproteobacteria, including Escherichia coli, Vibrio cholerae, and Colwellia psychrerythraea..
Probab=74.56  E-value=1.7  Score=22.61  Aligned_cols=51  Identities=24%  Similarity=0.354  Sum_probs=35.6

Q ss_pred             CCCCEEEECCCCHHHH--HHHHHHHHHHC-CCCCCCCCHHHHHHHHHHHCCCCCEEE
Q ss_conf             5880899818998999--99999999875-986210000135667652106665575
Q gi|254780563|r   25 TTKYLTLYTDQNQSVM--LPIIHSFEERT-GVKISPIYTSSIQRPPITQGSPVDVII   78 (195)
Q Consensus        25 ~~~~lvVYs~~~~~~~--~~~~~~Fek~t-gIkV~~~~~~~~~~~~~~~~~~~d~~~   78 (195)
                      -+++|||||--+.+..  -|-+.+|+++| -|..++.+|..+-..   .+...||-+
T Consensus        94 ~SG~LT~YSRPSfAQCWLVPri~~F~~~YPsIsL~~LTGNeNinf---qg~GIDvAI  147 (302)
T TIGR02036        94 LSGELTVYSRPSFAQCWLVPRIADFKKRYPSISLKVLTGNENINF---QGAGIDVAI  147 (302)
T ss_pred             CCCCEEECCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCEEC---CCCCCEEEE
T ss_conf             121020022553334433232321200387122110015353201---357503788


No 77 
>TIGR03042 PS_II_psbQ_bact photosystem II protein PsbQ. This protein through the member sll1638 from Synechocystis sp. PCC 6803, was shown to be part of the cyanobacteria photosystem II. It is homologous to (but quite diverged from) the chloroplast PsbQ protein, called oxygen-evolving enhancer protein 3 (OEE3). We designate this cyanobacteria protein PsbQ by homology.
Probab=73.16  E-value=4.9  Score=19.92  Aligned_cols=46  Identities=15%  Similarity=0.137  Sum_probs=26.0

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHH
Q ss_conf             25999999999999986124445880899818998999999999998
Q gi|254780563|r    3 KRTIYTYLLLLCGFTEAFSTENTTKYLTLYTDQNQSVMLPIIHSFEE   49 (195)
Q Consensus         3 kk~~~~~l~l~~~~~~~~~~~~~~~~lvVYs~~~~~~~~~~~~~Fek   49 (195)
                      ++.+...|++++.|+++|++..++. -.-||+..=+.++...+.|+.
T Consensus         2 Rsi~s~~L~~~~~fLvsC~gp~a~~-p~tysp~~l~~Iq~~~~~i~~   47 (142)
T TIGR03042         2 RSLASLLLVLLLTFLVSCSGPAAAV-PPTYSPAQLAQIQRQAEGIEA   47 (142)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCC-CCCCCHHHHHHHHHHHHHHHH
T ss_conf             7699999999999998838998889-998699999999999988999


No 78 
>PRK06760 hypothetical protein; Provisional
Probab=73.07  E-value=4.4  Score=20.16  Aligned_cols=65  Identities=20%  Similarity=0.219  Sum_probs=32.8

Q ss_pred             CHHHH--HHHHHHHHHHHHHHCC---CCCCCCEEEECCCCHHHHHHHHHHHHHHC--------------CCCCCCCCHHH
Q ss_conf             02599--9999999999986124---44588089981899899999999999875--------------98621000013
Q gi|254780563|r    2 FKRTI--YTYLLLLCGFTEAFST---ENTTKYLTLYTDQNQSVMLPIIHSFEERT--------------GVKISPIYTSS   62 (195)
Q Consensus         2 mkk~~--~~~l~l~~~~~~~~~~---~~~~~~lvVYs~~~~~~~~~~~~~Fek~t--------------gIkV~~~~~~~   62 (195)
                      |||++  +...++.+..+++|+-   ...++-+.+|.  ++..+.++++...+++              |-+|-+...++
T Consensus         1 MKK~l~i~i~~iis~~~lsaCS~~~~~~PANGvliiG--dE~~~~~I~d~yK~~tke~~~y~vK~g~~~~kkVLim~~sT   78 (223)
T PRK06760          1 MKKTLTIFMLTILLLISFSACSKKENSFPANGVLIIG--DENNISPIINRYQEITKENEVFSVKKGEVGNGQVLILNEST   78 (223)
T ss_pred             CCEEEEEHHHHHHHHHHHHHCCCCCCCCCCCEEEEEE--CHHHHHHHHHHHHHHHHHHHEEEEEEEEECCEEEEEEEHHH
T ss_conf             9506764999999999840033678789874379996--51677889998877643432046675137882799986189


Q ss_pred             HHHHHH
Q ss_conf             566765
Q gi|254780563|r   63 IQRPPI   68 (195)
Q Consensus        63 ~~~~~~   68 (195)
                      ++.+..
T Consensus        79 Ae~mvK   84 (223)
T PRK06760         79 AQALIK   84 (223)
T ss_pred             HHHHHH
T ss_conf             999976


No 79 
>PRK13528 outer membrane receptor FepA; Provisional
Probab=73.02  E-value=3.2  Score=20.96  Aligned_cols=35  Identities=9%  Similarity=-0.046  Sum_probs=15.2

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCC-----CCCEEEECCC
Q ss_conf             9025999999999999986124445-----8808998189
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFSTENT-----TKYLTLYTDQ   35 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~~~~-----~~~lvVYs~~   35 (195)
                      ||+++++-.|.++++.++...++++     ..|.||-|+.
T Consensus         3 ~~~~~~~~~~~~~~~~l~~~~~a~~~~~~~~~e~vVvt~~   42 (727)
T PRK13528          3 MRANKILWLLTVVLAGLNSQLSAAESSDDDNGETVVVEGT   42 (727)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEECCC
T ss_conf             3046699999999998750555653346778868998787


No 80 
>TIGR02747 TraV type IV conjugative transfer system protein TraV; InterPro: IPR014118   This entry includes TraV, which is a component of conjugative type IV secretion system. TraV is an outer membrane lipoprotein that is believed to interact with the secretin TraK , , . The alignment contains three conserved cysteines in the N-terminal half..
Probab=72.66  E-value=2.5  Score=21.57  Aligned_cols=22  Identities=14%  Similarity=0.150  Sum_probs=16.2

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             9025999999999999986124
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFST   22 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~   22 (195)
                      |||..++..+.++++++++|++
T Consensus         1 Mmr~~~L~~~~~~~f~LtGCsa   22 (174)
T TIGR02747         1 MMRLKVLLLLACVAFLLTGCSA   22 (174)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHH
T ss_conf             9067899999999872002577


No 81 
>pfam05170 AsmA AsmA family. The AsmA gene, whose product is involved in the assembly of outer membrane proteins in Escherichia coli. AsmA mutations were isolated as extragenic suppressors of an OmpF assembly mutant. AsmA may have a role in LPS biogenesis.
Probab=72.43  E-value=7.1  Score=19.00  Aligned_cols=50  Identities=10%  Similarity=0.043  Sum_probs=28.7

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             025999999999999986124445880899818998999999999998759862100
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTENTTKYLTLYTDQNQSVMLPIIHSFEERTGVKISPI   58 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~~~~~lvVYs~~~~~~~~~~~~~Fek~tgIkV~~~   58 (195)
                      |||.+..++++++++..+..       +.++.-.....-..+.++.+++||-++++.
T Consensus         1 Mk~~lk~l~~i~~~lv~~~~-------~l~~~~d~n~~k~~i~~~v~~~TGr~l~i~   50 (537)
T pfam05170         1 MKKALKILLIILIVLLLLII-------ALIALFDPNYFKPTIQQKVSAASGRPLQID   50 (537)
T ss_pred             CHHHHHHHHHHHHHHHHHHH-------HHEEEECHHHHHHHHHHHHHHHHCCEEEEC
T ss_conf             94589999999999999999-------860752889979999999999889859994


No 82 
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=72.24  E-value=7.5  Score=18.85  Aligned_cols=55  Identities=18%  Similarity=0.239  Sum_probs=37.2

Q ss_pred             CCCCEEEECC--CCHHHHHHHHHHHHHHC-CCCCCCCCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             5880899818--99899999999999875-9862100001356676521066655750
Q gi|254780563|r   25 TTKYLTLYTD--QNQSVMLPIIHSFEERT-GVKISPIYTSSIQRPPITQGSPVDVIIT   79 (195)
Q Consensus        25 ~~~~lvVYs~--~~~~~~~~~~~~Fek~t-gIkV~~~~~~~~~~~~~~~~~~~d~~~~   79 (195)
                      ..++|.|-.+  .....+.+++..|.+++ +|++++......+......+...|+.+.
T Consensus        89 ~~G~l~ig~~~~~~~~~l~~~l~~f~~~~P~i~i~l~~~~~~~~~~~l~~~~~D~~i~  146 (292)
T PRK11242         89 SRGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMPQERIEALLADDELDVGIA  146 (292)
T ss_pred             CCCEEEEECHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHCCCCCEEEE
T ss_conf             7765863024577888738998888864889734899768899999986798557998


No 83 
>COG3017 LolB Outer membrane lipoprotein involved in outer membrane biogenesis [Cell envelope biogenesis, outer membrane]
Probab=71.40  E-value=3.7  Score=20.64  Aligned_cols=30  Identities=20%  Similarity=0.196  Sum_probs=22.9

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCCCEE
Q ss_conf             902599999999999998612444588089
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFSTENTTKYLT   30 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~~~~~~~lv   30 (195)
                      |||+..+.++.++++++.+|+..++-...+
T Consensus         3 ~~~~~~~~l~~~As~LL~aC~~~~~~~~~~   32 (206)
T COG3017           3 MMKRLLFLLLALASLLLTACTLTASRPPNN   32 (206)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf             277787899999999997565667778777


No 84 
>PRK13483 enterobactin receptor protein; Provisional
Probab=71.13  E-value=7.7  Score=18.79  Aligned_cols=23  Identities=9%  Similarity=0.004  Sum_probs=11.2

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             90259999999999999861244
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFSTE   23 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~~   23 (195)
                      ||.|+-++.+.+.+++++++.+.
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~a~   23 (663)
T PRK13483          1 LLSRKKYLAQVIAALCLLPAVPV   23 (663)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHC
T ss_conf             96414479999999999777650


No 85 
>TIGR03525 GldK gliding motility-associated lipoprotein GldK. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldK is a lipoprotein linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae. Knockouts of GldK abolish the gliding phenotype. GldK is homologous to GldJ. There is a GldK homolog in Cytophaga hutchinsonii and several other species that has a different, shorter architecture and is represented by a separate model. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility.
Probab=70.57  E-value=3.4  Score=20.79  Aligned_cols=27  Identities=11%  Similarity=0.102  Sum_probs=13.1

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCEEE
Q ss_conf             025999999999999986124445880899
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTENTTKYLTL   31 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~~~~~lvV   31 (195)
                      |||.++.++++++++  +|++ ...+|||=
T Consensus         1 Mkk~~~~~~~~~~~~--SCg~-~~~GELvG   27 (449)
T TIGR03525         1 MKKYLVFAALVVLVY--SCGS-GDKGELVG   27 (449)
T ss_pred             CCHHHHHHHHHHHHH--HCCC-CCCCEEEE
T ss_conf             912489999999872--1058-99713873


No 86 
>PRK02889 tolB translocation protein TolB; Provisional
Probab=69.83  E-value=3.9  Score=20.46  Aligned_cols=32  Identities=6%  Similarity=0.058  Sum_probs=17.4

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEC
Q ss_conf             902599999999999998612444588089981
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFSTENTTKYLTLYT   33 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~~~~~~~lvVYs   33 (195)
                      ||+|..+..++.+|++++++.+.++ -++.|..
T Consensus         3 ~~~~l~~~~~~~~~l~~~~~~A~A~-L~IeIt~   34 (430)
T PRK02889          3 LMTKLGLRALVASCLIAAGGAAHAQ-LNVEITG   34 (430)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEE-EEEEEEC
T ss_conf             7998999999999998621020278-9999935


No 87 
>PRK10653 D-ribose transporter subunit RbsB; Provisional
Probab=68.66  E-value=9.1  Score=18.39  Aligned_cols=59  Identities=8%  Similarity=0.164  Sum_probs=30.2

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCEEE-ECCCCHHHHHHHHHHHH---HHCCCCCCCCCHH
Q ss_conf             025999999999999986124445880899-81899899999999999---8759862100001
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTENTTKYLTL-YTDQNQSVMLPIIHSFE---ERTGVKISPIYTS   61 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~~~~~lvV-Ys~~~~~~~~~~~~~Fe---k~tgIkV~~~~~~   61 (195)
                      ||| ++.++..++...+.++.+.+++++-| ....+...-..+++..|   ++.|+++.+....
T Consensus         3 ~~k-~~~~~~~~~~~~~~~a~a~a~~TIgvivp~i~npff~~v~~gie~~a~~~Gy~l~v~~s~   65 (295)
T PRK10653          3 MKK-LATLVSAVALSATVSANAMAKDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQ   65 (295)
T ss_pred             HHH-HHHHHHHHHHHHHCCCHHHCCCEEEEEECCCCCHHHHHHHHHHHHHHHHCCCEEEEEECC
T ss_conf             079-999999998765212177529979999489879799999999999999769989998399


No 88 
>PRK10833 putative assembly protein; Provisional
Probab=68.56  E-value=7.7  Score=18.79  Aligned_cols=50  Identities=20%  Similarity=0.323  Sum_probs=29.7

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             025999999999999986124445880899818998999999999998759862100
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTENTTKYLTLYTDQNQSVMLPIIHSFEERTGVKISPI   58 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~~~~~lvVYs~~~~~~~~~~~~~Fek~tgIkV~~~   58 (195)
                      |||.+....++++++.++..+      |++. =.+.+.-..+.++.+++||-++.+.
T Consensus         1 MKrll~~l~illvvvv~gl~a------Lv~l-vdPNd~k~~I~~qV~~~TGr~L~i~   50 (617)
T PRK10833          1 MRRFLTTLMILLVVLVAGLSA------LVLL-VNPNDFRAYMVKQVEARSGYQLQLD   50 (617)
T ss_pred             CCHHHHHHHHHHHHHHHHHHH------HHEE-ECHHHHHHHHHHHHHHHHCCEEEEC
T ss_conf             941899999999999999998------8150-4889979999999999779879987


No 89 
>PRK13513 putative outer membrane receptor; Provisional
Probab=68.12  E-value=9.3  Score=18.33  Aligned_cols=36  Identities=14%  Similarity=0.134  Sum_probs=19.6

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCC---CCCEEEECCCCH
Q ss_conf             025999999999999986124445---880899818998
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTENT---TKYLTLYTDQNQ   37 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~~---~~~lvVYs~~~~   37 (195)
                      |||..++++++++++++...++.+   -+|+||=..+.+
T Consensus         8 ~~~~~~~a~~~~~~~~~~~~aa~~~~~le~ivVTAtr~~   46 (660)
T PRK13513          8 FRKTHSAALVIAAVISSQGYAAEKTTPTDTMVVTASGFQ   46 (660)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCC
T ss_conf             437999999999987568863767889872999704874


No 90 
>PRK12696 flgH flagellar basal body L-ring protein; Reviewed
Probab=66.64  E-value=4.8  Score=19.97  Aligned_cols=20  Identities=5%  Similarity=0.064  Sum_probs=11.0

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             9025999999999999986124
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFST   22 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~   22 (195)
                      ||||.++..  ++++++++|+.
T Consensus         1 mm~~~l~~~--~~~~~L~GC~~   20 (238)
T PRK12696          1 MIRKLLAAS--CAVLLLSGCNA   20 (238)
T ss_pred             CHHHHHHHH--HHHHHHHCCCC
T ss_conf             958999999--99999516568


No 91 
>TIGR02544 III_secr_YscJ type III secretion apparatus lipoprotein, YscJ/HrcJ family; InterPro: IPR003282 Secretion of virulence factors in Gram-negative bacteria involves transportation of the protein across two membranes to reach the cell exterior. There have been four secretion systems described in animal enteropathogens such as Salmonella and Yersinia, with further sequence similarities in plant pathogens like Ralstonia and Erwinia.   The type III secretion system is of great interest as it is used to transport virulence factors from the pathogen directly into the host cell  and is only triggered when the bacterium comes into close contact with the host. The protein subunits of the system are very similar to those of bacterial flagellar biosynthesis . However, while the latter forms a ring structure to allow secretion of flagellin and is an integral part of the flagellum itself, type III subunits in the outer membrane translocate secreted proteins through a channel-like structure.    One of the outer membrane protein subunit families, termed "K" here for nomenclature purposes, aids in the structural assembly of the invasion complex . It is also described as a lipoprotein. Members of this family include the Salmonella PrgK and SsaJ genes, MxiJ from Shigella, YscJ from Yersinia, and from the plant enteropathogens NolT (Rhizobium) and HrcJ Erwinia). The flagellar M-ring protein FliF also shares a low level of similarity, presumably due to evolution of the type III secretion system from the flagellar biosynthetic pathway.; GO: 0009306 protein secretion.
Probab=66.21  E-value=10  Score=18.11  Aligned_cols=43  Identities=19%  Similarity=0.230  Sum_probs=28.7

Q ss_pred             HHHHHHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             9999999998612444588089981899899999999999875986210
Q gi|254780563|r    9 YLLLLCGFTEAFSTENTTKYLTLYTDQNQSVMLPIIHSFEERTGVKISP   57 (195)
Q Consensus         9 ~l~l~~~~~~~~~~~~~~~~lvVYs~~~~~~~~~~~~~Fek~tgIkV~~   57 (195)
                      +++++++++++|.     .++++|++.++...-+++.-... +||+.+-
T Consensus         6 ~~~~l~llL~GC~-----~~~~Ly~gL~e~eANe~lA~L~~-~gI~A~K   48 (203)
T TIGR02544         6 LLLLLLLLLTGCK-----VDLELYSGLSEREANEMLALLMR-HGIDAEK   48 (203)
T ss_pred             HHHHHHHHHHCCC-----CEEEEECCCCHHHHHHHHHHHHH-CCCCEEE
T ss_conf             9999999971787-----40565047898789999999996-6983453


No 92 
>TIGR00439 ftsX putative protein insertion permease FtsX; InterPro: IPR004513 FtsX is an integral membrane protein encoded in the same operon as signal recognition particle docking protein FtsY and FtsE. FtsE is a hydrophilic nucleotide-binding protein that associates with the inner membrane by means of association with FtsX; FtsE mutants are viable only in high salt, supporting possible roles in cell division, as previously indicated, or in transport.; GO: 0007049 cell cycle, 0016021 integral to membrane.
Probab=66.13  E-value=10  Score=18.10  Aligned_cols=78  Identities=19%  Similarity=0.272  Sum_probs=48.7

Q ss_pred             HHHHHHHHHHHHHHHHCC-------------CCCCCCEEEE--CCCCHHHHHHHHHHHHHHCCC-CCCCCCHHH------
Q ss_conf             999999999999986124-------------4458808998--189989999999999987598-621000013------
Q gi|254780563|r    5 TIYTYLLLLCGFTEAFST-------------ENTTKYLTLY--TDQNQSVMLPIIHSFEERTGV-KISPIYTSS------   62 (195)
Q Consensus         5 ~~~~~l~l~~~~~~~~~~-------------~~~~~~lvVY--s~~~~~~~~~~~~~Fek~tgI-kV~~~~~~~------   62 (195)
                      ++++.++++.+++....+             -..+.++|||  +..+++..+-+.+..+++-|+ +|+|++..+      
T Consensus        35 TlLT~~viAvslTlP~v~Yl~~kn~~~a~t~~ypspqiTvYl~k~l~~~~a~~Vv~~l~~~kgve~~~y~sred~L~Ef~  114 (314)
T TIGR00439        35 TLLTVLVIAVSLTLPLVSYLVYKNVQSALTQLYPSPQITVYLEKALAEEDADTVVSKLRRDKGVEKINYISREDALAEFK  114 (314)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHCHHHHHHHHHHHHHHCCCCHHHCCCHHHHHHHHH
T ss_conf             79999999999865799999988577774201788403578775013446899999998740620210113566778863


Q ss_pred             -----HHHHHHHHCCC-CCEEEE-CCH
Q ss_conf             -----56676521066-655750-422
Q gi|254780563|r   63 -----IQRPPITQGSP-VDVIIT-KDE   82 (195)
Q Consensus        63 -----~~~~~~~~~~~-~d~~~~-~d~   82 (195)
                           .+.+...++|| .||++- .+.
T Consensus       115 sWsgfg~~l~mLd~NPLPaV~iV~P~~  141 (314)
T TIGR00439       115 SWSGFGELLEMLDDNPLPAVVIVTPDS  141 (314)
T ss_pred             CCCCCCHHHHHHCCCCCCCEEEEECCC
T ss_conf             346430056764178797368870687


No 93 
>pfam10566 Glyco_hydro_97 Glycoside hydrolase 97. This is the 97th family of glycosidases, in this case bacterial. The central part of the GH97 family protein sequences represents a typical and complete (beta/alpha)8-barrel or catalytic TIM-barrel type domain. The N- and C-terminal parts of the sequences, mainly consisting of beta-strands, most probably form two additional non-catalytic domains with as yet unknown functions. The non-catalytic domains of glycosidases from the alpha-galactosidase and alpha-glucosidase superfamilies are also predominantly composed of beta-strands, and at least some of these domains are involved in oligomerisation and carbohydrate binding. In all known glycosidases with the (beta-alpha)8-barrel fold, the amino acid residues at the active site are located on the C-termini of the beta-strands.
Probab=65.66  E-value=5.2  Score=19.77  Aligned_cols=22  Identities=14%  Similarity=0.040  Sum_probs=12.3

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             0259999999999999861244
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTE   23 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~   23 (195)
                      |||.++..+++++++++++.++
T Consensus         1 mkk~~~~~~~~~~~~~~~~~~~   22 (643)
T pfam10566         1 MKKLTIILLAFLLLIGNLSLAA   22 (643)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHH
T ss_conf             9502578999999997656754


No 94 
>PRK02710 plastocyanin; Provisional
Probab=65.05  E-value=10  Score=18.09  Aligned_cols=34  Identities=15%  Similarity=0.046  Sum_probs=17.4

Q ss_pred             CCHHH--HHHHHHHHHHHHHHHCCCCCCCCEEEECC
Q ss_conf             90259--99999999999986124445880899818
Q gi|254780563|r    1 MFKRT--IYTYLLLLCGFTEAFSTENTTKYLTLYTD   34 (195)
Q Consensus         1 mmkk~--~~~~l~l~~~~~~~~~~~~~~~~lvVYs~   34 (195)
                      ||||.  +...|+++++..+.+...+.++++.|.-.
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~~a~A~~~~v~m~   36 (119)
T PRK02710          1 MAKRLRSIAAALVAVVSSFGLGVSSASAATVEVKMG   36 (119)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEC
T ss_conf             906889999999999999981257020252899975


No 95 
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=64.82  E-value=11  Score=17.95  Aligned_cols=57  Identities=14%  Similarity=0.185  Sum_probs=41.8

Q ss_pred             CCCCCCEEEECCCC--HHHHHHHHHHHHHHC-CCCCCCCCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             44588089981899--899999999999875-9862100001356676521066655750
Q gi|254780563|r   23 ENTTKYLTLYTDQN--QSVMLPIIHSFEERT-GVKISPIYTSSIQRPPITQGSPVDVIIT   79 (195)
Q Consensus        23 ~~~~~~lvVYs~~~--~~~~~~~~~~Fek~t-gIkV~~~~~~~~~~~~~~~~~~~d~~~~   79 (195)
                      ....++|.|.+..+  .....+++..|.++| +|++.+..++..+..........|+-+.
T Consensus        89 ~~~~G~L~Ig~~~t~a~~~LP~vi~~f~~~yP~V~l~l~~~~~~~l~e~l~~g~~Diai~  148 (327)
T PRK12680         89 RESQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAVV  148 (327)
T ss_pred             CCCCEEEEEEEECHHHHHHHHHHHHHHHHHCCCCEEEEEECCCHHHHHHHHCCCCCEEEE
T ss_conf             887337999984227777568999999986899679999898288999997899409994


No 96 
>PRK04792 tolB translocation protein TolB; Provisional
Probab=64.44  E-value=6  Score=19.40  Aligned_cols=17  Identities=41%  Similarity=0.686  Sum_probs=10.7

Q ss_pred             CCHHHHHHHHHHHHHHH
Q ss_conf             90259999999999999
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFT   17 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~   17 (195)
                      ||||.++.+++++++++
T Consensus         1 M~k~~~~~l~lll~~~s   17 (450)
T PRK04792          1 MLKRLILGLFVLLLSFS   17 (450)
T ss_pred             CCHHHHHHHHHHHHHHH
T ss_conf             93899999999999865


No 97 
>PRK13697 cytochrome c6; Provisional
Probab=63.83  E-value=5.2  Score=19.75  Aligned_cols=26  Identities=27%  Similarity=0.260  Sum_probs=17.6

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             02599999999999998612444588
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTENTTK   27 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~~~~   27 (195)
                      |||.+..+++.++++..++.+.+.+.
T Consensus         1 Mk~l~~~~l~~~~~~~~~~~~pA~Aa   26 (111)
T PRK13697          1 MKKILKLVLLTLLLLTFAFTSPAFAA   26 (111)
T ss_pred             CHHHHHHHHHHHHHHHHHCCCHHHHH
T ss_conf             97899999999999999803554441


No 98 
>pfam12262 Lipase_bact_N Bacterial virulence factor lipase N-terminal. This domain family is found in bacteria, and is typically between 258 and 271 amino acids in length. There are two conserved sequence motifs: DGT and DGWST. This family is the N-terminal region of bacterial virulence factor lipase. The N-terminal region contains a potential signalling sequence.
Probab=63.55  E-value=5.6  Score=19.58  Aligned_cols=24  Identities=13%  Similarity=0.195  Sum_probs=16.9

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             025999999999999986124445
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTENT   25 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~~   25 (195)
                      |||+|+..++..++.+++|+....
T Consensus         1 MKk~~l~~~i~SAL~LaGCg~~s~   24 (269)
T pfam12262         1 MKKKFLALLLASALLLAGCGDDTE   24 (269)
T ss_pred             CCHHHHHHHHHHHHHHCCCCCCCC
T ss_conf             924799999999864111579965


No 99 
>PRK12473 hypothetical protein; Provisional
Probab=62.19  E-value=12  Score=17.67  Aligned_cols=43  Identities=12%  Similarity=0.291  Sum_probs=26.8

Q ss_pred             CCCCCEEEECCCCHHHHHHHHHHHHHHC--------------CCCCCCCCHHHHHHHHH
Q ss_conf             4588089981899899999999999875--------------98621000013566765
Q gi|254780563|r   24 NTTKYLTLYTDQNQSVMLPIIHSFEERT--------------GVKISPIYTSSIQRPPI   68 (195)
Q Consensus        24 ~~~~~lvVYs~~~~~~~~~~~~~Fek~t--------------gIkV~~~~~~~~~~~~~   68 (195)
                      ..++-+++|.  ++..+.++++...+++              |-+|-+...++.+.+..
T Consensus        28 epANGvli~G--dE~~~~~Iid~yK~~~ke~e~f~vK~g~~~~~kVLim~ksTAe~miK   84 (193)
T PRK12473         28 EKANGFVLYG--DEEQVQQIMDKYKDEVKSKDFYKMKMGTLEGKKVLVMDKTTAEKMVK   84 (193)
T ss_pred             CCCCEEEEEE--CHHHHHHHHHHHHHHHHHHHEEEEEEEEECCCEEEEEECHHHHHHHH
T ss_conf             8987799996--56888999998777653300267898667781799983189999987


No 100
>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=61.69  E-value=12  Score=17.61  Aligned_cols=124  Identities=11%  Similarity=-0.024  Sum_probs=59.4

Q ss_pred             CCCCCCCEEE-E-CCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCEEEECCHHHHHHHHHHHCCCCC-C
Q ss_conf             4445880899-8-18998999999999998759862100001356676521066655750422332343310000123-4
Q gi|254780563|r   22 TENTTKYLTL-Y-TDQNQSVMLPIIHSFEERTGVKISPIYTSSIQRPPITQGSPVDVIITKDETSLALNEDLLHKLPA-H   98 (195)
Q Consensus        22 ~~~~~~~lvV-Y-s~~~~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~~~~~~~~~d~~~~~d~~~l~~~~~~l~~~~~-~   98 (195)
                      .+++.++|+| + ++.+......+.+.--++.|.+|+++..+.............|++...=.+.   ....+.++.. .
T Consensus         3 ~~a~~~~V~i~~~~W~s~~~~t~v~~~iLE~~GY~Ve~~~~~~~~~~~~la~GdiDv~~e~W~p~---~~~~~~~~~~~g   79 (290)
T TIGR03414         3 EPASCKTVRFADVGWTDITATTALASVLLEGLGYQPKVTLLSVPVTYAGLKDGDLDVFLGNWMPA---MEPDIKPYLESG   79 (290)
T ss_pred             CHHCCCCEEEEECCCCHHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHCCCCEEEEECCCCC---CHHHHHHHHHCC
T ss_conf             71009966996068648999999999999974996489967749999999769970787111478---577899886369


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCEEEEEEEHHHHCCCCCCCCHHHHCC--HHHCCEEEECCCCCC
Q ss_conf             22234720001222223443450588873344013445578888408--667685996289830
Q gi|254780563|r   99 LIKKNSFVLKNENKKLMRISFDTQVLAYSTKRIKIADLPKSVFDLTN--AQWKKRLSIAPNNIS  160 (195)
Q Consensus        99 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~P~sw~DL~~--p~~kG~i~~~~~~~s  160 (195)
                      ....+-..+          .....++.+ ++.+.... .+||.||.+  ..++|+|.--+++..
T Consensus        80 ~v~~lg~~~----------~~a~~g~~V-P~Yv~d~~-l~si~DL~~~~~~f~g~i~gi~~G~~  131 (290)
T TIGR03414        80 SVEVLGPNL----------EGAKYTLAV-PTYVADAG-LKSFADIAKFKDKLDGKIYGIEPGND  131 (290)
T ss_pred             CEEECCCCC----------CCCEEEEEE-CHHHHHCC-CCCHHHHHHCHHHCCCCEECCCCCCC
T ss_conf             689835666----------786378985-41477659-99999998586752997613679984


No 101
>COG5510 Predicted small secreted protein [Function unknown]
Probab=61.56  E-value=7.3  Score=18.93  Aligned_cols=20  Identities=35%  Similarity=0.438  Sum_probs=9.5

Q ss_pred             CCHHHHHHHH-HHH-HHHHHHH
Q ss_conf             9025999999-999-9999861
Q gi|254780563|r    1 MFKRTIYTYL-LLL-CGFTEAF   20 (195)
Q Consensus         1 mmkk~~~~~l-~l~-~~~~~~~   20 (195)
                      ||||.++..+ +++ +.++++|
T Consensus         1 mmk~t~l~i~~vll~s~llaaC   22 (44)
T COG5510           1 MMKKTILLIALVLLASTLLAAC   22 (44)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHH
T ss_conf             9048999999999999999886


No 102
>TIGR01902 dapE-lys-deAc N-acetyl-ornithine/N-acetyl-lysine deacetylase; InterPro: IPR010175   This clade of mainly archaeal and related bacterial species contains two characterised enzymes, an deacetylase with specificity for both N-acetyl-ornithine and N-acetyl-lysine from Thermus  which is found within a lysine biosynthesis operon, and a fusion protein with acetyl-glutamate kinase (an enzyme of ornithine biosynthesis) from Lactobacillus. It is possible that all of the sequences within this clade have dual specificity, or that a mix of specificities have evolved within this clade.; GO: 0008270 zinc ion binding, 0016811 hydrolase activity acting on carbon-nitrogen (but not peptide) bonds in linear amides, 0050897 cobalt ion binding, 0009085 lysine biosynthetic process, 0005737 cytoplasm.
Probab=60.75  E-value=7.8  Score=18.76  Aligned_cols=45  Identities=13%  Similarity=0.190  Sum_probs=32.4

Q ss_pred             CEEEECC-CCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCC
Q ss_conf             0899818-99899999999999875986210000135667652106
Q gi|254780563|r   28 YLTLYTD-QNQSVMLPIIHSFEERTGVKISPIYTSSIQRPPITQGS   72 (195)
Q Consensus        28 ~lvVYs~-~~~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~~~~~~~   72 (195)
                      =|.|||. .+|+.....+++..+++|||.+++....+-....+++.
T Consensus         6 ~l~IyspS~~E~~~a~fl~~~~~~~g~k~e~iD~~~n~~l~~g~g~   51 (352)
T TIGR01902         6 LLEIYSPSGKEEEAAKFLEELKKELGLKAEFIDEAGNVILKKGDGG   51 (352)
T ss_pred             CEECCCCCCCHHHHHHHHHHHHHHHCCCEEECCCCCCEEEEECCCC
T ss_conf             7543798711899999999999970883410467474784216885


No 103
>PRK10859 putative transglycosylase; Provisional
Probab=60.42  E-value=13  Score=17.48  Aligned_cols=41  Identities=15%  Similarity=0.167  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHHHCCCCCCCCCHHH-HHHHHHHHCCCCCEEEE
Q ss_conf             999999999987598621000013-56676521066655750
Q gi|254780563|r   39 VMLPIIHSFEERTGVKISPIYTSS-IQRPPITQGSPVDVIIT   79 (195)
Q Consensus        39 ~~~~~~~~Fek~tgIkV~~~~~~~-~~~~~~~~~~~~d~~~~   79 (195)
                      .-=++.+.|.+.-|++++++...+ .+.....+...+|+...
T Consensus        66 FEYELak~FA~~LGV~L~i~~~~~~~el~~~L~~G~~DiaAA  107 (507)
T PRK10859         66 LDYELAKQFADYLGVKLKVTVRQNISQLFDDLDNGNADLLAA  107 (507)
T ss_pred             HHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHCCCCCEEEC
T ss_conf             999999999998099179997499999999986799888955


No 104
>COG3015 CutF Uncharacterized lipoprotein NlpE involved in copper resistance [Cell envelope biogenesis, outer membrane / Inorganic ion transport and metabolism]
Probab=59.89  E-value=8.8  Score=18.47  Aligned_cols=33  Identities=15%  Similarity=0.173  Sum_probs=20.0

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCC-CCC---EEEECC
Q ss_conf             9025999999999999986124445-880---899818
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFSTENT-TKY---LTLYTD   34 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~~~~-~~~---lvVYs~   34 (195)
                      ||||.|++.+.++ +.+++|...++ +++   ..+|-+
T Consensus         1 mvkk~i~tl~a~~-l~l~gcnnr~~~~gt~v~k~v~Lg   37 (178)
T COG3015           1 MVKKAIVTLMAVI-LTLMGCNNRAEKDGTWVMKEVYLG   37 (178)
T ss_pred             CHHHHHHHHHHHH-HHHHCCCCHHHCCCCEEEEEEEEC
T ss_conf             9078999999999-998457763322675688888750


No 105
>COG0715 TauA ABC-type nitrate/sulfonate/bicarbonate transport systems, periplasmic components [Inorganic ion transport and metabolism]
Probab=58.93  E-value=14  Score=17.33  Aligned_cols=42  Identities=12%  Similarity=0.131  Sum_probs=21.3

Q ss_pred             HHHHHHHCCC-CCCCCCHHHHHHHH-HHHCCCCCEE--EECCHHHH
Q ss_conf             9999987598-62100001356676-5210666557--50422332
Q gi|254780563|r   44 IHSFEERTGV-KISPIYTSSIQRPP-ITQGSPVDVI--ITKDETSL   85 (195)
Q Consensus        44 ~~~Fek~tgI-kV~~~~~~~~~~~~-~~~~~~~d~~--~~~d~~~l   85 (195)
                      .+.|=++.|+ +|+++......... ..-....|..  ...+...+
T Consensus        51 ~kG~f~~~Gl~~V~~~~~~~~~~~~~~l~~G~~D~a~~~~~~~~~~   96 (335)
T COG0715          51 EKGFFKKEGLDDVELVEFTGGAPVLEALAAGALDFAVYYTGDTPLI   96 (335)
T ss_pred             HCCHHHHCCCCEEEEEECCCCHHHHHHHHCCCCCEEEECCCCHHHH
T ss_conf             7891777499758997079845799999769988874237855999


No 106
>COG4594 FecB ABC-type Fe3+-citrate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=58.40  E-value=11  Score=17.88  Aligned_cols=25  Identities=36%  Similarity=0.335  Sum_probs=17.7

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             9025999999999999986124445
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFSTENT   25 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~~~~   25 (195)
                      |++-.|..+|++++++.++|++...
T Consensus         3 ~~~~~~i~~lll~lllva~C~~s~~   27 (310)
T COG4594           3 MKKTAIILTLLLLLLLVAACSSSDN   27 (310)
T ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             5035999999999999977147676


No 107
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=57.84  E-value=15  Score=17.22  Aligned_cols=57  Identities=14%  Similarity=0.184  Sum_probs=39.5

Q ss_pred             CCCCCCEEEECCC--CHHHHHHHHHHHHHHC-CCCCCCCCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             4458808998189--9899999999999875-9862100001356676521066655750
Q gi|254780563|r   23 ENTTKYLTLYTDQ--NQSVMLPIIHSFEERT-GVKISPIYTSSIQRPPITQGSPVDVIIT   79 (195)
Q Consensus        23 ~~~~~~lvVYs~~--~~~~~~~~~~~Fek~t-gIkV~~~~~~~~~~~~~~~~~~~d~~~~   79 (195)
                      ....+++.|....  ......+++..|.+++ +|++++..+...+..........|+.++
T Consensus        91 ~~~~G~l~Ig~~~~~~~~~lp~~l~~f~~~~P~v~i~i~~~~~~~~~~~l~~g~~D~~i~  150 (302)
T PRK09791         91 GQLAGQINIGMGASISRSLMPAVISRFHQQHPQVKVRIMEGQLVSMINELRQGELDFTIN  150 (302)
T ss_pred             CCCCCEEEEEECHHHHHHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHCCCCCEEEE
T ss_conf             676633999862688987119999999998879779999899999999998799778996


No 108
>cd01477 vWA_F09G8-8_type VWA F09G8.8 type: Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of fold. The vWA domain, since its discovery, has drawn great interest because of its widespread occurrence and its involvement in a wide variety of important cellular functions. These include basal membrane formation, cell migration, cell differentiation, adhesion, haemostasis, signaling, chromosomal stability, malignant transformation and in immune defenses  In integrins these domains form heterodimers while in vWF it forms multimers. There are different interaction surfaces of this domain as seen by the various molecules it complexes with. Ligand binding in most cases is mediated by the presence of a metal ion dependent adhesion site termed as the MIDAS motif that is a characteristic feature of mo
Probab=57.59  E-value=11  Score=17.92  Aligned_cols=86  Identities=16%  Similarity=0.107  Sum_probs=41.7

Q ss_pred             CEEEECCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEHHHHCCCCC--CCCHHHHCCHHHCCEE
Q ss_conf             55750422332343310000123422234720001222223443450588873344013445--5788884086676859
Q gi|254780563|r   75 DVIITKDETSLALNEDLLHKLPAHLIKKNSFVLKNENKKLMRISFDTQVLAYSTKRIKIADL--PKSVFDLTNAQWKKRL  152 (195)
Q Consensus        75 d~~~~~d~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~n~~~~~~~~~--P~sw~DL~~p~~kG~i  152 (195)
                      |++...|....+...|+.+-. .....-....-+..-++--+-.-+...+.||.+.....++  .+||.||.+--+.-..
T Consensus        21 DVv~VVD~S~~mt~~gl~~V~-~~I~s~f~~~t~iGt~~~~pr~TRVGlVTYn~~AtvvAdLn~~~S~ddl~~~i~~~l~   99 (193)
T cd01477          21 DIVFVVDNSKGMTQGGLWQVR-ATISSLFGSSSQIGTDYDDPRSTRVGLVTYNSNATVVADLNDLQSFDDLYSQIQGSLT   99 (193)
T ss_pred             EEEEEEECCCCCCCCCHHHHH-HHHHHHHHCCCCCCCCCCCCCCEEEEEEEECCCCEEEECCCCCCCHHHHHHHHHHHHC
T ss_conf             899999678765621099999-9999997135403578899873389999967874598634545657889999988751


Q ss_pred             EECCCCCCH
Q ss_conf             962898304
Q gi|254780563|r  153 SIAPNNISF  161 (195)
Q Consensus       153 ~~~~~~~s~  161 (195)
                      -..++..++
T Consensus       100 ~vsss~~Sy  108 (193)
T cd01477         100 DVSSTNASY  108 (193)
T ss_pred             CCCCCCHHH
T ss_conf             466663127


No 109
>PRK09408 ompX outer membrane protein X; Provisional
Probab=57.08  E-value=12  Score=17.72  Aligned_cols=53  Identities=15%  Similarity=0.100  Sum_probs=27.4

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCEEE-ECCCCHHHHHHHHHHHHH-HCCCCCCCCCHH
Q ss_conf             025999999999999986124445880899-818998999999999998-759862100001
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTENTTKYLTL-YTDQNQSVMLPIIHSFEE-RTGVKISPIYTS   61 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~~~~~lvV-Ys~~~~~~~~~~~~~Fek-~tgIkV~~~~~~   61 (195)
                      |||++..+++...+....+++.+...+|.+ |.-..       ++.|.. -.|+.+++++.-
T Consensus         1 mkk~~~~s~~~~~~~~~a~~a~A~~sTvS~GYAQs~-------~~~~~n~l~G~NlKYrYE~   55 (171)
T PRK09408          1 MKKIACLSALAAVLAFTAGTAVAATSTVTGGYAQSD-------AQGVANKMGGFNLKYRYEE   55 (171)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEC-------CCCCCCCCCCEEEEEEEEE
T ss_conf             922478999999988566666425766987886420-------0134678674488876673


No 110
>PRK13618 psbV cytochrome c-550; Provisional
Probab=57.08  E-value=8.8  Score=18.46  Aligned_cols=59  Identities=12%  Similarity=0.014  Sum_probs=30.5

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCC-----CCCEEEE-CC------CCHHHHHHHHHHHHHHCC-CCCCCCC
Q ss_conf             9025999999999999986124445-----8808998-18------998999999999998759-8621000
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFSTENT-----TKYLTLY-TD------QNQSVMLPIIHSFEERTG-VKISPIY   59 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~~~~-----~~~lvVY-s~------~~~~~~~~~~~~Fek~tg-IkV~~~~   59 (195)
                      ||||.|+.++..++++.-...+.+.     +++.+|= +.      .+.+.+..=.+-|...++ +.+--+.
T Consensus         1 M~kr~i~~~va~v~~~~q~~~~~a~A~elde~trTVpln~~G~tv~ls~~q~k~GkrlFn~~C~~CH~gG~T   72 (163)
T PRK13618          1 MFRRLIGVVVATVLLTFQLIVGSATALELDEATRTVPLNAEGDTVTLSLKQVKEGKRLFQYACAQCHVGGVT   72 (163)
T ss_pred             CHHHHHHHHHHHHHHHHHHCCCHHHHHHCCHHHEEEEECCCCCEEEECHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             938999999999999986404505565436233155307999879976999988999999887641068603


No 111
>pfam01456 Mucin Mucin-like glycoprotein. This family of trypanosomal proteins resemble vertebrate mucins. The protein consists of three regions. The N and C terminii are conserved between all members of the family, whereas the central region is not well conserved and contains a large number of threonine residues which can be glycosylated. Indirect evidence suggested that these genes might encode the core protein of parasite mucins, glycoproteins that were proposed to be involved in the interaction with, and invasion of, mammalian host cells.
Probab=56.39  E-value=8.3  Score=18.61  Aligned_cols=28  Identities=18%  Similarity=0.058  Sum_probs=20.0

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             9025999999999999986124445880
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFSTENTTKY   28 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~~~~~~~   28 (195)
                      ||-++++-.|++++++.+.+.+..++++
T Consensus         1 MmTCRLLCAlLVLALCCCpsVCaTa~ee   28 (143)
T pfam01456         1 MMTCRLLCALLVLALCCCASVCATAQGE   28 (143)
T ss_pred             CHHHHHHHHHHHHHHHCCCCEEECCCCC
T ss_conf             9028899999999997142212313334


No 112
>PRK13619 psbV cytochrome c-550; Provisional
Probab=55.26  E-value=8.6  Score=18.52  Aligned_cols=59  Identities=14%  Similarity=0.029  Sum_probs=31.2

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCC-----CCCEEEE-CC------CCHHHHHHHHHHHHHHCC-CCCCCCC
Q ss_conf             9025999999999999986124445-----8808998-18------998999999999998759-8621000
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFSTENT-----TKYLTLY-TD------QNQSVMLPIIHSFEERTG-VKISPIY   59 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~~~~-----~~~lvVY-s~------~~~~~~~~~~~~Fek~tg-IkV~~~~   59 (195)
                      ||||.|+.++..++++.....+.+.     +++.+|= +.      .+.+.+..=.+-|...++ +.+--+.
T Consensus         1 M~kr~~~~~va~v~~~~q~~v~~a~A~elde~trTVpln~~G~tvtls~eqv~~GkrlFn~~C~~CH~gG~T   72 (161)
T PRK13619          1 MMKRFILVAIATVFFFLQFNVNSANALELTEKTRTIPLNEAGETTTLTSEQATNGQRLFVAECTQCHLQGKT   72 (161)
T ss_pred             CHHHHHHHHHHHHHHHHHCCCCHHHHHHCCHHHEEEECCCCCCEEEECHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             948999999999999851146606665436222156417999869965999988999999887640168603


No 113
>PRK09810 entericidin A; Provisional
Probab=54.90  E-value=7.3  Score=18.92  Aligned_cols=17  Identities=41%  Similarity=0.340  Sum_probs=9.8

Q ss_pred             CCHHHHHHHHHHHHHHH
Q ss_conf             90259999999999999
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFT   17 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~   17 (195)
                      ||||.+...|+....+.
T Consensus         1 mmkrli~lil~~~~ll~   17 (41)
T PRK09810          1 MMKRLIVLVLLASTLLT   17 (41)
T ss_pred             CHHHHHHHHHHHHHHHH
T ss_conf             93899999999999982


No 114
>TIGR01368 CPSaseIIsmall carbamoyl-phosphate synthase, small subunit; InterPro: IPR006274   Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates , . CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate . The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC).   Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain . CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites . The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain.   Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein . The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP . There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia . CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains .    This entry represents the small subunit of the glutamine-dependent form (6.3.5.5 from EC) of carbamoyl phosphate synthase, CPSase II. The small subunit catalyses the hydrolysis of glutamine to ammonia, which in turn used by the large chain to synthesize carbamoyl phosphate. The C-terminal domain of the small subunit of CPSase has glutamine amidotransferase activity. Note that the sequence from the mammalian urea cycle form has lost the active site Cys, resulting in an ammonia-dependent form, CPSase I (6.3.4.16 from EC). CPSases of pyrimidine biosynthesis, arginine biosynthesis, and the urea cycle may be encoded by one or by several genes, depending on the species. ; GO: 0004086 carbamoyl-phosphate synthase activity, 0006807 nitrogen compound metabolic process.
Probab=53.89  E-value=4.1  Score=20.34  Aligned_cols=12  Identities=8%  Similarity=0.293  Sum_probs=4.9

Q ss_pred             CCCCCCCCCHHH
Q ss_conf             598621000013
Q gi|254780563|r   51 TGVKISPIYTSS   62 (195)
Q Consensus        51 tgIkV~~~~~~~   62 (195)
                      .|++|.++-.+.
T Consensus       217 rG~~v~vVP~~~  228 (383)
T TIGR01368       217 RGCEVTVVPYDT  228 (383)
T ss_pred             CCCEEEEECCCC
T ss_conf             698799967899


No 115
>PRK09859 multidrug efflux system protein MdtE; Provisional
Probab=52.63  E-value=14  Score=17.30  Aligned_cols=24  Identities=21%  Similarity=0.268  Sum_probs=12.0

Q ss_pred             CCHH-HHHHHHHHHHHHHHHHCCCC
Q ss_conf             9025-99999999999998612444
Q gi|254780563|r    1 MFKR-TIYTYLLLLCGFTEAFSTEN   24 (195)
Q Consensus         1 mmkk-~~~~~l~l~~~~~~~~~~~~   24 (195)
                      |-|| +++.+|+++++++++|+...
T Consensus         1 m~~k~~~li~ll~~~~lL~gC~~~~   25 (385)
T PRK09859          1 MNRRRKLLIPLLFCGAMLTACDDKS   25 (385)
T ss_pred             CCCHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             9820678999999999995379997


No 116
>cd00614 CGS_like CGS_like: Cystathionine gamma-synthase is a PLP dependent enzyme and catalyzes the committed step of methionine biosynthesis. This pathway is unique to microorganisms and plants, rendering the enzyme an attractive target for the development of antimicrobials and herbicides. This subgroup also includes cystathionine gamma-lyases (CGL), O-acetylhomoserine sulfhydrylases and O-acetylhomoserine thiol lyases. CGL's are very similar to CGS's. Members of this group are widely distributed among all three forms of life.
Probab=52.27  E-value=18  Score=16.69  Aligned_cols=43  Identities=5%  Similarity=0.044  Sum_probs=32.2

Q ss_pred             CCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHH
Q ss_conf             5880899818998999999999998759862100001356676
Q gi|254780563|r   25 TTKYLTLYTDQNQSVMLPIIHSFEERTGVKISPIYTSSIQRPP   67 (195)
Q Consensus        25 ~~~~lvVYs~~~~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~~   67 (195)
                      .++.-+|.+..-+.....+++.+-++.||+|.++.....+...
T Consensus        77 ~~Gd~vl~~~~~Yg~t~~~~~~~l~~~Gi~v~~~d~~d~~~~~  119 (369)
T cd00614          77 KAGDHVVASDDLYGGTYRLFERLLPKLGIEVTFVDPDDPEALE  119 (369)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHCCCEEEEEECCCCHHHHH
T ss_conf             8899999957885239999997786089238976787868899


No 117
>PRK06767 methionine gamma-lyase; Provisional
Probab=51.05  E-value=19  Score=16.58  Aligned_cols=45  Identities=7%  Similarity=-0.096  Sum_probs=31.7

Q ss_pred             CCCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHH
Q ss_conf             458808998189989999999999987598621000013566765
Q gi|254780563|r   24 NTTKYLTLYTDQNQSVMLPIIHSFEERTGVKISPIYTSSIQRPPI   68 (195)
Q Consensus        24 ~~~~~lvVYs~~~~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~~~   68 (195)
                      ..++.-+|.+..-+.....+++.|-++.||+|.++...+.+....
T Consensus        97 l~~Gd~vv~~~~~Yg~T~~l~~~~~~~~gI~~~~~d~~~~~~~~~  141 (386)
T PRK06767         97 LKAGDHIICSNGLYGCTYGFLEVLEEKFMITHSFCDMETEADIEN  141 (386)
T ss_pred             CCCCCEEEECCCCCCCHHHHHHHHHHHCCEEEEEECCCCHHHHHH
T ss_conf             799998998379822346699998887375899968988899997


No 118
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=50.70  E-value=19  Score=16.54  Aligned_cols=58  Identities=19%  Similarity=0.229  Sum_probs=41.0

Q ss_pred             CCCCCCEEEECCCC--HHHHHHHHHHHHHHC-CCCCCCCCHHHHHHHHHHHCCCCCEEEEC
Q ss_conf             44588089981899--899999999999875-98621000013566765210666557504
Q gi|254780563|r   23 ENTTKYLTLYTDQN--QSVMLPIIHSFEERT-GVKISPIYTSSIQRPPITQGSPVDVIITK   80 (195)
Q Consensus        23 ~~~~~~lvVYs~~~--~~~~~~~~~~Fek~t-gIkV~~~~~~~~~~~~~~~~~~~d~~~~~   80 (195)
                      ....++|.|..+..  .....+++..|.++| +|++++..+++.+......+...|+.+..
T Consensus        63 ~~~~G~lri~~~~t~~~~~lp~~l~~f~~~~P~v~~~l~~~~~~~~~~~l~~g~~D~ai~~  123 (269)
T PRK11716         63 PSLSGELSLFCSVTAAYSHLPPILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAA  123 (269)
T ss_pred             CCCCCCEEEEECHHHHHHHCCHHHHHHHHHCCCCEEEEECCCHHHHHHHHHCCCCCEEEEE
T ss_conf             6876626998514887775467899999988894489842899999999986995589993


No 119
>PRK10802 peptidoglycan-associated outer membrane lipoprotein; Provisional
Probab=50.61  E-value=19  Score=16.57  Aligned_cols=23  Identities=17%  Similarity=0.150  Sum_probs=9.6

Q ss_pred             CCHHHHHHHHHHHHHH--HHHHCCC
Q ss_conf             9025999999999999--9861244
Q gi|254780563|r    1 MFKRTIYTYLLLLCGF--TEAFSTE   23 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~--~~~~~~~   23 (195)
                      |+=++++..|++++.+  +++|++.
T Consensus         1 M~~nk~~K~l~ia~~~l~LaACSS~   25 (173)
T PRK10802          1 MQLNKVLKGLMIALPVMAIAACSSN   25 (173)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             9607899999999999999855799


No 120
>PRK08861 cystathionine gamma-synthase; Provisional
Probab=50.49  E-value=19  Score=16.52  Aligned_cols=43  Identities=7%  Similarity=-0.013  Sum_probs=31.5

Q ss_pred             CCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHH
Q ss_conf             5880899818998999999999998759862100001356676
Q gi|254780563|r   25 TTKYLTLYTDQNQSVMLPIIHSFEERTGVKISPIYTSSIQRPP   67 (195)
Q Consensus        25 ~~~~lvVYs~~~~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~~   67 (195)
                      ..+.-+|.+..-+.....+++.+-++.||+|.++...+.+...
T Consensus        90 ~~Gd~iv~~~~~Yg~T~~l~~~~l~~~gi~~~~~d~~d~~~~~  132 (388)
T PRK08861         90 GPDDLIVAPHDCYGGTYRLFNTRANKGDFKVLFVDQSDAAALD  132 (388)
T ss_pred             CCCCEEEECCCCCCCHHHHHHHHHHHCCEEEEEECCCCCHHHH
T ss_conf             8999899868985506899998986288699998999827899


No 121
>PRK13484 putative iron-regulated outer membrane virulence protein; Provisional
Probab=50.31  E-value=19  Score=16.59  Aligned_cols=25  Identities=20%  Similarity=0.073  Sum_probs=14.0

Q ss_pred             CCCCCCCCCCCCCCCCEEEEEEEHH
Q ss_conf             2000122222344345058887334
Q gi|254780563|r  105 FVLKNENKKLMRISFDTQVLAYSTK  129 (195)
Q Consensus       105 ~~~~~~~~~~~~~~~~~~~~~~n~~  129 (195)
                      +.+|-+....+|-.....+|.+-++
T Consensus       135 EVlrGp~S~LYGs~A~GGVINiiTK  159 (682)
T PRK13484        135 EVIRGPMSSLYGSDAIGGVINIITK  159 (682)
T ss_pred             EEEECCCHHCCCCCCCCEEEEEEEC
T ss_conf             9996880103389987569999977


No 122
>PRK10866 outer membrane protein assembly complex subunit YfiO; Provisional
Probab=50.28  E-value=19  Score=16.59  Aligned_cols=25  Identities=24%  Similarity=0.210  Sum_probs=14.3

Q ss_pred             HHHHHHHHHCHHHHHHHHHHHHHCC
Q ss_conf             9999999608699999999986088
Q gi|254780563|r  164 LLNTMEQTPNKTVVQDFIKNITANE  188 (195)
Q Consensus       164 ~~~a~~~~~G~~~~~~~l~~l~~N~  188 (195)
                      ++.+....+=.+.+.+..+=|+.|.
T Consensus       218 l~eaY~~Lgl~~~A~~~~~vL~~N~  242 (243)
T PRK10866        218 MENAYRQMQLNAQADKVAKIIAANS  242 (243)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHC
T ss_conf             9999998699789999999996126


No 123
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=49.99  E-value=20  Score=16.48  Aligned_cols=55  Identities=18%  Similarity=0.181  Sum_probs=35.7

Q ss_pred             CCCCEEEECC--CCHHHHHHHHHHHHHHC-CCCCCCCCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             5880899818--99899999999999875-9862100001356676521066655750
Q gi|254780563|r   25 TTKYLTLYTD--QNQSVMLPIIHSFEERT-GVKISPIYTSSIQRPPITQGSPVDVIIT   79 (195)
Q Consensus        25 ~~~~lvVYs~--~~~~~~~~~~~~Fek~t-gIkV~~~~~~~~~~~~~~~~~~~d~~~~   79 (195)
                      ..++|.|-++  .......+++..|.+++ +|+|++..+++.+......+...|+.+.
T Consensus        91 ~~G~l~Ig~~~~~~~~~lp~~l~~f~~~~P~v~i~l~~~~~~~~~~~L~~g~~Dl~i~  148 (308)
T PRK12683         91 DSGRLTVATTHTQARYALPKVVRQFTEVFPKVHLALRQGSPQEIAEMLLNGEADIGIA  148 (308)
T ss_pred             CCCEEEECCCCHHHHHCCCHHHHHHHHHCCCCEEEEEECCHHHHHHHHHCCCCCEEEC
T ss_conf             7762420013201120168466899987899669996078699999997799778806


No 124
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=49.17  E-value=20  Score=16.40  Aligned_cols=41  Identities=20%  Similarity=0.223  Sum_probs=23.9

Q ss_pred             HHHHHHHHHHHHHC-CCCCCCCCHHHHHHHHHHHCCCCCEEE
Q ss_conf             99999999999875-986210000135667652106665575
Q gi|254780563|r   38 SVMLPIIHSFEERT-GVKISPIYTSSIQRPPITQGSPVDVII   78 (195)
Q Consensus        38 ~~~~~~~~~Fek~t-gIkV~~~~~~~~~~~~~~~~~~~d~~~   78 (195)
                      ....+++..|.+++ +|++++..+...+.....+....|+.+
T Consensus       110 ~~lp~~l~~f~~~~P~v~i~l~~~~~~~~~~~l~~g~~D~~i  151 (312)
T PRK10341        110 TFMSDMINKFKEVFPKAQVSMYEAQLSSFLPAIRDGRLDFAI  151 (312)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHCCCCEEEE
T ss_conf             999999999999888977999989999999999669861999


No 125
>PRK03757 hypothetical protein; Provisional
Probab=48.93  E-value=13  Score=17.54  Aligned_cols=16  Identities=25%  Similarity=0.220  Sum_probs=8.6

Q ss_pred             CHHHHHHHHHHHHHHH
Q ss_conf             0259999999999999
Q gi|254780563|r    2 FKRTIYTYLLLLCGFT   17 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~   17 (195)
                      |||.++.+++.+++++
T Consensus         1 mkk~~l~~~l~a~~~~   16 (191)
T PRK03757          1 MKKTLLGLTLGSLLFS   16 (191)
T ss_pred             CCHHHHHHHHHHHHHH
T ss_conf             9043999999999863


No 126
>PRK08248 O-acetylhomoserine aminocarboxypropyltransferase; Validated
Probab=48.85  E-value=20  Score=16.37  Aligned_cols=44  Identities=5%  Similarity=-0.050  Sum_probs=30.9

Q ss_pred             CCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHH
Q ss_conf             58808998189989999999999987598621000013566765
Q gi|254780563|r   25 TTKYLTLYTDQNQSVMLPIIHSFEERTGVKISPIYTSSIQRPPI   68 (195)
Q Consensus        25 ~~~~lvVYs~~~~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~~~   68 (195)
                      .++.-+|.+..-+.....+++.+-++.||+|.++.....+....
T Consensus       101 ~~Gdhiv~~~~~YggT~~l~~~~l~~~Gi~v~~vD~~d~~~~~~  144 (431)
T PRK08248        101 SAGDEIVSSSSLYGGTYNLFAHTLPKLGITVKFVDPSDPENFEA  144 (431)
T ss_pred             CCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEEECCCCHHHHHH
T ss_conf             77998997278648889998742323887999989977577997


No 127
>PRK01742 tolB translocation protein TolB; Provisional
Probab=47.92  E-value=16  Score=17.01  Aligned_cols=17  Identities=18%  Similarity=0.471  Sum_probs=9.2

Q ss_pred             CCHHHHHHHHHHHHHHH
Q ss_conf             90259999999999999
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFT   17 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~   17 (195)
                      ||||.+..+++++++++
T Consensus         3 m~~~~~~~~~~l~~~~~   19 (430)
T PRK01742          3 LLKRLVSVFAVLFAVIS   19 (430)
T ss_pred             HHHHHHHHHHHHHHHHH
T ss_conf             69999999999999987


No 128
>PRK10959 outer membrane protein W; Provisional
Probab=47.32  E-value=18  Score=16.68  Aligned_cols=29  Identities=7%  Similarity=0.045  Sum_probs=15.1

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCEEE
Q ss_conf             025999999999999986124445880899
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTENTTKYLTL   31 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~~~~~lvV   31 (195)
                      |||..+..+++. ++++..+.+.+++..+|
T Consensus         1 Mkk~~~a~~~~~-a~~s~~A~A~~aGd~~v   29 (212)
T PRK10959          1 MKKLTVAALAVA-TLLSGSAFAHEAGDFIV   29 (212)
T ss_pred             CCHHHHHHHHHH-HHHHHHHHHHHCCCEEE
T ss_conf             937899999999-87516778832799899


No 129
>TIGR03502 lipase_Pla1_cef extracellular lipase, Pla-1/cef family. Members of this protein family are bacterial lipoproteins largely from the Gammaproteobacteria. Characterized members are expressed in extracellularly and have esterase activity. Members include the lipase Pla-1 from Aeromonas hydrophila (AF092033) and CHO cell elongation factor (cef) from Vibrio hollisae
Probab=47.05  E-value=16  Score=16.95  Aligned_cols=21  Identities=5%  Similarity=-0.021  Sum_probs=14.8

Q ss_pred             CHHHHHHHHHHHHHHHHHHCC
Q ss_conf             025999999999999986124
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFST   22 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~   22 (195)
                      |||.|+..++..++.+.+|+.
T Consensus         1 MKk~~l~~~iasal~LagCGg   21 (792)
T TIGR03502         1 MKKLLLSLAIASALGLAGCGD   21 (792)
T ss_pred             CCHHHHHHHHHHHHHHHCCCC
T ss_conf             933789999999875004578


No 130
>COG3338 Cah Carbonic anhydrase [Inorganic ion transport and metabolism]
Probab=46.95  E-value=7.7  Score=18.81  Aligned_cols=52  Identities=13%  Similarity=0.148  Sum_probs=24.5

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCHHHHHH---HHHHHHH------HCCCCCC
Q ss_conf             02599999999999998612444588089981899899999---9999998------7598621
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTENTTKYLTLYTDQNQSVMLP---IIHSFEE------RTGVKIS   56 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~~~~~lvVYs~~~~~~~~~---~~~~Fek------~tgIkV~   56 (195)
                      |||+.+..+.+.+.+.+++.+.+.+   |-+.+..++.++.   +-..|+.      ++.|.++
T Consensus         1 Mkk~~l~~~~L~~~~~~~~ts~a~~---~~WgY~g~~GPEhWg~L~~df~~C~~Gk~QSPIdI~   61 (250)
T COG3338           1 MKKRFLIVLALGASLIGAETSPAAE---VHWGYTGKEGPEHWGELSPDFEACAEGKNQSPIDIE   61 (250)
T ss_pred             CCEEEEHHHHHHHHHHHHHCCCCCC---CCCCCCCCCCCHHHHHCCCHHHHHHCCCCCCCCCHH
T ss_conf             9423207898766454200264301---014656885805665408424566566647982377


No 131
>TIGR02740 TraF-like TraF-like protein; InterPro: IPR014111   This entry contains TraF-like proteins that are related to the F-type conjugation system pilus assembly proteins TraF (IPR014110 from INTERPRO)and TrbB (IPR014109 from INTERPRO) both of which exhibit a thioredoxin fold . The proteins in this entry have the same length and architecture as TraF, but lack the CXXC-motif found in TrbB that is believed to be responsible for the disulphide isomerase activity..
Probab=46.78  E-value=15  Score=17.20  Aligned_cols=29  Identities=24%  Similarity=0.510  Sum_probs=22.1

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCCCCCHHH
Q ss_conf             89989999999999987598621000013
Q gi|254780563|r   34 DQNQSVMLPIIHSFEERTGVKISPIYTSS   62 (195)
Q Consensus        34 ~~~~~~~~~~~~~Fek~tgIkV~~~~~~~   62 (195)
                      |..=+...++++.|+.+|||+|.-|+.++
T Consensus       207 C~~C~~~~pil~~~~~~YG~~V~pvS~DG  235 (306)
T TIGR02740       207 CPYCHAQAPILKAFEDRYGIEVLPVSVDG  235 (306)
T ss_pred             CCCHHHHHHHHHHHHHHCCCEEEEEEECC
T ss_conf             66226899999999973197089998458


No 132
>CHL00133 psbV photosystem II cytochrome c550; Validated
Probab=46.28  E-value=17  Score=16.82  Aligned_cols=59  Identities=20%  Similarity=0.227  Sum_probs=30.9

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCC-----CCEEEE-CC------CCHHHHHHHHHHHHHHCC-CCCCCCC
Q ss_conf             90259999999999999861244458-----808998-18------998999999999998759-8621000
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFSTENTT-----KYLTLY-TD------QNQSVMLPIIHSFEERTG-VKISPIY   59 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~~~~~-----~~lvVY-s~------~~~~~~~~~~~~Fek~tg-IkV~~~~   59 (195)
                      |+||.++.+.++..++...+...+.+     ++.+|= ..      .+.+.+..=.+-|...++ +.|--+.
T Consensus         1 M~kr~~~~~~~~~~~~~~~~~~~a~A~elde~trTV~l~~~G~tvtls~~q~k~GkrlFn~~C~~CH~GG~T   72 (163)
T CHL00133          1 MFKKSSWLFLLIGFLILVIFSTTASAIELDEATRTVPLDSSGNTVVLTPEQVKRGKRLFNASCGACHVGGIT   72 (163)
T ss_pred             CHHHHHHHHHHHHHHHHHHCCCCHHHHHCCHHHEEEEECCCCCEEEECHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             938999999999999997535615565436434156407999879977999998999999887651168603


No 133
>COG1638 DctP TRAP-type C4-dicarboxylate transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=45.60  E-value=23  Score=16.08  Aligned_cols=60  Identities=27%  Similarity=0.281  Sum_probs=25.8

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCCCEEE-ECC-----CC-HHHHHHHHHHHHHHCC--CCCCCCCHH
Q ss_conf             9025999999999999986124445880899-818-----99-8999999999998759--862100001
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFSTENTTKYLTL-YTD-----QN-QSVMLPIIHSFEERTG--VKISPIYTS   61 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~~~~~~~lvV-Ys~-----~~-~~~~~~~~~~Fek~tg--IkV~~~~~~   61 (195)
                      ||+...+...++++.++++ ++.+++..+++ +++     .+ ......+.+.-+++||  +++++...+
T Consensus         1 ~~~~~~~~~~~~~~~~~~~-~~~a~~~~~~l~~~~~~~~~~p~~~~~~~fa~~v~ekt~G~l~i~vfP~~   69 (332)
T COG1638           1 MMKLLALLLALLLAAAALA-SAAAAAGALVLRFSHVTPEGHPKGKAAKKFAELVEEKTGGRLKIEVFPNS   69 (332)
T ss_pred             CCCHHHHHHHHHHHHHHHH-HHHHHHCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHCCCEEEEEECCCC
T ss_conf             9513789999999999977-77874015488752357998807899999999999871993899976675


No 134
>PRK08474 F0F1 ATP synthase subunit delta; Validated
Probab=44.71  E-value=24  Score=16.00  Aligned_cols=47  Identities=9%  Similarity=0.102  Sum_probs=28.3

Q ss_pred             HHHHHHHHCCCCCCCCEEEECC--CCHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             9999986124445880899818--9989999999999987598621000
Q gi|254780563|r   13 LCGFTEAFSTENTTKYLTLYTD--QNQSVMLPIIHSFEERTGVKISPIY   59 (195)
Q Consensus        13 ~~~~~~~~~~~~~~~~lvVYs~--~~~~~~~~~~~~Fek~tgIkV~~~~   59 (195)
                      +-.|-.........-+.+|+|+  .+++..+.+.+++++++|-+|++..
T Consensus        90 ~~~f~~l~~~~~~~~~a~V~SA~~Ls~~q~~~i~~~L~kk~g~~v~l~~  138 (176)
T PRK08474         90 AKELERQLALKENEYVGVVYSKEELSQETLKKLEEKLSKKFNAKIKLKQ  138 (176)
T ss_pred             HHHHHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHCCEEEEEE
T ss_conf             9999999999779038999879999999999999999998789169996


No 135
>pfam02402 Lysis_col Lysis protein. These small bacterial proteins are required for colicin release and partial cell lysis. This family contains lysis proteins for several different forms of colicin. Bacillus subtilis lytA has been included in this family, the similarity is not highly significant, however it is also a short protein, that is involved in secretion of other proteins (Bateman A pers. obs.).
Probab=44.52  E-value=9.6  Score=18.24  Aligned_cols=21  Identities=24%  Similarity=0.390  Sum_probs=12.3

Q ss_pred             CHHHHHHHHHHHHHHHHHHCC
Q ss_conf             025999999999999986124
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFST   22 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~   22 (195)
                      |||.++..++++.+++++|.+
T Consensus         1 Mkki~~~~i~~~~~~L~aCQa   21 (46)
T pfam02402         1 MKKILFIGILLLTVLLSACQA   21 (46)
T ss_pred             CCEEEEHHHHHHHHHHHHHHH
T ss_conf             924201399999999998555


No 136
>PRK09934 putative fimbrial protein; Provisional
Probab=44.44  E-value=24  Score=15.97  Aligned_cols=29  Identities=7%  Similarity=-0.004  Sum_probs=14.6

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCEEE
Q ss_conf             025999999999999986124445880899
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTENTTKYLTL   31 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~~~~~lvV   31 (195)
                      |||.++..++.+++...++ ++...+..+|
T Consensus         1 mkk~~l~~~~~l~~~~~~~-aa~~~g~g~i   29 (171)
T PRK09934          1 MRRVFIAIFCGLLWSPLSQ-AASPLGEINI   29 (171)
T ss_pred             CHHHHHHHHHHHHHHHHHH-HCCCCCEEEE
T ss_conf             9268999999999863442-1135880589


No 137
>PRK02944 OxaA-like protein precursor; Validated
Probab=44.33  E-value=21  Score=16.31  Aligned_cols=23  Identities=17%  Similarity=0.183  Sum_probs=10.6

Q ss_pred             CHHHHHHHHH--HHHHHHHHHCCCC
Q ss_conf             0259999999--9999998612444
Q gi|254780563|r    2 FKRTIYTYLL--LLCGFTEAFSTEN   24 (195)
Q Consensus         2 mkk~~~~~l~--l~~~~~~~~~~~~   24 (195)
                      |||++...+.  .++.++++|+..+
T Consensus         1 mkk~~~~~~~~~~~~~~lsgC~~~~   25 (255)
T PRK02944          1 MKKKLGLLAMVVALMAILAGCSEVN   25 (255)
T ss_pred             CCHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             9289999999999999996246889


No 138
>PRK07504 O-succinylhomoserine sulfhydrylase; Reviewed
Probab=44.26  E-value=24  Score=15.96  Aligned_cols=43  Identities=5%  Similarity=-0.027  Sum_probs=32.3

Q ss_pred             CCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHH
Q ss_conf             5880899818998999999999998759862100001356676
Q gi|254780563|r   25 TTKYLTLYTDQNQSVMLPIIHSFEERTGVKISPIYTSSIQRPP   67 (195)
Q Consensus        25 ~~~~lvVYs~~~~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~~   67 (195)
                      +++.-+|.+..-+.....+++.+-++.||+|.++.....+...
T Consensus       102 ~~Gdhiv~~~~~Yg~t~~l~~~~l~~~Gi~~~~vd~~d~~~~~  144 (397)
T PRK07504        102 KAGDHVVAARALFGSCRYVVETLLPRYGIESTLVDGLDLDNWE  144 (397)
T ss_pred             CCCCEEEECCCCCHHHHHHHHHHHHCCCEEEEEECCCCHHHHH
T ss_conf             8999898558875569999999986078589987898858899


No 139
>PHA00019 phage assembly protein
Probab=43.09  E-value=25  Score=15.85  Aligned_cols=51  Identities=24%  Similarity=0.235  Sum_probs=26.3

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             9025999999999999986124445880899818998999999999998759862100
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFSTENTTKYLTLYTDQNQSVMLPIIHSFEERTGVKISPI   58 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~~~~~~~lvVYs~~~~~~~~~~~~~Fek~tgIkV~~~   58 (195)
                      |||+.|...|+.++.+.+. +    .+.+.+.=  ....+..+++.+.+.+|..+.+-
T Consensus         1 ~~~~~~~~~~~~~~~~~~~-s----~~~isl~f--~d~dIr~vl~~la~~tg~NiVi~   51 (428)
T PHA00019          1 MIKSIFAKMLLFLLMFLSF-S----SFALPVEL--NNSPIREFVSWYSQQTGKSVVLG   51 (428)
T ss_pred             CHHHHHHHHHHHHHHHHCC-C----CCEEEEEE--ECCCHHHHHHHHHHHHCCEEEEC
T ss_conf             9274899999999877405-6----74477885--08779999999998449739989


No 140
>COG0505 CarA Carbamoylphosphate synthase small subunit [Amino acid transport and metabolism / Nucleotide transport and metabolism]
Probab=42.69  E-value=22  Score=16.16  Aligned_cols=35  Identities=20%  Similarity=0.273  Sum_probs=16.6

Q ss_pred             HHHHHHHHCCCCC-CCCCHHHHHHHHHHHCCCCCEE
Q ss_conf             9999998759862-1000013566765210666557
Q gi|254780563|r   43 IIHSFEERTGVKI-SPIYTSSIQRPPITQGSPVDVI   77 (195)
Q Consensus        43 ~~~~Fek~tgIkV-~~~~~~~~~~~~~~~~~~~d~~   77 (195)
                      -+++|=|+.||-- .-+....+-+.+++++.....+
T Consensus        96 sL~~~Lk~~gipgI~GIDTRaLtr~iR~~G~m~~~I  131 (368)
T COG0505          96 SLDEYLKEEGIPGIAGIDTRALTRKIREKGAMKGVI  131 (368)
T ss_pred             CHHHHHHHCCCCCEECCCHHHHHHHHHHCCCCCEEE
T ss_conf             899999976997750551899999998669731376


No 141
>PRK12701 flgH flagellar basal body L-ring protein; Reviewed
Probab=41.08  E-value=27  Score=15.69  Aligned_cols=22  Identities=9%  Similarity=-0.065  Sum_probs=16.4

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             0259999999999999861244
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTE   23 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~   23 (195)
                      |+|..+.+.+++++++++|++.
T Consensus         1 m~r~~~~~~~la~~lL~GC~~~   22 (230)
T PRK12701          1 MNRLNIAVSCLATALLFGCEAL   22 (230)
T ss_pred             CCHHHHHHHHHHHHHHHCCCCC
T ss_conf             9258999999999997556688


No 142
>TIGR03302 OM_YfiO outer membrane assembly lipoprotein YfiO. Members of this protein family include YfiO, a near-essential protein of the outer membrane, part of a complex involved in protein insertion into the bacterial outer membrane. Many proteins in this family are annotated as ComL, based on the involvement of this protein in natural transformation with exogenous DNA in Neisseria gonorrhoeae. This protein family shows sequence similarity to, but is distinct from, the tol-pal system protein YbgF (TIGR02795).
Probab=40.99  E-value=27  Score=15.66  Aligned_cols=24  Identities=21%  Similarity=0.138  Sum_probs=15.8

Q ss_pred             HHHHHHHHHCHHHHHHHHHHHHHC
Q ss_conf             999999960869999999998608
Q gi|254780563|r  164 LLNTMEQTPNKTVVQDFIKNITAN  187 (195)
Q Consensus       164 ~~~a~~~~~G~~~~~~~l~~l~~N  187 (195)
                      ++.+.....-.+.+.+..+-|..|
T Consensus       209 l~eay~~lg~~~~A~~~~~~l~~n  232 (235)
T TIGR03302       209 LVEAYLALGLTDLAQDAAAVLGAN  232 (235)
T ss_pred             HHHHHHHCCCHHHHHHHHHHHHHC
T ss_conf             999999869989999999999753


No 143
>PRK10554 outer membrane porin protein C; Provisional
Probab=40.98  E-value=25  Score=15.88  Aligned_cols=32  Identities=16%  Similarity=0.178  Sum_probs=16.0

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCC-----CCCCEEEECC
Q ss_conf             02599999999999998612444-----5880899818
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTEN-----TTKYLTLYTD   34 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~-----~~~~lvVYs~   34 (195)
                      |||++++.++.+++++ +.+.++     .-.+|-||..
T Consensus         1 MKk~~LA~~i~all~a-g~a~AAeVYn~Dgn~Ldl~Gr   37 (373)
T PRK10554          1 MKVKVLSLLVPALLVA-GAANAAEIYNKDGNKLDLYGK   37 (373)
T ss_pred             CCHHHHHHHHHHHHHH-CCCCEEEEEECCCCEEEEEEE
T ss_conf             9540899999999860-753179999679988976308


No 144
>COG1512 Beta-propeller domains of methanol dehydrogenase type [General function prediction only]
Probab=40.94  E-value=27  Score=15.65  Aligned_cols=27  Identities=15%  Similarity=0.347  Sum_probs=19.0

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCCCCCH
Q ss_conf             899899999999999875986210000
Q gi|254780563|r   34 DQNQSVMLPIIHSFEERTGVKISPIYT   60 (195)
Q Consensus        34 ~~~~~~~~~~~~~Fek~tgIkV~~~~~   60 (195)
                      .......+.-++++|++++-+|.++.-
T Consensus        45 ~~e~~~Leq~l~~L~~kt~~QiaVv~v   71 (271)
T COG1512          45 AAERGALEQQLADLEQKTGAQIAVVTV   71 (271)
T ss_pred             HHHHHHHHHHHHHHHHCCCCEEEEEEE
T ss_conf             557778999999997355861899994


No 145
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=40.73  E-value=28  Score=15.64  Aligned_cols=55  Identities=11%  Similarity=0.033  Sum_probs=34.7

Q ss_pred             CCCCCEEEEC--CCCHHHHHHHHHHHHHHC-CCCCCCCCHHHHHHHHHHHCCCCCEEE
Q ss_conf             4588089981--899899999999999875-986210000135667652106665575
Q gi|254780563|r   24 NTTKYLTLYT--DQNQSVMLPIIHSFEERT-GVKISPIYTSSIQRPPITQGSPVDVII   78 (195)
Q Consensus        24 ~~~~~lvVYs--~~~~~~~~~~~~~Fek~t-gIkV~~~~~~~~~~~~~~~~~~~d~~~   78 (195)
                      ...++|.|=.  +.......+++..|.+++ +|++.+..+.+.+..........|+.+
T Consensus        88 ~~~G~lrig~~~~~~~~llp~~l~~f~~~~P~v~i~l~~~~~~~l~~~l~~g~~D~~i  145 (305)
T PRK11151         88 TMSGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAI  145 (305)
T ss_pred             CCCCEEEEEEHHHHHHHCCCHHHHHHHHCCCCCEEEEEECCCHHHHHHHHCCCCCEEE
T ss_conf             8764143110222333238277999862389837999988757778786578853799


No 146
>PRK07503 methionine gamma-lyase; Provisional
Probab=40.65  E-value=28  Score=15.63  Aligned_cols=44  Identities=9%  Similarity=0.020  Sum_probs=31.9

Q ss_pred             CCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHH
Q ss_conf             58808998189989999999999987598621000013566765
Q gi|254780563|r   25 TTKYLTLYTDQNQSVMLPIIHSFEERTGVKISPIYTSSIQRPPI   68 (195)
Q Consensus        25 ~~~~lvVYs~~~~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~~~   68 (195)
                      .++.-+|.+..-+.....+++.+-++.||+|.++...+.+...+
T Consensus       102 ~~Gdhiv~~~~~YGgt~~l~~~~l~~~Gi~~~~vd~~d~~~~~~  145 (403)
T PRK07503        102 RPGDEVIVGRTLYGCTFAFLHHGLGEFGVKVRHVDLTDAKALKA  145 (403)
T ss_pred             CCCCEEEECCCCCCCHHHHHHHHHHHCCEEEEEECCCCHHHHHH
T ss_conf             99998997688753289999844631775999868989899997


No 147
>COG2854 Ttg2D ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=40.38  E-value=27  Score=15.73  Aligned_cols=23  Identities=22%  Similarity=0.496  Sum_probs=13.1

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             90259999999999999861244
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFSTE   23 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~~   23 (195)
                      ||+|.++...+++.++++..+..
T Consensus         2 ~m~k~l~~~~ll~~a~a~~~~~~   24 (202)
T COG2854           2 MMKKSLTILALLVIAFASSLAAA   24 (202)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             38999999999999999888763


No 148
>PRK06460 hypothetical protein; Provisional
Probab=40.28  E-value=28  Score=15.59  Aligned_cols=55  Identities=13%  Similarity=0.055  Sum_probs=33.2

Q ss_pred             CCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             5880899818998999999999998759862100001356676521066655750
Q gi|254780563|r   25 TTKYLTLYTDQNQSVMLPIIHSFEERTGVKISPIYTSSIQRPPITQGSPVDVIIT   79 (195)
Q Consensus        25 ~~~~lvVYs~~~~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~~~~~~~~~d~~~~   79 (195)
                      +++.-+|.+..-+.....+++.+-++.||+|.++.....+...........+++.
T Consensus        82 ~~Gdhiv~~~~~Yg~t~~l~~~~l~~~Gv~v~~~d~~~~~~~~~~~~~~Tklv~~  136 (375)
T PRK06460         82 KPGSSVLIHRDMFGRSYRFFTDFLRNWGVKVEVARPGEENILEKIKNKRYDVVFV  136 (375)
T ss_pred             CCCCEEEECCCCCCCHHHHHHHHHHHCCEEEEEECCCCHHHHHHHCCCCCEEEEE
T ss_conf             8999899717875867999999987378677973899999999734767608999


No 149
>pfam07901 DUF1672 Protein of unknown function (DUF1672). This family is composed of hypothetical bacterial proteins of unknown function.
Probab=40.25  E-value=28  Score=15.59  Aligned_cols=21  Identities=19%  Similarity=0.184  Sum_probs=10.1

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             0259999999999999861244
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTE   23 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~   23 (195)
                      |||+|...++ +++++.+|+..
T Consensus         1 MkK~i~~il~-~~llL~GCs~m   21 (304)
T pfam07901         1 MRKLIKLILI-ATLLLSGCSTT   21 (304)
T ss_pred             CCHHHHHHHH-HHHHHCCCCCC
T ss_conf             9018999999-99997133445


No 150
>PRK10877 thiol:disulfide interchange protein DsbC; Provisional
Probab=40.17  E-value=28  Score=15.58  Aligned_cols=46  Identities=17%  Similarity=0.348  Sum_probs=24.8

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHH
Q ss_conf             025999999999999986124445880899818998999999999998759862100001356
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTENTTKYLTLYTDQNQSVMLPIIHSFEERTGVKISPIYTSSIQ   64 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~~~~~lvVYs~~~~~~~~~~~~~Fek~tgIkV~~~~~~~~~   64 (195)
                      |||.++.+.+++++++.    .+.+         ++   ..+.+.+++ .|++|.-+..+...
T Consensus         1 mkk~l~~~~~l~~~~s~----~a~a---------De---a~i~~~l~k-~g~~v~~V~~sPi~   46 (232)
T PRK10877          1 MKKGFMLFTLLAAAFSG----FAHA---------DD---AAIQQTLAK-LGIQSADIQPSPVA   46 (232)
T ss_pred             CCHHHHHHHHHHHHHHH----HHHC---------CH---HHHHHHHHH-CCCCCCEECCCCCC
T ss_conf             92669999999999862----5243---------79---999999998-39983135568999


No 151
>COG3417 FlgN Collagen-binding surface adhesin SpaP (antigen I/II family) [General function prediction only]
Probab=39.77  E-value=27  Score=15.68  Aligned_cols=22  Identities=41%  Similarity=0.522  Sum_probs=16.1

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             9025999999999999986124
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFST   22 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~   22 (195)
                      |-|.+++..++++++|..+|++
T Consensus         1 mtk~k~~~~il~~al~l~GCs~   22 (200)
T COG3417           1 MTKMKIYASILLLALFLSGCSS   22 (200)
T ss_pred             CCHHHHHHHHHHHHHHHHHCCC
T ss_conf             9257999999999999841136


No 152
>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=39.60  E-value=29  Score=15.53  Aligned_cols=119  Identities=14%  Similarity=0.170  Sum_probs=67.0

Q ss_pred             CCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCHH--HHHHH---HHHHCCCCCEEEECCHH-------HH--H-----
Q ss_conf             880899818998999999999998759862100001--35667---65210666557504223-------32--3-----
Q gi|254780563|r   26 TKYLTLYTDQNQSVMLPIIHSFEERTGVKISPIYTS--SIQRP---PITQGSPVDVIITKDET-------SL--A-----   86 (195)
Q Consensus        26 ~~~lvVYs~~~~~~~~~~~~~Fek~tgIkV~~~~~~--~~~~~---~~~~~~~~d~~~~~d~~-------~l--~-----   86 (195)
                      .+|=|+-|....-+.+.+.+=| ++.||||+|.+.+  +.++.   ...+....||++|.+..       +.  .     
T Consensus       446 ~~ERvLVTTLTKkMAEdLTdYl-~E~Gikv~YLHSeIdt~ER~eiirdLR~G~fDVLVGINLLREGLDlPEVSLVAILDA  524 (667)
T TIGR00631       446 RNERVLVTTLTKKMAEDLTDYL-KELGIKVRYLHSEIDTLERVEIIRDLRLGEFDVLVGINLLREGLDLPEVSLVAILDA  524 (667)
T ss_pred             CCCCEEEEEHHHHHHHHHHHHH-HCCCCEEEEECCHHHHHHHHHHHHHHCCCCCEEEEECCHHHCCCCCHHHHHHHHHCC
T ss_conf             2894899820167788999997-058837987145578999999999844788408860002002465114889976327


Q ss_pred             HHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCEE----------------EEEEEHHHHCCCC-CCCCHHHHCCH
Q ss_conf             433100001234222347200012222234434505----------------8887334401344-55788884086
Q gi|254780563|r   87 LNEDLLHKLPAHLIKKNSFVLKNENKKLMRISFDTQ----------------VLAYSTKRIKIAD-LPKSVFDLTNA  146 (195)
Q Consensus        87 ~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----------------~~~~n~~~~~~~~-~P~sw~DL~~p  146 (195)
                      .++| |.=..-+....+==..|+.+|...-++....                -+.||...-..++ .-|...|.++-
T Consensus       525 DKEG-FLRSerSLIQTIGRAARN~~G~VilYAD~iT~sM~~AI~ET~RRR~~Q~~YNe~HgItP~ti~K~i~~~~~~  600 (667)
T TIGR00631       525 DKEG-FLRSERSLIQTIGRAARNVNGKVILYADKITDSMQKAIEETERRRKIQIAYNEEHGITPQTIRKKIKDILDI  600 (667)
T ss_pred             CCCC-CCCCCCHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHH
T ss_conf             8889-986630278898887525796599972870078999999878889999999975389788540568887777


No 153
>TIGR01420 pilT_fam twitching motility protein; InterPro: IPR006321   These represent the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction . Members of this family may be found in some species that do not have type IV pili but have related structures for DNA uptake and natural transformation. ; GO: 0005524 ATP binding, 0006810 transport.
Probab=39.32  E-value=29  Score=15.51  Aligned_cols=40  Identities=20%  Similarity=0.170  Sum_probs=31.3

Q ss_pred             CCC-CCHHHHCCHHHCCEEEECCCCCCHHH-HHHHHHHHHCHH
Q ss_conf             455-78888408667685996289830499-999999960869
Q gi|254780563|r  135 DLP-KSVFDLTNAQWKKRLSIAPNNISFHR-LLNTMEQTPNKT  175 (195)
Q Consensus       135 ~~P-~sw~DL~~p~~kG~i~~~~~~~s~~~-~~~a~~~~~G~~  175 (195)
                      .+| .-..+|++.+ +|.|.+.-|.+||.+ -++||+.+-++.
T Consensus       113 GLP~~v~~~~a~~~-~GLiLVTGPTGSGKSTTlAsmIDyIN~~  154 (350)
T TIGR01420       113 GLPRPVLRELAERP-RGLILVTGPTGSGKSTTLASMIDYINKN  154 (350)
T ss_pred             CCCHHHHHHHHHCC-CCCEEEECCCCCCHHHHHHHHHHHHHCC
T ss_conf             79878999998366-9938987688986789999999787403


No 154
>PTZ00334 trans-sialidase; Provisional
Probab=38.76  E-value=20  Score=16.41  Aligned_cols=21  Identities=19%  Similarity=0.268  Sum_probs=11.6

Q ss_pred             CHHHHHHHHHHHHH-HHHHHCC
Q ss_conf             02599999999999-9986124
Q gi|254780563|r    2 FKRTIYTYLLLLCG-FTEAFST   22 (195)
Q Consensus         2 mkk~~~~~l~l~~~-~~~~~~~   22 (195)
                      |.|+.|.+.+|+++ ..+||++
T Consensus        39 MSRrvF~SAVLLLlvVmMCCgs   60 (780)
T PTZ00334         39 MSRRVFTSAVLLLLVVMMCCGS   60 (780)
T ss_pred             CCHHHHHHHHHHHHHHHEECCC
T ss_conf             5134467789999998420898


No 155
>PRK13731 conjugal transfer surface exclusion protein TraT; Provisional
Probab=38.58  E-value=20  Score=16.39  Aligned_cols=23  Identities=9%  Similarity=-0.064  Sum_probs=16.8

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             02599999999999998612444
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTEN   24 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~   24 (195)
                      |||.++..++..++++++|++..
T Consensus         3 ~kk~~~~~~~~~~l~lsGC~a~~   25 (243)
T PRK13731          3 TKKLMMVALVSSTLALSGCGAMS   25 (243)
T ss_pred             HHHHHHHHHHHHHHHHCCHHHHH
T ss_conf             37757999999999971568767


No 156
>COG2980 RlpB Rare lipoprotein B [Cell envelope biogenesis, outer membrane]
Probab=37.62  E-value=31  Score=15.35  Aligned_cols=68  Identities=12%  Similarity=0.067  Sum_probs=35.6

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCC--------CCCEEEECCCCH-HHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHH
Q ss_conf             025999999999999986124445--------880899818998-999999999998759862100001356676521
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTENT--------TKYLTLYTDQNQ-SVMLPIIHSFEERTGVKISPIYTSSIQRPPITQ   70 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~~--------~~~lvVYs~~~~-~~~~~~~~~Fek~tgIkV~~~~~~~~~~~~~~~   70 (195)
                      |++....+|+.++.++++|+-.-.        -.++.++++.++ ....++.... ..+||+|.-...+...+.+..+
T Consensus         1 M~~L~~~lL~~a~~~L~aCGFhLRg~~~ip~~l~~l~l~s~d~y~~l~r~vrr~L-~~n~v~vv~~~~~~p~Lri~se   77 (178)
T COG2980           1 MRKLKTLLLLAAVLLLAACGFHLRGTTQIPPELKTLSLESSDPYGPLTRAVRRQL-RLNGVDVVDTAKDVPVLRILSE   77 (178)
T ss_pred             CCCHHHHHHHHHHHHHHHCCEEECCCCCCCCCHHHEEEECCCCCCHHHHHHHHHH-HHCCCEEEECCCCCCEEEECCE
T ss_conf             9005899999999997334534317888994113315543689876899999999-9849645314778607886022


No 157
>PRK08249 cystathionine gamma-synthase; Provisional
Probab=37.51  E-value=31  Score=15.34  Aligned_cols=43  Identities=14%  Similarity=0.092  Sum_probs=31.3

Q ss_pred             CCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHH
Q ss_conf             5880899818998999999999998759862100001356676
Q gi|254780563|r   25 TTKYLTLYTDQNQSVMLPIIHSFEERTGVKISPIYTSSIQRPP   67 (195)
Q Consensus        25 ~~~~lvVYs~~~~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~~   67 (195)
                      .++.-+|.+..-+.....+++.+-++.||+|+++...+.+...
T Consensus       101 ~~Gd~vv~~~~~YggT~~l~~~~l~~~Gi~v~fvd~~d~~~~~  143 (398)
T PRK08249        101 SPGDRVVSIKDTYGGTNKIFEEFLPRMGVDVTLCETGDHEQIE  143 (398)
T ss_pred             CCCCEEEECCCCCHHHHHHHHHHHCCCCEEEEEECCCCHHHHH
T ss_conf             8999899818984379999997601598699987999869999


No 158
>TIGR02086 IPMI_arch 3-isopropylmalate dehydratase, large subunit; InterPro: IPR011826   3-isopropylmalate dehydratase (or isopropylmalate isomerase; 4.2.1.33 from EC) catalyses the stereo-specific isomerisation of 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. This enzyme performs the second step in the biosynthesis of leucine, and is present in most prokaryotes and many fungal species. The prokaryotic enzyme is a heterodimer composed of a large (LeuC) and small (LeuD) subunit, while the fungal form is a monomeric enzyme. Both forms of isopropylmalate are related and are part of the larger aconitase family . Aconitases are mostly monomeric proteins which share four domains in common and contain a single, labile [4Fe-4S] cluster. Three structural domains (1, 2 and 3) are tightly packed around the iron-sulphur cluster, while a fourth domain (4) forms a deep active-site cleft. The prokaryotic enzyme is encoded by two adjacent genes, leuC and leuD, corresponding to aconitase domains 1-3 and 4 respectively , . LeuC does not bind an iron-sulphur cluster. It is thought that some prokaryotic isopropylamalate dehydrogenases can also function as homoaconitase 4.2.1.36 from EC, converting cis-homoaconitate to homoisocitric acid in lysine biosynthesis . Homoaconitase has been identified in higher fungi (mitochondria) and several archaea and one thermophilic species of bacteria, Thermus thermophilus .    This entry represents the large subunit of 3-isopropylmalate dehydratase (LeuC), as well as homoaconitase enzymes, from prokaryotes. Homoaconitase, aconitase and 3-isopropylmalate dehydratase have similar overall structures and domain organisation . All are dehydratases that bind a [4Fe-4S]-cluster.   Information about related proteins can be found at Protein of the Month: Aconitase .; GO: 0003861 3-isopropylmalate dehydratase activity, 0051539 4 iron 4 sulfur cluster binding, 0009098 leucine biosynthetic process.
Probab=37.36  E-value=19  Score=16.61  Aligned_cols=47  Identities=17%  Similarity=0.250  Sum_probs=33.2

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCHHH-HHHHHHHH--CCCCCEEEECCHH
Q ss_conf             89999999999987598621000013-56676521--0666557504223
Q gi|254780563|r   37 QSVMLPIIHSFEERTGVKISPIYTSS-IQRPPITQ--GSPVDVIITKDET   83 (195)
Q Consensus        37 ~~~~~~~~~~Fek~tgIkV~~~~~~~-~~~~~~~~--~~~~d~~~~~d~~   83 (195)
                      -+-.+..+.+|-|+.||++-+.-+.. .=+++.++  ..|++++.++|+.
T Consensus        76 ~A~~Q~~~REF~K~~gI~~f~~~g~GIcHQ~L~E~Gya~PG~vvvG~DSH  125 (431)
T TIGR02086        76 AAELQKEIREFAKRHGIKVFFDVGEGICHQVLVEKGYAEPGMVVVGADSH  125 (431)
T ss_pred             HHHHHHHHHHHHHHCCCCEEEECCCEEEEEEEEECCCCCCCEEEEECCCC
T ss_conf             78877899988876687059987980277886530624776189952677


No 159
>pfam00988 CPSase_sm_chain Carbamoyl-phosphate synthase small chain, CPSase domain. The carbamoyl-phosphate synthase domain is in the amino terminus of protein. Carbamoyl-phosphate synthase catalyses the ATP-dependent synthesis of carbamyl-phosphate from glutamine or ammonia and bicarbonate. This important enzyme initiates both the urea cycle and the biosynthesis of arginine and/or pyrimidines. The carbamoyl-phosphate synthase (CPS) enzyme in prokaryotes is a heterodimer of a small and large chain. The small chain promotes the hydrolysis of glutamine to ammonia, which is used by the large chain to synthesize carbamoyl phosphate. See pfam00289. The small chain has a GATase domain in the carboxyl terminus. See pfam00117.
Probab=36.89  E-value=30  Score=15.46  Aligned_cols=27  Identities=11%  Similarity=0.320  Sum_probs=17.0

Q ss_pred             EEEEEEHHHHCCCCCCCCHHHHCCHHHCCEEEE
Q ss_conf             588873344013445578888408667685996
Q gi|254780563|r  122 QVLAYSTKRIKIADLPKSVFDLTNAQWKKRLSI  154 (195)
Q Consensus       122 ~~~~~n~~~~~~~~~P~sw~DL~~p~~kG~i~~  154 (195)
                      .-+++||-.....+.      |+||.|.|+|.+
T Consensus        26 GEvvFnT~mtGYqE~------lTDPSY~gQIl~   52 (131)
T pfam00988        26 GEVVFNTGMTGYQEI------LTDPSYAGQIVV   52 (131)
T ss_pred             EEEEEECCCCCCCEE------CCCCCCCCEEEE
T ss_conf             799997887654403------258765774899


No 160
>COG3065 Slp Starvation-inducible outer membrane lipoprotein [Cell envelope biogenesis, outer membrane]
Probab=36.73  E-value=26  Score=15.74  Aligned_cols=24  Identities=8%  Similarity=-0.147  Sum_probs=13.2

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             902599999999999998612444
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFSTEN   24 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~~~   24 (195)
                      ||+.++-+++..+|+++++|.+.-
T Consensus         4 ~m~~~~~~l~~~laflLsgC~tiP   27 (191)
T COG3065           4 QMNMKKGALIGTLAFLLSGCVTIP   27 (191)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             876479999999999976303578


No 161
>pfam06551 DUF1120 Protein of unknown function (DUF1120). This family consists of several hypothetical bacterial proteins of unknown function.
Probab=36.09  E-value=33  Score=15.21  Aligned_cols=31  Identities=13%  Similarity=0.029  Sum_probs=15.9

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCC--CCEEEE
Q ss_conf             0259999999999999861244458--808998
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTENTT--KYLTLY   32 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~~~--~~lvVY   32 (195)
                      |||.++..++++.++.++.++.+++  .+|.|-
T Consensus         1 mkK~l~~~~i~a~l~~~~ssa~aa~~ta~LkV~   33 (145)
T pfam06551         1 MKKNLAATAIAAGLAVLATSAQAADSTAVLKVT   33 (145)
T ss_pred             CCHHHHHHHHHHHHHHHHCCHHHCCCCCEEEEE
T ss_conf             923789999999999860314225774469999


No 162
>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=35.65  E-value=33  Score=15.17  Aligned_cols=56  Identities=20%  Similarity=0.230  Sum_probs=34.7

Q ss_pred             CCCCCCEEEECCCCHHHHHHHHHHHHHHC-CCCCCCCCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             44588089981899899999999999875-9862100001356676521066655750
Q gi|254780563|r   23 ENTTKYLTLYTDQNQSVMLPIIHSFEERT-GVKISPIYTSSIQRPPITQGSPVDVIIT   79 (195)
Q Consensus        23 ~~~~~~lvVYs~~~~~~~~~~~~~Fek~t-gIkV~~~~~~~~~~~~~~~~~~~d~~~~   79 (195)
                      ....+.+.|-+... ....+++..|.+++ +|++++..+...+......+...|+.+.
T Consensus        83 ~~~~g~l~ig~~~~-~~l~~~l~~f~~~~P~v~i~i~~~~~~~~~~~L~~~~~Di~i~  139 (279)
T TIGR03339        83 ALREGSLRIAATAP-YYVLDLVARFRQRYPGIEVSVRIGNSQEVLQALQSYRVDVAVS  139 (279)
T ss_pred             CCCCCEEEECCCHH-HHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHCCCEEEEEE
T ss_conf             78745168617517-7899999999985898605789558087775402596589997


No 163
>PRK12789 flgI flagellar basal body P-ring protein; Reviewed
Probab=35.42  E-value=15  Score=17.15  Aligned_cols=16  Identities=31%  Similarity=0.382  Sum_probs=9.2

Q ss_pred             CCHHHHHHHHHHHHHH
Q ss_conf             9025999999999999
Q gi|254780563|r    1 MFKRTIYTYLLLLCGF   16 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~   16 (195)
                      ||||.++..++.++.+
T Consensus         1 m~~~~~~~~~~~l~~~   16 (367)
T PRK12789          1 MIRRLLLAVLLALLAG   16 (367)
T ss_pred             CHHHHHHHHHHHHHHC
T ss_conf             9089999999999855


No 164
>TIGR02346 chap_CCT_theta T-complex protein 1, theta subunit; InterPro: IPR012721    Members of this eukaryotic family are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT theta chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes.; GO: 0005524 ATP binding, 0051082 unfolded protein binding, 0006457 protein folding.
Probab=34.49  E-value=31  Score=15.34  Aligned_cols=41  Identities=17%  Similarity=0.174  Sum_probs=32.7

Q ss_pred             CCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHH
Q ss_conf             880899818998999999999998759862100001356676
Q gi|254780563|r   26 TKYLTLYTDQNQSVMLPIIHSFEERTGVKISPIYTSSIQRPP   67 (195)
Q Consensus        26 ~~~lvVYs~~~~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~~   67 (195)
                      ++||.=||=..|..++.++++| ++.|++|-+..|+-++..+
T Consensus       264 A~ELlny~KgEE~~~e~~iK~i-ad~Gv~VIv~gG~v~d~Al  304 (554)
T TIGR02346       264 AEELLNYSKGEENQIEALIKAI-ADSGVKVIVTGGSVGDMAL  304 (554)
T ss_pred             HHHHCCCCCCHHHHHHHHHHHH-HHCCCEEEEECCCHHHHHH
T ss_conf             7866055702689999987899-8689859994684889999


No 165
>TIGR00232 tktlase_bact transketolase; InterPro: IPR005478     Transketolase (EC 2.2.1.1) (TK) catalyzes the reversible transfer of a two-carbon ketol unit from xylulose 5-phosphate to an aldose receptor, such as ribose 5-phosphate, to form sedoheptulose 7-phosphate and glyceraldehyde 3- phosphate. This enzyme, together with transaldolase, provides a link between the glycolytic and pentose-phosphate pathways. TK requires thiamine pyrophosphate as a cofactor.    This group includes two proteins from the yeast Saccharomyces cerevisiae but excludes dihydroxyactetone synthases (formaldehyde transketolases) from various yeasts and the even more distant mammalian transketolases. Among the family of thiamine diphosphate-dependent enzymes that includes transketolases, dihydroxyacetone synthases, pyruvate dehydrogenase E1-beta subunits, and deoxyxylulose-5-phosphate synthases, mammalian and bacterial transketolases seem not to be orthologous. ; GO: 0004802 transketolase activity.
Probab=34.33  E-value=14  Score=17.36  Aligned_cols=16  Identities=19%  Similarity=0.285  Sum_probs=6.4

Q ss_pred             HHHHHHHHHHHHCCCCC
Q ss_conf             99999999998759862
Q gi|254780563|r   39 VMLPIIHSFEERTGVKI   55 (195)
Q Consensus        39 ~~~~~~~~Fek~tgIkV   55 (195)
                      ..+.+.+-||. +|=+|
T Consensus       193 F~Edv~~RFeA-~gW~V  208 (675)
T TIGR00232       193 FSEDVKKRFEA-YGWEV  208 (675)
T ss_pred             HHHHHHHHHHH-CCCEE
T ss_conf             10014534410-58558


No 166
>PRK08114 cystathionine beta-lyase; Provisional
Probab=33.80  E-value=36  Score=14.99  Aligned_cols=54  Identities=9%  Similarity=-0.077  Sum_probs=35.2

Q ss_pred             CCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCEEE
Q ss_conf             588089981899899999999999875986210000135667652106665575
Q gi|254780563|r   25 TTKYLTLYTDQNQSVMLPIIHSFEERTGVKISPIYTSSIQRPPITQGSPVDVII   78 (195)
Q Consensus        25 ~~~~lvVYs~~~~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~~~~~~~~~d~~~   78 (195)
                      .++.-+|.+..-+.....+++.+-++.||+|.++...+.+...+.-.....+++
T Consensus        99 ~~Gd~il~~~~~YggT~~l~~~~l~~~Gi~v~~~d~~d~~~~~~~i~~~Tklv~  152 (395)
T PRK08114         99 EQGDHVLMTGTAYEPSQDFCSKILSKLGVTTTWFDPLIGADIAKLIQPNTKVVF  152 (395)
T ss_pred             CCCCEEEECCCCCHHHHHHHHHHHHHCCCEEEEECCCCHHHHHHHCCCCCEEEE
T ss_conf             899989976888568999999999875956998579999999974687754999


No 167
>PRK07810 O-succinylhomoserine sulfhydrylase; Provisional
Probab=33.65  E-value=36  Score=14.98  Aligned_cols=44  Identities=7%  Similarity=-0.074  Sum_probs=30.0

Q ss_pred             CCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHH
Q ss_conf             58808998189989999999999987598621000013566765
Q gi|254780563|r   25 TTKYLTLYTDQNQSVMLPIIHSFEERTGVKISPIYTSSIQRPPI   68 (195)
Q Consensus        25 ~~~~lvVYs~~~~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~~~   68 (195)
                      .++.-+|.+..-+.....+++.+-.+.||+|+++...+.+...+
T Consensus       110 ~~Gd~iv~~~~~YGgT~~l~~~~l~~~GI~~~~vd~~d~~~~~~  153 (406)
T PRK07810        110 GAGDRLVAARSLFGSCFVVCNEILPRWGVETVFVDGDDLSQWEE  153 (406)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHCCCEEEEEECCCCHHHHHH
T ss_conf             89998998379863779999977644874999968988599997


No 168
>COG2247 LytB Putative cell wall-binding domain [Cell envelope biogenesis, outer membrane]
Probab=33.60  E-value=36  Score=14.97  Aligned_cols=36  Identities=11%  Similarity=0.252  Sum_probs=21.7

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCC--EEEECCCCH
Q ss_conf             025999999999999986124445880--899818998
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTENTTKY--LTLYTDQNQ   37 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~~~~~--lvVYs~~~~   37 (195)
                      |+|.+-..+++++.+++..+..+++..  ++|-.++.+
T Consensus         1 Mrr~l~lll~~~l~l~s~~av~A~~~~~~~VIlvsDn~   38 (337)
T COG2247           1 MRRLLMLLLASLLALSSPPAVSAQSQNTTVVILVSDNE   38 (337)
T ss_pred             CCCHHHHHHHHHHHHHCCHHHHHHHCCCEEEEEECCHH
T ss_conf             91088999999999823044444414815999956607


No 169
>PRK13703 conjugal pilus assembly protein TraF; Provisional
Probab=33.56  E-value=35  Score=15.06  Aligned_cols=12  Identities=8%  Similarity=0.108  Sum_probs=4.3

Q ss_pred             CCCCCCCEEEEC
Q ss_conf             444588089981
Q gi|254780563|r   22 TENTTKYLTLYT   33 (195)
Q Consensus        22 ~~~~~~~lvVYs   33 (195)
                      ..+.+.-=-.|+
T Consensus        17 ~~~k~~Gw~WYn   28 (247)
T PRK13703         17 ASGKDAGWQWYN   28 (247)
T ss_pred             CCCCCCCCEECC
T ss_conf             556887614217


No 170
>PRK10808 outer membrane protein A; Reviewed
Probab=33.54  E-value=36  Score=14.97  Aligned_cols=18  Identities=28%  Similarity=0.492  Sum_probs=10.8

Q ss_pred             CHHHHHHHHHHHHHHHHH
Q ss_conf             025999999999999986
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEA   19 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~   19 (195)
                      |||.++..++.++++++.
T Consensus         1 MKKt~ial~va~a~~a~~   18 (347)
T PRK10808          1 MKKTAIAIAVALAGFATV   18 (347)
T ss_pred             CCHHHHHHHHHHHHHHHH
T ss_conf             946799999999977764


No 171
>pfam01441 Lipoprotein_6 Lipoprotein. Members of this family are lipoproteins that are probably involved in evasion of the host immune system by pathogens.
Probab=33.50  E-value=36  Score=14.96  Aligned_cols=24  Identities=8%  Similarity=0.110  Sum_probs=15.2

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             025999999999999986124445
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTENT   25 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~~   25 (195)
                      |||.-+..+++.+++.++|.....
T Consensus         1 MkkntlSAIlMTLflfiSCNNsG~   24 (209)
T pfam01441         1 MKKNTLSAILMTLFLFISCNNSGP   24 (209)
T ss_pred             CCHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             961379999999999831458999


No 172
>PRK09733 putative fimbrial protein; Provisional
Probab=33.35  E-value=36  Score=14.95  Aligned_cols=30  Identities=10%  Similarity=0.196  Sum_probs=17.7

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCEEEE
Q ss_conf             0259999999999999861244458808998
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTENTTKYLTLY   32 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~~~~~lvVY   32 (195)
                      |||.++..++.+++....++ ....++|+.-
T Consensus         2 mKk~ll~~~~~~~~s~~~~A-~~~~G~V~F~   31 (181)
T PRK09733          2 FKKSLLVAGVAMILSNNVFA-DEGHGIVKFK   31 (181)
T ss_pred             HHHHHHHHHHHHHHHHHHHH-HCCCCEEEEE
T ss_conf             06889999999998666576-4488689999


No 173
>PRK10159 outer membrane phosphoporin protein E; Provisional
Probab=33.14  E-value=24  Score=15.99  Aligned_cols=32  Identities=13%  Similarity=0.155  Sum_probs=15.6

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCC-----CCCCEEEECC
Q ss_conf             02599999999999998612444-----5880899818
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTEN-----TTKYLTLYTD   34 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~-----~~~~lvVYs~   34 (195)
                      |||++++.++.+++++ ..+.++     ...+|-||..
T Consensus         1 MKk~~lA~ai~a~l~s-~~a~AaeVYn~dg~~ldigGr   37 (351)
T PRK10159          1 MKKSTLALVVMGIVAS-ASVQAAEIYNKDGNKLDVYGK   37 (351)
T ss_pred             CCHHHHHHHHHHHHHC-CCCCEEEEEECCCCEEEEEEE
T ss_conf             9473899999999872-653179999789988978358


No 174
>pfam03971 IDH Monomeric isocitrate dehydrogenase. NADP(+)-dependent isocitrate dehydrogenase (ICD) is an important enzyme of the intermediary metabolism, as it controls the carbon flux within the citric acid cycle and supplies the cell with 2-oxoglutarate EC:1.1.1.42 and NADPH for biosynthetic purposes.
Probab=32.71  E-value=37  Score=14.89  Aligned_cols=32  Identities=25%  Similarity=0.552  Sum_probs=22.1

Q ss_pred             EEECCCCHHH------HHHHHHHHHHHCCCCCCCCCHH
Q ss_conf             9981899899------9999999998759862100001
Q gi|254780563|r   30 TLYTDQNQSV------MLPIIHSFEERTGVKISPIYTS   61 (195)
Q Consensus        30 vVYs~~~~~~------~~~~~~~Fek~tgIkV~~~~~~   61 (195)
                      +|||-.++..      .-|++++|.+..||.|+...-+
T Consensus         2 IiyT~tDEAPaLAT~SlLPIv~aF~~~agi~vet~DIS   39 (735)
T pfam03971         2 IIYTLTDEAPALATYSLLPIVKAFAASAGIDVETSDIS   39 (735)
T ss_pred             EEEECCCCHHHHHHHHHHHHHHHHHHHCCCEEEEEECC
T ss_conf             26624762688877777899999731318747730045


No 175
>COG4851 CamS Protein involved in sex pheromone biosynthesis [General function prediction only]
Probab=32.19  E-value=38  Score=14.83  Aligned_cols=23  Identities=4%  Similarity=0.255  Sum_probs=16.0

Q ss_pred             HHHHHHHCHHHHHHHHHHHHHCC
Q ss_conf             99999608699999999986088
Q gi|254780563|r  166 NTMEQTPNKTVVQDFIKNITANE  188 (195)
Q Consensus       166 ~a~~~~~G~~~~~~~l~~l~~N~  188 (195)
                      .+-+-..|++-+.+.+.+|+.++
T Consensus       199 ds~l~~qGekiaqeVlnRlR~~d  221 (382)
T COG4851         199 DSKLLEQGEKIAQEVLNRLRRED  221 (382)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             88899988999999999987526


No 176
>CHL00197 carA carbamoyl-phosphate synthase arginine-specific small subunit; Provisional
Probab=31.82  E-value=24  Score=15.96  Aligned_cols=23  Identities=13%  Similarity=-0.123  Sum_probs=10.5

Q ss_pred             CCHHHHCCHHHCCEEEECCCCCC
Q ss_conf             78888408667685996289830
Q gi|254780563|r  138 KSVFDLTNAQWKKRLSIAPNNIS  160 (195)
Q Consensus       138 ~sw~DL~~p~~kG~i~~~~~~~s  160 (195)
                      .++++...-+..|-+.---|+.+
T Consensus       226 ~~~~~I~~~~PDGIfLSNGPGDP  248 (383)
T CHL00197        226 STYQDIMAYQPDGILLSNGPGDP  248 (383)
T ss_pred             CCCCHHHCCCCCEEEECCCCCCH
T ss_conf             85113425688889978999997


No 177
>pfam08085 Entericidin Entericidin EcnA/B family. This family consists of the entericidin antidote/toxin peptides. The entericidin locus is activated in stationary phase under high osmolarity conditions by rho-S and simultaneously repressed by the osmoregulatory EnvZ/OmpR signal transduction pathway. The entericidin locus encodes tandem paralogous genes (ecnAB) and directs the synthesis of two small cell-envelope lipoproteins which can maintain plasmids in bacterial population by means of post-segregational killing.
Probab=31.52  E-value=39  Score=14.77  Aligned_cols=15  Identities=33%  Similarity=0.208  Sum_probs=7.4

Q ss_pred             CHHHHHHHHHHHHHH
Q ss_conf             025999999999999
Q gi|254780563|r    2 FKRTIYTYLLLLCGF   16 (195)
Q Consensus         2 mkk~~~~~l~l~~~~   16 (195)
                      |||.+...++++..+
T Consensus         1 Mk~~~~~~~~l~~~~   15 (42)
T pfam08085         1 MKKLIALLLALLLLA   15 (42)
T ss_pred             CHHHHHHHHHHHHHH
T ss_conf             923699999999999


No 178
>PRK00031 lolA outer-membrane lipoprotein carrier protein; Reviewed
Probab=31.45  E-value=26  Score=15.78  Aligned_cols=13  Identities=23%  Similarity=0.330  Sum_probs=6.7

Q ss_pred             CHHHHHHHHHHHH
Q ss_conf             0259999999999
Q gi|254780563|r    2 FKRTIYTYLLLLC   14 (195)
Q Consensus         2 mkk~~~~~l~l~~   14 (195)
                      |||.++..+++++
T Consensus         1 mk~~~~~~~~~~~   13 (201)
T PRK00031          1 MKKLLIAALLAAA   13 (201)
T ss_pred             CCHHHHHHHHHHH
T ss_conf             9159999999999


No 179
>PRK10510 putative outer membrane lipoprotein; Provisional
Probab=31.37  E-value=39  Score=14.75  Aligned_cols=22  Identities=14%  Similarity=0.283  Sum_probs=10.9

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             0259999999999999861244
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTE   23 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~   23 (195)
                      |||+++...+++++.+...+|.
T Consensus         1 m~~r~~lia~~~a~~l~lsgC~   22 (219)
T PRK10510          1 MKKRVYLIAAIVSGALAVSGCT   22 (219)
T ss_pred             CCHHHHHHHHHHHHHHHHHCCC
T ss_conf             9426899999999998741356


No 180
>COG3470 Tpd Uncharacterized protein probably involved in high-affinity Fe2+ transport [Inorganic ion transport and metabolism]
Probab=31.26  E-value=40  Score=14.74  Aligned_cols=28  Identities=14%  Similarity=0.186  Sum_probs=12.4

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCE
Q ss_conf             0259999999999999861244458808
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTENTTKYL   29 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~~~~~l   29 (195)
                      |+|.++..++++..++++....+..+|+
T Consensus         3 ~~k~l~~~~~~a~v~s~~a~~~a~~~E~   30 (179)
T COG3470           3 MKKLLLSAAILASVFSAPAEGAAAFKEV   30 (179)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             6899999999999974100002344634


No 181
>PRK11671 mltC murein transglycosylase C; Provisional
Probab=30.76  E-value=40  Score=14.69  Aligned_cols=18  Identities=17%  Similarity=0.074  Sum_probs=10.9

Q ss_pred             CCHHHHHHHHHHHHHHHH
Q ss_conf             902599999999999998
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTE   18 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~   18 (195)
                      ||||.+++++++.+..+|
T Consensus         1 ~~~k~~~~~~~~~~l~~c   18 (360)
T PRK11671          1 MMKKYLALALIAPLLISC   18 (360)
T ss_pred             CCHHHHHHHHHHHHHHHH
T ss_conf             914688999999999871


No 182
>PRK06234 methionine gamma-lyase; Provisional
Probab=30.06  E-value=41  Score=14.62  Aligned_cols=44  Identities=14%  Similarity=0.129  Sum_probs=30.5

Q ss_pred             CCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHH
Q ss_conf             58808998189989999999999987598621000013566765
Q gi|254780563|r   25 TTKYLTLYTDQNQSVMLPIIHSFEERTGVKISPIYTSSIQRPPI   68 (195)
Q Consensus        25 ~~~~lvVYs~~~~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~~~   68 (195)
                      .++.-+|.+..-+.....+++.+-++.||+|+++...+.+....
T Consensus       101 ~~Gdhiv~~~~~YGgT~~l~~~~l~~~Gi~~~~vd~~d~~~~~~  144 (399)
T PRK06234        101 KAGDHVVASDTLYGCTFALLNHGLTRYGVEVTFVDTSNLEEVRN  144 (399)
T ss_pred             CCCCEEEECCCCCHHHHHHHHHHHHCCCEEEEEECCCCHHHHHH
T ss_conf             89998997588720489999988651685788626889699996


No 183
>pfam01053 Cys_Met_Meta_PP Cys/Met metabolism PLP-dependent enzyme. This family includes enzymes involved in cysteine and methionine metabolism. The following are members: Cystathionine gamma-lyase, Cystathionine gamma-synthase, Cystathionine beta-lyase, Methionine gamma-lyase, OAH/OAS sulfhydrylase, O-succinylhomoserine sulfhydrylase All of these members participate is slightly different reactions. All these enzymes use PLP (pyridoxal-5'-phosphate) as a cofactor.
Probab=29.97  E-value=42  Score=14.61  Aligned_cols=44  Identities=11%  Similarity=0.089  Sum_probs=30.0

Q ss_pred             CCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHH
Q ss_conf             58808998189989999999999987598621000013566765
Q gi|254780563|r   25 TTKYLTLYTDQNQSVMLPIIHSFEERTGVKISPIYTSSIQRPPI   68 (195)
Q Consensus        25 ~~~~lvVYs~~~~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~~~   68 (195)
                      .++.-+|.+..-+.....+++.+-++.||+|.++.....+....
T Consensus        89 ~~Gd~il~~~~~Yg~t~~~~~~~l~~~Gi~v~~~d~~d~~~~~~  132 (381)
T pfam01053        89 KAGDHVVATDDLYGGTYRLFEKVLPRFGIEVTFVDPSDLDALEA  132 (381)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHCCCEEEEECCCCHHHHHH
T ss_conf             99998999578737589999998871585067626658678997


No 184
>PRK07811 cystathionine gamma-synthase; Provisional
Probab=29.58  E-value=42  Score=14.58  Aligned_cols=54  Identities=13%  Similarity=0.129  Sum_probs=34.4

Q ss_pred             CCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHCCCCCEEE
Q ss_conf             588089981899899999999999875986210000135667652106665575
Q gi|254780563|r   25 TTKYLTLYTDQNQSVMLPIIHSFEERTGVKISPIYTSSIQRPPITQGSPVDVII   78 (195)
Q Consensus        25 ~~~~lvVYs~~~~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~~~~~~~~~d~~~   78 (195)
                      .++.-+|.+..-+.....+++.+-++.||+|.++...+.+...+.-.....+++
T Consensus        95 ~~Gd~iv~~~~~YggT~~l~~~~l~~~Gi~~~~vd~~d~~~~~~~i~~~Tkli~  148 (386)
T PRK07811         95 RPGDHIVIPNDAYGGTFRLIDKVFTRWGVEYTPVDLSDLDAVRAAITPRTKLIW  148 (386)
T ss_pred             CCCCEEEECCCCCHHHHHHHHHHHHHCCEEEEEECCCCHHHHHHHCCCCCEEEE
T ss_conf             899989937876521999999998735804997788787889865588834999


No 185
>PRK12564 carbamoyl phosphate synthase small subunit; Reviewed
Probab=29.32  E-value=30  Score=15.44  Aligned_cols=23  Identities=0%  Similarity=-0.201  Sum_probs=13.2

Q ss_pred             CCHHHHCCHHHCCEEEECCCCCC
Q ss_conf             78888408667685996289830
Q gi|254780563|r  138 KSVFDLTNAQWKKRLSIAPNNIS  160 (195)
Q Consensus       138 ~sw~DL~~p~~kG~i~~~~~~~s  160 (195)
                      .++++..+-+..|-+.-.-|+.+
T Consensus       203 ~~~~~I~~~~pDGIflSNGPGDP  225 (355)
T PRK12564        203 TTAEEILALNPDGVFLSNGPGDP  225 (355)
T ss_pred             CCHHHHHCCCCCEEEECCCCCCH
T ss_conf             87657641488889967999996


No 186
>PRK13659 hypothetical protein; Provisional
Probab=28.92  E-value=43  Score=14.51  Aligned_cols=46  Identities=17%  Similarity=0.165  Sum_probs=24.8

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCEEEECCC---CHHHHHHHHHHH
Q ss_conf             0259999999999999861244458808998189---989999999999
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTENTTKYLTLYTDQ---NQSVMLPIIHSF   47 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~~~~~lvVYs~~---~~~~~~~~~~~F   47 (195)
                      -|+.++..+++++.+....++.++...|+|=++.   +.+....-.+++
T Consensus         5 ~kr~~L~~~ll~~~~~~~~s~~A~t~~~ii~~gd~a~ske~Arq~keqW   53 (112)
T PRK13659          5 SKRLLLLAMLLLLALVLTTSAHAETNKLVIESGDSAQSREQARQEKEQW   53 (112)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCEEEECCCCHHHHHHHHHHHHHHH
T ss_conf             7999999999999999986877632414320786163099999879867


No 187
>PRK08045 cystathionine gamma-synthase; Provisional
Probab=28.91  E-value=43  Score=14.51  Aligned_cols=42  Identities=10%  Similarity=-0.001  Sum_probs=31.0

Q ss_pred             CCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHH
Q ss_conf             588089981899899999999999875986210000135667
Q gi|254780563|r   25 TTKYLTLYTDQNQSVMLPIIHSFEERTGVKISPIYTSSIQRP   66 (195)
Q Consensus        25 ~~~~lvVYs~~~~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~   66 (195)
                      +++.-+|.+..-+.....+.+.+.++.||+|.++...+.+..
T Consensus        89 ~~Gd~vv~~~~~Yg~T~~l~~~~~~~~gi~v~~~d~~d~~~~  130 (386)
T PRK08045         89 KPGDLLVAPHDCYGGSYRLFDSLAKRGCYRVLFVDQGDEQAL  130 (386)
T ss_pred             CCCCEEEECCCCCHHHHHHHHHHHCCCCEEEEEECCCCHHHH
T ss_conf             999989983786348999999872079579999699998999


No 188
>PRK05967 cystathionine beta-lyase; Provisional
Probab=28.90  E-value=43  Score=14.51  Aligned_cols=43  Identities=12%  Similarity=-0.023  Sum_probs=30.6

Q ss_pred             CCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHH
Q ss_conf             5880899818998999999999998759862100001356676
Q gi|254780563|r   25 TTKYLTLYTDQNQSVMLPIIHSFEERTGVKISPIYTSSIQRPP   67 (195)
Q Consensus        25 ~~~~lvVYs~~~~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~~   67 (195)
                      .++.-+|.+..-+.....+++.+-++.||+|+++.....+...
T Consensus       101 ~~Gdhiv~~~~~YggT~~l~~~~l~~~Gi~v~~vd~~~~~~~~  143 (392)
T PRK05967        101 SAGDHALIVDSVYYPTRHFADTMLKRLGVEVEYYDPEIGAGIE  143 (392)
T ss_pred             CCCCEEEECCCCCCHHHHHHHHHHHHCCEEEEEECCCCHHHHH
T ss_conf             8998899448984458999999876368699998899999999


No 189
>PRK07050 cystathionine beta-lyase; Provisional
Probab=28.73  E-value=44  Score=14.49  Aligned_cols=43  Identities=7%  Similarity=-0.154  Sum_probs=29.6

Q ss_pred             CCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHH
Q ss_conf             5880899818998999999999998759862100001356676
Q gi|254780563|r   25 TTKYLTLYTDQNQSVMLPIIHSFEERTGVKISPIYTSSIQRPP   67 (195)
Q Consensus        25 ~~~~lvVYs~~~~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~~   67 (195)
                      .++.-+|.+..-+.....+++.|-++.||+|+++...+.+...
T Consensus       102 ~~Gd~vv~~~~~Yg~T~~~~~~~l~~~Gi~v~f~d~~d~~~~~  144 (394)
T PRK07050        102 KAGDDVLIPDNVYGPNRDFGEWLAKDFGITVRFYDPMIGAGIA  144 (394)
T ss_pred             CCCCEEEECCCCCHHHHHHHHHHHHCCCEEEEEECCCCHHHHH
T ss_conf             7998578356663338999998753188799997999989998


No 190
>PRK09915 putative outer membrane efflux protein MdtP; Provisional
Probab=28.63  E-value=41  Score=14.63  Aligned_cols=21  Identities=10%  Similarity=0.093  Sum_probs=14.2

Q ss_pred             CHHHHHHHHHHHHHHHHHHCC
Q ss_conf             025999999999999986124
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFST   22 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~   22 (195)
                      |||.++..++.++.++++|+.
T Consensus         6 ~~r~~~~~~l~~~~lLagC~~   26 (488)
T PRK09915          6 LSRLLLCSILGSTTLISGCAL   26 (488)
T ss_pred             HHHHHHHHHHHHHHHHCCCCC
T ss_conf             769999999999999752668


No 191
>PRK08475 F0F1 ATP synthase subunit B; Validated
Probab=28.58  E-value=44  Score=14.47  Aligned_cols=22  Identities=14%  Similarity=0.117  Sum_probs=10.4

Q ss_pred             HHHHHHHHHHHHHHC-CCCCCCC
Q ss_conf             899999999999875-9862100
Q gi|254780563|r   37 QSVMLPIIHSFEERT-GVKISPI   58 (195)
Q Consensus        37 ~~~~~~~~~~Fek~t-gIkV~~~   58 (195)
                      +-.-+|+...|.... +|.-.+.
T Consensus        43 yf~~kpi~~~l~~R~~~I~~~L~   65 (170)
T PRK08475         43 YFAAKPIKNFYKSRINSISKRLE   65 (170)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99287899999989999999999


No 192
>COG5633 Predicted periplasmic lipoprotein [General function prediction only]
Probab=28.32  E-value=33  Score=15.21  Aligned_cols=21  Identities=14%  Similarity=0.108  Sum_probs=11.2

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             02599999999999998612444
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTEN   24 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~   24 (195)
                      |||..+  +++.++++++|++..
T Consensus         1 Mrk~~~--~~l~~~lLvGCsS~~   21 (123)
T COG5633           1 MRKLCL--LSLALLLLVGCSSHQ   21 (123)
T ss_pred             CCEEHH--HHHHHHHHHCCCCCC
T ss_conf             930038--999999942047887


No 193
>pfam07424 TrbM TrbM. This family contains the bacterial protein TrbM (approximately 180 residues long). In Comamonas testosteroni T-2, TrbM is derived from the IncP1beta plasmid pTSA, which encodes the widespread genes for p-toluenesulfonate (TSA) degradation.
Probab=28.30  E-value=45  Score=14.45  Aligned_cols=12  Identities=8%  Similarity=0.121  Sum_probs=5.7

Q ss_pred             CHHHHCCHHHCC
Q ss_conf             888840866768
Q gi|254780563|r  139 SVFDLTNAQWKK  150 (195)
Q Consensus       139 sw~DL~~p~~kG  150 (195)
                      .|.|...|+|.|
T Consensus       149 ~YTD~~~~kYvc  160 (189)
T pfam07424       149 AYTDYHQPKYVC  160 (189)
T ss_pred             CCCCCCCCEEEE
T ss_conf             752136854540


No 194
>pfam04076 BOF Bacterial OB fold (BOF) protein. Proteins in this family form an OB-fold. Analysis of the predicted binding site of BOF family proteins implies that they lack nucleic acid-binding properties. They contain an predicted N-terminal signal peptide which indicates that they localize in the periplasm where they may function to bind proteins, small molecules, or other typical OB-fold ligands. As hypothesized for the distantly related OB-fold containing bacterial enterotoxins, the loss of nucleotide-binding function and the rapid evolution of the BOF ligand-binding site may be associated with the presence of BOF proteins in mobile genetic elements and their potential role in bacterial pathogenicity.
Probab=28.25  E-value=40  Score=14.73  Aligned_cols=17  Identities=12%  Similarity=0.100  Sum_probs=9.3

Q ss_pred             CHHHHHHHHHHHHHHHH
Q ss_conf             02599999999999998
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTE   18 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~   18 (195)
                      |||.++..++++++..+
T Consensus         1 MKK~~i~~~~~l~s~~~   17 (126)
T pfam04076         1 MKKLAIALASALASTSA   17 (126)
T ss_pred             CCHHHHHHHHHHHHCHH
T ss_conf             95689999999984678


No 195
>COG1204 Superfamily II helicase [General function prediction only]
Probab=28.23  E-value=45  Score=14.44  Aligned_cols=36  Identities=11%  Similarity=0.103  Sum_probs=31.2

Q ss_pred             CCEEEECCCCHHHHHHHHHHHH--HHCCCCCCCCCHHH
Q ss_conf             8089981899899999999999--87598621000013
Q gi|254780563|r   27 KYLTLYTDQNQSVMLPIIHSFE--ERTGVKISPIYTSS   62 (195)
Q Consensus        27 ~~lvVYs~~~~~~~~~~~~~Fe--k~tgIkV~~~~~~~   62 (195)
                      +.-+||..--..+..+..+.|+  ++.||+|...+++.
T Consensus        76 ~~k~vYivPlkALa~Ek~~~~~~~~~~GirV~~~TgD~  113 (766)
T COG1204          76 GGKVVYIVPLKALAEEKYEEFSRLEELGIRVGISTGDY  113 (766)
T ss_pred             CCCEEEEECHHHHHHHHHHHHHHHHHCCCEEEEECCCC
T ss_conf             98389990759999999998666886597799964886


No 196
>PRK13893 conjugal transfer protein TrbM; Provisional
Probab=28.22  E-value=30  Score=15.41  Aligned_cols=16  Identities=13%  Similarity=-0.168  Sum_probs=6.8

Q ss_pred             CCHHHHHHHHHHHHHH
Q ss_conf             9025999999999999
Q gi|254780563|r    1 MFKRTIYTYLLLLCGF   16 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~   16 (195)
                      |+||.+....++++.+
T Consensus         1 m~kk~l~~a~~~~a~~   16 (193)
T PRK13893          1 MKKKLLALAAAVAALG   16 (193)
T ss_pred             CCCHHHHHHHHHHHHC
T ss_conf             9614889999999970


No 197
>pfam06510 DUF1102 Protein of unknown function (DUF1102). This family consists of several hypothetical archaeal proteins of unknown function.
Probab=27.68  E-value=46  Score=14.38  Aligned_cols=23  Identities=26%  Similarity=0.007  Sum_probs=12.3

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             02599999999999998612444
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTEN   24 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~   24 (195)
                      |||.|-.+++++.+.++.+++++
T Consensus         1 Mkkl~gi~~ll~~l~L~vGa~an   23 (183)
T pfam06510         1 MKKLIGILLLLAGLGLVVGAGAN   23 (183)
T ss_pred             CHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             91489999999999954005653


No 198
>pfam08139 LPAM_1 Prokaryotic membrane lipoprotein lipid attachment site. In prokaryotes, membrane lipoproteins are synthesized with a precursor signal peptide, which is cleaved by a specific lipoprotein signal peptidase (signal peptidase II). The peptidase recognizes a conserved sequence and cuts upstream of a cysteine residue to which a glyceride-fatty acid lipid is attached.
Probab=27.46  E-value=43  Score=14.53  Aligned_cols=20  Identities=20%  Similarity=0.301  Sum_probs=9.2

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             0259999999999999861244
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTE   23 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~   23 (195)
                      |||.++.+++++.  +++|++.
T Consensus         1 Mkk~~~l~~~~l~--LagCas~   20 (26)
T pfam08139         1 MKKLLLLLLALLL--LAGCASX   20 (26)
T ss_pred             CHHHHHHHHHHHH--HHCCCCC
T ss_conf             9669999999999--8233200


No 199
>PRK06084 O-acetylhomoserine aminocarboxypropyltransferase; Validated
Probab=27.20  E-value=47  Score=14.33  Aligned_cols=43  Identities=7%  Similarity=-0.052  Sum_probs=29.3

Q ss_pred             CCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHH
Q ss_conf             5880899818998999999999998759862100001356676
Q gi|254780563|r   25 TTKYLTLYTDQNQSVMLPIIHSFEERTGVKISPIYTSSIQRPP   67 (195)
Q Consensus        25 ~~~~lvVYs~~~~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~~   67 (195)
                      ..+.-+|.+..-+.....+++.+-++.||+|.++.....+...
T Consensus        95 ~~Gd~iv~~~~~Yggt~~l~~~~l~~~gi~~~fvd~~d~~~~~  137 (424)
T PRK06084         95 EAGDNIVSVAKLYGGTYNLLAHTLPRIGIQTRFAAHDDIAALE  137 (424)
T ss_pred             CCCCEEEECCCCCCCHHHHHHHHHHHCCCEEEEECCCCHHHHH
T ss_conf             8999899827985638999999887468615995886779999


No 200
>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=26.83  E-value=45  Score=14.41  Aligned_cols=27  Identities=11%  Similarity=0.004  Sum_probs=19.6

Q ss_pred             HHHHHHHHCCCCCCCCCHHHHHHHHHH
Q ss_conf             999999875986210000135667652
Q gi|254780563|r   43 IIHSFEERTGVKISPIYTSSIQRPPIT   69 (195)
Q Consensus        43 ~~~~Fek~tgIkV~~~~~~~~~~~~~~   69 (195)
                      -.++|+|++|-.|.++..+++.-+.+.
T Consensus        20 rfda~aKe~gaTiDWRkFdSGadi~~A   46 (304)
T TIGR01729        20 RFDAYAKEAGATIDWRKFDSGADIVAA   46 (304)
T ss_pred             CHHHHHHCCCCEEEEEEECCHHHHHHH
T ss_conf             222454304880200110441655556


No 201
>pfam09358 UBA_e1_C Ubiquitin-activating enzyme e1 C-terminal domain. This presumed domain found at the C-terminus of Ubiquitin-activating enzyme e1 proteins is functionally uncharacterized.
Probab=26.56  E-value=43  Score=14.53  Aligned_cols=35  Identities=17%  Similarity=0.395  Sum_probs=24.0

Q ss_pred             CEEEECC---CCHHHHHHHHHHHHHHCCCCCCCCCHHH
Q ss_conf             0899818---9989999999999987598621000013
Q gi|254780563|r   28 YLTLYTD---QNQSVMLPIIHSFEERTGVKISPIYTSS   62 (195)
Q Consensus        28 ~lvVYs~---~~~~~~~~~~~~Fek~tgIkV~~~~~~~   62 (195)
                      +.+++.-   ...--.+.+++.|++++|++|..++.+.
T Consensus        30 ~~T~WDr~~v~~d~TL~~li~~f~~~~~lev~mis~g~   67 (124)
T pfam09358        30 EFTIWDRWEVNGDLTLQELIDYFEEKYGLEVTMLSQGV   67 (124)
T ss_pred             EEEEEEEEEECCCCCHHHHHHHHHHHHCCEEEEEEECC
T ss_conf             77457789987995099999999998196699997289


No 202
>PRK09973 putative outer membrane lipoprotein; Provisional
Probab=26.53  E-value=19  Score=16.58  Aligned_cols=28  Identities=11%  Similarity=-0.009  Sum_probs=14.8

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             9025999999999999986124445880
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFSTENTTKY   28 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~~~~~~~   28 (195)
                      |-+|..+...++...++++|++.++-++
T Consensus         1 mrtk~vlGaviLaS~LLaGCsn~~kv~q   28 (85)
T PRK09973          1 MKTIFTVGAVVLATCLLSGCVNEQKVNQ   28 (85)
T ss_pred             CCCEEHHHHHHHHHHHHHCCCCHHHHHH
T ss_conf             9602110699999999981555588999


No 203
>PRK10449 heat-inducible protein; Provisional
Probab=26.48  E-value=48  Score=14.25  Aligned_cols=21  Identities=14%  Similarity=0.216  Sum_probs=10.2

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             02599999999999998612444
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTEN   24 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~   24 (195)
                      |||. +. ++++..++++|++..
T Consensus         1 MKk~-l~-l~~~~llLagC~s~~   21 (140)
T PRK10449          1 MKKV-VA-LVALSLLMAGCVSSG   21 (140)
T ss_pred             CCHH-HH-HHHHHHHHHHCCCCC
T ss_conf             9034-99-999999997523899


No 204
>PRK11624 cdsA CDP-diglyceride synthase; Provisional
Probab=25.91  E-value=49  Score=14.19  Aligned_cols=17  Identities=24%  Similarity=0.268  Sum_probs=12.9

Q ss_pred             CCHHHHHHHHHHHHHHH
Q ss_conf             90259999999999999
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFT   17 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~   17 (195)
                      |||.|+++.++++..+.
T Consensus         1 MLk~RiiTalvli~i~i   17 (285)
T PRK11624          1 MLKYRLITAFVLIPVVI   17 (285)
T ss_pred             CCHHHHHHHHHHHHHHH
T ss_conf             94609999999999999


No 205
>PRK08605 D-lactate dehydrogenase; Validated
Probab=25.83  E-value=50  Score=14.18  Aligned_cols=32  Identities=16%  Similarity=0.344  Sum_probs=21.8

Q ss_pred             CEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCHH
Q ss_conf             0899818998999999999998759862100001
Q gi|254780563|r   28 YLTLYTDQNQSVMLPIIHSFEERTGVKISPIYTS   61 (195)
Q Consensus        28 ~lvVYs~~~~~~~~~~~~~Fek~tgIkV~~~~~~   61 (195)
                      .+.+|+-++.+  .+.++.|.+++|++|.+....
T Consensus         3 Ki~~~~~~~~e--~~~~~~~~~~~~~ev~~~~~~   34 (332)
T PRK08605          3 KIKLMSVRDED--APYIKAWAEKHHVEVDLTKEA   34 (332)
T ss_pred             EEEEEECCHHH--HHHHHHHHHHCCCEEEEECCC
T ss_conf             69998276656--999999888659079996699


No 206
>COG5455 Predicted integral membrane protein [Function unknown]
Probab=25.71  E-value=49  Score=14.20  Aligned_cols=27  Identities=15%  Similarity=0.208  Sum_probs=15.0

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             9025999999999999986124445880
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFSTENTTKY   28 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~~~~~~~   28 (195)
                      |||| |++.++...++++..+.++++.+
T Consensus         1 ~mkr-lv~~lla~s~~a~p~a~~q~~~~   27 (129)
T COG5455           1 NMKR-LVSALLAVSSVAAPMALAQQDGE   27 (129)
T ss_pred             CCHH-HHHHHHHHHHHHCCHHHCCCCCC
T ss_conf             9143-89999999985051110233643


No 207
>PRK12838 carbamoyl phosphate synthase small subunit; Reviewed
Probab=25.55  E-value=34  Score=15.12  Aligned_cols=23  Identities=13%  Similarity=-0.074  Sum_probs=11.5

Q ss_pred             CCHHHHCCHHHCCEEEECCCCCC
Q ss_conf             78888408667685996289830
Q gi|254780563|r  138 KSVFDLTNAQWKKRLSIAPNNIS  160 (195)
Q Consensus       138 ~sw~DL~~p~~kG~i~~~~~~~s  160 (195)
                      .+.+|+.+-+..|-+.---|+.+
T Consensus       199 ~~~~~i~~~~pDGiflSNGPGDP  221 (356)
T PRK12838        199 ASLEDIKNLNPDGIVLSNGPGDP  221 (356)
T ss_pred             CCCCHHHCCCCCEEEECCCCCCH
T ss_conf             87540232497489943899896


No 208
>PRK13524 outer membrane receptor FepA; Provisional
Probab=25.43  E-value=50  Score=14.17  Aligned_cols=23  Identities=17%  Similarity=0.150  Sum_probs=13.5

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             02599999999999998612444
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTEN   24 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~   24 (195)
                      |.|+++..|.+++++++.+++.+
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~   23 (742)
T PRK13524          1 MNKKISHSLALLVNLGIYGAAQA   23 (742)
T ss_pred             CCCHHHHHHHHHHHHHHCCCHHH
T ss_conf             98434668999999875442010


No 209
>TIGR01088 aroQ 3-dehydroquinate dehydratase, type II; InterPro: IPR001874 3-dehydroquinate dehydratase (4.2.1.10 from EC), or dehydroquinase, catalyzes the conversion of 3-dehydroquinate into 3-dehydroshikimate. It is the third step in the shikimate pathway for the biosynthesis of aromatic amino acids from chorismate. Two classes of dehydroquinases exist, known as types I and II. Class-II enzymes are homododecameric enzymes of about 17 kDa. They are found in some bacteria such as actinomycetales ,  and some fungi where they act in a catabolic pathway that allows the use of quinic acid as a carbon source.; GO: 0003855 3-dehydroquinate dehydratase activity, 0009073 aromatic amino acid family biosynthetic process.
Probab=25.38  E-value=51  Score=14.14  Aligned_cols=41  Identities=15%  Similarity=0.165  Sum_probs=33.6

Q ss_pred             CCCEEEECCCCHHHHHHHHHHHHHHCC--CCCCCCCHHH-HHHH
Q ss_conf             880899818998999999999998759--8621000013-5667
Q gi|254780563|r   26 TKYLTLYTDQNQSVMLPIIHSFEERTG--VKISPIYTSS-IQRP   66 (195)
Q Consensus        26 ~~~lvVYs~~~~~~~~~~~~~Fek~tg--IkV~~~~~~~-~~~~   66 (195)
                      ..|-.||.+.+=+.+.+.++.|-++.+  ++|+....+. .+++
T Consensus        15 ~REP~~YG~~tle~i~~~~~~~a~~~~ld~e~~~fQSN~EG~L~   58 (144)
T TIGR01088        15 LREPGVYGSQTLEEIEEILETFAAQLNLDVEVEFFQSNSEGELI   58 (144)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHCCCEEEEEEECCCCHHHHH
T ss_conf             74653247868789999999999853982789873044357899


No 210
>PRK08133 O-succinylhomoserine sulfhydrylase; Validated
Probab=25.34  E-value=51  Score=14.13  Aligned_cols=43  Identities=7%  Similarity=0.032  Sum_probs=29.1

Q ss_pred             CCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHH
Q ss_conf             5880899818998999999999998759862100001356676
Q gi|254780563|r   25 TTKYLTLYTDQNQSVMLPIIHSFEERTGVKISPIYTSSIQRPP   67 (195)
Q Consensus        25 ~~~~lvVYs~~~~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~~   67 (195)
                      ..+.-+|.+..-+.....+++.+-++.||+|+++...+.+...
T Consensus        98 ~~Gd~iv~~~~~Yggt~~l~~~~l~~~Gi~~~~vd~~d~~~~~  140 (391)
T PRK08133         98 QAGDHVVSSRSLFGSTLSLFEKIFARFGIETTFVDLTDLDAWR  140 (391)
T ss_pred             CCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEECCCCCHHHHH
T ss_conf             7999899678974538999998741078444467987999999


No 211
>PRK09028 cystathionine beta-lyase; Provisional
Probab=25.30  E-value=51  Score=14.13  Aligned_cols=42  Identities=7%  Similarity=-0.103  Sum_probs=28.8

Q ss_pred             CCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHH
Q ss_conf             588089981899899999999999875986210000135667
Q gi|254780563|r   25 TTKYLTLYTDQNQSVMLPIIHSFEERTGVKISPIYTSSIQRP   66 (195)
Q Consensus        25 ~~~~lvVYs~~~~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~   66 (195)
                      .++.-+|.+..-+.....+++.+-++.||+|.++.....+..
T Consensus        98 ~~Gdhiv~~~~~YggT~~l~~~~l~~~Gi~v~~vd~~~~~~~  139 (394)
T PRK09028         98 KAGDHLLMVDSCYEPTRDLCDKILAGFGIETTYYDPMIGEGI  139 (394)
T ss_pred             CCCCEEECCCCCCCCHHHHHHHHHHHCCEEEEEECCCCHHHH
T ss_conf             799878706998627799999888656747999579998999


No 212
>PRK06007 fliF flagellar MS-ring protein; Reviewed
Probab=25.30  E-value=51  Score=14.13  Aligned_cols=47  Identities=11%  Similarity=0.228  Sum_probs=32.1

Q ss_pred             HHHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             999999861244458808998189989999999999987598621000
Q gi|254780563|r   12 LLCGFTEAFSTENTTKYLTLYTDQNQSVMLPIIHSFEERTGVKISPIY   59 (195)
Q Consensus        12 l~~~~~~~~~~~~~~~~lvVYs~~~~~~~~~~~~~Fek~tgIkV~~~~   59 (195)
                      +++++..........+-.++|++.+.+-...++++.++ -||.-++..
T Consensus        34 ~i~~~~~l~~~~~~p~y~~L~~~l~~~da~~I~~~L~~-~gI~Y~l~~   80 (540)
T PRK06007         34 VIAAIVALVLWASRPDYRVLYSNLSDQDAGQIVAALDQ-AGIPYKVSS   80 (540)
T ss_pred             HHHHHHHHHHHHCCCCEEEECCCCCHHHHHHHHHHHHH-CCCCEEECC
T ss_conf             99999999984169972770289998999999999998-799759769


No 213
>pfam12354 Internalin_N Bacterial adhesion/invasion protein N terminal. This domain family is found in bacteria, and is approximately 60 amino acids in length. The family is found in association with pfam00560, pfam08191, pfam09479. There are two completely conserved residues (I and F) that may be functionally important. Internalin mediates bacterial adhesion and invasion of epithelial cells in the human intestine through specific interaction with its host cell receptor E-cadherin. This family is the N terminal of internalin, the cap domain of the protein. The cap domain is conserved between different internalin types. The cap domain does not interact with E cadherin, therefore its function is presumably structural: capping the hydrophobic core.
Probab=25.30  E-value=41  Score=14.64  Aligned_cols=32  Identities=16%  Similarity=-0.113  Sum_probs=11.2

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEE
Q ss_conf             90259999999999999861244458808998
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFSTENTTKYLTLY   32 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~~~~~~~lvVY   32 (195)
                      |.|+.++..++++...+..+.+-..+.+.-+.
T Consensus         1 mkk~~~lk~~l~~~lv~~i~~~i~~~~~~kvq   32 (57)
T pfam12354         1 MKKNNWLKNVLTLLLVLIISLCIGTSLGTKVQ   32 (57)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHEECCCCCEEE
T ss_conf             95116999999999999998624268982786


No 214
>pfam11777 DUF3316 Protein of unknown function (DUF3316). This family of bacterial proteins has no known function. Several members are, however, annotated as being putative acyl-CoA synthetase, but this could not be confirmed.
Probab=25.29  E-value=51  Score=14.13  Aligned_cols=19  Identities=37%  Similarity=0.303  Sum_probs=12.1

Q ss_pred             CHHHHHHHHHHHHHHHHHH
Q ss_conf             0259999999999999861
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAF   20 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~   20 (195)
                      |||.+++.++++++..+..
T Consensus         1 mKk~~ll~~~ll~s~~AfA   19 (114)
T pfam11777         1 MKKLILLALLLLLSATAFA   19 (114)
T ss_pred             CHHHHHHHHHHHHHHHHHH
T ss_conf             9108999999999888875


No 215
>pfam05079 DUF680 Protein of unknown function (DUF680). This family contains several uncharacterized proteins which seem to be found exclusively in Rhizobium loti.
Probab=25.16  E-value=39  Score=14.79  Aligned_cols=24  Identities=21%  Similarity=0.285  Sum_probs=15.2

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             025999999999999986124445
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFSTENT   25 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~~~~   25 (195)
                      |||.++....++++-...|+..+.
T Consensus         1 M~KiaLtaAAiL~asgsAFAGSD~   24 (73)
T pfam05079         1 MKKIALTAAAILAASGSAFAGSDN   24 (73)
T ss_pred             CCHHHHHHHHHHHHCCCCCCCCCC
T ss_conf             922489999999970652213565


No 216
>TIGR01431 adm_rel adenosine deaminase-related growth factor; InterPro: IPR006331   Members of this family have been described as secreted proteins with growth factor activity and regions of adenosine deaminase homology in insects, molluscs, and vertebrates ..
Probab=24.99  E-value=51  Score=14.09  Aligned_cols=148  Identities=16%  Similarity=0.156  Sum_probs=80.2

Q ss_pred             HHHHHHHHHHC----CCCCCCCC--HHHHHHH------HH-HHCCCCCEEEECCHHH-------HHH-HHHHHCCCCCCC
Q ss_conf             99999999875----98621000--0135667------65-2106665575042233-------234-331000012342
Q gi|254780563|r   41 LPIIHSFEERT----GVKISPIY--TSSIQRP------PI-TQGSPVDVIITKDETS-------LAL-NEDLLHKLPAHL   99 (195)
Q Consensus        41 ~~~~~~Fek~t----gIkV~~~~--~~~~~~~------~~-~~~~~~d~~~~~d~~~-------l~~-~~~~l~~~~~~~   99 (195)
                      +++.++|.+++    |+|+-|..  +.+.+.+      .. .+.-..|.+.|-|...       |.. .+.++.+-....
T Consensus       245 ~ev~~~F~~ehpdFiG~klIys~~R~~~~~~l~~~~~~~~~l~~kyPd~~~GFDLVG~Ed~~~~L~~y~~~Ll~~s~qnd  324 (486)
T TIGR01431       245 KEVTEKFKKEHPDFIGVKLIYSDLRSKDKEELAEYIKVAMELKKKYPDFVAGFDLVGQEDKGLSLLDYLDALLEPSKQND  324 (486)
T ss_pred             HHHHHHHHHHCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCCCCCCEEEECCCCCCCCCCCCHHHHHHHHCCCCCCCC
T ss_conf             99999998645134202443002578777788899999851511188658603334778977974455688411523375


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCEEE---EEEEHHHHCCC----------------C-----CCCCHH--HHCCHHHCCE--
Q ss_conf             223472000122222344345058---88733440134----------------4-----557888--8408667685--
Q gi|254780563|r  100 IKKNSFVLKNENKKLMRISFDTQV---LAYSTKRIKIA----------------D-----LPKSVF--DLTNAQWKKR--  151 (195)
Q Consensus       100 ~~~~~~~~~~~~~~~~~~~~~~~~---~~~n~~~~~~~----------------~-----~P~sw~--DL~~p~~kG~--  151 (195)
                      ..++|--|.-....|.|.......   +.-||.++...                +     .|=|=.  .|- ..+|++  
T Consensus       325 ~~~lpyFFHAGETnw~g~~vD~NL~DA~LLnTtRiGhGFAL~KHP~~~~~~K~~~iavEVnPISNQvL~LV-~D~RNHp~  403 (486)
T TIGR01431       325 KVKLPYFFHAGETNWQGTEVDENLVDALLLNTTRIGHGFALVKHPLVLKLVKEREIAVEVNPISNQVLKLV-ADLRNHPV  403 (486)
T ss_pred             CCCCCCEEECCCCCCCCCCHHHHHHHHHHHCCCEEECCCCHHHHHHHHHHHHHCCCCEEECCCHHHHHHHH-HHHCCCCC
T ss_conf             98798221045226777512289999998468414125421011699999986598477768145788875-33200101


Q ss_pred             ---------EEECCCC-----CC--HHHHHHHHHHHHCHHHHHHHHHHHHHCCC
Q ss_conf             ---------9962898-----30--49999999996086999999999860887
Q gi|254780563|r  152 ---------LSIAPNN-----IS--FHRLLNTMEQTPNKTVVQDFIKNITANEI  189 (195)
Q Consensus       152 ---------i~~~~~~-----~s--~~~~~~a~~~~~G~~~~~~~l~~l~~N~~  189 (195)
                               ++|++..     .+  .+.|-.+++...|.+.+...||+|.=|=+
T Consensus       404 a~L~A~~yP~VISsDdPa~w~a~pLSyDFY~~~m~las~~a~L~~LKqLalNSI  457 (486)
T TIGR01431       404 AILLADNYPMVISSDDPAFWGAKPLSYDFYVAFMGLASAKADLRTLKQLALNSI  457 (486)
T ss_pred             HHHHHCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             554326876687468853345888728999999961046034668999986411


No 217
>KOG0634 consensus
Probab=24.64  E-value=52  Score=14.05  Aligned_cols=34  Identities=6%  Similarity=0.033  Sum_probs=26.3

Q ss_pred             EEECCCCCCHHHHHHHHHHHHCHHHHHHHHHHHH
Q ss_conf             9962898304999999999608699999999986
Q gi|254780563|r  152 LSIAPNNISFHRLLNTMEQTPNKTVVQDFIKNIT  185 (195)
Q Consensus       152 i~~~~~~~s~~~~~~a~~~~~G~~~~~~~l~~l~  185 (195)
                      ++...+|+..+..+.+|+..+|++...+|++.|.
T Consensus       322 ~~t~~pSg~sq~iv~a~l~~wgqeG~~~wi~~l~  355 (472)
T KOG0634         322 VATSGPSGFSQGIVYAMLKRWGQEGFLRWIQHLR  355 (472)
T ss_pred             EEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             1003866410999999999988888999999999


No 218
>PRK13680 hypothetical protein; Provisional
Probab=24.32  E-value=53  Score=14.02  Aligned_cols=49  Identities=12%  Similarity=0.211  Sum_probs=22.2

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCC-CEEEEC--CCCHHHH-HHHHHHHHH
Q ss_conf             902599999999999998612444588-089981--8998999-999999998
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFSTENTTK-YLTLYT--DQNQSVM-LPIIHSFEE   49 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~~~~~~-~lvVYs--~~~~~~~-~~~~~~Fek   49 (195)
                      ||||+=++..++++++++.+++.+++. ..-+-+  +.+.+.+ ..+...|-.
T Consensus         4 ~mkk~G~~l~~lll~~s~~~~a~~ee~r~akf~~C~gL~~~qIAaqVKrDflQ   56 (121)
T PRK13680          4 NMKKRGALLVLLLLACSSVFSANAEESKSVKFPKCEGLDAAGIAASVKRDYQQ   56 (121)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             07665299999999988777665057653344545798989999999999987


No 219
>PRK09578 periplasmic multidrug efflux lipoprotein precursor; Reviewed
Probab=24.10  E-value=53  Score=13.99  Aligned_cols=21  Identities=10%  Similarity=-0.017  Sum_probs=11.2

Q ss_pred             HHHHHHHHHHHHHHHHHHCCC
Q ss_conf             259999999999999861244
Q gi|254780563|r    3 KRTIYTYLLLLCGFTEAFSTE   23 (195)
Q Consensus         3 kk~~~~~l~l~~~~~~~~~~~   23 (195)
                      +|++..+++++++++++|+..
T Consensus         6 r~~~~l~~l~~~~~L~gC~~~   26 (385)
T PRK09578          6 RRRLALAALVAAFALAGCGKG   26 (385)
T ss_pred             HHHHHHHHHHHHHHHHCCCCC
T ss_conf             799999999999998167999


No 220
>PRK10270 hypothetical protein; Provisional
Probab=23.98  E-value=54  Score=13.98  Aligned_cols=52  Identities=13%  Similarity=0.246  Sum_probs=28.5

Q ss_pred             CHHHHCCHHHCCEEEECCCCCCHHHH-HHHHHHHHC---HH---HHHHHHHHHHHCCCC
Q ss_conf             88884086676859962898304999-999999608---69---999999998608870
Q gi|254780563|r  139 SVFDLTNAQWKKRLSIAPNNISFHRL-LNTMEQTPN---KT---VVQDFIKNITANEIL  190 (195)
Q Consensus       139 sw~DL~~p~~kG~i~~~~~~~s~~~~-~~a~~~~~G---~~---~~~~~l~~l~~N~~~  190 (195)
                      ....-.+..|+++..--+..+....+ ++++++...   +|   -+.=|+.+|+.|+-.
T Consensus       184 ~~~~~~~~~~~~~~~~l~~~~~~e~ltlASIVEkEa~~~~er~~IA~Vf~NRL~~gM~L  242 (340)
T PRK10270        184 KMVKAVDSAWEGRADGLPYKDKNQLVTMASIIEKETAVASERDQVASVFINRLRIGMRL  242 (340)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCC
T ss_conf             99999999998641157867899999999999997427421278999999986239988


No 221
>PRK10287 thiosulfate:cyanide sulfurtransferase; Provisional
Probab=23.51  E-value=54  Score=13.97  Aligned_cols=13  Identities=31%  Similarity=0.669  Sum_probs=8.4

Q ss_pred             CCHHHHHHHHHHH
Q ss_conf             9025999999999
Q gi|254780563|r    1 MFKRTIYTYLLLL   13 (195)
Q Consensus         1 mmkk~~~~~l~l~   13 (195)
                      ||||.++..++++
T Consensus         1 ~~~~~~~~l~~~f   13 (104)
T PRK10287          1 MFKKGLLALALVF   13 (104)
T ss_pred             CCHHHHHHHHHHH
T ss_conf             9244799999999


No 222
>KOG0559 consensus
Probab=23.41  E-value=55  Score=13.91  Aligned_cols=19  Identities=21%  Similarity=0.307  Sum_probs=8.3

Q ss_pred             HHHHHHHHHHCCCCCCCCC
Q ss_conf             9999999987598621000
Q gi|254780563|r   41 LPIIHSFEERTGVKISPIY   59 (195)
Q Consensus        41 ~~~~~~Fek~tgIkV~~~~   59 (195)
                      ....++|-|+||+|.-+.+
T Consensus       270 k~ykdaf~kKhGvKlGfMs  288 (457)
T KOG0559         270 KQYKDAFLKKHGVKLGFMS  288 (457)
T ss_pred             HHHHHHHHHHHCCEEEEHH
T ss_conf             9989999987385043146


No 223
>TIGR01181 dTDP_gluc_dehyt dTDP-glucose 4,6-dehydratase; InterPro: IPR005888    The conversion of dTDP-glucose into dTDP-4-keto-6-deoxyglucose by Escherichia coli dTDP-glucose 4,6-dehydratase) takes place in the active site in three steps: dehydrogenation to dTDP-4-ketoglucose, dehydration to dTDP-4-ketoglucose-5,6-ene, and rereduction of C6 to the methyl group. The 4,6-dehydratase makes use of tightly bound NAD^+ as the coenzyme for transiently oxidizing the substrate, activating it for the dehydration step . This and other 4,6-dehydratases catalyze the first committed step in all 6-deoxysugar biosynthetic pathways described to date. Numerous 6-deoxysugars are used in bacterial lipopolysaccharide production as well as in the biosynthesis of a diverse array of secondary metabolites.; GO: 0008460 dTDP-glucose 46-dehydratase activity, 0009225 nucleotide-sugar metabolic process.
Probab=23.41  E-value=49  Score=14.21  Aligned_cols=28  Identities=7%  Similarity=0.163  Sum_probs=22.1

Q ss_pred             CCHHHHHHHHHHHHHHCCCCCCCCCHHH
Q ss_conf             9989999999999987598621000013
Q gi|254780563|r   35 QNQSVMLPIIHSFEERTGVKISPIYTSS   62 (195)
Q Consensus        35 ~~~~~~~~~~~~Fek~tgIkV~~~~~~~   62 (195)
                      .|.+..+.|+.+|.+-||+++.+...+.
T Consensus       163 ASKAasD~LVrAy~rTYGLp~~ITrCsN  190 (340)
T TIGR01181       163 ASKAASDLLVRAYHRTYGLPVLITRCSN  190 (340)
T ss_pred             HHHHHHHHHHHHHHHHCCCCEEEECCCC
T ss_conf             8898887898888875488605768855


No 224
>PRK01622 OxaA-like protein precursor; Validated
Probab=23.33  E-value=55  Score=13.91  Aligned_cols=21  Identities=29%  Similarity=0.244  Sum_probs=9.1

Q ss_pred             CCHH-H-HHHHHH-HHHHHHHHHC
Q ss_conf             9025-9-999999-9999998612
Q gi|254780563|r    1 MFKR-T-IYTYLL-LLCGFTEAFS   21 (195)
Q Consensus         1 mmkk-~-~~~~l~-l~~~~~~~~~   21 (195)
                      |||+ + ++.+++ .++.++++|+
T Consensus         1 m~k~~~~~l~~~~~~~~~~lsgc~   24 (266)
T PRK01622          1 MLKSYRAVLISLSLLLVFVLSGCS   24 (266)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             953889999999999999995468


No 225
>TIGR01347 sucB 2-oxoglutarate dehydrogenase, E2 component, dihydrolipoamide succinyltransferase; InterPro: IPR006255   These sequences describe the TCA cycle 2-oxoglutarate system E2 component, dihydrolipoamide succinyltransferase. It is closely related to the pyruvate dehydrogenase E2 component, dihydrolipoamide acetyltransferase. Members include the mitochondrial and Gram-negative bacterial forms. Mycobacterial candidates are highly derived, differ in having and extra copy of the lipoyl-binding domain at the N-terminus and are generally excluded from this group of sequences as are all examples of dihydrolipoamide acetyltransferase. ; GO: 0004149 dihydrolipoyllysine-residue succinyltransferase activity, 0006099 tricarboxylic acid cycle, 0045252 oxoglutarate dehydrogenase complex.
Probab=23.32  E-value=50  Score=14.15  Aligned_cols=23  Identities=22%  Similarity=0.313  Sum_probs=17.0

Q ss_pred             HHHHHHHHHHHHHHC-CCCCCCCC
Q ss_conf             899999999999875-98621000
Q gi|254780563|r   37 QSVMLPIIHSFEERT-GVKISPIY   59 (195)
Q Consensus        37 ~~~~~~~~~~Fek~t-gIkV~~~~   59 (195)
                      -++.+...|+|+|+| |||+=+-+
T Consensus       240 meLRK~yke~F~K~HdGvKLGFMS  263 (435)
T TIGR01347       240 MELRKRYKEEFEKKHDGVKLGFMS  263 (435)
T ss_pred             HHHHHHHHHHHHHHCCCCEECCCC
T ss_conf             999986334676530882242110


No 226
>COG3056 Uncharacterized lipoprotein [Cell envelope biogenesis, outer membrane]
Probab=22.99  E-value=56  Score=13.87  Aligned_cols=26  Identities=12%  Similarity=0.016  Sum_probs=11.9

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCEEE
Q ss_conf             99999999999986124445880899
Q gi|254780563|r    6 IYTYLLLLCGFTEAFSTENTTKYLTL   31 (195)
Q Consensus         6 ~~~~l~l~~~~~~~~~~~~~~~~lvV   31 (195)
                      ....|.++++++.+.+|+++..++.+
T Consensus        15 t~k~L~~laa~~lLagC~a~~~tl~~   40 (204)
T COG3056          15 TKKILFPLAAIFLLAGCAAPPTTLIV   40 (204)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCEEEC
T ss_conf             99999999999999753799750313


No 227
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=22.67  E-value=57  Score=13.83  Aligned_cols=55  Identities=15%  Similarity=0.158  Sum_probs=34.6

Q ss_pred             CCCEEEEC--CCCHHHHHHHHHHHHHHC-CCCCCCCCHHHHHHHHHHHCCCCCEEEEC
Q ss_conf             88089981--899899999999999875-98621000013566765210666557504
Q gi|254780563|r   26 TKYLTLYT--DQNQSVMLPIIHSFEERT-GVKISPIYTSSIQRPPITQGSPVDVIITK   80 (195)
Q Consensus        26 ~~~lvVYs--~~~~~~~~~~~~~Fek~t-gIkV~~~~~~~~~~~~~~~~~~~d~~~~~   80 (195)
                      .+.|.|=.  +.......+++..|.+++ +|+|++..+.+.+......+...|+.+..
T Consensus        89 ~~~l~ig~~~~~~~~~lp~~l~~f~~~~P~v~v~l~~~~~~~~~~~l~~g~~D~~i~~  146 (296)
T PRK09906         89 DRQLTIGFVPSAEVNLLPKVLPMFRLRHPDTLIELVSLINTQQEEKLRRGELDVGFMR  146 (296)
T ss_pred             CCEEEEEECHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCHHHHHHHHCCCCCEEEEE
T ss_conf             7138832122569999999999987408986348997580899999986997679873


No 228
>COG2984 ABC-type uncharacterized transport system, periplasmic component [General function prediction only]
Probab=22.56  E-value=57  Score=13.82  Aligned_cols=130  Identities=12%  Similarity=0.124  Sum_probs=52.0

Q ss_pred             CCHHHHH---HHHHHHHHHHHHHCCC-CCCCCEEEECCCCHHHHHHHHHHHHH---HCCC-CCCCC--CHH----HHHHH
Q ss_conf             9025999---9999999999861244-45880899818998999999999998---7598-62100--001----35667
Q gi|254780563|r    1 MFKRTIY---TYLLLLCGFTEAFSTE-NTTKYLTLYTDQNQSVMLPIIHSFEE---RTGV-KISPI--YTS----SIQRP   66 (195)
Q Consensus         1 mmkk~~~---~~l~l~~~~~~~~~~~-~~~~~lvVYs~~~~~~~~~~~~~Fek---~tgI-kV~~~--~~~----~~~~~   66 (195)
                      ||+|.+.   .+.+++++++...++. +...++-|....+-...++..+.|++   +-|+ .+++.  ...    +.+.+
T Consensus         1 ~~~~~~~~~~~~~~L~~~~l~~~~~~~~~~~~VaI~~~veHpaLd~~~~G~~~aLk~~G~~n~~i~~~na~~~~~~a~~i   80 (322)
T COG2984           1 MMLRSLSFYLFFAALALAFLSSAGSAAADQITVAITQFVEHPALDAAREGVKEALKDAGYKNVKIDYQNAQGDLGTAAQI   80 (322)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHH
T ss_conf             92688899999999999999741214444336889985066559999997899998648667289962477885789999


Q ss_pred             HHHH-CCCCCEEEECCHH---HHHH-HHH---HHCCCCCCCCCCCCCCCCCCCCCCCCCC------------------CC
Q ss_conf             6521-0666557504223---3234-331---0000123422234720001222223443------------------45
Q gi|254780563|r   67 PITQ-GSPVDVIITKDET---SLAL-NED---LLHKLPAHLIKKNSFVLKNENKKLMRIS------------------FD  120 (195)
Q Consensus        67 ~~~~-~~~~d~~~~~d~~---~l~~-~~~---~l~~~~~~~~~~~~~~~~~~~~~~~~~~------------------~~  120 (195)
                      .+.- ....|+++....+   .+.. -.+   ++.-...+......+.+.-+.+..+|..                  ..
T Consensus        81 arql~~~~~dviv~i~tp~Aq~~~s~~~~iPVV~aavtd~v~a~Lv~~~~~pg~NvTGvsD~~~v~q~i~lik~~~Pnak  160 (322)
T COG2984          81 ARQLVGDKPDVIVAIATPAAQALVSATKTIPVVFAAVTDPVGAKLVKSLEQPGGNVTGVSDLLPVAQQIELIKALLPNAK  160 (322)
T ss_pred             HHHHHCCCCCEEEECCCHHHHHHHHHCCCCCEEEECCCCHHHCCCCCCCCCCCCCEEECCCCCHHHHHHHHHHHHCCCCE
T ss_conf             99961479967996177899999984679887997257633235876444788843623775169999999998678870


Q ss_pred             EEEEEEEHHH
Q ss_conf             0588873344
Q gi|254780563|r  121 TQVLAYSTKR  130 (195)
Q Consensus       121 ~~~~~~n~~~  130 (195)
                      ..++.||+..
T Consensus       161 ~Igv~Y~p~E  170 (322)
T COG2984         161 SIGVLYNPGE  170 (322)
T ss_pred             EEEEEECCCC
T ss_conf             6999957988


No 229
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=22.47  E-value=58  Score=13.81  Aligned_cols=54  Identities=13%  Similarity=0.127  Sum_probs=33.7

Q ss_pred             CCCCEEEECC--CCHHHHHHHHHHHHHHC-CCCCCCCCHHHHHHHHHHHCCCCCEEE
Q ss_conf             5880899818--99899999999999875-986210000135667652106665575
Q gi|254780563|r   25 TTKYLTLYTD--QNQSVMLPIIHSFEERT-GVKISPIYTSSIQRPPITQGSPVDVII   78 (195)
Q Consensus        25 ~~~~lvVYs~--~~~~~~~~~~~~Fek~t-gIkV~~~~~~~~~~~~~~~~~~~d~~~   78 (195)
                      ..++|.|-..  .......+++..|.+++ ++++++....+.+.....+....|+.+
T Consensus        93 ~~g~lrI~~~~s~~~~~lp~~l~~f~~~~P~v~i~l~~~~~~~~~~~l~~~~~D~~i  149 (307)
T CHL00180         93 QGGTLIIGASQTTGTYLMPRLIGLFRQKYPQIAVQLQVHSTRRIAWSVANGQIDLAI  149 (307)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHCCCEEEEE
T ss_conf             258601010406666643588999999888997278977999999999879800999


No 230
>PRK10903 peptidyl-prolyl cis-trans isomerase A (rotamase A); Provisional
Probab=22.44  E-value=58  Score=13.80  Aligned_cols=34  Identities=18%  Similarity=0.092  Sum_probs=17.4

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCC--CEEEECC
Q ss_conf             902599999999999998612444588--0899818
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFSTENTTK--YLTLYTD   34 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~~~~~~--~lvVYs~   34 (195)
                      |++|.++....+++..+...++.++++  .+++=|+
T Consensus         1 ~~~~~~~~~~~~~~~~~~~~~~~~a~~~p~V~i~Ts   36 (190)
T PRK10903          1 MFKSTLAAMAAVFALSALSPAALAAKGDPHVLLTTS   36 (190)
T ss_pred             CHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEC
T ss_conf             968999999999998740354211379976999979


No 231
>cd00713 GltS Glutamine amidotransferases class-II (Gn-AT), glutamate synthase (GltS)-type. GltS is a homodimer that synthesizes L-glutamate from 2-oxoglutarate and L-glutamine, an important step in ammonia assimilation in bacteria, cyanobacteria and plants. The N-terminal glutaminase domain catalyzes the hydrolysis of glutamine to glutamic acid and ammonia, and has a fold similar to that of other glutamine amidotransferases such as glucosamine-fructose 6-phosphate synthase (GLMS or GFAT), glutamine phosphoribosylpyrophosphate (Prpp) amidotransferase (GPATase), asparagine synthetase B (AsnB), and beta lactam synthetase (beta-LS), as well as the Ntn hydrolase folds of the proteasomal alpha and beta subunits.
Probab=22.00  E-value=21  Score=16.29  Aligned_cols=69  Identities=9%  Similarity=0.131  Sum_probs=42.9

Q ss_pred             CCCCCCCEEEEEEEHHHHCCCCCCCCHHHHCCHHHCCEEEEC------CCCCCHH-HHHHHHHHHHCHH----HHHHHHH
Q ss_conf             234434505888733440134455788884086676859962------8983049-9999999960869----9999999
Q gi|254780563|r  114 LMRISFDTQVLAYSTKRIKIADLPKSVFDLTNAQWKKRLSIA------PNNISFH-RLLNTMEQTPNKT----VVQDFIK  182 (195)
Q Consensus       114 ~~~~~~~~~~~~~n~~~~~~~~~P~sw~DL~~p~~kG~i~~~------~~~~s~~-~~~~a~~~~~G~~----~~~~~l~  182 (195)
                      .+-.+.....++| +-.+...++++=|.||.||+|+-.+++-      ++.++.. +.=--++++.||=    ....|.+
T Consensus       166 fYi~SlSsrtIVY-KGml~~~ql~~fY~DL~d~~~~s~~al~H~RFSTNTfPsW~lAqPfR~laHNGEINTi~GN~nwm~  244 (413)
T cd00713         166 FYVCSLSSRTIVY-KGMLLPEQLGQFYPDLQDPRFESAFALVHSRFSTNTFPSWPLAQPFRYLAHNGEINTIRGNRNWMR  244 (413)
T ss_pred             EEEEECCCCEEEE-ECCCCHHHHHHHHHHHCCCCEEEEEEEEEEECCCCCCCCCCCCCCCHHHHCCCCCHHHHHHHHHHH
T ss_conf             6997535141786-412578999886166369765899987883056899998730275500002763001565799999


Q ss_pred             H
Q ss_conf             9
Q gi|254780563|r  183 N  183 (195)
Q Consensus       183 ~  183 (195)
                      +
T Consensus       245 a  245 (413)
T cd00713         245 A  245 (413)
T ss_pred             H
T ss_conf             8


No 232
>PRK12700 flgH flagellar basal body L-ring protein; Reviewed
Probab=21.99  E-value=59  Score=13.75  Aligned_cols=22  Identities=14%  Similarity=0.072  Sum_probs=9.7

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             9025999999999999986124
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFST   22 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~   22 (195)
                      ||=|.++-+++++++++.+.+|
T Consensus         1 ~~~~t~~Rl~~~~~~~~ll~GC   22 (230)
T PRK12700          1 MMLKTVLRLPVCAALLALAAGC   22 (230)
T ss_pred             CCHHHHHHHHHHHHHHHHHHCC
T ss_conf             9158899999999999997444


No 233
>PTZ00203 cathepsin L protease; Provisional
Probab=21.89  E-value=59  Score=13.74  Aligned_cols=44  Identities=11%  Similarity=0.218  Sum_probs=21.8

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             599999999999998612444588089981899899999999999875986
Q gi|254780563|r    4 RTIYTYLLLLCGFTEAFSTENTTKYLTLYTDQNQSVMLPIIHSFEERTGVK   54 (195)
Q Consensus         4 k~~~~~l~l~~~~~~~~~~~~~~~~lvVYs~~~~~~~~~~~~~Fek~tgIk   54 (195)
                      |..+..|+++|+++.+.++.+..    .|.   +.....+.++|.++++-+
T Consensus         5 ~~~~~~~~~~c~~~~~~~a~~~~----~~~---~~~~~~lF~~fk~~y~K~   48 (348)
T PTZ00203          5 RAALCAVAVVCVVLAAACAPARA----IYV---GTPAAALFEEFKRTYQRA   48 (348)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCC----CCC---CCHHHHHHHHHHHHCCCC
T ss_conf             77899999999999985256532----356---708999999999974984


No 234
>TIGR01626 ytfJ_HI0045 conserved hypothetical protein YtfJ-family, TIGR01626; InterPro: IPR006513   These are sequences from gamma proteobacteria that are related to the E. coli protein, YtfJ. .
Probab=21.81  E-value=60  Score=13.73  Aligned_cols=21  Identities=29%  Similarity=0.206  Sum_probs=12.7

Q ss_pred             CHHHHHHHHHHHHHHHHHHCC
Q ss_conf             025999999999999986124
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFST   22 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~~   22 (195)
                      ||++++..++++|+-.+.|+=
T Consensus         1 Mk~~~l~a~~~~~~p~~a~AH   21 (184)
T TIGR01626         1 MKKKKLLALLLVLLPILAFAH   21 (184)
T ss_pred             CCHHHHHHHHHHHHHHHHHHH
T ss_conf             914789999999987756542


No 235
>PRK11548 hypothetical protein; Provisional
Probab=21.75  E-value=60  Score=13.72  Aligned_cols=23  Identities=26%  Similarity=0.108  Sum_probs=11.4

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             90259999999999999861244
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFSTE   23 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~~   23 (195)
                      |-=|++..+.+++++++++|+..
T Consensus         1 m~~k~l~~a~ll~~lllsgCS~~   23 (113)
T PRK11548          1 MRCKTLTAAAAVLLMLTAGCSTL   23 (113)
T ss_pred             CCHHHHHHHHHHHHHHHCCCCCC
T ss_conf             92578899999999998011578


No 236
>PRK05968 hypothetical protein; Provisional
Probab=21.70  E-value=60  Score=13.71  Aligned_cols=44  Identities=7%  Similarity=0.004  Sum_probs=30.9

Q ss_pred             CCCCEEEECCCCHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHH
Q ss_conf             58808998189989999999999987598621000013566765
Q gi|254780563|r   25 TTKYLTLYTDQNQSVMLPIIHSFEERTGVKISPIYTSSIQRPPI   68 (195)
Q Consensus        25 ~~~~lvVYs~~~~~~~~~~~~~Fek~tgIkV~~~~~~~~~~~~~   68 (195)
                      .++.-+|.+..-+.....+++.+-++.||+|+++...+.+....
T Consensus       100 ~~Gd~iv~~~~~YggT~~l~~~~l~~~GI~v~~vd~~d~~~~~~  143 (389)
T PRK05968        100 EPGDRIVAVRHVYPDAYRLFGTLLKRMGVEVDYVDGRDEEAVAK  143 (389)
T ss_pred             CCCCEEEECCCCCCCHHHHHHHHHHCCCCEEEEECCCCHHHHHH
T ss_conf             89998985887667589999988860784699968999999996


No 237
>pfam06291 Lambda_Bor Bor protein. This family consists of several Bacteriophage lambda Bor and Escherichia coli Iss proteins. Expression of bor significantly increases the survival of the Escherichia coli host cell in animal serum. This property is a well known bacterial virulence determinant indeed, bor and its adjacent sequences are highly homologous to the iss serum resistance locus of the plasmid ColV2-K94, which confers virulence in animals. It has been suggested that lysogeny may generally have a role in bacterial survival in animal hosts, and perhaps in pathogenesis.
Probab=21.69  E-value=57  Score=13.83  Aligned_cols=18  Identities=11%  Similarity=0.283  Sum_probs=8.7

Q ss_pred             CHHHHHHHHHHHHHHHHHHC
Q ss_conf             02599999999999998612
Q gi|254780563|r    2 FKRTIYTYLLLLCGFTEAFS   21 (195)
Q Consensus         2 mkk~~~~~l~l~~~~~~~~~   21 (195)
                      |||..+.  ++++.++++|+
T Consensus         1 MKk~~~~--~~~allLtgCa   18 (97)
T pfam06291         1 MKKMLFA--AALALLITGCA   18 (97)
T ss_pred             CHHHHHH--HHHHHHHCCCC
T ss_conf             9225999--99999972133


No 238
>TIGR03519 Bac_Flav_fam_1 Bacteroidetes-specific putative membrane protein. This model describes a protein family unique to, and greatly expanded in, the Bacteriodetes. Species in this lineage include several, such as Cytophaga hutchinsonii and Flavobacterium johnsoniae, that exhibit a poorly understood rapid gliding phenotype. Several members of this protein family are found in operons with other genes whose loss leads to a loss a this motility.
Probab=21.12  E-value=62  Score=13.64  Aligned_cols=13  Identities=38%  Similarity=0.588  Sum_probs=6.7

Q ss_pred             CHHHHHHHHHHHH
Q ss_conf             0259999999999
Q gi|254780563|r    2 FKRTIYTYLLLLC   14 (195)
Q Consensus         2 mkk~~~~~l~l~~   14 (195)
                      |||.++..+++++
T Consensus         1 Mkki~l~~~~~~~   13 (292)
T TIGR03519         1 MKKILLLLLLLLL   13 (292)
T ss_pred             CCCHHHHHHHHHH
T ss_conf             9605788999999


No 239
>COG2913 OlmA Outer membrane lipoprotein OmlA (small protein A) [Cell envelope biogenesis, outer membrane]
Probab=21.08  E-value=62  Score=13.64  Aligned_cols=31  Identities=16%  Similarity=0.141  Sum_probs=12.4

Q ss_pred             CCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEC
Q ss_conf             902599999999999998612444588089981
Q gi|254780563|r    1 MFKRTIYTYLLLLCGFTEAFSTENTTKYLTLYT   33 (195)
Q Consensus         1 mmkk~~~~~l~l~~~~~~~~~~~~~~~~lvVYs   33 (195)
                      ||+++.......+++++++.+|...  +++.|.
T Consensus         2 ~~~~~~~~~~~a~l~~~als~Cst~--~~~~~~   32 (147)
T COG2913           2 MLMATAILAIAALLGAAALSGCSTL--KVVYYN   32 (147)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCC--CCCCCC
T ss_conf             5788889999999999983148754--222345


No 240
>COG2838 Icd Monomeric isocitrate dehydrogenase [Energy production and conversion]
Probab=20.25  E-value=64  Score=13.54  Aligned_cols=32  Identities=22%  Similarity=0.516  Sum_probs=21.7

Q ss_pred             EEEECCCCHH------HHHHHHHHHHHHCCCCCCCCCH
Q ss_conf             8998189989------9999999999875986210000
Q gi|254780563|r   29 LTLYTDQNQS------VMLPIIHSFEERTGVKISPIYT   60 (195)
Q Consensus        29 lvVYs~~~~~------~~~~~~~~Fek~tgIkV~~~~~   60 (195)
                      -+|||-.++.      ..-|++++|.+..||+|+...-
T Consensus         7 ~iiyT~TDEaP~LATysllPIv~Af~~~AgI~VetsDI   44 (744)
T COG2838           7 TIIYTLTDEAPALATYSLLPIVKAFAAPAGIDVETSDI   44 (744)
T ss_pred             EEEEEECCCCHHHHHHHHHHHHHHHHCCCCCCEEECCC
T ss_conf             58998347526777777789999961204775132222


Done!