Query         gi|254781101|ref|YP_003065514.1| UDP-N-acetylmuramoylalanyl-D-glutamyl-2, 6-diaminopimelate/D-alanyl-D-alanyl ligase [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 472
No_of_seqs    233 out of 8252
Neff          8.4 
Searched_HMMs 39220
Date          Mon May 30 05:07:56 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781101.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR01143 murF UDP-N-acetylmur 100.0       0       0  858.8  26.9  430   32-464     1-462 (462)
  2 PRK11929 putative bifunctional 100.0       0       0  839.1  31.2  431   24-466   511-945 (953)
  3 PRK10773 murF UDP-N-acetylmura 100.0       0       0  823.4  34.9  447    1-468     1-450 (452)
  4 PRK11930 putative bifunctional 100.0       0       0  805.3  31.2  453    5-468     3-460 (824)
  5 COG0770 MurF UDP-N-acetylmuram 100.0       0       0  769.0  30.4  450    4-467     2-451 (451)
  6 PRK00139 murE UDP-N-acetylmura 100.0       0       0  630.7  31.9  422    5-452     3-453 (481)
  7 PRK11929 putative bifunctional 100.0       0       0  592.5  24.9  416   24-452    26-473 (953)
  8 TIGR01085 murE UDP-N-acetylmur 100.0       0       0  568.8  24.8  419   24-452     1-470 (494)
  9 COG0769 MurE UDP-N-acetylmuram 100.0       0       0  424.8  19.5  408   28-452    11-447 (475)
 10 PRK00421 murC UDP-N-acetylmura 100.0       0       0  403.9  26.3  369   63-468    66-458 (459)
 11 PRK03803 murD UDP-N-acetylmura 100.0       0       0  400.9  24.2  330  105-464   106-447 (448)
 12 PRK02472 murD UDP-N-acetylmura 100.0       0       0  402.2  22.3  324  106-465   110-448 (450)
 13 PRK01368 murD UDP-N-acetylmura 100.0       0       0  402.0  21.8  336  101-467    97-449 (450)
 14 PRK02006 murD UDP-N-acetylmura 100.0       0       0  392.0  20.0  355   82-467    97-496 (501)
 15 PRK01390 murD UDP-N-acetylmura 100.0       0       0  392.9  17.4  322  106-464   112-456 (457)
 16 PRK04308 murD UDP-N-acetylmura 100.0       0       0  389.5  18.9  324  104-464   106-445 (445)
 17 PRK02705 murD UDP-N-acetylmura 100.0       0       0  389.0  19.2  334  101-467   102-458 (459)
 18 PRK01438 murD UDP-N-acetylmura 100.0       0       0  386.6  19.5  333  106-466   120-478 (481)
 19 PRK01710 murD UDP-N-acetylmura 100.0       0       0  388.3  16.5  322  106-464   115-458 (458)
 20 PRK03806 murD UDP-N-acetylmura 100.0       0       0  378.2  21.1  321  105-464   102-437 (438)
 21 COG0771 MurD UDP-N-acetylmuram 100.0       0       0  372.0  22.2  330  100-465   102-447 (448)
 22 PRK04663 murD UDP-N-acetylmura 100.0       0       0  372.5  20.5  319  106-464   106-437 (438)
 23 PRK03369 murD UDP-N-acetylmura 100.0       0       0  372.0  19.4  323  107-466   116-487 (487)
 24 PRK00141 murD UDP-N-acetylmura 100.0       0       0  369.8  21.0  326  107-467   122-471 (476)
 25 PRK04690 murD UDP-N-acetylmura 100.0       0       0  369.2  20.1  325  106-467   113-458 (468)
 26 TIGR01087 murD UDP-N-acetylmur 100.0       0       0  368.3  17.4  326  107-462   109-475 (476)
 27 TIGR01082 murC UDP-N-acetylmur 100.0       0       0  347.2  20.4  412    7-452    15-480 (491)
 28 COG0773 MurC UDP-N-acetylmuram 100.0       0       0  335.8  23.1  354   80-468    88-457 (459)
 29 PRK00683 murD UDP-N-acetylmura 100.0       0       0  338.2  18.8  301  106-465   100-415 (418)
 30 PRK03815 murD UDP-N-acetylmura 100.0   7E-45       0  316.2  18.8  311   95-464    78-401 (401)
 31 TIGR02068 cya_phycin_syn cyano 100.0   2E-44       0  313.3  13.1  436    6-466   334-872 (876)
 32 pfam08245 Mur_ligase_M Mur lig 100.0 2.3E-42       0  299.5   2.8  186  113-303     1-188 (188)
 33 TIGR01081 mpl UDP-N-acetylmura 100.0 1.4E-37 3.7E-42  267.8  13.6  397    8-468    38-458 (459)
 34 COG0285 FolC Folylpolyglutamat 100.0 4.1E-35   1E-39  251.6  17.7  331  104-467    40-424 (427)
 35 PRK10846 bifunctional folylpol 100.0 3.5E-35   9E-40  252.0  14.8  323   90-453    34-404 (416)
 36 TIGR01499 folC FolC bifunction 100.0 1.2E-33 3.1E-38  241.8  15.9  350   91-466     4-458 (460)
 37 KOG2525 consensus               99.9 1.8E-21 4.6E-26  161.3  17.2  323   90-452    55-481 (496)
 38 pfam01225 Mur_ligase Mur ligas  99.7 5.9E-17 1.5E-21  131.4   9.4   76   26-103     1-76  (76)
 39 pfam02875 Mur_ligase_C Mur lig  99.0 1.2E-09   3E-14   83.2   7.0   78  323-411     1-78  (87)
 40 PRK00892 lpxD UDP-3-O-[3-hydro  98.1 2.6E-05 6.5E-10   54.4   9.5   95    3-106     1-95  (343)
 41 COG1044 LpxD UDP-3-O-[3-hydrox  97.0   0.004   1E-07   39.9   7.1   96    3-107     2-97  (338)
 42 TIGR01853 lipid_A_lpxD UDP-3-O  96.0   0.036 9.3E-07   33.5   7.2   93    9-108     1-94  (336)
 43 PRK05439 pantothenate kinase;   95.3   0.017 4.2E-07   35.8   3.1   27  108-134    86-114 (312)
 44 pfam04613 LpxD UDP-3-O-[3-hydr  95.1    0.11 2.8E-06   30.4   6.7   70   24-101     2-71  (72)
 45 pfam07085 DRTGG DRTGG domain.   94.3    0.34 8.7E-06   27.1   7.9   87    9-99      1-103 (105)
 46 PRK00409 recombination and DNA  93.1    0.53 1.4E-05   25.9   7.1   45  271-321   466-510 (780)
 47 TIGR00313 cobQ cobyric acid sy  92.8   0.049 1.2E-06   32.7   1.4   41  153-194   116-165 (502)
 48 TIGR01069 mutS2 MutS2 family p  92.3    0.86 2.2E-05   24.5   7.2   42  429-472   765-814 (834)
 49 TIGR00670 asp_carb_tr aspartat  92.0    0.93 2.4E-05   24.2   7.5  114  341-471   137-269 (336)
 50 TIGR03453 partition_RepA plasm  91.6    0.12 3.1E-06   30.1   2.2   29  107-135   103-134 (387)
 51 TIGR02764 spore_ybaN_pdaB poly  91.4    0.19 4.9E-06   28.8   3.0  155  284-467    24-187 (198)
 52 TIGR01278 DPOR_BchB light-inde  91.3     1.1 2.8E-05   23.8   7.8   79  367-461   307-392 (562)
 53 TIGR00631 uvrb excinuclease AB  91.2    0.24   6E-06   28.2   3.4  110   93-217    16-162 (667)
 54 PRK13869 plasmid-partitioning   91.1    0.15 3.8E-06   29.5   2.3   29  107-135   120-151 (405)
 55 COG4109 Predicted transcriptio  91.0    0.43 1.1E-05   26.4   4.5   95    5-104    71-180 (432)
 56 TIGR02782 TrbB_P P-type conjug  91.0    0.15 3.9E-06   29.5   2.2   71   37-123    76-156 (315)
 57 TIGR01968 minD_bact septum sit  90.4    0.21 5.4E-06   28.5   2.5   30  109-138     2-34  (272)
 58 COG1419 FlhF Flagellar GTP-bin  90.3    0.98 2.5E-05   24.1   5.8   17   29-45     26-42  (407)
 59 COG1072 CoaA Panthothenate kin  90.2    0.15 3.8E-06   29.5   1.6   75   61-135    17-111 (283)
 60 PRK09841 cryptic autophosphory  90.0    0.34 8.7E-06   27.1   3.3   97  366-469   528-642 (726)
 61 COG1703 ArgK Putative periplas  89.4    0.51 1.3E-05   26.0   3.8   36  102-137    45-82  (323)
 62 COG4555 NatA ABC-type Na+ tran  89.1    0.71 1.8E-05   25.0   4.4   79  107-209    27-108 (245)
 63 COG0595 mRNA degradation ribon  88.9     1.7 4.4E-05   22.5   8.2   12   41-52     32-43  (555)
 64 PRK06761 hypothetical protein;  88.9    0.16 4.1E-06   29.3   0.9   33  112-145     9-43  (281)
 65 COG1936 Predicted nucleotide k  88.8    0.22 5.5E-06   28.4   1.6   21  109-130     1-23  (180)
 66 cd02040 NifH NifH gene encodes  88.8    0.31   8E-06   27.4   2.4   30  108-137     1-32  (270)
 67 PRK06731 flhF flagellar biosyn  88.6    0.21 5.3E-06   28.5   1.4   29  107-135    74-104 (270)
 68 PRK03839 putative kinase; Prov  88.4    0.27   7E-06   27.7   1.9   21  110-130     2-24  (180)
 69 cd02029 PRK_like Phosphoribulo  88.0    0.25 6.3E-06   28.0   1.5   26  110-135     1-28  (277)
 70 cd02026 PRK Phosphoribulokinas  88.0    0.21 5.4E-06   28.5   1.1   25  110-134     1-27  (273)
 71 PRK09435 arginine/ornithine tr  87.7    0.89 2.3E-05   24.4   4.1   40   98-137    39-80  (325)
 72 TIGR01313 therm_gnt_kin carboh  87.7    0.28   7E-06   27.7   1.5   25  110-135     3-27  (175)
 73 PRK11519 tyrosine kinase; Prov  87.0     1.3 3.2E-05   23.3   4.6   99  366-470   523-638 (720)
 74 COG4240 Predicted kinase [Gene  87.0     1.1 2.7E-05   23.9   4.2   49   87-135    29-79  (300)
 75 pfam06564 YhjQ YhjQ protein. T  86.6    0.44 1.1E-05   26.4   2.0   29  108-136     1-32  (244)
 76 cd02025 PanK Pantothenate kina  86.5    0.33 8.4E-06   27.2   1.3   24  110-133     1-26  (220)
 77 pfam06555 consensus             86.1     2.3 5.9E-05   21.6   5.5   34   81-117    10-43  (200)
 78 COG2403 Predicted GTPase [Gene  85.9    0.65 1.7E-05   25.3   2.6   32  106-137   124-159 (449)
 79 PRK10037 cell division protein  85.7    0.53 1.4E-05   25.8   2.1   43  110-152     6-53  (250)
 80 PRK00313 lpxK tetraacyldisacch  85.5    0.75 1.9E-05   24.8   2.8   31  105-135    48-82  (332)
 81 TIGR00750 lao LAO/AO transport  85.2    0.72 1.8E-05   25.0   2.6   31  107-137    37-69  (333)
 82 PRK09825 idnK D-gluconate kina  85.2    0.39   1E-05   26.7   1.2   24  109-133     7-30  (176)
 83 COG1763 MobB Molybdopterin-gua  85.0    0.64 1.6E-05   25.3   2.2   34  108-141     2-37  (161)
 84 PRK05480 uridine kinase; Provi  84.9    0.52 1.3E-05   25.9   1.7   26  107-132     5-32  (209)
 85 pfam02606 LpxK Tetraacyldisacc  84.7    0.86 2.2E-05   24.5   2.8   31  105-135    32-66  (318)
 86 COG0237 CoaE Dephospho-CoA kin  83.9    0.61 1.5E-05   25.5   1.7   21  108-128     2-24  (201)
 87 pfam01121 CoaE Dephospho-CoA k  83.9    0.53 1.4E-05   25.8   1.4   19  110-128     2-22  (179)
 88 PRK08853 DNA polymerase III su  83.8    0.36 9.2E-06   27.0   0.5   35   28-62     73-109 (717)
 89 cd02028 UMPK_like Uridine mono  83.6    0.57 1.5E-05   25.6   1.5   25  110-134     1-27  (179)
 90 PRK05259 consensus              83.1     3.4 8.6E-05   20.5   8.2   92  338-444   211-302 (310)
 91 PRK00652 lpxK tetraacyldisacch  83.1       1 2.5E-05   24.0   2.6   31  105-135    46-80  (334)
 92 cd02023 UMPK Uridine monophosp  83.0    0.48 1.2E-05   26.1   0.9   23  110-132     1-25  (198)
 93 PRK13764 ATPase; Provisional    82.9     1.1 2.7E-05   23.8   2.7   76  107-193   258-336 (605)
 94 PRK01906 tetraacyldisaccharide  82.7     1.2   3E-05   23.6   2.8   31  105-135    53-87  (339)
 95 pfam03308 ArgK ArgK protein. T  82.7     2.3 5.9E-05   21.6   4.3   31  107-137    28-60  (267)
 96 pfam00142 Fer4_NifH 4Fe-4S iro  82.7    0.91 2.3E-05   24.3   2.2   29  109-137     1-31  (269)
 97 COG3954 PrkB Phosphoribulokina  82.6     1.1 2.9E-05   23.7   2.7   28  106-133     3-32  (289)
 98 pfam00485 PRK Phosphoribulokin  82.4    0.58 1.5E-05   25.6   1.1   25  110-134     1-27  (196)
 99 PRK07003 DNA polymerase III su  82.1     0.4   1E-05   26.7   0.2   53    8-63     56-110 (816)
100 PRK10818 cell division inhibit  82.0       1 2.6E-05   24.0   2.3   29  108-136     2-33  (270)
101 TIGR03172 probable selenium-de  81.7    0.79   2E-05   24.7   1.6   26  110-135     1-26  (232)
102 COG2894 MinD Septum formation   81.5     1.2 3.2E-05   23.4   2.6   31  108-138     2-35  (272)
103 COG3367 Uncharacterized conser  81.1       1 2.5E-05   24.0   2.0  100   41-140    70-183 (339)
104 PRK07429 phosphoribulokinase;   81.1    0.92 2.3E-05   24.3   1.8   28  107-134     7-36  (331)
105 PRK11545 gntK gluconate kinase  81.0    0.64 1.6E-05   25.3   1.0   28  107-134     7-36  (177)
106 TIGR01420 pilT_fam twitching m  81.0       4  0.0001   20.0   6.0   67   41-122    73-143 (350)
107 TIGR01188 drrA daunorubicin re  80.8    0.75 1.9E-05   24.9   1.2   29  106-134    19-49  (343)
108 PRK00081 coaE dephospho-CoA ki  80.7    0.91 2.3E-05   24.3   1.6   21  108-128     2-24  (199)
109 PRK09270 frcK putative fructos  80.5     2.6 6.5E-05   21.3   3.9   28  107-134    33-62  (230)
110 PRK06696 uridine kinase; Valid  80.4     3.1 7.9E-05   20.8   4.3   43   93-135     9-55  (227)
111 PRK05648 DNA polymerase III su  80.2    0.62 1.6E-05   25.4   0.6   12  458-469   676-687 (705)
112 CHL00175 minD septum-site dete  79.9     1.3 3.4E-05   23.2   2.3   30  108-137    13-45  (279)
113 PRK08770 DNA polymerase III su  79.7    0.74 1.9E-05   24.9   0.9   12  458-469   639-650 (663)
114 COG0769 MurE UDP-N-acetylmuram  79.7    0.11 2.9E-06   30.3  -3.2   95  105-202    61-161 (475)
115 cd03114 ArgK-like The function  79.4    0.96 2.4E-05   24.2   1.4   27  110-136     1-29  (148)
116 TIGR03450 mycothiol_INO1 inosi  78.6     4.8 0.00012   19.5   5.5   11   28-38     51-61  (351)
117 PRK12323 DNA polymerase III su  78.5    0.67 1.7E-05   25.2   0.4   36   28-63     78-115 (721)
118 pfam07755 DUF1611 Protein of u  78.4     1.2 2.9E-05   23.6   1.6   98   38-136    33-144 (302)
119 PTZ00145 phosphoribosylpyropho  78.4     4.8 0.00012   19.5   6.9   73  324-408   325-399 (443)
120 PRK10751 molybdopterin-guanine  78.0     1.6   4E-05   22.8   2.1   34  108-141     2-37  (170)
121 PRK10799 putative hydrolase-ox  77.9     4.7 0.00012   19.6   4.6   64    6-74      2-66  (247)
122 cd02036 MinD Bacterial cell di  77.8     1.2 3.1E-05   23.5   1.6   27  110-136     1-30  (179)
123 PRK06872 DNA polymerase III su  77.8    0.99 2.5E-05   24.1   1.1   36   28-63     73-110 (696)
124 PRK11670 putative ATPase; Prov  77.6     1.6 4.2E-05   22.6   2.2   29  109-137   108-139 (369)
125 TIGR02087 LEUD_arch 3-isopropy  77.2     4.7 0.00012   19.6   4.4   53    7-72     27-83  (159)
126 TIGR03371 cellulose_yhjQ cellu  76.9     1.7 4.3E-05   22.6   2.1   29  108-136     1-32  (246)
127 cd02022 DPCK Dephospho-coenzym  76.7    0.99 2.5E-05   24.0   0.9   18  110-127     1-20  (179)
128 TIGR00713 hemL glutamate-1-sem  76.7     5.4 0.00014   19.2   6.6  312   57-468    73-431 (434)
129 TIGR02853 spore_dpaA dipicolin  76.7     1.2   3E-05   23.6   1.2   63  159-227    55-131 (288)
130 PRK13705 plasmid-partitioning   76.4     1.8 4.7E-05   22.3   2.1   29  107-135   105-136 (388)
131 TIGR03018 pepcterm_TyrKin exop  76.1     3.4 8.6E-05   20.6   3.4   30  106-135    33-66  (207)
132 TIGR02199 rfaE_dom_II rfaE bif  76.1     5.1 0.00013   19.3   4.4   24  398-421    74-98  (144)
133 TIGR02855 spore_yabG sporulati  75.9    0.84 2.1E-05   24.5   0.3   63  147-211   110-192 (292)
134 PRK01184 hypothetical protein;  75.7     1.7 4.2E-05   22.6   1.8   23  108-134     1-25  (183)
135 TIGR02407 ectoine_ectB diamino  75.7     1.1 2.9E-05   23.7   0.9   37  283-319   281-322 (413)
136 TIGR01846 type_I_sec_HlyB type  74.5     1.8 4.5E-05   22.4   1.6   36  414-449   612-656 (703)
137 TIGR01035 hemA glutamyl-tRNA r  73.5     6.5 0.00016   18.7   9.3   21   88-108    60-80  (436)
138 PTZ00301 uridine kinase; Provi  73.4     2.6 6.7E-05   21.2   2.3   24  107-130     2-27  (210)
139 COG5271 MDN1 AAA ATPase contai  73.2     1.9 4.9E-05   22.2   1.6   20  110-130   469-488 (4600)
140 TIGR00064 ftsY signal recognit  73.2     2.9 7.5E-05   20.9   2.5   31  106-136    80-112 (284)
141 PRK03333 coaE dephospho-CoA ki  73.2     1.8 4.6E-05   22.3   1.4   47  304-360   143-189 (394)
142 COG0572 Udk Uridine kinase [Nu  72.8       2 5.1E-05   22.0   1.6   26  108-133     8-35  (218)
143 PRK08233 hypothetical protein;  72.8     2.2 5.7E-05   21.7   1.8   24  107-130     2-27  (182)
144 PRK07994 DNA polymerase III su  72.7     1.4 3.5E-05   23.2   0.7   39   25-63     70-110 (643)
145 PRK05749 3-deoxy-D-manno-octul  72.6     6.8 0.00017   18.5   4.6   70  402-472   342-423 (423)
146 cd01983 Fer4_NifH The Fer4_Nif  72.6     2.1 5.4E-05   21.9   1.7   26  110-135     1-28  (99)
147 cd02117 NifH_like This family   72.3     2.8 7.2E-05   21.0   2.3   29  109-137     1-31  (212)
148 COG0552 FtsY Signal recognitio  72.1     3.3 8.4E-05   20.6   2.6   27  108-134   139-167 (340)
149 cd03116 MobB Molybdenum is an   71.8     2.7 6.9E-05   21.2   2.1   34  108-141     1-36  (159)
150 COG1855 ATPase (PilT family) [  71.4     5.5 0.00014   19.1   3.6   71  109-190   264-337 (604)
151 PRK02458 ribose-phosphate pyro  71.3     7.3 0.00018   18.3   8.7   60  338-409   220-279 (323)
152 PRK13507 formate--tetrahydrofo  71.1     6.5 0.00017   18.7   3.9   33  103-135    58-96  (587)
153 cd02034 CooC The accessory pro  71.0     2.6 6.7E-05   21.2   1.9   25  111-135     2-28  (116)
154 TIGR01526 nadR_NMN_Atrans nico  70.6     2.8 7.2E-05   21.1   2.0   56  384-442   273-328 (346)
155 PRK04183 glutamyl-tRNA(Gln) am  70.5     5.2 0.00013   19.3   3.3   12   23-34     14-25  (421)
156 cd01882 BMS1 Bms1.  Bms1 is an  70.2     4.8 0.00012   19.5   3.0   23  106-131    37-61  (225)
157 PRK07667 uridine kinase; Provi  69.8     3.1 7.9E-05   20.8   2.0   28  107-134    13-42  (190)
158 KOG0950 consensus               69.8     5.9 0.00015   18.9   3.4   82   35-122   519-601 (1008)
159 PHA02519 plasmid partition pro  69.8     3.3 8.4E-05   20.6   2.1   28  108-135   106-136 (387)
160 cd02024 NRK1 Nicotinamide ribo  69.7       2 5.1E-05   22.0   1.0   22  110-131     1-24  (187)
161 PRK03092 ribose-phosphate pyro  69.7     7.8  0.0002   18.1   9.8   91  338-444   203-293 (304)
162 TIGR02525 plasmid_TraJ plasmid  69.5     1.9 4.7E-05   22.3   0.8   53   78-137   124-177 (374)
163 PRK13230 nitrogenase reductase  69.1     2.2 5.5E-05   21.8   1.1   29  109-137     2-32  (292)
164 PRK10416 cell division protein  69.1       4  0.0001   20.0   2.5   24  330-353   342-365 (499)
165 PHA02518 ParA-like protein; Pr  68.9     3.1   8E-05   20.7   1.9   28  109-136     1-31  (211)
166 pfam03215 Rad17 Rad17 cell cyc  68.5     3.4 8.8E-05   20.5   2.0   44   87-133    27-72  (490)
167 TIGR00235 udk uridine kinase;   67.3     2.9 7.3E-05   21.0   1.4   25  108-132    10-40  (220)
168 COG1428 Deoxynucleoside kinase  67.2     3.4 8.7E-05   20.5   1.8   24  108-131     4-29  (216)
169 COG1663 LpxK Tetraacyldisaccha  66.7       9 0.00023   17.7   3.9   32  106-137    45-80  (336)
170 pfam01656 CbiA CobQ/CobB/MinD/  66.4     2.4   6E-05   21.6   0.8   23  114-136     7-29  (212)
171 cd03109 DTBS Dethiobiotin synt  65.7     2.2 5.5E-05   21.8   0.5   39  114-166     6-45  (134)
172 COG0125 Tmk Thymidylate kinase  65.4     4.1  0.0001   20.0   1.9   33  107-139     2-37  (208)
173 cd02037 MRP-like MRP (Multiple  65.4     3.6 9.1E-05   20.4   1.6   28  110-137     1-31  (169)
174 KOG1970 consensus               64.6     6.1 0.00016   18.8   2.7   46   87-133    90-137 (634)
175 PRK04923 ribose-phosphate pyro  64.5     9.9 0.00025   17.4   8.8   92  338-444   219-310 (319)
176 cd02038 FleN-like FleN is a me  64.5     3.8 9.7E-05   20.2   1.6   51  110-169     1-54  (139)
177 COG0132 BioD Dethiobiotin synt  64.3       5 0.00013   19.4   2.2   29  108-136     2-33  (223)
178 PRK13185 chlL protochlorophyll  63.9     5.2 0.00013   19.3   2.2   31  108-138     2-34  (269)
179 TIGR02528 EutP ethanolamine ut  63.8     4.7 0.00012   19.6   2.0   85  111-195     3-103 (144)
180 PRK03946 pdxA 4-hydroxythreoni  63.6     7.2 0.00018   18.3   2.9   10  349-358   287-296 (304)
181 TIGR02397 dnaX_nterm DNA polym  63.4     2.5 6.5E-05   21.4   0.5   60  112-178    40-104 (363)
182 PRK13506 formate--tetrahydrofo  63.2      10 0.00027   17.3   3.7   32  104-135    50-87  (577)
183 TIGR00347 bioD dethiobiotin sy  63.1     3.4 8.8E-05   20.5   1.2   26  113-138     2-30  (187)
184 PRK08356 hypothetical protein;  63.0     4.3 0.00011   19.9   1.6   28  109-140     6-35  (195)
185 TIGR01186 proV glycine betaine  63.0     2.2 5.6E-05   21.8   0.2   31  107-137    18-51  (372)
186 PRK13233 nifH nitrogenase redu  63.0     5.9 0.00015   18.9   2.3   31  108-138     2-35  (275)
187 TIGR02884 spore_pdaA delta-lac  62.9     6.5 0.00017   18.6   2.6   73  382-467   139-214 (225)
188 KOG3347 consensus               62.8     4.7 0.00012   19.6   1.8   26  109-134     8-35  (176)
189 TIGR01969 minD_arch cell divis  62.7     3.2 8.1E-05   20.7   0.9   23  115-137    10-32  (258)
190 cd01130 VirB11-like_ATPase Typ  62.6     4.8 0.00012   19.5   1.8   29   96-127    16-46  (186)
191 cd02021 GntK Gluconate kinase   62.6     2.7 6.8E-05   21.2   0.5   22  110-132     4-25  (150)
192 PRK12374 putative dithiobiotin  62.5       4  0.0001   20.1   1.4   27  111-137     5-34  (231)
193 KOG2792 consensus               62.3     4.6 0.00012   19.7   1.7   11  113-123    39-49  (280)
194 COG0455 flhG Antiactivator of   62.2     6.2 0.00016   18.8   2.3   29  108-136     2-34  (262)
195 pfam09140 MipZ ATPase MipZ. Mi  62.1     3.5 8.9E-05   20.4   1.0   28  110-137     2-32  (261)
196 cd00477 FTHFS Formyltetrahydro  62.0      11 0.00028   17.1   3.6   33  103-135    33-71  (524)
197 PRK08691 DNA polymerase III su  61.8     3.2 8.1E-05   20.7   0.8   53    8-63     56-110 (704)
198 PRK04507 consensus              61.2      10 0.00026   17.3   3.3   16  348-363   304-319 (323)
199 pfam08353 DUF1727 Domain of un  61.0      11 0.00029   17.0   5.8   96  349-449     4-103 (110)
200 COG3640 CooC CO dehydrogenase   60.7     5.7 0.00015   19.0   1.9   24  110-133     2-28  (255)
201 TIGR00986 3a0801s05tom22 mitoc  60.3     2.1 5.4E-05   21.9  -0.3   50  116-166    78-127 (152)
202 PRK00090 bioD dithiobiotin syn  60.2     5.1 0.00013   19.3   1.6   27  111-137     2-31  (223)
203 cd02042 ParA ParA and ParB of   60.1     4.1  0.0001   20.0   1.1   73  112-201     6-78  (104)
204 pfam03205 MobB Molybdopterin g  59.8     6.6 0.00017   18.6   2.1   27  109-135     1-29  (122)
205 COG1192 Soj ATPases involved i  59.5       5 0.00013   19.4   1.4   28  110-137     7-36  (259)
206 PRK13232 nifH nitrogenase redu  59.4     4.3 0.00011   19.8   1.1   29  109-137     2-32  (273)
207 cd03231 ABC_CcmA_heme_exporter  58.9     4.6 0.00012   19.6   1.2   27  106-132    24-52  (201)
208 cd02032 Bchl_like This family   58.8     4.3 0.00011   19.8   1.1   29  110-138     2-32  (267)
209 COG0540 PyrB Aspartate carbamo  58.7      12 0.00032   16.8   7.0   79  347-433   136-221 (316)
210 PRK13235 nifH nitrogenase redu  58.3     4.5 0.00011   19.7   1.1   30  109-138     2-33  (274)
211 TIGR02124 hypE hydrogenase exp  58.3      11 0.00028   17.2   3.0   51  299-377   261-312 (345)
212 TIGR03180 UraD_2 OHCU decarbox  58.0      12  0.0003   16.9   3.2   14  306-319    47-60  (158)
213 cd03289 ABCC_CFTR2 The CFTR su  58.0     5.7 0.00015   19.0   1.6   31  106-136    28-60  (275)
214 cd03280 ABC_MutS2 MutS2 homolo  58.0       9 0.00023   17.7   2.6   28  107-134    27-58  (200)
215 cd02035 ArsA ArsA ATPase funct  57.6     4.5 0.00012   19.7   1.0   23  114-136     7-29  (217)
216 pfam00448 SRP54 SRP54-type pro  57.5     8.4 0.00021   17.9   2.3   28  108-135     1-30  (196)
217 PRK00698 tmk thymidylate kinas  57.4     8.6 0.00022   17.9   2.4   29  107-135     2-32  (204)
218 cd00550 ArsA_ATPase Oxyanion-t  57.3     4.7 0.00012   19.6   1.1   27  110-136     2-30  (254)
219 PRK03367 consensus              57.1      13 0.00034   16.6   4.2   17  348-364   309-325 (329)
220 PRK01259 ribose-phosphate pyro  57.1      13 0.00034   16.6   9.3   60  338-409   210-269 (309)
221 COG3044 Predicted ATPase of th  56.8     8.6 0.00022   17.8   2.3   44    4-56      1-44  (554)
222 PRK13505 formate--tetrahydrofo  56.8      11 0.00028   17.2   2.8   33  103-135    49-87  (556)
223 PRK10437 carbonic anhydrase; P  56.7      10 0.00026   17.3   2.7   24   21-45     33-63  (220)
224 COG0001 HemL Glutamate-1-semia  56.6      10 0.00026   17.3   2.7   75  323-406   279-353 (432)
225 TIGR00382 clpX ATP-dependent C  56.4     3.8 9.8E-05   20.2   0.5   37   94-131   141-177 (452)
226 PRK03695 vitamin B12-transport  56.3     5.3 0.00013   19.2   1.1   30  107-136    22-53  (245)
227 pfam04166 PdxA Pyridoxal phosp  56.1      14 0.00035   16.5   3.8   11  348-358   286-296 (299)
228 pfam09818 ABC_ATPase Predicted  56.0      14 0.00035   16.5   3.6   20  390-411   330-349 (447)
229 TIGR03029 EpsG chain length de  55.9      14 0.00035   16.5   4.2  102   31-135     9-133 (274)
230 cd02033 BchX Chlorophyllide re  55.8     8.7 0.00022   17.8   2.2   32  107-138    30-63  (329)
231 pfam01268 FTHFS Formate--tetra  55.2      11 0.00029   17.1   2.7   32  104-135    50-87  (555)
232 PRK13540 cytochrome c biogenes  55.2     6.1 0.00015   18.9   1.3   27  106-132    25-53  (200)
233 TIGR02188 Ac_CoA_lig_AcsA acet  55.0      14 0.00036   16.4   6.0   82   36-118   286-379 (643)
234 COG3172 NadR Predicted ATPase/  55.0     7.1 0.00018   18.4   1.6   25  108-132     8-34  (187)
235 PRK08674 bifunctional phosphog  54.9      14 0.00037   16.4   5.9   84   33-119    27-116 (328)
236 PRK08099 nicotinamide-nucleoti  54.4      14 0.00035   16.5   3.1   74  391-467   329-408 (411)
237 PRK11860 bifunctional 3-phosph  54.2      15 0.00038   16.3   3.4   37    7-44     56-92  (662)
238 pfam09905 DUF2132 Uncharacteri  54.0       5 0.00013   19.4   0.7   47  306-364     7-53  (64)
239 cd03278 ABC_SMC_barmotin Barmo  53.9     9.4 0.00024   17.6   2.1   25  106-131    21-47  (197)
240 TIGR00503 prfC peptide chain r  53.6      10 0.00027   17.3   2.3   39  429-469   419-459 (530)
241 PRK00411 cdc6 cell division co  53.5      14 0.00037   16.4   3.0   41   93-134    37-83  (394)
242 TIGR02881 spore_V_K stage V sp  53.5     5.6 0.00014   19.1   0.9   18  117-134    53-70  (261)
243 PRK13541 cytochrome c biogenes  53.3     6.3 0.00016   18.7   1.2   31  106-136    24-57  (195)
244 PRK07078 hypothetical protein;  53.2     6.4 0.00016   18.7   1.1   20  114-133   250-269 (510)
245 cd03110 Fer4_NifH_child This p  52.7     6.6 0.00017   18.6   1.2   21  111-131     2-25  (179)
246 KOG2182 consensus               52.4      16  0.0004   16.1   7.3   99   32-135    77-194 (514)
247 TIGR03499 FlhF flagellar biosy  52.4      12 0.00032   16.8   2.5   28  421-449   251-278 (282)
248 PRK13236 nitrogenase reductase  52.3      11 0.00027   17.3   2.2   32  107-138     5-38  (295)
249 PRK09111 DNA polymerase III su  52.1     6.2 0.00016   18.8   0.9   22  111-132    48-71  (600)
250 COG1219 ClpX ATP-dependent pro  51.4     3.7 9.4E-05   20.3  -0.3   98  105-216    97-202 (408)
251 TIGR01281 DPOR_bchL light-inde  51.3     7.6 0.00019   18.2   1.3   29  110-138     2-32  (275)
252 cd05008 SIS_GlmS_GlmD_1 SIS (S  50.9      17 0.00042   16.0   4.0   37   33-69     40-78  (126)
253 COG0556 UvrB Helicase subunit   50.6      17 0.00043   15.9   3.0   13  109-122    36-48  (663)
254 cd03215 ABC_Carb_Monos_II This  50.4     8.3 0.00021   18.0   1.4   27  106-132    24-52  (182)
255 PRK04117 consensus              50.1      17 0.00043   15.9   8.9   90  338-445   213-302 (309)
256 PRK00023 cmk cytidylate kinase  50.1      10 0.00026   17.3   1.8   28  107-134     3-32  (225)
257 COG0462 PrsA Phosphoribosylpyr  50.1      17 0.00044   15.9   9.1   61  337-409   215-275 (314)
258 PRK13896 cobyrinic acid a,c-di  50.0      12  0.0003   16.9   2.1   28  110-137     5-33  (432)
259 PRK01999 consensus              49.7      17 0.00044   15.8   8.7   89  338-444   214-302 (311)
260 COG0489 Mrp ATPases involved i  49.5      13 0.00034   16.6   2.3   30  107-136    56-88  (265)
261 TIGR02253 CTE7 HAD superfamily  49.4      17 0.00044   15.8   5.1   74  357-449   119-192 (244)
262 TIGR02173 cyt_kin_arch cytidyl  49.4     9.5 0.00024   17.6   1.6   24  110-133     2-27  (173)
263 TIGR03238 dnd_assoc_3 dnd syst  49.4      17 0.00045   15.8   4.0   28   91-118    76-104 (504)
264 TIGR02640 gas_vesic_GvpN gas v  49.1     8.8 0.00022   17.8   1.3   51   89-142     5-55  (265)
265 pfam02374 ArsA_ATPase Anion-tr  49.1      14 0.00034   16.5   2.3   27  109-135     2-30  (304)
266 TIGR00176 mobB molybdopterin-g  49.1     8.6 0.00022   17.9   1.3   32  110-141     1-34  (165)
267 PRK01077 cobyrinic acid a,c-di  49.0      16  0.0004   16.1   2.6   30  108-137     3-35  (451)
268 cd03115 SRP The signal recogni  49.0      14 0.00035   16.5   2.3   26  110-135     2-29  (173)
269 cd00884 beta_CA_cladeB Carboni  49.0      18 0.00045   15.8   2.9   25   20-45     23-54  (190)
270 cd03220 ABC_KpsT_Wzt ABC_KpsT_  48.9     8.5 0.00022   17.9   1.2   27  106-132    46-74  (224)
271 TIGR01978 sufC FeS assembly AT  48.9      18 0.00045   15.8   3.2   33  106-142    24-58  (248)
272 PRK05298 excinuclease ABC subu  48.5      17 0.00044   15.8   2.8   33   90-123    17-50  (657)
273 cd03226 ABC_cobalt_CbiO_domain  48.1     8.9 0.00023   17.7   1.2   27  106-132    24-52  (205)
274 PRK04607 consensus              48.0      18 0.00047   15.7   2.9   17  347-363   310-326 (330)
275 CHL00072 chlL photochlorophyll  48.0     8.2 0.00021   18.0   1.0   28  111-138     3-32  (271)
276 cd03225 ABC_cobalt_CbiO_domain  47.9     9.2 0.00023   17.7   1.3   26  106-131    25-52  (211)
277 cd03237 ABC_RNaseL_inhibitor_d  47.9     8.8 0.00022   17.8   1.2   26  107-132    24-51  (246)
278 COG1880 CdhB CO dehydrogenase/  47.7      19 0.00047   15.6   8.4   16  183-198   108-123 (170)
279 PRK13477 bifunctional pantoate  47.7      12 0.00031   16.9   1.9   26  442-468   476-501 (512)
280 PRK04554 consensus              47.6      19 0.00047   15.6   9.2   92  338-444   217-308 (327)
281 KOG3022 consensus               47.5     8.8 0.00022   17.8   1.1   27  109-135    48-77  (300)
282 PRK10584 putative ABC transpor  47.5     8.9 0.00023   17.8   1.1   27  106-132    34-62  (228)
283 PRK02812 ribose-phosphate pyro  47.4      19 0.00048   15.6  10.5   61  337-409   231-292 (331)
284 PRK13650 cbiO cobalt transport  47.1     9.4 0.00024   17.6   1.2   27  106-132    28-56  (276)
285 PRK05632 phosphate acetyltrans  46.9      19 0.00049   15.6  10.1   95    6-101   219-334 (702)
286 COG1245 Predicted ATPase, RNas  46.8     2.5 6.3E-05   21.4  -1.8   86   38-131    30-125 (591)
287 PRK06942 glutamate-1-semialdeh  46.7     9.1 0.00023   17.7   1.1   51  344-403   296-346 (425)
288 cd00267 ABC_ATPase ABC (ATP-bi  46.5      11 0.00027   17.3   1.4   26  106-131    23-50  (157)
289 COG4152 ABC-type uncharacteriz  46.0      11 0.00029   17.0   1.5   32  106-137    26-60  (300)
290 PRK00615 glutamate-1-semialdeh  45.8     9.6 0.00024   17.5   1.1   53  341-402   297-349 (433)
291 PRK11247 ssuB aliphatic sulfon  45.7      10 0.00026   17.4   1.2   27  106-132    36-64  (257)
292 pfam01935 DUF87 Domain of unkn  45.6     9.7 0.00025   17.5   1.1   24  107-131    25-49  (218)
293 PRK13544 consensus              45.6      11 0.00027   17.3   1.3   27  106-132    25-53  (208)
294 TIGR02873 spore_ylxY probable   45.5      20 0.00051   15.4   4.2   40  428-467   216-257 (269)
295 cd03227 ABC_Class2 ABC-type Cl  45.5      16 0.00041   16.0   2.2   21  107-127    20-42  (162)
296 PRK13538 cytochrome c biogenes  45.4      10 0.00026   17.4   1.2   26  106-131    25-52  (204)
297 TIGR02475 CobW cobalamin biosy  45.2      12  0.0003   16.9   1.5   31  106-139     2-35  (349)
298 cd02019 NK Nucleoside/nucleoti  45.2      12  0.0003   16.9   1.5   21  110-130     1-23  (69)
299 PRK10824 hypothetical protein;  45.1      19 0.00048   15.6   2.5   14  311-324    56-69  (115)
300 cd03246 ABCC_Protease_Secretio  45.1      11 0.00028   17.2   1.3   26  106-131    26-53  (173)
301 PRK13234 nifH nitrogenase redu  45.0      16 0.00041   16.1   2.1   32  107-138     3-36  (293)
302 cd03269 ABC_putative_ATPase Th  45.0      12  0.0003   16.9   1.5   27  106-132    24-52  (210)
303 cd03247 ABCC_cytochrome_bd The  45.0      12 0.00032   16.8   1.6   26  106-131    26-53  (178)
304 cd03236 ABC_RNaseL_inhibitor_d  44.8      10 0.00026   17.3   1.1   26  107-132    25-52  (255)
305 PRK13546 teichoic acids export  44.7      11 0.00028   17.2   1.2   27  106-132    48-76  (264)
306 PRK13647 cbiO cobalt transport  44.6      11 0.00028   17.1   1.3   26  106-131    29-56  (273)
307 cd00883 beta_CA_cladeA Carboni  44.6      21 0.00053   15.3   4.7   26   20-46     22-54  (182)
308 PRK00232 pdxA 4-hydroxythreoni  44.6      21 0.00053   15.3   3.7   17  348-364   313-329 (334)
309 KOG3220 consensus               44.5      14 0.00036   16.4   1.8   22  109-134     2-25  (225)
310 PRK13652 cbiO cobalt transport  44.5      11 0.00028   17.1   1.2   27  106-132    28-56  (277)
311 TIGR01007 eps_fam capsular exo  44.2      16  0.0004   16.1   2.0   29  107-135    18-49  (207)
312 cd03248 ABCC_TAP TAP, the Tran  43.9      12 0.00031   16.9   1.4   26  106-131    38-65  (226)
313 KOG3354 consensus               43.8      11 0.00028   17.1   1.2   24  110-134    17-40  (191)
314 cd03222 ABC_RNaseL_inhibitor T  43.8      11 0.00029   17.1   1.2   27  106-132    23-51  (177)
315 KOG1324 consensus               43.7      21 0.00054   15.2   4.4   76  318-407    61-137 (190)
316 PRK13644 cbiO cobalt transport  43.7      12 0.00031   16.9   1.4   27  106-132    26-54  (274)
317 cd01672 TMPK Thymidine monopho  43.6      17 0.00043   15.9   2.1   26  110-135     2-29  (200)
318 PRK11831 putative ABC transpor  43.5      11 0.00029   17.1   1.2   27  106-132    32-60  (269)
319 COG1618 Predicted nucleotide k  43.4      16  0.0004   16.1   1.9   26  109-134     6-33  (179)
320 cd03240 ABC_Rad50 The catalyti  43.2      13 0.00034   16.6   1.5   22  106-127    20-43  (204)
321 PRK00553 ribose-phosphate pyro  43.1      22 0.00055   15.2  10.8  111  338-466   228-338 (340)
322 pfam07693 KAP_NTPase KAP famil  43.1      22 0.00056   15.2   3.6   38   96-133     6-47  (301)
323 PRK13637 cbiO cobalt transport  43.0      12  0.0003   16.9   1.2   27  106-132    31-59  (287)
324 PRK13632 cbiO cobalt transport  42.9      13 0.00032   16.8   1.3   27  106-132    34-62  (273)
325 cd03257 ABC_NikE_OppD_transpor  42.9      12 0.00031   16.9   1.2   26  106-131    29-56  (228)
326 cd04261 AAK_AKii-LysC-BS AAK_A  42.8      18 0.00045   15.8   2.1   16  107-122    31-46  (239)
327 pfam07015 VirC1 VirC1 protein.  42.7      11 0.00028   17.1   1.0   29  109-137     2-33  (231)
328 cd03216 ABC_Carb_Monos_I This   42.6      12 0.00031   16.9   1.2   26  106-131    24-51  (163)
329 PRK02270 consensus              42.5      22 0.00057   15.1  10.6   92  338-444   216-307 (327)
330 cd03228 ABCC_MRP_Like The MRP   42.4      13 0.00032   16.7   1.3   26  106-131    26-53  (171)
331 PRK06131 dihydroxy-acid dehydr  42.4      22 0.00057   15.1   3.3  147  296-456   279-449 (577)
332 PRK13651 cobalt transporter AT  42.3      13 0.00032   16.7   1.3   27  106-132    31-59  (304)
333 TIGR01521 FruBisAldo_II_B fruc  42.2      22 0.00057   15.1   4.5   17  303-319   251-267 (347)
334 PRK13633 cobalt transporter AT  41.9      13 0.00034   16.6   1.4   27  106-132    35-63  (281)
335 PRK09580 sufC cysteine desulfu  41.9      16 0.00042   16.0   1.8   37  337-375   164-201 (248)
336 PRK13639 cbiO cobalt transport  41.9      13 0.00032   16.8   1.2   31  106-136    26-59  (275)
337 PRK13543 cytochrome c biogenes  41.7      13 0.00032   16.7   1.2   26  107-132    36-63  (214)
338 TIGR03164 UHCUDC OHCU decarbox  41.7      23 0.00058   15.0   2.8   15  306-320    45-59  (157)
339 cd03219 ABC_Mj1267_LivG_branch  41.6      13 0.00033   16.6   1.3   27  106-132    24-52  (236)
340 PRK13409 putative ATPase RIL;   41.4      12 0.00031   16.8   1.1   26  107-132    98-125 (590)
341 cd02020 CMPK Cytidine monophos  41.4      12 0.00031   16.8   1.1   25  110-134     1-27  (147)
342 COG0373 HemA Glutamyl-tRNA red  41.3      23 0.00059   15.0   8.5   15  222-236   205-219 (414)
343 PRK13974 thymidylate kinase; P  41.2      21 0.00054   15.2   2.3   28  107-134     2-31  (212)
344 CHL00181 cbbX CbbX; Provisiona  41.2      23 0.00059   15.0   3.2   24  111-134    62-87  (287)
345 PRK13537 lipooligosaccharide t  41.0      13 0.00032   16.7   1.1   28  106-133    29-58  (304)
346 pfam00488 MutS_V MutS domain V  40.9      23 0.00058   15.0   2.4   28  107-134    41-72  (234)
347 PRK13631 cbiO cobalt transport  40.8      13 0.00034   16.6   1.2   28  106-133    50-79  (320)
348 KOG3308 consensus               40.8      15 0.00038   16.2   1.5   25  108-132     4-30  (225)
349 COG1131 CcmA ABC-type multidru  40.8      12 0.00032   16.8   1.0   26  107-132    30-57  (293)
350 PRK13646 cbiO cobalt transport  40.8      14 0.00036   16.4   1.3   27  106-132    31-59  (286)
351 PRK13640 cbiO cobalt transport  40.6      17 0.00042   16.0   1.7   27  106-132    32-60  (283)
352 COG4586 ABC-type uncharacteriz  40.2      17 0.00043   15.9   1.7   30  106-135    48-80  (325)
353 PRK13645 cbiO cobalt transport  40.0      15 0.00038   16.3   1.4   27  106-132    35-63  (289)
354 TIGR02533 type_II_gspE general  39.9      24 0.00062   14.9   3.6   20  110-132   247-268 (495)
355 PRK10771 thiQ thiamine transpo  39.9      14 0.00035   16.5   1.2   27  106-132    23-51  (233)
356 TIGR01405 polC_Gram_pos DNA po  39.9      14 0.00036   16.4   1.2   73  164-240   223-309 (1264)
357 COG1193 Mismatch repair ATPase  39.8      21 0.00054   15.3   2.1   37  278-320   463-499 (753)
358 PRK13542 consensus              39.6      14 0.00036   16.5   1.2   27  106-132    42-70  (224)
359 TIGR01124 ilvA_2Cterm threonin  39.5      25 0.00063   14.8   3.1   34   35-70     63-96  (508)
360 pfam02223 Thymidylate_kin Thym  39.4      11 0.00028   17.2   0.6   19  117-135     7-25  (186)
361 PRK04040 adenylate kinase; Pro  39.3      19 0.00048   15.6   1.8   30  108-137     2-33  (189)
362 COG2019 AdkA Archaeal adenylat  39.3      22 0.00057   15.1   2.2   23  108-130     4-28  (189)
363 PRK11629 lolD lipoprotein tran  39.2      14 0.00035   16.5   1.1   27  106-132    33-61  (233)
364 PRK10436 hypothetical protein;  39.1      25 0.00064   14.8   3.6   29  292-320   317-345 (461)
365 cd03235 ABC_Metallic_Cations A  38.9      15 0.00038   16.3   1.2   53  337-407   151-205 (213)
366 COG1797 CobB Cobyrinic acid a,  38.9      19 0.00048   15.6   1.7   26  110-135     4-30  (451)
367 COG2759 MIS1 Formyltetrahydrof  38.9      25 0.00064   14.8   3.0   31  105-135    49-85  (554)
368 pfam05577 Peptidase_S28 Serine  38.8      25 0.00064   14.8  10.4  105   25-135    13-135 (433)
369 PRK13849 putative crown gall t  38.8      14 0.00036   16.5   1.0   29  109-137     2-33  (231)
370 PRK13539 cytochrome c biogenes  38.7      15 0.00037   16.3   1.1   26  106-131    26-53  (206)
371 cd03250 ABCC_MRP_domain1 Domai  38.5      15 0.00038   16.3   1.2   25  106-130    29-55  (204)
372 PRK05563 DNA polymerase III su  38.5      11 0.00027   17.2   0.4   32  289-320   257-288 (541)
373 KOG4777 consensus               38.3     9.4 0.00024   17.6   0.1   56  107-168     6-71  (361)
374 PRK13634 cbiO cobalt transport  38.2      15 0.00039   16.2   1.2   27  106-132    18-46  (276)
375 PRK10895 putative ABC transpor  38.2      15 0.00039   16.2   1.2   27  106-132    27-55  (241)
376 COG1105 FruK Fructose-1-phosph  38.1      26 0.00066   14.7   4.4   29  218-246   128-162 (310)
377 PRK00856 pyrB aspartate carbam  38.0      26 0.00066   14.7   7.0   11   93-103    21-31  (304)
378 PRK09984 phosphonate/organopho  38.0      18 0.00046   15.7   1.5   26  106-131    28-55  (262)
379 pfam02562 PhoH PhoH-like prote  37.9      26 0.00066   14.7   2.6   39  336-380   119-157 (205)
380 PRK03846 adenylylsulfate kinas  37.9      26 0.00066   14.7   3.2   36  100-135    16-53  (198)
381 PRK13582 thrH phosphoserine ph  37.6      26 0.00067   14.6   4.8   24  421-444   179-202 (205)
382 PRK09473 oppD oligopeptide tra  37.5      15 0.00039   16.2   1.1   31  106-136    40-72  (330)
383 cd03230 ABC_DR_subfamily_A Thi  37.4      16 0.00042   16.0   1.2   37  337-375   114-151 (173)
384 PRK13649 cbiO cobalt transport  37.3      17 0.00044   15.9   1.3   27  106-132    31-59  (280)
385 cd03267 ABC_NatA_like Similar   37.2      17 0.00042   15.9   1.2   26  107-132    46-73  (236)
386 TIGR02798 ligK_PcmE 4-carboxy-  37.2      27 0.00068   14.6   3.3   19  185-203    77-95  (222)
387 PRK13642 cbiO cobalt transport  37.1      16 0.00042   16.0   1.2   27  106-132    31-59  (277)
388 TIGR01193 bacteriocin_ABC ABC-  36.9      11 0.00028   17.2   0.3   49   23-73     71-132 (710)
389 KOG0479 consensus               36.9      27 0.00069   14.6   3.7   77   39-120   288-373 (818)
390 PRK13768 GTPase; Provisional    36.8      15 0.00037   16.3   0.9  113  339-468   133-246 (253)
391 PRK13635 cbiO cobalt transport  36.7      17 0.00044   15.9   1.3   27  106-132    31-59  (279)
392 TIGR01950 SoxR redox-sensitive  36.7      16 0.00042   16.0   1.1   28  297-326    47-74  (142)
393 PRK13231 nitrogenase reductase  36.6      15 0.00038   16.3   0.9   29  109-137     3-33  (264)
394 cd03268 ABC_BcrA_bacitracin_re  36.6      17 0.00043   15.9   1.2   28  106-133    24-53  (208)
395 COG4917 EutP Ethanolamine util  36.5      27  0.0007   14.5   3.2   53  156-214    61-116 (148)
396 PRK13641 cbiO cobalt transport  36.4      17 0.00043   15.9   1.2   31  106-136    31-64  (286)
397 PRK13638 cbiO cobalt transport  36.3      17 0.00044   15.9   1.2   27  106-132    25-53  (271)
398 PRK11147 ABC transporter ATPas  36.1      18 0.00047   15.7   1.3   34   25-62     17-50  (632)
399 cd03224 ABC_TM1139_LivF_branch  36.0      17 0.00044   15.9   1.2   27  106-132    24-52  (222)
400 PRK11614 livF leucine/isoleuci  36.0      17 0.00043   15.9   1.1   26  106-131    29-56  (237)
401 pfam04851 ResIII Type III rest  36.0      28 0.00071   14.5   2.9   24  104-128    17-40  (103)
402 cd03293 ABC_NrtD_SsuB_transpor  35.6      18 0.00045   15.8   1.2   27  106-132    28-56  (220)
403 TIGR03522 GldA_ABC_ATP gliding  35.6      17 0.00045   15.8   1.1   28  106-133    26-55  (301)
404 TIGR00041 DTMP_kinase thymidyl  35.5      13 0.00033   16.7   0.5   23  117-139    13-37  (211)
405 PRK07560 elongation factor EF-  35.4      28 0.00073   14.4   3.1   13  350-362   404-416 (730)
406 PRK12367 short chain dehydroge  35.3      29 0.00073   14.4   2.5   33  105-138    14-46  (250)
407 COG1102 Cmk Cytidylate kinase   35.3      24  0.0006   14.9   1.8   22  110-131     2-25  (179)
408 PRK13636 cbiO cobalt transport  35.3      18 0.00047   15.7   1.2   26  106-131    30-57  (285)
409 cd03221 ABCF_EF-3 ABCF_EF-3  E  35.1      18 0.00045   15.8   1.1   26  106-131    24-51  (144)
410 COG0003 ArsA Predicted ATPase   35.1      17 0.00044   15.8   1.0   27  109-135     3-31  (322)
411 PRK13648 cbiO cobalt transport  34.9      19 0.00049   15.5   1.3   27  106-132    33-61  (269)
412 cd05213 NAD_bind_Glutamyl_tRNA  34.9      29 0.00074   14.4   6.5   89  348-453   156-249 (311)
413 KOG0927 consensus               34.9      29 0.00074   14.4   5.1   38  427-471   542-579 (614)
414 PRK11264 putative amino-acid A  34.8      19 0.00048   15.6   1.2   26  106-131    25-52  (248)
415 PRK10908 cell division protein  34.6      17 0.00044   15.9   1.0   27  106-132    26-54  (222)
416 KOG0447 consensus               34.6      22 0.00057   15.1   1.5   23  107-129   307-331 (980)
417 PRK00062 glutamate-1-semialdeh  34.6      20 0.00051   15.4   1.3   50  344-402   298-347 (429)
418 cd03244 ABCC_MRP_domain2 Domai  34.5      20  0.0005   15.5   1.3   26  106-131    28-55  (221)
419 pfam01784 NIF3 NIF3 (NGG1p int  34.5      29 0.00075   14.3   5.1   30  370-410   171-200 (238)
420 COG4167 SapF ABC-type antimicr  34.4      30 0.00075   14.3   2.2   48   84-131     3-64  (267)
421 cd03245 ABCC_bacteriocin_expor  34.4      21 0.00053   15.3   1.4   26  106-131    28-55  (220)
422 cd03233 ABC_PDR_domain1 The pl  34.3      19 0.00048   15.6   1.1   26  106-131    31-58  (202)
423 cd03369 ABCC_NFT1 Domain 2 of   34.3      26 0.00065   14.7   1.8   27  106-132    32-60  (207)
424 PRK03743 pdxA 4-hydroxythreoni  34.3      30 0.00076   14.3   3.7   20  347-366   310-329 (333)
425 PRK13946 shikimate kinase; Pro  34.2      18 0.00046   15.7   1.0   27  105-132    20-46  (195)
426 PRK13695 putative NTPase; Prov  34.2      26 0.00067   14.6   1.9   25  110-134     5-31  (174)
427 cd03379 beta_CA_cladeD Carboni  34.2      22 0.00056   15.1   1.5   15   31-45     10-31  (142)
428 TIGR01394 TypA_BipA GTP-bindin  34.2      19 0.00049   15.5   1.2   60   57-120   115-177 (609)
429 PRK01506 consensus              34.1      30 0.00076   14.3   8.2   91  338-444   219-309 (317)
430 PRK13643 cbiO cobalt transport  34.1      20 0.00051   15.4   1.2   27  106-132    30-58  (288)
431 cd03254 ABCC_Glucan_exporter_l  34.0      20  0.0005   15.5   1.2   26  106-131    27-54  (229)
432 TIGR00618 sbcc exonuclease Sbc  34.0      30 0.00077   14.3   2.2   27  107-135    29-57  (1063)
433 cd03255 ABC_MJ0796_Lo1CDE_FtsE  33.9      19  0.0005   15.5   1.2   27  106-132    28-56  (218)
434 PRK10247 putative ABC transpor  33.9      21 0.00053   15.3   1.3   27  106-132    31-59  (225)
435 TIGR03591 polynuc_phos polyrib  33.9      28 0.00072   14.4   2.0   42    6-47     10-51  (684)
436 cd04246 AAK_AK-DapG-like AAK_A  33.8      11 0.00029   17.0  -0.0   30   93-122    15-46  (239)
437 TIGR01307 pgm_bpd_ind 2,3-bisp  33.5      31 0.00078   14.2   6.3   73  391-466   436-513 (529)
438 pfam03142 Chitin_synth_2 Chiti  33.3      31 0.00078   14.2   3.4   18  114-131    69-86  (536)
439 PRK10246 exonuclease subunit S  33.2      31 0.00079   14.2   2.8   12  441-452   500-511 (1047)
440 cd01673 dNK Deoxyribonucleosid  33.1      22 0.00056   15.2   1.3   21  110-130     1-23  (193)
441 cd03265 ABC_DrrA DrrA is the A  33.0      21 0.00053   15.3   1.2   27  106-132    24-52  (220)
442 PRK13137 consensus              32.8      31  0.0008   14.1   4.9   53   91-152     5-62  (266)
443 PRK13948 shikimate kinase; Pro  32.8      13 0.00033   16.7   0.1   25  109-133    11-37  (182)
444 pfam05049 IIGP Interferon-indu  32.8      31  0.0008   14.1   3.7   35   90-124    16-53  (375)
445 PRK01909 pdxA 4-hydroxythreoni  32.7      31  0.0008   14.1   4.1   17  348-364   307-323 (329)
446 PRK00230 orotidine 5'-phosphat  32.7      31  0.0008   14.1   4.0   29  390-418   139-167 (231)
447 PRK09493 glnQ glutamine ABC tr  32.5      22 0.00055   15.2   1.2   26  106-131    25-52  (240)
448 PRK13548 hmuV hemin importer A  32.3      22 0.00057   15.1   1.3   26  106-131    26-53  (257)
449 TIGR01011 rpsB_bact ribosomal   32.3      32 0.00081   14.1   3.8   10  311-320   105-114 (227)
450 cd02030 NDUO42 NADH:Ubiquinone  32.2      23 0.00058   15.0   1.3   21  110-130     1-23  (219)
451 cd03251 ABCC_MsbA MsbA is an e  32.2      22 0.00056   15.2   1.2   25  106-130    26-52  (234)
452 PRK10762 D-ribose transporter   32.0      24 0.00061   14.9   1.4   51    1-62      1-51  (501)
453 KOG2749 consensus               31.9      32 0.00083   14.0   4.7   50   84-133    78-131 (415)
454 COG0288 CynT Carbonic anhydras  31.9      28 0.00072   14.4   1.7   24  101-124    84-107 (207)
455 PRK13549 xylose transporter AT  31.9      24 0.00061   14.9   1.4   51    1-62      2-52  (513)
456 PRK00676 hemA glutamyl-tRNA re  31.8      33 0.00083   14.0   5.3   22  432-453   311-332 (338)
457 cd03263 ABC_subfamily_A The AB  31.6      23 0.00059   15.0   1.2   27  106-132    26-54  (220)
458 pfam05711 TylF Macrocin-O-meth  31.6      30 0.00076   14.3   1.8   11  336-347   205-215 (249)
459 TIGR00259 TIGR00259 conserved   31.5      23 0.00059   15.0   1.2  138   45-219    12-177 (261)
460 PRK05472 redox-sensing transcr  31.5      33 0.00084   14.0   3.6   19  302-320    38-56  (211)
461 PRK11124 artP arginine transpo  31.4      23 0.00058   15.1   1.2   26  106-131    26-53  (242)
462 cd03214 ABC_Iron-Siderophores_  31.3      23 0.00059   15.0   1.2   26  106-131    23-50  (180)
463 cd03234 ABCG_White The White s  31.3      21 0.00054   15.2   1.0   27  106-132    31-59  (226)
464 PRK11300 livG leucine/isoleuci  31.1      23 0.00058   15.0   1.1   26  106-131    29-56  (255)
465 cd03217 ABC_FeS_Assembly ABC-t  31.1      29 0.00074   14.3   1.7   37  337-375   123-160 (200)
466 cd03249 ABC_MTABC3_MDL1_MDL2 M  30.9      27 0.00068   14.6   1.5   26  106-131    27-54  (238)
467 TIGR00379 cobB cobyrinic acid   30.9      27 0.00068   14.6   1.5  165  160-346    80-262 (464)
468 COG0763 LpxB Lipid A disacchar  30.8      34 0.00086   13.9   3.9   21   96-116    18-39  (381)
469 PRK13973 thymidylate kinase; P  30.6      34 0.00087   13.9   2.3   29  107-135     2-32  (216)
470 PRK02269 ribose-phosphate pyro  30.6      34 0.00087   13.9  11.2   60  338-409   219-278 (321)
471 TIGR02746 TraC-F-type type-IV   30.6      24 0.00061   14.9   1.2   77  337-418   735-816 (900)
472 PRK05342 clpX ATP-dependent pr  30.5      12 0.00031   16.9  -0.4   26  108-134   112-137 (411)
473 pfam02492 cobW CobW/HypB/UreG,  30.4      34 0.00086   13.9   1.9   21  109-132     1-23  (174)
474 PRK10744 phosphate transporter  30.3      34 0.00088   13.9   2.1   26  106-131    34-61  (257)
475 PRK11248 tauB taurine transpor  30.3      25 0.00063   14.8   1.2   27  106-132    25-53  (255)
476 PRK02224 chromosome segregatio  30.2      35 0.00088   13.9   2.3   25  106-130    21-47  (880)
477 cd03253 ABCC_ATM1_transporter   30.2      25 0.00063   14.8   1.2   25  107-131    26-52  (236)
478 PRK05312 pdxA 4-hydroxythreoni  30.2      35 0.00088   13.8   3.6   70   48-117   132-216 (336)
479 cd03223 ABCD_peroxisomal_ALDP   30.2      23  0.0006   15.0   1.1   25  107-131    26-52  (166)
480 PRK10575 iron-hydroxamate tran  30.1      26 0.00066   14.7   1.3   26  106-131    35-62  (265)
481 PRK05035 electron transport co  30.1      35 0.00088   13.8   3.6  110   23-152   191-320 (725)
482 PRK11288 araG L-arabinose tran  30.0      32 0.00083   14.0   1.8   22  106-127    28-51  (501)
483 cd03218 ABC_YhbG The ABC trans  29.9      26 0.00065   14.7   1.2   26  106-131    24-51  (232)
484 PRK10619 histidine/lysine/argi  29.9      26 0.00066   14.7   1.2   26  106-131    29-56  (257)
485 PRK09544 znuC high-affinity zi  29.8      25 0.00065   14.7   1.2   25  107-131    29-55  (251)
486 PRK11701 phnK phosphonates tra  29.7      26 0.00065   14.7   1.2   25  107-131    31-57  (258)
487 PRK07247 DNA polymerase III su  29.7      34 0.00087   13.9   1.8   85  164-248    23-116 (195)
488 cd06201 SiR_like2 Cytochrome p  29.7      35  0.0009   13.8   4.7   36  430-466   231-266 (289)
489 pfam00076 RRM_1 RNA recognitio  29.6      35  0.0009   13.8   2.4   61  307-372     9-69  (70)
490 cd03282 ABC_MSH4_euk MutS4 hom  29.6      35  0.0009   13.8   2.5   28  107-134    28-59  (204)
491 COG1121 ZnuC ABC-type Mn/Zn tr  29.5      35  0.0009   13.8   2.1   22  106-130    28-51  (254)
492 pfam05872 DUF853 Bacterial pro  29.5      25 0.00064   14.8   1.1   27  107-134    23-49  (504)
493 TIGR02153 gatD_arch glutamyl-t  29.5      36 0.00091   13.8   3.6   54   53-107   320-390 (413)
494 PRK00934 ribose-phosphate pyro  29.5      36 0.00091   13.8   9.5  161  294-464     7-176 (286)
495 PRK00168 coaD phosphopantethei  29.3      36 0.00091   13.7   6.3   76  371-455     2-92  (159)
496 PRK06031 phosphoribosyltransfe  29.2      36 0.00091   13.7   5.2   88  296-394    96-203 (233)
497 cd03243 ABC_MutS_homologs The   29.1      36 0.00092   13.7   2.3   24  107-130    28-53  (202)
498 PRK13813 orotidine 5'-phosphat  29.1      36 0.00092   13.7   4.3   59   35-105   157-215 (215)
499 PRK11022 dppD dipeptide transp  29.0      27 0.00069   14.6   1.2   32  107-138    32-65  (327)
500 PRK11557 putative DNA-binding   29.0      36 0.00092   13.7   4.7   62   35-96    175-238 (282)

No 1  
>TIGR01143 murF UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; InterPro: IPR005863   The bacterial cell wall provides strength and rigidity to counteract internal osmotic pressure, and protection against the environment. The peptidoglycan layer gives the cell wall its strength, and helps maintain the overall shape of the cell. The basic peptidoglycan structure of both Gram-positive and Gram-negative bacteria is comprised of a sheet of glycan chains connected by short cross-linking polypeptides. Biosynthesis of peptidoglycan is a multi-step (11-12 steps) process comprising three main stages:    (1) formation of UDP-N-acetylmuramic acid (UDPMurNAc) from N-acetylglucosamine (GlcNAc). (2) addition of a short polypeptide chain to the UDPMurNAc. (3) addition of a second GlcNAc to the disaccharide-pentapeptide building block and transport of this unit through the cytoplasmic membrane and incorporation into the growing peptidoglycan layer.    Stage two involves four key Mur ligase enzymes: MurC (6.3.2.8 from EC) , MurD (6.3.2.9 from EC) , MurE (6.3.2.13 from EC)  and MurF (6.3.2.10 from EC) . These four Mur ligases are responsible for the successive additions of L-alanine, D-glutamate, meso-diaminopimelate or L-lysine, and D-alanyl-D-alanine to UDP-N-acetylmuramic acid. All four Mur ligases are topologically similar to one another, even though they display low sequence identity. They are each composed of three domains: an N-terminal Rossmann-fold domain responsible for binding the UDPMurNAc substrate; a central domain (similar to ATP-binding domains of several ATPases and GTPases); and a C-terminal domain (similar to dihydrofolate reductase fold) that appears to be associated with binding the incoming amino acid. The conserved sequence motifs found in the four Mur enzymes also map to other members of the Mur ligase family, including folylpolyglutamate synthetase, cyanophycin synthetase and the capB enzyme from Bacillales .    This entry represents UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase (MurF, 6.3.2.15 from EC), which is required to catalyze the final step in the synthesis of the cytoplasmic precursor of the bacterial cell wall peptidoglycan.  ATP + UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate + D-alanyl-D-alanine = ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-6-carboxy-L-lysyl-D-alanyl-D-alanine.. The crystal structure of the MurF apo-enzyme has been determined and refined to 2.3 A resolution. It contains three consecutive open alpha/beta-sheet domains. The topology of the N-terminal domain of MurF is unique, while its central and C-terminal domains exhibit similar mononucleotide and dinucleotide-binding folds to MurD. The apo-enzyme of MurF crystal structure reveals an open conformation with the three domains juxtaposed in a crescent-like arrangement creating a wide-open space where substrates are expected to bind. As such, catalysis is not feasible and significant domain closure is expected upon substrate binding . ; GO: 0005524 ATP binding, 0008766 UDP-N-acetylmuramoylalanyl-D-glutamyl-26-diaminopimelate-D-alanyl-D-alanine ligase activity, 0008360 regulation of cell shape, 0009252 peptidoglycan biosynthetic process, 0009273 peptidoglycan-based cell wall biogenesis, 0051301 cell division, 0005737 cytoplasm.
Probab=100.00  E-value=0  Score=858.81  Aligned_cols=430  Identities=37%  Similarity=0.550  Sum_probs=402.5

Q ss_pred             EECCCCCCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEECCCCC----CCCCCCCCCEEEECCH-HHHHHHHHHHHHHCC
Q ss_conf             40222378988897168874768889999986988999855212----4554469728995998-999999999998306
Q gi|254781101|r   32 IDSRSIAPQEAFFAIKGPHYDGHDFILHAVQKGAGLVVVNTDMV----ASIGSLSIPVFGVDDV-LGALNKLAVAARLRS  106 (472)
Q Consensus        32 ~dSr~v~~g~lFval~g~~~DGh~~i~~A~~~Ga~~~i~~~~~~----~~~~~~~~~~i~v~d~-~~al~~la~~~~~~~  106 (472)
                      +|||+++||+|||||+|+|||||+||++|+++||.|+|+++++.    +...+...++|+|+|| +.||++||+++|.++
T Consensus         1 ~DSR~~~~g~LF~AL~G~~fDGH~F~~~A~~~GA~Avl~~r~v~~e~~~~~~~~~~~~~~V~DtV~~AL~~lA~~~~~~~   80 (462)
T TIGR01143         1 TDSRAIKPGDLFIALKGERFDGHDFVEQALAAGAVAVLVDREVESEVVKYNPDNGLPQILVDDTVLAALQALASAKREKF   80 (462)
T ss_pred             CCCCEECCCEEEEECCCCCCCHHHHHHHHHHCCCEEEEEEECCCEEEEECCCCCCCCEEEEECHHHHHHHHHHHHHHHHC
T ss_conf             98643158704750688998634679999857966999970777057510379985289980658999999999999743


Q ss_pred             CCC--EEEEECCCCCCHHHHHHHHHHHHHHC----CCCCHHHHHCCCCCCCHHCCCCCCCHHHHHCCCCCCCCCCCCCCC
Q ss_conf             993--99983036542012334677775201----122212211014574100012322144430156644332112122
Q gi|254781101|r  107 KAT--IIAITGSVGKTTTKEMLTIALSSIKK----TYACIGSYNNHIGVPLTLARMPVDVDFGIFELGMSHLGEIRFLTH  180 (472)
Q Consensus       107 ~~~--vI~ITGTnGKTTt~~~l~~iL~~~~~----~~~t~gn~Nn~iGvpltll~~~~~~~~~V~E~g~~~~gei~~L~~  180 (472)
                      +++  |||||||+||||||||+++||++.|+    |++|+|||||+||+|+|||++++++||+|+|||||++|||.+|++
T Consensus        81 ~~~~~~igiTGS~GKTTtKEm~~~iL~~~~~~~~aV~~t~GN~Nn~iGlPltlL~~~~~~~~aV~EmG~s~~GEI~~L~~  160 (462)
T TIGR01143        81 SAKRRVIGITGSSGKTTTKEMLAAILSHKYKDSEAVLATPGNFNNEIGLPLTLLRATEDHDYAVLEMGASHPGEIAYLAE  160 (462)
T ss_pred             CCCEEEEEEECCCCHHHHHHHHHHHHHHHCCCCCCEEECCCCCCCCHHHHHHHHCCCCCCCEEEEEECCCCCCCHHHHHH
T ss_conf             99758999856896067999999999853597532362488767613567887507888805999843898873789998


Q ss_pred             CCCCCEEEEEEECCCHHHH---HHHHHHHHHHHHHHCCCCCCCCHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCC-CC
Q ss_conf             3232202555312101234---4457888865433103762210121013424689987520123333322222222-22
Q gi|254781101|r  181 LVRPHIAVITTIAPAHLSN---FSGIEEIASAKAEIFEGLEKTGTIFLNYDDSFFELLKAKSHALGIKTIYSFGKSK-NA  256 (472)
Q Consensus       181 i~~P~iaiiTNI~~dHld~---~~s~e~i~~~K~~i~~~l~~~g~~ViN~Dd~~~~~l~~~~~~~~~~~i~~~g~~~-~a  256 (472)
                      |++|||+|||||+++||+.   |||+|.|++||.+||+++++++++|+|.||+++..|.......+...+++||.+. ..
T Consensus       161 i~~P~ia~itNi~~AHl~~F~~Fgs~~~Ia~aK~EI~~~~~~~~~a~~n~d~~~~~~~~~~~~~~~~~~~~~Fg~~~~~~  240 (462)
T TIGR01143       161 IAKPDIALITNIGEAHLEGFGDFGSLEGIAEAKGEILQGLKENGIAVINADDPALAKFKKRLKILNKAKVLSFGLEGKYA  240 (462)
T ss_pred             HHCCCEEEEECCHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCEEEECCCCHHHHHHHHHCCCCCCCCEEEECCCCCCC
T ss_conf             61998699917047876115787538999999999970789775898535256889999841115786478814777634


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCC-CCCCCCCHHHHHHHHCCCCHHHHHHHHCCCCCCCCCCCCEECC
Q ss_conf             222344211346510012456543221222-22222-3333221035676510121034554311476644331010003
Q gi|254781101|r  257 DFQLRKWKQCSEQSWMEVQLQGKSMEVVHH-GIGYH-MAQNMLMTLGIVSILTADVDTAIKALSVFHPKEGRGKRYRCAL  334 (472)
Q Consensus       257 d~~~~~i~~~~~~~~~~~~~~~~~~~~~l~-~~G~h-nv~NalaAia~~~~lGi~~~~i~~~L~~~~~~~GR~~~~~~~~  334 (472)
                      |++..++.....+..|++..+++.+.+.|| ++|.| |+.|+++|+|+++.+|++++++.++|..+++++||++...   
T Consensus       241 d~~~~~~~~~~~g~~f~~~~~~~~~~v~LP~~~G~h~n~~NalaA~Ala~~lG~~~~~~~~gL~~~~~~~gR~~~~~---  317 (462)
T TIGR01143       241 DVSAEDVSLSELGTGFTLVTPGGEIEVELPILLGRHPNVENALAAAALALALGLPLEEIAEGLSELKPVKGRLEVIQ---  317 (462)
T ss_pred             CEEEECCEECCCCCEEEEEECCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCEEEEE---
T ss_conf             36884321215333589986370899983112088188999999999999809888899989764278876507898---


Q ss_pred             CCCCEEEEEECCCCCCCCHHHHHHHHHHHHHCC-CCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCH--
Q ss_conf             653113310002565321012577787411102-68713885123541710589999999999864998999988038--
Q gi|254781101|r  335 NQGFFTLIDESYNANPASMKAAISVLSQISPHG-EGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFHV--  411 (472)
Q Consensus       335 ~~~~~~iIDDsYNAnP~S~~aal~~l~~~~~~~-~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~~--  411 (472)
                      ..++++||||||||||+||++||+.|..++..+ .+|||+|||||+|||+.+.++|+++++++...+++.||++|+.+  
T Consensus       318 ~~~g~~~IdD~YNAnp~Sm~AAl~~L~~~~~~~E~g~~~~VLG~M~ELG~~s~~~H~~vg~~a~~~~~~~~~~~G~~~~~  397 (462)
T TIGR01143       318 TKKGLTLIDDTYNANPDSMRAALDALARFPGKGEVGKKILVLGDMLELGELSEELHAEVGRYAAALGIDLVFLVGEEASP  397 (462)
T ss_pred             ECCCEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCC
T ss_conf             64874898441359889999999996138888863546899838453117999999999999986287389984773350


Q ss_pred             ---HHHHHHCCCC-----CCEEEECCHHHHHHHHH----HHCCCCCEEEEECCCHHHHHHHHHHH
Q ss_conf             ---9899851137-----97999789899999999----84478989999771325489999999
Q gi|254781101|r  412 ---LALKDALPRS-----IHVHYSETMDGLFLFIQ----SSLVDGDVVVVKSSNSCGFYRLINLL  464 (472)
Q Consensus       412 ---~~~~~~~~~~-----~~~~~~~~~e~a~~~l~----~~~~~gdiVLiKGSr~~~le~iv~~L  464 (472)
                         +.+.+.+...     ...++|.+.+++++.++    ....++|+||||||||++||+||+.|
T Consensus       398 ~~~~~~~~~~~~~e~~~~~~~~~f~~~~~l~~~L~~~~~~~~~~~~~vLvKGSR~~~le~vv~~L  462 (462)
T TIGR01143       398 NTVAVIADSLGSGEKLVKKQGKHFADKDELLAFLKDLNELQVGEGDVVLVKGSRSVKLEKVVEAL  462 (462)
T ss_pred             HHHHHHHHHHCCCCCCEEEEEEECCCHHHHHHHHHHHHHCCCCCCCEEEEECCCHHHHHHHHHCC
T ss_conf             26999999855896504688875179889999987533112578608999536423678998409


No 2  
>PRK11929 putative bifunctional UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase/UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase; Provisional
Probab=100.00  E-value=0  Score=839.08  Aligned_cols=431  Identities=29%  Similarity=0.410  Sum_probs=397.3

Q ss_pred             CCEEEEEEEECCCCCCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEECCCCCCCCCCCCCCEEEECCHHHHHHHHHHHHH
Q ss_conf             71474677402223789888971688747688899999869889998552124554469728995998999999999998
Q gi|254781101|r   24 QGFVNGISIDSRSIAPQEAFFAIKGPHYDGHDFILHAVQKGAGLVVVNTDMVASIGSLSIPVFGVDDVLGALNKLAVAAR  103 (472)
Q Consensus        24 ~~~i~~i~~dSr~v~~g~lFval~g~~~DGh~~i~~A~~~Ga~~~i~~~~~~~~~~~~~~~~i~v~d~~~al~~la~~~~  103 (472)
                      +....+||+|||+|+||++||||+|+++|||+||++|+++||+++|++++.    ...++|+|.|+|+++||++||++||
T Consensus       511 ~~~~~~isiDSR~v~~GdlFvAlkG~~~DGH~Fi~~Ai~~GA~~~vv~~~~----~~~~~p~I~V~Dt~~AL~~lA~~~r  586 (953)
T PRK11929        511 KEISGAVSTDSRSIGRGEIFVALKGENFDGHAYLPQAFSAGACAAVVAHQV----ADVALPQLVLGDTLAALGRMATAWR  586 (953)
T ss_pred             HHHCCCEEEECCCCCCCCEEEEEECCCCCHHHHHHHHHHCCCEEEEEECCC----CCCCCCEEEECCHHHHHHHHHHHHH
T ss_conf             876185674377368898899971487777999999998699799992566----6678897996898999999999999


Q ss_pred             HCCCCCEEEEECCCCCCHHHHHHHHHHHH----HHCCCCCHHHHHCCCCCCCHHCCCCCCCHHHHHCCCCCCCCCCCCCC
Q ss_conf             30699399983036542012334677775----20112221221101457410001232214443015664433211212
Q gi|254781101|r  104 LRSKATIIAITGSVGKTTTKEMLTIALSS----IKKTYACIGSYNNHIGVPLTLARMPVDVDFGIFELGMSHLGEIRFLT  179 (472)
Q Consensus       104 ~~~~~~vI~ITGTnGKTTt~~~l~~iL~~----~~~~~~t~gn~Nn~iGvpltll~~~~~~~~~V~E~g~~~~gei~~L~  179 (472)
                      .+++.+||||||||||||||+|++++|++    .|+|++|+|||||+||+|+|+++++++++++|+|||||++|||.+|+
T Consensus       587 ~~~~~~vIgITGSnGKTTTKeml~~iLs~~~~~~~~v~~t~gN~NN~iGvPltll~l~~~~~~aVlEmGms~~GEI~~L~  666 (953)
T PRK11929        587 SSFSLPVIAITGSNGKTTTKEMIAAILAQWQGDDGRVTATEGNFNNEIGVPLTLLRLRARHRAAVFELGMNHPGEIARLA  666 (953)
T ss_pred             HHCCCCEEEEECCCCHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCCCHHHHCCCCCCHHHHHHHCCCCCCHHHHHH
T ss_conf             75799789996788507899999999985177784388556743786667178757996346578765289622699860


Q ss_pred             CCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             23232202555312101234445788886543310376221012101342468998752012333332222222222222
Q gi|254781101|r  180 HLVRPHIAVITTIAPAHLSNFSGIEEIASAKAEIFEGLEKTGTIFLNYDDSFFELLKAKSHALGIKTIYSFGKSKNADFQ  259 (472)
Q Consensus       180 ~i~~P~iaiiTNI~~dHld~~~s~e~i~~~K~~i~~~l~~~g~~ViN~Dd~~~~~l~~~~~~~~~~~i~~~g~~~~ad~~  259 (472)
                      ++++||++|||||+++|||+|||+|+|+++|++||++++++|++|+|.||+++..+...+..... ..++|+.+..+|++
T Consensus       667 ~i~~PdiaVITNIg~aHLe~fgs~e~Ia~aK~eIf~~l~~~g~aIlN~DD~~~~~~~~~~~~~~i-~~fg~~~~~~adi~  745 (953)
T PRK11929        667 AIAAPTVALVTNAQREHQEFLHSVEAVARANGALINALPEDGIAVVNGDDPYAAIWAKLAGARRV-LRFGLSLQPGLDVY  745 (953)
T ss_pred             CCCCCCEEEEECCHHHHHHHHCCHHHHHHHHHHHHHCCCCCCEEEEECCCHHHHHHHHHHCCCCE-EEEEECCCCCCCEE
T ss_conf             62589778874456998766189999999999998315879799993886889999998457875-99985258987689


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHCCCCCCCCCCCCEECCCCCCE
Q ss_conf             34421134651001245654322122222222333322103567651012103455431147664433101000365311
Q gi|254781101|r  260 LRKWKQCSEQSWMEVQLQGKSMEVVHHGIGYHMAQNMLMTLGIVSILTADVDTAIKALSVFHPKEGRGKRYRCALNQGFF  339 (472)
Q Consensus       260 ~~~i~~~~~~~~~~~~~~~~~~~~~l~~~G~hnv~NalaAia~~~~lGi~~~~i~~~L~~~~~~~GR~~~~~~~~~~~~~  339 (472)
                      ..++.....+..+.+...++...+.++++|.||++|+++|++++..+|+++++|.++|.+|++++||+++.+.   .+++
T Consensus       746 ~~~i~~~~~g~~~~~~~~~~~~~v~l~l~G~hnv~NaLaAiAva~~lGi~~~~i~~~L~~~~~~~gR~e~~~~---~~g~  822 (953)
T PRK11929        746 AEDIVTQAAGTLCFVVTPAGSAYVDLPVPGEHNLRNALAAIAIGLAAGAPLHQIIAALEGFQAVKGRMQRRQL---SDGT  822 (953)
T ss_pred             EEEEEECCCCEEEEEEECCCEEEEEECCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCCCCCCEEEEE---CCCE
T ss_conf             9998986896499999789569999568979999999999999999399999999998669999998789995---7997


Q ss_pred             EEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHCC
Q ss_conf             33100025653210125777874111026871388512354171058999999999986499899998803898998511
Q gi|254781101|r  340 TLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFHVLALKDALP  419 (472)
Q Consensus       340 ~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~~~~~~~~~~  419 (472)
                      ++|||||||||+||++||++|..++   .+|||+|||||+|||+.++++|+++++++.+.++|.|+++|+.++.+.+.++
T Consensus       823 ~iIDDsYNANP~Sm~aAl~~L~~~~---~~~kiaVLGdM~ELG~~s~~~H~~ig~~~~~~~id~v~~vG~~~~~~~~~~~  899 (953)
T PRK11929        823 VIIDDTYNANPDSMRAAIDVLARLP---GPKRALVLGDMLELGDNGPAMHREVGDYAREHSIDALITLGEASRDAAHAFG  899 (953)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHCCC---CCCEEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECHHHHHHHHHCC
T ss_conf             9999784888999999999985287---9986999848500245789999999999997599999998657999986568


Q ss_pred             CCCCEEEECCHHHHHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHH
Q ss_conf             37979997898999999998447898999977132548999999998
Q gi|254781101|r  420 RSIHVHYSETMDGLFLFIQSSLVDGDVVVVKSSNSCGFYRLINLLLE  466 (472)
Q Consensus       420 ~~~~~~~~~~~e~a~~~l~~~~~~gdiVLiKGSr~~~le~iv~~L~~  466 (472)
                      .. ...+|++.+++...+++.+.+||+|||||||+|+||+||+.|+.
T Consensus       900 ~~-~~~~~~~~~~l~~~L~~~l~~~d~VLVKGSR~m~lE~iV~~l~~  945 (953)
T PRK11929        900 KA-ARACFASVDEIIAALRGLLPSSDIVLIKGSRFMRLERVVTAFST  945 (953)
T ss_pred             CC-CEEEECCHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHC
T ss_conf             46-57883999999999985589999999971560469999999972


No 3  
>PRK10773 murF UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Reviewed
Probab=100.00  E-value=0  Score=823.40  Aligned_cols=447  Identities=30%  Similarity=0.438  Sum_probs=414.6

Q ss_pred             CCCCCCHHHHHHHHCCEEECCCCCCEEEEEEEECCCCCCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEECCCCCCCCCC
Q ss_conf             95435678899872799952688714746774022237898889716887476888999998698899985521245544
Q gi|254781101|r    1 MNPLWTFHDLLQAIQGHSIGIVPQGFVNGISIDSRSIAPQEAFFAIKGPHYDGHDFILHAVQKGAGLVVVNTDMVASIGS   80 (472)
Q Consensus         1 m~~~~~~~~l~~~~~g~~~~~~~~~~i~~i~~dSr~v~~g~lFval~g~~~DGh~~i~~A~~~Ga~~~i~~~~~~~~~~~   80 (472)
                      |.+| |+++|+++++|+|++.  |.+|++|++|||+++||++||||+|+++|||+||++|+++||+++|++++.     +
T Consensus         1 m~~~-~l~~ia~~~~g~l~~~--d~~i~~i~~DSR~v~~g~lFvAl~G~~~DGh~fi~~Ai~~GA~aiv~~~~~-----~   72 (452)
T PRK10773          1 MISV-TLSQLADILNAELQGA--DITIDAVTTDTRKVTPGCLFVALKGERFDAHDFADQAKAAGAGALLVSRPL-----D   72 (452)
T ss_pred             CCCC-CHHHHHHHHCCEEECC--CCCEEEEEECCCCCCCCCEEEEECCCCCCHHHHHHHHHHCCCEEEEECCCC-----C
T ss_conf             9647-6999999869999889--815778996587179998899944798997999999998699899984766-----8


Q ss_pred             CCCCEEEECCHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCHHHHHCCCCCCCHHCCCCCCC
Q ss_conf             69728995998999999999998306993999830365420123346777752011222122110145741000123221
Q gi|254781101|r   81 LSIPVFGVDDVLGALNKLAVAARLRSKATIIAITGSVGKTTTKEMLTIALSSIKKTYACIGSYNNHIGVPLTLARMPVDV  160 (472)
Q Consensus        81 ~~~~~i~v~d~~~al~~la~~~~~~~~~~vI~ITGTnGKTTt~~~l~~iL~~~~~~~~t~gn~Nn~iGvpltll~~~~~~  160 (472)
                      .++|++.|+|+++||+.+|+++|.+++.++||||||||||||++|++++|++.|++++++||+||++|+|+|++++++++
T Consensus        73 ~~~~~i~V~d~~~al~~la~~~~~~~~~~vIgITGSnGKTTtk~~i~~iL~~~g~~~~t~gn~n~~iG~p~tl~~~~~~~  152 (452)
T PRK10773         73 IDLPQLIVKDTRLAFGQLAAWVRQQVPARVVALTGSSGKTSVKEMTAAILSQCGNTLYTAGNLNNDIGVPLTLLRLTPEY  152 (452)
T ss_pred             CCCCEEEECCHHHHHHHHHHHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHCCCCHH
T ss_conf             99998998999999999999875159975899991699625999999999972884124565268878660765079213


Q ss_pred             HHHHHCCCCCCCCCCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHCCCCHHHHHHHHHCC
Q ss_conf             44430156644332112122323220255531210123444578888654331037622101210134246899875201
Q gi|254781101|r  161 DFGIFELGMSHLGEIRFLTHLVRPHIAVITTIAPAHLSNFSGIEEIASAKAEIFEGLEKTGTIFLNYDDSFFELLKAKSH  240 (472)
Q Consensus       161 ~~~V~E~g~~~~gei~~L~~i~~P~iaiiTNI~~dHld~~~s~e~i~~~K~~i~~~l~~~g~~ViN~Dd~~~~~l~~~~~  240 (472)
                      +++|+|+|++++|||.+++++++||++|||||++||||+|||+|+|+++|++||++++++|++|+|.||+....+.....
T Consensus       153 ~~~v~E~g~~~~gei~~~~~~~~pdiaviTNI~~dHLd~~gs~e~~~~aK~~Lf~~l~~~g~~IlN~Dd~~~~~~~~~~~  232 (452)
T PRK10773        153 DYAVIELGANHQGEIAWTVSLTRPEAALVNNLAAAHLEGFGSLAGVAKAKGEIFTGLPENGIAIMNADNNDWLNWQSVIG  232 (452)
T ss_pred             HHHHHHHCCCCCCHHHHHHCCCCCCEEEEEECCHHHHHCCCCHHHHHHHHHHHHHCCCCCCEEEEECCCHHHHHHHHHHC
T ss_conf             35785323798535676640026675999842477654057699999999999817887989999798767999999837


Q ss_pred             CCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHC
Q ss_conf             2333332222222-222222344211346510012456543221222222223333221035676510121034554311
Q gi|254781101|r  241 ALGIKTIYSFGKS-KNADFQLRKWKQCSEQSWMEVQLQGKSMEVVHHGIGYHMAQNMLMTLGIVSILTADVDTAIKALSV  319 (472)
Q Consensus       241 ~~~~~~i~~~g~~-~~ad~~~~~i~~~~~~~~~~~~~~~~~~~~~l~~~G~hnv~NalaAia~~~~lGi~~~~i~~~L~~  319 (472)
                      .   +.+++|+.+ ..+|++..++.....+..|.+..+++.+++.+|++|.||++|+++|++++..+|+++++|.++|++
T Consensus       233 ~---~~v~~~~~~~~~~d~~~~~i~~~~~g~~f~l~~~~~~~~v~l~l~G~hnv~NalaAiava~~lG~~~~~i~~~L~~  309 (452)
T PRK10773        233 S---RKVWRFSPNAANSDFTATNIHVTSHGTEFTLHTPTGSVDVLLPLPGRHNIANALAAAALAMSVGATLDAVKAGLAN  309 (452)
T ss_pred             C---CEEEEECCCCCCCCEEEEEEEEECCCCEEEEEECCCEEEEEEECCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf             9---8289980687776189999999189418999967951899970761768998999999999859999999999972


Q ss_pred             CCCCCCCCCCCEECCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHC
Q ss_conf             47664433101000365311331000256532101257778741110268713885123541710589999999999864
Q gi|254781101|r  320 FHPKEGRGKRYRCALNQGFFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLY  399 (472)
Q Consensus       320 ~~~~~GR~~~~~~~~~~~~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~  399 (472)
                      |+|+||||++++.   .++.++|||||||||+||++||++|+.++    +|||+|||||+|||+.+.++|+++++++...
T Consensus       310 ~~~v~GRme~i~~---~~g~~iIdDsYNAnP~Sm~aal~~l~~~~----~~ki~VLGdM~ELG~~s~~~H~~v~~~~~~~  382 (452)
T PRK10773        310 LKAVPGRLFPIQL---AENQLLLDDSYNANVGSMTAAVQVLAEMP----GYRVLVVGDMAELGAESEACHRQVGEAAKAA  382 (452)
T ss_pred             CCCCCCCEEEEEC---CCEEEEEEECCCCCHHHHHHHHHHHHHCC----CCEEEEECCHHHCCCHHHHHHHHHHHHHHHC
T ss_conf             8998674079973---87089997425699799999999997577----9769998773772857899999999999976


Q ss_pred             CCCEEEEECCCHHHHHHHCCCCCCEEEECCHHHHHHHHHHHCCCCCE--EEEECCCHHHHHHHHHHHHHHC
Q ss_conf             99899998803898998511379799978989999999984478989--9997713254899999999850
Q gi|254781101|r  400 NISHVWLSGFHVLALKDALPRSIHVHYSETMDGLFLFIQSSLVDGDV--VVVKSSNSCGFYRLINLLLEEF  468 (472)
Q Consensus       400 ~~d~v~~~G~~~~~~~~~~~~~~~~~~~~~~e~a~~~l~~~~~~gdi--VLiKGSr~~~le~iv~~L~~~~  468 (472)
                      ++|.|+++|+.++.+.+....   ..+|++.+++...+.+.+.++|+  |||||||+|+||+|++.|+++.
T Consensus       383 ~id~v~~vG~~~~~~~~~~~~---~~~f~~~~~~~~~l~~~l~~~~~~~vLvKGSr~~~le~iv~~L~~~~  450 (452)
T PRK10773        383 GIDRVLSVGKLSQAISTASGV---GEHFADKTALIARLKALLAEQQVITILVKGSRSAAMEEVVRALQEKG  450 (452)
T ss_pred             CCCEEEEECHHHHHHHHHCCC---CCCCCCHHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHC
T ss_conf             999999988789999874187---63369999999999988744998489998575114999999999625


No 4  
>PRK11930 putative bifunctional UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase/alanine racemase; Provisional
Probab=100.00  E-value=0  Score=805.25  Aligned_cols=453  Identities=25%  Similarity=0.339  Sum_probs=411.9

Q ss_pred             CCHHHHHHHHCCEEECCC--CCCEEEEEEEECCCCC--CCCEEEECCCCCCCHHHHHHHHHHCCCEEEEECCCCCCCCCC
Q ss_conf             567889987279995268--8714746774022237--898889716887476888999998698899985521245544
Q gi|254781101|r    5 WTFHDLLQAIQGHSIGIV--PQGFVNGISIDSRSIA--PQEAFFAIKGPHYDGHDFILHAVQKGAGLVVVNTDMVASIGS   80 (472)
Q Consensus         5 ~~~~~l~~~~~g~~~~~~--~~~~i~~i~~dSr~v~--~g~lFval~g~~~DGh~~i~~A~~~Ga~~~i~~~~~~~~~~~   80 (472)
                      +|+++|++++||+.++..  +|..|++|++|||++.  +|+|||||+|+|+|||+||++|+++||+++|++++.......
T Consensus         3 ~~~~~i~~~~g~~~~g~~~~~~~~I~~i~tDSR~l~~~~~~LFvAL~Ger~DGH~fi~~A~~~GA~~~vv~~~~~~~~~~   82 (824)
T PRK11930          3 ISIEELIRVLGANRVGGKTEFDAFIDQLLIDSRSLSFPENTLFFALKGKRNDGHRYIQELYEKGVRNFVVSEIPKDLMEK   82 (824)
T ss_pred             EEHHHHHHHHCCEEECCCCCCCCEECEEEECCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHCCCEEEEEECCCCCCCCC
T ss_conf             40999998639788578888883236399358876579986899956788887999999998899099994566554557


Q ss_pred             CCCCEEEECCHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCHHHHHCCCCCCCHHCCCCCCC
Q ss_conf             69728995998999999999998306993999830365420123346777752011222122110145741000123221
Q gi|254781101|r   81 LSIPVFGVDDVLGALNKLAVAARLRSKATIIAITGSVGKTTTKEMLTIALSSIKKTYACIGSYNNHIGVPLTLARMPVDV  160 (472)
Q Consensus        81 ~~~~~i~v~d~~~al~~la~~~~~~~~~~vI~ITGTnGKTTt~~~l~~iL~~~~~~~~t~gn~Nn~iGvpltll~~~~~~  160 (472)
                      .+.++|.|+||++||++||++||+++++|||||||||||||||+||+++|+..++|++|+|||||+||||+|++++++++
T Consensus        83 ~~~~~i~V~Dtl~ALq~LA~~~R~~~~~~VIgITGSnGKTttKe~L~~iLs~~~~v~~T~gn~Nn~IGvPLTll~l~~~~  162 (824)
T PRK11930         83 KPANFLIVKNPLKALQKLAAYYRKQFDIPIIGITGSNGKTIVKEWLYQLLSPDYNIVRSPRSYNSQIGVPLSVWQMNEEH  162 (824)
T ss_pred             CCCCEEEECCHHHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHHCCCCEECCCCCCCCCCCHHHHHHCCCCCC
T ss_conf             88778998989999999999999748998999949997899999999997457868528876687425899986498458


Q ss_pred             HHHHHCCCCCCCCCCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHCCCCHHHHHHHHHCC
Q ss_conf             44430156644332112122323220255531210123444578888654331037622101210134246899875201
Q gi|254781101|r  161 DFGIFELGMSHLGEIRFLTHLVRPHIAVITTIAPAHLSNFSGIEEIASAKAEIFEGLEKTGTIFLNYDDSFFELLKAKSH  240 (472)
Q Consensus       161 ~~~V~E~g~~~~gei~~L~~i~~P~iaiiTNI~~dHld~~~s~e~i~~~K~~i~~~l~~~g~~ViN~Dd~~~~~l~~~~~  240 (472)
                      +++|+|||||++|||.+|+++++|+++|||||+++|+|+|||+|++++||.+||+++   +.+++|.||+....+.....
T Consensus       163 e~aVlEmG~s~~GEI~~L~~i~~P~igVITNIg~aHle~fgS~e~ia~eK~eL~~~~---~~~i~n~d~~~~~~~~~~~~  239 (824)
T PRK11930        163 ELGIFEAGISTMGEMEALQKIIKPTIGILTNIGGAHQENFFDIQEKCMEKLKLFKDC---DVIIYNGDNEEISNCIHKSN  239 (824)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHCCCEEEEECCCHHHHHHCCCHHHHHHHHHHHHHCC---CCEEEECCCHHHHHHHHHHC
T ss_conf             089999078981469999535279999990750987664589999999999976217---81799468578999997633


Q ss_pred             CCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHC
Q ss_conf             23333322222-22222222344211346510012456543221222222223333221035676510121034554311
Q gi|254781101|r  241 ALGIKTIYSFG-KSKNADFQLRKWKQCSEQSWMEVQLQGKSMEVVHHGIGYHMAQNMLMTLGIVSILTADVDTAIKALSV  319 (472)
Q Consensus       241 ~~~~~~i~~~g-~~~~ad~~~~~i~~~~~~~~~~~~~~~~~~~~~l~~~G~hnv~NalaAia~~~~lGi~~~~i~~~L~~  319 (472)
                      ...  ..++|+ .+..+++++..+....++..|.+.+.+....+.+|++|.||++|+++|++++..+|+++++|.++|++
T Consensus       240 ~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lp~~G~h~v~NAlaA~ava~~lGv~~~~i~~~L~~  317 (824)
T PRK11930        240 LTR--REIAWSRTDSEAPLYISRSEKKEFHTHIQYRYLGMDRYFQIPFIDDASIENSIHCLAVALYLMYSADQITKRFAR  317 (824)
T ss_pred             CCC--CEEEEECCCCCCCEEEEEEEECCCCEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf             676--289983478665346665430588169999968906999936998899999999999999839999999999841


Q ss_pred             CCCCCCCCCCCEECCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHC
Q ss_conf             47664433101000365311331000256532101257778741110268713885123541710589999999999864
Q gi|254781101|r  320 FHPKEGRGKRYRCALNQGFFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLY  399 (472)
Q Consensus       320 ~~~~~GR~~~~~~~~~~~~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~  399 (472)
                      |+|++||++..+   ..+++++|||||||||+||++||++|..++.  .+|||+|||||+|||..++.+|+++++++.+.
T Consensus       318 ~~p~~~Rlev~~---g~~g~~iIdDsYNAnP~Sm~aALdtL~~~~~--~~RrI~ILgDMlElG~~~~~ly~~Vg~l~~~~  392 (824)
T PRK11930        318 LEPVEMRLEVKE---GINNCTLINDSYNSDLASLDIALDFLERRKQ--SKKKTLILSDILQSGQSPEELYRKVAQLISSA  392 (824)
T ss_pred             CCCCCCEEEEEE---CCCCCEEEECCCCCCHHHHHHHHHHHHHCCC--CCCEEEEECCHHHCCCCCHHHHHHHHHHHHHC
T ss_conf             896545137999---7998099956666998999999999974035--78569998774432876078999999999976


Q ss_pred             CCCEEEEECCCHHHHHHHCCCCCCEEEECCHHHHHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHHHC
Q ss_conf             998999988038989985113797999789899999999844789899997713254899999999850
Q gi|254781101|r  400 NISHVWLSGFHVLALKDALPRSIHVHYSETMDGLFLFIQSSLVDGDVVVVKSSNSCGFYRLINLLLEEF  468 (472)
Q Consensus       400 ~~d~v~~~G~~~~~~~~~~~~~~~~~~~~~~e~a~~~l~~~~~~gdiVLiKGSr~~~le~iv~~L~~~~  468 (472)
                      ++|.++.+|++....+..+. .....+|.+.+++++.+.....++++||+||+|..+||++++.|.++-
T Consensus       393 ~i~~ligiG~~~~~~~~~~~-~~~~~~~~~~~~~l~~~~~~~~~~~~iLikGar~~~~e~i~~~l~~~~  460 (824)
T PRK11930        393 KINRVIGIGEEISSEAKKFE-GIEKYFFKDTEAFLASLEKKKFSNELILIKGSRKFQFEQISERLELKV  460 (824)
T ss_pred             CCCEEEEECHHHHHHHHHCC-CCCEEEECCHHHHHHCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHCC
T ss_conf             88789981889999998645-776589568999974274113689779980554566899999996455


No 5  
>COG0770 MurF UDP-N-acetylmuramyl pentapeptide synthase [Cell envelope biogenesis, outer membrane]
Probab=100.00  E-value=0  Score=769.01  Aligned_cols=450  Identities=39%  Similarity=0.551  Sum_probs=416.2

Q ss_pred             CCCHHHHHHHHCCEEECCCCCCEEEEEEEECCCCCCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEECCCCCCCCCCCCC
Q ss_conf             35678899872799952688714746774022237898889716887476888999998698899985521245544697
Q gi|254781101|r    4 LWTFHDLLQAIQGHSIGIVPQGFVNGISIDSRSIAPQEAFFAIKGPHYDGHDFILHAVQKGAGLVVVNTDMVASIGSLSI   83 (472)
Q Consensus         4 ~~~~~~l~~~~~g~~~~~~~~~~i~~i~~dSr~v~~g~lFval~g~~~DGh~~i~~A~~~Ga~~~i~~~~~~~~~~~~~~   83 (472)
                      +|++.+++.+++|.+++..+ ..++++++|||++.||++||||+|+++|||+|+++|+++||.+++++++....... ..
T Consensus         2 ~~~~~~~~~~~~~~~~~~~~-~~~~~v~~Dsr~v~~g~lF~al~G~~~Dgh~fi~~A~~~GA~a~~v~r~~~~~~~~-~~   79 (451)
T COG0770           2 LLTLDELADILGGALVGADP-VVVSGVSIDSRKVKPGDLFVALKGERFDGHDFIEQALAAGAAAVLVARPVLPPAIP-LV   79 (451)
T ss_pred             CCCHHHHHHHHCCCCCCCCC-CCEEEEEEECCCCCCCCEEEECCCCCCCCCCHHHHHHHCCCEEEEEECCCCCCCCC-CC
T ss_conf             30089999971781136740-00106995246678885238716763564221889984597799992576786656-52


Q ss_pred             CEEEECCHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCHHHHHCCCCCCCHHCCCCCCCHHH
Q ss_conf             28995998999999999998306993999830365420123346777752011222122110145741000123221444
Q gi|254781101|r   84 PVFGVDDVLGALNKLAVAARLRSKATIIAITGSVGKTTTKEMLTIALSSIKKTYACIGSYNNHIGVPLTLARMPVDVDFG  163 (472)
Q Consensus        84 ~~i~v~d~~~al~~la~~~~~~~~~~vI~ITGTnGKTTt~~~l~~iL~~~~~~~~t~gn~Nn~iGvpltll~~~~~~~~~  163 (472)
                       ++.|.|++++|++||++||++.+++|||||||+||||||+|++++|+..|+|++|+|||||+||+|+|+++++.++||+
T Consensus        80 -~~~V~d~~~al~~la~~~~~~~~~kvIaITGS~GKTTTKe~la~iL~~~~~v~~t~gn~Nn~iGlPltll~~~~~~e~~  158 (451)
T COG0770          80 -VLLVLDTLEALGKLAKAYRQKFNAKVIAITGSNGKTTTKEMLAAILSTKGKVHATPGNFNNEIGLPLTLLRLPADTEYA  158 (451)
T ss_pred             -EEEEHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHCCEEECCCCCCCCCCCCHHHHHHCCCCCCEE
T ss_conf             -5875999999999999999736996899958997076999999998636807467876686544156897477766479


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHCCCCHHHHHHHHHCCCCC
Q ss_conf             30156644332112122323220255531210123444578888654331037622101210134246899875201233
Q gi|254781101|r  164 IFELGMSHLGEIRFLTHLVRPHIAVITTIAPAHLSNFSGIEEIASAKAEIFEGLEKTGTIFLNYDDSFFELLKAKSHALG  243 (472)
Q Consensus       164 V~E~g~~~~gei~~L~~i~~P~iaiiTNI~~dHld~~~s~e~i~~~K~~i~~~l~~~g~~ViN~Dd~~~~~l~~~~~~~~  243 (472)
                      |+||||||+|||..|+.+++||+++||||+++|+++|||+|+++++|.+|+.+++++|++|+|.|+++...+....   .
T Consensus       159 VlEmG~~~~GeI~~l~~i~~P~iavItnIg~aHle~fgs~e~Ia~aK~Ei~~~~~~~g~ai~n~d~~~~~~~~~~~---~  235 (451)
T COG0770         159 VLEMGMNHPGEIAELSEIARPDIAVITNIGEAHLEGFGSREGIAEAKAEILAGLRPEGIAILNADNPLLKNWAAKI---G  235 (451)
T ss_pred             EEECCCCCCCCHHHHHCCCCCCEEEECCHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCEEEEECCCHHHHHHHHHC---C
T ss_conf             9986899777478884405898899838059998742889999999999981568786799878617778777635---7


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHCCCCC
Q ss_conf             33322222222222223442113465100124565432212222222233332210356765101210345543114766
Q gi|254781101|r  244 IKTIYSFGKSKNADFQLRKWKQCSEQSWMEVQLQGKSMEVVHHGIGYHMAQNMLMTLGIVSILTADVDTAIKALSVFHPK  323 (472)
Q Consensus       244 ~~~i~~~g~~~~ad~~~~~i~~~~~~~~~~~~~~~~~~~~~l~~~G~hnv~NalaAia~~~~lGi~~~~i~~~L~~~~~~  323 (472)
                      ..++++||.+..+|+++.++.....+..|.+..++....+.++++|+||+.|+++|+++++.+|++.++|+++|+.+.++
T Consensus       236 ~~~v~~fg~~~~~d~~~~~i~~~~~~~~f~~~~~~~~~~~~l~~~G~hn~~NalaA~a~a~~lG~~~e~i~~~L~~~~~~  315 (451)
T COG0770         236 NAKVLSFGLNNGGDFRATNIHLDEEGSSFTLDIEGGEAEFELPLPGRHNVTNALAAAALALELGLDLEEIAAGLKELKPV  315 (451)
T ss_pred             CCCEEEECCCCCCCEEEEEEEECCCCEEEEEEECCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCC
T ss_conf             87579976887775256778983885079998068337999457847689999999999998199999999999863788


Q ss_pred             CCCCCCCEECCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCE
Q ss_conf             44331010003653113310002565321012577787411102687138851235417105899999999998649989
Q gi|254781101|r  324 EGRGKRYRCALNQGFFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISH  403 (472)
Q Consensus       324 ~GR~~~~~~~~~~~~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~  403 (472)
                      +||+++.   ...++.++|||+|||||+||+++++.+..++..   ++|+|+|||+|||+.+.++|+++++++...++|.
T Consensus       316 ~gR~~~~---~~~~g~~iIdD~YNAnp~sm~aai~~l~~~~~~---~~i~VlGdM~ELG~~s~~~H~~v~~~~~~~~~d~  389 (451)
T COG0770         316 KGRLEVI---LLANGKTLIDDSYNANPDSMRAALDLLAALPGR---KGIAVLGDMLELGEESEELHEEVGEYAVEAGIDL  389 (451)
T ss_pred             CCCCEEE---ECCCCCEEEECCCCCCHHHHHHHHHHHHHCCCC---CCEEEECCHHHHCCCHHHHHHHHHHHHHHCCCEE
T ss_conf             8663367---648981899737889989999999999637668---8579947766638548999999999998569509


Q ss_pred             EEEECCCHHHHHHHCCCCCCEEEECCHHHHHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHHH
Q ss_conf             9998803898998511379799978989999999984478989999771325489999999985
Q gi|254781101|r  404 VWLSGFHVLALKDALPRSIHVHYSETMDGLFLFIQSSLVDGDVVVVKSSNSCGFYRLINLLLEE  467 (472)
Q Consensus       404 v~~~G~~~~~~~~~~~~~~~~~~~~~~e~a~~~l~~~~~~gdiVLiKGSr~~~le~iv~~L~~~  467 (472)
                      +|++|+.++.+.+.++..  ..+|.+.+++.+.+...++++|+|||||||+++||++++.|+++
T Consensus       390 v~~~G~~~~~i~~~~~~~--~~~f~~~~~l~~~l~~~l~~gd~vLvKgSr~~~le~vv~~l~~~  451 (451)
T COG0770         390 VFLVGELSKAIAEALGNK--GIYFADKEELITSLKALLRKGDVVLVKGSRGMKLEKVVDALLGK  451 (451)
T ss_pred             EEEECCCHHHHHHHCCCC--EEECCCHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHCC
T ss_conf             999762069999865777--58607779999999985677878999737646579999998319


No 6  
>PRK00139 murE UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase; Provisional
Probab=100.00  E-value=0  Score=630.72  Aligned_cols=422  Identities=26%  Similarity=0.321  Sum_probs=354.7

Q ss_pred             CCHHHHHHHHCCEEECCCCCCEEEEEEEECCCCCCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEECCCCCCCCCCCCCC
Q ss_conf             56788998727999526887147467740222378988897168874768889999986988999855212455446972
Q gi|254781101|r    5 WTFHDLLQAIQGHSIGIVPQGFVNGISIDSRSIAPQEAFFAIKGPHYDGHDFILHAVQKGAGLVVVNTDMVASIGSLSIP   84 (472)
Q Consensus         5 ~~~~~l~~~~~g~~~~~~~~~~i~~i~~dSr~v~~g~lFval~g~~~DGh~~i~~A~~~Ga~~~i~~~~~~~~~~~~~~~   84 (472)
                      -.|.+|++.+..   ....|..|++|++|||+|+||++|||++|+++|||+||++|+++||+++|++++.     ..++|
T Consensus         3 ~~l~~ll~~~~~---~~~~d~~i~gis~DSR~v~~g~lFval~G~~~DGh~fi~~Ai~~GA~avv~~~~~-----~~~~~   74 (481)
T PRK00139          3 MKLRDLLAPLKA---DHVLDVEITGLTYDSRKVKPGDLFVALPGHKVDGRDFIAQAIANGAAAVVAEPDV-----EAAVP   74 (481)
T ss_pred             CCHHHHHHHCCC---CCCCCCCEEEEEECCCCCCCCCEEEEECCCCCCHHHHHHHHHHCCCEEEEECCCC-----CCCCC
T ss_conf             468998623665---6788877779996377189997899916677898999999998699799984776-----78985


Q ss_pred             EEEECCHHHHHHHHHHHHHHC--CCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCHHHHHCCCCC-----------CC
Q ss_conf             899599899999999999830--69939998303654201233467777520112221221101457-----------41
Q gi|254781101|r   85 VFGVDDVLGALNKLAVAARLR--SKATIIAITGSVGKTTTKEMLTIALSSIKKTYACIGSYNNHIGV-----------PL  151 (472)
Q Consensus        85 ~i~v~d~~~al~~la~~~~~~--~~~~vI~ITGTnGKTTt~~~l~~iL~~~~~~~~t~gn~Nn~iGv-----------pl  151 (472)
                      +|.|+|++++|+.||+.|+.+  .+++|||||||||||||++|++++|+..|..+++.|+.+|.+|.           |+
T Consensus        75 ~i~V~d~~~al~~la~~~y~~~~~~l~vIgITGTnGKTTt~~~l~~iL~~~g~~~~~igT~g~~~~~~~~~~~lTTP~~l  154 (481)
T PRK00139         75 VIVVPDLRRALALLAAAFYGNPSDKLKLIGVTGTNGKTTTAYLIAQILRLLGKKAALIGTLGNGLGGTLIPSGLTTPEAL  154 (481)
T ss_pred             EEEECCHHHHHHHHHHHHHCCCHHCCCEEEEECCCCCHHHHHHHHHHHHHCCCCCEEECCCCEECCCEECCCCCCCCCHH
T ss_conf             99989999999999999870804318089995899843499999999987498631430221141873036678988768


Q ss_pred             HHCCC-----CCCCHHHHHCCCCCCCCCCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHC
Q ss_conf             00012-----3221444301566443321121223232202555312101234445788886543310376221012101
Q gi|254781101|r  152 TLARM-----PVDVDFGIFELGMSHLGEIRFLTHLVRPHIAVITTIAPAHLSNFSGIEEIASAKAEIFEGLEKTGTIFLN  226 (472)
Q Consensus       152 tll~~-----~~~~~~~V~E~g~~~~gei~~L~~i~~P~iaiiTNI~~dHld~~~s~e~i~~~K~~i~~~l~~~g~~ViN  226 (472)
                      ++.++     +.+++++|||+| ||.-++.++.. ++|++|+||||++||||+|||+|+|+++|.+||..+.+ +.+|+|
T Consensus       155 ~L~~~l~~~~e~g~~~~vmEvS-Shgl~q~Rv~g-i~fdiav~TNIs~DHLD~Hgs~e~Y~~aK~~Lf~~~~~-~~aViN  231 (481)
T PRK00139        155 DLQRLLAEAVDAGATHVAMEVS-SHALDQGRVDG-LTFDVAVFTNLTRDHLDYHGTMEDYFAAKALLFAELGL-KAAVIN  231 (481)
T ss_pred             HHHHHHHHHHHCCCCEEEEEEC-HHHHHHCCCCC-CCCCEEEEECCCHHHHCCCCCHHHHHHHHHHHHHCCCC-CCEEEE
T ss_conf             8999999999879977999843-03555221348-87568999657677853437899999999999746578-824994


Q ss_pred             CCCHHHHHHHHHCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHH
Q ss_conf             34246899875201233333222222-22222223442113465100124565432212222222233332210356765
Q gi|254781101|r  227 YDDSFFELLKAKSHALGIKTIYSFGK-SKNADFQLRKWKQCSEQSWMEVQLQGKSMEVVHHGIGYHMAQNMLMTLGIVSI  305 (472)
Q Consensus       227 ~Dd~~~~~l~~~~~~~~~~~i~~~g~-~~~ad~~~~~i~~~~~~~~~~~~~~~~~~~~~l~~~G~hnv~NalaAia~~~~  305 (472)
                      .||++...+......    .+++||. ++.+|+++.++.....+..|.+..+++.+++.++++|.||++|+++|++++..
T Consensus       232 ~DD~~~~~~~~~~~~----~~it~g~~~~~ad~~~~~i~~~~~g~~f~l~~~~~~~~v~l~l~G~hNv~NalaAiava~~  307 (481)
T PRK00139        232 ADDEVGARLLAALPA----TVVTYSIEDHGADLRATDIEFSAQGVSFTLVTPWGEGEVESPLIGRFNVSNLLAAIAALLA  307 (481)
T ss_pred             CCCHHHHHHHHHCCC----CCCEECCCCCCCEEEEEEEEECCCCEEEEEEECCEEEEEEECCCCHHHHHHHHHHHHHHHH
T ss_conf             688899999997178----8525404788860899999984896199999589379999678878889879999999998


Q ss_pred             HCCCCHHHHHHHHCCCCCCCCCCCCEECCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCH
Q ss_conf             10121034554311476644331010003653113310002565321012577787411102687138851235417105
Q gi|254781101|r  306 LTADVDTAIKALSVFHPKEGRGKRYRCALNQGFFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELS  385 (472)
Q Consensus       306 lGi~~~~i~~~L~~~~~~~GR~~~~~~~~~~~~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~  385 (472)
                      +|++.++|.++|++|++++||||++.   ..++.++|+| |||||+||+++|++|+.+.   ++|+|+|||    +|.++
T Consensus       308 lGi~~~~i~~~L~~~~~v~GRmE~i~---~~~~~~vivD-YAHtP~sl~~~L~~lr~~~---~~rli~VfG----~gG~R  376 (481)
T PRK00139        308 LGVPLEDILKALAKLRPVPGRMERVG---AGGGPLVIVD-YAHTPDALEKVLDALRPHA---KGRLICVFG----CGGDR  376 (481)
T ss_pred             CCCCHHHHHHHHHCCCCCCCCCEEEE---CCCCCEEEEE-CCCCHHHHHHHHHHHHHHC---CCCEEEEEC----CCCCC
T ss_conf             39898999999834999999868998---7999689997-6899899999999998764---898699989----86777


Q ss_pred             HHHHHHHHHHHHHCCCCEEEEECC-----CHHHHHHHCCC---CCCEEEECCHHHHHHHHHHHCCCCCEEEE--ECC
Q ss_conf             899999999998649989999880-----38989985113---79799978989999999984478989999--771
Q gi|254781101|r  386 QSFHIDLAEVLSLYNISHVWLSGF-----HVLALKDALPR---SIHVHYSETMDGLFLFIQSSLVDGDVVVV--KSS  452 (472)
Q Consensus       386 ~~~h~~i~~~~~~~~~d~v~~~G~-----~~~~~~~~~~~---~~~~~~~~~~e~a~~~l~~~~~~gdiVLi--KGS  452 (472)
                      ++..|..+..++....|.+|+.-+     +...+.+.+..   ..++....++++|++.+.+.+.+||+||+  ||.
T Consensus       377 d~~KR~~mg~ia~~~ad~vi~T~DnPr~Edp~~I~~~i~~g~~~~~~~~i~dR~~AI~~ai~~a~~~d~vliaGKGh  453 (481)
T PRK00139        377 DKGKRPLMGAIAERLADVVIVTSDNPRSEDPAAIIADILAGITHANAVVIEDRAEAIKYAIALAKPGDVVLIAGKGH  453 (481)
T ss_pred             CCHHHHHHHHHHHHCCCEEEECCCCCCCCCHHHHHHHHHHCCCCCCEEEECCHHHHHHHHHHHCCCCCEEEEEECCC
T ss_conf             70141899999997199899939998998999999999826987992897899999999998559999999973587


No 7  
>PRK11929 putative bifunctional UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase/UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase; Provisional
Probab=100.00  E-value=0  Score=592.53  Aligned_cols=416  Identities=24%  Similarity=0.312  Sum_probs=348.1

Q ss_pred             CCEEEEEEEECCCCCCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEECCCCCCCCCCCCCCEEEECCHHHHHHHHHHHHH
Q ss_conf             71474677402223789888971688747688899999869889998552124554469728995998999999999998
Q gi|254781101|r   24 QGFVNGISIDSRSIAPQEAFFAIKGPHYDGHDFILHAVQKGAGLVVVNTDMVASIGSLSIPVFGVDDVLGALNKLAVAAR  103 (472)
Q Consensus        24 ~~~i~~i~~dSr~v~~g~lFval~g~~~DGh~~i~~A~~~Ga~~~i~~~~~~~~~~~~~~~~i~v~d~~~al~~la~~~~  103 (472)
                      -..|..++.|||+|+||++|||++|.++|||+||++|+++||+++|++++.... ...++|+|.|+|++++|+.||+.++
T Consensus        26 ~~~~~~it~DSR~V~~G~lFvAl~G~~~DGh~fi~~Ai~~GA~aiv~e~~~~~~-~~~~~~~i~V~d~r~al~~la~~fy  104 (953)
T PRK11929         26 VAATADLRLDSREVAPGDVFVACRGGASDGRAFIDQALARGAAVVIYEAEGAPV-APAGCLALPVADLRKALGELADEWY  104 (953)
T ss_pred             CCCCCCCCCCCCCCCCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEEECCCCCC-CCCCCCEEEECCHHHHHHHHHHHHH
T ss_conf             776455656654179999899945287788999999998699799991664444-6789719997989999999999986


Q ss_pred             HCC--CCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCHHHHHCCCC------CCCH------H----CCC-CCCCHHHH
Q ss_conf             306--993999830365420123346777752011222122110145------7410------0----012-32214443
Q gi|254781101|r  104 LRS--KATIIAITGSVGKTTTKEMLTIALSSIKKTYACIGSYNNHIG------VPLT------L----ARM-PVDVDFGI  164 (472)
Q Consensus       104 ~~~--~~~vI~ITGTnGKTTt~~~l~~iL~~~~~~~~t~gn~Nn~iG------vplt------l----l~~-~~~~~~~V  164 (472)
                      .++  +.++||||||||||||++|++++|+..|..+++.|+.++.+|      .|+|      +    .+| +.+++++|
T Consensus       105 ~~ps~~l~vigVTGTNGKTTt~~~i~~il~~~g~~~~~iGTlg~~~~~~~~~~~~~TTP~~~~l~~~l~~~~~~g~~~~v  184 (953)
T PRK11929        105 GKPSQDLSVVAVTGTNGKTSCAQWLAQMLTRLGKPCGSIGTLGARLPDGQSLGGSLTTPDVITLHRLLARMRAAGADAVA  184 (953)
T ss_pred             CCCCCCCCEEEEECCCCHHHHHHHHHHHHHHCCCCEEEECCCCEECCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCEEE
T ss_conf             49675887899979997999999999999867998899832454058764467899994899999999999976997999


Q ss_pred             HCCCCCCCCCCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHCCCCHHHHHHHHHCCCCCC
Q ss_conf             01566443321121223232202555312101234445788886543310376221012101342468998752012333
Q gi|254781101|r  165 FELGMSHLGEIRFLTHLVRPHIAVITTIAPAHLSNFSGIEEIASAKAEIFEGLEKTGTIFLNYDDSFFELLKAKSHALGI  244 (472)
Q Consensus       165 ~E~g~~~~gei~~L~~i~~P~iaiiTNI~~dHld~~~s~e~i~~~K~~i~~~l~~~g~~ViN~Dd~~~~~l~~~~~~~~~  244 (472)
                      ||+| ||.-+..|+.. ++|++++|||+++||||||||+|+|+++|++||+.+++.+.+|+|.||++...+.......  
T Consensus       185 mEvS-SHgL~q~Rv~g-i~fdvaifTNls~DHLDyH~tme~Y~~aK~~LF~~l~~~~~aViN~Dd~~~~~l~~~~~~~--  260 (953)
T PRK11929        185 MEAS-SHGLEQGRLDG-IRFAVAGFTNLTRDHLDYHGTMEDYEQAKAALFEQWPPLGAAVINADDPAGERLLASLPAA--  260 (953)
T ss_pred             EEEC-HHHHHHHHHCC-CCCCEEEEECCCHHHHHHCCCHHHHHHHHHHHHHHHHCCCEEEEECCCHHHHHHHHHCCCC--
T ss_conf             9833-06776434208-7878899947976786654899999999999998741086699979888899999871278--


Q ss_pred             CCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHCCCCC
Q ss_conf             3322222-222222223442113465100124565432212222222233332210356765101210345543114766
Q gi|254781101|r  245 KTIYSFG-KSKNADFQLRKWKQCSEQSWMEVQLQGKSMEVVHHGIGYHMAQNMLMTLGIVSILTADVDTAIKALSVFHPK  323 (472)
Q Consensus       245 ~~i~~~g-~~~~ad~~~~~i~~~~~~~~~~~~~~~~~~~~~l~~~G~hnv~NalaAia~~~~lGi~~~~i~~~L~~~~~~  323 (472)
                       .+.+|+ .+.++|+++.++.....+..|.+.++++.+++.++++|+||++|+++|++++..+|+++++|.++|+.++|+
T Consensus       261 -~~~~~~~~~~~ad~~~~~i~~~~~g~~f~l~~~~~~~~~~~~L~G~fNv~N~laA~a~~~~~g~~~~~i~~~l~~~~~v  339 (953)
T PRK11929        261 -LLTGYALQGSPADVHAYDLQATAHGQVFTLALPDGEAQIVTGLLGRHNISNLLLVAGALSKLGWPLPQIARELAAVSPV  339 (953)
T ss_pred             -CEEEEECCCCCCCEEEEEEEECCCCCEEEEEECCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCC
T ss_conf             -5899933678774899999982898689999789279998068631249999999999998399999999988617998


Q ss_pred             CCCCCCCEECCC-CCCEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             443310100036-5311331000256532101257778741110268713885123541710589999999999864998
Q gi|254781101|r  324 EGRGKRYRCALN-QGFFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNIS  402 (472)
Q Consensus       324 ~GR~~~~~~~~~-~~~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d  402 (472)
                      |||||++..... .+...+||  |-++|+|++.+|++++.+. +..+|.|+|||    +|.++++..|.++..++....|
T Consensus       340 pGRmE~v~~~~~~~~~~viVD--YAHTpdAl~~~L~~lr~~~-~~~~rli~VfG----cgGdRD~~KRp~Mg~iA~~~aD  412 (953)
T PRK11929        340 DGRLERVGPTASAQGPLVVVD--YAHTPDALARALTALRPVA-EANGRLVCVFG----CGGNRDKGKRPEMGRIAAELAD  412 (953)
T ss_pred             CCCEEEEECCCCCCCCEEEEE--CCCCHHHHHHHHHHHHHHH-CCCCCEEEEEC----CCCCCCCCHHHHHHHHHHHHCC
T ss_conf             887599615666789669998--6789899999999999761-46980999989----8787761034899999998499


Q ss_pred             EEEEECC-----CHHHHHH----HCCCCCCEEEECCHHHHHHHHHHHCCCCCEEEE--ECC
Q ss_conf             9999880-----3898998----511379799978989999999984478989999--771
Q gi|254781101|r  403 HVWLSGF-----HVLALKD----ALPRSIHVHYSETMDGLFLFIQSSLVDGDVVVV--KSS  452 (472)
Q Consensus       403 ~v~~~G~-----~~~~~~~----~~~~~~~~~~~~~~e~a~~~l~~~~~~gdiVLi--KGS  452 (472)
                      .||+.-+     +...+.+    .+....++....++++|++++...+.+||+|||  ||.
T Consensus       413 ~viiT~DNPR~Edp~~I~~dI~~g~~~~~~~~~i~dR~~AI~~ai~~a~~~D~vliaGKGh  473 (953)
T PRK11929        413 RVIVTSDNPRDEAPEDIIDQILAGIPAGARALRQSDRALAIMQAIWMAKPGDVILLAGKGH  473 (953)
T ss_pred             EEEECCCCCCCCCHHHHHHHHHHCCCCCCCEEEECCHHHHHHHHHHHCCCCCEEEEEECCC
T ss_conf             8998689989999999999998565668866997799999999998479999899987686


No 8  
>TIGR01085 murE UDP-N-acetylmuramyl-tripeptide synthetases; InterPro: IPR005761   The bacterial cell wall provides strength and rigidity to counteract internal osmotic pressure, and protection against the environment. The peptidoglycan layer gives the cell wall its strength, and helps maintain the overall shape of the cell. The basic peptidoglycan structure of both Gram-positive and Gram-negative bacteria is comprised of a sheet of glycan chains connected by short cross-linking polypeptides. Biosynthesis of peptidoglycan is a multi-step (11-12 steps) process comprising three main stages:    (1) formation of UDP-N-acetylmuramic acid (UDPMurNAc) from N-acetylglucosamine (GlcNAc). (2) addition of a short polypeptide chain to the UDPMurNAc. (3) addition of a second GlcNAc to the disaccharide-pentapeptide building block and transport of this unit through the cytoplasmic membrane and incorporation into the growing peptidoglycan layer.    Stage two involves four key Mur ligase enzymes: MurC (6.3.2.8 from EC) , MurD (6.3.2.9 from EC) , MurE (6.3.2.13 from EC)  and MurF (6.3.2.10 from EC) . These four Mur ligases are responsible for the successive additions of L-alanine, D-glutamate, meso-diaminopimelate or L-lysine, and D-alanyl-D-alanine to UDP-N-acetylmuramic acid. All four Mur ligases are topologically similar to one another, even though they display low sequence identity. They are each composed of three domains: an N-terminal Rossmann-fold domain responsible for binding the UDPMurNAc substrate; a central domain (similar to ATP-binding domains of several ATPases and GTPases); and a C-terminal domain (similar to dihydrofolate reductase fold) that appears to be associated with binding the incoming amino acid. The conserved sequence motifs found in the four Mur enzymes also map to other members of the Mur ligase family, including folylpolyglutamate synthetase, cyanophycin synthetase and the capB enzyme from Bacillales .    This entry represents DP-N-acetylmuramoylalanyl-D-glutamate-2,6-diaminopimelate ligases (MurE; 6.3.2.13 from EC). An exception is found with Staphylococcus aureus, in which diaminopimelate is replaced by lysine in the peptidoglycan and MurE is (6.3.2.7 from EC). The Mycobacteria, part of the closest neighbouring branch outside of the low-GC Gram-positive bacteria, use diaminopimelate.; GO: 0005524 ATP binding, 0016881 acid-amino acid ligase activity, 0008360 regulation of cell shape, 0009252 peptidoglycan biosynthetic process, 0009273 peptidoglycan-based cell wall biogenesis, 0051301 cell division, 0005737 cytoplasm.
Probab=100.00  E-value=0  Score=568.76  Aligned_cols=419  Identities=26%  Similarity=0.314  Sum_probs=337.4

Q ss_pred             CCEEEEEEEECCCCCCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEECCCCCCCCC-CCCCCEEEECCH-HHHHHHHHHH
Q ss_conf             71474677402223789888971688747688899999869889998552124554-469728995998-9999999999
Q gi|254781101|r   24 QGFVNGISIDSRSIAPQEAFFAIKGPHYDGHDFILHAVQKGAGLVVVNTDMVASIG-SLSIPVFGVDDV-LGALNKLAVA  101 (472)
Q Consensus        24 ~~~i~~i~~dSr~v~~g~lFval~g~~~DGh~~i~~A~~~Ga~~~i~~~~~~~~~~-~~~~~~i~v~d~-~~al~~la~~  101 (472)
                      +..|++++.|||+|+||++|||++|.++|||+||++|+++||.++|+|++.. ... ..++|+|.|+|. +.++..+|..
T Consensus         1 ~~~~~~l~~~S~~V~~G~~F~A~~G~~~DG~~fi~~A~~~GA~aVv~e~~~~-~~~~~~~V~~i~~~d~~r~~~~~~A~~   79 (494)
T TIGR01085         1 DLEVTGLTLDSREVKPGDLFVAIKGTKVDGHDFIEEAIENGAVAVVVEREVD-YVAGRAGVPVIIVPDLKRHALSSLAAA   79 (494)
T ss_pred             CCEEECCCCCHHHCCCCCEEEEECCCCCCHHHHHHHHHHCCCEEEEECCCCC-CCCCCCCCEEEEECCHHHHHHHHHHHH
T ss_conf             9603110013001279967897125655848889999872988999806011-276434610799623135888999999


Q ss_pred             HHHCC--CCCEEEEECCCCCCHHHHHHHHHHHHHHCCC---CCHHH--H-HCCCC------CCC--H----HCCC-CCCC
Q ss_conf             98306--9939998303654201233467777520112---22122--1-10145------741--0----0012-3221
Q gi|254781101|r  102 ARLRS--KATIIAITGSVGKTTTKEMLTIALSSIKKTY---ACIGS--Y-NNHIG------VPL--T----LARM-PVDV  160 (472)
Q Consensus       102 ~~~~~--~~~vI~ITGTnGKTTt~~~l~~iL~~~~~~~---~t~gn--~-Nn~iG------vpl--t----ll~~-~~~~  160 (472)
                      ++..+  +.+|||||||||||||+.|++++|+..|+..   +|.|+  + |+.|.      .|-  +    |-+| +.++
T Consensus        80 fY~~Ps~~l~viGvTGTNGKTtt~~li~~~l~~~G~~tgliGT~g~~~~g~~~~~~~~~~TTP~~~~~q~~L~~~~~~g~  159 (494)
T TIGR01085        80 FYGHPSKKLKVIGVTGTNGKTTTTSLIAQLLELLGKKTGLIGTIGYRLGGNELIKDPASLTTPEALTLQKTLAEMVEAGA  159 (494)
T ss_pred             HHCCCCCCEEEEEEEECCCCHHHHHHHHHHHHHCCCEEEEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCC
T ss_conf             73485525168999712874489999999998679708998654530477631266555679971899999999996599


Q ss_pred             HHHHHCCCCCCCCCCC--CCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCC------CCHHHHCCCCHHH
Q ss_conf             4443015664433211--2122323220255531210123444578888654331037622------1012101342468
Q gi|254781101|r  161 DFGIFELGMSHLGEIR--FLTHLVRPHIAVITTIAPAHLSNFSGIEEIASAKAEIFEGLEK------TGTIFLNYDDSFF  232 (472)
Q Consensus       161 ~~~V~E~g~~~~gei~--~L~~i~~P~iaiiTNI~~dHld~~~s~e~i~~~K~~i~~~l~~------~g~~ViN~Dd~~~  232 (472)
                      +|+|||+| ||.-...  |+.. ++++++|||||+.||||||||||+|+.+|++||+....      -+.+|+|.||++.
T Consensus       160 ~~~v~EvS-SHaL~q~TARV~~-~~F~~~vFTNl~~DHLDfHgtmEnY~~aK~~LF~~~~~~~~~~~~~~aV~n~dD~~~  237 (494)
T TIGR01085       160 QYAVMEVS-SHALAQGTARVEG-VDFDAAVFTNLTRDHLDFHGTMENYFAAKAKLFTELGLKSDRRRARFAVINLDDEYG  237 (494)
T ss_pred             CEEEEEEE-HHHHHCCCCEEEC-CEEEEEEEECCCHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEECCHHH
T ss_conf             79999863-0124214211102-115799960788302340334899999998524400136775356611588645446


Q ss_pred             HHHHHHCCCCCCCCCCC-CCC--CCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCHHHHHHHHC-
Q ss_conf             99875201233333222-222--222222234421134651001245654-3221222222223333221035676510-
Q gi|254781101|r  233 ELLKAKSHALGIKTIYS-FGK--SKNADFQLRKWKQCSEQSWMEVQLQGK-SMEVVHHGIGYHMAQNMLMTLGIVSILT-  307 (472)
Q Consensus       233 ~~l~~~~~~~~~~~i~~-~g~--~~~ad~~~~~i~~~~~~~~~~~~~~~~-~~~~~l~~~G~hnv~NalaAia~~~~lG-  307 (472)
                      ..+..+......-.... ...  ....|+...+......+..+.+..+++ .+.+.+|++|+||++|+|||++++..+| 
T Consensus       238 ~~f~~~~~~~~~~~~~~~~A~~R~~~~~~~~~~~~~~~~G~~~~~~~~~g~~~~~~~~LiG~FNv~N~lAa~a~~~~~gg  317 (494)
T TIGR01085       238 AQFVKRLPKDITVSAITQKADWRGKAQDIKITDSGYSFEGQSFTFETPAGVEFKLHTPLIGRFNVYNLLAALATLLHLGG  317 (494)
T ss_pred             HHHHHHHHHHCEEEEEEECCCCCCCCCCCHHHCCCCEEEEEEEEEECCCCCEEEEEECCCHHHHHHHHHHHHHHHHHHCC
T ss_conf             99986102522577885042126311240110000103456667524675206887536136889999999999997338


Q ss_pred             CCCHHHHHHHHCCCCCCCCCCCCEECCCCCCEEEEEECCCCCCCCHHHHHHHHHHHH-HCCCCCCEEEECCHHHCCCCHH
Q ss_conf             121034554311476644331010003653113310002565321012577787411-1026871388512354171058
Q gi|254781101|r  308 ADVDTAIKALSVFHPKEGRGKRYRCALNQGFFTLIDESYNANPASMKAAISVLSQIS-PHGEGRRIAVLGDMCEMGELSQ  386 (472)
Q Consensus       308 i~~~~i~~~L~~~~~~~GR~~~~~~~~~~~~~~iIDDsYNAnP~S~~aal~~l~~~~-~~~~~r~i~VlG~m~ELG~~~~  386 (472)
                      +++++|.+.|+.|+|++||||++.... .+..+|||  |-|+|+||+.+|.+|+.+. ....+|+|+|||    +|.+++
T Consensus       318 ~~~~~~~~~l~~~~gv~GRmE~v~~~~-~~f~V~VD--YAHTPDaLek~L~~lr~~~~~~~~g~L~~vFG----cGGdRD  390 (494)
T TIGR01085       318 IDLEDIVAALEKLRGVPGRMELVDGGQ-QKFLVIVD--YAHTPDALEKVLRTLRAIKLKHKKGRLIVVFG----CGGDRD  390 (494)
T ss_pred             CCHHHHHHHHHHCCCCCCCCEEECCCC-CCCEEEEE--ECCCHHHHHHHHHHHHHHHHHCCCCCEEEEEE----CCCCCC
T ss_conf             889999989873489987312302789-99607997--14880589999999999984258982799981----578998


Q ss_pred             HHHHHHHHHHHHCCCCEEEEECCC-----HH----HHHHHCCCCCC---EEEECCHHHHHHHHHHHCCCCCEEEE--ECC
Q ss_conf             999999999986499899998803-----89----89985113797---99978989999999984478989999--771
Q gi|254781101|r  387 SFHIDLAEVLSLYNISHVWLSGFH-----VL----ALKDALPRSIH---VHYSETMDGLFLFIQSSLVDGDVVVV--KSS  452 (472)
Q Consensus       387 ~~h~~i~~~~~~~~~d~v~~~G~~-----~~----~~~~~~~~~~~---~~~~~~~e~a~~~l~~~~~~gdiVLi--KGS  452 (472)
                      +..|.++..++....|.+|+.-++     ..    .|..++.....   +....|+.+|++++.+.+++||+|||  ||=
T Consensus       391 r~KRplMG~iA~~~AD~~ilT~DNPR~Edp~~I~~Di~~G~~~~~~~~~~~~i~DR~~AI~~Ai~~A~~gD~VLiAGKGH  470 (494)
T TIGR01085       391 RGKRPLMGAIAEQLADLIILTSDNPRSEDPEQIIADILAGISEKEKDKDVVIIADRRQAIRKAISNAKAGDVVLIAGKGH  470 (494)
T ss_pred             CCCCHHHHHHHHHHCCEEEEECCCCCCCCHHHHHHHHHHHCCCCCCCCCEEEEHHHHHHHHHHHHHHCCCCEEEEECCCC
T ss_conf             44575899999982986898368854579799999999714776667515896017899999998404798899961577


No 9  
>COG0769 MurE UDP-N-acetylmuramyl tripeptide synthase [Cell envelope biogenesis, outer membrane]
Probab=100.00  E-value=0  Score=424.84  Aligned_cols=408  Identities=24%  Similarity=0.292  Sum_probs=316.7

Q ss_pred             EEEEEECCCCCCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEECCCCCCCCCCCCCCEEEECCHHHHHHHHHHHHHHCC-
Q ss_conf             4677402223789888971688747688899999869889998552124554469728995998999999999998306-
Q gi|254781101|r   28 NGISIDSRSIAPQEAFFAIKGPHYDGHDFILHAVQKGAGLVVVNTDMVASIGSLSIPVFGVDDVLGALNKLAVAARLRS-  106 (472)
Q Consensus        28 ~~i~~dSr~v~~g~lFval~g~~~DGh~~i~~A~~~Ga~~~i~~~~~~~~~~~~~~~~i~v~d~~~al~~la~~~~~~~-  106 (472)
                      +++++|||++++|++|+|++|.++|||+|+.+|+++|+.+++++.+.  .......|++.|.|++.++..+|..++..+ 
T Consensus        11 ~~l~~dsr~v~~g~lf~a~~g~~~~g~~~~~~a~~~Gavav~~~~~~--~~~~~~~~vi~V~~~~~~~~~~a~~~y~~ps   88 (475)
T COG0769          11 TGLTLDSRKVKEGDLFVAKPGTKVDGHDFIAGAIAPGAVAVVVEKDI--KLAEAGVPVIVVTGTNGKLTTLALAFYGLPS   88 (475)
T ss_pred             CCCCCCHHHCCCCCEEEEEECCCCCCCCCCHHHHHCCCEEEEECCCC--CCCCCCCCEEEECCCHHHHHHHHHHHCCCCC
T ss_conf             57622365637684799973235245344065762897799970555--5545678779986853777888998523865


Q ss_pred             -CCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCHHHHHCCC--CC--------CC--H---HCC--CCCCCHHHHHCCC
Q ss_conf             -99399983036542012334677775201122212211014--57--------41--0---001--2322144430156
Q gi|254781101|r  107 -KATIIAITGSVGKTTTKEMLTIALSSIKKTYACIGSYNNHI--GV--------PL--T---LAR--MPVDVDFGIFELG  168 (472)
Q Consensus       107 -~~~vI~ITGTnGKTTt~~~l~~iL~~~~~~~~t~gn~Nn~i--Gv--------pl--t---ll~--~~~~~~~~V~E~g  168 (472)
                       +.++||||||||||||++|++++++..|+..+..|.-.+++  |.        |-  .   +++  +++..+++++|++
T Consensus        89 ~~l~vigvTGTNgKTt~t~~~~~~~~~~g~~~~~~gT~g~~~~~~~~~~~~~tTP~~~~l~~~~~~~~d~~~e~~vmEvs  168 (475)
T COG0769          89 GKLKVIGVTGTNGKTTTTSLLAQILKKLGKKTALIGTEGDELSPGILEPTGLTTPEALDLQNLLRDLLDRGAEIAVMEVS  168 (475)
T ss_pred             CCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEEEEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCEEEEEEEC
T ss_conf             78518986387857999999999988629825899977663268863456678921789999999999738809998850


Q ss_pred             CCCCCCCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHCCCCHHHHHHHHHCCCCCCCCCC
Q ss_conf             64433211212232322025553121012344457888865433103762210121013424689987520123333322
Q gi|254781101|r  169 MSHLGEIRFLTHLVRPHIAVITTIAPAHLSNFSGIEEIASAKAEIFEGLEKTGTIFLNYDDSFFELLKAKSHALGIKTIY  248 (472)
Q Consensus       169 ~~~~gei~~L~~i~~P~iaiiTNI~~dHld~~~s~e~i~~~K~~i~~~l~~~g~~ViN~Dd~~~~~l~~~~~~~~~~~i~  248 (472)
                       ||.....++. -+..+++++||+++||||+|+++|+|..+|..+|+.+++.+.+|+|.||++...+......... ..+
T Consensus       169 -sh~l~~~Rv~-~~~f~v~~ftnls~DHlD~h~t~e~Y~~aK~~lf~~~~~~~~~Vin~dd~~~~~~~~~~~~~~~-~~~  245 (475)
T COG0769         169 -SHGLVQGRVE-GVTFDVGVFTNLSRDHLDYHGTMEYYGAAKAVLFESLPHSGEAVINPDDGHGLDYKERLKNALG-DYI  245 (475)
T ss_pred             -HHHHHHCCCC-CCEEEEECCCCCCHHHHHCCCCHHHHHHHHHHHHHCCCCCCCEEECCCCCHHHHHHHHHHHCCC-CEE
T ss_conf             -3479757865-6359886456656666523574999998898776405788747987788038889999985688-789


Q ss_pred             CCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHCCCCCCCCC
Q ss_conf             2222222222234-421134651001245654322122222222333322103567651012103455431147664433
Q gi|254781101|r  249 SFGKSKNADFQLR-KWKQCSEQSWMEVQLQGKSMEVVHHGIGYHMAQNMLMTLGIVSILTADVDTAIKALSVFHPKEGRG  327 (472)
Q Consensus       249 ~~g~~~~ad~~~~-~i~~~~~~~~~~~~~~~~~~~~~l~~~G~hnv~NalaAia~~~~lGi~~~~i~~~L~~~~~~~GR~  327 (472)
                      ++|.+.+...... .++....+..+.+...+....+.+|++|.||++|+|+|++++..+|+|+++|.++++++++++|||
T Consensus       246 ~~~~~~~~~~~~~~~i~~~~~g~~~~~~~~~~~~~~~~~L~G~fNv~NaLaA~a~~~~lG~~~e~i~~~l~~~~~v~GRm  325 (475)
T COG0769         246 TYGCDFKRPDLDYRGIEESSSGSDFVFEPSGGIGEYELPLPGLFNVYNALAAVAAALALGVDLEDILAGLETLKPVPGRM  325 (475)
T ss_pred             EECCCCCCCCHHHCCCEEEECCCEEEEECCCCCEEEEECCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCE
T ss_conf             96889963121222611421354058863787326860412277899999999999874999999999997468999860


Q ss_pred             CCCEECCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             10100036531133100025653210125777874111026871388512354171058999999999986499899998
Q gi|254781101|r  328 KRYRCALNQGFFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLS  407 (472)
Q Consensus       328 ~~~~~~~~~~~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~  407 (472)
                      +++...   +...+||  |-+||+|++++|++++.+   ..+|.|+|+|.    |.+.+.-.+.++..++....|.+++.
T Consensus       326 E~v~~~---~~~v~VD--yAHnPd~le~~L~~~~~~---~~g~li~VfG~----gGDrD~~kr~~mg~ia~~~ad~vivt  393 (475)
T COG0769         326 ELVNIG---GKLVIVD--YAHNPDGLEKALRAVRLH---AAGRLIVVFGC----GGDRDKSKRPDMGAIAEQLADIVIVT  393 (475)
T ss_pred             EEECCC---CCEEEEE--ECCCHHHHHHHHHHHHHH---CCCCEEEEECC----CCCCCCCCCHHHHHHHHHCCCCEEEC
T ss_conf             687389---9769999--534869999999998753---49848999776----68875343031599998559936991


Q ss_pred             C-----CCHHHHHHHC----CCCCCEEEECCHHHHHHHHHHHCCCCCEEEEECC
Q ss_conf             8-----0389899851----1379799978989999999984478989999771
Q gi|254781101|r  408 G-----FHVLALKDAL----PRSIHVHYSETMDGLFLFIQSSLVDGDVVVVKSS  452 (472)
Q Consensus       408 G-----~~~~~~~~~~----~~~~~~~~~~~~e~a~~~l~~~~~~gdiVLiKGS  452 (472)
                      -     ++...+.+.+    ....++....++++|+..+.+.++++|+|++-|.
T Consensus       394 ~dnpR~edp~~i~~~i~~g~~~~~~~~~~~dr~~AI~~ai~~a~~~D~vliagk  447 (475)
T COG0769         394 SDNPRSEDPAVILADILAGIEAPEKYEIIEDREEAIRKALDLAKEGDVVLIAGK  447 (475)
T ss_pred             CCCCCCCCHHHHHHHHHHCCCCCCCEEECHHHHHHHHHHHHHHCCCCEEEEEEE
T ss_conf             899887688999999983647664143011099999999986324887899642


No 10 
>PRK00421 murC UDP-N-acetylmuramate--L-alanine ligase; Provisional
Probab=100.00  E-value=0  Score=403.92  Aligned_cols=369  Identities=27%  Similarity=0.366  Sum_probs=275.3

Q ss_pred             CCCEEEEECCCCCCC------CCCCCCCEEEECCHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCC
Q ss_conf             698899985521245------54469728995998999999999998306993999830365420123346777752011
Q gi|254781101|r   63 KGAGLVVVNTDMVAS------IGSLSIPVFGVDDVLGALNKLAVAARLRSKATIIAITGSVGKTTTKEMLTIALSSIKKT  136 (472)
Q Consensus        63 ~Ga~~~i~~~~~~~~------~~~~~~~~i~v~d~~~al~~la~~~~~~~~~~vI~ITGTnGKTTt~~~l~~iL~~~~~~  136 (472)
                      .++-.+|++--..+.      ....++|++.-  + +.|..+   .   ...++||||||||||||+.|++++|+..|..
T Consensus        66 ~~~d~vV~Sp~I~~~~p~~~~a~~~gi~v~~~--~-e~l~~~---~---~~~~~IaVtGTnGKTTtT~ll~~il~~~g~~  136 (459)
T PRK00421         66 KGADVVVVSSAIKPDNPELVAARELGIPVVRR--A-EMLAEL---M---RLRTSIAVAGTHGKTTTTSLLAHVLAEAGLD  136 (459)
T ss_pred             CCCCEEEECCCCCCCCHHHHHHHHCCCCEEEH--H-HHHHHH---H---HCCCEEEEECCCCCCHHHHHHHHHHHHCCCC
T ss_conf             99999998998599899999999879979889--9-999999---8---2596499977888611899999999976998


Q ss_pred             --CCCHHHHHCCCCCCCHHCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             --222122110145741000123221444301566443321121223232202555312101234445788886543310
Q gi|254781101|r  137 --YACIGSYNNHIGVPLTLARMPVDVDFGIFELGMSHLGEIRFLTHLVRPHIAVITTIAPAHLSNFSGIEEIASAKAEIF  214 (472)
Q Consensus       137 --~~t~gn~Nn~iGvpltll~~~~~~~~~V~E~g~~~~gei~~L~~i~~P~iaiiTNI~~dHld~~~s~e~i~~~K~~i~  214 (472)
                        +...|+.++ +|.+   ..+ ++.+|+|+|+.-+. +  .+  .-++|+++|||||++||||+|+|+|+|+++|.+++
T Consensus       137 ~~~~iGg~~~~-~~~~---~~~-~~~~~~V~E~dE~d-~--sf--~~~~P~iavitNI~~DHLD~h~s~e~Y~~ak~~~~  206 (459)
T PRK00421        137 PTFIIGGILNA-AGTN---ARL-GSSDYFVAEADESD-R--SF--LKLHPDIAVVTNIDADHLDYYGDFEDLKDAFQEFA  206 (459)
T ss_pred             CEEEECCCCCC-CCCC---CCC-CCCCEEEEEECCCC-C--CH--HHCCCCEEEEECCCHHHHHHCCCHHHHHHHHHHHH
T ss_conf             74885753355-6654---525-88988999953541-4--36--44589899991798778656018999999999999


Q ss_pred             CCCCCCCHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCC
Q ss_conf             3762210121013424689987520123333322222222222223442113465100124565432-212222222233
Q gi|254781101|r  215 EGLEKTGTIFLNYDDSFFELLKAKSHALGIKTIYSFGKSKNADFQLRKWKQCSEQSWMEVQLQGKSM-EVVHHGIGYHMA  293 (472)
Q Consensus       215 ~~l~~~g~~ViN~Dd~~~~~l~~~~~~~~~~~i~~~g~~~~ad~~~~~i~~~~~~~~~~~~~~~~~~-~~~l~~~G~hnv  293 (472)
                      +.++++|.+|+|.||++...+......    .+++||.++++|+++.++.....+..|.+...+... .+.++++|.||+
T Consensus       207 ~~~~~~g~~ViN~DD~~~~~l~~~~~~----~vitfg~~~~~d~~~~~i~~~~~~~~f~~~~~~~~~~~~~l~l~G~HNv  282 (459)
T PRK00421        207 HNLPFYGALVACGDDPELRELLPRVDR----PVITYGFSEDADFRAENIRQDGGGSHFDVLREGEDLGDFTLPLPGRHNV  282 (459)
T ss_pred             HCCCCCCCEECCCCCHHHHHHHHHCCC----CCEEECCCCCCCEEEEEEEEECCCEEEEEEECCCEEEEEEECCCHHHHH
T ss_conf             719954721146879899998774388----6002356876666788899948923899983893788999568638899


Q ss_pred             CCCCCHHHHHHHHCCCCHHHHHHHHCCCCCCCCCCCCEECCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEE
Q ss_conf             33221035676510121034554311476644331010003653113310002565321012577787411102687138
Q gi|254781101|r  294 QNMLMTLGIVSILTADVDTAIKALSVFHPKEGRGKRYRCALNQGFFTLIDESYNANPASMKAAISVLSQISPHGEGRRIA  373 (472)
Q Consensus       294 ~NalaAia~~~~lGi~~~~i~~~L~~~~~~~GR~~~~~~~~~~~~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~  373 (472)
                      +|+++|+++|..+|++++.|.++|++|++++||+|..   ...+++++||| |+|||++++++|++++...+  .+|.|+
T Consensus       283 ~NalAAia~a~~lGi~~e~i~~aL~~F~Gv~~R~E~v---~~~~gv~~idD-YAH~P~~i~a~l~alr~~~~--~~rii~  356 (459)
T PRK00421        283 LNALAAIAVALELGIDDEAIRKALATFKGVKRRFEEK---GEVNGVVLIDD-YAHHPTEIKATLKAARQKYP--DKRIVA  356 (459)
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCEEEEEE---EECCCEEEEEE-CCCCHHHHHHHHHHHHHHCC--CCCEEE
T ss_conf             9999999999984999999999997535745027998---72288479973-56893899999999998768--996699


Q ss_pred             EECCHHHCCC--CHHHHHHHHHHHHHHCCCCEEEEE-----------CCCHHHHHHHCCCC--CCEEEECCHHHHHHHHH
Q ss_conf             8512354171--058999999999986499899998-----------80389899851137--97999789899999999
Q gi|254781101|r  374 VLGDMCEMGE--LSQSFHIDLAEVLSLYNISHVWLS-----------GFHVLALKDALPRS--IHVHYSETMDGLFLFIQ  438 (472)
Q Consensus       374 VlG~m~ELG~--~~~~~h~~i~~~~~~~~~d~v~~~-----------G~~~~~~~~~~~~~--~~~~~~~~~e~a~~~l~  438 (472)
                      |+.-    ..  +...+..++++.+.  .+|.|++.           |...+.+.+++...  .++.++++.+++++.+.
T Consensus       357 vfqP----h~~sR~~~~~~e~a~~l~--~aD~vil~~iy~a~E~~~~g~~~~~i~~~i~~~~~~~~~~~~~~~~ai~~~~  430 (459)
T PRK00421        357 VFQP----HRYSRTRDLFDEFAEVLS--DADEVILLDIYAAGEAPIPGVDSEDLARAIRKRGHVDVIFVPDVDDLAELLA  430 (459)
T ss_pred             EECC----CCHHHHHHHHHHHHHHHH--CCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEECCHHHHHHHHH
T ss_conf             9867----420548999999999987--1999998887588887657889999999998608988799699999999999


Q ss_pred             HHCCCCCEEEEECCCHHHHHHHHHHHHHHC
Q ss_conf             844789899997713254899999999850
Q gi|254781101|r  439 SSLVDGDVVVVKSSNSCGFYRLINLLLEEF  468 (472)
Q Consensus       439 ~~~~~gdiVLiKGSr~~~le~iv~~L~~~~  468 (472)
                      +.+++||+||++|...  +.++.+.|.+.+
T Consensus       431 ~~a~~gDvVL~~GaGd--~~~~~~~l~~~l  458 (459)
T PRK00421        431 DVLQPGDLVLTMGAGD--ITKLARALLELL  458 (459)
T ss_pred             HHCCCCCEEEEECCCC--HHHHHHHHHHHH
T ss_conf             8589989999979999--899999999965


No 11 
>PRK03803 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=100.00  E-value=0  Score=400.87  Aligned_cols=330  Identities=23%  Similarity=0.271  Sum_probs=257.2

Q ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCHHHHHCCCCCCCHHCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCC
Q ss_conf             06993999830365420123346777752011222122110145741000123221444301566443321121223232
Q gi|254781101|r  105 RSKATIIAITGSVGKTTTKEMLTIALSSIKKTYACIGSYNNHIGVPLTLARMPVDVDFGIFELGMSHLGEIRFLTHLVRP  184 (472)
Q Consensus       105 ~~~~~vI~ITGTnGKTTt~~~l~~iL~~~~~~~~t~gn~Nn~iGvpltll~~~~~~~~~V~E~g~~~~gei~~L~~i~~P  184 (472)
                      ..+.|+||||||||||||++|+++||+..|......||    ||+|+.-+ +.++.+++|+|++..+.   +. +.-++|
T Consensus       106 ~~~~~~IaVTGTnGKTTTtsli~~iL~~~g~~~~~gGN----iG~p~~~~-~~~~~~~~VlElSSfqL---~~-~~~~~p  176 (448)
T PRK03803        106 AAKAPIVAITGSNAKSTVTTLVGEMAKAAGKRVAVGGN----LGTPALDL-LSDDVELYVLELSSFQL---ET-TDQLNA  176 (448)
T ss_pred             HCCCCEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEEE----CCCHHHHH-HCCCCCEEEEECCCCHH---HC-CCCCCC
T ss_conf             17898899858998388999999999865983799403----27613665-25888789998664112---03-545686


Q ss_pred             CEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             20255531210123444578888654331037622101210134246899875201233333222222222222234421
Q gi|254781101|r  185 HIAVITTIAPAHLSNFSGIEEIASAKAEIFEGLEKTGTIFLNYDDSFFELLKAKSHALGIKTIYSFGKSKNADFQLRKWK  264 (472)
Q Consensus       185 ~iaiiTNI~~dHld~~~s~e~i~~~K~~i~~~l~~~g~~ViN~Dd~~~~~l~~~~~~~~~~~i~~~g~~~~ad~~~~~i~  264 (472)
                      +++|||||++||||||+|+|+|.++|.+||++.+.   +|+|.||+....+....     ...++|+.+.. ++....+.
T Consensus       177 ~iaVitNI~~DHLD~h~s~e~Y~~aK~~If~~~~~---~v~n~Dd~~~~~l~~~~-----~~~~~f~~~~~-~~~~~~~~  247 (448)
T PRK03803        177 EVATVLNISEDHLDRHGGMLAYHQAKHRIFRGAKQ---VVVNRDDALTRPLVADG-----TPCWSFGLNAP-DFGAFGLR  247 (448)
T ss_pred             CEEEEECCCHHHHHHHCCHHHHHHHHHHHHCCCCE---EEEECCHHHHHHHHHCC-----CCEEEEECCCC-CCCCCCEE
T ss_conf             28998358753654633899999998777538878---99958608888886548-----85799835776-51223169


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHCCCCCCCCCCCCEECCCCCCEEEEEE
Q ss_conf             13465100124565432212222222233332210356765101210345543114766443310100036531133100
Q gi|254781101|r  265 QCSEQSWMEVQLQGKSMEVVHHGIGYHMAQNMLMTLGIVSILTADVDTAIKALSVFHPKEGRGKRYRCALNQGFFTLIDE  344 (472)
Q Consensus       265 ~~~~~~~~~~~~~~~~~~~~l~~~G~hnv~NalaAia~~~~lGi~~~~i~~~L~~~~~~~GR~~~~~~~~~~~~~~iIDD  344 (472)
                      .......+............++++|.||++|+++|++++..+|++.+.|.++|++|+++|+|+|.+   ...+|+.+|||
T Consensus       248 ~~~g~~~~~~~~~~~~~~~~l~l~G~HN~~NalAA~a~a~~~Gi~~e~I~~aL~~F~Gl~hR~E~v---~~~~Gv~fiND  324 (448)
T PRK03803        248 EEDGEKYLAFGFERLLPVRELKIRGAHNQSNALAALALGEAAGLPMEAMLETLKEFKGLEHRCQWV---REVDGVRYYND  324 (448)
T ss_pred             ECCCEEEEECCCCCCCCHHHCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCEEEEEE---EECCCEEEEEC
T ss_conf             539839996165321433330767623599899999999982998789899886355712057999---96188899968


Q ss_pred             CCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHCCCCCCE
Q ss_conf             02565321012577787411102687138851235417105899999999998649989999880389899851137979
Q gi|254781101|r  345 SYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFHVLALKDALPRSIHV  424 (472)
Q Consensus       345 sYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~~~~~~~~~~~~~~~  424 (472)
                      |...||+|+.+||+.+...   ..++.|+|+|     |......+.++.+.+.+. +..++++|+....+.+.+....++
T Consensus       325 SKaTN~~at~~Al~~~~~~---~~~~iilI~G-----G~~K~~d~~~l~~~~~~~-v~~v~l~G~~~~~i~~~l~~~~~~  395 (448)
T PRK03803        325 SKGTNVGATLAAIEGLGAD---IEGKLVLIAG-----GQGKGADFSELREPVAKY-CRAVVLIGRDAELIEQALGDAVPL  395 (448)
T ss_pred             CCCCCHHHHHHHHHHHHHH---CCCCEEEEEC-----CCCCCCCHHHHHHHHHHC-CEEEEEECCCHHHHHHHHCCCCCE
T ss_conf             9989978999999964652---3686899937-----866666879999999736-609999795999999975068987


Q ss_pred             EEECCHHHHHHHHHHHCCCCCEEEEE---CC---------CHHHHHHHHHHH
Q ss_conf             99789899999999844789899997---71---------325489999999
Q gi|254781101|r  425 HYSETMDGLFLFIQSSLVDGDVVVVK---SS---------NSCGFYRLINLL  464 (472)
Q Consensus       425 ~~~~~~e~a~~~l~~~~~~gdiVLiK---GS---------r~~~le~iv~~L  464 (472)
                      ..++++++|+..+.+.+++||+||+.   .|         ||..|.++|+.|
T Consensus       396 ~~~~~l~~Av~~a~~~a~~gd~VLlSPa~aSfD~f~nyeeRG~~F~~~V~~L  447 (448)
T PRK03803        396 VRAATLEEAVTQAAELAQPGDAVLLSPACASLDMFKNFEERGRQFAQAVEGL  447 (448)
T ss_pred             EECCCHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             9949999999999985789898998974402013179999999999999975


No 12 
>PRK02472 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=100.00  E-value=0  Score=402.16  Aligned_cols=324  Identities=23%  Similarity=0.212  Sum_probs=252.3

Q ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCHHHHHCCCCCCCHHC-CCCCCCHHHHHCCCCCCCCCCCCCCCCCCC
Q ss_conf             6993999830365420123346777752011222122110145741000-123221444301566443321121223232
Q gi|254781101|r  106 SKATIIAITGSVGKTTTKEMLTIALSSIKKTYACIGSYNNHIGVPLTLA-RMPVDVDFGIFELGMSHLGEIRFLTHLVRP  184 (472)
Q Consensus       106 ~~~~vI~ITGTnGKTTt~~~l~~iL~~~~~~~~t~gn~Nn~iGvpltll-~~~~~~~~~V~E~g~~~~gei~~L~~i~~P  184 (472)
                      .+.++||||||||||||++|++++|+..|......||    ||.|++-+ .-....+|+|+|++..+   ++. +.-++|
T Consensus       110 ~~~~~IaVTGTnGKTTTt~ll~~iL~~~g~~~~~~GN----iG~p~~~~~~~~~~~d~~VlE~SSfq---l~~-~~~~~p  181 (450)
T PRK02472        110 SEAPIIGITGSNGKTTTTTLIAEMLNAGGQHGLLAGN----IGYPASEVAQKATADDTLVTELSSFQ---LMG-VETFRP  181 (450)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHHCCCCEEEEEE----CCCCCHHHHHCCCCCCEEEEEECCCC---HHH-HCCCCC
T ss_conf             1597899827999731999999999974997399941----67641245544789877999906551---410-022588


Q ss_pred             CEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCC-CCCCCC
Q ss_conf             2025553121012344457888865433103762210121013424689987520123333322222222222-223442
Q gi|254781101|r  185 HIAVITTIAPAHLSNFSGIEEIASAKAEIFEGLEKTGTIFLNYDDSFFELLKAKSHALGIKTIYSFGKSKNAD-FQLRKW  263 (472)
Q Consensus       185 ~iaiiTNI~~dHld~~~s~e~i~~~K~~i~~~l~~~g~~ViN~Dd~~~~~l~~~~~~~~~~~i~~~g~~~~ad-~~~~~i  263 (472)
                      +++|||||++||||||+|+|+|+++|.+||+++++++.+|+|.||+....+......    .+++|+.....+ .++.+ 
T Consensus       182 ~iavitNI~~DHLD~h~s~e~Y~~aK~~i~~~~~~~~~~v~n~Dd~~~~~l~~~~~~----~~i~fs~~~~~~~~~~~~-  256 (450)
T PRK02472        182 HIAVITNIFEAHLDYHGTFENYVAAKWNIQKNQTEDDYLVLNADQEEVKELAKQTKA----TVVPFSTTKEVDGAYIKD-  256 (450)
T ss_pred             CEEEEECCCHHHHHHHCCHHHHHHHHHHHHHCCCCCCEEEEECCCHHHHHHHHHCCC----EEEEECCCCCCCCCEEEC-
T ss_conf             689993688779766348999999999999559968779995887999999975797----089853675466517627-


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHCCCCCCCCCCCCEECCCCCCEEEEE
Q ss_conf             11346510012456543221222222223333221035676510121034554311476644331010003653113310
Q gi|254781101|r  264 KQCSEQSWMEVQLQGKSMEVVHHGIGYHMAQNMLMTLGIVSILTADVDTAIKALSVFHPKEGRGKRYRCALNQGFFTLID  343 (472)
Q Consensus       264 ~~~~~~~~~~~~~~~~~~~~~l~~~G~hnv~NalaAia~~~~lGi~~~~i~~~L~~~~~~~GR~~~~~~~~~~~~~~iID  343 (472)
                          +  .+.+..........++++|.||++|+++|+++|..+|++.+.|.++|++|+++|+|+|.+   ...+|+.+||
T Consensus       257 ----~--~~~~~~~~~~~~~~l~l~G~HN~~NalaAia~a~~lGi~~~~i~~aL~~F~Gl~hRlE~v---~~~~Gv~~iN  327 (450)
T PRK02472        257 ----G--ALYFKGEKIMAADDIVLPGEHNLENILAAIAVAKLAGVSNEAIAEVLSTFTGVKHRLQYV---GTINGRKFYN  327 (450)
T ss_pred             ----C--EEEECCEEEEEHHHCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCEEEEEE---EEECCEEEEE
T ss_conf             ----8--799888456642323677553499999999999982998789999987448843379999---9974778982


Q ss_pred             ECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHCCC-CC
Q ss_conf             00256532101257778741110268713885123541710589999999999864998999988038989985113-79
Q gi|254781101|r  344 ESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFHVLALKDALPR-SI  422 (472)
Q Consensus       344 DsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~~~~~~~~~~~-~~  422 (472)
                      ||...||+|+.+||+++.       .+.++|+|+     ........++.+.+.  +++.++++|+....+.+.+.. +.
T Consensus       328 DSKaTN~~at~~Al~~~~-------~~iilI~GG-----~~Kg~d~~~l~~~~~--~vk~v~~~G~~~~~i~~~~~~~~~  393 (450)
T PRK02472        328 DSKATNILATQKALSGFN-------QPVILLAGG-----LDRGNEFDELIPYLK--NVKAMVVFGETAPKLARAANKAGI  393 (450)
T ss_pred             CCCCCCHHHHHHHHHCCC-------CCEEEEEEC-----CCCCCCHHHHHHHHH--CCCEEEEECCCHHHHHHHHHHCCC
T ss_conf             688889999999984589-------987999915-----556888799999973--768999968899999999973797


Q ss_pred             CEEEECCHHHHHHHHHHHCCCCCEEEEE---CC---------CHHHHHHHHHHHH
Q ss_conf             7999789899999999844789899997---71---------3254899999999
Q gi|254781101|r  423 HVHYSETMDGLFLFIQSSLVDGDVVVVK---SS---------NSCGFYRLINLLL  465 (472)
Q Consensus       423 ~~~~~~~~e~a~~~l~~~~~~gdiVLiK---GS---------r~~~le~iv~~L~  465 (472)
                      .+..++++++|++.+.+.+++||+||+.   .|         ||..|.++|+.|+
T Consensus       394 ~~~~~~~l~~Av~~a~~~a~~gd~VLlSPa~aSfD~f~nyeeRG~~F~~~V~~L~  448 (450)
T PRK02472        394 TIVEADNVEDAVPKAYALSEPGDVILLSPACASWDQYKTFEERGDEFIDAVHELK  448 (450)
T ss_pred             EEEECCCHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCHHHHHHHHHHHHHHCC
T ss_conf             1898799999999999858895989979733050120599999999999999747


No 13 
>PRK01368 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=100.00  E-value=0  Score=402.01  Aligned_cols=336  Identities=18%  Similarity=0.242  Sum_probs=258.9

Q ss_pred             HHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCHHHHHCCCCCCCHHCCCCCCCHHHHHCCCCCCCCCCCCCCC
Q ss_conf             99830699399983036542012334677775201122212211014574100012322144430156644332112122
Q gi|254781101|r  101 AARLRSKATIIAITGSVGKTTTKEMLTIALSSIKKTYACIGSYNNHIGVPLTLARMPVDVDFGIFELGMSHLGEIRFLTH  180 (472)
Q Consensus       101 ~~~~~~~~~vI~ITGTnGKTTt~~~l~~iL~~~~~~~~t~gn~Nn~iGvpltll~~~~~~~~~V~E~g~~~~gei~~L~~  180 (472)
                      +++.....|+||||||||||||++|+++||+..|......||    ||+|+  +.+..+.+++|+|++..+   ++ .++
T Consensus        97 ~~~~~~~~~~IaITGTnGKTTTt~li~~iL~~~g~~~~~~GN----IG~p~--l~~~~~~d~~VlElSSfQ---l~-~~~  166 (450)
T PRK01368         97 LFEKSKNLKFIAITGTNGKSTTTALISHILNSNGLDYPVAGN----IGVPA--LQAKASKDGYVLELSSFQ---LD-LVK  166 (450)
T ss_pred             HHHHCCCCCEEEEECCCCCHHHHHHHHHHHHHCCCCEEEECC----CCHHH--HHCCCCCCEEEEEECCCC---HH-CCC
T ss_conf             997667997799968999748999999999975996289625----56366--525268975999935652---20-363


Q ss_pred             CCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             32322025553121012344457888865433103762210121013424689987520123333322222222222223
Q gi|254781101|r  181 LVRPHIAVITTIAPAHLSNFSGIEEIASAKAEIFEGLEKTGTIFLNYDDSFFELLKAKSHALGIKTIYSFGKSKNADFQL  260 (472)
Q Consensus       181 i~~P~iaiiTNI~~dHld~~~s~e~i~~~K~~i~~~l~~~g~~ViN~Dd~~~~~l~~~~~~~~~~~i~~~g~~~~ad~~~  260 (472)
                      -++|++||||||++||||||+|+|+|+++|.+||+++++++.+|+|.||++...+...........+++|+.....+.. 
T Consensus       167 ~~~p~iAVilNIs~DHLD~h~s~e~Y~~aK~~If~~~~~~~~~Vin~Dd~~~~~l~~~l~~~~~~~~i~f~~~~~~~~g-  245 (450)
T PRK01368        167 TFTAKIAVLLNITPDHLDRHQDMNGYIAAKSKIFDRMDKDSYAVINIDNDYCREIFIKLQQEQRIKLIPFSVTKILENG-  245 (450)
T ss_pred             CCCCCEEEEECCCHHHHHHHCCHHHHHHHHHHHHHCCCCCCEEEEECCCHHHHHHHHHHCCCCCEEEEEECCCCCCCCC-
T ss_conf             4798789994688779877268789999999999658988889997874889999986300455169740345324477-


Q ss_pred             CCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHCCCCCCCCCCCCEECCCCCCE
Q ss_conf             4421134651001245-654322122222222333322103567651012103455431147664433101000365311
Q gi|254781101|r  261 RKWKQCSEQSWMEVQL-QGKSMEVVHHGIGYHMAQNMLMTLGIVSILTADVDTAIKALSVFHPKEGRGKRYRCALNQGFF  339 (472)
Q Consensus       261 ~~i~~~~~~~~~~~~~-~~~~~~~~l~~~G~hnv~NalaAia~~~~lGi~~~~i~~~L~~~~~~~GR~~~~~~~~~~~~~  339 (472)
                        +....+........ ......+..+++|.||++|++||+++|..+|++.+.|.++|++|+++|+|+|.+   ...+++
T Consensus       246 --~~~~~~~~~~~~~~~~~~~~~~~~~L~G~HN~~NalAA~a~a~~lGi~~~~I~~aL~~F~glpHRlE~V---~~~~gv  320 (450)
T PRK01368        246 --ISVVDDKILDNFFDDISFKLPFNKNLQGKHNCENIAASYAVAKIIGVEPKKILESISSFQSLPHRMQYI---GSINNI  320 (450)
T ss_pred             --EEEECCEEEEECCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCHHHEEEEE---EEECCE
T ss_conf             --488547335520155330045211357565899999999999980997777787642467700146899---998999


Q ss_pred             EEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHCC
Q ss_conf             33100025653210125777874111026871388512354171058999999999986499899998803898998511
Q gi|254781101|r  340 TLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFHVLALKDALP  419 (472)
Q Consensus       340 ~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~~~~~~~~~~  419 (472)
                      .+||||...||+|+.+||+++.        +.++|+|+     ........++...+.  .+..++++|+....+.+.++
T Consensus       321 ~~iNDSKaTN~~a~~~Al~~~~--------~i~lI~GG-----~~K~~d~~~l~~~~~--~v~~~~l~G~~~~~~~~~~~  385 (450)
T PRK01368        321 SFYNDSKATNAISAVQSIKALD--------NIYWLAGG-----IPKEGGIEEIKPYFS--KIKKAYFYGQAKEMFANTAK  385 (450)
T ss_pred             EEECCCCCCCHHHHHHHHHCCC--------CEEEEEEC-----CCCCCCHHHHHHHHH--CCCEEEEECCCHHHHHHHCC
T ss_conf             9971788789999999985689--------73999941-----577788799998874--38799998978999998605


Q ss_pred             CCCCEEEECCHHHHHHHHHHHCCCCCE----EEEE---CC---------CHHHHHHHHHHHHHH
Q ss_conf             379799978989999999984478989----9997---71---------325489999999985
Q gi|254781101|r  420 RSIHVHYSETMDGLFLFIQSSLVDGDV----VVVK---SS---------NSCGFYRLINLLLEE  467 (472)
Q Consensus       420 ~~~~~~~~~~~e~a~~~l~~~~~~gdi----VLiK---GS---------r~~~le~iv~~L~~~  467 (472)
                      ....+..++++++++..+...+.++|.    ||+.   .|         ||..|-++|+.|.++
T Consensus       386 ~~~~~~~~~~l~~av~~a~~~a~~~~~~~~~VLlSPacaSfD~f~nye~RG~~F~~lv~~L~~~  449 (450)
T PRK01368        386 NIVDFVICDNLEQAFDLAYKDAVGDNAEVKNILLAPSCSSYDQFKNFEERGELFIKLSSILILE  449 (450)
T ss_pred             CCCCEEECCCHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHC
T ss_conf             8987696499999999999997557878997996860204013179999999999999998755


No 14 
>PRK02006 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=100.00  E-value=0  Score=391.97  Aligned_cols=355  Identities=21%  Similarity=0.226  Sum_probs=257.1

Q ss_pred             CCCEEEECCHHHHHHHHHHHHH-HCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCHHHHHCCCCCCCH-HC----C
Q ss_conf             9728995998999999999998-3069939998303654201233467777520112221221101457410-00----1
Q gi|254781101|r   82 SIPVFGVDDVLGALNKLAVAAR-LRSKATIIAITGSVGKTTTKEMLTIALSSIKKTYACIGSYNNHIGVPLT-LA----R  155 (472)
Q Consensus        82 ~~~~i~v~d~~~al~~la~~~~-~~~~~~vI~ITGTnGKTTt~~~l~~iL~~~~~~~~t~gn~Nn~iGvplt-ll----~  155 (472)
                      ++|++  .|..-+.+.+..... ..+.+++||||||||||||+.|++++|+..|......||    ||.|.. .+    .
T Consensus        97 gi~i~--~eiel~~~~~~~~~~~~~~~~~iIaVTGTnGKTTTt~li~~iL~~~g~~~~~~GN----IG~p~l~~l~~~~~  170 (501)
T PRK02006         97 GIPVW--GELELFAQALAALGASRGYAPKVLAITGTNGKTTTTSLTGLLCERAGKKVAVAGN----ISPAALDKLAEAID  170 (501)
T ss_pred             CCCEE--EHHHHHHHHHHHCCCCCCCCCCEEEEECCCCHHHHHHHHHHHHHHCCCCEEEECC----CCCHHHHHHHHHHC
T ss_conf             99587--6899999887630222356874899938996687999999999976997465256----46102677876422


Q ss_pred             CCCCCHHHHHCCCCCCCCCCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHCCCCHHHHHH
Q ss_conf             23221444301566443321121223232202555312101234445788886543310376221012101342468998
Q gi|254781101|r  156 MPVDVDFGIFELGMSHLGEIRFLTHLVRPHIAVITTIAPAHLSNFSGIEEIASAKAEIFEGLEKTGTIFLNYDDSFFELL  235 (472)
Q Consensus       156 ~~~~~~~~V~E~g~~~~gei~~L~~i~~P~iaiiTNI~~dHld~~~s~e~i~~~K~~i~~~l~~~g~~ViN~Dd~~~~~l  235 (472)
                      .....+++|+|++..+   ++. +.-++|+++|||||++||||||+|+|+|+++|.+||.   +.+.+|+|.||+....+
T Consensus       171 ~~~~~d~~VlElSSfQ---Le~-~~~~~p~vaVilNIs~DHLD~h~s~e~Y~~aK~rif~---~~~~~V~n~DD~~~~~~  243 (501)
T PRK02006        171 AAALPDVWVLELSSFQ---LET-THTFAPDAATVLNITQDHLDWHGSMAAYAAAKGRIFG---PATVRVLNRDDALVMAM  243 (501)
T ss_pred             CCCCCCEEEEEECHHH---HCC-CCCCCCCEEEEECCCHHHHHHHCCHHHHHHHHHHHHC---CCCEEEEECCCHHHHHH
T ss_conf             5776868999966467---575-6557967899907886564442379999999998723---48559994888889987


Q ss_pred             HHHCCCCCCCCCCCCCCCCC---CCCCCCCCC---------CCCC-CCCCCC--------CCCC----CCC-CCCCCCCC
Q ss_conf             75201233333222222222---222234421---------1346-510012--------4565----432-21222222
Q gi|254781101|r  236 KAKSHALGIKTIYSFGKSKN---ADFQLRKWK---------QCSE-QSWMEV--------QLQG----KSM-EVVHHGIG  289 (472)
Q Consensus       236 ~~~~~~~~~~~i~~~g~~~~---ad~~~~~i~---------~~~~-~~~~~~--------~~~~----~~~-~~~l~~~G  289 (472)
                      .......  ...++||.+..   .++......         .... ......        ....    ... .-.+++.|
T Consensus       244 ~~~~~~~--~~~~~fg~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~L~l~G  321 (501)
T PRK02006        244 APPAAAA--DAPVTFGLDEPAQDGDYGLLRENGMAWLVEAEDRDAADEPAPTRRRKKDAAPPPDIALKRLMPADALRIRG  321 (501)
T ss_pred             HHHCCCC--CEEEEECCCCCCCCCCEEEEECCCCEEEEECCCCCCCCCCHHHHHHCCCCCCCCCCCHHHCCCCHHCCCCC
T ss_conf             6650566--41688505775666540256237705787303221000000122102333444331011035520103567


Q ss_pred             CCCCCCCCCHHHHHHHHCCCCHHHHHHHHCCCCCCCCCCCCEECCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHCCCC
Q ss_conf             22333322103567651012103455431147664433101000365311331000256532101257778741110268
Q gi|254781101|r  290 YHMAQNMLMTLGIVSILTADVDTAIKALSVFHPKEGRGKRYRCALNQGFFTLIDESYNANPASMKAAISVLSQISPHGEG  369 (472)
Q Consensus       290 ~hnv~NalaAia~~~~lGi~~~~i~~~L~~~~~~~GR~~~~~~~~~~~~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~  369 (472)
                      .||++|++||+++|..+|++.+.|.++|++|+++|+|+|.+   ...+++.+||||...||+|+.+||+++.       +
T Consensus       322 ~HN~~NalAA~a~a~~lGi~~e~i~~aL~~F~GlpHR~E~V---~~~~gv~~iNDSKaTN~~at~~Al~s~~-------~  391 (501)
T PRK02006        322 LHNAANALAALALARAIGLPAAPLLHGLREYRGEPHRVEVI---ATIDDVDYVDDSKGTNVGATVAALDGLA-------Q  391 (501)
T ss_pred             CHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCCCCCCCEEEE---EEECCEEEECCCCCCCHHHHHHHHHHCC-------C
T ss_conf             20699999999999985998789876631557876525899---9967889973787789899999997078-------9


Q ss_pred             CCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHCCCC-CCEEEECCHHHHHHHHHHHCCCCCEEE
Q ss_conf             7138851235417105899999999998649989999880389899851137-979997898999999998447898999
Q gi|254781101|r  370 RRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFHVLALKDALPRS-IHVHYSETMDGLFLFIQSSLVDGDVVV  448 (472)
Q Consensus       370 r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~~~~~~~~~~~~-~~~~~~~~~e~a~~~l~~~~~~gdiVL  448 (472)
                      +.++|+|+     ......+.++.+.+.+. +..++++|+....+.+.+... ..+..++++++|+..+.+.+++||+||
T Consensus       392 ~iilI~GG-----~~K~~d~~~L~~~~~~~-~k~vil~G~~~~~i~~~l~~~~~~~~~~~~l~~Av~~a~~~a~~gd~VL  465 (501)
T PRK02006        392 RVVLIAGG-----DGKGQDFSPLAAPVARW-ARAVVLIGRDAPAIRAALADTGVPLVDAATLEEAVRAAAELAQPGDAVL  465 (501)
T ss_pred             CEEEEEEC-----CCCCCCHHHHHHHHHHH-CEEEEEECCCHHHHHHHHHCCCCEEEECCCHHHHHHHHHHHCCCCCEEE
T ss_conf             74999805-----77777979999999853-7099998989999999975179807985999999999997578979899


Q ss_pred             EE---CC---------CHHHHHHHHHHHHHH
Q ss_conf             97---71---------325489999999985
Q gi|254781101|r  449 VK---SS---------NSCGFYRLINLLLEE  467 (472)
Q Consensus       449 iK---GS---------r~~~le~iv~~L~~~  467 (472)
                      +.   .|         ||..|.++|+.|..+
T Consensus       466 lSPacaSfD~F~nyeeRG~~F~~~V~~L~~~  496 (501)
T PRK02006        466 LSPACASLDMFRNYAHRAQVFRAAVEELALD  496 (501)
T ss_pred             ECCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             8961103012069999999999999999985


No 15 
>PRK01390 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=100.00  E-value=0  Score=392.94  Aligned_cols=322  Identities=19%  Similarity=0.255  Sum_probs=241.0

Q ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCHHHHHCCCCCCCHHCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf             69939998303654201233467777520112221221101457410001232214443015664433211212232322
Q gi|254781101|r  106 SKATIIAITGSVGKTTTKEMLTIALSSIKKTYACIGSYNNHIGVPLTLARMPVDVDFGIFELGMSHLGEIRFLTHLVRPH  185 (472)
Q Consensus       106 ~~~~vI~ITGTnGKTTt~~~l~~iL~~~~~~~~t~gn~Nn~iGvpltll~~~~~~~~~V~E~g~~~~gei~~L~~i~~P~  185 (472)
                      ...|+||||||||||||++|++++|+..|......||    ||.|+.-+......+++|+|++..+   ++. +.-++|+
T Consensus       112 ~~~~iIaVTGTnGKTTTtsli~~iL~~~g~~~~~gGN----IG~p~l~l~~~~~~~~~VlElSSfQ---l~~-~~~~~p~  183 (457)
T PRK01390        112 PDAPFIAITGTNGKSTTTALIAHLLRQAGRDVQMGGN----IGTAILSLEPPKAGRVYVVECSSYQ---IDL-TPSLDPT  183 (457)
T ss_pred             CCCCEEEEECCCCHHHHHHHHHHHHHHCCCCEEEECC----CCHHHCCCCCCCCCCEEEEEECCCH---HHH-HHCCCCC
T ss_conf             7898899928996498999999999973998699666----2401112346889966999925752---654-4006998


Q ss_pred             EEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCC--CCCCCCCC
Q ss_conf             0255531210123444578888654331037622101210134246899875201233333222222222--22223442
Q gi|254781101|r  186 IAVITTIAPAHLSNFSGIEEIASAKAEIFEGLEKTGTIFLNYDDSFFELLKAKSHALGIKTIYSFGKSKN--ADFQLRKW  263 (472)
Q Consensus       186 iaiiTNI~~dHld~~~s~e~i~~~K~~i~~~l~~~g~~ViN~Dd~~~~~l~~~~~~~~~~~i~~~g~~~~--ad~~~~~i  263 (472)
                      ++|||||++||||||+|+|+|+++|.+||.+   .+.+|+|.||++...+......... .++.++....  ..++..+ 
T Consensus       184 iavitNI~~DHLD~h~s~e~Y~~aK~~i~~~---~~~~Vin~DD~~~~~l~~~~~~~~~-~~~~~s~~~~~~~g~~~~~-  258 (457)
T PRK01390        184 VGILLNLTPDHLDRHGTMEHYAAIKERLVAG---AGTAVIGVDDAYCQAIADRLERAGK-RVVRISVEKPLARGIYADG-  258 (457)
T ss_pred             EEEEECCCHHHHHHCCCHHHHHHHHHHHHCC---CCEEEEECCCHHHHHHHHHHHHCCC-EEEEEECCCCCCCCEEEEC-
T ss_conf             8999178877865508999999999998557---9869996888889999999876388-4999716765668649857-


Q ss_pred             CCCCCCCCCCCCCCCCCC---CC--CCCCCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHCCCCCCCCCCCCEECCCCCC
Q ss_conf             113465100124565432---21--2222222233332210356765101210345543114766443310100036531
Q gi|254781101|r  264 KQCSEQSWMEVQLQGKSM---EV--VHHGIGYHMAQNMLMTLGIVSILTADVDTAIKALSVFHPKEGRGKRYRCALNQGF  338 (472)
Q Consensus       264 ~~~~~~~~~~~~~~~~~~---~~--~l~~~G~hnv~NalaAia~~~~lGi~~~~i~~~L~~~~~~~GR~~~~~~~~~~~~  338 (472)
                           ...+.. ..+...   ++  ..+++|.||++|+++|+++|..+|++.+.|.++|++|+++|+|+|.+   ...+|
T Consensus       259 -----~~~~~~-~~~~~~~~~~~~~~~~L~G~HN~~NalAAia~a~~lGi~~e~i~~aL~~F~Gl~hR~E~V---~~~~G  329 (457)
T PRK01390        259 -----GKLVRA-TGGARHEIADLAGIGSLRGRHNAQNAAAAVAACLALGVSPEEIQAGLRSFPGLAHRMEQV---GRRGK  329 (457)
T ss_pred             -----CEEEEC-CCCCEEEEEEHHHCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCEEEE---EECCC
T ss_conf             -----889984-798345443143234577542699999999999981898999999997489999852797---54278


Q ss_pred             EEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHC
Q ss_conf             13310002565321012577787411102687138851235417105899999999998649989999880389899851
Q gi|254781101|r  339 FTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFHVLALKDAL  418 (472)
Q Consensus       339 ~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~~~~~~~~~  418 (472)
                      +++||||...||+|+.+||+++.        +.++|+|+.     .......++.+.+.  .+..++++|+....+.+.+
T Consensus       330 v~~iNDSKaTN~~at~~Al~s~~--------~i~lI~GG~-----~K~~d~~~l~~~~~--~v~~~~liG~~~~~~~~~l  394 (457)
T PRK01390        330 VLFVNDSKATNADAAAPALSSFP--------NIYWIAGGK-----PKAGGIESLAPFFP--RIAKAYLIGEAAEEFAATL  394 (457)
T ss_pred             CEEECCCCCCCHHHHHHHHHCCC--------CEEEEECCC-----CCCCCHHHHHHHHH--CCCEEEEECCCHHHHHHHH
T ss_conf             33853776789899999997378--------859994504-----78889799999874--3359999898889999987


Q ss_pred             CCCCCEEEECCHHHHHHHHHHHC----CCCCEEEEE---CC---------CHHHHHHHHHHH
Q ss_conf             13797999789899999999844----789899997---71---------325489999999
Q gi|254781101|r  419 PRSIHVHYSETMDGLFLFIQSSL----VDGDVVVVK---SS---------NSCGFYRLINLL  464 (472)
Q Consensus       419 ~~~~~~~~~~~~e~a~~~l~~~~----~~gdiVLiK---GS---------r~~~le~iv~~L  464 (472)
                      ....+...++++++++..+.+.+    .+||+||+.   .|         ||..|.++|+.|
T Consensus       395 ~~~~~~~~~~~l~~av~~a~~~a~~~~~~gd~VLlSPacaSfD~f~nyeeRG~~Fk~~V~~L  456 (457)
T PRK01390        395 GGAVPYEISGTLEAAVAAAARDAAASGAPEPVVLLSPACASFDQFKNFEVRGDAFRELVQAL  456 (457)
T ss_pred             HCCCCEEECCCHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCCCHHHHHHHHHHHHHHC
T ss_conf             36798798598999999999999851899998997962404014269999999999999868


No 16 
>PRK04308 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=100.00  E-value=0  Score=389.50  Aligned_cols=324  Identities=23%  Similarity=0.284  Sum_probs=250.7

Q ss_pred             HCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCHHHHHCCCCCCCHHCC---CCCCCHHHHHCCCCCCCCCCCCCCC
Q ss_conf             3069939998303654201233467777520112221221101457410001---2322144430156644332112122
Q gi|254781101|r  104 LRSKATIIAITGSVGKTTTKEMLTIALSSIKKTYACIGSYNNHIGVPLTLAR---MPVDVDFGIFELGMSHLGEIRFLTH  180 (472)
Q Consensus       104 ~~~~~~vI~ITGTnGKTTt~~~l~~iL~~~~~~~~t~gn~Nn~iGvpltll~---~~~~~~~~V~E~g~~~~gei~~L~~  180 (472)
                      .+...++||||||||||||+.|++++|+..|......||    ||.|+.-..   ...+.+++|+|++..+   ++. +.
T Consensus       106 ~~~~~~~IaVTGTnGKTTTtsli~~iL~~~g~~~~~~GN----iG~p~~~~~~~~~~~~~d~~VlElSSfq---l~~-~~  177 (445)
T PRK04308        106 NRRGDKVIAITGSNGKTTVTSLVGYLCIKCGLDTVIAGN----IGTPVLEAELQREGKKADVWVLELSSFQ---LEN-TE  177 (445)
T ss_pred             HCCCCCEEEEECCCCCHHHHHHHHHHHHHCCCCEEEEEE----CCCCCHHHHHHHCCCCCCEEEEEEECCC---CCC-CC
T ss_conf             416995799948998377999999999975996299850----3752111144432787867999960334---466-55


Q ss_pred             CCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             32322025553121012344457888865433103762210121013424689987520123333322222222222223
Q gi|254781101|r  181 LVRPHIAVITTIAPAHLSNFSGIEEIASAKAEIFEGLEKTGTIFLNYDDSFFELLKAKSHALGIKTIYSFGKSKNADFQL  260 (472)
Q Consensus       181 i~~P~iaiiTNI~~dHld~~~s~e~i~~~K~~i~~~l~~~g~~ViN~Dd~~~~~l~~~~~~~~~~~i~~~g~~~~ad~~~  260 (472)
                      -++|+++|||||++||||||+|+|+|+++|.+||+   ..+.+|+|.||+....+....     ..+.+|+.+..+|+.+
T Consensus       178 ~~~p~iavitNi~~DHLD~h~s~e~Y~~aK~~if~---~~~~~vln~dd~~~~~~~~~~-----~~v~~~~~~~~~d~~~  249 (445)
T PRK04308        178 SLRPTAATVLNISEDHLDRYDDLLDYAHTKAKIFR---GDGVQVLNADDAFCRAMKRAG-----REVKWFSLEHEADFWL  249 (445)
T ss_pred             CCCCCEEEECCCCHHHHHHHCCHHHHHHHHHHHCC---CCCEEEECCCCHHHHHHHHCC-----CCEEEEECCCCCCEEE
T ss_conf             43763899858985675453599999999997445---797799938719999998669-----9569981376563689


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHCCCCCCCCCCCCEECCCCCCEE
Q ss_conf             44211346510012456543221222222223333221035676510121034554311476644331010003653113
Q gi|254781101|r  261 RKWKQCSEQSWMEVQLQGKSMEVVHHGIGYHMAQNMLMTLGIVSILTADVDTAIKALSVFHPKEGRGKRYRCALNQGFFT  340 (472)
Q Consensus       261 ~~i~~~~~~~~~~~~~~~~~~~~~l~~~G~hnv~NalaAia~~~~lGi~~~~i~~~L~~~~~~~GR~~~~~~~~~~~~~~  340 (472)
                      ...     ...+............++++|.||++|+++|+++|..+|++.+.|.++|++|+++|+|+|.+   ...+|++
T Consensus       250 ~~~-----~~~~~~~~~~l~~~~~l~l~G~HN~~NalAAia~a~~lGi~~~~I~~aL~~F~Gl~hR~E~v---~~~~GV~  321 (445)
T PRK04308        250 ERE-----TGRLKQGNEDLIATQDIPLQGLHNAANVMAAVALCEAVGLPREALLEHVKTFQGLPHRVEKI---GEKNGVV  321 (445)
T ss_pred             ECC-----CCEEEECCCEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCEEEE---EEECCEE
T ss_conf             616-----63797468114543025667654798899999999982998899999987579999862899---8648988


Q ss_pred             EEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHCCC
Q ss_conf             31000256532101257778741110268713885123541710589999999999864998999988038989985113
Q gi|254781101|r  341 LIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFHVLALKDALPR  420 (472)
Q Consensus       341 iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~~~~~~~~~~~  420 (472)
                      +||||...||+|+.+||+++.       ++.++|+|     |........++.+.+.+. +..|+++|+....+.+.+..
T Consensus       322 ~iNDSKaTn~~at~~Al~~~~-------~~i~lI~G-----G~~Kg~d~~~l~~~~~~~-~~~v~~~G~~~~~i~~~l~~  388 (445)
T PRK04308        322 FIDDSKGTNVGATAAAIAGLQ-------NPLFVILG-----GMGKGQDFTPLRDALAGK-AKGVFLIGVDAPQIRRDLDG  388 (445)
T ss_pred             EEECCCCCCHHHHHHHHHHCC-------CCEEEEEC-----CCCCCCCHHHHHHHHHHH-CEEEEEECCCHHHHHHHHHH
T ss_conf             980798888899999998277-------97799976-----766777869999998752-56999989799999998863


Q ss_pred             -CCCEEEECCHHHHHHHHHHHCCCCCEEEEE---CC---------CHHHHHHHHHHH
Q ss_conf             -797999789899999999844789899997---71---------325489999999
Q gi|254781101|r  421 -SIHVHYSETMDGLFLFIQSSLVDGDVVVVK---SS---------NSCGFYRLINLL  464 (472)
Q Consensus       421 -~~~~~~~~~~e~a~~~l~~~~~~gdiVLiK---GS---------r~~~le~iv~~L  464 (472)
                       +..+..++++++|+..+.+.+++||+||+.   .|         ||..|.+.|++|
T Consensus       389 ~~~~~~~~~~l~~Av~~a~~~a~~g~~VLlSPa~aSfD~f~nye~RG~~F~~~v~~L  445 (445)
T PRK04308        389 CGLNLTDCATLEEAVQTAYAQAEAGDIVLLSPACASFDMFKGYAHRSEVFIEAFKAL  445 (445)
T ss_pred             CCCCEEECCCHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCHHHHHHHHHHHHHHC
T ss_conf             798558768799999999974889898998973404013079999999999999739


No 17 
>PRK02705 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=100.00  E-value=0  Score=389.00  Aligned_cols=334  Identities=21%  Similarity=0.211  Sum_probs=246.6

Q ss_pred             HHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCHHHHHCCCCCCCHHCC-----CCCCCHHHHHCCCCCCCCCC
Q ss_conf             9983069939998303654201233467777520112221221101457410001-----23221444301566443321
Q gi|254781101|r  101 AARLRSKATIIAITGSVGKTTTKEMLTIALSSIKKTYACIGSYNNHIGVPLTLAR-----MPVDVDFGIFELGMSHLGEI  175 (472)
Q Consensus       101 ~~~~~~~~~vI~ITGTnGKTTt~~~l~~iL~~~~~~~~t~gn~Nn~iGvpltll~-----~~~~~~~~V~E~g~~~~gei  175 (472)
                      +|+...+.++||||||||||||++|+++||+..|......||    ||.|++-+.     -....||+|+|++..+   +
T Consensus       102 ~~~~~~~~~~IaVTGTnGKTTTt~ll~~iL~~~g~~~~~~GN----IG~p~~~~~l~~~~~~~~~d~~VlE~SSfQ---L  174 (459)
T PRK02705        102 AWRALKHIPWVGITGTNGKTTVTHLLAHILQAAGLNAPMCGN----IGYAACELALLRSGKAEKPDWIVAELSSYQ---I  174 (459)
T ss_pred             HHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHCCCCCEEECC----CCCCHHHHHHHCCCCCCCCCEEEEECCHHH---H
T ss_conf             999850497577717897278999999999983998536401----376204444213467887657999757133---1


Q ss_pred             CCCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCC
Q ss_conf             12122323220255531210123444578888654331037622101210134246899875201233333222222222
Q gi|254781101|r  176 RFLTHLVRPHIAVITTIAPAHLSNFSGIEEIASAKAEIFEGLEKTGTIFLNYDDSFFELLKAKSHALGIKTIYSFGKSKN  255 (472)
Q Consensus       176 ~~L~~i~~P~iaiiTNI~~dHld~~~s~e~i~~~K~~i~~~l~~~g~~ViN~Dd~~~~~l~~~~~~~~~~~i~~~g~~~~  255 (472)
                      +. +.-++|+++|||||++||||||+|+|+|+++|.+|++   ..+.+|+|.||+.+.........    ..+.......
T Consensus       175 e~-~~~~~p~iavitNI~~DHLD~h~s~e~Y~~aK~~i~~---~~~~~V~N~DD~~l~~~~~~~~~----~~~~~~~~~~  246 (459)
T PRK02705        175 ES-SPELAPKIGIWTTFTPDHLERHGTLENYFAIKASLLE---RSEIRILNGDDPYLRQGRSSWPK----GYWVSTQGKK  246 (459)
T ss_pred             CC-CCCCCCCEEEEECCCHHHHHHHHHHHHHHHHHHHHHC---CCCEEEEECCCHHHHHHHHHCCC----CEEEECCCCC
T ss_conf             33-6677877899966887787664217789999997506---59889993887999998764377----4799655641


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHCCCCCCCCCCCCEECC
Q ss_conf             2222344211346510012456543221-222222223333221035676510121034554311476644331010003
Q gi|254781101|r  256 ADFQLRKWKQCSEQSWMEVQLQGKSMEV-VHHGIGYHMAQNMLMTLGIVSILTADVDTAIKALSVFHPKEGRGKRYRCAL  334 (472)
Q Consensus       256 ad~~~~~i~~~~~~~~~~~~~~~~~~~~-~l~~~G~hnv~NalaAia~~~~lGi~~~~i~~~L~~~~~~~GR~~~~~~~~  334 (472)
                      .+..........++  +.....+..+.+ .++++|.||++|+++|+++|..+|++.+.|.++|++|+++|||+|.+   .
T Consensus       247 ~~~~~~~~~~~~~~--~i~~~~~~~~~~~~l~l~G~HN~~NalAAia~a~~lGi~~e~I~~aL~~F~GlpHRlE~V---~  321 (459)
T PRK02705        247 SLLDQADFWIDQEG--WVVERGEPLFPLEALKMPGAHNLQNLLLAVAAARLAGLSAEAIAKALRSFPGVPHRLERI---G  321 (459)
T ss_pred             CCCCCCCEEECCCC--EEEECCEEEEEHHHCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCEEEE---E
T ss_conf             12111444882698--799778056540421687676899999999999985886366788875089999853898---7


Q ss_pred             CCCCEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHHHH
Q ss_conf             65311331000256532101257778741110268713885123541710589999999999864998999988038989
Q gi|254781101|r  335 NQGFFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFHVLAL  414 (472)
Q Consensus       335 ~~~~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~~~~~  414 (472)
                      ..+|+.+||||...||+|+.+||+++.       ++.|+|+|+     ........++.+.+.. .+..|+++|+....+
T Consensus       322 ~~~gV~fiNDSKaTN~~a~~~Al~~~~-------~~iilI~GG-----~~K~~d~~~l~~~~~~-~v~~v~~~G~~~~~i  388 (459)
T PRK02705        322 TINGIDFINDSKATNYDAAEVGLKAVP-------GPIILIAGG-----EAKQGDDSAWLKQIKA-KAAAVLLFGEAAPEL  388 (459)
T ss_pred             ECCCEEEECCCCCCCHHHHHHHHHHCC-------CCEEEEECC-----CCCCCCHHHHHHHHHH-CCEEEEEECCCHHHH
T ss_conf             428878972787889899999998289-------986999567-----6667873999999864-061999989899999


Q ss_pred             HHHCCCC---CCEEEECCHHHHHHHHHHHCCCCC--EEEEE---CC---------CHHHHHHHHHHHHHH
Q ss_conf             9851137---979997898999999998447898--99997---71---------325489999999985
Q gi|254781101|r  415 KDALPRS---IHVHYSETMDGLFLFIQSSLVDGD--VVVVK---SS---------NSCGFYRLINLLLEE  467 (472)
Q Consensus       415 ~~~~~~~---~~~~~~~~~e~a~~~l~~~~~~gd--iVLiK---GS---------r~~~le~iv~~L~~~  467 (472)
                      .+.+...   ..+..++++++|++.+.+.+.++|  +||+.   .|         ||..|.++|+.|.+.
T Consensus       389 ~~~l~~~~~~~~~~~~~~l~~Av~~a~~~a~~~~~~~VLlSPacaSfD~f~nyeeRG~~F~~~V~~l~~~  458 (459)
T PRK02705        389 AQLLQESGYTGEIEIVETLDEAVNRAFELAKELQAKSVLLSPACASFDQYQNFEERGDHFRQLIQELLKV  458 (459)
T ss_pred             HHHHHHCCCCCCEEECCCHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHCC
T ss_conf             9999736998776985999999999999876589998996874401013279999999999999998616


No 18 
>PRK01438 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=100.00  E-value=0  Score=386.59  Aligned_cols=333  Identities=23%  Similarity=0.279  Sum_probs=247.1

Q ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCHHHHHCCCCCCCH-HCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCC
Q ss_conf             69939998303654201233467777520112221221101457410-00123221444301566443321121223232
Q gi|254781101|r  106 SKATIIAITGSVGKTTTKEMLTIALSSIKKTYACIGSYNNHIGVPLT-LARMPVDVDFGIFELGMSHLGEIRFLTHLVRP  184 (472)
Q Consensus       106 ~~~~vI~ITGTnGKTTt~~~l~~iL~~~~~~~~t~gn~Nn~iGvplt-ll~~~~~~~~~V~E~g~~~~gei~~L~~i~~P  184 (472)
                      ...|+||||||||||||++|+++||+..|......||    ||+|+. .+.-+.+.+++|+|++..+   ++. +.-++|
T Consensus       120 ~~~~~IaVTGTnGKTTTtsli~~iL~~~g~~~~~~GN----IG~p~l~~~~~~~~~d~~V~ElSSfq---L~~-~~~~~p  191 (481)
T PRK01438        120 TPAPWLAVTGTNGKTTTVQMLASILRAAGLRAAAVGN----IGVPVLDAVRGPDGYDVLAVELSSFQ---LHW-APSVRP  191 (481)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHHHHCCCCEEEEEE----CCHHHHHHHCCCCCCCEEEEECCCCC---CCC-CCCCCC
T ss_conf             8887899938997460999999999966997079962----56777764228888608999804765---133-445576


Q ss_pred             CEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCC--CCCCCCC
Q ss_conf             20255531210123444578888654331037622101210134246899875201233333222222222--2222344
Q gi|254781101|r  185 HIAVITTIAPAHLSNFSGIEEIASAKAEIFEGLEKTGTIFLNYDDSFFELLKAKSHALGIKTIYSFGKSKN--ADFQLRK  262 (472)
Q Consensus       185 ~iaiiTNI~~dHld~~~s~e~i~~~K~~i~~~l~~~g~~ViN~Dd~~~~~l~~~~~~~~~~~i~~~g~~~~--ad~~~~~  262 (472)
                      +++|||||++||||||+|+|+|+++|.+||.+...  .+|+|.||+....+............++|+.+..  .++...+
T Consensus       192 ~iavitNIs~DHLD~h~s~e~Y~~aK~~If~~~~~--~~v~n~dD~~~~~l~~~~~~~~~~~~i~f~~~~~~~~~~~~~~  269 (481)
T PRK01438        192 HSAAVLNLAPDHLDWHGSMEAYAADKGRVYEGNTV--ACVYNVADPATEDLVREADVVEGARAIGFTLGTPGPSDLGIVD  269 (481)
T ss_pred             CEEEEECCCHHHHHHHCCHHHHHHHHHHHHCCCCE--EEEEECCCHHHHHHHHHCCCCCCCCEEEEECCCCCCCCCCEEC
T ss_conf             48997068777866523598999999998627851--4997057788999998602244770788735888712012103


Q ss_pred             CCCCCCCCCCCCCC-CC-CCC-CCCCCCCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHCCCCCCCCCCCCEECCCCCCE
Q ss_conf             21134651001245-65-432-2122222222333322103567651012103455431147664433101000365311
Q gi|254781101|r  263 WKQCSEQSWMEVQL-QG-KSM-EVVHHGIGYHMAQNMLMTLGIVSILTADVDTAIKALSVFHPKEGRGKRYRCALNQGFF  339 (472)
Q Consensus       263 i~~~~~~~~~~~~~-~~-~~~-~~~l~~~G~hnv~NalaAia~~~~lGi~~~~i~~~L~~~~~~~GR~~~~~~~~~~~~~  339 (472)
                      ....+. ..+.-.. .. ... .-.++++|.||++|+++|++++..+|++.+.|.++|++|+++|+|+|.+   ...+|+
T Consensus       270 ~~~~~~-~~~~~~~~~~~~~~~~~~l~l~G~HN~~NalAA~a~a~~lGi~~~~i~~aL~~F~Gl~hR~E~v---~~~~GV  345 (481)
T PRK01438        270 GILVDR-AFVEDRFTSAQELATLSDVGPAAPHNVANALAAAALARAFGVSPAAVRDGLRAFRPDAHRIEHV---ADADGV  345 (481)
T ss_pred             CEEEEC-EEEEECCCCCCCCCCHHHCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCEEEEE---EEECCE
T ss_conf             455302-0343023453000106640676576999999999999982998899998886348977337899---999999


Q ss_pred             EEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHCC
Q ss_conf             33100025653210125777874111026871388512354171058999999999986499899998803898998511
Q gi|254781101|r  340 TLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFHVLALKDALP  419 (472)
Q Consensus       340 ~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~~~~~~~~~~  419 (472)
                      .+||||+..||+|+.+||+++.        ..++|+|+     ........++.+.+.. .+..++++|+....+.+.+.
T Consensus       346 ~fiNDSKaTN~~A~~~AL~~~~--------~i~lI~GG-----~~Kg~d~~~l~~~~~~-~vk~~~l~G~~~~~i~~~~~  411 (481)
T PRK01438        346 TYVDDSKATNPHAAEASLAAYP--------SVVWIAGG-----LAKGAHFDDLVRAHAA-RLRGVVLIGADRALIREALA  411 (481)
T ss_pred             EEECCCCCCCHHHHHHHHHHCC--------CEEEEECC-----CCCCCCHHHHHHHHHH-HCEEEEEECCCHHHHHHHHH
T ss_conf             9980688789889999987249--------88999378-----6578898999999860-13399997789999999997


Q ss_pred             CCC---CEE-----EECCHHHHHHHHHHHCCCCCEEEEE---CC---------CHHHHHHHHHHHHH
Q ss_conf             379---799-----9789899999999844789899997---71---------32548999999998
Q gi|254781101|r  420 RSI---HVH-----YSETMDGLFLFIQSSLVDGDVVVVK---SS---------NSCGFYRLINLLLE  466 (472)
Q Consensus       420 ~~~---~~~-----~~~~~e~a~~~l~~~~~~gdiVLiK---GS---------r~~~le~iv~~L~~  466 (472)
                      ...   .+.     ..+++++|++.+.+..++||+||+.   .|         ||..|.++|++|..
T Consensus       412 ~~~~~~~~~~~~~~~~~~l~~av~~a~~~a~~gd~VLlSPacaSfD~f~nyeeRG~~Fk~~V~~l~g  478 (481)
T PRK01438        412 RHAPDVPVVDVDRTDTEAMARAVRLAARLARPGDTVLLAPACASMDMFTNYAERGEAFAAAVRHLLG  478 (481)
T ss_pred             HCCCCCCEEEECCCHHHHHHHHHHHHHHHCCCCCEEEECCHHHCCCCCCCHHHHHHHHHHHHHHHHC
T ss_conf             2289874577310237899999999996389989899895000202206999999999999997237


No 19 
>PRK01710 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=100.00  E-value=0  Score=388.29  Aligned_cols=322  Identities=20%  Similarity=0.242  Sum_probs=245.0

Q ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCHHHHHCCCCCCCH-HCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCC
Q ss_conf             69939998303654201233467777520112221221101457410-00123221444301566443321121223232
Q gi|254781101|r  106 SKATIIAITGSVGKTTTKEMLTIALSSIKKTYACIGSYNNHIGVPLT-LARMPVDVDFGIFELGMSHLGEIRFLTHLVRP  184 (472)
Q Consensus       106 ~~~~vI~ITGTnGKTTt~~~l~~iL~~~~~~~~t~gn~Nn~iGvplt-ll~~~~~~~~~V~E~g~~~~gei~~L~~i~~P  184 (472)
                      .+.++||||||||||||++|++++|+..|......||    ||.|+. .+.-..+.+++|+|++..+   +..+ + ++|
T Consensus       115 ~~~~~IaVTGTnGKTTTtsmi~~iL~~~g~~~~~gGN----iG~p~~~~~~~~~~~d~~V~E~SS~q---l~~~-~-~~P  185 (458)
T PRK01710        115 CPAKVFGITGSDGKTTTTTLIYEMLKEEGYKTWVGGN----IGTPLFSNIEEIKEEDKVVLELSSFQ---LMTM-D-VSP  185 (458)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHHHHCCCCEEEECC----CCCHHHHHHHHCCCCCEEEEEECHHH---HHHC-C-CCC
T ss_conf             7587799936898478999999999984997585166----26446888850578866999932155---5305-4-688


Q ss_pred             CEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCC--CCCCCC
Q ss_conf             202555312101234445788886543310376221012101342468998752012333332222222222--222344
Q gi|254781101|r  185 HIAVITTIAPAHLSNFSGIEEIASAKAEIFEGLEKTGTIFLNYDDSFFELLKAKSHALGIKTIYSFGKSKNA--DFQLRK  262 (472)
Q Consensus       185 ~iaiiTNI~~dHld~~~s~e~i~~~K~~i~~~l~~~g~~ViN~Dd~~~~~l~~~~~~~~~~~i~~~g~~~~a--d~~~~~  262 (472)
                      +++|||||++||||||+|+|+|+++|.+||+++++++.+|+|.||+....+......    .+++|+.+...  +.+..+
T Consensus       186 ~iaVitNi~~DHLD~h~s~e~Y~~aK~~i~~~~~~~~~~i~n~Dd~~~~~~~~~~~~----~~~~f~~~~~~~~~~~~~~  261 (458)
T PRK01710        186 EVAVVTNLSPNHLDVHKDMEEYVDAKKNIFKYQSSNDLLVLNKDNEITNGMEKEAKG----DVVKFSRKEKLKEGAYYKD  261 (458)
T ss_pred             CEEEEECCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCHHHHHHHHHCCC----CEEEECCCCCCCCCCEEEC
T ss_conf             789983588536506541999999999999638877379993786999998776368----7899536654566736766


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHCCCCCCCCCCCCEECCCCCCEEEE
Q ss_conf             21134651001245654322122222222333322103567651012103455431147664433101000365311331
Q gi|254781101|r  263 WKQCSEQSWMEVQLQGKSMEVVHHGIGYHMAQNMLMTLGIVSILTADVDTAIKALSVFHPKEGRGKRYRCALNQGFFTLI  342 (472)
Q Consensus       263 i~~~~~~~~~~~~~~~~~~~~~l~~~G~hnv~NalaAia~~~~lGi~~~~i~~~L~~~~~~~GR~~~~~~~~~~~~~~iI  342 (472)
                           .  ...+..........++++|.||++|++||++++. +|++.+.|.++|++|+++|+|+|.+   ...+++++|
T Consensus       262 -----~--~~~~~~~~~~~~~~l~l~G~HN~~N~lAA~aa~~-~gi~~e~i~~aL~~F~Gl~hR~E~v---~~~~gv~~i  330 (458)
T PRK01710        262 -----G--KLYIRGKEVCKKDDIKLKGMHNVENLLAAFCAVN-DDVSIESMKKVATTFTGVEHRCEFV---REINGVKYY  330 (458)
T ss_pred             -----C--EEEECCCEECCHHHCCCCCHHHHHHHHHHHHHHH-CCCCHHHHHHHHHHCCCHHHHHEEE---EEECCEEEE
T ss_conf             -----8--8998784011324216776544999999999998-1999999999987543534231465---787476798


Q ss_pred             EECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHCCC--
Q ss_conf             000256532101257778741110268713885123541710589999999999864998999988038989985113--
Q gi|254781101|r  343 DESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFHVLALKDALPR--  420 (472)
Q Consensus       343 DDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~~~~~~~~~~~--  420 (472)
                      |||+..||+|+.+||+++.       ++.++|+|+     ........++.+.+.+ .+..++++|+....+.+.+.+  
T Consensus       331 NDSkaTn~~s~~~AL~~~~-------~~iilI~GG-----~~K~~d~~~l~~~~~~-~~k~vi~~G~~~~~i~~~l~~~~  397 (458)
T PRK01710        331 NDSIASSPTRTLAGLNAFE-------KPVILIAGG-----YDKKIPFEPLAEEGYE-KIKILILMGDTKNKIKEAFKKVE  397 (458)
T ss_pred             ECCCCCCHHHHHHHHHCCC-------CCEEEEECC-----CCCCCCHHHHHHHHHH-HCCEEEEECCCHHHHHHHHHHHH
T ss_conf             1576689899999997167-------772999646-----5667886999998763-05299997887799999998766


Q ss_pred             -----CCCEEEECCHHHHHHHHHHHCCCCCEEEEE---CC---------CHHHHHHHHHHH
Q ss_conf             -----797999789899999999844789899997---71---------325489999999
Q gi|254781101|r  421 -----SIHVHYSETMDGLFLFIQSSLVDGDVVVVK---SS---------NSCGFYRLINLL  464 (472)
Q Consensus       421 -----~~~~~~~~~~e~a~~~l~~~~~~gdiVLiK---GS---------r~~~le~iv~~L  464 (472)
                           ...+..++++++|+..+.+.+++||+||+.   .|         ||..|.++|+.|
T Consensus       398 ~~~~~~~~~~~~~~l~~Av~~a~~~a~~gd~VLlSPa~aSfD~f~nfeeRG~~F~~~V~~L  458 (458)
T PRK01710        398 EEKGIKIPIVIVNSLEEAVKVAKNIAEKGDIITLSPACASFDMFPNFEIRGNKFKEIVNNL  458 (458)
T ss_pred             HHCCCCCCEEHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCHHHHHHHHHHHHHHC
T ss_conf             6316886523373599999999975889798998973311035269999999999999739


No 20 
>PRK03806 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=100.00  E-value=0  Score=378.19  Aligned_cols=321  Identities=23%  Similarity=0.325  Sum_probs=242.6

Q ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCHHHHHCCCCCCCHHCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCC
Q ss_conf             06993999830365420123346777752011222122110145741000123221444301566443321121223232
Q gi|254781101|r  105 RSKATIIAITGSVGKTTTKEMLTIALSSIKKTYACIGSYNNHIGVPLTLARMPVDVDFGIFELGMSHLGEIRFLTHLVRP  184 (472)
Q Consensus       105 ~~~~~vI~ITGTnGKTTt~~~l~~iL~~~~~~~~t~gn~Nn~iGvpltll~~~~~~~~~V~E~g~~~~gei~~L~~i~~P  184 (472)
                      ..+.++||||||||||||+.|++++|+..|......||    ||.|..-+ +..+.|++|+|++..+   ++. +.-++|
T Consensus       102 ~~~~~iIaVTGTnGKTTTt~li~~iL~~~g~~~~~gGN----iG~p~~~~-~~~~~d~~VlElSSfQ---Le~-~~~~~p  172 (438)
T PRK03806        102 EAQAPIVAITGSNGKSTVTTLVGEMAKAAGVNVGVGGN----IGLPALML-LDQDCELYVLELSSFQ---LET-TSSLQA  172 (438)
T ss_pred             CCCCCEEEEECCCCCHHHHHHHHHHHHHCCCCEEEEEC----CCCCHHHH-HCCCCCEEEEECCCCC---CCC-CCCCCC
T ss_conf             27998899948998489999999999865997567715----77527775-1376757998324533---002-354576


Q ss_pred             CEEEEEEECCCHHHHHH-HHHHHHHHHHHHCCCCCCCCHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             20255531210123444-57888865433103762210121013424689987520123333322222222222223442
Q gi|254781101|r  185 HIAVITTIAPAHLSNFS-GIEEIASAKAEIFEGLEKTGTIFLNYDDSFFELLKAKSHALGIKTIYSFGKSKNADFQLRKW  263 (472)
Q Consensus       185 ~iaiiTNI~~dHld~~~-s~e~i~~~K~~i~~~l~~~g~~ViN~Dd~~~~~l~~~~~~~~~~~i~~~g~~~~ad~~~~~i  263 (472)
                      +++|||||++||||+|+ ++|+|+++|.+||++.   +.+|+|.||+....+....     ...++||.+. .++.+.. 
T Consensus       173 ~vavilNi~~DHLDr~~~s~e~Y~~aK~rI~~~~---~~~v~n~dD~~~~~~~~~~-----~~~i~fg~~~-~~~~~~~-  242 (438)
T PRK03806        173 VAATILNVTEDHMDRYPFGLQQYRAAKLRIYENA---KVCVVNADDALTMPVRGAD-----ERCVSFGVNM-GDYHLNR-  242 (438)
T ss_pred             CEEEEECCCHHHHHHHHHHHHHHHHHHHHHHCCC---CEEEECCCCHHHHHHHHCC-----CCEEEEECCC-CCEEEEE-
T ss_conf             3788635888788776545999999999886279---6899947518779864035-----6558982356-6436760-


Q ss_pred             CCCCCCCCCCCCCCCCC-C-CCCCCCCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHCCCCCCCCCCCCEECCCCCCEEE
Q ss_conf             11346510012456543-2-212222222233332210356765101210345543114766443310100036531133
Q gi|254781101|r  264 KQCSEQSWMEVQLQGKS-M-EVVHHGIGYHMAQNMLMTLGIVSILTADVDTAIKALSVFHPKEGRGKRYRCALNQGFFTL  341 (472)
Q Consensus       264 ~~~~~~~~~~~~~~~~~-~-~~~l~~~G~hnv~NalaAia~~~~lGi~~~~i~~~L~~~~~~~GR~~~~~~~~~~~~~~i  341 (472)
                        ......+.  ..+.. . .-.++++|.||++|+++|+++|..+|++.+.|.++|.+|+++|+|+|.+   ...+|+++
T Consensus       243 --~~~~~~~~--~~~~~~~~~~~l~l~G~HN~~NalaA~a~a~~lGi~~e~i~~aL~sF~gl~HRlE~v---~~~~gv~f  315 (438)
T PRK03806        243 --QQGETWLR--VKGEKVLNVKEMKLSGRHNYTNALAALALADAVGIPRASSLKALTTFTGLPHRFQLV---LEHNGVRW  315 (438)
T ss_pred             --CCCCEEEE--ECCEEEEECHHCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCCEEEE---EEECCEEE
T ss_conf             --57736897--378035401212666720498899999999983999899865520479999733899---99799999


Q ss_pred             EEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHCCCC
Q ss_conf             10002565321012577787411102687138851235417105899999999998649989999880389899851137
Q gi|254781101|r  342 IDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFHVLALKDALPRS  421 (472)
Q Consensus       342 IDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~~~~~~~~~~~~  421 (472)
                      ||||...||+|+.+||+++..     .++.++|+|++     .....+.++.+.+... ...++++|+....+.+.....
T Consensus       316 iNDSKaTN~~a~~~Al~s~~~-----~~~i~lI~GG~-----~K~~d~~~l~~~~~~~-~~~~~~~G~~~~~~~~~~~~~  384 (438)
T PRK03806        316 INDSKATNVGSTEAALNGLHV-----DGTLHLLLGGD-----GKSADFSPLARYLNGD-NIRLYCFGRDGAQLAALRPEV  384 (438)
T ss_pred             EECCCCCCHHHHHHHHHHCCC-----CCCEEEEECCC-----CCCCCHHHHHHHHHCC-CEEEEEECCCHHHHHHHCCCC
T ss_conf             989721589999999982620-----39779995477-----5557879999986126-569999777889999641220


Q ss_pred             CCEEEECCHHHHHHHHHHHCCCCCEEEEE---CC---------CHHHHHHHHHHH
Q ss_conf             97999789899999999844789899997---71---------325489999999
Q gi|254781101|r  422 IHVHYSETMDGLFLFIQSSLVDGDVVVVK---SS---------NSCGFYRLINLL  464 (472)
Q Consensus       422 ~~~~~~~~~e~a~~~l~~~~~~gdiVLiK---GS---------r~~~le~iv~~L  464 (472)
                        ...++++++|++.+.+.+++||+||+.   .|         ||..|.++|++|
T Consensus       385 --~~~~~~l~~Av~~a~~~a~~gd~VLlSPacaSfD~f~nye~RG~~F~~lv~~L  437 (438)
T PRK03806        385 --AQLTETMEQAMRLLAPRVQPGDMVLLSPACASLDQFKNFEQRGDEFARLAKEL  437 (438)
T ss_pred             --CHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCHHHHHHHHHHHHHHC
T ss_conf             --41540099999999986689998998974503014249999999999999962


No 21 
>COG0771 MurD UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell envelope biogenesis, outer membrane]
Probab=100.00  E-value=0  Score=372.02  Aligned_cols=330  Identities=25%  Similarity=0.264  Sum_probs=251.0

Q ss_pred             HHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCHHHHHCCCCCCCH-HCCCCCCCHHHHHCCCCCCCCCCCCC
Q ss_conf             99983069939998303654201233467777520112221221101457410-00123221444301566443321121
Q gi|254781101|r  100 VAARLRSKATIIAITGSVGKTTTKEMLTIALSSIKKTYACIGSYNNHIGVPLT-LARMPVDVDFGIFELGMSHLGEIRFL  178 (472)
Q Consensus       100 ~~~~~~~~~~vI~ITGTnGKTTt~~~l~~iL~~~~~~~~t~gn~Nn~iGvplt-ll~~~~~~~~~V~E~g~~~~gei~~L  178 (472)
                      -++|.....|+||||||||||||+.|++++|+..|....-.||    ||+|.. ++.-.++.|++|+|+|.-+   ++. 
T Consensus       102 L~~r~~~~~p~vaITGTNGKTTTTsli~~~l~~~G~~~~lgGN----IG~p~l~~~~~~~~~d~~VlElSSfQ---L~~-  173 (448)
T COG0771         102 LFYRLSGEAPIVAITGTNGKTTTTSLIAHLLKAAGLDALLGGN----IGTPALELLEQAEPADVYVLELSSFQ---LET-  173 (448)
T ss_pred             HHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHCCCCCEECCC----CCCCHHHHHCCCCCCCEEEEECCCCC---CCC-
T ss_conf             8987448999899979996288999999999855998321351----67137876201578987999924555---165-


Q ss_pred             CCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCC--
Q ss_conf             223232202555312101234445788886543310376221012101342468998752012333332222222222--
Q gi|254781101|r  179 THLVRPHIAVITTIAPAHLSNFSGIEEIASAKAEIFEGLEKTGTIFLNYDDSFFELLKAKSHALGIKTIYSFGKSKNA--  256 (472)
Q Consensus       179 ~~i~~P~iaiiTNI~~dHld~~~s~e~i~~~K~~i~~~l~~~g~~ViN~Dd~~~~~l~~~~~~~~~~~i~~~g~~~~a--  256 (472)
                      +.-++|++++||||++||||||+|||+|+.+|++|++++.+  ++|+|.||++...+....   ....+.+|+..+..  
T Consensus       174 ~~~~~P~iavilNi~~DHLD~H~s~e~Y~~aK~~i~~~~~~--~~Vin~dd~~~~~~~~~~---~~~~~~~fs~~~~~~~  248 (448)
T COG0771         174 TSSLRPEIAVILNISEDHLDRHGSMENYAAAKLRILEGQTE--VAVINADDAYLKTLADEA---TKARVIWFSFGEPLAD  248 (448)
T ss_pred             CCCCCCCEEEEECCCHHHHHHCCCHHHHHHHHHHHHCCCCC--EEEEECCCHHHHHHHHHC---CCCEEEEEECCCCCCC
T ss_conf             76678557999448877865606999999999999838962--799837727776544303---6632688974664556


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHCCCCCCCCCCCCEECCCC
Q ss_conf             22234421134651001245654322122222222333322103567651012103455431147664433101000365
Q gi|254781101|r  257 DFQLRKWKQCSEQSWMEVQLQGKSMEVVHHGIGYHMAQNMLMTLGIVSILTADVDTAIKALSVFHPKEGRGKRYRCALNQ  336 (472)
Q Consensus       257 d~~~~~i~~~~~~~~~~~~~~~~~~~~~l~~~G~hnv~NalaAia~~~~lGi~~~~i~~~L~~~~~~~GR~~~~~~~~~~  336 (472)
                      .+++.+-...       +....-...-.++++|.||++|+++|+++|..+|++.+.|.+.|++|++++||+|.+   ...
T Consensus       249 ~~~~~~~~~~-------~~~~~i~~~~~l~l~G~hn~~N~lAa~a~a~~~gv~~e~i~~~L~~F~gl~HR~e~v---~~~  318 (448)
T COG0771         249 GDYIYDGKLV-------FKGEKLLPADELKLPGAHNLENALAALALARALGVPPEAILEALSSFTGLPHRLEFV---GEK  318 (448)
T ss_pred             CCEEECCHHC-------CCCCCCCCHHHCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCEEEE---EEC
T ss_conf             6334340110-------353000334215875452499899999999983999899999997389998622798---861


Q ss_pred             CCEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHH
Q ss_conf             31133100025653210125777874111026871388512354171058999999999986499899998803898998
Q gi|254781101|r  337 GFFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFHVLALKD  416 (472)
Q Consensus       337 ~~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~~~~~~~  416 (472)
                      +++.+||||...||+|..+||..+.       ++.++|+|+.     .....-..+.+.+... ...++++|+....+..
T Consensus       319 ~gv~f~NDSKATN~~At~~AL~~~~-------~~v~lI~GG~-----~Kg~df~~L~~~~~~~-~~~~~~~G~~~~~i~~  385 (448)
T COG0771         319 DGVLFINDSKATNVDATLAALSGFD-------GPVILIAGGD-----DKGADFSPLAEILAKV-IKKLVLIGEDAEKIAA  385 (448)
T ss_pred             CCEEEECCCCCCCHHHHHHHHHCCC-------CCEEEEECCC-----CCCCCHHHHHHHHHHC-CEEEEEECCCHHHHHH
T ss_conf             9889960787888889999997189-------9779997777-----8888816889977415-5599994788899999


Q ss_pred             HCCCCCC-EEEECCHHHHHHHHHHHCCCCCEEEEE---CC---------CHHHHHHHHHHHH
Q ss_conf             5113797-999789899999999844789899997---71---------3254899999999
Q gi|254781101|r  417 ALPRSIH-VHYSETMDGLFLFIQSSLVDGDVVVVK---SS---------NSCGFYRLINLLL  465 (472)
Q Consensus       417 ~~~~~~~-~~~~~~~e~a~~~l~~~~~~gdiVLiK---GS---------r~~~le~iv~~L~  465 (472)
                      .+++... ...++++++|++.+.+.+.+||+||+.   .|         ||..|.+.+..|.
T Consensus       386 ~l~~~~~~~~~~~~le~Av~~a~~~a~~gd~VLLSPacASfDqf~~feeRG~~F~~~v~~l~  447 (448)
T COG0771         386 ALKEAGPSLVICETLEEAVQLARELAQPGDVVLLSPACASFDQFKNFEERGEEFKELVSELG  447 (448)
T ss_pred             HHHHCCCCEEECCCHHHHHHHHHHHHCCCCEEEECCCCCCHHHHCCHHHHHHHHHHHHHHHC
T ss_conf             98752785361476999999999872589869976442164222379999999999999854


No 22 
>PRK04663 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=100.00  E-value=0  Score=372.50  Aligned_cols=319  Identities=21%  Similarity=0.234  Sum_probs=238.6

Q ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCHHHHHCCCCCCCHHCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf             69939998303654201233467777520112221221101457410001232214443015664433211212232322
Q gi|254781101|r  106 SKATIIAITGSVGKTTTKEMLTIALSSIKKTYACIGSYNNHIGVPLTLARMPVDVDFGIFELGMSHLGEIRFLTHLVRPH  185 (472)
Q Consensus       106 ~~~~vI~ITGTnGKTTt~~~l~~iL~~~~~~~~t~gn~Nn~iGvpltll~~~~~~~~~V~E~g~~~~gei~~L~~i~~P~  185 (472)
                      .+.++||||||||||||++|++++|+..|......||    ||.|..-+ +..+.|++|+|++..+.   +. +.-++|+
T Consensus       106 ~~~~iIaVTGTnGKTTTtsli~~iL~~~g~~~~~gGN----iG~p~~~~-~~~~~d~~VlElSSfQL---e~-~~~~~p~  176 (438)
T PRK04663        106 VDKPVIAITGSNGKSTVTDLTGVMAKAAGVKVAVGGN----IGVPALDL-LEQDAELYVLELSSFQL---ET-TSSLKLK  176 (438)
T ss_pred             CCCCEEEEECCCCHHHHHHHHHHHHHHCCCCCEEEEE----CCCHHHHH-HHCCCCEEEEECCCCCH---HH-HCCCCCC
T ss_conf             5897899948998289999999999828997068721----57168875-30469789984451014---34-0356863


Q ss_pred             EEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             02555312101234445788886543310376221012101342468998752012333332222222222222344211
Q gi|254781101|r  186 IAVITTIAPAHLSNFSGIEEIASAKAEIFEGLEKTGTIFLNYDDSFFELLKAKSHALGIKTIYSFGKSKNADFQLRKWKQ  265 (472)
Q Consensus       186 iaiiTNI~~dHld~~~s~e~i~~~K~~i~~~l~~~g~~ViN~Dd~~~~~l~~~~~~~~~~~i~~~g~~~~ad~~~~~i~~  265 (472)
                      ++|||||++||||||+|+|+|.++|.+||++.   ..+|+|.||+....  ...    ...+++||.+.. ++....   
T Consensus       177 iavilNIs~DHLD~h~s~e~Y~~aK~rIf~~~---~~~Ivn~dd~~~~~--~~~----~~~~~~fg~~~~-~~~~~~---  243 (438)
T PRK04663        177 AAAFLNLSEDHMDRYQGMADYRQAKLRIFDHA---ELAVVNRDDKQTYP--DTA----SLQLVTFGFDQQ-EYGLIE---  243 (438)
T ss_pred             CHHHHCCCHHHHHHHCCHHHHHHHHHHHHCCC---CEEEECCCHHHHHH--HHC----CCCEEEEECCCC-CCCEEE---
T ss_conf             33440688768777369999999999985369---78998653598887--760----785799604620-165597---


Q ss_pred             CCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHCCCCCCCCCCCCEECCCCCCEEEEEE
Q ss_conf             34651001245654-32212222222233332210356765101210345543114766443310100036531133100
Q gi|254781101|r  266 CSEQSWMEVQLQGK-SMEVVHHGIGYHMAQNMLMTLGIVSILTADVDTAIKALSVFHPKEGRGKRYRCALNQGFFTLIDE  344 (472)
Q Consensus       266 ~~~~~~~~~~~~~~-~~~~~l~~~G~hnv~NalaAia~~~~lGi~~~~i~~~L~~~~~~~GR~~~~~~~~~~~~~~iIDD  344 (472)
                       ..+..+....... .....++++|.||++|+++|+++|..+|++.+.|.++|++|+++|+|+|.+   ...+++++|||
T Consensus       244 -~~~~~~~~~~~~~~~~~~~l~l~G~HN~~NalaA~a~a~~lGi~~e~I~~aL~~F~glpHRlE~v---~~~~gv~~iND  319 (438)
T PRK04663        244 -HQGREWLADNGQPVLASNELKLVGKHNVANSLVVLALLDAAGIDYRKTLDALKSYNGLTHRCQVV---ADNRGIKWVND  319 (438)
T ss_pred             -ECCEEEEEECCEEEEEHHHHCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCCEEEE---EEECCEEEECC
T ss_conf             -27869998588776631430566455687799999999983999789865653358988752899---99899999747


Q ss_pred             CCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHCCCCCCE
Q ss_conf             02565321012577787411102687138851235417105899999999998649989999880389899851137979
Q gi|254781101|r  345 SYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFHVLALKDALPRSIHV  424 (472)
Q Consensus       345 sYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~~~~~~~~~~~~~~~  424 (472)
                      |...||+|+.+||++++.     +++.++|+|+     ........++.+.+.+. ...++++|+....+....   ...
T Consensus       320 SKaTN~~a~~~Al~~~~~-----~~~i~lI~GG-----~~Kg~d~~~l~~~~~~~-~~~~~~~G~~~~~~~~~~---~~~  385 (438)
T PRK04663        320 SKATNVASTLAALSGLNL-----EGKLYLLVGG-----VGKGADFSELKPVLATL-NLQLCCFGEDGDQFMPLH---PSA  385 (438)
T ss_pred             CCCCCHHHHHHHHHHCCC-----CCCEEEEECC-----CCCCCCHHHHHHHHHHC-CEEEEEECCCHHHHHHHC---CCC
T ss_conf             877887899999983677-----7847999657-----66666879999998523-769999888899997432---453


Q ss_pred             EEECCHHHHHHHHHHHCCCCCEEEEE---CC---------CHHHHHHHHHHH
Q ss_conf             99789899999999844789899997---71---------325489999999
Q gi|254781101|r  425 HYSETMDGLFLFIQSSLVDGDVVVVK---SS---------NSCGFYRLINLL  464 (472)
Q Consensus       425 ~~~~~~e~a~~~l~~~~~~gdiVLiK---GS---------r~~~le~iv~~L  464 (472)
                      ..++++++|+..+.+.+++||+||+.   .|         ||..|.++|+.|
T Consensus       386 ~~~~~l~~Av~~a~~~a~~gd~vLlSPacaSfD~F~nyeeRG~~F~~lv~~l  437 (438)
T PRK04663        386 RRFETMEDAIESISPQLKSGDMVMLSPACASFDQFANFMARGDAFAELAKQY  437 (438)
T ss_pred             EECCCHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             4406799999999986779998998974403003069999999999999974


No 23 
>PRK03369 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=100.00  E-value=0  Score=371.98  Aligned_cols=323  Identities=19%  Similarity=0.190  Sum_probs=236.0

Q ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCHHHHHCCCCCCCHHCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCE
Q ss_conf             99399983036542012334677775201122212211014574100012322144430156644332112122323220
Q gi|254781101|r  107 KATIIAITGSVGKTTTKEMLTIALSSIKKTYACIGSYNNHIGVPLTLARMPVDVDFGIFELGMSHLGEIRFLTHLVRPHI  186 (472)
Q Consensus       107 ~~~vI~ITGTnGKTTt~~~l~~iL~~~~~~~~t~gn~Nn~iGvpltll~~~~~~~~~V~E~g~~~~gei~~L~~i~~P~i  186 (472)
                      ..++||||||||||||++|++++|+..|......||    ||.|+.- .++++.+++|+|++..+   ++. +.-++|++
T Consensus       116 ~~~~IaVTGTnGKTTttsli~~iL~~~g~~~~~~GN----iG~p~~~-~~~~~~~~~V~ElSSfq---l~~-~~~~~p~i  186 (487)
T PRK03369        116 PRRWLVVTGTNGKTTTTSMLHAMLRAAGRRSVLCGN----IGSPVLD-VLDEPAELLAVELSSFQ---LHW-APSLRPEA  186 (487)
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHCCCCEEEEEC----CCHHHHH-HCCCCCCEEEEEECCCC---CCC-CCCCCCCE
T ss_conf             665599979887278999999999858998599813----6657664-12478858999813654---344-66668547


Q ss_pred             EEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCC--CCCCCCCCCCCC
Q ss_conf             255531210123444578888654331037622101210134246899875201233333222222--222222234421
Q gi|254781101|r  187 AVITTIAPAHLSNFSGIEEIASAKAEIFEGLEKTGTIFLNYDDSFFELLKAKSHALGIKTIYSFGK--SKNADFQLRKWK  264 (472)
Q Consensus       187 aiiTNI~~dHld~~~s~e~i~~~K~~i~~~l~~~g~~ViN~Dd~~~~~l~~~~~~~~~~~i~~~g~--~~~ad~~~~~i~  264 (472)
                      +|||||++||||||+|+|+|.++|.+||.    ++++|+|.||+....+.......   ..+.|+.  ....++...+..
T Consensus       187 aVitNI~~DHLD~h~s~e~Y~~aK~ri~~----~~~~v~n~DD~~~~~l~~~~~~~---~~~~~~~~~~~~~~~~~~~~~  259 (487)
T PRK03369        187 GAVLNIAEDHLDWHGTMAAYAAAKARALT----GRVAVAGLDDSRAAALLDTAPAP---VRVGFRLGEPAAGELGVRDGH  259 (487)
T ss_pred             EEECCCCHHHHHHCCCHHHHHHHHHHHHC----CCEEEEECCCHHHHHHHHHCCCC---EEEEEECCCCCCCCEEEECCE
T ss_conf             88527887787542899999999755733----98799968768899997427876---799653278764421265368


Q ss_pred             CCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHCCCCCCCCCCCCEECCCCCCEEEEE
Q ss_conf             134651001245654322-1222222223333221035676510121034554311476644331010003653113310
Q gi|254781101|r  265 QCSEQSWMEVQLQGKSME-VVHHGIGYHMAQNMLMTLGIVSILTADVDTAIKALSVFHPKEGRGKRYRCALNQGFFTLID  343 (472)
Q Consensus       265 ~~~~~~~~~~~~~~~~~~-~~l~~~G~hnv~NalaAia~~~~lGi~~~~i~~~L~~~~~~~GR~~~~~~~~~~~~~~iID  343 (472)
                      .....    +........ -.++++|.||++|+++|++++..+|++.+.|.++|++|+++|+|+|.+   ...+|+.+||
T Consensus       260 ~~~~~----~~~~~~~~~~~~l~l~G~HNv~NalAA~a~a~~lGi~~~~i~~aL~~F~glphR~E~v---~~~~Gv~fiN  332 (487)
T PRK03369        260 LVDRA----FADDLTLAPVDSIPVPGPVGVLDALAAAALARAVGVPAGAIADALASFRVGRHRAEVV---AVADGITYVD  332 (487)
T ss_pred             EEEEE----CCCCCEEEEHHHCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCEEEE---EEECCEEEEE
T ss_conf             99841----3677367246645886353699899999999984999999999998579999852899---9999999982


Q ss_pred             ECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHCCCCCC
Q ss_conf             00256532101257778741110268713885123541710589999999999864998999988038989985113797
Q gi|254781101|r  344 ESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFHVLALKDALPRSIH  423 (472)
Q Consensus       344 DsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~~~~~~~~~~~~~~  423 (472)
                      ||+..||+|+.+||+++.        +.++|+|+.     .......++.+.+... +..++++|+....+.+.+.+...
T Consensus       333 DSKaTn~~a~~~Al~s~~--------~iilI~GG~-----~Kg~~~~~L~~~~~~~-v~~v~l~G~d~~~i~~~l~~~~~  398 (487)
T PRK03369        333 DSKATNPHAARASILAYP--------RVVWIAGGL-----LKGASVDALVAEMASR-LVGAVLIGRDRAVVAEALSRHAP  398 (487)
T ss_pred             CCCCCCHHHHHHHHHHCC--------CEEEECCCC-----CCCCCHHHHHHHHHHH-EEEEEEECCCHHHHHHHHHHHCC
T ss_conf             576689889999986155--------508961554-----3677707789999754-25999978888999999974277


Q ss_pred             ---E---EE----------------------------ECCHHHHHHHHHHHCCCCCEEEEE---CC---------CHHHH
Q ss_conf             ---9---99----------------------------789899999999844789899997---71---------32548
Q gi|254781101|r  424 ---V---HY----------------------------SETMDGLFLFIQSSLVDGDVVVVK---SS---------NSCGF  457 (472)
Q Consensus       424 ---~---~~----------------------------~~~~e~a~~~l~~~~~~gdiVLiK---GS---------r~~~l  457 (472)
                         +   ..                            ..++++|++.+.+.+++||+||+.   .|         ||..|
T Consensus       399 ~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~AV~~A~~~a~~GdvVLLSPacaSfD~f~nye~RG~~F  478 (487)
T PRK03369        399 DVPVVEVVTGEDAGMPATPEACVLDVTKVDDAGGTLGDAVMTAAVAAARGLARPGDTVLLAPAGASFDQFTGYADRGDAF  478 (487)
T ss_pred             CCCCEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHCCCCCEEEECCHHHCHHCCCCHHHHHHHH
T ss_conf             66521331132222100134544333321001120357799999999997489999899795553410307999999999


Q ss_pred             HHHHHHHHH
Q ss_conf             999999998
Q gi|254781101|r  458 YRLINLLLE  466 (472)
Q Consensus       458 e~iv~~L~~  466 (472)
                      .++|++|.+
T Consensus       479 ~~~V~~l~~  487 (487)
T PRK03369        479 AAAVRAAIR  487 (487)
T ss_pred             HHHHHHHHC
T ss_conf             999999759


No 24 
>PRK00141 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=100.00  E-value=0  Score=369.81  Aligned_cols=326  Identities=20%  Similarity=0.209  Sum_probs=239.0

Q ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCHHHHHCCCCCCCH-HCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf             9939998303654201233467777520112221221101457410-001232214443015664433211212232322
Q gi|254781101|r  107 KATIIAITGSVGKTTTKEMLTIALSSIKKTYACIGSYNNHIGVPLT-LARMPVDVDFGIFELGMSHLGEIRFLTHLVRPH  185 (472)
Q Consensus       107 ~~~vI~ITGTnGKTTt~~~l~~iL~~~~~~~~t~gn~Nn~iGvplt-ll~~~~~~~~~V~E~g~~~~gei~~L~~i~~P~  185 (472)
                      +.++||||||||||||++|+++||++.|......||    ||+|++ .+...+..+++|+|++..+   ++. +.-++|+
T Consensus       122 ~~~~IaVTGTnGKTTTtsli~~iL~~~g~~~~~~GN----IG~p~~~~l~~~~~~d~~VlElSSfQ---L~~-~~~~~p~  193 (476)
T PRK00141        122 PRTWLAVTGTNGKTTTTAMLAAMMQAGGFAAVAVGN----IGIPVSAALVAQNRIDVLVAELSSFQ---LHW-APTFTPD  193 (476)
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHCCCCCEEEEE----CCCHHHHHHHCCCCCCEEEEECCCCH---HCC-CCCCCCC
T ss_conf             776388968996798999999999837997289950----67246666525787758999778201---200-2236865


Q ss_pred             EEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCC--CCCCCC
Q ss_conf             025553121012344457888865433103762210121013424689987520123333322222222222--223442
Q gi|254781101|r  186 IAVITTIAPAHLSNFSGIEEIASAKAEIFEGLEKTGTIFLNYDDSFFELLKAKSHALGIKTIYSFGKSKNAD--FQLRKW  263 (472)
Q Consensus       186 iaiiTNI~~dHld~~~s~e~i~~~K~~i~~~l~~~g~~ViN~Dd~~~~~l~~~~~~~~~~~i~~~g~~~~ad--~~~~~i  263 (472)
                      ++|||||++||||||+|+|+|+++|.+||++    ...|+|.||+....+......   ..+++|+.+...+  +...+.
T Consensus       194 iaVilNIs~DHLD~h~s~e~Y~~aK~kI~~~----~~~vi~~Dd~~~~~~~~~~~~---~~~~~~s~~~~~~~~~~~~~~  266 (476)
T PRK00141        194 AGVVLNLAEDHIDWHGSMRDYALDKARVLTA----PVAVIGADDPYVVELTREADL---SGLIGFTLGEPAEGQVGVRAG  266 (476)
T ss_pred             EEEEECCCHHHHHHHCCHHHHHHHHHHHHCC----CCEEEECCCHHHHHHHHHCCC---CCEEEECCCCCCCCCEEEECC
T ss_conf             8987268878986626999999999987348----824997787899998874478---867985278755352447768


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHCCCCCCCCCCCCEECCCCCCEEEEE
Q ss_conf             11346510012456543221222222223333221035676510121034554311476644331010003653113310
Q gi|254781101|r  264 KQCSEQSWMEVQLQGKSMEVVHHGIGYHMAQNMLMTLGIVSILTADVDTAIKALSVFHPKEGRGKRYRCALNQGFFTLID  343 (472)
Q Consensus       264 ~~~~~~~~~~~~~~~~~~~~~l~~~G~hnv~NalaAia~~~~lGi~~~~i~~~L~~~~~~~GR~~~~~~~~~~~~~~iID  343 (472)
                      .............   ...-.++++|.||++|+++|++++..+|++.+.|.++|++|+++|+|+|.   ....+++.+||
T Consensus       267 ~~~~~~~~~~~~l---~~~~~l~~~G~HNl~NalAA~a~a~~lGi~~e~I~~aL~~F~gl~HR~E~---v~~~~gV~fiN  340 (476)
T PRK00141        267 ELVDNAFGDNVVL---ASADGINPAGPAGVLDALAAAAVARSQGVAPEAIARALAGFEVAGHRGQV---VAEHDGVHFID  340 (476)
T ss_pred             EEEEEECCCCCEE---CCHHHCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCEEE---EEEECCEEEEC
T ss_conf             8998515775032---12432377653359999999999998499999999999856898861279---99989999981


Q ss_pred             ECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHCCCC--
Q ss_conf             002565321012577787411102687138851235417105899999999998649989999880389899851137--
Q gi|254781101|r  344 ESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFHVLALKDALPRS--  421 (472)
Q Consensus       344 DsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~~~~~~~~~~~~--  421 (472)
                      ||...||+|+.+||++++        +.++|+|+     ........++.+.+.. .+..++++|+....+.+.+...  
T Consensus       341 DSKaTN~~at~~AL~~~~--------~iilI~GG-----~~Kg~d~~~l~~~~~~-~vk~v~l~G~~~~~i~~~l~~~~~  406 (476)
T PRK00141        341 NSKATNPHAADSALAGHE--------SVIWVAGG-----QLKGADIDELIATHGG-RIKAALVLGADRAEIVAAVKEHAP  406 (476)
T ss_pred             CCCCCCHHHHHHHHHHCC--------CCEEEECC-----CCCCCCHHHHHHHHHH-HCEEEEEECCCHHHHHHHHHHHCC
T ss_conf             798999899999997288--------73999447-----6577787999999863-310999976898999999985478


Q ss_pred             -CCEEEE------CCHHHHHHHHHHHCCCCCEEEEE---CC---------CHHHHHHHHHHHHHH
Q ss_conf             -979997------89899999999844789899997---71---------325489999999985
Q gi|254781101|r  422 -IHVHYS------ETMDGLFLFIQSSLVDGDVVVVK---SS---------NSCGFYRLINLLLEE  467 (472)
Q Consensus       422 -~~~~~~------~~~e~a~~~l~~~~~~gdiVLiK---GS---------r~~~le~iv~~L~~~  467 (472)
                       ..+...      +++++|+..+.+...+||+||+.   .|         ||..|.+.|..+.+-
T Consensus       407 ~~~~~~~~~~~~~~~l~~av~~a~~~a~~gd~VLLSPacaSfD~f~nyeeRG~~F~~~V~~~~~~  471 (476)
T PRK00141        407 DAPVTVTDKTDPEEAMREAVAAAFSLAEPGDSVVLAPAAASLDMYTGMGQRGDLFAHYIIGTIKG  471 (476)
T ss_pred             CCCEEEEECCCHHHHHHHHHHHHHHHCCCCCEEEECCHHHHHCCCCCHHHHHHHHHHHHHHHHCC
T ss_conf             88268861545788999999999973889898998945430205179999999999999999713


No 25 
>PRK04690 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=100.00  E-value=0  Score=369.19  Aligned_cols=325  Identities=19%  Similarity=0.205  Sum_probs=239.1

Q ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCHHHHHCCCCCCCH-HCCCCCCCHHHHHCCCCCCCCCCCCCC-CCCC
Q ss_conf             69939998303654201233467777520112221221101457410-001232214443015664433211212-2323
Q gi|254781101|r  106 SKATIIAITGSVGKTTTKEMLTIALSSIKKTYACIGSYNNHIGVPLT-LARMPVDVDFGIFELGMSHLGEIRFLT-HLVR  183 (472)
Q Consensus       106 ~~~~vI~ITGTnGKTTt~~~l~~iL~~~~~~~~t~gn~Nn~iGvplt-ll~~~~~~~~~V~E~g~~~~gei~~L~-~i~~  183 (472)
                      +..++||||||||||||+.|+++||+..|......||    ||.|+. ++.-.+..+++|+|+|..+   ++.+. ..++
T Consensus       113 ~~~k~IaVTGTNGKTTTt~ll~~iL~~~g~~~~~~GN----IG~P~~~~~~~~~~~d~~VlElSSfQ---Le~~~~~~~~  185 (468)
T PRK04690        113 SVPGAVCVTGTKGKSTTTALLAHLLRAAGHRTALVGN----IGQPLLEVLAPQPAPAYWAIELSSYQ---TGDVGRSGAR  185 (468)
T ss_pred             CCCCEEEEECCCCHHHHHHHHHHHHHHCCCCEEEECC----CCHHHHHHHCCCCCCCEEEEEECCCH---HHHHHHCCCC
T ss_conf             6787899969985899999999999857998289867----76446765324788857999943205---7654531478


Q ss_pred             CCEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             22025553121012344457888865433103762210121013424689987520123333322222222222223442
Q gi|254781101|r  184 PHIAVITTIAPAHLSNFSGIEEIASAKAEIFEGLEKTGTIFLNYDDSFFELLKAKSHALGIKTIYSFGKSKNADFQLRKW  263 (472)
Q Consensus       184 P~iaiiTNI~~dHld~~~s~e~i~~~K~~i~~~l~~~g~~ViN~Dd~~~~~l~~~~~~~~~~~i~~~g~~~~ad~~~~~i  263 (472)
                      |+++|||||++||||||+|+|+|+++|.+||.+..++ .+++|.||+....+..     ....+++|+....  +.....
T Consensus       186 p~iavilNispDHLDrHgs~e~Y~~aK~~If~~~~~~-~~vin~~D~~~~~~~~-----~~~~v~~~~~~~~--~~~~~~  257 (468)
T PRK04690        186 PELAVVLNLFPEHLDWHGGEARYVRDKLSLVTEGRPR-IALLNAADPRLAALQL-----PDSEVRWFNHPDG--WHVRGD  257 (468)
T ss_pred             CCEEEEECCCHHHHHHCCCHHHHHHHHHHHHHCCCCC-EEEEECCCHHHHHHHC-----CCCCEEEECCCCC--EEECCC
T ss_conf             7787530488878746089999999999999657997-7999788889997525-----7784699517775--376066


Q ss_pred             C-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHCCCCCCCCCCCCEECCCCCCEEEE
Q ss_conf             1-134651001245654322122222222333322103567651012103455431147664433101000365311331
Q gi|254781101|r  264 K-QCSEQSWMEVQLQGKSMEVVHHGIGYHMAQNMLMTLGIVSILTADVDTAIKALSVFHPKEGRGKRYRCALNQGFFTLI  342 (472)
Q Consensus       264 ~-~~~~~~~~~~~~~~~~~~~~l~~~G~hnv~NalaAia~~~~lGi~~~~i~~~L~~~~~~~GR~~~~~~~~~~~~~~iI  342 (472)
                      . ...+...+        ....++++|.||++|+++|++++..+|++.+.|.++|++|+++|+|+|.+   ...+++.+|
T Consensus       258 ~~~~~~~~~~--------~~~~l~L~G~HN~~NalAA~a~a~~lGv~~~~I~~aL~sF~glpHRlE~v---~~~~gv~fi  326 (468)
T PRK04690        258 VVYRGEQAIF--------DTANVPLPGRHNRGNLCAVLAALEALGLDAAALAPAAASFRPLPNRLQEL---GSVDGITYV  326 (468)
T ss_pred             EEEECCCCEE--------CCCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCEEEE---EEECCEEEE
T ss_conf             7883562011--------11236777700487699999999983898899999874267999752799---998999997


Q ss_pred             EECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHCCC--
Q ss_conf             000256532101257778741110268713885123541710589999999999864998999988038989985113--
Q gi|254781101|r  343 DESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFHVLALKDALPR--  420 (472)
Q Consensus       343 DDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~~~~~~~~~~~--  420 (472)
                      |||...||+|+.+||+++..      .+.++|+|+     ......+.++.+.+.+...-.|+++|+....+.+.+..  
T Consensus       327 NDSKATN~~a~~~AL~~f~~------~~iilI~GG-----~~Kg~d~~~l~~~~~~~~~~~vi~~G~~~~~i~~~~~~~~  395 (468)
T PRK04690        327 NDSISTTPHASLAALDCFAG------RRVALLVGG-----HDRGLDWTDFAAHMAQQAPLEIVTMGANGPRIHALLAPLA  395 (468)
T ss_pred             CCCCCCCHHHHHHHHHHCCC------CCEEEEECC-----CCCCCCHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHCC
T ss_conf             37877898999999972766------857999736-----7667787999999863376899997478899999975234


Q ss_pred             ---CCCEEEECCHHHHHHHHHHH-CCCCCEEEEE---CC---------CHHHHHHHHHHHHHH
Q ss_conf             ---79799978989999999984-4789899997---71---------325489999999985
Q gi|254781101|r  421 ---SIHVHYSETMDGLFLFIQSS-LVDGDVVVVK---SS---------NSCGFYRLINLLLEE  467 (472)
Q Consensus       421 ---~~~~~~~~~~e~a~~~l~~~-~~~gdiVLiK---GS---------r~~~le~iv~~L~~~  467 (472)
                         ...+..++++++|+..+.+. ..+||+||+.   .|         ||..|.+++..+-..
T Consensus       396 ~~~~~~~~~~~~l~~Av~~a~~~~~~~gd~VLLSPacASfD~F~nyeeRG~~Fk~L~~~~~~~  458 (468)
T PRK04690        396 DAGRFGLHAADDLPHAMALARTALGAQGGVVLLSPGAPSFGAYRDYVARGRHFAQLAGFDPAA  458 (468)
T ss_pred             CCCCEEEEECCCHHHHHHHHHHHCCCCCCEEEECCHHHCCCCCCCHHHHHHHHHHHHCCCHHH
T ss_conf             456310254067999999999960589998997953115004179999999999987808777


No 26 
>TIGR01087 murD UDP-N-acetylmuramoylalanine--D-glutamate ligase; InterPro: IPR005762   The bacterial cell wall provides strength and rigidity to counteract internal osmotic pressure, and protection against the environment. The peptidoglycan layer gives the cell wall its strength, and helps maintain the overall shape of the cell. The basic peptidoglycan structure of both Gram-positive and Gram-negative bacteria is comprised of a sheet of glycan chains connected by short cross-linking polypeptides. Biosynthesis of peptidoglycan is a multi-step (11-12 steps) process comprising three main stages:    (1) formation of UDP-N-acetylmuramic acid (UDPMurNAc) from N-acetylglucosamine (GlcNAc). (2) addition of a short polypeptide chain to the UDPMurNAc. (3) addition of a second GlcNAc to the disaccharide-pentapeptide building block and transport of this unit through the cytoplasmic membrane and incorporation into the growing peptidoglycan layer.    Stage two involves four key Mur ligase enzymes: MurC (6.3.2.8 from EC) , MurD (6.3.2.9 from EC) , MurE (6.3.2.13 from EC)  and MurF (6.3.2.10 from EC) . These four Mur ligases are responsible for the successive additions of L-alanine, D-glutamate, meso-diaminopimelate or L-lysine, and D-alanyl-D-alanine to UDP-N-acetylmuramic acid. All four Mur ligases are topologically similar to one another, even though they display low sequence identity. They are each composed of three domains: an N-terminal Rossmann-fold domain responsible for binding the UDPMurNAc substrate; a central domain (similar to ATP-binding domains of several ATPases and GTPases); and a C-terminal domain (similar to dihydrofolate reductase fold) that appears to be associated with binding the incoming amino acid. The conserved sequence motifs found in the four Mur enzymes also map to other members of the Mur ligase family, including folylpolyglutamate synthetase, cyanophycin synthetase and the capB enzyme from Bacillales .    This entry represents UDP-N-acetylmuramoylalanine-D-glutamate ligase (MurD). MurD catalyses the addition of d-glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-l-alanine. ; GO: 0005524 ATP binding, 0008764 UDP-N-acetylmuramoylalanine-D-glutamate ligase activity, 0008360 regulation of cell shape, 0009252 peptidoglycan biosynthetic process, 0009273 peptidoglycan-based cell wall biogenesis, 0051301 cell division, 0005737 cytoplasm.
Probab=100.00  E-value=0  Score=368.33  Aligned_cols=326  Identities=24%  Similarity=0.277  Sum_probs=246.9

Q ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCHHHHHCCCCCC-CHHCCCCCCCHHHHHCCCCCCCCCCCCCCCCCC--
Q ss_conf             99399983036542012334677775201122212211014574-100012322144430156644332112122323--
Q gi|254781101|r  107 KATIIAITGSVGKTTTKEMLTIALSSIKKTYACIGSYNNHIGVP-LTLARMPVDVDFGIFELGMSHLGEIRFLTHLVR--  183 (472)
Q Consensus       107 ~~~vI~ITGTnGKTTt~~~l~~iL~~~~~~~~t~gn~Nn~iGvp-ltll~~~~~~~~~V~E~g~~~~gei~~L~~i~~--  183 (472)
                      +.|+||||||||||||+.|++++|+..|......||    ||+| +..+.- ++.+++|+|+|.-+   ++.+- =++  
T Consensus       109 ~~~~~aITGTnGKtTTT~L~~~~L~~~G~~a~~gGN----IG~p~L~~~~~-~~~~~~VlElSSFQ---L~~~~-~~~p~  179 (476)
T TIGR01087       109 PAKVVAITGTNGKTTTTSLLYHLLKAAGLKAVLGGN----IGTPALEVLDQ-EGAELYVLELSSFQ---LETTE-SLRPA  179 (476)
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHHHCCCCEEEECC----CCCHHHHHHCC-CCCCEEEEEECCHH---HCCCC-CCCCC
T ss_conf             873799972686079999999999846997786257----88125553105-88966999700032---04575-55665


Q ss_pred             CCEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHCCC---CHHHHHHHHHCCCCCCCCCCCCCCCC---CCC
Q ss_conf             220255531210123444578888654331037622101210134---24689987520123333322222222---222
Q gi|254781101|r  184 PHIAVITTIAPAHLSNFSGIEEIASAKAEIFEGLEKTGTIFLNYD---DSFFELLKAKSHALGIKTIYSFGKSK---NAD  257 (472)
Q Consensus       184 P~iaiiTNI~~dHld~~~s~e~i~~~K~~i~~~l~~~g~~ViN~D---d~~~~~l~~~~~~~~~~~i~~~g~~~---~ad  257 (472)
                      |.+++||||++||||||+|||+|.++|++|+.+++.++++|+|.|   ++.+........   . ++++|+..+   ..+
T Consensus       180 p~i~~~lNi~~DHLD~h~~~~~Y~~aK~~i~~~~~~~d~~v~n~d~~~~~~~~~~~~~~~---~-~~~~~~~~~CP~~~~  255 (476)
T TIGR01087       180 PEIALILNISEDHLDWHGSFEDYVAAKLKIFARQTEGDVAVLNADQAYDPRFTRLEKKSK---A-QVVLFSVEKCPAEAE  255 (476)
T ss_pred             CEEEEEECCCHHHHCCCCCHHHHHHHHHHHHCCCCCCCEEEEECCCCCCCHHHHCCCCCC---C-EEEEECCCCCCHHHH
T ss_conf             124687066356301107988999998898525998767988120025504652124675---3-078740445808899


Q ss_pred             CCCCCCCCCCCCCCCCCCCC--------CCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCC----CHHHHHHHHCCCCCCC
Q ss_conf             22344211346510012456--------54322122222222333322103567651012----1034554311476644
Q gi|254781101|r  258 FQLRKWKQCSEQSWMEVQLQ--------GKSMEVVHHGIGYHMAQNMLMTLGIVSILTAD----VDTAIKALSVFHPKEG  325 (472)
Q Consensus       258 ~~~~~i~~~~~~~~~~~~~~--------~~~~~~~l~~~G~hnv~NalaAia~~~~lGi~----~~~i~~~L~~~~~~~G  325 (472)
                      ..+   ...+++..+...-.        .-......+++|.||++|+++|++++..+|++    .+.+.+.|++|++++|
T Consensus       256 ~~l---~~~~~~~~l~~~~e~~~~C~~~~~~~~~~~~l~g~h~~~n~laa~ala~~~g~~~~~~~~~~~~~l~~F~~~~H  332 (476)
T TIGR01087       256 QGL---EIRDGKEYLKPNDENDFACDDLTILPCEELKLLGLHNAENILAAIALAKSLGLNSDEELEAILEALRSFKGLPH  332 (476)
T ss_pred             HHH---HHCCCCEEECCCCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCCCC
T ss_conf             764---12388526336787630000112433215676788899999999999998288976016899999984579876


Q ss_pred             CCCCCEECCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEE
Q ss_conf             33101000365311331000256532101257778741110268713885123541710589999999999864998999
Q gi|254781101|r  326 RGKRYRCALNQGFFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVW  405 (472)
Q Consensus       326 R~~~~~~~~~~~~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~  405 (472)
                      |+|.   ....+|+.+||||--.||+|+.+||..++.     ++|.++|+|++     +.......+.+.+... ...++
T Consensus       333 RlE~---~~~~~G~~f~NDSKATn~~At~~AL~~~~~-----~~~~~LI~GG~-----~KG~df~~L~~~~~~~-~~~~~  398 (476)
T TIGR01087       333 RLEY---VGQKNGVHFINDSKATNVHATLAALSALKN-----PKRVILIVGGD-----DKGADFSPLAPALKKK-VKAVL  398 (476)
T ss_pred             CEEE---EEECCCEEEEECCCCCCHHHHHHHHHHCCC-----CCEEEEEEECC-----CCCCCHHHHHHHHCCC-EEEEE
T ss_conf             2688---777285479825621218999999984799-----97189996034-----6899848999984365-07999


Q ss_pred             EECCCHHHHHHHCCCCCCEE------EECCHHHHHHHHHHHCCCC--CEEEE---ECC---------CHHHHHHHHH
Q ss_conf             98803898998511379799------9789899999999844789--89999---771---------3254899999
Q gi|254781101|r  406 LSGFHVLALKDALPRSIHVH------YSETMDGLFLFIQSSLVDG--DVVVV---KSS---------NSCGFYRLIN  462 (472)
Q Consensus       406 ~~G~~~~~~~~~~~~~~~~~------~~~~~e~a~~~l~~~~~~g--diVLi---KGS---------r~~~le~iv~  462 (472)
                      ++|+....+++.++......      .++++++|++.+.+.+++|  |+||+   ++|         ||..|-++|+
T Consensus       399 ~~G~~~~~~~~~l~~~~~~~~~~~~~~~~~l~~Av~~a~~~~~~g~~d~vLLSPacASFDqF~~y~eRGe~F~~~v~  475 (476)
T TIGR01087       399 AIGEDAAKIAKLLKEIGLVVKYGEETLVESLEEAVQAAREVAKEGNADVVLLSPACASFDQFKSYEERGEKFKELVR  475 (476)
T ss_pred             EECCCHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCCCHHHHCCHHHHHHHHHHHHH
T ss_conf             85354789999863427643546530577899999999997127997679888641217773038888899999981


No 27 
>TIGR01082 murC UDP-N-acetylmuramate--alanine ligase; InterPro: IPR005758   The bacterial cell wall provides strength and rigidity to counteract internal osmotic pressure, and protection against the environment. The peptidoglycan layer gives the cell wall its strength, and helps maintain the overall shape of the cell. The basic peptidoglycan structure of both Gram-positive and Gram-negative bacteria is comprised of a sheet of glycan chains connected by short cross-linking polypeptides. Biosynthesis of peptidoglycan is a multi-step (11-12 steps) process comprising three main stages:    (1) formation of UDP-N-acetylmuramic acid (UDPMurNAc) from N-acetylglucosamine (GlcNAc). (2) addition of a short polypeptide chain to the UDPMurNAc. (3) addition of a second GlcNAc to the disaccharide-pentapeptide building block and transport of this unit through the cytoplasmic membrane and incorporation into the growing peptidoglycan layer.    Stage two involves four key Mur ligase enzymes: MurC (6.3.2.8 from EC) , MurD (6.3.2.9 from EC) , MurE (6.3.2.13 from EC)  and MurF (6.3.2.10 from EC) . These four Mur ligases are responsible for the successive additions of L-alanine, D-glutamate, meso-diaminopimelate or L-lysine, and D-alanyl-D-alanine to UDP-N-acetylmuramic acid. All four Mur ligases are topologically similar to one another, even though they display low sequence identity. They are each composed of three domains: an N-terminal Rossmann-fold domain responsible for binding the UDPMurNAc substrate; a central domain (similar to ATP-binding domains of several ATPases and GTPases); and a C-terminal domain (similar to dihydrofolate reductase fold) that appears to be associated with binding the incoming amino acid. The conserved sequence motifs found in the four Mur enzymes also map to other members of the Mur ligase family, including folylpolyglutamate synthetase, cyanophycin synthetase and the capB enzyme from Bacillales .    This entry represents UDP-N-acetylmuramate-alanine ligase (MurC). MurC is an essential, cytoplasmic peptidoglycan biosynthetic enzyme, catalyzes the ATP-dependent ligation of L-alanine (Ala) and UDP-N-acetylmuramic acid (UNAM) to form UDP-N-acetylmuramyl-L-alanine (UNAM-Ala). The enzyme is a nonribosomal peptide ligase which utilises ATP to form an amide bond between L-alanine and UNAM.1 Mechanistic studies on the Escherichia coli MurC enzyme using oxygen isotope analyses demonstrated that the enzyme-catalyzed reaction proceeds through an acyl phosphate UNAM intermediate prior to L-alanine addition.; GO: 0005524 ATP binding, 0008763 UDP-N-acetylmuramate-L-alanine ligase activity, 0008360 regulation of cell shape, 0009252 peptidoglycan biosynthetic process, 0009273 peptidoglycan-based cell wall biogenesis, 0051301 cell division, 0005737 cytoplasm.
Probab=100.00  E-value=0  Score=347.19  Aligned_cols=412  Identities=23%  Similarity=0.301  Sum_probs=290.2

Q ss_pred             HHHHHHHHCCEEECCCCCCEEEEEEEECCCCCCCCEEEECCCCCCCHHHHHHHHHHC----CCEEEEEC-CCCCCC----
Q ss_conf             788998727999526887147467740222378988897168874768889999986----98899985-521245----
Q gi|254781101|r    7 FHDLLQAIQGHSIGIVPQGFVNGISIDSRSIAPQEAFFAIKGPHYDGHDFILHAVQK----GAGLVVVN-TDMVAS----   77 (472)
Q Consensus         7 ~~~l~~~~~g~~~~~~~~~~i~~i~~dSr~v~~g~lFval~g~~~DGh~~i~~A~~~----Ga~~~i~~-~~~~~~----   77 (472)
                      +.+++..-|.+..+ . |  |..-.|..+.++.-.+=|.+      | .|-.+.++.    ++..||++ .-..+.    
T Consensus        15 lA~~L~~~G~~VsG-S-D--~~~~~y~t~~L~~~Gi~I~~------g-~h~~~n~~~~p~g~~~vVv~S~~Ai~~~NpEi   83 (491)
T TIGR01082        15 LAEILLNRGYKVSG-S-D--IAENAYTTKRLEALGIKIYI------G-EHSAENLDDLPTGAADVVVVSAAAIKEDNPEI   83 (491)
T ss_pred             HHHHHHHCCCCEEE-E-E--CCCCCCHHHHHHHCCCEECC------C-CCCHHHHCCCCCCCCCEEEEEEECCCCCCHHH
T ss_conf             99999857890877-2-0--33563158999867876627------9-96779820367897437998640337888889


Q ss_pred             --CCCCCCCEEEECCHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHC--CCCCHHHHHCCCCCCCHH
Q ss_conf             --5446972899599899999999999830699399983036542012334677775201--122212211014574100
Q gi|254781101|r   78 --IGSLSIPVFGVDDVLGALNKLAVAARLRSKATIIAITGSVGKTTTKEMLTIALSSIKK--TYACIGSYNNHIGVPLTL  153 (472)
Q Consensus        78 --~~~~~~~~i~v~d~~~al~~la~~~~~~~~~~vI~ITGTnGKTTt~~~l~~iL~~~~~--~~~t~gn~Nn~iGvpltl  153 (472)
                        .....+|++.=   -++|++|-   +.+ + .-||||||+||||||+||+++|+..|.  ++-..|..+. .|   +=
T Consensus        84 ~~A~~~~IPv~~R---~~~Lael~---~~~-k-~~iaVaGtHGKTTTTamia~~~~~aGLdPt~~~GG~~~~-~~---~N  151 (491)
T TIGR01082        84 VEAKERGIPVIRR---AEMLAELM---RKR-K-ESIAVAGTHGKTTTTAMIAVILKEAGLDPTVIVGGEVKE-AG---TN  151 (491)
T ss_pred             HHHHHCCCCEECH---HHHHHHHH---HHH-C-CEEEEECCCCCHHHHHHHHHHHHHCCCCCCEEECCCCCC-CC---CC
T ss_conf             9999648881337---89999998---620-8-707998368725689999999984499976898664366-57---74


Q ss_pred             CCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCEEEEEEECCCHHH--HHHHHHHHHHHHHHHCCCCCCCCHHHHCCCCHH
Q ss_conf             012322144430156644332112122323220255531210123--444578888654331037622101210134246
Q gi|254781101|r  154 ARMPVDVDFGIFELGMSHLGEIRFLTHLVRPHIAVITTIAPAHLS--NFSGIEEIASAKAEIFEGLEKTGTIFLNYDDSF  231 (472)
Q Consensus       154 l~~~~~~~~~V~E~g~~~~gei~~L~~i~~P~iaiiTNI~~dHld--~~~s~e~i~~~K~~i~~~l~~~g~~ViN~Dd~~  231 (472)
                      .++-...+|+|.|+-=|..+   ..---++|+++|||||.+||+|  |++|+|.+.++..+.+.++++.|.+|+|.|||.
T Consensus       152 a~~g~~~~~lvaEaDESd~~---~sFl~~~P~~ai~TNie~DH~D~tY~~~~E~~~~aF~~F~~~l~~~G~~v~c~DD~~  228 (491)
T TIGR01082       152 ARLGSSGEYLVAEADESDRS---ASFLHLQPEVAIVTNIEPDHLDNTYGSSLERLKAAFEKFIHNLPFYGLAVICADDPV  228 (491)
T ss_pred             EEECCCCCEEEEEEEECCCC---CCHHCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCHH
T ss_conf             35714686799998723776---401206985799747774347766645789999999999982788879999838654


Q ss_pred             HHHHHHHCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCC--------CCCCCCCCCCCCCCCCCCCHHHH
Q ss_conf             8998752012333332222222-22222234421134651001245654--------32212222222233332210356
Q gi|254781101|r  232 FELLKAKSHALGIKTIYSFGKS-KNADFQLRKWKQCSEQSWMEVQLQGK--------SMEVVHHGIGYHMAQNMLMTLGI  302 (472)
Q Consensus       232 ~~~l~~~~~~~~~~~i~~~g~~-~~ad~~~~~i~~~~~~~~~~~~~~~~--------~~~~~l~~~G~hnv~NalaAia~  302 (472)
                      ++.+...+.......+++++.+ +++|+++.++........|.+.....        ..++.++++|.||+.|++||+|+
T Consensus       229 ~~~l~~~~~~~r~d~~~~y~~~~~~~~~~~~~~~~~~~~~~f~v~~~~~~~~~~~~G~~~~~~~~pG~HNvLNAlAA~av  308 (491)
T TIGR01082       229 LRKLVPKATESRKDVVITYGGSGEDADIRAENIQQSGAEFEFSVRLKGKLGEATTEGPLEFKLNLPGRHNVLNALAAIAV  308 (491)
T ss_pred             HHHHHHHHHHCCCEEEEECCCCCCCCEEEEEEEEECCCEEEEEEEECCCCCCCEEEEEEEEEEECCCCCCHHHHHHHHHH
T ss_conf             78776355533870478668777641477887432264589999970452201110027999803872006789999988


Q ss_pred             HHHHCCCC---------HHHHHHHHCCCCCCCCCCCCEECCCCCC------EEEEEECCCCCCCCHHHHHHHHHHHHHCC
Q ss_conf             76510121---------0345543114766443310100036531------13310002565321012577787411102
Q gi|254781101|r  303 VSILTADV---------DTAIKALSVFHPKEGRGKRYRCALNQGF------FTLIDESYNANPASMKAAISVLSQISPHG  367 (472)
Q Consensus       303 ~~~lGi~~---------~~i~~~L~~~~~~~GR~~~~~~~~~~~~------~~iIDDsYNAnP~S~~aal~~l~~~~~~~  367 (472)
                      |..+|++.         +.|+++|.+|+++..|++..   ...++      +++||| |.+||+.++++|+++++..+.+
T Consensus       309 a~~~g~~~~G~~~~~~~~~I~~~L~~F~G~~RRf~~~---g~~~~~~n~g~~~~~DD-YAHHPtEi~aTl~aAr~~~~~k  384 (491)
T TIGR01082       309 ALELGLDFYGKVIVDFLEAIKRALANFQGVKRRFEIL---GECNGGNNNGTVLLIDD-YAHHPTEIKATLAAARQVYPDK  384 (491)
T ss_pred             HHHHCCCCCCCEEEEHHHHHHHHHHCCCCCCHHHHHH---HHCCCCCCCCEEEEEEC-CCCCHHHHHHHHHHHHHHHCCC
T ss_conf             8872212368556415899999985068973101201---00278987527999965-8999789999999998752117


Q ss_pred             CCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCC-CCEEEEE-----------CCCHHHHHHHCCC---CCCEEEECCHHH
Q ss_conf             687138851235417105899999999998649-9899998-----------8038989985113---797999789899
Q gi|254781101|r  368 EGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYN-ISHVWLS-----------GFHVLALKDALPR---SIHVHYSETMDG  432 (472)
Q Consensus       368 ~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~-~d~v~~~-----------G~~~~~~~~~~~~---~~~~~~~~~~e~  432 (472)
                      .+|.++||=.=  .=.+...+..+.++.+.  . +|.|++.           |...+.+.+.+..   .....|++++++
T Consensus       385 ~~r~v~~FQPH--rYsRT~~~~~~F~~~L~--~haD~l~~~diY~A~E~~~~g~~~~~l~~~~~~~~~~~~~~f~~~~~~  460 (491)
T TIGR01082       385 NRRIVVVFQPH--RYSRTKDLFDDFAKVLS--DHADELILLDIYAAGEEPIAGIDGKSLARKITQKKGKEEPYFVPDLAE  460 (491)
T ss_pred             CCEEEEEECCC--CHHHHHHHHHHHHHHHH--HCCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCHHHH
T ss_conf             95799997498--56789988999999997--308999981532113677678778999999862578777610421778


Q ss_pred             HHHHHHHHCCCCCEEEEECC
Q ss_conf             99999984478989999771
Q gi|254781101|r  433 LFLFIQSSLVDGDVVVVKSS  452 (472)
Q Consensus       433 a~~~l~~~~~~gdiVLiKGS  452 (472)
                      ..+.+...+.+||++|..|.
T Consensus       461 ~~~~l~~~~~~GD~~~~~GA  480 (491)
T TIGR01082       461 VVEFLAEVLQSGDLILTMGA  480 (491)
T ss_pred             HHHHHHHHCCCCCEEEEECC
T ss_conf             99999997169989999605


No 28 
>COG0773 MurC UDP-N-acetylmuramate-alanine ligase [Cell envelope biogenesis, outer membrane]
Probab=100.00  E-value=0  Score=335.79  Aligned_cols=354  Identities=23%  Similarity=0.295  Sum_probs=263.8

Q ss_pred             CCCCCEEEECCHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHC--CCCCHHHHHCCCCCCCHHCCCC
Q ss_conf             46972899599899999999999830699399983036542012334677775201--1222122110145741000123
Q gi|254781101|r   80 SLSIPVFGVDDVLGALNKLAVAARLRSKATIIAITGSVGKTTTKEMLTIALSSIKK--TYACIGSYNNHIGVPLTLARMP  157 (472)
Q Consensus        80 ~~~~~~i~v~d~~~al~~la~~~~~~~~~~vI~ITGTnGKTTt~~~l~~iL~~~~~--~~~t~gn~Nn~iGvpltll~~~  157 (472)
                      ...+|++.-   -+.|.+   ..+.   -..|||+||+|||||++|++++|...|.  ++...|..|+ .|.     ++.
T Consensus        88 e~~ipi~~r---~e~L~e---lm~~---~~~iaVaGTHGKTTTTsmla~vl~~~gldPtf~iGG~~~~-~g~-----na~  152 (459)
T COG0773          88 ERGIPVISR---AEMLAE---LMRF---RTSIAVAGTHGKTTTTSMLAWVLEAAGLDPTFLIGGILKN-FGT-----NAR  152 (459)
T ss_pred             HCCCCEECH---HHHHHH---HHHC---CEEEEEECCCCCHHHHHHHHHHHHHCCCCCEEEECCCCCC-CCC-----CCC
T ss_conf             859981628---999999---9707---7169994788754089999999986799987997774455-776-----554


Q ss_pred             C-CCHHHHHCCCCCCCCCCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHCCCCHHHHHHH
Q ss_conf             2-214443015664433211212232322025553121012344457888865433103762210121013424689987
Q gi|254781101|r  158 V-DVDFGIFELGMSHLGEIRFLTHLVRPHIAVITTIAPAHLSNFSGIEEIASAKAEIFEGLEKTGTIFLNYDDSFFELLK  236 (472)
Q Consensus       158 ~-~~~~~V~E~g~~~~gei~~L~~i~~P~iaiiTNI~~dHld~~~s~e~i~~~K~~i~~~l~~~g~~ViN~Dd~~~~~l~  236 (472)
                      . +.+|.|+|.--|.     .----.+|+++|+|||..||+|+|++++++.++-.+++++++..|.+|+|.|||.++.+.
T Consensus       153 ~g~~~~fV~EADEsD-----~sFl~~~P~~aIvTNid~DH~D~y~~~~~i~~~F~~f~~~vp~~G~~v~~~dd~~l~~l~  227 (459)
T COG0773         153 LGSGDYFVAEADESD-----SSFLHYNPRVAIVTNIEFDHLDYYGDLEAIKQAFHHFVRNVPFYGRAVVCGDDPNLRELL  227 (459)
T ss_pred             CCCCCEEEEEECCCC-----CCCCCCCCCEEEEECCCCCCHHHHCCHHHHHHHHHHHHHHCCCCCEEEEECCCHHHHHHH
T ss_conf             588864999951541-----650248897899807883400121899999999999998388665599978888899987


Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCHHHHH
Q ss_conf             5201233333222222222222234421134651001245654-322122222222333322103567651012103455
Q gi|254781101|r  237 AKSHALGIKTIYSFGKSKNADFQLRKWKQCSEQSWMEVQLQGK-SMEVVHHGIGYHMAQNMLMTLGIVSILTADVDTAIK  315 (472)
Q Consensus       237 ~~~~~~~~~~i~~~g~~~~ad~~~~~i~~~~~~~~~~~~~~~~-~~~~~l~~~G~hnv~NalaAia~~~~lGi~~~~i~~  315 (472)
                      .+..+   ..+++||.+..+||++.++.....++.|.+...++ ..++.++++|+||+.|+++|++++..+|++.+.|++
T Consensus       228 ~~~~~---~~v~tyG~~~~ad~~a~ni~~~~~~~~F~V~~~g~~~~~~~l~~pG~HNvlNAlaaia~a~~~Gi~~~~i~~  304 (459)
T COG0773         228 SRGCW---SPVVTYGFDDEADWRAENIRQDGSGTTFDVLFRGEELGEVKLPLPGRHNVLNALAAIAVARELGIDPEAIAE  304 (459)
T ss_pred             HCCCC---CCEEEECCCCCCCEEEEEEEEECCCCEEEEEECCCEEEEEEECCCCHHHHHHHHHHHHHHHHCCCCHHHHHH
T ss_conf             22258---737942478767289997687066427999986855679997267622688899999999984999899999


Q ss_pred             HHHCCCCCCCCCCCCEECCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHH
Q ss_conf             43114766443310100036531133100025653210125777874111026871388512354171058999999999
Q gi|254781101|r  316 ALSVFHPKEGRGKRYRCALNQGFFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEV  395 (472)
Q Consensus       316 ~L~~~~~~~GR~~~~~~~~~~~~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~  395 (472)
                      +|.+|+++..|   +++....+++++||| |.++|+.+++.|+++++..+. .+|.++|+--=  .-.+...++.+..+.
T Consensus       305 aL~~F~GvkRR---fe~~g~~~~~~viDD-YaHHPtEI~aTL~aaR~~~~~-~~rIvaifQPH--rySRt~~~~~dF~~~  377 (459)
T COG0773         305 ALASFQGVKRR---FELKGEVNGVTVIDD-YAHHPTEIKATLAAARQKVPG-GKRIVAVFQPH--RYSRTRDLLDDFAKA  377 (459)
T ss_pred             HHHHCCCCCEE---EEEEEEECCEEEEEC-CCCCHHHHHHHHHHHHHHCCC-CCEEEEEECCC--CHHHHHHHHHHHHHH
T ss_conf             99738896413---688646887899856-888979999999999976588-86699997787--317589999999988


Q ss_pred             HHHCCCCEEEEEC-----CC-------HHHHHHHCCCCCCEEEECCHHHHHHHHHHHCCCCCEEEEECCCHHHHHHHHHH
Q ss_conf             9864998999988-----03-------89899851137979997898999999998447898999977132548999999
Q gi|254781101|r  396 LSLYNISHVWLSG-----FH-------VLALKDALPRSIHVHYSETMDGLFLFIQSSLVDGDVVVVKSSNSCGFYRLINL  463 (472)
Q Consensus       396 ~~~~~~d~v~~~G-----~~-------~~~~~~~~~~~~~~~~~~~~e~a~~~l~~~~~~gdiVLiKGSr~~~le~iv~~  463 (472)
                      .  ..+|.|++..     ++       ...+.+.+....+.. +++.+++...+.+.+++||+||+.|.=.  +.++...
T Consensus       378 l--~~AD~v~l~~VY~A~e~~~~g~~~~~~l~~~i~~~~~~~-~~~~~~~~~~l~~~~~~gD~il~mGAGd--i~~~~~~  452 (459)
T COG0773         378 L--SDADEVILLDVYAAGEEPIEGDVSSEDLAEKIRQPGHVD-VPDLDDLVELLAKVAQPGDVILFMGAGD--IGKIARE  452 (459)
T ss_pred             H--HCCCEEEEECCCCCCCCCCCCCCCHHHHHHHHHCCCCCC-CCCHHHHHHHHHHHCCCCCEEEEECCCC--HHHHHHH
T ss_conf             8--519999996233357888767753999999851377014-7888899999996478999899966884--7889999


Q ss_pred             HHHHC
Q ss_conf             99850
Q gi|254781101|r  464 LLEEF  468 (472)
Q Consensus       464 L~~~~  468 (472)
                      +++++
T Consensus       453 ~~~~l  457 (459)
T COG0773         453 LLEAL  457 (459)
T ss_pred             HHHHH
T ss_conf             99875


No 29 
>PRK00683 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=100.00  E-value=0  Score=338.16  Aligned_cols=301  Identities=18%  Similarity=0.200  Sum_probs=225.1

Q ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCHHHHHCCCCCCCHHCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf             69939998303654201233467777520112221221101457410001232214443015664433211212232322
Q gi|254781101|r  106 SKATIIAITGSVGKTTTKEMLTIALSSIKKTYACIGSYNNHIGVPLTLARMPVDVDFGIFELGMSHLGEIRFLTHLVRPH  185 (472)
Q Consensus       106 ~~~~vI~ITGTnGKTTt~~~l~~iL~~~~~~~~t~gn~Nn~iGvpltll~~~~~~~~~V~E~g~~~~gei~~L~~i~~P~  185 (472)
                      .+.|+||||||||||||++|++++|+..|......||    ||+|+  +..-.+.++.|+|+|..+.   +. .....|.
T Consensus       100 ~~~~~IaITGTNGKTTTt~ll~~iL~~~g~~~~~~GN----IG~p~--l~~~~~~~~~VlElSSfQL---~~-~~~~~p~  169 (418)
T PRK00683        100 QRYPSLGITGSTGKTTTILFLEHLLRTLGIPAFAMGN----IGLPI--LDGMQQPGVRVVEISSFQL---AD-QEESIPV  169 (418)
T ss_pred             CCCCEEEEECCCCCEEHHHHHHHHHHHCCCCCEEEEC----CCHHH--HHHHCCCCCEEEEEEHHHH---HH-HHHCCCC
T ss_conf             4798799976898660999999999867998188803----46577--7643258946998312423---21-2430776


Q ss_pred             E--EEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             0--25553121012344457888865433103762210121013424689987520123333322222222222223442
Q gi|254781101|r  186 I--AVITTIAPAHLSNFSGIEEIASAKAEIFEGLEKTGTIFLNYDDSFFELLKAKSHALGIKTIYSFGKSKNADFQLRKW  263 (472)
Q Consensus       186 i--aiiTNI~~dHld~~~s~e~i~~~K~~i~~~l~~~g~~ViN~Dd~~~~~l~~~~~~~~~~~i~~~g~~~~ad~~~~~i  263 (472)
                      +  ||||||++||||||+|+|+|+++|.+|+..++....++++.+...........              ++..      
T Consensus       170 ~~~avilNis~DHLD~H~s~e~Y~~aK~~I~~~~~~~~~~~~~~~~~~~~~~~~~~--------------~~~~------  229 (418)
T PRK00683        170 LSGGMILNISDNHLDYHGNLDAYFQAKQNIAKCLRNPDDLWVGDERSLGNSYLEYV--------------QEIM------  229 (418)
T ss_pred             CCHHHHCCCCCCHHCCCCCHHHHHHHHHHHHHHCCCCCCEEECCCCCCCHHHHHHH--------------HHHH------
T ss_conf             22121015784241221689999999999998467976468525411017888877--------------7777------


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHH-HCCCCHHHHHHHHCCCCCCCCCCCCEECCCCCCEEEE
Q ss_conf             113465100124565432212222222233332210356765-1012103455431147664433101000365311331
Q gi|254781101|r  264 KQCSEQSWMEVQLQGKSMEVVHHGIGYHMAQNMLMTLGIVSI-LTADVDTAIKALSVFHPKEGRGKRYRCALNQGFFTLI  342 (472)
Q Consensus       264 ~~~~~~~~~~~~~~~~~~~~~l~~~G~hnv~NalaAia~~~~-lGi~~~~i~~~L~~~~~~~GR~~~~~~~~~~~~~~iI  342 (472)
                      .....             ...+...+.||.+|+++|++++.. .|++.+.+.++|++|+++|+|+|.+   ...+|+.+|
T Consensus       230 ~~~~~-------------~~~l~~~~~hn~~N~~aA~a~a~~~~~i~~~~i~~al~~F~glpHR~E~v---~~~~Gv~fi  293 (418)
T PRK00683        230 RLLDK-------------GSALKPLYLHDRYNYCAAYALANEVFPISPESFLEAVATFEKPPHRMEYL---GEKDGVHYI  293 (418)
T ss_pred             HHHCC-------------CCCCCCCCCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCCEEEE---EEECCCEEE
T ss_conf             77445-------------31016544032988999999999857999999999997348841113688---881782376


Q ss_pred             EECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHCCCCC
Q ss_conf             00025653210125777874111026871388512354171058999999999986499899998803898998511379
Q gi|254781101|r  343 DESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFHVLALKDALPRSI  422 (472)
Q Consensus       343 DDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~~~~~~~~~~~~~  422 (472)
                      |||...||+|+.+||+++..       +.|+|+|+     ........++.+.+.+. +..++++|+....+.+.+....
T Consensus       294 NDSKaTN~~a~~~AL~s~~~-------~iilI~GG-----~~K~~d~~~L~~~~~~~-vk~v~~~G~~~~~i~~~l~~~~  360 (418)
T PRK00683        294 NDSKATTVSAVEKALLAVGK-------DVIVILGG-----RNKGGDFPSLLPVLRQT-AKHVVAMGECRQEIAQALSEKF  360 (418)
T ss_pred             CCCCCCCHHHHHHHHHHCCC-------CCEEEECC-----CCCCCCHHHHHHHHHHC-CCEEEEECCCHHHHHHHHHCCC
T ss_conf             37767898999999985678-------85899757-----87667869999998631-8499996889999999875699


Q ss_pred             CEEEECCHHHHHHHHHHHCCCCCEEEEE---CC---------CHHHHHHHHHHHH
Q ss_conf             7999789899999999844789899997---71---------3254899999999
Q gi|254781101|r  423 HVHYSETMDGLFLFIQSSLVDGDVVVVK---SS---------NSCGFYRLINLLL  465 (472)
Q Consensus       423 ~~~~~~~~e~a~~~l~~~~~~gdiVLiK---GS---------r~~~le~iv~~L~  465 (472)
                      ++..++++++|+..+.+.+++||+||+.   .|         ||..|.++|..|+
T Consensus       361 ~~~~~~~l~eAv~~a~~~a~~gd~VLLSPacaSfD~F~nyeeRG~~Fk~lV~~l~  415 (418)
T PRK00683        361 PLTVVKDLQEAVSCAQEIAQPGDVILLSPGCASFDQFRSFEERGAYFKQLVGEME  415 (418)
T ss_pred             CEEECCCHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             8798598999999999847898989989755010021599999999999999732


No 30 
>PRK03815 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=100.00  E-value=7e-45  Score=316.23  Aligned_cols=311  Identities=17%  Similarity=0.182  Sum_probs=219.4

Q ss_pred             HHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCHHHHHCCCCCCCHHCCCCCCCHHHHHCCCCCCCCC
Q ss_conf             99999999830699399983036542012334677775201122212211014574100012322144430156644332
Q gi|254781101|r   95 LNKLAVAARLRSKATIIAITGSVGKTTTKEMLTIALSSIKKTYACIGSYNNHIGVPLTLARMPVDVDFGIFELGMSHLGE  174 (472)
Q Consensus        95 l~~la~~~~~~~~~~vI~ITGTnGKTTt~~~l~~iL~~~~~~~~t~gn~Nn~iGvpltll~~~~~~~~~V~E~g~~~~ge  174 (472)
                      ..++--+++  +.+++||||||||||||+.|+.++|+..+.  ...||    ||.|+  +.+.++.+++|+|+|..+   
T Consensus        78 ~seiel~~~--~~~~~I~ITGTNGKsTtt~li~~iL~~~g~--~~~GN----IG~Pl--~~~~~~~~~~VlElSSfQ---  144 (401)
T PRK03815         78 ISEYDYFYS--FMPFSIWISGTNGKTTTTQMLTHLLEDFGA--VSGGN----IGTPL--AELDPNAKIWVLETSSFT---  144 (401)
T ss_pred             HHHHHHHHH--CCCCCEEEECCCCHHHHHHHHHHHHHHCCC--CEECC----CCHHH--HHCCCCCCEEEEEECHHH---
T ss_conf             149999985--278748998477778999999999986698--13041----66438--862877887999934454---


Q ss_pred             CCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             11212232322025553121012344457888865433103762210121013424689987520123333322222222
Q gi|254781101|r  175 IRFLTHLVRPHIAVITTIAPAHLSNFSGIEEIASAKAEIFEGLEKTGTIFLNYDDSFFELLKAKSHALGIKTIYSFGKSK  254 (472)
Q Consensus       175 i~~L~~i~~P~iaiiTNI~~dHld~~~s~e~i~~~K~~i~~~l~~~g~~ViN~Dd~~~~~l~~~~~~~~~~~i~~~g~~~  254 (472)
                      ++. +.-++|+++|+|||++||||||+|+|+|+++|.+||.++++++.+++|.+.....         .....++|....
T Consensus       145 Le~-~~~~~p~iavilNis~DHLDrH~s~e~Y~~aK~~I~~~~~~~~~~i~~~~~~~~~---------~~~~~i~~~~~~  214 (401)
T PRK03815        145 LHY-TNKAKPNIYLLLPITPDHLSWHGSFENYEKAKLKPLKLMNEGSVAILPKKYKETP---------TKAQKISYEDEE  214 (401)
T ss_pred             CCC-CCCCCCCEEEEECCCCCHHCCCCCHHHHHHHHHHHHHHCCCCCEEEECHHHCCCC---------CCCEEEEECCHH
T ss_conf             066-7566876898836882052362689999999999996288776799722330476---------661799726627


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHCCCCCCCCCCCCEECC
Q ss_conf             22222344211346510012456543221222222223333221035676510121034554311476644331010003
Q gi|254781101|r  255 NADFQLRKWKQCSEQSWMEVQLQGKSMEVVHHGIGYHMAQNMLMTLGIVSILTADVDTAIKALSVFHPKEGRGKRYRCAL  334 (472)
Q Consensus       255 ~ad~~~~~i~~~~~~~~~~~~~~~~~~~~~l~~~G~hnv~NalaAia~~~~lGi~~~~i~~~L~~~~~~~GR~~~~~~~~  334 (472)
                      .  ..          ..+.+  ..    -.+.+.|.|+..++ +|+  +....+..+.+.++|++|+++|+|+|.+   .
T Consensus       215 ~--~~----------~~~~i--~~----~~i~~~~~~~~~~~-~a~--~~~~~~~~~~~~~~l~~F~gl~HRlE~v---~  270 (401)
T PRK03815        215 D--LA----------EKFGI--DT----EKINFKGPFLLDAL-LAL--AVEKILFDENDYERLNAFVIEAHKLEEF---R  270 (401)
T ss_pred             H--HH----------HHCCC--CH----HHCCCCHHHHHHHH-HHH--HHHHCCCCHHHHHHHHHCCCCCCCEEEE---E
T ss_conf             7--78----------76588--77----87056458999999-999--9985566355899998489988853899---9


Q ss_pred             CCCCEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHHHH
Q ss_conf             65311331000256532101257778741110268713885123541710589999999999864998999988038989
Q gi|254781101|r  335 NQGFFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFHVLAL  414 (472)
Q Consensus       335 ~~~~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~~~~~  414 (472)
                      ..+|+.+||||...||+|+.+||+++..      .+.++|+|+     ........++.+.+... +..++++|+....+
T Consensus       271 ~~~gv~fiNDSKATN~~At~~Al~~~~~------~~iilI~GG-----~~Kg~d~~~L~~~i~~~-~~~v~~~G~~~~~i  338 (401)
T PRK03815        271 DKQGRLWVDDSKATNIDATIQALKRYKD------KKIHLILGG-----DDKGVDLTPLFEELKNF-DIEIYAIGSNAEKI  338 (401)
T ss_pred             EECCEEEECCCCCCCHHHHHHHHHHCCC------CCEEEEECC-----CCCCCCHHHHHHHHHHH-CEEEEEECCCHHHH
T ss_conf             8489899668878988999999983767------867999637-----65567879999997640-56999987899999


Q ss_pred             HHHCCC-CCCEEEECCHHHHHHHHHHHCCCCCEEEEE---CC---------CHHHHHHHHHHH
Q ss_conf             985113-797999789899999999844789899997---71---------325489999999
Q gi|254781101|r  415 KDALPR-SIHVHYSETMDGLFLFIQSSLVDGDVVVVK---SS---------NSCGFYRLINLL  464 (472)
Q Consensus       415 ~~~~~~-~~~~~~~~~~e~a~~~l~~~~~~gdiVLiK---GS---------r~~~le~iv~~L  464 (472)
                      .+.+.. +..+..++++++|+..+.+.+++||+||+.   .|         ||..|.++|+.|
T Consensus       339 ~~~~~~~~~~~~~~~~l~eAv~~a~~~a~~gdvVLLSPacASfD~FknyeeRG~~Fk~~V~~L  401 (401)
T PRK03815        339 LALAKEFNIKAQKCEFLEKAVNEIKKVLKQNEVALLSPAAASLDQFSSYAERGEKFKEFVLKL  401 (401)
T ss_pred             HHHHHHCCCCEEECCCHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCHHHHHHHHHHHHHHC
T ss_conf             999875698469828699999999985789798998974403002069999999999999739


No 31 
>TIGR02068 cya_phycin_syn cyanophycin synthetase; InterPro: IPR011810    Cyanophycin is an insoluble storage polymer for carbon, nitrogen, and energy, found in most Cyanobacteria. The polymer has a backbone of L-aspartic acid, with most Asp side chain carboxyl groups attached to L-arginine. The polymer is made by this enzyme, cyanophycin synthetase, and degraded by cyanophycinase. Heterologously expressed cyanophycin synthetase in Escherichia coli produces a closely related, water-soluble polymer with some Arg replaced by Lys. It is unclear whether enzymes that produce soluble cyanophycin-like polymers in vivo in non-Cyanobacterial species should be designated as cyanophycin synthetase itself or as a related enzyme. Cyanophycin synthesis is analogous to polyhydroxyalkanoic acid (PHA) biosynthesis, except that PHA polymers lack nitrogen and may be made under nitrogen-limiting conditions .; GO: 0005524 ATP binding, 0016874 ligase activity, 0009059 macromolecule biosynthetic process.
Probab=100.00  E-value=2e-44  Score=313.29  Aligned_cols=436  Identities=23%  Similarity=0.291  Sum_probs=283.2

Q ss_pred             CHHHHH-HHHCCEEEC-CCCCCEEEEEEEECCCC--------------CCCCEEEECC--------------CCCCCHHH
Q ss_conf             678899-872799952-68871474677402223--------------7898889716--------------88747688
Q gi|254781101|r    6 TFHDLL-QAIQGHSIG-IVPQGFVNGISIDSRSI--------------APQEAFFAIK--------------GPHYDGHD   55 (472)
Q Consensus         6 ~~~~l~-~~~~g~~~~-~~~~~~i~~i~~dSr~v--------------~~g~lFval~--------------g~~~DGh~   55 (472)
                      |++||. +.+|..... .-.+...+.|..|+=..              .+|.. |-|+              ....|.|.
T Consensus       334 Ti~eLiG~~~N~DP~RG~Gh~~~Ltki~~D~~~~~~L~kqG~~ldsVp~kG~~-V~Lr~~ANLSTGG~A~DrTDeiHP~~  412 (876)
T TIGR02068       334 TIEELIGEQINKDPLRGDGHDKPLTKIRLDSVAKLVLAKQGLTLDSVPAKGRI-VYLRATANLSTGGVAIDRTDEIHPEN  412 (876)
T ss_pred             HHHHHHHHHHCCCCCCCCCCCCCCCCEEHHHHHHHHHHHCCCCCCCHHHCCCE-EEEECCCCCCCCCEEEECCCCCCHHH
T ss_conf             07664057646777888866778883433079999998549751154540978-88632477445873162257538458


Q ss_pred             HHHHHHHCCCEEE--------EECCCCCCCCCCCCCCEEEECC-HHHHH---------HHHHHHH-------HHCCCCCE
Q ss_conf             8999998698899--------9855212455446972899599-89999---------9999999-------83069939
Q gi|254781101|r   56 FILHAVQKGAGLV--------VVNTDMVASIGSLSIPVFGVDD-VLGAL---------NKLAVAA-------RLRSKATI  110 (472)
Q Consensus        56 ~i~~A~~~Ga~~~--------i~~~~~~~~~~~~~~~~i~v~d-~~~al---------~~la~~~-------~~~~~~~v  110 (472)
                       +.-|. .=|..|        |+..+...++.+.+=.++.|+= |=--|         +..|++.       .+....||
T Consensus       413 -~~~a~-~aAk~iGLDiaG~D~v~~di~~PL~~~~G~iVEVNAaPGlrMH~~PS~G~pR~Va~Ai~d~LFP~~~~grIPi  490 (876)
T TIGR02068       413 -IAIAV-RAAKIIGLDIAGVDVVTEDISKPLRDTDGAIVEVNAAPGLRMHLAPSQGKPRNVAKAIVDMLFPEEDDGRIPI  490 (876)
T ss_pred             -HHHHH-HHHHEEEEEECCEEECCCCCCCCHHHCCCEEEEEECCCCHHHCCCCCCCCCCCCCHHHHHHCCCCCCCCCEEE
T ss_conf             -99998-7520000012122200310003745459729998567663444677774698710268752288878983448


Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCC---CHHHHHCCC----C---CCCHHCC--CCCCCHHHHHCCCCCCCCCCCCC
Q ss_conf             9983036542012334677775201122---212211014----5---7410001--23221444301566443321121
Q gi|254781101|r  111 IAITGSVGKTTTKEMLTIALSSIKKTYA---CIGSYNNHI----G---VPLTLAR--MPVDVDFGIFELGMSHLGEIRFL  178 (472)
Q Consensus       111 I~ITGTnGKTTt~~~l~~iL~~~~~~~~---t~gn~Nn~i----G---vpltll~--~~~~~~~~V~E~g~~~~gei~~L  178 (472)
                      |+||||||||||+.|++|||+..|++++   |.|-|=++-    |   =|.|.-+  ++++.|.||+|..   .|-|-+-
T Consensus       491 V~vTGTNGKTt~~RL~Ahil~~~G~~vG~T~tDG~Yi~~~~v~~GDntGP~SAr~~L~d~~VdaAVLEta---rGGiLR~  567 (876)
T TIGR02068       491 VAVTGTNGKTTTTRLVAHILKQTGKVVGMTTTDGVYIGKKLVEKGDNTGPKSARRILADPTVDAAVLETA---RGGILRE  567 (876)
T ss_pred             EEEECCCCCHHHHHHHHHHHHHCCCEEEEEECCCEEECCEEEECCCCCCHHHHHHCCCCCCEEEEEEECC---CCCCCCC
T ss_conf             8872689835578899999985698276420376775576662478987157301227888018998627---8722066


Q ss_pred             -CCCCCCCEEEEEEEC-CCHHHHHH--HHHHHHHHHHHHCCCCCCCCHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             -223232202555312-10123444--57888865433103762210121013424689987520123333322222222
Q gi|254781101|r  179 -THLVRPHIAVITTIA-PAHLSNFS--GIEEIASAKAEIFEGLEKTGTIFLNYDDSFFELLKAKSHALGIKTIYSFGKSK  254 (472)
Q Consensus       179 -~~i~~P~iaiiTNI~-~dHld~~~--s~e~i~~~K~~i~~~l~~~g~~ViN~Dd~~~~~l~~~~~~~~~~~i~~~g~~~  254 (472)
                       -.+=..+++|+|||+ .|||+.+.  ++|+.+.-|.-+.+.+.++|.+|+|+|||....|+++++.    .|.+|+.++
T Consensus       568 GLafD~c~VGvVtNi~~~DHLG~~dInt~e~La~Vk~vv~e~V~pDG~AVLNA~DP~va~mA~~~~G----~i~YF~~~~  643 (876)
T TIGR02068       568 GLAFDRCDVGVVTNIADGDHLGLGDINTIEDLADVKRVVVEVVKPDGYAVLNADDPMVAAMAEKCKG----KIAYFSMDP  643 (876)
T ss_pred             CCCCCCCCCEEEEECCCCCCCCCCCCHHHHHHHHHEEEEEEEECCCCCEEECCCCCHHHHHHHHCCC----CEEEEECCC
T ss_conf             5010321416898337766357886004788875101267888589827864788557999842896----189862186


Q ss_pred             CCCCCCCC-----CCCCCCCCCCCCCCCC--------CCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHCCC
Q ss_conf             22222344-----2113465100124565--------4322122222222333322103567651012103455431147
Q gi|254781101|r  255 NADFQLRK-----WKQCSEQSWMEVQLQG--------KSMEVVHHGIGYHMAQNMLMTLGIVSILTADVDTAIKALSVFH  321 (472)
Q Consensus       255 ~ad~~~~~-----i~~~~~~~~~~~~~~~--------~~~~~~l~~~G~hnv~NalaAia~~~~lGi~~~~i~~~L~~~~  321 (472)
                      +...-..+     .-..-+...+.+--.+        ...+++...--.||++|+|||+++++.+++|.|.|+++|+.|.
T Consensus       644 ~~~~~~~H~~~G~~avy~~~G~ivia~G~~~~~~~~~~~iPlT~GG~~~F~ieN~LAA~aAA~~~~v~ie~Ir~G~~tF~  723 (876)
T TIGR02068       644 NNPTVAKHIAKGGRAVYYENGYIVIAKGGAEVAIARIAEIPLTMGGRVAFQIENALAAVAAAWALGVDIELIRAGIRTFK  723 (876)
T ss_pred             CHHHHHHHHHCCCEEEEEECCEEEEEECCCCHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCC
T ss_conf             25899999855989999867879997478322678997288675771578888999999998534898999998987330


Q ss_pred             ----CCCCCCCCCEECCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHH
Q ss_conf             ----6644331010003653113310002565321012577787411102687138851235417105899999999998
Q gi|254781101|r  322 ----PKEGRGKRYRCALNQGFFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLS  397 (472)
Q Consensus       322 ----~~~GR~~~~~~~~~~~~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~  397 (472)
                          .-||||..|++.   +...++|  |.|||+|+++.+++.++++   .+||+.|+|..   ||+.++.=.++++.+.
T Consensus       724 ~d~~~~PGrfnLFn~~---~~~~lvD--Y~HNp~~~~av~~a~~~~~---A~rr~gV~ggp---GDR~De~l~~~G~~~g  792 (876)
T TIGR02068       724 ADAAQAPGRFNLFNLG---GAHVLVD--YGHNPAAIEAVVEAIRNLP---ARRRIGVIGGP---GDRRDEDLVKLGEILG  792 (876)
T ss_pred             CHHHCCCCEEEEEECC---CCEEEEE--CCCCHHHHHHHHHHHHHCC---CCCEEEEEECC---CCCCHHHHHHHHHHHH
T ss_conf             1010689503222258---8289996--5779789999999996178---78478998078---7786588999999975


Q ss_pred             HCCCCEEEEEC-----------CCHHHHHHHCCCCC-CEEEEC---CHHHHHHHHHHHCCCCCEEEEECCCHHHHHHHHH
Q ss_conf             64998999988-----------03898998511379-799978---9899999999844789899997713254899999
Q gi|254781101|r  398 LYNISHVWLSG-----------FHVLALKDALPRSI-HVHYSE---TMDGLFLFIQSSLVDGDVVVVKSSNSCGFYRLIN  462 (472)
Q Consensus       398 ~~~~d~v~~~G-----------~~~~~~~~~~~~~~-~~~~~~---~~e~a~~~l~~~~~~gdiVLiKGSr~~~le~iv~  462 (472)
                      . .||.|++..           +-..-+.+.+.+.. +...++   +--+|++...+.+.+||++||---   +.++.++
T Consensus       793 ~-~FD~i~~keD~~~rGkR~~G~a~~Ll~~G~~~~~~~~~~i~~i~de~~Ai~~~L~~~~~GdL~vi~~e---~~~~a~~  868 (876)
T TIGR02068       793 G-AFDQIILKEDDDLRGKRARGEAAALLRQGLIQAAMRKAAIEEILDETEAIKAALDSLEAGDLVVILPE---SVERAIK  868 (876)
T ss_pred             H-CCCEEEEECCCCCCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECC---CCHHHHH
T ss_conf             4-06879996274535788873589999963530577656799998899999999842146886999702---1003566


Q ss_pred             HHHH
Q ss_conf             9998
Q gi|254781101|r  463 LLLE  466 (472)
Q Consensus       463 ~L~~  466 (472)
                      .+..
T Consensus       869 ~i~~  872 (876)
T TIGR02068       869 LIEE  872 (876)
T ss_pred             HHHH
T ss_conf             7665


No 32 
>pfam08245 Mur_ligase_M Mur ligase middle domain.
Probab=100.00  E-value=2.3e-42  Score=299.51  Aligned_cols=186  Identities=36%  Similarity=0.470  Sum_probs=167.7

Q ss_pred             EECCCCCCHHHHHHHHHHHHHHCCCCCHHHHHCCCCCCCHHCCCC-CCCHHHHHCCCCCCCCCCCCCCCCCCCCEEEEEE
Q ss_conf             830365420123346777752011222122110145741000123-2214443015664433211212232322025553
Q gi|254781101|r  113 ITGSVGKTTTKEMLTIALSSIKKTYACIGSYNNHIGVPLTLARMP-VDVDFGIFELGMSHLGEIRFLTHLVRPHIAVITT  191 (472)
Q Consensus       113 ITGTnGKTTt~~~l~~iL~~~~~~~~t~gn~Nn~iGvpltll~~~-~~~~~~V~E~g~~~~gei~~L~~i~~P~iaiiTN  191 (472)
                      ||||||||||++|++++|+..|.++.+.||+|+.||+|++++++. .+++|+|+|+|+++.++ .+|..+.+|+++||||
T Consensus         1 VTGT~GKTTt~~ml~~iL~~~g~~~~~~g~~~~~ig~~~~~~~~~~~~~~~~V~E~~~~~~~~-~~l~~~~~P~iaviTN   79 (188)
T pfam08245         1 ITGTNGKTTTTELIAALLSAAGGVVGTGGNTNNAIGLPLLLALMERKGADYAVLELSSFGLGE-GRLEGLAKPDIAVITN   79 (188)
T ss_pred             CCCCCCHHHHHHHHHHHHHHCCCCEEEECCCCCHHHHHHHHHHHHHCCCCEEEEEECCCCCCH-HHHCCCCCCCEEEEEC
T ss_conf             937586899999999999838998998388474577999997666469968999832777107-6552777899999945


Q ss_pred             ECCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             12101234445788886543310376221012101342468998752012333332222222222222344211346510
Q gi|254781101|r  192 IAPAHLSNFSGIEEIASAKAEIFEGLEKTGTIFLNYDDSFFELLKAKSHALGIKTIYSFGKSKNADFQLRKWKQCSEQSW  271 (472)
Q Consensus       192 I~~dHld~~~s~e~i~~~K~~i~~~l~~~g~~ViN~Dd~~~~~l~~~~~~~~~~~i~~~g~~~~ad~~~~~i~~~~~~~~  271 (472)
                      |++||||+|+|+|+|+++|.+||+++++++.+|+|.||+....+.....    ..+++||.++++|++..++.....+..
T Consensus        80 i~~DHld~~~s~e~~~~~K~~i~~~~~~~g~~v~n~Dd~~~~~~~~~~~----~~~~t~g~~~~~d~~~~~i~~~~~~~~  155 (188)
T pfam08245        80 ISPDHLDYHGTMENYAAAKAEIFEGLPEDGIAVINADDPELAKRLKNAG----AKVITFGLENEADDRAANIYVSSEGGK  155 (188)
T ss_pred             CHHHHHHHHCCHHHHHHHHHHHHHCCCCCCEEEEECCCHHHHHHHHHCC----CCEEEEECCCCCCEEEEEEEECCCCCE
T ss_conf             7655646621799999999999972999999999898888999998669----846998568765604467899589968


Q ss_pred             CCC-CCCCCCCCCCCCCCCCCCCCCCCCHHHHH
Q ss_conf             012-45654322122222222333322103567
Q gi|254781101|r  272 MEV-QLQGKSMEVVHHGIGYHMAQNMLMTLGIV  303 (472)
Q Consensus       272 ~~~-~~~~~~~~~~l~~~G~hnv~NalaAia~~  303 (472)
                      |.+ ..++...++.++++|+||++|+++|+++|
T Consensus       156 ~~~~~~~~~~~~~~l~l~G~HNv~NalaAia~A  188 (188)
T pfam08245       156 IVLFTVPGGELEISLPLPGRHNVYNALAALAAA  188 (188)
T ss_pred             EEEEECCCEEEEEEECCCCHHHHHHHHHHHHHC
T ss_conf             999962993899998866399999999999959


No 33 
>TIGR01081 mpl UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase; InterPro: IPR005757    The tripeptide L-ananyl-gamma-D-glutamyl-meso-diaminopimelic acid is efficiently re-cycled during the formation of bacterial cell wall murein. UDP-N-acetylmuramate:L-alanyl-gamma-D-glutamyl-meso-diaminopimelate ligase is an essential enzyme in this process which links the tripeptide to UDP-N-acetylmuramate.; GO: 0016874 ligase activity, 0007047 cell wall organization and biogenesis.
Probab=100.00  E-value=1.4e-37  Score=267.81  Aligned_cols=397  Identities=23%  Similarity=0.293  Sum_probs=280.8

Q ss_pred             HHHHHHHCCEEECCCCCCEEEEEEEECCCCCC--CCEEEECCCCCCCHHHHHHHHHHCCCEEEEECCCCCCCCCCCCCCE
Q ss_conf             88998727999526887147467740222378--9888971688747688899999869889998552124554469728
Q gi|254781101|r    8 HDLLQAIQGHSIGIVPQGFVNGISIDSRSIAP--QEAFFAIKGPHYDGHDFILHAVQKGAGLVVVNTDMVASIGSLSIPV   85 (472)
Q Consensus         8 ~~l~~~~~g~~~~~~~~~~i~~i~~dSr~v~~--g~lFval~g~~~DGh~~i~~A~~~Ga~~~i~~~~~~~~~~~~~~~~   85 (472)
                      +++++..|-+++.+          ||.-++.|  .|++|- =-...-|++-++..++++-.++             .-|+
T Consensus        38 ST~LE~~GIe~~~g----------fD~~QL~~~~pD~~vi-GNa~~RG~p~VE~vL~~nl~Y~-------------SGPQ   93 (459)
T TIGR01081        38 STLLEAQGIEIIEG----------FDAAQLEPFKPDLVVI-GNAMKRGNPCVEAVLEKNLPYT-------------SGPQ   93 (459)
T ss_pred             HHHHHHCCCEEECC----------CCHHHCCCCCCCEEEE-CCCCCCCCHHHHHHHHCCCCCC-------------CCCC
T ss_conf             68887557303227----------7844400348887998-4633167446789872689502-------------1751


Q ss_pred             EEECCHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHC-----CCCCHHHHHCCCCCCCHHCC-----
Q ss_conf             99599899999999999830699399983036542012334677775201-----12221221101457410001-----
Q gi|254781101|r   86 FGVDDVLGALNKLAVAARLRSKATIIAITGSVGKTTTKEMLTIALSSIKK-----TYACIGSYNNHIGVPLTLAR-----  155 (472)
Q Consensus        86 i~v~d~~~al~~la~~~~~~~~~~vI~ITGTnGKTTt~~~l~~iL~~~~~-----~~~t~gn~Nn~iGvpltll~-----  155 (472)
                      +.-+..+          |   +--|+||.||+|||||+.|++++|+..|-     +-+-+|||    |+.--|=+     
T Consensus        94 WL~d~~L----------~---drWVlaV~GTHGKTTT~~M~~WvLE~~G~~pGFliGGv~gNF----gvSArLg~~pr~d  156 (459)
T TIGR01081        94 WLHDFVL----------R---DRWVLAVAGTHGKTTTASMLAWVLEQCGLKPGFLIGGVPGNF----GVSARLGETPRQD  156 (459)
T ss_pred             HHHHHHH----------H---CCEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCEECCCCCCC----CEEEECCCCCCCC
T ss_conf             0563342----------1---342789507886046889999999863798872673424534----2142068775667


Q ss_pred             CCCCCHHHHHCCCCCCCC--CCCCCCCCC--CCCEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHCCCCHH
Q ss_conf             232214443015664433--211212232--3220255531210123444578888654331037622101210134246
Q gi|254781101|r  156 MPVDVDFGIFELGMSHLG--EIRFLTHLV--RPHIAVITTIAPAHLSNFSGIEEIASAKAEIFEGLEKTGTIFLNYDDSF  231 (472)
Q Consensus       156 ~~~~~~~~V~E~g~~~~g--ei~~L~~i~--~P~iaiiTNI~~dHld~~~s~e~i~~~K~~i~~~l~~~g~~ViN~Dd~~  231 (472)
                      -+...+|+|+|.-  ...  =.++-++++  +|...|+.|+..||-|.|.+++.|.+..-.|++.+|..|.+|.|..+..
T Consensus       157 p~~~S~fFviEAD--EYD~AFFDKRSKFVHY~PRTlvlNNleFDHADIFddL~AI~~QFHhlvR~vP~~G~i~~~~~~~~  234 (459)
T TIGR01081       157 PNSQSPFFVIEAD--EYDTAFFDKRSKFVHYRPRTLVLNNLEFDHADIFDDLKAIQRQFHHLVRTVPGEGLILAPERDQS  234 (459)
T ss_pred             CCCCCCEEEEECC--CCCCCCCCCCCCEEECCCCEEEEECCCCCHHHHHHHHHHHHHCCCEEEEEECCCCEEECCCHHHH
T ss_conf             4546875799535--65651002543312027600145155544455787689987403068896468864843501468


Q ss_pred             HHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCHHHHHHHHCCCC
Q ss_conf             89987520123333322222222222223442113465100124565432-21222222223333221035676510121
Q gi|254781101|r  232 FELLKAKSHALGIKTIYSFGKSKNADFQLRKWKQCSEQSWMEVQLQGKSM-EVVHHGIGYHMAQNMLMTLGIVSILTADV  310 (472)
Q Consensus       232 ~~~l~~~~~~~~~~~i~~~g~~~~ad~~~~~i~~~~~~~~~~~~~~~~~~-~~~l~~~G~hnv~NalaAia~~~~lGi~~  310 (472)
                      ++....+-++....   .+|  ++..|++..+  ..+++.|.+-..|+.. ++++.+.|+||..|+|+|+|+++..|+++
T Consensus       235 l~~~l~~GCWs~~e---~~G--~~~~W~A~~~--~~D~S~f~Vll~G~~vg~VkW~lvG~HN~~NaL~aIAAArHvGV~~  307 (459)
T TIGR01081       235 LKDTLAKGCWSEQE---FLG--EQGEWQAEKI--TADASEFEVLLDGEKVGEVKWSLVGEHNMHNALMAIAAARHVGVAI  307 (459)
T ss_pred             HHHHHHHCCCCCHH---CCC--CCCCHHHHHH--CCCCHHHHHHHCCCEEEEEEEEECCCCCHHHHHHHHHHHHCCCCCH
T ss_conf             99998606872011---246--7775057654--0451000220178436776533304600135899998742167687


Q ss_pred             HHHHHHHHCCCCCCCCCCCCEECCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEEC----CHHHCCCCHH
Q ss_conf             034554311476644331010003653113310002565321012577787411102687138851----2354171058
Q gi|254781101|r  311 DTAIKALSVFHPKEGRGKRYRCALNQGFFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLG----DMCEMGELSQ  386 (472)
Q Consensus       311 ~~i~~~L~~~~~~~GR~~~~~~~~~~~~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG----~m~ELG~~~~  386 (472)
                      +...++|-.|.-.+   +|+|++.+.|+++++|| +-++|+++.+.|..|++- .-...|.++||=    .|+ ||-..+
T Consensus       308 ~~Ac~ALG~F~N~k---RRlE~kG~~Ng~TVYDD-FAHHP~AI~~Tl~~LR~k-VGG~~rIlAVLEPRSnTMK-lG~~K~  381 (459)
T TIGR01081       308 EDACEALGSFVNAK---RRLELKGEANGVTVYDD-FAHHPTAIEATLAALRDK-VGGGARILAVLEPRSNTMK-LGVHKD  381 (459)
T ss_pred             HHHHHHHCCCCCCC---EEEEEEEEEEEEEEECC-CCCCHHHHHHHHHHHHHH-CCCCCEEEEEECCCCCCCC-CCCCHH
T ss_conf             89998703200120---01567211313787327-667868999999998752-3997069998778744100-343255


Q ss_pred             HHHHHHHHHHHHCCCCEEEEECCC-HHH-HHHHCCC-CCCEEEECCHHHHHHHHHHHCCCCCEEEEECCCHHHHHHHHHH
Q ss_conf             999999999986499899998803-898-9985113-7979997898999999998447898999977132548999999
Q gi|254781101|r  387 SFHIDLAEVLSLYNISHVWLSGFH-VLA-LKDALPR-SIHVHYSETMDGLFLFIQSSLVDGDVVVVKSSNSCGFYRLINL  463 (472)
Q Consensus       387 ~~h~~i~~~~~~~~~d~v~~~G~~-~~~-~~~~~~~-~~~~~~~~~~e~a~~~l~~~~~~gdiVLiKGSr~~~le~iv~~  463 (472)
                      .    +...+.  ..|.||++-.. ..+ .++.+.. ..+..+-.+++++++.+.+.++++|-|||. ||| .|+-|.++
T Consensus       382 ~----la~sL~--~AD~Vf~~~p~~~~W~V~e~~~~~~~p~~~~~~~D~~v~~ivk~A~~gD~ILVM-SNG-gFgGIH~K  453 (459)
T TIGR01081       382 D----LAPSLG--RADEVFLLQPEQIPWEVAEVAEQCVQPANVSADLDELVAMIVKEAQPGDHILVM-SNG-GFGGIHGK  453 (459)
T ss_pred             H----HHHHHH--HCCEEEEECCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEE-ECC-CCCHHHHH
T ss_conf             6----667666--003565316898870599999860240211010789999999605888758997-468-86406899


Q ss_pred             HHHHC
Q ss_conf             99850
Q gi|254781101|r  464 LLEEF  468 (472)
Q Consensus       464 L~~~~  468 (472)
                      |++++
T Consensus       454 lL~~L  458 (459)
T TIGR01081       454 LLDAL  458 (459)
T ss_pred             HHHHC
T ss_conf             99852


No 34 
>COG0285 FolC Folylpolyglutamate synthase [Coenzyme metabolism]
Probab=100.00  E-value=4.1e-35  Score=251.59  Aligned_cols=331  Identities=21%  Similarity=0.296  Sum_probs=223.4

Q ss_pred             HCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCC---CCCH--HHHHCCC---CCCCH-----------------------
Q ss_conf             306993999830365420123346777752011---2221--2211014---57410-----------------------
Q gi|254781101|r  104 LRSKATIIAITGSVGKTTTKEMLTIALSSIKKT---YACI--GSYNNHI---GVPLT-----------------------  152 (472)
Q Consensus       104 ~~~~~~vI~ITGTnGKTTt~~~l~~iL~~~~~~---~~t~--gn~Nn~i---Gvplt-----------------------  152 (472)
                      .+..+++|.|+|||||.||+.|+.+||.+.|-.   +.||  -+||-.|   |-|++                       
T Consensus        40 P~~~~~vIhVaGTNGKGSt~afl~siL~~aG~~VG~yTSPHL~~~~ERI~ing~~Isd~~~~~~~~~ve~~~~~~~~~~~  119 (427)
T COG0285          40 PQKSPPVIHVAGTNGKGSTCAFLESILREAGYKVGVYTSPHLLSFNERIRINGEPISDEELAAAFERVEEAAGSLDLISL  119 (427)
T ss_pred             CCCCCCEEEEECCCCCHHHHHHHHHHHHHCCCCCEEECCCCCCCCCEEEEECCEECCHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf             72149869993789842499999999997598714678876076421799999988899999999999997523666787


Q ss_pred             -HCC----------CCCCCHHHHHCCCCCCCCCCCCCCCCCCCCEEEEEEECCCHHHHHH-HHHHHHHHHHHHCCCCCCC
Q ss_conf             -001----------2322144430156644332112122323220255531210123444-5788886543310376221
Q gi|254781101|r  153 -LAR----------MPVDVDFGIFELGMSHLGEIRFLTHLVRPHIAVITTIAPAHLSNFS-GIEEIASAKAEIFEGLEKT  220 (472)
Q Consensus       153 -ll~----------~~~~~~~~V~E~g~~~~gei~~L~~i~~P~iaiiTNI~~dHld~~~-s~e~i~~~K~~i~~~l~~~  220 (472)
                       .++          .+.+.|++|+|+|+.  |..+. ++++.|.+++||+|+.||.+++| |+|.|+.||+.|++.-.| 
T Consensus       120 T~FE~~Ta~Af~~F~~~~vD~aIlEVGLG--GRlDA-TNVi~p~vsvIT~I~lDH~~~LG~tie~IA~EKAGI~k~g~P-  195 (427)
T COG0285         120 TYFEVLTAMAFLYFAEAKVDVAILEVGLG--GRLDA-TNVIEPDVSVITSIGLDHTAFLGDTLESIAREKAGIIKAGKP-  195 (427)
T ss_pred             CHHHHHHHHHHHHHHHCCCCEEEEECCCC--CCCCC-HHCCCCCEEEECCCCHHHHHHHCCCHHHHHHHHHCCCCCCCC-
T ss_conf             47999999999999768999899960556--66443-221687668976647257888686699999986401257995-


Q ss_pred             CHHHHCC-CCH-HHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCC
Q ss_conf             0121013-424-6899875201233333222222222222234421134651001245654322122222222-333322
Q gi|254781101|r  221 GTIFLNY-DDS-FFELLKAKSHALGIKTIYSFGKSKNADFQLRKWKQCSEQSWMEVQLQGKSMEVVHHGIGYH-MAQNML  297 (472)
Q Consensus       221 g~~ViN~-Dd~-~~~~l~~~~~~~~~~~i~~~g~~~~ad~~~~~i~~~~~~~~~~~~~~~~~~~~~l~~~G~h-nv~Nal  297 (472)
                        +|+-. +.| ....+.+++...... +..++.    ++....     .+..|.+...+....+.+|++|.| |+.|+.
T Consensus       196 --~v~~~~~~p~a~~vi~~~a~~~~~~-~~~~~~----~~~~~~-----~~~~~~~~~~~~~~~~~lp~l~~~~Q~~NAa  263 (427)
T COG0285         196 --AVIGEQQPPEALNVIAERAEELGAP-LFVLGP----DFQVLE-----EGNGFSFQGGGGLLDLPLPLLGGHHQIENAA  263 (427)
T ss_pred             --EEECCCCCHHHHHHHHHHHHHCCCC-EEECCC----CHHHCC-----CCCEEEEECCCEEEEECCCCCCCCHHHHHHH
T ss_conf             --7988889878999999998751897-465173----322104-----6526887337704554166566305788899


Q ss_pred             CHHHHHHHHCC--CCHHHHHHHHCCCCCCCCCCCCEECCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEE
Q ss_conf             10356765101--2103455431147664433101000365311331000256532101257778741110268713885
Q gi|254781101|r  298 MTLGIVSILTA--DVDTAIKALSVFHPKEGRGKRYRCALNQGFFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVL  375 (472)
Q Consensus       298 aAia~~~~lGi--~~~~i~~~L~~~~~~~GR~~~~~~~~~~~~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~Vl  375 (472)
                      .|++++..++.  +.+.|.++|++.. +|||+|++..    +...++|-.  +||+|+++..++|+......+ +.++|+
T Consensus       264 ~Ai~al~~l~~~i~~~~i~~gl~~~~-wpGR~e~l~~----~p~i~lDgA--HNp~aa~~La~~l~~~~~~~~-~~~~v~  335 (427)
T COG0285         264 LAIAALEALGKEISEEAIRKGLANVD-WPGRLERLSE----NPLILLDGA--HNPHAARALAETLKTLFNDRP-RLTLVF  335 (427)
T ss_pred             HHHHHHHHHCCCCCHHHHHHHHHHCC-CCCEEEEECC----CCEEEEECC--CCHHHHHHHHHHHHHHHCCCC-CEEEEE
T ss_conf             99999998314288999999998676-8733788337----974999888--999999999999997733577-528999


Q ss_pred             CCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECC------CHHHHHHHCCCCCCEEEECCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             1235417105899999999998649989999880------3898998511379799978989999999984478989999
Q gi|254781101|r  376 GDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGF------HVLALKDALPRSIHVHYSETMDGLFLFIQSSLVDGDVVVV  449 (472)
Q Consensus       376 G~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~------~~~~~~~~~~~~~~~~~~~~~e~a~~~l~~~~~~gdiVLi  449 (472)
                      |.+      .++.+..+.+.+... .+.+++...      ....+.+......... .++.+++++.+.+....+|.|||
T Consensus       336 g~l------~dKd~~~~l~~L~~~-~~~~~~~~~~~~ra~~~~~l~~~~~~~~~~~-~~~~~~a~~~~~~~~~~~~~ilV  407 (427)
T COG0285         336 GML------KDKDIAGMLAALLPI-VDEIYTTPLPWPRALDAEELLAFAGERGGVE-LDDVAEALELALEKADEDDLVLV  407 (427)
T ss_pred             EEE------CCCCHHHHHHHHHCC-CCEEEECCCCCCCCCCHHHHHHHHHHHCCCC-HHHHHHHHHHHHHHCCCCCEEEE
T ss_conf             832------588889999974064-7689982589735489999999987635785-00399999999971579974999


Q ss_pred             ECCCHHHHHHHHHHHHHH
Q ss_conf             771325489999999985
Q gi|254781101|r  450 KSSNSCGFYRLINLLLEE  467 (472)
Q Consensus       450 KGSr~~~le~iv~~L~~~  467 (472)
                      .||-.. ...+.+.+.++
T Consensus       408 ~GSly~-~~ev~~~~~~~  424 (427)
T COG0285         408 TGSLYL-AGEVLELLKKR  424 (427)
T ss_pred             EECHHH-HHHHHHHHHCC
T ss_conf             823999-99999996335


No 35 
>PRK10846 bifunctional folylpolyglutamate synthase/ dihydrofolate synthase; Provisional
Probab=100.00  E-value=3.5e-35  Score=251.99  Aligned_cols=323  Identities=18%  Similarity=0.173  Sum_probs=208.5

Q ss_pred             CHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCC---CH--HHHHCCC---CCC-----------
Q ss_conf             9899999999999830699399983036542012334677775201122---21--2211014---574-----------
Q gi|254781101|r   90 DVLGALNKLAVAARLRSKATIIAITGSVGKTTTKEMLTIALSSIKKTYA---CI--GSYNNHI---GVP-----------  150 (472)
Q Consensus        90 d~~~al~~la~~~~~~~~~~vI~ITGTnGKTTt~~~l~~iL~~~~~~~~---t~--gn~Nn~i---Gvp-----------  150 (472)
                      .+++.|.+|+.   .+...++|.|+|||||.||+.|++++|++.|..++   ||  -+||-.|   |.|           
T Consensus        34 ri~~ll~~lg~---p~~~~~~IhVaGTNGKGSt~~~l~~il~~~G~~vG~ftSPHl~~~~ERi~ing~~Is~~~~~~~~~  110 (416)
T PRK10846         34 RVSQVAARLDV---LKPAPFVFTVAGTNGKGTTCRTLESILMAAGYRVGVYSSPHLVRYTERVRVQGQELPESAHTASFA  110 (416)
T ss_pred             HHHHHHHHCCC---CCCCCCEEEEECCCCHHHHHHHHHHHHHHCCCCCCEECCCCCCCEEEEEEECCCCCCHHHHHHHHH
T ss_conf             99999997299---865799899968855799999999999987997307788867951015679991289899999999


Q ss_pred             ----------CHHCC----------CCCCCHHHHHCCCCCCCCCCCCCCCCCCCCEEEEEEECCCHHHHHH-HHHHHHHH
Q ss_conf             ----------10001----------2322144430156644332112122323220255531210123444-57888865
Q gi|254781101|r  151 ----------LTLAR----------MPVDVDFGIFELGMSHLGEIRFLTHLVRPHIAVITTIAPAHLSNFS-GIEEIASA  209 (472)
Q Consensus       151 ----------ltll~----------~~~~~~~~V~E~g~~~~gei~~L~~i~~P~iaiiTNI~~dHld~~~-s~e~i~~~  209 (472)
                                +|.++          .+.+.|++|+|+|+.+  ..+. ++++.|+++|||||+.||++++| |+|+|+.|
T Consensus       111 ~v~~~~~~~~lT~FE~~T~~A~~~F~~~~vD~aVlEvGLGG--rlDA-TNvi~~~vsvIT~IglDH~~~LG~Tle~IA~E  187 (416)
T PRK10846        111 EIEAARGDISLTYFEYGTLSALWLFKQAQLDVVILEVGLGG--RLDA-TNIVDADVAVITSIALDHTDWLGPDRESIGRE  187 (416)
T ss_pred             HHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCCE--EEHH-HCCCCCCEEEECCCCHHHHHHHCCCHHHHHHH
T ss_conf             98875068887699999999999998569998999835751--3432-13888877998870476420017999999998


Q ss_pred             HHHHCCCCCCCCHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             43310376221012101342468998752012333332222222222222344211346510012456543221222222
Q gi|254781101|r  210 KAEIFEGLEKTGTIFLNYDDSFFELLKAKSHALGIKTIYSFGKSKNADFQLRKWKQCSEQSWMEVQLQGKSMEVVHHGIG  289 (472)
Q Consensus       210 K~~i~~~l~~~g~~ViN~Dd~~~~~l~~~~~~~~~~~i~~~g~~~~ad~~~~~i~~~~~~~~~~~~~~~~~~~~~l~~~G  289 (472)
                      |+.|++   ++..+|+. +......+.+.+...+. .++.++.    |+..     ...+..+.+......+ -.+++ +
T Consensus       188 KAGIik---~g~pvV~g-~~~~~~~i~~~a~~~~a-~l~~~~~----d~~~-----~~~~~~~~~~~~~~~~-~~l~l-~  251 (416)
T PRK10846        188 KAGIFR---SEKPAVVG-EPEMPSTIADVAQEKGA-LLQRRGV----DWNY-----SVTDHDWAFSDGDGTL-ENLPL-P  251 (416)
T ss_pred             HHHHHC---CCCEEEEC-CCCHHHHHHHHHHHCCC-CEEECCC----CEEE-----EECCCEEEEECCCCCC-CCCCC-C
T ss_conf             753422---79808985-85378999999997099-7798178----4079-----8538737997588625-24888-6


Q ss_pred             CCCCCCCCCHHHHHHHHC--CCCHHHHHHHHCCCCCCCCCCCCEECCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHCC
Q ss_conf             223333221035676510--121034554311476644331010003653113310002565321012577787411102
Q gi|254781101|r  290 YHMAQNMLMTLGIVSILT--ADVDTAIKALSVFHPKEGRGKRYRCALNQGFFTLIDESYNANPASMKAAISVLSQISPHG  367 (472)
Q Consensus       290 ~hnv~NalaAia~~~~lG--i~~~~i~~~L~~~~~~~GR~~~~~~~~~~~~~~iIDDsYNAnP~S~~aal~~l~~~~~~~  367 (472)
                      .++..|+..|+++...++  ++.+.+.++|.+.. +|||+|++.    .+...++|-+  |||+++++..++++.+..  
T Consensus       252 ~~~~~Naa~Al~al~~~~~~i~~~~i~~gL~~~~-wpGR~e~i~----~~p~iiLDgA--HN~~aa~~L~~~l~~~~~--  322 (416)
T PRK10846        252 NVPQPNAATALAALRASGLEVSENAIRDGIASAI-LPGRFQIVS----ESPRVIFDVA--HNPHAAEYLTGRLKALPK--  322 (416)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHCC-CCCCEEEEC----CCCCEEEECC--CCHHHHHHHHHHHHHCCC--
T ss_conf             5799999999999997399999999999998577-787512414----7985777778--599999999999996077--


Q ss_pred             CCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECC------CHHHHHHHCCCCCCEEEECCHHHHHHHHHHHC
Q ss_conf             687138851235417105899999999998649989999880------38989985113797999789899999999844
Q gi|254781101|r  368 EGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGF------HVLALKDALPRSIHVHYSETMDGLFLFIQSSL  441 (472)
Q Consensus       368 ~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~------~~~~~~~~~~~~~~~~~~~~~e~a~~~l~~~~  441 (472)
                      .+|.++|+|-|      .++.+..+.+.+... +|.++++..      ....+.+.+..   ...+++.+++++.+.+..
T Consensus       323 ~~k~~~V~g~l------~dKD~~~~l~~L~~~-~d~~~~~~~~~~Ra~~~~~L~~~l~~---~~~~~~~~~A~~~al~~a  392 (416)
T PRK10846        323 NGRVLAVIGML------HDKDIAGTLAWLKSV-VDDWYCAPLEGPRGATAEQLLEHLGN---GKSFDSVAQAWDAAMADA  392 (416)
T ss_pred             CCCEEEEEECC------CCCCHHHHHHHHHHH-CCEEEEECCCCCCCCCHHHHHHHHHC---CCCCCCHHHHHHHHHHHC
T ss_conf             99689998413------789999999986644-68999958999777999999998602---766699999999999847


Q ss_pred             CCCCEEEEECCC
Q ss_conf             789899997713
Q gi|254781101|r  442 VDGDVVVVKSSN  453 (472)
Q Consensus       442 ~~gdiVLiKGSr  453 (472)
                      +++|+|||.||-
T Consensus       393 ~~~d~IlV~GSl  404 (416)
T PRK10846        393 KPEDTVLVCGSF  404 (416)
T ss_pred             CCCCEEEEECHH
T ss_conf             999859997139


No 36 
>TIGR01499 folC FolC bifunctional protein; InterPro: IPR001645   Folylpolyglutamate synthase 6.3.2.17 from EC (FPGS) is responsible for the addition of a polyglutamate tail to folate and folate derivatives, is an ATP-dependent enzyme isolated from eukaryotic and bacterial sources, where it plays a key role in the retention of the intracellular folate pool Its sequence is moderately conserved between prokaryotes (gene folC) and eukaryotes.   FPGS belongs to a protein family that contains a number of related peptidoglycan synthetases (Mur) 6.3.2. from EC (see ).   A crystal structure of the MgATP complex of the enzyme from Lactobacillus casei reveals that folylpolyglutamate synthetase is a modular protein consisting of two domains, one with a typical mononucleotide-binding fold and the other strikingly similar to the folate-binding enzyme dihydrofolate reductase. The active site of the enzyme is located in a large interdomain cleft adjacent to an ATP-binding P-loop motif. Opposite this site, in the C domain, a cavity likely to be the folate binding site has been identified, and inspection of this cavity and the surrounding protein structure suggests that the glutamate tail of the substrate may project into the active site. A further feature of the structure is a well defined Omega loop, which contributes both to the active site and to interdomain interactions .; GO: 0004326 tetrahydrofolylpolyglutamate synthase activity, 0005524 ATP binding, 0009396 folic acid and derivative biosynthetic process.
Probab=100.00  E-value=1.2e-33  Score=241.81  Aligned_cols=350  Identities=20%  Similarity=0.251  Sum_probs=223.2

Q ss_pred             HHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHH-HHHHCCC---CCH--HHHHCCC---CCCCH---------
Q ss_conf             8999999999998306993999830365420123346777-7520112---221--2211014---57410---------
Q gi|254781101|r   91 VLGALNKLAVAARLRSKATIIAITGSVGKTTTKEMLTIAL-SSIKKTY---ACI--GSYNNHI---GVPLT---------  152 (472)
Q Consensus        91 ~~~al~~la~~~~~~~~~~vI~ITGTnGKTTt~~~l~~iL-~~~~~~~---~t~--gn~Nn~i---Gvplt---------  152 (472)
                      .++.|..|+.-..+.-..|+|.|+|||||.||..||++|| +..|-.+   .||  -.||-.|   |.|++         
T Consensus         4 ~~~ll~~LG~P~~~~~a~~~IHVaGTNGKGST~a~l~~iL~~~~G~~VG~fTSPHl~~f~ERI~~nG~~i~d~~~~~~~~   83 (460)
T TIGR01499         4 MKKLLEALGNPHQDLNALPVIHVAGTNGKGSTCAFLESILREAAGYKVGLFTSPHLVSFNERIRVNGEPISDEELAQAFE   83 (460)
T ss_pred             HHHHHHHCCCCHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHCCCEEEEEECCEEEEEEEEEEECCEECCHHHHHHHHH
T ss_conf             88999970887379248977999720687589999999988753977888873738742234789885768899999999


Q ss_pred             -------------------------HCC----CC-CCCHHHHHCCCCCCCCCCCCCCCCCC-CCEEEEEEECCCHHHHHH
Q ss_conf             -------------------------001----23-22144430156644332112122323-220255531210123444
Q gi|254781101|r  153 -------------------------LAR----MP-VDVDFGIFELGMSHLGEIRFLTHLVR-PHIAVITTIAPAHLSNFS  201 (472)
Q Consensus       153 -------------------------ll~----~~-~~~~~~V~E~g~~~~gei~~L~~i~~-P~iaiiTNI~~dHld~~~  201 (472)
                                               ++.    .+ ..+|++|+|+|+.  |+.|. ++++. |.+++||+|+.||.+++|
T Consensus        84 ~~~~~~~~~~~~~~~~~~t~FE~~T~~Af~~F~~~~~vd~av~EVGlG--GrlDa-TNv~~~p~~~~iT~ig~DH~~~LG  160 (460)
T TIGR01499        84 QVRPILKKLSQETEYSQPTFFELLTLLAFLYFAQLAQVDVAVLEVGLG--GRLDA-TNVVEKPLVSVITSIGLDHTEILG  160 (460)
T ss_pred             HHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEECCC--CCCCC-CCCCCCCEEEEECCCCHHHHHHHC
T ss_conf             999987533101358777789999999999999850882899987376--54455-441138637997277768886505


Q ss_pred             -HHHHHHHHHHHHCCCCCCCCHHHHCC-CC-HHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             -57888865433103762210121013-42-4689987520123333322222222222223442113465100124565
Q gi|254781101|r  202 -GIEEIASAKAEIFEGLEKTGTIFLNY-DD-SFFELLKAKSHALGIKTIYSFGKSKNADFQLRKWKQCSEQSWMEVQLQG  278 (472)
Q Consensus       202 -s~e~i~~~K~~i~~~l~~~g~~ViN~-Dd-~~~~~l~~~~~~~~~~~i~~~g~~~~ad~~~~~i~~~~~~~~~~~~~~~  278 (472)
                       |+++||.+|+.|++.-.|   +|+.. +. +....+.+++...+...++.++.    ++.+........+..+.+....
T Consensus       161 ~t~~~IA~eKAGI~k~g~P---~v~~~~~~~ea~~v~~~~A~~~~~~~l~~~~~----~~~~~~~~~~~~g~~~~~~~~~  233 (460)
T TIGR01499       161 DTLEEIAWEKAGIIKEGVP---IVTGEVQEPEALEVLKKKAEEKGAAPLQVVGK----DFDIKEKDENLNGEKFSFSGEN  233 (460)
T ss_pred             CCHHHHHHHHHHHHCCCCC---EEEECCCCHHHHHHHHHHHHHHCCCEEEEECC----CCCCCCCCCCCCCCEEEECCCC
T ss_conf             3379999974576216765---68714886689999999999716860465034----1322111122465212223555


Q ss_pred             C-CCCC--CCCCCCCCCCCCCCCHHHHHHHHC------CCCHHHH-HHHHCCCCCCCCCCCCEECCCC---CCEEEEEEC
Q ss_conf             4-3221--222222223333221035676510------1210345-5431147664433101000365---311331000
Q gi|254781101|r  279 K-SMEV--VHHGIGYHMAQNMLMTLGIVSILT------ADVDTAI-KALSVFHPKEGRGKRYRCALNQ---GFFTLIDES  345 (472)
Q Consensus       279 ~-~~~~--~l~~~G~hnv~NalaAia~~~~lG------i~~~~i~-~~L~~~~~~~GR~~~~~~~~~~---~~~~iIDDs  345 (472)
                      . ...+  .++++|.|++.|+..|+.++..++      ++...++ +||.+.. +|||+|+++.....   +...+||-+
T Consensus       234 ~~~~~~~~~~~L~G~~Q~~Na~~A~~~~~~l~~~~~~~~~~~~~~~~GL~~~~-wpGR~e~~~~~~~~~~~~p~~~lDGA  312 (460)
T TIGR01499       234 LFLEPLLAKLSLLGDHQAENAALALAALEVLGKQSSEKLSEAAIRSEGLASTI-WPGRLEILSEDKDAKAANPNILLDGA  312 (460)
T ss_pred             CCCHHCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHC-CCCCEEEEECCCCHHHCCCEEEEECC
T ss_conf             42100135556567999999999999999850235666676678889888511-12201133035412233871799527


Q ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCC----E-EEEECCC------HHHH
Q ss_conf             256532101257778741110268713885123541710589999999999864998----9-9998803------8989
Q gi|254781101|r  346 YNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNIS----H-VWLSGFH------VLAL  414 (472)
Q Consensus       346 YNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d----~-v~~~G~~------~~~~  414 (472)
                        |||+|++++.++++. ......+..+|+|-+.      ++....+...+... ++    . +++....      ...+
T Consensus       313 --HNp~~~~~l~~~~~~-~~~~~~~~~~~~~~l~------~Kd~~~~l~~L~~~-~~~i~~~~~~~~~~~~~~a~~~~~~  382 (460)
T TIGR01499       313 --HNPHSAEALVEWLKE-KEFNGRPITLLFGALA------DKDAAAMLALLREL-VPKIFEEIVYVTPFDYPRALDAADL  382 (460)
T ss_pred             --CCHHHHHHHHHHHHH-HHHCCCCCEEEEEECC------CCCHHHHHHHHHHH-HHHHHCEEEEECCCCCCCCCCHHHH
T ss_conf             --687899999999999-8626997188886113------68878998887874-3565221768617786233675789


Q ss_pred             HHHCCCCC-C-----EEEECCHHHHHHHH---------------------HH--HCCCCCEEEEECCCHHHHHHHHHHHH
Q ss_conf             98511379-7-----99978989999999---------------------98--44789899997713254899999999
Q gi|254781101|r  415 KDALPRSI-H-----VHYSETMDGLFLFI---------------------QS--SLVDGDVVVVKSSNSCGFYRLINLLL  465 (472)
Q Consensus       415 ~~~~~~~~-~-----~~~~~~~e~a~~~l---------------------~~--~~~~gdiVLiKGSr~~~le~iv~~L~  465 (472)
                      .+...... .     ....++..++++..                     ++  ....++.|||.||..     +|-.++
T Consensus       383 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~~~~~lVtGSly-----Lvg~v~  457 (460)
T TIGR01499       383 EAAAEAFGSEELEKAAETVSSWREALELAEKLDEAQKVSALIEIAYLLVALEKEKAKADDLILVTGSLY-----LVGEVR  457 (460)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCEEEEEHHH-----HHHHHH
T ss_conf             999974054156677876730899997166787655102457789888888750567677378872599-----999999


Q ss_pred             H
Q ss_conf             8
Q gi|254781101|r  466 E  466 (472)
Q Consensus       466 ~  466 (472)
                      +
T Consensus       458 ~  458 (460)
T TIGR01499       458 K  458 (460)
T ss_pred             H
T ss_conf             8


No 37 
>KOG2525 consensus
Probab=99.89  E-value=1.8e-21  Score=161.27  Aligned_cols=323  Identities=19%  Similarity=0.176  Sum_probs=192.7

Q ss_pred             CHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCC---CCCHH--HHHCCC---CCCCH---------
Q ss_conf             98999999999998306993999830365420123346777752011---22212--211014---57410---------
Q gi|254781101|r   90 DVLGALNKLAVAARLRSKATIIAITGSVGKTTTKEMLTIALSSIKKT---YACIG--SYNNHI---GVPLT---------  152 (472)
Q Consensus        90 d~~~al~~la~~~~~~~~~~vI~ITGTnGKTTt~~~l~~iL~~~~~~---~~t~g--n~Nn~i---Gvplt---------  152 (472)
                      ..++.|..++-- -++.+..||.|+||+||.||..++.+||++.|..   +.||-  +-.-.|   |.|+|         
T Consensus        55 ~m~~~L~~lg~p-~d~~~l~iIHVAGTkGKGStcaF~~SILr~~g~rtG~yTSPHLl~vrErIriNGqpIS~e~F~~~f~  133 (496)
T KOG2525          55 RMRKLLERLGNP-EDQNSLNIIHVAGTKGKGSTCAFTESILRQQGLRTGFYTSPHLLSVRERIRINGQPISEEKFTKYFW  133 (496)
T ss_pred             HHHHHHHHHCCH-HHHHHEEEEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCHHHCCHHHEEEECCEECCHHHHHHHHH
T ss_conf             999999970986-5443224799823789864589899999842636632268001553245888998789999999999


Q ss_pred             ------------------------HCC----CCCCCHHHHHCCCCCCCCCCCCCCCCCCCCEEEEEEECCCHHHHHH-HH
Q ss_conf             ------------------------001----2322144430156644332112122323220255531210123444-57
Q gi|254781101|r  153 ------------------------LAR----MPVDVDFGIFELGMSHLGEIRFLTHLVRPHIAVITTIAPAHLSNFS-GI  203 (472)
Q Consensus       153 ------------------------ll~----~~~~~~~~V~E~g~~~~gei~~L~~i~~P~iaiiTNI~~dHld~~~-s~  203 (472)
                                              ++.    ..+++|++|+|+|+.  |+.+...-|-+|-++.||+|+-||++.+| ++
T Consensus       134 ~v~~~lk~~~~~~~~~p~yF~fLT~lAF~~F~~enVdvaViEvGlG--G~~DaTNvI~kpvvcgITslG~DH~~~LG~tL  211 (496)
T KOG2525         134 EVYERLKSTKLKEVSMPTYFEFLTLLAFHVFVKENVDVAVIEVGLG--GELDATNVIEKPVVCGITSLGLDHTSFLGNTL  211 (496)
T ss_pred             HHHHHHHHHHCCCCCCCCHHHHHHHHHHEEEEECCCCEEEEEECCC--CCCCCCCCCCCCEEEEEEECCCCHHHHHHHHH
T ss_conf             9999887763065678735556675442015555886899984356--66566533136458998405775288886589


Q ss_pred             HHHHHHHHHHCCCCCCCCHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             88886543310376221012101342468998752012333332222222222222344211346510012456543221
Q gi|254781101|r  204 EEIASAKAEIFEGLEKTGTIFLNYDDSFFELLKAKSHALGIKTIYSFGKSKNADFQLRKWKQCSEQSWMEVQLQGKSMEV  283 (472)
Q Consensus       204 e~i~~~K~~i~~~l~~~g~~ViN~Dd~~~~~l~~~~~~~~~~~i~~~g~~~~ad~~~~~i~~~~~~~~~~~~~~~~~~~~  283 (472)
                      ++|+.+|+.||+.-.|-.  ....++...+.+.+++.......-+   ..+              .....+      -..
T Consensus       212 ~eIA~eKAGIfK~gvpaf--t~~q~~e~~nvL~~ra~e~~~~L~~---v~p--------------~~~~~l------s~~  266 (496)
T KOG2525         212 SEIAWEKAGIFKEGVPAF--TVPQPPEALNVLKERASELGVPLFV---VPP--------------LEAYEL------SGV  266 (496)
T ss_pred             HHHHHHHCCCCCCCCCEE--ECCCCHHHHHHHHHHHHHCCCCCEE---CCC--------------CHHHHH------CCC
T ss_conf             999887446240588548--7588578899999988733788355---388--------------146550------487


Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHH----C---------------CCCHHHHHHHHCCCCCCCCCCCCEECCCCCCEEEEEE
Q ss_conf             22222222333322103567651----0---------------1210345543114766443310100036531133100
Q gi|254781101|r  284 VHHGIGYHMAQNMLMTLGIVSIL----T---------------ADVDTAIKALSVFHPKEGRGKRYRCALNQGFFTLIDE  344 (472)
Q Consensus       284 ~l~~~G~hnv~NalaAia~~~~l----G---------------i~~~~i~~~L~~~~~~~GR~~~~~~~~~~~~~~iIDD  344 (472)
                      .+.+.|.|+..|+..|+.++...    |               ++ +....||.++. +|||.|+++.  +.+...++|.
T Consensus       267 ~lgl~g~hq~~na~lA~~L~~~~~~~~~~~~~~~~~~~~~~~~i~-~~~l~GL~~~~-wPGR~qil~~--~~~~~~llDG  342 (496)
T KOG2525         267 NLGLIGTHQWSNASLAVQLASEWLIQNGRVAEGVLDALQTSGLIP-PAFLSGLASTD-WPGRLQILEY--GRGVTWLLDG  342 (496)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCC-HHHHCCHHHCC-CCCCEEEEEC--CCCCEEEECC
T ss_conf             654006513443578988899999863850105787322366789-89961203245-7870689862--8985799658


Q ss_pred             CCCCCCCCHHHHHHHHHH-HHHCCCCC-CEEEECCHHHCCCCHHHHHHHHHHHHHH-----CCCCEEEEECCC-------
Q ss_conf             025653210125777874-11102687-1388512354171058999999999986-----499899998803-------
Q gi|254781101|r  345 SYNANPASMKAAISVLSQ-ISPHGEGR-RIAVLGDMCEMGELSQSFHIDLAEVLSL-----YNISHVWLSGFH-------  410 (472)
Q Consensus       345 sYNAnP~S~~aal~~l~~-~~~~~~~r-~i~VlG~m~ELG~~~~~~h~~i~~~~~~-----~~~d~v~~~G~~-------  410 (472)
                      +  +||+||+++-+.++. ++...+.+ +|+++-.|   |++...   .+.+.+..     ..++.|+++.-.       
T Consensus       343 A--Ht~eSaea~~~w~~~~~~~~~~~~~~illfn~t---~~~d~~---~Ll~~L~~~~~~~~~F~~Vvf~Pni~~~~~~~  414 (496)
T KOG2525         343 A--HTKESAEACAKWFRKAVRGLKKLTSLILLFNCT---SDRDPP---LLLPLLKPDAVIGTRFSSVVFMPNITSSSPVG  414 (496)
T ss_pred             C--CCHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEC---CCCCHH---HHHHHHCCCCCCCCCCCEEEECCCCCCCCCCC
T ss_conf             9--998999999999999853677765269999803---776647---67677454654344514178524431158766


Q ss_pred             HH-----------HH------H----HHCC----CCCCEEEECCHHHHHHHHHHHCCCCCEEEEECC
Q ss_conf             89-----------89------9----8511----379799978989999999984478989999771
Q gi|254781101|r  411 VL-----------AL------K----DALP----RSIHVHYSETMDGLFLFIQSSLVDGDVVVVKSS  452 (472)
Q Consensus       411 ~~-----------~~------~----~~~~----~~~~~~~~~~~e~a~~~l~~~~~~gdiVLiKGS  452 (472)
                      ..           .+      .    +...    .......+.++..|.+.+....+.-+-+.|.||
T Consensus       415 ~~d~~~~~~s~~~~l~~q~~L~~~w~~l~~~~~~~~~~~~V~~sL~~a~~~Lr~~~~~s~~~~V~gs  481 (496)
T KOG2525         415 SADSISLNTSTEEQLNWQNDLQSVWEELKESEGKTEDPSIVFGSLYLAYELLRDDQHLSPRIEVLGS  481 (496)
T ss_pred             CHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCHHHHHHHHHHCCCCCCEEEEEEE
T ss_conf             6455415677268777758999999998655887313236734599999999842777770899988


No 38 
>pfam01225 Mur_ligase Mur ligase family, catalytic domain. This family contains a number of related ligase enzymes which have EC numbers 6.3.2.*. This family includes: MurC, MurD, MurE, MurF, Mpl and FolC. MurC, MurD, Mure and MurF catalyse consecutive steps in the synthesis of peptidoglycan. Peptidoglycan consists of a sheet of two sugar derivatives, with one of these N-acetylmuramic acid attaching to a small pentapeptide. The pentapeptide is is made of L-alanine, D-glutamic acid, Meso-diaminopimelic acid and D-alanyl alanine. The peptide moiety is synthesized by successively adding these amino acids to UDP-N-acetylmuramic acid. MurC transfers the L-alanine, MurD transfers the D-glutamate, MurE transfers the diaminopimelic acid, and MurF transfers the D-alanyl alanine. This family also includes Folylpolyglutamate synthase that transfers glutamate to folylpolyglutamate.
Probab=99.71  E-value=5.9e-17  Score=131.39  Aligned_cols=76  Identities=34%  Similarity=0.350  Sum_probs=67.8

Q ss_pred             EEEEEEEECCCCCCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEECCCCCCCCCCCCCCEEEECCHHHHHHHHHHHHH
Q ss_conf             474677402223789888971688747688899999869889998552124554469728995998999999999998
Q gi|254781101|r   26 FVNGISIDSRSIAPQEAFFAIKGPHYDGHDFILHAVQKGAGLVVVNTDMVASIGSLSIPVFGVDDVLGALNKLAVAAR  103 (472)
Q Consensus        26 ~i~~i~~dSr~v~~g~lFval~g~~~DGh~~i~~A~~~Ga~~~i~~~~~~~~~~~~~~~~i~v~d~~~al~~la~~~~  103 (472)
                      +|+++++|||++++|++|||++|.++|||+|+++|+++||.+++++....  ....++|+|.|+|++++|+++|+.++
T Consensus         1 eI~~i~~dSr~v~~g~lF~a~~G~~~dG~~fi~~a~~~GA~ai~~~~~~~--~~~~~~~~i~v~d~~~aL~~la~~fy   76 (76)
T pfam01225         1 EIHFIGIDSRGMSPGALFLALKGYRVDGSDFAESAIALGAVAVVSSAIPR--DPNPEVPGIPVIDRREALAELAARFY   76 (76)
T ss_pred             CCCEEEECCCCCCCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEECCCCC--CCCCCCCEEEECCHHHHHHHHHHHHC
T ss_conf             90658878772799999998077867999999999980998999936545--67999739998999999999999769


No 39 
>pfam02875 Mur_ligase_C Mur ligase family, glutamate ligase domain. This family contains a number of related ligase enzymes which have EC numbers 6.3.2.*. This family includes: MurC, MurD, MurE, MurF, Mpl and FolC. MurC, MurD, Mure and MurF catalyse consecutive steps in the synthesis of peptidoglycan. Peptidoglycan consists of a sheet of two sugar derivatives, with one of these N-acetylmuramic acid attaching to a small pentapeptide. The pentapeptide is is made of L-alanine, D-glutamic acid, Meso-diaminopimelic acid and D-alanyl alanine. The peptide moiety is synthesized by successively adding these amino acids to UDP-N-acetylmuramic acid. MurC transfers the L-alanine, MurD transfers the D-glutamate, MurE transfers the diaminopimelic acid, and MurF transfers the D-alanyl alanine. This family also includes Folylpolyglutamate synthase that transfers glutamate to folylpolyglutamate.
Probab=99.00  E-value=1.2e-09  Score=83.15  Aligned_cols=78  Identities=28%  Similarity=0.375  Sum_probs=61.8

Q ss_pred             CCCCCCCCEECCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             64433101000365311331000256532101257778741110268713885123541710589999999999864998
Q gi|254781101|r  323 KEGRGKRYRCALNQGFFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNIS  402 (472)
Q Consensus       323 ~~GR~~~~~~~~~~~~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d  402 (472)
                      +|||||++..   .+++++|+| |++||+||+++|++++++   ..+|+|+|+|.|   |++..+.|.++++.+... .|
T Consensus         1 vpGR~e~i~~---~~~~~vi~D-yaHnp~~~~a~l~~~~~~---~~~r~i~V~G~~---g~r~~~~r~~~g~~a~~~-ad   69 (87)
T pfam02875         1 VPGRLEVVGE---NNGVLVIDD-YAHNPDALEAALQALKEL---FDGRLILVFGAG---GDRDAEFHALLGALAAAL-AD   69 (87)
T ss_pred             CCCCCEEEEC---CCCCEEEEE-CCCCHHHHHHHHHHHHHC---CCCCEEEEECCC---CCCCHHHHHHHHHHHHHC-CC
T ss_conf             9997389865---899789996-789969999999999862---688789999998---888678999999999971-99


Q ss_pred             EEEEECCCH
Q ss_conf             999988038
Q gi|254781101|r  403 HVWLSGFHV  411 (472)
Q Consensus       403 ~v~~~G~~~  411 (472)
                      .|++.+++.
T Consensus        70 ~viit~~~p   78 (87)
T pfam02875        70 VVILTGDYP   78 (87)
T ss_pred             EEEECCCCC
T ss_conf             999999889


No 40 
>PRK00892 lpxD UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional
Probab=98.15  E-value=2.6e-05  Score=54.41  Aligned_cols=95  Identities=16%  Similarity=0.169  Sum_probs=75.3

Q ss_pred             CCCCHHHHHHHHCCEEECCCCCCEEEEEEEECCCCCCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEECCCCCCCCCCCC
Q ss_conf             43567889987279995268871474677402223789888971688747688899999869889998552124554469
Q gi|254781101|r    3 PLWTFHDLLQAIQGHSIGIVPQGFVNGISIDSRSIAPQEAFFAIKGPHYDGHDFILHAVQKGAGLVVVNTDMVASIGSLS   82 (472)
Q Consensus         3 ~~~~~~~l~~~~~g~~~~~~~~~~i~~i~~dSr~v~~g~lFval~g~~~DGh~~i~~A~~~Ga~~~i~~~~~~~~~~~~~   82 (472)
                      |-+||+|||+.++|++.+ +++..|++++ +-.+.++++|=|+-      ..+|++.+.+-.|+++|+.++..... +.+
T Consensus         1 ~s~tL~eIA~~lgg~l~G-d~d~~I~gva-~l~~A~~~~IsF~~------~~ky~~~L~~tkAsavIv~~~~~~~~-~~~   71 (343)
T PRK00892          1 PSLTLAELAEQLGAELHG-DGDIEITGLA-PLDEAGPGQLSFLD------NPKYRKQLKDTQAGAVIVSPDDAEKV-PAH   71 (343)
T ss_pred             CCCCHHHHHHHHCCEEEC-CCCCEEECCC-CHHHCCCCCEEEEE------CHHHHHHHHCCCCEEEEECHHHHHHC-CCC
T ss_conf             963199999975999977-9982796454-96668998099995------88888887557874999547888557-588


Q ss_pred             CCEEEECCHHHHHHHHHHHHHHCC
Q ss_conf             728995998999999999998306
Q gi|254781101|r   83 IPVFGVDDVLGALNKLAVAARLRS  106 (472)
Q Consensus        83 ~~~i~v~d~~~al~~la~~~~~~~  106 (472)
                      .++|.|+||+.++.++...++.+.
T Consensus        72 ~~~Iiv~nP~~afaki~~lF~~~~   95 (343)
T PRK00892         72 RAALVVKNPYLAFARVAQLFDTPP   95 (343)
T ss_pred             CCEEEECCHHHHHHHHHHHHCCCC
T ss_conf             738998998999999999746764


No 41 
>COG1044 LpxD UDP-3-O-[3-hydroxymyristoyl]
Probab=96.96  E-value=0.004  Score=39.92  Aligned_cols=96  Identities=19%  Similarity=0.184  Sum_probs=73.6

Q ss_pred             CCCCHHHHHHHHCCEEECCCCCCEEEEEEEECCCCCCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEECCCCCCCCCCCC
Q ss_conf             43567889987279995268871474677402223789888971688747688899999869889998552124554469
Q gi|254781101|r    3 PLWTFHDLLQAIQGHSIGIVPQGFVNGISIDSRSIAPQEAFFAIKGPHYDGHDFILHAVQKGAGLVVVNTDMVASIGSLS   82 (472)
Q Consensus         3 ~~~~~~~l~~~~~g~~~~~~~~~~i~~i~~dSr~v~~g~lFval~g~~~DGh~~i~~A~~~Ga~~~i~~~~~~~~~~~~~   82 (472)
                      +.++|+||++.+++++.+.. +..++++.-=. +..+++++|.      |+-+|.++...-.|.+++++..... .....
T Consensus         2 ~~~~l~~la~~~~~e~~g~~-~~~i~~va~l~-~a~~~~i~f~------~~~ky~~~l~~s~Agaviv~~~~~~-~~~~~   72 (338)
T COG1044           2 PSYTLAELAQQLGAELRGDG-DRVITGVAPLD-EAQPGDISFL------ANPKYRKELKTSRAGAVIVSAKDAA-FAPAK   72 (338)
T ss_pred             CCCHHHHHHHHHCCEEECCC-CEEEECCCHHH-HCCCCCCEEE------CCHHHHHHCCCCCCCEEEECHHHHH-CCCCC
T ss_conf             52009999975183882578-42562013244-4484451562------2733343112376758995589972-06668


Q ss_pred             CCEEEECCHHHHHHHHHHHHHHCCC
Q ss_conf             7289959989999999999983069
Q gi|254781101|r   83 IPVFGVDDVLGALNKLAVAARLRSK  107 (472)
Q Consensus        83 ~~~i~v~d~~~al~~la~~~~~~~~  107 (472)
                      .+.+.+.||..+++.++..+...++
T Consensus        73 ~~~Lv~~~P~~~fA~~~~~f~~~~~   97 (338)
T COG1044          73 KNALVVKDPYLAFAKVAQLFYRPFN   97 (338)
T ss_pred             CEEEEECCCHHHHHHHHHHHCCCCC
T ss_conf             7089948806789999988514776


No 42 
>TIGR01853 lipid_A_lpxD UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; InterPro: IPR007691 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase (2.3.1 from EC) catalyses an early step in lipid A biosynthesis : UDP-3-O-(3-hydroxytetradecanoyl)glucosamine + (R)-3-hydroxytetradecanoyl- [acyl carrier protein] = UDP-2,3-bis(3-hydroxytetradecanoyl)glucosamine + [acyl carrier protein]  Members of this family also contain a hexapeptide repeat (IPR001451 from INTERPRO). This entry represents the non-repeating region of LPXD proteins.; GO: 0016747 transferase activity transferring groups other than amino-acyl groups, 0009245 lipid A biosynthetic process.
Probab=96.04  E-value=0.036  Score=33.55  Aligned_cols=93  Identities=16%  Similarity=0.132  Sum_probs=72.3

Q ss_pred             HHHHHHCCEEECC-CCCCEEEEEEEECCCCCCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEECCCCCCCCCCCCCCEEE
Q ss_conf             8998727999526-887147467740222378988897168874768889999986988999855212455446972899
Q gi|254781101|r    9 DLLQAIQGHSIGI-VPQGFVNGISIDSRSIAPQEAFFAIKGPHYDGHDFILHAVQKGAGLVVVNTDMVASIGSLSIPVFG   87 (472)
Q Consensus         9 ~l~~~~~g~~~~~-~~~~~i~~i~~dSr~v~~g~lFval~g~~~DGh~~i~~A~~~Ga~~~i~~~~~~~~~~~~~~~~i~   87 (472)
                      ||++.++++|-+. .-|..|++++.= .+.++.+|=|+-      .-+|.+++.+..|.+++++++..........+.|.
T Consensus         1 ela~~~~~El~g~a~g~~~i~~v~~l-~~A~~~~itF~~------n~K~~~~l~~~~AgAv~~~~~~~~~~~~~~~~~L~   73 (336)
T TIGR01853         1 ELAERLGAELKGDAEGDIKISGVAPL-EKAKAEHITFLA------NPKYLKELKSSKAGAVIVSADDQSKLVPKKCAALV   73 (336)
T ss_pred             CCHHHCCCEEECCCCCCEEEEEECCC-CCCCCCCEEEEC------CHHHHHHHHCCCCEEEEEEHHHCCCCCCCCCCEEE
T ss_conf             90442085023566676688530763-358802266533------80478765157740799715661785523250578


Q ss_pred             ECCHHHHHHHHHHHHHHCCCC
Q ss_conf             599899999999999830699
Q gi|254781101|r   88 VDDVLGALNKLAVAARLRSKA  108 (472)
Q Consensus        88 v~d~~~al~~la~~~~~~~~~  108 (472)
                      |+||..++++++.++..+.+.
T Consensus        74 v~~P~l~fA~~~~~F~~~~~~   94 (336)
T TIGR01853        74 VKDPYLAFAKVAELFDPPPKR   94 (336)
T ss_pred             ECCCHHHHHHHHHHHCCCCCC
T ss_conf             178179999999860887650


No 43 
>PRK05439 pantothenate kinase; Provisional
Probab=95.26  E-value=0.017  Score=35.82  Aligned_cols=27  Identities=48%  Similarity=0.594  Sum_probs=23.1

Q ss_pred             CCEEEEECC--CCCCHHHHHHHHHHHHHH
Q ss_conf             939998303--654201233467777520
Q gi|254781101|r  108 ATIIAITGS--VGKTTTKEMLTIALSSIK  134 (472)
Q Consensus       108 ~~vI~ITGT--nGKTTt~~~l~~iL~~~~  134 (472)
                      +-|||||||  .||+||+.+|..+|+.-.
T Consensus        86 PfIIGIaGSVAVGKSTtARlLq~LL~r~~  114 (312)
T PRK05439         86 PFIIGIAGSVAVGKSTTARLLQALLSRWP  114 (312)
T ss_pred             CEEEEEEEEEECCHHHHHHHHHHHHHCCC
T ss_conf             98999762010262889999999995078


No 44 
>pfam04613 LpxD UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD. UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase (EC 2.3.1.-) catalyses an early step in lipid A biosynthesis: UDP-3-O-(3-hydroxytetradecanoyl)glucosamine + (R)-3-hydroxytetradecanoyl- [acyl carrier protein] - UDP-2,3-bis(3-hydroxytetradecanoyl)glucosamine + [acyl carrier protein]. Members of this family also contain a hexapeptide repeat (pfam00132). This family constitutes the non-repeating region of LPXD proteins.
Probab=95.06  E-value=0.11  Score=30.43  Aligned_cols=70  Identities=19%  Similarity=0.213  Sum_probs=50.9

Q ss_pred             CCEEEEEEEECCCCCCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEECCCCCCCCCCCCCCEEEECCHHHHHHHHHHH
Q ss_conf             714746774022237898889716887476888999998698899985521245544697289959989999999999
Q gi|254781101|r   24 QGFVNGISIDSRSIAPQEAFFAIKGPHYDGHDFILHAVQKGAGLVVVNTDMVASIGSLSIPVFGVDDVLGALNKLAVA  101 (472)
Q Consensus        24 ~~~i~~i~~dSr~v~~g~lFval~g~~~DGh~~i~~A~~~Ga~~~i~~~~~~~~~~~~~~~~i~v~d~~~al~~la~~  101 (472)
                      +..|++++. =.+.++|++=|.      +..+|.+++.+-.|+++|+..+.... ...+.+.|+|+||+.++.+++..
T Consensus         2 d~~I~~va~-l~~A~~~~isF~------~n~ky~~~l~~t~A~aviv~~~~~~~-~~~~~~~Iiv~nP~~afa~i~~l   71 (72)
T pfam04613         2 DREISGIAP-LEEAGPGDISFL------ANPKYLKQLKTTKASAVIVTPDFADL-VPEGIALLVVKNPYLAFAKLLQL   71 (72)
T ss_pred             CCEEECCCC-HHHCCCCCEEEE------CCHHHHHHHHHCCCCEEEECHHHHHH-CCCCCCEEEECCHHHHHHHHHHH
T ss_conf             947804547-643899978996------68878999986889899973788745-76898689989989999999975


No 45 
>pfam07085 DRTGG DRTGG domain. This presumed domain is about 120 amino acids in length. It is found associated with CBS domains pfam00571, as well as the CbiA domain pfam01656. The function of this domain is unknown. It is named the DRTGG domain after some of the most conserved residues. This domain may be very distantly related to a pair of CBS domains. There are no significant sequence similarities, but its length and association with CBS domains supports this idea (Bateman A, pers. obs.).
Probab=94.34  E-value=0.34  Score=27.11  Aligned_cols=87  Identities=15%  Similarity=0.219  Sum_probs=56.0

Q ss_pred             HHHHHHCCEEECCCCC--CEEEEEEEECC-------CCCCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEECCCCCCC--
Q ss_conf             8998727999526887--14746774022-------237898889716887476888999998698899985521245--
Q gi|254781101|r    9 DLLQAIQGHSIGIVPQ--GFVNGISIDSR-------SIAPQEAFFAIKGPHYDGHDFILHAVQKGAGLVVVNTDMVAS--   77 (472)
Q Consensus         9 ~l~~~~~g~~~~~~~~--~~i~~i~~dSr-------~v~~g~lFval~g~~~DGh~~i~~A~~~Ga~~~i~~~~~~~~--   77 (472)
                      +|++.++|+++++.+.  ..+.++.+-..       .+++|++.+ .+|.|.|-   +..|+++|++++|......+.  
T Consensus         1 ~I~~~L~g~vl~g~~~~~~~v~~~~igAm~~~~~l~~~~~g~lvI-~~gdR~di---~~~a~~~~~~~iIlTgg~~p~~~   76 (105)
T pfam07085         1 DIAEILGAEVLNGGEGLLRRVGKVVIGAMSVENMLEYLRPGDLVI-TPGDREDI---QLAALLAGIAGLILTGGFEPSEE   76 (105)
T ss_pred             CHHHHCCCEEEECCCCCCCCCCCEEEEECCHHHHHHHHCCCCEEE-EECCCHHH---HHHHHHHCCCEEEEECCCCCCHH
T ss_conf             957866999997686654205869999878999998606897999-92796899---99999824878999489898999


Q ss_pred             ----CCCCCCCEEEEC-CHHHHHHHHH
Q ss_conf             ----544697289959-9899999999
Q gi|254781101|r   78 ----IGSLSIPVFGVD-DVLGALNKLA   99 (472)
Q Consensus        78 ----~~~~~~~~i~v~-d~~~al~~la   99 (472)
                          ....++|++.++ |+.++-..+.
T Consensus        77 v~~la~~~~ipii~t~~dT~~ta~~i~  103 (105)
T pfam07085        77 VLKLAEEAGLPVLSTPYDTFTTARRIN  103 (105)
T ss_pred             HHHHHHHCCCEEEEECCCHHHHHHHHH
T ss_conf             999998779839996688999999985


No 46 
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=93.14  E-value=0.53  Score=25.85  Aligned_cols=45  Identities=11%  Similarity=0.017  Sum_probs=28.8

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHCCC
Q ss_conf             001245654322122222222333322103567651012103455431147
Q gi|254781101|r  271 WMEVQLQGKSMEVVHHGIGYHMAQNMLMTLGIVSILTADVDTAIKALSVFH  321 (472)
Q Consensus       271 ~~~~~~~~~~~~~~l~~~G~hnv~NalaAia~~~~lGi~~~~i~~~L~~~~  321 (472)
                      .|....-.-.|.+.+..+|.-|      |+.+|.-+|+|.+-|..+-+.+.
T Consensus       466 ~FD~~tl~PtYrl~~G~pG~S~------A~~IA~rlGlp~~ii~~A~~~l~  510 (780)
T PRK00409        466 EFDEETLRPTYRLLIGIPGRSN------AFEIAKRLGLPPNIIEEAKKVYG  510 (780)
T ss_pred             EECCCCCCCCEEEECCCCCCCH------HHHHHHHHCCCHHHHHHHHHHHC
T ss_conf             8740237860687059997636------99999992979999999998856


No 47 
>TIGR00313 cobQ cobyric acid synthase CobQ; InterPro: IPR004459 Cobyric acid synthase (CobQ) catalyses amidations at positions B, D, E, and G on adenosylcobyrinic A,C-diamide in the biosynthesis of cobalamin. NH(2) groups are provided by glutamine, and one molecule of ATP is hydrogenolysed for each amidation .; GO: 0003824 catalytic activity, 0009236 cobalamin biosynthetic process.
Probab=92.83  E-value=0.049  Score=32.70  Aligned_cols=41  Identities=20%  Similarity=0.354  Sum_probs=26.4

Q ss_pred             HCCCCCCCHHHHHCCCCCCCCCCC---------CCCCCCCCCEEEEEEECC
Q ss_conf             001232214443015664433211---------212232322025553121
Q gi|254781101|r  153 LARMPVDVDFGIFELGMSHLGEIR---------FLTHLVRPHIAVITTIAP  194 (472)
Q Consensus       153 ll~~~~~~~~~V~E~g~~~~gei~---------~L~~i~~P~iaiiTNI~~  194 (472)
                      +.-|..+.||.|+| |+.++-||.         +.+++++|++-++--|.+
T Consensus       116 le~L~~~Yd~vv~E-GAGS~AEINL~~rDLaN~~iA~~~~A~~iLvADIDR  165 (502)
T TIGR00313       116 LEILAEEYDLVVIE-GAGSPAEINLKERDLANMRIAELADADVILVADIDR  165 (502)
T ss_pred             HHHHHCCCCEEEEE-CCCCCCCCCCCCCCCHHHHHHHHCCCCEEEEEECCC
T ss_conf             98752028889982-688710005331572247898643976799975077


No 48 
>TIGR01069 mutS2 MutS2 family protein; InterPro: IPR005747   Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication . MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base . MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch . MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level . Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA.    MutS is a modular protein with a complex structure , and is composed of:    N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts.    Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions . Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts .    This entry represents a family of MutS proteins.; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0045005 maintenance of fidelity during DNA-dependent DNA replication.
Probab=92.27  E-value=0.86  Score=24.47  Aligned_cols=42  Identities=21%  Similarity=0.358  Sum_probs=24.6

Q ss_pred             CHHHHHHHHHHH----CCCC-CEEEE---ECCCHHHHHHHHHHHHHHCCCCC
Q ss_conf             989999999984----4789-89999---77132548999999998505779
Q gi|254781101|r  429 TMDGLFLFIQSS----LVDG-DVVVV---KSSNSCGFYRLINLLLEEFPAIQ  472 (472)
Q Consensus       429 ~~e~a~~~l~~~----~~~g-diVLi---KGSr~~~le~iv~~L~~~~~~~~  472 (472)
                      +.|+|++.+.+.    +..| ..|.|   ||| | .|++.|+.++++.|.|+
T Consensus       765 R~E~Al~~LeK~l~~A~laG~~~v~IIHGKG~-G-~L~~~V~e~Lk~h~~Vk  814 (834)
T TIGR01069       765 RSEEALDRLEKFLDDALLAGYEVVEIIHGKGS-G-KLRKGVQELLKNHPKVK  814 (834)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCEEEEEEECCC-C-HHHHHHHHHHHCCCCEE
T ss_conf             27999999999999998789847899840266-5-05688998986299546


No 49 
>TIGR00670 asp_carb_tr aspartate carbamoyltransferase; InterPro: IPR002082   Aspartate carbamoyltransferase (ATCase) catalyses the formation of carbamoyl-aspartate in the pyrimidine biosynthesis pathway, by the association of aspartate and carbamoyl-phosphate. This is the commitment step in the Escherichia coli pathway and is regulated by feedback inhibition by CTP, the final product of the pathway.   The structural organisation of the ATCase protein varies considerably between different organisms. In bacteria such as E. coli, Salmonella typhimurium and Serratia marcescens, the ATCase is a dodecamer of 2 catalytic (c) trimers and 3 regulatory (r) dimers. The catalytic domains are coded for by the pyrB gene, and the regulatory domains by pyrI. In Gram-positive bacteria such as Bacillus subtilis, ATCase exists as a trimer of catalytic subunits, but unlike in E. coli, it neither contains nor binds to regulatory subunits. In eukaryotes, ATCase is found as a single domain in a multifunctional enzyme that contains activity for glutamine amidotransferase, carbamoylphosphate synthetase, dihydroorotase, and aspartate carbamoyltransferase. ; GO: 0004070 aspartate carbamoyltransferase activity, 0006207 'de novo' pyrimidine base biosynthetic process.
Probab=92.04  E-value=0.93  Score=24.25  Aligned_cols=114  Identities=18%  Similarity=0.335  Sum_probs=71.0

Q ss_pred             EEE--ECCCCCCCCHHHHHH--HHHHHHH-------CCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             310--002565321012577--7874111-------02687138851235417105899999999998649989999880
Q gi|254781101|r  341 LID--ESYNANPASMKAAIS--VLSQISP-------HGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGF  409 (472)
Q Consensus       341 iID--DsYNAnP~S~~aal~--~l~~~~~-------~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~  409 (472)
                      |||  |--|.||+  ++.|+  |+.+.-.       ..+|.+|+++||.+    ++..-|..+ ..++..+--.|+++++
T Consensus       137 viNAGDG~~qHPT--Q~LLDLyTi~~~fGPDnP~l~~~~Gl~iA~vGDlk----ygRtvhS~~-~~L~~f~~~~v~l~sP  209 (336)
T TIGR00670       137 VINAGDGSGQHPT--QTLLDLYTIYEEFGPDNPALERLDGLKIALVGDLK----YGRTVHSLI-KALALFGNAEVYLISP  209 (336)
T ss_pred             EEECCCCCCCCCC--HHHHHHHHHHHHHCCCCCCHHHCCCCEEEEEEECC----CCHHHHHHH-HHHHHHCCCEEEEECC
T ss_conf             6636878787975--34788999998718886303222885799984312----024766788-9986518956998677


Q ss_pred             CH----HHHHHHCC-CCCCEEEECCHHHHHHHHHHHCCCCCEE---EEECCCHHHHHHHHHHHHHHCCCC
Q ss_conf             38----98998511-3797999789899999999844789899---997713254899999999850577
Q gi|254781101|r  410 HV----LALKDALP-RSIHVHYSETMDGLFLFIQSSLVDGDVV---VVKSSNSCGFYRLINLLLEEFPAI  471 (472)
Q Consensus       410 ~~----~~~~~~~~-~~~~~~~~~~~e~a~~~l~~~~~~gdiV---LiKGSr~~~le~iv~~L~~~~~~~  471 (472)
                      +.    +.+.+.+. ++..+....+++|+       +..=||+   .+.  | .+-||+-....++|..|
T Consensus       210 ~~LrmP~~~~e~~~~~G~~~~~~~~l~e~-------~~~~DVlkiWY~t--R-iQkER~~~~d~~ey~~~  269 (336)
T TIGR00670       210 EELRMPKEILEDLKAKGVKVRETESLEEV-------IDEADVLKIWYVT--R-IQKERFPEDDPEEYEKV  269 (336)
T ss_pred             HHHHCHHHHHHHHHHCCCEEEEEEEHHHH-------HCCCCEEEEEEEE--C-CCCCCCCCCCHHHHHHH
T ss_conf             24306178899985289628995224344-------2157847886420--0-11123788788999841


No 50 
>TIGR03453 partition_RepA plasmid partitioning protein RepA. Members of this family are the RepA (or ParA) protein involved in replicon partitioning. All known examples occur in bacterial species with two or more replicons, on a plasmid or the smaller chromosome. Note that an apparent exception may be seen as a pseudomolecule from assembly of an incompletely sequenced genome. Members of this family belong to a larger family that also includes the enzyme cobyrinic acid a,c-diamide synthase, but assignment of that name to members of this family would be in error.
Probab=91.60  E-value=0.12  Score=30.07  Aligned_cols=29  Identities=38%  Similarity=0.398  Sum_probs=26.2

Q ss_pred             CCCEEEEE---CCCCCCHHHHHHHHHHHHHHC
Q ss_conf             99399983---036542012334677775201
Q gi|254781101|r  107 KATIIAIT---GSVGKTTTKEMLTIALSSIKK  135 (472)
Q Consensus       107 ~~~vI~IT---GTnGKTTt~~~l~~iL~~~~~  135 (472)
                      +++||+|.   |-.|||||+-.+++.|...|.
T Consensus       103 ~~~VIav~N~KGGVGKTTtav~LA~~LA~~G~  134 (387)
T TIGR03453       103 HLQVIAVTNFKGGSGKTTTSAHLAQYLALRGY  134 (387)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHHCCC
T ss_conf             88089997888765699999999999997799


No 51 
>TIGR02764 spore_ybaN_pdaB polysaccharide deacetylase family sporulation protein PdaB; InterPro: IPR014132   This entry describes the YbaN protein family, also called PdaB and SpoVIE, of Gram-positive bacteria. Although ybaN null mutants have only a mild sporulation defect, ybaN/ytrI double mutants show drastically reduced sporulation efficiencies. This synthetic defect suggests the role of this sigmaE-controlled gene in sporulation had been masked by functional redundancy. Members of this family are homologous to a characterised polysaccharide deacetylase; the exact function this protein family is unknown..
Probab=91.38  E-value=0.19  Score=28.79  Aligned_cols=155  Identities=14%  Similarity=0.137  Sum_probs=82.9

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHCCCCCCCCCCCCEECCCCCCEEEEEECCCC-CCCCHHHHHHHHHH
Q ss_conf             22222222333322103567651012103455431147664433101000365311331000256-53210125777874
Q gi|254781101|r  284 VHHGIGYHMAQNMLMTLGIVSILTADVDTAIKALSVFHPKEGRGKRYRCALNQGFFTLIDESYNA-NPASMKAAISVLSQ  362 (472)
Q Consensus       284 ~l~~~G~hnv~NalaAia~~~~lGi~~~~i~~~L~~~~~~~GR~~~~~~~~~~~~~~iIDDsYNA-nP~S~~aal~~l~~  362 (472)
                      -|..+-..++.||.+=+...++=--| |.+++ |-...   -|++  |+  +..+....|  |+. .++-++.=|..-.+
T Consensus        24 IL~~L~~~~vk~ATFFlsG~Wae~hP-elvk~-lveI~---~~GH--EI--GsHgY~h~~--~~~l~~E~ikkd~~~a~~   92 (198)
T TIGR02764        24 ILDTLKEEDVKNATFFLSGSWAERHP-ELVKE-LVEIV---KDGH--EI--GSHGYRHKN--YTTLEDEKIKKDLLRAQE   92 (198)
T ss_pred             HHHHHHHCCCCCCCCEEEHHHHHCCH-HHHHH-HHHHH---HCCC--CC--CCCCCCCCC--CCCCCHHHHHHHHHHHHH
T ss_conf             76667655885333024315761277-89999-99998---4484--30--335421242--125876489999999888


Q ss_pred             HHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEE--CCCHHHHHHHCCCCCCEEEECCHHHHHHHHHHH
Q ss_conf             111026871388512354171058999999999986499899998--803898998511379799978989999999984
Q gi|254781101|r  363 ISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLS--GFHVLALKDALPRSIHVHYSETMDGLFLFIQSS  440 (472)
Q Consensus       363 ~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~--G~~~~~~~~~~~~~~~~~~~~~~e~a~~~l~~~  440 (472)
                      .-.+-.|+..-+|=-.  -|.+.    ..+.+.+.+.+...|.+-  =+ ..+-+           =+..|..+....+.
T Consensus        93 ~i~~~~g~~p~LlRpP--~G~fn----~~~~~~ae~~GY~~V~WsWHvd-S~DWk-----------NPG~e~iv~~V~~~  154 (198)
T TIGR02764        93 IIEKLTGKKPTLLRPP--NGAFN----KAVLKLAESLGYTVVHWSWHVD-SLDWK-----------NPGVESIVDRVVKN  154 (198)
T ss_pred             HHHHHCCCCEEEEECC--CCCCC----HHHHHHHHHCCCCEEEEECCCC-CCCCC-----------CCCEEHHHHHHHCC
T ss_conf             8865105550165688--98604----6899999973991898624558-83545-----------78610001113312


Q ss_pred             CCCCCEEEEE-CCCHH-----HHHHHHHHHHHH
Q ss_conf             4789899997-71325-----489999999985
Q gi|254781101|r  441 LVDGDVVVVK-SSNSC-----GFYRLINLLLEE  467 (472)
Q Consensus       441 ~~~gdiVLiK-GSr~~-----~le~iv~~L~~~  467 (472)
                      +++|||||+= ||.+.     .|.+|++.|+++
T Consensus       155 ~~~GdIiL~HDASd~~KqT~~ALp~Ii~~LK~~  187 (198)
T TIGR02764       155 TKPGDIILLHDASDSAKQTVKALPEIIKKLKEK  187 (198)
T ss_pred             CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHC
T ss_conf             799856987634879744177899998998754


No 52 
>TIGR01278 DPOR_BchB light-independent protochlorophyllide reductase, B subunit; InterPro: IPR005969    Synonym: dark protochlorophyllide reductase    Protochlorophyllide reductase catalyzes the reductive formation of chlorophyllide from protochlorophyllide during biosynthesis of chlorophylls and bacteriochlorophylls. The light-independent (dark) form of protochlorophyllide reductase plays a key role in the ability of gymnosperms, algae, and photosynthetic bacteria to form chlorophyll in the dark. Genetic and sequence analyses have indicated that dark protochlorophyllide reductase consists of three protein subunits that exhibit significant sequence similarity to the three subunits of nitrogenase, which catalyzes the reductive formation of ammonia from dinitrogen. Dark protochlorophyllide reductase activity was shown to be dependent on the presence of all three subunits, ATP, and the reductant dithionite .; GO: 0016730 oxidoreductase activity acting on iron-sulfur proteins as donors, 0015995 chlorophyll biosynthetic process, 0019685 photosynthesis dark reaction.
Probab=91.32  E-value=1.1  Score=23.75  Aligned_cols=79  Identities=20%  Similarity=0.228  Sum_probs=53.2

Q ss_pred             CCCCCEEEECCHHHCCCCHHHHHHHHHHHHH-HCCCCEEEEECCCHHHHHHHCC----C-CC-CEEEECCHHHHHHHHHH
Q ss_conf             2687138851235417105899999999998-6499899998803898998511----3-79-79997898999999998
Q gi|254781101|r  367 GEGRRIAVLGDMCEMGELSQSFHIDLAEVLS-LYNISHVWLSGFHVLALKDALP----R-SI-HVHYSETMDGLFLFIQS  439 (472)
Q Consensus       367 ~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~-~~~~d~v~~~G~~~~~~~~~~~----~-~~-~~~~~~~~e~a~~~l~~  439 (472)
                      -.|||.+||||      .+.-  -.|.+.++ +.++ .|++.|...+..++.++    . .. .+.+.|+..++.+.+. 
T Consensus       307 L~GKra~VFGD------~tHa--vg~T~~L~~ElG~-~vv~AGTY~k~~a~wvr~~~~gY~dGEvlv~ddf~~v~~~I~-  376 (562)
T TIGR01278       307 LTGKRAFVFGD------ATHA--VGVTKLLRDELGI-HVVGAGTYCKEQADWVREQVAGYVDGEVLVTDDFQEVADAIA-  376 (562)
T ss_pred             CCCCCEEEECC------CHHH--HHHHHHHHHHCCC-EEEEECCCCHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHH-
T ss_conf             15884698678------4489--9999998863791-798724798668999999983038824888253588999998-


Q ss_pred             HCCCCCEEEEECCCHHHHHHHH
Q ss_conf             4478989999771325489999
Q gi|254781101|r  440 SLVDGDVVVVKSSNSCGFYRLI  461 (472)
Q Consensus       440 ~~~~gdiVLiKGSr~~~le~iv  461 (472)
                      .+.|. +||     |++|||=+
T Consensus       377 ~~~P~-lv~-----GTQMERH~  392 (562)
T TIGR01278       377 ALEPE-LVL-----GTQMERHV  392 (562)
T ss_pred             HHCCC-CEE-----CCCHHHHH
T ss_conf             60852-010-----56425677


No 53 
>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=91.22  E-value=0.24  Score=28.18  Aligned_cols=110  Identities=25%  Similarity=0.322  Sum_probs=56.2

Q ss_pred             HHHHHHHHHHHH-CCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCHHHHHCCCCCCCHHC-CC--------CCC-CH
Q ss_conf             999999999983-06993999830365420123346777752011222122110145741000-12--------322-14
Q gi|254781101|r   93 GALNKLAVAARL-RSKATIIAITGSVGKTTTKEMLTIALSSIKKTYACIGSYNNHIGVPLTLA-RM--------PVD-VD  161 (472)
Q Consensus        93 ~al~~la~~~~~-~~~~~vI~ITGTnGKTTt~~~l~~iL~~~~~~~~t~gn~Nn~iGvpltll-~~--------~~~-~~  161 (472)
                      +|-..|...... ....+..||||| |||=|.+.+=+=++..--|.+--+          ||+ +|        |++ .+
T Consensus        16 ~AI~~L~~~l~~G~~~QtLLGvTGs-GKTFT~AnVIa~~~rPTLV~aHNK----------TLAAQLY~EfKefFPeNAVE   84 (667)
T TIGR00631        16 KAIAKLVEGLEAGEKEQTLLGVTGS-GKTFTMANVIAQVQRPTLVLAHNK----------TLAAQLYNEFKEFFPENAVE   84 (667)
T ss_pred             HHHHHHHHHHHCCCCCEEEEEEECC-CHHHHHHHHHHHHCCCEEEECCCH----------HHHHHHHHHHHHHCCCCCEE
T ss_conf             9999999998568871478532148-627889899998479849985777----------67999999998638677245


Q ss_pred             HHH------------------HC--CCCCCCCCCCCC-----CC-CCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             443------------------01--566443321121-----22-32322025553121012344457888865433103
Q gi|254781101|r  162 FGI------------------FE--LGMSHLGEIRFL-----TH-LVRPHIAVITTIAPAHLSNFSGIEEIASAKAEIFE  215 (472)
Q Consensus       162 ~~V------------------~E--~g~~~~gei~~L-----~~-i~~P~iaiiTNI~~dHld~~~s~e~i~~~K~~i~~  215 (472)
                      |+|                  ||  .++|.  ||++|     .. +-+.|+-|+=+||.  +=.+|+-+.|.+--..|-.
T Consensus        85 YFvSYYDYYQPEAYvP~~DtyIEKdaSINd--eIerlR~SAT~SLl~RrDVIVVASVSc--IYGLG~P~~Y~~~~~~l~v  160 (667)
T TIGR00631        85 YFVSYYDYYQPEAYVPSKDTYIEKDASIND--EIERLRLSATKSLLERRDVIVVASVSC--IYGLGSPEEYLKMVLHLEV  160 (667)
T ss_pred             EEEECCCCCCCCCCCCCCCCEEECCCCHHH--HHHHHHHHHHHHHCCCCCEEEEEEEEE--ECCCCCCHHHHCCEEEEEE
T ss_conf             255203237873214798841304553004--676778898886423787899987552--0688882556422786540


Q ss_pred             CC
Q ss_conf             76
Q gi|254781101|r  216 GL  217 (472)
Q Consensus       216 ~l  217 (472)
                      +.
T Consensus       161 G~  162 (667)
T TIGR00631       161 GK  162 (667)
T ss_pred             CC
T ss_conf             78


No 54 
>PRK13869 plasmid-partitioning protein RepA; Provisional
Probab=91.09  E-value=0.15  Score=29.48  Aligned_cols=29  Identities=38%  Similarity=0.403  Sum_probs=25.9

Q ss_pred             CCCEEEEE---CCCCCCHHHHHHHHHHHHHHC
Q ss_conf             99399983---036542012334677775201
Q gi|254781101|r  107 KATIIAIT---GSVGKTTTKEMLTIALSSIKK  135 (472)
Q Consensus       107 ~~~vI~IT---GTnGKTTt~~~l~~iL~~~~~  135 (472)
                      +++||+|.   |-.|||||+--|++.|...|.
T Consensus       120 ~~kVIaVaN~KGGVGKTTtav~LA~~LA~~G~  151 (405)
T PRK13869        120 HLQVIAVTNFKGGSGKTTTSAHLAQYLALQGY  151 (405)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHHCCC
T ss_conf             98289997888776599999999999997799


No 55 
>COG4109 Predicted transcriptional regulator containing CBS domains [Transcription]
Probab=90.97  E-value=0.43  Score=26.43  Aligned_cols=95  Identities=18%  Similarity=0.311  Sum_probs=54.6

Q ss_pred             CCHHHHHHHHCCEEECCCCC--CEEEEEEEEC-------CCCCCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEEC----
Q ss_conf             56788998727999526887--1474677402-------2237898889716887476888999998698899985----
Q gi|254781101|r    5 WTFHDLLQAIQGHSIGIVPQ--GFVNGISIDS-------RSIAPQEAFFAIKGPHYDGHDFILHAVQKGAGLVVVN----   71 (472)
Q Consensus         5 ~~~~~l~~~~~g~~~~~~~~--~~i~~i~~dS-------r~v~~g~lFval~g~~~DGh~~i~~A~~~Ga~~~i~~----   71 (472)
                      +|..+|+.++.|+.+++..-  ..++.|++.-       |-+.||.|.+  .|.|.|-|..   |+++|++..++-    
T Consensus        71 LTf~Eiv~iidgqVLgG~~Gl~k~~sKFvIGAMt~~~i~rY~~~g~LlI--VGnR~~iq~l---AL~~~~AVLvTGGF~~  145 (432)
T COG4109          71 LTFAEIVNIIDGQVLGGRAGLEKELSKFVIGAMTLDAILRYLDPGGLLI--VGNREDIQLL---ALENGNAVLVTGGFDV  145 (432)
T ss_pred             HHHHHHHHHHCCCEECCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCEEE--EECHHHHHHH---HHHCCCEEEEECCCCC
T ss_conf             1199998762350432632266654665043521988996107895699--9468999999---9864985999579886


Q ss_pred             -CCCCCCCCCCCCCEEEEC-CHHHHHHHHHHHHHH
Q ss_conf             -521245544697289959-989999999999983
Q gi|254781101|r   72 -TDMVASIGSLSIPVFGVD-DVLGALNKLAVAARL  104 (472)
Q Consensus        72 -~~~~~~~~~~~~~~i~v~-d~~~al~~la~~~~~  104 (472)
                       ++........++|++... |+...-..+-++..+
T Consensus       146 s~evi~lAne~~lPvlstsYDTFTVAtmIN~Al~n  180 (432)
T COG4109         146 SDEVIKLANEKGLPVLSTSYDTFTVATMINKALSN  180 (432)
T ss_pred             CHHHHHHHCCCCCCEEEECCCCEEHHHHHHHHHHH
T ss_conf             58899764014884487045213099999899877


No 56 
>TIGR02782 TrbB_P P-type conjugative transfer ATPase TrbB; InterPro: IPR014149   This entry represents TrbB, a protein, which is encoded in the trb locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for plasmid conjugative transfer . TrbB is a homologue of the vir system VirB11 ATPase , and the Flp pilus system ATPase TadA ..
Probab=90.96  E-value=0.15  Score=29.46  Aligned_cols=71  Identities=30%  Similarity=0.351  Sum_probs=42.1

Q ss_pred             CCCCCEEEECC--CCCCCHH--------HHHHHHHHCCCEEEEECCCCCCCCCCCCCCEEEECCHHHHHHHHHHHHHHCC
Q ss_conf             37898889716--8874768--------8899999869889998552124554469728995998999999999998306
Q gi|254781101|r   37 IAPQEAFFAIK--GPHYDGH--------DFILHAVQKGAGLVVVNTDMVASIGSLSIPVFGVDDVLGALNKLAVAARLRS  106 (472)
Q Consensus        37 v~~g~lFval~--g~~~DGh--------~~i~~A~~~Ga~~~i~~~~~~~~~~~~~~~~i~v~d~~~al~~la~~~~~~~  106 (472)
                      +-+|.|  +|.  |+||-|-        .|   +|.+-|..+++=++|++..       |.   +-..+..|..+...+-
T Consensus        76 ivegEL--PldflGsRFeGl~PPVV~~p~F---~IRkkA~~vfTLDdYV~~g-------im---taaQ~d~l~~Av~ar~  140 (315)
T TIGR02782        76 IVEGEL--PLDFLGSRFEGLLPPVVEAPSF---AIRKKAVRVFTLDDYVEAG-------IM---TAAQRDVLREAVAARK  140 (315)
T ss_pred             EEEECC--CCCHHHCCCCCCCCCCCCCCCC---HHCCCCCCCCCCHHHHHHC-------CC---CHHHHHHHHHHHHHCC
T ss_conf             266107--5111201100468775565510---1110224104707776404-------45---5789999999997129


Q ss_pred             CCCEEEEECCCCCCHHH
Q ss_conf             99399983036542012
Q gi|254781101|r  107 KATIIAITGSVGKTTTK  123 (472)
Q Consensus       107 ~~~vI~ITGTnGKTTt~  123 (472)
                      +.-|+|=||| ||||-+
T Consensus       141 NIlv~GGTGS-GKTTLa  156 (315)
T TIGR02782       141 NILVVGGTGS-GKTTLA  156 (315)
T ss_pred             CEEEECCCCC-CHHHHH
T ss_conf             8899814588-579999


No 57 
>TIGR01968 minD_bact septum site-determining protein MinD; InterPro: IPR010223   This entry describes the bacterial and chloroplast form of MinD, a multifunctional cell division protein that guides correct placement of the septum. In Escherichia coli, the cell division site is determined by the cooperative activity of min operon products MinC, MinD, and MinE . MinD is a membrane-associated ATPase and is a septum site-determining factor through the activation and regulation of MinC and MinE. MinD is also known to undergo a rapid pole-to-pole oscillation movement in vivo as observed by fluorescent microscopy. In plants, chloroplast division requires the dimerisation of stromal MinD . The homologous archaeal MinD proteins, with many archaeal genomes having two or more forms, are described by a separate model.; GO: 0016887 ATPase activity, 0000918 selection of site for barrier septum formation.
Probab=90.42  E-value=0.21  Score=28.48  Aligned_cols=30  Identities=47%  Similarity=0.586  Sum_probs=24.6

Q ss_pred             CEEEEE---CCCCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             399983---036542012334677775201122
Q gi|254781101|r  109 TIIAIT---GSVGKTTTKEMLTIALSSIKKTYA  138 (472)
Q Consensus       109 ~vI~IT---GTnGKTTt~~~l~~iL~~~~~~~~  138 (472)
                      +||-||   |-.|||||+.=|..-|...|+.+.
T Consensus         2 ~viViTSGKGGVGKTTtTANlG~aLA~lG~kVv   34 (272)
T TIGR01968         2 RVIVITSGKGGVGKTTTTANLGTALARLGKKVV   34 (272)
T ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEE
T ss_conf             589998178897735898999999996198289


No 58 
>COG1419 FlhF Flagellar GTP-binding protein [Cell motility and secretion]
Probab=90.28  E-value=0.98  Score=24.08  Aligned_cols=17  Identities=12%  Similarity=0.100  Sum_probs=12.7

Q ss_pred             EEEEECCCCCCCCEEEE
Q ss_conf             67740222378988897
Q gi|254781101|r   29 GISIDSRSIAPQEAFFA   45 (472)
Q Consensus        29 ~i~~dSr~v~~g~lFva   45 (472)
                      .+-++||.+++|..|..
T Consensus        26 AvIls~r~i~~g~~~~~   42 (407)
T COG1419          26 AVILSNRRIKKGGFLGL   42 (407)
T ss_pred             CEEEECCEECCCCEEEE
T ss_conf             18854336347825632


No 59 
>COG1072 CoaA Panthothenate kinase [Coenzyme metabolism]
Probab=90.16  E-value=0.15  Score=29.46  Aligned_cols=75  Identities=25%  Similarity=0.296  Sum_probs=48.2

Q ss_pred             HHCCCEEEEECCCCCC-CCCCCCCCEEEECCHHHHHHHHHHHHHH-----------------CCCCCEEEEECCC--CCC
Q ss_conf             9869889998552124-5544697289959989999999999983-----------------0699399983036--542
Q gi|254781101|r   61 VQKGAGLVVVNTDMVA-SIGSLSIPVFGVDDVLGALNKLAVAARL-----------------RSKATIIAITGSV--GKT  120 (472)
Q Consensus        61 ~~~Ga~~~i~~~~~~~-~~~~~~~~~i~v~d~~~al~~la~~~~~-----------------~~~~~vI~ITGTn--GKT  120 (472)
                      +.+-+...+++.+... ...+..+.+..|+++..-|.+|...+..                 ...+-||||.||.  ||+
T Consensus        17 ~~~~~~~~lt~~e~~~~~~ln~~~~l~eV~~iylpL~~l~~~~~~~~~~~~~~~~~~l~~~~~~~pfIIgiaGsvavGKS   96 (283)
T COG1072          17 LRASTPLTLTEEELKRLRGLNEPISLDEVEDIYLPLSRLLQLYVEARERLFAELLRFLGTNNQQRPFIIGIAGSVAVGKS   96 (283)
T ss_pred             HHHCCCCCCCHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCCHH
T ss_conf             54058642678999886067889779999999999999999999889988999999834668888879996057665577


Q ss_pred             HHHHHHHHHHHHHHC
Q ss_conf             012334677775201
Q gi|254781101|r  121 TTKEMLTIALSSIKK  135 (472)
Q Consensus       121 Tt~~~l~~iL~~~~~  135 (472)
                      ||+..+..+|+..+.
T Consensus        97 T~ar~L~~ll~~~~~  111 (283)
T COG1072          97 TTARILQALLSRWPE  111 (283)
T ss_pred             HHHHHHHHHHHHCCC
T ss_conf             899999999963889


No 60 
>PRK09841 cryptic autophosphorylating protein tyrosine kinase Etk; Provisional
Probab=90.04  E-value=0.34  Score=27.11  Aligned_cols=97  Identities=12%  Similarity=0.134  Sum_probs=48.5

Q ss_pred             CCCCCCEEEECCH-HHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHHH--HHHHCCCCCC---EEEE---CCHHHHHHH
Q ss_conf             0268713885123-54171058999999999986499899998803898--9985113797---9997---898999999
Q gi|254781101|r  366 HGEGRRIAVLGDM-CEMGELSQSFHIDLAEVLSLYNISHVWLSGFHVLA--LKDALPRSIH---VHYS---ETMDGLFLF  436 (472)
Q Consensus       366 ~~~~r~i~VlG~m-~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~~~~--~~~~~~~~~~---~~~~---~~~e~a~~~  436 (472)
                      ....|.|+|.+.. +| |+-.-  -..++..++..+ .+|.+++-+++.  +...+.....   ..+.   .+.++++. 
T Consensus       528 ~~~~kvi~vTS~~pgE-GKSt~--a~nLA~~~A~~G-~rvLLID~DlRrp~l~~~~~~~~~~GLs~~L~g~~~~~~~i~-  602 (726)
T PRK09841        528 ETENNILMITGATPDS-GKTFV--SSTLAAVIAQSD-QKVLFIDADLRRGYSHNLFTVSNEHGLSEYLAGKDELNKVIQ-  602 (726)
T ss_pred             CCCCCEEEEECCCCCC-CHHHH--HHHHHHHHHHCC-CEEEEECCCCCCCCHHHHCCCCCCCCHHHHHCCCCCHHHHCC-
T ss_conf             8888689997799999-77999--999999998479-959998288777107761599999877998389998899330-


Q ss_pred             HHHHCCCCCEEEEECC---------CHHHHHHHHHHHHHHCC
Q ss_conf             9984478989999771---------32548999999998505
Q gi|254781101|r  437 IQSSLVDGDVVVVKSS---------NSCGFYRLINLLLEEFP  469 (472)
Q Consensus       437 l~~~~~~gdiVLiKGS---------r~~~le~iv~~L~~~~~  469 (472)
                        ....+|=-||-.|.         -+-+|+.+++.|.++|-
T Consensus       603 --~~~~~~ldvl~aG~~p~nP~elL~s~~~~~ll~~l~~~yD  642 (726)
T PRK09841        603 --HFGKGGFDVITRGQVPPNPSELLMRDRMRQLLEWANDHYD  642 (726)
T ss_pred             --CCCCCCEEEEECCCCCCCHHHHHCCHHHHHHHHHHHHCCC
T ss_conf             --2798998998289999798999587699999999981399


No 61 
>COG1703 ArgK Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]
Probab=89.45  E-value=0.51  Score=25.95  Aligned_cols=36  Identities=31%  Similarity=0.290  Sum_probs=27.5

Q ss_pred             HHHCCCCCEEEEECC--CCCCHHHHHHHHHHHHHHCCC
Q ss_conf             983069939998303--654201233467777520112
Q gi|254781101|r  102 ARLRSKATIIAITGS--VGKTTTKEMLTIALSSIKKTY  137 (472)
Q Consensus       102 ~~~~~~~~vI~ITGT--nGKTTt~~~l~~iL~~~~~~~  137 (472)
                      +-..-+..+|||||+  .||+|..+-+..-|...|..+
T Consensus        45 ~p~tG~a~viGITG~PGaGKSTli~~L~~~l~~~G~rV   82 (323)
T COG1703          45 YPRTGNAHVIGITGVPGAGKSTLIEALGRELRERGHRV   82 (323)
T ss_pred             HHCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHCCCEE
T ss_conf             31179983787317998866889999999999779678


No 62 
>COG4555 NatA ABC-type Na+ transport system, ATPase component [Energy production and conversion / Inorganic ion transport and metabolism]
Probab=89.12  E-value=0.71  Score=25.00  Aligned_cols=79  Identities=24%  Similarity=0.310  Sum_probs=43.5

Q ss_pred             CCCEEEEECCC--CCCHHHHHHHHHHHH-HHCCCCCHHHHHCCCCCCCHHCCCCCCCHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf             99399983036--542012334677775-201122212211014574100012322144430156644332112122323
Q gi|254781101|r  107 KATIIAITGSV--GKTTTKEMLTIALSS-IKKTYACIGSYNNHIGVPLTLARMPVDVDFGIFELGMSHLGEIRFLTHLVR  183 (472)
Q Consensus       107 ~~~vI~ITGTn--GKTTt~~~l~~iL~~-~~~~~~t~gn~Nn~iGvpltll~~~~~~~~~V~E~g~~~~gei~~L~~i~~  183 (472)
                      ++.|.|+-|-|  ||||+-.||+.+|.. .|++.. .       |     ..+..+...+.=++|... |+..-..+   
T Consensus        27 ~Gei~GlLG~NGAGKTT~LRmiatlL~P~~G~v~i-d-------g-----~d~~~~p~~vrr~IGVl~-~e~glY~R---   89 (245)
T COG4555          27 EGEITGLLGENGAGKTTLLRMIATLLIPDSGKVTI-D-------G-----VDTVRDPSFVRRKIGVLF-GERGLYAR---   89 (245)
T ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHCCCCCCEEEE-E-------E-----CCCCCCHHHHHHHCCEEC-CCCCHHHH---
T ss_conf             66499987689887123799999832588864998-4-------0-----021017187752021313-77670355---


Q ss_pred             CCEEEEEEECCCHHHHHHHHHHHHHH
Q ss_conf             22025553121012344457888865
Q gi|254781101|r  184 PHIAVITTIAPAHLSNFSGIEEIASA  209 (472)
Q Consensus       184 P~iaiiTNI~~dHld~~~s~e~i~~~  209 (472)
                           +|  ..+|+-||+-+.+....
T Consensus        90 -----lT--~rEnl~~Fa~L~~l~~~  108 (245)
T COG4555          90 -----LT--ARENLKYFARLNGLSRK  108 (245)
T ss_pred             -----HH--HHHHHHHHHHHHHHHHH
T ss_conf             -----30--89999999999624026


No 63 
>COG0595 mRNA degradation ribonucleases J1/J2 (metallo-beta-lactamase superfamily) [Translation, ribosomal structure and biogenesis; Replication, recombination and repair]
Probab=88.94  E-value=1.7  Score=22.48  Aligned_cols=12  Identities=8%  Similarity=0.219  Sum_probs=5.4

Q ss_pred             CEEEECCCCCCC
Q ss_conf             888971688747
Q gi|254781101|r   41 EAFFAIKGPHYD   52 (472)
Q Consensus        41 ~lFval~g~~~D   52 (472)
                      ++|+-=-|.+++
T Consensus        32 ~i~i~D~G~~fp   43 (555)
T COG0595          32 DIIILDAGLKFP   43 (555)
T ss_pred             CEEEEECCCCCC
T ss_conf             689997765668


No 64 
>PRK06761 hypothetical protein; Provisional
Probab=88.92  E-value=0.16  Score=29.31  Aligned_cols=33  Identities=33%  Similarity=0.474  Sum_probs=23.4

Q ss_pred             EEECCCCCCHHHHHHHHHHHHHHCC--CCCHHHHHC
Q ss_conf             9830365420123346777752011--222122110
Q gi|254781101|r  112 AITGSVGKTTTKEMLTIALSSIKKT--YACIGSYNN  145 (472)
Q Consensus       112 ~ITGTnGKTTt~~~l~~iL~~~~~~--~~t~gn~Nn  145 (472)
                      ||-| .|||||.+|+...|++.|.-  +...|+.++
T Consensus         9 GlPG-sGKSTta~~l~d~L~~~g~~v~~~~Egd~~h   43 (281)
T PRK06761          9 GLPG-FGKSTTAHLLNDKLSQLKIEVELFVEGDLNH   43 (281)
T ss_pred             CCCC-CCHHHHHHHHHHHHHHCCCCEEEEEECCCCC
T ss_conf             6899-9801499999999986698538995078999


No 65 
>COG1936 Predicted nucleotide kinase (related to CMP and AMP kinases) [Nucleotide transport and metabolism]
Probab=88.80  E-value=0.22  Score=28.42  Aligned_cols=21  Identities=57%  Similarity=0.800  Sum_probs=17.3

Q ss_pred             CEEEEECC--CCCCHHHHHHHHHH
Q ss_conf             39998303--65420123346777
Q gi|254781101|r  109 TIIAITGS--VGKTTTKEMLTIAL  130 (472)
Q Consensus       109 ~vI~ITGT--nGKTTt~~~l~~iL  130 (472)
                      +.|+||||  .||||++..|+ -|
T Consensus         1 m~I~ITGTPGvGKTT~~~~L~-~l   23 (180)
T COG1936           1 MLIAITGTPGVGKTTVCKLLR-EL   23 (180)
T ss_pred             CEEEEECCCCCCHHHHHHHHH-HH
T ss_conf             937993799986687999999-82


No 66 
>cd02040 NifH NifH gene encodes component II (iron protein) of nitrogenase. Nitrogenase is responsible for the biological nitrogen fixation, i.e. reduction of molecular nitrogen to ammonia. NifH consists of two oxygen-sensitive metallosulfur proteins: the mollybdenum-iron (alternatively, vanadium-iron or iron-iron) protein (commonly referred to as component 1), and the iron protein (commonly referred to as component 2). The iron protein is a homodimer, with an Fe4S4 cluster bound between the subunits and two ATP-binding domains. It supplies energy by ATP hydrolysis, and transfers electrons from reduced ferredoxin or flavodoxin to component 1 for the reduction of molecular nitrogen to ammonia.
Probab=88.79  E-value=0.31  Score=27.37  Aligned_cols=30  Identities=40%  Similarity=0.531  Sum_probs=25.2

Q ss_pred             CCEEEEEC--CCCCCHHHHHHHHHHHHHHCCC
Q ss_conf             93999830--3654201233467777520112
Q gi|254781101|r  108 ATIIAITG--SVGKTTTKEMLTIALSSIKKTY  137 (472)
Q Consensus       108 ~~vI~ITG--TnGKTTt~~~l~~iL~~~~~~~  137 (472)
                      .++|||+|  -.|||||+--|+..|.+.|+.+
T Consensus         1 ~r~Iai~GKGGVGKTTtavNLA~aLa~~GkkV   32 (270)
T cd02040           1 MRQIAIYGKGGIGKSTTTQNLSAALAEMGKKV   32 (270)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHHCCCEE
T ss_conf             95899979985778999999999999879949


No 67 
>PRK06731 flhF flagellar biosynthesis regulator FlhF; Validated
Probab=88.64  E-value=0.21  Score=28.52  Aligned_cols=29  Identities=34%  Similarity=0.438  Sum_probs=19.0

Q ss_pred             CCCEEEEECCC--CCCHHHHHHHHHHHHHHC
Q ss_conf             99399983036--542012334677775201
Q gi|254781101|r  107 KATIIAITGSV--GKTTTKEMLTIALSSIKK  135 (472)
Q Consensus       107 ~~~vI~ITGTn--GKTTt~~~l~~iL~~~~~  135 (472)
                      ++++|..-|-+  |||||..=|++.+...++
T Consensus        74 ~~~vI~lvG~~G~GKTTT~AKLA~~~~~~~~  104 (270)
T PRK06731         74 EVQTIALIGPTGVGKTTTLAKMAWQFHGKKK  104 (270)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHCCC
T ss_conf             9818999888989889999999999986799


No 68 
>PRK03839 putative kinase; Provisional
Probab=88.42  E-value=0.27  Score=27.75  Aligned_cols=21  Identities=62%  Similarity=0.828  Sum_probs=17.3

Q ss_pred             EEEEECC--CCCCHHHHHHHHHH
Q ss_conf             9998303--65420123346777
Q gi|254781101|r  110 IIAITGS--VGKTTTKEMLTIAL  130 (472)
Q Consensus       110 vI~ITGT--nGKTTt~~~l~~iL  130 (472)
                      +|+||||  .||||.+..|+.-|
T Consensus         2 ~I~ITGTPGtGKTTva~~La~~l   24 (180)
T PRK03839          2 IIAITGTPGVGKTTISKLLAEKL   24 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHH
T ss_conf             89997899999899999999976


No 69 
>cd02029 PRK_like Phosphoribulokinase-like (PRK-like) is a family of proteins similar to phosphoribulokinase (PRK), the enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes. PRK catalyzes the phosphorylation of D-ribulose 5-phosphate to form D-ribulose 1, 5-biphosphate, using ATP and NADPH produced by the primary reactions of photosynthesis.
Probab=88.03  E-value=0.25  Score=28.03  Aligned_cols=26  Identities=35%  Similarity=0.429  Sum_probs=21.6

Q ss_pred             EEEEECCC--CCCHHHHHHHHHHHHHHC
Q ss_conf             99983036--542012334677775201
Q gi|254781101|r  110 IIAITGSV--GKTTTKEMLTIALSSIKK  135 (472)
Q Consensus       110 vI~ITGTn--GKTTt~~~l~~iL~~~~~  135 (472)
                      |||||||.  ||||++.-+.+|+...+.
T Consensus         1 IIaVtGsSGAGtsTv~r~f~~IF~re~v   28 (277)
T cd02029           1 VIAVTGSSGAGTTTVKRAFEHIFAREGI   28 (277)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHHCCC
T ss_conf             9899338888478799999998720588


No 70 
>cd02026 PRK Phosphoribulokinase (PRK) is an enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes. This enzyme catalyzes the phosphorylation of D-ribulose 5-phosphate to form D-ribulose 1, 5-biphosphate, using ATP and NADPH produced by the primary reactions of photosynthesis.
Probab=88.00  E-value=0.21  Score=28.50  Aligned_cols=25  Identities=36%  Similarity=0.384  Sum_probs=20.8

Q ss_pred             EEEEECCC--CCCHHHHHHHHHHHHHH
Q ss_conf             99983036--54201233467777520
Q gi|254781101|r  110 IIAITGSV--GKTTTKEMLTIALSSIK  134 (472)
Q Consensus       110 vI~ITGTn--GKTTt~~~l~~iL~~~~  134 (472)
                      ||||||+.  ||||++..+.++|....
T Consensus         1 IIgVaG~SGSGKTTv~~~i~~ifg~~~   27 (273)
T cd02026           1 IIGVAGDSGCGKSTFLRRLTSLFGSDL   27 (273)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHCCCC
T ss_conf             989978887869999999999858487


No 71 
>PRK09435 arginine/ornithine transport system ATPase; Provisional
Probab=87.73  E-value=0.89  Score=24.36  Aligned_cols=40  Identities=33%  Similarity=0.287  Sum_probs=27.2

Q ss_pred             HHHHHHHCCCCCEEEEECC--CCCCHHHHHHHHHHHHHHCCC
Q ss_conf             9999983069939998303--654201233467777520112
Q gi|254781101|r   98 LAVAARLRSKATIIAITGS--VGKTTTKEMLTIALSSIKKTY  137 (472)
Q Consensus        98 la~~~~~~~~~~vI~ITGT--nGKTTt~~~l~~iL~~~~~~~  137 (472)
                      +...+...-+..+|||||+  .||+|..+-+...|...++.+
T Consensus        39 l~~l~~~~g~a~~iGiTG~pG~GKStli~~l~~~~~~~g~~v   80 (325)
T PRK09435         39 LDALLPHTGNALRIGITGVPGVGKSTFIEALGMHLIEQGHKV   80 (325)
T ss_pred             HHHHHHCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCEE
T ss_conf             998630179825997427999868899999999999679858


No 72 
>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family; InterPro: IPR006001    This family of proteins includes thermoresistant and thermosensitve isozymes of gluconate kinase (gluconokinase) in E. coli and other related proteins; members of this family are often named by similarity to the thermostable isozyme. These proteins show homology to shikimate kinases and adenylate kinases but not to gluconate kinases from the FGGY family of carbohydrate kinases (IPR000577 from INTERPRO).; GO: 0016301 kinase activity, 0005975 carbohydrate metabolic process.
Probab=87.72  E-value=0.28  Score=27.73  Aligned_cols=25  Identities=32%  Similarity=0.515  Sum_probs=19.5

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC
Q ss_conf             99983036542012334677775201
Q gi|254781101|r  110 IIAITGSVGKTTTKEMLTIALSSIKK  135 (472)
Q Consensus       110 vI~ITGTnGKTTt~~~l~~iL~~~~~  135 (472)
                      ++||.|| ||||+..-+++-|.+.|+
T Consensus         3 lmGvaG~-GKs~~a~~l~~~lg~iyP   27 (175)
T TIGR01313         3 LMGVAGS-GKSTIASALAHRLGDIYP   27 (175)
T ss_pred             EECCCCC-CHHHHHHHHHHHHHHHCC
T ss_conf             7602786-288999999998543157


No 73 
>PRK11519 tyrosine kinase; Provisional
Probab=86.97  E-value=1.3  Score=23.34  Aligned_cols=99  Identities=13%  Similarity=0.126  Sum_probs=48.3

Q ss_pred             CCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHHH--HHHHCCCCC-C--EEEE---CCHHHHHHHH
Q ss_conf             026871388512354171058999999999986499899998803898--998511379-7--9997---8989999999
Q gi|254781101|r  366 HGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFHVLA--LKDALPRSI-H--VHYS---ETMDGLFLFI  437 (472)
Q Consensus       366 ~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~~~~--~~~~~~~~~-~--~~~~---~~~e~a~~~l  437 (472)
                      ...+|.|+|.+..-.=|+-.-  -..++..++..+ .+|.+++-+++.  +.+.+.... .  ..+.   .+.++++   
T Consensus       523 ~~~~~vi~vTS~~pgEGKSt~--a~nLA~~~A~~G-~rvLLID~DlRrp~l~~~~~~~~~~GLs~~L~g~~~~~~~i---  596 (720)
T PRK11519        523 QAQNNVLMMTGVSPSIGKTFV--CANLAAVISQTN-KRVLLIDCDMRKGYTHELLGTNNVNGLSEILIGQGDITTAA---  596 (720)
T ss_pred             CCCCCEEEEEECCCCCCHHHH--HHHHHHHHHHCC-CEEEEEECCCCCCHHHHHCCCCCCCCHHHHCCCCCCHHHHC---
T ss_conf             888767999708999978999--999999998379-91999938777701677539999998599807999789970---


Q ss_pred             HHHCCCCCEEEEECCC---------HHHHHHHHHHHHHHCCC
Q ss_conf             9844789899997713---------25489999999985057
Q gi|254781101|r  438 QSSLVDGDVVVVKSSN---------SCGFYRLINLLLEEFPA  470 (472)
Q Consensus       438 ~~~~~~gdiVLiKGSr---------~~~le~iv~~L~~~~~~  470 (472)
                      ...-.++=-||-.|..         +-+|..+++.|+++|.-
T Consensus       597 ~~~~~~~l~vl~~G~~~pnp~elL~s~~~~~ll~~l~~~yD~  638 (720)
T PRK11519        597 KPTSIANFDLIPRGQVPPNPSELLMSERFAELVAWASKNYDL  638 (720)
T ss_pred             CCCCCCCEEEECCCCCCCCHHHHHCCHHHHHHHHHHHHHCCE
T ss_conf             357989989976999994989983875999999999852999


No 74 
>COG4240 Predicted kinase [General function prediction only]
Probab=86.96  E-value=1.1  Score=23.86  Aligned_cols=49  Identities=29%  Similarity=0.325  Sum_probs=37.1

Q ss_pred             EECCHHHHHHHHHHHHHHCCCCCEEEEECCC--CCCHHHHHHHHHHHHHHC
Q ss_conf             9599899999999999830699399983036--542012334677775201
Q gi|254781101|r   87 GVDDVLGALNKLAVAARLRSKATIIAITGSV--GKTTTKEMLTIALSSIKK  135 (472)
Q Consensus        87 ~v~d~~~al~~la~~~~~~~~~~vI~ITGTn--GKTTt~~~l~~iL~~~~~  135 (472)
                      .++=....+.+++.++-+.-.+-++||.|+-  ||||++..|..+|...|.
T Consensus        29 ~~dl~Lpll~Kiap~~qe~grPli~gisGpQGSGKStls~~i~~~L~~kg~   79 (300)
T COG4240          29 AQDLHLPLLAKIAPWAQERGRPLIVGISGPQGSGKSTLSALIVRLLAAKGL   79 (300)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCC
T ss_conf             999877889864454421279639985268887653599999999997365


No 75 
>pfam06564 YhjQ YhjQ protein. This family consists of several bacterial YhjQ proteins. The function of this family is unknown. However, the family does contain a P-loop sequence motif suggesting a nucleotide binding function.
Probab=86.55  E-value=0.44  Score=26.38  Aligned_cols=29  Identities=28%  Similarity=0.487  Sum_probs=24.0

Q ss_pred             CCEEEE---ECCCCCCHHHHHHHHHHHHHHCC
Q ss_conf             939998---30365420123346777752011
Q gi|254781101|r  108 ATIIAI---TGSVGKTTTKEMLTIALSSIKKT  136 (472)
Q Consensus       108 ~~vI~I---TGTnGKTTt~~~l~~iL~~~~~~  136 (472)
                      ++||+|   -|-.|||||+--|++.|...|+.
T Consensus         1 MkiIai~s~KGGVGKTT~t~nLa~aLa~~G~r   32 (244)
T pfam06564         1 MAVLALQGVRGGVGTTSLTAALGWALQQLGES   32 (244)
T ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHCCCC
T ss_conf             92999966999861999999999999977995


No 76 
>cd02025 PanK Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway. The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.
Probab=86.47  E-value=0.33  Score=27.23  Aligned_cols=24  Identities=54%  Similarity=0.686  Sum_probs=19.9

Q ss_pred             EEEEECC--CCCCHHHHHHHHHHHHH
Q ss_conf             9998303--65420123346777752
Q gi|254781101|r  110 IIAITGS--VGKTTTKEMLTIALSSI  133 (472)
Q Consensus       110 vI~ITGT--nGKTTt~~~l~~iL~~~  133 (472)
                      +|||+|.  .||||++..+..+|...
T Consensus         1 IIGIaG~sgSGKST~a~~l~~~l~~~   26 (220)
T cd02025           1 IIGIAGSVAVGKSTTARVLQALLSRW   26 (220)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHHC
T ss_conf             98978899877999999999986002


No 77 
>pfam06555 consensus
Probab=86.12  E-value=2.3  Score=21.64  Aligned_cols=34  Identities=15%  Similarity=0.221  Sum_probs=22.0

Q ss_pred             CCCCEEEECCHHHHHHHHHHHHHHCCCCCEEEEECCC
Q ss_conf             6972899599899999999999830699399983036
Q gi|254781101|r   81 LSIPVFGVDDVLGALNKLAVAARLRSKATIIAITGSV  117 (472)
Q Consensus        81 ~~~~~i~v~d~~~al~~la~~~~~~~~~~vI~ITGTn  117 (472)
                      .++....|++..+|+..+-...   ++...|+.-||.
T Consensus        10 ~~f~~~~~~t~eeA~~~~~~lI---~~g~sV~~GGS~   43 (200)
T pfam06555        10 NNFEAYYVENKEEALELILELI---PEGSTVGFGGSM   43 (200)
T ss_pred             CCCEEEEECCHHHHHHHHHHHC---CCCCEEEECCHH
T ss_conf             8987999799999999999868---998999869317


No 78 
>COG2403 Predicted GTPase [General function prediction only]
Probab=85.92  E-value=0.65  Score=25.26  Aligned_cols=32  Identities=22%  Similarity=0.345  Sum_probs=26.5

Q ss_pred             CCCCEEEEECC---CCCCHHHHHHHHHHHHHH-CCC
Q ss_conf             69939998303---654201233467777520-112
Q gi|254781101|r  106 SKATIIAITGS---VGKTTTKEMLTIALSSIK-KTY  137 (472)
Q Consensus       106 ~~~~vI~ITGT---nGKTTt~~~l~~iL~~~~-~~~  137 (472)
                      ..-|+|+||||   .|||++..+++++|++.| +++
T Consensus       124 ~ekPviaV~atrtg~GKsaVS~~v~r~l~ergyrv~  159 (449)
T COG2403         124 LEKPVIAVTATRTGVGKSAVSRYVARLLRERGYRVC  159 (449)
T ss_pred             HCCCEEEEEEECCCCCHHHHHHHHHHHHHHCCCCEE
T ss_conf             148559999723665567888999999986698237


No 79 
>PRK10037 cell division protein; Provisional
Probab=85.66  E-value=0.53  Score=25.84  Aligned_cols=43  Identities=23%  Similarity=0.398  Sum_probs=29.2

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCC----CCHHH-HHCCCCCCCH
Q ss_conf             9998303654201233467777520112----22122-1101457410
Q gi|254781101|r  110 IIAITGSVGKTTTKEMLTIALSSIKKTY----ACIGS-YNNHIGVPLT  152 (472)
Q Consensus       110 vI~ITGTnGKTTt~~~l~~iL~~~~~~~----~t~gn-~Nn~iGvplt  152 (472)
                      +.++.|-.||||++.-|++.|...|+.+    ..+.| +.-+.|+|++
T Consensus         6 l~s~kGGVGkTTltAnLA~aL~~~g~~VlaID~dpqN~Lrlhfg~~~~   53 (250)
T PRK10037          6 LQGVRGGVGTTSITAALAWSLQMLGENVLVIDACPDNLLRLSFNVDFT   53 (250)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHCCCCCC
T ss_conf             960788876899999999999977991899957825667875499854


No 80 
>PRK00313 lpxK tetraacyldisaccharide 4'-kinase; Provisional
Probab=85.51  E-value=0.75  Score=24.84  Aligned_cols=31  Identities=23%  Similarity=0.220  Sum_probs=26.9

Q ss_pred             CCCCCEEEE----ECCCCCCHHHHHHHHHHHHHHC
Q ss_conf             069939998----3036542012334677775201
Q gi|254781101|r  105 RSKATIIAI----TGSVGKTTTKEMLTIALSSIKK  135 (472)
Q Consensus       105 ~~~~~vI~I----TGTnGKTTt~~~l~~iL~~~~~  135 (472)
                      +++.|||.|    .|-.|||-+..+|+..|++.|.
T Consensus        48 ~~~vPVI~VGNitvGGTGKTP~v~~La~~L~~~G~   82 (332)
T PRK00313         48 RAPVPVIVVGNITVGGTGKTPLILWLIEHCRRRGL   82 (332)
T ss_pred             CCCCCEEEECCEEECCCCHHHHHHHHHHHHHHCCC
T ss_conf             58998999878735887777999999999997799


No 81 
>TIGR00750 lao LAO/AO transport system ATPase; InterPro: IPR005129   Bacterial periplasmic transport systems require the function of a specific substrate-binding protein, located in the periplasm, and several cytoplasmic membrane transport components. In Escherichia coli K-12, the arginine-ornithine transport system requires an arginine-ornithine-binding protein and the lysine-arginine-ornithine (LAO) transport system includes a LAO-binding protein. Both periplasmic proteins can be phosphorylated by a single kinase, ArgK  resulting in reduced levels of transport activity of the periplasmic transport systems that include each of the binding proteins. The ArgK protein acts as an ATPase enzyme and as a kinase..
Probab=85.23  E-value=0.72  Score=24.96  Aligned_cols=31  Identities=32%  Similarity=0.407  Sum_probs=25.9

Q ss_pred             CCCEEEEECC--CCCCHHHHHHHHHHHHHHCCC
Q ss_conf             9939998303--654201233467777520112
Q gi|254781101|r  107 KATIIAITGS--VGKTTTKEMLTIALSSIKKTY  137 (472)
Q Consensus       107 ~~~vI~ITGT--nGKTTt~~~l~~iL~~~~~~~  137 (472)
                      +..+|||||.  .||+|.-+-+..-|...|..+
T Consensus        37 nA~~vG~TG~PGaGKSTl~~~l~~~lrRrG~~V   69 (333)
T TIGR00750        37 NAHVVGITGVPGAGKSTLVEKLIMELRRRGLKV   69 (333)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHCCCEE
T ss_conf             907876646888857779999989997659768


No 82 
>PRK09825 idnK D-gluconate kinase; Provisional
Probab=85.18  E-value=0.39  Score=26.70  Aligned_cols=24  Identities=21%  Similarity=0.422  Sum_probs=17.9

Q ss_pred             CEEEEECCCCCCHHHHHHHHHHHHH
Q ss_conf             3999830365420123346777752
Q gi|254781101|r  109 TIIAITGSVGKTTTKEMLTIALSSI  133 (472)
Q Consensus       109 ~vI~ITGTnGKTTt~~~l~~iL~~~  133 (472)
                      -|.||.|| ||||+...|++-|.-.
T Consensus         7 VVmGVsGs-GKSTvg~~LA~~L~~~   30 (176)
T PRK09825          7 ILMGVSGS-GKSLIGSKIAALFSAK   30 (176)
T ss_pred             EEEECCCC-CHHHHHHHHHHHHCCC
T ss_conf             99828989-9899999999995987


No 83 
>COG1763 MobB Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme metabolism]
Probab=85.00  E-value=0.64  Score=25.30  Aligned_cols=34  Identities=32%  Similarity=0.309  Sum_probs=26.5

Q ss_pred             CCEEEEECC--CCCCHHHHHHHHHHHHHHCCCCCHH
Q ss_conf             939998303--6542012334677775201122212
Q gi|254781101|r  108 ATIIAITGS--VGKTTTKEMLTIALSSIKKTYACIG  141 (472)
Q Consensus       108 ~~vI~ITGT--nGKTTt~~~l~~iL~~~~~~~~t~g  141 (472)
                      ++|++|+|.  .||||..+=+...|++.|..+++..
T Consensus         2 ~~Il~ivG~k~SGKTTLie~lv~~L~~~G~rVa~iK   37 (161)
T COG1763           2 MKILGIVGYKNSGKTTLIEKLVRKLKARGYRVATVK   37 (161)
T ss_pred             CCEEEEEECCCCCHHHHHHHHHHHHHHCCCEEEEEE
T ss_conf             728999962799734289999999975793799998


No 84 
>PRK05480 uridine kinase; Provisional
Probab=84.88  E-value=0.52  Score=25.92  Aligned_cols=26  Identities=35%  Similarity=0.480  Sum_probs=20.9

Q ss_pred             CCCEEEEECC--CCCCHHHHHHHHHHHH
Q ss_conf             9939998303--6542012334677775
Q gi|254781101|r  107 KATIIAITGS--VGKTTTKEMLTIALSS  132 (472)
Q Consensus       107 ~~~vI~ITGT--nGKTTt~~~l~~iL~~  132 (472)
                      ++-+|||+|.  .||||.+..|...|..
T Consensus         5 ~P~iIgIaG~SgSGKTT~a~~L~~~l~~   32 (209)
T PRK05480          5 QPIIIGIAGGSGSGKTTVASTIYEELGD   32 (209)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHCCC
T ss_conf             9889999899977899999999998086


No 85 
>pfam02606 LpxK Tetraacyldisaccharide-1-P 4'-kinase. This family consists of tetraacyldisaccharide-1-P 4'-kinase also known as Lipid-A 4'-kinase or Lipid A biosynthesis protein LpxK, EC:2.7.1.130. This enzyme catalyses the reaction: ATP + 2,3-bis(3-hydroxytetradecanoyl)-D -glucosaminyl-(beta-D-1,6)-2,3-bis(3-hydroxytetradecanoyl)-D-glu cosam inyl beta-phosphate <= ADP + 2,3,2',3'-tetrakis(3-hydroxytetradecanoyl)-D- glucosaminyl-1,6-beta-D-glucosamine 1,4'-bisphosphate. This enzyme is involved in the synthesis of lipid A portion of the bacterial lipopolysaccharide layer (LPS). The family contains a P-loop motif at the N terminus.
Probab=84.72  E-value=0.86  Score=24.46  Aligned_cols=31  Identities=26%  Similarity=0.276  Sum_probs=26.8

Q ss_pred             CCCCCEEEE----ECCCCCCHHHHHHHHHHHHHHC
Q ss_conf             069939998----3036542012334677775201
Q gi|254781101|r  105 RSKATIIAI----TGSVGKTTTKEMLTIALSSIKK  135 (472)
Q Consensus       105 ~~~~~vI~I----TGTnGKTTt~~~l~~iL~~~~~  135 (472)
                      +++.|||.|    .|-.|||-++.+++..|++.|.
T Consensus        32 ~~~vpVI~VGNit~GGtGKTP~v~~l~~~l~~~g~   66 (318)
T pfam02606        32 RLPVPVIVVGNITVGGTGKTPLVIALAELLRARGL   66 (318)
T ss_pred             CCCCCEEEECCEEECCCCHHHHHHHHHHHHHHCCC
T ss_conf             48999999989845887858999999999997699


No 86 
>COG0237 CoaE Dephospho-CoA kinase [Coenzyme metabolism]
Probab=83.88  E-value=0.61  Score=25.46  Aligned_cols=21  Identities=38%  Similarity=0.585  Sum_probs=17.2

Q ss_pred             CCEEEEECC--CCCCHHHHHHHH
Q ss_conf             939998303--654201233467
Q gi|254781101|r  108 ATIIAITGS--VGKTTTKEMLTI  128 (472)
Q Consensus       108 ~~vI~ITGT--nGKTTt~~~l~~  128 (472)
                      ..+||+||+  .||||+..+++.
T Consensus         2 ~~iIglTG~igsGKStva~~~~~   24 (201)
T COG0237           2 MLIIGLTGGIGSGKSTVAKILAE   24 (201)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH
T ss_conf             64999957887788999999997


No 87 
>pfam01121 CoaE Dephospho-CoA kinase. This family catalyses the phosphorylation of the 3'-hydroxyl group of dephosphocoenzyme A to form Coenzyme A EC:2.7.1.24. This enzyme uses ATP in its reaction.
Probab=83.87  E-value=0.53  Score=25.85  Aligned_cols=19  Identities=32%  Similarity=0.611  Sum_probs=15.6

Q ss_pred             EEEEECC--CCCCHHHHHHHH
Q ss_conf             9998303--654201233467
Q gi|254781101|r  110 IIAITGS--VGKTTTKEMLTI  128 (472)
Q Consensus       110 vI~ITGT--nGKTTt~~~l~~  128 (472)
                      +|||||.  .||||+..++..
T Consensus         2 iIgiTG~IgsGKStv~~~l~~   22 (179)
T pfam01121         2 IVGLTGGIGSGKSTVANLFAD   22 (179)
T ss_pred             EEEEECCCCCCHHHHHHHHHH
T ss_conf             899857864789999999998


No 88 
>PRK08853 DNA polymerase III subunits gamma and tau; Validated
Probab=83.77  E-value=0.36  Score=26.95  Aligned_cols=35  Identities=9%  Similarity=0.069  Sum_probs=14.5

Q ss_pred             EEEEEECCCCCCCCE--EEECCCCCCCHHHHHHHHHH
Q ss_conf             467740222378988--89716887476888999998
Q gi|254781101|r   28 NGISIDSRSIAPQEA--FFAIKGPHYDGHDFILHAVQ   62 (472)
Q Consensus        28 ~~i~~dSr~v~~g~l--Fval~g~~~DGh~~i~~A~~   62 (472)
                      .|.|..-+.+..|..  ++-+.+....|-+-+.+.++
T Consensus        73 cg~C~~C~~i~~g~~~d~~EiDaAs~~~vdd~rel~~  109 (717)
T PRK08853         73 CGQCATCKEIDEGRFVDLLEIDAASRTKVEDTRELLD  109 (717)
T ss_pred             CCCCCCHHHHHCCCCCCEEEECCCCCCCHHHHHHHHH
T ss_conf             8887026767447877524540565678899999998


No 89 
>cd02028 UMPK_like Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).
Probab=83.63  E-value=0.57  Score=25.64  Aligned_cols=25  Identities=32%  Similarity=0.410  Sum_probs=21.0

Q ss_pred             EEEEECC--CCCCHHHHHHHHHHHHHH
Q ss_conf             9998303--654201233467777520
Q gi|254781101|r  110 IIAITGS--VGKTTTKEMLTIALSSIK  134 (472)
Q Consensus       110 vI~ITGT--nGKTTt~~~l~~iL~~~~  134 (472)
                      +|||+|-  .||||.+..|...|...+
T Consensus         1 iIgIaG~SgSGKTT~a~~L~~~l~~~~   27 (179)
T cd02028           1 VVGIAGPSGSGKTTFAKKLSNQLRVNG   27 (179)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHHCC
T ss_conf             989989897789999999999984648


No 90 
>PRK05259 consensus
Probab=83.13  E-value=3.4  Score=20.55  Aligned_cols=92  Identities=12%  Similarity=0.054  Sum_probs=41.6

Q ss_pred             CEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHH
Q ss_conf             11331000256532101257778741110268713885123541710589999999999864998999988038989985
Q gi|254781101|r  338 FFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFHVLALKDA  417 (472)
Q Consensus       338 ~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~~~~~~~~  417 (472)
                      .+.++||== .+-.++..|.+.|+..   + -++|.+...=   |-.+..-.    +.+...+++.|++.-.-..  .+.
T Consensus       211 ~~IIvDDiI-dTGgTl~~aa~~Lk~~---G-A~~V~~~~TH---gvfs~~A~----~ri~~s~i~~vvvTdTi~~--~~~  276 (310)
T PRK05259        211 DCILIDDIV-DSGGTLCNAAEALLAN---G-ANSVTAYITH---GVLSGGAV----ARIASSKLKELVITDSIQP--TEA  276 (310)
T ss_pred             EEEEECCHH-HCHHHHHHHHHHHHHC---C-CCEEEEEEEC---CCCCCHHH----HHHHCCCCCEEEEECCCCC--CHH
T ss_conf             489517344-1688999999999877---9-9869999978---53685699----9986289978999389788--845


Q ss_pred             CCCCCCEEEECCHHHHHHHHHHHCCCC
Q ss_conf             113797999789899999999844789
Q gi|254781101|r  418 LPRSIHVHYSETMDGLFLFIQSSLVDG  444 (472)
Q Consensus       418 ~~~~~~~~~~~~~e~a~~~l~~~~~~g  444 (472)
                      .++..++...+ ...++..+...+..|
T Consensus       277 ~~~~~kl~vls-va~llAeaI~r~~~~  302 (310)
T PRK05259        277 VNDAPNIRVLS-IAPLIGEAIRRTAAE  302 (310)
T ss_pred             HHCCCCCEEEE-HHHHHHHHHHHHHCC
T ss_conf             70589939998-299999999998679


No 91 
>PRK00652 lpxK tetraacyldisaccharide 4'-kinase; Reviewed
Probab=83.08  E-value=1  Score=24.03  Aligned_cols=31  Identities=26%  Similarity=0.285  Sum_probs=26.7

Q ss_pred             CCCCCEEEE----ECCCCCCHHHHHHHHHHHHHHC
Q ss_conf             069939998----3036542012334677775201
Q gi|254781101|r  105 RSKATIIAI----TGSVGKTTTKEMLTIALSSIKK  135 (472)
Q Consensus       105 ~~~~~vI~I----TGTnGKTTt~~~l~~iL~~~~~  135 (472)
                      +++.|||.|    +|..|||-++.+++..|...|.
T Consensus        46 ~~~vpVI~VGNitvGGtGKTP~v~~la~~l~~~g~   80 (334)
T PRK00652         46 RFPVPVISVGNLTVGGNGKTPVVIWLAEQLQARGV   80 (334)
T ss_pred             CCCCCEEEEECEEECCCCHHHHHHHHHHHHHHCCC
T ss_conf             58998999908887887779999999999997699


No 92 
>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP. This kinase also catalyzes the phosphorylation of several cytotoxic ribonucleoside analogs such as 5-flurrouridine and cyclopentenyl-cytidine.
Probab=83.05  E-value=0.48  Score=26.11  Aligned_cols=23  Identities=43%  Similarity=0.576  Sum_probs=18.6

Q ss_pred             EEEEECC--CCCCHHHHHHHHHHHH
Q ss_conf             9998303--6542012334677775
Q gi|254781101|r  110 IIAITGS--VGKTTTKEMLTIALSS  132 (472)
Q Consensus       110 vI~ITGT--nGKTTt~~~l~~iL~~  132 (472)
                      +|||+|.  .||||++..|...|..
T Consensus         1 iIgI~G~sgsGKTT~a~~L~~~l~~   25 (198)
T cd02023           1 IIGIAGGSGSGKTTVAEEIIEQLGN   25 (198)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHCC
T ss_conf             9898899988599999999998099


No 93 
>PRK13764 ATPase; Provisional
Probab=82.93  E-value=1.1  Score=23.84  Aligned_cols=76  Identities=25%  Similarity=0.373  Sum_probs=47.4

Q ss_pred             CCCEEEEECC--CCCCHHHHHHHHHHHHHHCCCCCHHHHHCCCCCCCHHCCCCC-CCHHHHHCCCCCCCCCCCCCCCCCC
Q ss_conf             9939998303--654201233467777520112221221101457410001232-2144430156644332112122323
Q gi|254781101|r  107 KATIIAITGS--VGKTTTKEMLTIALSSIKKTYACIGSYNNHIGVPLTLARMPV-DVDFGIFELGMSHLGEIRFLTHLVR  183 (472)
Q Consensus       107 ~~~vI~ITGT--nGKTTt~~~l~~iL~~~~~~~~t~gn~Nn~iGvpltll~~~~-~~~~~V~E~g~~~~gei~~L~~i~~  183 (472)
                      +..=|=|.|+  .||||-..-++..|...+++++|..+       |-- +++++ =++|+-+|-+|...+||--   +++
T Consensus       258 ~a~GilIaG~PGaGKsTfaqalA~~~~~~g~iVKTmEs-------PRD-l~v~~~iTQy~~l~g~~e~t~diLl---LvR  326 (605)
T PRK13764        258 RAEGILIAGAPGAGKSTFAQALAEFYADMGKIVKTMES-------PRD-LQVPPEITQYTPLEGSMEETADILL---LVR  326 (605)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEECCC-------CCC-CCCCCCCCEECCCCCCHHHHEEEEE---EEC
T ss_conf             36649997799997789999999999847978983248-------623-6689542052435688777300678---854


Q ss_pred             CCEEEEEEEC
Q ss_conf             2202555312
Q gi|254781101|r  184 PHIAVITTIA  193 (472)
Q Consensus       184 P~iaiiTNI~  193 (472)
                      ||+.|+--+-
T Consensus       327 PDytifDE~R  336 (605)
T PRK13764        327 PDYTIFDEMR  336 (605)
T ss_pred             CCCEEEEEHH
T ss_conf             8826640020


No 94 
>PRK01906 tetraacyldisaccharide 4'-kinase; Provisional
Probab=82.71  E-value=1.2  Score=23.61  Aligned_cols=31  Identities=26%  Similarity=0.284  Sum_probs=26.8

Q ss_pred             CCCCCEEEE----ECCCCCCHHHHHHHHHHHHHHC
Q ss_conf             069939998----3036542012334677775201
Q gi|254781101|r  105 RSKATIIAI----TGSVGKTTTKEMLTIALSSIKK  135 (472)
Q Consensus       105 ~~~~~vI~I----TGTnGKTTt~~~l~~iL~~~~~  135 (472)
                      +++.|||.|    .|-.|||-++.+++..|++.|.
T Consensus        53 ~~~vPVI~VGNitvGGTGKTP~vi~L~~~L~~~G~   87 (339)
T PRK01906         53 DVGVPVVVVGNVTVGGTGKTPTVIALVDALRAAGF   87 (339)
T ss_pred             CCCCCEEEECCEEECCCCHHHHHHHHHHHHHHCCC
T ss_conf             48999999868876887577999999999997699


No 95 
>pfam03308 ArgK ArgK protein. The ArgK protein acts as an ATPase enzyme and as a kinase, and phosphorylates periplasmic binding proteins involved in the LAO (lysine, arginine, ornithine)/AO transport systems.
Probab=82.69  E-value=2.3  Score=21.61  Aligned_cols=31  Identities=32%  Similarity=0.392  Sum_probs=22.8

Q ss_pred             CCCEEEEECC--CCCCHHHHHHHHHHHHHHCCC
Q ss_conf             9939998303--654201233467777520112
Q gi|254781101|r  107 KATIIAITGS--VGKTTTKEMLTIALSSIKKTY  137 (472)
Q Consensus       107 ~~~vI~ITGT--nGKTTt~~~l~~iL~~~~~~~  137 (472)
                      +..+|||||+  .||+|..+-+...|...++.+
T Consensus        28 ~a~~iGiTG~PGaGKStli~~l~~~~~~~g~~v   60 (267)
T pfam03308        28 RAHRVGITGVPGAGKSTLIEALGMELRRRGHRV   60 (267)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHCCCEE
T ss_conf             955998768998879999999999999689868


No 96 
>pfam00142 Fer4_NifH 4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family.
Probab=82.68  E-value=0.91  Score=24.31  Aligned_cols=29  Identities=38%  Similarity=0.494  Sum_probs=24.2

Q ss_pred             CEEEEEC--CCCCCHHHHHHHHHHHHHHCCC
Q ss_conf             3999830--3654201233467777520112
Q gi|254781101|r  109 TIIAITG--SVGKTTTKEMLTIALSSIKKTY  137 (472)
Q Consensus       109 ~vI~ITG--TnGKTTt~~~l~~iL~~~~~~~  137 (472)
                      ++|||+|  -.|||||+-=|+..|.+.|+.+
T Consensus         1 r~iai~GKGGVGKTTtsvNLA~aLA~~GkrV   31 (269)
T pfam00142         1 RKIAIYGKGGIGKSTTSQNTSAALAEMGKKV   31 (269)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHCCCEE
T ss_conf             9589989997688999999999999879909


No 97 
>COG3954 PrkB Phosphoribulokinase [Energy production and conversion]
Probab=82.64  E-value=1.1  Score=23.70  Aligned_cols=28  Identities=36%  Similarity=0.498  Sum_probs=19.4

Q ss_pred             CCCCEEEEECCCCC--CHHHHHHHHHHHHH
Q ss_conf             69939998303654--20123346777752
Q gi|254781101|r  106 SKATIIAITGSVGK--TTTKEMLTIALSSI  133 (472)
Q Consensus       106 ~~~~vI~ITGTnGK--TTt~~~l~~iL~~~  133 (472)
                      .+.|+|+||||.|-  |||+.-...|+++.
T Consensus         3 aKhPiIavTGSSGAGTTTts~aFrKiF~~~   32 (289)
T COG3954           3 AKHPVIAVTGSSGAGTTTTSLAFRKIFAQL   32 (289)
T ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHHHC
T ss_conf             778668884478887544899999999851


No 98 
>pfam00485 PRK Phosphoribulokinase / Uridine kinase family. In Arabidopsis the region carries two binding domains, a phosphoribosylpyrophosphate-binding domain and, at the very C-terminus, a uracil-binding domain.
Probab=82.43  E-value=0.58  Score=25.61  Aligned_cols=25  Identities=32%  Similarity=0.442  Sum_probs=21.1

Q ss_pred             EEEEECC--CCCCHHHHHHHHHHHHHH
Q ss_conf             9998303--654201233467777520
Q gi|254781101|r  110 IIAITGS--VGKTTTKEMLTIALSSIK  134 (472)
Q Consensus       110 vI~ITGT--nGKTTt~~~l~~iL~~~~  134 (472)
                      +|||+|.  .||||.+..|...|...+
T Consensus         1 iIgIaG~SgSGKTT~a~~L~~~l~~~~   27 (196)
T pfam00485         1 IIGVAGSSGAGKTTVARTFVSIFGREG   27 (196)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHCCCC
T ss_conf             989989985719999999999966058


No 99 
>PRK07003 DNA polymerase III subunits gamma and tau; Validated
Probab=82.05  E-value=0.4  Score=26.65  Aligned_cols=53  Identities=11%  Similarity=0.135  Sum_probs=30.5

Q ss_pred             HHHHHHHCCEEECCCCCCEEEEEEEECCCCCCCCE--EEECCCCCCCHHHHHHHHHHC
Q ss_conf             88998727999526887147467740222378988--897168874768889999986
Q gi|254781101|r    8 HDLLQAIQGHSIGIVPQGFVNGISIDSRSIAPQEA--FFAIKGPHYDGHDFILHAVQK   63 (472)
Q Consensus         8 ~~l~~~~~g~~~~~~~~~~i~~i~~dSr~v~~g~l--Fval~g~~~DGh~~i~~A~~~   63 (472)
                      +-+++.++-   .......-.|.|..-+.|..|..  ++-+.+....|-+-+.+.+++
T Consensus        56 Ri~Ak~lnC---~~~~~~~pcg~C~~C~~i~~g~~~d~iEiDaAS~~~vd~~r~l~~~  110 (816)
T PRK07003         56 RIFAKALNC---ETGVTSQPCGVCRACREIDEGRFVDYVEMDAASNRGVDEMAALLER  110 (816)
T ss_pred             HHHHHHHCC---CCCCCCCCCCCCHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHH
T ss_conf             999998678---9999989787755578775588775478635543576899999986


No 100
>PRK10818 cell division inhibitor MinD; Provisional
Probab=82.00  E-value=1  Score=24.00  Aligned_cols=29  Identities=41%  Similarity=0.583  Sum_probs=24.1

Q ss_pred             CCEEEEE---CCCCCCHHHHHHHHHHHHHHCC
Q ss_conf             9399983---0365420123346777752011
Q gi|254781101|r  108 ATIIAIT---GSVGKTTTKEMLTIALSSIKKT  136 (472)
Q Consensus       108 ~~vI~IT---GTnGKTTt~~~l~~iL~~~~~~  136 (472)
                      .+||+|+   |-.|||||+--|+..|...|+.
T Consensus         2 ~rvIaV~s~KGGVGKTT~avNLA~aLA~~G~k   33 (270)
T PRK10818          2 ARIIVVTSGKGGVGKTTSSAAIATGLAQKGKK   33 (270)
T ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHCCCC
T ss_conf             74999978999841899999999999977996


No 101
>TIGR03172 probable selenium-dependent hydroxylase accessory protein YqeC. This uncharacterized protein family includes YqeC from Escherichia coli. A phylogenetic profiling analysis shows correlation with SelD, the selenium donor protein, even in species where SelD contributes to neither selenocysteine nor selenouridine biosynthesis. Instead, this family, and families TIGR03309 and TIGR03310 appear to mark selenium-dependent molybdenum hydroxylase maturation systems.
Probab=81.70  E-value=0.79  Score=24.70  Aligned_cols=26  Identities=31%  Similarity=0.293  Sum_probs=23.6

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHC
Q ss_conf             99983036542012334677775201
Q gi|254781101|r  110 IIAITGSVGKTTTKEMLTIALSSIKK  135 (472)
Q Consensus       110 vI~ITGTnGKTTt~~~l~~iL~~~~~  135 (472)
                      ||+++|.=||||+-..|+.-|+..|+
T Consensus         1 VIs~VGaGGKTS~m~~LA~e~~~~G~   26 (232)
T TIGR03172         1 VIAFVGAGGKTSTMFWLAAEYRKEGY   26 (232)
T ss_pred             CEEEECCCCHHHHHHHHHHHHHHCCC
T ss_conf             98998898799999999999987699


No 102
>COG2894 MinD Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]
Probab=81.53  E-value=1.2  Score=23.42  Aligned_cols=31  Identities=45%  Similarity=0.584  Sum_probs=24.7

Q ss_pred             CCEEEEE---CCCCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             9399983---036542012334677775201122
Q gi|254781101|r  108 ATIIAIT---GSVGKTTTKEMLTIALSSIKKTYA  138 (472)
Q Consensus       108 ~~vI~IT---GTnGKTTt~~~l~~iL~~~~~~~~  138 (472)
                      .++|-||   |-.|||||+.-++.-|...|+.+.
T Consensus         2 ~~iIVvTSGKGGVGKTTttAnig~aLA~~GkKv~   35 (272)
T COG2894           2 ARIIVVTSGKGGVGKTTTTANIGTALAQLGKKVV   35 (272)
T ss_pred             CEEEEEECCCCCCCCCCHHHHHHHHHHHCCCEEE
T ss_conf             6499994488876743106778999997398599


No 103
>COG3367 Uncharacterized conserved protein [Function unknown]
Probab=81.11  E-value=1  Score=24.03  Aligned_cols=100  Identities=17%  Similarity=0.188  Sum_probs=56.8

Q ss_pred             CEEEE--CCC-CCCCHH-HHHHHHHHCCCEEE------EECCCCC-CCCCCCCCCEEEECCHHHHHHHHHHHHHHCCCCC
Q ss_conf             88897--168-874768-88999998698899------9855212-4554469728995998999999999998306993
Q gi|254781101|r   41 EAFFA--IKG-PHYDGH-DFILHAVQKGAGLV------VVNTDMV-ASIGSLSIPVFGVDDVLGALNKLAVAARLRSKAT  109 (472)
Q Consensus        41 ~lFva--l~g-~~~DGh-~~i~~A~~~Ga~~~------i~~~~~~-~~~~~~~~~~i~v~d~~~al~~la~~~~~~~~~~  109 (472)
                      .+-|+  .+| .-.+-. .|+.+|+++|...+      +.+.|.. ......+..+.-|.++..-|..+.----.+-+.+
T Consensus        70 ~liIgia~~gG~~~~~~~~~i~eAl~~G~nVvsglh~~ls~dp~~~k~A~~~G~rl~dvR~p~~~l~~~~tG~~~k~~a~  149 (339)
T COG3367          70 ALIIGIAPPGGVLPESWREYIVEALEAGMNVVSGLHSFLSDDPEFVKLAERTGVRLDDVRKPPLDLEYLCTGMARKVDAK  149 (339)
T ss_pred             EEEEEEECCCCCCCHHHHHHHHHHHHHCCHHHHHHHHHHHCCHHHHHHHHHCCCEEEEECCCCCCHHHHCCCCCCCCCCC
T ss_conf             48999615888575788999999998373166555777611868999998719756762267420334304751146776


Q ss_pred             EEEEECC---CCCCHHHHHHHHHHHHHHCCCCCH
Q ss_conf             9998303---654201233467777520112221
Q gi|254781101|r  110 IIAITGS---VGKTTTKEMLTIALSSIKKTYACI  140 (472)
Q Consensus       110 vI~ITGT---nGKTTt~~~l~~iL~~~~~~~~t~  140 (472)
                      +|.+-||   .||-||+--|...++..|......
T Consensus       150 ~V~vvGTd~~vGKrTTa~~L~~~~~e~G~~a~fv  183 (339)
T COG3367         150 VVLVVGTDCAVGKRTTALELREAAREEGIKAGFV  183 (339)
T ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCEE
T ss_conf             8999335632104388999999999709863157


No 104
>PRK07429 phosphoribulokinase; Provisional
Probab=81.09  E-value=0.92  Score=24.27  Aligned_cols=28  Identities=25%  Similarity=0.334  Sum_probs=22.8

Q ss_pred             CCCEEEEECC--CCCCHHHHHHHHHHHHHH
Q ss_conf             9939998303--654201233467777520
Q gi|254781101|r  107 KATIIAITGS--VGKTTTKEMLTIALSSIK  134 (472)
Q Consensus       107 ~~~vI~ITGT--nGKTTt~~~l~~iL~~~~  134 (472)
                      ++-+|||+|.  .||||.+.-|..+|....
T Consensus         7 rP~IIGIAGgSGSGKTTv~r~I~~~fg~~~   36 (331)
T PRK07429          7 RPVIIGVAGDSGCGKSTFLRRLADLFGEEL   36 (331)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHCCCC
T ss_conf             998999857887789999999999838887


No 105
>PRK11545 gntK gluconate kinase 1; Provisional
Probab=81.04  E-value=0.64  Score=25.30  Aligned_cols=28  Identities=18%  Similarity=0.256  Sum_probs=18.0

Q ss_pred             CCCEEEEECC--CCCCHHHHHHHHHHHHHH
Q ss_conf             9939998303--654201233467777520
Q gi|254781101|r  107 KATIIAITGS--VGKTTTKEMLTIALSSIK  134 (472)
Q Consensus       107 ~~~vI~ITGT--nGKTTt~~~l~~iL~~~~  134 (472)
                      +..+|-|.|-  .||||+...|++-|.-.+
T Consensus         7 ~~~iiVVMGVsGsGKSTig~~LA~~l~~~f   36 (177)
T PRK11545          7 DHHIYVLMGVSGSGKSAVASAVAHQLHAAF   36 (177)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHCCCE
T ss_conf             875999984798999999999999819985


No 106
>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=81.02  E-value=4  Score=20.05  Aligned_cols=67  Identities=28%  Similarity=0.404  Sum_probs=28.7

Q ss_pred             CEEEECCCC-CCCHHHHHHHHHHCCCEEEEECCCCCCCCCCCCCCEEEE-CCHHHHHHHHHHHHHHCCCCCEEEEECC--
Q ss_conf             888971688-747688899999869889998552124554469728995-9989999999999983069939998303--
Q gi|254781101|r   41 EAFFAIKGP-HYDGHDFILHAVQKGAGLVVVNTDMVASIGSLSIPVFGV-DDVLGALNKLAVAARLRSKATIIAITGS--  116 (472)
Q Consensus        41 ~lFval~g~-~~DGh~~i~~A~~~Ga~~~i~~~~~~~~~~~~~~~~i~v-~d~~~al~~la~~~~~~~~~~vI~ITGT--  116 (472)
                      |.=+.++|. ||=+|-|.    ++|+.+.+-..      .+..+|-+.- .=|+..|.++|..    ..+ .|=|||-  
T Consensus        73 Dfs~~~~~~~RfRvN~f~----QRg~~a~vlR~------ip~~Ip~fe~LGLP~~v~~~~a~~----~~G-LiLVTGPTG  137 (350)
T TIGR01420        73 DFSFSLPGLARFRVNAFK----QRGGVALVLRL------IPSKIPTFEELGLPRPVLRELAER----PRG-LILVTGPTG  137 (350)
T ss_pred             CEEEEECCCCEEEEHHHH----HCCHHHHHHHH------CCCCCCCHHHCCCCHHHHHHHHHC----CCC-CEEEECCCC
T ss_conf             446630673221220323----50006423231------153462166637987899999836----699-389876889


Q ss_pred             CCCCHH
Q ss_conf             654201
Q gi|254781101|r  117 VGKTTT  122 (472)
Q Consensus       117 nGKTTt  122 (472)
                      .|||||
T Consensus       138 SGKSTT  143 (350)
T TIGR01420       138 SGKSTT  143 (350)
T ss_pred             CCHHHH
T ss_conf             867899


No 107
>TIGR01188 drrA daunorubicin resistance ABC transporter, ATP-binding protein; InterPro: IPR005894   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 family contains the daunorubicin resistance ABC transporter, ATP binding subunit in bacteria and archaea. This model is restricted in its scope to preferentially recognize the ATP binding subunit associated with effux of the drug, daunorubicin. In other words it functions as an ATP dependent antiporter. .
Probab=80.79  E-value=0.75  Score=24.88  Aligned_cols=29  Identities=34%  Similarity=0.450  Sum_probs=24.7

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHHHH
Q ss_conf             699399983036--54201233467777520
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSSIK  134 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~~~  134 (472)
                      ..+.|+|+=|=|  |||||..||..+|+...
T Consensus        19 ~~G~vfGfLGPNGAGKTTti~mLtTll~P~s   49 (343)
T TIGR01188        19 REGEVFGFLGPNGAGKTTTIRMLTTLLKPTS   49 (343)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHCCCCCCCC
T ss_conf             0624899768799851335634102557998


No 108
>PRK00081 coaE dephospho-CoA kinase; Reviewed
Probab=80.66  E-value=0.91  Score=24.29  Aligned_cols=21  Identities=33%  Similarity=0.548  Sum_probs=16.4

Q ss_pred             CCEEEEECC--CCCCHHHHHHHH
Q ss_conf             939998303--654201233467
Q gi|254781101|r  108 ATIIAITGS--VGKTTTKEMLTI  128 (472)
Q Consensus       108 ~~vI~ITGT--nGKTTt~~~l~~  128 (472)
                      ..+|||||.  .||||+..++..
T Consensus         2 m~~IgiTG~igsGKStv~~~l~~   24 (199)
T PRK00081          2 MLIIGLTGGIGSGKSTVANIFAE   24 (199)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH
T ss_conf             78999578887779999999998


No 109
>PRK09270 frcK putative fructose transport system kinase; Reviewed
Probab=80.53  E-value=2.6  Score=21.34  Aligned_cols=28  Identities=39%  Similarity=0.497  Sum_probs=22.8

Q ss_pred             CCCEEEEECC--CCCCHHHHHHHHHHHHHH
Q ss_conf             9939998303--654201233467777520
Q gi|254781101|r  107 KATIIAITGS--VGKTTTKEMLTIALSSIK  134 (472)
Q Consensus       107 ~~~vI~ITGT--nGKTTt~~~l~~iL~~~~  134 (472)
                      +..+|||+|.  .||||+++.+...|+..+
T Consensus        33 rR~lIgIaG~pGSGKSTlA~~l~~~L~~~~   62 (230)
T PRK09270         33 RRTVVGIAGPPGAGKSTLAETLWEALSQQG   62 (230)
T ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHHHCC
T ss_conf             718999989998899999999999986237


No 110
>PRK06696 uridine kinase; Validated
Probab=80.38  E-value=3.1  Score=20.79  Aligned_cols=43  Identities=21%  Similarity=0.213  Sum_probs=30.7

Q ss_pred             HHHHHHHHHHHHC-C-CCCEEEEEC--CCCCCHHHHHHHHHHHHHHC
Q ss_conf             9999999999830-6-993999830--36542012334677775201
Q gi|254781101|r   93 GALNKLAVAARLR-S-KATIIAITG--SVGKTTTKEMLTIALSSIKK  135 (472)
Q Consensus        93 ~al~~la~~~~~~-~-~~~vI~ITG--TnGKTTt~~~l~~iL~~~~~  135 (472)
                      +.+.+||...... + ..-+|||.|  -.||||.+.-|+..|.+.|.
T Consensus         9 ~~~~~~~~~i~~~~p~rpl~VgIdG~~gSGKTTlA~~La~~L~~~G~   55 (227)
T PRK06696          9 QVVKEIANHILTLNLTRPLRVAIDGITASGKTTFANELAEEIKKRGR   55 (227)
T ss_pred             HHHHHHHHHHHHCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCC
T ss_conf             89999999998359998689997789987879999999999974699


No 111
>PRK05648 DNA polymerase III subunits gamma and tau; Reviewed
Probab=80.19  E-value=0.62  Score=25.42  Aligned_cols=12  Identities=25%  Similarity=0.495  Sum_probs=5.6

Q ss_pred             HHHHHHHHHHCC
Q ss_conf             999999998505
Q gi|254781101|r  458 YRLINLLLEEFP  469 (472)
Q Consensus       458 e~iv~~L~~~~~  469 (472)
                      +..|+.|+++|-
T Consensus       676 DP~VQ~L~q~Fg  687 (705)
T PRK05648        676 DPLIQQMIQQFG  687 (705)
T ss_pred             CHHHHHHHHHCC
T ss_conf             989999999819


No 112
>CHL00175 minD septum-site determining protein; Validated
Probab=79.87  E-value=1.3  Score=23.19  Aligned_cols=30  Identities=40%  Similarity=0.546  Sum_probs=24.4

Q ss_pred             CCEEEEE---CCCCCCHHHHHHHHHHHHHHCCC
Q ss_conf             9399983---03654201233467777520112
Q gi|254781101|r  108 ATIIAIT---GSVGKTTTKEMLTIALSSIKKTY  137 (472)
Q Consensus       108 ~~vI~IT---GTnGKTTt~~~l~~iL~~~~~~~  137 (472)
                      .+||+|+   |-.|||||+.-++..|.+.|+.+
T Consensus        13 ~kiIaV~s~KGGVGKTT~a~NLa~aLA~~G~kV   45 (279)
T CHL00175         13 TRIIVITSGKGGVGKTTTTANLGMSIARLGYRV   45 (279)
T ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHCCCCE
T ss_conf             869999748998448999999999999789988


No 113
>PRK08770 DNA polymerase III subunits gamma and tau; Validated
Probab=79.73  E-value=0.74  Score=24.90  Aligned_cols=12  Identities=17%  Similarity=0.246  Sum_probs=6.5

Q ss_pred             HHHHHHHHHHCC
Q ss_conf             999999998505
Q gi|254781101|r  458 YRLINLLLEEFP  469 (472)
Q Consensus       458 e~iv~~L~~~~~  469 (472)
                      +-+|+.|+++|-
T Consensus       639 DP~VQ~L~q~Fg  650 (663)
T PRK08770        639 DPTVQLLIQQQG  650 (663)
T ss_pred             CHHHHHHHHHHC
T ss_conf             989999999729


No 114
>COG0769 MurE UDP-N-acetylmuramyl tripeptide synthase [Cell envelope biogenesis, outer membrane]
Probab=79.66  E-value=0.11  Score=30.26  Aligned_cols=95  Identities=22%  Similarity=0.196  Sum_probs=53.5

Q ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHHHH-HCCCCCHHHHHCCCCCCCHHC---C-CCCCCHHHHHCC-CCCCCCCCCCC
Q ss_conf             06993999830365420123346777752-011222122110145741000---1-232214443015-66443321121
Q gi|254781101|r  105 RSKATIIAITGSVGKTTTKEMLTIALSSI-KKTYACIGSYNNHIGVPLTLA---R-MPVDVDFGIFEL-GMSHLGEIRFL  178 (472)
Q Consensus       105 ~~~~~vI~ITGTnGKTTt~~~l~~iL~~~-~~~~~t~gn~Nn~iGvpltll---~-~~~~~~~~V~E~-g~~~~gei~~L  178 (472)
                      ....++|.|+|++||+++..+....+.+. .++....|. |..=++-..+.   + ....+.+++.|. +++ +|... -
T Consensus        61 ~~~~~vi~V~~~~~~~~~~a~~~y~~ps~~l~vigvTGT-NgKTt~t~~~~~~~~~~g~~~~~~gT~g~~~~-~~~~~-~  137 (475)
T COG0769          61 EAGVPVIVVTGTNGKLTTLALAFYGLPSGKLKVIGVTGT-NGKTTTTSLLAQILKKLGKKTALIGTEGDELS-PGILE-P  137 (475)
T ss_pred             CCCCCEEEECCCHHHHHHHHHHHCCCCCCCCEEEEECCC-CCHHHHHHHHHHHHHHCCCCEEEEEEEEEECC-CCCCC-C
T ss_conf             567877998685377788899852386578518986387-85799999999998862982589997766326-88634-5


Q ss_pred             CCCCCCCEEEEEEECCCHHHHHHH
Q ss_conf             223232202555312101234445
Q gi|254781101|r  179 THLVRPHIAVITTIAPAHLSNFSG  202 (472)
Q Consensus       179 ~~i~~P~iaiiTNI~~dHld~~~s  202 (472)
                      +....|+.-.++|+..+++|..++
T Consensus       138 ~~~tTP~~~~l~~~~~~~~d~~~e  161 (475)
T COG0769         138 TGLTTPEALDLQNLLRDLLDRGAE  161 (475)
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCE
T ss_conf             667892178999999999973880


No 115
>cd03114 ArgK-like The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and ornithine (AO system) and lysine, arginine and ornithine (LAO) transport systems.
Probab=79.36  E-value=0.96  Score=24.15  Aligned_cols=27  Identities=41%  Similarity=0.517  Sum_probs=20.5

Q ss_pred             EEEEECC--CCCCHHHHHHHHHHHHHHCC
Q ss_conf             9998303--65420123346777752011
Q gi|254781101|r  110 IIAITGS--VGKTTTKEMLTIALSSIKKT  136 (472)
Q Consensus       110 vI~ITGT--nGKTTt~~~l~~iL~~~~~~  136 (472)
                      ||||||+  .||||..+-+...|...++.
T Consensus         1 viGitG~pGaGKStLi~~l~~~~~~~g~~   29 (148)
T cd03114           1 VIGITGVPGAGKSTLIDALITALRARGKR   29 (148)
T ss_pred             CEEECCCCCCCHHHHHHHHHHHHHHCCCE
T ss_conf             97625899787899999999999978983


No 116
>TIGR03450 mycothiol_INO1 inositol 1-phosphate synthase, Actinobacterial type. This enzyme, inositol 1-phosphate synthase as found in Actinobacteria, produces an essential precursor for several different products, including mycothiol, which is a glutathione analog, and phosphatidylinositol, which is a phospholipid.
Probab=78.55  E-value=4.8  Score=19.54  Aligned_cols=11  Identities=9%  Similarity=0.516  Sum_probs=5.1

Q ss_pred             EEEEEECCCCC
Q ss_conf             46774022237
Q gi|254781101|r   28 NGISIDSRSIA   38 (472)
Q Consensus        28 ~~i~~dSr~v~   38 (472)
                      .++-.|.|+|.
T Consensus        51 aafDVD~~KVG   61 (351)
T TIGR03450        51 AAFDVDAKKVG   61 (351)
T ss_pred             EEEECCCCCCC
T ss_conf             99732704047


No 117
>PRK12323 DNA polymerase III subunits gamma and tau; Provisional
Probab=78.47  E-value=0.67  Score=25.20  Aligned_cols=36  Identities=11%  Similarity=0.191  Sum_probs=18.2

Q ss_pred             EEEEEECCCCCCCCE--EEECCCCCCCHHHHHHHHHHC
Q ss_conf             467740222378988--897168874768889999986
Q gi|254781101|r   28 NGISIDSRSIAPQEA--FFAIKGPHYDGHDFILHAVQK   63 (472)
Q Consensus        28 ~~i~~dSr~v~~g~l--Fval~g~~~DGh~~i~~A~~~   63 (472)
                      .|.|..-+.|..|.-  ++=+.+....|-+-+.+.+++
T Consensus        78 cg~C~~C~~i~~g~~~d~~EiDaas~~~v~~~r~l~~~  115 (721)
T PRK12323         78 CGQCRACTEIDAGRFVDYIEMDAASNRGVDEMAQLLDQ  115 (721)
T ss_pred             CCCCHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHH
T ss_conf             87765468775689876477436767888999999985


No 118
>pfam07755 DUF1611 Protein of unknown function (DUF1611). This region is found in a number of hypothetical bacterial and archaeal proteins. The region is approximately 350 residues long. A member of this family is thought to associate with another subunit to form an H+-transporting ATPase, but no evidence has been found to support this.
Probab=78.38  E-value=1.2  Score=23.62  Aligned_cols=98  Identities=21%  Similarity=0.229  Sum_probs=55.2

Q ss_pred             CCCCEEE--ECCCCCCCHH--HHHHHHHHCCCEEE------EECCCCC-CCCCCCCCCEEEECCHHHHHHHHHHHHHHCC
Q ss_conf             7898889--7168874768--88999998698899------9855212-4554469728995998999999999998306
Q gi|254781101|r   38 APQEAFF--AIKGPHYDGH--DFILHAVQKGAGLV------VVNTDMV-ASIGSLSIPVFGVDDVLGALNKLAVAARLRS  106 (472)
Q Consensus        38 ~~g~lFv--al~g~~~DGh--~~i~~A~~~Ga~~~------i~~~~~~-~~~~~~~~~~i~v~d~~~al~~la~~~~~~~  106 (472)
                      .+..+.+  |-.|-...-+  ..|.+|+++|-..+      +.+.+.. ......++.++-|..+...+ .++.......
T Consensus        33 g~~~liiGiA~~GG~lp~~w~~~i~~Ai~~GldIvsGLH~~L~ddp~l~~~A~~~g~~i~DvR~p~~~~-~~~~g~~~~~  111 (302)
T pfam07755        33 GADTLIIGIAPSGGVLPEAWREVLLEALEAGLDVVSGLHEFLSDDPELAAAAKKHGVQIIDVRKPPVDL-PVATGKAREV  111 (302)
T ss_pred             CCCEEEEEECCCCCCCCHHHHHHHHHHHHCCCCEEHHHHHHHHCCHHHHHHHHHCCCEEEEECCCCCCC-CCCCCCCCCC
T ss_conf             999899974168884898999999999982892623357775148989999998699799915899988-6576840147


Q ss_pred             CCCEEEEECC---CCCCHHHHHHHHHHHHHHCC
Q ss_conf             9939998303---65420123346777752011
Q gi|254781101|r  107 KATIIAITGS---VGKTTTKEMLTIALSSIKKT  136 (472)
Q Consensus       107 ~~~vI~ITGT---nGKTTt~~~l~~iL~~~~~~  136 (472)
                      +.++|.+-||   .||-||+-.|.+-|++.|..
T Consensus       112 ~~~rvl~vGTDcavGK~tTal~l~~~l~~~Gi~  144 (302)
T pfam07755       112 KAKRVLTVGTDCAVGKMTTALELERALRERGLN  144 (302)
T ss_pred             CCCEEEEEECCCCHHHHHHHHHHHHHHHHCCCC
T ss_conf             987899960573340789999999999977998


No 119
>PTZ00145 phosphoribosylpyrophosphate synthetase; Provisional
Probab=78.37  E-value=4.8  Score=19.50  Aligned_cols=73  Identities=14%  Similarity=0.155  Sum_probs=31.4

Q ss_pred             CCCCCCCEECCCCC--CEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCC
Q ss_conf             44331010003653--1133100025653210125777874111026871388512354171058999999999986499
Q gi|254781101|r  324 EGRGKRYRCALNQG--FFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNI  401 (472)
Q Consensus       324 ~GR~~~~~~~~~~~--~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~  401 (472)
                      ++..+.+.+.++..  .+.++||== .+-.++..|.+.|+..   + -++|.+...=   |-.+..-    .+.+....+
T Consensus       325 ~neve~m~iIGDVkGK~~IIVDDmI-DTgGTL~~AA~~Lke~---G-Ak~VyA~aTH---GVfSg~A----ierI~~S~I  392 (443)
T PTZ00145        325 PNEIEKMDLVGNVYDSDVIIVDDMI-DTSGTLCEAAKQLKKH---G-ARRVFAFATH---GLFSGPA----IDRIEKSPL  392 (443)
T ss_pred             CCCEEEEEEEECCCCCEEEEECCCC-CCCHHHHHHHHHHHHC---C-CCEEEEEEEC---CCCCHHH----HHHHHCCCC
T ss_conf             9936653557502798789967743-4556799999999967---9-9879999977---3078548----989754899


Q ss_pred             CEEEEEC
Q ss_conf             8999988
Q gi|254781101|r  402 SHVWLSG  408 (472)
Q Consensus       402 d~v~~~G  408 (472)
                      +.|++.-
T Consensus       393 ~evVVTD  399 (443)
T PTZ00145        393 EEVVVTD  399 (443)
T ss_pred             CEEEECC
T ss_conf             7899878


No 120
>PRK10751 molybdopterin-guanine dinucleotide biosynthesis protein B; Provisional
Probab=77.95  E-value=1.6  Score=22.76  Aligned_cols=34  Identities=29%  Similarity=0.214  Sum_probs=26.0

Q ss_pred             CCEEEEECC--CCCCHHHHHHHHHHHHHHCCCCCHH
Q ss_conf             939998303--6542012334677775201122212
Q gi|254781101|r  108 ATIIAITGS--VGKTTTKEMLTIALSSIKKTYACIG  141 (472)
Q Consensus       108 ~~vI~ITGT--nGKTTt~~~l~~iL~~~~~~~~t~g  141 (472)
                      .|||||+|.  .||||..+=+-..|...|-.+++.+
T Consensus         2 ~Pii~ivG~s~SGKTTLi~kli~~l~~~G~rV~~IK   37 (170)
T PRK10751          2 IPLLAIAAWSGTGKTTLLKKLIPALCARGIRPGLIK   37 (170)
T ss_pred             CCEEEEEECCCCCHHHHHHHHHHHHHHCCCEEEEEE
T ss_conf             877999946999999999999999998798499994


No 121
>PRK10799 putative hydrolase-oxidase; Provisional
Probab=77.91  E-value=4.7  Score=19.57  Aligned_cols=64  Identities=17%  Similarity=0.225  Sum_probs=49.1

Q ss_pred             CHHHHHHHHCCEEE-CCCCCCEEEEEEEECCCCCCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEECCCC
Q ss_conf             67889987279995-2688714746774022237898889716887476888999998698899985521
Q gi|254781101|r    6 TFHDLLQAIQGHSI-GIVPQGFVNGISIDSRSIAPQEAFFAIKGPHYDGHDFILHAVQKGAGLVVVNTDM   74 (472)
Q Consensus         6 ~~~~l~~~~~g~~~-~~~~~~~i~~i~~dSr~v~~g~lFval~g~~~DGh~~i~~A~~~Ga~~~i~~~~~   74 (472)
                      .++||.+.+...+- ....|+.-+|+..++|+ .-.-+.+|+.-.    -.-+++|+++||-++|+..|.
T Consensus         2 k~~El~~~l~~~l~~~~~~D~d~~GLqV~~~~-eV~kI~~alD~t----~~vi~eAi~~~aDliitHHpl   66 (247)
T PRK10799          2 KNTELEQLINEKLNSAAISDYAPNGLQVEGKE-TVQKIVTGVTAS----QALLDEAVRLQADAVIVHHGY   66 (247)
T ss_pred             CHHHHHHHHHHHCCHHHCCCCCCCEEEECCCC-CCCEEEEEECCC----HHHHHHHHHCCCCEEEECCCC
T ss_conf             58999999985679966058897645877987-511899995698----999999998599999986740


No 122
>cd02036 MinD Bacterial cell division requires the formation of a septum at mid-cell. The site is determined by the min operon products MinC, MinD and MinE. MinC is a nonspecific inhibitor of the septum protein FtsZ. MinE is the supressor of MinC. MinD plays a pivotal role, selecting the mid-cell over other sites through the activation and regulation of MinC and MinE. MinD is a membrane-associated ATPase, related to nitrogenase iron protein. More distantly related proteins include flagellar biosynthesis proteins and ParA chromosome partitioning proteins. MinD is a monomer.
Probab=77.82  E-value=1.2  Score=23.47  Aligned_cols=27  Identities=44%  Similarity=0.594  Sum_probs=21.9

Q ss_pred             EEEEE---CCCCCCHHHHHHHHHHHHHHCC
Q ss_conf             99983---0365420123346777752011
Q gi|254781101|r  110 IIAIT---GSVGKTTTKEMLTIALSSIKKT  136 (472)
Q Consensus       110 vI~IT---GTnGKTTt~~~l~~iL~~~~~~  136 (472)
                      ||+|.   |-.||||++.-|+..|.+.|+.
T Consensus         1 iIav~s~KGGVGKTT~a~NLA~aLa~~g~~   30 (179)
T cd02036           1 VIVVTSGKGGVGKTTTTANLGTALAQLGYK   30 (179)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHHHCCCC
T ss_conf             989973999870999999999999977991


No 123
>PRK06872 DNA polymerase III subunits gamma and tau; Provisional
Probab=77.80  E-value=0.99  Score=24.06  Aligned_cols=36  Identities=8%  Similarity=0.076  Sum_probs=15.0

Q ss_pred             EEEEEECCCCCCCCE--EEECCCCCCCHHHHHHHHHHC
Q ss_conf             467740222378988--897168874768889999986
Q gi|254781101|r   28 NGISIDSRSIAPQEA--FFAIKGPHYDGHDFILHAVQK   63 (472)
Q Consensus        28 ~~i~~dSr~v~~g~l--Fval~g~~~DGh~~i~~A~~~   63 (472)
                      .|.|..-+.+..|.-  ++-+.+....|-+-+.+.+++
T Consensus        73 cg~c~~c~~i~~g~~~d~~eidaas~~~v~~~r~l~~~  110 (696)
T PRK06872         73 CGECENCKAIEEGNFIDLIEIDAASRTKVEDTRELLDN  110 (696)
T ss_pred             CCCCHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHH
T ss_conf             88862257674478775467505655788999999984


No 124
>PRK11670 putative ATPase; Provisional
Probab=77.61  E-value=1.6  Score=22.62  Aligned_cols=29  Identities=38%  Similarity=0.547  Sum_probs=24.8

Q ss_pred             CEEEEE---CCCCCCHHHHHHHHHHHHHHCCC
Q ss_conf             399983---03654201233467777520112
Q gi|254781101|r  109 TIIAIT---GSVGKTTTKEMLTIALSSIKKTY  137 (472)
Q Consensus       109 ~vI~IT---GTnGKTTt~~~l~~iL~~~~~~~  137 (472)
                      .||+|+   |-.|||||+.-|+..|.+.|..+
T Consensus       108 ~vIAVaSGKGGVGKSTvavNLA~ALA~~G~kV  139 (369)
T PRK11670        108 NIIAVSSGKGGVGKSSTAVNLALALAAEGAKV  139 (369)
T ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHHCCCCE
T ss_conf             89999858998889999999999999669937


No 125
>TIGR02087 LEUD_arch 3-isopropylmalate dehydratase, small subunit; InterPro: IPR011827   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 is most closely related to the 3-isopropylmalate dehydratase IPR004431 from INTERPRO. It also includes members, which cluster with other genes of leucine biosynthesis.    The structure of the Pyrococcus horikoshii small subunit (O59393 from SWISSPROT) has recently been determined . As expected the structure of this polypeptide is similar to that of aconitase domain 4, though one alpha helix is replaced by a short loop with relatively high temperature factor values. This loop region is thought to be important for substrate recognition. Unlike other aconitase family proteins, this subunit formed a tetramer through disulphide linkages, though it is not expected to interfere with its interaction with the large subunit. These disulphide linkages would be expected to confer thermostability on the enzyme, reflecting the thermophilic lifestyle of the organism.; GO: 0003861 3-isopropylmalate dehydratase activity, 0009098 leucine biosynthetic process, 0009316 3-isopropylmalate dehydratase complex.
Probab=77.17  E-value=4.7  Score=19.60  Aligned_cols=53  Identities=19%  Similarity=0.330  Sum_probs=27.7

Q ss_pred             HHHHHHHHCCEEECCCCCCEEEEEEEECCCCCCCCEEEECCCCCCC-H--HHHHHHHHH-CCCEEEEECC
Q ss_conf             7889987279995268871474677402223789888971688747-6--888999998-6988999855
Q gi|254781101|r    7 FHDLLQAIQGHSIGIVPQGFVNGISIDSRSIAPQEAFFAIKGPHYD-G--HDFILHAVQ-KGAGLVVVNT   72 (472)
Q Consensus         7 ~~~l~~~~~g~~~~~~~~~~i~~i~~dSr~v~~g~lFval~g~~~D-G--h~~i~~A~~-~Ga~~~i~~~   72 (472)
                      .++||+..   ..+-+|+..        ++|++||+-||  |++|= |  ..=+.-|++ .|..|+|++.
T Consensus        27 ~~eLA~ha---M~g~~PeF~--------~kvr~GDviVA--GkNFGcGSSREQA~~ALK~aGv~aviA~S   83 (159)
T TIGR02087        27 PDELASHA---MEGIDPEFA--------KKVREGDVIVA--GKNFGCGSSREQAALALKAAGVAAVIAES   83 (159)
T ss_pred             HHHHHHHC---CCCCCCCHH--------HHCCCCCEEEE--CCCCCCCCCHHHHHHHHHHCCEEEEEEEE
T ss_conf             78899870---558996313--------40789978871--41647788778899999747904898520


No 126
>TIGR03371 cellulose_yhjQ cellulose synthase operon protein YhjQ. Members of this family are the YhjQ protein, found immediately upsteam of bacterial cellulose synthase (bcs) genes in a broad range of bacteria, including both copies of the bcs locus in Klebsiella pneumoniae. In several species it is seen clearly as part of the bcs operon. It is identified as a probable component of the bacterial cellulose metabolic process not only by gene location, but also by partial phylogenetic profiling, or Haft-Selengut algorithm (PMID:16930487), based on a bacterial cellulose biosynthesis genome property profile. Cellulose plays an important role in biofilm formation and structural integrity in some bacteria. Mutants in yhjQ in Escherichia coli, show altered morphology an growth, but the function of YhjQ has not yet been determined.
Probab=76.94  E-value=1.7  Score=22.56  Aligned_cols=29  Identities=38%  Similarity=0.528  Sum_probs=23.4

Q ss_pred             CCEEEEE---CCCCCCHHHHHHHHHHHHHHCC
Q ss_conf             9399983---0365420123346777752011
Q gi|254781101|r  108 ATIIAIT---GSVGKTTTKEMLTIALSSIKKT  136 (472)
Q Consensus       108 ~~vI~IT---GTnGKTTt~~~l~~iL~~~~~~  136 (472)
                      +++|+|+   |-.|||||+--|++.|.+.|+.
T Consensus         1 MkiIav~n~KGGVGKTT~avNLA~~La~~G~r   32 (246)
T TIGR03371         1 MKVIAIVGIKGGVGRTTLTAALASALKLLGEP   32 (246)
T ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHCCCC
T ss_conf             93999975999854999999999999968997


No 127
>cd02022 DPCK Dephospho-coenzyme A kinase (DPCK, EC 2.7.1.24) catalyzes the phosphorylation of dephosphocoenzyme A (dCoA) to yield CoA, which is the final step in CoA biosynthesis.
Probab=76.74  E-value=0.99  Score=24.05  Aligned_cols=18  Identities=44%  Similarity=0.765  Sum_probs=14.5

Q ss_pred             EEEEECC--CCCCHHHHHHH
Q ss_conf             9998303--65420123346
Q gi|254781101|r  110 IIAITGS--VGKTTTKEMLT  127 (472)
Q Consensus       110 vI~ITGT--nGKTTt~~~l~  127 (472)
                      +|||||.  .||||+..++.
T Consensus         1 iigiTG~igSGKStv~~~l~   20 (179)
T cd02022           1 IIGLTGGIGSGKSTVAKLLK   20 (179)
T ss_pred             CEEEECCCCCCHHHHHHHHH
T ss_conf             98863787578999999999


No 128
>TIGR00713 hemL glutamate-1-semialdehyde-2,1-aminomutase; InterPro: IPR004639   Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway . The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including vitamin B12, haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin .   The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes: (1) condensation of succinyl CoA and glycine (C4 pathway) using ALA synthase (2.3.1.37 from EC), or (2) decarboxylation of glutamate (C5 pathway) via three different enzymes, glutamyl-tRNA synthetase (6.1.1.17 from EC) to charge a tRNA with glutamate, glutamyl-tRNA reductase (1.2.1.70 from EC) to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and GSA aminotransferase (5.4.3.8 from EC) to catalyse a transamination reaction to produce ALA.   The second stage is to convert ALA to uroporphyrinogen III, the first macrocyclic tetrapyrrolic structure in the pathway. This is achieved by the action of three enzymes in one common pathway: porphobilinogen (PBG) synthase (or ALA dehydratase, 4.2.1.24 from EC) to condense two ALA molecules to generate porphobilinogen; hydroxymethylbilane synthase (or PBG deaminase, 2.5.1.61 from EC) to polymerise four PBG molecules into preuroporphyrinogen (tetrapyrrole structure); and uroporphyrinogen III synthase (4.2.1.75 from EC) to link two pyrrole units together (rings A and D) to yield uroporphyrinogen III.   Uroporphyrinogen III is the first branch point of the pathway. To synthesise cobalamin (vitamin B12), sirohaem, and coenzyme F430, uroporphyrinogen III needs to be converted into precorrin-2 by the action of uroporphyrinogen III methyltransferase (2.1.1.107 from EC). To synthesise haem and chlorophyll, uroporphyrinogen III needs to be decarboxylated into coproporphyrinogen III by the action of uroporphyrinogen III decarboxylase (4.1.1.37 from EC) .   This entry represents glutamate-1-semialdehyde (GSA) aminotransferase (5.4.3.8 from EC), which catalyse a transamination reaction to produce 5-aminoaevulinic acid during the first stage of tetrapyrrole biosynthesis by the C5 pathway , . This enzyme has a high degree of similarity to amino acid transaminases, and is classed as a class III aminotransferase.; GO: 0042286 glutamate-1-semialdehyde 21-aminomutase activity, 0033014 tetrapyrrole biosynthetic process.
Probab=76.72  E-value=5.4  Score=19.20  Aligned_cols=312  Identities=21%  Similarity=0.234  Sum_probs=145.7

Q ss_pred             HHHHHHCCCEEEEECCCCC-------CCCCCC--CCCEEEECCHHHHHH--HHHHHHHHCCCCCEEEEECCC-CCCHHHH
Q ss_conf             9999986988999855212-------455446--972899599899999--999999830699399983036-5420123
Q gi|254781101|r   57 ILHAVQKGAGLVVVNTDMV-------ASIGSL--SIPVFGVDDVLGALN--KLAVAARLRSKATIIAITGSV-GKTTTKE  124 (472)
Q Consensus        57 i~~A~~~Ga~~~i~~~~~~-------~~~~~~--~~~~i~v~d~~~al~--~la~~~~~~~~~~vI~ITGTn-GKTTt~~  124 (472)
                      |.+++++|-+.-.......       ...+..  +..-++=+-|+..|.  +||+.+-.|.  ++|=.-|+. |=     
T Consensus        73 v~e~lerG~syG~PtE~Ei~lA~~i~~~v~~~t~e~vRfVnSGTEATMsAvRLARG~TGR~--~IiKFeGcYHGh-----  145 (434)
T TIGR00713        73 VKEALERGTSYGAPTEAEILLAKEIISRVPSVTEEMVRFVNSGTEATMSAVRLARGFTGRD--KIIKFEGCYHGH-----  145 (434)
T ss_pred             HHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCCCCEEEEECCCCHHHHHHHHHHHHCCCCC--CEEEECCCCCCC-----
T ss_conf             9999973012689988999999999864055546516862176488999999863105887--278861764101-----


Q ss_pred             HHHHHHHHHHCCCCCHHH---HHCCCCCCCHHCC----CCCCCHHHHHCCCCCCCCCCCCCCCCCCCCEEEEEEECCCHH
Q ss_conf             346777752011222122---1101457410001----232214443015664433211212232322025553121012
Q gi|254781101|r  125 MLTIALSSIKKTYACIGS---YNNHIGVPLTLAR----MPVDVDFGIFELGMSHLGEIRFLTHLVRPHIAVITTIAPAHL  197 (472)
Q Consensus       125 ~l~~iL~~~~~~~~t~gn---~Nn~iGvpltll~----~~~~~~~~V~E~g~~~~gei~~L~~i~~P~iaiiTNI~~dHl  197 (472)
                       -=.+|-.+|.-..|.||   -|| .|+|-...+    ++=+.-=++=|+ +.+.|          .+||.|        
T Consensus       146 -~D~lLv~AGSGaaT~g~CG~P~S-pGvP~~~~k~Tl~~PYND~~a~~~~-f~~~G----------~~iAgv--------  204 (434)
T TIGR00713       146 -HDALLVKAGSGAATLGSCGLPTS-PGVPEDFAKLTLVLPYNDLEALEEA-FEEYG----------EEIAGV--------  204 (434)
T ss_pred             -HHHHCCCCCCHHHCCCCCCCCCC-CCCHHHHHHHCCCCCCCCHHHHHHH-HHHCC----------CCEEEE--------
T ss_conf             -23200354521010468877888-8870114311340451738999999-98679----------834378--------


Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             34445788886543310376221012101342468998752012333332222222222222344211346510012456
Q gi|254781101|r  198 SNFSGIEEIASAKAEIFEGLEKTGTIFLNYDDSFFELLKAKSHALGIKTIYSFGKSKNADFQLRKWKQCSEQSWMEVQLQ  277 (472)
Q Consensus       198 d~~~s~e~i~~~K~~i~~~l~~~g~~ViN~Dd~~~~~l~~~~~~~~~~~i~~~g~~~~ad~~~~~i~~~~~~~~~~~~~~  277 (472)
                                     |++-+.-| .-|++-...++..+++.+...+.-.|+    |    =-++         -|.+...
T Consensus       205 ---------------IvEPv~GN-mGvvpP~~eFL~~Lr~lt~e~g~LLI~----D----EV~T---------GFRva~~  251 (434)
T TIGR00713       205 ---------------IVEPVAGN-MGVVPPKKEFLEGLRELTEEYGALLIF----D----EVIT---------GFRVALG  251 (434)
T ss_pred             ---------------EECCCCCC-CCCCCCCCCHHHHHHHHHHHHCCEEEE----E----CCCC---------HHHCCHH
T ss_conf             ---------------86120257-666488522358999999872957755----0----2210---------1221332


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCHHHHHHHH--CCCCHHHHHHHHCCCCCCCCCCCCEECCCCCCEEEEEECCCCCCCCHHH
Q ss_conf             54322122222222333322103567651--0121034554311476644331010003653113310002565321012
Q gi|254781101|r  278 GKSMEVVHHGIGYHMAQNMLMTLGIVSIL--TADVDTAIKALSVFHPKEGRGKRYRCALNQGFFTLIDESYNANPASMKA  355 (472)
Q Consensus       278 ~~~~~~~l~~~G~hnv~NalaAia~~~~l--Gi~~~~i~~~L~~~~~~~GR~~~~~~~~~~~~~~iIDDsYNAnP~S~~a  355 (472)
                      |-+        +.|+|.==|  +++.+.+  |+|.-          -.-||-+.|+-..=.|.+ +==-+.|.||-||-|
T Consensus       252 GAQ--------~yfgV~PDl--~~lGKI~GGGlP~g----------A~gGrrEiM~~laP~G~v-YQAGTlsGNPlam~A  310 (434)
T TIGR00713       252 GAQ--------EYFGVEPDL--TTLGKIIGGGLPVG----------AFGGRREIMERLAPEGPV-YQAGTLSGNPLAMAA  310 (434)
T ss_pred             HCC--------HHCCCCCCC--EEECHHHCCCCCCE----------EECCCHHHHHHHCCCCCC-CCCCCCCCCHHHHHH
T ss_conf             150--------113787410--34233233764510----------122675688431788774-456435558899999


Q ss_pred             HHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEE---------EC--CCHHHHHHHCCCCCCE
Q ss_conf             577787411102687138851235417105899999999998649989999---------88--0389899851137979
Q gi|254781101|r  356 AISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWL---------SG--FHVLALKDALPRSIHV  424 (472)
Q Consensus       356 al~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~---------~G--~~~~~~~~~~~~~~~~  424 (472)
                      -+.+|+.+.....-  +      .+|-...+.+.+.|-+.+.+.++..-+.         ++  +......++.+     
T Consensus       311 G~atLk~~~~~~~~--Y------~~l~~~~~~L~~g~~e~l~~~gip~~~~~~gSMf~~FFtd~~~V~ny~~A~~-----  377 (434)
T TIGR00713       311 GLATLKLLDEEKGV--Y------TELDELAKRLAEGLSEVLEDKGIPHTVNRVGSMFSLFFTDEEEVTNYADAKK-----  377 (434)
T ss_pred             HHHHHHHHHCCCCH--H------HHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCEEEEEECCCCCCCCHHHHHH-----
T ss_conf             99999985348883--4------8999999999999999998279858995044004566577889878899988-----


Q ss_pred             EEECCHHHHHHHHHHHCCCCCEEEEECC----------CH-HHHH----HHHHHHHHHC
Q ss_conf             9978989999999984478989999771----------32-5489----9999999850
Q gi|254781101|r  425 HYSETMDGLFLFIQSSLVDGDVVVVKSS----------NS-CGFY----RLINLLLEEF  468 (472)
Q Consensus       425 ~~~~~~e~a~~~l~~~~~~gdiVLiKGS----------r~-~~le----~iv~~L~~~~  468 (472)
                         .|.|...++....+.+|  |.+--|          +. -.+|    ..++++.+-|
T Consensus       378 ---SD~e~F~~Ff~~mL~~G--VylpPS~FEa~F~S~AH~~E~i~yaq~~ti~a~~~~f  431 (434)
T TIGR00713       378 ---SDTELFAKFFHEMLEKG--VYLPPSQFEACFISAAHTEEDIEYAQTNTIEAAEEVF  431 (434)
T ss_pred             ---HHHHHHHHHHHHHHHCC--CCCCCCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             ---61898899999998588--8789872115551677772117899999999999998


No 129
>TIGR02853 spore_dpaA dipicolinic acid synthetase, A subunit; InterPro: IPR014215   This predicted Rossman fold-containing protein is the A subunit of dipicolinic acid synthetase as found in most, though not all, endospore-forming low-GC Gram-positive bacteria; it is absent in Clostridium. The B subunit is represented by IPR014214 from INTERPRO. This protein is also known as SpoVFA..
Probab=76.71  E-value=1.2  Score=23.59  Aligned_cols=63  Identities=22%  Similarity=0.384  Sum_probs=44.0

Q ss_pred             CCHHHHHCC-CCCCCCCCC-------------CCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHH
Q ss_conf             214443015-664433211-------------212232322025553121012344457888865433103762210121
Q gi|254781101|r  159 DVDFGIFEL-GMSHLGEIR-------------FLTHLVRPHIAVITTIAPAHLSNFSGIEEIASAKAEIFEGLEKTGTIF  224 (472)
Q Consensus       159 ~~~~~V~E~-g~~~~gei~-------------~L~~i~~P~iaiiTNI~~dHld~~~s~e~i~~~K~~i~~~l~~~g~~V  224 (472)
                      +.|..|+=| |+|+.|.+.             .+.+ ++++..|+|-|+.+||+.+-     ..++.+|++-+..+.++|
T Consensus        55 ~~DvviLPv~G~~~~G~v~t~f~~~~~~l~~~~~~~-~~~~~~~~~Gisn~yL~~l~-----~~a~~~Li~l~erDdvAI  128 (288)
T TIGR02853        55 TLDVVILPVQGVSQDGKVATVFSNEKVVLKPELLEE-TKKHCTIYVGISNDYLEELA-----AEAGVKLIELFERDDVAI  128 (288)
T ss_pred             CCCEEEECCCCCCCCCEEEEECCCCCEEECHHHHHH-CCCCEEEEECCCCHHHHHHH-----HHCCCCEEEECCCCCEEE
T ss_conf             666788167885998848741158721646689952-07943899737765899999-----871960241003575334


Q ss_pred             HCC
Q ss_conf             013
Q gi|254781101|r  225 LNY  227 (472)
Q Consensus       225 iN~  227 (472)
                      ||.
T Consensus       129 YNS  131 (288)
T TIGR02853       129 YNS  131 (288)
T ss_pred             ECC
T ss_conf             458


No 130
>PRK13705 plasmid-partitioning protein SopA; Provisional
Probab=76.40  E-value=1.8  Score=22.28  Aligned_cols=29  Identities=24%  Similarity=0.220  Sum_probs=24.6

Q ss_pred             CCCEEEEE---CCCCCCHHHHHHHHHHHHHHC
Q ss_conf             99399983---036542012334677775201
Q gi|254781101|r  107 KATIIAIT---GSVGKTTTKEMLTIALSSIKK  135 (472)
Q Consensus       107 ~~~vI~IT---GTnGKTTt~~~l~~iL~~~~~  135 (472)
                      ++.||+|.   |-.|||||+--|++.|...|.
T Consensus       105 ~~~VIAVaNqKGGvGKTTTavnLA~~LAl~G~  136 (388)
T PRK13705        105 FPPVIGVAAHKGGVYKTSVSVHLAQDLALKGL  136 (388)
T ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCC
T ss_conf             87289995278885599999999999997799


No 131
>TIGR03018 pepcterm_TyrKin exopolysaccharide/PEPCTERM locus tyrosine autokinase. Members of this protein family are related to a known protein-tyrosine autokinase and to numerous homologs from exopolysaccharide biosynthesis region proteins, many of which are designated as chain length determinants. Most members of this family contain a short region, immediately C-terminal to the region modeled here, with an abundance of Tyr residues. These C-terminal tyrosine residues are likely to be autophosphorylation sites. Some members of this family are fusion proteins.
Probab=76.09  E-value=3.4  Score=20.55  Aligned_cols=30  Identities=33%  Similarity=0.399  Sum_probs=24.1

Q ss_pred             CCCCEEEEECC---CCCCHHHHHHHHHHHHH-HC
Q ss_conf             69939998303---65420123346777752-01
Q gi|254781101|r  106 SKATIIAITGS---VGKTTTKEMLTIALSSI-KK  135 (472)
Q Consensus       106 ~~~~vI~ITGT---nGKTTt~~~l~~iL~~~-~~  135 (472)
                      -+.++|+||.+   .||||+..-++..|... ++
T Consensus        33 ~~~kvi~VTS~~pgeGKTtva~nLA~~lA~~~~~   66 (207)
T TIGR03018        33 KNNNLIMVTSSLPGEGKSFTAINLAISLAQEYDK   66 (207)
T ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHHCCC
T ss_conf             7880999978999998899999999999972498


No 132
>TIGR02199 rfaE_dom_II rfaE bifunctional protein, domain II; InterPro: IPR011914    RfaE is a protein involved in the biosynthesis of ADP-L-glycero-D-manno-heptose, a precursor for LPS inner core biosynthesis. RfaE is a bifunctional protein in Escherichia coli, and separate proteins in some other genome. Domain I (IPR011913 from INTERPRO) is suggested to act in D-glycero-D-manno-heptose 1-phosphate biosynthesis, while domain II (this family) adds ADP to yield ADP-D-glycero-D-manno-heptose .; GO: 0016773 phosphotransferase activity alcohol group as acceptor, 0016779 nucleotidyltransferase activity, 0005975 carbohydrate metabolic process.
Probab=76.08  E-value=5.1  Score=19.33  Aligned_cols=24  Identities=17%  Similarity=0.094  Sum_probs=11.7

Q ss_pred             HCCCCEEEEECCCH-HHHHHHCCCC
Q ss_conf             64998999988038-9899851137
Q gi|254781101|r  398 LYNISHVWLSGFHV-LALKDALPRS  421 (472)
Q Consensus       398 ~~~~d~v~~~G~~~-~~~~~~~~~~  421 (472)
                      -..+|.|+.+.|+. ..+-..+++.
T Consensus        74 L~~VD~VV~F~EDTP~~LI~~~~Pd   98 (144)
T TIGR02199        74 LSSVDYVVIFDEDTPEELIEELKPD   98 (144)
T ss_pred             CCCEEEEEECCCCCHHHHHHHHCCC
T ss_conf             7850037863898968999862962


No 133
>TIGR02855 spore_yabG sporulation peptidase YabG; InterPro: IPR008764   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.     The peptidases families associated with clan U- have an unknown catalytic mechanism as the protein fold of the active site domain and the active site residues have not been reported.   This is a group of peptidases belong to MEROPS peptidase family U57 (clan U-). The type example is the YabG protein of Bacillus subtilis. This is a protease involved in the synthesis and maturation of the spore coat proteins SpoIVA and YrbA of Bacillus subtilis ..
Probab=75.91  E-value=0.84  Score=24.53  Aligned_cols=63  Identities=24%  Similarity=0.362  Sum_probs=37.1

Q ss_pred             CCCCCHHCCCCCCCHHH--HHC----CCC----------CCCCCCCCCCCCCCCCEEEEEEECCCHH----HHHHHHHHH
Q ss_conf             45741000123221444--301----566----------4433211212232322025553121012----344457888
Q gi|254781101|r  147 IGVPLTLARMPVDVDFG--IFE----LGM----------SHLGEIRFLTHLVRPHIAVITTIAPAHL----SNFSGIEEI  206 (472)
Q Consensus       147 iGvpltll~~~~~~~~~--V~E----~g~----------~~~gei~~L~~i~~P~iaiiTNI~~dHl----d~~~s~e~i  206 (472)
                      .+.|==+|-++.|..|.  .++    +|+          ..|-.|..|-+-++|||.|||  |+|=.    ....++++|
T Consensus       110 F~~PGrVLH~DGD~~YL~~C~~~Y~~~gv~V~G~~~~E~emPe~v~~L~~~~~PDIlViT--GHDa~~K~~~~~~DL~aY  187 (292)
T TIGR02855       110 FGMPGRVLHIDGDPEYLRKCLKLYKKLGVPVVGIHCKEKEMPEKVLDLIEEVRPDILVIT--GHDAYSKNKGNYGDLNAY  187 (292)
T ss_pred             CCCCCEEEEECCCHHHHHHHHHHHHHCCCCEEEEEEEECCCCHHHHHHHHHHCCCEEEEE--CCCCEEECCCCHHHHHHC
T ss_conf             248864774228888999999988661972799998412180889999973099789994--666302167871136423


Q ss_pred             HHHHH
Q ss_conf             86543
Q gi|254781101|r  207 ASAKA  211 (472)
Q Consensus       207 ~~~K~  211 (472)
                      ...|-
T Consensus       188 RhSky  192 (292)
T TIGR02855       188 RHSKY  192 (292)
T ss_pred             CCCHH
T ss_conf             66568


No 134
>PRK01184 hypothetical protein; Provisional
Probab=75.71  E-value=1.7  Score=22.58  Aligned_cols=23  Identities=26%  Similarity=0.372  Sum_probs=16.8

Q ss_pred             CCEEEEECCC--CCCHHHHHHHHHHHHHH
Q ss_conf             9399983036--54201233467777520
Q gi|254781101|r  108 ATIIAITGSV--GKTTTKEMLTIALSSIK  134 (472)
Q Consensus       108 ~~vI~ITGTn--GKTTt~~~l~~iL~~~~  134 (472)
                      ..+||+||..  ||||+.++    |++.|
T Consensus         1 M~iIGlTG~iGSGKstva~i----~~e~G   25 (183)
T PRK01184          1 MMIIIVTGMPGSGKGEFSKI----ARELG   25 (183)
T ss_pred             CEEEEEECCCCCCHHHHHHH----HHHCC
T ss_conf             93999968998878999999----99779


No 135
>TIGR02407 ectoine_ectB diaminobutyrate--2-oxoglutarate aminotransferase; InterPro: IPR012773    Members of this family of class III pyridoxal-phosphate-dependent aminotransferases are diaminobutyrate--2-oxoglutarate aminotransferase (2.6.1.76 from EC) that catalyze the first step in ectoine biosynthesis from L-aspartate beta-semialdehyde. This family is readily separated phylogenetically from enzymes with the same substrate and product but involved in other process such as siderophore (Q9Z3R2 from SWISSPROT) or 1,3-diaminopropane (P44951 from SWISSPROT) biosynthesis. Ectoine is a compatible solute particularly effective in conferring salt tolerance.; GO: 0030170 pyridoxal phosphate binding, 0047307 diaminobutyrate-pyruvate transaminase activity, 0019491 ectoine biosynthetic process.
Probab=75.69  E-value=1.1  Score=23.67  Aligned_cols=37  Identities=16%  Similarity=0.004  Sum_probs=16.7

Q ss_pred             CCCCCCCCCCC----CCCCCHHHHH-HHHCCCCHHHHHHHHC
Q ss_conf             12222222233----3322103567-6510121034554311
Q gi|254781101|r  283 VVHHGIGYHMA----QNMLMTLGIV-SILTADVDTAIKALSV  319 (472)
Q Consensus       283 ~~l~~~G~hnv----~NalaAia~~-~~lGi~~~~i~~~L~~  319 (472)
                      +..--||+||=    .|.+...|.+ +..=...++..+.+..
T Consensus       281 ~D~W~PGEHNGTFRGNNlAFVtA~aAL~~yW~Dd~f~~~v~~  322 (413)
T TIGR02407       281 LDVWKPGEHNGTFRGNNLAFVTATAALEYYWSDDAFEKAVQR  322 (413)
T ss_pred             CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHH
T ss_conf             674678877886466527899999999984896268999999


No 136
>TIGR01846 type_I_sec_HlyB type I secretion system ATPase; InterPro: IPR010132   Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This entry contains one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N terminus, but rather carry signals located toward the extreme C terminus to direct type I secretion.; GO: 0005524 ATP binding, 0008565 protein transporter activity, 0015031 protein transport, 0016021 integral to membrane.
Probab=74.51  E-value=1.8  Score=22.42  Aligned_cols=36  Identities=8%  Similarity=0.102  Sum_probs=16.3

Q ss_pred             HHHHCCCCCCEEEECCH---------HHHHHHHHHHCCCCCEEEE
Q ss_conf             99851137979997898---------9999999984478989999
Q gi|254781101|r  414 LKDALPRSIHVHYSETM---------DGLFLFIQSSLVDGDVVVV  449 (472)
Q Consensus       414 ~~~~~~~~~~~~~~~~~---------e~a~~~l~~~~~~gdiVLi  449 (472)
                      ++-++-.++++-.||.-         +.+...+.+.++-=.+|.|
T Consensus       612 iARALv~nPrILifDEATSALDYESE~~Im~Nm~~Ic~GRTVIiI  656 (703)
T TIGR01846       612 IARALVANPRILIFDEATSALDYESEAVIMRNMREICRGRTVIII  656 (703)
T ss_pred             HHHHHHCCCCEEEHHHHHCCCCHHHHHHHHHHHHHHHCCCEEEEE
T ss_conf             999973589467201131221476899999755887459827974


No 137
>TIGR01035 hemA glutamyl-tRNA reductase; InterPro: IPR000343   Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway . The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including vitamin B12, haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin .   The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes: (1) condensation of succinyl CoA and glycine (C4 pathway) using ALA synthase (2.3.1.37 from EC), or (2) decarboxylation of glutamate (C5 pathway) via three different enzymes, glutamyl-tRNA synthetase (6.1.1.17 from EC) to charge a tRNA with glutamate, glutamyl-tRNA reductase (1.2.1.70 from EC) to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and GSA aminotransferase (5.4.3.8 from EC) to catalyse a transamination reaction to produce ALA.   The second stage is to convert ALA to uroporphyrinogen III, the first macrocyclic tetrapyrrolic structure in the pathway. This is achieved by the action of three enzymes in one common pathway: porphobilinogen (PBG) synthase (or ALA dehydratase, 4.2.1.24 from EC) to condense two ALA molecules to generate porphobilinogen; hydroxymethylbilane synthase (or PBG deaminase, 2.5.1.61 from EC) to polymerise four PBG molecules into preuroporphyrinogen (tetrapyrrole structure); and uroporphyrinogen III synthase (4.2.1.75 from EC) to link two pyrrole units together (rings A and D) to yield uroporphyrinogen III.   Uroporphyrinogen III is the first branch point of the pathway. To synthesise cobalamin (vitamin B12), sirohaem, and coenzyme F430, uroporphyrinogen III needs to be converted into precorrin-2 by the action of uroporphyrinogen III methyltransferase (2.1.1.107 from EC). To synthesise haem and chlorophyll, uroporphyrinogen III needs to be decarboxylated into coproporphyrinogen III by the action of uroporphyrinogen III decarboxylase (4.1.1.37 from EC) .   This entry represents glutamyl-tRNA reductase (1.2.1.70 from EC), which reduces glutamyl-tRNA to glutamate-1-semialdehyde during the first stage of tetrapyrrole biosynthesis by the C5 pathway , . This enzyme required NADPH as a coenzyme.; GO: 0008883 glutamyl-tRNA reductase activity, 0050661 NADP binding, 0033014 tetrapyrrole biosynthetic process.
Probab=73.52  E-value=6.5  Score=18.67  Aligned_cols=21  Identities=10%  Similarity=-0.013  Sum_probs=8.4

Q ss_pred             ECCHHHHHHHHHHHHHHCCCC
Q ss_conf             599899999999999830699
Q gi|254781101|r   88 VDDVLGALNKLAVAARLRSKA  108 (472)
Q Consensus        88 v~d~~~al~~la~~~~~~~~~  108 (472)
                      |++.......|.++..+..++
T Consensus        60 v~~~~~~~~~l~~~La~~~~~   80 (436)
T TIGR01035        60 VENLEEGKSALLKILAEYKNL   80 (436)
T ss_pred             HHHHHHHHHHHHHHHHHHCCC
T ss_conf             876889999999998762367


No 138
>PTZ00301 uridine kinase; Provisional
Probab=73.38  E-value=2.6  Score=21.25  Aligned_cols=24  Identities=29%  Similarity=0.508  Sum_probs=17.0

Q ss_pred             CCCEEEEECC--CCCCHHHHHHHHHH
Q ss_conf             9939998303--65420123346777
Q gi|254781101|r  107 KATIIAITGS--VGKTTTKEMLTIAL  130 (472)
Q Consensus       107 ~~~vI~ITGT--nGKTTt~~~l~~iL  130 (472)
                      ++.||||+|-  .||||.+.-+..-|
T Consensus         2 ~~~iIgIaGgSgSGKTT~a~~i~~~l   27 (210)
T PTZ00301          2 PCTVIGISGASGSGKSSLSTNIVSEL   27 (210)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             98899996887678999999999998


No 139
>COG5271 MDN1 AAA ATPase containing von Willebrand factor type A (vWA) domain [General function prediction only]
Probab=73.22  E-value=1.9  Score=22.16  Aligned_cols=20  Identities=40%  Similarity=0.649  Sum_probs=8.2

Q ss_pred             EEEEECCCCCCHHHHHHHHHH
Q ss_conf             999830365420123346777
Q gi|254781101|r  110 IIAITGSVGKTTTKEMLTIAL  130 (472)
Q Consensus       110 vI~ITGTnGKTTt~~~l~~iL  130 (472)
                      .||=||| ||||+...++-+|
T Consensus       469 LVGeTGt-GKTT~IQ~La~~l  488 (4600)
T COG5271         469 LVGETGT-GKTTMIQYLALKL  488 (4600)
T ss_pred             EEECCCC-CHHHHHHHHHHHH
T ss_conf             8714887-6546999999986


No 140
>TIGR00064 ftsY signal recognition particle-docking protein FtsY; InterPro: IPR004390   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 family includes the cell division ABC transporter and the periplasmic substrate-binding protein FtsY. There is a weak division between FtsY and SRP54; both are GTPases. In Escherichia coli, ftsY is an essential gene located in an operon with cell division genes ftsE and ftsX, but its apparent function is as the signal recognition particle docking protein.; GO: 0005525 GTP binding.
Probab=73.21  E-value=2.9  Score=20.93  Aligned_cols=31  Identities=35%  Similarity=0.383  Sum_probs=25.2

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHHHHCC
Q ss_conf             699399983036--5420123346777752011
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSSIKKT  136 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~~~~~  136 (472)
                      -++.||-+.|=|  |||||-.=|++.|.+.|+.
T Consensus        80 ~kp~Vil~VGVNG~GKTTTIaKLA~~l~~~Gk~  112 (284)
T TIGR00064        80 KKPNVILFVGVNGVGKTTTIAKLANKLKKQGKS  112 (284)
T ss_pred             CCCEEEEEEEEECCCHHHHHHHHHHHHHHCCCE
T ss_conf             897799998440886010288999999874990


No 141
>PRK03333 coaE dephospho-CoA kinase/unknown domain fusion protein; Provisional
Probab=73.20  E-value=1.8  Score=22.35  Aligned_cols=47  Identities=17%  Similarity=0.161  Sum_probs=28.2

Q ss_pred             HHHCCCCHHHHHHHHCCCCCCCCCCCCEECCCCCCEEEEEECCCCCCCCHHHHHHHH
Q ss_conf             651012103455431147664433101000365311331000256532101257778
Q gi|254781101|r  304 SILTADVDTAIKALSVFHPKEGRGKRYRCALNQGFFTLIDESYNANPASMKAAISVL  360 (472)
Q Consensus       304 ~~lGi~~~~i~~~L~~~~~~~GR~~~~~~~~~~~~~~iIDDsYNAnP~S~~aal~~l  360 (472)
                      ..-|++.+++...+..--+.+   +|...    -. .+||.|  -+++.+...++.|
T Consensus       143 ~r~gls~~~A~aRIaaQ~~~e---~r~a~----AD-~VIDNs--Gt~~~l~~~v~~l  189 (394)
T PRK03333        143 EQRGMAEADARARIAAQASDE---QRRAA----AD-VWLDNS--GTPEELVEAVRDL  189 (394)
T ss_pred             HCCCCCHHHHHHHHHHCCCHH---HHHHH----CC-EEEECC--CCHHHHHHHHHHH
T ss_conf             637989999999999479999---99985----99-999698--9999999999999


No 142
>COG0572 Udk Uridine kinase [Nucleotide transport and metabolism]
Probab=72.81  E-value=2  Score=22.03  Aligned_cols=26  Identities=38%  Similarity=0.456  Sum_probs=20.9

Q ss_pred             CCEEEEECC--CCCCHHHHHHHHHHHHH
Q ss_conf             939998303--65420123346777752
Q gi|254781101|r  108 ATIIAITGS--VGKTTTKEMLTIALSSI  133 (472)
Q Consensus       108 ~~vI~ITGT--nGKTTt~~~l~~iL~~~  133 (472)
                      .-+|||+|-  .||||.+..|...|+..
T Consensus         8 ~iiIgIaG~SgSGKTTv~~~l~~~~~~~   35 (218)
T COG0572           8 VIIIGIAGGSGSGKTTVAKELSEQLGVE   35 (218)
T ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHCCC
T ss_conf             6999986798778899999999982867


No 143
>PRK08233 hypothetical protein; Provisional
Probab=72.80  E-value=2.2  Score=21.71  Aligned_cols=24  Identities=50%  Similarity=0.511  Sum_probs=17.6

Q ss_pred             CCCEEEEECC--CCCCHHHHHHHHHH
Q ss_conf             9939998303--65420123346777
Q gi|254781101|r  107 KATIIAITGS--VGKTTTKEMLTIAL  130 (472)
Q Consensus       107 ~~~vI~ITGT--nGKTTt~~~l~~iL  130 (472)
                      ++.||||+|-  .||||.++-|..-|
T Consensus         2 kp~IIgIaGgSgSGKTtla~~l~~~l   27 (182)
T PRK08233          2 KTKIITIAAVSGGGKTTLTERLTHKL   27 (182)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHC
T ss_conf             98899996888678999999999974


No 144
>PRK07994 DNA polymerase III subunits gamma and tau; Validated
Probab=72.74  E-value=1.4  Score=23.15  Aligned_cols=39  Identities=10%  Similarity=0.089  Sum_probs=22.4

Q ss_pred             CEEEEEEEECCCCCCCCE--EEECCCCCCCHHHHHHHHHHC
Q ss_conf             147467740222378988--897168874768889999986
Q gi|254781101|r   25 GFVNGISIDSRSIAPQEA--FFAIKGPHYDGHDFILHAVQK   63 (472)
Q Consensus        25 ~~i~~i~~dSr~v~~g~l--Fval~g~~~DGh~~i~~A~~~   63 (472)
                      ..-.|.|..-+.+..|..  ++-+.+....|-+.+.+.+++
T Consensus        70 ~~pcg~c~~c~~i~~g~~~d~~eidaas~~~vd~~rel~~~  110 (643)
T PRK07994         70 ATPCGVCDNCREIEQGRFVDLIEIDAASRTKVEDTRDLLDN  110 (643)
T ss_pred             CCCCCCCHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHH
T ss_conf             99787677689886589887588636777888999999984


No 145
>PRK05749 3-deoxy-D-manno-octulosonic-acid transferase; Reviewed
Probab=72.64  E-value=6.8  Score=18.54  Aligned_cols=70  Identities=21%  Similarity=0.236  Sum_probs=46.6

Q ss_pred             CEEEEECCCH---HHHHHHCCCCCCEEEECCHHHHHHHHHHHCCCCCEE---------EEECCCHHHHHHHHHHHHHHCC
Q ss_conf             8999988038---989985113797999789899999999844789899---------9977132548999999998505
Q gi|254781101|r  402 SHVWLSGFHV---LALKDALPRSIHVHYSETMDGLFLFIQSSLVDGDVV---------VVKSSNSCGFYRLINLLLEEFP  469 (472)
Q Consensus       402 d~v~~~G~~~---~~~~~~~~~~~~~~~~~~~e~a~~~l~~~~~~gdiV---------LiKGSr~~~le~iv~~L~~~~~  469 (472)
                      ..-+++|+..   +++.+.+....-+..+++.+++.+.+...+...+.-         .+...+| ..+++++.|.+-+|
T Consensus       342 g~pvi~GP~~~nf~e~~~~L~~~g~~~~v~~~~eL~~~~~~ll~~~~~~~~~~~~a~~~v~~~~G-at~r~~~~i~~~L~  420 (423)
T PRK05749        342 GVPVISGPHTFNFKEIFERLLQAGAAIQVEDAEDLAKAVSSLLTDPDAREAMGEAGVAFLKQNRG-ALQRTLQLLKPYLP  420 (423)
T ss_pred             CCCEEECCCCCCHHHHHHHHHHCCCEEEECCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCC-HHHHHHHHHHHHCC
T ss_conf             99889993832779999999978995896899999999999976999999999999999997847-99999999997635


Q ss_pred             CCC
Q ss_conf             779
Q gi|254781101|r  470 AIQ  472 (472)
Q Consensus       470 ~~~  472 (472)
                      .+|
T Consensus       421 ~~~  423 (423)
T PRK05749        421 PLK  423 (423)
T ss_pred             CCC
T ss_conf             789


No 146
>cd01983 Fer4_NifH The Fer4_NifH superfamily contains a variety of proteins which share a common ATP-binding domain. Functionally, proteins in this superfamily use the energy from hydrolysis of NTP to transfer electron or ion.
Probab=72.57  E-value=2.1  Score=21.90  Aligned_cols=26  Identities=46%  Similarity=0.576  Sum_probs=20.7

Q ss_pred             EEEEECC--CCCCHHHHHHHHHHHHHHC
Q ss_conf             9998303--6542012334677775201
Q gi|254781101|r  110 IIAITGS--VGKTTTKEMLTIALSSIKK  135 (472)
Q Consensus       110 vI~ITGT--nGKTTt~~~l~~iL~~~~~  135 (472)
                      +|.++|.  .||||++..++..|.+.|.
T Consensus         1 ~i~~~~~kGvGKTT~a~~La~~la~~g~   28 (99)
T cd01983           1 VIVVTGKGGVGKTTLAANLAAALAKRGK   28 (99)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHHCCC
T ss_conf             9898589977689999999999998899


No 147
>cd02117 NifH_like This family contains the NifH (iron protein) of nitrogenase, L subunit (BchL/ChlL) of the  protochlorophyllide reductase and the BchX subunit of the Chlorophyllide reductase. Members of this family use energey from ATP hydrolysis and transfer electrons through a Fe4-S4 cluster to other subunit for reduction of substrate.
Probab=72.32  E-value=2.8  Score=21.03  Aligned_cols=29  Identities=41%  Similarity=0.557  Sum_probs=23.6

Q ss_pred             CEEEEEC--CCCCCHHHHHHHHHHHHHHCCC
Q ss_conf             3999830--3654201233467777520112
Q gi|254781101|r  109 TIIAITG--SVGKTTTKEMLTIALSSIKKTY  137 (472)
Q Consensus       109 ~vI~ITG--TnGKTTt~~~l~~iL~~~~~~~  137 (472)
                      +.|||.|  -.|||||+.-|+..|.+.|+.+
T Consensus         1 ~~iaiyGKGGVGKTTts~NLaaaLA~~G~rV   31 (212)
T cd02117           1 RQIAIYGKGGIGKSTTSQNLSAALAEMGKKV   31 (212)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHCCCEE
T ss_conf             9599988983568778999999999869969


No 148
>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]
Probab=72.07  E-value=3.3  Score=20.62  Aligned_cols=27  Identities=33%  Similarity=0.295  Sum_probs=13.6

Q ss_pred             CCEEEEECCC--CCCHHHHHHHHHHHHHH
Q ss_conf             9399983036--54201233467777520
Q gi|254781101|r  108 ATIIAITGSV--GKTTTKEMLTIALSSIK  134 (472)
Q Consensus       108 ~~vI~ITGTn--GKTTt~~~l~~iL~~~~  134 (472)
                      +.||-+.|-|  |||||-.=|++.|.+.|
T Consensus       139 p~Vil~vGVNG~GKTTTIaKLA~~l~~~g  167 (340)
T COG0552         139 PFVILFVGVNGVGKTTTIAKLAKYLKQQG  167 (340)
T ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHHHCC
T ss_conf             67999993488863717999999999789


No 149
>cd03116 MobB Molybdenum is an essential trace element in the form of molybdenum cofactor (Moco) which is associated with the metabolism of nitrogen, carbon and sulfur by redox active enzymes. In E. coli, the synthesis of Moco involves genes from several loci: moa, mob, mod, moe and mog. The mob locus contains mobA and mobB genes. MobB catalyzes the attachment of the guanine dinucleotide to molybdopterin.
Probab=71.80  E-value=2.7  Score=21.16  Aligned_cols=34  Identities=38%  Similarity=0.337  Sum_probs=26.1

Q ss_pred             CCEEEEECC--CCCCHHHHHHHHHHHHHHCCCCCHH
Q ss_conf             939998303--6542012334677775201122212
Q gi|254781101|r  108 ATIIAITGS--VGKTTTKEMLTIALSSIKKTYACIG  141 (472)
Q Consensus       108 ~~vI~ITGT--nGKTTt~~~l~~iL~~~~~~~~t~g  141 (472)
                      +++|+|.|-  .||||..+=+-..|...|-.+++..
T Consensus         1 mkii~ivG~snSGKTTLi~kli~~l~~~G~~V~~iK   36 (159)
T cd03116           1 MKVIGFVGYSGSGKTTLLEKLIPALSARGLRVAVIK   36 (159)
T ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHHHCCCEEEEEE
T ss_conf             929999967999999999999999997798598997


No 150
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=71.41  E-value=5.5  Score=19.13  Aligned_cols=71  Identities=25%  Similarity=0.319  Sum_probs=44.4

Q ss_pred             CEEEEECC--CCCCHHHHHHHHHHHHHHCCCCCHHHHHCCCCCCCHHCCCCC-CCHHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf             39998303--654201233467777520112221221101457410001232-214443015664433211212232322
Q gi|254781101|r  109 TIIAITGS--VGKTTTKEMLTIALSSIKKTYACIGSYNNHIGVPLTLARMPV-DVDFGIFELGMSHLGEIRFLTHLVRPH  185 (472)
Q Consensus       109 ~vI~ITGT--nGKTTt~~~l~~iL~~~~~~~~t~gn~Nn~iGvpltll~~~~-~~~~~V~E~g~~~~gei~~L~~i~~P~  185 (472)
                      .=|=|.|.  .||||-..-++..+...|++++|..+       |-- +++++ =++|+=+|-.|...++|--   +++||
T Consensus       264 eGILIAG~PGaGKsTFaqAlAefy~~~GkiVKTmEs-------PRD-l~v~~eITQYs~l~g~me~t~DiLL---LvRPD  332 (604)
T COG1855         264 EGILIAGAPGAGKSTFAQALAEFYASQGKIVKTMES-------PRD-LQVSPEITQYSPLEGDMEKTADILL---LVRPD  332 (604)
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHHHHCCCEEEECCC-------CCC-CCCCHHHHHCCCCCCCHHHHCCEEE---EECCC
T ss_conf             646995699997468999999999866968863247-------513-5688666320644564555233799---96588


Q ss_pred             EEEEE
Q ss_conf             02555
Q gi|254781101|r  186 IAVIT  190 (472)
Q Consensus       186 iaiiT  190 (472)
                      +.|+-
T Consensus       333 YTIyD  337 (604)
T COG1855         333 YTIYD  337 (604)
T ss_pred             CEEHH
T ss_conf             45103


No 151
>PRK02458 ribose-phosphate pyrophosphokinase; Provisional
Probab=71.28  E-value=7.3  Score=18.34  Aligned_cols=60  Identities=22%  Similarity=0.271  Sum_probs=31.5

Q ss_pred             CEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             113310002565321012577787411102687138851235417105899999999998649989999880
Q gi|254781101|r  338 FFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGF  409 (472)
Q Consensus       338 ~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~  409 (472)
                      .+.++||== .+-.++..|.+.|+..   + -++|.+...=   |-.+..-    .+.+...+++.|+..-.
T Consensus       220 ~vIIVDDiI-dTGgTl~~aa~~Lk~~---G-A~~V~~~~TH---glfs~~A----~~rl~~s~i~~ivvTnT  279 (323)
T PRK02458        220 KAILIDDIL-NTGKTFAEAAKILERS---G-ATEIYAVASH---GLFAGGA----AEVLETAPIKEILVTDS  279 (323)
T ss_pred             EEEEECCHH-HHHHHHHHHHHHHHHC---C-CCEEEEEEEC---CCCCHHH----HHHHHCCCCCEEEECCC
T ss_conf             678762023-2248899999999964---9-9768999976---4257079----99986499868998589


No 152
>PRK13507 formate--tetrahydrofolate ligase; Provisional
Probab=71.15  E-value=6.5  Score=18.66  Aligned_cols=33  Identities=30%  Similarity=0.304  Sum_probs=26.2

Q ss_pred             HHCCCCCEEEEECCC------CCCHHHHHHHHHHHHHHC
Q ss_conf             830699399983036------542012334677775201
Q gi|254781101|r  103 RLRSKATIIAITGSV------GKTTTKEMLTIALSSIKK  135 (472)
Q Consensus       103 ~~~~~~~vI~ITGTn------GKTTt~~~l~~iL~~~~~  135 (472)
                      .++.+++.|-||+.+      |||||+==|++-|...|+
T Consensus        58 ~~~~~gklILVTaitPTP~GEGKTTttIGL~~aL~~lgk   96 (587)
T PRK13507         58 KDRPDGKYIDVTAITPTPLGEGKSTTTMGLVQGLGKRGK   96 (587)
T ss_pred             CCCCCCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCC
T ss_conf             048996399998468888889862105629999986088


No 153
>cd02034 CooC The accessory protein CooC, which contains a nucleotide-binding domain (P-loop) near the N-terminus, participates in the maturation of the nickel center of carbon monoxide dehydrogenase (CODH). CODH from Rhodospirillum rubrum catalyzes the reversible oxidation of CO to CO2. CODH contains a nickel-iron-sulfur cluster (C-center) and an iron-sulfur cluster (B-center). CO oxidation occurs at the C-center. Three accessory proteins encoded by cooCTJ genes are involved in nickel incorporation into a nickel site. CooC functions as a nickel insertase that mobilizes nickel to apoCODH using energy released from ATP hydrolysis. CooC is a homodimer and has NTPase activities. Mutation at the P-loop abolishs its function.
Probab=70.99  E-value=2.6  Score=21.24  Aligned_cols=25  Identities=52%  Similarity=0.603  Sum_probs=19.8

Q ss_pred             EEEEC--CCCCCHHHHHHHHHHHHHHC
Q ss_conf             99830--36542012334677775201
Q gi|254781101|r  111 IAITG--SVGKTTTKEMLTIALSSIKK  135 (472)
Q Consensus       111 I~ITG--TnGKTTt~~~l~~iL~~~~~  135 (472)
                      |+|+|  -.||||++.++++.|.+.++
T Consensus         2 ia~~GKGGvGKtt~~~~la~~l~~~g~   28 (116)
T cd02034           2 IAITGKGGVGKTTIAALLARYLAEKGK   28 (116)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCC
T ss_conf             789889977499999999999997899


No 154
>TIGR01526 nadR_NMN_Atrans nicotinamide-nucleotide adenylyltransferase; InterPro: IPR006417   The NadR protein of Escherichia coli and closely related bacteria is both enzyme and regulatory protein. The first 60 or so amino acids, N-terminal region is a DNA-binding helix-turn-helix domain (IPR001387 from INTERPRO) responsible for repressing the nadAB genes of NAD de novo biosynthesis. The NadR homologs in Mycobacterium tuberculosis, Haemophilus influenzae, and others appear to lack the repressor domain. NadR has recently been shown to act as an enzyme of the salvage pathway of NAD biosynthesis, nicotinamide-nucleotide adenylyltransferase; members of this family are presumed to share this activity. E. coli NadR has also been found to regulate the import of its substrate, nicotinamide ribonucleotide, but it is not known if the other members of this family share that activity.  ; GO: 0003677 DNA binding, 0030528 transcription regulator activity, 0006810 transport, 0019363 pyridine nucleotide biosynthetic process, 0045449 regulation of transcription.
Probab=70.65  E-value=2.8  Score=21.05  Aligned_cols=56  Identities=14%  Similarity=0.104  Sum_probs=28.2

Q ss_pred             CHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHCCCCCCEEEECCHHHHHHHHHHHCC
Q ss_conf             05899999999998649989999880389899851137979997898999999998447
Q gi|254781101|r  384 LSQSFHIDLAEVLSLYNISHVWLSGFHVLALKDALPRSIHVHYSETMDGLFLFIQSSLV  442 (472)
Q Consensus       384 ~~~~~h~~i~~~~~~~~~d~v~~~G~~~~~~~~~~~~~~~~~~~~~~e~a~~~l~~~~~  442 (472)
                      +-+++|=.+-+.+++..+|.++++-.+...+.+.+..-   ..-.++.+..+.+.+.+.
T Consensus       273 Dfeql~P~~~~~i~~~r~DL~ll~~p~tew~~Dg~R~l---~~~~~R~~F~~~l~~~L~  328 (346)
T TIGR01526       273 DFEQLHPFLKKTIAEYRFDLTLLLKPNTEWVDDGLRSL---GSEESRKEFQELLERALA  328 (346)
T ss_pred             CHHHCCHHHHHHHHHCCCCEEEEECCCCCEECCCCCCC---CCHHHHHHHHHHHHHHHH
T ss_conf             54450627887763278847997279987342885207---743227899999999999


No 155
>PRK04183 glutamyl-tRNA(Gln) amidotransferase subunit D; Validated
Probab=70.53  E-value=5.2  Score=19.31  Aligned_cols=12  Identities=25%  Similarity=0.274  Sum_probs=7.3

Q ss_pred             CCCEEEEEEEEC
Q ss_conf             871474677402
Q gi|254781101|r   23 PQGFVNGISIDS   34 (472)
Q Consensus        23 ~~~~i~~i~~dS   34 (472)
                      .+..+.|+-..|
T Consensus        14 ~~~~~~g~~~p~   25 (421)
T PRK04183         14 EGTVYEGILMPS   25 (421)
T ss_pred             CCEEEEEEEECC
T ss_conf             997999998178


No 156
>cd01882 BMS1 Bms1.  Bms1 is an essential, evolutionarily conserved, nucleolar protein.  Its depletion interferes with processing of the 35S pre-rRNA at sites A0, A1, and A2, and the formation of 40S subunits.  Bms1, the putative endonuclease Rc11, and the essential U3 small nucleolar RNA form a stable subcomplex that is believed to control an early step in the formation of the 40S subumit.  The C-terminal domain of Bms1 contains a GTPase-activating protein (GAP) that functions intramolecularly.  It is believed that Rc11 activates Bms1 by acting as a guanine-nucleotide exchange factor (GEF) to promote GDP/GTP exchange, and that activated (GTP-bound) Bms1 delivers Rc11 to the preribosomes.
Probab=70.16  E-value=4.8  Score=19.52  Aligned_cols=23  Identities=30%  Similarity=0.525  Sum_probs=15.4

Q ss_pred             CCCCEEEEECC--CCCCHHHHHHHHHHH
Q ss_conf             69939998303--654201233467777
Q gi|254781101|r  106 SKATIIAITGS--VGKTTTKEMLTIALS  131 (472)
Q Consensus       106 ~~~~vI~ITGT--nGKTTt~~~l~~iL~  131 (472)
                      +++-+|+|-|.  .||||.   +.++.+
T Consensus        37 pPP~vVavvGPpgvGKtTL---iksLvk   61 (225)
T cd01882          37 PPPLVVAVVGPPGVGKTTL---IKSLVK   61 (225)
T ss_pred             CCCEEEEEECCCCCCHHHH---HHHHHH
T ss_conf             9996999989899778899---999999


No 157
>PRK07667 uridine kinase; Provisional
Probab=69.84  E-value=3.1  Score=20.77  Aligned_cols=28  Identities=29%  Similarity=0.262  Sum_probs=21.8

Q ss_pred             CCCEEEEECC--CCCCHHHHHHHHHHHHHH
Q ss_conf             9939998303--654201233467777520
Q gi|254781101|r  107 KATIIAITGS--VGKTTTKEMLTIALSSIK  134 (472)
Q Consensus       107 ~~~vI~ITGT--nGKTTt~~~l~~iL~~~~  134 (472)
                      +--+|||.|-  .||||.+.-|+..|...+
T Consensus        13 ~r~iIgIaG~sgSGKTTla~~L~~~l~~~~   42 (190)
T PRK07667         13 NRFILGIDGLSRSGKTTFVANLKENMKQEG   42 (190)
T ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHHHCC
T ss_conf             869999779897889999999999986659


No 158
>KOG0950 consensus
Probab=69.83  E-value=5.9  Score=18.94  Aligned_cols=82  Identities=20%  Similarity=0.191  Sum_probs=44.6

Q ss_pred             CCCCCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEECCCCCC-CCCCCCCCEEEECCHHHHHHHHHHHHHHCCCCCEEEE
Q ss_conf             223789888971688747688899999869889998552124-5544697289959989999999999983069939998
Q gi|254781101|r   35 RSIAPQEAFFAIKGPHYDGHDFILHAVQKGAGLVVVNTDMVA-SIGSLSIPVFGVDDVLGALNKLAVAARLRSKATIIAI  113 (472)
Q Consensus        35 r~v~~g~lFval~g~~~DGh~~i~~A~~~Ga~~~i~~~~~~~-~~~~~~~~~i~v~d~~~al~~la~~~~~~~~~~vI~I  113 (472)
                      +.+.-|-.|.- -|..+|+.++|++|+.+|...+++..+... .......++|.-. |.-.-..+.+.   +|+ +.+|.
T Consensus       519 ~ti~~GvAyHh-aGLT~eER~~iE~afr~g~i~vl~aTSTlaaGVNLPArRVIira-P~~g~~~l~~~---~Yk-QM~GR  592 (1008)
T KOG0950         519 KTIPYGVAYHH-AGLTSEEREIIEAAFREGNIFVLVATSTLAAGVNLPARRVIIRA-PYVGREFLTRL---EYK-QMVGR  592 (1008)
T ss_pred             EECCCCCEECC-CCCCCCHHHHHHHHHHHCCEEEEEECCHHHCCCCCCCCEEEEEC-CCCCCCHHHHH---HHH-HHHHH
T ss_conf             02003533034-44650068889999974676999943446406868751158747-75462300024---677-65302


Q ss_pred             ECCCCCCHH
Q ss_conf             303654201
Q gi|254781101|r  114 TGSVGKTTT  122 (472)
Q Consensus       114 TGTnGKTTt  122 (472)
                      ||..|..|.
T Consensus       593 AGR~gidT~  601 (1008)
T KOG0950         593 AGRTGIDTL  601 (1008)
T ss_pred             HHHCCCCCC
T ss_conf             000334657


No 159
>PHA02519 plasmid partition protein SopA; Reviewed
Probab=69.76  E-value=3.3  Score=20.61  Aligned_cols=28  Identities=21%  Similarity=0.204  Sum_probs=23.7

Q ss_pred             CCEEEEE---CCCCCCHHHHHHHHHHHHHHC
Q ss_conf             9399983---036542012334677775201
Q gi|254781101|r  108 ATIIAIT---GSVGKTTTKEMLTIALSSIKK  135 (472)
Q Consensus       108 ~~vI~IT---GTnGKTTt~~~l~~iL~~~~~  135 (472)
                      +-||+|.   |-.|||||+--|++.|...|.
T Consensus       106 ~~VIAVaN~KGGVGKTTTavnLA~~LAl~G~  136 (387)
T PHA02519        106 PVVLAVMSHKGGVYKTSSAVHTAQWLALQGH  136 (387)
T ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHHHCCC
T ss_conf             5289986168877699999999999997699


No 160
>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+). This enzyme catalyzes the phosphorylation of nicotinamide riboside (NR) to form nicotinamide mononucleotide (NMN). It defines the NR salvage pathway of NAD+ biosynthesis in addition to the pathways through nicotinic acid mononucleotide (NaMN). This enzyme can also phosphorylate the anticancer drug tiazofurin, which is an analog of nicotinamide riboside.
Probab=69.75  E-value=2  Score=22.03  Aligned_cols=22  Identities=41%  Similarity=0.607  Sum_probs=17.1

Q ss_pred             EEEEECC--CCCCHHHHHHHHHHH
Q ss_conf             9998303--654201233467777
Q gi|254781101|r  110 IIAITGS--VGKTTTKEMLTIALS  131 (472)
Q Consensus       110 vI~ITGT--nGKTTt~~~l~~iL~  131 (472)
                      ||||+|.  .||||.+..|...|.
T Consensus         1 iIgIaG~S~SGKTTla~~L~~~l~   24 (187)
T cd02024           1 IVGISGVTNSGKTTLAKLLQRILP   24 (187)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHCC
T ss_conf             989968888759999999999879


No 161
>PRK03092 ribose-phosphate pyrophosphokinase; Provisional
Probab=69.67  E-value=7.8  Score=18.11  Aligned_cols=91  Identities=15%  Similarity=0.201  Sum_probs=40.9

Q ss_pred             CEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHH
Q ss_conf             11331000256532101257778741110268713885123541710589999999999864998999988038989985
Q gi|254781101|r  338 FFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFHVLALKDA  417 (472)
Q Consensus       338 ~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~~~~~~~~  417 (472)
                      .+.++||== .+-.++..|.+.|+.   .+. ++|.+...=   |-.+..-    .+.+.+.+++.|+..-.-..  .+.
T Consensus       203 ~viIVDDiI-~TGgTl~~aa~~Lk~---~GA-~~V~~~~TH---glfs~~A----~~rl~~s~i~~iv~TnTip~--~~~  268 (304)
T PRK03092        203 TCVLVDDMI-DTGGTIAGAVEALKE---AGA-KDVIIAATH---GVLSDPA----AERLKNCGAREVVVTNTLPI--PEE  268 (304)
T ss_pred             EEEEECCHH-HCCHHHHHHHHHHHH---CCC-CEEEEEEEC---CCCCHHH----HHHHHHCCCCEEEEECCCCC--CCC
T ss_conf             599977645-437359999999986---699-839999979---3459679----99997389987998188038--620


Q ss_pred             CCCCCCEEEECCHHHHHHHHHHHCCCC
Q ss_conf             113797999789899999999844789
Q gi|254781101|r  418 LPRSIHVHYSETMDGLFLFIQSSLVDG  444 (472)
Q Consensus       418 ~~~~~~~~~~~~~e~a~~~l~~~~~~g  444 (472)
                       ....++...+ +..++..+...+..|
T Consensus       269 -~~~~ki~~~s-va~llAeaI~ri~~~  293 (304)
T PRK03092        269 -KRFDKLTVLS-IAPLLARAIREVFED  293 (304)
T ss_pred             -CCCCCEEEEE-HHHHHHHHHHHHHCC
T ss_conf             -0689829998-199999999998669


No 162
>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ; InterPro: IPR013364    Proteins in this entry are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase (IPR013363 from INTERPRO) of a type-IV secretion-like system of the obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii..
Probab=69.46  E-value=1.9  Score=22.26  Aligned_cols=53  Identities=25%  Similarity=0.227  Sum_probs=31.5

Q ss_pred             CCCCCCCEEEECCHHHHHHHHHHHHHHCCC-CCEEEEECCCCCCHHHHHHHHHHHHHHCCC
Q ss_conf             544697289959989999999999983069-939998303654201233467777520112
Q gi|254781101|r   78 IGSLSIPVFGVDDVLGALNKLAVAARLRSK-ATIIAITGSVGKTTTKEMLTIALSSIKKTY  137 (472)
Q Consensus        78 ~~~~~~~~i~v~d~~~al~~la~~~~~~~~-~~vI~ITGTnGKTTt~~~l~~iL~~~~~~~  137 (472)
                      ..+.++|.|.--+.++-|-+   ....... +-|-|.||| ||+|   ++|+|.+..+++.
T Consensus       124 vips~IP~L~~MgiE~DLf~---alLP~~GLGLiCG~TGS-GKST---l~AaiY~~~l~t~  177 (374)
T TIGR02525       124 VIPSDIPDLKKMGIEPDLFE---ALLPKAGLGLICGETGS-GKST---LAAAIYRHCLETY  177 (374)
T ss_pred             HCCCCCCCHHHCCCCHHHHH---HHCCCCCCEEECCCCCC-CHHH---HHHHHHHHHCCCC
T ss_conf             05566651323478768998---70500378022177897-2899---9999999850748


No 163
>PRK13230 nitrogenase reductase-like protein; Reviewed
Probab=69.13  E-value=2.2  Score=21.80  Aligned_cols=29  Identities=41%  Similarity=0.404  Sum_probs=23.2

Q ss_pred             CEEEEE--CCCCCCHHHHHHHHHHHHHHCCC
Q ss_conf             399983--03654201233467777520112
Q gi|254781101|r  109 TIIAIT--GSVGKTTTKEMLTIALSSIKKTY  137 (472)
Q Consensus       109 ~vI~IT--GTnGKTTt~~~l~~iL~~~~~~~  137 (472)
                      +-|||-  |-.|||||+-=|+..|...|+.+
T Consensus         2 ~~ia~yGKGGVGKTTTavNLAaALA~~GkkV   32 (292)
T PRK13230          2 KQIAFYGKGGIGKSTTVCNLAAALSKSGKKV   32 (292)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHCCCEE
T ss_conf             6799917998578989999999999879959


No 164
>PRK10416 cell division protein FtsY; Provisional
Probab=69.06  E-value=4  Score=20.04  Aligned_cols=24  Identities=17%  Similarity=0.152  Sum_probs=12.3

Q ss_pred             CEECCCCCCEEEEEECCCCCCCCH
Q ss_conf             100036531133100025653210
Q gi|254781101|r  330 YRCALNQGFFTLIDESYNANPASM  353 (472)
Q Consensus       330 ~~~~~~~~~~~iIDDsYNAnP~S~  353 (472)
                      +++.....++-+|-..++++|.|+
T Consensus       342 L~~w~~r~~v~vi~~~~g~Dpa~V  365 (499)
T PRK10416        342 LQVWGQRNNIPVIAQHTGADSASV  365 (499)
T ss_pred             HHHHHCCCCCEEEECCCCCCHHHH
T ss_conf             999842457369836899997999


No 165
>PHA02518 ParA-like protein; Provisional
Probab=68.92  E-value=3.1  Score=20.74  Aligned_cols=28  Identities=36%  Similarity=0.375  Sum_probs=21.9

Q ss_pred             CEEEEE---CCCCCCHHHHHHHHHHHHHHCC
Q ss_conf             399983---0365420123346777752011
Q gi|254781101|r  109 TIIAIT---GSVGKTTTKEMLTIALSSIKKT  136 (472)
Q Consensus       109 ~vI~IT---GTnGKTTt~~~l~~iL~~~~~~  136 (472)
                      +||+|.   |-.|||||+--|+..|...|+.
T Consensus         1 KIIav~n~KGGvGKTT~a~nLA~~la~~G~~   31 (211)
T PHA02518          1 KIIAVLNQKGGAGKTTVATNLASWLHADGHK   31 (211)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHHHCCCC
T ss_conf             9899980899974999999999999978994


No 166
>pfam03215 Rad17 Rad17 cell cycle checkpoint protein.
Probab=68.51  E-value=3.4  Score=20.48  Aligned_cols=44  Identities=27%  Similarity=0.295  Sum_probs=29.6

Q ss_pred             EECCHHHHHHHHHHHHHHCCCCCEEEEECC--CCCCHHHHHHHHHHHHH
Q ss_conf             959989999999999983069939998303--65420123346777752
Q gi|254781101|r   87 GVDDVLGALNKLAVAARLRSKATIIAITGS--VGKTTTKEMLTIALSSI  133 (472)
Q Consensus        87 ~v~d~~~al~~la~~~~~~~~~~vI~ITGT--nGKTTt~~~l~~iL~~~  133 (472)
                      +|+|++..|....   ..+.+.++.-+||-  .|||||..+|+.-|.-.
T Consensus        27 KV~eV~~WL~~~~---~~~~~~~iLlLtGPaG~GKTTTI~lLAkeLG~e   72 (490)
T pfam03215        27 KIAEVDHWLKAVF---LESNKQLILLLTGPSGCGKSTTVKVLSKELGIE   72 (490)
T ss_pred             HHHHHHHHHHHHH---CCCCCCEEEEEECCCCCCHHHHHHHHHHHHCCE
T ss_conf             3999999999985---477773189987989988999999999975968


No 167
>TIGR00235 udk uridine kinase; InterPro: IPR000764   Uridine kinase (pyrimidine ribonucleoside kinase) is the rate-limiting enzyme in the pyrimidine salvage pathway. It catalyzes the following reaction:  ATP + Uridine = ADP + UMP  A cDNA for uridine kinase from mouse brain was found which encodes a protein of 277 amino acids. A truncated form of the cDNA was expressed in Escherichia coli, and shown to display uridine kinase activity and to readily form a tetramer, the most active form of the wild-type enzyme. Sequence analysis has identified three ATP-binding site consensus motifs. The predicted secondary structure, and sequence comparison with kinases of known structure, is consistent with uridine kinase having the alpha/beta core nucleotide-binding fold common to many kinases .; GO: 0005524 ATP binding, 0016773 phosphotransferase activity alcohol group as acceptor.
Probab=67.31  E-value=2.9  Score=20.99  Aligned_cols=25  Identities=36%  Similarity=0.478  Sum_probs=21.7

Q ss_pred             CCEEEEECC--CCC----CHHHHHHHHHHHH
Q ss_conf             939998303--654----2012334677775
Q gi|254781101|r  108 ATIIAITGS--VGK----TTTKEMLTIALSS  132 (472)
Q Consensus       108 ~~vI~ITGT--nGK----TTt~~~l~~iL~~  132 (472)
                      +-+|||+|.  .||    ||+.++|.+.|..
T Consensus        10 c~iigI~GgSgSGKs~iATtV~~~i~~~~~~   40 (220)
T TIGR00235        10 CIIIGISGGSGSGKSLIATTVARKIYEQLGK   40 (220)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHHHHHHCC
T ss_conf             1799701766101567899999999998314


No 168
>COG1428 Deoxynucleoside kinases [Nucleotide transport and metabolism]
Probab=67.23  E-value=3.4  Score=20.49  Aligned_cols=24  Identities=38%  Similarity=0.512  Sum_probs=19.3

Q ss_pred             CCEEEEECC--CCCCHHHHHHHHHHH
Q ss_conf             939998303--654201233467777
Q gi|254781101|r  108 ATIIAITGS--VGKTTTKEMLTIALS  131 (472)
Q Consensus       108 ~~vI~ITGT--nGKTTt~~~l~~iL~  131 (472)
                      .++|+|.|+  .||||.+++|++=|.
T Consensus         4 ~~~IvI~G~IG~GKSTLa~~La~~l~   29 (216)
T COG1428           4 AMVIVIEGMIGAGKSTLAQALAEHLG   29 (216)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHC
T ss_conf             60899844644687899999998838


No 169
>COG1663 LpxK Tetraacyldisaccharide-1-P 4'-kinase [Cell envelope biogenesis, outer membrane]
Probab=66.67  E-value=9  Score=17.71  Aligned_cols=32  Identities=25%  Similarity=0.298  Sum_probs=26.6

Q ss_pred             CCCCEEEE----ECCCCCCHHHHHHHHHHHHHHCCC
Q ss_conf             69939998----303654201233467777520112
Q gi|254781101|r  106 SKATIIAI----TGSVGKTTTKEMLTIALSSIKKTY  137 (472)
Q Consensus       106 ~~~~vI~I----TGTnGKTTt~~~l~~iL~~~~~~~  137 (472)
                      .+.|||.|    -|-+|||-+.-+|+.-|++.|-..
T Consensus        45 ~pvPVI~VGNltvGGtGKTP~vi~la~~l~~rG~~~   80 (336)
T COG1663          45 APVPVICVGNLTVGGTGKTPVVIWLAEALQARGVRV   80 (336)
T ss_pred             CCCCEEEECCEEECCCCCCHHHHHHHHHHHHCCCEE
T ss_conf             788789985577778996889999999998669736


No 170
>pfam01656 CbiA CobQ/CobB/MinD/ParA nucleotide binding domain. This family consists of various cobyrinic acid a,c-diamide synthases. These include CbiA and CbiP from S.typhimurium, and CobQ from R. capsulatus. These amidases catalyse amidations to various side chains of hydrogenobyrinic acid or cobyrinic acid a,c-diamide in the biosynthesis of cobalamin (vitamin B12) from uroporphyrinogen III. Vitamin B12 is an important cofactor and an essential nutrient for many plants and animals and is primarily produced by bacteria. The family also contains dethiobiotin synthetases as well as the plasmid partitioning proteins of the MinD/ParA family.
Probab=66.41  E-value=2.4  Score=21.57  Aligned_cols=23  Identities=39%  Similarity=0.369  Sum_probs=19.0

Q ss_pred             ECCCCCCHHHHHHHHHHHHHHCC
Q ss_conf             30365420123346777752011
Q gi|254781101|r  114 TGSVGKTTTKEMLTIALSSIKKT  136 (472)
Q Consensus       114 TGTnGKTTt~~~l~~iL~~~~~~  136 (472)
                      -|-.||||++..+++.|.+.|+.
T Consensus         7 KGGVGKTT~a~nLA~~la~~G~r   29 (212)
T pfam01656         7 KGGVGKTTLAANLARALAKRGYR   29 (212)
T ss_pred             CCCHHHHHHHHHHHHHHHHCCCC
T ss_conf             99806999999999999978997


No 171
>cd03109 DTBS Dethiobiotin synthetase (DTBS) is the penultimate enzyme in the biotin biosynthesis pathway in Escherichia coli and other microorganisms. The enzyme catalyzes formation of the ureido ring of dethiobiotin from (7R,8S)-7,8-diaminononanoic acid (DAPA) and carbon dioxide. The enzyme utilizes carbon dioxide instead of hydrogen carbonate as substrate and is dependent on ATP and divalent metal ions as cofactors.
Probab=65.72  E-value=2.2  Score=21.83  Aligned_cols=39  Identities=33%  Similarity=0.434  Sum_probs=26.8

Q ss_pred             ECC-CCCCHHHHHHHHHHHHHHCCCCCHHHHHCCCCCCCHHCCCCCCCHHHHHC
Q ss_conf             303-65420123346777752011222122110145741000123221444301
Q gi|254781101|r  114 TGS-VGKTTTKEMLTIALSSIKKTYACIGSYNNHIGVPLTLARMPVDVDFGIFE  166 (472)
Q Consensus       114 TGT-nGKTTt~~~l~~iL~~~~~~~~t~gn~Nn~iGvpltll~~~~~~~~~V~E  166 (472)
                      ||| .|||.++..+...|++.|......+        |      -..+|+.++|
T Consensus         6 TdT~VGKT~vt~~l~~~l~~~G~~v~~~K--------P------v~t~D~vlVE   45 (134)
T cd03109           6 TGTDIGKTVATAILARALKEKGYRVAPLK--------P------VQTYDFVLVE   45 (134)
T ss_pred             CCCCCCHHHHHHHHHHHHHHCCCCEEEEC--------H------HHCCCEEEEE
T ss_conf             78887689999999999997799177875--------6------6727989998


No 172
>COG0125 Tmk Thymidylate kinase [Nucleotide transport and metabolism]
Probab=65.39  E-value=4.1  Score=19.99  Aligned_cols=33  Identities=36%  Similarity=0.404  Sum_probs=26.2

Q ss_pred             CCCEEEEECC--CCCCHHHHHHHHHHHHHH-CCCCC
Q ss_conf             9939998303--654201233467777520-11222
Q gi|254781101|r  107 KATIIAITGS--VGKTTTKEMLTIALSSIK-KTYAC  139 (472)
Q Consensus       107 ~~~vI~ITGT--nGKTTt~~~l~~iL~~~~-~~~~t  139 (472)
                      ++..|+|.|-  .||||..++++..|...| +|+.|
T Consensus         2 ~g~fI~iEGiDGaGKTT~~~~L~~~l~~~g~~v~~t   37 (208)
T COG0125           2 KGMFIVIEGIDGAGKTTQAELLKERLEERGIKVVLT   37 (208)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEE
T ss_conf             962999978888988999999999999829807998


No 173
>cd02037 MRP-like MRP (Multiple Resistance and pH adaptation) is a homologue of the Fer4_NifH superfamily. Like the other members of the superfamily, MRP contains a ATP-binding domain at the N-termini. It is found in bacteria as a membrane-spanning protein and functions as a Na+/H+ antiporter.
Probab=65.39  E-value=3.6  Score=20.36  Aligned_cols=28  Identities=36%  Similarity=0.540  Sum_probs=21.3

Q ss_pred             EEEEE---CCCCCCHHHHHHHHHHHHHHCCC
Q ss_conf             99983---03654201233467777520112
Q gi|254781101|r  110 IIAIT---GSVGKTTTKEMLTIALSSIKKTY  137 (472)
Q Consensus       110 vI~IT---GTnGKTTt~~~l~~iL~~~~~~~  137 (472)
                      ||+|+   |-.||||++..++..|.+.|+.+
T Consensus         1 vi~v~s~kggvgkst~~~~la~~l~~~g~~v   31 (169)
T cd02037           1 VIAVMSGKGGVGKSTVAVNLALALAKLGYKV   31 (169)
T ss_pred             CEEEECCCCCCCHHHHHHHHHHHHHHCCCCE
T ss_conf             9899749998819999999999999879978


No 174
>KOG1970 consensus
Probab=64.57  E-value=6.1  Score=18.84  Aligned_cols=46  Identities=24%  Similarity=0.328  Sum_probs=33.5

Q ss_pred             EECCHHHHHHHHHHHHHHCCCCCEEEEECC--CCCCHHHHHHHHHHHHH
Q ss_conf             959989999999999983069939998303--65420123346777752
Q gi|254781101|r   87 GVDDVLGALNKLAVAARLRSKATIIAITGS--VGKTTTKEMLTIALSSI  133 (472)
Q Consensus        87 ~v~d~~~al~~la~~~~~~~~~~vI~ITGT--nGKTTt~~~l~~iL~~~  133 (472)
                      .++++..+|..+ .....+....+.=+||-  +|||||...|+..|.-.
T Consensus        90 KI~eVk~WL~~~-~~~~~~l~~~iLLltGPsGcGKSTtvkvLskelg~~  137 (634)
T KOG1970          90 KISEVKQWLKQV-AEFTPKLGSRILLLTGPSGCGKSTTVKVLSKELGYQ  137 (634)
T ss_pred             HHHHHHHHHHHH-HHHCCCCCCEEEEEECCCCCCCHHHHHHHHHHHCCE
T ss_conf             489999999999-974536676079985798887131999999864802


No 175
>PRK04923 ribose-phosphate pyrophosphokinase; Provisional
Probab=64.52  E-value=9.9  Score=17.45  Aligned_cols=92  Identities=14%  Similarity=0.123  Sum_probs=42.0

Q ss_pred             CEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHH
Q ss_conf             11331000256532101257778741110268713885123541710589999999999864998999988038989985
Q gi|254781101|r  338 FFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFHVLALKDA  417 (472)
Q Consensus       338 ~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~~~~~~~~  417 (472)
                      .+.++||-= .+-.+|..|.+.|++.   +. ++|.+...=   |-.+..-.    +.+...+++.|+..-.-..  .+.
T Consensus       219 ~~IIVDDiI-dTGgTl~~aa~~Lk~~---GA-~~V~~~~TH---glfs~~A~----~rl~~s~i~~ivvTnTip~--~~~  284 (319)
T PRK04923        219 TCVLVDDLV-DTAGTLCAAAAALKQR---GA-LKVVAYITH---PVLSGPAV----DNINNSQLDELVVTDTIPL--SEA  284 (319)
T ss_pred             EEEEECCHH-CCCHHHHHHHHHHHHC---CC-CEEEEEEEC---CCCCHHHH----HHHHHCCCCEEEEECCCCC--CHH
T ss_conf             699966432-0651299999999875---99-868999979---76886799----9997089988998289658--622


Q ss_pred             CCCCCCEEEECCHHHHHHHHHHHCCCC
Q ss_conf             113797999789899999999844789
Q gi|254781101|r  418 LPRSIHVHYSETMDGLFLFIQSSLVDG  444 (472)
Q Consensus       418 ~~~~~~~~~~~~~e~a~~~l~~~~~~g  444 (472)
                      .+...++...+ ...++..+...+..|
T Consensus       285 ~~~~~kl~vls-va~llA~aI~ri~~~  310 (319)
T PRK04923        285 ARTCAKIRQLS-VAELLAETIRRIAFG  310 (319)
T ss_pred             HCCCCCCEEEE-HHHHHHHHHHHHHCC
T ss_conf             33589838997-389999999998679


No 176
>cd02038 FleN-like FleN is a member of the Fer4_NifH superfamily. It shares the common function as an ATPase, with the ATP-binding domain at the N-terminus. In Pseudomonas aeruginosa, FleN gene is involved in regulating the number of flagella and chemotactic motility by influencing FleQ activity.
Probab=64.49  E-value=3.8  Score=20.19  Aligned_cols=51  Identities=35%  Similarity=0.604  Sum_probs=33.2

Q ss_pred             EEEEE---CCCCCCHHHHHHHHHHHHHHCCCCCHHHHHCCCCCCCHHCCCCCCCHHHHHCCCC
Q ss_conf             99983---0365420123346777752011222122110145741000123221444301566
Q gi|254781101|r  110 IIAIT---GSVGKTTTKEMLTIALSSIKKTYACIGSYNNHIGVPLTLARMPVDVDFGIFELGM  169 (472)
Q Consensus       110 vI~IT---GTnGKTTt~~~l~~iL~~~~~~~~t~gn~Nn~iGvpltll~~~~~~~~~V~E~g~  169 (472)
                      ||+|+   |-.||||++--++..|.+.|+.+.-.   --++|++    +  -+.||.++.+++
T Consensus         1 vi~v~sgKgGvGkt~~~~nLa~~la~~G~~vll~---D~D~g~a----n--~~~D~viiD~~a   54 (139)
T cd02038           1 IIAVTSGKGGVGKTNISANLALALAKLGKRVLLL---DADLGLA----N--LDYDYIIIDTGA   54 (139)
T ss_pred             CEEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEE---ECCCCCC----C--CCCCEEEEECCC
T ss_conf             9899649999839999999999999789969999---8989996----5--799999994899


No 177
>COG0132 BioD Dethiobiotin synthetase [Coenzyme metabolism]
Probab=64.34  E-value=5  Score=19.42  Aligned_cols=29  Identities=28%  Similarity=0.277  Sum_probs=23.5

Q ss_pred             CCEEEEECCC---CCCHHHHHHHHHHHHHHCC
Q ss_conf             9399983036---5420123346777752011
Q gi|254781101|r  108 ATIIAITGSV---GKTTTKEMLTIALSSIKKT  136 (472)
Q Consensus       108 ~~vI~ITGTn---GKTTt~~~l~~iL~~~~~~  136 (472)
                      .+.+=||||.   |||.++..|++.|++.|..
T Consensus         2 ~~~~fVtGTDT~VGKTv~S~aL~~~l~~~g~~   33 (223)
T COG0132           2 MKRFFVTGTDTGVGKTVVSAALAQALKQQGYS   33 (223)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHCCCC
T ss_conf             73699982799964999999999999968970


No 178
>PRK13185 chlL protochlorophyllide reductase iron-sulfur ATP-binding protein; Provisional
Probab=63.90  E-value=5.2  Score=19.29  Aligned_cols=31  Identities=35%  Similarity=0.536  Sum_probs=24.8

Q ss_pred             CCEEEEECC--CCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             939998303--6542012334677775201122
Q gi|254781101|r  108 ATIIAITGS--VGKTTTKEMLTIALSSIKKTYA  138 (472)
Q Consensus       108 ~~vI~ITGT--nGKTTt~~~l~~iL~~~~~~~~  138 (472)
                      ..+|||.|-  -|||||+.-++..|...|+.+-
T Consensus         2 ~~~iaiyGKGGIGKSTttaNlsaALA~~GkkV~   34 (269)
T PRK13185          2 ALVLAVYGKGGIGKSTTSSNLSAALAKLGKKVL   34 (269)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEE
T ss_conf             539999789954788899999999997699389


No 179
>TIGR02528 EutP ethanolamine utilization protein, EutP; InterPro: IPR012381   Members of this family function in ethanolamine  and propanediol  degradation pathways. Both pathways require coenzyme B12 (adenosylcobalamin, AdoCbl). Bacteria that harbour these pathways can use ethanolamine as a source of carbon and nitrogen, or propanediol as a sole carbon and energy source, respectively.  The exact roles of the EutP and PduV proteins in these respective pathways are not yet determined. Members of this family contain P-loop consensus motifs in the N-terminal part, and are distantly related to various GTPases and ATPases, including ATPase components of transport systems.  Propanediol degradation is thought to be important for the natural Salmonella populations, since propanediol is produced by the fermentation of the common plant sugars rhamnose and fucose , . More than 10f the Salmonella enterica genome is devoted to the utilisation of propanediol and cobalamin biosynthesis. In vivo expression technology has indicated that propanediol utilisation (pdu) genes may be important for growth in host tissues, and competitive index studies with mice have shown that pdu mutations confer a virulence defect , . The pdu operon is contiguous and co-regulated with the cobalamin (B12) biosynthesis cob operon, indicating that propanediol catabolism may be the primary reason for de novo B12 synthesis in Salmonella , , . Please see IPR003207 from INTERPRO, IPR003208 from INTERPRO, IPR009204 from INTERPRO, IPR009191 from INTERPRO, IPR009192 from INTERPRO for more details on the propanediol utilisation pathway and the pdu operon.; GO: 0005524 ATP binding, 0006576 biogenic amine metabolic process.
Probab=63.77  E-value=4.7  Score=19.57  Aligned_cols=85  Identities=25%  Similarity=0.235  Sum_probs=37.7

Q ss_pred             EEEECC--CCCCHHHHHHHHHHHHHHC----------CCCCHHHHHCCCCCCCHHCCCCCCCHHHHHCCCCCCCCC-C--
Q ss_conf             998303--6542012334677775201----------122212211014574100012322144430156644332-1--
Q gi|254781101|r  111 IAITGS--VGKTTTKEMLTIALSSIKK----------TYACIGSYNNHIGVPLTLARMPVDVDFGIFELGMSHLGE-I--  175 (472)
Q Consensus       111 I~ITGT--nGKTTt~~~l~~iL~~~~~----------~~~t~gn~Nn~iGvpltll~~~~~~~~~V~E~g~~~~ge-i--  175 (472)
                      |.+-|+  +||||.+.-|.--=-..-|          ..-|||-|-++=+.--+|+-.-.|.|+.++=.+++..-. +  
T Consensus         3 ~~f~G~~gCGKTTL~q~L~g~~~~YKKTQAvE~~~k~~IDTPGEY~enr~~Y~AL~vtaaDAd~i~lV~~a~~~~~~f~P   82 (144)
T TIGR02528         3 IMFIGSVGCGKTTLTQALQGEEIKYKKTQAVEYKDKEAIDTPGEYVENRRYYSALIVTAADADVIALVQSATDEESRFSP   82 (144)
T ss_pred             EEEEECCCCCHHHHHHHCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHCCEEEEEEECCCCCCCCCCC
T ss_conf             78871588874435431168732102334454258886559850015752378888887210236677357764223785


Q ss_pred             CCCCCCCC-CCEEEEEEECCC
Q ss_conf             12122323-220255531210
Q gi|254781101|r  176 RFLTHLVR-PHIAVITTIAPA  195 (472)
Q Consensus       176 ~~L~~i~~-P~iaiiTNI~~d  195 (472)
                      ..++=+.+ |-|||||=+..+
T Consensus        83 gF~~~f~kK~~IG~vTK~DLA  103 (144)
T TIGR02528        83 GFASIFVKKEVIGIVTKIDLA  103 (144)
T ss_pred             CCCCCCCCCCEEEEEEECCCC
T ss_conf             000236788634788403788


No 180
>PRK03946 pdxA 4-hydroxythreonine-4-phosphate dehydrogenase; Provisional
Probab=63.61  E-value=7.2  Score=18.35  Aligned_cols=10  Identities=40%  Similarity=0.321  Sum_probs=3.4

Q ss_pred             CCCCHHHHHH
Q ss_conf             5321012577
Q gi|254781101|r  349 NPASMKAAIS  358 (472)
Q Consensus       349 nP~S~~aal~  358 (472)
                      ||.||.+|++
T Consensus       287 ~~~s~~~Ai~  296 (304)
T PRK03946        287 NTKSYLNAIK  296 (304)
T ss_pred             CHHHHHHHHH
T ss_conf             9699999999


No 181
>TIGR02397 dnaX_nterm DNA polymerase III, subunits gamma and tau; InterPro: IPR012763    This entry represents the well-conserved first N-terminal domain of DnaX, approx. 365 aa. The full-length product of the dnaX gene in Escherichia coli encodes the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the extreme thermophile Thermus thermophilis.; GO: 0003887 DNA-directed DNA polymerase activity, 0005524 ATP binding, 0006260 DNA replication, 0009360 DNA polymerase III complex.
Probab=63.39  E-value=2.5  Score=21.35  Aligned_cols=60  Identities=20%  Similarity=0.238  Sum_probs=33.4

Q ss_pred             EEECC--CCCCHHHHHHHHHHHHHHCCCCCHHHHHCCCCCCCHHCCCCCCCHHHHHCC-CCCCCC--CCCCC
Q ss_conf             98303--654201233467777520112221221101457410001232214443015-664433--21121
Q gi|254781101|r  112 AITGS--VGKTTTKEMLTIALSSIKKTYACIGSYNNHIGVPLTLARMPVDVDFGIFEL-GMSHLG--EIRFL  178 (472)
Q Consensus       112 ~ITGT--nGKTTt~~~l~~iL~~~~~~~~t~gn~Nn~iGvpltll~~~~~~~~~V~E~-g~~~~g--ei~~L  178 (472)
                      =-||+  .||||++..+|..|.-. .....|=|-      +-+-.....+.-.=|+|+ |+|+-|  ||..|
T Consensus        40 LF~GpRGtGKTS~ARIfAKaLNC~-~~~~~PCn~------C~~C~~i~~g~~~DviEiDAASN~gVD~IR~l  104 (363)
T TIGR02397        40 LFSGPRGTGKTSIARIFAKALNCQ-GPDGEPCNE------CESCKEINSGSSLDVIEIDAASNNGVDDIREL  104 (363)
T ss_pred             EECCCCCCCHHHHHHHHHHHHCCC-CCCCCCCCC------CCHHHHHHCCCCCCEEEECCCCCCCHHHHHHH
T ss_conf             502859976355899999986588-787787777------50227765289866688648656878899999


No 182
>PRK13506 formate--tetrahydrofolate ligase; Provisional
Probab=63.15  E-value=10  Score=17.28  Aligned_cols=32  Identities=28%  Similarity=0.365  Sum_probs=26.0

Q ss_pred             HCCCCCEEEEECCC------CCCHHHHHHHHHHHHHHC
Q ss_conf             30699399983036------542012334677775201
Q gi|254781101|r  104 LRSKATIIAITGSV------GKTTTKEMLTIALSSIKK  135 (472)
Q Consensus       104 ~~~~~~vI~ITGTn------GKTTt~~~l~~iL~~~~~  135 (472)
                      .+.+++.|-||+.+      |||||+==|++-|...|+
T Consensus        50 ~~~~gklilVTaitPTP~GEGKTTttIGL~~aL~~lgk   87 (577)
T PRK13506         50 DQPKGKLVIVTAVTPTPLGEGKTVTTIGLTQGLNALGQ   87 (577)
T ss_pred             CCCCCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCC
T ss_conf             38996499998568988989841109879999987198


No 183
>TIGR00347 bioD dethiobiotin synthase; InterPro: IPR004472 The enzyme is involved in biotin biosynthesis and catalyses the reaction (CO2 + 7,8-diaminononanoate + ATP = dethiobiotin + phosphate + ADP). The enzyme binds ATP and requires magnesium as a co-factor. The Thr residue at position seven of the seed alignment is necessary for the binding of ATP.; GO: 0004141 dethiobiotin synthase activity, 0005524 ATP binding, 0009102 biotin biosynthetic process.
Probab=63.14  E-value=3.4  Score=20.48  Aligned_cols=26  Identities=31%  Similarity=0.414  Sum_probs=21.6

Q ss_pred             EECC---CCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             8303---6542012334677775201122
Q gi|254781101|r  113 ITGS---VGKTTTKEMLTIALSSIKKTYA  138 (472)
Q Consensus       113 ITGT---nGKTTt~~~l~~iL~~~~~~~~  138 (472)
                      ||||   .|||-++..|++-|++.|..++
T Consensus         2 vTGtDT~VGKT~~ss~La~~lk~~G~~~g   30 (187)
T TIGR00347         2 VTGTDTGVGKTVVSSALAKKLKKAGYSVG   30 (187)
T ss_pred             CEEEECCCCHHHHHHHHHHHHHHCCCCEE
T ss_conf             10224586178998999999997598525


No 184
>PRK08356 hypothetical protein; Provisional
Probab=63.05  E-value=4.3  Score=19.87  Aligned_cols=28  Identities=29%  Similarity=0.445  Sum_probs=18.7

Q ss_pred             CEEEEECCC--CCCHHHHHHHHHHHHHHCCCCCH
Q ss_conf             399983036--54201233467777520112221
Q gi|254781101|r  109 TIIAITGSV--GKTTTKEMLTIALSSIKKTYACI  140 (472)
Q Consensus       109 ~vI~ITGTn--GKTTt~~~l~~iL~~~~~~~~t~  140 (472)
                      -+|||||-+  ||+|++.++    +..|-++.+.
T Consensus         6 mIIgitG~~gSGK~tva~~l----~~~G~~~~s~   35 (195)
T PRK08356          6 MIVGIAGKIAAGKTTVAKFL----EELGFCRISC   35 (195)
T ss_pred             EEEEEECCCCCCHHHHHHHH----HHCCCEEEEC
T ss_conf             69998589988789999999----9869928842


No 185
>TIGR01186 proV glycine betaine/L-proline transport ATP binding subunit; InterPro: IPR005892   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 family comprises the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporters is the obligatory coupling of ATP hydrolysis to substrate translocation.   Functionally, this transport system is involved in osmoregulation. Under conditions of stress, the organism recruits this transport system to accumulate glycine betaine and other solutes which offer osmo-protection. It has been demonstrated that glycine betaine uptake is accompanied by symport with sodium ions. The locus has been named variously as proU or opuA. A gene library from L. lactis functionally complements an Escherichia coli proU mutant. The complementing locus is similar to a opuA locus in Bacillus subtlis. This clarifies the differences in nomenclature.; GO: 0005524 ATP binding, 0015171 amino acid transmembrane transporter activity, 0006865 amino acid transport, 0016020 membrane.
Probab=62.97  E-value=2.2  Score=21.75  Aligned_cols=31  Identities=29%  Similarity=0.426  Sum_probs=20.7

Q ss_pred             CCCEEEEECC--CCCCHHHHHHHHHHHH-HHCCC
Q ss_conf             9939998303--6542012334677775-20112
Q gi|254781101|r  107 KATIIAITGS--VGKTTTKEMLTIALSS-IKKTY  137 (472)
Q Consensus       107 ~~~vI~ITGT--nGKTTt~~~l~~iL~~-~~~~~  137 (472)
                      ++-++.|-|-  +||||+..||..+.+. +|+++
T Consensus        18 ~GEi~vi~GlSGsGKsT~vrmlNRLIEPt~G~i~   51 (372)
T TIGR01186        18 KGEIFVIMGLSGSGKSTLVRMLNRLIEPTAGQIF   51 (372)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHCCCCCCCCEE
T ss_conf             5438999778998578999998722577787467


No 186
>PRK13233 nifH nitrogenase reductase; Reviewed
Probab=62.95  E-value=5.9  Score=18.95  Aligned_cols=31  Identities=32%  Similarity=0.384  Sum_probs=23.7

Q ss_pred             CCEEEEEC--CCCCCHHHHHHHHHHHH-HHCCCC
Q ss_conf             93999830--36542012334677775-201122
Q gi|254781101|r  108 ATIIAITG--SVGKTTTKEMLTIALSS-IKKTYA  138 (472)
Q Consensus       108 ~~vI~ITG--TnGKTTt~~~l~~iL~~-~~~~~~  138 (472)
                      .+.|||.|  -.|||||+.=|+..|.. .|+.+-
T Consensus         2 ~~~iaiyGKGGIGKSTTt~NLaaALA~l~GkrVl   35 (275)
T PRK13233          2 TRKIAIYGKGGIGKSTTTQNTAAAMAHFHDKKVF   35 (275)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHHHCCCEEE
T ss_conf             7389998998544654599999999964798899


No 187
>TIGR02884 spore_pdaA delta-lactam-biosynthetic de-N-acetylase; InterPro: IPR014235    Muramic delta-lactam is an unusual constituent of peptidoglycan, found only in bacterial spores, in the peptidoglycan wall or spore cortex. This entry represents a subset of the larger polysaccharide deacetylase family that is specifically involved in delta-lactam biosynthesis. PdaA from Bacillus subtilis acts immediately after CwlD, an N-acetylmuramoyl-L-alanine amidase and performs a de-N-acetylation. PdaA may also perform the subsequent transpeptidation that leads to lactam ring formation, as heterologous expression in Escherichia coli of CwlD and PdaA together is sufficient for delta-lactam production..
Probab=62.93  E-value=6.5  Score=18.63  Aligned_cols=73  Identities=15%  Similarity=0.150  Sum_probs=48.4

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHCCCCCCEEEECCHHHHHHHHHHHCCCCCEEEE---ECCCHHHHH
Q ss_conf             71058999999999986499899998803898998511379799978989999999984478989999---771325489
Q gi|254781101|r  382 GELSQSFHIDLAEVLSLYNISHVWLSGFHVLALKDALPRSIHVHYSETMDGLFLFIQSSLVDGDVVVV---KSSNSCGFY  458 (472)
Q Consensus       382 G~~~~~~h~~i~~~~~~~~~d~v~~~G~~~~~~~~~~~~~~~~~~~~~~e~a~~~l~~~~~~gdiVLi---KGSr~~~le  458 (472)
                      |.+|+.    -..+-.+.+...||+.=...         .-.+..-...++|-..+.+.++||.|+|+   +--|+..|+
T Consensus       139 G~fSE~----tL~~t~~LGY~~vFWSlAy~---------DW~~D~Q~G~~~A~~~im~~~HpGai~LLHAVS~dNA~aLd  205 (225)
T TIGR02884       139 GKFSER----TLAYTKELGYKTVFWSLAYK---------DWEVDKQKGKEYAYKQIMKKIHPGAILLLHAVSKDNAEALD  205 (225)
T ss_pred             CCCHHH----HHHHHHHCCCCEEEEEEEEC---------CCCCCCCCCHHHHHHHHHHHCCCHHHHHHHCCCHHHHHHHH
T ss_conf             754057----89999974882110012202---------67769877877788777541570241332314745899999


Q ss_pred             HHHHHHHHH
Q ss_conf             999999985
Q gi|254781101|r  459 RLINLLLEE  467 (472)
Q Consensus       459 ~iv~~L~~~  467 (472)
                      +|++.|+++
T Consensus       206 ~~i~~lk~~  214 (225)
T TIGR02884       206 EIIKDLKEQ  214 (225)
T ss_pred             HHHHHHHHC
T ss_conf             999999865


No 188
>KOG3347 consensus
Probab=62.81  E-value=4.7  Score=19.60  Aligned_cols=26  Identities=31%  Similarity=0.277  Sum_probs=19.2

Q ss_pred             CEEEEECC--CCCCHHHHHHHHHHHHHH
Q ss_conf             39998303--654201233467777520
Q gi|254781101|r  109 TIIAITGS--VGKTTTKEMLTIALSSIK  134 (472)
Q Consensus       109 ~vI~ITGT--nGKTTt~~~l~~iL~~~~  134 (472)
                      |-|-||||  .||||+.+-++..+.-.+
T Consensus         8 PNILvtGTPG~GKstl~~~lae~~~~~~   35 (176)
T KOG3347           8 PNILVTGTPGTGKSTLAERLAEKTGLEY   35 (176)
T ss_pred             CCEEEECCCCCCCHHHHHHHHHHHCCCE
T ss_conf             8879867999880259999999739856


No 189
>TIGR01969 minD_arch cell division ATPase MinD; InterPro: IPR010224   Proper placement of the bacterial cell division site requires the site-specific inactivation of other potential division sites. In Escherichia coli, selection of the correct mid-cell site is mediated by the MinC, MinD and MinE proteins. Several members of this family are found in archaeal genomes but their function is uncharacterised. More distantly related proteins include flagellar biosynthesis proteins and ParA chromosome partitioning proteins.    This entry represents the archaeal MinD family. The exact roles of the various archaeal MinD homologs are unknown. .
Probab=62.68  E-value=3.2  Score=20.70  Aligned_cols=23  Identities=39%  Similarity=0.531  Sum_probs=20.0

Q ss_pred             CCCCCCHHHHHHHHHHHHHHCCC
Q ss_conf             03654201233467777520112
Q gi|254781101|r  115 GSVGKTTTKEMLTIALSSIKKTY  137 (472)
Q Consensus       115 GTnGKTTt~~~l~~iL~~~~~~~  137 (472)
                      |-.|||||+.=|+--|.+.|+.+
T Consensus        10 GGtGKTT~tANLgVALA~~Gk~V   32 (258)
T TIGR01969        10 GGTGKTTITANLGVALAKLGKKV   32 (258)
T ss_pred             CCCCHHHEEEHHHHHHHHCCCEE
T ss_conf             89861400000778898609768


No 190
>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB.  This alignment contains the C-terminal domain, which is the ATPase.
Probab=62.61  E-value=4.8  Score=19.51  Aligned_cols=29  Identities=38%  Similarity=0.412  Sum_probs=14.0

Q ss_pred             HHHHHHHHHCCCCCEEEEECC--CCCCHHHHHHH
Q ss_conf             999999983069939998303--65420123346
Q gi|254781101|r   96 NKLAVAARLRSKATIIAITGS--VGKTTTKEMLT  127 (472)
Q Consensus        96 ~~la~~~~~~~~~~vI~ITGT--nGKTTt~~~l~  127 (472)
                      .-|....+.+.+   |-|+|.  .||||+-..+.
T Consensus        16 ~~L~~~v~~~~n---IlIsG~tGSGKTTll~al~   46 (186)
T cd01130          16 AYLWLAVEARKN---ILISGGTGSGKTTLLNALL   46 (186)
T ss_pred             HHHHHHHHCCCC---EEEECCCCCCHHHHHHHHH
T ss_conf             999999985998---9998999998999999999


No 191
>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate. The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.
Probab=62.60  E-value=2.7  Score=21.23  Aligned_cols=22  Identities=32%  Similarity=0.599  Sum_probs=14.7

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHH
Q ss_conf             99983036542012334677775
Q gi|254781101|r  110 IIAITGSVGKTTTKEMLTIALSS  132 (472)
Q Consensus       110 vI~ITGTnGKTTt~~~l~~iL~~  132 (472)
                      |.||.|| ||||+...|+.-|..
T Consensus         4 v~GvsGs-GKSTia~~La~~lg~   25 (150)
T cd02021           4 VMGVSGS-GKSTVGKALAERLGA   25 (150)
T ss_pred             EECCCCC-CHHHHHHHHHHHHCC
T ss_conf             9918999-999999999997199


No 192
>PRK12374 putative dithiobiotin synthetase; Provisional
Probab=62.51  E-value=4  Score=20.06  Aligned_cols=27  Identities=44%  Similarity=0.493  Sum_probs=20.7

Q ss_pred             EEEECC---CCCCHHHHHHHHHHHHHHCCC
Q ss_conf             998303---654201233467777520112
Q gi|254781101|r  111 IAITGS---VGKTTTKEMLTIALSSIKKTY  137 (472)
Q Consensus       111 I~ITGT---nGKTTt~~~l~~iL~~~~~~~  137 (472)
                      +=||||   .|||.++..|.+.|++.|..+
T Consensus         5 ~FITGTDTdVGKT~vsaaL~~~l~~~G~~v   34 (231)
T PRK12374          5 FFITGTDTSVGKTVVSRALLQALASQGKSV   34 (231)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCCE
T ss_conf             799878999539999999999999789948


No 193
>KOG2792 consensus
Probab=62.27  E-value=4.6  Score=19.67  Aligned_cols=11  Identities=9%  Similarity=0.135  Sum_probs=5.7

Q ss_pred             EECCCCCCHHH
Q ss_conf             83036542012
Q gi|254781101|r  113 ITGSVGKTTTK  123 (472)
Q Consensus       113 ITGTnGKTTt~  123 (472)
                      ++.+||++..+
T Consensus        39 ~~~~~~~s~~~   49 (280)
T KOG2792          39 LLETNGLSPLA   49 (280)
T ss_pred             EECCCCCCCCC
T ss_conf             32257888756


No 194
>COG0455 flhG Antiactivator of flagellar biosynthesis FleN, an ATPase [Cell motility]
Probab=62.19  E-value=6.2  Score=18.80  Aligned_cols=29  Identities=34%  Similarity=0.390  Sum_probs=21.6

Q ss_pred             CCEEEEE---CCCCCCHHHHHH-HHHHHHHHCC
Q ss_conf             9399983---036542012334-6777752011
Q gi|254781101|r  108 ATIIAIT---GSVGKTTTKEML-TIALSSIKKT  136 (472)
Q Consensus       108 ~~vI~IT---GTnGKTTt~~~l-~~iL~~~~~~  136 (472)
                      .++|+|+   |-.||||++.-+ +.+++..+++
T Consensus         2 ~~~Iav~SgKGGvGKTtitanlga~~~~~~~k~   34 (262)
T COG0455           2 TKVIAVVSGKGGVGKTTITANLGAALAALGGKV   34 (262)
T ss_pred             CEEEEEEECCCCCCHHHHHHHHHHHHHHHCCCE
T ss_conf             789999845887568989986999999648976


No 195
>pfam09140 MipZ ATPase MipZ. MipZ is an ATPase that forms a complex with the chromosome partitioning protein ParB near the chromosomal origin of replication. It is responsible for the temporal and spatial regulation of FtsZ ring formation.
Probab=62.08  E-value=3.5  Score=20.43  Aligned_cols=28  Identities=29%  Similarity=0.441  Sum_probs=22.4

Q ss_pred             EEEE---ECCCCCCHHHHHHHHHHHHHHCCC
Q ss_conf             9998---303654201233467777520112
Q gi|254781101|r  110 IIAI---TGSVGKTTTKEMLTIALSSIKKTY  137 (472)
Q Consensus       110 vI~I---TGTnGKTTt~~~l~~iL~~~~~~~  137 (472)
                      ||+|   -|-.|||||+--++..|...|+.+
T Consensus         2 IIaVaNqKGGvGKTTtavnLA~aLA~~G~rV   32 (261)
T pfam09140         2 VIVVGNEKGGSGKSTTAVHVAVALLYLGARV   32 (261)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCCE
T ss_conf             7999717898729999999999999889978


No 196
>cd00477 FTHFS Formyltetrahydrofolate synthetase (FTHFS) catalyzes the ATP-dependent activation of formate ion via its addition to the N10 position of tetrahydrofolate. FTHFS is a highly expressed key enzyme in both the Wood-Ljungdahl pathway of autotrophic CO2 fixation (acetogenesis) and the glycine synthase/reductase pathways of purinolysis. The key physiological role of this enzyme in acetogens is to catalyze the formylation of tetrahydrofolate, an initial step in the reduction of carbon dioxide and other one-carbon precursors to acetate. In purinolytic organisms, the enzymatic reaction is reversed, liberating formate from 10-formyltetrahydrofolate with concurrent production of ATP.
Probab=61.98  E-value=11  Score=17.15  Aligned_cols=33  Identities=36%  Similarity=0.371  Sum_probs=26.6

Q ss_pred             HHCCCCCEEEEECCC------CCCHHHHHHHHHHHHHHC
Q ss_conf             830699399983036------542012334677775201
Q gi|254781101|r  103 RLRSKATIIAITGSV------GKTTTKEMLTIALSSIKK  135 (472)
Q Consensus       103 ~~~~~~~vI~ITGTn------GKTTt~~~l~~iL~~~~~  135 (472)
                      .++.+++.|-||+-+      |||||+==|.+-|...|+
T Consensus        33 ~~~~~gklilVTaitPTP~GEGKTTttIGL~~aL~~~gk   71 (524)
T cd00477          33 EKRPDGKLILVTAITPTPAGEGKTTTTIGLAQALNAHGK   71 (524)
T ss_pred             CCCCCCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCC
T ss_conf             348995599998468888888853109989999987366


No 197
>PRK08691 DNA polymerase III subunits gamma and tau; Validated
Probab=61.82  E-value=3.2  Score=20.71  Aligned_cols=53  Identities=15%  Similarity=0.198  Sum_probs=23.9

Q ss_pred             HHHHHHHCCEEECCCCCCEEEEEEEECCCCCCCCE--EEECCCCCCCHHHHHHHHHHC
Q ss_conf             88998727999526887147467740222378988--897168874768889999986
Q gi|254781101|r    8 HDLLQAIQGHSIGIVPQGFVNGISIDSRSIAPQEA--FFAIKGPHYDGHDFILHAVQK   63 (472)
Q Consensus         8 ~~l~~~~~g~~~~~~~~~~i~~i~~dSr~v~~g~l--Fval~g~~~DGh~~i~~A~~~   63 (472)
                      +-+++.++   +.......-.|.|..-+.|..|.-  ++=+.+....|-+-+.+.+++
T Consensus        56 ri~Ak~lN---C~~~~~~~pCg~C~~C~~i~~g~~~D~~EiDaAs~~~vdd~R~l~~~  110 (704)
T PRK08691         56 RILAKSLN---CENAQHGEPCGVCQSCTQIDAGRYVDLLEIDAASNTGIDNIREVLEN  110 (704)
T ss_pred             HHHHHHHC---CCCCCCCCCCCCCHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHH
T ss_conf             99999967---99999999787777678785589987477424544588999999985


No 198
>PRK04507 consensus
Probab=61.21  E-value=10  Score=17.32  Aligned_cols=16  Identities=31%  Similarity=0.582  Sum_probs=7.8

Q ss_pred             CCCCCHHHHHHHHHHH
Q ss_conf             6532101257778741
Q gi|254781101|r  348 ANPASMKAAISVLSQI  363 (472)
Q Consensus       348 AnP~S~~aal~~l~~~  363 (472)
                      |||.||.+|++.-.++
T Consensus       304 A~~~s~~~Ai~la~~~  319 (323)
T PRK04507        304 ADPSSLMAATALCARL  319 (323)
T ss_pred             CCHHHHHHHHHHHHHH
T ss_conf             9969999999999999


No 199
>pfam08353 DUF1727 Domain of unknown function (DUF1727). This domain of unknown function is found at the C-terminus of bacterial proteins which include UDP-N-acetylmuramyl tripeptide synthase and the related Mur ligase.
Probab=61.05  E-value=11  Score=17.04  Aligned_cols=96  Identities=17%  Similarity=0.139  Sum_probs=53.7

Q ss_pred             CCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHCCC----CCCE
Q ss_conf             532101257778741110268713885123541710589999999999864998999988038989985113----7979
Q gi|254781101|r  349 NPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFHVLALKDALPR----SIHV  424 (472)
Q Consensus       349 nP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~~~~~~~~~~~----~~~~  424 (472)
                      ||.++..+|+.+..-+.  +...++.+-|-.-=|.+-..+..-=.+.+.. .+..+++.|..+..++--++-    ..++
T Consensus         4 NP~G~~~~l~~i~~~~~--~~~~~~~lNd~~aDG~DvSWiWDvdFE~L~~-~~~~vivsG~Ra~DmAlRLkyAGv~~~~i   80 (110)
T pfam08353         4 NPAGLNEVLDMLATDPG--PKSLVILLNDNYADGRDVSWIWDVDFEKLNQ-NIRNIVVSGERAYDMALRLKYAGVPEEKI   80 (110)
T ss_pred             CCHHHHHHHHHHHCCCC--CCEEEEEECCCCCCCCCCCEEEECCHHHHCC-CCCEEEEECCCHHHHHHHEEECCCCHHHE
T ss_conf             83769999999853899--8549999658577886563640456778354-77679997352999786723368377781


Q ss_pred             EEECCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             9978989999999984478989999
Q gi|254781101|r  425 HYSETMDGLFLFIQSSLVDGDVVVV  449 (472)
Q Consensus       425 ~~~~~~e~a~~~l~~~~~~gdiVLi  449 (472)
                      ...++.+++++.+..  .+++.+.+
T Consensus        81 ~v~~d~~~ai~~~~~--~~~~~~yi  103 (110)
T pfam08353        81 IVEPDLEQAIEAIEE--SPTKTVYI  103 (110)
T ss_pred             EECCCHHHHHHHHHH--CCCCEEEE
T ss_conf             762899999999986--89981999


No 200
>COG3640 CooC CO dehydrogenase maturation factor [Cell division and chromosome partitioning]
Probab=60.69  E-value=5.7  Score=19.03  Aligned_cols=24  Identities=54%  Similarity=0.553  Sum_probs=18.3

Q ss_pred             EEEEECC--CCCCHHHHH-HHHHHHHH
Q ss_conf             9998303--654201233-46777752
Q gi|254781101|r  110 IIAITGS--VGKTTTKEM-LTIALSSI  133 (472)
Q Consensus       110 vI~ITGT--nGKTTt~~~-l~~iL~~~  133 (472)
                      .|||||-  .||||.+.+ +..+++..
T Consensus         2 kIaI~GKGG~GKTtiaalll~~l~~~~   28 (255)
T COG3640           2 KIAITGKGGVGKTTIAALLLKRLLSKG   28 (255)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCC
T ss_conf             699965997658999999999998648


No 201
>TIGR00986 3a0801s05tom22 mitochondrial import receptor subunit; InterPro: IPR005683    The mitochondrial protein translocase (MPT) family, which brings nuclearly encoded preproteins into mitochondria, is very complex with 19 currently identified protein constituents. These proteins include several chaperone proteins, four proteins of the outer membrane translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three "motor" proteins.The inner membrane translocase is formed of a complex with a number of proteins, including the Tim17, Tim23 and Tim44 subunits. This family is specific for the Tom22 proteins. ; GO: 0015450 P-P-bond-hydrolysis-driven protein transmembrane transporter activity, 0006886 intracellular protein transport, 0005741 mitochondrial outer membrane.
Probab=60.25  E-value=2.1  Score=21.89  Aligned_cols=50  Identities=20%  Similarity=0.202  Sum_probs=33.5

Q ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCHHHHHCCCCCCCHHCCCCCCCHHHHHC
Q ss_conf             365420123346777752011222122110145741000123221444301
Q gi|254781101|r  116 SVGKTTTKEMLTIALSSIKKTYACIGSYNNHIGVPLTLARMPVDVDFGIFE  166 (472)
Q Consensus       116 TnGKTTt~~~l~~iL~~~~~~~~t~gn~Nn~iGvpltll~~~~~~~~~V~E  166 (472)
                      +|+=.||+.++...+...|+..++...--=.||||+++ .+.++..|+-+|
T Consensus        78 ~~~~~ttt~fv~~~~~f~G~~aW~~stsaLLlGVPf~~-s~~eeq~l~emE  127 (152)
T TIGR00986        78 ADKYSTTTSFVKKLLSFAGKAAWAVSTSALLLGVPFAL-SLAEEQQLIEME  127 (152)
T ss_pred             CCCHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHH
T ss_conf             01100255899999876044578999989998889999-999876899998


No 202
>PRK00090 bioD dithiobiotin synthetase; Reviewed
Probab=60.21  E-value=5.1  Score=19.35  Aligned_cols=27  Identities=33%  Similarity=0.396  Sum_probs=21.4

Q ss_pred             EEEECC---CCCCHHHHHHHHHHHHHHCCC
Q ss_conf             998303---654201233467777520112
Q gi|254781101|r  111 IAITGS---VGKTTTKEMLTIALSSIKKTY  137 (472)
Q Consensus       111 I~ITGT---nGKTTt~~~l~~iL~~~~~~~  137 (472)
                      |=||||   .|||+++..|.+.|++.|..+
T Consensus         2 ifI~GT~T~vGKT~vt~~L~~~l~~~G~~v   31 (223)
T PRK00090          2 LFVTGTDTGVGKTVVTAALAQALREQGYRV   31 (223)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCCE
T ss_conf             899868999769999999999999789948


No 203
>cd02042 ParA ParA and ParB of Caulobacter crescentus belong to a conserved family of bacterial proteins implicated in chromosome segregation. ParB binds to DNA sequences adjacent to the origin of replication and localizes to opposite cell poles shortly following the initiation of DNA replication. ParB regulates the ParA ATPase activity by promoting nucleotide exchange in a fashion reminiscent of the exchange factors of eukaryotic G proteins. ADP-bound ParA binds single-stranded DNA, whereas the ATP-bound form dissociates ParB from its DNA binding sites. Increasing the fraction of ParA-ADP in the cell inhibits cell division, suggesting that this simple nucleotide switch may regulate cytokinesis. ParA shares sequence similarity to a conserved and widespread family of ATPases which includes the repA protein of the repABC operon in R. etli Sym plasmid. This operon is involved in the plasmid replication and partition.
Probab=60.05  E-value=4.1  Score=19.99  Aligned_cols=73  Identities=29%  Similarity=0.320  Sum_probs=43.5

Q ss_pred             EEECCCCCCHHHHHHHHHHHHHHCCCCCHHHHHCCCCCCCHHCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCCEEEEEE
Q ss_conf             98303654201233467777520112221221101457410001232214443015664433211212232322025553
Q gi|254781101|r  112 AITGSVGKTTTKEMLTIALSSIKKTYACIGSYNNHIGVPLTLARMPVDVDFGIFELGMSHLGEIRFLTHLVRPHIAVITT  191 (472)
Q Consensus       112 ~ITGTnGKTTt~~~l~~iL~~~~~~~~t~gn~Nn~iGvpltll~~~~~~~~~V~E~g~~~~gei~~L~~i~~P~iaiiTN  191 (472)
                      .--|-.||||++-.++..|...|..+              -+..++++.|+.++-...+ .+.... .-+..-|. +|.-
T Consensus         6 n~KGGvGKtt~~~~la~~~a~~g~~v--------------l~iD~DpQyD~iiIDtpp~-~~~~~~-~al~~aD~-viiP   68 (104)
T cd02042           6 NQKGGVGKTTTAVNLAAALARRGKRV--------------LLIDLDPQYDYIIIDTPPS-LGLLTR-NALAAADL-VLIP   68 (104)
T ss_pred             ECCCCCCHHHHHHHHHHHHHHCCCEE--------------EEEECCCCCCEEEEECCCC-CCHHHH-HHHHHCCE-EEEE
T ss_conf             38998768999999999999779929--------------9997798888899979499-989999-99997899-9998


Q ss_pred             ECCCHHHHHH
Q ss_conf             1210123444
Q gi|254781101|r  192 IAPAHLSNFS  201 (472)
Q Consensus       192 I~~dHld~~~  201 (472)
                      +.++-.+..+
T Consensus        69 ~~p~~~~~~~   78 (104)
T cd02042          69 VQPSPLDLDG   78 (104)
T ss_pred             CCCCHHHHHH
T ss_conf             3698899999


No 204
>pfam03205 MobB Molybdopterin guanine dinucleotide synthesis protein B. This protein contains a P-loop.
Probab=59.83  E-value=6.6  Score=18.60  Aligned_cols=27  Identities=30%  Similarity=0.267  Sum_probs=21.0

Q ss_pred             CEEEEECC--CCCCHHHHHHHHHHHHHHC
Q ss_conf             39998303--6542012334677775201
Q gi|254781101|r  109 TIIAITGS--VGKTTTKEMLTIALSSIKK  135 (472)
Q Consensus       109 ~vI~ITGT--nGKTTt~~~l~~iL~~~~~  135 (472)
                      |+|.|.|.  .||||...+|...|...|.
T Consensus         1 p~v~i~G~~~sGKttl~~~L~~~~~~~g~   29 (122)
T pfam03205         1 PIVLVVGPKDSGKTTLIRKLLNYLKRRGY   29 (122)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHCCC
T ss_conf             97999948999899999999999998799


No 205
>COG1192 Soj ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]
Probab=59.47  E-value=5  Score=19.43  Aligned_cols=28  Identities=39%  Similarity=0.387  Sum_probs=20.7

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHH-HH-CCC
Q ss_conf             99983036542012334677775-20-112
Q gi|254781101|r  110 IIAITGSVGKTTTKEMLTIALSS-IK-KTY  137 (472)
Q Consensus       110 vI~ITGTnGKTTt~~~l~~iL~~-~~-~~~  137 (472)
                      |...-|-.|||||+-.++..|.. .+ +|.
T Consensus         7 v~n~KGGvGKTT~a~nLa~~La~~~~~kVL   36 (259)
T COG1192           7 VANQKGGVGKTTTAVNLAAALAKRGGKKVL   36 (259)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHHCCCCEE
T ss_conf             985788851999999999999983899789


No 206
>PRK13232 nifH nitrogenase reductase; Reviewed
Probab=59.38  E-value=4.3  Score=19.84  Aligned_cols=29  Identities=45%  Similarity=0.573  Sum_probs=22.9

Q ss_pred             CEEEEE--CCCCCCHHHHHHHHHHHHHHCCC
Q ss_conf             399983--03654201233467777520112
Q gi|254781101|r  109 TIIAIT--GSVGKTTTKEMLTIALSSIKKTY  137 (472)
Q Consensus       109 ~vI~IT--GTnGKTTt~~~l~~iL~~~~~~~  137 (472)
                      +-|||-  |-.|||||+.=|+..|...|+.+
T Consensus         2 ~~iaiyGKGGVGKSTTt~NLaAALA~~GkkV   32 (273)
T PRK13232          2 RQIAIYGKGGIGKSTTTQNLTAALSTMGNKI   32 (273)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHCCCEE
T ss_conf             5799979986658878999999999779969


No 207
>cd03231 ABC_CcmA_heme_exporter CcmA, the ATP-binding component of the bacterial CcmAB transporter.  The CCM family is involved in bacterial cytochrome c biogenesis.  Cytochrome c maturation in E. coli requires the ccm operon, which encodes eight membrane proteins (CcmABCDEFGH).  CcmE is a periplasmic heme chaperone that binds heme covalently and transfers it onto apocytochrome c in the presence of CcmF, CcmG, and CcmH.  The CcmAB proteins represent an ABC transporter and the CcmCD proteins participate in heme transfer to CcmE.
Probab=58.92  E-value=4.6  Score=19.62  Aligned_cols=27  Identities=26%  Similarity=0.313  Sum_probs=21.3

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++||+|.|  ||||.-.++.-+++.
T Consensus        24 ~~Ge~~~l~G~NGsGKSTLlk~i~Gl~~p   52 (201)
T cd03231          24 AAGEALQVTGPNGSGKTTLLRILAGLSPP   52 (201)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             79959999999999999999999667788


No 208
>cd02032 Bchl_like This family of proteins contains bchL and chlL. Protochlorophyllide reductase catalyzes the reductive formation of chlorophyllide from protochlorophyllide during biosynthesis of chlorophylls and bacteriochlorophylls. Three genes, bchL, bchN and bchB, are involved in light-independent protochlorophyllide reduction in bacteriochlorophyll biosynthesis. In cyanobacteria, algae, and gymnosperms, three similar genes, chlL, chlN and chlB are involved in protochlorophyllide reduction during chlorophylls biosynthesis. BchL/chlL, bchN/chlN and bchB/chlB exhibit significant sequence similarity to the nifH, nifD and nifK subunits of nitrogenase, respectively. Nitrogenase catalyzes the reductive formation of ammonia from dinitrogen.
Probab=58.79  E-value=4.3  Score=19.82  Aligned_cols=29  Identities=34%  Similarity=0.549  Sum_probs=22.8

Q ss_pred             EEEEE--CCCCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             99983--036542012334677775201122
Q gi|254781101|r  110 IIAIT--GSVGKTTTKEMLTIALSSIKKTYA  138 (472)
Q Consensus       110 vI~IT--GTnGKTTt~~~l~~iL~~~~~~~~  138 (472)
                      .|||-  |-.|||||+.-++..|...|+.+-
T Consensus         2 kiaiyGKGGIGKSTttaNl~aaLA~~G~kVl   32 (267)
T cd02032           2 VLAVYGKGGIGKSTTSSNLSVALAKRGKKVL   32 (267)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCEEE
T ss_conf             7999779965787789999999998799599


No 209
>COG0540 PyrB Aspartate carbamoyltransferase, catalytic chain [Nucleotide transport and metabolism]
Probab=58.70  E-value=12  Score=16.78  Aligned_cols=79  Identities=19%  Similarity=0.299  Sum_probs=36.9

Q ss_pred             CCCCCCHHHHHH--HHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHH----HHHHHCCC
Q ss_conf             565321012577--787411102687138851235417105899999999998649989999880389----89985113
Q gi|254781101|r  347 NANPASMKAAIS--VLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFHVL----ALKDALPR  420 (472)
Q Consensus       347 NAnP~S~~aal~--~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~~~----~~~~~~~~  420 (472)
                      +.+|+  ++.|+  ++++......|.+|+++||.+    ++.--|.. ...+...+ -.|+++|+..-    .+.+.+..
T Consensus       136 ~qHPT--Q~LLDl~TI~~~~G~~~gl~iaivGDlk----hsRva~S~-~~~L~~~g-a~v~lvsP~~L~~p~~i~~~l~~  207 (316)
T COG0540         136 HQHPT--QALLDLYTIREEFGRLDGLKIAIVGDLK----HSRVAHSN-IQALKRFG-AEVYLVSPETLLPPEYILEELEE  207 (316)
T ss_pred             CCCCC--HHHHHHHHHHHHHCCCCCCEEEEECCCC----CHHHHHHH-HHHHHHCC-CEEEEECCHHHCCCHHHHHHHHH
T ss_conf             98952--8999999999984876794799982544----11888877-99999819-87999886586794657888762


Q ss_pred             C-CCEEEECCHHHH
Q ss_conf             7-979997898999
Q gi|254781101|r  421 S-IHVHYSETMDGL  433 (472)
Q Consensus       421 ~-~~~~~~~~~e~a  433 (472)
                      . ....+.+..+++
T Consensus       208 ~~~~~~~~~~~e~~  221 (316)
T COG0540         208 KGGVVVEHDSDEEV  221 (316)
T ss_pred             CCCEEEEECCHHHH
T ss_conf             48527981466664


No 210
>PRK13235 nifH nitrogenase reductase; Reviewed
Probab=58.33  E-value=4.5  Score=19.73  Aligned_cols=30  Identities=30%  Similarity=0.444  Sum_probs=23.1

Q ss_pred             CEEEE--ECCCCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             39998--3036542012334677775201122
Q gi|254781101|r  109 TIIAI--TGSVGKTTTKEMLTIALSSIKKTYA  138 (472)
Q Consensus       109 ~vI~I--TGTnGKTTt~~~l~~iL~~~~~~~~  138 (472)
                      +-|||  -|-.|||||+.=|+..|...|+.+-
T Consensus         2 ~~iaiyGKGGVGKSTtt~NLaAALA~~GkkVl   33 (274)
T PRK13235          2 RKVAIYGKGGIGKSTTTQNTVAGLAEMGKKVM   33 (274)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHCCCEEE
T ss_conf             67999799855476789999999997899799


No 211
>TIGR02124 hypE hydrogenase expression/formation protein HypE; InterPro: IPR011854    This family contains HypE (or HupE), a protein required for expression of catalytically active hydrogenase in many systems. It appears to be an accessory protein involved in maturation rather than a regulatory protein involved in expression. HypE shows considerable homology to the thiamine-monophosphate kinase ThiL (IPR006283 from INTERPRO) and other enzymes..
Probab=58.27  E-value=11  Score=17.18  Aligned_cols=51  Identities=24%  Similarity=0.398  Sum_probs=26.1

Q ss_pred             HHHHHHHHCCCCHHHHHHHHCCCCCCCCCCCCEECCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEE-EECC
Q ss_conf             035676510121034554311476644331010003653113310002565321012577787411102687138-8512
Q gi|254781101|r  299 TLGIVSILTADVDTAIKALSVFHPKEGRGKRYRCALNQGFFTLIDESYNANPASMKAAISVLSQISPHGEGRRIA-VLGD  377 (472)
Q Consensus       299 Aia~~~~lGi~~~~i~~~L~~~~~~~GR~~~~~~~~~~~~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~-VlG~  377 (472)
                      .-++|..||+++=.++                    |.|.+.++-+     |+.-..+|+.|+.   ++.||=-. |+|.
T Consensus       261 V~gaCE~LGldPl~lA--------------------NEG~~v~~V~-----~E~A~~vLe~lk~---hp~G~~A~YiIG~  312 (345)
T TIGR02124       261 VKGACELLGLDPLYLA--------------------NEGKLVLAVP-----PEAAEKVLEILKS---HPLGKDAAYIIGE  312 (345)
T ss_pred             HHHHHHHHCCCHHHHH--------------------CCCEEEEEEC-----HHHHHHHHHHHHH---CCCCCCCCEEEEE
T ss_conf             9999986170325420--------------------4762899828-----3779999999860---7764332156301


No 212
>TIGR03180 UraD_2 OHCU decarboxylase. Previously thought to only proceed spontaneously, the decarboxylation of 2-oxo-4-hydroxy-4-carboxy--5-ureidoimidazoline (OHCU) has been recently been shown to be catalyzed by this enzyme in Mus musculus. Homologs of this enzyme are found adjacent to and fused with uricase in a number of prokaryotes and are represented by this model. This model is a separate (but related) clade from that represented by TIGR3164. This model places a second homolog in streptomyces species which (are not in the vicinity of other urate catabolism associated genes) below the trusted cutoff.
Probab=58.01  E-value=12  Score=16.91  Aligned_cols=14  Identities=14%  Similarity=0.060  Sum_probs=5.6

Q ss_pred             HCCCCHHHHHHHHC
Q ss_conf             10121034554311
Q gi|254781101|r  306 LTADVDTAIKALSV  319 (472)
Q Consensus       306 lGi~~~~i~~~L~~  319 (472)
                      .+.+.++..+.|..
T Consensus        47 ~~~~~~~~l~~l~~   60 (158)
T TIGR03180        47 QNLSEQDLFEALAG   60 (158)
T ss_pred             HHCCHHHHHHHHHH
T ss_conf             81999999999980


No 213
>cd03289 ABCC_CFTR2 The CFTR subfamily domain 2.  The cystic fibrosis transmembrane regulator (CFTR), the product of the gene mutated in patients with cystic fibrosis, has adapted the ABC transporter structural motif to form a tightly regulated anion channel at the apical surface of many epithelia.  Use of the term assembly of a functional ion channel implies the coming together of subunits or at least smaller not-yet functional components of the active whole.  In fact, on the basis of current knowledge only the CFTR polypeptide itself is required to form an ATP- and protein kinase A-dependent low-conductance chloride channel of the type present in the apical membrane of many epithelial cells.  CFTR displays the typical organization (IM-ABC)2 and carries a characteristic hydrophilic R-domain that separates IM1-ABC1 from IM2-ABC2.
Probab=57.99  E-value=5.7  Score=19.01  Aligned_cols=31  Identities=19%  Similarity=0.224  Sum_probs=22.4

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHHHHCC
Q ss_conf             699399983036--5420123346777752011
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSSIKKT  136 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~~~~~  136 (472)
                      .++..|||.|.+  ||||.-.+|..++...|.+
T Consensus        28 ~~Ge~vaIvG~sGsGKSTLl~lL~gl~~~~G~I   60 (275)
T cd03289          28 SPGQRVGLLGRTGSGKSTLLSAFLRLLNTEGDI   60 (275)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHCCCCCEE
T ss_conf             799999999999997999999996035789539


No 214
>cd03280 ABC_MutS2 MutS2 homologs in bacteria and eukaryotes.  The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch.  Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily.  MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes.  The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis.  All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action.  MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, a
Probab=57.98  E-value=9  Score=17.71  Aligned_cols=28  Identities=29%  Similarity=0.393  Sum_probs=18.7

Q ss_pred             CCCEEEEECCC--CCCHHHHH--HHHHHHHHH
Q ss_conf             99399983036--54201233--467777520
Q gi|254781101|r  107 KATIIAITGSV--GKTTTKEM--LTIALSSIK  134 (472)
Q Consensus       107 ~~~vI~ITGTn--GKTTt~~~--l~~iL~~~~  134 (472)
                      +.+++=|||.|  ||||.-..  +..+|.+.|
T Consensus        27 ~~~~~iiTGpN~sGKSt~lk~i~l~~iLAq~G   58 (200)
T cd03280          27 NKRVLVITGPNAGGKTVTLKTLGLLTLMAQSG   58 (200)
T ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHHHC
T ss_conf             93399998898775099999999999999977


No 215
>cd02035 ArsA ArsA ATPase functionas as an efflux pump located on the inner membrane of the cell. This ATP-driven oxyanion pump catalyzes the extrusion of arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces resistance to the toxic agents. The pump is composed of two subunits, the catalytic ArsA subunit and the membrane subunit ArsB, which are encoded by arsA and arsB genes respectively. Arsenic efflux in bacteria is catalyzed by either ArsB alone or by ArsAB complex. The ATP-coupled pump, however, is more efficient. ArsA is composed of two homologous halves, A1 and A2, connected by a short linker sequence.
Probab=57.57  E-value=4.5  Score=19.68  Aligned_cols=23  Identities=35%  Similarity=0.439  Sum_probs=19.0

Q ss_pred             ECCCCCCHHHHHHHHHHHHHHCC
Q ss_conf             30365420123346777752011
Q gi|254781101|r  114 TGSVGKTTTKEMLTIALSSIKKT  136 (472)
Q Consensus       114 TGTnGKTTt~~~l~~iL~~~~~~  136 (472)
                      -|-.||||++.-++..|+..|+.
T Consensus         7 KGGVGKTTvAaalA~~lA~~G~r   29 (217)
T cd02035           7 KGGVGKTTIAAATAVRLAEEGKK   29 (217)
T ss_pred             CCCCCHHHHHHHHHHHHHHCCCE
T ss_conf             99661999999999999968994


No 216
>pfam00448 SRP54 SRP54-type protein, GTPase domain. This family includes relatives of the G-domain of the SRP54 family of proteins.
Probab=57.52  E-value=8.4  Score=17.92  Aligned_cols=28  Identities=36%  Similarity=0.386  Sum_probs=19.0

Q ss_pred             CCEEEEECCC--CCCHHHHHHHHHHHHHHC
Q ss_conf             9399983036--542012334677775201
Q gi|254781101|r  108 ATIIAITGSV--GKTTTKEMLTIALSSIKK  135 (472)
Q Consensus       108 ~~vI~ITGTn--GKTTt~~~l~~iL~~~~~  135 (472)
                      +.||++.|-+  |||||..=|+..+...++
T Consensus         1 P~vi~lvGptGvGKTTTiaKLAa~~~~~~~   30 (196)
T pfam00448         1 PNVILLVGLQGSGKTTTIAKLAAYLKKQGK   30 (196)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCC
T ss_conf             969999899999889999999999997799


No 217
>PRK00698 tmk thymidylate kinase; Validated
Probab=57.36  E-value=8.6  Score=17.85  Aligned_cols=29  Identities=31%  Similarity=0.467  Sum_probs=24.1

Q ss_pred             CCCEEEEECC--CCCCHHHHHHHHHHHHHHC
Q ss_conf             9939998303--6542012334677775201
Q gi|254781101|r  107 KATIIAITGS--VGKTTTKEMLTIALSSIKK  135 (472)
Q Consensus       107 ~~~vI~ITGT--nGKTTt~~~l~~iL~~~~~  135 (472)
                      ++..|+|-|-  .||||...+|+.-|...|.
T Consensus         2 kG~fIviEGiDGsGKsTq~~~L~~~L~~~g~   32 (204)
T PRK00698          2 RGMFITIEGIDGAGKSTQIELLAERLEEQGR   32 (204)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHCCC
T ss_conf             8319999889999899999999999996799


No 218
>cd00550 ArsA_ATPase Oxyanion-translocating ATPase (ArsA).  This ATPase is involved in transport of arsenite, antimonite or other oxyanions across biological membranes in all three kingdoms of life.  ArsA contains a highly conserved AAA motif present in the AAA+ ATPase superfamily associated with a variety of cellular activities.   To form a functional ATP-driven pump, ArsA interacts with the permease ArsB, which is a channel-forming integral membrane protein. One of the most interesting features of ArsA is the allosteric activation by its transport substrates.  A divalent cation, typically Mg2+, is required for its enzymatic activity.
Probab=57.33  E-value=4.7  Score=19.55  Aligned_cols=27  Identities=33%  Similarity=0.400  Sum_probs=20.6

Q ss_pred             EEEEE--CCCCCCHHHHHHHHHHHHHHCC
Q ss_conf             99983--0365420123346777752011
Q gi|254781101|r  110 IIAIT--GSVGKTTTKEMLTIALSSIKKT  136 (472)
Q Consensus       110 vI~IT--GTnGKTTt~~~l~~iL~~~~~~  136 (472)
                      +|=+|  |-.||||++.-++.-|...|+.
T Consensus         2 ~i~~~GKGGVGKTT~AaalA~~lA~~G~k   30 (254)
T cd00550           2 YIFFGGKGGVGKTTISAATAVRLAEQGKK   30 (254)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCE
T ss_conf             89996898554899999999999968994


No 219
>PRK03367 consensus
Probab=57.11  E-value=13  Score=16.61  Aligned_cols=17  Identities=18%  Similarity=0.251  Sum_probs=8.7

Q ss_pred             CCCCCHHHHHHHHHHHH
Q ss_conf             65321012577787411
Q gi|254781101|r  348 ANPASMKAAISVLSQIS  364 (472)
Q Consensus       348 AnP~S~~aal~~l~~~~  364 (472)
                      |||.||.+|++.-.++.
T Consensus       309 A~~~s~~~Ai~~A~~~~  325 (329)
T PRK03367        309 ADVGSFITALNLAIKMI  325 (329)
T ss_pred             CCHHHHHHHHHHHHHHH
T ss_conf             99699999999999998


No 220
>PRK01259 ribose-phosphate pyrophosphokinase; Provisional
Probab=57.06  E-value=13  Score=16.60  Aligned_cols=60  Identities=15%  Similarity=0.143  Sum_probs=30.3

Q ss_pred             CEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             113310002565321012577787411102687138851235417105899999999998649989999880
Q gi|254781101|r  338 FFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGF  409 (472)
Q Consensus       338 ~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~  409 (472)
                      .+.++||== .+-.+|..|.+.|+..   +. ++|.+...=   |-.+..-    .+.+...+++.|+..-.
T Consensus       210 ~vIIvDDiI-~TGgTl~~aa~~Lk~~---GA-~~V~~~~TH---glfs~~A----~~rl~~s~i~~iv~TnT  269 (309)
T PRK01259        210 DCILVDDMI-DTGGTLCKAAEALKER---GA-KSVFAYATH---PVLSGGA----AERIANSVLDELVVTDS  269 (309)
T ss_pred             EEEEECCHH-HCCHHHHHHHHHHHHC---CC-CEEEEEEEC---HHCCHHH----HHHHHHCCCCEEEEECC
T ss_conf             399976534-3456599999999756---99-669999876---3139459----99987089988998189


No 221
>COG3044 Predicted ATPase of the ABC class [General function prediction only]
Probab=56.78  E-value=8.6  Score=17.84  Aligned_cols=44  Identities=11%  Similarity=0.205  Sum_probs=19.2

Q ss_pred             CCCHHHHHHHHCCEEECCCCCCEEEEEEEECCCCCCCCEEEECCCCCCCHHHH
Q ss_conf             35678899872799952688714746774022237898889716887476888
Q gi|254781101|r    4 LWTFHDLLQAIQGHSIGIVPQGFVNGISIDSRSIAPQEAFFAIKGPHYDGHDF   56 (472)
Q Consensus         4 ~~~~~~l~~~~~g~~~~~~~~~~i~~i~~dSr~v~~g~lFval~g~~~DGh~~   56 (472)
                      |..+.+.++-+.|+-....  ..+++-+.       +-..+|+++.+..+.-|
T Consensus         1 m~~leevlr~L~g~~y~ay--k~lTg~s~-------d~g~yavr~~d~q~dpv   44 (554)
T COG3044           1 MDRLEEVLRKLEGQNYRAY--KQLTGASY-------DFGDYAVRIDDIQSDPV   44 (554)
T ss_pred             CCCHHHHHHHHHCCCCHHH--HHHCCCCC-------CCCEEEEECCCCCCCCC
T ss_conf             9328999987624530136--76424444-------65405897345666633


No 222
>PRK13505 formate--tetrahydrofolate ligase; Provisional
Probab=56.77  E-value=11  Score=17.15  Aligned_cols=33  Identities=33%  Similarity=0.329  Sum_probs=25.4

Q ss_pred             HHCCCCCEEEEECCC------CCCHHHHHHHHHHHHHHC
Q ss_conf             830699399983036------542012334677775201
Q gi|254781101|r  103 RLRSKATIIAITGSV------GKTTTKEMLTIALSSIKK  135 (472)
Q Consensus       103 ~~~~~~~vI~ITGTn------GKTTt~~~l~~iL~~~~~  135 (472)
                      ..+.+++.|-||+-+      |||||+==|++-|...|+
T Consensus        49 ~~~~~gklIlVTaitPTP~GEGKTTttIGL~~aL~~lgk   87 (556)
T PRK13505         49 KDKKDGKLILVTAINPTPAGEGKTTVTVGLGDALNKIGK   87 (556)
T ss_pred             CCCCCCEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHCC
T ss_conf             248996399998458888888863017989999987187


No 223
>PRK10437 carbonic anhydrase; Provisional
Probab=56.69  E-value=10  Score=17.31  Aligned_cols=24  Identities=33%  Similarity=0.425  Sum_probs=13.5

Q ss_pred             CCCCCEEEEEEEECCC-------CCCCCEEEE
Q ss_conf             6887147467740222-------378988897
Q gi|254781101|r   21 IVPQGFVNGISIDSRS-------IAPQEAFFA   45 (472)
Q Consensus        21 ~~~~~~i~~i~~dSr~-------v~~g~lFva   45 (472)
                      ..|...+=+ |.|||-       .+||++||-
T Consensus        33 Q~P~~L~Ig-CsDSRV~p~~I~~~~PGelFV~   63 (220)
T PRK10437         33 QKPRFLWIG-CSDSRVPAERLTGLEPGELFVH   63 (220)
T ss_pred             CCCCEEEEE-ECCCCCCHHHHCCCCCCCEEEE
T ss_conf             999849997-3377889999738998667899


No 224
>COG0001 HemL Glutamate-1-semialdehyde aminotransferase [Coenzyme metabolism]
Probab=56.63  E-value=10  Score=17.31  Aligned_cols=75  Identities=15%  Similarity=0.092  Sum_probs=45.5

Q ss_pred             CCCCCCCCEECCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             64433101000365311331000256532101257778741110268713885123541710589999999999864998
Q gi|254781101|r  323 KEGRGKRYRCALNQGFFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNIS  402 (472)
Q Consensus       323 ~~GR~~~~~~~~~~~~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d  402 (472)
                      +-||-+.++..... +..+-..+++.||.+|.+.+.+|..+.....     +.-.|.   ...+.+...+-+.+.+.+++
T Consensus       279 ~gGr~eiM~~~~p~-g~vyqaGT~sgnplamaAG~atl~~l~~~~~-----~y~~l~---~~~~~L~~gl~~~~~~~g~~  349 (432)
T COG0001         279 FGGRAEIMEQLAPL-GPVYQAGTLSGNPLAMAAGLATLEELMTEEG-----VYERLD---ALGERLAEGLRAAAERHGIP  349 (432)
T ss_pred             ECCHHHHHHHHCCC-CCCCCCCCCCCCHHHHHHHHHHHHHHHHCCC-----HHHHHH---HHHHHHHHHHHHHHHHHCCC
T ss_conf             25699999632778-8764567778868999999999999873651-----899999---99999999999999983998


Q ss_pred             EEEE
Q ss_conf             9999
Q gi|254781101|r  403 HVWL  406 (472)
Q Consensus       403 ~v~~  406 (472)
                      ..+.
T Consensus       350 ~~v~  353 (432)
T COG0001         350 LTVN  353 (432)
T ss_pred             EEEE
T ss_conf             5886


No 225
>TIGR00382 clpX ATP-dependent Clp protease, ATP-binding subunit ClpX; InterPro: IPR004487   ClpX is a member of the HSP (heat-shock protein) 100 family. Gel filtration and electron microscopy showed that ClpX subunits associate to form a six-membered ring that is stabilized by binding of ATP or nonhydrolyzable analogs of ATP . It functions as an ATP-depedent  molecular chaperone and is the regulatory subunit of the ClpXP protease .   ClpXP is involved in DNA damage repair, stationary-phase gene expression, and ssrA-mediated protein quality control. To date more than 50 proteins include transcription factors, metabolic enzymes, and proteins involved in the starvation and oxidative stress responses have been identified as substrates .    The N-terminal domain of ClpX is a C4-type zinc binding domain (ZBD) involved in substrate recognition. ZBD forms a very stable dimer that is essential for promoting the degradation of some typical ClpXP substrates such as lO and MuA .  ; GO: 0005515 protein binding, 0005524 ATP binding, 0016887 ATPase activity, 0015031 protein transport.
Probab=56.42  E-value=3.8  Score=20.17  Aligned_cols=37  Identities=32%  Similarity=0.359  Sum_probs=22.7

Q ss_pred             HHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHH
Q ss_conf             99999999983069939998303654201233467777
Q gi|254781101|r   94 ALNKLAVAARLRSKATIIAITGSVGKTTTKEMLTIALS  131 (472)
Q Consensus        94 al~~la~~~~~~~~~~vI~ITGTnGKTTt~~~l~~iL~  131 (472)
                      -|..+-.-=..++++-.||=||| |||-.+.-||..|.
T Consensus       141 elehleeVEL~KSNILLiGPTGS-GKTLLAqTLA~~L~  177 (452)
T TIGR00382       141 ELEHLEEVELSKSNILLIGPTGS-GKTLLAQTLARILN  177 (452)
T ss_pred             HHHHHHHHHHHCCCEEEECCCCC-CHHHHHHHHHHHCC
T ss_conf             35444443330066245468885-26899999998738


No 226
>PRK03695 vitamin B12-transporter ATPase; Provisional
Probab=56.26  E-value=5.3  Score=19.24  Aligned_cols=30  Identities=23%  Similarity=0.272  Sum_probs=21.6

Q ss_pred             CCCEEEEECCC--CCCHHHHHHHHHHHHHHCC
Q ss_conf             99399983036--5420123346777752011
Q gi|254781101|r  107 KATIIAITGSV--GKTTTKEMLTIALSSIKKT  136 (472)
Q Consensus       107 ~~~vI~ITGTn--GKTTt~~~l~~iL~~~~~~  136 (472)
                      ++.++||.|.|  ||||.-.++.-++...|.+
T Consensus        22 ~Ge~v~iiGpNGaGKSTLlk~i~Gl~p~~G~I   53 (245)
T PRK03695         22 AGEILHLVGPNGAGKSTLLARMAGLLSGSGEI   53 (245)
T ss_pred             CCCEEEEECCCCCHHHHHHHHHHCCCCCCCEE
T ss_conf             99899999789941999999984668889659


No 227
>pfam04166 PdxA Pyridoxal phosphate biosynthetic protein PdxA. In Escherichia coli the coenzyme pyridoxal 5'-phosphate is synthesized de novo by a pathway that is thought to involve the condensation of 4-(phosphohydroxy)-L-threonine and 1-deoxy-D-xylulose, catalysed by the enzymes PdxA and PdxJ, to form either pyridoxine (vitamin B6) or pyridoxine 5'-phosphate.
Probab=56.09  E-value=14  Score=16.50  Aligned_cols=11  Identities=45%  Similarity=0.706  Sum_probs=4.6

Q ss_pred             CCCCCHHHHHH
Q ss_conf             65321012577
Q gi|254781101|r  348 ANPASMKAAIS  358 (472)
Q Consensus       348 AnP~S~~aal~  358 (472)
                      |||.||.+|++
T Consensus       286 A~~~s~~~Ai~  296 (299)
T pfam04166       286 ADPGSLIAALK  296 (299)
T ss_pred             CCHHHHHHHHH
T ss_conf             99699999999


No 228
>pfam09818 ABC_ATPase Predicted ATPase of the ABC class. Members of this family include various bacterial predicted ABC class ATPases.
Probab=56.01  E-value=14  Score=16.49  Aligned_cols=20  Identities=15%  Similarity=0.102  Sum_probs=10.5

Q ss_pred             HHHHHHHHHCCCCEEEEECCCH
Q ss_conf             9999999864998999988038
Q gi|254781101|r  390 IDLAEVLSLYNISHVWLSGFHV  411 (472)
Q Consensus       390 ~~i~~~~~~~~~d~v~~~G~~~  411 (472)
                      ..|.+.+ +.+. .++++.|+.
T Consensus       330 AnI~Eal-EaGa-~~lLIDEDT  349 (447)
T pfam09818       330 ANIQEAL-EAGA-SLLLIDEDT  349 (447)
T ss_pred             HHHHHHH-HCCC-CEEEECCCC
T ss_conf             9999999-7489-789983564


No 229
>TIGR03029 EpsG chain length determinant protein tyrosine kinase EpsG. The proteins in this family are homologs of the EpsG protein found in Methylobacillus strain 12S and are generally found in operons with other Eps homologs. The protein is believed to function as the protein tyrosine kinase component of the chain length regulator (along with the transmembrane component EpsF).
Probab=55.91  E-value=14  Score=16.48  Aligned_cols=102  Identities=18%  Similarity=0.221  Sum_probs=52.2

Q ss_pred             EEECCCCCCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEECCCCCCC-CCCCCCCEEEECCH----------------HH
Q ss_conf             74022237898889716887476888999998698899985521245-54469728995998----------------99
Q gi|254781101|r   31 SIDSRSIAPQEAFFAIKGPHYDGHDFILHAVQKGAGLVVVNTDMVAS-IGSLSIPVFGVDDV----------------LG   93 (472)
Q Consensus        31 ~~dSr~v~~g~lFval~g~~~DGh~~i~~A~~~Ga~~~i~~~~~~~~-~~~~~~~~i~v~d~----------------~~   93 (472)
                      -.++..+.+.++==+++-.+..|-.|=+.|++-|   +|++.+.... ....+.|++...|.                -+
T Consensus         9 l~~~g~i~~~~~~~~l~~q~~~g~rfGea~~~lg---~~t~~di~~als~q~~~py~~~~~~~~~~~l~aa~~P~s~~~E   85 (274)
T TIGR03029         9 LLDAGKLSEDEAERILRLQKQENIRFGEAALRLG---LINEDDIRQALSRQFEYPYLPPNDGSFSPDLIAAYQPFSPQVE   85 (274)
T ss_pred             HHHCCCCCHHHHHHHHHHHHHHCCCHHHHHHHCC---CCCHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHCCCCHHHH
T ss_conf             9982998999999999999984866899999819---9769999999998628987784557889899877389988999


Q ss_pred             HHHHHHHHHHH---CCCCCEEEEECC---CCCCHHHHHHHHHHHHHHC
Q ss_conf             99999999983---069939998303---6542012334677775201
Q gi|254781101|r   94 ALNKLAVAARL---RSKATIIAITGS---VGKTTTKEMLTIALSSIKK  135 (472)
Q Consensus        94 al~~la~~~~~---~~~~~vI~ITGT---nGKTTt~~~l~~iL~~~~~  135 (472)
                      +++.|-....-   ..+.+.++||..   .|||||..=++..|.+.|+
T Consensus        86 a~R~lRs~l~~~~~~~~~~~LaItS~~pGEGKS~vAaNLA~~~Aq~G~  133 (274)
T TIGR03029        86 ALRALRSQLMLRWFSEGRKALAVVSAKSGEGCSYIAANLAIVFSQLGE  133 (274)
T ss_pred             HHHHHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHHCCC
T ss_conf             999999999998457888389996899999899999999999996799


No 230
>cd02033 BchX Chlorophyllide reductase converts chlorophylls into bacteriochlorophylls by reducing the chlorin B-ring. This family contains the X subunit of this three-subunit enzyme. Sequence and structure similarity between bchX, protochlorophyllide reductase L subunit (bchL and chlL) and nitrogenase Fe protein (nifH gene) suggest their functional similarity. Members of the BchX family serve as the unique electron donors to their respective catalytic subunits (bchN-bchB, bchY-bchZ and nitrogenase component 1). Mechanistically, they hydrolyze ATP and transfer electrons through a Fe4-S4 cluster.
Probab=55.82  E-value=8.7  Score=17.82  Aligned_cols=32  Identities=34%  Similarity=0.414  Sum_probs=25.7

Q ss_pred             CCCEEEEEC--CCCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             993999830--36542012334677775201122
Q gi|254781101|r  107 KATIIAITG--SVGKTTTKEMLTIALSSIKKTYA  138 (472)
Q Consensus       107 ~~~vI~ITG--TnGKTTt~~~l~~iL~~~~~~~~  138 (472)
                      +.++|||=|  --||+||+.-++..|...|+.+-
T Consensus        30 ~~~~IAiYGKGGIGKSTts~NlsAAlA~~GkkVm   63 (329)
T cd02033          30 KTQIIAIYGKGGIGKSFTLANLSYMMAQQGKRVL   63 (329)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEE
T ss_conf             4549999768843561688999999997799699


No 231
>pfam01268 FTHFS Formate--tetrahydrofolate ligase.
Probab=55.19  E-value=11  Score=17.08  Aligned_cols=32  Identities=38%  Similarity=0.379  Sum_probs=24.8

Q ss_pred             HCCCCCEEEEECCC------CCCHHHHHHHHHHHHHHC
Q ss_conf             30699399983036------542012334677775201
Q gi|254781101|r  104 LRSKATIIAITGSV------GKTTTKEMLTIALSSIKK  135 (472)
Q Consensus       104 ~~~~~~vI~ITGTn------GKTTt~~~l~~iL~~~~~  135 (472)
                      .+.+++.|-||+-+      |||||+==|++-|...|+
T Consensus        50 ~~~~gklilVTaitPTP~GEGKTTttIGL~~aL~~lgk   87 (555)
T pfam01268        50 DRPDGKLILVTAITPTPAGEGKTTTTIGLGQALNRLGK   87 (555)
T ss_pred             CCCCCEEEEEEECCCCCCCCCCCEEHHHHHHHHHHHCC
T ss_conf             48985399998457888888863023659999986287


No 232
>PRK13540 cytochrome c biogenesis protein CcmA; Provisional
Probab=55.19  E-value=6.1  Score=18.86  Aligned_cols=27  Identities=26%  Similarity=0.397  Sum_probs=21.5

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.+++++|-|  ||||.-.++.-+++.
T Consensus        25 ~~G~i~~l~G~NGaGKSTLlkli~Gl~~p   53 (200)
T PRK13540         25 PAGGLLHLKGSNGAGKTTLLKLIAGLLNP   53 (200)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             79979999889998799999999778588


No 233
>TIGR02188 Ac_CoA_lig_AcsA acetate--CoA ligase; InterPro: IPR011904   Acetyl-CoA synthetase (also known as acetate-CoA ligase and acetyl-activating enzyme) is a ubiquitous enzyme, found in both prokaryotes and eukaryotes, which catalyses the formation of acetyl-CoA from acetate, coenzyme A (CoA) and ATP as shown below : ATP + acetate + CoA = AMP + diphosphate + acetyl-CoA The activity of this enzyme is crucial for maintaining the required levels of acetyl-CoA, a key intermediate in many important biosynthetic and catabolic processes. It is especially important in eukayotic species as it is the only route for the activation of acetate to acetyl-CoA in these organisms (some prokaryotic species can also activate acetate by either acetate kinase/phosphotransacetylase or by ADP-forming acetyl-CoA synthase). Eukaryotes typically have two isoforms of acetyl-CoA synthase, a cytosolic form involved in biosynthetic processes and a mitochondrial form primarily involved in energy generation.   The crystal structures of a eukaryotic (Q01574 from SWISSPROT, from yeast) and bacterial (Q8ZKF6 from SWISSPROT, from Salmonella) form of this enzyme have been determined , . The yeast enzyme is trimeric, while the bacterial enzyme is monomeric. The trimeric state of the yeast protein may be unique to this organism however, as the residues involved in the trimer interface are poorly conserved in other sequences. Despite differences in the oligomeric state of the two enzyme, the structures of the monomers are almost identical. A large N-terminal domain (~500 residues) containing two parallel beta sheets is followed by a small (~110 residues) C-terminal domain containing a three-stranded beta sheet with helices. The active site occurs at the domain interface, with its contents determining the orientation of the C-terminal domain.; GO: 0003987 acetate-CoA ligase activity, 0016208 AMP binding.
Probab=54.99  E-value=14  Score=16.38  Aligned_cols=82  Identities=20%  Similarity=0.317  Sum_probs=50.1

Q ss_pred             CCCCCCEEEECCCC--CCCHHHHHHH-HHHCCCEEEEECCCCCCC--------CCCCCCCEEEEC-CHHHHHHHHHHHHH
Q ss_conf             23789888971688--7476888999-998698899985521245--------544697289959-98999999999998
Q gi|254781101|r   36 SIAPQEAFFAIKGP--HYDGHDFILH-AVQKGAGLVVVNTDMVAS--------IGSLSIPVFGVD-DVLGALNKLAVAAR  103 (472)
Q Consensus        36 ~v~~g~lFval~g~--~~DGh~~i~~-A~~~Ga~~~i~~~~~~~~--------~~~~~~~~i~v~-d~~~al~~la~~~~  103 (472)
                      +++|+|+|.|- +.  -.-||.||=- =+.+||+.++-|--...+        .....+.++..+ =..++|.+++..+.
T Consensus       286 D~~d~D~fWCT-ADvGWiTGHSYiVYGPL~~GAT~~mfEG~P~YP~~~R~W~~iekh~vtiFYTAPTAIR~L~r~G~~~~  364 (643)
T TIGR02188       286 DIKDGDIFWCT-ADVGWITGHSYIVYGPLANGATTLMFEGVPTYPDAGRFWEIIEKHKVTIFYTAPTAIRALMRLGDEWV  364 (643)
T ss_pred             ECCCCCEEEEE-CCEEEEECCHHHHHHHHHCCCEEEEECCCCCCCCCCCEEEEEEECCCCEEECCHHHHHHHHHHCCHHH
T ss_conf             03799626862-11200205324012422115317874377833278767855331576503315689999986111213


Q ss_pred             HCCCCCEEEEECCCC
Q ss_conf             306993999830365
Q gi|254781101|r  104 LRSKATIIAITGSVG  118 (472)
Q Consensus       104 ~~~~~~vI~ITGTnG  118 (472)
                      ++++.-=.=|=||.|
T Consensus       365 ~k~DlSSLR~LGSVG  379 (643)
T TIGR02188       365 KKHDLSSLRLLGSVG  379 (643)
T ss_pred             HHCCCCCEEECCCCC
T ss_conf             441764001502568


No 234
>COG3172 NadR Predicted ATPase/kinase involved in NAD metabolism [Coenzyme metabolism]
Probab=54.96  E-value=7.1  Score=18.41  Aligned_cols=25  Identities=28%  Similarity=0.395  Sum_probs=19.2

Q ss_pred             CCEEEEECC--CCCCHHHHHHHHHHHH
Q ss_conf             939998303--6542012334677775
Q gi|254781101|r  108 ATIIAITGS--VGKTTTKEMLTIALSS  132 (472)
Q Consensus       108 ~~vI~ITGT--nGKTTt~~~l~~iL~~  132 (472)
                      .|+|+|+|+  .||||...-++.+++.
T Consensus         8 ~K~VailG~ESsGKStLv~kLA~~fnt   34 (187)
T COG3172           8 VKTVAILGGESSGKSTLVNKLANIFNT   34 (187)
T ss_pred             HEEEEEECCCCCCHHHHHHHHHHHHCC
T ss_conf             513556457665717999999999688


No 235
>PRK08674 bifunctional phosphoglucose/phosphomannose isomerase; Validated
Probab=54.93  E-value=14  Score=16.38  Aligned_cols=84  Identities=25%  Similarity=0.196  Sum_probs=50.0

Q ss_pred             ECCCCCC-CCEEEECCCCCCCHHHHHHHHHHCCC-EEEEECCCCCC-CCCCCCCCEEEEC---CHHHHHHHHHHHHHHCC
Q ss_conf             0222378-98889716887476888999998698-89998552124-5544697289959---98999999999998306
Q gi|254781101|r   33 DSRSIAP-QEAFFAIKGPHYDGHDFILHAVQKGA-GLVVVNTDMVA-SIGSLSIPVFGVD---DVLGALNKLAVAARLRS  106 (472)
Q Consensus        33 dSr~v~~-g~lFval~g~~~DGh~~i~~A~~~Ga-~~~i~~~~~~~-~~~~~~~~~i~v~---d~~~al~~la~~~~~~~  106 (472)
                      .+++++| ..+.||==|-..-|-+++...+...+ .-+++.+++.. .-.+.+.-+|.|+   +|.+.|..+..+.++  
T Consensus        27 ~~~~~~~~~~Ivi~GmGGS~i~Gdv~~~l~~~~~~iPv~v~~~y~lP~~v~~~tLVIavSySGnTeETL~a~~~A~~r--  104 (328)
T PRK08674         27 IEVEIEPYDNIVISGMGGSGIGGDLLRSLLLDEWKKPVFVVRDYFLPAFVDRKTLVIAVSYSGNTEETLSAVEQAKKR--  104 (328)
T ss_pred             CHHCCCCCCEEEEEECCHHHHHHHHHHHHHHCCCCCCEEEECCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHC--
T ss_conf             110147657299995756489999999998447998679855887998658885799982899977999999999975--


Q ss_pred             CCCEEEEECCCCC
Q ss_conf             9939998303654
Q gi|254781101|r  107 KATIIAITGSVGK  119 (472)
Q Consensus       107 ~~~vI~ITGTnGK  119 (472)
                      ..++|+|| |.||
T Consensus       105 ga~vi~It-sGG~  116 (328)
T PRK08674        105 GAKIIAIT-SGGK  116 (328)
T ss_pred             CCCEEEEE-CCCC
T ss_conf             99589994-8970


No 236
>PRK08099 nicotinamide-nucleotide adenylyltransferase; Provisional
Probab=54.43  E-value=14  Score=16.47  Aligned_cols=74  Identities=19%  Similarity=0.184  Sum_probs=43.3

Q ss_pred             HHHHHHHHCCCCEEEEECCCHHHHHHHCCCCCCEEEECCHHHHHHHHHHHCCCCC--EEEEE-CCCHHHHHH---HHHHH
Q ss_conf             9999998649989999880389899851137979997898999999998447898--99997-713254899---99999
Q gi|254781101|r  391 DLAEVLSLYNISHVWLSGFHVLALKDALPRSIHVHYSETMDGLFLFIQSSLVDGD--VVVVK-SSNSCGFYR---LINLL  464 (472)
Q Consensus       391 ~i~~~~~~~~~d~v~~~G~~~~~~~~~~~~~~~~~~~~~~e~a~~~l~~~~~~gd--iVLiK-GSr~~~le~---iv~~L  464 (472)
                      .+.+.+.+...|.+++...+..+..+.+.+-.   ..+++++.-+.+++.+.+..  .+.+. ||---++++   ++++|
T Consensus       329 ~l~~~a~~~~yDL~Lll~~DvpwVdDGlRd~~---~~~~R~~f~~~lk~lL~k~ni~yv~I~~~~y~eR~~kAi~~Id~l  405 (411)
T PRK08099        329 FVQALIDEYRFDLVILLENNTPWVADGLRSLG---SSVDRKRFQNLLVEMLEENNIEYVRVESPDYDARFLRCVELVDQM  405 (411)
T ss_pred             HHHHHHHHCCCCEEEEECCCCCCCCCCCCCCC---CHHHHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHHH
T ss_conf             99999863587789980899875567876667---888999999999999998199769971788899999999999999


Q ss_pred             HHH
Q ss_conf             985
Q gi|254781101|r  465 LEE  467 (472)
Q Consensus       465 ~~~  467 (472)
                      +++
T Consensus       406 L~~  408 (411)
T PRK08099        406 LGE  408 (411)
T ss_pred             HHC
T ss_conf             714


No 237
>PRK11860 bifunctional 3-phosphoshikimate 1-carboxyvinyltransferase/cytidine monophosphate kinase; Provisional
Probab=54.17  E-value=15  Score=16.30  Aligned_cols=37  Identities=11%  Similarity=0.098  Sum_probs=20.1

Q ss_pred             HHHHHHHHCCEEECCCCCCEEEEEEEECCCCCCCCEEE
Q ss_conf             78899872799952688714746774022237898889
Q gi|254781101|r    7 FHDLLQAIQGHSIGIVPQGFVNGISIDSRSIAPQEAFF   44 (472)
Q Consensus         7 ~~~l~~~~~g~~~~~~~~~~i~~i~~dSr~v~~g~lFv   44 (472)
                      .-+.++.+|..+........|+|... .....+..+++
T Consensus        56 ti~al~~LG~~I~~~~~~~~I~G~g~-~~~~~~~~l~~   92 (662)
T PRK11860         56 MLDALRQLGCGVEQAGDTVRITGLGG-QLPVKKADLFL   92 (662)
T ss_pred             HHHHHHHCCCEEEECCCEEEEEECCC-CCCCCCCEEEC
T ss_conf             99999986996996599899990788-87899865773


No 238
>pfam09905 DUF2132 Uncharacterized conserved protein (DUF2132). This domain, found in various hypothetical prokaryotic proteins, has no known function.
Probab=53.99  E-value=5  Score=19.42  Aligned_cols=47  Identities=21%  Similarity=0.334  Sum_probs=33.2

Q ss_pred             HCCCCHHHHHHHHCCCCCCCCCCCCEECCCCCCEEEEEECCCCCCCCHHHHHHHHHHHH
Q ss_conf             10121034554311476644331010003653113310002565321012577787411
Q gi|254781101|r  306 LTADVDTAIKALSVFHPKEGRGKRYRCALNQGFFTLIDESYNANPASMKAAISVLSQIS  364 (472)
Q Consensus       306 lGi~~~~i~~~L~~~~~~~GR~~~~~~~~~~~~~~iIDDsYNAnP~S~~aal~~l~~~~  364 (472)
                      -|+.++.|...|...-++++-.+++++           .|++.|| |++++|++|+..+
T Consensus         7 HGvtLe~il~~Lv~~yGW~~L~~~i~i-----------~CF~~~P-sikSSLkFLRkTp   53 (64)
T pfam09905         7 HGLKLETILTELVEHYGWEELGERINI-----------NCFKNNP-SIKSSLKFLRKTP   53 (64)
T ss_pred             CCCHHHHHHHHHHHHHCHHHHHHHCCC-----------CCCCCCC-CHHHHHHHHHCCH
T ss_conf             400399999999998698999845571-----------5178999-6688999991598


No 239
>cd03278 ABC_SMC_barmotin Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function.  Barmotin belongs to the SMC protein family.  SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains.  Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins.  The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases.  The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, w
Probab=53.86  E-value=9.4  Score=17.58  Aligned_cols=25  Identities=24%  Similarity=0.403  Sum_probs=18.9

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHH
Q ss_conf             699399983036--54201233467777
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALS  131 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~  131 (472)
                      +++ ++||.|-|  ||||.-.++..+|.
T Consensus        21 p~G-itaIvGpsGsGKSTLl~~i~~~lg   47 (197)
T cd03278          21 PPG-LTAIVGPNGSGKSNIIDAIRWVLG   47 (197)
T ss_pred             CCC-EEEEECCCCCCHHHHHHHHHHHHC
T ss_conf             898-289999999988999999998747


No 240
>TIGR00503 prfC peptide chain release factor 3; InterPro: IPR004548   Peptide chain release factor 3 increases the formation of ribosomal termination complexes and stimulates activity of RF-1 and RF-2. It binds to guanine nucleotides and has a strong preference for UGA stop codons. This translation releasing factor, RF-3 (prfC) was originally described as stop codon-independent, in contrast to peptide chain release factor 1 (RF-1, prfA) and RF-2 (prfB). RF-1 and RF-2 are closely related to each other, while RF-3 is similar to elongation factors EF-Tu and EF-G; RF-1 is active at UAA and UAG and RF-2 is active at UAA and UGA. All bacteria and organelles have RF-1. The Mycoplasmas and organelles, which translate UGA as Trp rather than as a stop codon, lack RF-2. RF-3, in contrast, seems to be rare among bacteria and is found so far only in Escherichia coli and some other gamma subdivision Proteobacteria, in Synechocystis sp. (strain PCC 6803), and in Staphylococcus aureus.; GO: 0005525 GTP binding, 0016149 translation release factor activity codon specific, 0006415 translational termination, 0005737 cytoplasm.
Probab=53.60  E-value=10  Score=17.30  Aligned_cols=39  Identities=18%  Similarity=0.220  Sum_probs=24.0

Q ss_pred             CHHHHHHHHHHHCCC-CCEEEE-ECCCHHHHHHHHHHHHHHCC
Q ss_conf             989999999984478-989999-77132548999999998505
Q gi|254781101|r  429 TMDGLFLFIQSSLVD-GDVVVV-KSSNSCGFYRLINLLLEEFP  469 (472)
Q Consensus       429 ~~e~a~~~l~~~~~~-gdiVLi-KGSr~~~le~iv~~L~~~~~  469 (472)
                      +-|-|++.+.+.... -|.|+- -|.  .+||-++..|+++|-
T Consensus       419 ~EEGAVQv~~~l~~~krD~I~~AVG~--LQF~VV~~RL~~EY~  459 (530)
T TIGR00503       419 SEEGAVQVLRPLDNNKRDLIVGAVGV--LQFDVVVYRLKEEYN  459 (530)
T ss_pred             CCCCHHHHHHHHHHCCCCEEEEECCH--HHHHHHHHHHHCCCC
T ss_conf             22643232311321477605542011--468899887300134


No 241
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=53.52  E-value=14  Score=16.37  Aligned_cols=41  Identities=29%  Similarity=0.351  Sum_probs=22.1

Q ss_pred             HHHHHHHHHHHH----CCCCC--EEEEECCCCCCHHHHHHHHHHHHHH
Q ss_conf             999999999983----06993--9998303654201233467777520
Q gi|254781101|r   93 GALNKLAVAARL----RSKAT--IIAITGSVGKTTTKEMLTIALSSIK  134 (472)
Q Consensus        93 ~al~~la~~~~~----~~~~~--vI~ITGTnGKTTt~~~l~~iL~~~~  134 (472)
                      +-+.+++.+...    ..+..  +.|.+|| |||+|...+..-|+...
T Consensus        37 ~Ei~~l~~~l~~~l~g~~~~n~~I~G~pGT-GKT~~vk~v~~~l~~~~   83 (394)
T PRK00411         37 EQIEELAFALRPALRGSRPSNVLILGPPGT-GKTTTVKKVFEELEEAA   83 (394)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCEEEECCCCC-CHHHHHHHHHHHHHHHC
T ss_conf             999999999999975999984799889999-89999999999999746


No 242
>TIGR02881 spore_V_K stage V sporulation protein K; InterPro: IPR014232   Proteins in this entry include the stage V sporulation protein K (SpoVK), a close homologue of the Rubisco expression protein CbbX (IPR000470 from INTERPRO), and are members of an ATPase family associated with various cellular activities. These proteins are strictly limited to bacterial endospore-forming species, but are not found universally among members of this group; they are missing from the Clostridium species..
Probab=53.46  E-value=5.6  Score=19.06  Aligned_cols=18  Identities=28%  Similarity=0.423  Sum_probs=15.3

Q ss_pred             CCCCHHHHHHHHHHHHHH
Q ss_conf             654201233467777520
Q gi|254781101|r  117 VGKTTTKEMLTIALSSIK  134 (472)
Q Consensus       117 nGKTTt~~~l~~iL~~~~  134 (472)
                      -||||++.+|+.++..-+
T Consensus        53 TGKTTVAR~~gklf~emn   70 (261)
T TIGR02881        53 TGKTTVARLLGKLFKEMN   70 (261)
T ss_pred             CCHHHHHHHHHHHHHHCC
T ss_conf             843899999999985337


No 243
>PRK13541 cytochrome c biogenesis protein CcmA; Provisional
Probab=53.34  E-value=6.3  Score=18.73  Aligned_cols=31  Identities=19%  Similarity=0.246  Sum_probs=23.1

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH-HHCC
Q ss_conf             699399983036--542012334677775-2011
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS-IKKT  136 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~-~~~~  136 (472)
                      .++.+++|+|.|  ||||.-.++.-+++. .|.+
T Consensus        24 ~~G~i~~i~G~NGsGKSTLlk~i~Gl~~p~~G~I   57 (195)
T PRK13541         24 LPSAITYIKGANGCGKSSLLRMIAGIMQPSSGNI   57 (195)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCCCCEEE
T ss_conf             7997999999999819999999967988984089


No 244
>PRK07078 hypothetical protein; Validated
Probab=53.20  E-value=6.4  Score=18.72  Aligned_cols=20  Identities=30%  Similarity=0.386  Sum_probs=11.3

Q ss_pred             ECCCCCCHHHHHHHHHHHHH
Q ss_conf             30365420123346777752
Q gi|254781101|r  114 TGSVGKTTTKEMLTIALSSI  133 (472)
Q Consensus       114 TGTnGKTTt~~~l~~iL~~~  133 (472)
                      +|.|||+|.-+.|..+|...
T Consensus       250 ~G~NGKStf~~vl~~lLGdY  269 (510)
T PRK07078        250 TGANGKSVFVNTLATILGDY  269 (510)
T ss_pred             CCCCCHHHHHHHHHHHHHHH
T ss_conf             89884789999999986566


No 245
>cd03110 Fer4_NifH_child This protein family's function is unkown. It contains nucleotide binding site. It uses NTP as energy source to transfer electron or ion.
Probab=52.66  E-value=6.6  Score=18.62  Aligned_cols=21  Identities=43%  Similarity=0.585  Sum_probs=15.4

Q ss_pred             EEEE---CCCCCCHHHHHHHHHHH
Q ss_conf             9983---03654201233467777
Q gi|254781101|r  111 IAIT---GSVGKTTTKEMLTIALS  131 (472)
Q Consensus       111 I~IT---GTnGKTTt~~~l~~iL~  131 (472)
                      |+|+   |-.||||++.-|+..|.
T Consensus         2 IaV~SgKGGVGKTT~a~nLA~~l~   25 (179)
T cd03110           2 IAVISGKGGTGKTTVTAALAALLK   25 (179)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHCC
T ss_conf             899958998609999999999742


No 246
>KOG2182 consensus
Probab=52.43  E-value=16  Score=16.12  Aligned_cols=99  Identities=20%  Similarity=0.202  Sum_probs=63.0

Q ss_pred             EECCCCCC-CCEEEECCCCC--------CCHHHHHHHHHHCCCEEEEECCCCCC---CCCCCCCCEEEECCHHHHHHHHH
Q ss_conf             40222378-98889716887--------47688899999869889998552124---55446972899599899999999
Q gi|254781101|r   32 IDSRSIAP-QEAFFAIKGPH--------YDGHDFILHAVQKGAGLVVVNTDMVA---SIGSLSIPVFGVDDVLGALNKLA   99 (472)
Q Consensus        32 ~dSr~v~~-g~lFval~g~~--------~DGh~~i~~A~~~Ga~~~i~~~~~~~---~~~~~~~~~i~v~d~~~al~~la   99 (472)
                      .++.-.++ |-+|..|-|+-        ..+..+..-|.+-||.++..|...-.   +..+.+.+-++.=..++||..+|
T Consensus        77 ~n~~~~~~~gPiFLmIGGEgp~~~~wv~~~~~~~~~~AkkfgA~v~~lEHRFYG~S~P~~~~st~nlk~LSs~QALaDla  156 (514)
T KOG2182          77 NNNQWAKPGGPIFLMIGGEGPESDKWVGNENLTWLQWAKKFGATVFQLEHRFYGQSSPIGDLSTSNLKYLSSLQALADLA  156 (514)
T ss_pred             ECCCCCCCCCCEEEEECCCCCCCCCCCCCCCCHHHHHHHHHCCEEEEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             01201369996699976778778873356760699999982982688640003667788877640056660898999899


Q ss_pred             HHHHHC---C----CCCEEEEECCCCCCHHHHHHHHHHHHHHC
Q ss_conf             999830---6----99399983036542012334677775201
Q gi|254781101|r  100 VAARLR---S----KATIIAITGSVGKTTTKEMLTIALSSIKK  135 (472)
Q Consensus       100 ~~~~~~---~----~~~vI~ITGTnGKTTt~~~l~~iL~~~~~  135 (472)
                      .+....   +    +.|.|..-||.-=     .|+.-.++.++
T Consensus       157 ~fI~~~n~k~n~~~~~~WitFGgSYsG-----sLsAW~R~~yP  194 (514)
T KOG2182         157 EFIKAMNAKFNFSDDSKWITFGGSYSG-----SLSAWFREKYP  194 (514)
T ss_pred             HHHHHHHHHCCCCCCCCEEEECCCCHH-----HHHHHHHHHCC
T ss_conf             999998765277789976997887700-----89999987583


No 247
>TIGR03499 FlhF flagellar biosynthetic protein FlhF.
Probab=52.42  E-value=12  Score=16.80  Aligned_cols=28  Identities=18%  Similarity=0.309  Sum_probs=22.6

Q ss_pred             CCCEEEECCHHHHHHHHHHHCCCCCEEEE
Q ss_conf             79799978989999999984478989999
Q gi|254781101|r  421 SIHVHYSETMDGLFLFIQSSLVDGDVVVV  449 (472)
Q Consensus       421 ~~~~~~~~~~e~a~~~l~~~~~~gdiVLi  449 (472)
                      +.++....+.+++-+.+.. +...|+|||
T Consensus       251 ~vp~~vv~~~~~l~~~l~~-~~~~d~IlI  278 (282)
T TIGR03499       251 GVPVKVARDPKELAKALER-LRDKDLILI  278 (282)
T ss_pred             CCEEEEECCHHHHHHHHHH-CCCCCEEEE
T ss_conf             9748993999999999986-579899998


No 248
>PRK13236 nitrogenase reductase; Reviewed
Probab=52.28  E-value=11  Score=17.26  Aligned_cols=32  Identities=25%  Similarity=0.348  Sum_probs=25.6

Q ss_pred             CCCEEEEEC--CCCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             993999830--36542012334677775201122
Q gi|254781101|r  107 KATIIAITG--SVGKTTTKEMLTIALSSIKKTYA  138 (472)
Q Consensus       107 ~~~vI~ITG--TnGKTTt~~~l~~iL~~~~~~~~  138 (472)
                      +.+-|||=|  --||+||+.-++..|.+.|+.+-
T Consensus         5 ~mk~IAiYGKGGIGKSTts~NlsAAlA~~G~rVl   38 (295)
T PRK13236          5 NIRQIAFYGKGGIGKSTTSQNTLAAMAEMGQRIL   38 (295)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHCCCEEE
T ss_conf             7618999679843475789999999997799699


No 249
>PRK09111 DNA polymerase III subunits gamma and tau; Validated
Probab=52.12  E-value=6.2  Score=18.80  Aligned_cols=22  Identities=50%  Similarity=0.637  Sum_probs=15.6

Q ss_pred             EEEECC--CCCCHHHHHHHHHHHH
Q ss_conf             998303--6542012334677775
Q gi|254781101|r  111 IAITGS--VGKTTTKEMLTIALSS  132 (472)
Q Consensus       111 I~ITGT--nGKTTt~~~l~~iL~~  132 (472)
                      .=.||+  .|||||..+++..|.-
T Consensus        48 ~l~~g~rg~gktt~ari~a~~lnc   71 (600)
T PRK09111         48 FMLTGVRGVGKTTTARILARALNY   71 (600)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCC
T ss_conf             764578987899999999999669


No 250
>COG1219 ClpX ATP-dependent protease Clp, ATPase subunit [Posttranslational modification, protein turnover, chaperones]
Probab=51.41  E-value=3.7  Score=20.27  Aligned_cols=98  Identities=27%  Similarity=0.295  Sum_probs=51.2

Q ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHHHHHC----CCCCHHHHHCCCC--CCCHHCCCCCCCHH--HHHCCCCCCCCCCC
Q ss_conf             0699399983036542012334677775201----1222122110145--74100012322144--43015664433211
Q gi|254781101|r  105 RSKATIIAITGSVGKTTTKEMLTIALSSIKK----TYACIGSYNNHIG--VPLTLARMPVDVDF--GIFELGMSHLGEIR  176 (472)
Q Consensus       105 ~~~~~vI~ITGTnGKTTt~~~l~~iL~~~~~----~~~t~gn~Nn~iG--vpltll~~~~~~~~--~V~E~g~~~~gei~  176 (472)
                      +++.-+||=||| |||-...-|+.+|.-.+.    |.-|..-|   +|  |.--++++=-.+||  .--|-|+-+..||+
T Consensus        97 KSNILLiGPTGs-GKTlLAqTLAk~LnVPFaiADATtLTEAGY---VGEDVENillkLlqaadydV~rAerGIIyIDEID  172 (408)
T COG1219          97 KSNILLIGPTGS-GKTLLAQTLAKILNVPFAIADATTLTEAGY---VGEDVENILLKLLQAADYDVERAERGIIYIDEID  172 (408)
T ss_pred             ECCEEEECCCCC-CHHHHHHHHHHHHCCCEEECCCCCHHHCCC---CCHHHHHHHHHHHHHCCCCHHHHHCCEEEEECHH
T ss_conf             031799888997-577999999998489847514441210663---5500899999999876458888828859985102


Q ss_pred             CCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             2122323220255531210123444578888654331037
Q gi|254781101|r  177 FLTHLVRPHIAVITTIAPAHLSNFSGIEEIASAKAEIFEG  216 (472)
Q Consensus       177 ~L~~i~~P~iaiiTNI~~dHld~~~s~e~i~~~K~~i~~~  216 (472)
                      ..++-.. +.    +|++|     -|=|.+.++=++|+++
T Consensus       173 KIarkSe-n~----SITRD-----VSGEGVQQALLKiiEG  202 (408)
T COG1219         173 KIARKSE-NP----SITRD-----VSGEGVQQALLKIIEG  202 (408)
T ss_pred             HHHCCCC-CC----CCCCC-----CCCHHHHHHHHHHHCC
T ss_conf             5420578-98----72343-----6735899999999707


No 251
>TIGR01281 DPOR_bchL light-independent protochlorophyllide reductase, iron-sulfur ATP-binding protein; InterPro: IPR005971    Synonym: dark protochlorophyllide reductase    Protochlorophyllide reductase catalyzes the reductive formation of chlorophyllide from protochlorophyllide during biosynthesis of chlorophylls and bacteriochlorophylls. The light-independent (dark) form of protochlorophyllide reductase plays a key role in the ability of gymnosperms, algae, and photosynthetic bacteria to form chlorophyll in the dark. Genetic and sequence analyses have indicated that dark protochlorophyllide reductase consists of three protein subunits that exhibit significant sequence similarity to the three subunits of nitrogenase, which catalyzes the reductive formation of ammonia from dinitrogen. Dark protochlorophyllide reductase activity was shown to be dependent on the presence of all three subunits, ATP, and the reductant dithionite.    The BchL peptide (ChlL in chloroplast and cyanobacteria) is an ATP-binding iron-sulphur protein of the dark form protochlorophyllide reductase, an enzyme similar to nitrogenase . ; GO: 0005524 ATP binding, 0016730 oxidoreductase activity acting on iron-sulfur proteins as donors, 0015995 chlorophyll biosynthetic process, 0019685 photosynthesis dark reaction.
Probab=51.26  E-value=7.6  Score=18.20  Aligned_cols=29  Identities=38%  Similarity=0.586  Sum_probs=22.7

Q ss_pred             EEEE--ECCCCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             9998--3036542012334677775201122
Q gi|254781101|r  110 IIAI--TGSVGKTTTKEMLTIALSSIKKTYA  138 (472)
Q Consensus       110 vI~I--TGTnGKTTt~~~l~~iL~~~~~~~~  138 (472)
                      ++||  =|--||+||+.=|+..|+..|+.+-
T Consensus         2 ~lAvYGKGGiGKSTTssNLSvA~A~~GkkVl   32 (275)
T TIGR01281         2 ILAVYGKGGIGKSTTSSNLSVALAKKGKKVL   32 (275)
T ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHCCCEEE
T ss_conf             6888638887700467899999984699189


No 252
>cd05008 SIS_GlmS_GlmD_1 SIS (Sugar ISomerase) domain repeat 1 found in Glucosamine 6-phosphate synthase (GlmS) and Glucosamine-6-phosphate deaminase (GlmD). The SIS domain is found in many phosphosugar isomerases and phosphosugar binding proteins. GlmS contains a N-terminal glutaminase domain and two C-terminal SIS domains and catalyzes the first step in hexosamine metabolism, converting fructose 6-phosphate into glucosamine 6-phosphate using glutamine as nitrogen source. The glutaminase domain hydrolyzes glutamine to glutamate and ammonia. Ammonia is transferred through a channel to the isomerase domain for glucosamine 6-phosphate synthesis. The end product of the pathway is N-acetylglucosamine, which plays multiple roles in eukaryotic cells including being a building block of bacterial and fungal cell walls. In the absence of glutamine, GlmS catalyzes the isomerization of fructose 6-phosphate into glucose 6- phosphate (PGI-like activity). Glucosamine-6-phosphate deaminase (GlmD) cont
Probab=50.94  E-value=17  Score=15.97  Aligned_cols=37  Identities=24%  Similarity=0.207  Sum_probs=18.9

Q ss_pred             ECCCCCCCCEEEECC--CCCCCHHHHHHHHHHCCCEEEE
Q ss_conf             022237898889716--8874768889999986988999
Q gi|254781101|r   33 DSRSIAPQEAFFAIK--GPHYDGHDFILHAVQKGAGLVV   69 (472)
Q Consensus        33 dSr~v~~g~lFval~--g~~~DGh~~i~~A~~~Ga~~~i   69 (472)
                      ..+.+.+++++|++-  |+..|=.+-++.|.++|+..+.
T Consensus        40 ~~~~~~~~~lvI~iS~SG~t~e~i~a~~~a~~~g~~~i~   78 (126)
T cd05008          40 RRPLLDEDTLVIAISQSGETADTLAALRLAKEKGAKTVA   78 (126)
T ss_pred             CCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHCCCCEEE
T ss_conf             478899985999986897980078899999982994898


No 253
>COG0556 UvrB Helicase subunit of the DNA excision repair complex [DNA replication, recombination, and repair]
Probab=50.58  E-value=17  Score=15.93  Aligned_cols=13  Identities=62%  Similarity=0.912  Sum_probs=6.0

Q ss_pred             CEEEEECCCCCCHH
Q ss_conf             39998303654201
Q gi|254781101|r  109 TIIAITGSVGKTTT  122 (472)
Q Consensus       109 ~vI~ITGTnGKTTt  122 (472)
                      ...||||| |||=|
T Consensus        36 tLLGvTGS-GKTfT   48 (663)
T COG0556          36 TLLGVTGS-GKTFT   48 (663)
T ss_pred             EEEEECCC-CCHHH
T ss_conf             88620368-83107


No 254
>cd03215 ABC_Carb_Monos_II This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos).  The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis.  In members of Carb_Monos family the single hydrophobic gene product forms a homodimer, while the ABC protein represents a fusion of two nucleotide-binding domains.  However, it is assumed that two copies of the ABC domains are present in the assembled transporter.
Probab=50.41  E-value=8.3  Score=17.95  Aligned_cols=27  Identities=30%  Similarity=0.326  Sum_probs=21.4

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++|+.|.|  ||||+-.++.-++..
T Consensus        24 ~~GEi~~liG~nGaGKSTll~~l~G~~~p   52 (182)
T cd03215          24 RAGEIVGIAGLVGNGQTELAEALFGLRPP   52 (182)
T ss_pred             CCCCEEEEECCCCCCCCHHHHHHCCCCCC
T ss_conf             59969999888999926377876698678


No 255
>PRK04117 consensus
Probab=50.12  E-value=17  Score=15.88  Aligned_cols=90  Identities=13%  Similarity=0.130  Sum_probs=41.1

Q ss_pred             CEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHH
Q ss_conf             11331000256532101257778741110268713885123541710589999999999864998999988038989985
Q gi|254781101|r  338 FFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFHVLALKDA  417 (472)
Q Consensus       338 ~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~~~~~~~~  417 (472)
                      .+.++||== .+-.+|..|.+.|+..   +. ++|.+...=   |-.+..-    .+.+...+++.++..-.-..  .  
T Consensus       213 ~vIIVDDiI-~TGgTi~~aa~~L~~~---GA-~~V~~~~TH---glfs~~A----~~rl~~s~i~~ivvTnTip~--~--  276 (309)
T PRK04117        213 DVILVDDMI-DTAGTIVKAAEALKEK---GA-TSVMACCTH---AVLSGPA----YERIAKGALDELVVTNTIPL--K--  276 (309)
T ss_pred             EEEEECCHH-HHHHHHHHHHHHHHHC---CC-CEEEEEEEC---CCCCCHH----HHHHHHCCCCEEEECCCCCC--C--
T ss_conf             689757256-5279999999999866---99-748999945---5458369----99998389978998289877--4--


Q ss_pred             CCCCCCEEEECCHHHHHHHHHHHCCCCC
Q ss_conf             1137979997898999999998447898
Q gi|254781101|r  418 LPRSIHVHYSETMDGLFLFIQSSLVDGD  445 (472)
Q Consensus       418 ~~~~~~~~~~~~~e~a~~~l~~~~~~gd  445 (472)
                       +...++... +...++..+...+..|.
T Consensus       277 -~~~~kl~~i-sVa~llAeaI~ri~~~~  302 (309)
T PRK04117        277 -EELPKIKVL-SVAPLFAEVIRRVYHNE  302 (309)
T ss_pred             -CCCCCEEEE-EHHHHHHHHHHHHHCCC
T ss_conf             -459980998-83999999999986799


No 256
>PRK00023 cmk cytidylate kinase; Provisional
Probab=50.08  E-value=10  Score=17.33  Aligned_cols=28  Identities=39%  Similarity=0.466  Sum_probs=22.1

Q ss_pred             CCCEEEEECC--CCCCHHHHHHHHHHHHHH
Q ss_conf             9939998303--654201233467777520
Q gi|254781101|r  107 KATIIAITGS--VGKTTTKEMLTIALSSIK  134 (472)
Q Consensus       107 ~~~vI~ITGT--nGKTTt~~~l~~iL~~~~  134 (472)
                      +.+||+|-|.  .||||+..+++.-|.-.+
T Consensus         3 ~~iIIaIDGpagSGKST~ak~lA~~L~~~y   32 (225)
T PRK00023          3 KAPVIAIDGPAGSGKGTVAKILAKKLGFHY   32 (225)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHCCCE
T ss_conf             897899658986787899999999939887


No 257
>COG0462 PrsA Phosphoribosylpyrophosphate synthetase [Nucleotide transport and metabolism / Amino acid transport and metabolism]
Probab=50.06  E-value=17  Score=15.88  Aligned_cols=61  Identities=15%  Similarity=0.186  Sum_probs=33.0

Q ss_pred             CCEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             3113310002565321012577787411102687138851235417105899999999998649989999880
Q gi|254781101|r  337 GFFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGF  409 (472)
Q Consensus       337 ~~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~  409 (472)
                      ..+.++||=- ++...|-.|-+.|++.    +-+++.+...-   |-.+..    ..+.+....++.|+..-.
T Consensus       215 k~~iiVDDiI-dTgGTi~~Aa~~Lk~~----GAk~V~a~~tH---~vfs~~----a~~~l~~~~i~~vivTnT  275 (314)
T COG0462         215 KDVVIVDDII-DTGGTIAKAAKALKER----GAKKVYAAATH---GVFSGA----ALERLEASAIDEVIVTDT  275 (314)
T ss_pred             CEEEEEECCC-CCCHHHHHHHHHHHHC----CCCEEEEEEEC---HHHCHH----HHHHHHCCCCCEEEEECC
T ss_conf             8799993651-3656899999999977----99759999983---660708----999986488767998278


No 258
>PRK13896 cobyrinic acid a,c-diamide synthase; Provisional
Probab=50.02  E-value=12  Score=16.95  Aligned_cols=28  Identities=32%  Similarity=0.279  Sum_probs=16.9

Q ss_pred             EEEEECC-CCCCHHHHHHHHHHHHHHCCC
Q ss_conf             9998303-654201233467777520112
Q gi|254781101|r  110 IIAITGS-VGKTTTKEMLTIALSSIKKTY  137 (472)
Q Consensus       110 vI~ITGT-nGKTTt~~~l~~iL~~~~~~~  137 (472)
                      +||=|.| .||||++--|...|++.|..+
T Consensus         5 lIAa~~SgsGKTtvt~gL~~aL~~rG~~V   33 (432)
T PRK13896          5 VLAGTSSGVGKTVATLAVLQALADAGYDV   33 (432)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCCC
T ss_conf             99778999989999999999999784963


No 259
>PRK01999 consensus
Probab=49.70  E-value=17  Score=15.84  Aligned_cols=89  Identities=10%  Similarity=0.189  Sum_probs=39.6

Q ss_pred             CEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHH
Q ss_conf             11331000256532101257778741110268713885123541710589999999999864998999988038989985
Q gi|254781101|r  338 FFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFHVLALKDA  417 (472)
Q Consensus       338 ~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~~~~~~~~  417 (472)
                      .+.++||== .+-.+|..+.+.|+..   +. ++|.+...=   |-.+..-    .+.+...+++.++..-.-..  .  
T Consensus       214 ~~IIVDDiI-dTGgTl~~aa~~L~~~---GA-~~V~~~~TH---glfs~~A----~~rl~~s~i~~iv~TdTip~--~--  277 (311)
T PRK01999        214 NVILVDDMV-DTAGTITKAADLMMEK---GA-KSVRAIASH---AVMSGPA----SERVENSKLTEMIFTDSIPY--R--  277 (311)
T ss_pred             EEEEECCHH-HHHHHHHHHHHHHHHC---CC-CEEEEEEEC---CCCCCHH----HHHHHHCCCCEEEECCCCCC--C--
T ss_conf             699975444-4347899999999855---99-738999945---5458559----99997489988998378558--5--


Q ss_pred             CCCCCCEEEECCHHHHHHHHHHHCCCC
Q ss_conf             113797999789899999999844789
Q gi|254781101|r  418 LPRSIHVHYSETMDGLFLFIQSSLVDG  444 (472)
Q Consensus       418 ~~~~~~~~~~~~~e~a~~~l~~~~~~g  444 (472)
                       +...++...+ ...++..+...+..|
T Consensus       278 -~~~~k~~vis-va~llAeaI~ri~~~  302 (311)
T PRK01999        278 -KKCSKVKVLS-VADLFAEAIKRVMNN  302 (311)
T ss_pred             -CCCCCCEEEE-HHHHHHHHHHHHHCC
T ss_conf             -5699848987-689999999998679


No 260
>COG0489 Mrp ATPases involved in chromosome partitioning [Cell division and chromosome partitioning]
Probab=49.51  E-value=13  Score=16.62  Aligned_cols=30  Identities=37%  Similarity=0.481  Sum_probs=24.6

Q ss_pred             CCCEEEEECC---CCCCHHHHHHHHHHHHHHCC
Q ss_conf             9939998303---65420123346777752011
Q gi|254781101|r  107 KATIIAITGS---VGKTTTKEMLTIALSSIKKT  136 (472)
Q Consensus       107 ~~~vI~ITGT---nGKTTt~~~l~~iL~~~~~~  136 (472)
                      ...+|+||.+   .|||||+..|+..|.+.|+.
T Consensus        56 ~~~~I~V~S~kgGvGKStva~nLA~alA~~G~r   88 (265)
T COG0489          56 VKNVIAVTSGKGGVGKSTVAVNLAAALAQLGKR   88 (265)
T ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCE
T ss_conf             661899975899875689999999999963993


No 261
>TIGR02253 CTE7 HAD superfamily (subfamily IA) hydrolase, TIGR02253; InterPro: IPR011950    This family of sequences from archaea and metazoans includes the human uncharacterised protein CTE7. Pyrococcus species appear to have three different forms of this enzyme, so it is unclear whether all members of this family have the same function. This family is a member of the haloacid dehalogenase (HAD) superfamily of hydrolases which are characterised by three conserved sequence motifs. By virtue of an alpha helical domain in-between the first and second conserved motif, this family is a member of subfamily IA ..
Probab=49.44  E-value=17  Score=15.81  Aligned_cols=74  Identities=14%  Similarity=0.078  Sum_probs=37.8

Q ss_pred             HHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHCCCCCCEEEECCHHHHHHH
Q ss_conf             77787411102687138851235417105899999999998649989999880389899851137979997898999999
Q gi|254781101|r  357 ISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFHVLALKDALPRSIHVHYSETMDGLFLF  436 (472)
Q Consensus       357 l~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~~~~~~~~~~~~~~~~~~~~~e~a~~~  436 (472)
                      .++|..++.  .|.+++++.+    |... ....+|...=...-||.|++.++..     ..+++..+     +..|++.
T Consensus       119 ~~~L~~LR~--~Gy~Lg~iT~----G~~~-~Q~eKl~~lg~~~fFD~V~~s~e~g-----~~KPhP~I-----F~~Al~~  181 (244)
T TIGR02253       119 VDTLMELRE--SGYRLGLITD----GLTV-KQWEKLERLGIRDFFDAVITSEELG-----VEKPHPKI-----FYAALRR  181 (244)
T ss_pred             HHHHHHHHH--CCCEEEEEEC----CCHH-HHHHHHHHHCCCCCCCEEEECCCCC-----CCCCCHHH-----HHHHHHH
T ss_conf             899999986--4778899866----8778-9999999827753577057224447-----76978589-----9999997


Q ss_pred             HHHHCCCCCEEEE
Q ss_conf             9984478989999
Q gi|254781101|r  437 IQSSLVDGDVVVV  449 (472)
Q Consensus       437 l~~~~~~gdiVLi  449 (472)
                      +  .++|+|.|+|
T Consensus       182 ~--gV~p~eaVmV  192 (244)
T TIGR02253       182 L--GVKPEEAVMV  192 (244)
T ss_pred             H--CCCCCCEEEE
T ss_conf             0--8893666676


No 262
>TIGR02173 cyt_kin_arch cytidylate kinase, putative; InterPro: IPR011892    Proteins in this family are believed to be cytidylate kinase. Members of this family are found in the archaea and in spirochaetes, and differ considerably from the common bacterial form of cytidylate kinase described by IPR003136 from INTERPRO.; GO: 0004127 cytidylate kinase activity, 0005524 ATP binding, 0006139 nucleobase nucleoside nucleotide and nucleic acid metabolic process.
Probab=49.39  E-value=9.5  Score=17.56  Aligned_cols=24  Identities=46%  Similarity=0.580  Sum_probs=19.5

Q ss_pred             EEEEECC--CCCCHHHHHHHHHHHHH
Q ss_conf             9998303--65420123346777752
Q gi|254781101|r  110 IIAITGS--VGKTTTKEMLTIALSSI  133 (472)
Q Consensus       110 vI~ITGT--nGKTTt~~~l~~iL~~~  133 (472)
                      +|.|.|-  .||||++.+|+.-|+-.
T Consensus         2 ~I~ISGpPGSGktTvA~~lA~~Lsl~   27 (173)
T TIGR02173         2 IITISGPPGSGKTTVAKILAEKLSLK   27 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHCCCC
T ss_conf             78873589686478999999863983


No 263
>TIGR03238 dnd_assoc_3 dnd system-associated protein 3. cereus E33L, Hahella chejuensis KCTC 2396, Pseudoalteromonas haloplanktis TAC12, and Escherichia coli B7A.
Probab=49.38  E-value=17  Score=15.81  Aligned_cols=28  Identities=18%  Similarity=0.288  Sum_probs=14.9

Q ss_pred             HHHHHHHHHHHHHHCCCCCEEEE-ECCCC
Q ss_conf             89999999999983069939998-30365
Q gi|254781101|r   91 VLGALNKLAVAARLRSKATIIAI-TGSVG  118 (472)
Q Consensus        91 ~~~al~~la~~~~~~~~~~vI~I-TGTnG  118 (472)
                      ..++|.++=..+.+..++-+||| +|+=|
T Consensus        76 AieTL~e~l~~f~~s~~plIvaINlG~L~  104 (504)
T TIGR03238        76 AMETLDEIFDGFNQSNKPLIVGINMGMLH  104 (504)
T ss_pred             HHHHHHHHHHHHHCCCCCEEEEEEHHHHH
T ss_conf             99999999998545699779998455443


No 264
>TIGR02640 gas_vesic_GvpN gas vesicle protein GvpN; InterPro: IPR013462    The GvpN protein is associated with the production of gas vesicles produced in some prokaryotes to give cells buoyancy , . It belongs to a larger family of ATPases .; GO: 0000166 nucleotide binding, 0005524 ATP binding, 0031412 gas vesicle organization and biogenesis, 0031411 gas vesicle.
Probab=49.15  E-value=8.8  Score=17.79  Aligned_cols=51  Identities=16%  Similarity=0.074  Sum_probs=30.0

Q ss_pred             CCHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCHHH
Q ss_conf             998999999999998306993999830365420123346777752011222122
Q gi|254781101|r   89 DDVLGALNKLAVAARLRSKATIIAITGSVGKTTTKEMLTIALSSIKKTYACIGS  142 (472)
Q Consensus        89 ~d~~~al~~la~~~~~~~~~~vI~ITGTnGKTTt~~~l~~iL~~~~~~~~t~gn  142 (472)
                      +.+.....+.-+|.-.-++...+|=||| ||||.+--+|.-+..  +|..--|+
T Consensus         5 ~~v~~v~~R~l~yL~~G~PvHl~GPaG~-GKT~LA~hvA~~r~R--PV~l~~Gd   55 (265)
T TIGR02640         5 DAVKRVTSRALRYLKSGYPVHLRGPAGT-GKTTLAMHVARKRDR--PVVLINGD   55 (265)
T ss_pred             HHHHHHHHHHHHHHCCCCCEEEECCCCC-CHHHHHHHHHHHCCC--CEEEEECC
T ss_conf             2379999987663227886674478885-568999999973689--68998658


No 265
>pfam02374 ArsA_ATPase Anion-transporting ATPase. This Pfam family represents a conserved domain, which is sometimes repeated, in an anion-transporting ATPase. The ATPase is involved in the removal of arsenate, antimonite, and arsenate from the cell.
Probab=49.13  E-value=14  Score=16.55  Aligned_cols=27  Identities=37%  Similarity=0.363  Sum_probs=20.9

Q ss_pred             CEEEEECC--CCCCHHHHHHHHHHHHHHC
Q ss_conf             39998303--6542012334677775201
Q gi|254781101|r  109 TIIAITGS--VGKTTTKEMLTIALSSIKK  135 (472)
Q Consensus       109 ~vI~ITGT--nGKTTt~~~l~~iL~~~~~  135 (472)
                      ++|=+||-  .||||++.-++-.+...|+
T Consensus         2 r~i~~~GKGGVGKTT~AaA~A~~~A~~G~   30 (304)
T pfam02374         2 RWIFFGGKGGVGKTTVSCATAVRLSEQGK   30 (304)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHCCC
T ss_conf             19999579857489999999999995899


No 266
>TIGR00176 mobB molybdopterin-guanine dinucleotide biosynthesis protein B; InterPro: IPR004435   The majority of molybdenum-containing enzymes utilise a molybdenum cofactor (MoCF or Moco) consisting of a Mo atom coordinated via a cisdithiolene moiety to molybdopterin (MPT). MoCF is ubiquitous in nature, and the pathway for MoCF biosynthesis is conserved in all three domains of life. MoCF-containing enzymes function as oxidoreductases in carbon, nitrogen, and sulphur metabolism , .    In Escherichia coli, biosynthesis of MoCF is a three stage process. It begins with the MoaA and MoaC conversion of GTP to the meta-stable pterin intermediate precursor Z. The second stage involves MPT synthase (MoaD and MoaE), which coverts precursor Z to MPT; MoeB is involved in the recycling of MPT synthase. The final step in MoCF synthesis is the attachment of mononuclear Mo to MPT, a process that requires MoeA and which is enhanced by MogA in an Mg2 ATP-dependent manner . MoCF is the active co-factor in eukaryotic and some prokaryotic molybdoenzymes, but the majority of bacterial enzymes requiring MoCF, need a modification of MTP for it to be active; MobA is involved in the attachment of a nucleotide monophosphate to MPT resulting in the MGD co-factor, the active co-factor for most prokaryotic molybdoenzymes. Bacterial two-hybrid studies have revealed the close interactions between MoeA, MogA, and MobA in the synthesis of MoCF . Moreover the close functional association of MoeA and MogA in the synthesis of MoCF is supported by fact that the known eukaryotic homologues to MoeA and MogA exist as fusion proteins: CNX1 () of Arabidopsis thaliana (Mouse-ear cress), mammalian Gephryin (e.g. Q9NQX3 from SWISSPROT) and Drosophila melanogaster (Fruit fly) Cinnamon (P39205 from SWISSPROT) .   The MobB domain is similar to that of the urease accessory protein UreG and the hydrogenase accessory protein HypB, both GTP hydrolases involved in loading nickel into the metallocentres of their respective target enzymes. It is involved in the final step of molybdenum-cofactor biosynthesis. While its precise function has not been identified it is thought to be involved in the transfer of a guanine dinucleotide moiety to molybdopterin, as it shows GTP-binding and weak GTPase activity . The MobB protein (P32125 from SWISSPROT) from Escherichia coli, which is comprised of this domain, is a homodimer . Each molecule is composed of two distinct regions - an outer region comprised of 6 beta-strands and three alpha helices, and an inner region comprised of a two-strand beta hairpin followed by an alpha helix. These regions require interaction with the second monomer to allow proper folding to occur. The two monomers are intertwined and form an extensive 16-stranded beta-sheet. While the active site could not be positively identified, the presence of highly conserved residues suggests the substrate binding site occurs in the central solvent channel.; GO: 0005525 GTP binding, 0006777 Mo-molybdopterin cofactor biosynthetic process.
Probab=49.10  E-value=8.6  Score=17.86  Aligned_cols=32  Identities=38%  Similarity=0.357  Sum_probs=23.3

Q ss_pred             EEEEECC--CCCCHHHHHHHHHHHHHHCCCCCHH
Q ss_conf             9998303--6542012334677775201122212
Q gi|254781101|r  110 IIAITGS--VGKTTTKEMLTIALSSIKKTYACIG  141 (472)
Q Consensus       110 vI~ITGT--nGKTTt~~~l~~iL~~~~~~~~t~g  141 (472)
                      |++|+|-  .||||.-+-+...|+..|-++.+.+
T Consensus         1 v~~i~G~k~SGKTtL~~~l~~~L~~~Gy~V~~IK   34 (165)
T TIGR00176         1 VLQIVGYKNSGKTTLIERLVKALKARGYRVATIK   34 (165)
T ss_pred             CEEEEEECCCCHHHHHHHHHHHHHCCCCCEEEEE
T ss_conf             9378962588678999999999970799508986


No 267
>PRK01077 cobyrinic acid a,c-diamide synthase; Validated
Probab=49.01  E-value=16  Score=16.12  Aligned_cols=30  Identities=27%  Similarity=0.165  Sum_probs=20.4

Q ss_pred             CCEEEEECC---CCCCHHHHHHHHHHHHHHCCC
Q ss_conf             939998303---654201233467777520112
Q gi|254781101|r  108 ATIIAITGS---VGKTTTKEMLTIALSSIKKTY  137 (472)
Q Consensus       108 ~~vI~ITGT---nGKTTt~~~l~~iL~~~~~~~  137 (472)
                      .|-|=|.||   .||||.+.-|..+|++.|..+
T Consensus         3 ~p~lmI~gt~S~~GKT~vt~gL~r~l~~rG~~V   35 (451)
T PRK01077          3 MPALVIAAPASGSGKTTVTLGLMRALRRRGLRV   35 (451)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHCCCCC
T ss_conf             887999868999978999999999999687945


No 268
>cd03115 SRP The signal recognition particle (SRP) mediates the transport to or across the plasma membrane in bacteria and the endoplasmic reticulum in eukaryotes. SRP recognizes N-terminal sighnal sequences of newly synthesized polypeptides at the ribosome. The SRP-polypeptide complex is then targeted to the membrane by an interaction between SRP and its cognated receptor (SR). In mammals, SRP consists of six protein subunits and a 7SL RNA. One of these subunits is a 54 kd protein (SRP54), which is a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 is a multidomain protein that consists of an N-terminal domain, followed by a central G (GTPase) domain and a C-terminal M domain.
Probab=48.96  E-value=14  Score=16.53  Aligned_cols=26  Identities=38%  Similarity=0.470  Sum_probs=17.4

Q ss_pred             EEEEECCC--CCCHHHHHHHHHHHHHHC
Q ss_conf             99983036--542012334677775201
Q gi|254781101|r  110 IIAITGSV--GKTTTKEMLTIALSSIKK  135 (472)
Q Consensus       110 vI~ITGTn--GKTTt~~~l~~iL~~~~~  135 (472)
                      ||.+.|-+  |||||..=+++-+...++
T Consensus         2 Vi~lvGptGvGKTTTiaKLA~~~~~~~~   29 (173)
T cd03115           2 VILLVGLQGVGKTTTAAKLALYLKKKGK   29 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCC
T ss_conf             9999899999889999999999997699


No 269
>cd00884 beta_CA_cladeB Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. CAs are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionarily distinct families of CAs (the alpha-, beta-, and gamma-CAs) which show no significant sequence identity or structural similarity.  Within the beta-CA family there are four evolutionarily distinct clades (A through D). The beta-CAs are multimeric enzymes (forming dimers,tetramers,hexamers and octamers) which are present in higher plants, algae, fungi, archaea and prokaryotes.
Probab=48.96  E-value=18  Score=15.77  Aligned_cols=25  Identities=32%  Similarity=0.499  Sum_probs=16.9

Q ss_pred             CCCCCCEEEEEEEECCC-------CCCCCEEEE
Q ss_conf             26887147467740222-------378988897
Q gi|254781101|r   20 GIVPQGFVNGISIDSRS-------IAPQEAFFA   45 (472)
Q Consensus        20 ~~~~~~~i~~i~~dSr~-------v~~g~lFva   45 (472)
                      +..|...+=+ |.|||-       ..|||+||.
T Consensus        23 gQ~P~a~vi~-CsDSRV~pe~if~~~~GdlFVv   54 (190)
T cd00884          23 GQSPKALFIA-CSDSRVVPALITQTQPGELFVV   54 (190)
T ss_pred             CCCCCEEEEE-EECCCCCHHHHHCCCCCCEEEE
T ss_conf             8999679998-6535899999828999767998


No 270
>cd03220 ABC_KpsT_Wzt ABC_KpsT_Wzt   The KpsT/Wzt ABC transporter subfamily is involved in extracellular polysaccharide export.  Among the variety of membrane-linked or extracellular polysaccharides excreted by bacteria, only capsular polysaccharides, lipopolysaccharides, and teichoic acids have been shown to be exported by ABC transporters.  A typical system is made of a conserved integral membrane and an ABC.  In addition to these proteins, capsular polysaccharide exporter systems require two 'accessory' proteins to perform their function: a periplasmic (E.coli) or a lipid-anchored outer membrane protein called OMA (Neisseria meningitidis and Haemophilus influenzae) and a cytoplasmic membrane protein MPA2.
Probab=48.90  E-value=8.5  Score=17.87  Aligned_cols=27  Identities=22%  Similarity=0.319  Sum_probs=22.3

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++-++||.|.|  ||||+-.++.-++..
T Consensus        46 ~~GeivgilG~NGaGKSTLl~~i~Gl~~p   74 (224)
T cd03220          46 PRGERIGLIGRNGAGKSTLLRLLAGIYPP   74 (224)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             38989999979998199999999758777


No 271
>TIGR01978 sufC FeS assembly ATPase SufC; InterPro: IPR010230   Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems.   The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly .   The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets.   In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen .   This entry represents SufC, which acts as an ATPase in the SUF system. SufC belongs to the ATP-binding cassette transporter family (IPR003439 from INTERPRO) but is no longer thought to be part of a transporter. The complex is reported as cytosolic or associated with the membrane.; GO: 0005524 ATP binding, 0006810 transport.
Probab=48.85  E-value=18  Score=15.76  Aligned_cols=33  Identities=33%  Similarity=0.404  Sum_probs=23.3

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHHHHCCCCCHHH
Q ss_conf             699399983036--5420123346777752011222122
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSSIKKTYACIGS  142 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~~~~~~~t~gn  142 (472)
                      .++.|.||-|=|  ||+|    |+.+|.....+--|.|+
T Consensus        24 ~~GE~HAiMGPNGsGKST----L~~~iaGhp~y~vt~G~   58 (248)
T TIGR01978        24 KKGEIHAIMGPNGSGKST----LSKTIAGHPKYEVTSGT   58 (248)
T ss_pred             CCCEEEEEECCCCCCHHH----HHHHHHCCCCEEEEEEE
T ss_conf             685179986889984788----87776179933784208


No 272
>PRK05298 excinuclease ABC subunit B; Provisional
Probab=48.54  E-value=17  Score=15.82  Aligned_cols=33  Identities=33%  Similarity=0.404  Sum_probs=19.8

Q ss_pred             CHHHHHHHHHHHHHHC-CCCCEEEEECCCCCCHHH
Q ss_conf             9899999999999830-699399983036542012
Q gi|254781101|r   90 DVLGALNKLAVAARLR-SKATIIAITGSVGKTTTK  123 (472)
Q Consensus        90 d~~~al~~la~~~~~~-~~~~vI~ITGTnGKTTt~  123 (472)
                      |--+|..+|.....+. ....+.||||| |||=|-
T Consensus        17 DQP~AI~~L~~gi~~g~~~Q~LlGvTGS-GKTfTm   50 (657)
T PRK05298         17 DQPQAIAELVEGIESGEKHQTLLGVTGS-GKTFTM   50 (657)
T ss_pred             CCHHHHHHHHHHHHCCCCEEEEECCCCC-CHHHHH
T ss_conf             8799999999899749963699703678-566899


No 273
>cd03226 ABC_cobalt_CbiO_domain2 Domain II of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota.  The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed.  The CbiMNQO family ABC transport system is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways.  Most cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO.  Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.
Probab=48.10  E-value=8.9  Score=17.74  Aligned_cols=27  Identities=37%  Similarity=0.459  Sum_probs=21.5

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++||.|.|  ||||.-.++.-+++.
T Consensus        24 ~~Gei~~iiG~nGaGKSTLl~~i~Gl~~p   52 (205)
T cd03226          24 YAGEIIALTGKNGAGKTTLAKILAGLIKE   52 (205)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             69989999889999899999999568577


No 274
>PRK04607 consensus
Probab=48.04  E-value=18  Score=15.67  Aligned_cols=17  Identities=18%  Similarity=0.378  Sum_probs=10.3

Q ss_pred             CCCCCCHHHHHHHHHHH
Q ss_conf             56532101257778741
Q gi|254781101|r  347 NANPASMKAAISVLSQI  363 (472)
Q Consensus       347 NAnP~S~~aal~~l~~~  363 (472)
                      .|||.||.+|++.-.++
T Consensus       310 ~A~~~S~~~Ai~~A~~~  326 (330)
T PRK04607        310 QADTGSFRTALTHAIEL  326 (330)
T ss_pred             CCCHHHHHHHHHHHHHH
T ss_conf             89969999999999999


No 275
>CHL00072 chlL photochlorophyllide reductase subunit L
Probab=47.96  E-value=8.2  Score=17.97  Aligned_cols=28  Identities=39%  Similarity=0.501  Sum_probs=21.8

Q ss_pred             EEEE--CCCCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             9983--036542012334677775201122
Q gi|254781101|r  111 IAIT--GSVGKTTTKEMLTIALSSIKKTYA  138 (472)
Q Consensus       111 I~IT--GTnGKTTt~~~l~~iL~~~~~~~~  138 (472)
                      |||-  |--|||||+.=++..|...|+.+-
T Consensus         3 iaiyGKGGIGKSTtsaNlsaaLA~~GkkVl   32 (271)
T CHL00072          3 IAVYGKGGIGKSTTSCNISIALARRGKKVL   32 (271)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCEEE
T ss_conf             999789854485889999999998799799


No 276
>cd03225 ABC_cobalt_CbiO_domain1 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota.  The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed.  This ABC transport system of the CbiMNQO family is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways.  Most of cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO.  Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.
Probab=47.87  E-value=9.2  Score=17.65  Aligned_cols=26  Identities=31%  Similarity=0.414  Sum_probs=20.5

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHH
Q ss_conf             699399983036--54201233467777
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALS  131 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~  131 (472)
                      ..+.++||.|.|  ||||+-.++.-++.
T Consensus        25 ~~Gei~~iiG~nGaGKSTLlk~i~Gl~~   52 (211)
T cd03225          25 KKGEFVLIVGPNGSGKSTLLRLLNGLLG   52 (211)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCC
T ss_conf             4997999988999989999999964677


No 277
>cd03237 ABC_RNaseL_inhibitor_domain2 The ATPase domain 2 of RNase L inhibitor.  The ABC ATPase, RNase L inhibitor (RLI), is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids.  RLI's are not transport proteins and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family.  Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains which are arranged to form two composite active sites in their interface cleft.  RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity of more than 48%.  The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.
Probab=47.87  E-value=8.8  Score=17.78  Aligned_cols=26  Identities=38%  Similarity=0.488  Sum_probs=20.5

Q ss_pred             CCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             99399983036--542012334677775
Q gi|254781101|r  107 KATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       107 ~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      ++.++||.|-|  ||||.-.+++-+++.
T Consensus        24 ~GEiv~liGpNGaGKSTLlk~l~Gll~p   51 (246)
T cd03237          24 ESEVIGILGPNGIGKTTFIKMLAGVLKP   51 (246)
T ss_pred             CCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             7989999979997699999999778788


No 278
>COG1880 CdhB CO dehydrogenase/acetyl-CoA synthase epsilon subunit [Energy production and conversion]
Probab=47.71  E-value=19  Score=15.64  Aligned_cols=16  Identities=13%  Similarity=-0.033  Sum_probs=9.3

Q ss_pred             CCCEEEEEEECCCHHH
Q ss_conf             3220255531210123
Q gi|254781101|r  183 RPHIAVITTIAPAHLS  198 (472)
Q Consensus       183 ~P~iaiiTNI~~dHld  198 (472)
                      ++|..|+|..-..|++
T Consensus       108 ~yDlviflG~~~yy~s  123 (170)
T COG1880         108 NYDLVIFLGSIYYYLS  123 (170)
T ss_pred             CCCEEEEEECCHHHHH
T ss_conf             8456999702299999


No 279
>PRK13477 bifunctional pantoate ligase/cytidylate kinase; Provisional
Probab=47.70  E-value=12  Score=16.86  Aligned_cols=26  Identities=4%  Similarity=0.250  Sum_probs=16.5

Q ss_pred             CCCCEEEEECCCHHHHHHHHHHHHHHC
Q ss_conf             789899997713254899999999850
Q gi|254781101|r  442 VDGDVVVVKSSNSCGFYRLINLLLEEF  468 (472)
Q Consensus       442 ~~gdiVLiKGSr~~~le~iv~~L~~~~  468 (472)
                      .+.|-|+|--|+ +-.|++++++.+-|
T Consensus       476 ~A~DAi~IDTs~-lsieeVv~kI~~l~  501 (512)
T PRK13477        476 KADDAIELITDG-LSIEEVVDKIIDLY  501 (512)
T ss_pred             CCCCEEEEECCC-CCHHHHHHHHHHHH
T ss_conf             589848998999-99999999999999


No 280
>PRK04554 consensus
Probab=47.60  E-value=19  Score=15.63  Aligned_cols=92  Identities=13%  Similarity=0.165  Sum_probs=43.2

Q ss_pred             CEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHH
Q ss_conf             11331000256532101257778741110268713885123541710589999999999864998999988038989985
Q gi|254781101|r  338 FFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFHVLALKDA  417 (472)
Q Consensus       338 ~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~~~~~~~~  417 (472)
                      .+.++||=- .+..++..|.+.|+..   +. ++|.+...=   |-.+..-    .+.+...+++.+++.-.-...  +.
T Consensus       217 ~~IIVDDiI-dTGgTl~~aa~~Lk~~---GA-~~V~~~aTH---glfs~~A----~~rl~~s~i~~ivvTnTIp~~--~~  282 (327)
T PRK04554        217 TCLIVDDMI-DTANTLCKAAVALKER---GA-ERVLAYASH---AVFSGEA----VSRIASSEIDQVVVTDTIPLS--EA  282 (327)
T ss_pred             EEEECCCCC-CCHHHHHHHHHHHHHC---CC-CEEEEEEEC---CCCCCHH----HHHHHHCCCCEEEEECCCCCC--HH
T ss_conf             367204321-3506799999999976---99-878999879---1606339----999971899789991897687--45


Q ss_pred             CCCCCCEEEECCHHHHHHHHHHHCCCC
Q ss_conf             113797999789899999999844789
Q gi|254781101|r  418 LPRSIHVHYSETMDGLFLFIQSSLVDG  444 (472)
Q Consensus       418 ~~~~~~~~~~~~~e~a~~~l~~~~~~g  444 (472)
                      .+...++...+ ...++..+...+..|
T Consensus       283 ~~~~~Ki~vls-va~llAeaI~rih~~  308 (327)
T PRK04554        283 AKNCDRIRQVT-IAGLLAETVRRISNE  308 (327)
T ss_pred             HCCCCCEEEEE-HHHHHHHHHHHHHCC
T ss_conf             62589809988-899999999998679


No 281
>KOG3022 consensus
Probab=47.52  E-value=8.8  Score=17.77  Aligned_cols=27  Identities=44%  Similarity=0.556  Sum_probs=22.2

Q ss_pred             CEEEEE---CCCCCCHHHHHHHHHHHHHHC
Q ss_conf             399983---036542012334677775201
Q gi|254781101|r  109 TIIAIT---GSVGKTTTKEMLTIALSSIKK  135 (472)
Q Consensus       109 ~vI~IT---GTnGKTTt~~~l~~iL~~~~~  135 (472)
                      .+|.|+   |-.|||||+.+++..|+..+.
T Consensus        48 ~iI~VlSGKGGVGKSTvt~nla~~La~~g~   77 (300)
T KOG3022          48 HIILVLSGKGGVGKSTVTVNLALALASEGK   77 (300)
T ss_pred             EEEEEEECCCCCCHHHHHHHHHHHHHCCCC
T ss_conf             589998678877616899999999861797


No 282
>PRK10584 putative ABC transporter ATP-binding protein YbbA; Provisional
Probab=47.45  E-value=8.9  Score=17.76  Aligned_cols=27  Identities=26%  Similarity=0.319  Sum_probs=21.1

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++||+|.|  ||||.-.++.-++..
T Consensus        34 ~~GE~v~ivG~sGsGKSTLl~~i~Gl~~p   62 (228)
T PRK10584         34 KRGETIALIGESGSGKSTLLAILAGLDDG   62 (228)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             99989999999985899999999669999


No 283
>PRK02812 ribose-phosphate pyrophosphokinase; Provisional
Probab=47.36  E-value=19  Score=15.61  Aligned_cols=61  Identities=16%  Similarity=0.208  Sum_probs=28.7

Q ss_pred             CCEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCC-CEEEEECC
Q ss_conf             31133100025653210125777874111026871388512354171058999999999986499-89999880
Q gi|254781101|r  337 GFFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNI-SHVWLSGF  409 (472)
Q Consensus       337 ~~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~-d~v~~~G~  409 (472)
                      ..+.++||== .+-.++..|.+.|+.   .+. ++|.+.-.=   |-.+..-    .+.+.+.++ +.|+..-.
T Consensus       231 r~~IIVDDiI-dTGgTl~~aa~~Lk~---~GA-~~V~a~aTH---gvfsg~A----~~rl~~s~ii~~vvvTdT  292 (331)
T PRK02812        231 KTAILVDDMI-DTGGTICEGARLLRK---EGA-KRVYACATH---AVFSPPA----IERLSASGLFEEVIVTNT  292 (331)
T ss_pred             CEEEEECCHH-HHHHHHHHHHHHHHH---CCC-CEEEEEEEC---CCCCHHH----HHHHHHCCCCCEEEEECC
T ss_conf             5189962144-227999999999985---799-878999989---6558779----999972897677998089


No 284
>PRK13650 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=47.05  E-value=9.4  Score=17.59  Aligned_cols=27  Identities=26%  Similarity=0.395  Sum_probs=21.7

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++||.|.|  ||||+..++.-++..
T Consensus        28 ~~GE~vaivG~nGsGKSTL~~~l~Gll~p   56 (276)
T PRK13650         28 KQGEWLSIIGHNGSGKSTTVRLIDGLLEA   56 (276)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             89989999999998799999999738898


No 285
>PRK05632 phosphate acetyltransferase; Reviewed
Probab=46.94  E-value=19  Score=15.56  Aligned_cols=95  Identities=16%  Similarity=0.150  Sum_probs=50.6

Q ss_pred             CHHHHHHHHCCEEECCCC--CCEEEEEEEECCCC-------CCCCEEEECCCCCCCHHHHHHHHHHCCC--EEEEECCCC
Q ss_conf             678899872799952688--71474677402223-------7898889716887476888999998698--899985521
Q gi|254781101|r    6 TFHDLLQAIQGHSIGIVP--QGFVNGISIDSRSI-------APQEAFFAIKGPHYDGHDFILHAVQKGA--GLVVVNTDM   74 (472)
Q Consensus         6 ~~~~l~~~~~g~~~~~~~--~~~i~~i~~dSr~v-------~~g~lFval~g~~~DGh~~i~~A~~~Ga--~~~i~~~~~   74 (472)
                      ++.|+++.++|+++++..  +..+.++.+-.+.+       ++|.|-| .+|.|.|=-.=.-.|..+|.  ++++..-..
T Consensus       219 rV~DIa~~L~A~vL~g~e~ldR~V~~vvV~Am~v~N~L~~L~~GsLVI-TPGDRsDIil~~~~a~~~~~~~agi~ltgg~  297 (702)
T PRK05632        219 RVIDIAKHLGATVINGGDLLTRRVRSVTVCARSIPNMLEHLKPGSLVV-TPGDRSDVILAACLAAMNGVPIAGLLLTGGY  297 (702)
T ss_pred             CHHHHHHHHCCEEECCCCHHCCEEEEEEEEEEECHHHHHCCCCCCEEE-CCCCHHHHHHHHHHHHCCCCCEEEEEECCCC
T ss_conf             299999983989965752102465049999700555561068995798-1685789999999984169980599961898


Q ss_pred             CC---------CCCCCCCCEEEEC-CHHHHHHHHHHH
Q ss_conf             24---------5544697289959-989999999999
Q gi|254781101|r   75 VA---------SIGSLSIPVFGVD-DVLGALNKLAVA  101 (472)
Q Consensus        75 ~~---------~~~~~~~~~i~v~-d~~~al~~la~~  101 (472)
                      .+         ......+|++.|+ |+.+....++..
T Consensus       298 ~~~~~i~~l~~~~~~~~lpil~~~~~t~~ta~~l~~~  334 (702)
T PRK05632        298 EPDPRIAKLCEGAFETGLPILSVDTNTYQTALRLQSF  334 (702)
T ss_pred             CCCHHHHHHHHHHCCCCCCEEEECCCHHHHHHHHHHC
T ss_conf             9878999999864238988799568769999999745


No 286
>COG1245 Predicted ATPase, RNase L inhibitor (RLI) homolog [General function prediction only]
Probab=46.78  E-value=2.5  Score=21.45  Aligned_cols=86  Identities=21%  Similarity=0.337  Sum_probs=43.1

Q ss_pred             CCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEECCCCCCCCCCCCCCEEEECCHHH--HHHHHHH----HHHHC--CCCC
Q ss_conf             78988897168874768889999986988999855212455446972899599899--9999999----99830--6993
Q gi|254781101|r   38 APQEAFFAIKGPHYDGHDFILHAVQKGAGLVVVNTDMVASIGSLSIPVFGVDDVLG--ALNKLAV----AARLR--SKAT  109 (472)
Q Consensus        38 ~~g~lFval~g~~~DGh~~i~~A~~~Ga~~~i~~~~~~~~~~~~~~~~i~v~d~~~--al~~la~----~~~~~--~~~~  109 (472)
                      +.|..=|.+...  +|-.+|.+.+=-||..++-..|..      .+.++-..+-++  ...+.+.    .|+-.  -+++
T Consensus        30 rtg~~~I~i~~~--~gkpvIsE~lCiGCGICvkkCPF~------AI~IvnLP~eLe~e~vHRYg~NgFkL~~LP~pr~G~  101 (591)
T COG1245          30 RTGKETIEIDED--TGKPVISEELCIGCGICVKKCPFD------AISIVNLPEELEEEVVHRYGVNGFKLYRLPTPRPGK  101 (591)
T ss_pred             CCCCEEEEECCC--CCCCEEEHHHHCCCHHHHCCCCCC------EEEEECCCHHHCCCCEEECCCCCEEEECCCCCCCCC
T ss_conf             578726995477--798436764423203431348866------178843834643443044057743784578788884


Q ss_pred             EEEEECCC--CCCHHHHHHHHHHH
Q ss_conf             99983036--54201233467777
Q gi|254781101|r  110 IIAITGSV--GKTTTKEMLTIALS  131 (472)
Q Consensus       110 vI~ITGTn--GKTTt~~~l~~iL~  131 (472)
                      |+||-|+|  ||||+...|+--|.
T Consensus       102 V~GilG~NGiGKsTalkILaGel~  125 (591)
T COG1245         102 VVGILGPNGIGKSTALKILAGELK  125 (591)
T ss_pred             EEEEECCCCCCHHHHHHHHHCCCC
T ss_conf             799876897657889999747607


No 287
>PRK06942 glutamate-1-semialdehyde 2,1-aminomutase; Validated
Probab=46.72  E-value=9.1  Score=17.68  Aligned_cols=51  Identities=16%  Similarity=0.240  Sum_probs=30.8

Q ss_pred             ECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCE
Q ss_conf             002565321012577787411102687138851235417105899999999998649989
Q gi|254781101|r  344 ESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISH  403 (472)
Q Consensus       344 DsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~  403 (472)
                      -+||.||.||.+++.+|+.+....      ++..+.++|   +.+-..+-+.+.+.++..
T Consensus       296 gTf~gnp~a~AAalatL~~~~~~~------~~~~~~~~g---~~L~~gl~~~~~~~g~~~  346 (425)
T PRK06942        296 GTLSGNPIAVAAGLKTLRLIQAPG------FYDALAAQT---RRLADGLAAEARAAGVPF  346 (425)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHCCC------HHHHHHHHH---HHHHHHHHHHHHHCCCCE
T ss_conf             899878799999999999984567------999999999---999999999999779988


No 288
>cd00267 ABC_ATPase ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.  The nucleotide-binding domain shows the highest similarity between all members of the family.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=46.50  E-value=11  Score=17.27  Aligned_cols=26  Identities=27%  Similarity=0.374  Sum_probs=19.4

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHH
Q ss_conf             699399983036--54201233467777
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALS  131 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~  131 (472)
                      .++.+++|+|.|  ||||+-.++.-++.
T Consensus        23 ~~Ge~~~i~G~nGaGKSTLl~~l~gl~~   50 (157)
T cd00267          23 KAGEIVALVGPNGSGKSTLLRAIAGLLK   50 (157)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCC
T ss_conf             7997999987889998999999958847


No 289
>COG4152 ABC-type uncharacterized transport system, ATPase component [General function prediction only]
Probab=45.99  E-value=11  Score=17.04  Aligned_cols=32  Identities=28%  Similarity=0.272  Sum_probs=25.7

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH-HHCCC
Q ss_conf             699399983036--542012334677775-20112
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS-IKKTY  137 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~-~~~~~  137 (472)
                      ..+.+.|.-|-|  |||||-.|+-.+|+. .|...
T Consensus        26 ~~G~i~GllG~NGAGKTTtfRmILglle~~~G~I~   60 (300)
T COG4152          26 PPGEIFGLLGPNGAGKTTTFRMILGLLEPTEGEIT   60 (300)
T ss_pred             CCCEEEEEECCCCCCCCCHHHHHHCCCCCCCCEEE
T ss_conf             48717876658889732339998645786676689


No 290
>PRK00615 glutamate-1-semialdehyde aminotransferase; Provisional
Probab=45.83  E-value=9.6  Score=17.53  Aligned_cols=53  Identities=15%  Similarity=0.298  Sum_probs=31.1

Q ss_pred             EEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             31000256532101257778741110268713885123541710589999999999864998
Q gi|254781101|r  341 LIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNIS  402 (472)
Q Consensus       341 iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d  402 (472)
                      +.--+||.||.||.+++.+|..+....      +...+.++|++   +-..+-+.+.+.++.
T Consensus       297 ~~~gTf~gnpla~AAa~AtL~~l~~~~------~~~~~~~~g~~---l~~gl~~~~~~~g~~  349 (433)
T PRK00615        297 FQAGTLSGNPLAMAAGKASIELCREEG------FYTQLSNLEQL---FLSPIEEMIRSQGFP  349 (433)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHCCC------HHHHHHHHHHH---HHHHHHHHHHHCCCC
T ss_conf             546887406999999999999983578------99999999999---999999999976998


No 291
>PRK11247 ssuB aliphatic sulfonates transport ATP-binding subunit; Provisional
Probab=45.71  E-value=10  Score=17.41  Aligned_cols=27  Identities=22%  Similarity=0.336  Sum_probs=21.0

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++|+.|-|  ||||+-.++.-++..
T Consensus        36 ~~GEiv~LiG~nGaGKSTLlr~i~Gl~~p   64 (257)
T PRK11247         36 PAGQFVAVVGRSGCGKSTLLRLLAGLETP   64 (257)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             79989999989988899999999658988


No 292
>pfam01935 DUF87 Domain of unknown function DUF87. The function of this prokaryotic domain is unknown. It contains several conserved aspartates and histidines that could be metal ligands.
Probab=45.58  E-value=9.7  Score=17.49  Aligned_cols=24  Identities=38%  Similarity=0.491  Sum_probs=15.4

Q ss_pred             CCCEEEEECCCCCCHHHH-HHHHHHH
Q ss_conf             993999830365420123-3467777
Q gi|254781101|r  107 KATIIAITGSVGKTTTKE-MLTIALS  131 (472)
Q Consensus       107 ~~~vI~ITGTnGKTTt~~-~l~~iL~  131 (472)
                      +.-|+|.||| |||.|.. ++..+++
T Consensus        25 H~aIlg~TGs-GKS~tv~vLl~~l~~   49 (218)
T pfam01935        25 HFAILGSTGS-GKSNTVAVLLEELLE   49 (218)
T ss_pred             HEEEECCCCC-CHHHHHHHHHHHHHH
T ss_conf             1478726999-769999999999985


No 293
>PRK13544 consensus
Probab=45.57  E-value=11  Score=17.27  Aligned_cols=27  Identities=19%  Similarity=0.316  Sum_probs=21.3

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++|+.|.|  ||||.-.+++-++..
T Consensus        25 ~~Gei~~l~G~NGsGKSTLl~~i~Gl~~p   53 (208)
T PRK13544         25 KQNSLTLVIGNNGSGKTSLLRLLAGLIPI   53 (208)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             29949999999999899999999588068


No 294
>TIGR02873 spore_ylxY probable sporulation protein, polysaccharide deacetylase family; InterPro: IPR014228   Members of this entry include YlxY, and are related to IPR014132 from INTERPRO, which represents a subset of the polysaccharide deacetylase family found in a species if, and only if, the species forms endospores e.g. Bacillus subtilis or Clostridium tetani. Proteins in this entry are likewise restricted to spore-formers, but are not universally found among endospore-forming species..
Probab=45.49  E-value=20  Score=15.42  Aligned_cols=40  Identities=23%  Similarity=0.247  Sum_probs=35.0

Q ss_pred             CCHHHHHHHHHHHCCCCCEEEE--ECCCHHHHHHHHHHHHHH
Q ss_conf             8989999999984478989999--771325489999999985
Q gi|254781101|r  428 ETMDGLFLFIQSSLVDGDVVVV--KSSNSCGFYRLINLLLEE  467 (472)
Q Consensus       428 ~~~e~a~~~l~~~~~~gdiVLi--KGSr~~~le~iv~~L~~~  467 (472)
                      ++.+..++.+.+-++||.+||-  ..|-..+||.++..|++|
T Consensus       216 P~p~vl~~Rvl~KiHpGA~vLMHPT~Ssa~gLe~lIt~ikek  257 (269)
T TIGR02873       216 PEPSVLVDRVLSKIHPGAMVLMHPTESSAEGLEELITKIKEK  257 (269)
T ss_pred             CCHHHHHHHHHHHCCCCCEEECCCCCHHHHHHHHHHHHHHHC
T ss_conf             874689888774068986576489976689999998999762


No 295
>cd03227 ABC_Class2 ABC-type Class 2 contains systems involved in cellular processes other than transport.  These families are characterised by the fact that the ABC subunit is made up of duplicated, fused ABC modules (ABC2).  No known transmembrane proteins or domains are associated with these proteins.
Probab=45.49  E-value=16  Score=16.02  Aligned_cols=21  Identities=29%  Similarity=0.488  Sum_probs=15.0

Q ss_pred             CCCEEEEECCC--CCCHHHHHHH
Q ss_conf             99399983036--5420123346
Q gi|254781101|r  107 KATIIAITGSV--GKTTTKEMLT  127 (472)
Q Consensus       107 ~~~vI~ITGTn--GKTTt~~~l~  127 (472)
                      +..++.|||.|  ||||.-..++
T Consensus        20 ~g~~~iItGpN~sGKSt~Lr~i~   42 (162)
T cd03227          20 EGSLTIITGPNGSGKSTILDAIG   42 (162)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHH
T ss_conf             98689998998775799999999


No 296
>PRK13538 cytochrome c biogenesis protein CcmA; Provisional
Probab=45.37  E-value=10  Score=17.37  Aligned_cols=26  Identities=23%  Similarity=0.336  Sum_probs=20.5

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHH
Q ss_conf             699399983036--54201233467777
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALS  131 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~  131 (472)
                      .++.++||.|.|  ||||.-.++.-++.
T Consensus        25 ~~Ge~~~l~G~NGaGKSTLl~~l~Gl~~   52 (204)
T PRK13538         25 NAGELVQIEGPNGAGKTSLLRILAGLAR   52 (204)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCC
T ss_conf             7998999999999859999999976888


No 297
>TIGR02475 CobW cobalamin biosynthesis protein CobW; InterPro: IPR012824   Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase . In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase .    There are at least two distinct cobalamin biosynthetic pathways in bacteria :  Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway ; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis ; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii shermanii.     Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) . There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans.   This entry represents CobW proteins, which are generally found proximal to the trimeric cobaltochelatase subunit CobN, an essential protein for vitamin B12 (cobalamin) biosynthesis . They contain a P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. CobW might be involved in cobalt reduction leading to cobalt(I) corrinoids.; GO: 0009236 cobalamin biosynthetic process.
Probab=45.17  E-value=12  Score=16.91  Aligned_cols=31  Identities=32%  Similarity=0.415  Sum_probs=22.8

Q ss_pred             CCCCEEEEECC--CCCCHHHHHHHHHHHH-HHCCCCC
Q ss_conf             69939998303--6542012334677775-2011222
Q gi|254781101|r  106 SKATIIAITGS--VGKTTTKEMLTIALSS-IKKTYAC  139 (472)
Q Consensus       106 ~~~~vI~ITGT--nGKTTt~~~l~~iL~~-~~~~~~t  139 (472)
                      .|.|+-=|||=  .||||   |++|+|+- .|+..+-
T Consensus         2 ~KiPvTvvTGFLGaGKTT---LiRhlL~NA~GkRiAv   35 (349)
T TIGR02475         2 AKIPVTVVTGFLGAGKTT---LIRHLLENAEGKRIAV   35 (349)
T ss_pred             CCCCEEEEECCCCCCHHH---HHHHHHHCCCCCEEEE
T ss_conf             732327873756761589---9999971747876999


No 298
>cd02019 NK Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate.
Probab=45.17  E-value=12  Score=16.92  Aligned_cols=21  Identities=52%  Similarity=0.664  Sum_probs=17.6

Q ss_pred             EEEEECC--CCCCHHHHHHHHHH
Q ss_conf             9998303--65420123346777
Q gi|254781101|r  110 IIAITGS--VGKTTTKEMLTIAL  130 (472)
Q Consensus       110 vI~ITGT--nGKTTt~~~l~~iL  130 (472)
                      +|+|+|.  .||||+..-+++.|
T Consensus         1 ~I~I~G~~gsGKsT~a~~l~~~l   23 (69)
T cd02019           1 IIAITGGSGSGKSTVAKKLAEQL   23 (69)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHH
T ss_conf             97883688887258999999995


No 299
>PRK10824 hypothetical protein; Provisional
Probab=45.13  E-value=19  Score=15.57  Aligned_cols=14  Identities=7%  Similarity=-0.050  Sum_probs=5.9

Q ss_pred             HHHHHHHHCCCCCC
Q ss_conf             03455431147664
Q gi|254781101|r  311 DTAIKALSVFHPKE  324 (472)
Q Consensus       311 ~~i~~~L~~~~~~~  324 (472)
                      ++++++|+.|..+|
T Consensus        56 ~~ir~~lk~~s~WP   69 (115)
T PRK10824         56 PDIRAELPKYANWP   69 (115)
T ss_pred             HHHHHHHHHHCCCC
T ss_conf             88999989981997


No 300
>cd03246 ABCC_Protease_Secretion This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain.  They export degradative enzymes by using a type I protein secretion system and  lack an N-terminal signal peptide, but contain a C-terminal secretion signal.  The Type I secretion apparatus is made up of three components, an ABC transporter, a membrane fusion protein (MFP), and an outer membrane protein (OMP).  For the HlyA transporter complex, HlyB (ABC transporter) and HlyD (MFP) reside in the inner membrane of E. coli.  The OMP component is TolC, which is thought to interact with the MFP to form a continuous channel across the periplasm from the cytoplasm to the exterior.  HlyB belongs to the family of ABC transporters, which are ubiquitous, ATP-dependent transmembrane pumps or channels.  The spectrum of transport substra
Probab=45.08  E-value=11  Score=17.16  Aligned_cols=26  Identities=27%  Similarity=0.356  Sum_probs=18.7

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHH
Q ss_conf             699399983036--54201233467777
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALS  131 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~  131 (472)
                      .++..+||+|.+  ||||...++.-++.
T Consensus        26 ~~G~~vaIvG~sGsGKSTLl~ll~gl~~   53 (173)
T cd03246          26 EPGESLAIIGPSGSGKSTLARLILGLLR   53 (173)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCC
T ss_conf             5999999999999809999999966666


No 301
>PRK13234 nifH nitrogenase reductase; Reviewed
Probab=45.00  E-value=16  Score=16.06  Aligned_cols=32  Identities=28%  Similarity=0.325  Sum_probs=25.1

Q ss_pred             CCCEEEEEC--CCCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             993999830--36542012334677775201122
Q gi|254781101|r  107 KATIIAITG--SVGKTTTKEMLTIALSSIKKTYA  138 (472)
Q Consensus       107 ~~~vI~ITG--TnGKTTt~~~l~~iL~~~~~~~~  138 (472)
                      +.+-|||=|  --||+||+.-++..|...|+.+-
T Consensus         3 ~mr~IAiYGKGGIGKSTtssNlsAAlA~~G~rVl   36 (293)
T PRK13234          3 ALRQIAFYGKGGIGKSTTSQNTLAALVEMGQKIL   36 (293)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHCCCEEE
T ss_conf             7757999779844587789999999997799699


No 302
>cd03269 ABC_putative_ATPase This subfamily is involved in drug resistance, nodulation, lipid transport, and bacteriocin and lantibiotic immunity.  In eubacteria and archaea, the typical organization consists of one ABC and one or two IMs.  Eukaryote systems of the ABCA subfamily display ABC domains strongly similar to this family.  ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules.  The nucleotide binding domain shows the highest similarity between all members of the family.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=44.98  E-value=12  Score=16.91  Aligned_cols=27  Identities=33%  Similarity=0.406  Sum_probs=22.2

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++|+-|-|  ||||+-.++.-++..
T Consensus        24 ~~Gei~gllG~NGaGKTTll~~i~Gl~~p   52 (210)
T cd03269          24 EKGEIFGLLGPNGAGKTTTIRMILGIILP   52 (210)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             79959999989998499999999600266


No 303
>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis.  The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd quinol oxidase and for periplasmic c-type cytochromes.  CydCD were proposed to determine a heterooligomeric complex important for heme export into the periplasm or to be involved in the maintenance of the proper redox state of the periplasmic space.  In Bacillus subtilius, the absence of CydCD does not affect the presence of halo-cytochrome c in the membrane and this observation suggests that CydCD proteins are not involved in the export of heme in this organism.
Probab=44.98  E-value=12  Score=16.79  Aligned_cols=26  Identities=35%  Similarity=0.436  Sum_probs=19.7

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHH
Q ss_conf             699399983036--54201233467777
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALS  131 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~  131 (472)
                      .++..+||.|.|  ||||.-.++..++.
T Consensus        26 ~~Ge~~aivG~sGsGKSTLl~~l~G~~~   53 (178)
T cd03247          26 KQGEKIALLGRSGSGKSTLLQLLTGDLK   53 (178)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHHCCC
T ss_conf             6999999999998759999999986176


No 304
>cd03236 ABC_RNaseL_inhibitor_domain1 The ATPase domain 1 of RNase L inhibitor.  The ABC ATPase, RNase L inhibitor (RLI), is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids.  RLI s are not transport proteins and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family.  Structurally, RLIs have an N-terminal Fe-S domain and two nucleotide binding domains which are arranged to form two composite active sites in their interface cleft.  RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity more than 48%.  The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.
Probab=44.83  E-value=10  Score=17.34  Aligned_cols=26  Identities=23%  Similarity=0.461  Sum_probs=20.2

Q ss_pred             CCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             99399983036--542012334677775
Q gi|254781101|r  107 KATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       107 ~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      ++.++||.|.|  ||||.-.+|+-++..
T Consensus        25 ~GEi~gLiGpNGaGKSTLlk~i~Gll~P   52 (255)
T cd03236          25 EGQVLGLVGPNGIGKSTALKILAGKLKP   52 (255)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             9809999899997099999999679868


No 305
>PRK13546 teichoic acids export protein ATP-binding subunit; Provisional
Probab=44.66  E-value=11  Score=17.19  Aligned_cols=27  Identities=26%  Similarity=0.417  Sum_probs=21.4

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++|+-|.|  ||||+-.+++-++..
T Consensus        48 ~~GEivgllG~NGaGKSTLlk~I~Gl~~P   76 (264)
T PRK13546         48 YEGDVIGLVGINGSGKSTLSNIIGGSLSP   76 (264)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             59989999989986199999999679888


No 306
>PRK13647 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=44.63  E-value=11  Score=17.13  Aligned_cols=26  Identities=27%  Similarity=0.230  Sum_probs=20.4

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHH
Q ss_conf             699399983036--54201233467777
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALS  131 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~  131 (472)
                      .++.++||.|-|  ||||+-.++.-++.
T Consensus        29 ~~Ge~~aiiG~NGsGKSTLl~~l~Gl~~   56 (273)
T PRK13647         29 PEGSKTAILGPNGAGKSTLLLHLNGIYT   56 (273)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCC
T ss_conf             8998999999999759999999966988


No 307
>cd00883 beta_CA_cladeA Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. CAs are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionarily distinct families of CAs (the alpha-, beta-, and gamma-CAs) which show no significant sequence identity or structural similarity.  Within the beta-CA family there are four evolutionarily distinct clades (A through D). The beta-CAs are multimeric enzymes (forming dimers,tetramers,hexamers and octamers) which are present in higher plants, algae, fungi, archaea and prokaryotes.
Probab=44.58  E-value=21  Score=15.33  Aligned_cols=26  Identities=35%  Similarity=0.487  Sum_probs=17.2

Q ss_pred             CCCCCCEEEEEEEECCC-------CCCCCEEEEC
Q ss_conf             26887147467740222-------3789888971
Q gi|254781101|r   20 GIVPQGFVNGISIDSRS-------IAPQEAFFAI   46 (472)
Q Consensus        20 ~~~~~~~i~~i~~dSr~-------v~~g~lFval   46 (472)
                      +..|...+=+ |.|||-       ..|||+|+.-
T Consensus        22 gQ~P~a~vi~-CsDSRv~pe~ifd~~~GdlFvvR   54 (182)
T cd00883          22 GQTPEYLWIG-CSDSRVPENTILGLLPGEVFVHR   54 (182)
T ss_pred             CCCCCEEEEE-ECCCCCCHHHHCCCCCCCEEEEE
T ss_conf             8999669998-64789899998099997679997


No 308
>PRK00232 pdxA 4-hydroxythreonine-4-phosphate dehydrogenase; Reviewed
Probab=44.57  E-value=21  Score=15.33  Aligned_cols=17  Identities=18%  Similarity=0.307  Sum_probs=10.0

Q ss_pred             CCCCCHHHHHHHHHHHH
Q ss_conf             65321012577787411
Q gi|254781101|r  348 ANPASMKAAISVLSQIS  364 (472)
Q Consensus       348 AnP~S~~aal~~l~~~~  364 (472)
                      |||.||.+|++.-..+.
T Consensus       313 A~~~s~~~Ai~~A~~~a  329 (334)
T PRK00232        313 ADVGSFITALNLAIRMA  329 (334)
T ss_pred             CCHHHHHHHHHHHHHHH
T ss_conf             99699999999999999


No 309
>KOG3220 consensus
Probab=44.51  E-value=14  Score=16.45  Aligned_cols=22  Identities=27%  Similarity=0.561  Sum_probs=15.7

Q ss_pred             CEEEEECC--CCCCHHHHHHHHHHHHHH
Q ss_conf             39998303--654201233467777520
Q gi|254781101|r  109 TIIAITGS--VGKTTTKEMLTIALSSIK  134 (472)
Q Consensus       109 ~vI~ITGT--nGKTTt~~~l~~iL~~~~  134 (472)
                      .+||+||+  .||||+    .+.|++.|
T Consensus         2 ~iVGLTGgiatGKStV----s~~f~~~G   25 (225)
T KOG3220           2 LIVGLTGGIATGKSTV----SQVFKALG   25 (225)
T ss_pred             EEEEEECCCCCCHHHH----HHHHHHCC
T ss_conf             6999405656673799----99999749


No 310
>PRK13652 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=44.48  E-value=11  Score=17.15  Aligned_cols=27  Identities=26%  Similarity=0.308  Sum_probs=21.8

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++|+.|-|  ||||+-.++.-++..
T Consensus        28 ~~Ge~~aliG~NGaGKSTLl~~i~Gll~p   56 (277)
T PRK13652         28 GRKQRIAVIGPNGAGKSTLFKHFNGILKP   56 (277)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             89989999999994799999999669999


No 311
>TIGR01007 eps_fam capsular exopolysaccharide family; InterPro: IPR005702    This family describes the capsular exopolysaccharide proteins in bacteria. The exopolysaccharide gene cluster consists of several genes which encode a number of proteins which regulate the exoploysaccharide biosynthesis (EPS). At least 13 genes EpsA to EpsM in streptococcus species seem to direct the EPS proteins and share high homology. ; GO: 0030234 enzyme regulator activity, 0045227 capsule polysaccharide biosynthetic process.
Probab=44.23  E-value=16  Score=16.10  Aligned_cols=29  Identities=21%  Similarity=0.350  Sum_probs=24.5

Q ss_pred             CCCEEEEECC---CCCCHHHHHHHHHHHHHHC
Q ss_conf             9939998303---6542012334677775201
Q gi|254781101|r  107 KATIIAITGS---VGKTTTKEMLTIALSSIKK  135 (472)
Q Consensus       107 ~~~vI~ITGT---nGKTTt~~~l~~iL~~~~~  135 (472)
                      ..|+++||=.   -|||||..=+|.-+.+.|.
T Consensus        18 e~K~l~itS~~~~eGKsT~S~NiA~~fAqaGy   49 (207)
T TIGR01007        18 EIKVLLITSVKAGEGKSTTSANIAVSFAQAGY   49 (207)
T ss_pred             CEEEEEEEECCCCCCCEEEEHHHHHHHHHCCC
T ss_conf             70589984110588862410788999985685


No 312
>cd03248 ABCC_TAP TAP, the Transporter Associated with Antigen Processing; TAP is essential for peptide delivery from the cytosol into the lumen of the endoplasmic reticulum (ER), where these peptides are loaded on major histocompatibility complex (MHC) I molecules.  Loaded MHC I leave the ER and display their antigenic cargo on the cell surface to cytotoxic T cells.  Subsequently, virus-infected or malignantly transformed cells can be eliminated.  TAP belongs to the large family of ATP-binding cassette (ABC) transporters, which translocate a vast variety of solutes across membranes.
Probab=43.91  E-value=12  Score=16.88  Aligned_cols=26  Identities=23%  Similarity=0.350  Sum_probs=20.6

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHH
Q ss_conf             699399983036--54201233467777
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALS  131 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~  131 (472)
                      .++..+||.|.+  ||||...++..++.
T Consensus        38 ~~Ge~vaIvG~sGsGKSTL~~ll~gl~~   65 (226)
T cd03248          38 HPGEVTALVGPSGSGKSTVVALLENFYQ   65 (226)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCC
T ss_conf             2999999999999849999999964546


No 313
>KOG3354 consensus
Probab=43.77  E-value=11  Score=17.13  Aligned_cols=24  Identities=29%  Similarity=0.443  Sum_probs=16.2

Q ss_pred             EEEEECCCCCCHHHHHHHHHHHHHH
Q ss_conf             9998303654201233467777520
Q gi|254781101|r  110 IIAITGSVGKTTTKEMLTIALSSIK  134 (472)
Q Consensus       110 vI~ITGTnGKTTt~~~l~~iL~~~~  134 (472)
                      |+||.|| ||||..-++.+-|+-.+
T Consensus        17 vmGvsGs-GKSTigk~L~~~l~~~F   40 (191)
T KOG3354          17 VMGVSGS-GKSTIGKALSEELGLKF   40 (191)
T ss_pred             EEECCCC-CHHHHHHHHHHHHCCCC
T ss_conf             9835887-74459999999858862


No 314
>cd03222 ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibitor (RLI) is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids.  RLI's are not transport proteins, and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family.  Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains, which are arranged to form two composite active sites in their interface cleft.  RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity more than 48%.  The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.
Probab=43.77  E-value=11  Score=17.08  Aligned_cols=27  Identities=33%  Similarity=0.470  Sum_probs=19.4

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++-++||.|-|  ||||+-.|++-++..
T Consensus        23 ~~GEiv~ilGpNGaGKSTllk~i~G~l~p   51 (177)
T cd03222          23 KEGEVIGIVGPNGTGKTTAVKILAGQLIP   51 (177)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             89989999899999999999999688678


No 315
>KOG1324 consensus
Probab=43.75  E-value=21  Score=15.25  Aligned_cols=76  Identities=16%  Similarity=0.192  Sum_probs=36.8

Q ss_pred             HCCCCCCCCCCCCEECCCCCCEEEEEE-CCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHH
Q ss_conf             114766443310100036531133100-0256532101257778741110268713885123541710589999999999
Q gi|254781101|r  318 SVFHPKEGRGKRYRCALNQGFFTLIDE-SYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVL  396 (472)
Q Consensus       318 ~~~~~~~GR~~~~~~~~~~~~~~iIDD-sYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~  396 (472)
                      .++.|++||+...=.......+ ..++ .|  --.|+.+||+.|..-+....--+|.|+|+     ..   .+++   .+
T Consensus        61 ~k~RPL~gRiNiVLSR~~~~~~-~~t~~~~--~~~slesAl~lL~~pp~~~~ve~vfvIGG-----~~---vy~~---al  126 (190)
T KOG1324          61 EKFRPLPGRINVVLSRSLKEDF-APTENVF--LSSSLESALDLLEEPPSSNSVEMVFVIGG-----SE---VYSE---AL  126 (190)
T ss_pred             CCCCCCCCCEEEEEECCCCCCC-CCCCCEE--EECCHHHHHHHHCCCCCCCCEEEEEEECC-----HH---HHHH---HH
T ss_conf             3458899855799944667566-7756789--83139999985138853352147999868-----89---9999---87


Q ss_pred             HHCCCCEEEEE
Q ss_conf             86499899998
Q gi|254781101|r  397 SLYNISHVWLS  407 (472)
Q Consensus       397 ~~~~~d~v~~~  407 (472)
                      ....+|.+++.
T Consensus       127 ~~p~~~~i~~T  137 (190)
T KOG1324         127 NSPRCDAIHIT  137 (190)
T ss_pred             CCCCCCEEEEE
T ss_conf             38775528988


No 316
>PRK13644 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=43.71  E-value=12  Score=16.86  Aligned_cols=27  Identities=33%  Similarity=0.327  Sum_probs=21.5

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++||.|-|  ||||...++.-++..
T Consensus        26 ~~Ge~vaiiG~nGsGKSTL~~~l~Gll~P   54 (274)
T PRK13644         26 KKGEYIGIIGKNGSGKSTLALHLNGLLRP   54 (274)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             48999999999998099999999706858


No 317
>cd01672 TMPK Thymidine monophosphate kinase (TMPK), also known as thymidylate kinase, catalyzes the phosphorylation of thymidine monophosphate (TMP) to thymidine diphosphate (TDP) utilizing ATP as its preferred phophoryl donor. TMPK represents the rate-limiting step in either de novo or salvage biosynthesis of thymidine triphosphate (TTP).
Probab=43.55  E-value=17  Score=15.89  Aligned_cols=26  Identities=35%  Similarity=0.382  Sum_probs=21.1

Q ss_pred             EEEEECC--CCCCHHHHHHHHHHHHHHC
Q ss_conf             9998303--6542012334677775201
Q gi|254781101|r  110 IIAITGS--VGKTTTKEMLTIALSSIKK  135 (472)
Q Consensus       110 vI~ITGT--nGKTTt~~~l~~iL~~~~~  135 (472)
                      .|+|-|-  .||||...+|+.-|...|.
T Consensus         2 ~IviEG~dGsGKsT~~~~L~~~L~~~g~   29 (200)
T cd01672           2 FIVFEGIDGAGKTTLIELLAERLEARGY   29 (200)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCC
T ss_conf             8999899899999999999999997799


No 318
>PRK11831 putative ABC transporter ATP-binding protein YrbF; Provisional
Probab=43.47  E-value=11  Score=17.09  Aligned_cols=27  Identities=30%  Similarity=0.431  Sum_probs=21.2

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++||.|-|  ||||+-.++.-++..
T Consensus        32 ~~Gei~~iiGpnGsGKSTLlk~i~Gl~~p   60 (269)
T PRK11831         32 PRGKITAIMGPSGIGKTTLLRLIGGQIAP   60 (269)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             79989999939997599999999679888


No 319
>COG1618 Predicted nucleotide kinase [Nucleotide transport and metabolism]
Probab=43.36  E-value=16  Score=16.10  Aligned_cols=26  Identities=38%  Similarity=0.309  Sum_probs=21.3

Q ss_pred             CEEEEECC--CCCCHHHHHHHHHHHHHH
Q ss_conf             39998303--654201233467777520
Q gi|254781101|r  109 TIIAITGS--VGKTTTKEMLTIALSSIK  134 (472)
Q Consensus       109 ~vI~ITGT--nGKTTt~~~l~~iL~~~~  134 (472)
                      --|+|||.  .||||...-++..|+..|
T Consensus         6 mki~ITG~PGvGKtTl~~ki~e~L~~~g   33 (179)
T COG1618           6 MKIFITGRPGVGKTTLVLKIAEKLREKG   33 (179)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCC
T ss_conf             5999867998458999999999998559


No 320
>cd03240 ABC_Rad50 The catalytic domains of Rad50 are similar to the ATP-binding cassette of ABC transporters, but are not associated with membrane-spanning domains.  The conserved ATP-binding motifs common to Rad50 and the ABC transporter family include the Walker A and Walker B motifs, the Q loop, a histidine residue in the switch region, a D-loop, and a conserved LSGG sequence.  This conserved sequence, LSGG, is the most specific and characteristic motif of this family and is thus known as the ABC signature sequence.
Probab=43.20  E-value=13  Score=16.56  Aligned_cols=22  Identities=36%  Similarity=0.362  Sum_probs=16.4

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHH
Q ss_conf             699399983036--5420123346
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLT  127 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~  127 (472)
                      +...+++|.|-|  ||||.-.++.
T Consensus        20 f~~~itaivG~NGaGKSTLl~~i~   43 (204)
T cd03240          20 FFSPLTLIVGQNGAGKTTIIEALK   43 (204)
T ss_pred             EECCEEEEECCCCCCHHHHHHHHH
T ss_conf             508889999899999999999986


No 321
>PRK00553 ribose-phosphate pyrophosphokinase; Provisional
Probab=43.13  E-value=22  Score=15.18  Aligned_cols=111  Identities=14%  Similarity=0.193  Sum_probs=51.3

Q ss_pred             CEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHH
Q ss_conf             11331000256532101257778741110268713885123541710589999999999864998999988038989985
Q gi|254781101|r  338 FFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFHVLALKDA  417 (472)
Q Consensus       338 ~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~~~~~~~~  417 (472)
                      .+.++||== .+-.++..|.+.|++   . +-++|.+...=   |-.+..--+.+.+...+..+|.|+..-.-...   .
T Consensus       228 ~vIIVDDiI-dTGgTl~~aa~~Lk~---~-GA~~V~a~aTH---gvfsg~A~eri~~~~~~~~i~~vvvTnTip~~---~  296 (340)
T PRK00553        228 NCLIVDDMI-DTGGTVIAAAKLLKK---Q-KAKKVCVMATH---GLFNKNAIQLFDEAFKKKLIDKLFVSNSIPQT---K  296 (340)
T ss_pred             EEEEECCHH-HHHHHHHHHHHHHHH---C-CCCEEEEEEEC---CCCCHHHHHHHHHCCCCCCCCEEEECCCCCCH---H
T ss_conf             489525244-312569999999998---7-99879999979---51485799999852025776589985788772---5


Q ss_pred             CCCCCCEEEECCHHHHHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHH
Q ss_conf             1137979997898999999998447898999977132548999999998
Q gi|254781101|r  418 LPRSIHVHYSETMDGLFLFIQSSLVDGDVVVVKSSNSCGFYRLINLLLE  466 (472)
Q Consensus       418 ~~~~~~~~~~~~~e~a~~~l~~~~~~gdiVLiKGSr~~~le~iv~~L~~  466 (472)
                      .....++... +...++..+...+..|.      |=+.=|.+..+-.+|
T Consensus       297 ~~~~~kl~vl-sva~llaeaI~ri~~~~------SvS~LF~~~~~~~~~  338 (340)
T PRK00553        297 FEKKPQFKVV-DLAHLYEEVLLCYANGG------SISAIYTRHIEWIKK  338 (340)
T ss_pred             HHCCCCCEEE-EHHHHHHHHHHHHHCCC------CHHHHHHHHHHHHHH
T ss_conf             6559982998-77999999999986799------689987740998862


No 322
>pfam07693 KAP_NTPase KAP family P-loop domain. The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals. Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side.
Probab=43.06  E-value=22  Score=15.18  Aligned_cols=38  Identities=26%  Similarity=0.282  Sum_probs=27.6

Q ss_pred             HHHHHHHHHCC--CCCEEEEECC--CCCCHHHHHHHHHHHHH
Q ss_conf             99999998306--9939998303--65420123346777752
Q gi|254781101|r   96 NKLAVAARLRS--KATIIAITGS--VGKTTTKEMLTIALSSI  133 (472)
Q Consensus        96 ~~la~~~~~~~--~~~vI~ITGT--nGKTTt~~~l~~iL~~~  133 (472)
                      ..||.......  .+-+|||.|.  .||||.-.|+.+-|++.
T Consensus         6 ~~la~~i~~~~~~~~~vIgl~G~WGsGKTs~l~~~~~~L~~~   47 (301)
T pfam07693         6 ENLAKLLVEPSLAPGFVIGLYGAWGSGKTSFLNLLEDELKEF   47 (301)
T ss_pred             HHHHHHHHCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHC
T ss_conf             999999957778999799998989999999999999998613


No 323
>PRK13637 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=43.02  E-value=12  Score=16.95  Aligned_cols=27  Identities=26%  Similarity=0.375  Sum_probs=21.7

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++||.|-|  ||||+..++.-++..
T Consensus        31 ~~GE~v~iiG~nGsGKSTLl~~l~GLl~p   59 (287)
T PRK13637         31 EDGEFVALIGHTGSGKSTLIQHLNGLLKP   59 (287)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             79989999999993999999999739988


No 324
>PRK13632 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=42.91  E-value=13  Score=16.76  Aligned_cols=27  Identities=33%  Similarity=0.452  Sum_probs=22.0

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++||.|-|  ||||...++.-++..
T Consensus        34 ~~Ge~vaivG~nGsGKSTLlk~l~Gll~p   62 (273)
T PRK13632         34 NEGEYVAILGHNGSGKSTISKILTGLLKP   62 (273)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             49989999999998699999999738778


No 325
>cd03257 ABC_NikE_OppD_transporters The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE).  The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane components (NikB and NikC), and two ATPase (NikD and NikE).  The NikABCDE transporter is synthesized under anaerobic conditions to meet the increased demand for nickel resulting from hydrogenase synthesis.  The molecular mechanism of nickel uptake in many bacteria and most archaea is not known.  Many other members of this ABC family are also involved in the uptake of dipeptides and oligopeptides.  The oligopeptide transport system (Opp) is a five-component ABC transport composed of a membrane-anchored substrate binding proteins (SRP), OppA, two transmembrane proteins, OppB and OppC, and two ATP-binding domains, OppD and OppF.
Probab=42.90  E-value=12  Score=16.90  Aligned_cols=26  Identities=23%  Similarity=0.344  Sum_probs=21.3

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHH
Q ss_conf             699399983036--54201233467777
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALS  131 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~  131 (472)
                      .++.++||.|.|  ||||+-.++.-++.
T Consensus        29 ~~Ge~~~iiG~sGsGKSTLl~~i~Gl~~   56 (228)
T cd03257          29 KKGETLGLVGESGSGKSTLARAILGLLK   56 (228)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCC
T ss_conf             6998999999999869999999972898


No 326
>cd04261 AAK_AKii-LysC-BS AAK_AKii-LysC-BS: Amino Acid Kinase Superfamily (AAK), AKii; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis 168, and the lysine plus threonine-sensitive aspartokinase of Corynebacterium glutamicum, and related sequences. In B. subtilis 168, the regulation of the diaminopimelate (Dap)-lysine biosynthetic pathway involves dual control by Dap and lysine, effected through separate Dap- and lysine-sensitive aspartokinase isoenzymes. The B. subtilis 168 AKII is induced by methionine, and repressed and inhibited by lysine. Although Corynebacterium glutamicum is known to contain a single aspartokinase isoenzyme type, both the succinylase and dehydrogenase variant pathways of DAP-lysine synthesis operate simultaneously in this organism. In this organism and other various Gram-positive bacteria, the DAP-lysine pathway is feedback regulated by the concerted action of lysine and 
Probab=42.82  E-value=18  Score=15.78  Aligned_cols=16  Identities=19%  Similarity=0.451  Sum_probs=9.9

Q ss_pred             CCCEEEEECCCCCCHH
Q ss_conf             9939998303654201
Q gi|254781101|r  107 KATIIAITGSVGKTTT  122 (472)
Q Consensus       107 ~~~vI~ITGTnGKTTt  122 (472)
                      +.+++-|.+--||+|-
T Consensus        31 ~~~vvVVvSA~gg~Td   46 (239)
T cd04261          31 GNQVVVVVSAMGGTTD   46 (239)
T ss_pred             CCCEEEEECCCCCCHH
T ss_conf             9928999779875368


No 327
>pfam07015 VirC1 VirC1 protein. This family consists of several bacterial VirC1 proteins. In Agrobacterium tumefaciens, a cis-active 24-base-pair sequence adjacent to the right border of the T-DNA, called overdrive, stimulates tumour formation by increasing the level of T-DNA processing. It is thought that the virC operon which enhances T-DNA processing probably does so because the VirC1 protein interacts with overdrive. It has now been shown that the virC1 gene product binds to overdrive but not to the right border of T-DNA.
Probab=42.73  E-value=11  Score=17.14  Aligned_cols=29  Identities=38%  Similarity=0.360  Sum_probs=21.9

Q ss_pred             CEEEEE---CCCCCCHHHHHHHHHHHHHHCCC
Q ss_conf             399983---03654201233467777520112
Q gi|254781101|r  109 TIIAIT---GSVGKTTTKEMLTIALSSIKKTY  137 (472)
Q Consensus       109 ~vI~IT---GTnGKTTt~~~l~~iL~~~~~~~  137 (472)
                      +||.+.   |-.||||+.-.|+.-|...|..+
T Consensus         2 ~vi~~~~~KGG~GKtT~a~~la~~~~~~g~~V   33 (231)
T pfam07015         2 QLITFCSFKGGAGKTTALMGLCSALASDGKRV   33 (231)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCEE
T ss_conf             37999617998659999999999999689959


No 328
>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos).  The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis.  Pentoses include xylose, arabinose, and ribose.  Important hexoses include glucose, galactose, and fructose.  In members of the Carb_monos family, the single hydrophobic gene product forms a homodimer while the ABC protein represents a fusion of two nucleotide-binding domains.  However, it is assumed that two copies of the ABC domains are present in the assembled transporter.
Probab=42.58  E-value=12  Score=16.86  Aligned_cols=26  Identities=23%  Similarity=0.348  Sum_probs=19.1

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHH
Q ss_conf             699399983036--54201233467777
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALS  131 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~  131 (472)
                      .++.++|+.|.|  ||||+-.++.-++.
T Consensus        24 ~~Gei~~lvG~nGaGKSTl~~~i~Gl~~   51 (163)
T cd03216          24 RRGEVHALLGENGAGKSTLMKILSGLYK   51 (163)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCC
T ss_conf             7998999998899899999999957768


No 329
>PRK02270 consensus
Probab=42.45  E-value=22  Score=15.12  Aligned_cols=92  Identities=14%  Similarity=0.141  Sum_probs=41.4

Q ss_pred             CEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHH
Q ss_conf             11331000256532101257778741110268713885123541710589999999999864998999988038989985
Q gi|254781101|r  338 FFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFHVLALKDA  417 (472)
Q Consensus       338 ~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~~~~~~~~  417 (472)
                      .+.++||== .+-.++..|.+.|+.   .+. ++|.+.-.=   |-.+..    ..+.+....++.|+..-.-.  ..+.
T Consensus       216 ~~IIVDDiI-dTGgTl~~aa~~Lk~---~GA-~~V~~~aTH---gvfs~~----a~~~~~~s~i~~ivvTnTip--~~~~  281 (327)
T PRK02270        216 NAVIIDDII-DTGGTIINAAEVLKE---KGA-KKIVLAATH---GLFSKG----FEIFEENPNIDKVIITNSID--NKEL  281 (327)
T ss_pred             EEEEECCCC-CCHHHHHHHHHHHHH---CCC-CEEEEEEEC---HHCCCH----HHHHHHCCCCCEEEEECCCC--CCHH
T ss_conf             489976700-054779999999998---799-879999977---443804----99996589987899938866--8433


Q ss_pred             CCCCCCEEEECCHHHHHHHHHHHCCCC
Q ss_conf             113797999789899999999844789
Q gi|254781101|r  418 LPRSIHVHYSETMDGLFLFIQSSLVDG  444 (472)
Q Consensus       418 ~~~~~~~~~~~~~e~a~~~l~~~~~~g  444 (472)
                      .+...++... +...++..+...+..|
T Consensus       282 ~~~~~kl~vl-sva~llaeaI~ri~~~  307 (327)
T PRK02270        282 AKKFKKLLIV-SLAEFLSKVILACIFS  307 (327)
T ss_pred             HHCCCCEEEE-EHHHHHHHHHHHHHCC
T ss_conf             5028982998-8799999999998679


No 330
>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export.  They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins.  The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities.  The MRP-like family, simlar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD).  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=42.42  E-value=13  Score=16.75  Aligned_cols=26  Identities=27%  Similarity=0.351  Sum_probs=19.4

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHH
Q ss_conf             699399983036--54201233467777
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALS  131 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~  131 (472)
                      .++.++||.|.+  ||||.-.++.-+++
T Consensus        26 ~~Ge~i~ivG~sGsGKSTLl~ll~gl~~   53 (171)
T cd03228          26 KPGEKVAIVGPSGSGKSTLLKLLLRLYD   53 (171)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCC
T ss_conf             5998999999999839999999976775


No 331
>PRK06131 dihydroxy-acid dehydratase; Validated
Probab=42.40  E-value=22  Score=15.11  Aligned_cols=147  Identities=15%  Similarity=0.110  Sum_probs=70.7

Q ss_pred             CCCHHHHHHHHCCCC--HHHHHHHHCCCCCCCCCCCCEECCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEE
Q ss_conf             221035676510121--034554311476644331010003653113310002565321012577787411102687138
Q gi|254781101|r  296 MLMTLGIVSILTADV--DTAIKALSVFHPKEGRGKRYRCALNQGFFTLIDESYNANPASMKAAISVLSQISPHGEGRRIA  373 (472)
Q Consensus       296 alaAia~~~~lGi~~--~~i~~~L~~~~~~~GR~~~~~~~~~~~~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~  373 (472)
                      ++.-+|++...|+++  +++ +.++.-.  |   ....+.  .+|-..+.|-|+|  ..+.+.++.|..+- +  +-...
T Consensus       279 vLHL~AIA~eaGi~l~l~df-d~is~~~--P---~l~~l~--P~G~~~~~d~~~a--GGvp~vmk~L~~lL-~--~d~~T  345 (577)
T PRK06131        279 VIHLIAIAGRAGVELDLDDW-DRIGRDV--P---VLVNLQ--PSGEYLMEDFYYA--GGLPAVLRELGELL-H--LDALT  345 (577)
T ss_pred             HHHHHHHHHHHCCCCCHHHH-HHHHCCC--C---EEEEEC--CCCCCHHHHHHHC--CCHHHHHHHHHHHC-C--CCCCC
T ss_conf             88899999973899999999-9870678--7---787733--6764029888873--79999999999750-6--88875


Q ss_pred             EECC-HHHCCCCHHHHHHHHHHHHH----HCCCCEEEEECCCHHH---HH------HHCCCCCCEEEECCHHHHHHHHHH
Q ss_conf             8512-35417105899999999998----6499899998803898---99------851137979997898999999998
Q gi|254781101|r  374 VLGD-MCEMGELSQSFHIDLAEVLS----LYNISHVWLSGFHVLA---LK------DALPRSIHVHYSETMDGLFLFIQS  439 (472)
Q Consensus       374 VlG~-m~ELG~~~~~~h~~i~~~~~----~~~~d~v~~~G~~~~~---~~------~~~~~~~~~~~~~~~e~a~~~l~~  439 (472)
                      |-|. +.|.=+..+..-+++++-+.    ..+ -..++.|.-+..   ++      +...-..++..|++.|++.+.+..
T Consensus       346 VtG~tl~e~l~~~~~~~~~VIr~~~~P~~~~G-gl~iL~GNLAP~GaVvK~sav~~~~~~~~G~A~VF~~ee~~~~ai~~  424 (577)
T PRK06131        346 VNGKTLGENLAGAEIYNDDVIRPLDNPLKPEG-GIAVLRGNLAPDGAVIKPSAASPELLKHEGRAVVFEDYEDYKARIDD  424 (577)
T ss_pred             CCCCCHHHHHHCCCCCCCCEECCCCCCCCCCC-CEEEECCCCCCCCEEEEECCCCCCCEEEEEEEEEECCHHHHHHHHHC
T ss_conf             27986999970687789774666565656778-88982266578852675201473112787425775799999999848


Q ss_pred             H---CCCCCEEEE-----ECCCHHH
Q ss_conf             4---478989999-----7713254
Q gi|254781101|r  440 S---LVDGDVVVV-----KSSNSCG  456 (472)
Q Consensus       440 ~---~~~gdiVLi-----KGSr~~~  456 (472)
                      .   .++||+|.+     ||..||.
T Consensus       425 ~~l~i~~gdVvViR~eGPkGgPGMp  449 (577)
T PRK06131        425 PDLDVDEDSVLVLRNAGPKGYPGMP  449 (577)
T ss_pred             CCCCCCCCEEEEEECCCCCCCCCCC
T ss_conf             7767877259999566898999873


No 332
>PRK13651 cobalt transporter ATP-binding subunit; Provisional
Probab=42.27  E-value=13  Score=16.72  Aligned_cols=27  Identities=41%  Similarity=0.470  Sum_probs=21.5

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++||.|.|  ||||...++.-+|..
T Consensus        31 ~~GE~v~IiG~nGsGKSTL~k~l~Gll~P   59 (304)
T PRK13651         31 NQGEFIAIIGQTGSGKTTFIEHLNALLLP   59 (304)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             59989999879998599999999669998


No 333
>TIGR01521 FruBisAldo_II_B fructose-bisphosphate aldolase, class II, Calvin cycle subtype; InterPro: IPR006412   Members of this family are class II examples of the enzyme fructose-bisphosphate aldolase, an enzyme both of glycolysis and (in the opposite direction) of the Calvin cycle of CO2 fixation. A deep split separates the tightly conserved yeast/Escherichia coli/Mycobacterium subtype (all species lacking the Calvin cycle) represented by IPR006411 from INTERPRO from a broader group of aldolases that includes both tagatose- and fructose-bisphosphate aldolases. This family represents a distinct, elongated, very well conserved subtype within the latter group. Most species with this aldolase subtype have the Calvin cycle.; GO: 0004332 fructose-bisphosphate aldolase activity, 0006096 glycolysis.
Probab=42.18  E-value=22  Score=15.09  Aligned_cols=17  Identities=12%  Similarity=0.198  Sum_probs=12.7

Q ss_pred             HHHHCCCCHHHHHHHHC
Q ss_conf             76510121034554311
Q gi|254781101|r  303 VSILTADVDTAIKALSV  319 (472)
Q Consensus       303 ~~~lGi~~~~i~~~L~~  319 (472)
                      -...|+|.++|.++++.
T Consensus       251 ~etyGvPveei~~Gi~~  267 (347)
T TIGR01521       251 KETYGVPVEEIVKGIKY  267 (347)
T ss_pred             CCCCCCCHHHHHHHHHH
T ss_conf             31247868998867762


No 334
>PRK13633 cobalt transporter ATP-binding subunit; Provisional
Probab=41.94  E-value=13  Score=16.56  Aligned_cols=27  Identities=26%  Similarity=0.381  Sum_probs=21.1

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++||.|.|  ||||...++.-++..
T Consensus        35 ~~GE~v~iiG~nGsGKSTL~r~l~gl~~P   63 (281)
T PRK13633         35 KKGEFLVILGHNGSGKSTIAKHMNALLLP   63 (281)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             79989999999998499999999758878


No 335
>PRK09580 sufC cysteine desulfurase ATPase component; Reviewed
Probab=41.92  E-value=16  Score=15.99  Aligned_cols=37  Identities=14%  Similarity=0.230  Sum_probs=22.8

Q ss_pred             CCEEEEEECCCC-CCCCHHHHHHHHHHHHHCCCCCCEEEE
Q ss_conf             311331000256-532101257778741110268713885
Q gi|254781101|r  337 GFFTLIDESYNA-NPASMKAAISVLSQISPHGEGRRIAVL  375 (472)
Q Consensus       337 ~~~~iIDDsYNA-nP~S~~aal~~l~~~~~~~~~r~i~Vl  375 (472)
                      ..+.++|..-++ +|.+.+...+.++.++.  .++-++++
T Consensus       164 P~lllLDEPtsgLD~~~~~~i~~~i~~l~~--~~~tviiv  201 (248)
T PRK09580        164 PELCILDESDSGLDIDALKIVADGVNSLRD--GKRSFIIV  201 (248)
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHHHHHHH--CCCEEEEE
T ss_conf             998999796223999999999999999983--89999999


No 336
>PRK13639 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=41.85  E-value=13  Score=16.75  Aligned_cols=31  Identities=29%  Similarity=0.260  Sum_probs=22.9

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHH-HHHCC
Q ss_conf             699399983036--54201233467777-52011
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALS-SIKKT  136 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~-~~~~~  136 (472)
                      .++.++||.|-|  ||||+..++.-++. ..|.+
T Consensus        26 ~~Ge~vaiiG~nGsGKSTLl~~l~Gll~P~~G~I   59 (275)
T PRK13639         26 EEGEMIAILGPNGAGKSTLFLHFNGILKPSSGSV   59 (275)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCCCCEEE
T ss_conf             8998999999999649999999973989996399


No 337
>PRK13543 cytochrome c biogenesis protein CcmA; Provisional
Probab=41.71  E-value=13  Score=16.75  Aligned_cols=26  Identities=27%  Similarity=0.308  Sum_probs=20.3

Q ss_pred             CCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             99399983036--542012334677775
Q gi|254781101|r  107 KATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       107 ~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      ++.+++|.|.|  ||||.-.+++-++..
T Consensus        36 ~Ge~~~l~GpNGaGKTTLlr~l~Gl~~p   63 (214)
T PRK13543         36 AGEALLVQGDNGAGKTTLLRVLAGLLHV   63 (214)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             8989999999998799999999769778


No 338
>TIGR03164 UHCUDC OHCU decarboxylase. Previously thought to only proceed spontaneously, the decarboxylation of 2-oxo-4-hydroxy-4-carboxy--5-ureidoimidazoline (OHCU) has been recently been shown to be catalyzed by this enzyme in Mus musculus. Homologs of this enzyme are found adjacent to and fused with uricase in a number of prokaryotes and are represented by this model.
Probab=41.71  E-value=23  Score=15.04  Aligned_cols=15  Identities=7%  Similarity=0.131  Sum_probs=6.3

Q ss_pred             HCCCCHHHHHHHHCC
Q ss_conf             101210345543114
Q gi|254781101|r  306 LTADVDTAIKALSVF  320 (472)
Q Consensus       306 lGi~~~~i~~~L~~~  320 (472)
                      ...+.++..+.|...
T Consensus        45 ~~~~~~~~l~ll~aH   59 (157)
T TIGR03164        45 RAASPEQQLALIRAH   59 (157)
T ss_pred             HHCCHHHHHHHHHHC
T ss_conf             959999999999869


No 339
>cd03219 ABC_Mj1267_LivG_branched The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine.  MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E. coli  branched-chain amino acid transporter.  MJ1267 contains an insertion from residues 114 to 123 characteristic of LivG (Leucine-Isoleucine-Valine) homologs.  The branched-chain amino acid transporter from E. coli comprises a heterodimer of ABCs (LivF and LivG), a heterodimer of six-helix TM domains (LivM and LivH), and one of two alternative soluble periplasmic substrate binding proteins (LivK or LivJ).
Probab=41.58  E-value=13  Score=16.63  Aligned_cols=27  Identities=26%  Similarity=0.304  Sum_probs=21.3

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++||.|.|  ||||+-.++.-++..
T Consensus        24 ~~Gei~gliG~nGaGKSTL~~~i~Gl~~p   52 (236)
T cd03219          24 RPGEIHGLIGPNGAGKTTLFNLISGFLRP   52 (236)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             89989999989997399999999679878


No 340
>PRK13409 putative ATPase RIL; Provisional
Probab=41.40  E-value=12  Score=16.85  Aligned_cols=26  Identities=27%  Similarity=0.415  Sum_probs=20.6

Q ss_pred             CCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             99399983036--542012334677775
Q gi|254781101|r  107 KATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       107 ~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .+.|+|+-|.|  ||||+--+|+-.|..
T Consensus        98 ~G~v~GLiG~NGaGKST~lkILsG~l~P  125 (590)
T PRK13409         98 EGKVTGILGPNGIGKSTAVKILSGELIP  125 (590)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             9878998899999899999999587148


No 341
>cd02020 CMPK Cytidine monophosphate kinase (CMPK) catalyzes the reversible phosphorylation of cytidine monophosphate (CMP) to produce cytidine diphosphate (CDP), using ATP as the preferred phosphoryl donor.
Probab=41.36  E-value=12  Score=16.82  Aligned_cols=25  Identities=40%  Similarity=0.501  Sum_probs=19.2

Q ss_pred             EEEEECC--CCCCHHHHHHHHHHHHHH
Q ss_conf             9998303--654201233467777520
Q gi|254781101|r  110 IIAITGS--VGKTTTKEMLTIALSSIK  134 (472)
Q Consensus       110 vI~ITGT--nGKTTt~~~l~~iL~~~~  134 (472)
                      +|+|-|.  .||||+..+|+.-|.-.+
T Consensus         1 iIaIdGpagsGKsT~ak~lA~~l~~~~   27 (147)
T cd02020           1 IIAIDGPAGSGKSTVAKLLAKKLGLPY   27 (147)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHCCEE
T ss_conf             988868997898999999999909907


No 342
>COG0373 HemA Glutamyl-tRNA reductase [Coenzyme metabolism]
Probab=41.35  E-value=23  Score=15.01  Aligned_cols=15  Identities=20%  Similarity=-0.093  Sum_probs=5.7

Q ss_pred             HHHHCCCCHHHHHHH
Q ss_conf             121013424689987
Q gi|254781101|r  222 TIFLNYDDSFFELLK  236 (472)
Q Consensus       222 ~~ViN~Dd~~~~~l~  236 (472)
                      ..|.|..-.....+.
T Consensus       205 i~IaNRT~erA~~La  219 (414)
T COG0373         205 ITIANRTLERAEELA  219 (414)
T ss_pred             EEEECCCHHHHHHHH
T ss_conf             999758789999999


No 343
>PRK13974 thymidylate kinase; Provisional
Probab=41.23  E-value=21  Score=15.24  Aligned_cols=28  Identities=36%  Similarity=0.406  Sum_probs=22.9

Q ss_pred             CCCEEEEECC--CCCCHHHHHHHHHHHHHH
Q ss_conf             9939998303--654201233467777520
Q gi|254781101|r  107 KATIIAITGS--VGKTTTKEMLTIALSSIK  134 (472)
Q Consensus       107 ~~~vI~ITGT--nGKTTt~~~l~~iL~~~~  134 (472)
                      +++.|.+-|.  .||||-..+|+.-|.+.|
T Consensus         2 ~G~fIv~EGiDGsGKsTq~~~L~~~L~~~g   31 (212)
T PRK13974          2 KGKFIVLEGIDGCGKTTQIDHLSKWLPSSG   31 (212)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHCC
T ss_conf             941999889999989999999999998658


No 344
>CHL00181 cbbX CbbX; Provisional
Probab=41.21  E-value=23  Score=14.99  Aligned_cols=24  Identities=33%  Similarity=0.397  Sum_probs=18.8

Q ss_pred             EEEECC--CCCCHHHHHHHHHHHHHH
Q ss_conf             998303--654201233467777520
Q gi|254781101|r  111 IAITGS--VGKTTTKEMLTIALSSIK  134 (472)
Q Consensus       111 I~ITGT--nGKTTt~~~l~~iL~~~~  134 (472)
                      ...+|-  .||||++.+++.+|...|
T Consensus        62 ~vF~GnPGTGKTTVARl~a~il~~lG   87 (287)
T CHL00181         62 MSFTGSPGTGKTTVALKMADILYRLG   87 (287)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCC
T ss_conf             88878998679999999999999869


No 345
>PRK13537 lipooligosaccharide transporter ATP-binding subunit; Provisional
Probab=41.00  E-value=13  Score=16.73  Aligned_cols=28  Identities=29%  Similarity=0.234  Sum_probs=22.5

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHHH
Q ss_conf             699399983036--5420123346777752
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSSI  133 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~~  133 (472)
                      .++.++|+-|-|  |||||-.|+.-++...
T Consensus        29 ~~Gei~gllGpNGAGKTTli~~l~Gl~~p~   58 (304)
T PRK13537         29 QPGECFGLLGPNGAGKTTTLKMLLGLTHPD   58 (304)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCCC
T ss_conf             699599999998972999999997795689


No 346
>pfam00488 MutS_V MutS domain V. This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam01624, pfam05188, pfam05192 and pfam05190. The mutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. The aligned region corresponds with domain V of Thermus aquaticus MutS, which contains a Walker A motif, and is structurally similar to the ATPase domain of ABC transporters.
Probab=40.89  E-value=23  Score=15.03  Aligned_cols=28  Identities=32%  Similarity=0.506  Sum_probs=18.9

Q ss_pred             CCCEEEEECCC--CCCHHHHH--HHHHHHHHH
Q ss_conf             99399983036--54201233--467777520
Q gi|254781101|r  107 KATIIAITGSV--GKTTTKEM--LTIALSSIK  134 (472)
Q Consensus       107 ~~~vI~ITGTn--GKTTt~~~--l~~iL~~~~  134 (472)
                      ..+++=|||.|  ||||.--.  +..+|.+.|
T Consensus        41 ~~~~~iiTGpN~sGKSt~Lk~igl~~~lAq~G   72 (234)
T pfam00488        41 RSRILLITGPNMGGKSTYLRQVALIVIMAQIG   72 (234)
T ss_pred             CEEEEEEECCCCCCCHHHHHHHHHHHHHHHHC
T ss_conf             61699997887776199999999999999836


No 347
>PRK13631 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=40.80  E-value=13  Score=16.57  Aligned_cols=28  Identities=29%  Similarity=0.279  Sum_probs=22.0

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHHH
Q ss_conf             699399983036--5420123346777752
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSSI  133 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~~  133 (472)
                      .++.++||-|.|  ||||+..++.-++...
T Consensus        50 ~~Ge~vaIIG~nGsGKSTL~~~l~Gll~p~   79 (320)
T PRK13631         50 EKNKIYFIIGNSGSGKSTLVTHFNGLIKSK   79 (320)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCCC
T ss_conf             599899999499984999999997588899


No 348
>KOG3308 consensus
Probab=40.80  E-value=15  Score=16.23  Aligned_cols=25  Identities=32%  Similarity=0.438  Sum_probs=18.0

Q ss_pred             CCEEEEECC--CCCCHHHHHHHHHHHH
Q ss_conf             939998303--6542012334677775
Q gi|254781101|r  108 ATIIAITGS--VGKTTTKEMLTIALSS  132 (472)
Q Consensus       108 ~~vI~ITGT--nGKTTt~~~l~~iL~~  132 (472)
                      .-||||.|-  .||||.+..+...|..
T Consensus         4 ~~ivgiSG~TnsGKTTLak~l~~~f~~   30 (225)
T KOG3308           4 TLIVGISGCTNSGKTTLAKSLHRFFPG   30 (225)
T ss_pred             EEEEEEECCCCCCHHHHHHHHHHHCCC
T ss_conf             899986424678776899999987368


No 349
>COG1131 CcmA ABC-type multidrug transport system, ATPase component [Defense mechanisms]
Probab=40.79  E-value=12  Score=16.80  Aligned_cols=26  Identities=31%  Similarity=0.387  Sum_probs=21.4

Q ss_pred             CCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             99399983036--542012334677775
Q gi|254781101|r  107 KATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       107 ~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      ++.++|+.|-|  ||||+-.|+..+++.
T Consensus        30 ~Gei~gllG~NGAGKTTllk~l~Gl~~p   57 (293)
T COG1131          30 PGEIFGLLGPNGAGKTTLLKILAGLLKP   57 (293)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             8959999899999899999999679778


No 350
>PRK13646 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=40.78  E-value=14  Score=16.45  Aligned_cols=27  Identities=26%  Similarity=0.369  Sum_probs=21.5

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++||.|-|  ||||...++.-++..
T Consensus        31 ~~Ge~~aiiG~nGsGKSTLl~~l~GLl~p   59 (286)
T PRK13646         31 EQGKYYAIVGQTGSGKSTLIQNINALLKP   59 (286)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             69989999999998199999999707888


No 351
>PRK13640 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=40.61  E-value=17  Score=15.95  Aligned_cols=27  Identities=22%  Similarity=0.356  Sum_probs=21.7

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++||.|.|  ||||...++.-+|..
T Consensus        32 ~~Ge~vaiiG~nGsGKSTL~~~l~Gll~P   60 (283)
T PRK13640         32 PRGSWTALIGHNGSGKSTISKLINGLLLP   60 (283)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             89999999999998799999999640378


No 352
>COG4586 ABC-type uncharacterized transport system, ATPase component [General function prediction only]
Probab=40.19  E-value=17  Score=15.89  Aligned_cols=30  Identities=40%  Similarity=0.444  Sum_probs=22.5

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH-HHC
Q ss_conf             699399983036--542012334677775-201
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS-IKK  135 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~-~~~  135 (472)
                      +++.++|.-|-|  |||||--||.-++.. .|+
T Consensus        48 P~G~ivgflGaNGAGKSTtLKmLTGll~p~~G~   80 (325)
T COG4586          48 PKGEIVGFLGANGAGKSTTLKMLTGLLLPTSGK   80 (325)
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHCCCCCCCCE
T ss_conf             898689887588886033398973860368875


No 353
>PRK13645 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=40.01  E-value=15  Score=16.27  Aligned_cols=27  Identities=22%  Similarity=0.359  Sum_probs=20.6

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++||.|.|  ||||...++.-++..
T Consensus        35 ~~Ge~~aIiG~nGsGKSTL~~~l~Gll~p   63 (289)
T PRK13645         35 KKNKVTCVIGTTGSGKSTMIQLTNGLIIS   63 (289)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             89989999999995799999999659889


No 354
>TIGR02533 type_II_gspE general secretory pathway protein E; InterPro: IPR013369    GspE, the E protein of the type II secretion system, is also referred to as the main terminal branch of the general secretion pathway. ; GO: 0005524 ATP binding, 0008565 protein transporter activity, 0015628 protein secretion by the type II secretion system, 0015627 type II protein secretion system complex.
Probab=39.88  E-value=24  Score=14.86  Aligned_cols=20  Identities=65%  Similarity=0.757  Sum_probs=9.7

Q ss_pred             EEEEECC--CCCCHHHHHHHHHHHH
Q ss_conf             9998303--6542012334677775
Q gi|254781101|r  110 IIAITGS--VGKTTTKEMLTIALSS  132 (472)
Q Consensus       110 vI~ITGT--nGKTTt~~~l~~iL~~  132 (472)
                      +|=|||=  .|||||   |+..|+.
T Consensus       247 IiLVTGPTGSGKtTT---LYaaL~~  268 (495)
T TIGR02533       247 IILVTGPTGSGKTTT---LYAALSR  268 (495)
T ss_pred             EEEECCCCCCCHHHH---HHHHHHH
T ss_conf             188417789852588---9999986


No 355
>PRK10771 thiQ thiamine transporter ATP-binding subunit; Provisional
Probab=39.88  E-value=14  Score=16.49  Aligned_cols=27  Identities=26%  Similarity=0.399  Sum_probs=21.7

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++||.|-|  ||||.-.++.-++..
T Consensus        23 ~~GE~v~iiG~nGaGKSTLl~~i~Gll~p   51 (233)
T PRK10771         23 ERGEQVAILGPSGAGKSTLLNLIAGFLTP   51 (233)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             89989999999998199999999659999


No 356
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha subunit, Gram-positive type; InterPro: IPR006308   These are the polypeptide chains of DNA polymerase III. Full-length homologs of this protein are restricted to the Gram-positive lineages, including the Mycoplasmas. This protein is designated alpha chain and given the gene symbol polC, but is not a full-length homolog of other polC genes. The N-terminal region of about 200 amino acids is rich in low-complexity sequence and poorly alignable. ; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0005737 cytoplasm.
Probab=39.87  E-value=14  Score=16.45  Aligned_cols=73  Identities=23%  Similarity=0.373  Sum_probs=46.4

Q ss_pred             HHCCCCC--CCC-C-CCCCCCCCCCC------EEEEEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHH----CCCC
Q ss_conf             3015664--433-2-11212232322------0255531210123444578888654331037622101210----1342
Q gi|254781101|r  164 IFELGMS--HLG-E-IRFLTHLVRPH------IAVITTIAPAHLSNFSGIEEIASAKAEIFEGLEKTGTIFL----NYDD  229 (472)
Q Consensus       164 V~E~g~~--~~g-e-i~~L~~i~~P~------iaiiTNI~~dHld~~~s~e~i~~~K~~i~~~l~~~g~~Vi----N~Dd  229 (472)
                      |+|+|+.  +-| + |++...+++|+      +.=+|||+.|||+.=.+.|....+-.++++.    .++|.    |.|-
T Consensus       223 iIE~gA~k~~nGk~ii~~~~~FikP~~~l~~~~~elT~ITq~ml~n~~~~~~vL~k~~~f~~d----~ilVAHNGasFD~  298 (1264)
T TIGR01405       223 IIEFGAVKVKNGKRIIDKFQFFIKPKEPLSAFVTELTGITQDMLENAPEIEEVLEKFKEFLKD----SILVAHNGASFDI  298 (1264)
T ss_pred             EEEEEEEEEECCCEEEEEHHHHCCCCCCCCCCEEEECCCCHHHHCCCCCHHHHHHHHHHHHCC----EEEEECCCCCCCH
T ss_conf             467875887468576231232328875467542662466479737984178999999997697----5888627610366


Q ss_pred             HHHHHHHHHCC
Q ss_conf             46899875201
Q gi|254781101|r  230 SFFELLKAKSH  240 (472)
Q Consensus       230 ~~~~~l~~~~~  240 (472)
                      ++++...++..
T Consensus       299 ~Fl~~~~~k~~  309 (1264)
T TIGR01405       299 GFLNTNFEKVG  309 (1264)
T ss_pred             HHHHHHHHHCC
T ss_conf             88988987627


No 357
>COG1193 Mismatch repair ATPase (MutS family) [DNA replication, recombination, and repair]
Probab=39.78  E-value=21  Score=15.26  Aligned_cols=37  Identities=14%  Similarity=0.038  Sum_probs=20.1

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHCC
Q ss_conf             5432212222222233332210356765101210345543114
Q gi|254781101|r  278 GKSMEVVHHGIGYHMAQNMLMTLGIVSILTADVDTAIKALSVF  320 (472)
Q Consensus       278 ~~~~~~~l~~~G~hnv~NalaAia~~~~lGi~~~~i~~~L~~~  320 (472)
                      ...+.+....+|+-|      |+.++..+|++...|.++...+
T Consensus       463 ~ptY~l~~G~~g~S~------Af~ia~rlGl~~~iie~a~~~~  499 (753)
T COG1193         463 RPTYRLLEGVPGRSN------AFDIALRLGLPEPIIEEAKTEF  499 (753)
T ss_pred             HHHHHHHCCCCCCCH------HHHHHHHCCCCHHHHHHHHHHC
T ss_conf             677887607866102------7999998399889999987750


No 358
>PRK13542 consensus
Probab=39.65  E-value=14  Score=16.45  Aligned_cols=27  Identities=19%  Similarity=0.365  Sum_probs=20.4

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++||.|-|  ||||.-.++.-++..
T Consensus        42 ~~Gei~~liGpNGaGKTTLlk~l~Gll~p   70 (224)
T PRK13542         42 APGDLLQVMGPNGSGKTSLLRVLSGLMPP   70 (224)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             59979999999999999999999579788


No 359
>TIGR01124 ilvA_2Cterm threonine ammonia-lyase, biosynthetic; InterPro: IPR005787    Serine and threonine dehydratases ,  are functionally and structurally related pyridoxal-phosphate dependent enzymes. L-serine dehydratase () and D-serine dehydratase () catalyze the dehydratation of L-serine (respectively D-serine) into ammonia and pyruvate. Threonine dehydratase () (TDH) catalyzes the dehydratation of threonine into alpha-ketobutarate and ammonia. In Escherichia coli and other microorganisms, two classes of TDH are known to exist. One is involved in the biosynthesis of isoleucine, the other in hydroxamino acid catabolism. Threonine synthase () is also a pyridoxal-phosphate enzyme, it catalyzes the transformation of homoserine-phosphate into threonine. It has been shown  that threonine synthase is distantly related to the serine/threonine dehydratases. In all these enzymes, the pyridoxal-phosphate group is attached to a lysine residue.    This family describes a form of threonine dehydratase, with two copies of the threonine dehydratase C-terminal domain IPR001721 from INTERPRO. Members with known function participate in isoleucine biosynthesis and are inhibited by isoleucine.; GO: 0004794 L-threonine ammonia-lyase activity, 0009097 isoleucine biosynthetic process.
Probab=39.46  E-value=25  Score=14.82  Aligned_cols=34  Identities=24%  Similarity=0.261  Sum_probs=14.3

Q ss_pred             CCCCCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEE
Q ss_conf             223789888971688747688899999869889998
Q gi|254781101|r   35 RSIAPQEAFFAIKGPHYDGHDFILHAVQKGAGLVVV   70 (472)
Q Consensus        35 r~v~~g~lFval~g~~~DGh~~i~~A~~~Ga~~~i~   70 (472)
                      .+-+--.+=-|=-|.+.=|=-|  .|-+-|.+|+||
T Consensus        63 ~E~~A~GVIaASAGNHAQGVAl--sa~~LG~~A~IV   96 (508)
T TIGR01124        63 AEQRARGVIAASAGNHAQGVAL--SAEKLGLKAVIV   96 (508)
T ss_pred             HHHHCCCEEECCCCCHHHHHHH--HHHHCCCCEEEE
T ss_conf             7584182012024545789987--663179726987


No 360
>pfam02223 Thymidylate_kin Thymidylate kinase.
Probab=39.41  E-value=11  Score=17.19  Aligned_cols=19  Identities=37%  Similarity=0.368  Sum_probs=16.5

Q ss_pred             CCCCHHHHHHHHHHHHHHC
Q ss_conf             6542012334677775201
Q gi|254781101|r  117 VGKTTTKEMLTIALSSIKK  135 (472)
Q Consensus       117 nGKTTt~~~l~~iL~~~~~  135 (472)
                      .||||...+|+.-|+..|.
T Consensus         7 sGKsTq~~~L~~~L~~~g~   25 (186)
T pfam02223         7 AGKTTQAELLKERLKEQGI   25 (186)
T ss_pred             CCHHHHHHHHHHHHHHCCC
T ss_conf             8999999999999998799


No 361
>PRK04040 adenylate kinase; Provisional
Probab=39.33  E-value=19  Score=15.60  Aligned_cols=30  Identities=30%  Similarity=0.299  Sum_probs=21.4

Q ss_pred             CCEEEEECC--CCCCHHHHHHHHHHHHHHCCC
Q ss_conf             939998303--654201233467777520112
Q gi|254781101|r  108 ATIIAITGS--VGKTTTKEMLTIALSSIKKTY  137 (472)
Q Consensus       108 ~~vI~ITGT--nGKTTt~~~l~~iL~~~~~~~  137 (472)
                      +++|-|||-  .||||+...+...|...++.+
T Consensus         2 ~k~VvvtGiPGvGKTTv~~~~~~~l~~~~~~v   33 (189)
T PRK04040          2 MKVVVVTGVPGVGKTTVLNKALEKLKEDYKIV   33 (189)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHCCCCEEE
T ss_conf             41899975898878999999999723587598


No 362
>COG2019 AdkA Archaeal adenylate kinase [Nucleotide transport and metabolism]
Probab=39.30  E-value=22  Score=15.12  Aligned_cols=23  Identities=39%  Similarity=0.538  Sum_probs=18.7

Q ss_pred             CCEEEEECC--CCCCHHHHHHHHHH
Q ss_conf             939998303--65420123346777
Q gi|254781101|r  108 ATIIAITGS--VGKTTTKEMLTIAL  130 (472)
Q Consensus       108 ~~vI~ITGT--nGKTTt~~~l~~iL  130 (472)
                      .+++.|||-  .||||+.......|
T Consensus         4 ~kvvvitGVpGvGKTTVl~~~~~~l   28 (189)
T COG2019           4 RKVVVITGVPGVGKTTVLKIALKEL   28 (189)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             5599997579887266999999877


No 363
>PRK11629 lolD lipoprotein transporter ATP-binding subunit; Provisional
Probab=39.22  E-value=14  Score=16.48  Aligned_cols=27  Identities=30%  Similarity=0.370  Sum_probs=21.1

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++||.|-|  ||||.-.+++-++..
T Consensus        33 ~~GE~v~iiG~sGsGKSTLl~~i~Gl~~p   61 (233)
T PRK11629         33 GEGEMMAIVGSSGSGKSTLLHLLGGLDTP   61 (233)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             89989999999994099999999669999


No 364
>PRK10436 hypothetical protein; Provisional
Probab=39.10  E-value=25  Score=14.78  Aligned_cols=29  Identities=14%  Similarity=-0.033  Sum_probs=16.3

Q ss_pred             CCCCCCCHHHHHHHHCCCCHHHHHHHHCC
Q ss_conf             33332210356765101210345543114
Q gi|254781101|r  292 MAQNMLMTLGIVSILTADVDTAIKALSVF  320 (472)
Q Consensus       292 nv~NalaAia~~~~lGi~~~~i~~~L~~~  320 (472)
                      +..++..|+.=...+|+++..+...|..+
T Consensus       317 Htnda~~ai~RL~~mgi~~~lla~~L~~V  345 (461)
T PRK10436        317 HTNSTSETLIRLQQMGVARWMISSALTLV  345 (461)
T ss_pred             CCCCHHHHHHHHHHCCCCHHHHHHHHHHE
T ss_conf             26977889999998399888999866334


No 365
>cd03235 ABC_Metallic_Cations ABC component of the metal-type transporters.  This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc.  The ATPases of this group of transporters are very similar to members of iron-siderophore uptake family suggesting that they share a common ancestor.  The best characterized metal-type ABC transporters are the YfeABCD system of Y. pestis, the SitABCD system of Salmonella enterica serovar Typhimurium, and the SitABCD transporter of Shigella flexneri.  Moreover other uncharacterized homologs of these metal-type transporters are mainly found in pathogens like Haemophilus or enteroinvasive E. coli isolates.
Probab=38.94  E-value=15  Score=16.28  Aligned_cols=53  Identities=25%  Similarity=0.435  Sum_probs=31.4

Q ss_pred             CCEEEEEECCCC-CCCCHHHHHHHHHHHHHCCCCCCEEEEC-CHHHCCCCHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             311331000256-5321012577787411102687138851-2354171058999999999986499899998
Q gi|254781101|r  337 GFFTLIDESYNA-NPASMKAAISVLSQISPHGEGRRIAVLG-DMCEMGELSQSFHIDLAEVLSLYNISHVWLS  407 (472)
Q Consensus       337 ~~~~iIDDsYNA-nP~S~~aal~~l~~~~~~~~~r~i~VlG-~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~  407 (472)
                      ..+.+.|...++ +|.+....++.++.+..  .++-+++.- +|               +.+.+. +|+|++.
T Consensus       151 P~lLlLDEPtsgLD~~~~~~~~~~i~~l~~--~g~tii~vtHdl---------------~~~~~~-~drii~l  205 (213)
T cd03235         151 PDLLLLDEPFAGVDPKTQEDIYELLRELRR--EGMTILVVTHDL---------------GLVLEY-FDRVLLL  205 (213)
T ss_pred             CCEEEECCCCCCCCHHHHHHHHHHHHHHHH--CCCEEEEEECCH---------------HHHHHH-CCEEEEE
T ss_conf             999998188667899999999999999996--899999990798---------------999997-9999999


No 366
>COG1797 CobB Cobyrinic acid a,c-diamide synthase [Coenzyme metabolism]
Probab=38.92  E-value=19  Score=15.58  Aligned_cols=26  Identities=42%  Similarity=0.247  Sum_probs=17.7

Q ss_pred             EEEEECC-CCCCHHHHHHHHHHHHHHC
Q ss_conf             9998303-6542012334677775201
Q gi|254781101|r  110 IIAITGS-VGKTTTKEMLTIALSSIKK  135 (472)
Q Consensus       110 vI~ITGT-nGKTTt~~~l~~iL~~~~~  135 (472)
                      +||=|.| .||||++--|-..|+..|.
T Consensus         4 vIAg~~SG~GKTTvT~glm~aL~~rg~   30 (451)
T COG1797           4 VIAGTSSGSGKTTVTLGLMRALRRRGL   30 (451)
T ss_pred             EEECCCCCCCHHHHHHHHHHHHHHCCC
T ss_conf             995488888589999999999986687


No 367
>COG2759 MIS1 Formyltetrahydrofolate synthetase [Nucleotide transport and metabolism]
Probab=38.90  E-value=25  Score=14.76  Aligned_cols=31  Identities=35%  Similarity=0.408  Sum_probs=21.8

Q ss_pred             CCCCCEEEEECCC------CCCHHHHHHHHHHHHHHC
Q ss_conf             0699399983036------542012334677775201
Q gi|254781101|r  105 RSKATIIAITGSV------GKTTTKEMLTIALSSIKK  135 (472)
Q Consensus       105 ~~~~~vI~ITGTn------GKTTt~~~l~~iL~~~~~  135 (472)
                      +.+++.|-||+-|      |||||+-=|.+-|...|+
T Consensus        49 k~~gKlILVTaitPTPaGEGKsTttiGL~~al~~lgK   85 (554)
T COG2759          49 KPDGKLILVTAITPTPAGEGKTTTTIGLVDALNKLGK   85 (554)
T ss_pred             CCCCEEEEEEECCCCCCCCCCCEEEEHHHHHHHHCCC
T ss_conf             8886089998257888888861254248999986186


No 368
>pfam05577 Peptidase_S28 Serine carboxypeptidase S28. These serine proteases include several eukaryotic enzymes such as lysosomal Pro-X carboxypeptidase, dipeptidyl-peptidase II, and thymus-specific serine peptidase.
Probab=38.82  E-value=25  Score=14.75  Aligned_cols=105  Identities=18%  Similarity=0.152  Sum_probs=64.4

Q ss_pred             CEEEEEEEECCCCCCCC-EEEECCCCC-------CCHHHHHHHHHHCCCEEEEECCCCCCCCC---CCCCCEEEECCHHH
Q ss_conf             14746774022237898-889716887-------47688899999869889998552124554---46972899599899
Q gi|254781101|r   25 GFVNGISIDSRSIAPQE-AFFAIKGPH-------YDGHDFILHAVQKGAGLVVVNTDMVASIG---SLSIPVFGVDDVLG   93 (472)
Q Consensus        25 ~~i~~i~~dSr~v~~g~-lFval~g~~-------~DGh~~i~~A~~~Ga~~~i~~~~~~~~~~---~~~~~~i~v~d~~~   93 (472)
                      ++-..--++++--++|. +||-+-|+-       ..| ...+-|-+-||..++.|..+-....   +.....+.-=.+.+
T Consensus        13 TF~qRY~~n~~y~~~ggPifly~gGE~~~~~~~~~~g-~~~~lA~~~~a~~v~lEHRYYG~S~P~~~~s~enL~yLt~~Q   91 (433)
T pfam05577        13 TFQQRYFYNDQHYRNGGPIFLMIGGEGPESASWVRNG-HWLDLAKEFGALVFSLEHRFYGQSKPIGDLSTANLRYLSSLQ   91 (433)
T ss_pred             EEEEEEEEECCEECCCCCEEEEECCCCCCCCCCCCCC-HHHHHHHHHCCEEEEEEEECCCCCCCCCCCCCCCCCCCCHHH
T ss_conf             7887799855684699978999899876752311362-899999983996999851035036688998811236478999


Q ss_pred             HHHHHHHHHH---HC----CCCCEEEEECCCCCCHHHHHHHHHHHHHHC
Q ss_conf             9999999998---30----699399983036542012334677775201
Q gi|254781101|r   94 ALNKLAVAAR---LR----SKATIIAITGSVGKTTTKEMLTIALSSIKK  135 (472)
Q Consensus        94 al~~la~~~~---~~----~~~~vI~ITGTnGKTTt~~~l~~iL~~~~~  135 (472)
                      ||..+|.+..   .+    .+.|+|.+-||.|     -||+.-++..++
T Consensus        92 ALaD~a~Fi~~~k~~~~~~~~~pwI~~GGSY~-----G~LaAw~R~kYP  135 (433)
T pfam05577        92 ALADVASFIKAMNQKFNGLSSSKWITFGGSYS-----GSLAAWARKKYP  135 (433)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCCEEEECCCCH-----HHHHHHHHHHCC
T ss_conf             99999999999998637889999899878608-----799999998688


No 369
>PRK13849 putative crown gall tumor protein VirC1; Provisional
Probab=38.78  E-value=14  Score=16.46  Aligned_cols=29  Identities=34%  Similarity=0.359  Sum_probs=21.7

Q ss_pred             CEEEEE---CCCCCCHHHHHHHHHHHHHHCCC
Q ss_conf             399983---03654201233467777520112
Q gi|254781101|r  109 TIIAIT---GSVGKTTTKEMLTIALSSIKKTY  137 (472)
Q Consensus       109 ~vI~IT---GTnGKTTt~~~l~~iL~~~~~~~  137 (472)
                      +||.+.   |-.||||+.-.++..|...|+.+
T Consensus         2 ~vi~~~~~KGG~GKtT~a~~la~~~~~~g~~v   33 (231)
T PRK13849          2 KLLTFCSFKGGAGKTTALMGLCAALASDGKRV   33 (231)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHCCCEE
T ss_conf             37999618998769999999999999789959


No 370
>PRK13539 cytochrome c biogenesis protein CcmA; Provisional
Probab=38.68  E-value=15  Score=16.33  Aligned_cols=26  Identities=31%  Similarity=0.401  Sum_probs=19.6

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHH
Q ss_conf             699399983036--54201233467777
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALS  131 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~  131 (472)
                      .++.++|+.|-|  ||||.-.++.-++.
T Consensus        26 ~~Gei~~l~G~NGaGKTTLlk~i~Gl~~   53 (206)
T PRK13539         26 AAGEALVLTGPNGSGKTTLLRLLAGLLP   53 (206)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCC
T ss_conf             6994999989999989999999958878


No 371
>cd03250 ABCC_MRP_domain1 Domain 1 of the ABC subfamily C.  This family is also known as MRP (mulrtidrug resisitance-associated protein).  Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear.  The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.
Probab=38.51  E-value=15  Score=16.27  Aligned_cols=25  Identities=36%  Similarity=0.505  Sum_probs=17.8

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHH
Q ss_conf             699399983036--5420123346777
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIAL  130 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL  130 (472)
                      .++.++||.|.|  ||||.-.++.-++
T Consensus        29 ~~Ge~~~IvG~sGsGKSTLl~~i~G~~   55 (204)
T cd03250          29 PKGELVAIVGPVGSGKSSLLSALLGEL   55 (204)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHCCCC
T ss_conf             699899999999985899999981895


No 372
>PRK05563 DNA polymerase III subunits gamma and tau; Validated
Probab=38.48  E-value=11  Score=17.23  Aligned_cols=32  Identities=13%  Similarity=0.039  Sum_probs=16.4

Q ss_pred             CCCCCCCCCCHHHHHHHHCCCCHHHHHHHHCC
Q ss_conf             22233332210356765101210345543114
Q gi|254781101|r  289 GYHMAQNMLMTLGIVSILTADVDTAIKALSVF  320 (472)
Q Consensus       289 G~hnv~NalaAia~~~~lGi~~~~i~~~L~~~  320 (472)
                      -..+..+++..+--....|.++..+.+.|..+
T Consensus       257 ~~~d~~~~l~~~~~i~~~G~d~~~fl~dLi~~  288 (541)
T PRK05563        257 IEKDIEKSMEIIDDIVLSGKDIYNFIKDLITH  288 (541)
T ss_pred             HCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf             85899999999999998699999999999999


No 373
>KOG4777 consensus
Probab=38.32  E-value=9.4  Score=17.58  Aligned_cols=56  Identities=23%  Similarity=0.333  Sum_probs=25.4

Q ss_pred             CCCEEEEECCCCCCHHHH----------HHHHHHHHHHCCCCCHHHHHCCCCCCCHHCCCCCCCHHHHHCCC
Q ss_conf             993999830365420123----------34677775201122212211014574100012322144430156
Q gi|254781101|r  107 KATIIAITGSVGKTTTKE----------MLTIALSSIKKTYACIGSYNNHIGVPLTLARMPVDVDFGIFELG  168 (472)
Q Consensus       107 ~~~vI~ITGTnGKTTt~~----------~l~~iL~~~~~~~~t~gn~Nn~iGvpltll~~~~~~~~~V~E~g  168 (472)
                      ..+|+|.||+.|.--..-          ||..--+++|+.++-.+|+-..+-+|      ++-++|.|-|.-
T Consensus         6 ~a~vlGaTGaVGQrFi~lLsdhP~f~ikvLgAS~RSAGK~ya~a~~wkqt~~lp------~~~~e~~V~ec~   71 (361)
T KOG4777           6 SAPVLGATGAVGQRFISLLSDHPYFSIKVLGASKRSAGKRYAFAGNWKQTDLLP------ESAHEYTVEECT   71 (361)
T ss_pred             CCCEEECCCHHHHHHHHHHCCCCCCEEEEECCCCCCCCCCEEECCCCHHCCCCC------CHHHHHHHHHCC
T ss_conf             355210343147789998616985134230133314698157604411202465------034341375558


No 374
>PRK13634 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=38.18  E-value=15  Score=16.18  Aligned_cols=27  Identities=30%  Similarity=0.386  Sum_probs=21.6

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++||.|-|  ||||...++.-++..
T Consensus        18 ~~Ge~vaiiG~sGsGKSTLl~~l~GLl~P   46 (276)
T PRK13634         18 PSGSYVAIIGHTGSGKSTLLQHLNGLLKP   46 (276)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             89989999999996999999999749998


No 375
>PRK10895 putative ABC transporter ATP-binding protein YhbG; Provisional
Probab=38.16  E-value=15  Score=16.22  Aligned_cols=27  Identities=30%  Similarity=0.364  Sum_probs=21.4

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++|+.|-|  ||||+-.++.-++..
T Consensus        27 ~~Gei~~liGpNGaGKSTLl~~i~Gl~~~   55 (241)
T PRK10895         27 NSGEIVGLLGPNGAGKTTTFYMVVGIVPR   55 (241)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             39979999889998699999999678888


No 376
>COG1105 FruK Fructose-1-phosphate kinase and related fructose-6-phosphate kinase (PfkB) [Carbohydrate transport and metabolism]
Probab=38.14  E-value=26  Score=14.68  Aligned_cols=29  Identities=17%  Similarity=0.146  Sum_probs=12.0

Q ss_pred             CCCCHHHHCCC------CHHHHHHHHHCCCCCCCC
Q ss_conf             22101210134------246899875201233333
Q gi|254781101|r  218 EKTGTIFLNYD------DSFFELLKAKSHALGIKT  246 (472)
Q Consensus       218 ~~~g~~ViN~D------d~~~~~l~~~~~~~~~~~  246 (472)
                      .+...+|++..      ..++..+...++..+.+.
T Consensus       128 ~~~d~VvlsGSlP~g~~~d~y~~li~~~~~~g~~v  162 (310)
T COG1105         128 ESDDIVVLSGSLPPGVPPDAYAELIRILRQQGAKV  162 (310)
T ss_pred             CCCCEEEEECCCCCCCCHHHHHHHHHHHHHCCCEE
T ss_conf             64889999088999999799999999998659839


No 377
>PRK00856 pyrB aspartate carbamoyltransferase catalytic subunit; Provisional
Probab=38.03  E-value=26  Score=14.67  Aligned_cols=11  Identities=18%  Similarity=-0.031  Sum_probs=4.2

Q ss_pred             HHHHHHHHHHH
Q ss_conf             99999999998
Q gi|254781101|r   93 GALNKLAVAAR  103 (472)
Q Consensus        93 ~al~~la~~~~  103 (472)
                      ..+-.+|..+.
T Consensus        21 ~~ll~~A~~~K   31 (304)
T PRK00856         21 ELLLDTAEQFK   31 (304)
T ss_pred             HHHHHHHHHHH
T ss_conf             99999999997


No 378
>PRK09984 phosphonate/organophosphate ester transporter subunit; Provisional
Probab=38.00  E-value=18  Score=15.72  Aligned_cols=26  Identities=23%  Similarity=0.385  Sum_probs=21.1

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHH
Q ss_conf             699399983036--54201233467777
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALS  131 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~  131 (472)
                      .++.++||-|.|  ||||+-.++.-++.
T Consensus        28 ~~GE~~~iiGpNGaGKSTLlk~i~Gll~   55 (262)
T PRK09984         28 HHGEMVALLGPSGSGKSTLLRHLSGLIT   55 (262)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCC
T ss_conf             7998999998999609999999975677


No 379
>pfam02562 PhoH PhoH-like protein. PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation.
Probab=37.94  E-value=26  Score=14.66  Aligned_cols=39  Identities=31%  Similarity=0.603  Sum_probs=26.4

Q ss_pred             CCCEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHH
Q ss_conf             531133100025653210125777874111026871388512354
Q gi|254781101|r  336 QGFFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCE  380 (472)
Q Consensus       336 ~~~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~E  380 (472)
                      .+.+.|+|.+=|.+|..++..|.   .+   ..+-|+++.||..+
T Consensus       119 ~n~~iIvDEaQN~t~~~lk~ilT---Ri---G~~SK~vi~GD~~Q  157 (205)
T pfam02562       119 NDAFIILDEAQNTTPEQMKMFLT---RI---GFNSKMVVTGDITQ  157 (205)
T ss_pred             CCCEEEEECHHCCCHHHHHHHHH---HC---CCCCEEEEECCHHH
T ss_conf             56889997221399999999984---21---79968999478665


No 380
>PRK03846 adenylylsulfate kinase; Provisional
Probab=37.90  E-value=26  Score=14.66  Aligned_cols=36  Identities=25%  Similarity=0.233  Sum_probs=27.7

Q ss_pred             HHHHHCCCCCEEEEECC--CCCCHHHHHHHHHHHHHHC
Q ss_conf             99983069939998303--6542012334677775201
Q gi|254781101|r  100 VAARLRSKATIIAITGS--VGKTTTKEMLTIALSSIKK  135 (472)
Q Consensus       100 ~~~~~~~~~~vI~ITGT--nGKTTt~~~l~~iL~~~~~  135 (472)
                      +..+...++.||=+||=  .||||....+..-|...+.
T Consensus        16 r~~~~~~kg~viWlTGLSGSGKTTlA~~L~~~L~~~~~   53 (198)
T PRK03846         16 REQLHGHKGVVLWFTGLSGSGKSTVAGALEEALHELGV   53 (198)
T ss_pred             HHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCC
T ss_conf             99986899869998799999889999999999997599


No 381
>PRK13582 thrH phosphoserine phosphatase; Provisional
Probab=37.56  E-value=26  Score=14.62  Aligned_cols=24  Identities=17%  Similarity=0.041  Sum_probs=17.7

Q ss_pred             CCCEEEECCHHHHHHHHHHHCCCC
Q ss_conf             797999789899999999844789
Q gi|254781101|r  421 SIHVHYSETMDGLFLFIQSSLVDG  444 (472)
Q Consensus       421 ~~~~~~~~~~e~a~~~l~~~~~~g  444 (472)
                      ..++..+++.+++...+.+....|
T Consensus       179 ap~~~~~~~y~el~~~i~~~~~~~  202 (205)
T PRK13582        179 FPQFPVVHDYDDLKKEIDKASARG  202 (205)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHCCC
T ss_conf             889953068999999999974367


No 382
>PRK09473 oppD oligopeptide transporter ATP-binding component; Provisional
Probab=37.49  E-value=15  Score=16.22  Aligned_cols=31  Identities=23%  Similarity=0.251  Sum_probs=23.7

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHHHHCC
Q ss_conf             699399983036--5420123346777752011
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSSIKKT  136 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~~~~~  136 (472)
                      .++.++||-|-+  ||||+..++..+|...+.+
T Consensus        40 ~~GEilgivGeSGsGKSTl~~~i~gll~~~~~~   72 (330)
T PRK09473         40 RAGETLGIVGESGSGKSQTAFALMGLLAANGRI   72 (330)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCCCCCE
T ss_conf             899899998689877999999997688888833


No 383
>cd03230 ABC_DR_subfamily_A This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity.  In bacteria and archaea, these transporters usually include an ATP-binding protein and one or two integral membrane proteins.  Eukaryote systems of the ABCA subfamily display ABC domains that are quite similar to this family.  The ATP-binding domain shows the highest similarity between all members of the ABC transporter family.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=37.39  E-value=16  Score=15.98  Aligned_cols=37  Identities=19%  Similarity=0.359  Sum_probs=23.3

Q ss_pred             CCEEEEEECCCC-CCCCHHHHHHHHHHHHHCCCCCCEEEE
Q ss_conf             311331000256-532101257778741110268713885
Q gi|254781101|r  337 GFFTLIDESYNA-NPASMKAAISVLSQISPHGEGRRIAVL  375 (472)
Q Consensus       337 ~~~~iIDDsYNA-nP~S~~aal~~l~~~~~~~~~r~i~Vl  375 (472)
                      ..+.++|.-.+. +|.+.+...+.++.+...  ++-|++.
T Consensus       114 p~lllLDEPt~gLD~~~~~~i~~~i~~l~~~--g~tvi~~  151 (173)
T cd03230         114 PELLILDEPTSGLDPESRREFWELLRELKKE--GKTILLS  151 (173)
T ss_pred             CCEEEECCCCCCCCHHHHHHHHHHHHHHHHC--CCEEEEE
T ss_conf             9999990886579999999999999999968--9999999


No 384
>PRK13649 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=37.30  E-value=17  Score=15.86  Aligned_cols=27  Identities=22%  Similarity=0.260  Sum_probs=21.1

Q ss_pred             CCCCEEEEECCCC--CCHHHHHHHHHHHH
Q ss_conf             6993999830365--42012334677775
Q gi|254781101|r  106 SKATIIAITGSVG--KTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTnG--KTTt~~~l~~iL~~  132 (472)
                      .++.++||.|.||  |||+..++.-++..
T Consensus        31 ~~Ge~~aiiG~nGsGKSTLl~~l~Gl~~p   59 (280)
T PRK13649         31 LDGSYTAFIGHTGSGKSTIMQLLNGLHVP   59 (280)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             79989999959998699999999669998


No 385
>cd03267 ABC_NatA_like Similar in sequence to NatA, this is the ATPase component of a bacterial ABC-type Na+ transport system called NatAB, which catalyzes ATP-dependent electrogenic Na+ extrusion without mechanically coupled to proton or K+ uptake.  NatB possess six putative membrane spanning regions at its C-terminus.  In B. subtilis, NatAB is inducible by agents such as ethanol and protonophores, which lower the protonmotive force across the membrane.  The closest sequence similarity to NatA is exhibited by DrrA of the two-component daunomycin- and doxorubicin-efflux system.  Hence, the functional NatAB is presumably assembled with two copies of the single ATP-binding protein and the single intergral membrane protein.
Probab=37.21  E-value=17  Score=15.95  Aligned_cols=26  Identities=38%  Similarity=0.510  Sum_probs=21.2

Q ss_pred             CCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             99399983036--542012334677775
Q gi|254781101|r  107 KATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       107 ~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .+.++|+-|-|  ||||+-.++.-++..
T Consensus        46 ~Gei~gLlGpNGaGKSTllk~l~Gl~~p   73 (236)
T cd03267          46 KGEIVGFIGPNGAGKTTTLKILSGLLQP   73 (236)
T ss_pred             CCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             8959999999983099999999649488


No 386
>TIGR02798 ligK_PcmE 4-carboxy-4-hydroxy-2-oxoadipate aldolase/oxaloacetate decarboxylase; InterPro: IPR014165   This entry represents 4-carboxy-4-hydroxy-2-oxoadipate aldolase, also called 4-oxalocitramalate aldolase. This enzyme of the protocatechuate 4,5-cleavage pathway converts its substrate to pyruvate plus oxaloacetate. Protocatechuate is an intermediate in many pathways for degrading aromatic compounds, including lignin and fluorene. LigK gene has been shown to be, not only a 4-carboxy-4-hydroxy-2-oxoadipate aldolase but also the enzyme of the following step, oxaloacetate decarboxylase..
Probab=37.18  E-value=27  Score=14.59  Aligned_cols=19  Identities=16%  Similarity=0.263  Sum_probs=6.7

Q ss_pred             CEEEEEEECCCHHHHHHHH
Q ss_conf             2025553121012344457
Q gi|254781101|r  185 HIAVITTIAPAHLSNFSGI  203 (472)
Q Consensus       185 ~iaiiTNI~~dHld~~~s~  203 (472)
                      |+.+...-++..=+|||++
T Consensus        77 d~~~~~~t~~~~dG~fG~l   95 (222)
T TIGR02798        77 DVVVAAVTAESEDGYFGDL   95 (222)
T ss_pred             CEEEEECCCCCCCCCHHHH
T ss_conf             7799842666666611558


No 387
>PRK13642 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=37.09  E-value=16  Score=15.97  Aligned_cols=27  Identities=26%  Similarity=0.422  Sum_probs=21.8

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++||-|-|  ||||+..++.-++..
T Consensus        31 ~~Ge~~aiiG~sGsGKSTL~~~l~Gl~~~   59 (277)
T PRK13642         31 TKGEWVSIIGQNGSGKSTTARLIDGLFEE   59 (277)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             89989999999996899999999638998


No 388
>TIGR01193 bacteriocin_ABC ABC-type bacteriocin transporter; InterPro: IPR005897   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 family contains ABC-type bacteriocin transporter. In general, bacteriocins are agents which are responsible for killing or inhibiting the closely related species or even different strains of the same species. Bacteriocins are encoded by bacterial plasmids. Bacteriocins are named after the species and hence in literature one encounters various names e.g., leucocin from Leuconostic geldium; pedicocin from Pedicoccus acidilactici; sakacin from Lactobacillus sake etc.    Peptide bacteriocins are exported across the cytoplasmic membrane by a dedicated ATP-binding cassette (ABC) transporter. These ABC-transporters have an N-terminal peptidase domain that belong to MEROPS peptidase family C39 (clan CA); a central multi-pass transmembrane region and a C-terminal ABC transporter domain. These transporters have dual function: (i) they remove the N-terminal leader peptide from its bacteriocin precursor by cleavage at a Gly-Gly bond and (ii) transport the mature bacteriocin across the cytoplasmic membrane. This represents a novel strategy for secretion of bacterial proteins . Many bacteria are known to regulate diverse physiological processes through this system, such as bioluminescence, regulation of sporulation, virulence factor expression, antibiotics production, competence for genetic transformation, and activation of biofilm formation .; GO: 0008234 cysteine-type peptidase activity, 0019534 toxin transporter activity, 0006810 transport, 0016020 membrane.
Probab=36.94  E-value=11  Score=17.18  Aligned_cols=49  Identities=16%  Similarity=0.302  Sum_probs=20.8

Q ss_pred             CCCEEEEEEEECC--------CCCCCCEEEECCCCCCC-----HHHHHHHHHHCCCEEEEECCC
Q ss_conf             8714746774022--------23789888971688747-----688899999869889998552
Q gi|254781101|r   23 PQGFVNGISIDSR--------SIAPQEAFFAIKGPHYD-----GHDFILHAVQKGAGLVVVNTD   73 (472)
Q Consensus        23 ~~~~i~~i~~dSr--------~v~~g~lFval~g~~~D-----Gh~~i~~A~~~Ga~~~i~~~~   73 (472)
                      |-.+|-||-=+-+        .+++++++||=|....-     =.+|.++=  =|.+.++...+
T Consensus        71 ~~PfIaHV~K~~K~pHYYVvy~~~kn~l~IaDPDpTvg~TK~sK~~F~~EW--TGi~i~i~p~~  132 (710)
T TIGR01193        71 PLPFIAHVIKEGKLPHYYVVYGVTKNSLLIADPDPTVGITKISKEDFEEEW--TGIAIFIAPTP  132 (710)
T ss_pred             CCCEEEEEEECCCCCCEEEEEEEECCEEEEECCCCCCCCEEECHHHHCCCC--CEEEEEEECCC
T ss_conf             997699998078521237897333366788268869762112378840326--40577763788


No 389
>KOG0479 consensus
Probab=36.89  E-value=27  Score=14.56  Aligned_cols=77  Identities=26%  Similarity=0.226  Sum_probs=44.7

Q ss_pred             CCCEEEECC---CCCCCHHHHHHHHHH----CCCEEEEECCCCCCCCCCCCCCEEEECCHHHHHHHHHHHHHHCCCCCEE
Q ss_conf             898889716---887476888999998----6988999855212455446972899599899999999999830699399
Q gi|254781101|r   39 PQEAFFAIK---GPHYDGHDFILHAVQ----KGAGLVVVNTDMVASIGSLSIPVFGVDDVLGALNKLAVAARLRSKATII  111 (472)
Q Consensus        39 ~g~lFval~---g~~~DGh~~i~~A~~----~Ga~~~i~~~~~~~~~~~~~~~~i~v~d~~~al~~la~~~~~~~~~~vI  111 (472)
                      ..++|=-|-   ...-.||+|+++|+-    -|.--.+-+-    ....-++.++.|.||-.|=.+|=++..+- .+.-|
T Consensus       288 ~kdiFdlLa~SLAPSI~GH~~vKkAillLLlGGvEk~L~NG----shlRGDINiLlvGDPSvAKSQLLRyVLnt-AplAI  362 (818)
T KOG0479         288 KKDIFDLLARSLAPSIYGHDYVKKAILLLLLGGVEKNLENG----SHLRGDINILLVGDPSVAKSQLLRYVLNT-APLAI  362 (818)
T ss_pred             CCCHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCEECCCCC----CEECCCEEEEEECCCHHHHHHHHHHHHHC-CCCCC
T ss_conf             17889998650376203579999999999854501205788----62225203898469527899999999841-54001


Q ss_pred             EEEC--CCCCC
Q ss_conf             9830--36542
Q gi|254781101|r  112 AITG--SVGKT  120 (472)
Q Consensus       112 ~ITG--TnGKT  120 (472)
                      +-||  |.|-.
T Consensus       363 ~TTGRGSSGVG  373 (818)
T KOG0479         363 ATTGRGSSGVG  373 (818)
T ss_pred             CCCCCCCCCCC
T ss_conf             03688877755


No 390
>PRK13768 GTPase; Provisional
Probab=36.75  E-value=15  Score=16.34  Aligned_cols=113  Identities=21%  Similarity=0.190  Sum_probs=52.3

Q ss_pred             EEEEEECCCCCCCCHHH-HHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHH
Q ss_conf             13310002565321012-57778741110268713885123541710589999999999864998999988038989985
Q gi|254781101|r  339 FTLIDESYNANPASMKA-AISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFHVLALKDA  417 (472)
Q Consensus       339 ~~iIDDsYNAnP~S~~a-al~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~~~~~~~~  417 (472)
                      +-++|-.+-.+|....+ .|.+++.+. +-.-..|.||.-+-=+++   +...++.+|..            +...+.+.
T Consensus       133 v~l~D~~~~~~~~~fiS~~L~a~s~m~-~l~lP~inVlsK~Dll~~---~~~~~i~~~~~------------D~~~l~~~  196 (253)
T PRK13768        133 VYLIDAVLAKDPSDFVSLLLLALSVQL-RLGLPQIPVLNKIDLLSE---EELERIRKWLE------------DPETLLEE  196 (253)
T ss_pred             EEEECHHHHCCHHHHHHHHHHHHHHHH-HCCCCEEEEEEHHHCCCH---HHHHHHHHHHC------------CHHHHHHH
T ss_conf             998450563788799999999999999-739997998676862783---77999999862------------99999999


Q ss_pred             CCCCCCEEEECCHHHHHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHHHC
Q ss_conf             113797999789899999999844789899997713254899999999850
Q gi|254781101|r  418 LPRSIHVHYSETMDGLFLFIQSSLVDGDVVVVKSSNSCGFYRLINLLLEEF  468 (472)
Q Consensus       418 ~~~~~~~~~~~~~e~a~~~l~~~~~~gdiVLiKGSr~~~le~iv~~L~~~~  468 (472)
                      +..... ...+-.+++...+.+....-..|-+....+.+|+.+..++.+-|
T Consensus       197 l~~~~~-~~~~l~~~l~~~l~e~~~~v~~ipvS~~~~eg~~~l~~~I~~~~  246 (253)
T PRK13768        197 LKLDKG-VQGDLAEELLSALEESGIPVRVIPVSAKTGEGFEELYALLQEVF  246 (253)
T ss_pred             HHCCCC-HHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             850611-58999999999999846666527756898787999999999996


No 391
>PRK13635 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=36.73  E-value=17  Score=15.85  Aligned_cols=27  Identities=30%  Similarity=0.357  Sum_probs=21.1

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++||.|.|  ||||...++.-++..
T Consensus        31 ~~GE~vaivG~nGsGKSTL~k~l~Gl~~p   59 (279)
T PRK13635         31 YEGEWVAIVGHNGSGKSTLAKLLNGLLLP   59 (279)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             79989999999996599999999728888


No 392
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR; InterPro: IPR010211   SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulphur cluster activates SoxR. The physiological role in Escherichia coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In Escherichia coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0005506 iron ion binding, 0006118 electron transport, 0006355 regulation of transcription DNA-dependent, 0006979 response to oxidative stress.
Probab=36.72  E-value=16  Score=16.00  Aligned_cols=28  Identities=18%  Similarity=0.310  Sum_probs=22.8

Q ss_pred             CCHHHHHHHHCCCCHHHHHHHHCCCCCCCC
Q ss_conf             210356765101210345543114766443
Q gi|254781101|r  297 LMTLGIVSILTADVDTAIKALSVFHPKEGR  326 (472)
Q Consensus       297 laAia~~~~lGi~~~~i~~~L~~~~~~~GR  326 (472)
                      .+.|-+|...|+|+++|.++|..+  |+||
T Consensus        47 Va~Ik~AQ~vGipL~~I~~ALa~L--P~gr   74 (142)
T TIGR01950        47 VAVIKVAQRVGIPLAEIAEALAEL--PEGR   74 (142)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHHHC--CCCC
T ss_conf             674332332589888999999734--6889


No 393
>PRK13231 nitrogenase reductase-like protein; Reviewed
Probab=36.65  E-value=15  Score=16.26  Aligned_cols=29  Identities=41%  Similarity=0.440  Sum_probs=20.8

Q ss_pred             CEEEEE--CCCCCCHHHHHHHHHHHHHHCCC
Q ss_conf             399983--03654201233467777520112
Q gi|254781101|r  109 TIIAIT--GSVGKTTTKEMLTIALSSIKKTY  137 (472)
Q Consensus       109 ~vI~IT--GTnGKTTt~~~l~~iL~~~~~~~  137 (472)
                      +-|||-  |-.|||||+.-|+..|....+|.
T Consensus         3 ~~iAiyGKGGIGKSTt~~NlaaalA~g~rVl   33 (264)
T PRK13231          3 KKIAIYGKGGIGKSTTVSNMAAAYSSDNSTL   33 (264)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHCCCCEE
T ss_conf             2899978985478889999999998799779


No 394
>cd03268 ABC_BcrA_bacitracin_resist The BcrA subfamily represents ABC transporters involved in peptide antibiotic resistance.  Bacitracin is a dodecapeptide antibiotic produced by B. licheniformis and B. subtilis.  The synthesis of bacitracin is non-ribosomally catalyzed by a multienzyme complex BcrABC.  Bacitracin has potent antibiotic activity against gram-positive bacteria.  The inhibition of peptidoglycan biosynthesis is the best characterized bacterial effect of bacitracin.  The bacitracin resistance of B. licheniformis is mediated by the ABC transporter Bcr which is composed of two identical BcrA ATP-binding subunits and one each of the integral membrane proteins, BcrB and BcrC.  B. subtilis cells carrying bcr genes on high-copy number plasmids develop collateral detergent sensitivity, a similar phenomenon in human cells with overexpressed multi-drug resistance P-glycoprotein.
Probab=36.64  E-value=17  Score=15.89  Aligned_cols=28  Identities=29%  Similarity=0.322  Sum_probs=21.9

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHHH
Q ss_conf             699399983036--5420123346777752
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSSI  133 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~~  133 (472)
                      .++.++|+-|-|  ||||+-.++.-++...
T Consensus        24 ~~Gei~gllG~NGaGKSTLl~~i~Gl~~p~   53 (208)
T cd03268          24 KKGEIYGFLGPNGAGKTTTMKIILGLIKPD   53 (208)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCCC
T ss_conf             698199999999999999999995783789


No 395
>COG4917 EutP Ethanolamine utilization protein [Amino acid transport and metabolism]
Probab=36.52  E-value=27  Score=14.52  Aligned_cols=53  Identities=23%  Similarity=0.129  Sum_probs=25.3

Q ss_pred             CCCCCHHHHHCCCCCCCCC---CCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             2322144430156644332---1121223232202555312101234445788886543310
Q gi|254781101|r  156 MPVDVDFGIFELGMSHLGE---IRFLTHLVRPHIAVITTIAPAHLSNFSGIEEIASAKAEIF  214 (472)
Q Consensus       156 ~~~~~~~~V~E~g~~~~ge---i~~L~~i~~P~iaiiTNI~~dHld~~~s~e~i~~~K~~i~  214 (472)
                      +..+.++.++=-+++++-.   -..++-..+|.||++|-+...      ..++|...|.-|.
T Consensus        61 t~~dadvi~~v~~and~~s~f~p~f~~~~~k~vIgvVTK~DLa------ed~dI~~~~~~L~  116 (148)
T COG4917          61 TLQDADVIIYVHAANDPESRFPPGFLDIGVKKVIGVVTKADLA------EDADISLVKRWLR  116 (148)
T ss_pred             HHHCCCEEEEEECCCCCCCCCCCCCCCCCCCCEEEEEECCCCC------CHHHHHHHHHHHH
T ss_conf             7611332554300268444488421344666558998603466------4676899999999


No 396
>PRK13641 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=36.39  E-value=17  Score=15.89  Aligned_cols=31  Identities=26%  Similarity=0.386  Sum_probs=22.8

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHH-HHHCC
Q ss_conf             699399983036--54201233467777-52011
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALS-SIKKT  136 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~-~~~~~  136 (472)
                      .++.++||.|-|  ||||.-.++.-++. ..|.+
T Consensus        31 ~~Ge~~~iiG~nGsGKSTLl~~l~Gll~P~sG~V   64 (286)
T PRK13641         31 EDGSFVALIGHTGSGKSTLMQHFNALLKPSSGKI   64 (286)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCCCCEEE
T ss_conf             6999999999998399999999965989885499


No 397
>PRK13638 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=36.31  E-value=17  Score=15.87  Aligned_cols=27  Identities=26%  Similarity=0.268  Sum_probs=21.1

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++||.|-|  ||||+-.++.-+++.
T Consensus        25 ~~Gei~~liGpNGaGKSTLlk~l~Gl~~p   53 (271)
T PRK13638         25 SLSPVTGLVGANGCGKSTLFMNLSGLLRP   53 (271)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             38979999999998099999999668888


No 398
>PRK11147 ABC transporter ATPase component; Reviewed
Probab=36.12  E-value=18  Score=15.67  Aligned_cols=34  Identities=12%  Similarity=0.305  Sum_probs=22.0

Q ss_pred             CEEEEEEEECCCCCCCCEEEECCCCCCCHHHHHHHHHH
Q ss_conf             14746774022237898889716887476888999998
Q gi|254781101|r   25 GFVNGISIDSRSIAPQEAFFAIKGPHYDGHDFILHAVQ   62 (472)
Q Consensus        25 ~~i~~i~~dSr~v~~g~lFval~g~~~DGh~~i~~A~~   62 (472)
                      ..++++++   .|.+|+. +||-|.+--|-.=+-.++.
T Consensus        17 ~ll~~vsl---~I~~Ge~-vgLVG~NGsGKSTLl~iL~   50 (632)
T PRK11147         17 PLLDNAEL---HIEDNER-VCLVGRNGAGKSTLMKILS   50 (632)
T ss_pred             EEEECCEE---EECCCCE-EEEECCCCCHHHHHHHHHH
T ss_conf             68986259---9989989-9999999987999999983


No 399
>cd03224 ABC_TM1139_LivF_branched LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids.  The  E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a heterodimer of six-helix TM domains (LivM and LivH), and one of two alternative soluble periplasmic substrate binding proteins (LivK or LivJ).  ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.
Probab=36.04  E-value=17  Score=15.87  Aligned_cols=27  Identities=30%  Similarity=0.378  Sum_probs=20.9

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++|+.|-|  ||||+-.++.-+++.
T Consensus        24 ~~Gei~~liG~nGaGKSTLl~~i~Gl~~p   52 (222)
T cd03224          24 PEGEIVALLGRNGAGKTTLLKTIMGLLPP   52 (222)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             89989999999998599999999779889


No 400
>PRK11614 livF leucine/isoleucine/valine transporter ATP-binding subunit; Provisional
Probab=35.98  E-value=17  Score=15.90  Aligned_cols=26  Identities=27%  Similarity=0.314  Sum_probs=19.6

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHH
Q ss_conf             699399983036--54201233467777
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALS  131 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~  131 (472)
                      .++.++|+.|.|  ||||+-.++.-+++
T Consensus        29 ~~Gei~~liG~NGaGKSTLl~~i~G~~~   56 (237)
T PRK11614         29 NQGEIVTLIGANGAGKTTLLGTLCGDPR   56 (237)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCC
T ss_conf             6997999987999759999999967998


No 401
>pfam04851 ResIII Type III restriction enzyme, res subunit.
Probab=35.95  E-value=28  Score=14.46  Aligned_cols=24  Identities=38%  Similarity=0.461  Sum_probs=12.4

Q ss_pred             HCCCCCEEEEECCCCCCHHHHHHHH
Q ss_conf             3069939998303654201233467
Q gi|254781101|r  104 LRSKATIIAITGSVGKTTTKEMLTI  128 (472)
Q Consensus       104 ~~~~~~vI~ITGTnGKTTt~~~l~~  128 (472)
                      ++..+-+++-||| |||.+...+..
T Consensus        17 ~~~~~~i~~pTGs-GKT~~~~~~i~   40 (103)
T pfam04851        17 EKKRGLIVMATGS-GKTLTAAKLIA   40 (103)
T ss_pred             HCCCEEEEECCCC-CHHHHHHHHHH
T ss_conf             6398699958999-87999999999


No 402
>cd03293 ABC_NrtD_SsuB_transporters NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively.  ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.  The nucleotide binding domain shows the highest similarity between all members of the family.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=35.64  E-value=18  Score=15.77  Aligned_cols=27  Identities=19%  Similarity=0.316  Sum_probs=21.4

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++||.|-|  ||||.-.+++-++..
T Consensus        28 ~~Ge~~~iiGpsGsGKSTLl~~i~Gl~~p   56 (220)
T cd03293          28 EEGEFVALVGPSGCGKSTLLRIIAGLERP   56 (220)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             79989999999995799999999759998


No 403
>TIGR03522 GldA_ABC_ATP gliding motility-associated ABC transporter ATP-binding subunit GldA. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldA is an ABC transporter ATP-binding protein (pfam00005) linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Knockouts of GldA abolish the gliding phenotype. 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=35.64  E-value=17  Score=15.81  Aligned_cols=28  Identities=32%  Similarity=0.406  Sum_probs=22.2

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHHH
Q ss_conf             699399983036--5420123346777752
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSSI  133 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~~  133 (472)
                      .++.++|+-|-|  ||||+-.|+.-++...
T Consensus        26 ~~Gei~gllGpNGAGKTTl~~~l~Gl~~p~   55 (301)
T TIGR03522        26 QKGRIVGFLGPNGAGKSTTMKIITGYLPPD   55 (301)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCCC
T ss_conf             598199999999981999999996795689


No 404
>TIGR00041 DTMP_kinase thymidylate kinase; InterPro: IPR000062   Thymidylate kinase (2.7.4.9 from EC; dTMP kinase) catalyzes the phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP) in the presence of ATP and magnesium:   ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate    Thymidylate kinase is an ubiquitous enzyme of about 25 Kd and is important in the dTTP synthesis pathway for DNA synthesis. The function of dTMP kinase in eukaryotes comes from the study of a cell cycle mutant, cdc8, in Saccharomyces cerevisiae Saccharomyces cerevisiae. Structural and functional analyses suggest that the cDNA codes for authentic human dTMP kinase. The mRNA levels and enzyme activities corresponded to cell cycle progression and cell growth stages. ; GO: 0004798 thymidylate kinase activity, 0005524 ATP binding, 0006233 dTDP biosynthetic process, 0006235 dTTP biosynthetic process.
Probab=35.55  E-value=13  Score=16.66  Aligned_cols=23  Identities=30%  Similarity=0.265  Sum_probs=17.8

Q ss_pred             CCCCHHHHHHHHHHHH-HH-CCCCC
Q ss_conf             6542012334677775-20-11222
Q gi|254781101|r  117 VGKTTTKEMLTIALSS-IK-KTYAC  139 (472)
Q Consensus       117 nGKTTt~~~l~~iL~~-~~-~~~~t  139 (472)
                      .||||..+.+...|.. .| .++.|
T Consensus        13 aGKTT~~~~l~~~l~~l~g~~~~~t   37 (211)
T TIGR00041        13 AGKTTQLNLLKKLLKELEGYKVLFT   37 (211)
T ss_pred             CCHHHHHHHHHHHHHHHCCCEEEEE
T ss_conf             7589999999999775138347887


No 405
>PRK07560 elongation factor EF-2; Reviewed
Probab=35.43  E-value=28  Score=14.41  Aligned_cols=13  Identities=8%  Similarity=0.171  Sum_probs=5.7

Q ss_pred             CCCHHHHHHHHHH
Q ss_conf             3210125777874
Q gi|254781101|r  350 PASMKAAISVLSQ  362 (472)
Q Consensus       350 P~S~~aal~~l~~  362 (472)
                      .+.+..+|+-|..
T Consensus       404 ~~kL~~aL~~L~~  416 (730)
T PRK07560        404 LPKLIEVLRQLAK  416 (730)
T ss_pred             HHHHHHHHHHHHH
T ss_conf             9999999999884


No 406
>PRK12367 short chain dehydrogenase; Provisional
Probab=35.28  E-value=29  Score=14.39  Aligned_cols=33  Identities=24%  Similarity=0.247  Sum_probs=19.4

Q ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             0699399983036542012334677775201122
Q gi|254781101|r  105 RSKATIIAITGSVGKTTTKEMLTIALSSIKKTYA  138 (472)
Q Consensus       105 ~~~~~vI~ITGTnGKTTt~~~l~~iL~~~~~~~~  138 (472)
                      .++.+.|||||-+|= -=++++.+..+...+|.+
T Consensus        14 ~~kgKtIgITGAsGa-LG~AL~k~f~~~GakVIa   46 (250)
T PRK12367         14 RWNGKRIGITGASGA-LGKALTKLFRAKGAKVIG   46 (250)
T ss_pred             CCCCCEEEEECCCCH-HHHHHHHHHHHCCCEEEE
T ss_conf             638987999678738-999999999988998999


No 407
>COG1102 Cmk Cytidylate kinase [Nucleotide transport and metabolism]
Probab=35.27  E-value=24  Score=14.94  Aligned_cols=22  Identities=41%  Similarity=0.531  Sum_probs=17.1

Q ss_pred             EEEEECC--CCCCHHHHHHHHHHH
Q ss_conf             9998303--654201233467777
Q gi|254781101|r  110 IIAITGS--VGKTTTKEMLTIALS  131 (472)
Q Consensus       110 vI~ITGT--nGKTTt~~~l~~iL~  131 (472)
                      +|.|.|-  .||||+..+|+..|.
T Consensus         2 ~ItIsG~pGsG~TTva~~lAe~~g   25 (179)
T COG1102           2 VITISGLPGSGKTTVARELAEHLG   25 (179)
T ss_pred             EEEECCCCCCCCHHHHHHHHHHHC
T ss_conf             799617999970279999999829


No 408
>PRK13636 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=35.26  E-value=18  Score=15.68  Aligned_cols=26  Identities=35%  Similarity=0.362  Sum_probs=21.0

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHH
Q ss_conf             699399983036--54201233467777
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALS  131 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~  131 (472)
                      .++.++||-|.|  ||||.-.++.-++.
T Consensus        30 ~~Ge~~aiiG~NGaGKSTLl~~i~Gll~   57 (285)
T PRK13636         30 KKGEVTAILGGNGAGKSTLFQNLNGILK   57 (285)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCC
T ss_conf             7998999999999809999999965988


No 409
>cd03221 ABCF_EF-3 ABCF_EF-3  Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth.  EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated release of the deacylated tRNA from the E site.  The reaction requires ATP hydrolysis.  EF-3 contains two ATP nucleotide binding sequence (NBS) motifs.  NBSI is sufficient for the intrinsic ATPase activity. NBSII is essential for the ribosome-stimulated functions.
Probab=35.09  E-value=18  Score=15.78  Aligned_cols=26  Identities=23%  Similarity=0.353  Sum_probs=18.1

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHH
Q ss_conf             699399983036--54201233467777
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALS  131 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~  131 (472)
                      .+..++|+.|-|  ||||.-.++.-.+.
T Consensus        24 ~~ge~~~l~G~NGsGKTTl~~~l~G~~~   51 (144)
T cd03221          24 NPGDRIGLVGRNGAGKSTLLKLIAGELE   51 (144)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCC
T ss_conf             7999999998999849999999848988


No 410
>COG0003 ArsA Predicted ATPase involved in chromosome partitioning [Cell division and chromosome partitioning]
Probab=35.09  E-value=17  Score=15.85  Aligned_cols=27  Identities=37%  Similarity=0.485  Sum_probs=20.3

Q ss_pred             CEEEEE--CCCCCCHHHHHHHHHHHHHHC
Q ss_conf             399983--036542012334677775201
Q gi|254781101|r  109 TIIAIT--GSVGKTTTKEMLTIALSSIKK  135 (472)
Q Consensus       109 ~vI~IT--GTnGKTTt~~~l~~iL~~~~~  135 (472)
                      +++-+|  |-.||||++.-++--|.+.|+
T Consensus         3 riv~f~GKGGVGKTT~aaA~A~~lA~~g~   31 (322)
T COG0003           3 RIVFFTGKGGVGKTTIAAATAVKLAESGK   31 (322)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCC
T ss_conf             79999368854589999999999997599


No 411
>PRK13648 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=34.94  E-value=19  Score=15.53  Aligned_cols=27  Identities=22%  Similarity=0.261  Sum_probs=20.5

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++||.|.|  ||||...++.-++..
T Consensus        33 ~~Ge~vaiiG~sGsGKSTLl~ll~Gl~~p   61 (269)
T PRK13648         33 PKGQWTSIVGHNGSGKSTIAKLMIGIEKV   61 (269)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             59989999999999799999999649799


No 412
>cd05213 NAD_bind_Glutamyl_tRNA_reduct NADP-binding domain of glutamyl-tRNA reductase. Glutamyl-tRNA reductase catalyzes the conversion of glutamyl-tRNA to glutamate-1-semialdehyde, initiating the synthesis of tetrapyrrole. Whereas tRNAs are generally associated with peptide bond formation in protein translation, here the tRNA activates glutamate in the initiation of tetrapyrrole biosynthesis in archaea, plants and many bacteria. In the first step, activated glutamate is reduced to glutamate-1-semi-aldehyde via the NADPH dependent glutamyl-tRNA reductase. Glutamyl-tRNA reductase forms a V-shaped dimer. Each monomer has 3 domains: an N-terminal catalytic domain, a classic nucleotide binding domain, and a C-terminal dimerization domain. Although the representative structure 1GPJ lacks a bound NADPH, a theoretical binding pocket has been described. (PMID 11172694). Amino acid dehydrogenase (DH)-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, 
Probab=34.93  E-value=29  Score=14.35  Aligned_cols=89  Identities=19%  Similarity=0.289  Sum_probs=48.4

Q ss_pred             CCCCCHHH-HHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCC---HHHHHHHCCCCCC
Q ss_conf             65321012-5777874111026871388512354171058999999999986499899998803---8989985113797
Q gi|254781101|r  348 ANPASMKA-AISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFH---VLALKDALPRSIH  423 (472)
Q Consensus       348 AnP~S~~a-al~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~---~~~~~~~~~~~~~  423 (472)
                      .+|.|+-. |++........-.+++++|+|.    |+-.    +.+.+.+.+.++..+++..-.   +..+++.+  +..
T Consensus       156 ~~~vSv~~~av~~a~~~~~~l~~~~vLviGa----Gem~----~l~~~~L~~~g~~~i~v~nRt~~ra~~la~~~--g~~  225 (311)
T cd05213         156 RGAVSISSAAVELAEKIFGNLKGKKVLVIGA----GEMG----ELAAKHLAAKGVAEITIANRTYERAEELAKEL--GGN  225 (311)
T ss_pred             CCCCCHHHHHHHHHHHHHCCCCCCEEEEECC----CHHH----HHHHHHHHHCCCCEEEEECCCHHHHHHHHHHC--CCE
T ss_conf             8988899999999998718721167999868----7999----99999999659982599768678999999974--989


Q ss_pred             EEEECCHHHHHHHHHHHCCCCCEEEEE-CCC
Q ss_conf             999789899999999844789899997-713
Q gi|254781101|r  424 VHYSETMDGLFLFIQSSLVDGDVVVVK-SSN  453 (472)
Q Consensus       424 ~~~~~~~e~a~~~l~~~~~~gdiVLiK-GSr  453 (472)
                        .. ..++    +.+.+..-|+|... ||-
T Consensus       226 --~~-~~~~----l~~~l~~~DvvisaT~s~  249 (311)
T cd05213         226 --AV-PLDE----LLELLNEADVVISATGAP  249 (311)
T ss_pred             --EE-CHHH----HHHHHHHCCEEEEECCCC
T ss_conf             --97-2999----999997689999927999


No 413
>KOG0927 consensus
Probab=34.92  E-value=29  Score=14.35  Aligned_cols=38  Identities=39%  Similarity=0.435  Sum_probs=21.3

Q ss_pred             ECCHHHHHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHHHCCCC
Q ss_conf             789899999999844789899997713254899999999850577
Q gi|254781101|r  427 SETMDGLFLFIQSSLVDGDVVVVKSSNSCGFYRLINLLLEEFPAI  471 (472)
Q Consensus       427 ~~~~e~a~~~l~~~~~~gdiVLiKGSr~~~le~iv~~L~~~~~~~  471 (472)
                      .++.+.+.+++.+  -+|.+||+  |+-+   +++.+.-++.|.+
T Consensus       542 i~tid~laeaiNe--~~Ggvv~v--SHDf---rlI~qVaeEi~~c  579 (614)
T KOG0927         542 IETIDALAEAINE--FPGGVVLV--SHDF---RLISQVAEEIWVC  579 (614)
T ss_pred             CHHHHHHHHHHHC--CCCCEEEE--ECHH---HHHHHHHHHHHHH
T ss_conf             5069999999852--67851553--2123---4899887776701


No 414
>PRK11264 putative amino-acid ABC transporter ATP-binding protein YecC; Provisional
Probab=34.76  E-value=19  Score=15.60  Aligned_cols=26  Identities=27%  Similarity=0.400  Sum_probs=19.9

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHH
Q ss_conf             699399983036--54201233467777
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALS  131 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~  131 (472)
                      .++.++||.|.|  ||||.-.++.-++.
T Consensus        25 ~~Ge~~aliG~sGsGKSTLl~~l~gl~~   52 (248)
T PRK11264         25 KPGEVVAIIGPSGSGKTTLLRCINLLEQ   52 (248)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCC
T ss_conf             7998999999999809999999975899


No 415
>PRK10908 cell division protein FtsE; Provisional
Probab=34.61  E-value=17  Score=15.86  Aligned_cols=27  Identities=19%  Similarity=0.230  Sum_probs=21.6

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++||.|-|  ||||+-.++.-++..
T Consensus        26 ~~Ge~~~liG~nGsGKSTLl~~i~Gl~~p   54 (222)
T PRK10908         26 RPGEMAFLTGHSGAGKSTLLKLICGIERP   54 (222)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             69989999999980799999999659999


No 416
>KOG0447 consensus
Probab=34.59  E-value=22  Score=15.12  Aligned_cols=23  Identities=35%  Similarity=0.520  Sum_probs=15.0

Q ss_pred             CCCEEEEEC--CCCCCHHHHHHHHH
Q ss_conf             993999830--36542012334677
Q gi|254781101|r  107 KATIIAITG--SVGKTTTKEMLTIA  129 (472)
Q Consensus       107 ~~~vI~ITG--TnGKTTt~~~l~~i  129 (472)
                      +.|.|-|-|  |.||||+-+|+++.
T Consensus       307 hLPRVVVVGDQSaGKTSVLEmiAqA  331 (980)
T KOG0447         307 HLPRVVVVGDQSAGKTSVLEMIAQA  331 (980)
T ss_pred             CCCEEEEECCCCCCCHHHHHHHHHH
T ss_conf             6862799756666622899999874


No 417
>PRK00062 glutamate-1-semialdehyde aminotransferase; Provisional
Probab=34.56  E-value=20  Score=15.40  Aligned_cols=50  Identities=20%  Similarity=0.309  Sum_probs=28.9

Q ss_pred             ECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             00256532101257778741110268713885123541710589999999999864998
Q gi|254781101|r  344 ESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNIS  402 (472)
Q Consensus       344 DsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d  402 (472)
                      -+|+.||.||.+++.+|+.+....      ++..+.++|++   +.+.+-+.+.+.++.
T Consensus       298 gTf~gnpla~AAa~a~L~~l~~~~------l~~~~~~~G~~---l~~~l~~~~~~~~~~  347 (429)
T PRK00062        298 GTLSGNPLAMAAGLATLRLLDQEG------VYETLDALTDR---LAEGLKEAAEKAGIP  347 (429)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHCC------HHHHHHHHHHH---HHHHHHHHHHHCCCC
T ss_conf             878888799999999999997357------99999999999---999999999877998


No 418
>cd03244 ABCC_MRP_domain2 Domain 2 of the ABC subfamily C.  This family is also known as MRP (mulrtidrug resisitance-associated protein).  Some of the MRP members have five additional transmembrane segments in their N-terminus, but the function of these additional membrane-spanning domains is not clear.  The MRP was found in the multidrug-resistance lung cancer cell in which p-glycoprotein was not overexpressed.  MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.
Probab=34.55  E-value=20  Score=15.46  Aligned_cols=26  Identities=19%  Similarity=0.231  Sum_probs=19.8

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHH
Q ss_conf             699399983036--54201233467777
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALS  131 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~  131 (472)
                      .++.++||.|-|  ||||.-.++.-++.
T Consensus        28 ~~Ge~v~ivG~sGsGKSTLl~ll~gl~~   55 (221)
T cd03244          28 KPGEKVGIVGRTGSGKSSLLLALFRLVE   55 (221)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCC
T ss_conf             6998999999999989999999967971


No 419
>pfam01784 NIF3 NIF3 (NGG1p interacting factor 3). This family contains several NIF3 (NGG1p interacting factor 3) protein homologues. NIF3 interacts with the yeast transcriptional coactivator NGG1p which is part of the ADA complex, the exact function of this interaction is unknown.
Probab=34.51  E-value=29  Score=14.31  Aligned_cols=30  Identities=23%  Similarity=0.342  Sum_probs=15.5

Q ss_pred             CCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
Q ss_conf             71388512354171058999999999986499899998803
Q gi|254781101|r  370 RRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFH  410 (472)
Q Consensus       370 r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~  410 (472)
                      ++++|.|     |..+.     +.+.+...++| +|+.|+-
T Consensus       171 ~~Vai~~-----GsG~~-----~i~~a~~~gaD-~~ITGd~  200 (238)
T pfam01784       171 KKVAICG-----GSGSS-----LIEEAKAKGAD-LLITGEL  200 (238)
T ss_pred             EEEEEEC-----CCCHH-----HHHHHHHCCCC-EEEECCC
T ss_conf             6899974-----66677-----89998757996-9997688


No 420
>COG4167 SapF ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]
Probab=34.43  E-value=30  Score=14.30  Aligned_cols=48  Identities=21%  Similarity=0.257  Sum_probs=28.8

Q ss_pred             CEEEECCHHHHHHHHHHHHHHC-C-----------CCCEEEEECCC--CCCHHHHHHHHHHH
Q ss_conf             2899599899999999999830-6-----------99399983036--54201233467777
Q gi|254781101|r   84 PVFGVDDVLGALNKLAVAARLR-S-----------KATIIAITGSV--GKTTTKEMLTIALS  131 (472)
Q Consensus        84 ~~i~v~d~~~al~~la~~~~~~-~-----------~~~vI~ITGTn--GKTTt~~~l~~iL~  131 (472)
                      +.+.|+|.-+.+..-+..+|.+ +           ....+||-|-|  ||+|...|++-+..
T Consensus         3 ~LLeV~nLsKtF~~~~~lf~r~~~~AV~~vSFtL~~~QTlaiIG~NGSGKSTLakMlaGmi~   64 (267)
T COG4167           3 TLLEVRNLSKTFRYRTGLFRRQTVEAVKPVSFTLREGQTLAIIGENGSGKSTLAKMLAGMIE   64 (267)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEECCCCEEEEECCCCCCHHHHHHHHHCCCC
T ss_conf             12221433443333354555644520041578960796799982699747589999835558


No 421
>cd03245 ABCC_bacteriocin_exporters ABC-type bacteriocin exporters. Many non-lantibiotic bacteriocins of lactic acid bacteria are produced as precursors which have N-terminal leader peptides that share similarities in amino acid sequence and contain a conserved processing site of two glycine residues in positions -1 and -2.  A dedicated ATP-binding cassette (ABC) transporter is responsible for the proteolytic cleavage of the leader peptides and subsequent translocation of the bacteriocins across the cytoplasmic membrane.
Probab=34.37  E-value=21  Score=15.29  Aligned_cols=26  Identities=31%  Similarity=0.383  Sum_probs=19.8

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHH
Q ss_conf             699399983036--54201233467777
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALS  131 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~  131 (472)
                      .++..|||.|.+  ||||...++.-++.
T Consensus        28 ~~G~~v~ivG~sGsGKSTLl~ll~gl~~   55 (220)
T cd03245          28 RAGEKVAIIGRVGSGKSTLLKLLAGLYK   55 (220)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCC
T ss_conf             7999999999999859999999967254


No 422
>cd03233 ABC_PDR_domain1 The pleiotropic drug resistance (PDR) family of ATP-binding cassette (ABC) transporters.  PDR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes.  This PDR subfamily represents domain I of its (ABC-IM)2 organization.  ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules.  The nucleotide-binding domain shows the highest similarity between all members of the family.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=34.34  E-value=19  Score=15.62  Aligned_cols=26  Identities=15%  Similarity=0.203  Sum_probs=19.5

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHH
Q ss_conf             699399983036--54201233467777
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALS  131 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~  131 (472)
                      .++.++||.|.|  ||||.-.+|+-++.
T Consensus        31 ~~Gei~~llG~nGsGKSTLl~~l~G~~~   58 (202)
T cd03233          31 KPGEMVLVLGRPGSGCSTLLKALANRTE   58 (202)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHCCCC
T ss_conf             0984999998999988999999837878


No 423
>cd03369 ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-type transporter 1).  NFT1 belongs to the MRP (mulrtidrug resisitance-associated protein) family of ABC transporters.  Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear.  The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed.  MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions such as glutathione, glucuronate, and sulfate.
Probab=34.29  E-value=26  Score=14.71  Aligned_cols=27  Identities=30%  Similarity=0.276  Sum_probs=20.3

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++..|||.|-|  ||||.-.++.-++..
T Consensus        32 ~~Ge~v~ivG~sGsGKSTLl~ll~g~~~p   60 (207)
T cd03369          32 KAGEKIGIVGRTGAGKSTLILALFRFLEA   60 (207)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHCCC
T ss_conf             69999999999998799999999987288


No 424
>PRK03743 pdxA 4-hydroxythreonine-4-phosphate dehydrogenase; Validated
Probab=34.29  E-value=30  Score=14.29  Aligned_cols=20  Identities=30%  Similarity=0.451  Sum_probs=13.7

Q ss_pred             CCCCCCHHHHHHHHHHHHHC
Q ss_conf             56532101257778741110
Q gi|254781101|r  347 NANPASMKAAISVLSQISPH  366 (472)
Q Consensus       347 NAnP~S~~aal~~l~~~~~~  366 (472)
                      .|||.||.+|++...++..+
T Consensus       310 ~A~~~s~~~Ai~~a~~~a~~  329 (333)
T PRK03743        310 IASSVSMEEAIKLAAKYAPK  329 (333)
T ss_pred             CCCHHHHHHHHHHHHHHHHH
T ss_conf             89969999999999999987


No 425
>PRK13946 shikimate kinase; Provisional
Probab=34.25  E-value=18  Score=15.73  Aligned_cols=27  Identities=22%  Similarity=0.433  Sum_probs=17.9

Q ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHHH
Q ss_conf             0699399983036542012334677775
Q gi|254781101|r  105 RSKATIIAITGSVGKTTTKEMLTIALSS  132 (472)
Q Consensus       105 ~~~~~vI~ITGTnGKTTt~~~l~~iL~~  132 (472)
                      +-+.-+||..| .||||+-..|+..|.-
T Consensus        20 kknIvLIG~mG-sGKStvGk~LA~~L~~   46 (195)
T PRK13946         20 KRTVVLVGLMG-AGKSTVGRRLATMLGL   46 (195)
T ss_pred             CCCEEEECCCC-CCHHHHHHHHHHHHCC
T ss_conf             99589989999-9889999999999797


No 426
>PRK13695 putative NTPase; Provisional
Probab=34.18  E-value=26  Score=14.64  Aligned_cols=25  Identities=40%  Similarity=0.340  Sum_probs=14.9

Q ss_pred             EEEEECC--CCCCHHHHHHHHHHHHHH
Q ss_conf             9998303--654201233467777520
Q gi|254781101|r  110 IIAITGS--VGKTTTKEMLTIALSSIK  134 (472)
Q Consensus       110 vI~ITGT--nGKTTt~~~l~~iL~~~~  134 (472)
                      -|.|||-  .||||...=+...|+..+
T Consensus         5 kI~iTG~PGvGKTTli~Kv~~~L~~~g   31 (174)
T PRK13695          5 RIGITGMPGVGKTTLVLKIAELLAREG   31 (174)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCC
T ss_conf             999878999889999999999986369


No 427
>cd03379 beta_CA_cladeD Carbonic anhydrases (CA) are zinc-containing enzymes that catalyze the reversible hydration of carbon dioxide in a two-step mechanism in which the nucleophilic attack of a zinc-bound hydroxide ion on carbon dioxide is followed by the regeneration of an active site by ionization of the zinc-bound water molecule and removal of a proton from the active site. CAs are ubiquitous enzymes involved in fundamental processes like photosynthesis, respiration, pH homeostasis and ion transport. There are three evolutionarily distinct families of CAs (the alpha-, beta-, and gamma-CAs) which show no significant sequence identity or structural similarity.  Within the beta-CA family there are four evolutionarily distinct clades (A through D). The beta-CAs are multimeric enzymes (forming dimers,tetramers,hexamers and octamers) which are present in higher plants, algae, fungi, archaea and prokaryotes.
Probab=34.18  E-value=22  Score=15.13  Aligned_cols=15  Identities=20%  Similarity=0.251  Sum_probs=11.1

Q ss_pred             EEECCC-------CCCCCEEEE
Q ss_conf             740222-------378988897
Q gi|254781101|r   31 SIDSRS-------IAPQEAFFA   45 (472)
Q Consensus        31 ~~dSr~-------v~~g~lFva   45 (472)
                      |.|||-       .+||++|+.
T Consensus        10 C~DSRv~p~~i~~~~pGdlfv~   31 (142)
T cd03379          10 CMDARLDPEKALGLKLGDAKVI   31 (142)
T ss_pred             ECCCCCCHHHHCCCCCCCEEEE
T ss_conf             6254879899709998747999


No 428
>TIGR01394 TypA_BipA GTP-binding protein TypA; InterPro: IPR006298   This bacterial (and Arabidopsis) protein, termed TypA or BipA, is a GTP-binding protein. It is phosphorylated on a tyrosine residue under some cellular conditions. Mutants show altered regulation of some pathways, but the precise function is unknown.; GO: 0005525 GTP binding, 0005622 intracellular.
Probab=34.16  E-value=19  Score=15.53  Aligned_cols=60  Identities=20%  Similarity=0.182  Sum_probs=35.4

Q ss_pred             HHHHHHCCCEEEEECCCCCCCCCCCCCCEEEECCHHHHHHHHHHHHHHCCCCCEE---EEECCCCCC
Q ss_conf             9999986988999855212455446972899599899999999999830699399---983036542
Q gi|254781101|r   57 ILHAVQKGAGLVVVNTDMVASIGSLSIPVFGVDDVLGALNKLAVAARLRSKATII---AITGSVGKT  120 (472)
Q Consensus        57 i~~A~~~Ga~~~i~~~~~~~~~~~~~~~~i~v~d~~~al~~la~~~~~~~~~~vI---~ITGTnGKT  120 (472)
                      +.+|++.|=.-|||=.....+   ...|--+|+-++.-+.+|++. -+|.+.|+|   |..|....+
T Consensus       115 L~KAL~~gLkPIVViNKiDrp---~ARP~eV~d~vFDLF~~LgA~-deQLDFP~vYASa~~G~A~l~  177 (609)
T TIGR01394       115 LKKALELGLKPIVVINKIDRP---SARPDEVVDEVFDLFIELGAD-DEQLDFPIVYASARAGWASLD  177 (609)
T ss_pred             HHHHHHCCCCEEEEECCCCCC---CCCHHHHHHHHHHHHHHCCCC-CCCCCHHHHHHHHCCCCCCCC
T ss_conf             999995689369997134788---788378875787888853888-001012567665236720144


No 429
>PRK01506 consensus
Probab=34.12  E-value=30  Score=14.27  Aligned_cols=91  Identities=16%  Similarity=0.117  Sum_probs=41.2

Q ss_pred             CEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHHH
Q ss_conf             11331000256532101257778741110268713885123541710589999999999864998999988038989985
Q gi|254781101|r  338 FFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFHVLALKDA  417 (472)
Q Consensus       338 ~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~~~~~~~~  417 (472)
                      .+.|+||== .+-.+|..|.+.|+..   +. ++|.+...=   |-.+..-    .+.+...+++.+++.-.-..  -+.
T Consensus       219 ~vIIVDDiI-~TGgTl~~aa~~Lk~~---GA-~~V~~~~TH---glfs~~A----~~rl~~s~i~~iv~TnTip~--p~~  284 (317)
T PRK01506        219 TAILIDDII-DTAGTITLAANALVEN---GA-SEVYACCTH---PVLSGPA----IERIQNSKIKELVVTNSIVL--PEE  284 (317)
T ss_pred             EEEEECCHH-HCCCHHHHHHHHHHHC---CC-CEEEEEEEC---CCCCCHH----HHHHHCCCCCEEEEECCCCC--CHH
T ss_conf             278751322-1350599999999865---99-758999977---0068179----99986189988999388448--612


Q ss_pred             CCCCCCEEEECCHHHHHHHHHHHCCCC
Q ss_conf             113797999789899999999844789
Q gi|254781101|r  418 LPRSIHVHYSETMDGLFLFIQSSLVDG  444 (472)
Q Consensus       418 ~~~~~~~~~~~~~e~a~~~l~~~~~~g  444 (472)
                       +...++... +...++..+...+..|
T Consensus       285 -~~~~kl~vl-sva~llAeaI~ri~~~  309 (317)
T PRK01506        285 -KKIDKVHEL-SVAPLIAEAIIRVYEE  309 (317)
T ss_pred             -HCCCCCEEE-EHHHHHHHHHHHHHCC
T ss_conf             -337983998-8499999999998679


No 430
>PRK13643 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=34.10  E-value=20  Score=15.43  Aligned_cols=27  Identities=30%  Similarity=0.362  Sum_probs=21.5

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++||-|.|  ||||...++.-++..
T Consensus        30 ~~Ge~vaiiG~nGsGKSTLl~~l~Gll~p   58 (288)
T PRK13643         30 KKGSYTALIGHTGSGKSTLLQHLNGLLQP   58 (288)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             59989999999994799999999748888


No 431
>cd03254 ABCC_Glucan_exporter_like Glucan exporter ATP-binding protein.  In A. tumefaciens cyclic beta-1, 2-glucan must be transported into the periplasmic space to exert its action as a virluence factor.  This subfamily belongs to the MRP-like family and is involved in drug, peptide, and lipid export.  The MRP-like family, similar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains each composed of six transmembrane (TM) helices and two nucleotide-binding domains (NBD).  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=34.04  E-value=20  Score=15.48  Aligned_cols=26  Identities=31%  Similarity=0.387  Sum_probs=19.7

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHH
Q ss_conf             699399983036--54201233467777
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALS  131 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~  131 (472)
                      .++..|||+|.+  ||||.-.++.-++.
T Consensus        27 ~~Ge~vaivG~sGsGKSTLl~ll~gl~~   54 (229)
T cd03254          27 KPGETVAIVGPTGAGKTTLINLLMRFYD   54 (229)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCC
T ss_conf             7999999999999809999999966866


No 432
>TIGR00618 sbcc exonuclease SbcC; InterPro: IPR004592 All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. SbcC may have nuclease activity that is functionally related to one of the nuclease activities of the RecBCD enzyme (IPR004586 from INTERPRO).; GO: 0004527 exonuclease activity, 0006259 DNA metabolic process.
Probab=33.97  E-value=30  Score=14.25  Aligned_cols=27  Identities=33%  Similarity=0.469  Sum_probs=19.8

Q ss_pred             CCCEEEEECCC--CCCHHHHHHHHHHHHHHC
Q ss_conf             99399983036--542012334677775201
Q gi|254781101|r  107 KATIIAITGSV--GKTTTKEMLTIALSSIKK  135 (472)
Q Consensus       107 ~~~vI~ITGTn--GKTTt~~~l~~iL~~~~~  135 (472)
                      ..++..|+|++  ||||.-+-|.+.|  .|+
T Consensus        29 sl~~f~i~G~tGAGKtsLldAI~yAL--YGk   57 (1063)
T TIGR00618        29 SLKLFVICGKTGAGKTSLLDAITYAL--YGK   57 (1063)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHH--CCC
T ss_conf             25736777889983545999999987--288


No 433
>cd03255 ABC_MJ0796_Lo1CDE_FtsE This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE).  They are clustered together phylogenetically.  MacAB is an exporter that confers resistance to macrolides, while the LolCDE system is not a transporter at all.  An FtsE null mutants showed filamentous growth and appeared viable on high salt medium only, indicating a role for FtsE in cell division and/or salt transport.  The LolCDE complex catalyses the release of lipoproteins from the cytoplasmic membrane prior to their targeting to the outer membrane.
Probab=33.90  E-value=19  Score=15.50  Aligned_cols=27  Identities=30%  Similarity=0.341  Sum_probs=21.6

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      ..+.++||.|-|  ||||+-.+++-++..
T Consensus        28 ~~Ge~~~iiG~sGsGKTTll~~i~Gl~~p   56 (218)
T cd03255          28 EKGEFVAIVGPSGSGKSTLLNILGGLDRP   56 (218)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             69989999999998699999999669999


No 434
>PRK10247 putative ABC transporter ATP-binding protein YbbL; Provisional
Probab=33.88  E-value=21  Score=15.32  Aligned_cols=27  Identities=26%  Similarity=0.358  Sum_probs=20.6

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++||.|-|  ||||.-.++.-++..
T Consensus        31 ~~Ge~~~i~G~sGsGKSTLlk~i~gl~~p   59 (225)
T PRK10247         31 RAGEFKLITGPSGCGKSTLLKIVASLISP   59 (225)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             59969999999999999999999646688


No 435
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=33.86  E-value=28  Score=14.44  Aligned_cols=42  Identities=10%  Similarity=0.140  Sum_probs=27.0

Q ss_pred             CHHHHHHHHCCEEECCCCCCEEEEEEEECCCCCCCCEEEECC
Q ss_conf             678899872799952688714746774022237898889716
Q gi|254781101|r    6 TFHDLLQAIQGHSIGIVPQGFVNGISIDSRSIAPQEAFFAIK   47 (472)
Q Consensus         6 ~~~~l~~~~~g~~~~~~~~~~i~~i~~dSr~v~~g~lFval~   47 (472)
                      ....+|+--+|..+-..-++.+=....-|++.++|.=||+|.
T Consensus        10 etGklAkqA~GsV~v~~GdT~VL~T~~~~~~~~~~~DFfPLt   51 (684)
T TIGR03591        10 ETGKIARQADGAVVVRYGDTVVLVTVVAAKEAKEGQDFFPLT   51 (684)
T ss_pred             ECCHHHHHCCCEEEEEECCEEEEEEEEECCCCCCCCCCCCCE
T ss_conf             745335416842999989969999998148888999977754


No 436
>cd04246 AAK_AK-DapG-like AAK_AK-DapG-like: Amino Acid Kinase Superfamily (AAK), AK-DapG-like; this CD includes the N-terminal catalytic aspartokinase (AK) domain of the diaminopimelate-sensitive aspartokinase isoenzyme AKI (DapG), a monofunctional enzymes found in Bacilli (Bacillus subtilis 168), Clostridia, and Actinobacteria bacterial species, as well as, the catalytic AK domain of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis 168, the lysine plus threonine-sensitive aspartokinase of Corynebacterium glutamicum, and related isoenzymes. In Bacillus subtilis, the regulation of the diaminopimelate-lysine biosynthetic pathway involves dual control by diaminopimelate and lysine, effected through separate diaminopimelate- and lysine-sensitive aspartokinase isoenzymes. The role of the AKI isoenzyme is most likely to provide a constant level of aspartyl-beta-phosphate for the biosynthesis of diaminopimelate for peptidoglycan synthesis and dipicolinate during sporulati
Probab=33.81  E-value=11  Score=17.02  Aligned_cols=30  Identities=13%  Similarity=0.286  Sum_probs=15.9

Q ss_pred             HHHHHHHHHHHHC--CCCCEEEEECCCCCCHH
Q ss_conf             9999999999830--69939998303654201
Q gi|254781101|r   93 GALNKLAVAARLR--SKATIIAITGSVGKTTT  122 (472)
Q Consensus        93 ~al~~la~~~~~~--~~~~vI~ITGTnGKTTt  122 (472)
                      +.+.++|....+.  ...+++-|.+--|++|-
T Consensus        15 e~i~~va~iI~~~~~~g~~viVVvSA~gg~Td   46 (239)
T cd04246          15 ERIKRVAERIKKAVKKGYQVVVVVSAMGGTTD   46 (239)
T ss_pred             HHHHHHHHHHHHHHHCCCEEEEEECCCCCCHH
T ss_conf             99999999999998679829999848986567


No 437
>TIGR01307 pgm_bpd_ind 2,3-bisphosphoglycerate-independent phosphoglycerate mutase; InterPro: IPR005995   This 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (iPGAM) is a metalloenzyme found particularly in eubacteria and higher plants. It is distantly related to archaeal iPGAM (IPR004456 from INTERPRO) and distinct from the unrelated cofactor-dependent PGAM (PIRSF001490 from PIRSF). Activity has been demonstrated for proteins from a variety of organisms, including Pseudomonas syringae pv. tomato , Bacillus subtilis , Bacillus stearothermophilus , maize , castor bean , and Trypanosoma brucei . The structure of the B. stearothermophilus enzyme (PDB:1EJJ) has two domains . Residues 1-76 and 311-511 form the phosphatase domain, containing the active site residue and two metal-binding sites. This domain is similar to alkaline phosphatase (PDB:1ALK) and arylsulphatase (PDB:1AUK), which are members of the SCOP alkaline phosphatase-like superfamily, but there is meagre sequence similarity outside of the metal-binding segments. Residues 77-310 form the phosphotransferase domain, which is poorly conserved (or perhaps unrelated) in the archaeal enzymes.; GO: 0004619 phosphoglycerate mutase activity, 0006007 glucose catabolic process.
Probab=33.49  E-value=31  Score=14.20  Aligned_cols=73  Identities=12%  Similarity=0.128  Sum_probs=31.6

Q ss_pred             HHHHHHHHCCCCEEEEECC-CHHHHHHHCC-CCCCEEEECCHHHHHHH--HHHHCCCCCEEEEE-CCCHHHHHHHHHHHH
Q ss_conf             9999998649989999880-3898998511-37979997898999999--99844789899997-713254899999999
Q gi|254781101|r  391 DLAEVLSLYNISHVWLSGF-HVLALKDALP-RSIHVHYSETMDGLFLF--IQSSLVDGDVVVVK-SSNSCGFYRLINLLL  465 (472)
Q Consensus       391 ~i~~~~~~~~~d~v~~~G~-~~~~~~~~~~-~~~~~~~~~~~e~a~~~--l~~~~~~gdiVLiK-GSr~~~le~iv~~L~  465 (472)
                      +|.+.+.+.+...+++..- ++..+.+.-. +....+.++.+--++--  -.+.-+.||+.++| |.   .|..|+..++
T Consensus       436 ri~~~~~~~g~~~llTADHGNAE~M~De~~G~P~T~HT~npVPfv~~~GeGrk~~~~G~~~~~~eGG---~L~dIAPT~L  512 (529)
T TIGR01307       436 RIVEACKKVGGTLLLTADHGNAEEMKDENGGNPHTAHTTNPVPFVYVGGEGRKIPKNGDVKLVREGG---VLADIAPTIL  512 (529)
T ss_pred             HHHHHHHHCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCEECCCCCCEEEEECCC---CCCCHHHHHH
T ss_conf             9999997489629996055660016788887730115578634688588430456787764541674---4213578899


Q ss_pred             H
Q ss_conf             8
Q gi|254781101|r  466 E  466 (472)
Q Consensus       466 ~  466 (472)
                      +
T Consensus       513 ~  513 (529)
T TIGR01307       513 D  513 (529)
T ss_pred             H
T ss_conf             9


No 438
>pfam03142 Chitin_synth_2 Chitin synthase. Members of this family are fungal chitin synthase EC:2.4.1.16 enzymes. They catalyse chitin synthesis as follows: UDP-N-acetyl-D-glucosamine + {(1,4)-(N-acetyl-beta-D-glucosaminyl)}(N) <= UDP + {(1,4)-(N-acetyl-beta-D-glucosaminyl)}(N+1).
Probab=33.31  E-value=31  Score=14.19  Aligned_cols=18  Identities=17%  Similarity=0.257  Sum_probs=7.2

Q ss_pred             ECCCCCCHHHHHHHHHHH
Q ss_conf             303654201233467777
Q gi|254781101|r  114 TGSVGKTTTKEMLTIALS  131 (472)
Q Consensus       114 TGTnGKTTt~~~l~~iL~  131 (472)
                      +|+--.-||-+.+-.+|.
T Consensus        69 ~G~G~~~~Tp~i~l~im~   86 (536)
T pfam03142        69 KGSGNDRSTPDIVLDMMK   86 (536)
T ss_pred             CCCCCCCCCHHHHHHHHH
T ss_conf             158888781799999850


No 439
>PRK10246 exonuclease subunit SbcC; Provisional
Probab=33.19  E-value=31  Score=14.17  Aligned_cols=12  Identities=25%  Similarity=0.216  Sum_probs=4.2

Q ss_pred             CCCCCEEEEECC
Q ss_conf             478989999771
Q gi|254781101|r  441 LVDGDVVVVKSS  452 (472)
Q Consensus       441 ~~~gdiVLiKGS  452 (472)
                      +.+|+-.-||||
T Consensus       500 L~~G~pCPVCGS  511 (1047)
T PRK10246        500 LQAGQPCPLCGS  511 (1047)
T ss_pred             CCCCCCCCCCCC
T ss_conf             479998999999


No 440
>cd01673 dNK Deoxyribonucleoside kinase (dNK) catalyzes the phosphorylation of deoxyribonucleosides to yield corresponding monophosphates (dNMPs). This family consists of various deoxynucleoside kinases including deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC 2.7.1.113), adenosine (EC 2.7.1.76), and thymidine (EC 2.7.1.21) kinases. They are key enzymes in the salvage of deoxyribonucleosides originating from extra- or intracellular breakdown of DNA.
Probab=33.11  E-value=22  Score=15.17  Aligned_cols=21  Identities=33%  Similarity=0.544  Sum_probs=14.8

Q ss_pred             EEEEECC--CCCCHHHHHHHHHH
Q ss_conf             9998303--65420123346777
Q gi|254781101|r  110 IIAITGS--VGKTTTKEMLTIAL  130 (472)
Q Consensus       110 vI~ITGT--nGKTTt~~~l~~iL  130 (472)
                      +|+|-|.  .||||...+|+..|
T Consensus         1 lI~iEG~iGsGKSTl~~~L~~~~   23 (193)
T cd01673           1 VIVVEGNIGAGKSTLAKELAEHL   23 (193)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHH
T ss_conf             98998888888999999999966


No 441
>cd03265 ABC_DrrA DrrA is the ATP-binding protein component of a bacterial exporter complex that confers resistance to the antibiotics daunorubicin and doxorubicin.  In addition to DrrA, the complex includes an integral membrane protein called DrrB.  DrrA belongs to the ABC family of transporters and shares sequence and functional similarities with a protein found in cancer cells called  P-glycoprotein.  ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.  The nucleotide binding domain shows the highest similarity between all members of the family.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=33.03  E-value=21  Score=15.32  Aligned_cols=27  Identities=41%  Similarity=0.551  Sum_probs=22.2

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++|+-|-|  ||||+-.|+.-+++.
T Consensus        24 ~~Gei~gllGpNGAGKSTll~~i~Gl~~p   52 (220)
T cd03265          24 RRGEIFGLLGPNGAGKTTTIKMLTTLLKP   52 (220)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             89839999999987199999999769788


No 442
>PRK13137 consensus
Probab=32.79  E-value=31  Score=14.13  Aligned_cols=53  Identities=15%  Similarity=0.197  Sum_probs=21.8

Q ss_pred             HHHHHHHHHHHHHH---CCCCCEE-EE-ECCCCCCHHHHHHHHHHHHHHCCCCCHHHHHCCCCCCCH
Q ss_conf             89999999999983---0699399-98-303654201233467777520112221221101457410
Q gi|254781101|r   91 VLGALNKLAVAARL---RSKATII-AI-TGSVGKTTTKEMLTIALSSIKKTYACIGSYNNHIGVPLT  152 (472)
Q Consensus        91 ~~~al~~la~~~~~---~~~~~vI-~I-TGTnGKTTt~~~l~~iL~~~~~~~~t~gn~Nn~iGvplt  152 (472)
                      +.+.|.++-..+.+   +-..-.| =+ .|--...++.+.+..+.  .+...       =+||+|+|
T Consensus         5 ~~~~m~Ri~~~F~~~k~~~~~ali~yitaG~P~~~~s~~~~~~l~--~gaDi-------iElGiPFS   62 (266)
T PRK13137          5 TNRGVQRLHAAFARARAEGRAAFIPFLTAGYPSAAGFLQVAEELL--AYADL-------LEVGIPYS   62 (266)
T ss_pred             CHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHH--CCCCE-------EEECCCCC
T ss_conf             020488999999999976995388786681888789999999997--38998-------99789988


No 443
>PRK13948 shikimate kinase; Provisional
Probab=32.78  E-value=13  Score=16.66  Aligned_cols=25  Identities=32%  Similarity=0.343  Sum_probs=15.9

Q ss_pred             CEEEEECC--CCCCHHHHHHHHHHHHH
Q ss_conf             39998303--65420123346777752
Q gi|254781101|r  109 TIIAITGS--VGKTTTKEMLTIALSSI  133 (472)
Q Consensus       109 ~vI~ITGT--nGKTTt~~~l~~iL~~~  133 (472)
                      +.|...|=  .||||+-..|+..|.-.
T Consensus        11 ~~IvLIG~mGsGKStiGk~LA~~l~~~   37 (182)
T PRK13948         11 TFVALAGFMGTGKSRIGWELSRALALH   37 (182)
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHHCCC
T ss_conf             818988999998899999999996959


No 444
>pfam05049 IIGP Interferon-inducible GTPase (IIGP). Interferon-inducible GTPase (IIGP) is thought to play a role in in intracellular defence. IIGP is predominantly associated with the Golgi apparatus and also localizes to the endoplasmic reticulum and exerts a distinct role in IFN-induced intracellular membrane trafficking or processing.
Probab=32.77  E-value=31  Score=14.13  Aligned_cols=35  Identities=26%  Similarity=0.283  Sum_probs=18.9

Q ss_pred             CHHHHHHHHHHHHHHCCCCC-EEEEECC--CCCCHHHH
Q ss_conf             98999999999998306993-9998303--65420123
Q gi|254781101|r   90 DVLGALNKLAVAARLRSKAT-IIAITGS--VGKTTTKE  124 (472)
Q Consensus        90 d~~~al~~la~~~~~~~~~~-vI~ITGT--nGKTTt~~  124 (472)
                      |..++...+-.......+.+ -|||||-  +||+|--.
T Consensus        16 ~l~~a~s~I~e~L~~~~~~~lnIavtGesG~GkSsfIN   53 (375)
T pfam05049        16 NLQKVVSIIKKAIQEISSAPLKIAVTGDSGNGKSSFIN   53 (375)
T ss_pred             CHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHHH
T ss_conf             98999999999997544382479985489986789999


No 445
>PRK01909 pdxA 4-hydroxythreonine-4-phosphate dehydrogenase; Validated
Probab=32.75  E-value=31  Score=14.13  Aligned_cols=17  Identities=41%  Similarity=0.546  Sum_probs=8.6

Q ss_pred             CCCCCHHHHHHHHHHHH
Q ss_conf             65321012577787411
Q gi|254781101|r  348 ANPASMKAAISVLSQIS  364 (472)
Q Consensus       348 AnP~S~~aal~~l~~~~  364 (472)
                      |||.||.+|++.-..+.
T Consensus       307 A~~~s~~~Ai~~A~~~a  323 (329)
T PRK01909        307 ADPGSMIAAIDTAVTMA  323 (329)
T ss_pred             CCHHHHHHHHHHHHHHH
T ss_conf             99699999999999999


No 446
>PRK00230 orotidine 5'-phosphate decarboxylase; Reviewed
Probab=32.68  E-value=31  Score=14.12  Aligned_cols=29  Identities=24%  Similarity=0.229  Sum_probs=17.1

Q ss_pred             HHHHHHHHHCCCCEEEEECCCHHHHHHHC
Q ss_conf             99999998649989999880389899851
Q gi|254781101|r  390 IDLAEVLSLYNISHVWLSGFHVLALKDAL  418 (472)
Q Consensus       390 ~~i~~~~~~~~~d~v~~~G~~~~~~~~~~  418 (472)
                      ..+++.+.+.++|-+++.+.+...+++..
T Consensus       139 ~~~a~~a~~~g~dGiVcs~~e~~~ir~~~  167 (231)
T PRK00230        139 LRLAKLAQEAGLDGVVCSAQEAAALREAT  167 (231)
T ss_pred             HHHHHHHHHHCCCEEECCHHHHHHHHHHC
T ss_conf             99999999969984863888999998645


No 447
>PRK09493 glnQ glutamine ABC transporter ATP-binding protein; Reviewed
Probab=32.49  E-value=22  Score=15.19  Aligned_cols=26  Identities=19%  Similarity=0.327  Sum_probs=20.2

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHH
Q ss_conf             699399983036--54201233467777
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALS  131 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~  131 (472)
                      .++.+++|.|-|  ||||+-.++.-++.
T Consensus        25 ~~Ge~~~liG~nGsGKSTll~~i~Gl~~   52 (240)
T PRK09493         25 DQGEVVVIIGPSGSGKSTLLRCINKLEE   52 (240)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCC
T ss_conf             7998999999999809999999963899


No 448
>PRK13548 hmuV hemin importer ATP-binding subunit; Provisional
Probab=32.32  E-value=22  Score=15.09  Aligned_cols=26  Identities=31%  Similarity=0.401  Sum_probs=20.1

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHH
Q ss_conf             699399983036--54201233467777
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALS  131 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~  131 (472)
                      ..+.++||-|-|  ||||.-.++.-++.
T Consensus        26 ~~Gei~~liGpNGaGKSTLlk~i~Gl~~   53 (257)
T PRK13548         26 RPGEVVAILGPNGAGKSTLLRALSGELP   53 (257)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCC
T ss_conf             6998999999999879999999856757


No 449
>TIGR01011 rpsB_bact ribosomal protein S2; InterPro: IPR005706   Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.    Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , .    This family describes the bacterial, mitochondrial and chloroplast forms of ribosomal protein S2.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=32.27  E-value=32  Score=14.07  Aligned_cols=10  Identities=20%  Similarity=0.245  Sum_probs=4.0

Q ss_pred             HHHHHHHHCC
Q ss_conf             0345543114
Q gi|254781101|r  311 DTAIKALSVF  320 (472)
Q Consensus       311 ~~i~~~L~~~  320 (472)
                      ++|++++..+
T Consensus       105 ~TirkSi~kL  114 (227)
T TIGR01011       105 KTIRKSIKKL  114 (227)
T ss_pred             HHHHHHHHHH
T ss_conf             9999999999


No 450
>cd02030 NDUO42 NADH:Ubiquinone oxioreductase, 42 kDa (NDUO42) is a family of proteins that are highly similar to deoxyribonucleoside kinases (dNK). Members of this family have been identified as one of the subunits of NADH:Ubiquinone oxioreductase (complex I), a multi-protein complex located in the inner mitochondrial membrane. The main function of the complex is to transport electrons from NADH to ubiquinone, which is accompanied by the translocation of protons from the mitochondrial matrix to the inter membrane space.
Probab=32.19  E-value=23  Score=15.03  Aligned_cols=21  Identities=29%  Similarity=0.463  Sum_probs=15.4

Q ss_pred             EEEEECC--CCCCHHHHHHHHHH
Q ss_conf             9998303--65420123346777
Q gi|254781101|r  110 IIAITGS--VGKTTTKEMLTIAL  130 (472)
Q Consensus       110 vI~ITGT--nGKTTt~~~l~~iL  130 (472)
                      +|+|-|.  .||||...+|+.-|
T Consensus         1 iI~IEGnIG~GKTTl~~~La~~l   23 (219)
T cd02030           1 VITVDGNIASGKGKLAKELAEKL   23 (219)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHH
T ss_conf             98996785679999999999985


No 451
>cd03251 ABCC_MsbA MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins.  ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.  The nucleotide binding domain shows the highest similarity between all members of the family.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=32.19  E-value=22  Score=15.15  Aligned_cols=25  Identities=20%  Similarity=0.359  Sum_probs=17.5

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHH
Q ss_conf             699399983036--5420123346777
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIAL  130 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL  130 (472)
                      .++..|||+|.+  ||||.-.++..++
T Consensus        26 ~~Ge~i~IvG~sGsGKSTLl~ll~gl~   52 (234)
T cd03251          26 PAGETVALVGPSGSGKSTLVNLIPRFY   52 (234)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCC
T ss_conf             799999999899982999999996676


No 452
>PRK10762 D-ribose transporter ATP binding protein; Provisional
Probab=32.01  E-value=24  Score=14.89  Aligned_cols=51  Identities=18%  Similarity=0.396  Sum_probs=29.7

Q ss_pred             CCCCCCHHHHHHHHCCEEECCCCCCEEEEEEEECCCCCCCCEEEECCCCCCCHHHHHHHHHH
Q ss_conf             95435678899872799952688714746774022237898889716887476888999998
Q gi|254781101|r    1 MNPLWTFHDLLQAIQGHSIGIVPQGFVNGISIDSRSIAPQEAFFAIKGPHYDGHDFILHAVQ   62 (472)
Q Consensus         1 m~~~~~~~~l~~~~~g~~~~~~~~~~i~~i~~dSr~v~~g~lFval~g~~~DGh~~i~~A~~   62 (472)
                      |.||..++.+...-++..       -.+++++   .+.+|.+ ++|-|.+--|-.=+-.++.
T Consensus         1 M~~il~v~~l~k~y~~~~-------aL~~vsl---~i~~Gei-~~liG~nGaGKSTL~~~l~   51 (501)
T PRK10762          1 MEALLQLKGIDKAFPGVK-------ALSGAAL---NVYPGRV-MALVGENGAGKSTLMKVLT   51 (501)
T ss_pred             CCEEEEEEEEEEEECCEE-------EECCEEE---EECCCCE-EEEECCCCCHHHHHHHHHH
T ss_conf             961599963599999999-------8855478---9989969-9998999982999999995


No 453
>KOG2749 consensus
Probab=31.91  E-value=32  Score=14.04  Aligned_cols=50  Identities=22%  Similarity=0.210  Sum_probs=27.3

Q ss_pred             CEEEECCHHHHHHHHHHHHHH-CCCCC-EEEEECCC-CCCHHHHHHH-HHHHHH
Q ss_conf             289959989999999999983-06993-99983036-5420123346-777752
Q gi|254781101|r   84 PVFGVDDVLGALNKLAVAARL-RSKAT-IIAITGSV-GKTTTKEMLT-IALSSI  133 (472)
Q Consensus        84 ~~i~v~d~~~al~~la~~~~~-~~~~~-vI~ITGTn-GKTTt~~~l~-~iL~~~  133 (472)
                      |...-=|...+|......+-. ...+| ++-|-+|+ ||||.+.||- ..+++.
T Consensus        78 pM~~ylNlH~ale~~R~~~e~~~~~GPrv~vVGp~d~GKsTl~r~L~nyavk~g  131 (415)
T KOG2749          78 PMVLYLNLHAALEKRRMQAEEESSYGPRVMVVGPTDVGKSTLCRILLNYAVKQG  131 (415)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHHHCC
T ss_conf             730001399999998665542002597799989876566789999999998717


No 454
>COG0288 CynT Carbonic anhydrase [Inorganic ion transport and metabolism]
Probab=31.89  E-value=28  Score=14.45  Aligned_cols=24  Identities=17%  Similarity=0.040  Sum_probs=13.5

Q ss_pred             HHHHCCCCCEEEEECCCCCCHHHH
Q ss_conf             998306993999830365420123
Q gi|254781101|r  101 AARLRSKATIIAITGSVGKTTTKE  124 (472)
Q Consensus       101 ~~~~~~~~~vI~ITGTnGKTTt~~  124 (472)
                      +.-...+.+-|=|.|-.|...++.
T Consensus        84 yAv~~L~v~~IiV~GH~~CGav~a  107 (207)
T COG0288          84 YAVYVLGVKEIIVCGHTDCGAVKA  107 (207)
T ss_pred             HHHHHCCCCEEEEECCCCCHHHHH
T ss_conf             999974998899966898478770


No 455
>PRK13549 xylose transporter ATP-binding subunit; Provisional
Probab=31.88  E-value=24  Score=14.89  Aligned_cols=51  Identities=16%  Similarity=0.318  Sum_probs=29.9

Q ss_pred             CCCCCCHHHHHHHHCCEEECCCCCCEEEEEEEECCCCCCCCEEEECCCCCCCHHHHHHHHHH
Q ss_conf             95435678899872799952688714746774022237898889716887476888999998
Q gi|254781101|r    1 MNPLWTFHDLLQAIQGHSIGIVPQGFVNGISIDSRSIAPQEAFFAIKGPHYDGHDFILHAVQ   62 (472)
Q Consensus         1 m~~~~~~~~l~~~~~g~~~~~~~~~~i~~i~~dSr~v~~g~lFval~g~~~DGh~~i~~A~~   62 (472)
                      |.||..++.+-..-++.       .-+++|++   ++.+|.+ ++|-|.+--|-.=+-.++.
T Consensus         2 m~~ll~v~~l~~~~g~~-------~aL~~vsl---~i~~Ge~-~~lvG~nGsGKSTL~~~l~   52 (513)
T PRK13549          2 MPYLLEMKNITKTFGGV-------KALDNISL---RVRAGEI-VSLCGENGAGKSTLMKVLS   52 (513)
T ss_pred             CCHHEEEEEEEEEECCE-------EEECCEEE---EECCCCE-EEEECCCCCHHHHHHHHHH
T ss_conf             60687996179998999-------99756389---9889979-9998999972999999995


No 456
>PRK00676 hemA glutamyl-tRNA reductase; Validated
Probab=31.80  E-value=33  Score=14.02  Aligned_cols=22  Identities=9%  Similarity=0.027  Sum_probs=11.7

Q ss_pred             HHHHHHHHHCCCCCEEEEECCC
Q ss_conf             9999999844789899997713
Q gi|254781101|r  432 GLFLFIQSSLVDGDVVVVKSSN  453 (472)
Q Consensus       432 ~a~~~l~~~~~~gdiVLiKGSr  453 (472)
                      ..++.+++.....|+|-+.+-|
T Consensus       311 ~~~e~~~~~~~~~~~~~~~~~~  332 (338)
T PRK00676        311 KQWESYEKKSSHIDCVQINAPR  332 (338)
T ss_pred             HHHHHHHHHCCCCCCHHHCCCC
T ss_conf             9999998650558802312686


No 457
>cd03263 ABC_subfamily_A The ABCA subfamily mediates the transport of a variety of lipid compounds.  Mutations of members of ABCA subfamily are associated with human genetic diseases, such as, familial high-density lipoprotein (HDL) deficiency, neonatal surfactant deficiency, degenerative retinopathies, and congenital keratinization disorders.  The ABCA1 protein is involved in disorders of cholesterol transport and high-density lipoprotein (HDL) biosynthesis.  The ABCA4 (ABCR) protein transports vitamin A derivatives in the outer segments of photoreceptor cells, and therefore, performs a crucial step in the visual cycle.  The ABCA genes are not present in yeast.  However, evolutionary studies of ABCA genes indicate that they arose as transporters that subsequently duplicated and that certain sets of ABCA genes were lost in different eukaryotic lineages.
Probab=31.62  E-value=23  Score=15.03  Aligned_cols=27  Identities=44%  Similarity=0.492  Sum_probs=21.2

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++|+-|-|  ||||+-.++.-++..
T Consensus        26 ~~Gei~~llG~NGaGKSTLl~~i~Gl~~p   54 (220)
T cd03263          26 YKGEIFGLLGHNGAGKTTTLKMLTGELRP   54 (220)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             49959999989997399999999669878


No 458
>pfam05711 TylF Macrocin-O-methyltransferase (TylF). This family consists of bacterial macrocin O-methyltransferase (TylF) proteins. TylF is responsible for the methylation of macrocin to produce tylosin. Tylosin is a macrolide antibiotic used in veterinary medicine to treat infections caused by Gram-positive bacteria and as an animal growth promoter in the swine industry. It is produced by several Streptomyces species. As with other macrolides, the antibiotic activity of tylosin is due to the inhibition of protein biosynthesis by a mechanism that involves the binding of tylosin to the ribosome, preventing the formation of the mRNA-aminoacyl-tRNA-ribosome complex.
Probab=31.59  E-value=30  Score=14.27  Aligned_cols=11  Identities=36%  Similarity=0.833  Sum_probs=6.1

Q ss_pred             CCCEEEEEECCC
Q ss_conf             531133100025
Q gi|254781101|r  336 QGFFTLIDESYN  347 (472)
Q Consensus       336 ~~~~~iIDDsYN  347 (472)
                      .||+.+||| |+
T Consensus       205 ~GG~iiiDD-Y~  215 (249)
T pfam05711       205 PGGFVIVDD-YC  215 (249)
T ss_pred             CCCEEEEEC-CC
T ss_conf             882899926-89


No 459
>TIGR00259 TIGR00259 conserved hypothetical protein TIGR00259; InterPro: IPR005137   Photosystem I (PSI) is a large protein complex embedded within the photosynthetic thylakoid membrane. It consists of 11 subunits, ~100 chlorophyll a molecules, 2 phylloquinones, and 3 Fe4S4-clusters. The three dimensional structure of the PSI complex has been resolved at 2.5 A , which allows the precise localisation of each cofactor. PSI together with photosystem II (PSII) catalyses the light-induced steps in oxygenic photosynthesis - a process found in cyanobacteria, eukaryotic algae (e.g. red algae, green algae) and higher plants.   To date, three thylakoid proteins involved in the stable accumulation of PSI have been identified: BtpA , Ycf3 , , and Ycf4 (IPR003359 from INTERPRO) . Because translation of the psaA and psaB mRNAs encoding the two reaction centre polypeptides, of PSI and PSII respectively, is not affected in mutant strains lacking functional ycf3 and ycf4, the products of these two genes appear to act at a post-translational step of PSI biosynthesis. These gene products are therefore involved either in the stabilisation or in the assembly of the PSI complex. However, their exact roles remain unknown. The BtpA protein appears to act at the level of PSI stabilisation . It is an extrinsic membrane protein located on the cytoplasmic side of the thylakoid membrane , . Homologs of BtpA are found in the crenarchaeota and euryarchaeota, where their function remains unknown. The Ycf4 protein is firmly associated with the thylakoid membrane, presumably through a transmembrane domain . Ycf4 co-fractionates with a protein complex larger than PSI upon sucrose density gradient centrifugation of solubilised thylakoids . The Ycf3 protein is loosely associated with the thylakoid membrane and can be released from the membrane with sodium carbonate. This suggests that Ycf3 is not part of a stable complex and that it probably interacts transiently with its partners . Ycf3 contains a number of tetratrico peptide repeats (TPR, IPR001440 from INTERPRO); TPR is a structural motif present in a wide range of proteins, which mediates proteinprotein interactions.  .
Probab=31.47  E-value=23  Score=14.98  Aligned_cols=138  Identities=20%  Similarity=0.334  Sum_probs=78.2

Q ss_pred             ECCCCC-CCHH----HHHHHH-------HHCCCEEEEECCCCCCCCCCCCCCEEE--E-CCHHHHHHHHHHHHHHCCCCC
Q ss_conf             716887-4768----889999-------986988999855212455446972899--5-998999999999998306993
Q gi|254781101|r   45 AIKGPH-YDGH----DFILHA-------VQKGAGLVVVNTDMVASIGSLSIPVFG--V-DDVLGALNKLAVAARLRSKAT  109 (472)
Q Consensus        45 al~g~~-~DGh----~~i~~A-------~~~Ga~~~i~~~~~~~~~~~~~~~~i~--v-~d~~~al~~la~~~~~~~~~~  109 (472)
                      +|||+. +|++    .=|+.|       -+-|+=+++.|...       +.|+..  | ..+..||..++....+.-..|
T Consensus        12 pLPGs~~~~~~lGl~~vid~A~~da~aL~~GG~DAv~~eN~f-------d~PF~kq~v~~~tvAAMa~I~~~l~~~v~~P   84 (261)
T TIGR00259        12 PLPGSPSFDDNLGLNAVIDKAVKDAKALEEGGVDAVILENFF-------DAPFLKQEVDPETVAAMAVIAKELKEDVSIP   84 (261)
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEECCC-------CCCCCCCCCCHHHHHHHHHHHHHHHHCCCCC
T ss_conf             876397638755648999999999999985698789985246-------8697765056344318899999887512046


Q ss_pred             EEEEECCCCCCHHHHHHH----------HHHHHHHCCCCCHHHHHCCCCCCCHHCCCCCCCHHHHHCCCCCCCCCCCCCC
Q ss_conf             999830365420123346----------7777520112221221101457410001232214443015664433211212
Q gi|254781101|r  110 IIAITGSVGKTTTKEMLT----------IALSSIKKTYACIGSYNNHIGVPLTLARMPVDVDFGIFELGMSHLGEIRFLT  179 (472)
Q Consensus       110 vI~ITGTnGKTTt~~~l~----------~iL~~~~~~~~t~gn~Nn~iGvpltll~~~~~~~~~V~E~g~~~~gei~~L~  179 (472)
                      + ||          ..|.          ..-...+-.+      |-.-|+.        -+|.-|+|   ...||+-++.
T Consensus        85 l-Gi----------NvLrNDa~aa~~iA~~v~A~FiRV------n~L~G~~--------~sD~G~~e---g~a~E~~ry~  136 (261)
T TIGR00259        85 L-GI----------NVLRNDAVAALAIAKAVGAKFIRV------NVLTGVA--------ASDQGIIE---GNAGELLRYK  136 (261)
T ss_pred             C-CE----------EEECCCHHHHHHHHHHHCCCEEEE------EEEEEEE--------ECCCCCEE---CCHHHHHHHH
T ss_conf             4-10----------121234777898867647726898------5332125--------53674000---4165433433


Q ss_pred             CCCCC-CEEEEEEECCCHHHHHH--HHHHHHHHHHHHCCCCCC
Q ss_conf             23232-20255531210123444--578888654331037622
Q gi|254781101|r  180 HLVRP-HIAVITTIAPAHLSNFS--GIEEIASAKAEIFEGLEK  219 (472)
Q Consensus       180 ~i~~P-~iaiiTNI~~dHld~~~--s~e~i~~~K~~i~~~l~~  219 (472)
                      +.+.. ++.|+-||-..|--+||  +++.+..  .-+++++..
T Consensus       137 ~~~~sG~v~~ladv~vkhA~~lG~~~l~~~~~--~Tver~laD  177 (261)
T TIGR00259       137 KLLGSGEVKILADVVVKHAVHLGNRDLESIVL--DTVERGLAD  177 (261)
T ss_pred             HCCCCCCEEEEECCCHHHCCCCCCCCHHHHHH--HHHHHCCCC
T ss_conf             12676645630315245210258836688986--445416988


No 460
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=31.46  E-value=33  Score=13.99  Aligned_cols=19  Identities=26%  Similarity=0.322  Sum_probs=7.6

Q ss_pred             HHHHHCCCCHHHHHHHHCC
Q ss_conf             6765101210345543114
Q gi|254781101|r  302 IVSILTADVDTAIKALSVF  320 (472)
Q Consensus       302 ~~~~lGi~~~~i~~~L~~~  320 (472)
                      ++..+|+++.+|++-|+.|
T Consensus        38 La~~~gi~~~qVRKDls~f   56 (211)
T PRK05472         38 LAEAVGVDSAQIRKDLSYF   56 (211)
T ss_pred             HHHHHCCCHHHHHHHHHHH
T ss_conf             9999698999999899986


No 461
>PRK11124 artP arginine transporter ATP-binding subunit; Provisional
Probab=31.44  E-value=23  Score=15.06  Aligned_cols=26  Identities=15%  Similarity=0.327  Sum_probs=19.3

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHH
Q ss_conf             699399983036--54201233467777
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALS  131 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~  131 (472)
                      .++.++||.|-|  ||||+-.++.-++.
T Consensus        26 ~~Ge~~~iiG~nGaGKSTLl~~l~gl~~   53 (242)
T PRK11124         26 PQGETLVLLGPSGAGKSSLLRVLNLLEM   53 (242)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCC
T ss_conf             7998999999999719999999965888


No 462
>cd03214 ABC_Iron-Siderophores_B12_Hemin ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea.  Only very few species lack representatives of the siderophore family transporters.  The E. coli BtuCD protein is an ABC transporter mediating vitamin B12 uptake.  The two ATP-binding cassettes (BtuD) are in close contact with each other, as are the two membrane-spanning subunits (BtuC); this arrangement is distinct from that observed for the E. coli lipid flippase MsbA.  The BtuC subunits provide 20 transmembrane helices grouped around a translocation pathway that is closed to the cytoplasm by a gate region, whereas the dimer arrangement of the BtuD subunits resembles the ATP-bound form of the Rad50 DNA repair enzyme.  A prominent cytoplasmic loop of BtuC forms the contact region with the ATP-binding cassette and represent a conserved motif among the ABC transporters.
Probab=31.35  E-value=23  Score=14.98  Aligned_cols=26  Identities=31%  Similarity=0.377  Sum_probs=19.5

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHH
Q ss_conf             699399983036--54201233467777
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALS  131 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~  131 (472)
                      .++.++||.|-|  ||||.-.++.-++.
T Consensus        23 ~~Ge~~~liG~nGsGKTTLl~~i~G~~~   50 (180)
T cd03214          23 EAGEIVGILGPNGAGKSTLLKTLAGLLK   50 (180)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCC
T ss_conf             6997999998999889999999957989


No 463
>cd03234 ABCG_White The White subfamily represents ABC transporters homologous to the Drosophila white gene, which acts as a dimeric importer for eye pigment precursors.  The eye pigmentation of Drosophila is developed from the synthesis and deposition in the cells of red pigments, which are synthesized from guanine, and brown pigments, which are synthesized from tryptophan.  The pigment precursors are encoded by the white, brown, and scarlet genes, respectively.  Evidence from genetic and biochemical studies suggest that the White and Brown proteins function as heterodimers to import guanine, while the White and Scarlet proteins function to import tryptophan.  However, a recent study also suggests that White may be involved in the transport of a metabolite, such as 3-hydroxykynurenine, across intracellular membranes.  Mammalian ABC transporters belonging to the White subfamily (ABCG1, ABCG5, and ABCG8) have been shown to be involved in the regulation of lipid-trafficking mechanisms in 
Probab=31.27  E-value=21  Score=15.24  Aligned_cols=27  Identities=30%  Similarity=0.425  Sum_probs=20.7

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.++||-|-|  ||||+-.++.-++..
T Consensus        31 ~~Ge~~~ilGpnGsGKSTLl~~i~G~~~~   59 (226)
T cd03234          31 ESGQVMAILGSSGSGKTTLLDAISGRVEG   59 (226)
T ss_pred             ECCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             18809999989996099999999678978


No 464
>PRK11300 livG leucine/isoleucine/valine transporter ATP-binding subunit; Provisional
Probab=31.10  E-value=23  Score=15.04  Aligned_cols=26  Identities=27%  Similarity=0.339  Sum_probs=20.1

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHH
Q ss_conf             699399983036--54201233467777
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALS  131 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~  131 (472)
                      ..+.++||-|-|  ||||+-.++.-++.
T Consensus        29 ~~Gei~~liGpnGaGKSTL~~~i~Gl~~   56 (255)
T PRK11300         29 REQEVVSLIGPNGAGKTTVFNCLTGFYK   56 (255)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCC
T ss_conf             9997999998999649999999967988


No 465
>cd03217 ABC_FeS_Assembly ABC-type transport system involved in Fe-S cluster assembly, ATPase component.  Biosynthesis of iron-sulfur clusters (Fe-S) depends on multiprotein systems.  The SUF system of E. coli and Erwinia chrysanthemi is important for Fe-S biogenesis under stressful conditions.  The SUF system is made of six proteins: SufC is an atypical cytoplasmic ABC-ATPase, which forms a complex with SufB and SufD; SufA plays the role of a scaffold protein for assembly of iron-sulfur clusters and delivery to target proteins; SufS is a cysteine desulfurase which mobilizes the sulfur atom from cysteine and provides it to the cluster; SufE has no associated function yet.
Probab=31.05  E-value=29  Score=14.34  Aligned_cols=37  Identities=11%  Similarity=0.376  Sum_probs=23.7

Q ss_pred             CCEEEEEECCCC-CCCCHHHHHHHHHHHHHCCCCCCEEEE
Q ss_conf             311331000256-532101257778741110268713885
Q gi|254781101|r  337 GFFTLIDESYNA-NPASMKAAISVLSQISPHGEGRRIAVL  375 (472)
Q Consensus       337 ~~~~iIDDsYNA-nP~S~~aal~~l~~~~~~~~~r~i~Vl  375 (472)
                      ..+.+.|.-.++ +|.+.+...+.++.+..+  ++-+++.
T Consensus       123 P~lllLDEPtsgLD~~~~~~i~~~i~~l~~~--g~tiiii  160 (200)
T cd03217         123 PDLAILDEPDSGLDIDALRLVAEVINKLREE--GKSVLII  160 (200)
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHHHHHHHC--CCEEEEE
T ss_conf             9999996962269999999999999999857--9999999


No 466
>cd03249 ABC_MTABC3_MDL1_MDL2 MTABC3 (also known as ABCB6) is a mitochondrial ATP-binding cassette protein involved in iron homeostasis and one of four ABC transporters expressed in the mitochondrial inner membrane, the other three being MDL1(ABC7), MDL2, and ATM1.  In fact, the yeast MDL1 (multidrug resistance-like protein 1) and MDL2 (multidrug resistance-like protein 2) transporters are also included in this CD.  MDL1 is an ATP-dependent permease that acts as a high-copy suppressor of ATM1 and is thought to have a role in resistance to oxidative stress. Interestingly, subfamily B is more closely related to the carboxyl-terminal component of subfamily C than the two halves of ABCC molecules are with one another.
Probab=30.93  E-value=27  Score=14.58  Aligned_cols=26  Identities=27%  Similarity=0.395  Sum_probs=19.0

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHH
Q ss_conf             699399983036--54201233467777
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALS  131 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~  131 (472)
                      .++..|||+|.+  ||||...+|..++.
T Consensus        27 ~~G~~iaIvG~sGsGKSTLl~ll~gl~~   54 (238)
T cd03249          27 PPGKTVALVGSSGCGKSTVVSLLERFYD   54 (238)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHCCC
T ss_conf             6999999999999989999999823861


No 467
>TIGR00379 cobB cobyrinic acid a,c-diamide synthase; InterPro: IPR004484 This family describes cobyrinic acid a,c-diamide synthase, the cobB (cbiA in Salmonella) protein of cobalamin biosynthesis. It is responsible for the amidation of cobyrinic acid to cobyrinic acid a,c-diamide via the intermediate formation of cobyrinic acid c-monoamide or hydrogenobrynic acid. NH(2) groups are provided by glutamine and one molecule of ATP hydrogenolyzed for each amidation .; GO: 0042242 cobyrinic acid ac-diamide synthase activity, 0009236 cobalamin biosynthetic process.
Probab=30.88  E-value=27  Score=14.58  Aligned_cols=165  Identities=15%  Similarity=0.196  Sum_probs=72.3

Q ss_pred             CHHHHHC--C----CC--CCCCCC---CCCCCCCCCCEEEEEEECCCHHHHHHHHHHHHHHHHHHCC-CCCCCCHHHHCC
Q ss_conf             1444301--5----66--443321---1212232322025553121012344457888865433103-762210121013
Q gi|254781101|r  160 VDFGIFE--L----GM--SHLGEI---RFLTHLVRPHIAVITTIAPAHLSNFSGIEEIASAKAEIFE-GLEKTGTIFLNY  227 (472)
Q Consensus       160 ~~~~V~E--~----g~--~~~gei---~~L~~i~~P~iaiiTNI~~dHld~~~s~e~i~~~K~~i~~-~l~~~g~~ViN~  227 (472)
                      .+++|+|  +    |+  +..+|+   ...+++++-=|..+-|...  |  -+|--+++.=-. .|+ +++-.|+ |+|.
T Consensus        80 s~~s~IEGv~GLYdg~Py~a~~d~gStA~vAk~L~~PvvLv~n~~~--L--~~saaAiv~Gy~-~fdp~V~l~GV-ILN~  153 (464)
T TIGR00379        80 SDVSIIEGVRGLYDGIPYSAISDKGSTASVAKALDAPVVLVVNAKR--L--SRSAAAIVLGYR-SFDPDVKLKGV-ILNR  153 (464)
T ss_pred             CCEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCEEEEEECCH--H--HHHHHHHHHHHH-HCCCCCEEEEE-EEEE
T ss_conf             9657972741343676887768775188999986598899995640--3--357867764134-30898317878-8731


Q ss_pred             --CCHHHHHHHHHCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHH
Q ss_conf             --4246899875201233-3332222222222222344211346510012456543221222222223333221035676
Q gi|254781101|r  228 --DDSFFELLKAKSHALG-IKTIYSFGKSKNADFQLRKWKQCSEQSWMEVQLQGKSMEVVHHGIGYHMAQNMLMTLGIVS  304 (472)
Q Consensus       228 --Dd~~~~~l~~~~~~~~-~~~i~~~g~~~~ad~~~~~i~~~~~~~~~~~~~~~~~~~~~l~~~G~hnv~NalaAia~~~  304 (472)
                        .+.+...++..-.... ...|+.+= -.+.|+.+.     ....-..-+.+.  .        +-......--++-+.
T Consensus       154 V~~~rH~~k~k~A~e~L~Pgi~vlG~~-pR~~~l~~p-----~RHLGLVpa~E~--l--------~~~~~~~~~~la~~~  217 (464)
T TIGR00379       154 VGSERHLEKLKTAVEKLAPGIEVLGVI-PRKEDLKVP-----DRHLGLVPAVER--L--------DEIIQQILDWLAEVV  217 (464)
T ss_pred             ECCHHHHHHHHHHHHHHCCCCEEEEEE-ECCCCCCCC-----CCCCCCCCCCCC--C--------CHHHHHHHHHHHHHH
T ss_conf             077446899999988636894588777-367532147-----754653166135--3--------178999999999999


Q ss_pred             HHCCCCHHHHHHHHCCCCCCCCCCCCEECCCCCC--EEE-EEECC
Q ss_conf             5101210345543114766443310100036531--133-10002
Q gi|254781101|r  305 ILTADVDTAIKALSVFHPKEGRGKRYRCALNQGF--FTL-IDESY  346 (472)
Q Consensus       305 ~lGi~~~~i~~~L~~~~~~~GR~~~~~~~~~~~~--~~i-IDDsY  346 (472)
                      +--+|+++|.+-+++-...++-++.+....+.+.  +-| +|.++
T Consensus       218 e~~lD~~kl~~i~~~~~~~~~~~~~~~~~~~~~~~kiava~D~aF  262 (464)
T TIGR00379       218 EKYLDLDKLLEIAEKARELDSEMELLWEDENKKYVKIAVARDQAF  262 (464)
T ss_pred             HHHCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEEEEEEECCC
T ss_conf             974497798887406787777521012345677237899973321


No 468
>COG0763 LpxB Lipid A disaccharide synthetase [Cell envelope biogenesis, outer membrane]
Probab=30.82  E-value=34  Score=13.92  Aligned_cols=21  Identities=19%  Similarity=0.311  Sum_probs=12.0

Q ss_pred             HHHHHHHHHCC-CCCEEEEECC
Q ss_conf             99999998306-9939998303
Q gi|254781101|r   96 NKLAVAARLRS-KATIIAITGS  116 (472)
Q Consensus        96 ~~la~~~~~~~-~~~vI~ITGT  116 (472)
                      ..|-+..+.++ +...+||.|-
T Consensus        18 a~LikaLk~~~~~~efvGvgG~   39 (381)
T COG0763          18 AGLIKALKARYPDVEFVGVGGE   39 (381)
T ss_pred             HHHHHHHHHHCCCEEEEEECCH
T ss_conf             9999999863898389981767


No 469
>PRK13973 thymidylate kinase; Provisional
Probab=30.64  E-value=34  Score=13.90  Aligned_cols=29  Identities=24%  Similarity=0.389  Sum_probs=23.0

Q ss_pred             CCCEEEEECC--CCCCHHHHHHHHHHHHHHC
Q ss_conf             9939998303--6542012334677775201
Q gi|254781101|r  107 KATIIAITGS--VGKTTTKEMLTIALSSIKK  135 (472)
Q Consensus       107 ~~~vI~ITGT--nGKTTt~~~l~~iL~~~~~  135 (472)
                      +++.|.+-|.  .||||-..+|+.-|...|.
T Consensus         2 kG~fIv~EGiDGsGKsTq~~~L~~~L~~~g~   32 (216)
T PRK13973          2 RGRFITFEGGEGAGKSTQIRLLAERLRAAGY   32 (216)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHCCC
T ss_conf             8249998899999899999999999997799


No 470
>PRK02269 ribose-phosphate pyrophosphokinase; Provisional
Probab=30.62  E-value=34  Score=13.90  Aligned_cols=60  Identities=15%  Similarity=0.112  Sum_probs=31.5

Q ss_pred             CEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECC
Q ss_conf             113310002565321012577787411102687138851235417105899999999998649989999880
Q gi|254781101|r  338 FFTLIDESYNANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGF  409 (472)
Q Consensus       338 ~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~  409 (472)
                      .+.|+||== .+-.++..|.+.|+.   .+. ++|.+...=   |-.+..-    .+.+...+++.|+..-.
T Consensus       219 ~vIIVDDiI-dTGgTl~~aa~~Lk~---~GA-~~V~~~~TH---gvfs~~A----~~rl~~s~i~~ivvTdT  278 (321)
T PRK02269        219 KCILIDDMI-DTAGTICHAADALAE---AGA-TAVYASCTH---PVLSGPA----LDNIQKSAIEKLIVLDT  278 (321)
T ss_pred             EEEEECCHH-HCHHHHHHHHHHHHH---CCC-CEEEEEEEC---CCCCHHH----HHHHHCCCCCEEEEECC
T ss_conf             699966243-142669999999984---899-827999978---0278479----99986089988998089


No 471
>TIGR02746 TraC-F-type type-IV secretion system protein TraC; InterPro: IPR014117   The proteins in this entry are found in the F, P and I-like type IV secretion systems. Gene symbols include TraC (F-type), TrbE/VirB4 (P-type) and TraU (I-type). The proteins contain the Walker A and B motifs and so are putative nucleotide triphosphatases..
Probab=30.58  E-value=24  Score=14.90  Aligned_cols=77  Identities=14%  Similarity=0.080  Sum_probs=34.3

Q ss_pred             CCEEEEEECC-----CCCCCCHHHHHHHHHHHHHCCCCCCEEEECCHHHCCCCHHHHHHHHHHHHHHCCCCEEEEECCCH
Q ss_conf             3113310002-----56532101257778741110268713885123541710589999999999864998999988038
Q gi|254781101|r  337 GFFTLIDESY-----NANPASMKAAISVLSQISPHGEGRRIAVLGDMCEMGELSQSFHIDLAEVLSLYNISHVWLSGFHV  411 (472)
Q Consensus       337 ~~~~iIDDsY-----NAnP~S~~aal~~l~~~~~~~~~r~i~VlG~m~ELG~~~~~~h~~i~~~~~~~~~d~v~~~G~~~  411 (472)
                      ..+.|||-+|     ++||.+. ..|++......+..|=.+.|.=.   +.|.-.+--.+=++.+.. +-|..++..-..
T Consensus       735 rK~~~iDEAW~Ll~~g~~~~~~-~FIE~gyRr~RK~~Ga~~tiTQ~---~~D~~~dka~~~arA~ya-NS~~~iiL~Q~~  809 (900)
T TIGR02746       735 RKILIIDEAWSLLDDGANPQAA-NFIETGYRRARKYGGAFITITQG---IEDFYSDKASPEARAAYA-NSDWKIILRQSA  809 (900)
T ss_pred             CEEEEEHHHHHHHHCCCCCHHH-HHHHHHHHCCHHHCCCEEEEECC---EEHHHCCCCCHHHHHHHH-CCCEEEEECCCH
T ss_conf             5167644248987427851358-98887632011116436899644---001000347988999884-533004127886


Q ss_pred             HHHHHHC
Q ss_conf             9899851
Q gi|254781101|r  412 LALKDAL  418 (472)
Q Consensus       412 ~~~~~~~  418 (472)
                      +.+.+..
T Consensus       810 ~~~~~~~  816 (900)
T TIGR02746       810 ESIEKLK  816 (900)
T ss_pred             HHHHHHH
T ss_conf             4789999


No 472
>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional
Probab=30.52  E-value=12  Score=16.89  Aligned_cols=26  Identities=35%  Similarity=0.305  Sum_probs=17.8

Q ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHHH
Q ss_conf             939998303654201233467777520
Q gi|254781101|r  108 ATIIAITGSVGKTTTKEMLTIALSSIK  134 (472)
Q Consensus       108 ~~vI~ITGTnGKTTt~~~l~~iL~~~~  134 (472)
                      .-.||=||| |||-...-|+.+|.-.+
T Consensus       112 ILliGPTG~-GKTlla~tLAk~l~vPF  137 (411)
T PRK05342        112 ILLIGPTGS-GKTLLAQTLARILNVPF  137 (411)
T ss_pred             EEEECCCCC-CHHHHHHHHHHHHCCCE
T ss_conf             899899997-78899999999869998


No 473
>pfam02492 cobW CobW/HypB/UreG, nucleotide-binding domain. This domain is found in HypB, a hydrogenase expression / formation protein, and UreG a urease accessory protein. Both these proteins contain a P-loop nucleotide binding motif. HypB has GTPase activity and is a guanine nucleotide binding protein. It is not known whether UreG binds GTP or some other nucleotide. Both enzymes are involved in nickel binding. HypB can store nickel and is required for nickel dependent hydrogenase expression. UreG is required for functional incorporation of the urease nickel metallocenter. GTP hydrolysis may required by these proteins for nickel incorporation into other nickel proteins. This family of domains also contains P47K, a Pseudomonas chlororaphis protein needed for nitrile hydratase expression, and the cobW gene product, which may be involved in cobalamin biosynthesis in Pseudomonas denitrificans.
Probab=30.44  E-value=34  Score=13.91  Aligned_cols=21  Identities=38%  Similarity=0.528  Sum_probs=15.6

Q ss_pred             CEEEEECC--CCCCHHHHHHHHHHHH
Q ss_conf             39998303--6542012334677775
Q gi|254781101|r  109 TIIAITGS--VGKTTTKEMLTIALSS  132 (472)
Q Consensus       109 ~vI~ITGT--nGKTTt~~~l~~iL~~  132 (472)
                      ||+-|||-  .||||   ++.++|+.
T Consensus         1 Pv~iitGFLGsGKTT---ll~~ll~~   23 (174)
T pfam02492         1 PVTVLTGFLGSGKTT---LLEHLLRD   23 (174)
T ss_pred             CEEEEECCCCCCHHH---HHHHHHHH
T ss_conf             969993488788999---99999984


No 474
>PRK10744 phosphate transporter subunit; Provisional
Probab=30.32  E-value=34  Score=13.86  Aligned_cols=26  Identities=23%  Similarity=0.327  Sum_probs=20.9

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHH
Q ss_conf             699399983036--54201233467777
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALS  131 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~  131 (472)
                      .++.++|+-|-|  ||||+-.++.-++.
T Consensus        34 ~~Ge~~~liG~nGaGKSTLlk~i~gl~~   61 (257)
T PRK10744         34 AKNQVTAFIGPSGCGKSTLLRTFNKMYE   61 (257)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHHC
T ss_conf             8998999999999819999999987651


No 475
>PRK11248 tauB taurine transporter ATP-binding subunit; Provisional
Probab=30.26  E-value=25  Score=14.82  Aligned_cols=27  Identities=19%  Similarity=0.353  Sum_probs=21.5

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHHHH
Q ss_conf             699399983036--542012334677775
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIALSS  132 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL~~  132 (472)
                      .++.+++|.|-|  ||||+-.+++-++..
T Consensus        25 ~~Ge~~~lvGpnGaGKSTLl~~i~Gl~~p   53 (255)
T PRK11248         25 ESGELLVVLGPSGCGKTTLLNLIAGFVPP   53 (255)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             69989999999984699999999759988


No 476
>PRK02224 chromosome segregation protein; Provisional
Probab=30.21  E-value=35  Score=13.85  Aligned_cols=25  Identities=28%  Similarity=0.299  Sum_probs=0.0

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHH
Q ss_conf             699399983036--5420123346777
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLTIAL  130 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~~iL  130 (472)
                      |+..+.+|+|-|  ||||.-+-|.+.|
T Consensus        21 F~~Gi~~I~G~NGsGKSsIldAI~~aL   47 (880)
T PRK02224         21 LEDGVTVIHGLNGSGKSSLLEACFFAL   47 (880)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             699858998999998899999999998


No 477
>cd03253 ABCC_ATM1_transporter ATM1 is an ABC transporter that is expressed in the mitochondria.  Although the specific function of ATM1 is unknown, its disruption results in the accumulation of excess mitochondrial iron, loss of mitochondrial cytochromes, oxidative damage to mitochondrial DNA, and decreased levels of cytosolic heme proteins.  ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.  The nucleotide binding domain shows the highest similarity between all members of the family.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=30.21  E-value=25  Score=14.82  Aligned_cols=25  Identities=28%  Similarity=0.341  Sum_probs=0.0

Q ss_pred             CCCEEEEECCC--CCCHHHHHHHHHHH
Q ss_conf             99399983036--54201233467777
Q gi|254781101|r  107 KATIIAITGSV--GKTTTKEMLTIALS  131 (472)
Q Consensus       107 ~~~vI~ITGTn--GKTTt~~~l~~iL~  131 (472)
                      ++..+||.|.+  ||||...++.-++.
T Consensus        26 ~Ge~v~ivG~sGsGKSTLl~ll~gl~~   52 (236)
T cd03253          26 AGKKVAIVGPSGSGKSTILRLLFRFYD   52 (236)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHCCCCC
T ss_conf             999999999999989999999743854


No 478
>PRK05312 pdxA 4-hydroxythreonine-4-phosphate dehydrogenase; Provisional
Probab=30.18  E-value=35  Score=13.85  Aligned_cols=70  Identities=19%  Similarity=0.280  Sum_probs=0.0

Q ss_pred             CCCCCHH-HHHHHH------HHCCCEEEEECCCCCCCCCCCCCCEEEECC------HHHHHHHHHHHHHHCC--CCCEEE
Q ss_conf             8874768-889999------986988999855212455446972899599------8999999999998306--993999
Q gi|254781101|r   48 GPHYDGH-DFILHA------VQKGAGLVVVNTDMVASIGSLSIPVFGVDD------VLGALNKLAVAARLRS--KATIIA  112 (472)
Q Consensus        48 g~~~DGh-~~i~~A------~~~Ga~~~i~~~~~~~~~~~~~~~~i~v~d------~~~al~~la~~~~~~~--~~~vI~  112 (472)
                      |.+|.|| +|+.+.      ...-....++............+|.-.|.+      ..+.+..+....+..+  +-|.||
T Consensus       132 G~~f~GHTE~LA~l~g~~~~~~~~~vMml~~~~LrV~l~TtHIpLk~V~~~It~~~I~~~i~l~~~~L~~~fgi~~PrIa  211 (336)
T PRK05312        132 GFAFPGHTEFLAELAGVALGKPVQPVMMLAGPQLRVVPVTIHIPLRDVPAALTTELIVATARITAADLRRRFGIAAPRLA  211 (336)
T ss_pred             CCCCCCHHHHHHHHHCCCCCCCCCEEEEEECCCCEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEE
T ss_conf             78889869999998554446777426886158736888533505999976544899999999999999985498887289


Q ss_pred             EECCC
Q ss_conf             83036
Q gi|254781101|r  113 ITGSV  117 (472)
Q Consensus       113 ITGTn  117 (472)
                      |+|=|
T Consensus       212 V~GLN  216 (336)
T PRK05312        212 VAGLN  216 (336)
T ss_pred             EEEEC
T ss_conf             99708


No 479
>cd03223 ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome.  The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation.  To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes.  X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family.  The disease is characterized by a striking and unpredictable variation in phenotypic expression.  Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asympt
Probab=30.16  E-value=23  Score=14.97  Aligned_cols=25  Identities=24%  Similarity=0.243  Sum_probs=0.0

Q ss_pred             CCCEEEEECCC--CCCHHHHHHHHHHH
Q ss_conf             99399983036--54201233467777
Q gi|254781101|r  107 KATIIAITGSV--GKTTTKEMLTIALS  131 (472)
Q Consensus       107 ~~~vI~ITGTn--GKTTt~~~l~~iL~  131 (472)
                      ++..++|+|.|  ||||.-.++.-++.
T Consensus        26 ~Ge~v~i~G~sGsGKSTLl~~l~Gl~~   52 (166)
T cd03223          26 PGDRLLITGPSGTGKSSLFRALAGLWP   52 (166)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHCCCCC
T ss_conf             999999995899988999999869876


No 480
>PRK10575 iron-hydroxamate transporter ATP-binding subunit; Provisional
Probab=30.12  E-value=26  Score=14.70  Aligned_cols=26  Identities=23%  Similarity=0.314  Sum_probs=0.0

Q ss_pred             CCCCEEEEECCCC--CCHHHHHHHHHHH
Q ss_conf             6993999830365--4201233467777
Q gi|254781101|r  106 SKATIIAITGSVG--KTTTKEMLTIALS  131 (472)
Q Consensus       106 ~~~~vI~ITGTnG--KTTt~~~l~~iL~  131 (472)
                      .++.++||.|-||  |||.-.++.-++.
T Consensus        35 ~~Ge~~~liG~NGaGKSTLl~~l~gl~~   62 (265)
T PRK10575         35 PAGKVTGLIGHNGSGKSTLLKMLGRHQP   62 (265)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCC
T ss_conf             7998999999999809999999956889


No 481
>PRK05035 electron transport complex protein RnfC; Provisional
Probab=30.09  E-value=35  Score=13.84  Aligned_cols=110  Identities=17%  Similarity=0.231  Sum_probs=0.0

Q ss_pred             CCCEEEEEEEECCCCCCCCEEEECCCCCCCHHHHHHHHH--HCCCEEEEECCCCC-----------------CCCCCCCC
Q ss_conf             871474677402223789888971688747688899999--86988999855212-----------------45544697
Q gi|254781101|r   23 PQGFVNGISIDSRSIAPQEAFFAIKGPHYDGHDFILHAV--QKGAGLVVVNTDMV-----------------ASIGSLSI   83 (472)
Q Consensus        23 ~~~~i~~i~~dSr~v~~g~lFval~g~~~DGh~~i~~A~--~~Ga~~~i~~~~~~-----------------~~~~~~~~   83 (472)
                      ++..|.|+.+=-+-+.+.-+.|+|...+-+.-.-+..|+  ..+....++...|+                 ......++
T Consensus       191 a~eIi~Gi~Il~~~l~~~~~iIgIEdNKPeAI~al~~a~~~~~~i~V~~lptkYPqGgEKqLI~~lTGreVP~G~lPadv  270 (725)
T PRK05035        191 ADEILEGIRILAHILQPKEVLIGIEDNKPEAIAALRAALAGADDIRVRVIPTKYPSGGEKQLIQILTGKEVPSGGRPADI  270 (725)
T ss_pred             HHHHHHHHHHHHHHHCCCEEEEEEECCCHHHHHHHHHHHCCCCCEEEEECCCCCCCCHHHHHHHHHHCCCCCCCCCCCCC
T ss_conf             99999999999998399879999838989999999997466998599981787999489999999949746899987656


Q ss_pred             CEEEECCHHHHHHHHHHHHHHCCCC-CEEEEECCCCCCHHHHHHHHHHHHHHCCCCCHHHHHCCCCCCCH
Q ss_conf             2899599899999999999830699-39998303654201233467777520112221221101457410
Q gi|254781101|r   84 PVFGVDDVLGALNKLAVAARLRSKA-TIIAITGSVGKTTTKEMLTIALSSIKKTYACIGSYNNHIGVPLT  152 (472)
Q Consensus        84 ~~i~v~d~~~al~~la~~~~~~~~~-~vI~ITGTnGKTTt~~~l~~iL~~~~~~~~t~gn~Nn~iGvplt  152 (472)
                      -++ |.|+-.++.-.-.....++-. +||-|||..                   +..+|||.-.||.|++
T Consensus       271 Gvv-v~NVgTa~AI~~Av~~G~PLieRvVTVTG~a-------------------v~~P~N~~v~iGTPv~  320 (725)
T PRK05035        271 GVL-MQNVGTAYAIKRAVIDGEPLIERVVTLTGEA-------------------VARPGNVWARLGTPVR  320 (725)
T ss_pred             CEE-EECHHHHHHHHHHHHCCCCEEEEEEEEECCC-------------------CCCCCEEEEECCCCHH
T ss_conf             659-8668999999999974997468999974675-------------------4899728997999599


No 482
>PRK11288 araG L-arabinose transporter ATP-binding protein; Provisional
Probab=30.01  E-value=32  Score=14.04  Aligned_cols=22  Identities=27%  Similarity=0.450  Sum_probs=0.0

Q ss_pred             CCCCEEEEECCC--CCCHHHHHHH
Q ss_conf             699399983036--5420123346
Q gi|254781101|r  106 SKATIIAITGSV--GKTTTKEMLT  127 (472)
Q Consensus       106 ~~~~vI~ITGTn--GKTTt~~~l~  127 (472)
                      .++.++|+.|.|  ||||...++.
T Consensus        28 ~~Ge~~~lvG~nGaGKSTL~~~l~   51 (501)
T PRK11288         28 RAGQVHALMGENGAGKSTLLKILS   51 (501)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHH
T ss_conf             898199998999981999999984


No 483
>cd03218 ABC_YhbG The ABC transporters belonging to the YhbG family are similar to members of the Mj1267_LivG family, which is involved in the transport of branched-chain amino acids.  The genes yhbG and yhbN are located in a single operon and may function together in cell envelope during biogenesis.  YhbG is the putative ATP-binding cassette component and YhbN is the putative periplasmic-binding protein.  Depletion of each gene product leads to growth arrest, irreversible cell damage and loss of viability in E. coli.  The YhbG homolog (NtrA) is essential in Rhizobium meliloti, a symbiotic nitrogen-fixing bacterium.
Probab=29.91  E-value=26  Score=14.70  Aligned_cols=26  Identities=31%  Similarity=0.392  Sum_probs=0.0

Q ss_pred             CCCCEEEEECCCC--CCHHHHHHHHHHH
Q ss_conf             6993999830365--4201233467777
Q gi|254781101|r  106 SKATIIAITGSVG--KTTTKEMLTIALS  131 (472)
Q Consensus       106 ~~~~vI~ITGTnG--KTTt~~~l~~iL~  131 (472)
                      .++.++|+-|-||  |||+-.++.-+++
T Consensus        24 ~~Gei~~llGpNGAGKSTll~~i~Gl~~   51 (232)
T cd03218          24 KQGEIVGLLGPNGAGKTTTFYMIVGLVK   51 (232)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCC
T ss_conf             9995999999999619999999977999


No 484
>PRK10619 histidine/lysine/arginine/ornithine transporter subunit; Provisional
Probab=29.90  E-value=26  Score=14.67  Aligned_cols=26  Identities=27%  Similarity=0.383  Sum_probs=0.0

Q ss_pred             CCCCEEEEECCCC--CCHHHHHHHHHHH
Q ss_conf             6993999830365--4201233467777
Q gi|254781101|r  106 SKATIIAITGSVG--KTTTKEMLTIALS  131 (472)
Q Consensus       106 ~~~~vI~ITGTnG--KTTt~~~l~~iL~  131 (472)
                      .++.++||-|-||  |||.-.++.-+..
T Consensus        29 ~~Gei~~iiG~sGsGKSTLl~~i~gl~~   56 (257)
T PRK10619         29 NAGDVISIIGSSGSGKSTFLRCINFLEK   56 (257)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCC
T ss_conf             7997999998999819999999965999


No 485
>PRK09544 znuC high-affinity zinc transporter ATPase; Reviewed
Probab=29.83  E-value=25  Score=14.73  Aligned_cols=25  Identities=20%  Similarity=0.324  Sum_probs=0.0

Q ss_pred             CCCEEEEECCC--CCCHHHHHHHHHHH
Q ss_conf             99399983036--54201233467777
Q gi|254781101|r  107 KATIIAITGSV--GKTTTKEMLTIALS  131 (472)
Q Consensus       107 ~~~vI~ITGTn--GKTTt~~~l~~iL~  131 (472)
                      ++.++|+.|-|  ||||.-.++.-++.
T Consensus        29 ~Gei~~LiGpNGaGKSTLlk~I~Gl~~   55 (251)
T PRK09544         29 PGKILTLLGPNGAGKSTLVRVVLGLVA   55 (251)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHCCCC
T ss_conf             997999998999889999999966888


No 486
>PRK11701 phnK phosphonates transport ATP-binding protein; Provisional
Probab=29.74  E-value=26  Score=14.72  Aligned_cols=25  Identities=32%  Similarity=0.492  Sum_probs=0.0

Q ss_pred             CCCEEEEECCC--CCCHHHHHHHHHHH
Q ss_conf             99399983036--54201233467777
Q gi|254781101|r  107 KATIIAITGSV--GKTTTKEMLTIALS  131 (472)
Q Consensus       107 ~~~vI~ITGTn--GKTTt~~~l~~iL~  131 (472)
                      ++.++||.|-|  ||||.-.++.-++.
T Consensus        31 ~GEi~~iiG~nGaGKSTLl~~i~G~~~   57 (258)
T PRK11701         31 PGEVLGIVGESGSGKTTLLNALSARLA   57 (258)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHCCCC
T ss_conf             997999988899889999999856788


No 487
>PRK07247 DNA polymerase III subunit epsilon; Validated
Probab=29.68  E-value=34  Score=13.88  Aligned_cols=85  Identities=14%  Similarity=0.150  Sum_probs=0.0

Q ss_pred             HHCCCC---CCCCCCCCCCCCCCCCEEE------EEEECCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHCCCCHHHHH
Q ss_conf             301566---4433211212232322025------5531210123444578888654331037622101210134246899
Q gi|254781101|r  164 IFELGM---SHLGEIRFLTHLVRPHIAV------ITTIAPAHLSNFSGIEEIASAKAEIFEGLEKTGTIFLNYDDSFFEL  234 (472)
Q Consensus       164 V~E~g~---~~~gei~~L~~i~~P~iai------iTNI~~dHld~~~s~e~i~~~K~~i~~~l~~~g~~ViN~Dd~~~~~  234 (472)
                      |+|+|+   .....++....+++|..-|      +|+|+.+.+..=.+++++..+-.+.+...+--+.-+.+.|-++...
T Consensus        23 IIEIgAVk~~~g~ivd~F~slVnP~~~I~~~i~~lTGIt~~~v~~aP~~~eVl~~f~~Figd~~lVaHNa~~FD~~fL~~  102 (195)
T PRK07247         23 IIQVSAVKYDHHKEVDSFDTYVYTDVPLQSFINGLTGITADKIAAAPKVEEVLAAFKNFVGELPLIGYNAQKSDLPILAE  102 (195)
T ss_pred             EEEEEEEEEECCEEEEEEEEEECCCCCCCHHHHHCCCCCHHHHHCCCCHHHHHHHHHHHHCCCEEEEECCCHHHHHHHHH
T ss_conf             69999999989989999983566989999555413598999983599999999999999689918990884514999999


Q ss_pred             HHHHCCCCCCCCCC
Q ss_conf             87520123333322
Q gi|254781101|r  235 LKAKSHALGIKTIY  248 (472)
Q Consensus       235 l~~~~~~~~~~~i~  248 (472)
                      .............+
T Consensus       103 ~~~~~~~~~~~~~~  116 (195)
T PRK07247        103 NGLDLRDQYQVDLF  116 (195)
T ss_pred             HHHHHCCCCCCCHH
T ss_conf             87741577668569


No 488
>cd06201 SiR_like2 Cytochrome p450- like alpha subunits of E. coli sulfite reductase (SiR) multimerize with beta subunits to catalyze the NADPH dependent reduction of sulfite to sulfide.  Beta subunits have an Fe4S4 cluster and a siroheme, while the alpha subunits (cysJ gene) are of the cytochrome p450 (CyPor) family having FAD and FMN as prosthetic groups and utilizing NADPH.  Cypor (including cyt -450 reductase, nitric oxide synthase, and methionine synthase reductase) are ferredoxin reductase (FNR)-like proteins with an additional N-terminal  FMN domain and a connecting sub-domain inserted within the flavin binding portion of the FNR-like domain. The connecting domain orients the N-terminal FMN domain with the C-terminal FNR domain. NADPH cytochrome p450 reductase (CYPOR) serves as an electron donor in several oxygenase systems and is a component of nitric oxide synthases and methionine synthase reductases. CYPOR transfers two electrons from NADPH to the heme of cytochrome p450 via F
Probab=29.67  E-value=35  Score=13.79  Aligned_cols=36  Identities=17%  Similarity=0.156  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHCCCCCEEEEECCCHHHHHHHHHHHHH
Q ss_conf             8999999998447898999977132548999999998
Q gi|254781101|r  430 MDGLFLFIQSSLVDGDVVVVKSSNSCGFYRLINLLLE  466 (472)
Q Consensus       430 ~e~a~~~l~~~~~~gdiVLiKGSr~~~le~iv~~L~~  466 (472)
                      +.+-.+.+.+.+..|..|+|+||+.|. .-|.+.|.+
T Consensus       231 l~~~~~~v~~~l~~ga~iyVCGs~~Ma-~~V~~aL~~  266 (289)
T cd06201         231 LRADAERLRRLIEDGAQIMVCGSRAMA-QGVAAVLEE  266 (289)
T ss_pred             HHHHHHHHHHHHHCCCEEEEECCCHHH-HHHHHHHHH
T ss_conf             999899999999889899994896089-999999999


No 489
>pfam00076 RRM_1 RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain). The RRM motif is probably diagnostic of an RNA binding protein. RRMs are found in a variety of RNA binding proteins, including various hnRNP proteins, proteins implicated in regulation of alternative splicing, and protein components of snRNPs. The motif also appears in a few single stranded DNA binding proteins. The RRM structure consists of four strands and two helices arranged in an alpha/beta sandwich, with a third helix present during RNA binding in some cases The C-terminal beta strand (4th strand) and final helix are hard to align and have been omitted in the SEED alignment The LA proteins have an N terminal rrm which is included in the seed. There is a second region towards the C terminus that has some features characteristic of a rrm but does not appear to have the important structural core of a rrm. The LA proteins are one of the main autoantigens in Systemic lupus erythematosus (SLE), an autoimmune disea
Probab=29.58  E-value=35  Score=13.78  Aligned_cols=61  Identities=15%  Similarity=0.179  Sum_probs=0.0

Q ss_pred             CCCCHHHHHHHHCCCCCCCCCCCCEECCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCE
Q ss_conf             012103455431147664433101000365311331000256532101257778741110268713
Q gi|254781101|r  307 TADVDTAIKALSVFHPKEGRGKRYRCALNQGFFTLIDESYNANPASMKAAISVLSQISPHGEGRRI  372 (472)
Q Consensus       307 Gi~~~~i~~~L~~~~~~~GR~~~~~~~~~~~~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i  372 (472)
                      .++.+++.+-++.|.++..-.-...-.....+.-+|.  | .++++...|++.+...  .-.||+|
T Consensus         9 ~~t~~~l~~~F~~~G~v~~v~i~~~~~g~~~g~afV~--f-~~~~~A~~Ai~~lng~--~~~gr~i   69 (70)
T pfam00076         9 DTTEEDLKDLFSKFGPIESIKIVRDETGRSKGFAFVE--F-EDEEDAEKALEALNGK--ELGGREL   69 (70)
T ss_pred             CCCHHHHHHHHHHHCCCCCCCEEECCCCCCCCCEEEE--E-CCHHHHHHHHHHHCCC--EECCCCC
T ss_conf             5889999999998398142422223578878977999--8-8999999999985999--8396099


No 490
>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes.  The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch.  Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily.  MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined.  Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes.  The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis.  All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action.  MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c
Probab=29.55  E-value=35  Score=13.78  Aligned_cols=28  Identities=29%  Similarity=0.339  Sum_probs=0.0

Q ss_pred             CCCEEEEECCC--CCCHHHHH--HHHHHHHHH
Q ss_conf             99399983036--54201233--467777520
Q gi|254781101|r  107 KATIIAITGSV--GKTTTKEM--LTIALSSIK  134 (472)
Q Consensus       107 ~~~vI~ITGTn--GKTTt~~~--l~~iL~~~~  134 (472)
                      ..+++=|||.|  ||||.-..  +..+|.+.|
T Consensus        28 ~~~~~iITGpN~gGKSt~Lktigl~~ilAq~G   59 (204)
T cd03282          28 SSRFHIITGPNMSGKSTYLKQIALLAIMAQIG   59 (204)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHHHHC
T ss_conf             72599998999887199999999999999968


No 491
>COG1121 ZnuC ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]
Probab=29.52  E-value=35  Score=13.78  Aligned_cols=22  Identities=41%  Similarity=0.602  Sum_probs=0.0

Q ss_pred             CCCCEEEEECCCC--CCHHHHHHHHHH
Q ss_conf             6993999830365--420123346777
Q gi|254781101|r  106 SKATIIAITGSVG--KTTTKEMLTIAL  130 (472)
Q Consensus       106 ~~~~vI~ITGTnG--KTTt~~~l~~iL  130 (472)
                      .++.++||.|-||  |||   ++..+|
T Consensus        28 ~~G~~~~iiGPNGaGKST---LlK~iL   51 (254)
T COG1121          28 EKGEITALIGPNGAGKST---LLKAIL   51 (254)
T ss_pred             CCCCEEEEECCCCCCHHH---HHHHHH
T ss_conf             489689999998888899---999996


No 492
>pfam05872 DUF853 Bacterial protein of unknown function (DUF853). This family consists of several bacterial proteins of unknown function. One member from Brucella melitensis is thought to be an ATPase.
Probab=29.50  E-value=25  Score=14.75  Aligned_cols=27  Identities=33%  Similarity=0.434  Sum_probs=0.0

Q ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHH
Q ss_conf             9939998303654201233467777520
Q gi|254781101|r  107 KATIIAITGSVGKTTTKEMLTIALSSIK  134 (472)
Q Consensus       107 ~~~vI~ITGTnGKTTt~~~l~~iL~~~~  134 (472)
                      ++-|-|-||| |||-|-..++.-|+..|
T Consensus        23 HGLiaGATGT-GKTvTLq~lAE~~S~~G   49 (504)
T pfam05872        23 HGLIAGATGT-GKTVTLQVLAESFSDAG   49 (504)
T ss_pred             CCEECCCCCC-CHHHHHHHHHHHHHHCC
T ss_conf             1662265778-61789999999874549


No 493
>TIGR02153 gatD_arch glutamyl-tRNA(Gln) amidotransferase, subunit D; InterPro: IPR011878    This peptide is found only in the Archaea. It is part of a heterodimer, with GatD (IPR004414 from INTERPRO), that acts as an amidotransferase on misacylated Glu-tRNA(Gln) to produce Gln-tRNA(Gln). The analogous amidotransferase found in bacteria is the GatABC system, although GatABC homologs in the Archaea appear to act instead on Asp-tRNA(Asn) .; GO: 0006450 regulation of translational fidelity.
Probab=29.48  E-value=36  Score=13.77  Aligned_cols=54  Identities=22%  Similarity=0.142  Sum_probs=0.0

Q ss_pred             HH------HHHHHHHHCCCEEEEECCC---------CCCCCCCCCCCEEEECC--HHHHHHHHHHHHHHCCC
Q ss_conf             68------8899999869889998552---------12455446972899599--89999999999983069
Q gi|254781101|r   53 GH------DFILHAVQKGAGLVVVNTD---------MVASIGSLSIPVFGVDD--VLGALNKLAVAARLRSK  107 (472)
Q Consensus        53 Gh------~~i~~A~~~Ga~~~i~~~~---------~~~~~~~~~~~~i~v~d--~~~al~~la~~~~~~~~  107 (472)
                      ||      ++|+.|.+.|...+++++.         |.-.-.-...=+|-.+|  |..||.+| .|.+.+++
T Consensus       320 GHvs~~~ip~i~ra~d~Gv~V~MTSQClyGRVNlnVY~TGR~Ll~aGVIp~EDMlPEvAyVKL-MWvLg~~~  390 (413)
T TIGR02153       320 GHVSEDWIPSIKRATDDGVPVVMTSQCLYGRVNLNVYSTGRELLKAGVIPGEDMLPEVAYVKL-MWVLGQTD  390 (413)
T ss_pred             CCCHHHHHHHHHHHHHCCCEEEEEEEEECCEECCCCCCCHHHHHHCCCCCCCCCCHHHHHHHH-HHHHCCCC
T ss_conf             555235899999987589689996114335050753433489997587278888769999999-99746898


No 494
>PRK00934 ribose-phosphate pyrophosphokinase; Provisional
Probab=29.47  E-value=36  Score=13.77  Aligned_cols=161  Identities=14%  Similarity=0.086  Sum_probs=0.0

Q ss_pred             CCCCCHHHHHHHHCCCCHHHHHHHHCCCCCCCCCCCCEECCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCCEE
Q ss_conf             33221035676510121034554311476644331010003653113310002565321012577787411102687138
Q gi|254781101|r  294 QNMLMTLGIVSILTADVDTAIKALSVFHPKEGRGKRYRCALNQGFFTLIDESYNANPASMKAAISVLSQISPHGEGRRIA  373 (472)
Q Consensus       294 ~NalaAia~~~~lGi~~~~i~~~L~~~~~~~GR~~~~~~~~~~~~~~iIDDsYNAnP~S~~aal~~l~~~~~~~~~r~i~  373 (472)
                      .|-..|-.+|..||+++-.+.  +..|.--+-..+..+-..+ ..+.++..++..| +.+...|-.+..++.....|.++
T Consensus         7 s~~~La~~ia~~Lg~~l~~~~--~~~F~DGE~~v~i~~~vrg-~dV~i~~~~~~~n-d~lmELll~i~A~r~a~A~~It~   82 (286)
T PRK00934          7 GSQNLAAEVAKLLNSELARVE--TKKFPDGELYVRVDEELGG-EDIVIISTQYPQD-ENLIELILLLDALRDEGVKSITL   82 (286)
T ss_pred             CCHHHHHHHHHHHCCCCEEEE--EEECCCCCEEEEECCCCCC-CEEEEEECCCCCC-HHHHHHHHHHHHHHHCCCCEEEE
T ss_conf             989999999998699714128--8988999889986887799-8699991899984-79999999999998758973899


Q ss_pred             EECCHHHCCCCHHHH------HHHHHHHHHHCCCCEEEEECCCHHHHHHHCCCCCCEEEECCHHHHHHHHHHHCCCCCEE
Q ss_conf             851235417105899------99999999864998999988038989985113797999789899999999844789899
Q gi|254781101|r  374 VLGDMCEMGELSQSF------HIDLAEVLSLYNISHVWLSGFHVLALKDALPRSIHVHYSETMDGLFLFIQSSLVDGDVV  447 (472)
Q Consensus       374 VlG~m~ELG~~~~~~------h~~i~~~~~~~~~d~v~~~G~~~~~~~~~~~~~~~~~~~~~~e~a~~~l~~~~~~gdiV  447 (472)
                      |+.-|.-.-.+....      -+-+++.+... +|.|+++.-+...+...+  ..++........+.++++.  ..++.+
T Consensus        83 ViPY~~YsRQDr~~~~ge~isak~va~ll~~~-~d~vitvDlH~~~i~~fF--~~p~~nl~~~~~~~~~~~~--~~~~~v  157 (286)
T PRK00934         83 VAPYLAYARQDRRFKEGEPISIKALAKVYSSY-YDEIITINIHEEHTLEFF--DIPFTNLSAMPAIAEYIKE--KLVDPL  157 (286)
T ss_pred             ECCCCCCCCCCCCCCCCCCCCHHHHHHHHHHH-CCEEEEEECCHHHHHHCC--CCCCCCCCCCHHHHHHHHH--HCCCCE
T ss_conf             83465533464346899865089999999753-174699947887884046--8983111057145899984--388878


Q ss_pred             EE---ECCCHHHHHHHHHHH
Q ss_conf             99---771325489999999
Q gi|254781101|r  448 VV---KSSNSCGFYRLINLL  464 (472)
Q Consensus       448 Li---KGSr~~~le~iv~~L  464 (472)
                      ++   .|+.. +-+.+.+.|
T Consensus       158 VVsPD~G~~~-ra~~~a~~L  176 (286)
T PRK00934        158 VLAPDKGALE-RAKEVAEIL  176 (286)
T ss_pred             EECCCCCHHH-HHHHHHHHH
T ss_conf             9847974899-999999975


No 495
>PRK00168 coaD phosphopantetheine adenylyltransferase; Provisional
Probab=29.29  E-value=36  Score=13.75  Aligned_cols=76  Identities=20%  Similarity=0.242  Sum_probs=0.0

Q ss_pred             CEEEECCHHHCCCCHHHH--HHHHHHHHHHCCCCEEEEE-------------CCCHHHHHHHCCCCCCEEEECCHHHHHH
Q ss_conf             138851235417105899--9999999986499899998-------------8038989985113797999789899999
Q gi|254781101|r  371 RIAVLGDMCEMGELSQSF--HIDLAEVLSLYNISHVWLS-------------GFHVLALKDALPRSIHVHYSETMDGLFL  435 (472)
Q Consensus       371 ~i~VlG~m~ELG~~~~~~--h~~i~~~~~~~~~d~v~~~-------------G~~~~~~~~~~~~~~~~~~~~~~e~a~~  435 (472)
                      |++|++     |...+-.  |..|.+.+.+. +|.|+..             .+..+-+.+++....++....--.-.++
T Consensus         2 riai~p-----GSFDPit~GHldii~ra~~l-fD~viv~v~~Np~K~~~f~~eeR~~mi~~~~~~~~nv~V~~~~gL~vd   75 (159)
T PRK00168          2 KIAIYP-----GSFDPITNGHLDIIERASKL-FDEVIVAVAINPSKKPLFSLEERVELIREVTAHLPNVEVVGFDGLLVD   75 (159)
T ss_pred             CEEEEC-----CCCCCCCHHHHHHHHHHHHH-CCEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCCEEEEECCCHHHH
T ss_conf             489947-----26798844799999999986-799999405698877778999999999998515899799943650323


Q ss_pred             HHHHHCCCCCEEEEECCCHH
Q ss_conf             99984478989999771325
Q gi|254781101|r  436 FIQSSLVDGDVVVVKSSNSC  455 (472)
Q Consensus       436 ~l~~~~~~gdiVLiKGSr~~  455 (472)
                      ++++.   |..++++|-|..
T Consensus        76 ~ak~~---~a~~iiRGlR~~   92 (159)
T PRK00168         76 FAREV---GATVIVRGLRAV   92 (159)
T ss_pred             HHHHC---CCEEEEEECCCC
T ss_conf             57766---984999605640


No 496
>PRK06031 phosphoribosyltransferase; Provisional
Probab=29.22  E-value=36  Score=13.74  Aligned_cols=88  Identities=25%  Similarity=0.289  Sum_probs=0.0

Q ss_pred             CCCHHHHHHHHCCCC-------------HHHHHHHHCCCCCCCCCCCCEE------CCCCCCEEEEEECCCCCCCCHHHH
Q ss_conf             221035676510121-------------0345543114766443310100------036531133100025653210125
Q gi|254781101|r  296 MLMTLGIVSILTADV-------------DTAIKALSVFHPKEGRGKRYRC------ALNQGFFTLIDESYNANPASMKAA  356 (472)
Q Consensus       296 alaAia~~~~lGi~~-------------~~i~~~L~~~~~~~GR~~~~~~------~~~~~~~~iIDDsYNAnP~S~~aa  356 (472)
                      +..|.++++.+|.+.             ++....++++.. |+-..|+.+      ......+.+|||.- ++-.|+.++
T Consensus        96 l~lA~~Var~LG~~rYVplg~SrKfwy~d~Ls~~vsSITt-p~~~krlylDp~~lpLl~GrRV~lVDDVI-SSG~Si~a~  173 (233)
T PRK06031         96 LTLAAAVARKLGHTRYVPLGTSRKFWYDDELSVPLSSITT-PDQGKRLYIDPRMLPLLRGRRVALIDDVI-SSGASIVAA  173 (233)
T ss_pred             CHHHHHHHHHCCCCCEEECCCCCCCCHHHHHCCCEECCCC-CCCCCEEEECHHHHHHHCCCEEEEEECHH-CCCHHHHHH
T ss_conf             0458999997097636765647753313443551000358-88773156774441243287799982122-155659999


Q ss_pred             HHHHHHHHHCCCCCCEEEEC-CHHHCCCCHHHHHHHHHH
Q ss_conf             77787411102687138851-235417105899999999
Q gi|254781101|r  357 ISVLSQISPHGEGRRIAVLG-DMCEMGELSQSFHIDLAE  394 (472)
Q Consensus       357 l~~l~~~~~~~~~r~i~VlG-~m~ELG~~~~~~h~~i~~  394 (472)
                      |+.|...-.+     ++.+| .|.|    ++.++..+..
T Consensus       174 l~LL~~~G~e-----~v~igvaM~Q----~erWre~l~a  203 (233)
T PRK06031        174 LRLLATCGIE-----PAGIGAAMLQ----SERWRESLAA  203 (233)
T ss_pred             HHHHHHCCCC-----EEEEEEEEHH----HHHHHHHHHH
T ss_conf             9999975997-----3788763214----4567787751


No 497
>cd03243 ABC_MutS_homologs The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch.  Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily.  MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined.  Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes.  The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis.  All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action.  MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA stru
Probab=29.10  E-value=36  Score=13.73  Aligned_cols=24  Identities=29%  Similarity=0.468  Sum_probs=0.0

Q ss_pred             CCCEEEEECCC--CCCHHHHHHHHHH
Q ss_conf             99399983036--5420123346777
Q gi|254781101|r  107 KATIIAITGSV--GKTTTKEMLTIAL  130 (472)
Q Consensus       107 ~~~vI~ITGTn--GKTTt~~~l~~iL  130 (472)
                      +.+++-|||.|  ||||.-..++...
T Consensus        28 ~~~~~iiTGpN~sGKSt~lkti~l~~   53 (202)
T cd03243          28 SGRLLLITGPNMGGKSTYLRSIGLAV   53 (202)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             98289998998875399999999999


No 498
>PRK13813 orotidine 5'-phosphate decarboxylase; Provisional
Probab=29.08  E-value=36  Score=13.73  Aligned_cols=59  Identities=19%  Similarity=0.193  Sum_probs=0.0

Q ss_pred             CCCCCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEECCCCCCCCCCCCCCEEEECCHHHHHHHHHHHHHHC
Q ss_conf             22378988897168874768889999986988999855212455446972899599899999999999830
Q gi|254781101|r   35 RSIAPQEAFFAIKGPHYDGHDFILHAVQKGAGLVVVNTDMVASIGSLSIPVFGVDDVLGALNKLAVAARLR  105 (472)
Q Consensus        35 r~v~~g~lFval~g~~~DGh~~i~~A~~~Ga~~~i~~~~~~~~~~~~~~~~i~v~d~~~al~~la~~~~~~  105 (472)
                      |+.-+.++.+--+|-+..|.. ..+|+++||..+|+           ..|+..-+||.++..++-+....+
T Consensus       157 r~~~~~~~~ivtPGI~~~~~~-~~~ai~~Gad~iVV-----------GR~It~A~dP~~aa~~i~~~i~g~  215 (215)
T PRK13813        157 RRRLGDDLKIISPGIGAQGGK-ASDAIKAGADYVIV-----------GRSIYNAADPREAAKKIREEILGK  215 (215)
T ss_pred             HHHCCCCCEEECCCCCCCCCC-HHHHHHHCCCEEEE-----------CCCCCCCCCHHHHHHHHHHHHCCC
T ss_conf             986288746985761679999-89999818999998-----------943358999999999999986799


No 499
>PRK11022 dppD dipeptide transporter ATP-binding subunit; Provisional
Probab=29.01  E-value=27  Score=14.57  Aligned_cols=32  Identities=16%  Similarity=0.282  Sum_probs=0.0

Q ss_pred             CCCEEEEECCCC--CCHHHHHHHHHHHHHHCCCC
Q ss_conf             993999830365--42012334677775201122
Q gi|254781101|r  107 KATIIAITGSVG--KTTTKEMLTIALSSIKKTYA  138 (472)
Q Consensus       107 ~~~vI~ITGTnG--KTTt~~~l~~iL~~~~~~~~  138 (472)
                      .+.++||-|-+|  |||+...+.-+|...+++..
T Consensus        32 ~GEilgivGeSGsGKSTl~~~ilgll~~~~~~~~   65 (327)
T PRK11022         32 QGEVVGIVGESGSGKSVSSLAIMGLIDYPGRVMA   65 (327)
T ss_pred             CCCEEEEECCCCCHHHHHHHHHHCCCCCCCCEEE
T ss_conf             9999999999987899999999748898997654


No 500
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=28.97  E-value=36  Score=13.71  Aligned_cols=62  Identities=11%  Similarity=0.101  Sum_probs=0.0

Q ss_pred             CCCCCCCEEEECC--CCCCCHHHHHHHHHHCCCEEEEECCCCCCCCCCCCCCEEEECCHHHHHH
Q ss_conf             2237898889716--8874768889999986988999855212455446972899599899999
Q gi|254781101|r   35 RSIAPQEAFFAIK--GPHYDGHDFILHAVQKGAGLVVVNTDMVASIGSLSIPVFGVDDVLGALN   96 (472)
Q Consensus        35 r~v~~g~lFval~--g~~~DGh~~i~~A~~~Ga~~~i~~~~~~~~~~~~~~~~i~v~d~~~al~   96 (472)
                      +.+.|+|++|++-  |...+=.+.++.|.++||..+.+......+.....--.+.+......+.
T Consensus       175 ~~l~~~Dv~I~iS~sG~t~~~~~~~~~Ak~~Ga~iIaIT~~~~spLa~~aD~~L~~~~~e~~~~  238 (282)
T PRK11557        175 QALSPDDLLLAISYSGERRELNLAADEALRVGGKVLAITGFTPNALQQRASHCLYTIAEEQATR  238 (282)
T ss_pred             HHCCCCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEECCCCCCCHHHHCCEEEEECCCCCCCC
T ss_conf             8189999899985999978999999999987993999729899815886999998478531013


Done!