Query         gi|254780901|ref|YP_003065314.1| single-stranded-DNA-specific exonuclease protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 600
No_of_seqs    191 out of 2089
Neff          6.5 
Searched_HMMs 39220
Date          Mon May 30 01:55:05 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780901.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR00644 recJ single-stranded 100.0       0       0 1274.7  50.9  551   39-589     1-705 (705)
  2 PRK11070 ssDNA exonuclease Rec 100.0       0       0 1262.4  56.0  547   36-592    16-574 (574)
  3 COG0608 RecJ Single-stranded D 100.0       0       0  776.7  33.2  466   64-551     9-476 (491)
  4 pfam01368 DHH DHH family. It i  99.7 9.9E-17 2.5E-21  150.8  13.7  150   88-250     1-156 (156)
  5 COG1107 Archaea-specific RecJ-  99.5 1.5E-11 3.9E-16  110.2  18.3  341   73-462   324-708 (715)
  6 COG0618 Exopolyphosphatase-rel  99.3 7.3E-08 1.9E-12   81.4  25.9  301   80-466     4-326 (332)
  7 COG2404 Predicted phosphohydro  98.6 9.9E-06 2.5E-10   64.8  16.0  303   94-462     1-317 (339)
  8 COG3887 Predicted signaling pr  98.3 0.00093 2.4E-08   49.3  22.0  301   75-470   323-653 (655)
  9 pfam02272 DHHA1 DHHA1 domain.   98.1 2.6E-06 6.6E-11   69.3   3.9   65  395-461     1-68  (69)
 10 pfam02724 CDC45 CDC45-like pro  96.1   0.039 9.9E-07   36.7   7.4   85   94-184     1-86  (584)
 11 PRK02947 hypothetical protein;  95.9    0.19   5E-06   31.2  12.9  153   73-233    22-217 (247)
 12 cd04492 YhaM_OBF_like YhaM_OBF  95.9   0.084 2.1E-06   34.1   8.5   79  510-597     3-81  (83)
 13 PRK00286 xseA exodeoxyribonucl  95.7    0.21 5.4E-06   30.9  10.1   21  307-327   245-265 (443)
 14 LOAD_cdc45 consensus            95.6   0.094 2.4E-06   33.7   7.8   88   91-184    13-101 (578)
 15 cd04489 ExoVII_LU_OBF ExoVII_L  95.2    0.17 4.5E-06   31.6   8.3   71  517-592     7-77  (78)
 16 TIGR03316 ygeW probable carbam  94.8     0.3 7.7E-06   29.7   8.5   52  105-156    52-104 (357)
 17 CHL00162 thiG thiamin biosynth  94.7    0.45 1.1E-05   28.4   9.3  103   62-178   113-216 (267)
 18 PRK00208 thiG thiazole synthas  94.4    0.45 1.2E-05   28.3   8.5  103   61-177    99-202 (256)
 19 cd04728 ThiG Thiazole synthase  94.2    0.58 1.5E-05   27.5   9.0  103   61-177    98-201 (248)
 20 pfam03345 DDOST_48kD Oligosacc  94.0    0.62 1.6E-05   27.3  10.3   95   90-185    14-136 (439)
 21 pfam05690 ThiG Thiazole biosyn  94.0    0.63 1.6E-05   27.2   9.2  103   61-177    97-200 (246)
 22 PRK11840 bifunctional sulfur c  94.0    0.63 1.6E-05   27.2   9.3   26  106-131    94-119 (327)
 23 TIGR00486 TIGR00486 conserved   93.9     0.1 2.6E-06   33.4   4.4   31  150-184    48-78  (325)
 24 PRK13480 3'-5' exoribonuclease  93.7    0.47 1.2E-05   28.2   7.5   37  271-315   120-156 (314)
 25 COG1570 XseA Exonuclease VII,   93.4    0.77   2E-05   26.5   9.4   18  210-227   101-118 (440)
 26 COG2022 ThiG Uncharacterized e  93.4    0.71 1.8E-05   26.8   8.0  103   61-177   105-208 (262)
 27 PTZ00254 40S ribosomal protein  93.1    0.84 2.1E-05   26.2  11.2   89   78-178    58-146 (242)
 28 TIGR00064 ftsY signal recognit  92.8    0.94 2.4E-05   25.8  10.0  139   25-180    19-172 (284)
 29 KOG3108 consensus               92.4     1.1 2.7E-05   25.5   9.3   90  500-596    52-149 (265)
 30 COG0052 RpsB Ribosomal protein  92.3     1.1 2.7E-05   25.4   9.8  135   75-227    47-225 (252)
 31 TIGR02188 Ac_CoA_lig_AcsA acet  92.1    0.79   2E-05   26.4   6.9  340   71-470    99-588 (643)
 32 KOG2475 consensus               92.1     1.1 2.9E-05   25.2   7.8  104   76-185     6-111 (587)
 33 cd01539 PBP1_GGBP Periplasmic   91.4    0.77   2E-05   26.5   6.1   73  115-188    24-97  (303)
 34 PRK00252 alaS alanyl-tRNA synt  90.6     1.5 3.9E-05   24.2  14.7   96  369-465   761-861 (864)
 35 cd00079 HELICc Helicase superf  90.6     1.5 3.9E-05   24.2   8.1   77   77-160    13-89  (131)
 36 PRK07200 aspartate/ornithine c  90.6     1.6   4E-05   24.1   8.6   48  107-154    71-119 (395)
 37 pfam06506 PrpR_N Propionate ca  90.3     1.6 4.1E-05   24.0   6.9  132   26-180    17-148 (169)
 38 PRK13936 phosphoheptose isomer  90.2     1.7 4.2E-05   23.9   7.8  104   76-183    27-148 (197)
 39 PRK05427 putative manganese-de  90.1       1 2.7E-05   25.5   5.9   88   93-186     2-104 (311)
 40 pfam02571 CbiJ Precorrin-6x re  89.8     1.8 4.5E-05   23.7   8.0   22   94-120     2-23  (246)
 41 cd06313 PBP1_ABC_sugar_binding  89.7     1.8 4.6E-05   23.6   6.9   67  114-183    23-90  (272)
 42 cd06368 PBP1_iGluR_non_NMDA_li  89.2       2   5E-05   23.4   7.9   33  147-179    60-92  (324)
 43 cd06317 PBP1_ABC_sugar_binding  88.9       2 5.2E-05   23.2   7.6   70  114-186    24-94  (275)
 44 pfam00977 His_biosynth Histidi  88.5     2.2 5.5E-05   23.0   6.6   69  112-181    34-103 (229)
 45 PRK00414 gmhA phosphoheptose i  88.4     2.2 5.6E-05   23.0   9.6  112   67-182    19-147 (192)
 46 COG4821 Uncharacterized protei  88.4     1.1 2.9E-05   25.2   5.0   98   74-180    20-138 (243)
 47 pfam10740 DUF2529 Protein of u  88.2     2.2 5.7E-05   22.9   7.0  109   77-198    23-135 (172)
 48 cd06380 PBP1_iGluR_AMPA N-term  88.2     2.3 5.8E-05   22.9   7.0   47  132-179    46-92  (382)
 49 PRK10355 xylF D-xylose transpo  87.7     1.6 4.2E-05   24.0   5.5   46  138-183    70-116 (330)
 50 cd06393 PBP1_iGluR_Kainate_Glu  87.7     2.4 6.1E-05   22.7   7.9   10  168-177    91-100 (384)
 51 PRK04523 N-acetylornithine car  87.6     2.4 6.2E-05   22.6   6.5   11  172-182   104-114 (335)
 52 PRK02255 putrescine carbamoylt  87.3     2.5 6.4E-05   22.5   6.7   31  106-136    54-85  (341)
 53 cd05006 SIS_GmhA Phosphoheptos  87.1     2.6 6.6E-05   22.4   8.3  105   75-183    16-138 (177)
 54 PRK13585 1-(5-phosphoribosyl)-  87.0     2.6 6.6E-05   22.4   7.3   71  111-182    35-106 (240)
 55 COG1737 RpiR Transcriptional r  86.8     2.7 6.8E-05   22.3  13.8  187   29-227    38-258 (281)
 56 TIGR02691 arsC_pI258_fam arsen  86.8       1 2.6E-05   25.6   4.0   70  104-179     6-75  (129)
 57 KOG0781 consensus               86.0     2.9 7.4E-05   22.0   7.1   35   76-117    74-108 (587)
 58 cd06312 PBP1_ABC_sugar_binding  86.0     2.9 7.4E-05   22.0   7.6   81  115-197    25-106 (271)
 59 PRK01710 murD UDP-N-acetylmura  85.5     3.1 7.8E-05   21.8   9.7   88   76-177     3-105 (458)
 60 PRK03092 ribose-phosphate pyro  85.5     2.2 5.6E-05   22.9   5.2   78   85-162    30-119 (304)
 61 cd01425 RPS2 Ribosomal protein  85.4     3.1 7.9E-05   21.8  10.6   97   74-178    38-155 (193)
 62 PRK09701 D-allose transporter   85.3     2.1 5.4E-05   23.1   5.0   68  116-184    50-118 (311)
 63 PRK01747 mnmC 5-methylaminomet  85.1     3.2 8.1E-05   21.7   6.3  128   83-226   185-332 (660)
 64 COG0552 FtsY Signal recognitio  85.0     3.2 8.2E-05   21.7   7.0   19  384-403   301-319 (340)
 65 PRK05299 rpsB 30S ribosomal pr  84.9     3.2 8.3E-05   21.6  10.7  100   75-182    47-190 (255)
 66 COG5235 RFA2 Single-stranded D  84.5     3.4 8.6E-05   21.5   8.0   72  367-444    56-136 (258)
 67 pfam09547 Spore_IV_A Stage IV   84.5       2   5E-05   23.4   4.5   33  384-416   366-400 (492)
 68 cd04723 HisA_HisF Phosphoribos  84.1     3.5 8.9E-05   21.4   6.3   67  112-180    40-107 (233)
 69 PRK03806 murD UDP-N-acetylmura  84.0     3.5   9E-05   21.3   6.1   74   91-177     5-93  (438)
 70 PRK00779 ornithine carbamoyltr  83.8     3.6 9.2E-05   21.3   8.3   37  174-211   100-140 (308)
 71 cd06316 PBP1_ABC_sugar_binding  83.7     3.6 9.2E-05   21.3   6.4   81  115-197    24-106 (294)
 72 cd03109 DTBS Dethiobiotin synt  83.5     3.7 9.4E-05   21.2   8.1   82   95-176     1-99  (134)
 73 cd04732 HisA HisA.  Phosphorib  83.5     3.7 9.4E-05   21.2   7.0   68  111-179    33-101 (234)
 74 cd05013 SIS_RpiR RpiR-like pro  83.4     3.7 9.5E-05   21.2  12.1  108   77-199     2-114 (139)
 75 PRK03515 ornithine carbamoyltr  83.3     3.7 9.5E-05   21.2   7.8   25  105-129    55-80  (334)
 76 PRK01506 consensus              83.3     2.3 5.9E-05   22.8   4.5   75   87-162    52-139 (317)
 77 pfam00148 Oxidored_nitro Nitro  83.3     3.8 9.6E-05   21.1  10.0   24   75-98     56-81  (398)
 78 TIGR01334 modD modD protein; I  83.2     3.7 9.4E-05   21.2   5.5   23  106-128    45-67  (277)
 79 PRK01132 consensus              82.6     2.8   7E-05   22.2   4.7   68   91-158    46-123 (286)
 80 cd01968 Nitrogenase_NifE_I Nit  82.3       4  0.0001   20.9  10.8   47   73-125    66-122 (410)
 81 COG0365 Acs Acyl-coenzyme A sy  82.3     4.1  0.0001   20.9   8.4   98   73-181    41-147 (528)
 82 PRK04128 1-(5-phosphoribosyl)-  82.3     4.1  0.0001   20.9   7.1   63  116-180    39-102 (228)
 83 TIGR00461 gcvP glycine dehydro  81.7    0.43 1.1E-05   28.5   0.2  150   79-257    51-250 (965)
 84 PRK05038 consensus              81.7     3.5 8.8E-05   21.4   4.9   74   87-161    46-133 (315)
 85 cd06305 PBP1_methylthioribose_  81.5     4.3 0.00011   20.7   6.6   69  113-184    22-91  (273)
 86 PRK10416 cell division protein  81.4     4.3 0.00011   20.6   7.0   36  367-402   294-331 (499)
 87 PRK09428 pssA phosphatidylseri  81.3     4.3 0.00011   20.7   5.3   74   79-155    59-144 (444)
 88 cd06324 PBP1_ABC_sugar_binding  81.3     4.4 0.00011   20.6   8.4   49  139-187    46-96  (305)
 89 COG3980 spsG Spore coat polysa  81.3     4.4 0.00011   20.6   6.7  120   94-214     2-139 (318)
 90 PRK01999 consensus              81.1     2.9 7.4E-05   22.0   4.3   76   85-161    46-133 (311)
 91 cd06342 PBP1_ABC_LIVBP_like Ty  80.3     4.7 0.00012   20.4  10.6   36  142-177    59-94  (334)
 92 PRK00934 ribose-phosphate pyro  80.1     4.2 0.00011   20.8   4.9   74   87-161    42-126 (286)
 93 PRK08341 amidophosphoribosyltr  79.9     4.8 0.00012   20.3   6.8   36   92-138     2-37  (442)
 94 COG1023 Gnd Predicted 6-phosph  79.7     4.4 0.00011   20.6   4.9   67  104-177    42-116 (300)
 95 cd06302 PBP1_LsrB_Quorum_Sensi  79.6     4.7 0.00012   20.4   5.0   64  116-181    25-89  (298)
 96 PRK13530 arsenate reductase; P  79.6     4.9 0.00013   20.2   6.4   55   92-152     3-59  (133)
 97 PRK13371 4-hydroxy-3-methylbut  79.6     4.9 0.00013   20.2   9.5  141   32-187    20-178 (392)
 98 PRK09454 ugpQ cytoplasmic glyc  79.5     4.6 0.00012   20.4   4.9   28  162-189    24-51  (249)
 99 TIGR01326 OAH_OAS_sulfhy O-ace  79.4       5 0.00013   20.2   5.7  248   77-404    81-356 (434)
100 TIGR03572 WbuZ glycosyl amidat  79.4       5 0.00013   20.2   6.6   73  111-184    34-107 (232)
101 COG0683 LivK ABC-type branched  79.3       5 0.00013   20.1   9.5  101   78-184   135-238 (366)
102 cd06338 PBP1_ABC_ligand_bindin  79.2       5 0.00013   20.1  10.0   79   93-175   142-222 (345)
103 cd01538 PBP1_ABC_xylose_bindin  78.9     5.2 0.00013   20.0   7.0   67  115-184    24-91  (288)
104 PRK13937 phosphoheptose isomer  78.8     5.2 0.00013   20.0   8.2  104   74-181    24-145 (192)
105 COG2099 CobK Precorrin-6x redu  78.8     3.7 9.4E-05   21.2   4.3   34  149-182   196-231 (257)
106 COG2248 Predicted hydrolase (m  78.7     5.2 0.00013   20.0   9.6   37   61-97     35-71  (304)
107 pfam01784 NIF3 NIF3 (NGG1p int  78.5     4.4 0.00011   20.6   4.6   29  150-181    33-61  (238)
108 PRK13586 1-(5-phosphoribosyl)-  78.5     5.3 0.00014   20.0   7.2   71  110-182    32-103 (231)
109 cd06319 PBP1_ABC_sugar_binding  78.4     5.3 0.00014   20.0   5.9   44  139-182    45-89  (277)
110 cd06330 PBP1_Arsenic_SBP_like   78.3     5.4 0.00014   19.9   8.7   38  141-178    58-96  (346)
111 cd06309 PBP1_YtfQ_like Peripla  78.2     5.4 0.00014   19.9   8.1   46  139-184    45-91  (273)
112 PRK04117 consensus              78.2     5.4 0.00014   19.9   5.2   74   88-162    47-133 (309)
113 PRK13938 phosphoheptose isomer  78.1     5.4 0.00014   19.9   8.3  112   68-183    21-150 (196)
114 pfam02401 LYTB LytB protein. T  78.1     5.4 0.00014   19.9   9.0  102   76-184    11-122 (280)
115 COG0327 Uncharacterized conser  78.1     3.6 9.3E-05   21.2   4.1   30  150-182    37-66  (250)
116 PRK08507 prephenate dehydrogen  77.6     5.6 0.00014   19.8   6.8   40  313-352   220-259 (275)
117 PRK00087 4-hydroxy-3-methylbut  77.5     5.6 0.00014   19.8   8.7  105   76-186    13-127 (670)
118 cd01979 Pchlide_reductase_N Pc  77.4     5.6 0.00014   19.8   4.8  152    9-177    10-184 (396)
119 cd06308 PBP1_sensor_kinase_lik  77.3     5.7 0.00014   19.7   5.2   47  139-185    46-93  (270)
120 PRK11460 esterase YpfH; Provis  77.2     5.7 0.00015   19.7   5.8   18  445-462   190-207 (230)
121 PRK07199 phosphoribosylpyropho  77.1     5.8 0.00015   19.7   7.5   70   89-159    47-127 (301)
122 PRK06084 O-acetylhomoserine am  77.0     5.8 0.00015   19.7   8.6  118   77-213    82-210 (424)
123 PRK02102 ornithine carbamoyltr  76.6     5.9 0.00015   19.6   8.1   15  115-129    67-81  (331)
124 cd06335 PBP1_ABC_ligand_bindin  76.5       6 0.00015   19.6  10.7   88   93-184   139-228 (347)
125 TIGR01011 rpsB_bact ribosomal   76.4       6 0.00015   19.6   8.6  117   73-208    44-204 (227)
126 PRK01395 V-type ATP synthase s  76.1     4.3 0.00011   20.7   3.9   62   93-169     4-66  (104)
127 cd06300 PBP1_ABC_sugar_binding  75.8       4  0.0001   20.9   3.8   44  139-182    50-94  (272)
128 cd06310 PBP1_ABC_sugar_binding  75.8     6.2 0.00016   19.4   6.3   69  114-183    23-92  (273)
129 PRK04308 murD UDP-N-acetylmura  75.8     6.2 0.00016   19.4   6.9   31   91-126     4-34  (445)
130 cd02922 FCB2_FMN Flavocytochro  75.7     6.2 0.00016   19.4   5.0   79   76-167    80-163 (344)
131 cd06326 PBP1_STKc_like Type I   75.6     6.3 0.00016   19.4  10.7   83   93-179   137-221 (336)
132 TIGR02707 butyr_kinase butyrat  75.5     1.9 4.8E-05   23.5   2.0   46  382-427   106-157 (353)
133 cd01537 PBP1_Repressors_Sugar_  75.4     6.3 0.00016   19.4   8.2   69  113-184    22-90  (264)
134 PRK03379 vitamin B12-transport  75.3     4.2 0.00011   20.8   3.7   38  142-180    70-107 (265)
135 COG1110 Reverse gyrase [DNA re  75.1     6.4 0.00016   19.3  14.2  118  304-430   532-699 (1187)
136 TIGR01678 FAD_lactone_ox sugar  74.9     4.7 0.00012   20.3   3.9   79   76-176    22-105 (505)
137 COG0078 ArgF Ornithine carbamo  74.8     6.6 0.00017   19.2   8.9   91   71-168    16-115 (310)
138 cd06306 PBP1_TorT-like TorT-li  74.8     6.6 0.00017   19.2   5.7   68  116-184    25-92  (268)
139 PRK10610 chemotaxis regulatory  74.7       2   5E-05   23.3   1.9   89  149-242    29-117 (129)
140 pfam00185 OTCace Aspartate/orn  74.7     6.6 0.00017   19.2   6.3   78   91-182     1-82  (155)
141 cd06382 PBP1_iGluR_Kainate N-t  74.3     6.7 0.00017   19.2   8.0   48  134-182    49-96  (327)
142 cd06314 PBP1_tmGBP Periplasmic  74.3     6.7 0.00017   19.2   6.0   66  116-184    24-90  (271)
143 PRK00553 ribose-phosphate pyro  73.9     6.9 0.00017   19.1   8.1  117   17-161    17-146 (340)
144 PRK13812 orotate phosphoribosy  73.8     6.9 0.00018   19.1   6.1  106   58-177    30-138 (174)
145 cd06321 PBP1_ABC_sugar_binding  73.8     6.9 0.00018   19.1   7.1   68  116-184    25-93  (271)
146 PRK04148 hypothetical protein;  73.7     6.1 0.00016   19.5   4.3   32  151-184    18-50  (135)
147 PRK00141 murD UDP-N-acetylmura  73.7     6.9 0.00018   19.1   6.4   78   93-177    18-104 (476)
148 pfam00926 DHBP_synthase 3,4-di  73.5       7 0.00018   19.0   5.8   91   82-172     1-105 (193)
149 PRK01045 ispH 4-hydroxy-3-meth  73.0     7.2 0.00018   18.9   9.5  103   76-185    13-125 (304)
150 PRK10799 putative hydrolase-ox  73.0     7.2 0.00018   18.9   8.2   29  150-181    36-64  (247)
151 PRK10653 D-ribose transporter   73.0     7.2 0.00018   18.9   6.7   49  139-187    72-121 (295)
152 cd03466 Nitrogenase_NifN_2 Nit  72.8     7.2 0.00018   18.9   8.0   26   74-99     65-92  (429)
153 cd06318 PBP1_ABC_sugar_binding  72.7     7.3 0.00019   18.9   7.3   45  139-183    45-90  (282)
154 cd06322 PBP1_ABC_sugar_binding  72.1     7.5 0.00019   18.8   7.2   46  139-184    45-91  (267)
155 PRK08057 cobalt-precorrin-6x r  72.1     7.5 0.00019   18.8   4.7   19   94-117     3-21  (241)
156 cd06348 PBP1_ABC_ligand_bindin  72.0     7.5 0.00019   18.8  10.1   10  168-177    86-95  (344)
157 PRK12562 ornithine carbamoyltr  71.9     7.6 0.00019   18.8   8.2   34  106-139    56-90  (334)
158 PRK10841 hybrid sensory kinase  71.8     5.8 0.00015   19.6   3.8   41  171-211   239-282 (947)
159 cd04478 RPA2_DBD_D RPA2_DBD_D:  71.6     7.7  0.0002   18.7   8.4   65  527-596    16-81  (95)
160 PRK10886 DnaA initiator-associ  71.5     7.7  0.0002   18.7   8.4  105   76-183    25-146 (196)
161 smart00481 POLIIIAc DNA polyme  71.1     7.8  0.0002   18.6   4.7   50  129-178     6-59  (67)
162 PRK02145 consensus              71.1     7.9  0.0002   18.6   6.6   74  109-183    33-107 (257)
163 COG3010 NanE Putative N-acetyl  71.1     7.9  0.0002   18.6   8.9  113   69-186    29-160 (229)
164 PRK03369 murD UDP-N-acetylmura  71.0     7.9  0.0002   18.6   7.7   33   89-126     9-41  (487)
165 PRK02269 ribose-phosphate pyro  70.9     7.9  0.0002   18.6   8.1   73   92-164    52-137 (321)
166 cd06311 PBP1_ABC_sugar_binding  70.5     8.1 0.00021   18.5   4.9   45  139-183    50-95  (274)
167 cd02812 PcrB_like PcrB_like pr  70.2     8.2 0.00021   18.5   8.3   46  137-182   161-206 (219)
168 PRK13809 orotate phosphoribosy  70.1     8.2 0.00021   18.5   5.1   73  105-177    73-149 (206)
169 PRK04923 ribose-phosphate pyro  70.0     8.3 0.00021   18.5   5.1   74   89-163    51-138 (319)
170 PRK13587 1-(5-phosphoribosyl)-  70.0     8.3 0.00021   18.5   7.7   83   98-181    20-106 (234)
171 cd06320 PBP1_allose_binding Pe  69.5     8.5 0.00022   18.4   6.6   69  113-182    22-91  (275)
172 PRK02270 consensus              69.3     8.5 0.00022   18.3   5.1   80   85-164    46-137 (327)
173 PRK04284 ornithine carbamoyltr  68.9     8.7 0.00022   18.3   7.7   22  115-136    66-87  (332)
174 PRK03604 moaC bifunctional mol  68.8     8.5 0.00022   18.4   4.1   46  446-496   184-230 (301)
175 PRK11337 DNA-binding transcrip  68.8     8.7 0.00022   18.3  12.2  160   30-199    50-242 (293)
176 PRK05793 amidophosphoribosyltr  68.5     8.8 0.00022   18.2   9.3   39   92-138    15-53  (472)
177 pfam01336 tRNA_anti OB-fold nu  68.5     8.8 0.00022   18.2   9.4   70  517-592     6-75  (75)
178 cd01524 RHOD_Pyr_redox Member   68.2     8.2 0.00021   18.5   3.9   32   89-124    48-79  (90)
179 PRK07208 hypothetical protein;  68.1     8.8 0.00023   18.2   4.1   31   91-126     2-32  (474)
180 PRK05858 hypothetical protein;  68.1       9 0.00023   18.2   9.7  103   80-182   193-297 (543)
181 TIGR02634 xylF D-xylose ABC tr  67.7     9.1 0.00023   18.1   7.1   72  109-183    17-89  (307)
182 KOG2754 consensus               67.7     9.1 0.00023   18.1  10.5   97   90-189    21-146 (443)
183 PRK01368 murD UDP-N-acetylmura  67.6     9.2 0.00023   18.1   5.9   75   90-177     4-91  (450)
184 PRK00865 glutamate racemase; P  67.5     9.2 0.00023   18.1   7.8   81   92-177     2-92  (262)
185 pfam05728 UPF0227 Uncharacteri  67.5     9.2 0.00023   18.1   4.4   24  381-404    67-90  (187)
186 PRK01659 consensus              67.5     9.2 0.00024   18.1   6.3   75  109-184    32-107 (252)
187 PRK02458 ribose-phosphate pyro  67.3     9.3 0.00024   18.1   7.9  125   12-164     4-141 (323)
188 TIGR01055 parE_Gneg DNA topois  67.2     6.5 0.00017   19.3   3.2   70  277-346   300-393 (647)
189 cd01534 4RHOD_Repeat_3 Member   67.0     6.6 0.00017   19.2   3.2   41  141-181    47-88  (95)
190 KOG4131 consensus               67.0     6.8 0.00017   19.1   3.3   31  150-183    46-76  (272)
191 TIGR01162 purE phosphoribosyla  67.0     9.4 0.00024   18.0   4.2   47  113-163    18-67  (159)
192 PRK00910 ribB 3,4-dihydroxy-2-  66.5     9.6 0.00024   17.9   6.2   92   81-172    16-122 (218)
193 pfam08981 consensus             66.5       9 0.00023   18.2   3.8   20  369-394    27-46  (181)
194 PRK03220 consensus              66.2     9.7 0.00025   17.9   6.9   70  112-182    36-106 (257)
195 cd00758 MoCF_BD MoCF_BD: molyb  66.2     9.7 0.00025   17.9   5.0   99  107-219    19-124 (133)
196 pfam01070 FMN_dh FMN-dependent  66.2     9.5 0.00024   18.0   3.9   40  140-182   159-199 (301)
197 PRK01438 murD UDP-N-acetylmura  66.1     9.8 0.00025   17.9   9.2   31   91-126    13-43  (481)
198 cd06301 PBP1_rhizopine_binding  66.1     9.8 0.00025   17.9   5.8   45  139-183    46-91  (272)
199 cd05126 Mth938 Mth938 domain.   66.0     9.8 0.00025   17.9   5.5   49  132-181    41-94  (117)
200 cd02750 MopB_Nitrate-R-NarG-li  66.0     9.8 0.00025   17.9   8.3  114   78-196    91-221 (461)
201 PRK02621 consensus              65.5      10 0.00025   17.8   6.4   73  110-183    33-106 (254)
202 PRK12311 rpsB 30S ribosomal pr  65.5      10 0.00026   17.8   9.8   96   75-178    49-187 (332)
203 COG4213 XylF ABC-type xylose t  65.5      10 0.00026   17.8   4.9   73  110-185    45-118 (341)
204 PRK09104 hypothetical protein;  65.4     7.4 0.00019   18.8   3.2   19  313-331   332-350 (465)
205 PRK00748 1-(5-phosphoribosyl)-  65.2      10 0.00026   17.8   6.7   69  112-181    34-103 (241)
206 PRK05259 consensus              64.9      10 0.00026   17.7   7.5   73   91-163    46-131 (310)
207 cd06349 PBP1_ABC_ligand_bindin  64.8      10 0.00026   17.7  11.0   80   93-176   136-217 (340)
208 COG1087 GalE UDP-glucose 4-epi  64.7      10 0.00026   17.7   6.4   13  170-182    21-33  (329)
209 cd01144 BtuF Cobalamin binding  64.7     8.8 0.00022   18.2   3.5   39  142-181    50-88  (245)
210 TIGR02836 spore_IV_A stage IV   64.7      10 0.00026   17.7   4.3   66  383-466   365-434 (492)
211 cd06303 PBP1_LuxPQ_Quorum_Sens  64.5      10 0.00027   17.7   8.0  110  110-231    20-133 (280)
212 COG1029 FwdB Formylmethanofura  64.5      10 0.00027   17.7   6.6   81   77-164    64-153 (429)
213 cd06268 PBP1_ABC_transporter_L  64.0      11 0.00027   17.6  10.0   82   93-176   136-217 (298)
214 cd04482 RPA2_OBF_like RPA2_OBF  63.9      11 0.00027   17.6   9.0   61  514-575     4-64  (91)
215 KOG3857 consensus               63.6      11 0.00027   17.6   4.8   63  124-187    44-112 (465)
216 cd01536 PBP1_ABC_sugar_binding  63.6      11 0.00027   17.5   7.3   70  113-185    22-92  (267)
217 PRK01713 ornithine carbamoyltr  63.5      11 0.00028   17.5   8.1   50  105-154    56-106 (334)
218 TIGR02061 aprA adenylylsulfate  63.3     2.5 6.5E-05   22.5   0.5  157  266-465   432-589 (651)
219 PRK04020 rps2P 30S ribosomal p  63.1      11 0.00028   17.5  11.2  130   77-227    47-183 (204)
220 cd01540 PBP1_arabinose_binding  63.1      11 0.00028   17.5   7.2   49  139-187    44-93  (289)
221 cd02811 IDI-2_FMN Isopentenyl-  62.9      11 0.00028   17.5   3.7   43  140-183   168-212 (326)
222 KOG4730 consensus               62.6      11 0.00029   17.4   5.4   78   76-175    57-135 (518)
223 PRK09802 DNA-binding transcrip  62.4      11 0.00029   17.4   7.5   53  412-464   162-214 (269)
224 cd00886 MogA_MoaB MogA_MoaB fa  62.4      11 0.00029   17.4   4.3   63   95-163     5-73  (152)
225 PRK00455 pyrE orotate phosphor  61.9      11 0.00029   17.3   4.8  107   59-177    33-142 (200)
226 PRK07502 cyclohexadienyl dehyd  61.6      12  0.0003   17.3   7.4   35  313-347   233-267 (307)
227 PRK07417 arogenate dehydrogena  61.4      12  0.0003   17.3   7.4   45  305-349   213-259 (280)
228 PRK02812 ribose-phosphate pyro  61.2      12  0.0003   17.2   7.8  121   16-164    20-153 (331)
229 cd04729 NanE N-acetylmannosami  61.1      12  0.0003   17.2   8.4  110   69-182    23-152 (219)
230 COG0648 Nfo Endonuclease IV [D  60.9      12  0.0003   17.2   6.0  136  371-519   103-250 (280)
231 PRK11107 hybrid sensory histid  60.8      12 0.00031   17.2   3.8   33   75-107    61-95  (920)
232 PRK05437 isopentenyl pyrophosp  60.5      12 0.00031   17.2   4.0   38  134-171   195-232 (351)
233 PRK10434 srlR DNA-bindng trans  60.5      12 0.00031   17.2   8.4   34  414-447   150-183 (256)
234 PRK01259 ribose-phosphate pyro  60.2      12 0.00031   17.1   7.5   70   92-161    47-129 (309)
235 PRK11557 putative DNA-binding   60.1      12 0.00031   17.1  13.2  145   29-183    36-217 (282)
236 TIGR02955 TMAO_TorT TMAO reduc  59.9      12 0.00031   17.1   4.7   96  122-219     1-113 (304)
237 cd06323 PBP1_ribose_binding Pe  59.9      12 0.00032   17.1   7.7   68  114-184    23-91  (268)
238 PRK04169 geranylgeranylglycery  59.9      12 0.00032   17.1   6.6   10  188-197   114-123 (229)
239 COG1560 HtrB Lauroyl/myristoyl  59.5     4.4 0.00011   20.6   1.2   11  139-149   112-122 (308)
240 PRK01033 imidazole glycerol ph  59.5      13 0.00032   17.0   6.8   72  112-184    35-107 (253)
241 cd06354 PBP1_BmpA_PnrA_like Pe  59.4      13 0.00032   17.0   6.0   89  112-213    24-114 (265)
242 cd01028 TOPRIM_TopoIA TOPRIM_T  59.4      13 0.00032   17.0   5.2   65   76-147    75-140 (142)
243 PRK11071 esterase YqiA; Provis  59.4      13 0.00032   17.0   4.9   33  367-404    60-92  (190)
244 PRK06781 amidophosphoribosyltr  59.3      13 0.00032   17.0   8.4   37   92-138     9-45  (471)
245 cd06327 PBP1_SBP_like_1 Peripl  59.3      13 0.00032   17.0   8.3   40  142-181    58-98  (334)
246 cd06343 PBP1_ABC_ligand_bindin  58.8      13 0.00033   16.9   8.1   13  490-502   317-329 (362)
247 cd01030 TOPRIM_TopoIIA_like TO  58.7      13 0.00033   17.0   3.5   29   91-119    72-100 (115)
248 PRK09279 pyruvate phosphate di  58.6      13 0.00033   16.9   5.0   36  368-403   424-474 (875)
249 cd06451 AGAT_like Alanine-glyo  58.3      13 0.00033   16.9   8.8   99   72-181    52-161 (356)
250 PRK02083 imidazole glycerol ph  58.1      13 0.00034   16.9   6.6   72  112-184    35-107 (253)
251 PRK01792 ribB 3,4-dihydroxy-2-  58.1      13 0.00034   16.9   7.1   94   77-170    11-119 (214)
252 PRK01390 murD UDP-N-acetylmura  58.1      13 0.00034   16.9   7.7   32   90-126     7-38  (457)
253 COG1137 YhbG ABC-type (unclass  58.0     5.9 0.00015   19.6   1.7   65  367-445   157-221 (243)
254 cd03366 TOPRIM_TopoIIA_GyrB TO  57.8      13 0.00033   16.9   3.4   30   90-119    70-99  (114)
255 PRK02472 murD UDP-N-acetylmura  57.7      13 0.00034   16.8   9.2   31   91-126     8-38  (450)
256 COG0761 lytB 4-Hydroxy-3-methy  57.6      13 0.00034   16.8   9.9  108   70-184     7-125 (294)
257 PRK07349 amidophosphoribosyltr  57.6      13 0.00034   16.8   9.5   27   92-119    26-52  (495)
258 PRK03675 consensus              57.3      14 0.00035   16.8   5.9   69   91-159    41-121 (279)
259 PRK06545 prephenate dehydrogen  57.1      14 0.00035   16.8   7.4   78  314-393   223-312 (357)
260 TIGR02116 toxin_Txe_YoeB addic  57.0      14 0.00035   16.7   4.5   49  490-541    24-73  (82)
261 cd04731 HisF The cyclase subun  56.8      14 0.00035   16.7   6.4   72  112-184    32-104 (243)
262 PRK09534 btuF corrinoid ABC tr  56.8      14 0.00035   16.7   4.0   86   72-179    60-147 (364)
263 PRK01641 leuD isopropylmalate   56.7      11 0.00028   17.5   2.8   49  130-178    47-99  (201)
264 PRK07907 hypothetical protein;  56.7      14 0.00035   16.7   3.8   13   41-53     36-48  (437)
265 TIGR01670 YrbI-phosphatas 3-de  56.3     3.2 8.1E-05   21.7   0.0   66  102-180     7-73  (154)
266 pfam04131 NanE Putative N-acet  56.3      14 0.00036   16.7   7.2   83   94-182    35-121 (192)
267 TIGR01734 D-ala-DACP-lig D-ala  56.2      14 0.00036   16.6   4.7  102   72-187    29-147 (513)
268 cd06346 PBP1_ABC_ligand_bindin  56.2      14 0.00036   16.6  10.9   12   76-87     21-32  (312)
269 PRK08617 acetolactate synthase  56.1      14 0.00036   16.6   9.3  101   79-181   188-300 (552)
270 PRK08327 acetolactate synthase  56.1      14 0.00036   16.6   8.6   81   80-160   208-290 (568)
271 TIGR00734 hisAF_rel hisA/hisF   56.0      14 0.00036   16.6   4.5  146  112-278    41-199 (230)
272 PRK03353 ribB 3,4-dihydroxy-2-  55.9      14 0.00036   16.6   5.7   91   80-170    14-119 (217)
273 TIGR01179 galE UDP-glucose 4-e  55.8     4.6 0.00012   20.5   0.8   19  292-315   283-301 (341)
274 PRK04663 murD UDP-N-acetylmura  55.6      14 0.00037   16.6   6.0   30   93-127     8-37  (438)
275 cd06328 PBP1_SBP_like_2 Peripl  55.0      15 0.00037   16.5  11.1   83   90-176   134-219 (333)
276 PRK05588 histidinol-phosphatas  54.7      13 0.00032   17.0   2.9   24  161-184    18-41  (256)
277 cd06329 PBP1_SBP_like_3 Peripl  54.6      15 0.00038   16.5  10.2   15  142-156    59-73  (342)
278 COG3051 CitF Citrate lyase, al  54.5     5.5 0.00014   19.9   1.0   66  109-181    81-149 (513)
279 cd01965 Nitrogenase_MoFe_beta_  54.4      15 0.00038   16.4   6.8  125   44-179    37-188 (428)
280 pfam08288 PIGA PIGA (GPI ancho  54.3     8.3 0.00021   18.4   1.9   45  140-184    40-86  (90)
281 PRK08134 O-acetylhomoserine am  54.3      15 0.00038   16.4   8.3   95   77-183    88-188 (433)
282 PRK12360 4-hydroxy-3-methylbut  54.2      15 0.00038   16.4   9.4  109   72-186     8-129 (281)
283 COG0796 MurI Glutamate racemas  54.1      15 0.00039   16.4   6.9   82   91-177     4-95  (269)
284 PRK08574 cystathionine gamma-s  54.1      15 0.00039   16.4   9.8   89   77-178    77-172 (384)
285 pfam03686 UPF0146 Uncharacteri  54.0      15 0.00039   16.4   5.0   56  142-199     5-65  (127)
286 PRK07272 amidophosphoribosyltr  53.9      15 0.00039   16.4   8.9   36   92-137     9-44  (484)
287 COG0496 SurE Predicted acid ph  53.9      15 0.00039   16.4   5.7  182  151-407     2-200 (252)
288 cd05805 MPG1_transferase GTP-m  53.4      11 0.00027   17.6   2.4   49  137-188    50-101 (441)
289 PRK12367 short chain dehydroge  53.4      15  0.0004   16.3   8.0   82   87-184    12-93  (250)
290 TIGR00040 yfcE phosphodiestera  53.4      12 0.00031   17.1   2.6  114   80-197    14-140 (170)
291 pfam07592 Transposase_36 Rhodo  53.3      15 0.00037   16.5   3.0  162   14-187    18-226 (311)
292 cd01990 Alpha_ANH_like_I This   53.3      16  0.0004   16.3   7.9   96  152-291    27-126 (202)
293 pfam01522 Polysacc_deac_1 Poly  53.2      16  0.0004   16.3   6.4   26  104-129    14-40  (123)
294 PRK00055 ribonuclease Z; Revie  53.1      16  0.0004   16.3   5.0   15  154-168    32-46  (259)
295 cd01714 ETF_beta The electron   53.1      16  0.0004   16.3   6.3   79   71-156    34-115 (202)
296 cd06299 PBP1_LacI_like_13 Liga  53.1      16  0.0004   16.3   7.4   69  114-186    23-91  (265)
297 KOG4165 consensus               53.1     9.5 0.00024   18.0   2.0   17   71-87     69-85  (433)
298 CHL00176 ftsH cell division pr  52.9      16  0.0004   16.3   6.7   12  186-197   207-218 (631)
299 PRK06725 acetolactate synthase  52.9      16  0.0004   16.3   5.7   77   81-158   203-289 (570)
300 TIGR02151 IPP_isom_2 isopenten  52.7      16  0.0004   16.2   3.8   89   78-173   141-237 (349)
301 pfam00072 Response_reg Respons  52.7     9.1 0.00023   18.1   1.9   95  140-242    12-107 (111)
302 PRK12726 flagellar biosynthesi  52.6      16 0.00041   16.2   7.2   37  366-402   204-242 (407)
303 pfam01751 Toprim Toprim domain  52.6      16 0.00041   16.2   4.9   42   82-124    43-84  (89)
304 cd06289 PBP1_MalI_like Ligand-  52.4      16 0.00041   16.2   7.6   71  115-188    24-94  (268)
305 PRK00724 formate dehydrogenase  52.0      16 0.00041   16.2   4.0   19  386-404   233-251 (262)
306 cd02511 Beta4Glucosyltransfera  52.0      16 0.00041   16.2   4.8   27  150-177    26-52  (229)
307 cd01141 TroA_d Periplasmic bin  52.0      16 0.00041   16.2   4.6   38  142-180    62-99  (186)
308 cd04597 CBS_pair_DRTGG_assoc2   51.9      16 0.00042   16.1   6.0   77  101-182     3-98  (113)
309 PRK07574 formate dehydrogenase  51.6      16 0.00042   16.1   7.7  250   72-426    47-299 (385)
310 PRK00197 proA gamma-glutamyl p  51.6      16 0.00041   16.2   3.0   35  411-457   317-352 (416)
311 TIGR01302 IMP_dehydrog inosine  50.7      17 0.00043   16.0   3.4   70  368-442   188-265 (476)
312 TIGR00441 gmhA phosphoheptose   50.7      17 0.00043   16.0   3.3  118   73-199    20-164 (186)
313 COG0037 MesJ tRNA(Ile)-lysidin  50.5      17 0.00043   16.0   9.1  102   79-184     4-131 (298)
314 PRK02705 murD UDP-N-acetylmura  50.3      17 0.00044   16.0   6.6   33   89-124   106-139 (459)
315 cd06390 PBP1_iGluR_AMPA_GluR1   50.1      17 0.00044   16.0   7.6   12  451-462   270-281 (364)
316 COG3383 Uncharacterized anaero  50.0      17 0.00044   15.9   6.2  134   57-203   316-478 (978)
317 cd06394 PBP1_iGluR_Kainate_KA1  50.0      17 0.00044   15.9   7.6   13  168-180    85-97  (333)
318 PRK08525 amidophosphoribosyltr  49.9      17 0.00044   15.9   8.9   32   97-138     4-35  (445)
319 cd01139 TroA_f Periplasmic bin  49.7      18 0.00045   15.9   4.4   41  142-182    84-127 (342)
320 PRK13915 putative glucosyl-3-p  49.7      18 0.00045   15.9   4.1   55  119-177    29-87  (307)
321 COG0033 Pgm Phosphoglucomutase  49.6      18 0.00045   15.9   6.6   57  132-188    61-129 (524)
322 cd01987 USP_OKCHK USP domain i  49.4      18 0.00045   15.9   8.6   84   94-184     1-96  (124)
323 COG0622 Predicted phosphoester  49.4      18 0.00045   15.9   5.9   93   94-198    31-135 (172)
324 PRK05211 consensus              49.2      18 0.00045   15.8   7.2   73  111-184    25-98  (248)
325 cd06070 H2MP_like-2 Putative [  49.2      18 0.00045   15.8   4.5   55  130-192    10-64  (140)
326 TIGR03394 indol_phenyl_DC indo  49.2      18 0.00045   15.8   4.1   85   76-161   185-280 (535)
327 PRK07945 hypothetical protein;  49.1      18 0.00046   15.8   3.9   15  168-182   119-134 (335)
328 cd04509 PBP1_ABC_transporter_G  49.0      18 0.00046   15.8  10.2   30  149-178    67-96  (299)
329 PRK09246 amidophosphoribosyltr  49.0      18 0.00046   15.8   5.2   11  132-142   182-192 (503)
330 pfam00318 Ribosomal_S2 Ribosom  49.0      18 0.00046   15.8  10.4   99   74-181    38-169 (205)
331 cd00003 PNPsynthase Pyridoxine  48.9      18 0.00046   15.8   7.3   74  100-177    64-148 (234)
332 PRK06015 keto-hydroxyglutarate  48.8      18 0.00046   15.8   7.9   96   78-183     1-97  (212)
333 cd01391 Periplasmic_Binding_Pr  48.6      18 0.00046   15.8   7.5   49  138-186    47-95  (269)
334 cd06333 PBP1_ABC-type_HAAT_lik  48.6      18 0.00046   15.8  10.4   36  142-177    58-94  (312)
335 TIGR01082 murC UDP-N-acetylmur  48.5      18 0.00046   15.8   5.6   87   43-132    37-146 (491)
336 cd03365 TOPRIM_TopoIIA TOPRIM_  48.5      18 0.00046   15.8   3.4   30   90-119    75-104 (120)
337 PRK09191 two-component respons  48.3      15 0.00037   16.5   2.4  114  292-412   105-227 (261)
338 PRK05939 hypothetical protein;  48.3      18 0.00047   15.7   8.9   93   77-182    70-168 (396)
339 PRK13435 response regulator; P  48.1      15 0.00039   16.4   2.4   86  351-470    35-121 (141)
340 PRK00683 murD UDP-N-acetylmura  47.9      19 0.00047   15.7   5.9   29   93-124   103-132 (418)
341 cd06366 PBP1_GABAb_receptor Li  47.8      19 0.00048   15.7   9.1   75   74-177    17-94  (350)
342 PRK08072 nicotinate-nucleotide  47.8      14 0.00036   16.6   2.2   14  274-287   132-145 (277)
343 cd03361 TOPRIM_TopoIA_RevGyr T  47.7      19 0.00048   15.7   6.8   68   75-148   102-169 (170)
344 PRK08322 acetolactate synthase  47.6      19 0.00048   15.7  10.2   81   80-161   184-274 (547)
345 cd06347 PBP1_ABC_ligand_bindin  47.5      19 0.00048   15.7  11.1   36  142-177    59-95  (334)
346 PTZ00170 D-ribulose-5-phosphat  47.5      19 0.00048   15.7   4.0   63  106-177    47-115 (224)
347 cd01448 TST_Repeat_1 Thiosulfa  47.4      19 0.00048   15.7   5.5   50   71-123    57-107 (122)
348 PRK04281 consensus              47.3      19 0.00048   15.6   6.7   73  110-183    33-106 (254)
349 pfam00205 TPP_enzyme_M Thiamin  47.3      19 0.00048   15.6   8.5   75   83-158     2-86  (138)
350 PRK11302 DNA-binding transcrip  47.2      19 0.00048   15.6  14.2   89   82-180   118-210 (284)
351 PRK08392 hypothetical protein;  46.9      19 0.00049   15.6   6.7   23  159-181    12-36  (215)
352 TIGR02902 spore_lonB ATP-depen  46.9      19 0.00049   15.6   3.4   44   71-117    60-108 (532)
353 PRK09558 ushA bifunctional UDP  46.8      19 0.00049   15.6   4.8   58   77-135    56-124 (551)
354 pfam10498 IFT57 Intra-flagella  46.8      14 0.00036   16.7   2.1   64   75-142    42-105 (355)
355 PRK01362 putative translaldola  46.8      19 0.00049   15.6   8.5   86   78-177    39-126 (214)
356 cd02772 MopB_NDH-1_NuoG2 MopB_  46.7      19 0.00049   15.6   8.6   99   77-181    70-189 (414)
357 COG0279 GmhA Phosphoheptose is  46.7      18 0.00047   15.7   2.7  104   75-182    24-145 (176)
358 TIGR02478 6PF1K_euk 6-phosphof  46.7      13 0.00034   16.9   1.9  407   40-496   118-657 (777)
359 TIGR03669 urea_ABC_arch urea A  46.5      19  0.0005   15.6  10.6   39  143-182    61-101 (374)
360 PRK04554 consensus              46.2      20  0.0005   15.5   5.8   76   85-161    47-136 (327)
361 COG1227 PPX1 Inorganic pyropho  46.1      20  0.0005   15.5   9.2   26   93-119     2-29  (311)
362 pfam03060 NPD 2-nitropropane d  46.1      20  0.0005   15.5   5.2   64  114-188   108-172 (330)
363 PRK01130 N-acetylmannosamine-6  45.8      20 0.00051   15.5   8.1  110   69-182    19-148 (222)
364 COG0462 PrsA Phosphoribosylpyr  45.8      20 0.00051   15.5   5.3   74   85-159    45-131 (314)
365 PRK11778 putative periplasmic   45.7      16  0.0004   16.3   2.2   39  121-159   103-143 (317)
366 pfam00994 MoCF_biosynth Probab  45.7      20 0.00051   15.5   4.8   45  107-156    17-63  (140)
367 PRK13597 imidazole glycerol ph  45.5      20 0.00051   15.4   6.8   72  110-182    34-106 (252)
368 CHL00067 rps2 ribosomal protei  45.4      20 0.00051   15.4  10.4  101   74-183    46-191 (227)
369 COG1699 Uncharacterized protei  45.3      16 0.00041   16.2   2.2   56  150-206    14-71  (146)
370 cd01149 HutB Hemin binding pro  45.3      20 0.00052   15.4   4.1   37  142-179    51-87  (235)
371 PRK07494 2-octaprenyl-6-methox  45.2      20 0.00052   15.4   3.8   14  388-401   269-282 (386)
372 PRK09935 transcriptional regul  45.0      20 0.00052   15.4   5.0  110  135-251    12-121 (210)
373 PRK09959 hybrid sensory histid  44.9      21 0.00052   15.4   3.8   12   41-52    213-224 (1197)
374 TIGR00093 TIGR00093 conserved   44.7      11 0.00028   17.5   1.3   31  301-332    29-59  (185)
375 TIGR02134 transald_staph trans  44.5      21 0.00053   15.3   5.3   65  113-178    77-141 (237)
376 KOG1111 consensus               44.5      14 0.00036   16.6   1.8   34  151-184    89-125 (426)
377 pfam00782 DSPc Dual specificit  44.2      21 0.00053   15.3   3.2   49   60-112    40-88  (131)
378 cd02765 MopB_4 The MopB_4 CD i  44.1      21 0.00054   15.3   6.9   39  142-184   154-199 (567)
379 PRK09123 amidophosphoribosyltr  44.1      21 0.00054   15.3   6.6   37   92-138    11-47  (480)
380 cd01977 Nitrogenase_VFe_alpha   43.8      21 0.00054   15.3  11.3   27   73-99     67-96  (415)
381 COG1606 ATP-utilizing enzymes   43.6      21 0.00054   15.2   8.6  143   79-297     4-155 (269)
382 TIGR01584 citF citrate lyase,   43.6      12 0.00031   17.2   1.3  113  436-572   375-495 (496)
383 PRK07324 transaminase; Validat  43.5      21 0.00055   15.2   5.7   96   76-178    87-191 (373)
384 PRK09860 putative alcohol dehy  43.5      21 0.00055   15.2   7.1   14  497-510   357-370 (383)
385 cd04488 RecG_wedge_OBF RecG_we  43.4      22 0.00055   15.2   7.1   60  517-584     5-67  (75)
386 cd04730 NPD_like 2-Nitropropan  43.3      22 0.00055   15.2   7.6   65  112-187    72-136 (236)
387 COG1504 Uncharacterized conser  43.3      22 0.00055   15.2   4.7   44  135-179    47-95  (121)
388 PRK02747 consensus              43.3      22 0.00055   15.2   6.5   73  110-183    33-106 (257)
389 pfam00436 SSB Single-strand bi  43.3      22 0.00055   15.2   6.1   49  540-590    49-102 (104)
390 cd04409 RhoGAP_PARG1 RhoGAP_PA  43.2      22 0.00055   15.2   3.9   67   37-120    14-83  (211)
391 PRK09028 cystathionine beta-ly  43.1      22 0.00055   15.2   9.3   95   76-182    84-184 (394)
392 pfam02634 FdhD-NarQ FdhD/NarQ   42.9      22 0.00056   15.2   4.1   19  386-404   204-222 (235)
393 PRK09016 quinolinate phosphori  42.9      15 0.00037   16.5   1.7   13  274-286   153-165 (296)
394 KOG1404 consensus               42.8      19  0.0005   15.6   2.3   66   89-172    36-101 (442)
395 PRK08508 biotin synthase; Prov  42.5      22 0.00056   15.1   4.3   79   72-186    36-122 (279)
396 TIGR03479 DMSO_red_II_alp DMSO  42.5      22 0.00056   15.1   6.2  120   78-203   141-281 (912)
397 cd06296 PBP1_CatR_like Ligand-  42.5      22 0.00056   15.1   7.4   65  115-183    24-88  (270)
398 TIGR01524 ATPase-IIIB_Mg magne  42.4      18 0.00047   15.8   2.1   20  252-271   478-497 (892)
399 cd05313 NAD_bind_2_Glu_DH NAD(  42.2      22 0.00057   15.1   5.3   56  120-177   119-174 (254)
400 cd04390 RhoGAP_ARHGAP22_24_25   42.0      22 0.00057   15.1   3.4   17  290-306   151-167 (199)
401 PRK07979 acetolactate synthase  42.0      23 0.00057   15.0   5.7   79   79-158   193-281 (574)
402 COG0644 FixC Dehydrogenases (f  42.0      23 0.00057   15.0   3.2   42  156-197     9-50  (396)
403 TIGR03407 urea_ABC_UrtA urea A  41.8      23 0.00058   15.0  10.0   15   74-88     20-34  (359)
404 PRK08182 single-stranded DNA-b  41.6      23 0.00058   15.0   7.5   55  535-591    50-109 (148)
405 cd04376 RhoGAP_ARHGAP6 RhoGAP_  41.5      23 0.00058   15.0   3.2   45   73-119    31-75  (206)
406 TIGR03151 enACPred_II putative  41.5      23 0.00058   15.0   5.4   51  133-187    93-143 (307)
407 pfam04723 GRDA Glycine reducta  41.5      23 0.00058   15.0   2.6   76   89-169     2-84  (150)
408 cd01523 RHOD_Lact_B Member of   41.3      23 0.00059   15.0   3.8   38  141-179    54-91  (100)
409 PRK10618 phosphotransfer inter  41.3     8.2 0.00021   18.5   0.2   45   91-135   100-167 (881)
410 cd04382 RhoGAP_MgcRacGAP RhoGA  41.2      23 0.00059   15.0   3.8   17  290-306   143-159 (193)
411 TIGR02238 recomb_DMC1 meiotic   41.1      23 0.00059   15.0   2.8   14  388-401   230-243 (314)
412 cd06341 PBP1_ABC_ligand_bindin  41.0      23 0.00059   14.9   9.7   77   95-175   136-214 (341)
413 PRK00758 GMP synthase subunit   40.7      23  0.0006   14.9   3.5   44  153-197     2-49  (184)
414 cd01143 YvrC Periplasmic bindi  40.7      23  0.0006   14.9   4.2   37  142-180    53-89  (195)
415 PRK13958 N-(5'-phosphoribosyl)  40.6      19 0.00049   15.6   2.0   20  158-177     6-25  (207)
416 PRK05742 nicotinate-nucleotide  40.6      16 0.00041   16.2   1.6   14  274-287   134-147 (277)
417 PRK12480 D-lactate dehydrogena  40.6      24  0.0006   14.9   3.9   51  368-426   199-249 (330)
418 PRK01222 N-(5'-phosphoribosyl)  40.5      19 0.00049   15.6   2.0   20  158-177     8-27  (212)
419 PRK10524 prpE propionyl-CoA sy  40.3      24 0.00061   14.9   9.2  101   74-184    86-201 (629)
420 PRK09418 bifunctional 2',3'-cy  40.3      24 0.00061   14.9   6.1   68   76-147    66-153 (780)
421 PRK08979 acetolactate synthase  40.1      24 0.00061   14.8   5.5   76   81-158   195-281 (572)
422 pfam04223 CitF Citrate lyase,   40.1      11 0.00029   17.4   0.7  132  383-526   302-438 (466)
423 PRK07710 acetolactate synthase  40.0      24 0.00061   14.8   5.7   79   80-159   203-291 (571)
424 TIGR01241 FtsH_fam ATP-depende  39.7      13 0.00032   17.0   0.9   16  141-157   143-158 (505)
425 cd06355 PBP1_FmdD_like Peripla  39.6      24 0.00062   14.8   9.3   10   77-86     22-31  (348)
426 cd06360 PBP1_alkylbenzenes_lik  39.6      24 0.00062   14.8   9.6   36  142-177    57-93  (336)
427 cd01967 Nitrogenase_MoFe_alpha  39.6      24 0.00062   14.8   6.5   25   74-98     68-94  (406)
428 cd03796 GT1_PIG-A_like This fa  39.5      24 0.00062   14.8   8.1   99   75-182    13-122 (398)
429 TIGR02169 SMC_prok_A chromosom  39.5      24 0.00062   14.8   4.1   62  484-547  1060-1126(1202)
430 PRK12843 putative FAD-binding   39.3      23 0.00057   15.0   2.2   86  448-545   441-531 (576)
431 PRK06559 nicotinate-nucleotide  39.2      20 0.00052   15.4   1.9   13  275-287   142-154 (290)
432 PRK09484 3-deoxy-D-manno-octul  39.1      25 0.00063   14.7   3.8   76   91-182    22-98  (186)
433 PRK06388 amidophosphoribosyltr  39.0      25 0.00063   14.7   5.3   38   91-138    16-53  (474)
434 pfam01497 Peripla_BP_2 Peripla  38.9      25 0.00063   14.7   4.4   38  142-180    53-90  (236)
435 pfam00697 PRAI N-(5'phosphorib  38.7      23 0.00057   15.0   2.1   22  158-179     4-25  (195)
436 PRK00014 ribB 3,4-dihydroxy-2-  38.6      25 0.00064   14.7   6.4   35   66-105    10-44  (230)
437 PRK05265 pyridoxine 5'-phospha  38.6      25 0.00064   14.7   7.0   64  111-177    77-151 (240)
438 PRK02039 consensus              38.4      25 0.00065   14.7   7.6   71   92-162    52-136 (316)
439 cd01571 NAPRTase_B Nicotinate   38.1      26 0.00065   14.6   9.4   93  158-286    39-132 (302)
440 cd06358 PBP1_NHase Type I peri  38.0      26 0.00065   14.6   9.6   36  142-178    59-95  (333)
441 pfam03009 GDPD Glycerophosphor  38.0      26 0.00065   14.6   4.8   29  161-189    11-39  (238)
442 TIGR03307 PhnP phosphonate met  37.8      17 0.00044   16.0   1.4   32  149-180   154-185 (249)
443 PRK13265 glycine/sarcosine/bet  37.8      26 0.00066   14.6   2.8   76   89-169     3-85  (157)
444 COG1646 Predicted phosphate-bi  37.7      26 0.00066   14.6   8.2   51   71-126    23-76  (240)
445 PRK07631 amidophosphoribosyltr  37.7      26 0.00066   14.6   5.2   37   92-138     9-45  (475)
446 COG0013 AlaS Alanyl-tRNA synth  37.5      26 0.00066   14.6  13.3   99  367-466   774-877 (879)
447 cd03817 GT1_UGDG_like This fam  37.5      26 0.00066   14.6   8.5   38  144-181    79-116 (374)
448 cd06282 PBP1_GntR_like_2 Ligan  37.5      26 0.00067   14.5   6.9   67  113-182    22-88  (266)
449 COG1634 Uncharacterized Rossma  37.3      24 0.00062   14.8   2.1   47  150-204    73-126 (232)
450 cd01966 Nitrogenase_NifN_1 Nit  37.2      26 0.00067   14.5   4.8  126   43-179    36-190 (417)
451 cd00156 REC Signal receiver do  37.2      26 0.00067   14.5   2.6   45  141-189    12-57  (113)
452 COG3848 Phosphohistidine swive  37.2      26 0.00067   14.5   2.3   39  137-178    41-79  (111)
453 KOG2187 consensus               37.2      26 0.00067   14.5   3.6   18   76-93     74-91  (534)
454 PRK06460 hypothetical protein;  37.1      26 0.00067   14.5   9.2   94   77-182    69-168 (375)
455 COG3222 Uncharacterized protei  37.0      26 0.00067   14.5   6.8   84   82-176    94-182 (211)
456 TIGR02153 gatD_arch glutamyl-t  37.0      27 0.00068   14.5   4.6  100  292-430    92-203 (413)
457 TIGR00381 cdhD CO dehydrogenas  36.9     8.5 0.00022   18.4  -0.3   24  249-272   251-274 (401)
458 COG1255 Uncharacterized protei  36.6      27 0.00068   14.5   4.0   95  143-260     6-107 (129)
459 TIGR01324 cysta_beta_ly_B cyst  36.5      27 0.00069   14.4   6.4   73   77-160    79-152 (389)
460 PRK10906 DNA-binding transcrip  36.5      27 0.00069   14.4   6.4   90  409-498   144-244 (252)
461 pfam04015 DUF362 Domain of unk  36.4      27 0.00069   14.4   6.8   23  319-341   213-235 (262)
462 PRK11091 aerobic respiration c  36.3      24  0.0006   14.9   1.9   53  174-229   431-486 (779)
463 cd06270 PBP1_GalS_like Ligand   36.2      27 0.00069   14.4   7.4   68  114-185    23-90  (268)
464 cd06267 PBP1_LacI_sugar_bindin  36.2      27 0.00069   14.4   7.1   68  114-185    23-90  (264)
465 TIGR01918 various_sel_PB selen  35.9      27  0.0007   14.4   2.3   28  135-163    30-57  (433)
466 COG1778 Low specificity phosph  35.9      14 0.00037   16.6   0.8   72   91-178     6-78  (170)
467 PRK09490 metH B12-dependent me  35.8      28  0.0007   14.4  16.0   29  132-161   285-318 (1229)
468 cd03362 TOPRIM_TopoIA_TopoIII   35.8      28  0.0007   14.4   6.9   64   76-147    83-149 (151)
469 PTZ00237 acetyl-CoA synthetase  35.7      28  0.0007   14.4   6.2   54  110-164   103-179 (649)
470 cd06331 PBP1_AmiC_like Type I   35.7      28 0.00071   14.3  10.3   37  142-178    59-96  (333)
471 pfam07085 DRTGG DRTGG domain.   35.6      28 0.00071   14.3   7.4   64  112-184    31-96  (105)
472 cd00405 PRAI Phosphoribosylant  35.6      27 0.00068   14.5   2.1   20  158-177     4-23  (203)
473 cd06277 PBP1_LacI_like_1 Ligan  35.5      28 0.00071   14.3   7.5   46  139-186    48-93  (268)
474 PRK13810 orotate phosphoribosy  35.4      28 0.00071   14.3   5.2  106   58-177    43-153 (187)
475 PRK09259 putative oxalyl-CoA d  35.3      28 0.00072   14.3   9.8   80   80-159   204-285 (572)
476 PRK08745 ribulose-phosphate 3-  35.2      28 0.00072   14.3   7.5   87   77-177    17-114 (223)
477 cd06340 PBP1_ABC_ligand_bindin  35.1      28 0.00072   14.3  10.1   31  148-178    69-99  (347)
478 cd03814 GT1_like_2 This family  35.0      28 0.00072   14.3  10.0   38  144-181    78-115 (364)
479 cd01445 TST_Repeats Thiosulfat  34.9      28 0.00072   14.3   5.2   53   73-126    75-129 (138)
480 PRK01424 S-adenosylmethionine:  34.9      28 0.00072   14.3   3.7   10  384-393   276-285 (366)
481 cd07035 TPP_PYR_POX_like Pyrim  34.9      28 0.00073   14.3   5.7   70  301-403    23-93  (155)
482 PRK00830 consensus              34.7      29 0.00073   14.2   6.0   72  111-183    38-110 (273)
483 TIGR02104 pulA_typeI pullulana  34.7      29 0.00073   14.2   4.6  138  255-415   241-413 (655)
484 PRK06752 single-stranded DNA-b  34.6      29 0.00073   14.2   7.4   54  540-595    48-106 (112)
485 PRK11192 ATP-dependent RNA hel  34.6      29 0.00073   14.2   7.2  117   35-180     6-132 (417)
486 PRK08249 cystathionine gamma-s  34.6      29 0.00073   14.2   9.2   93   77-182    88-187 (398)
487 cd06304 PBP1_BmpA_like Peripla  34.5      29 0.00073   14.2   7.9   89  114-215    25-115 (260)
488 TIGR03360 VI_minor_1 type VI s  34.5      29 0.00073   14.2   3.2   57  404-463   126-182 (185)
489 cd06337 PBP1_ABC_ligand_bindin  34.4      29 0.00074   14.2  15.1   10  168-177    88-97  (357)
490 COG0677 WecC UDP-N-acetyl-D-ma  34.4      29 0.00074   14.2   8.6   14  413-426   339-352 (436)
491 PRK08266 hypothetical protein;  34.3      29 0.00074   14.2   5.9   70  106-181     1-72  (531)
492 PRK10437 carbonic anhydrase; P  34.3      24 0.00061   14.8   1.7   17   93-109    91-107 (220)
493 COG1692 Calcineurin-like phosp  34.3      29 0.00074   14.2   6.2   58   94-153     2-63  (266)
494 cd05800 PGM_like2 This PGM-lik  34.2      29 0.00074   14.2   4.0   47  142-189   166-212 (461)
495 COG2826 Tra8 Transposase and i  34.1     9.4 0.00024   18.0  -0.4   85   98-184   164-255 (318)
496 TIGR02298 HpaD_Fe 3,4-dihydrox  34.0      19 0.00048   15.6   1.1   23  160-182    92-116 (343)
497 cd01545 PBP1_SalR Ligand-bindi  33.9      29 0.00075   14.1   7.6   75  112-189    21-96  (270)
498 PRK07525 sulfoacetaldehyde ace  33.8      29 0.00075   14.1   5.3   68  106-179     6-74  (589)
499 pfam04800 ETC_C1_NDUFA4 ETC co  33.8      29 0.00073   14.2   2.0   38  161-207    57-94  (101)
500 TIGR03254 oxalate_oxc oxalyl-C  33.6      30 0.00076   14.1   9.6   80   79-158   193-274 (554)

No 1  
>TIGR00644 recJ single-stranded-DNA-specific exonuclease RecJ; InterPro: IPR004610 All proteins in this family are 5'-3' single-strand DNA exonucleases. These proteins are used in some aspects of mismatch repair, recombination, and recombinational repair. RecJ is a single-stranded DNA-specific endonuclease which is required for many types of recombination events, although the stringency of the requirement for RecJ appears to vary with the type of recombinational event monitored, and the other recombination gene products which are available.; GO: 0008409 5'-3' exonuclease activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=100.00  E-value=0  Score=1274.67  Aligned_cols=551  Identities=38%  Similarity=0.669  Sum_probs=523.8

Q ss_pred             CCHHHHHHHHHCCCC-HHHHHHHCCCCHHHCCCCHHHCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHH
Q ss_conf             999999999967889-7898866196677718995561487999999999997799799994078861528999999999
Q gi|254780901|r   39 IPDIVARVLVNRNVS-IDYAKDFLNPSIRLLMPDPLILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLS  117 (600)
Q Consensus        39 ~~~~~a~iL~~Rgi~-~~~~~~fL~p~l~~l~~dP~~l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~  117 (600)
                      +++++|+||+|||++ .++++.||.|++.+++|+|++|+||+|||+||.+|++++|||+|||||||||+||||||+++|+
T Consensus         1 ~~~~~a~~L~~Rg~~~~~~~~~fl~~~~~~l~~~p~~l~dm~kAv~ri~~A~~~~eki~i~GDyDvDGiTSt~~l~~~L~   80 (705)
T TIGR00644         1 LSPILAQILVSRGIKDAEELENFLEPDLSHLHDPPFLLKDMEKAVERIIEAIENNEKILIFGDYDVDGITSTAILVEFLR   80 (705)
T ss_pred             CCHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCCCCHHCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHH
T ss_conf             94689999985587798999842145456887870211436899999999997289389996175226899999999999


Q ss_pred             HCC--CCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCC-CCCCCCCCCEEE
Q ss_conf             769--94799807874336688978988742026868999648876234555554179827996154-476555672565
Q gi|254780901|r  118 HCS--VNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHH-QVKSEEIPAYAL  194 (600)
Q Consensus       118 ~~g--~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH-~~~~~~p~a~ai  194 (600)
                      .+|  ..+.||||||++||||+|++++++++++|++|||||||||++++|+++|+++|+|||||||| ++++.+|+|+||
T Consensus        81 ~lGp~~~~~~~IPnR~~egYG~~~~~~~~~~~~G~~LiiTVD~Gi~a~~e~~~a~~~G~dVIVtDHHC~~~~~lP~a~Ai  160 (705)
T TIGR00644        81 ELGPYVQVDYYIPNRFTEGYGLSPEALRELKENGVSLIITVDNGISAHEEIEYAKELGIDVIVTDHHCLPPETLPEAAAI  160 (705)
T ss_pred             HCCCCCEEEEEECCCCCCCCCCCHHHHHHHHHCCCEEEEECCCCHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCCCCEE
T ss_conf             50997324666266357777889899999986698399982687426999999986698199972567984899865057


Q ss_pred             ECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHC-----------------------------------------------
Q ss_conf             237888864334430478899999999999702-----------------------------------------------
Q gi|254780901|r  195 VNPNRLDDLSGQGHLCAAGVVFLVLVLIYRILR-----------------------------------------------  227 (600)
Q Consensus       195 vNP~~~~~~~p~~~l~gaGvaf~l~~al~~~l~-----------------------------------------------  227 (600)
                      ||||+++|+||+|+|||||||||||+||.+.++                                               
T Consensus       161 vNP~~~~~~yP~k~LaGvGVaFkl~~AL~~~~~~~Y~~~~VlL~~~~~~~~~~~~A~~~~N~~~~~~L~~~~~~~L~~S~  240 (705)
T TIGR00644       161 VNPKRPDCNYPFKELAGVGVAFKLVTALLEELRDLYSKNLVLLFLRKVKNEIILEAVKINNYILKDRLLTVKNDMLLNSN  240 (705)
T ss_pred             EECCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCCEEEHHHHHHHHHHHHHHHHCCCCCCCCHH
T ss_conf             71675889988314678899999999999733311135768998740377113014567338988877624777666603


Q ss_pred             --------------------------------------------------------------------------CCCCCC
Q ss_conf             --------------------------------------------------------------------------148876
Q gi|254780901|r  228 --------------------------------------------------------------------------QDNKVP  233 (600)
Q Consensus       228 --------------------------------------------------------------------------~~~~~~  233 (600)
                                                                                                ..+.+.
T Consensus       241 ~~~~~~~~~~~~~~~~~~~L~~~~~~~~~~~~T~~~~~~~~~~~~~~R~~L~~~~~~~~~~~~~~~~~~~y~~l~~~~f~  320 (705)
T TIGR00644       241 KLLAVLEVIVIDEKVVRTELLKKFFAKFINIFTIVISRNAIKKYQNERKLLRDKIFARKYFKRKVEIKIKYIILKRGWFE  320 (705)
T ss_pred             HHHHHHEEEEEECHHHHHHHHHHHCCCCCCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEEECCCCC
T ss_conf             46432101156441578999987503354000002113443068325678878887654101351000025775247341


Q ss_pred             ---CHHHHHHHHHHHHHHHHHCCCCCC--CCCHHHHHHHHHHHHHC-----CCCCHHHHHHHHCCCC-C-CCHHHHHHHH
Q ss_conf             ---407799999998775420111144--41189999878877516-----8874357898708886-4-2423456667
Q gi|254780901|r  234 ---LNFDLLSLLDLVALATVCDVVPLI--GLNRAYVVKGLMVARRQ-----GNPGLKALIERVNISS-P-ITAENLGYMI  301 (600)
Q Consensus       234 ---~~~~l~~~ldlvaiGTvaD~vpL~--~eNR~lvk~GL~~l~~~-----~~~gl~~L~~~~~~~~-~-i~~~di~f~i  301 (600)
                         ..+++.+||||||||||||||||.  +|||+||++||+.|+++     +|+||++|++.+++++ + ++++||||.|
T Consensus       321 ~~~~~~~~~~~LdLVAiGtiAD~~~L~~Y~eNR~lv~~Gl~~~~~~~~~~~~r~Glk~L~~~~~~~~~~~~~~~~igF~I  400 (705)
T TIGR00644       321 KDKLKPDLLKLLDLVAIGTIADVMPLTEYGENRALVKKGLKALNKGADGKRKRPGLKALLKVAGFDKKKDLSSTDIGFSI  400 (705)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHCCCCCCCCCEEEHHHHH
T ss_conf             46663005767878776466302110233431899999999986288885320789999998146666674013113124


Q ss_pred             HHHCCHHHHHCCCCCCCEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC--CCCCCEEEEECCCCC
Q ss_conf             743062333121222210020342589999999999899999999999999999998752112--434750262057858
Q gi|254780901|r  302 GPSINAGGRIGESNLGSRLLISDDSQELEMLAMKLDVLNQNRRLMESAMLEQAEAKVLTQCDD--IQQASVIVVEGDRWH  379 (600)
Q Consensus       302 aPrINAaGRl~~a~~av~lL~~~d~~~a~~la~~L~~lN~~Rk~~e~~i~~~a~~~~~~~~~~--~~~~~~ivv~~~~wh  379 (600)
                      ||||||+|||++|+.|++||+|+|+.+|.++|++|+++|++||.+|+.++++|..++.++.+.  ..+++++|+++++||
T Consensus       401 gPriNA~GRl~~a~~a~~LL~~~d~~~a~~la~~l~~~N~~Rk~i~~~~~~ea~~~~~~~~~~~~l~~~~~~V~~~~~WH  480 (705)
T TIGR00644       401 GPRINAAGRLGDASLAVELLLTDDPKQARELAEELDELNEERKKIEQEVLKEAEKIAEAELEKSDLTNDSVIVVAKENWH  480 (705)
T ss_pred             HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEECCCC
T ss_conf             43664343027746789864130389999999999998899999999999999999984144234457812899617868


Q ss_pred             HHHHHHHHHHHHHHHHCEEEEEEECCC-C-EEEEEEECCCCCCHHHHHHHHCC--CCCCCCCCCCCCCCCEEECCCCHHH
Q ss_conf             122222278998842010799886379-8-37999864898618888885303--3530115653222314642221588
Q gi|254780901|r  380 PGIVGLLAARLKEKFGRPSFAISFEED-G-KGIGSGRSIEGFDIGKMVSFAVE--EGILVKGGGHAMAAGLTVERVNFGR  455 (600)
Q Consensus       380 ~GViGIVAsrL~e~y~kP~iv~s~~~d-g-~~kGS~RSi~g~~l~~~l~~~~~--~~ll~~~GGH~~AaG~ti~~~~l~~  455 (600)
                      +||+|||||||+|+|+|||+|++.+++ | .+|||+||++|+|++++++...+  .++|.+||||+|||||||++++|+.
T Consensus       481 ~GV~GIvAsrL~~~~~KP~~v~~~~~~~g~~~KGS~RSi~~~~l~~~l~~~~~~~a~l~~~~GGH~~AAGl~~~~~~l~~  560 (705)
T TIGR00644       481 PGVLGIVASRLAETFNKPVIVLAIDEEKGVIAKGSARSISGIDLLDLLSELREKGAGLLLKFGGHAMAAGLTLKRENLEE  560 (705)
T ss_pred             CCHHHHHHHHHHHHHCCCEEEEECCCCCCEEEEEEECCCCCCCHHHHHHHHHHCCCHHHHCCCCCHHHCCCCCCHHHHHH
T ss_conf             63187788889886389789998389985799877202133106989976520130133127880465055566621189


Q ss_pred             HHHHHHHHHHHHC-CHHHCCCCEEEEEEECHHHCCHHHHHHHHHCC-CCCCCCCCCEEEECCEEEEE---EEEEC--CCE
Q ss_conf             9999999998622-64433771476044346897999999998518-46789998468427809988---88847--964
Q gi|254780901|r  456 LCDFFQKFAHNIV-PALITTPVFKIDGVLNASAVNIALIDMLESAG-PYGAGNPNPVFAFPNHKLQS---IRVVN--LAH  528 (600)
Q Consensus       456 f~~~l~~~~~~~~-~~~~~~~~l~iD~el~~~~i~~~l~~~L~~le-PFG~gNpeP~F~~~~~~i~~---~r~vG--k~H  528 (600)
                      |++.|++.+.+.. ..+..++...+|++|++++++.+++++|+.|+ |||+|||+|+|.+++++|..   .+.+|  ++|
T Consensus       561 f~~~l~~~~~~~~~~~~~~~~~~~~D~~l~~~~~~~~l~~~~~~l~~PfG~gNp~P~f~~~~~~~~~~~~~~~~g~~~~H  640 (705)
T TIGR00644       561 FREKLEEKFKKSLEADESFEEILEVDAELKAEEITRELIEQLEKLEDPFGQGNPEPLFLLKNLRVEEEQIIKLIGKDENH  640 (705)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCEEECCEECHHHCCHHHHHHHHHHCCCCCCCCCCCEEEECCEEECCCHHHHHHCCCCCC
T ss_conf             99999999987520122202320102243378538789999998505457889664276222021364277661546561


Q ss_pred             EEEEEECCC----CCEEEEEEECCCCCCHHHHHHCCCCCEEEEEEEEEEEEECCCCEEEEEEEEE
Q ss_conf             999998499----8779999977878701235530699879999997665457811058999980
Q gi|254780901|r  529 LQMTFESQD----SETLQAIAFRVYGTPLGEFLMQSRGKRMHVTGHLCVNYWRGSKRCQLRVLDA  589 (600)
Q Consensus       529 lkl~l~~~~----g~~i~aI~Fn~~~~~~~~~~~~~~g~~idii~~l~~N~~~G~~s~QL~I~Di  589 (600)
                      ++|.|...+    |+.++||+|++.++++.+.+....+..+|++|++++|+|+|++++||+|.|+
T Consensus       641 ~k~~l~~~~~~p~g~~~~ai~f~~~~~~~~~~~~~~~~~~~~~~g~l~~n~~~g~~~~ql~i~d~  705 (705)
T TIGR00644       641 LKLSLKSGEQGPDGKNIEAIAFNAGEKPLIQLLELNLGRPLDVAGKLSINEWRGREKPQLIIQDL  705 (705)
T ss_pred             EEEEEECCCCCCCCCEEEEEEEECCCCCCCCHHHCCCCCEEEEEEEEEEEEECCCCEEEEEEECC
T ss_conf             78998507768987367789871577221121213688578999998765006863045677229


No 2  
>PRK11070 ssDNA exonuclease RecJ; Provisional
Probab=100.00  E-value=0  Score=1262.37  Aligned_cols=547  Identities=33%  Similarity=0.496  Sum_probs=505.1

Q ss_pred             HHCCCHHHHHHHHHCCCC-HHHHHHHCCCCHHHCCCCHHHCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHH
Q ss_conf             819999999999967889-7898866196677718995561487999999999997799799994078861528999999
Q gi|254780901|r   36 KHAIPDIVARVLVNRNVS-IDYAKDFLNPSIRLLMPDPLILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMR  114 (600)
Q Consensus        36 ~~~~~~~~a~iL~~Rgi~-~~~~~~fL~p~l~~l~~dP~~l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~  114 (600)
                      ...+||++|++|+||||+ .++    ++|++++++ +|++|+||++||+||.+||+++|||+|||||||||+||||||++
T Consensus        16 ~~~i~p~~a~lL~~RGi~~~~~----~~~~l~~l~-~p~~l~dm~~Av~ri~~Ai~~~ekI~I~GDYDvDGiTstaiL~~   90 (574)
T PRK11070         16 PAELPPLLRRLYASRGVRSAQE----LERSVKGLL-PWQQLSGIEKAVEILYNAFREGTRIIVVGDFDADGATSTALSVL   90 (574)
T ss_pred             CCCCCHHHHHHHHHCCCCCHHH----HHHHHHHCC-CHHHCCCHHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHH
T ss_conf             6667999999999779999999----847777479-92351399999999999998799499993478606799999999


Q ss_pred             HHHHCCCC-EEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCCCCCCCCCEE
Q ss_conf             99976994-79980787433668897898874202686899964887623455555417982799615447655567256
Q gi|254780901|r  115 FLSHCSVN-ANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKSEEIPAYA  193 (600)
Q Consensus       115 ~L~~~g~~-v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~~~~~~p~a~a  193 (600)
                      +|+.+|++ |.||||||++||||+|.+++++++++|++|||||||||+++++|++|+++||||||||||+|++++|+|+|
T Consensus        91 ~l~~~g~~~v~y~IP~R~~eGYGl~~~~i~~~~~~g~~LiITvDcGi~a~e~i~~a~~~GidvIVtDHH~~~~~lP~a~a  170 (574)
T PRK11070         91 ALRSLGCSNIDYLVPNRFEDGYGLSPEVVDQAHARGAQLIVTVDNGISSHAGVAHAKSLGIPVIVTDHHLPGDTLPAADA  170 (574)
T ss_pred             HHHHCCCCCEEEECCCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHCCCCEEEECCCCCCCCCCCCCE
T ss_conf             99986997169979898767879799999999965999999957853029999999977999999789999765887516


Q ss_pred             EECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCC----CHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHH
Q ss_conf             5237888864334430478899999999999702148876----407799999998775420111144411899998788
Q gi|254780901|r  194 LVNPNRLDDLSGQGHLCAAGVVFLVLVLIYRILRQDNKVP----LNFDLLSLLDLVALATVCDVVPLIGLNRAYVVKGLM  269 (600)
Q Consensus       194 ivNP~~~~~~~p~~~l~gaGvaf~l~~al~~~l~~~~~~~----~~~~l~~~ldlvaiGTvaD~vpL~~eNR~lvk~GL~  269 (600)
                      +|||+++||+||||+||||||||||++||++.+++.+.+.    ..+++.+||||||||||||||||.+|||+||++||+
T Consensus       171 ivNP~~~~~~yp~k~L~G~GVafkl~~al~~~l~~~~~~~~~~~~~~~l~~~ldlvalgTvaD~vpL~~eNR~lV~~GL~  250 (574)
T PRK11070        171 IINPNLRDCNFPSKSLAGVGVAFYLMLALRTFLRDQGWFDERGIAIPNLAELLDLVALGTVADVVPLDANNRILVWQGLS  250 (574)
T ss_pred             EECCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHH
T ss_conf             65789789899986655024999999999999876342444178807799999898676654012342058999999999


Q ss_pred             HHHHCC-CCCHHHHHHHHCCC-CCCCHHHHHHHHHHHCCHHHHHCCCCCCCEEEECCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             775168-87435789870888-6424234566677430623331212222100203425899999999998999999999
Q gi|254780901|r  270 VARRQG-NPGLKALIERVNIS-SPITAENLGYMIGPSINAGGRIGESNLGSRLLISDDSQELEMLAMKLDVLNQNRRLME  347 (600)
Q Consensus       270 ~l~~~~-~~gl~~L~~~~~~~-~~i~~~di~f~iaPrINAaGRl~~a~~av~lL~~~d~~~a~~la~~L~~lN~~Rk~~e  347 (600)
                      .|++++ ||||++|++.++++ .++|++||||+|||||||+|||++|..|++||+++|+.+|..+|++|+++|++||++|
T Consensus       251 ~l~~~~~r~Gl~aL~~~~~~~~~~i~~~dIgF~iaPriNAaGRl~~a~~av~LL~~~d~~~A~~la~~L~~~N~~Rk~ie  330 (574)
T PRK11070        251 RIRAGKCRPGIKALLEVANRDAQKLAASDLGFALGPRLNAAGRLDDMSVGVALLLCDNIGEARVLANELDALNQTRKEIE  330 (574)
T ss_pred             HHHHCCCCHHHHHHHHHHCCCCCCCCHHHEEEEEECCCCCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99757998579999997177878787534114656122156776533899998808999999999999999899999999


Q ss_pred             HHHHHHHHHHHHHHHCC-CCCCCEEEEECCCCCHHHHHHHHHHHHHHHHCEEEEEEECCCCEEEEEEECCCCCCHHHHHH
Q ss_conf             99999999998752112-43475026205785812222227899884201079988637983799986489861888888
Q gi|254780901|r  348 SAMLEQAEAKVLTQCDD-IQQASVIVVEGDRWHPGIVGLLAARLKEKFGRPSFAISFEEDGKGIGSGRSIEGFDIGKMVS  426 (600)
Q Consensus       348 ~~i~~~a~~~~~~~~~~-~~~~~~ivv~~~~wh~GViGIVAsrL~e~y~kP~iv~s~~~dg~~kGS~RSi~g~~l~~~l~  426 (600)
                      ++|+++|.+++...... ...+..||+++++||+||+|||||||+|+|+|||||++..+||.+||||||++||||+++|.
T Consensus       331 ~~i~~eA~~~~e~~~~~~~~~~~~ivl~~~~WH~GViGIVAsRL~e~y~rP~ivl~~~~dG~~kGS~RSi~g~~l~~aL~  410 (574)
T PRK11070        331 QGMQVEALTLCEKLERSSDTLPGGLAMYHPEWHQGVVGILASRIKERFHRPVIAFAPAGDGTLKGSGRSIQGLHMRDALE  410 (574)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCEEEEEECCCCEEEEEECCCCCCCHHHHHH
T ss_conf             99999999999987634676771699964886750699999999999799889999878972786421789976899999


Q ss_pred             HHCC--CCCCCCCCCCCCCCCEEECCCCHHHHHHHHHHHHHHHCCHHHCCCCEEEEEEECHHHCCHHHHHHHHHCCCCCC
Q ss_conf             5303--35301156532223146422215889999999998622644337714760443468979999999985184678
Q gi|254780901|r  427 FAVE--EGILVKGGGHAMAAGLTVERVNFGRLCDFFQKFAHNIVPALITTPVFKIDGVLNASAVNIALIDMLESAGPYGA  504 (600)
Q Consensus       427 ~~~~--~~ll~~~GGH~~AaG~ti~~~~l~~f~~~l~~~~~~~~~~~~~~~~l~iD~el~~~~i~~~l~~~L~~lePFG~  504 (600)
                      .|+.  .++|++||||+||||||++++++++|+++|++++.+++..+..++.+.+|++++++++|.+++++|++|+|||+
T Consensus       411 ~~~~~~~~lL~~fGGH~~AAG~tl~~~~l~~f~~~l~~~~~~~~~~~~~~~~l~~D~~l~~~~i~~~l~~~L~~lePFG~  490 (574)
T PRK11070        411 RLDTLYPGLILKFGGHAMAAGLSLEEDKFELFQQRFGELVTEWLDPSLLQGEVVSDGELSPAEMSMEVAELLRDAGPWGQ  490 (574)
T ss_pred             HHHHHCHHHHHHCCCCCCCCEEEECHHHHHHHHHHHHHHHHHHCCHHHCCCEEEEEEEECHHHCCHHHHHHHHHCCCCCC
T ss_conf             99864744564266755223015769999999999999999745876558727896572758689999999996497899


Q ss_pred             CCCCCEEEECCEEEEEEEEECCCEEEEEEEC-CCCCEEEEEEECCCCCCHHHHHHCCCCCEEEEEEEEEEEEECCCCEEE
Q ss_conf             9998468427809988888479649999984-998779999977878701235530699879999997665457811058
Q gi|254780901|r  505 GNPNPVFAFPNHKLQSIRVVNLAHLQMTFES-QDSETLQAIAFRVYGTPLGEFLMQSRGKRMHVTGHLCVNYWRGSKRCQ  583 (600)
Q Consensus       505 gNpeP~F~~~~~~i~~~r~vGk~Hlkl~l~~-~~g~~i~aI~Fn~~~~~~~~~~~~~~g~~idii~~l~~N~~~G~~s~Q  583 (600)
                      |||+|+|..+ +++.+.|.+|++|+|+.+++ ++++.++|||||+.....    ....+..+|++|+|++|+|||++++|
T Consensus       491 gNp~P~F~~~-~~v~~~r~vG~~Hlkl~l~~~~~~~~i~aI~F~~~~~~~----~~~~~~~vdi~~~l~iN~w~G~~s~Q  565 (574)
T PRK11070        491 MFPEPLFDGR-FRLLQQRLVGERHLKVMVEPVGGGPLLDGIAFNVDTTLW----PDNSVREVELAYKLDINEFRGNRSLQ  565 (574)
T ss_pred             CCCCCEEEEE-EEEEEEEEECCCCEEEEEEECCCCEEEEEEEECCCCCCC----CCCCCCEEEEEEEEEEEEECCCCEEE
T ss_conf             9998677201-489986770688479999967998589999968953225----43679889999998788789927289


Q ss_pred             EEEEEEEEC
Q ss_conf             999980111
Q gi|254780901|r  584 LRVLDASPV  592 (600)
Q Consensus       584 L~I~Di~p~  592 (600)
                      |+|+||+|+
T Consensus       566 L~I~Di~P~  574 (574)
T PRK11070        566 LIIDHIWPI  574 (574)
T ss_pred             EEEEEEECC
T ss_conf             999987787


No 3  
>COG0608 RecJ Single-stranded DNA-specific exonuclease [DNA replication, recombination, and repair]
Probab=100.00  E-value=0  Score=776.75  Aligned_cols=466  Identities=39%  Similarity=0.607  Sum_probs=434.7

Q ss_pred             CHHHCCCCHHHCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHH
Q ss_conf             67771899556148799999999999779979999407886152899999999976994799807874336688978988
Q gi|254780901|r   64 SIRLLMPDPLILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLME  143 (600)
Q Consensus        64 ~l~~l~~dP~~l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~  143 (600)
                      .++.+ ++|+.+++|++|++|+.+|++++++|+|||||||||+||+|||+++|+.+|+++.|+||+|+++|||    +++
T Consensus         9 ~~~~~-~~~~~l~~~~~a~~~i~~ai~~~~~I~I~~d~DaDGitS~ail~~~L~~~g~~~~~~ip~~~~~~~g----~~~   83 (491)
T COG0608           9 DLSLL-LDPFLLKDMEKAAARIAEAIEKGEKILIYGDYDADGITSAAILAKALRRLGADVDYYIPNRFEEGYG----AIR   83 (491)
T ss_pred             HHHCC-CCHHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEECCCCCCCCCH----HHH
T ss_conf             77446-8856687599999999999966986999787885177899999999997698268974774455530----676


Q ss_pred             HHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             74202686899964887623455555417982799615447655567256523788886433443047889999999999
Q gi|254780901|r  144 KFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKSEEIPAYALVNPNRLDDLSGQGHLCAAGVVFLVLVLIY  223 (600)
Q Consensus       144 ~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~~~~~~p~a~aivNP~~~~~~~p~~~l~gaGvaf~l~~al~  223 (600)
                      .+++++++|||||||||++++++.+++++|++|||||||.+++++|+++++|||++++|+||++++|||||+|++++++.
T Consensus        84 ~~~~~~~~liItvD~G~~~~~~i~~~~~~g~~vIVtDHH~~~~~~p~~~~ivNP~~~~~~~~~~~lag~gv~f~l~~al~  163 (491)
T COG0608          84 KLKEEGADLIITVDNGSGSLEEIARAKELGIDVIVTDHHPPGEELPDAVAIVNPNLPGCDYPFKELAGVGVAFKLARALL  163 (491)
T ss_pred             HHHHCCCCEEEEECCCCCHHHHHHHHHHCCCCEEEECCCCCCCCCCCCCEEECCCCCCCCCCCCCEEHHHHHHHHHHHHH
T ss_conf             55650898899977997379999998736997899789999776886526858887887876100105699999999998


Q ss_pred             HHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHCCCC-CCCHHHHHHHHH
Q ss_conf             9702148876407799999998775420111144411899998788775168874357898708886-424234566677
Q gi|254780901|r  224 RILRQDNKVPLNFDLLSLLDLVALATVCDVVPLIGLNRAYVVKGLMVARRQGNPGLKALIERVNISS-PITAENLGYMIG  302 (600)
Q Consensus       224 ~~l~~~~~~~~~~~l~~~ldlvaiGTvaD~vpL~~eNR~lvk~GL~~l~~~~~~gl~~L~~~~~~~~-~i~~~di~f~ia  302 (600)
                      +.++           .+|++||+|||||||||+.++||.+|+.||+.++...++|+++|++.++++. ++++.+++|.++
T Consensus       164 ~~~~-----------~~ll~l~alGtv~D~~~l~~~nr~~v~~gl~~~~~~~~~gi~~ll~~~~~~~~~~~~~~i~~~~~  232 (491)
T COG0608         164 EELR-----------KDLLDLVALGTVADVQPLTGENRILVNQGLKRLRKSGRPGIKALLKLAGRDTRQPTASDIGFIIG  232 (491)
T ss_pred             HHHH-----------HHHHHHHHHHHHHCCEECCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCEEEEEEEC
T ss_conf             6524-----------54688988852110101651269999999998764144559999988375557885001231112


Q ss_pred             HHCCHHHHHCCCCCCCEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCHHH
Q ss_conf             43062333121222210020342589999999999899999999999999999998752112434750262057858122
Q gi|254780901|r  303 PSINAGGRIGESNLGSRLLISDDSQELEMLAMKLDVLNQNRRLMESAMLEQAEAKVLTQCDDIQQASVIVVEGDRWHPGI  382 (600)
Q Consensus       303 PrINAaGRl~~a~~av~lL~~~d~~~a~~la~~L~~lN~~Rk~~e~~i~~~a~~~~~~~~~~~~~~~~ivv~~~~wh~GV  382 (600)
                      |||||+||++++..++.|+++++..++..++.+++..|++||.++++++.++.+........  ...++|++.+.||+||
T Consensus       233 P~ina~gr~~d~~~~~~L~~~~~~~~~~~~~~~~~~~n~erk~i~~~~~~~a~~~~~~~~~~--~~~~i~~~~~~~~~gv  310 (491)
T COG0608         233 PRINAAGRLGDAKAGVELLLTEDDEKAESLAEELELLNEERKKIENELLKEAIKIVEALEES--GEYVIVVSEEEWHPGV  310 (491)
T ss_pred             CCCCCCCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC--CCEEEEEECCCCCCHH
T ss_conf             54265565584668888622898055667999999858999999999999999875421245--8628998337867316


Q ss_pred             HHHHHHHHHHHHHCEEEEEEECCCCEEEEEEECCC-CCCHHHHHHHHCCCCCCCCCCCCCCCCCEEECCCCHHHHHHHHH
Q ss_conf             22227899884201079988637983799986489-86188888853033530115653222314642221588999999
Q gi|254780901|r  383 VGLLAARLKEKFGRPSFAISFEEDGKGIGSGRSIE-GFDIGKMVSFAVEEGILVKGGGHAMAAGLTVERVNFGRLCDFFQ  461 (600)
Q Consensus       383 iGIVAsrL~e~y~kP~iv~s~~~dg~~kGS~RSi~-g~~l~~~l~~~~~~~ll~~~GGH~~AaG~ti~~~~l~~f~~~l~  461 (600)
                      +||+||||+++|+||+++++...++.+|||+||++ ++++++.+..+.+..++.+||||++|||+++..++++.|+..+.
T Consensus       311 ~givas~l~~~~~rp~~~~~~~~~~~~kgs~rsi~~~~~~~~~l~~~~~~~~~~~~gGh~~aagl~~~~~~~~~~~~~~~  390 (491)
T COG0608         311 LGIVASRLLNAFGRPVIVLAGDAEGGAKGSARSIAKGIDLRKLLRKGRSKLLLEKFGGHAMAAGLSLKEENLEEFRGILG  390 (491)
T ss_pred             HHHHHHHHHHHHCCCEEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHCCHHHHHCCCCCCCCCCEEEECCCHHHHHHHHH
T ss_conf             99999999998589648860355445654200225566599999863306666505884322855897243488999999


Q ss_pred             HHHHHHCCHHHCCCCEEEEEEECHHHCCHHHHHHHHHCCCCCCCCCCCEEEECCEEEEEEEEECCCEEEEEEECCCCCEE
Q ss_conf             99986226443377147604434689799999999851846789998468427809988888479649999984998779
Q gi|254780901|r  462 KFAHNIVPALITTPVFKIDGVLNASAVNIALIDMLESAGPYGAGNPNPVFAFPNHKLQSIRVVNLAHLQMTFESQDSETL  541 (600)
Q Consensus       462 ~~~~~~~~~~~~~~~l~iD~el~~~~i~~~l~~~L~~lePFG~gNpeP~F~~~~~~i~~~r~vGk~Hlkl~l~~~~g~~i  541 (600)
                      +.+...+......+...+|..++.++++..++..++.++|||+|||+|+|..++..+...+.+|  |+++.+....+  .
T Consensus       391 ~~~~~~~~~~~~~~~~~id~~~~~~~~~~~~~~~~~~~~p~g~g~~~p~~~~~~~~~~~~~~~g--H~~~~~~~~~~--~  466 (491)
T COG0608         391 EIASMILDKEELREKLEIDFALKDEDITLELVSALETLEPFGQGNPLPLFLRKAAEVVGGRGGG--HLKAAGANIPK--L  466 (491)
T ss_pred             HHHHHHHHHCCCCCCCEEEEECCCCCCCHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCCCCCC--EEEEEECCCCC--C
T ss_conf             9999875520467663365433633004999998754487447995567767766662365546--37898546687--3


Q ss_pred             EEEEECCCCC
Q ss_conf             9999778787
Q gi|254780901|r  542 QAIAFRVYGT  551 (600)
Q Consensus       542 ~aI~Fn~~~~  551 (600)
                      ++++|+....
T Consensus       467 ~~~~F~~~~~  476 (491)
T COG0608         467 DAIEFLKDLD  476 (491)
T ss_pred             CHHHHHHHHH
T ss_conf             0888764435


No 4  
>pfam01368 DHH DHH family. It is predicted that this family of proteins all perform a phosphoesterase function. It included the single stranded DNA exonuclease RecJ.
Probab=99.74  E-value=9.9e-17  Score=150.81  Aligned_cols=150  Identities=38%  Similarity=0.563  Sum_probs=121.5

Q ss_pred             HHHCCCCEEEEECC--CCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCC--CCCCHHHHHHHHHC--CCCEEEEECCCCC
Q ss_conf             99779979999407--886152899999999976994799807874336--68897898874202--6868999648876
Q gi|254780901|r   88 AIYNSEKIMIFGDY--DVDGAASVALMMRFLSHCSVNANMYIPDRIVDG--YGPNPSLMEKFINE--GAQLIITVDCGST  161 (600)
Q Consensus        88 ai~~~ekI~I~gDy--D~DGitstail~~~L~~~g~~v~~~IP~R~~eG--YGl~~~~i~~~~~~--g~~LiItvD~Gi~  161 (600)
                      ||+++++|+|+||+  |.||++|+..|+.+|+++|.++.+++|.+..++  |++....++...+.  ..+|+|+||||+.
T Consensus         1 ai~~~~~i~i~~H~~pD~DaigS~~~l~~~L~~~gk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~dlvI~vD~~~~   80 (156)
T pfam01368         1 AIKEGEKILIVGHYNPDADGIGSAAALALALKRLGAEKDYVVPPREIEGKFYGLSDEIVEDIAEEKGKADLLITVDTGST   80 (156)
T ss_pred             CCCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCEEECCCCCCCHHHCCCCHHHHHHHHHCCCCCCEEEEECCCCH
T ss_conf             97679889997479988748899999999999839964685589888723306778899999853789898999769953


Q ss_pred             CHHHHHHHHHCCCCEEEECCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHH
Q ss_conf             23455555417982799615447655567256523788886433443047889999999999970214887640779999
Q gi|254780901|r  162 SYDALQYATNQGIDVIVIDHHQVKSEEIPAYALVNPNRLDDLSGQGHLCAAGVVFLVLVLIYRILRQDNKVPLNFDLLSL  241 (600)
Q Consensus       162 ~~e~i~~a~~~GidvIVtDHH~~~~~~p~a~aivNP~~~~~~~p~~~l~gaGvaf~l~~al~~~l~~~~~~~~~~~l~~~  241 (600)
                      +....+.++..+..+||+|||.+++...  +.+|||+..+   ++.+.+++++++++...+.. ++.    +..   .++
T Consensus        81 ~r~~~~~~~~~~~~~ivIDHH~~~~~~~--~~~in~~~~~---~~v~~~asst~elv~~~~~~-~~~----~~~---~~~  147 (156)
T pfam01368        81 AREEIELAKLLGIDVIVIDHHEPPENDL--PPIINPADLG---PYIDLSASSTAELVAEALLG-LEL----KLN---RNL  147 (156)
T ss_pred             HHHHHHHHHHCCCCEEEEECCCCCCCCC--CCCCCCCCCC---CCCCCCCCCHHHHHHHHHHH-CCC----CCC---HHH
T ss_conf             5554699998699789983687877776--5223734356---66587706599999999998-489----766---999


Q ss_pred             HHHHHHHHH
Q ss_conf             999877542
Q gi|254780901|r  242 LDLVALATV  250 (600)
Q Consensus       242 ldlvaiGTv  250 (600)
                      .++..+|+|
T Consensus       148 A~~l~~Giv  156 (156)
T pfam01368       148 ADLLALGIV  156 (156)
T ss_pred             HHHHHHCCC
T ss_conf             999995169


No 5  
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=99.48  E-value=1.5e-11  Score=110.23  Aligned_cols=341  Identities=23%  Similarity=0.276  Sum_probs=191.6

Q ss_pred             HHCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHH----CC--CCEEEEECCCCC---CCCCCC-----
Q ss_conf             5614879999999999977997999940788615289999999997----69--947998078743---366889-----
Q gi|254780901|r   73 LILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSH----CS--VNANMYIPDRIV---DGYGPN-----  138 (600)
Q Consensus        73 ~~l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~----~g--~~v~~~IP~R~~---eGYGl~-----  138 (600)
                      -+.++|-+++..|.+|+-.+.+|.|--.-|+||+|+..-|-++|..    .+  .+..||.-.|.-   -=|-|-     
T Consensus       324 ~L~p~m~~vAk~irrAV~egRPIiiRHHaDaDG~~agvAlE~AilplI~d~~~d~DAeyh~~KRrPskAPfYeleDvtrD  403 (715)
T COG1107         324 ALKPDMVDVAKEIRRAVLEGRPIIIRHHADADGYCAGVALEKAILPLIEDVHPDEDAEYHLFKRRPSKAPFYELEDVTRD  403 (715)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCEEEECCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCCCCCEEHHHHHHH
T ss_conf             75188999999999987347836996456766520026689988999987279802456776338666873037766646


Q ss_pred             -HHHHHHHHHCC--CCEEEEECCCCC--CHHHHHHHHHCCCCEEEECCCCCCCCCCC--CEEEECCCCCCCCCCCCCHHH
Q ss_conf             -78988742026--868999648876--23455555417982799615447655567--256523788886433443047
Q gi|254780901|r  139 -PSLMEKFINEG--AQLIITVDCGST--SYDALQYATNQGIDVIVIDHHQVKSEEIP--AYALVNPNRLDDLSGQGHLCA  211 (600)
Q Consensus       139 -~~~i~~~~~~g--~~LiItvD~Gi~--~~e~i~~a~~~GidvIVtDHH~~~~~~p~--a~aivNP~~~~~~~p~~~l~g  211 (600)
                       ..++|.+...|  .-|++.||||++  +..++..++--|++++|+|||-|.+....  -+..|||...+.+|+.   ..
T Consensus       404 l~~aLED~~RhGqKlPL~VlvDnGsTeEDipA~~~~k~Ygi~ivVVDHH~Pde~vvD~yvd~HVNPy~vGgd~~i---ta  480 (715)
T COG1107         404 LNFALEDAHRHGQKLPLLVLVDNGSTEEDIPAIKQLKAYGIDIVVVDHHYPDEAVVDEYVDVHVNPYLVGGDSNI---TA  480 (715)
T ss_pred             HHHHHHHHHHCCCCCCEEEEECCCCCCCCCHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHCCCHHHCCCCCCC---CH
T ss_conf             889999999608756569997689864462789888754997899717889603334566631275440787676---61


Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCHHH--------HHHHHHHHHHCCCCCHHHHH
Q ss_conf             8899999999999702148876407799999998775420111144411899--------99878877516887435789
Q gi|254780901|r  212 AGVVFLVLVLIYRILRQDNKVPLNFDLLSLLDLVALATVCDVVPLIGLNRAY--------VVKGLMVARRQGNPGLKALI  283 (600)
Q Consensus       212 aGvaf~l~~al~~~l~~~~~~~~~~~l~~~ldlvaiGTvaD~vpL~~eNR~l--------vk~GL~~l~~~~~~gl~~L~  283 (600)
                      -.    |+.-+.+.++..-    .   .++.-|-|++.++|-..--.--++|        -+.-|+.|..          
T Consensus       481 G~----L~vEiArmInp~v----~---d~ikHLPaVA~~gD~a~ape~~~Ylela~~~gyd~e~L~~ia~----------  539 (715)
T COG1107         481 GM----LCVEIARMINPEV----E---DDIKHLPAVAGVGDRAKAPEAEQYLELAAERGYDREDLEKIAL----------  539 (715)
T ss_pred             HH----HHHHHHHHCCCCH----H---HHHHCCCCEEEECCCCCCHHHHHHHHHHHHCCCCHHHHHHHHH----------
T ss_conf             37----8999999719244----5---5653374113424654574678999988762789899999999----------


Q ss_pred             HHHCCCCCCCHHHHHHHHHHHCCHHHHHCCCCCCCEEEE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             870888642423456667743062333121222210020-3425899999999998999999999999999999987521
Q gi|254780901|r  284 ERVNISSPITAENLGYMIGPSINAGGRIGESNLGSRLLI-SDDSQELEMLAMKLDVLNQNRRLMESAMLEQAEAKVLTQC  362 (600)
Q Consensus       284 ~~~~~~~~i~~~di~f~iaPrINAaGRl~~a~~av~lL~-~~d~~~a~~la~~L~~lN~~Rk~~e~~i~~~a~~~~~~~~  362 (600)
                       ..    .+.+..+.|.     +..|=|.      ++|- +.|...-..++..|.+.-   ++..+..++.|+..++.+.
T Consensus       540 -av----d~EaFylrf~-----~gr~ii~------DIL~~~gd~~rH~~Lvd~L~~q~---~~~ve~qL~aa~~~vk~~~  600 (715)
T COG1107         540 -AV----DYEAFYLRFM-----DGRGIIA------DILGTTGDADRHRELVDHLYEQA---KEAVEEQLRAALPHVKSER  600 (715)
T ss_pred             -HH----HHHHHHHHHC-----CCCHHHH------HHHHCCCCHHHHHHHHHHHHHHH---HHHHHHHHHHHHHCCCEEE
T ss_conf             -87----6798886516-----6540799------98631353257899999999999---9999999997641343266


Q ss_pred             CCCCCCCEE--EEECCCC-------CHH-HHHHHHHHHHHHHHC-EEEEEEECCCCEEEEEEECCCC-CCHHHHHHHHCC
Q ss_conf             124347502--6205785-------812-222227899884201-0799886379837999864898-618888885303
Q gi|254780901|r  363 DDIQQASVI--VVEGDRW-------HPG-IVGLLAARLKEKFGR-PSFAISFEEDGKGIGSGRSIEG-FDIGKMVSFAVE  430 (600)
Q Consensus       363 ~~~~~~~~i--vv~~~~w-------h~G-ViGIVAsrL~e~y~k-P~iv~s~~~dg~~kGS~RSi~g-~~l~~~l~~~~~  430 (600)
                        ..+ .++  .+--+++       .+| ..|.+--++.++|+. |++-++...|   -+-.||-.. |||..+..++.+
T Consensus       601 --l~n-Gi~~~tlDVE~yahkFtfP~pGk~~g~~HD~~~q~~g~~pivtlgyGpD---f~viRa~d~~~dl~~IV~~l~e  674 (715)
T COG1107         601 --LPN-GIAFNTLDVENYAHKFTFPPPGKLSGEVHDRLVQKYGEDPIVTLGYGPD---FAVIRATDAVFDLNRIVKELEE  674 (715)
T ss_pred             --CCC-CEEEEEEEHHHCCCCCCCCCCCCCCHHHHHHHHHHCCCCCEEEEECCCC---EEEEECCCCCCCHHHHHHHHHH
T ss_conf             --258-6378986253413456579986442266533443047775256311786---1477046641458899999975


Q ss_pred             C--CCCCCCCCCCCCCCEEECCCCHHHHHHHHHH
Q ss_conf             3--5301156532223146422215889999999
Q gi|254780901|r  431 E--GILVKGGGHAMAAGLTVERVNFGRLCDFFQK  462 (600)
Q Consensus       431 ~--~ll~~~GGH~~AaG~ti~~~~l~~f~~~l~~  462 (600)
                      .  .--..+|||.-|.-+..-...=.+...+|-+
T Consensus       675 e~p~a~v~ggGh~~~Gsikfveg~R~~Vl~a~~e  708 (715)
T COG1107         675 ELPEAGVDGGGHETAGSIKFVEGLRKEVLGAFAE  708 (715)
T ss_pred             HCCCCCCCCCCCEEECCCHHHHHHHHHHHHHHHH
T ss_conf             4510244789833303027876535557999999


No 6  
>COG0618 Exopolyphosphatase-related proteins [General function prediction only]
Probab=99.26  E-value=7.3e-08  Score=81.43  Aligned_cols=301  Identities=19%  Similarity=0.189  Sum_probs=147.6

Q ss_pred             HHHHHHHHHHHCCCCEEEEEC--CCCCHHHHHHHHHHHHHHCCCCEEEE-EC---C----CCCCCCCCCHHHHHHHHHCC
Q ss_conf             999999999977997999940--78861528999999999769947998-07---8----74336688978988742026
Q gi|254780901|r   80 KAARRIVQAIYNSEKIMIFGD--YDVDGAASVALMMRFLSHCSVNANMY-IP---D----RIVDGYGPNPSLMEKFINEG  149 (600)
Q Consensus        80 ~A~~ri~~ai~~~ekI~I~gD--yD~DGitstail~~~L~~~g~~v~~~-IP---~----R~~eGYGl~~~~i~~~~~~g  149 (600)
                      .-...+.+.++..++|.|+++  .|.|-+.|..-|.++|+..|.+...+ ..   +    ++...++...+.........
T Consensus         4 ~~~~~~~~~i~~~~~i~i~~H~nPD~DalgSa~aL~~ll~~~~~~~~v~~~G~~~~~e~~~~~~~~~~~~~~~~~~~~~~   83 (332)
T COG0618           4 RDLAELLELIKAHDKILILTHENPDPDALGSALALAELLKDLGKNKEVLYVGPITHPENRAFLNLLGDELERIEDDPLDD   83 (332)
T ss_pred             HHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHCCCCCCCCCCCCCCC
T ss_conf             68999999974569689996789995389999999999998399864998267568516777663155312356666667


Q ss_pred             CCEEEEECCCC-CCHHHHHHHHHCCCCEEEECCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             86899964887-62345555541798279961544765556725652378888643344304788999999999997021
Q gi|254780901|r  150 AQLIITVDCGS-TSYDALQYATNQGIDVIVIDHHQVKSEEIPAYALVNPNRLDDLSGQGHLCAAGVVFLVLVLIYRILRQ  228 (600)
Q Consensus       150 ~~LiItvD~Gi-~~~e~i~~a~~~GidvIVtDHH~~~~~~p~a~aivNP~~~~~~~p~~~l~gaGvaf~l~~al~~~l~~  228 (600)
                      ++++|+|||.. ............ -.+||+|||...++.+..+..|.|..         -|.+.+.+.+.+...     
T Consensus        84 ~~~~iivDt~~~~ri~~~~~~~~~-~~~ivIDHH~~~~~~~~~~~~i~~~~---------~ataeii~~~~~~~~-----  148 (332)
T COG0618          84 YDLVIIVDTANLPRIGDQELLLDS-KKVIVIDHHPGNNDIYGDFVWIDPSA---------GATAEIIAELLKEAG-----  148 (332)
T ss_pred             CCEEEEECCCCCCCCCCCCCCCCC-CCEEEEECCCCCCCCCCCEEEECCCC---------CHHHHHHHHHHHHCC-----
T ss_conf             778999738997766643322356-75699848999888778627873687---------518999999999839-----


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCC-CCHHHHHHHHCCCCCCCHHHHHHHHHHHCCH
Q ss_conf             488764077999999987754201111444118999987887751688-7435789870888642423456667743062
Q gi|254780901|r  229 DNKVPLNFDLLSLLDLVALATVCDVVPLIGLNRAYVVKGLMVARRQGN-PGLKALIERVNISSPITAENLGYMIGPSINA  307 (600)
Q Consensus       229 ~~~~~~~~~l~~~ldlvaiGTvaD~vpL~~eNR~lvk~GL~~l~~~~~-~gl~~L~~~~~~~~~i~~~di~f~iaPrINA  307 (600)
                         .+.......   +...|.+.|--.+...|.            +.+ .-+.+++...+.+.    .+           
T Consensus       149 ---~~~~~~~At---~L~~GI~tDTg~F~~~~t------------~~~~~~~a~~L~~~g~~~----~~-----------  195 (332)
T COG0618         149 ---IDLDPLVAT---ALLLGIRTDTGRFRYANT------------TADTLAAAALLVEAGADL----LE-----------  195 (332)
T ss_pred             ---CCCCHHHHH---HHHHHHHHHHCCCCCCCC------------CHHHHHHHHHHHHCCCCH----HH-----------
T ss_conf             ---995689999---999767750113354889------------836999999999769988----99-----------


Q ss_pred             HHHHCCCCCCCEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC-CEEEEECCCC--CHHHHH
Q ss_conf             3331212222100203425899999999998999999999999999999987521124347-5026205785--812222
Q gi|254780901|r  308 GGRIGESNLGSRLLISDDSQELEMLAMKLDVLNQNRRLMESAMLEQAEAKVLTQCDDIQQA-SVIVVEGDRW--HPGIVG  384 (600)
Q Consensus       308 aGRl~~a~~av~lL~~~d~~~a~~la~~L~~lN~~Rk~~e~~i~~~a~~~~~~~~~~~~~~-~~ivv~~~~w--h~GViG  384 (600)
                               .++............+..              .+++        ......+. -.+.+....+  ......
T Consensus       196 ---------v~~~~~~~~~~~~~~l~~--------------~i~~--------~~~~~~~g~~~~~~~~~~~~~~~~~~~  244 (332)
T COG0618         196 ---------VLELPLERSSETLLKLAA--------------YILK--------NNRIVENGVAYVSLVGDILEEFGDTLA  244 (332)
T ss_pred             ---------HHHHHHCCCCHHHHHHHH--------------HHHH--------HHEEECCCEEEEEEEEEEHHHCCCCHH
T ss_conf             ---------984120358678999999--------------9997--------651511663999997443123157688


Q ss_pred             HHHHHHHHH---HHCEEEEEEECC-CCEEEEEEECCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCEEECC---CCHHHHH
Q ss_conf             227899884---201079988637-983799986489861888888530335301156532223146422---2158899
Q gi|254780901|r  385 LLAARLKEK---FGRPSFAISFEE-DGKGIGSGRSIEGFDIGKMVSFAVEEGILVKGGGHAMAAGLTVER---VNFGRLC  457 (600)
Q Consensus       385 IVAsrL~e~---y~kP~iv~s~~~-dg~~kGS~RSi~g~~l~~~l~~~~~~~ll~~~GGH~~AaG~ti~~---~~l~~f~  457 (600)
                      -.+..+..-   -...+.++..++ ++.++-|-||.+..++.+....       -.+|||+.|||++++.   +..+.+.
T Consensus       245 ~~~~~v~~l~~i~~~~v~~~~~~~~~~~~r~~~rs~~~~~v~~~A~~-------~gGGGH~~AaG~~i~~~~~~~~~~l~  317 (332)
T COG0618         245 EAADFVLLLENISTAKVWGIFKDEEDGSIRVSDRSKGIGNVNEIAFK-------FGGGGHALAAGARIPLGILESADDLL  317 (332)
T ss_pred             HHHHHHHHHHCCCEEEEEEEEEECCCCEEEEEEEECCCHHHHHHHHH-------CCCCCCCCCCEEEECCCHHHHHHHHH
T ss_conf             89999988625440699999985133179997576585428999756-------38998611366786353145699999


Q ss_pred             HHHHHHHHH
Q ss_conf             999999986
Q gi|254780901|r  458 DFFQKFAHN  466 (600)
Q Consensus       458 ~~l~~~~~~  466 (600)
                      +.+.+.+..
T Consensus       318 ~~l~~~l~~  326 (332)
T COG0618         318 KLLEAALKK  326 (332)
T ss_pred             HHHHHHHHH
T ss_conf             999999998


No 7  
>COG2404 Predicted phosphohydrolase (DHH superfamily) [General function prediction only]
Probab=98.59  E-value=9.9e-06  Score=64.75  Aligned_cols=303  Identities=22%  Similarity=0.237  Sum_probs=138.9

Q ss_pred             CEEEEECCCCCHHHHHHHHHHHHHH-C-CCCEEEEECCCCCCCCCCCHHHHHHHHHCCC-CEEEEECCCCCC--HHH-HH
Q ss_conf             7999940788615289999999997-6-9947998078743366889789887420268-689996488762--345-55
Q gi|254780901|r   94 KIMIFGDYDVDGAASVALMMRFLSH-C-SVNANMYIPDRIVDGYGPNPSLMEKFINEGA-QLIITVDCGSTS--YDA-LQ  167 (600)
Q Consensus        94 kI~I~gDyD~DGitstail~~~L~~-~-g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~-~LiItvD~Gi~~--~e~-i~  167 (600)
                      .+.||.+-|.||+.++++...++.. . .++.....|+++..       .++.+.+.+. +++..-|++...  .++ ++
T Consensus         1 ~y~i~sH~DlDG~acaaV~k~~~gk~vyn~n~~~~~~~~i~~-------~l~~~~~~~~~~~i~i~DL~~n~d~~e~~~~   73 (339)
T COG2404           1 VYHIYSHNDLDGYACAAVVKRFFGKNVYNANFGREVSARINS-------ILESAEESGIGDAILISDLDVNLDRFEELVE   73 (339)
T ss_pred             CEEEEECCCCCHHHHHHHHHHHHHHCCCCHHHHCCCHHHHHH-------HHHHHHHHCCCCEEEEEECCCCCCHHHHHHH
T ss_conf             979995388522889999999831034541441244288999-------9989986256653777541558210389999


Q ss_pred             HHH---HCCCCEEEECCCCCCCC----CCCCEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHH
Q ss_conf             554---17982799615447655----56725652378888643344304788999999999997021488764077999
Q gi|254780901|r  168 YAT---NQGIDVIVIDHHQVKSE----EIPAYALVNPNRLDDLSGQGHLCAAGVVFLVLVLIYRILRQDNKVPLNFDLLS  240 (600)
Q Consensus       168 ~a~---~~GidvIVtDHH~~~~~----~p~a~aivNP~~~~~~~p~~~l~gaGvaf~l~~al~~~l~~~~~~~~~~~l~~  240 (600)
                      .++   ..|..|.-+|||.-..+    .+.+..-+.        -..-.|+++|.|...... ..+ +    | .--+.+
T Consensus        74 ~l~~~~~~~~kv~wiDHH~t~~e~~~e~~~~~v~~~--------~D~~rcaa~vvy~~l~~~-~~~-e----~-~~~~~~  138 (339)
T COG2404          74 KLKEATNKGTKVKWIDHHKTANETKEEVREAGVSVY--------VDDSRCAAGVVYEYLKPH-EIL-E----P-TLFLEQ  138 (339)
T ss_pred             HHHHHHHCCCCEEEECCCCCCCHHHHHHHHCCCEEE--------ECCCCHHHHHHHHEECCC-CCC-C----C-HHHHHH
T ss_conf             999876357735875010135445898653280899--------777202112233000502-257-7----0-356999


Q ss_pred             HHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCHHHHHCCCCCCCEE
Q ss_conf             99998775420111144411899998788775168874357898708886424234566677430623331212222100
Q gi|254780901|r  241 LLDLVALATVCDVVPLIGLNRAYVVKGLMVARRQGNPGLKALIERVNISSPITAENLGYMIGPSINAGGRIGESNLGSRL  320 (600)
Q Consensus       241 ~ldlvaiGTvaD~vpL~~eNR~lvk~GL~~l~~~~~~gl~~L~~~~~~~~~i~~~di~f~iaPrINAaGRl~~a~~av~l  320 (600)
                         ||.+-.=.|+=--.+.+       |..+.+     ...|.+..-   +.+....-+...+-.|=.-++-.    ...
T Consensus       139 ---lve~v~s~DiW~~e~~~-------~~~~~~-----~~~l~r~~~---d~~~~~~~l~~~e~~~~~l~k~~----~gi  196 (339)
T COG2404         139 ---LVELVRSVDIWLWEDYG-------LGMIPQ-----GSELNRFMF---DDNQWEYLLGDGEEYKDYLKKFN----AGI  196 (339)
T ss_pred             ---HHHHHCCCCHHHCCCCC-------CCCCCC-----HHHHHHHHH---CCHHHHHHHCCHHHHHHHHHHHH----CCC
T ss_conf             ---99985251121124763-------201100-----236778764---00577776113599999999850----575


Q ss_pred             EECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHCEEE
Q ss_conf             2034258999999999989999999999999999999875-211243475026205785812222227899884201079
Q gi|254780901|r  321 LISDDSQELEMLAMKLDVLNQNRRLMESAMLEQAEAKVLT-QCDDIQQASVIVVEGDRWHPGIVGLLAARLKEKFGRPSF  399 (600)
Q Consensus       321 L~~~d~~~a~~la~~L~~lN~~Rk~~e~~i~~~a~~~~~~-~~~~~~~~~~ivv~~~~wh~GViGIVAsrL~e~y~kP~i  399 (600)
                      |..++-.    .   +.+.--.|.  ..+.+..+.+++.. +.++. ...+-+.|.  -++|..-..+++..+.|+--+ 
T Consensus       197 ~~de~~~----~---~l~~~~~~~--~~~~l~~~~krv~~~~i~~~-~~~~~i~y~--~~~g~~s~~~g~~~~~~~d~v-  263 (339)
T COG2404         197 LWDEVLD----Y---ILQIAVGRD--KIETLSNASKRVVTITIDDK-KHVVEIYYR--GPGGYDSSIMGQTDELYNDFV-  263 (339)
T ss_pred             CCHHHHH----H---HHHHHHHCC--HHHHHHHHHHHHHHHCCCCC-EEEEEEEEC--CCCCCCHHHCCCHHHHHCCEE-
T ss_conf             5288899----9---999886002--36789999976732101341-566899952--799841332154144202105-


Q ss_pred             EEEECCCCEEEEEEECCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCEEECCCCHHHHHHHHHH
Q ss_conf             988637983799986489861888888530335301156532223146422215889999999
Q gi|254780901|r  400 AISFEEDGKGIGSGRSIEGFDIGKMVSFAVEEGILVKGGGHAMAAGLTVERVNFGRLCDFFQK  462 (600)
Q Consensus       400 v~s~~~dg~~kGS~RSi~g~~l~~~l~~~~~~~ll~~~GGH~~AaG~ti~~~~l~~f~~~l~~  462 (600)
                      |+....|+.  -|-||-+.+|........+.  ....+|||+.||| .    ++..|.++++-
T Consensus       264 v~~~~~d~~--i~~~Sk~~~n~~~~~a~~~~--~~~gGGGH~nAaG-~----~~~~f~~~~n~  317 (339)
T COG2404         264 VFVLRSDSG--ISDRSKNNANVNIDVAEIAQ--VQYGGGGHPNAAG-G----KIARFAEKFNY  317 (339)
T ss_pred             EEECCCCCC--CCCCCCCCCCCCHHHHHHHH--HHCCCCCCCCCCC-C----HHHHHHHHHHH
T ss_conf             784147876--66410136763135777888--5138999855442-2----77889875008


No 8  
>COG3887 Predicted signaling protein consisting of a modified GGDEF domain and a DHH domain [Signal transduction mechanisms]
Probab=98.27  E-value=0.00093  Score=49.32  Aligned_cols=301  Identities=16%  Similarity=0.239  Sum_probs=152.1

Q ss_pred             CCCHHHHHHHHHHHHHCCCCEEEEEC--CCCCHHHHHHHHHHHHHHCCCCEEEEE-CCCCCCCCCCCHHHHHHHHH--CC
Q ss_conf             14879999999999977997999940--788615289999999997699479980-78743366889789887420--26
Q gi|254780901|r   75 LTDCDKAARRIVQAIYNSEKIMIFGD--YDVDGAASVALMMRFLSHCSVNANMYI-PDRIVDGYGPNPSLMEKFIN--EG  149 (600)
Q Consensus        75 l~dm~~A~~ri~~ai~~~ekI~I~gD--yD~DGitstail~~~L~~~g~~v~~~I-P~R~~eGYGl~~~~i~~~~~--~g  149 (600)
                      -+.|..|.   .+-|....++.|+|+  -|.|-+-|+.=|.++....+-+...++ |.-+..   =.+++|+++.+  ++
T Consensus       323 aRvis~al---~d~i~e~d~VfImGHk~pDmDalGsAig~~~~A~~~~~~a~~v~dp~~~~p---dveRai~~i~~~~e~  396 (655)
T COG3887         323 ARVISTAL---SDIIKESDNVFIMGHKFPDMDALGSAIGMQKFASMNNKEAFAVLDPEDMSP---DVERAINEIEKNSEG  396 (655)
T ss_pred             HHHHHHHH---HHHHHHCCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCH---HHHHHHHHHHHCCHH
T ss_conf             99999999---999852274899816888757777899999999734656279977222684---699999999726205


Q ss_pred             CCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCCCCCC-------CCCEEEECCCCCCCCCCCCCH-----HHHHHHHH
Q ss_conf             868999648876234555554179827996154476555-------672565237888864334430-----47889999
Q gi|254780901|r  150 AQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKSEE-------IPAYALVNPNRLDDLSGQGHL-----CAAGVVFL  217 (600)
Q Consensus       150 ~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~~~~~~-------p~a~aivNP~~~~~~~p~~~l-----~gaGvaf~  217 (600)
                      .+.+||++-      +.+ +...+--+++.|||.|.-.+       ...+.||.-||.+.+||...+     ++|.-|=-
T Consensus       397 ~~~fit~~~------A~~-l~t~~sLLviVDt~k~s~vl~~~~~~~~~kvVViDHHRR~e~f~~n~~l~YiEsyASStsE  469 (655)
T COG3887         397 KTRFITPSD------AME-LSTERSLLVIVDTHKPSLVLNEEFLDKFEKVVVIDHHRRDEDFISNPLLVYIESYASSTSE  469 (655)
T ss_pred             HHEECCHHH------HHH-CCCCCCEEEEEECCCCCEECCHHHHHHHCEEEEEECCCCCCCCCCCHHHHHHCCCCCCHHH
T ss_conf             432355999------863-2687708999936882000389999763028997344355443234277631367651889


Q ss_pred             HHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCC-H--HHHHHHHCC--CC-C
Q ss_conf             9999999702148876407799999998775420111144411899998788775168874-3--578987088--86-4
Q gi|254780901|r  218 VLVLIYRILRQDNKVPLNFDLLSLLDLVALATVCDVVPLIGLNRAYVVKGLMVARRQGNPG-L--KALIERVNI--SS-P  291 (600)
Q Consensus       218 l~~al~~~l~~~~~~~~~~~l~~~ldlvaiGTvaD~vpL~~eNR~lvk~GL~~l~~~~~~g-l--~~L~~~~~~--~~-~  291 (600)
                      |+                                             .+=|+..++..+.. +  .+|+  +|+  ++ .
T Consensus       470 LV---------------------------------------------TEliqyq~~~~kl~~ieAt~Ll--AGI~vDTKn  502 (655)
T COG3887         470 LV---------------------------------------------TELIQYQPKKQKLSPIEATALL--AGIIVDTKN  502 (655)
T ss_pred             HH---------------------------------------------HHHHHHCCHHCCCCHHHHHHHH--HCEEEECCC
T ss_conf             99---------------------------------------------9999717431132578999987--325882365


Q ss_pred             C--CHHHHHHHHHHHCCHHHHHCCCCCCCEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             2--42345666774306233312122221002034258999999999989999999999999999999875211243475
Q gi|254780901|r  292 I--TAENLGYMIGPSINAGGRIGESNLGSRLLISDDSQELEMLAMKLDVLNQNRRLMESAMLEQAEAKVLTQCDDIQQAS  369 (600)
Q Consensus       292 i--~~~di~f~iaPrINAaGRl~~a~~av~lL~~~d~~~a~~la~~L~~lN~~Rk~~e~~i~~~a~~~~~~~~~~~~~~~  369 (600)
                      +  ++..=.|-.|--|-+-|-  |. ..++-++.+|.+          .. .+|.++    .+.++         .-.+.
T Consensus       503 Ft~rTgsRTFdAAsyLRs~Ga--Dt-iliq~~lk~d~e----------~y-~k~~el----I~~~~---------~~~~g  555 (655)
T COG3887         503 FTLRTGSRTFDAASYLRSRGA--DT-ILIQKFLKTDFE----------EY-IKRSEL----IENAR---------VYKDG  555 (655)
T ss_pred             CEEECCCCEEHHHHHHHHCCC--CH-HHHHHHHHHHHH----------HH-HHHHHH----HHHHH---------CCCCC
T ss_conf             234036511158999986387--67-999999876199----------99-999999----98777---------10697


Q ss_pred             EEEEECCCCCHHHHHHHHHHHHHH----HH-CEEEEEEECCCCEEEEEEECCCCCCHHHHHHHHCCCCCCCCCCCCCCCC
Q ss_conf             026205785812222227899884----20-1079988637983799986489861888888530335301156532223
Q gi|254780901|r  370 VIVVEGDRWHPGIVGLLAARLKEK----FG-RPSFAISFEEDGKGIGSGRSIEGFDIGKMVSFAVEEGILVKGGGHAMAA  444 (600)
Q Consensus       370 ~ivv~~~~wh~GViGIVAsrL~e~----y~-kP~iv~s~~~dg~~kGS~RSi~g~~l~~~l~~~~~~~ll~~~GGH~~Aa  444 (600)
                      +.+-+++. |+-.--+++++-+++    -+ +.+||++...+|..--|+||-+++|+--++..+       .+|||=.+|
T Consensus       556 iaiA~~~~-~e~~~~viiaqAAD~lLsm~Gv~ASFVvak~~~~~i~ISaRS~g~iNVQ~ImEaL-------GGGGH~tnA  627 (655)
T COG3887         556 IAIATGSK-DEAYSNVIIAQAADTLLSMAGVEASFVVAKRTDGLISISARSLGKINVQVIMEAL-------GGGGHLTNA  627 (655)
T ss_pred             EEEEECCH-HHHHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCEEEEEECCCCCCHHHHHHHHH-------CCCCHHHHH
T ss_conf             69995335-5431088999989988513172278999983697599972025774088999873-------686316677


Q ss_pred             CEEECCCCHHHHHHHHHHHHHHHCCH
Q ss_conf             14642221588999999999862264
Q gi|254780901|r  445 GLTVERVNFGRLCDFFQKFAHNIVPA  470 (600)
Q Consensus       445 G~ti~~~~l~~f~~~l~~~~~~~~~~  470 (600)
                      +..++.--+++..+.|.+.+.+.+.+
T Consensus       628 Atql~~~t~~ea~~~L~~aI~~~~~e  653 (655)
T COG3887         628 ATQLKDVTLEEALEQLQEAIDEYLEE  653 (655)
T ss_pred             HHHHCCCCHHHHHHHHHHHHHHHHCC
T ss_conf             77511364999999999999998505


No 9  
>pfam02272 DHHA1 DHHA1 domain. This domain is often found adjacent to the DHH domain pfam01368 and is called DHHA1 for DHH associated domain. This domain is diagnostic of DHH subfamily 1 members. This domains is also found in alanyl tRNA synthetase, suggesting that this domain may have an RNA binding function. The domain is about 60 residues long and contains a conserved GG motif.
Probab=98.12  E-value=2.6e-06  Score=69.30  Aligned_cols=65  Identities=28%  Similarity=0.378  Sum_probs=54.8

Q ss_pred             HCEEEEEEECCCCEEEEEEECCCCCCHH--HHHHHHCCCCCCCCCCCCCCCCCEEECCCC-HHHHHHHHH
Q ss_conf             0107998863798379998648986188--888853033530115653222314642221-588999999
Q gi|254780901|r  395 GRPSFAISFEEDGKGIGSGRSIEGFDIG--KMVSFAVEEGILVKGGGHAMAAGLTVERVN-FGRLCDFFQ  461 (600)
Q Consensus       395 ~kP~iv~s~~~dg~~kGS~RSi~g~~l~--~~l~~~~~~~ll~~~GGH~~AaG~ti~~~~-l~~f~~~l~  461 (600)
                      .+|+++++. +++.+++|+||.++++..  ++++.+++. +.-++|||++|||++++... +++|.+.+.
T Consensus         1 ~~~vi~~~~-~~~k~~~s~rs~~~~~~~~~~i~~~~~~~-~gG~GGGh~~aAg~~~~~~~~~~~~~~~~~   68 (69)
T pfam02272         1 DKPVVLFAE-EDGKVKVSARSSKGLDVKGGELLKEVAEI-LGGGGGGHPDAAGAGGKDPSKLEEALELLE   68 (69)
T ss_pred             CCEEEEEEE-CCCEEEEEEEECHHHHHHHHHHHHHHHHH-HCCCCCCCHHHHHCCCCCHHHHHHHHHHHH
T ss_conf             955999981-49959999996578887899999999999-389889975676158998788999999834


No 10 
>pfam02724 CDC45 CDC45-like protein. CDC45 is an essential gene required for initiation of DNA replication in S. cerevisiae, forming a complex with MCM5/CDC46. Homologues of CDC45 have been identified in human, mouse and smut fungus among others.
Probab=96.05  E-value=0.039  Score=36.66  Aligned_cols=85  Identities=22%  Similarity=0.486  Sum_probs=63.5

Q ss_pred             CEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHH-HC
Q ss_conf             79999407886152899999999976994799807874336688978988742026868999648876234555554-17
Q gi|254780901|r   94 KIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYAT-NQ  172 (600)
Q Consensus        94 kI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~-~~  172 (600)
                      .|+|+.=+|||.+||+-||...|+.-.+....+ |   ..||+=-..+.++..++ +.-+|.+-||-+ .+-.+.+. .-
T Consensus         1 ~Vlilva~DvDALCA~kILt~Llk~D~I~y~l~-P---V~gy~eL~~~~~e~~~~-~~~vilIncGa~-vDL~~~l~~~~   74 (584)
T pfam02724         1 SVLVLVALDVDALCACKILTSLLKCDLIQYQLV-P---VSGYGELKRAYQELDED-IKSVILINCGGM-VDLLEFLQLDE   74 (584)
T ss_pred             CEEEEEECCCHHHHHHHHHHHHHHHCCCCEEEE-E---ECCHHHHHHHHHHHHHC-CCEEEEEECCCC-EEHHHHCCCCC
T ss_conf             989999088079999999999986558865899-6---07899999999987521-528999905860-03998719999


Q ss_pred             CCCEEEECCCCC
Q ss_conf             982799615447
Q gi|254780901|r  173 GIDVIVIDHHQV  184 (600)
Q Consensus       173 GidvIVtDHH~~  184 (600)
                      ++.|.|+|.|.|
T Consensus        75 ~~~v~ViDsHRP   86 (584)
T pfam02724        75 DVIVYVIDSHRP   86 (584)
T ss_pred             CEEEEEEECCCC
T ss_conf             649999558898


No 11 
>PRK02947 hypothetical protein; Provisional
Probab=95.94  E-value=0.19  Score=31.20  Aligned_cols=153  Identities=16%  Similarity=0.246  Sum_probs=88.9

Q ss_pred             HHCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCC--CEEEEEC---------------CCCCCCC
Q ss_conf             5614879999999999977997999940788615289999999997699--4799807---------------8743366
Q gi|254780901|r   73 LILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSV--NANMYIP---------------DRIVDGY  135 (600)
Q Consensus        73 ~~l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~--~v~~~IP---------------~R~~eGY  135 (600)
                      .....|++|++.+.++|+++-.|.+||-    | -|..+.-+.+-+.|.  .+.....               .| .+||
T Consensus        22 ~q~~~I~~Aa~~ia~si~~gg~i~~fGt----G-HS~~~a~E~f~RAGGla~~~pI~~~~l~~~~g~~~s~~~ER-~~g~   95 (247)
T PRK02947         22 TQADAIKQAADLVADSIANGGRIYVFGT----G-HSHMAAEEVFYRAGGLAPFNPILEPSLMLHEGAVASSYLER-IEGY   95 (247)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCEEEEECC----C-CHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHC-CCCH
T ss_conf             9999999999999999975997999888----5-16489998741147643313003411025478666531222-5509


Q ss_pred             CCCHHHHHHHHHCCCC-EEEEECCCCC--CHHHHHHHHHCCCCEEEEC---C-------CCCCC------------CCCC
Q ss_conf             8897898874202686-8999648876--2345555541798279961---5-------44765------------5567
Q gi|254780901|r  136 GPNPSLMEKFINEGAQ-LIITVDCGST--SYDALQYATNQGIDVIVID---H-------HQVKS------------EEIP  190 (600)
Q Consensus       136 Gl~~~~i~~~~~~g~~-LiItvD~Gi~--~~e~i~~a~~~GidvIVtD---H-------H~~~~------------~~p~  190 (600)
                      |  ...++...-..-| +||.--.|.+  ..|...+||++|+.||.+-   |       |....            -.|+
T Consensus        96 a--~~il~~~~i~~~Dvlii~SnSG~N~~pVE~A~~ak~~G~~VIaiTS~~~s~~~~srH~SGkkL~d~aDiviDN~~p~  173 (247)
T PRK02947         96 A--KLILDRYPIRPGDVLIIVSNSGRNAVPIEMALEAKERGAKVIAVTSLAYSKSVASRHSSGKRLYEVADVVIDNGAPK  173 (247)
T ss_pred             H--HHHHHHCCCCCCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEECHHHHCCCCCCCCCCCEEHHHCCEEEECCCCC
T ss_conf             9--99998679999988999967877768999999999869969999667881678998976671156366786579998


Q ss_pred             CEEEEC-CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             256523-7888864334430478899999999999702148876
Q gi|254780901|r  191 AYALVN-PNRLDDLSGQGHLCAAGVVFLVLVLIYRILRQDNKVP  233 (600)
Q Consensus       191 a~aivN-P~~~~~~~p~~~l~gaGvaf~l~~al~~~l~~~~~~~  233 (600)
                      .+|++. |.....-.|...++|+-++..++....+.|.+.+..|
T Consensus       174 GDA~l~i~g~~~kvgp~STi~g~~i~n~i~~e~~~~L~~~G~~p  217 (247)
T PRK02947        174 GDAVLEIEGLEAKVGPTSTVVGVAILNAIFAEAAEELVERGIDP  217 (247)
T ss_pred             CCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             76589878977775757789999999999999999999779999


No 12 
>cd04492 YhaM_OBF_like YhaM_OBF_like: A subfamily of OB folds similar to that found in Bacillus subtilis YhaM and Staphylococcus aureus cmp-binding factor-1 (SaCBF1). Both these proteins are 3'-to-5'exoribonucleases. YhaM requires Mn2+ or Co2+ for activity and is inactive in the presence of Mg2+. YhaM also has a Mn2+ dependent 3'-to-5'single-stranded DNA exonuclease activity. SaCBF is also a double-stranded DNA binding protein, binding specifically to cmp, the replication enhancer found in S. aureus plasmid pT181. Proteins in this group combine an N-terminal OB fold with a C-terminal HD domain. The HD domain is found in metal-dependent phosphohydrolases.
Probab=95.87  E-value=0.084  Score=34.05  Aligned_cols=79  Identities=19%  Similarity=0.243  Sum_probs=54.9

Q ss_pred             EEEECCEEEEEEEEECCCEEEEEEECCCCCEEEEEEECCCCCCHHHHHHCCCCCEEEEEEEEEEEEECCCCEEEEEEEEE
Q ss_conf             68427809988888479649999984998779999977878701235530699879999997665457811058999980
Q gi|254780901|r  510 VFAFPNHKLQSIRVVNLAHLQMTFESQDSETLQAIAFRVYGTPLGEFLMQSRGKRMHVTGHLCVNYWRGSKRCQLRVLDA  589 (600)
Q Consensus       510 ~F~~~~~~i~~~r~vGk~Hlkl~l~~~~g~~i~aI~Fn~~~~~~~~~~~~~~g~~idii~~l~~N~~~G~~s~QL~I~Di  589 (600)
                      .|++++..+. ...-|+.-+.+.|.+..| .++|..|...+...   .....|..+.+-++..  .|+|  ++||.|..|
T Consensus         3 ~fli~~~~~~-~tk~G~~Yl~l~L~D~tG-~I~ak~W~~~~~~~---~~~~~g~~V~v~G~v~--~y~g--~~Ql~I~~i   73 (83)
T cd04492           3 FFLIKSKELR-TAKNGKPYLALTLQDKTG-EIEAKLWDASEEDE---EKFKPGDIVHVKGRVE--EYRG--RLQLKIQRI   73 (83)
T ss_pred             EEEEEEHHHH-CCCCCCCEEEEEEECCCC-EEEEEECCCCHHHH---HCCCCCCEEEEEEEEE--EECC--CEEEEEEEE
T ss_conf             9999980100-057999178999987887-68888857886788---3078999999999998--8899--510899896


Q ss_pred             EECCCCCC
Q ss_conf             11131126
Q gi|254780901|r  590 SPVEGHHF  597 (600)
Q Consensus       590 ~p~e~~~~  597 (600)
                      +|++.+..
T Consensus        74 ~~~~~~d~   81 (83)
T cd04492          74 RLVTEEDG   81 (83)
T ss_pred             EECCCCCC
T ss_conf             89983447


No 13 
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=95.73  E-value=0.21  Score=30.93  Aligned_cols=21  Identities=19%  Similarity=0.314  Sum_probs=11.3

Q ss_pred             HHHHHCCCCCCCEEEECCCHH
Q ss_conf             233312122221002034258
Q gi|254780901|r  307 AGGRIGESNLGSRLLISDDSQ  327 (600)
Q Consensus       307 AaGRl~~a~~av~lL~~~d~~  327 (600)
                      |-=|-..|.-|-++++.+-.+
T Consensus       245 AD~Ra~TPTaAAe~~~p~~~e  265 (443)
T PRK00286        245 ADLRAPTPTAAAELVVPDQAE  265 (443)
T ss_pred             HHCCCCCHHHHHHHHCCCHHH
T ss_conf             540379969999986531999


No 14 
>LOAD_cdc45 consensus
Probab=95.58  E-value=0.094  Score=33.67  Aligned_cols=88  Identities=16%  Similarity=0.363  Sum_probs=60.9

Q ss_pred             CCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCC-CHHHHHHH
Q ss_conf             79979999407886152899999999976994799807874336688978988742026868999648876-23455555
Q gi|254780901|r   91 NSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGST-SYDALQYA  169 (600)
Q Consensus        91 ~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~-~~e~i~~a  169 (600)
                      ++..|+|+.=+|||.+||+-||...|+.=.+.... +|   ..||+=-..+..+..++ +.-+|.+.||-+ +..++-. 
T Consensus        13 ~r~sVlilva~DvDALCA~kILt~Llk~D~I~y~l-vP---V~Gy~dL~~~~~e~~~~-~~~vilIncGg~~DL~~~l~-   86 (578)
T LOAD_cdc45       13 SRSSVLLVVALDVDALCATKILQALFKCDHIQYTI-VP---VSGYSELERAFLEHQED-IKYVILINCGAVVDLLETLQ-   86 (578)
T ss_pred             CCCEEEEEECCCCHHHHHHHHHHHHHHHCCCCEEE-EE---ECCHHHHHHHHHHHCCC-CCEEEEEECCCCEEHHHHCC-
T ss_conf             88769999828817989999999998544887589-98---47899999999973677-54799990687327888609-


Q ss_pred             HHCCCCEEEECCCCC
Q ss_conf             417982799615447
Q gi|254780901|r  170 TNQGIDVIVIDHHQV  184 (600)
Q Consensus       170 ~~~GidvIVtDHH~~  184 (600)
                      -.-.+.+-|+|.|.|
T Consensus        87 ~~~~~~vyViDsHRP  101 (578)
T LOAD_cdc45       87 IPPDVIIFVIDSHRP  101 (578)
T ss_pred             CCCCCEEEEEECCCC
T ss_conf             998718999347898


No 15 
>cd04489 ExoVII_LU_OBF ExoVII_LU_OBF: A subfamily of OB folds corresponding to the N-terminal OB-fold domain of Escherichia coli exodeoxyribonuclease VII (ExoVII) large subunit. E. coli ExoVII is composed of two non-identical subunits. E. coli ExoVII is a single-strand-specific exonuclease which degrades ssDNA from both 3-prime and 5-prime ends. ExoVII plays a role in methyl-directed mismatch repair in vivo. ExoVII may also guard the genome from mutagenesis by removing excess ssDNA, since the build up of ssDNA would lead to SOS induction and PolIV-dependent mutagenesis.
Probab=95.25  E-value=0.17  Score=31.56  Aligned_cols=71  Identities=21%  Similarity=0.416  Sum_probs=49.6

Q ss_pred             EEEEEEEECCCEEEEEEECCCCCEEEEEEECCCCCCHHHHHHCCCCCEEEEEEEEEEEEECCCCEEEEEEEEEEEC
Q ss_conf             9988888479649999984998779999977878701235530699879999997665457811058999980111
Q gi|254780901|r  517 KLQSIRVVNLAHLQMTFESQDSETLQAIAFRVYGTPLGEFLMQSRGKRMHVTGHLCVNYWRGSKRCQLRVLDASPV  592 (600)
Q Consensus       517 ~i~~~r~vGk~Hlkl~l~~~~g~~i~aI~Fn~~~~~~~~~~~~~~g~~idii~~l~~N~~~G~~s~QL~I~Di~p~  592 (600)
                      +|.+.+.-..+|+=|.|++.+ ..++++.|+..-...+  .....|..+-+.+  +++.|..+-++||.+.+|+|+
T Consensus         7 EIs~~~~~~sGh~Yf~LkD~~-a~i~~v~~~~~~~~~~--~~~~~G~~V~v~g--~~~~y~~~G~~ql~v~~i~~~   77 (78)
T cd04489           7 EISNLKRPSSGHLYFTLKDED-ASIRCVMWRSNARRLG--FPLEEGMEVLVRG--KVSFYEPRGGYQLIVEEIEPA   77 (78)
T ss_pred             EECCCEECCCCEEEEEEECCC-EEEEEEEEHHHHHHCC--CCCCCCCEEEEEE--EEEEECCCCEEEEEEEEEEEC
T ss_conf             988558289963999994788-1999999667883279--9988998999999--999998984099999999978


No 16 
>TIGR03316 ygeW probable carbamoyltransferase YgeW. Members of this protein family include the ygeW gene product of Escherichia coli. The function is unknown. Members show homology to ornithine carbamoyltransferase (TIGR00658) and aspartate carbamoyltransferase (carbamoyltransferase), and therefore may belong to the carbamoyltransferases in function. Members often are found in a large, conserved genomic region associated with purine catabolism.
Probab=94.80  E-value=0.3  Score=29.71  Aligned_cols=52  Identities=12%  Similarity=-0.024  Sum_probs=24.4

Q ss_pred             HHHHHHHHHH-HHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEE
Q ss_conf             1528999999-999769947998078743366889789887420268689996
Q gi|254780901|r  105 GAASVALMMR-FLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITV  156 (600)
Q Consensus       105 Gitstail~~-~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItv  156 (600)
                      --|=|-+=.+ +..++|..+.+.=|+-.+-|.|-+..=.-+....-++.|+.-
T Consensus        52 pSTRTR~SFe~A~~~LGg~~i~l~~~~ss~~kGEsv~DTarvls~y~D~IviR  104 (357)
T TIGR03316        52 NSTRTRFSFASAMNLLGLHAQDLDEGKSQIGHGETVRETAEMISFFADGIGIR  104 (357)
T ss_pred             CCCCHHHHHHHHHHHCCCEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEEEE
T ss_conf             98403899999999859959997832244768988799999999638889998


No 17 
>CHL00162 thiG thiamin biosynthesis protein G; Validated
Probab=94.72  E-value=0.45  Score=28.36  Aligned_cols=103  Identities=20%  Similarity=0.288  Sum_probs=70.0

Q ss_pred             CCCHHHCCCCHHHCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCC-CHH
Q ss_conf             9667771899556148799999999999779979999407886152899999999976994799807874336688-978
Q gi|254780901|r   62 NPSIRLLMPDPLILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGP-NPS  140 (600)
Q Consensus        62 ~p~l~~l~~dP~~l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl-~~~  140 (600)
                      -++-++|+|||+..   -+|++.+   ++++=+++-|..-|       -++.+-|...|..+..=...-.--|-|+ |+.
T Consensus       113 i~D~~tLlPD~~et---l~Aae~L---v~eGF~VlpY~~dD-------~v~akrLe~~Gc~avMPlgsPIGSg~Gl~n~~  179 (267)
T CHL00162        113 IPDPKYLLPDPIGT---LKAAEFL---VRKGFTVLPYINAD-------PVLAKQLEDIGCATVMPLGSPIGSGQGLQNLL  179 (267)
T ss_pred             ECCCCCCCCCHHHH---HHHHHHH---HHCCCEEEEECCCC-------HHHHHHHHHCCCEEEEECCCCCCCCCCCCCHH
T ss_conf             27987779887899---9999999---97899998954899-------89999998659868863455123688758999


Q ss_pred             HHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEE
Q ss_conf             98874202686899964887623455555417982799
Q gi|254780901|r  141 LMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIV  178 (600)
Q Consensus       141 ~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIV  178 (600)
                      .++.+.++ +++-+.||-||..--....|.|+|.|-+.
T Consensus       180 ~l~~i~e~-~~vPvIVDAGiG~pSdAa~aMElG~DaVL  216 (267)
T CHL00162        180 NLQIIIEN-AKIPVIIDAGIGTPSEASQAMELGASGVL  216 (267)
T ss_pred             HHHHHHHC-CCCCEEEECCCCCHHHHHHHHHCCCCEEE
T ss_conf             99999964-89988996898967888999974677787


No 18 
>PRK00208 thiG thiazole synthase; Reviewed
Probab=94.38  E-value=0.45  Score=28.32  Aligned_cols=103  Identities=23%  Similarity=0.312  Sum_probs=69.9

Q ss_pred             CCCCHHHCCCCHHHCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCC-CH
Q ss_conf             19667771899556148799999999999779979999407886152899999999976994799807874336688-97
Q gi|254780901|r   61 LNPSIRLLMPDPLILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGP-NP  139 (600)
Q Consensus        61 L~p~l~~l~~dP~~l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl-~~  139 (600)
                      .-++-++|+|||+..   -+|++.+   ++++=+++-|..-|       -++.+-|...|..+..=..+-.--|-|+ |+
T Consensus        99 Vi~D~~~LlPD~~et---l~Aae~L---v~eGF~VlpY~~~D-------~v~akrLe~~Gc~avMPlgsPIGSg~Gl~n~  165 (256)
T PRK00208         99 VIGDDKTLLPDPIET---LKAAEIL---VKEGFVVLPYCTDD-------PVLAKRLEEAGCAAVMPLGAPIGSGLGLLNP  165 (256)
T ss_pred             EECCCCCCCCCHHHH---HHHHHHH---HHCCCEEEEECCCC-------HHHHHHHHHCCCEEEEECCCCCCCCCCCCCH
T ss_conf             817976779886899---9999999---98899897867889-------8999999974953452045643479887999


Q ss_pred             HHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEE
Q ss_conf             89887420268689996488762345555541798279
Q gi|254780901|r  140 SLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVI  177 (600)
Q Consensus       140 ~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvI  177 (600)
                      ..++.+.++ .++-+.||-||..--....|.|+|.|-+
T Consensus       166 ~~l~~i~e~-~~vPvIVDAGiG~pS~Aa~AMElG~DaV  202 (256)
T PRK00208        166 YNLRIIIEQ-ADVPVIVDAGIGTPSDAAQAMELGADAV  202 (256)
T ss_pred             HHHHHHHHH-CCCCEEEECCCCCHHHHHHHHHCCCCEE
T ss_conf             999999986-7998898578897667899986255432


No 19 
>cd04728 ThiG Thiazole synthase (ThiG) is the tetrameric enzyme that is involved in the formation of the thiazole moiety of thiamin pyrophosphate, an essential ubiquitous cofactor that plays an important role in carbohydrate and amino acid metabolism. ThiG catalyzes the formation of thiazole from 1-deoxy-D-xylulose 5-phosphate (DXP) and dehydroglycine, with the help of the sulfur carrier protein ThiS that carries the sulfur needed for thiazole assembly on its carboxy terminus (ThiS-COSH).
Probab=94.17  E-value=0.58  Score=27.48  Aligned_cols=103  Identities=23%  Similarity=0.313  Sum_probs=70.1

Q ss_pred             CCCCHHHCCCCHHHCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCC-CH
Q ss_conf             19667771899556148799999999999779979999407886152899999999976994799807874336688-97
Q gi|254780901|r   61 LNPSIRLLMPDPLILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGP-NP  139 (600)
Q Consensus        61 L~p~l~~l~~dP~~l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl-~~  139 (600)
                      .-|+-++|+|||+.   .-+|++.+   ++++=+++-|..-|       -++.+-|...|..+..=...-.--|-|+ |+
T Consensus        98 Vi~D~~~LlPD~~e---Tl~Aae~L---v~~GF~VlpY~~~D-------~v~akrLe~~Gc~avMPlgsPIGSg~Gl~n~  164 (248)
T cd04728          98 VIGDDKTLLPDPIE---TLKAAEIL---VKEGFTVLPYCTDD-------PVLAKRLEDAGCAAVMPLGSPIGSGQGLLNP  164 (248)
T ss_pred             EECCCCCCCCCHHH---HHHHHHHH---HHCCCEEEEECCCC-------HHHHHHHHHCCCEEEEECCCCCCCCCCCCCH
T ss_conf             81797677988689---99999999---98899897867889-------9999999974953452045643479887999


Q ss_pred             HHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEE
Q ss_conf             89887420268689996488762345555541798279
Q gi|254780901|r  140 SLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVI  177 (600)
Q Consensus       140 ~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvI  177 (600)
                      ..++.+.++ .++-+.||-||..--....|.|+|.|-+
T Consensus       165 ~~l~~i~e~-~~vPvIVDAGiG~pS~Aa~aMElG~daV  201 (248)
T cd04728         165 YNLRIIIER-ADVPVIVDAGIGTPSDAAQAMELGADAV  201 (248)
T ss_pred             HHHHHHHHH-CCCCEEEECCCCCHHHHHHHHHCCCCEE
T ss_conf             999999984-7998898479997567899987265533


No 20 
>pfam03345 DDOST_48kD Oligosaccharyltransferase 48 kDa subunit beta. Members of this family are involved in asparagine-linked protein glycosylation. In particular, dolichyl-diphosphooligosaccharide-protein glycosyltransferase (DDOST), also known as oligosaccharyltransferase EC:2.4.1.119, transfers the high-mannose sugar GlcNAc(2)-Man(9)-Glc(3) from a dolichol-linked donor to an asparagine acceptor in a consensus Asn-X-Ser/Thr motif. In most eukaryotes, the DDOST complex is composed of three subunits, which in humans are described as a 48kD subunit, ribophorin I, and ribophorin II. However, the yeast DDOST appears to consist of six subunits (alpha, beta, gamma, delta, epsilon, zeta). The yeast beta subunit is a 45kD polypeptide, previously discovered as the Wbp1 protein, with known sequence similarity to the human 48kD subunit and the other orthologues. This family includes the 48kD-like subunits from several eukaryotes; it also includes the yeast DDOST beta subunit Wbp1.
Probab=94.01  E-value=0.62  Score=27.25  Aligned_cols=95  Identities=16%  Similarity=0.336  Sum_probs=68.9

Q ss_pred             HCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCC---------------------CCCCCC--CCHHHHHHHH
Q ss_conf             77997999940788615289999999997699479980787---------------------433668--8978988742
Q gi|254780901|r   90 YNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDR---------------------IVDGYG--PNPSLMEKFI  146 (600)
Q Consensus        90 ~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R---------------------~~eGYG--l~~~~i~~~~  146 (600)
                      ..+.+.++.-|-..+- .+-++..+-|+.-|.++.+..|+-                     -.++.|  |+.+.+-+..
T Consensus        14 ~~g~r~LVlld~~~~k-~~~S~F~~~L~~rG~~lt~~~~~d~~l~L~~~Ge~lYDhlIlf~p~~k~~g~~ls~~~l~~Fi   92 (439)
T pfam03345        14 SSGGRTLVVLDSLSEK-ETYSTFFKSLESRGYELTFKTPKDESLSLFKYGERLYDHLILFPPKSKGLGPSLSPKKLLDFI   92 (439)
T ss_pred             CCCCEEEEEECCCCCH-HHHHHHHHHHHHCCCEEEEECCCCCCCEEECCCCCCCCEEEEECCCHHHHCCCCCHHHHHHHH
T ss_conf             6897189994576315-679999999986796489955888752200078300346999366414407778989999998


Q ss_pred             HCCCCEEEEECCCCCCHHHHHHHHHCCCCE-----EEECCCCCC
Q ss_conf             026868999648876234555554179827-----996154476
Q gi|254780901|r  147 NEGAQLIITVDCGSTSYDALQYATNQGIDV-----IVIDHHQVK  185 (600)
Q Consensus       147 ~~g~~LiItvD~Gi~~~e~i~~a~~~Gidv-----IVtDHH~~~  185 (600)
                      ++|-+++++.+.+...-.--+.|++.||++     .|+||+.-.
T Consensus        93 d~GGNilva~s~~~~~~~ir~l~~E~gi~~~~~~~~viDHfnyd  136 (439)
T pfam03345        93 DKGGNVLVALSSETTPDAIRELLSELGIELDERNTVVVDHFNYD  136 (439)
T ss_pred             HCCCCEEEEECCCCCCHHHHHHHHHCCCEECCCCCEEEECCCCC
T ss_conf             68997999938876758999999985915678898677414676


No 21 
>pfam05690 ThiG Thiazole biosynthesis protein ThiG. This family consists of several bacterial thiazole biosynthesis protein G sequences. ThiG, together with ThiF and ThiH, is proposed to be involved in the synthesis of 4-methyl-5-(b-hydroxyethyl)thiazole (THZ) which is an intermediate in the thiazole production pathway.
Probab=93.97  E-value=0.63  Score=27.20  Aligned_cols=103  Identities=25%  Similarity=0.347  Sum_probs=70.9

Q ss_pred             CCCCHHHCCCCHHHCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCC-CH
Q ss_conf             19667771899556148799999999999779979999407886152899999999976994799807874336688-97
Q gi|254780901|r   61 LNPSIRLLMPDPLILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGP-NP  139 (600)
Q Consensus        61 L~p~l~~l~~dP~~l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl-~~  139 (600)
                      .-++-+.|+|||+..   -+|++.+   ++++=+++-|..-|       -++.+-|...|..+..=...-.--|-|+ |+
T Consensus        97 Vi~D~~~LlPD~~et---l~Aae~L---v~eGF~VlpY~~~D-------~v~akrLed~Gc~avMPlgsPIGSg~Gl~n~  163 (246)
T pfam05690        97 VIGDSKTLLPDPIET---LKAAEIL---VKEGFTVLPYTTDD-------PVLARRLEEAGCAAVMPLGAPIGSGLGLRNP  163 (246)
T ss_pred             EECCCCCCCCCHHHH---HHHHHHH---HHCCCEEEEECCCC-------HHHHHHHHHCCCEEEEECCCCCCCCCCCCCH
T ss_conf             826988779887899---9999999---97899898861799-------8999999875984986224401368886899


Q ss_pred             HHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEE
Q ss_conf             89887420268689996488762345555541798279
Q gi|254780901|r  140 SLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVI  177 (600)
Q Consensus       140 ~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvI  177 (600)
                      ..++.+.++ .++-+.||-||..--....|.|+|.|-+
T Consensus       164 ~~l~~i~e~-~~vPvIVDAGiG~pS~Aa~aMElG~DaV  200 (246)
T pfam05690       164 ENLRIIIEE-ADVPVIVDAGIGTPSDAAQAMELGADAV  200 (246)
T ss_pred             HHHHHHHHH-CCCCEEEECCCCCHHHHHHHHHCCCCEE
T ss_conf             999999996-7998898489896788999997456777


No 22 
>PRK11840 bifunctional sulfur carrier protein/thiazole synthase protein; Provisional
Probab=93.95  E-value=0.63  Score=27.18  Aligned_cols=26  Identities=4%  Similarity=-0.075  Sum_probs=13.4

Q ss_pred             HHHHHHHHHHHHHCCCCEEEEECCCC
Q ss_conf             52899999999976994799807874
Q gi|254780901|r  106 AASVALMMRFLSHCSVNANMYIPDRI  131 (600)
Q Consensus       106 itstail~~~L~~~g~~v~~~IP~R~  131 (600)
                      ..|-.++.++++.-|+++...--.|.
T Consensus        94 y~s~~~~~~ai~aSgaeivTVAlRR~  119 (327)
T PRK11840         94 YKDFEETAAAVEASGAEIVTVAVRRV  119 (327)
T ss_pred             CCCHHHHHHHHHHHCCCEEEEEEEEE
T ss_conf             99999999999985897699999742


No 23 
>TIGR00486 TIGR00486 conserved hypothetical protein TIGR00486; InterPro: IPR002678   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=93.88  E-value=0.1  Score=33.41  Aligned_cols=31  Identities=26%  Similarity=0.504  Sum_probs=24.3

Q ss_pred             CCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCC
Q ss_conf             86899964887623455555417982799615447
Q gi|254780901|r  150 AQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQV  184 (600)
Q Consensus       150 ~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~~  184 (600)
                      -+++++||.   +.+-+..|.+.|.|+||| ||-+
T Consensus        48 ~kv~~~vD~---s~~~~~~A~~~~~d~i~~-HHp~   78 (325)
T TIGR00486        48 KKVLVAVDA---SESVAKEAKEKNADLIIT-HHPL   78 (325)
T ss_pred             HHHHHHHHH---HHHHHHHHHHCCCCEEEE-ECCC
T ss_conf             455667778---999999998537979998-0786


No 24 
>PRK13480 3'-5' exoribonuclease YhaM; Provisional
Probab=93.71  E-value=0.47  Score=28.21  Aligned_cols=37  Identities=11%  Similarity=0.108  Sum_probs=17.5

Q ss_pred             HHHCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHHCCHHHHHCCCC
Q ss_conf             751688743578987088864242345666774306233312122
Q gi|254780901|r  271 ARRQGNPGLKALIERVNISSPITAENLGYMIGPSINAGGRIGESN  315 (600)
Q Consensus       271 l~~~~~~gl~~L~~~~~~~~~i~~~di~f~iaPrINAaGRl~~a~  315 (600)
                      +.+-.++.|+.|++..-  .   ...-.|..+|   ||-++-+|.
T Consensus       120 i~~I~~~~l~~lv~~~~--~---~~~~~f~~~P---AA~~~HHay  156 (314)
T PRK13480        120 IFEMENPNIQRITRHLL--K---KYQEEFLDYP---AATKNHHEF  156 (314)
T ss_pred             HHHCCCHHHHHHHHHHH--H---HHHHHHHHCC---HHHHHCCCC
T ss_conf             99858988999999999--9---9999998397---888604133


No 25 
>COG1570 XseA Exonuclease VII, large subunit [DNA replication, recombination, and repair]
Probab=93.42  E-value=0.77  Score=26.52  Aligned_cols=18  Identities=17%  Similarity=0.324  Sum_probs=7.1

Q ss_pred             HHHHHHHHHHHHHHHHHC
Q ss_conf             478899999999999702
Q gi|254780901|r  210 CAAGVVFLVLVLIYRILR  227 (600)
Q Consensus       210 ~gaGvaf~l~~al~~~l~  227 (600)
                      +|.|--+.-...+.++|.
T Consensus       101 ~G~G~L~~~~E~lK~kL~  118 (440)
T COG1570         101 AGLGALYLAFEQLKAKLA  118 (440)
T ss_pred             CCHHHHHHHHHHHHHHHH
T ss_conf             872589999999999998


No 26 
>COG2022 ThiG Uncharacterized enzyme of thiazole biosynthesis [Nucleotide transport and metabolism]
Probab=93.39  E-value=0.71  Score=26.78  Aligned_cols=103  Identities=25%  Similarity=0.344  Sum_probs=65.6

Q ss_pred             CCCCHHHCCCCHHHCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCC-H
Q ss_conf             196677718995561487999999999997799799994078861528999999999769947998078743366889-7
Q gi|254780901|r   61 LNPSIRLLMPDPLILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPN-P  139 (600)
Q Consensus        61 L~p~l~~l~~dP~~l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~-~  139 (600)
                      .-++-+.|+|||+..   -+|++.+   ++.+=.++-|.--|       -++.+-|...|.....=.-.-.--|-|+. +
T Consensus       105 Vi~d~~tLlPD~~et---l~Aae~L---v~eGF~VlPY~~dD-------~v~arrLee~GcaavMPl~aPIGSg~G~~n~  171 (262)
T COG2022         105 VIGDEKTLLPDPIET---LKAAEQL---VKEGFVVLPYTTDD-------PVLARRLEEAGCAAVMPLGAPIGSGLGLQNP  171 (262)
T ss_pred             EECCCCCCCCCHHHH---HHHHHHH---HHCCCEEEECCCCC-------HHHHHHHHHCCCEEECCCCCCCCCCCCCCCH
T ss_conf             936876548875789---9999999---86798885036887-------8999999864966863356656678675788


Q ss_pred             HHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEE
Q ss_conf             89887420268689996488762345555541798279
Q gi|254780901|r  140 SLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVI  177 (600)
Q Consensus       140 ~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvI  177 (600)
                      ..++-+.++ .++=|.||-||..-.....+.++|.|-+
T Consensus       172 ~~l~iiie~-a~VPviVDAGiG~pSdAa~aMElG~DaV  208 (262)
T COG2022         172 YNLEIIIEE-ADVPVIVDAGIGTPSDAAQAMELGADAV  208 (262)
T ss_pred             HHHHHHHHH-CCCCEEEECCCCCHHHHHHHHHHCCCEE
T ss_conf             999999973-8998898679897668899986055432


No 27 
>PTZ00254 40S ribosomal protein SA; Provisional
Probab=93.15  E-value=0.84  Score=26.22  Aligned_cols=89  Identities=26%  Similarity=0.344  Sum_probs=59.1

Q ss_pred             HHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEEC
Q ss_conf             79999999999977997999940788615289999999997699479980787433668897898874202686899964
Q gi|254780901|r   78 CDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVD  157 (600)
Q Consensus        78 m~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD  157 (600)
                      +..|+.-| .++++...|+++|-   --....+++ +|-...|.   +||..|+.-|-=-| .....+.  .++|+|.+|
T Consensus        58 L~~Aa~~i-~~i~~~~~Il~V~t---r~~~q~aV~-kfA~~tG~---~~i~~Rw~pGtlTN-~i~~~f~--eP~lliV~D  126 (242)
T PTZ00254         58 IKLAARVI-AAVENPADVVVVSS---RPYGQRAIL-KFSQYTGA---SFIAGRFTPGTFTN-QIQKKFQ--EPRLLIVTD  126 (242)
T ss_pred             HHHHHHHH-HHHCCCCCEEEEEC---CHHHHHHHH-HHHHHHCC---CEEECCCCCCCCCC-HHHHCCC--CCCEEEEEC
T ss_conf             99999999-98647997799983---889879999-99999799---42405127866468-7665246--888899966


Q ss_pred             CCCCCHHHHHHHHHCCCCEEE
Q ss_conf             887623455555417982799
Q gi|254780901|r  158 CGSTSYDALQYATNQGIDVIV  178 (600)
Q Consensus       158 ~Gi~~~e~i~~a~~~GidvIV  178 (600)
                      -- .++.+|..|...||-||=
T Consensus       127 P~-~d~~AV~EA~~~nIPvIa  146 (242)
T PTZ00254        127 PR-TDHQAIREASYVNIPVIA  146 (242)
T ss_pred             CC-CCHHHHHHHHHCCCCEEE
T ss_conf             75-440899999985998898


No 28 
>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=92.78  E-value=0.94  Score=25.84  Aligned_cols=139  Identities=21%  Similarity=0.324  Sum_probs=92.8

Q ss_pred             CCHHHHHHHHHHHCCCHHHHHHHHHCCCC-HHHHHHHCCCCHHHCCCCHHHCCCHHHHHHHHHHHHHCCCC--EEEEECC
Q ss_conf             89889999998819999999999967889-78988661966777189955614879999999999977997--9999407
Q gi|254780901|r   25 EGINRALAITQKHAIPDIVARVLVNRNVS-IDYAKDFLNPSIRLLMPDPLILTDCDKAARRIVQAIYNSEK--IMIFGDY  101 (600)
Q Consensus        25 ~~~~~~~~l~~~~~~~~~~a~iL~~Rgi~-~~~~~~fL~p~l~~l~~dP~~l~dm~~A~~ri~~ai~~~ek--I~I~gDy  101 (600)
                      -.++-+.++..      -+-.-+..|.++ .++.+.++.-.+.+.+ .+..-++-.--...+....+.++.  |+++|  
T Consensus        19 v~~~~v~~i~~------~l~~~~~~~~~~~~~~~~e~~~~~l~~~~-~~~~~~~~~~~~~~~~~~~~~~kp~Vil~VG--   89 (284)
T TIGR00064        19 VGLEVVEKIIE------ELKKELVGKKVKDEEKLKEILKEALKEIL-KEILDKDTLLDLEQIEELPEEKKPNVILFVG--   89 (284)
T ss_pred             CCHHHHHHHHH------HHHHHHCCCCCCCHHHHHHHHHHHHHHHH-HHCCCCCHHHHHHHHHHCCCCCCCEEEEEEE--
T ss_conf             51899999999------98875403557707899999999999987-4112321133443344301478977999984--


Q ss_pred             CCCH---HHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHC----CCCEEEEECCC-C----CCHHHHHHH
Q ss_conf             8861---5289999999997699479980787433668897898874202----68689996488-7----623455555
Q gi|254780901|r  102 DVDG---AASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINE----GAQLIITVDCG-S----TSYDALQYA  169 (600)
Q Consensus       102 D~DG---itstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~----g~~LiItvD~G-i----~~~e~i~~a  169 (600)
                       |=|   +|+-|=|.+.|++-|.+|-.-=-|-|.      ..++|++...    |++ ||+---| +    -.+++|..|
T Consensus        90 -VNG~GKTTTIaKLA~~l~~~Gk~V~laAgDTFR------AAA~EQL~~Wa~R~gv~-vi~~~~gn~DPAaV~fDAi~~A  161 (284)
T TIGR00064        90 -VNGVGKTTTIAKLANKLKKQGKSVLLAAGDTFR------AAAIEQLEVWAKRLGVD-VIKQKEGNADPAAVIFDAIQAA  161 (284)
T ss_pred             -EECCCHHHHHHHHHHHHHHCCCEEEEECCCHHH------HHHHHHHHHHHHHHCCE-EEECCCCCCCCHHHHHHHHHHH
T ss_conf             -408860102889999998749908998275247------99999999989883875-5407889887178999989999


Q ss_pred             HHCCCCEEEEC
Q ss_conf             41798279961
Q gi|254780901|r  170 TNQGIDVIVID  180 (600)
Q Consensus       170 ~~~GidvIVtD  180 (600)
                      +++|+||+++|
T Consensus       162 k~~niDvvliD  172 (284)
T TIGR00064       162 KARNIDVVLID  172 (284)
T ss_pred             HHCCCCEEEEE
T ss_conf             87499789973


No 29 
>KOG3108 consensus
Probab=92.37  E-value=1.1  Score=25.46  Aligned_cols=90  Identities=19%  Similarity=0.312  Sum_probs=63.7

Q ss_pred             CCCCCCCCCCEEEECCEEEEEEEEEC--------CCEEEEEEECCCCCEEEEEEECCCCCCHHHHHHCCCCCEEEEEEEE
Q ss_conf             84678999846842780998888847--------9649999984998779999977878701235530699879999997
Q gi|254780901|r  500 GPYGAGNPNPVFAFPNHKLQSIRVVN--------LAHLQMTFESQDSETLQAIAFRVYGTPLGEFLMQSRGKRMHVTGHL  571 (600)
Q Consensus       500 ePFG~gNpeP~F~~~~~~i~~~r~vG--------k~Hlkl~l~~~~g~~i~aI~Fn~~~~~~~~~~~~~~g~~idii~~l  571 (600)
                      .+.+...+  .|.+.++++..+-+||        ..+..+.+.+..|. +++--|...+....+......+..+.+.+.|
T Consensus        52 s~~~~~~~--~~~i~~~~v~~v~~VGivr~~e~~~t~i~y~I~D~tg~-id~r~W~~~~~~~~e~~~l~~~~yVkv~G~L  128 (265)
T KOG3108          52 SSTQDDDS--VFKIGGVEVSAVSIVGIVRNIEKSATNITYEIEDGTGQ-IDVRQWFHDNAESEEMPALETGTYVKVYGHL  128 (265)
T ss_pred             CCCCCCCC--CEEECCEEEEEEEEEEEEEECEECCCCEEEEEECCCCE-EEEEECCCCCCHHHHCCCCCCCCEEEEECCC
T ss_conf             01322566--27886799888899999970202676149998268650-7888703553022217412447579964010


Q ss_pred             EEEEECCCCEEEEEEEEEEECCCCC
Q ss_conf             6654578110589999801113112
Q gi|254780901|r  572 CVNYWRGSKRCQLRVLDASPVEGHH  596 (600)
Q Consensus       572 ~~N~~~G~~s~QL~I~Di~p~e~~~  596 (600)
                      +.  |+|+++++  +.-|+|+|..+
T Consensus       129 k~--f~Gk~sl~--~fkI~pv~D~N  149 (265)
T KOG3108         129 KP--FQGKKSLQ--VFKIRPVEDFN  149 (265)
T ss_pred             CC--CCCCEEEE--EEEEEEEECCC
T ss_conf             48--89952677--87655540377


No 30 
>COG0052 RpsB Ribosomal protein S2 [Translation, ribosomal structure and biogenesis]
Probab=92.34  E-value=1.1  Score=25.43  Aligned_cols=135  Identities=18%  Similarity=0.238  Sum_probs=81.1

Q ss_pred             CCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCC--H--HHHHHHH----
Q ss_conf             1487999999999997799799994078861528999999999769947998078743366889--7--8988742----
Q gi|254780901|r   75 LTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPN--P--SLMEKFI----  146 (600)
Q Consensus        75 l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~--~--~~i~~~~----  146 (600)
                      ++-+..|..-+.+...++.+|+..|--    --+.-++.++-+..|   .|||.+|+--|-=-|  .  ..++++.    
T Consensus        47 ~~~l~~A~~~v~~~~~~~g~ILfVgTK----~~a~~~V~~~A~r~g---~~yV~~RwLgG~LTN~~ti~~si~rl~~lE~  119 (252)
T COG0052          47 LERLREAYKFLRRIAANGGKILFVGTK----KQAQEPVKEFAERTG---AYYVNGRWLGGMLTNFKTIRKSIKRLKELEK  119 (252)
T ss_pred             HHHHHHHHHHHHHHHCCCCEEEEEECH----HHHHHHHHHHHHHHC---CCEECCCCCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             999999999999997289979999520----887899999999959---9513276437424474058889999999998


Q ss_pred             --HCC--------------------------------CCEEEEECCCCCCHHHHHHHHHCCCCEEE-ECCCCCCCCCCCC
Q ss_conf             --026--------------------------------86899964887623455555417982799-6154476555672
Q gi|254780901|r  147 --NEG--------------------------------AQLIITVDCGSTSYDALQYATNQGIDVIV-IDHHQVKSEEIPA  191 (600)
Q Consensus       147 --~~g--------------------------------~~LiItvD~Gi~~~e~i~~a~~~GidvIV-tDHH~~~~~~p~a  191 (600)
                        ++|                                +++++.+|-. ...-+|..|+.+||.||- +|--..|+..   
T Consensus       120 ~~~~~~~~~tKkE~l~l~re~~kL~k~lgGIk~m~~~Pd~l~ViDp~-~e~iAv~EA~klgIPVvAlvDTn~dpd~V---  195 (252)
T COG0052         120 MEEDGFDGLTKKEALMLTRELEKLEKSLGGIKDMKGLPDVLFVIDPR-KEKIAVKEANKLGIPVVALVDTNCDPDGV---  195 (252)
T ss_pred             HHHCCCCCCCHHHHHHHHHHHHHHHHHHCCHHHCCCCCCEEEEECCC-HHHHHHHHHHHCCCCEEEEECCCCCCCCC---
T ss_conf             76414321007888877778999987401411126799989996881-76899999997599989984189997657---


Q ss_pred             EEEECCCCCCCCCCCCCH-HHHHHHHHHHHHHHHHHC
Q ss_conf             565237888864334430-478899999999999702
Q gi|254780901|r  192 YALVNPNRLDDLSGQGHL-CAAGVVFLVLVLIYRILR  227 (600)
Q Consensus       192 ~aivNP~~~~~~~p~~~l-~gaGvaf~l~~al~~~l~  227 (600)
                       -++=|-   .+   +.+ |-+=+.++++.++.+...
T Consensus       196 -D~~IP~---Nd---da~rsi~Li~~~lA~ai~e~r~  225 (252)
T COG0052         196 -DYVIPG---ND---DAIRSIALIYWLLARAILEGRG  225 (252)
T ss_pred             -CEEECC---CC---HHHHHHHHHHHHHHHHHHHHHC
T ss_conf             -655228---87---0898999999999999998743


No 31 
>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=92.13  E-value=0.79  Score=26.44  Aligned_cols=340  Identities=18%  Similarity=0.209  Sum_probs=174.4

Q ss_pred             CHHHCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHH-HHHHHCC
Q ss_conf             955614879999999999977997999940788615289999999997699479980787433668897898-8742026
Q gi|254780901|r   71 DPLILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLM-EKFINEG  149 (600)
Q Consensus        71 dP~~l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i-~~~~~~g  149 (600)
                      --.|+...-|.|+-|+.-|+++.+++||    .==|-=++|...+-.++||-.+...    -   |+|.+++ +++.+.+
T Consensus        99 Y~eL~~~Vcr~An~LK~GvkkGD~V~IY----mPMiPEa~~AMLACaRIGA~HSVVF----g---GFSa~aL~~Ri~Da~  167 (643)
T TIGR02188        99 YRELHREVCRFANVLKLGVKKGDRVAIY----MPMIPEAAIAMLACARIGAIHSVVF----G---GFSAEALADRINDAG  167 (643)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCCEEEEE----CCCCHHHHHHHHHHHHCCCEEEEEC----C---CCCHHHHHHHHHCCC
T ss_conf             8899899999999974476468878995----7881899999988643685267872----5---774789988753277


Q ss_pred             CCEEEEECCCCCCHHH------HHHHHH-C-----CC-CEEEECCCCCC-C------------CCCC-CEEEECCCCCCC
Q ss_conf             8689996488762345------555541-7-----98-27996154476-5------------5567-256523788886
Q gi|254780901|r  150 AQLIITVDCGSTSYDA------LQYATN-Q-----GI-DVIVIDHHQVK-S------------EEIP-AYALVNPNRLDD  202 (600)
Q Consensus       150 ~~LiItvD~Gi~~~e~------i~~a~~-~-----Gi-dvIVtDHH~~~-~------------~~p~-a~aivNP~~~~~  202 (600)
                      ++++||.|-|..--..      ++.|-+ -     -+ .|||.=|---+ .            .... +-+-+-|...+.
T Consensus       168 ak~VITAD~g~RgGK~~~LK~~VD~AL~~~~~~~~~V~~VlV~~RtG~~~~~w~~GRD~wwh~l~~~~~~~~c~Pe~m~s  247 (643)
T TIGR02188       168 AKLVITADEGLRGGKVIPLKAIVDEALEKCPDTCPSVEKVLVVRRTGGPVVPWVEGRDVWWHELVAKGQSAECEPEPMDS  247 (643)
T ss_pred             CCEEEECCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCCCCCCCCCHHHHHHCCCCCCCCCCCCCCC
T ss_conf             75899437740588643036899999960786745300678998558887775488876068985378878246541787


Q ss_pred             CCCCCCHHHHHHH------------HHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCC-----------CCC---
Q ss_conf             4334430478899------------99999999970214887640779999999877542011-----------114---
Q gi|254780901|r  203 LSGQGHLCAAGVV------------FLVLVLIYRILRQDNKVPLNFDLLSLLDLVALATVCDV-----------VPL---  256 (600)
Q Consensus       203 ~~p~~~l~gaGva------------f~l~~al~~~l~~~~~~~~~~~l~~~ldlvaiGTvaD~-----------vpL---  256 (600)
                      +-|.--|=.+|-+            |+|-.++--++--+-+        +- |  --..-|||           -||   
T Consensus       248 EDPLFiLYTSGSTGKPKGv~HttgGYll~a~~T~k~VFD~~--------d~-D--~fWCTADvGWiTGHSYiVYGPL~~G  316 (643)
T TIGR02188       248 EDPLFILYTSGSTGKPKGVLHTTGGYLLYAAMTMKYVFDIK--------DG-D--IFWCTADVGWITGHSYIVYGPLANG  316 (643)
T ss_pred             CCCHHHHHCCCCCCCCCCCEECCHHHHHHHHCCEEEEEECC--------CC-C--EEEEECCEEEEECCHHHHHHHHHCC
T ss_conf             66026763478778887214341779988732146764037--------99-6--2686211200205324012422115


Q ss_pred             ------------------------CCCC---------HHHHHHHHHHHHHCCCCCHHHHHHHHCCCCCCCH---------
Q ss_conf             ------------------------4411---------8999987887751688743578987088864242---------
Q gi|254780901|r  257 ------------------------IGLN---------RAYVVKGLMVARRQGNPGLKALIERVNISSPITA---------  294 (600)
Q Consensus       257 ------------------------~~eN---------R~lvk~GL~~l~~~~~~gl~~L~~~~~~~~~i~~---------  294 (600)
                                              .+.|         |.|.|.|-+..++..+--||-|=.   +-.+||.         
T Consensus       317 AT~~mfEG~P~YP~~~R~W~~iekh~vtiFYTAPTAIR~L~r~G~~~~~k~DlSSLR~LGS---VGEPINPEAW~WY~~~  393 (643)
T TIGR02188       317 ATTLMFEGVPTYPDAGRFWEIIEKHKVTIFYTAPTAIRALMRLGDEWVKKHDLSSLRLLGS---VGEPINPEAWMWYYKV  393 (643)
T ss_pred             CEEEEECCCCCCCCCCCEEEEEEECCCCEEECCHHHHHHHHHHCCHHHHHCCCCCEEECCC---CCCCCCHHHHHHHHHC
T ss_conf             3178743778332787678553315765033156899999861112134417640015025---6888764478899870


Q ss_pred             ---------------HHHHHHHHHHCCHHHHH--CCC---CCCCEEEECC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             ---------------34566677430623331--212---2221002034-25899999999998999999999999999
Q gi|254780901|r  295 ---------------ENLGYMIGPSINAGGRI--GES---NLGSRLLISD-DSQELEMLAMKLDVLNQNRRLMESAMLEQ  353 (600)
Q Consensus       295 ---------------~di~f~iaPrINAaGRl--~~a---~~av~lL~~~-d~~~a~~la~~L~~lN~~Rk~~e~~i~~~  353 (600)
                                     ++=|..|.|+==++-=+  |+|   -.+++-=+-| +...                         
T Consensus       394 vG~~~CpiVDTWWQTETGgimItPlPG~~~p~KPGSAt~PffGi~p~~vDP~~G~-------------------------  448 (643)
T TIGR02188       394 VGKERCPIVDTWWQTETGGIMITPLPGAATPTKPGSATLPFFGIEPAVVDPEEGK-------------------------  448 (643)
T ss_pred             CCCCEEEEECCCCCCCCHHHHHCCCHHHHHHCCCCCCCCCCCCCEEEEECCCCCC-------------------------
T ss_conf             4895200761654510025334040125763487768748887247887189885-------------------------


Q ss_pred             HHHHHHHHHCCCCCC-CEEEEECCCCCHHHHHHH--HHHHHHHHHC--EE---EEEE-----ECCCCEEEEEEECC----
Q ss_conf             999987521124347-502620578581222222--7899884201--07---9988-----63798379998648----
Q gi|254780901|r  354 AEAKVLTQCDDIQQA-SVIVVEGDRWHPGIVGLL--AARLKEKFGR--PS---FAIS-----FEEDGKGIGSGRSI----  416 (600)
Q Consensus       354 a~~~~~~~~~~~~~~-~~ivv~~~~wh~GViGIV--AsrL~e~y~k--P~---iv~s-----~~~dg~~kGS~RSi----  416 (600)
                         .+.  - ..... .+||+..| |+.=+-+|=  =.|..+.|-+  |-   .=||     .|+||+.=--||-=    
T Consensus       449 ---~~~--G-~~~~g~G~LvI~~P-WPsm~RtiyGDh~Rf~~tYf~~~~~~G~~YFtGDGA~rD~DGY~WI~GRvDDViN  521 (643)
T TIGR02188       449 ---EVE--G-PGEGGAGYLVIKQP-WPSMLRTIYGDHERFVETYFSPFPGKGKYYFTGDGARRDKDGYIWITGRVDDVIN  521 (643)
T ss_pred             ---EEC--C-CCCCCCEEEEECCC-CCCHHCCCCCCCHHHHHCCCCCCCCCCCEEEECCCEEECCCCCEEEEEEEEEEEE
T ss_conf             ---733--7-77677507887788-8520022468832567505324789986367366002558988799415612865


Q ss_pred             -CC-----CCHHHHHHHHCCCCCCC--------CCCCCCCCCCEEECCC--CHHHHHHHHHHHHHHHCCH
Q ss_conf             -98-----61888888530335301--------1565322231464222--1588999999999862264
Q gi|254780901|r  417 -EG-----FDIGKMVSFAVEEGILV--------KGGGHAMAAGLTVERV--NFGRLCDFFQKFAHNIVPA  470 (600)
Q Consensus       417 -~g-----~~l~~~l~~~~~~~ll~--------~~GGH~~AaG~ti~~~--~l~~f~~~l~~~~~~~~~~  470 (600)
                       .|     .-|-.||-  +|+..=+        .-=|-.-.|=++|+..  .=+ |++.|.+.+.+.+..
T Consensus       522 VSGHRLGTaEiESALv--~Hp~VAEAAVVG~pd~iKGq~i~AFV~L~~~~~~~~-l~~EL~~~Vr~~IGp  588 (643)
T TIGR02188       522 VSGHRLGTAEIESALV--SHPAVAEAAVVGIPDDIKGQAIYAFVTLKDGVEPDD-LRKELRKHVRKEIGP  588 (643)
T ss_pred             ECCCCCCHHHHHHHHH--CCCCCCEEEEECCCCCCCCCEEEEEEEECCCCCCCH-HHHHHHHHHHHHCCC
T ss_conf             1565654689999985--685555456206788864456899998558887336-999999999986077


No 32 
>KOG2475 consensus
Probab=92.06  E-value=1.1  Score=25.20  Aligned_cols=104  Identities=21%  Similarity=0.374  Sum_probs=61.3

Q ss_pred             CCHHHHHHHHHHHHHC-CCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEE
Q ss_conf             4879999999999977-997999940788615289999999997699479980787433668897898874202686899
Q gi|254780901|r   76 TDCDKAARRIVQAIYN-SEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLII  154 (600)
Q Consensus        76 ~dm~~A~~ri~~ai~~-~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiI  154 (600)
                      ++..++-.+|.+.-.. .-.++|+--+|+|-+|+|-||...|+.=...... +|   ..||-=-..+.-+. ++.+.-+|
T Consensus         6 ~~~~~~y~ki~~~~~S~s~~vlifVs~DiDALCA~kiLt~Llk~D~iqysi-vP---VsG~~elek~~~e~-~e~~~~ii   80 (587)
T KOG2475           6 SDFREFYNKIKEGSRSLSCPVLIFVSLDIDALCATKILTHLLKCDHIQYSI-VP---VSGWSELEKAFLEL-QEQIKYII   80 (587)
T ss_pred             HHHHHHHHHHHHCCCCCCCCEEEEEECCHHHHHHHHHHHHHHHCCCCCEEE-EE---ECCHHHHHHHHHHH-CCCCEEEE
T ss_conf             778999999983344678747999835805888999999997026653047-87---33568999999853-36851999


Q ss_pred             EECCCCCCHHHHHHHH-HCCCCEEEECCCCCC
Q ss_conf             9648876234555554-179827996154476
Q gi|254780901|r  155 TVDCGSTSYDALQYAT-NQGIDVIVIDHHQVK  185 (600)
Q Consensus       155 tvD~Gi~~~e~i~~a~-~~GidvIVtDHH~~~  185 (600)
                      -+-||.. .+-.+++. -.-.++-|+|-|.|-
T Consensus        81 LiNcG~~-vDL~~~L~~P~e~~~fViDSHRP~  111 (587)
T KOG2475          81 LINCGAT-VDLTRLLQPPSEDVIFVIDSHRPF  111 (587)
T ss_pred             EECCCCC-HHHHHHHCCCCCCEEEEEECCCCC
T ss_conf             9657741-009988179642528997078974


No 33 
>cd01539 PBP1_GGBP Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species. Periplasmic glucose/galactose-binding protein (GGBP) involved in chemotaxis towards, and active transport of, glucose and galactose in various bacterial species. GGBP is a member of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic GGBP is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.
Probab=91.36  E-value=0.77  Score=26.53  Aligned_cols=73  Identities=11%  Similarity=0.145  Sum_probs=46.5

Q ss_pred             HHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCC-CHHHHHHHHHCCCCEEEECCCCCCCCC
Q ss_conf             99976994799807874336688978988742026868999648876-234555554179827996154476555
Q gi|254780901|r  115 FLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGST-SYDALQYATNQGIDVIVIDHHQVKSEE  188 (600)
Q Consensus       115 ~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~-~~e~i~~a~~~GidvIVtDHH~~~~~~  188 (600)
                      +.+..|.++.+.+++--.+ .--....|+.++.+|++.||..-+-+. ..+.++.|++.||.||+.|+.......
T Consensus        24 ~a~e~g~~v~~~~~da~~D-~~~Q~~~Ie~~I~qgvD~Iii~p~d~~~~~~~i~~A~~agIPVI~~d~~~~~~~~   97 (303)
T cd01539          24 IQKENGGKVEFTFYDAKNN-QSTQNEQIDTALAKGVDLLAVNLVDPTAAQTVINKAKQKNIPVIFFNREPEEEDI   97 (303)
T ss_pred             HHHHHCCCEEEEEECCCCC-HHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHCCCEEEEECCCCCHHHC
T ss_conf             9998599579997078789-9999999999997599999994687334899999999669849998787661220


No 34 
>PRK00252 alaS alanyl-tRNA synthetase; Reviewed
Probab=90.63  E-value=1.5  Score=24.17  Aligned_cols=96  Identities=22%  Similarity=0.293  Sum_probs=37.0

Q ss_pred             CEEEEECCCCCHHHHHHHHHHHHHHHHCEEEEEEECCCCEE---EEEEEC-CCCCCHHHHHHHHCCCCCCCCCCCCC-CC
Q ss_conf             50262057858122222278998842010799886379837---999864-89861888888530335301156532-22
Q gi|254780901|r  369 SVIVVEGDRWHPGIVGLLAARLKEKFGRPSFAISFEEDGKG---IGSGRS-IEGFDIGKMVSFAVEEGILVKGGGHA-MA  443 (600)
Q Consensus       369 ~~ivv~~~~wh~GViGIVAsrL~e~y~kP~iv~s~~~dg~~---kGS~RS-i~g~~l~~~l~~~~~~~ll~~~GGH~-~A  443 (600)
                      ++++..-++.....+--+|..+.+++..-++++.-..++..   .++..+ ..+++..++++.++.. +-.++||-+ +|
T Consensus       761 ~~i~~~~~~~d~k~Lr~l~~~l~~k~~~~vvil~s~~~~K~~~vv~vs~~~~~~i~A~~lvk~i~~~-~gGkGGGkp~~A  839 (864)
T PRK00252        761 KVLAAQLDGVDAKDLRTLADDLKNKLGSGVVVLASVADGKVSLVVGVTKDLTKGLKAGDLVKELAAI-VGGKGGGRPDMA  839 (864)
T ss_pred             EEEEEEECCCCHHHHHHHHHHHHHHCCCEEEEEEEECCCEEEEEEEECHHHCCCCCHHHHHHHHHHH-CCCCCCCCHHHE
T ss_conf             9999990699999999999999965699699999803990899999897872798889999999986-599657935746


Q ss_pred             CCEEECCCCHHHHHHHHHHHHH
Q ss_conf             3146422215889999999998
Q gi|254780901|r  444 AGLTVERVNFGRLCDFFQKFAH  465 (600)
Q Consensus       444 aG~ti~~~~l~~f~~~l~~~~~  465 (600)
                      -|=.-..+++++..+...+.++
T Consensus       840 QgGG~~~~~l~~al~~a~~~l~  861 (864)
T PRK00252        840 QAGGKDPAKLDEALAAVKEWLK  861 (864)
T ss_pred             ECCCCCHHHHHHHHHHHHHHHH
T ss_conf             6389987899999999999998


No 35 
>cd00079 HELICc Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may not be an autonomously folding unit, but an integral part of the helicase; 4 helicase superfamilies at present according to the organization of their signature motifs; all helicases share the ability to unwind nucleic acid duplexes with a distinct directional polarity; they utilize the free energy from nucleoside triphosphate hydrolysis to fuel their translocation along DNA, unwinding the duplex in the process
Probab=90.62  E-value=1.5  Score=24.16  Aligned_cols=77  Identities=9%  Similarity=0.174  Sum_probs=54.1

Q ss_pred             CHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEE
Q ss_conf             87999999999997799799994078861528999999999769947998078743366889789887420268689996
Q gi|254780901|r   77 DCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITV  156 (600)
Q Consensus        77 dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItv  156 (600)
                      -++...+.|.+.+++++|+.||.    ......-.+.+.|+..+.++.++--+- ..  ---...++++.+...+++++.
T Consensus        13 K~~~l~~~i~~~~~~~~kviIF~----~~~~~~~~l~~~L~~~~~~~~~~~~~~-~~--~~R~~~~~~F~~~~~~ilv~t   85 (131)
T cd00079          13 KLEALLELLKEHLKKGGKVLIFC----PSKKMLDELAELLRKPGIKVAALHGDG-SQ--EEREEVLKDFREGEIVVLVAT   85 (131)
T ss_pred             HHHHHHHHHHHHHHCCCEEEEEE----CCHHHHHHHHHHHHHCCCCEEEEECCC-CH--HHHHHHHHHHHHHCEEEEEEE
T ss_conf             99999999999997899099997----889999999999955899899998999-99--999999999775401048875


Q ss_pred             CCCC
Q ss_conf             4887
Q gi|254780901|r  157 DCGS  160 (600)
Q Consensus       157 D~Gi  160 (600)
                      |.+.
T Consensus        86 ~~~~   89 (131)
T cd00079          86 DVIA   89 (131)
T ss_pred             ECCE
T ss_conf             1120


No 36 
>PRK07200 aspartate/ornithine carbamoyltransferase family protein; Validated
Probab=90.56  E-value=1.6  Score=24.12  Aligned_cols=48  Identities=10%  Similarity=-0.052  Sum_probs=21.2

Q ss_pred             HHHHHHHH-HHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEE
Q ss_conf             28999999-9997699479980787433668897898874202686899
Q gi|254780901|r  107 ASVALMMR-FLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLII  154 (600)
Q Consensus       107 tstail~~-~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiI  154 (600)
                      |-|-.-++ +..++|..+.|.=|+-.+=|+|-+.+=..++...=++.|.
T Consensus        71 TRTR~SFEva~~~LGg~~~yL~p~~~QlG~gEsi~DTArVLsR~~D~I~  119 (395)
T PRK07200         71 TRTRFSYASALNLLGLAQQDLDEGKSQIAHGETVRETANMISFCADAIG  119 (395)
T ss_pred             CHHHHHHHHHHHHCCCCEEEECCCCCCCCCCCCHHHHHHHHHHHHHEEE
T ss_conf             3468999999997799769738987627799888999999985502588


No 37 
>pfam06506 PrpR_N Propionate catabolism activator. This domain is found at the N terminus of several sigma54- dependent transcriptional activators including PrpR, which activates catabolism of propionate.
Probab=90.29  E-value=1.6  Score=24.03  Aligned_cols=132  Identities=14%  Similarity=0.169  Sum_probs=76.5

Q ss_pred             CHHHHHHHHHHHCCCHHHHHHHHHCCCCHHHHHHHCCCCHHHCCCCHHHCCCHHHHHHHHHHHHHCCCCEEEEECCCCCH
Q ss_conf             98899999988199999999999678897898866196677718995561487999999999997799799994078861
Q gi|254780901|r   26 GINRALAITQKHAIPDIVARVLVNRNVSIDYAKDFLNPSIRLLMPDPLILTDCDKAARRIVQAIYNSEKIMIFGDYDVDG  105 (600)
Q Consensus        26 ~~~~~~~l~~~~~~~~~~a~iL~~Rgi~~~~~~~fL~p~l~~l~~dP~~l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DG  105 (600)
                      +++....+++++-  .-=+.++++||-+..-++..++--.-..   |..-.||=+|..   +|.+-+.+|.+.|-...  
T Consensus        17 ~l~~av~~a~~~~--~~g~dvIIsRGgta~~ir~~~~iPVv~I---~~s~~Dil~al~---~a~~~~~kiavvg~~~~--   86 (169)
T pfam06506        17 GLEDAVEVARALV--AEGVDVIISRGGTAAYLRDRLSVPVVEI---KVSGFDLLRALA---RARRYGGRIGLVGYENI--   86 (169)
T ss_pred             CHHHHHHHHHHHH--HCCCCEEEECCHHHHHHHHHCCCCEEEE---ECCHHHHHHHHH---HHHHHCCCEEEEECCCC--
T ss_conf             7899999999999--7799599989658999998589988998---278869999999---99975897999927630--


Q ss_pred             HHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEEC
Q ss_conf             528999999999769947998078743366889789887420268689996488762345555541798279961
Q gi|254780901|r  106 AASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVID  180 (600)
Q Consensus       106 itstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtD  180 (600)
                       +..  +..+-..++.++..+..+...|    -...+++++++|++.+|    |  +.-..++|++.|+..+.+.
T Consensus        87 -~~~--~~~~~~il~~~i~~~~~~~~~e----~~~~i~~l~~~G~~vvV----G--~~~~~~~A~~~Gl~~vli~  148 (169)
T pfam06506        87 -IPG--LKALSELLGLDIVQRAYQSEEE----ARAAVKELKAQGIKVIV----G--DGLVCDLAEQAGLQGVLIY  148 (169)
T ss_pred             -CHH--HHHHHHHHCCCEEEEEECCHHH----HHHHHHHHHHCCCEEEE----C--CCHHHHHHHHCCCCEEEEE
T ss_conf             -368--9999999699359999668899----99999999986995998----5--8289999998399579996


No 38 
>PRK13936 phosphoheptose isomerase; Provisional
Probab=90.21  E-value=1.7  Score=23.91  Aligned_cols=104  Identities=21%  Similarity=0.337  Sum_probs=60.5

Q ss_pred             CCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHH--HHHHHHCC-----CCEEEEEC-----CCCCCCCCCCHHHHH
Q ss_conf             4879999999999977997999940788615289999--99999769-----94799807-----874336688978988
Q gi|254780901|r   76 TDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALM--MRFLSHCS-----VNANMYIP-----DRIVDGYGPNPSLME  143 (600)
Q Consensus        76 ~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail--~~~L~~~g-----~~v~~~IP-----~R~~eGYGl~~~~i~  143 (600)
                      +.+++|++.|.+++.++.||.++|   .-|-.+.|-.  .+++..+.     ..+...-.     .-+...||...-.-+
T Consensus        27 ~~i~~aa~~i~~~~~~g~ki~~~G---NGgSaa~A~h~a~el~~~~~~~r~~lpai~L~~d~~~lTai~ND~g~~~vf~r  103 (197)
T PRK13936         27 PPIAQAVELMVQALLNEGKILACG---NGGSAADAQHFSSELLNRFERERPSLPAIALTTDSSTLTAIANDYSYNEVFSK  103 (197)
T ss_pred             HHHHHHHHHHHHHHHCCCEEEEEE---CCHHHHHHHHHHHHHHCHHHCCCCCCCEEEECCCCHHHHCCCCCCCHHHHHHH
T ss_conf             999999999999998799899996---87899999999999866541278887557643674011010278789999999


Q ss_pred             HH---HHCCCCEEEEEC-CCCC--CHHHHHHHHHCCCCEEEECCCC
Q ss_conf             74---202686899964-8876--2345555541798279961544
Q gi|254780901|r  144 KF---INEGAQLIITVD-CGST--SYDALQYATNQGIDVIVIDHHQ  183 (600)
Q Consensus       144 ~~---~~~g~~LiItvD-~Gi~--~~e~i~~a~~~GidvIVtDHH~  183 (600)
                      .+   ...| +++|... .|-+  =.+++++|+++|+.||..==..
T Consensus       104 Ql~a~~~~g-Dili~iS~SGnS~Nii~A~~~A~~~g~~~i~ltG~d  148 (197)
T PRK13936        104 QVRALGQPG-DVLLAISTSGNSANVIQAIQAAHEREMHVVALTGRD  148 (197)
T ss_pred             HHHHHCCCC-CEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEECCC
T ss_conf             999838999-989999699999899999999998599599998168


No 39 
>PRK05427 putative manganese-dependent inorganic pyrophosphatase; Provisional
Probab=90.11  E-value=1  Score=25.48  Aligned_cols=88  Identities=25%  Similarity=0.335  Sum_probs=45.4

Q ss_pred             CCEEEEEC--CCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCC----------CCCCCH-HHHHHHHHCCCCEEEEECCC
Q ss_conf             97999940--788615289999999997699479980787433----------668897-89887420268689996488
Q gi|254780901|r   93 EKIMIFGD--YDVDGAASVALMMRFLSHCSVNANMYIPDRIVD----------GYGPNP-SLMEKFINEGAQLIITVDCG  159 (600)
Q Consensus        93 ekI~I~gD--yD~DGitstail~~~L~~~g~~v~~~IP~R~~e----------GYGl~~-~~i~~~~~~g~~LiItvD~G  159 (600)
                      ++|.|+|+  -|.|.|+|+-.+..++++.|..-  ++|-|.-+          -+|+.. +.++.+.....+=+|-||.-
T Consensus         2 ~~i~V~Gh~npDtDSI~SAIayA~l~~~~g~~~--~~p~r~g~ln~Et~fvL~~~gv~~p~li~~v~~~~~~~viLVDHN   79 (311)
T PRK05427          2 MKIYVFGHKNPDTDSICSAIAYAYLKNKLGEDA--AVAVRLGEPNPETQFVLDYFGVEAPELITDVAPEVSDKVILVDHN   79 (311)
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCC--CEEECCCCCCHHHHHHHHHCCCCCHHHHHHHCCCCCCEEEEEECC
T ss_conf             827994189887779999999999998509986--226012797988999999859995478874122557739998589


Q ss_pred             CC--CHHHHHHHHHCCCCEEEECCCCCCC
Q ss_conf             76--2345555541798279961544765
Q gi|254780901|r  160 ST--SYDALQYATNQGIDVIVIDHHQVKS  186 (600)
Q Consensus       160 i~--~~e~i~~a~~~GidvIVtDHH~~~~  186 (600)
                      -.  +.+.++.+    -=+-|+|||...+
T Consensus        80 e~~q~v~~i~~a----~Iv~IIDHHr~g~  104 (311)
T PRK05427         80 EFQQSVDGIEEA----EILEIIDHHRLGN  104 (311)
T ss_pred             CCCCCCCCCCCC----EEEEEEECCCCCC
T ss_conf             722264665425----2799961476788


No 40 
>pfam02571 CbiJ Precorrin-6x reductase CbiJ/CobK. This family consists of Precorrin-6x reductase EC:1.3.1.54. This enzyme catalyses the reaction: precorrin-6Y + NADP(+) <= precorrin-6X + NADPH. CbiJ and CobK both catalyse the reduction of macocycle in the colbalmin biosynthesis pathway.
Probab=89.82  E-value=1.8  Score=23.69  Aligned_cols=22  Identities=23%  Similarity=0.498  Sum_probs=12.3

Q ss_pred             CEEEEECCCCCHHHHHHHHHHHHHHCC
Q ss_conf             799994078861528999999999769
Q gi|254780901|r   94 KIMIFGDYDVDGAASVALMMRFLSHCS  120 (600)
Q Consensus        94 kI~I~gDyD~DGitstail~~~L~~~g  120 (600)
                      +|+|+|     |+|=+--+.+.|...|
T Consensus         2 ~Ililg-----GT~e~r~la~~L~~~g   23 (246)
T pfam02571         2 RILILG-----GTTEARALAAALAAAG   23 (246)
T ss_pred             EEEEEE-----ECHHHHHHHHHHHHCC
T ss_conf             699997-----3689999999998569


No 41 
>cd06313 PBP1_ABC_sugar_binding_like_5 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=89.72  E-value=1.8  Score=23.63  Aligned_cols=67  Identities=21%  Similarity=0.127  Sum_probs=46.8

Q ss_pred             HHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCC-CCHHHHHHHHHCCCCEEEECCCC
Q ss_conf             99997699479980787433668897898874202686899964887-62345555541798279961544
Q gi|254780901|r  114 RFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGS-TSYDALQYATNQGIDVIVIDHHQ  183 (600)
Q Consensus       114 ~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi-~~~e~i~~a~~~GidvIVtDHH~  183 (600)
                      ++-+.+|.++.++-|+--   ..-....|+.++.+|++.||..-+.. +..+.++.|++.||.||..|.-.
T Consensus        23 ~aA~e~Gv~v~~~~a~~D---~~~Q~~~Ie~~I~~gvD~Iiv~p~d~~a~~~~~~~A~~aGIpVV~~d~~~   90 (272)
T cd06313          23 EAGKLLGVDVTWYGGALD---AVKQVAAIENMASQGWDFIAVDPLGIGTLTEAVQKAIARGIPVIDMGTLI   90 (272)
T ss_pred             HHHHHCCCEEEEECCCCC---HHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHCCCEEEEECCCC
T ss_conf             999981998999869999---99999999999985999999968887899999999998699899974777


No 42 
>cd06368 PBP1_iGluR_non_NMDA_like N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the non-NMDA (N-methyl-d-asparate) subtypes of ionotropic glutamate receptors. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the non-NMDA (N-methyl-d-asparate) subtypes of ionotropic glutamate receptors. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR.  Glutamate mediates the majority of excitatory synaptic transmission in the central nervous system via two broad classes of ionotropic receptors, characterized by their response to glutamate agonists: N-methyl-d -aspartate (NMDA) and non-NMDA receptors. NMDA receptors
Probab=89.21  E-value=2  Score=23.36  Aligned_cols=33  Identities=15%  Similarity=0.153  Sum_probs=11.3

Q ss_pred             HCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEE
Q ss_conf             026868999648876234555554179827996
Q gi|254780901|r  147 NEGAQLIITVDCGSTSYDALQYATNQGIDVIVI  179 (600)
Q Consensus       147 ~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVt  179 (600)
                      +.|+--|+..=...++.--...+.++.|-.|-+
T Consensus        60 ~~gV~AI~Gp~~~~~~~~v~si~~~~~vP~i~~   92 (324)
T cd06368          60 SQGVAAIFGPSSSSSANTVQSICDALEIPHITT   92 (324)
T ss_pred             HCCCEEEECCCCHHHHHHHHHHHHHCCCCEEEE
T ss_conf             549589998897568999999863326855882


No 43 
>cd06317 PBP1_ABC_sugar_binding_like_8 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Pperiplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=88.89  E-value=2  Score=23.20  Aligned_cols=70  Identities=16%  Similarity=0.146  Sum_probs=43.6

Q ss_pred             HHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCC-CCHHHHHHHHHCCCCEEEECCCCCCC
Q ss_conf             99997699479980787433668897898874202686899964887-62345555541798279961544765
Q gi|254780901|r  114 RFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGS-TSYDALQYATNQGIDVIVIDHHQVKS  186 (600)
Q Consensus       114 ~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi-~~~e~i~~a~~~GidvIVtDHH~~~~  186 (600)
                      ++.+.+|.++.+.=++.-.+   -..+.++.++.++++-||.+-+.. ...+.++.|++.||.||..|...+..
T Consensus        24 ~~A~~~G~~~~v~~~~~d~~---~q~~~i~~~i~~~vd~Iii~p~d~~~~~~~i~~a~~agIpVv~~d~~~~~~   94 (275)
T cd06317          24 AAAEEDGVEVIVLDANGDVA---RQAAQVEDLIAQKVDGIILWPTDGQAYIPGLRKAKQAGIPVVITNSNISEK   94 (275)
T ss_pred             HHHHHCCCEEEEECCCCCHH---HHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHCCCEEEEECCCCCCC
T ss_conf             99997699899977999999---999999999975999999967871245799999998699499976888766


No 44 
>pfam00977 His_biosynth Histidine biosynthesis protein. Proteins involved in steps 4 and 6 of the histidine biosynthesis pathway are contained in this family. Histidine is formed by several complex and distinct biochemical reactions catalysed by eight enzymes. The enzymes in this Pfam entry are called His6 and His7 in eukaryotes and HisA and HisF in prokaryotes. The structure of HisA is known to be a TIM barrel fold. In some archaeal HisA proteins the TIM barrel is composed of two tandem repeats of a half barrel. This family belong to the common phosphate binding site TIM barrel family.
Probab=88.51  E-value=2.2  Score=23.02  Aligned_cols=69  Identities=17%  Similarity=0.264  Sum_probs=52.5

Q ss_pred             HHHHHHHCCCCEEEEE-CCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECC
Q ss_conf             9999997699479980-787433668897898874202686899964887623455555417982799615
Q gi|254780901|r  112 MMRFLSHCSVNANMYI-PDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDH  181 (600)
Q Consensus       112 l~~~L~~~g~~v~~~I-P~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDH  181 (600)
                      +.+.+...|++--|.+ -+...+|.+.|.+.++++.+. +.+=|+++-|+++.+.++.+-+.|.+=||+--
T Consensus        34 ~a~~~~~~g~d~i~ivDLda~~~~~~~n~~~i~~i~~~-~~~pi~vgGGIrs~e~~~~~l~~Ga~kvvigs  103 (229)
T pfam00977        34 LAKRYEEEGADELHFVDLDAAKEGRPVNLDLIEEIAEE-VFIPVQVGGGIRSLEDAERLLSAGADKVIIGT  103 (229)
T ss_pred             HHHHHHHCCCCEEEEEECCCCCCCCHHHHHHHHHHHHH-CCCCEEEECCEEEHHHHHHHHHCCCCEEEECC
T ss_conf             99999987999899996866302681069999999986-69878996456118999999976998999586


No 45 
>PRK00414 gmhA phosphoheptose isomerase; Reviewed
Probab=88.44  E-value=2.2  Score=22.98  Aligned_cols=112  Identities=15%  Similarity=0.245  Sum_probs=60.8

Q ss_pred             HCCCCHHHCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHH--HHHHHHCCCC-----EEEEECC-----CCCCC
Q ss_conf             7189955614879999999999977997999940788615289999--9999976994-----7998078-----74336
Q gi|254780901|r   67 LLMPDPLILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALM--MRFLSHCSVN-----ANMYIPD-----RIVDG  134 (600)
Q Consensus        67 ~l~~dP~~l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail--~~~L~~~g~~-----v~~~IP~-----R~~eG  134 (600)
                      .+..+-..+..+++|++.|.++++++.||.++|.   -|-.|.|--  .++...+..+     +... -+     -+...
T Consensus        19 ~~~~~~~~~~~I~~aa~~i~~~~~~g~kI~~cGN---GGSaa~A~Hfa~dl~~~~~~~r~~l~ai~L-sd~s~lTa~~ND   94 (192)
T PRK00414         19 NFLKDDANIHAIQRAAVLIADSFKAGGKVLSCGN---GGSHCDAMHFAEELTGRYRENRPGYPAIAI-SDVSHLSCVSND   94 (192)
T ss_pred             HHHHCHHHHHHHHHHHHHHHHHHHCCCEEEEEEC---CHHHHHHHHHHHHHHCCCCCCCCCCCEEEC-CCHHHHHHHCCC
T ss_conf             9971564499999999999999987997999968---588999999999874631446665432532-767775010076


Q ss_pred             CCCCHHHHHHHHH--CCCCEEEEECCCCC---CHHHHHHHHHCCCCEEEECCC
Q ss_conf             6889789887420--26868999648876---234555554179827996154
Q gi|254780901|r  135 YGPNPSLMEKFIN--EGAQLIITVDCGST---SYDALQYATNQGIDVIVIDHH  182 (600)
Q Consensus       135 YGl~~~~i~~~~~--~g~~LiItvD~Gi~---~~e~i~~a~~~GidvIVtDHH  182 (600)
                      ||...-..+.+..  +.-+++|..-.+=+   =.+++++|+++|+.+|..==.
T Consensus        95 ~g~e~iF~~Ql~~~~~~gDvLi~iS~SGnS~Nii~A~~~Ak~~g~~~i~ltG~  147 (192)
T PRK00414         95 FGYDYVFSRYVEAVGREGDVLLGISTSGNSGNIIKAIEAAREKGMKVITLTGK  147 (192)
T ss_pred             CCHHHHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCEEEEEECC
T ss_conf             64889999999981789999999768999999999999999889989999779


No 46 
>COG4821 Uncharacterized protein containing SIS (Sugar ISomerase) phosphosugar binding domain [General function prediction only]
Probab=88.38  E-value=1.1  Score=25.18  Aligned_cols=98  Identities=23%  Similarity=0.498  Sum_probs=56.4

Q ss_pred             HCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCC------------------CCEEEEECCCCCCCC
Q ss_conf             61487999999999997799799994078861528999999999769------------------947998078743366
Q gi|254780901|r   74 ILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCS------------------VNANMYIPDRIVDGY  135 (600)
Q Consensus        74 ~l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g------------------~~v~~~IP~R~~eGY  135 (600)
                      .-..|.+|+..+.++|.|+..|-+||-    | -|..+--+..-+.|                  +....|. .| .|||
T Consensus        20 ~a~~i~kaa~lVAesi~n~g~i~~FG~----G-HShm~aeEv~yRAGGLa~~~pIL~~plMLhega~ass~l-Er-ieg~   92 (243)
T COG4821          20 QAENIKKAAKLVAESIMNDGRIYVFGS----G-HSHMLAEEVFYRAGGLAPIKPILMEPLMLHEGAVASSYL-ER-IEGY   92 (243)
T ss_pred             HHHHHHHHHHHHHHHHHCCCEEEEECC----C-HHHHHHHHHHHHCCCCCCCCCCCCCHHHHCCCCCCCCHH-HH-HHHH
T ss_conf             999999999999999854987999648----6-288999999864378001132147716521352100045-76-5317


Q ss_pred             CCCHHHHHHHHHCCCCEEEEE-CCCCC--CHHHHHHHHHCCCCEEEEC
Q ss_conf             889789887420268689996-48876--2345555541798279961
Q gi|254780901|r  136 GPNPSLMEKFINEGAQLIITV-DCGST--SYDALQYATNQGIDVIVID  180 (600)
Q Consensus       136 Gl~~~~i~~~~~~g~~LiItv-D~Gi~--~~e~i~~a~~~GidvIVtD  180 (600)
                      +  +..+.+..-..-+.+|.+ -.|-+  -.|..+++++.|..||+.-
T Consensus        93 ~--~~~l~~~~i~~~DVliviSnSGrNpvpie~A~~~rekGa~vI~vT  138 (243)
T COG4821          93 A--KLFLHRLQIRPNDVLIVISNSGRNPVPIEVAEYAREKGAKVIAVT  138 (243)
T ss_pred             H--HHHHHHHCCCCCCEEEEEECCCCCCCCHHHHHHHHHCCCEEEEEE
T ss_conf             7--778999668878889998079989844389999986597699985


No 47 
>pfam10740 DUF2529 Protein of unknown function (DUF2529). This family is conserved in the Bacillales. The function is not known. Several members are annotated as being YWJG, a protein expressed downstream of pyrG, a gene encoding for cytidine triphosphate synthetase.
Probab=88.22  E-value=2.2  Score=22.89  Aligned_cols=109  Identities=17%  Similarity=0.181  Sum_probs=62.8

Q ss_pred             CHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCC-CCCCCCHHHHHHHHHCCCCEEEE
Q ss_conf             87999999999997799799994078861528999999999769947998078743-36688978988742026868999
Q gi|254780901|r   77 DCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIV-DGYGPNPSLMEKFINEGAQLIIT  155 (600)
Q Consensus        77 dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~-eGYGl~~~~i~~~~~~g~~LiIt  155 (600)
                      +++.|+.+|+||+--.-+|-|+|.-|.+|+.+-|+.       |.+-.... .|+. |     .....++-+..--|+++
T Consensus        23 ~iEdaARlLAQAiigeG~VYi~G~~Em~~v~~eal~-------g~E~l~~~-k~l~~~-----~~~~~~~t~tDRVLlfs   89 (172)
T pfam10740        23 AIEDGARLLAQAIIGEGNVYIKGFNEMEAVELEALE-------GVEPLPSA-KPLPLD-----ATEFADITETDRVLLFS   89 (172)
T ss_pred             HHHHHHHHHHHHHHCCCEEEEEECCHHHHHHHHHHC-------CCCCCCCC-CCCCCC-----CCCCCCCCCCCEEEEEC
T ss_conf             699999999999726977999725469989999972-------87767544-337555-----66510077557699976


Q ss_pred             ECCCCC-CHHHHHHHHHCCCCEEEEC-CCCCCCCCCC-CEEEECCC
Q ss_conf             648876-2345555541798279961-5447655567-25652378
Q gi|254780901|r  156 VDCGST-SYDALQYATNQGIDVIVID-HHQVKSEEIP-AYALVNPN  198 (600)
Q Consensus       156 vD~Gi~-~~e~i~~a~~~GidvIVtD-HH~~~~~~p~-a~aivNP~  198 (600)
                      ..++-. +..-++.+.+.|++++.+- ++.-...+++ ++..||-+
T Consensus        90 ~~~~d~e~~~~a~~L~~~gi~~v~Vs~~~~~~~~l~~~~~vhId~~  135 (172)
T pfam10740        90 RFSNDEEAVALAKKLYDQGIDVVAVSPNAKEGDSLADHADVHIDLK  135 (172)
T ss_pred             CCCCCHHHHHHHHHHHHCCCCEEEEECCCCCCCCCHHHEEEEEECC
T ss_conf             9999789999999999869988998168888876144402667647


No 48 
>cd06380 PBP1_iGluR_AMPA N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the AMPA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor, a member of the glutamate-receptor ion channels (iGluRs). AMPA receptors are the major mediators of excitatory synaptic transmission in the central nervous system.  While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR.  AMPA receptors consist of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an important roles in mediating the rapid excita
Probab=88.17  E-value=2.3  Score=22.86  Aligned_cols=47  Identities=13%  Similarity=0.136  Sum_probs=25.6

Q ss_pred             CCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEE
Q ss_conf             336688978988742026868999648876234555554179827996
Q gi|254780901|r  132 VDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVI  179 (600)
Q Consensus       132 ~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVt  179 (600)
                      .+.|.+...+-+ ..+.|+--||-.=...++.--...++++.|-.|-+
T Consensus        46 ~dsf~~~~~~C~-~l~~gV~AI~Gp~s~~~~~~v~si~~~l~IP~I~~   92 (382)
T cd06380          46 SDSFALTNAICS-QLSRGVFAIFGSYDKSSVNTLTSYSDALHVPFITP   92 (382)
T ss_pred             CCHHHHHHHHHH-HHHCCCEEEECCCCHHHHHHHHHHHHCCCCCEEEE
T ss_conf             887999999999-98649589997785647999999973468976860


No 49 
>PRK10355 xylF D-xylose transporter subunit XylF; Provisional
Probab=87.73  E-value=1.6  Score=23.97  Aligned_cols=46  Identities=22%  Similarity=0.411  Sum_probs=34.5

Q ss_pred             CHHHHHHHHHCCCCEEEEECCCCC-CHHHHHHHHHCCCCEEEECCCC
Q ss_conf             978988742026868999648876-2345555541798279961544
Q gi|254780901|r  138 NPSLMEKFINEGAQLIITVDCGST-SYDALQYATNQGIDVIVIDHHQ  183 (600)
Q Consensus       138 ~~~~i~~~~~~g~~LiItvD~Gi~-~~e~i~~a~~~GidvIVtDHH~  183 (600)
                      ...-||.++.+|++.||.+-+-.. ....++.|++.||.||..|.-.
T Consensus        70 Qi~qIe~~I~qgvdaIiv~p~D~~al~~~v~~A~~aGIPVI~~D~~i  116 (330)
T PRK10355         70 QMSQIENMINRGVDVLVIIPYNGQVLSNVIKEAKQEGIKVLAYDRMI  116 (330)
T ss_pred             HHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHCCCEEEEECCCC
T ss_conf             99999999985999999969987888999999998799499957877


No 50 
>cd06393 PBP1_iGluR_Kainate_GluR5_7 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR5-7 subunits of Kainate receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR5-7 subunits of Kainate receptor. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. There are five types of kainate receptors, GluR5, GluR6, GluR7, KA1, and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeric receptor channels activated
Probab=87.72  E-value=2.4  Score=22.67  Aligned_cols=10  Identities=10%  Similarity=0.069  Sum_probs=3.6

Q ss_pred             HHHHCCCCEE
Q ss_conf             5541798279
Q gi|254780901|r  168 YATNQGIDVI  177 (600)
Q Consensus       168 ~a~~~GidvI  177 (600)
                      .|.++.|--|
T Consensus        91 ic~~l~IPhi  100 (384)
T cd06393          91 ICNALEVPHI  100 (384)
T ss_pred             HHCCCCCCEE
T ss_conf             8535668716


No 51 
>PRK04523 N-acetylornithine carbamoyltransferase; Reviewed
Probab=87.62  E-value=2.4  Score=22.62  Aligned_cols=11  Identities=18%  Similarity=0.295  Sum_probs=6.6

Q ss_pred             CCCCEEEECCC
Q ss_conf             79827996154
Q gi|254780901|r  172 QGIDVIVIDHH  182 (600)
Q Consensus       172 ~GidvIVtDHH  182 (600)
                      .-.|+||.=|+
T Consensus       104 ~y~D~iviR~~  114 (335)
T PRK04523        104 RYVDLIGVRAF  114 (335)
T ss_pred             HCCCEEEEECC
T ss_conf             43989999325


No 52 
>PRK02255 putrescine carbamoyltransferase; Provisional
Probab=87.34  E-value=2.5  Score=22.51  Aligned_cols=31  Identities=13%  Similarity=0.150  Sum_probs=17.1

Q ss_pred             HHHHHHHHH-HHHHCCCCEEEEECCCCCCCCC
Q ss_conf             528999999-9997699479980787433668
Q gi|254780901|r  106 AASVALMMR-FLSHCSVNANMYIPDRIVDGYG  136 (600)
Q Consensus       106 itstail~~-~L~~~g~~v~~~IP~R~~eGYG  136 (600)
                      -|=|-+=.+ +.+++|..+.+.=|+..+-|-|
T Consensus        54 STRTR~SFE~A~~~LGg~~i~l~~~~~sl~kg   85 (341)
T PRK02255         54 STRTRVSFETAMTQLGGHAQYLAPGQIHLGGH   85 (341)
T ss_pred             CCHHHHHHHHHHHHCCCCEEECCCCCCCCCCC
T ss_conf             71079999999998599799827654457887


No 53 
>cd05006 SIS_GmhA Phosphoheptose isomerase is a member of the SIS (Sugar ISomerase) superfamily. Phosphoheptose isomerase catalyzes the isomerization of sedoheptulose 7-phosphate into D-glycero-D-mannoheptose 7-phosphate. This is the first step of the biosynthesis of gram-negative bacteria inner core lipopolysaccharide precursor, L-glycero-D-mannoheptose (Gmh).
Probab=87.06  E-value=2.6  Score=22.40  Aligned_cols=105  Identities=21%  Similarity=0.369  Sum_probs=57.9

Q ss_pred             CCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHH--HHHHHHHHCCCC-----EEEEECC-----CCCCCCCCCHHHH
Q ss_conf             148799999999999779979999407886152899--999999976994-----7998078-----7433668897898
Q gi|254780901|r   75 LTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVA--LMMRFLSHCSVN-----ANMYIPD-----RIVDGYGPNPSLM  142 (600)
Q Consensus        75 l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitsta--il~~~L~~~g~~-----v~~~IP~-----R~~eGYGl~~~~i  142 (600)
                      -..++++++.|.+++.++.||.++|.   -|-.++|  +...+.+.+..+     +...-.+     -+...||...-..
T Consensus        16 ~~~i~~~~~~i~~~~~~g~kI~~~GN---GgSa~~A~H~a~dl~~~~~~~r~~l~aisL~~~~~~~ta~~ND~~~~~if~   92 (177)
T cd05006          16 AEAIEQAAQLLAEALLNGGKILICGN---GGSAADAQHFAAELVKRFEKERPGLPAIALTTDTSILTAIANDYGYEEVFS   92 (177)
T ss_pred             HHHHHHHHHHHHHHHHCCCEEEEEEC---CHHHHHHHHHHHHHHCCCCCCCCCEEEEECCCCHHHHHHHHCCCCHHHHHH
T ss_conf             89999999999999987998999968---740888999999873576668887017976787788888756532999999


Q ss_pred             HH---HHHCCCCEEEEECCCCC---CHHHHHHHHHCCCCEEEECCCC
Q ss_conf             87---42026868999648876---2345555541798279961544
Q gi|254780901|r  143 EK---FINEGAQLIITVDCGST---SYDALQYATNQGIDVIVIDHHQ  183 (600)
Q Consensus       143 ~~---~~~~g~~LiItvD~Gi~---~~e~i~~a~~~GidvIVtDHH~  183 (600)
                      +.   +... -|++|.....-.   =.+++++|+++|+.+|..=-..
T Consensus        93 ~ql~~~~~~-gDili~iS~sG~s~nii~a~~~ak~~g~~~i~ltg~~  138 (177)
T cd05006          93 RQVEALGQP-GDVLIGISTSGNSPNVLKALEAAKERGMKTIALTGRD  138 (177)
T ss_pred             HHHHHHCCC-CCEEEEECCCCCCHHHHHHHHHHHHCCCEEEEEECCC
T ss_conf             999974468-9889998189999899999999998799899998789


No 54 
>PRK13585 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; Provisional
Probab=87.00  E-value=2.6  Score=22.37  Aligned_cols=71  Identities=14%  Similarity=0.257  Sum_probs=55.0

Q ss_pred             HHHHHHHHCCCCEEEEE-CCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCC
Q ss_conf             99999997699479980-7874336688978988742026868999648876234555554179827996154
Q gi|254780901|r  111 LMMRFLSHCSVNANMYI-PDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHH  182 (600)
Q Consensus       111 il~~~L~~~g~~v~~~I-P~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH  182 (600)
                      -+.+.+...|++--|++ =+.-.+|.+.|.+.|+++.+. +.+=|+++-||.+.+.++.+-+.|.+-+|+--.
T Consensus        35 ~~a~~~~~~Ga~~lhivDLd~a~~g~~~n~~~I~~i~~~-~~~pi~vGGGIrs~~~i~~~l~~Ga~kvvigs~  106 (240)
T PRK13585         35 EVAKRWVDAGAKTLHLVDLDGAFEGSRKNADIIEKIVEA-TDVSIQLGGGIRSVEDAASLLDLGVDRVILGTA  106 (240)
T ss_pred             HHHHHHHHCCCCEEEEEECCCCCCCCCCHHHHHHHHHHH-CCCCEEEECCCCCHHHHHHHHHCCCCEEEECCC
T ss_conf             999999987999799998977211894449999999973-797789978858799999999769989993981


No 55 
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=86.83  E-value=2.7  Score=22.30  Aligned_cols=187  Identities=16%  Similarity=0.179  Sum_probs=95.9

Q ss_pred             HHHHHHHHHCCCH-HHHHHHHHCCCC-HHHHHHHCCCCHHH---------CC-CCHH-HCC----------------CHH
Q ss_conf             9999998819999-999999967889-78988661966777---------18-9955-614----------------879
Q gi|254780901|r   29 RALAITQKHAIPD-IVARVLVNRNVS-IDYAKDFLNPSIRL---------LM-PDPL-ILT----------------DCD   79 (600)
Q Consensus        29 ~~~~l~~~~~~~~-~~a~iL~~Rgi~-~~~~~~fL~p~l~~---------l~-~dP~-~l~----------------dm~   79 (600)
                      .+..|+++.|+|+ .+.|..-.=|++ -.+.+..|.-.+..         .. .+|. .+.                --+
T Consensus        38 si~elA~~a~VS~aTv~Rf~~kLGf~Gf~efk~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~t~~~l~~  117 (281)
T COG1737          38 SIAELAERAGVSPATVVRFARKLGFEGFSEFKLALAQELAEGRAQLLREIAEDDGPESILEKLLAANIAALERTLNLLDE  117 (281)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCH
T ss_conf             49999988199888999999985999889999999999763333100002456754689999999999999999853689


Q ss_pred             HHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEE-CC
Q ss_conf             99999999997799799994078861528999999999769947998078743366889789887420268689996-48
Q gi|254780901|r   80 KAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITV-DC  158 (600)
Q Consensus        80 ~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItv-D~  158 (600)
                      +..++..+.+.+-++|.+|| .=.=|..+.- +...|..+|.++.++     .+.++.. ..+..+.++  +++|.. -+
T Consensus       118 ~~l~~av~~L~~A~rI~~~G-~g~S~~vA~~-~~~~l~~ig~~~~~~-----~d~~~~~-~~~~~~~~~--Dv~i~iS~s  187 (281)
T COG1737         118 EALERAVELLAKARRIYFFG-LGSSGLVASD-LAYKLMRIGLNVVAL-----SDTHGQL-MQLALLTPG--DVVIAISFS  187 (281)
T ss_pred             HHHHHHHHHHHCCCCEEEEE-CCCHHHHHHH-HHHHHHHCCCCEEEE-----CCCHHHH-HHHHHCCCC--CEEEEEECC
T ss_conf             99999999997069579996-4835999999-999999819966996-----6841799-999838999--889998489


Q ss_pred             CCC--CHHHHHHHHHCCCCEEE-ECC-CCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             876--23455555417982799-615-4476555672565237888864334430478899999999999702
Q gi|254780901|r  159 GST--SYDALQYATNQGIDVIV-IDH-HQVKSEEIPAYALVNPNRLDDLSGQGHLCAAGVVFLVLVLIYRILR  227 (600)
Q Consensus       159 Gi~--~~e~i~~a~~~GidvIV-tDH-H~~~~~~p~a~aivNP~~~~~~~p~~~l~gaGvaf~l~~al~~~l~  227 (600)
                      |-+  -.+.++.|+++|..||- ||. +.|-.+.- -+.+..|.-....+. ...+.-.....++.+|...+.
T Consensus       188 G~t~e~i~~a~~ak~~ga~vIaiT~~~~spla~~A-d~~L~~~~~~~~~~~-~~~~s~~a~l~l~d~L~~~~~  258 (281)
T COG1737         188 GYTREIVEAAELAKERGAKVIAITDSADSPLAKLA-DIVLLVPVAEESFFR-SPISSRIAQLALIDALITAVA  258 (281)
T ss_pred             CCCHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHC-CEEEEECCCCCCCCC-CCCHHHHHHHHHHHHHHHHHH
T ss_conf             99689999999999779929998399999366654-778871267632225-560788999999999999999


No 56 
>TIGR02691 arsC_pI258_fam arsenate reductase (thioredoxin); InterPro: IPR014064   This family describes the well-studied thioredoxin-dependent arsenate reductase of Staphylococcus aureus plasmid pI258 and other mechanistically similar arsenate reductases. The mechanism involves an intramolecular disulphide bond cascade, and aligned members of this family have four absolutely conserved Cys residues. This group of arsenate reductases belongs to the low-molecular weight protein-tyrosine phosphatase family (IPR000106 from INTERPRO), as does a group of glutathione/glutaredoxin type arsenate reductases (IPR014062 from INTERPRO). At least two other, non-homologous groups of arsenate reductases involved in arsenical resistance are also known. This enzyme reduces arsenate to arsenite, which may be more toxic but which is more easily exported..
Probab=86.76  E-value=1  Score=25.58  Aligned_cols=70  Identities=13%  Similarity=0.184  Sum_probs=38.9

Q ss_pred             CHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEE
Q ss_conf             6152899999999976994799807874336688978988742026868999648876234555554179827996
Q gi|254780901|r  104 DGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVI  179 (600)
Q Consensus       104 DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVt  179 (600)
                      -|=+--+=|.+..-+....-.|-+-+---|-||||+.+|+-+.|.|+++=   + -+|..=--+++++-  |+|||
T Consensus         6 TGNSCRSQmAEG~gk~~L~~~w~V~SAGiE~HGlNP~Av~~M~E~giDIS---~-q~S~lID~~~L~~a--dlVvT   75 (129)
T TIGR02691         6 TGNSCRSQMAEGWGKKYLGDKWEVYSAGIEAHGLNPKAVKAMKEVGIDIS---N-QTSDLIDLDILNKA--DLVVT   75 (129)
T ss_pred             CCCCCHHHHHHHHHHHHCCCCCEEEECCCCCCCCCHHHHHHHCCCCCCCC---C-CCCHHHHHHHHHCC--CEEEE
T ss_conf             27530557779999874688616653553124878678764112774433---4-42024457776217--87876


No 57 
>KOG0781 consensus
Probab=86.04  E-value=2.9  Score=22.01  Aligned_cols=35  Identities=9%  Similarity=0.148  Sum_probs=14.5

Q ss_pred             CCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHH
Q ss_conf             487999999999997799799994078861528999999999
Q gi|254780901|r   76 TDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLS  117 (600)
Q Consensus        76 ~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~  117 (600)
                      +.|.=+..++....+...     +-||.  .+...++.+++.
T Consensus        74 ~~L~yv~~ll~~v~~~f~-----~~~~~--~~~~~l~~n~~~  108 (587)
T KOG0781          74 LTLTYVDKLLNDVLNLFR-----EKYDT--QSALSLLNNTFD  108 (587)
T ss_pred             CHHHHHHHHHHHHHHHHH-----HHHCC--CHHHHHHHHHHH
T ss_conf             211338878999999999-----87343--017776400477


No 58 
>cd06312 PBP1_ABC_sugar_binding_like_4 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=85.98  E-value=2.9  Score=21.99  Aligned_cols=81  Identities=21%  Similarity=0.176  Sum_probs=48.7

Q ss_pred             HHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCC-CCCHHHHHHHHHCCCCEEEECCCCCCCCCCCCEE
Q ss_conf             999769947998078743366889789887420268689996488-7623455555417982799615447655567256
Q gi|254780901|r  115 FLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCG-STSYDALQYATNQGIDVIVIDHHQVKSEEIPAYA  193 (600)
Q Consensus       115 ~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~G-i~~~e~i~~a~~~GidvIVtDHH~~~~~~p~a~a  193 (600)
                      +-+.+|.++.+.-|...+  .--....++.+...+++-||..-.- ....+.++.|++.||.||..|-..+.....+..+
T Consensus        25 aA~~~Gv~v~~~~~~~~d--~~~Q~~~i~~~i~~~vDaIii~p~~~~~~~~~i~~a~~agIpVv~~ds~~~~~~~~~~~~  102 (271)
T cd06312          25 AAKDLGVDVEYRGPETFD--VADMARLIEAAIAAKPDGIVVTIPDPDALDPAIKRAVAAGIPVISFNAGDPKYKELGALA  102 (271)
T ss_pred             HHHHHCCEEEEEECCCCC--HHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHCCCEEEEEECCCCCCCCCCEEE
T ss_conf             999969989999689899--999999999999759998999378830026999999965986999947886434455389


Q ss_pred             EECC
Q ss_conf             5237
Q gi|254780901|r  194 LVNP  197 (600)
Q Consensus       194 ivNP  197 (600)
                      .|-+
T Consensus       103 ~vg~  106 (271)
T cd06312         103 YVGQ  106 (271)
T ss_pred             EECC
T ss_conf             9727


No 59 
>PRK01710 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=85.54  E-value=3.1  Score=21.84  Aligned_cols=88  Identities=17%  Similarity=0.303  Sum_probs=52.9

Q ss_pred             CCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCC----------CCCCCHH----H
Q ss_conf             4879999999999977997999940788615289999999997699479980787433----------6688978----9
Q gi|254780901|r   76 TDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVD----------GYGPNPS----L  141 (600)
Q Consensus        76 ~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~e----------GYGl~~~----~  141 (600)
                      +||.+--+.     -+++||+|+|=    |+|+-|+. ++|...|++|..+=- +..+          ..|+...    .
T Consensus         3 ~~~~~~~~~-----l~~kkv~i~Gl----G~sG~a~a-~~L~~~g~~v~~~D~-~~~~~~~~~~~~l~~~gi~~~~g~~~   71 (458)
T PRK01710          3 RDFNEFKDF-----IKNKKVAVVGI----GVSNIPLI-KFLVKLGAKVTAFDK-KSEEELGEISLELKEKGVNLELGENY   71 (458)
T ss_pred             CHHHHHHHH-----HCCCEEEEEEE----CHHHHHHH-HHHHHCCCEEEEEEC-CCCHHHHHHHHHHHHCCCEEEECCCH
T ss_conf             348999999-----78996999978----78899999-999978897999989-88431489999998579989957840


Q ss_pred             HHHHHHCCCCEEEEECCCCC-CHHHHHHHHHCCCCEE
Q ss_conf             88742026868999648876-2345555541798279
Q gi|254780901|r  142 MEKFINEGAQLIITVDCGST-SYDALQYATNQGIDVI  177 (600)
Q Consensus       142 i~~~~~~g~~LiItvD~Gi~-~~e~i~~a~~~GidvI  177 (600)
                      .+.+  .+++++|. =-||+ +++++..|+++|+.|+
T Consensus        72 ~~~~--~~~d~vv~-SPgI~~~~p~~~~a~~~gi~v~  105 (458)
T PRK01710         72 LDKL--TGFDVIFK-TPSMRIDSPELVKAKEEGAYIT  105 (458)
T ss_pred             HHHC--CCCCEEEE-CCCCCCCCHHHHHHHHCCCCEE
T ss_conf             5423--78888998-9987998999999998799374


No 60 
>PRK03092 ribose-phosphate pyrophosphokinase; Provisional
Probab=85.52  E-value=2.2  Score=22.94  Aligned_cols=78  Identities=14%  Similarity=0.213  Sum_probs=54.6

Q ss_pred             HHHHHHCCCCEEEEECCCC--CHHHHHHHHHHHHHHCCC-CEEEEEC--------CCCCCCCCCCHHHHHHHHH-CCCCE
Q ss_conf             9999977997999940788--615289999999997699-4799807--------8743366889789887420-26868
Q gi|254780901|r   85 IVQAIYNSEKIMIFGDYDV--DGAASVALMMRFLSHCSV-NANMYIP--------DRIVDGYGPNPSLMEKFIN-EGAQL  152 (600)
Q Consensus        85 i~~ai~~~ekI~I~gDyD~--DGitstail~~~L~~~g~-~v~~~IP--------~R~~eGYGl~~~~i~~~~~-~g~~L  152 (600)
                      +.+.+..+.-+.|..-++-  |.+.-.-+|..+++..|+ ++...+|        .|+..|-.++...+-++.+ .|++-
T Consensus        30 i~~~vrg~dV~Ivqs~~~p~nd~lmELll~i~alk~~~A~~It~ViPY~~YsRQDr~~~~ge~isa~~va~lL~~~G~d~  109 (304)
T PRK03092         30 FEESVRGCDAFVLQSHPAPVNKWLMEQLIMIDALKRASAKRITVVLPFYPYARQDKKHRGREPISARLVADLLKTAGADR  109 (304)
T ss_pred             ECCCCCCCEEEEECCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCE
T ss_conf             47876798489991799995188999999999999758972799805776005877778877522999999886148881


Q ss_pred             EEEECCCCCC
Q ss_conf             9996488762
Q gi|254780901|r  153 IITVDCGSTS  162 (600)
Q Consensus       153 iItvD~Gi~~  162 (600)
                      +||+|.-...
T Consensus       110 vitvDlH~~~  119 (304)
T PRK03092        110 IMTVDLHTDQ  119 (304)
T ss_pred             EEEECCCHHH
T ss_conf             7996577599


No 61 
>cd01425 RPS2 Ribosomal protein S2 (RPS2), involved in formation of the translation initiation complex, where it might contact the messenger RNA and several components of the ribosome. It has been shown that in Escherichia coli RPS2 is essential for the binding of ribosomal protein S1 to the 30s ribosomal subunit. In humans, most likely in all vertebrates, and perhaps in all metazoans, the protein also functions as the 67 kDa laminin receptor (LAMR1 or 67LR), which is formed from a 37 kDa precursor, and is overexpressed in many tumors. 67LR is a cell surface receptor which interacts with a variety of ligands, laminin-1 and others. It is assumed that the ligand interactions are mediated via the conserved C-terminus, which becomes extracellular as the protein undergoes conformational changes which are not well understood. Specifically, a conserved palindromic motif, LMWWML, may participate in the interactions. 67LR plays essential roles in the adhesion of cells to the basement membrane an
Probab=85.39  E-value=3.1  Score=21.79  Aligned_cols=97  Identities=22%  Similarity=0.268  Sum_probs=63.2

Q ss_pred             HCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHH----H----
Q ss_conf             61487999999999997799799994078861528999999999769947998078743366889789887----4----
Q gi|254780901|r   74 ILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEK----F----  145 (600)
Q Consensus        74 ~l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~----~----  145 (600)
                      .+.-+.+|...+.+...++.+|+++|.-.    -+.-+..++.+..+.   +|+..|..-|-=-|...+..    +    
T Consensus        38 T~~~L~~A~~~i~~~~~~~g~ILfVgtk~----~~~~~v~~~a~~~~~---~yv~~rWigG~LTN~~~~~~~i~~~~~~~  110 (193)
T cd01425          38 TLEKLRLALNFIANIAAKGGKILFVGTKP----QAQRAVKKFAERTGS---FYVNGRWLGGTLTNWKTIRKSIKRLKKLE  110 (193)
T ss_pred             HHHHHHHHHHHHHHHHHCCCEEEEEECCH----HHHHHHHHHHHHCCC---EEECCEECCCCCCCHHHHHHHHHHHHHHH
T ss_conf             99999999999999997599599997578----999999999998399---45448575877248888866899888754


Q ss_pred             -------------HHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEE
Q ss_conf             -------------202686899964887623455555417982799
Q gi|254780901|r  146 -------------INEGAQLIITVDCGSTSYDALQYATNQGIDVIV  178 (600)
Q Consensus       146 -------------~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIV  178 (600)
                                   ...-++++|.+|- ..+..+|..|+.+||-||=
T Consensus       111 ~~k~~~~~~g~~~~~~~Pdliiv~d~-~~~~~ai~Ea~~l~IPvI~  155 (193)
T cd01425         111 KEKLEKNLGGIKDMFRLPDLVIVLDP-RKEHQAIREASKLGIPVIA  155 (193)
T ss_pred             HHHHHHHCCCHHHCCCCCCEEEEECC-CCCHHHHHHHHHHCCCEEE
T ss_conf             22566520340101669998999889-8416899999861875578


No 62 
>PRK09701 D-allose transporter subunit; Provisional
Probab=85.32  E-value=2.1  Score=23.07  Aligned_cols=68  Identities=15%  Similarity=0.152  Sum_probs=44.1

Q ss_pred             HHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECC-CCCCHHHHHHHHHCCCCEEEECCCCC
Q ss_conf             9976994799807874336688978988742026868999648-87623455555417982799615447
Q gi|254780901|r  116 LSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDC-GSTSYDALQYATNQGIDVIVIDHHQV  184 (600)
Q Consensus       116 L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~-Gi~~~e~i~~a~~~GidvIVtDHH~~  184 (600)
                      -+.+|.++.++.++--.+ .--....|+.++.+|++-||..-+ .......++.|++.||.||..|--..
T Consensus        50 Ak~~G~~v~v~~~~~~~D-~~~Qi~~Ie~~I~~gvdaIii~p~d~~a~~~~i~~A~~aGIpVV~~D~~v~  118 (311)
T PRK09701         50 AKTLGVSVDIFASPSEGD-FQSQLQLFEDLSNKNYKGIAFAPLSSVNLVMPVARAWKKGIYLVNLDEKID  118 (311)
T ss_pred             HHHHCCEEEEEECCCCCC-HHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHCCCCEEECCCCCC
T ss_conf             998699799992798789-999999999999759999999189877889999999977991896367667


No 63 
>PRK01747 mnmC 5-methylaminomethyl-2-thiouridine methyltransferase; Reviewed
Probab=85.11  E-value=3.2  Score=21.69  Aligned_cols=128  Identities=13%  Similarity=0.190  Sum_probs=78.4

Q ss_pred             HHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHH----------------
Q ss_conf             9999999779979999407886152899999999976994799807874336688978988742----------------
Q gi|254780901|r   83 RRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFI----------------  146 (600)
Q Consensus        83 ~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~----------------  146 (600)
                      ..|.+....+-.+.-|        |++....+.|+..|.+|.=      ..|+|--.+.+.-..                
T Consensus       185 ~~~~~~~~~~~~~~T~--------taag~Vrr~L~~~GF~v~k------~~G~~~Kreml~g~~~~~~~~~~~~~w~~~~  250 (660)
T PRK01747        185 NALARLARPGATLATF--------TSAGFVRRGLQEAGFTVKK------VKGFGRKREMLVGVLEQSLPPPLAAPWFARP  250 (660)
T ss_pred             HHHHHHCCCCCEEEEE--------CCHHHHHHHHHHCCCEEEE------CCCCCCCCCEEEEECCCCCCCCCCCCCCCCC
T ss_conf             9999972899758863--------0458999999978966986------6778874403687716776777788642466


Q ss_pred             --HCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCCCCCCC--CCEEEECCCCCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             --0268689996488762345555541798279961544765556--725652378888643344304788999999999
Q gi|254780901|r  147 --NEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKSEEI--PAYALVNPNRLDDLSGQGHLCAAGVVFLVLVLI  222 (600)
Q Consensus       147 --~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~~~~~~p--~a~aivNP~~~~~~~p~~~l~gaGvaf~l~~al  222 (600)
                        ....+=++.+--||...--.-.+.++|++|.|.|-|.-+...-  ....++.|+....+.+...++-++  |.++...
T Consensus       251 ~~~~~~~~VaVIGAGIAGas~A~~LA~rG~~VtVlDr~~~~A~gASGn~aG~l~P~ls~~~~~~sr~~~~a--~~~a~~~  328 (660)
T PRK01747        251 HSSKRNRDAAIIGGGIAGAALALALARRGWQVTLYEADEAPAQGASGNRQGALYPLLSKDDNALSRFFRAA--FLFARRF  328 (660)
T ss_pred             CCCCCCCCEEEECCHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCCCCCEEEECCCCCCCCHHHHHHHHH--HHHHHHH
T ss_conf             65578871899893899999999999789968999479875655666731267402578997689999999--9999999


Q ss_pred             HHHH
Q ss_conf             9970
Q gi|254780901|r  223 YRIL  226 (600)
Q Consensus       223 ~~~l  226 (600)
                      ++.+
T Consensus       329 ~~~l  332 (660)
T PRK01747        329 YDLE  332 (660)
T ss_pred             HHHH
T ss_conf             9987


No 64 
>COG0552 FtsY Signal recognition particle GTPase [Intracellular trafficking and secretion]
Probab=85.05  E-value=3.2  Score=21.67  Aligned_cols=19  Identities=21%  Similarity=0.420  Sum_probs=9.7

Q ss_pred             HHHHHHHHHHHHCEEEEEEE
Q ss_conf             22278998842010799886
Q gi|254780901|r  384 GLLAARLKEKFGRPSFAISF  403 (600)
Q Consensus       384 GIVAsrL~e~y~kP~iv~s~  403 (600)
                      |++-+ ++.++++|+..+..
T Consensus       301 G~il~-I~~~l~~PI~fiGv  319 (340)
T COG0552         301 GIILS-IAYELGIPIKFIGV  319 (340)
T ss_pred             CEEEE-HHHHHCCCEEEEEC
T ss_conf             24350-88886999799857


No 65 
>PRK05299 rpsB 30S ribosomal protein S2; Provisional
Probab=84.93  E-value=3.2  Score=21.64  Aligned_cols=100  Identities=19%  Similarity=0.264  Sum_probs=62.3

Q ss_pred             CCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHH----HHH------
Q ss_conf             1487999999999997799799994078861528999999999769947998078743366889789----887------
Q gi|254780901|r   75 LTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSL----MEK------  144 (600)
Q Consensus        75 l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~----i~~------  144 (600)
                      +.-+.+|...+.+...++.+|+..|--    --+.-++.++-...|   .|||.+|..-|-=-|-..    +.+      
T Consensus        47 ~~~L~~A~~~l~~~~~~gg~iLFVgTk----~q~~~~V~~~A~~~~---~~yV~~RWlGG~LTN~~tI~~~i~~l~~l~~  119 (255)
T PRK05299         47 VPMLDEAYNFVRDVAANGGKILFVGTK----KQAQEIIAEEAERCG---QPYVNHRWLGGMLTNFKTIRKSIKRLKELEK  119 (255)
T ss_pred             HHHHHHHHHHHHHHHHCCCCEEEEECC----HHHHHHHHHHHHHCC---CCEECCCCCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             999999999999999769936999665----878999999999839---9704387278653378888779999999998


Q ss_pred             ------------------------HH---------HCCCCEEEEECCCCCCHHHHHHHHHCCCCEEE-ECCC
Q ss_conf             ------------------------42---------02686899964887623455555417982799-6154
Q gi|254780901|r  145 ------------------------FI---------NEGAQLIITVDCGSTSYDALQYATNQGIDVIV-IDHH  182 (600)
Q Consensus       145 ------------------------~~---------~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIV-tDHH  182 (600)
                                              +.         ..-++++|.+|.. ..+-+|..|+.+||.||= +|-.
T Consensus       120 ~~~~~~~~~~tKKE~~~~~r~~~kL~k~~~Gi~~m~~lPd~viv~d~~-~e~~AV~EA~kl~IPvI~ivDTn  190 (255)
T PRK05299        120 MEEDGTFEKLTKKEALMLTRELEKLEKSLGGIKDMGGLPDALFVVDPN-KEHIAVKEARKLGIPVVAIVDTN  190 (255)
T ss_pred             HHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCC-CCHHHHHHHHHCCCCEEEEECCC
T ss_conf             872340544558999988777888998654053243199879984785-33799999997599888762489


No 66 
>COG5235 RFA2 Single-stranded DNA-binding replication protein A (RPA), medium (30 kD) subunit [DNA replication, recombination, and repair]
Probab=84.51  E-value=3.4  Score=21.50  Aligned_cols=72  Identities=17%  Similarity=0.151  Sum_probs=29.7

Q ss_pred             CCCEEEEECCCCCHHHHHHHHHHHHHHHHCEEEEEEECCCCEEEEEEECCCCCCHHHHHHHHCC---C------CCCCCC
Q ss_conf             4750262057858122222278998842010799886379837999864898618888885303---3------530115
Q gi|254780901|r  367 QASVIVVEGDRWHPGIVGLLAARLKEKFGRPSFAISFEEDGKGIGSGRSIEGFDIGKMVSFAVE---E------GILVKG  437 (600)
Q Consensus       367 ~~~~ivv~~~~wh~GViGIVAsrL~e~y~kP~iv~s~~~dg~~kGS~RSi~g~~l~~~l~~~~~---~------~ll~~~  437 (600)
                      +.++++=..+=-|.-.+|.|-+--...-   -..+.+ +||.+---+|--++.+--+..  |.+   .      +-+-.|
T Consensus        56 d~~f~vd~~Ev~~V~fVGvvrni~~~tt---n~~~~i-EDGTG~Ievr~W~~~~~~~e~--~~d~~~~~yvkV~G~lk~F  129 (258)
T COG5235          56 DSTFLVDSAEVTNVQFVGVVRNIKTSTT---NSMFVI-EDGTGSIEVRFWPGNSYEEEQ--CKDLEEQNYVKVNGSLKTF  129 (258)
T ss_pred             CCCEEECCEEEEEEEEEEEEEEEEECCC---CEEEEE-ECCCCEEEEEECCCCCHHHHH--CCCCCCCCEEEEECCEEEE
T ss_conf             7855662418866899999984010345---418999-348742898856887237775--4343326679994211220


Q ss_pred             CCCCCCC
Q ss_conf             6532223
Q gi|254780901|r  438 GGHAMAA  444 (600)
Q Consensus       438 GGH~~Aa  444 (600)
                      +|-..-+
T Consensus       130 ~GK~~I~  136 (258)
T COG5235         130 NGKRSIS  136 (258)
T ss_pred             CCEEEEE
T ss_conf             7805774


No 67 
>pfam09547 Spore_IV_A Stage IV sporulation protein A (spore_IV_A). SpoIVA is designated stage IV sporulation protein A. It acts in the mother cell compartment and plays a role in spore coat morphogenesis. A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species.
Probab=84.47  E-value=2  Score=23.35  Aligned_cols=33  Identities=27%  Similarity=0.337  Sum_probs=19.1

Q ss_pred             HHHHHHHHH-HHHCEEEEEEECCCC-EEEEEEECC
Q ss_conf             222789988-420107998863798-379998648
Q gi|254780901|r  384 GLLAARLKE-KFGRPSFAISFEEDG-KGIGSGRSI  416 (600)
Q Consensus       384 GIVAsrL~e-~y~kP~iv~s~~~dg-~~kGS~RSi  416 (600)
                      |+|+-.+-| ..--|.+|=.-..=| .+|.||-|+
T Consensus       366 GvV~P~l~e~~LeePeiIkqG~k~GVklkA~APSi  400 (492)
T pfam09547       366 GVVAPQLEEMTLEEPEIIKQGNRFGVKLKASAPSL  400 (492)
T ss_pred             EEECCCCCCCCCCCCEEEEECCCCCEEEEECCCCH
T ss_conf             78478734250578728756683317988427713


No 68 
>cd04723 HisA_HisF Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase (HisA) and the cyclase subunit of imidazoleglycerol phosphate synthase (HisF). The ProFAR isomerase catalyzes the fourth step in histidine biosynthesis, an isomerisation of the aminoaldose moiety of ProFAR to the aminoketose of PRFAR (N-(5'-phospho-D-1'-ribulosylformimino)-5-amino-1-(5''-phospho-ribosyl)-4-imidazolecarboxamide). In bacteria and archaea, ProFAR isomerase is encoded by the HisA gene. The Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)-formimino-5-aminoimidazole-4-carboxamide ribonucleotide (PRFAR) to imidazole glycerol phosphate (ImGP) and 5'-(5-aminoimidazole-4-carboxamide) ribonucleotide (AICAR). This conversion involves two tightly coupled reactions in distinct active sites of IGPS. The two catalytic domains can be fused, like in fungi and pl
Probab=84.09  E-value=3.5  Score=21.37  Aligned_cols=67  Identities=18%  Similarity=0.195  Sum_probs=47.2

Q ss_pred             HHHHHHHCCCCEEEEE-CCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEEC
Q ss_conf             9999997699479980-78743366889789887420268689996488762345555541798279961
Q gi|254780901|r  112 MMRFLSHCSVNANMYI-PDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVID  180 (600)
Q Consensus       112 l~~~L~~~g~~v~~~I-P~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtD  180 (600)
                      +.+.+...|++--|.+ =+. .+|-+.|.+.++++.+. +.+=|+++.||++.+.++.+-+.|.|-+|+-
T Consensus        40 ~a~~~~~~ga~~lhivDLda-~~g~~~n~~~I~~i~~~-~~~pi~vGGGIrs~~~~~~~l~~Gadkvvig  107 (233)
T cd04723          40 VARAYKELGFRGLYIADLDA-IMGRGDNDEAIRELAAA-WPLGLWVDGGIRSLENAQEWLKRGASRVIVG  107 (233)
T ss_pred             HHHHHHHCCCCEEEEEECCC-CCCCCCHHHHHHHHHHH-CCCCEEEECCCCCHHHHHHHHHCCCCEEECC
T ss_conf             99999987989899997865-46997539999999987-8998899702276999999986072015245


No 69 
>PRK03806 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=83.97  E-value=3.5  Score=21.34  Aligned_cols=74  Identities=20%  Similarity=0.372  Sum_probs=43.3

Q ss_pred             CCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHH--------------HCCCCEEEEE
Q ss_conf             79979999407886152899999999976994799807874336688978988742--------------0268689996
Q gi|254780901|r   91 NSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFI--------------NEGAQLIITV  156 (600)
Q Consensus        91 ~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~--------------~~g~~LiItv  156 (600)
                      ++++|+|+|    =|.|+-+.. ++|...|++|..+=- |      .++...+.+.              -.+++++| +
T Consensus         5 ~~k~v~V~G----lG~sG~s~~-~~L~~~G~~v~~~D~-~------~~~~~~~~l~~~~~~~~g~~~~~~~~~~d~vV-~   71 (438)
T PRK03806          5 QGKNVVIIG----LGLTGLSCV-DFFLARGVTPRVMDT-R------MTPPGLDKLPENVERHTGSLNDEWLLAADLIV-A   71 (438)
T ss_pred             CCCEEEEEE----ECHHHHHHH-HHHHHCCCEEEEEEC-C------CCCHHHHHHHCCCCEEECCCCHHHHCCCCEEE-E
T ss_conf             899899994----578889999-999978996999989-9------99005788645884665777966806799999-8


Q ss_pred             CCCCC-CHHHHHHHHHCCCCEE
Q ss_conf             48876-2345555541798279
Q gi|254780901|r  157 DCGST-SYDALQYATNQGIDVI  177 (600)
Q Consensus       157 D~Gi~-~~e~i~~a~~~GidvI  177 (600)
                      =-||. +++.+..|++.|+.|+
T Consensus        72 SPGI~~~~p~~~~a~~~~i~i~   93 (438)
T PRK03806         72 SPGIALAHPSLSAAADAGVEIV   93 (438)
T ss_pred             CCCCCCCCHHHHHHHHCCCCEE
T ss_conf             9978998989999998799477


No 70 
>PRK00779 ornithine carbamoyltransferase; Provisional
Probab=83.78  E-value=3.6  Score=21.28  Aligned_cols=37  Identities=19%  Similarity=0.168  Sum_probs=18.5

Q ss_pred             CCEEEECCCCCCC--CCC--CCEEEECCCCCCCCCCCCCHHH
Q ss_conf             8279961544765--556--7256523788886433443047
Q gi|254780901|r  174 IDVIVIDHHQVKS--EEI--PAYALVNPNRLDDLSGQGHLCA  211 (600)
Q Consensus       174 idvIVtDHH~~~~--~~p--~a~aivNP~~~~~~~p~~~l~g  211 (600)
                      .|+||.=||....  +.-  ....|||- ..|...|...|+-
T Consensus       100 ~D~iviR~~~~~~~~~~a~~~~vPVINa-~~d~~HPtQaL~D  140 (308)
T PRK00779        100 VDAIMIRTFEHETLEELAEYSTVPVING-LTDLSHPCQILAD  140 (308)
T ss_pred             CCEEEEECCCCCHHHHHHHHCCCCEEEC-CCCCCCCHHHHHH
T ss_conf             7799993243011899987489878967-8887673899999


No 71 
>cd06316 PBP1_ABC_sugar_binding_like_7 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=83.75  E-value=3.6  Score=21.27  Aligned_cols=81  Identities=12%  Similarity=0.101  Sum_probs=48.3

Q ss_pred             HHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEE-EECCCCCCHHHHHHHHHCCCCEEEECCCCCCCCCCCC-E
Q ss_conf             9997699479980787433668897898874202686899-9648876234555554179827996154476555672-5
Q gi|254780901|r  115 FLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLII-TVDCGSTSYDALQYATNQGIDVIVIDHHQVKSEEIPA-Y  192 (600)
Q Consensus       115 ~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiI-tvD~Gi~~~e~i~~a~~~GidvIVtDHH~~~~~~p~a-~  192 (600)
                      ..+.+|.++.+..+...+  -.-....|+.++..|++-|| ++-........++.|++.||.||..|.-.+..+.+.. .
T Consensus        24 aA~~lG~~v~~~~da~~d--~~~Q~~~i~~~I~~gvDaIii~p~d~~a~~~~v~~A~~aGIpVv~~d~~~~~~~~~~~~~  101 (294)
T cd06316          24 EFAKLGIEVVATTDAQFD--PAKQVADIETTISQKPDIIISIPVDPVSTAAAYKKVAEAGIKLVFMDNVPSGLEHGKDYA  101 (294)
T ss_pred             HHHHHCCEEEEECCCCCC--HHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHCCCCEEEECCCCCCCCCCCCEE
T ss_conf             999839989996699889--999999999999859999999388867879999999981996798326777777777479


Q ss_pred             EEECC
Q ss_conf             65237
Q gi|254780901|r  193 ALVNP  197 (600)
Q Consensus       193 aivNP  197 (600)
                      +.|..
T Consensus       102 ~~v~~  106 (294)
T cd06316         102 GIVTD  106 (294)
T ss_pred             EEEEC
T ss_conf             99948


No 72 
>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=83.53  E-value=3.7  Score=21.21  Aligned_cols=82  Identities=22%  Similarity=0.282  Sum_probs=50.0

Q ss_pred             EEEEE-CCCCCHHHHHHHHHHHHHHCCCCEEEEECCC-----CCCCCC-----CC--HHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             99994-0788615289999999997699479980787-----433668-----89--78988742026868999648876
Q gi|254780901|r   95 IMIFG-DYDVDGAASVALMMRFLSHCSVNANMYIPDR-----IVDGYG-----PN--PSLMEKFINEGAQLIITVDCGST  161 (600)
Q Consensus        95 I~I~g-DyD~DGitstail~~~L~~~g~~v~~~IP~R-----~~eGYG-----l~--~~~i~~~~~~g~~LiItvD~Gi~  161 (600)
                      |+++| |-|+-=...|+.|.++|++.|.++.++=|-.     +-||-|     ++  .-..+-+++.+...|+.++.+-.
T Consensus         1 ~~~~GTdT~VGKT~vt~~l~~~l~~~G~~v~~~KPv~t~D~vlVEGaGG~~vPl~~~~~~~Dl~~~l~~pvIlV~~~~LG   80 (134)
T cd03109           1 IMGFGTGTDIGKTVATAILARALKEKGYRVAPLKPVQTYDFVLVEGAGGLCVPLKEDFTNADVAKELNLPAILVTSAGLG   80 (134)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEECHHHCCCEEEEECCCCEEECCCCCCCHHHHHHHHCCCEEEEECCCCC
T ss_conf             95752788876899999999999977991778756672798999889774600389862999999709998999778878


Q ss_pred             CHH----HHHHHHHCCCCE
Q ss_conf             234----555554179827
Q gi|254780901|r  162 SYD----ALQYATNQGIDV  176 (600)
Q Consensus       162 ~~e----~i~~a~~~Gidv  176 (600)
                      +..    .+++++++|+.+
T Consensus        81 ~INhtlLt~eal~~~gi~v   99 (134)
T cd03109          81 SINHAFLTIEAARIKGIIL   99 (134)
T ss_pred             HHHHHHHHHHHHHHCCCCE
T ss_conf             5899999999999879928


No 73 
>cd04732 HisA HisA.  Phosphoribosylformimino-5-aminoimidazole carboxamide ribonucleotide (ProFAR) isomerase catalyzes the fourth step in histidine biosynthesis, an isomerisation of the aminoaldose moiety of ProFAR to the aminoketose of PRFAR (N-(5'-phospho-D-1'-ribulosylformimino)-5-amino-1-(5''-phospho-ribosyl)-4-imidazolecarboxamide). In bacteria and archaea, ProFAR isomerase is encoded by the HisA gene.
Probab=83.48  E-value=3.7  Score=21.19  Aligned_cols=68  Identities=15%  Similarity=0.213  Sum_probs=51.6

Q ss_pred             HHHHHHHHCCCCEEEEE-CCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEE
Q ss_conf             99999997699479980-7874336688978988742026868999648876234555554179827996
Q gi|254780901|r  111 LMMRFLSHCSVNANMYI-PDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVI  179 (600)
Q Consensus       111 il~~~L~~~g~~v~~~I-P~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVt  179 (600)
                      -+.+.+...|++--|.+ =+...+|.|.|.+.|+++.+. +.+=||++-||.+.+.++.+-+.|.|-||+
T Consensus        33 ~~a~~~~~~g~d~l~i~DLdaa~~~~~~n~~~I~~I~~~-~~~pi~vGGGIrs~~~~~~l~~~Ga~kvvi  101 (234)
T cd04732          33 EVAKKWEEAGAKWLHVVDLDGAKGGEPVNLELIEEIVKA-VGIPVQVGGGIRSLEDIERLLDLGVSRVII  101 (234)
T ss_pred             HHHHHHHHCCCCEEEEEECCCHHHCCCCHHHHHHHHHHH-CCCCEEECCCCCCHHHHHHHHHCCCCEEEE
T ss_conf             999999986999899996753030891159999999976-795689737717599999998648871897


No 74 
>cd05013 SIS_RpiR RpiR-like protein. RpiR contains a SIS (Sugar ISomerase) domain, which is found in many phosphosugar isomerases and phosphosugar binding proteins. In E. coli, rpiR negatively regulates the expression of rpiB gene. Both rpiB and rpiA are ribose phosphate isomerases that catalyze the reversible reactions of ribose 5-phosphate into ribulose 5-phosphate.
Probab=83.36  E-value=3.7  Score=21.16  Aligned_cols=108  Identities=16%  Similarity=0.178  Sum_probs=54.5

Q ss_pred             CHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEE
Q ss_conf             87999999999997799799994078861528999999999769947998078743366889789887420268689996
Q gi|254780901|r   77 DCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITV  156 (600)
Q Consensus        77 dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItv  156 (600)
                      .+++++++    |.+.++|.+||--.  ....+.-+...|..+|..+.++ ++    . +........+. . -+++|.+
T Consensus         2 ~i~~~~~~----i~~a~~I~i~G~G~--S~~~A~~~~~~l~~~g~~~~~~-~~----~-~~~~~~~~~~~-~-~d~~i~i   67 (139)
T cd05013           2 ALEKAVDL----LAKARRIYIFGVGS--SGLVAEYLAYKLLRLGKPVVLL-SD----P-HLQLMSAANLT-P-GDVVIAI   67 (139)
T ss_pred             HHHHHHHH----HHCCCEEEEEECCH--HHHHHHHHHHHHCCCCCEEEEC-CC----H-HHHHHHHHCCC-C-CCEEEEE
T ss_conf             79999999----97599289998081--5999999999972589827987-96----2-77888874599-9-9999997


Q ss_pred             CCCCC---CHHHHHHHHHCCCCEEE-ECCCCCCCCCCCCEE-EECCCC
Q ss_conf             48876---23455555417982799-615447655567256-523788
Q gi|254780901|r  157 DCGST---SYDALQYATNQGIDVIV-IDHHQVKSEEIPAYA-LVNPNR  199 (600)
Q Consensus       157 D~Gi~---~~e~i~~a~~~GidvIV-tDHH~~~~~~p~a~a-ivNP~~  199 (600)
                      ...-.   ..+.++.|+++|+.+|. ||.+..+-.. -++. +.-|..
T Consensus        68 S~sg~~~~~~~~~~~ak~~g~~ii~IT~~~~s~l~~-~ad~~l~~~~~  114 (139)
T cd05013          68 SFSGETKETVEAAEIAKERGAKVIAITDSANSPLAK-LADIVLLVSSE  114 (139)
T ss_pred             CCCCCCHHHHHHHHHHHHCCCEEEEEECCCCCHHHH-HCCEEEECCCC
T ss_conf             686363789999999998699799997999997799-69999982886


No 75 
>PRK03515 ornithine carbamoyltransferase subunit I; Provisional
Probab=83.35  E-value=3.7  Score=21.16  Aligned_cols=25  Identities=4%  Similarity=-0.031  Sum_probs=11.5

Q ss_pred             HHHHHHHHHH-HHHHCCCCEEEEECC
Q ss_conf             1528999999-999769947998078
Q gi|254780901|r  105 GAASVALMMR-FLSHCSVNANMYIPD  129 (600)
Q Consensus       105 Gitstail~~-~L~~~g~~v~~~IP~  129 (600)
                      .-|=|-+=.+ +.+++|.++.+.=|+
T Consensus        55 pSTRTR~SFE~A~~~LGg~~i~l~~~   80 (334)
T PRK03515         55 DSTRTRCSFEVAAYDQGARVTYLGPS   80 (334)
T ss_pred             CCCHHHHHHHHHHHHCCCEEEEECCC
T ss_conf             87037999999999829929996775


No 76 
>PRK01506 consensus
Probab=83.28  E-value=2.3  Score=22.77  Aligned_cols=75  Identities=19%  Similarity=0.300  Sum_probs=53.2

Q ss_pred             HHHHCCCCEEEE-ECCC--CCHHHHHHHHHHHHHHCCCC-EEEEEC--------CCCCCCCCCCHHHHHHHHH-CCCCEE
Q ss_conf             999779979999-4078--86152899999999976994-799807--------8743366889789887420-268689
Q gi|254780901|r   87 QAIYNSEKIMIF-GDYD--VDGAASVALMMRFLSHCSVN-ANMYIP--------DRIVDGYGPNPSLMEKFIN-EGAQLI  153 (600)
Q Consensus        87 ~ai~~~ekI~I~-gDyD--~DGitstail~~~L~~~g~~-v~~~IP--------~R~~eGYGl~~~~i~~~~~-~g~~Li  153 (600)
                      +.++ ++.+.|+ .-+.  -|.+.-.-+|..+++..|++ +...+|        .|+..|=.++...+-++.+ .|++-+
T Consensus        52 ~~vr-g~dV~ivqs~~~p~nd~lmELll~i~a~r~~gA~~It~ViPY~~YaRQDr~~~~ge~isak~vA~ll~~~G~d~v  130 (317)
T PRK01506         52 ESIR-GCDVFIIQSTSAPVNEHIMELLIMIDALKRASAKTINIVIPYYGYARQDRKARSREPITAKLVANLLETAGATRV  130 (317)
T ss_pred             CCCC-CCEEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCEEHHHHHHHHHCCCCCEE
T ss_conf             8778-982899858999920899999999999887389748996267652437643358876138988878741588537


Q ss_pred             EEECCCCCC
Q ss_conf             996488762
Q gi|254780901|r  154 ITVDCGSTS  162 (600)
Q Consensus       154 ItvD~Gi~~  162 (600)
                      ||+|--...
T Consensus       131 itvDlH~~~  139 (317)
T PRK01506        131 ITLDLHAPQ  139 (317)
T ss_pred             EEECCCCHH
T ss_conf             996278487


No 77 
>pfam00148 Oxidored_nitro Nitrogenase component 1 type Oxidoreductase.
Probab=83.27  E-value=3.8  Score=21.13  Aligned_cols=24  Identities=17%  Similarity=0.220  Sum_probs=11.8

Q ss_pred             CCCHHHHHHHHHHHHHCC--CCEEEE
Q ss_conf             148799999999999779--979999
Q gi|254780901|r   75 LTDCDKAARRIVQAIYNS--EKIMIF   98 (600)
Q Consensus        75 l~dm~~A~~ri~~ai~~~--ekI~I~   98 (600)
                      |-+.++-.+-|.++.++.  +-|+|+
T Consensus        56 ~Gg~~kL~~~i~~~~~~~~p~~I~v~   81 (398)
T pfam00148        56 FGGEEKLEEAIREADKRYKPKAIFVY   81 (398)
T ss_pred             CCCHHHHHHHHHHHHHHCCCCEEEEE
T ss_conf             58599999999999973599789997


No 78 
>TIGR01334 modD modD protein; InterPro: IPR006242   The gene modD for a member of this family is found with molybdenum transport genes modABC in Rhodobacter capsulatus. However, disruption of modD causes only a 4-fold (rather than 500-fold for modA, modB, modC) change in the external molybdenum concentration required to suppress an alternative nitrogenase. ModD proteins are highly similar to nicotinate-nucleotide pyrophosphorylase (also called quinolinate phosphoribosyltransferase). Their function is unknown. ; GO: 0016763 transferase activity transferring pentosyl groups.
Probab=83.21  E-value=3.7  Score=21.19  Aligned_cols=23  Identities=9%  Similarity=0.303  Sum_probs=10.0

Q ss_pred             HHHHHHHHHHHHHCCCCEEEEEC
Q ss_conf             52899999999976994799807
Q gi|254780901|r  106 AASVALMMRFLSHCSVNANMYIP  128 (600)
Q Consensus       106 itstail~~~L~~~g~~v~~~IP  128 (600)
                      ++|.++-.+.|+++|+.+.++||
T Consensus        45 vsgvs~A~klL~~Lg~~id~av~   67 (277)
T TIGR01334        45 VSGVSVAAKLLKKLGLSIDVAVK   67 (277)
T ss_pred             EEHHHHHHHHHHHCCCCEEEECC
T ss_conf             43188999999860897000027


No 79 
>PRK01132 consensus
Probab=82.57  E-value=2.8  Score=22.17  Aligned_cols=68  Identities=18%  Similarity=0.266  Sum_probs=46.3

Q ss_pred             CCCCEEEEECCCC-CHHHHHHHHHHHHHHCCCC-EEEEEC--------CCCCCCCCCCHHHHHHHHHCCCCEEEEECC
Q ss_conf             7997999940788-6152899999999976994-799807--------874336688978988742026868999648
Q gi|254780901|r   91 NSEKIMIFGDYDV-DGAASVALMMRFLSHCSVN-ANMYIP--------DRIVDGYGPNPSLMEKFINEGAQLIITVDC  158 (600)
Q Consensus        91 ~~ekI~I~gDyD~-DGitstail~~~L~~~g~~-v~~~IP--------~R~~eGYGl~~~~i~~~~~~g~~LiItvD~  158 (600)
                      +++.+.|.+.... |-+.-.-+|..+++..|++ +...+|        .|+..|--++...+.++.+.+.+-+||+|-
T Consensus        46 rg~dV~iv~s~~~n~~lmELll~idAlr~~~A~rIt~ViPY~~YsRQDr~~~~ge~isak~vA~ll~~~~d~vitvDl  123 (286)
T PRK01132         46 KGRDVFIIGNTHHDAELIEMILLLSAAYDYKPKSVNIIAPYYGYARQHQRYNPGEPISSQIFTEIIESYSDSIATVDI  123 (286)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCEEEEEEC
T ss_conf             898799988899977699999999999874887279982465423323235898963099999998741666999824


No 80 
>cd01968 Nitrogenase_NifE_I Nitrogenase_NifE_I: a subgroup of the NifE subunit of the NifEN complex: NifE forms an alpha2beta2 tetramer with NifN.  NifE and NifN are structurally homologous to nitrogenase MoFe protein alpha and beta subunits respectively.  NifEN participates in the synthesis of the iron-molybdenum cofactor (FeMoco) of the MoFe protein.  NifB-co (an iron and sulfur containing precursor of the FeMoco) from NifB is transferred to the NifEN complex where it is further processed to FeMoco. The NifEN bound precursor of FeMoco has been identified as a molybdenum-free, iron- and sulfur- containing analog of FeMoco. It has been suggested that this NifEN bound precursor also acts as a cofactor precursor in nitrogenase systems which require a cofactor other than FeMoco: i.e. iron-vanadium cofactor (FeVco) or iron only cofactor (FeFeco).
Probab=82.35  E-value=4  Score=20.88  Aligned_cols=47  Identities=17%  Similarity=0.304  Sum_probs=23.4

Q ss_pred             HHCCCHHHHHHHHHHHHHCC--CCEEEE--------ECCCCCHHHHHHHHHHHHHHCCCCEEE
Q ss_conf             56148799999999999779--979999--------407886152899999999976994799
Q gi|254780901|r   73 LILTDCDKAARRIVQAIYNS--EKIMIF--------GDYDVDGAASVALMMRFLSHCSVNANM  125 (600)
Q Consensus        73 ~~l~dm~~A~~ri~~ai~~~--ekI~I~--------gDyD~DGitstail~~~L~~~g~~v~~  125 (600)
                      --|-+.++--+-|.++++.-  +-|.|+        || |++++.     .++-+..+..+.+
T Consensus        66 ~VfGG~~~L~~~I~~~~~~~~P~~I~v~tTC~~e~IGD-Di~~v~-----~~~~~~~~~pvv~  122 (410)
T cd01968          66 VIFGGEKKLYKAILEIIERYHPKAVFVYSTCVVALIGD-DIDAVC-----KTASEKFGIPVIP  122 (410)
T ss_pred             EEECCHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHCC-CHHHHH-----HHHHHHHCCCEEE
T ss_conf             56573999999999999854998899975670887356-399999-----9988861997798


No 81 
>COG0365 Acs Acyl-coenzyme A synthetases/AMP-(fatty) acid ligases [Lipid metabolism]
Probab=82.32  E-value=4.1  Score=20.87  Aligned_cols=98  Identities=12%  Similarity=0.238  Sum_probs=69.7

Q ss_pred             HHCCCHHHHHHHHHHHHH-----CCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHH-HHH
Q ss_conf             561487999999999997-----79979999407886152899999999976994799807874336688978988-742
Q gi|254780901|r   73 LILTDCDKAARRIVQAIY-----NSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLME-KFI  146 (600)
Q Consensus        73 ~~l~dm~~A~~ri~~ai~-----~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~-~~~  146 (600)
                      ..+.++.+.+.|+..++.     .+.++.||    ...+--+++...+.-++|+-.....|       |++.+++. ++.
T Consensus        41 ~Ty~~L~~~v~r~A~~L~~~~gvkGDrV~iy----mp~~pe~~~a~LA~~riGAI~~~vf~-------~f~~~al~~Ri~  109 (528)
T COG0365          41 LTYGDLRREVARLANALKDLGGVKGDRVAIY----MPNSPEAVIALLATARIGAIPAVVSP-------GLSAEAVADRIA  109 (528)
T ss_pred             EEHHHHHHHHHHHHHHHHHHCCCCCCEEEEE----CCCCHHHHHHHHHHHHCCCEEEECCC-------CCCHHHHHHHHH
T ss_conf             7899999999999999998489987889998----38989999999999981987761156-------879899999997


Q ss_pred             HCCCCEEEEECCCCCCHHHHHHHH---HCCCCEEEECC
Q ss_conf             026868999648876234555554---17982799615
Q gi|254780901|r  147 NEGAQLIITVDCGSTSYDALQYAT---NQGIDVIVIDH  181 (600)
Q Consensus       147 ~~g~~LiItvD~Gi~~~e~i~~a~---~~GidvIVtDH  181 (600)
                      ..+++++||.|.+.....++....   +.-..+||.+.
T Consensus       110 d~~~k~vit~d~~~~~gk~~~~~~~~~~~~~~~iv~~r  147 (528)
T COG0365         110 DLGPKVLIADDGTFRNGKEIALLEDADAVLSSVVVVPR  147 (528)
T ss_pred             CCCCCEEEEECCCCCCCCCCCCHHHHHHHHCCEEEECC
T ss_conf             24988899815644566432422678875122688414


No 82 
>PRK04128 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; Provisional
Probab=82.28  E-value=4.1  Score=20.86  Aligned_cols=63  Identities=22%  Similarity=0.393  Sum_probs=48.3

Q ss_pred             HHHCCCCEEEEE-CCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEEC
Q ss_conf             997699479980-78743366889789887420268689996488762345555541798279961
Q gi|254780901|r  116 LSHCSVNANMYI-PDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVID  180 (600)
Q Consensus       116 L~~~g~~v~~~I-P~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtD  180 (600)
                      +... ++--|.+ -+.-.+|.+.|.+.++++.++ +.+=|+++.||.+.+.++.+-+.|.+-+|.-
T Consensus        39 ~~~~-a~~lhivDLd~a~~g~~~n~~~I~~i~~~-~~~piqvGGGIrs~e~i~~~l~~Ga~kViig  102 (228)
T PRK04128         39 FSEY-VDKIHVVDLDGAFEGKPKNLDVVKNIIEE-TGLKVQVGGGFRTYESIKDAYEIGVENVIIG  102 (228)
T ss_pred             HHHC-CCEEEEEECCCCCCCCCCHHHHHHHHHHH-CCCEEEECCCCCCHHHHHHHHHCCCCEEEEC
T ss_conf             9966-99899998803014983269999999865-4962897386077999999996899769814


No 83 
>TIGR00461 gcvP glycine dehydrogenase; InterPro: IPR003437   This family consists of glycine cleavage system P-proteins (1.4.4.2 from EC) from bacterial, mammalian and plant sources. The P protein is part of the glycine decarboxylase multienzyme complex (2.1.2.10 from EC (GDC) also annotated as glycine cleavage system or glycine synthase. The P protein binds the alpha-amino group of glycine through its pyridoxal phosphate cofactor, carbon dioxide is released and the remaining methylamin moiety is then transferred to the lipoamide cofactor of the H protein. GDC consists of four proteins P, H, L and T . The reaction catalysed by this protein is:    Glycine + lipoylprotein = S-aminomethyldihydrolipoylprotein + CO2 ; GO: 0004375 glycine dehydrogenase (decarboxylating) activity, 0006544 glycine metabolic process, 0005961 glycine dehydrogenase complex (decarboxylating).
Probab=81.71  E-value=0.43  Score=28.53  Aligned_cols=150  Identities=23%  Similarity=0.272  Sum_probs=79.7

Q ss_pred             HHHHHHHHHHHHCCCC--EEEE-ECCCCCHHHHHHHHHHHHHHCCC--CEEEEECCCCCCCCCCCHHHHHHHHH------
Q ss_conf             9999999999977997--9999-40788615289999999997699--47998078743366889789887420------
Q gi|254780901|r   79 DKAARRIVQAIYNSEK--IMIF-GDYDVDGAASVALMMRFLSHCSV--NANMYIPDRIVDGYGPNPSLMEKFIN------  147 (600)
Q Consensus        79 ~~A~~ri~~ai~~~ek--I~I~-gDyD~DGitstail~~~L~~~g~--~v~~~IP~R~~eGYGl~~~~i~~~~~------  147 (600)
                      |.++--=.++|.++.+  +.=| |-==-|-++==.|+.+.|+.=|.  -.+.|-|.       ++...+|-+.+      
T Consensus        51 Ey~ala~Lk~IAskN~y~f~syIG~GYy~tilPPVI~RN~LEnPgWYTaYTPYQpE-------isQGRLEALLNFQtvv~  123 (965)
T TIGR00461        51 EYEALAELKKIASKNKYKFKSYIGMGYYDTILPPVIQRNLLENPGWYTAYTPYQPE-------ISQGRLEALLNFQTVVL  123 (965)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCH-------HHHHHHHHHHHHHHHHH
T ss_conf             89999999998730871687401355144516704643124787843467886501-------32468999873444543


Q ss_pred             C-------CCCEEEEECCCCCCHHH-----------------------------H-HHHHHCCCCEEEECCCCCCCCCCC
Q ss_conf             2-------68689996488762345-----------------------------5-555417982799615447655567
Q gi|254780901|r  148 E-------GAQLIITVDCGSTSYDA-----------------------------L-QYATNQGIDVIVIDHHQVKSEEIP  190 (600)
Q Consensus       148 ~-------g~~LiItvD~Gi~~~e~-----------------------------i-~~a~~~GidvIVtDHH~~~~~~p~  190 (600)
                      +       +++|+   |=|+.+.|+                             | .+|+-.||+|||-|||.+....  
T Consensus       124 DLTGL~~AnASLL---DEgTAAaEAMals~~vSk~Knan~ffva~d~HpQT~~V~~TRA~pfgiEvIv~D~~~~~~~~--  198 (965)
T TIGR00461       124 DLTGLEVANASLL---DEGTAAAEAMALSFRVSKKKNANKFFVAKDVHPQTLEVVKTRAKPFGIEVIVDDASDVKKAV--  198 (965)
T ss_pred             HCCCHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHCCCHHHHCCCCCCHHHHHHCCCCCCEEEEECCHHHHHHHH--
T ss_conf             0024346545332---17889999999987642222110110210377343688752403145168863445556544--


Q ss_pred             CEEEECCCCCCCCCCCCCHHHHHHHH--HHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             25652378888643344304788999--99999999702148876407799999998775420111144
Q gi|254780901|r  191 AYALVNPNRLDDLSGQGHLCAAGVVF--LVLVLIYRILRQDNKVPLNFDLLSLLDLVALATVCDVVPLI  257 (600)
Q Consensus       191 a~aivNP~~~~~~~p~~~l~gaGvaf--~l~~al~~~l~~~~~~~~~~~l~~~ldlvaiGTvaD~vpL~  257 (600)
                       +.+-||...||--  .+-+..|-.|  -=+.+|..++..+.-            ||+++  ||+|.|+
T Consensus       199 -dvfknPdvsG~Ll--QypaTdG~i~PPddy~~lid~lhshk~------------lvsvA--aD~maLt  250 (965)
T TIGR00461       199 -DVFKNPDVSGVLL--QYPATDGEIYPPDDYKALIDKLHSHKA------------LVSVA--ADLMALT  250 (965)
T ss_pred             -HHHCCCCCCEEEE--ECCCCCCCCCCCHHHHHHHHHHHCCHH------------HHHHH--HHHHHHH
T ss_conf             -3321777441576--235777723686228999998741301------------24678--7899998


No 84 
>PRK05038 consensus
Probab=81.71  E-value=3.5  Score=21.41  Aligned_cols=74  Identities=19%  Similarity=0.355  Sum_probs=51.5

Q ss_pred             HHHHCCCCEEEE-ECCC--CCHHHHHHHHHHHHHHCCC-CEEEEEC-------C-CCCCCC-CCCHHHHHHHHHC-CCCE
Q ss_conf             999779979999-4078--8615289999999997699-4799807-------8-743366-8897898874202-6868
Q gi|254780901|r   87 QAIYNSEKIMIF-GDYD--VDGAASVALMMRFLSHCSV-NANMYIP-------D-RIVDGY-GPNPSLMEKFINE-GAQL  152 (600)
Q Consensus        87 ~ai~~~ekI~I~-gDyD--~DGitstail~~~L~~~g~-~v~~~IP-------~-R~~eGY-Gl~~~~i~~~~~~-g~~L  152 (600)
                      +.+. ++.+.|. .-+.  =|.+.-.-+|..++++.|+ ++...+|       + |+..|- .++...+-++.+. |++-
T Consensus        46 ~~vr-g~dV~ivqs~~~p~nd~lmELll~idA~r~a~A~~It~ViPY~~YaRQDr~~~~g~~pIsak~vA~ll~~~g~d~  124 (315)
T PRK05038         46 ENVR-GGDVFIIQSTCAPTNDNLMELVVMVDALRRASAGRITAVIPYFGYARQDRRVRSARVPITAKVVADFLSSVGVDR  124 (315)
T ss_pred             CCCC-CCCEEEECCCCCCCCHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCCCCCCCEEHHHHHHHHHHCCCCE
T ss_conf             8778-995899858999951789999999999987388726998325432347755568888701999999998538875


Q ss_pred             EEEECCCCC
Q ss_conf             999648876
Q gi|254780901|r  153 IITVDCGST  161 (600)
Q Consensus       153 iItvD~Gi~  161 (600)
                      +||+|--..
T Consensus       125 vitvDlH~~  133 (315)
T PRK05038        125 VLTVDLHAE  133 (315)
T ss_pred             EEEECCCHH
T ss_conf             999658858


No 85 
>cd06305 PBP1_methylthioribose_binding_like Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Methylthioribose-binding protein-like of ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. The sugar-binding domain of the periplasmic proteins in this group is also homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR), DNA-binding transcriptional repressors such as LacI and GalR.
Probab=81.54  E-value=4.3  Score=20.67  Aligned_cols=69  Identities=13%  Similarity=0.074  Sum_probs=43.8

Q ss_pred             HHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEE-ECCCCCCHHHHHHHHHCCCCEEEECCCCC
Q ss_conf             9999976994799807874336688978988742026868999-64887623455555417982799615447
Q gi|254780901|r  113 MRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIIT-VDCGSTSYDALQYATNQGIDVIVIDHHQV  184 (600)
Q Consensus       113 ~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiIt-vD~Gi~~~e~i~~a~~~GidvIVtDHH~~  184 (600)
                      -...+.+|.++.++=.+- +  ---....|+.+...+++-||. .-...+..+.++.|++.||.||..|--.+
T Consensus        22 ~~~A~~~G~~~~v~d~~~-d--~~~Q~~~i~~~i~~~vDgIii~p~d~~~~~~~l~~a~~aGIPVV~~d~~~~   91 (273)
T cd06305          22 KAEAEALGGDLRVYDAGG-D--DAKQADQIDQAIAQKVDAIIIQHGRAEVLKPWVKRALDAGIPVVAFDVDSD   91 (273)
T ss_pred             HHHHHHCCCEEEEECCCC-C--HHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHCCCCEEEECCCCC
T ss_conf             999997499899973999-9--999999999999859999999468714448999999985997899817767


No 86 
>PRK10416 cell division protein FtsY; Provisional
Probab=81.40  E-value=4.3  Score=20.63  Aligned_cols=36  Identities=19%  Similarity=0.196  Sum_probs=18.5

Q ss_pred             CCCEEEEECCCC--CHHHHHHHHHHHHHHHHCEEEEEE
Q ss_conf             475026205785--812222227899884201079988
Q gi|254780901|r  367 QASVIVVEGDRW--HPGIVGLLAARLKEKFGRPSFAIS  402 (600)
Q Consensus       367 ~~~~ivv~~~~w--h~GViGIVAsrL~e~y~kP~iv~s  402 (600)
                      .+.+|++.+-|.  ..--+|=+|.++..+=+++.++-+
T Consensus       294 ~P~VIl~vGvNG~GKTTTigKLA~~~~~~gkkVllaA~  331 (499)
T PRK10416        294 TPFVILMVGVNGVGKTTTIGKLARQFEQQGKSVMLAAG  331 (499)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEE
T ss_conf             98799997478787898999999999977995378840


No 87 
>PRK09428 pssA phosphatidylserine synthase; Provisional
Probab=81.34  E-value=4.3  Score=20.65  Aligned_cols=74  Identities=11%  Similarity=0.217  Sum_probs=48.2

Q ss_pred             HHHHHHHHHHHHCC--CCEEEEECCC---------CCHHHHHHHHHHHHHHCCCCEE-EEECCCCCCCCCCCHHHHHHHH
Q ss_conf             99999999999779--9799994078---------8615289999999997699479-9807874336688978988742
Q gi|254780901|r   79 DKAARRIVQAIYNS--EKIMIFGDYD---------VDGAASVALMMRFLSHCSVNAN-MYIPDRIVDGYGPNPSLMEKFI  146 (600)
Q Consensus        79 ~~A~~ri~~ai~~~--ekI~I~gDyD---------~DGitstail~~~L~~~g~~v~-~~IP~R~~eGYGl~~~~i~~~~  146 (600)
                      .+-++.|.+|..++  =+|.|.-||=         .-..|+++++...++..+.++. |.||.|+.|+.|+..  +.-..
T Consensus        59 ~Ell~aL~~Ak~~np~L~V~ILvD~~RgtRg~ig~~~~~~na~~y~~l~~~~~~~v~i~gvP~r~nE~~GvqH--mK~yi  136 (444)
T PRK09428         59 REILDALYEAKQQNPELDIKVLVDWHRAQRGLIGAAKSNTNADWYCRMAQEYGHDVPVYGVPVNTREAFGVLH--LKGFI  136 (444)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCEEECCCHHHHHHHHHE--EEEEE
T ss_conf             9999999999976899879999987875667766678986288879899875997554307820655442231--47998


Q ss_pred             HCCCCEEEE
Q ss_conf             026868999
Q gi|254780901|r  147 NEGAQLIIT  155 (600)
Q Consensus       147 ~~g~~LiIt  155 (600)
                      -++ .+|++
T Consensus       137 fDD-~vi~S  144 (444)
T PRK09428        137 IDD-TVLYS  144 (444)
T ss_pred             ECC-CEEEE
T ss_conf             558-57983


No 88 
>cd06324 PBP1_ABC_sugar_binding_like_13 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=81.30  E-value=4.4  Score=20.61  Aligned_cols=49  Identities=10%  Similarity=0.228  Sum_probs=32.4

Q ss_pred             HHHHHHHHHC--CCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCCCCC
Q ss_conf             7898874202--686899964887623455555417982799615447655
Q gi|254780901|r  139 PSLMEKFINE--GAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKSE  187 (600)
Q Consensus       139 ~~~i~~~~~~--g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~~~~~  187 (600)
                      ...++.++..  +++.||.+.....+.+.++.|++.||.||++|-..++..
T Consensus        46 ~~~ie~~I~~~~~vd~Iii~p~~~~~~~~l~~A~~agIPVv~~d~~~~~~~   96 (305)
T cd06324          46 LQQARTILQRPDKPDALIFTNEKSVAPELLRLAEGAGVKLFLVNSGLTEAQ   96 (305)
T ss_pred             HHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHCCCEEEEECCCCCHHH
T ss_conf             999999983637970999879620018999999976983999658888365


No 89 
>COG3980 spsG Spore coat polysaccharide biosynthesis protein, predicted glycosyltransferase [Cell envelope biogenesis, outer membrane]
Probab=81.30  E-value=4.4  Score=20.61  Aligned_cols=120  Identities=15%  Similarity=0.122  Sum_probs=73.9

Q ss_pred             CEEEEECCCCC----HHHHHHHHHHHHHHCCCCEEEEE-------CCCCCCCCCCCHHHH-HHHHHCCCCEEEEECCCCC
Q ss_conf             79999407886----15289999999997699479980-------787433668897898-8742026868999648876
Q gi|254780901|r   94 KIMIFGDYDVD----GAASVALMMRFLSHCSVNANMYI-------PDRIVDGYGPNPSLM-EKFINEGAQLIITVDCGST  161 (600)
Q Consensus        94 kI~I~gDyD~D----Gitstail~~~L~~~g~~v~~~I-------P~R~~eGYGl~~~~i-~~~~~~g~~LiItvD~Gi~  161 (600)
                      +|.|..|--.+    -+.-+--|.+.|+..|..+.|+-       ||...+|.+...-.- +.+++...+++||=+-|++
T Consensus         2 ~V~i~~Dgg~~iGmGHV~R~l~LA~~l~k~~~~~~fl~k~~~e~~~~~~~~~f~~~~~~~~n~ik~~k~d~lI~Dsygl~   81 (318)
T COG3980           2 KVLIRCDGGLEIGMGHVMRTLTLARELEKRGFACLFLTKQDIEAIIHKVYEGFKVLEGRGNNLIKEEKFDLLIFDSYGLN   81 (318)
T ss_pred             CEEEEECCCCCCCCCHHHHHHHHHHHHHHCCCEEEEECCCCHHHHHHHHHHHCCCEEEECCCCCCCCCCCEEEEECCCCC
T ss_conf             57999268755575134559999999985174688840662564215666510430023364100366778999426888


Q ss_pred             CHHHHHHHHHCCCCEEEECCCCCCCCCCCCEEEECCCCCCCCC----CCC--CHHHHHH
Q ss_conf             2345555541798279961544765556725652378888643----344--3047889
Q gi|254780901|r  162 SYDALQYATNQGIDVIVIDHHQVKSEEIPAYALVNPNRLDDLS----GQG--HLCAAGV  214 (600)
Q Consensus       162 ~~e~i~~a~~~GidvIVtDHH~~~~~~p~a~aivNP~~~~~~~----p~~--~l~gaGv  214 (600)
                      +-..=....+.|-..++.|--.++.-- ..+.+|||.+.+..|    |++  .++|.+-
T Consensus        82 ~dd~k~ik~e~~~k~l~fDd~~~~~~~-d~d~ivN~~~~a~~~y~~v~~k~~~~lGp~y  139 (318)
T COG3980          82 ADDFKLIKEEAGSKILIFDDENAKSFK-DNDLIVNAILNANDYYGLVPNKTRYYLGPGY  139 (318)
T ss_pred             HHHHHHHHHHHCCCEEEECCCCCCCHH-HHHHHHHHHHCCHHHCCCCCCCEEEEECCCC
T ss_conf             789999889738817996477764225-6673545553511220536766379965871


No 90 
>PRK01999 consensus
Probab=81.12  E-value=2.9  Score=22.00  Aligned_cols=76  Identities=16%  Similarity=0.235  Sum_probs=48.2

Q ss_pred             HHHHHHCCCCEEEEEC--CCCCHHHHHHHHHHHHHHCCCC-EEEEECC--------CCCCCCCCCHHHHHHHHH-CCCCE
Q ss_conf             9999977997999940--7886152899999999976994-7998078--------743366889789887420-26868
Q gi|254780901|r   85 IVQAIYNSEKIMIFGD--YDVDGAASVALMMRFLSHCSVN-ANMYIPD--------RIVDGYGPNPSLMEKFIN-EGAQL  152 (600)
Q Consensus        85 i~~ai~~~ekI~I~gD--yD~DGitstail~~~L~~~g~~-v~~~IP~--------R~~eGYGl~~~~i~~~~~-~g~~L  152 (600)
                      +.+.++ ++.+.|+-.  -+.|.+.-..+|..++++.|++ +...+|-        ++..|--++...+-++.+ .|++-
T Consensus        46 i~~~vr-g~dV~ivqs~~p~~d~lmELll~~dA~r~~~A~~It~ViPY~~YaRQDr~~~~~e~isak~va~lL~~~G~d~  124 (311)
T PRK01999         46 YEESIR-GADVFLVQSTFPNSDNLMELLLMIDAAKRASARSITAVIPYFGWARQDRKDKPRVSIGAKLVADLLSVAGIDR  124 (311)
T ss_pred             ECCCCC-CCEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCEEHHHHHHHHHCCCCCE
T ss_conf             178767-9838998899998168999999998898658863899625544333766568998676777443430157865


Q ss_pred             EEEECCCCC
Q ss_conf             999648876
Q gi|254780901|r  153 IITVDCGST  161 (600)
Q Consensus       153 iItvD~Gi~  161 (600)
                      +||+|--..
T Consensus       125 vitvDlH~~  133 (311)
T PRK01999        125 LITMDLHAD  133 (311)
T ss_pred             EEEEECCCH
T ss_conf             899826838


No 91 
>cd06342 PBP1_ABC_LIVBP_like Type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine). This subgroup includes the type I periplasmic ligand-binding domain of ABC (Atpase Binding Cassette)-type active transport systems that are involved in the transport of all three branched chain aliphatic amino acids (leucine, isoleucine and valine). This subgroup also includes a leucine-specific binding protein (or LivK), which is very similar in sequence and structure to leucine-isoleucine-valine binding protein (LIVBP). ABC-type active transport systems are transmembrane proteins that function in the transport of diverse sets of substrates across extra- and intracellular membranes, including carbohydrates, amino acids, inorganic ions, dipeptides and oligopeptides, metabolic products, lipids and sterols, and heme, to name a few.
Probab=80.28  E-value=4.7  Score=20.37  Aligned_cols=36  Identities=17%  Similarity=0.245  Sum_probs=13.3

Q ss_pred             HHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEE
Q ss_conf             887420268689996488762345555541798279
Q gi|254780901|r  142 MEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVI  177 (600)
Q Consensus       142 i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvI  177 (600)
                      .+++.++++..||-.-|...+......+.+.|+-+|
T Consensus        59 a~~li~~~v~aiiG~~~s~~~~a~~~~~~~~~vp~i   94 (334)
T cd06342          59 AQKLVDDGVVGVVGHLNSGVTIPASPIYADAGIVMI   94 (334)
T ss_pred             HHHHHHCCCCEEECCCCHHHHHHHHHHHHHHCCEEE
T ss_conf             999997698488646647878875578997397030


No 92 
>PRK00934 ribose-phosphate pyrophosphokinase; Provisional
Probab=80.13  E-value=4.2  Score=20.77  Aligned_cols=74  Identities=19%  Similarity=0.261  Sum_probs=52.6

Q ss_pred             HHHHCCCCEEEEEC-CCC-CHHHHHHHHHHHHHHCCCC-EEEEECC--------CCCCCCCCCHHHHHHHHHCCCCEEEE
Q ss_conf             99977997999940-788-6152899999999976994-7998078--------74336688978988742026868999
Q gi|254780901|r   87 QAIYNSEKIMIFGD-YDV-DGAASVALMMRFLSHCSVN-ANMYIPD--------RIVDGYGPNPSLMEKFINEGAQLIIT  155 (600)
Q Consensus        87 ~ai~~~ekI~I~gD-yD~-DGitstail~~~L~~~g~~-v~~~IP~--------R~~eGYGl~~~~i~~~~~~g~~LiIt  155 (600)
                      +.+. ++.+.|... +.+ |.+.-.-+|..+++..|++ +...+|-        |+..|--++...+.++.+.+++-+||
T Consensus        42 ~~vr-g~dV~i~~~~~~~nd~lmELll~i~A~r~a~A~~It~ViPY~~YsRQDr~~~~ge~isak~va~ll~~~~d~vit  120 (286)
T PRK00934         42 EELG-GEDIVIISTQYPQDENLIELILLLDALRDEGVKSITLVAPYLAYARQDRRFKEGEPISIKALAKVYSSYYDEIIT  120 (286)
T ss_pred             CCCC-CCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCEEEE
T ss_conf             8779-986999918999847999999999999875897389983465533464346899865089999999753174699


Q ss_pred             ECCCCC
Q ss_conf             648876
Q gi|254780901|r  156 VDCGST  161 (600)
Q Consensus       156 vD~Gi~  161 (600)
                      +|--..
T Consensus       121 vDlH~~  126 (286)
T PRK00934        121 INIHEE  126 (286)
T ss_pred             EECCHH
T ss_conf             947887


No 93 
>PRK08341 amidophosphoribosyltransferase; Provisional
Probab=79.87  E-value=4.8  Score=20.27  Aligned_cols=36  Identities=25%  Similarity=0.201  Sum_probs=19.5

Q ss_pred             CCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCC
Q ss_conf             99799994078861528999999999769947998078743366889
Q gi|254780901|r   92 SEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPN  138 (600)
Q Consensus        92 ~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~  138 (600)
                      +|.=.|+|=|--|   +...++..|..+        -||=+|+.|+.
T Consensus         2 ~eeCGIfGv~s~d---~~~~~~~GL~~L--------QHRGqesaGIa   37 (442)
T PRK08341          2 REKCGIFAAYSEN---APKKAYYGLIAL--------QHRGQEGAGIS   37 (442)
T ss_pred             CCCCEEEEEECCC---CHHHHHHHHHHH--------HCCCCCEEEEE
T ss_conf             7475389998896---289999999986--------16773410499


No 94 
>COG1023 Gnd Predicted 6-phosphogluconate dehydrogenase [Carbohydrate transport and metabolism]
Probab=79.71  E-value=4.4  Score=20.58  Aligned_cols=67  Identities=19%  Similarity=0.443  Sum_probs=39.7

Q ss_pred             CHHHHHHHHHHHHHHCCCC--EEEEECCCCCCCCCCCHHHHHHHHHC--CCCEEEEECCCCCCHHH-HH---HHHHCCCC
Q ss_conf             6152899999999976994--79980787433668897898874202--68689996488762345-55---55417982
Q gi|254780901|r  104 DGAASVALMMRFLSHCSVN--ANMYIPDRIVDGYGPNPSLMEKFINE--GAQLIITVDCGSTSYDA-LQ---YATNQGID  175 (600)
Q Consensus       104 DGitstail~~~L~~~g~~--v~~~IP~R~~eGYGl~~~~i~~~~~~--g~~LiItvD~Gi~~~e~-i~---~a~~~Gid  175 (600)
                      +|+|.++-|.+++..+++.  |-..+|.-  +   +...+++++...  .-+.||  |-|-|.+.. +.   .+++.||.
T Consensus        42 ~ga~~a~sl~el~~~L~~pr~vWlMvPag--~---it~~vi~~la~~L~~GDivI--DGGNS~y~Ds~rr~~~l~~kgi~  114 (300)
T COG1023          42 EGATGAASLDELVAKLSAPRIVWLMVPAG--D---ITDAVIDDLAPLLSAGDIVI--DGGNSNYKDSLRRAKLLAEKGIH  114 (300)
T ss_pred             CCCCCCCCHHHHHHHCCCCCEEEEECCCC--C---CHHHHHHHHHHHCCCCCEEE--ECCCCCHHHHHHHHHHHHHCCCE
T ss_conf             57754367999997469874799973377--7---36899999885367888898--78863257789999988765971


Q ss_pred             EE
Q ss_conf             79
Q gi|254780901|r  176 VI  177 (600)
Q Consensus       176 vI  177 (600)
                      .+
T Consensus       115 fl  116 (300)
T COG1023         115 FL  116 (300)
T ss_pred             EE
T ss_conf             78


No 95 
>cd06302 PBP1_LsrB_Quorum_Sensing Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs. Periplasmic binding domain of autoinducer-2 (AI-2) receptor LsrB from Salmonella typhimurium and its close homologs from other bacteria. The members of this group are homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transporters of many sugar based solutes in bacteria and archaea and that are a member of the type I periplasmic binding protein superfamily.  LsrB binds a chemically distinct form of the AI-2 signal that lacks boron, in contrast to the Vibrio harveyi AI-2 signaling molecule that has an unusual furanosyl borate diester. Hence, many bacteria coordinate their gene expression according to the local density of their population by producing species specific AI-2. This process of quorum sensing allows LsrB to function as a periplasmic AI-2 binding p
Probab=79.63  E-value=4.7  Score=20.36  Aligned_cols=64  Identities=22%  Similarity=0.240  Sum_probs=41.6

Q ss_pred             HHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCC-CHHHHHHHHHCCCCEEEECC
Q ss_conf             9976994799807874336688978988742026868999648876-23455555417982799615
Q gi|254780901|r  116 LSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGST-SYDALQYATNQGIDVIVIDH  181 (600)
Q Consensus       116 L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~-~~e~i~~a~~~GidvIVtDH  181 (600)
                      -+.+|.++.|.-|...+  -.-..+.|+.++.+|++.||..-.-.. ..+.++.|++.||.||..|-
T Consensus        25 A~e~G~~v~~~~~~~~D--~~~Q~~~ie~~Ia~gvDaIii~p~d~~a~~~~i~~A~~aGIpVv~~Ds   89 (298)
T cd06302          25 AKELGVDAIYVGPTTAD--AAGQVQIIEDLIAQGVDAIAVVPNDPDALEPVLKKAREAGIKVVTHDS   89 (298)
T ss_pred             HHHHCCEEEEECCCCCC--HHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHCCCEEEEECC
T ss_conf             99979999998899899--999999999999739988999068778889999999867986998268


No 96 
>PRK13530 arsenate reductase; Provisional
Probab=79.61  E-value=4.9  Score=20.21  Aligned_cols=55  Identities=16%  Similarity=0.267  Sum_probs=36.0

Q ss_pred             CCCEEEEECCCCCHHHHHHHHHHHHH-H-CCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCE
Q ss_conf             99799994078861528999999999-7-6994799807874336688978988742026868
Q gi|254780901|r   92 SEKIMIFGDYDVDGAASVALMMRFLS-H-CSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQL  152 (600)
Q Consensus        92 ~ekI~I~gDyD~DGitstail~~~L~-~-~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~L  152 (600)
                      +++|+..    |-|=++-+.|.++|- . .|..+..+-  --.++.|+|+.+++-+.+.|.++
T Consensus         3 kk~VLFv----Ct~Ns~RSqmAEal~~~~~~~~~~v~S--AG~~~~~v~p~ai~vm~e~Gidi   59 (133)
T PRK13530          3 KKTIYFL----CTGNSCRSQMAEGWGKQYLGDEWNVYS--AGIEAHGVNPNAIKAMKEVGIDI   59 (133)
T ss_pred             CCEEEEE----ECCCCHHHHHHHHHHHHHCCCCEEEEE--CCCCCCCCCHHHHHHHHHCCCCC
T ss_conf             8879999----599627889999999986589669980--67787786989999999869165


No 97 
>PRK13371 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Provisional
Probab=79.59  E-value=4.9  Score=20.21  Aligned_cols=141  Identities=11%  Similarity=0.163  Sum_probs=90.9

Q ss_pred             HHHHHHCCCHHHHHHHHHCCC-CHHHHHHHCCCCHHHCCCCHHHC-CCHHHHHHHHHHHHHC--CCCEEEEECCCCCHHH
Q ss_conf             999881999999999996788-97898866196677718995561-4879999999999977--9979999407886152
Q gi|254780901|r   32 AITQKHAIPDIVARVLVNRNV-SIDYAKDFLNPSIRLLMPDPLIL-TDCDKAARRIVQAIYN--SEKIMIFGDYDVDGAA  107 (600)
Q Consensus        32 ~l~~~~~~~~~~a~iL~~Rgi-~~~~~~~fL~p~l~~l~~dP~~l-~dm~~A~~ri~~ai~~--~ekI~I~gDyD~DGit  107 (600)
                      .+.+.| -|+++.++=.|-.. +...    +.-.|    ...|.| -+.++|++...+|++.  +++|.+.|+     |-
T Consensus        20 ~~~~~y-~s~~i~~~~~~~~~~~~g~----~~i~L----A~~~GFC~GVeRAI~ia~ea~~~~p~~~Iy~~ge-----II   85 (392)
T PRK13371         20 ALESAY-QSSLIQSIRDNGYVLQRGD----VTIKL----AEAFGFCWGVERAVAMAYETRRHFPDERIWITNE-----II   85 (392)
T ss_pred             HHHHHH-HHHHHHHHHHCCCEEEECC----EEEEE----HHHCCCCCCHHHHHHHHHHHHHHCCCCCEEEECC-----CC
T ss_conf             999888-7899999997497675577----79996----6546875358999999999998689997897178-----74


Q ss_pred             HHHHHHHHHHHCCCCEEEEE-----CCCCCC-------CCCCCHHHHHHHHHCCCCEEEEECCCC--CCHHHHHHHHHCC
Q ss_conf             89999999997699479980-----787433-------668897898874202686899964887--6234555554179
Q gi|254780901|r  108 SVALMMRFLSHCSVNANMYI-----PDRIVD-------GYGPNPSLMEKFINEGAQLIITVDCGS--TSYDALQYATNQG  173 (600)
Q Consensus       108 stail~~~L~~~g~~v~~~I-----P~R~~e-------GYGl~~~~i~~~~~~g~~LiItvD~Gi--~~~e~i~~a~~~G  173 (600)
                      ----..+-|+..|+.+..-.     .+...+       -||.+++.++.+.+.|..++ -.-|.-  .-+..++...+.|
T Consensus        86 HNp~Vv~~L~~~Gv~~i~~~~~~kd~~~v~~gdvVIi~AHGvs~~v~~~l~~kgl~iv-DATCP~V~KV~~~v~k~~k~g  164 (392)
T PRK13371         86 HNPSVNQHLREMGVKFIPVEQGVKDFSVVTPGDVVILPAFGATVQEMQLLHEKGCHIV-DTTCPWVSKVWNTVEKHKKHG  164 (392)
T ss_pred             CCHHHHHHHHHCCCEEEECCCCCCCCCCCCCCCEEEEECCCCCHHHHHHHHHCCCEEE-ECCCCCCHHHHHHHHHHHHCC
T ss_conf             6979999999779999624566663200899998999699999789999998899799-689836199999999999689


Q ss_pred             CCEEEECCCCCCCC
Q ss_conf             82799615447655
Q gi|254780901|r  174 IDVIVIDHHQVKSE  187 (600)
Q Consensus       174 idvIVtDHH~~~~~  187 (600)
                      ..+||.-|+.-|+.
T Consensus       165 y~iII~G~~~HpEv  178 (392)
T PRK13371        165 FTSIIHGKYKHEET  178 (392)
T ss_pred             CEEEEECCCCCCCE
T ss_conf             85999778898715


No 98 
>PRK09454 ugpQ cytoplasmic glycerophosphodiester phosphodiesterase; Provisional
Probab=79.46  E-value=4.6  Score=20.43  Aligned_cols=28  Identities=18%  Similarity=0.226  Sum_probs=20.1

Q ss_pred             CHHHHHHHHHCCCCEEEECCCCCCCCCC
Q ss_conf             2345555541798279961544765556
Q gi|254780901|r  162 SYDALQYATNQGIDVIVIDHHQVKSEEI  189 (600)
Q Consensus       162 ~~e~i~~a~~~GidvIVtDHH~~~~~~p  189 (600)
                      ..++.+.|.++|.|.|=+|=|.-.+..|
T Consensus        24 Tl~Af~~A~~~G~d~iE~DV~lTkDg~~   51 (249)
T PRK09454         24 TLAAIDVGARYGHKMIEFDAKLSADGVI   51 (249)
T ss_pred             HHHHHHHHHHCCCCEEEEEEEECCCCCE
T ss_conf             4999999998499999998569689999


No 99 
>TIGR01326 OAH_OAS_sulfhy O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase; InterPro: IPR006235   This family of sequences is a distinct clade of the Cys/Met metabolism pyridoxal phosphate-dependent enzyme superfamily. Members include examples of OAH/OAS sulfhydrylase, an enzyme with activity both as O-acetylhomoserine sulfhydrylase (OAH, 2.5.1.49 from EC) and O-acetylserine sulfhydrylase (OAS, 2.5.1.47 from EC). An alternate name for OAH sulfhydrylase is homocysteine synthase.; GO: 0016765 transferase activity transferring alkyl or aryl (other than methyl) groups, 0006520 amino acid metabolic process.
Probab=79.43  E-value=5  Score=20.17  Aligned_cols=248  Identities=17%  Similarity=0.216  Sum_probs=130.5

Q ss_pred             CHHHHHHHHHHHHHCCCCEE----EEECCCCCHHHHH-HHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCC
Q ss_conf             87999999999997799799----9940788615289-999999997699479980787433668897898874202686
Q gi|254780901|r   77 DCDKAARRIVQAIYNSEKIM----IFGDYDVDGAASV-ALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQ  151 (600)
Q Consensus        77 dm~~A~~ri~~ai~~~ekI~----I~gDyD~DGitst-ail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~  151 (600)
                      +|..-.-=|..-...+..|+    +||        +| .++.-.|++||++|.+.=++-       .++.+++++.++++
T Consensus        81 G~AA~~~Ailnla~AGDnIVsS~~LYG--------GTynLF~~TlkrlGIevrFvd~dd-------~pe~~~k~id~nTK  145 (434)
T TIGR01326        81 GQAAITYAILNLAQAGDNIVSSSYLYG--------GTYNLFKHTLKRLGIEVRFVDGDD-------DPEELEKAIDENTK  145 (434)
T ss_pred             HHHHHHHHHHHHHHCCCCEEECCCCCC--------HHHHHHHHHHHHCCEEEEEECCCC-------CHHHHHHHCCCCCE
T ss_conf             579999999999726982698064442--------257899995554481488727888-------87899976066751


Q ss_pred             EEEE-----ECCCCCCHHHHH-HHHHC--CCCEEEECCCCCCCCCCCC-EEEECCCCCCCC----CCCCCHHHHHHHHHH
Q ss_conf             8999-----648876234555-55417--9827996154476555672-565237888864----334430478899999
Q gi|254780901|r  152 LIIT-----VDCGSTSYDALQ-YATNQ--GIDVIVIDHHQVKSEEIPA-YALVNPNRLDDL----SGQGHLCAAGVVFLV  218 (600)
Q Consensus       152 LiIt-----vD~Gi~~~e~i~-~a~~~--GidvIVtDHH~~~~~~p~a-~aivNP~~~~~~----~p~~~l~gaGvaf~l  218 (600)
                      .+-.     ...=+-++|+|. .|++.  ||-+|      +.++..-+ | +|.|=.+|-+    +--|+|.|=|.|-  
T Consensus       146 Avf~EtIgNP~~~v~Die~~a~~Ah~~PhgvPli------VDNT~atpGY-L~rPi~hGADIVvhSaTK~iGGHG~ai--  216 (434)
T TIGR01326       146 AVFAETIGNPALNVPDIEAVAEVAHAHPHGVPLI------VDNTFATPGY-LCRPIDHGADIVVHSATKYIGGHGTAI--  216 (434)
T ss_pred             EEEEECCCCCCCCCCCHHHHHHHHHHCCCCCEEE------EECCCCCCCC-CCCHHHCCCCEEEEEECCCCCCCEEEE--
T ss_conf             8984012387767678589999998678983488------7478687641-006456498679961001012631465--


Q ss_pred             HHHHHHHHCCCCCC-CCHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHH--HHHCCCCCCCHH
Q ss_conf             99999970214887-640779999999877542011114441189999878877516887435789--870888642423
Q gi|254780901|r  219 LVLIYRILRQDNKV-PLNFDLLSLLDLVALATVCDVVPLIGLNRAYVVKGLMVARRQGNPGLKALI--ERVNISSPITAE  295 (600)
Q Consensus       219 ~~al~~~l~~~~~~-~~~~~l~~~ldlvaiGTvaD~vpL~~eNR~lvk~GL~~l~~~~~~gl~~L~--~~~~~~~~i~~~  295 (600)
                          --.+-+.+++ +|..+-.                     |      ...|+. +.|+..=|.  +..+--.++-..
T Consensus       217 ----GG~ivD~G~FndW~~~~g---------------------k------FP~f~~-PdpsYHGl~f~E~~g~~~~~G~~  264 (434)
T TIGR01326       217 ----GGVIVDGGKFNDWANNPG---------------------K------FPLFTT-PDPSYHGLVFTETFGEFEGLGLG  264 (434)
T ss_pred             ----EEEEEECCCCCCCCCCCC---------------------C------CCCCCC-CCCCCCCCEEEECCCCCCCCCCC
T ss_conf             ----047882675563014787---------------------4------777888-88865871265315575777850


Q ss_pred             HHHHHHHHHCCHHHHHCCCCCCCEEE----ECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEE
Q ss_conf             45666774306233312122221002----03425899999999998999999999999999999987521124347502
Q gi|254780901|r  296 NLGYMIGPSINAGGRIGESNLGSRLL----ISDDSQELEMLAMKLDVLNQNRRLMESAMLEQAEAKVLTQCDDIQQASVI  371 (600)
Q Consensus       296 di~f~iaPrINAaGRl~~a~~av~lL----~~~d~~~a~~la~~L~~lN~~Rk~~e~~i~~~a~~~~~~~~~~~~~~~~i  371 (600)
                      .++|.+-=|             |++|    -+-+|.-|..+.+=||.|==+=.+-.+.-.+-|+     .++  ..+.|-
T Consensus       265 ~~Afi~~~R-------------v~~LRD~Gaa~sPFnAFLllQGLETLsLR~ERH~~NA~kVA~-----fL~--~Hp~V~  324 (434)
T TIGR01326       265 NIAFIVKAR-------------VQLLRDLGAALSPFNAFLLLQGLETLSLRMERHVENALKVAE-----FLE--AHPKVA  324 (434)
T ss_pred             CHHEEEEEE-------------EEECHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HHH--CCCCCC
T ss_conf             000034446-------------742210033401789999998666787678888899999999-----972--788445


Q ss_pred             EEECCCCCHHHHHHHHHHHHHHHH---CEEEEEEEC
Q ss_conf             620578581222222789988420---107998863
Q gi|254780901|r  372 VVEGDRWHPGIVGLLAARLKEKFG---RPSFAISFE  404 (600)
Q Consensus       372 vv~~~~wh~GViGIVAsrL~e~y~---kP~iv~s~~  404 (600)
                      .|.-|    |+--=.--.++++|-   ++.-|+|..
T Consensus       325 wV~YP----GL~s~~~h~lAkkYl~~G~~G~vLsFe  356 (434)
T TIGR01326       325 WVNYP----GLASHPHHALAKKYLPKGLFGAVLSFE  356 (434)
T ss_pred             CCCCC----CCCCCHHHHHHHHHHCCCCEEEEEECC
T ss_conf             13488----878875378899874179426787413


No 100
>TIGR03572 WbuZ glycosyl amidation-associated protein WbuZ. This clade of sequences is highly similar to the HisF protein, but generally represents the second HisF homolog in the genome where the other is an authentic HisF observed in the context of a complete histidine biosynthesis operon. The similarity between these WbuZ sequences and true HisFs is such that often the closest match by BLAST of a WbuZ is a HisF. Only by making a multiple sequence alignment is the homology relationship among the WbuZ sequences made apparent. WbuZ genes are invariably observed in the presence of a homolog of the HisH protein (designated WbuY) and a proposed N-acetyl sugar amidotransferase designated in WbuX in E. coli, IfnA in P. aeriginosa and PseA in C. jejuni. Similarly, this trio of genes is invariably found in the context of saccharide biosynthesis loci. It has been shown that the WbuYZ homologs are not essential components of the activity expressed by WbuX, leading to the proposal that these to pr
Probab=79.43  E-value=5  Score=20.17  Aligned_cols=73  Identities=18%  Similarity=0.208  Sum_probs=50.6

Q ss_pred             HHHHHHHHCCCCEEEEE-CCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCC
Q ss_conf             99999997699479980-787433668897898874202686899964887623455555417982799615447
Q gi|254780901|r  111 LMMRFLSHCSVNANMYI-PDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQV  184 (600)
Q Consensus       111 il~~~L~~~g~~v~~~I-P~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~~  184 (600)
                      -+.+.+...|++--+.+ =++-.+|-..|.+.|+++.++ +.+=|++.-||.+.+.++.+-+.|.|-||+--...
T Consensus        34 ~~ak~~~~~g~d~lhivDld~a~~~~~~n~~~I~~i~~~-~~ipi~vGGGIrs~e~~~~ll~~GadkViigs~a~  107 (232)
T TIGR03572        34 NAARIYNAKGADELIVLDIDASKRGREPLFELISNLAEE-CFMPLTVGGGIRSLEDAKKLLSLGADKVSINTAAL  107 (232)
T ss_pred             HHHHHHHHCCCCEEEEEECCCCCCCCCCHHHHHHHHHHH-CCCCEEEEECEEEHHHHHHHHHCCCCEEEECHHHH
T ss_conf             999999986999999996876434882179999999997-29858997133038999999976996899345452


No 101
>COG0683 LivK ABC-type branched-chain amino acid transport systems, periplasmic component [Amino acid transport and metabolism]
Probab=79.33  E-value=5  Score=20.15  Aligned_cols=101  Identities=19%  Similarity=0.201  Sum_probs=66.8

Q ss_pred             HHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEE---EECCCCCCCCCCCHHHHHHHHHCCCCEEE
Q ss_conf             799999999999779979999407886152899999999976994799---80787433668897898874202686899
Q gi|254780901|r   78 CDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANM---YIPDRIVDGYGPNPSLMEKFINEGAQLII  154 (600)
Q Consensus        78 m~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~---~IP~R~~eGYGl~~~~i~~~~~~g~~LiI  154 (600)
                      +..+++.+.+.... +++.|+++-|+-|-.-...+.+.|+..|.++..   |.|.  . ..  -...+.+++..+++.|+
T Consensus       135 ~~~~~~~l~~~~~~-k~v~ii~~~~~yg~~~~~~~~~~l~~~G~~~~~~~~~~~~--~-~~--~~~~v~~i~~~~~d~v~  208 (366)
T COG0683         135 AAAAADYLVKKGGK-KRVAIIGDDYAYGEGLADAFKAALKALGGEVVVEEVYAPG--D-TD--FSALVAKIKAAGPDAVL  208 (366)
T ss_pred             HHHHHHHHHHHCCC-CEEEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCC--C-CC--HHHHHHHHHHCCCCEEE
T ss_conf             99999999973788-5799994798777899999999999659933234565878--8-79--99999998756999999


Q ss_pred             EECCCCCCHHHHHHHHHCCCCEEEECCCCC
Q ss_conf             964887623455555417982799615447
Q gi|254780901|r  155 TVDCGSTSYDALQYATNQGIDVIVIDHHQV  184 (600)
Q Consensus       155 tvD~Gi~~~e~i~~a~~~GidvIVtDHH~~  184 (600)
                      ..-.|.....-++.++++|++..+.=....
T Consensus       209 ~~~~~~~~~~~~r~~~~~G~~~~~~~~~~~  238 (366)
T COG0683         209 VGGYGPDAALFLRQAREQGLKAKLIGGDGA  238 (366)
T ss_pred             ECCCCCCHHHHHHHHHHCCCCCEEEECCCC
T ss_conf             878876369999999976887504413666


No 102
>cd06338 PBP1_ABC_ligand_binding_like_5 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT); however their ligand specificity has not been determined experimentally.
Probab=79.24  E-value=5  Score=20.13  Aligned_cols=79  Identities=11%  Similarity=0.050  Sum_probs=35.5

Q ss_pred             CCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEE--CCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHH
Q ss_conf             97999940788615289999999997699479980--7874336688978988742026868999648876234555554
Q gi|254780901|r   93 EKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYI--PDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYAT  170 (600)
Q Consensus        93 ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~I--P~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~  170 (600)
                      +++.|+.+-|.-|......+.+.++..|.++....  |.-.+|   + ...+.+++..+++.|+..-.+.....-+..++
T Consensus       142 k~vaii~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~~D---f-~~~l~~i~~~~pd~i~~~~~~~~~~~~~~q~~  217 (345)
T cd06338         142 KKVAILYADDPFSQDVAEGAREKAEAAGLEVVYDETYPPGTAD---L-SPLISKAKAAGPDAVVVAGHFPDAVLLVRQMK  217 (345)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHCCCEEEEEEEECCCCCC---H-HHHHHHHHHCCCCEEEECCCCCHHHHHHHHHH
T ss_conf             6899996486303689999999998659749999971798765---8-99999998679999999077715999999999


Q ss_pred             HCCCC
Q ss_conf             17982
Q gi|254780901|r  171 NQGID  175 (600)
Q Consensus       171 ~~Gid  175 (600)
                      +.|++
T Consensus       218 ~~G~~  222 (345)
T cd06338         218 ELGYN  222 (345)
T ss_pred             HCCCC
T ss_conf             76999


No 103
>cd01538 PBP1_ABC_xylose_binding Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily. Periplasmic xylose-binding component of the ABC-type transport systems that belong to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein (PBP1) superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, the periplasmic xylose-binding protein is homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR.
Probab=78.88  E-value=5.2  Score=20.05  Aligned_cols=67  Identities=18%  Similarity=0.216  Sum_probs=41.8

Q ss_pred             HHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCC-CCCHHHHHHHHHCCCCEEEECCCCC
Q ss_conf             999769947998078743366889789887420268689996488-7623455555417982799615447
Q gi|254780901|r  115 FLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCG-STSYDALQYATNQGIDVIVIDHHQV  184 (600)
Q Consensus       115 ~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~G-i~~~e~i~~a~~~GidvIVtDHH~~  184 (600)
                      +.+.+|.++.+.=++.-   ..-....|+.+..++++.||..=+- .+..+.++.|++.||.||..|.-.+
T Consensus        24 ~A~e~G~~v~~~~~~~d---~~~Q~~~i~~lia~~vD~Iii~p~d~~a~~~~l~~a~~agIPVV~~D~~i~   91 (288)
T cd01538          24 ALKELGAEVIVQNANGD---PAKQISQIENMIAKGVDVLVIAPVDGEALASAVEKAADAGIPVIAYDRLIL   91 (288)
T ss_pred             HHHHCCCEEEEECCCCC---HHHHHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHCCCEEEEECCCCC
T ss_conf             99976998999718999---999999999999849989998677534439999999975999999877678


No 104
>PRK13937 phosphoheptose isomerase; Provisional
Probab=78.81  E-value=5.2  Score=20.04  Aligned_cols=104  Identities=21%  Similarity=0.349  Sum_probs=57.7

Q ss_pred             HCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHH--HHHHHHHCCC-----CEEEEECCC-----CCCCCCCCHHH
Q ss_conf             61487999999999997799799994078861528999--9999997699-----479980787-----43366889789
Q gi|254780901|r   74 ILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVAL--MMRFLSHCSV-----NANMYIPDR-----IVDGYGPNPSL  141 (600)
Q Consensus        74 ~l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstai--l~~~L~~~g~-----~v~~~IP~R-----~~eGYGl~~~~  141 (600)
                      ....++++++.|.+++.++.||.++|   --|-.++|-  ..+++..+..     .+...-.+-     +..-||...-.
T Consensus        24 ~~~~I~~~a~~i~~~~~~g~kI~~~G---NGGSaa~A~Hfa~dl~~~~~~~r~~lpaisL~~d~~~lTA~~ND~g~~~if  100 (192)
T PRK13937         24 LLAAIAKIAEALIEALASGGKLLLCG---NGGSAADAQHIAAELVGRYKKERPALPAIALTTDTSALTAIGNDYGYERVF  100 (192)
T ss_pred             HHHHHHHHHHHHHHHHHCCCEEEEEE---CCHHHHHHHHHHHHHHCCCCCCCCCCCEEECCCCHHHHHHHHCCCCHHHHH
T ss_conf             49999999999999998799899996---863188899999999641355789853577678828777642778789999


Q ss_pred             HHH---HHHCCCCEEEEEC-CCCC--CHHHHHHHHHCCCCEEEECC
Q ss_conf             887---4202686899964-8876--23455555417982799615
Q gi|254780901|r  142 MEK---FINEGAQLIITVD-CGST--SYDALQYATNQGIDVIVIDH  181 (600)
Q Consensus       142 i~~---~~~~g~~LiItvD-~Gi~--~~e~i~~a~~~GidvIVtDH  181 (600)
                      -+.   +...| |++|..- .|-|  =.+++++|+++|+.||..==
T Consensus       101 ~~ql~~~~~~g-Dili~iS~SGnS~Nii~A~~~A~~~g~~~i~ltG  145 (192)
T PRK13937        101 ARQVEALGRPG-DVLIGISTSGNSPNVLAALEKARELGMTTIGLTG  145 (192)
T ss_pred             HHHHHHCCCCC-CEEEEECCCCCCHHHHHHHHHHHHCCCEEEEEEC
T ss_conf             99999557889-8899977999997999999999987997999988


No 105
>COG2099 CobK Precorrin-6x reductase [Coenzyme metabolism]
Probab=78.80  E-value=3.7  Score=21.19  Aligned_cols=34  Identities=26%  Similarity=0.572  Sum_probs=13.9

Q ss_pred             CCCEEEEECCCCC--CHHHHHHHHHCCCCEEEECCC
Q ss_conf             6868999648876--234555554179827996154
Q gi|254780901|r  149 GAQLIITVDCGST--SYDALQYATNQGIDVIVIDHH  182 (600)
Q Consensus       149 g~~LiItvD~Gi~--~~e~i~~a~~~GidvIVtDHH  182 (600)
                      +++.|||=|.|-+  ..+-++.|.++||.||++.-+
T Consensus       196 ~id~vItK~SG~~Gg~~~Ki~aA~eLgi~VI~I~Rp  231 (257)
T COG2099         196 RIDVVVTKNSGGAGGTYEKIEAARELGIPVIMIERP  231 (257)
T ss_pred             CCCEEEECCCCCCCCCHHHHHHHHHCCCCEEEEECC
T ss_conf             888999826776667389899999869938999467


No 106
>COG2248 Predicted hydrolase (metallo-beta-lactamase superfamily) [General function prediction only]
Probab=78.72  E-value=5.2  Score=20.02  Aligned_cols=37  Identities=24%  Similarity=0.224  Sum_probs=19.8

Q ss_pred             CCCCHHHCCCCHHHCCCHHHHHHHHHHHHHCCCCEEE
Q ss_conf             1966777189955614879999999999977997999
Q gi|254780901|r   61 LNPSIRLLMPDPLILTDCDKAARRIVQAIYNSEKIMI   97 (600)
Q Consensus        61 L~p~l~~l~~dP~~l~dm~~A~~ri~~ai~~~ekI~I   97 (600)
                      |-|+-..|.|.|-.|.-+.++.+.|.+..+.-+-|.|
T Consensus        35 LaPkRy~LPPh~~E~erl~~~r~~i~~~ak~a~VitI   71 (304)
T COG2248          35 LAPKRYGLPPHQRELERLRQAREKIQRYAKKADVITI   71 (304)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCEEEE
T ss_conf             4853468998879999999999999999864888998


No 107
>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=78.49  E-value=4.4  Score=20.62  Aligned_cols=29  Identities=21%  Similarity=0.568  Sum_probs=23.5

Q ss_pred             CCEEEEECCCCCCHHHHHHHHHCCCCEEEECC
Q ss_conf             86899964887623455555417982799615
Q gi|254780901|r  150 AQLIITVDCGSTSYDALQYATNQGIDVIVIDH  181 (600)
Q Consensus       150 ~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDH  181 (600)
                      .+.++|+|.   ..+-++.|.+.|.|+|||-|
T Consensus        33 ~~I~~~lD~---t~~vi~~A~~~~~dlIItHH   61 (238)
T pfam01784        33 KKILVALDA---TEEVIEEAIENGADLIITHH   61 (238)
T ss_pred             CEEEEEEEC---CHHHHHHHHHCCCCEEEECC
T ss_conf             889999829---99999999977999999738


No 108
>PRK13586 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; Provisional
Probab=78.49  E-value=5.3  Score=19.97  Aligned_cols=71  Identities=14%  Similarity=0.132  Sum_probs=52.4

Q ss_pred             HHHHHHHHHCCCCEEEEE-CCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCC
Q ss_conf             999999997699479980-7874336688978988742026868999648876234555554179827996154
Q gi|254780901|r  110 ALMMRFLSHCSVNANMYI-PDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHH  182 (600)
Q Consensus       110 ail~~~L~~~g~~v~~~I-P~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH  182 (600)
                      .-+.+.+...|++--+.+ -+. .+|-+.|.+.++++.+. +.+-|++..||.+.+.++.+-+.|.+-||+--.
T Consensus        32 ~~~a~~~~~~Ga~~lhvvDLda-a~g~~~N~~~I~~i~~~-~~~piqvGGGIrs~e~~~~~l~~Ga~kViigS~  103 (231)
T PRK13586         32 LKIAEELYNEGYDSIHVVDLDA-AEGKGDNEEYIKRICKI-GFSWIQVGGGIRDVEKAERLLSYDCSAIVMSTL  103 (231)
T ss_pred             HHHHHHHHHCCCCEEEEEECCC-CCCCCCHHHHHHHHHHH-CCCCEEEECCCCCHHHHHHHHHCCCCEEEECHH
T ss_conf             9999999987999899996715-68998439999999974-598579856717699999999779988997688


No 109
>cd06319 PBP1_ABC_sugar_binding_like_10 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=78.42  E-value=5.3  Score=19.95  Aligned_cols=44  Identities=23%  Similarity=0.255  Sum_probs=31.5

Q ss_pred             HHHHHHHHHCCCCEEEEE-CCCCCCHHHHHHHHHCCCCEEEECCC
Q ss_conf             789887420268689996-48876234555554179827996154
Q gi|254780901|r  139 PSLMEKFINEGAQLIITV-DCGSTSYDALQYATNQGIDVIVIDHH  182 (600)
Q Consensus       139 ~~~i~~~~~~g~~LiItv-D~Gi~~~e~i~~a~~~GidvIVtDHH  182 (600)
                      .+.++.+...+++-||.. -......+.++.|++.||-|+..|--
T Consensus        45 ~~~i~~~i~~~vDgIii~p~~~~~~~~~~~~a~~~gIPvv~~d~~   89 (277)
T cd06319          45 LENLRTAIDKGVSGIIISPTNSSAAVTLLKLAAQAKIPVVIADIG   89 (277)
T ss_pred             HHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHCCCCEEEEECC
T ss_conf             999999996699879964777411099999999769978998658


No 110
>cd06330 PBP1_Arsenic_SBP_like Periplasmic solute-binding domain of active transport proteins. Periplasmic solute-binding domain of active transport proteins found in bacteria and Archaea that is predicted to be involved in the efflux of toxic compounds.  Members of this subgroup include proteins from Herminiimonas arsenicoxydans, which is resistant to arsenic and various heavy metals such as cadmium and zinc. Moreover, they show significant sequence similarity to the cluster of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and thus are likely to exhibit a ligand-binding mode similar to that of the amide sensor protein AmiC from Pseudomonas aeruginosa.
Probab=78.28  E-value=5.4  Score=19.92  Aligned_cols=38  Identities=16%  Similarity=0.241  Sum_probs=22.7

Q ss_pred             HHHHHH-HCCCCEEEEECCCCCCHHHHHHHHHCCCCEEE
Q ss_conf             988742-02686899964887623455555417982799
Q gi|254780901|r  141 LMEKFI-NEGAQLIITVDCGSTSYDALQYATNQGIDVIV  178 (600)
Q Consensus       141 ~i~~~~-~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIV  178 (600)
                      ..+++. ++++..||..-|...+......+.+.|+-+|.
T Consensus        58 ~a~~Li~~d~V~aiiG~~~S~~~~av~~~~~~~~ip~i~   96 (346)
T cd06330          58 EARELVENEGVDMLIGLISSGVALAVAPVAEELKVFFIA   96 (346)
T ss_pred             HHHHHHHCCCCEEEECCCCCHHHHHHHHHHHHCCCCEEE
T ss_conf             999999618966997787757789999999983985784


No 111
>cd06309 PBP1_YtfQ_like Periplasmic binding domain of ABC-type YtfQ-like transport systems. Periplasmic binding domain of ABC-type YtfQ-like transport systems. The YtfQ protein from Escherichia coli is up-regulated under glucose-limited conditions and shares homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their ligand specificity is not determined experimentally.
Probab=78.20  E-value=5.4  Score=19.91  Aligned_cols=46  Identities=30%  Similarity=0.380  Sum_probs=34.7

Q ss_pred             HHHHHHHHHCCCCEEEEECCCCCC-HHHHHHHHHCCCCEEEECCCCC
Q ss_conf             789887420268689996488762-3455555417982799615447
Q gi|254780901|r  139 PSLMEKFINEGAQLIITVDCGSTS-YDALQYATNQGIDVIVIDHHQV  184 (600)
Q Consensus       139 ~~~i~~~~~~g~~LiItvD~Gi~~-~e~i~~a~~~GidvIVtDHH~~  184 (600)
                      ...|+.+...+++-||.+-+-.++ .+.++.+++.||.||.+|+...
T Consensus        45 ~~~i~~li~~~vDgIii~p~~~~~~~~~l~~a~~agIPvV~~d~~~~   91 (273)
T cd06309          45 ISAIRSFIAQGVDVIILAPVVETGWDPVLKEAKAAGIPVILVDRGVD   91 (273)
T ss_pred             HHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHCCCCEEEECCCCC
T ss_conf             99999999759999998057654358999999974998899826776


No 112
>PRK04117 consensus
Probab=78.16  E-value=5.4  Score=19.90  Aligned_cols=74  Identities=15%  Similarity=0.275  Sum_probs=51.8

Q ss_pred             HHHCCCCEEEEE-CC-CC-CHHHHHHHHHHHHHHCCCC-EEEEECC--------CCCCCCCCCHHHHHHHHHC-CCCEEE
Q ss_conf             997799799994-07-88-6152899999999976994-7998078--------7433668897898874202-686899
Q gi|254780901|r   88 AIYNSEKIMIFG-DY-DV-DGAASVALMMRFLSHCSVN-ANMYIPD--------RIVDGYGPNPSLMEKFINE-GAQLII  154 (600)
Q Consensus        88 ai~~~ekI~I~g-Dy-D~-DGitstail~~~L~~~g~~-v~~~IP~--------R~~eGYGl~~~~i~~~~~~-g~~LiI  154 (600)
                      .+. ++.+.|+. -+ .+ |.+.-.-+|..+++..|++ +...+|-        |+..|=.++...+-++.+. |++-+|
T Consensus        47 ~vr-g~dV~ivqs~~~p~nd~lmELll~~~a~r~agA~~It~ViPY~~YsRQDr~~~~ge~isak~vA~lL~~~G~d~vi  125 (309)
T PRK04117         47 SVR-GKDVFIIQPTCAPANDNLMELLIMTDALRRSSANSITAVVPYFGYARQDRKAAPRVPITAKLVANLMQAAGIDRVV  125 (309)
T ss_pred             CCC-CCCEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCEEE
T ss_conf             778-9988999179998248899999999999874897388960355002144456999870189999888642776589


Q ss_pred             EECCCCCC
Q ss_conf             96488762
Q gi|254780901|r  155 TVDCGSTS  162 (600)
Q Consensus       155 tvD~Gi~~  162 (600)
                      |+|--...
T Consensus       126 tvDlH~~~  133 (309)
T PRK04117        126 TMDLHAGQ  133 (309)
T ss_pred             EECCCHHH
T ss_conf             96178688


No 113
>PRK13938 phosphoheptose isomerase; Provisional
Probab=78.14  E-value=5.4  Score=19.89  Aligned_cols=112  Identities=15%  Similarity=0.346  Sum_probs=61.5

Q ss_pred             CCCCHHHCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHH--HHHHHHCCCC-----EEEEECC-----CCCCCC
Q ss_conf             189955614879999999999977997999940788615289999--9999976994-----7998078-----743366
Q gi|254780901|r   68 LMPDPLILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALM--MRFLSHCSVN-----ANMYIPD-----RIVDGY  135 (600)
Q Consensus        68 l~~dP~~l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail--~~~L~~~g~~-----v~~~IP~-----R~~eGY  135 (600)
                      +..+..++..++++++.|.++++++.||.++|.   -|-.|.|--  .+++..+..+     +...-.|     -+..-|
T Consensus        21 ~~~~~~~~~~i~~~~~~i~~~~~~g~kI~~cGN---GGSaa~A~Hfa~el~~~~~~~R~~lpaiaL~~n~s~lTAiaND~   97 (196)
T PRK13938         21 ILNDRVLLEAARAIGDRLIAGYRAGARVFMCGN---GGSAADAQHFAAELTGHLIFDRPPLGAEALHANSSHLTAVANDY   97 (196)
T ss_pred             HHHCHHHHHHHHHHHHHHHHHHHCCCEEEEEEC---CHHHHHHHHHHHHHHHHCCCCCCCCCEEECCCCCHHHHHHHCCC
T ss_conf             982522099999999999999987998999968---68899999999998633357899847454478807888876247


Q ss_pred             CCCHHH---HHHHHHCCCCEEEEEC-CCCC--CHHHHHHHHHCCCCEEEECCCC
Q ss_conf             889789---8874202686899964-8876--2345555541798279961544
Q gi|254780901|r  136 GPNPSL---MEKFINEGAQLIITVD-CGST--SYDALQYATNQGIDVIVIDHHQ  183 (600)
Q Consensus       136 Gl~~~~---i~~~~~~g~~LiItvD-~Gi~--~~e~i~~a~~~GidvIVtDHH~  183 (600)
                      |...-.   ++.+.+.| |++|..- .|-|  =.+++++|+++|+.+|..=-..
T Consensus        98 gye~vF~rQl~al~~~g-DvLi~iStSGnS~NIi~A~~~Ak~~g~~~i~ltG~~  150 (196)
T PRK13938         98 DYDTVFARALEGSARPG-DTLFAISTSGNSMSVLRAAKTARELGVTVVAMTGES  150 (196)
T ss_pred             CHHHHHHHHHHHCCCCC-CEEEEECCCCCCHHHHHHHHHHHHCCCEEEEEECCC
T ss_conf             89999999999716899-989997799999999999999998799899998899


No 114
>pfam02401 LYTB LytB protein. The mevalonate-independent 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway for isoprenoid biosynthesis is essential in many eubacteria, plants, and the malaria parasite. The LytB gene is involved in the trunk line of the MEP pathway.
Probab=78.13  E-value=5.4  Score=19.89  Aligned_cols=102  Identities=18%  Similarity=0.283  Sum_probs=59.1

Q ss_pred             CCHHHHHHHHHHHHHC-CCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCC-------CCCCHHHHHHHHH
Q ss_conf             4879999999999977-9979999407886152899999999976994799807874336-------6889789887420
Q gi|254780901|r   76 TDCDKAARRIVQAIYN-SEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDG-------YGPNPSLMEKFIN  147 (600)
Q Consensus        76 ~dm~~A~~ri~~ai~~-~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eG-------YGl~~~~i~~~~~  147 (600)
                      -+..+|++...++.++ +++|.++|+     +.----..+-|+..|..+.--+. .+.+|       ||.+++..+++.+
T Consensus        11 ~GV~rAi~~a~~~~~~~~~~vy~lG~-----iVHN~~vv~~L~~~Gv~~v~~~~-~i~~g~~ViirAHGv~~~~~~~a~~   84 (280)
T pfam02401        11 AGVKRAIQIAERALQKSGGPVYVRGE-----IVHNRHVVNRLRERGAIFVEELK-EVPEGATVIFSAHGVSPEVREEAKE   84 (280)
T ss_pred             CCHHHHHHHHHHHHHHCCCCEEEECC-----CCCCHHHHHHHHHCCCEEECCCC-CCCCCCEEEEECCCCCHHHHHHHHH
T ss_conf             13999999999999876997798377-----76498999999988399813613-3787888999399999899999997


Q ss_pred             CCCCEEEEECCC--CCCHHHHHHHHHCCCCEEEECCCCC
Q ss_conf             268689996488--7623455555417982799615447
Q gi|254780901|r  148 EGAQLIITVDCG--STSYDALQYATNQGIDVIVIDHHQV  184 (600)
Q Consensus       148 ~g~~LiItvD~G--i~~~e~i~~a~~~GidvIVtDHH~~  184 (600)
                      .|..++ -.-|-  ...+..++...+.|-.+||.-|+.-
T Consensus        85 ~gl~vi-DaTCP~V~kvh~~v~~~~~~Gy~iiiiG~~~H  122 (280)
T pfam02401        85 RGLQVI-DATCPLVTKVHNAVERMAKKGYHVILIGHKNH  122 (280)
T ss_pred             CCCEEE-ECCCCCHHHHHHHHHHHHHCCCEEEEEECCCC
T ss_conf             499299-37080157999999999868987999837987


No 115
>COG0327 Uncharacterized conserved protein [Function unknown]
Probab=78.12  E-value=3.6  Score=21.24  Aligned_cols=30  Identities=20%  Similarity=0.490  Sum_probs=24.8

Q ss_pred             CCEEEEECCCCCCHHHHHHHHHCCCCEEEECCC
Q ss_conf             868999648876234555554179827996154
Q gi|254780901|r  150 AQLIITVDCGSTSYDALQYATNQGIDVIVIDHH  182 (600)
Q Consensus       150 ~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH  182 (600)
                      -+++++||+   +.+-++.|.+.|.|+||+.|=
T Consensus        37 ~kV~~avd~---t~~vi~~Ai~~~ad~ii~HHp   66 (250)
T COG0327          37 KKVAVALDA---TLAVLDEAIELGADLLIVHHP   66 (250)
T ss_pred             CEEEEHHHC---CHHHHHHHHHCCCCEEEECCC
T ss_conf             101132640---698899998658688871582


No 116
>PRK08507 prephenate dehydrogenase; Validated
Probab=77.60  E-value=5.6  Score=19.78  Aligned_cols=40  Identities=18%  Similarity=0.218  Sum_probs=21.5

Q ss_pred             CCCCCCEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1222210020342589999999999899999999999999
Q gi|254780901|r  313 ESNLGSRLLISDDSQELEMLAMKLDVLNQNRRLMESAMLE  352 (600)
Q Consensus       313 ~a~~av~lL~~~d~~~a~~la~~L~~lN~~Rk~~e~~i~~  352 (600)
                      +|.+--+++++....-...+-+..+++++-|..++..-.+
T Consensus       220 ~p~mW~dI~~~N~~~i~~~l~~f~~~L~~l~~~l~~~d~~  259 (275)
T PRK08507        220 SPLMWEDIFKQNKDNVLEAIDFFEKELEQAKELIENEDWE  259 (275)
T ss_pred             CHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHCCHH
T ss_conf             9899999999788999999999999999999999816999


No 117
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=77.48  E-value=5.6  Score=19.76  Aligned_cols=105  Identities=15%  Similarity=0.290  Sum_probs=72.0

Q ss_pred             CCHHHHHHHHHHHHHC-CCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCC-------CCCCHHHHHHHHH
Q ss_conf             4879999999999977-9979999407886152899999999976994799807874336-------6889789887420
Q gi|254780901|r   76 TDCDKAARRIVQAIYN-SEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDG-------YGPNPSLMEKFIN  147 (600)
Q Consensus        76 ~dm~~A~~ri~~ai~~-~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eG-------YGl~~~~i~~~~~  147 (600)
                      -+..+|++...++.++ +.+|..+|+     +----...+-|+..|..+.-.+.+...+|       ||.+++..+.+.+
T Consensus        13 ~GV~rAI~~a~~~~~~~~~~vytlG~-----iIHN~~Vv~~L~~~Gv~~v~~~~~~~~~~~~VIIrAHGv~p~v~~~~~~   87 (670)
T PRK00087         13 FGVKRAVDTAIETLEEGKKKIYTLGP-----LIHNNQVVEELKRKGIEPIEEIEDELNEGDTIIIRSHGVPPEVLEKLKD   87 (670)
T ss_pred             CCHHHHHHHHHHHHHHCCCCEEEECC-----CCCCHHHHHHHHHCCCEEECCCCCCCCCCCEEEEECCCCCHHHHHHHHH
T ss_conf             08899999999999852997898288-----8689799999998869991676565799799999289999899999998


Q ss_pred             CCCCEEEEECCCC--CCHHHHHHHHHCCCCEEEECCCCCCC
Q ss_conf             2686899964887--62345555541798279961544765
Q gi|254780901|r  148 EGAQLIITVDCGS--TSYDALQYATNQGIDVIVIDHHQVKS  186 (600)
Q Consensus       148 ~g~~LiItvD~Gi--~~~e~i~~a~~~GidvIVtDHH~~~~  186 (600)
                      .|..++ -.-|-.  ..+..++...+.|-.+||.-|+.-|+
T Consensus        88 ~g~~vv-DATCP~V~Kvh~~~~~~~~~Gy~iviiG~~~HpE  127 (670)
T PRK00087         88 KGLKVI-DATCPFVKNIQKLAKKYYEEGYQIVIVGDKNHPE  127 (670)
T ss_pred             CCCEEE-ECCCCCCHHHHHHHHHHHHCCCEEEEECCCCCCH
T ss_conf             799599-6788262899999999997879899987999954


No 118
>cd01979 Pchlide_reductase_N Pchlide_reductase_N: N protein of the NB protein complex of Protochlorophyllide (Pchlide)_reductase. Pchlide reductase catalyzes the reductive formation of chlorophyllide (chlide) from protochlorophyllide (pchlide) during biosynthesis of chlorophylls and bacteriochlorophylls. This group contains both the light-independent Pchlide reductase (DPOR) and light-dependent Pchlide reductase (LPOR).  Angiosperms contain only LPOR, cyanobacteria, algae and gymnosperms contain both DPOR and LPOR, primitive anoxygenic photosynthetic bacteria contain only DPOR. NB is structurally similar to the FeMo protein of nitrogenase, forming an N2B2 heterotetramer. N and B are homologous to the FeMo alpha and beta subunits respectively. Also in common with nitrogenase in vitro DPOR activity requires ATP hydrolysis and dithoionite or ferredoxin as electron donor. The NB protein complex may serve as a catalytic site for Pchlide reduction similar to MoFe for nitrogen reduction.
Probab=77.37  E-value=5.6  Score=19.77  Aligned_cols=152  Identities=15%  Similarity=0.169  Sum_probs=62.0

Q ss_pred             HHCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHH-CCC-CHHHHHHHCCCCHHHCCCCHHHCCC----HHHHH
Q ss_conf             11047887341157888988999999881999999999996-788-9789886619667771899556148----79999
Q gi|254780901|r    9 VECSISGFRWVSLLGQEGINRALAITQKHAIPDIVARVLVN-RNV-SIDYAKDFLNPSIRLLMPDPLILTD----CDKAA   82 (600)
Q Consensus         9 ~~~s~~~~rW~~~~~~~~~~~~~~l~~~~~~~~~~a~iL~~-Rgi-~~~~~~~fL~p~l~~l~~dP~~l~d----m~~A~   82 (600)
                      +=|++|+--|..++.++-.-    |.   .-|...|-+++| ||+ .-.+ .+|=...+++  .|-..+-|    +++++
T Consensus        10 ~fc~lt~i~wl~~kI~Daff----LV---vG~~tCah~~q~a~Gvmifae-pRf~ta~leE--~Dl~~~~~~~~eL~r~v   79 (396)
T cd01979          10 TFCGLACVAWLYQKIEDSFF----LV---VGTKTCAHFLQNALGVMIFAE-PRFAMAELEE--GDLSALLNDYAELDRVV   79 (396)
T ss_pred             CCCCHHHHHHHHHHHCCCCE----EE---ECCCHHHHHHHHHHCCEEECC-CCCCCCCCCC--HHHHHCCCCHHHHHHHH
T ss_conf             25523639999986331003----64---337506767664102454357-4322230462--05542369669999999


Q ss_pred             HHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHH--------HHCCCCEEEEECCC----CCCCCCCCHHH-HHHHHH--
Q ss_conf             9999999779979999407886152899999999--------97699479980787----43366889789-887420--
Q gi|254780901|r   83 RRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFL--------SHCSVNANMYIPDR----IVDGYGPNPSL-MEKFIN--  147 (600)
Q Consensus        83 ~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L--------~~~g~~v~~~IP~R----~~eGYGl~~~~-i~~~~~--  147 (600)
                      +.|.+--... .|.+||      .|-+-++..=|        ...|..|..|--+=    |+.||---..+ +..+.+  
T Consensus        80 ~~i~~~r~p~-~iFlvg------tCpseVIk~DLe~~A~rls~~~~v~Vv~vs~sGiettFTQGEDa~LaAlvp~~P~~~  152 (396)
T cd01979          80 TQIKRDRNPS-VIFLIG------SCTTEVIKMDLEGAAPRLSAEIGVPILVASASGLDYTFTQGEDTVLAALVPRCPEKP  152 (396)
T ss_pred             HHHHHHCCCC-EEEEEC------CCCHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCC
T ss_conf             9999748994-799972------585777752499998875326795599952687547576799999999986474323


Q ss_pred             -CCCCEEEEECCCCCCHHHH-HHHHHCCCCEE
Q ss_conf             -2686899964887623455-55541798279
Q gi|254780901|r  148 -EGAQLIITVDCGSTSYDAL-QYATNQGIDVI  177 (600)
Q Consensus       148 -~g~~LiItvD~Gi~~~e~i-~~a~~~GidvI  177 (600)
                       ...+|++.-+---.-.+++ .+++++||.|+
T Consensus       153 ~~~~~LvlvGsl~d~vedq~~~ll~~lGI~vv  184 (396)
T cd01979         153 SPERSLVLVGSLPDIVEDQLRRELEQLGIPVV  184 (396)
T ss_pred             CCCCCEEEEEECCCHHHHHHHHHHHHCCCCEE
T ss_conf             78886489970581689999999997699246


No 119
>cd06308 PBP1_sensor_kinase_like Periplasmic binding domain of two-component sensor kinase signaling systems. Periplasmic binding domain of two-component sensor kinase signaling systems, some of which are fused with a C-terminal histidine kinase A domain (HisK) and/or a signal receiver domain (REC). Members of this group share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily and are predicted to be involved in sensing of environmental stimuli; their substrate specificities, however, are not known in detail.
Probab=77.31  E-value=5.7  Score=19.72  Aligned_cols=47  Identities=26%  Similarity=0.397  Sum_probs=33.9

Q ss_pred             HHHHHHHHHCCCCEEEEECC-CCCCHHHHHHHHHCCCCEEEECCCCCC
Q ss_conf             78988742026868999648-876234555554179827996154476
Q gi|254780901|r  139 PSLMEKFINEGAQLIITVDC-GSTSYDALQYATNQGIDVIVIDHHQVK  185 (600)
Q Consensus       139 ~~~i~~~~~~g~~LiItvD~-Gi~~~e~i~~a~~~GidvIVtDHH~~~  185 (600)
                      ...++.+..++++.||.+-. +....+.++.|++.||.||..|....+
T Consensus        46 ~~~ie~li~~~vD~iiv~p~d~~~~~~~l~~a~~agIPVV~~d~~~~~   93 (270)
T cd06308          46 VADIENFIRQGVDLLIISPNEAAPLTPVVEEAYRAGIPVILLDRKILS   93 (270)
T ss_pred             HHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHCCCCEEEECCCCCC
T ss_conf             999999998499999996488520089999999859919994588888


No 120
>PRK11460 esterase YpfH; Provisional
Probab=77.16  E-value=5.7  Score=19.69  Aligned_cols=18  Identities=11%  Similarity=0.054  Sum_probs=7.2

Q ss_pred             CEEECCCCHHHHHHHHHH
Q ss_conf             146422215889999999
Q gi|254780901|r  445 GLTVERVNFGRLCDFFQK  462 (600)
Q Consensus       445 G~ti~~~~l~~f~~~l~~  462 (600)
                      |=+|..+-++.-.+++.+
T Consensus       190 GH~I~~egl~~a~~FLk~  207 (230)
T PRK11460        190 GHAIDPRLMQFALDRLRY  207 (230)
T ss_pred             CCCCCHHHHHHHHHHHHH
T ss_conf             998899999999999987


No 121
>PRK07199 phosphoribosylpyrophosphate synthetase; Provisional
Probab=77.06  E-value=5.8  Score=19.67  Aligned_cols=70  Identities=10%  Similarity=0.125  Sum_probs=51.7

Q ss_pred             HHCCCCEEEEEC-CC-CCHHHHHHHHHHHHHHCCC-CEEEEEC--------CCCCCCCCCCHHHHHHHHHCCCCEEEEEC
Q ss_conf             977997999940-78-8615289999999997699-4799807--------87433668897898874202686899964
Q gi|254780901|r   89 IYNSEKIMIFGD-YD-VDGAASVALMMRFLSHCSV-NANMYIP--------DRIVDGYGPNPSLMEKFINEGAQLIITVD  157 (600)
Q Consensus        89 i~~~ekI~I~gD-yD-~DGitstail~~~L~~~g~-~v~~~IP--------~R~~eGYGl~~~~i~~~~~~g~~LiItvD  157 (600)
                      +. ++.+.|..- .+ -|.+.-.-+|..++++.|+ ++...||        .++..|=-++...+-++.+.|++-+||+|
T Consensus        47 vr-g~dV~iiqs~~~pnd~lmELll~idA~r~a~A~~It~ViPY~~YaRQDr~~~~ge~isak~vA~ll~~~~d~vitvD  125 (301)
T PRK07199         47 VA-GRTVVLVCSLDQPDEKLLPLLFAAEAARELGARRVVLVAPYLAYMRQDIRFHPGEAISSRHFARLLSGSFDRLITVD  125 (301)
T ss_pred             CC-CCEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCCCHHCCCCCCCCCCCCCHHHHHHHHHHHCCEEEEEC
T ss_conf             77-98389988999973889999999999987488748998156621013223479985108999999985277689970


Q ss_pred             CC
Q ss_conf             88
Q gi|254780901|r  158 CG  159 (600)
Q Consensus       158 ~G  159 (600)
                      .=
T Consensus       126 lH  127 (301)
T PRK07199        126 PH  127 (301)
T ss_pred             CC
T ss_conf             45


No 122
>PRK06084 O-acetylhomoserine aminocarboxypropyltransferase; Validated
Probab=76.96  E-value=5.8  Score=19.65  Aligned_cols=118  Identities=15%  Similarity=0.227  Sum_probs=61.4

Q ss_pred             CHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEE
Q ss_conf             87999999999997799799994078861528999999999769947998078743366889789887420268689996
Q gi|254780901|r   77 DCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITV  156 (600)
Q Consensus        77 dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItv  156 (600)
                      +|.....-+..-.+.+..|++-.  |+=|-| ..++.++|..+|.++.++=|+        +.+.++.++..++++|. +
T Consensus        82 GMaAIs~~ll~ll~~Gd~iv~~~--~~Yggt-~~l~~~~l~~~gi~~~fvd~~--------d~~~~~~~i~~~Tklv~-~  149 (424)
T PRK06084         82 GMAAITYAIQTVAEAGDNIVSVA--KLYGGT-YNLLAHTLPRIGIQTRFAAHD--------DIAALEALIDERTKAVF-C  149 (424)
T ss_pred             HHHHHHHHHHHHCCCCCEEEECC--CCCCCH-HHHHHHHHHHCCCEEEEECCC--------CHHHHHHHCCCCCEEEE-E
T ss_conf             89999999998418999899827--985638-999999887468615995886--------77999975487651899-8


Q ss_pred             CC------CCCCHHHHH-HHHHCCCCEEEECCCCCCCCCCCCEEEECCCCCCCCC----CCCCHHHHH
Q ss_conf             48------876234555-5541798279961544765556725652378888643----344304788
Q gi|254780901|r  157 DC------GSTSYDALQ-YATNQGIDVIVIDHHQVKSEEIPAYALVNPNRLDDLS----GQGHLCAAG  213 (600)
Q Consensus       157 D~------Gi~~~e~i~-~a~~~GidvIVtDHH~~~~~~p~a~aivNP~~~~~~~----p~~~l~gaG  213 (600)
                      ..      -+.+.++|. .|++.|+-++ .|.--.+.      ...||-..|.+.    --|+++|-|
T Consensus       150 EsP~NPtl~v~DI~~i~~iA~~~g~~~v-VDNT~atP------~~~~Pl~~GaDivvhS~TKYi~GHs  210 (424)
T PRK06084        150 ESIGNPAGNIVDLQALADAAHRHGVPLI-VDNTVATP------VLCRPFEHGADIVVHSLTKYMGGHG  210 (424)
T ss_pred             ECCCCCCCEECCHHHHHHHHHHCCCEEE-EECCCCCC------CCCCHHHHCCCEEEEECCEECCCCC
T ss_conf             4389998650378999999987499599-54576352------3268045289889996652205887


No 123
>PRK02102 ornithine carbamoyltransferase; Validated
Probab=76.63  E-value=5.9  Score=19.59  Aligned_cols=15  Identities=7%  Similarity=0.025  Sum_probs=7.7

Q ss_pred             HHHHCCCCEEEEECC
Q ss_conf             999769947998078
Q gi|254780901|r  115 FLSHCSVNANMYIPD  129 (600)
Q Consensus       115 ~L~~~g~~v~~~IP~  129 (600)
                      +.+++|+++.+.=++
T Consensus        67 A~~~LGg~~i~l~~~   81 (331)
T PRK02102         67 AAIDLGAHVTYLGPN   81 (331)
T ss_pred             HHHHCCCEEEECCCC
T ss_conf             999859909957875


No 124
>cd06335 PBP1_ABC_ligand_binding_like_2 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=76.45  E-value=6  Score=19.56  Aligned_cols=88  Identities=17%  Similarity=0.103  Sum_probs=56.7

Q ss_pred             CCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEE--CCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHH
Q ss_conf             97999940788615289999999997699479980--7874336688978988742026868999648876234555554
Q gi|254780901|r   93 EKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYI--PDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYAT  170 (600)
Q Consensus        93 ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~I--P~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~  170 (600)
                      +||.|+.+-|.=|......+.+.++..|.++....  |.--+|   ++ ..+.+++..+++.|+.+-.|.....-+.-++
T Consensus       139 kkvai~~~d~~~G~~~~~~~~~~~~~~G~~vv~~~~~~~~~~D---f~-~~l~~i~~~~pD~V~~~~~~~~~~~~~~q~~  214 (347)
T cd06335         139 KKVALLLDNTGWGRSNRKDLTAALAARGLKPVAVEWFNWGDKD---MT-AQLLRAKAAGADAIIIVGNGPEGAQIANGMA  214 (347)
T ss_pred             CEEEEEEECCHHHHHHHHHHHHHHHHCCCEEEEEEEECCCCCC---HH-HHHHHHHHCCCCEEEEECCCHHHHHHHHHHH
T ss_conf             6699997076366899999999998659867578840799834---89-9999998669999999477617999999999


Q ss_pred             HCCCCEEEECCCCC
Q ss_conf             17982799615447
Q gi|254780901|r  171 NQGIDVIVIDHHQV  184 (600)
Q Consensus       171 ~~GidvIVtDHH~~  184 (600)
                      ++|+++-+.-+.-+
T Consensus       215 ~~G~~~~~~g~~~~  228 (347)
T cd06335         215 KLGWKVPIISHWGL  228 (347)
T ss_pred             HCCCCCCEEEECCC
T ss_conf             71999767941477


No 125
>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=76.44  E-value=6  Score=19.55  Aligned_cols=117  Identities=18%  Similarity=0.243  Sum_probs=74.8

Q ss_pred             HHCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCC---------------------
Q ss_conf             56148799999999999779979999407886152899999999976994799807874---------------------
Q gi|254780901|r   73 LILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRI---------------------  131 (600)
Q Consensus        73 ~~l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~---------------------  131 (600)
                      -.+.-|++|.+.+.+.+.++.+|+=.|=-   ---|.-++.++-+++|   .|||-+|=                     
T Consensus        44 kT~~~~~~Ay~~v~~~~~~gg~iLFVGTK---NkQA~~~i~~~A~r~g---~~YVn~RWLGGMLTNf~TirkSi~kL~~l  117 (227)
T TIGR01011        44 KTLQLLEEAYNFVREVVANGGKILFVGTK---NKQAKEIIKEEAERCG---MFYVNQRWLGGMLTNFKTIRKSIKKLKKL  117 (227)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCEEEEEECH---HHHHHHHHHHHHHHCC---CCEECCCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999819958885165---8899999999998748---96211333464002479999999999999


Q ss_pred             --------------CCCCCCCHHHHHHHHHC--C-------CCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCCCCCC
Q ss_conf             --------------33668897898874202--6-------868999648876234555554179827996154476555
Q gi|254780901|r  132 --------------VDGYGPNPSLMEKFINE--G-------AQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKSEE  188 (600)
Q Consensus       132 --------------~eGYGl~~~~i~~~~~~--g-------~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~~~~~~  188 (600)
                                    +|.-.|+.+ .+++...  |       +++|+.+|.. -=+=||..|+.+||-||=     +=++-
T Consensus       118 E~~~~~g~~~~LtKKE~~~L~Re-~~KL~k~LgGIk~M~~lPd~l~viD~~-~E~IAv~EA~kLgIPvvA-----~vDTN  190 (227)
T TIGR01011       118 EKMEEDGTFDVLTKKEILMLSRE-KEKLEKNLGGIKDMKKLPDLLFVIDPR-KEKIAVAEARKLGIPVVA-----IVDTN  190 (227)
T ss_pred             HHHHHHCCCCCCCCCCHHHHHHH-HHHHHHHHHHHHHHHCCCCEEEEECCC-CCHHHHHHHHHCCCCEEE-----EECCC
T ss_conf             98776133124770007767899-999865530025453169708997482-106899997337997898-----70478


Q ss_pred             CCCEEEECCCCCCCCCCCCC
Q ss_conf             67256523788886433443
Q gi|254780901|r  189 IPAYALVNPNRLDDLSGQGH  208 (600)
Q Consensus       189 p~a~aivNP~~~~~~~p~~~  208 (600)
                            +||-.-|+.=|.-+
T Consensus       191 ------CdPd~vD~~IPgND  204 (227)
T TIGR01011       191 ------CDPDVVDYPIPGND  204 (227)
T ss_pred             ------CCCCCCCCCCCCCC
T ss_conf             ------88886650257973


No 126
>PRK01395 V-type ATP synthase subunit F; Provisional
Probab=76.05  E-value=4.3  Score=20.71  Aligned_cols=62  Identities=18%  Similarity=0.178  Sum_probs=35.8

Q ss_pred             CCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCE-EEEECCCCCCHHHHHHH
Q ss_conf             979999407886152899999999976994799807874336688978988742026868-99964887623455555
Q gi|254780901|r   93 EKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQL-IITVDCGSTSYDALQYA  169 (600)
Q Consensus        93 ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~L-iItvD~Gi~~~e~i~~a  169 (600)
                      -||.|.||||.         ...|+.+|.++......  +|    -.+.++++.++++.+ +||=++.-.--+.+++.
T Consensus         4 yKIaVvGd~Ds---------vlgF~~lG~dvfpv~~~--eE----a~~~l~~La~~~y~II~ITE~~a~~i~~~i~~y   66 (104)
T PRK01395          4 YKIGVIGDKDS---------ILPFKALGFDVFPVIEE--QE----ARNTLRKLAMEDYAIIYITEDIAKDIPETIERY   66 (104)
T ss_pred             EEEEEECCHHH---------HHHHHHCCEEEEECCCH--HH----HHHHHHHHHHCCEEEEEEEHHHHHHHHHHHHHH
T ss_conf             17999868578---------78888658047854887--99----999999998679279997299984569999998


No 127
>cd06300 PBP1_ABC_sugar_binding_like_1 Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily. Periplasmic sugar-binding component of uncharacterized ABC-type transport systems that are members of the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily, which consists of two alpha/beta globular domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding. Members of this group are predicted to be involved in the transport of sugar-containing molecules across cellular and organellar membranes; however their substrate specificity is not known in detail.
Probab=75.85  E-value=4  Score=20.91  Aligned_cols=44  Identities=23%  Similarity=0.305  Sum_probs=34.2

Q ss_pred             HHHHHHHHHCCCCEEEEECCCCC-CHHHHHHHHHCCCCEEEECCC
Q ss_conf             78988742026868999648876-234555554179827996154
Q gi|254780901|r  139 PSLMEKFINEGAQLIITVDCGST-SYDALQYATNQGIDVIVIDHH  182 (600)
Q Consensus       139 ~~~i~~~~~~g~~LiItvD~Gi~-~~e~i~~a~~~GidvIVtDHH  182 (600)
                      ...|+.+..+|++.||..-...+ ..+.++.|++.||.||+.|--
T Consensus        50 ~~~ie~~I~qgvD~Iiv~p~d~~a~~~~l~~A~~aGIpVV~~d~~   94 (272)
T cd06300          50 IADIRNLIAQGVDAIIINPASPTALNPVIEEACEAGIPVVSFDGT   94 (272)
T ss_pred             HHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHCCCEEEEECCC
T ss_conf             999999998599999997897678899999999859969996687


No 128
>cd06310 PBP1_ABC_sugar_binding_like_2 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=75.80  E-value=6.2  Score=19.43  Aligned_cols=69  Identities=22%  Similarity=0.269  Sum_probs=41.5

Q ss_pred             HHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCC-CCHHHHHHHHHCCCCEEEECCCC
Q ss_conf             99997699479980787433668897898874202686899964887-62345555541798279961544
Q gi|254780901|r  114 RFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGS-TSYDALQYATNQGIDVIVIDHHQ  183 (600)
Q Consensus       114 ~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi-~~~e~i~~a~~~GidvIVtDHH~  183 (600)
                      ++.+.+|.++.++-|+.-.+ -.-..+.++.+...+++-||..-... ...+.++.|.+.||.||..|--.
T Consensus        23 ~aA~~~G~~v~~~~~~~~~d-~~~q~~~i~~~i~~~vDgIii~p~~~~~~~~~l~~a~~~gIPvV~~d~~~   92 (273)
T cd06310          23 AAAKELGVKVTFQGPASETD-VAGQVNLLENAIARGPDAILLAPTDAKALVPPLKEAKDAGIPVVLIDSGL   92 (273)
T ss_pred             HHHHHCCCEEEEECCCCCCC-HHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHCCCCEEEEECCC
T ss_conf             99998099899972899789-99999999999974999999916871447999999998499858980333


No 129
>PRK04308 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=75.75  E-value=6.2  Score=19.42  Aligned_cols=31  Identities=19%  Similarity=0.530  Sum_probs=16.9

Q ss_pred             CCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             799799994078861528999999999769947998
Q gi|254780901|r   91 NSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMY  126 (600)
Q Consensus        91 ~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~  126 (600)
                      ++++|+|+|    =|.|+-+. .++|...|++|..+
T Consensus         4 ~~k~v~viG----lG~sG~s~-a~~L~~~G~~v~~~   34 (445)
T PRK04308          4 QNKKILVAG----LGGTGISM-IAYLRKNGAEVAAY   34 (445)
T ss_pred             CCCEEEEEE----ECHHHHHH-HHHHHHCCCEEEEE
T ss_conf             999899999----89999999-99999789919999


No 130
>cd02922 FCB2_FMN Flavocytochrome b2 (FCB2) FMN-binding domain.  FCB2 (AKA L-lactate:cytochrome c oxidoreductase) is a respiratory enzyme located in the intermembrane space of fungal mitochondria which catalyzes the oxidation of L-lactate to pyruvate. FCB2 also participates in a short electron-transport chain involving cytochrome c and cytochrome oxidase which ultimately directs the reducing equivalents gained from L-lactate oxidation to oxygen, yielding one molecule of ATP for every L-lactate molecule consumed. FCB2  is composed of 2 domains: a C-terminal flavin-binding domain, which includes the active site for lacate oxidation, and an N-terminal b2-cytochrome domain, required for efficient cytochrome c reduction. FCB2 is a homotetramer and contains two noncovalently bound cofactors, FMN and heme per subunit.
Probab=75.72  E-value=6.2  Score=19.42  Aligned_cols=79  Identities=11%  Similarity=0.150  Sum_probs=41.5

Q ss_pred             CCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHC--CCC--EEEEECCCCCCCCCCCHHHHHHHHHCCCC
Q ss_conf             48799999999999779979999407886152899999999976--994--79980787433668897898874202686
Q gi|254780901|r   76 TDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHC--SVN--ANMYIPDRIVDGYGPNPSLMEKFINEGAQ  151 (600)
Q Consensus        76 ~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~--g~~--v~~~IP~R~~eGYGl~~~~i~~~~~~g~~  151 (600)
                      ++-|.++.|-   -.+.....+..      ..|+.-|-+.-+..  +..  ...|++.-    ..++.+.++++.+.|++
T Consensus        80 p~gE~a~Ara---A~~~gi~~~lS------t~ss~slEdVa~a~~~~~~~wfQLY~~~d----r~~~~~li~RA~~aG~~  146 (344)
T cd02922          80 PDGELNLARA---AGKHGILQMIS------TNASCSLEEIVDARPPDQPLFFQLYVNKD----RTKTEELLKRAEKLGAK  146 (344)
T ss_pred             CCHHHHHHHH---HHHCCCCEEEE------CCCCCCHHHHHHHCCCCCCEEEEEECCCC----HHHHHHHHHHHHHCCCC
T ss_conf             8456999999---99748865740------57778889999865689866999824776----79999999999986998


Q ss_pred             -EEEEECCCCCCHHHHH
Q ss_conf             -8999648876234555
Q gi|254780901|r  152 -LIITVDCGSTSYDALQ  167 (600)
Q Consensus       152 -LiItvD~Gi~~~e~i~  167 (600)
                       |++|||.-.....+-+
T Consensus       147 alvlTvD~p~~G~R~rd  163 (344)
T cd02922         147 AIFLTVDAPVLGKRERD  163 (344)
T ss_pred             EEEEECCCCCCCCCHHH
T ss_conf             89995678887752266


No 131
>cd06326 PBP1_STKc_like Type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins. The type I periplasmic binding domain of uncharacterized extracellular ligand-binding proteins, some of which contain a conserved catalytic serine/threonine protein kinase (STKc) domain in the N-terminal region. Members of this group are sequence-similar to the branched-chain amino acid ABC transporter leucine-isoleucine-valine-binding protein (LIVBP); their ligand specificity has not been determined experimentally, however.
Probab=75.58  E-value=6.3  Score=19.39  Aligned_cols=83  Identities=13%  Similarity=0.119  Sum_probs=38.4

Q ss_pred             CCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEE--CCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHH
Q ss_conf             97999940788615289999999997699479980--7874336688978988742026868999648876234555554
Q gi|254780901|r   93 EKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYI--PDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYAT  170 (600)
Q Consensus        93 ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~I--P~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~  170 (600)
                      +||.|+.+-+.-|.....-+.+.++..|.++....  |.--+|   + ...+.+++..+++.|+..-.|-....-+.-++
T Consensus       137 kkvavl~~d~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~~D---f-s~~l~~i~~~~pD~v~~~~~~~~~~~~~~q~~  212 (336)
T cd06326         137 KRIAVFYQDDAFGKDGLAGVEKALAARGLKPVATASYERNTAD---V-AAAVAQLAAARPQAVIMVGAYKAAAAFIRALR  212 (336)
T ss_pred             CEEEEEECCCHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCC---H-HHHHHHHHHCCCCEEEEECCCHHHHHHHHHHH
T ss_conf             7599993587588999999999999779937999986899877---7-99999998479799999278279999999999


Q ss_pred             HCCCCEEEE
Q ss_conf             179827996
Q gi|254780901|r  171 NQGIDVIVI  179 (600)
Q Consensus       171 ~~GidvIVt  179 (600)
                      +.|++..+.
T Consensus       213 ~~G~~~~~~  221 (336)
T cd06326         213 KAGGGAQFY  221 (336)
T ss_pred             HCCCCCEEE
T ss_conf             769997599


No 132
>TIGR02707 butyr_kinase butyrate kinase; InterPro: IPR011245   This group represents bacterial butyrate kinase, an enzyme that facilitates the formation of butyryl-CoA by phosphorylating butyrate in the presence of ATP to form butyryl phosphate . The final steps in butyrate synthesis by anaerobic bacteria can occur via butyrate kinase and phosphotransbutyrylase or via butyryl-CoA:acetate CoA-transferase, the latter providing the dominant route for butyrate formation in human colonic bacteria .; GO: 0005524 ATP binding, 0047761 butyrate kinase activity, 0016310 phosphorylation, 0005737 cytoplasm.
Probab=75.46  E-value=1.9  Score=23.49  Aligned_cols=46  Identities=22%  Similarity=0.294  Sum_probs=34.9

Q ss_pred             HHHHHHHHHHHHHH-CEEEEEEE---CC-CCEEEEEEE-CCCCCCHHHHHHH
Q ss_conf             22222789988420-10799886---37-983799986-4898618888885
Q gi|254780901|r  382 IVGLLAARLKEKFG-RPSFAISF---EE-DGKGIGSGR-SIEGFDIGKMVSF  427 (600)
Q Consensus       382 ViGIVAsrL~e~y~-kP~iv~s~---~~-dg~~kGS~R-Si~g~~l~~~l~~  427 (600)
                      +=||+|.+|+++|+ .|++++=+   || +.++|=||- -++--+++.||++
T Consensus       106 LGaIIA~~lA~~~~diPafIVDPVVVDEledvARISG~P~i~RkSIfHALNq  157 (353)
T TIGR02707       106 LGAIIARELADELNDIPAFIVDPVVVDELEDVARISGLPEIERKSIFHALNQ  157 (353)
T ss_pred             HHHHHHHHHHHHCCCCCEEEECCCEECCCCCHHHHCCCCCCCCEEHHHHHHH
T ss_conf             6899999987651894358826833505510132138898641104444338


No 133
>cd01537 PBP1_Repressors_Sugar_Binding_like Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems. Ligand-binding domain of the LacI-GalR family of transcription regulators and the sugar-binding domain of ABC-type transport systems, all of which contain the type I periplasmic binding protein-like fold. Their specific ligands include lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor; in general the sugar binding domain in this family binds a sugar, which in turn changes the DNA binding activity of the repressor domain.  The core structure of the periplasmic binding proteins is classified into two types and they differ in number and order of beta strands in each domain: type I, which has six beta strands, and type II, which has five beta strands. These two distinct structural arrangem
Probab=75.43  E-value=6.3  Score=19.36  Aligned_cols=69  Identities=17%  Similarity=0.176  Sum_probs=46.0

Q ss_pred             HHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCC
Q ss_conf             999997699479980787433668897898874202686899964887623455555417982799615447
Q gi|254780901|r  113 MRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQV  184 (600)
Q Consensus       113 ~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~~  184 (600)
                      .+.++..|.++.....+.-.   --....++.+...+++-||.+-+-.++.+.++.+.+.|+.++.+|....
T Consensus        22 ~~~a~~~gy~~~~~~~~~~~---~~~~~~i~~~~~~~vDgiIi~~~~~~~~~~~~~~~~~~ipvV~~~~~~~   90 (264)
T cd01537          22 EEAAKAAGYQVLLANSQNDA---EKQLSALENLIARGVDGIIIAPSDLTAPTIVKLARKAGIPVVLVDRDIP   90 (264)
T ss_pred             HHHHHHCCCEEEEEECCCCH---HHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCC
T ss_conf             99999869989999799998---9999999999976999999967988868999999975997999856678


No 134
>PRK03379 vitamin B12-transporter protein BtuF; Provisional
Probab=75.33  E-value=4.2  Score=20.79  Aligned_cols=38  Identities=18%  Similarity=0.376  Sum_probs=20.3

Q ss_pred             HHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEEC
Q ss_conf             887420268689996488762345555541798279961
Q gi|254780901|r  142 MEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVID  180 (600)
Q Consensus       142 i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtD  180 (600)
                      +|++..-.++|||+-+.| ...+.++.++++||.|+++|
T Consensus        70 ~E~IlaL~PDLVia~~~~-~~~~~~~~L~~~GI~v~~~~  107 (265)
T PRK03379         70 LERIVALKPDLVLAWRGG-NAERQVDQLASLGIKVMWVD  107 (265)
T ss_pred             HHHHHHHCCCEEEEECCC-CCHHHHHHHHHCCCEEEECC
T ss_conf             999996399989995688-95899999981697588359


No 135
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=75.11  E-value=6.4  Score=19.30  Aligned_cols=118  Identities=20%  Similarity=0.225  Sum_probs=58.9

Q ss_pred             HCCHHHHH-----CCCCCCCEEEECCCHHHHHHHHHHHH--------------HHHHHHHHHHHHHHHHHHHHH----HH
Q ss_conf             30623331-----21222210020342589999999999--------------899999999999999999998----75
Q gi|254780901|r  304 SINAGGRI-----GESNLGSRLLISDDSQELEMLAMKLD--------------VLNQNRRLMESAMLEQAEAKV----LT  360 (600)
Q Consensus       304 rINAaGRl-----~~a~~av~lL~~~d~~~a~~la~~L~--------------~lN~~Rk~~e~~i~~~a~~~~----~~  360 (600)
                      -|-|.||-     |--..++...+.+|++--..+-++|.              .+++-.+++++.= +.....+    .+
T Consensus       532 YIQaSGRtSRLyaGglTkGlSvvlvdd~~~f~~L~krm~~~~~e~e~k~l~evdL~el~reIdEdR-~~~r~~~~g~~~~  610 (1187)
T COG1110         532 YIQASGRTSRLYAGGLTKGLSVVLVDDPEVFEGLIKRMSWKFIEIEFKEISEVDLEELLREIDEDR-ERVRRVLEGKLKE  610 (1187)
T ss_pred             HEECCCHHHHHHCCCCCCCEEEEEECCHHHHHHHHHHHHHHHCCCCEEECCCCCHHHHHHHHHHHH-HHHHHHHHCCCHH
T ss_conf             310266176654266346228999568899999999998751234230521147999999977668-9998887243112


Q ss_pred             HHCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHCEEEEEE--------ECCCCE------------------EEEEEE
Q ss_conf             211243475026205785812222227899884201079988--------637983------------------799986
Q gi|254780901|r  361 QCDDIQQASVIVVEGDRWHPGIVGLLAARLKEKFGRPSFAIS--------FEEDGK------------------GIGSGR  414 (600)
Q Consensus       361 ~~~~~~~~~~ivv~~~~wh~GViGIVAsrL~e~y~kP~iv~s--------~~~dg~------------------~kGS~R  414 (600)
                      +..+.-....+||.+|+        =|--++.-|+||..-.-        ..+|++                  ..|=..
T Consensus       611 ~~~dlvkt~L~IVESPn--------KARTIA~FFgrPS~R~~~~~~vYEv~~gD~vL~ItAS~GHv~DLvt~~g~hGvl~  682 (1187)
T COG1110         611 ETKDLVKTALMIVESPN--------KARTIASFFGRPSVRRLGGGVVYEVAIGDLVLTITASGGHVFDLVTEPGVHGVLV  682 (1187)
T ss_pred             HHHHHHHCEEEEEECCH--------HHHHHHHHHCCCCEEEECCEEEEEEECCCEEEEEEECCCEEEEEECCCCCCEEEC
T ss_conf             33321101589996771--------8889999848962355479068999618758999953871688631465210560


Q ss_pred             CCC-CCCHHHHHHHHCC
Q ss_conf             489-8618888885303
Q gi|254780901|r  415 SIE-GFDIGKMVSFAVE  430 (600)
Q Consensus       415 Si~-g~~l~~~l~~~~~  430 (600)
                      -.+ -+.+|+.+..|.+
T Consensus       683 ~~~~~vPvY~tIKrC~d  699 (1187)
T COG1110         683 KDGKYVPVYDTIKRCRD  699 (1187)
T ss_pred             CCCCEEEHHHHHHHHHH
T ss_conf             58706862788888851


No 136
>TIGR01678 FAD_lactone_ox sugar 1,4-lactone oxidases; InterPro: IPR010031   This entry identifies a family of at least two different sugar 1,4 lactone oxidases, both involved in synthesising ascorbic acid or a derivative. These include L-gulonolactone oxidase (1.1.3.8 from EC) from rat and D-arabinono-1,4-lactone oxidase (1.1.3.37 from EC) from Saccharomyces cerevisiae. Members are proposed to have the cofactor FAD covalently bound at a site specified by IPR006093 from INTERPRO.; GO: 0016899 oxidoreductase activity acting on the CH-OH group of donors oxygen as acceptor, 0009058 biosynthetic process.
Probab=74.90  E-value=4.7  Score=20.34  Aligned_cols=79  Identities=16%  Similarity=0.253  Sum_probs=57.9

Q ss_pred             CCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHC-C----C
Q ss_conf             4879999999999977997999940788615289999999997699479980787433668897898874202-6----8
Q gi|254780901|r   76 TDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINE-G----A  150 (600)
Q Consensus        76 ~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~-g----~  150 (600)
                      +-+|+.+|.+..|-.+++||.+.|                   -|.-..=..   .++||=++..-++++.+- .    .
T Consensus        22 ~s~eevrE~l~~Ar~~~Kk~~vVG-------------------~GHSPSdi~---cTdg~l~~ldkmnkV~~fd~~Pelh   79 (505)
T TIGR01678        22 KSVEEVREVLADAREAEKKVKVVG-------------------AGHSPSDIV---CTDGFLVSLDKMNKVLKFDKEPELH   79 (505)
T ss_pred             CCHHHHHHHHHHHHHCCCEEEEEC-------------------CCCCCCCCE---ECCCHHEECCCCCCEEEECCCCCCC
T ss_conf             729999999999874698389975-------------------777823215---4260210012245101552786632


Q ss_pred             CEEEEECCCCCCHHHHHHHHHCCCCE
Q ss_conf             68999648876234555554179827
Q gi|254780901|r  151 QLIITVDCGSTSYDALQYATNQGIDV  176 (600)
Q Consensus       151 ~LiItvD~Gi~~~e~i~~a~~~Gidv  176 (600)
                      ++=||||.||.=.+--+.+.++|.-+
T Consensus        80 ~~~iTV~AGirlyql~e~L~~~Gys~  105 (505)
T TIGR01678        80 KKDITVEAGIRLYQLQEILDEKGYSL  105 (505)
T ss_pred             CCCEEHHHHHHHHHHHHHHHHCCCCE
T ss_conf             20111655256866458975248710


No 137
>COG0078 ArgF Ornithine carbamoyltransferase [Amino acid transport and metabolism]
Probab=74.76  E-value=6.6  Score=19.24  Aligned_cols=91  Identities=14%  Similarity=0.098  Sum_probs=46.7

Q ss_pred             CHHHCCCHHHHHHHHHHHHHCC-------CC-EEEEECCCCCHHHHHHHHHH-HHHHCCCCEEEEECCCCCCCCCCCHHH
Q ss_conf             9556148799999999999779-------97-99994078861528999999-999769947998078743366889789
Q gi|254780901|r   71 DPLILTDCDKAARRIVQAIYNS-------EK-IMIFGDYDVDGAASVALMMR-FLSHCSVNANMYIPDRIVDGYGPNPSL  141 (600)
Q Consensus        71 dP~~l~dm~~A~~ri~~ai~~~-------ek-I~I~gDyD~DGitstail~~-~L~~~g~~v~~~IP~R~~eGYGl~~~~  141 (600)
                      +|..+..+=.-+.-+.++..++       +. .+||-    .--|-|=.-++ +..++|..+.|.=|+-.+=|.|-+..=
T Consensus        16 t~~El~~ll~~A~~lK~~~~~~~~~~~~gk~laliFe----K~STRTR~SFe~a~~qlGg~~~~l~~~~~Qlgr~Esi~D   91 (310)
T COG0078          16 TPEELEALLDLAAELKAAKKAGKELKLKGKNLALIFE----KTSTRTRVSFEVAATQLGGHAIYLGPGDSQLGRGESIKD   91 (310)
T ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEEC----CCCCHHHHHHHHHHHHCCCCEEEECCCCCCCCCCCCHHH
T ss_conf             9999999999999998745158742568965999964----898404544999999768964870887552678996788


Q ss_pred             HHHHHHCCCCEEEEECCCCCCHHHHHH
Q ss_conf             887420268689996488762345555
Q gi|254780901|r  142 MEKFINEGAQLIITVDCGSTSYDALQY  168 (600)
Q Consensus       142 i~~~~~~g~~LiItvD~Gi~~~e~i~~  168 (600)
                      ..++...-++-|..=..   .++.++.
T Consensus        92 TArVLsr~~D~I~~R~~---~~~~v~~  115 (310)
T COG0078          92 TARVLSRMVDAIMIRGF---SHETLEE  115 (310)
T ss_pred             HHHHHHHHHHEEEEECC---CHHHHHH
T ss_conf             99999855025778535---4899999


No 138
>cd06306 PBP1_TorT-like TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. TorT-like proteins, a periplasmic binding protein family that activates induction of the Tor respiratory system upon trimethylamine N-oxide (TMAO) electron-acceptor binding in bacteria. The Tor respiratory system is consists of three proteins (TorC, TorA, and TorD) and is induced in the presence of TMAO. The TMAO control is tightly regulated by three proteins: TorS, TorT, and TorR. Thus, the disruption of any of these proteins can abolish the Tor respiratory induction. TorT shares homology with the sugar-binding domain of the type I periplasmic binding proteins. The members of TorT-like family bind TMAO or related compounds and are predicted to be involved in signal transduction and/or substrate transport.
Probab=74.75  E-value=6.6  Score=19.24  Aligned_cols=68  Identities=12%  Similarity=0.106  Sum_probs=44.5

Q ss_pred             HHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCC
Q ss_conf             997699479980787433668897898874202686899964887623455555417982799615447
Q gi|254780901|r  116 LSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQV  184 (600)
Q Consensus       116 L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~~  184 (600)
                      -+.+|.++.++-|.-..+ -.-....|+.+...|++.||..-....+..++..+.+.||-||.+|--.+
T Consensus        25 A~e~G~~v~~~~~~~~~d-~~~Qi~~ie~~i~~gvDaIii~p~d~~al~~~~~a~~agIPVV~~d~~i~   92 (268)
T cd06306          25 AKRLGVSLKLLEAGGYPN-LAKQIAQLEDCAAWGADAILLGAVSPDGLNEILQQVAASIPVIALVNDIN   92 (268)
T ss_pred             HHHHCCEEEEEECCCCCC-HHHHHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHCCCEEEEEECCCC
T ss_conf             999699799995899999-99999999999983999999867986777899999986982999945778


No 139
>PRK10610 chemotaxis regulatory protein CheY; Provisional
Probab=74.73  E-value=2  Score=23.35  Aligned_cols=89  Identities=11%  Similarity=0.044  Sum_probs=39.9

Q ss_pred             CCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             68689996488762345555541798279961544765556725652378888643344304788999999999997021
Q gi|254780901|r  149 GAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKSEEIPAYALVNPNRLDDLSGQGHLCAAGVVFLVLVLIYRILRQ  228 (600)
Q Consensus       149 g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~~~~~~p~a~aivNP~~~~~~~p~~~l~gaGvaf~l~~al~~~l~~  228 (600)
                      |..-+.++.+   ..++++.+++...|+|++|.|.|.-........+.-+.....-|.--++|.+-.-....++.  .+-
T Consensus        29 g~~~v~~a~~---g~~al~~~~~~~~Dlil~D~~MP~~dG~el~~~ir~~~~~~~~Pii~~T~~~~~~~~~~a~~--~Ga  103 (129)
T PRK10610         29 GFNNVEEAED---GVDALNKLQAGGFGFVISDWNMPNMDGLELLKTIRADGAMSALPVLMVTAEAKKENIIAAAQ--AGA  103 (129)
T ss_pred             CCCEEEEECC---HHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHCCCCCCCCEEEEECCCCHHHHHHHHH--CCC
T ss_conf             9978999899---99999999858999999818999998999999998577778996899988689999999998--699


Q ss_pred             CCCCCCHHHHHHHH
Q ss_conf             48876407799999
Q gi|254780901|r  229 DNKVPLNFDLLSLL  242 (600)
Q Consensus       229 ~~~~~~~~~l~~~l  242 (600)
                      ++.+.+.++..++.
T Consensus       104 ~~yl~KP~~~~~L~  117 (129)
T PRK10610        104 SGYVVKPFTAATLE  117 (129)
T ss_pred             CEEEECCCCHHHHH
T ss_conf             88998989999999


No 140
>pfam00185 OTCace Aspartate/ornithine carbamoyltransferase, Asp/Orn binding domain.
Probab=74.65  E-value=6.6  Score=19.22  Aligned_cols=78  Identities=23%  Similarity=0.426  Sum_probs=46.2

Q ss_pred             CCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHC----CCCEEEEECCCCCCHHHH
Q ss_conf             7997999940788615289999999997699479980787433668897898874202----686899964887623455
Q gi|254780901|r   91 NSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINE----GAQLIITVDCGSTSYDAL  166 (600)
Q Consensus        91 ~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~----g~~LiItvD~Gi~~~e~i  166 (600)
                      ++.+|+++||.-. +=++-+ +..++..+|.++.+.-|.    ||-+.++.++.+.+.    +. ..+++-   ++.++ 
T Consensus         1 ~g~~i~~vGD~~~-~rv~~S-~~~~~~~~g~~v~i~~P~----~~~~~~~~~~~~~~~~~~~~~-~~~~~~---~d~~~-   69 (155)
T pfam00185         1 DGLKVAIVGDGKH-NRVAHS-LILALAKFGMEVVLVAPK----GLPPDPELVDEAKKNALKSGG-ISITVT---DDLEE-   69 (155)
T ss_pred             CCCEEEEECCCCC-CHHHHH-HHHHHHHCCCEEEEECCC----CCCCCHHHHHHHHHHHHHCCC-CEEEEE---CCHHH-
T ss_conf             9989999837872-749999-999999849989998785----238888999999999886289-749998---49999-


Q ss_pred             HHHHHCCCCEEEECCC
Q ss_conf             5554179827996154
Q gi|254780901|r  167 QYATNQGIDVIVIDHH  182 (600)
Q Consensus       167 ~~a~~~GidvIVtDHH  182 (600)
                       .+  .+.|||.||-=
T Consensus        70 -al--~~aDvvyt~~w   82 (155)
T pfam00185        70 -AL--KGADVVYTDRW   82 (155)
T ss_pred             -HH--CCCCEEEEEEE
T ss_conf             -84--53999999765


No 141
>cd06382 PBP1_iGluR_Kainate N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the kainate receptors. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the kainate receptors, non-NMDA ionotropic receptors which respond to the neurotransmitter glutamate.  While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. Kainate receptors have five subunits, GluR5, GluR6, GluR7, KA1, and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeri
Probab=74.34  E-value=6.7  Score=19.16  Aligned_cols=48  Identities=10%  Similarity=0.160  Sum_probs=21.0

Q ss_pred             CCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCC
Q ss_conf             6688978988742026868999648876234555554179827996154
Q gi|254780901|r  134 GYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHH  182 (600)
Q Consensus       134 GYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH  182 (600)
                      .|-....+-+ +.+.|+--|+-.-+..+++---..|.++.|-.|-|.=.
T Consensus        49 sF~~~~~~C~-~l~~GV~AI~Gp~s~~~~~~v~sic~~l~IP~i~~~~~   96 (327)
T cd06382          49 SFETTKKVCD-LLQQGVAAIFGPSSSEASSIVQSICDAKEIPHIQTRWD   96 (327)
T ss_pred             HHHHHHHHHH-HHHCCCEEEECCCCHHHHHHHHHHHHHCCCCEEEECCC
T ss_conf             1799999999-88549389996787237899999874316852683578


No 142
>cd06314 PBP1_tmGBP Periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs. Periplasmic sugar-binding domain of Thermotoga maritima glucose-binding protein (tmGBP) and its close homologs from other bacteria. They are a member of the type I periplasmic binding protein superfamily which consists of two domains connected by a three-stranded hinge. TmGBP is specific for glucose and its binding pocket is buried at the interface of the two domains. TmGBP also exhibits high thermostability and the highest structural similarity to E. coli glucose binding protein (ecGBP).
Probab=74.27  E-value=6.7  Score=19.15  Aligned_cols=66  Identities=21%  Similarity=0.265  Sum_probs=40.3

Q ss_pred             HHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEEC-CCCCCHHHHHHHHHCCCCEEEECCCCC
Q ss_conf             997699479980787433668897898874202686899964-887623455555417982799615447
Q gi|254780901|r  116 LSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVD-CGSTSYDALQYATNQGIDVIVIDHHQV  184 (600)
Q Consensus       116 L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD-~Gi~~~e~i~~a~~~GidvIVtDHH~~  184 (600)
                      -+.+|.++.+..|...+  ---..+.++.+..+|++-||..= ...+..+.++.|. .||-||..|...+
T Consensus        24 A~e~Gv~v~~~~~~~~d--~~~Q~~~i~~~i~~~vDaIii~p~d~~~~~~~~~~a~-agIpVv~~d~~~~   90 (271)
T cd06314          24 GKELGVDVEFVVPQQGT--VNAQLRMLEDLIAEGVDGIAISPIDPKAVIPALNKAA-AGIKLITTDSDAP   90 (271)
T ss_pred             HHHHCCEEEEEECCCCC--HHHHHHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHH-CCCCEEEEECCCC
T ss_conf             99859989999689999--9999999999997599999992687455699999996-5998899807888


No 143
>PRK00553 ribose-phosphate pyrophosphokinase; Provisional
Probab=73.88  E-value=6.9  Score=19.09  Aligned_cols=117  Identities=15%  Similarity=0.171  Sum_probs=66.9

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHCCCCHHHHHHHCCCCHHHCCCCHHHCCCHHHHHHHHHHHHHCCCCEE
Q ss_conf             34115788898899999988199999999999678897898866196677718995561487999999999997799799
Q gi|254780901|r   17 RWVSLLGQEGINRALAITQKHAIPDIVARVLVNRNVSIDYAKDFLNPSIRLLMPDPLILTDCDKAARRIVQAIYNSEKIM   96 (600)
Q Consensus        17 rW~~~~~~~~~~~~~~l~~~~~~~~~~a~iL~~Rgi~~~~~~~fL~p~l~~l~~dP~~l~dm~~A~~ri~~ai~~~ekI~   96 (600)
                      .-.....+...+.+..+++.+|++..-           -+.+.|=         |=...-       |+.+.+. ++.+.
T Consensus        17 n~~ifsgss~~~LA~~Ia~~Lg~~l~~-----------~~~~~F~---------DGE~~v-------~i~e~VR-g~dV~   68 (340)
T PRK00553         17 NHVIFSLSKAKKLVDSICRKLSMKPGE-----------IVIQKFA---------DGETYI-------RFDESVR-NKDVV   68 (340)
T ss_pred             CEEEEECCCCHHHHHHHHHHHCCCCCC-----------EEEEECC---------CCCEEE-------EECCCCC-CCCEE
T ss_conf             679997799889999999985997413-----------1789879---------997898-------5278768-99889


Q ss_pred             EEECC--CC-CHHHHHHHHHHHHHHCCCC-EEEEEC--------CCCCCCCCCCHHHHHHHHHC-CCCEEEEECCCCC
Q ss_conf             99407--88-6152899999999976994-799807--------87433668897898874202-6868999648876
Q gi|254780901|r   97 IFGDY--DV-DGAASVALMMRFLSHCSVN-ANMYIP--------DRIVDGYGPNPSLMEKFINE-GAQLIITVDCGST  161 (600)
Q Consensus        97 I~gDy--D~-DGitstail~~~L~~~g~~-v~~~IP--------~R~~eGYGl~~~~i~~~~~~-g~~LiItvD~Gi~  161 (600)
                      |...-  ++ |-+.-.-+|..++++.|++ +...||        .|+..|-.++...+-++.+. |++-+||+|--..
T Consensus        69 Iiqs~~~pvnd~lmELll~idA~rrasA~~It~ViPY~~YaRQDrk~~~repIsak~vA~lL~~~G~drvitvDlH~~  146 (340)
T PRK00553         69 IFQSTCSPVNDSLMELLIAIDALKRGSAKSITAILPYYGYARQDRKTAGREPITSKLVADLLTKAGVTRVTLTDIHSD  146 (340)
T ss_pred             EECCCCCCCCHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCEEEEECCCHH
T ss_conf             987899995268999999999998707882699966666554787678999843999985676358856998435658


No 144
>PRK13812 orotate phosphoribosyltransferase; Provisional
Probab=73.83  E-value=6.9  Score=19.08  Aligned_cols=106  Identities=19%  Similarity=0.327  Sum_probs=56.8

Q ss_pred             HHHCCCCHHHCCCCHHHCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCC
Q ss_conf             86619667771899556148799999999999779979999407886152899999999976994799807874336688
Q gi|254780901|r   58 KDFLNPSIRLLMPDPLILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGP  137 (600)
Q Consensus        58 ~~fL~p~l~~l~~dP~~l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl  137 (600)
                      ..|++..  .+..+|..+   .+.++.+.+.+....  .|.| -..-|+.-++.+..   ..+.  -+.+..+...+||.
T Consensus        30 ~~Y~d~~--~~~~~P~~~---~~i~~~~~~~i~~~~--~i~G-~~~ggip~a~~ia~---~~~~--p~~~vRke~K~hG~   96 (174)
T PRK13812         30 EYYVDKY--LFETDPECL---SAIAAAFADRIDEDT--TLAG-VALGAVPLVAATAT---EAGV--PYVIARKQAKEYGT   96 (174)
T ss_pred             HHHCCCC--HHHCCHHHH---HHHHHHHHHHHCCCC--EEEC-CCCCCHHHHHHHHH---HHCC--CEEEEEECCCCCCC
T ss_conf             2344380--441799999---999999998604216--3867-55243999999999---8299--88999843677664


Q ss_pred             CHHHHHHHHHCCCCEEEE---ECCCCCCHHHHHHHHHCCCCEE
Q ss_conf             978988742026868999---6488762345555541798279
Q gi|254780901|r  138 NPSLMEKFINEGAQLIIT---VDCGSTSYDALQYATNQGIDVI  177 (600)
Q Consensus       138 ~~~~i~~~~~~g~~LiIt---vD~Gi~~~e~i~~a~~~GidvI  177 (600)
                      ... ++--.+.|-+.+|.   +-.|.|..+.++.+++.|..|+
T Consensus        97 ~~~-ieG~~~~g~rVlivEDViTTG~S~~eai~~l~~~G~~V~  138 (174)
T PRK13812         97 GNR-IEGRLDDGEEVVVLEDIATTGQSAVDAVEALRDAGATVN  138 (174)
T ss_pred             CCC-CCCCCCCCCEEEEEEEEECCCCCHHHHHHHHHHCCCEEE
T ss_conf             430-313235786699998644578019999999998799799


No 145
>cd06321 PBP1_ABC_sugar_binding_like_11 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=73.77  E-value=6.9  Score=19.07  Aligned_cols=68  Identities=19%  Similarity=0.211  Sum_probs=39.7

Q ss_pred             HHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCC-CHHHHHHHHHCCCCEEEECCCCC
Q ss_conf             9976994799807874336688978988742026868999648876-23455555417982799615447
Q gi|254780901|r  116 LSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGST-SYDALQYATNQGIDVIVIDHHQV  184 (600)
Q Consensus       116 L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~-~~e~i~~a~~~GidvIVtDHH~~  184 (600)
                      .+..|..+...+++.-.+ -.-..+.++.+...+++.||..-.... ..+.++.+++.||-|+..|...+
T Consensus        25 a~~~g~~~~v~~~~~~~d-~~~q~~~i~~li~~~vDgIii~~~~~~~~~~~i~~a~~~gIpvV~~d~~~~   93 (271)
T cd06321          25 AKKLNPGVKVTVVSADYD-LNKQVSQIDNFIAAKVDLILLNAVDSKGIAPAVKRAQAAGIVVVAVDVAAE   93 (271)
T ss_pred             HHHCCCCEEEEEECCCCC-HHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHCCCEEEEEEECCC
T ss_conf             997199769998079889-999999999999749988999347840359999999974991899860589


No 146
>PRK04148 hypothetical protein; Provisional
Probab=73.73  E-value=6.1  Score=19.47  Aligned_cols=32  Identities=31%  Similarity=0.373  Sum_probs=21.9

Q ss_pred             CEEEEECCCCCCHHHHH-HHHHCCCCEEEECCCCC
Q ss_conf             68999648876234555-55417982799615447
Q gi|254780901|r  151 QLIITVDCGSTSYDALQ-YATNQGIDVIVIDHHQV  184 (600)
Q Consensus       151 ~LiItvD~Gi~~~e~i~-~a~~~GidvIVtDHH~~  184 (600)
                      .-|+-|  |+...-+++ .+++.|.||++||-|..
T Consensus        18 ~kIvEv--GIGf~~~vA~~L~e~g~dv~~~Din~~   50 (135)
T PRK04148         18 GKIAEL--GIGFYFKVAKKLKESGFDVIVIDINKK   50 (135)
T ss_pred             CEEEEE--ECCCCHHHHHHHHHCCCCEEEEECCHH
T ss_conf             738999--236667899999874998899957655


No 147
>PRK00141 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=73.73  E-value=6.9  Score=19.06  Aligned_cols=78  Identities=13%  Similarity=0.235  Sum_probs=40.7

Q ss_pred             CCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECC-----CCCCCCCCCHHH---HHHHHHCCCCEEEEECCCCC-CH
Q ss_conf             9799994078861528999999999769947998078-----743366889789---88742026868999648876-23
Q gi|254780901|r   93 EKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPD-----RIVDGYGPNPSL---MEKFINEGAQLIITVDCGST-SY  163 (600)
Q Consensus        93 ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~-----R~~eGYGl~~~~---i~~~~~~g~~LiItvD~Gi~-~~  163 (600)
                      .||+|+|    =|.|+-++ .++|...|++|..+=-+     +..+..|...-.   .... -++++++| +=-||. .+
T Consensus        18 ~kvlV~G----lG~SG~s~-a~~L~~~G~~v~~~D~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~d~vV-~SPGI~~~~   90 (476)
T PRK00141         18 GRVLVAG----AGVSGLGI-AKMLSELGCDVVVADDNETQRHMLIEVVDVADISTAQASDA-LDSYSIVV-TSPGWRPDS   90 (476)
T ss_pred             CCEEEEE----ECHHHHHH-HHHHHHCCCEEEEEECCCCHHHHHHHHCCCCEECCCCHHHH-HCCCCEEE-ECCCCCCCC
T ss_conf             9889992----27889999-99999789979999899870357887479856515530656-46899999-899789979


Q ss_pred             HHHHHHHHCCCCEE
Q ss_conf             45555541798279
Q gi|254780901|r  164 DALQYATNQGIDVI  177 (600)
Q Consensus       164 e~i~~a~~~GidvI  177 (600)
                      +.+..|+++||.||
T Consensus        91 p~l~~a~~~gi~vi  104 (476)
T PRK00141         91 PLLVDAQSAGLEVI  104 (476)
T ss_pred             HHHHHHHHCCCCEE
T ss_conf             99999998799577


No 148
>pfam00926 DHBP_synthase 3,4-dihydroxy-2-butanone 4-phosphate synthase. 3,4-Dihydroxy-2-butanone 4-phosphate is biosynthesized from ribulose 5-phosphate and serves as the biosynthetic precursor for the xylene ring of riboflavin. Sometimes found as a bifunctional enzyme with pfam00925.
Probab=73.50  E-value=7  Score=19.02  Aligned_cols=91  Identities=14%  Similarity=0.167  Sum_probs=47.8

Q ss_pred             HHHHHHHHHCCCCEEEEECCC----CCHH-----HHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCE
Q ss_conf             999999997799799994078----8615-----2899999999976994799807874336688978988742026868
Q gi|254780901|r   82 ARRIVQAIYNSEKIMIFGDYD----VDGA-----ASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQL  152 (600)
Q Consensus        82 ~~ri~~ai~~~ekI~I~gDyD----~DGi-----tstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~L  152 (600)
                      ++...+++++++.|.|+-|.|    .|=+     .....+....+..+.-++.-++...-+--||..-.-..-...+..-
T Consensus         1 ie~ai~al~~G~~Viv~D~~~REnEgdlv~~Ae~~t~e~i~fm~~~~~Glic~a~~~~~~~~LgLp~m~~~n~~~~~t~F   80 (193)
T pfam00926         1 IEEAIEALKAGKPVIVVDDEDRENEGDLVIAAEKVTPESVNFMIRHARGLICVALTEERADRLGLPPMVDRNTDRFGTAF   80 (193)
T ss_pred             CHHHHHHHHCCCEEEEEECCCCCCCCCEEEEHHHCCHHHHHHHHHHCCCCEEEECCHHHHHHCCCCCCCCCCCCCCCCCE
T ss_conf             97899999879959999489987642489784449999999999958977797169999976699565555678878875


Q ss_pred             EEEEC-----CCCCCHHHHHHHHHC
Q ss_conf             99964-----887623455555417
Q gi|254780901|r  153 IITVD-----CGSTSYDALQYATNQ  172 (600)
Q Consensus       153 iItvD-----~Gi~~~e~i~~a~~~  172 (600)
                      -++||     .|||+.+...-.+.+
T Consensus        81 tvsvd~~~~~TGISa~DRa~Tir~l  105 (193)
T pfam00926        81 TVSVDAKGTTTGISAADRALTIRAL  105 (193)
T ss_pred             EEEEECCCCCCCCCHHHHHHHHHHH
T ss_conf             9888648887897899999999998


No 149
>PRK01045 ispH 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Reviewed
Probab=73.02  E-value=7.2  Score=18.94  Aligned_cols=103  Identities=17%  Similarity=0.245  Sum_probs=63.4

Q ss_pred             CCHHHHHHHHHHHHHC-CCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCC-------CCCCHHHHHHHHH
Q ss_conf             4879999999999977-9979999407886152899999999976994799807874336-------6889789887420
Q gi|254780901|r   76 TDCDKAARRIVQAIYN-SEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDG-------YGPNPSLMEKFIN  147 (600)
Q Consensus        76 ~dm~~A~~ri~~ai~~-~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eG-------YGl~~~~i~~~~~  147 (600)
                      .+..+|++...++.++ +++|..+|+     +.---...+-|+..|..+.-- ++...+|       ||.+++..+++.+
T Consensus        13 ~GV~rAi~~a~~~~~~~~~~iytlG~-----iIHN~~vv~~L~~~Gv~~v~~-~~~v~~~~~ViirAHGi~~~~~~~~~~   86 (304)
T PRK01045         13 AGVDRAIEIVERALEKYGAPIYVRHE-----IVHNKYVVERLKKKGAIFVEE-LDEVPDGAIVIFSAHGVSPAVREEAKE   86 (304)
T ss_pred             CCHHHHHHHHHHHHHHCCCCEEEECC-----CCCCHHHHHHHHHCCCEEECC-CCCCCCCCEEEEECCCCCHHHHHHHHH
T ss_conf             25999999999999854996898478-----864989999999886999615-566899998999778998999999996


Q ss_pred             CCCCEEEEECCCC--CCHHHHHHHHHCCCCEEEECCCCCC
Q ss_conf             2686899964887--6234555554179827996154476
Q gi|254780901|r  148 EGAQLIITVDCGS--TSYDALQYATNQGIDVIVIDHHQVK  185 (600)
Q Consensus       148 ~g~~LiItvD~Gi--~~~e~i~~a~~~GidvIVtDHH~~~  185 (600)
                      .|..++= .-|-.  ..+..++...+.|-.+||.-++.-|
T Consensus        87 ~g~~viD-aTCP~V~k~~~~v~~~~~~Gy~iviiG~~~Hp  125 (304)
T PRK01045         87 RGLTVID-ATCPLVTKVHKEVARMSREGYEIILIGHKGHP  125 (304)
T ss_pred             CCCCEEE-CCCCCHHHHHHHHHHHHHCCCEEEEECCCCCH
T ss_conf             5997770-50830589999999998589889998178988


No 150
>PRK10799 putative hydrolase-oxidase; Provisional
Probab=73.00  E-value=7.2  Score=18.93  Aligned_cols=29  Identities=21%  Similarity=0.351  Sum_probs=23.7

Q ss_pred             CCEEEEECCCCCCHHHHHHHHHCCCCEEEECC
Q ss_conf             86899964887623455555417982799615
Q gi|254780901|r  150 AQLIITVDCGSTSYDALQYATNQGIDVIVIDH  181 (600)
Q Consensus       150 ~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDH  181 (600)
                      .+..++||.   .-+-|+.|-+.|.|.|||-|
T Consensus        36 ~kI~~alD~---t~~vi~eAi~~~aDliitHH   64 (247)
T PRK10799         36 QKIVTGVTA---SQALLDEAVRLQADAVIVHH   64 (247)
T ss_pred             CEEEEEECC---CHHHHHHHHHCCCCEEEECC
T ss_conf             189999569---89999999985999999867


No 151
>PRK10653 D-ribose transporter subunit RbsB; Provisional
Probab=73.00  E-value=7.2  Score=18.93  Aligned_cols=49  Identities=18%  Similarity=0.306  Sum_probs=32.8

Q ss_pred             HHHHHHHHHCCCCEEEEECC-CCCCHHHHHHHHHCCCCEEEECCCCCCCC
Q ss_conf             78988742026868999648-87623455555417982799615447655
Q gi|254780901|r  139 PSLMEKFINEGAQLIITVDC-GSTSYDALQYATNQGIDVIVIDHHQVKSE  187 (600)
Q Consensus       139 ~~~i~~~~~~g~~LiItvD~-Gi~~~e~i~~a~~~GidvIVtDHH~~~~~  187 (600)
                      .+.++.+..++++.||..-. .....+.++.+++.||.||..|...+..+
T Consensus        72 ~~~i~~li~~~vdgiii~p~d~~~~~~~~~~a~~~gIPvV~~d~~~~~~~  121 (295)
T PRK10653         72 LANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLDRGATKGE  121 (295)
T ss_pred             HHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHHCCCEEEEEEECCCCCC
T ss_conf             99999999769988998477706569999999976981999951278877


No 152
>cd03466 Nitrogenase_NifN_2 Nitrogenase_nifN_2: A subgroup of the NifN subunit of the NifEN complex: NifN forms an alpha2beta2 tetramer with NifE.  NifN and nifE are structurally homologous to nitrogenase MoFe protein beta and alpha subunits respectively.  NifEN participates in the synthesis of the iron-molybdenum cofactor (FeMoco) of the MoFe protein.  NifB-co (an iron and sulfur containing precursor of the FeMoco) from NifB is transferred to the NifEN complex where it is further processed to FeMoco. The nifEN bound precursor of FeMoco has been identified as a molybdenum-free, iron- and sulfur- containing analog of FeMoco. It has been suggested that this nifEN bound precursor also acts as a cofactor precursor in nitrogenase systems which require a cofactor other than FeMoco: i.e. iron-vanadium cofactor (FeVco) or iron only cofactor (FeFeco). This group also contains the Clostidium fused NifN-NifB protein.
Probab=72.83  E-value=7.2  Score=18.91  Aligned_cols=26  Identities=12%  Similarity=0.052  Sum_probs=13.8

Q ss_pred             HCCCHHHHHHHHHHHHHCCCC--EEEEE
Q ss_conf             614879999999999977997--99994
Q gi|254780901|r   74 ILTDCDKAARRIVQAIYNSEK--IMIFG   99 (600)
Q Consensus        74 ~l~dm~~A~~ri~~ai~~~ek--I~I~g   99 (600)
                      -|-+.++-.+-|.++++.-+.  |.|+.
T Consensus        65 VfGGe~kL~~aI~~~~~~~~P~~i~V~s   92 (429)
T cd03466          65 VYGGEKNLKKGLKNVIEQYNPEVIGIAT   92 (429)
T ss_pred             EECHHHHHHHHHHHHHHHCCCCEEEEEC
T ss_conf             7675999999999999841998899965


No 153
>cd06318 PBP1_ABC_sugar_binding_like_9 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=72.71  E-value=7.3  Score=18.89  Aligned_cols=45  Identities=20%  Similarity=0.321  Sum_probs=33.1

Q ss_pred             HHHHHHHHHCCCCEEEEECCCCC-CHHHHHHHHHCCCCEEEECCCC
Q ss_conf             78988742026868999648876-2345555541798279961544
Q gi|254780901|r  139 PSLMEKFINEGAQLIITVDCGST-SYDALQYATNQGIDVIVIDHHQ  183 (600)
Q Consensus       139 ~~~i~~~~~~g~~LiItvD~Gi~-~~e~i~~a~~~GidvIVtDHH~  183 (600)
                      ...|+.++.+|++.||..-+... ....++.|++.||.||..|.-.
T Consensus        45 ~~~i~~~i~~~vd~iii~~~d~~~~~~~~~~a~~aGIPVv~~d~~~   90 (282)
T cd06318          45 IADVEDLLTRGVNVLIINPVDPEGLVPAVAAAKAAGVPVVVVDSSI   90 (282)
T ss_pred             HHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHCCCCEEEECCCC
T ss_conf             9999999976998799811680566999999997799889973777


No 154
>cd06322 PBP1_ABC_sugar_binding_like_12 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. This group includes the periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consist of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=72.15  E-value=7.5  Score=18.79  Aligned_cols=46  Identities=28%  Similarity=0.294  Sum_probs=32.8

Q ss_pred             HHHHHHHHHCCCCEEEEECCCC-CCHHHHHHHHHCCCCEEEECCCCC
Q ss_conf             7898874202686899964887-623455555417982799615447
Q gi|254780901|r  139 PSLMEKFINEGAQLIITVDCGS-TSYDALQYATNQGIDVIVIDHHQV  184 (600)
Q Consensus       139 ~~~i~~~~~~g~~LiItvD~Gi-~~~e~i~~a~~~GidvIVtDHH~~  184 (600)
                      .+.++.+...+++-||.+-+.. .....++.+.+.||.||..|....
T Consensus        45 ~~~i~~li~~~vDgiIi~p~~~~~~~~~~~~~~~~gIPvV~~d~~~~   91 (267)
T cd06322          45 LSDVEDFITKKVDAIVLSPVDSKGIRAAIAKAKKAGIPVITVDIAAE   91 (267)
T ss_pred             HHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHCCCCEEEEECCCC
T ss_conf             99999999749999999067610106999999975997899834655


No 155
>PRK08057 cobalt-precorrin-6x reductase; Reviewed
Probab=72.13  E-value=7.5  Score=18.79  Aligned_cols=19  Identities=26%  Similarity=0.655  Sum_probs=9.3

Q ss_pred             CEEEEECCCCCHHHHHHHHHHHHH
Q ss_conf             799994078861528999999999
Q gi|254780901|r   94 KIMIFGDYDVDGAASVALMMRFLS  117 (600)
Q Consensus        94 kI~I~gDyD~DGitstail~~~L~  117 (600)
                      +|+|+|     |+|=+--|.+.|.
T Consensus         3 ~Ililg-----GT~Egr~la~~L~   21 (241)
T PRK08057          3 RILLLG-----GTSEARALARALA   21 (241)
T ss_pred             EEEEEE-----CHHHHHHHHHHHH
T ss_conf             599996-----7089999999974


No 156
>cd06348 PBP1_ABC_ligand_binding_like_13 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=72.00  E-value=7.5  Score=18.77  Aligned_cols=10  Identities=30%  Similarity=0.574  Sum_probs=4.2

Q ss_pred             HHHHCCCCEE
Q ss_conf             5541798279
Q gi|254780901|r  168 YATNQGIDVI  177 (600)
Q Consensus       168 ~a~~~GidvI  177 (600)
                      .+.+.|+-+|
T Consensus        86 v~~~~~vp~i   95 (344)
T cd06348          86 IAERAGVPVV   95 (344)
T ss_pred             HHHHCCCCEE
T ss_conf             9987599276


No 157
>PRK12562 ornithine carbamoyltransferase subunit F; Provisional
Probab=71.90  E-value=7.6  Score=18.75  Aligned_cols=34  Identities=6%  Similarity=-0.091  Sum_probs=18.5

Q ss_pred             HHHHHHHHH-HHHHCCCCEEEEECCCCCCCCCCCH
Q ss_conf             528999999-9997699479980787433668897
Q gi|254780901|r  106 AASVALMMR-FLSHCSVNANMYIPDRIVDGYGPNP  139 (600)
Q Consensus       106 itstail~~-~L~~~g~~v~~~IP~R~~eGYGl~~  139 (600)
                      -|=|-+=++ +.+++|.++.+.=|+-.+=|.|-+.
T Consensus        56 STRTR~SFE~A~~~LGg~~i~l~~~~s~~~kgEsl   90 (334)
T PRK12562         56 STRTRCSFEVAAYDQGARVTYLGPSGSQIGHKESI   90 (334)
T ss_pred             CCHHHHHHHHHHHHCCCCEEEECCCCCCCCCCCCH
T ss_conf             70479999999998599789858764527899888


No 158
>PRK10841 hybrid sensory kinase in two-component regulatory system with RcsB and YojN; Provisional
Probab=71.79  E-value=5.8  Score=19.63  Aligned_cols=41  Identities=15%  Similarity=0.132  Sum_probs=16.8

Q ss_pred             HCCCCEEEECCCCCCCC-CC--CCEEEECCCCCCCCCCCCCHHH
Q ss_conf             17982799615447655-56--7256523788886433443047
Q gi|254780901|r  171 NQGIDVIVIDHHQVKSE-EI--PAYALVNPNRLDDLSGQGHLCA  211 (600)
Q Consensus       171 ~~GidvIVtDHH~~~~~-~p--~a~aivNP~~~~~~~p~~~l~g  211 (600)
                      .+-+.+-++|+-.-|-- .|  +...-..+..++...-|.+-.|
T Consensus       239 ~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~fg~~~~  282 (947)
T PRK10841        239 TLPMGVTLLDENNHPLLSLTGPERYIKADPRWMQERSWFGYTDG  282 (947)
T ss_pred             CCCEEEEEECCCCCEEEECCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             88558999879997778647888864433356777552464688


No 159
>cd04478 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA dam
Probab=71.56  E-value=7.7  Score=18.70  Aligned_cols=65  Identities=17%  Similarity=0.268  Sum_probs=44.9

Q ss_pred             CEEEEEEECCCCCEEEEEEECCCCCC-HHHHHHCCCCCEEEEEEEEEEEEECCCCEEEEEEEEEEECCCCC
Q ss_conf             64999998499877999997787870-12355306998799999976654578110589999801113112
Q gi|254780901|r  527 AHLQMTFESQDSETLQAIAFRVYGTP-LGEFLMQSRGKRMHVTGHLCVNYWRGSKRCQLRVLDASPVEGHH  596 (600)
Q Consensus       527 ~Hlkl~l~~~~g~~i~aI~Fn~~~~~-~~~~~~~~~g~~idii~~l~~N~~~G~~s~QL~I~Di~p~e~~~  596 (600)
                      ..+.+.+.|..| .+++..|--.+.. .........|..+.+.++++.  |+|+++  +.+-.+||+++.+
T Consensus        16 t~~~y~idDgTG-~i~~~~w~~~~~~~~~~~~~i~~g~YVrV~G~lk~--f~~~~~--I~~~~irpv~d~N   81 (95)
T cd04478          16 TNITYTIDDGTG-TIEVRQWLDDDNDDSSEVEPIEEGTYVRVFGNLKS--FQGKKS--IMAFSIRPVTDFN   81 (95)
T ss_pred             CEEEEEEECCCC-CEEEEEECCCCCCCCCCCCCCCCCCEEEEEEEEEE--ECCEEE--EEEEEEEEECCCC
T ss_conf             579999987987-39999963778764222443326989999999800--289137--9999999937975


No 160
>PRK10886 DnaA initiator-associating protein DiaA; Provisional
Probab=71.48  E-value=7.7  Score=18.69  Aligned_cols=105  Identities=14%  Similarity=0.244  Sum_probs=57.2

Q ss_pred             CCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHH--HHHHHHHHCCCC-----EEEEEC-----CCCCCCCCCCHHHHH
Q ss_conf             48799999999999779979999407886152899--999999976994-----799807-----874336688978988
Q gi|254780901|r   76 TDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVA--LMMRFLSHCSVN-----ANMYIP-----DRIVDGYGPNPSLME  143 (600)
Q Consensus        76 ~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitsta--il~~~L~~~g~~-----v~~~IP-----~R~~eGYGl~~~~i~  143 (600)
                      ..+++|++.|.+++.++.||.++|.   -|-.+.|  +..+++..+..+     +...-.     .-+...||...-..+
T Consensus        25 ~~I~~aa~~i~~~l~~g~ki~~cGN---GGSaa~A~Hfa~el~~~f~~~R~~lpai~L~~d~s~lTai~ND~~~~~vF~r  101 (196)
T PRK10886         25 DAISRAAMTLVQSLLNGNKILCCGN---GTSAANAQHFAASMINRFETERPSLPAIALNTDNVVLTAIANDRLHDEVYAK  101 (196)
T ss_pred             HHHHHHHHHHHHHHHCCCEEEEEEC---CHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCCHHHHHHHCCCCHHHHHHH
T ss_conf             9999999999999987997999868---4748899999999964655689884056632670565431166779999999


Q ss_pred             HHHHC--CCCEEEEE-CCCCC--CHHHHHHHHHCCCCEEEECCCC
Q ss_conf             74202--68689996-48876--2345555541798279961544
Q gi|254780901|r  144 KFINE--GAQLIITV-DCGST--SYDALQYATNQGIDVIVIDHHQ  183 (600)
Q Consensus       144 ~~~~~--g~~LiItv-D~Gi~--~~e~i~~a~~~GidvIVtDHH~  183 (600)
                      .+..-  .-+++|.. -.|-|  =.+++++|+++||.||..==..
T Consensus       102 Ql~alg~~gDiLi~iStSGnS~Nii~Ai~~A~~~g~~~i~ltG~~  146 (196)
T PRK10886        102 QVRALGHAGDVLLAISTRGNSRDIVKAVEAAVTRDMTIVALTGYD  146 (196)
T ss_pred             HHHHHCCCCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEECCC
T ss_conf             999856799989999489999899999999998899899997688


No 161
>smart00481 POLIIIAc DNA polymerase alpha chain like domain. DNA polymerase alpha chain like domain, incl. family of hypothetical proteins
Probab=71.14  E-value=7.8  Score=18.63  Aligned_cols=50  Identities=22%  Similarity=0.288  Sum_probs=35.0

Q ss_pred             CCCC--CCCCCCHHHHHHHHHCCCCEEEEECCCC--CCHHHHHHHHHCCCCEEE
Q ss_conf             8743--3668897898874202686899964887--623455555417982799
Q gi|254780901|r  129 DRIV--DGYGPNPSLMEKFINEGAQLIITVDCGS--TSYDALQYATNQGIDVIV  178 (600)
Q Consensus       129 ~R~~--eGYGl~~~~i~~~~~~g~~LiItvD~Gi--~~~e~i~~a~~~GidvIV  178 (600)
                      ..++  +|..--.+.++.+++.|.+.+-.+|.+.  +..+..+++++.||.+|+
T Consensus         6 T~~S~~dg~~~~~~lv~~a~~~g~~~vaiTDh~~~~g~~~~~~~~~~~gi~~I~   59 (67)
T smart00481        6 SDYSLLDGALSPEELVKRAKELGLKAIAITDHGNLFGAVEFYKAAKKAGIKPII   59 (67)
T ss_pred             CCCCHHHCCCCHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHCCCEEEE
T ss_conf             658565636899999999998799889996788644699999999986997999


No 162
>PRK02145 consensus
Probab=71.11  E-value=7.9  Score=18.63  Aligned_cols=74  Identities=14%  Similarity=0.201  Sum_probs=58.7

Q ss_pred             HHHHHHHHHHCCCCEEEEEC-CCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCC
Q ss_conf             99999999976994799807-8743366889789887420268689996488762345555541798279961544
Q gi|254780901|r  109 VALMMRFLSHCSVNANMYIP-DRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQ  183 (600)
Q Consensus       109 tail~~~L~~~g~~v~~~IP-~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~  183 (600)
                      -.-+.+.+...|++--+.+- ++..+|...+.+.++++.+. +.+=|++-=||.+.+.++.+-+.|.|=||+.-..
T Consensus        33 P~~~a~~~~~~GadelhivDld~a~~~~~~~~~~I~~i~~~-~~iPi~vGGGIrs~e~~~~ll~~GadkVii~s~a  107 (257)
T PRK02145         33 PVEIARRYDEQGADELTFLDITATSDGRDLILPIIEAVASQ-VFIPLTVGGGVRAVEDVRRLLNAGADKVSMNSSA  107 (257)
T ss_pred             HHHHHHHHHHCCCCEEEEEECCCCCCCCHHHHHHHHHHHHH-CCCCEEEECCCCCHHHHHHHHHCCCCEEEEHHHH
T ss_conf             99999999987999899997888766754089999999965-6874896277304688999998199889841556


No 163
>COG3010 NanE Putative N-acetylmannosamine-6-phosphate epimerase [Carbohydrate transport and metabolism]
Probab=71.07  E-value=7.9  Score=18.62  Aligned_cols=113  Identities=19%  Similarity=0.227  Sum_probs=77.3

Q ss_pred             CCCHHHCCCHHHHHH------------HHHHHHHCCCCEEEEE----CCCCC--HHHHHHHHHHHHHHCCCCEEEEE-CC
Q ss_conf             899556148799999------------9999997799799994----07886--15289999999997699479980-78
Q gi|254780901|r   69 MPDPLILTDCDKAAR------------RIVQAIYNSEKIMIFG----DYDVD--GAASVALMMRFLSHCSVNANMYI-PD  129 (600)
Q Consensus        69 ~~dP~~l~dm~~A~~------------ri~~ai~~~ekI~I~g----DyD~D--Gitstail~~~L~~~g~~v~~~I-P~  129 (600)
                      +++|+.+.-|-+|+.            +=.+||++.-.+-|+|    ||+--  =||.|.==++.|-..|+++-.+= -.
T Consensus        29 l~~~~iv~~mA~Aa~~gGAvgiR~~gv~dIkai~~~v~vPIIGIiKrd~~~s~v~ITptlkeVd~L~~~Ga~IIA~DaT~  108 (229)
T COG3010          29 LDSPEIVAAMALAAEQGGAVGIRIEGVEDIKAIRAVVDVPIIGIIKRDYPDSPVRITPTLKEVDALAEAGADIIAFDATD  108 (229)
T ss_pred             CCCHHHHHHHHHHHHHCCCCEEEECCHHHHHHHHHHCCCCEEEEEECCCCCCCCEECCCHHHHHHHHHCCCCEEEEECCC
T ss_conf             76565999999999857862686120656999986178876888805899999355661899999997799099962556


Q ss_pred             CCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCCCC
Q ss_conf             743366889789887420268689996488762345555541798279961544765
Q gi|254780901|r  130 RIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKS  186 (600)
Q Consensus       130 R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~~~~  186 (600)
                      |-. .-|--.+.+.+  ...+..++..||.  ++|+.-+|.++|+|.|=|--+--.+
T Consensus       109 R~R-P~~~~~~~i~~--~k~~~~l~MAD~S--t~ee~l~a~~~G~D~IGTTLsGYT~  160 (229)
T COG3010         109 RPR-PDGDLEELIAR--IKYPGQLAMADCS--TFEEGLNAHKLGFDIIGTTLSGYTG  160 (229)
T ss_pred             CCC-CCCHHHHHHHH--HHCCCCEEEECCC--CHHHHHHHHHCCCCEEECCCCCCCC
T ss_conf             879-84359999997--3357947873259--8888888997399678224201468


No 164
>PRK03369 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=70.96  E-value=7.9  Score=18.60  Aligned_cols=33  Identities=12%  Similarity=0.309  Sum_probs=22.4

Q ss_pred             HHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             97799799994078861528999999999769947998
Q gi|254780901|r   89 IYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMY  126 (600)
Q Consensus        89 i~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~  126 (600)
                      ..++++|+|+|    =|.|+-| ..++|...|++|..+
T Consensus         9 ~~~Gk~V~V~G----lG~sG~a-~a~~L~~~G~~v~~~   41 (487)
T PRK03369          9 LTPGAPVLVAG----AGVTGRA-VLAALTRFGARPTVC   41 (487)
T ss_pred             CCCCCEEEEEE----ECHHHHH-HHHHHHHCCCEEEEE
T ss_conf             57989899991----5683899-999999786979999


No 165
>PRK02269 ribose-phosphate pyrophosphokinase; Provisional
Probab=70.85  E-value=7.9  Score=18.59  Aligned_cols=73  Identities=16%  Similarity=0.318  Sum_probs=53.0

Q ss_pred             CCCEEEEE-CCC-C-CHHHHHHHHHHHHHHCCCC-EEEEEC--------CCCCCCCCCCHHHHHHHHH-CCCCEEEEECC
Q ss_conf             99799994-078-8-6152899999999976994-799807--------8743366889789887420-26868999648
Q gi|254780901|r   92 SEKIMIFG-DYD-V-DGAASVALMMRFLSHCSVN-ANMYIP--------DRIVDGYGPNPSLMEKFIN-EGAQLIITVDC  158 (600)
Q Consensus        92 ~ekI~I~g-DyD-~-DGitstail~~~L~~~g~~-v~~~IP--------~R~~eGYGl~~~~i~~~~~-~g~~LiItvD~  158 (600)
                      ++.+.|.. =+. + |.+.-.-+|..+++..|++ +...+|        .|+..|--++...+-++.+ .|++-|||+|-
T Consensus        52 g~dV~ivqs~~~pvnd~lmELll~idAlr~a~A~~It~ViPY~~YaRQDr~~~~ge~isak~vA~lL~~~g~d~vitvDl  131 (321)
T PRK02269         52 GHHVFILQSTSSPVNDNLMEILIMVDALKRASAESISVVMPYYGYARQDRKARSREPITSKLVANMLEVAGVDRLLTVDL  131 (321)
T ss_pred             CCEEEEECCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEECC
T ss_conf             98089990799995379999999999998748973999813553130454457899726999999887448777999626


Q ss_pred             CCCCHH
Q ss_conf             876234
Q gi|254780901|r  159 GSTSYD  164 (600)
Q Consensus       159 Gi~~~e  164 (600)
                      -....+
T Consensus       132 H~~~i~  137 (321)
T PRK02269        132 HAAQIQ  137 (321)
T ss_pred             CCHHHH
T ss_conf             747776


No 166
>cd06311 PBP1_ABC_sugar_binding_like_3 Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems. Periplasmic sugar-binding domain of uncharacterized ABC-type transport systems that share homology with a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily, which consists of two domains connected by a three-stranded hinge. The substrate specificity of this group is not known, but it is predicted to be involved in the transport of sugar-containing molecules and chemotaxis.
Probab=70.46  E-value=8.1  Score=18.52  Aligned_cols=45  Identities=20%  Similarity=0.257  Sum_probs=33.7

Q ss_pred             HHHHHHHHHCCCCEEEEECCCC-CCHHHHHHHHHCCCCEEEECCCC
Q ss_conf             7898874202686899964887-62345555541798279961544
Q gi|254780901|r  139 PSLMEKFINEGAQLIITVDCGS-TSYDALQYATNQGIDVIVIDHHQ  183 (600)
Q Consensus       139 ~~~i~~~~~~g~~LiItvD~Gi-~~~e~i~~a~~~GidvIVtDHH~  183 (600)
                      ...|+.++.+|++.||..=.-. .....++.|++.||.||..|.-.
T Consensus        50 ~~~ie~lI~qgvDaIiv~p~d~~a~~~~v~~a~~aGIpVV~~D~~~   95 (274)
T cd06311          50 NAQQDLLINRKIDALVILPFESAPLTQPVAKAKKAGIFVVVVDRGL   95 (274)
T ss_pred             HHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHHCCCEEEEECCCC
T ss_conf             9999999974999999957977888999999998699799978888


No 167
>cd02812 PcrB_like PcrB_like proteins. One member of this family, a protein from Archaeoglobus fulgidus, has been characterized as a (S)-3-O-geranylgeranylglyceryl phosphate synthase (AfGGGPS). AfGGGPS catalyzes the formation of an ether linkage between sn-glycerol-1-phosphate (G1P) and geranylgeranyl diphosphate (GGPP), the committed step in archaeal lipid biosynthesis. Therefore, it has been proposed that PcrB-like proteins are either prenyltransferases or are involved in lipoteichoic acid biosynthesis although the exact function is still unknown.
Probab=70.15  E-value=8.2  Score=18.48  Aligned_cols=46  Identities=17%  Similarity=0.190  Sum_probs=23.0

Q ss_pred             CCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCC
Q ss_conf             8978988742026868999648876234555554179827996154
Q gi|254780901|r  137 PNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHH  182 (600)
Q Consensus       137 l~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH  182 (600)
                      .+++.|+.+++.=.+..+.|-=||.+.|....+.+.|-|+||+--.
T Consensus       161 v~~e~V~~vk~~l~~~~LivGGGIrs~e~a~~~~~AgAD~IVvGn~  206 (219)
T cd02812         161 GPPEVVRAVKKVLGDTPLIVGGGIRSGEQAKEMAEAGADTIVVGNI  206 (219)
T ss_pred             CCHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHCCCCEEEECCC
T ss_conf             9999999999846797099928979999999999869999998872


No 168
>PRK13809 orotate phosphoribosyltransferase; Provisional
Probab=70.10  E-value=8.2  Score=18.47  Aligned_cols=73  Identities=16%  Similarity=0.261  Sum_probs=41.4

Q ss_pred             HHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHH-HHHHHHCCCCEEEEEC---CCCCCHHHHHHHHHCCCCEE
Q ss_conf             1528999999999769947998078743366889789-8874202686899964---88762345555541798279
Q gi|254780901|r  105 GAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSL-MEKFINEGAQLIITVD---CGSTSYDALQYATNQGIDVI  177 (600)
Q Consensus       105 Gitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~-i~~~~~~g~~LiItvD---~Gi~~~e~i~~a~~~GidvI  177 (600)
                      |++-++|-.-+.-....++-+.+..+...+||-.... +|-....|-+.+|.=|   .|.|..++++.+++.|..|.
T Consensus        73 Gv~~ggip~A~~ia~~~~~P~~~vRke~K~~g~~~~i~iEG~~~~G~kVvvIEDViTTGgSil~ai~~lr~~G~~V~  149 (206)
T PRK13809         73 GVPYTALTLATSISLKYNIPMVLRRKELQNVDPSDAIKVEGLFTPGQTCLVINDMVSSGKSIIETAVALEENGLVVR  149 (206)
T ss_pred             CCCHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCEEEECCCCCCCCEEEEEEEEECCCHHHHHHHHHHHHCCCEEE
T ss_conf             43133899999999860998388744545678676025335778998899997334468009999999998799699


No 169
>PRK04923 ribose-phosphate pyrophosphokinase; Provisional
Probab=70.01  E-value=8.3  Score=18.46  Aligned_cols=74  Identities=18%  Similarity=0.297  Sum_probs=50.0

Q ss_pred             HHCCCCEEEEE--CCCC-CHHHHHHHHHHHHHHCCC-CEEEEEC-------C-CCCCCC-CCCHHHHHHHHHC-CCCEEE
Q ss_conf             97799799994--0788-615289999999997699-4799807-------8-743366-8897898874202-686899
Q gi|254780901|r   89 IYNSEKIMIFG--DYDV-DGAASVALMMRFLSHCSV-NANMYIP-------D-RIVDGY-GPNPSLMEKFINE-GAQLII  154 (600)
Q Consensus        89 i~~~ekI~I~g--DyD~-DGitstail~~~L~~~g~-~v~~~IP-------~-R~~eGY-Gl~~~~i~~~~~~-g~~LiI  154 (600)
                      +. ++.+.|+-  ..++ |-+.-..+|..+|+..|+ ++...+|       + ++.+|- .++...+-++.+. |++-+|
T Consensus        51 vr-g~dv~ivqs~~~~~nd~lmELll~idAlr~a~A~rIt~ViPY~~YsRQDr~~~~g~~pIsak~vA~lL~~~gvdrvi  129 (319)
T PRK04923         51 VR-RQEVFVIQPTCAPSAENLMELLVLIDALKRASASSVTAVIPYFGYSRQDRRMRSSRVPITAKVAAKMICAMGADRVL  129 (319)
T ss_pred             CC-CCCEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEECCCCHHHCCCCCCCCCCCEEHHHHHHHHCCCCCCEEE
T ss_conf             57-99889993799980789999999999998758872799832553200013346676870299999886125876279


Q ss_pred             EECCCCCCH
Q ss_conf             964887623
Q gi|254780901|r  155 TVDCGSTSY  163 (600)
Q Consensus       155 tvD~Gi~~~  163 (600)
                      |+|.-+...
T Consensus       130 tvDlH~~qi  138 (319)
T PRK04923        130 TVDLHADQI  138 (319)
T ss_pred             EECCCHHHH
T ss_conf             844887998


No 170
>PRK13587 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; Provisional
Probab=69.99  E-value=8.3  Score=18.45  Aligned_cols=83  Identities=13%  Similarity=0.090  Sum_probs=53.0

Q ss_pred             EECCCCCHHHHHH--HHHHHH-HHCCCCEEEEE-CCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCC
Q ss_conf             9407886152899--999999-97699479980-7874336688978988742026868999648876234555554179
Q gi|254780901|r   98 FGDYDVDGAASVA--LMMRFL-SHCSVNANMYI-PDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQG  173 (600)
Q Consensus        98 ~gDyD~DGitsta--il~~~L-~~~g~~v~~~I-P~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~G  173 (600)
                      -||||..=.-+..  -....+ +.-|++--+.+ -+.-..|-..|.+.|+++.+. +++-|.|-=||.+.+.++.+-+.|
T Consensus        20 qG~~~~~~~~~~~~~~~~~~~~~~~Ga~~lHvVDLdgA~~g~~~n~~~I~~i~~~-~~~~iqvGGGIRs~e~i~~~l~~G   98 (234)
T PRK13587         20 EGKYDSEEKMSRSAEESIAYYSQFECVNRIHIVDLIGAKAQHAREFDYIKSLRRL-TTKDIEVGGGIRTKSQIMDYFAAG   98 (234)
T ss_pred             CCCCCCCEECCCCHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCHHHHHHHHHHH-CCCCEEEECCCCCHHHHHHHHHCC
T ss_conf             5879996484799999999999838998899997876468974379999999843-798679846547599999999768


Q ss_pred             CCEEEECC
Q ss_conf             82799615
Q gi|254780901|r  174 IDVIVIDH  181 (600)
Q Consensus       174 idvIVtDH  181 (600)
                      .+-+|+--
T Consensus        99 ~~rViigT  106 (234)
T PRK13587         99 INYCIVGT  106 (234)
T ss_pred             CCEEEECC
T ss_conf             99999888


No 171
>cd06320 PBP1_allose_binding Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. Periplasmic allose-binding domain of bacterial transport systems that function as a primary receptor of active transport and chemotaxis. The members of this group are belonging to a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily.  Like other periplasmic receptors of the ABC-type transport systems, the allose-binding protein consists of two alpha/beta domains connected by a three-stranded hinge. This Venus flytrap-like domain undergoes transition from an open to a closed conformational state upon ligand binding.
Probab=69.47  E-value=8.5  Score=18.37  Aligned_cols=69  Identities=17%  Similarity=0.192  Sum_probs=43.8

Q ss_pred             HHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCC-CHHHHHHHHHCCCCEEEECCC
Q ss_conf             9999976994799807874336688978988742026868999648876-234555554179827996154
Q gi|254780901|r  113 MRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGST-SYDALQYATNQGIDVIVIDHH  182 (600)
Q Consensus       113 ~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~-~~e~i~~a~~~GidvIVtDHH  182 (600)
                      -+..+.+|.++.++.++--.+ .--....++.+..+|++-||..-.... ..+.++.|++.||.||..|.-
T Consensus        22 e~~a~~~G~~v~v~~~~~~~d-~~~q~~~i~~~i~~~vdgii~~p~~~~~~~~~~~~a~~~gIpvv~~d~~   91 (275)
T cd06320          22 ENEAKKLGVSVDIQAAPSEGD-QQGQLSIAENMINKGYKGLLFSPISDVNLVPAVERAKKKGIPVVNVNDK   91 (275)
T ss_pred             HHHHHHCCCEEEEEECCCCCC-HHHHHHHHHHHHHCCCCEEEECCCCCHHHHHHHHHHHHCCCEEEEECCC
T ss_conf             999997499899996899758-9999999999997499879876788065699999998679909992688


No 172
>PRK02270 consensus
Probab=69.26  E-value=8.5  Score=18.34  Aligned_cols=80  Identities=19%  Similarity=0.292  Sum_probs=54.1

Q ss_pred             HHHHHHCCCCEEEEE-CCCC-CHHHHHHHHHHHHHHCCCC-EEEEEC-------CC-CCCCCCCCHHHHHHHHH-CCCCE
Q ss_conf             999997799799994-0788-6152899999999976994-799807-------87-43366889789887420-26868
Q gi|254780901|r   85 IVQAIYNSEKIMIFG-DYDV-DGAASVALMMRFLSHCSVN-ANMYIP-------DR-IVDGYGPNPSLMEKFIN-EGAQL  152 (600)
Q Consensus        85 i~~ai~~~ekI~I~g-DyD~-DGitstail~~~L~~~g~~-v~~~IP-------~R-~~eGYGl~~~~i~~~~~-~g~~L  152 (600)
                      +.+.+..+.-..|.. ..++ |-+.-..+|..++++.|++ +...||       +| +..|--++...+-++.+ .|++-
T Consensus        46 i~esvrg~dV~ivqs~~~pvnd~lmELll~idA~rrasA~~It~ViPY~~YaRQDrk~~~repIsaklvA~lL~~~G~d~  125 (327)
T PRK02270         46 SKETVRNRDVFIVASTSRPVNENIMELLIFIDSLKRASAKEINVILSYYGYARQDRKSSGRQPIGAKLVADLLEKAGATK  125 (327)
T ss_pred             ECCCCCCCEEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCE
T ss_conf             27877898089987899993178999999999998738872589712544344777668998633999999885247864


Q ss_pred             EEEECCCCCCHH
Q ss_conf             999648876234
Q gi|254780901|r  153 IITVDCGSTSYD  164 (600)
Q Consensus       153 iItvD~Gi~~~e  164 (600)
                      +||+|--+...+
T Consensus       126 vitvDlH~~qiq  137 (327)
T PRK02270        126 IISVDLHNPSIQ  137 (327)
T ss_pred             EEEECCCHHHHH
T ss_conf             788435768885


No 173
>PRK04284 ornithine carbamoyltransferase; Provisional
Probab=68.87  E-value=8.7  Score=18.29  Aligned_cols=22  Identities=9%  Similarity=-0.064  Sum_probs=11.0

Q ss_pred             HHHHCCCCEEEEECCCCCCCCC
Q ss_conf             9997699479980787433668
Q gi|254780901|r  115 FLSHCSVNANMYIPDRIVDGYG  136 (600)
Q Consensus       115 ~L~~~g~~v~~~IP~R~~eGYG  136 (600)
                      +.+++|.++.+.=|+-.+-|.|
T Consensus        66 A~~~LGg~~i~l~~~~s~~~kg   87 (332)
T PRK04284         66 AAHDQGAHVTYLGPTGSQMGKK   87 (332)
T ss_pred             HHHHCCCCEEEECCCCCCCCCC
T ss_conf             9998599689848864527887


No 174
>PRK03604 moaC bifunctional molybdenum cofactor biosynthesis protein C/molybdopterin-binding protein; Provisional
Probab=68.85  E-value=8.5  Score=18.37  Aligned_cols=46  Identities=13%  Similarity=0.146  Sum_probs=21.2

Q ss_pred             EEECCCCHHHHHHHHHHHHHHHCCHHHCCCCEEEEE-EECHHHCCHHHHHHH
Q ss_conf             464222158899999999986226443377147604-434689799999999
Q gi|254780901|r  446 LTVERVNFGRLCDFFQKFAHNIVPALITTPVFKIDG-VLNASAVNIALIDML  496 (600)
Q Consensus       446 ~ti~~~~l~~f~~~l~~~~~~~~~~~~~~~~l~iD~-el~~~~i~~~l~~~L  496 (600)
                      ..+=+|..+..++.+.+.+.+..     .-.+..-+ -+.+.++|++-...+
T Consensus       184 ~~vVPDd~~~I~~~l~~~~~~~~-----dlIlTtGGTG~s~RDvTpEAt~~v  230 (301)
T PRK03604        184 YQIIPDEPEEIAAAVQAWIAEGV-----ELIITTGGTGLGPRDVTVETLEPL  230 (301)
T ss_pred             EEEECCCHHHHHHHHHHHHHCCC-----CEEEEECCCCCCCCCCCHHHHHHH
T ss_conf             28968988999999999997799-----799970897789997888999987


No 175
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=68.84  E-value=8.7  Score=18.28  Aligned_cols=160  Identities=15%  Similarity=0.221  Sum_probs=75.8

Q ss_pred             HHHHHHHHCCCH-HHHHHHHHCCCC-HHHHHHHC----CCCHHHCC------CCHHHC-CC--------H--------HH
Q ss_conf             999998819999-999999967889-78988661----96677718------995561-48--------7--------99
Q gi|254780901|r   30 ALAITQKHAIPD-IVARVLVNRNVS-IDYAKDFL----NPSIRLLM------PDPLIL-TD--------C--------DK   80 (600)
Q Consensus        30 ~~~l~~~~~~~~-~~a~iL~~Rgi~-~~~~~~fL----~p~l~~l~------~dP~~l-~d--------m--------~~   80 (600)
                      +..|++..+.|+ .+.|....=|++ -.+.+..|    ......+.      ..|..+ ..        +        .+
T Consensus        50 i~eLA~~~~vS~aTVvRf~kkLGf~Gf~efK~~l~~~~~~~~~~~~~~~~~~d~~~~i~~k~~~~~~~~l~~t~~~ld~~  129 (293)
T PRK11337         50 LKDVAEALAVSEAMIVKVAKLLGFSGFRNLRSALEDYFSQSEQVLPSELSFDDAPQDVVNKVFNISLQTIMEGQSIVNVD  129 (293)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCHH
T ss_conf             99999895998889999999957897899999999998603233345478788899999999999999999999726999


Q ss_pred             HHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEEC-CC
Q ss_conf             99999999977997999940788615289999999997699479980787433668897898874202686899964-88
Q gi|254780901|r   81 AARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVD-CG  159 (600)
Q Consensus        81 A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD-~G  159 (600)
                      ..+++.+.|.+-++|.|||= -.-+..+.- +..-|..+|..+.++-     |.| +.......+. . -+++|.+. .|
T Consensus       130 ~i~~av~li~~A~~I~i~G~-G~S~~vA~~-~~~kl~rlG~~~~~~~-----d~~-~~~~~a~~l~-~-~Dv~i~iS~sG  199 (293)
T PRK11337        130 EIHRAARFFYQARQRDLYGA-GGSNAICAD-VQHKFLRIGVRCQAYP-----DAH-IMMMSASLLQ-E-GDVVLVVSHSG  199 (293)
T ss_pred             HHHHHHHHHHHCCCEEEEEE-CCHHHHHHH-HHHHHHHCCCEEEEEC-----CHH-HHHHHHHHCC-C-CCEEEEEECCC
T ss_conf             99999999982797089985-726999999-9999998598047647-----778-9999997189-9-98899981899


Q ss_pred             CC--CHHHHHHHHHCCCCEEE-ECCCCCCCCCCCCEEEECCCC
Q ss_conf             76--23455555417982799-615447655567256523788
Q gi|254780901|r  160 ST--SYDALQYATNQGIDVIV-IDHHQVKSEEIPAYALVNPNR  199 (600)
Q Consensus       160 i~--~~e~i~~a~~~GidvIV-tDHH~~~~~~p~a~aivNP~~  199 (600)
                      -+  -.+.++.|+++|+.||. ||+..-|=-.-.-+++.-|..
T Consensus       200 ~t~e~i~~~~~Ak~~Ga~vI~IT~~~~SpLa~~aD~vL~~~~~  242 (293)
T PRK11337        200 RTSDVKAAVELAKQNGAKIICITHSYHSPIAKLADYIICSPAP  242 (293)
T ss_pred             CCHHHHHHHHHHHHCCCEEEEECCCCCCHHHHHCCEEEECCCC
T ss_conf             9889999999999879949997699998468958998864887


No 176
>PRK05793 amidophosphoribosyltransferase; Provisional
Probab=68.55  E-value=8.8  Score=18.24  Aligned_cols=39  Identities=15%  Similarity=0.127  Sum_probs=27.4

Q ss_pred             CCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCC
Q ss_conf             99799994078861528999999999769947998078743366889
Q gi|254780901|r   92 SEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPN  138 (600)
Q Consensus        92 ~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~  138 (600)
                      +|.=.|+|=|-.+......++|..|..+        -||=+|+.|+.
T Consensus        15 ~eeCGI~GI~~~~~~~~~~~~y~GL~aL--------QHRGQesaGIa   53 (472)
T PRK05793         15 KEECGVFGVFSNKEIDVASITYYGLYAL--------QHRGQESAGIA   53 (472)
T ss_pred             CCCCEEEEEECCCCHHHHHHHHHHHHHH--------HCCCCCEEEEE
T ss_conf             6676389999688440699999999986--------36787757899


No 177
>pfam01336 tRNA_anti OB-fold nucleic acid binding domain. This family contains OB-fold domains that bind to nucleic acids. The family includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl -tRNA synthetases (See pfam00152). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule EC:6.1.1.-. This family also includes part of RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family. This domain is also found at the C-terminus of bacterial DNA polymerase III alpha chain.
Probab=68.52  E-value=8.8  Score=18.23  Aligned_cols=70  Identities=17%  Similarity=0.184  Sum_probs=48.2

Q ss_pred             EEEEEEEECCCEEEEEEECCCCCEEEEEEECCCCCCHHHHHHCCCCCEEEEEEEEEEEEECCCCEEEEEEEEEEEC
Q ss_conf             9988888479649999984998779999977878701235530699879999997665457811058999980111
Q gi|254780901|r  517 KLQSIRVVNLAHLQMTFESQDSETLQAIAFRVYGTPLGEFLMQSRGKRMHVTGHLCVNYWRGSKRCQLRVLDASPV  592 (600)
Q Consensus       517 ~i~~~r~vGk~Hlkl~l~~~~g~~i~aI~Fn~~~~~~~~~~~~~~g~~idii~~l~~N~~~G~~s~QL~I~Di~p~  592 (600)
                      .|.+.+.-+++++.+.+.|.. ..+++++|+....  ........|..+.+.++++.+  ++. .+|+.+.++++.
T Consensus         6 ~V~~~~~~~~~~~~~~l~D~t-g~i~~~~~~~~~~--~~~~~l~~g~~v~v~G~v~~~--~~~-~~~i~~~~i~~~   75 (75)
T pfam01336         6 RVTSVRRSGGKVAFLTLRDGT-GSIQVVLFKEEAE--KLAKKLKEGDVVLVTGKVKKR--PGG-ELELVVEEIEVL   75 (75)
T ss_pred             EEEEEEECCCCEEEEEEEECC-EEEEEEEEHHHHH--HHHHCCCCCCEEEEEEEEEEC--CCC-CEEEEEEEEEEC
T ss_conf             999518879998999999799-3999999523868--886328989899999999997--499-899999899979


No 178
>cd01524 RHOD_Pyr_redox Member of the Rhodanese Homology Domain superfamily. Included in this CD are the Lactococcus lactis NADH oxidase, Bacillus cereus NADH dehydrogenase, and Bacteroides thetaiotaomicron pyridine nucleotide-disulphide oxidoreductase, and similar rhodanese-like domains found C-terminal of the pyridine nucleotide-disulphide oxidoreductase (Pyr-redox) domain and the Pyr-redox dimerization domain.
Probab=68.20  E-value=8.2  Score=18.49  Aligned_cols=32  Identities=13%  Similarity=0.319  Sum_probs=18.5

Q ss_pred             HHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEE
Q ss_conf             977997999940788615289999999997699479
Q gi|254780901|r   89 IYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNAN  124 (600)
Q Consensus        89 i~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~  124 (600)
                      +..+++|.+|.   .-|..| +.....|+..|.+|.
T Consensus        48 l~k~~~ivv~C---~~G~rS-~~aa~~L~~~G~~v~   79 (90)
T cd01524          48 LPKDKEIIVYC---AVGLRG-YIAARILTQNGFKVK   79 (90)
T ss_pred             HCCCCEEEEEC---CCCCHH-HHHHHHHHHCCCCEE
T ss_conf             61587099988---998059-999999998699889


No 179
>PRK07208 hypothetical protein; Provisional
Probab=68.15  E-value=8.8  Score=18.23  Aligned_cols=31  Identities=13%  Similarity=0.320  Sum_probs=21.9

Q ss_pred             CCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             799799994078861528999999999769947998
Q gi|254780901|r   91 NSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMY  126 (600)
Q Consensus        91 ~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~  126 (600)
                      +++||+|.|    =|+|+.+..++. .+.|.+|..+
T Consensus         2 ~~kkv~IiG----AG~~GL~aA~~L-~~~g~~v~vl   32 (474)
T PRK07208          2 EKKSVVIIG----AGPAGLTAAYEL-VKRGYPVTIL   32 (474)
T ss_pred             CCCEEEEEC----CCHHHHHHHHHH-HHCCCCEEEE
T ss_conf             987599989----768999999999-8689975999


No 180
>PRK05858 hypothetical protein; Provisional
Probab=68.13  E-value=9  Score=18.18  Aligned_cols=103  Identities=13%  Similarity=0.040  Sum_probs=52.2

Q ss_pred             HHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCC--CCCCCCCCHHHHHHHHHCCCCEEEEEC
Q ss_conf             999999999977997999940788615289999999997699479980787--433668897898874202686899964
Q gi|254780901|r   80 KAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDR--IVDGYGPNPSLMEKFINEGAQLIITVD  157 (600)
Q Consensus        80 ~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R--~~eGYGl~~~~i~~~~~~g~~LiItvD  157 (600)
                      ++++++.+.+.+-++-+|+....+.---+..-+.++...+|+-|..-...|  +.+.|-+.........-...+++|.+.
T Consensus       193 ~~i~~a~~~L~~AkrPvii~G~gv~~~~a~~~l~~lae~lg~Pv~tt~~gkg~~p~~hpl~~~~~~~~~l~~aDlil~iG  272 (543)
T PRK05858        193 DALDRAAGLLSTAQRPVIMAGTNVWWGHAEAALLRLAEELHIPVLMNGMARGVVPADHPLAFSRARSKALGEADVALVVG  272 (543)
T ss_pred             HHHHHHHHHHHHCCCCEEEECCCCCCCCHHHHHHHHHHHHCCCEEECCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEEC
T ss_conf             99999999998279978996864223333999999999869977875555776888770456578998855699899965


Q ss_pred             CCCCCHHHHHHHHHCCCCEEEECCC
Q ss_conf             8876234555554179827996154
Q gi|254780901|r  158 CGSTSYDALQYATNQGIDVIVIDHH  182 (600)
Q Consensus       158 ~Gi~~~e~i~~a~~~GidvIVtDHH  182 (600)
                      +.....-.....-.....+|..|-.
T Consensus       273 ~~l~~~~~~~~~~~~~~~~i~vd~~  297 (543)
T PRK05858        273 VPMDFRLGFGGVFGSTTQLVVVDRA  297 (543)
T ss_pred             CCCCEECCCCCCCCCCCEEEEEECC
T ss_conf             7654111565435887649996178


No 181
>TIGR02634 xylF D-xylose ABC transporter, substrate-binding protein; InterPro: IPR013456   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).     This entry represents the D-xylose ABC transporter substrate-binding protein which is a periplasmic (when in Gram-negative bacteria) binding protein for D-xylose import by a high-affinity ATP-binding cassette (ABC) transporter..
Probab=67.71  E-value=9.1  Score=18.12  Aligned_cols=72  Identities=19%  Similarity=0.216  Sum_probs=53.5

Q ss_pred             HHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCC-EEEEECCCCCCHHHHHHHHHCCCCEEEECCCC
Q ss_conf             9999999997699479980787433668897898874202686-89996488762345555541798279961544
Q gi|254780901|r  109 VALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQ-LIITVDCGSTSYDALQYATNQGIDVIVIDHHQ  183 (600)
Q Consensus       109 tail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~-LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~  183 (600)
                      -+++...+..+|+++..-=-+--+   --...-||.+...|++ |||..-+|..=-..|..|++.||.|+--|-=.
T Consensus        17 ~~~~~~~~E~~gAK~~~~~A~~~~---~~Q~S~iE~li~~gv~vlvi~~~~~~vl~~~~~~A~~~GI~V~aYDRLI   89 (307)
T TIGR02634        17 RDIFVAKAESLGAKVFVQSANGNE---AKQLSQIENLIARGVDVLVIIPYNGEVLSNAVQEAKKEGIKVLAYDRLI   89 (307)
T ss_pred             HHHHHHHHHHCCCCEEEECCCCCC---HHHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHCCCEEEEEECCC
T ss_conf             999999986349828985267740---2347889999867980999953686037889999987798088730111


No 182
>KOG2754 consensus
Probab=67.67  E-value=9.1  Score=18.11  Aligned_cols=97  Identities=19%  Similarity=0.296  Sum_probs=63.4

Q ss_pred             HCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEE-----------------------ECCCCCCCCCCCHHHHHHHH
Q ss_conf             7799799994078861528999999999769947998-----------------------07874336688978988742
Q gi|254780901|r   90 YNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMY-----------------------IPDRIVDGYGPNPSLMEKFI  146 (600)
Q Consensus        90 ~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~-----------------------IP~R~~eGYGl~~~~i~~~~  146 (600)
                      ...-+.++..|-+.+ ..+.++..+-|+.-|.++.|.                       -|.-..-|=-++.+.+-+..
T Consensus        21 ~~~~RtLVL~d~~~~-~ethSvFl~sLkdRgf~L~~~~a~dssl~L~~Ygq~LyDnlIifap~~e~fgg~is~k~l~~Fv   99 (443)
T KOG2754          21 SQAARTLVLLDNLAV-KETHSVFLKSLKDRGFKLTYKLADDSSLALFKYGQRLYDNLIIFAPSVENFGGSISVKSLAKFV   99 (443)
T ss_pred             CCCCCEEEEEECCCC-CCCHHHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHHHCCEEEECCCHHHCCCCCCHHHHHHHH
T ss_conf             036737999622000-1103545645875694048974377315788753576546799467435407878989999998


Q ss_pred             HCCCCEEEEECCCCCCHHHHH-HHHHCCCC-----EEEECCCCCCCCCC
Q ss_conf             026868999648876234555-55417982-----79961544765556
Q gi|254780901|r  147 NEGAQLIITVDCGSTSYDALQ-YATNQGID-----VIVIDHHQVKSEEI  189 (600)
Q Consensus       147 ~~g~~LiItvD~Gi~~~e~i~-~a~~~Gid-----vIVtDHH~~~~~~p  189 (600)
                      +.|-++++..  |+..-+.|. .+++.||+     ..|+|||.-....+
T Consensus       100 d~gGnvlv~a--ss~~~d~iRe~~~E~g~~~~e~~~~ViDH~~~d~s~~  146 (443)
T KOG2754         100 DSGGNVLVAA--SSAIGDAIREFASECGIEFDEEGAAVIDHHNYDVSSD  146 (443)
T ss_pred             HCCCCEEEEC--CCCCCHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCC
T ss_conf             4798489984--7766478999999729650746662454430113578


No 183
>PRK01368 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=67.55  E-value=9.2  Score=18.09  Aligned_cols=75  Identities=17%  Similarity=0.194  Sum_probs=38.0

Q ss_pred             HCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHH------------HHCCCCEEEEEC
Q ss_conf             77997999940788615289999999997699479980787433668897898874------------202686899964
Q gi|254780901|r   90 YNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKF------------INEGAQLIITVD  157 (600)
Q Consensus        90 ~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~------------~~~g~~LiItvD  157 (600)
                      -+++||+|+|    =|.|+-|. .++|+..+..+.+. -.+      -+.+..++.            .-.++++||. =
T Consensus         4 ~~~K~v~V~G----lG~sG~a~-~~~L~~~~~~~~~d-d~~------~~~~~~~~~~~~~~~~~~~~~~~~~~d~iV~-S   70 (450)
T PRK01368          4 HTKQKIGVFG----LGKTGISV-YEELQNKYDLIVYD-DLK------ANRDIFEELFSKNAIIALSDSRWQNLDKIVL-S   70 (450)
T ss_pred             CCCCEEEEEE----ECHHHHHH-HHHHHHCCCEEEEE-CCC------CCHHHHHHHHCCCCEECCCCCCHHCCCEEEE-C
T ss_conf             6899089995----87879999-99997199989998-996------5647899752148360257111521999998-9


Q ss_pred             CCCC-CHHHHHHHHHCCCCEE
Q ss_conf             8876-2345555541798279
Q gi|254780901|r  158 CGST-SYDALQYATNQGIDVI  177 (600)
Q Consensus       158 ~Gi~-~~e~i~~a~~~GidvI  177 (600)
                      -||. +++.+..|+++||.|+
T Consensus        71 PGI~~~~p~~~~a~~~~i~i~   91 (450)
T PRK01368         71 PGIPLTHEIVKIAKNFNIPIT   91 (450)
T ss_pred             CCCCCCCHHHHHHHHCCCCEE
T ss_conf             961998999999998799587


No 184
>PRK00865 glutamate racemase; Provisional
Probab=67.53  E-value=9.2  Score=18.09  Aligned_cols=81  Identities=19%  Similarity=0.384  Sum_probs=57.9

Q ss_pred             CCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCC---------CHHHHHHHHHCCCCEEEEECCCCCC
Q ss_conf             9979999407886152899999999976994799807874336688---------9789887420268689996488762
Q gi|254780901|r   92 SEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGP---------NPSLMEKFINEGAQLIITVDCGSTS  162 (600)
Q Consensus        92 ~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl---------~~~~i~~~~~~g~~LiItvD~Gi~~  162 (600)
                      +.+|.||-    -|+-+-+++....+.+-..-.+|+.|.-.-.||-         ..+.++.+.+.++++||. =|-+.+
T Consensus         2 ~~pIGiFD----SGvGGLtVl~~l~~~lP~e~~iY~gD~a~~PYG~ks~~~I~~~~~~i~~~l~~~~~k~iVi-ACNTas   76 (262)
T PRK00865          2 NAPIGVFD----SGVGGLTVLREIRRQLPDEHIIYVGDTARFPYGEKSEEEIRERTLEIVEFLLEQGVKMLVI-ACNTAS   76 (262)
T ss_pred             CCCEEEEE----CCCCHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEE-ECCCHH
T ss_conf             99789986----8988799999999978999989982378899898999999999999999999779989998-167378


Q ss_pred             HHHHHHHHHC-CCCEE
Q ss_conf             3455555417-98279
Q gi|254780901|r  163 YDALQYATNQ-GIDVI  177 (600)
Q Consensus       163 ~e~i~~a~~~-GidvI  177 (600)
                      .-+++.+++. .+.+|
T Consensus        77 a~al~~lr~~~~iPii   92 (262)
T PRK00865         77 AVALEDLRERLDIPVV   92 (262)
T ss_pred             HHHHHHHHHHCCCCEE
T ss_conf             9999999964799779


No 185
>pfam05728 UPF0227 Uncharacterized protein family (UPF0227). Despite being classed as uncharacterized proteins, the members of this family are almost certainly enzymes that are distantly related to the pfam00561.
Probab=67.49  E-value=9.2  Score=18.08  Aligned_cols=24  Identities=17%  Similarity=0.134  Sum_probs=19.2

Q ss_pred             HHHHHHHHHHHHHHHCEEEEEEEC
Q ss_conf             222222789988420107998863
Q gi|254780901|r  381 GIVGLLAARLKEKFGRPSFAISFE  404 (600)
Q Consensus       381 GViGIVAsrL~e~y~kP~iv~s~~  404 (600)
                      .+=|--|..|+|+|+.|++++.+.
T Consensus        67 SLGGfyAt~lae~~~~~aVLINPA   90 (187)
T pfam05728        67 SLGGYYATWLGFRCGLRQVLFNPA   90 (187)
T ss_pred             CCHHHHHHHHHHHCCCCEEEECCC
T ss_conf             707999999998639877997589


No 186
>PRK01659 consensus
Probab=67.45  E-value=9.2  Score=18.08  Aligned_cols=75  Identities=15%  Similarity=0.200  Sum_probs=57.0

Q ss_pred             HHHHHHHHHHCCCCEEEEE-CCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCC
Q ss_conf             9999999997699479980-787433668897898874202686899964887623455555417982799615447
Q gi|254780901|r  109 VALMMRFLSHCSVNANMYI-PDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQV  184 (600)
Q Consensus       109 tail~~~L~~~g~~v~~~I-P~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~~  184 (600)
                      -.-+.+.+...|++--+++ -++-.+|...|.+.++++.+. +.+=||+.=||.+.+.++.+-+.|.|-||+.-...
T Consensus        32 P~~~ak~~~~~Gad~ihivDld~a~~g~~~n~~~I~~i~~~-~~ipi~vGGGIrs~e~~~~~l~~GadkViigs~a~  107 (252)
T PRK01659         32 PVEIAAAYNEAGADELVFLDITATHEGRKTMVDVVEKVAAK-VFIPLTVGGGISSVKDMKRLLRAGADKVSINSAAV  107 (252)
T ss_pred             HHHHHHHHHHCCCCEEEEEECCCCCCCCHHHHHHHHHHHHH-CCCCEEEECCEECHHHHHHHHHCCCCEEEECHHHH
T ss_conf             99999999987999999994676656886489999999975-69747996332006888898744885598317775


No 187
>PRK02458 ribose-phosphate pyrophosphokinase; Provisional
Probab=67.29  E-value=9.3  Score=18.06  Aligned_cols=125  Identities=18%  Similarity=0.209  Sum_probs=75.4

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHCCCCHHHHHHHCCCCHHHCCCCHHHCCCHHHHHHHHHHHHHC
Q ss_conf             47887341157888988999999881999999999996788978988661966777189955614879999999999977
Q gi|254780901|r   12 SISGFRWVSLLGQEGINRALAITQKHAIPDIVARVLVNRNVSIDYAKDFLNPSIRLLMPDPLILTDCDKAARRIVQAIYN   91 (600)
Q Consensus        12 s~~~~rW~~~~~~~~~~~~~~l~~~~~~~~~~a~iL~~Rgi~~~~~~~fL~p~l~~l~~dP~~l~dm~~A~~ri~~ai~~   91 (600)
                      -.+.++-.....+...+.+..+++.+|++-.           .-+.+.|=         |      =|--+ |+.+.+ +
T Consensus         4 ~~~~~~~~ifsgss~~~La~~ia~~Lg~~l~-----------~~~~~~Fp---------D------GE~~v-~i~e~V-r   55 (323)
T PRK02458          4 RYADKQIKLFSLNSNLPIAEKIAKAAGIPLG-----------KLSSRQFS---------D------GEIMI-NIEESV-R   55 (323)
T ss_pred             CCCCCCEEEEECCCCHHHHHHHHHHHCCCCC-----------CEEEEECC---------C------CCEEE-EECCCC-C
T ss_conf             4579975999799999999999999689841-----------21889889---------9------98898-647877-8


Q ss_pred             CCCEEEEECC--CC-CHHHHHHHHHHHHHHCCCC-EEEEEC-------CC-CCCCCCCCHHHHHHHH-HCCCCEEEEECC
Q ss_conf             9979999407--88-6152899999999976994-799807-------87-4336688978988742-026868999648
Q gi|254780901|r   92 SEKIMIFGDY--DV-DGAASVALMMRFLSHCSVN-ANMYIP-------DR-IVDGYGPNPSLMEKFI-NEGAQLIITVDC  158 (600)
Q Consensus        92 ~ekI~I~gDy--D~-DGitstail~~~L~~~g~~-v~~~IP-------~R-~~eGYGl~~~~i~~~~-~~g~~LiItvD~  158 (600)
                      ++.+.|....  .+ |-+.-.-+|..++++.|++ +...+|       +| +.+|-.++...+-++. ..|++-+||+|-
T Consensus        56 g~dV~iiqs~~~p~nd~lmELll~idA~r~agA~~It~ViPY~~YaRQDr~~~~gepIsak~vA~lL~~~G~d~vitvDl  135 (323)
T PRK02458         56 GDDIYIIQSTSFPVNDHLWELLIMIDACKRASANTVNVVLPYFGYARQDRIAKPREPITAKLVANMLVKAGVDRVLTLDL  135 (323)
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCEEEEECC
T ss_conf             98389986899893089999999999998738871899832465454776658998741999999987538865788427


Q ss_pred             CCCCHH
Q ss_conf             876234
Q gi|254780901|r  159 GSTSYD  164 (600)
Q Consensus       159 Gi~~~e  164 (600)
                      -....+
T Consensus       136 H~~~i~  141 (323)
T PRK02458        136 HAVQVQ  141 (323)
T ss_pred             CCHHHH
T ss_conf             818774


No 188
>TIGR01055 parE_Gneg DNA topoisomerase IV, B subunit; InterPro: IPR005737   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils .   This entry represents subunit B (parE) of topoisomerase IV from Gram negative bacteria. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication . Topoisomerase IV consists of two polypeptide subunits, parC (subunit A), which is homologous to gyrA of topoisomerase II, and parE (subunit B), which is homologous to gyrB of topoisomerase II.   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0005694 chromosome.
Probab=67.17  E-value=6.5  Score=19.27  Aligned_cols=70  Identities=24%  Similarity=0.307  Sum_probs=44.1

Q ss_pred             CCHHHHHHHHCCC---CCCCHHHH----HHHHH-----H--------HCCHHH--HH--CCCCCCCEEEECCCHHHHHHH
Q ss_conf             7435789870888---64242345----66677-----4--------306233--31--212222100203425899999
Q gi|254780901|r  277 PGLKALIERVNIS---SPITAENL----GYMIG-----P--------SINAGG--RI--GESNLGSRLLISDDSQELEML  332 (600)
Q Consensus       277 ~gl~~L~~~~~~~---~~i~~~di----~f~ia-----P--------rINAaG--Rl--~~a~~av~lL~~~d~~~a~~l  332 (600)
                      -++++.++..++.   -++|++||    +|.+.     |        ||-+-+  .+  +--..++.++++.|...|+.+
T Consensus       300 ~a~~~f~E~~~~~P~~~~Lt~eDI~~~~s~vLS~~~~~p~F~GQTKE~L~S~~~a~~V~~v~KD~F~~~L~~~~~~A~~L  379 (647)
T TIGR01055       300 DALREFCEMRNLLPRGVKLTAEDILDRCSYVLSIKMQDPQFAGQTKERLSSRQVAKLVSGVIKDAFDLWLNQNVQLAEKL  379 (647)
T ss_pred             HHHHHHHHHHCCCCCEEECCHHHHHHHHHEEEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999888751886402210888873111014556655665775312331313578877778778888741107889999


Q ss_pred             HHHHHHHHHHHHHH
Q ss_conf             99999899999999
Q gi|254780901|r  333 AMKLDVLNQNRRLM  346 (600)
Q Consensus       333 a~~L~~lN~~Rk~~  346 (600)
                      ++..-..-+.||.+
T Consensus       380 ~E~~I~~A~~Rrn~  393 (647)
T TIGR01055       380 AEIAISSAQRRRNK  393 (647)
T ss_pred             HHHHHHHHHHHHHH
T ss_conf             99998888877654


No 189
>cd01534 4RHOD_Repeat_3 Member of the Rhodanese Homology Domain superfamily, repeat 3. This CD includes putative rhodanese-related sulfurtransferases which contain 4 copies of the Rhodanese Homology Domain. This CD aligns the 3rd repeat which does not contain the putative catalytic Cys residue.
Probab=67.02  E-value=6.6  Score=19.23  Aligned_cols=41  Identities=20%  Similarity=0.358  Sum_probs=30.1

Q ss_pred             HHHHHH-HCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECC
Q ss_conf             988742-02686899964887623455555417982799615
Q gi|254780901|r  141 LMEKFI-NEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDH  181 (600)
Q Consensus       141 ~i~~~~-~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDH  181 (600)
                      .++++. ..+..+++.|..|..|..+...++++|.+|.+.+-
T Consensus        47 ~~~~~~~~k~~~ivl~C~~G~RS~~AA~~L~~~G~~v~~L~G   88 (95)
T cd01534          47 ETDHFAPVRGARIVLADDDGVRADMTASWLAQMGWEVYVLEG   88 (95)
T ss_pred             HHHHHCCCCCCEEEEECCCCCCHHHHHHHHHHCCCCEEEECC
T ss_conf             765424668983999859998799999999986997699578


No 190
>KOG4131 consensus
Probab=67.01  E-value=6.8  Score=19.11  Aligned_cols=31  Identities=19%  Similarity=0.246  Sum_probs=19.0

Q ss_pred             CCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCC
Q ss_conf             8689996488762345555541798279961544
Q gi|254780901|r  150 AQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQ  183 (600)
Q Consensus       150 ~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~  183 (600)
                      -+++.|.|---+=   .+.|.+.+.++||-=|-.
T Consensus        46 ~kVlLT~DLTe~V---~eEa~ek~~e~IvAYHP~   76 (272)
T KOG4131          46 KKVLLTNDLTESV---AEEALEKNAESIVAYHPP   76 (272)
T ss_pred             CEEEEECCCHHHH---HHHHHHHCCCEEEEECCC
T ss_conf             3466750030899---999997077466763675


No 191
>TIGR01162 purE phosphoribosylaminoimidazole carboxylase, catalytic subunit; InterPro: IPR000031   Phosphoribosylaminoimidazole carboxylase is a fusion protein in plants and fungi, but consists of two non-interacting proteins in bacteria, PurK and PurE. PurK, N5-carboxyaminoimidazole ribonucleotide (N5_CAIR) synthetase, catalyzes the conversion of 5-aminoimidazole ribonucleotide (AIR), ATP, and bicarbonate to N5-CAIR, ADP, and Pi. PurE converts N5-CAIR to CAIR, the sixth step of de novo purine biosynthesis. In the presence of high concentrations of bicarbonate, PurE is reported able to convert AIR to CAIR directly and without ATP. Some members of this family contain two copies of this domain . The crystal structure of PurE indicates a unique quaternary structure that confirms the octameric nature of the enzyme .; GO: 0004638 phosphoribosylaminoimidazole carboxylase activity, 0006189 'de novo' IMP biosynthetic process, 0009320 phosphoribosylaminoimidazole carboxylase complex.
Probab=67.00  E-value=9.4  Score=18.01  Aligned_cols=47  Identities=13%  Similarity=0.193  Sum_probs=33.1

Q ss_pred             HHHHHHCCCCEEEEE--CCCCCCCCCCCHHHHHHHHHCCC-CEEEEECCCCCCH
Q ss_conf             999997699479980--78743366889789887420268-6899964887623
Q gi|254780901|r  113 MRFLSHCSVNANMYI--PDRIVDGYGPNPSLMEKFINEGA-QLIITVDCGSTSY  163 (600)
Q Consensus       113 ~~~L~~~g~~v~~~I--P~R~~eGYGl~~~~i~~~~~~g~-~LiItvD~Gi~~~  163 (600)
                      .++|+.||..++..|  +||.-|   .-.+.++++.+.|. +.||.+ .|-++|
T Consensus        18 ~~~L~~fgi~~e~~V~SAHRTP~---~~~~ya~~a~~~G~P~ViIAg-AGgaAH   67 (159)
T TIGR01162        18 AEILEEFGIPYELRVVSAHRTPE---LMFEYAKEAEERGIPKVIIAG-AGGAAH   67 (159)
T ss_pred             HHHHHHCCCCEEEEEECCCCCHH---HHHHHHHHHHHCCCCEEEEEC-CCCCCC
T ss_conf             99998559966789860677808---899999999867899799840-351133


No 192
>PRK00910 ribB 3,4-dihydroxy-2-butanone 4-phosphate synthase; Provisional
Probab=66.51  E-value=9.6  Score=17.95  Aligned_cols=92  Identities=12%  Similarity=0.244  Sum_probs=45.4

Q ss_pred             HHHHHHHHHHCCCCEEEEECCCCCH----HH----HHHHHHHHH-HHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCC
Q ss_conf             9999999997799799994078861----52----899999999-97699479980787433668897898874202686
Q gi|254780901|r   81 AARRIVQAIYNSEKIMIFGDYDVDG----AA----SVALMMRFL-SHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQ  151 (600)
Q Consensus        81 A~~ri~~ai~~~ekI~I~gDyD~DG----it----stail~~~L-~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~  151 (600)
                      -++...+++++++.|.|+-|-|=.+    +.    .|.=...|+ +..+.-++.-++...-+.-||..-....-...++.
T Consensus        16 ~Ie~Ai~al~~Gk~Viv~DdedREnEgDlv~aAe~~t~e~i~fm~~~~~GliC~~~~~~~~~~L~Lp~mv~~~~~~~~ta   95 (218)
T PRK00910         16 RVENALQALREGRGVLLLDDEDRENEGDIIYSVEHLTNAQMALMIRECSGIVCLCLTDEQANKLELPPMVVNNNSANQTA   95 (218)
T ss_pred             HHHHHHHHHHCCCEEEEEECCCCCCHHCEEEEHHHCCHHHHHHHHHHCCCCEEEECCHHHHHHCCCCCCCCCCCCCCCCC
T ss_conf             29999999988995999978998761416867664999999999995997199647999997779986567888878876


Q ss_pred             EEEEEC------CCCCCHHHHHHHHHC
Q ss_conf             899964------887623455555417
Q gi|254780901|r  152 LIITVD------CGSTSYDALQYATNQ  172 (600)
Q Consensus       152 LiItvD------~Gi~~~e~i~~a~~~  172 (600)
                      .-++||      .|||+.+...-.+.+
T Consensus        96 ftvsvda~~g~tTGISa~DRa~TIr~l  122 (218)
T PRK00910         96 FTVSIEAKHGVTTGVSAQDRVTTIKTA  122 (218)
T ss_pred             CEEEEEECCCCCCCCCHHHHHHHHHHH
T ss_conf             268876047876884889999999997


No 193
>pfam08981 consensus
Probab=66.48  E-value=9  Score=18.18  Aligned_cols=20  Identities=30%  Similarity=0.328  Sum_probs=8.7

Q ss_pred             CEEEEECCCCCHHHHHHHHHHHHHHH
Q ss_conf             50262057858122222278998842
Q gi|254780901|r  369 SVIVVEGDRWHPGIVGLLAARLKEKF  394 (600)
Q Consensus       369 ~~ivv~~~~wh~GViGIVAsrL~e~y  394 (600)
                      +-+||++..      |=.|-++.+.+
T Consensus        27 ~~iVvASss------G~TA~k~~e~~   46 (181)
T pfam08981        27 KHIVVASSS------GETALKAAEAL   46 (181)
T ss_pred             CEEEEEECC------CHHHHHHHHHH
T ss_conf             769998078------77999999871


No 194
>PRK03220 consensus
Probab=66.18  E-value=9.7  Score=17.90  Aligned_cols=70  Identities=9%  Similarity=0.165  Sum_probs=50.0

Q ss_pred             HHHHHHHCCCCEEEEE-CCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCC
Q ss_conf             9999997699479980-7874336688978988742026868999648876234555554179827996154
Q gi|254780901|r  112 MMRFLSHCSVNANMYI-PDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHH  182 (600)
Q Consensus       112 l~~~L~~~g~~v~~~I-P~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH  182 (600)
                      +.+.+...|++--+.+ .+.-..|-..|.+.++++.++ +.+=||+-.||.+.+.++.+-+.|.|=||+--.
T Consensus        36 ~a~~~~~~G~d~lhivDld~a~~g~~~n~~~I~~i~~~-~~~pi~vGGGIrs~e~~~~ll~~GadkVvigs~  106 (257)
T PRK03220         36 LAAVYDAEGADELTFLDVTASSSGRATMLDVVRRTAEQ-VFIPLTVGGGVRTVEDVDSLLRAGADKVSVNTA  106 (257)
T ss_pred             HHHHHHHCCCCEEEEEECCCCCCCCHHHHHHHHHHHHC-CCCCEEEECCCCCHHHHHHHHHCCCCEEECHHH
T ss_conf             99999986999899990888756763079999999850-696489847858799999999819750872066


No 195
>cd00758 MoCF_BD MoCF_BD: molybdenum cofactor (MoCF) binding domain (BD). This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor, like MoaB, MogA, and MoeA. The domain is presumed to bind molybdopterin.
Probab=66.17  E-value=9.7  Score=17.90  Aligned_cols=99  Identities=12%  Similarity=0.051  Sum_probs=50.8

Q ss_pred             HHHHHHHHHHHHCCCCEEEE--ECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHH----HHHHCCCCEEEEC
Q ss_conf             28999999999769947998--07874336688978988742026868999648876234555----5541798279961
Q gi|254780901|r  107 ASVALMMRFLSHCSVNANMY--IPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQ----YATNQGIDVIVID  180 (600)
Q Consensus       107 tstail~~~L~~~g~~v~~~--IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~----~a~~~GidvIVtD  180 (600)
                      +++..|...|+..|.++.++  +|+...+    -.++++++.+ .+++|||.  |-++..+-+    ...++|-..+.. 
T Consensus        19 sn~~~l~~~l~~~G~~v~~~~iv~Dd~~~----i~~~l~~~~~-~~DlIItt--GG~s~g~~D~t~~~l~~~g~~~~~~-   90 (133)
T cd00758          19 TNGPALEALLEDLGCEVIYAGVVPDDADS----IRAALIEASR-EADLVLTT--GGTGVGRRDVTPEALAELGEREAHG-   90 (133)
T ss_pred             HHHHHHHHHHHHCCCEEEEEEEECCCHHH----HHHHHHHHHH-CCCEEEEC--CCCCCCCCCCHHHHHHHHCCCEEEE-
T ss_conf             37999999999889979898898979999----9999999861-49999993--8866798851899999853928888-


Q ss_pred             CCC-CCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             544-765556725652378888643344304788999999
Q gi|254780901|r  181 HHQ-VKSEEIPAYALVNPNRLDDLSGQGHLCAAGVVFLVL  219 (600)
Q Consensus       181 HH~-~~~~~p~a~aivNP~~~~~~~p~~~l~gaGvaf~l~  219 (600)
                      |.. ...-.|-.+++++-+      +.-.|.|.=+|-+.+
T Consensus        91 ~~v~~~PG~p~~~g~~~~~------~v~~LPG~P~aa~~~  124 (133)
T cd00758          91 KGVALAPGSRTAFGIIGKV------LIINLPGSPKSALTT  124 (133)
T ss_pred             EEEEEEECCEEEEEEECCE------EEEECCCCHHHHHHH
T ss_conf             7654530670689999999------999889998999999


No 196
>pfam01070 FMN_dh FMN-dependent dehydrogenase.
Probab=66.15  E-value=9.5  Score=17.99  Aligned_cols=40  Identities=23%  Similarity=0.371  Sum_probs=24.9

Q ss_pred             HHHHHHHHC-CCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCC
Q ss_conf             898874202-6868999648876234555554179827996154
Q gi|254780901|r  140 SLMEKFINE-GAQLIITVDCGSTSYDALQYATNQGIDVIVIDHH  182 (600)
Q Consensus       140 ~~i~~~~~~-g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH  182 (600)
                      +.++.+.+. +..+||-   ||-+.+....|.+.|+|-|+.-.|
T Consensus       159 ~~i~~l~~~~~~PvivK---GI~s~eDA~~a~~~Gv~~I~VSnH  199 (301)
T pfam01070       159 DDLAWLRDQWKGPLVLK---GILSPEDAKRAVEAGVDGIVVSNH  199 (301)
T ss_pred             HHHHHHHHHCCCCEEEE---CCCCHHHHHHHHHCCCCEEEECCC
T ss_conf             99999998669988998---289999999999859999996499


No 197
>PRK01438 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=66.10  E-value=9.8  Score=17.89  Aligned_cols=31  Identities=10%  Similarity=0.202  Sum_probs=20.1

Q ss_pred             CCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             799799994078861528999999999769947998
Q gi|254780901|r   91 NSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMY  126 (600)
Q Consensus        91 ~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~  126 (600)
                      ++++|+|+|    =|.|+-+. .++|...|++|..+
T Consensus        13 ~gk~v~V~G----lG~sG~s~-a~~L~~~G~~v~~~   43 (481)
T PRK01438         13 SGLRVVVAG----LGVSGFPA-ADALHELGASVTVV   43 (481)
T ss_pred             CCCEEEEEE----ECHHHHHH-HHHHHHCCCEEEEE
T ss_conf             899899995----75889999-99999679989999


No 198
>cd06301 PBP1_rhizopine_binding_like Periplasmic binding proteins specific to rhizopines. Periplasmic binding proteins specific to rhizopines, which are simple sugar-like compounds produced in the nodules induced by the symbiotic root nodule bacteria, such as Rhizobium and Sinorhizobium. Rhizopine-binding-like proteins from other bacteria are also included. Two inositol based rhizopine compounds are known to date: L-3-O-methly-scyllo-inosamine (3-O-MSI) and scyllo-inosamine. Bacterial strains that can metabolize rhizopine have a greater competitive advantage in nodulation and rhizopine synthesis is regulated by NifA/NtrA regulatory transcription activators which are maximally expressed at the onset of nitrogen fixation in bacteroids. The members of this group belong to the pentose/hexose sugar-binding protein family of the type I periplasmic binding protein superfamily.
Probab=66.09  E-value=9.8  Score=17.89  Aligned_cols=45  Identities=24%  Similarity=0.426  Sum_probs=33.4

Q ss_pred             HHHHHHHHHCCCCEEEEECCCC-CCHHHHHHHHHCCCCEEEECCCC
Q ss_conf             7898874202686899964887-62345555541798279961544
Q gi|254780901|r  139 PSLMEKFINEGAQLIITVDCGS-TSYDALQYATNQGIDVIVIDHHQ  183 (600)
Q Consensus       139 ~~~i~~~~~~g~~LiItvD~Gi-~~~e~i~~a~~~GidvIVtDHH~  183 (600)
                      .+.|+.+...+++-||.+-+-. +..+.++.|.+.||.||..|...
T Consensus        46 ~~~i~~li~~~vDgIii~p~d~~~~~~~~~~a~~agIPvV~~d~~~   91 (272)
T cd06301          46 LSQVENFIAQGVDAIIVVPVDTAATAPIVKAANAAGIPLVYVNRRP   91 (272)
T ss_pred             HHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHCCCCEEEEECCC
T ss_conf             9999999985999999955882111899999998699889993566


No 199
>cd05126 Mth938 Mth938 domain. Mth938 is a hypothetical protein encoded by the Methanobacterium thermoautotrophicum (Mth) genome. This protein crystallizes as a dimer, although it is monomeric in solution, with one disulfide bond in each monomer. The function of the protein has not been determined.
Probab=66.04  E-value=9.8  Score=17.88  Aligned_cols=49  Identities=20%  Similarity=0.524  Sum_probs=37.5

Q ss_pred             CCCCCCCHHHHHHHHHCCCCEEEEECCCCC-----CHHHHHHHHHCCCCEEEECC
Q ss_conf             336688978988742026868999648876-----23455555417982799615
Q gi|254780901|r  132 VDGYGPNPSLMEKFINEGAQLIITVDCGST-----SYDALQYATNQGIDVIVIDH  181 (600)
Q Consensus       132 ~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~-----~~e~i~~a~~~GidvIVtDH  181 (600)
                      ..+++++++-++.+.+.+++.|| +-+|.+     .-+..+++++.||.|++.|-
T Consensus        41 ~~~h~l~~~dl~~ll~~~~evlv-iGTG~~g~l~v~p~~~~~l~~~gi~v~~~~T   94 (117)
T cd05126          41 GTSHGLQPEELEELLEEGVEVIV-IGTGQSGALKVPPETVEKLEKRGVEVLVLPT   94 (117)
T ss_pred             CCCCCCCHHHHHHHHHCCCCEEE-ECCCCCCCCCCCHHHHHHHHHCCCCEEEECH
T ss_conf             77898899999999971999999-8589686564899999999975981898375


No 200
>cd02750 MopB_Nitrate-R-NarG-like Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to nitrite and forms part of a redox loop generating a proton-motive force. Found in prokaryotes and some archaea, NarGHI usually functions as a heterotrimer. The alpha chain contains the molybdenum cofactor-containing Mo-bisMGD catalytic subunit. Members of the MopB_Nitrate-R-NarG-like CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=65.96  E-value=9.8  Score=17.87  Aligned_cols=114  Identities=21%  Similarity=0.141  Sum_probs=54.3

Q ss_pred             HHHHHHHHHHHHHCC--CCEEEEECCCCCHHHHHHHHHHHHHHCCCC-EEEEE--CCC-----CCCCCCCCHHHHHHHHH
Q ss_conf             799999999999779--979999407886152899999999976994-79980--787-----43366889789887420
Q gi|254780901|r   78 CDKAARRIVQAIYNS--EKIMIFGDYDVDGAASVALMMRFLSHCSVN-ANMYI--PDR-----IVDGYGPNPSLMEKFIN  147 (600)
Q Consensus        78 m~~A~~ri~~ai~~~--ekI~I~gDyD~DGitstail~~~L~~~g~~-v~~~I--P~R-----~~eGYGl~~~~i~~~~~  147 (600)
                      ++..++++.+.+++.  +.|..++-.-.-|-.+-+...++++.+|.. ..++.  .+.     ..-|.+.......++  
T Consensus        91 ld~IA~kl~~i~~~~G~~~i~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~~D~--  168 (461)
T cd02750          91 LELIADAIIDTIKKYGPDRVIGFSPIPAMSMVSYAAGSRFASLIGGVSLSFYDWYGDLPPGSPQTWGEQTDVPESADW--  168 (461)
T ss_pred             HHHHHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHEECCCCCCCHHHH--
T ss_conf             999999999999961996499964786404888999999999848976788657674889999883278888987788--


Q ss_pred             CCCCEEEEECCCCCCH-------HHHHHHHHCCCCEEEECCCCCCCCCCCCEEEEC
Q ss_conf             2686899964887623-------455555417982799615447655567256523
Q gi|254780901|r  148 EGAQLIITVDCGSTSY-------DALQYATNQGIDVIVIDHHQVKSEEIPAYALVN  196 (600)
Q Consensus       148 ~g~~LiItvD~Gi~~~-------e~i~~a~~~GidvIVtDHH~~~~~~p~a~aivN  196 (600)
                      .++++||..  |++..       .-+..|+++|..+||+|....+ .-..|+.-+-
T Consensus       169 ~~a~~il~~--G~N~~~~~~~~~~~i~~ar~~GaklivIDPr~t~-ta~~AD~~l~  221 (461)
T cd02750         169 YNADYIIMW--GSNVPVTRTPDAHFLTEARYNGAKVVVVSPDYSP-SAKHADLWVP  221 (461)
T ss_pred             HCCCEEEEE--CCCHHHHCCHHHHHHHHHHHCCCEEEEECCCCCH-HHHHHCCCCC
T ss_conf             439789995--6787883645469999999779979992699987-8997270468


No 201
>PRK02621 consensus
Probab=65.53  E-value=10  Score=17.81  Aligned_cols=73  Identities=11%  Similarity=0.181  Sum_probs=54.9

Q ss_pred             HHHHHHHHHCCCCEEEEEC-CCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCC
Q ss_conf             9999999976994799807-8743366889789887420268689996488762345555541798279961544
Q gi|254780901|r  110 ALMMRFLSHCSVNANMYIP-DRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQ  183 (600)
Q Consensus       110 ail~~~L~~~g~~v~~~IP-~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~  183 (600)
                      .-+.+.+...|++--+.+- ++-.+|-..+.+.++++.+. +.+=|++.-||.+.+.++.+-+.|.|=||+.-..
T Consensus        33 ~~~ak~~~~~gad~lhivDld~a~~~~~~~~~~I~~i~~~-~~ipi~vGGGIrs~e~~~~ll~~GadkVii~s~a  106 (254)
T PRK02621         33 VELACRYSQAGADELVFLDITATHEGRATLIDVVYRTAEQ-VFIPLTVGGGISSLEGIKELLRAGADKVSLNSAA  106 (254)
T ss_pred             HHHHHHHHHCCCCEEEEEECCCCCCCCHHHHHHHHHHHHH-CCCCEEEECCEEEHHHHHHHHHCCCCEEEECCHH
T ss_conf             9999999985999999982667656754289999999986-7985899633535799999997499989998867


No 202
>PRK12311 rpsB 30S ribosomal protein S2; Provisional
Probab=65.46  E-value=10  Score=17.80  Aligned_cols=96  Identities=15%  Similarity=0.204  Sum_probs=60.5

Q ss_pred             CCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHH----HHHH-----
Q ss_conf             1487999999999997799799994078861528999999999769947998078743366889789----8874-----
Q gi|254780901|r   75 LTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSL----MEKF-----  145 (600)
Q Consensus        75 l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~----i~~~-----  145 (600)
                      .+-+.+|.+-+.+...++.+|+.+|---    -+.-++.++-++.|.   |||-+|---|-=-|-..    |+++     
T Consensus        49 ~~~L~~A~~~v~~ia~~Gg~ILFVGTK~----qa~~~V~~~A~r~~~---~YVn~RWLGGtLTN~~TI~~sI~rL~~le~  121 (332)
T PRK12311         49 VPLLHRALQAVSDTVAKGGRVLFVGTKR----QAQDAVADAAKRSAQ---YFVNSRWLGGTLTNWKTISGSIKRLRKLDE  121 (332)
T ss_pred             HHHHHHHHHHHHHHHHCCCEEEEEECCH----HHHHHHHHHHHHCCC---CEEECCCCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             9999999999999996699799986878----899999999998399---657340027635559999999999999999


Q ss_pred             -------------------------H-------H--CCCCEEEEECCCCCCHHHHHHHHHCCCCEEE
Q ss_conf             -------------------------2-------0--2686899964887623455555417982799
Q gi|254780901|r  146 -------------------------I-------N--EGAQLIITVDCGSTSYDALQYATNQGIDVIV  178 (600)
Q Consensus       146 -------------------------~-------~--~g~~LiItvD~Gi~~~e~i~~a~~~GidvIV  178 (600)
                                               .       +  .=++++|.+|.. ...-+|..|+.+||.||-
T Consensus       122 ~~~~g~~~~ltKKE~l~l~Re~~KL~k~lgGIk~M~~lPDlvfViD~~-kE~iAV~EA~kLgIPvIa  187 (332)
T PRK12311        122 VLSSGDAGAYTKKERLTLQRERDKLDRSLGGIKDMGGLPDLIFVIDTN-KEDIAIQEAQRLGIPVAA  187 (332)
T ss_pred             HHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCC-CCHHHHHHHHHCCCCEEE
T ss_conf             861265233587889999879999998546254205599989996897-338999999980979899


No 203
>COG4213 XylF ABC-type xylose transport system, periplasmic component [Carbohydrate transport and metabolism]
Probab=65.45  E-value=10  Score=17.80  Aligned_cols=73  Identities=21%  Similarity=0.270  Sum_probs=50.2

Q ss_pred             HHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCC-EEEEECCCCCCHHHHHHHHHCCCCEEEECCCCCC
Q ss_conf             999999997699479980787433668897898874202686-8999648876234555554179827996154476
Q gi|254780901|r  110 ALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQ-LIITVDCGSTSYDALQYATNQGIDVIVIDHHQVK  185 (600)
Q Consensus       110 ail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~-LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~~~  185 (600)
                      ..++..++.+|+++.+---+-   --.-...-||.+..+|++ |+|-.=.|.+.-+.++.|++.||.||--|.-...
T Consensus        45 ~~~~~~~e~~g~k~~~q~A~~---~~~~Q~~qien~i~qg~~vlvi~a~d~~~l~~~i~~A~~~gikViaYDRlI~n  118 (341)
T COG4213          45 DAFVKKAEALGAKVDVQSADG---DEEKQLAQIENMINQGVKVLVIGAIDGGVLSNAVEKAKSEGIKVIAYDRLINN  118 (341)
T ss_pred             HHHHHHHHHCCCHHHHHHHCC---CHHHHHHHHHHHHHCCCCEEEEEECCCHHHHHHHHHHHHCCCEEEEEECCCCC
T ss_conf             889999986243230343225---71679999999873599789998135325899999998759949974010026


No 204
>PRK09104 hypothetical protein; Validated
Probab=65.36  E-value=7.4  Score=18.81  Aligned_cols=19  Identities=16%  Similarity=0.284  Sum_probs=9.3

Q ss_pred             CCCCCCEEEECCCHHHHHH
Q ss_conf             1222210020342589999
Q gi|254780901|r  313 ESNLGSRLLISDDSQELEM  331 (600)
Q Consensus       313 ~a~~av~lL~~~d~~~a~~  331 (600)
                      .+.+.++|.-..|++++.+
T Consensus       332 ~akl~~RlvP~qdp~~v~~  350 (465)
T PRK09104        332 SAKVSFRLVGGQDPAKIRE  350 (465)
T ss_pred             EEEEEEEECCCCCHHHHHH
T ss_conf             9999999689999999999


No 205
>PRK00748 1-(5-phosphoribosyl)-5-[(5-phosphoribosylamino)methylideneamino] imidazole-4-carboxamide isomerase; Validated
Probab=65.18  E-value=10  Score=17.76  Aligned_cols=69  Identities=12%  Similarity=0.187  Sum_probs=50.4

Q ss_pred             HHHHHHHCCCCEEEEE-CCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECC
Q ss_conf             9999997699479980-787433668897898874202686899964887623455555417982799615
Q gi|254780901|r  112 MMRFLSHCSVNANMYI-PDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDH  181 (600)
Q Consensus       112 l~~~L~~~g~~v~~~I-P~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDH  181 (600)
                      +.+.+...|++--+++ -+.-.+|-+.|.+.++++.+. +.+=|++.-||.+.+.++.+-+.|.|-+|+--
T Consensus        34 ~A~~~~~~Ga~~lhvvDLd~A~~g~~~n~~~I~~i~~~-~~~pi~vGGGIrs~e~~~~~l~~GadkVvigS  103 (241)
T PRK00748         34 QAQAWQDQGAEWLHLVDLDGAFAGRPVNLELIEAIVAA-VDIPVQLGGGIRDLETVEAYLDAGVARVIIGT  103 (241)
T ss_pred             HHHHHHHCCCCEEEEEECCCCCCCCCCHHHHHHHHHHH-CCCCEEEECCCCCHHHHHHHHHCCCCEEEECC
T ss_conf             99999987999899997854202882079999999986-79999982770749999999976977588647


No 206
>PRK05259 consensus
Probab=64.95  E-value=10  Score=17.73  Aligned_cols=73  Identities=19%  Similarity=0.301  Sum_probs=51.8

Q ss_pred             CCCCEEEEEC--CCC-CHHHHHHHHHHHHHHCCC-CEEEEECC--------CCCCCCCCCHHHHHHHHH-CCCCEEEEEC
Q ss_conf             7997999940--788-615289999999997699-47998078--------743366889789887420-2686899964
Q gi|254780901|r   91 NSEKIMIFGD--YDV-DGAASVALMMRFLSHCSV-NANMYIPD--------RIVDGYGPNPSLMEKFIN-EGAQLIITVD  157 (600)
Q Consensus        91 ~~ekI~I~gD--yD~-DGitstail~~~L~~~g~-~v~~~IP~--------R~~eGYGl~~~~i~~~~~-~g~~LiItvD  157 (600)
                      +++.+.|+..  +.+ |-+.-.-++..+++..|+ ++...||-        |+..|--++...+-++.+ .|++-+||+|
T Consensus        46 rg~dV~ivqs~~~p~nd~lmELll~i~A~r~~~A~~It~ViPY~~YsRQDr~~~~~e~isak~vA~lL~~~G~d~vitvD  125 (310)
T PRK05259         46 RGEDVFVIQSTSYPANDHLMELLIMIDALRRSSARRITAVIPYFGYARQDRKPGPRTPISAKLVANLITEAGADRVLTLD  125 (310)
T ss_pred             CCCCEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCCCCCCEEHHHHHHHHHCCCCCEEEEEC
T ss_conf             89988999079998408899999999999873887179994145511155778999866588875112104776689962


Q ss_pred             CCCCCH
Q ss_conf             887623
Q gi|254780901|r  158 CGSTSY  163 (600)
Q Consensus       158 ~Gi~~~  163 (600)
                      --....
T Consensus       126 lH~~~i  131 (310)
T PRK05259        126 LHAGQI  131 (310)
T ss_pred             CCCHHH
T ss_conf             785777


No 207
>cd06349 PBP1_ABC_ligand_binding_like_14 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=64.83  E-value=10  Score=17.72  Aligned_cols=80  Identities=13%  Similarity=0.097  Sum_probs=35.0

Q ss_pred             CCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEE--CCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHH
Q ss_conf             97999940788615289999999997699479980--7874336688978988742026868999648876234555554
Q gi|254780901|r   93 EKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYI--PDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYAT  170 (600)
Q Consensus        93 ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~I--P~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~  170 (600)
                      +++.++..-+.-|........+.++..|.++....  |.-.+|    -...+.++++.+++.|+.+..|.....-+..++
T Consensus       136 k~v~i~~~~~~~g~~~~~~~~~~~~~~g~~iv~~~~~~~~~~d----~s~~v~~l~~~~~d~v~~~~~~~~~~~~~~~~~  211 (340)
T cd06349         136 KKVAILSVNTDWGRTSADIFVKAAEKLGGQVVAHEEYVPGEKD----FRPTITRLRDANPDAIILISYYNDGAPIARQAR  211 (340)
T ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCC----HHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHH
T ss_conf             3799983686177899999999999749969998625866675----799999998669999999157535999999999


Q ss_pred             HCCCCE
Q ss_conf             179827
Q gi|254780901|r  171 NQGIDV  176 (600)
Q Consensus       171 ~~Gidv  176 (600)
                      +.|.+.
T Consensus       212 ~~G~~~  217 (340)
T cd06349         212 AVGLDI  217 (340)
T ss_pred             HCCCCC
T ss_conf             769997


No 208
>COG1087 GalE UDP-glucose 4-epimerase [Cell envelope biogenesis, outer membrane]
Probab=64.73  E-value=10  Score=17.70  Aligned_cols=13  Identities=31%  Similarity=0.598  Sum_probs=6.1

Q ss_pred             HHCCCCEEEECCC
Q ss_conf             4179827996154
Q gi|254780901|r  170 TNQGIDVIVIDHH  182 (600)
Q Consensus       170 ~~~GidvIVtDHH  182 (600)
                      .+.|.+|+|.|.-
T Consensus        21 l~~G~~vvV~DNL   33 (329)
T COG1087          21 LKTGHEVVVLDNL   33 (329)
T ss_pred             HHCCCEEEEEECC
T ss_conf             9789848999568


No 209
>cd01144 BtuF Cobalamin binding protein BtuF.  These proteins have been shown to function as initial receptors in ABC transport of vitamin B12 (cobalamin) in eubacterial and some archaeal species.  They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism.  A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains. In addition, these proteins sometimes have a low complexity region containing a metal-binding histidine-rich motif (repetitive HDH sequence).
Probab=64.70  E-value=8.8  Score=18.23  Aligned_cols=39  Identities=18%  Similarity=0.278  Sum_probs=27.5

Q ss_pred             HHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECC
Q ss_conf             8874202686899964887623455555417982799615
Q gi|254780901|r  142 MEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDH  181 (600)
Q Consensus       142 i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDH  181 (600)
                      +|.+.+-.++|||+- .+....+.++.+++.|+.|++++.
T Consensus        50 ~E~I~~L~PDLVi~~-~~~~~~~~~~~l~~~gi~v~~~~~   88 (245)
T cd01144          50 LERVLALKPDLVIAW-DDCNVCAVVDQLRAAGIPVLVSEP   88 (245)
T ss_pred             HHHHHCCCCCEEEEE-CCCCHHHHHHHHHCCCCEEEEECC
T ss_conf             999952599647742-687768899987604976998489


No 210
>TIGR02836 spore_IV_A stage IV sporulation protein A; InterPro: IPR014201   This entry is designated stage IV sporulation protein A. It acts in the mother cell compartment and plays a role in spore coat morphogenesis . A comparative genome analysis of all sequenced genomes of Firmicutes shows that the proteins are strictly conserved among the sub-set of endospore-forming species. .
Probab=64.66  E-value=10  Score=17.69  Aligned_cols=66  Identities=18%  Similarity=0.198  Sum_probs=40.7

Q ss_pred             HHHHHHHHHH-HHHCEEEEEEECCC--C-EEEEEEECCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCEEECCCCHHHHHH
Q ss_conf             2222789988-42010799886379--8-379998648986188888853033530115653222314642221588999
Q gi|254780901|r  383 VGLLAARLKE-KFGRPSFAISFEED--G-KGIGSGRSIEGFDIGKMVSFAVEEGILVKGGGHAMAAGLTVERVNFGRLCD  458 (600)
Q Consensus       383 iGIVAsrL~e-~y~kP~iv~s~~~d--g-~~kGS~RSi~g~~l~~~l~~~~~~~ll~~~GGH~~AaG~ti~~~~l~~f~~  458 (600)
                      .|+||.+|.| ++-+|=||=  .++  | .+|.||   +.+|+..+--..-=...+..             +.+=++|.+
T Consensus       365 yGvvap~L~eM~LeePEivr--QG~RFGVrLkAsA---PS~H~ik~Di~~E~~PiiGT-------------EkqSEeLVk  426 (492)
T TIGR02836       365 YGVVAPELEEMKLEEPEIVR--QGNRFGVRLKASA---PSLHIIKADIETEITPIIGT-------------EKQSEELVK  426 (492)
T ss_pred             CEEECCCCCCCCCCCCCEEE--ECCCCEEEEEEEC---CCCEEEECCCCEECCCCCCC-------------CCCCHHHHH
T ss_conf             30441761347898870676--2883125754104---76002330300010564367-------------423178999


Q ss_pred             HHHHHHHH
Q ss_conf             99999986
Q gi|254780901|r  459 FFQKFAHN  466 (600)
Q Consensus       459 ~l~~~~~~  466 (600)
                      ++-+.+.+
T Consensus       427 Yll~~FE~  434 (492)
T TIGR02836       427 YLLEQFEE  434 (492)
T ss_pred             HHHHHHHH
T ss_conf             99898762


No 211
>cd06303 PBP1_LuxPQ_Quorum_Sensing Periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs. Periplasmic binding protein (LuxP) of autoinducer-2 (AI-2) receptor LuxPQ from Vibrio harveyi and its close homologs from other bacteria. The members of this group are highly homologous to a family of periplasmic pentose/hexose sugar-binding proteins that function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea, and that are members of the type I periplasmic binding protein superfamily. The Vibrio harveyi AI-2 receptor consists of two polypeptides, LuxP and LuxQ:  LuxP is a periplasmic binding protein that binds AI-2 by clamping it between two domains, LuxQ is an integral membrane protein belonging to the two-component sensor kinase family. Unlike AI-2 bound to the LsrB receptor in Salmonella typhimurium, the Vibrio harveyi AI-2 signaling molecule has an unusual furanosyl borate 
Probab=64.52  E-value=10  Score=17.67  Aligned_cols=110  Identities=11%  Similarity=0.089  Sum_probs=60.3

Q ss_pred             HHHHHHHHHCCCCE--EEEECCCCCCCCCCCHHHHHHHHHCCCC-EEEEECCCCCCHHHHH-HHHHCCCCEEEECCCCCC
Q ss_conf             99999999769947--9980787433668897898874202686-8999648876234555-554179827996154476
Q gi|254780901|r  110 ALMMRFLSHCSVNA--NMYIPDRIVDGYGPNPSLMEKFINEGAQ-LIITVDCGSTSYDALQ-YATNQGIDVIVIDHHQVK  185 (600)
Q Consensus       110 ail~~~L~~~g~~v--~~~IP~R~~eGYGl~~~~i~~~~~~g~~-LiItvD~Gi~~~e~i~-~a~~~GidvIVtDHH~~~  185 (600)
                      .-+-..+..+|.++  ..|-+..-.| +-.....+++++..+++ +++|+|. +.....|. .+++.++.+||.|=+.|.
T Consensus        20 ~g~e~~a~eLGI~~ei~~~~~~~~~D-~~~Q~~~le~~i~~~~D~Ii~tp~~-~~~~~~I~~~~~~~~~kliv~ni~tp~   97 (280)
T cd06303          20 ASFTARLEELNIPYELTQFSSRPGID-HRLQSQQLNEALQSKPDYLIFTLDS-LRHRKLIERVLASGKTKIILQNITTPV   97 (280)
T ss_pred             HHHHHHHHHCCCCEEEEEECCCCCCC-HHHHHHHHHHHHHCCCCEEEEECCC-HHHHHHHHHHHHCCCCCEEEEECCCCC
T ss_conf             99999999849986998814788747-9999999999985379989991680-566778999997489958999478861


Q ss_pred             CCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             5556725652378888643344304788999999999997021488
Q gi|254780901|r  186 SEEIPAYALVNPNRLDDLSGQGHLCAAGVVFLVLVLIYRILRQDNK  231 (600)
Q Consensus       186 ~~~p~a~aivNP~~~~~~~p~~~l~gaGvaf~l~~al~~~l~~~~~  231 (600)
                      ...-.       .+++.-..|.+..|+   .+++..+.+.++..++
T Consensus        98 ~~~~~-------~~p~~yvg~Dn~~gg---~~~a~~l~~~lg~~g~  133 (280)
T cd06303          98 KAWLK-------HQPLLYVGFDHAAGA---RLLADYFIKRYPNHAR  133 (280)
T ss_pred             HHHHC-------CCCCEEECCCHHHHH---HHHHHHHHHHCCCCCE
T ss_conf             23404-------687558707639999---9999999997599975


No 212
>COG1029 FwdB Formylmethanofuran dehydrogenase subunit B [Energy production and conversion]
Probab=64.51  E-value=10  Score=17.67  Aligned_cols=81  Identities=15%  Similarity=0.243  Sum_probs=43.9

Q ss_pred             CHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHH---------H
Q ss_conf             8799999999999779979999407886152899999999976994799807874336688978988742---------0
Q gi|254780901|r   77 DCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFI---------N  147 (600)
Q Consensus        77 dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~---------~  147 (600)
                      +-++|+++-.+-+.+-++.++||= +.--.-+.++-.+.-..+|+-    |-+--+-.+|.+..++.+.-         .
T Consensus        64 ~~deAie~Aa~ILv~aKrPllyg~-s~tscEA~~~gielaE~~gav----iD~~asvchGp~~~alqe~g~p~~TlgevK  138 (429)
T COG1029          64 DYDEAIEKAAEILVNAKRPLLYGW-SSTSCEAQELGIELAEKLGAV----IDSNASVCHGPSVLALQEAGKPTATLGEVK  138 (429)
T ss_pred             CHHHHHHHHHHHHHHCCCCEEECC-CCCHHHHHHHHHHHHHHHCCE----ECCCCCCCCCHHHHHHHHCCCCCCCHHHHC
T ss_conf             499999999999982678526235-532188999999999873727----747874005657889985598665512212


Q ss_pred             CCCCEEEEECCCCCCHH
Q ss_conf             26868999648876234
Q gi|254780901|r  148 EGAQLIITVDCGSTSYD  164 (600)
Q Consensus       148 ~g~~LiItvD~Gi~~~e  164 (600)
                      +..++||--  |++-.+
T Consensus       139 NraDviVyW--GtNP~~  153 (429)
T COG1029         139 NRADVIVYW--GTNPMH  153 (429)
T ss_pred             CCCCEEEEE--CCCCCC
T ss_conf             566589995--788432


No 213
>cd06268 PBP1_ABC_transporter_LIVBP_like Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type I periplasmic binding fold protein superfamily. Periplasmic binding domain of ATP-binding cassette transporter-like systems that belong to the type I periplasmic binding fold protein superfamily. They are mostly present in archaea and eubacteria, and are primarily involved in scavenging solutes from the environment. ABC-type transporters couple ATP hydrolysis with the uptake and efflux of a wide range of substrates across bacterial membranes, including amino acids, peptides, lipids and sterols, and various drugs. These systems are comprised of transmembrane domains, nucleotide binding domains, and in most bacterial uptake systems, periplasmic binding proteins (PBPs) which transfer the ligand to the extracellular gate of the transmembrane domains. These PBPs bind their substrates selectively and with high affinity.  Members of this group include ABC
Probab=63.97  E-value=11  Score=17.60  Aligned_cols=82  Identities=17%  Similarity=0.104  Sum_probs=38.3

Q ss_pred             CCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHC
Q ss_conf             97999940788615289999999997699479980787433668897898874202686899964887623455555417
Q gi|254780901|r   93 EKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQ  172 (600)
Q Consensus        93 ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~  172 (600)
                      ++|.|..+-|.-|.....-+.+.++..|.++...++.....  .=-...+.++...+++.|+..-.+.....-+..+++.
T Consensus       136 ~~vaiv~~d~~~g~~~~~~~~~~~~~~g~~v~~~~~~~~~~--~d~~~~i~~l~~~~pd~v~~~~~~~~~~~~~~~~~~~  213 (298)
T cd06268         136 KKVAIIYDDYAYGRGLAAAFREALKKLGGEVVAEETYPPGA--TDFSPLIAKLKAAGPDAVFLAGYGGDAALFLKQAREA  213 (298)
T ss_pred             CEEEEECCCCHHHHHHHHHHHHHHHHCCCEEEEEEECCCCC--CCHHHHHHHHHHCCCCEEEECCCCHHHHHHHHHHHHC
T ss_conf             58999778734679999999998997499899999648765--7779999999976999999917626789999999982


Q ss_pred             CCCE
Q ss_conf             9827
Q gi|254780901|r  173 GIDV  176 (600)
Q Consensus       173 Gidv  176 (600)
                      |.+.
T Consensus       214 g~~~  217 (298)
T cd06268         214 GLKV  217 (298)
T ss_pred             CCCC
T ss_conf             9997


No 214
>cd04482 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle depende
Probab=63.91  E-value=11  Score=17.59  Aligned_cols=61  Identities=10%  Similarity=0.118  Sum_probs=42.9

Q ss_pred             CCEEEEEEEEECCCEEEEEEECCCCCEEEEEEECCCCCCHHHHHHCCCCCEEEEEEEEEEEE
Q ss_conf             78099888884796499999849987799999778787012355306998799999976654
Q gi|254780901|r  514 PNHKLQSIRVVNLAHLQMTFESQDSETLQAIAFRVYGTPLGEFLMQSRGKRMHVTGHLCVNY  575 (600)
Q Consensus       514 ~~~~i~~~r~vGk~Hlkl~l~~~~g~~i~aI~Fn~~~~~~~~~~~~~~g~~idii~~l~~N~  575 (600)
                      .+......+.+.++|+.+.+.+.++ .++.++|.-.+.-..-......|+.+.+.+..+.+.
T Consensus         4 ~G~V~~~P~~i~GGHv~~~v~~~~~-~i~~~afepTg~~r~~~r~L~~GD~I~v~G~v~~~~   64 (91)
T cd04482           4 TGKVVEEPRTIEGGHVFFKISDGTG-EIDCAAYEPTKEFRDVVRLLIPGDEVTVYGSVRPGT   64 (91)
T ss_pred             EEEEECCEEEECCCEEEEEEEECCC-EEEEEEECCCCHHHHHHHHCCCCCEEEEEEEECCCC
T ss_conf             9999786489528749999993998-899999987750889997389999999999987898


No 215
>KOG3857 consensus
Probab=63.63  E-value=11  Score=17.56  Aligned_cols=63  Identities=25%  Similarity=0.298  Sum_probs=40.8

Q ss_pred             EEEECCCCCCCCCCCHHHHHHHHHCCCC--EEEEECCCCCCHHHH----HHHHHCCCCEEEECCCCCCCC
Q ss_conf             9980787433668897898874202686--899964887623455----555417982799615447655
Q gi|254780901|r  124 NMYIPDRIVDGYGPNPSLMEKFINEGAQ--LIITVDCGSTSYDAL----QYATNQGIDVIVIDHHQVKSE  187 (600)
Q Consensus       124 ~~~IP~R~~eGYGl~~~~i~~~~~~g~~--LiItvD~Gi~~~e~i----~~a~~~GidvIVtDHH~~~~~  187 (600)
                      .+|||+-..-|-|...++-.+++..|.+  ||+| |-|+.....+    +.+.++||.+-|-|--.|...
T Consensus        44 f~m~~s~~rfG~gv~~Evg~dikn~gaKk~llvT-Dkni~~~~~~~~a~~~L~~~~I~~~vyD~v~~ePt  112 (465)
T KOG3857          44 FFMIPSTSRFGKGVLAEVGDDIKNLGAKKTLLVT-DKNIAKLGLVKVAQDSLEENGINVEVYDKVQPEPT  112 (465)
T ss_pred             EEECCCHHHHCCHHHHHHHHHHHHCCCCCEEEEE-CCCHHHCCCHHHHHHHHHHCCCCEEEECCCCCCCC
T ss_conf             7861513320611689999998715744258960-77744414178999999975981697247647986


No 216
>cd01536 PBP1_ABC_sugar_binding_like Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily. Periplasmic sugar-binding domain of active transport systems that are members of the type I periplasmic binding protein (PBP1) superfamily. The members of this family function as the primary receptors for chemotaxis and transport of many sugar based solutes in bacteria and archaea. The sugar binding domain is also homologous to the ligand-binding domain of eukaryotic receptors such as glutamate receptor (GluR) and DNA-binding transcriptional repressors such as LacI and GalR. Moreover, this periplasmic binding domain, also known as Venus flytrap domain, undergoes transition from an open to a closed conformational state upon the binding of ligands such as lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. This family also includes the periplasmic binding domain of autoinducer-2 (AI-2
Probab=63.57  E-value=11  Score=17.55  Aligned_cols=70  Identities=21%  Similarity=0.178  Sum_probs=42.2

Q ss_pred             HHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCC-CHHHHHHHHHCCCCEEEECCCCCC
Q ss_conf             9999976994799807874336688978988742026868999648876-234555554179827996154476
Q gi|254780901|r  113 MRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGST-SYDALQYATNQGIDVIVIDHHQVK  185 (600)
Q Consensus       113 ~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~-~~e~i~~a~~~GidvIVtDHH~~~  185 (600)
                      .++++..|.++.+.-.+.-.+   -..+.++.+...+++-||.+-.... ..+.++.+++.||-|+..|...+.
T Consensus        22 ~~~a~~~g~~~~~~~~~~~~~---~e~~~i~~~~~~~vdgiI~~~~~~~~~~~~~~~~~~~~iPvV~~d~~~~~   92 (267)
T cd01536          22 EAAAKELGVELIVLDAQNDVS---KQIQQIEDLIAQGVDGIIISPVDSAALTPALKKANAAGIPVVTVDSDIDG   92 (267)
T ss_pred             HHHHHHCCCEEEEEECCCCHH---HHHHHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHCCCCEEEEECCCCC
T ss_conf             999998499999996999999---99999999997599999993158415589999999879969998256678


No 217
>PRK01713 ornithine carbamoyltransferase; Provisional
Probab=63.53  E-value=11  Score=17.54  Aligned_cols=50  Identities=6%  Similarity=-0.077  Sum_probs=22.9

Q ss_pred             HHHHHHHHHH-HHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEE
Q ss_conf             1528999999-9997699479980787433668897898874202686899
Q gi|254780901|r  105 GAASVALMMR-FLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLII  154 (600)
Q Consensus       105 Gitstail~~-~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiI  154 (600)
                      --|=|-+=++ +..++|.++.+.=|+-.+-|.|-+..=.-+....-++.|+
T Consensus        56 pSTRTR~SFE~A~~~LGg~~i~l~~~~s~~~kgEsl~Dta~vls~~~D~iv  106 (334)
T PRK01713         56 TSTRTRCAFEVAAYDQGAQVTYIDPTSSQIGHKESMKDTARVLGRMYDAIE  106 (334)
T ss_pred             CCHHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCCHHHHHHHHHHHCCEEE
T ss_conf             962689999999998599099847512457899899999999996285899


No 218
>TIGR02061 aprA adenylylsulfate reductase, alpha subunit; InterPro: IPR011803    During dissimilatory sulphate reduction or sulphur oxidation, adenylylsulphate (APS) reductase catalyzes reversibly the two-electron reduction of APS to sulphite and AMP. Found in several bacterial lineages and in Archaeoglobales, APS reductase is a heterodimer composed of an alpha subunit containing a noncovalently bound FAD, and a beta subunit containing two [4Fe-4S] clusters. This entry describes the alpha subunit of APS reductase, which shares a common evolutionary origin with fumarate reductase/succinate dehydrogenase flavoproteins..
Probab=63.34  E-value=2.5  Score=22.47  Aligned_cols=157  Identities=15%  Similarity=0.164  Sum_probs=69.9

Q ss_pred             HHHHHHHHCCCCCHHHHHHHHCCCC-CCCHHHHHHHHHHHCCHHHHHCCCCCCCEEEECCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             8788775168874357898708886-424234566677430623331212222100203425899999999998999999
Q gi|254780901|r  266 KGLMVARRQGNPGLKALIERVNISS-PITAENLGYMIGPSINAGGRIGESNLGSRLLISDDSQELEMLAMKLDVLNQNRR  344 (600)
Q Consensus       266 ~GL~~l~~~~~~gl~~L~~~~~~~~-~i~~~di~f~iaPrINAaGRl~~a~~av~lL~~~d~~~a~~la~~L~~lN~~Rk  344 (600)
                      .|++.=+-|.--||=+.-+..+-+. +++|..         =+=|||. |..++++.+.-..+-...-+..++++   ||
T Consensus       432 nG~~YNRMTTVeGLF~~gD~vGa~pHkFSSGS---------ftEGR~A-aKaavr~ildG~k~~~~~~da~~Eel---kk  498 (651)
T TIGR02061       432 NGKKYNRMTTVEGLFAIGDAVGASPHKFSSGS---------FTEGRLA-AKAAVRYILDGKKEGKEVSDAVVEEL---KK  498 (651)
T ss_pred             CCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCC---------CHHHHHH-HHHHHHHHHCCCCCCCCCCHHHHHHH---HH
T ss_conf             88612542120146530134688886677664---------1578899-99997775336788885438899999---99


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHCEEEEEEECCCCEEEEEEECCCCCCHHHH
Q ss_conf             99999999999998752112434750262057858122222278998842010799886379837999864898618888
Q gi|254780901|r  345 LMESAMLEQAEAKVLTQCDDIQQASVIVVEGDRWHPGIVGLLAARLKEKFGRPSFAISFEEDGKGIGSGRSIEGFDIGKM  424 (600)
Q Consensus       345 ~~e~~i~~~a~~~~~~~~~~~~~~~~ivv~~~~wh~GViGIVAsrL~e~y~kP~iv~s~~~dg~~kGS~RSi~g~~l~~~  424 (600)
                      ++=+=+.. -++.-.....+.-|+..|.   |  .+|+.=++  |+.++|.-=+-+.=...+.++-      .|+++..+
T Consensus       499 ~~Y~Pme~-f~~yk~~sTa~~VNPnYI~---P--~qgl~RL~--K~~DEY~gGv~t~Y~Tne~lL~------~gl~lla~  564 (651)
T TIGR02061       499 EVYKPMER-FREYKDESTADSVNPNYIL---P--KQGLVRLQ--KLMDEYAGGVATIYKTNEKLLD------IGLELLAL  564 (651)
T ss_pred             HHCCHHHH-HHHHHHHCCCCCCCCCCCC---C--HHHHHHHH--HHHHHCCCCEEEEEHHHHHHHH------HHHHHHHH
T ss_conf             85122678-8887652278887877447---5--34556765--4432106850465430388999------99999877


Q ss_pred             HHHHCCCCCCCCCCCCCCCCCEEECCCCHHHHHHHHHHHHH
Q ss_conf             88530335301156532223146422215889999999998
Q gi|254780901|r  425 VSFAVEEGILVKGGGHAMAAGLTVERVNFGRLCDFFQKFAH  465 (600)
Q Consensus       425 l~~~~~~~ll~~~GGH~~AaG~ti~~~~l~~f~~~l~~~~~  465 (600)
                      |.+-     +.           .|...+|+++.+..+.+=.
T Consensus       565 leED-----le-----------KLAArdlHELlRaWEl~HR  589 (651)
T TIGR02061       565 LEED-----LE-----------KLAARDLHELLRAWELKHR  589 (651)
T ss_pred             HHHH-----HH-----------HHHHHHHHHHHHHHHHHHH
T ss_conf             6411-----77-----------8878778899988887658


No 219
>PRK04020 rps2P 30S ribosomal protein S2; Provisional
Probab=63.12  E-value=11  Score=17.49  Aligned_cols=130  Identities=22%  Similarity=0.257  Sum_probs=71.0

Q ss_pred             CHHHHHHHHHHHHH-----CCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCC
Q ss_conf             87999999999997-----7997999940788615289999999997699479980787433668897898874202686
Q gi|254780901|r   77 DCDKAARRIVQAIY-----NSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQ  151 (600)
Q Consensus        77 dm~~A~~ri~~ai~-----~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~  151 (600)
                      |+++-.++|..|.+     .+++|+..|-   - -.+.-+..++-+..|.   +|+..|..-|-==| ..++...+  ++
T Consensus        47 DL~kT~~~L~~A~~~l~~~~~~~ILfVgt---k-~qa~~~v~~~A~~~g~---~yv~~RWlgG~LTN-~~l~~~~e--Pd  116 (204)
T PRK04020         47 DVRKTDERIRIAAKFLSRYEPEKILVVSS---R-QYGQKPVKKFAEVVGA---KAITGRFIPGTLTN-PSLKGYIE--PD  116 (204)
T ss_pred             CHHHHHHHHHHHHHHHHHCCCCEEEEEEC---C-HHHHHHHHHHHHHHCC---EEECCCCCCCCCCC-HHHCCCCC--CC
T ss_conf             39999999999999999607984999979---8-9999999999999699---06826227986568-31302568--99


Q ss_pred             EEEEECCCCCCHHHHHHHHHCCCCEEE-ECCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHH-HHHHHHHHHHHHHHC
Q ss_conf             899964887623455555417982799-6154476555672565237888864334430478-899999999999702
Q gi|254780901|r  152 LIITVDCGSTSYDALQYATNQGIDVIV-IDHHQVKSEEIPAYALVNPNRLDDLSGQGHLCAA-GVVFLVLVLIYRILR  227 (600)
Q Consensus       152 LiItvD~Gi~~~e~i~~a~~~GidvIV-tDHH~~~~~~p~a~aivNP~~~~~~~p~~~l~ga-Gvaf~l~~al~~~l~  227 (600)
                      ++|.+|-- ..+.+|..|+.+||.||= .|--..|...    -+.=|-    +  .+..-.. =+.|.|+.++.+.-+
T Consensus       117 lliV~Dp~-~e~~AV~EA~~l~IPvIaivDTn~dp~~V----dy~IP~----N--Dds~~SI~Li~~lLa~ail~~kg  183 (204)
T PRK04020        117 VLVVTDPR-GDAQAVKEAIEIGIPVVALCDTDNLTSNV----DLVIPT----N--NKGRKALALIYWLLAREILRERG  183 (204)
T ss_pred             EEEEECCC-CCHHHHHHHHHCCCCEEEEECCCCCCHHC----CEEEEC----C--CCCHHHHHHHHHHHHHHHHHHCC
T ss_conf             89997886-30489999987699989982799891115----736516----8--83073899999999999999739


No 220
>cd01540 PBP1_arabinose_binding Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. Periplasmic L-arabinose-binding protein (ABP), a member of a family of pentose/hexose sugar-binding proteins of the type I periplasmic binding protein superfamily. ABP is only involved in transport contrary to other related sugar-binding proteins such as the glucose/galactose-binding protein (GGBP) and the ribose-binding protein (RBP), both of which are involved in chemotaxis as well as transport. The periplasmic ABP consists of two alpha/beta globular domains connected by a three-stranded hinge, a Venus flytrap-like domain, which undergoes a transition from an open to a closed conformational state upon ligand binding. Moreover, ABP is homologous to the ligand-binding domain of eukaryotic receptors such as metabotropic glutamate receptor (mGluR) and DNA-binding transcriptional repressors such a
Probab=63.11  E-value=11  Score=17.49  Aligned_cols=49  Identities=16%  Similarity=0.185  Sum_probs=36.0

Q ss_pred             HHHHHHHHHCCCCEEEEECCCCCCHHH-HHHHHHCCCCEEEECCCCCCCC
Q ss_conf             789887420268689996488762345-5555417982799615447655
Q gi|254780901|r  139 PSLMEKFINEGAQLIITVDCGSTSYDA-LQYATNQGIDVIVIDHHQVKSE  187 (600)
Q Consensus       139 ~~~i~~~~~~g~~LiItvD~Gi~~~e~-i~~a~~~GidvIVtDHH~~~~~  187 (600)
                      ...++.++.+|++-||.+-+..++..+ ++.|++.||.||..|+-.+...
T Consensus        44 ~~~ie~~i~qgvd~iii~p~d~~~~~~~v~~A~~agIpVv~~D~~~~~~~   93 (289)
T cd01540          44 LSAIDNLGAQGAKGFVICVPDVKLGPAIVAKAKAYNMKVVAVDDRLVDAD   93 (289)
T ss_pred             HHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHCCCEEEEECCCCCCCC
T ss_conf             99999999858988999278710018999999987986999346455655


No 221
>cd02811 IDI-2_FMN Isopentenyl-diphosphate:dimethylallyl diphosphate isomerase type 2 (IDI-2) FMN-binding domain. Two types of IDIs have been characterized at present. The long known IDI-1 is only dependent on divalent metals for activity, whereas IDI-2 requires a metal, FMN and NADPH. IDI-2 catalyzes the interconversion of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) in the mevalonate pathway.
Probab=62.92  E-value=11  Score=17.46  Aligned_cols=43  Identities=14%  Similarity=0.326  Sum_probs=26.2

Q ss_pred             HHHHHHHHC-CCCEEEE-ECCCCCCHHHHHHHHHCCCCEEEECCCC
Q ss_conf             898874202-6868999-6488762345555541798279961544
Q gi|254780901|r  140 SLMEKFINE-GAQLIIT-VDCGSTSYDALQYATNQGIDVIVIDHHQ  183 (600)
Q Consensus       140 ~~i~~~~~~-g~~LiIt-vD~Gi~~~e~i~~a~~~GidvIVtDHH~  183 (600)
                      +.|+.+.+. ++-+|+- |-||++ .|.+..+.+.|++-|+.=.|=
T Consensus       168 ~~I~~l~~~~~vPVIvKeVG~Gis-~eda~~l~~~Gv~~IdVSghG  212 (326)
T cd02811         168 ERIEELVKALSVPVIVKEVGFGIS-RETAKRLADAGVKAIDVAGAG  212 (326)
T ss_pred             HHHHHHHHHCCCCEEEEECCCCCC-HHHHHHHHHCCCCEEEECCCC
T ss_conf             999999984799858852478999-999999996799999978999


No 222
>KOG4730 consensus
Probab=62.59  E-value=11  Score=17.42  Aligned_cols=78  Identities=14%  Similarity=0.155  Sum_probs=56.4

Q ss_pred             CCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCC-EEE
Q ss_conf             4879999999999977997999940788615289999999997699479980787433668897898874202686-899
Q gi|254780901|r   76 TDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQ-LII  154 (600)
Q Consensus        76 ~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~-LiI  154 (600)
                      +..++-++.++.|-+++.||.+.| |--   |-.            +..      .++|+=+|...+++..+-.+. +-+
T Consensus        57 ~teaeL~~lVa~A~~a~~kirvVg-~gH---Sp~------------~l~------ctdg~lisl~~lnkVv~~dpe~~tv  114 (518)
T KOG4730          57 KTEAELVELVAAATEAGKKIRVVG-SGH---SPS------------KLV------CTDGLLISLDKLNKVVEFDPELKTV  114 (518)
T ss_pred             CCHHHHHHHHHHHHHCCCEEEEEC-CCC---CCC------------CCE------ECCCCEEEHHHHCCCEEECCHHCEE
T ss_conf             879999999999987486589851-567---877------------633------0465477766632312547302047


Q ss_pred             EECCCCCCHHHHHHHHHCCCC
Q ss_conf             964887623455555417982
Q gi|254780901|r  155 TVDCGSTSYDALQYATNQGID  175 (600)
Q Consensus       155 tvD~Gi~~~e~i~~a~~~Gid  175 (600)
                      |||.|++=.+-|+.+.+.|..
T Consensus       115 TV~aGirlrQLie~~~~~Gls  135 (518)
T KOG4730         115 TVQAGIRLRQLIEELAKLGLS  135 (518)
T ss_pred             EECCCCCHHHHHHHHHHCCCC
T ss_conf             712082899999999864845


No 223
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=62.41  E-value=11  Score=17.40  Aligned_cols=53  Identities=11%  Similarity=0.068  Sum_probs=22.0

Q ss_pred             EEECCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCEEECCCCHHHHHHHHHHHH
Q ss_conf             98648986188888853033530115653222314642221588999999999
Q gi|254780901|r  412 SGRSIEGFDIGKMVSFAVEEGILVKGGGHAMAAGLTVERVNFGRLCDFFQKFA  464 (600)
Q Consensus       412 S~RSi~g~~l~~~l~~~~~~~ll~~~GGH~~AaG~ti~~~~l~~f~~~l~~~~  464 (600)
                      ..+|.-|-...+.+....-.-.|..-.|=..-.|++-....-..+++.+-+.+
T Consensus       162 ~~~s~~G~~a~~~l~~~~~d~aFlg~~gi~~~~G~t~~~~~ea~~kr~~i~~a  214 (269)
T PRK09802        162 QSQSFYGDQAEQSLQNYHFDMLFLGVDAIDLERGVSTHNEDEARLNRRMCEVA  214 (269)
T ss_pred             CCCCEECHHHHHHHHHCCCCEEEECCCEECCCCCCCCCCHHHHHHHHHHHHHC
T ss_conf             77726678999999836689999847665589975739999999999999955


No 224
>cd00886 MogA_MoaB MogA_MoaB family. Members of this family are involved in biosynthesis of the molybdenum cofactor (MoCF) an essential cofactor of a diverse group of redox enzymes. MoCF biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea, and eukaryotes. MoCF contains a tricyclic pyranopterin, termed molybdopterin (MPT).  MogA, together with MoeA, is responsible for the metal incorporation into MPT, the third step in MoCF biosynthesis. The plant homolog Cnx1 is a MoeA-MogA fusion protein.  The mammalian homolog gephyrin is a MogA-MoeA fusion protein, that plays a critical role in postsynaptic anchoring of inhibitory glycine receptors and major GABAa receptor subtypes. In contrast, MoaB shows high similarity to MogA, but little is known about its physiological role. All well studied members of this family form highly stable trimers.
Probab=62.38  E-value=11  Score=17.40  Aligned_cols=63  Identities=21%  Similarity=0.398  Sum_probs=37.8

Q ss_pred             EEEEECCCCCH---HHHHHHHHHHHHHCCCCEEEE--ECCCCCCCCCCCHHHHHHHHH-CCCCEEEEECCCCCCH
Q ss_conf             99994078861---528999999999769947998--078743366889789887420-2686899964887623
Q gi|254780901|r   95 IMIFGDYDVDG---AASVALMMRFLSHCSVNANMY--IPDRIVDGYGPNPSLMEKFIN-EGAQLIITVDCGSTSY  163 (600)
Q Consensus        95 I~I~gDyD~DG---itstail~~~L~~~g~~v~~~--IP~R~~eGYGl~~~~i~~~~~-~g~~LiItvD~Gi~~~  163 (600)
                      |...+|-=.-|   =+|+..+.+.|+..|.++..|  ||+-..+   + ...+.++.+ .++++|||.  |=+..
T Consensus         5 Vitvsd~~~~G~~~D~sG~~l~~~l~~~G~~v~~~~ivpDd~~~---I-~~~l~~~~~~~~~DlIitt--GGTG~   73 (152)
T cd00886           5 VLTVSDTRSAGEAEDRSGPALVELLEEAGHEVVAYEIVPDDKDE---I-REALIEWADEDGVDLILTT--GGTGL   73 (152)
T ss_pred             EEEECCCCCCCCCCCCHHHHHHHHHHHCCCEEEEEEEECCCHHH---H-HHHHHHHHHCCCCCEEEEC--CCCCC
T ss_conf             99988877679987756999999998749978899995999899---9-9999999853698889966--85558


No 225
>PRK00455 pyrE orotate phosphoribosyltransferase; Validated
Probab=61.95  E-value=11  Score=17.34  Aligned_cols=107  Identities=17%  Similarity=0.254  Sum_probs=55.9

Q ss_pred             HHCCCCHHHCCCCHHHCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCC
Q ss_conf             66196677718995561487999999999997799799994078861528999999999769947998078743366889
Q gi|254780901|r   59 DFLNPSIRLLMPDPLILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPN  138 (600)
Q Consensus        59 ~fL~p~l~~l~~dP~~l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~  138 (600)
                      -|++..  .+..+|..+.   ..++.+.+.|.+.+-=+|.      |.+-.+|..-+.-....++.+.+..|...+||..
T Consensus        33 ~Y~d~~--~l~~~p~~~~---~i~~~~~~~i~~~~~d~I~------G~a~ggipia~~ia~~l~~p~~~~Rke~K~hG~~  101 (200)
T PRK00455         33 YYFDCR--KLFNYPEALA---LLGRFLAEAIKDSGIDFVA------GPATGGIPLAAAVARALDLPMIFVRKEAKDHGEG  101 (200)
T ss_pred             HHHCCH--HHHHCHHHHH---HHHHHHHHHHHHCCCCEEE------ECCCCHHHHHHHHHHHCCCCEEEEECCCCCCCCC
T ss_conf             671888--9886999999---9999999997544998997------3331068999999997299879997057755658


Q ss_pred             HHHHHHHHHCCCCEEEEEC---CCCCCHHHHHHHHHCCCCEE
Q ss_conf             7898874202686899964---88762345555541798279
Q gi|254780901|r  139 PSLMEKFINEGAQLIITVD---CGSTSYDALQYATNQGIDVI  177 (600)
Q Consensus       139 ~~~i~~~~~~g~~LiItvD---~Gi~~~e~i~~a~~~GidvI  177 (600)
                      .. ++--...|-+.+|.=|   .|.|..+.++.+++.|..|+
T Consensus       102 ~~-ieG~~~~g~~VliVeDViTtG~S~~~ai~~l~~~G~~V~  142 (200)
T PRK00455        102 RQ-IEGALLKGKRVLVVEDVITTGGSVLEAVEAIRAAGAEVV  142 (200)
T ss_pred             CE-EECCCCCCCCEEEEEEHHHCCCCHHHHHHHHHHCCCEEE
T ss_conf             66-642445545348876301047019999999998799799


No 226
>PRK07502 cyclohexadienyl dehydrogenase; Validated
Probab=61.56  E-value=12  Score=17.29  Aligned_cols=35  Identities=17%  Similarity=0.265  Sum_probs=17.8

Q ss_pred             CCCCCCEEEECCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             12222100203425899999999998999999999
Q gi|254780901|r  313 ESNLGSRLLISDDSQELEMLAMKLDVLNQNRRLME  347 (600)
Q Consensus       313 ~a~~av~lL~~~d~~~a~~la~~L~~lN~~Rk~~e  347 (600)
                      ++.+-.++|+++.+.-...+-...+++++-|..++
T Consensus       233 ~p~mW~dI~~~N~~~il~~ld~~~~~L~~l~~~i~  267 (307)
T PRK07502        233 DPTMWRDVFLHNKDAVLEMLGRFTEDLAALQRAIR  267 (307)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             85799999998099999999999999999999998


No 227
>PRK07417 arogenate dehydrogenase; Reviewed
Probab=61.37  E-value=12  Score=17.27  Aligned_cols=45  Identities=20%  Similarity=0.181  Sum_probs=21.4

Q ss_pred             CCHHHHHC--CCCCCCEEEECCCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             06233312--1222210020342589999999999899999999999
Q gi|254780901|r  305 INAGGRIG--ESNLGSRLLISDDSQELEMLAMKLDVLNQNRRLMESA  349 (600)
Q Consensus       305 INAaGRl~--~a~~av~lL~~~d~~~a~~la~~L~~lN~~Rk~~e~~  349 (600)
                      +--..|+.  +|.+-.+++++..+.-...+-+..++++.-|..+++.
T Consensus       213 frD~TRIA~s~p~mW~dI~~~N~~~i~~~l~~~~~~L~~l~~~l~~~  259 (280)
T PRK07417        213 FADTSRVGGGNPELGVMMAEYNRAALLRSLASYRWSLDQLEEAILQE  259 (280)
T ss_pred             HHHCCEECCCCHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             43300003799799999999788999999999999999999999807


No 228
>PRK02812 ribose-phosphate pyrophosphokinase; Provisional
Probab=61.18  E-value=12  Score=17.24  Aligned_cols=121  Identities=17%  Similarity=0.193  Sum_probs=71.4

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHCCCCHHHHHHHCCCCHHHCCCCHHHCCCHHHHHHHHHHHHHCCCCE
Q ss_conf             73411578889889999998819999999999967889789886619667771899556148799999999999779979
Q gi|254780901|r   16 FRWVSLLGQEGINRALAITQKHAIPDIVARVLVNRNVSIDYAKDFLNPSIRLLMPDPLILTDCDKAARRIVQAIYNSEKI   95 (600)
Q Consensus        16 ~rW~~~~~~~~~~~~~~l~~~~~~~~~~a~iL~~Rgi~~~~~~~fL~p~l~~l~~dP~~l~dm~~A~~ri~~ai~~~ekI   95 (600)
                      .+-.....+.+.+.+..+++.+|++.--.           +.+.|         ||=...      + ++.+-++ ++.+
T Consensus        20 ~~~~ifsg~s~~~La~~Ia~~Lg~~l~~~-----------~~~kF---------~DGE~~------v-~i~esVr-g~dV   71 (331)
T PRK02812         20 NRLRLFSGSSNPALAQEVARYLGIDLGPM-----------IRKRF---------ADGELY------V-QIQESIR-GCDV   71 (331)
T ss_pred             CCEEEEECCCCHHHHHHHHHHHCCCCCCE-----------EEEEC---------CCCCEE------E-EECCCCC-CCEE
T ss_conf             98899978999999999999968985340-----------78988---------999889------8-6568778-8769


Q ss_pred             EEEE--CCCC-CHHHHHHHHHHHHHHCCCC-EEEEEC-------C-CCCCCCCCCHHHHHHHH-HCCCCEEEEECCCCCC
Q ss_conf             9994--0788-6152899999999976994-799807-------8-74336688978988742-0268689996488762
Q gi|254780901|r   96 MIFG--DYDV-DGAASVALMMRFLSHCSVN-ANMYIP-------D-RIVDGYGPNPSLMEKFI-NEGAQLIITVDCGSTS  162 (600)
Q Consensus        96 ~I~g--DyD~-DGitstail~~~L~~~g~~-v~~~IP-------~-R~~eGYGl~~~~i~~~~-~~g~~LiItvD~Gi~~  162 (600)
                      .|.-  -.++ |.+.-.-+|..++++.+++ +...||       + ++..|-.++...+-++. ..|++-+||+|--...
T Consensus        72 ~iiqs~~~pvnd~lmELll~idA~krasA~~It~ViPY~~YaRQDrk~~~re~IsaklvA~lL~~aG~d~vitvDlH~~q  151 (331)
T PRK02812         72 YLIQPTCAPVNDHLMELLIMVDACRRASARQITAVIPYYGYARADRKTAGRESITAKLVANLITKAGVDRVLAMDLHSAQ  151 (331)
T ss_pred             EEECCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCEEEEECCCHHH
T ss_conf             99837999841899999999999877578727998325543556766689998349999978873488758873466288


Q ss_pred             HH
Q ss_conf             34
Q gi|254780901|r  163 YD  164 (600)
Q Consensus       163 ~e  164 (600)
                      .+
T Consensus       152 iq  153 (331)
T PRK02812        152 IQ  153 (331)
T ss_pred             HH
T ss_conf             86


No 229
>cd04729 NanE N-acetylmannosamine-6-phosphate epimerase (NanE) converts N-acetylmannosamine-6-phosphate to N-acetylglucosamine-6-phosphate. This reaction is part of the pathway that allows the usage of sialic acid as a carbohydrate source. Sialic acids are a family of related sugars that are found as a component of glycoproteins, gangliosides, and other sialoglycoconjugates.
Probab=61.08  E-value=12  Score=17.23  Aligned_cols=110  Identities=19%  Similarity=0.222  Sum_probs=74.8

Q ss_pred             CCCHHHCCCHHHHHHH------------HHHHHHCCCCEEEEE----CCCCC--HHHHHHHHHHHHHHCCCCEEEEE-CC
Q ss_conf             8995561487999999------------999997799799994----07886--15289999999997699479980-78
Q gi|254780901|r   69 MPDPLILTDCDKAARR------------IVQAIYNSEKIMIFG----DYDVD--GAASVALMMRFLSHCSVNANMYI-PD  129 (600)
Q Consensus        69 ~~dP~~l~dm~~A~~r------------i~~ai~~~ekI~I~g----DyD~D--Gitstail~~~L~~~g~~v~~~I-P~  129 (600)
                      +++|+.|.-|-+|+..            =.+||+..-.+-|+|    ||+--  =||.|.==...|-..|+++--.= -+
T Consensus        23 l~~~~im~~mA~Aa~~gGA~giR~~~~~dI~aIk~~v~lPIIGi~K~~~~~s~VyITPt~~ev~~l~~aGadiIA~DaT~  102 (219)
T cd04729          23 LHSPEIMAAMALAAVQGGAVGIRANGVEDIRAIRARVDLPIIGLIKRDYPDSEVYITPTIEEVDALAAAGADIIALDATD  102 (219)
T ss_pred             CCCHHHHHHHHHHHHHCCCEEEEECCHHHHHHHHHCCCCCEEEEEECCCCCCCEEECCCHHHHHHHHHCCCCEEEEECCC
T ss_conf             68778999999999978963998089889999983289988999956889998456688999999998599999994678


Q ss_pred             CCCCCCCCC-HHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCC
Q ss_conf             743366889-78988742026868999648876234555554179827996154
Q gi|254780901|r  130 RIVDGYGPN-PSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHH  182 (600)
Q Consensus       130 R~~eGYGl~-~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH  182 (600)
                      | .-..|.+ .+.++.+++++ +.++..||.  ..|+...|.++|.|+|-|--.
T Consensus       103 R-~RP~g~~l~~~i~~i~~~~-~~l~MAD~s--t~ee~~~A~~~G~D~vgTTL~  152 (219)
T cd04729         103 R-PRPDGETLAELIKRIHEEY-NCLLMADIS--TLEEALNAAKLGFDIIGTTLS  152 (219)
T ss_pred             C-CCCCCCCHHHHHHHHHHHH-CCEEEEECC--CHHHHHHHHHCCCCEEECCCC
T ss_conf             8-7989978999999999986-977887548--899999999849989970214


No 230
>COG0648 Nfo Endonuclease IV [DNA replication, recombination, and repair]
Probab=60.90  E-value=12  Score=17.21  Aligned_cols=136  Identities=14%  Similarity=0.185  Sum_probs=71.2

Q ss_pred             EEEECCCCCHHH-----HHHHHHHHHHHHH-CEEEEEEECCCCEEEEEEECCCCCCHHHHHHHHCCCC---CCCCCCCCC
Q ss_conf             262057858122-----2222789988420-1079988637983799986489861888888530335---301156532
Q gi|254780901|r  371 IVVEGDRWHPGI-----VGLLAARLKEKFG-RPSFAISFEEDGKGIGSGRSIEGFDIGKMVSFAVEEG---ILVKGGGHA  441 (600)
Q Consensus       371 ivv~~~~wh~GV-----iGIVAsrL~e~y~-kP~iv~s~~~dg~~kGS~RSi~g~~l~~~l~~~~~~~---ll~~~GGH~  441 (600)
                      .++..|+.|.|-     +--|+.-|.+... ..++++-..--|...+=+++.+  +|.++++.+.+..   .-.-+ -|.
T Consensus       103 ~lv~HpG~~~~~~~e~~l~~i~~~Ln~~~~~~~v~i~~e~~agegs~~g~~F~--~L~eii~~~~~~~~igvCiDt-cH~  179 (280)
T COG0648         103 LLVFHPGSYLGQGKEEGLNRIAEALNELLEEEGVIILLENTAGEGSGKGTQFG--ELAEIIDLIEEKERIGVCIDT-CHA  179 (280)
T ss_pred             EEEECCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCHH--HHHHHHHHHCCCCCEEEEEEC-HHH
T ss_conf             89977750147888999999999999985014872898774466676564224--199999863365754999871-204


Q ss_pred             CCCCEEECCCCHHHHHHHHHHHHHHHCCHHHCCCCEEEEEEECHHHCCHHHHHHHHHCCCCCCCCCC---CEEEECCEEE
Q ss_conf             2231464222158899999999986226443377147604434689799999999851846789998---4684278099
Q gi|254780901|r  442 MAAGLTVERVNFGRLCDFFQKFAHNIVPALITTPVFKIDGVLNASAVNIALIDMLESAGPYGAGNPN---PVFAFPNHKL  518 (600)
Q Consensus       442 ~AaG~ti~~~~l~~f~~~l~~~~~~~~~~~~~~~~l~iD~el~~~~i~~~l~~~L~~lePFG~gNpe---P~F~~~~~~i  518 (600)
                      .|+|.-+..+  +.|.+.|++.-+. +..+       ++..+.+++....+=..-++.+|.|.|+.-   ..+.+.+.++
T Consensus       180 ~Aagy~~~~~--~~~~~vl~~~d~~-~G~~-------~~~~~Hlndsk~~~G~~kDRH~~ig~G~ig~e~l~~~~~d~~~  249 (280)
T COG0648         180 FAAGYDIITE--EDFEKVLNEFDKV-LGLE-------YLKHIHLNDSKYPLGSNKDRHENIGEGYIGFEALRKILKDFRI  249 (280)
T ss_pred             HHCCCCCCCH--HHHHHHHHHHHHH-HCHH-------HHEEEEECCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCC
T ss_conf             4354785757--8899999999998-5714-------3306763376143665511123567899885899999812120


Q ss_pred             E
Q ss_conf             8
Q gi|254780901|r  519 Q  519 (600)
Q Consensus       519 ~  519 (600)
                      .
T Consensus       250 ~  250 (280)
T COG0648         250 D  250 (280)
T ss_pred             C
T ss_conf             5


No 231
>PRK11107 hybrid sensory histidine kinase BarA; Provisional
Probab=60.81  E-value=12  Score=17.20  Aligned_cols=33  Identities=9%  Similarity=0.221  Sum_probs=16.3

Q ss_pred             CCCHHHHHHHHHHHHH-CCCC-EEEEECCCCCHHH
Q ss_conf             1487999999999997-7997-9999407886152
Q gi|254780901|r   75 LTDCDKAARRIVQAIY-NSEK-IMIFGDYDVDGAA  107 (600)
Q Consensus        75 l~dm~~A~~ri~~ai~-~~ek-I~I~gDyD~DGit  107 (600)
                      +.+=.+..+|+..+.. ++.. |.-..=||.||-.
T Consensus        61 ~~~n~~~l~~l~~~~~~~~~~~v~~i~i~d~~~~l   95 (920)
T PRK11107         61 SLQNRESVRRLISVLHRRHSDIVRSIAVFDENNRL   95 (920)
T ss_pred             HHCCHHHHHHHHHHHHHCCCCCEEEEEEECCCCCE
T ss_conf             63699999999999874288746899999689988


No 232
>PRK05437 isopentenyl pyrophosphate isomerase; Provisional
Probab=60.50  E-value=12  Score=17.16  Aligned_cols=38  Identities=21%  Similarity=0.411  Sum_probs=16.3

Q ss_pred             CCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHH
Q ss_conf             66889789887420268689996488762345555541
Q gi|254780901|r  134 GYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATN  171 (600)
Q Consensus       134 GYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~  171 (600)
                      |+|++.+.+.++.+.|++-|..--.|=|++..|+..+.
T Consensus       195 G~Gis~e~a~~l~~~Gv~~IdVsg~GGTnf~~IE~~R~  232 (351)
T PRK05437        195 GFGISKETAKRLADAGVKAIDVAGAGGTSWAAVENYRA  232 (351)
T ss_pred             CCCCCHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHH
T ss_conf             57889999999996799999957998855799998871


No 233
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=60.47  E-value=12  Score=17.15  Aligned_cols=34  Identities=18%  Similarity=0.211  Sum_probs=11.9

Q ss_pred             ECCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCEE
Q ss_conf             6489861888888530335301156532223146
Q gi|254780901|r  414 RSIEGFDIGKMVSFAVEEGILVKGGGHAMAAGLT  447 (600)
Q Consensus       414 RSi~g~~l~~~l~~~~~~~ll~~~GGH~~AaG~t  447 (600)
                      +|.-|....+.+....-.-.|..-+|=....|+|
T Consensus       150 ~s~~G~~a~~~l~~~~~d~aFig~~gi~~~~g~t  183 (256)
T PRK10434        150 ASFHGQLAENAFEHFTFDKLFMGTDGIDLNAGVT  183 (256)
T ss_pred             CCCCCHHHHHHHHHHCCCEEEEECCCCCCCCCCC
T ss_conf             7320599999987527878998446065788846


No 234
>PRK01259 ribose-phosphate pyrophosphokinase; Provisional
Probab=60.24  E-value=12  Score=17.13  Aligned_cols=70  Identities=19%  Similarity=0.286  Sum_probs=47.5

Q ss_pred             CCCEEEEE--CCCC-CHHHHHHHHHHHHHHCCC-CEEEEECC--------CCCCCCCCCHHHHHHHHHC-CCCEEEEECC
Q ss_conf             99799994--0788-615289999999997699-47998078--------7433668897898874202-6868999648
Q gi|254780901|r   92 SEKIMIFG--DYDV-DGAASVALMMRFLSHCSV-NANMYIPD--------RIVDGYGPNPSLMEKFINE-GAQLIITVDC  158 (600)
Q Consensus        92 ~ekI~I~g--DyD~-DGitstail~~~L~~~g~-~v~~~IP~--------R~~eGYGl~~~~i~~~~~~-g~~LiItvD~  158 (600)
                      ++.+.|+.  ...+ |-+.-.-++..++++.|+ ++...+|-        ++..|=-++...+-++.+. |++-+||+|-
T Consensus        47 g~dV~ivqs~~~p~nd~lmElll~i~A~r~a~A~~It~ViPY~~Y~RQDr~~~~re~isak~va~ll~~~G~d~vit~Dl  126 (309)
T PRK01259         47 GKDVFIIQSTCAPTNDNLMELLIMIDALRRASAGRITAVIPYFGYARQDRKASARVPITAKLVANLLSSAGADRVLTVDL  126 (309)
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCCCEEHHHHHHHHHHCCCCEEEEEEC
T ss_conf             98289986799995177999999999998748871799724665036877779998675999999985237873899816


Q ss_pred             CCC
Q ss_conf             876
Q gi|254780901|r  159 GST  161 (600)
Q Consensus       159 Gi~  161 (600)
                      =..
T Consensus       127 H~~  129 (309)
T PRK01259        127 HAD  129 (309)
T ss_pred             CHH
T ss_conf             767


No 235
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=60.11  E-value=12  Score=17.11  Aligned_cols=145  Identities=12%  Similarity=0.119  Sum_probs=71.2

Q ss_pred             HHHHHHHHHCCCH-HHHHHHHHCCCC-HHHHHHHCCCCHHHC-------CCCHHHCCC----------------H-----
Q ss_conf             9999998819999-999999967889-789886619667771-------899556148----------------7-----
Q gi|254780901|r   29 RALAITQKHAIPD-IVARVLVNRNVS-IDYAKDFLNPSIRLL-------MPDPLILTD----------------C-----   78 (600)
Q Consensus        29 ~~~~l~~~~~~~~-~~a~iL~~Rgi~-~~~~~~fL~p~l~~l-------~~dP~~l~d----------------m-----   78 (600)
                      .+..|+++.+.|+ .+.|..-.=|++ -.+.+..|.-.+...       ..+|..-.|                +     
T Consensus        36 si~eLA~~~~vS~aTVvRf~kkLGf~Gf~efK~~l~~~~~~~~~~~~~~~~~~~~~~d~~~~i~~~~~~~~~~~l~~t~~  115 (282)
T PRK11557         36 SSQQLANEAGVSQSSVVKFAQKLGYKGFPALKLALSEALASQPEPPSVPVHNQIRGDDPLRLVGEKLIKENTAAMYATLD  115 (282)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             69999989699988999999993899899999999999861456433421244676775999999999999999999983


Q ss_pred             ---HHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEE
Q ss_conf             ---99999999999779979999407886152899999999976994799807874336688978988742026868999
Q gi|254780901|r   79 ---DKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIIT  155 (600)
Q Consensus        79 ---~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiIt  155 (600)
                         .+..++..+.|.+-++|.|||-- .-+..+-- +..-|.++|.++.++     .+.|... .....+.++  +++|.
T Consensus       116 ~~~~~~l~~av~~i~~A~~I~i~G~G-~S~~vA~~-~~~kl~rig~~~~~~-----~d~~~~~-~~~~~l~~~--Dv~I~  185 (282)
T PRK11557        116 VNSEEKLHECVTMLRSARRIILTGIG-ASGLVAQN-FAWKLMKIGINAVAE-----RDMHALL-ATVQALSPD--DLLLA  185 (282)
T ss_pred             CCCHHHHHHHHHHHHCCCCEEEEECC-CHHHHHHH-HHHHHHHHCCCEEEC-----CCHHHHH-HHHHHCCCC--CEEEE
T ss_conf             36899999999999648958999704-36999999-999999809963740-----8868999-999818999--98999


Q ss_pred             EC-CCCC--CHHHHHHHHHCCCCEEE-ECCCC
Q ss_conf             64-8876--23455555417982799-61544
Q gi|254780901|r  156 VD-CGST--SYDALQYATNQGIDVIV-IDHHQ  183 (600)
Q Consensus       156 vD-~Gi~--~~e~i~~a~~~GidvIV-tDHH~  183 (600)
                      +. .|-+  -.+.++.|+++|..+|. ||...
T Consensus       186 iS~sG~t~~~~~~~~~Ak~~Ga~iIaIT~~~~  217 (282)
T PRK11557        186 ISYSGERRELNLAADEALRVGGKVLAITGFTP  217 (282)
T ss_pred             EECCCCCHHHHHHHHHHHHCCCEEEEECCCCC
T ss_conf             85999978999999999987993999729899


No 236
>TIGR02955 TMAO_TorT TMAO reductase system periplasmic protein TorT; InterPro: IPR014301   Members of this entry are the periplasmic protein TorT that, together with the TorS/TorR histidine kinase/response regulator system, regulates expression of the torCAD operon for trimethylamine N-oxide reductase (TMAO reductase). It appears to bind an inducer for TMAO reductase and shows homology to a periplasmic D-ribose binding protein..
Probab=59.94  E-value=12  Score=17.09  Aligned_cols=96  Identities=20%  Similarity=0.341  Sum_probs=68.4

Q ss_pred             CEEEEECCCCCCCC--CCCHHHHHHHHHCCCCEEEEECCCC-----CCHHHHHHHHHCCCCEEEECCCCCC---------
Q ss_conf             47998078743366--8897898874202686899964887-----6234555554179827996154476---------
Q gi|254780901|r  122 NANMYIPDRIVDGY--GPNPSLMEKFINEGAQLIITVDCGS-----TSYDALQYATNQGIDVIVIDHHQVK---------  185 (600)
Q Consensus       122 ~v~~~IP~R~~eGY--Gl~~~~i~~~~~~g~~LiItvD~Gi-----~~~e~i~~a~~~GidvIVtDHH~~~---------  185 (600)
                      +.+...|| ++|.|  ++|=..+|.++..|++|=+ .|.|.     ....+|+.|..-|-|-|+.===.+.         
T Consensus         1 KLCAlYPH-LKDSYWLSiNYGM~e~Ak~~~v~L~V-lEAGGY~~~~~Q~~Qi~~C~~wgadAILLG~V~~~~~~~~L~~~   78 (304)
T TIGR02955         1 KLCALYPH-LKDSYWLSINYGMVEQAKKLGVELKV-LEAGGYPNLDKQLAQIEQCVSWGADAILLGTVSPEALNQDLAQL   78 (304)
T ss_pred             CCEEEECC-CHHHHHHHHHHHHHHHHHHHCCCEEE-ECCCCCHHHHHHHHHHHHHHHCCCCEEEECCCCHHHHCCCCHHH
T ss_conf             91475075-11346653126589999970984799-70688700789999999863079858996156856620230435


Q ss_pred             CCCCCCEEEECCCCCCCC-CCCCCHHHHHHHHHHH
Q ss_conf             555672565237888864-3344304788999999
Q gi|254780901|r  186 SEEIPAYALVNPNRLDDL-SGQGHLCAAGVVFLVL  219 (600)
Q Consensus       186 ~~~p~a~aivNP~~~~~~-~p~~~l~gaGvaf~l~  219 (600)
                      ..-.|-+|+||-=..+.+ --.--.+-+||-|+-|
T Consensus        79 ~~~~PVfalVN~l~~~~P~~~~~~~g~vGV~WY~M  113 (304)
T TIGR02955        79 TKSIPVFALVNQLDSNQPEAKEHVKGRVGVDWYQM  113 (304)
T ss_pred             HCCCCCEEEECCCCCCCCCCCCEEEEEECCCHHHH
T ss_conf             08846032213314655855540302236863331


No 237
>cd06323 PBP1_ribose_binding Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Periplasmic sugar-binding domain of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein (ttRBP) and its mesophilic homologs. Members of this group are belonging to the type I periplasmic binding protein superfamily, whose members are involved in chemotaxis, ATP-binding cassette transport, and intercellular communication in central nervous system. The thermophilic and mesophilic ribose-binding proteins are structurally very similar, but differ substantially in thermal stability.
Probab=59.90  E-value=12  Score=17.08  Aligned_cols=68  Identities=19%  Similarity=0.189  Sum_probs=41.9

Q ss_pred             HHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCC-CHHHHHHHHHCCCCEEEECCCCC
Q ss_conf             999976994799807874336688978988742026868999648876-23455555417982799615447
Q gi|254780901|r  114 RFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGST-SYDALQYATNQGIDVIVIDHHQV  184 (600)
Q Consensus       114 ~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~-~~e~i~~a~~~GidvIVtDHH~~  184 (600)
                      +.++..|.++.+.-.+...+   -..+.++.+...+++-||.+=++.. ..+.++.+++.|+-|+..|+...
T Consensus        23 ~~a~~~Gy~~~i~~s~~~~~---~e~~~i~~l~~~~vdgiI~~p~~~~~~~~~i~~~~~~~iPvV~id~~~~   91 (268)
T cd06323          23 KEAKELGYELTVLDAQNDAA---KQLNDIEDLITRGVDAIIINPTDSDAVVPAVKAANEAGIPVFTIDREAN   91 (268)
T ss_pred             HHHHHCCCEEEEEECCCCHH---HHHHHHHHHHHCCCCEEEECCCCCCCCHHHHHHHHHCCCCEEEECCCCC
T ss_conf             99997599899981999999---9999999999649998997565421246999999976996899636667


No 238
>PRK04169 geranylgeranylglyceryl phosphate synthase-like protein; Reviewed
Probab=59.90  E-value=12  Score=17.08  Aligned_cols=10  Identities=30%  Similarity=0.557  Sum_probs=4.4

Q ss_pred             CCCCEEEECC
Q ss_conf             5672565237
Q gi|254780901|r  188 EIPAYALVNP  197 (600)
Q Consensus       188 ~p~a~aivNP  197 (600)
                      .|.+|.++||
T Consensus       114 ip~gYiv~~~  123 (229)
T PRK04169        114 IPEGYIVLNP  123 (229)
T ss_pred             CCEEEEEECC
T ss_conf             4458999879


No 239
>COG1560 HtrB Lauroyl/myristoyl acyltransferase [Cell envelope biogenesis, outer membrane]
Probab=59.52  E-value=4.4  Score=20.62  Aligned_cols=11  Identities=18%  Similarity=0.344  Sum_probs=4.3

Q ss_pred             HHHHHHHHHCC
Q ss_conf             78988742026
Q gi|254780901|r  139 PSLMEKFINEG  149 (600)
Q Consensus       139 ~~~i~~~~~~g  149 (600)
                      .+.++++.++|
T Consensus       112 ~e~l~e~l~~~  122 (308)
T COG1560         112 LEHLEEALANG  122 (308)
T ss_pred             HHHHHHHHHCC
T ss_conf             88999999759


No 240
>PRK01033 imidazole glycerol phosphate synthase subunit HisF; Provisional
Probab=59.47  E-value=13  Score=17.03  Aligned_cols=72  Identities=15%  Similarity=0.269  Sum_probs=46.3

Q ss_pred             HHHHHHHCCCCEEEEEC-CCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCC
Q ss_conf             99999976994799807-87433668897898874202686899964887623455555417982799615447
Q gi|254780901|r  112 MMRFLSHCSVNANMYIP-DRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQV  184 (600)
Q Consensus       112 l~~~L~~~g~~v~~~IP-~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~~  184 (600)
                      +.+.+...|++--+.+- +.-.+|-..|.+.|+++.+. +.+=||+--||.+.+.++.+-+.|.|=||+.-...
T Consensus        35 ~ak~f~~~GadelhivDld~a~~g~~~n~~~I~~I~~~-~~ipi~vGGGIrs~e~~~~ll~~GadkViigs~a~  107 (253)
T PRK01033         35 AVRIFNEKEADELIVLDIDASRKGREPNYELIENLASE-CFMPLCYGGGIKTVEQAKRIFSLGVEKVSISTAAL  107 (253)
T ss_pred             HHHHHHHCCCCEEEEEECCCCCCCCCCHHHHHHHHHHH-CCCCEEEECCCCCHHHHHHHHHCCCCEEEECCHHH
T ss_conf             99999987999899994745424880169999999987-69988986881216888999867986699998786


No 241
>cd06354 PBP1_BmpA_PnrA_like Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea. Periplasmic binding domain of basic membrane lipoprotein, PnrA, in Treponema pallidum and its homologs from other bacteria and Archaea. The PnrA lipoprotein, also known as Tp0319 or TmpC, represents a novel family of bacterial purine nucleoside receptor encoded within an ATP-binding cassette (ABC) transport system (pnrABCDE). It shows a striking structural similarity to another basic membrane lipoprotein Med which regulates the competence transcription factor gene, comK, in Bacillus subtilis. The members of PnrA-like subgroup are likely to have similar nucleoside-binding functions and a similar type I periplasmic sugar-binding protein-like fold.
Probab=59.44  E-value=13  Score=17.03  Aligned_cols=89  Identities=19%  Similarity=0.157  Sum_probs=53.3

Q ss_pred             HHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHH-HHHC-CCCEEEECCCCCCCCCC
Q ss_conf             999999769947998078743366889789887420268689996488762345555-5417-98279961544765556
Q gi|254780901|r  112 MMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQY-ATNQ-GIDVIVIDHHQVKSEEI  189 (600)
Q Consensus       112 l~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~-a~~~-GidvIVtDHH~~~~~~p  189 (600)
                      +.++-+.+|.++.|+-|.-..|    -.+.++.+.++|++|||++  |..-.+.+.. |.+. .+..+++|.+..   .+
T Consensus        24 ~~~~~~~~g~~~~~~e~~~~~d----~~~~~~~~~~~g~~lIi~~--g~~~~~~~~~vA~~~Pd~~F~~id~~~~---~~   94 (265)
T cd06354          24 LERAAKELGIEYKYVESKSDAD----YEPNLEQLADAGYDLIVGV--GFLLADALKEVAKQYPDQKFAIIDAVVD---DP   94 (265)
T ss_pred             HHHHHHHHCCEEEEEECCCHHH----HHHHHHHHHHCCCCEEEEC--CHHHHHHHHHHHHHCCCCEEEEECCCCC---CC
T ss_conf             9999998699389993799899----9999999998799999991--7567899999999789987999568768---89


Q ss_pred             CCEEEECCCCCCCCCCCCCHHHHH
Q ss_conf             725652378888643344304788
Q gi|254780901|r  190 PAYALVNPNRLDDLSGQGHLCAAG  213 (600)
Q Consensus       190 ~a~aivNP~~~~~~~p~~~l~gaG  213 (600)
                      +.+.-+..+.    +.-.+|+|.-
T Consensus        95 ~Nv~~~~~~~----~e~~ylaG~~  114 (265)
T cd06354          95 PNVASIVFKE----EEGSFLAGYL  114 (265)
T ss_pred             CCEEEEECCH----HHHHHHHHHH
T ss_conf             9788997304----6788999999


No 242
>cd01028 TOPRIM_TopoIA TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IA family of DNA topoisomerases (TopoIA).  This subgroup contains proteins similar to the Type I DNA topoisomerases: E. coli topisomerases I and III, eukaryotic topoisomerase III and, ATP-dependent reverse gyrase found in archaea and thermophilic bacteria.   Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA. These enzymes cleave one strand of the DNA duplex, covalently link to the 5' phosphoryl end of the DNA break and allow the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP.  The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD).  For topoisomerases the conserved glutamate is believed to act as a general b
Probab=59.40  E-value=13  Score=17.02  Aligned_cols=65  Identities=14%  Similarity=0.204  Sum_probs=47.7

Q ss_pred             CCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCC-CEEEEECCCCCCCCCCCHHHHHHHHH
Q ss_conf             4879999999999977997999940788615289999999997699-47998078743366889789887420
Q gi|254780901|r   76 TDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSV-NANMYIPDRIVDGYGPNPSLMEKFIN  147 (600)
Q Consensus        76 ~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~-~v~~~IP~R~~eGYGl~~~~i~~~~~  147 (600)
                      ++-.+....|.+.+++...|.+.+|+|-.|   -.|-++.++.++. +..+. --+|++   ++++.|.++.+
T Consensus        75 ~~~~~~~~~i~~l~~~~d~iiiAtD~DrEG---E~I~~~i~~~~~~~~~~v~-R~~fss---lT~~~I~~A~~  140 (142)
T cd01028          75 PDKKKQLKALKKLAKKADEIVLATDPDREG---ELIAWEILEVLKCDNKPVK-RAWFSE---ITPKAIREAFK  140 (142)
T ss_pred             CCHHHHHHHHHHHHHHCCEEEECCCCCCCH---HHHHHHHHHHHCCCCCCCE-EEEEEC---CCHHHHHHHHH
T ss_conf             656999999999986199999888998227---9999999999578899927-899835---79999999997


No 243
>PRK11071 esterase YqiA; Provisional
Probab=59.37  E-value=13  Score=17.02  Aligned_cols=33  Identities=21%  Similarity=0.247  Sum_probs=24.4

Q ss_pred             CCCEEEEECCCCCHHHHHHHHHHHHHHHHCEEEEEEEC
Q ss_conf             47502620578581222222789988420107998863
Q gi|254780901|r  367 QASVIVVEGDRWHPGIVGLLAARLKEKFGRPSFAISFE  404 (600)
Q Consensus       367 ~~~~ivv~~~~wh~GViGIVAsrL~e~y~kP~iv~s~~  404 (600)
                      ..++.++-+     .+=|--|.-|+|+|+.|++++.+.
T Consensus        60 ~~~~~lIGS-----SLGGfyAt~Laeky~~~aVLINPA   92 (190)
T PRK11071         60 GDSLGLVGS-----SLGGYYATWLSQCFMLPAVVVNPA   92 (190)
T ss_pred             CCCEEEEEC-----CHHHHHHHHHHHHHCCCEEEECCC
T ss_conf             997699955-----858999999999858987997167


No 244
>PRK06781 amidophosphoribosyltransferase; Provisional
Probab=59.32  E-value=13  Score=17.01  Aligned_cols=37  Identities=19%  Similarity=0.213  Sum_probs=21.7

Q ss_pred             CCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCC
Q ss_conf             99799994078861528999999999769947998078743366889
Q gi|254780901|r   92 SEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPN  138 (600)
Q Consensus        92 ~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~  138 (600)
                      +|.=.|+|=|..+-  ++.+++..|..+        -||=+|+.|+.
T Consensus         9 ~eeCGI~Gi~~~~~--~~~~~~~gL~~L--------QHRGqeSaGIa   45 (471)
T PRK06781          9 NEECGVFGIWGHEN--AAQVSYYGLHSL--------QHRGQEGAGIV   45 (471)
T ss_pred             CCCCEEEEEECCCC--HHHHHHHHHHHH--------HCCCCCEEEEE
T ss_conf             76753899988812--399999999987--------35751330699


No 245
>cd06327 PBP1_SBP_like_1 Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family. Periplasmic solute-binding domain of active transport proteins that belong to the type I periplasmic binding fold protein family. Solute binding proteins are the primary specific receptors that initiate uptake of a broad range of solutes, including amino acids, peptides and inorganic ions. The members are predicted to have a similar function to an active transport system for short chain amides and urea by sequence comparison and phylogenetic analysis. Moreover, this binding domain has high sequence identity to the family of hydrophobic amino acid transporters (HAAT), and thus may also be involved in transport of amino acids.
Probab=59.25  E-value=13  Score=17.01  Aligned_cols=40  Identities=15%  Similarity=0.235  Sum_probs=18.3

Q ss_pred             HHHHHH-CCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECC
Q ss_conf             887420-2686899964887623455555417982799615
Q gi|254780901|r  142 MEKFIN-EGAQLIITVDCGSTSYDALQYATNQGIDVIVIDH  181 (600)
Q Consensus       142 i~~~~~-~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDH  181 (600)
                      .+++.+ +++..||-..+...+......+.+.|+-+|.+.-
T Consensus        58 a~~Lv~~~~V~aviG~~~S~~~~a~~~~~~~~~vp~i~~~a   98 (334)
T cd06327          58 AREWIDRDGVDMIVGGPNSAVALAVQEVAREKKKIYIVTGA   98 (334)
T ss_pred             HHHHHHCCCCCEECCCCCCHHHHHHHHHHHHCCCEEEECCC
T ss_conf             99998457971431787818889889999982975650377


No 246
>cd06343 PBP1_ABC_ligand_binding_like_8 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=58.79  E-value=13  Score=16.95  Aligned_cols=13  Identities=15%  Similarity=0.061  Sum_probs=6.8

Q ss_pred             HHHHHHHHHCCCC
Q ss_conf             9999999851846
Q gi|254780901|r  490 IALIDMLESAGPY  502 (600)
Q Consensus       490 ~~l~~~L~~lePF  502 (600)
                      ..+.+.|+.+.-|
T Consensus       317 ~~v~~ALe~l~~~  329 (362)
T cd06343         317 ENIMKQAESLKDV  329 (362)
T ss_pred             HHHHHHHHHCCCC
T ss_conf             9999999816787


No 247
>cd01030 TOPRIM_TopoIIA_like TOPRIM_TopoIIA_like: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA.  These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings.  The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general base in strand joining and as a general acid in strand cleavage by topisomerases.  The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=58.75  E-value=13  Score=16.97  Aligned_cols=29  Identities=34%  Similarity=0.542  Sum_probs=23.7

Q ss_pred             CCCCEEEEECCCCCHHHHHHHHHHHHHHC
Q ss_conf             79979999407886152899999999976
Q gi|254780901|r   91 NSEKIMIFGDYDVDGAASVALMMRFLSHC  119 (600)
Q Consensus        91 ~~ekI~I~gDyD~DGitstail~~~L~~~  119 (600)
                      +=.||.|..|-|+||.-=..+|..++-.+
T Consensus        72 RYgkIii~tDaD~DG~HI~~Lll~ff~~~  100 (115)
T cd01030          72 RYGKIIIMTDADVDGSHIRTLLLTFFYRF  100 (115)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHHHHHH
T ss_conf             62744898789997579999999999998


No 248
>PRK09279 pyruvate phosphate dikinase; Provisional
Probab=58.63  E-value=13  Score=16.93  Aligned_cols=36  Identities=28%  Similarity=0.362  Sum_probs=25.1

Q ss_pred             CCEEEEE---CCCCCHHHH---HHH---------HHHHHHHHHCEEEEEEE
Q ss_conf             7502620---578581222---222---------78998842010799886
Q gi|254780901|r  368 ASVIVVE---GDRWHPGIV---GLL---------AARLKEKFGRPSFAISF  403 (600)
Q Consensus       368 ~~~ivv~---~~~wh~GVi---GIV---------AsrL~e~y~kP~iv~s~  403 (600)
                      .++|.|.   +|+|-+++.   |||         |+-++.++++||+|-+-
T Consensus       424 e~vILV~~~T~Pdd~~~M~~A~aIvT~~GG~TsHAAIVaReLGiPaVVG~~  474 (875)
T PRK09279        424 EKVILVRIETSPEDIHGMHAAEGILTARGGMTSHAAVVARGMGKPCVVGAG  474 (875)
T ss_pred             CCEEEEECCCCHHHHHHHHHHCEEEECCCCCCHHHHHHHHHCCCCEEECCC
T ss_conf             956999688880047788773034654798612999999872997562455


No 249
>cd06451 AGAT_like Alanine-glyoxylate aminotransferase (AGAT) family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD correspond to alanine-glyoxylate aminotransferase (AGAT), serine-glyoxylate aminotransferase (SGAT), and 3-hydroxykynurenine transaminase (HKT). AGAT is a homodimeric protein, which catalyses the transamination of glyoxylate to glycine, and SGAT converts serine and glyoxylate to hydroxypyruvate and glycine. HKT catalyzes the PLP-dependent transamination of 3-hydroxykynurenine, a potentially toxic metabolite of the kynurenine pathway.
Probab=58.28  E-value=13  Score=16.89  Aligned_cols=99  Identities=9%  Similarity=0.184  Sum_probs=60.2

Q ss_pred             HHHCCC-HHHHHHHHH-HHHHCCCCEEE--EECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHH
Q ss_conf             556148-799999999-99977997999--94078861528999999999769947998078743366889789887420
Q gi|254780901|r   72 PLILTD-CDKAARRIV-QAIYNSEKIMI--FGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFIN  147 (600)
Q Consensus        72 P~~l~d-m~~A~~ri~-~ai~~~ekI~I--~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~  147 (600)
                      +..|.+ -.-|.+.+. ..+..+.|+++  .|-|=       .-+.+..+.+|.++..+-   +..|..++.+.+++..+
T Consensus        52 ~v~~~gsgt~a~ea~~~n~~~~~~kvlv~~~G~fg-------~r~~~~a~~~g~~~~~i~---~~~~~~~~~~~v~~~l~  121 (356)
T cd06451          52 TFLLSGSGTGAMEAALSNLLEPGDKVLVGVNGVFG-------DRWADMAERYGADVDVVE---KPWGEAVSPEEIAEALE  121 (356)
T ss_pred             EEEEECCHHHHHHHHHHHCCCCCCCEEEEEEEECC-------CCHHHHHHHCCCCEEEEE---CCCCCCCCHHHHHHHHH
T ss_conf             89995770899999998526888814788530405-------416764411597239986---89999789899998863


Q ss_pred             -CCCCEEEEECCCCC-----CHHHH-HHHHHCCCCEEEECC
Q ss_conf             -26868999648876-----23455-555417982799615
Q gi|254780901|r  148 -EGAQLIITVDCGST-----SYDAL-QYATNQGIDVIVIDH  181 (600)
Q Consensus       148 -~g~~LiItvD~Gi~-----~~e~i-~~a~~~GidvIVtDH  181 (600)
                       .+++++..|-|-++     +.++| +.+++.|.-++ .|=
T Consensus       122 ~~~~~~v~~~h~etstG~~~~l~~i~~~~~~~~~~~~-vDa  161 (356)
T cd06451         122 QHDIKAVTLTHNETSTGVLNPLEGIGALAKKHDALLI-VDA  161 (356)
T ss_pred             CCCCCEEEEECCCCCCCCCCCHHHHHHHHHHCCEEEE-EEC
T ss_conf             3896589996653651014775889998741572799-725


No 250
>PRK02083 imidazole glycerol phosphate synthase subunit HisF; Provisional
Probab=58.15  E-value=13  Score=16.87  Aligned_cols=72  Identities=14%  Similarity=0.223  Sum_probs=52.1

Q ss_pred             HHHHHHHCCCCEEEEE-CCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCC
Q ss_conf             9999997699479980-787433668897898874202686899964887623455555417982799615447
Q gi|254780901|r  112 MMRFLSHCSVNANMYI-PDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQV  184 (600)
Q Consensus       112 l~~~L~~~g~~v~~~I-P~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~~  184 (600)
                      +.+.+...|++--+.+ =++-.+|-+.+.+.++++.+. +.+=||+.=||.+.+.++.+-+.|.|-||+.-...
T Consensus        35 ~a~~~~~~gadel~ivDld~s~~~~~~~~~~I~~i~~~-~~~pi~vGGGIrs~e~~~~ll~~GadkVvigs~a~  107 (253)
T PRK02083         35 LAKRYDEEGADELVFLDITASSEGRDTMKDVVERVAEQ-VFIPLTVGGGIRSVEDARRLLRAGADKVSINSAAV  107 (253)
T ss_pred             HHHHHHHCCCCEEEEEECCCCCCCCHHHHHHHHHHHHH-CCCCEEEECCCCCHHHHHHHHHCCCCEEEECCHHH
T ss_conf             99999987999899995626645774179999999986-39877851762138987689877987899998465


No 251
>PRK01792 ribB 3,4-dihydroxy-2-butanone 4-phosphate synthase; Provisional
Probab=58.13  E-value=13  Score=16.87  Aligned_cols=94  Identities=12%  Similarity=0.210  Sum_probs=46.6

Q ss_pred             CHHHHHHHHHHHHHCCCCEEEEECCCCCHH---------HHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHH
Q ss_conf             879999999999977997999940788615---------28999999999769947998078743366889789887420
Q gi|254780901|r   77 DCDKAARRIVQAIYNSEKIMIFGDYDVDGA---------ASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFIN  147 (600)
Q Consensus        77 dm~~A~~ri~~ai~~~ekI~I~gDyD~DGi---------tstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~  147 (600)
                      .-++-|++..+++++++.|.|+-|.|=.+-         .....+...++.-+.-++.-++...-+--||..-.-..-..
T Consensus        11 ~~~~~V~~Ai~alr~G~~Viv~Dd~dREnEgDlv~aAe~~T~e~i~fm~~~~~GliCva~~~~~~~~L~Lp~mv~~n~~~   90 (214)
T PRK01792         11 TSEERVINAINAFKQGNGVLVLDDEDRENEGDLIFPAETITPEQMAKLIRYGSGIVCLCITDELCQQLDLPPMVQHNTSV   90 (214)
T ss_pred             CHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCEEEEHHHCCHHHHHHHHHHCCCCEEEECCHHHHHHCCCCCCCCCCCCC
T ss_conf             97889999999998799699982899876406796855499999999999589778973699999777990214667788


Q ss_pred             CCCCEEEEEC------CCCCCHHHHHHHH
Q ss_conf             2686899964------8876234555554
Q gi|254780901|r  148 EGAQLIITVD------CGSTSYDALQYAT  170 (600)
Q Consensus       148 ~g~~LiItvD------~Gi~~~e~i~~a~  170 (600)
                      .++.--++||      .|||+.+...-.+
T Consensus        91 ~~taFtvsvd~~~g~~TGISa~DRa~TIr  119 (214)
T PRK01792         91 NKTAFTVTIEAAKGVSTGVSAADRVTTIQ  119 (214)
T ss_pred             CCCCEEEEEECCCCCCCCCCHHHHHHHHH
T ss_conf             88877999965789768869899999999


No 252
>PRK01390 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=58.10  E-value=13  Score=16.87  Aligned_cols=32  Identities=19%  Similarity=0.407  Sum_probs=24.6

Q ss_pred             HCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             7799799994078861528999999999769947998
Q gi|254780901|r   90 YNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMY  126 (600)
Q Consensus        90 ~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~  126 (600)
                      -++++|.|+|    =|.|+-|. .++|...|++|..+
T Consensus         7 ~~gk~v~v~G----lG~sG~s~-a~~L~~~G~~V~~~   38 (457)
T PRK01390          7 FKGKTVALFG----LGGSGLAT-ARALKAGGAEVIAW   38 (457)
T ss_pred             CCCCEEEEEE----ECHHHHHH-HHHHHHCCCEEEEE
T ss_conf             2899899994----36999999-99999789979999


No 253
>COG1137 YhbG ABC-type (unclassified) transport system, ATPase component [General function prediction only]
Probab=58.03  E-value=5.9  Score=19.57  Aligned_cols=65  Identities=12%  Similarity=0.341  Sum_probs=27.1

Q ss_pred             CCCEEEEECCCCCHHHHHHHHHHHHHHHHCEEEEEEECCCCEEEEEEECCCCCCHHHHHHHHCCCCCCCCCCCCCCCCC
Q ss_conf             4750262057858122222278998842010799886379837999864898618888885303353011565322231
Q gi|254780901|r  367 QASVIVVEGDRWHPGIVGLLAARLKEKFGRPSFAISFEEDGKGIGSGRSIEGFDIGKMVSFAVEEGILVKGGGHAMAAG  445 (600)
Q Consensus       367 ~~~~ivv~~~~wh~GViGIVAsrL~e~y~kP~iv~s~~~dg~~kGS~RSi~g~~l~~~l~~~~~~~ll~~~GGH~~AaG  445 (600)
                      ++.++.+..|  -.||=-|.-+-+..--.      ...+.|+    |=-|..-|..+.|+-|. +-+++ +-||-.|-|
T Consensus       157 ~P~fiLLDEP--FAGVDPiaV~dIq~iI~------~L~~rgi----GvLITDHNVREtL~i~d-RaYIi-~~G~vla~G  221 (243)
T COG1137         157 NPKFILLDEP--FAGVDPIAVIDIQRIIK------HLKDRGI----GVLITDHNVRETLDICD-RAYII-SDGKVLAEG  221 (243)
T ss_pred             CCCEEEECCC--CCCCCCHHHHHHHHHHH------HHHHCCC----EEEECCCCHHHHHHHHH-EEEEE-ECCEEEECC
T ss_conf             9978994687--56899402999999999------9986796----59971663888873200-48998-657588437


No 254
>cd03366 TOPRIM_TopoIIA_GyrB TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA.  These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings.  DNA gyrase is more effective at relaxing supercoils than decatentating DNA.  DNA gyrase in addition inserts negative supercoils in the presence of ATP.  The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general base in strand joining and as a general acid in strand cleava
Probab=57.81  E-value=13  Score=16.92  Aligned_cols=30  Identities=37%  Similarity=0.545  Sum_probs=24.4

Q ss_pred             HCCCCEEEEECCCCCHHHHHHHHHHHHHHC
Q ss_conf             779979999407886152899999999976
Q gi|254780901|r   90 YNSEKIMIFGDYDVDGAASVALMMRFLSHC  119 (600)
Q Consensus        90 ~~~ekI~I~gDyD~DGitstail~~~L~~~  119 (600)
                      -+=.||+|..|-|+||.-=..+|..++-.+
T Consensus        70 LRYgkIiImtDaD~DG~HI~~Lli~ff~~~   99 (114)
T cd03366          70 LRYHKIIIMTDADVDGAHIRTLLLTFFFRY   99 (114)
T ss_pred             CCCCEEEEEECCCCCCHHHHHHHHHHHHHH
T ss_conf             787869999689988068999999999998


No 255
>PRK02472 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=57.67  E-value=13  Score=16.81  Aligned_cols=31  Identities=16%  Similarity=0.359  Sum_probs=23.1

Q ss_pred             CCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEE
Q ss_conf             799799994078861528999999999769947998
Q gi|254780901|r   91 NSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMY  126 (600)
Q Consensus        91 ~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~  126 (600)
                      ++++|+|+|    =|.|+-+. .++|...|++|..+
T Consensus         8 ~~k~i~viG----lG~sG~s~-a~~L~~~G~~V~~~   38 (450)
T PRK02472          8 QNKKVLVLG----LAKSGYAA-AKLLHKLGANVTVN   38 (450)
T ss_pred             CCCEEEEEE----ECHHHHHH-HHHHHHCCCEEEEE
T ss_conf             899899997----78999999-99999886989998


No 256
>COG0761 lytB 4-Hydroxy-3-methylbut-2-enyl diphosphate reductase IspH [Lipid metabolism]
Probab=57.63  E-value=13  Score=16.81  Aligned_cols=108  Identities=18%  Similarity=0.276  Sum_probs=71.9

Q ss_pred             CCHHHC-CCHHHHHHHHHHHHHC-CCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCC-------CCCCHH
Q ss_conf             995561-4879999999999977-9979999407886152899999999976994799807874336-------688978
Q gi|254780901|r   70 PDPLIL-TDCDKAARRIVQAIYN-SEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDG-------YGPNPS  140 (600)
Q Consensus        70 ~dP~~l-~dm~~A~~ri~~ai~~-~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eG-------YGl~~~  140 (600)
                      -+|..| -+.++|++...+|++. +.+|.|.|-     |-----..+.|+..|+...- -++...+|       ||.++.
T Consensus         7 A~prGFCaGV~RAI~ive~al~~~g~pIyv~~e-----IVHN~~Vv~~L~~~g~~fve-~l~e~p~~~~VIfsAHGVs~~   80 (294)
T COG0761           7 AKPRGFCAGVDRAIQIVERALEEYGAPIYVRHE-----IVHNRYVVDRLREKGAIFVE-ELDEVPDGATVIFSAHGVSPA   80 (294)
T ss_pred             ECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEC-----CCCCHHHHHHHHHCCCEECC-CCCCCCCCCEEEEECCCCCHH
T ss_conf             358863040899999999999971998589700-----22588999999975988613-210299998799977999989


Q ss_pred             HHHHHHHCCCCEEEEECCC--CCCHHHHHHHHHCCCCEEEECCCCC
Q ss_conf             9887420268689996488--7623455555417982799615447
Q gi|254780901|r  141 LMEKFINEGAQLIITVDCG--STSYDALQYATNQGIDVIVIDHHQV  184 (600)
Q Consensus       141 ~i~~~~~~g~~LiItvD~G--i~~~e~i~~a~~~GidvIVtDHH~~  184 (600)
                      ..+.+.+.|.. +|-.-|.  +.-|.++....+.|.++|++-|---
T Consensus        81 v~~~a~~r~l~-v~DATCPlVtKvh~~v~~~~~~G~~iIliG~~gH  125 (294)
T COG0761          81 VREEAKERGLK-VIDATCPLVTKVHKEVERYAREGYEIILIGHKGH  125 (294)
T ss_pred             HHHHHHHCCCE-EEECCCCCCHHHHHHHHHHHHCCCEEEEECCCCC
T ss_conf             99999877997-9946897516999999999858988999726999


No 257
>PRK07349 amidophosphoribosyltransferase; Provisional
Probab=57.62  E-value=13  Score=16.81  Aligned_cols=27  Identities=22%  Similarity=0.135  Sum_probs=10.9

Q ss_pred             CCCEEEEECCCCCHHHHHHHHHHHHHHC
Q ss_conf             9979999407886152899999999976
Q gi|254780901|r   92 SEKIMIFGDYDVDGAASVALMMRFLSHC  119 (600)
Q Consensus        92 ~ekI~I~gDyD~DGitstail~~~L~~~  119 (600)
                      +|.=.|||=|-.+ -..+.++|..|..+
T Consensus        26 ~eeCGVfGi~s~~-~~va~~~y~GL~aL   52 (495)
T PRK07349         26 EEACGVFGIYAPG-EEVAKLTYFGLYAL   52 (495)
T ss_pred             CCCCEEEEEECCC-CCHHHHHHHHHHHH
T ss_conf             6468089997599-35689999999987


No 258
>PRK03675 consensus
Probab=57.26  E-value=14  Score=16.77  Aligned_cols=69  Identities=12%  Similarity=0.129  Sum_probs=47.5

Q ss_pred             CCCCEEEEE--CCCC-CHHHHHHHHHHHHHHCCC-CEEEEECC--------CCCCCCCCCHHHHHHHHHCCCCEEEEECC
Q ss_conf             799799994--0788-615289999999997699-47998078--------74336688978988742026868999648
Q gi|254780901|r   91 NSEKIMIFG--DYDV-DGAASVALMMRFLSHCSV-NANMYIPD--------RIVDGYGPNPSLMEKFINEGAQLIITVDC  158 (600)
Q Consensus        91 ~~ekI~I~g--DyD~-DGitstail~~~L~~~g~-~v~~~IP~--------R~~eGYGl~~~~i~~~~~~g~~LiItvD~  158 (600)
                      +++.+.|+.  .+++ |-+.-.-+|..++++.|+ ++...+|-        |+..|--++...+-++...+++-+||+|.
T Consensus        41 ~g~dv~iiqs~~~p~nd~lmELll~~dAlr~a~A~~It~ViPY~~YaRQDr~~~~gepisak~va~ll~~~~d~vitvDl  120 (279)
T PRK03675         41 NGDEAIVVQSTYYPQDEKLIEALLLGDALREAGFEKLKLVVPYLAYSRQDRVTKEGEPISVRAVMKMLGLYYDELYVFDI  120 (279)
T ss_pred             CCCCEEEECCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCEEEEEEC
T ss_conf             89828998789999736799999999999982787279993467523224224799861499999997521276999826


Q ss_pred             C
Q ss_conf             8
Q gi|254780901|r  159 G  159 (600)
Q Consensus       159 G  159 (600)
                      -
T Consensus       121 H  121 (279)
T PRK03675        121 H  121 (279)
T ss_pred             C
T ss_conf             8


No 259
>PRK06545 prephenate dehydrogenase; Validated
Probab=57.14  E-value=14  Score=16.75  Aligned_cols=78  Identities=19%  Similarity=0.311  Sum_probs=36.5

Q ss_pred             CCCCCEEEECCCHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHCC-----CCCCCEEEEECCCCCHH
Q ss_conf             22221002034258999999999989999999999-------9999999998752112-----43475026205785812
Q gi|254780901|r  314 SNLGSRLLISDDSQELEMLAMKLDVLNQNRRLMES-------AMLEQAEAKVLTQCDD-----IQQASVIVVEGDRWHPG  381 (600)
Q Consensus       314 a~~av~lL~~~d~~~a~~la~~L~~lN~~Rk~~e~-------~i~~~a~~~~~~~~~~-----~~~~~~ivv~~~~wh~G  381 (600)
                      |.+=-++|+++.+.-...+-+..++|++-|..++.       +.++++.+. ....+.     ...-.-++|.-++ ++|
T Consensus       223 P~mW~dI~~~N~~~il~~L~~~~~~L~~~~~~l~~~d~~~l~~~~~~a~~~-R~~ip~~~~g~~~~~~~l~v~i~D-~pG  300 (357)
T PRK06545        223 PDMWRDILLSNAEPLLDALDEWIEELDRARDALESGDAGSIAEFFDAGKAG-RDRLPGKHGGAIPSFYDLYVDVPD-EPG  300 (357)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHH-HHHCCCCCCCCCCCCEEEEEECCC-CCC
T ss_conf             379999999839999999999999999999999808999999999999999-983887668999861899987899-998


Q ss_pred             HHHHHHHHHHHH
Q ss_conf             222227899884
Q gi|254780901|r  382 IVGLLAARLKEK  393 (600)
Q Consensus       382 ViGIVAsrL~e~  393 (600)
                      +++-+++-+.+.
T Consensus       301 ~la~l~~~l~~~  312 (357)
T PRK06545        301 VIAKVTRILAEE  312 (357)
T ss_pred             HHHHHHHHHHHC
T ss_conf             799999999986


No 260
>TIGR02116 toxin_Txe_YoeB addiction module toxin, Txe/YoeB family; InterPro: IPR009614   The Axe-Txe pair in Enterococcus faecium and the homologous YefM-YoeB pair in Escherichia coli have been shown to act as an antitoxin-toxin pair. This family describes the toxin component. Nearly every example found is next to an identifiable antitoxin, as indicated by match to  ..
Probab=57.01  E-value=14  Score=16.74  Aligned_cols=49  Identities=20%  Similarity=0.335  Sum_probs=35.2

Q ss_pred             HHHHHHHHHCCCC-CCCCCCCEEEECCEEEEEEEEECCCEEEEEEECCCCCEE
Q ss_conf             9999999851846-789998468427809988888479649999984998779
Q gi|254780901|r  490 IALIDMLESAGPY-GAGNPNPVFAFPNHKLQSIRVVNLAHLQMTFESQDSETL  541 (600)
Q Consensus       490 ~~l~~~L~~lePF-G~gNpeP~F~~~~~~i~~~r~vGk~Hlkl~l~~~~g~~i  541 (600)
                      .+|++.+.+ .|| |.|=|||+=.  ++.=...|.+...|--......+.+.+
T Consensus        24 ~~Li~~~~r-dPf~g~gkpEpLk~--~l~G~wSRRI~~eHRLVY~V~d~~k~v   73 (82)
T TIGR02116        24 NELIKDVKR-DPFKGIGKPEPLKG--DLSGYWSRRITDEHRLVYLVEDDEKVV   73 (82)
T ss_pred             HHHHHHHCC-CCCCCCCCCCCCCC--CCCCCCCCCCCCCCEEEEEEECCCEEE
T ss_conf             999998548-89605867899887--889843032275650577875794268


No 261
>cd04731 HisF The cyclase subunit of imidazoleglycerol phosphate synthase (HisF). Imidazole glycerol phosphate synthase (IGPS) catalyzes the fifth step of histidine biosynthesis, the formation of the imidazole ring. IGPS converts N1-(5'-phosphoribulosyl)-formimino-5-aminoimidazole-4-carboxamide ribonucleotide (PRFAR) to imidazole glycerol phosphate (ImGP) and 5'-(5-aminoimidazole-4-carboxamide) ribonucleotide (AICAR). This conversion involves two tightly coupled reactions in distinct active sites of IGPS. The two catalytic domains can be fused, like in fungi and plants, or peformed by a heterodimer (HisH-glutaminase and HisF-cyclase), like in bacteria.
Probab=56.81  E-value=14  Score=16.71  Aligned_cols=72  Identities=15%  Similarity=0.229  Sum_probs=51.5

Q ss_pred             HHHHHHHCCCCEEEEE-CCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCC
Q ss_conf             9999997699479980-787433668897898874202686899964887623455555417982799615447
Q gi|254780901|r  112 MMRFLSHCSVNANMYI-PDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQV  184 (600)
Q Consensus       112 l~~~L~~~g~~v~~~I-P~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~~  184 (600)
                      +.+.+...|++--+.+ =++-.+|.+.|.+.++++.+. +.+=|++-=||.+.+.++.+-+.|.|=||+.-...
T Consensus        32 ~a~~~~~~gadelhivDld~a~~g~~~n~~~i~~i~~~-~~~pi~vGGGIrs~~~~~~~l~~GadkVvigs~~~  104 (243)
T cd04731          32 LAKRYNEQGADELVFLDITASSEGRETMLDVVERVAEE-VFIPLTVGGGIRSLEDARRLLRAGADKVSINSAAV  104 (243)
T ss_pred             HHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHHH-CCCCEEEEEEEEEHHHHHHHHHCCCCEEEECCCCC
T ss_conf             99999986999999970673203770079999999986-79868998506647999999977997899898442


No 262
>PRK09534 btuF corrinoid ABC transporter substrate-binding protein; Reviewed
Probab=56.79  E-value=14  Score=16.71  Aligned_cols=86  Identities=14%  Similarity=0.264  Sum_probs=45.5

Q ss_pred             HHHCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCC--CCCCHHHHHHHHHCC
Q ss_conf             556148799999999999779979999407886152899999999976994799807874336--688978988742026
Q gi|254780901|r   72 PLILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDG--YGPNPSLMEKFINEG  149 (600)
Q Consensus        72 P~~l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eG--YGl~~~~i~~~~~~g  149 (600)
                      |...=-+.-...-+.=|+-.+.+|.=..|||--           ...  ++-   .| +..-|  +++|   +|++..-+
T Consensus        60 PeRIVSL~PS~TEiLfALG~gDkvVGVt~y~dY-----------P~~--a~~---~~-~V~~~~~~~~N---vE~IiaL~  119 (364)
T PRK09534         60 PERVVTLNPSAAQTMWELGDRDAVVGVSQYGSY-----------LDG--AEQ---RT-NVSGGQPFQVN---VEAVVGLD  119 (364)
T ss_pred             CCEEEECCCCHHHHHHHHCCCCCEEEEECCCCC-----------CHH--HHH---CC-CCCCCCCCCCC---HHHHHCCC
T ss_conf             876886481088999983689808986144568-----------533--442---36-36667878879---99996169


Q ss_pred             CCEEEEECCCCCCHHHHHHHHHCCCCEEEE
Q ss_conf             868999648876234555554179827996
Q gi|254780901|r  150 AQLIITVDCGSTSYDALQYATNQGIDVIVI  179 (600)
Q Consensus       150 ~~LiItvD~Gi~~~e~i~~a~~~GidvIVt  179 (600)
                      ++|+|..  +....+.++.+++.||.|++.
T Consensus       120 PDLVla~--~~~~~~~v~~L~~~GI~V~v~  147 (364)
T PRK09534        120 PDLVLAP--NTVRNDTVTRLRSAGITVFQF  147 (364)
T ss_pred             CCEEEEC--CCCCHHHHHHHHHCCCEEEEE
T ss_conf             9889965--877567899999769969991


No 263
>PRK01641 leuD isopropylmalate isomerase small subunit; Provisional
Probab=56.69  E-value=11  Score=17.47  Aligned_cols=49  Identities=27%  Similarity=0.505  Sum_probs=31.6

Q ss_pred             CCCCCCCCCHHHH-HHHHHCCCCEEEEEC---CCCCCHHHHHHHHHCCCCEEE
Q ss_conf             7433668897898-874202686899964---887623455555417982799
Q gi|254780901|r  130 RIVDGYGPNPSLM-EKFINEGAQLIITVD---CGSTSYDALQYATNQGIDVIV  178 (600)
Q Consensus       130 R~~eGYGl~~~~i-~~~~~~g~~LiItvD---~Gi~~~e~i~~a~~~GidvIV  178 (600)
                      |+.++-.++++.+ ++-.-.+.+.+|+=+   ||||-.-++-.+++.|+.+||
T Consensus        47 R~~~~g~~~~dF~LN~~~~~~a~ILvag~NFGCGSSREhAvwAL~d~Gir~VI   99 (201)
T PRK01641         47 RYLDDGQPNPDFVLNQPRYQGASILLAGENFGCGSSREHAPWALADYGFRVVI   99 (201)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCCHHHHHHHHHHCCCCEEE
T ss_conf             14689997877556775668981899678767775088999999985998999


No 264
>PRK07907 hypothetical protein; Provisional
Probab=56.68  E-value=14  Score=16.70  Aligned_cols=13  Identities=23%  Similarity=0.322  Sum_probs=8.4

Q ss_pred             HHHHHHHHHCCCC
Q ss_conf             9999999967889
Q gi|254780901|r   41 DIVARVLVNRNVS   53 (600)
Q Consensus        41 ~~~a~iL~~Rgi~   53 (600)
                      .+++..|..+|+.
T Consensus        36 ~~l~~~l~~~G~~   48 (437)
T PRK07907         36 EAVADLLREAGFD   48 (437)
T ss_pred             HHHHHHHHHCCCC
T ss_conf             9999999967997


No 265
>TIGR01670 YrbI-phosphatas 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase, YrbI family; InterPro: IPR010023    This entry is a part of the haloacid dehalogenase (HAD) superfamily of hydrolases from beta, gamma and epsilon proteobacteria, Aquifex, Fusobacterium, Porphyromonas and Methanosarcina. All characterised members of the HAD-superfamily hydrolase, subfamily IIIA and most characterised members of the HAD superfamily are phosphatases. HAD superfamily phosphatases contain active site residues in several conserved catalytic motifs , all of which are found conserved in this family.    Lipopolysaccharides of Gram-negative bacteria consist of a heteropolysaccharide component (O-antigen) and a hydrophobic component (lipid A). Linking the two portions is 3-Deoxy-D-manno-octulosonate (KDO), an 8-carbon sugar. Biosynthesis of KDO linked to lipid A proceeds via five steps, one of which involves removal of a phosphate from KDO 8-P via the action of KDO 8-P phosphatase (3.1.3.45 from EC; IPR008230 from INTERPRO) . One member of this family, the YrbI protein from Haemophilus influenzae has been cloned, expressed, purified and found to be an active phosphatase. Furthermore, its crystal structure has been determined .   The sequence from Methanosarcina acetivorans, Q8TJL6 from SWISSPROT, is distinctive in that it is linked to an N-terminal cytidylyltransferase domain (IPR003329 from INTERPRO) and is annotated as acylneuraminate cytidylyltransferase. This may give some clue as the function of these phosphatases. Several eukaryotic sequences are also closely related to this family; one such sequence is the CMP-N-acetylneuraminic acid synthetase from mouse, but in this case as in the others the phosphatase domain is clearly inactive as many of the active site residues are not conserved.; GO: 0019143 3-deoxy-manno-octulosonate-8-phosphatase activity, 0009103 lipopolysaccharide biosynthetic process.
Probab=56.33  E-value=3.2  Score=21.70  Aligned_cols=66  Identities=21%  Similarity=0.328  Sum_probs=37.6

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCE-EEEECCCCCCHHHHHHHHHCCCCEEEEC
Q ss_conf             886152899999999976994799807874336688978988742026868-9996488762345555541798279961
Q gi|254780901|r  102 DVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQL-IITVDCGSTSYDALQYATNQGIDVIVID  180 (600)
Q Consensus       102 D~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~L-iItvD~Gi~~~e~i~~a~~~GidvIVtD  180 (600)
                      |+||+-|=-.+|-+  .-|-.+..|   -..||||     |+-+...|.++ |||   |=.+.--.++++++||..+=+=
T Consensus         7 DvDGvLtDGkiyyt--~nGE~iK~F---NV~DG~g-----I~~~lk~gi~~AiIt---GR~~~~v~~R~k~Lgi~~lY~G   73 (154)
T TIGR01670         7 DVDGVLTDGKIYYT--ENGEEIKAF---NVKDGIG-----IKLLLKLGIKVAIIT---GRDAKLVEKRLKELGIKELYQG   73 (154)
T ss_pred             ECCCEEECCEEEEC--CCCCEEEEE---CCCCCHH-----HHHHHHCCCEEEEEE---CCCCHHHHHHHHHCCCEEEECC
T ss_conf             42723106706663--888443120---1545289-----999997498698981---7987568988877582032058


No 266
>pfam04131 NanE Putative N-acetylmannosamine-6-phosphate epimerase. This family represents a putative ManNAc-6-P-to-GlcNAc-6P epimerase in the N-acetylmannosamine (ManNAc) utilisation pathway found mainly in pathogenic bacteria.
Probab=56.32  E-value=14  Score=16.65  Aligned_cols=83  Identities=16%  Similarity=0.194  Sum_probs=54.5

Q ss_pred             CEEEEE-CCCCC--HHHHHHHHHHHHHHCCCCEEEEE-CCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHH
Q ss_conf             799994-07886--15289999999997699479980-787433668897898874202686899964887623455555
Q gi|254780901|r   94 KIMIFG-DYDVD--GAASVALMMRFLSHCSVNANMYI-PDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYA  169 (600)
Q Consensus        94 kI~I~g-DyD~D--Gitstail~~~L~~~g~~v~~~I-P~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a  169 (600)
                      -|.|+- ||+-.  =||.|.=-.+.|-..|+++--.= -+|-. ...+ .+.++.+++.+  .++..||.  +.|+...|
T Consensus        35 IIGi~K~~~~~~~VyITPt~~ev~~l~~aGadiIA~DaT~R~R-P~~~-~~lv~~i~~~~--~l~MAD~s--t~eea~~A  108 (192)
T pfam04131        35 IIGIVKRDLPDSPVRITPTMKDIDELANAGADIIALDGTDRPR-PVDI-ESFIKRIKEKG--QLAMADCS--TFEEGLNA  108 (192)
T ss_pred             EEEEEECCCCCCCCEECCCHHHHHHHHHCCCCEEEEECCCCCC-CCCH-HHHHHHHHHHC--CEEEEECC--CHHHHHHH
T ss_conf             7999856789998165588999999998599999984678989-7589-99999999819--98899749--99999999


Q ss_pred             HHCCCCEEEECCC
Q ss_conf             4179827996154
Q gi|254780901|r  170 TNQGIDVIVIDHH  182 (600)
Q Consensus       170 ~~~GidvIVtDHH  182 (600)
                      .++|.|+|-|--.
T Consensus       109 ~~~G~D~I~TTL~  121 (192)
T pfam04131       109 HKLGVDIVGTTLS  121 (192)
T ss_pred             HHCCCCEEECCCC
T ss_conf             9859999982325


No 267
>TIGR01734 D-ala-DACP-lig D-alanine-activating enzyme; InterPro: IPR010072   This entry represents the enzyme (also called D-alanine-D-alanyl carrier protein ligase) which activates D-alanine as an adenylate via the reaction D-ala + ATP to D-ala-AMP + PPi, and further catalyses the condensation of the amino acid adenylate with the D-alanyl carrier protein (D-ala-ACP). The D-alanine is then further transferred to teichoic acid in the biosynthesis of lipoteichoic acid (LTA) and wall teichoic acid (WTA) in Gram-positive bacteria, both polysacchatides .; GO: 0016208 AMP binding, 0047473 D-alanine-poly(phosphoribitol) ligase activity, 0019350 teichoic acid biosynthetic process.
Probab=56.21  E-value=14  Score=16.64  Aligned_cols=102  Identities=20%  Similarity=0.286  Sum_probs=59.9

Q ss_pred             HHHCCCHHHHHHHHHHH-HHCCC-CEEEEECCCCCHHHHHHHHHHHHHHCC---CCEEEEECCCCCCCCCCCHHHHHHHH
Q ss_conf             55614879999999999-97799-799994078861528999999999769---94799807874336688978988742
Q gi|254780901|r   72 PLILTDCDKAARRIVQA-IYNSE-KIMIFGDYDVDGAASVALMMRFLSHCS---VNANMYIPDRIVDGYGPNPSLMEKFI  146 (600)
Q Consensus        72 P~~l~dm~~A~~ri~~a-i~~~e-kI~I~gDyD~DGitstail~~~L~~~g---~~v~~~IP~R~~eGYGl~~~~i~~~~  146 (600)
                      -.|+.+-++.+.+|.+- +.+++ +|.|||.-+=+=+  .+.|  ++..-|   +-|..|+|.          +.|++++
T Consensus        29 ~~L~~~Sd~la~~i~~~~l~~k~kPiivfG~~~~~Ml--~~fl--g~~KsGhaYiPvD~s~P~----------ERi~~I~   94 (513)
T TIGR01734        29 QQLKEQSDRLAAFIQERLLPEKEKPIIVFGHMEPEML--VAFL--GSIKSGHAYIPVDTSIPL----------ERIEQIK   94 (513)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCEEEECCCCHHHH--HHHH--HHHHCCCCCCCCCCCCCH----------HHHHHHH
T ss_conf             8999999999999986057666775788648868999--9999--975168964343668816----------7999998


Q ss_pred             HC-CCCEEEEEC--------CC--CCCHHHHHHHHHCCC-CEEEECCCCCCCC
Q ss_conf             02-686899964--------88--762345555541798-2799615447655
Q gi|254780901|r  147 NE-GAQLIITVD--------CG--STSYDALQYATNQGI-DVIVIDHHQVKSE  187 (600)
Q Consensus       147 ~~-g~~LiItvD--------~G--i~~~e~i~~a~~~Gi-dvIVtDHH~~~~~  187 (600)
                      +. ++.++|++-        ..  +=..++.+.|.+.+- .+...||---.++
T Consensus        95 ~~a~p~~vi~~~~ls~~~~~~~~~~~~~~~~~~~~~~~~G~~~~~~~~V~~dD  147 (513)
T TIGR01734        95 EAAKPELVIETAELSIDLVETETDVITLEALEDALTSGAGPAVDFDHAVKGDD  147 (513)
T ss_pred             HHCCCCEEEEECCCCCCCCCCCCCEECHHHHHHHHHHCCCCCCCCCCCCCCCC
T ss_conf             63381127431137753111467511189999999706878642100005799


No 268
>cd06346 PBP1_ABC_ligand_binding_like_11 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=56.21  E-value=14  Score=16.64  Aligned_cols=12  Identities=8%  Similarity=0.199  Sum_probs=4.4

Q ss_pred             CCHHHHHHHHHH
Q ss_conf             487999999999
Q gi|254780901|r   76 TDCDKAARRIVQ   87 (600)
Q Consensus        76 ~dm~~A~~ri~~   87 (600)
                      ++++-|++.|.+
T Consensus        21 ~g~~lAveeiNa   32 (312)
T cd06346          21 DAAELAVKEVNA   32 (312)
T ss_pred             HHHHHHHHHHHH
T ss_conf             999999999986


No 269
>PRK08617 acetolactate synthase; Reviewed
Probab=56.08  E-value=14  Score=16.63  Aligned_cols=101  Identities=18%  Similarity=0.294  Sum_probs=51.4

Q ss_pred             HHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEE------ECCCCCC---C-CCC--CHHHHHHHH
Q ss_conf             999999999997799799994078861528999999999769947998------0787433---6-688--978988742
Q gi|254780901|r   79 DKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMY------IPDRIVD---G-YGP--NPSLMEKFI  146 (600)
Q Consensus        79 ~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~------IP~R~~e---G-YGl--~~~~i~~~~  146 (600)
                      ++.++++.+.+.+-++.+|+..+.+----+...+.++.+.+++.|..-      +|+-...   | .|+  +.. .+.+.
T Consensus       188 ~~~i~~a~~~L~~AkrPvii~G~g~~~~~~~~~l~~lae~~~iPv~tt~~gkg~i~~~h~~~~~G~~G~~~~~~-~~~~l  266 (552)
T PRK08617        188 PEDINYLAELIKNAKLPVLLLGMRASDPEVTAAIRRLLERTNLPVVETFQAAGVISRELEDHFFGRVGLFRNQP-GDELL  266 (552)
T ss_pred             HHHHHHHHHHHHHCCCCEEEECHHHCCHHHHHHHHHHHHHHCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCHH-HHHHH
T ss_conf             99999999999846587488322233364999999988874984884467773669765524255246657699-99998


Q ss_pred             HCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECC
Q ss_conf             02686899964887623455555417982799615
Q gi|254780901|r  147 NEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDH  181 (600)
Q Consensus       147 ~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDH  181 (600)
                      + .+|+||++.+....+..-.+.......+|.+|.
T Consensus       267 ~-~aDlvl~lG~~~~~~~~~~~~~~~~~~ii~id~  300 (552)
T PRK08617        267 K-KADLVITIGYDPIEYEPRNWNKEGDRTIIHIDE  300 (552)
T ss_pred             H-HCCEEEEEECCCCCCCCCCCCCCCCCEEEEEEC
T ss_conf             6-178589972465201542357789975999718


No 270
>PRK08327 acetolactate synthase catalytic subunit; Validated
Probab=56.06  E-value=14  Score=16.62  Aligned_cols=81  Identities=16%  Similarity=0.099  Sum_probs=46.2

Q ss_pred             HHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCC--CCCCCCCCHHHHHHHHHCCCCEEEEEC
Q ss_conf             999999999977997999940788615289999999997699479980787--433668897898874202686899964
Q gi|254780901|r   80 KAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDR--IVDGYGPNPSLMEKFINEGAQLIITVD  157 (600)
Q Consensus        80 ~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R--~~eGYGl~~~~i~~~~~~g~~LiItvD  157 (600)
                      ++++++.+.+.+-++-+|+...-+----+..-|.++.+.+|+.|....+.|  +.+.+++.........-..++|+|.++
T Consensus       208 ~~l~~~~~~l~~AkrPvii~G~G~~~~~a~~~l~~lae~lg~PV~tt~~~~~~~~~~hpl~~G~~~~~~l~~aDlvl~vG  287 (568)
T PRK08327        208 EDIQRAAEMLAAAERPVIITQRGGRRAEAFASLDRLAEELGIPVVEYNGEVVNIPSDHPLFLGGDDKADLADADLVLVVD  287 (568)
T ss_pred             HHHHHHHHHHHHCCCCEEECCCCCCHHHHHHHHHHHHHHCCCCEEECCCCCCCCCCCCCCCCCHHHHHHHHHCCEEEEEC
T ss_conf             99999999998367974751787335789999999987549967955765664699887655667787875088999946


Q ss_pred             CCC
Q ss_conf             887
Q gi|254780901|r  158 CGS  160 (600)
Q Consensus       158 ~Gi  160 (600)
                      |-.
T Consensus       288 ~~~  290 (568)
T PRK08327        288 SEV  290 (568)
T ss_pred             CCC
T ss_conf             777


No 271
>TIGR00734 hisAF_rel hisA/hisF family protein; InterPro: IPR004650   This family of proteins has so far been found in three archaeal species: Methanobacterium thermoautotrophicum, Methanococcus jannaschii, and Archaeoglobus fulgidus. Proteins are homologous to phosphoribosylformimino-5-aminoimidazole carboxamide ribotide isomerase (HisA) and, with lower similarity, to the cyclase HisF, both of which are enzymes of histidine biosynthesis. Each species with this protein also encodes HisA. However, the function of proteins in this group is unknown..
Probab=56.02  E-value=14  Score=16.62  Aligned_cols=146  Identities=22%  Similarity=0.193  Sum_probs=80.4

Q ss_pred             HHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHC---CCCEEE-ECCCCCC--
Q ss_conf             9999997699479980787433668897898874202686899964887623455555417---982799-6154476--
Q gi|254780901|r  112 MMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQ---GIDVIV-IDHHQVK--  185 (600)
Q Consensus       112 l~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~---GidvIV-tDHH~~~--  185 (600)
                      ..+.++..|++.-|.===-+-.|-|=|-+++.++-.....+|  +|||..|-|+.+..+..   .=-+|| |.-=+..  
T Consensus        41 ~ak~~~e~gar~iYiADLd~I~G~GdNf~~~~~~~~~~~e~I--~D~GvrS~EdLE~~~f~l~~~~R~vVaTETl~~~el  118 (230)
T TIGR00734        41 VAKALKEIGARSIYIADLDAIVGLGDNFELVKKVDKVVEELI--VDIGVRSREDLETLKFVLEKDDRVVVATETLDSTEL  118 (230)
T ss_pred             HHHHHHHCCCCEEEEEEHHHHCCCCCHHHHHHHHHHHCCHHE--EECCCCCHHHHHHCCCCCCCCCCEEEEECCHHHHHH
T ss_conf             999998638846863410022268854899988632220012--413556845443103675635636886245046789


Q ss_pred             -----CCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHH--HHHHHHHHHHHCCCCCCC
Q ss_conf             -----5556725652378888643344304788999999999997021488764077999--999987754201111444
Q gi|254780901|r  186 -----SEEIPAYALVNPNRLDDLSGQGHLCAAGVVFLVLVLIYRILRQDNKVPLNFDLLS--LLDLVALATVCDVVPLIG  258 (600)
Q Consensus       186 -----~~~p~a~aivNP~~~~~~~p~~~l~gaGvaf~l~~al~~~l~~~~~~~~~~~l~~--~ldlvaiGTvaD~vpL~~  258 (600)
                           ...||.-.+|.=     ++-.+.|...+.-- -+..++..+       ..++++.  .||.-|+|      ...|
T Consensus       119 l~e~~rnyPPer~VVSl-----DfK~~~L~~~~l~~-~leevrd~l-------~~f~~~GlI~LdI~sVG------t~~G  179 (230)
T TIGR00734       119 LKEILRNYPPERIVVSL-----DFKEKRLDASSLEE-SLEEVRDLL-------NSFDLDGLIVLDISSVG------TSKG  179 (230)
T ss_pred             HHHHHHCCCCCCEEEEE-----EEECCCCCCCCCHH-HHHHHHHHC-------CCCCCCEEEEECCCCCC------CCCC
T ss_conf             99986158986379998-----40055200013045-688887530-------66310137983363305------6778


Q ss_pred             CCHHHHHHHHHHHHHCCCCC
Q ss_conf             11899998788775168874
Q gi|254780901|r  259 LNRAYVVKGLMVARRQGNPG  278 (600)
Q Consensus       259 eNR~lvk~GL~~l~~~~~~g  278 (600)
                      -||-+.+.-|...++.-.+|
T Consensus       180 ~n~ell~~~l~l~e~PV~~G  199 (230)
T TIGR00734       180 VNLELLKKVLELSERPVILG  199 (230)
T ss_pred             CCHHHHHHHHHHHCCCEEEC
T ss_conf             78889998864424871406


No 272
>PRK03353 ribB 3,4-dihydroxy-2-butanone 4-phosphate synthase; Provisional
Probab=55.87  E-value=14  Score=16.60  Aligned_cols=91  Identities=12%  Similarity=0.183  Sum_probs=42.0

Q ss_pred             HHHHHHHHHHHCCCCEEEEECCCCCHH---------HHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCC
Q ss_conf             999999999977997999940788615---------28999999999769947998078743366889789887420268
Q gi|254780901|r   80 KAARRIVQAIYNSEKIMIFGDYDVDGA---------ASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGA  150 (600)
Q Consensus        80 ~A~~ri~~ai~~~ekI~I~gDyD~DGi---------tstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~  150 (600)
                      .-++...+|+++++.|.|+-|.|-.+-         .....+....+.-+.-++.-++...-+--||..-.-..--..+.
T Consensus        14 ~~Ie~Ai~al~~G~~Viv~Dd~dREnEgDlv~aAe~~t~e~v~fm~~~~~GliCv~~~~~~~~~L~Lp~m~~~n~~~~~t   93 (217)
T PRK03353         14 ERVEAALDALREGRGVLVLDDEDRENEGDMIFAAETMTVEQMALTIRHGSGIVCLCLTEERRKQLDLPMMVENNTSQYGT   93 (217)
T ss_pred             CHHHHHHHHHHCCCEEEEEECCCCCCCCCEEEEHHHCCHHHHHHHHHHCCCCEEECCCHHHHHHCCCCCCCCCCCCCCCC
T ss_conf             15999999998799599983899876406897854399999999999579978835999999867996756877664578


Q ss_pred             CEEEEEC------CCCCCHHHHHHHH
Q ss_conf             6899964------8876234555554
Q gi|254780901|r  151 QLIITVD------CGSTSYDALQYAT  170 (600)
Q Consensus       151 ~LiItvD------~Gi~~~e~i~~a~  170 (600)
                      .--++||      .|||+.+...-.+
T Consensus        94 aFtvsvd~~~g~~TGISa~DRa~Tir  119 (217)
T PRK03353         94 AFTVTIEAAEGVTTGVSAADRITTIR  119 (217)
T ss_pred             CCEEEEEEECCCCCCCCHHHHHHHHH
T ss_conf             75155523058878879899999899


No 273
>TIGR01179 galE UDP-glucose 4-epimerase; InterPro: IPR005886    Synonym: UDP-galactose 4-epimerase UDP-glucose 4-epimerase (5.1.3.2 from EC) interconverts UDP-glucose and UDP-galactose which are precursors of glucose- and galactose-containing exopolysaccharides (EPS). A set of related proteins, some of which are tentatively identified as UDP-glucose-4-epimerase in Thermotoga maritima, Bacillus halodurans, and several archaea, but deeply branched from this set and lacking experimental evidence, are excluded and described by a separate model. ; GO: 0003978 UDP-glucose 4-epimerase activity, 0006012 galactose metabolic process.
Probab=55.78  E-value=4.6  Score=20.45  Aligned_cols=19  Identities=16%  Similarity=0.506  Sum_probs=8.9

Q ss_pred             CCHHHHHHHHHHHCCHHHHHCCCC
Q ss_conf             242345666774306233312122
Q gi|254780901|r  292 ITAENLGYMIGPSINAGGRIGESN  315 (600)
Q Consensus       292 i~~~di~f~iaPrINAaGRl~~a~  315 (600)
                      +|-.+|-+.++||     |-||+-
T Consensus       283 vsG~~~~~~~~~R-----R~GDpa  301 (341)
T TIGR01179       283 VSGKDIPVELAPR-----RPGDPA  301 (341)
T ss_pred             HCCCEEEEEECCC-----CCCCCC
T ss_conf             1098137887687-----798845


No 274
>PRK04663 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=55.58  E-value=14  Score=16.57  Aligned_cols=30  Identities=10%  Similarity=0.367  Sum_probs=18.9

Q ss_pred             CCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEE
Q ss_conf             97999940788615289999999997699479980
Q gi|254780901|r   93 EKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYI  127 (600)
Q Consensus        93 ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~I  127 (600)
                      +||+|+|    =|.|+-| ..++|...+..+.+++
T Consensus         8 KkvlV~G----lG~sG~s-~a~~L~~~~~~~~v~~   37 (438)
T PRK04663          8 KNVVVVG----LGITGLS-VVKHLRKTQPQLTVKV   37 (438)
T ss_pred             CEEEEEE----ECHHHHH-HHHHHHHCCCCCEEEE
T ss_conf             7499990----6785899-9999996699846999


No 275
>cd06328 PBP1_SBP_like_2 Periplasmic solute-binding domain of active transport proteins found in gram-negative and gram-positive bacteria. Periplasmic solute-binding domain of active transport proteins found in gram-negative and gram-positive bacteria. Members of this group are initial receptors in the process of active transport across cellular membrane, but their substrate specificities are not known in detail. However, they closely resemble the group of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and thus are likely to exhibit a ligand-binding mode similar to that of the amide sensor protein AmiC from Pseudomonas aeruginosa. Moreover, this binding domain has high sequence identity to the family of hydrophobic amino acid transporters (HAAT), and thus it may also be involved in transport of amino acids.
Probab=55.05  E-value=15  Score=16.51  Aligned_cols=83  Identities=14%  Similarity=0.165  Sum_probs=47.2

Q ss_pred             HCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEE--ECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCC-HHHH
Q ss_conf             7799799994078861528999999999769947998--078743366889789887420268689996488762-3455
Q gi|254780901|r   90 YNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMY--IPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTS-YDAL  166 (600)
Q Consensus        90 ~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~--IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~-~e~i  166 (600)
                      +++.|+.+.++-+.-|......+.+.++..|.++...  .|...+|   ++ ..+.++++.++++++.+-.|..+ ...+
T Consensus       134 ~~~kkva~i~~d~~~g~~~~~~~~~~~~~~g~~iv~~~~~~~~~~D---f~-~~i~~i~~~~pd~v~~~~~~~~~~~~~~  209 (333)
T cd06328         134 KPGKKIATLAQDYAFGRDGVAAFKAALEKLGAAIVTEEYAPTDTTD---FT-PYAQRLLDALKKVLFVIWAGAGGPWPKL  209 (333)
T ss_pred             HCCCEEEEEECCCHHHHHHHHHHHHHHHHCCCEEEEEEECCCCCCC---HH-HHHHHHHHCCCCEEEEECCCCHHHHHHH
T ss_conf             3698899996785576999999999999739969999826888877---79-9999998669999999357862699999


Q ss_pred             HHHHHCCCCE
Q ss_conf             5554179827
Q gi|254780901|r  167 QYATNQGIDV  176 (600)
Q Consensus       167 ~~a~~~Gidv  176 (600)
                      ..+...|...
T Consensus       210 ~~~~~~~~~~  219 (333)
T cd06328         210 QQMGVLGYGI  219 (333)
T ss_pred             HHHHHCCCCC
T ss_conf             9998659997


No 276
>PRK05588 histidinol-phosphatase; Provisional
Probab=54.65  E-value=13  Score=16.99  Aligned_cols=24  Identities=17%  Similarity=0.416  Sum_probs=17.2

Q ss_pred             CCHHHHHHHHHCCCCEEEECCCCC
Q ss_conf             623455555417982799615447
Q gi|254780901|r  161 TSYDALQYATNQGIDVIVIDHHQV  184 (600)
Q Consensus       161 ~~~e~i~~a~~~GidvIVtDHH~~  184 (600)
                      +-.+-++.|.++|+++|+|||...
T Consensus        18 ~~ee~v~~Ai~~Gl~~i~TdH~d~   41 (256)
T PRK05588         18 KIEEAIKKAKKNNLGIIITEHMDL   41 (256)
T ss_pred             CHHHHHHHHHHCCCCEEEECCCCC
T ss_conf             699999999986998899668888


No 277
>cd06329 PBP1_SBP_like_3 Periplasmic solute-binding domain of active transport proteins. Periplasmic solute-binding domain of active transport proteins found in bacteria and Archaea. Members of this group are initial receptors in the process of active transport across cellular membrane, but their substrate specificities are not known in detail. However, they closely resemble the group of AmiC and active transport systems for short-chain amides and urea (FmdDEF), and thus are likely to exhibit a ligand-binding mode similar to that of the amide sensor protein AmiC from Pseudomonas aeruginosa. Moreover, this binding domain has high sequence identity to the family of hydrophobic amino acid transporters (HAAT), and thus it may also be involved in transport of amino acids.
Probab=54.65  E-value=15  Score=16.46  Aligned_cols=15  Identities=27%  Similarity=0.576  Sum_probs=7.6

Q ss_pred             HHHHHHCCCCEEEEE
Q ss_conf             887420268689996
Q gi|254780901|r  142 MEKFINEGAQLIITV  156 (600)
Q Consensus       142 i~~~~~~g~~LiItv  156 (600)
                      .+++.++++.++|-.
T Consensus        59 a~~Li~~~v~~iiG~   73 (342)
T cd06329          59 AQKAIDDGVRLVVQG   73 (342)
T ss_pred             HHHHHHCCCCEEECC
T ss_conf             999997699499889


No 278
>COG3051 CitF Citrate lyase, alpha subunit [Energy production and conversion]
Probab=54.47  E-value=5.5  Score=19.85  Aligned_cols=66  Identities=18%  Similarity=0.287  Sum_probs=34.0

Q ss_pred             HHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCC---CEEEECC
Q ss_conf             999999999769947998078743366889789887420268689996488762345555541798---2799615
Q gi|254780901|r  109 VALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGI---DVIVIDH  181 (600)
Q Consensus       109 tail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~Gi---dvIVtDH  181 (600)
                      .-...+.+-.+|.+-...-|+-+.+-+   ...+|.+ +.|+--=|+ -.|..  ..+...-++|+   .|+|--|
T Consensus        81 vN~Vm~~Ia~mGfKnLtlA~SSl~~~h---~pliehI-knGVVt~I~-sSGlR--g~lg~~IS~Gll~~PV~i~SH  149 (513)
T COG3051          81 VNMVMDVIAKMGFKNLTLASSSLSDCH---APLVEHI-KNGVVTRIY-SSGLR--GPLGEEISRGLLAEPVQIHSH  149 (513)
T ss_pred             HHHHHHHHHHHCCCCEEECCCHHHHHH---HHHHHHH-HCCEEEEEE-ECCCC--CHHHHHHHHHHHHCCEEEECC
T ss_conf             999999999718552155341333311---7899998-627765675-05556--267899854675098699626


No 279
>cd01965 Nitrogenase_MoFe_beta_like Nitrogenase_MoFe_beta_like: Nitrogenase MoFe protein, beta subunit_like. The nitrogenase enzyme catalyzes the ATP-dependent reduction of dinitrogen (N2) to ammonia.  This group contains the beta subunits of component 1 of the three known genetically distinct types of nitrogenase systems: a molybdenum-dependent  nitrogenase (Mo-nitrogenase), a vanadium-dependent nitrogenase (V-nitrogenase), and an iron-only nitrogenase (Fe-nitrogenase). These nitrogenase systems consist of component 1 (MoFe protein, VFe protein or, FeFe protein respectively) and, component 2 (Fe protein). The most widespread and best characterized of these systems is the Mo-nitrogenase. MoFe is an alpha2beta2 tetramer, the alternative nitrogenases are alpha2beta2delta2 hexamers having  alpha and beta subunits similar to the alpha and beta subunits of MoFe. For MoFe, each alphabeta pair contains one P-cluster (at the alphabeta interface) and, one molecule of iron molybdenum cofactor (Fe
Probab=54.38  E-value=15  Score=16.43  Aligned_cols=125  Identities=17%  Similarity=0.260  Sum_probs=53.7

Q ss_pred             HHHHHHCCCCHHHHHHHCCCCHHHCCCCHHHCCCHHHHHHHHHHHHHCCCC--EEEE--------ECCCCCHHHHHHHHH
Q ss_conf             999996788978988661966777189955614879999999999977997--9999--------407886152899999
Q gi|254780901|r   44 ARVLVNRNVSIDYAKDFLNPSIRLLMPDPLILTDCDKAARRIVQAIYNSEK--IMIF--------GDYDVDGAASVALMM  113 (600)
Q Consensus        44 a~iL~~Rgi~~~~~~~fL~p~l~~l~~dP~~l~dm~~A~~ri~~ai~~~ek--I~I~--------gDyD~DGitstail~  113 (600)
                      ++.+..|.+... +.  + + ..++..+---|-+-++-.+-|.++.++...  |.|+        || |++|+..     
T Consensus        37 ~~~~~~rh~~e~-~~--~-~-sT~l~E~~~VfGG~~~L~~ai~~~~~~~~P~~I~V~ttC~se~IGD-Di~~v~~-----  105 (428)
T cd01965          37 ARVLFTRHFKEP-IP--I-A-STSMTEDAAVFGGEDNLIEALKNLLSRYKPDVIGVLTTCLTETIGD-DVAGFIK-----  105 (428)
T ss_pred             HHHHHHCCCCCC-CC--C-C-CCCCCCCCEEECCHHHHHHHHHHHHHHCCCCEEEEECCCHHHHHCC-CHHHHHH-----
T ss_conf             999985245789-78--7-6-5568866155063899999999999844998899976766886367-5899999-----


Q ss_pred             HHHHH----CCCCEEEE-ECC---CCCCCCCCCHHHH-HHHHHC-------CCCEEEEECCCCCCHHHHH-HHHHCCCCE
Q ss_conf             99997----69947998-078---7433668897898-874202-------6868999648876234555-554179827
Q gi|254780901|r  114 RFLSH----CSVNANMY-IPD---RIVDGYGPNPSLM-EKFINE-------GAQLIITVDCGSTSYDALQ-YATNQGIDV  176 (600)
Q Consensus       114 ~~L~~----~g~~v~~~-IP~---R~~eGYGl~~~~i-~~~~~~-------g~~LiItvD~Gi~~~e~i~-~a~~~Gidv  176 (600)
                      ++-..    .+..+.+. -|.   ....||..-.+++ +.+...       .+.+|..+-+--.+.++++ .+.+.|+++
T Consensus       106 ~~~~~~~~~~~~~vi~v~tpgf~Gs~~~G~~~a~~ai~~~~~~~~~~~~~~~vNli~~~~~~~~D~~eik~ll~~~Gl~v  185 (428)
T cd01965         106 EFRAEGPEPADFPVVYASTPSFKGSHETGYDNAVKAIIEQLAKPSEVKKNGKVNLLPGFPLTPGDVREIKRILEAFGLEP  185 (428)
T ss_pred             HHHHHCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCEEEECCCCCCCHHHHHHHHHHHHCCCCE
T ss_conf             99984466679848996089867759999999999999984678788899947997686788245999999999849916


Q ss_pred             EEE
Q ss_conf             996
Q gi|254780901|r  177 IVI  179 (600)
Q Consensus       177 IVt  179 (600)
                      +++
T Consensus       186 ~~l  188 (428)
T cd01965         186 IIL  188 (428)
T ss_pred             EEE
T ss_conf             981


No 280
>pfam08288 PIGA PIGA (GPI anchor biosynthesis). This domain is found on phosphatidylinositol n-acetylglucosaminyltransferase proteins. These proteins are involved in GPI anchor biosynthesis and are associated with disease the paroxysmal nocturnal haemoglobinuria.
Probab=54.31  E-value=8.3  Score=18.44  Aligned_cols=45  Identities=18%  Similarity=0.335  Sum_probs=29.3

Q ss_pred             HHHHH-HHHCCCCEEEEECC-CCCCHHHHHHHHHCCCCEEEECCCCC
Q ss_conf             89887-42026868999648-87623455555417982799615447
Q gi|254780901|r  140 SLMEK-FINEGAQLIITVDC-GSTSYDALQYATNQGIDVIVIDHHQV  184 (600)
Q Consensus       140 ~~i~~-~~~~g~~LiItvD~-Gi~~~e~i~~a~~~GidvIVtDHH~~  184 (600)
                      ..+.. +..+.++++=-=-. .+-++|++-.|+.+|+.++-|||-.-
T Consensus        40 Pl~R~IliRE~I~IVHgH~a~S~l~hEailhA~tmGlktVfTDHSLF   86 (90)
T pfam08288        40 PLFRNILIRERIDIVHGHQAFSTLAHEAILHARTMGLKTVFTDHSLF   86 (90)
T ss_pred             HHHHHHHHHHCCEEEEEEHHHHHHHHHHHHHHHHCCCCEEEECCCCC
T ss_conf             99999998726219972177777788999999866981785245323


No 281
>PRK08134 O-acetylhomoserine aminocarboxypropyltransferase; Validated
Probab=54.29  E-value=15  Score=16.42  Aligned_cols=95  Identities=13%  Similarity=0.141  Sum_probs=52.8

Q ss_pred             CHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEE-
Q ss_conf             8799999999999779979999407886152899999999976994799807874336688978988742026868999-
Q gi|254780901|r   77 DCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIIT-  155 (600)
Q Consensus        77 dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiIt-  155 (600)
                      +|.....-+..-.+.+..|++-.  ++=|-| ..++.+.|..+|.++.|+=|.        +.+.++.+...++++|.. 
T Consensus        88 GmaAis~~l~~ll~~Gd~iv~~~--~~YggT-~~l~~~~l~~~Gi~~~~vd~~--------d~~~~~~~i~~~Tklv~~E  156 (433)
T PRK08134         88 GQAALHLAIATLMGAGSHIVASS--ALYGGS-HNLLHYTLPRFGIETTFVKPR--------DIDGWRAAIRPNTRLLFGE  156 (433)
T ss_pred             HHHHHHHHHHHHCCCCCEEEECC--CEECCH-HHHHHHHHHHCCEEEEEECCC--------CHHHHHHHCCCCCEEEEEE
T ss_conf             89999999997489999899718--807737-999998776348379998897--------8467887559875289985


Q ss_pred             ----ECCCCCCHHHHH-HHHHCCCCEEEECCCC
Q ss_conf             ----648876234555-5541798279961544
Q gi|254780901|r  156 ----VDCGSTSYDALQ-YATNQGIDVIVIDHHQ  183 (600)
Q Consensus       156 ----vD~Gi~~~e~i~-~a~~~GidvIVtDHH~  183 (600)
                          .-.-+.+.++|. .|++.|+-+|| |.--
T Consensus       157 spsNP~l~v~Di~aia~iA~~~g~~~vV-DNT~  188 (433)
T PRK08134        157 TLGNPGLEVLDIPTVAAIAHEAGVPLLV-DSTF  188 (433)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHCCCEEEE-ECCC
T ss_conf             3899975035899999999756761997-1665


No 282
>PRK12360 4-hydroxy-3-methylbut-2-enyl diphosphate reductase; Provisional
Probab=54.19  E-value=15  Score=16.41  Aligned_cols=109  Identities=15%  Similarity=0.195  Sum_probs=72.1

Q ss_pred             HHHC-CCHHHHHHHHHHHHHCC--CCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEE-CCCCCCC-------CCCCHH
Q ss_conf             5561-48799999999999779--97999940788615289999999997699479980-7874336-------688978
Q gi|254780901|r   72 PLIL-TDCDKAARRIVQAIYNS--EKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYI-PDRIVDG-------YGPNPS  140 (600)
Q Consensus        72 P~~l-~dm~~A~~ri~~ai~~~--ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~I-P~R~~eG-------YGl~~~  140 (600)
                      |..| .+..+|++...++.+++  ++|.++|+     +.----..+.|+..|.++.... -+...+|       ||.+++
T Consensus         8 ~~GFC~GV~rAi~~a~~~~~~~~~~~vy~lG~-----iVHN~~vv~~L~~~Gv~~v~~~~~~~~~~~~~ViirAHGv~~~   82 (281)
T PRK12360          8 NAGFCFGVKRAIDTAYKEIEKNDKKKIYTLGP-----LIHNNQVVSDLEEKGVKVIEESDLDSLKKGDVVIIRSHGVSKK   82 (281)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHCCCCCEEEECC-----CCCCHHHHHHHHHCCCEEEECCCCCCCCCCCEEEEECCCCCHH
T ss_conf             99868149999999999999769996898377-----7679899999997799798134202379999899989999989


Q ss_pred             HHHHHHHCCCCEEEEECCC--CCCHHHHHHHHHCCCCEEEECCCCCCC
Q ss_conf             9887420268689996488--762345555541798279961544765
Q gi|254780901|r  141 LMEKFINEGAQLIITVDCG--STSYDALQYATNQGIDVIVIDHHQVKS  186 (600)
Q Consensus       141 ~i~~~~~~g~~LiItvD~G--i~~~e~i~~a~~~GidvIVtDHH~~~~  186 (600)
                      ..+++.+.|..++= .-|.  ...+..++...+.|..+||.-|+.-|+
T Consensus        83 ~~~~a~~~g~~viD-aTCP~V~kvh~~v~~~~~~Gy~viiiG~~~HpE  129 (281)
T PRK12360         83 VYKDLTDKGLEVID-ATCPFVKKIQNIVEEYYNKGYKIIIVGDPNHPE  129 (281)
T ss_pred             HHHHHHHCCCCEEC-CCCCCHHHHHHHHHHHHHCCCEEEEECCCCCHH
T ss_conf             99999965998770-518105799999999997899799971689877


No 283
>COG0796 MurI Glutamate racemase [Cell envelope biogenesis, outer membrane]
Probab=54.10  E-value=15  Score=16.40  Aligned_cols=82  Identities=17%  Similarity=0.347  Sum_probs=60.9

Q ss_pred             CCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCC---------HHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             799799994078861528999999999769947998078743366889---------78988742026868999648876
Q gi|254780901|r   91 NSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPN---------PSLMEKFINEGAQLIITVDCGST  161 (600)
Q Consensus        91 ~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~---------~~~i~~~~~~g~~LiItvD~Gi~  161 (600)
                      .+.+|.||-    -|+-+-+++.+..+++-.+-.+|+-|.-.-.||.-         .++++.+.+.+++++|. =|-+.
T Consensus         4 ~~~~IgvFD----SGVGGLsVlrei~~~LP~e~~iY~~D~a~~PYG~ks~e~I~~~~~~i~~~l~~~~ik~lVI-ACNTA   78 (269)
T COG0796           4 PQPPIGVFD----SGVGGLSVLREIRRQLPDEDIIYVGDTARFPYGEKSEEEIRERTLEIVDFLLERGIKALVI-ACNTA   78 (269)
T ss_pred             CCCEEEEEE----CCCCHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEEE-ECCHH
T ss_conf             668189997----8987089999999978998689981477899998999999999999999999729988999-66517


Q ss_pred             CHHHHHHHHHC-CCCEE
Q ss_conf             23455555417-98279
Q gi|254780901|r  162 SYDALQYATNQ-GIDVI  177 (600)
Q Consensus       162 ~~e~i~~a~~~-GidvI  177 (600)
                      +.-+++.+++. .+-|+
T Consensus        79 Sa~al~~LR~~~~iPVv   95 (269)
T COG0796          79 SAVALEDLREKFDIPVV   95 (269)
T ss_pred             HHHHHHHHHHHCCCCEE
T ss_conf             89999999986799989


No 284
>PRK08574 cystathionine gamma-synthase; Provisional
Probab=54.09  E-value=15  Score=16.40  Aligned_cols=89  Identities=11%  Similarity=0.209  Sum_probs=45.9

Q ss_pred             CHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEE
Q ss_conf             87999999999997799799994078861528999999999769947998078743366889789887420268689996
Q gi|254780901|r   77 DCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITV  156 (600)
Q Consensus        77 dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItv  156 (600)
                      +|..-..-+....+.+..|++-.  |+=|-|  .-+.+.|.++|.++.++-|+-        .+.++.++..+++||.. 
T Consensus        77 GmaAi~~~ll~~l~~Gd~il~~~--~~Yg~t--~~l~~~l~~~Gi~v~~~~~~~--------~~~~~~~~~~~Tklv~~-  143 (384)
T PRK08574         77 GMAAISTLFFSLLKAGDEVVLPM--EAYGTT--LRLLKSLEKFGVRVRLAYPST--------EDLIEAIKESRTKLVFI-  143 (384)
T ss_pred             HHHHHHHHHHHHCCCCCEEEECC--CCCHHH--HHHHHHHHHHCCEEEEECCCC--------HHHHHHHCCCCCEEEEE-
T ss_conf             79999999998168999899848--971459--999999986085799948997--------89999744788549999-


Q ss_pred             CCC------CCCHHHH-HHHHHCCCCEEE
Q ss_conf             488------7623455-555417982799
Q gi|254780901|r  157 DCG------STSYDAL-QYATNQGIDVIV  178 (600)
Q Consensus       157 D~G------i~~~e~i-~~a~~~GidvIV  178 (600)
                      .+=      +.+.+++ +.|++.|+-+||
T Consensus       144 EspsNP~l~v~Di~~ia~iA~~~g~~~vv  172 (384)
T PRK08574        144 ETITNPTLRVIDVPEVAKAAKDLGAILVV  172 (384)
T ss_pred             ECCCCCCCCCCCHHHHHHHHHHCCCEEEE
T ss_conf             88999876347859999999775985997


No 285
>pfam03686 UPF0146 Uncharacterized protein family (UPF0146). The function of this family of proteins is unknown.
Probab=54.02  E-value=15  Score=16.39  Aligned_cols=56  Identities=21%  Similarity=0.322  Sum_probs=34.4

Q ss_pred             HHHHHHC-CCCEEEEECCCCCCHHHH-HHHHHCCCCEEEECCCCCCC-CCCC--CEEEECCCC
Q ss_conf             8874202-686899964887623455-55541798279961544765-5567--256523788
Q gi|254780901|r  142 MEKFINE-GAQLIITVDCGSTSYDAL-QYATNQGIDVIVIDHHQVKS-EEIP--AYALVNPNR  199 (600)
Q Consensus       142 i~~~~~~-g~~LiItvD~Gi~~~e~i-~~a~~~GidvIVtDHH~~~~-~~p~--a~aivNP~~  199 (600)
                      .+.+++. ...-|+-|  |+...-++ ..+++.|+||++||-|+..- ...+  .+=|.||+.
T Consensus         5 a~~ia~~~~~gkiVEV--GIG~~~~vA~~L~~~g~dv~~tDi~~~av~~gl~~v~DDif~P~~   65 (127)
T pfam03686         5 AEYIARENARGKVVEV--GIGFFLDVAKRLAERGFDVLATDINEKAVPEGLRFVVDDITNPNI   65 (127)
T ss_pred             HHHHHHHCCCCCEEEE--ECCCCHHHHHHHHHCCCCEEEEECCCCCCCCCCCEEECCCCCCCH
T ss_conf             9998741878858999--136888999999985996899977765766788878725889898


No 286
>PRK07272 amidophosphoribosyltransferase; Provisional
Probab=53.91  E-value=15  Score=16.38  Aligned_cols=36  Identities=22%  Similarity=0.216  Sum_probs=19.3

Q ss_pred             CCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCC
Q ss_conf             9979999407886152899999999976994799807874336688
Q gi|254780901|r   92 SEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGP  137 (600)
Q Consensus        92 ~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl  137 (600)
                      +|.=.|+|=|..+  -++.+++..|..+        -||=+|+.|+
T Consensus         9 ~eeCGIfGi~~~~--~~~~~ly~gL~aL--------QHRGQeSaGI   44 (484)
T PRK07272          9 NEECGVFGIWGHP--DAAQLTYFGLHSL--------QHRGQEGAGI   44 (484)
T ss_pred             CCCCEEEEEECCH--HHHHHHHHHHHHH--------HCCCCCCCEE
T ss_conf             7676079998883--0399999999987--------5477020359


No 287
>COG0496 SurE Predicted acid phosphatase [General function prediction only]
Probab=53.85  E-value=15  Score=16.37  Aligned_cols=182  Identities=16%  Similarity=0.166  Sum_probs=82.1

Q ss_pred             CEEEEECCCCCCHHHHHHHHHC--CCCEEEECCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             6899964887623455555417--98279961544765556725652378888643344304788999999999997021
Q gi|254780901|r  151 QLIITVDCGSTSYDALQYATNQ--GIDVIVIDHHQVKSEEIPAYALVNPNRLDDLSGQGHLCAAGVVFLVLVLIYRILRQ  228 (600)
Q Consensus       151 ~LiItvD~Gi~~~e~i~~a~~~--GidvIVtDHH~~~~~~p~a~aivNP~~~~~~~p~~~l~gaGvaf~l~~al~~~l~~  228 (600)
                      ++|||=|-|+.|---...++.+  +-||                .||=|.        .+-||+|-+.-+...++-.--+
T Consensus         2 rILlTNDDGi~a~Gi~aL~~al~~~~dV----------------~VVAP~--------~~qSg~s~slTl~~Plr~~~~~   57 (252)
T COG0496           2 RILLTNDDGIHAPGIRALARALREGADV----------------TVVAPD--------REQSGASHSLTLHEPLRVRQVD   57 (252)
T ss_pred             EEEEECCCCCCCHHHHHHHHHHHHCCCE----------------EEECCC--------CCCCCCCCCCCCCCCCEEEEEC
T ss_conf             4999668865777799999998627979----------------998269--------8774543440035672324723


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHCCC-CC------CCHHHHHHHH
Q ss_conf             4887640779999999877542011114441189999878877516887435789870888-64------2423456667
Q gi|254780901|r  229 DNKVPLNFDLLSLLDLVALATVCDVVPLIGLNRAYVVKGLMVARRQGNPGLKALIERVNIS-SP------ITAENLGYMI  301 (600)
Q Consensus       229 ~~~~~~~~~l~~~ldlvaiGTvaD~vpL~~eNR~lvk~GL~~l~~~~~~gl~~L~~~~~~~-~~------i~~~di~f~i  301 (600)
                               .   -.++.-||=+|+|          +.||..+-+...|-|    -.++++ +.      +.+.++|   
T Consensus        58 ---------~---~~~av~GTPaDCV----------~lal~~l~~~~~pDL----VvSGIN~G~Nlg~dv~ySGTVa---  108 (252)
T COG0496          58 ---------N---GAYAVNGTPADCV----------ILGLNELLKEPRPDL----VVSGINAGANLGDDVIYSGTVA---  108 (252)
T ss_pred             ---------C---CEEEECCCHHHHH----------HHHHHHHCCCCCCCE----EEECCCCCCCCCCCEEEEEHHH---
T ss_conf             ---------6---5289358818999----------999998646789998----9967647886551134201499---


Q ss_pred             HHHCCHHHHHCCCCCCCEEEECCC-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEE
Q ss_conf             743062333121222210020342-------5899999999998999999999999999999987521124347502620
Q gi|254780901|r  302 GPSINAGGRIGESNLGSRLLISDD-------SQELEMLAMKLDVLNQNRRLMESAMLEQAEAKVLTQCDDIQQASVIVVE  374 (600)
Q Consensus       302 aPrINAaGRl~~a~~av~lL~~~d-------~~~a~~la~~L~~lN~~Rk~~e~~i~~~a~~~~~~~~~~~~~~~~ivv~  374 (600)
                       --+-|+- +|-+..|+.+.....       -+.|.+++..                  ..+.+...  ......++-+.
T Consensus       109 -aA~Ea~~-~GipsIA~S~~~~~~~~~~~~~~e~A~~~~~~------------------lv~~l~~~--p~~~~~llNVN  166 (252)
T COG0496         109 -AAMEAAL-LGIPAIAISLAYREAFGKQDVDFETAAKVARA------------------LVEALLAN--PLPPDTLLNVN  166 (252)
T ss_pred             -HHHHHHH-CCCCCEEEEEHHHCCCCCCCCCHHHHHHHHHH------------------HHHHHHHC--CCCCCCEEEEE
T ss_conf             -9999987-29642365410001355544367999999999------------------99999838--89988289986


Q ss_pred             CCCCC-HHHHHHHHHHHHHHHHCEEEEEEECCCC
Q ss_conf             57858-1222222789988420107998863798
Q gi|254780901|r  375 GDRWH-PGIVGLLAARLKEKFGRPSFAISFEEDG  407 (600)
Q Consensus       375 ~~~wh-~GViGIVAsrL~e~y~kP~iv~s~~~dg  407 (600)
                      -|+++ +-+-|+.-.|+..+.+.+.+.-..+..|
T Consensus       167 iP~~~~~~~~gi~vtr~g~~~~~~~~~~r~dprG  200 (252)
T COG0496         167 IPNLPLEEIKGIRVTRLGRRRYAEPVEERTDPRG  200 (252)
T ss_pred             CCCCCCCCCCCEEEEECHHHHCCCCCCEEECCCC
T ss_conf             7999722368679984236433676323368999


No 288
>cd05805 MPG1_transferase GTP-mannose-1-phosphate guanyltransferase (MPG1 transferase), also known as GDP-mannose pyrophosphorylase, is a bifunctional enzyme with both phosphomannose isomerase (PMI) activity and GDP-mannose phosphorylase (GMP) activity.  The protein contains an N-terminal NTP transferase domain, an L-beta-H domain, and a C-terminal PGM-like domain that belongs to the alpha-D-phosphohexomutase superfamily.  This subfamily is limited to bacteria and archaea. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Members of this group appear to lack conserved residues necessary for metal binding and catalytic activity. Other members of this superfamily include the phosphoglucomutases (PGM1 and PGM2), phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional 
Probab=53.43  E-value=11  Score=17.55  Aligned_cols=49  Identities=16%  Similarity=0.245  Sum_probs=31.4

Q ss_pred             CCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHH-HHCCCC--EEEECCCCCCCCC
Q ss_conf             897898874202686899964887623455555-417982--7996154476555
Q gi|254780901|r  137 PNPSLMEKFINEGAQLIITVDCGSTSYDALQYA-TNQGID--VIVIDHHQVKSEE  188 (600)
Q Consensus       137 l~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a-~~~Gid--vIVtDHH~~~~~~  188 (600)
                      +....+.-+...|++.+   |+|....+.+.++ +..+.+  |+||=.|.|++..
T Consensus        50 l~~a~~~gl~~~G~~V~---~~g~~pTP~~~~a~~~~~~~~GI~ITASHnp~~~n  101 (441)
T cd05805          50 LKRALISGLLSTGVNVR---DLGALPLPVARYAIRFLGASGGIHVRTSPDDPDKV  101 (441)
T ss_pred             HHHHHHHHHHHCCCEEE---EECCCCHHHHHHHHHHCCCCEEEEEECCCCCHHCC
T ss_conf             99999999998699499---90787718999999855998389984478972004


No 289
>PRK12367 short chain dehydrogenase; Provisional
Probab=53.41  E-value=15  Score=16.32  Aligned_cols=82  Identities=23%  Similarity=0.344  Sum_probs=54.9

Q ss_pred             HHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHH
Q ss_conf             99977997999940788615289999999997699479980787433668897898874202686899964887623455
Q gi|254780901|r   87 QAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDAL  166 (600)
Q Consensus        87 ~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i  166 (600)
                      ....++++|+|-|   +-|.-+-|++..+ ++.|++|.-+--+...     +    .....+++.=.|...||  ..+++
T Consensus        12 ~~~~kgKtIgITG---AsGaLG~AL~k~f-~~~GakVIalTh~~~~-----~----~~~~~~~p~~wi~W~cG--~E~~L   76 (250)
T PRK12367         12 NSRWNGKRIGITG---ASGALGKALTKLF-RAKGAKVIGLTHSKIN-----N----SEISDESPNEWVSWECG--KESSL   76 (250)
T ss_pred             CCCCCCCEEEEEC---CCCHHHHHHHHHH-HHCCCEEEEEECCCCC-----C----CCCCCCCCCEEEEEECC--CHHHH
T ss_conf             5563898799967---8738999999999-9889989998368888-----7----54556789528984349--98999


Q ss_pred             HHHHHCCCCEEEECCCCC
Q ss_conf             555417982799615447
Q gi|254780901|r  167 QYATNQGIDVIVIDHHQV  184 (600)
Q Consensus       167 ~~a~~~GidvIVtDHH~~  184 (600)
                      +..-+ .+|++|.-|-.-
T Consensus        77 ~~~Lk-kiDILILNHGIn   93 (250)
T PRK12367         77 DKTLA-KIDVLILNHGIN   93 (250)
T ss_pred             HHHHH-HCCEEEECCCCC
T ss_conf             99987-588999838777


No 290
>TIGR00040 yfcE phosphodiesterase, MJ0936 family; InterPro: IPR000979   Members of this largely uncharacterised family share a motif approximating DXH(X25)GDXXD(X25)GNHD as found in several phosphoesterases, including the nucleases SbcD and Mre11, and a family of uncharacterised archaeal putative phosphoesterases. In this family, the His residue in GNHD portion of the motif is not conserved. The member MJ0936, one of two from Methanococcus jannaschii, was shown  to act on model phosphodiesterase substrates; a divalent cation was required. The following uncharacterised proteins are members of the fsmily: Escherichia coli hypothetical protein yfcE; Bacillus subtilis hypothetical protein ysnB; Mycoplasma genitalium and Mycoplasma pneumoniae hypothetical protein MG207; and M. jannaschii hypothetical proteins MJ0623 and MJ0936. .
Probab=53.37  E-value=12  Score=17.10  Aligned_cols=114  Identities=19%  Similarity=0.228  Sum_probs=67.9

Q ss_pred             HHHHHHHHHH---HCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCC---CCCCHHHHHHHHH------
Q ss_conf             9999999999---779979999407886152899999999976994799807874336---6889789887420------
Q gi|254780901|r   80 KAARRIVQAI---YNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDG---YGPNPSLMEKFIN------  147 (600)
Q Consensus        80 ~A~~ri~~ai---~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eG---YGl~~~~i~~~~~------  147 (600)
                      +|.++-.++.   .+=+.|.+.||.=  --|++.-..+.+..+..++...-.|  .||   -.+....+-++-.      
T Consensus        14 ~A~e~~~~~~~~~~~~D~viH~GD~~--N~~~s~~~l~~~~~~~~~~~aV~GN--~D~~~~~~~~~~~~~~~e~~~f~~~   89 (170)
T TIGR00040        14 RATELPVEAFDKESNVDLVIHAGDLT--NSYKSPFVLKEFEDLAAKVIAVRGN--NDGKEREELPEEEIFEVEGIKFGLV   89 (170)
T ss_pred             CCCHHHHHHHHHHCCCCEEEEECCCC--CCCCCHHHHHHHHHCCCCEEEEECC--CCCCCCCCCCHHHHHHCCCEEEEEE
T ss_conf             33157999998751887999921432--3557878999886313858999678--9982000000344422388027998


Q ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECC-CCCCCCCCCCEEEECC
Q ss_conf             2686899964887623455555417982799615-4476555672565237
Q gi|254780901|r  148 EGAQLIITVDCGSTSYDALQYATNQGIDVIVIDH-HQVKSEEIPAYALVNP  197 (600)
Q Consensus       148 ~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDH-H~~~~~~p~a~aivNP  197 (600)
                      .|..+.+-.|-|--...-...+++.+.||+|.=| |.+--+.-...-+|||
T Consensus        90 hg~~~~~~~~~g~~~~~L~~~~~~~~~DVli~GHTH~~~~e~~~~~l~~NP  140 (170)
T TIGR00040        90 HGDLVYPRGDLGHWYLVLEYLAKELGVDVLIFGHTHIPVAEELRGILLINP  140 (170)
T ss_pred             ECCEEEECCCCCHHHHHHHHHHHHCCCEEEEECCCCEEEEEECCCEEEEEC
T ss_conf             578564244677113556767766284089988714000011276888818


No 291
>pfam07592 Transposase_36 Rhodopirellula transposase. These transposases are found in the planctomycete Rhodopirellula baltica, the cyanobacterium Nostoc, and the Gram-positive bacterium Streptomyces.
Probab=53.32  E-value=15  Score=16.51  Aligned_cols=162  Identities=19%  Similarity=0.320  Sum_probs=70.7

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHCCC---HHHHHHHHHCCCCHHHHHHHCCCCHHHCCCCHHHCCCHHHHHHHHHHHHH
Q ss_conf             887341157888988999999881999---99999999678897898866196677718995561487999999999997
Q gi|254780901|r   14 SGFRWVSLLGQEGINRALAITQKHAIP---DIVARVLVNRNVSIDYAKDFLNPSIRLLMPDPLILTDCDKAARRIVQAIY   90 (600)
Q Consensus        14 ~~~rW~~~~~~~~~~~~~~l~~~~~~~---~~~a~iL~~Rgi~~~~~~~fL~p~l~~l~~dP~~l~dm~~A~~ri~~ai~   90 (600)
                      |..||..+....   .+.+| .+.|.+   ..++++|-..|++......-+.-.   -+||-.  .-.+---++..++..
T Consensus        18 splrWT~kS~r~---la~eL-~~~G~~vs~~tV~~lL~~~GysLq~~~Kt~eg~---~hpDRd--aQF~~In~~~~~~~~   88 (311)
T pfam07592        18 SPLRWTRKSTRK---LAEEL-NQRGYKVSRETVGRLLNELGYSLQANVKTKEGK---KHPDRD--AQFEQINERVKEFDN   88 (311)
T ss_pred             CCCEEEHHHHHH---HHHHH-HHCCCCCCHHHHHHHHHHCCCCHHHHHCCCCCC---CCCCHH--HHHHHHHHHHHHHHH
T ss_conf             986531204999---99999-975987428899999987492113223236788---899816--789999999999876


Q ss_pred             CCCCEE--------EEECCCCCHHHH-------HHHHHHHHHH-CCC--CEEEEECCCCCCCC---CCCHH-------HH
Q ss_conf             799799--------994078861528-------9999999997-699--47998078743366---88978-------98
Q gi|254780901|r   91 NSEKIM--------IFGDYDVDGAAS-------VALMMRFLSH-CSV--NANMYIPDRIVDGY---GPNPS-------LM  142 (600)
Q Consensus        91 ~~ekI~--------I~gDyD~DGits-------tail~~~L~~-~g~--~v~~~IP~R~~eGY---Gl~~~-------~i  142 (600)
                      .++++.        ..|+|.-.|-+=       .+.-..|... +|.  ....|-+.+ .+|+   |.+.+       .|
T Consensus        89 ~g~PvISVDtKkKeliG~~~n~G~~w~~~g~p~~v~~HDf~~~~~gk~iPyGiYD~~~-n~g~V~vgt~~dTa~FaV~si  167 (311)
T pfam07592        89 NGQPVISVDTKKKELIGEFKNSGKEWTKKGAPVEVLDHDFPDKALGTAIPYGIYDVGA-NTGWVSVGTDHDTAEFAVESI  167 (311)
T ss_pred             CCCCEEEEECHHHHHHCCCCCCCCEECCCCCCCEECCCCCCCCCCCCCCCCEEEECCC-CEEEEEEEECCCHHHHHHHHH
T ss_conf             6995788743024552677889854230799504114667664578115641366588-727999820665289999999


Q ss_pred             HHHHHC--------CCCEEEEECCCCCCH--------HHHHHHHHCCCCEEEECCCCCCCC
Q ss_conf             874202--------686899964887623--------455555417982799615447655
Q gi|254780901|r  143 EKFINE--------GAQLIITVDCGSTSY--------DALQYATNQGIDVIVIDHHQVKSE  187 (600)
Q Consensus       143 ~~~~~~--------g~~LiItvD~Gi~~~--------e~i~~a~~~GidvIVtDHH~~~~~  187 (600)
                      +.-.++        -..|+||+|||-++.        +-+++|++.|+.+=|  -|-||..
T Consensus       168 ~~WW~~~g~~~yp~a~~LlItaD~GgsN~~R~r~wk~~Lq~lA~e~gl~I~v--~h~PPgt  226 (311)
T pfam07592       168 RRWWDEMGKKRYPHAKELLITADCGGSNGSRRRLWKKRLQELANETGLPIQV--CHYPPGT  226 (311)
T ss_pred             HHHHHHCCCCCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHHHHHCCEEEE--EECCCCC
T ss_conf             9999973875588520799976788766427789999999999973974799--8359987


No 292
>cd01990 Alpha_ANH_like_I This is a subfamily of Adenine nucleotide alpha hydrolases superfamily. Adenine nucleotide alpha hydrolases superfamily  includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which  binds to Adenosine group.  This subfamily   of proteins probably binds ATP. This domain is about 200 amino acids long with a strongly conserved motif SGGKD at the N terminus.
Probab=53.31  E-value=16  Score=16.31  Aligned_cols=96  Identities=31%  Similarity=0.395  Sum_probs=52.6

Q ss_pred             EEEEECCCCCCHHHHH----HHHHCCCCEEEECCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             8999648876234555----554179827996154476555672565237888864334430478899999999999702
Q gi|254780901|r  152 LIITVDCGSTSYDALQ----YATNQGIDVIVIDHHQVKSEEIPAYALVNPNRLDDLSGQGHLCAAGVVFLVLVLIYRILR  227 (600)
Q Consensus       152 LiItvD~Gi~~~e~i~----~a~~~GidvIVtDHH~~~~~~p~a~aivNP~~~~~~~p~~~l~gaGvaf~l~~al~~~l~  227 (600)
                      +-||+|+|.-.-.+.+    .|++.|++.+++|-++...+.   + .-||..      --+.|.-.+ |..+..+.+..+
T Consensus        27 ~aV~~~s~~~~~~E~e~a~~~a~~~gi~~~~i~~~~l~~~~---~-~~N~~~------RCy~CK~~l-~~~l~~~a~~~g   95 (202)
T cd01990          27 LAVTATSPLFPRRELEEAKRLAKEIGIRHEVIETDELDDPE---F-AKNPPD------RCYLCKKAL-YEALKEIAEELG   95 (202)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHCCCCEEEEECCHHHHHH---H-CCCCHH------HHHHHHHHH-HHHHHHHHHHCC
T ss_conf             99997279899789999999998639857997341110165---5-459755------622998999-999999999679


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCC
Q ss_conf             1488764077999999987754201111444118999987887751688743578987088864
Q gi|254780901|r  228 QDNKVPLNFDLLSLLDLVALATVCDVVPLIGLNRAYVVKGLMVARRQGNPGLKALIERVNISSP  291 (600)
Q Consensus       228 ~~~~~~~~~~l~~~ldlvaiGTvaD~vpL~~eNR~lvk~GL~~l~~~~~~gl~~L~~~~~~~~~  291 (600)
                                    .+.++=||.+|=.  .                ..|||++|+.+ .++..+
T Consensus        96 --------------~~~v~dGtn~dDl--~----------------d~RPGl~A~~e-~~v~sP  126 (202)
T cd01990          96 --------------LDVVLDGTNADDL--G----------------DYRPGLKALRE-LGVRSP  126 (202)
T ss_pred             --------------CCEEEECCCCCCC--C----------------CCCCCHHHHHH-CCCCCC
T ss_conf             --------------9789415757632--3----------------55786889987-699885


No 293
>pfam01522 Polysacc_deac_1 Polysaccharide deacetylase. This domain is found in polysaccharide deacetylase. This family of polysaccharide deacetylases includes NodB (nodulation protein B from Rhizobium) which is a chitooligosaccharide deacetylase. It also includes chitin deacetylase from yeast, and endoxylanases which hydrolyses glucosidic bonds in xylan.
Probab=53.18  E-value=16  Score=16.29  Aligned_cols=26  Identities=19%  Similarity=0.423  Sum_probs=10.8

Q ss_pred             CHHHH-HHHHHHHHHHCCCCEEEEECC
Q ss_conf             61528-999999999769947998078
Q gi|254780901|r  104 DGAAS-VALMMRFLSHCSVNANMYIPD  129 (600)
Q Consensus       104 DGits-tail~~~L~~~g~~v~~~IP~  129 (600)
                      ||-.+ +.-+...|++.+...+++++.
T Consensus        14 DG~~~~~~~~l~~L~~~~i~aTfFv~~   40 (123)
T pfam01522        14 DGPPDNTPRILDVLKKYGVPATFFVIG   40 (123)
T ss_pred             CCCHHHHHHHHHHHHHCCCCEEEEECC
T ss_conf             797351999999999829986997247


No 294
>PRK00055 ribonuclease Z; Reviewed
Probab=53.15  E-value=16  Score=16.29  Aligned_cols=15  Identities=20%  Similarity=0.392  Sum_probs=9.8

Q ss_pred             EEECCCCCCHHHHHH
Q ss_conf             996488762345555
Q gi|254780901|r  154 ITVDCGSTSYDALQY  168 (600)
Q Consensus       154 ItvD~Gi~~~e~i~~  168 (600)
                      |-+|||.....++..
T Consensus        32 iliD~G~G~~~~l~~   46 (259)
T PRK00055         32 WLFDCGEGTQRQMLR   46 (259)
T ss_pred             EEEECCCHHHHHHHH
T ss_conf             999588159999998


No 295
>cd01714 ETF_beta The electron transfer flavoprotein (ETF) serves as a specific electron acceptor for various mitochondrial dehydrogenases. ETF transfers electrons to the main respiratory chain via ETF-ubiquinone oxidoreductase. ETF is an heterodimer that consists of an alpha and a beta subunit which binds one molecule of FAD per dimer . A similar system also exists in some bacteria.  The homologous pair of proteins (FixA/FixB) are essential for nitrogen fixation. The beta subunit protein is distantly related to and forms a heterodimer with the alpha subunit.
Probab=53.14  E-value=16  Score=16.29  Aligned_cols=79  Identities=15%  Similarity=0.256  Sum_probs=46.8

Q ss_pred             CHHHCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCC---CCCCHHHHHHHHH
Q ss_conf             9556148799999999999779979999407886152899999999976994799807874336---6889789887420
Q gi|254780901|r   71 DPLILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDG---YGPNPSLMEKFIN  147 (600)
Q Consensus        71 dP~~l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eG---YGl~~~~i~~~~~  147 (600)
                      |||...-+|.|. ||.++.  +-++.++.   +-+-.+...|.++| .+|++--++|-++-.+|   +....-.-+.+..
T Consensus        34 n~~D~~AlE~Al-rlke~~--g~~Vtvls---vGp~~a~~~Lr~al-AmGaD~ai~i~d~~~~~~D~~~tA~~La~~i~~  106 (202)
T cd01714          34 NPYDEYAVEEAL-RLKEKY--GGEVTVVS---MGPPQAEEALREAL-AMGADRAILVSDRAFAGADTLATAKALAAAIKK  106 (202)
T ss_pred             CCCCHHHHHHHH-HHHHCC--CCEEEEEE---ECCHHHHHHHHHHH-HHCCCEEEEECCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             954389999999-986603--98899999---37478899999999-708983599806555666989999999999987


Q ss_pred             CCCCEEEEE
Q ss_conf             268689996
Q gi|254780901|r  148 EGAQLIITV  156 (600)
Q Consensus       148 ~g~~LiItv  156 (600)
                      .+++||++=
T Consensus       107 ~~~DLIl~G  115 (202)
T cd01714         107 IGVDLILTG  115 (202)
T ss_pred             CCCCEEEEE
T ss_conf             599889995


No 296
>cd06299 PBP1_LacI_like_13 Ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia. This group includes the ligand-binding domain of DNA-binding regulatory protein from Corynebacterium glutamicum which has a unique ability to produce significant amounts of L-glutamate directly from cheap sugar and ammonia.  This regulatory protein is a member of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial trans
Probab=53.08  E-value=16  Score=16.28  Aligned_cols=69  Identities=17%  Similarity=0.210  Sum_probs=41.0

Q ss_pred             HHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCCCC
Q ss_conf             9999769947998078743366889789887420268689996488762345555541798279961544765
Q gi|254780901|r  114 RFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKS  186 (600)
Q Consensus       114 ~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~~~~  186 (600)
                      +.++..|.++....-+.-.+   ...+.++.+.+.+++=+|.+..+. +-+.+..+.+.|+.++..|...+..
T Consensus        23 ~~~~~~gy~~ll~~s~~~~~---~e~~~l~~l~~~~vDGiIi~~~~~-~~~~~~~l~~~~iPvV~id~~~~~~   91 (265)
T cd06299          23 DAASAAGYSTIIGNSDENPE---TENRYLDNLLSQRVDGIIVVPHEQ-SAEQLEDLLKRGIPVVFVDREITGS   91 (265)
T ss_pred             HHHHHCCCEEEEEECCCCHH---HHHHHHHHHHHCCCCEEEEEECCC-CHHHHHHHHHCCCCEEEECCCCCCC
T ss_conf             99998599899997899989---999999999947999999980679-9899999996699899837868999


No 297
>KOG4165 consensus
Probab=53.05  E-value=9.5  Score=17.99  Aligned_cols=17  Identities=18%  Similarity=0.305  Sum_probs=6.9

Q ss_pred             CHHHCCCHHHHHHHHHH
Q ss_conf             95561487999999999
Q gi|254780901|r   71 DPLILTDCDKAARRIVQ   87 (600)
Q Consensus        71 dP~~l~dm~~A~~ri~~   87 (600)
                      .|..+..|-..+.-|.+
T Consensus        69 ~~~K~~sl~~g~~~ia~   85 (433)
T KOG4165          69 SPGKISSLAAGLRQIAE   85 (433)
T ss_pred             CHHHHHHHHHHHHHHHH
T ss_conf             86878999999999885


No 298
>CHL00176 ftsH cell division protein; Validated
Probab=52.90  E-value=16  Score=16.26  Aligned_cols=12  Identities=25%  Similarity=0.279  Sum_probs=5.7

Q ss_pred             CCCCCCEEEECC
Q ss_conf             555672565237
Q gi|254780901|r  186 SEEIPAYALVNP  197 (600)
Q Consensus       186 ~~~p~a~aivNP  197 (600)
                      ...|..+.++-|
T Consensus       207 ak~PkGvLL~Gp  218 (631)
T CHL00176        207 AKIPKGVLLVGP  218 (631)
T ss_pred             CCCCCEEEEECC
T ss_conf             968965898898


No 299
>PRK06725 acetolactate synthase 3 catalytic subunit; Validated
Probab=52.89  E-value=16  Score=16.26  Aligned_cols=77  Identities=10%  Similarity=0.183  Sum_probs=41.0

Q ss_pred             HHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCC--CCCC-------CCCCHH-HHHHHHHCCC
Q ss_conf             99999999977997999940788615289999999997699479980787--4336-------688978-9887420268
Q gi|254780901|r   81 AARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDR--IVDG-------YGPNPS-LMEKFINEGA  150 (600)
Q Consensus        81 A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R--~~eG-------YGl~~~-~i~~~~~~g~  150 (600)
                      .++++.++|.+-++.+|+...-+.---+..-|.++.+.+++-|......|  +.+.       +|.... ....+.+ .+
T Consensus       203 ~l~~a~~~L~~AkrPvil~G~Gv~~~~a~~~l~~lae~~~~PV~tt~~gkg~~~~~hpl~~G~~G~~g~~~a~~~~~-~a  281 (570)
T PRK06725        203 KLREVAKAISKAKRPLLYIGGGVIHSGGSDELIKFARENRIPVVSTLMGLGAYPPGDPLFLGMLGMHGTYAANMAVT-EC  281 (570)
T ss_pred             HHHHHHHHHHHCCCCEEECCCCCCCCCHHHHHHHHHHHHCCCEEECCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHH-CC
T ss_conf             99999999985689879836760046489999999998699899424568889999855578777767799999873-18


Q ss_pred             CEEEEECC
Q ss_conf             68999648
Q gi|254780901|r  151 QLIITVDC  158 (600)
Q Consensus       151 ~LiItvD~  158 (600)
                      ||||++-+
T Consensus       282 Dlvl~iG~  289 (570)
T PRK06725        282 DLLLALGV  289 (570)
T ss_pred             CEEEEECC
T ss_conf             87874055


No 300
>TIGR02151 IPP_isom_2 isopentenyl-diphosphate delta-isomerase, type 2; InterPro: IPR011179   This group represents the bacterial and archaeal isopentenyl-diphosphate delta-isomerase (IPP isomerase). IPP isomerase catalyses the interconversion of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), and is a key enzyme in the biosynthesis of isoprenoids via the mevalonate pathway. The bacterial and archaeal IPP isomerase (type 2 enzyme) differs from that found in eukaryotes (type 1 enzyme), and requires NADPH, magnesium, and FMN for activity , .; GO: 0004452 isopentenyl-diphosphate delta-isomerase activity, 0010181 FMN binding, 0008299 isoprenoid biosynthetic process, 0005737 cytoplasm.
Probab=52.75  E-value=16  Score=16.24  Aligned_cols=89  Identities=20%  Similarity=0.227  Sum_probs=50.9

Q ss_pred             HHHHHHHHH-HHH-----HCCCCEEEEECCCC-CHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCC
Q ss_conf             799999999-999-----77997999940788-61528999999999769947998078743366889789887420268
Q gi|254780901|r   78 CDKAARRIV-QAI-----YNSEKIMIFGDYDV-DGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGA  150 (600)
Q Consensus        78 m~~A~~ri~-~ai-----~~~ekI~I~gDyD~-DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~  150 (600)
                      ..+|++.|. +|+     --.|-+.-=||-+- -|+.-  =+-+.-+++...|-.-     +=|+|+|.+.+.++.+-|+
T Consensus       141 ~~~aid~i~AdAL~iHlN~~QE~vqpEGDr~F~~G~l~--~i~~~~~~~~vPVIvK-----EvG~G~S~e~a~~L~~~Gv  213 (349)
T TIGR02151       141 AQEAIDMIEADALAIHLNVLQELVQPEGDRNFSKGWLE--KIAEICSAVSVPVIVK-----EVGFGISKEVAKLLADAGV  213 (349)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHH--HHHHHHHHCCCCEEEE-----ECCCCCCHHHHHHHHHCCE
T ss_conf             99999875101335543233025579997015653899--9999996528987998-----2157998899999987890


Q ss_pred             CEEEEECCCCCCHHHHHHHH-HCC
Q ss_conf             68999648876234555554-179
Q gi|254780901|r  151 QLIITVDCGSTSYDALQYAT-NQG  173 (600)
Q Consensus       151 ~LiItvD~Gi~~~e~i~~a~-~~G  173 (600)
                      +-|=.--.|=|++-.||..+ .++
T Consensus       214 ~aiDv~G~GGTswa~vE~~Rr~~~  237 (349)
T TIGR02151       214 KAIDVSGAGGTSWAAVENYRRAKE  237 (349)
T ss_pred             EEEEECCCCCCCHHHHHHHHHHCC
T ss_conf             088707876755999998875157


No 301
>pfam00072 Response_reg Response regulator receiver domain. This domain receives the signal from the sensor partner in bacterial two-component systems. It is usually found N-terminal to a DNA binding effector domain.
Probab=52.67  E-value=9.1  Score=18.13  Aligned_cols=95  Identities=16%  Similarity=0.152  Sum_probs=40.7

Q ss_pred             HHHHHHHH-CCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             89887420-26868999648876234555554179827996154476555672565237888864334430478899999
Q gi|254780901|r  140 SLMEKFIN-EGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKSEEIPAYALVNPNRLDDLSGQGHLCAAGVVFLV  218 (600)
Q Consensus       140 ~~i~~~~~-~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~~~~~~p~a~aivNP~~~~~~~p~~~l~gaGvaf~l  218 (600)
                      ..+..+.+ .|+. +.++.+   ..++++.+.+...|+|++|.+.|.-.......-+.-  .+..-|.--++|-+-.-..
T Consensus        12 ~~l~~~L~~~g~~-v~~a~~---g~~al~~~~~~~~dlvi~Di~mP~~dG~el~~~ir~--~~~~~piI~~T~~~~~~~~   85 (111)
T pfam00072        12 ELLRQLLEKEGYV-VAEADD---GEEALELLKEKRPDLILLDIRMPGMDGLELLRRIRR--RPPTTPVIVLTAHGDEEDA   85 (111)
T ss_pred             HHHHHHHHHCCCE-EEEECC---HHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHH--CCCCCEEEEEECCCCHHHH
T ss_conf             9999999988999-999899---999999998479989999536899501579999973--5999809999750899999


Q ss_pred             HHHHHHHHCCCCCCCCHHHHHHHH
Q ss_conf             999999702148876407799999
Q gi|254780901|r  219 LVLIYRILRQDNKVPLNFDLLSLL  242 (600)
Q Consensus       219 ~~al~~~l~~~~~~~~~~~l~~~l  242 (600)
                      .+++  ..+-.+.+.+.++..+++
T Consensus        86 ~~a~--~~Ga~~yl~KP~~~~~L~  107 (111)
T pfam00072        86 VEAL--KAGANDFLSKPFDPEELV  107 (111)
T ss_pred             HHHH--HCCCCEEEECCCCHHHHH
T ss_conf             9999--779877994999989999


No 302
>PRK12726 flagellar biosynthesis regulator FlhF; Provisional
Probab=52.65  E-value=16  Score=16.23  Aligned_cols=37  Identities=14%  Similarity=0.112  Sum_probs=20.1

Q ss_pred             CCCCEEEEECCCC--CHHHHHHHHHHHHHHHHCEEEEEE
Q ss_conf             3475026205785--812222227899884201079988
Q gi|254780901|r  366 QQASVIVVEGDRW--HPGIVGLLAARLKEKFGRPSFAIS  402 (600)
Q Consensus       366 ~~~~~ivv~~~~w--h~GViGIVAsrL~e~y~kP~iv~s  402 (600)
                      +...||.+.+++.  ..--+|=.|.+++.+=.++.++-+
T Consensus       204 ~~g~VIaLVGvnGvGKTTTiAKLA~~l~~~gkkV~LVAa  242 (407)
T PRK12726        204 SNHRIISLIGQTGVGKTTTLVKLGWQLLKQNRTVGFITT  242 (407)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEC
T ss_conf             369089998999897899999999999977991799970


No 303
>pfam01751 Toprim Toprim domain. This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyse the relaxation of DNA supercoiling by causing transient double strand breaks.
Probab=52.60  E-value=16  Score=16.23  Aligned_cols=42  Identities=12%  Similarity=0.187  Sum_probs=32.0

Q ss_pred             HHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEE
Q ss_conf             9999999977997999940788615289999999997699479
Q gi|254780901|r   82 ARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNAN  124 (600)
Q Consensus        82 ~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~  124 (600)
                      +..+.+..++. .|.|..|.|.+|-..+.-+.+.|+..+.++.
T Consensus        43 ~~~l~~~~~~~-eViiatD~D~eGe~~a~~l~~~l~~~~~~v~   84 (89)
T pfam01751        43 LKLLKKLAKKD-EVILATDPDREGEAIAWKLLELLKPLGKKVR   84 (89)
T ss_pred             HHHHHHHHCCC-EEEEECCCCHHHHHHHHHHHHHHHHCCCCEE
T ss_conf             99999862377-4999879894899999999998312298169


No 304
>cd06289 PBP1_MalI_like Ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. This group includes the ligand-binding domain of MalI, a transcription regulator of the maltose system of Escherichia coli and its close homologs from other bacteria. They are members of the LacI-GalR family of repressor proteins which are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold.  As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=52.40  E-value=16  Score=16.20  Aligned_cols=71  Identities=18%  Similarity=0.238  Sum_probs=41.2

Q ss_pred             HHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCCCCCC
Q ss_conf             99976994799807874336688978988742026868999648876234555554179827996154476555
Q gi|254780901|r  115 FLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKSEE  188 (600)
Q Consensus       115 ~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~~~~~~  188 (600)
                      .++..|.++.....+.-.+   .-.+.++.+...+++=+|.+-.--++.+.++.+++.|+.+++.|.+.+....
T Consensus        24 ~a~~~gy~lll~~t~~~~~---~e~~~i~~l~~~~vDGiIi~~~~~~~~~~~~~l~~~~iPvV~i~~~~~~~~~   94 (268)
T cd06289          24 VLEEAGYTVFLANSGEDVE---RQEQLLSTMLEHGVAGIILCPAAGTSPDLLKRLAESGIPVVLVAREVAGAPF   94 (268)
T ss_pred             HHHHCCCEEEEEECCCCHH---HHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCCCCCC
T ss_conf             9998699899995899989---9999999999659998999468889999999999759989983676799998


No 305
>PRK00724 formate dehydrogenase accessory protein; Reviewed
Probab=52.01  E-value=16  Score=16.16  Aligned_cols=19  Identities=26%  Similarity=0.324  Sum_probs=11.7

Q ss_pred             HHHHHHHHHHCEEEEEEEC
Q ss_conf             2789988420107998863
Q gi|254780901|r  386 LAARLKEKFGRPSFAISFE  404 (600)
Q Consensus       386 VAsrL~e~y~kP~iv~s~~  404 (600)
                      .|-.++++++-.-+-|+..
T Consensus       233 lAvelA~~~giTLigf~R~  251 (262)
T PRK00724        233 LAVELAEELGLTLVGFARG  251 (262)
T ss_pred             HHHHHHHHCCCEEEEEECC
T ss_conf             9999999819989999618


No 306
>cd02511 Beta4Glucosyltransferase UDP-glucose LOS-beta-1,4 glucosyltransferase is required for biosynthesis of lipooligosaccharide. UDP-glucose: lipooligosaccharide (LOS)  beta-1-4-glucosyltransferase catalyzes the addition of the first residue, glucose, of the lacto-N-neotetrase structure to HepI of the LOS inner core.  LOS is the major constituent of the outer leaflet of the outer membrane of gram-positive bacteria. It consists of a short oligosaccharide chain of variable composition (alpha chain) attached to a branched inner core which is lined in turn to lipid A. Beta 1,4 glucosyltransferase is required to attach the alpha chain to the inner core.
Probab=51.98  E-value=16  Score=16.16  Aligned_cols=27  Identities=37%  Similarity=0.469  Sum_probs=20.1

Q ss_pred             CCEEEEECCCCCCHHHHHHHHHCCCCEE
Q ss_conf             8689996488762345555541798279
Q gi|254780901|r  150 AQLIITVDCGSTSYDALQYATNQGIDVI  177 (600)
Q Consensus       150 ~~LiItvD~Gi~~~e~i~~a~~~GidvI  177 (600)
                      ++=||.||+||++.- ++.|++.|..|+
T Consensus        26 ~deiivvDs~StD~T-~~ia~~~~~~v~   52 (229)
T cd02511          26 VDEIIVVDSGSTDRT-VEIAKEYGAKVY   52 (229)
T ss_pred             CCEEEEEECCCCCCH-HHHHHHCCCEEE
T ss_conf             988999959798752-999998499089


No 307
>cd01141 TroA_d Periplasmic binding protein TroA_d.  These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea.  They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism.  A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains.
Probab=51.97  E-value=16  Score=16.16  Aligned_cols=38  Identities=21%  Similarity=0.320  Sum_probs=21.8

Q ss_pred             HHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEEC
Q ss_conf             887420268689996488762345555541798279961
Q gi|254780901|r  142 MEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVID  180 (600)
Q Consensus       142 i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtD  180 (600)
                      +|.+.+-.++|||+-+ +..+.+.++.+.+.||.|++++
T Consensus        62 ~E~ilaL~PDlVi~~~-~~~~~~~~~~L~~~gI~v~~~~   99 (186)
T cd01141          62 VELIVALKPDLVILYG-GFQAQTILDKLEQLGIPVLYVN   99 (186)
T ss_pred             HHHHHHHCCCEEEEEC-CCCCHHHHHHHHHCCCCEEEEE
T ss_conf             9999970999999958-8786789999996499579960


No 308
>cd04597 CBS_pair_DRTGG_assoc2 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with a DRTGG domain upstream. The function of the DRTGG domain, named after its conserved residues, is unknown. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.
Probab=51.86  E-value=16  Score=16.14  Aligned_cols=77  Identities=21%  Similarity=0.229  Sum_probs=49.2

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHH---HHHHHHC---------------CCCEEEEECCCCCC
Q ss_conf             78861528999999999769947998078743366889789---8874202---------------68689996488762
Q gi|254780901|r  101 YDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSL---MEKFINE---------------GAQLIITVDCGSTS  162 (600)
Q Consensus       101 yD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~---i~~~~~~---------------g~~LiItvD~Gi~~  162 (600)
                      -|.|-|+|+--...+.+..|..  -|+|-|.-|   +|.+.   ++++--+               -.+-++|+...++-
T Consensus         3 PDtDsi~sAi~ya~l~~~~~~~--~~~~~r~G~---~n~et~~vL~~f~~~~P~li~~v~~qV~DIm~~~~vti~~~~sl   77 (113)
T cd04597           3 PDTDSVASAIAYAHLKRRQGMD--NVTAARLGE---PNPQTRYVLEYLGIEPPILLADVHPRVRDVINRKPVTARPNDPL   77 (113)
T ss_pred             CCHHHHHHHHHHHHHHHHCCCC--CEEEECCCC---CCHHHHHHHHHCCCCCCEECCCCCCHHHHHCCCCCCCCCCCCCH
T ss_conf             8568899999999999761888--637730689---99899999998499998002156505666313788341999829


Q ss_pred             HHHHHHHHHCCCC-EEEECCC
Q ss_conf             3455555417982-7996154
Q gi|254780901|r  163 YDALQYATNQGID-VIVIDHH  182 (600)
Q Consensus       163 ~e~i~~a~~~Gid-vIVtDHH  182 (600)
                      .++.+...++++. +-|+|.+
T Consensus        78 ~eA~~lM~e~~i~~LPVVD~~   98 (113)
T cd04597          78 REALNLMHEHNIRTLPVVDDD   98 (113)
T ss_pred             HHHHHHHHHCCCCEEEEECCC
T ss_conf             999999998499878698899


No 309
>PRK07574 formate dehydrogenase; Provisional
Probab=51.62  E-value=16  Score=16.12  Aligned_cols=250  Identities=16%  Similarity=0.182  Sum_probs=124.4

Q ss_pred             HHHCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCC
Q ss_conf             55614879999999999977997999940788615289999999997699479980787433668897898874202686
Q gi|254780901|r   72 PLILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQ  151 (600)
Q Consensus        72 P~~l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~  151 (600)
                      |-.|-+.-...--|.+.++.+-.=+|..+ |-||-.|  -+-+-|  -.++|..--|  |--. =++.+.|++++.  -+
T Consensus        47 p~~llg~~~~elglr~~le~~gh~~v~t~-dk~g~~~--~~~~~l--~da~ivis~p--f~p~-ylT~E~IekApn--LK  116 (385)
T PRK07574         47 PGELLGSVSGELGLRTFLEERGHELVVTS-DKDGPDS--VFEREL--PDADVVISQP--FWPA-YLTAERIAKAPN--LK  116 (385)
T ss_pred             CCCEEEECCCHHHHHHHHHHCCCEEEEEC-CCCCCCC--HHHHHC--CCCEEEECCC--CCCC-CCCHHHHHCCCC--CE
T ss_conf             76212223330105888985591699965-8889850--677515--7763997458--8732-114999943886--73


Q ss_pred             EEEEECCCCCCHHHHHHHHHCCCCEEEECCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             89996488762345555541798279961544765556725652378888643344304788999999999997021488
Q gi|254780901|r  152 LIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKSEEIPAYALVNPNRLDDLSGQGHLCAAGVVFLVLVLIYRILRQDNK  231 (600)
Q Consensus       152 LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~~~~~~p~a~aivNP~~~~~~~p~~~l~gaGvaf~l~~al~~~l~~~~~  231 (600)
                      |++|.--|+.+. -++.|+++||.|.                  |  -++++    ..+-|--++.++.++.|.+...  
T Consensus       117 li~tAGVG~DnI-DL~AA~erGI~V~------------------n--vpG~N----s~SVAEhtv~liLal~R~i~~~--  169 (385)
T PRK07574        117 LAITAGIGSDHV-DLQAASEHNITVA------------------E--VTGSN----SISVAEHVVMMILALVRNYLPS--  169 (385)
T ss_pred             EEEEEEECCCHH-HHHHHHHCCCEEE------------------E--CCCCC----HHHHHHHHHHHHHHHHCCCHHH--
T ss_conf             999942047245-4998997899999------------------5--99987----1999999999999997588889--


Q ss_pred             CCCHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHH-HHHHHHCCCCCHHHHHHHHCCC-CCCCHHHHHHHHHHHCCHHH
Q ss_conf             764077999999987754201111444118999987-8877516887435789870888-64242345666774306233
Q gi|254780901|r  232 VPLNFDLLSLLDLVALATVCDVVPLIGLNRAYVVKG-LMVARRQGNPGLKALIERVNIS-SPITAENLGYMIGPSINAGG  309 (600)
Q Consensus       232 ~~~~~~l~~~ldlvaiGTvaD~vpL~~eNR~lvk~G-L~~l~~~~~~gl~~L~~~~~~~-~~i~~~di~f~iaPrINAaG  309 (600)
                                                  + ..++.| ... ......+    .+..+-. +-+-...||-.++-|+-+-|
T Consensus       170 ----------------------------~-~~v~~G~W~~-a~~~~~~----~EL~GKTlGIVG~GrIG~~VArra~aFg  215 (385)
T PRK07574        170 ----------------------------H-RQVVDGGWNI-ADCVSRS----YDLEGMTVGTVGAGRIGLAVLRRLKPFD  215 (385)
T ss_pred             ----------------------------H-HHHHCCCCCH-HHCCCCC----EECCCCEEEEECCCHHHHHHHHHHHHCC
T ss_conf             ----------------------------9-9998499851-2125664----3268998999897889999999999779


Q ss_pred             HHCCCCCCCEEEECCCHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCHHHHHHHHH
Q ss_conf             312122221002034258-9999999999899999999999999999998752112434750262057858122222278
Q gi|254780901|r  310 RIGESNLGSRLLISDDSQ-ELEMLAMKLDVLNQNRRLMESAMLEQAEAKVLTQCDDIQQASVIVVEGDRWHPGIVGLLAA  388 (600)
Q Consensus       310 Rl~~a~~av~lL~~~d~~-~a~~la~~L~~lN~~Rk~~e~~i~~~a~~~~~~~~~~~~~~~~ivv~~~~wh~GViGIVAs  388 (600)
                              ++++-.+ +. ......++   +|-++.       ...++ +..      .-.++.+..| -++.--+++-.
T Consensus       216 --------m~Vl~yD-p~~l~~~~e~~---lg~~~~-------~slde-Ll~------~sDvVslh~P-Lt~eT~~Lin~  268 (385)
T PRK07574        216 --------VTLHYTD-RHRLPAEVEQE---LGLTYH-------PDVDS-LVS------VCDVVTIHCP-LHPETEHLFDK  268 (385)
T ss_pred             --------CEEEEEC-CCCCCHHHHHH---CCCCCC-------CCHHH-HHH------HCCEEEECCC-CCHHHHHHCCH
T ss_conf             --------9899858-86698899997---198656-------89999-986------2896998667-98577401029


Q ss_pred             HHHHHHHCEEEEEEECCCCEEEEEEECCCCCCHHHHHH
Q ss_conf             99884201079988637983799986489861888888
Q gi|254780901|r  389 RLKEKFGRPSFAISFEEDGKGIGSGRSIEGFDIGKMVS  426 (600)
Q Consensus       389 rL~e~y~kP~iv~s~~~dg~~kGS~RSi~g~~l~~~l~  426 (600)
                      +.-.+.++-++++..     ++|..  ++.-.|.++|.
T Consensus       269 ~~l~~MK~ga~LVNt-----ARG~i--VDe~AL~~AL~  299 (385)
T PRK07574        269 DVLSRMKRGSYLVNT-----ARGKI--VDRDAVVEALE  299 (385)
T ss_pred             HHHHCCCCCCEEEEC-----CCCHH--CCHHHHHHHHH
T ss_conf             999438998189988-----86110--19999999997


No 310
>PRK00197 proA gamma-glutamyl phosphate reductase; Provisional
Probab=51.57  E-value=16  Score=16.21  Aligned_cols=35  Identities=14%  Similarity=0.226  Sum_probs=16.9

Q ss_pred             EEEECCCCCCHHHHHHHHCCCCCCCCCC-CCCCCCCEEECCCCHHHHH
Q ss_conf             9986489861888888530335301156-5322231464222158899
Q gi|254780901|r  411 GSGRSIEGFDIGKMVSFAVEEGILVKGG-GHAMAAGLTVERVNFGRLC  457 (600)
Q Consensus       411 GS~RSi~g~~l~~~l~~~~~~~ll~~~G-GH~~AaG~ti~~~~l~~f~  457 (600)
                      -|.+-+.+  +-+|+...      .+|| ||..+ =+|   ++...-.
T Consensus       317 lsv~~V~~--~deAI~hi------n~~~sght~~-I~T---~d~~~a~  352 (416)
T PRK00197        317 LAVKVVDG--LDEAIAHI------NEYGSHHSEA-IVT---EDYSAAR  352 (416)
T ss_pred             EEEEEECC--HHHHHHHH------HHCCCCCCCE-EEE---CCHHHHH
T ss_conf             16999699--99999999------8518998615-798---8999999


No 311
>TIGR01302 IMP_dehydrog inosine-5'-monophosphate dehydrogenase; InterPro: IPR005990    Synonyms: Inosine-5'-monophosphate dehydrogenase, Inosinic acid dehydrogenase     IMP dehydrogenase (1.1.1.205 from EC,IMPDH) catalyzes the rate-limiting reaction of de novo GTP biosynthesis, the NAD-dependent reduction of IMP into XMP .  Inosine 5-phosphate + NAD+ + H2O = xanthosine 5-phosphate + NADH     IMP dehydrogenase is associated with cell proliferation and is a possible target for cancer chemotherapy. Mammalian and bacterial IMPDHs are tetramers of identical chains. There are two IMP dehydrogenase isozymes in humans . IMP dehydrogenase nearly always contains a long insertion that has two CBS domains within it and adopts a TIM barrel structure.; GO: 0003938 IMP dehydrogenase activity, 0006177 GMP biosynthetic process.
Probab=50.75  E-value=17  Score=16.02  Aligned_cols=70  Identities=21%  Similarity=0.341  Sum_probs=30.4

Q ss_pred             CCEEEEECCCCCHHHHHHHHHH-HHHHHHCEEEEEEEC---CCC-EEEEEEECCCCCCHHHHHH--HH-CCCCCCCCCCC
Q ss_conf             7502620578581222222789-988420107998863---798-3799986489861888888--53-03353011565
Q gi|254780901|r  368 ASVIVVEGDRWHPGIVGLLAAR-LKEKFGRPSFAISFE---EDG-KGIGSGRSIEGFDIGKMVS--FA-VEEGILVKGGG  439 (600)
Q Consensus       368 ~~~ivv~~~~wh~GViGIVAsr-L~e~y~kP~iv~s~~---~dg-~~kGS~RSi~g~~l~~~l~--~~-~~~~ll~~~GG  439 (600)
                      .++.||..++   -++|+|.-+ +.+.-..|--.  .+   ++| +..|-|=|+..+|.--+-.  ++ .+--++..-.|
T Consensus       188 ekLpvVd~~~---~lVgLiT~~Di~~~~~~P~A~--kd~vG~~GrL~VgAAvg~r~~D~~R~~~L~~AGvDv~viDsshG  262 (476)
T TIGR01302       188 EKLPVVDKDG---ELVGLITVKDIVKRREFPHAS--KDTVGENGRLIVGAAVGTREDDLERAEALVEAGVDVIVIDSSHG  262 (476)
T ss_pred             CEEEEECCCC---CEEEEEEHHHHHHHHHCCCCC--CCCCCCCCEEEEEEEECCCCCCHHHHHHHHHCCCCEEEEECCCC
T ss_conf             5047882789---889998644788986388877--88748886089998846898618999999965965899816654


Q ss_pred             CCC
Q ss_conf             322
Q gi|254780901|r  440 HAM  442 (600)
Q Consensus       440 H~~  442 (600)
                      |+.
T Consensus       263 hs~  265 (476)
T TIGR01302       263 HSI  265 (476)
T ss_pred             CCH
T ss_conf             537


No 312
>TIGR00441 gmhA phosphoheptose isomerase; InterPro: IPR004515 Phosphoheptose isomerase is involved in lipopolysaccharide biosynthesis, and more specifically in the synthesis of glyceromannoheptose 7-phosphate. It may also have a role in virulence in Haemophilus ducreyi.; GO: 0008968 phosphoheptose isomerase activity, 0009244 lipopolysaccharide core region biosynthetic process, 0005737 cytoplasm.
Probab=50.66  E-value=17  Score=16.01  Aligned_cols=118  Identities=17%  Similarity=0.331  Sum_probs=65.4

Q ss_pred             HHCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCC---------------CCEE--EEECCCCCCCC
Q ss_conf             561487999999999997799799994078861528999999999769---------------9479--98078743366
Q gi|254780901|r   73 LILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCS---------------VNAN--MYIPDRIVDGY  135 (600)
Q Consensus        73 ~~l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g---------------~~v~--~~IP~R~~eGY  135 (600)
                      -...-+++||..|.+..+++.||+++|    -|-+++==+--+-...|               .++.  .-|-|    -|
T Consensus        20 ~~~~Ai~~aa~ll~~~l~~GgK~L~CG----NGgSaadAqHFAaEl~GRf~~eR~glPAIAL~tD~S~Ltai~N----Dy   91 (186)
T TIGR00441        20 ALIEAIQRAALLLVQSLKNGGKILICG----NGGSAADAQHFAAELVGRFKLERPGLPAIALNTDISILTAIAN----DY   91 (186)
T ss_pred             CHHHHHHHHHHHHHHHHHCCCCEEEEC----CCCCHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHCCC----HH
T ss_conf             508899999999999998089089856----8504335888999871640002677646777622353232001----10


Q ss_pred             CCCHHHHHHHHHC-C--CCEEEEE---CCCCCCHHHHHHHHHCCCCEEEECCCC---CCCC-CCCCEEEECCCC
Q ss_conf             8897898874202-6--8689996---488762345555541798279961544---7655-567256523788
Q gi|254780901|r  136 GPNPSLMEKFINE-G--AQLIITV---DCGSTSYDALQYATNQGIDVIVIDHHQ---VKSE-EIPAYALVNPNR  199 (600)
Q Consensus       136 Gl~~~~i~~~~~~-g--~~LiItv---D~Gi~~~e~i~~a~~~GidvIVtDHH~---~~~~-~p~a~aivNP~~  199 (600)
                      |.. +++.+-.+. |  -|.++-.   -|...=..+++.||++||.||=.==-.   ..+- .|.-++++=|..
T Consensus        92 gyd-~vF~RqVEAlG~~GDVL~GiSTSGNS~NvlkA~~~Ak~~gm~~i~L~G~dGGk~~~l~GPqD~~l~VP~~  164 (186)
T TIGR00441        92 GYD-EVFSRQVEALGQEGDVLLGISTSGNSKNVLKAIEAAKDKGMKTIALTGKDGGKLAGLAGPQDVELRVPSK  164 (186)
T ss_pred             HHH-HHHHHHHHHCCCCCCEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCCCCCCEEEECCCC
T ss_conf             256-7877776632889868887424767088999999884579669997217863113357888605676788


No 313
>COG0037 MesJ tRNA(Ile)-lysidine synthase MesJ [Cell cycle control, cell division, chromosome partitioning]
Probab=50.54  E-value=17  Score=15.99  Aligned_cols=102  Identities=26%  Similarity=0.362  Sum_probs=54.5

Q ss_pred             HHHHHHHHHHHHCC----CCEEEEECCCCCHHHHHHHHHHHHHHCC-CCE-EEEECCCCCCCCCCCH-HHHHHHHHC-CC
Q ss_conf             99999999999779----9799994078861528999999999769-947-9980787433668897-898874202-68
Q gi|254780901|r   79 DKAARRIVQAIYNS----EKIMIFGDYDVDGAASVALMMRFLSHCS-VNA-NMYIPDRIVDGYGPNP-SLMEKFINE-GA  150 (600)
Q Consensus        79 ~~A~~ri~~ai~~~----ekI~I~gDyD~DGitstail~~~L~~~g-~~v-~~~IP~R~~eGYGl~~-~~i~~~~~~-g~  150 (600)
                      ++...++.+++...    ++|+|--   -=|--|+++|+...+..+ .++ -.+|.+.+.. |+-.. ..++++.+. ++
T Consensus         4 ~~~~~~v~~~i~~~~~~~~~ilVav---SGGkDS~~ll~~L~~l~~~~~~~a~~Vd~~~~~-~~~~~~~~~~~~~~~~~~   79 (298)
T COG0037           4 EKLERKVKRAIREFNLIEYKILVAV---SGGKDSLALLHLLKELGRRIEVEAVHVDHGLRG-YSDQEAELVEKLCEKLGI   79 (298)
T ss_pred             HHHHHHHHHHHHHHCCCCCCEEEEE---CCCHHHHHHHHHHHHHCCCCEEEEEEECCCCCC-CCHHHHHHHHHHHHHCCC
T ss_conf             8999999999987256678589993---787899999999998422573899997089886-432899999999996499


Q ss_pred             CEEEE-EC--CCCC-----CHHH----------HHHHHHCCCCEEEECCCCC
Q ss_conf             68999-64--8876-----2345----------5555417982799615447
Q gi|254780901|r  151 QLIIT-VD--CGST-----SYDA----------LQYATNQGIDVIVIDHHQV  184 (600)
Q Consensus       151 ~LiIt-vD--~Gi~-----~~e~----------i~~a~~~GidvIVtDHH~~  184 (600)
                      .+++. ++  -+..     +.+.          -+.|++.|.++|+|=||.-
T Consensus        80 ~~~v~~~~~~~~~~~~~~~~~c~~c~~~R~~~l~~~a~~~g~~~i~tgH~~d  131 (298)
T COG0037          80 PLIVERVTDDLGRETLDGKSICAACRRLRRGLLYKIAKELGADKIATGHHLD  131 (298)
T ss_pred             CEEEEEHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCEEEECCCHH
T ss_conf             8488620454310024676787999999999999999985999898567846


No 314
>PRK02705 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=50.25  E-value=17  Score=15.96  Aligned_cols=33  Identities=21%  Similarity=0.309  Sum_probs=16.2

Q ss_pred             HHCCCCEEEEECCCCCHH-HHHHHHHHHHHHCCCCEE
Q ss_conf             977997999940788615-289999999997699479
Q gi|254780901|r   89 IYNSEKIMIFGDYDVDGA-ASVALMMRFLSHCSVNAN  124 (600)
Q Consensus        89 i~~~ekI~I~gDyD~DGi-tstail~~~L~~~g~~v~  124 (600)
                      +.+..-|+|=|   ..|= |-|+++...|+..|.++.
T Consensus       106 ~~~~~~IaVTG---TnGKTTTt~ll~~iL~~~g~~~~  139 (459)
T PRK02705        106 LKHIPWVGITG---TNGKTTVTHLLAHILQAAGLNAP  139 (459)
T ss_pred             HCCCCEEEEEC---CCCCHHHHHHHHHHHHHCCCCCE
T ss_conf             50497577717---89727899999999998399853


No 315
>cd06390 PBP1_iGluR_AMPA_GluR1 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR1 subunit of the AMPA receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the GluR1 subunit of the AMPA (alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid) receptor. The AMPA receptor is a member of the glutamate-receptor ion channels (iGluRs) which are the major mediators of excitatory synaptic transmission in the central nervous system. AMPA receptors are composed of four types of subunits (GluR1, GluR2, GluR3, and GluR4) which combine to form a tetramer and play an  important role in mediating the rapid excitatory synaptic current. Furthermore, this N-terminal domain of the iGluRs has homology with LIVBP, a bacterial periplasmic binding protein, as well as with the structurally related glutamate-binding domain of the G-protein-coupled metabotropic receptors (mGluRs).
Probab=50.14  E-value=17  Score=15.95  Aligned_cols=12  Identities=17%  Similarity=0.246  Sum_probs=4.7

Q ss_pred             CCHHHHHHHHHH
Q ss_conf             215889999999
Q gi|254780901|r  451 VNFGRLCDFFQK  462 (600)
Q Consensus       451 ~~l~~f~~~l~~  462 (600)
                      |-+-.|.+++..
T Consensus       270 DAV~v~a~al~~  281 (364)
T cd06390         270 DGVRVMAEAFQN  281 (364)
T ss_pred             HHHHHHHHHHHH
T ss_conf             999999999999


No 316
>COG3383 Uncharacterized anaerobic dehydrogenase [General function prediction only]
Probab=50.03  E-value=17  Score=15.94  Aligned_cols=134  Identities=20%  Similarity=0.289  Sum_probs=78.7

Q ss_pred             HHHHCCCCHHHCCCCHHHCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHH-------HHHHHHHHH-CCC-CEE---
Q ss_conf             88661966777189955614879999999999977997999940788615289-------999999997-699-479---
Q gi|254780901|r   57 AKDFLNPSIRLLMPDPLILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASV-------ALMMRFLSH-CSV-NAN---  124 (600)
Q Consensus        57 ~~~fL~p~l~~l~~dP~~l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitst-------ail~~~L~~-~g~-~v~---  124 (600)
                      -++...|-+..  .++|.--.-++|...+++-..+  .=--||---.-||+|+       -++.+..++ +|. +|.   
T Consensus       316 ~dRit~PlIR~--~~~f~evsWeEAl~~vA~rl~~--ik~~yg~dsigfI~Ssk~TNEE~Yl~QKLaR~v~gtNNVDncs  391 (978)
T COG3383         316 RDRITKPLIRE--GDRFREVSWEEALDLVASRLRE--IKEKYGGDSIGFIASSKCTNEENYLMQKLARQVFGTNNVDNCS  391 (978)
T ss_pred             HHHHCCCCCCC--CCCEEEEEHHHHHHHHHHHHHH--HHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCH
T ss_conf             66735662512--8943562099999999999888--8887386532136147777589999999999974468853201


Q ss_pred             -EEE-C-----CCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHH-------HHHHHH-CCCCEEEECCC--CCCCC
Q ss_conf             -980-7-----8743366889789887420268689996488762345-------555541-79827996154--47655
Q gi|254780901|r  125 -MYI-P-----DRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDA-------LQYATN-QGIDVIVIDHH--QVKSE  187 (600)
Q Consensus       125 -~~I-P-----~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~-------i~~a~~-~GidvIVtDHH--~~~~~  187 (600)
                       |.- |     .| +-|||-....|+++...  +|++.+  |.+-.|.       ++.|.. +|-.+||.|--  +..+ 
T Consensus       392 R~CqsPa~~gL~r-TvG~g~dsgsi~dve~a--d~vliI--G~N~te~HPV~asr~kra~k~~G~KliV~D~R~~emae-  465 (978)
T COG3383         392 RYCQSPATDGLFR-TVGSGADSGSIEDVEGA--DLVLII--GANPTEGHPVLASRLKRAHKLRGQKLIVIDPRKHEMAE-  465 (978)
T ss_pred             HHCCCCCCCCCHH-EEECCCCCCCHHHHHHC--CEEEEE--CCCCCCCCCCHHHHHHHHHHHCCCEEEEECCCHHHHHH-
T ss_conf             1006864464031-05436778888888507--759997--67877668508999999998459749995363667777-


Q ss_pred             CCCCEEEECCCCCCCC
Q ss_conf             5672565237888864
Q gi|254780901|r  188 EIPAYALVNPNRLDDL  203 (600)
Q Consensus       188 ~p~a~aivNP~~~~~~  203 (600)
                        .|+..++|+ ++.+
T Consensus       466 --rAdlf~~pk-pGtd  478 (978)
T COG3383         466 --RADLFLHPK-PGTD  478 (978)
T ss_pred             --HHHCCCCCC-CCCC
T ss_conf             --553005899-9964


No 317
>cd06394 PBP1_iGluR_Kainate_KA1_2 N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the KA1 and KA2 subunits of Kainate receptor. N-terminal leucine/isoleucine/valine-binding protein (LIVBP)-like domain of the KA1 and KA2 subunits of Kainate receptor. While this N-terminal domain belongs to the periplasmic-binding fold type I superfamily, the glutamate-binding domain of the iGluR is structurally homologous to the periplasmic-binding fold type II. The LIVBP-like domain of iGluRs is thought to play a role in the initial assembly of iGluR subunits, but it is not well understood how this domain is arranged and functions in intact iGluR. There are five types of kainate receptors, GluR5, GluR6, GluR7, KA1, and KA2, which are structurally similar to AMPA and NMDA subunits of ionotropic glutamate receptors. KA1 and KA2 subunits can only form functional receptors with one of the GluR5-7 subunits. Moreover, GluR5-7 can also form functional homomeric receptor channels act
Probab=50.00  E-value=17  Score=15.93  Aligned_cols=13  Identities=8%  Similarity=0.107  Sum_probs=5.9

Q ss_pred             HHHHCCCCEEEEC
Q ss_conf             5541798279961
Q gi|254780901|r  168 YATNQGIDVIVID  180 (600)
Q Consensus       168 ~a~~~GidvIVtD  180 (600)
                      .|.++.|--|-|+
T Consensus        85 iC~al~IPhi~~~   97 (333)
T cd06394          85 ICGEKEIPHFKVG   97 (333)
T ss_pred             HHCCCCCCEEECC
T ss_conf             8446799808615


No 318
>PRK08525 amidophosphoribosyltransferase; Provisional
Probab=49.94  E-value=17  Score=15.93  Aligned_cols=32  Identities=13%  Similarity=0.093  Sum_probs=15.0

Q ss_pred             EEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCC
Q ss_conf             994078861528999999999769947998078743366889
Q gi|254780901|r   97 IFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPN  138 (600)
Q Consensus        97 I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~  138 (600)
                      |+|=|..+.  ++.+++..|..+        -||=+|+.|+.
T Consensus         4 I~Gi~~~~~--~~~~~~~gL~~L--------QHRGqdsaGIa   35 (445)
T PRK08525          4 VVGVINSKN--AAKYAYYALFAM--------QHRGQEASGIS   35 (445)
T ss_pred             EEEEECCCC--HHHHHHHHHHHH--------HCCCCCCCEEE
T ss_conf             999988852--399999999986--------44661401699


No 319
>cd01139 TroA_f Periplasmic binding protein TroA_f.  These proteins are predicted to function as initial receptors in the ABC metal ion uptake in eubacteria and archaea.  They belong to the TroA superfamily of helical backbone metal receptor proteins that share a distinct fold and ligand binding mechanism.  A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind their ligands in the cleft between these domains.
Probab=49.71  E-value=18  Score=15.90  Aligned_cols=41  Identities=22%  Similarity=0.307  Sum_probs=30.0

Q ss_pred             HHHHHHCCCCEEEEECCCC---CCHHHHHHHHHCCCCEEEECCC
Q ss_conf             8874202686899964887---6234555554179827996154
Q gi|254780901|r  142 MEKFINEGAQLIITVDCGS---TSYDALQYATNQGIDVIVIDHH  182 (600)
Q Consensus       142 i~~~~~~g~~LiItvD~Gi---~~~e~i~~a~~~GidvIVtDHH  182 (600)
                      +|++.+-.++++|....+.   ...+.++.+.+.||.|+++|.+
T Consensus        84 ~E~il~l~PDvVi~~~~~~~~~~~~~~~~~l~~~GIpVv~~~~~  127 (342)
T cd01139          84 VEKVLTLKPDLVILNIWAKTTAEESGILEKLEQAGIPVVFVDFR  127 (342)
T ss_pred             HHHHHHCCCCEEEEECCCCCCCCCHHHHHHHHHCCCCEEEEECC
T ss_conf             99996219988999443456544567999999719988999468


No 320
>PRK13915 putative glucosyl-3-phosphoglycerate synthase; Provisional
Probab=49.67  E-value=18  Score=15.90  Aligned_cols=55  Identities=18%  Similarity=0.209  Sum_probs=33.3

Q ss_pred             CCCCEEEEECCCCCCCCCCCHHH-HHHHHHC---CCCEEEEECCCCCCHHHHHHHHHCCCCEE
Q ss_conf             69947998078743366889789-8874202---68689996488762345555541798279
Q gi|254780901|r  119 CSVNANMYIPDRIVDGYGPNPSL-MEKFINE---GAQLIITVDCGSTSYDALQYATNQGIDVI  177 (600)
Q Consensus       119 ~g~~v~~~IP~R~~eGYGl~~~~-i~~~~~~---g~~LiItvD~Gi~~~e~i~~a~~~GidvI  177 (600)
                      -|..|...||-+-.|   -+... ++.+.+.   -++=||.+|.||++.-+ +.|++.|.+|+
T Consensus        29 ~~~~VSVvlPalNEe---~TVg~vv~~i~~~~~~lvDEviVvDsgStD~Ta-~~A~~aGA~V~   87 (307)
T PRK13915         29 AGRTVSVVLPALNEE---ATVGKVVDSIRPLLVGLVDELIVIDSGSTDDTA-IRAAAAGARVV   87 (307)
T ss_pred             CCCEEEEEECCCCHH---HHHHHHHHHHHHHHCCCCCEEEEECCCCCCCHH-HHHHHHCCEEE
T ss_conf             798699993477657---779999999988505887569997799976589-99998199798


No 321
>COG0033 Pgm Phosphoglucomutase [Carbohydrate transport and metabolism]
Probab=49.58  E-value=18  Score=15.89  Aligned_cols=57  Identities=14%  Similarity=0.124  Sum_probs=43.4

Q ss_pred             CCCCCCCHHHHHHH----HHCCCCEEEEECCCCCCHHHHHHHHH--------CCCCEEEECCCCCCCCC
Q ss_conf             33668897898874----20268689996488762345555541--------79827996154476555
Q gi|254780901|r  132 VDGYGPNPSLMEKF----INEGAQLIITVDCGSTSYDALQYATN--------QGIDVIVIDHHQVKSEE  188 (600)
Q Consensus       132 ~eGYGl~~~~i~~~----~~~g~~LiItvD~Gi~~~e~i~~a~~--------~GidvIVtDHH~~~~~~  188 (600)
                      .||+.+|.+++..+    +.+|+.-|+.-++|+++..++..+--        .|=-+|+|--|.||++.
T Consensus        61 ~D~~~~se~a~~~~lev~aANgv~~iv~~~~g~~~TPAaSh~I~t~n~k~k~~~~GIvlT~SHNPP~D~  129 (524)
T COG0033          61 GDTHALSEPAIQSALEVLAANGVEVIVQGQGGFTPTPAASHAILTHNGKYKALADGIVLTPSHNPPEDG  129 (524)
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCEEEEECCCCCCCCHHHHHHHHHHCCCCCCCCCEEEECCCCCCCCCC
T ss_conf             886401589999999999735845999468982576377778986055456657807975798995447


No 322
>cd01987 USP_OKCHK USP domain is located between the N-terminal sensor domain and C-terminal catalytic domain of this Osmosensitive K+ channel histidine kinase family. The family of KdpD sensor kinase proteins regulates the kdpFABC operon responsible for potassium transport. The USP domain is homologous to the universal stress protein Usp Usp is a small cytoplasmic bacterial protein whose expression is enhanced when the cell is exposed to stress agents. Usp enhances the rate of cell survival during prolonged exposure to such conditions, and may provide a general "stress endurance" activity.
Probab=49.43  E-value=18  Score=15.87  Aligned_cols=84  Identities=12%  Similarity=0.141  Sum_probs=45.5

Q ss_pred             CEEEEECCCCCHHHHHHHHHHHH---HHCCCCE--EEEECCCCCCCCCCCHH---HHHH----HHHCCCCEEEEECCCCC
Q ss_conf             79999407886152899999999---9769947--99807874336688978---9887----42026868999648876
Q gi|254780901|r   94 KIMIFGDYDVDGAASVALMMRFL---SHCSVNA--NMYIPDRIVDGYGPNPS---LMEK----FINEGAQLIITVDCGST  161 (600)
Q Consensus        94 kI~I~gDyD~DGitstail~~~L---~~~g~~v--~~~IP~R~~eGYGl~~~---~i~~----~~~~g~~LiItvD~Gi~  161 (600)
                      ||+++-|+   .-+|-.++-.+.   +.++++.  -|..+.+..   .++..   .+++    +.+-|...++.. .+--
T Consensus         1 rILV~vd~---s~~s~~lir~a~rlA~~~~a~l~vl~V~~~~~~---~~~~~~~~~l~~~~~la~~lga~~~~~~-~~d~   73 (124)
T cd01987           1 RILVCISG---GPNAERLIRRAARLADRLKAPWYVVYVETPRLN---RLSEAERRRLAEALRLAEELGAEVVTLP-GDDV   73 (124)
T ss_pred             CEEEEECC---CHHHHHHHHHHHHHHHHCCCCEEEEEEECCCCC---CCCHHHHHHHHHHHHHHHHCCCEEEEEE-CCCH
T ss_conf             99999589---850799999999999964998999999559756---5897999999999999998599899994-7998


Q ss_pred             CHHHHHHHHHCCCCEEEECCCCC
Q ss_conf             23455555417982799615447
Q gi|254780901|r  162 SYDALQYATNQGIDVIVIDHHQV  184 (600)
Q Consensus       162 ~~e~i~~a~~~GidvIVtDHH~~  184 (600)
                      +..-+++|++.|+|.||.-+|--
T Consensus        74 ~~~I~~~A~~~~~t~IVlG~~~~   96 (124)
T cd01987          74 AEAIVEFAREHNVTQIVVGKSRR   96 (124)
T ss_pred             HHHHHHHHHHCCCCEEEECCCCC
T ss_conf             99999999984998999768988


No 323
>COG0622 Predicted phosphoesterase [General function prediction only]
Probab=49.39  E-value=18  Score=15.87  Aligned_cols=93  Identities=23%  Similarity=0.291  Sum_probs=48.5

Q ss_pred             CEEEEECCCCCHHHHHHHHHHHHHH-CCCCEEEEECCCCCCCC----CCCHHHHHHHHHCCCCEEEEECCCC-----CCH
Q ss_conf             7999940788615289999999997-69947998078743366----8897898874202686899964887-----623
Q gi|254780901|r   94 KIMIFGDYDVDGAASVALMMRFLSH-CSVNANMYIPDRIVDGY----GPNPSLMEKFINEGAQLIITVDCGS-----TSY  163 (600)
Q Consensus        94 kI~I~gDyD~DGitstail~~~L~~-~g~~v~~~IP~R~~eGY----Gl~~~~i~~~~~~g~~LiItvD~Gi-----~~~  163 (600)
                      -|...||+=..+.      ...|.. +.+++.+.-.|  .|+.    ++....  .+.-.|.++.+|  -|-     .+.
T Consensus        31 ~vih~GD~~~~~~------~~~l~~~~~~~i~~V~GN--~D~~~~~~~~p~~~--~~~~~g~ki~l~--HGh~~~~~~~~   98 (172)
T COG0622          31 AVIHAGDSTSPFT------LDALEGGLAAKLIAVRGN--CDGEVDQEELPEEL--VLEVGGVKIFLT--HGHLYFVKTDL   98 (172)
T ss_pred             EEEECCCCCCCCC------HHHHHHCCCCCEEEEECC--CCCCCCCCCCCHHH--EEEECCEEEEEE--CCCCCCCCCCH
T ss_conf             9998997577233------787741136636999777--88751013599658--689888999998--89834667688


Q ss_pred             HH-HHHHHHCCCCEEEECC-CCCCCCCCCCEEEECCC
Q ss_conf             45-5555417982799615-44765556725652378
Q gi|254780901|r  164 DA-LQYATNQGIDVIVIDH-HQVKSEEIPAYALVNPN  198 (600)
Q Consensus       164 e~-i~~a~~~GidvIVtDH-H~~~~~~p~a~aivNP~  198 (600)
                      .. -..|++.+.||+|.=| |.|..+.-....+|||=
T Consensus        99 ~~l~~la~~~~~Dvli~GHTH~p~~~~~~~i~~vNPG  135 (172)
T COG0622          99 SLLEYLAKELGADVLIFGHTHKPVAEKVGGILLVNPG  135 (172)
T ss_pred             HHHHHHHHHCCCCEEEECCCCCCEEEEECCEEEECCC
T ss_conf             8999999746998999798675408998999998499


No 324
>PRK05211 consensus
Probab=49.24  E-value=18  Score=15.85  Aligned_cols=73  Identities=14%  Similarity=0.140  Sum_probs=53.9

Q ss_pred             HHHHHHHHCCCCEEEEE-CCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCC
Q ss_conf             99999997699479980-787433668897898874202686899964887623455555417982799615447
Q gi|254780901|r  111 LMMRFLSHCSVNANMYI-PDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQV  184 (600)
Q Consensus       111 il~~~L~~~g~~v~~~I-P~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~~  184 (600)
                      -+.+.+...|++--+++ =+.-.+|...|.+.|+++.+. +.+=|||--||.+.+.++.+-+.|.|=|++--...
T Consensus        25 ~~ak~~~~~gadelhivDld~a~~g~~~n~~~I~~i~~~-~~~Pl~vGGGIrs~~~i~~ll~~GadkViigs~a~   98 (248)
T PRK05211         25 PLAKRYAEEGADELVFYDITASSDGRVVDKSWVSRVAEV-IDIPFCVAGGIKSVEDAREILSFGADKISINSPAL   98 (248)
T ss_pred             HHHHHHHHCCCCEEEEEECCCCCCCCCCHHHHHHHHHHH-CCCCEEEECCCCCHHHHHHHHHCCCCEEEECCHHH
T ss_conf             999999986999899997867767872149999999976-79858962780138999999987998899897676


No 325
>cd06070 H2MP_like-2 Putative [NiFe] hydrogenase-specific C-terminal protease. Sequence comparison shows similarity to hydrogenase specific C-terminal endopeptidases, also called Hydrogen Maturation Proteases (H2MP). Maturation of [FeNi] hydrogenases includes formation of the nickel metallocenter, proteolytic processing and assembly with other subunits. Hydrogenase maturation endopeptidases are responsible for the proteolytic processing, liberating a short C-terminal peptide by cleaving after a His or an Arg residue, e.g., HycI (E. coli) is involved  in processing of HypE (the large subunit of hydrogenases 3). This cleavage is nickel dependent.
Probab=49.18  E-value=18  Score=15.84  Aligned_cols=55  Identities=29%  Similarity=0.300  Sum_probs=36.7

Q ss_pred             CCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCCCCCCCCCE
Q ss_conf             743366889789887420268689996488762345555541798279961544765556725
Q gi|254780901|r  130 RIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKSEEIPAY  192 (600)
Q Consensus       130 R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~~~~~~p~a~  192 (600)
                      |-+||-|  ..+++.+.+.++.+   .|+|+...+-+.+..... .+||.|=-  ....+|..
T Consensus        10 ~gDDGvG--~~vv~~L~~~~v~v---iD~Gt~g~~l~~~l~~~d-~vIiVDAv--~~g~~pG~   64 (140)
T cd06070          10 YGDDGFG--SCLAEALEQCGAPV---FDGGLDGFGLLSHLENYD-IVIFIDVA--VIDEDVGV   64 (140)
T ss_pred             CCCCCHH--HHHHHHHHHCCCEE---EEECCCHHHHHHHHHCCC-EEEEEEEE--CCCCCCCE
T ss_conf             2538689--99999998639859---992585899999982799-89999511--16899827


No 326
>TIGR03394 indol_phenyl_DC indolepyruvate/phenylpyruvate decarboxylase, Azospirillum family. A family of closely related, thiamine pyrophosphate-dependent enzymes includes indolepyruvate decarboxylase (EC 4.1.1.74), phenylpyruvate decarboxylase (EC 4.1.1.43), pyruvate decarboxylase (EC 4.1.1.1), branched-chain alpha-ketoacid decarboxylase, etc.. Members of this group of homologs may overlap in specificity. This model represents a clade that includes a Azospirillum brasilense member active as both phenylpyruvate decarboxylase and indolepyruvate decarboxylase.
Probab=49.17  E-value=18  Score=15.84  Aligned_cols=85  Identities=11%  Similarity=0.123  Sum_probs=46.1

Q ss_pred             CCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEE------ECCC--CCCC-C-CCCH-HHHHH
Q ss_conf             487999999999997799799994078861528999999999769947998------0787--4336-6-8897-89887
Q gi|254780901|r   76 TDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMY------IPDR--IVDG-Y-GPNP-SLMEK  144 (600)
Q Consensus        76 ~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~------IP~R--~~eG-Y-Gl~~-~~i~~  144 (600)
                      .-.+.+++.+.+.+.+-++-+|+.-.-+.---+..-+.++.+.+|+-|..-      +|+.  ..-| | |... ....+
T Consensus       185 ~~~~~~~~~~~~~l~~A~rPvi~~G~Gv~~~~a~~~l~~lae~l~~PV~tt~~gkG~i~~~~~~~~G~~~G~~g~~~~~~  264 (535)
T TIGR03394       185 DALDACADEVLARMRSATSPVMMVCVEVRRYGLEAKVAELAQRLGVPVVTTFMGRGLLADAPTPPLGTYLGVAGDAELSR  264 (535)
T ss_pred             CHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHHHHCCCCCCHHHHH
T ss_conf             51268999999999855688299831400245799999999972888442645564689998413300055557899998


Q ss_pred             HHHCCCCEEEEECCCCC
Q ss_conf             42026868999648876
Q gi|254780901|r  145 FINEGAQLIITVDCGST  161 (600)
Q Consensus       145 ~~~~g~~LiItvD~Gi~  161 (600)
                      +.+ +.||||.+-+..+
T Consensus       265 ~l~-~aDlvl~lG~~l~  280 (535)
T TIGR03394       265 LVE-ESDGLLLLGVILS  280 (535)
T ss_pred             HHC-CCCEEEEECCCCC
T ss_conf             750-7999999367777


No 327
>PRK07945 hypothetical protein; Provisional
Probab=49.09  E-value=18  Score=15.83  Aligned_cols=15  Identities=27%  Similarity=0.353  Sum_probs=5.5

Q ss_pred             HHHHCCCCEE-EECCC
Q ss_conf             5541798279-96154
Q gi|254780901|r  168 YATNQGIDVI-VIDHH  182 (600)
Q Consensus       168 ~a~~~GidvI-VtDHH  182 (600)
                      .|+++|-+-| ||||-
T Consensus       119 aA~~lGyeYlaITDHS  134 (335)
T PRK07945        119 TAAALGHEYCALTDHS  134 (335)
T ss_pred             HHHHCCCEEEEECCCC
T ss_conf             9998398279980488


No 328
>cd04509 PBP1_ABC_transporter_GCPR_C_like Family C of G-protein coupled receptors and their close homologs, the type I periplasmic-binding proteins of ATP-binding cassette transporter-like systems. This CD includes members of the family C of G-protein coupled receptors and their close homologs, the type I periplasmic-binding proteins of ATP-binding cassette transporter-like systems.  The family C GPCR includes glutamate/glycine-gated ion channels such as the NMDA receptor, G-protein-coupled receptors, metabotropic glutamate, GABA-B, calcium sensing, phermone receptors, and atrial natriuretic peptide-guanylate cyclase receptors. The glutamate receptors that form cation-selective ion channels, iGluR, can be classified into three different subgroups according to their binding-affinity for the agonists NMDA (N-methyl-D-asparate), AMPA (alpha-amino-3-dihydro-5-methyl-3-oxo-4-isoxazolepropionic acid), and kainate. L-glutamate is a major neurotransmitter in the brain of vertebrates and acts th
Probab=49.04  E-value=18  Score=15.83  Aligned_cols=30  Identities=13%  Similarity=0.149  Sum_probs=13.6

Q ss_pred             CCCEEEEECCCCCCHHHHHHHHHCCCCEEE
Q ss_conf             686899964887623455555417982799
Q gi|254780901|r  149 GAQLIITVDCGSTSYDALQYATNQGIDVIV  178 (600)
Q Consensus       149 g~~LiItvD~Gi~~~e~i~~a~~~GidvIV  178 (600)
                      ++..||...|...+......+.+.++-+|.
T Consensus        67 ~v~~iiG~~~s~~~~a~~~~~~~~~vp~i~   96 (299)
T cd04509          67 GVDALVGPVSSGVALAVAPVAEALKIPLIS   96 (299)
T ss_pred             CCEEEECCCCCHHHHHHHHHHHHHCCCEEC
T ss_conf             946997788748899999999982894222


No 329
>PRK09246 amidophosphoribosyltransferase; Provisional
Probab=48.99  E-value=18  Score=15.82  Aligned_cols=11  Identities=27%  Similarity=0.404  Sum_probs=4.6

Q ss_pred             CCCCCCCHHHH
Q ss_conf             33668897898
Q gi|254780901|r  132 VDGYGPNPSLM  142 (600)
Q Consensus       132 ~eGYGl~~~~i  142 (600)
                      .|.||+-+-.+
T Consensus       182 RDp~GiRPL~l  192 (503)
T PRK09246        182 RDPHGIRPLVL  192 (503)
T ss_pred             ECCCCCCCEEE
T ss_conf             88888764277


No 330
>pfam00318 Ribosomal_S2 Ribosomal protein S2.
Probab=48.97  E-value=18  Score=15.82  Aligned_cols=99  Identities=24%  Similarity=0.302  Sum_probs=62.5

Q ss_pred             HCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHH----------
Q ss_conf             6148799999999999779979999407886152899999999976994799807874336688978988----------
Q gi|254780901|r   74 ILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLME----------  143 (600)
Q Consensus        74 ~l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~----------  143 (600)
                      .+.-+.+|...+.....++.+|++.|--.    -+.-++.++.+..|.   +|+..|..-|-=-|...+.          
T Consensus        38 T~~~L~~A~~~i~~i~~~~~~iLfVgTk~----~~~~~v~~~a~~~~~---~yv~~rWigG~LTN~~~i~~~~~~l~~~~  110 (205)
T pfam00318        38 TLEKLRKAANFIKEIAAKGGKILFVGTKK----QAQEAVKKFAKRTGQ---FYVNGRWLGGTLTNWKTIKKSIKKLEELS  110 (205)
T ss_pred             HHHHHHHHHHHHHHHHHCCCEEEEEECCH----HHHHHHHHHHHHHCC---CCCCCCCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             99999999999999996698289997778----999999999998399---74316433872366999988887777654


Q ss_pred             ----------------------HHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEE-ECC
Q ss_conf             ----------------------74202686899964887623455555417982799-615
Q gi|254780901|r  144 ----------------------KFINEGAQLIITVDCGSTSYDALQYATNQGIDVIV-IDH  181 (600)
Q Consensus       144 ----------------------~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIV-tDH  181 (600)
                                            .+. .-++++|.+|.. .+.-+|..|+.+||-+|= .|-
T Consensus       111 kk~~~~~~~~~~kl~k~~~Gi~~~~-~~Pd~vii~d~~-~~~~ai~Ea~~l~IP~I~ivDT  169 (205)
T pfam00318       111 KKEALKLKRELEKLEKYLGGIKNMK-KLPDLVIVVDPN-KEHIAIKEASKLGIPVIAIVDT  169 (205)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHH-HCCCEEEEECCC-CCHHHHHHHHHCCCCEEEECCC
T ss_conf             7888888889999998454354450-089869985786-4538999998759975654059


No 331
>cd00003 PNPsynthase Pyridoxine 5'-phosphate (PNP) synthase domain; pyridoxal 5'-phosphate is the active form of vitamin B6 that acts as an essential, ubiquitous coenzyme in amino acid metabolism. In bacteria, formation of pyridoxine 5'-phosphate is a step in the biosynthesis of vitamin B6. PNP synthase, a homooctameric enzyme, catalyzes the final step in PNP biosynthesis, the condensation of 1-amino-acetone 3-phosphate and 1-deoxy-D-xylulose 5-phosphate. PNP synthase adopts a TIM barrel topology, intersubunit contacts are mediated by three ''extra'' helices, generating a tetramer of symmetric dimers with shared active sites; the open state has been proposed to accept substrates and to release products, while most of the catalytic events are likely to occur in the closed state; a hydrophilic channel running through the center of the barrel was identified as the essential structural feature that enables PNP synthase to release water molecules produced during the reaction from the closed,
Probab=48.94  E-value=18  Score=15.82  Aligned_cols=74  Identities=14%  Similarity=0.298  Sum_probs=52.1

Q ss_pred             CCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCC---CCCCC--------HHHHHHHHHCCCCEEEEECCCCCCHHHHHH
Q ss_conf             0788615289999999997699479980787433---66889--------789887420268689996488762345555
Q gi|254780901|r  100 DYDVDGAASVALMMRFLSHCSVNANMYIPDRIVD---GYGPN--------PSLMEKFINEGAQLIITVDCGSTSYDALQY  168 (600)
Q Consensus       100 DyD~DGitstail~~~L~~~g~~v~~~IP~R~~e---GYGl~--------~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~  168 (600)
                      .+...|.. |.=|.+.......+-.+.+|++-.|   ..|++        .+.++++++.|...=+++|-   +.++++.
T Consensus        64 ~lNlE~a~-~~emi~ia~~~kP~~vtLVPe~r~elTTegGld~~~~~~~L~~~i~~lk~~~IrvSLFIDP---d~~qi~~  139 (234)
T cd00003          64 ELNLEMAP-TEEMLEIALEVKPHQVTLVPEKREELTTEGGLDVAGQAEKLKPIIERLKDAGIRVSLFIDP---DPEQIEA  139 (234)
T ss_pred             CEEECCCC-CHHHHHHHHHCCCCEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCEEEEEECC---CHHHHHH
T ss_conf             54661279-3899999998499878987888786417889266547889999999998659827997279---8789999


Q ss_pred             HHHCCCCEE
Q ss_conf             541798279
Q gi|254780901|r  169 ATNQGIDVI  177 (600)
Q Consensus       169 a~~~GidvI  177 (600)
                      |++.|.|.|
T Consensus       140 a~~~Gad~V  148 (234)
T cd00003         140 AKEVGADRV  148 (234)
T ss_pred             HHHHCCCEE
T ss_conf             998493999


No 332
>PRK06015 keto-hydroxyglutarate-aldolase/keto-deoxy-phosphogluconate aldolase; Provisional
Probab=48.79  E-value=18  Score=15.80  Aligned_cols=96  Identities=15%  Similarity=0.170  Sum_probs=64.6

Q ss_pred             HHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEEC
Q ss_conf             79999999999977997999940788615289999999997699479980787433668897898874202686899964
Q gi|254780901|r   78 CDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVD  157 (600)
Q Consensus        78 m~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD  157 (600)
                      |.+-.+.+.+.+++..-|.|+-   .|-...+.-+.++|..-|.++.- |.-|..    -..++|+.+.++-.+++|=+ 
T Consensus         1 m~~k~~~i~~~l~~~~iipVlr---~~~~~~a~~~~~al~~gGi~~iE-ITlrt~----~a~~~I~~l~~~~p~~~vGa-   71 (212)
T PRK06015          1 MSQKTEKLLSILKGQPVIPVLL---IDDVEHAVPLARALARGGLPAIE-ITLRTP----AALDAIRAVAAEVEEAIVGA-   71 (212)
T ss_pred             CCCCHHHHHHHHHHCCEEEEEE---CCCHHHHHHHHHHHHHCCCCEEE-EECCCC----CHHHHHHHHHHHCCCCEEEE-
T ss_conf             9721999999998799799997---79999999999999987998899-968995----19999999998699967954-


Q ss_pred             CCC-CCHHHHHHHHHCCCCEEEECCCC
Q ss_conf             887-62345555541798279961544
Q gi|254780901|r  158 CGS-TSYDALQYATNQGIDVIVIDHHQ  183 (600)
Q Consensus       158 ~Gi-~~~e~i~~a~~~GidvIVtDHH~  183 (600)
                       |+ .+.++++.+.+.|.+.||+=|-.
T Consensus        72 -GTVl~~e~~~~a~~aGA~FiVSP~~~   97 (212)
T PRK06015         72 -GTILNAKQFEDAAKAGSRFIVSPGTT   97 (212)
T ss_pred             -EECCCHHHHHHHHHCCCCEEECCCCC
T ss_conf             -21156999999998499899858999


No 333
>cd01391 Periplasmic_Binding_Protein_Type_1 Type 1 periplasmic binding fold superfamily. Type 1 periplasmic binding fold superfamily. This model and hierarchy represent the ligand binding domains of the LacI family of transcriptional regulators, periplasmic binding proteins of the ABC-type transport systems, the family C G-protein couples receptors (GPCRs), membrane bound guanylyl cyclases including the family of natriuretic peptide receptors (NPRs), and the N-terminal leucine/isoleucine/valine- binding protein  (LIVBP)-like domains of the ionotropic glutamate receptors (iGluRs). In LacI-like transcriptional regulator and the bacterial periplasmic binding proteins the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions.  Periplasmic sugar binding proteins are one of the components of ABC transporters and are involved in the active transport of water-soluble ligands. The LacI family of proteins con
Probab=48.62  E-value=18  Score=15.78  Aligned_cols=49  Identities=20%  Similarity=0.310  Sum_probs=36.0

Q ss_pred             CHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCCCC
Q ss_conf             9789887420268689996488762345555541798279961544765
Q gi|254780901|r  138 NPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKS  186 (600)
Q Consensus       138 ~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~~~~  186 (600)
                      ..+.++.+...+++.||..-+...+......+++.|+-+|.+|--.++.
T Consensus        47 ~~~~i~~l~~~~vd~ii~~~~~~~~~~~~~~~~~~~iPvv~~~~~~~~~   95 (269)
T cd01391          47 ALEALRDLIQQGVDGIIGPPSSSSALAVVELAAAAGIPVVSLDATAPDL   95 (269)
T ss_pred             HHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHCCCEEEEECCCCCCC
T ss_conf             9999999997499999946887444899999997698199967887877


No 334
>cd06333 PBP1_ABC-type_HAAT_like Type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids. This subgroup includes the type I periplasmic binding component of ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in uptake of amino acids. Members of this subgroup are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine-binding protein (LIVBP); their ligand specificity has not been determined experimentally, however.
Probab=48.56  E-value=18  Score=15.77  Aligned_cols=36  Identities=17%  Similarity=0.196  Sum_probs=15.5

Q ss_pred             HHHHHH-CCCCEEEEECCCCCCHHHHHHHHHCCCCEE
Q ss_conf             887420-268689996488762345555541798279
Q gi|254780901|r  142 MEKFIN-EGAQLIITVDCGSTSYDALQYATNQGIDVI  177 (600)
Q Consensus       142 i~~~~~-~g~~LiItvD~Gi~~~e~i~~a~~~GidvI  177 (600)
                      .+++.+ +++..||..-+...+......+.+.|+-+|
T Consensus        58 a~~li~~~~V~~ivG~~~S~~~~a~~~~~~~~~vp~i   94 (312)
T cd06333          58 ARKLIEEDKVDAIIGPSTTPATMAVAPVAEEAKTPMI   94 (312)
T ss_pred             HHHHHHHCCCEEEECCCCCHHHHHHHHHHHHCCCEEE
T ss_conf             9998651793398668773778888999997498699


No 335
>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=48.53  E-value=18  Score=15.77  Aligned_cols=87  Identities=11%  Similarity=0.200  Sum_probs=56.5

Q ss_pred             HHHHHHHCCCC--HH-HHHHHCCC----CHHHCCC----CHHHCCCHHHHHH----------HHHHHHHCC-CCEEEEEC
Q ss_conf             99999967889--78-98866196----6777189----9556148799999----------999999779-97999940
Q gi|254780901|r   43 VARVLVNRNVS--ID-YAKDFLNP----SIRLLMP----DPLILTDCDKAAR----------RIVQAIYNS-EKIMIFGD  100 (600)
Q Consensus        43 ~a~iL~~Rgi~--~~-~~~~fL~p----~l~~l~~----dP~~l~dm~~A~~----------ri~~ai~~~-ekI~I~gD  100 (600)
                      ..+.|.++|++  .. ...+-|..    ..+-...    -|..-|.+.+|-+          -|.+-++.+ +.|.|-| 
T Consensus        37 ~t~~L~~~Gi~I~~g~h~~~n~~~~p~g~~~vVv~S~~Ai~~~NpEi~~A~~~~IPv~~R~~~Lael~~~~k~~iaVaG-  115 (491)
T TIGR01082        37 TTKRLEALGIKIYIGEHSAENLDDLPTGAADVVVVSAAAIKEDNPEIVEAKERGIPVIRRAEMLAELMRKRKESIAVAG-  115 (491)
T ss_pred             HHHHHHHCCCEECCCCCCHHHHCCCCCCCCCEEEEEEECCCCCCHHHHHHHHCCCCEECHHHHHHHHHHHHCCEEEEEC-
T ss_conf             5899986787662799677982036789743799864033788888999996488813378999999862087079983-


Q ss_pred             CCCCH-HHHHHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             78861-528999999999769947998078743
Q gi|254780901|r  101 YDVDG-AASVALMMRFLSHCSVNANMYIPDRIV  132 (600)
Q Consensus       101 yD~DG-itstail~~~L~~~g~~v~~~IP~R~~  132 (600)
                        ++| +|-||++...++.+|.+.+..|....+
T Consensus       116 --tHGKTTTTamia~~~~~aGLdPt~~~GG~~~  146 (491)
T TIGR01082       116 --THGKTTTTAMIAVILKEAGLDPTVIVGGEVK  146 (491)
T ss_pred             --CCCCHHHHHHHHHHHHHCCCCCCEEECCCCC
T ss_conf             --6872568999999998449997689866436


No 336
>cd03365 TOPRIM_TopoIIA TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA.  These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings.  The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in strand joining and as a general acid in strand cleavage by topisomerases.  The DXD motif may co-ordinate Mg2+, a cofact
Probab=48.52  E-value=18  Score=15.77  Aligned_cols=30  Identities=27%  Similarity=0.494  Sum_probs=23.3

Q ss_pred             HCCCCEEEEECCCCCHHHHHHHHHHHHHHC
Q ss_conf             779979999407886152899999999976
Q gi|254780901|r   90 YNSEKIMIFGDYDVDGAASVALMMRFLSHC  119 (600)
Q Consensus        90 ~~~ekI~I~gDyD~DGitstail~~~L~~~  119 (600)
                      -+=.||.|..|-|+||.-=..+|..++-.+
T Consensus        75 LRYgkIiI~tDaDvDG~HI~~LlltfF~~~  104 (120)
T cd03365          75 LRYGRLMIMTDQDHDGSHIKGLLINFIHSF  104 (120)
T ss_pred             CCCCEEEEEECCCCCHHHHHHHHHHHHHHH
T ss_conf             788858998789886578999999999998


No 337
>PRK09191 two-component response regulator; Provisional
Probab=48.33  E-value=15  Score=16.53  Aligned_cols=114  Identities=14%  Similarity=0.140  Sum_probs=57.6

Q ss_pred             CCHHHHHHHHH-------HHCCHHHHHCCCCCCCEEEECCCH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             24234566677-------430623331212222100203425-8999999999989999999999999999999875211
Q gi|254780901|r  292 ITAENLGYMIG-------PSINAGGRIGESNLGSRLLISDDS-QELEMLAMKLDVLNQNRRLMESAMLEQAEAKVLTQCD  363 (600)
Q Consensus       292 i~~~di~f~ia-------PrINAaGRl~~a~~av~lL~~~d~-~~a~~la~~L~~lN~~Rk~~e~~i~~~a~~~~~~~~~  363 (600)
                      ++..+++..++       -+++.|.+-=+...+-+.|+-+|+ --|..+...|+++.-+=-- ...-.++|.+.+..   
T Consensus       105 Fs~~eaA~Il~v~~~e~~~l~~~A~~ei~~~~~~rILIVEDE~lIAmdLe~~l~~lG~~V~G-iA~t~~eAl~la~~---  180 (261)
T PRK09191        105 FSEEEAAEILGVDPAEVAALLDDASREIARQVATSVLIIEDEPIIAMDLEQLVESLGHRVVG-IARTRAEAVALAKK---  180 (261)
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCEEEECCCHHHHHHHHHHHHHCCCEEEE-EECCHHHHHHHHHC---
T ss_conf             98899999978999999999999999997374788799858599999999999987996787-62789999999742---


Q ss_pred             CCCCCCEEEEECCCCCHHHHHH-HHHHHHHHHHCEEEEEEECCCCEEEEE
Q ss_conf             2434750262057858122222-278998842010799886379837999
Q gi|254780901|r  364 DIQQASVIVVEGDRWHPGIVGL-LAARLKEKFGRPSFAISFEEDGKGIGS  412 (600)
Q Consensus       364 ~~~~~~~ivv~~~~wh~GViGI-VAsrL~e~y~kP~iv~s~~~dg~~kGS  412 (600)
                         ..+-+++.+=+..-|.-|| +|.++.++++.|+|.+|--.+...+|.
T Consensus       181 ---~~PDlvL~DI~L~d~~sGIdaa~~I~~~~~iPvIFiTAyperlltg~  227 (261)
T PRK09191        181 ---TRPGLILADIQLADGSSGIDAVNDILKTFDVPVIFITAFPERLLTGE  227 (261)
T ss_pred             ---CCCCEEEEEEECCCCCCHHHHHHHHHHHCCCCEEEECCCHHHHCCCC
T ss_conf             ---59898999534799987999999999828999899777846530278


No 338
>PRK05939 hypothetical protein; Provisional
Probab=48.26  E-value=18  Score=15.74  Aligned_cols=93  Identities=9%  Similarity=0.142  Sum_probs=55.4

Q ss_pred             CHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEE
Q ss_conf             87999999999997799799994078861528999999999769947998078743366889789887420268689996
Q gi|254780901|r   77 DCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITV  156 (600)
Q Consensus        77 dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItv  156 (600)
                      +|..-..-+..-.+.+..|++-  .++=|-|  -.+.+.|..+|+++.++=|.        ..+.++++...+++||..=
T Consensus        70 GMaAi~~~l~~ll~~Gd~il~~--~~~YG~t--~~l~~~l~~~GI~v~~vd~~--------d~~~~~~ai~~~Tklv~~E  137 (396)
T PRK05939         70 GMAAIAAVFLTLLRAGDHLVSS--QYLFGNT--NSLLGTLQGLGVEVTMVDAT--------DVQQVAAAIRPNTRMVFVE  137 (396)
T ss_pred             HHHHHHHHHHHHCCCCCEEEEC--CCCCCHH--HHHHHHHHHCCEEEEEECCC--------CHHHHHHHHCCCCCEEEEE
T ss_conf             9999999999835889889953--8869229--99999865318699998897--------9899998618566189998


Q ss_pred             -----CCCCCCHHHHH-HHHHCCCCEEEECCC
Q ss_conf             -----48876234555-554179827996154
Q gi|254780901|r  157 -----DCGSTSYDALQ-YATNQGIDVIVIDHH  182 (600)
Q Consensus       157 -----D~Gi~~~e~i~-~a~~~GidvIVtDHH  182 (600)
                           -.-+.+.++|. .|++.|+-++ .|.-
T Consensus       138 spsNP~l~v~Di~~i~~ia~~~g~~~v-VDNT  168 (396)
T PRK05939        138 TIANPGTQVADLAGIGALCRERGLVYV-VDNT  168 (396)
T ss_pred             ECCCCCCCCCCHHHHHHHHHHCCCEEE-EECC
T ss_conf             089998707589999999998399799-9777


No 339
>PRK13435 response regulator; Provisional
Probab=48.13  E-value=15  Score=16.40  Aligned_cols=86  Identities=21%  Similarity=0.160  Sum_probs=54.3

Q ss_pred             HHHHHHHHHHHHCCCCCCCEEEEECCCCCHHHHHH-HHHHHHHHHHCEEEEEEECCCCEEEEEEECCCCCCHHHHHHHHC
Q ss_conf             99999998752112434750262057858122222-27899884201079988637983799986489861888888530
Q gi|254780901|r  351 LEQAEAKVLTQCDDIQQASVIVVEGDRWHPGIVGL-LAARLKEKFGRPSFAISFEEDGKGIGSGRSIEGFDIGKMVSFAV  429 (600)
Q Consensus       351 ~~~a~~~~~~~~~~~~~~~~ivv~~~~wh~GViGI-VAsrL~e~y~kP~iv~s~~~dg~~kGS~RSi~g~~l~~~l~~~~  429 (600)
                      .++|.+.+...     .+. +++-+=+-+.|.-|+ ++.+|.+.++-|+|.+|-..              +   ...   
T Consensus        35 ~~eAl~~~~~~-----~PD-lvllDi~LpdG~~G~e~~r~l~~~~~ipvI~lTa~~--------------d---~~~---   88 (141)
T PRK13435         35 SEQALALGRRA-----QPD-VALVDIRLADGPTGVEVARRLSIDGGVEVIFMTANP--------------E---RVG---   88 (141)
T ss_pred             HHHHHHHHHCC-----CCC-EEEECCCCCCCCCHHHHHHHHHHCCCCCEEEEECCH--------------H---HHH---
T ss_conf             99999997659-----998-999788789999899999999875998389997779--------------9---860---


Q ss_pred             CCCCCCCCCCCCCCCCEEECCCCHHHHHHHHHHHHHHHCCH
Q ss_conf             33530115653222314642221588999999999862264
Q gi|254780901|r  430 EEGILVKGGGHAMAAGLTVERVNFGRLCDFFQKFAHNIVPA  470 (600)
Q Consensus       430 ~~~ll~~~GGH~~AaG~ti~~~~l~~f~~~l~~~~~~~~~~  470 (600)
                      .  ..      +.|.++-.|+-..+++..++...+..+..+
T Consensus        89 ~--~~------aGA~dyl~KPf~~~eL~~ai~~~~~rr~~~  121 (141)
T PRK13435         89 H--DF------AGALGVIAKPYSLRQVARALSYVAARRVDD  121 (141)
T ss_pred             H--HH------CCCCCEEECCCCHHHHHHHHHHHHHHCCCC
T ss_conf             1--34------599858989999899999999999715689


No 340
>PRK00683 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=47.90  E-value=19  Score=15.70  Aligned_cols=29  Identities=17%  Similarity=0.309  Sum_probs=15.9

Q ss_pred             CCEEEEECCCCCH-HHHHHHHHHHHHHCCCCEE
Q ss_conf             9799994078861-5289999999997699479
Q gi|254780901|r   93 EKIMIFGDYDVDG-AASVALMMRFLSHCSVNAN  124 (600)
Q Consensus        93 ekI~I~gDyD~DG-itstail~~~L~~~g~~v~  124 (600)
                      ..|+|-|   ..| .|-|+++...|+..|.++.
T Consensus       103 ~~IaITG---TNGKTTTt~ll~~iL~~~g~~~~  132 (418)
T PRK00683        103 PSLGITG---STGKTTTILFLEHLLRTLGIPAF  132 (418)
T ss_pred             CEEEEEC---CCCCEEHHHHHHHHHHHCCCCCE
T ss_conf             8799976---89866099999999986799818


No 341
>cd06366 PBP1_GABAb_receptor Ligand-binding domain of GABAb receptors, which are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA). Ligand-binding domain of GABAb receptors, which are metabotropic transmembrane receptors for gamma-aminobutyric acid (GABA). GABA is the major inhibitory neurotransmitter in the mammalian CNS and, like glutamate and other transmitters, acts via both ligand gated ion channels (GABAa receptors) and G-protein coupled receptors (GABAb). GABAa receptors are members of the ionotropic receptor superfamily which includes alpha-adrenergic and glycine receptors. The GABAb receptor is a member of a receptor superfamily which includes the mGlu receptors. The GABAb receptor is coupled to G alpha_i proteins, and activation causes a decrease in calcium, an increase in potassium membrane conductance, and inhibition of cAMP formation. The response is thus inhibitory and leads to hyperpolarization and decreased neurotransmitter release, for example.
Probab=47.81  E-value=19  Score=15.69  Aligned_cols=75  Identities=16%  Similarity=0.191  Sum_probs=35.6

Q ss_pred             HCCCHHHHHHHHHHHH--HCC-CCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCC
Q ss_conf             6148799999999999--779-9799994078861528999999999769947998078743366889789887420268
Q gi|254780901|r   74 ILTDCDKAARRIVQAI--YNS-EKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGA  150 (600)
Q Consensus        74 ~l~dm~~A~~ri~~ai--~~~-ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~  150 (600)
                      ..+.|+-|++.|.+.-  ..+ +-.+++.|.-+|-..+.....+.+.                             .+++
T Consensus        17 ~~~a~~lAi~~iN~~~~il~~~~l~l~~~D~~~~~~~a~~~a~~li~-----------------------------~~~v   67 (350)
T cd06366          17 ALPAIEMALEDVNADNSILPGYRLVLHVRDSKCDPVQAASAALDLLE-----------------------------NKPV   67 (350)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCCHHHHHHHHHHHHH-----------------------------CCCC
T ss_conf             99999999999985899899977999998689997999999999985-----------------------------1796


Q ss_pred             CEEEEECCCCCCHHHHHHHHHCCCCEE
Q ss_conf             689996488762345555541798279
Q gi|254780901|r  151 QLIITVDCGSTSYDALQYATNQGIDVI  177 (600)
Q Consensus       151 ~LiItvD~Gi~~~e~i~~a~~~GidvI  177 (600)
                      ..||=.-|...+..-...+.+.++-+|
T Consensus        68 ~aiiGp~~S~~~~~va~v~~~~~ip~i   94 (350)
T cd06366          68 VAIIGPQCSSVAEFVAEVANEWNVPVL   94 (350)
T ss_pred             EEEEECCCCHHHHHHHHHHHHCCCEEE
T ss_conf             799935644888978887651371250


No 342
>PRK08072 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=47.79  E-value=14  Score=16.61  Aligned_cols=14  Identities=21%  Similarity=0.396  Sum_probs=9.9

Q ss_pred             CCCCCHHHHHHHHC
Q ss_conf             68874357898708
Q gi|254780901|r  274 QGNPGLKALIERVN  287 (600)
Q Consensus       274 ~~~~gl~~L~~~~~  287 (600)
                      ...||+|.|-+.+=
T Consensus       132 KT~PGlR~l~k~AV  145 (277)
T PRK08072        132 KTTPGLRMFDKYAV  145 (277)
T ss_pred             CCCCCCHHHHHHHH
T ss_conf             77877539999999


No 343
>cd03361 TOPRIM_TopoIA_RevGyr TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to the ATP-dependent reverse gyrase found in archaea and thermophilic bacteria.   Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD).  For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=47.66  E-value=19  Score=15.68  Aligned_cols=68  Identities=10%  Similarity=0.082  Sum_probs=45.9

Q ss_pred             CCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHC
Q ss_conf             14879999999999977997999940788615289999999997699479980787433668897898874202
Q gi|254780901|r   75 LTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINE  148 (600)
Q Consensus        75 l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~  148 (600)
                      .++-.+.+.-|.+..++-..|.|-.|+|--|=.=+.=+++.|+....++ +.+  +|.|   +++.+|.++.++
T Consensus       102 ~~~k~k~v~~lk~lak~ad~v~lATD~DREGEaIa~hi~~~l~~~~~~~-~Ri--~F~e---ITk~aI~~A~~n  169 (170)
T cd03361         102 IDDKLETLEALRELALEVDEVLIATDPDTEGEKIAWDVYLALRPYNKNI-KRA--EFHE---VTRRAILEALRN  169 (170)
T ss_pred             CCCHHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHCCCCCCE-EEE--EECC---CCHHHHHHHHHC
T ss_conf             7548999999999986089799857998222299999999955758981-578--9746---599999999968


No 344
>PRK08322 acetolactate synthase; Reviewed
Probab=47.57  E-value=19  Score=15.67  Aligned_cols=81  Identities=21%  Similarity=0.239  Sum_probs=45.5

Q ss_pred             HHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEE------ECCCCC--CC-CCCCH-HHHHHHHHCC
Q ss_conf             99999999997799799994078861528999999999769947998------078743--36-68897-8988742026
Q gi|254780901|r   80 KAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMY------IPDRIV--DG-YGPNP-SLMEKFINEG  149 (600)
Q Consensus        80 ~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~------IP~R~~--eG-YGl~~-~~i~~~~~~g  149 (600)
                      +.++++.+.|.+-++.+|+..+-+.---+..-|.++.+.+|+.|..-      +|+.-.  -| +|+.. +.+..+.+ .
T Consensus       184 ~~l~~a~~~L~~AkrPvIi~G~g~~~~~a~~~l~~lae~l~~PV~tt~~gkg~~p~~hp~~~G~~g~~~~~~~~~~i~-~  262 (547)
T PRK08322        184 KAIERAAEAIQAAKNPLILIGAGANRKTASKALTEFVDKTGIPFFTTQMGKGVIPETHPLSLGTAGLSQGDYVHCAIE-H  262 (547)
T ss_pred             HHHHHHHHHHHHCCCCEEECCCCCCCHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCCCCCCCCCCCCHHHHHHHH-C
T ss_conf             999999999972689789868885734099999999998299789604677777988741145554456699998776-4


Q ss_pred             CCEEEEECCCCC
Q ss_conf             868999648876
Q gi|254780901|r  150 AQLIITVDCGST  161 (600)
Q Consensus       150 ~~LiItvD~Gi~  161 (600)
                      +||+|++.+-..
T Consensus       263 aDlvl~iG~~l~  274 (547)
T PRK08322        263 ADLIINVGHDVI  274 (547)
T ss_pred             CCEEEEECCCCC
T ss_conf             986898154256


No 345
>cd06347 PBP1_ABC_ligand_binding_like_12 Type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (Atpase Binding Cassette)-type active transport systems that are predicted to be involved in uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); however its ligand specificity has not been determined experimentally.
Probab=47.51  E-value=19  Score=15.66  Aligned_cols=36  Identities=17%  Similarity=0.203  Sum_probs=16.7

Q ss_pred             HHHHHH-CCCCEEEEECCCCCCHHHHHHHHHCCCCEE
Q ss_conf             887420-268689996488762345555541798279
Q gi|254780901|r  142 MEKFIN-EGAQLIITVDCGSTSYDALQYATNQGIDVI  177 (600)
Q Consensus       142 i~~~~~-~g~~LiItvD~Gi~~~e~i~~a~~~GidvI  177 (600)
                      .+++.+ +++..||-.-+...+......+.+.|+-+|
T Consensus        59 a~~Lv~~d~V~aviG~~~S~~~~a~~~~~~~~~vp~i   95 (334)
T cd06347          59 ATRLIDQDKVVAIIGPVTSGATLAAGPIAEDAKVPMI   95 (334)
T ss_pred             HHHHHHHCCCEEEECCCCHHHHHHHHHHHHHHCCEEE
T ss_conf             9999975797799767856878988999997196487


No 346
>PTZ00170 D-ribulose-5-phosphate 3-epimerase; Provisional
Probab=47.46  E-value=19  Score=15.65  Aligned_cols=63  Identities=11%  Similarity=0.173  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHHHH-C-C--CCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCC--CCHHHHHHHHHCCCCEE
Q ss_conf             5289999999997-6-9--9479980787433668897898874202686899964887--62345555541798279
Q gi|254780901|r  106 AASVALMMRFLSH-C-S--VNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGS--TSYDALQYATNQGIDVI  177 (600)
Q Consensus       106 itstail~~~L~~-~-g--~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi--~~~e~i~~a~~~GidvI  177 (600)
                      +|=..-+++.++. . .  .+|+.++-+        ....++++.+.|++.|+ +-.-+  ...+-++++++.|+.+-
T Consensus        47 ~t~g~~~v~~ir~~~~~~~lDvHLMv~~--------P~~~i~~~~~~gad~I~-~H~E~~~~~~~~i~~ik~~g~k~G  115 (224)
T PTZ00170         47 LSFGPPVVSSLRKHLPNTFLDVHLMVSD--------PERWVDSFAKAGASQFT-FHIEATEDPKAVARKIRAAGMQVG  115 (224)
T ss_pred             CCCCHHHHHHHHHHCCCCCEEEEEEECC--------HHHHHHHHHHCCCCEEE-ECCCCCCCHHHHHHHHHHHCCCEE
T ss_conf             5749789999997179986468998638--------88879999862896799-850013399999999997147645


No 347
>cd01448 TST_Repeat_1 Thiosulfate sulfurtransferase (TST), N-terminal, inactive domain. TST contains 2 copies of the Rhodanese Homology Domain; this is the 1st repeat, which does not contain the catalytically active Cys residue. The role of the 1st repeat is uncertain, but it is believed to be involved in protein interaction.
Probab=47.43  E-value=19  Score=15.65  Aligned_cols=50  Identities=16%  Similarity=0.179  Sum_probs=36.6

Q ss_pred             CHHHCCCHHHHHHHHHHH-HHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCE
Q ss_conf             955614879999999999-97799799994078861528999999999769947
Q gi|254780901|r   71 DPLILTDCDKAARRIVQA-IYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNA  123 (600)
Q Consensus        71 dP~~l~dm~~A~~ri~~a-i~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v  123 (600)
                      -|+.+++.++..+.+.++ |.++.+|++|+   ..|..+++-++-.|+.+|.+-
T Consensus        57 ~~~~l~~~~~l~~~l~~~GI~~~~~VV~Y~---~~~~~~a~r~~w~L~~~G~~~  107 (122)
T cd01448          57 GPHMLPSPEEFAELLGSLGISNDDTVVVYD---DGGGFFAARAWWTLRYFGHEN  107 (122)
T ss_pred             CCCCCCCHHHHHHHHHHHCCCCCCEEEEEE---CCCCHHHHHHHHHHHHCCCCC
T ss_conf             887788989999999980988897599980---898738999999999839987


No 348
>PRK04281 consensus
Probab=47.30  E-value=19  Score=15.64  Aligned_cols=73  Identities=12%  Similarity=0.155  Sum_probs=52.5

Q ss_pred             HHHHHHHHHCCCCEEEEEC-CCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCC
Q ss_conf             9999999976994799807-8743366889789887420268689996488762345555541798279961544
Q gi|254780901|r  110 ALMMRFLSHCSVNANMYIP-DRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQ  183 (600)
Q Consensus       110 ail~~~L~~~g~~v~~~IP-~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~  183 (600)
                      .-+.+.+...|++--+.+- +.-.+|-..+.+.++++.+. +.+=||+-=||.+.+.++.+-+.|.|=||+--..
T Consensus        33 ~~~ak~~~~~GadelhivDld~a~~~~~~~~~~I~~i~~~-~~vpi~vGGGIrs~e~~~~ll~~GadkViigs~a  106 (254)
T PRK04281         33 VEAAKRYNGEGADELTFLDITASSDNRDTILHIIEEVAGQ-VFIPLTVGGGVRTVADIRRLLNAGADKVSINTAA  106 (254)
T ss_pred             HHHHHHHHHCCCCEEEEEECCCCCCCCHHHHHHHHHHHHH-CCCCEEEECCEEECHHHHHHHHCCCCEEEECHHH
T ss_conf             9999999986999999996889877753089999999850-7962899777545188999997699889977767


No 349
>pfam00205 TPP_enzyme_M Thiamine pyrophosphate enzyme, central domain. The central domain of TPP enzymes contains a 2-fold Rossman fold.
Probab=47.29  E-value=19  Score=15.63  Aligned_cols=75  Identities=9%  Similarity=0.177  Sum_probs=46.1

Q ss_pred             HHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEE------ECCCCC--CCC-CCC-HHHHHHHHHCCCCE
Q ss_conf             99999997799799994078861528999999999769947998------078743--366-889-78988742026868
Q gi|254780901|r   83 RRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMY------IPDRIV--DGY-GPN-PSLMEKFINEGAQL  152 (600)
Q Consensus        83 ~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~------IP~R~~--eGY-Gl~-~~~i~~~~~~g~~L  152 (600)
                      +++.+.|.+-++.+|+....+..-.+..-+.++.+.+|+.|..-      +|++-.  =|| |.. .....++.+ +++|
T Consensus         2 ~~~~~~l~~AkrPvii~G~g~~~~~a~~~l~~lae~~~~Pv~~t~~~~~~~~~~hp~~~G~~g~~~~~~~~~~l~-~aDl   80 (138)
T pfam00205         2 EKAAELLAAAKRPVILVGGGVRRSGASEELRALAEKLGIPVVTTLMGKGAFPEDHPLYLGMLGMHGTPAANEALE-EADL   80 (138)
T ss_pred             HHHHHHHHHCCCEEEEECCCCCHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCCCCCCCCCCCCHHHHHHHH-CCCE
T ss_conf             899999996899199989783522189999999998499879211125678988865577577657799986553-3999


Q ss_pred             EEEECC
Q ss_conf             999648
Q gi|254780901|r  153 IITVDC  158 (600)
Q Consensus       153 iItvD~  158 (600)
                      ||++.+
T Consensus        81 vl~lG~   86 (138)
T pfam00205        81 VLAIGA   86 (138)
T ss_pred             EEEECC
T ss_conf             999788


No 350
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=47.22  E-value=19  Score=15.63  Aligned_cols=89  Identities=17%  Similarity=0.155  Sum_probs=46.9

Q ss_pred             HHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCC
Q ss_conf             99999999779979999407886152899999999976994799807874336688978988742026868999648876
Q gi|254780901|r   82 ARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGST  161 (600)
Q Consensus        82 ~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~  161 (600)
                      .++..+.|.+-++|.+||-- .-+..+.-. ..-|.++|..+.++     .+.|   ...+.-.....-+++|.....=.
T Consensus       118 l~~av~li~~A~~I~i~G~G-~S~~vA~~~-~~kl~r~g~~~~~~-----~d~~---~~~~~a~~~~~~Dvvi~iS~sG~  187 (284)
T PRK11302        118 INRAVDLLTQAKKISFFGLG-ASAAVAHDA-QNKFFRFNVPVVYF-----DDIV---MQRMSCMNSSDGDVVVLISHTGR  187 (284)
T ss_pred             HHHHHHHHHCCCEEEEEECC-CCHHHHHHH-HHHHHHCCCCEEEC-----CCHH---HHHHHHHHCCCCCEEEEECCCCC
T ss_conf             99999999718958999648-509999999-99998439814642-----8789---99999971999888999737999


Q ss_pred             ---CHHHHHHHHHCCCCEEE-EC
Q ss_conf             ---23455555417982799-61
Q gi|254780901|r  162 ---SYDALQYATNQGIDVIV-ID  180 (600)
Q Consensus       162 ---~~e~i~~a~~~GidvIV-tD  180 (600)
                         -.+.++.|+++|+.||. |+
T Consensus       188 t~e~i~~~~~Ak~~ga~vIaIT~  210 (284)
T PRK11302        188 TKSLVELAQLARENGATVIGITA  210 (284)
T ss_pred             CHHHHHHHHHHHHCCCCEEEECC
T ss_conf             87999999999987995899779


No 351
>PRK08392 hypothetical protein; Provisional
Probab=46.93  E-value=19  Score=15.59  Aligned_cols=23  Identities=26%  Similarity=0.595  Sum_probs=13.8

Q ss_pred             CCCCHHH-HHHHHHCCCCEE-EECC
Q ss_conf             8762345-555541798279-9615
Q gi|254780901|r  159 GSTSYDA-LQYATNQGIDVI-VIDH  181 (600)
Q Consensus       159 Gi~~~e~-i~~a~~~GidvI-VtDH  181 (600)
                      |.+..++ ++.|+++|++.| ||||
T Consensus        12 g~~ti~E~~~aA~~~Gl~~i~ITDH   36 (215)
T PRK08392         12 GIGSVRDNVAWAEKRGLKLLGISDH   36 (215)
T ss_pred             CCCCHHHHHHHHHHCCCCEEEEECC
T ss_conf             7787999999999879948998069


No 352
>TIGR02902 spore_lonB ATP-dependent protease LonB; InterPro: IPR014251   This entry represents LonB, a paralog of the ATP-dependent protease La (LonA, IPR004815 from INTERPRO). LonB proteins are unassigned peptidases belonging to the MEROPS peptidase family S16 (lon protease family, clan SJ) and are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore during sporulation, under control of sigmaF . The lonB gene, despite being located immediately upstream of lonA, was shown to be monocistronic. LonB appears to be involved in the post-translation control of sigmaH, but lonB mutation did not produce an obvious sporulation defect under the conditions tested . Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and these are excluded from this entry. .
Probab=46.91  E-value=19  Score=15.59  Aligned_cols=44  Identities=18%  Similarity=0.345  Sum_probs=30.1

Q ss_pred             CHHHCC---CHHHHHHHHHHHH--HCCCCEEEEECCCCCHHHHHHHHHHHHH
Q ss_conf             955614---8799999999999--7799799994078861528999999999
Q gi|254780901|r   71 DPLILT---DCDKAARRIVQAI--YNSEKIMIFGDYDVDGAASVALMMRFLS  117 (600)
Q Consensus        71 dP~~l~---dm~~A~~ri~~ai--~~~ekI~I~gDyD~DGitstail~~~L~  117 (600)
                      =|..|.   +=++...-|..|+  -|=+++-|||   -=|+==||=.-..|+
T Consensus        60 RP~SF~EIiGQe~GI~ALKAALCGPNPQHVIiYG---PPGVGKTAAARLVLe  108 (532)
T TIGR02902        60 RPKSFDEIIGQEEGIKALKAALCGPNPQHVIIYG---PPGVGKTAAARLVLE  108 (532)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHCCCCCCCEEEEEC---CCCCCHHHHHHHHHH
T ss_conf             7776332567355689999860686896389878---869617899999999


No 353
>PRK09558 ushA bifunctional UDP-sugar hydrolase/5'-nucleotidase periplasmic precursor; Reviewed
Probab=46.84  E-value=19  Score=15.58  Aligned_cols=58  Identities=10%  Similarity=0.022  Sum_probs=29.8

Q ss_pred             CHHHHHHHHHHHHH----CCCC-EEEE-ECCCCCHHHHH-----HHHHHHHHHCCCCEEEEECCCCCCCC
Q ss_conf             87999999999997----7997-9999-40788615289-----99999999769947998078743366
Q gi|254780901|r   77 DCDKAARRIVQAIY----NSEK-IMIF-GDYDVDGAASV-----ALMMRFLSHCSVNANMYIPDRIVDGY  135 (600)
Q Consensus        77 dm~~A~~ri~~ai~----~~ek-I~I~-gDyD~DGitst-----ail~~~L~~~g~~v~~~IP~R~~eGY  135 (600)
                      ++.+.+..|.+..+    ++.. |++- ||. .-|...+     .-+.+++..+|.++...=.|-|..|+
T Consensus        56 G~a~~at~i~~~R~e~~a~~~n~llldaGD~-~qGt~~s~l~~g~p~i~~mN~lgyDa~tlGNHEFD~G~  124 (551)
T PRK09558         56 GLAARKTLVDQIRKEVAAEGGSVLLLSGGDI-NTGVPESDLQDAEPDFRGMNLIGYDAMAVGNHEFDNPL  124 (551)
T ss_pred             CHHHHHHHHHHHHHHHHCCCCCEEEEECCCC-CCCCCCCHHCCCCHHHHHHHCCCCCEEEECCCCCCCCH
T ss_conf             7999999999999998525998799958855-56774604228807999986189888977754455787


No 354
>pfam10498 IFT57 Intra-flagellar transport protein 57. Eukaryotic cilia and flagella are specialized organelles found at the periphery of cells of diverse organisms. Intra-flagellar transport (IFT) is required for the assembly and maintenance of eukaryotic cilia and flagella, and consists of the bidirectional movement of large protein particles between the base and the distal tip of the organelle. IFT particles contain multiple copies of two distinct protein complexes, A and B, which contain at least 6 and 11 protein subunits. IFT57 is part of complex B but is not, however, required for the core subunits to stay associated. This protein is known as Huntington-interacting protein-1 in humans.
Probab=46.84  E-value=14  Score=16.67  Aligned_cols=64  Identities=13%  Similarity=0.207  Sum_probs=44.7

Q ss_pred             CCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHH
Q ss_conf             14879999999999977997999940788615289999999997699479980787433668897898
Q gi|254780901|r   75 LTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLM  142 (600)
Q Consensus        75 l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i  142 (600)
                      |.=...-+.+|..  ..+.+.--.+.|| |=.|.++=+...|+.+|..+.+ =|+|+.-|||-..=.|
T Consensus        42 F~~Ft~L~~WL~~--~~g~~~~~P~e~D-DPn~t~~~Il~~lk~~g~~~dF-~P~kLk~G~Ge~v~~V  105 (355)
T pfam10498        42 FYYFTSLCAWLMS--KAGRKFEQPQEFD-DPNATASNILNELKAIGIPVDF-PPNKLKSGSGEIVCYV  105 (355)
T ss_pred             HHHHHHHHHHHHH--HCCCCCCCCCCCC-CHHHHHHHHHHHHHHCCCCCCC-CHHHHHCCCCHHHHHH
T ss_conf             9999999999998--6499899975447-8789999999999963999998-9677645777189999


No 355
>PRK01362 putative translaldolase; Provisional
Probab=46.79  E-value=19  Score=15.58  Aligned_cols=86  Identities=15%  Similarity=0.183  Sum_probs=53.4

Q ss_pred             HHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHH--HHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEE
Q ss_conf             79999999999977997999940788615289999999--9976994799807874336688978988742026868999
Q gi|254780901|r   78 CDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRF--LSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIIT  155 (600)
Q Consensus        78 m~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~--L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiIt  155 (600)
                      ..+.+..|.+.+..  .|.+    .|.|-+.-.++-++  |..++.++...||- ..+|    ..++.++..+|+++-+|
T Consensus        39 ~~~~~~~i~~~~~~--~is~----ev~~~~~~~m~~qA~~l~~~~~nv~VKIP~-t~~G----l~ai~~L~~~Gi~vn~T  107 (214)
T PRK01362         39 FKEVIKEICSIVDG--PVSA----EVIALDAEGMIKEGRELAKIAPNVVVKIPM-TTEG----LKAVKALSKEGIKTNVT  107 (214)
T ss_pred             HHHHHHHHHHHCCC--CEEE----EECCCHHHHHHHHHHHHHHHCCCEEEECCC-CHHH----HHHHHHHHHCCCCEEEE
T ss_conf             89999999873179--7579----963641999999999999848776998189-6669----99999999849975766


Q ss_pred             ECCCCCCHHHHHHHHHCCCCEE
Q ss_conf             6488762345555541798279
Q gi|254780901|r  156 VDCGSTSYDALQYATNQGIDVI  177 (600)
Q Consensus       156 vD~Gi~~~e~i~~a~~~GidvI  177 (600)
                         .+-+..+.-.|...|.+.|
T Consensus       108 ---ai~s~~Qa~~Aa~aga~yi  126 (214)
T PRK01362        108 ---LCFSANQALLAAKAGATYV  126 (214)
T ss_pred             ---ECCCHHHHHHHHHCCCCEE
T ss_conf             ---4588999999987599689


No 356
>cd02772 MopB_NDH-1_NuoG2 MopB_NDH-1_NuoG2: The second domain of the NuoG subunit of the NADH-quinone oxidoreductase/NADH dehydrogenase-1 (NDH-1), found in beta- and gammaproteobacteria. The NDH-1 is the first energy-transducting complex in the respiratory chain and functions as a redox pump that uses the redox energy to translocate H+ ions across the membrane, resulting in a significant contribution to energy production. In Escherichia coli NDH-1, the largest subunit is encoded by the nuoG gene, and is part of the 14 distinct subunits constituting the functional enzyme. The NuoG subunit is made of two domains: the first contains three binding sites for FeS clusters (the fer2 domain), the second domain (this CD), is of unknown function or, as postulated, has lost an ancestral formate dehydrogenase activity that became redundant during the evolution of the complex I enzyme. Although only vestigial sequence evidence remains of a molybdopterin binding site, this protein domain belongs to t
Probab=46.68  E-value=19  Score=15.57  Aligned_cols=99  Identities=12%  Similarity=0.159  Sum_probs=54.5

Q ss_pred             CHHHH----HHHHHHHHHC--CCCEEEEECCCCCHHHHHHHHHHHHHHCCCC-EEEEECCC-------CCCCCCCCHHHH
Q ss_conf             87999----9999999977--9979999407886152899999999976994-79980787-------433668897898
Q gi|254780901|r   77 DCDKA----ARRIVQAIYN--SEKIMIFGDYDVDGAASVALMMRFLSHCSVN-ANMYIPDR-------IVDGYGPNPSLM  142 (600)
Q Consensus        77 dm~~A----~~ri~~ai~~--~ekI~I~gDyD~DGitstail~~~L~~~g~~-v~~~IP~R-------~~eGYGl~~~~i  142 (600)
                      ..++|    +++|.+.+++  .+.|.+|+.-.... -...++.++++.+|.+ +.+..-+.       +.-+.|++.. +
T Consensus        70 sWdeAl~~ia~kl~~i~~~~G~~sia~~~s~~~~~-E~~~~~~kf~~~lGt~n~d~~~~~~~~~~~~~~~~~~~~~~~-~  147 (414)
T cd02772          70 DWETALEYVAEGLSAIIKKHGADQIGALASPHSTL-EELYLLQKLARGLGSDNIDHRLRQSDFRDDAKASGAPWLGMP-I  147 (414)
T ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCCCEECCCCCCH-HHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHCCCCCCCCC-H
T ss_conf             79999999999999999874875331304898868-999999999997699762454234442145653248777998-8


Q ss_pred             HHHHHCCCCEEEEECCCCCCHHH-------HHHHHHCCCCEEEECC
Q ss_conf             87420268689996488762345-------5555417982799615
Q gi|254780901|r  143 EKFINEGAQLIITVDCGSTSYDA-------LQYATNQGIDVIVIDH  181 (600)
Q Consensus       143 ~~~~~~g~~LiItvD~Gi~~~e~-------i~~a~~~GidvIVtDH  181 (600)
                      +++.+  .++|+.+  |+.-.++       +..++++|..+||+|.
T Consensus       148 ~Di~~--ad~ivl~--G~n~~~~~Pil~~rir~a~k~gaklividP  189 (414)
T cd02772         148 AEISE--LDRVLVI--GSNLRKEHPLLAQRLRQAVKKGAKLSAINP  189 (414)
T ss_pred             HHHHH--CCEEEEE--CCCHHHHHHHHHHHHHHHHHCCCEEEEECC
T ss_conf             88985--9989998--588788759999999999987998999868


No 357
>COG0279 GmhA Phosphoheptose isomerase [Carbohydrate transport and metabolism]
Probab=46.68  E-value=18  Score=15.73  Aligned_cols=104  Identities=26%  Similarity=0.449  Sum_probs=54.6

Q ss_pred             CCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHH------HHHHHHHHC-CCCE-----EEEECCCCCCCCCCCHH--
Q ss_conf             148799999999999779979999407886152899------999999976-9947-----99807874336688978--
Q gi|254780901|r   75 LTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVA------LMMRFLSHC-SVNA-----NMYIPDRIVDGYGPNPS--  140 (600)
Q Consensus        75 l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitsta------il~~~L~~~-g~~v-----~~~IP~R~~eGYGl~~~--  140 (600)
                      ...+++|+..+.++..++.||+++|-   -|-.+-|      ++-+|-+.- +...     ..-+-.-..--||...=  
T Consensus        24 ~~~I~~aa~~i~~~l~~G~Kvl~cGN---GgSaadAqHfaaEl~gRf~~eR~~lpaIaLt~dsS~lTai~NDy~yd~vFs  100 (176)
T COG0279          24 IEAIERAAQLLVQSLLNGNKVLACGN---GGSAADAQHFAAELTGRFEKERPSLPAIALSTDSSVLTAIANDYGYDEVFS  100 (176)
T ss_pred             HHHHHHHHHHHHHHHHCCCEEEEECC---CCCHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCHHHHHHHCCCCHHHHHH
T ss_conf             99999999999999976997999769---852451899999986078752789873686426377765650455889999


Q ss_pred             -HHHHHHHCCCCEEEEE-CCC--CCCHHHHHHHHHCCCCEEEECCC
Q ss_conf             -9887420268689996-488--76234555554179827996154
Q gi|254780901|r  141 -LMEKFINEGAQLIITV-DCG--STSYDALQYATNQGIDVIVIDHH  182 (600)
Q Consensus       141 -~i~~~~~~g~~LiItv-D~G--i~~~e~i~~a~~~GidvIVtDHH  182 (600)
                       -++-+-..| +++|-. -.|  -+=..+++.|+++||.||..---
T Consensus       101 RqveA~g~~G-DvLigISTSGNS~nVi~Ai~~Ak~~gm~vI~ltG~  145 (176)
T COG0279         101 RQVEALGQPG-DVLIGISTSGNSKNVLKAIEAAKEKGMTVIALTGK  145 (176)
T ss_pred             HHHHHCCCCC-CEEEEEECCCCCHHHHHHHHHHHHCCCEEEEEECC
T ss_conf             9999527888-78999817999778999999998769879999558


No 358
>TIGR02478 6PF1K_euk 6-phosphofructokinase; InterPro: IPR009161    Members of this family are eukaryotic (with one exception) ATP-dependent 6-phosphofructokinases (2.7.1.11 from EC) in which two tandem copies of the phosphofructokinase are found . Members are found, often including several isozymes, in animals and fungi and in the bacterium Propionibacterium acnes KPA171202 (a human skin commensal).   Phosphofructokinase (PFK) catalyses the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate, which then enters the Embden-Meyerhof pathway. PFK is a key regulatory enzyme in glycolysis.   For additional information please see , , .; GO: 0003872 6-phosphofructokinase activity, 0006096 glycolysis, 0005737 cytoplasm.
Probab=46.67  E-value=13  Score=16.85  Aligned_cols=407  Identities=18%  Similarity=0.204  Sum_probs=190.3

Q ss_pred             CHHHHHHHHHCCCCHHHHHHH--CC-----CCHHHCCCCHHHC-CCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHH
Q ss_conf             999999999678897898866--19-----6677718995561-487999999999997799799994078861528999
Q gi|254780901|r   40 PDIVARVLVNRNVSIDYAKDF--LN-----PSIRLLMPDPLIL-TDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVAL  111 (600)
Q Consensus        40 ~~~~a~iL~~Rgi~~~~~~~f--L~-----p~l~~l~~dP~~l-~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstai  111 (600)
                      |.|+..|+.+-.|+.|+++.|  |+     -|++|.+.. ..+ =+-+-|..||.+|              +|.|.+||.
T Consensus       118 ~~L~~EL~~~g~It~Eq~~~~~~L~IvGlVGSIDND~~g-TD~TIGadSaLhRIcEa--------------~D~i~~TA~  182 (777)
T TIGR02478       118 PSLLEELVDTGKITAEQAKEHRHLTIVGLVGSIDNDMCG-TDMTIGADSALHRICEA--------------IDAISSTAQ  182 (777)
T ss_pred             HHHHHHHHHCCCCCHHHHHCCCCCCEEEEEECCCCCCCC-CCCCCCCCCHHHHHHHH--------------HCHHHHCCC
T ss_conf             158899731586647999507864067752110167564-78630224123347654--------------330440430


Q ss_pred             H---------------HHHHH---HCCCCEEEEECCCCCCCCC-CCHHH---HHHHHHCC--CCEEEEECCC--------
Q ss_conf             9---------------99999---7699479980787433668-89789---88742026--8689996488--------
Q gi|254780901|r  112 M---------------MRFLS---HCSVNANMYIPDRIVDGYG-PNPSL---MEKFINEG--AQLIITVDCG--------  159 (600)
Q Consensus       112 l---------------~~~L~---~~g~~v~~~IP~R~~eGYG-l~~~~---i~~~~~~g--~~LiItvD~G--------  159 (600)
                      =               |.+|-   ..|||..+ ||.|=-+ =| =..++   +.+--+.|  -++|| |==|        
T Consensus       183 SHqR~FVvEVMGRHCGyLAL~AaiAtgADyvF-iPE~PP~-~~~W~d~lc~~l~~~R~~GkR~~iVi-VAEGA~D~~~~p  259 (777)
T TIGR02478       183 SHQRAFVVEVMGRHCGYLALMAAIATGADYVF-IPERPPE-EGDWEDQLCAKLKRNRKAGKRKNIVI-VAEGAIDRELNP  259 (777)
T ss_pred             CCCCEEEEEECCCCHHHHHHHHHHHHHHCEEE-CCCCCCC-CCCCHHHHHHHHHHHHHCCCCCEEEE-EEECEECCCCCC
T ss_conf             01765999874884258999999886220022-4786898-88768899899888773689640799-842105467779


Q ss_pred             CCCHHHHHHH-HHCCCCEEEECCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHHH
Q ss_conf             7623455555-417982799615447655567256523788886433443047889999999999970214887640779
Q gi|254780901|r  160 STSYDALQYA-TNQGIDVIVIDHHQVKSEEIPAYALVNPNRLDDLSGQGHLCAAGVVFLVLVLIYRILRQDNKVPLNFDL  238 (600)
Q Consensus       160 i~~~e~i~~a-~~~GidvIVtDHH~~~~~~p~a~aivNP~~~~~~~p~~~l~gaGvaf~l~~al~~~l~~~~~~~~~~~l  238 (600)
                      ||+.+==+.+ .++++|+=||=             +=|=+|-|.+.-|.-+-++   ++=+.|+...|.-.....-.   
T Consensus       260 Itse~VK~vl~~~L~lDtRiT~-------------LGHVQRGG~PsA~DR~Lat---~~GvEAV~avL~~tpe~~Ga---  320 (777)
T TIGR02478       260 ITSEDVKDVLVERLGLDTRITV-------------LGHVQRGGAPSAYDRILAT---LQGVEAVLAVLESTPETEGA---  320 (777)
T ss_pred             CCHHHHHHHHHHHCCCCEEEEE-------------CCCCCCCCCHHHHHHHHHH---HHHHHHHHHHHCCCCCCCCC---
T ss_conf             6889898886440184024766-------------0522468872289999998---64499999997268776874---


Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCHHH----H------HHHHHHHHHCCC--------C----CHHHHHHHHCCC--CC-CC
Q ss_conf             9999998775420111144411899----9------987887751688--------7----435789870888--64-24
Q gi|254780901|r  239 LSLLDLVALATVCDVVPLIGLNRAY----V------VKGLMVARRQGN--------P----GLKALIERVNIS--SP-IT  293 (600)
Q Consensus       239 ~~~ldlvaiGTvaD~vpL~~eNR~l----v------k~GL~~l~~~~~--------~----gl~~L~~~~~~~--~~-i~  293 (600)
                          -...=-|++=|+.|.+ |++.    +      |.==+.|.+...        +    -+..+...+..+  .. ..
T Consensus       321 ----vvtGqk~ps~VI~l~g-NkI~R~PL~~~V~~T~~V~~~i~~~~f~~A~~LRg~eF~~~~~~~~~~s~~~~~~~~~~  395 (777)
T TIGR02478       321 ----VVTGQKTPSPVISLRG-NKIVRKPLVEAVRQTKTVAKAIKERRFDEAVRLRGREFVENLATFLELSKPDQDKKLVP  395 (777)
T ss_pred             ----EEECCCCCCEEEEECC-CEEEECHHHHHHHHHHHHHHHHHCCCCHHHHHCCCHHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf             ----7615435551475068-70221318899998999899873177545872357235775444776203378886777


Q ss_pred             --HHHHHHHHH--------HHCCHHHHH--------CCCCCCCE----EEECCC-H----HHHHHHHHHHHHH-------
Q ss_conf             --234566677--------430623331--------21222210----020342-5----8999999999989-------
Q gi|254780901|r  294 --AENLGYMIG--------PSINAGGRI--------GESNLGSR----LLISDD-S----QELEMLAMKLDVL-------  339 (600)
Q Consensus       294 --~~di~f~ia--------PrINAaGRl--------~~a~~av~----lL~~~d-~----~~a~~la~~L~~l-------  339 (600)
                        .+-++|+||        +=+|||-|=        |+--.|+.    =|...| .    .--+--+.+.+..       
T Consensus       396 ~~~~r~~~R~AIihvGAPA~GMNaA~R~avr~~~~~Gh~v~aI~nGf~GL~~~~DDtPicsvrEL~W~dV~gW~~~GGS~  475 (777)
T TIGR02478       396 SKADRLNLRVAIIHVGAPAGGMNAATRAAVRYALARGHTVIAIHNGFSGLARGDDDTPICSVRELTWSDVEGWVGEGGSE  475 (777)
T ss_pred             CCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEEECCCHHCCCCCCCCCEEEEEEECCCCCHHHHCCCCCC
T ss_conf             54356742079996488853023999999999850698799981684100228889743312220234442334288762


Q ss_pred             -HHHHHHH-HHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCHHHHHHHHHHHH-HHHHCEEEEE--EECCCCEEEEEEE
Q ss_conf             -9999999-999999999998752112434750262057858122222278998-8420107998--8637983799986
Q gi|254780901|r  340 -NQNRRLM-ESAMLEQAEAKVLTQCDDIQQASVIVVEGDRWHPGIVGLLAARLK-EKFGRPSFAI--SFEEDGKGIGSGR  414 (600)
Q Consensus       340 -N~~Rk~~-e~~i~~~a~~~~~~~~~~~~~~~~ivv~~~~wh~GViGIVAsrL~-e~y~kP~iv~--s~~~dg~~kGS~R  414 (600)
                       =.+|.-= +..+-.-|.     .+++++-+-.||+-+=.=-+++.=|.+.|-. ..|.-|.+++  |+++|  .=||--
T Consensus       476 lGTnR~lP~~~d~~~iA~-----~f~~~kiDgL~IIGGFEAf~al~qL~~aR~~YP~F~IPmv~iPATISNN--VPGTe~  548 (777)
T TIGR02478       476 LGTNRELPNGKDLGEIAY-----KFQKHKIDGLLIIGGFEAFEALLQLEQAREKYPAFRIPMVVIPATISNN--VPGTEY  548 (777)
T ss_pred             CCCCCCCCCCCCHHHHHH-----HHHHCCCCEEEEECCHHHHHHHHHHHHHHHHCCCCCCCEEEECCEEECC--CCCCCC
T ss_conf             167789778653899999-----9986098879997603688999999999861885578857866601077--872443


Q ss_pred             CCCCC-CHHHHHHHHC---C-------C-CCCCCCCCCCC--------CCC---EEECCC--CHHHHHHHHHHHHHHHCC
Q ss_conf             48986-1888888530---3-------3-53011565322--------231---464222--158899999999986226
Q gi|254780901|r  415 SIEGF-DIGKMVSFAV---E-------E-GILVKGGGHAM--------AAG---LTVERV--NFGRLCDFFQKFAHNIVP  469 (600)
Q Consensus       415 Si~g~-~l~~~l~~~~---~-------~-~ll~~~GGH~~--------AaG---~ti~~~--~l~~f~~~l~~~~~~~~~  469 (600)
                      |.+-- =|.++...|.   +       + =..+--||-..        |+|   .-++++  +|..+++-+...-++ +.
T Consensus       549 SLG~DTaLN~i~~~cD~IkqSA~askrRvFVvEtmGG~sGYLAt~~GLa~GA~a~Yi~Eegi~l~~L~~Di~~L~~~-fa  627 (777)
T TIGR02478       549 SLGSDTALNEITEYCDKIKQSASASKRRVFVVETMGGYSGYLATMAGLATGADAAYIPEEGISLKDLQEDIEHLKEK-FA  627 (777)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEECCCHHHHHHHHHHHHCCEEEEECCCCCCHHHHHHHHHHHHHH-HH
T ss_conf             02201577789987263223530114756999970897168999998864624788647897889999999999986-30


Q ss_pred             H---HHCCCCEEEEEEECHHHCCHHHHHHH
Q ss_conf             4---43377147604434689799999999
Q gi|254780901|r  470 A---LITTPVFKIDGVLNASAVNIALIDML  496 (600)
Q Consensus       470 ~---~~~~~~l~iD~el~~~~i~~~l~~~L  496 (600)
                      .   ......|.+=.|-.-+..|-+++..|
T Consensus       628 ~~~g~n~~~~L~lRNE~AS~~ytTd~i~~i  657 (777)
T TIGR02478       628 EGAGKNRAGKLILRNENASKNYTTDFIARI  657 (777)
T ss_pred             CCCCCCCCCCEEEECCCCCCCCCHHHHHHH
T ss_conf             047863014316640223312275899999


No 359
>TIGR03669 urea_ABC_arch urea ABC transporter, substrate-binding protein, archaeal type. Members of this protein family are identified as the substrate-binding protein of a urea ABC transport system by similarity to a known urea transporter from Corynebacterium glutamicum, operon structure, proximity of its operons to urease (urea-utilization protein) operons, and by Partial Phylogenetic Profiling vs. urea utilization.
Probab=46.54  E-value=19  Score=15.55  Aligned_cols=39  Identities=8%  Similarity=0.097  Sum_probs=15.9

Q ss_pred             HHHHH-CCCCEEEEECCCCCCHHHH-HHHHHCCCCEEEECCC
Q ss_conf             87420-2686899964887623455-5554179827996154
Q gi|254780901|r  143 EKFIN-EGAQLIITVDCGSTSYDAL-QYATNQGIDVIVIDHH  182 (600)
Q Consensus       143 ~~~~~-~g~~LiItvD~Gi~~~e~i-~~a~~~GidvIVtDHH  182 (600)
                      +++.. ++++.|+-+-+ |+...++ ..+.+.++-.+.+.+.
T Consensus        61 ~kLi~~d~V~~v~G~~~-S~~~~Av~p~~~~~~~~~~~~~~~  101 (374)
T TIGR03669        61 RRLLNRDKVDALWAGYS-SATREAIRPIIDRNEQLYFYTNQY  101 (374)
T ss_pred             HHHHHHCCCEEEECCCC-CHHHHHHHHHHHHCCCEEEEECCC
T ss_conf             99996489449984667-177788788998608516981355


No 360
>PRK04554 consensus
Probab=46.21  E-value=20  Score=15.52  Aligned_cols=76  Identities=17%  Similarity=0.253  Sum_probs=47.8

Q ss_pred             HHHHHHCCCCEEEEE-CC-CC-CHHHHHHHHHHHHHHCCC-CEEEEECC-------C-CCCCCC-CCHHHHHHHH-HCCC
Q ss_conf             999997799799994-07-88-615289999999997699-47998078-------7-433668-8978988742-0268
Q gi|254780901|r   85 IVQAIYNSEKIMIFG-DY-DV-DGAASVALMMRFLSHCSV-NANMYIPD-------R-IVDGYG-PNPSLMEKFI-NEGA  150 (600)
Q Consensus        85 i~~ai~~~ekI~I~g-Dy-D~-DGitstail~~~L~~~g~-~v~~~IP~-------R-~~eGYG-l~~~~i~~~~-~~g~  150 (600)
                      +.+-+. ++.+.|+- =+ ++ |-+.-.-+|..++++.|+ ++...+|-       | +..|-. ++...+-++. ..|+
T Consensus        47 i~esVr-g~dV~iiqs~~~~~nd~lmELll~idA~rra~A~~It~ViPY~~YaRQDr~~~~gr~pIsak~vA~lL~~~G~  125 (327)
T PRK04554         47 LLENVR-GRDVFILQPTCAPTNDNLMEILTMADALKRASAGRITTAIPYFGYARQDRRPRSVRVPISAKLVANMLYSAGI  125 (327)
T ss_pred             ECCCCC-CCEEEEEECCCCCHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCC
T ss_conf             178778-9818999179998247799999999999872887279994465643367665788675129999855762598


Q ss_pred             CEEEEECCCCC
Q ss_conf             68999648876
Q gi|254780901|r  151 QLIITVDCGST  161 (600)
Q Consensus       151 ~LiItvD~Gi~  161 (600)
                      +-+||+|--..
T Consensus       126 d~vitvDlH~~  136 (327)
T PRK04554        126 DRVLTVDLHAD  136 (327)
T ss_pred             CCCEEECCCHH
T ss_conf             85047626848


No 361
>COG1227 PPX1 Inorganic pyrophosphatase/exopolyphosphatase [Energy production and conversion]
Probab=46.10  E-value=20  Score=15.50  Aligned_cols=26  Identities=35%  Similarity=0.585  Sum_probs=19.0

Q ss_pred             CCEEEEEC--CCCCHHHHHHHHHHHHHHC
Q ss_conf             97999940--7886152899999999976
Q gi|254780901|r   93 EKIMIFGD--YDVDGAASVALMMRFLSHC  119 (600)
Q Consensus        93 ekI~I~gD--yD~DGitstail~~~L~~~  119 (600)
                      .+|.++|.  -|.|-++| ||.|-++.+.
T Consensus         2 ~~~~v~Gh~npDtDsi~S-ai~~ay~~~~   29 (311)
T COG1227           2 SKILVVGHENPDTDSIAS-AIVYAYLLNA   29 (311)
T ss_pred             CCEEEECCCCCCHHHHHH-HHHHHHHHHH
T ss_conf             617871687854788989-9999999987


No 362
>pfam03060 NPD 2-nitropropane dioxygenase. Members of this family catalyse the denitrification of a number of nitroalkanes using either FAD or FMN as a cofactor.
Probab=46.09  E-value=20  Score=15.50  Aligned_cols=64  Identities=22%  Similarity=0.336  Sum_probs=44.8

Q ss_pred             HHHHHCCCCEEEEECCCCCCCCCCCHH-HHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCCCCCC
Q ss_conf             999976994799807874336688978-988742026868999648876234555554179827996154476555
Q gi|254780901|r  114 RFLSHCSVNANMYIPDRIVDGYGPNPS-LMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKSEE  188 (600)
Q Consensus       114 ~~L~~~g~~v~~~IP~R~~eGYGl~~~-~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~~~~~~  188 (600)
                      ..+...+.++.       .-++|+..+ .++++++.|+.++.+|    ++.++...+.+.|.|+||.-=++..+..
T Consensus       108 ~~~~~~~~~~v-------~~~~G~p~~~~v~~~~~~G~~v~~~v----~s~~~A~~a~~~G~D~iV~qG~eAGGH~  172 (330)
T pfam03060       108 DSLKDAKPKVV-------SFGFGLPPEDVIERLKESGTKVIPTV----SSAKEARKAEAAGADAVVAQGPEAGGHR  172 (330)
T ss_pred             HHHHHCCCCEE-------EECCCCCHHHHHHHHHHCCCEEEEEC----CCHHHHHHHHHCCCCEEEEECCCCCCCC
T ss_conf             99997499999-------98998982799999998799899981----8999999999819998999667667778


No 363
>PRK01130 N-acetylmannosamine-6-phosphate 2-epimerase; Provisional
Probab=45.83  E-value=20  Score=15.47  Aligned_cols=110  Identities=18%  Similarity=0.207  Sum_probs=71.4

Q ss_pred             CCCHHHCCCHHHHHHH------------HHHHHHCCCCEEEEE----CCCCC--HHHHHHHHHHHHHHCCCCEEEEE-CC
Q ss_conf             8995561487999999------------999997799799994----07886--15289999999997699479980-78
Q gi|254780901|r   69 MPDPLILTDCDKAARR------------IVQAIYNSEKIMIFG----DYDVD--GAASVALMMRFLSHCSVNANMYI-PD  129 (600)
Q Consensus        69 ~~dP~~l~dm~~A~~r------------i~~ai~~~ekI~I~g----DyD~D--Gitstail~~~L~~~g~~v~~~I-P~  129 (600)
                      +++|+.|.-|-+|+..            =.++|+..-.+-|+|    ||+--  =||.|.==...|-..|+++--.= -+
T Consensus        19 l~~~~im~~mA~Aa~~gGA~giR~~~~~dI~aik~~v~lPIIGi~K~~~~~s~VyITPt~~ev~~l~~aGadiIA~DaT~   98 (222)
T PRK01130         19 LHSPEIMAAMALAAEQGGAVGIRANGVEDIKAIREVVDVPIIGIIKRDYPDSEVYITPTLKEVDALAAAGADIIALDATL   98 (222)
T ss_pred             CCCHHHHHHHHHHHHHCCCEEEECCCHHHHHHHHHHCCCCEEEEEECCCCCCCEEECCCHHHHHHHHHCCCCEEEEECCC
T ss_conf             78879999999999968962997189889999998479987999954689997375176999999998699999984678


Q ss_pred             CCCCCCCCCH-HHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCC
Q ss_conf             7433668897-8988742026868999648876234555554179827996154
Q gi|254780901|r  130 RIVDGYGPNP-SLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHH  182 (600)
Q Consensus       130 R~~eGYGl~~-~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH  182 (600)
                      | .-..|.+. +.++.++++- +.++..||.  +.|+...|.++|.|+|=|--.
T Consensus        99 R-~RP~g~~~~~~i~~i~~~~-~~l~MAD~s--t~eea~~A~~~G~D~V~TTLs  148 (222)
T PRK01130         99 R-PRPDGETLAELVKRIKEKP-GQLLMADCS--TLEEGLAAAKLGFDFIGTTLS  148 (222)
T ss_pred             C-CCCCCCCHHHHHHHHHHHH-CCEEEEECC--CHHHHHHHHHCCCCEEECCCC
T ss_conf             9-8989968999999999982-987898548--899999999849999972334


No 364
>COG0462 PrsA Phosphoribosylpyrophosphate synthetase [Nucleotide transport and metabolism / Amino acid transport and metabolism]
Probab=45.83  E-value=20  Score=15.47  Aligned_cols=74  Identities=19%  Similarity=0.283  Sum_probs=46.3

Q ss_pred             HHHHHHCCCCEEEEE-CCC--CCHHHHHHHHHHHHHHCCC-CEEEEECC--------CCCCCCCCCHHHHHHHHHC-CCC
Q ss_conf             999997799799994-078--8615289999999997699-47998078--------7433668897898874202-686
Q gi|254780901|r   85 IVQAIYNSEKIMIFG-DYD--VDGAASVALMMRFLSHCSV-NANMYIPD--------RIVDGYGPNPSLMEKFINE-GAQ  151 (600)
Q Consensus        85 i~~ai~~~ekI~I~g-DyD--~DGitstail~~~L~~~g~-~v~~~IP~--------R~~eGYGl~~~~i~~~~~~-g~~  151 (600)
                      |.+.+. ++.+.|+- .+.  =|-+.-.-||..++++.++ .++..||-        ++..|=-++..++-++.+. |++
T Consensus        45 i~EsVr-g~dVfI~qs~~~pvnd~lmELLi~idA~k~asA~~It~ViPY~gYARQDk~~~~repIsaklvA~lL~~aG~d  123 (314)
T COG0462          45 IEESVR-GKDVFIIQSTSPPVNDNLMELLIMIDALKRASAKRITAVIPYFGYARQDKAFKPREPISAKLVANLLETAGAD  123 (314)
T ss_pred             ECCCCC-CCEEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCHHHCCCCCCCCCCCEEHHHHHHHHHHCCCC
T ss_conf             426526-8769999089998688999999999998865886589993165132257656899977299999999972998


Q ss_pred             EEEEECCC
Q ss_conf             89996488
Q gi|254780901|r  152 LIITVDCG  159 (600)
Q Consensus       152 LiItvD~G  159 (600)
                      -|+|+|--
T Consensus       124 rv~TvDlH  131 (314)
T COG0462         124 RVLTVDLH  131 (314)
T ss_pred             EEEEEECC
T ss_conf             69997078


No 365
>PRK11778 putative periplasmic protease; Provisional
Probab=45.74  E-value=16  Score=16.25  Aligned_cols=39  Identities=26%  Similarity=0.466  Sum_probs=30.8

Q ss_pred             CCEEEEE--CCCCCCCCCCCHHHHHHHHHCCCCEEEEECCC
Q ss_conf             9479980--78743366889789887420268689996488
Q gi|254780901|r  121 VNANMYI--PDRIVDGYGPNPSLMEKFINEGAQLIITVDCG  159 (600)
Q Consensus       121 ~~v~~~I--P~R~~eGYGl~~~~i~~~~~~g~~LiItvD~G  159 (600)
                      -+|...+  |--...||||-..-++++.+.|..|.|.||.=
T Consensus       103 DeV~~rles~GG~v~~yglaasql~rlr~~~i~ltv~vd~V  143 (317)
T PRK11778        103 DEVLLRLESPGGVVHGYGLAASQLQRLRDAGIPLTVCVDKV  143 (317)
T ss_pred             CEEEEEEECCCCEEEHHHHHHHHHHHHHHCCCCEEEEEEEE
T ss_conf             86999997899566605779999999986799289997013


No 366
>pfam00994 MoCF_biosynth Probable molybdopterin binding domain. This domain is found a variety of proteins involved in biosynthesis of molybdopterin cofactor. The domain is presumed to bind molybdopterin. The structure of this domain is known, and it forms an alpha/beta structure. In the known structure of Gephyrin this domain mediates trimerisation.
Probab=45.68  E-value=20  Score=15.46  Aligned_cols=45  Identities=18%  Similarity=0.278  Sum_probs=29.6

Q ss_pred             HHHHHHHHHHHHCCCCEEEE--ECCCCCCCCCCCHHHHHHHHHCCCCEEEEE
Q ss_conf             28999999999769947998--078743366889789887420268689996
Q gi|254780901|r  107 ASVALMMRFLSHCSVNANMY--IPDRIVDGYGPNPSLMEKFINEGAQLIITV  156 (600)
Q Consensus       107 tstail~~~L~~~g~~v~~~--IP~R~~eGYGl~~~~i~~~~~~g~~LiItv  156 (600)
                      |++..|...|+..|.++.++  +|+...+    -.+++++.. +++++|||.
T Consensus        17 sn~~~l~~~l~~~G~~v~~~~~v~Dd~~~----i~~~l~~~~-~~~Dliitt   63 (140)
T pfam00994        17 TNGPLLAALLREAGAEVIRYGIVPDDPEA----IKEALAAAA-DEADVVITT   63 (140)
T ss_pred             HHHHHHHHHHHHCCCEEEEEEEECCCHHH----HHHHHHHHH-CCCCEEEEC
T ss_conf             69999999999879937799897889999----999999973-269999987


No 367
>PRK13597 imidazole glycerol phosphate synthase subunit HisF; Provisional
Probab=45.51  E-value=20  Score=15.44  Aligned_cols=72  Identities=10%  Similarity=0.123  Sum_probs=49.3

Q ss_pred             HHHHHHHHHCCCCEEEEE-CCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCC
Q ss_conf             999999997699479980-7874336688978988742026868999648876234555554179827996154
Q gi|254780901|r  110 ALMMRFLSHCSVNANMYI-PDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHH  182 (600)
Q Consensus       110 ail~~~L~~~g~~v~~~I-P~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH  182 (600)
                      .-+.+.+...|++--+.+ -+.-.+|-..|.+.++++.+. +.+=||+-=||.+.+.++.+-+.|.|=||+--.
T Consensus        34 ~~~a~~~~~~Gad~lhlvDld~a~~~~~~n~~~I~~i~~~-~~vpiqvGGGIrs~e~~~~ll~~GadkViigS~  106 (252)
T PRK13597         34 VEAARAYDEAGADELVFLDISATHEERAILLDVVARVAER-VFIPLTVGGGVRSLEDARKLLLSGADKVSVNSA  106 (252)
T ss_pred             HHHHHHHHHCCCCEEEEEECCCCCCCCHHHHHHHHHHHHH-CCCCEEEECCCCCHHHHHHHHHCCCCEEEECHH
T ss_conf             9999999986999999995646666866379999999862-698289847713089999998569877983266


No 368
>CHL00067 rps2 ribosomal protein S2
Probab=45.39  E-value=20  Score=15.43  Aligned_cols=101  Identities=19%  Similarity=0.232  Sum_probs=59.5

Q ss_pred             HCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHH-----------
Q ss_conf             614879999999999977997999940788615289999999997699479980787433668897898-----------
Q gi|254780901|r   74 ILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLM-----------  142 (600)
Q Consensus        74 ~l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i-----------  142 (600)
                      .+.-+.+|..-+.+...++.+|+..|-.-    -+.-++.++....|   .+||.+|---|-=-|-..+           
T Consensus        46 T~~~L~~A~~~i~~~~~~~g~ILfVgTk~----~~~~~i~~~A~~~~---~~yV~~rWlgG~LTN~~ti~k~i~~l~~l~  118 (227)
T CHL00067         46 TARFLSEACDLVFDAASRGKKFLFVGTKK----QAADLVASAAIRAR---CHYVNKKWLGGMLTNWSTTKTRLKKLRDLR  118 (227)
T ss_pred             HHHHHHHHHHHHHHHHHCCCEEEEEECCH----HHHHHHHHHHHHHC---CCEEECCCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             99999999999999985499479997658----78999999999819---971537642874447899977999999999


Q ss_pred             ---------------------------------HHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEE-ECCCC
Q ss_conf             ---------------------------------874202686899964887623455555417982799-61544
Q gi|254780901|r  143 ---------------------------------EKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIV-IDHHQ  183 (600)
Q Consensus       143 ---------------------------------~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIV-tDHH~  183 (600)
                                                       ..+ ..-++++|.+|.- ...-+|..|+.+||.||- .|-..
T Consensus       119 ~~~~~~~~~~~~KKe~~~~~~~~~kL~k~~~Gi~~m-~~lPd~iii~d~~-~e~~ai~Ea~kL~IPvIaivDTn~  191 (227)
T CHL00067        119 MEEKTGLFNRLPKKEAAILKRQLSRLQKYLGGIKYM-TKLPDIVIIVDQQ-EEYTALRECIKLGIPTISIVDTNC  191 (227)
T ss_pred             HHHHCCCHHCCCHHHHHHHHHHHHHHHHHHHHHHHH-HCCCCEEEEECCC-CCHHHHHHHHHCCCCEEEEEECCC
T ss_conf             976245231020789998888898999875315456-2089769996775-337999999875999899963899


No 369
>COG1699 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=45.34  E-value=16  Score=16.21  Aligned_cols=56  Identities=18%  Similarity=0.195  Sum_probs=36.1

Q ss_pred             CCEEEEECCCCCCHHHHHHHHHCCCCE-EEECCCCCCCCCC-CCEEEECCCCCCCCCCC
Q ss_conf             868999648876234555554179827-9961544765556-72565237888864334
Q gi|254780901|r  150 AQLIITVDCGSTSYDALQYATNQGIDV-IVIDHHQVKSEEI-PAYALVNPNRLDDLSGQ  206 (600)
Q Consensus       150 ~~LiItvD~Gi~~~e~i~~a~~~Gidv-IVtDHH~~~~~~p-~a~aivNP~~~~~~~p~  206 (600)
                      -..+|++++||..+|.+..-.=.+++= ...=|-+ ..+-+ -++.+|||-..-.+|.+
T Consensus        14 ~~~ii~~~~gI~GFE~~kkf~L~~i~e~fp~~~~q-s~~~~~lsFivvnPf~~r~dYe~   71 (146)
T COG1699          14 EEMIIDFKAGILGFEHIKKFILVKIDEVFPRLHSQ-SLKDSDLSFIVVNPFLFRPDYEF   71 (146)
T ss_pred             CCEEEEECCCCCCCEEEEEEEEECCHHCCEEEEEE-CCCCCCEEEEEECCCEECCCCCC
T ss_conf             34079741785561000068996402422247872-17865257999765134365545


No 370
>cd01149 HutB Hemin binding protein HutB.  These proteins have been shown to function as initial receptors in ABC transport of hemin and hemoproteins in many eubacterial species.  They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains.
Probab=45.26  E-value=20  Score=15.41  Aligned_cols=37  Identities=19%  Similarity=0.281  Sum_probs=19.5

Q ss_pred             HHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEE
Q ss_conf             88742026868999648876234555554179827996
Q gi|254780901|r  142 MEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVI  179 (600)
Q Consensus       142 i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVt  179 (600)
                      +|.+..-.++|||+- .+....+.++.+.+.||.|+++
T Consensus        51 ~E~il~l~PDLVi~~-~~~~~~~~~~~L~~~gi~v~~~   87 (235)
T cd01149          51 AEGVLSLKPTLVIAS-DEAGPPEALDQLRAAGVPVVTV   87 (235)
T ss_pred             HHHHHHCCCCEEEEE-CCCCHHHHHHHHHHCCCCEEEC
T ss_conf             999973799889981-7768399999999629907955


No 371
>PRK07494 2-octaprenyl-6-methoxyphenyl hydroxylase; Provisional
Probab=45.16  E-value=20  Score=15.40  Aligned_cols=14  Identities=14%  Similarity=0.273  Sum_probs=6.2

Q ss_pred             HHHHHHHHCEEEEE
Q ss_conf             89988420107998
Q gi|254780901|r  388 ARLKEKFGRPSFAI  401 (600)
Q Consensus       388 srL~e~y~kP~iv~  401 (600)
                      .+.+++|.++=+++
T Consensus       269 ~~~a~~~~~~Rv~L  282 (386)
T PRK07494        269 GLVPHRFAANRTAL  282 (386)
T ss_pred             HHHHHHHHCCCEEE
T ss_conf             41156651688278


No 372
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=45.03  E-value=20  Score=15.39  Aligned_cols=110  Identities=11%  Similarity=0.101  Sum_probs=54.5

Q ss_pred             CCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHH
Q ss_conf             68897898874202686899964887623455555417982799615447655567256523788886433443047889
Q gi|254780901|r  135 YGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKSEEIPAYALVNPNRLDDLSGQGHLCAAGV  214 (600)
Q Consensus       135 YGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~~~~~~p~a~aivNP~~~~~~~p~~~l~gaGv  214 (600)
                      +-+-...+..+.+....+-+..-+ .+..+.++.+.+...||+++|-+.|.........-+.-..++  -+.=-+++..-
T Consensus        12 h~l~r~gl~~~l~~~~~~~vv~~a-~~~~~~~~~l~~~~~DvvllD~~lp~~~g~~~i~~i~~~~p~--~~ilvls~~~~   88 (210)
T PRK09935         12 HPIVRMSIEVLLQKNSNIQVVLKT-DDSRITIDYLRTYPVDLVILDIELPGTDGFTLLKRIKQIQET--VKVLFLSSKSE   88 (210)
T ss_pred             CHHHHHHHHHHHHCCCCEEEEEEE-CCHHHHHHHHHHCCCCEEEECCCCCCCCCCCHHHHHHHHCCC--CCEEEEECCCC
T ss_conf             699999999999629892899998-999999999974799999988999998864056789873899--70899717672


Q ss_pred             HHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999702148876407799999998775420
Q gi|254780901|r  215 VFLVLVLIYRILRQDNKVPLNFDLLSLLDLVALATVC  251 (600)
Q Consensus       215 af~l~~al~~~l~~~~~~~~~~~l~~~ldlvaiGTva  251 (600)
                      ..+...++.  .+-.+.+++..+..+++  .||-+|.
T Consensus        89 ~~~~~~a~~--~Ga~g~l~K~~~~~~l~--~ai~~v~  121 (210)
T PRK09935         89 CFYAGRAIR--AGANGFVSKRKDLNDIY--NAVQMIL  121 (210)
T ss_pred             HHHHHHHHH--CCCCEEEECCCCHHHHH--HHHHHHH
T ss_conf             999999996--68776886789999999--9999998


No 373
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=44.86  E-value=21  Score=15.37  Aligned_cols=12  Identities=17%  Similarity=0.526  Sum_probs=6.3

Q ss_pred             HHHHHHHHHCCC
Q ss_conf             999999996788
Q gi|254780901|r   41 DIVARVLVNRNV   52 (600)
Q Consensus        41 ~~~a~iL~~Rgi   52 (600)
                      .+.+..|++|++
T Consensus       213 ~~s~~~li~~~~  224 (1197)
T PRK09959        213 NIITSSMISRYF  224 (1197)
T ss_pred             HHHHHHHHHHHC
T ss_conf             999999997440


No 374
>TIGR00093 TIGR00093 conserved hypothetical protein; InterPro: IPR000748   Pseudouridine synthases are responsible for the synthesis of pseudouridine from uracil in ribosomal RNA. Several bacterial proteins from the Rsu family of pseudouridine synthases  have been shown to share regions of similarities, including Escherichia coli and Haemophilus influenzae 16S pseudouridylate 516 synthase (gene rsuA); E. coli hypothetical proteins yciL and ymfC and the corresponding H. influenzae proteins HI1199 and HI0694 respectively; Aquifex aeolicus hypothetical proteins AQ_554 and AQ_1464; Bacillus subtilis hypothetical proteins ypuL and ytzF; Borrelia burgdorferi hypothetical protein BB0129; Helicobacter pylori hypothetical protein HP1459; and Synechocystis sp. (strain PCC 6803) hypothetical proteins slr0361 and slr0612. These are proteins of from 25 to 40 kD which contain a number of conserved regions in their central section.; GO: 0003723 RNA binding, 0004730 pseudouridylate synthase activity, 0001522 pseudouridine synthesis.
Probab=44.70  E-value=11  Score=17.46  Aligned_cols=31  Identities=29%  Similarity=0.396  Sum_probs=21.4

Q ss_pred             HHHHCCHHHHHCCCCCCCEEEECCCHHHHHHH
Q ss_conf             77430623331212222100203425899999
Q gi|254780901|r  301 IGPSINAGGRIGESNLGSRLLISDDSQELEML  332 (600)
Q Consensus       301 iaPrINAaGRl~~a~~av~lL~~~d~~~a~~l  332 (600)
                      -+.++-|+||||-.+.++=||+ +|-+-+.++
T Consensus        29 ~~~~~~a~GRLD~ds~GLlLLT-~~G~L~~RL   59 (185)
T TIGR00093        29 RGKRLHAVGRLDRDSEGLLLLT-NDGELQHRL   59 (185)
T ss_pred             CCCCEEEEECCCCCCCCEEEEC-CCHHHHHHH
T ss_conf             0574677402674562038990-697999987


No 375
>TIGR02134 transald_staph transaldolase; InterPro: IPR011861    This small family of proteins belong to the transaldolases. Coxiella and Staphylococcus lack members of the known transaldolase families and appear to require a transaldolase activity for completion of the pentose phosphate pathway..
Probab=44.53  E-value=21  Score=15.33  Aligned_cols=65  Identities=20%  Similarity=0.243  Sum_probs=47.1

Q ss_pred             HHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEE
Q ss_conf             999997699479980787433668897898874202686899964887623455555417982799
Q gi|254780901|r  113 MRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIV  178 (600)
Q Consensus       113 ~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIV  178 (600)
                      .+.+..+|-+|...||=--+.|- .+.++|+++-++|++|=||.=.-++..++|-.+-..|+-.||
T Consensus        77 A~~ias~GnNV~vKIPvtntkGe-sT~PlIqkLSadgi~LNvTA~~TieQv~~v~~~~t~gvP~iV  141 (237)
T TIGR02134        77 AEKIASYGNNVYVKIPVTNTKGE-STIPLIQKLSADGIKLNVTAVYTIEQVKKVVEALTEGVPAIV  141 (237)
T ss_pred             HHHHHHHCCCEEEEEEEECCCCC-CCCHHHHHHHHCCCEEEEEEECCHHHHHHHHHHHHCCCCCEE
T ss_conf             99998707932788412418895-153078664024866754354025889999998745898179


No 376
>KOG1111 consensus
Probab=44.52  E-value=14  Score=16.63  Aligned_cols=34  Identities=21%  Similarity=0.295  Sum_probs=23.3

Q ss_pred             CEEEEECCCC---CCHHHHHHHHHCCCCEEEECCCCC
Q ss_conf             6899964887---623455555417982799615447
Q gi|254780901|r  151 QLIITVDCGS---TSYDALQYATNQGIDVIVIDHHQV  184 (600)
Q Consensus       151 ~LiItvD~Gi---~~~e~i~~a~~~GidvIVtDHH~~  184 (600)
                      +.-|..--++   -++|++-+|+..|..+++|||-.-
T Consensus        89 ~I~ivhghs~fS~lahe~l~hartMGlktVfTdHSlf  125 (426)
T KOG1111          89 RIEIVHGHSPFSYLAHEALMHARTMGLKTVFTDHSLF  125 (426)
T ss_pred             CEEEEECCCHHHHHHHHHHHHHHHCCCEEEEECCCCC
T ss_conf             1689965770888999999988745825998524311


No 377
>pfam00782 DSPc Dual specificity phosphatase, catalytic domain. Ser/Thr and Tyr protein phosphatases. The enzyme's tertiary fold is highly similar to that of tyrosine-specific phosphatases, except for a "recognition" region.
Probab=44.22  E-value=21  Score=15.30  Aligned_cols=49  Identities=18%  Similarity=0.175  Sum_probs=29.7

Q ss_pred             HCCCCHHHCCCCHHHCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHH
Q ss_conf             61966777189955614879999999999977997999940788615289999
Q gi|254780901|r   60 FLNPSIRLLMPDPLILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALM  112 (600)
Q Consensus        60 fL~p~l~~l~~dP~~l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail  112 (600)
                      +++-.+.+. ++....+.++++++.|.++++++++|+|+-   .-|++=++.+
T Consensus        40 yl~i~i~D~-~~~~i~~~~~~~~~fI~~~~~~g~~VLVHC---~~G~sRS~~i   88 (131)
T pfam00782        40 YLGIPVEDN-HETNISKYLPEAVEFIDDAIQKGGKVLVHC---QAGISRSATL   88 (131)
T ss_pred             EEEEECCCC-CCCCHHHHHHHHHHHHHHHHHCCCCEEEEC---CCCCCCHHHH
T ss_conf             999875209-998779999999999999986499699999---9987401999


No 378
>cd02765 MopB_4 The MopB_4 CD includes a group of related uncharacterized bacterial and archaeal molybdopterin-binding oxidoreductase-like domains with a putative N-terminal iron-sulfur [4Fe-4S] cluster binding site and molybdopterin cofactor binding site. These members belong to the molybdopterin_binding (MopB) superfamily of proteins
Probab=44.11  E-value=21  Score=15.28  Aligned_cols=39  Identities=26%  Similarity=0.371  Sum_probs=25.6

Q ss_pred             HHHHHHCCCCEEEEECCCCCC-------HHHHHHHHHCCCCEEEECCCCC
Q ss_conf             887420268689996488762-------3455555417982799615447
Q gi|254780901|r  142 MEKFINEGAQLIITVDCGSTS-------YDALQYATNQGIDVIVIDHHQV  184 (600)
Q Consensus       142 i~~~~~~g~~LiItvD~Gi~~-------~e~i~~a~~~GidvIVtDHH~~  184 (600)
                      +.++.  ++++||..  |.+-       ...+..|+++|..+||+|-..-
T Consensus       154 ~~D~~--~a~~il~~--G~Np~~~~~~~~~~~~~ak~~G~klIvIDPr~t  199 (567)
T cd02765         154 ITDWV--NAKTIIIW--GSNILETQFQDAEFFLDARENGAKIVVIDPVYS  199 (567)
T ss_pred             HHHHH--HCCEEEEE--CCCCHHHCCCHHHHHHHHHHCCCEEEEEECCCC
T ss_conf             56786--39899999--988246361079999999866983999938526


No 379
>PRK09123 amidophosphoribosyltransferase; Provisional
Probab=44.10  E-value=21  Score=15.28  Aligned_cols=37  Identities=19%  Similarity=0.146  Sum_probs=18.6

Q ss_pred             CCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCC
Q ss_conf             99799994078861528999999999769947998078743366889
Q gi|254780901|r   92 SEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPN  138 (600)
Q Consensus        92 ~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~  138 (600)
                      +|.=.|+|=|..+  -++.+++..|..+        -||=+|+.|+.
T Consensus        11 ~eeCGIfGi~~~~--~~a~~~~~gL~aL--------QHRGQesaGIa   47 (480)
T PRK09123         11 REECGVFGIFGHP--DAAAITALGLHAL--------QHRGQEAAGIV   47 (480)
T ss_pred             CCCCEEEEEECCH--HHHHHHHHHHHHH--------HCCCCCCCEEE
T ss_conf             6676289999781--5499999999997--------53785611499


No 380
>cd01977 Nitrogenase_VFe_alpha Nitrogenase_VFe_alpha -like: Nitrogenase VFe protein, alpha subunit like. This group contains proteins similar to the alpha subunits of,  the VFe protein of the vanadium-dependent (V-) nitrogenase and the FeFe protein of the iron only (Fe-) nitrogenase Nitrogenase catalyzes the ATP-dependent reduction of dinitrogen (N2) to ammonia. In addition to V- and Fe- nitrogenases there is a molybdenum (Mo)-dependent nitrogenase which is the most widespread and best characterized of these systems.  These systems consist of component 1 (VFe protein, FeFe protein or, MoFe protein  respectively) and, component 2 (Fe protein). MoFe is an alpha2beta2 tetramer, V-and Fe- nitrogenases are alpha2beta2delta2 hexamers. The alpha and beta subunits of VFe and FeFe are similar to the alpha and beta subunits of MoFe. For MoFe each alphabeta pair contains one P-cluster (at the alphabeta interface) and, one molecule of iron molybdenum cofactor (FeMoco) contained within the alpha sub
Probab=43.81  E-value=21  Score=15.25  Aligned_cols=27  Identities=11%  Similarity=0.320  Sum_probs=17.0

Q ss_pred             HHCCCHHHHHHHHHHHHHCC-CC--EEEEE
Q ss_conf             56148799999999999779-97--99994
Q gi|254780901|r   73 LILTDCDKAARRIVQAIYNS-EK--IMIFG   99 (600)
Q Consensus        73 ~~l~dm~~A~~ri~~ai~~~-ek--I~I~g   99 (600)
                      --|-+.++-.+-|.++.+.- +.  |.|+.
T Consensus        67 ~VfGG~~kL~~~I~~~~~~yP~~k~I~V~t   96 (415)
T cd01977          67 VVFGGEKKLKKNIIEAFKEFPDIKRMTVYT   96 (415)
T ss_pred             EECCHHHHHHHHHHHHHHHCCCCCEEEEEC
T ss_conf             231749999999999998579965699976


No 381
>COG1606 ATP-utilizing enzymes of the PP-loop superfamily [General function prediction only]
Probab=43.62  E-value=21  Score=15.23  Aligned_cols=143  Identities=25%  Similarity=0.275  Sum_probs=75.5

Q ss_pred             HHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECC
Q ss_conf             99999999999779979999407886152899999999976994799807874336688978988742026868999648
Q gi|254780901|r   79 DKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDC  158 (600)
Q Consensus        79 ~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~  158 (600)
                      .+-.+++.++++..+++.|-=   --|+-||.++.-+-..+|-+|                            +-+|+|.
T Consensus         4 ~~Kl~~l~~~ik~~~kv~vAf---SGGvDSslLa~la~~~lG~~v----------------------------~AvTv~s   52 (269)
T COG1606           4 LSKLERLKKAIKEKKKVVVAF---SGGVDSSLLAKLAKEALGDNV----------------------------VAVTVDS   52 (269)
T ss_pred             HHHHHHHHHHHHHCCEEEEEE---CCCCCHHHHHHHHHHHHCCCE----------------------------EEEEEEC
T ss_conf             799999999986437399996---588427999999999735646----------------------------9999716


Q ss_pred             CCCCHHHH----HHHHHCCCCEEEECCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             87623455----55541798279961544765556725652378888643344304788999999999997021488764
Q gi|254780901|r  159 GSTSYDAL----QYATNQGIDVIVIDHHQVKSEEIPAYALVNPNRLDDLSGQGHLCAAGVVFLVLVLIYRILRQDNKVPL  234 (600)
Q Consensus       159 Gi~~~e~i----~~a~~~GidvIVtDHH~~~~~~p~a~aivNP~~~~~~~p~~~l~gaGvaf~l~~al~~~l~~~~~~~~  234 (600)
                      ......++    ..|++.||.--|++--...   | .+ .-||- .-|     ++|---|-=.    |.+...+.+    
T Consensus        53 P~~p~~e~e~A~~~A~~iGi~H~~i~~~~~~---~-~~-~~n~~-~rC-----Y~CK~~v~~~----l~~~a~~~G----  113 (269)
T COG1606          53 PYIPRREIEEAKNIAKEIGIRHEFIKMNRMD---P-EF-KENPE-NRC-----YLCKRAVYST----LVEEAEKRG----  113 (269)
T ss_pred             CCCCHHHHHHHHHHHHHHCCCCEEEEHHHCC---H-HH-CCCCC-CCC-----HHHHHHHHHH----HHHHHHHCC----
T ss_conf             8777666067899999948762465500025---2-33-04998-735-----5778999999----999999739----


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHCCCCC-----CCHHHH
Q ss_conf             077999999987754201111444118999987887751688743578987088864-----242345
Q gi|254780901|r  235 NFDLLSLLDLVALATVCDVVPLIGLNRAYVVKGLMVARRQGNPGLKALIERVNISSP-----ITAENL  297 (600)
Q Consensus       235 ~~~l~~~ldlvaiGTvaD~vpL~~eNR~lvk~GL~~l~~~~~~gl~~L~~~~~~~~~-----i~~~di  297 (600)
                             .|.|+=||=||  .|.+                -|||++|+-+. ++..+     ++-.+|
T Consensus       114 -------yd~V~dGtNas--Dl~~----------------~RPG~rA~kE~-gi~sPl~e~gitk~eI  155 (269)
T COG1606         114 -------YDVVADGTNAS--DLFD----------------YRPGLRALKEL-GIRSPLAEFGITKKEI  155 (269)
T ss_pred             -------CCEEEECCCHH--HHCC----------------CCCCHHHHHHC-CCCCHHHHHCCCHHHH
T ss_conf             -------98897477578--7337----------------88302357760-7777188839759999


No 382
>TIGR01584 citF citrate lyase, alpha subunit; InterPro: IPR006472   These sequences, from both Gram-positive and Gram-negative bacteria, represent the alpha subunit of the holoenzyme citrate lyase composed of alpha (2.8.3.10 from EC), beta, and acyl carrier protein subunits in a stoichiometric relationship of 6:6:6. Citrate lyase is an enzyme which converts citrate to oxaloacetate. In bacteria, this reaction is involved in citrate fermentation. The alpha subunit catalyzes the reaction Acetyl-CoA + citrate = acetate + (3S)-citryl-CoA. The protein from Lactococcus lactis subsp. lactis has been experimentally characterised . ; GO: 0008814 citrate CoA-transferase activity, 0006084 acetyl-CoA metabolic process, 0005737 cytoplasm, 0009346 citrate lyase complex.
Probab=43.61  E-value=12  Score=17.17  Aligned_cols=113  Identities=14%  Similarity=0.217  Sum_probs=63.8

Q ss_pred             CCCCCCC-CCCEEECCCCHHHHHHHHHHHHHHH---CCHHHCCCCEEEEEEECHH---HCCHHHHHHHHHCCCCCCCCCC
Q ss_conf             1565322-2314642221588999999999862---2644337714760443468---9799999999851846789998
Q gi|254780901|r  436 KGGGHAM-AAGLTVERVNFGRLCDFFQKFAHNI---VPALITTPVFKIDGVLNAS---AVNIALIDMLESAGPYGAGNPN  508 (600)
Q Consensus       436 ~~GGH~~-AaG~ti~~~~l~~f~~~l~~~~~~~---~~~~~~~~~l~iD~el~~~---~i~~~l~~~L~~lePFG~gNpe  508 (600)
                      .-|||.= |||-.+.----|..|-|+--.+.+-   .++-+....+-.|.=+..+   --+.+|++.|+      ..---
T Consensus       375 A~GGH~DTAA~Ak~~iI~APLvRGRIptvV~~V~TviTPGe~vDvlvTd~GvavNdklpkr~dL~e~L~------~~~~i  448 (496)
T TIGR01584       375 ASGGHQDTAAGAKLSIIVAPLVRGRIPTVVEKVTTVITPGESVDVLVTDIGVAVNDKLPKRKDLIEKLS------SKKGI  448 (496)
T ss_pred             CCCCCCCCCHHEEEEEEECCHHHCCCCEEECCCEEEECCCCCEEEEECCCCEEECCCCCCCHHHHHHHC------CCCCC
T ss_conf             747762100100876664332307756575796069848884338981421797388898743688741------67988


Q ss_pred             CEEEECCEEEEEEEEECCC-EEEEEEECCCCCEEEEEEECCCCCCHHHHHHCCCCCEEEEEEEEE
Q ss_conf             4684278099888884796-499999849987799999778787012355306998799999976
Q gi|254780901|r  509 PVFAFPNHKLQSIRVVNLA-HLQMTFESQDSETLQAIAFRVYGTPLGEFLMQSRGKRMHVTGHLC  572 (600)
Q Consensus       509 P~F~~~~~~i~~~r~vGk~-Hlkl~l~~~~g~~i~aI~Fn~~~~~~~~~~~~~~g~~idii~~l~  572 (600)
                      |+|-++.++=.-.++.||- -++|+  +   +.+-.|-+             ..|.-+|++++++
T Consensus       449 p~~tIEeL~e~A~~~tGkP~pieFt--d---~vVavveY-------------RDGS~iDvi~~VK  495 (496)
T TIGR01584       449 PLYTIEELKEKAEEITGKPEPIEFT--D---KVVAVVEY-------------RDGSIIDVIKKVK  495 (496)
T ss_pred             CEECHHHHHHHHHHHCCCCCCCEEC--C---EEEEEEEE-------------CCCCEEEEEEECC
T ss_conf             2443899999999727898850132--7---37999983-------------5876877355306


No 383
>PRK07324 transaminase; Validated
Probab=43.52  E-value=21  Score=15.22  Aligned_cols=96  Identities=11%  Similarity=0.123  Sum_probs=48.5

Q ss_pred             CCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEE
Q ss_conf             48799999999999779979999407886152899999999976994799807874336688978988742026868999
Q gi|254780901|r   76 TDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIIT  155 (600)
Q Consensus        76 ~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiIt  155 (600)
                      .+-..|...+..++-+.--.+|+-+-   +.   .-++...+.+|+++.. +|-...+||.+..+.++.+...++++++.
T Consensus        87 ~Ga~~Al~l~~~~l~~pGD~Viv~~P---~Y---~~~~~~~~~~G~~v~~-~~l~~~~~~~~Dl~~l~~~i~~~tkliil  159 (373)
T PRK07324         87 NGATGANHLVLYALIEPGDHVISVYP---TY---QQLYDIPESLGAEVDY-WKLREENGWLPDLDELKRLVRPNTKLICI  159 (373)
T ss_pred             CCHHHHHHHHHHHHCCCCCEEEECCC---CC---HHHHHHHHHCCCEEEE-CCCCCCCCCCCCHHHHHHHCCCCCEEEEE
T ss_conf             87899999999997599998998899---85---7799999983987654-07672259887999999618878769997


Q ss_pred             EC----CCCC-CHHH----HHHHHHCCCCEEE
Q ss_conf             64----8876-2345----5555417982799
Q gi|254780901|r  156 VD----CGST-SYDA----LQYATNQGIDVIV  178 (600)
Q Consensus       156 vD----~Gi~-~~e~----i~~a~~~GidvIV  178 (600)
                      +.    +|.. +.++    ++.|++.|+-+|.
T Consensus       160 ~nP~NPTG~v~s~e~l~~l~~la~~~~i~iis  191 (373)
T PRK07324        160 NNANNPTGALMDRAFLEEIVEIAKSVDAYVLS  191 (373)
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHCCCEEEEE
T ss_conf             99979889778899999999875417859981


No 384
>PRK09860 putative alcohol dehydrogenase; Provisional
Probab=43.46  E-value=21  Score=15.21  Aligned_cols=14  Identities=21%  Similarity=0.219  Sum_probs=8.3

Q ss_pred             HHCCCCCCCCCCCE
Q ss_conf             85184678999846
Q gi|254780901|r  497 ESAGPYGAGNPNPV  510 (600)
Q Consensus       497 ~~lePFG~gNpeP~  510 (600)
                      -.-.+++.+||.|.
T Consensus       357 a~~d~~~~~NPr~~  370 (383)
T PRK09860        357 ALKDACGFTNPIQA  370 (383)
T ss_pred             HHHCCCCCCCCCCC
T ss_conf             99661357999779


No 385
>cd04488 RecG_wedge_OBF RecG_wedge_OBF: A subfamily of OB folds corresponding to the OB fold found in the N-terminal (wedge) domain of Escherichia coli RecG. RecG is a branched-DNA-specific helicase, which catalyzes the interconversion of a DNA replication fork to a four-stranded (Holliday) junction in vivo and in vitro. This interconversion provides a route to repair stalled forks. The RecG monomer contains three domains. The N-terminal domain is named for its wedge structure, and may provide the specificity of RecG for binding branched-DNA structures. During the reversal of fork to Holliday junction, the wedge domain is fixed at the junction of the fork where the leading and lagging strand duplex arms meet, and is thought to promote the unwinding of the nascent leading and lagging strands. In order to form the Holliday junction, these nascent strands would be annealed, and the parental strands reannealed. The wedge domain may also be a processivity factor of RecG on these branched cha
Probab=43.37  E-value=22  Score=15.20  Aligned_cols=60  Identities=27%  Similarity=0.367  Sum_probs=36.8

Q ss_pred             EEEEEEEEC---CCEEEEEEECCCCCEEEEEEECCCCCCHHHHHHCCCCCEEEEEEEEEEEEECCCCEEEE
Q ss_conf             998888847---96499999849987799999778787012355306998799999976654578110589
Q gi|254780901|r  517 KLQSIRVVN---LAHLQMTFESQDSETLQAIAFRVYGTPLGEFLMQSRGKRMHVTGHLCVNYWRGSKRCQL  584 (600)
Q Consensus       517 ~i~~~r~vG---k~Hlkl~l~~~~g~~i~aI~Fn~~~~~~~~~~~~~~g~~idii~~l~~N~~~G~~s~QL  584 (600)
                      +|.......   ++-++..+.|..| .++++|||.... .  ......|..+-+.++++.  |+|  .+|+
T Consensus         5 ~I~~~~~~~~~~r~~l~~~v~D~tg-~i~l~~Fn~~~~-~--~~~~~~G~~v~v~Gkv~~--~~~--~~q~   67 (75)
T cd04488           5 TVVSVEVVPRRGRRRLKVTLSDGTG-TLTLVFFNFQPY-L--KKQLPPGTRVRVSGKVKR--FRG--GLQI   67 (75)
T ss_pred             EEEEEEEECCCCCEEEEEEEEECCC-EEEEEEECCCHH-H--HHHCCCCCEEEEEEEEEE--CCC--EEEE
T ss_conf             9999885458997089999996998-899999899779-9--953889999999999971--399--9999


No 386
>cd04730 NPD_like 2-Nitropropane dioxygenase (NPD), one of the nitroalkane oxidizing enzyme families, catalyzes oxidative denitrification of nitroalkanes to their corresponding carbonyl compounds and nitrites. NDP is a member of the NAD(P)H-dependent flavin oxidoreductase family that reduce a range of alternative electron acceptors. Most use FAD/FMN as a cofactor and NAD(P)H as electron donor. Some contain 4Fe-4S cluster to transfer electron from FAD to FMN.
Probab=43.32  E-value=22  Score=15.20  Aligned_cols=65  Identities=22%  Similarity=0.322  Sum_probs=44.4

Q ss_pred             HHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCCCCC
Q ss_conf             9999997699479980787433668897898874202686899964887623455555417982799615447655
Q gi|254780901|r  112 MMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKSE  187 (600)
Q Consensus       112 l~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~~~~~  187 (600)
                      +.+.+...+.++..       -+.|...+.++.+++.|+.++.+|    ++.++...+.+.|.|.||.--++..+.
T Consensus        72 ~~~~~~~~~v~~v~-------~~~g~p~~~v~~l~~~g~~v~~~v----~s~~~A~~a~~~GaD~iv~qG~eAGGH  136 (236)
T cd04730          72 LLEVALEEGVPVVS-------FSFGPPAEVVERLKAAGIKVIPTV----TSVEEARKAEAAGADALVAQGAEAGGH  136 (236)
T ss_pred             HHHHHHHCCCCEEE-------ECCCCCHHHHHHHHHCCCEEEEEC----CCHHHHHHHHHCCCCEEEEECCCCCCC
T ss_conf             99999976999999-------879897899999998299899958----989999999981899899977777778


No 387
>COG1504 Uncharacterized conserved protein [Function unknown]
Probab=43.29  E-value=22  Score=15.20  Aligned_cols=44  Identities=25%  Similarity=0.459  Sum_probs=35.0

Q ss_pred             CCCCHHHHHHHHHCCCCEEEEECCCCC-----CHHHHHHHHHCCCCEEEE
Q ss_conf             688978988742026868999648876-----234555554179827996
Q gi|254780901|r  135 YGPNPSLMEKFINEGAQLIITVDCGST-----SYDALQYATNQGIDVIVI  179 (600)
Q Consensus       135 YGl~~~~i~~~~~~g~~LiItvD~Gi~-----~~e~i~~a~~~GidvIVt  179 (600)
                      |-+..+-++++.+.++..|| |-.|.+     +-++.++.++.|+.||+.
T Consensus        47 Hkl~~eEle~~lee~~E~iv-vGTG~~G~l~l~~ea~e~~r~k~~~vi~~   95 (121)
T COG1504          47 HKLALEELEELLEEGPEVIV-VGTGQSGMLELSEEAREFFRKKGCEVIEL   95 (121)
T ss_pred             CCCCHHHHHHHHHCCCCEEE-EECCCEEEEEECHHHHHHHHHCCCEEEEE
T ss_conf             34699999999860996899-91484258995899999998549707982


No 388
>PRK02747 consensus
Probab=43.27  E-value=22  Score=15.19  Aligned_cols=73  Identities=12%  Similarity=0.164  Sum_probs=50.4

Q ss_pred             HHHHHHHHHCCCCEEEEE-CCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCC
Q ss_conf             999999997699479980-78743366889789887420268689996488762345555541798279961544
Q gi|254780901|r  110 ALMMRFLSHCSVNANMYI-PDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQ  183 (600)
Q Consensus       110 ail~~~L~~~g~~v~~~I-P~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~  183 (600)
                      .-+.+.+...|++--+++ -+.-.+|-..+.+.++++.+. +.+=|++-=||.+.+.++.+-+.|.|=||+.-..
T Consensus        33 ~~~ak~~~~~Gadelh~vDl~~a~~~~~~~~~lI~~i~~~-~~ipi~vGGGIrs~e~~~~ll~~GadkViigs~a  106 (257)
T PRK02747         33 VEAARAYDAAGADELCFLDITASHENRGTMLDVVARTAEQ-CFMPLTVGGGVRTVDDIRKLLLAGADKVSINSAA  106 (257)
T ss_pred             HHHHHHHHHCCCCEEEEEECCCCCCCCHHHHHHHHHHHHH-CCCCEEEECCCCCHHHHHHHHHCCCCEEEECHHH
T ss_conf             9999999986999899994767756755289999999986-6998898488207388789987699689834446


No 389
>pfam00436 SSB Single-strand binding protein family. This family includes single stranded binding proteins and also the primosomal replication protein N (PriB). PriB forms a complex with PriA, PriC and ssDNA.
Probab=43.26  E-value=22  Score=15.19  Aligned_cols=49  Identities=10%  Similarity=0.211  Sum_probs=35.4

Q ss_pred             EEEEEEECCCCCCHHHHHHCCCCCEEEEEEEEEEEEECCC-----CEEEEEEEEEE
Q ss_conf             7999997787870123553069987999999766545781-----10589999801
Q gi|254780901|r  540 TLQAIAFRVYGTPLGEFLMQSRGKRMHVTGHLCVNYWRGS-----KRCQLRVLDAS  590 (600)
Q Consensus       540 ~i~aI~Fn~~~~~~~~~~~~~~g~~idii~~l~~N~~~G~-----~s~QL~I~Di~  590 (600)
                      .+++.+|+-......+.  ...|..+-+.+++..+.|.++     .++++.+.+|.
T Consensus        49 ~~~v~~~g~~A~~~~~~--l~KG~~V~V~G~l~~~~~~~~~G~~r~~~~v~~~~i~  102 (104)
T pfam00436        49 FIRVVVWGKLAENAAEY--LKKGSLVYVEGRLRTRKYEDQEGQKRYVTEIVADNVQ  102 (104)
T ss_pred             EEEEEECCHHHHHHHHC--CCCCCEEEEEEEEEEEEEECCCCCEEEEEEEEEEEEE
T ss_conf             99877305446543122--7899799999997811379999989999999999999


No 390
>cd04409 RhoGAP_PARG1 RhoGAP_PARG1: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of PARG1 (PTPL1-associated RhoGAP1). PARG1 was originally cloned as an interaction partner of PTPL1, an intracellular protein-tyrosine phosphatase. PARG1 interacts with Rap2, also a member of the Ras small GTPase superfamily whose exact function is unknown, and shows strong preference for Rho. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=43.19  E-value=22  Score=15.18  Aligned_cols=67  Identities=12%  Similarity=0.247  Sum_probs=45.6

Q ss_pred             HCCCHHHHHHH---HHCCCCHHHHHHHCCCCHHHCCCCHHHCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHH
Q ss_conf             19999999999---967889789886619667771899556148799999999999779979999407886152899999
Q gi|254780901|r   37 HAIPDIVARVL---VNRNVSIDYAKDFLNPSIRLLMPDPLILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMM  113 (600)
Q Consensus        37 ~~~~~~~a~iL---~~Rgi~~~~~~~fL~p~l~~l~~dP~~l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~  113 (600)
                      -++|.++.+.+   ..||++.+               .-|...+-...++.+.++++++..+.-+.+||+  -+-+++|.
T Consensus        14 ~~IP~ii~~ci~~le~~gl~~e---------------GIfR~sGs~~~v~~L~~~~~~~~~~~~~~~~~~--h~va~lLK   76 (211)
T cd04409          14 DGIPFIIKKCTSEIESRALCLK---------------GIYRVNGAKSRVEKLCQAFENGKDLVELSELSP--HDISNVLK   76 (211)
T ss_pred             CCCCHHHHHHHHHHHHHCCCCC---------------CEEECCCCHHHHHHHHHHHHCCCCCCCCCCCCH--HHHHHHHH
T ss_conf             9988799999999998389878---------------803168848999999999976997534010889--99999999


Q ss_pred             HHHHHCC
Q ss_conf             9999769
Q gi|254780901|r  114 RFLSHCS  120 (600)
Q Consensus       114 ~~L~~~g  120 (600)
                      .||+.+-
T Consensus        77 ~yLReLP   83 (211)
T cd04409          77 LYLRQLP   83 (211)
T ss_pred             HHHHHCC
T ss_conf             9998389


No 391
>PRK09028 cystathionine beta-lyase; Provisional
Probab=43.06  E-value=22  Score=15.17  Aligned_cols=95  Identities=11%  Similarity=0.201  Sum_probs=54.1

Q ss_pred             CCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEE
Q ss_conf             48799999999999779979999407886152899999999976994799807874336688978988742026868999
Q gi|254780901|r   76 TDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIIT  155 (600)
Q Consensus        76 ~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiIt  155 (600)
                      .+|.....-+....+.+.+|++-.  |+=|-| ..++.+.|.++|.++.++=|.        +.+.+++++..++++|..
T Consensus        84 SGmaAi~~~ll~ll~~Gdhiv~~~--~~YggT-~~l~~~~l~~~Gi~v~~vd~~--------~~~~~~~~i~~~Tklv~~  152 (394)
T PRK09028         84 SGAAAISNALLSFLKAGDHLLMVD--SCYEPT-RDLCDKILAGFGIETTYYDPM--------IGEGIRELIRPNTKVLFL  152 (394)
T ss_pred             CHHHHHHHHHHHHHCCCCEEECCC--CCCCCH-HHHHHHHHHHCCEEEEEECCC--------CHHHHHHHCCCCCEEEEE
T ss_conf             999999999999847998787069--986277-999998886567479995799--------989998536877269999


Q ss_pred             ECC-----CCCCHHHHH-HHHHCCCCEEEECCC
Q ss_conf             648-----876234555-554179827996154
Q gi|254780901|r  156 VDC-----GSTSYDALQ-YATNQGIDVIVIDHH  182 (600)
Q Consensus       156 vD~-----Gi~~~e~i~-~a~~~GidvIVtDHH  182 (600)
                      =--     -+.+.++|. .|++.|+-+| .|.-
T Consensus       153 EtpsNP~l~v~Di~~ia~iA~~~g~~~v-VDNT  184 (394)
T PRK09028        153 ESPGSITMEVQDVPTLSRIAHEHDIVVM-LDNT  184 (394)
T ss_pred             ECCCCCCCCCCCHHHHHHHHHHCCCEEE-ECCC
T ss_conf             5589987523689999999998398799-6376


No 392
>pfam02634 FdhD-NarQ FdhD/NarQ family. Nitrate assimilation protein, NarQ, and FdhD are required for formate dehydrogenase activity.
Probab=42.89  E-value=22  Score=15.15  Aligned_cols=19  Identities=26%  Similarity=0.321  Sum_probs=12.4

Q ss_pred             HHHHHHHHHHCEEEEEEEC
Q ss_conf             2789988420107998863
Q gi|254780901|r  386 LAARLKEKFGRPSFAISFE  404 (600)
Q Consensus       386 VAsrL~e~y~kP~iv~s~~  404 (600)
                      .|-.++++++-.-+-|...
T Consensus       204 lAv~lA~~~giTLigf~R~  222 (235)
T pfam02634       204 LAVELAEELGITLVGFARG  222 (235)
T ss_pred             HHHHHHHHCCCEEEEEEEC
T ss_conf             9999999829989999718


No 393
>PRK09016 quinolinate phosphoribosyltransferase; Validated
Probab=42.87  E-value=15  Score=16.53  Aligned_cols=13  Identities=23%  Similarity=0.526  Sum_probs=9.0

Q ss_pred             CCCCCHHHHHHHH
Q ss_conf             6887435789870
Q gi|254780901|r  274 QGNPGLKALIERV  286 (600)
Q Consensus       274 ~~~~gl~~L~~~~  286 (600)
                      ..-||||.|-+.+
T Consensus       153 KT~PGlR~leKyA  165 (296)
T PRK09016        153 KTLPGLRSALKYA  165 (296)
T ss_pred             CCCCCCHHHHHHH
T ss_conf             6687640999999


No 394
>KOG1404 consensus
Probab=42.84  E-value=19  Score=15.55  Aligned_cols=66  Identities=17%  Similarity=0.225  Sum_probs=33.8

Q ss_pred             HHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHH
Q ss_conf             97799799994078861528999999999769947998078743366889789887420268689996488762345555
Q gi|254780901|r   89 IYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQY  168 (600)
Q Consensus        89 i~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~  168 (600)
                      |-+.|.-.+|   |-+|       .++|..++.-+.....|      + ++++++-+.++-..|..| -.|-.+....++
T Consensus        36 Iv~~~~~yly---De~G-------~ryLD~f~Gi~tvslGH------c-hP~v~~a~~kQl~~l~H~-t~~~~~~pi~~~   97 (442)
T KOG1404          36 IVRGEGQYLY---DEEG-------RRYLDAFGGIVTVSLGH------C-HPDVVAAAVKQLKKLYHT-TSGYLNPPIHDL   97 (442)
T ss_pred             EEECCEEEEE---CCCC-------CEEEHHHCCEEEEECCC------C-CHHHHHHHHHHHHHHEEE-ECCCCCCCHHHH
T ss_conf             7844267998---6888-------65002208748997378------8-847899999864532873-012148708999


Q ss_pred             HHHC
Q ss_conf             5417
Q gi|254780901|r  169 ATNQ  172 (600)
Q Consensus       169 a~~~  172 (600)
                      |..+
T Consensus        98 Ae~L  101 (442)
T KOG1404          98 AEAL  101 (442)
T ss_pred             HHHH
T ss_conf             9999


No 395
>PRK08508 biotin synthase; Provisional
Probab=42.54  E-value=22  Score=15.11  Aligned_cols=79  Identities=15%  Similarity=0.152  Sum_probs=52.7

Q ss_pred             HHHCCCHHHHHHHHHHHHHCCCC-EEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCH-------HHHH
Q ss_conf             55614879999999999977997-999940788615289999999997699479980787433668897-------8988
Q gi|254780901|r   72 PLILTDCDKAARRIVQAIYNSEK-IMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNP-------SLME  143 (600)
Q Consensus        72 P~~l~dm~~A~~ri~~ai~~~ek-I~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~-------~~i~  143 (600)
                      .+.|.+.++.++.-.+|.+++-. .++..                                 -|.|++.       ++++
T Consensus        36 ~Y~l~~~eeIl~~A~~a~~~G~~rf~lv~---------------------------------sg~~~~~~~~e~v~~~v~   82 (279)
T PRK08508         36 RYKRKEIEQIVQEAKMARANGALGFCLVT---------------------------------AGRGLDDKKLEYVAKAAK   82 (279)
T ss_pred             EECCCCHHHHHHHHHHHHHCCCCEEEEEE---------------------------------ECCCCCHHHHHHHHHHHH
T ss_conf             10789999999999999975997689998---------------------------------236887544999999999


Q ss_pred             HHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCCCC
Q ss_conf             7420268689996488762345555541798279961544765
Q gi|254780901|r  144 KFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKS  186 (600)
Q Consensus       144 ~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~~~~  186 (600)
                      .+++...++-+++=+|.-+.|+...+++.|+|-.   ||....
T Consensus        83 ~Ik~~~~~l~~c~slG~l~~e~~~~LkeAGvdrY---~hNlET  122 (279)
T PRK08508         83 AVKKEVPGLHLIACNGMASVEQLKELKKAGIFSY---NHNLET  122 (279)
T ss_pred             HHHHCCCCEEEEEECCCCCHHHHHHHHHCCCCEE---CCCCCC
T ss_conf             9863379935761178579999999998397123---076676


No 396
>TIGR03479 DMSO_red_II_alp DMSO reductase family type II enzyme, molybdopterin subunit. This model represents the molybdopterin subunit, typically called the alpha subunit, of various proteins that also contain an iron-sulfur subunit and a heme b subunit. The group includes two distinct but very closely related periplasmic proteins of anaerobic respiration, selenate reductase and chlorate reductase. Other members of this family include dimethyl sulphide dehydrogenase, ethylbenzene dehydrogenase, and an archaeal respiratory nitrate reductase. This alpha subunit has a twin-arginine translocation (TAT) signal for Sec-independent translocation across the plasma membrane.
Probab=42.52  E-value=22  Score=15.11  Aligned_cols=120  Identities=19%  Similarity=0.134  Sum_probs=61.7

Q ss_pred             HHHHHHHHHHHH----HC--CCCEEEEECCCCCHHHHHHHHHHHHHHCCCC-EEEEE-----CCCCCCCCCCCHHH--HH
Q ss_conf             799999999999----77--9979999407886152899999999976994-79980-----78743366889789--88
Q gi|254780901|r   78 CDKAARRIVQAI----YN--SEKIMIFGDYDVDGAASVALMMRFLSHCSVN-ANMYI-----PDRIVDGYGPNPSL--ME  143 (600)
Q Consensus        78 m~~A~~ri~~ai----~~--~ekI~I~gDyD~DGitstail~~~L~~~g~~-v~~~I-----P~R~~eGYGl~~~~--i~  143 (600)
                      =|+|.+.|.+++    ++  .+.|..+.-.-.-|..+.+-..+++..+|.- ..+|.     |-=....||-....  ..
T Consensus       141 WDEA~~~IA~~l~~~~~~yGp~~i~~~~~~~~~~~~~~~~~~r~~~l~Gg~~~~~~~~~~d~~~~~~~~~G~~~~~~~~~  220 (912)
T TIGR03479       141 WDEALTEIADKIIDTFEAQGPDGISLDTPHPHMAPISFAAGSRFANLIGGVSPDIFDDYGDLYTGAFHTFGKAHDSATSD  220 (912)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHEEECCCCCCCHH
T ss_conf             99999999998999999659972999788853115666899999997088578864455753564563560166789844


Q ss_pred             HHHHCCCCEEEEECCCCC-------CHHHHHHHHHCCCCEEEECCCCCCCCCCCCEEEECCCCCCCC
Q ss_conf             742026868999648876-------234555554179827996154476555672565237888864
Q gi|254780901|r  144 KFINEGAQLIITVDCGST-------SYDALQYATNQGIDVIVIDHHQVKSEEIPAYALVNPNRLDDL  203 (600)
Q Consensus       144 ~~~~~g~~LiItvD~Gi~-------~~e~i~~a~~~GidvIVtDHH~~~~~~p~a~aivNP~~~~~~  203 (600)
                      +.  .+.++||..  |++       +..-+..|+++|..|||+|=.-- +.-..|+--|.+ +++.+
T Consensus       221 D~--~ns~~ii~w--G~Np~~t~~~~~~~~~ear~~GaKvIvIDPryt-~tA~~AD~Wlpi-rPGTD  281 (912)
T TIGR03479       221 DW--FNADYIIMW--GSNPSVTRIPDAHFLSEARYNGARVVSIAPDYN-PSTIHADLWLPV-RVGTD  281 (912)
T ss_pred             HH--HCCCEEEEE--CCCHHHHCCCHHHHHHHHHHCCCEEEEECCCCC-HHHHHHCEEECC-CCCCH
T ss_conf             77--548889998--989578266458999999977997999948870-678961830177-79977


No 397
>cd06296 PBP1_CatR_like Ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. This group includes the ligand-binding domain of a LacI-like transcriptional regulator, CatR which is involved in catechol degradation. This group belongs to the the LacI-GalR family repressors that are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=42.47  E-value=22  Score=15.10  Aligned_cols=65  Identities=14%  Similarity=0.144  Sum_probs=38.3

Q ss_pred             HHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCC
Q ss_conf             999769947998078743366889789887420268689996488762345555541798279961544
Q gi|254780901|r  115 FLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQ  183 (600)
Q Consensus       115 ~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~  183 (600)
                      .++..|.++.....+.-.+   ...+.++.+...+++=||.+.... +-..++.+++.|+.++++|.+.
T Consensus        24 ~~~~~gy~~ll~~~~~~~~---~e~~~i~~l~~~~vdgiIi~~~~~-~~~~~~~l~~~~iPvV~id~~~   88 (270)
T cd06296          24 AAAAAGYDVVLSESGRRTS---PERQWVERLSARRTDGVILVTPEL-TSAQRAALRRTGIPFVVVDPAG   88 (270)
T ss_pred             HHHHCCCEEEEEECCCCHH---HHHHHHHHHHHCCCCEEEEECCCC-CHHHHHHHHHCCCCEEEECCCC
T ss_conf             9998499899997999969---999999999954999999906889-9999999997499999987888


No 398
>TIGR01524 ATPase-IIIB_Mg magnesium-translocating P-type ATPase; InterPro: IPR006415   This group describes the magnesium translocating P-type ATPase found in a limited number of bacterial species and best described in Salmonella typhimurium, which contains two isoforms . These transporters are active in low external Mg2+ concentrations and pump the ion into the cytoplasm. The magnesium ATPases have been classified as type IIIB by a phylogenetic analysis .; GO: 0015444 magnesium-importing ATPase activity, 0015693 magnesium ion transport, 0016021 integral to membrane.
Probab=42.39  E-value=18  Score=15.76  Aligned_cols=20  Identities=15%  Similarity=-0.051  Sum_probs=7.8

Q ss_pred             CCCCCCCCCHHHHHHHHHHH
Q ss_conf             11114441189999878877
Q gi|254780901|r  252 DVVPLIGLNRAYVVKGLMVA  271 (600)
Q Consensus       252 D~vpL~~eNR~lvk~GL~~l  271 (600)
                      |||||.+..|..++.--+.+
T Consensus       478 ~vv~L~e~~~~~l~~~t~~~  497 (892)
T TIGR01524       478 AVVALDESEKERLKDVTEEL  497 (892)
T ss_pred             CEECCCHHHHHHHHHHHHHH
T ss_conf             03037625789999999874


No 399
>cd05313 NAD_bind_2_Glu_DH NAD(P) binding domain of glutamate dehydrogenase, subgroup 2. Amino acid dehydrogenase (DH) is a widely distributed family of enzymes that catalyzes the oxidative deamination of an amino acid to its keto acid and ammonia with concomitant reduction of NADP+. Glutamate DH is a multidomain enzyme that catalyzes the reaction from glutamate to 2-oxyoglutarate and ammonia in the presence of NAD or NADP. It is present in all organisms. Enzymes involved in ammonia asimilation are typically NADP+-dependent, while those involved in glutamate catabolism are generally NAD+-dependent. Amino acid DH-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate, leucine, and phenylalanine DHs, methylene tetrahydrofolate DH, methylene-tetrahydromethanopterin DH, methylene-tetrahydropholate DH/cyclohydrolase, Shikimate DH-like proteins, malate oxidoreductases, and glutamyl tRNA reductase. Amino acid DHs catalyze the deamination of amino acids t
Probab=42.16  E-value=22  Score=15.07  Aligned_cols=56  Identities=9%  Similarity=0.127  Sum_probs=41.3

Q ss_pred             CCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEE
Q ss_conf             9947998078743366889789887420268689996488762345555541798279
Q gi|254780901|r  120 SVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVI  177 (600)
Q Consensus       120 g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvI  177 (600)
                      ..++...||--+.  .-++.+..+++...|+++|+--=||=+.-|+-+.++++||.||
T Consensus       119 ~~~cDIliPaA~e--n~I~~~nA~~i~a~~ck~IvEgANgP~T~eAd~iL~~kGI~vi  174 (254)
T cd05313         119 EVPCDIAFPCATQ--NEVDAEDAKLLVKNGCKYVAEGANMPCTAEAIEVFRQAGVLFA  174 (254)
T ss_pred             HCCCCEEEECCCC--CCCCHHHHHHHHHCCCEEEEECCCCCCCHHHHHHHHHCCCEEE
T ss_conf             3047699743546--6789999999996798299865889998789999998898896


No 400
>cd04390 RhoGAP_ARHGAP22_24_25 RhoGAP_ARHGAP22_24_25:  GTPase-activator protein (GAP) domain for Rho-like GTPases found in ARHGAP22, 24 and 25-like proteins; longer isoforms of these proteins contain an additional N-terminal pleckstrin homology (PH) domain. ARHGAP25 (KIA0053) has been identified as a GAP for Rac1 and Cdc42. Short isoforms (without the PH domain) of ARHGAP24, called RC-GAP72 and p73RhoGAP, and of ARHGAP22, called p68RacGAP, has been shown to be involved in angiogenesis and endothelial cell capillary formation. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the r
Probab=42.03  E-value=22  Score=15.06  Aligned_cols=17  Identities=29%  Similarity=0.612  Sum_probs=13.5

Q ss_pred             CCCCHHHHHHHHHHHCC
Q ss_conf             64242345666774306
Q gi|254780901|r  290 SPITAENLGYMIGPSIN  306 (600)
Q Consensus       290 ~~i~~~di~f~iaPrIN  306 (600)
                      ++.++..++-.+||-|=
T Consensus       151 NkM~~~NLAivf~P~Ll  167 (199)
T cd04390         151 NKMSVQNLATVFGPNIL  167 (199)
T ss_pred             CCCCHHHHHHHHCCHHC
T ss_conf             48983888887524307


No 401
>PRK07979 acetolactate synthase 3 catalytic subunit; Validated
Probab=41.98  E-value=23  Score=15.05  Aligned_cols=79  Identities=14%  Similarity=0.175  Sum_probs=41.9

Q ss_pred             HHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEE------ECCCC--CCC-CCCCHH-HHHHHHHC
Q ss_conf             999999999997799799994078861528999999999769947998------07874--336-688978-98874202
Q gi|254780901|r   79 DKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMY------IPDRI--VDG-YGPNPS-LMEKFINE  148 (600)
Q Consensus        79 ~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~------IP~R~--~eG-YGl~~~-~i~~~~~~  148 (600)
                      +..++++.+.+.+-++-+|+...-+----+..-+.++.+.+|+.|..-      +|+.-  .-| +|+.-. ....+.+ 
T Consensus       193 ~~~i~~a~~~L~~AkrPvIi~G~g~~~~~a~~~l~~lae~l~~PV~tt~~gkg~~~~~hp~~~G~~G~~g~~~~~~~l~-  271 (574)
T PRK07979        193 KGQIKRALQTLVAAKKPVVYVGGGAINAACHQQLKELVEKLNLPVVSSLMGLGAFPATHRQSLGMLGMHGTYEANMTMH-  271 (574)
T ss_pred             HHHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCCCCCCCCCCCCHHHHHHHH-
T ss_conf             9999999999972799889982773435489999999987198778740456789987742267777778689999984-


Q ss_pred             CCCEEEEECC
Q ss_conf             6868999648
Q gi|254780901|r  149 GAQLIITVDC  158 (600)
Q Consensus       149 g~~LiItvD~  158 (600)
                      ++||||.+.+
T Consensus       272 ~aDlvl~lG~  281 (574)
T PRK07979        272 NADVIFAVGV  281 (574)
T ss_pred             CCCEEEEEEE
T ss_conf             3886999985


No 402
>COG0644 FixC Dehydrogenases (flavoproteins) [Energy production and conversion]
Probab=41.97  E-value=23  Score=15.05  Aligned_cols=42  Identities=19%  Similarity=0.290  Sum_probs=21.4

Q ss_pred             ECCCCCCHHHHHHHHHCCCCEEEECCCCCCCCCCCCEEEECC
Q ss_conf             648876234555554179827996154476555672565237
Q gi|254780901|r  156 VDCGSTSYDALQYATNQGIDVIVIDHHQVKSEEIPAYALVNP  197 (600)
Q Consensus       156 vD~Gi~~~e~i~~a~~~GidvIVtDHH~~~~~~p~a~aivNP  197 (600)
                      |--|.+---+...+++.|++|+|.|.|..+...+-+-..+.|
T Consensus         9 VGaGPAGs~aA~~la~~G~~VlvlEk~~~~G~k~~~~~~~~~   50 (396)
T COG0644           9 VGAGPAGSSAARRLAKAGLDVLVLEKGSEPGAKPCCGGGLSP   50 (396)
T ss_pred             ECCCHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCCCCCCCH
T ss_conf             897889999999998579929999657889998767666787


No 403
>TIGR03407 urea_ABC_UrtA urea ABC transporter, urea binding protein. Members of this protein family are ABC transporter substrate-binding proteins associated with urea transport and metabolism. This protein is found in a conserved five-gene transport operon typically found adjacent to urease genes. It was shown in Cyanobacteria that disruption leads to the loss of high-affinity urea transport activity. Members of this protein family tend to have the twin-arginine signal for Sec-independent transport across the plasma membrane.
Probab=41.80  E-value=23  Score=15.03  Aligned_cols=15  Identities=13%  Similarity=-0.062  Sum_probs=7.1

Q ss_pred             HCCCHHHHHHHHHHH
Q ss_conf             614879999999999
Q gi|254780901|r   74 ILTDCDKAARRIVQA   88 (600)
Q Consensus        74 ~l~dm~~A~~ri~~a   88 (600)
                      ...+++-|++.|.++
T Consensus        20 ~~~g~~lAveeiNa~   34 (359)
T TIGR03407        20 LKDAELMAIEEINAS   34 (359)
T ss_pred             HHHHHHHHHHHHHHC
T ss_conf             999999999999860


No 404
>PRK08182 single-stranded DNA-binding protein; Provisional
Probab=41.57  E-value=23  Score=15.01  Aligned_cols=55  Identities=9%  Similarity=0.139  Sum_probs=39.1

Q ss_pred             CCCCCEEEEEEECCCCCCHHHHHHCCCCCEEEEEEEEEEEEECCC-----CEEEEEEEEEEE
Q ss_conf             499877999997787870123553069987999999766545781-----105899998011
Q gi|254780901|r  535 SQDSETLQAIAFRVYGTPLGEFLMQSRGKRMHVTGHLCVNYWRGS-----KRCQLRVLDASP  591 (600)
Q Consensus       535 ~~~g~~i~aI~Fn~~~~~~~~~~~~~~g~~idii~~l~~N~~~G~-----~s~QL~I~Di~p  591 (600)
                      +.++..+.+.+|+-......+++  ..|..+-|.++|..+.|..+     .++++...++.-
T Consensus        50 d~~~~W~~V~~Wg~~AE~~a~~L--~KG~~V~V~Grl~~~~W~dkdG~~R~~~eV~Ad~v~~  109 (148)
T PRK08182         50 DRGGFWAPVELWHRDAEHWARLY--QKGMRVLVEGRMERDEWTDNEDNERVTFKVEARRVGI  109 (148)
T ss_pred             ECCCEEEEEEEEHHHHHHHHHHH--CCCCEEEEEEEEEECCCCCCCCCEEEEEEEEEEEEEE
T ss_conf             66647999998736999999987--3899899998986013477999878899999868883


No 405
>cd04376 RhoGAP_ARHGAP6 RhoGAP_ARHGAP6: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain of ArhGAP6-like proteins. ArhGAP6 shows GAP activity towards RhoA, but not towards Cdc42 and Rac1. ArhGAP6 is often deleted in microphthalmia with linear skin defects syndrome (MLS); MLS is a severe X-linked developmental disorder. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway. GTPases generally have a low intrinsic GTPase hydrolytic activity but there are family-specific groups of GAPs that enhance the rate of GTP hydrolysis by several orders of magnitude.
Probab=41.54  E-value=23  Score=15.00  Aligned_cols=45  Identities=13%  Similarity=0.225  Sum_probs=24.8

Q ss_pred             HHCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHC
Q ss_conf             56148799999999999779979999407886152899999999976
Q gi|254780901|r   73 LILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHC  119 (600)
Q Consensus        73 ~~l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~  119 (600)
                      |...+-...++.+.+++++++.+.+..++|+  -+-+++|..||+.+
T Consensus        31 FR~sGs~~~i~~L~~~~d~g~~~~~~~~~~~--h~vA~lLK~flReL   75 (206)
T cd04376          31 FRVGSSKKRVRQLREEFDRGIDVVLDENHSV--HDVAALLKEFFRDM   75 (206)
T ss_pred             EECCCCHHHHHHHHHHHHCCCCCCCCCCCCH--HHHHHHHHHHHHHC
T ss_conf             2488869999999999864898776556889--99999999999868


No 406
>TIGR03151 enACPred_II putative enoyl-(acyl-carrier-protein) reductase II. This oxidoreductase of the 2-nitropropane dioxygenase family (pfam03060) is commonly found in apparent operons with genes involved in fatty acid biosynthesis. Furthermore, this genomic context generally includes the fabG 3-oxoacyl-[ACP] reductase and lacks the fabI enoyl-[ACP] reductase.
Probab=41.49  E-value=23  Score=15.00  Aligned_cols=51  Identities=16%  Similarity=0.287  Sum_probs=39.0

Q ss_pred             CCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCCCCC
Q ss_conf             3668897898874202686899964887623455555417982799615447655
Q gi|254780901|r  133 DGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKSE  187 (600)
Q Consensus       133 eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~~~~~  187 (600)
                      -+.|...+.++.+++.|+.++.+|  |  +.+....+.+.|.|+||..-++..+.
T Consensus        93 ~~~G~p~~~~~~~~~~g~~v~~~v--~--s~~~A~~a~~~G~D~iV~qG~EAGGH  143 (307)
T TIGR03151        93 TGAGNPGKYIPRLKENGVKVIPVV--A--SVALAKRMEKAGADAVIAEGMESGGH  143 (307)
T ss_pred             ECCCCCHHHHHHHHHCCCEEEEEE--C--CHHHHHHHHHCCCCEEEEECCCCCCC
T ss_conf             279996899999998599799981--8--99999999964999999745544687


No 407
>pfam04723 GRDA Glycine reductase complex selenoprotein A. Found in clostridia, this protein contains one active site selenocysteine and catalyses the reductive deamination of glycine, which is coupled to the esterification of orthophosphate resulting in the formation of ATP. A member of this family may also exist in Treponema denticola.
Probab=41.47  E-value=23  Score=14.99  Aligned_cols=76  Identities=22%  Similarity=0.395  Sum_probs=45.4

Q ss_pred             HHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCC-CCC----CCHHHHHHHHHC-CCC-EEEEECCCCC
Q ss_conf             977997999940788615289999999997699479980787433-668----897898874202-686-8999648876
Q gi|254780901|r   89 IYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVD-GYG----PNPSLMEKFINE-GAQ-LIITVDCGST  161 (600)
Q Consensus        89 i~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~e-GYG----l~~~~i~~~~~~-g~~-LiItvD~Gi~  161 (600)
                      +-.++|+.|+||  -||+-+-|| -.+++..|++|.|---.-|.- .-|    -|...+.++.++ |.. +++..  |.+
T Consensus         2 ~l~gKkviiiGd--RDGiPgpai-e~c~k~~gaevvfs~TECFVctaagaMDLEnQ~rVK~~aEk~G~ENvvVvl--Gaa   76 (150)
T pfam04723         2 IFQGKKVIIIGD--RDGIPGPAI-EECLKSIGAEVAFSSTECFVUTAAGAMDLENQQKVKDATESIGAENLVVLL--GAA   76 (150)
T ss_pred             CCCCCEEEEEEC--CCCCCCHHH-HHHHHCCCCEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHCCCCCEEEEE--CCC
T ss_conf             667866999816--889974889-999854596699974356776064412268789999999870975289996--466


Q ss_pred             CHHHHHHH
Q ss_conf             23455555
Q gi|254780901|r  162 SYDALQYA  169 (600)
Q Consensus       162 ~~e~i~~a  169 (600)
                      ..|....+
T Consensus        77 eaE~agla   84 (150)
T pfam04723        77 EAESAGLA   84 (150)
T ss_pred             CHHHCCCE
T ss_conf             70011443


No 408
>cd01523 RHOD_Lact_B Member of the Rhodanese Homology Domain superfamily. This CD includes predicted proteins with rhodanese-like domains found N-terminal of the metallo-beta-lactamase domain.
Probab=41.32  E-value=23  Score=14.98  Aligned_cols=38  Identities=11%  Similarity=0.221  Sum_probs=22.2

Q ss_pred             HHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEE
Q ss_conf             988742026868999648876234555554179827996
Q gi|254780901|r  141 LMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVI  179 (600)
Q Consensus       141 ~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVt  179 (600)
                      .++.+.+ +-.+++.|..|..|..+...++++|.+|...
T Consensus        54 ~~~~lp~-d~~ivv~C~~G~rS~~aa~~L~~~G~~v~~L   91 (100)
T cd01523          54 ILDQLPD-DQEVTVICAKEGSSQFVAELLAERGYDVDYL   91 (100)
T ss_pred             HHHHCCC-CCEEEEEECCCHHHHHHHHHHHHCCCEEEEE
T ss_conf             9964789-9839999289656999999999879837983


No 409
>PRK10618 phosphotransfer intermediate protein in two-component regulatory system with RcsBC; Provisional
Probab=41.28  E-value=8.2  Score=18.49  Aligned_cols=45  Identities=20%  Similarity=0.383  Sum_probs=32.7

Q ss_pred             CCCCEEEEECCCCCHHHHHHHHHHHHHH-CCCCE----EEEEC------------------CCCCCCC
Q ss_conf             7997999940788615289999999997-69947----99807------------------8743366
Q gi|254780901|r   91 NSEKIMIFGDYDVDGAASVALMMRFLSH-CSVNA----NMYIP------------------DRIVDGY  135 (600)
Q Consensus        91 ~~ekI~I~gDyD~DGitstail~~~L~~-~g~~v----~~~IP------------------~R~~eGY  135 (600)
                      ++---.|||-+|---...|.=|.++|.. .|++-    -||..                  .||+|.|
T Consensus       100 ~ktDAlIFG~h~~atl~ma~rlS~YLdilWGA~n~~~SMYYLNGqDNsLiLItT~plk~~~~rfKESy  167 (881)
T PRK10618        100 RKTEALIFGSHDSATLEMTQRMSTYLDTLWGAENVPWSMYYLNGQDNSLILISTLPLKDLTSRFKESY  167 (881)
T ss_pred             CEEEEEEECCCCHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCEEEEECCCCCCCHHHHHHHH
T ss_conf             61337996588706899999999889877343777521578607988579997454456155544557


No 410
>cd04382 RhoGAP_MgcRacGAP RhoGAP_MgcRacGAP: RhoGAP (GTPase-activator protein [GAP] for Rho-like small GTPases) domain present in MgcRacGAP proteins. MgcRacGAP plays an important dual role in cytokinesis: i) it is part of centralspindlin-complex, together with the mitotic kinesin MKLP1, which is critical for the structure of the central spindle by promoting microtuble bundling. ii) after phosphorylation by aurora B MgcRacGAP becomes an effective regulator of RhoA and plays an important role in the assembly of the contractile ring and the initiation of cytokinesis. MgcRacGAP-like proteins contain a N-terminal C1-like domain, and a C-terminal RhoGAP domain. Small GTPases cluster into distinct families, and all act as molecular switches, active in their GTP-bound form but inactive when GDP-bound. The Rho family of GTPases activates effectors involved in a wide variety of developmental processes, including regulation of cytoskeleton formation, cell proliferation and the JNK signaling pathway
Probab=41.22  E-value=23  Score=14.97  Aligned_cols=17  Identities=29%  Similarity=0.563  Sum_probs=12.8

Q ss_pred             CCCCHHHHHHHHHHHCC
Q ss_conf             64242345666774306
Q gi|254780901|r  290 SPITAENLGYMIGPSIN  306 (600)
Q Consensus       290 ~~i~~~di~f~iaPrIN  306 (600)
                      ++.++..++-.+||-|=
T Consensus       143 NkM~~~NLAivf~P~L~  159 (193)
T cd04382         143 CKMDINNLARVFGPTIV  159 (193)
T ss_pred             CCCCHHHHHHHCCCHHC
T ss_conf             35955155721131327


No 411
>TIGR02238 recomb_DMC1 meiotic recombinase Dmc1; InterPro: IPR011940    This entry describes DMC1, a subfamily of a larger family of DNA repair and recombination proteins. It is eukaryotic only and most closely related to eukaryotic RAD51. It also resembles archaeal RadA (IPR011938 from INTERPRO) and RadB (IPR011939 from INTERPRO) and bacterial RecA. It has been characterised for human as a recombinase active only in meiosis .; GO: 0003677 DNA binding, 0005524 ATP binding, 0008094 DNA-dependent ATPase activity, 0007131 meiotic recombination, 0005634 nucleus.
Probab=41.11  E-value=23  Score=14.95  Aligned_cols=14  Identities=29%  Similarity=0.536  Sum_probs=8.0

Q ss_pred             HHHHHHHHCEEEEE
Q ss_conf             89988420107998
Q gi|254780901|r  388 ARLKEKFGRPSFAI  401 (600)
Q Consensus       388 srL~e~y~kP~iv~  401 (600)
                      .||+|+||.-+++-
T Consensus       230 ~~~sEefNvAv~~T  243 (314)
T TIGR02238       230 NKLSEEFNVAVFVT  243 (314)
T ss_pred             HHHHHHHHHHHEEE
T ss_conf             76546640232001


No 412
>cd06341 PBP1_ABC_ligand_binding_like_7 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=41.00  E-value=23  Score=14.94  Aligned_cols=77  Identities=21%  Similarity=0.249  Sum_probs=29.3

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEEC--CCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHC
Q ss_conf             9999407886152899999999976994799807--87433668897898874202686899964887623455555417
Q gi|254780901|r   95 IMIFGDYDVDGAASVALMMRFLSHCSVNANMYIP--DRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQ  172 (600)
Q Consensus        95 I~I~gDyD~DGitstail~~~L~~~g~~v~~~IP--~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~  172 (600)
                      +.++.+.+.-|-.....+...++..|.++....+  .--.|   + ...+.+++..+++.|+++=.+-....-++.++++
T Consensus       136 ~~~~~~~~~~g~~~~~~~~~~~~~~G~~vv~~~~~~~~~~D---~-~~~v~~l~~~~pd~V~~~~~~~~~~~~~k~~~~~  211 (341)
T cd06341         136 VALVTALSAAVSAAAALLARSLAAAGVSVAGIVVITATAPD---P-TPQAQQAAAAGADAIITVLDAAVCASVLKAVRAA  211 (341)
T ss_pred             EEEEECCCHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCC---H-HHHHHHHHHCCCCEEEEECCCHHHHHHHHHHHHC
T ss_conf             99993583588999999999999759954578744899987---7-8999999856969999906847899999999976


Q ss_pred             CCC
Q ss_conf             982
Q gi|254780901|r  173 GID  175 (600)
Q Consensus       173 Gid  175 (600)
                      |++
T Consensus       212 G~~  214 (341)
T cd06341         212 GLT  214 (341)
T ss_pred             CCC
T ss_conf             999


No 413
>PRK00758 GMP synthase subunit A; Validated
Probab=40.73  E-value=23  Score=14.91  Aligned_cols=44  Identities=16%  Similarity=0.199  Sum_probs=29.9

Q ss_pred             EEEECCCCCCH-HHHHHHHHCCCCEEEECCCCCCCC---CCCCEEEECC
Q ss_conf             99964887623-455555417982799615447655---5672565237
Q gi|254780901|r  153 IITVDCGSTSY-DALQYATNQGIDVIVIDHHQVKSE---EIPAYALVNP  197 (600)
Q Consensus       153 iItvD~Gi~~~-e~i~~a~~~GidvIVtDHH~~~~~---~p~a~aivNP  197 (600)
                      |+.+|||.+-. --+.+++++|++|.|..+..+.++   .|++ .++-|
T Consensus         2 IlviD~~dsft~ni~~~l~~~g~~v~v~~~~~~~~~i~~~~dg-iilS~   49 (184)
T PRK00758          2 ILVINNGGQYNHLIHRTLRYLGVDAKIIPNTTPLEEIKAEPDG-IILSG   49 (184)
T ss_pred             EEEEECCCHHHHHHHHHHHHCCCEEEEEECCCCHHHHHHCCCE-EEECC
T ss_conf             9999898638999999999789928999598989999638998-99889


No 414
>cd01143 YvrC Periplasmic binding protein YvrC.  These proteins are predicted to function as initial receptors in ABC transport of metal ions in eubacteria and archaea.  They belong to the TroA superfamily of periplasmic metal binding proteins that share a distinct fold and ligand binding mechanism. A typical TroA protein is comprised of two globular subdomains connected by a single helix and can bind the metal ion in the cleft between these domains.
Probab=40.71  E-value=23  Score=14.91  Aligned_cols=37  Identities=27%  Similarity=0.428  Sum_probs=22.6

Q ss_pred             HHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEEC
Q ss_conf             887420268689996488762345555541798279961
Q gi|254780901|r  142 MEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVID  180 (600)
Q Consensus       142 i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtD  180 (600)
                      +|.+..-.++|||+..  ....+.++.+.+.|+.|++++
T Consensus        53 ~E~i~~l~PDLVi~~~--~~~~~~~~~L~~~gi~v~~~~   89 (195)
T cd01143          53 VEKIVALKPDLVIVSS--SSLAELLEKLKDAGIPVVVLP   89 (195)
T ss_pred             HHHHHCCCCCEEEEEC--CCCHHHHHHHHHCCCEEEEEC
T ss_conf             9999616999999827--874779999864188599975


No 415
>PRK13958 N-(5'-phosphoribosyl)anthranilate isomerase; Provisional
Probab=40.64  E-value=19  Score=15.60  Aligned_cols=20  Identities=40%  Similarity=0.556  Sum_probs=16.8

Q ss_pred             CCCCCHHHHHHHHHCCCCEE
Q ss_conf             88762345555541798279
Q gi|254780901|r  158 CGSTSYDALQYATNQGIDVI  177 (600)
Q Consensus       158 ~Gi~~~e~i~~a~~~GidvI  177 (600)
                      ||+++.+.+..|.++|.|-|
T Consensus         6 CGit~~eda~~a~~~gaD~i   25 (207)
T PRK13958          6 CGFTSIKDVTAASQLPIDAI   25 (207)
T ss_pred             ECCCCHHHHHHHHHCCCCEE
T ss_conf             18997999999996899999


No 416
>PRK05742 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=40.61  E-value=16  Score=16.20  Aligned_cols=14  Identities=21%  Similarity=0.271  Sum_probs=9.6

Q ss_pred             CCCCCHHHHHHHHC
Q ss_conf             68874357898708
Q gi|254780901|r  274 QGNPGLKALIERVN  287 (600)
Q Consensus       274 ~~~~gl~~L~~~~~  287 (600)
                      ...||+|.|.+.+=
T Consensus       134 KT~PGlR~lek~AV  147 (277)
T PRK05742        134 KTLPGLRLAQKYAV  147 (277)
T ss_pred             CCCCCHHHHHHHHH
T ss_conf             87852799999999


No 417
>PRK12480 D-lactate dehydrogenase; Provisional
Probab=40.59  E-value=24  Score=14.90  Aligned_cols=51  Identities=14%  Similarity=0.139  Sum_probs=32.1

Q ss_pred             CCEEEEECCCCCHHHHHHHHHHHHHHHHCEEEEEEECCCCEEEEEEECCCCCCHHHHHH
Q ss_conf             75026205785812222227899884201079988637983799986489861888888
Q gi|254780901|r  368 ASVIVVEGDRWHPGIVGLLAARLKEKFGRPSFAISFEEDGKGIGSGRSIEGFDIGKMVS  426 (600)
Q Consensus       368 ~~~ivv~~~~wh~GViGIVAsrL~e~y~kP~iv~s~~~dg~~kGS~RSi~g~~l~~~l~  426 (600)
                      ..+|.+.-|- .+.--++|-...-.+.++-++++..     ++|+.  ++.-+|.++|+
T Consensus       199 sDiIslh~Pl-t~~T~~lIn~~~l~~MK~~ailINt-----aRG~i--Vde~aL~~AL~  249 (330)
T PRK12480        199 ADIISLHVPA-NKESYHLFDKAMFDHVKKGAILVNA-----ARGAV--INTPDLIAAVN  249 (330)
T ss_pred             CCEEEECCCC-CHHHHCCHHHHHHHHCCCCCEEEEC-----CCCCC--CCHHHHHHHHH
T ss_conf             9999973768-5331200489999757999769972-----78633--19999999997


No 418
>PRK01222 N-(5'-phosphoribosyl)anthranilate isomerase; Provisional
Probab=40.52  E-value=19  Score=15.62  Aligned_cols=20  Identities=35%  Similarity=0.549  Sum_probs=16.7

Q ss_pred             CCCCCHHHHHHHHHCCCCEE
Q ss_conf             88762345555541798279
Q gi|254780901|r  158 CGSTSYDALQYATNQGIDVI  177 (600)
Q Consensus       158 ~Gi~~~e~i~~a~~~GidvI  177 (600)
                      ||+++.+.++++.++|.|-+
T Consensus         8 CGit~~eda~~~~~~gad~i   27 (212)
T PRK01222          8 CGITTPEDALAAAEAGADAI   27 (212)
T ss_pred             ECCCCHHHHHHHHHCCCCEE
T ss_conf             18995999999995799989


No 419
>PRK10524 prpE propionyl-CoA synthetase; Provisional
Probab=40.34  E-value=24  Score=14.87  Aligned_cols=101  Identities=16%  Similarity=0.285  Sum_probs=51.9

Q ss_pred             HCCCHHHHHHHHHHHH-----HCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHC
Q ss_conf             6148799999999999-----77997999940788615289999999997699479980787433668897898874202
Q gi|254780901|r   74 ILTDCDKAARRIVQAI-----YNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINE  148 (600)
Q Consensus        74 ~l~dm~~A~~ri~~ai-----~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~  148 (600)
                      .+.++.+-++|+..++     +.+.+|+||-    .-.--+.+.+.+..++|+-....     .-+|+. .+....+...
T Consensus        86 TY~eL~~~v~rlA~~L~~~GV~~GDrVai~l----pn~~E~via~lA~~kiGAv~vpv-----~~~~~~-~~l~~rl~~~  155 (629)
T PRK10524         86 TFRQLHDEVNRMAAMLRSLGVQRGDRVLIYM----PMIAEAAFAMLACARIGAIHSVV-----FGGFAS-HSLAARIDDA  155 (629)
T ss_pred             EHHHHHHHHHHHHHHHHHCCCCCCCEEEEEC----CCHHHHHHHHHHHHHHCEEEECC-----CCCCCH-HHHHHHHHCC
T ss_conf             7999999999999999974959999999985----88499999999999969599732-----777767-8899987322


Q ss_pred             CCCEEEEECCCCCCHH----------HHHHHHHCCCCEEEECCCCC
Q ss_conf             6868999648876234----------55555417982799615447
Q gi|254780901|r  149 GAQLIITVDCGSTSYD----------ALQYATNQGIDVIVIDHHQV  184 (600)
Q Consensus       149 g~~LiItvD~Gi~~~e----------~i~~a~~~GidvIVtDHH~~  184 (600)
                      +++++||.|.+.....          .+..+....-.|++.|....
T Consensus       156 ~pk~lit~d~~~~~gk~v~~~~~l~~~~~~~~~~~~~vi~~~~~~~  201 (629)
T PRK10524        156 KPKLIVSADAGARGGKVVPYKPLLDEAIAQAQHKPEHVLLVDRGLA  201 (629)
T ss_pred             CCEEEECCCHHHHCCCCCCCHHHHHHHHHHCCCCCCEEEEECCCCC
T ss_conf             4145521301210375332167899999752578747999747777


No 420
>PRK09418 bifunctional 2',3'-cyclic nucleotide 2'-phosphodiesterase/3'-nucleotidase precursor protein; Reviewed
Probab=40.29  E-value=24  Score=14.86  Aligned_cols=68  Identities=16%  Similarity=0.244  Sum_probs=39.5

Q ss_pred             CCHHHHHHHHHHHHHCCCCEEEE-----------ECCCC-------CHHHH--HHHHHHHHHHCCCCEEEEECCCCCCCC
Q ss_conf             48799999999999779979999-----------40788-------61528--999999999769947998078743366
Q gi|254780901|r   76 TDCDKAARRIVQAIYNSEKIMIF-----------GDYDV-------DGAAS--VALMMRFLSHCSVNANMYIPDRIVDGY  135 (600)
Q Consensus        76 ~dm~~A~~ri~~ai~~~ekI~I~-----------gDyD~-------DGits--tail~~~L~~~g~~v~~~IP~R~~eGY  135 (600)
                      -++.+.+..|.++..+....+++           |||-+       +|+..  +-=|+.++..+|.++-..=-|-|.  |
T Consensus        66 ~GLar~ATLIk~aRaE~~NslLvDNGD~IQGtPlgdy~A~~~~~~~~~~~~g~~HPmi~AMN~LgYDA~tLGNHEFN--Y  143 (780)
T PRK09418         66 VGLVQTATLVNKAREEAKNSVLFDDGDALQGTPLGDYVANKINDPKKPVDPSYTHPLYRLMNLMKYDVISLGNHEFN--Y  143 (780)
T ss_pred             CCHHHHHHHHHHHHHHCCCEEEEECCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHCCCCEECCCCCCCC--C
T ss_conf             67999999999999648982999687301587078999763234446777777688999987539877514465543--6


Q ss_pred             CCCHHHHHHHHH
Q ss_conf             889789887420
Q gi|254780901|r  136 GPNPSLMEKFIN  147 (600)
Q Consensus       136 Gl~~~~i~~~~~  147 (600)
                      ||  +.+++...
T Consensus       144 GL--d~L~k~l~  153 (780)
T PRK09418        144 GL--DYLNKVIS  153 (780)
T ss_pred             CH--HHHHHHHH
T ss_conf             88--99999985


No 421
>PRK08979 acetolactate synthase 3 catalytic subunit; Validated
Probab=40.14  E-value=24  Score=14.85  Aligned_cols=76  Identities=13%  Similarity=0.131  Sum_probs=38.2

Q ss_pred             HHHHHHHHHHCCCC-EEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCC--CCCC-------CCCCHH-HHHHHHHCC
Q ss_conf             99999999977997-999940788615289999999997699479980787--4336-------688978-988742026
Q gi|254780901|r   81 AARRIVQAIYNSEK-IMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDR--IVDG-------YGPNPS-LMEKFINEG  149 (600)
Q Consensus        81 A~~ri~~ai~~~ek-I~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R--~~eG-------YGl~~~-~i~~~~~~g  149 (600)
                      .+++..+.+.+-++ +.+.| .-+-.--+..-+.++...+|+.|..-...|  +.+.       +|+... ....+. ++
T Consensus       195 ~i~~a~~~L~~A~rPvil~G-~g~~~~~a~~~l~~lae~lg~PV~tt~~gkg~~p~~hp~~~G~~G~~g~~~a~~~~-~~  272 (572)
T PRK08979        195 QIRRGLQALLAAKKPVLYVG-GGAIISGCDKQILALAEKLNIPVVSTLMGLGAFPGTHKNSLGMLGMHGRYEANMAM-HN  272 (572)
T ss_pred             HHHHHHHHHHHCCCCEEEEC-CCCCCCCHHHHHHHHHHHHCCCEEECCCCCCCCCCCCCCCCCCCCCCCCHHHHHHH-HH
T ss_conf             99999999982799889978-75353568999999998639975522026789998886556778777769999998-41


Q ss_pred             CCEEEEECC
Q ss_conf             868999648
Q gi|254780901|r  150 AQLIITVDC  158 (600)
Q Consensus       150 ~~LiItvD~  158 (600)
                      +||||.+-+
T Consensus       273 aDlvl~lG~  281 (572)
T PRK08979        273 ADLIFGIGV  281 (572)
T ss_pred             CCEEEEECC
T ss_conf             878998256


No 422
>pfam04223 CitF Citrate lyase, alpha subunit (CitF). In citrate-utilising prokaryotes, citrate lyase EC:4.1.3.6 cleaves intracellular citrate into acetate and oxaloacetate, and is organized as a functional complex consisting of alpha, beta, and gamma subunits. The gamma subunit serves as an acyl carrier protein (ACP), and has a 2'-(5''-phosphoribosyl)-3'-dephospho-CoA prosthetic group. The citrate lyase is active only if this prosthetic group is acetylated; this acetylation is catalysed by an acetate:SH-citrate lyase ligase. The alpha subunit substitutes citryl for the acetyl group to form citryl-S-ACP. The beta subunit completes the reaction by cleaving the citryl to yield oxaloacetate and (regenerated) acetyl-S-ACP. This family represents the alpha subunit EC:2.8.3.10.
Probab=40.06  E-value=11  Score=17.39  Aligned_cols=132  Identities=15%  Similarity=0.159  Sum_probs=66.2

Q ss_pred             HHHHHHHHHHHHHCEEEEEEECCCCEEEEEEECCC-CCCHHHHHHHHCCCCCCCCCCCCCC-CCCEEECCCCHHHHHHHH
Q ss_conf             22227899884201079988637983799986489-8618888885303353011565322-231464222158899999
Q gi|254780901|r  383 VGLLAARLKEKFGRPSFAISFEEDGKGIGSGRSIE-GFDIGKMVSFAVEEGILVKGGGHAM-AAGLTVERVNFGRLCDFF  460 (600)
Q Consensus       383 iGIVAsrL~e~y~kP~iv~s~~~dg~~kGS~RSi~-g~~l~~~l~~~~~~~ll~~~GGH~~-AaG~ti~~~~l~~f~~~l  460 (600)
                      +-|-||.-+.-++|-++|=..  | ...-|+--++ +||.. .+. -++--+.-.-|||+- |||-.+..---+.++.++
T Consensus       302 ~eisas~YAnP~~kga~vn~L--D-vviL~AlEiD~~FNVN-V~T-gSdGvi~GasGGH~DTAagAkltIivaPL~rgRi  376 (466)
T pfam04223       302 IEIDANQYANPSSKGASVDRL--D-VVILSALEIDTKFNVN-VMT-GSDGVIRGASGGHCDTAAAAKLSIIVAPLVRGRI  376 (466)
T ss_pred             EEECHHHHCCCCCCCCEECCC--C-EEEEEEEEEECCCCEE-EEE-CCCCEECCCCCCCCHHHHHCCCEEEEEHHHCCCC
T ss_conf             488677715888888540224--5-7998613640576226-887-8986581687888344652674799704444888


Q ss_pred             HHHHHHHC---CHHHCCCCEEEEEEECHHHCCHHHHHHHHHCCCCCCCCCCCEEEECCEEEEEEEEECC
Q ss_conf             99998622---6443377147604434689799999999851846789998468427809988888479
Q gi|254780901|r  461 QKFAHNIV---PALITTPVFKIDGVLNASAVNIALIDMLESAGPYGAGNPNPVFAFPNHKLQSIRVVNL  526 (600)
Q Consensus       461 ~~~~~~~~---~~~~~~~~l~iD~el~~~~i~~~l~~~L~~lePFG~gNpeP~F~~~~~~i~~~r~vGk  526 (600)
                      -..+.+..   +.-.....+..|.-+..+-...+|++.|+..       .-|++-++.++=.-.++.|+
T Consensus       377 p~ivd~Vttv~TPGetVDVvVTe~GIAVNP~R~dL~e~l~~a-------~lp~~~IeeL~~~A~~i~G~  438 (466)
T pfam04223       377 PTVVDKVTTVITPGSSVDVLVTEHGIAINPNRPDLIERLSEA-------PLPVVTIEELQERAYLITGK  438 (466)
T ss_pred             CEEECCEEEECCCCCCEEEEEECCCEEECCCCHHHHHHHHHC-------CCCEEEHHHHHHHHHHHCCC
T ss_conf             878677137868998154899237466588988999999858-------99853599999999985399


No 423
>PRK07710 acetolactate synthase catalytic subunit; Reviewed
Probab=39.95  E-value=24  Score=14.83  Aligned_cols=79  Identities=19%  Similarity=0.236  Sum_probs=47.8

Q ss_pred             HHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEE------CCC--CCCC-CCCCHH-HHHHHHHCC
Q ss_conf             999999999977997999940788615289999999997699479980------787--4336-688978-988742026
Q gi|254780901|r   80 KAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYI------PDR--IVDG-YGPNPS-LMEKFINEG  149 (600)
Q Consensus        80 ~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~I------P~R--~~eG-YGl~~~-~i~~~~~~g  149 (600)
                      ..++++.+++.+-++.+|+...-+.---+..-|.++...+|+-|..-.      |+.  +.-| +|+... ....+.+ .
T Consensus       203 ~~i~~~~~~L~~AkrPvIl~G~g~~~~~a~~~l~~lae~~~~Pv~tt~~gkg~~~~~hpl~~G~~g~~g~~~a~~~~~-~  281 (571)
T PRK07710        203 LQIRKLVEAISVAKKPLILAGAGVLHAKASKELTSFARQYEIPVVHTLLGLGGFPADDELFLGMGGMHGSYTANMALY-E  281 (571)
T ss_pred             HHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCCCCCCCCCCCCHHHHHHHH-C
T ss_conf             999999999971899789986884625699999999998789999824557878999966588777667689999973-6


Q ss_pred             CCEEEEECCC
Q ss_conf             8689996488
Q gi|254780901|r  150 AQLIITVDCG  159 (600)
Q Consensus       150 ~~LiItvD~G  159 (600)
                      ++|||.+.|-
T Consensus       282 aDlvl~lG~~  291 (571)
T PRK07710        282 CDLLINIGAR  291 (571)
T ss_pred             CCEEEEECCC
T ss_conf             9879993565


No 424
>TIGR01241 FtsH_fam ATP-dependent metallopeptidase HflB; InterPro: IPR005936   Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases .   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.    This group of metallopeptidases belong to MEROPS peptidase family M41 (FtsH endopeptidase family, clan MA(E)). The predicted active site residues for members of this family and thermolysin, the type example for clan MA, occur in the motif HEXXH.    FtsH is a membrane-anchored ATP-dependent protease that degrades misfolded or misassembled membrane proteins as well as a subset of cytoplasmic regulatory proteins. FtsH is a 647-residue protein of 70 kDa, with two putative transmembrane segments towards its N terminus which anchor the protein to the membrane, giving rise to a periplasmic domain of 70 residues and a cytoplasmic segment of 520 residues containing the ATPase and protease domains . ; GO: 0004222 metalloendopeptidase activity, 0030163 protein catabolic process, 0016020 membrane.
Probab=39.65  E-value=13  Score=17.03  Aligned_cols=16  Identities=38%  Similarity=0.465  Sum_probs=8.6

Q ss_pred             HHHHHHHCCCCEEEEEC
Q ss_conf             98874202686899964
Q gi|254780901|r  141 LMEKFINEGAQLIITVD  157 (600)
Q Consensus       141 ~i~~~~~~g~~LiItvD  157 (600)
                      ++++++++ .--||+.|
T Consensus       143 LFeqAK~n-APCIIFID  158 (505)
T TIGR01241       143 LFEQAKKN-APCIIFID  158 (505)
T ss_pred             HHHHHHHH-CCCEEEEE
T ss_conf             57999971-89705640


No 425
>cd06355 PBP1_FmdD_like Periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF). This group includes the periplasmic component (FmdD) of an active transport system for short-chain amides and urea (FmdDEF), found in Methylophilus methylotrophus, and its homologs from other bacteria. FmdD, a type I periplasmic binding protein, is induced by short-chain amides and urea and repressed by excess ammonia, while FmdE and FmdF are hydrophobic transmembrane proteins. FmdDEF is predicted to be an ATP-dependent transporter and closely resembles the periplasmic binding protein and the two transmembrane proteins present in various hydrophobic amino acid-binding transport systems.
Probab=39.61  E-value=24  Score=14.79  Aligned_cols=10  Identities=20%  Similarity=-0.170  Sum_probs=3.7

Q ss_pred             CHHHHHHHHH
Q ss_conf             8799999999
Q gi|254780901|r   77 DCDKAARRIV   86 (600)
Q Consensus        77 dm~~A~~ri~   86 (600)
                      +++-|++.|.
T Consensus        22 g~~lAveeiN   31 (348)
T cd06355          22 AELLAIEEIN   31 (348)
T ss_pred             HHHHHHHHHH
T ss_conf             9999999998


No 426
>cd06360 PBP1_alkylbenzenes_like Type I periplasmic binding component of active transport systems that are predicted be involved in anaerobic biodegradation of alkylbenzenes such as toluene and ethylbenzene. This group includes the type I periplasmic binding component of active transport systems that are predicted be involved in anaerobic biodegradation of alkylbenzenes such as toluene and ethylbenzene; their substrate specificity is not well characterized, however.
Probab=39.59  E-value=24  Score=14.79  Aligned_cols=36  Identities=11%  Similarity=0.249  Sum_probs=17.8

Q ss_pred             HHHHHH-CCCCEEEEECCCCCCHHHHHHHHHCCCCEE
Q ss_conf             887420-268689996488762345555541798279
Q gi|254780901|r  142 MEKFIN-EGAQLIITVDCGSTSYDALQYATNQGIDVI  177 (600)
Q Consensus       142 i~~~~~-~g~~LiItvD~Gi~~~e~i~~a~~~GidvI  177 (600)
                      ++++.+ +++..||-.-+...+......+.+.|+-+|
T Consensus        57 a~~Li~~d~V~aiiG~~~S~~~~a~~~~~~~~~vp~i   93 (336)
T cd06360          57 ARKLIEQDKVDVVVGPVHSGEALAMVKVLREPGTPLI   93 (336)
T ss_pred             HHHHHHCCCCEEEECCCCCHHHHHHHHHHHHCCCEEE
T ss_conf             9999854996388557670765533399985095343


No 427
>cd01967 Nitrogenase_MoFe_alpha_like Nitrogenase_MoFe_alpha_like: Nitrogenase MoFe protein, alpha subunit_like. The nitrogenase enzyme catalyzes the ATP-dependent reduction of dinitrogen to ammonia.  Three genetically distinct types of nitrogenase systems are known to exist: a molybdenum-dependent  nitrogenase (Mo-nitrogenase), a vanadium dependent nitrogenase (V-nitrogenase), and an iron-only nitrogenase (Fe-nitrogenase). These nitrogenase systems consist of component 1 (MoFe protein, VFe protein or, FeFe protein respectively) and, component 2 (Fe protein). This group contains the alpha subunit of component 1 of all three different forms. The most widespread and best characterized of these systems is the Mo-nitrogenase. MoFe is an alpha2beta2 tetramer, the alternative nitrogenases are alpha2beta2delta2 hexamers having  alpha and beta subunits similar to the alpha and beta subunits of MoFe.  The role of the delta subunit is unknown. For MoFe, each alphabeta pair of subunits contains one
Probab=39.55  E-value=24  Score=14.78  Aligned_cols=25  Identities=16%  Similarity=0.248  Sum_probs=14.7

Q ss_pred             HCCCHHHHHHHHHHHHHCCCC--EEEE
Q ss_conf             614879999999999977997--9999
Q gi|254780901|r   74 ILTDCDKAARRIVQAIYNSEK--IMIF   98 (600)
Q Consensus        74 ~l~dm~~A~~ri~~ai~~~ek--I~I~   98 (600)
                      -|-+.++-.+-|.+++++-++  |.|+
T Consensus        68 VfGg~~~L~~~i~~~~~~~~P~~i~V~   94 (406)
T cd01967          68 VFGGEKKLKKAIKEAYERFPPKAIFVY   94 (406)
T ss_pred             CCCCHHHHHHHHHHHHHHCCCCEEEEE
T ss_conf             048099999999999985699789997


No 428
>cd03796 GT1_PIG-A_like This family is most closely related to the GT1 family of glycosyltransferases. Phosphatidylinositol glycan-class A (PIG-A), an X-linked gene in humans, is necessary for the synthesis of N-acetylglucosaminyl-phosphatidylinositol, a very early intermediate in glycosyl phosphatidylinositol (GPI)-anchor biosynthesis. The GPI-anchor is an important cellular structure that facilitates the attachment of many proteins to cell surfaces. Somatic mutations in PIG-A have been associated with Paroxysmal Nocturnal Hemoglobinuria (PNH), an acquired hematological disorder.
Probab=39.53  E-value=24  Score=14.78  Aligned_cols=99  Identities=19%  Similarity=0.326  Sum_probs=50.7

Q ss_pred             CCCHHHHHHHHHHHH-HCCCCEEEEEC-CC-CCHHHHHHHHHHHHHHCCCCEEEEECCCCCCC---CC---CCHHHHHH-
Q ss_conf             148799999999999-77997999940-78-86152899999999976994799807874336---68---89789887-
Q gi|254780901|r   75 LTDCDKAARRIVQAI-YNSEKIMIFGD-YD-VDGAASVALMMRFLSHCSVNANMYIPDRIVDG---YG---PNPSLMEK-  144 (600)
Q Consensus        75 l~dm~~A~~ri~~ai-~~~ekI~I~gD-yD-~DGitstail~~~L~~~g~~v~~~IP~R~~eG---YG---l~~~~i~~-  144 (600)
                      +-+++..+..+.+++ +.+-.+.|+.. |+ ..|+       +.+ .-|.+| |++|.+-.-.   +.   .+...+.. 
T Consensus        13 iGG~e~~v~~La~~L~~~Gh~V~Vit~~~~~~~~~-------~~~-~~g~~V-~~~p~~~~~~~~~~~~~~~~~~~~r~~   83 (398)
T cd03796          13 LGGVETHIYQLSQCLIKRGHKVVVITHAYGNRVGI-------RYL-TNGLKV-YYLPFVVFYNQSTLPTFFGTFPLLRNI   83 (398)
T ss_pred             CCCHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCC-------EEE-CCCCEE-EECCCCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             99779999999999997699899996899988774-------685-388469-975663345631167798889999999


Q ss_pred             HHHCCCCEEEEECCCCC-CHHHHHHHHHCCCCEEEECCC
Q ss_conf             42026868999648876-234555554179827996154
Q gi|254780901|r  145 FINEGAQLIITVDCGST-SYDALQYATNQGIDVIVIDHH  182 (600)
Q Consensus       145 ~~~~g~~LiItvD~Gi~-~~e~i~~a~~~GidvIVtDHH  182 (600)
                      +...++++|-+-...+. +...+-.++..|+.++.|+|.
T Consensus        84 ~~~~~~DIIH~H~~~~~l~~~~~~~ar~~g~~~V~T~H~  122 (398)
T cd03796          84 LIRERITIVHGHQAFSALAHEALLHARTMGLKTVFTDHS  122 (398)
T ss_pred             HHHCCCCEEEECCHHHHHHHHHHHHHHHCCCCEEEEECC
T ss_conf             976799889989626889999999987559978998344


No 429
>TIGR02169 SMC_prok_A chromosome segregation protein SMC; InterPro: IPR011891   The SMC (structural maintenance of chromosomes) family of proteins, exist in virtually all organisms including both bacteria and archaea. The SMC proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms and form three types of heterodimer (SMC1SMC3, SMC2SMC4, SMC5SMC6), which are core components of large multiprotein complexes. The best known complexes are cohesin, which is responsible for sister-chromatid cohesion, and condensin, which is required for full chromosome condensation in mitosis.     SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and share a five-domain structure, with globular N- and C-terminal (IPR003395 from INTERPRO) domains separated by a long (circa 100 nm or 900 residues) coiled coil segment in the centre of which is a globular ''hinge'' domain, characterised by a set of four highly conserved glycine residues that are typical of flexible regions in a protein. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T), 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 (XXXXD, where X is any hydrophobic residue), and a LSGG motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases .    All SMC proteins appear to form dimers, either forming homodimers with themselves, as in the case of prokaryotic SMC proteins, or heterodimers between different but related SMC proteins. The dimers are arranged in an antiparallel alignment. This orientation brings the N- and C-terminal globular domains (from either different or identical protamers) together, which unites an ATP binding site (Walker A motif) within the N-terminal domain with a Walker B motif (DA box) within the C-terminal domain, to form a potentially functional ATPase. Protein interaction and microscopy data suggest that SMC dimers form a ring-like structure which might embrace DNA molecules. Non-SMC subunits associate with the SMC amino- and carboxy-terminal domains. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences.   SMCs share not only sequence similarity but also structural similarity with ABC proteins. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression .    This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by IPR011890 from INTERPRO. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent ..
Probab=39.50  E-value=24  Score=14.78  Aligned_cols=62  Identities=23%  Similarity=0.340  Sum_probs=47.7

Q ss_pred             CHHHCCHHHHHHHHHCCCCCCC-----CCCCEEEECCEEEEEEEEECCCEEEEEEECCCCCEEEEEEEC
Q ss_conf             4689799999999851846789-----998468427809988888479649999984998779999977
Q gi|254780901|r  484 NASAVNIALIDMLESAGPYGAG-----NPNPVFAFPNHKLQSIRVVNLAHLQMTFESQDSETLQAIAFR  547 (600)
Q Consensus       484 ~~~~i~~~l~~~L~~lePFG~g-----NpeP~F~~~~~~i~~~r~vGk~Hlkl~l~~~~g~~i~aI~Fn  547 (600)
                      .+..||..|-.-...|.|=|.|     ||+==|. -++.+ .+++-||.=.|+-=.++|-+++-|++|=
T Consensus      1060 aF~~IN~~f~~iF~~LSP~G~g~L~Le~PdDPF~-GGl~l-~a~P~~K~vqrleAMSGGEKSLtALsFI 1126 (1202)
T TIGR02169      1060 AFEAINENFKEIFAELSPGGTGELILENPDDPFA-GGLEL-KAKPKGKPVQRLEAMSGGEKSLTALSFI 1126 (1202)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCC-CCCEE-EEEECCCCEEEHHHCCCCHHHHHHHHHH
T ss_conf             9999999999999853889824654358887436-87178-8873788502022103838999999999


No 430
>PRK12843 putative FAD-binding dehydrogenase; Reviewed
Probab=39.34  E-value=23  Score=15.05  Aligned_cols=86  Identities=9%  Similarity=0.051  Sum_probs=37.4

Q ss_pred             ECCCCHHHHHHHHHHHHHHHCCHHHCCC-CEEEEEEEC--HHHCCHHHHHHHHHCCCCCCCCCCCEEEECCEEEEEEEEE
Q ss_conf             4222158899999999986226443377-147604434--6897999999998518467899984684278099888884
Q gi|254780901|r  448 VERVNFGRLCDFFQKFAHNIVPALITTP-VFKIDGVLN--ASAVNIALIDMLESAGPYGAGNPNPVFAFPNHKLQSIRVV  524 (600)
Q Consensus       448 i~~~~l~~f~~~l~~~~~~~~~~~~~~~-~l~iD~el~--~~~i~~~l~~~L~~lePFG~gNpeP~F~~~~~~i~~~r~v  524 (600)
                      ++.+.|.+=.++.|+++..-. +.++.+ ...++--..  ....++       .|.|.-   .-|.+.++ +...-.-++
T Consensus       441 id~~~L~~TV~ryN~~~~~G~-D~dFgk~~~~~~~~~g~~~~~~~p-------~L~pI~---~~PfYA~~-~~p~~~~T~  508 (576)
T PRK12843        441 IDPAALAATVQRHNQSARTGI-DPDFGRGATAYSRMNGDAMIGPNP-------NLGPIE---TAPFYAVR-LYPGDIGAA  508 (576)
T ss_pred             CCHHHHHHHHHHHHHHHHCCC-CCCCCCCCCCHHCCCCCCCCCCCC-------CCCCCC---CCCEEEEE-EECCCCCCC
T ss_conf             699999999999998875299-966587743010235664457785-------647366---79969999-861204537


Q ss_pred             CCC--EEEEEEECCCCCEEEEEE
Q ss_conf             796--499999849987799999
Q gi|254780901|r  525 NLA--HLQMTFESQDSETLQAIA  545 (600)
Q Consensus       525 Gk~--Hlkl~l~~~~g~~i~aI~  545 (600)
                      |+=  -.++.+.+.+|+.|++++
T Consensus       509 GGl~id~~~qVLd~dg~pIpGLY  531 (576)
T PRK12843        509 TGLVTDADARVLNADGQPISGLY  531 (576)
T ss_pred             CCEEECCCCCEECCCCCEECCEE
T ss_conf             78108998744899988829975


No 431
>PRK06559 nicotinate-nucleotide pyrophosphorylase; Provisional
Probab=39.17  E-value=20  Score=15.38  Aligned_cols=13  Identities=15%  Similarity=0.245  Sum_probs=9.4

Q ss_pred             CCCCHHHHHHHHC
Q ss_conf             8874357898708
Q gi|254780901|r  275 GNPGLKALIERVN  287 (600)
Q Consensus       275 ~~~gl~~L~~~~~  287 (600)
                      .-||+|.|.+.+=
T Consensus       142 T~PGlR~l~kyAV  154 (290)
T PRK06559        142 TTPNLRLFEKYAV  154 (290)
T ss_pred             CCCCCHHHHHHHH
T ss_conf             8855079999999


No 432
>PRK09484 3-deoxy-D-manno-octulosonate 8-phosphate phosphatase; Provisional
Probab=39.11  E-value=25  Score=14.73  Aligned_cols=76  Identities=25%  Similarity=0.379  Sum_probs=37.2

Q ss_pred             CCCCEEEEECCCCCHH-HHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHH
Q ss_conf             7997999940788615-289999999997699479980787433668897898874202686899964887623455555
Q gi|254780901|r   91 NSEKIMIFGDYDVDGA-ASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYA  169 (600)
Q Consensus        91 ~~ekI~I~gDyD~DGi-tstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a  169 (600)
                      ++=|.+|+   |+||+ |-..+.+   ..-|-+...|  | ..||+|+     ..+.+.|..+.|.-  |-++.--..++
T Consensus        22 ~~IKl~i~---DvDGVLTDG~i~~---~~~G~e~k~f--~-~~DG~gi-----~~l~~~Gi~v~iIS--g~~s~~v~~Ra   85 (186)
T PRK09484         22 ENIKLLIC---DVDGVFSDGLIYM---GNNGEELKAF--N-TRDGYGI-----RCLLTSGIEVAIIT--GRKSKIVEDRM   85 (186)
T ss_pred             HCCCEEEE---CCEECEECCCEEE---CCCCCEEEEE--E-CCHHHHH-----HHHHHCCCEEEEEE--CCCCHHHHHHH
T ss_conf             68989998---4716407890898---7999799999--7-5275999-----99998799699994--78888999999


Q ss_pred             HHCCCCEEEECCC
Q ss_conf             4179827996154
Q gi|254780901|r  170 TNQGIDVIVIDHH  182 (600)
Q Consensus       170 ~~~GidvIVtDHH  182 (600)
                      +++||+.+..-.+
T Consensus        86 ~~Lgi~~~~~g~~   98 (186)
T PRK09484         86 TTLGITHIYQGQS   98 (186)
T ss_pred             HHHCCCEEEECHH
T ss_conf             9618988993707


No 433
>PRK06388 amidophosphoribosyltransferase; Provisional
Probab=38.99  E-value=25  Score=14.72  Aligned_cols=38  Identities=16%  Similarity=0.086  Sum_probs=23.5

Q ss_pred             CCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCC
Q ss_conf             799799994078861528999999999769947998078743366889
Q gi|254780901|r   91 NSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPN  138 (600)
Q Consensus        91 ~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~  138 (600)
                      -+|.=.|+|=|..  -.+...++..|..+        -||-+|+.|+.
T Consensus        16 ~~eeCGI~Gi~~~--~~~~~~~~~gL~aL--------QHRGQESaGIa   53 (474)
T PRK06388         16 PSEDCAVVGFKGG--INAYSPIITALRTL--------QHRGQESAGMA   53 (474)
T ss_pred             CCCCCEEEEEECC--CCHHHHHHHHHHHH--------HHCCHHHCEEE
T ss_conf             3757638999898--44899999999997--------72354244799


No 434
>pfam01497 Peripla_BP_2 Periplasmic binding protein. This family includes bacterial periplasmic binding proteins. Several of which are involved in iron transport.
Probab=38.88  E-value=25  Score=14.71  Aligned_cols=38  Identities=21%  Similarity=0.198  Sum_probs=24.5

Q ss_pred             HHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEEC
Q ss_conf             887420268689996488762345555541798279961
Q gi|254780901|r  142 MEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVID  180 (600)
Q Consensus       142 i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtD  180 (600)
                      +|.+..-.++|||+ +.+....+......+.|+.|++.|
T Consensus        53 ~E~i~~l~PDlVi~-~~~~~~~~~~~~~~~~gipvv~~~   90 (236)
T pfam01497        53 VEKLAALKPDLIIG-SAGIGLTDKAYELLSLIIPTVIFE   90 (236)
T ss_pred             HHHHHHCCCCEEEE-ECCCCCHHHHHHHHHCCCCEEEEC
T ss_conf             99997159998997-267673689999995799789942


No 435
>pfam00697 PRAI N-(5'phosphoribosyl)anthranilate (PRA) isomerase.
Probab=38.74  E-value=23  Score=15.05  Aligned_cols=22  Identities=27%  Similarity=0.472  Sum_probs=17.0

Q ss_pred             CCCCCHHHHHHHHHCCCCEEEE
Q ss_conf             8876234555554179827996
Q gi|254780901|r  158 CGSTSYDALQYATNQGIDVIVI  179 (600)
Q Consensus       158 ~Gi~~~e~i~~a~~~GidvIVt  179 (600)
                      ||+++.+.+.++.++|.|-|=.
T Consensus         4 CGit~~ed~~~~~~~gad~iGf   25 (195)
T pfam00697         4 CGLTRIEDVVAAVPAGADYLGL   25 (195)
T ss_pred             CCCCCHHHHHHHHHCCCCEEEE
T ss_conf             8889799999999589999988


No 436
>PRK00014 ribB 3,4-dihydroxy-2-butanone 4-phosphate synthase; Provisional
Probab=38.60  E-value=25  Score=14.68  Aligned_cols=35  Identities=17%  Similarity=0.415  Sum_probs=23.1

Q ss_pred             HHCCCCHHHCCCHHHHHHHHHHHHHCCCCEEEEECCCCCH
Q ss_conf             7718995561487999999999997799799994078861
Q gi|254780901|r   66 RLLMPDPLILTDCDKAARRIVQAIYNSEKIMIFGDYDVDG  105 (600)
Q Consensus        66 ~~l~~dP~~l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DG  105 (600)
                      +.+..+|+.     --++.-.+++++++.|.|+-|.|=.+
T Consensus        10 ~~~~~~~~~-----s~Ie~AI~alr~Gk~VIv~DdedREn   44 (230)
T PRK00014         10 SPLFAQPFA-----TRLERALQHLRIGRPVILMDDFDREN   44 (230)
T ss_pred             CCCCCCCCH-----HHHHHHHHHHHCCCEEEEEECCCCCC
T ss_conf             534589644-----08999999998799699980899876


No 437
>PRK05265 pyridoxine 5'-phosphate synthase; Provisional
Probab=38.56  E-value=25  Score=14.67  Aligned_cols=64  Identities=14%  Similarity=0.252  Sum_probs=47.6

Q ss_pred             HHHHHHHHCCCCEEEEECCCCCC---CCCCCH--------HHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEE
Q ss_conf             99999997699479980787433---668897--------89887420268689996488762345555541798279
Q gi|254780901|r  111 LMMRFLSHCSVNANMYIPDRIVD---GYGPNP--------SLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVI  177 (600)
Q Consensus       111 il~~~L~~~g~~v~~~IP~R~~e---GYGl~~--------~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvI  177 (600)
                      =|.+.......+-.+.+|++-.|   -.|++.        +.++++++.|+..=+++|-   +.++++.|++.|.|.|
T Consensus        77 e~i~ia~~~kP~qvtLVPe~r~e~TTegGld~~~~~~~L~~~i~~lk~~gIrvSLFiDP---d~~~i~~a~~~Gad~V  151 (240)
T PRK05265         77 EMLDIALEIKPHQVTLVPEKREELTTEGGLDVAGQFDKLKPAIARLKDAGIRVSLFIDP---DPEQIEAAAEVGADRI  151 (240)
T ss_pred             HHHHHHHHCCCCEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCEEEEEECC---CHHHHHHHHHHCCCEE
T ss_conf             89999998499859988899886267889377657899999999998659817997279---8789999998493999


No 438
>PRK02039 consensus
Probab=38.37  E-value=25  Score=14.65  Aligned_cols=71  Identities=17%  Similarity=0.287  Sum_probs=46.9

Q ss_pred             CCCEEEEE-CC-C-CCHHHHHHHHHHHHHHCCC-CEEEEECC-------C-CCCCC-CCCHHHHHHHHH-CCCCEEEEEC
Q ss_conf             99799994-07-8-8615289999999997699-47998078-------7-43366-889789887420-2686899964
Q gi|254780901|r   92 SEKIMIFG-DY-D-VDGAASVALMMRFLSHCSV-NANMYIPD-------R-IVDGY-GPNPSLMEKFIN-EGAQLIITVD  157 (600)
Q Consensus        92 ~ekI~I~g-Dy-D-~DGitstail~~~L~~~g~-~v~~~IP~-------R-~~eGY-Gl~~~~i~~~~~-~g~~LiItvD  157 (600)
                      ++.+.|.. -+ . =|.+.-.-+|..++++.|+ ++...||-       | +..|- .++...+-++.+ .|++-+||+|
T Consensus        52 g~dV~ivqs~~~p~nd~lmELll~idA~r~a~A~~It~ViPY~~YaRQDr~~~~gr~pisak~vA~ll~~aG~d~vitvD  131 (316)
T PRK02039         52 GKDVFVLQSTCAPTNDNLMELMIMVDALKRASAGRITAAIPYFGYARQDRRPRSARVAISAKVVANMLEIAGVERIITMD  131 (316)
T ss_pred             CCCEEEECCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCEEEEEC
T ss_conf             99889992899982078999999999998738874899842545334776556887653099999876232777048852


Q ss_pred             CCCCC
Q ss_conf             88762
Q gi|254780901|r  158 CGSTS  162 (600)
Q Consensus       158 ~Gi~~  162 (600)
                      --...
T Consensus       132 lH~~q  136 (316)
T PRK02039        132 LHADQ  136 (316)
T ss_pred             CCHHH
T ss_conf             78388


No 439
>cd01571 NAPRTase_B Nicotinate phosphoribosyltransferase (NAPRTase), subgroup B. Nicotinate phosphoribosyltransferase catalyses the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid, this is the first, and also rate limiting, reaction in the NAD salvage synthesis. This salvage pathway serves to recycle NAD degradation products.
Probab=38.10  E-value=26  Score=14.62  Aligned_cols=93  Identities=18%  Similarity=0.201  Sum_probs=39.7

Q ss_pred             CCCCCHHHHHHHHHCCCCEEEECCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCHHH
Q ss_conf             88762345555541798279961544765556725652378888643344304788999999999997021488764077
Q gi|254780901|r  158 CGSTSYDALQYATNQGIDVIVIDHHQVKSEEIPAYALVNPNRLDDLSGQGHLCAAGVVFLVLVLIYRILRQDNKVPLNFD  237 (600)
Q Consensus       158 ~Gi~~~e~i~~a~~~GidvIVtDHH~~~~~~p~a~aivNP~~~~~~~p~~~l~gaGvaf~l~~al~~~l~~~~~~~~~~~  237 (600)
                      ||+  .|.+++++...++|    |..+.++      ++.|+.     |.-.+.|--.-+.++.-.               
T Consensus        39 aGl--~ev~~~l~~~~~~v----~a~~EG~------~v~p~e-----pvl~I~Gp~~~~~~lEt~---------------   86 (302)
T cd01571          39 CGL--EEVLALLEGLPVKV----YALPEGT------IFNPKE-----PVLRIEGPYQDFGELETA---------------   86 (302)
T ss_pred             ECH--HHHHHHHHCCCEEE----EECCCCC------EECCCC-----CEEEEEECHHHHHHHHHH---------------
T ss_conf             529--99999984598079----9808988------845998-----579999719999999999---------------


Q ss_pred             HHHHHHH-HHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHH
Q ss_conf             9999999-877542011114441189999878877516887435789870
Q gi|254780901|r  238 LLSLLDL-VALATVCDVVPLIGLNRAYVVKGLMVARRQGNPGLKALIERV  286 (600)
Q Consensus       238 l~~~ldl-vaiGTvaD~vpL~~eNR~lvk~GL~~l~~~~~~gl~~L~~~~  286 (600)
                      +..+|.. -.|+|-|--+-..-.++.++-.|.++    .+|+.+.+...+
T Consensus        87 lLn~l~~~S~IAT~a~r~v~aA~~~~v~~fg~Rr----~~p~~~~~~~rA  132 (302)
T cd01571          87 ILGILARASSIATNAARVKLAAGDKPVISFGDRR----DHPAIQPMDGRA  132 (302)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCC----CCHHHHHHHHHH
T ss_conf             9988758889999999999974999389744533----596578998688


No 440
>cd06358 PBP1_NHase Type I periplasmic-binding protein of the nitrile hydratase (NHase) system that selectively converts nitriles to corresponding amides. This group includes the type I periplasmic-binding protein of the nitrile hydratase (NHase) system that selectively converts nitriles to corresponding amides, which are subsequently converted by amidases to yield free carboxylic acids and ammonia. NHases from bacteria and fungi have been purified and characterized. In Rhodococcus sp., the nitrile hydratase operon consists of six genes encoding NHase regulator 2, NHase regulator 1, amidase, NHase alpha subunit, NHase beta subunit, and NHase activator. The operon produces a constitutive hydratase that has a broad substrate spectrum: aliphatic and aromatic nitriles, mononitriles and dinitriles, hydroxynitriles and amino-nitriles, and a constitutive amidase of equally low substrate specificity. NHases are metalloenzymes containing either cobalt or iron, and therefore can be classified int
Probab=38.03  E-value=26  Score=14.61  Aligned_cols=36  Identities=14%  Similarity=0.196  Sum_probs=13.0

Q ss_pred             HHHHHH-CCCCEEEEECCCCCCHHHHHHHHHCCCCEEE
Q ss_conf             887420-2686899964887623455555417982799
Q gi|254780901|r  142 MEKFIN-EGAQLIITVDCGSTSYDALQYATNQGIDVIV  178 (600)
Q Consensus       142 i~~~~~-~g~~LiItvD~Gi~~~e~i~~a~~~GidvIV  178 (600)
                      .+++.+ +++..||-. .+++...++.-+.+.++-.|.
T Consensus        59 a~kLi~~~~V~aviG~-~~S~~~~A~~~~~~~~vp~i~   95 (333)
T cd06358          59 AARLVDEGGVDAIIGW-HTSAVRNAVAPVVAGRVPYVY   95 (333)
T ss_pred             HHHHHHCCCEEEEECC-CCCHHHHHHHHHHHCCCCEEE
T ss_conf             9999975990899877-440778988999976993897


No 441
>pfam03009 GDPD Glycerophosphoryl diester phosphodiesterase family. E. coli has two sequence related isozymes of glycerophosphoryl diester phosphodiesterase (GDPD) - periplasmic and cytosolic. This family also includes agrocinopine synthase, the similarity to GDPD has been noted. This family appears to have weak but not significant matches to mammalian phospholipase C pfam00388, which suggests that this family may adopt a TIM barrel fold.
Probab=38.03  E-value=26  Score=14.61  Aligned_cols=29  Identities=24%  Similarity=0.217  Sum_probs=21.9

Q ss_pred             CCHHHHHHHHHCCCCEEEECCCCCCCCCC
Q ss_conf             62345555541798279961544765556
Q gi|254780901|r  161 TSYDALQYATNQGIDVIVIDHHQVKSEEI  189 (600)
Q Consensus       161 ~~~e~i~~a~~~GidvIVtDHH~~~~~~p  189 (600)
                      +..++.+.|.+.|.|.|=+|=|.-.+..|
T Consensus        11 NTl~Af~~A~~~G~d~iE~DV~~TkDg~~   39 (238)
T pfam03009        11 NTLLAFRKAAEAGADYIEFDVQLTKDGVP   39 (238)
T ss_pred             CHHHHHHHHHHCCCCEEEEEEEECCCCCE
T ss_conf             34999999998698999987758469999


No 442
>TIGR03307 PhnP phosphonate metabolism protein PhnP. This family of proteins found in operons encoding phosphonate C-P lyase systems as is observed in E. coli and is a member of the metallo-beta-lactamase superfamily (pfam00753). As defined by this model, all instances of this protein are associated with the C-P lyase, but not all genomes containing the C-P lyase system contain phnP.
Probab=37.84  E-value=17  Score=15.96  Aligned_cols=32  Identities=22%  Similarity=0.445  Sum_probs=19.8

Q ss_pred             CCCEEEEECCCCCCHHHHHHHHHCCCCEEEEC
Q ss_conf             68689996488762345555541798279961
Q gi|254780901|r  149 GAQLIITVDCGSTSYDALQYATNQGIDVIVID  180 (600)
Q Consensus       149 g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtD  180 (600)
                      |-++..+.||+.=..+..++++..++|++|.|
T Consensus       154 g~~~aY~tD~~~ip~es~~~L~~~~lD~li~d  185 (249)
T TIGR03307       154 GQRLAYLTDTAGLPPDTEAFLKNHPLDLLILD  185 (249)
T ss_pred             CCEEEEECCCCCCCHHHHHHHCCCCCCEEEEC
T ss_conf             95599967888779899999728998889962


No 443
>PRK13265 glycine/sarcosine/betaine reductase complex protein A; Reviewed
Probab=37.76  E-value=26  Score=14.58  Aligned_cols=76  Identities=20%  Similarity=0.400  Sum_probs=45.4

Q ss_pred             HHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCC-CCC----CCHHHHHHHHHC-CCC-EEEEECCCCC
Q ss_conf             977997999940788615289999999997699479980787433-668----897898874202-686-8999648876
Q gi|254780901|r   89 IYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVD-GYG----PNPSLMEKFINE-GAQ-LIITVDCGST  161 (600)
Q Consensus        89 i~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~e-GYG----l~~~~i~~~~~~-g~~-LiItvD~Gi~  161 (600)
                      +-.++|+.|+||  -||+-+-|| -.+++..|++|.|---.-|.- .-|    -|...+.++.++ |+. +++..  |.+
T Consensus         3 ~l~gKkviiiGd--RDGiPgpai-~~c~k~~gaevvfs~TECFVctaagaMDLEnQ~rVK~~aek~G~ENvvVvl--Gaa   77 (157)
T PRK13265          3 LFEGKKVIIIGD--RDGIPGPAI-EECIKGTGAEVVFSSTECFVUTAAGAMDLENQKRVKDLTEKHGAENIVVIL--GAA   77 (157)
T ss_pred             CCCCCEEEEEEC--CCCCCCHHH-HHHHHCCCCEEEEEEEEEEEEECCCCCCHHHHHHHHHHHHHCCCCCEEEEE--CCC
T ss_conf             556866999816--889974889-999853596599974356775064412268789999999870975289996--466


Q ss_pred             CHHHHHHH
Q ss_conf             23455555
Q gi|254780901|r  162 SYDALQYA  169 (600)
Q Consensus       162 ~~e~i~~a  169 (600)
                      ..|....+
T Consensus        78 eaE~agla   85 (157)
T PRK13265         78 EAEAAGLA   85 (157)
T ss_pred             CHHHCCCE
T ss_conf             70011443


No 444
>COG1646 Predicted phosphate-binding enzymes, TIM-barrel fold [General function prediction only]
Probab=37.72  E-value=26  Score=14.58  Aligned_cols=51  Identities=14%  Similarity=0.257  Sum_probs=22.3

Q ss_pred             CHHHCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHH--HHHHHH-HCCCCEEEE
Q ss_conf             95561487999999999997799799994078861528999--999999-769947998
Q gi|254780901|r   71 DPLILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVAL--MMRFLS-HCSVNANMY  126 (600)
Q Consensus        71 dP~~l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstai--l~~~L~-~~g~~v~~~  126 (600)
                      ||..-   +.+.+....+.+.+---.+.|  --||+|...+  +++.++ +....+-.+
T Consensus        23 DP~k~---~~~~ei~~~~~~~GTDaImIG--GS~gvt~~~~~~~v~~ik~~~~lPvilf   76 (240)
T COG1646          23 DPDKT---EEADEIAEAAAEAGTDAIMIG--GSDGVTEENVDNVVEAIKERTDLPVILF   76 (240)
T ss_pred             CCCCC---CCCHHHHHHHHHCCCCEEEEC--CCCCCCHHHHHHHHHHHHHHCCCCEEEE
T ss_conf             76323---452899999997399889977--8556447999999999975069988993


No 445
>PRK07631 amidophosphoribosyltransferase; Provisional
Probab=37.70  E-value=26  Score=14.58  Aligned_cols=37  Identities=19%  Similarity=0.225  Sum_probs=19.6

Q ss_pred             CCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCC
Q ss_conf             99799994078861528999999999769947998078743366889
Q gi|254780901|r   92 SEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPN  138 (600)
Q Consensus        92 ~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~  138 (600)
                      +|.=.|+|=|..+  -+..+++..|..+        -||=+|+.|+.
T Consensus         9 ~eeCGI~Gi~~~~--d~~~~~y~GL~~L--------QHRGQesaGIa   45 (475)
T PRK07631          9 NEECGVFGIWGHE--EAAQITYYGLHSL--------QHRGQEGAGIV   45 (475)
T ss_pred             CCCCEEEEEECCC--CHHHHHHHHHHHH--------HCCCCCEEEEE
T ss_conf             7676289999880--2299999999986--------24760232799


No 446
>COG0013 AlaS Alanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=37.53  E-value=26  Score=14.56  Aligned_cols=99  Identities=21%  Similarity=0.248  Sum_probs=56.9

Q ss_pred             CCCEEEEECCCCCHHHHHHHHHHHHHHHHCEEEEEEECCCCEE-EEEEEC---CCCCCHHHHHHHHCCCCCCCCCCCCC-
Q ss_conf             4750262057858122222278998842010799886379837-999864---89861888888530335301156532-
Q gi|254780901|r  367 QASVIVVEGDRWHPGIVGLLAARLKEKFGRPSFAISFEEDGKG-IGSGRS---IEGFDIGKMVSFAVEEGILVKGGGHA-  441 (600)
Q Consensus       367 ~~~~ivv~~~~wh~GViGIVAsrL~e~y~kP~iv~s~~~dg~~-kGS~RS---i~g~~l~~~l~~~~~~~ll~~~GGH~-  441 (600)
                      ..++++..-.+-..+-+.-+|.+|+.+....++++.-..++.. ...+-|   ..+++..++++.++.. +-.++||-+ 
T Consensus       774 g~~~~~~~~~~~d~~~Lr~~a~~lk~k~~~~vivl~~~~~~Kv~~~~~v~~~~~~~~~a~~lvk~la~~-~gG~GGGr~d  852 (879)
T COG0013         774 GVKVLAKEVDGADMKELREIADDLKKKLGSAVIVLASVADGKVSLVVAVSKDLTDKVKAGELVKELAAI-VGGKGGGRPD  852 (879)
T ss_pred             CEEEEEEEECCCCHHHHHHHHHHHHHHCCCCEEEEEEECCCEEEEEEEECHHHHCCCCHHHHHHHHHHH-CCCCCCCCHH
T ss_conf             879999994478989999999999750478379999852770899999651441354899999999986-2998889625


Q ss_pred             CCCCEEECCCCHHHHHHHHHHHHHH
Q ss_conf             2231464222158899999999986
Q gi|254780901|r  442 MAAGLTVERVNFGRLCDFFQKFAHN  466 (600)
Q Consensus       442 ~AaG~ti~~~~l~~f~~~l~~~~~~  466 (600)
                      +|-|-.=...++++..+.+.+.+.+
T Consensus       853 ~Aqggg~d~~~~~~al~~~~~~~~~  877 (879)
T COG0013         853 MAQGGGKDPEKLDEALELVIEWVKE  877 (879)
T ss_pred             HHEECCCCCCCHHHHHHHHHHHHHH
T ss_conf             5211789833289999999999984


No 447
>cd03817 GT1_UGDG_like This family is most closely related to the GT1 family of glycosyltransferases. UDP-glucose-diacylglycerol glucosyltransferase (UGDG; also known as 1,2-diacylglycerol 3-glucosyltransferase) catalyzes the transfer of glucose from UDP-glucose to 1,2-diacylglycerol forming 3-D-glucosyl-1,2-diacylglycerol.
Probab=37.48  E-value=26  Score=14.55  Aligned_cols=38  Identities=24%  Similarity=0.197  Sum_probs=16.5

Q ss_pred             HHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECC
Q ss_conf             74202686899964887623455555417982799615
Q gi|254780901|r  144 KFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDH  181 (600)
Q Consensus       144 ~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDH  181 (600)
                      .+.+.++++|.+-..-....-+...++..++.+|.|=|
T Consensus        79 ~~~~~~~DvIh~~~~~~~~~~a~~~~~~~~ip~V~t~H  116 (374)
T cd03817          79 ILKELGPDIVHTHTPFSLGLLGLRVARKLGIPVVATYH  116 (374)
T ss_pred             HHHHCCCCEEEECCHHHHHHHHHHHHHHCCCCEEEEEC
T ss_conf             99866999999878258899999999974995999955


No 448
>cd06282 PBP1_GntR_like_2 Ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. This group includes the ligand-binding domain of putative DNA transcription repressors highly similar to that of the repressor specific for gluconate (GntR) which is a member of the LacI-GalR family of bacterial transcription regulators. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold.  As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding
Probab=37.45  E-value=26  Score=14.55  Aligned_cols=67  Identities=7%  Similarity=0.070  Sum_probs=40.9

Q ss_pred             HHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCC
Q ss_conf             9999976994799807874336688978988742026868999648876234555554179827996154
Q gi|254780901|r  113 MRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHH  182 (600)
Q Consensus       113 ~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH  182 (600)
                      -..++..|.++.....+--.+   .-.+.++.+.+.+++=+|.+=++.+..+.++.+++.|+-|++.|.-
T Consensus        22 e~~~~~~Gy~~~i~~t~~~~~---~e~~~i~~l~~~~vdGiIi~~~~~~~~~~~~~l~~~~iPvV~~~~~   88 (266)
T cd06282          22 QEEARAAGYSLLLATTDYDAE---READAVETLLRQRVDGLILTVADAATSPALDLLDAERVPYVLAYND   88 (266)
T ss_pred             HHHHHHCCCEEEEEECCCCHH---HHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEEECC
T ss_conf             999998799899997999979---9999999999659987999637877559999998559978999504


No 449
>COG1634 Uncharacterized Rossmann fold enzyme [General function prediction only]
Probab=37.32  E-value=24  Score=14.77  Aligned_cols=47  Identities=23%  Similarity=0.376  Sum_probs=23.7

Q ss_pred             CCEEEEECCCCCCHHHHHHHHHCCC--CEEEECCCCCCCCCC-----CCEEEECCCCCCCCC
Q ss_conf             8689996488762345555541798--279961544765556-----725652378888643
Q gi|254780901|r  150 AQLIITVDCGSTSYDALQYATNQGI--DVIVIDHHQVKSEEI-----PAYALVNPNRLDDLS  204 (600)
Q Consensus       150 ~~LiItvD~Gi~~~e~i~~a~~~Gi--dvIVtDHH~~~~~~p-----~a~aivNP~~~~~~~  204 (600)
                      ...+|+.|      -++..+.+.|+  |+||||---.++.+.     -...+||-|  |+++
T Consensus        73 ~~~vi~Ad------gA~~~l~~~gi~pDiiVTDlDgd~e~~~~~~~~g~i~VVHAH--GDNi  126 (232)
T COG1634          73 SEVVIAAD------GAVSALLERGIRPDIIVTDLDGDPEDLLSCTAKGSIVVVHAH--GDNI  126 (232)
T ss_pred             CCEEEECC------HHHHHHHHCCCCCCEEEECCCCCHHHHHHHHCCCCEEEEEEC--CCCH
T ss_conf             53599556------899999985997757970598898899875336977999946--8677


No 450
>cd01966 Nitrogenase_NifN_1 Nitrogenase_nifN1: A subgroup of the NifN subunit of the NifEN complex: NifN forms an alpha2beta2 tetramer with NifE.  NifN and nifE are structurally homologous to nitrogenase MoFe protein beta and alpha subunits respectively.  NifEN participates in the synthesis of the iron-molybdenum cofactor (FeMoco) of the MoFe protein.  NifB-co (an iron and sulfur containing precursor of the FeMoco) from NifB is transferred to the NifEN complex where it is further processed to FeMoco. The nifEN bound precursor of FeMoco has been identified as a molybdenum-free, iron- and sulfur- containing analog of FeMoco. It has been suggested that this nifEN bound precursor also acts as a cofactor precursor in nitrogenase systems which require a cofactor other than FeMoco: i.e. iron-vanadium cofactor (FeVco) or iron only cofactor (FeFeco).
Probab=37.23  E-value=26  Score=14.52  Aligned_cols=126  Identities=18%  Similarity=0.279  Sum_probs=61.4

Q ss_pred             HHHHHHHCCCCHHHHHHHCCCCHHHCCCCHHHCCCHHHHHHHHHHHHHCCCC--EEEE--------ECCCCCHHHHHHHH
Q ss_conf             9999996788978988661966777189955614879999999999977997--9999--------40788615289999
Q gi|254780901|r   43 VARVLVNRNVSIDYAKDFLNPSIRLLMPDPLILTDCDKAARRIVQAIYNSEK--IMIF--------GDYDVDGAASVALM  112 (600)
Q Consensus        43 ~a~iL~~Rgi~~~~~~~fL~p~l~~l~~dP~~l~dm~~A~~ri~~ai~~~ek--I~I~--------gDyD~DGitstail  112 (600)
                      ..+.+.+|.+.+.-.   + + ..++..+---|-+.++-.+-|..+++.-+.  |.|+        || |++++...   
T Consensus        36 ~~~~~~~rhf~ep~~---~-~-sT~l~E~~~VfGG~~~L~~~I~~~~~~y~P~~I~V~tTC~se~IGD-Di~~vv~~---  106 (417)
T cd01966          36 FAKVLLVRHFKEPIP---L-Q-TTAMDEVSTILGGGENLEEALDTLAERAKPKVIGLLSTGLTETRGE-DIAGALKQ---  106 (417)
T ss_pred             HHHHHHHCCCCCCCC---C-C-CCCCCCCCEEECCHHHHHHHHHHHHHHCCCCEEEEECCCHHHHCCC-CHHHHHHH---
T ss_conf             799986265789868---7-7-6788878656673899999999999852987799965531433077-78999999---


Q ss_pred             HHHHHHC----CCCEEEE-ECC---CCCCCCCCCHHHH-HHHHHC----C-----CCEEEEECCCCCCHHHHHH-HHHCC
Q ss_conf             9999976----9947998-078---7433668897898-874202----6-----8689996488762345555-54179
Q gi|254780901|r  113 MRFLSHC----SVNANMY-IPD---RIVDGYGPNPSLM-EKFINE----G-----AQLIITVDCGSTSYDALQY-ATNQG  173 (600)
Q Consensus       113 ~~~L~~~----g~~v~~~-IP~---R~~eGYGl~~~~i-~~~~~~----g-----~~LiItvD~Gi~~~e~i~~-a~~~G  173 (600)
                        +-...    +..+.+. -|.   -...||-.-.+++ +.+...    .     +.||--..+.-.+.++++. +.+.|
T Consensus       107 --~~~~~~~~~~~pvi~v~tpgF~Gs~~~Gy~~a~~aii~~~~~~~~~~~~~~~~iNli~g~~~~pgDl~eik~ll~~~G  184 (417)
T cd01966         107 --FRAEHPELADVPVVYVSTPDFEGSLEDGWAAAVEAIIEALVEPGSRTVTDPRQVNLLPGAHLTPGDVEELKDIIEAFG  184 (417)
T ss_pred             --HHHHCCCCCCCCEEEECCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEECCCCCCCHHHHHHHHHHHHHCC
T ss_conf             --997446557984685168764563788999999999987436878777778835881564688777999999999829


Q ss_pred             CCEEEE
Q ss_conf             827996
Q gi|254780901|r  174 IDVIVI  179 (600)
Q Consensus       174 idvIVt  179 (600)
                      ++++|+
T Consensus       185 l~~~il  190 (417)
T cd01966         185 LEPIIL  190 (417)
T ss_pred             CCEEEE
T ss_conf             956982


No 451
>cd00156 REC Signal receiver domain; originally thought to be unique to bacteria (CheY, OmpR, NtrC, and PhoB), now recently identified in eukaroytes ETR1 Arabidopsis thaliana; this domain receives the signal from the sensor partner in a two-component systems; contains a phosphoacceptor site that is phosphorylated by histidine kinase homologs; usually found N-terminal to a DNA binding effector domain; forms homodimers
Probab=37.20  E-value=26  Score=14.52  Aligned_cols=45  Identities=16%  Similarity=0.366  Sum_probs=24.3

Q ss_pred             HHHHHHHC-CCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCCCCCCC
Q ss_conf             98874202-68689996488762345555541798279961544765556
Q gi|254780901|r  141 LMEKFINE-GAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKSEEI  189 (600)
Q Consensus       141 ~i~~~~~~-g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~~~~~~p  189 (600)
                      .+..+.+. |.. +.++++   ..++++.+.+...|+|++|-+.|.-...
T Consensus        12 ~l~~~L~~~g~~-v~~a~~---g~~al~~~~~~~~dlvi~D~~mP~~~G~   57 (113)
T cd00156          12 LLRRLLEKEGYE-VVEAED---GEEALALLAEEKPDLILLDIMMPGMDGL   57 (113)
T ss_pred             HHHHHHHHCCCE-EEEECC---HHHHHHHHHHCCCCEEEECCCCCCCCCH
T ss_conf             999999988999-999899---9999999875799999977999898726


No 452
>COG3848 Phosphohistidine swiveling domain [Signal transduction mechanisms]
Probab=37.18  E-value=26  Score=14.52  Aligned_cols=39  Identities=31%  Similarity=0.376  Sum_probs=28.6

Q ss_pred             CCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEE
Q ss_conf             897898874202686899964887623455555417982799
Q gi|254780901|r  137 PNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIV  178 (600)
Q Consensus       137 l~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIV  178 (600)
                      ...+.+..+-+  ..-|||-|.|+++|.++- ..++|+.|||
T Consensus        41 td~d~v~~~eK--a~aiItee~glTshaAVv-gl~LgvPvIv   79 (111)
T COG3848          41 TDADFVPALEK--AAAIITEEGGLTSHAAVV-GLELGVPVIV   79 (111)
T ss_pred             CCHHHHHHHHH--HHEEEECCCCCCCCCEEE-EEECCCCEEE
T ss_conf             77446789986--300685047745542016-7524996798


No 453
>KOG2187 consensus
Probab=37.17  E-value=26  Score=14.52  Aligned_cols=18  Identities=22%  Similarity=0.290  Sum_probs=9.6

Q ss_pred             CCHHHHHHHHHHHHHCCC
Q ss_conf             487999999999997799
Q gi|254780901|r   76 TDCDKAARRIVQAIYNSE   93 (600)
Q Consensus        76 ~dm~~A~~ri~~ai~~~e   93 (600)
                      .++++|..++.....++-
T Consensus        74 ~~~~ka~~~v~g~~~k~~   91 (534)
T KOG2187          74 SDAGKAINLVDGLLYKGF   91 (534)
T ss_pred             CHHHHHHHHHHHHHHHHH
T ss_conf             423557898751002200


No 454
>PRK06460 hypothetical protein; Provisional
Probab=37.14  E-value=26  Score=14.51  Aligned_cols=94  Identities=16%  Similarity=0.274  Sum_probs=56.8

Q ss_pred             CHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEE
Q ss_conf             87999999999997799799994078861528999999999769947998078743366889789887420268689996
Q gi|254780901|r   77 DCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITV  156 (600)
Q Consensus        77 dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItv  156 (600)
                      +|.....-+....+.+..|++-.  ++=|-| ..++.++|..+|.++.++=|.        ..+.+++++..+++||..=
T Consensus        69 GmaAi~~~l~~~l~~Gdhiv~~~--~~Yg~t-~~l~~~~l~~~Gv~v~~~d~~--------~~~~~~~~~~~~Tklv~~E  137 (375)
T PRK06460         69 GMGAISTTLLTLLKPGSSVLIHR--DMFGRS-YRFFTDFLRNWGVKVEVARPG--------EENILEKIKNKRYDVVFVE  137 (375)
T ss_pred             HHHHHHHHHHHHHCCCCEEEECC--CCCCCH-HHHHHHHHHHCCEEEEEECCC--------CHHHHHHHCCCCCEEEEEE
T ss_conf             99999999999728999899717--875867-999999987378677973899--------9999997347676089998


Q ss_pred             CC-----CCCCHHHHH-HHHHCCCCEEEECCC
Q ss_conf             48-----876234555-554179827996154
Q gi|254780901|r  157 DC-----GSTSYDALQ-YATNQGIDVIVIDHH  182 (600)
Q Consensus       157 D~-----Gi~~~e~i~-~a~~~GidvIVtDHH  182 (600)
                      --     -+.+.++|. .|+++|+-++| |.-
T Consensus       138 spsNP~l~v~Di~~i~~ia~~~gi~~vV-DNT  168 (375)
T PRK06460        138 TISNPLLRVIDIPELSKACKENGALLIV-DST  168 (375)
T ss_pred             CCCCCCCCCCCCHHHHHHHHHCCCEEEE-ECC
T ss_conf             8999876405858999999874993897-567


No 455
>COG3222 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.03  E-value=26  Score=14.50  Aligned_cols=84  Identities=23%  Similarity=0.295  Sum_probs=44.5

Q ss_pred             HHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCC---CCCHHHHHHHHHCCCCEEEEECC
Q ss_conf             999999997799799994078861528999999999769947998078743366---88978988742026868999648
Q gi|254780901|r   82 ARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGY---GPNPSLMEKFINEGAQLIITVDC  158 (600)
Q Consensus        82 ~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGY---Gl~~~~i~~~~~~g~~LiItvD~  158 (600)
                      +.-...|....++++|+| .||-|+|+-- |-.+++.++-- .....--+.-||   ||.. ..-.       +.=.+|.
T Consensus        94 ars~~~a~~~~~~VliIg-~DcP~lt~el-La~a~taL~~~-paVLGpa~dGGy~llgLrr-~~pe-------~fe~ipw  162 (211)
T COG3222          94 ARSHVDAFDGSYPVLIIG-MDCPGLTAEL-LADAFTALLQI-PAVLGPAFDGGYYLLGLRR-FAPE-------LFEAIPW  162 (211)
T ss_pred             HHHHHHHHCCCCCEEEEE-CCCCCCCHHH-HHHHHHHHHCC-CCEECCCCCCCEEEEEEEC-CCHH-------HHHCCCC
T ss_conf             999999756887279982-5897647999-99999997147-6102222258378997310-4899-------9950888


Q ss_pred             CCCCHHH--HHHHHHCCCCE
Q ss_conf             8762345--55554179827
Q gi|254780901|r  159 GSTSYDA--LQYATNQGIDV  176 (600)
Q Consensus       159 Gi~~~e~--i~~a~~~Gidv  176 (600)
                      |....-+  ++.++++|+++
T Consensus       163 g~~~v~~lTl~~lrqng~~~  182 (211)
T COG3222         163 GTPDVLELTLKALRQNGIDV  182 (211)
T ss_pred             CCCHHHHHHHHHHHHCCCCC
T ss_conf             87459999999999749961


No 456
>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=36.96  E-value=27  Score=14.49  Aligned_cols=100  Identities=21%  Similarity=0.243  Sum_probs=44.1

Q ss_pred             CCHHHHHHHHHHHCCHHHHHC--CCCCCCEEEECC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             242345666774306233312--122221002034-25899999999998999999999999999999987521124347
Q gi|254780901|r  292 ITAENLGYMIGPSINAGGRIG--ESNLGSRLLISD-DSQELEMLAMKLDVLNQNRRLMESAMLEQAEAKVLTQCDDIQQA  368 (600)
Q Consensus       292 i~~~di~f~iaPrINAaGRl~--~a~~av~lL~~~-d~~~a~~la~~L~~lN~~Rk~~e~~i~~~a~~~~~~~~~~~~~~  368 (600)
                      +|+++| |.-.|=|+   |+.  +|..-+..|.++ .|+.+.++|++.-                      +..++ .+.
T Consensus        92 ftAeel-~~~~PEL~---~iAni~a~~~~niLSENMkP~~W~~IA~~V~----------------------~al~~-G~~  144 (413)
T TIGR02153        92 FTAEEL-ARAVPELL---EIANIKARAVFNILSENMKPEYWIKIAEAVA----------------------KALEE-GAD  144 (413)
T ss_pred             CCHHHH-HHHCCCHH---EECCCCEEEEEHHCCCCCCHHHHHHHHHHHH----------------------HHHCC-CCC
T ss_conf             398999-86174002---0124310560001077888589999999999----------------------98408-995


Q ss_pred             CEEEEECCCCCHHHHHHHHHHHHHHHHC--EE-EEEEECCCCEEEEEEECC------CCCCHHHHHHHHCC
Q ss_conf             5026205785812222227899884201--07-998863798379998648------98618888885303
Q gi|254780901|r  369 SVIVVEGDRWHPGIVGLLAARLKEKFGR--PS-FAISFEEDGKGIGSGRSI------EGFDIGKMVSFAVE  430 (600)
Q Consensus       369 ~~ivv~~~~wh~GViGIVAsrL~e~y~k--P~-iv~s~~~dg~~kGS~RSi------~g~~l~~~l~~~~~  430 (600)
                      -|+|..+-+    -..=-||=|+=.|..  |+ ||        ..||=||-      .-+||..+...+..
T Consensus       145 GVVvaHGTD----TM~YTAaALSFm~~~Gl~~PvV--------lVGAQRSSDRPSSDAa~NL~~A~~~A~~  203 (413)
T TIGR02153       145 GVVVAHGTD----TMAYTAAALSFMFKTGLPVPVV--------LVGAQRSSDRPSSDAALNLIAAVRAATS  203 (413)
T ss_pred             EEEEEECCC----HHHHHHHHHHHHHHCCCCCCEE--------EECCCCCCCCCCCHHHHHHHHHHHHHCC
T ss_conf             389941587----4689999999999716999889--------9857435888731379999999998336


No 457
>TIGR00381 cdhD CO dehydrogenase/acetyl-CoA synthase, delta subunit; InterPro: IPR004486 This is the small subunit of a heterodimer which catalyzes the reaction CO + H2O + Acceptor = CO2 + Reduced acceptor and is involved in the synthesis of acetyl-CoA from CO2 and H2.; GO: 0006730 one-carbon compound metabolic process.
Probab=36.91  E-value=8.5  Score=18.38  Aligned_cols=24  Identities=25%  Similarity=0.290  Sum_probs=18.1

Q ss_pred             HHHCCCCCCCCCHHHHHHHHHHHH
Q ss_conf             420111144411899998788775
Q gi|254780901|r  249 TVCDVVPLIGLNRAYVVKGLMVAR  272 (600)
Q Consensus       249 TvaD~vpL~~eNR~lvk~GL~~l~  272 (600)
                      |+-|+=-=...||+|+|.|++.-+
T Consensus       251 ~~mD~N~qktLNRyLlk~gl~p~d  274 (401)
T TIGR00381       251 AIMDINMQKTLNRYLLKRGLKPRD  274 (401)
T ss_pred             HHCCCCHHHHHHHHHHHHHCCCCC
T ss_conf             112800144676999984148677


No 458
>COG1255 Uncharacterized protein conserved in archaea [Function unknown]
Probab=36.61  E-value=27  Score=14.45  Aligned_cols=95  Identities=23%  Similarity=0.323  Sum_probs=53.0

Q ss_pred             HHHH-HCCCCEEEEECCCCCCHHHHH-HHHHCCCCEEEECCCCCCCC-CCC--CEEEECCCCCCCCCCCCCHHHHHHHHH
Q ss_conf             8742-026868999648876234555-55417982799615447655-567--256523788886433443047889999
Q gi|254780901|r  143 EKFI-NEGAQLIITVDCGSTSYDALQ-YATNQGIDVIVIDHHQVKSE-EIP--AYALVNPNRLDDLSGQGHLCAAGVVFL  217 (600)
Q Consensus       143 ~~~~-~~g~~LiItvD~Gi~~~e~i~-~a~~~GidvIVtDHH~~~~~-~p~--a~aivNP~~~~~~~p~~~l~gaGvaf~  217 (600)
                      +.++ +.+..-++-|  ||..+-.++ +++++|+||+.||-.+.... ...  -+-+.||++.              .|+
T Consensus         6 ~~iAre~~~gkVvEV--GiG~~~~VA~~L~e~g~dv~atDI~~~~a~~g~~~v~DDitnP~~~--------------iY~   69 (129)
T COG1255           6 EYIARENARGKVVEV--GIGFFLDVAKRLAERGFDVLATDINEKTAPEGLRFVVDDITNPNIS--------------IYE   69 (129)
T ss_pred             HHHHHHHCCCCEEEE--CCCHHHHHHHHHHHCCCCEEEEECCCCCCCCCCEEEECCCCCCCHH--------------HHH
T ss_conf             999987058837998--1411799999999748868998523013765533887247796477--------------762


Q ss_pred             HHHHHHHHHCCCCCCCCHHHHHHH-HHHH-HHHHHHCCCCCCCCC
Q ss_conf             999999970214887640779999-9998-775420111144411
Q gi|254780901|r  218 VLVLIYRILRQDNKVPLNFDLLSL-LDLV-ALATVCDVVPLIGLN  260 (600)
Q Consensus       218 l~~al~~~l~~~~~~~~~~~l~~~-ldlv-aiGTvaD~vpL~~eN  260 (600)
                      =+.++++.     .  ..+++..+ ||++ ++|.=+=.+||.||-
T Consensus        70 ~A~lIYSi-----R--pppEl~~~ildva~aVga~l~I~pL~Ge~  107 (129)
T COG1255          70 GADLIYSI-----R--PPPELQSAILDVAKAVGAPLYIKPLTGEP  107 (129)
T ss_pred             CCCCEEEC-----C--CCHHHHHHHHHHHHHHCCCEEEEECCCCC
T ss_conf             70012662-----7--98899899999998609978997168997


No 459
>TIGR01324 cysta_beta_ly_B cystathionine beta-lyase; InterPro: IPR006233   Cystathionine beta-lyase (alternate name: beta-cystathionase) is one of several pyridoxal-dependent enzymes of cysteine, methionine, and homocysteine metabolism. This enzyme is involved in the biosynthesis of Met from Cys .; GO: 0004121 cystathionine beta-lyase activity, 0006520 amino acid metabolic process, 0005737 cytoplasm.
Probab=36.50  E-value=27  Score=14.44  Aligned_cols=73  Identities=10%  Similarity=0.211  Sum_probs=36.5

Q ss_pred             CHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHH-HHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEE
Q ss_conf             87999999999997799799994078861528999999-99976994799807874336688978988742026868999
Q gi|254780901|r   77 DCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMR-FLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIIT  155 (600)
Q Consensus        77 dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~-~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiIt  155 (600)
                      ++-....-|..-++.+..++|.+=    -.-=|---++ .|+++|.++.||=|+       ++++.|--+++-++++|++
T Consensus        79 GlAAvT~~~LafvkaGDhvL~vds----aY~PTr~Fcd~vLkr~gv~~~YYDP~-------igPe~ia~Li~pnTkv~fl  147 (389)
T TIGR01324        79 GLAAVTNALLAFVKAGDHVLVVDS----AYKPTRRFCDIVLKRLGVEVEYYDPK-------IGPEDIAALIKPNTKVVFL  147 (389)
T ss_pred             CHHHHHHHHHHHHHCCCEEEEECC----CCCHHHHHHHHHHHHHCEEEEEECCC-------CCHHHHHHHCCCCCEEEEE
T ss_conf             557888999988743883798646----46115899988753634458872788-------6888898740888448998


Q ss_pred             ECCCC
Q ss_conf             64887
Q gi|254780901|r  156 VDCGS  160 (600)
Q Consensus       156 vD~Gi  160 (600)
                      ===||
T Consensus       148 EaP~S  152 (389)
T TIGR01324       148 EAPAS  152 (389)
T ss_pred             ECCCC
T ss_conf             37874


No 460
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=36.50  E-value=27  Score=14.44  Aligned_cols=90  Identities=9%  Similarity=-0.027  Sum_probs=37.5

Q ss_pred             EEEEEECCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCEEECCCCHHHHHHHHHHHHHHHCCHHHCC-----------CCE
Q ss_conf             799986489861888888530335301156532223146422215889999999998622644337-----------714
Q gi|254780901|r  409 GIGSGRSIEGFDIGKMVSFAVEEGILVKGGGHAMAAGLTVERVNFGRLCDFFQKFAHNIVPALITT-----------PVF  477 (600)
Q Consensus       409 ~kGS~RSi~g~~l~~~l~~~~~~~ll~~~GGH~~AaG~ti~~~~l~~f~~~l~~~~~~~~~~~~~~-----------~~l  477 (600)
                      ++-.-+|.-|-.-.+.+....-.-.|..-.|=....|+|-....-..+++.+-+.+.+.+--.+..           +.-
T Consensus       144 ~~~~~~~~~G~~a~~~l~~~~~d~afig~~gi~~~~g~t~~~~~ea~~kr~mi~~a~~~illaDssKfg~~~~~~~~~l~  223 (252)
T PRK10906        144 LRSRDGGIIGEATLDFISQFRLDFGILGISGIDSDGSLLEFDYHEVRTKRAIIENSRHVMLVVDHSKFGRNAMVNMGSIS  223 (252)
T ss_pred             EECCCCCEECHHHHHHHHHCCEEEEEEECCEECCCCCCCCCCHHHHHHHHHHHHHCCCEEEEECCCCCCCCCCEEEECHH
T ss_conf             85788743068899999706602999616512689873359999999999999961968999873303881416984779


Q ss_pred             EEEEEECHHHCCHHHHHHHHH
Q ss_conf             760443468979999999985
Q gi|254780901|r  478 KIDGVLNASAVNIALIDMLES  498 (600)
Q Consensus       478 ~iD~el~~~~i~~~l~~~L~~  498 (600)
                      .+|..+.-...+.++.+.|+.
T Consensus       224 ~id~lITD~~~~~~~~~~l~~  244 (252)
T PRK10906        224 MVDAVYTDQLPPASVMQVITD  244 (252)
T ss_pred             HCCEEEECCCCCHHHHHHHHH
T ss_conf             899999894999999999998


No 461
>pfam04015 DUF362 Domain of unknown function (DUF362). Sometimes present in iron-sulphur proteins.
Probab=36.39  E-value=27  Score=14.43  Aligned_cols=23  Identities=22%  Similarity=0.293  Sum_probs=16.6

Q ss_pred             EEEECCCHHHHHHHHHHHHHHHH
Q ss_conf             00203425899999999998999
Q gi|254780901|r  319 RLLISDDSQELEMLAMKLDVLNQ  341 (600)
Q Consensus       319 ~lL~~~d~~~a~~la~~L~~lN~  341 (600)
                      -++.++|+-.....+.+|-.++-
T Consensus       213 ~llas~D~vAlD~v~a~llG~~p  235 (262)
T pfam04015       213 LLIASNDVVALDAVIVALLGIDP  235 (262)
T ss_pred             EEEEECCHHHHHHHHHHHHCCCH
T ss_conf             69994889999999999809982


No 462
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=36.30  E-value=24  Score=14.87  Aligned_cols=53  Identities=15%  Similarity=0.102  Sum_probs=27.4

Q ss_pred             CCEEEECCCC--CCCCCCCCEEEECCC-CCCCCCCCCCHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             8279961544--765556725652378-8886433443047889999999999970214
Q gi|254780901|r  174 IDVIVIDHHQ--VKSEEIPAYALVNPN-RLDDLSGQGHLCAAGVVFLVLVLIYRILRQD  229 (600)
Q Consensus       174 idvIVtDHH~--~~~~~p~a~aivNP~-~~~~~~p~~~l~gaGvaf~l~~al~~~l~~~  229 (600)
                      +.+-|.|.=.  |++..+   -|..|- |.+.....++..|+|+-.-++..|.+.++..
T Consensus       431 l~f~V~DTGiGI~~e~l~---~IF~~F~Q~~~s~~~r~~~GTGLGLaI~k~LvelMGG~  486 (779)
T PRK11091        431 LHFEVEDSGIGIPEDELD---KIFAMYYQVKDSHGGKPATGTGIGLAVSRRLAQNMGGD  486 (779)
T ss_pred             EEEEEEECCCCCCHHHHH---HHHCCCEECCCCCCCCCCCCCCHHHHHHHHHHHHCCCE
T ss_conf             999999579999999999---87057560667877767788760799999999984997


No 463
>cd06270 PBP1_GalS_like Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Ligand binding domain of DNA transcription iso-repressor GalS, which is one of two regulatory proteins involved in galactose transport and metabolism. Transcription of the galactose regulon genes is regulated by Gal iso-repressor (GalS) and Gal repressor (GalR) in different ways, but both repressors recognize the same DNA binding site in the absence of D-galactose. GalS is a dimeric protein like GalR,and its major role is in regulating expression of the high-affinity galactose transporter encoded by the mgl operon, whereas GalR is the exclusive regulator of galactose permease, the low-affinity galactose transporter. GalS and GalR are members of the LacI-GalR family of transcription regulators and both contain the type I periplasmic binding protein-like fold. Hence, they are homologous to the periplasmic sugar bindi
Probab=36.24  E-value=27  Score=14.41  Aligned_cols=68  Identities=12%  Similarity=0.077  Sum_probs=39.8

Q ss_pred             HHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCCC
Q ss_conf             999976994799807874336688978988742026868999648876234555554179827996154476
Q gi|254780901|r  114 RFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVK  185 (600)
Q Consensus       114 ~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~~~  185 (600)
                      +.++..|.++..+.-+.-.+   ...+.++.+.+.+++=||..-.+. +.+.+..+.+.|+-+++.|.+.+.
T Consensus        23 ~~~~~~gy~~ll~~s~~~~~---~e~~~l~~l~~~~vdGiIi~~~~~-~~~~~~~l~~~~~PvV~i~~~~~~   90 (268)
T cd06270          23 SVARKAGKHLIITAGHHSAE---KEREAIEFLLERRCDALILHSKAL-SDDELIELAAQVPPLVLINRHIPG   90 (268)
T ss_pred             HHHHHCCCEEEEEECCCCHH---HHHHHHHHHHHCCCCEEEEECCCC-CHHHHHHHHHCCCCEEEECCCCCC
T ss_conf             99998599999995899989---999999999965999999952779-989999999649989998676899


No 464
>cd06267 PBP1_LacI_sugar_binding_like Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily. Ligand binding domain of the LacI tanscriptional regulator family belonging to the type I periplasmic-binding fold protein superfamily.  In most cases, ligands are monosaccharide including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars. The LacI family of proteins consists of transcriptional regulators related to the lac repressor. In this case, the domain sugar binding changes the DNA binding activity of the repressor domain.
Probab=36.23  E-value=27  Score=14.41  Aligned_cols=68  Identities=13%  Similarity=0.103  Sum_probs=41.3

Q ss_pred             HHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCCC
Q ss_conf             999976994799807874336688978988742026868999648876234555554179827996154476
Q gi|254780901|r  114 RFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVK  185 (600)
Q Consensus       114 ~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~~~  185 (600)
                      +.++..|.++..+.-+.-.   -.....++.+...+++-+|.+.... +.+.+..+++.|+.+|..|.....
T Consensus        23 ~~a~~~gy~~~i~~~~~~~---~~~~~~i~~l~~~~vDgiIi~~~~~-~~~~~~~~~~~~iPvV~~~~~~~~   90 (264)
T cd06267          23 EAAREAGYSVLLCNSDEDP---EKEREALELLLSRRVDGIILAPSRL-DDELLEELAALGIPVVLVDRPLDG   90 (264)
T ss_pred             HHHHHCCCEEEEEECCCCH---HHHHHHHHHHHHCCCCEEEECCCCC-CHHHHHHHHHCCCCEEEEEECCCC
T ss_conf             9999869989999789998---9999999999957999999678889-989999999869988999604799


No 465
>TIGR01918 various_sel_PB selenoprotein B, glycine/betaine/sarcosine/D-proline reductase family; InterPro: IPR010187   This entry represents selenoprotein B of glycine reductase, sarcosine reductase, betaine reductase, D-proline reductase, and perhaps others. All members are expected to contain an internal UGA codon, encoding selenocysteine, which may be misinterpreted as a stop codon.; GO: 0030699 glycine reductase activity, 0050485 oxidoreductase activity acting on X-H and Y-H to form an X-Y bond with a disulfide as acceptor, 0030700 glycine reductase complex.
Probab=35.94  E-value=27  Score=14.38  Aligned_cols=28  Identities=25%  Similarity=0.519  Sum_probs=15.6

Q ss_pred             CCCCHHHHHHHHHCCCCEEEEECCCCCCH
Q ss_conf             68897898874202686899964887623
Q gi|254780901|r  135 YGPNPSLMEKFINEGAQLIITVDCGSTSY  163 (600)
Q Consensus       135 YGl~~~~i~~~~~~g~~LiItvD~Gi~~~  163 (600)
                      -|++.. +++++++...++-||=||=+=+
T Consensus        30 ~p~s~~-L~~lle~DAEv~~~vvCGD~f~   57 (433)
T TIGR01918        30 PPISQQ-LNKLLEEDAEVVATVVCGDSFF   57 (433)
T ss_pred             CCHHHH-HHHHHCCCCEEEEEEEECCCHH
T ss_conf             726788-7654037743899998277201


No 466
>COG1778 Low specificity phosphatase (HAD superfamily) [General function prediction only]
Probab=35.93  E-value=14  Score=16.57  Aligned_cols=72  Identities=25%  Similarity=0.415  Sum_probs=42.0

Q ss_pred             CCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCE-EEEECCCCCCHHHHHHH
Q ss_conf             79979999407886152899999999976994799807874336688978988742026868-99964887623455555
Q gi|254780901|r   91 NSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQL-IITVDCGSTSYDALQYA  169 (600)
Q Consensus        91 ~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~L-iItvD~Gi~~~e~i~~a  169 (600)
                      .+=|.+|+   ||||+-+---||-  ..-|-....|   ...||||     |..+.+.|.+. |||   |-.+----.++
T Consensus         6 ~~IkLli~---DVDGvLTDG~ly~--~~~Gee~KaF---nv~DG~G-----ik~l~~~Gi~vAIIT---Gr~s~ive~Ra   69 (170)
T COG1778           6 KNIKLLIL---DVDGVLTDGKLYY--DENGEEIKAF---NVRDGHG-----IKLLLKSGIKVAIIT---GRDSPIVEKRA   69 (170)
T ss_pred             HHCEEEEE---ECCCEEECCEEEE--CCCCCEEEEE---ECCCCHH-----HHHHHHCCCEEEEEE---CCCCHHHHHHH
T ss_conf             31328999---4564056674888--4897565433---0357699-----999998599289996---78787899999


Q ss_pred             HHCCCCEEE
Q ss_conf             417982799
Q gi|254780901|r  170 TNQGIDVIV  178 (600)
Q Consensus       170 ~~~GidvIV  178 (600)
                      +++||+-+.
T Consensus        70 ~~LGI~~~~   78 (170)
T COG1778          70 KDLGIKHLY   78 (170)
T ss_pred             HHCCCCEEE
T ss_conf             975970024


No 467
>PRK09490 metH B12-dependent methionine synthase; Provisional
Probab=35.83  E-value=28  Score=14.36  Aligned_cols=29  Identities=28%  Similarity=0.598  Sum_probs=13.5

Q ss_pred             CCCCCCCHHHHHH----HHHCC-CCEEEEECCCCC
Q ss_conf             3366889789887----42026-868999648876
Q gi|254780901|r  132 VDGYGPNPSLMEK----FINEG-AQLIITVDCGST  161 (600)
Q Consensus       132 ~eGYGl~~~~i~~----~~~~g-~~LiItvD~Gi~  161 (600)
                      ..||-++++-+..    +.+.| +++|=-| ||++
T Consensus       285 ~g~Y~~tPee~a~~~~~f~~~g~vnivGGC-CGTT  318 (1229)
T PRK09490        285 FGEYDETPEEMAAQIEEFAESGFLNIVGGC-CGTT  318 (1229)
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCEECCCC-CCCC
T ss_conf             898889999999999999984980054766-7999


No 468
>cd03362 TOPRIM_TopoIA_TopoIII TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III.   Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap.  The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD).  For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=35.76  E-value=28  Score=14.36  Aligned_cols=64  Identities=13%  Similarity=0.131  Sum_probs=47.3

Q ss_pred             CCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCC--CE-EEEECCCCCCCCCCCHHHHHHHHH
Q ss_conf             4879999999999977997999940788615289999999997699--47-998078743366889789887420
Q gi|254780901|r   76 TDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSV--NA-NMYIPDRIVDGYGPNPSLMEKFIN  147 (600)
Q Consensus        76 ~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~--~v-~~~IP~R~~eGYGl~~~~i~~~~~  147 (600)
                      ++..+-...|.+...+-..|.+.+|+|--|   -.|-++.+..++.  +. .+.+  +|++   +++..|.++.+
T Consensus        83 ~~~~~~~~~ik~l~~~ad~ii~atD~DrEG---E~I~~ei~~~~~~~~~~~v~R~--~fs~---lT~~~I~~A~~  149 (151)
T cd03362          83 KGKKKQFKVLKKLAKRADEIVIATDADREG---ELIGREILEYAKCVKRKPVKRA--WFSS---LTPKAIRRAFK  149 (151)
T ss_pred             CCHHHHHHHHHHHHHHCCEEEECCCCCCCH---HHHHHHHHHHHCCCCCCCEEEE--EEEC---CCHHHHHHHHH
T ss_conf             548999999999985399899877887204---5999999998488889856899--9804---89999999997


No 469
>PTZ00237 acetyl-CoA synthetase; Provisional
Probab=35.72  E-value=28  Score=14.35  Aligned_cols=54  Identities=26%  Similarity=0.468  Sum_probs=30.6

Q ss_pred             HHHHHHHHHCCC----CEEEEECCC-------------------CCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHH
Q ss_conf             999999997699----479980787-------------------4336688978988742026868999648876234
Q gi|254780901|r  110 ALMMRFLSHCSV----NANMYIPDR-------------------IVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYD  164 (600)
Q Consensus       110 ail~~~L~~~g~----~v~~~IP~R-------------------~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e  164 (600)
                      .-+..+|+.+|.    .|-.|.|+.                   ..-|||. .++..++...+++++||.|.+....+
T Consensus       103 ~r~A~~L~~lGV~kGDrVai~mpn~~E~via~lA~~riGAV~~~~~~~~~~-~~l~~ri~~~~pkvlit~~~~~~~~~  179 (649)
T PTZ00237        103 CEFSRVLLNLNISKNDNVLIYMANTLEPLIAMLSCARIGATHCVLFDGYSV-KSLIDRIETITPKLIITTNYGILNDE  179 (649)
T ss_pred             HHHHHHHHHCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCEEECCCCCCCH-HHHHHHHHHCCCCEEECCCCCEECCC
T ss_conf             999999997397989999998488299999999999949298466997798-99999998521118840441100673


No 470
>cd06331 PBP1_AmiC_like Type I periplasmic components of amide-binding protein (AmiC) and the active transport system for short-chain and urea (FmdDEF). This group includes the type I periplasmic components of amide-binding protein (AmiC) and the active transport system for short-chain and urea (FmdDEF), found in bacteria and Archaea. AmiC controls expression of the amidase operon by a ligand-triggered conformational switch. In the absence of ligand or presence of butyramide (repressor), AmiC (the ligand sensor and negative regulator) adopts an open conformation and inhibits the transcription antitermination function of AmiR by direct protein-protein interaction.  In the presence of inducing ligands such as acetamide, AmiC adopts a closed conformation which disrupts a silencing AmiC-AmiR complex and the expression of amidase and other genes of the operon is induced. FmdDEF is predicted to be an ATP-dependent transporter and closely resembles the periplasmic binding protein and the two t
Probab=35.66  E-value=28  Score=14.35  Aligned_cols=37  Identities=5%  Similarity=0.060  Sum_probs=17.3

Q ss_pred             HHHHH-HCCCCEEEEECCCCCCHHHHHHHHHCCCCEEE
Q ss_conf             88742-02686899964887623455555417982799
Q gi|254780901|r  142 MEKFI-NEGAQLIITVDCGSTSYDALQYATNQGIDVIV  178 (600)
Q Consensus       142 i~~~~-~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIV  178 (600)
                      .+++. ++++..||-.-+...+......+.+.++-+|.
T Consensus        59 a~~Li~~d~V~~iiG~~~S~~~~A~~~~~~~~~vp~i~   96 (333)
T cd06331          59 ARRLIRDDKVDAVFGCYTSASRKAVLPVVERGRGLLFY   96 (333)
T ss_pred             HHHHHHHCCCEEEECCCCCHHHHHHCHHHHHCCCCEEE
T ss_conf             99999728964996687607777643078875997780


No 471
>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=35.64  E-value=28  Score=14.34  Aligned_cols=64  Identities=19%  Similarity=0.213  Sum_probs=39.5

Q ss_pred             HHHHHHHCCCCEEEEEC-CCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCC-CHHHHHHHHHCCCCEEEECCCCC
Q ss_conf             99999976994799807-874336688978988742026868999648876-23455555417982799615447
Q gi|254780901|r  112 MMRFLSHCSVNANMYIP-DRIVDGYGPNPSLMEKFINEGAQLIITVDCGST-SYDALQYATNQGIDVIVIDHHQV  184 (600)
Q Consensus       112 l~~~L~~~g~~v~~~IP-~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~-~~e~i~~a~~~GidvIVtDHH~~  184 (600)
                      +-.++..+....-..+| +|        .+.+..+.+.++..+|.+ +|.. +-+-++.|++.|+-+|.|.++..
T Consensus        31 ~~~~l~~~~~g~lvI~~gdR--------~di~~~a~~~~~~~iIlT-gg~~p~~~v~~la~~~~ipii~t~~dT~   96 (105)
T pfam07085        31 VENMLEYLRPGDLVITPGDR--------EDIQLAALLAGIAGLILT-GGFEPSEEVLKLAEEAGLPVLSTPYDTF   96 (105)
T ss_pred             HHHHHHHHCCCCEEEEECCC--------HHHHHHHHHHCCCEEEEE-CCCCCCHHHHHHHHHCCCEEEEECCCHH
T ss_conf             99999860689799992796--------899999998248789994-8989899999999877983999668899


No 472
>cd00405 PRAI Phosphoribosylanthranilate isomerase (PRAI) catalyzes the fourth step of the tryptophan biosynthesis, the conversion of N-(5'- phosphoribosyl)-anthranilate (PRA) to 1-(o-carboxyphenylamino)- 1-deoxyribulose 5-phosphate (CdRP). Most PRAIs are monomeric, monofunctional and thermolabile, but in some thermophile organisms PRAI is dimeric for reasons of stability and in others it is fused to other components of the tryptophan biosynthesis pathway to form multifunctional enzymes.
Probab=35.57  E-value=27  Score=14.46  Aligned_cols=20  Identities=35%  Similarity=0.601  Sum_probs=12.4

Q ss_pred             CCCCCHHHHHHHHHCCCCEE
Q ss_conf             88762345555541798279
Q gi|254780901|r  158 CGSTSYDALQYATNQGIDVI  177 (600)
Q Consensus       158 ~Gi~~~e~i~~a~~~GidvI  177 (600)
                      ||+++.+.++.+.++|+|-+
T Consensus         4 CGit~~~d~~~~~~~g~d~i   23 (203)
T cd00405           4 CGITTLEDALAAAEAGADAI   23 (203)
T ss_pred             CCCCCHHHHHHHHHCCCCEE
T ss_conf             88895999999985799989


No 473
>cd06277 PBP1_LacI_like_1 Ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. This group includes the ligand-binding domain of uncharacterized DNA-binding regulatory proteins that are members of the LacI-GalR family of bacterial transcription repressors. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the sugar-binding domain of ABC-type transport systems that contain the type I periplasmic binding protein-like fold.  As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand binding which in turn changes the DNA binding affinity of the repressor.
Probab=35.52  E-value=28  Score=14.33  Aligned_cols=46  Identities=20%  Similarity=0.225  Sum_probs=30.9

Q ss_pred             HHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCCCC
Q ss_conf             789887420268689996488762345555541798279961544765
Q gi|254780901|r  139 PSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKS  186 (600)
Q Consensus       139 ~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~~~~  186 (600)
                      .+.++.+.+..++=+|.+  |..+-+.++.+.+.|+-+++.|.+.+..
T Consensus        48 ~~~~~~l~~~~vdGiI~~--~~~~~~~~~~l~~~~~P~V~id~~~~~~   93 (268)
T cd06277          48 FELPSFLEDGKVDGIILL--GGISTEYIKEIKELGIPFVLVDHYIPNE   93 (268)
T ss_pred             HHHHHHHHHCCCCEEEEE--CCCCHHHHHHHHHCCCCEEEECCCCCCC
T ss_conf             999999994898789997--8999799999997599899967768999


No 474
>PRK13810 orotate phosphoribosyltransferase; Provisional
Probab=35.39  E-value=28  Score=14.32  Aligned_cols=106  Identities=17%  Similarity=0.203  Sum_probs=54.0

Q ss_pred             HHHCCCCHHHCCCCHHHCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHH-HH-HHCCCCEEEEECCCCCCCC
Q ss_conf             866196677718995561487999999999997799799994078861528999999-99-9769947998078743366
Q gi|254780901|r   58 KDFLNPSIRLLMPDPLILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMR-FL-SHCSVNANMYIPDRIVDGY  135 (600)
Q Consensus        58 ~~fL~p~l~~l~~dP~~l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~-~L-~~~g~~v~~~IP~R~~eGY  135 (600)
                      ..|++..  .+..+|..+.-   .++.+.+.++.-+.=.|.      |.+-++|-.- .+ ...+....|  ..+...+|
T Consensus        43 ~~Y~d~r--~~~~~p~~~~~---i~~~~~~~i~~~~~d~I~------G~a~Ggipla~~va~~~~~p~~~--vRke~K~~  109 (187)
T PRK13810         43 KYYIDIK--KASTDPKTLKL---IARQAALRIKEMDVDTIA------GVELGGVPLATAVSLETGLPLLI--VRKSVKDY  109 (187)
T ss_pred             CHHCCCH--HHHCCHHHHHH---HHHHHHHHCCCCCCCEEE------CCCCCHHHHHHHHHHHHCCCEEE--EEECCCCC
T ss_conf             1235194--45478999999---999999844114987794------31101279999999981998699--98337764


Q ss_pred             CCCHHHHHHHHHCCCCEEEEEC---CCCCCHHHHHHHHHCCCCEE
Q ss_conf             8897898874202686899964---88762345555541798279
Q gi|254780901|r  136 GPNPSLMEKFINEGAQLIITVD---CGSTSYDALQYATNQGIDVI  177 (600)
Q Consensus       136 Gl~~~~i~~~~~~g~~LiItvD---~Gi~~~e~i~~a~~~GidvI  177 (600)
                      |.... ++--...|-+.+|.=|   .|.|..+.++.+++.|..|+
T Consensus       110 G~~~~-ieG~~~~g~rVlvVEDViTTGgS~~eai~~l~~~G~~V~  153 (187)
T PRK13810        110 GTKSR-FVGDLKPEDRIVMLEDVTTSGGSVRDAIEVVREAGAIVK  153 (187)
T ss_pred             CCCCE-EEEECCCCCEEEEEEEEECCCCCHHHHHHHHHHCCCEEE
T ss_conf             43435-885047998899998543568239999999998899799


No 475
>PRK09259 putative oxalyl-CoA decarboxylase; Validated
Probab=35.27  E-value=28  Score=14.30  Aligned_cols=80  Identities=11%  Similarity=0.125  Sum_probs=46.5

Q ss_pred             HHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCC--CCCCCCCCHHHHHHHHHCCCCEEEEEC
Q ss_conf             999999999977997999940788615289999999997699479980787--433668897898874202686899964
Q gi|254780901|r   80 KAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDR--IVDGYGPNPSLMEKFINEGAQLIITVD  157 (600)
Q Consensus        80 ~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R--~~eGYGl~~~~i~~~~~~g~~LiItvD  157 (600)
                      ++++++.+.+.+-++.+|+.-.-+---.+..-|.++.+.+|+.|..-...|  +.|.|-++........-+.+|+||.+.
T Consensus       204 ~~i~~a~~~L~~AkrPvIi~G~G~~~~~a~~~l~~lae~l~iPV~tt~~gkg~~p~~hpl~~G~~~~~~l~~aDlvl~iG  283 (572)
T PRK09259        204 DAVDRAIDLLKKAKRPLIILGKGAAYAQADEQIREFVESTGIPFLPMSMAKGLLPDTHPQSAAAARSFALANADVVLLVG  283 (572)
T ss_pred             HHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHHCCCEEECCCCCCCCCCCCCCCHHHHHHHHHHCCCEEEEEC
T ss_conf             99999999997279809998878145548999999999739976753435676888674114689999883198899982


Q ss_pred             CC
Q ss_conf             88
Q gi|254780901|r  158 CG  159 (600)
Q Consensus       158 ~G  159 (600)
                      |-
T Consensus       284 ~~  285 (572)
T PRK09259        284 AR  285 (572)
T ss_pred             CC
T ss_conf             67


No 476
>PRK08745 ribulose-phosphate 3-epimerase; Provisional
Probab=35.21  E-value=28  Score=14.29  Aligned_cols=87  Identities=11%  Similarity=0.226  Sum_probs=46.8

Q ss_pred             CHHHHHHHHHHHHHCCCCEEEEECCCC-CH-----HHHHHHHHHHHHHCC--C--CEEEEECCCCCCCCCCCHHHHHHHH
Q ss_conf             879999999999977997999940788-61-----528999999999769--9--4799807874336688978988742
Q gi|254780901|r   77 DCDKAARRIVQAIYNSEKIMIFGDYDV-DG-----AASVALMMRFLSHCS--V--NANMYIPDRIVDGYGPNPSLMEKFI  146 (600)
Q Consensus        77 dm~~A~~ri~~ai~~~ekI~I~gDyD~-DG-----itstail~~~L~~~g--~--~v~~~IP~R~~eGYGl~~~~i~~~~  146 (600)
                      ++++.++++.+   .+-..   =++|+ ||     +|-..-+.+.++...  .  +++..+-+        ....++.+.
T Consensus        17 ~L~~ei~~l~~---~g~d~---iHiDImDG~FVpN~t~g~~~i~~ir~~~~~~plDvHLMv~~--------P~~~i~~~~   82 (223)
T PRK08745         17 RLGEEVDNVLK---AGADW---VHFDVMDNHYVPNLTIGPMVCQALRKHGITAPIDVHLMVEP--------VDRIVPDFA   82 (223)
T ss_pred             HHHHHHHHHHH---CCCCE---EEEECCCCCCCCCCCCCHHHHHHHHHHCCCCCEEEEEEECC--------HHHHHHHHH
T ss_conf             99999999997---69998---99827679707755709599999996189975377898339--------899999999


Q ss_pred             HCCCCEE-EEECCCCCCHHHHHHHHHCCCCEE
Q ss_conf             0268689-996488762345555541798279
Q gi|254780901|r  147 NEGAQLI-ITVDCGSTSYDALQYATNQGIDVI  177 (600)
Q Consensus       147 ~~g~~Li-ItvD~Gi~~~e~i~~a~~~GidvI  177 (600)
                      +.|++.| +-+.+...-++-+...++.|+.+-
T Consensus        83 ~aGad~i~~H~Ea~~~~~~~i~~ik~~g~k~G  114 (223)
T PRK08745         83 DAGATTISFHPEASRHVHRTIQLIKSHGCQAG  114 (223)
T ss_pred             HCCCCEEEEEECCCCCHHHHHHHHHHCCCCEE
T ss_conf             73997899960644299999999998398446


No 477
>cd06340 PBP1_ABC_ligand_binding_like_6 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=35.12  E-value=28  Score=14.28  Aligned_cols=31  Identities=23%  Similarity=0.307  Sum_probs=11.7

Q ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCEEE
Q ss_conf             2686899964887623455555417982799
Q gi|254780901|r  148 EGAQLIITVDCGSTSYDALQYATNQGIDVIV  178 (600)
Q Consensus       148 ~g~~LiItvD~Gi~~~e~i~~a~~~GidvIV  178 (600)
                      +++..||-.-|...+......+.+.|+-+|.
T Consensus        69 d~V~aviG~~~S~~~~a~~~v~~~~~vp~i~   99 (347)
T cd06340          69 EGVVALVGAYQSAVTLAASQVAERYGVPFVV   99 (347)
T ss_pred             CCCEEEECCCCCHHHHHHHHHHHHHCEEEEE
T ss_conf             8946974576737666646999862845880


No 478
>cd03814 GT1_like_2 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homolog
Probab=35.01  E-value=28  Score=14.27  Aligned_cols=38  Identities=21%  Similarity=0.203  Sum_probs=23.9

Q ss_pred             HHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECC
Q ss_conf             74202686899964887623455555417982799615
Q gi|254780901|r  144 KFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDH  181 (600)
Q Consensus       144 ~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDH  181 (600)
                      .+.+..+++|.+.+-+.....+...++..|+.+|+|=|
T Consensus        78 ~~~~~~pDiIh~~~~~~~~~~a~~~~~~~~ip~i~~~H  115 (364)
T cd03814          78 LLDAFAPDVVHIATPGPLGLAALRAARRLGIPVVTSYH  115 (364)
T ss_pred             HHHHCCCCEEEECCCCHHHHHHHHHHHHCCCCEEEEEC
T ss_conf             99865999999878416789999999975997899974


No 479
>cd01445 TST_Repeats Thiosulfate sulfurtransferases (TST) contain 2 copies of the Rhodanese Homology Domain. Only the second repeat contains the catalytically active Cys residue. The role of the 1st repeat is uncertain, but believed to be involved in protein interaction. This CD aligns the 1st and 2nd repeats.
Probab=34.94  E-value=28  Score=14.26  Aligned_cols=53  Identities=9%  Similarity=0.079  Sum_probs=30.9

Q ss_pred             HHCCCHHHHHHHHHHH-HHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCC-CEEEE
Q ss_conf             5614879999999999-977997999940788615289999999997699-47998
Q gi|254780901|r   73 LILTDCDKAARRIVQA-IYNSEKIMIFGDYDVDGAASVALMMRFLSHCSV-NANMY  126 (600)
Q Consensus        73 ~~l~dm~~A~~ri~~a-i~~~ekI~I~gDyD~DGitstail~~~L~~~g~-~v~~~  126 (600)
                      +.++.-++-.+.+.+. |.+.+.|.+|.--|+-|+|| +.++-+|+.+|. +|..|
T Consensus        75 ~~lp~~~~f~~~~~~lGI~~~~~vVvycg~~~sGvtA-~r~ww~l~~~G~~~V~vy  129 (138)
T cd01445          75 SMEPSEAEFAAMFEAKGIDLDKHLIATDGDDLGGFTA-CHIALAARLCGHPDVAIL  129 (138)
T ss_pred             CCCCCHHHHHHHHHHCCCCCCCCEEEEECCCCCCHHH-HHHHHHHHHCCCCCCEEC
T ss_conf             8888999999999982999898089983898850199-999999998299981682


No 480
>PRK01424 S-adenosylmethionine:tRNA ribosyltransferase-isomerase; Provisional
Probab=34.93  E-value=28  Score=14.26  Aligned_cols=10  Identities=30%  Similarity=0.282  Sum_probs=3.8

Q ss_pred             HHHHHHHHHH
Q ss_conf             2227899884
Q gi|254780901|r  384 GLLAARLKEK  393 (600)
Q Consensus       384 GIVAsrL~e~  393 (600)
                      |--+-|..|.
T Consensus       276 GTT~vRaLEs  285 (366)
T PRK01424        276 GTTTLRTLES  285 (366)
T ss_pred             ECCHHHHHHH
T ss_conf             4516887887


No 481
>cd07035 TPP_PYR_POX_like Pyrimidine (PYR) binding domain of POX and related proteins. Thiamine pyrophosphate (TPP family), pyrimidine (PYR) binding domain of pyruvate oxidase (POX) and related protiens subfamily. The PYR domain is found in many key metabolic enzymes which use TPP (also known as thiamine diphosphate) as a cofactor. TPP binds in the cleft formed by a PYR domain and a PP domain. The PYR domain, binds the aminopyrimidine ring of TPP, the PP domain binds the diphosphate residue. A polar interaction between the conserved glutamate of the PYR domain and the N1' of the TPP aminopyrimidine ring is shared by most TPP-dependent enzymes, and participates in the activation of TPP. For glyoxylate carboligase, which belongs to this subfamily, but lacks this conserved glutamate, the rate of the initial TPP activation step is reduced but the ensuing steps of the enzymic reaction proceed efficiently. The PYR and PP domains have a common fold, but do not share strong sequence conservatio
Probab=34.88  E-value=28  Score=14.26  Aligned_cols=70  Identities=24%  Similarity=0.293  Sum_probs=33.5

Q ss_pred             HHHHCCHHHHHCCCCCCCEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEE-ECCCCC
Q ss_conf             7743062333121222210020342589999999999899999999999999999998752112434750262-057858
Q gi|254780901|r  301 IGPSINAGGRIGESNLGSRLLISDDSQELEMLAMKLDVLNQNRRLMESAMLEQAEAKVLTQCDDIQQASVIVV-EGDRWH  379 (600)
Q Consensus       301 iaPrINAaGRl~~a~~av~lL~~~d~~~a~~la~~L~~lN~~Rk~~e~~i~~~a~~~~~~~~~~~~~~~~ivv-~~~~wh  379 (600)
                      +.|.+++..     ...+++..+.++..|--.|.-.                   .++.      ....++++ .+++.-
T Consensus        23 ~~~l~~~~~-----~~~i~~i~~~~E~~A~~~A~g~-------------------~~~t------g~~~v~~~~~gpG~~   72 (155)
T cd07035          23 ILPLLDALA-----RSGIRYILVRHEQGAVGMADGY-------------------ARAT------GKPGVVLVTSGPGLT   72 (155)
T ss_pred             HHHHHHHHH-----HCCCEEEEECCHHHHHHHHHHH-------------------HHHC------CCCEEEEEECCHHHH
T ss_conf             699999865-----0798799878779999999999-------------------9865------997599982776888


Q ss_pred             HHHHHHHHHHHHHHHHCEEEEEEE
Q ss_conf             122222278998842010799886
Q gi|254780901|r  380 PGIVGLLAARLKEKFGRPSFAISF  403 (600)
Q Consensus       380 ~GViGIVAsrL~e~y~kP~iv~s~  403 (600)
                      .++.||......   +-|+++++-
T Consensus        73 n~~~~l~~A~~~---~~Pvl~i~g   93 (155)
T cd07035          73 NAVTGLANAYLD---SIPLLVITG   93 (155)
T ss_pred             HHHHHHHHHHHC---CCCEEEEEC
T ss_conf             788999999983---898089946


No 482
>PRK00830 consensus
Probab=34.70  E-value=29  Score=14.24  Aligned_cols=72  Identities=13%  Similarity=0.190  Sum_probs=49.9

Q ss_pred             HHHHHHHHCCCCEEEEE-CCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCC
Q ss_conf             99999997699479980-78743366889789887420268689996488762345555541798279961544
Q gi|254780901|r  111 LMMRFLSHCSVNANMYI-PDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQ  183 (600)
Q Consensus       111 il~~~L~~~g~~v~~~I-P~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~  183 (600)
                      -+.+.+..-|++--+++ =++-.+|-..+.+.|+++.+. +.+=|||-=||.+.+.++.+-+.|.|=||+--..
T Consensus        38 ~~ak~~~~~gadelhivDld~a~~g~~~~~~~I~~i~~~-~~~pi~vGGGIrs~e~~~~ll~~GadkVvIgS~a  110 (273)
T PRK00830         38 ELAKRYYEDGADELVFLDITASHEGRATMIDVIERTAEE-VFIPLTVGGGIRSIEDIRQILRAGADKVSVNTAA  110 (273)
T ss_pred             HHHHHHHHCCCCEEEEEEEECCCCCCCCHHHHHHHHHHH-CCCCEEEECCEEECCCHHHHHHCCCCEEECHHHH
T ss_conf             999999987999899995324646884279999999986-6995896088437732899997698639837989


No 483
>TIGR02104 pulA_typeI pullulanase, type I; InterPro: IPR011840    Pullulan is an unusual, industrially important polysaccharide in which short alpha-1,4 chains (maltotriose) are connected in alpha-1,6 linkages. Enzymes that cleave alpha-1,6 linkages in pullulan and release maltotriose are called pullulanases although pullulan itself may not be the natural substrate. This family consists of pullulanases related to the entries in IPR011838 from INTERPRO and IPR011839 from INTERPRO but having a different domain architecture with shorter sequences. Members are called type I pullulanases ..
Probab=34.65  E-value=29  Score=14.23  Aligned_cols=138  Identities=16%  Similarity=0.243  Sum_probs=75.1

Q ss_pred             CCCCCCHHH-HHHHHHHHHHCCCCCHHHHHHHHCCCCCCCH-HHHHH-HHHH----HCCHHHHHCCC-----CCCCEEEE
Q ss_conf             144411899-9987887751688743578987088864242-34566-6774----30623331212-----22210020
Q gi|254780901|r  255 PLIGLNRAY-VVKGLMVARRQGNPGLKALIERVNISSPITA-ENLGY-MIGP----SINAGGRIGES-----NLGSRLLI  322 (600)
Q Consensus       255 pL~~eNR~l-vk~GL~~l~~~~~~gl~~L~~~~~~~~~i~~-~di~f-~iaP----rINAaGRl~~a-----~~av~lL~  322 (600)
                      |-..-+|+. +|+-++.+   ..-||+.+|++.= +-..+. ++=.| ++.|    |.|.-|-+.+.     +.|-|=.+
T Consensus       241 P~~P~~RI~ELKqmi~~l---H~~GirVImDVVY-NH~y~~G~~S~Fek~VPgYyyR~~~~G~~~NGtGvGNdtASEr~M  316 (655)
T TIGR02104       241 PYDPATRILELKQMIQAL---HENGIRVIMDVVY-NHTYSRGEESPFEKTVPGYYYRYNEDGTFSNGTGVGNDTASEREM  316 (655)
T ss_pred             CCCCCCHHHHHHHHHHHH---HHCCCEEEEEECC-CCCCCCCCCCCHHHCCCCHHEEECCCCCCCCCCCCCCCCCCCCHH
T ss_conf             887730767888999999---8668879985024-760334675850003872111147888824764354760000222


Q ss_pred             CC-CHHHHHHH----------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCHHHHHH
Q ss_conf             34-25899999----------------99999899999999999999999998752112434750262057858122222
Q gi|254780901|r  323 SD-DSQELEML----------------AMKLDVLNQNRRLMESAMLEQAEAKVLTQCDDIQQASVIVVEGDRWHPGIVGL  385 (600)
Q Consensus       323 ~~-d~~~a~~l----------------a~~L~~lN~~Rk~~e~~i~~~a~~~~~~~~~~~~~~~~ivv~~~~wh~GViGI  385 (600)
                      .. =.-+.-.+                .-..+.+|.=|+++.                  +-++.|+||||+|--+=++|
T Consensus       317 ~RKfIvDSv~YW~~EYniDGFRFDLMGihD~~TMn~ir~~l~------------------~Idp~IlLyGEGWDl~~tpL  378 (655)
T TIGR02104       317 MRKFIVDSVLYWVKEYNIDGFRFDLMGIHDIETMNEIRKALN------------------KIDPSILLYGEGWDLGGTPL  378 (655)
T ss_pred             HHHHHHHHEEEEEEEECCCCCHHHHCCHHHHHHHHHHHHHHH------------------HCCCCEEEECCCCCCCCCCC
T ss_conf             005424401012001046762010123436999999999985------------------33983799745778767888


Q ss_pred             HHHHHH---HHHHCEEEEEEECC--CCEEEE-EEEC
Q ss_conf             278998---84201079988637--983799-9864
Q gi|254780901|r  386 LAARLK---EKFGRPSFAISFEE--DGKGIG-SGRS  415 (600)
Q Consensus       386 VAsrL~---e~y~kP~iv~s~~~--dg~~kG-S~RS  415 (600)
                      -+.+-+   ..+.-|-|.+=-|+  |+ +|| |.=.
T Consensus       379 ~~~~KA~~~NA~~mp~Ia~FND~fRDa-lKGasvF~  413 (655)
T TIGR02104       379 PPEQKATKANAYQMPGIAFFNDEFRDA-LKGASVFD  413 (655)
T ss_pred             CHHHHHHHHHHHHCCCEEECCCCCCCC-CCCCCCCC
T ss_conf             832235898898558323015632365-00454357


No 484
>PRK06752 single-stranded DNA-binding protein; Validated
Probab=34.64  E-value=29  Score=14.23  Aligned_cols=54  Identities=13%  Similarity=0.318  Sum_probs=40.5

Q ss_pred             EEEEEEECCCCCCHHHHHHCCCCCEEEEEEEEEEEEECCC-----CEEEEEEEEEEECCCC
Q ss_conf             7999997787870123553069987999999766545781-----1058999980111311
Q gi|254780901|r  540 TLQAIAFRVYGTPLGEFLMQSRGKRMHVTGHLCVNYWRGS-----KRCQLRVLDASPVEGH  595 (600)
Q Consensus       540 ~i~aI~Fn~~~~~~~~~~~~~~g~~idii~~l~~N~~~G~-----~s~QL~I~Di~p~e~~  595 (600)
                      .++++.|+-......+++  ..|..+-+-++++.+.|.++     .+.++.+..+...+..
T Consensus        48 f~~~~~w~k~Ae~~~~yl--~KG~~V~v~Grl~~~~y~~~~G~~~~~~eVvv~~v~fL~~k  106 (112)
T PRK06752         48 FINCVVWRKSAENVTEYC--TKGSLVGITGRIHTSNYEDDQGKRIYRTEVVIESITFLERR  106 (112)
T ss_pred             EEEEEEECHHHHHHHHHH--CCCCEEEEEEEEECCCEECCCCCEEEEEEEEEEEEEECCCC
T ss_conf             999999965898999984--79999999999984610999997999999999999977578


No 485
>PRK11192 ATP-dependent RNA helicase SrmB; Provisional
Probab=34.61  E-value=29  Score=14.23  Aligned_cols=117  Identities=12%  Similarity=0.190  Sum_probs=55.9

Q ss_pred             HHHCCCHHHHHHHHHCCCCHHHHHHHCCCCHHHCCCCHHHCCCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHH
Q ss_conf             88199999999999678897898866196677718995561487999999999997799799994078861528999999
Q gi|254780901|r   35 QKHAIPDIVARVLVNRNVSIDYAKDFLNPSIRLLMPDPLILTDCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMR  114 (600)
Q Consensus        35 ~~~~~~~~~a~iL~~Rgi~~~~~~~fL~p~l~~l~~dP~~l~dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~  114 (600)
                      +++++++.+.+-|...||+.               |.|     +++.+   ..++-+++.+++.. ---=|=|.+.+|--
T Consensus         6 ~~l~L~~~l~~~L~~~g~~~---------------pT~-----IQ~~a---Ip~il~g~dvl~~A-~TGSGKTlaylLPi   61 (417)
T PRK11192          6 EELDLDPSLLEALQDKGYTR---------------PTA-----IQAEA---IPPALDGRDVLGSA-PTGTGKTAAFLLPA   61 (417)
T ss_pred             HHCCCCHHHHHHHHHCCCCC---------------CCH-----HHHHH---HHHHHCCCCEEEEC-CCCCHHHHHHHHHH
T ss_conf             77798999999999779999---------------999-----99999---99997799889989-99867999999999


Q ss_pred             H--H-H----HC-CCCEEEEECCCCCCCCCCCHHHHHHH--HHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEEC
Q ss_conf             9--9-9----76-99479980787433668897898874--20268689996488762345555541798279961
Q gi|254780901|r  115 F--L-S----HC-SVNANMYIPDRIVDGYGPNPSLMEKF--INEGAQLIITVDCGSTSYDALQYATNQGIDVIVID  180 (600)
Q Consensus       115 ~--L-~----~~-g~~v~~~IP~R~~eGYGl~~~~i~~~--~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtD  180 (600)
                      .  | .    .- ...+-+..|.|.-     -.-..+.+  ...+..+-+.+=+|-.+.......-..|.|++|.-
T Consensus        62 l~~l~~~~~~~~~~~~~LIl~PTrEL-----a~Qi~~~~~~l~~~~~i~~~~i~Gg~~~~~q~~~l~~~~dIlV~T  132 (417)
T PRK11192         62 LQHLLDFPRRKSGPPRILILTPTREL-----AMQVADQARELAKHTHLDIATITGGVAYMNHAEVFSENQDIVVAT  132 (417)
T ss_pred             HHHHHHHHCCCCCCCEEEEEECHHHH-----HHHHHHHHHHHHCCCCCCEEEEECCCCHHHHHHHHHCCCCEEEEC
T ss_conf             99987521036899649999471999-----999999999864005730599856878799999983699989978


No 486
>PRK08249 cystathionine gamma-synthase; Provisional
Probab=34.61  E-value=29  Score=14.23  Aligned_cols=93  Identities=17%  Similarity=0.279  Sum_probs=50.6

Q ss_pred             CHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEE
Q ss_conf             87999999999997799799994078861528999999999769947998078743366889789887420268689996
Q gi|254780901|r   77 DCDKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITV  156 (600)
Q Consensus        77 dm~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItv  156 (600)
                      +|.....-+...++.+..|++-.  ++=|-| -.++.++|.++|.++.++=|.        ..+.++.....++++|.. 
T Consensus        88 GmaAis~~l~~ll~~Gd~vv~~~--~~YggT-~~l~~~~l~~~Gi~v~fvd~~--------d~~~~~~ai~~~Tklv~~-  155 (398)
T PRK08249         88 GMAAISNTLYTFLSPGDRVVSIK--DTYGGT-NKIFEEFLPRMGVDVTLCETG--------DHEQIEREIAKGCDLLYL-  155 (398)
T ss_pred             HHHHHHHHHHHHHCCCCEEEECC--CCCHHH-HHHHHHHHCCCCEEEEEECCC--------CHHHHHHHCCCCCEEEEE-
T ss_conf             89999999999718999899818--984379-999997601598699987999--------869999855888618998-


Q ss_pred             CCC------CCCHHHHH-HHHHCCCCEEEECCC
Q ss_conf             488------76234555-554179827996154
Q gi|254780901|r  157 DCG------STSYDALQ-YATNQGIDVIVIDHH  182 (600)
Q Consensus       157 D~G------i~~~e~i~-~a~~~GidvIVtDHH  182 (600)
                      ..=      +.+.++|. .|++.|+-++| |.-
T Consensus       156 EtpsNP~l~v~Di~~ia~iA~~~g~~~vV-DNT  187 (398)
T PRK08249        156 ETPTNPTLKITDIRRLSAAAHEVGALVVV-DNT  187 (398)
T ss_pred             ECCCCCCCEEECHHHHHHHHHHCCCEEEE-ECC
T ss_conf             44899974666479999999874996998-477


No 487
>cd06304 PBP1_BmpA_like Periplasmic binding component of a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria. Periplasmic binding component of a family of basic membrane lipoproteins from Borrelia and various putative lipoproteins from other bacteria. These outer membrane proteins include Med, a cell-surface localized protein regulating the competence transcription factor gene comK in Bacillus subtilis, and PnrA, a periplasmic purine nucleoside binding protein of an ATP-binding cassette (ABC) transport system in Treponema pallidum. All contain the type I periplasmic sugar-binding protein-like fold.
Probab=34.54  E-value=29  Score=14.22  Aligned_cols=89  Identities=17%  Similarity=0.109  Sum_probs=51.5

Q ss_pred             HHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHH-HHHH-CCCCEEEECCCCCCCCCCCC
Q ss_conf             999976994799807874336688978988742026868999648876234555-5541-79827996154476555672
Q gi|254780901|r  114 RFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQ-YATN-QGIDVIVIDHHQVKSEEIPA  191 (600)
Q Consensus       114 ~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~-~a~~-~GidvIVtDHH~~~~~~p~a  191 (600)
                      ++-+.+|.++.++=+.-..+    -.+.++.+.++|++|||++  |..-.+.+. .|.+ -.+..++.|-+...   ++.
T Consensus        25 ~~~~~~g~~~~~~e~~~~~d----~~~~~~~~~~~g~~lIi~~--g~~~~~~~~~~A~~~P~~~F~~~~~~~~~---~~N   95 (260)
T cd06304          25 KAEKELGVEVKYVESVEDAD----YEPNLRQLAAQGYDLIFGV--GFGFMDAVEKVAKEYPDVKFAIIDGVVDA---PPN   95 (260)
T ss_pred             HHHHHHCCEEEEEECCCHHH----HHHHHHHHHHCCCCEEEEC--CHHHHHHHHHHHHHCCCCEEEEECCCCCC---CCC
T ss_conf             99998698599990699899----9999999998799999993--67777999999998899879996465688---897


Q ss_pred             EEEECCCCCCCCCCCCCHHHHHHH
Q ss_conf             565237888864334430478899
Q gi|254780901|r  192 YALVNPNRLDDLSGQGHLCAAGVV  215 (600)
Q Consensus       192 ~aivNP~~~~~~~p~~~l~gaGva  215 (600)
                      +.-+..+.    +.-.+|+|+--+
T Consensus        96 v~~~~~~~----~e~~ylaG~~Aa  115 (260)
T cd06304          96 VASYVFRE----YEGSYLAGVLAA  115 (260)
T ss_pred             EEEEECCC----CHHHHHHHHHHH
T ss_conf             89997643----023589999999


No 488
>TIGR03360 VI_minor_1 type VI secretion-associated protein, VC_A0118 family. Members of this protein family, including VC_A0118 from Vibrio cholerae El Tor N16961, are restricted to a subset of bacteria with the type VI secretion system, and are encoded among the type VI-associated pathogenicity islands. However, many species with type VI secretion lack a member of this family. This lack suggests that members of this family may be targets rather than components of the type VI secretion system.
Probab=34.49  E-value=29  Score=14.21  Aligned_cols=57  Identities=23%  Similarity=0.299  Sum_probs=41.6

Q ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCEEECCCCHHHHHHHHHHH
Q ss_conf             379837999864898618888885303353011565322231464222158899999999
Q gi|254780901|r  404 EEDGKGIGSGRSIEGFDIGKMVSFAVEEGILVKGGGHAMAAGLTVERVNFGRLCDFFQKF  463 (600)
Q Consensus       404 ~~dg~~kGS~RSi~g~~l~~~l~~~~~~~ll~~~GGH~~AaG~ti~~~~l~~f~~~l~~~  463 (600)
                      +++|+.--|+|..++++..+.+-..  +-|-.+ +.+..+-|+++....+..-.+-+-+.
T Consensus       126 re~G~ll~sgRGLpaIe~iK~l~~~--~~L~lr-s~~~~~dgL~Fd~~gL~~ai~PLR~a  182 (185)
T TIGR03360       126 RENGLLLESGRGLPAIEEIKRLIGA--RRLTVR-GDNGAADGLRFDLSGLNEALDPLRQQ  182 (185)
T ss_pred             CCCCEEEECCCCCHHHHHHHHHHCC--CEEEEE-CCCCCCCCEEEEHHHHHHHHHHHHHH
T ss_conf             4896498637993699999998479--869997-58987552688825268888999986


No 489
>cd06337 PBP1_ABC_ligand_binding_like_4 Type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. This subgroup includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type active transport systems that are predicted to be involved in transport of amino acids, peptides, or inorganic ions. Members of this group are sequence-similar to members of the family of ABC-type hydrophobic amino acid transporters, such as leucine-isoleucine-valine-binding protein (LIVBP); however their ligand specificity has not been determined experimentally.
Probab=34.41  E-value=29  Score=14.20  Aligned_cols=10  Identities=20%  Similarity=0.405  Sum_probs=4.0

Q ss_pred             HHHHCCCCEE
Q ss_conf             5541798279
Q gi|254780901|r  168 YATNQGIDVI  177 (600)
Q Consensus       168 ~a~~~GidvI  177 (600)
                      .+.+.|+-.|
T Consensus        88 ~~~~~~vp~i   97 (357)
T cd06337          88 QCEANGVPCI   97 (357)
T ss_pred             HHHHHCCCEE
T ss_conf             9998399778


No 490
>COG0677 WecC UDP-N-acetyl-D-mannosaminuronate dehydrogenase [Cell envelope biogenesis, outer membrane]
Probab=34.41  E-value=29  Score=14.20  Aligned_cols=14  Identities=21%  Similarity=0.261  Sum_probs=5.8

Q ss_pred             EECCCCCCHHHHHH
Q ss_conf             86489861888888
Q gi|254780901|r  413 GRSIEGFDIGKMVS  426 (600)
Q Consensus       413 ~RSi~g~~l~~~l~  426 (600)
                      .|--+.+++.+.|.
T Consensus       339 ~ReSPa~~ii~~l~  352 (436)
T COG0677         339 LRESPALDIIELLE  352 (436)
T ss_pred             CCCCCHHHHHHHHH
T ss_conf             01483589999999


No 491
>PRK08266 hypothetical protein; Provisional
Probab=34.33  E-value=29  Score=14.19  Aligned_cols=70  Identities=19%  Similarity=0.173  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCC--CCEEEEECCCCCCHHHHHHHHHCCCCEEEECC
Q ss_conf             52899999999976994799807874336688978988742026--86899964887623455555417982799615
Q gi|254780901|r  106 AASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEG--AQLIITVDCGSTSYDALQYATNQGIDVIVIDH  181 (600)
Q Consensus       106 itstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g--~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDH  181 (600)
                      +|++-+|.++|++.|.+..|-+|-      +-+...++.+.+.+  .++|.+.+=....+-+-.|++..|--.+++=|
T Consensus         1 mtg~~~l~~~L~~~Gv~~vFg~pG------~~~~~l~dal~~~~~~i~~v~~~hE~~A~~~A~gyar~tg~~gv~~~t   72 (531)
T PRK08266          1 MTGGEAIVRGLVAHGVDTVFGIPG------AQLYGLFDALAKAADQIRFIGTRHEQAAGYMAFGYARSTGRPGVFSVV   72 (531)
T ss_pred             CCHHHHHHHHHHHCCCCEEEECCC------CCHHHHHHHHHHCCCCCEEEEECCHHHHHHHHHHHHHHHCCCEEEEEC
T ss_conf             958999999999879989998489------555999999996589966991287899999999999997997899982


No 492
>PRK10437 carbonic anhydrase; Provisional
Probab=34.30  E-value=24  Score=14.83  Aligned_cols=17  Identities=35%  Similarity=0.718  Sum_probs=0.0

Q ss_pred             CCEEEEECCCCCHHHHH
Q ss_conf             97999940788615289
Q gi|254780901|r   93 EKIMIFGDYDVDGAASV  109 (600)
Q Consensus        93 ekI~I~gDyD~DGitst  109 (600)
                      +.|.|+|+|+|-|+.+.
T Consensus        91 ~~IIVcGHs~CGgv~A~  107 (220)
T PRK10437         91 EHIIICGHYGCGGVQAA  107 (220)
T ss_pred             CEEEEECCCCCCHHHHH
T ss_conf             87999558764057888


No 493
>COG1692 Calcineurin-like phosphoesterase [General function prediction only]
Probab=34.27  E-value=29  Score=14.19  Aligned_cols=58  Identities=21%  Similarity=0.437  Sum_probs=0.0

Q ss_pred             CEEEEECCCCCHHHHHHHHHHHH----HHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEE
Q ss_conf             79999407886152899999999----9769947998078743366889789887420268689
Q gi|254780901|r   94 KIMIFGDYDVDGAASVALMMRFL----SHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLI  153 (600)
Q Consensus        94 kI~I~gDyD~DGitstail~~~L----~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~Li  153 (600)
                      ||++.|  |+=|-++--.+.+.|    +....++...=..--.-|.|+++...+.+++.|++.+
T Consensus         2 riLfiG--DvvGk~Gr~~v~~~Lp~lk~kyk~dfvI~N~ENaa~G~Git~k~y~~l~~~G~dvi   63 (266)
T COG1692           2 RILFIG--DVVGKPGRKAVKEHLPQLKSKYKIDFVIVNGENAAGGFGITEKIYKELLEAGADVI   63 (266)
T ss_pred             EEEEEE--CCCCCCHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCHHHHHHHHHHCCCEE
T ss_conf             489982--22473128999987077787506738998573045776777999999998588789


No 494
>cd05800 PGM_like2 This PGM-like (phosphoglucomutase-like) protein of unknown function belongs to the alpha-D-phosphohexomutase superfamily and is found in both archaea and bacteria. The alpha-D-phosphohexomutases include several related enzymes that catalyze a reversible intramolecular phosphoryl transfer on their sugar substrates. Other members of this superfamily include phosphoglucosamine mutase (PNGM), phosphoacetylglucosamine mutase (PAGM), the bacterial phosphomannomutase ManB, the bacterial phosphoglucosamine mutase GlmM, and the bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM). Each of these enzymes has four structural domains (subdomains) with a centrally located active site formed by four loops, one from each subdomain. All four subdomains are included in this alignment model.
Probab=34.23  E-value=29  Score=14.18  Aligned_cols=47  Identities=15%  Similarity=0.136  Sum_probs=0.0

Q ss_pred             HHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCCCCCCC
Q ss_conf             887420268689996488762345555541798279961544765556
Q gi|254780901|r  142 MEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKSEEI  189 (600)
Q Consensus       142 i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~~~~~~p  189 (600)
                      ++.+...+.+++|.+.+|++..-.-..+.++|++|+.+ |..|.+..|
T Consensus       166 ~~~i~~~~lkIvid~~~G~~~~~~~~ll~~lg~~v~~~-~~~~d~~f~  212 (461)
T cd05800         166 LEAIREAGLKVVVDPMYGAGAGYLEELLRGAGVDVEEI-RAERDPLFG  212 (461)
T ss_pred             HHHHHCCCCEEEEECCCCHHHHHHHHHHHHHCCEEEEE-CCCCCCCCC
T ss_conf             55551269779998899656655899998609749997-771479999


No 495
>COG2826 Tra8 Transposase and inactivated derivatives, IS30 family [DNA replication, recombination, and repair]
Probab=34.13  E-value=9.4  Score=18.03  Aligned_cols=85  Identities=18%  Similarity=0.127  Sum_probs=0.0

Q ss_pred             EECCCCCHHHH-----HHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHC--CCCEEEEECCCCCCHHHHHHHH
Q ss_conf             94078861528-----9999999997699479980787433668897898874202--6868999648876234555554
Q gi|254780901|r   98 FGDYDVDGAAS-----VALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINE--GAQLIITVDCGSTSYDALQYAT  170 (600)
Q Consensus        98 ~gDyD~DGits-----tail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~--g~~LiItvD~Gi~~~e~i~~a~  170 (600)
                      +|+|.+|=+..     ++|+...=+.--..+-..+|+|..  +.++..+++.+..-  ...-=||.|+|+--..-.+...
T Consensus       164 ~GHWE~D~vv~~~~~~~~l~tLveRksR~~ii~k~~~~~s--~~v~~~l~~~~~~~p~~~r~SiT~DrG~Efa~~~~l~~  241 (318)
T COG2826         164 FGHWEGDTVVGLRTKNSNLLTLVERKTRYTIIRKLDSRTS--QPVNARLKDIMKKLPFFLRKSITFDRGTEFARHSELEK  241 (318)
T ss_pred             CCCEEEEEEEECCCCCCEEEEEEEEEEEEEEEEECCCCCC--HHHHHHHHHHHHCCCCHHHEEEECCCCHHHHHHHHHHH
T ss_conf             5731311443204676336898630254788774587643--04899999985026603420020158645687888886


Q ss_pred             HCCCCEEEECCCCC
Q ss_conf             17982799615447
Q gi|254780901|r  171 NQGIDVIVIDHHQV  184 (600)
Q Consensus       171 ~~GidvIVtDHH~~  184 (600)
                      .+|++|--.|-|.|
T Consensus       242 ~l~~~vyfcdp~ap  255 (318)
T COG2826         242 RLGADVYFADPYAS  255 (318)
T ss_pred             HCCCCEEECCCCCC
T ss_conf             23881586389981


No 496
>TIGR02298 HpaD_Fe 3,4-dihydroxyphenylacetate 2,3-dioxygenase; InterPro: IPR011984    This enzyme catalyses the ring-opening step in the degradation of 4-hydroxyphenylacetate ..
Probab=33.96  E-value=19  Score=15.65  Aligned_cols=23  Identities=30%  Similarity=0.508  Sum_probs=0.0

Q ss_pred             CCCHHHH-HHHHHCCCCEEE-ECCC
Q ss_conf             7623455-555417982799-6154
Q gi|254780901|r  160 STSYDAL-QYATNQGIDVIV-IDHH  182 (600)
Q Consensus       160 i~~~e~i-~~a~~~GidvIV-tDHH  182 (600)
                      |..+.|| ++|||+|+|+|| .|=|
T Consensus        92 idghkEi~~rakE~~VdTivVfDtH  116 (343)
T TIGR02298        92 IDGHKEISRRAKEMGVDTIVVFDTH  116 (343)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEECCH
T ss_conf             9998888643100468669996320


No 497
>cd01545 PBP1_SalR Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. Ligand-binding domain of DNA transcription repressor SalR, a member of the LacI-GalR family of bacterial transcription regulators. The SalR binds to glucose based compound Salicin which is chemically related to aspirin. The ligand-binding of SalR is structurally homologous to the periplasmic sugar-binding domain of ABC-transporters and both domains contain the type I periplasmic binding protein-like fold. The LacI-GalR family repressors are composed of two functional domains: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal ligand-binding domain, which is homologous to the type I periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcription repressor undergoes a conformational change upon ligand bind
Probab=33.94  E-value=29  Score=14.15  Aligned_cols=75  Identities=8%  Similarity=-0.011  Sum_probs=0.0

Q ss_pred             HHHHHHHCCCCEEEE-ECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCCCCCCC
Q ss_conf             999999769947998-078743366889789887420268689996488762345555541798279961544765556
Q gi|254780901|r  112 MMRFLSHCSVNANMY-IPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQGIDVIVIDHHQVKSEEI  189 (600)
Q Consensus       112 l~~~L~~~g~~v~~~-IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~GidvIVtDHH~~~~~~p  189 (600)
                      +.+.++..|..+... .-+.-.+   .....++.+.+.+++-+|.+.+...+.+-++.+++.|+.++..|...+....+
T Consensus        21 i~~~~~~~GY~~~i~~~~~~~~~---~~~~~~~~l~~~~vdGiIl~~~~~~~~~~~~~l~~~~iPvV~i~~~~~~~~~~   96 (270)
T cd01545          21 ALDACRDTGYQLVIEPCDSGSPD---LAERVRALLQRSRVDGVILTPPLSDNPELLDLLDEAGVPYVRIAPGTPDPDSP   96 (270)
T ss_pred             HHHHHHHCCCEEEEEECCCCCHH---HHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCCCCEEEECCCCCCCCCC
T ss_conf             99999984998999969999989---99999999996699989994788899999999997799799987887789997


No 498
>PRK07525 sulfoacetaldehyde acetyltransferase; Validated
Probab=33.81  E-value=29  Score=14.13  Aligned_cols=68  Identities=12%  Similarity=0.097  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHCC-CCEEEE
Q ss_conf             52899999999976994799807874336688978988742026868999648876234555554179-827996
Q gi|254780901|r  106 AASVALMMRFLSHCSVNANMYIPDRIVDGYGPNPSLMEKFINEGAQLIITVDCGSTSYDALQYATNQG-IDVIVI  179 (600)
Q Consensus       106 itstail~~~L~~~g~~v~~~IP~R~~eGYGl~~~~i~~~~~~g~~LiItvD~Gi~~~e~i~~a~~~G-idvIVt  179 (600)
                      +|.+-.+.++|+..|.+..|=+|-      +-+...++.+.+.|.+.|.+..=....+-+-.|++-.| .-|+++
T Consensus         6 mt~aeaiv~~L~~~GV~~vFG~pG------~~~~~~~d~~~~~~i~~I~~rhE~~A~~mAdgyar~tg~~gv~~~   74 (589)
T PRK07525          6 MTPSEAFVETLQAHGITHAFGIIG------SAFMDASDLFPPAGIRFIDVAHEQNAGHMADGYTRVTGRMGMVIG   74 (589)
T ss_pred             EEHHHHHHHHHHHCCCCEEEECCC------HHHHHHHHHHHHCCCEEEEECCHHHHHHHHHHHHHHHCCCEEEEE
T ss_conf             679999999999879989997886------407999997775598198209789999999999999799889999


No 499
>pfam04800 ETC_C1_NDUFA4 ETC complex I subunit conserved region. Family of pankaryotic NADH-ubiquinone oxidoreductase subunits (EC:1.6.5.3) (EC:1.6.99.3) from complex I of the electron transport chain initially identified in Neurospora crassa as a 21 kDa protein.
Probab=33.76  E-value=29  Score=14.25  Aligned_cols=38  Identities=21%  Similarity=0.205  Sum_probs=0.0

Q ss_pred             CCHHHHHHHHHCCCCEEEECCCCCCCCCCCCEEEECCCCCCCCCCCC
Q ss_conf             62345555541798279961544765556725652378888643344
Q gi|254780901|r  161 TSYDALQYATNQGIDVIVIDHHQVKSEEIPAYALVNPNRLDDLSGQG  207 (600)
Q Consensus       161 ~~~e~i~~a~~~GidvIVtDHH~~~~~~p~a~aivNP~~~~~~~p~~  207 (600)
                      +-.++|+||..+|++..|.+-+..         -+.|+-..++|.+.
T Consensus        57 skE~Ai~YA~k~gi~y~V~ep~~r---------k~~~KsYadNF~~~   94 (101)
T pfam04800        57 TKEAAIAFAERQGWEYDVEEPNAP---------KAKPKAYSDNFSWN   94 (101)
T ss_pred             CHHHHHHHHHHCCCEEEEECCCCC---------CCCCCCHHHHCCCC
T ss_conf             999999999984982899578866---------57745588967777


No 500
>TIGR03254 oxalate_oxc oxalyl-CoA decarboxylase. In a number of bacteria, including Oxalobacter formigenes from the human gut, a two-gene operon of oxc (oxalyl-CoA decarboxylase) and frc (formyl-CoA transferase) encodes a system for degrading and therefore detoxifying oxalate. Members of this family are the thiamine pyrophosphate (TPP)-containing enzyme oxalyl-CoA decarboxylase.
Probab=33.63  E-value=30  Score=14.11  Aligned_cols=80  Identities=11%  Similarity=0.128  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHCCCCEEEEECCCCCHHHHHHHHHHHHHHCCCCEEEEECCC--CCCCCCCCHHHHHHHHHCCCCEEEEE
Q ss_conf             9999999999977997999940788615289999999997699479980787--43366889789887420268689996
Q gi|254780901|r   79 DKAARRIVQAIYNSEKIMIFGDYDVDGAASVALMMRFLSHCSVNANMYIPDR--IVDGYGPNPSLMEKFINEGAQLIITV  156 (600)
Q Consensus        79 ~~A~~ri~~ai~~~ekI~I~gDyD~DGitstail~~~L~~~g~~v~~~IP~R--~~eGYGl~~~~i~~~~~~g~~LiItv  156 (600)
                      ...++++.+.+.+-++.+|+..+-+.---+..-+.++.+.+++-|......|  +.|.|-++........-+..||||.+
T Consensus       193 ~~~i~~a~~~L~~AkrPvIi~G~g~~~~~a~~~l~~lae~~~iPv~tt~~gkg~~~~~hp~~~g~~~~~~l~~aDlvl~l  272 (554)
T TIGR03254       193 PDSVDRAVELLKDAKRPLILLGKGAAYAQADEEIREFVEKTGIPFLPMSMAKGLLPDTHPQSAAAARSFALAEADVVMLV  272 (554)
T ss_pred             HHHHHHHHHHHHHCCCCEEEECCCCCHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCCCCHHHHHHHHHCCCCEEEEE
T ss_conf             99999999999827996899688621444899999999972983896245477478888743568998774658799993


Q ss_pred             CC
Q ss_conf             48
Q gi|254780901|r  157 DC  158 (600)
Q Consensus       157 D~  158 (600)
                      .|
T Consensus       273 G~  274 (554)
T TIGR03254       273 GA  274 (554)
T ss_pred             CC
T ss_conf             36


Done!