Query         gi|254781225|ref|YP_003065638.1| P4 family phage/plasmid primase [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 789
No_of_seqs    322 out of 861
Neff          8.2 
Searched_HMMs 39220
Date          Mon May 30 07:05:57 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254781225.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK07078 hypothetical protein; 100.0       0       0  726.2  41.2  427  305-774    70-499 (510)
  2 COG3378 Phage associated DNA p 100.0       0       0  532.5  28.0  347  415-773   139-498 (517)
  3 TIGR01613 primase_Cterm phage/ 100.0       0       0  407.2  22.1  302  427-736     1-314 (316)
  4 pfam09250 Prim-Pol Bifunctiona  99.9 7.1E-21 1.8E-25  156.4  14.8  140   10-153     1-149 (161)
  5 pfam08706 D5_N D5 N terminal l  99.9 1.2E-20   3E-25  154.9  14.1  143  315-478     3-145 (145)
  6 cd04859 Prim_Pol Prim_Pol: Pri  99.8 6.8E-20 1.7E-24  149.8  15.0  143   18-171     1-151 (152)
  7 pfam08707 PriCT_2 Primase C te  99.2 6.7E-11 1.7E-15   90.1   7.3   61  224-293    13-73  (74)
  8 cd00525 AE_Prim_S_like AE_Prim  99.0   2E-09 5.1E-14   80.3   7.5  113   18-149     1-133 (136)
  9 COG4983 Uncharacterized conser  99.0 5.1E-10 1.3E-14   84.2   4.1  419   34-517    51-494 (495)
 10 pfam05272 VirE Virulence-assoc  98.9 2.1E-08 5.3E-13   73.5  10.6  181  465-663     9-196 (198)
 11 pfam01057 Parvo_NS1 Parvovirus  98.2 3.3E-05 8.5E-10   52.3  11.0  193  445-661    61-261 (271)
 12 pfam04735 Baculo_helicase Bacu  98.1 3.5E-06 8.9E-11   58.8   5.1  139  490-639   867-1007(1173)
 13 COG5545 Predicted P-loop ATPas  98.1 3.8E-05 9.6E-10   51.9  10.0  182  465-672   159-347 (517)
 14 pfam00519 PPV_E1_C Papillomavi  98.0 0.00012   3E-09   48.7  10.2  156  463-637   228-385 (432)
 15 pfam03288 Pox_D5 Poxvirus D5 p  97.5 0.00016   4E-09   47.8   5.1   54  689-745     1-55  (88)
 16 PRK03992 proteasome-activating  97.5  0.0053 1.3E-07   37.7  12.5  209  411-627    52-294 (390)
 17 smart00763 AAA_PrkA PrkA AAA d  97.2  0.0011 2.9E-08   42.1   6.3   55  475-529    52-106 (361)
 18 KOG3712 consensus               97.2  0.0009 2.3E-08   42.8   5.7   11  649-659   573-583 (736)
 19 pfam05496 RuvB_N Holliday junc  97.0   0.026 6.6E-07   33.1  11.8  145  473-628    23-171 (234)
 20 pfam08298 AAA_PrkA PrkA AAA do  96.7  0.0043 1.1E-07   38.3   5.5   55  475-529    59-113 (358)
 21 PRK00440 rfc replication facto  96.5    0.01 2.6E-07   35.7   6.6  135  472-635    14-160 (318)
 22 pfam02257 RFX_DNA_binding RFX   96.3   0.012   3E-07   35.3   6.0   65  693-762     8-72  (73)
 23 KOG0743 consensus               96.3    0.02 5.1E-07   33.8   6.9   87  480-573   215-301 (457)
 24 TIGR02673 FtsE cell division A  96.2  0.0048 1.2E-07   37.9   3.3   79  500-585    27-110 (215)
 25 PRK04195 replication factor C   96.1   0.028 7.1E-07   32.9   7.0  142  472-636    12-162 (403)
 26 PRK00411 cdc6 cell division co  96.1   0.095 2.4E-06   29.3  15.5  273  479-772    36-374 (394)
 27 pfam00004 AAA ATPase family as  96.1  0.0042 1.1E-07   38.4   2.5  123  504-633     1-130 (131)
 28 TIGR00960 3a0501s02 Type II (G  95.9  0.0065 1.7E-07   37.1   3.0   27  500-526    28-54  (216)
 29 cd00009 AAA The AAA+ (ATPases   95.9   0.012   3E-07   35.3   4.1  122  500-632    18-149 (151)
 30 pfam07728 AAA_5 AAA domain (dy  95.8   0.015 3.8E-07   34.7   4.3  123  504-627     2-139 (139)
 31 PRK13531 regulatory ATPase Rav  95.7   0.065 1.7E-06   30.4   7.5   48  577-632   387-434 (498)
 32 COG1222 RPT1 ATP-dependent 26S  95.7    0.15 3.8E-06   28.1  10.9  208  410-625    70-309 (406)
 33 PRK13341 recombination factor   95.3   0.016 4.2E-07   34.4   3.2   41  133-175   136-178 (726)
 34 pfam06431 Polyoma_lg_T_C Polyo  94.6     0.3 7.6E-06   26.0   9.6  179  485-692   140-341 (417)
 35 PRK13900 type IV secretion sys  94.6    0.17 4.4E-06   27.6   6.7   85  435-527   102-186 (332)
 36 TIGR02788 VirB11 P-type DNA tr  94.4    0.16 4.1E-06   27.8   6.3   92  430-529    87-186 (328)
 37 TIGR01242 26Sp45 26S proteasom  94.1   0.062 1.6E-06   30.6   3.6  221  410-635    41-295 (364)
 38 COG2884 FtsE Predicted ATPase   93.9   0.054 1.4E-06   30.9   3.1   28  498-525    25-52  (223)
 39 TIGR02982 heterocyst_DevA ABC   93.8   0.054 1.4E-06   31.0   2.9   17  427-443   203-219 (220)
 40 COG0419 SbcC ATPase involved i  93.8    0.02 5.1E-07   33.8   0.7   16   46-61     19-34  (908)
 41 PRK12402 replication factor C   93.7    0.26 6.7E-06   26.4   6.3   49  472-526    13-61  (337)
 42 TIGR03346 chaperone_ClpB ATP-d  93.6    0.47 1.2E-05   24.7  10.5  155  445-612   530-717 (852)
 43 COG1136 SalX ABC-type antimicr  93.6   0.057 1.5E-06   30.8   2.7   28  499-526    29-56  (226)
 44 TIGR03420 DnaA_homol_Hda DnaA   93.5    0.39 9.9E-06   25.3   6.8   94  457-568     5-100 (226)
 45 PRK10865 protein disaggregatio  93.4    0.51 1.3E-05   24.5   9.9  155  445-612   533-720 (857)
 46 PRK10733 hflB ATP-dependent me  93.3    0.52 1.3E-05   24.4   8.2  166  454-633   145-322 (644)
 47 PRK00080 ruvB Holliday junctio  93.1    0.48 1.2E-05   24.7   6.8  141  467-629    22-173 (328)
 48 KOG1970 consensus               93.0    0.28 7.1E-06   26.2   5.4   22  454-476   258-279 (634)
 49 cd03278 ABC_SMC_barmotin Barmo  92.8    0.12 3.1E-06   28.6   3.5   26  503-528    24-49  (197)
 50 pfam07726 AAA_3 ATPase family   92.8   0.094 2.4E-06   29.4   2.8  120  504-629     2-131 (131)
 51 PRK07261 topology modulation p  92.8    0.11 2.8E-06   28.9   3.2   25  504-528     3-27  (171)
 52 COG3839 MalK ABC-type sugar tr  92.7   0.082 2.1E-06   29.7   2.4   15  126-140    22-37  (338)
 53 cd03239 ABC_SMC_head The struc  92.7    0.18 4.5E-06   27.5   4.1   31  501-531    22-52  (178)
 54 TIGR03345 VI_ClpV1 type VI sec  92.7    0.63 1.6E-05   23.9  10.3  151  449-612   535-718 (852)
 55 pfam05621 TniB Bacterial TniB   92.6    0.18 4.7E-06   27.4   4.1   50  478-527    23-87  (302)
 56 TIGR02881 spore_V_K stage V sp  92.6    0.23 5.8E-06   26.8   4.5  158  471-639     3-178 (261)
 57 TIGR02211 LolD_lipo_ex lipopro  92.6   0.082 2.1E-06   29.8   2.3   22  503-524    33-54  (221)
 58 PRK07429 phosphoribulokinase;   92.5    0.17 4.5E-06   27.6   3.9   42  481-522   265-310 (331)
 59 PRK08118 topology modulation p  92.5    0.13 3.2E-06   28.5   3.2   98  504-627     4-101 (167)
 60 cd03292 ABC_FtsE_transporter F  92.4     0.1 2.6E-06   29.2   2.6   29  499-527    25-53  (214)
 61 pfam00437 GSPII_E Type II/IV s  92.3    0.26 6.6E-06   26.4   4.6   41  479-527   125-165 (283)
 62 PRK05480 uridine kinase; Provi  92.3    0.19 4.9E-06   27.3   3.9   36  499-534     4-39  (209)
 63 TIGR00602 rad24 checkpoint pro  92.3    0.21 5.4E-06   27.0   4.1   21  455-476   291-311 (670)
 64 cd01130 VirB11-like_ATPase Typ  92.1    0.29 7.4E-06   26.1   4.7   48  471-526     3-50  (186)
 65 TIGR03608 L_ocin_972_ABC putat  92.1    0.12   3E-06   28.7   2.6   29  499-527    22-50  (206)
 66 PRK13851 type IV secretion sys  91.9    0.41   1E-05   25.1   5.2   49  471-527   140-188 (343)
 67 TIGR02315 ABC_phnC phosphonate  91.8    0.15 3.8E-06   28.0   2.9   25  502-526    29-53  (253)
 68 PRK00091 miaA tRNA delta(2)-is  91.8    0.14 3.5E-06   28.3   2.7   73  501-576     4-76  (304)
 69 cd03260 ABC_PstB_phosphate_tra  91.7    0.18 4.5E-06   27.5   3.2   28  499-526    24-51  (227)
 70 PRK08939 primosomal protein Dn  91.7    0.61 1.6E-05   23.9   5.9  138  429-569    83-229 (306)
 71 PRK04220 2-phosphoglycerate ki  91.7    0.76 1.9E-05   23.3   6.4   51  485-535    76-126 (306)
 72 pfam01078 Mg_chelatase Magnesi  91.7    0.68 1.7E-05   23.6   6.1  131  474-615     3-161 (207)
 73 TIGR00972 3a0107s01c2 phosphat  91.6    0.21 5.4E-06   27.0   3.4   25  500-524    26-50  (248)
 74 KOG0651 consensus               91.5     0.3 7.8E-06   26.0   4.2  131  497-632   162-302 (388)
 75 TIGR01186 proV glycine betaine  91.5    0.17 4.4E-06   27.6   2.9   10  131-140    18-27  (372)
 76 TIGR00455 apsK adenylylsulfate  91.4    0.19 4.8E-06   27.4   3.0   29  501-529    19-47  (187)
 77 cd03256 ABC_PhnC_transporter A  91.4    0.15 3.9E-06   28.0   2.5   29  499-527    25-53  (241)
 78 pfam05049 IIGP Interferon-indu  91.3    0.39 9.9E-06   25.3   4.6   14   79-92     22-35  (375)
 79 cd03237 ABC_RNaseL_inhibitor_d  91.3    0.17 4.4E-06   27.6   2.7   33  496-528    20-52  (246)
 80 PRK10744 phosphate transporter  91.3     0.5 1.3E-05   24.6   5.1   29  499-527    34-62  (257)
 81 TIGR00968 3a0106s01 sulfate AB  91.3    0.16 4.1E-06   27.8   2.5   26  499-524    24-49  (241)
 82 cd03298 ABC_ThiQ_thiamine_tran  91.3    0.15 3.9E-06   27.9   2.4   28  500-527    23-50  (211)
 83 pfam00910 RNA_helicase RNA hel  91.2    0.33 8.4E-06   25.7   4.1  101  504-612     1-105 (105)
 84 cd03262 ABC_HisP_GlnQ_permease  91.2    0.17 4.3E-06   27.7   2.6   28  499-526    24-51  (213)
 85 PRK11545 gntK gluconate kinase  91.1    0.31   8E-06   25.9   3.9   33  495-527     2-34  (177)
 86 PRK10646 putative ATPase; Prov  91.1    0.76 1.9E-05   23.3   5.9   59  478-540     9-67  (153)
 87 TIGR01846 type_I_sec_HlyB type  91.1    0.16   4E-06   27.9   2.4   47  494-540   484-531 (703)
 88 pfam00493 MCM MCM2/3/5 family.  91.1    0.94 2.4E-05   22.7   9.8  161  468-630    14-201 (327)
 89 TIGR01277 thiQ thiamine ABC tr  91.0    0.17 4.4E-06   27.6   2.5   23  505-527    28-50  (213)
 90 COG2255 RuvB Holliday junction  91.0    0.97 2.5E-05   22.6   6.3  127  472-612    24-160 (332)
 91 pfam00485 PRK Phosphoribulokin  90.8    0.22 5.7E-06   26.9   2.9   29  504-532     2-30  (196)
 92 CHL00176 ftsH cell division pr  90.7       1 2.6E-05   22.5   8.4  165  454-633   170-347 (631)
 93 cd00227 CPT Chloramphenicol (C  90.6    0.37 9.4E-06   25.4   3.9   34  502-535     3-37  (175)
 94 COG0324 MiaA tRNA delta(2)-iso  90.5    0.83 2.1E-05   23.1   5.6   70  503-575     5-74  (308)
 95 PRK10247 putative ABC transpor  90.5    0.24 6.1E-06   26.7   2.8   29  499-527    31-59  (225)
 96 cd03293 ABC_NrtD_SsuB_transpor  90.4    0.21 5.3E-06   27.1   2.4   29  499-527    28-56  (220)
 97 pfam08800 VirE_N VirE N-termin  90.4    0.76 1.9E-05   23.3   5.3   46   63-108    31-77  (136)
 98 pfam00503 G-alpha G-protein al  90.4    0.29 7.4E-06   26.1   3.2   47  481-527   295-343 (350)
 99 COG0802 Predicted ATPase or ki  90.3    0.72 1.8E-05   23.5   5.2   60  477-540     5-65  (149)
100 cd03296 ABC_CysA_sulfate_impor  90.3    0.21 5.4E-06   27.0   2.4   29  499-527    26-54  (239)
101 PRK10535 macrolide transporter  90.2    0.35 8.8E-06   25.6   3.5   13  689-701   565-577 (648)
102 PRK13648 cbiO cobalt transport  90.2    0.25 6.5E-06   26.5   2.7   29  500-528    34-62  (269)
103 PRK13407 bchI magnesium chelat  90.2    0.95 2.4E-05   22.7   5.7  126  503-634    31-201 (334)
104 cd03299 ABC_ModC_like Archeal   90.1    0.23 5.8E-06   26.8   2.5   29  499-527    23-51  (235)
105 COG1116 TauB ABC-type nitrate/  90.1    0.22 5.7E-06   26.9   2.4   22  503-524    31-52  (248)
106 cd03226 ABC_cobalt_CbiO_domain  90.1    0.26 6.5E-06   26.5   2.7   30  499-528    24-53  (205)
107 cd03229 ABC_Class3 This class   90.1    0.24 6.1E-06   26.7   2.5   29  499-527    24-52  (178)
108 PRK11248 tauB taurine transpor  90.0    0.23 5.9E-06   26.8   2.5   23  503-525    29-51  (255)
109 TIGR00618 sbcc exonuclease Sbc  90.0    0.31 7.8E-06   26.0   3.1   16  460-475   534-549 (1063)
110 PHA02244 ATPase-like protein    90.0     1.1 2.7E-05   22.4   5.8  130  501-634   119-260 (383)
111 cd03234 ABCG_White The White s  90.0    0.19   5E-06   27.3   2.0   30  498-527    30-59  (226)
112 PRK08903 hypothetical protein;  89.9    0.63 1.6E-05   23.9   4.6  138  457-628     8-147 (227)
113 PRK09270 frcK putative fructos  89.9     1.1 2.9E-05   22.2   5.9   33  497-529    30-62  (230)
114 PRK13646 cbiO cobalt transport  89.9    0.29 7.3E-06   26.1   2.9   30  499-528    31-60  (286)
115 PRK06893 DNA replication initi  89.9     1.1 2.9E-05   22.2   5.9   87  467-568    13-101 (229)
116 PRK13540 cytochrome c biogenes  89.9    0.25 6.4E-06   26.5   2.5   29  500-528    26-54  (200)
117 cd03257 ABC_NikE_OppD_transpor  89.8    0.26 6.6E-06   26.4   2.6   29  499-527    29-57  (228)
118 cd03261 ABC_Org_Solvent_Resist  89.8    0.25 6.5E-06   26.5   2.5   28  499-526    24-51  (235)
119 cd03300 ABC_PotA_N PotA is an   89.8    0.25 6.3E-06   26.6   2.4   27  500-526    25-51  (232)
120 cd03231 ABC_CcmA_heme_exporter  89.8    0.29 7.3E-06   26.1   2.8   29  500-528    25-53  (201)
121 pfam09079 Cdc6_C CDC6, C termi  89.7     1.1 2.9E-05   22.2   5.8   64  705-772    12-75  (85)
122 cd03297 ABC_ModC_molybdenum_tr  89.7    0.26 6.7E-06   26.4   2.5   25  501-525    23-47  (214)
123 cd00066 G-alpha G protein alph  89.7    0.35   9E-06   25.5   3.2   19  509-527   295-313 (317)
124 COG0470 HolB ATPase involved i  89.6    0.54 1.4E-05   24.3   4.1  129  486-634    10-167 (325)
125 smart00275 G_alpha G protein a  89.6    0.35   9E-06   25.5   3.1   47  480-526   287-335 (342)
126 PRK13644 cbiO cobalt transport  89.6     0.3 7.6E-06   26.0   2.7   24  502-525    29-52  (274)
127 PRK10771 thiQ thiamine transpo  89.6    0.29 7.4E-06   26.1   2.7   31  498-528    22-52  (233)
128 PRK13833 conjugal transfer pro  89.6       1 2.6E-05   22.5   5.5   49  469-525   120-168 (323)
129 pfam07931 CPT Chloramphenicol   89.6    0.45 1.1E-05   24.9   3.7   34  502-535     2-36  (174)
130 TIGR00929 VirB4_CagE type IV s  89.6    0.32 8.1E-06   25.9   2.9   26  505-530   520-545 (931)
131 cd03249 ABC_MTABC3_MDL1_MDL2 M  89.6    0.31 7.8E-06   26.0   2.8   26  501-526    29-54  (238)
132 PRK13634 cbiO cobalt transport  89.6    0.26 6.6E-06   26.4   2.4   29  499-527    18-46  (276)
133 PRK10584 putative ABC transpor  89.5    0.26 6.5E-06   26.5   2.4   30  499-528    34-63  (228)
134 PRK13651 cobalt transporter AT  89.5    0.28 7.1E-06   26.2   2.5   27  501-527    33-59  (304)
135 PRK05642 DNA replication initi  89.4     1.3 3.3E-05   21.8   6.7   97  457-568     9-107 (234)
136 cd03255 ABC_MJ0796_Lo1CDE_FtsE  89.3    0.28 7.2E-06   26.2   2.4   30  499-528    28-57  (218)
137 cd03295 ABC_OpuCA_Osmoprotecti  89.3    0.28 7.3E-06   26.2   2.5   28  499-526    25-52  (242)
138 TIGR01087 murD UDP-N-acetylmur  89.3    0.28   7E-06   26.3   2.4   50  466-525    80-132 (476)
139 cd02023 UMPK Uridine monophosp  89.3    0.33 8.3E-06   25.8   2.8   31  504-534     2-32  (198)
140 cd03254 ABCC_Glucan_exporter_l  89.3     0.3 7.5E-06   26.1   2.5   27  500-526    28-54  (229)
141 COG2766 PrkA Putative Ser prot  89.3    0.73 1.9E-05   23.4   4.5   13  103-115   104-116 (649)
142 PRK01156 chromosome segregatio  89.3    0.53 1.3E-05   24.4   3.8   10   51-60     22-31  (895)
143 cd04104 p47_IIGP_like p47 (47-  89.2    0.26 6.5E-06   26.5   2.2   22  503-524     3-24  (197)
144 PRK13541 cytochrome c biogenes  89.2    0.29 7.5E-06   26.1   2.5   29  499-527    24-52  (195)
145 PRK11629 lolD lipoprotein tran  89.2     0.3 7.5E-06   26.1   2.5   29  499-527    33-61  (233)
146 COG1125 OpuBA ABC-type proline  89.2    0.35 8.8E-06   25.6   2.8   14  226-239    71-84  (309)
147 PRK13641 cbiO cobalt transport  89.2    0.28 7.2E-06   26.2   2.4   29  499-527    31-59  (286)
148 cd02026 PRK Phosphoribulokinas  89.2    0.32 8.3E-06   25.8   2.7  160  505-699     3-165 (273)
149 PRK10908 cell division protein  89.1    0.29 7.3E-06   26.1   2.4   29  499-527    26-54  (222)
150 cd03301 ABC_MalK_N The N-termi  89.1    0.31 7.8E-06   26.0   2.5   28  499-526    24-51  (213)
151 cd03227 ABC_Class2 ABC-type Cl  89.1    0.41   1E-05   25.1   3.2   26  501-526    21-46  (162)
152 cd03233 ABC_PDR_domain1 The pl  89.1    0.26 6.7E-06   26.4   2.2   31  498-528    30-60  (202)
153 PRK13538 cytochrome c biogenes  89.1    0.34 8.7E-06   25.6   2.7   30  499-528    25-54  (204)
154 cd03263 ABC_subfamily_A The AB  89.1    0.31   8E-06   25.9   2.5   29  499-527    26-54  (220)
155 PRK09493 glnQ glutamine ABC tr  89.0    0.33 8.3E-06   25.8   2.6   27  500-526    26-52  (240)
156 COG0444 DppD ABC-type dipeptid  89.0    0.52 1.3E-05   24.5   3.6   13  224-236   156-168 (316)
157 PRK13637 cbiO cobalt transport  89.0     0.3 7.8E-06   26.0   2.4   29  499-527    31-59  (287)
158 PRK06217 hypothetical protein;  89.0    0.42 1.1E-05   25.0   3.2   26  504-529     4-29  (185)
159 cd03247 ABCC_cytochrome_bd The  89.0    0.39 9.9E-06   25.3   3.0   29  500-528    27-55  (178)
160 PRK13544 consensus              89.0    0.35 8.9E-06   25.6   2.7   30  499-528    25-54  (208)
161 cd03289 ABCC_CFTR2 The CFTR su  88.9    0.41   1E-05   25.1   3.1   26  501-526    30-55  (275)
162 cd03248 ABCC_TAP TAP, the Tran  88.9    0.34 8.6E-06   25.7   2.6   28  499-526    38-65  (226)
163 cd03251 ABCC_MsbA MsbA is an e  88.9    0.33 8.3E-06   25.8   2.5   26  501-526    28-53  (234)
164 cd03225 ABC_cobalt_CbiO_domain  88.9    0.38 9.8E-06   25.3   2.9   30  499-528    25-54  (211)
165 TIGR01420 pilT_fam twitching m  88.9    0.33 8.4E-06   25.8   2.5   24  215-239    79-102 (350)
166 cd03294 ABC_Pro_Gly_Bertaine T  88.9    0.31   8E-06   25.9   2.4   27  500-526    49-75  (269)
167 PRK13643 cbiO cobalt transport  88.9    0.32 8.3E-06   25.8   2.5   29  499-527    30-58  (288)
168 COG4619 ABC-type uncharacteriz  88.8    0.37 9.5E-06   25.4   2.8   27  501-527    29-55  (223)
169 COG0714 MoxR-like ATPases [Gen  88.8     1.3 3.4E-05   21.7   5.6  145  469-630    18-183 (329)
170 cd03246 ABCC_Protease_Secretio  88.8    0.34 8.7E-06   25.7   2.6   29  499-527    26-54  (173)
171 cd03228 ABCC_MRP_Like The MRP   88.8    0.34 8.6E-06   25.7   2.5   29  499-527    26-54  (171)
172 PRK10846 bifunctional folylpol  88.7     1.3 3.2E-05   21.9   5.4   10   80-89     34-43  (416)
173 cd03236 ABC_RNaseL_inhibitor_d  88.7    0.33 8.4E-06   25.7   2.5   26  501-526    26-51  (255)
174 PRK11701 phnK phosphonates tra  88.7    0.35 8.9E-06   25.6   2.5   27  501-527    32-58  (258)
175 PRK13635 cbiO cobalt transport  88.7    0.36 9.1E-06   25.5   2.6   25  502-526    34-58  (279)
176 PRK13633 cobalt transporter AT  88.6    0.36 9.1E-06   25.5   2.5   24  502-525    38-61  (281)
177 PRK13649 cbiO cobalt transport  88.5    0.34 8.8E-06   25.6   2.5   28  499-526    31-58  (280)
178 PRK13543 cytochrome c biogenes  88.5    0.36 9.3E-06   25.5   2.6   29  500-528    36-64  (214)
179 TIGR02173 cyt_kin_arch cytidyl  88.5    0.72 1.8E-05   23.5   4.1  101  503-618     2-107 (173)
180 cd03253 ABCC_ATM1_transporter   88.5    0.33 8.5E-06   25.7   2.3   24  502-525    28-51  (236)
181 cd03235 ABC_Metallic_Cations A  88.5    0.37 9.4E-06   25.4   2.6   29  499-527    23-51  (213)
182 cd03369 ABCC_NFT1 Domain 2 of   88.5    0.51 1.3E-05   24.5   3.3   28  500-527    33-60  (207)
183 pfam07724 AAA_2 AAA domain (Cd  88.5     1.2 3.1E-05   22.0   5.2  108  501-612     3-125 (168)
184 PRK13636 cbiO cobalt transport  88.4    0.37 9.4E-06   25.4   2.5   26  501-526    32-57  (285)
185 COG1123 ATPase components of v  88.4     0.7 1.8E-05   23.6   3.9   29  499-527   315-343 (539)
186 PRK13548 hmuV hemin importer A  88.4    0.38 9.6E-06   25.3   2.6   29  500-528    27-55  (257)
187 COG3911 Predicted ATPase [Gene  88.3    0.52 1.3E-05   24.4   3.3   25  500-524     8-32  (183)
188 PRK09984 phosphonate/organopho  88.3    0.39 9.8E-06   25.3   2.6   26  500-525    29-54  (262)
189 PRK13639 cbiO cobalt transport  88.3    0.38 9.7E-06   25.3   2.6   28  500-527    27-54  (275)
190 TIGR00955 3a01204 Pigment prec  88.3    0.47 1.2E-05   24.7   3.0   14  225-238   205-220 (671)
191 PRK10789 putative multidrug tr  88.3    0.57 1.4E-05   24.2   3.4   32  498-529   338-369 (569)
192 cd03244 ABCC_MRP_domain2 Domai  88.2    0.38 9.7E-06   25.3   2.5   28  500-527    29-56  (221)
193 PRK11231 fecE iron-dicitrate t  88.2    0.41 1.1E-05   25.1   2.7   30  499-528    26-55  (255)
194 PRK10851 sulfate/thiosulfate t  88.1    0.38 9.6E-06   25.4   2.4   14  605-618   321-334 (352)
195 pfam06414 Zeta_toxin Zeta toxi  88.1    0.74 1.9E-05   23.4   3.9   31  499-529    10-40  (191)
196 pfam02367 UPF0079 Uncharacteri  88.1    0.61 1.6E-05   23.9   3.5   45  493-537     7-52  (123)
197 COG0563 Adk Adenylate kinase a  88.1    0.52 1.3E-05   24.4   3.1   41  674-718   133-173 (178)
198 PRK13640 cbiO cobalt transport  88.0    0.42 1.1E-05   25.0   2.6   28  500-527    33-60  (283)
199 PRK11247 ssuB aliphatic sulfon  88.0    0.39   1E-05   25.2   2.4   26  501-526    38-63  (257)
200 PRK05291 trmE tRNA modificatio  88.0     1.6 4.1E-05   21.2   5.8   43  481-523   195-238 (445)
201 PRK13650 cbiO cobalt transport  88.0    0.41 1.1E-05   25.1   2.6   25  502-526    31-55  (276)
202 PRK06762 hypothetical protein;  87.9    0.64 1.6E-05   23.8   3.5   28  501-528     2-29  (166)
203 PRK10869 recombination and rep  87.9    0.55 1.4E-05   24.3   3.2  136  428-587   385-527 (553)
204 cd03245 ABCC_bacteriocin_expor  87.9    0.43 1.1E-05   25.0   2.6   27  501-527    30-56  (220)
205 cd03290 ABCC_SUR1_N The SUR do  87.9    0.43 1.1E-05   25.0   2.6   28  500-527    26-53  (218)
206 PRK07667 uridine kinase; Provi  87.9     0.7 1.8E-05   23.6   3.7   32  498-529    10-42  (190)
207 KOG0728 consensus               87.9     1.6 4.2E-05   21.1   9.0  121  498-626   178-306 (404)
208 COG3840 ThiQ ABC-type thiamine  87.8     0.5 1.3E-05   24.6   2.9   23  502-524    26-48  (231)
209 cd03291 ABCC_CFTR1 The CFTR su  87.8    0.41   1E-05   25.1   2.4   24  502-525    64-87  (282)
210 cd03252 ABCC_Hemolysin The ABC  87.8    0.41   1E-05   25.1   2.4   25  502-526    29-53  (237)
211 cd03258 ABC_MetN_methionine_tr  87.7    0.37 9.5E-06   25.4   2.2   25  501-525    31-55  (233)
212 TIGR03258 PhnT 2-aminoethylpho  87.7    0.41   1E-05   25.1   2.4   10  130-139    29-38  (362)
213 PRK13631 cbiO cobalt transport  87.7    0.45 1.2E-05   24.8   2.6   29  499-527    50-78  (320)
214 PRK13894 conjugal transfer ATP  87.6     1.7 4.3E-05   21.0   5.7   48  470-525   126-173 (320)
215 PRK13645 cbiO cobalt transport  87.6    0.44 1.1E-05   24.9   2.5   29  499-527    35-63  (289)
216 PRK10790 putative multidrug tr  87.6    0.67 1.7E-05   23.7   3.4   31  498-528   364-394 (593)
217 PRK10522 multidrug transporter  87.6    0.41   1E-05   25.1   2.3   31  498-528   346-376 (547)
218 pfam06048 DUF927 Domain of unk  87.6     1.7 4.3E-05   21.0  10.9  119  458-584   146-267 (284)
219 cd03224 ABC_TM1139_LivF_branch  87.6    0.44 1.1E-05   24.9   2.5   29  500-528    25-53  (222)
220 cd00267 ABC_ATPase ABC (ATP-bi  87.6    0.43 1.1E-05   25.0   2.4   27  500-526    24-50  (157)
221 TIGR02928 TIGR02928 orc1/cdc6   87.6     1.7 4.4E-05   21.0   5.6  284  455-765     7-378 (383)
222 PRK11831 putative ABC transpor  87.5    0.43 1.1E-05   25.0   2.4   26  501-526    34-59  (269)
223 cd03223 ABCD_peroxisomal_ALDP   87.5    0.36 9.1E-06   25.5   2.0   27  499-525    25-51  (166)
224 cd03214 ABC_Iron-Siderophores_  87.5    0.46 1.2E-05   24.8   2.6   29  499-527    23-51  (180)
225 PRK09536 btuD corrinoid ABC tr  87.5    0.45 1.1E-05   24.9   2.5   50  502-563   265-314 (409)
226 PRK13652 cbiO cobalt transport  87.5    0.43 1.1E-05   25.0   2.4   27  500-526    29-55  (277)
227 COG1660 Predicted P-loop-conta  87.4       1 2.5E-05   22.6   4.2   17  502-518   243-260 (286)
228 TIGR01448 recD_rel helicase, R  87.3    0.64 1.6E-05   23.8   3.2   82  499-600   363-444 (769)
229 COG1126 GlnQ ABC-type polar am  87.3    0.47 1.2E-05   24.7   2.5   12  465-476   228-239 (240)
230 COG1121 ZnuC ABC-type Mn/Zn tr  87.3    0.49 1.3E-05   24.6   2.6   29  500-528    29-57  (254)
231 PRK10619 histidine/lysine/argi  87.2    0.48 1.2E-05   24.7   2.5   25  501-525    31-55  (257)
232 PRK10253 iron-enterobactin tra  87.2    0.45 1.2E-05   24.8   2.4   29  499-527    31-59  (265)
233 TIGR03263 guanyl_kin guanylate  87.2    0.71 1.8E-05   23.5   3.4   27  502-528     2-28  (180)
234 PRK09544 znuC high-affinity zi  87.2    0.49 1.3E-05   24.6   2.6   28  500-527    29-56  (251)
235 PRK10575 iron-hydroxamate tran  87.2    0.51 1.3E-05   24.5   2.6   28  500-527    36-63  (265)
236 PRK11264 putative amino-acid A  87.2     0.5 1.3E-05   24.5   2.6   22  503-524    29-50  (248)
237 PRK13547 hmuV hemin importer A  87.1    0.47 1.2E-05   24.7   2.5   27  500-526    26-52  (273)
238 cd03288 ABCC_SUR2 The SUR doma  87.1    0.57 1.5E-05   24.2   2.9   14  508-521    54-67  (257)
239 PRK11650 ugpC glycerol-3-phosp  87.1    0.46 1.2E-05   24.8   2.4   10  130-139    28-37  (358)
240 CHL00095 clpC Clp protease ATP  87.1     1.8 4.6E-05   20.8   9.8  164  445-612   474-661 (823)
241 PRK13642 cbiO cobalt transport  87.0    0.49 1.3E-05   24.6   2.5   27  501-527    33-59  (277)
242 PRK13657 cyclic beta-1,2-gluca  87.0    0.68 1.7E-05   23.6   3.2   30  499-528   359-388 (585)
243 PRK10078 ribose 1,5-bisphospho  87.0    0.67 1.7E-05   23.7   3.1   26  502-527     3-28  (184)
244 PRK11124 artP arginine transpo  87.0    0.52 1.3E-05   24.4   2.6   25  501-525    28-52  (242)
245 cd03250 ABCC_MRP_domain1 Domai  86.9    0.44 1.1E-05   24.9   2.2   26  500-525    30-55  (204)
246 cd03213 ABCG_EPDR ABCG transpo  86.9     0.4   1E-05   25.2   2.0   28  498-525    32-59  (194)
247 COG1120 FepC ABC-type cobalami  86.9     0.5 1.3E-05   24.6   2.5   30  499-528    26-55  (258)
248 pfam00625 Guanylate_kin Guanyl  86.9     0.7 1.8E-05   23.6   3.2   56  502-568     2-57  (182)
249 PRK13768 GTPase; Provisional    86.9    0.75 1.9E-05   23.4   3.4   24  503-526     4-27  (253)
250 COG4615 PvdE ABC-type sideroph  86.8    0.64 1.6E-05   23.8   3.0   30  499-528   347-376 (546)
251 PRK11176 lipid transporter ATP  86.8    0.65 1.7E-05   23.8   3.0   31  498-528   365-395 (581)
252 PRK02224 chromosome segregatio  86.8     1.1 2.8E-05   22.3   4.2   11   51-61     22-32  (880)
253 PRK10895 putative ABC transpor  86.7    0.52 1.3E-05   24.4   2.5   29  500-528    28-56  (241)
254 PRK13638 cbiO cobalt transport  86.7    0.57 1.5E-05   24.2   2.7   26  502-527    28-53  (271)
255 COG0464 SpoVK ATPases of the A  86.7     1.5 3.9E-05   21.3   4.8   72  498-569   273-346 (494)
256 pfam08419 consensus             86.6     1.3 3.3E-05   21.8   4.5   40  483-523    57-97  (116)
257 cd03267 ABC_NatA_like Similar   86.6    0.54 1.4E-05   24.3   2.5   30  498-527    44-73  (236)
258 PRK13546 teichoic acids export  86.6    0.52 1.3E-05   24.4   2.4   29  499-527    48-76  (264)
259 cd03222 ABC_RNaseL_inhibitor T  86.6    0.53 1.3E-05   24.4   2.5   30  497-526    21-50  (177)
260 cd03240 ABC_Rad50 The catalyti  86.6    0.67 1.7E-05   23.7   3.0   25  501-525    22-46  (204)
261 COG1117 PstB ABC-type phosphat  86.6    0.73 1.9E-05   23.5   3.2   30  496-525    28-57  (253)
262 PRK08084 DNA replication initi  86.5     1.9 4.9E-05   20.6   5.4  133  467-627    19-156 (235)
263 cd03220 ABC_KpsT_Wzt ABC_KpsT_  86.5    0.56 1.4E-05   24.2   2.6   28  500-527    47-74  (224)
264 TIGR03411 urea_trans_UrtD urea  86.5    0.54 1.4E-05   24.3   2.5   28  500-527    27-54  (242)
265 TIGR02868 CydC ABC transporter  86.4    0.78   2E-05   23.3   3.2   25  503-527   389-413 (566)
266 PRK11614 livF leucine/isoleuci  86.4    0.55 1.4E-05   24.3   2.5   28  500-527    30-57  (237)
267 cd03221 ABCF_EF-3 ABCF_EF-3  E  86.4    0.59 1.5E-05   24.1   2.6   67  499-570    24-100 (144)
268 TIGR01189 ccmA heme ABC export  86.4    0.69 1.8E-05   23.6   3.0   11  245-255    92-102 (204)
269 cd01850 CDC_Septin CDC/Septin.  86.3    0.59 1.5E-05   24.1   2.6   29  497-525   112-141 (276)
270 cd03232 ABC_PDR_domain2 The pl  86.3    0.56 1.4E-05   24.2   2.5   26  498-523    30-55  (192)
271 cd03259 ABC_Carb_Solutes_like   86.3    0.58 1.5E-05   24.1   2.5   29  499-527    24-52  (213)
272 cd03285 ABC_MSH2_euk MutS2 hom  86.3       1 2.6E-05   22.4   3.8   26  499-524    28-53  (222)
273 PRK06851 hypothetical protein;  86.3     1.6 4.2E-05   21.1   4.8   48  470-525   192-239 (368)
274 PRK13542 consensus              86.2    0.58 1.5E-05   24.1   2.5   27  501-527    44-70  (224)
275 cd03269 ABC_putative_ATPase Th  86.2    0.69 1.7E-05   23.6   2.9   30  499-528    24-53  (210)
276 PRK11034 clpA ATP-dependent Cl  86.2       2 5.2E-05   20.5  10.1  152  447-612   425-607 (758)
277 TIGR00958 3a01208 antigen pept  86.1     1.3 3.3E-05   21.8   4.3   65  494-568   552-617 (770)
278 cd03280 ABC_MutS2 MutS2 homolo  86.1    0.99 2.5E-05   22.6   3.7   24  500-523    27-50  (200)
279 cd03217 ABC_FeS_Assembly ABC-t  86.0    0.68 1.7E-05   23.7   2.8   26  499-524    24-49  (200)
280 PRK11432 fbpC ferric transport  86.0    0.56 1.4E-05   24.2   2.3   10  130-139    30-39  (351)
281 PRK11160 cysteine/glutathione   86.0    0.66 1.7E-05   23.7   2.7   30  499-528   365-394 (575)
282 PRK13891 conjugal transfer pro  86.0       1 2.5E-05   22.6   3.6   28  504-531   491-518 (852)
283 PRK05416 hypothetical protein;  86.0     1.2   3E-05   22.1   4.0   58  467-527   211-275 (292)
284 PRK10787 DNA-binding ATP-depen  86.0     2.1 5.3E-05   20.4   6.8  207  451-689   294-538 (784)
285 TIGR03265 PhnT2 putative 2-ami  86.0    0.59 1.5E-05   24.1   2.4   10  130-139    28-37  (353)
286 PRK10261 glutathione transport  85.9     1.1 2.8E-05   22.3   3.8   29  499-527   348-376 (623)
287 cd03264 ABC_drug_resistance_li  85.9     0.6 1.5E-05   24.0   2.4   25  503-527    27-51  (211)
288 cd02025 PanK Pantothenate kina  85.8    0.66 1.7E-05   23.8   2.6   22  506-527     4-25  (220)
289 PRK06761 hypothetical protein;  85.8    0.82 2.1E-05   23.1   3.1   26  502-527     3-28  (281)
290 cd03230 ABC_DR_subfamily_A Thi  85.8    0.65 1.6E-05   23.8   2.6   30  499-528    24-53  (173)
291 PRK11300 livG leucine/isoleuci  85.8    0.62 1.6E-05   23.9   2.5   28  500-527    30-57  (255)
292 cd01853 Toc34_like Toc34-like   85.8     1.6   4E-05   21.3   4.5  146  476-640     8-165 (249)
293 cd03241 ABC_RecN RecN ATPase i  85.8    0.86 2.2E-05   23.0   3.2   29  501-529    21-49  (276)
294 TIGR01192 chvA glucan exporter  85.7    0.68 1.7E-05   23.7   2.7   36  502-537   362-398 (592)
295 TIGR01143 murF UDP-N-acetylmur  85.7    0.79   2E-05   23.2   3.0   21   80-100    71-94  (462)
296 cd03268 ABC_BcrA_bacitracin_re  85.7    0.68 1.7E-05   23.7   2.6   31  499-529    24-54  (208)
297 CHL00131 ycf16 sulfate ABC tra  85.7    0.75 1.9E-05   23.4   2.8   24  500-523    31-54  (252)
298 cd03284 ABC_MutS1 MutS1 homolo  85.6     1.1 2.9E-05   22.2   3.8   25  500-524    29-53  (216)
299 cd03218 ABC_YhbG The ABC trans  85.6    0.64 1.6E-05   23.8   2.5   26  502-527    27-52  (232)
300 cd03281 ABC_MSH5_euk MutS5 hom  85.6       1 2.6E-05   22.4   3.5   26  499-524    27-52  (213)
301 COG3910 Predicted ATPase [Gene  85.6    0.72 1.8E-05   23.5   2.7   24  503-526    39-62  (233)
302 cd03265 ABC_DrrA DrrA is the A  85.6    0.69 1.8E-05   23.6   2.6   31  499-529    24-54  (220)
303 PRK00139 murE UDP-N-acetylmura  85.5     1.8 4.7E-05   20.8   4.8   87  501-598   364-457 (481)
304 KOG2655 consensus               85.5    0.65 1.7E-05   23.8   2.5   30  497-526   127-157 (366)
305 COG3172 NadR Predicted ATPase/  85.5     0.9 2.3E-05   22.9   3.2   28  500-527     7-34  (187)
306 TIGR02204 MsbA_rel ABC transpo  85.4    0.61 1.5E-05   24.0   2.3   40  499-538   364-404 (576)
307 cd03266 ABC_NatA_sodium_export  85.3    0.68 1.7E-05   23.7   2.5   30  499-528    29-58  (218)
308 PRK06620 hypothetical protein;  85.3     1.3 3.2E-05   21.9   3.9   49  479-529    24-72  (214)
309 PRK03695 vitamin B12-transport  85.3    0.67 1.7E-05   23.7   2.5   29  498-526    20-48  (245)
310 COG0529 CysC Adenylylsulfate k  85.3       1 2.7E-05   22.4   3.4   27  501-527    23-49  (197)
311 COG0572 Udk Uridine kinase [Nu  85.3     1.1 2.9E-05   22.2   3.6   35  500-534     6-41  (218)
312 TIGR03410 urea_trans_UrtE urea  85.2    0.67 1.7E-05   23.7   2.4   28  500-527    25-52  (230)
313 TIGR02857 CydD ABC transporter  85.2     0.8   2E-05   23.2   2.8   31  499-529   376-406 (570)
314 pfam00735 Septin Septin. Membe  85.1    0.74 1.9E-05   23.4   2.6   31  496-526   109-140 (280)
315 PRK00300 gmk guanylate kinase;  85.1    0.63 1.6E-05   23.9   2.2   67  499-576     5-71  (208)
316 COG1101 PhnK ABC-type uncharac  85.1    0.76 1.9E-05   23.3   2.6   15  126-141    27-41  (263)
317 PRK09580 sufC cysteine desulfu  85.0    0.87 2.2E-05   23.0   2.9   23  502-524    28-50  (248)
318 TIGR00630 uvra excinuclease AB  85.0    0.69 1.8E-05   23.6   2.4   28  498-525   662-690 (956)
319 COG1122 CbiO ABC-type cobalt t  85.0    0.56 1.4E-05   24.2   1.9   30  499-528    28-57  (235)
320 cd03282 ABC_MSH4_euk MutS4 hom  85.0     1.3 3.3E-05   21.8   3.8   26  499-524    27-52  (204)
321 COG0194 Gmk Guanylate kinase [  85.0    0.95 2.4E-05   22.7   3.1   56  500-568     3-58  (191)
322 pfam03668 ATP_bind_2 P-loop AT  84.9     1.3 3.3E-05   21.8   3.8   60  467-526   205-268 (284)
323 TIGR02203 MsbA_lipidA lipid A   84.9    0.64 1.6E-05   23.8   2.2   60  498-567   385-445 (603)
324 PRK11144 modC molybdate transp  84.9    0.73 1.9E-05   23.4   2.5   21  432-452   196-217 (352)
325 TIGR01526 nadR_NMN_Atrans nico  84.8     1.1 2.8E-05   22.2   3.4   27  499-525   173-199 (346)
326 cd03286 ABC_MSH6_euk MutS6 hom  84.8     1.3 3.3E-05   21.8   3.7   26  499-524    28-53  (218)
327 TIGR03015 pepcterm_ATPase puta  84.7     1.2 3.1E-05   22.0   3.6   29  498-526    40-68  (269)
328 PRK09825 idnK D-gluconate kina  84.6     1.2   3E-05   22.1   3.4   25  502-526     4-28  (176)
329 PRK13539 cytochrome c biogenes  84.6    0.74 1.9E-05   23.4   2.4   27  500-526    27-53  (206)
330 KOG0739 consensus               84.6     1.8 4.6E-05   20.8   4.4  130  493-633   158-299 (439)
331 cd03216 ABC_Carb_Monos_I This   84.6    0.78   2E-05   23.3   2.5   29  500-528    25-53  (163)
332 TIGR00150 TIGR00150 conserved   84.5     2.4 6.1E-05   20.0   5.6   64  477-540     2-68  (147)
333 cd03279 ABC_sbcCD SbcCD and ot  84.5     1.1 2.9E-05   22.2   3.4   25  501-525    28-52  (213)
334 KOG0058 consensus               84.5    0.98 2.5E-05   22.6   3.0   31  499-529   492-522 (716)
335 PRK03839 putative kinase; Prov  84.5     1.2   3E-05   22.1   3.4   25  503-527     2-26  (180)
336 cd01131 PilT Pilus retraction   84.5     1.2   3E-05   22.1   3.4   26  502-527     2-27  (198)
337 PRK10938 putative molybdenum t  84.4    0.77   2E-05   23.3   2.4   26  499-524   284-309 (490)
338 COG2256 MGS1 ATPase related to  84.3       1 2.5E-05   22.6   3.0   12  442-453   383-394 (436)
339 COG0606 Predicted ATPase with   84.3     1.6 4.2E-05   21.1   4.1  147  473-632   178-353 (490)
340 COG3842 PotA ABC-type spermidi  84.3       1 2.5E-05   22.6   3.0   15  429-443   201-215 (352)
341 cd03219 ABC_Mj1267_LivG_branch  84.2    0.81 2.1E-05   23.2   2.5   29  499-527    24-52  (236)
342 PRK10762 D-ribose transporter   84.2    0.82 2.1E-05   23.1   2.5   30  499-528   276-305 (501)
343 PRK00064 recF recombination pr  84.2     1.5 3.9E-05   21.3   3.9   21  488-508   247-267 (355)
344 KOG0082 consensus               84.2     1.1 2.7E-05   22.3   3.1   45  481-526   299-345 (354)
345 cd03283 ABC_MutS-like MutS-lik  84.1     1.2 3.1E-05   22.0   3.3   24  501-524    25-48  (199)
346 cd03287 ABC_MSH3_euk MutS3 hom  83.9     1.5 3.8E-05   21.4   3.7   25  500-524    30-54  (222)
347 COG4604 CeuD ABC-type enteroch  83.8     1.2 3.1E-05   22.0   3.3   22  505-526    31-52  (252)
348 cd02028 UMPK_like Uridine mono  83.8    0.77   2E-05   23.3   2.2   26  504-529     2-27  (179)
349 cd03243 ABC_MutS_homologs The   83.8     1.3 3.3E-05   21.8   3.4   24  501-524    29-52  (202)
350 PRK13873 conjugal transfer ATP  83.8     1.2 2.9E-05   22.1   3.1   52  503-562   443-494 (815)
351 smart00382 AAA ATPases associa  83.8     1.3 3.2E-05   21.9   3.3   27  502-528     3-29  (148)
352 PRK13549 xylose transporter AT  83.7    0.88 2.2E-05   22.9   2.5   28  499-526   286-313 (513)
353 cd03215 ABC_Carb_Monos_II This  83.7    0.54 1.4E-05   24.3   1.4   30  499-528    24-53  (182)
354 PRK11929 putative bifunctional  83.7     1.9 4.8E-05   20.7   4.2   39  483-526   575-614 (953)
355 cd01858 NGP_1 NGP-1.  Autoanti  83.6     2.6 6.7E-05   19.8   5.7   25  498-522    99-123 (157)
356 cd00071 GMPK Guanosine monopho  83.5     0.8   2E-05   23.2   2.2   27  503-529     1-27  (137)
357 PRK13830 conjugal transfer pro  83.5     1.2   3E-05   22.1   3.0   54  503-564   458-511 (818)
358 TIGR03269 met_CoM_red_A2 methy  83.4    0.93 2.4E-05   22.7   2.5   32  498-529   307-338 (520)
359 TIGR01978 sufC FeS assembly AT  83.3       1 2.5E-05   22.5   2.6   11  250-260   136-146 (248)
360 PRK10875 recD exonuclease V su  83.3     2.7 6.9E-05   19.7   5.8   19  509-527   444-462 (607)
361 KOG0729 consensus               83.3       2 5.1E-05   20.5   4.2  155  457-625   173-335 (435)
362 pfam00488 MutS_V MutS domain V  83.3     1.6 4.2E-05   21.1   3.7   24  501-524    42-65  (234)
363 cd02021 GntK Gluconate kinase   83.2     1.1 2.9E-05   22.2   2.9   26  503-528     1-26  (150)
364 COG4962 CpaF Flp pilus assembl  83.2     2.7   7E-05   19.6   5.9   50  469-526   149-198 (355)
365 cd02024 NRK1 Nicotinamide ribo  83.0     1.1 2.9E-05   22.2   2.8   24  505-528     3-26  (187)
366 COG1196 Smc Chromosome segrega  83.0     1.3 3.2E-05   21.9   3.1   10  468-477   530-539 (1163)
367 PRK07952 DNA replication prote  82.9     2.8 7.1E-05   19.6   5.4  118  502-633    97-229 (242)
368 TIGR01166 cbiO cobalt ABC tran  82.9     1.4 3.6E-05   21.6   3.2   63  499-569    16-79  (190)
369 COG3451 VirB4 Type IV secretor  82.8     1.2 3.1E-05   22.0   2.9   27  503-529   438-464 (796)
370 cd03271 ABC_UvrA_II The excisi  82.7     1.2 3.1E-05   22.0   2.9   23  499-521    19-41  (261)
371 cd03242 ABC_RecF RecF is a rec  82.7     1.8 4.7E-05   20.8   3.8   26  501-526    21-46  (270)
372 COG2274 SunT ABC-type bacterio  82.6       1 2.6E-05   22.4   2.5   31  499-529   497-527 (709)
373 PRK09700 D-allose transporter   82.6       1 2.6E-05   22.5   2.5   31  498-528   286-316 (510)
374 PRK10636 putative ABC transpor  82.5    0.89 2.3E-05   22.9   2.1   26  502-527   339-364 (638)
375 PRK05541 adenylylsulfate kinas  82.5     1.9 4.9E-05   20.6   3.8   30  499-528     5-34  (176)
376 PRK10982 galactose/methyl gala  82.4     1.1 2.7E-05   22.3   2.5   29  499-527   272-300 (491)
377 TIGR01842 type_I_sec_PrtD type  82.4     1.1 2.8E-05   22.2   2.6   89  422-540   307-396 (556)
378 COG1131 CcmA ABC-type multidru  82.3     1.1 2.7E-05   22.3   2.5   24  503-526    33-56  (293)
379 PRK02006 murD UDP-N-acetylmura  82.3     2.9 7.5E-05   19.4   5.4   10  442-451   353-362 (501)
380 KOG0979 consensus               82.2     1.3 3.4E-05   21.7   2.9   29   73-101    50-78  (1072)
381 COG3638 ABC-type phosphate/pho  82.2     1.2 2.9E-05   22.1   2.6   24  502-525    31-54  (258)
382 KOG0738 consensus               82.2       3 7.6E-05   19.4   5.9  252  450-726   201-489 (491)
383 PRK11174 cysteine/glutathione   82.2     1.4 3.5E-05   21.6   3.0   27  499-525   374-400 (588)
384 COG4172 ABC-type uncharacteriz  82.1     2.3 5.9E-05   20.1   4.1   59  503-568   315-373 (534)
385 KOG0055 consensus               82.1     1.5 3.8E-05   21.4   3.2   27  500-526  1015-1041(1228)
386 PRK11147 ABC transporter ATPas  82.1       1 2.6E-05   22.4   2.3   27  502-528   346-372 (632)
387 PRK11819 putative ABC transpor  82.0     1.2   3E-05   22.1   2.6   26  502-527   351-376 (556)
388 CHL00181 cbbX CbbX; Provisiona  81.9       3 7.7E-05   19.3   7.9  102  465-567    13-131 (287)
389 COG4778 PhnL ABC-type phosphon  81.8     1.3 3.3E-05   21.8   2.7   12  253-264   146-157 (235)
390 PRK13898 type IV secretion sys  81.8     2.1 5.4E-05   20.4   3.8   55  503-566   448-502 (800)
391 TIGR00635 ruvB Holliday juncti  81.7     3.1 7.9E-05   19.3   6.4   95  473-576     3-99  (305)
392 TIGR02533 type_II_gspE general  81.6    0.89 2.3E-05   22.9   1.8   86  415-520   173-264 (495)
393 COG4088 Predicted nucleotide k  81.6     1.3 3.4E-05   21.7   2.8   11  486-496   248-258 (261)
394 PRK13948 shikimate kinase; Pro  81.5     1.8 4.6E-05   20.9   3.4   32  498-529     7-38  (182)
395 COG0465 HflB ATP-dependent Zn   81.5     3.1   8E-05   19.2   5.9   17  505-521   347-363 (596)
396 PRK13853 type IV secretion sys  81.4     1.3 3.3E-05   21.8   2.6   55  504-564   429-484 (789)
397 TIGR02397 dnaX_nterm DNA polym  81.4     2.6 6.6E-05   19.8   4.2  144  473-634    13-174 (363)
398 cd01428 ADK Adenylate kinase (  81.3     1.7 4.3E-05   21.0   3.2   24  504-527     2-25  (194)
399 PRK11153 metN DL-methionine tr  81.2     1.2 3.2E-05   21.9   2.5   12  467-478   235-246 (343)
400 COG1132 MdlB ABC-type multidru  81.1     1.7 4.4E-05   21.0   3.2   30  500-529   354-383 (567)
401 COG4913 Uncharacterized protei  81.0     1.4 3.5E-05   21.6   2.6   35   20-59      7-44  (1104)
402 PRK06696 uridine kinase; Valid  80.8     3.3 8.4E-05   19.1   5.7   30  500-529    25-54  (227)
403 PRK13545 tagH teichoic acids e  80.8    0.93 2.4E-05   22.7   1.7   55  574-637   365-421 (549)
404 PRK07940 DNA polymerase III su  80.8     3.3 8.5E-05   19.1   5.7   54  473-526     4-64  (395)
405 PRK09435 arginine/ornithine tr  80.7     3.3 8.5E-05   19.1   5.8   40  485-525    34-73  (325)
406 COG1100 GTPase SAR1 and relate  80.5     1.4 3.6E-05   21.6   2.6   22  502-523     6-27  (219)
407 TIGR02633 xylG D-xylose ABC tr  80.5     1.2 3.1E-05   22.0   2.2   86  497-593   394-488 (501)
408 TIGR01351 adk adenylate kinase  80.5     1.9 4.8E-05   20.7   3.2   27  674-700   175-201 (232)
409 TIGR02142 modC_ABC molybdate A  80.3     1.1 2.9E-05   22.2   2.0   15  223-237   133-147 (361)
410 TIGR02525 plasmid_TraJ plasmid  80.3     1.5 3.8E-05   21.4   2.6   56   40-99      6-77  (374)
411 cd03114 ArgK-like The function  80.2     1.3 3.3E-05   21.8   2.3   21  506-526     4-24  (148)
412 TIGR00382 clpX ATP-dependent C  80.2     1.9 4.8E-05   20.7   3.1  129  504-637   155-315 (452)
413 cd01855 YqeH YqeH.  YqeH is an  80.2     2.9 7.3E-05   19.5   4.1   38  480-525   114-151 (190)
414 smart00534 MUTSac ATPase domai  80.1     1.7 4.3E-05   21.1   2.8   22  503-524     1-22  (185)
415 pfam10236 DAP3 Mitochondrial r  80.0     3.5 8.9E-05   18.9   5.0   20  161-180    81-100 (274)
416 PRK11288 araG L-arabinose tran  80.0     1.4 3.6E-05   21.6   2.4   31  498-528   276-306 (501)
417 cd02029 PRK_like Phosphoribulo  80.0     1.5 3.9E-05   21.3   2.6   27  505-531     3-29  (277)
418 COG4559 ABC-type hemin transpo  79.8     1.7 4.2E-05   21.1   2.7   11  508-518    34-44  (259)
419 PRK02496 adk adenylate kinase;  79.8     2.4 6.1E-05   20.0   3.6   36  664-699   123-158 (185)
420 COG1149 MinD superfamily P-loo  79.8     2.1 5.4E-05   20.4   3.3   25  503-527     4-28  (284)
421 TIGR03375 type_I_sec_LssB type  79.8     1.3 3.3E-05   21.8   2.2   29  501-529   491-519 (694)
422 KOG1051 consensus               79.7     3.6 9.2E-05   18.9   8.4  140  469-612   556-710 (898)
423 PRK05563 DNA polymerase III su  79.6     3.6 9.2E-05   18.8   5.9   20  161-180   127-146 (541)
424 PRK03846 adenylylsulfate kinas  79.6     2.6 6.8E-05   19.7   3.7   29  499-527    22-50  (198)
425 COG1134 TagH ABC-type polysacc  79.6     1.1 2.8E-05   22.3   1.7   21  505-525    57-77  (249)
426 KOG0061 consensus               79.5     1.5 3.8E-05   21.4   2.4   26  228-253   205-241 (613)
427 COG0237 CoaE Dephospho-CoA kin  79.4     2.2 5.7E-05   20.2   3.3   78  502-588     3-80  (201)
428 PRK04690 murD UDP-N-acetylmura  79.4     1.3 3.2E-05   21.9   2.0   14  577-590   447-460 (468)
429 COG5019 CDC3 Septin family pro  79.4     1.6 4.1E-05   21.2   2.6   32  495-526   129-161 (373)
430 COG1703 ArgK Putative periplas  79.3     2.6 6.6E-05   19.8   3.6   33  494-526    44-76  (323)
431 cd03275 ABC_SMC1_euk Eukaryoti  79.2     2.1 5.4E-05   20.4   3.1   29  501-529    22-50  (247)
432 KOG0018 consensus               79.2     1.8 4.6E-05   20.8   2.8   54  504-565   533-586 (1141)
433 KOG0730 consensus               79.2     1.7 4.5E-05   20.9   2.7  127  498-633   465-602 (693)
434 PRK00889 adenylylsulfate kinas  79.1     2.6 6.7E-05   19.8   3.6   28  501-528     4-31  (175)
435 PRK08233 hypothetical protein;  79.1     2.8 7.2E-05   19.5   3.7   30  502-531     4-33  (182)
436 cd03238 ABC_UvrA The excision   78.9     2.4   6E-05   20.1   3.3   24  499-522    19-42  (176)
437 PRK13409 putative ATPase RIL;   78.6     1.6   4E-05   21.3   2.3   28  500-527   364-391 (590)
438 COG1119 ModF ABC-type molybden  78.6     2.2 5.6E-05   20.3   3.1   13  508-520    64-76  (257)
439 cd01673 dNK Deoxyribonucleosid  78.5       2 5.2E-05   20.5   2.9   24  504-527     2-25  (193)
440 cd01129 PulE-GspE PulE/GspE Th  78.4     3.9   1E-04   18.6   5.6   44  473-523    59-102 (264)
441 cd03276 ABC_SMC6_euk Eukaryoti  78.4     3.2 8.3E-05   19.2   3.9   30  501-530    21-50  (198)
442 TIGR02237 recomb_radB DNA repa  78.4     1.9 4.8E-05   20.7   2.7   70  494-595     5-74  (223)
443 TIGR01193 bacteriocin_ABC ABC-  78.3     1.4 3.6E-05   21.6   2.0   54   86-139    67-131 (710)
444 TIGR02746 TraC-F-type type-IV   78.3       4  0.0001   18.6   4.3  170  505-730   493-681 (900)
445 pfam10662 PduV-EutP Ethanolami  78.3     1.8 4.7E-05   20.8   2.6   21  504-527     4-24  (143)
446 COG0466 Lon ATP-dependent Lon   78.3       4  0.0001   18.6   7.0  202  450-690   294-541 (782)
447 TIGR00634 recN DNA repair prot  78.3     1.6   4E-05   21.2   2.2  153  410-588   406-580 (605)
448 PTZ00088 adenylate kinase 1; P  78.2     2.4 6.1E-05   20.0   3.1   28  674-701   172-200 (225)
449 KOG0652 consensus               78.2       4  0.0001   18.6   7.3  131  498-635   202-342 (424)
450 cd02019 NK Nucleoside/nucleoti  78.2     2.2 5.5E-05   20.3   2.9   24  504-527     2-25  (69)
451 pfam03193 DUF258 Protein of un  78.2     1.9 4.8E-05   20.7   2.6   16  505-520    39-54  (161)
452 TIGR01313 therm_gnt_kin carboh  78.2     1.7 4.3E-05   21.0   2.4   23  214-236    45-68  (175)
453 KOG2203 consensus               78.1       3 7.6E-05   19.4   3.6   12   64-75     89-100 (772)
454 COG4525 TauB ABC-type taurine   78.1     1.9 4.8E-05   20.7   2.6   18  506-523    36-53  (259)
455 PRK09862 putative ATP-dependen  77.8     3.7 9.5E-05   18.7   4.1  134  473-616   190-350 (506)
456 KOG2028 consensus               77.8     4.1  0.0001   18.5  10.3   43  710-752   469-516 (554)
457 PRK00131 aroK shikimate kinase  77.7     2.5 6.5E-05   19.8   3.2   29  501-529     4-32  (175)
458 COG0488 Uup ATPase components   77.7       2   5E-05   20.6   2.6   26  503-528   350-375 (530)
459 pfam05970 DUF889 PIF1 helicase  77.6     1.7 4.3E-05   21.1   2.2   11  557-567   308-318 (418)
460 PRK11784 tRNA 2-selenouridine   77.5     4.2 0.00011   18.4   5.0   53  480-545   125-177 (333)
461 smart00072 GuKc Guanylate kina  77.5     2.6 6.6E-05   19.8   3.1   57  501-568     2-58  (184)
462 PRK00279 adk adenylate kinase;  77.4     2.6 6.7E-05   19.7   3.2   27  674-700   163-189 (215)
463 PTZ00265 multidrug resistance   77.4     1.9 4.9E-05   20.6   2.5   28  499-526  1193-1220(1467)
464 pfam03266 DUF265 Protein of un  77.4     2.5 6.4E-05   19.9   3.0   25  504-528     2-26  (168)
465 pfam01583 APS_kinase Adenylyls  77.2     3.2 8.2E-05   19.2   3.6   26  502-527     3-28  (157)
466 COG4175 ProV ABC-type proline/  77.2     2.2 5.6E-05   20.3   2.7   19  126-146    49-67  (386)
467 PRK03815 murD UDP-N-acetylmura  77.1     1.5 3.9E-05   21.3   1.9   18  509-526    95-112 (401)
468 PRK08451 DNA polymerase III su  77.0     4.3 0.00011   18.3   6.1   22  161-182   125-146 (523)
469 COG1159 Era GTPase [General fu  76.9     2.4   6E-05   20.1   2.8   17  503-519     8-24  (298)
470 pfam03205 MobB Molybdopterin g  76.7     2.8 7.2E-05   19.6   3.2   22  504-525     3-24  (122)
471 KOG1969 consensus               76.6     2.8 7.1E-05   19.6   3.1   40  497-537   322-361 (877)
472 TIGR02030 BchI-ChlI magnesium   76.4     2.6 6.7E-05   19.8   2.9   24  504-527    28-51  (340)
473 COG0396 sufC Cysteine desulfur  76.4     2.5 6.4E-05   19.9   2.8   20  503-522    32-51  (251)
474 pfam03308 ArgK ArgK protein. T  76.4     3.7 9.3E-05   18.8   3.7   32  494-525    22-53  (267)
475 COG4988 CydD ABC-type transpor  76.4     2.2 5.6E-05   20.3   2.6   27  502-528   348-374 (559)
476 TIGR02729 Obg_CgtA GTP-binding  76.4     1.5 3.9E-05   21.3   1.7   32  506-537   163-197 (296)
477 PRK04040 adenylate kinase; Pro  76.4     3.9   1E-04   18.6   3.8   55  502-556     3-58  (189)
478 PRK00089 era GTP-binding prote  76.3     3.3 8.4E-05   19.1   3.4   28  494-521     1-28  (296)
479 PRK10418 nikD nickel transport  76.3       2 5.1E-05   20.5   2.3   23  503-525    31-53  (254)
480 KOG3347 consensus               76.3     2.6 6.5E-05   19.8   2.9   23  504-526    10-32  (176)
481 COG4598 HisP ABC-type histidin  76.2     2.8 7.2E-05   19.6   3.1   22  503-524    34-55  (256)
482 TIGR01187 potA polyamine ABC t  76.2     1.3 3.3E-05   21.8   1.3   17  506-522     1-17  (331)
483 PRK10773 murF UDP-N-acetylmura  76.2     3.4 8.8E-05   19.0   3.5   51  480-535    81-132 (452)
484 PRK13946 shikimate kinase; Pro  76.1       3 7.7E-05   19.4   3.2   23  504-526    23-45  (195)
485 COG0497 RecN ATPase involved i  76.1     2.8 7.2E-05   19.5   3.0   31  503-533    24-54  (557)
486 KOG0991 consensus               76.1     4.5 0.00012   18.2   4.8   65  473-543    26-91  (333)
487 PRK00141 murD UDP-N-acetylmura  76.0     1.8 4.6E-05   20.8   2.0   17  509-525   129-145 (476)
488 PRK05896 DNA polymerase III su  76.0     4.6 0.00012   18.2   6.1   48  473-525    15-62  (613)
489 cd01854 YjeQ_engC YjeQ/EngC.    75.9     2.3   6E-05   20.1   2.6   20  502-521   162-181 (287)
490 PRK08727 hypothetical protein;  75.9     4.6 0.00012   18.1   7.6  103  451-568     1-103 (233)
491 PRK05057 aroK shikimate kinase  75.8     3.2 8.2E-05   19.2   3.3   28  499-526     2-29  (172)
492 cd00464 SK Shikimate kinase (S  75.6     3.2 8.1E-05   19.2   3.2   23  504-526     2-24  (154)
493 pfam00350 Dynamin_N Dynamin fa  75.6       2   5E-05   20.6   2.1   18  504-521     1-18  (168)
494 PRK05506 bifunctional sulfate   75.5     3.7 9.4E-05   18.8   3.5   24  502-525   444-467 (613)
495 cd04164 trmE TrmE (MnmE, ThdF,  75.4     2.7 6.8E-05   19.7   2.7   19  504-522     4-22  (157)
496 TIGR00750 lao LAO/AO transport  75.3     2.4 6.1E-05   20.0   2.5   20  506-525    43-62  (333)
497 PRK02705 murD UDP-N-acetylmura  75.3     1.8 4.7E-05   20.8   1.9   17  509-525   115-131 (459)
498 PRK01889 ribosome-associated G  75.2     2.5 6.5E-05   19.9   2.6   20  502-521   195-214 (353)
499 PRK06547 hypothetical protein;  75.2     3.9  0.0001   18.6   3.6   33  502-534    16-48  (184)
500 PRK01390 murD UDP-N-acetylmura  75.2       2   5E-05   20.6   2.0   17  509-525   120-136 (457)

No 1  
>PRK07078 hypothetical protein; Validated
Probab=100.00  E-value=0  Score=726.23  Aligned_cols=427  Identities=22%  Similarity=0.311  Sum_probs=357.2

Q ss_pred             CCCCHHHHHHHHHHHCCCEEEEEEECCEEEEECCCEEEEECCHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHHH
Q ss_conf             55330478999987089839999617814686088057741312201344589999999999999865410123014889
Q gi|254781225|r  305 SRFSDAYNKAMFSIYKKGHFLYTADTKAWYKKDKNNVYIWSLTLDKITASIMNFLVSMKEDVFDLSEEPEDNNKNSKSPR  384 (789)
Q Consensus       305 ~~~~d~~~~~~~~~~~~~~~~~~~~~~~wy~~~~~~~~~~~g~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  384 (789)
                      ...++...+..|...+.+.++|+.+.+.|        ++|+|.+|+......-     ...++.+..++....+. .+..
T Consensus        70 ~~~t~~~~a~~f~~~y~~~~ry~~~~~~w--------~~w~g~~W~~d~~~~a-----~~~~r~~~~~~~~~~~~-~~~~  135 (510)
T PRK07078         70 SPATEDALALAFTRRYADDWRYCALWGKW--------LVWTGVRWNPERTLAA-----FHLIRGICREAALKAES-PRLA  135 (510)
T ss_pred             CCCCHHHHHHHHHHHHCCCEEEEECCCCE--------EEECCCEECCCCCHHH-----HHHHHHHHHHHHHHCCC-HHHH
T ss_conf             99746689999999840326766034717--------9975846225764259-----99999999999873443-8788


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHCCCCCCEEEECCCEEECCCCCCCCCCHHHHCCEECCCCCCCCC
Q ss_conf             98756877762000267999987411000012320220579717660793797438885589865501001378888757
Q gi|254781225|r  385 FWFNTDYRRQNVEENSKAKSTAQSLEAGSIFSITSDLLDSSSRFLGEQDGILDLETGQKVKPTKELYITKSTGTPFVEGE  464 (789)
Q Consensus       385 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ld~~~~ll~~~NGv~dl~t~~~~~~~~~~~~t~~~~~~y~~~a  464 (789)
                      .      +.+..   .....+...+.......++.++||+||+||||+|||+||+||+|++|+|+|++|+++++.  |.+
T Consensus       136 ~------~~~~~---~~~~~v~~~ar~~~~~~~~~e~~D~dp~lLn~~nGvvDLrTG~lr~h~p~d~iTk~t~v~--P~a  204 (510)
T PRK07078        136 A------KLASS---STVGGVERLARSDRRHAATAEEWDADPWLLNTPGGVVDLRTGRLRPHRREDRMTKLTTAT--PAG  204 (510)
T ss_pred             H------HHHHH---HHHHHHHHHHHHCCCCCCCHHHHCCCCHHHCCCCEEEECCCCCCCCCCHHHCEEEECCCC--CCC
T ss_conf             8------98765---678999999841833347977855894310799817989779727899878445300368--789


Q ss_pred             CHHHHHHHHHHHC-CCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCC
Q ss_conf             9478999998887-999999999999999975987433799997078862578999999972330003442676420124
Q gi|254781225|r  465 PSQEFLDLVSGYF-ESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRP  543 (789)
Q Consensus       465 ~~p~~~~~l~~~~-~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~  543 (789)
                      +||.|++||++|| +|+|+++|||+++||||+|.+++|+++|++|+|+||||||+++|+.|||+|+.+....+++.. ++
T Consensus       205 ~cP~W~~FL~~if~gD~eli~fLQr~~GY~LtG~t~Eq~lf~l~G~G~NGKStf~~vl~~lLGdYa~t~~~~tl~~~-~~  283 (510)
T PRK07078        205 DCPTWRQFLAEVTGGDAALQAYLQRMAGYALTGDTSEHALFFLYGTGANGKSVFVNTLATILGDYAANAAMDTFMET-RG  283 (510)
T ss_pred             CCCHHHHHHHHHHCCCHHHHHHHHHHHHHEECCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHC-CC
T ss_conf             89379999999848999999999999757633787733899997589884789999999986566304898999634-68


Q ss_pred             CCCCCCCHHHHHHCCCEEEEEECCCCCCCCCCCEEEEEECCCEEEEEECCCCCCEEEECCEEEEEECCCCCCCCCCCCCE
Q ss_conf             55556898899738980999934677760131002454159858732104786068714528999738863426798416
Q gi|254781225|r  544 PEAGKANPSLIRLMGSRIVIISETNENDEINAAKIKQMTGGDCMTARLNYGNTYSESPASFTPFIVPNKHLFVRNPDDAW  623 (789)
Q Consensus       544 ~~~~~~~~~la~l~g~r~~~~~E~~~~~~~~~~~~K~ltggD~i~ar~~~~~~~~~~~p~~~~~~~~N~~P~~~~~d~~~  623 (789)
                         +.++++||+|.|+|+++++|+++|.++++++||+|||||+|+||++|++.| +|.|+|++||+|||+|.+++.|+|+
T Consensus       284 ---~~~~~dlA~L~GaRlV~asE~eeG~rl~Ea~IKqLTGGD~ItAR~l~~d~f-eF~P~fkL~l~tNhlP~i~~~D~gi  359 (510)
T PRK07078        284 ---DRHPTDLAGLRGARFVSAIETEQGRRWAESKVKQLTGGDKISARFMRQDFF-EFTPQFKLLIAGNHKPAIRNVDEAM  359 (510)
T ss_pred             ---CCCCHHHHHCCCCEEEEEECCCCCCCHHHHHHHEECCCCEEEEECCCCCCE-EECCCEEEEEECCCCCCCCCCCHHH
T ss_conf             ---999878883379818996548865004477454301797267420257754-8512438999737877577888201


Q ss_pred             EEEEEEEECCCCCC--CCCCCHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCHHHHHHHHHE
Q ss_conf             64689996588788--8787833422012044799999999999998788988788999999999984263888875432
Q gi|254781225|r  624 WRRYIVIPFDKPIA--NRDASFAQKLETKYTLEAKKWFLKGVKAYISKGLDVDIPEVCLKAKEEERQGTDTYQAWIDDCC  701 (789)
Q Consensus       624 ~rR~~iipF~~~~~--~~d~~~~~~~~~~e~~~i~~w~l~g~~~~~~~g~~~~~p~~v~~a~~~y~~~~D~v~~fi~e~c  701 (789)
                      |||++||||+++|+  ++|++|.++| ..|.+|||+|+|+||++|+++||  ..|++|.+|+++|+.++|+|++||+|||
T Consensus       360 WRRi~vIPF~~~f~~~~~D~~L~~KL-~aE~pGIL~W~IeG~~~wq~~GL--~~P~~V~~At~eYr~e~D~vg~Fl~EcC  436 (510)
T PRK07078        360 KRRLHLIPFTVTVPPERRDKRLQEKL-LAERDGILAWAVEGCLDWQRNGL--DPPQSVVDATEEYFEAEDALGQWLEERC  436 (510)
T ss_pred             EEEEEEEEEEEECCCCCCCHHHHHHH-HHHHHHHHHHHHHHHHHHHHCCC--CCCHHHHHHHHHHHHHCCHHHHHHHHHE
T ss_conf             44799987455368656483589999-97348999999999999998299--9988999999999984686988877647


Q ss_pred             EECCCCEECHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCCCCCCEEEECCCCCCCCEEEEEEECCC
Q ss_conf             6268841117999999999998504667555452568999986354233310010256765208997986566
Q gi|254781225|r  702 DIGENLWEESHSLAKSYSEYREQELNYDRKRISTRTVTLNLKQKGFIGGIKREKIEKEWKSKRIIKGLKLKPA  774 (789)
Q Consensus       702 e~~~~~~~~~~~l~~~y~~~~~~~~~~~~~~~s~~~~~~~l~~~g~~~~~~~~~~~~~~~~~r~~~Gi~Lk~~  774 (789)
                      +++++..++..+||++|++||+++|+   .++|++.|+..|.++||...       +...+.|+|+||+||+.
T Consensus       437 ~v~~~~~~~~~eLY~aYr~Wc~~nGe---~~~s~~~F~~~L~~~GF~~~-------r~~~g~r~~~Gi~lk~~  499 (510)
T PRK07078        437 VREANAKETTADLFADWKEWAERAGE---FVGSQKRFSELLITRGFEKW-------RLHGGVRGFSGLSLKPK  499 (510)
T ss_pred             EECCCCEEEHHHHHHHHHHHHHHCCC---CCCCHHHHHHHHHHCCCCCC-------CCCCCCCEEEEEEECCC
T ss_conf             98899704089999999999998498---74419999999997688600-------36698212775675358


No 2  
>COG3378 Phage associated DNA primase [General function prediction only]
Probab=100.00  E-value=0  Score=532.46  Aligned_cols=347  Identities=25%  Similarity=0.382  Sum_probs=309.3

Q ss_pred             CCCCHHHCCCCCCEEEECCCEEECCCCCCCCCCHHHHCCEECCCCCCCCCC----HHHHHHHHHHHC-CCHHHHHHHHHH
Q ss_conf             123202205797176607937974388855898655010013788887579----478999998887-999999999999
Q gi|254781225|r  415 FSITSDLLDSSSRFLGEQDGILDLETGQKVKPTKELYITKSTGTPFVEGEP----SQEFLDLVSGYF-ESEEVMDYFTRC  489 (789)
Q Consensus       415 ~~~~~~~ld~~~~ll~~~NGv~dl~t~~~~~~~~~~~~t~~~~~~y~~~a~----~p~~~~~l~~~~-~d~e~~~~l~~~  489 (789)
                      +.+.....|.+|+||||+|||+||+||+|+||+|++++|+.+++.|.+.+.    ||.|.+||.+++ +|.|++.++|++
T Consensus       139 ~~~~~~~~~~~p~li~~~NGv~dl~tgql~ph~~~~~~t~~~~~~y~~~~~~~~~~p~~~~~L~~~~~~d~el~~ll~~i  218 (517)
T COG3378         139 KAATPKQQDPDPHLINFANGVLDLRTGQLEPHDPEDRFTRIIPVDYTDPAADPSHCPKWREWLDRVAGGDPELRNLLQRI  218 (517)
T ss_pred             CCCCCCCCCCCCCEEECCCCEEECCCCCCCCCCCCHHEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCCCHHHHHHHHHH
T ss_conf             13460003699775501682377330233647821204674234446875555568509999987615788899999999


Q ss_pred             HHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCCCCCHHHHHHCCCEEEEEECCCC
Q ss_conf             99997598743379999707886257899999997233000344267642012455556898899738980999934677
Q gi|254781225|r  490 VGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEAGKANPSLIRLMGSRIVIISETNE  569 (789)
Q Consensus       490 ~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~~~~~~~~la~l~g~r~~~~~E~~~  569 (789)
                      +||+|+|.+++|++++++|+|+||||||.++|+.|+|.||+++.+...|..     ..+.++++|.|.|+|++.++|.++
T Consensus       219 ~g~~l~g~~~~~k~~~l~G~G~nGKstf~~li~~llG~~n~~s~~~~~~~~-----~~~~~~~~A~Lvg~~~v~~~E~~k  293 (517)
T COG3378         219 IGASLTGRVSEQKLFWLYGPGGNGKSTFVDLISNLLGRYNVTSAPLTDLEA-----DDRHPFGLAALVGKRLVTVSETEK  293 (517)
T ss_pred             HHHEECCCCCCEEEEEEECCCCCCHHHHHHHHHHHHCCCHHCCCCHHHHHH-----HCCCCCHHHHHHCCEEEEECCCCC
T ss_conf             766006753400479997689987389999999984542110362887753-----204863388761755787047653


Q ss_pred             CCCCCCCEEEEEECCCEEEEEECCCCCCEEEECCEEEEEECCCCCCCCCCCCCEEEEEEEEECCCCCCCC--CCCHHHHH
Q ss_conf             7601310024541598587321047860687145289997388634267984166468999658878887--87833422
Q gi|254781225|r  570 NDEINAAKIKQMTGGDCMTARLNYGNTYSESPASFTPFIVPNKHLFVRNPDDAWWRRYIVIPFDKPIANR--DASFAQKL  647 (789)
Q Consensus       570 ~~~~~~~~~K~ltggD~i~ar~~~~~~~~~~~p~~~~~~~~N~~P~~~~~d~~~~rR~~iipF~~~~~~~--d~~~~~~~  647 (789)
                      +...+++.||+|||||.|+||+||+++| +|.|++++++++||+|++++.|.|||||+++|||+++|+..  |..+.+++
T Consensus       294 g~l~~~~~lK~ltgGD~i~a~~K~kd~~-~f~p~a~~i~~~N~~P~~~~~d~ai~rR~~ivpF~~~f~~~~~d~~l~~kl  372 (517)
T COG3378         294 GRLDDEGKLKALTGGDVISAERKRKDFF-SFTPNAKLIQATNHPPRIRGDDEAIWRRLLIVPFEKQFPPAERDDKLDEKL  372 (517)
T ss_pred             CCCCCCCCEEEECCCCEEEEHHCCCCCE-EECCCEEEEEECCCCCCCCCCCHHHHHEEEEEECCCCCCCCCCCHHHHHHH
T ss_conf             3003556636642587032011057844-751451788732889721364154232257875566678844315576888


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCHHHHHHHHHEEECCCCEECHH------HHHHHHHHH
Q ss_conf             01204479999999999999878898878899999999998426388887543262688411179------999999999
Q gi|254781225|r  648 ETKYTLEAKKWFLKGVKAYISKGLDVDIPEVCLKAKEEERQGTDTYQAWIDDCCDIGENLWEESH------SLAKSYSEY  721 (789)
Q Consensus       648 ~~~e~~~i~~w~l~g~~~~~~~g~~~~~p~~v~~a~~~y~~~~D~v~~fi~e~ce~~~~~~~~~~------~l~~~y~~~  721 (789)
                       ..|.++||+|+|+|+.+|+.+|+  ..|+++.+++++|++++|+|.+|++|||+..+....+..      +||.+|.+|
T Consensus       373 -~~E~~~IL~~~v~g~~~~~~~g~--~~pq~~~~~~ee~k~~~D~v~~F~~d~~~~~~~~~~~~~~~~~~~~ly~~y~~w  449 (517)
T COG3378         373 -AAERPGILNWLVAGFLDLQREGL--DQPQAVLDALEEYKRENDPVFQFCDDECVLGETDGTPTAFDNIVLELYEAYQEW  449 (517)
T ss_pred             -HHHHHHHHHHHHHHHHHHHHCCC--CCHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             -87438899999999888876168--955667999998887322799999887431544331114135667899999999


Q ss_pred             HHHCCCCCCCCCCHHHHHHHHHHCCCCCCCCEEEECCCCCCCCEEEEEEECC
Q ss_conf             9850466755545256899998635423331001025676520899798656
Q gi|254781225|r  722 REQELNYDRKRISTRTVTLNLKQKGFIGGIKREKIEKEWKSKRIIKGLKLKP  773 (789)
Q Consensus       722 ~~~~~~~~~~~~s~~~~~~~l~~~g~~~~~~~~~~~~~~~~~r~~~Gi~Lk~  773 (789)
                      |+.+|-  ..++|++.|...|...+...+.++.+. ..+.+.+.-.++..++
T Consensus       450 ~e~~G~--~~~~s~~~F~~~l~~~~v~~~r~~~~~-~~t~g~~~~~~L~~~~  498 (517)
T COG3378         450 CEANGY--VVELSKTRFGKELPTKGVPKGRKRHQG-ETTAGGRGGVDLDEQP  498 (517)
T ss_pred             HHHCCC--CCCCHHHHHHCCCCCCCCCCCCEEEEC-CCCCCCCCCCCCCCCC
T ss_conf             975697--112226555223552122034123421-3578753434342235


No 3  
>TIGR01613 primase_Cterm phage/plasmid primase, P4 family, C-terminal domain; InterPro: IPR006500   These sequences form a clade within a larger family of proteins from viruses of bacteria and animals. Members of the family that contain this domain are found in phage and the plasmids of bacteria and archaea. .
Probab=100.00  E-value=0  Score=407.15  Aligned_cols=302  Identities=25%  Similarity=0.425  Sum_probs=273.1

Q ss_pred             CEEEECCCEEECCCCCCCCCCHHHHCC-EECCCCCCCCCCHHHHHH-----HHHHHC-CCHHHHHHHHHHHHHHHCCCCC
Q ss_conf             176607937974388855898655010-013788887579478999-----998887-9999999999999999759874
Q gi|254781225|r  427 RFLGEQDGILDLETGQKVKPTKELYIT-KSTGTPFVEGEPSQEFLD-----LVSGYF-ESEEVMDYFTRCVGMALLGGNK  499 (789)
Q Consensus       427 ~ll~~~NGv~dl~t~~~~~~~~~~~~t-~~~~~~y~~~a~~p~~~~-----~l~~~~-~d~e~~~~l~~~~g~~l~g~~~  499 (789)
                      ++|+++|||+|++|++|++|+|+...+ ..+++.|++++.||.|..     ||.++| +|.++++|+|+++||+|+|.+.
T Consensus         1 ~~~~~~ng~~~~~~~~l~~~~~~~~~~~~~~~~~y~~~~~~p~~~~w~~~~~l~~~~~gd~~~~~~~~~~~g~~~~g~~~   80 (316)
T TIGR01613         1 YLLNVGNGVYDLRTGELLPHDPDEDHTTRKITTEYDPDADCPTWNGWDPDAFLLELFGGDNELVEYLQRLAGYSLTGNYT   80 (316)
T ss_pred             CCCCCCCCEEECCCCCCCCCCCCHHEEEECCCCCCCCCCCCCCCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCC
T ss_conf             93114751254225733535761020120113432676666300146624678876257168999999997322023200


Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCCCCCHHHHHHCCCEEEEEECCCCC-CCCCCCEE
Q ss_conf             33799997078862578999999972330003442676420124555568988997389809999346777-60131002
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEAGKANPSLIRLMGSRIVIISETNEN-DEINAAKI  578 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~~~~~~~~la~l~g~r~~~~~E~~~~-~~~~~~~~  578 (789)
                      +|++++++|.|+||||||.++|..++|+|++.......+....    ..+++.++.|.|+|+++.+|+..+ .+++++.+
T Consensus        81 ~~~~~~l~G~G~~Gk~~~~~~l~~~~G~~~~~~~~~~~~~~~~----~~~~~~~~~l~g~~~~~~~~~~~g~~~~~~~~~  156 (316)
T TIGR01613        81 EQKLFFLYGNGGNGKSTFQDLLSNLLGDYATNAVASLFLEELA----SEHRFGLARLEGKRLVIGDEVEKGVYRLDESTV  156 (316)
T ss_pred             EEEEEEEEECCCCCHHHHHHHHHHHHCCHHCCCHHHHHHHHHH----HCCCCHHHHHCCCEEEEECCCCCCCEEECCCCE
T ss_conf             0256778625888436899999998341000201356777665----213300232103237862366745232012222


Q ss_pred             EEEECCCEEEEEECCCCCCEEEECCEEEEEECCCCCCCCCCCCCEEEEEEEEECCCCCCCC---CCCHHHHHCCCCHHHH
Q ss_conf             4541598587321047860687145289997388634267984166468999658878887---8783342201204479
Q gi|254781225|r  579 KQMTGGDCMTARLNYGNTYSESPASFTPFIVPNKHLFVRNPDDAWWRRYIVIPFDKPIANR---DASFAQKLETKYTLEA  655 (789)
Q Consensus       579 K~ltggD~i~ar~~~~~~~~~~~p~~~~~~~~N~~P~~~~~d~~~~rR~~iipF~~~~~~~---d~~~~~~~~~~e~~~i  655 (789)
                      |++||||++++|++++++| +|.|.+++++++||+|.+++.+.|+|||+++|||++.|+..   +..+.+++...|.++|
T Consensus       157 k~l~ggd~~~~~~~~~~~~-~~~~~~~~~~~~n~~P~~~~~~~~~~rr~~~~pf~~~~~~~~~~~~~~~~~~~l~~~~~~  235 (316)
T TIGR01613       157 KSLTGGDTVTARFKNKDPF-EFTPSFTLVLATNHLPRIKGFDGGIWRRLRIIPFTKVIPGEKKANKKLKEDLILNEGDGI  235 (316)
T ss_pred             EEECCCCEEEEEECCCCHH-HHHCCCEEEEECCCCCCCCCCCCCEEEEEEEEEEEEECCCCHHCCHHHHHHHHHHCCHHH
T ss_conf             1111673357641477401-110152145521676655787631011346631322138510000678888875210478


Q ss_pred             HHHHHHHHHHHHHCCCCCC-CCHHHHHHHHHHHHHCCHHHHHHHHHEEECCCCEECHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             9999999999998788988-788999999999984263888875432626884111799999999999850466755545
Q gi|254781225|r  656 KKWFLKGVKAYISKGLDVD-IPEVCLKAKEEERQGTDTYQAWIDDCCDIGENLWEESHSLAKSYSEYREQELNYDRKRIS  734 (789)
Q Consensus       656 ~~w~l~g~~~~~~~g~~~~-~p~~v~~a~~~y~~~~D~v~~fi~e~ce~~~~~~~~~~~l~~~y~~~~~~~~~~~~~~~s  734 (789)
                      ++|+++|+..++..+ .+. .|+++.+++++|++++|+|..|++|||....+..++...+|..|..||.+.+.  .+.++
T Consensus       236 ~~~~~~g~~~~~~~~-~~~p~p~~~~~~~~~~~~~~d~~~~f~~~~~~~~~~~~~~~~~~~~~~~~w~~~~g~--~~~~~  312 (316)
T TIGR01613       236 LAWAVEGIRLWLRFG-DFSPEPKAVLEATEEYKEENDPVGRFLEECCDDEEGEKVPTRFVYEAYKEWCEEGGE--YPLLS  312 (316)
T ss_pred             HHHHHHHHHHHHHCC-CCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCC--CCCCC
T ss_conf             999998754443101-368875889999987630120578877765202133113467888889999872586--13410


Q ss_pred             HH
Q ss_conf             25
Q gi|254781225|r  735 TR  736 (789)
Q Consensus       735 ~~  736 (789)
                      ++
T Consensus       313 ~~  314 (316)
T TIGR01613       313 KN  314 (316)
T ss_pred             CC
T ss_conf             24


No 4  
>pfam09250 Prim-Pol Bifunctional DNA primase/polymerase, N-terminal. Members of this family adopt a structure consisting of a core of antiparallel beta sheets. They are found in various bacterial hypothetical proteins, and have been shown to harbour both primase and polymerase activities.
Probab=99.87  E-value=7.1e-21  Score=156.38  Aligned_cols=140  Identities=25%  Similarity=0.370  Sum_probs=100.4

Q ss_pred             HHHHHHCCCEEEEECCCCCCCCCCCCCCCCCCCHHHHHHH----HHCCEEEEECCCCCCEEEEEEECCCCHHHH-HHHHH
Q ss_conf             8999977985977356778787756545656898999742----007889992347798799996468812567-89998
Q gi|254781225|r   10 AKQAIHNGFKLIPLRLGDKRPQRLGKWEEQLLSSEKIDKL----PACGFGFVCGVGEQPLYAFDIDSKDEKTAN-TFKDT   84 (789)
Q Consensus        10 ~~~~i~~G~~viPi~pg~KrP~~~~~w~~~~~~~~~i~~~----~~~giGi~~G~~s~glv~iDiD~~d~~~~~-~~~~~   84 (789)
                      |.+|+++||.|||+.|++|+|....+|++...+.+++.+|    +.+||||.||.  +|+++||||..++..+. .+...
T Consensus         1 a~~~~~~G~~v~Pl~p~~K~P~~~~g~~~at~d~~~i~~w~~~~p~~nigv~~g~--~~lvviDiD~~~~~~~l~~l~~~   78 (161)
T pfam09250         1 ALRYAANGWAVLPLDPGSKKPLDPKGWQDATTDPAEIRRWWARNPGANIGLPTGR--SGLVVLDVDTKAGGDALAALERA   78 (161)
T ss_pred             CHHHHHCCCEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCEEEECCC--CCEEEEECCCCCCHHHHHHHHHH
T ss_conf             9779879698956699987799987320268999999999860999528887089--85799957676544899999985


Q ss_pred             HHHCCCCCEEEECCCCCEEEEEEECCCCCCCCCC---CCCCCCCEEEECCC-CEEEECCCCCCCCCCEEECCC
Q ss_conf             7641899769967889659999507310244544---44576753485268-438804776888874575177
Q gi|254781225|r   85 FEILHGTPIVRIGQKPKILIPFRMNKEGIKKKKT---TESTQGHLDILGCG-QYFVAYNIHPKTKKEYTWTTP  153 (789)
Q Consensus        85 ~~~l~g~p~~~~g~~~~~~~~yr~~~~~~~~~~~---~~~~~~~iEi~~~G-~q~V~~gshp~Tg~~Y~w~~~  153 (789)
                      ...+..+..++++ .++.|++|++|+........   .....+++||+++| +|+|++||.+..| .|+|..+
T Consensus        79 ~~~lp~t~~~~T~-~gG~H~~fr~p~~~~~~~~~~~~~~~~~~gvDir~~g~~yvv~ppS~~~~g-~Y~w~~~  149 (161)
T pfam09250        79 GGPLPPTLVVRTP-SGGRHLYFRVPDGPELKRNLLFAKDGGGGGIDIRAGGGGYVVAPPSVHPGG-PYEWTGG  149 (161)
T ss_pred             CCCCCCCEEEECC-CCCEEEEEECCCCCCCCCCCCCCCCCCCCCEEEECCCCCEEEECCCCCCCE-EEEEECC
T ss_conf             4888886168889-997799997788864367522102678998798538962899579537983-2898159


No 5  
>pfam08706 D5_N D5 N terminal like. This domain is found in D5 proteins of DNA viruses and bacteriophage P4 DNA primases phages.
Probab=99.86  E-value=1.2e-20  Score=154.87  Aligned_cols=143  Identities=19%  Similarity=0.192  Sum_probs=94.3

Q ss_pred             HHHHHCCCEEEEEEECCEEEEECCCEEEEECCHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHH
Q ss_conf             99870898399996178146860880577413122013445899999999999998654101230148899875687776
Q gi|254781225|r  315 MFSIYKKGHFLYTADTKAWYKKDKNNVYIWSLTLDKITASIMNFLVSMKEDVFDLSEEPEDNNKNSKSPRFWFNTDYRRQ  394 (789)
Q Consensus       315 ~~~~~~~~~~~~~~~~~~wy~~~~~~~~~~~g~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  394 (789)
                      ++....++.++|++..+.||.        |+|.+|+..... .....+...+..+..+...      .. .+....   .
T Consensus         3 ~~~~~~~~~l~y~~~~~~W~~--------~~g~~W~~d~~~-~v~~~~~~~~~~~~~~~~~------~~-~~~~~~---~   63 (145)
T pfam08706         3 RLADRYGKDLRYVPGTGGWYV--------WDGKRWEEDSKK-AIRELADKLLRLILEEAEA------AK-ELRKFA---K   63 (145)
T ss_pred             HHHHHHCCEEEEECCCCCEEE--------ECCCEEEECCHH-HHHHHHHHHHHHHHHHHHH------HH-HHHHHH---H
T ss_conf             899983993899778792899--------789894168588-9999999999999999999------99-999999---9


Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCHHHCCCCCCEEEECCCEEECCCCCCCCCCHHHHCCEECCCCCCCCCCHHHHHHHHH
Q ss_conf             20002679999874110000123202205797176607937974388855898655010013788887579478999998
Q gi|254781225|r  395 NVEENSKAKSTAQSLEAGSIFSITSDLLDSSSRFLGEQDGILDLETGQKVKPTKELYITKSTGTPFVEGEPSQEFLDLVS  474 (789)
Q Consensus       395 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ld~~~~ll~~~NGv~dl~t~~~~~~~~~~~~t~~~~~~y~~~a~~p~~~~~l~  474 (789)
                      .......+.++...+.+.  +.+..+.||++|++|||+||||||+||+|++|+|++++|++++++|+|+++||.|++||+
T Consensus        64 ~~~~~~~i~~~~~~~~~~--~~~~~~~~D~~p~ll~~~NGv~DL~tg~l~~h~p~~~~T~~~~v~y~p~a~~p~~~~fL~  141 (145)
T pfam08706        64 RSRSKSGVKNVLREAKAM--LDVTLDELDADPYLLNFPNGVLDLRTGELRPHDPEDRLTKITPVDYDPDADCPLWKQFLE  141 (145)
T ss_pred             HHCCHHHHHHHHHHHHHH--CCCCHHHHCCCCCEECCCCEEEECCCCCCCCCCHHHHEEECCCCCCCCCCCCHHHHHHHH
T ss_conf             850677899999984042--367988946997873799858989899578899778154425878898998878999999


Q ss_pred             HHCC
Q ss_conf             8879
Q gi|254781225|r  475 GYFE  478 (789)
Q Consensus       475 ~~~~  478 (789)
                      ++|+
T Consensus       142 ~i~~  145 (145)
T pfam08706       142 DIFG  145 (145)
T ss_pred             HHHC
T ss_conf             9739


No 6  
>cd04859 Prim_Pol Prim_Pol: Primase-polymerase (primpol) domain of the type found in bifunctional replicases from archaeal plasmids, including ORF904 protein of the crenarchaeal plasmid pRN1 from Sulfolobus islandicus (pRN1 primpol). These primpol domains belong to the archaeal/eukaryal primase (AEP) superfamily. This group includes archaeal plasmids and bacteriophage AEPs. The ORF904 protein is a multifunctional protein having ATPase, primase and DNA polymerase activity, and may play a role in the replication of the archaeal plasmid. The pRN1 primpol domain exhibits DNA polymerase and primase activities; a cluster of active site residues (three acidic residues, and a histidine) is required for both these activities. For pRN1 primpol, the primase activity prefers dNTPs to rNTPs; incorporation of dNTPs requires rNTP as cofactor. The pRN1 primpol contains an unusual zinc-binding stem, which is not conserved in other members of this group.
Probab=99.85  E-value=6.8e-20  Score=149.84  Aligned_cols=143  Identities=27%  Similarity=0.355  Sum_probs=101.3

Q ss_pred             CEEEEECCCCCCCCCCCCCCCC--CCCHHHHHHH----HHCCEEEEECCCCCCEEEEEEECCCCHHHH-HHHHHHHHCCC
Q ss_conf             8597735677878775654565--6898999742----007889992347798799996468812567-89998764189
Q gi|254781225|r   18 FKLIPLRLGDKRPQRLGKWEEQ--LLSSEKIDKL----PACGFGFVCGVGEQPLYAFDIDSKDEKTAN-TFKDTFEILHG   90 (789)
Q Consensus        18 ~~viPi~pg~KrP~~~~~w~~~--~~~~~~i~~~----~~~giGi~~G~~s~glv~iDiD~~d~~~~~-~~~~~~~~l~g   90 (789)
                      |+|||+.|++|+|.. .+|+..  ..+.++|.+|    +.+||||.||.  +||++||||+.+..... .....+..+..
T Consensus         1 ~~v~P~~~~~K~P~~-~~~~~~~at~d~~~i~~w~~~~p~~niGi~~G~--sglvviDiD~~~~~~~~~~~~~~~~~l~~   77 (152)
T cd04859           1 FAVIPLDPGSKRPLI-KGWPKDAATTDPEQIEAWWRDGPDANIGLRTGP--SGLVVIDIDVKHDGAAALAALAELGKLPP   77 (152)
T ss_pred             CEEEECCCCCCCCCC-CCCCCCCCCCCHHHHHHHHHHCCCCCEEEECCC--CCEEEEECCCCCCCHHHHHHHHHCCCCCC
T ss_conf             907746899871896-998874673999999999985998448888288--87799973267763468998776157787


Q ss_pred             -CCEEEECCCCCEEEEEEECCCCCCCCCCCCCCCCCEEEECCCCEEEECCCCCCCCCCEEECCCCCCCCCCCCCCCCHHH
Q ss_conf             -9769967889659999507310244544445767534852684388047768888745751776558722164689999
Q gi|254781225|r   91 -TPIVRIGQKPKILIPFRMNKEGIKKKKTTESTQGHLDILGCGQYFVAYNIHPKTKKEYTWTTPPHRFKVEDTPLLSEED  169 (789)
Q Consensus        91 -~p~~~~g~~~~~~~~yr~~~~~~~~~~~~~~~~~~iEi~~~G~q~V~~gshp~Tg~~Y~w~~~~~~~~~~~~P~i~~~~  169 (789)
                       ++.++++ .++.|++|+.|+...... ......+++|||+.|+|+|++||+|.+|++|.|..      ..+++.+|+|+
T Consensus        78 ~t~~~~T~-~gG~H~~f~~p~~~~~~~-~~~~~~~~vDir~~g~yvV~pPS~~~~g~~y~~~~------~~~~~~~P~wl  149 (152)
T cd04859          78 LTLTVRTG-SGGRHLYFRVPDGVPVKS-VKGKGGPGIDIRGGGGYVVAPPSVHPGGGYYVWKS------TVDPAPAPEWL  149 (152)
T ss_pred             CCEEEECC-CCCEEEEEECCCCCCCCC-CCCCCCCCEEEEECCCEEECCCCCCCCCCEEEECC------CCCCCCCCHHH
T ss_conf             77478869-994499998999862233-22476786789835988981786848964698089------99866788678


Q ss_pred             HH
Q ss_conf             99
Q gi|254781225|r  170 VE  171 (789)
Q Consensus       170 ~~  171 (789)
                      ++
T Consensus       150 ~~  151 (152)
T cd04859         150 LD  151 (152)
T ss_pred             HC
T ss_conf             63


No 7  
>pfam08707 PriCT_2 Primase C terminal 2 (PriCT-2). This alpha helical domain is found at the C terminal of primases.
Probab=99.19  E-value=6.7e-11  Score=90.12  Aligned_cols=61  Identities=36%  Similarity=0.656  Sum_probs=51.9

Q ss_pred             CCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHH
Q ss_conf             8888999999998621678156899999974035788978998864320101245676666415889987
Q gi|254781225|r  224 GSHDEWIPVVMAVHHETRGSSKGKEIARRWSKQGSTYDEENFNYKWDTFDFEEIGDTAKKRSTFTSLFYH  293 (789)
Q Consensus       224 ~dyd~W~~vg~al~~~~~~~~~~l~lw~~wS~~~~~y~~~~~~~~w~sf~~~~~~~~~~~~~~~~~~~~~  293 (789)
                      ++|++|++|||||||++  +++++++|++||+++++|++.+|+++|++|..       .+..++.++++.
T Consensus        13 ~dy~~W~~vG~aL~~~~--~~~~~~lw~~wS~~~~ky~~~~~~~~W~sf~~-------~~~itigTl~~~   73 (74)
T pfam08707        13 DDYDSWLRVGMALKHEF--GEEGLELWDEWSAKSSKYDPGECERKWDSFKR-------PGGITIGTLFYL   73 (74)
T ss_pred             CCHHHHHHHHHHHHHCC--CHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCC-------CCCCCHHHHHHH
T ss_conf             88899999999998266--65799999999746565883789999983779-------999348889986


No 8  
>cd00525 AE_Prim_S_like AE_Prim_S_like: primase domain similar to that found in the small subunit of archaeal and eukaryotic (A/E) DNA primases. The replication machineries of A/Es are distinct from that of bacteria. Primases are DNA-dependent RNA polymerases which synthesis the short RNA primers required for DNA replication. In eukaryotes, this small catalytically active primase subunit (p50) and a larger primase subunit (p60), referred to jointly as the core primase, associate with the B subunit and the DNA polymerase alpha subunit in a complex, called Pol alpha-pri. In addition to its catalytic role in replication, eukaryotic DNA primase may play a role in coupling replication to DNA damage repair and in checkpoint control during S phase. Pfu41 and Pfu46 comprise the primase complex of the archaea Pyrococcus furiosus; these proteins have sequence identity to the eukaryotic p50 and p60 primase proteins respectively. Pfu41 preferentially uses dNTPs as substrate. Pfu46 regulates the pri
Probab=98.98  E-value=2e-09  Score=80.31  Aligned_cols=113  Identities=21%  Similarity=0.252  Sum_probs=76.8

Q ss_pred             CEEEEECCCCCCCCCCCCCCC-CCCCHHHHHHH----HHCCEEEEECCC----CCCEEEEEEECCCC---HHHHHHHHHH
Q ss_conf             859773567787877565456-56898999742----007889992347----79879999646881---2567899987
Q gi|254781225|r   18 FKLIPLRLGDKRPQRLGKWEE-QLLSSEKIDKL----PACGFGFVCGVG----EQPLYAFDIDSKDE---KTANTFKDTF   85 (789)
Q Consensus        18 ~~viPi~pg~KrP~~~~~w~~-~~~~~~~i~~~----~~~giGi~~G~~----s~glv~iDiD~~d~---~~~~~~~~~~   85 (789)
                      +.++|+.++.|.|.. .+|+. ...+.+++..|    +..|||+.||..    ..+++++|||..+.   +........+
T Consensus         1 r~~~p~~~~~k~p~~-~~~~~~~~~~~~~~~~w~~~~~~~~i~~~~~~~~~~~~~~~lv~DlD~~~~~~~~~~~~~a~~~   79 (136)
T cd00525           1 RPVSPIRPPGKGPFQ-RHWPFGATTDDAEILAWLANLPPGNIGLSLGRYDKLWKPDLLVFDLDPDDYDCWEDVKEAALLL   79 (136)
T ss_pred             CCCCCCCCCCCCCCC-CCCCCCCCCCHHHHHHHHHHCCCEEEECCCCCCCCCCCCCEEEEECCCCCCCCHHHHHHHHHHH
T ss_conf             984455789888766-7886547558099999886338575017766567567998799826899999899999999999


Q ss_pred             HHCCC-----CCEEEECCCCCEEEEEEECCCCCCCCCCCCCCCCCEEEECC--CCEEEECCCCCC-CCCCEE
Q ss_conf             64189-----97699678896599995073102445444457675348526--843880477688-887457
Q gi|254781225|r   86 EILHG-----TPIVRIGQKPKILIPFRMNKEGIKKKKTTESTQGHLDILGC--GQYFVAYNIHPK-TKKEYT  149 (789)
Q Consensus        86 ~~l~g-----~p~~~~g~~~~~~~~yr~~~~~~~~~~~~~~~~~~iEi~~~--G~q~V~~gshp~-Tg~~Y~  149 (789)
                      .++..     +..++||+ ++.|++|+.                 +|++++  |+++|+|+|++. .+..+.
T Consensus        80 ~~ll~~~~~~~~~~~TG~-~G~H~~~~~-----------------iD~~~~~~~~~~v~p~S~~~~~~~~p~  133 (136)
T cd00525          80 RELLDEDGLNTLVVTSGS-RGLHVYVRL-----------------IDIRVNARGRLLVAPPSVHPRPGGPPS  133 (136)
T ss_pred             HHHHHHCCCCEEEECCCC-CEEEEEEEC-----------------CHHHCCCCCCEEECCCCCCCCCCCCCC
T ss_conf             999988499554374389-834999976-----------------456435789727636556689989787


No 9  
>COG4983 Uncharacterized conserved protein [Function unknown]
Probab=98.97  E-value=5.1e-10  Score=84.24  Aligned_cols=419  Identities=11%  Similarity=0.016  Sum_probs=193.2

Q ss_pred             CCCCCCCCCHHHHHHHHHCCEEEEECCCCCCEEEEEEECCC----CHHHHHHHHHHHHCCCCCEEEECCCCCEEEEEEEC
Q ss_conf             65456568989997420078899923477987999964688----12567899987641899769967889659999507
Q gi|254781225|r   34 GKWEEQLLSSEKIDKLPACGFGFVCGVGEQPLYAFDIDSKD----EKTANTFKDTFEILHGTPIVRIGQKPKILIPFRMN  109 (789)
Q Consensus        34 ~~w~~~~~~~~~i~~~~~~giGi~~G~~s~glv~iDiD~~d----~~~~~~~~~~~~~l~g~p~~~~g~~~~~~~~yr~~  109 (789)
                      .+|++++++++++.++.-+|||+++..+ +++|.||+|+..    +++.....+....+.++. ...+.+|.++|++-.-
T Consensus        51 ~TWsdf~tavralt~y~fdGIGFvFaen-~~~v~iDlDgcrd~~tGel~~~A~e~ir~l~nSy-tE~S~SGtGiHiigkg  128 (495)
T COG4983          51 ETWSDFNTAVRALTEYDFDGIGFVFAEN-NDDVPIDLDGCRDLDTGELKKSAQEKIRDLLNSY-TEFSESGTGIHIIGKG  128 (495)
T ss_pred             CHHHHHHHHHHHHHHCCCCCEEEEECCC-CCCCCCCCCCCEECCCCCCCHHHHHHHHHHHHHH-HHCCCCCCEEEEEEEC
T ss_conf             2010138899998724556436896037-8986636410242345665666788887645566-5125688627999505


Q ss_pred             CCCCCCCCCCCCCCCCEEEECCCCEEEECC-CCCCCCCCEEECC-CCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             310244544445767534852684388047-7688887457517-76558722164689999999997620012434543
Q gi|254781225|r  110 KEGIKKKKTTESTQGHLDILGCGQYFVAYN-IHPKTKKEYTWTT-PPHRFKVEDTPLLSEEDVEYLFKFFQEITVPLVKD  187 (789)
Q Consensus       110 ~~~~~~~~~~~~~~~~iEi~~~G~q~V~~g-shp~Tg~~Y~w~~-~~~~~~~~~~P~i~~~~~~~l~~~~~~~~~~~~~~  187 (789)
                          ...+-...+.+..|++.++|+++..| -.+++-+   -++ ....+....---+.....+.+...+....-+....
T Consensus       129 ----~~~p~gGrR~gn~EmY~d~rF~~ftg~~vldn~r---~vneA~~ai~~~~~kwig~d~~~~l~~~~~~sng~~k~~  201 (495)
T COG4983         129 ----EGIPIGGRRYGNPEMYADCRFGEFTGVDVLDNKR---CVNEAGNAISVSGDKWIGADPTQFLFEAYQESNGEAKSL  201 (495)
T ss_pred             ----CCCCCCCCCCCCHHHCCCCCEEEECCCCCCCCCC---CCCHHHHHHHHCCCCCCCCCCHHHHHHHHHHHCCCCCHH
T ss_conf             ----6235665567882014555337640641145732---111466666630773016880898988777524562034


Q ss_pred             CCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHH---------------CCCCCHHHHHHHHH
Q ss_conf             234554322234542000368898732101221114888899999999862---------------16781568999999
Q gi|254781225|r  188 KKSIIPSKTWTNNNNRQYTNREITAFLSCFGEEFYNGSHDEWIPVVMAVHH---------------ETRGSSKGKEIARR  252 (789)
Q Consensus       188 ~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~dyd~W~~vg~al~~---------------~~~~~~~~l~lw~~  252 (789)
                      .++...          ....+....+.+....    +++.+......||.|               .++.+...++.   
T Consensus       202 ~s~~~~----------sk~gA~fk~lfdgs~~----g~~~shS~AD~Alanmlafwtgd~av~i~~fgrS~lg~ReK---  264 (495)
T COG4983         202 SSSTGK----------SKLGADFKELFDGSDI----GDALSHSNADCALANMLAFWTGDFAVHIWDFGRSGLGLREK---  264 (495)
T ss_pred             HHCCCC----------CCCCCHHHHHCCCCCC----CCCCCCCCHHHHHHHHHHHHCCCCEEEHHHHHCCCCCHHHH---
T ss_conf             412643----------1224337774787444----67623343346776658865077534402230243531434---


Q ss_pred             HHCCCCCCC---HHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCEEEEEEE
Q ss_conf             740357889---78998864320101245676666415889987663045444555533047899998708983999961
Q gi|254781225|r  253 WSKQGSTYD---EENFNYKWDTFDFEEIGDTAKKRSTFTSLFYHHGKLIPKGLLASRFSDAYNKAMFSIYKKGHFLYTAD  329 (789)
Q Consensus       253 wS~~~~~y~---~~~~~~~w~sf~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~~~~~~~~  329 (789)
                      |++...+-+   +..|+..|+.-...      .........+...++.. ......+ +  ....+++.-.....+|..+
T Consensus       265 w~r~r~~t~n~a~ri~q~iygrS~~~------q~Gve~et~~~~~kd~~-w~v~~~~-n--v~p~~~a~~e~~a~r~~~~  334 (495)
T COG4983         265 WSRGRSKTDNQAERIIQDIYGRSASE------QQGVEVETLIHYAKDGG-WTVPTRS-N--VTPQSQANGETKALREAID  334 (495)
T ss_pred             HHCCCCCCHHHHHHHHHHHHCCCHHC------CCCCCCHHEEHHHHCCC-CEECCCC-C--CCHHHHHHHCCCEEEEECC
T ss_conf             43046630248888888774620010------58852000001454078-2521555-6--7788875320460788404


Q ss_pred             CCEEEEECCCEEEEECCHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             78146860880577413122013445899999999999998654101230148899875687776200026799998741
Q gi|254781225|r  330 TKAWYKKDKNNVYIWSLTLDKITASIMNFLVSMKEDVFDLSEEPEDNNKNSKSPRFWFNTDYRRQNVEENSKAKSTAQSL  409 (789)
Q Consensus       330 ~~~wy~~~~~~~~~~~g~~w~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  409 (789)
                      . .|+.......       -+....+++......  ++.....+         .+.  ............. ..++  .+
T Consensus       335 ~-s~id~~~ktv-------t~~~v~~~n~~e~~~--~~~~~~~i---------~~a--~g~~vi~~~~es~-g~g~--~l  390 (495)
T COG4983         335 S-SWIDLDSKTV-------TVQSVEGYNASELVD--VFQKSGNI---------LEA--CGHEVISAIGESD-GGGE--FL  390 (495)
T ss_pred             C-CEECCCCCEE-------EEEECCCCCHHHHHH--HHHCCCHH---------HHH--CCCEEEEECCCCC-CCCC--CH
T ss_conf             7-6011556637-------897405545787777--77312066---------664--4832787336788-8764--21


Q ss_pred             CCCCCCCCCHHHCCCCCCEEEECCCEEECCCCCCCCCCHHHHCCEECCCCCCCCCCHHHHHHHHHHHC-CCHHHHHHHHH
Q ss_conf             10000123202205797176607937974388855898655010013788887579478999998887-99999999999
Q gi|254781225|r  410 EAGSIFSITSDLLDSSSRFLGEQDGILDLETGQKVKPTKELYITKSTGTPFVEGEPSQEFLDLVSGYF-ESEEVMDYFTR  488 (789)
Q Consensus       410 ~~~~~~~~~~~~ld~~~~ll~~~NGv~dl~t~~~~~~~~~~~~t~~~~~~y~~~a~~p~~~~~l~~~~-~d~e~~~~l~~  488 (789)
                      +..+......+..+.--..++..|+-+.+.|++...|+.....+.+.+..+-.++..+.|..++...+ .|..++.|++-
T Consensus       391 ~~~~~~~~~~dgrk~~~~~ls~~~~~lip~ta~~~~~t~~~a~~~~r~i~l~~~~~~~~~~~tg~~r~wls~~L~py~~g  470 (495)
T COG4983         391 DDSGNGWTVEDGRKNPYAHLSPLSNQLIPNTALAELPTHRVAYLPKREIWLWCDDGVWKPNGTGWVRQWLSEYLGPYYSG  470 (495)
T ss_pred             HCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCEEEECCCCHHHHHHCCCEECCCCCCCEECCCCCCCHHHHHHHHHHHHHH
T ss_conf             10268765743345735452334311165640223563332220003133134567152034331012456777888888


Q ss_pred             HHHHHHCCCCCCCEEEEEEECCCCCHHHH
Q ss_conf             99999759874337999970788625789
Q gi|254781225|r  489 CVGMALLGGNKAQRFIHIRGVGGSGKSTL  517 (789)
Q Consensus       489 ~~g~~l~g~~~~~~~~~~~G~G~nGKSt~  517 (789)
                      ++++     ...+.+++..+.+.+++|++
T Consensus       471 ~v~~-----ev~dq~~nr~lv~e~~~~~~  494 (495)
T COG4983         471 HIRR-----EVMDQLQNRSLVEEQRFGGG  494 (495)
T ss_pred             HHHH-----HHHHHHHHHHHHHHHCCCCC
T ss_conf             8888-----99999988776665114468


No 10 
>pfam05272 VirE Virulence-associated protein E. This family contains several bacterial virulence-associated protein E like proteins.
Probab=98.91  E-value=2.1e-08  Score=73.55  Aligned_cols=181  Identities=18%  Similarity=0.216  Sum_probs=125.7

Q ss_pred             CHHHHHHHHHHHCC--CHHHH-----HHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHH
Q ss_conf             94789999988879--99999-----999999999975987433799997078862578999999972330003442676
Q gi|254781225|r  465 PSQEFLDLVSGYFE--SEEVM-----DYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASD  537 (789)
Q Consensus       465 ~~p~~~~~l~~~~~--d~e~~-----~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~  537 (789)
                      -.|++..++.+.++  |.+.-     .+|.-+++-++.++.....+++|.|+.|-|||||++.|.   ++++..+...  
T Consensus         9 G~~Ri~~l~~~~~g~~d~~~~~~~~~~wligaVaR~~~pG~k~d~vlvL~G~QG~gKStf~~~L~---~~~~~d~~~~--   83 (198)
T pfam05272         9 GIPRIETLFIDYLGAEDSLYTREVSKLFLIGAVARVYEPGCKFDHVLILQGAQGSGKSTFLKKLG---GEWFTDSIRS--   83 (198)
T ss_pred             CCCHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCHHHHHHHHH---HHHCCCCCCC--
T ss_conf             81179999999629997599999999999999999977897677678998898678999999973---7751565557--


Q ss_pred             HHHCCCCCCCCCCHHHHHHCCCEEEEEECCCCCCCCCCCEEEEEECCCEEEEEECCCCCCEEEECCEEEEEECCCCCCCC
Q ss_conf             42012455556898899738980999934677760131002454159858732104786068714528999738863426
Q gi|254781225|r  538 IMQNRPPEAGKANPSLIRLMGSRIVIISETNENDEINAAKIKQMTGGDCMTARLNYGNTYSESPASFTPFIVPNKHLFVR  617 (789)
Q Consensus       538 ~~~~~~~~~~~~~~~la~l~g~r~~~~~E~~~~~~~~~~~~K~ltggD~i~ar~~~~~~~~~~~p~~~~~~~~N~~P~~~  617 (789)
                      .         .....+..+.+.-++-++|.+.-.+-+.+.+|++.+-.....|..|+.....++-.+.++-.||+....+
T Consensus        84 ~---------~~kD~~~~l~~~wi~el~El~~~~k~~~~~lK~fls~~~d~~R~pY~~~~~~~pR~~vfigTtN~~~~L~  154 (198)
T pfam05272        84 F---------EGKDAYEKLQGVWIVEIAELDGFSKAEVEAIKAFITRTVDSFRAPYGRRAESFPRQCVFVGTTNRDEFLK  154 (198)
T ss_pred             C---------CCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCHHHCCHHCCCCCCEECCEEEEEEEECCCCCCCC
T ss_conf             6---------7738999999878732598751365329999998454131231022356400654799999638876557


Q ss_pred             CCCCCEEEEEEEEECCCCCCCCCCCHHHHHCCCCHHHHHHHHHHHH
Q ss_conf             7984166468999658878887878334220120447999999999
Q gi|254781225|r  618 NPDDAWWRRYIVIPFDKPIANRDASFAQKLETKYTLEAKKWFLKGV  663 (789)
Q Consensus       618 ~~d~~~~rR~~iipF~~~~~~~d~~~~~~~~~~e~~~i~~w~l~g~  663 (789)
                      |.+.  -||+.+|+-...+...-.  ..+....+...+.+-|+.-+
T Consensus       155 D~TG--nRRF~pi~v~~~~~~~~~--~~d~l~~~rdqlWAeA~~~Y  196 (198)
T pfam05272       155 DPTG--NRRFWPVKVGKKINIKHP--VSELLDEVRDQLWAEAVWYY  196 (198)
T ss_pred             CCCC--CEEEEEEEECCCCCCCCC--CHHHHHHHHHHHHHHHHHHH
T ss_conf             9999--816899996885455767--55777999999999999997


No 11 
>pfam01057 Parvo_NS1 Parvovirus non-structural protein NS1. This family also contains the NS2 protein. Parvoviruses encode two non-structural proteins, NS1 and NS2. The mRNA for NS2 contains the coding sequence for the first 87 amino acids of NS1, then by an alternative splicing mechanism mRNA from a different reading frame, encoding the last 78 amino acids, makes up the full length of the NS2 mRNA. NS1, is the major non-structural protein. It is essential for DNA replication. It is an 83-kDa nuclear phosphoprotein. It has DNA helicase and ATPase activity.
Probab=98.21  E-value=3.3e-05  Score=52.27  Aligned_cols=193  Identities=14%  Similarity=0.082  Sum_probs=117.8

Q ss_pred             CCCHHHHCCEECCCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             89865501001378888757947899999888799999999999999997598743379999707886257899999997
Q gi|254781225|r  445 KPTKELYITKSTGTPFVEGEPSQEFLDLVSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYA  524 (789)
Q Consensus       445 ~~~~~~~~t~~~~~~y~~~a~~p~~~~~l~~~~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~l  524 (789)
                      .+...+|+....+....+... ..+.++|..-==|+....   .++-.-|......+-.+.++|+.+.|||-|...|...
T Consensus        61 ~~~~~~~l~~~~~~~~~~i~~-N~~~~l~~~~gy~P~~~g---~~l~~w~~k~~~krN~i~~~Gp~~TGks~la~ai~~~  136 (271)
T pfam01057        61 TKTALDYLAKPEVTANFDIEE-NRIYQLLSLNGYNPAEVG---QVLLAWLSKQGGKRNTVWFYGPASTGKTNLAQAIAHA  136 (271)
T ss_pred             CCCHHHHHHCCCCCCCCCCCC-CHHHHHHHHCCCCHHHHH---HHHHHHHHCCCCCCCEEEEECCCCCCHHHHHHHHHHH
T ss_conf             575999850678886566441-789999998499989999---9999998447888756999889876789999999986


Q ss_pred             HCCCCCCCCCHHHHHHCCCCCCCCCCHHHHHHCCCEEEEEECCCCCCCCCCCEEEEEECCCEEEEEECCCCCCEEEECCE
Q ss_conf             23300034426764201245555689889973898099993467776013100245415985873210478606871452
Q gi|254781225|r  525 FGNQYVINAEASDIMQNRPPEAGKANPSLIRLMGSRIVIISETNENDEINAAKIKQMTGGDCMTARLNYGNTYSESPASF  604 (789)
Q Consensus       525 lG~~~~~~~~~~~~~~~~~~~~~~~~~~la~l~g~r~~~~~E~~~~~~~~~~~~K~ltggD~i~ar~~~~~~~~~~~p~~  604 (789)
                      ++.|.+..-.             +.++-+..+.++.+..-.|.......- ..+|++.||..|....|+++. ++..+.-
T Consensus       137 ~~~~g~v~~~-------------N~~fp~~d~~~~~~~wwee~~~~~~~v-e~~r~il~G~~i~vD~k~k~~-~~l~~~P  201 (271)
T pfam01057       137 VPLYGCVNWT-------------NENFPFNDCPNKLLIWWEEGLMTVKVV-ELAKAILGGTDVRVDQKCKGS-VEIEPTP  201 (271)
T ss_pred             CCCEEEECCC-------------CCCCCCCCCCCCEEEEECCCCCCHHHH-HHHHHHHCCCCCEEECCCCCC-CCCCCCC
T ss_conf             8952785178-------------778876446547899980788718899-999997299962563478980-0237997


Q ss_pred             EEEEECCCCC-CCCC-------CCCCEEEEEEEEECCCCCCCCCCCHHHHHCCCCHHHHHHHHHH
Q ss_conf             8999738863-4267-------9841664689996588788878783342201204479999999
Q gi|254781225|r  605 TPFIVPNKHL-FVRN-------PDDAWWRRYIVIPFDKPIANRDASFAQKLETKYTLEAKKWFLK  661 (789)
Q Consensus       605 ~~~~~~N~~P-~~~~-------~d~~~~rR~~iipF~~~~~~~d~~~~~~~~~~e~~~i~~w~l~  661 (789)
                      . ++.+|+-- .+.+       +..++-.|+..+-|...++..    ...+...|....+.|+-.
T Consensus       202 v-iiTsn~di~~v~~g~~~s~~Ha~~Lk~rm~~~~~~~~l~~~----fg~it~~d~~~f~~W~~~  261 (271)
T pfam01057       202 V-IITSNHDITLVVDGNTTSFEHAQPLKDRMYKFNLTKRLPPA----FGLITKEDVRQFLQWSEN  261 (271)
T ss_pred             E-EEEECCCEEEEEECCCCCHHHHHHHHHHEEEEEECCCCCCC----CCCCCHHHHHHHHHHHHH
T ss_conf             8-99827857999868753577777876536898857674887----785489999999999860


No 12 
>pfam04735 Baculo_helicase Baculovirus DNA helicase.
Probab=98.15  E-value=3.5e-06  Score=58.78  Aligned_cols=139  Identities=17%  Similarity=0.272  Sum_probs=94.2

Q ss_pred             HHHHH-CCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCCCCCHHHHHHCCCEEEEEECCC
Q ss_conf             99997-59874337999970788625789999999723300034426764201245555689889973898099993467
Q gi|254781225|r  490 VGMAL-LGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEAGKANPSLIRLMGSRIVIISETN  568 (789)
Q Consensus       490 ~g~~l-~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~~~~~~~~la~l~g~r~~~~~E~~  568 (789)
                      +|.+| ++...+++++.+.|..+.|||+|.+|+..++=-+   .-+...-+..+    ...+.--+...-.-|=++.|..
T Consensus       867 F~ASLaIPtDYEK~clyL~g~PnsGKSSffELLd~iivvh---K~D~~~Y~~~k----ket~emev~k~~SQLYviNE~k  939 (1173)
T pfam04735       867 FCASLAIPTDYEKMCLYLNGKPNCGKSSFFELLDKIILVH---KHDKEKYTLSK----KETDEMEVKKLESQLYVINEAK  939 (1173)
T ss_pred             HHHHCCCCCCCCEEEEEECCCCCCCCHHHHHHHHHEEEEE---ECCHHHCCCCC----CCCCHHHHHHHHHHHHHHHHHH
T ss_conf             6301168875211799914889997132899862058998---43555326888----8887889998874777888998


Q ss_pred             CCCCCCCCEEEEEECC-CEEEEEECCCCCCEEEECCEEEEEECCCCCCCCCCCCCEEEEEEEEECCCCCCCC
Q ss_conf             7760131002454159-8587321047860687145289997388634267984166468999658878887
Q gi|254781225|r  569 ENDEINAAKIKQMTGG-DCMTARLNYGNTYSESPASFTPFIVPNKHLFVRNPDDAWWRRYIVIPFDKPIANR  639 (789)
Q Consensus       569 ~~~~~~~~~~K~ltgg-D~i~ar~~~~~~~~~~~p~~~~~~~~N~~P~~~~~d~~~~rR~~iipF~~~~~~~  639 (789)
                         ..+.+.||+..-. -.-+|+++|+-.. .|.-++|+++.-|.+..|.|-|.|...|+.+|=|++.|.+.
T Consensus       940 ---~cs~sffK~~ADSTKsdsv~rkY~g~q-kyeaNYK~lIvNNkpL~I~DYDkgv~NRf~ivY~DH~F~e~ 1007 (1173)
T pfam04735       940 ---KCSKSFFKSIADSTKSDSACRKYGGSE-KYEANYKLLIVNNKPLYISDYDKGVRNRFGQIYTDHEFEEN 1007 (1173)
T ss_pred             ---HHHHHHHHCCCCCCCHHHHHHCCCHHH-HHHHCCEEEEECCCEEEEECCCHHHHHCEEEEEECCCCCCC
T ss_conf             ---852887431333431021132143366-42300528998387037605655544224789723211438


No 13 
>COG5545 Predicted P-loop ATPase and inactivated derivatives [General function prediction only]
Probab=98.13  E-value=3.8e-05  Score=51.93  Aligned_cols=182  Identities=18%  Similarity=0.256  Sum_probs=129.1

Q ss_pred             CHHHHHHHHHHHCC--CHHHH-----HHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHH
Q ss_conf             94789999988879--99999-----999999999975987433799997078862578999999972330003442676
Q gi|254781225|r  465 PSQEFLDLVSGYFE--SEEVM-----DYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASD  537 (789)
Q Consensus       465 ~~p~~~~~l~~~~~--d~e~~-----~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~  537 (789)
                      ..|+.+..+...||  |.++.     .|+--+++-++-++.+...+++|.|+-++|||||+.   .|+|.|-.+-.....
T Consensus       159 ~v~r~~~l~~dyfGa~ds~l~~~~~k~f~VgAVarv~~Pg~K~Df~l~L~G~Qgs~KsTfl~---~l~G~~wftd~~~~~  235 (517)
T COG5545         159 GVPRVETLLIDYFGASDSTLARQASKCFMVGAVARVLWPGAKVDFMLVLEGPQGSHKSTFLS---ELFGTYWFTDTAESP  235 (517)
T ss_pred             CCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCCCHHH---HHCCCEEEECCCCCC
T ss_conf             96279898898727887389999998899999998737887520689974477777322699---861860340345588


Q ss_pred             HHHCCCCCCCCCCHHHHHHCCCEEEEEECCCCCCCCCCCEEEEEECCCEEEEEECCCCCCEEEECCEEEEEECCCCCCCC
Q ss_conf             42012455556898899738980999934677760131002454159858732104786068714528999738863426
Q gi|254781225|r  538 IMQNRPPEAGKANPSLIRLMGSRIVIISETNENDEINAAKIKQMTGGDCMTARLNYGNTYSESPASFTPFIVPNKHLFVR  617 (789)
Q Consensus       538 ~~~~~~~~~~~~~~~la~l~g~r~~~~~E~~~~~~~~~~~~K~ltggD~i~ar~~~~~~~~~~~p~~~~~~~~N~~P~~~  617 (789)
                       +         -..++..+.+.-.+-..|.+...+.+.+-||...+.-..+-|..|+.....|.-.+.++=.|||.--.+
T Consensus       236 -t---------~KD~~~~i~~~wive~~Em~s~~K~dvt~lK~fitr~~dsfRaPYgt~~e~y~r~~V~vgTTN~~Eylk  305 (517)
T COG5545         236 -T---------GKDFYQVIQGCWIVEIGEMDSFGKADVTALKVFITRRTDSFRAPYGTLPESYRRECVFVGTTNDREYLK  305 (517)
T ss_pred             -C---------CCHHHHHHHHHHEEEHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCCCCHHHCCCCEEEEECCCHHHHHC
T ss_conf             -8---------505999976553341055554268878999999987036301765688555466517972156687610


Q ss_pred             CCCCCEEEEEEEEECCCCCCCCCCCHHHHHCCCCHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             7984166468999658878887878334220120447999999999999987889
Q gi|254781225|r  618 NPDDAWWRRYIVIPFDKPIANRDASFAQKLETKYTLEAKKWFLKGVKAYISKGLD  672 (789)
Q Consensus       618 ~~d~~~~rR~~iipF~~~~~~~d~~~~~~~~~~e~~~i~~w~l~g~~~~~~~g~~  672 (789)
                      |.+.|  ||+.+|.-.+.++..      .+ ..|..  .-|+-  +..++.+|+.
T Consensus       306 D~TG~--RRFlpV~~~k~v~~~------~~-v~erD--q~Wae--aV~~y~~gf~  347 (517)
T COG5545         306 DATGG--RRFLPVRADKNVDVS------RI-VAERD--QLWAE--AVQLYLDGFP  347 (517)
T ss_pred             CCCCC--EEEEEEEECCCCCHH------HH-HHHHH--HHHHH--HHHHHHCCCC
T ss_conf             67787--367888765767655------54-46789--99999--9999864785


No 14 
>pfam00519 PPV_E1_C Papillomavirus helicase. This protein is a DNA helicase that is required for initiation of viral DNA replication. This protein forms a complex with the E2 protein pfam00508.
Probab=97.98  E-value=0.00012  Score=48.66  Aligned_cols=156  Identities=15%  Similarity=0.205  Sum_probs=107.5

Q ss_pred             CCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCC
Q ss_conf             57947899999888799999999999999997598743379999707886257899999997233000344267642012
Q gi|254781225|r  463 GEPSQEFLDLVSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNR  542 (789)
Q Consensus       463 ~a~~p~~~~~l~~~~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~  542 (789)
                      +.....+.+||.-  .+-+.+.||. .+-.-|-|..+ +.++.++|+.++|||.|..-|.+.||..-.+-+         
T Consensus       228 ~GdWk~Iv~FLry--Q~iefi~Fl~-alk~fLkg~PK-knCivi~GPPnTGKS~F~mSLi~fL~G~ViSfv---------  294 (432)
T pfam00519       228 EGDWKPIVKFLRY--QGIEFISFLS-ALKDFLKGIPK-KNCLVIYGPPDTGKSMFCMSLIKFLGGKVISFV---------  294 (432)
T ss_pred             CCCHHHHHHHHHH--CCCCHHHHHH-HHHHHHCCCCC-CCEEEEECCCCCCHHHHHHHHHHHHCCEEEEEE---------
T ss_conf             9976789888832--7713999999-99999648985-246999899996676899999998498699961---------


Q ss_pred             CCCCCCCCHHHHHHCCCEEEEEECCCCC--CCCCCCEEEEEECCCEEEEEECCCCCCEEEECCEEEEEECCCCCCCCCCC
Q ss_conf             4555568988997389809999346777--60131002454159858732104786068714528999738863426798
Q gi|254781225|r  543 PPEAGKANPSLIRLMGSRIVIISETNEN--DEINAAKIKQMTGGDCMTARLNYGNTYSESPASFTPFIVPNKHLFVRNPD  620 (789)
Q Consensus       543 ~~~~~~~~~~la~l~g~r~~~~~E~~~~--~~~~~~~~K~ltggD~i~ar~~~~~~~~~~~p~~~~~~~~N~~P~~~~~d  620 (789)
                        ++ ...|-|.-|..++++.++|.-..  ..+++ .+....-|.+|....||+.+. +.+-- -|++.||--+.-.+.=
T Consensus       295 --Ns-kShFWLqPL~daKiallDDAT~~CW~Y~D~-ylRN~LDGN~vsiD~KHkap~-QiK~P-PLLiTsNidv~~d~~~  368 (432)
T pfam00519       295 --NS-KSHFWLQPLADAKIALLDDATHACWDYIDT-YLRNALDGNPVSIDRKHKAPV-QIKCP-PLLITSNIDVKADDRY  368 (432)
T ss_pred             --CC-CCCCCCCCHHHCCEEEEECCCHHHHHHHHH-HHHHCCCCCCEEEECCCCCCH-HCCCC-CEEEEECCCCCCCCCH
T ss_conf             --48-773022735327464220660888999999-876134788134552357742-02578-6588705787866321


Q ss_pred             CCEEEEEEEEECCCCCC
Q ss_conf             41664689996588788
Q gi|254781225|r  621 DAWWRRYIVIPFDKPIA  637 (789)
Q Consensus       621 ~~~~rR~~iipF~~~~~  637 (789)
                      .=+-.|+.++.|+++||
T Consensus       369 ~YLhSRi~~f~F~n~fP  385 (432)
T pfam00519       369 KYLHSRITVFEFPNPFP  385 (432)
T ss_pred             HHHHHEEEEEECCCCCC
T ss_conf             53343168997489887


No 15 
>pfam03288 Pox_D5 Poxvirus D5 protein-like. This family includes D5 from Poxviruses which is necessary for viral DNA replication, and is a nucleic acid independent nucleoside triphosphatase. Members of this family are also found outside of poxviruses. This domain is a DNA-binding winged HTH domain.
Probab=97.53  E-value=0.00016  Score=47.78  Aligned_cols=54  Identities=17%  Similarity=0.166  Sum_probs=49.0

Q ss_pred             HCCHHHHHHHHHEEECCCCEECHHHHHHHHHHHHHHCCCCCCCC-CCHHHHHHHHHHC
Q ss_conf             42638888754326268841117999999999998504667555-4525689999863
Q gi|254781225|r  689 GTDTYQAWIDDCCDIGENLWEESHSLAKSYSEYREQELNYDRKR-ISTRTVTLNLKQK  745 (789)
Q Consensus       689 ~~D~v~~fi~e~ce~~~~~~~~~~~l~~~y~~~~~~~~~~~~~~-~s~~~~~~~l~~~  745 (789)
                      ++|+|..|+++||+......+++..+|.+|.+||+.+|-   .+ ++.+.|.++|.+.
T Consensus         1 ~nD~v~dF~~~~~~~~~s~~vP~~~ly~~y~~~~e~~g~---~~~L~~~~F~~~l~~~   55 (88)
T pfam03288         1 DNDPVPDFAEELFVLFKSDRVPSDFLYEAYKAWCEKNGY---VPVLSKRTFQQRLAKH   55 (88)
T ss_pred             CCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHCCC---CCCCHHHHHHHHHHHH
T ss_conf             986099999999764546407599999999999998599---7752177999999987


No 16 
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=97.50  E-value=0.0053  Score=37.68  Aligned_cols=209  Identities=16%  Similarity=0.167  Sum_probs=107.5

Q ss_pred             CCCCCCCCHHHCCCCCCEEEECCCE---EECCC----CCCCCCC------HHHHCCEECCCCCCCCCCHHHHH----HHH
Q ss_conf             0000123202205797176607937---97438----8855898------65501001378888757947899----999
Q gi|254781225|r  411 AGSIFSITSDLLDSSSRFLGEQDGI---LDLET----GQKVKPT------KELYITKSTGTPFVEGEPSQEFL----DLV  473 (789)
Q Consensus       411 ~~~~~~~~~~~ld~~~~ll~~~NGv---~dl~t----~~~~~~~------~~~~~t~~~~~~y~~~a~~p~~~----~~l  473 (789)
                      +-..+....+.+|.+..++-..+|-   +....    ..+.|++      ..+-+-.+++-++||....-...    -..
T Consensus        52 ~p~~vg~~~~~~~~~~~iv~~~~g~~~~v~~~~~~~~~~l~pg~~V~l~~~~~~i~~~l~~~~d~~v~~m~v~e~P~v~~  131 (390)
T PRK03992         52 PPLIVATVLEVLDDGRVVVKSSTGPQFVVTVSSFVDRDKLKPGARVALNQQTLAIVEVLPSEKDPRVRAMEVIESPDVTY  131 (390)
T ss_pred             CCCEEEEEEEEECCCEEEEEECCCCEEEEECCCCCCHHHCCCCCEEEECCCCCEEEEECCCCCCCCCCCCCCCCCCCCCH
T ss_conf             99489999998379749999789987999657876888879999899853530305646888786211042147999984


Q ss_pred             HHHCCCHHHHHHHHHHHHHHHCC-------CCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCC
Q ss_conf             88879999999999999999759-------87433799997078862578999999972330003442676420124555
Q gi|254781225|r  474 SGYFESEEVMDYFTRCVGMALLG-------GNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEA  546 (789)
Q Consensus       474 ~~~~~d~e~~~~l~~~~g~~l~g-------~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~~  546 (789)
                      ++|=|=++.+.-+++.+=+-|..       +....+=++|||+.|+||+.+...+..-.|-.........+++. .-..+
T Consensus       132 ~dIGGl~~~k~el~E~velPl~~pe~f~~~Gi~pPkGvLLyGPPGtGKTllAkAvA~e~~~~fi~v~~s~l~sk-~vGes  210 (390)
T PRK03992        132 EDIGGLDEQIREVREAVELPLKNPELFEEVGIEPPKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVQK-FIGEG  210 (390)
T ss_pred             HHHCCHHHHHHHHHHHHHHHHHCHHHHHHCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCEEEEEHHHHHHC-CCCHH
T ss_conf             66149899999999999998659899997699999727868989997899999999874888799667997524-54179


Q ss_pred             C---CCCHHHHHHCCCEEEEEECCCCCCCCCCCEEEEEECCCEEEE----EECC-CCCCEEEECCEEEEEECCCCCCCCC
Q ss_conf             5---689889973898099993467776013100245415985873----2104-7860687145289997388634267
Q gi|254781225|r  547 G---KANPSLIRLMGSRIVIISETNENDEINAAKIKQMTGGDCMTA----RLNY-GNTYSESPASFTPFIVPNKHLFVRN  618 (789)
Q Consensus       547 ~---~~~~~la~l~g~r~~~~~E~~~~~~~~~~~~K~ltggD~i~a----r~~~-~~~~~~~~p~~~~~~~~N~~P~~~~  618 (789)
                      .   ..-|++|+-..--+++++|.+.   +...+.-.-++||.-.-    ..+. -+.| .-.....++.+||+   ...
T Consensus       211 ek~vr~lF~~Ar~~aP~IiFiDEiDa---i~~~R~~~~~~g~~ev~r~l~qLL~emDG~-~~~~~V~VIaATNr---pd~  283 (390)
T PRK03992        211 ARLVRELFELAREKAPSIIFIDEIDA---IAAKRTDSGTSGDREVQRTLMQLLAEMDGF-DPRGNVKIIAATNR---PDI  283 (390)
T ss_pred             HHHHHHHHHHHHHHCCCEEEHHHHHH---HHCCCCCCCCCCCHHHHHHHHHHHHHCCCC-CCCCCEEEEEECCC---CHH
T ss_conf             99999999999970990897143256---633567788862088999999999974487-77788279960698---100


Q ss_pred             CCCCEEE--EE
Q ss_conf             9841664--68
Q gi|254781225|r  619 PDDAWWR--RY  627 (789)
Q Consensus       619 ~d~~~~r--R~  627 (789)
                      -|.|+.|  |+
T Consensus       284 LDpAllRpGRF  294 (390)
T PRK03992        284 LDPALLRPGRF  294 (390)
T ss_pred             CCHHHHCCCCC
T ss_conf             59777547765


No 17 
>smart00763 AAA_PrkA PrkA AAA domain. This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.
Probab=97.22  E-value=0.0011  Score=42.11  Aligned_cols=55  Identities=24%  Similarity=0.388  Sum_probs=46.6

Q ss_pred             HHCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCC
Q ss_conf             8879999999999999999759874337999970788625789999999723300
Q gi|254781225|r  475 GYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQY  529 (789)
Q Consensus       475 ~~~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~  529 (789)
                      ++||-++.++-+-.++..+.-|.-..+..++|.||-|+|||||.+.|...|=.|.
T Consensus        52 ~~fG~e~~i~~~V~~~k~AA~g~~~~k~IllL~GPvGsGKStl~~~Lk~~lE~ys  106 (361)
T smart00763       52 DFFGMEEAIERFVNYFKSAAQGLEERKQILYLLGPVGGGKSSLVECLKRGLEEYS  106 (361)
T ss_pred             HHCCCHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHH
T ss_conf             3116489999999999999844671256999988998877999999999999862


No 18 
>KOG3712 consensus
Probab=97.20  E-value=0.0009  Score=42.76  Aligned_cols=11  Identities=9%  Similarity=0.295  Sum_probs=7.0

Q ss_pred             CCCHHHHHHHH
Q ss_conf             12044799999
Q gi|254781225|r  649 TKYTLEAKKWF  659 (789)
Q Consensus       649 ~~e~~~i~~w~  659 (789)
                      ......|+.||
T Consensus       573 lq~~s~ie~~a  583 (736)
T KOG3712         573 LQQQSDIEVWA  583 (736)
T ss_pred             HHHHHHHHHHH
T ss_conf             98765899999


No 19 
>pfam05496 RuvB_N Holliday junction DNA helicase ruvB N-terminus. The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein. This family contains the N-terminal region of the protein.
Probab=96.99  E-value=0.026  Score=33.07  Aligned_cols=145  Identities=15%  Similarity=0.171  Sum_probs=75.2

Q ss_pred             HHHHCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCC-CCCCHHHHHHCCCCCCCCCCH
Q ss_conf             9888799999999999999997598743379999707886257899999997233000-344267642012455556898
Q gi|254781225|r  473 VSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYV-INAEASDIMQNRPPEAGKANP  551 (789)
Q Consensus       473 l~~~~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~-~~~~~~~~~~~~~~~~~~~~~  551 (789)
                      |++++|-+.+..-+..++-.+........- ++++|+.|.||+|+..+|.+.++.... .+.+  .+....     .-..
T Consensus        23 l~e~vGQehl~~~l~~~i~a~~~~~~~l~h-~lf~GPPG~GKTTlAriiAk~~~~~~~~~s~~--~i~~~~-----di~~   94 (234)
T pfam05496        23 LDEYIGQEKVKENLKIFIEAAKKRGEALDH-VLLYGPPGLGKTTLANIIANEMGVNIRITSGP--ALEKPG-----DLAA   94 (234)
T ss_pred             HHHCCCHHHHHHHHHHHHHHHHHCCCCCCE-EEEECCCCCCHHHHHHHHHHHHCCCEEEECCH--HHHHHH-----HHHH
T ss_conf             666069499999999999988742777662-78878999988899999998408753761426--664389-----9999


Q ss_pred             HHHHHCCCEEEEEECCCCCCCCC-CCEEEEEECCCE-EE-EEECCCCCCEEEECCEEEEEECCCCCCCCCCCCCEEEEEE
Q ss_conf             89973898099993467776013-100245415985-87-3210478606871452899973886342679841664689
Q gi|254781225|r  552 SLIRLMGSRIVIISETNENDEIN-AAKIKQMTGGDC-MT-ARLNYGNTYSESPASFTPFIVPNKHLFVRNPDDAWWRRYI  628 (789)
Q Consensus       552 ~la~l~g~r~~~~~E~~~~~~~~-~~~~K~ltggD~-i~-ar~~~~~~~~~~~p~~~~~~~~N~~P~~~~~d~~~~rR~~  628 (789)
                      .+..+...-+.+++|...-.+.- +..+..+-.|-- |. ...........-.|.|+++.+|.+.+.+.   ..+..|+-
T Consensus        95 ~l~~~~~~~ILFIDEIHr~nK~qqd~Llp~vE~g~i~i~ig~~~~A~~~~~e~P~FtLIgATTe~~~l~---~pl~sR~~  171 (234)
T pfam05496        95 ILTNLEPGDVLFIDEIHRLNRAVEEILYPAMEDFRLDIVIGKGPSARSIRLDLPPFTLVGATTRAGLLT---SPLRDRFG  171 (234)
T ss_pred             HHHHCCCCCEEEEECHHHCCHHHHHHCCCCCCCCEEEEEECCCCCCEEEECCCCCEEEEEECCCCCCCC---HHHHHHHH
T ss_conf             998458998899966543587688744553346169999636766324652689759985215666477---77997621


No 20 
>pfam08298 AAA_PrkA PrkA AAA domain. This is a family of PrkA bacterial and archaeal serine kinases approximately 630 residues long. This is the N-terminal AAA domain.
Probab=96.68  E-value=0.0043  Score=38.25  Aligned_cols=55  Identities=22%  Similarity=0.292  Sum_probs=45.5

Q ss_pred             HHCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCC
Q ss_conf             8879999999999999999759874337999970788625789999999723300
Q gi|254781225|r  475 GYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQY  529 (789)
Q Consensus       475 ~~~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~  529 (789)
                      ++||-++.++-+-.++..+..|.-..+..+.|.|+-|+|||+|.+.|...|=.|.
T Consensus        59 dffGme~~i~~iV~~~ksAA~g~e~~kqIllL~GPVGsGKSsl~e~LK~glE~y~  113 (358)
T pfam08298        59 DFFGMEETIERIVNYFRHAAQGLEERKQILYLLGPVGGGKSSLAERLKKLLELVP  113 (358)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCCHHHHHHHHHHHHCCCC
T ss_conf             2001599999999999999723672105899977898775899999998720586


No 21 
>PRK00440 rfc replication factor C small subunit; Reviewed
Probab=96.52  E-value=0.01  Score=35.73  Aligned_cols=135  Identities=18%  Similarity=0.204  Sum_probs=73.0

Q ss_pred             HHHHHCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHH-HHCCCCC---CCCCHHHHHHCCCCCCC
Q ss_conf             9988879999999999999999759874337999970788625789999999-7233000---34426764201245555
Q gi|254781225|r  472 LVSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKY-AFGNQYV---INAEASDIMQNRPPEAG  547 (789)
Q Consensus       472 ~l~~~~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~-llG~~~~---~~~~~~~~~~~~~~~~~  547 (789)
                      -|+++.|.++.++.++.++-   .+... +  ++++|+.|.||+|+..++.+ ++|+...   .-.+.+.   .++-  .
T Consensus        14 ~l~di~g~~~~~~~L~~~i~---~~~~p-h--lLf~GppG~GKTt~a~~la~~l~~~~~~~~~lelnasd---~r~i--d   82 (318)
T PRK00440         14 SLDEVVGQEEIVERLKSFVK---EKNMP-H--LLFAGPPGTGKTTAALALARELYGEYWRENFLELNASD---ERGI--D   82 (318)
T ss_pred             CHHHHCCCHHHHHHHHHHHH---CCCCC-E--EEEECCCCCCHHHHHHHHHHHHCCCCCCCCEEEECCCC---CCCH--H
T ss_conf             89994196999999999998---79986-6--98889599889999999999976986434768951645---6671--7


Q ss_pred             CCCH---HHHHH---CC--CEEEEEECCCCCCCCCCCEEEEEECCCEEEEEECCCCCCEEEECCEEEEEECCCCCCCCCC
Q ss_conf             6898---89973---89--8099993467776013100245415985873210478606871452899973886342679
Q gi|254781225|r  548 KANP---SLIRL---MG--SRIVIISETNENDEINAAKIKQMTGGDCMTARLNYGNTYSESPASFTPFIVPNKHLFVRNP  619 (789)
Q Consensus       548 ~~~~---~la~l---~g--~r~~~~~E~~~~~~~~~~~~K~ltggD~i~ar~~~~~~~~~~~p~~~~~~~~N~~P~~~~~  619 (789)
                      -.+.   +.++.   .+  .++++++|.+.-..-....+           |    +...++..+..+++.||+.-++-  
T Consensus        83 ~vr~~i~~~~~~~~~~~~~~kiiiiDE~d~l~~~aq~aL-----------~----~~mE~~~~~~~fil~~n~~~kii--  145 (318)
T PRK00440         83 VIRNKIKEFARTAPVGGAPFKIIFLDEADNLTSDAQQAL-----------R----RTMEMYSQTTRFILSCNYSSKII--  145 (318)
T ss_pred             HHHHHHHHHHHHCCCCCCCEEEEEEECCCCCCHHHHHHH-----------H----HHHHCCCCCCEEEEECCCCCCCC--
T ss_conf             899999999972677899738999868553225567888-----------7----64310566625886348833376--


Q ss_pred             CCCEEEEEEEEECCCC
Q ss_conf             8416646899965887
Q gi|254781225|r  620 DDAWWRRYIVIPFDKP  635 (789)
Q Consensus       620 d~~~~rR~~iipF~~~  635 (789)
                       ..+-.|...|.|+..
T Consensus       146 -~~i~SRc~~i~f~~~  160 (318)
T PRK00440        146 -DPIQSRCAVFRFSPL  160 (318)
T ss_pred             -CCHHHHHEEEECCCC
T ss_conf             -155655101115789


No 22 
>pfam02257 RFX_DNA_binding RFX DNA-binding domain. RFX is a regulatory factor which binds to the X box of MHC class II genes and is essential for their expression. The DNA-binding domain of RFX is the central domain of the protein and binds ssDNA as either a monomer or homodimer.
Probab=96.34  E-value=0.012  Score=35.31  Aligned_cols=65  Identities=17%  Similarity=0.244  Sum_probs=52.1

Q ss_pred             HHHHHHHHEEECCCCEECHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCCCCCCEEEECCCCCC
Q ss_conf             8888754326268841117999999999998504667555452568999986354233310010256765
Q gi|254781225|r  693 YQAWIDDCCDIGENLWEESHSLAKSYSEYREQELNYDRKRISTRTVTLNLKQKGFIGGIKREKIEKEWKS  762 (789)
Q Consensus       693 v~~fi~e~ce~~~~~~~~~~~l~~~y~~~~~~~~~~~~~~~s~~~~~~~l~~~g~~~~~~~~~~~~~~~~  762 (789)
                      --+||.+.||..++..++...+|..|..+|+++.   .+|++..+|++-++.. | .+++..+...++++
T Consensus         8 a~~WL~~~~e~~~~~~lPR~~vY~~Y~~~C~~~~---~~pl~~AsFGKliR~v-F-P~lktRRLGtRG~S   72 (73)
T pfam02257         8 ALQWLRDNCEESEGSSLPRNRVYAHYVSHCAELG---LKPLSAASFGKLIRSV-F-PGLKTRRLGTRGQS   72 (73)
T ss_pred             HHHHHHHHCEECCCCCCCCHHHHHHHHHHHHHCC---CCCCCHHHHHHHHHHH-C-CCCCCCCCCCCCCC
T ss_conf             9999997744289972350899999999999739---9747787899999998-8-89630105667788


No 23 
>KOG0743 consensus
Probab=96.27  E-value=0.02  Score=33.83  Aligned_cols=87  Identities=14%  Similarity=0.218  Sum_probs=54.5

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCCCCCHHHHHHCCC
Q ss_conf             99999999999999759874337999970788625789999999723300034426764201245555689889973898
Q gi|254781225|r  480 EEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEAGKANPSLIRLMGS  559 (789)
Q Consensus       480 ~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~~~~~~~~la~l~g~  559 (789)
                      +++.+|+..---|.=+|. ....=..||||.|.|||+|+..|.+-|+ |.+-.+.++....    ++ .-+-=|....++
T Consensus       215 ~Dl~~F~k~k~~YkrvGk-awKRGYLLYGPPGTGKSS~IaAmAn~L~-ydIydLeLt~v~~----n~-dLr~LL~~t~~k  287 (457)
T KOG0743         215 DDLDDFIKGKDFYKRVGK-AWKRGYLLYGPPGTGKSSFIAAMANYLN-YDIYDLELTEVKL----DS-DLRHLLLATPNK  287 (457)
T ss_pred             HHHHHHHHCCHHHHHCCC-CCCCCCEEECCCCCCHHHHHHHHHHHCC-CCEEEEEECCCCC----CH-HHHHHHHHCCCC
T ss_conf             999999722357886484-5000412047999988899999972058-7367744002368----38-999999728997


Q ss_pred             EEEEEECCCCCCCC
Q ss_conf             09999346777601
Q gi|254781225|r  560 RIVIISETNENDEI  573 (789)
Q Consensus       560 r~~~~~E~~~~~~~  573 (789)
                      -++++.|.+..--+
T Consensus       288 SIivIEDIDcs~~l  301 (457)
T KOG0743         288 SILLIEDIDCSFDL  301 (457)
T ss_pred             CEEEEEECCCCCCC
T ss_conf             18999612432304


No 24 
>TIGR02673 FtsE cell division ATP-binding protein FtsE; InterPro: IPR005286   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).     FtsE is an ABC transporter ATP-binding protein. This protein and its permease partner FtsX, localize to the cell division site. In a number of species, the ftsEX gene pair is located next to ftsY, which encodes the signal recognition particle-docki ng protein.; GO: 0005524 ATP binding, 0051301 cell division.
Probab=96.17  E-value=0.0048  Score=37.93  Aligned_cols=79  Identities=20%  Similarity=0.242  Sum_probs=49.2

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHCCCCC-CCCCHHHHHHCCCCCCCCCCHHHHHHCCCEEEEEECC----CCCCCCC
Q ss_conf             3379999707886257899999997233000-3442676420124555568988997389809999346----7776013
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFGNQYV-INAEASDIMQNRPPEAGKANPSLIRLMGSRIVIISET----NENDEIN  574 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~-~~~~~~~~~~~~~~~~~~~~~~la~l~g~r~~~~~E~----~~~~~~~  574 (789)
                      .--|+|++|+.|.|||||++||...+-.+.. ..+.-..++.-       ..-+|+.|+-+-=++++|-    +..-.-|
T Consensus        27 kG~F~FLtG~SGAGKttLLKLl~~~~~P~~G~v~~~G~~~~~l-------~~~~~P~LRR~iGvvFQDf~LL~~rTv~eN   99 (215)
T TIGR02673        27 KGEFLFLTGPSGAGKTTLLKLLYGALTPSRGQVRVAGEDVSRL-------RGRQLPLLRRRIGVVFQDFRLLPDRTVYEN   99 (215)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHCCCCCCEEEECCEECCCC-------CCCCCHHHHCCCCEEEECCCCCCCCCHHHH
T ss_conf             7740788727786178999999852698758088887404667-------756431221315437842211011661341


Q ss_pred             CCEEEEEECCC
Q ss_conf             10024541598
Q gi|254781225|r  575 AAKIKQMTGGD  585 (789)
Q Consensus       575 ~~~~K~ltggD  585 (789)
                      .+.-=.+.|-.
T Consensus       100 VAl~L~V~G~~  110 (215)
T TIGR02673       100 VALPLEVRGKK  110 (215)
T ss_pred             CCHHHHCCCCC
T ss_conf             12101113888


No 25 
>PRK04195 replication factor C large subunit; Provisional
Probab=96.12  E-value=0.028  Score=32.87  Aligned_cols=142  Identities=15%  Similarity=0.200  Sum_probs=77.6

Q ss_pred             HHHHHCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHH------HHHCCCCC
Q ss_conf             998887999999999999999975987433799997078862578999999972330003442676------42012455
Q gi|254781225|r  472 LVSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASD------IMQNRPPE  545 (789)
Q Consensus       472 ~l~~~~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~------~~~~~~~~  545 (789)
                      .+.++.+++..++-+..|+-.-+.|.. .++.++++||.|.||+|+..+|.+-+|-. +.-.+.+.      +..--...
T Consensus        12 ~~~divg~~~~v~~l~~Wl~~w~~g~~-~~k~lLL~GPpGvGKTT~a~~lAk~~g~~-viElNASD~R~~~~I~~~i~~~   89 (403)
T PRK04195         12 SLSDVVGNEKAKKQLREWIESWLKGKP-PKKALLLYGPPGVGKTSLAHALANDYGWE-VIELNASDQRTKDVIERVAGEA   89 (403)
T ss_pred             CHHHHHCCHHHHHHHHHHHHHHHCCCC-CCCEEEEECCCCCCHHHHHHHHHHHHCCC-EEEECCCCCCCHHHHHHHHHHH
T ss_conf             899985889999999999999873996-57469988939987999999999984998-5997710114789999999987


Q ss_pred             CCCCCHHHHHHC--CCEEEEEECCCCCCC-CCCCEEEEEECCCEEEEEECCCCCCEEEECCEEEEEECCCCCCCCCCCCC
Q ss_conf             556898899738--980999934677760-13100245415985873210478606871452899973886342679841
Q gi|254781225|r  546 AGKANPSLIRLM--GSRIVIISETNENDE-INAAKIKQMTGGDCMTARLNYGNTYSESPASFTPFIVPNKHLFVRNPDDA  622 (789)
Q Consensus       546 ~~~~~~~la~l~--g~r~~~~~E~~~~~~-~~~~~~K~ltggD~i~ar~~~~~~~~~~~p~~~~~~~~N~~P~~~~~d~~  622 (789)
                      +.  +   ..+.  .+++++++|.+.-.. -+.+-+..|.        ..-++.      ..-+++.||+.-..  .-..
T Consensus        90 ~~--~---~sl~~~~~KlIIlDEvD~l~~~~d~gg~~al~--------~~ik~s------~~PiIli~Nd~~~~--~~~~  148 (403)
T PRK04195         90 ST--S---GSLFGAKRKLILLDEVDGIHGNADRGGVRAIL--------EIIKKA------KNPIILTANDPYDP--SLRP  148 (403)
T ss_pred             HH--C---CCCCCCCCEEEEEECCCCCCCHHHHHHHHHHH--------HHHHCC------CCEEEEEECCCCCC--CHHH
T ss_conf             60--6---88778873499963434457244479999999--------998548------87089982684556--7177


Q ss_pred             EEEEEEEEECCCCC
Q ss_conf             66468999658878
Q gi|254781225|r  623 WWRRYIVIPFDKPI  636 (789)
Q Consensus       623 ~~rR~~iipF~~~~  636 (789)
                      +-.|..+|.|...-
T Consensus       149 lrs~c~~i~F~~~~  162 (403)
T PRK04195        149 LRNACLMIEFKRLS  162 (403)
T ss_pred             HHHHHHHCCCCCCC
T ss_conf             99766122179949


No 26 
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=96.11  E-value=0.095  Score=29.33  Aligned_cols=273  Identities=16%  Similarity=0.134  Sum_probs=132.2

Q ss_pred             CHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCC---------CCCCC-H-----HH---HHH
Q ss_conf             999999999999999759874337999970788625789999999723300---------03442-6-----76---420
Q gi|254781225|r  479 SEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQY---------VINAE-A-----SD---IMQ  540 (789)
Q Consensus       479 d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~---------~~~~~-~-----~~---~~~  540 (789)
                      |+| ++-+..++.-++.|....  -++++|+.|.|||+....+..-+....         +.... .     .+   +.+
T Consensus        36 e~E-i~~l~~~l~~~l~g~~~~--n~~I~G~pGTGKT~~vk~v~~~l~~~~~~~~~vyINc~~~~t~~~i~~~i~~~L~~  112 (394)
T PRK00411         36 EEQ-IEELAFALRPALRGSRPS--NVLILGPPGTGKTTTVKKVFEELEEAALKVVYVYINCQIDRTRYAILSEIARSLFG  112 (394)
T ss_pred             HHH-HHHHHHHHHHHHCCCCCC--CEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHCC
T ss_conf             999-999999999997599998--47998899998999999999999974689659999696689899999999999569


Q ss_pred             CCCCCCCCCCHHHHH-----H--CC-CEEEEEECCCCCCCCC-CCEEEEEECCCEEEEEECCCCCCEEEECCEEEEEECC
Q ss_conf             124555568988997-----3--89-8099993467776013-1002454159858732104786068714528999738
Q gi|254781225|r  541 NRPPEAGKANPSLIR-----L--MG-SRIVIISETNENDEIN-AAKIKQMTGGDCMTARLNYGNTYSESPASFTPFIVPN  611 (789)
Q Consensus       541 ~~~~~~~~~~~~la~-----l--~g-~r~~~~~E~~~~~~~~-~~~~K~ltggD~i~ar~~~~~~~~~~~p~~~~~~~~N  611 (789)
                      ...+..|-+..++..     +  .+ ..+++.+|.+.=..-+ ...+-+|+       |- +.. .  -.....++..+|
T Consensus       113 ~~~p~~G~s~~~~~~~l~~~l~~~~~~~ivvLDEiD~L~~~~~~~vLY~L~-------r~-~~~-~--~~~~~~vI~IsN  181 (394)
T PRK00411        113 HPPPSSGLSFDELFDKIAEYLDERDRVLIVALDDINYLVEKEGNDVLYSLL-------RA-HEE-Y--PGARIGVIGISS  181 (394)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCHHHHHHH-------HC-CCC-C--CCCCEEEEEEEC
T ss_conf             989877878999999999986166975899996554020366508999998-------54-022-6--887389999976


Q ss_pred             CCCCCCCCCCCEEEEE--EEEECCC----CCC----CC------CCCHHHHHC------CCCHHHHHHHHHHHHHH----
Q ss_conf             8634267984166468--9996588----788----87------878334220------12044799999999999----
Q gi|254781225|r  612 KHLFVRNPDDAWWRRY--IVIPFDK----PIA----NR------DASFAQKLE------TKYTLEAKKWFLKGVKA----  665 (789)
Q Consensus       612 ~~P~~~~~d~~~~rR~--~iipF~~----~~~----~~------d~~~~~~~~------~~e~~~i~~w~l~g~~~----  665 (789)
                      .+.-..--|.-+-.|+  ..|.|+-    ++.    .+      +.-+.+.-.      .....|=...||+-|++    
T Consensus       182 ~~~~~~~Ldprv~S~l~~~~i~F~PY~~~qL~~IL~~R~~~af~~gv~~~~~i~~~A~~~a~~~GDaR~Aldllr~A~e~  261 (394)
T PRK00411        182 DLTFLYILDPRVKSVFGPEEIVFPPYTADEIFDILKDRVEEGFYPGVVSDEVLELIADLTGREHGDARVAIDLLRRAGEI  261 (394)
T ss_pred             CCCHHHHHHHHHHCCCCCEEEEECCCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHH
T ss_conf             87177664077750278628985899989999999999984145567897899999999855047589999999999999


Q ss_pred             HHHCCCCCCCCHHHHHHHHHHHHHCCHHHHHHHHH-----------EEE--CCCCEECHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             99878898878899999999998426388887543-----------262--68841117999999999998504667555
Q gi|254781225|r  666 YISKGLDVDIPEVCLKAKEEERQGTDTYQAWIDDC-----------CDI--GENLWEESHSLAKSYSEYREQELNYDRKR  732 (789)
Q Consensus       666 ~~~~g~~~~~p~~v~~a~~~y~~~~D~v~~fi~e~-----------ce~--~~~~~~~~~~l~~~y~~~~~~~~~~~~~~  732 (789)
                      ..++|......+.|+.|.++.  +.+.+..-|...           |..  .....+..+++|+.|...|+..   +.++
T Consensus       262 Ae~~g~~~Vt~~hV~~A~~~~--~~~~~~~~i~~L~~~~klvL~ai~~~~~~~~~~~~~g~vy~~Y~~lc~~~---~~~~  336 (394)
T PRK00411        262 AEREGSRKVTEEDVRKAYEKS--EPVHLEEVLRTLPLHEKLLLLAIVRLLEKGAPYVTTGEVYEEYKELCEEL---GYEP  336 (394)
T ss_pred             HHHHCCCCCCHHHHHHHHHHH--HCCHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHC---CCCC
T ss_conf             997189965899999999986--00008899873899899999999998517887663899999999999973---9988


Q ss_pred             CCHHHHHHHHHHCCCCCCCCEEEECCCCCCCCEEEEEEEC
Q ss_conf             4525689999863542333100102567652089979865
Q gi|254781225|r  733 ISTRTVTLNLKQKGFIGGIKREKIEKEWKSKRIIKGLKLK  772 (789)
Q Consensus       733 ~s~~~~~~~l~~~g~~~~~~~~~~~~~~~~~r~~~Gi~Lk  772 (789)
                      ++.+.|..-+.++...|-+..+...++ +.+|. +-+.|.
T Consensus       337 ls~~~~~~~l~~L~~~giI~~~~~~~G-~~Gr~-~~i~L~  374 (394)
T PRK00411        337 RSHTRFYEYLNKLDMLGLINTRYTGKG-GRGRT-RLISLS  374 (394)
T ss_pred             CCHHHHHHHHHHHHHCCCEEEEEECCC-CCCCE-EEEEEC
T ss_conf             879999999999986798588875488-88852-699962


No 27 
>pfam00004 AAA ATPase family associated with various cellular activities (AAA). AAA family proteins often perform chaperone-like functions that assist in the assembly, operation, or disassembly of protein complexes.
Probab=96.05  E-value=0.0042  Score=38.36  Aligned_cols=123  Identities=15%  Similarity=0.233  Sum_probs=58.4

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHC-CCCCCC--CCCHHHHHHCCCEEEEEECCCCCCCCCCCEEEE
Q ss_conf             99970788625789999999723300034426764201-245555--689889973898099993467776013100245
Q gi|254781225|r  504 IHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQN-RPPEAG--KANPSLIRLMGSRIVIISETNENDEINAAKIKQ  580 (789)
Q Consensus       504 ~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~-~~~~~~--~~~~~la~l~g~r~~~~~E~~~~~~~~~~~~K~  580 (789)
                      ++++|+-|+|||++.+.+.+-+|-.... .+...+... .+....  ..-++.|+.....+++++|.+.--.   ..-+.
T Consensus         1 iLl~GppGtGKT~~a~~la~~~~~~~~~-v~~~~~~~~~~g~~~~~i~~~f~~a~~~~p~Il~iDe~d~l~~---~~~~~   76 (131)
T pfam00004         1 LLLYGPPGTGKTTLAKAVAKELGAPFIE-ISGSELVSKYVGESEKRLRELFEAAKKLAPCVIFIDEIDALAG---SRGSG   76 (131)
T ss_pred             CEEECCCCCCHHHHHHHHHHHHCCCCEE-CCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEECHHHHHHC---CCCCC
T ss_conf             9878999999999999999997898533-2420122233450688899999999974991898311677751---67888


Q ss_pred             EEC-CCEEEEEEC-CCCCCEEEECCEEEEEECCCCCCCCCCCCCEEE-EE-EEEECC
Q ss_conf             415-985873210-478606871452899973886342679841664-68-999658
Q gi|254781225|r  581 MTG-GDCMTARLN-YGNTYSESPASFTPFIVPNKHLFVRNPDDAWWR-RY-IVIPFD  633 (789)
Q Consensus       581 ltg-gD~i~ar~~-~~~~~~~~~p~~~~~~~~N~~P~~~~~d~~~~r-R~-~iipF~  633 (789)
                      -.+ ...+....+ .-+.+..-.....++.+||++-   .-|.++.| |+ .+|.|+
T Consensus        77 ~~~~~~~~~~~ll~~ld~~~~~~~~v~~I~tTN~~~---~ld~al~r~Rfd~~i~~p  130 (131)
T pfam00004        77 GDSESRRVVNQLLTELDGFTSSLSKVIVIAATNRPD---KLDPALLRGRFDRIIEFP  130 (131)
T ss_pred             CCCCCHHHHHHHHHHHHHCCCCCCCEEEEEECCCHH---HCCHHHHCCCCEEEEEEC
T ss_conf             887513268789999850224688769999759904---499779628332899806


No 28 
>TIGR00960 3a0501s02 Type II (General) Secretory Pathway (IISP) Family protein; InterPro: IPR013505   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).     FtsE is an ABC transporter ATP-binding protein. This protein and its permease partner FtsX, localize to the cell division site. In a number of species, the ftsEX gene pair is located next to ftsY, which encodes the signal recognition particle-docki ng protein.; GO: 0005524 ATP binding, 0051301 cell division.
Probab=95.94  E-value=0.0065  Score=37.07  Aligned_cols=27  Identities=33%  Similarity=0.437  Sum_probs=22.9

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             337999970788625789999999723
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      .--|.|+.|..|+|||||++||..+--
T Consensus        28 kGem~fL~GHSGaGKST~lkLi~~~~~   54 (216)
T TIGR00960        28 KGEMVFLVGHSGAGKSTLLKLILGIEK   54 (216)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHCC
T ss_conf             850799856888607899999985228


No 29 
>cd00009 AAA The AAA+ (ATPases Associated with a wide variety of cellular Activities) superfamily represents an ancient group of ATPases belonging to the ASCE (for additional strand, catalytic E) division of the P-loop NTPase fold. The ASCE division also includes ABC, RecA-like, VirD4-like, PilT-like, and SF1/2 helicases. Members of the AAA+ ATPases function as molecular chaperons, ATPase subunits of proteases, helicases, or nucleic-acid stimulated ATPases. The AAA+ proteins contain several distinct features in addition to the conserved alpha-beta-alpha core domain structure and the Walker A and B motifs of the P-loop NTPases.
Probab=95.86  E-value=0.012  Score=35.35  Aligned_cols=122  Identities=18%  Similarity=0.186  Sum_probs=63.9

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHC--CCCCCCCCHHHHHH-CCCCCCC-----CCCHHHHHHCCCEEEEEECCCCCC
Q ss_conf             337999970788625789999999723--30003442676420-1245555-----689889973898099993467776
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFG--NQYVINAEASDIMQ-NRPPEAG-----KANPSLIRLMGSRIVIISETNEND  571 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG--~~~~~~~~~~~~~~-~~~~~~~-----~~~~~la~l~g~r~~~~~E~~~~~  571 (789)
                      ...-++++|+.|.|||++...|...++  .+.....+...+.. .......     .............+++++|.+.-.
T Consensus        18 ~~~~ill~GppGtGKT~la~~ia~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vl~iDEi~~l~   97 (151)
T cd00009          18 PPKNLLLYGPPGTGKTTLARAIANELFRPGAPFLYLNASDLLEGLVVAELFGHFLVRLLFELAEKAKPGVLFIDEIDSLS   97 (151)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEEEHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEECHHHCC
T ss_conf             99808998999988659999999971213798278547770467777576057788989999997699869820166559


Q ss_pred             C-CCCCEEEEEECCCEEEEEECCCCCCEEEECCEEEEEECCCCCCCCCCCCCEEEEE-EEEEC
Q ss_conf             0-1310024541598587321047860687145289997388634267984166468-99965
Q gi|254781225|r  572 E-INAAKIKQMTGGDCMTARLNYGNTYSESPASFTPFIVPNKHLFVRNPDDAWWRRY-IVIPF  632 (789)
Q Consensus       572 ~-~~~~~~K~ltggD~i~ar~~~~~~~~~~~p~~~~~~~~N~~P~~~~~d~~~~rR~-~iipF  632 (789)
                      . .....+..|--        .. . .........++++||+.+. .+.+.+++.|+ ..|.|
T Consensus        98 ~~~~~~~~~~l~~--------~~-~-~~~~~~~~~vI~~tn~~~~-~~~~~~~~~R~~~~i~~  149 (151)
T cd00009          98 RGAQNALLRVLET--------LN-D-LRIDRENVRVIGATNRPLL-GDLDRALYDRLDIRIVI  149 (151)
T ss_pred             HHHHHHHHHHHHH--------HC-C-CCCCCCCEEEEEEECCCCC-CCHHHHHHCCCCEEEEC
T ss_conf             9999999999987--------15-7-5406788899995289988-68377642559869863


No 30 
>pfam07728 AAA_5 AAA domain (dynein-related subfamily). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.
Probab=95.78  E-value=0.015  Score=34.67  Aligned_cols=123  Identities=15%  Similarity=0.168  Sum_probs=63.1

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH-CC-CCCCCC----CHHHHHHCCCCCCCC----CCHHHHHHCCCEEEEEECCCCCCCC
Q ss_conf             9997078862578999999972-33-000344----267642012455556----8988997389809999346777601
Q gi|254781225|r  504 IHIRGVGGSGKSTLMNLIKYAF-GN-QYVINA----EASDIMQNRPPEAGK----ANPSLIRLMGSRIVIISETNENDEI  573 (789)
Q Consensus       504 ~~~~G~G~nGKSt~~~~l~~ll-G~-~~~~~~----~~~~~~~~~~~~~~~----~~~~la~l~g~r~~~~~E~~~~~~~  573 (789)
                      ++++|+.+.|||++...+...+ |. +.....    +...+.+......+.    ..+-+..+....+++++|.+.-..-
T Consensus         2 vll~Gp~G~GKT~la~~la~~l~~~~~~~i~~~~~~~~~dl~G~~~~~~~~~~~~~g~l~~a~~~g~vl~lDEin~a~~~   81 (139)
T pfam07728         2 VLLVGPPGTGKSELAERLAAALSNRPVFYVQLTRDTTEEDLKGRRNIANGTTSWVDGPLVRAAREGEIAVLDEINRANPD   81 (139)
T ss_pred             EEEECCCCCHHHHHHHHHHHHCCCCCCHHHCCCCCCCHHHCCCCEECCCCCEEEECCHHHCCCCCCCEEEECCHHHCCHH
T ss_conf             89998997569999999999807983111214655652220573423799357815514101012868996343448999


Q ss_pred             CCCEEEEEECCCEEEEEEC----CCCCCEEEECCEEEEEECCCCCC-CCCCCCCEEEEE
Q ss_conf             3100245415985873210----47860687145289997388634-267984166468
Q gi|254781225|r  574 NAAKIKQMTGGDCMTARLN----YGNTYSESPASFTPFIVPNKHLF-VRNPDDAWWRRY  627 (789)
Q Consensus       574 ~~~~~K~ltggD~i~ar~~----~~~~~~~~~p~~~~~~~~N~~P~-~~~~d~~~~rR~  627 (789)
                      -...|-++.-...+..-..    .... ....+.|.+|.++|..+. ...-|.|+.+|+
T Consensus        82 v~~~L~~~le~~~~~~~~~~~~~~~~~-~~~~~~f~viaT~N~~~~g~~~l~~Al~~RF  139 (139)
T pfam07728        82 VLNSLLSLLDERRLLLPEGGELVKVAP-DDFAKRFRLIATMNPLDRGLNELSPALRSRF  139 (139)
T ss_pred             HHHHHHHHHCCCEEEECCCCEEECCCC-CCCCCCEEEEEEECCCCCCCCCCCHHHHCCC
T ss_conf             999999997489698368972733666-6789996999975896547800998997509


No 31 
>PRK13531 regulatory ATPase RavA; Provisional
Probab=95.74  E-value=0.065  Score=30.44  Aligned_cols=48  Identities=15%  Similarity=0.230  Sum_probs=27.4

Q ss_pred             EEEEEECCCEEEEEECCCCCCEEEECCEEEEEECCCCCCCCCCCCCEEEEEEEEEC
Q ss_conf             02454159858732104786068714528999738863426798416646899965
Q gi|254781225|r  577 KIKQMTGGDCMTARLNYGNTYSESPASFTPFIVPNKHLFVRNPDDAWWRRYIVIPF  632 (789)
Q Consensus       577 ~~K~ltggD~i~ar~~~~~~~~~~~p~~~~~~~~N~~P~~~~~d~~~~rR~~iipF  632 (789)
                      .-+.+-.|+.|.++- ++.+|   .-...+-+-+.+...++|.+    ||-..+-.
T Consensus       387 l~~wl~kg~ei~~~l-ng~gf---~~~l~~evd~~~~L~i~Dis----~~~~~l~l  434 (498)
T PRK13531        387 LEQWLSKGGEIRGKL-NGIGF---AQKLNLEVDSAQHLVVRDVS----LQGSTLAL  434 (498)
T ss_pred             HHHHHHCCCEEEEEE-CCCCC---CEEEEEEECCCCCEEEEECC----CCCEEEEE
T ss_conf             888874298479985-58887---50356777555766787426----78435772


No 32 
>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]
Probab=95.65  E-value=0.15  Score=28.06  Aligned_cols=208  Identities=16%  Similarity=0.171  Sum_probs=114.3

Q ss_pred             CCCCCCCCCHHHCCCCCCEEEECCC---EEECCCC----CCCCC------CHHHHCCEECCCCCCCCCCHHHHHH----H
Q ss_conf             1000012320220579717660793---7974388----85589------8655010013788887579478999----9
Q gi|254781225|r  410 EAGSIFSITSDLLDSSSRFLGEQDG---ILDLETG----QKVKP------TKELYITKSTGTPFVEGEPSQEFLD----L  472 (789)
Q Consensus       410 ~~~~~~~~~~~~ld~~~~ll~~~NG---v~dl~t~----~~~~~------~~~~~~t~~~~~~y~~~a~~p~~~~----~  472 (789)
                      .+-..+....+.+|.+..++....|   |+.+...    .+.|+      ...+-+-.++|-++||....-..++    .
T Consensus        70 ~~pl~vg~v~e~id~~~~iVks~~g~~~vV~i~~~vd~~~L~pG~rVal~~~s~~Iv~vLp~~~Dp~V~~M~v~e~Pdvt  149 (406)
T COG1222          70 EPPLIVGTVLEVLDDGRAIVKSSTGPKFVVNILSFVDRDLLEPGMRVALNRDSYSIVRVLPPEVDPRVSVMEVEEKPDVT  149 (406)
T ss_pred             CCCCEEEEEEEECCCCEEEEEECCCCEEEEECCCCCCHHHCCCCCEEEECCCCCEEEEECCCCCCCHHHEEEECCCCCCC
T ss_conf             89956899999817861899707997188734687698786998889985776145661787557620200112589878


Q ss_pred             HHHHCCCHHHHHHHHHHHHHHHCC-------CCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCC
Q ss_conf             988879999999999999999759-------8743379999707886257899999997233000344267642012455
Q gi|254781225|r  473 VSGYFESEEVMDYFTRCVGMALLG-------GNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPE  545 (789)
Q Consensus       473 l~~~~~d~e~~~~l~~~~g~~l~g-------~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~  545 (789)
                      ..+|=|=++.++=+.+.+-.-|..       +....+=++|||+.|+||+.+...+.+--.....-.+...+. ++.-..
T Consensus       150 Y~dIGGL~~Qi~EirE~VELPL~~PElF~~~GI~PPKGVLLYGPPGTGKTLLAkAVA~~T~AtFIrvvgSElV-qKYiGE  228 (406)
T COG1222         150 YEDIGGLDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTLLAKAVANQTDATFIRVVGSELV-QKYIGE  228 (406)
T ss_pred             HHHCCCHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCEEEECCCCCCHHHHHHHHHHCCCCEEEEECCHHHH-HHHHCC
T ss_conf             6533588999999999840336688899974999997127668999758899999872058669994219999-998341


Q ss_pred             CC---CCCHHHHHHCCCEEEEEECCCCCCCCCCCEEEEEECCCEEEEEECC-----CCCCEEEECCEEEEEECCCCCCCC
Q ss_conf             55---6898899738980999934677760131002454159858732104-----786068714528999738863426
Q gi|254781225|r  546 AG---KANPSLIRLMGSRIVIISETNENDEINAAKIKQMTGGDCMTARLNY-----GNTYSESPASFTPFIVPNKHLFVR  617 (789)
Q Consensus       546 ~~---~~~~~la~l~g~r~~~~~E~~~~~~~~~~~~K~ltggD~i~ar~~~-----~~~~~~~~p~~~~~~~~N~~P~~~  617 (789)
                      +.   .--|.+|+-+---+++++|.+.   +.+.++-+-||||.=.-|-+-     -+.| .-.-..+++++||.   +.
T Consensus       229 GaRlVRelF~lArekaPsIIFiDEIDA---Ig~kR~d~~t~gDrEVQRTmleLL~qlDGF-D~~~nvKVI~ATNR---~D  301 (406)
T COG1222         229 GARLVRELFELAREKAPSIIFIDEIDA---IGAKRFDSGTSGDREVQRTMLELLNQLDGF-DPRGNVKVIMATNR---PD  301 (406)
T ss_pred             CHHHHHHHHHHHHHCCCEEEEEECHHH---HHCCCCCCCCCCHHHHHHHHHHHHHHCCCC-CCCCCEEEEEECCC---CC
T ss_conf             169999999987414984999831122---311113688885099999999999860588-97887689985588---55


Q ss_pred             CCCCCEEE
Q ss_conf             79841664
Q gi|254781225|r  618 NPDDAWWR  625 (789)
Q Consensus       618 ~~d~~~~r  625 (789)
                      --|.|+-|
T Consensus       302 ~LDPALLR  309 (406)
T COG1222         302 ILDPALLR  309 (406)
T ss_pred             CCCHHHCC
T ss_conf             55766508


No 33 
>PRK13341 recombination factor protein RarA/unknown domain fusion protein; Reviewed
Probab=95.32  E-value=0.016  Score=34.41  Aligned_cols=41  Identities=20%  Similarity=0.178  Sum_probs=15.5

Q ss_pred             CEEEECCCCCCCCCCEEECCCCC--CCCCCCCCCCCHHHHHHHHH
Q ss_conf             43880477688887457517765--58722164689999999997
Q gi|254781225|r  133 QYFVAYNIHPKTKKEYTWTTPPH--RFKVEDTPLLSEEDVEYLFK  175 (789)
Q Consensus       133 ~q~V~~gshp~Tg~~Y~w~~~~~--~~~~~~~P~i~~~~~~~l~~  175 (789)
                      +.++.-|+  .|-.||.-+++..  -..+-.+-.++...+..+++
T Consensus       136 G~i~LIGA--TTENP~F~vn~ALlSR~~vf~L~~L~~~dl~~il~  178 (726)
T PRK13341        136 GTVTLIGA--TTENPYFEVNKALVSRSRLFRLKSLEDEDLHQLLK  178 (726)
T ss_pred             CEEEEEEE--CCCCCCEEECHHHHHHCEEEEECCCCHHHHHHHHH
T ss_conf             83899970--47897436429888323466743899999999999


No 34 
>pfam06431 Polyoma_lg_T_C Polyomavirus large T antigen C-terminus.
Probab=94.60  E-value=0.3  Score=26.04  Aligned_cols=179  Identities=15%  Similarity=0.157  Sum_probs=98.2

Q ss_pred             HHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCC-CCCCHHHHHHCCCCCCCCCCHHHHHHCCCEEEE
Q ss_conf             9999999997598743379999707886257899999997233000-344267642012455556898899738980999
Q gi|254781225|r  485 YFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYV-INAEASDIMQNRPPEAGKANPSLIRLMGSRIVI  563 (789)
Q Consensus       485 ~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~-~~~~~~~~~~~~~~~~~~~~~~la~l~g~r~~~  563 (789)
                      .+++++- +++-+...+..+++.||=++||+|+...|..++|..+- +..+.           ..-+|||......-+|+
T Consensus       140 ~i~~~lk-~~v~N~PKkRy~lFkGPvNsGKTTlAAAlldLcgGkaLNIN~P~-----------dkL~FELG~AIDQfmVv  207 (417)
T pfam06431       140 VIYDFLK-CIVYNIPKKRYWLFKGPIDSGKTTLAAALLDLCGGKALNVNLPL-----------ERLNFELGVAIDQFMVV  207 (417)
T ss_pred             HHHHHHH-HHHCCCCCCEEEEEECCCCCCHHHHHHHHHHHCCCCEEECCCCH-----------HHCCHHHCCEEEEEEEE
T ss_conf             9999999-99618874115887678677748799999986368612047985-----------64453530021104788


Q ss_pred             EECCCCCCCC-C----CC----EEE----EEECCCEEEEEECCCCCCEE-EECCEEEEEECCCCCCCCCCCCCEEEEE-E
Q ss_conf             9346777601-3----10----024----54159858732104786068-7145289997388634267984166468-9
Q gi|254781225|r  564 ISETNENDEI-N----AA----KIK----QMTGGDCMTARLNYGNTYSE-SPASFTPFIVPNKHLFVRNPDDAWWRRY-I  628 (789)
Q Consensus       564 ~~E~~~~~~~-~----~~----~~K----~ltggD~i~ar~~~~~~~~~-~~p~~~~~~~~N~~P~~~~~d~~~~rR~-~  628 (789)
                      ..++. |..- +    .+    .+-    -|-|-=++.-++||.+.-++ |+|.   ++.+|+-..-..    ++-|+ .
T Consensus       208 FEDVK-Gq~~~~k~Lp~G~Gi~NLDNLRDyLDGsV~VNLEKKH~NKrsQIFPPg---IVTmNeY~iP~T----l~~RF~~  279 (417)
T pfam06431       208 FEDVK-GTGAESRDLPSGHGINNLDNLRDYLDGSVKVNLEKKHLNKRTQIFPPG---IVTMNEYSVPKT----LQARFVR  279 (417)
T ss_pred             EEECC-CCCCCCCCCCCCCCCCCHHHHHHHHCCCEEECHHHHHCCCCCCCCCCC---EEEECCCCCCHH----HHHHHHH
T ss_conf             75247-876655689999885321557775157411034453036653148996---663056666266----7656440


Q ss_pred             EEECCCCCCCCCCCHHHHHCCCCHHHH-------HHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCH
Q ss_conf             996588788878783342201204479-------9999999999998788988788999999999984263
Q gi|254781225|r  629 VIPFDKPIANRDASFAQKLETKYTLEA-------KKWFLKGVKAYISKGLDVDIPEVCLKAKEEERQGTDT  692 (789)
Q Consensus       629 iipF~~~~~~~d~~~~~~~~~~e~~~i-------~~w~l~g~~~~~~~g~~~~~p~~v~~a~~~y~~~~D~  692 (789)
                      +|.|..     ..++.+-|...|....       +.++|  ++.|..---.|  -+++.+....|++.-|.
T Consensus       280 ~l~F~~-----k~~L~~sL~~~~~l~~~RILQSG~TlLL--lLIw~~pv~~F--~~~iq~~V~~WKe~ld~  341 (417)
T pfam06431       280 QIDFRP-----KDYLRKSLERSEFLLEKRILQSGMTLLL--LLIWFRPVADF--AQSIQSRIVEWKERLDK  341 (417)
T ss_pred             EECCCH-----HHHHHHHHHCCHHHHHHHHHHCCHHHHH--HHHHHCCHHHH--HHHHHHHHHHHHHHHHH
T ss_conf             235765-----6999999851889989999701389999--99996868777--69999999999999998


No 35 
>PRK13900 type IV secretion system ATPase VirB11; Provisional
Probab=94.55  E-value=0.17  Score=27.61  Aligned_cols=85  Identities=14%  Similarity=0.153  Sum_probs=46.8

Q ss_pred             EEECCCCCCCCCCHHHHCCEECCCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCH
Q ss_conf             79743888558986550100137888875794789999988879999999999999999759874337999970788625
Q gi|254781225|r  435 ILDLETGQKVKPTKELYITKSTGTPFVEGEPSQEFLDLVSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGK  514 (789)
Q Consensus       435 v~dl~t~~~~~~~~~~~~t~~~~~~y~~~a~~p~~~~~l~~~~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGK  514 (789)
                      .+-++.....+.+.++|...-+--.-............|.+.+.+.++.+||+.++        +..+=+++.|..++||
T Consensus       102 ~ltIRk~~~~~~tl~dl~~~G~~~~~~~~~~~~~~~~~l~~~~~~~~~~~fL~~aV--------~~r~NilI~G~TgSGK  173 (332)
T PRK13900        102 IYSIRKPSGMQLTLDDYEKMGAFDETATESLVDEDDVILNELLAEKKIKEFLEHAV--------ISKKNIIISGGTSTGK  173 (332)
T ss_pred             EEEEECCCCCCCCHHHHHHCCCCCHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH--------HCCCCEEEECCCCCCH
T ss_conf             79997888888999999864986655542013415677887641057999999998--------6487199988889889


Q ss_pred             HHHHHHHHHHHCC
Q ss_conf             7899999997233
Q gi|254781225|r  515 STLMNLIKYAFGN  527 (789)
Q Consensus       515 St~~~~l~~llG~  527 (789)
                      +||++.|...+..
T Consensus       174 TTll~aL~~~ip~  186 (332)
T PRK13900        174 TTFTNAALREIPA  186 (332)
T ss_pred             HHHHHHHHHCCCC
T ss_conf             9999999835895


No 36 
>TIGR02788 VirB11 P-type DNA transfer ATPase VirB11; InterPro: IPR014155   This entry contains VirB11, a protein that is found in the vir locus of Agrobacterium Ti plasmids where it is involved in the type IV secretion system for DNA transfer . VirB11 is believed to be an ATPase  and is a homologue of the P-like conjugation system TrbB protein and the Flp pilus system protein TadA ..
Probab=94.41  E-value=0.16  Score=27.78  Aligned_cols=92  Identities=12%  Similarity=0.191  Sum_probs=63.7

Q ss_pred             EECCC-EE--ECCCCCCCCCCHHHHCCEEC-----CCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             60793-79--74388855898655010013-----788887579478999998887999999999999999975987433
Q gi|254781225|r  430 GEQDG-IL--DLETGQKVKPTKELYITKST-----GTPFVEGEPSQEFLDLVSGYFESEEVMDYFTRCVGMALLGGNKAQ  501 (789)
Q Consensus       430 ~~~NG-v~--dl~t~~~~~~~~~~~~t~~~-----~~~y~~~a~~p~~~~~l~~~~~d~e~~~~l~~~~g~~l~g~~~~~  501 (789)
                      +|.+| ++  =++...+...+-+||-..-.     ++.-....++..+++=|.+.....+..+||..++        ..+
T Consensus        87 Ac~~~eTvs~tIRKpS~~~~sL~dy~~~G~F~~ar~~~~~~~~~~~d~~~~L~el~~~g~~~~Fl~~Ai--------~~~  158 (328)
T TIGR02788        87 ACENDETVSITIRKPSLVDLSLDDYEEKGFFDTARAVVVPASTELSDKDEELLELLDAGDIKEFLRLAI--------ASR  158 (328)
T ss_pred             CCCCCCEEEEEEECCCCCCCCHHHHHHCCCCCEEEEEECCCCCCCCHHHHHHHHHHHCCCHHHHHHHHH--------HCC
T ss_conf             758988589999526444554799962798544777631443443468999999986288879999998--------738


Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHHCCCC
Q ss_conf             7999970788625789999999723300
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYAFGNQY  529 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~llG~~~  529 (789)
                      +=+|+.|..++||+||+|.|-+.++..-
T Consensus       159 knIii~GGTgSGKTTf~kal~~~IP~~E  186 (328)
T TIGR02788       159 KNIIISGGTGSGKTTFLKALVKEIPKDE  186 (328)
T ss_pred             CEEEEEECCCCHHHHHHHHHHHCCCCCC
T ss_conf             9199990689718999999973276225


No 37 
>TIGR01242 26Sp45 26S proteasome subunit P45 family; InterPro: IPR005937    Intracellular proteins, including short-lived proteins such as cyclin, Mos, Myc, p53, NF-kappaB, and IkappaB, are degraded by the ubiquitin-proteasome system. The 26S proteasome (a 2 MDa complex) is made up of two subcomplexes: the 20S proteasome and the regulatory complex. The former is a 700 kDa cylindrical protease complex consisting of four stacks of heptameric rings with 28 subunits (i.e., 7777) with molecular masses of about 20-35 kDa, whereas the latter is a 700-1000 kDa complex consisting of at least 18 subunits with molecular masses of 28-110 kDa, including 6 putative ATPases (Rpt1-Rpt6) and 12 non-ATPase subunits (Rpn1-12).     Members of the 26S proteasome subunit P45 family: ATPase p45/Sug1/Rpt6 may be phosphorylated within the proteasome. This phosphorylation event may play a key role in ATP-dependent proteolysis because a good correlation exists between the inhibition pattern of protein kinase inhibitors against the phosphorylation of p45 and that against the ATP-dependent proteolytic activity , .   More information about these protein can be found at Protein of the Month: AAA ATPases .; GO: 0016787 hydrolase activity, 0030163 protein catabolic process, 0005634 nucleus, 0005737 cytoplasm.
Probab=94.08  E-value=0.062  Score=30.57  Aligned_cols=221  Identities=14%  Similarity=0.172  Sum_probs=124.7

Q ss_pred             CCCCCCCCCHHHCCCCCCEEEECCC---EEECC----CCCCCCCCH------HHHCCEECCCCCCCCCCHHHHHH----H
Q ss_conf             1000012320220579717660793---79743----888558986------55010013788887579478999----9
Q gi|254781225|r  410 EAGSIFSITSDLLDSSSRFLGEQDG---ILDLE----TGQKVKPTK------ELYITKSTGTPFVEGEPSQEFLD----L  472 (789)
Q Consensus       410 ~~~~~~~~~~~~ld~~~~ll~~~NG---v~dl~----t~~~~~~~~------~~~~t~~~~~~y~~~a~~p~~~~----~  472 (789)
                      .|-....+..+.+|.+.-.+--.+|   |++..    ..+|.|+..      ..-+--++|..+||....=+..+    +
T Consensus        41 ~PP~~~~~V~~~~~~~rvvVks~tGP~fvv~~~~~i~~~~L~PG~~VaLn~~t~~iV~vLP~~kDp~v~~~EV~E~P~V~  120 (364)
T TIGR01242        41 SPPLIVGTVVEVLDDDRVVVKSSTGPKFVVNVSAFIDRKELKPGARVALNQQTLAIVDVLPTSKDPLVKGMEVEERPNVS  120 (364)
T ss_pred             CCCEEEEEEEEEECCCEEEEECCCCCEEEEEHHCCCCHHHCCCCCEEEECCCCEEEEEECCCCCCCEEEEEEEECCCCEE
T ss_conf             89827887543214863799637985000000012362026886567423784289984678878657877762178233


Q ss_pred             HHHHCCCHHHHHHHHHHHHHHH--------CCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCC
Q ss_conf             9888799999999999999997--------59874337999970788625789999999723300034426764201245
Q gi|254781225|r  473 VSGYFESEEVMDYFTRCVGMAL--------LGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPP  544 (789)
Q Consensus       473 l~~~~~d~e~~~~l~~~~g~~l--------~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~  544 (789)
                      .++|=|=++-++=+.+.+-.=|        +| ..-.+=+.||||.|.||+.+...+.+=.-..++-.+...+..+--|.
T Consensus       121 y~diGGL~~Q~~E~~E~v~LPlk~PeLF~~vG-I~PPKGvLLyGPPGtGKTLlAKAvA~et~ATFIrvVgSElV~KyIGE  199 (364)
T TIGR01242       121 YEDIGGLEKQIREIREAVELPLKKPELFEEVG-IEPPKGVLLYGPPGTGKTLLAKAVAHETNATFIRVVGSELVRKYIGE  199 (364)
T ss_pred             EECCCCHHHHHHHHHHHHHCCCCCCHHHHHCC-CCCCCCEEEECCCCCCHHHHHHHHHCCCCCEEEEEEHHHHHHHHHCC
T ss_conf             40267878999999888734688831677628-89898657007579768899998631455126886044444444133


Q ss_pred             CC--CCCCHHHHHHCCCEEEEEECCCCCCCCCCCEEEEEECCCEEEEEECCC-----CCCEEEECCEEEEEECCCCCCCC
Q ss_conf             55--568988997389809999346777601310024541598587321047-----86068714528999738863426
Q gi|254781225|r  545 EA--GKANPSLIRLMGSRIVIISETNENDEINAAKIKQMTGGDCMTARLNYG-----NTYSESPASFTPFIVPNKHLFVR  617 (789)
Q Consensus       545 ~~--~~~~~~la~l~g~r~~~~~E~~~~~~~~~~~~K~ltggD~i~ar~~~~-----~~~~~~~p~~~~~~~~N~~P~~~  617 (789)
                      .+  -..-|.||+=+-=-+++++|.+   .+.+-+++..||||.=.-|-+-+     +.| +-.-..+++-+||.+=.+.
T Consensus       200 GArLV~~~F~LAkEKaPsIiFIDEiD---AiaakR~~~~TsGdREV~RTlmQLLAElDGF-d~rg~VkviaATNR~DilD  275 (364)
T TIGR01242       200 GARLVREVFELAKEKAPSIIFIDEID---AIAAKRVDSSTSGDREVQRTLMQLLAELDGF-DPRGNVKVIAATNRPDILD  275 (364)
T ss_pred             HHHHHHHHHHHHHCCCCCEEEEECHH---HHHHHHCCCCCCCCHHHHHHHHHHHHHHCCC-CCCCCEEEEEECCCCHHCC
T ss_conf             16899999998530698168610133---3543211467787315788999999752488-8767616887207620204


Q ss_pred             CC--CCCEEEEEEEEECCCC
Q ss_conf             79--8416646899965887
Q gi|254781225|r  618 NP--DDAWWRRYIVIPFDKP  635 (789)
Q Consensus       618 ~~--d~~~~rR~~iipF~~~  635 (789)
                      ..  =-|=+.|++=||.+..
T Consensus       276 PA~LRPGRFDR~IEVPlP~~  295 (364)
T TIGR01242       276 PAILRPGRFDRIIEVPLPDF  295 (364)
T ss_pred             CCCCCCCCCCCEEECCCCCC
T ss_conf             32148886132573169783


No 38 
>COG2884 FtsE Predicted ATPase involved in cell division [Cell division and chromosome partitioning]
Probab=93.92  E-value=0.054  Score=30.94  Aligned_cols=28  Identities=36%  Similarity=0.491  Sum_probs=23.2

Q ss_pred             CCCCEEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             7433799997078862578999999972
Q gi|254781225|r  498 NKAQRFIHIRGVGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       498 ~~~~~~~~~~G~G~nGKSt~~~~l~~ll  525 (789)
                      ...--|.|++|+.+.|||||+++|....
T Consensus        25 i~~Gef~fl~GpSGAGKSTllkLi~~~e   52 (223)
T COG2884          25 IPKGEFVFLTGPSGAGKSTLLKLIYGEE   52 (223)
T ss_pred             ECCCEEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             4686089986788887899999998413


No 39 
>TIGR02982 heterocyst_DevA ABC exporter ATP-binding subunit, DevA family; InterPro: IPR014324   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 ATP-binding subunit DevA, found mostly in the Cyanobacteria, but also in the Planctomycetes. Cyanobacterial examples are involved in heterocyst formation, by which some fraction of members of the colony undergo a developmental change and become capable of nitrogen fixation. The ABC transporter encoded by the devBCA operon is induced by nitrogen deficiency and is necessary for the formation of the laminated layer which envelops heterocysts , . It is thought to be involved in the export of either the heterocyst-specific glycolipids found in the laminated layer, or an enzyme essential for their formation..
Probab=93.84  E-value=0.054  Score=30.97  Aligned_cols=17  Identities=35%  Similarity=0.599  Sum_probs=7.5

Q ss_pred             CEEEECCCEEECCCCCC
Q ss_conf             17660793797438885
Q gi|254781225|r  427 RFLGEQDGILDLETGQK  443 (789)
Q Consensus       427 ~ll~~~NGv~dl~t~~~  443 (789)
                      ..|.+++=++.++.|++
T Consensus       203 RIlDvADRI~~MEdG~L  219 (220)
T TIGR02982       203 RILDVADRIVQMEDGKL  219 (220)
T ss_pred             CHHHHHHHHHHCCCCCC
T ss_conf             12006544421168635


No 40 
>COG0419 SbcC ATPase involved in DNA repair [DNA replication, recombination, and repair]
Probab=93.83  E-value=0.02  Score=33.83  Aligned_cols=16  Identities=31%  Similarity=0.472  Sum_probs=9.9

Q ss_pred             HHHHHHCCEEEEECCC
Q ss_conf             9742007889992347
Q gi|254781225|r   46 IDKLPACGFGFVCGVG   61 (789)
Q Consensus        46 i~~~~~~giGi~~G~~   61 (789)
                      +..+...||-+++|+.
T Consensus        19 ~~~~f~~gi~lI~G~n   34 (908)
T COG0419          19 IEKLFDSGIFLIVGPN   34 (908)
T ss_pred             CCCCCCCCEEEEECCC
T ss_conf             2315788837998999


No 41 
>PRK12402 replication factor C small subunit 2; Reviewed
Probab=93.74  E-value=0.26  Score=26.39  Aligned_cols=49  Identities=20%  Similarity=0.321  Sum_probs=37.4

Q ss_pred             HHHHHCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             9988879999999999999999759874337999970788625789999999723
Q gi|254781225|r  472 LVSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       472 ~l~~~~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      .|+++.|.++.+..|..++.   .|... +  ++++||.|.||+|...++.+-++
T Consensus        13 ~~~dvvGq~~i~~~L~~~~~---~~~~p-h--lLf~GPpG~GKTt~A~~lA~~l~   61 (337)
T PRK12402         13 LFEDILGQESVVDHLSALAA---SGNLP-H--LVVYGPSGSGKTAAVRALARELY   61 (337)
T ss_pred             CHHHHCCCHHHHHHHHHHHH---CCCCC-E--EEEECCCCCCHHHHHHHHHHHHC
T ss_conf             79980397999999999997---79987-6--98889298489999999999967


No 42 
>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB. Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.
Probab=93.60  E-value=0.47  Score=24.75  Aligned_cols=155  Identities=15%  Similarity=0.228  Sum_probs=93.2

Q ss_pred             CCCHHHHCCEECCCCCCCC--CC---HHHHHHHHHH-HCCCHHHHHHHHHHHHHHHCCCC---CCCEEEEEEECCCCCHH
Q ss_conf             8986550100137888875--79---4789999988-87999999999999999975987---43379999707886257
Q gi|254781225|r  445 KPTKELYITKSTGTPFVEG--EP---SQEFLDLVSG-YFESEEVMDYFTRCVGMALLGGN---KAQRFIHIRGVGGSGKS  515 (789)
Q Consensus       445 ~~~~~~~~t~~~~~~y~~~--a~---~p~~~~~l~~-~~~d~e~~~~l~~~~g~~l~g~~---~~~~~~~~~G~G~nGKS  515 (789)
                      +.+-...++..++++-..-  .+   --..++.|.+ ++|-++.++-+-+.+-.+-.|-.   +.---|++.||.|-||+
T Consensus       530 ~~~ia~vvs~~tgIPv~~~~~~e~~~L~~Le~~L~~rViGQd~AI~~I~~aI~~sraGL~dp~rP~GsFlf~GptGvGKT  609 (852)
T TIGR03346       530 AEEIAEVVSRWTGIPVSKMLEGEREKLLHMEEVLHERVVGQDEAVEAVSDAIRRSRAGLSDPNRPIGSFLFLGPTGVGKT  609 (852)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHH
T ss_conf             99999999999688667666547999987888899897170999999999999997188889997458998678877689


Q ss_pred             HHHHHHHHH-HCCC-CCCCCCHHHHHHCCCCCCCCCCHHHHHHCCC----------------------EEEEEECCCCCC
Q ss_conf             899999997-2330-0034426764201245555689889973898----------------------099993467776
Q gi|254781225|r  516 TLMNLIKYA-FGNQ-YVINAEASDIMQNRPPEAGKANPSLIRLMGS----------------------RIVIISETNEND  571 (789)
Q Consensus       516 t~~~~l~~l-lG~~-~~~~~~~~~~~~~~~~~~~~~~~~la~l~g~----------------------r~~~~~E~~~~~  571 (789)
                      -+...|... ||+. +....+.+.+..         ...+++|.|+                      -++..+|.++-.
T Consensus       610 ELAKaLAe~Lfg~~~~LIriDMSEy~E---------~hsvsrLiGaPPGYVGy~egG~Lte~vr~~PysVvL~DEIEKAh  680 (852)
T TIGR03346       610 ELAKALAEFLFDDEDAMVRIDMSEYME---------KHSVARLIGAPPGYVGYEEGGQLTEAVRRKPYSVVLFDEVEKAH  680 (852)
T ss_pred             HHHHHHHHHHHCCCCCEEEECHHHHCC---------HHHHHHHCCCCCCCCCCCCCCEECHHHHHCCCEEEEECCHHHHC
T ss_conf             999999999855852069843044301---------22477855899976776878742398981988799853054307


Q ss_pred             CCCCCEEEEEECCCEEEEEECCCCCCEEEECCEEEEEECCC
Q ss_conf             01310024541598587321047860687145289997388
Q gi|254781225|r  572 EINAAKIKQMTGGDCMTARLNYGNTYSESPASFTPFIVPNK  612 (789)
Q Consensus       572 ~~~~~~~K~ltggD~i~ar~~~~~~~~~~~p~~~~~~~~N~  612 (789)
                      .---..|-|+-....++-  -.++. +.|+.+ .++|.||-
T Consensus       681 ~~V~~~lLQilD~G~ltD--~~Gr~-vdF~Nt-iiimTSN~  717 (852)
T TIGR03346       681 PDVFNVLLQVLDDGRLTD--GQGRT-VDFRNT-VIIMTSNL  717 (852)
T ss_pred             HHHHHHHHHHHCCCEEEC--CCCCE-EEEEEE-EEEEECCC
T ss_conf             689999998823674307--99988-853556-89861540


No 43 
>COG1136 SalX ABC-type antimicrobial peptide transport system, ATPase component [Defense mechanisms]
Probab=93.57  E-value=0.057  Score=30.80  Aligned_cols=28  Identities=46%  Similarity=0.576  Sum_probs=22.6

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             4337999970788625789999999723
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      ..--|+.+.|+.|+|||||+++|..+.-
T Consensus        29 ~~Ge~vaI~GpSGSGKSTLLniig~ld~   56 (226)
T COG1136          29 EAGEFVAIVGPSGSGKSTLLNLLGGLDK   56 (226)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCC
T ss_conf             4998999989999989999999964667


No 44 
>TIGR03420 DnaA_homol_Hda DnaA regulatory inactivator Hda. Members of this protein family are Hda (Homologous to DnaA). These proteins are about half the length of DnaA and homologous over length of Hda. In the model species Escherichia coli, the initiation of DNA replication requires DnaA bound to ATP rather than ADP; Hda helps facilitate the conversion of DnaA-ATP to DnaA-ADP.
Probab=93.48  E-value=0.39  Score=25.27  Aligned_cols=94  Identities=19%  Similarity=0.279  Sum_probs=49.7

Q ss_pred             CCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCCCC--CC
Q ss_conf             7888875794789999988879999999999999999759874337999970788625789999999723300034--42
Q gi|254781225|r  457 GTPFVEGEPSQEFLDLVSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVIN--AE  534 (789)
Q Consensus       457 ~~~y~~~a~~p~~~~~l~~~~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~--~~  534 (789)
                      ++..++..   .|+.|+..  ++...+.-+.+++.      .....++++||+.|+|||-+++.+.+-+.......  .+
T Consensus         5 ~~~l~~~~---tfdnFi~~--~N~~~~~~l~~~~~------~~~~~~l~i~G~~GsGKTHLl~a~~~~~~~~~~~~~yl~   73 (226)
T TIGR03420         5 DVGLPDDP---TFDNFYAG--GNAELLAALRQLAA------GKGDRFLYLWGESGSGKSHLLQAACAAAEERGKSAIYLP   73 (226)
T ss_pred             CCCCCCCC---CHHCCCCC--CHHHHHHHHHHHHH------CCCCCEEEEECCCCCCHHHHHHHHHHHHHCCCCCEEEEC
T ss_conf             99999987---63123658--67999999998764------668886999899999889999999999862699579952


Q ss_pred             HHHHHHCCCCCCCCCCHHHHHHCCCEEEEEECCC
Q ss_conf             6764201245555689889973898099993467
Q gi|254781225|r  535 ASDIMQNRPPEAGKANPSLIRLMGSRIVIISETN  568 (789)
Q Consensus       535 ~~~~~~~~~~~~~~~~~~la~l~g~r~~~~~E~~  568 (789)
                      ...+...       ....+-.+...-++++.+.+
T Consensus        74 ~~~~~~~-------~~~~l~~l~~~d~l~iDDi~  100 (226)
T TIGR03420        74 LAELAQA-------DPEVLEGLEQADLVCLDDVE  100 (226)
T ss_pred             HHHHHHH-------HHHHHHHCCCCCEEEEECHH
T ss_conf             9998775-------39999727448999996633


No 45 
>PRK10865 protein disaggregation chaperone; Provisional
Probab=93.36  E-value=0.51  Score=24.50  Aligned_cols=155  Identities=15%  Similarity=0.214  Sum_probs=94.2

Q ss_pred             CCCHHHHCCEECCCCCCCCC--CHH---HHHHHHHH-HCCCHHHHHHHHHHHHHHHCCCCC---CCEEEEEEECCCCCHH
Q ss_conf             89865501001378888757--947---89999988-879999999999999999759874---3379999707886257
Q gi|254781225|r  445 KPTKELYITKSTGTPFVEGE--PSQ---EFLDLVSG-YFESEEVMDYFTRCVGMALLGGNK---AQRFIHIRGVGGSGKS  515 (789)
Q Consensus       445 ~~~~~~~~t~~~~~~y~~~a--~~p---~~~~~l~~-~~~d~e~~~~l~~~~g~~l~g~~~---~~~~~~~~G~G~nGKS  515 (789)
                      +.+-...++..++++-..-.  +..   ..++-|.+ ++|-.+.++-+-..+--+-.|-..   .---|++.||.|-||+
T Consensus       533 ~~~ia~vvs~~TgIPv~~l~~~e~~~L~~le~~L~~rViGQd~AI~~v~~aI~~sraGL~dp~rPiGsFLFlGPTGVGKT  612 (857)
T PRK10865        533 DAEIAEVLARWTGIPVSRMLESEREKLLRMEQELHHRVIGQNEAVEAVSNAIRRSRAGLSDPNRPIGSFLFLGPTGVGKT  612 (857)
T ss_pred             HHHHHHHHHHHHCCCCHHCCCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCCCCHH
T ss_conf             99999999999689830213105899999999998785280999999999999986389999997389998689878889


Q ss_pred             HHHHHHHHH-HCCCC-CCCCCHHHHHHCCCCCCCCCCHHHHHHCCC----------------------EEEEEECCCCCC
Q ss_conf             899999997-23300-034426764201245555689889973898----------------------099993467776
Q gi|254781225|r  516 TLMNLIKYA-FGNQY-VINAEASDIMQNRPPEAGKANPSLIRLMGS----------------------RIVIISETNEND  571 (789)
Q Consensus       516 t~~~~l~~l-lG~~~-~~~~~~~~~~~~~~~~~~~~~~~la~l~g~----------------------r~~~~~E~~~~~  571 (789)
                      -+...|... ||+.. ....+.+.+..         ...+++|.|+                      -++..+|.++-.
T Consensus       613 ElAK~LA~~LF~~e~~liriDMSEy~E---------~hsVSrLiGaPPGYVGy~eGG~LTeaVRr~PySVvLfDEIEKAH  683 (857)
T PRK10865        613 ELCKALANFMFDSDDAMVRIDMSEFME---------KHSVSRLVGAPPGYVGYEEGGYLTEAVRRRPYSVILLDEVEKAH  683 (857)
T ss_pred             HHHHHHHHHHHCCHHHEEEECCHHHCC---------CHHHHHHCCCCCCCCCCCCCCCHHHHHHHCCCEEEEEHHHHHHC
T ss_conf             999999999838933425625332113---------01276755899876675778811099981987788632576638


Q ss_pred             CCCCCEEEEEECCCEEEEEECCCCCCEEEECCEEEEEECCC
Q ss_conf             01310024541598587321047860687145289997388
Q gi|254781225|r  572 EINAAKIKQMTGGDCMTARLNYGNTYSESPASFTPFIVPNK  612 (789)
Q Consensus       572 ~~~~~~~K~ltggD~i~ar~~~~~~~~~~~p~~~~~~~~N~  612 (789)
                      .---..|-|+.-...++=  -.++. +.|+.+ .++|.||-
T Consensus       684 pdV~nilLQvlD~G~LtD--~~Gr~-vdF~Nt-IIImTSN~  720 (857)
T PRK10865        684 PDVFNILLQVLDDGRLTD--GQGRT-VDFRNT-VVIMTSNL  720 (857)
T ss_pred             HHHHHHHHHHHCCCEEEC--CCCCE-EEEEEE-EEEECCCH
T ss_conf             589999998703683207--99988-851334-89964623


No 46 
>PRK10733 hflB ATP-dependent metalloprotease; Reviewed
Probab=93.27  E-value=0.52  Score=24.40  Aligned_cols=166  Identities=17%  Similarity=0.156  Sum_probs=80.2

Q ss_pred             EECCCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCC
Q ss_conf             01378888757947899999888799999999999999997598743379999707886257899999997233000344
Q gi|254781225|r  454 KSTGTPFVEGEPSQEFLDLVSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINA  533 (789)
Q Consensus       454 ~~~~~~y~~~a~~p~~~~~l~~~~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~  533 (789)
                      ....+.|+.-|-|.+-.+-|      .|+++||..-=-|.-.| .+-.+=++|+|+.+.||+.|...+..=-|--..+..
T Consensus       145 ~~~~vtF~DVaG~~eaK~el------~EiVdfLk~P~k~~~~G-ak~PkGvLL~GPPGtGKTlLAkAvAgEa~vpF~~~s  217 (644)
T PRK10733        145 DQIKTTFADVAGCDEAKEEV------AELVEYLREPSRFQKLG-GKIPKGVLMVGPPGTGKTLLAKAIAGEAKVPFFTIS  217 (644)
T ss_pred             CCCCCCCCCCCCCHHHHHHH------HHHHHHHHCHHHHHHCC-CCCCCCEEEECCCCCCHHHHHHHHHCCCCCEEEEEE
T ss_conf             78987710408978999999------99999812979999749-979985177798998778999998645598089978


Q ss_pred             CHHHHHHCCCCCCCC--CCHHHHHHCCCEEEEEECCCCCCCCCCCEEEEEECCCEEEEEECC-----CCCCEEEECCEEE
Q ss_conf             267642012455556--898899738980999934677760131002454159858732104-----7860687145289
Q gi|254781225|r  534 EASDIMQNRPPEAGK--ANPSLIRLMGSRIVIISETNENDEINAAKIKQMTGGDCMTARLNY-----GNTYSESPASFTP  606 (789)
Q Consensus       534 ~~~~~~~~~~~~~~~--~~~~la~l~g~r~~~~~E~~~~~~~~~~~~K~ltggD~i~ar~~~-----~~~~~~~~p~~~~  606 (789)
                      ...+.+.--+..+..  .-|+.|+-.--.+++++|.+.-.+-..   ..+.||..-.-+-++     -+.|. - ....+
T Consensus       218 gsef~e~~vGvga~rVR~lF~~Ar~~aP~IIFIDEiDaig~~R~---~~~~gg~~e~~~tlNqlL~EmDGf~-~-~~~Vi  292 (644)
T PRK10733        218 GSDFVEMFVGVGASRVRDMFEQAKKAAPCIIFIDEIDAVGRQRG---AGLGGGHDEREQTLNQMLVEMDGFE-G-NEGII  292 (644)
T ss_pred             HHHHHHEEEECCHHHHHHHHHHHHHCCCEEEEEECHHCCCCCCC---CCCCCCCHHHHHHHHHHHHHHHCCC-C-CCCEE
T ss_conf             47730222530689999999999966997999953220366678---9888983288878999999954888-8-78769


Q ss_pred             EEECCCCCCCCCCCCCEEE-----EEEEEECC
Q ss_conf             9973886342679841664-----68999658
Q gi|254781225|r  607 FIVPNKHLFVRNPDDAWWR-----RYIVIPFD  633 (789)
Q Consensus       607 ~~~~N~~P~~~~~d~~~~r-----R~~iipF~  633 (789)
                      ++++.+.|.+  -|.|+-|     |.+.||.+
T Consensus       293 viaATNrpd~--LD~ALlRPGRFDr~I~V~lP  322 (644)
T PRK10733        293 VIAATNRPDV--LDPALLRPGRFDRQVVVGLP  322 (644)
T ss_pred             EEEECCCCCC--CCHHHHCCCCCCEEEEECCC
T ss_conf             9962699755--47777168886559997798


No 47 
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=93.13  E-value=0.48  Score=24.68  Aligned_cols=141  Identities=19%  Similarity=0.254  Sum_probs=80.3

Q ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCC-CCEEEEEEECCCCCHHHHHHHHHHHHCCCCC-CCCCHHHHHHCCCC
Q ss_conf             789999988879999999999999999759874-3379999707886257899999997233000-34426764201245
Q gi|254781225|r  467 QEFLDLVSGYFESEEVMDYFTRCVGMALLGGNK-AQRFIHIRGVGGSGKSTLMNLIKYAFGNQYV-INAEASDIMQNRPP  544 (789)
Q Consensus       467 p~~~~~l~~~~~d~e~~~~l~~~~g~~l~g~~~-~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~-~~~~~~~~~~~~~~  544 (789)
                      ..|.+|+    |-+++.+-+.-++..+-...-. .|  ++++|+.|-||+|+..+|.+-+|.... ++.+.  +..    
T Consensus        22 ~~l~efi----GQ~~i~~~L~v~i~Aak~r~e~ldH--~Ll~GPPGlGKTTLA~iiA~E~~~~~~~tsGP~--lek----   89 (328)
T PRK00080         22 KSLDEFI----GQEKVKENLKIFIEAAKKRGEALDH--VLLYGPPGLGKTTLANIIANEMGVNIRITSGPA--LEK----   89 (328)
T ss_pred             CCHHHCC----CHHHHHHHHHHHHHHHHHCCCCCCC--EEEECCCCCCHHHHHHHHHHHHCCCCEECCCCC--CCC----
T ss_conf             8576635----9599999999999999964999880--576588998899999999998688815624500--167----


Q ss_pred             CCCCCCHHHHHHCCCEEEEEECCCCCCCCCCC---------EEEEEECCCEEEEEECCCCCCEEEECCEEEEEECCCCCC
Q ss_conf             55568988997389809999346777601310---------024541598587321047860687145289997388634
Q gi|254781225|r  545 EAGKANPSLIRLMGSRIVIISETNENDEINAA---------KIKQMTGGDCMTARLNYGNTYSESPASFTPFIVPNKHLF  615 (789)
Q Consensus       545 ~~~~~~~~la~l~g~r~~~~~E~~~~~~~~~~---------~~K~ltggD~i~ar~~~~~~~~~~~p~~~~~~~~N~~P~  615 (789)
                       .+.--.-|..|...-+.+++|...=.+.-+.         .+--++|.+ -.||-..    . -.|.|+|+-+|-..=.
T Consensus        90 -~~DL~~iLt~l~~~dvLFIDEIHRl~~~vEE~LY~AMEDf~iDi~iG~g-~~Ar~~~----i-~L~pFTLIGATTr~g~  162 (328)
T PRK00080         90 -AGDLAALLTNLEEGDVLFIDEIHRLSPVVEEILYPAMEDFRLDIMIGKG-PAARSIR----L-DLPPFTLIGATTRAGL  162 (328)
T ss_pred             -HHHHHHHHHHCCCCCEEEEHHHHHCCHHHHHHHHHHHHHCEEEEEECCC-CCCEEEE----C-CCCCEEEEECCCCCCC
T ss_conf             -4789999960887876765065324888998857987752345786478-6532455----5-8998347401367665


Q ss_pred             CCCCCCCEEEEEEE
Q ss_conf             26798416646899
Q gi|254781225|r  616 VRNPDDAWWRRYIV  629 (789)
Q Consensus       616 ~~~~d~~~~rR~~i  629 (789)
                         -+.-+..|+-+
T Consensus       163 ---Ls~PLrdRFGi  173 (328)
T PRK00080        163 ---LTSPLRDRFGI  173 (328)
T ss_pred             ---CCHHHHHHCCC
T ss_conf             ---77678975793


No 48 
>KOG1970 consensus
Probab=92.97  E-value=0.28  Score=26.25  Aligned_cols=22  Identities=9%  Similarity=0.169  Sum_probs=10.2

Q ss_pred             EECCCCCCCCCCHHHHHHHHHHH
Q ss_conf             01378888757947899999888
Q gi|254781225|r  454 KSTGTPFVEGEPSQEFLDLVSGY  476 (789)
Q Consensus       454 ~~~~~~y~~~a~~p~~~~~l~~~  476 (789)
                      .+..+.|+|-|+. ...++|..|
T Consensus       258 ri~~IsFNPIa~T-~MKK~L~ri  279 (634)
T KOG1970         258 RISNISFNPIAPT-IMKKFLKRI  279 (634)
T ss_pred             CCCEEEECCCCHH-HHHHHHHHH
T ss_conf             8524761577679-999999999


No 49 
>cd03278 ABC_SMC_barmotin Barmotin is a tight junction-associated protein expressed in rat epithelial cells which is thought to have an important regulatory role in tight junction barrier function.  Barmotin belongs to the SMC protein family.  SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains.  Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins.  The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases.  The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, w
Probab=92.84  E-value=0.12  Score=28.61  Aligned_cols=26  Identities=38%  Similarity=0.750  Sum_probs=22.9

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             99997078862578999999972330
Q gi|254781225|r  503 FIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       503 ~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      +.-+.|+-|+||||++++|..++|..
T Consensus        24 itaIvGpsGsGKSTLl~~i~~~lg~~   49 (197)
T cd03278          24 LTAIVGPNGSGKSNIIDAIRWVLGEQ   49 (197)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCCC
T ss_conf             28999999998899999999874777


No 50 
>pfam07726 AAA_3 ATPase family associated with various cellular activities (AAA). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.
Probab=92.82  E-value=0.094  Score=29.38  Aligned_cols=120  Identities=17%  Similarity=0.221  Sum_probs=55.7

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHCCCCC-CCCC----HHHHHHCC--CCCCCCCCHHHHHHCCCEEEEEECCCCCCCCCCC
Q ss_conf             999707886257899999997233000-3442----67642012--4555568988997389809999346777601310
Q gi|254781225|r  504 IHIRGVGGSGKSTLMNLIKYAFGNQYV-INAE----ASDIMQNR--PPEAGKANPSLIRLMGSRIVIISETNENDEINAA  576 (789)
Q Consensus       504 ~~~~G~G~nGKSt~~~~l~~llG~~~~-~~~~----~~~~~~~~--~~~~~~~~~~la~l~g~r~~~~~E~~~~~~~~~~  576 (789)
                      +++.|+-+.|||++...+...+|.... .+.+    .+.+.+..  ....+...+.-..+. ..+++++|.+.-..---+
T Consensus         2 VLL~GppG~GKT~l~~~lA~~~~~~~~~i~~~~~~~~~Dl~G~~~~~~~~~~~~~~~G~l~-~~vl~lDEin~a~~~v~~   80 (131)
T pfam07726         2 VLLEGVPGLAKTLLARTLARSLGLDFRRIQFTPDLLPSDITGTEVYDQKTREFEFRPGPIF-ANVLLADEINRAPPKTQS   80 (131)
T ss_pred             EEEECCCCCHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCEEECCCCCEEEEECCCCC-CCCEEEEHHHCCCHHHHH
T ss_conf             8789899876999999999995998168883377670003684542378740898457310-370564012039989999


Q ss_pred             EEEEEECCCEEEEEECCCCCCEEEECCEEEEEECCCCCCC---CCCCCCEEEEEEE
Q ss_conf             0245415985873210478606871452899973886342---6798416646899
Q gi|254781225|r  577 KIKQMTGGDCMTARLNYGNTYSESPASFTPFIVPNKHLFV---RNPDDAWWRRYIV  629 (789)
Q Consensus       577 ~~K~ltggD~i~ar~~~~~~~~~~~p~~~~~~~~N~~P~~---~~~d~~~~rR~~i  629 (789)
                      .+-++.-.-.++.   .+.. ....+.|.+|.+.|- ...   ..-+.|+..|+++
T Consensus        81 ~Ll~~l~er~v~~---~g~~-~~~p~~f~viAt~NP-~e~~G~~~L~~al~dRF~~  131 (131)
T pfam07726        81 ALLEAMQERQVTI---GGET-HPLPEPFFVLATQNP-IEQEGTYPLPEAQLDRFLM  131 (131)
T ss_pred             HHHHHHHCEEEEE---CCEE-EECCCCEEEEECCCC-CCCCCCEECCHHHHCCCCC
T ss_conf             9997632649977---9988-527998499971698-7555764499889656158


No 51 
>PRK07261 topology modulation protein; Provisional
Probab=92.78  E-value=0.11  Score=28.86  Aligned_cols=25  Identities=40%  Similarity=0.565  Sum_probs=21.8

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             9997078862578999999972330
Q gi|254781225|r  504 IHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       504 ~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      ++++|++|+|||||..-|...+|--
T Consensus         3 I~IiG~sGsGKSTlAr~L~~~~~ip   27 (171)
T PRK07261          3 IAIIGYSGSGKSTLARFLGQHYNCP   27 (171)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCC
T ss_conf             9998899986899999999987979


No 52 
>COG3839 MalK ABC-type sugar transport systems, ATPase components [Carbohydrate transport and metabolism]
Probab=92.72  E-value=0.082  Score=29.74  Aligned_cols=15  Identities=13%  Similarity=0.425  Sum_probs=8.2

Q ss_pred             EEE-ECCCCEEEECCC
Q ss_conf             348-526843880477
Q gi|254781225|r  126 LDI-LGCGQYFVAYNI  140 (789)
Q Consensus       126 iEi-~~~G~q~V~~gs  140 (789)
                      +++ ..+|.++|.-|.
T Consensus        22 i~l~i~~Gef~vllGP   37 (338)
T COG3839          22 VNLDIEDGEFVVLLGP   37 (338)
T ss_pred             CEEEECCCCEEEEECC
T ss_conf             2689747979999899


No 53 
>cd03239 ABC_SMC_head The structural maintenance of chromosomes (SMC) proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms.  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 each has five distinct domains: amino- and carboxy-terminal globular domains, which contain sequences characteristic of ATPases, two coiled-coil regions separating the terminal domains , and a central flexible hinge.  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.
Probab=92.70  E-value=0.18  Score=27.53  Aligned_cols=31  Identities=32%  Similarity=0.544  Sum_probs=26.9

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHCCCCCC
Q ss_conf             3799997078862578999999972330003
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYAFGNQYVI  531 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~  531 (789)
                      ..+..++|+-++|||++++.|+-+||..+..
T Consensus        22 ~~~~~ivG~nGsGKSni~~ai~~~~g~~~~~   52 (178)
T cd03239          22 NSFNAIVGPNGSGKSNIVDAICFVLGGKAAK   52 (178)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHCCCHHH
T ss_conf             9817998999887789999999998664276


No 54 
>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family. Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.
Probab=92.67  E-value=0.63  Score=23.86  Aligned_cols=151  Identities=16%  Similarity=0.206  Sum_probs=90.2

Q ss_pred             HHHCCEECCCCCCCC-----CCHHHHHHHHHH-HCCCHHHHHHHHHHHHHHHCCCCCC---CEEEEEEECCCCCHHHHHH
Q ss_conf             550100137888875-----794789999988-8799999999999999997598743---3799997078862578999
Q gi|254781225|r  449 ELYITKSTGTPFVEG-----EPSQEFLDLVSG-YFESEEVMDYFTRCVGMALLGGNKA---QRFIHIRGVGGSGKSTLMN  519 (789)
Q Consensus       449 ~~~~t~~~~~~y~~~-----a~~p~~~~~l~~-~~~d~e~~~~l~~~~g~~l~g~~~~---~~~~~~~G~G~nGKSt~~~  519 (789)
                      ...++..++++-..-     ..--..++.|.+ ++|-++.++-+-+.+--+-.|-...   ---|++.||.|-||+-+..
T Consensus       535 a~vvs~~tgIPv~~l~~~e~~~l~~le~~L~~~ViGQ~~Av~~v~~ai~~sraGl~d~~rPigsFLFlGPTGVGKTElAK  614 (852)
T TIGR03345       535 AEVVADWTGIPVGRMVRDEIEAVLSLPDRLAERVIGQDHALEAIAERIRTARAGLEDPRKPLGVFLLVGPSGVGKTETAL  614 (852)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHHHH
T ss_conf             99999996898788617888888867999999972849999999999999871799999985689987899877899999


Q ss_pred             HHHHHH-CCC-CCCCCCHHHHHHCCCCCCCCCCHHHHHHCCC----------------------EEEEEECCCCCCCCCC
Q ss_conf             999972-330-0034426764201245555689889973898----------------------0999934677760131
Q gi|254781225|r  520 LIKYAF-GNQ-YVINAEASDIMQNRPPEAGKANPSLIRLMGS----------------------RIVIISETNENDEINA  575 (789)
Q Consensus       520 ~l~~ll-G~~-~~~~~~~~~~~~~~~~~~~~~~~~la~l~g~----------------------r~~~~~E~~~~~~~~~  575 (789)
                      .|...| |+. +..-.+.+.+..         ...+++|.|+                      -++..+|.++-..---
T Consensus       615 ~LA~~LFg~e~~liR~DMSEy~E---------~hsvsrLiGaPPGYVGy~eGG~LTe~Vrr~PysVvLfDEIEKAHpdV~  685 (852)
T TIGR03345       615 ALAELLYGGEQNLITINMSEFQE---------AHTVSRLKGSPPGYVGYGEGGVLTEAVRRKPYSVVLLDEVEKAHPDVL  685 (852)
T ss_pred             HHHHHHCCCCCCEEEECCHHHCC---------HHHHHHHCCCCCCCCCCCCCCHHHHHHHHCCCEEEEECHHHHCCHHHH
T ss_conf             99999719861147842243210---------436878638999766748777210988809986888611300288999


Q ss_pred             CEEEEEECCCEEEEEECCCCCCEEEECCEEEEEECCC
Q ss_conf             0024541598587321047860687145289997388
Q gi|254781225|r  576 AKIKQMTGGDCMTARLNYGNTYSESPASFTPFIVPNK  612 (789)
Q Consensus       576 ~~~K~ltggD~i~ar~~~~~~~~~~~p~~~~~~~~N~  612 (789)
                      ..|-|+.-...++=.  .++. +.|+.+ .++|.||-
T Consensus       686 nilLQvlD~G~LtD~--~Gr~-vdF~Nt-IIImTSN~  718 (852)
T TIGR03345       686 ELFYQVFDKGVMEDG--EGRE-IDFKNT-VILLTSNA  718 (852)
T ss_pred             HHHHHHHCCCEEECC--CCCE-EECEEE-EEEECCCH
T ss_conf             999987246777579--9998-845212-99975724


No 55 
>pfam05621 TniB Bacterial TniB protein. This family consists of several bacterial TniB NTP-binding proteins. TniB is a probable ATP-binding protein which is involved in Tn5053 mercury resistance transposition.
Probab=92.63  E-value=0.18  Score=27.42  Aligned_cols=50  Identities=18%  Similarity=0.290  Sum_probs=32.1

Q ss_pred             CCHHHHHHHH--HHHHHH-----------H--CCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             9999999999--999999-----------7--598743379999707886257899999997233
Q gi|254781225|r  478 ESEEVMDYFT--RCVGMA-----------L--LGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       478 ~d~e~~~~l~--~~~g~~-----------l--~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      +|+|.+.|++  +|+||.           |  .+....--.++++|+.+||||++++-.....+.
T Consensus        23 s~~eRI~~i~~~rWIgY~~A~~~L~~Le~Ll~~P~~~Rmp~lLlvGdsnnGKT~Iv~rF~~~hp~   87 (302)
T pfam05621        23 PADERIQRIRADRWIGYPRAVEALNRLEALYAWPNKQRMPNLLLVGPTNNGKSMIVEKFRRAHPA   87 (302)
T ss_pred             CHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEECCCCCHHHHHHHHHHHCCC
T ss_conf             98999999757853277899999999999984686468875588707988789999999996799


No 56 
>TIGR02881 spore_V_K stage V sporulation protein K; InterPro: IPR014232   Proteins in this entry include the stage V sporulation protein K (SpoVK), a close homologue of the Rubisco expression protein CbbX (IPR000470 from INTERPRO), and are members of an ATPase family associated with various cellular activities. These proteins are strictly limited to bacterial endospore-forming species, but are not found universally among members of this group; they are missing from the Clostridium species..
Probab=92.58  E-value=0.23  Score=26.83  Aligned_cols=158  Identities=13%  Similarity=0.218  Sum_probs=80.1

Q ss_pred             HHHHHHCCCHHHHHHHHHHHHHHHCCCCC--------CC-EEEEEEECCCCCHHHHHHHHHHHHCCCCCCCC-------C
Q ss_conf             99988879999999999999999759874--------33-79999707886257899999997233000344-------2
Q gi|254781225|r  471 DLVSGYFESEEVMDYFTRCVGMALLGGNK--------AQ-RFIHIRGVGGSGKSTLMNLIKYAFGNQYVINA-------E  534 (789)
Q Consensus       471 ~~l~~~~~d~e~~~~l~~~~g~~l~g~~~--------~~-~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~-------~  534 (789)
                      +-|+..+|=.++.+.++++-++..+..-+        .+ ..+|+.|..|+||+|...+|..+|-+=++-+-       .
T Consensus         3 ~EL~~~vGL~~vK~~i~EiYA~i~i~~kR~~~GLk~~~~~LHMiFKGNPGTGKTTVAR~~gklf~emnvL~KGH~iE~ER   82 (261)
T TIGR02881         3 RELSRLVGLDEVKELIKEIYAWIQINEKRKEEGLKTSKQVLHMIFKGNPGTGKTTVARLLGKLFKEMNVLSKGHLIEVER   82 (261)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCEEEEEE
T ss_conf             23564048889999999999999998888751011488447877427866843899999999985337567886788762


Q ss_pred             HHHHHHCCCCCCCCCCHHHHHHCCCEEEEEECCCCCCCCCCCEEEEEECCCEEEEEECCCCCCEEEECCEEEEEEC--CC
Q ss_conf             6764201245555689889973898099993467776013100245415985873210478606871452899973--88
Q gi|254781225|r  535 ASDIMQNRPPEAGKANPSLIRLMGSRIVIISETNENDEINAAKIKQMTGGDCMTARLNYGNTYSESPASFTPFIVP--NK  612 (789)
Q Consensus       535 ~~~~~~~~~~~~~~~~~~la~l~g~r~~~~~E~~~~~~~~~~~~K~ltggD~i~ar~~~~~~~~~~~p~~~~~~~~--N~  612 (789)
                      .-++..--|-++-..+..+-+..|- +.+++|.=.=.+-.+-=|    |-+-|..=-|.   .-+-...|.+|+++  .+
T Consensus        83 ADLVGEYIGHTAqkTRe~~kkA~GG-vLFiDEAYSLaRGGEKDF----GKEAIDtLVK~---mEd~~~~lvlILAGY~~E  154 (261)
T TIGR02881        83 ADLVGEYIGHTAQKTREVIKKALGG-VLFIDEAYSLARGGEKDF----GKEAIDTLVKA---MEDQRNELVLILAGYSDE  154 (261)
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHCCC-CHHHHHHHHHHCCCCCCC----CCHHHHHHHHH---HHHCCCCEEEEEECCHHH
T ss_conf             2212232030048999999986388-005577777614888876----62088899998---761569868997087689


Q ss_pred             CCCCCCCCCCEEEEEEEEECCCCCCCC
Q ss_conf             634267984166468999658878887
Q gi|254781225|r  613 HLFVRNPDDAWWRRYIVIPFDKPIANR  639 (789)
Q Consensus       613 ~P~~~~~d~~~~rR~~iipF~~~~~~~  639 (789)
                      |-.|=..-.|+-.|+   |+.-.|||=
T Consensus       155 M~yFL~~NPGL~SRF---Pi~i~FPdY  178 (261)
T TIGR02881       155 MDYFLSLNPGLRSRF---PISIDFPDY  178 (261)
T ss_pred             HHHHHHCCCCCCCCC---CCEEECCCC
T ss_conf             999862077977766---505418899


No 57 
>TIGR02211 LolD_lipo_ex lipoprotein releasing system, ATP-binding protein; InterPro: IPR011924   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 LolD, a member of the ABC transporter family. LolD is involved in localization of lipoproteins in some bacteria. It works with a transmembrane protein LolC, which in some species is a paralogous pair LolC and LolE. Depending on the residue immediately following the modified N-terminal Cys residue, the nascent lipoprotein may be carried further by LolA and LolB to the outer membrane, or remain at the inner membrane. Excluded from this entry are homologs from the archaeal genus Methanosarcina .; GO: 0005524 ATP binding, 0006810 transport, 0016020 membrane.
Probab=92.58  E-value=0.082  Score=29.75  Aligned_cols=22  Identities=45%  Similarity=0.653  Sum_probs=15.1

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             9999707886257899999997
Q gi|254781225|r  503 FIHIRGVGGSGKSTLMNLIKYA  524 (789)
Q Consensus       503 ~~~~~G~G~nGKSt~~~~l~~l  524 (789)
                      .+.++|..|+|||||+.+|..|
T Consensus        33 ~~~IvG~SGSGKSTLLHlLGGL   54 (221)
T TIGR02211        33 IVAIVGSSGSGKSTLLHLLGGL   54 (221)
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
T ss_conf             3798736787168999987306


No 58 
>PRK07429 phosphoribulokinase; Provisional
Probab=92.54  E-value=0.17  Score=27.58  Aligned_cols=42  Identities=19%  Similarity=0.215  Sum_probs=15.0

Q ss_pred             HHHHHHHHHHHHH---HCCCCCCCEEEEEEECC-CCCHHHHHHHHH
Q ss_conf             9999999999999---75987433799997078-862578999999
Q gi|254781225|r  481 EVMDYFTRCVGMA---LLGGNKAQRFIHIRGVG-GSGKSTLMNLIK  522 (789)
Q Consensus       481 e~~~~l~~~~g~~---l~g~~~~~~~~~~~G~G-~nGKSt~~~~l~  522 (789)
                      |-+.|+...+.-.   .+|...++..-.---+| +||-+.|.-++.
T Consensus       265 ~~~~~~E~~l~~~~~k~~g~~t~~~~~~~~~~gs~ngt~l~Q~l~~  310 (331)
T PRK07429        265 EEVIYLEDHLSNTSTKYYGETTELLLSHPDYPGSNNGTGLFQLLIG  310 (331)
T ss_pred             HHHHHHHHHHHCCCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHH
T ss_conf             9999999997535772146568998738678887540699999999


No 59 
>PRK08118 topology modulation protein; Reviewed
Probab=92.53  E-value=0.13  Score=28.51  Aligned_cols=98  Identities=22%  Similarity=0.156  Sum_probs=50.9

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCCCCCHHHHHHCCCEEEEEECCCCCCCCCCCEEEEEEC
Q ss_conf             99970788625789999999723300034426764201245555689889973898099993467776013100245415
Q gi|254781225|r  504 IHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEAGKANPSLIRLMGSRIVIISETNENDEINAAKIKQMTG  583 (789)
Q Consensus       504 ~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~~~~~~~~la~l~g~r~~~~~E~~~~~~~~~~~~K~ltg  583 (789)
                      ++++|+.|+|||||..-|...+|--. ..++......+-.                      +.+. +. -...++.++.
T Consensus         4 I~IiG~~GsGKSTlAr~L~~~~~ip~-~~LD~l~w~~~w~----------------------~~~~-~e-~~~~~~~~~~   58 (167)
T PRK08118          4 IILIGSGGSGKSTLARQLGEKLNIPV-HHLDALFWKPNWE----------------------GVPK-EE-QRTVQNELVK   58 (167)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCCE-EECCCEEECCCCC----------------------CCCH-HH-HHHHHHHHHH
T ss_conf             99988999879999999999889697-9644347668994----------------------6888-99-9999999983


Q ss_pred             CCEEEEEECCCCCCEEEECCEEEEEECCCCCCCCCCCCCEEEEE
Q ss_conf             98587321047860687145289997388634267984166468
Q gi|254781225|r  584 GDCMTARLNYGNTYSESPASFTPFIVPNKHLFVRNPDDAWWRRY  627 (789)
Q Consensus       584 gD~i~ar~~~~~~~~~~~p~~~~~~~~N~~P~~~~~d~~~~rR~  627 (789)
                      +|.=-.++.|........+.+..++.-+ +|...-.-..+.|++
T Consensus        59 ~~~WIidGny~~~~~~r~~~aD~iI~Ld-~p~~~~~~r~~kR~~  101 (167)
T PRK08118         59 EDEWIIDGNYGGTMDIRLNAADTIIFLD-IPRTICLYRAFKRRV  101 (167)
T ss_pred             CCCEEEECCCHHHHHHHHHHCCEEEEEC-CCHHHHHHHHHHHHH
T ss_conf             8987994771779987797699999985-989999999999999


No 60 
>cd03292 ABC_FtsE_transporter FtsE is a hydrophilic nucleotide-binding protein that binds FtsX to form a heterodimeric ATP-binding cassette (ABC)-type transporter that associates with the bacterial inner membrane.  The FtsE/X transporter is thought to be involved in cell division and is important for assembly or stability of the septal ring.
Probab=92.44  E-value=0.1  Score=29.18  Aligned_cols=29  Identities=38%  Similarity=0.487  Sum_probs=23.2

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             43379999707886257899999997233
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ..--|+.+.|+.|+||||++++|..+.-.
T Consensus        25 ~~Ge~v~i~GpSGsGKSTLl~~i~gl~~p   53 (214)
T cd03292          25 SAGEFVFLVGPSGAGKSTLLKLIYKEELP   53 (214)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             59989999979995399999999629898


No 61 
>pfam00437 GSPII_E Type II/IV secretion system protein. This family contains both type II and type IV pathway secretion proteins from bacteria. VirB11 ATPase is a subunit of the Agrobacterium tumefaciens transfer DNA (T-DNA) transfer system, a type IV secretion pathway required for delivery of T-DNA and effector proteins to plant cells during infection.
Probab=92.30  E-value=0.26  Score=26.44  Aligned_cols=41  Identities=24%  Similarity=0.465  Sum_probs=29.3

Q ss_pred             CHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             9999999999999997598743379999707886257899999997233
Q gi|254781225|r  479 SEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       479 d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ++++..|++.++        +.+..+++.|+.++||||+++.+...+..
T Consensus       125 ~~~~~~~L~~~v--------~~~~~ilIsG~TGSGKTT~l~all~~i~~  165 (283)
T pfam00437       125 DADIAEFLRQAV--------QARGNILVSGGTGSGKTTLLYALLNEINT  165 (283)
T ss_pred             HHHHHHHHHHHH--------HCCCEEEEECCCCCCHHHHHHHHHHHCCC
T ss_conf             599999999999--------81975999889999889999999984087


No 62 
>PRK05480 uridine kinase; Provisional
Probab=92.30  E-value=0.19  Score=27.31  Aligned_cols=36  Identities=31%  Similarity=0.406  Sum_probs=27.4

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             433799997078862578999999972330003442
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAE  534 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~  534 (789)
                      +....+-+.|+.++|||||.+.|...||...++.++
T Consensus         4 k~P~iIgIaG~SgSGKTT~a~~L~~~l~~~~v~vi~   39 (209)
T PRK05480          4 KQPIIIGIAGGSGSGKTTVASTIYEELGDESIAVIS   39 (209)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHCCCCCEEEEE
T ss_conf             898899998999778999999999980868759995


No 63 
>TIGR00602 rad24 checkpoint protein rad24; InterPro: IPR004582    To be effective as a mechanism that preserves genomic integrity, the DNA damage checkpoint must be extremely sensitive in its ability to detect DNA damage. In Saccharomyces cerevisiae the Ddc1/Rad17/Mec3 complex and Rad24 are DNA damage checkpoint components which may promote checkpoint activation by "sensing" DNA damage directly . Rad24 shares sequence homology with RF-c, a protein that recognises DNA template/RNA primer hybrids during DNA replication. The Ddc1 complex has structural homology to proliferating-cell nuclear antigen (PCNA), which clamps onto DNA and confers processivity to DNA polymerases delta and epsilon. Rad24 is postulated to recognise DNA lesions and then recruit the Ddc1 complex to generate checkpoint signals. ; GO: 0006281 DNA repair, 0007049 cell cycle, 0005634 nucleus.
Probab=92.28  E-value=0.21  Score=27.03  Aligned_cols=21  Identities=10%  Similarity=0.118  Sum_probs=8.4

Q ss_pred             ECCCCCCCCCCHHHHHHHHHHH
Q ss_conf             1378888757947899999888
Q gi|254781225|r  455 STGTPFVEGEPSQEFLDLVSGY  476 (789)
Q Consensus       455 ~~~~~y~~~a~~p~~~~~l~~~  476 (789)
                      +..+.|+|=|+ -...+||+.|
T Consensus       291 ~~~i~FNPiap-T~mkK~L~~I  311 (670)
T TIGR00602       291 VSNIKFNPIAP-TLMKKFLNRI  311 (670)
T ss_pred             CCCEECCCCCH-HHHHHHHHHH
T ss_conf             13100178717-8999985556


No 64 
>cd01130 VirB11-like_ATPase Type IV secretory pathway component VirB11, and related ATPases. The homohexamer, VirB11 is one of eleven Vir proteins, which are required for T-pilus biogenesis and virulence in the transfer of T-DNA from the Ti (tumor-inducing) plasmid of bacterial to plant cells. The pilus is a fibrous cell surface organelle, which mediates adhesion between bacteria during conjugative transfer or between bacteria and host eukaryotic cells during infection. VirB11- related ATPases include the archaeal flagella biosynthesis protein and the pilus assembly proteins CpaF/TadA and TrbB.  This alignment contains the C-terminal domain, which is the ATPase.
Probab=92.14  E-value=0.29  Score=26.09  Aligned_cols=48  Identities=33%  Similarity=0.325  Sum_probs=33.0

Q ss_pred             HHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             99988879999999999999999759874337999970788625789999999723
Q gi|254781225|r  471 DLVSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       471 ~~l~~~~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      +++..=+-++++.+||+.++        +..+-+++.|+.++||||+++.|...+.
T Consensus         3 dlv~~G~~~~~~~~~L~~~v--------~~~~nIlIsG~tGSGKTTll~al~~~i~   50 (186)
T cd01130           3 DLIAQGTFSPLQAAYLWLAV--------EARKNILISGGTGSGKTTLLNALLAFIP   50 (186)
T ss_pred             HHHHCCCCCHHHHHHHHHHH--------HCCCCEEEECCCCCCHHHHHHHHHHHCC
T ss_conf             78866999999999999999--------8599899989999989999999996133


No 65 
>TIGR03608 L_ocin_972_ABC putative bacteriocin export ABC transporter, lactococcin 972 group. A gene pair with a fairly wide distribution consists of a polypeptide related to the lactococcin 972 (see TIGR01653) and multiple-membrane-spanning putative immunity protein (see TIGR01654). This model represents a small clade within the ABC transporters that regularly are found adjacent to these bacteriocin system gene pairs and are likely serve as export proteins.
Probab=92.07  E-value=0.12  Score=28.74  Aligned_cols=29  Identities=38%  Similarity=0.529  Sum_probs=23.7

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             43379999707886257899999997233
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ..-.++.+.|+.|+|||||+++|..+.-.
T Consensus        22 ~~Ge~~~i~GpSGsGKSTLL~~i~gl~~p   50 (206)
T TIGR03608        22 EKGKMVAIVGESGSGKSTLLNIIGLLEKP   50 (206)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             69989999879997099999999759998


No 66 
>PRK13851 type IV secretion system protein VirB11; Provisional
Probab=91.93  E-value=0.41  Score=25.13  Aligned_cols=49  Identities=18%  Similarity=0.361  Sum_probs=32.4

Q ss_pred             HHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             999888799999999999999997598743379999707886257899999997233
Q gi|254781225|r  471 DLVSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       471 ~~l~~~~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ..+...+...++.+||+.++-        ..+=+++.|..++||+||+|.|...+..
T Consensus       140 ~~l~~~~~~~~~~~fL~~aV~--------~r~NIlIsGgTGSGKTTllnALl~~IP~  188 (343)
T PRK13851        140 EAILRHYDNGDLEAFLHACVV--------GRLTMLLCGPTGSGKTTMSKTLISAIPP  188 (343)
T ss_pred             HHHHHCCCCHHHHHHHHHHHH--------CCCCEEEECCCCCCHHHHHHHHHHCCCC
T ss_conf             787750243779999999997--------6988999888986199999999962896


No 67 
>TIGR02315 ABC_phnC phosphonate ABC transporter, ATP-binding protein; InterPro: IPR012693   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).     Phosphonates are a class of phosphorus-containing organic compound with a stable direct C-P bond rather than a C-O-P linkage. A number of bacterial species have operons, typically about 14 genes in size, with genes for ATP-dependent transport of phosphonates, degradation, and regulation of the expression of the system. Members of this protein family are the ATP-binding cassette component of tripartite ABC transporters of phosphonates.; GO: 0005524 ATP binding, 0015416 phosphonate transmembrane-transporting ATPase activity, 0015716 phosphonate transport, 0016020 membrane.
Probab=91.85  E-value=0.15  Score=28.00  Aligned_cols=25  Identities=36%  Similarity=0.594  Sum_probs=20.6

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             7999970788625789999999723
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      =|+-++|+.|.|||||+..|-.|..
T Consensus        29 E~~~~IG~SGAGKSTLLR~iNrL~~   53 (253)
T TIGR02315        29 EFVAVIGPSGAGKSTLLRCINRLVE   53 (253)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHCC
T ss_conf             1799973788726799987753026


No 68 
>PRK00091 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; Reviewed
Probab=91.84  E-value=0.14  Score=28.30  Aligned_cols=73  Identities=21%  Similarity=0.339  Sum_probs=32.6

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCCCCCHHHHHHCCCEEEEEECCCCCCCCCCC
Q ss_conf             3799997078862578999999972330003442676420124555568988997389809999346777601310
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEAGKANPSLIRLMGSRIVIISETNENDEINAA  576 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~~~~~~~~la~l~g~r~~~~~E~~~~~~~~~~  576 (789)
                      ++.+++.|+.++|||-+.--|...++.. +.+.+..++-.  +...|.+.|....+.+.+--.++-.+.+...+.+
T Consensus         4 ~~ii~i~GpTasGKs~la~~la~~~~~e-IIsaDS~QvYk--~l~IgTakps~~e~~~i~Hhli~~~~~~e~~sv~   76 (304)
T PRK00091          4 PKLIVLVGPTASGKTALAIELAKRLNGE-IISVDSMQVYR--GMDIGTAKPTAEELAGVPHHLIDILDPTESYSAA   76 (304)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHCCCE-EEEECHHHHHC--CCCEEECCCCHHHHCCCCCEEEEEECCCCCEEHH
T ss_conf             9779998988658999999999987998-99412688749--9986889999999818981243456588754499


No 69 
>cd03260 ABC_PstB_phosphate_transporter Phosphate uptake is of fundamental importance in the cell physiology of bacteria because phosphate is required as a nutrient.  The Pst system of E. coli comprises four distinct subunits encoded by the pstS, pstA, pstB, and pstC genes.  The PstS protein is a phosphate-binding protein located in the periplasmic space. P stA and PstC are hydrophobic and they form the transmembrane portion of the Pst system.  PstB is the catalytic subunit, which couples the energy of ATP hydrolysis to the import of phosphate across cellular membranes through the Pst system, often referred as ABC-protein.  PstB belongs to one of the largest superfamilies of proteins characterized by a highly conserved adenosine triphosphate (ATP) binding cassette (ABC), which is also a nucleotide binding domain (NBD).
Probab=91.74  E-value=0.18  Score=27.52  Aligned_cols=28  Identities=29%  Similarity=0.400  Sum_probs=22.8

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             4337999970788625789999999723
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      ..-.++.+.|+.|+||||++++|..++-
T Consensus        24 ~~Ge~~~iiG~SGsGKSTll~~i~gL~~   51 (227)
T cd03260          24 PKGEITALIGPSGCGKSTLLRLLNRLND   51 (227)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHHH
T ss_conf             7998999999999819999999974450


No 70 
>PRK08939 primosomal protein DnaI; Reviewed
Probab=91.72  E-value=0.61  Score=23.95  Aligned_cols=138  Identities=12%  Similarity=0.153  Sum_probs=78.9

Q ss_pred             EEECCCEEECC---CCCCCCCCHHHHCCEECCCCCCCCCCHHHHHHHHHHHC-CCHHHHHHHHHHHHHHHCC-CCCCCEE
Q ss_conf             66079379743---88855898655010013788887579478999998887-9999999999999999759-8743379
Q gi|254781225|r  429 LGEQDGILDLE---TGQKVKPTKELYITKSTGTPFVEGEPSQEFLDLVSGYF-ESEEVMDYFTRCVGMALLG-GNKAQRF  503 (789)
Q Consensus       429 l~~~NGv~dl~---t~~~~~~~~~~~~t~~~~~~y~~~a~~p~~~~~l~~~~-~d~e~~~~l~~~~g~~l~g-~~~~~~~  503 (789)
                      |-+.+|.+|++   |.+.+.++.+..+...+..-|-|..   ....-|.++- .|.+...-+..+.-++-.- ....++=
T Consensus        83 L~~~~~~idv~Y~pc~~~~~~~~~~~~~~~i~s~~mpk~---i~~as~~d~~~~d~~R~~a~~~a~~F~~~y~~~~~~kG  159 (306)
T PRK08939         83 LVMNGGYIDVSYLPTPEKIEADEERAIEERIQSIYMPKD---LLQATLADIDLDDLDRLDALMAALDFLEAYKPGEKVKG  159 (306)
T ss_pred             EEEECCEEEEEEECCHHHHHHHHHHHHHHHHHHCCCCHH---HHCCCHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCCE
T ss_conf             786388778987048999999999999998776357799---98098986488977899999999999997376988877


Q ss_pred             EEEEECCCCCHHHHHHHHHHHHCCCC--CCCCC-HHHHHHCC-CCCCCCCCHHHHHHCCCEEEEEECCCC
Q ss_conf             99970788625789999999723300--03442-67642012-455556898899738980999934677
Q gi|254781225|r  504 IHIRGVGGSGKSTLMNLIKYAFGNQY--VINAE-ASDIMQNR-PPEAGKANPSLIRLMGSRIVIISETNE  569 (789)
Q Consensus       504 ~~~~G~G~nGKSt~~~~l~~llG~~~--~~~~~-~~~~~~~~-~~~~~~~~~~la~l~g~r~~~~~E~~~  569 (789)
                      +.++|+-|.|||-++..|.+-|-...  +..+. ..++..-+ .-..+.-...+-.++.+.+.+++|...
T Consensus       160 lyl~G~~G~GKTyL~~aian~La~~g~~v~~v~~p~~~~~lK~s~~d~s~~~~i~~~k~~~vLiLDDiGa  229 (306)
T PRK08939        160 LYLYGDFGVGKTYLLAAIANELAKKGVSSTLVHFPEFIRELKNAISDGSVKEKIDAVKEAPVLMLDDIGA  229 (306)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEHHHHHHHHHHHHCCCCHHHHHHHHHCCCEEEEECCCC
T ss_conf             8898999998999999999999986992999875999999999864898899999984499899844465


No 71 
>PRK04220 2-phosphoglycerate kinase; Provisional
Probab=91.69  E-value=0.76  Score=23.34  Aligned_cols=51  Identities=22%  Similarity=0.255  Sum_probs=36.5

Q ss_pred             HHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCH
Q ss_conf             999999999759874337999970788625789999999723300034426
Q gi|254781225|r  485 YFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEA  535 (789)
Q Consensus       485 ~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~  535 (789)
                      +.+++.-..-....+....+++-|+.|-||||+...|..=||=..+.+.+.
T Consensus        76 ~a~rY~~~r~~r~~~~pliILigGtsGvGKSTlA~~LA~rLgI~~visTD~  126 (306)
T PRK04220         76 IAEKYLLWRRIRKSKEPIIILIGGASGVGTSTIAFELASRLGIRSVIGTDS  126 (306)
T ss_pred             HHHHHHHHHHHHCCCCCEEEEEECCCCCCHHHHHHHHHHHHCCCEEECCHH
T ss_conf             999999999985369987999858998878999999999709883422216


No 72 
>pfam01078 Mg_chelatase Magnesium chelatase, subunit ChlI. Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg2+ into protoporphyrin IX. This is the first unique step in the synthesis of (bacterio)chlorophyll. Due to this, it is thought that Mg-chelatase has an important role in channelling inter- mediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weight between 38-42 kDa.
Probab=91.68  E-value=0.68  Score=23.63  Aligned_cols=131  Identities=18%  Similarity=0.133  Sum_probs=65.2

Q ss_pred             HHHCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCC-CCCCH-------------HHHH
Q ss_conf             888799999999999999997598743379999707886257899999997233000-34426-------------7642
Q gi|254781225|r  474 SGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYV-INAEA-------------SDIM  539 (789)
Q Consensus       474 ~~~~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~-~~~~~-------------~~~~  539 (789)
                      .+|.|-+..++    .+-.+..|..    -++++|+-+.|||++.+.+..+|.+-.. .....             .++.
T Consensus         3 ~di~GQ~~akr----Al~iAaaG~H----~lLl~GpPG~GKTmlA~rl~~iLP~l~~~e~le~~~i~S~~g~~~~~~l~~   74 (207)
T pfam01078         3 ADVKGQEQAKR----ALEIAAAGGH----NLLMIGPPGSGKTMLAKRLPGILPPLTEQEALEVTAIHSVAGLGGDGGLIR   74 (207)
T ss_pred             HHHCCCHHHHH----HHHHHHCCCC----CEEEECCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCC
T ss_conf             68638599999----9999854787----589788998029999976301489987899887776423036877777445


Q ss_pred             HCCCC-------------CCCCCCHHHHHHCCCEEEEEECCCCCCCCC-CCEEEEEECCCEEEEEECCCCCCEEEECCEE
Q ss_conf             01245-------------555689889973898099993467776013-1002454159858732104786068714528
Q gi|254781225|r  540 QNRPP-------------EAGKANPSLIRLMGSRIVIISETNENDEIN-AAKIKQMTGGDCMTARLNYGNTYSESPASFT  605 (789)
Q Consensus       540 ~~~~~-------------~~~~~~~~la~l~g~r~~~~~E~~~~~~~~-~~~~K~ltggD~i~ar~~~~~~~~~~~p~~~  605 (789)
                      ..-+.             ....+.|....|.+.-+.+.+|..+-.+-- +++..-|-.| .|+..+-. . .++|.-.|.
T Consensus        75 ~rPfr~PHhs~s~~aliGGg~~~~PGeIslAH~GVLFLDE~~Ef~~~vle~LrqpLE~~-~v~IsRa~-~-~~~~PA~f~  151 (207)
T pfam01078        75 RRPFRAPHHSASAAALVGGGSIPRPGEISLAHNGVLFLDELPEFSRRVLESLRQPLEDG-EITISRAR-A-KVTFPARFQ  151 (207)
T ss_pred             CCCCCCCCCCCCHHHCCCCCCCCCCCCEEECCCCEEEECCHHHCCHHHHHHHHHHHCCC-CEEEEECC-C-EEEECCCEE
T ss_conf             79865788764363322688889997066636878884764653988999998766049-48999567-5-898604348


Q ss_pred             EEEECCCCCC
Q ss_conf             9997388634
Q gi|254781225|r  606 PFIVPNKHLF  615 (789)
Q Consensus       606 ~~~~~N~~P~  615 (789)
                      ++.++|-=|-
T Consensus       152 LvaA~NPCpC  161 (207)
T pfam01078       152 LVAAMNPCPC  161 (207)
T ss_pred             EEEECCCCCC
T ss_conf             8885057777


No 73 
>TIGR00972 3a0107s01c2 phosphate ABC transporter, ATP-binding protein; InterPro: IPR005670   This is a family of phosphate transport system permease proteins.; GO: 0005315 inorganic phosphate transmembrane transporter activity, 0015114 phosphate transmembrane transporter activity, 0006817 phosphate transport, 0016020 membrane.
Probab=91.57  E-value=0.21  Score=27.03  Aligned_cols=25  Identities=28%  Similarity=0.446  Sum_probs=15.9

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             3379999707886257899999997
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYA  524 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~l  524 (789)
                      ....--++||.|.|||||++.|-.|
T Consensus        26 ~n~vTAlIGPSGCGKSTlLR~lNRM   50 (248)
T TIGR00972        26 KNQVTALIGPSGCGKSTLLRSLNRM   50 (248)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH
T ss_conf             7705898778898678999998877


No 74 
>KOG0651 consensus
Probab=91.54  E-value=0.3  Score=25.97  Aligned_cols=131  Identities=15%  Similarity=0.182  Sum_probs=75.5

Q ss_pred             CCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCCC---CCHHHHHHCCCEEEEEECCCCCCCC
Q ss_conf             8743379999707886257899999997233000344267642012455556---8988997389809999346777601
Q gi|254781225|r  497 GNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEAGK---ANPSLIRLMGSRIVIISETNENDEI  573 (789)
Q Consensus       497 ~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~~~~---~~~~la~l~g~r~~~~~E~~~~~~~  573 (789)
                      +.+..+-+.+||+.+.||+-+.+++.+-+|-.....++..+.++.-+ +++.   -.+--|+-.-...++++|.+.+..-
T Consensus       162 gIk~Pkg~ll~GppGtGKTlla~~Vaa~mg~nfl~v~ss~lv~kyiG-EsaRlIRemf~yA~~~~pciifmdeiDAigGR  240 (388)
T KOG0651         162 GIKPPKGLLLYGPPGTGKTLLARAVAATMGVNFLKVVSSALVDKYIG-ESARLIRDMFRYAREVIPCIIFMDEIDAIGGR  240 (388)
T ss_pred             CCCCCCEEEEECCCCCCHHHHHHHHHHHCCCCEEEEEHHHHHHHHCC-CHHHHHHHHHHHHHHHCCEEEEEHHHHHHCCE
T ss_conf             77788256876799986459999999865985477447666330026-57889999997786527557751012311457


Q ss_pred             CCCEEEEEECCCEEEEEECC-----CCCCEEEECCEEEEEECCCCCCCCCC--CCCEEEEEEEEEC
Q ss_conf             31002454159858732104-----78606871452899973886342679--8416646899965
Q gi|254781225|r  574 NAAKIKQMTGGDCMTARLNY-----GNTYSESPASFTPFIVPNKHLFVRNP--DDAWWRRYIVIPF  632 (789)
Q Consensus       574 ~~~~~K~ltggD~i~ar~~~-----~~~~~~~~p~~~~~~~~N~~P~~~~~--d~~~~rR~~iipF  632 (789)
                         ++-+.|..|.+..|-+-     -+.| ......+++|++|..-.....  -.|=..|.+-||-
T Consensus       241 ---r~se~Ts~dreiqrTLMeLlnqmdgf-d~l~rVk~ImatNrpdtLdpaLlRpGRldrk~~iPl  302 (388)
T KOG0651         241 ---RFSEGTSSDREIQRTLMELLNQMDGF-DTLHRVKTIMATNRPDTLDPALLRPGRLDRKVEIPL  302 (388)
T ss_pred             ---EECCCCCHHHHHHHHHHHHHHHHCCC-HHCCCCCEEEECCCCCCCCHHHCCCCCCCCEECCCC
T ss_conf             ---73355520599999999998742140-120663179853886656655428752111002688


No 75 
>TIGR01186 proV glycine betaine/L-proline transport ATP binding subunit; InterPro: IPR005892   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).     This family comprises the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea. This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily. The characteristic feature of these transporters is the obligatory coupling of ATP hydrolysis to substrate translocation.   Functionally, this transport system is involved in osmoregulation. Under conditions of stress, the organism recruits this transport system to accumulate glycine betaine and other solutes which offer osmo-protection. It has been demonstrated that glycine betaine uptake is accompanied by symport with sodium ions. The locus has been named variously as proU or opuA. A gene library from L. lactis functionally complements an Escherichia coli proU mutant. The complementing locus is similar to a opuA locus in Bacillus subtlis. This clarifies the differences in nomenclature.; GO: 0005524 ATP binding, 0015171 amino acid transmembrane transporter activity, 0006865 amino acid transport, 0016020 membrane.
Probab=91.50  E-value=0.17  Score=27.63  Aligned_cols=10  Identities=30%  Similarity=0.580  Sum_probs=4.7

Q ss_pred             CCCEEEECCC
Q ss_conf             6843880477
Q gi|254781225|r  131 CGQYFVAYNI  140 (789)
Q Consensus       131 ~G~q~V~~gs  140 (789)
                      .|-.||.+|-
T Consensus        18 ~GEi~vi~Gl   27 (372)
T TIGR01186        18 KGEIFVIMGL   27 (372)
T ss_pred             CCEEEEEECC
T ss_conf             5438999778


No 76 
>TIGR00455 apsK adenylylsulfate kinase; InterPro: IPR002891 Enzyme that catalyses the phosphorylation of adenylylsulphate to 3'-phosphoadenylylsulphate. This domain contains an ATP binding P-loop motif .; GO: 0005524 ATP binding, 0016301 kinase activity, 0016772 transferase activity transferring phosphorus-containing groups, 0000103 sulfate assimilation.
Probab=91.41  E-value=0.19  Score=27.38  Aligned_cols=29  Identities=28%  Similarity=0.455  Sum_probs=24.8

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHCCCC
Q ss_conf             37999970788625789999999723300
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYAFGNQY  529 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~llG~~~  529 (789)
                      -+.+.|+|..++||||+.+.+...|=+.+
T Consensus        19 g~vlWlTGLSGsGKsTiA~Al~~~L~~~G   47 (187)
T TIGR00455        19 GVVLWLTGLSGSGKSTIANALEKKLEKKG   47 (187)
T ss_pred             EEEEEEECCCCCHHHHHHHHHHHHHHHCC
T ss_conf             38985116885635799999999999669


No 77 
>cd03256 ABC_PhnC_transporter ABC-type phosphate/phosphonate transport system.  Phosphonates are a class of organophosphorus compounds characterized by a chemically stable carbon-to-phosphorus (C-P) bond.  Phosphonates are widespread among naturally occurring compounds in all kingdoms of wildlife, but only procaryotic microorganisms are able to cleave this bond.  Certain bacteria such as E. coli can use alkylphosphonates as a phosphorus source.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=91.36  E-value=0.15  Score=27.97  Aligned_cols=29  Identities=28%  Similarity=0.461  Sum_probs=22.6

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             43379999707886257899999997233
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ..-.++.+.|+-|+||||++++|..++-.
T Consensus        25 ~~Ge~~~iiGpsGsGKSTLl~~i~gl~~p   53 (241)
T cd03256          25 NPGEFVALIGPSGAGKSTLLRCLNGLVEP   53 (241)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             99989999999983399999999749999


No 78 
>pfam05049 IIGP Interferon-inducible GTPase (IIGP). Interferon-inducible GTPase (IIGP) is thought to play a role in in intracellular defence. IIGP is predominantly associated with the Golgi apparatus and also localizes to the endoplasmic reticulum and exerts a distinct role in IFN-induced intracellular membrane trafficking or processing.
Probab=91.34  E-value=0.39  Score=25.26  Aligned_cols=14  Identities=14%  Similarity=0.401  Sum_probs=6.2

Q ss_pred             HHHHHHHHHCCCCC
Q ss_conf             78999876418997
Q gi|254781225|r   79 NTFKDTFEILHGTP   92 (789)
Q Consensus        79 ~~~~~~~~~l~g~p   92 (789)
                      ..+.+.+......|
T Consensus        22 s~I~e~L~~~~~~~   35 (375)
T pfam05049        22 SIIKKAIQEISSAP   35 (375)
T ss_pred             HHHHHHHHHHHCCC
T ss_conf             99999997544382


No 79 
>cd03237 ABC_RNaseL_inhibitor_domain2 The ATPase domain 2 of RNase L inhibitor.  The ABC ATPase, RNase L inhibitor (RLI), is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids.  RLI's are not transport proteins and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family.  Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains which are arranged to form two composite active sites in their interface cleft.  RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity of more than 48%.  The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.
Probab=91.32  E-value=0.17  Score=27.63  Aligned_cols=33  Identities=24%  Similarity=0.412  Sum_probs=25.6

Q ss_pred             CCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             987433799997078862578999999972330
Q gi|254781225|r  496 GGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       496 g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      |....-.++-+.|+-|.|||||+++|..++-..
T Consensus        20 Gti~~GEiv~liGpNGaGKSTLlk~l~Gll~p~   52 (246)
T cd03237          20 GSISESEVIGILGPNGIGKTTFIKMLAGVLKPD   52 (246)
T ss_pred             CCCCCCCEEEEECCCCCHHHHHHHHHHCCCCCC
T ss_conf             846579899999799976999999997787888


No 80 
>PRK10744 phosphate transporter subunit; Provisional
Probab=91.26  E-value=0.5  Score=24.57  Aligned_cols=29  Identities=24%  Similarity=0.360  Sum_probs=22.8

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             43379999707886257899999997233
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ....++-+.|+-|.||||++++|..+++-
T Consensus        34 ~~Ge~~~liG~nGaGKSTLlk~i~gl~~l   62 (257)
T PRK10744         34 AKNQVTAFIGPSGCGKSTLLRTFNKMYEL   62 (257)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHHCC
T ss_conf             89989999999998199999999876512


No 81 
>TIGR00968 3a0106s01 sulfate ABC transporter, ATP-binding protein; InterPro: IPR005666   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).     These proteins are involved in the transmembrane transport of sulphate and thiosulphate.; GO: 0042626 ATPase activity coupled to transmembrane movement of substances, 0006810 transport, 0016020 membrane.
Probab=91.26  E-value=0.16  Score=27.82  Aligned_cols=26  Identities=35%  Similarity=0.507  Sum_probs=21.0

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             43379999707886257899999997
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYA  524 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~l  524 (789)
                      ..-.++-|.||.|+||||++.+|..|
T Consensus        24 ~~G~lvaLLGPSGSGKsTLLR~iAGL   49 (241)
T TIGR00968        24 PTGSLVALLGPSGSGKSTLLRVIAGL   49 (241)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHCC
T ss_conf             38527985468987378999998357


No 82 
>cd03298 ABC_ThiQ_thiamine_transporter ABC-type thiamine tranport system; part of the binding-protein-dependent transport system tbpA-thiPQ for thiamine and TPP.  Probably responsible for the translocation of thiamine across the membrane. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.  The nucleotide binding domain shows the highest similarity between all members of the family.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=91.26  E-value=0.15  Score=27.94  Aligned_cols=28  Identities=43%  Similarity=0.421  Sum_probs=22.7

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             3379999707886257899999997233
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      .-.++.+.|+.+.||||++++|..++-.
T Consensus        23 ~Ge~~~ilGpSGsGKSTLl~li~Gl~~p   50 (211)
T cd03298          23 QGEITAIVGPSGSGKSTLLNLIAGFETP   50 (211)
T ss_pred             CCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             9989999999995599999999769998


No 83 
>pfam00910 RNA_helicase RNA helicase. This family includes RNA helicases thought to be involved in duplex unwinding during viral RNA replication. Members of this family are found in a variety of single stranded RNA viruses.
Probab=91.20  E-value=0.33  Score=25.74  Aligned_cols=101  Identities=20%  Similarity=0.275  Sum_probs=54.2

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCCCCCHHHHHHCCCEEEEEECCCCCCC--CCCCEEEEE
Q ss_conf             999707886257899999997233000344267642012455556898899738980999934677760--131002454
Q gi|254781225|r  504 IHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEAGKANPSLIRLMGSRIVIISETNENDE--INAAKIKQM  581 (789)
Q Consensus       504 ~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~~~~~~~~la~l~g~r~~~~~E~~~~~~--~~~~~~K~l  581 (789)
                      +.++|+.+.|||++.+.|...+.+.-..........  +.+..    .---.-.|-..+++.|......  ..+..+-+|
T Consensus         1 i~l~G~~G~GKS~~a~~la~~~~~~~~~~~~~~~Y~--~~~~~----~~wdgY~gq~vvi~DD~~~~~~~~~~~~~~~~l   74 (105)
T pfam00910         1 IWLYGPPGCGKSTLAKYLARALLDHLGLPKKDSVYS--RNPDD----DFWDGYTGQPVVIIDDFGQNPDGPSDEAELIRL   74 (105)
T ss_pred             CEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEE--CCCCC----CCCCCCCCCEEEEEECCCCCCCCCHHHHHHHHH
T ss_conf             989799989889999999999999837787897796--78877----656788998579996577788862889999987


Q ss_pred             ECCCEEEEEEC--CCCCCEEEECCEEEEEECCC
Q ss_conf             15985873210--47860687145289997388
Q gi|254781225|r  582 TGGDCMTARLN--YGNTYSESPASFTPFIVPNK  612 (789)
Q Consensus       582 tggD~i~ar~~--~~~~~~~~~p~~~~~~~~N~  612 (789)
                      ....+......  -.+. ..|.+.+. ++.||.
T Consensus        75 vs~~p~~~~ma~le~Kg-~~f~s~~v-i~tsN~  105 (105)
T pfam00910        75 VSSTPYPPPMAALEEKG-TPFTSKFV-IVTSNF  105 (105)
T ss_pred             HCCCCCCCCCCCHHHCC-CCCCCCEE-EEECCC
T ss_conf             56998388866761488-84468889-994799


No 84 
>cd03262 ABC_HisP_GlnQ_permeases HisP and GlnQ are the ATP-binding components of the bacterial periplasmic histidine and glutamine permeases, repectively.  Histidine permease is a multisubunit complex containing the HisQ and HisM integral membrane subunits and two copies of HisP.  HisP has properties intermediate between those of integral and peripheral membrane proteins and is accessible from both sides of the membrane, presumably by its interaction with HisQ and HisM.  The two HisP subunits form a homodimer within the complex.  The domain structure of the amino acid uptake systems is typical for prokaryote extracellular solute binding protein-dependent uptake systems.  All of the amino acid uptake systems also have at least one, and in a few cases, two extracellular solute binding proteins located in the periplasm of Gram-negative bacteria, or attached to the cell membrane of Gram-positive bacteria.  The best-studied member of the PAAT (polar amino acid transport) family is the HisJQM
Probab=91.18  E-value=0.17  Score=27.67  Aligned_cols=28  Identities=39%  Similarity=0.453  Sum_probs=22.2

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             4337999970788625789999999723
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      ..--++.+.|+.++||||++++|..+.-
T Consensus        24 ~~Ge~~~ivGpSGsGKSTLL~~i~gL~~   51 (213)
T cd03262          24 KKGEVVVIIGPSGSGKSTLLRCINLLEE   51 (213)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCC
T ss_conf             8998999999998449999999981999


No 85 
>PRK11545 gntK gluconate kinase 1; Provisional
Probab=91.15  E-value=0.31  Score=25.88  Aligned_cols=33  Identities=24%  Similarity=0.347  Sum_probs=28.3

Q ss_pred             CCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             598743379999707886257899999997233
Q gi|254781225|r  495 LGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       495 ~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      +-.+..+..+++-|..|.||||+.+.|..-||-
T Consensus         2 ~~~~~~~~iiVVMGVsGsGKSTig~~LA~~l~~   34 (177)
T PRK11545          2 STTNHDHHIYVLMGVSGSGKSAVASAVAHQLHA   34 (177)
T ss_pred             CCCCCCCEEEEEECCCCCCHHHHHHHHHHHHCC
T ss_conf             656788759999847989999999999998199


No 86 
>PRK10646 putative ATPase; Provisional
Probab=91.15  E-value=0.76  Score=23.34  Aligned_cols=59  Identities=22%  Similarity=0.221  Sum_probs=41.9

Q ss_pred             CCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHH
Q ss_conf             999999999999999975987433799997078862578999999972330003442676420
Q gi|254781225|r  478 ESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQ  540 (789)
Q Consensus       478 ~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~  540 (789)
                      +|++--.-+-+.+|.+|.+.    ..+.|.|.=+.||+||..-+...+|......+|+..+.+
T Consensus         9 ~de~~T~~lg~~la~~l~~g----~vi~L~G~LGaGKTtf~r~i~~~lg~~~~V~SPTf~lv~   67 (153)
T PRK10646          9 PDEQATLDLGERVAKACDGA----TVIYLYGDLGAGKTTFSRGFLQALGHQGNVKSPTYTLVE   67 (153)
T ss_pred             CCHHHHHHHHHHHHHHCCCC----CEEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCCEEEEE
T ss_conf             89999999999999768999----799998888789999999999984997862699764799


No 87 
>TIGR01846 type_I_sec_HlyB type I secretion system ATPase; InterPro: IPR010132   Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This entry contains one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N terminus, but rather carry signals located toward the extreme C terminus to direct type I secretion.; GO: 0005524 ATP binding, 0008565 protein transporter activity, 0015031 protein transport, 0016021 integral to membrane.
Probab=91.12  E-value=0.16  Score=27.87  Aligned_cols=47  Identities=30%  Similarity=0.347  Sum_probs=32.2

Q ss_pred             HCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCC-CCCCCHHHHHH
Q ss_conf             759874337999970788625789999999723300-03442676420
Q gi|254781225|r  494 LLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQY-VINAEASDIMQ  540 (789)
Q Consensus       494 l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~-~~~~~~~~~~~  540 (789)
                      |+=+.+.--++=.+|+.|+||||+.+|++.+.=... -.-++..++..
T Consensus       484 l~L~I~~Ge~IGIvGpSGSGKSTLTKL~QRLYtP~~GqVLVDG~DLA~  531 (703)
T TIGR01846       484 LSLDIKPGEVIGIVGPSGSGKSTLTKLLQRLYTPEHGQVLVDGVDLAI  531 (703)
T ss_pred             CCCCCCCCEEEEEECCCCCCHHHHHHHHHHHCCCCCCEEEECCCCCCC
T ss_conf             687657865799872789867899999886148888747770300010


No 88 
>pfam00493 MCM MCM2/3/5 family.
Probab=91.10  E-value=0.94  Score=22.71  Aligned_cols=161  Identities=16%  Similarity=0.191  Sum_probs=72.1

Q ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHHCCCC----------CCCEEEEEEECCCCCHHHHHHHHHHHHCCC-CCC-C-CC
Q ss_conf             8999998887999999999999999975987----------433799997078862578999999972330-003-4-42
Q gi|254781225|r  468 EFLDLVSGYFESEEVMDYFTRCVGMALLGGN----------KAQRFIHIRGVGGSGKSTLMNLIKYAFGNQ-YVI-N-AE  534 (789)
Q Consensus       468 ~~~~~l~~~~~d~e~~~~l~~~~g~~l~g~~----------~~~~~~~~~G~G~nGKSt~~~~l~~llG~~-~~~-~-~~  534 (789)
                      .++.+++.+.|.--=.+.+...+-..|.|++          +-..-+.+.|..+.|||+|+..+..+...- +++ . ++
T Consensus        14 ~~~~l~~siaP~i~G~~~vK~ai~l~l~gg~~~~~~~~~~~Rg~ihiLLvGdPG~gKSqlLk~~~~~~pr~~~tsg~~ss   93 (327)
T pfam00493        14 IYDKLARSIAPSIYGHEDVKKAILLQLFGGVKKNLPDGTRLRGDINVLLVGDPGTAKSQLLKYVAKLAPRAVYTSGKGSS   93 (327)
T ss_pred             HHHHHHHHHCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHCCCCEEECCCCCC
T ss_conf             99999998597124987999999999808987658888620365118984699815609999999868870883177665


Q ss_pred             HHHHHH--CCCCCCCCCCHH--HHHHCCCEEEEEECCCCCCCCCCCEEEEEECCCEEEEEECCCCCCEEEECCEEEEEEC
Q ss_conf             676420--124555568988--9973898099993467776013100245415985873210478606871452899973
Q gi|254781225|r  535 ASDIMQ--NRPPEAGKANPS--LIRLMGSRIVIISETNENDEINAAKIKQMTGGDCMTARLNYGNTYSESPASFTPFIVP  610 (789)
Q Consensus       535 ~~~~~~--~~~~~~~~~~~~--la~l~g~r~~~~~E~~~~~~~~~~~~K~ltggD~i~ar~~~~~~~~~~~p~~~~~~~~  610 (789)
                      ..-++.  .+....|.-..+  ..-|...-++.++|.++-..-+-+.|-+..-.-.|+..+- +-. .+.+-.+.++-++
T Consensus        94 ~~GLTa~~~~d~~~~~~~leaGalvlAd~Gv~cIDEfdk~~~~d~saL~EAMEqqtVsIaKa-Gi~-~tL~ar~sVlAaa  171 (327)
T pfam00493        94 AAGLTAAVVRDPDTGEWTLEAGALVLADGGVCCIDEFDKMNEEDRVAIHEAMEQQTISIAKA-GIV-ATLNARCSVLAAA  171 (327)
T ss_pred             CCCCEEEEEEECCCCCEEEECCCEEECCCCEEEEECCCCCCHHHHHHHHHHHHHCEEEEECC-CEE-EEECCCCEEEEEE
T ss_conf             67761589980688836983684775589827850055588767999999998681776338-538-9725871799852


Q ss_pred             CCCCCCC----------CCCCCEEEEEEEE
Q ss_conf             8863426----------7984166468999
Q gi|254781225|r  611 NKHLFVR----------NPDDAWWRRYIVI  630 (789)
Q Consensus       611 N~~P~~~----------~~d~~~~rR~~ii  630 (789)
                      |-.-..-          +-..++..|+-+|
T Consensus       172 NP~~g~yd~~~~~~~ni~Lp~~lLsRFDLi  201 (327)
T pfam00493       172 NPIFGRYDPKKSVAENINLPPPLLSRFDLI  201 (327)
T ss_pred             CCCCCCCCCCCCHHHHCCCCHHHHCCEEEE
T ss_conf             776773788889888558976774501079


No 89 
>TIGR01277 thiQ thiamine ABC transporter, ATP-binding protein; InterPro: IPR005968   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).     Thiamine pyrophosphate (TPP) is a required cofactor synthesized de novo in Salmonella typhimurium. The primary role for TPP is in central metabolism as an electron carrier and nucleophile for such enzymes as pyruvate dehydrogenase (1.2.4.1 from EC), acetolactate synthase (4.1.3.18 from EC), and alpha-ketoglutarate dehydrogenase (1.2.4.2 from EC).    Despite its importance in cellular physiology, neither the de novo biosynthetic pathway nor the salvage systems for thiamine are fully understood in any organism.    The model describes thiamine ABC transporter, ATP-binding protein, believed to be involved in the specific translocation of thiamine and its phosphoesters across the inner membrane The protein belongs to the larger ABC transport system which consists of at least three components: the inner membrane permease; thiamine binding protein and an ATP-binding subunit. This protein is found so far only in Proteobacteria, and is found in complete genomes only if the ThiB and ThiP subunits are also found. It has been experimentally demonstrated that mutants in the various steps in the de novo synthesis of thiamine and its biologically active form, namely thiamine pyrophosphate can be exogenously supplemented with thiamine, thiamine monophosphate or thiamine pyrophosphate. ; GO: 0005524 ATP binding, 0042626 ATPase activity coupled to transmembrane movement of substances, 0006810 transport, 0009276 1-2nm peptidoglycan-based cell wall.
Probab=91.04  E-value=0.17  Score=27.60  Aligned_cols=23  Identities=48%  Similarity=0.589  Sum_probs=17.1

Q ss_pred             EEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             99707886257899999997233
Q gi|254781225|r  505 HIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       505 ~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      -+.|+.|.||||++|+|..-+-.
T Consensus        28 Ai~GpSGAGKSTLLnLiAGF~~P   50 (213)
T TIGR01277        28 AILGPSGAGKSTLLNLIAGFLEP   50 (213)
T ss_pred             EEECCCCCCHHHHHHHHHHHCCC
T ss_conf             88758986278898778640477


No 90 
>COG2255 RuvB Holliday junction resolvasome, helicase subunit [DNA replication, recombination, and repair]
Probab=90.97  E-value=0.97  Score=22.63  Aligned_cols=127  Identities=18%  Similarity=0.225  Sum_probs=69.7

Q ss_pred             HHHHHCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCC-CCCCCHHHHHHCCCCCCCCCC
Q ss_conf             9988879999999999999999759874337999970788625789999999723300-034426764201245555689
Q gi|254781225|r  472 LVSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQY-VINAEASDIMQNRPPEAGKAN  550 (789)
Q Consensus       472 ~l~~~~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~-~~~~~~~~~~~~~~~~~~~~~  550 (789)
                      .|.+..|-+.+.+-++-++-.+-..+.... .+.++|+.+-||+|+.++|.+=+|-.- +++.+...-.       |.--
T Consensus        24 ~l~efiGQ~~vk~~L~ifI~AAk~r~e~lD-HvLl~GPPGlGKTTLA~IIA~Emgvn~k~tsGp~leK~-------gDla   95 (332)
T COG2255          24 TLDEFIGQEKVKEQLQIFIKAAKKRGEALD-HVLLFGPPGLGKTTLAHIIANELGVNLKITSGPALEKP-------GDLA   95 (332)
T ss_pred             CHHHHCCHHHHHHHHHHHHHHHHHCCCCCC-EEEEECCCCCCHHHHHHHHHHHHCCCEEECCCCCCCCH-------HHHH
T ss_conf             488851839999999999999984498767-47864799876888999999985677376366201572-------6599


Q ss_pred             HHHHHHCCCEEEEEECCCCCCCCCCCE---------EEEEECCCEEEEEECCCCCCEEEECCEEEEEECCC
Q ss_conf             889973898099993467776013100---------24541598587321047860687145289997388
Q gi|254781225|r  551 PSLIRLMGSRIVIISETNENDEINAAK---------IKQMTGGDCMTARLNYGNTYSESPASFTPFIVPNK  612 (789)
Q Consensus       551 ~~la~l~g~r~~~~~E~~~~~~~~~~~---------~K~ltggD~i~ar~~~~~~~~~~~p~~~~~~~~N~  612 (789)
                      --|..|.-.-..+++|...-...-+..         +--+.|.++- ||-.     .--.|-|+++=+|-.
T Consensus        96 aiLt~Le~~DVLFIDEIHrl~~~vEE~LYpaMEDf~lDI~IG~gp~-Arsv-----~ldLppFTLIGATTr  160 (332)
T COG2255          96 AILTNLEEGDVLFIDEIHRLSPAVEEVLYPAMEDFRLDIIIGKGPA-ARSI-----RLDLPPFTLIGATTR  160 (332)
T ss_pred             HHHHCCCCCCEEEEEHHHHCCHHHHHHHHHHHHHEEEEEEECCCCC-CCEE-----ECCCCCEEEEEECCC
T ss_conf             9986398677677725531474289896467531057789724875-5347-----637998137510134


No 91 
>pfam00485 PRK Phosphoribulokinase / Uridine kinase family. In Arabidopsis the region carries two binding domains, a phosphoribosylpyrophosphate-binding domain and, at the very C-terminus, a uracil-binding domain.
Probab=90.77  E-value=0.22  Score=26.86  Aligned_cols=29  Identities=31%  Similarity=0.477  Sum_probs=23.6

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHCCCCCCC
Q ss_conf             99970788625789999999723300034
Q gi|254781225|r  504 IHIRGVGGSGKSTLMNLIKYAFGNQYVIN  532 (789)
Q Consensus       504 ~~~~G~G~nGKSt~~~~l~~llG~~~~~~  532 (789)
                      +-+.|+.++|||||.+.|...||...+..
T Consensus         2 IgIaG~SgSGKTT~a~~L~~~l~~~~~~~   30 (196)
T pfam00485         2 IGVAGSSGAGKTTVARTFVSIFGREGVPA   30 (196)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCCCCCC
T ss_conf             89989985719999999999966058776


No 92 
>CHL00176 ftsH cell division protein; Validated
Probab=90.70  E-value=1  Score=22.47  Aligned_cols=165  Identities=17%  Similarity=0.169  Sum_probs=85.0

Q ss_pred             EECCCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCC
Q ss_conf             01378888757947899999888799999999999999997598743379999707886257899999997233000344
Q gi|254781225|r  454 KSTGTPFVEGEPSQEFLDLVSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINA  533 (789)
Q Consensus       454 ~~~~~~y~~~a~~p~~~~~l~~~~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~  533 (789)
                      ..+.+.|+.-|-|.+-.+-|      .|+++||..---|.-.| .+-.+=++|+||.++||+.+...+..=-|--..+..
T Consensus       170 ~~~~vtF~DVaG~~eaK~el------~EivdfLk~P~k~~~~G-ak~PkGvLL~GpPGTGKTlLAkAvAgEa~vpF~~~s  242 (631)
T CHL00176        170 AKTGITFNDVAGVEEAKEEL------EEVVTFLKKPERFTAVG-AKIPKGVLLVGPPGTGKTLLAKAIAGEAEVPFFSIS  242 (631)
T ss_pred             CCCCCCCCCCCCCHHHHHHH------HHHHHHHCCHHHHHHCC-CCCCCEEEEECCCCCCHHHHHHHHHCCCCCCEEEEE
T ss_conf             89997753228858999999------99999835958876449-968965898898998788999998565588469988


Q ss_pred             CHHHHHHCCCCCCC--CCCHHHHHHCCCEEEEEECCCCCCCCCCCEEEEEECC-CEEEEEECC-----CCCCEEEECCEE
Q ss_conf             26764201245555--6898899738980999934677760131002454159-858732104-----786068714528
Q gi|254781225|r  534 EASDIMQNRPPEAG--KANPSLIRLMGSRIVIISETNENDEINAAKIKQMTGG-DCMTARLNY-----GNTYSESPASFT  605 (789)
Q Consensus       534 ~~~~~~~~~~~~~~--~~~~~la~l~g~r~~~~~E~~~~~~~~~~~~K~ltgg-D~i~ar~~~-----~~~~~~~~p~~~  605 (789)
                      ...+.+.--+-.+.  ..-|+.|+-.--.+++++|.+.-.+-..   ..+.|| |.- -+-++     -+.|. -...-.
T Consensus       243 gs~F~e~~vGvga~rVR~LF~~Ar~~aP~IiFIDEiDaig~~Rg---~~~~gg~~e~-e~tlnqLL~emDGf~-~~~gVi  317 (631)
T CHL00176        243 GSEFVEMFVGVGAARVRDLFKKAKENSPCIVFIDEIDAVGRQRG---AGVGGGNDER-EQTLNQLLTEMDGFE-GNKGVI  317 (631)
T ss_pred             HHHHHHHHCCHHHHHHHHHHHHHHHCCCEEEEEEEEEEEEECCC---CCCCCCCCHH-HHHHHHHHHHHCCCC-CCCCEE
T ss_conf             37855642155589999999999863996999871012011478---9888985089-999999999842888-788869


Q ss_pred             EEEECCCCCCCCCCCCCEEE-----EEEEEECC
Q ss_conf             99973886342679841664-----68999658
Q gi|254781225|r  606 PFIVPNKHLFVRNPDDAWWR-----RYIVIPFD  633 (789)
Q Consensus       606 ~~~~~N~~P~~~~~d~~~~r-----R~~iipF~  633 (789)
                      ++-+||+ |.  .-|.|+-|     |-+.||.+
T Consensus       318 ViaATNr-pd--~LDpALlRPGRFDR~I~V~lP  347 (631)
T CHL00176        318 VIAATNR-ID--ILDAALLRPGRFDRQVTVSLP  347 (631)
T ss_pred             EEEECCC-CC--CCCHHHCCCCCCCEEEEECCC
T ss_conf             9982588-55--456866268877549982698


No 93 
>cd00227 CPT Chloramphenicol (Cm) phosphotransferase (CPT). Cm-inactivating enzyme; modifies the primary (C-3) hydroxyl of the antibiotic. Related structurally to shikimate kinase II.
Probab=90.55  E-value=0.37  Score=25.41  Aligned_cols=34  Identities=18%  Similarity=0.429  Sum_probs=27.3

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHHCCCC-CCCCCH
Q ss_conf             7999970788625789999999723300-034426
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYAFGNQY-VINAEA  535 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~llG~~~-~~~~~~  535 (789)
                      ++++|.|++++|||++...|+.++..-. ..+.+.
T Consensus         3 ~II~LNG~SSSGKSsiAraLQ~~l~~p~~h~~vD~   37 (175)
T cd00227           3 RIIILNGGSSAGKSSIARALQSVLAEPWLHFGVDS   37 (175)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHCCCCEEEEEHHH
T ss_conf             49998689989889999999984767568841858


No 94 
>COG0324 MiaA tRNA delta(2)-isopentenylpyrophosphate transferase [Translation, ribosomal structure and biogenesis]
Probab=90.47  E-value=0.83  Score=23.09  Aligned_cols=70  Identities=27%  Similarity=0.422  Sum_probs=26.0

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCCCCCHHHHHHCCCEEEEEECCCCCCCCCC
Q ss_conf             9999707886257899999997233000344267642012455556898899738980999934677760131
Q gi|254781225|r  503 FIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEAGKANPSLIRLMGSRIVIISETNENDEINA  575 (789)
Q Consensus       503 ~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~~~~~~~~la~l~g~r~~~~~E~~~~~~~~~  575 (789)
                      .+++.||.+.|||-+.--|..-+|.. +.+.+..++-  ++.+.|.++|....+.|..--.++..+..+..++
T Consensus         5 ~i~I~GPTAsGKT~lai~LAk~~~~e-IIs~DSmQvY--r~mdIGTAKps~~e~~~vpHhliDi~~p~e~ysa   74 (308)
T COG0324           5 LIVIAGPTASGKTALAIALAKRLGGE-IISLDSMQVY--RGLDIGTAKPSLEELAGVPHHLIDIRDPTESYSA   74 (308)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHCCCC-EEECCHHHHC--CCCCCCCCCCCHHHHCCCCEEEECCCCCCCCCCH
T ss_conf             79998988757789999999982992-8930235531--8886307999999985899787545683225549


No 95 
>PRK10247 putative ABC transporter ATP-binding protein YbbL; Provisional
Probab=90.45  E-value=0.24  Score=26.66  Aligned_cols=29  Identities=34%  Similarity=0.555  Sum_probs=22.6

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             43379999707886257899999997233
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ..-.++.+.|+-|.|||||+++|..++-.
T Consensus        31 ~~Ge~~~i~G~sGsGKSTLlk~i~gl~~p   59 (225)
T PRK10247         31 RAGEFKLITGPSGCGKSTLLKIVASLISP   59 (225)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             59969999999999999999999646688


No 96 
>cd03293 ABC_NrtD_SsuB_transporters NrtD and SsuB are the ATP-binding subunits of the bacterial ABC-type nitrate and sulfonate transport systems, respectively.  ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.  The nucleotide binding domain shows the highest similarity between all members of the family.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=90.39  E-value=0.21  Score=27.09  Aligned_cols=29  Identities=31%  Similarity=0.456  Sum_probs=23.4

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             43379999707886257899999997233
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ..--++.+.|+.|+||||++++|..++-.
T Consensus        28 ~~Ge~~~iiGpsGsGKSTLl~~i~Gl~~p   56 (220)
T cd03293          28 EEGEFVALVGPSGCGKSTLLRIIAGLERP   56 (220)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             79989999999995799999999759998


No 97 
>pfam08800 VirE_N VirE N-terminal domain. This presumed domain is found at the N-terminus of VirE proteins.
Probab=90.39  E-value=0.76  Score=23.35  Aligned_cols=46  Identities=20%  Similarity=0.211  Sum_probs=23.4

Q ss_pred             CCEEEEEEECCCCHHHHHHHHHHHHCCCCCEEEECCCCC-EEEEEEE
Q ss_conf             987999964688125678999876418997699678896-5999950
Q gi|254781225|r   63 QPLYAFDIDSKDEKTANTFKDTFEILHGTPIVRIGQKPK-ILIPFRM  108 (789)
Q Consensus        63 ~glv~iDiD~~d~~~~~~~~~~~~~l~g~p~~~~g~~~~-~~~~yr~  108 (789)
                      +|+++||||+.+.+-...+.+.+....-+-.+-++.+|+ ..++.++
T Consensus        31 sgli~lDiD~l~~ee~~~~r~~l~~dp~t~~~FvSpSG~GvKi~V~~   77 (136)
T pfam08800        31 NGLVCLDVDHLAKEELERVKQKAAALPYTVLAFISSSGRGVKIWVRF   77 (136)
T ss_pred             CCEEEEEECCCCHHHHHHHHHHHHCCCCEEEEEECCCCCEEEEEEEE
T ss_conf             88089982899989999999998469948999985799879999997


No 98 
>pfam00503 G-alpha G-protein alpha subunit. G proteins couple receptors of extracellular signals to intracellular signaling pathways. The G protein alpha subunit binds guanyl nucleotide and is a weak GTPase.
Probab=90.36  E-value=0.29  Score=26.12  Aligned_cols=47  Identities=4%  Similarity=-0.016  Sum_probs=20.0

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCEEEEEEE--CCCCCHHHHHHHHHHHHCC
Q ss_conf             9999999999999759874337999970--7886257899999997233
Q gi|254781225|r  481 EVMDYFTRCVGMALLGGNKAQRFIHIRG--VGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       481 e~~~~l~~~~g~~l~g~~~~~~~~~~~G--~G~nGKSt~~~~l~~llG~  527 (789)
                      +.+.|+...+-...........+..++-  ...|=+-||-.+-..++..
T Consensus       295 ~~~~fi~~kF~~~~~~~~~r~iy~h~T~AtDt~~i~~vf~~v~d~Il~~  343 (350)
T pfam00503       295 AAKEFIKKKFVSLNRNNPKKEIYSHFTCATDTENIRFVFDAVKDIILQE  343 (350)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999975679889826652153205088999999999999999


No 99 
>COG0802 Predicted ATPase or kinase [General function prediction only]
Probab=90.35  E-value=0.72  Score=23.51  Aligned_cols=60  Identities=25%  Similarity=0.277  Sum_probs=42.5

Q ss_pred             CCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHC-CCCCCCCCHHHHHH
Q ss_conf             79999999999999999759874337999970788625789999999723-30003442676420
Q gi|254781225|r  477 FESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFG-NQYVINAEASDIMQ  540 (789)
Q Consensus       477 ~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG-~~~~~~~~~~~~~~  540 (789)
                      +.|++-..-+-+.+|..|    ...-.+.|.|.=+.||+||..-|..-|| +.++.|++.+++..
T Consensus         5 ~~~~~~t~~lg~~l~~~l----~~g~Vv~L~GdLGAGKTtf~rgi~~~Lg~~~~V~SPTFtlv~~   65 (149)
T COG0802           5 LPDEEATLALGERLAEAL----KAGDVVLLSGDLGAGKTTLVRGIAKGLGVDGNVKSPTFTLVEE   65 (149)
T ss_pred             CCCHHHHHHHHHHHHHHC----CCCCEEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCCEEEEHH
T ss_conf             289999999999999657----8998899977876885999999999749997524987610121


No 100
>cd03296 ABC_CysA_sulfate_importer Part of the ABC transporter complex cysAWTP involved in sulfate import.  Responsible for energy coupling to the transport system.  The complex is composed of two ATP-binding proteins (cysA), two transmembrane proteins (cysT and cysW), and a solute-binding protein (cysP).  ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.  The nucleotide binding domain shows the highest similarity between all members of the family.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=90.29  E-value=0.21  Score=27.02  Aligned_cols=29  Identities=31%  Similarity=0.418  Sum_probs=22.1

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             43379999707886257899999997233
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ..--++.+.|+.++||||++++|..+...
T Consensus        26 ~~Ge~~~iiGpSGsGKSTll~~i~Gl~~p   54 (239)
T cd03296          26 PSGELVALLGPSGSGKTTLLRLIAGLERP   54 (239)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             89989999999997799999999769999


No 101
>PRK10535 macrolide transporter ATP-binding /permease protein; Provisional
Probab=90.22  E-value=0.35  Score=25.61  Aligned_cols=13  Identities=15%  Similarity=0.386  Sum_probs=7.3

Q ss_pred             HCCHHHHHHHHHE
Q ss_conf             4263888875432
Q gi|254781225|r  689 GTDTYQAWIDDCC  701 (789)
Q Consensus       689 ~~D~v~~fi~e~c  701 (789)
                      ..|.+.+|+-|+.
T Consensus       565 ~~dI~~qFL~Ea~  577 (648)
T PRK10535        565 ASDVLQQFLIEAV  577 (648)
T ss_pred             HHHHHHHHHHHHH
T ss_conf             8899999999999


No 102
>PRK13648 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=90.15  E-value=0.25  Score=26.51  Aligned_cols=29  Identities=31%  Similarity=0.346  Sum_probs=19.1

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             33799997078862578999999972330
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      ...++-+.|+-|.||||++++|..++...
T Consensus        34 ~Ge~vaiiG~sGsGKSTLl~ll~Gl~~p~   62 (269)
T PRK13648         34 KGQWTSIVGHNGSGKSTIAKLMIGIEKVK   62 (269)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHCCCCCC
T ss_conf             99899999999997999999996497998


No 103
>PRK13407 bchI magnesium chelatase subunit I; Provisional
Probab=90.15  E-value=0.95  Score=22.68  Aligned_cols=126  Identities=16%  Similarity=0.153  Sum_probs=67.9

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHCCCCCC------C--------------------------CCHHHHHHCC--------
Q ss_conf             99997078862578999999972330003------4--------------------------4267642012--------
Q gi|254781225|r  503 FIHIRGVGGSGKSTLMNLIKYAFGNQYVI------N--------------------------AEASDIMQNR--------  542 (789)
Q Consensus       503 ~~~~~G~G~nGKSt~~~~l~~llG~~~~~------~--------------------------~~~~~~~~~~--------  542 (789)
                      =+++.|+-|+||||+..-+..+|.+-...      +                          ++... +..+        
T Consensus        31 gvLi~G~~GtgKStlaR~l~~iLP~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~v~lPl~a-tedr~~G~ldie  109 (334)
T PRK13407         31 GVLVFGDRGTGKSTAVRALAALLPLIKAVEGCPVNSARPEDCPEWAEVSSTTMVERPTPVIDLPLGA-TEDRVVGALDIE  109 (334)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHCCCCCHHCCCCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCHH
T ss_conf             0899789986599999999972899511036755667742113343114555344899876789999-986644742188


Q ss_pred             -C--CCCCCCCHHHHHHCCCEEEEEECCCCCC-CCCCCEEEEEECCCEEEEEECCCCCCEEEECCEEEEEECCCCCCCCC
Q ss_conf             -4--5555689889973898099993467776-01310024541598587321047860687145289997388634267
Q gi|254781225|r  543 -P--PEAGKANPSLIRLMGSRIVIISETNEND-EINAAKIKQMTGGDCMTARLNYGNTYSESPASFTPFIVPNKHLFVRN  618 (789)
Q Consensus       543 -~--~~~~~~~~~la~l~g~r~~~~~E~~~~~-~~~~~~~K~ltggD~i~ar~~~~~~~~~~~p~~~~~~~~N~~P~~~~  618 (789)
                       .  .......|.+..+.+.-+.+++|.+.-. .+-+.++-.+-.|. ++.++- +-. +.+.-.|.+|-+.|-  .=..
T Consensus       110 ~al~~G~~~~~PGlLa~Ah~GVLylDEinll~~~vld~Ll~~~e~G~-~~IeRe-g~s-~~~ParF~LVatmNP--eEg~  184 (334)
T PRK13407        110 RALTRGEKAFEPGLLARANRGYLYIDEVNLLEDHIVDLLLDVAQSGE-NVVERE-GLS-IRHPARFVLVGSGNP--EEGE  184 (334)
T ss_pred             HHHHCCCCCCCCCHHHHCCCCEEEEECHHHCCHHHHHHHHHHHHCCC-EEEEEC-CEE-EECCCCCEEEEEECC--CCCC
T ss_conf             88626987788605434028867872053333889999998871695-799977-634-603662658982088--8777


Q ss_pred             CCCCEEEEEEE-EECCC
Q ss_conf             98416646899-96588
Q gi|254781225|r  619 PDDAWWRRYIV-IPFDK  634 (789)
Q Consensus       619 ~d~~~~rR~~i-ipF~~  634 (789)
                      -...+-.|+-+ |....
T Consensus       185 Lrp~lLDRf~l~v~v~~  201 (334)
T PRK13407        185 LRPQLLDRFGLSVEVRS  201 (334)
T ss_pred             CCHHHHHHHCEEEEECC
T ss_conf             59899836100687148


No 104
>cd03299 ABC_ModC_like Archeal protein closely related to ModC.  ModC is an ABC-type transporter and the ATPase component of a molybdate transport system that also includes the periplasmic binding protein ModA and the membrane protein ModB.  ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.  The nucleotide binding domain shows the highest similarity between all members of the family.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=90.13  E-value=0.23  Score=26.84  Aligned_cols=29  Identities=31%  Similarity=0.374  Sum_probs=21.8

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             43379999707886257899999997233
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ..-.++.+.|+.|.||||++++|..++-.
T Consensus        23 ~~Ge~~~iiGpSGsGKSTLlr~i~Gl~~p   51 (235)
T cd03299          23 ERGDYFVILGPTGSGKSVLLETIAGFIKP   51 (235)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             89989999999963599999999749999


No 105
>COG1116 TauB ABC-type nitrate/sulfonate/bicarbonate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=90.12  E-value=0.22  Score=26.86  Aligned_cols=22  Identities=50%  Similarity=0.712  Sum_probs=7.7

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             9999707886257899999997
Q gi|254781225|r  503 FIHIRGVGGSGKSTLMNLIKYA  524 (789)
Q Consensus       503 ~~~~~G~G~nGKSt~~~~l~~l  524 (789)
                      |+-+.|+.|-||||++++|..+
T Consensus        31 fvsilGpSGcGKSTLLriiAGL   52 (248)
T COG1116          31 FVAILGPSGCGKSTLLRLIAGL   52 (248)
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
T ss_conf             9999899978899999999687


No 106
>cd03226 ABC_cobalt_CbiO_domain2 Domain II of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota.  The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed.  The CbiMNQO family ABC transport system is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways.  Most cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO.  Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.
Probab=90.08  E-value=0.26  Score=26.47  Aligned_cols=30  Identities=27%  Similarity=0.428  Sum_probs=24.3

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             433799997078862578999999972330
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      ..--++.+.|+-|+||||++++|..++...
T Consensus        24 ~~Gei~~iiG~nGaGKSTLl~~i~Gl~~p~   53 (205)
T cd03226          24 YAGEIIALTGKNGAGKTTLAKILAGLIKES   53 (205)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCCC
T ss_conf             699899998899998999999995685777


No 107
>cd03229 ABC_Class3 This class is comprised of all BPD (Binding Protein Dependent) systems that are largely represented in archaea and eubacteria and are primarily involved in scavenging solutes from the environment.  ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.  The nucleotide binding domain shows the highest similarity between all members of the family.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=90.07  E-value=0.24  Score=26.68  Aligned_cols=29  Identities=34%  Similarity=0.390  Sum_probs=23.9

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             43379999707886257899999997233
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ..-.++.+.|+.++||||++++|..+.-.
T Consensus        24 ~~Ge~~~ivGpSG~GKSTllr~i~Gl~~p   52 (178)
T cd03229          24 EAGEIVALLGPSGSGKSTLLRCIAGLEEP   52 (178)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             89989999999998399999999859999


No 108
>PRK11248 tauB taurine transporter ATP-binding subunit; Provisional
Probab=90.05  E-value=0.23  Score=26.78  Aligned_cols=23  Identities=39%  Similarity=0.600  Sum_probs=10.3

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             99997078862578999999972
Q gi|254781225|r  503 FIHIRGVGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       503 ~~~~~G~G~nGKSt~~~~l~~ll  525 (789)
                      ++-+.|+-|.||||++++|..++
T Consensus        29 ~~~lvGpnGaGKSTLl~~i~Gl~   51 (255)
T PRK11248         29 LLVVLGPSGCGKTTLLNLIAGFV   51 (255)
T ss_pred             EEEEECCCCCHHHHHHHHHHCCC
T ss_conf             99999999846999999997599


No 109
>TIGR00618 sbcc exonuclease SbcC; InterPro: IPR004592 All proteins in this family for which functions are known are part of an exonuclease complex with sbcD homologs. This complex is involved in the initiation of recombination to regulate the levels of palindromic sequences in DNA. SbcC may have nuclease activity that is functionally related to one of the nuclease activities of the RecBCD enzyme (IPR004586 from INTERPRO).; GO: 0004527 exonuclease activity, 0006259 DNA metabolic process.
Probab=90.00  E-value=0.31  Score=25.96  Aligned_cols=16  Identities=6%  Similarity=0.077  Sum_probs=7.7

Q ss_pred             CCCCCCHHHHHHHHHH
Q ss_conf             8875794789999988
Q gi|254781225|r  460 FVEGEPSQEFLDLVSG  475 (789)
Q Consensus       460 y~~~a~~p~~~~~l~~  475 (789)
                      +.|.+.|+.....+..
T Consensus       534 ~~~~~~~~~~~~~~~~  549 (1063)
T TIGR00618       534 LLPGADTSRLEAGEDE  549 (1063)
T ss_pred             HCCCCCCHHHHHHHHH
T ss_conf             2689861589999999


No 110
>PHA02244 ATPase-like protein
Probab=90.00  E-value=1.1  Score=22.38  Aligned_cols=130  Identities=15%  Similarity=0.134  Sum_probs=82.9

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHCC--CC-CCCCCHHHHHHCCCCCCCCCCHHHHHH-CCCEEEEEECCCCCCCCCCC
Q ss_conf             379999707886257899999997233--00-034426764201245555689889973-89809999346777601310
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYAFGN--QY-VINAEASDIMQNRPPEAGKANPSLIRL-MGSRIVIISETNENDEINAA  576 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~llG~--~~-~~~~~~~~~~~~~~~~~~~~~~~la~l-~g~r~~~~~E~~~~~~~~~~  576 (789)
                      -.-+++.|+.++||.....-|...|--  |. .+......+.+-..+++.-+...+.+. ..--+....|.+.+..-.-.
T Consensus       119 nipV~L~G~AGsGKt~~A~qIA~aLdl~FYf~gAI~~ef~L~Gf~DAnG~yh~T~f~kaFk~GGLfLlDEiDASnP~aL~  198 (383)
T PHA02244        119 NIPVFLKGGAGSGKNHIAEQIAEALDLDFYFMNAIMDEFELKGFIDANGKFHETPFYEAFKKGGLFFIDEIDASIPEALI  198 (383)
T ss_pred             CCCEEEECCCCCCHHHHHHHHHHHHCCCCEECHHHHHHHHCCCEECCCCCEECCHHHHHHHCCCEEEEEHHCCCCHHHHH
T ss_conf             98569975888863489999999858882441323013430125648996726389999861887997320044879999


Q ss_pred             EEEEEECCCEEEEEECCCCCCEEEECCEEEEEECCCCCCC-------CC-CCCCEEEEEEEEECCC
Q ss_conf             0245415985873210478606871452899973886342-------67-9841664689996588
Q gi|254781225|r  577 KIKQMTGGDCMTARLNYGNTYSESPASFTPFIVPNKHLFV-------RN-PDDAWWRRYIVIPFDK  634 (789)
Q Consensus       577 ~~K~ltggD~i~ar~~~~~~~~~~~p~~~~~~~~N~~P~~-------~~-~d~~~~rR~~iipF~~  634 (789)
                      .|-+-+.++.+  ++.  +..+..-+.|.++-++|..=.-       +. -|.|...|+..|||..
T Consensus       199 ~lNaALAN~fm--~FP--dG~V~~HedFr~IAagNT~G~Gad~~YVGRnqLD~ATLDRFv~ie~~Y  260 (383)
T PHA02244        199 IINSAIANKFF--DFA--DERVTAHEDFRVISAGNTLGKGADHIYVARNKIDGATLDRFAPIEFDY  260 (383)
T ss_pred             HHHHHHHCCCC--CCC--CCHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCHHHHHHEEECCCCC
T ss_conf             99899864763--476--421100576389972465677887221144545646462036445683


No 111
>cd03234 ABCG_White The White subfamily represents ABC transporters homologous to the Drosophila white gene, which acts as a dimeric importer for eye pigment precursors.  The eye pigmentation of Drosophila is developed from the synthesis and deposition in the cells of red pigments, which are synthesized from guanine, and brown pigments, which are synthesized from tryptophan.  The pigment precursors are encoded by the white, brown, and scarlet genes, respectively.  Evidence from genetic and biochemical studies suggest that the White and Brown proteins function as heterodimers to import guanine, while the White and Scarlet proteins function to import tryptophan.  However, a recent study also suggests that White may be involved in the transport of a metabolite, such as 3-hydroxykynurenine, across intracellular membranes.  Mammalian ABC transporters belonging to the White subfamily (ABCG1, ABCG5, and ABCG8) have been shown to be involved in the regulation of lipid-trafficking mechanisms in 
Probab=89.97  E-value=0.19  Score=27.26  Aligned_cols=30  Identities=30%  Similarity=0.443  Sum_probs=23.5

Q ss_pred             CCCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             743379999707886257899999997233
Q gi|254781225|r  498 NKAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       498 ~~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      .....++-+.|+-++||||++++|..++..
T Consensus        30 i~~Ge~~~ilGpnGsGKSTLl~~i~G~~~~   59 (226)
T cd03234          30 VESGQVMAILGSSGSGKTTLLDAISGRVEG   59 (226)
T ss_pred             EECCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             918809999989996099999999678978


No 112
>PRK08903 hypothetical protein; Validated
Probab=89.94  E-value=0.63  Score=23.88  Aligned_cols=138  Identities=12%  Similarity=0.120  Sum_probs=66.6

Q ss_pred             CCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHH
Q ss_conf             78888757947899999888799999999999999997598743379999707886257899999997233000344267
Q gi|254781225|r  457 GTPFVEGEPSQEFLDLVSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEAS  536 (789)
Q Consensus       457 ~~~y~~~a~~p~~~~~l~~~~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~  536 (789)
                      ++.++|..   .|+.|+..  ++..++..+.++..    .... ..++++||+.|+|||=++..+.+-.......+.-  
T Consensus         8 ~~~l~~~~---tfdnFv~g--~n~~~~~~l~~~~~----~~~~-~~~l~i~G~~G~GKTHLl~a~~~~~~~~~~~~~y--   75 (227)
T PRK08903          8 DLGPPPPP---TFDNFIAG--ENAELVTRLRELAA----GPVA-DRFFYLWGEAGSGRSHLLQALVAAASEGGKNARY--   75 (227)
T ss_pred             CCCCCCCC---CHHCCCCC--CHHHHHHHHHHHHH----CCCC-CCEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEE--
T ss_conf             99999987---64315577--75999999998874----3887-8669998999998889999999999806997499--


Q ss_pred             HHHHCCCCCCCCCCHHHHHHCCCEEEEEECCCCCCCCCCCEEEEEECCCEEEEEECCCCCCEEEE--CCEEEEEECCCCC
Q ss_conf             64201245555689889973898099993467776013100245415985873210478606871--4528999738863
Q gi|254781225|r  537 DIMQNRPPEAGKANPSLIRLMGSRIVIISETNENDEINAAKIKQMTGGDCMTARLNYGNTYSESP--ASFTPFIVPNKHL  614 (789)
Q Consensus       537 ~~~~~~~~~~~~~~~~la~l~g~r~~~~~E~~~~~~~~~~~~K~ltggD~i~ar~~~~~~~~~~~--p~~~~~~~~N~~P  614 (789)
                       +...      .....+.......++++.+.+.   ++         ++. . ..+| .-+....  -...++++++..|
T Consensus        76 -l~~~------~~~~~~~~~~~~d~l~iDDi~~---i~---------~~~-q-~~lF-~l~N~~~~~~~~~ll~s~~~~p  133 (227)
T PRK08903         76 -LDPA------SPLLAFDFDPRAELYAVDDVER---LD---------DAQ-Q-IALF-NLFNRVRAHGKTALLVAGPAAP  133 (227)
T ss_pred             -ECCC------CCHHHHHHHHCCCEEEEECCCC---CC---------CHH-H-HHHH-HHHHHHHHCCCCEEEECCCCCH
T ss_conf             -6511------0457774200189899964114---89---------569-9-9999-9999999729948997189971


Q ss_pred             CCCCCCCCEEEEEE
Q ss_conf             42679841664689
Q gi|254781225|r  615 FVRNPDDAWWRRYI  628 (789)
Q Consensus       615 ~~~~~d~~~~rR~~  628 (789)
                      ..-+...-+-.|+.
T Consensus       134 ~~l~~~~DL~SRl~  147 (227)
T PRK08903        134 LALDVREDLRTRLG  147 (227)
T ss_pred             HHCCCCHHHHHHHH
T ss_conf             20120089999993


No 113
>PRK09270 frcK putative fructose transport system kinase; Reviewed
Probab=89.93  E-value=1.1  Score=22.18  Aligned_cols=33  Identities=30%  Similarity=0.353  Sum_probs=25.8

Q ss_pred             CCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCC
Q ss_conf             874337999970788625789999999723300
Q gi|254781225|r  497 GNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQY  529 (789)
Q Consensus       497 ~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~  529 (789)
                      ......++-+-|+.++|||||.+.|...|+...
T Consensus        30 ~~~rR~lIgIaG~pGSGKSTlA~~l~~~L~~~~   62 (230)
T PRK09270         30 EPQRRTVVGIAGPPGAGKSTLAETLWEALSQQG   62 (230)
T ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHCC
T ss_conf             999718999989998899999999999986237


No 114
>PRK13646 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=89.92  E-value=0.29  Score=26.13  Aligned_cols=30  Identities=33%  Similarity=0.459  Sum_probs=22.7

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             433799997078862578999999972330
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      ..-.++-+.|+.|+||||++++|..++...
T Consensus        31 ~~Ge~~aiiG~nGsGKSTLl~~l~GLl~p~   60 (286)
T PRK13646         31 EQGKYYAIVGQTGSGKSTLIQNINALLKPT   60 (286)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCCC
T ss_conf             699899999999981999999997078888


No 115
>PRK06893 DNA replication initiation factor; Validated
Probab=89.90  E-value=1.1  Score=22.20  Aligned_cols=87  Identities=18%  Similarity=0.167  Sum_probs=46.8

Q ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCC--CCCCHHHHHHCCCC
Q ss_conf             7899999888799999999999999997598743379999707886257899999997233000--34426764201245
Q gi|254781225|r  467 QEFLDLVSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYV--INAEASDIMQNRPP  544 (789)
Q Consensus       467 p~~~~~l~~~~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~--~~~~~~~~~~~~~~  544 (789)
                      +.|+.|+..  .+.+++..+++.+.      .....++++||+.|+|||-+++.+.+-+-..+.  .-.+..... ..  
T Consensus        13 ~tfdnF~~~--~n~~~~~~l~~~~~------~~~~~~l~i~G~~gsGKTHLLqa~~~~~~~~~~~~~yi~~~~~~-~~--   81 (229)
T PRK06893         13 ETLDNFYSD--NNLLLLDSLRKNFI------DLKQPFFYIWGGKSSGKSHLLKAVSNHYLLNQRTAIYIPLSKSQ-YF--   81 (229)
T ss_pred             CCHHCCCCC--CHHHHHHHHHHHCC------CCCCCEEEEECCCCCCHHHHHHHHHHHHHHHCCCEEEEEHHHHH-HC--
T ss_conf             654315468--74999999997550------24698799989999988999999999999718985999737756-40--


Q ss_pred             CCCCCCHHHHHHCCCEEEEEECCC
Q ss_conf             555689889973898099993467
Q gi|254781225|r  545 EAGKANPSLIRLMGSRIVIISETN  568 (789)
Q Consensus       545 ~~~~~~~~la~l~g~r~~~~~E~~  568 (789)
                          ....+..+...-++++++.+
T Consensus        82 ----~~~~l~~l~~~d~l~iDDi~  101 (229)
T PRK06893         82 ----SPAVLENLEQQDLVCLDDLQ  101 (229)
T ss_pred             ----CHHHHHHHHHCCEEEEECHH
T ss_conf             ----69999876547979996723


No 116
>PRK13540 cytochrome c biogenesis protein CcmA; Provisional
Probab=89.88  E-value=0.25  Score=26.54  Aligned_cols=29  Identities=34%  Similarity=0.660  Sum_probs=23.8

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             33799997078862578999999972330
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      .-.++.+.|+-|+||||++++|..++-..
T Consensus        26 ~G~i~~l~G~NGaGKSTLlkli~Gl~~p~   54 (200)
T PRK13540         26 AGGLLHLKGSNGAGKTTLLKLIAGLLNPE   54 (200)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHCCCCCC
T ss_conf             99799998899987999999997785889


No 117
>cd03257 ABC_NikE_OppD_transporters The ABC transporter subfamily specific for the transport of dipeptides, oligopeptides (OppD), and nickel (NikDE).  The NikABCDE system of E. coli belongs to this family and is composed of the periplasmic binding protein NikA, two integral membrane components (NikB and NikC), and two ATPase (NikD and NikE).  The NikABCDE transporter is synthesized under anaerobic conditions to meet the increased demand for nickel resulting from hydrogenase synthesis.  The molecular mechanism of nickel uptake in many bacteria and most archaea is not known.  Many other members of this ABC family are also involved in the uptake of dipeptides and oligopeptides.  The oligopeptide transport system (Opp) is a five-component ABC transport composed of a membrane-anchored substrate binding proteins (SRP), OppA, two transmembrane proteins, OppB and OppC, and two ATP-binding domains, OppD and OppF.
Probab=89.83  E-value=0.26  Score=26.44  Aligned_cols=29  Identities=34%  Similarity=0.343  Sum_probs=22.9

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             43379999707886257899999997233
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ...-++-+.|+.|+||||++++|..++-.
T Consensus        29 ~~Ge~~~iiG~sGsGKSTLl~~i~Gl~~p   57 (228)
T cd03257          29 KKGETLGLVGESGSGKSTLARAILGLLKP   57 (228)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             69989999999998699999999728987


No 118
>cd03261 ABC_Org_Solvent_Resistant ABC (ATP-binding cassette) transport system involved in resistant to organic solvents; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.  The nucleotide binding domain shows the highest similarity between all members of the family.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=89.82  E-value=0.25  Score=26.49  Aligned_cols=28  Identities=39%  Similarity=0.522  Sum_probs=19.6

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             4337999970788625789999999723
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      ..-.++-+.|+.|+||||++++|..++-
T Consensus        24 ~~Ge~~~iiG~SGsGKSTll~~i~gL~~   51 (235)
T cd03261          24 RRGEILAIIGPSGSGKSTLLRLIVGLLR   51 (235)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCC
T ss_conf             7998999999999729999999975999


No 119
>cd03300 ABC_PotA_N PotA is an ABC-type transporter and the ATPase component of the spermidine/putrescine-preferential uptake system consisting of PotA, -B, -C, and -D.  PotA has two domains with the N-terminal domain containing the ATPase activity and the residues required for homodimerization with PotA and heterdimerization with PotB.  ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.  The nucleotide binding domain shows the highest similarity between all members of the family.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=89.80  E-value=0.25  Score=26.59  Aligned_cols=27  Identities=33%  Similarity=0.455  Sum_probs=19.4

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             337999970788625789999999723
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      .-.++.+.|+.|+||||++++|..+.-
T Consensus        25 ~Ge~~~iiGpSGsGKSTllr~i~Gl~~   51 (232)
T cd03300          25 EGEFFTLLGPSGCGKTTLLRLIAGFET   51 (232)
T ss_pred             CCCEEEEECCCCCHHHHHHHHHHCCCC
T ss_conf             998999999999839999999977999


No 120
>cd03231 ABC_CcmA_heme_exporter CcmA, the ATP-binding component of the bacterial CcmAB transporter.  The CCM family is involved in bacterial cytochrome c biogenesis.  Cytochrome c maturation in E. coli requires the ccm operon, which encodes eight membrane proteins (CcmABCDEFGH).  CcmE is a periplasmic heme chaperone that binds heme covalently and transfers it onto apocytochrome c in the presence of CcmF, CcmG, and CcmH.  The CcmAB proteins represent an ABC transporter and the CcmCD proteins participate in heme transfer to CcmE.
Probab=89.77  E-value=0.29  Score=26.15  Aligned_cols=29  Identities=28%  Similarity=0.397  Sum_probs=23.8

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             33799997078862578999999972330
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      .-.++.+.|+-|.|||||+++|..++-..
T Consensus        25 ~Ge~~~l~G~NGsGKSTLlk~i~Gl~~p~   53 (201)
T cd03231          25 AGEALQVTGPNGSGKTTLLRILAGLSPPL   53 (201)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHCCCCCC
T ss_conf             99599999999999999999996677888


No 121
>pfam09079 Cdc6_C CDC6, C terminal. The C terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity.
Probab=89.68  E-value=1.1  Score=22.16  Aligned_cols=64  Identities=16%  Similarity=0.209  Sum_probs=44.9

Q ss_pred             CCCEECHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCCCCCCEEEECCCCCCCCEEEEEEEC
Q ss_conf             88411179999999999985046675554525689999863542333100102567652089979865
Q gi|254781225|r  705 ENLWEESHSLAKSYSEYREQELNYDRKRISTRTVTLNLKQKGFIGGIKREKIEKEWKSKRIIKGLKLK  772 (789)
Q Consensus       705 ~~~~~~~~~l~~~y~~~~~~~~~~~~~~~s~~~~~~~l~~~g~~~~~~~~~~~~~~~~~r~~~Gi~Lk  772 (789)
                      ........++|+.|.+-|+..   +..++|++.|..-+.++.+.|-+..+...++.+.+| .+-++|.
T Consensus        12 ~~~~~~tg~vy~~Y~~lc~~~---~~~~lt~rr~~~~l~~L~~~gii~~~~~~~G~~~G~-~~~~~L~   75 (85)
T pfam09079        12 GTPETTTGEVYEVYKELCEEL---GVDPLTQRRISDLLSELEMLGILETEVVSRGRGGGR-TKKISLN   75 (85)
T ss_pred             CCCCCCHHHHHHHHHHHHHHH---CCCCCCHHHHHHHHHHHHHCCCCEEEEECCCCCCCE-EEEEEEC
T ss_conf             999872789999999999982---987652999999999999658500578148867864-7899833


No 122
>cd03297 ABC_ModC_molybdenum_transporter ModC is an ABC-type transporter and the ATPase component of a molybdate transport system that also includes the periplasmic binding protein ModA and the membrane protein ModB. ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules. The nucleotide binding domain shows the highest similarity between all members of the family.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=89.67  E-value=0.26  Score=26.41  Aligned_cols=25  Identities=36%  Similarity=0.406  Sum_probs=20.7

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             3799997078862578999999972
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~ll  525 (789)
                      .-++-+.|+.+.||||++++|..+.
T Consensus        23 ge~~~iiGpSGsGKSTll~~i~GL~   47 (214)
T cd03297          23 EEVTGIFGASGAGKSTLLRCIAGLE   47 (214)
T ss_pred             CCEEEEECCCCCHHHHHHHHHHCCC
T ss_conf             9799999999735999999998499


No 123
>cd00066 G-alpha G protein alpha subunit.  The alpha subunit of G proteins contains the guanine nucleotide binding site. The heterotrimeric GNP-binding proteins are signal transducers that communicate signals from many hormones, neurotransmitters, chemokines, and autocrine and paracrine factors. Extracellular signals are received by receptors, which activate the G proteins, which in turn route the signals to several distinct intracellular signaling pathways. The alpha subunit of G proteins is a weak GTPase. In the resting state, heterotrimeric G proteins are associated at the cytosolic face of the plasma membrane and the alpha subunit binds to GDP. Upon activation by a receptor GDP is replaced with GTP, and the G-alpha/GTP complex dissociates from the beta and gamma subunits. This results in activation of downstream signaling pathways, such as cAMP synthesis by adenylyl cyclase, which is terminated when GTP is hydrolized and the heterotrimers reconstitute.
Probab=89.66  E-value=0.35  Score=25.54  Aligned_cols=19  Identities=5%  Similarity=-0.108  Sum_probs=9.9

Q ss_pred             CCCCCHHHHHHHHHHHHCC
Q ss_conf             7886257899999997233
Q gi|254781225|r  509 VGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       509 ~G~nGKSt~~~~l~~llG~  527 (789)
                      ...|=+.||-.+-..++..
T Consensus       295 Dt~~i~~vf~~v~d~I~~~  313 (317)
T cd00066         295 DTENIRFVFDAVKDIILQN  313 (317)
T ss_pred             CHHHHHHHHHHHHHHHHHH
T ss_conf             5289999999999999998


No 124
>COG0470 HolB ATPase involved in DNA replication [DNA replication, recombination, and repair]
Probab=89.65  E-value=0.54  Score=24.30  Aligned_cols=129  Identities=19%  Similarity=0.164  Sum_probs=62.3

Q ss_pred             HHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCC-C-----------------CCCHHHHHHCCCCCCC
Q ss_conf             999999997598743379999707886257899999997233000-3-----------------4426764201245555
Q gi|254781225|r  486 FTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYV-I-----------------NAEASDIMQNRPPEAG  547 (789)
Q Consensus       486 l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~-~-----------------~~~~~~~~~~~~~~~~  547 (789)
                      +++...+..... +.+..++++|+-+.||+|+...+...++.... .                 ..+...+........+
T Consensus        10 ~~~l~~~~~~~~-~~~halL~~Gp~G~Gktt~a~~lA~~l~~~~~~~~~~~~~~~~~~~~~~~~~~d~lel~~s~~~~~~   88 (325)
T COG0470          10 VKRLLVQALESG-RLPHALLFYGPPGVGKTTAALALAKELLCENPTGLLPCGHCRSCKLIPAGNHPDFLELNPSDLRKID   88 (325)
T ss_pred             HHHHHHHHHHCC-CCCCCEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCCCCCEEEECCCCCCCCC
T ss_conf             999999998658-8876100379999978999999999965866433455200224443202568865997732133330


Q ss_pred             CCCHH----HHH-------HCCCEEEEEECCCCCCCCCCCEEEEEECCCEEEEEECCCCCCEEEECCEEEEEECCCCCCC
Q ss_conf             68988----997-------3898099993467776013100245415985873210478606871452899973886342
Q gi|254781225|r  548 KANPS----LIR-------LMGSRIVIISETNENDEINAAKIKQMTGGDCMTARLNYGNTYSESPASFTPFIVPNKHLFV  616 (789)
Q Consensus       548 ~~~~~----la~-------l~g~r~~~~~E~~~~~~~~~~~~K~ltggD~i~ar~~~~~~~~~~~p~~~~~~~~N~~P~~  616 (789)
                       ..-+    +++       .-+.+++++.|.+.-..            |...|  + .+...+......+++.||..-.+
T Consensus        89 -i~~~~vr~~~~~~~~~~~~~~~kviiidead~mt~------------~A~na--l-lk~lEep~~~~~~il~~n~~~~i  152 (325)
T COG0470          89 -IIVEQVRELAEFLSESPLEGGYKVVIIDEADKLTE------------DAANA--L-LKTLEEPPKNTRFILITNDPSKI  152 (325)
T ss_pred             -CHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCH------------HHHHH--H-HHHCCCCCCCEEEEEEECCHHHC
T ss_conf             -06999999998604465667726999732032698------------88876--7-54332488871699974985556


Q ss_pred             CCCCCCEEEEEEEEECCC
Q ss_conf             679841664689996588
Q gi|254781225|r  617 RNPDDAWWRRYIVIPFDK  634 (789)
Q Consensus       617 ~~~d~~~~rR~~iipF~~  634 (789)
                      ..   -+-.|..+|.|..
T Consensus       153 l~---tI~SRc~~i~f~~  167 (325)
T COG0470         153 LP---TIRSRCQRIRFKP  167 (325)
T ss_pred             HH---HHHHHEEEEECCC
T ss_conf             47---8775607887677


No 125
>smart00275 G_alpha G protein alpha subunit. Subunit of G proteins that contains the guanine nucleotide binding site
Probab=89.64  E-value=0.35  Score=25.54  Aligned_cols=47  Identities=4%  Similarity=-0.019  Sum_probs=20.6

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCEEEEEEE--CCCCCHHHHHHHHHHHHC
Q ss_conf             99999999999999759874337999970--788625789999999723
Q gi|254781225|r  480 EEVMDYFTRCVGMALLGGNKAQRFIHIRG--VGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       480 ~e~~~~l~~~~g~~l~g~~~~~~~~~~~G--~G~nGKSt~~~~l~~llG  526 (789)
                      ++...|+...+-...........+..++=  ...|=+-||..+-..++.
T Consensus       287 ~~~~~fi~~~F~~~~~~~~~r~~y~h~T~AtDt~~i~~vf~~v~d~Il~  335 (342)
T smart00275      287 EAAAKFIKQKFLRLNRNSSRKSIYHHFTCATDTRNIRVVFDAVKDIILQ  335 (342)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCEEEEECCEECHHHHHHHHHHHHHHHHH
T ss_conf             9999999999998577988972686667314508899999999999999


No 126
>PRK13644 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=89.62  E-value=0.3  Score=26.04  Aligned_cols=24  Identities=42%  Similarity=0.516  Sum_probs=12.4

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             799997078862578999999972
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~ll  525 (789)
                      .++-+.|+-|+||||++++|..++
T Consensus        29 e~vaiiG~nGsGKSTL~~~l~Gll   52 (274)
T PRK13644         29 EYIGIIGKNGSGKSTLALHLNGLL   52 (274)
T ss_pred             CEEEEECCCCCHHHHHHHHHHCCC
T ss_conf             999999999980999999997068


No 127
>PRK10771 thiQ thiamine transporter ATP-binding subunit; Provisional
Probab=89.62  E-value=0.29  Score=26.10  Aligned_cols=31  Identities=35%  Similarity=0.414  Sum_probs=24.8

Q ss_pred             CCCCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             7433799997078862578999999972330
Q gi|254781225|r  498 NKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       498 ~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      ...-.++-+.|+-|.||||++++|..++...
T Consensus        22 i~~GE~v~iiG~nGaGKSTLl~~i~Gll~p~   52 (233)
T PRK10771         22 VERGEQVAILGPSGAGKSTLLNLIAGFLTPA   52 (233)
T ss_pred             ECCCCEEEEECCCCCHHHHHHHHHHCCCCCC
T ss_conf             8899899999999981999999996599998


No 128
>PRK13833 conjugal transfer protein TrbB; Provisional
Probab=89.62  E-value=1  Score=22.53  Aligned_cols=49  Identities=27%  Similarity=0.285  Sum_probs=32.6

Q ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             999998887999999999999999975987433799997078862578999999972
Q gi|254781225|r  469 FLDLVSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       469 ~~~~l~~~~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~ll  525 (789)
                      .++++..=+-.++..+||..++        +.++-++..|..++||+||+|.|...+
T Consensus       120 l~dlv~~g~~t~~~~~~L~~aV--------~~r~nilVsGgTGSGKTTllnaL~~~i  168 (323)
T PRK13833        120 LDDYVRSKVMTEAQASTIRSAI--------SSRLNIVISGGTGSGKTTLANAVIAEI  168 (323)
T ss_pred             HHHHHHCCCCCHHHHHHHHHHH--------HCCCCEEEECCCCCCHHHHHHHHHHHH
T ss_conf             9999876999999999999999--------818968999177775689999999864


No 129
>pfam07931 CPT Chloramphenicol phosphotransferase-like protein. The members of this family are all similar to chloramphenicol 3-O phosphotransferase (CPT) expressed by Streptomyces venezuelae. Chloramphenicol (Cm) is a metabolite produced by this bacterium that can inhibit ribosomal peptidyl transferase activity and therefore protein production. By transferring a phosphate group to the C-3 hydroxyl group of Cm, CPT inactivates this potentially lethal metabolite.
Probab=89.61  E-value=0.45  Score=24.86  Aligned_cols=34  Identities=24%  Similarity=0.429  Sum_probs=27.0

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHHCCCC-CCCCCH
Q ss_conf             7999970788625789999999723300-034426
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYAFGNQY-VINAEA  535 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~llG~~~-~~~~~~  535 (789)
                      .+++|.|++++|||++...|+.++..-. ..+.+.
T Consensus         2 ~II~LNG~SSsGKSsiAraLQ~~l~~p~~h~~vD~   36 (174)
T pfam07931         2 RIILLNGGSSSGKSSIARALQDILDGPWLHFGVDA   36 (174)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHCCCCEEEEEHHH
T ss_conf             19997489988879999999984747467642858


No 130
>TIGR00929 VirB4_CagE type IV secretion/conjugal transfer ATPase, VirB4 family; InterPro: IPR004346   This family includes the Helicobacter pylori protein CagE (see examples), which together with other proteins from the cag pathogenicity island (PAI), encodes a type IV transporter secretion system. The precise role of CagE is not known, but studies in animal models have shown that it is essential for pathogenesis in Helicobacter pylori induced gastritis and peptic ulceration . Indeed, the expression of the cag PAI has been shown to be essential for stimulating human gastric epithelial cell apoptosis in vitro .    Similar type IV transport systems are also found in other bacteria. This family includes proteins from the trb and Vir conjugal transfer systems in Agrobacterium tumefaciens and homologues of VirB proteins from other species.; GO: 0005524 ATP binding.
Probab=89.61  E-value=0.32  Score=25.85  Aligned_cols=26  Identities=35%  Similarity=0.415  Sum_probs=23.1

Q ss_pred             EEEECCCCCHHHHHHHHHHHHCCCCC
Q ss_conf             99707886257899999997233000
Q gi|254781225|r  505 HIRGVGGSGKSTLMNLIKYAFGNQYV  530 (789)
Q Consensus       505 ~~~G~G~nGKSt~~~~l~~llG~~~~  530 (789)
                      +++|+.|+|||||++.|.+-++.|..
T Consensus       520 ~IfG~~G~GKTtLl~fL~a~~~ky~~  545 (931)
T TIGR00929       520 LIFGPTGSGKTTLLNFLLAQLQKYKP  545 (931)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHCCCC
T ss_conf             78888898469999999999742488


No 131
>cd03249 ABC_MTABC3_MDL1_MDL2 MTABC3 (also known as ABCB6) is a mitochondrial ATP-binding cassette protein involved in iron homeostasis and one of four ABC transporters expressed in the mitochondrial inner membrane, the other three being MDL1(ABC7), MDL2, and ATM1.  In fact, the yeast MDL1 (multidrug resistance-like protein 1) and MDL2 (multidrug resistance-like protein 2) transporters are also included in this CD.  MDL1 is an ATP-dependent permease that acts as a high-copy suppressor of ATM1 and is thought to have a role in resistance to oxidative stress. Interestingly, subfamily B is more closely related to the carboxyl-terminal component of subfamily C than the two halves of ABCC molecules are with one another.
Probab=89.60  E-value=0.31  Score=25.96  Aligned_cols=26  Identities=27%  Similarity=0.554  Sum_probs=16.9

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             37999970788625789999999723
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      -.++.++|+-|+||||++++|..++-
T Consensus        29 G~~iaIvG~sGsGKSTLl~ll~gl~~   54 (238)
T cd03249          29 GKTVALVGSSGCGKSTVVSLLERFYD   54 (238)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHCCC
T ss_conf             99999999999989999999823861


No 132
>PRK13634 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=89.59  E-value=0.26  Score=26.44  Aligned_cols=29  Identities=31%  Similarity=0.450  Sum_probs=21.9

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             43379999707886257899999997233
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ..-.++-+.|+.|+||||++++|..++-.
T Consensus        18 ~~Ge~vaiiG~sGsGKSTLl~~l~GLl~P   46 (276)
T PRK13634         18 PSGSYVAIIGHTGSGKSTLLQHLNGLLKP   46 (276)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             89989999999996999999999749998


No 133
>PRK10584 putative ABC transporter ATP-binding protein YbbA; Provisional
Probab=89.54  E-value=0.26  Score=26.46  Aligned_cols=30  Identities=33%  Similarity=0.385  Sum_probs=23.5

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             433799997078862578999999972330
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      ...-++-+.|+-|+||||++++|..++-..
T Consensus        34 ~~GE~v~ivG~sGsGKSTLl~~i~Gl~~p~   63 (228)
T PRK10584         34 KRGETIALIGESGSGKSTLLAILAGLDDGS   63 (228)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCCC
T ss_conf             999899999999858999999996699999


No 134
>PRK13651 cobalt transporter ATP-binding subunit; Provisional
Probab=89.51  E-value=0.28  Score=26.23  Aligned_cols=27  Identities=33%  Similarity=0.472  Sum_probs=16.9

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             379999707886257899999997233
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      --++-+.|+-|+|||||+++|..++-.
T Consensus        33 GE~v~IiG~nGsGKSTL~k~l~Gll~P   59 (304)
T PRK13651         33 GEFIAIIGQTGSGKTTFIEHLNALLLP   59 (304)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             989999879998599999999669998


No 135
>PRK05642 DNA replication initiation factor; Validated
Probab=89.36  E-value=1.3  Score=21.76  Aligned_cols=97  Identities=16%  Similarity=0.304  Sum_probs=53.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCC--CCCCC
Q ss_conf             7888875794789999988879999999999999999759874337999970788625789999999723300--03442
Q gi|254781225|r  457 GTPFVEGEPSQEFLDLVSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQY--VINAE  534 (789)
Q Consensus       457 ~~~y~~~a~~p~~~~~l~~~~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~--~~~~~  534 (789)
                      ++..++.   ..|+.|+..  .+.....++.+++--   .......+++++|+.|+|||-++..++.-+...+  +.-.+
T Consensus         9 ~~~l~~~---~tfdnFi~g--~N~~a~~~~~~l~~~---~~~~~~~~l~i~G~~G~GKTHLL~A~~~~~~~~~~~~~yl~   80 (234)
T PRK05642          9 GVRLRDD---ATFANYYPG--ANAAALGYVERLCEA---DAGWTESLIYLWGKDGVGRSHLLQAACLRFEQRGEPAVYLP   80 (234)
T ss_pred             CCCCCCC---CCHHCCCCC--CCHHHHHHHHHHHHC---CCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEEE
T ss_conf             9999997---773035718--759999999998760---67877883899889999889999999999980799679978


Q ss_pred             HHHHHHCCCCCCCCCCHHHHHHCCCEEEEEECCC
Q ss_conf             6764201245555689889973898099993467
Q gi|254781225|r  535 ASDIMQNRPPEAGKANPSLIRLMGSRIVIISETN  568 (789)
Q Consensus       535 ~~~~~~~~~~~~~~~~~~la~l~g~r~~~~~E~~  568 (789)
                      ...+...       ....+-.+...-++++++.+
T Consensus        81 ~~~~~~~-------~~~~~~~l~~~d~l~IDDi~  107 (234)
T PRK05642         81 LAELLDR-------GPELLDNLEQYELVCIDDLD  107 (234)
T ss_pred             HHHHHHH-------HHHHHHHHHHCCEEEEECHH
T ss_conf             9998754-------49998624227989893645


No 136
>cd03255 ABC_MJ0796_Lo1CDE_FtsE This family is comprised of MJ0796 ATP-binding cassette, macrolide-specific ABC-type efflux carrier (MacAB), and proteins involved in cell division (FtsE), and release of liporoteins from the cytoplasmic membrane (LolCDE).  They are clustered together phylogenetically.  MacAB is an exporter that confers resistance to macrolides, while the LolCDE system is not a transporter at all.  An FtsE null mutants showed filamentous growth and appeared viable on high salt medium only, indicating a role for FtsE in cell division and/or salt transport.  The LolCDE complex catalyses the release of lipoproteins from the cytoplasmic membrane prior to their targeting to the outer membrane.
Probab=89.32  E-value=0.28  Score=26.20  Aligned_cols=30  Identities=37%  Similarity=0.484  Sum_probs=23.5

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             433799997078862578999999972330
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      .+-.++.+.|+.|+|||||+++|..++-..
T Consensus        28 ~~Ge~~~iiG~sGsGKTTll~~i~Gl~~p~   57 (218)
T cd03255          28 EKGEFVAIVGPSGSGKSTLLNILGGLDRPT   57 (218)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCCC
T ss_conf             699899999999986999999996699999


No 137
>cd03295 ABC_OpuCA_Osmoprotection OpuCA is a the ATP binding component of a bacterial solute transporter that serves a protective role to cells growing in a hyperosmolar environment.  ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.  The nucleotide binding domain shows the highest similarity between all members of the family.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition, to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=89.32  E-value=0.28  Score=26.17  Aligned_cols=28  Identities=32%  Similarity=0.515  Sum_probs=19.7

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             4337999970788625789999999723
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      ....++.+.|+.|.||||++++|..++-
T Consensus        25 ~~Ge~~~ilGpSG~GKSTllr~i~gl~~   52 (242)
T cd03295          25 AKGEFLVLIGPSGSGKTTTMKMINRLIE   52 (242)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCC
T ss_conf             6998999999999569999999975999


No 138
>TIGR01087 murD UDP-N-acetylmuramoylalanine--D-glutamate ligase; InterPro: IPR005762   The bacterial cell wall provides strength and rigidity to counteract internal osmotic pressure, and protection against the environment. The peptidoglycan layer gives the cell wall its strength, and helps maintain the overall shape of the cell. The basic peptidoglycan structure of both Gram-positive and Gram-negative bacteria is comprised of a sheet of glycan chains connected by short cross-linking polypeptides. Biosynthesis of peptidoglycan is a multi-step (11-12 steps) process comprising three main stages:    (1) formation of UDP-N-acetylmuramic acid (UDPMurNAc) from N-acetylglucosamine (GlcNAc). (2) addition of a short polypeptide chain to the UDPMurNAc. (3) addition of a second GlcNAc to the disaccharide-pentapeptide building block and transport of this unit through the cytoplasmic membrane and incorporation into the growing peptidoglycan layer.    Stage two involves four key Mur ligase enzymes: MurC (6.3.2.8 from EC) , MurD (6.3.2.9 from EC) , MurE (6.3.2.13 from EC)  and MurF (6.3.2.10 from EC) . These four Mur ligases are responsible for the successive additions of L-alanine, D-glutamate, meso-diaminopimelate or L-lysine, and D-alanyl-D-alanine to UDP-N-acetylmuramic acid. All four Mur ligases are topologically similar to one another, even though they display low sequence identity. They are each composed of three domains: an N-terminal Rossmann-fold domain responsible for binding the UDPMurNAc substrate; a central domain (similar to ATP-binding domains of several ATPases and GTPases); and a C-terminal domain (similar to dihydrofolate reductase fold) that appears to be associated with binding the incoming amino acid. The conserved sequence motifs found in the four Mur enzymes also map to other members of the Mur ligase family, including folylpolyglutamate synthetase, cyanophycin synthetase and the capB enzyme from Bacillales .    This entry represents UDP-N-acetylmuramoylalanine-D-glutamate ligase (MurD). MurD catalyses the addition of d-glutamate to the nucleotide precursor UDP-N-acetylmuramoyl-l-alanine. ; GO: 0005524 ATP binding, 0008764 UDP-N-acetylmuramoylalanine-D-glutamate ligase activity, 0008360 regulation of cell shape, 0009252 peptidoglycan biosynthetic process, 0009273 peptidoglycan-based cell wall biogenesis, 0051301 cell division, 0005737 cytoplasm.
Probab=89.30  E-value=0.28  Score=26.26  Aligned_cols=50  Identities=16%  Similarity=0.149  Sum_probs=27.5

Q ss_pred             HHHHHHHHH---HHCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             478999998---887999999999999999975987433799997078862578999999972
Q gi|254781225|r  466 SQEFLDLVS---GYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       466 ~p~~~~~l~---~~~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~ll  525 (789)
                      .|.+.++..   .|.+|=|+   +.+.     .-.....+++-+  +|.|||||...++..||
T Consensus        80 hp~~~~a~~~g~~v~gdi~L---~~~~-----~~~~~~~~~~aI--TGTnGKtTTT~L~~~~L  132 (476)
T TIGR01087        80 HPLVQAAAKRGIPVVGDIEL---ALRL-----VDFPEPAKVVAI--TGTNGKTTTTSLLYHLL  132 (476)
T ss_pred             CHHHHHHHHCCCEEEEHHHH---HHHH-----CCCCCCCCEEEE--ECCCCHHHHHHHHHHHH
T ss_conf             77999999669808986799---9974-----157898737999--72686079999999999


No 139
>cd02023 UMPK Uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK), catalyzes the reversible phosphoryl transfer from ATP to uridine or cytidine to yield UMP or CMP. In the primidine nucleotide-salvage pathway, this enzyme combined with nucleoside diphosphate kinases further phosphorylates UMP and CMP to form UTP and CTP. This kinase also catalyzes the phosphorylation of several cytotoxic ribonucleoside analogs such as 5-flurrouridine and cyclopentenyl-cytidine.
Probab=89.30  E-value=0.33  Score=25.78  Aligned_cols=31  Identities=39%  Similarity=0.471  Sum_probs=24.0

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             9997078862578999999972330003442
Q gi|254781225|r  504 IHIRGVGGSGKSTLMNLIKYAFGNQYVINAE  534 (789)
Q Consensus       504 ~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~  534 (789)
                      +-+.|+.++|||||.+.|...|+...++.++
T Consensus         2 IgI~G~sgsGKTT~a~~L~~~l~~~~v~~i~   32 (198)
T cd02023           2 IGIAGGSGSGKTTVAEEIIEQLGNPKVVIIS   32 (198)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCCCEEEEE
T ss_conf             8988999885999999999980999858997


No 140
>cd03254 ABCC_Glucan_exporter_like Glucan exporter ATP-binding protein.  In A. tumefaciens cyclic beta-1, 2-glucan must be transported into the periplasmic space to exert its action as a virluence factor.  This subfamily belongs to the MRP-like family and is involved in drug, peptide, and lipid export.  The MRP-like family, similar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains each composed of six transmembrane (TM) helices and two nucleotide-binding domains (NBD).  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=89.27  E-value=0.3  Score=26.06  Aligned_cols=27  Identities=33%  Similarity=0.541  Sum_probs=17.7

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             337999970788625789999999723
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      ...++.++|+-++|||||+++|..++-
T Consensus        28 ~Ge~vaivG~sGsGKSTLl~ll~gl~~   54 (229)
T cd03254          28 PGETVAIVGPTGAGKTTLINLLMRFYD   54 (229)
T ss_pred             CCCEEEEECCCCCHHHHHHHHHHCCCC
T ss_conf             999999999999809999999966866


No 141
>COG2766 PrkA Putative Ser protein kinase [Signal transduction mechanisms]
Probab=89.27  E-value=0.73  Score=23.44  Aligned_cols=13  Identities=23%  Similarity=0.204  Sum_probs=4.6

Q ss_pred             EEEEEECCCCCCC
Q ss_conf             9999507310244
Q gi|254781225|r  103 LIPFRMNKEGIKK  115 (789)
Q Consensus       103 ~~~yr~~~~~~~~  115 (789)
                      +++|-+-+.+-++
T Consensus       104 qiL~LlGPVggGK  116 (649)
T COG2766         104 QILYLLGPVGGGK  116 (649)
T ss_pred             HHHEEECCCCCCH
T ss_conf             5530435678766


No 142
>PRK01156 chromosome segregation protein; Provisional
Probab=89.27  E-value=0.53  Score=24.39  Aligned_cols=10  Identities=20%  Similarity=0.524  Sum_probs=5.9

Q ss_pred             HCCEEEEECC
Q ss_conf             0788999234
Q gi|254781225|r   51 ACGFGFVCGV   60 (789)
Q Consensus        51 ~~giGi~~G~   60 (789)
                      ..|+=+++|+
T Consensus        22 ~~Gi~~I~G~   31 (895)
T PRK01156         22 DTGINIITGK   31 (895)
T ss_pred             CCCCEEEECC
T ss_conf             9992788899


No 143
>cd04104 p47_IIGP_like p47 (47-kDa) family.  The p47 GTPase family consists of several highly homologous proteins, including IGTP, TGTP/Mg21, IRG-47, GTPI, LRG-47, and IIGP1.  They are found in higher eukaryotes where they play a role in immune resistance against intracellular pathogens.  p47 proteins exist at low resting levels in mouse cells, but are strongly induced by Type II interferon (IFN-gamma).  ITGP is critical for resistance to Toxoplasma gondii infection and in involved in inhibition of Coxsackievirus-B3-induced apoptosis.  TGTP was shown to limit vesicular stomatitis virus (VSV) infection of fibroblasts in vitro.  IRG-47 is involved in resistance to T. gondii infection.  LRG-47 has been implicated in resistance to T. gondii, Listeria monocytogenes, Leishmania, and mycobacterial infections.  IIGP1 has been shown to localize to the ER and to the Golgi membranes in IFN-induced cells and inflamed tissues.  In macrophages, IIGP1 interacts with hook3, a microtubule binding protei
Probab=89.23  E-value=0.26  Score=26.48  Aligned_cols=22  Identities=32%  Similarity=0.576  Sum_probs=19.5

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             9999707886257899999997
Q gi|254781225|r  503 FIHIRGVGGSGKSTLMNLIKYA  524 (789)
Q Consensus       503 ~~~~~G~G~nGKSt~~~~l~~l  524 (789)
                      -+.++|..|+|||+|+|.++.+
T Consensus         3 ~iaVtGesGaGKSSfINAlRGl   24 (197)
T cd04104           3 NIAVTGESGAGKSSFINALRGV   24 (197)
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
T ss_conf             7999558998689999998688


No 144
>PRK13541 cytochrome c biogenesis protein CcmA; Provisional
Probab=89.21  E-value=0.29  Score=26.07  Aligned_cols=29  Identities=28%  Similarity=0.442  Sum_probs=23.7

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             43379999707886257899999997233
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ....+..+.|+-|+|||||+++|..++-.
T Consensus        24 ~~G~i~~i~G~NGsGKSTLlk~i~Gl~~p   52 (195)
T PRK13541         24 LPSAITYIKGANGCGKSSLLRMIAGIMQP   52 (195)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             79979999999998199999999679889


No 145
>PRK11629 lolD lipoprotein transporter ATP-binding subunit; Provisional
Probab=89.21  E-value=0.3  Score=26.05  Aligned_cols=29  Identities=34%  Similarity=0.402  Sum_probs=22.6

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             43379999707886257899999997233
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ..--++-+.|+-|+||||++++|..+.-.
T Consensus        33 ~~GE~v~iiG~sGsGKSTLl~~i~Gl~~p   61 (233)
T PRK11629         33 GEGEMMAIVGSSGSGKSTLLHLLGGLDTP   61 (233)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             89989999999994099999999669999


No 146
>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]
Probab=89.20  E-value=0.35  Score=25.60  Aligned_cols=14  Identities=0%  Similarity=-0.097  Sum_probs=7.4

Q ss_pred             HHHHHHHHHHHHHC
Q ss_conf             88999999998621
Q gi|254781225|r  226 HDEWIPVVMAVHHE  239 (789)
Q Consensus       226 yd~W~~vg~al~~~  239 (789)
                      +.-...+|.++.++
T Consensus        71 ~~LRr~IGYviQqi   84 (309)
T COG1125          71 VELRRKIGYVIQQI   84 (309)
T ss_pred             HHHHHHHHHHHHHC
T ss_conf             99987533542221


No 147
>PRK13641 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=89.19  E-value=0.28  Score=26.20  Aligned_cols=29  Identities=34%  Similarity=0.480  Sum_probs=22.4

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             43379999707886257899999997233
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ..-.++-+.|+-|+||||++++|..++-.
T Consensus        31 ~~Ge~~~iiG~nGsGKSTLl~~l~Gll~P   59 (286)
T PRK13641         31 EDGSFVALIGHTGSGKSTLMQHFNALLKP   59 (286)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             69999999999983999999999659898


No 148
>cd02026 PRK Phosphoribulokinase (PRK) is an enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes. This enzyme catalyzes the phosphorylation of D-ribulose 5-phosphate to form D-ribulose 1, 5-biphosphate, using ATP and NADPH produced by the primary reactions of photosynthesis.
Probab=89.18  E-value=0.32  Score=25.79  Aligned_cols=160  Identities=16%  Similarity=0.211  Sum_probs=75.8

Q ss_pred             EEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCCCCCHHHHHHCCCEEEEEECCCCCCC-CCCCEEEEEEC
Q ss_conf             99707886257899999997233000344267642012455556898899738980999934677760-13100245415
Q gi|254781225|r  505 HIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEAGKANPSLIRLMGSRIVIISETNENDE-INAAKIKQMTG  583 (789)
Q Consensus       505 ~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~~~~~~~~la~l~g~r~~~~~E~~~~~~-~~~~~~K~ltg  583 (789)
                      =+.|..++||||+.+.|..+||...++.+..-..-.    -   .+.+...   +.+.. ..|+..+. +-...++.|-.
T Consensus         3 gVaG~SGSGKTTv~~~i~~ifg~~~v~vI~~D~Yhr----~---dr~~r~~---~~~t~-~~P~And~dll~~~l~~Lk~   71 (273)
T cd02026           3 GVAGDSGCGKSTFLRRLTSLFGSDLVTVICLDDYHS----L---DRKGRKE---TGITA-LDPRANNFDLMYEQLKALKE   71 (273)
T ss_pred             EEECCCCCCHHHHHHHHHHHHCCCCEEEEECCCCCC----C---CHHHHHH---HCCCC-CCCCHHHHHHHHHHHHHHHC
T ss_conf             997888786999999999985848769996577788----9---9899987---18776-89752349999999999985


Q ss_pred             CCEEEEEECCCCCCEEEECCEEEEEECCCCCCCCCCCCCEEEEEEEEECCCCCCCCCC-CHH-HHHCCCCHHHHHHHHHH
Q ss_conf             9858732104786068714528999738863426798416646899965887888787-833-42201204479999999
Q gi|254781225|r  584 GDCMTARLNYGNTYSESPASFTPFIVPNKHLFVRNPDDAWWRRYIVIPFDKPIANRDA-SFA-QKLETKYTLEAKKWFLK  661 (789)
Q Consensus       584 gD~i~ar~~~~~~~~~~~p~~~~~~~~N~~P~~~~~d~~~~rR~~iipF~~~~~~~d~-~~~-~~~~~~e~~~i~~w~l~  661 (789)
                      |-+|... .|.-..-.|.|.-          .+..      ..+++++=-+.+.+++. ++. -+. --....-+.|+-+
T Consensus        72 Gk~i~~P-vYdh~tg~~~~~e----------~i~p------~diII~EGLh~l~~~~lrdl~DLkI-fVD~d~dlr~~rK  133 (273)
T cd02026          72 GQAIEKP-IYNHVTGLIDPPE----------LIKP------TKIVVIEGLHPLYDERVRELLDFSV-YLDISDEVKFAWK  133 (273)
T ss_pred             CCCCCCC-CCCCCCCCCCCCE----------EECC------CCEEEEECEECCCCHHHHHHHCEEE-EECCCHHHHHHHH
T ss_conf             9953432-2214589657756----------5068------7479992200026688986607468-8568764799998


Q ss_pred             HHHHHHHCCCCCCCCHHHHHHHHHHHHHCCHHHHHHHH
Q ss_conf             99999987889887889999999999842638888754
Q gi|254781225|r  662 GVKAYISKGLDVDIPEVCLKAKEEERQGTDTYQAWIDD  699 (789)
Q Consensus       662 g~~~~~~~g~~~~~p~~v~~a~~~y~~~~D~v~~fi~e  699 (789)
                      -.+...+.|..   .++|.+.   +.+.+....+||.=
T Consensus       134 I~RD~~ERGyS---~E~V~~~---I~rR~pDy~~yI~P  165 (273)
T cd02026         134 IQRDMAERGHS---LEDVLAS---IEARKPDFEAYIDP  165 (273)
T ss_pred             HHHHHHHHCCC---HHHHHHH---HHHHHHHHHHHCCC
T ss_conf             77667664889---9999999---98604788975075


No 149
>PRK10908 cell division protein FtsE; Provisional
Probab=89.15  E-value=0.29  Score=26.14  Aligned_cols=29  Identities=31%  Similarity=0.405  Sum_probs=23.6

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             43379999707886257899999997233
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ..--++.+.|+-++||||++++|..++-.
T Consensus        26 ~~Ge~~~liG~nGsGKSTLl~~i~Gl~~p   54 (222)
T PRK10908         26 RPGEMAFLTGHSGAGKSTLLKLICGIERP   54 (222)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             69989999999980799999999659999


No 150
>cd03301 ABC_MalK_N The N-terminal ATPase domain of the maltose transporter, MalK.  ATP binding cassette (ABC) proteins function from bacteria to human, mediating the translocation of substances into and out of cells or organelles.  ABC transporters contain two transmembrane-spanning domains (TMDs) or subunits and two nucleotide binding domains (NBDs) or subunits that couple transport to the hydrolysis of ATP.  In the maltose transport system, the periplasmic maltose binding protein (MBP) stimulates the ATPase activity of the membrane-associated transporter, which consists of two transmembrane subunits, MalF and MalG, and two copies of the ATP binding subunit, MalK, and becomes tightly bound to the transporter in the catalytic transition state, ensuring that maltose is passed to the transporter as ATP is hydrolyzed.
Probab=89.13  E-value=0.31  Score=25.97  Aligned_cols=28  Identities=25%  Similarity=0.375  Sum_probs=21.8

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             4337999970788625789999999723
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      ..--++.+.|+.+.||||++++|..+.-
T Consensus        24 ~~Ge~~~i~GpSG~GKSTlLr~iaGl~~   51 (213)
T cd03301          24 ADGEFVVLLGPSGCGKTTTLRMIAGLEE   51 (213)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCC
T ss_conf             6998999999998809999999976999


No 151
>cd03227 ABC_Class2 ABC-type Class 2 contains systems involved in cellular processes other than transport.  These families are characterised by the fact that the ABC subunit is made up of duplicated, fused ABC modules (ABC2).  No known transmembrane proteins or domains are associated with these proteins.
Probab=89.13  E-value=0.41  Score=25.11  Aligned_cols=26  Identities=42%  Similarity=0.652  Sum_probs=22.0

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             37999970788625789999999723
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      ..+++++|+-+.||||+++.+.-+++
T Consensus        21 g~~~iItGpN~sGKSt~Lr~i~l~~~   46 (162)
T cd03227          21 GSLTIITGPNGSGKSTILDAIGLALG   46 (162)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHH
T ss_conf             86899989987757999999999999


No 152
>cd03233 ABC_PDR_domain1 The pleiotropic drug resistance (PDR) family of ATP-binding cassette (ABC) transporters.  PDR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes.  This PDR subfamily represents domain I of its (ABC-IM)2 organization.  ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules.  The nucleotide-binding domain shows the highest similarity between all members of the family.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=89.12  E-value=0.26  Score=26.42  Aligned_cols=31  Identities=26%  Similarity=0.320  Sum_probs=24.2

Q ss_pred             CCCCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             7433799997078862578999999972330
Q gi|254781225|r  498 NKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       498 ~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      ...-.++.+.|+-+.||||++++|..++..+
T Consensus        30 i~~Gei~~llG~nGsGKSTLl~~l~G~~~~~   60 (202)
T cd03233          30 VKPGEMVLVLGRPGSGCSTLLKALANRTEGN   60 (202)
T ss_pred             ECCCEEEEEECCCCCCHHHHHHHHHCCCCCC
T ss_conf             8098499999899998899999983787898


No 153
>PRK13538 cytochrome c biogenesis protein CcmA; Provisional
Probab=89.12  E-value=0.34  Score=25.65  Aligned_cols=30  Identities=23%  Similarity=0.476  Sum_probs=23.4

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             433799997078862578999999972330
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      ..-.++-+.|+-++||||++++|..++-..
T Consensus        25 ~~Ge~~~l~G~NGaGKSTLl~~l~Gl~~p~   54 (204)
T PRK13538         25 NAGELVQIEGPNGAGKTSLLRILAGLARPD   54 (204)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCCC
T ss_conf             799899999999985999999997688888


No 154
>cd03263 ABC_subfamily_A The ABCA subfamily mediates the transport of a variety of lipid compounds.  Mutations of members of ABCA subfamily are associated with human genetic diseases, such as, familial high-density lipoprotein (HDL) deficiency, neonatal surfactant deficiency, degenerative retinopathies, and congenital keratinization disorders.  The ABCA1 protein is involved in disorders of cholesterol transport and high-density lipoprotein (HDL) biosynthesis.  The ABCA4 (ABCR) protein transports vitamin A derivatives in the outer segments of photoreceptor cells, and therefore, performs a crucial step in the visual cycle.  The ABCA genes are not present in yeast.  However, evolutionary studies of ABCA genes indicate that they arose as transporters that subsequently duplicated and that certain sets of ABCA genes were lost in different eukaryotic lineages.
Probab=89.07  E-value=0.31  Score=25.89  Aligned_cols=29  Identities=17%  Similarity=0.331  Sum_probs=22.8

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             43379999707886257899999997233
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ..-.++-+.|+-++||||++++|..++-.
T Consensus        26 ~~Gei~~llG~NGaGKSTLl~~i~Gl~~p   54 (220)
T cd03263          26 YKGEIFGLLGHNGAGKTTTLKMLTGELRP   54 (220)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             49959999989997399999999669878


No 155
>PRK09493 glnQ glutamine ABC transporter ATP-binding protein; Reviewed
Probab=89.04  E-value=0.33  Score=25.77  Aligned_cols=27  Identities=37%  Similarity=0.407  Sum_probs=16.4

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             337999970788625789999999723
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      ...++.+.|+-|+||||++++|..++.
T Consensus        26 ~Ge~~~liG~nGsGKSTll~~i~Gl~~   52 (240)
T PRK09493         26 QGEVVVIIGPSGSGKSTLLRCINKLEE   52 (240)
T ss_pred             CCCEEEEECCCCCHHHHHHHHHHCCCC
T ss_conf             998999999999809999999963899


No 156
>COG0444 DppD ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]
Probab=89.00  E-value=0.52  Score=24.45  Aligned_cols=13  Identities=23%  Similarity=0.460  Sum_probs=5.2

Q ss_pred             CCHHHHHHHHHHH
Q ss_conf             8888999999998
Q gi|254781225|r  224 GSHDEWIPVVMAV  236 (789)
Q Consensus       224 ~dyd~W~~vg~al  236 (789)
                      ++-...+.+.|||
T Consensus       156 GGMrQRV~IAmal  168 (316)
T COG0444         156 GGMRQRVMIAMAL  168 (316)
T ss_pred             CCHHHHHHHHHHH
T ss_conf             7189999999998


No 157
>PRK13637 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=89.00  E-value=0.3  Score=25.97  Aligned_cols=29  Identities=31%  Similarity=0.466  Sum_probs=22.3

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             43379999707886257899999997233
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ..--++-+.|+-|+||||++++|..++-.
T Consensus        31 ~~GE~v~iiG~nGsGKSTLl~~l~GLl~p   59 (287)
T PRK13637         31 EDGEFVALIGHTGSGKSTLIQHLNGLLKP   59 (287)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             79989999999993999999999739988


No 158
>PRK06217 hypothetical protein; Validated
Probab=88.99  E-value=0.42  Score=25.03  Aligned_cols=26  Identities=38%  Similarity=0.491  Sum_probs=22.3

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHCCCC
Q ss_conf             99970788625789999999723300
Q gi|254781225|r  504 IHIRGVGGSGKSTLMNLIKYAFGNQY  529 (789)
Q Consensus       504 ~~~~G~G~nGKSt~~~~l~~llG~~~  529 (789)
                      ++++|.+++|||||...|...+|-..
T Consensus         4 I~i~G~sGsGkSTla~~La~~l~~~~   29 (185)
T PRK06217          4 IHITGASGSGTTTLGAALAEALDLPH   29 (185)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCCCE
T ss_conf             99978998878999999999759896


No 159
>cd03247 ABCC_cytochrome_bd The CYD subfamily implicated in cytochrome bd biogenesis.  The CydC and CydD proteins are important for the formation of cytochrome bd terminal oxidase of E. coli and it has been proposed that they were necessary for biosynthesis of the cytochrome bd quinol oxidase and for periplasmic c-type cytochromes.  CydCD were proposed to determine a heterooligomeric complex important for heme export into the periplasm or to be involved in the maintenance of the proper redox state of the periplasmic space.  In Bacillus subtilius, the absence of CydCD does not affect the presence of halo-cytochrome c in the membrane and this observation suggests that CydCD proteins are not involved in the export of heme in this organism.
Probab=88.98  E-value=0.39  Score=25.28  Aligned_cols=29  Identities=38%  Similarity=0.470  Sum_probs=23.3

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             33799997078862578999999972330
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      .-.++.+.|+-++||||++++|..++-..
T Consensus        27 ~Ge~~aivG~sGsGKSTLl~~l~G~~~p~   55 (178)
T cd03247          27 QGEKIALLGRSGSGKSTLLQLLTGDLKPQ   55 (178)
T ss_pred             CCCEEEEECCCCCHHHHHHHHHHHCCCCC
T ss_conf             99999999999875999999998617667


No 160
>PRK13544 consensus
Probab=88.98  E-value=0.35  Score=25.59  Aligned_cols=30  Identities=27%  Similarity=0.390  Sum_probs=24.6

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             433799997078862578999999972330
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      .....+.+.|+-|+||||++++|..++...
T Consensus        25 ~~Gei~~l~G~NGsGKSTLl~~i~Gl~~p~   54 (208)
T PRK13544         25 KQNSLTLVIGNNGSGKTSLLRLLAGLIPIT   54 (208)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCCC
T ss_conf             299499999999998999999995880689


No 161
>cd03289 ABCC_CFTR2 The CFTR subfamily domain 2.  The cystic fibrosis transmembrane regulator (CFTR), the product of the gene mutated in patients with cystic fibrosis, has adapted the ABC transporter structural motif to form a tightly regulated anion channel at the apical surface of many epithelia.  Use of the term assembly of a functional ion channel implies the coming together of subunits or at least smaller not-yet functional components of the active whole.  In fact, on the basis of current knowledge only the CFTR polypeptide itself is required to form an ATP- and protein kinase A-dependent low-conductance chloride channel of the type present in the apical membrane of many epithelial cells.  CFTR displays the typical organization (IM-ABC)2 and carries a characteristic hydrophilic R-domain that separates IM1-ABC1 from IM2-ABC2.
Probab=88.94  E-value=0.41  Score=25.11  Aligned_cols=26  Identities=31%  Similarity=0.401  Sum_probs=17.9

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             37999970788625789999999723
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      ...+-+.|+-|+||||++++|..++.
T Consensus        30 Ge~vaIvG~sGsGKSTLl~lL~gl~~   55 (275)
T cd03289          30 GQRVGLLGRTGSGKSTLLSAFLRLLN   55 (275)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHCC
T ss_conf             99999999999979999999960357


No 162
>cd03248 ABCC_TAP TAP, the Transporter Associated with Antigen Processing; TAP is essential for peptide delivery from the cytosol into the lumen of the endoplasmic reticulum (ER), where these peptides are loaded on major histocompatibility complex (MHC) I molecules.  Loaded MHC I leave the ER and display their antigenic cargo on the cell surface to cytotoxic T cells.  Subsequently, virus-infected or malignantly transformed cells can be eliminated.  TAP belongs to the large family of ATP-binding cassette (ABC) transporters, which translocate a vast variety of solutes across membranes.
Probab=88.93  E-value=0.34  Score=25.68  Aligned_cols=28  Identities=29%  Similarity=0.475  Sum_probs=20.4

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             4337999970788625789999999723
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      ....++.+.|+-++||||++++|..++-
T Consensus        38 ~~Ge~vaIvG~sGsGKSTL~~ll~gl~~   65 (226)
T cd03248          38 HPGEVTALVGPSGSGKSTVVALLENFYQ   65 (226)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCC
T ss_conf             2999999999999849999999964546


No 163
>cd03251 ABCC_MsbA MsbA is an essential ABC transporter, closely related to eukaryotic MDR proteins.  ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.  The nucleotide binding domain shows the highest similarity between all members of the family.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=88.90  E-value=0.33  Score=25.77  Aligned_cols=26  Identities=42%  Similarity=0.599  Sum_probs=15.8

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             37999970788625789999999723
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      -.++.++|+.|+|||||+++|..++-
T Consensus        28 Ge~i~IvG~sGsGKSTLl~ll~gl~~   53 (234)
T cd03251          28 GETVALVGPSGSGKSTLVNLIPRFYD   53 (234)
T ss_pred             CCEEEEECCCCCHHHHHHHHHHCCCC
T ss_conf             99999998999829999999966766


No 164
>cd03225 ABC_cobalt_CbiO_domain1 Domain I of the ABC component of a cobalt transport family found in bacteria, archaea, and eukaryota.  The transition metal cobalt is an essential component of many enzymes and must be transported into cells in appropriate amounts when needed.  This ABC transport system of the CbiMNQO family is involved in cobalt transport in association with the cobalamin (vitamin B12) biosynthetic pathways.  Most of cobalt (Cbi) transport systems possess a separate CbiN component, the cobalt-binding periplasmic protein, and they are encoded by the conserved gene cluster cbiMNQO.  Both the CbiM and CbiQ proteins are integral cytoplasmic membrane proteins, and the CbiO protein has the linker peptide and the Walker A and B motifs commonly found in the ATPase components of the ABC-type transport systems.
Probab=88.90  E-value=0.38  Score=25.31  Aligned_cols=30  Identities=43%  Similarity=0.646  Sum_probs=23.1

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             433799997078862578999999972330
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      ..-.++-+.|+-|+||||++++|..++-.+
T Consensus        25 ~~Gei~~iiG~nGaGKSTLlk~i~Gl~~p~   54 (211)
T cd03225          25 KKGEFVLIVGPNGSGKSTLLRLLNGLLGPT   54 (211)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCCC
T ss_conf             499799998899998999999996467798


No 165
>TIGR01420 pilT_fam twitching motility protein; InterPro: IPR006321   These represent the PilT subfamily of proteins related to GspE, a protein involved in type II secretion (also called the General Secretion Pathway). PilT is an apparent cytosolic ATPase associated with type IV pilus systems. It is not required for pilin biogenesis, but is required for twitching motility and social gliding behaviors, shown in some species, powered by pilus retraction . Members of this family may be found in some species that do not have type IV pili but have related structures for DNA uptake and natural transformation. ; GO: 0005524 ATP binding, 0006810 transport.
Probab=88.90  E-value=0.33  Score=25.76  Aligned_cols=24  Identities=8%  Similarity=-0.053  Sum_probs=10.3

Q ss_pred             HHCCCCCCCCCHHHHHHHHHHHHHC
Q ss_conf             1012211148888999999998621
Q gi|254781225|r  215 SCFGEEFYNGSHDEWIPVVMAVHHE  239 (789)
Q Consensus       215 ~~~~~~~~~~dyd~W~~vg~al~~~  239 (789)
                      +...-.+.|. |...-.++++|--+
T Consensus        79 ~~~~RfRvN~-f~QRg~~a~vlR~i  102 (350)
T TIGR01420        79 PGLARFRVNA-FKQRGGVALVLRLI  102 (350)
T ss_pred             CCCCEEEEHH-HHHCCHHHHHHHHC
T ss_conf             6732212203-23500064232311


No 166
>cd03294 ABC_Pro_Gly_Bertaine This family comprises the glycine betaine/L-proline ATP binding subunit in bacteria and its equivalents in archaea.  This transport system belong to the larger ATP-Binding Cassette (ABC) transporter superfamily.  The characteristic feature of these transporters is the obligatory coupling of ATP hydrolysis to substrate translocation.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=88.87  E-value=0.31  Score=25.90  Aligned_cols=27  Identities=37%  Similarity=0.512  Sum_probs=16.8

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             337999970788625789999999723
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      ..-++.+.|+.|.||||++++|..+.-
T Consensus        49 ~GE~~~ivG~SGsGKSTLLr~i~GL~~   75 (269)
T cd03294          49 EGEIFVIMGLSGSGKSTLLRCINRLIE   75 (269)
T ss_pred             CCCEEEEECCCCCHHHHHHHHHHCCCC
T ss_conf             999999998998489999999975999


No 167
>PRK13643 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=88.86  E-value=0.32  Score=25.79  Aligned_cols=29  Identities=31%  Similarity=0.422  Sum_probs=22.9

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             43379999707886257899999997233
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ..-.++-+.|+-|+||||++++|..++-.
T Consensus        30 ~~Ge~vaiiG~nGsGKSTLl~~l~Gll~p   58 (288)
T PRK13643         30 KKGSYTALIGHTGSGKSTLLQHLNGLLQP   58 (288)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             59989999999994799999999748888


No 168
>COG4619 ABC-type uncharacterized transport system, ATPase component [General function prediction only]
Probab=88.82  E-value=0.37  Score=25.39  Aligned_cols=27  Identities=37%  Similarity=0.621  Sum_probs=22.8

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             379999707886257899999997233
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      --+..++|+.+.|||||+..++.+...
T Consensus        29 Ge~iaitGPSG~GKStllk~va~Lisp   55 (223)
T COG4619          29 GEFIAITGPSGCGKSTLLKIVASLISP   55 (223)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHCCCC
T ss_conf             854887678876688999999813699


No 169
>COG0714 MoxR-like ATPases [General function prediction only]
Probab=88.80  E-value=1.3  Score=21.74  Aligned_cols=145  Identities=17%  Similarity=0.198  Sum_probs=71.2

Q ss_pred             HHHHHHHH-CCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCC-CCCCCHHHHHHC-CCCC
Q ss_conf             99999888-79999999999999999759874337999970788625789999999723300-034426764201-2455
Q gi|254781225|r  469 FLDLVSGY-FESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQY-VINAEASDIMQN-RPPE  545 (789)
Q Consensus       469 ~~~~l~~~-~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~-~~~~~~~~~~~~-~~~~  545 (789)
                      ....+.+. +++++.+.   ..+-..+.|.     -+++.|+-|.|||++...+...+|-.. .......+.... .+  
T Consensus        18 ~~~~~~~~~~g~~~~~~---~~l~a~~~~~-----~vll~G~PG~gKT~la~~lA~~l~~~~~~i~~t~~l~p~d~~G--   87 (329)
T COG0714          18 IRSELEKVVVGDEEVIE---LALLALLAGG-----HVLLEGPPGVGKTLLARALARALGLPFVRIQCTPDLLPSDLLG--   87 (329)
T ss_pred             HHHHCCCCCCCCHHHHH---HHHHHHHCCC-----CEEEECCCCCCHHHHHHHHHHHHCCCCEEEECCCCCCHHHHCC--
T ss_conf             66522565526699999---9999998599-----7787798987779999999998389818995689988888205--


Q ss_pred             CCCCCHHHHH--------------HCCC--EEEEEECCCCCCCCCCCEEEEEECCCEEEEEECCCCCCEEEECCEEEEEE
Q ss_conf             5568988997--------------3898--09999346777601310024541598587321047860687145289997
Q gi|254781225|r  546 AGKANPSLIR--------------LMGS--RIVIISETNENDEINAAKIKQMTGGDCMTARLNYGNTYSESPASFTPFIV  609 (789)
Q Consensus       546 ~~~~~~~la~--------------l~g~--r~~~~~E~~~~~~~~~~~~K~ltggD~i~ar~~~~~~~~~~~p~~~~~~~  609 (789)
                          ......              +...  .+++++|.+....--.+.+-++...-.++.-....   ..+.+-|.++.+
T Consensus        88 ----~~~~~~~~~~~~~~~~~~gpl~~~~~~ill~DEInra~p~~q~aLl~~l~e~~vt~~~~~~---~~~~~~f~viaT  160 (329)
T COG0714          88 ----TYAYAALLLEPGEFRFVPGPLFAAVRVILLLDEINRAPPEVQNALLEALEERQVTVPGLTT---IRLPPPFIVIAT  160 (329)
T ss_pred             ----HHHHHHHHCCCCEEEEECCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHCEEEECCCCC---CCCCCCCEEEEE
T ss_conf             ----6888766425771898468733451338998703458988999999999726897079665---337998789982


Q ss_pred             CCCCCCCCCC--CCCEEEEEEEE
Q ss_conf             3886342679--84166468999
Q gi|254781225|r  610 PNKHLFVRNP--DDAWWRRYIVI  630 (789)
Q Consensus       610 ~N~~P~~~~~--d~~~~rR~~ii  630 (789)
                      +|..+.-...  .+|+.+|+.+.
T Consensus       161 ~Np~e~~g~~~l~eA~ldRf~~~  183 (329)
T COG0714         161 QNPGEYEGTYPLPEALLDRFLLR  183 (329)
T ss_pred             CCCCCCCCCCCCCHHHHCCCEEE
T ss_conf             68676578878998888103887


No 170
>cd03246 ABCC_Protease_Secretion This family represents the ABC component of the protease secretion system PrtD, a 60-kDa integral membrane protein sharing 37% identity with HlyB, the ABC component of the alpha-hemolysin secretion pathway, in the C-terminal domain.  They export degradative enzymes by using a type I protein secretion system and  lack an N-terminal signal peptide, but contain a C-terminal secretion signal.  The Type I secretion apparatus is made up of three components, an ABC transporter, a membrane fusion protein (MFP), and an outer membrane protein (OMP).  For the HlyA transporter complex, HlyB (ABC transporter) and HlyD (MFP) reside in the inner membrane of E. coli.  The OMP component is TolC, which is thought to interact with the MFP to form a continuous channel across the periplasm from the cytoplasm to the exterior.  HlyB belongs to the family of ABC transporters, which are ubiquitous, ATP-dependent transmembrane pumps or channels.  The spectrum of transport substra
Probab=88.80  E-value=0.34  Score=25.65  Aligned_cols=29  Identities=38%  Similarity=0.399  Sum_probs=23.5

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             43379999707886257899999997233
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ..-.++.+.|+-++||||++++|..++-.
T Consensus        26 ~~G~~vaIvG~sGsGKSTLl~ll~gl~~p   54 (173)
T cd03246          26 EPGESLAIIGPSGSGKSTLARLILGLLRP   54 (173)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             59999999999998099999999666667


No 171
>cd03228 ABCC_MRP_Like The MRP (Mutidrug Resistance Protein)-like transporters are involved in drug, peptide, and lipid export.  They belong to the subfamily C of the ATP-binding cassette (ABC) superfamily of transport proteins.  The ABCC subfamily contains transporters with a diverse functional spectrum that includes ion transport, cell surface receptor, and toxin secretion activities.  The MRP-like family, simlar to all ABC proteins, have a common four-domain core structure constituted by two membrane-spanning domains, each composed of six transmembrane (TM) helices, and two nucleotide-binding domains (NBD).  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=88.77  E-value=0.34  Score=25.67  Aligned_cols=29  Identities=38%  Similarity=0.529  Sum_probs=23.5

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             43379999707886257899999997233
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ..-.++-+.|+-|+||||++++|..++-.
T Consensus        26 ~~Ge~i~ivG~sGsGKSTLl~ll~gl~~p   54 (171)
T cd03228          26 KPGEKVAIVGPSGSGKSTLLKLLLRLYDP   54 (171)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             59989999999998399999999767758


No 172
>PRK10846 bifunctional folylpolyglutamate synthase/ dihydrofolate synthase; Provisional
Probab=88.74  E-value=1.3  Score=21.89  Aligned_cols=10  Identities=10%  Similarity=0.022  Sum_probs=5.2

Q ss_pred             HHHHHHHHCC
Q ss_conf             8999876418
Q gi|254781225|r   80 TFKDTFEILH   89 (789)
Q Consensus        80 ~~~~~~~~l~   89 (789)
                      ++...++.|.
T Consensus        34 ri~~ll~~lg   43 (416)
T PRK10846         34 RVSQVAARLD   43 (416)
T ss_pred             HHHHHHHHCC
T ss_conf             9999999729


No 173
>cd03236 ABC_RNaseL_inhibitor_domain1 The ATPase domain 1 of RNase L inhibitor.  The ABC ATPase, RNase L inhibitor (RLI), is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids.  RLI s are not transport proteins and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family.  Structurally, RLIs have an N-terminal Fe-S domain and two nucleotide binding domains which are arranged to form two composite active sites in their interface cleft.  RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity more than 48%.  The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.
Probab=88.71  E-value=0.33  Score=25.73  Aligned_cols=26  Identities=23%  Similarity=0.404  Sum_probs=16.8

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             37999970788625789999999723
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      --++-+.|+-|.|||||+++|..++-
T Consensus        26 GEi~gLiGpNGaGKSTLlk~i~Gll~   51 (255)
T cd03236          26 GQVLGLVGPNGIGKSTALKILAGKLK   51 (255)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHCCCC
T ss_conf             80999989999709999999967986


No 174
>PRK11701 phnK phosphonates transport ATP-binding protein; Provisional
Probab=88.67  E-value=0.35  Score=25.59  Aligned_cols=27  Identities=33%  Similarity=0.516  Sum_probs=18.4

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             379999707886257899999997233
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      .-++-+.|+-|+||||++++|..++-.
T Consensus        32 GEi~~iiG~nGaGKSTLl~~i~G~~~p   58 (258)
T PRK11701         32 GEVLGIVGESGSGKTTLLNALSARLAP   58 (258)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             979999888998899999998567888


No 175
>PRK13635 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=88.66  E-value=0.36  Score=25.52  Aligned_cols=25  Identities=40%  Similarity=0.543  Sum_probs=12.9

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             7999970788625789999999723
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      -++-+.|+-|+||||++++|..++-
T Consensus        34 E~vaivG~nGsGKSTL~k~l~Gl~~   58 (279)
T PRK13635         34 EWVAIVGHNGSGKSTLAKLLNGLLL   58 (279)
T ss_pred             CEEEEECCCCCHHHHHHHHHHCCCC
T ss_conf             8999999999659999999972888


No 176
>PRK13633 cobalt transporter ATP-binding subunit; Provisional
Probab=88.56  E-value=0.36  Score=25.52  Aligned_cols=24  Identities=38%  Similarity=0.573  Sum_probs=11.7

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             799997078862578999999972
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~ll  525 (789)
                      -++-+.|+.|+||||++++|..++
T Consensus        38 E~v~iiG~nGsGKSTL~r~l~gl~   61 (281)
T PRK13633         38 EFLVILGHNGSGKSTIAKHMNALL   61 (281)
T ss_pred             CEEEEECCCCCHHHHHHHHHHCCC
T ss_conf             899999999984999999997588


No 177
>PRK13649 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=88.54  E-value=0.34  Score=25.61  Aligned_cols=28  Identities=32%  Similarity=0.386  Sum_probs=22.3

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             4337999970788625789999999723
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      ....++-+.|+-|+||||++++|..++-
T Consensus        31 ~~Ge~~aiiG~nGsGKSTLl~~l~Gl~~   58 (280)
T PRK13649         31 LDGSYTAFIGHTGSGKSTIMQLLNGLHV   58 (280)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCC
T ss_conf             7998999995999869999999966999


No 178
>PRK13543 cytochrome c biogenesis protein CcmA; Provisional
Probab=88.54  E-value=0.36  Score=25.46  Aligned_cols=29  Identities=24%  Similarity=0.424  Sum_probs=22.7

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             33799997078862578999999972330
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      .--++.+.|+-|.||||++++|..++-..
T Consensus        36 ~Ge~~~l~GpNGaGKTTLlr~l~Gl~~p~   64 (214)
T PRK13543         36 AGEALLVQGDNGAGKTTLLRVLAGLLHVE   64 (214)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHCCCCCC
T ss_conf             89899999999987999999997697788


No 179
>TIGR02173 cyt_kin_arch cytidylate kinase, putative; InterPro: IPR011892    Proteins in this family are believed to be cytidylate kinase. Members of this family are found in the archaea and in spirochaetes, and differ considerably from the common bacterial form of cytidylate kinase described by IPR003136 from INTERPRO.; GO: 0004127 cytidylate kinase activity, 0005524 ATP binding, 0006139 nucleobase nucleoside nucleotide and nucleic acid metabolic process.
Probab=88.51  E-value=0.72  Score=23.51  Aligned_cols=101  Identities=16%  Similarity=0.200  Sum_probs=56.7

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCCCCCHHHHHHCCCEEEEEECCCCCCCCCCCEEEEEE
Q ss_conf             99997078862578999999972330003442676420124555568988997389809999346777601310024541
Q gi|254781225|r  503 FIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEAGKANPSLIRLMGSRIVIISETNENDEINAAKIKQMT  582 (789)
Q Consensus       503 ~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~~~~~~~~la~l~g~r~~~~~E~~~~~~~~~~~~K~lt  582 (789)
                      .+..-|+.|+||||....|..-||=..+++-..-.|+++++.+-       ..     ...+.|-++=++.=...++.+.
T Consensus         2 ~I~ISGpPGSGktTvA~~lA~~Lsl~~iSaG~iRelA~~~Gldl-------~E-----~~~aee~~eIDk~iD~~~~E~A   69 (173)
T TIGR02173         2 IITISGPPGSGKTTVAKILAEKLSLKLISAGDIRELAEKMGLDL-------AE-----SKYAEENPEIDKKIDRRIREIA   69 (173)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHCCCCEECCCHHHHHHHHCCCCH-------HH-----HHHHCCCCCCCHHHHHHHHHHH
T ss_conf             78873589686478999999863983120200788986429887-------77-----3443058631167537885543


Q ss_pred             -CCCEEEEEECCCCCCEEE----ECCEEEEEECCCCCCCCC
Q ss_conf             -598587321047860687----145289997388634267
Q gi|254781225|r  583 -GGDCMTARLNYGNTYSES----PASFTPFIVPNKHLFVRN  618 (789)
Q Consensus       583 -ggD~i~ar~~~~~~~~~~----~p~~~~~~~~N~~P~~~~  618 (789)
                       +.+.|..+.-= -.++.-    .+=.++|  -+-.|.++-
T Consensus        70 ~~~~nvvlEsrl-agW~~~~nG~yaD~~iy--L~A~levRA  107 (173)
T TIGR02173        70 EKEKNVVLESRL-AGWILKKNGEYADVKIY--LKAPLEVRA  107 (173)
T ss_pred             CCCCCEEEEEHH-HHHHCCCCCCCCCEEEE--ECCCHHHHH
T ss_conf             048966885205-43311578896756788--608833324


No 180
>cd03253 ABCC_ATM1_transporter ATM1 is an ABC transporter that is expressed in the mitochondria.  Although the specific function of ATM1 is unknown, its disruption results in the accumulation of excess mitochondrial iron, loss of mitochondrial cytochromes, oxidative damage to mitochondrial DNA, and decreased levels of cytosolic heme proteins.  ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.  The nucleotide binding domain shows the highest similarity between all members of the family.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=88.49  E-value=0.33  Score=25.72  Aligned_cols=24  Identities=38%  Similarity=0.592  Sum_probs=14.7

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             799997078862578999999972
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~ll  525 (789)
                      .++.+.|+-++||||++++|..++
T Consensus        28 e~v~ivG~sGsGKSTLl~ll~gl~   51 (236)
T cd03253          28 KKVAIVGPSGSGKSTILRLLFRFY   51 (236)
T ss_pred             CEEEEECCCCCCHHHHHHHHCCCC
T ss_conf             999999999998999999974385


No 181
>cd03235 ABC_Metallic_Cations ABC component of the metal-type transporters.  This family includes transporters involved in the uptake of various metallic cations such as iron, manganese, and zinc.  The ATPases of this group of transporters are very similar to members of iron-siderophore uptake family suggesting that they share a common ancestor.  The best characterized metal-type ABC transporters are the YfeABCD system of Y. pestis, the SitABCD system of Salmonella enterica serovar Typhimurium, and the SitABCD transporter of Shigella flexneri.  Moreover other uncharacterized homologs of these metal-type transporters are mainly found in pathogens like Haemophilus or enteroinvasive E. coli isolates.
Probab=88.49  E-value=0.37  Score=25.41  Aligned_cols=29  Identities=38%  Similarity=0.511  Sum_probs=23.6

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             43379999707886257899999997233
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ..-.++-+.|+-|.||||++++|..++-.
T Consensus        23 ~~Ge~~~liGpNGaGKSTllk~i~Gl~~p   51 (213)
T cd03235          23 KPGEFLAIVGPNGAGKSTLLKAILGLLKP   51 (213)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             59989999999998699999999768788


No 182
>cd03369 ABCC_NFT1 Domain 2 of NFT1 (New full-length MRP-type transporter 1).  NFT1 belongs to the MRP (mulrtidrug resisitance-associated protein) family of ABC transporters.  Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear.  The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed.  MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions such as glutathione, glucuronate, and sulfate.
Probab=88.48  E-value=0.51  Score=24.49  Aligned_cols=28  Identities=36%  Similarity=0.328  Sum_probs=22.2

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             3379999707886257899999997233
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      .-.++-+.|+-+.||||++++|..++-.
T Consensus        33 ~Ge~v~ivG~sGsGKSTLl~ll~g~~~p   60 (207)
T cd03369          33 AGEKIGIVGRTGAGKSTLILALFRFLEA   60 (207)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHCCC
T ss_conf             9999999999998799999999987288


No 183
>pfam07724 AAA_2 AAA domain (Cdc48 subfamily). This Pfam entry includes some of the AAA proteins not detected by the pfam00004 model.
Probab=88.47  E-value=1.2  Score=21.98  Aligned_cols=108  Identities=19%  Similarity=0.157  Sum_probs=51.8

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHCC--CCCCCCCHHHHHHC------CC-------CCCCCCCHHHHHHCCCEEEEEE
Q ss_conf             379999707886257899999997233--00034426764201------24-------5555689889973898099993
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYAFGN--QYVINAEASDIMQN------RP-------PEAGKANPSLIRLMGSRIVIIS  565 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~llG~--~~~~~~~~~~~~~~------~~-------~~~~~~~~~la~l~g~r~~~~~  565 (789)
                      ..-+++.|+.+.||+.+...+..++..  ......+...+...      .+       ...++.-.+..+-..-.+++++
T Consensus         3 ~~~~l~~GPsGvGKT~lAk~la~~l~~~~~~~i~~dm~e~~~~~~v~~l~g~~~gyvg~~~~G~l~~~v~~~p~~VillD   82 (168)
T pfam07724         3 IGSFLFLGPTGVGKTELAKALAELLFGDERALIRIDMSEYMEEHSVSRLIGAPPGYVGYEEGGQLTEAVRRKPYSIVLID   82 (168)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHCCCCCCEEEECCCCCCCHHHHHHHCCCCCCCCCCCCCCCHHHHHHHCCCCEEEEH
T ss_conf             37999889899899999999999967985344885575654256999870589987262426507899983898489865


Q ss_pred             CCCCCCCCCCCEEEEEECCCEEEEEECCCCCCEEEECCEEEEEECCC
Q ss_conf             46777601310024541598587321047860687145289997388
Q gi|254781225|r  566 ETNENDEINAAKIKQMTGGDCMTARLNYGNTYSESPASFTPFIVPNK  612 (789)
Q Consensus       566 E~~~~~~~~~~~~K~ltggD~i~ar~~~~~~~~~~~p~~~~~~~~N~  612 (789)
                      |.++-..---..|-++.-+..++  ..++.. +.|.. ..+++.||-
T Consensus        83 EIeKa~~~V~~~LL~ild~g~~~--d~~g~~-v~~~n-~i~i~Tsn~  125 (168)
T pfam07724        83 EIEKAHPGVQNDLLQILEGGTLT--DKQGRK-VDFRN-TLFIMTGNF  125 (168)
T ss_pred             HHHHHCHHHHHHHHHHCCCCCEE--CCCCCE-EECCC-EEEEECCCC
T ss_conf             77665899999999870587063--699967-84464-799976873


No 184
>PRK13636 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=88.42  E-value=0.37  Score=25.42  Aligned_cols=26  Identities=31%  Similarity=0.371  Sum_probs=16.2

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             37999970788625789999999723
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      -.++-+.|+-|+||||++++|..++-
T Consensus        32 Ge~~aiiG~NGaGKSTLl~~i~Gll~   57 (285)
T PRK13636         32 GEVTAILGGNGAGKSTLFQNLNGILK   57 (285)
T ss_pred             CCEEEEECCCCCHHHHHHHHHHCCCC
T ss_conf             98999999999809999999965988


No 185
>COG1123 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]
Probab=88.37  E-value=0.7  Score=23.58  Aligned_cols=29  Identities=28%  Similarity=0.387  Sum_probs=22.6

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             43379999707886257899999997233
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      +.--.+=+.|..|+||||+..+|..++-.
T Consensus       315 ~~GE~lglVGeSGsGKSTlar~i~gL~~P  343 (539)
T COG1123         315 REGETLGLVGESGSGKSTLARILAGLLPP  343 (539)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             38878999889999989999999487788


No 186
>PRK13548 hmuV hemin importer ATP-binding subunit; Provisional
Probab=88.36  E-value=0.38  Score=25.35  Aligned_cols=29  Identities=28%  Similarity=0.413  Sum_probs=20.7

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             33799997078862578999999972330
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      .-.++-+.|+-|+||||++++|..++-..
T Consensus        27 ~Gei~~liGpNGaGKSTLlk~i~Gl~~p~   55 (257)
T PRK13548         27 PGEVVAILGPNGAGKSTLLRALSGELPPS   55 (257)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHCCCCCC
T ss_conf             99899999999987999999985675778


No 187
>COG3911 Predicted ATPase [General function prediction only]
Probab=88.34  E-value=0.52  Score=24.41  Aligned_cols=25  Identities=28%  Similarity=0.441  Sum_probs=22.2

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             3379999707886257899999997
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYA  524 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~l  524 (789)
                      .++++|+.|..+.||||+++.|...
T Consensus         8 R~~~fIltGgpGaGKTtLL~aLa~~   32 (183)
T COG3911           8 RHKRFILTGGPGAGKTTLLAALARA   32 (183)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHC
T ss_conf             5338998379997689999999975


No 188
>PRK09984 phosphonate/organophosphate ester transporter subunit; Provisional
Probab=88.33  E-value=0.39  Score=25.29  Aligned_cols=26  Identities=31%  Similarity=0.456  Sum_probs=20.7

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             33799997078862578999999972
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~ll  525 (789)
                      .--++-+.|+-|.||||++++|..++
T Consensus        29 ~GE~~~iiGpNGaGKSTLlk~i~Gll   54 (262)
T PRK09984         29 HGEMVALLGPSGSGKSTLLRHLSGLI   54 (262)
T ss_pred             CCCEEEEECCCCCHHHHHHHHHHCCC
T ss_conf             99899999899960999999997567


No 189
>PRK13639 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=88.33  E-value=0.38  Score=25.32  Aligned_cols=28  Identities=32%  Similarity=0.372  Sum_probs=19.7

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             3379999707886257899999997233
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      .-.++-+.|+-|+||||++++|..++-.
T Consensus        27 ~Ge~vaiiG~nGsGKSTLl~~l~Gll~P   54 (275)
T PRK13639         27 EGEMIAILGPNGAGKSTLFLHFNGILKP   54 (275)
T ss_pred             CCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             9989999999996499999999739899


No 190
>TIGR00955 3a01204 Pigment precourser permease; InterPro: IPR005284   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 different parts of a membrane-spanning permease system necessary for the transport of pigment precursor into pigment cells responsible for eye color. White protein dimerises with brown protein for the transport of guanine and with scarlet protein for the transport of tryptophan.; GO: 0006810 transport.
Probab=88.31  E-value=0.47  Score=24.75  Aligned_cols=14  Identities=21%  Similarity=0.401  Sum_probs=5.4

Q ss_pred             CHHHHH--HHHHHHHH
Q ss_conf             888999--99999862
Q gi|254781225|r  225 SHDEWI--PVVMAVHH  238 (789)
Q Consensus       225 dyd~W~--~vg~al~~  238 (789)
                      +.|+..  .|..+|++
T Consensus       205 GLDSfmA~~Vv~~L~~  220 (671)
T TIGR00955       205 GLDSFMAYSVVQVLKG  220 (671)
T ss_pred             HHHHHHHHHHHHHHHH
T ss_conf             3459999999999999


No 191
>PRK10789 putative multidrug transporter membrane\ATP-binding components; Provisional
Probab=88.28  E-value=0.57  Score=24.19  Aligned_cols=32  Identities=41%  Similarity=0.519  Sum_probs=26.0

Q ss_pred             CCCCEEEEEEECCCCCHHHHHHHHHHHHCCCC
Q ss_conf             74337999970788625789999999723300
Q gi|254781225|r  498 NKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQY  529 (789)
Q Consensus       498 ~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~  529 (789)
                      ......+-+.|+.|+||||++++|..++-.+.
T Consensus       338 I~~Ge~vaIVG~SGsGKSTLl~LL~g~y~p~~  369 (569)
T PRK10789        338 LKPGQMLGICGPTGSGKSTLLSLIQRHFDVSE  369 (569)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHHHHHHCCC
T ss_conf             88997899879999987999999997764267


No 192
>cd03244 ABCC_MRP_domain2 Domain 2 of the ABC subfamily C.  This family is also known as MRP (mulrtidrug resisitance-associated protein).  Some of the MRP members have five additional transmembrane segments in their N-terminus, but the function of these additional membrane-spanning domains is not clear.  The MRP was found in the multidrug-resistance lung cancer cell in which p-glycoprotein was not overexpressed.  MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.
Probab=88.23  E-value=0.38  Score=25.33  Aligned_cols=28  Identities=29%  Similarity=0.255  Sum_probs=21.7

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             3379999707886257899999997233
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      .-.++-+.|+-++||||++++|..++-.
T Consensus        29 ~Ge~v~ivG~sGsGKSTLl~ll~gl~~p   56 (221)
T cd03244          29 PGEKVGIVGRTGSGKSSLLLALFRLVEL   56 (221)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             9989999999999899999999679718


No 193
>PRK11231 fecE iron-dicitrate transporter ATP-binding subunit; Provisional
Probab=88.22  E-value=0.41  Score=25.10  Aligned_cols=30  Identities=27%  Similarity=0.384  Sum_probs=23.5

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             433799997078862578999999972330
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      ..-.++-+.|+-|+||||++++|..++-..
T Consensus        26 ~~Gei~~liGpNGaGKSTLlk~i~Gl~~p~   55 (255)
T PRK11231         26 PTGKITALIGPNGCGKSTLLKCFARLLTPQ   55 (255)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCCC
T ss_conf             899799999999981999999997598888


No 194
>PRK10851 sulfate/thiosulfate transporter subunit; Provisional
Probab=88.09  E-value=0.38  Score=25.35  Aligned_cols=14  Identities=7%  Similarity=-0.126  Sum_probs=6.9

Q ss_pred             EEEEECCCCCCCCC
Q ss_conf             89997388634267
Q gi|254781225|r  605 TPFIVPNKHLFVRN  618 (789)
Q Consensus       605 ~~~~~~N~~P~~~~  618 (789)
                      ++.+...+.|...+
T Consensus       321 ~~~~~~~~~~~~G~  334 (352)
T PRK10851        321 TVVMHGDDAPQRGE  334 (352)
T ss_pred             EEEECCCCCCCCCC
T ss_conf             99927987899999


No 195
>pfam06414 Zeta_toxin Zeta toxin. This family consists of several bacterial zeta toxin proteins. Zeta toxin is thought to be part of a postregulational killing system in bacteria. It relies on antitoxin/toxin systems that secure stable inheritance of low and medium copy number plasmids during cell division and kill cells that have lost the plasmid.
Probab=88.07  E-value=0.74  Score=23.41  Aligned_cols=31  Identities=19%  Similarity=0.308  Sum_probs=25.3

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCCCC
Q ss_conf             4337999970788625789999999723300
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGNQY  529 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~  529 (789)
                      ...+++|+-|..|+|||++.+.+..-++..+
T Consensus        10 ~~Pkai~laG~pGAGKS~~~~~~~~~~~~~~   40 (191)
T pfam06414        10 ERPVAVLLGGQPGAGKTELARALLEELGGGN   40 (191)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHCCCCC
T ss_conf             6987999957998888999999987537899


No 196
>pfam02367 UPF0079 Uncharacterized P-loop hydrolase UPF0079. This uncharacterized family contains a P-loop.
Probab=88.07  E-value=0.61  Score=23.95  Aligned_cols=45  Identities=22%  Similarity=0.180  Sum_probs=31.1

Q ss_pred             HHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCC-CCCCCHHH
Q ss_conf             9759874337999970788625789999999723300-03442676
Q gi|254781225|r  493 ALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQY-VINAEASD  537 (789)
Q Consensus       493 ~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~-~~~~~~~~  537 (789)
                      .|....+....+.|.|+=+.||+||..-+..-||-.. ++|++..+
T Consensus         7 ~ia~~l~~G~vi~L~G~LGaGKTtfvr~i~~~lg~~~~V~SPTF~l   52 (123)
T pfam02367         7 RLAQLLKAGDVVLLSGDLGAGKTTFVRGLAKGLGITGNVTSPTFTL   52 (123)
T ss_pred             HHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCCEEE
T ss_conf             9997689997999988877889999999999859988737995588


No 197
>COG0563 Adk Adenylate kinase and related kinases [Nucleotide transport and metabolism]
Probab=88.06  E-value=0.52  Score=24.42  Aligned_cols=41  Identities=15%  Similarity=0.061  Sum_probs=27.3

Q ss_pred             CCCHHHHHHHHHHHHHCCHHHHHHHHHEEECCCCEECHHHHHHHH
Q ss_conf             878899999999998426388887543262688411179999999
Q gi|254781225|r  674 DIPEVCLKAKEEERQGTDTYQAWIDDCCDIGENLWEESHSLAKSY  718 (789)
Q Consensus       674 ~~p~~v~~a~~~y~~~~D~v~~fi~e~ce~~~~~~~~~~~l~~~y  718 (789)
                      ..++.++.-...|...+.++-.+..  +.++.  ..+..++++.+
T Consensus       133 d~~~~~~~R~~~y~~~~~pl~~~y~--~~id~--~~~i~~v~~~i  173 (178)
T COG0563         133 DNEETVKKRLKVYHEQTAPLIEYYS--VTIDG--SGEIEEVLADI  173 (178)
T ss_pred             CCHHHHHHHHHHHHHCCCCEEEEEE--ECCCC--CCCHHHHHHHH
T ss_conf             6789999999998754683477775--11467--78899999999


No 198
>PRK13640 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=88.04  E-value=0.42  Score=25.03  Aligned_cols=28  Identities=32%  Similarity=0.377  Sum_probs=19.3

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             3379999707886257899999997233
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      .-.++-+.|+-|.||||++.+|..++-.
T Consensus        33 ~Ge~vaiiG~nGsGKSTL~~~l~Gll~P   60 (283)
T PRK13640         33 RGSWTALIGHNGSGKSTISKLINGLLLP   60 (283)
T ss_pred             CCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             9999999999998799999999640378


No 199
>PRK11247 ssuB aliphatic sulfonates transport ATP-binding subunit; Provisional
Probab=87.98  E-value=0.39  Score=25.25  Aligned_cols=26  Identities=35%  Similarity=0.519  Sum_probs=14.4

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             37999970788625789999999723
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      ..++-+.|+-|.||||++++|..++.
T Consensus        38 GEiv~LiG~nGaGKSTLlr~i~Gl~~   63 (257)
T PRK11247         38 GQFVAVVGRSGCGKSTLLRLLAGLET   63 (257)
T ss_pred             CCEEEEECCCCCHHHHHHHHHHCCCC
T ss_conf             98999998998889999999965898


No 200
>PRK05291 trmE tRNA modification GTPase TrmE; Reviewed
Probab=87.97  E-value=1.6  Score=21.16  Aligned_cols=43  Identities=23%  Similarity=0.258  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHHHHHCCC-CCCCEEEEEEECCCCCHHHHHHHHHH
Q ss_conf             99999999999997598-74337999970788625789999999
Q gi|254781225|r  481 EVMDYFTRCVGMALLGG-NKAQRFIHIRGVGGSGKSTLMNLIKY  523 (789)
Q Consensus       481 e~~~~l~~~~g~~l~g~-~~~~~~~~~~G~G~nGKSt~~~~l~~  523 (789)
                      .++.-+..++...-.|. .++..-+.+.|+.+.|||+|+|.|..
T Consensus       195 ~l~~~i~~ll~~~~~g~~l~~G~~v~i~G~PN~GKSSL~N~L~~  238 (445)
T PRK05291        195 ELIAELEKLLASAKQGELLREGLKVVIAGRPNVGKSSLLNALLG  238 (445)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCEEEEECCCCCCHHHHHHHHHC
T ss_conf             99999999999987417863598699889998768999999857


No 201
>PRK13650 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=87.96  E-value=0.41  Score=25.09  Aligned_cols=25  Identities=40%  Similarity=0.555  Sum_probs=14.8

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             7999970788625789999999723
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      -++-+.|+-|+||||++++|..++-
T Consensus        31 E~vaivG~nGsGKSTL~~~l~Gll~   55 (276)
T PRK13650         31 EWLSIIGHNGSGKSTTVRLIDGLLE   55 (276)
T ss_pred             CEEEEECCCCCHHHHHHHHHHCCCC
T ss_conf             8999999999879999999973889


No 202
>PRK06762 hypothetical protein; Provisional
Probab=87.93  E-value=0.64  Score=23.83  Aligned_cols=28  Identities=36%  Similarity=0.595  Sum_probs=25.4

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             3799997078862578999999972330
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      .+++++-|+.++||||+..-|+.-||..
T Consensus         2 t~LIiiRGNSgSGKtT~Ak~L~~~~G~g   29 (166)
T PRK06762          2 TTLIIIRGNSGSGKTTIAKQLQERLGRG   29 (166)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHCCC
T ss_conf             5289997888888789999999986888


No 203
>PRK10869 recombination and repair protein; Provisional
Probab=87.93  E-value=0.55  Score=24.25  Aligned_cols=136  Identities=10%  Similarity=0.080  Sum_probs=63.2

Q ss_pred             EEEECCCEEECCC----CCCCCCCHHHHCCEECCCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCEE
Q ss_conf             7660793797438----885589865501001378888757947899999888799999999999999997598743379
Q gi|254781225|r  428 FLGEQDGILDLET----GQKVKPTKELYITKSTGTPFVEGEPSQEFLDLVSGYFESEEVMDYFTRCVGMALLGGNKAQRF  503 (789)
Q Consensus       428 ll~~~NGv~dl~t----~~~~~~~~~~~~t~~~~~~y~~~a~~p~~~~~l~~~~~d~e~~~~l~~~~g~~l~g~~~~~~~  503 (789)
                      -|+++|+.+++.-    ..+.++- .|-+....  .-+|..+.    +=|..|----|+-+.+..+ -.++........+
T Consensus       385 ~L~M~~a~F~i~i~~~~~~~~~~G-~d~vefl~--s~N~G~~~----~pL~kiASGGElSRimLAl-k~v~a~~~~~~tl  456 (553)
T PRK10869        385 ELSMPHGKFTIDVKFDEHHLSADG-ADRIEFRV--TTNPGQPL----QPIAKVASGGELSRIALAI-QVITARKMETPAL  456 (553)
T ss_pred             CCCCCCCEEEEEEECCCCCCCCCC-CEEEEEEE--ECCCCCCC----CCHHHHCCHHHHHHHHHHH-HHHHHCCCCCCEE
T ss_conf             029997489999961766789998-63899999--52899997----6177763660899999999-9997057999828


Q ss_pred             EEE---EECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCCCCCHHHHHHCCCEEEEEECCCCCCCCCCCEEEE
Q ss_conf             999---70788625789999999723300034426764201245555689889973898099993467776013100245
Q gi|254781225|r  504 IHI---RGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEAGKANPSLIRLMGSRIVIISETNENDEINAAKIKQ  580 (789)
Q Consensus       504 ~~~---~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~~~~~~~~la~l~g~r~~~~~E~~~~~~~~~~~~K~  580 (789)
                      +|=   .|.||.==..+.+.|..+=-.+-+..+              -+.|.+|......+.|.-+...+..  .+.++.
T Consensus       457 IFDEID~GigG~~a~~vg~~L~~ls~~~QVi~I--------------THlpQvAa~ad~H~~V~K~~~~~~t--~t~i~~  520 (553)
T PRK10869        457 IFDEVDVGISGPTAAVVGKLLRQLGESTQVMCV--------------THLPQVAGCGHQHMFVSKETDGGMT--ETHMQP  520 (553)
T ss_pred             EEECCCCCCCHHHHHHHHHHHHHHHCCCEEEEE--------------CCHHHHHHCCCCEEEEEEECCCCEE--EEEEEE
T ss_conf             985788899879999999999998529879998--------------0369998544877899997379826--898788


Q ss_pred             EECCCEE
Q ss_conf             4159858
Q gi|254781225|r  581 MTGGDCM  587 (789)
Q Consensus       581 ltggD~i  587 (789)
                      |++.+.+
T Consensus       521 L~~~eRv  527 (553)
T PRK10869        521 LDKKARL  527 (553)
T ss_pred             CCHHHHH
T ss_conf             9840799


No 204
>cd03245 ABCC_bacteriocin_exporters ABC-type bacteriocin exporters. Many non-lantibiotic bacteriocins of lactic acid bacteria are produced as precursors which have N-terminal leader peptides that share similarities in amino acid sequence and contain a conserved processing site of two glycine residues in positions -1 and -2.  A dedicated ATP-binding cassette (ABC) transporter is responsible for the proteolytic cleavage of the leader peptides and subsequent translocation of the bacteriocins across the cytoplasmic membrane.
Probab=87.93  E-value=0.43  Score=24.98  Aligned_cols=27  Identities=37%  Similarity=0.452  Sum_probs=18.8

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             379999707886257899999997233
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ..++-+.|+-++||||++++|..++-.
T Consensus        30 G~~v~ivG~sGsGKSTLl~ll~gl~~p   56 (220)
T cd03245          30 GEKVAIIGRVGSGKSTLLKLLAGLYKP   56 (220)
T ss_pred             CCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             999999999998599999999672547


No 205
>cd03290 ABCC_SUR1_N The SUR domain 1.  The sulfonylurea receptor SUR is an ATP transporter of the ABCC/MRP family with tandem ATPase binding domains.  Unlike other ABC proteins, it has no intrinsic transport function, neither active nor passive, but associates with the potassium channel proteins Kir6.1 or Kir6.2 to form the ATP-sensitive potassium (K(ATP)) channel.  Within the channel complex, SUR serves as a regulatory subunit that fine-tunes the gating of Kir6.x in response to alterations in cellular metabolism.  It constitutes a major pharmaceutical target as it binds numerous drugs, K(ATP) channel openers and blockers, capable of up- or down-regulating channel activity.
Probab=87.91  E-value=0.43  Score=25.00  Aligned_cols=28  Identities=29%  Similarity=0.320  Sum_probs=20.5

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             3379999707886257899999997233
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      .-.++.+.|+-++||||++++|..++-.
T Consensus        26 ~Ge~~~IvG~sGsGKSTLl~~l~g~~~~   53 (218)
T cd03290          26 TGQLTMIVGQVGCGKSSLLLAILGEMQT   53 (218)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             9999999999998099999998555656


No 206
>PRK07667 uridine kinase; Provisional
Probab=87.90  E-value=0.7  Score=23.56  Aligned_cols=32  Identities=31%  Similarity=0.419  Sum_probs=24.4

Q ss_pred             CCCCEEEEE-EECCCCCHHHHHHHHHHHHCCCC
Q ss_conf             743379999-70788625789999999723300
Q gi|254781225|r  498 NKAQRFIHI-RGVGGSGKSTLMNLIKYAFGNQY  529 (789)
Q Consensus       498 ~~~~~~~~~-~G~G~nGKSt~~~~l~~llG~~~  529 (789)
                      -+++.|+|- -|..++|||||.+-|...|+...
T Consensus        10 ~~~~r~iIgIaG~sgSGKTTla~~L~~~l~~~~   42 (190)
T PRK07667         10 HKENRFILGIDGLSRSGKTTFVANLKENMKQEG   42 (190)
T ss_pred             CCCCEEEEEEECCCCCCHHHHHHHHHHHHHHCC
T ss_conf             759869999779897889999999999986659


No 207
>KOG0728 consensus
Probab=87.85  E-value=1.6  Score=21.12  Aligned_cols=121  Identities=18%  Similarity=0.283  Sum_probs=73.2

Q ss_pred             CCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCC---CCCHHHHHHCCCEEEEEECCCCCCCCC
Q ss_conf             74337999970788625789999999723300034426764201245555---689889973898099993467776013
Q gi|254781225|r  498 NKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEAG---KANPSLIRLMGSRIVIISETNENDEIN  574 (789)
Q Consensus       498 ~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~~~---~~~~~la~l~g~r~~~~~E~~~~~~~~  574 (789)
                      ....+=+++||+.+.||..+.....+----.. .-++.+.+-++.-...+   ..-|.+|+-..--+++++|.+.   +.
T Consensus       178 IaQPKGvlLygppgtGktLlaraVahht~c~f-irvsgselvqk~igegsrmvrelfvmarehapsiifmdeids---ig  253 (404)
T KOG0728         178 IAQPKGVLLYGPPGTGKTLLARAVAHHTDCTF-IRVSGSELVQKYIGEGSRMVRELFVMAREHAPSIIFMDEIDS---IG  253 (404)
T ss_pred             CCCCCCEEEECCCCCCHHHHHHHHHHHCCEEE-EEECHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEHHCCC---CC
T ss_conf             78876048846999756299999875414079-996449999998501389999999998750882675000012---12


Q ss_pred             CCEEEEEECCCEEEEEEC----C-CCCCEEEECCEEEEEECCCCCCCCCCCCCEEEE
Q ss_conf             100245415985873210----4-786068714528999738863426798416646
Q gi|254781225|r  575 AAKIKQMTGGDCMTARLN----Y-GNTYSESPASFTPFIVPNKHLFVRNPDDAWWRR  626 (789)
Q Consensus       575 ~~~~K~ltggD~i~ar~~----~-~~~~~~~~p~~~~~~~~N~~P~~~~~d~~~~rR  626 (789)
                      .+++-.-+|||.-.-|-+    + -+.| +...+.+++|+||.   +.--|.|+.|-
T Consensus       254 s~r~e~~~ggdsevqrtmlellnqldgf-eatknikvimatnr---idild~allrp  306 (404)
T KOG0728         254 SSRVESGSGGDSEVQRTMLELLNQLDGF-EATKNIKVIMATNR---IDILDPALLRP  306 (404)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHCCCC-CCCCCEEEEEECCC---CCCCCHHHCCC
T ss_conf             3434578986389999999999740240-00366269984164---22246866387


No 208
>COG3840 ThiQ ABC-type thiamine transport system, ATPase component [Coenzyme metabolism]
Probab=87.80  E-value=0.5  Score=24.57  Aligned_cols=23  Identities=48%  Similarity=0.650  Sum_probs=17.0

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             79999707886257899999997
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYA  524 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~l  524 (789)
                      -..-+.|+.+.||||++|+|...
T Consensus        26 e~vAi~GpSGaGKSTLLnLIAGF   48 (231)
T COG3840          26 EIVAILGPSGAGKSTLLNLIAGF   48 (231)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHC
T ss_conf             57999778886578899998742


No 209
>cd03291 ABCC_CFTR1 The CFTR subfamily domain 1.  The cystic fibrosis transmembrane regulator (CFTR), the product of the gene mutated in patients with cystic fibrosis, has adapted the ABC transporter structural motif to form a tightly regulated anion channel at the apical surface of many epithelia.  Use of the term assembly of a functional ion channel implies the coming together of subunits, or at least smaller not-yet functional components of the active whole.  In fact, on the basis of current knowledge only the CFTR polypeptide itself is required to form an ATP- and protein kinase A-dependent low-conductance chloride channel of the type present in the apical membrane of many epithelial cells.  CFTR displays the typical organization (IM-ABC)2 and carries a characteristic hydrophilic R-domain that separates IM1-ABC1 from IM2-ABC2.
Probab=87.77  E-value=0.41  Score=25.10  Aligned_cols=24  Identities=38%  Similarity=0.589  Sum_probs=12.2

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             799997078862578999999972
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~ll  525 (789)
                      ..+-+.|+.|+||||++++|..++
T Consensus        64 e~vaIVG~sGSGKSTLl~lL~gl~   87 (282)
T cd03291          64 EMLAITGSTGSGKTSLLMLILGEL   87 (282)
T ss_pred             CEEEEECCCCCHHHHHHHHHHCCC
T ss_conf             999999999981999999995787


No 210
>cd03252 ABCC_Hemolysin The ABC-transporter hemolysin B is a central component of the secretion machinery that translocates the toxin, hemolysin A, in a Sec-independent fashion across both membranes of E. coli.  The hemolysin A (HlyA) transport machinery is composed of the ATP-binding cassette (ABC) transporter HlyB located in the inner membrane, hemolysin D (HlyD), also anchored in the inner membrane, and TolC, which resides in the outer membrane.  HlyD apparently forms a continuous channel that bridges the entire periplasm, interacting with TolC and HlyB.  This arrangement prevents the appearance of periplasmic intermediates of HlyA during substrate transport.  Little is known about the molecular details of HlyA transport, but it is evident that ATP-hydrolysis by the ABC-transporter HlyB is a necessary source of energy.
Probab=87.77  E-value=0.41  Score=25.10  Aligned_cols=25  Identities=44%  Similarity=0.586  Sum_probs=14.2

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             7999970788625789999999723
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      .++-+.|+-++|||||+++|..++-
T Consensus        29 ~~vaivG~sGsGKSTll~ll~gl~~   53 (237)
T cd03252          29 EVVGIVGRSGSGKSTLTKLIQRFYV   53 (237)
T ss_pred             CEEEEECCCCCHHHHHHHHHHCCCC
T ss_conf             9999999999859999999967765


No 211
>cd03258 ABC_MetN_methionine_transporter MetN (also known as YusC) is an ABC-type transporter encoded by metN of the metNPQ operon in Bacillus subtilis that is involved in methionine transport.  Other members of this system include the MetP permease and  the MetQ substrate binding protein.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=87.74  E-value=0.37  Score=25.38  Aligned_cols=25  Identities=36%  Similarity=0.398  Sum_probs=14.1

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             3799997078862578999999972
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~ll  525 (789)
                      -.++-+.|+.|+||||++++|..+.
T Consensus        31 Ge~~~ivG~SGsGKSTllr~i~gL~   55 (233)
T cd03258          31 GEIFGIIGRSGAGKSTLIRCINGLE   55 (233)
T ss_pred             CCEEEEECCCCCHHHHHHHHHHCCC
T ss_conf             9999998898058999999996799


No 212
>TIGR03258 PhnT 2-aminoethylphosphonate ABC transport system, ATP-binding component PhnT. This ATP-binding component of an ABC transport system is found in Salmonella and Burkholderia lineages in the vicinity of enzymes for the breakdown of 2-aminoethylphosphonate.
Probab=87.73  E-value=0.41  Score=25.12  Aligned_cols=10  Identities=10%  Similarity=0.288  Sum_probs=5.3

Q ss_pred             CCCCEEEECC
Q ss_conf             2684388047
Q gi|254781225|r  130 GCGQYFVAYN  139 (789)
Q Consensus       130 ~~G~q~V~~g  139 (789)
                      ..|.++++-|
T Consensus        29 ~~GE~~~llG   38 (362)
T TIGR03258        29 EAGELLALIG   38 (362)
T ss_pred             CCCCEEEEEC
T ss_conf             9998999999


No 213
>PRK13631 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=87.69  E-value=0.45  Score=24.83  Aligned_cols=29  Identities=31%  Similarity=0.411  Sum_probs=21.5

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             43379999707886257899999997233
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ..-.++-+.|+.|+||||++++|..++-.
T Consensus        50 ~~Ge~vaIIG~nGsGKSTL~~~l~Gll~p   78 (320)
T PRK13631         50 EKNKIYFIIGNSGSGKSTLVTHFNGLIKS   78 (320)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             59989999949998499999999758889


No 214
>PRK13894 conjugal transfer ATPase TrbB; Provisional
Probab=87.64  E-value=1.7  Score=21.03  Aligned_cols=48  Identities=31%  Similarity=0.324  Sum_probs=31.0

Q ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             99998887999999999999999975987433799997078862578999999972
Q gi|254781225|r  470 LDLVSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       470 ~~~l~~~~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~ll  525 (789)
                      ++++..=+-+.+..+||..++        +..+-+++.|..++||+||++.+..-+
T Consensus       126 ~dlv~~G~~~~~~a~~L~~~V--------~~r~nilI~G~TgsGKTTll~all~~i  173 (320)
T PRK13894        126 DQYVERGIMTAEQREAIIAAV--------RAHRNILVIGGTGSGKTTLVNAIINEM  173 (320)
T ss_pred             HHHHHCCCCCHHHHHHHHHHH--------HCCCCEEEECCCCCCHHHHHHHHHHHH
T ss_conf             999876999999999999999--------728758998588865689999998632


No 215
>PRK13645 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=87.59  E-value=0.44  Score=24.91  Aligned_cols=29  Identities=31%  Similarity=0.418  Sum_probs=23.0

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             43379999707886257899999997233
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ....++-+.|+-|+||||++++|..++-.
T Consensus        35 ~~Ge~~aIiG~nGsGKSTL~~~l~Gll~p   63 (289)
T PRK13645         35 KKNKVTCVIGTTGSGKSTMIQLTNGLIIS   63 (289)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             89989999999995799999999659889


No 216
>PRK10790 putative multidrug transporter membrane\ATP-binding components; Provisional
Probab=87.58  E-value=0.67  Score=23.68  Aligned_cols=31  Identities=32%  Similarity=0.441  Sum_probs=24.9

Q ss_pred             CCCCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             7433799997078862578999999972330
Q gi|254781225|r  498 NKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       498 ~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      ...-..+-+.|+.|+||||++++|..++-..
T Consensus       364 I~~Ge~vaIVG~SGsGKSTL~~LL~rly~p~  394 (593)
T PRK10790        364 VPSRNFVALVGHTGSGKSTLASLLMGYYPLT  394 (593)
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHHCCCC
T ss_conf             4899789987999886899999999855678


No 217
>PRK10522 multidrug transporter membrane component/ATP-binding component; Provisional
Probab=87.58  E-value=0.41  Score=25.14  Aligned_cols=31  Identities=35%  Similarity=0.431  Sum_probs=24.3

Q ss_pred             CCCCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             7433799997078862578999999972330
Q gi|254781225|r  498 NKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       498 ~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      ...-..+-+.|+.|+||||++++|..++-..
T Consensus       346 i~~Ge~vaiVG~SGsGKSTL~~LL~r~y~p~  376 (547)
T PRK10522        346 IKRGELLFLIGGNGSGKSTLAMLLTGLYQPQ  376 (547)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHHCCCCCC
T ss_conf             8599889998999997799999982896699


No 218
>pfam06048 DUF927 Domain of unknown function (DUF927). Family of bacterial proteins of unknown function.
Probab=87.58  E-value=1.7  Score=21.01  Aligned_cols=119  Identities=15%  Similarity=0.148  Sum_probs=75.2

Q ss_pred             CCCCCCCCHHHHHHHHHHHC-CCHHHHHHHHHHHHHHHCCCCC-CCEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCH
Q ss_conf             88887579478999998887-9999999999999999759874-337999970788625789999999723300034426
Q gi|254781225|r  458 TPFVEGEPSQEFLDLVSGYF-ESEEVMDYFTRCVGMALLGGNK-AQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEA  535 (789)
Q Consensus       458 ~~y~~~a~~p~~~~~l~~~~-~d~e~~~~l~~~~g~~l~g~~~-~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~  535 (789)
                      -.|.+.-+-..|.+-+.... ++..++-.+-..++..|..-.. +-..+-++|..+.||||.+++...+.|+....    
T Consensus       146 ~~~~~~GTl~~W~~~v~~~~~gn~~~~~~v~~afa~pLl~~~~~~~~~~hl~g~Ss~GKTt~~~~AaSvwG~p~~~----  221 (284)
T pfam06048       146 DGLSQKGTLDEWRREVAALCVGNPLLILAVSAALAAPLLKLLGLEGGGFHFVGDSSTGKTTALKLAASVWGNPDTL----  221 (284)
T ss_pred             HCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHHCCHHHH----
T ss_conf             2133787999999999999758989999999998999999858985599986589876689999887661482887----


Q ss_pred             HHHHHCCCCCCCCCCHHHHHHCCCEEEEEECCCCCCCCCC-CEEEEEECC
Q ss_conf             7642012455556898899738980999934677760131-002454159
Q gi|254781225|r  536 SDIMQNRPPEAGKANPSLIRLMGSRIVIISETNENDEINA-AKIKQMTGG  584 (789)
Q Consensus       536 ~~~~~~~~~~~~~~~~~la~l~g~r~~~~~E~~~~~~~~~-~~~K~ltgg  584 (789)
                       ..+- + .+ .+.-...|.+..-.+.+.+|..+.+.-.. ..+-+|+.|
T Consensus       222 -~~sw-~-~T-~n~le~~a~~~nd~~l~lDE~~~~~~~~~~~~~Y~l~nG  267 (284)
T pfam06048       222 -IRSW-R-ST-ANGLEATASEHNDTPLILDEISEADPREVGGAVYMLANG  267 (284)
T ss_pred             -HHHH-H-HH-HHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHHCC
T ss_conf             -3107-6-46-999999999847985576226678988997775234279


No 219
>cd03224 ABC_TM1139_LivF_branched LivF (TM1139) is part of the LIV-I bacterial ABC-type two-component transport system that imports neutral, branched-chain amino acids.  The  E. coli branched-chain amino acid transporter comprises a heterodimer of ABC transporters (LivF and LivG), a heterodimer of six-helix TM domains (LivM and LivH), and one of two alternative soluble periplasmic substrate binding proteins (LivK or LivJ).  ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.
Probab=87.56  E-value=0.44  Score=24.89  Aligned_cols=29  Identities=24%  Similarity=0.398  Sum_probs=22.1

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             33799997078862578999999972330
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      .--++-+.|+-++||||++++|..++-..
T Consensus        25 ~Gei~~liG~nGaGKSTLl~~i~Gl~~p~   53 (222)
T cd03224          25 EGEIVALLGRNGAGKTTLLKTIMGLLPPR   53 (222)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHCCCCCC
T ss_conf             99899999999985999999997798899


No 220
>cd00267 ABC_ATPase ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.  The nucleotide-binding domain shows the highest similarity between all members of the family.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=87.55  E-value=0.43  Score=24.99  Aligned_cols=27  Identities=37%  Similarity=0.490  Sum_probs=23.0

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             337999970788625789999999723
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      .-.++.+.|+.+.||||++++|..++-
T Consensus        24 ~Ge~~~i~G~nGaGKSTLl~~l~gl~~   50 (157)
T cd00267          24 AGEIVALVGPNGSGKSTLLRAIAGLLK   50 (157)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHCCCC
T ss_conf             997999987889998999999958847


No 221
>TIGR02928 TIGR02928 orc1/cdc6 family replication initiation protein; InterPro: IPR014277   This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. The proteins in this entry are found exclusively in the archaea. Several members may be found in a genome and interact with each other..
Probab=87.55  E-value=1.7  Score=21.00  Aligned_cols=284  Identities=16%  Similarity=0.167  Sum_probs=148.0

Q ss_pred             ECCCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHC-CCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCC----
Q ss_conf             13788887579478999998887999999999999999975-9874337999970788625789999999723300----
Q gi|254781225|r  455 STGTPFVEGEPSQEFLDLVSGYFESEEVMDYFTRCVGMALL-GGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQY----  529 (789)
Q Consensus       455 ~~~~~y~~~a~~p~~~~~l~~~~~d~e~~~~l~~~~g~~l~-g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~----  529 (789)
                      .+..+|.|++.         .|.+=+|-|+-+...+.-+|. |....-  +|+||..|.|||...+-+.+.|=..+    
T Consensus         7 ~L~~dY~Pden---------~i~hRdeqI~~l~~~L~~~l~PG~~P~N--i~iYGkTGtGKT~vt~~v~~~l~~~~~~~d   75 (383)
T TIGR02928         7 LLEPDYVPDEN---------RIVHRDEQIEELAKALRPILRPGSRPSN--IFIYGKTGTGKTAVTKYVMKELEEAAEDRD   75 (383)
T ss_pred             CCCCCCCCCCC---------CCCCCHHHHHHHHHHHHHHHCCCCCCCC--EEEECCCCCCHHHHHHHHHHHHHHHHHCCC
T ss_conf             37757702742---------4668678999999998875067489872--588788898788999999999999862269


Q ss_pred             ---CCC----------------CCHHHH----HHCCCCCCCCCC--------HHHH-HHCCCEEEEEECCCCC-CCCCCC
Q ss_conf             ---034----------------426764----201245555689--------8899-7389809999346777-601310
Q gi|254781225|r  530 ---VIN----------------AEASDI----MQNRPPEAGKAN--------PSLI-RLMGSRIVIISETNEN-DEINAA  576 (789)
Q Consensus       530 ---~~~----------------~~~~~~----~~~~~~~~~~~~--------~~la-~l~g~r~~~~~E~~~~-~~~~~~  576 (789)
                         ++.                .=...+    .+...+..|-+.        ..|. ...+.-+++.+|.+.= ..-+..
T Consensus        76 ~~D~~~~~~NC~~~~T~y~~~~~L~~~ln~~~~~~~vP~tG~s~~~~~~~l~~~l~~~~~~~~~ivLDEiD~Lv~~~~d~  155 (383)
T TIGR02928        76 VRDVSTVYINCQILDTSYQVLVELANQLNRRGSGEEVPTTGLSTSEVFRELYKELNRERGDSLIIVLDEIDKLVRKDDDD  155 (383)
T ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCEEEEEECCCCHHHCCCCCC
T ss_conf             97158999778546846999999999851577888898877878999999999983201887999862310221588888


Q ss_pred             -----EEEEEECCCEEEEEECCCCCCEEEECCEEEEEECCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCC-H----HHH
Q ss_conf             -----024541598587321047860687145289997388634267984166468999658878887878-3----342
Q gi|254781225|r  577 -----KIKQMTGGDCMTARLNYGNTYSESPASFTPFIVPNKHLFVRNPDDAWWRRYIVIPFDKPIANRDAS-F----AQK  646 (789)
Q Consensus       577 -----~~K~ltggD~i~ar~~~~~~~~~~~p~~~~~~~~N~~P~~~~~d~~~~rR~~iipF~~~~~~~d~~-~----~~~  646 (789)
                           .|-+|+       |.. .+.-.+-. .--+|-.||..=-...-|.=+-..  +.|=+-.||.=|.+ |    .++
T Consensus       156 PAyS~~LY~L~-------Ra~-~~~~~~~~-~vgvIgISND~~f~~~Ld~RVkSs--L~~eei~FpPYdA~eL~~IL~~R  224 (383)
T TIGR02928       156 PAYSKLLYQLS-------RAR-ENGDLENA-KVGVIGISNDLKFRENLDPRVKSS--LCEEEIVFPPYDAEELRDILENR  224 (383)
T ss_pred             HHHHHHHHHHH-------HHH-HCCCCCCC-CEEEEEEECCCHHHHHCCCCEECC--CCCCCCEECCCCHHHHHHHHHHH
T ss_conf             07878853433-------100-03577885-348999865714364457530132--48740040798869999999720


Q ss_pred             H-CCCCHHHHH-------------------HHHHHHHHH----HHHCCC-CCCCCHHHHHHHHHHHHHCCHHHHHHHHH-
Q ss_conf             2-012044799-------------------999999999----998788-98878899999999998426388887543-
Q gi|254781225|r  647 L-ETKYTLEAK-------------------KWFLKGVKA----YISKGL-DVDIPEVCLKAKEEERQGTDTYQAWIDDC-  700 (789)
Q Consensus       647 ~-~~~e~~~i~-------------------~w~l~g~~~----~~~~g~-~~~~p~~v~~a~~~y~~~~D~v~~fi~e~-  700 (789)
                      . ...-..|++                   .-||+=++.    ..++|- .++ -+.|++|.+.. -|.|-+..-|.+- 
T Consensus       225 ~v~~AF~dGvl~d~VI~lcAA~aAq~hGDAR~AiDLLR~AGe~A~~~g~~~Vt-~~HV~~A~e~~-PE~~r~~e~~~~Lp  302 (383)
T TIGR02928       225 AVEKAFYDGVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVT-EDHVEEAQEKI-PEVDRVLELIRGLP  302 (383)
T ss_pred             HHHHCCCCCCCCHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCH-HHHHHHHHHHC-CHHHHHHHHHHCCC
T ss_conf             31203368854622799999986206787899999999876875315763100-88899999832-22889999860798


Q ss_pred             ------------EEEC--CCCEECHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHCCCCCCCCEEEECCCCCCCCE
Q ss_conf             ------------2626--8841117999999999998504667555452568999986354233310010256765208
Q gi|254781225|r  701 ------------CDIG--ENLWEESHSLAKSYSEYREQELNYDRKRISTRTVTLNLKQKGFIGGIKREKIEKEWKSKRI  765 (789)
Q Consensus       701 ------------ce~~--~~~~~~~~~l~~~y~~~~~~~~~~~~~~~s~~~~~~~l~~~g~~~~~~~~~~~~~~~~~r~  765 (789)
                                  ....  ...+..++++|+.|.+-|+..   +.-|++++.+..-|.++-+.|-+..+...++.-.+|+
T Consensus       303 ~h~k~~L~A~~~l~~~~~~~~~~~t~~vY~~Y~~~c~~~---~~dpl~~rR~~~~l~eL~~LG~~~~~~~~~G~g~G~~  378 (383)
T TIGR02928       303 THSKLVLLAIANLAAESPEEDPFRTGEVYEVYKELCEDI---GVDPLTQRRISDLLNELDMLGLVEAEERNKGRGGGRT  378 (383)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCEEEEHHHHHHHHHHHHHH---CCCCCCHHHHHHHHHHHHHCCCEEEEEEECCCCCCEE
T ss_conf             679999999999985167887366127789999998762---6776614679998876766073345677426776436


No 222
>PRK11831 putative ABC transporter ATP-binding protein YrbF; Provisional
Probab=87.54  E-value=0.43  Score=24.99  Aligned_cols=26  Identities=35%  Similarity=0.497  Sum_probs=14.7

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             37999970788625789999999723
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      ..++-+.|+-|.||||++++|..++-
T Consensus        34 Gei~~iiGpnGsGKSTLlk~i~Gl~~   59 (269)
T PRK11831         34 GKITAIMGPSGIGKTTLLRLIGGQIA   59 (269)
T ss_pred             CCEEEEECCCCCHHHHHHHHHHCCCC
T ss_conf             98999993999759999999967988


No 223
>cd03223 ABCD_peroxisomal_ALDP Peroxisomal ATP-binding cassette transporter (Pat) is involved in the import of very long-chain fatty acids (VLCFA) into the peroxisome.  The peroxisomal membrane forms a permeability barrier for a wide variety of metabolites required for and formed during fatty acid beta-oxidation.  To communicate with the cytoplasm and mitochondria, peroxisomes need dedicated proteins to transport such hydrophilic molecules across their membranes.  X-linked adrenoleukodystrophy (X-ALD) is caused by mutations in the ALD gene, which encodes ALDP (adrenoleukodystrophy protein ), a peroxisomal integral membrane protein that is a member of the ATP-binding cassette (ABC) transporter protein family.  The disease is characterized by a striking and unpredictable variation in phenotypic expression.  Phenotypes include the rapidly progressive childhood cerebral form (CCALD), the milder adult form, adrenomyeloneuropathy (AMN), and variants without neurologic involvement (i.e. asympt
Probab=87.53  E-value=0.36  Score=25.50  Aligned_cols=27  Identities=30%  Similarity=0.445  Sum_probs=21.2

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             433799997078862578999999972
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~ll  525 (789)
                      ..-.++.+.|+-+.||||++++|..++
T Consensus        25 ~~Ge~v~i~G~sGsGKSTLl~~l~Gl~   51 (166)
T cd03223          25 KPGDRLLITGPSGTGKSSLFRALAGLW   51 (166)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHCCCC
T ss_conf             899999999589998899999986987


No 224
>cd03214 ABC_Iron-Siderophores_B12_Hemin ABC transporters, involved in the uptake of siderophores, heme, and vitamin B12, are widely conserved in bacteria and archaea.  Only very few species lack representatives of the siderophore family transporters.  The E. coli BtuCD protein is an ABC transporter mediating vitamin B12 uptake.  The two ATP-binding cassettes (BtuD) are in close contact with each other, as are the two membrane-spanning subunits (BtuC); this arrangement is distinct from that observed for the E. coli lipid flippase MsbA.  The BtuC subunits provide 20 transmembrane helices grouped around a translocation pathway that is closed to the cytoplasm by a gate region, whereas the dimer arrangement of the BtuD subunits resembles the ATP-bound form of the Rad50 DNA repair enzyme.  A prominent cytoplasmic loop of BtuC forms the contact region with the ATP-binding cassette and represent a conserved motif among the ABC transporters.
Probab=87.50  E-value=0.46  Score=24.76  Aligned_cols=29  Identities=31%  Similarity=0.442  Sum_probs=24.1

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             43379999707886257899999997233
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ....++-+.|+-++||||++++|..++-.
T Consensus        23 ~~Ge~~~liG~nGsGKTTLl~~i~G~~~~   51 (180)
T cd03214          23 EAGEIVGILGPNGAGKSTLLKTLAGLLKP   51 (180)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             69979999989998899999999579899


No 225
>PRK09536 btuD corrinoid ABC transporter ATPase; Reviewed
Probab=87.47  E-value=0.45  Score=24.86  Aligned_cols=50  Identities=18%  Similarity=0.272  Sum_probs=28.8

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCCCCCHHHHHHCCCEEEE
Q ss_conf             79999707886257899999997233000344267642012455556898899738980999
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEAGKANPSLIRLMGSRIVI  563 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~~~~~~~~la~l~g~r~~~  563 (789)
                      .-++.+|.|+.|-..+-.+.+.=+.   ++.-.+..         +....+.|+..+...+.
T Consensus       265 ~~vhvi~ggg~g~~~~r~L~~~g~~---v~~Gvl~~---------~D~d~~~A~~l~~~~v~  314 (409)
T PRK09536        265 TSVHVVGGGQPAAPAVSRLVSAGAS---VSVGPVPA---------GDTAAETARRVGCEAVT  314 (409)
T ss_pred             CEEEEECCCCCHHHHHHHHHHCCCC---EEEECCCC---------CCCHHHHHHHCCCCEEE
T ss_conf             6299988997369999999987981---69842767---------65248999971985785


No 226
>PRK13652 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=87.46  E-value=0.43  Score=24.98  Aligned_cols=27  Identities=30%  Similarity=0.407  Sum_probs=16.9

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             337999970788625789999999723
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      ...++-+.|+-|.||||++++|..++-
T Consensus        29 ~Ge~~aliG~NGaGKSTLl~~i~Gll~   55 (277)
T PRK13652         29 RKQRIAVIGPNGAGKSTLFKHFNGILK   55 (277)
T ss_pred             CCCEEEEECCCCCHHHHHHHHHHCCCC
T ss_conf             998999999999479999999966999


No 227
>COG1660 Predicted P-loop-containing kinase [General function prediction only]
Probab=87.39  E-value=1  Score=22.55  Aligned_cols=17  Identities=24%  Similarity=0.397  Sum_probs=10.6

Q ss_pred             EEEEEEE-CCCCCHHHHH
Q ss_conf             7999970-7886257899
Q gi|254781225|r  502 RFIHIRG-VGGSGKSTLM  518 (789)
Q Consensus       502 ~~~~~~G-~G~nGKSt~~  518 (789)
                      -+.|.+| +||---||.+
T Consensus       243 ~lTIaIGCTGGqHRSV~i  260 (286)
T COG1660         243 YLTIAIGCTGGQHRSVYI  260 (286)
T ss_pred             EEEEEECCCCCCCCHHHH
T ss_conf             999997147986205899


No 228
>TIGR01448 recD_rel helicase, RecD/TraA family; InterPro: IPR006345   These sequences represent a family similar to RecD, the exodeoxyribonuclease V alpha chain of IPR006344 from INTERPRO. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD. .
Probab=87.34  E-value=0.64  Score=23.82  Aligned_cols=82  Identities=17%  Similarity=0.256  Sum_probs=48.9

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCCCCCHHHHHHCCCEEEEEECCCCCCCCCCCEE
Q ss_conf             43379999707886257899999997233000344267642012455556898899738980999934677760131002
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEAGKANPSLIRLMGSRIVIISETNENDEINAAKI  578 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~~~~~~~~la~l~g~r~~~~~E~~~~~~~~~~~~  578 (789)
                      ..++.+||+|..|.||||.++-|-.++-.  ..+++.   ..+.     ..+      ..-....|+-+  |+  ++-++
T Consensus       363 ~~~Kv~iLTGGPGTGKtT~t~~i~~~~~~--~~gl~l---~~~~-----~vn------dd~~v~LaAPT--Gr--AAkRl  422 (769)
T TIGR01448       363 IQDKVVILTGGPGTGKTTITKAIIELYEE--LKGLDL---DKDD-----YVN------DDLPVVLAAPT--GR--AAKRL  422 (769)
T ss_pred             HCCCEEEEECCCCCCHHHHHHHHHHHHHH--HCCCCC---CCCC-----CCC------CCCEEEEECCC--HH--HHHHC
T ss_conf             60948998577888616899999999987--168775---5312-----456------77648873774--37--88851


Q ss_pred             EEEECCCEEEEEECCCCCCEEE
Q ss_conf             4541598587321047860687
Q gi|254781225|r  579 KQMTGGDCMTARLNYGNTYSES  600 (789)
Q Consensus       579 K~ltggD~i~ar~~~~~~~~~~  600 (789)
                      .++||-...|.=++-+..+-++
T Consensus       423 ~E~TG~~a~TIHRLlG~~~~~~  444 (769)
T TIGR01448       423 AEVTGLEALTIHRLLGYGSDTK  444 (769)
T ss_pred             CCCCCCHHHHHHHHHCCCCCCC
T ss_conf             1002621234778636898887


No 229
>COG1126 GlnQ ABC-type polar amino acid transport system, ATPase component [Amino acid transport and metabolism]
Probab=87.31  E-value=0.47  Score=24.73  Aligned_cols=12  Identities=17%  Similarity=0.124  Sum_probs=6.1

Q ss_pred             CHHHHHHHHHHH
Q ss_conf             947899999888
Q gi|254781225|r  465 PSQEFLDLVSGY  476 (789)
Q Consensus       465 ~~p~~~~~l~~~  476 (789)
                      ..|+..+||.++
T Consensus       228 ~~~R~~~FL~~i  239 (240)
T COG1126         228 KSERTRQFLSKI  239 (240)
T ss_pred             CCHHHHHHHHHH
T ss_conf             998999999851


No 230
>COG1121 ZnuC ABC-type Mn/Zn transport systems, ATPase component [Inorganic ion transport and metabolism]
Probab=87.31  E-value=0.49  Score=24.59  Aligned_cols=29  Identities=28%  Similarity=0.343  Sum_probs=22.5

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             33799997078862578999999972330
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      .-.|.-++|+-+.|||||+.+|..++-.+
T Consensus        29 ~G~~~~iiGPNGaGKSTLlK~iLGll~p~   57 (254)
T COG1121          29 KGEITALIGPNGAGKSTLLKAILGLLKPS   57 (254)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHCCCCCC
T ss_conf             89689999998888899999996787677


No 231
>PRK10619 histidine/lysine/arginine/ornithine transporter subunit; Provisional
Probab=87.21  E-value=0.48  Score=24.65  Aligned_cols=25  Identities=40%  Similarity=0.559  Sum_probs=15.7

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             3799997078862578999999972
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~ll  525 (789)
                      --++-+.|+-|+||||++++|..+.
T Consensus        31 Gei~~iiG~sGsGKSTLl~~i~gl~   55 (257)
T PRK10619         31 GDVISIIGSSGSGKSTFLRCINFLE   55 (257)
T ss_pred             CCEEEEECCCCCHHHHHHHHHHCCC
T ss_conf             9799999899981999999996599


No 232
>PRK10253 iron-enterobactin transporter ATP-binding protein; Provisional
Probab=87.20  E-value=0.45  Score=24.81  Aligned_cols=29  Identities=31%  Similarity=0.433  Sum_probs=22.0

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             43379999707886257899999997233
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ..-.++-+.|+-|.||||++++|..++-.
T Consensus        31 ~~Ge~~~iiGpNGaGKSTLlk~i~Gll~p   59 (265)
T PRK10253         31 PDGHFTAIIGPNGCGKSTLLRTLSRLMTP   59 (265)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             59979999999883999999999749888


No 233
>TIGR03263 guanyl_kin guanylate kinase. Members of this family are the enzyme guanylate kinase, also called GMP kinase. This enzyme transfers a phosphate from ATP to GMP, yielding ADP and GDP.
Probab=87.19  E-value=0.71  Score=23.54  Aligned_cols=27  Identities=37%  Similarity=0.374  Sum_probs=23.0

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             799997078862578999999972330
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      +++++.|+.|.||+|+++.|..-..+.
T Consensus         2 ~livl~GpsG~GK~tl~~~l~~~~~~~   28 (180)
T TIGR03263         2 LLIVISGPSGVGKSTLVKALLEEDPNL   28 (180)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHCCCC
T ss_conf             399998999889999999999768994


No 234
>PRK09544 znuC high-affinity zinc transporter ATPase; Reviewed
Probab=87.18  E-value=0.49  Score=24.58  Aligned_cols=28  Identities=25%  Similarity=0.438  Sum_probs=22.1

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             3379999707886257899999997233
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      .-.++-+.|+-|.||||++++|..++-.
T Consensus        29 ~Gei~~LiGpNGaGKSTLlk~I~Gl~~p   56 (251)
T PRK09544         29 PGKILTLLGPNGAGKSTLVRVVLGLVAP   56 (251)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             9979999989998899999999668889


No 235
>PRK10575 iron-hydroxamate transporter ATP-binding subunit; Provisional
Probab=87.16  E-value=0.51  Score=24.48  Aligned_cols=28  Identities=32%  Similarity=0.421  Sum_probs=19.0

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             3379999707886257899999997233
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ...++-+.|+-|+||||++++|..++..
T Consensus        36 ~Ge~~~liG~NGaGKSTLl~~l~gl~~p   63 (265)
T PRK10575         36 AGKVTGLIGHNGSGKSTLLKMLGRHQPP   63 (265)
T ss_pred             CCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             9989999999998099999999568899


No 236
>PRK11264 putative amino-acid ABC transporter ATP-binding protein YecC; Provisional
Probab=87.16  E-value=0.5  Score=24.55  Aligned_cols=22  Identities=41%  Similarity=0.622  Sum_probs=9.6

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             9999707886257899999997
Q gi|254781225|r  503 FIHIRGVGGSGKSTLMNLIKYA  524 (789)
Q Consensus       503 ~~~~~G~G~nGKSt~~~~l~~l  524 (789)
                      ++-+.|+-|+||||++++|..+
T Consensus        29 ~~aliG~sGsGKSTLl~~l~gl   50 (248)
T PRK11264         29 VVAIIGPSGSGKTTLLRCINLL   50 (248)
T ss_pred             EEEEECCCCCCHHHHHHHHHCC
T ss_conf             9999999998099999999758


No 237
>PRK13547 hmuV hemin importer ATP-binding subunit; Provisional
Probab=87.15  E-value=0.47  Score=24.71  Aligned_cols=27  Identities=30%  Similarity=0.485  Sum_probs=20.2

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             337999970788625789999999723
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      .-.++-+.|+-|+||||++++|..++.
T Consensus        26 ~Ge~~aliG~nGaGKSTLl~~i~G~l~   52 (273)
T PRK13547         26 PGRVTALLGRNGAGKSTLLKVLAGELT   52 (273)
T ss_pred             CCCEEEEECCCCCHHHHHHHHHHCCCC
T ss_conf             998999999999769999999956788


No 238
>cd03288 ABCC_SUR2 The SUR domain 2.  The sulfonylurea receptor SUR is an ATP binding cassette (ABC) protein of the ABCC/MRP family.  Unlike other ABC proteins, it has no intrinsic transport function, neither active nor passive, but associates with the potassium channel proteins Kir6.1 or Kir6.2 to form the ATP-sensitive potassium (K(ATP)) channel.  Within the channel complex, SUR serves as a regulatory subunit that fine-tunes the gating of Kir6.x in response to alterations in cellular metabolism.  It constitutes a major pharmaceutical target as it binds numerous drugs, K(ATP) channel openers and blockers, capable of up- or down-regulating channel activity.
Probab=87.14  E-value=0.57  Score=24.17  Aligned_cols=14  Identities=50%  Similarity=0.601  Sum_probs=4.5

Q ss_pred             ECCCCCHHHHHHHH
Q ss_conf             07886257899999
Q gi|254781225|r  508 GVGGSGKSTLMNLI  521 (789)
Q Consensus       508 G~G~nGKSt~~~~l  521 (789)
                      |+-+.|||||+++|
T Consensus        54 G~sGsGKSTL~~ll   67 (257)
T cd03288          54 GRTGSGKSSLSLAF   67 (257)
T ss_pred             CCCCCCHHHHHHHH
T ss_conf             99998199999999


No 239
>PRK11650 ugpC glycerol-3-phosphate transporter ATP-binding subunit; Provisional
Probab=87.11  E-value=0.46  Score=24.77  Aligned_cols=10  Identities=20%  Similarity=0.441  Sum_probs=4.9

Q ss_pred             CCCCEEEECC
Q ss_conf             2684388047
Q gi|254781225|r  130 GCGQYFVAYN  139 (789)
Q Consensus       130 ~~G~q~V~~g  139 (789)
                      ..|..+++-|
T Consensus        28 ~~Ge~~~llG   37 (358)
T PRK11650         28 ADGEFIVLVG   37 (358)
T ss_pred             CCCCEEEEEC
T ss_conf             8998999999


No 240
>CHL00095 clpC Clp protease ATP binding subunit
Probab=87.10  E-value=1.8  Score=20.84  Aligned_cols=164  Identities=15%  Similarity=0.166  Sum_probs=92.5

Q ss_pred             CCCHHHHCCEECCCCCCCCCC-----HHHHHHHHHH-HCCCHHHHHHHHHHHHHHHCCCCC---CCEEEEEEECCCCCHH
Q ss_conf             898655010013788887579-----4789999988-879999999999999999759874---3379999707886257
Q gi|254781225|r  445 KPTKELYITKSTGTPFVEGEP-----SQEFLDLVSG-YFESEEVMDYFTRCVGMALLGGNK---AQRFIHIRGVGGSGKS  515 (789)
Q Consensus       445 ~~~~~~~~t~~~~~~y~~~a~-----~p~~~~~l~~-~~~d~e~~~~l~~~~g~~l~g~~~---~~~~~~~~G~G~nGKS  515 (789)
                      +.+-...++..++++-..-..     --..++.|.+ ++|-++.++-+-..+--+-.|-..   .---|++.||.|-||+
T Consensus       474 ~~dI~~vvs~~tgiPv~~~~~~e~~~l~~le~~L~~~ViGQd~AI~~vs~ai~rsraGl~~~~rPigsFlf~GPTGvGKT  553 (823)
T CHL00095        474 EKDIAEIVSAWTGIPVNKLTKSESEKLIHMEETLHKRIIGQDEAVVAVSKAIRRARVGLKNPNRPIASFIFCGPTGVGKT  553 (823)
T ss_pred             HHHHHHHHHHHHCCCHHHHCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHH
T ss_conf             99999999998689847633458899987888787784076999999999999997089989997468998789988779


Q ss_pred             HHHHHHHHH-HCCCC-CCCCCHHHHHHCC-------------CCCCCCCCHHHHHHCCCEEEEEECCCCCCCCCCCEEEE
Q ss_conf             899999997-23300-0344267642012-------------45555689889973898099993467776013100245
Q gi|254781225|r  516 TLMNLIKYA-FGNQY-VINAEASDIMQNR-------------PPEAGKANPSLIRLMGSRIVIISETNENDEINAAKIKQ  580 (789)
Q Consensus       516 t~~~~l~~l-lG~~~-~~~~~~~~~~~~~-------------~~~~~~~~~~la~l~g~r~~~~~E~~~~~~~~~~~~K~  580 (789)
                      -+...|... ||+.. ..-.+.+.....-             |-..|+--.+-.+-+.--++..+|.++-..---..|-|
T Consensus       554 ElAK~LA~~LFg~e~~liR~DMSEy~E~hsvsrLIGaPPGYVGy~eGG~LTeaVrr~PysVvLfDEIEKAHpdV~nilLQ  633 (823)
T CHL00095        554 ELTKALASYFFGSEEAMIRLDMSEYMEKHTVSKLIGSPPGYVGYNEGGQLTEAVRKKPYTVVLFDEIEKAHPDIFNLLLQ  633 (823)
T ss_pred             HHHHHHHHHHCCCCCCEEEECCCCCCCCCCHHHHCCCCCCCCCCCCCCCHHHHHHCCCCEEEEECHHHHCCHHHHHHHHH
T ss_conf             99999999974782025885351015542076745899876677878820198871998699862131138899998876


Q ss_pred             EECCCEEEEEECCCCCCEEEECCEEEEEECCC
Q ss_conf             41598587321047860687145289997388
Q gi|254781225|r  581 MTGGDCMTARLNYGNTYSESPASFTPFIVPNK  612 (789)
Q Consensus       581 ltggD~i~ar~~~~~~~~~~~p~~~~~~~~N~  612 (789)
                      +.....++-.  .++. +.|+.+ .++|.||-
T Consensus       634 vlDdG~LtD~--~Gr~-vdF~Nt-IIImTSNl  661 (823)
T CHL00095        634 ILDDGRLTDS--KGRT-IDFKNT-LIIMTSNL  661 (823)
T ss_pred             HCCCCCCCCC--CCCE-EECEEE-EEEECCCC
T ss_conf             5168843489--9998-843103-99971650


No 241
>PRK13642 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=87.03  E-value=0.49  Score=24.59  Aligned_cols=27  Identities=41%  Similarity=0.556  Sum_probs=18.5

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             379999707886257899999997233
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      -.++-+.|+-|+||||++.+|..++..
T Consensus        33 Ge~~aiiG~sGsGKSTL~~~l~Gl~~~   59 (277)
T PRK13642         33 GEWVSIIGQNGSGKSTTARLIDGLFEE   59 (277)
T ss_pred             CCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             989999999996899999999638998


No 242
>PRK13657 cyclic beta-1,2-glucan ABC transporter; Provisional
Probab=86.99  E-value=0.68  Score=23.64  Aligned_cols=30  Identities=43%  Similarity=0.633  Sum_probs=24.1

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             433799997078862578999999972330
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      .....+-+.|+.|+||||++++|..++-.+
T Consensus       359 ~~Ge~vaiVG~SGsGKSTL~~LL~gly~p~  388 (585)
T PRK13657        359 KPGQTVAIVGPTGAGKSTLINLLHRVFDPQ  388 (585)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHCCCC
T ss_conf             599889998898986999999986015788


No 243
>PRK10078 ribose 1,5-bisphosphokinase; Provisional
Probab=86.96  E-value=0.67  Score=23.72  Aligned_cols=26  Identities=27%  Similarity=0.500  Sum_probs=21.4

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             79999707886257899999997233
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      +++++.||.|.||||+++-|..-...
T Consensus         3 ~LivvsgPSGaGK~Tli~~l~~~~~~   28 (184)
T PRK10078          3 KLIWLMGPSGSGKDSLLAALRQREQT   28 (184)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHCCCC
T ss_conf             09999899869999999999844899


No 244
>PRK11124 artP arginine transporter ATP-binding subunit; Provisional
Probab=86.96  E-value=0.52  Score=24.44  Aligned_cols=25  Identities=24%  Similarity=0.433  Sum_probs=16.3

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             3799997078862578999999972
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~ll  525 (789)
                      -.++-+.|+-|+||||++++|..+.
T Consensus        28 Ge~~~iiG~nGaGKSTLl~~l~gl~   52 (242)
T PRK11124         28 GETLVLLGPSGAGKSSLLRVLNLLE   52 (242)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHCCC
T ss_conf             9899999999971999999996588


No 245
>cd03250 ABCC_MRP_domain1 Domain 1 of the ABC subfamily C.  This family is also known as MRP (mulrtidrug resisitance-associated protein).  Some of the MRP members have five additional transmembrane segments in their N-terminas, but the function of these additional membrane-spanning domains is not clear.  The MRP was found in the multidrug-resisting lung cancer cell in which p-glycoprotein was not overexpressed. MRP exports glutathione by drug stimulation, as well as, certain substrates in conjugated forms with anions, such as glutathione, glucuronate, and sulfate.
Probab=86.92  E-value=0.44  Score=24.93  Aligned_cols=26  Identities=31%  Similarity=0.441  Sum_probs=20.0

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             33799997078862578999999972
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~ll  525 (789)
                      .-.++-+.|+-|.||||++++|..++
T Consensus        30 ~Ge~~~IvG~sGsGKSTLl~~i~G~~   55 (204)
T cd03250          30 KGELVAIVGPVGSGKSSLLSALLGEL   55 (204)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHCCCC
T ss_conf             99899999999985899999981895


No 246
>cd03213 ABCG_EPDR ABCG transporters are involved in eye pigment (EP) precursor transport, regulation of lipid-trafficking mechanisms, and pleiotropic drug resistance (DR).  DR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes.  Compared to other members of the ABC transporter subfamilies, the ABCG transporter family is composed of proteins that have an ATP-binding cassette domain at the N-terminus and a TM (transmembrane) domain at the C-terminus.
Probab=86.90  E-value=0.4  Score=25.18  Aligned_cols=28  Identities=36%  Similarity=0.440  Sum_probs=22.3

Q ss_pred             CCCCEEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             7433799997078862578999999972
Q gi|254781225|r  498 NKAQRFIHIRGVGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       498 ~~~~~~~~~~G~G~nGKSt~~~~l~~ll  525 (789)
                      ...-.++.+.|+-++||||++++|..++
T Consensus        32 v~~Gei~~ilGpnGaGKSTLl~~l~Gl~   59 (194)
T cd03213          32 AKPGELTAIMGPSGAGKSTLLNALAGRR   59 (194)
T ss_pred             EECCEEEEEECCCCCHHHHHHHHHHCCC
T ss_conf             9088199999899951999999985777


No 247
>COG1120 FepC ABC-type cobalamin/Fe3+-siderophores transport systems, ATPase components [Inorganic ion transport and metabolism / Coenzyme metabolism]
Probab=86.90  E-value=0.5  Score=24.57  Aligned_cols=30  Identities=30%  Similarity=0.362  Sum_probs=23.3

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             433799997078862578999999972330
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      ....+.-+.|+-|.||||+++.|..++-..
T Consensus        26 ~~G~i~~iiGpNG~GKSTLLk~l~~~l~p~   55 (258)
T COG1120          26 PKGEITGILGPNGSGKSTLLKCLAGLLKPK   55 (258)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCCC
T ss_conf             599799998998889999999986567888


No 248
>pfam00625 Guanylate_kin Guanylate kinase.
Probab=86.89  E-value=0.7  Score=23.59  Aligned_cols=56  Identities=23%  Similarity=0.427  Sum_probs=36.3

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCCCCCHHHHHHCCCEEEEEECCC
Q ss_conf             7999970788625789999999723300034426764201245555689889973898099993467
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEAGKANPSLIRLMGSRIVIISETN  568 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~~~~~~~~la~l~g~r~~~~~E~~  568 (789)
                      +++++.|+.+.||+|+++.|..-+++....+.+-  ++  |.+..+       ...|.-..++++..
T Consensus         2 klivl~GPSG~GK~tl~~~L~~~~~~~~~~~vs~--TT--R~~R~~-------E~~G~dY~Fvs~~~   57 (182)
T pfam00625         2 RPIVLSGPSGVGKSHIKKALLDEYPEKFGYSVSH--TT--RPPRPG-------EVDGKDYHFVSKEE   57 (182)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHCCCCEEEEEEE--EC--CCCCCC-------CCCCCEEEEECHHH
T ss_conf             8699989899999999999998486673445765--54--799987-------87896579965899


No 249
>PRK13768 GTPase; Provisional
Probab=86.89  E-value=0.75  Score=23.37  Aligned_cols=24  Identities=29%  Similarity=0.487  Sum_probs=14.2

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             999970788625789999999723
Q gi|254781225|r  503 FIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       503 ~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      ..+..|+.|+|||||...+..-+-
T Consensus         4 ~~~ViGpaGSGKsT~~~~l~~~l~   27 (253)
T PRK13768          4 IVFFLGTAGSGKTTLVGALSDWLE   27 (253)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHH
T ss_conf             899989999988999999999999


No 250
>COG4615 PvdE ABC-type siderophore export system, fused ATPase and permease components [Secondary metabolites biosynthesis, transport, and catabolism / Inorganic ion transport and metabolism]
Probab=86.81  E-value=0.64  Score=23.82  Aligned_cols=30  Identities=37%  Similarity=0.480  Sum_probs=24.3

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             433799997078862578999999972330
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      +.--++|++|.-++|||||+.++..+.-..
T Consensus       347 krGelvFliG~NGsGKST~~~LLtGL~~Pq  376 (546)
T COG4615         347 KRGELVFLIGGNGSGKSTLAMLLTGLYQPQ  376 (546)
T ss_pred             ECCCEEEEECCCCCCHHHHHHHHHHCCCCC
T ss_conf             337389998889963889999997066888


No 251
>PRK11176 lipid transporter ATP-binding/permease protein; Provisional
Probab=86.76  E-value=0.65  Score=23.79  Aligned_cols=31  Identities=32%  Similarity=0.452  Sum_probs=25.1

Q ss_pred             CCCCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             7433799997078862578999999972330
Q gi|254781225|r  498 NKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       498 ~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      ......+-+.|+.|+||||++++|..++-.+
T Consensus       365 I~~G~~vaiVG~SGsGKSTL~~LL~gly~p~  395 (581)
T PRK11176        365 IPAGKTVALVGRSGSGKSTIANLLTRFYDID  395 (581)
T ss_pred             CCCCCEEECCCCCCCCHHHHHHHHHHHCCCC
T ss_conf             7999443122899986789999998536678


No 252
>PRK02224 chromosome segregation protein; Provisional
Probab=86.75  E-value=1.1  Score=22.26  Aligned_cols=11  Identities=18%  Similarity=0.398  Sum_probs=6.1

Q ss_pred             HCCEEEEECCC
Q ss_conf             07889992347
Q gi|254781225|r   51 ACGFGFVCGVG   61 (789)
Q Consensus        51 ~~giGi~~G~~   61 (789)
                      ..||=+++|++
T Consensus        22 ~~Gi~~I~G~N   32 (880)
T PRK02224         22 EDGVTVIHGLN   32 (880)
T ss_pred             CCCEEEEECCC
T ss_conf             99858998999


No 253
>PRK10895 putative ABC transporter ATP-binding protein YhbG; Provisional
Probab=86.75  E-value=0.52  Score=24.41  Aligned_cols=29  Identities=17%  Similarity=0.329  Sum_probs=21.4

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             33799997078862578999999972330
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      .--++-+.|+-++||||++++|..++...
T Consensus        28 ~Gei~~liGpNGaGKSTLl~~i~Gl~~~~   56 (241)
T PRK10895         28 SGEIVGLLGPNGAGKTTTFYMVVGIVPRD   56 (241)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHCCCCCC
T ss_conf             99799998899986999999996788888


No 254
>PRK13638 cbiO cobalt transporter ATP-binding subunit; Provisional
Probab=86.70  E-value=0.57  Score=24.17  Aligned_cols=26  Identities=27%  Similarity=0.316  Sum_probs=15.6

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             79999707886257899999997233
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      .++-+.|+-|+||||++++|..++-.
T Consensus        28 ei~~liGpNGaGKSTLlk~l~Gl~~p   53 (271)
T PRK13638         28 PVTGLVGANGCGKSTLFMNLSGLLRP   53 (271)
T ss_pred             CEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             79999999998099999999668888


No 255
>COG0464 SpoVK ATPases of the AAA+ class [Posttranslational modification, protein turnover, chaperones]
Probab=86.68  E-value=1.5  Score=21.34  Aligned_cols=72  Identities=13%  Similarity=0.157  Sum_probs=46.1

Q ss_pred             CCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCC--CCCCHHHHHHCCCEEEEEECCCC
Q ss_conf             7433799997078862578999999972330003442676420124555--56898899738980999934677
Q gi|254781225|r  498 NKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEA--GKANPSLIRLMGSRIVIISETNE  569 (789)
Q Consensus       498 ~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~~--~~~~~~la~l~g~r~~~~~E~~~  569 (789)
                      .+..+.++++|+-++||+.+...+..-++-...+.....++++--+...  -..-+..|+..-...++++|.+.
T Consensus       273 ~~~~~giLl~GpPGtGKT~lAkava~~~~~~fi~v~~~~l~sk~vGesek~ir~~F~~A~~~~p~iifiDEiDs  346 (494)
T COG0464         273 LRPPKGVLLYGPPGTGKTLLAKAVALESRSRFISVKGSELLSKWVGESEKNIRELFEKARKLAPSIIFIDEIDS  346 (494)
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEHHHHHH
T ss_conf             98883699988999758999999875449824884335554077659999999999999966998897488666


No 256
>pfam08419 consensus
Probab=86.65  E-value=1.3  Score=21.79  Aligned_cols=40  Identities=23%  Similarity=0.311  Sum_probs=25.2

Q ss_pred             HHHHHHHHHHHHCCCCCCCEEEEEEEC-CCCCHHHHHHHHHH
Q ss_conf             999999999997598743379999707-88625789999999
Q gi|254781225|r  483 MDYFTRCVGMALLGGNKAQRFIHIRGV-GGSGKSTLMNLIKY  523 (789)
Q Consensus       483 ~~~l~~~~g~~l~g~~~~~~~~~~~G~-G~nGKSt~~~~l~~  523 (789)
                      ..+-.++.. .|........++..||+ |+.|||||..-|..
T Consensus        57 k~WQ~~l~~-~l~~~PddRtI~Wvygp~GgeGKStfak~L~~   97 (116)
T pfam08419        57 RPWQDEVES-LLEEEPDDRTIIWVYGPNGGEGKSTFAKHLGL   97 (116)
T ss_pred             CHHHHHHHH-HHHCCCCCCEEEEEECCCCCCCHHHHHHHHHH
T ss_conf             169999999-98369987469999858998664288886420


No 257
>cd03267 ABC_NatA_like Similar in sequence to NatA, this is the ATPase component of a bacterial ABC-type Na+ transport system called NatAB, which catalyzes ATP-dependent electrogenic Na+ extrusion without mechanically coupled to proton or K+ uptake.  NatB possess six putative membrane spanning regions at its C-terminus.  In B. subtilis, NatAB is inducible by agents such as ethanol and protonophores, which lower the protonmotive force across the membrane.  The closest sequence similarity to NatA is exhibited by DrrA of the two-component daunomycin- and doxorubicin-efflux system.  Hence, the functional NatAB is presumably assembled with two copies of the single ATP-binding protein and the single intergral membrane protein.
Probab=86.63  E-value=0.54  Score=24.31  Aligned_cols=30  Identities=17%  Similarity=0.316  Sum_probs=24.1

Q ss_pred             CCCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             743379999707886257899999997233
Q gi|254781225|r  498 NKAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       498 ~~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ...--++-+.|+-+.||||++++|..++-.
T Consensus        44 i~~Gei~gLlGpNGaGKSTllk~l~Gl~~p   73 (236)
T cd03267          44 IEKGEIVGFIGPNGAGKTTTLKILSGLLQP   73 (236)
T ss_pred             ECCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             848959999999983099999999649488


No 258
>PRK13546 teichoic acids export protein ATP-binding subunit; Provisional
Probab=86.59  E-value=0.52  Score=24.42  Aligned_cols=29  Identities=38%  Similarity=0.509  Sum_probs=22.8

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             43379999707886257899999997233
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ..--++-+.|+-|+||||++++|..++-.
T Consensus        48 ~~GEivgllG~NGaGKSTLlk~I~Gl~~P   76 (264)
T PRK13546         48 YEGDVIGLVGINGSGKSTLSNIIGGSLSP   76 (264)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             59989999989986199999999679888


No 259
>cd03222 ABC_RNaseL_inhibitor The ABC ATPase RNase L inhibitor (RLI) is a key enzyme in ribosomal biogenesis, formation of translation preinitiation complexes, and assembly of HIV capsids.  RLI's are not transport proteins, and thus cluster with a group of soluble proteins that lack the transmembrane components commonly found in other members of the family.  Structurally, RLI's have an N-terminal Fe-S domain and two nucleotide-binding domains, which are arranged to form two composite active sites in their interface cleft.  RLI is one of the most conserved enzymes between archaea and eukaryotes with a sequence identity more than 48%.  The high degree of evolutionary conservation suggests that RLI performs a central role in archaeal and eukaryotic physiology.
Probab=86.58  E-value=0.53  Score=24.38  Aligned_cols=30  Identities=27%  Similarity=0.319  Sum_probs=24.1

Q ss_pred             CCCCCEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             874337999970788625789999999723
Q gi|254781225|r  497 GNKAQRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       497 ~~~~~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      ....--++-+.|+-+.||||++++|..++-
T Consensus        21 ~v~~GEiv~ilGpNGaGKSTllk~i~G~l~   50 (177)
T cd03222          21 VVKEGEVIGIVGPNGTGKTTAVKILAGQLI   50 (177)
T ss_pred             CCCCCCEEEEECCCCCCHHHHHHHHHCCCC
T ss_conf             558998999989999999999999968867


No 260
>cd03240 ABC_Rad50 The catalytic domains of Rad50 are similar to the ATP-binding cassette of ABC transporters, but are not associated with membrane-spanning domains.  The conserved ATP-binding motifs common to Rad50 and the ABC transporter family include the Walker A and Walker B motifs, the Q loop, a histidine residue in the switch region, a D-loop, and a conserved LSGG sequence.  This conserved sequence, LSGG, is the most specific and characteristic motif of this family and is thus known as the ABC signature sequence.
Probab=86.58  E-value=0.67  Score=23.68  Aligned_cols=25  Identities=36%  Similarity=0.680  Sum_probs=20.2

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             3799997078862578999999972
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~ll  525 (789)
                      .-+..+.|+-|.||||+++.|...+
T Consensus        22 ~~itaivG~NGaGKSTLl~~i~~~l   46 (204)
T cd03240          22 SPLTLIVGQNGAGKTTIIEALKYAL   46 (204)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHCC
T ss_conf             8889999899999999999986304


No 261
>COG1117 PstB ABC-type phosphate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=86.55  E-value=0.73  Score=23.45  Aligned_cols=30  Identities=23%  Similarity=0.273  Sum_probs=22.2

Q ss_pred             CCCCCCEEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             987433799997078862578999999972
Q gi|254781225|r  496 GGNKAQRFIHIRGVGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       496 g~~~~~~~~~~~G~G~nGKSt~~~~l~~ll  525 (789)
                      -.....+..-++||.|.|||||+..+-.|.
T Consensus        28 l~i~~~~VTAlIGPSGcGKST~LR~lNRmn   57 (253)
T COG1117          28 LDIPKNKVTALIGPSGCGKSTLLRCLNRMN   57 (253)
T ss_pred             EECCCCCEEEEECCCCCCHHHHHHHHHHHC
T ss_conf             214578069988898867888999987541


No 262
>PRK08084 DNA replication initiation factor; Provisional
Probab=86.55  E-value=1.9  Score=20.64  Aligned_cols=133  Identities=14%  Similarity=0.137  Sum_probs=63.6

Q ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCC--CCCCCHHHHHHCCCC
Q ss_conf             789999988879999999999999999759874337999970788625789999999723300--034426764201245
Q gi|254781225|r  467 QEFLDLVSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQY--VINAEASDIMQNRPP  544 (789)
Q Consensus       467 p~~~~~l~~~~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~--~~~~~~~~~~~~~~~  544 (789)
                      +.|+.|+..  ++.++..-++..+    .+  ....++++||+.|.|||-+++.+++-+...+  +.-++...... .  
T Consensus        19 ~tfdnFi~g--~n~~~~~al~~~~----~~--~~~~~l~l~G~~G~GKTHLLqA~~~~~~~~~~~~~yl~~~~~~~-~--   87 (235)
T PRK08084         19 ETFASFYPG--DNDSLLAALQNVL----RQ--EHSGYIYLWGREGAGRSHLLHAACAELSQRGDAVGYVPLDKRAW-F--   87 (235)
T ss_pred             CCHHCCCCC--CCHHHHHHHHHHH----HC--CCCCEEEEECCCCCCHHHHHHHHHHHHHCCCCCEEEEEHHHHHH-H--
T ss_conf             663023448--8699999999998----57--89876999899998889999999999970798579987798665-1--


Q ss_pred             CCCCCCHHHHHHCCCEEEEEECCCCCCCCCCCEEEEEECCCEEEEEECCCCCCEEEECC--EEEEEECCCCCCCCC-CCC
Q ss_conf             55568988997389809999346777601310024541598587321047860687145--289997388634267-984
Q gi|254781225|r  545 EAGKANPSLIRLMGSRIVIISETNENDEINAAKIKQMTGGDCMTARLNYGNTYSESPAS--FTPFIVPNKHLFVRN-PDD  621 (789)
Q Consensus       545 ~~~~~~~~la~l~g~r~~~~~E~~~~~~~~~~~~K~ltggD~i~ar~~~~~~~~~~~p~--~~~~~~~N~~P~~~~-~d~  621 (789)
                          .+..+..+...-++.+++.+.           +.|. .-.-+.+| .-|....-.  ..++++++..|.--+ ...
T Consensus        88 ----~~~~l~~l~~~dll~iDDi~~-----------i~g~-~~~ee~lF-~l~N~~~~~g~~~ll~ts~~~P~~l~~~l~  150 (235)
T PRK08084         88 ----VPEVLEGMEQLSLVCIDNIEC-----------IAGD-ELWEMAIF-DLYNRILESGKTRLLITGDRPPRQLNLGLP  150 (235)
T ss_pred             ----HHHHHHHHHHCCEEEEECHHH-----------HCCC-HHHHHHHH-HHHHHHHHHCCCEEEEECCCCHHHCCCCCH
T ss_conf             ----799998764189899827455-----------4699-78999999-999999984896699967988243023128


Q ss_pred             CEEEEE
Q ss_conf             166468
Q gi|254781225|r  622 AWWRRY  627 (789)
Q Consensus       622 ~~~rR~  627 (789)
                      -+-.|+
T Consensus       151 DL~SRl  156 (235)
T PRK08084        151 DLASRL  156 (235)
T ss_pred             HHHHHH
T ss_conf             899999


No 263
>cd03220 ABC_KpsT_Wzt ABC_KpsT_Wzt   The KpsT/Wzt ABC transporter subfamily is involved in extracellular polysaccharide export.  Among the variety of membrane-linked or extracellular polysaccharides excreted by bacteria, only capsular polysaccharides, lipopolysaccharides, and teichoic acids have been shown to be exported by ABC transporters.  A typical system is made of a conserved integral membrane and an ABC.  In addition to these proteins, capsular polysaccharide exporter systems require two 'accessory' proteins to perform their function: a periplasmic (E.coli) or a lipid-anchored outer membrane protein called OMA (Neisseria meningitidis and Haemophilus influenzae) and a cytoplasmic membrane protein MPA2.
Probab=86.55  E-value=0.56  Score=24.21  Aligned_cols=28  Identities=32%  Similarity=0.443  Sum_probs=19.9

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             3379999707886257899999997233
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      .--++-+.|+-++||||++++|..++-.
T Consensus        47 ~GeivgilG~NGaGKSTLl~~i~Gl~~p   74 (224)
T cd03220          47 RGERIGLIGRNGAGKSTLLRLLAGIYPP   74 (224)
T ss_pred             CCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             8989999979998199999999758777


No 264
>TIGR03411 urea_trans_UrtD urea ABC transporter, ATP-binding protein UrtD. Members of this protein family are ABC transporter ATP-binding subunits 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.
Probab=86.53  E-value=0.54  Score=24.30  Aligned_cols=28  Identities=29%  Similarity=0.386  Sum_probs=19.4

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             3379999707886257899999997233
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      .--++-+.|+-++||||++++|..++-.
T Consensus        27 ~Gei~~liGpNGaGKSTLl~~i~Gl~~p   54 (242)
T TIGR03411        27 PGELRVIIGPNGAGKTTMMDVITGKTRP   54 (242)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             9989999989997599999999679578


No 265
>TIGR02868 CydC ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydC; InterPro: IPR014223   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 CydC, a member of a heterodimeric ATP-binding cassette-type transporter (ABC transporter). It is involved in the export of glutathione from the cytoplasm to the periplasm and is required for the assembly of both cytochrome c and cytochrome bd , , .; GO: 0042626 ATPase activity coupled to transmembrane movement of substances, 0006810 transport, 0016021 integral to membrane.
Probab=86.42  E-value=0.78  Score=23.28  Aligned_cols=25  Identities=36%  Similarity=0.441  Sum_probs=21.4

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             9999707886257899999997233
Q gi|254781225|r  503 FIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       503 ~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      =+-+.|+.|.||||++.+|..++-.
T Consensus       389 r~Ai~G~SG~GKsTLL~~L~G~l~P  413 (566)
T TIGR02868       389 RVAILGPSGSGKSTLLATLAGLLDP  413 (566)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHCCC
T ss_conf             0898668876578999999840289


No 266
>PRK11614 livF leucine/isoleucine/valine transporter ATP-binding subunit; Provisional
Probab=86.41  E-value=0.55  Score=24.25  Aligned_cols=28  Identities=21%  Similarity=0.341  Sum_probs=19.5

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             3379999707886257899999997233
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      .--++-+.|+-++||||++++|..++-.
T Consensus        30 ~Gei~~liG~NGaGKSTLl~~i~G~~~~   57 (237)
T PRK11614         30 QGEIVTLIGANGAGKTTLLGTLCGDPRA   57 (237)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             9979999879997599999999679988


No 267
>cd03221 ABCF_EF-3 ABCF_EF-3  Elongation factor 3 (EF-3) is a cytosolic protein required by fungal ribosomes for in vitro protein synthesis and for in vivo growth.  EF-3 stimulates the binding of the EF-1: GTP: aa-tRNA ternary complex to the ribosomal A site by facilitated release of the deacylated tRNA from the E site.  The reaction requires ATP hydrolysis.  EF-3 contains two ATP nucleotide binding sequence (NBS) motifs.  NBSI is sufficient for the intrinsic ATPase activity. NBSII is essential for the ribosome-stimulated functions.
Probab=86.36  E-value=0.59  Score=24.08  Aligned_cols=67  Identities=22%  Similarity=0.298  Sum_probs=40.0

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCCCCCCC--C------CHHHHHHCCCCCCCCCCHHHHHH--CCCEEEEEECCC
Q ss_conf             4337999970788625789999999723300034--4------26764201245555689889973--898099993467
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVIN--A------EASDIMQNRPPEAGKANPSLIRL--MGSRIVIISETN  568 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~--~------~~~~~~~~~~~~~~~~~~~la~l--~g~r~~~~~E~~  568 (789)
                      .....+.++|+-+.|||||+++|..++.......  .      -...+++.     -..+-.+|+.  ....+.+.+||.
T Consensus        24 ~~ge~~~l~G~NGsGKTTl~~~l~G~~~~~~G~i~~~~~~~i~y~~QLSgG-----qkqr~~la~al~~~p~iliLDEPt   98 (144)
T cd03221          24 NPGDRIGLVGRNGAGKSTLLKLIAGELEPDEGIVTWGSTVKIGYFEQLSGG-----EKMRLALAKLLLENPNLLLLDEPT   98 (144)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCCCCEEEEECCCCEEEEEHHCCHH-----HHHHHHHHHHHCCCCCEEEEECCC
T ss_conf             799999999899984999999984898898509999996089987007999-----999999999972599899995775


Q ss_pred             CC
Q ss_conf             77
Q gi|254781225|r  569 EN  570 (789)
Q Consensus       569 ~~  570 (789)
                      .+
T Consensus        99 ~~  100 (144)
T cd03221          99 NH  100 (144)
T ss_pred             CC
T ss_conf             55


No 268
>TIGR01189 ccmA heme ABC exporter, ATP-binding protein CcmA; InterPro: IPR005895   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).     This family contains the cytochrome c biogenesis protein encoded by ccmA in bacteria and one arabidopsis protein, possibly encoded by an organelle. Bacterial c-type cytochromes are located on the periplasmic side of the cytoplasmic membrane. Several gene products encoded in a locus designated as 'ccm' are implicated in the transport and assembly of the functional cytochrome C. This cluster includes genes: ccmA;B;C;D;E;F;G and H. The post-translational pathway includes the transport of a heme moiety, the secretion of the apoprotein and the covalent attachment of the heme with the apoprotein. The proteins ccmA and B represent an ABC transporter; ccmC and D participate in heme transfer to ccmE, which functions as a periplasmic heme chaperone. The presence of ccmF, G and H is suggested to be obligatory for the final functional assembly of cytochrome c.; GO: 0005215 transporter activity, 0017004 cytochrome complex assembly, 0030288 outer membrane-bounded periplasmic space.
Probab=86.35  E-value=0.69  Score=23.59  Aligned_cols=11  Identities=0%  Similarity=-0.169  Sum_probs=5.0

Q ss_pred             HHHHHHHHHHC
Q ss_conf             68999999740
Q gi|254781225|r  245 KGKEIARRWSK  255 (789)
Q Consensus       245 ~~l~lw~~wS~  255 (789)
                      |=|.+|..+..
T Consensus        92 ENL~F~~~~~~  102 (204)
T TIGR01189        92 ENLQFWAAIHG  102 (204)
T ss_pred             HHHHHHHHHHH
T ss_conf             87999999852


No 269
>cd01850 CDC_Septin CDC/Septin.  Septins are a conserved family of GTP-binding proteins associated with diverse processes in dividing and non-dividing cells.  They were first discovered in the budding yeast S. cerevisiae as a set of genes (CDC3, CDC10, CDC11 and CDC12) required for normal bud morphology. Septins are also present in metazoan cells, where they are required for cytokinesis in some systems, and implicated in a variety of other processes involving organization of the cell cortex and exocytosis.  In humans, 12 septin genes generate dozens of polypeptides, many of which comprise heterooligomeric complexes. Since septin mutants are commonly defective in cytokinesis and formation of the neck formation of the neck filaments/septin rings, septins have been considered to be the primary constituents of the neck filaments.  Septins belong to the GTPase superfamily for their conserved GTPase motifs and enzymatic activities.
Probab=86.34  E-value=0.59  Score=24.08  Aligned_cols=29  Identities=14%  Similarity=0.221  Sum_probs=10.5

Q ss_pred             CCCCCEEEEEEECCCCCHHHH-HHHHHHHH
Q ss_conf             874337999970788625789-99999972
Q gi|254781225|r  497 GNKAQRFIHIRGVGGSGKSTL-MNLIKYAF  525 (789)
Q Consensus       497 ~~~~~~~~~~~G~G~nGKSt~-~~~l~~ll  525 (789)
                      +++-++++.++-|.+.|=+-+ +.+|+.|-
T Consensus       112 D~RVH~cLYFI~Ptgh~L~~lDi~~mk~Ls  141 (276)
T cd01850         112 DTRVHACLYFIEPTGHGLKPLDIEFMKRLS  141 (276)
T ss_pred             CCCEEEEEEEECCCCCCCCHHHHHHHHHHC
T ss_conf             774489999967888888799999999962


No 270
>cd03232 ABC_PDR_domain2 The pleiotropic drug resistance-like (PDR) family of ATP-binding cassette (ABC) transporters. PDR is a well-described phenomenon occurring in fungi and shares several similarities with processes in bacteria and higher eukaryotes.  This PDR subfamily represents domain I of its (ABC-IM)2 organization.  ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules.  The nucleotide binding domain shows the highest similarity between all members of the family.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=86.30  E-value=0.56  Score=24.20  Aligned_cols=26  Identities=27%  Similarity=0.483  Sum_probs=20.6

Q ss_pred             CCCCEEEEEEECCCCCHHHHHHHHHH
Q ss_conf             74337999970788625789999999
Q gi|254781225|r  498 NKAQRFIHIRGVGGSGKSTLMNLIKY  523 (789)
Q Consensus       498 ~~~~~~~~~~G~G~nGKSt~~~~l~~  523 (789)
                      ...-.++-+.|+-+.||||++++|..
T Consensus        30 i~~Ge~~~llGpnGaGKSTLl~~l~g   55 (192)
T cd03232          30 VKPGTLTALMGESGAGKTTLLDVLAG   55 (192)
T ss_pred             EECCEEEEEECCCCCCHHHHHHHHHC
T ss_conf             92883999999999988999999837


No 271
>cd03259 ABC_Carb_Solutes_like ABC Carbohydrate and Solute Transporters-like subgroup.  This family is comprised of proteins involved in the transport of apparently unrelated solutes and proteins specific for di- and oligosaccharides and polyols.  ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules.  The nucleotide-binding domain shows the highest similarity between all members of the family.   ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=86.30  E-value=0.58  Score=24.13  Aligned_cols=29  Identities=31%  Similarity=0.460  Sum_probs=22.1

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             43379999707886257899999997233
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ...-++-+.|+-++||||++++|..+.-.
T Consensus        24 ~~Gei~~iiGpnGaGKSTl~~~i~Gl~~p   52 (213)
T cd03259          24 EPGEFLALLGPSGCGKTTLLRLIAGLERP   52 (213)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             89989999999997399999999759998


No 272
>cd03285 ABC_MSH2_euk MutS2 homolog in eukaryotes.  The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch.  Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily.  MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined.  Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes.  The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis.  All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action.  MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c
Probab=86.29  E-value=1  Score=22.43  Aligned_cols=26  Identities=35%  Similarity=0.432  Sum_probs=21.0

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             43379999707886257899999997
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYA  524 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~l  524 (789)
                      ..+.+++++|+-..||||++..+.-+
T Consensus        28 ~~~~i~iiTGpN~sGKSt~lk~i~l~   53 (222)
T cd03285          28 GKSRFLIITGPNMGGKSTYIRQIGVI   53 (222)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH
T ss_conf             98259999899988718999999999


No 273
>PRK06851 hypothetical protein; Provisional
Probab=86.27  E-value=1.6  Score=21.12  Aligned_cols=48  Identities=17%  Similarity=0.197  Sum_probs=29.3

Q ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             99998887999999999999999975987433799997078862578999999972
Q gi|254781225|r  470 LDLVSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       470 ~~~l~~~~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~ll  525 (789)
                      ..|+..+.|+-. +.|+..+     +.  .-...+++.|.-++||||+++.|....
T Consensus       192 hlF~~A~TP~G~-v~~i~~l-----~~--~~~~~y~ikG~pGtGKstlL~~i~~~A  239 (368)
T PRK06851        192 HLFLGAITPKGA-VDHVPSL-----TE--GVKNRYFLKGRPGTGKSTMLKKVAKAA  239 (368)
T ss_pred             EEECCCCCCCCH-HHHHHHH-----HH--CCCEEEEECCCCCCCHHHHHHHHHHHH
T ss_conf             132235799964-5147878-----60--678699981899987799999999999


No 274
>PRK13542 consensus
Probab=86.20  E-value=0.58  Score=24.12  Aligned_cols=27  Identities=22%  Similarity=0.477  Sum_probs=19.0

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             379999707886257899999997233
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      --++-+.|+-|.|||||+++|..++-.
T Consensus        44 Gei~~liGpNGaGKTTLlk~l~Gll~p   70 (224)
T PRK13542         44 GDLLQVMGPNGSGKTSLLRVLSGLMPP   70 (224)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             979999999999999999999579788


No 275
>cd03269 ABC_putative_ATPase This subfamily is involved in drug resistance, nodulation, lipid transport, and bacteriocin and lantibiotic immunity.  In eubacteria and archaea, the typical organization consists of one ABC and one or two IMs.  Eukaryote systems of the ABCA subfamily display ABC domains strongly similar to this family.  ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides and more complex organic molecules.  The nucleotide binding domain shows the highest similarity between all members of the family.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=86.20  E-value=0.69  Score=23.63  Aligned_cols=30  Identities=20%  Similarity=0.292  Sum_probs=23.9

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             433799997078862578999999972330
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      ..-.++-+.|+-++||||++++|..++-..
T Consensus        24 ~~Gei~gllG~NGaGKTTll~~i~Gl~~p~   53 (210)
T cd03269          24 EKGEIFGLLGPNGAGKTTTIRMILGIILPD   53 (210)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCCC
T ss_conf             799599999899984999999996002668


No 276
>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional
Probab=86.16  E-value=2  Score=20.51  Aligned_cols=152  Identities=16%  Similarity=0.250  Sum_probs=88.4

Q ss_pred             CHHHHCCEECCCCCCCC-----CCHHHHHHHHHH-HCCCHHHHHHHHHHHHHHHCCCC---CCCEEEEEEECCCCCHHHH
Q ss_conf             86550100137888875-----794789999988-87999999999999999975987---4337999970788625789
Q gi|254781225|r  447 TKELYITKSTGTPFVEG-----EPSQEFLDLVSG-YFESEEVMDYFTRCVGMALLGGN---KAQRFIHIRGVGGSGKSTL  517 (789)
Q Consensus       447 ~~~~~~t~~~~~~y~~~-----a~~p~~~~~l~~-~~~d~e~~~~l~~~~g~~l~g~~---~~~~~~~~~G~G~nGKSt~  517 (789)
                      +-+..+...+.++-..-     ..--..++.|.+ ++|.++.++-+-+.+-.+-.|-.   +.---|++.||.|-||+-+
T Consensus       425 di~~vv~~~t~ip~~~~~~~~~~~l~~le~~l~~~viGQ~~Ai~~v~~ai~~~raGL~~~~rPigsFlf~GPTGVGKTEl  504 (758)
T PRK11034        425 DIESVVARIARIPEKSVSQSDRDTLKNLGDRLKMLVFGQDKAIEALTEAIKMSRAGLGHEHKPVGSFLFAGPTGVGKTEV  504 (758)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCHHHH
T ss_conf             99999987503607677677999999899998778745499999999999998638889999705899978998777999


Q ss_pred             HHHHHHHHCCCCCCCCCHHHHHHCCCCCCCCCCHHHHHHCCC----------------------EEEEEECCCCCCCCCC
Q ss_conf             999999723300034426764201245555689889973898----------------------0999934677760131
Q gi|254781225|r  518 MNLIKYAFGNQYVINAEASDIMQNRPPEAGKANPSLIRLMGS----------------------RIVIISETNENDEINA  575 (789)
Q Consensus       518 ~~~l~~llG~~~~~~~~~~~~~~~~~~~~~~~~~~la~l~g~----------------------r~~~~~E~~~~~~~~~  575 (789)
                      ...|...|+.. ..-.+.+....         ...+++|.|+                      -++..+|.++-..---
T Consensus       505 ak~LA~~L~~~-lir~DMSEy~e---------~hsvsrLiGaPPGYVGy~eGG~Lte~Vr~~PysVvL~DEIEKAhpdV~  574 (758)
T PRK11034        505 TVQLSKALGIE-LLRFDMSEYME---------RHTVSRLIGAPPGYVGFDQGGLLTDAVIKHPHAVLLLDEIEKAHPDVF  574 (758)
T ss_pred             HHHHHHHHHHH-HHCCCHHHHCC---------HHHHHHHCCCCCCCCCCCCCCCCCHHHHHCCCEEEEEHHHHHHCHHHH
T ss_conf             99999998667-72142665312---------014777448998666767777012878739877997336756398999


Q ss_pred             CEEEEEECCCEEEEEECCCCCCEEEECCEEEEEECCC
Q ss_conf             0024541598587321047860687145289997388
Q gi|254781225|r  576 AKIKQMTGGDCMTARLNYGNTYSESPASFTPFIVPNK  612 (789)
Q Consensus       576 ~~~K~ltggD~i~ar~~~~~~~~~~~p~~~~~~~~N~  612 (789)
                      ..|-|+.....++-  -.++. +.|+.+ .++|.+|-
T Consensus       575 nilLQvlD~G~LtD--~~Gr~-vdF~Nt-iIImTSN~  607 (758)
T PRK11034        575 NLLLQVMDNGTLTD--NNGRK-ADFRNV-VLVMTTNA  607 (758)
T ss_pred             HHHHHHCCCCCCCC--CCCCE-EECEEE-EEEEECCC
T ss_conf             98873237783017--99998-844001-99982561


No 277
>TIGR00958 3a01208 antigen peptide transporter 2; InterPro: IPR005293   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).     Proteins of this family are involved in the transport of antigens from the cytoplasm to a membrane-bound compartment for association with MHC class I molecules.; GO: 0005215 transporter activity, 0006810 transport.
Probab=86.14  E-value=1.3  Score=21.80  Aligned_cols=65  Identities=18%  Similarity=0.133  Sum_probs=38.1

Q ss_pred             HCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCC-CCCCHHHHHHCCCCCCCCCCHHHHHHCCCEEEEEECCC
Q ss_conf             7598743379999707886257899999997233000-34426764201245555689889973898099993467
Q gi|254781225|r  494 LLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYV-INAEASDIMQNRPPEAGKANPSLIRLMGSRIVIISETN  568 (789)
Q Consensus       494 l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~-~~~~~~~~~~~~~~~~~~~~~~la~l~g~r~~~~~E~~  568 (789)
                      ||=..+.-.-.-+.||-|+||||.+-+|+++.-.... ..++..-+.+          .|=-.|.-+-..+.+||-
T Consensus       552 LtFt~~PG~vvALVGPsGsGKStvaaLL~n~Y~Pt~G~vLlDg~Pl~~----------y~H~YLH~~V~~VgQEPv  617 (770)
T TIGR00958       552 LTFTLEPGEVVALVGPSGSGKSTVAALLQNLYQPTGGQVLLDGVPLSQ----------YDHHYLHRQVALVGQEPV  617 (770)
T ss_pred             CCEEECCCEEEEEECCCCCCHHHHHHHHHHCCCCCCCEEEECCCCHHH----------HCCEECCCEEEEEECCCE
T ss_conf             743653862599865899839999999985578986568776846133----------265010002543320543


No 278
>cd03280 ABC_MutS2 MutS2 homologs in bacteria and eukaryotes.  The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch.  Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily.  MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined. Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes.  The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis.  All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action.  MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, a
Probab=86.14  E-value=0.99  Score=22.58  Aligned_cols=24  Identities=21%  Similarity=0.428  Sum_probs=19.6

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHH
Q ss_conf             337999970788625789999999
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKY  523 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~  523 (789)
                      .+.+++++|+-..|||||++.+.-
T Consensus        27 ~~~~~iiTGpN~sGKSt~lk~i~l   50 (200)
T cd03280          27 NKRVLVITGPNAGGKTVTLKTLGL   50 (200)
T ss_pred             CCEEEEEECCCCCCCHHHHHHHHH
T ss_conf             933999988987750999999999


No 279
>cd03217 ABC_FeS_Assembly ABC-type transport system involved in Fe-S cluster assembly, ATPase component.  Biosynthesis of iron-sulfur clusters (Fe-S) depends on multiprotein systems.  The SUF system of E. coli and Erwinia chrysanthemi is important for Fe-S biogenesis under stressful conditions.  The SUF system is made of six proteins: SufC is an atypical cytoplasmic ABC-ATPase, which forms a complex with SufB and SufD; SufA plays the role of a scaffold protein for assembly of iron-sulfur clusters and delivery to target proteins; SufS is a cysteine desulfurase which mobilizes the sulfur atom from cysteine and provides it to the cluster; SufE has no associated function yet.
Probab=86.02  E-value=0.68  Score=23.65  Aligned_cols=26  Identities=38%  Similarity=0.379  Sum_probs=20.9

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             43379999707886257899999997
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYA  524 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~l  524 (789)
                      ..-.++-+.|+-++||||++++|..+
T Consensus        24 ~~Gei~~iiGpnGaGKSTLl~~i~G~   49 (200)
T cd03217          24 KKGEVHALMGPNGSGKSTLAKTIMGH   49 (200)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHCCC
T ss_conf             79989999968999999999997077


No 280
>PRK11432 fbpC ferric transporter ATP-binding subunit; Provisional
Probab=86.01  E-value=0.56  Score=24.24  Aligned_cols=10  Identities=10%  Similarity=0.076  Sum_probs=4.8

Q ss_pred             CCCCEEEECC
Q ss_conf             2684388047
Q gi|254781225|r  130 GCGQYFVAYN  139 (789)
Q Consensus       130 ~~G~q~V~~g  139 (789)
                      ..|..+++-|
T Consensus        30 ~~Ge~~~llG   39 (351)
T PRK11432         30 KQGTMVTLLG   39 (351)
T ss_pred             CCCCEEEEEC
T ss_conf             8998999999


No 281
>PRK11160 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed
Probab=86.01  E-value=0.66  Score=23.74  Aligned_cols=30  Identities=40%  Similarity=0.554  Sum_probs=24.0

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             433799997078862578999999972330
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      ..-..+-+.|+.|.||||++++|...+-.+
T Consensus       365 ~~Ge~vaiVG~SGsGKSTL~~LL~r~ydp~  394 (575)
T PRK11160        365 KAGEKVALLGRTGCGKSTLLQLLTRAWDPQ  394 (575)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCCC
T ss_conf             699889998899975999999986236789


No 282
>PRK13891 conjugal transfer protein TrbE; Provisional
Probab=85.97  E-value=1  Score=22.55  Aligned_cols=28  Identities=25%  Similarity=0.316  Sum_probs=23.9

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHCCCCCC
Q ss_conf             9997078862578999999972330003
Q gi|254781225|r  504 IHIRGVGGSGKSTLMNLIKYAFGNQYVI  531 (789)
Q Consensus       504 ~~~~G~G~nGKSt~~~~l~~llG~~~~~  531 (789)
                      .+++|+.|.|||||+++|..-+..|...
T Consensus       491 TlIiGpTGaGKTvll~fL~aQ~~rY~~~  518 (852)
T PRK13891        491 TFMFGPTGAGKSTHLGIIAAQLRRYAGM  518 (852)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCC
T ss_conf             0787899998899999999997441898


No 283
>PRK05416 hypothetical protein; Provisional
Probab=85.97  E-value=1.2  Score=22.07  Aligned_cols=58  Identities=17%  Similarity=0.204  Sum_probs=28.2

Q ss_pred             HHHHHHHHHHCCCHHHHH---HHHHHHHHHHCCCCCCCE--EEEEEE-CCCCCHHHH-HHHHHHHHCC
Q ss_conf             789999988879999999---999999999759874337--999970-788625789-9999997233
Q gi|254781225|r  467 QEFLDLVSGYFESEEVMD---YFTRCVGMALLGGNKAQR--FIHIRG-VGGSGKSTL-MNLIKYAFGN  527 (789)
Q Consensus       467 p~~~~~l~~~~~d~e~~~---~l~~~~g~~l~g~~~~~~--~~~~~G-~G~nGKSt~-~~~l~~llG~  527 (789)
                      +...+|+.+   +++..+   .+..++.+.|-.-..+.+  +.|-+| +||-=-||+ .+.+..-|.+
T Consensus       211 ~~V~~yv~~---~~~~~~f~~~i~~~l~~~lp~y~~egk~yltIaiGCTGG~HRSV~~ae~l~~~l~~  275 (292)
T PRK05416        211 KPVADYVLA---QPEVEEFLDQIRDLLEFWLPGYRREGKSYLTIAIGCTGGQHRSVAIAERLAERLRA  275 (292)
T ss_pred             HHHHHHHHC---CCHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHC
T ss_conf             589999974---92299999999999999999999849977999975889871799999999999857


No 284
>PRK10787 DNA-binding ATP-dependent protease La; Provisional
Probab=85.97  E-value=2.1  Score=20.45  Aligned_cols=207  Identities=17%  Similarity=0.198  Sum_probs=106.5

Q ss_pred             HCCEECCCCCCCCCC----HHHHHHHHHHH-CCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             010013788887579----47899999888-7999999999999999975987433799997078862578999999972
Q gi|254781225|r  451 YITKSTGTPFVEGEP----SQEFLDLVSGY-FESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       451 ~~t~~~~~~y~~~a~----~p~~~~~l~~~-~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~ll  525 (789)
                      |+-+.+..+|.....    ...-.+-|++= +|=+.+.+.+.++++-.-......--.+-|+|+.|-||+.+..-|...|
T Consensus       294 YLd~l~~LPW~~~t~d~~dl~~A~~iLd~dHyGL~~vKeRile~lAv~~~~~~~kg~IlclvGpPGvGKTSl~~sIA~al  373 (784)
T PRK10787        294 YIDWMVQVPWNARSKVKKDLRQAQEILDTDHYGLERVKDRILEYLAVQSRVNKIKGPILCLVGPPGVGKTSLGQSIAKAT  373 (784)
T ss_pred             HHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             99999759988887875699999998765430657799999999999986246778779964699877246999999985


Q ss_pred             CCCCC-CCCCHHHHHHCCCCCCCCCCHHHHHHCCCEEEEEECCCCCCCCCC----------------CEEEEEECCCEEE
Q ss_conf             33000-344267642012455556898899738980999934677760131----------------0024541598587
Q gi|254781225|r  526 GNQYV-INAEASDIMQNRPPEAGKANPSLIRLMGSRIVIISETNENDEINA----------------AKIKQMTGGDCMT  588 (789)
Q Consensus       526 G~~~~-~~~~~~~~~~~~~~~~~~~~~~la~l~g~r~~~~~E~~~~~~~~~----------------~~~K~ltggD~i~  588 (789)
                      |..++ .++-             +. -+-|.++|-|-.++.-.+ |+.+..                .++=+=.-||+-.
T Consensus       374 ~r~f~rislG-------------Gv-~DeaeirGHrrTYvgamp-Grii~~l~~a~~~nPv~llDEiDK~~~~~~Gdp~s  438 (784)
T PRK10787        374 GRKYVRMALG-------------GV-RDEAEIRGHRRTYIGSMP-GKLIQKMAKVGVKNPLFLLDEIDKMSSDMRGDPAS  438 (784)
T ss_pred             CCCEEEEECC-------------CC-CCHHHHCCCCCCCCCCCC-HHHHHHHHHHCCCCCEEEEHHHHHHCCCCCCCHHH
T ss_conf             8986998068-------------87-888882564334344368-38999999748988566500355522455899889


Q ss_pred             E---------EECCCCCCE--EEECCEEEEEECCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCHHHHHCCCCHHHHH-
Q ss_conf             3---------210478606--8714528999738863426798416646899965887888787833422012044799-
Q gi|254781225|r  589 A---------RLNYGNTYS--ESPASFTPFIVPNKHLFVRNPDDAWWRRYIVIPFDKPIANRDASFAQKLETKYTLEAK-  656 (789)
Q Consensus       589 a---------r~~~~~~~~--~~~p~~~~~~~~N~~P~~~~~d~~~~rR~~iipF~~~~~~~d~~~~~~~~~~e~~~i~-  656 (789)
                      |         ..-|.+.|.  .|.....+|++|-+--   +-...+..||-+|.+..-..            .|+..|. 
T Consensus       439 alLEvLDpeQN~~F~Dhyl~~~~DlS~v~Fi~TaN~~---~ip~pLlDRmE~i~~~gYt~------------~eK~~Ia~  503 (784)
T PRK10787        439 ALLEVLDPEQNVAFSDHYLEVDYDLSDVMFVATSNSM---NIPAPLLDRMEVIRLSGYTE------------DEKLNIAK  503 (784)
T ss_pred             HHHHHCCHHHCCCCCCCEEECCCCHHHEEEEEECCCC---CCCHHHHHHEEEEEECCCCH------------HHHHHHHH
T ss_conf             9998459765564000322046452225899732767---78767763121554116767------------88999999


Q ss_pred             HHHHHHHHHHHHCCCCC---CC-CHHHHHHHHHHHHH
Q ss_conf             99999999999878898---87-88999999999984
Q gi|254781225|r  657 KWFLKGVKAYISKGLDV---DI-PEVCLKAKEEERQG  689 (789)
Q Consensus       657 ~w~l~g~~~~~~~g~~~---~~-p~~v~~a~~~y~~~  689 (789)
                      ++++  .+...++|++.   .. .+++....+.|-+|
T Consensus       504 ~~l~--p~~~~~~gl~~~~~~~~~~~~~~ii~~ytrE  538 (784)
T PRK10787        504 RHLL--PKQIERNALKKGELTVDDSAIIGIIRYYTRE  538 (784)
T ss_pred             HHCH--HHHHHHHCCCCCCCCCCHHHHHHHHHHCCCC
T ss_conf             7453--9999982899656743999999987533654


No 285
>TIGR03265 PhnT2 putative 2-aminoethylphosphonate ABC transport system, ATP-binding protein component. This ABC transporter ATP-binding protein is found in a number of genomes in operon-like contexts strongly suggesting a substrate specificity for 2-aminoethylphosphonate (2-AEP). The characterized PhnSTUV system is absent in the genomes in which this system is found. These genomes encode systems for the catabolism of 2-AEP, making the need for a 2-AEP-specific transporter likely.
Probab=85.95  E-value=0.59  Score=24.08  Aligned_cols=10  Identities=10%  Similarity=0.295  Sum_probs=5.1

Q ss_pred             CCCCEEEECC
Q ss_conf             2684388047
Q gi|254781225|r  130 GCGQYFVAYN  139 (789)
Q Consensus       130 ~~G~q~V~~g  139 (789)
                      ..|.++++.|
T Consensus        28 ~~Ge~~~llG   37 (353)
T TIGR03265        28 KKGEFVCLLG   37 (353)
T ss_pred             CCCCEEEEEC
T ss_conf             8999999999


No 286
>PRK10261 glutathione transporter ATP-binding protein; Provisional
Probab=85.88  E-value=1.1  Score=22.31  Aligned_cols=29  Identities=24%  Similarity=0.209  Sum_probs=23.2

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             43379999707886257899999997233
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ..--.+-+.|.-++||||+..+|..++-.
T Consensus       348 ~~GE~l~lvG~sGsGKSTl~r~l~gl~~~  376 (623)
T PRK10261        348 WPGETLSLVGESGSGKSTTGRALLRLVES  376 (623)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             89958999767876689999998566466


No 287
>cd03264 ABC_drug_resistance_like ABC-type multidrug transport system, ATPase component.  The biological function of this family is not well characterized, but display ABC domains similar to members of ABCA subfamily.  ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.  The nucleotide binding domain shows the highest similarity between all members of the family.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=85.86  E-value=0.6  Score=24.00  Aligned_cols=25  Identities=28%  Similarity=0.438  Sum_probs=20.0

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             9999707886257899999997233
Q gi|254781225|r  503 FIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       503 ~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ++-+.|+-+.||||++++|..++-.
T Consensus        27 i~gllGpNGAGKSTll~~i~Gl~~p   51 (211)
T cd03264          27 MYGLLGPNGAGKTTLMRILATLTPP   51 (211)
T ss_pred             EEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             5999999982399999999759668


No 288
>cd02025 PanK Pantothenate kinase (PanK) catalyzes the phosphorylation of pantothenic acid to form 4'-phosphopantothenic, which is the first of five steps in coenzyme A (CoA) biosynthetic pathway. The reaction carried out by this enzyme is a key regulatory point in CoA biosynthesis.
Probab=85.85  E-value=0.66  Score=23.75  Aligned_cols=22  Identities=27%  Similarity=0.356  Sum_probs=19.4

Q ss_pred             EEECCCCCHHHHHHHHHHHHCC
Q ss_conf             9707886257899999997233
Q gi|254781225|r  506 IRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       506 ~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      +.|+.++||||+.+.|+.+|+.
T Consensus         4 IaG~sgSGKST~a~~l~~~l~~   25 (220)
T cd02025           4 IAGSVAVGKSTTARVLQALLSR   25 (220)
T ss_pred             EECCCCCCHHHHHHHHHHHHHH
T ss_conf             7889987799999999998600


No 289
>PRK06761 hypothetical protein; Provisional
Probab=85.84  E-value=0.82  Score=23.11  Aligned_cols=26  Identities=35%  Similarity=0.548  Sum_probs=14.6

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             79999707886257899999997233
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      +++|.-|-.|+||||+.+.+...|-.
T Consensus         3 kLIiIEGlPGsGKSTta~~l~d~L~~   28 (281)
T PRK06761          3 KLIIIEGLPGFGKSTTAHLLNDKLSQ   28 (281)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHH
T ss_conf             17999668999801499999999986


No 290
>cd03230 ABC_DR_subfamily_A This family of ATP-binding proteins belongs to a multisubunit transporter involved in drug resistance (BcrA and DrrA), nodulation, lipid transport, and lantibiotic immunity.  In bacteria and archaea, these transporters usually include an ATP-binding protein and one or two integral membrane proteins.  Eukaryote systems of the ABCA subfamily display ABC domains that are quite similar to this family.  The ATP-binding domain shows the highest similarity between all members of the ABC transporter family.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=85.82  E-value=0.65  Score=23.81  Aligned_cols=30  Identities=23%  Similarity=0.380  Sum_probs=24.2

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             433799997078862578999999972330
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      ..-.++-+.|+-++||||++++|..++-..
T Consensus        24 ~~Gei~gl~G~NGaGKSTLl~~i~Gl~~p~   53 (173)
T cd03230          24 EKGEIYGLLGPNGAGKTTLIKIILGLLKPD   53 (173)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCCC
T ss_conf             799399998789979999999997685778


No 291
>PRK11300 livG leucine/isoleucine/valine transporter ATP-binding subunit; Provisional
Probab=85.80  E-value=0.62  Score=23.93  Aligned_cols=28  Identities=25%  Similarity=0.460  Sum_probs=20.5

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             3379999707886257899999997233
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      .--++-+.|+-++||||++++|..++-.
T Consensus        30 ~Gei~~liGpnGaGKSTL~~~i~Gl~~p   57 (255)
T PRK11300         30 EQEVVSLIGPNGAGKTTVFNCLTGFYKP   57 (255)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             9979999989996499999999679889


No 292
>cd01853 Toc34_like Toc34-like (Translocon at the Outer-envelope membrane of Chloroplasts).  This family contains several Toc proteins, including Toc34, Toc33, Toc120, Toc159, Toc86, Toc125, and Toc90.  The Toc complex at the outer envelope membrane of chloroplasts is a molecular machine of ~500 kDa that contains a single Toc159 protein, four Toc75 molecules, and four or five copies of Toc34. Toc64 and Toc12 are associated with the translocon, but do not appear to be part of the core complex.  The Toc translocon initiates the import of nuclear-encoded preproteins from the cytosol into the organelle.  Toc34 and Toc159 are both GTPases, while Toc75 is a beta-barrel integral membrane protein.  Toc159 is equally distributed between a soluble cytoplasmic form and a membrane-inserted form, suggesting that assembly of the Toc complex is dynamic.  Toc34 and Toc75 act sequentially to mediate docking and insertion of Toc159 resulting in assembly of the functional translocon.
Probab=85.76  E-value=1.6  Score=21.27  Aligned_cols=146  Identities=18%  Similarity=0.159  Sum_probs=77.6

Q ss_pred             HCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCCCCCHHHHH
Q ss_conf             87999999999999999975987433799997078862578999999972330003442676420124555568988997
Q gi|254781225|r  476 YFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEAGKANPSLIR  555 (789)
Q Consensus       476 ~~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~~~~~~~~la~  555 (789)
                      .|+|.... -+.+..+ .+.......+-+++.|.++-|||..+|-   +||+.. +..+.+.-+..+....+.      .
T Consensus         8 ~~~~a~~~-~~~el~a-~~~~~~~~sltILvlGKtGVGKSsTINS---ifgE~~-~~~~aF~~~t~r~~~v~~------t   75 (249)
T cd01853           8 FFPDAAQT-KALELEA-KGKEELDFSLTILVLGKTGVGKSSTINS---IFGERK-AATSAFQSETLRVREVSG------T   75 (249)
T ss_pred             CCCHHHHH-HHHHHHH-CCCCCCCCEEEEEEEECCCCCHHHHHHH---HCCCCC-CCCCCCCCCCCCEEEEEE------E
T ss_conf             08688999-9999985-1352456436999980687645776776---508541-344776778865089987------5


Q ss_pred             HCCCEEEEEECCC--CC---CCCCCC---EEEEEECCCEEEEEECCCCCCEEEECCEEEEEECCCCCCCCCC----CCCE
Q ss_conf             3898099993467--77---601310---0245415985873210478606871452899973886342679----8416
Q gi|254781225|r  556 LMGSRIVIISETN--EN---DEINAA---KIKQMTGGDCMTARLNYGNTYSESPASFTPFIVPNKHLFVRNP----DDAW  623 (789)
Q Consensus       556 l~g~r~~~~~E~~--~~---~~~~~~---~~K~ltggD~i~ar~~~~~~~~~~~p~~~~~~~~N~~P~~~~~----d~~~  623 (789)
                      ..|-++++++-|.  ++   ...|..   .+|..+-+-++.+ -+|-+-. ..     .=+-.+++|.++.-    ..+|
T Consensus        76 v~G~kl~iIDTPGL~~~~~~~~~N~k~l~~iKr~l~~~~~Dv-vLYvDRL-D~-----~r~d~~D~~ll~~iT~~fG~~I  148 (249)
T cd01853          76 VDGFKLNIIDTPGLLESVMDQRVNRKILSSIKRYLKKKTPDV-VLYVDRL-DM-----YRRDYLDLPLLRAITDSFGPSI  148 (249)
T ss_pred             ECCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCE-EEEEECC-CC-----CCCCCCHHHHHHHHHHHHHHHH
T ss_conf             334489986089877665422130999999999962899978-9998457-66-----2458642899999998767888


Q ss_pred             EEEEEEEECCCCCCCCC
Q ss_conf             64689996588788878
Q gi|254781225|r  624 WRRYIVIPFDKPIANRD  640 (789)
Q Consensus       624 ~rR~~iipF~~~~~~~d  640 (789)
                      |+|.+|+=-..+....|
T Consensus       149 W~naivvLTHa~~~pPd  165 (249)
T cd01853         149 WRNAIVVLTHAASSPPD  165 (249)
T ss_pred             HHHHHEEEECCCCCCCC
T ss_conf             75454035346648999


No 293
>cd03241 ABC_RecN RecN ATPase involved in DNA repair; ABC (ATP-binding cassette) transporter nucleotide-binding domain; ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules.  The nucleotide binding domain shows the highest similarity between all members of the family.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=85.76  E-value=0.86  Score=22.96  Aligned_cols=29  Identities=24%  Similarity=0.497  Sum_probs=22.8

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHCCCC
Q ss_conf             37999970788625789999999723300
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYAFGNQY  529 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~llG~~~  529 (789)
                      .-|-+++|..|.|||.+++.|.-++|..+
T Consensus        21 ~GlnVlTGETGAGKSIlidAL~lllG~Ra   49 (276)
T cd03241          21 EGLTVLTGETGAGKSILLDALSLLLGGRA   49 (276)
T ss_pred             CCCEEEECCCCCCHHHHHHHHHHHHCCCC
T ss_conf             99758878998889999999999628998


No 294
>TIGR01192 chvA glucan exporter ATP-binding protein; InterPro: IPR005896   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).     This family contains glucan exporter ATP binding protein in bacteria. It belongs to the larger ABC transporter superfamily with the characteristic ATP binding motif. In general, this protein is in some ways implicated in osmo-regulation and is suggested to participate in the export of glucan from the cytoplasm to periplasm. The cyclic beta-1,2-glucan in the bacterial periplasmic space is suggested to confer the property of high osmolority. It has also been demonstrated that mutants in this loci have lost functions of virulence and motility. It is unclear as to how virulence and osmo-adaptaion are related. ; GO: 0005215 transporter activity, 0006810 transport.
Probab=85.73  E-value=0.68  Score=23.66  Aligned_cols=36  Identities=31%  Similarity=0.512  Sum_probs=25.3

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHHCCCC-CCCCCHHH
Q ss_conf             7999970788625789999999723300-03442676
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYAFGNQY-VINAEASD  537 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~llG~~~-~~~~~~~~  537 (789)
                      .-+-+.||.|.||+|++|+|+.+.-+.. ....+-..
T Consensus       362 ~TvAIVGPTGAGKTTLiNLLQRVydP~~G~I~IDG~~  398 (592)
T TIGR01192       362 QTVAIVGPTGAGKTTLINLLQRVYDPKVGQILIDGID  398 (592)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHCCCCCCEEEECCEE
T ss_conf             5689877899717899887753106986548872424


No 295
>TIGR01143 murF UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; InterPro: IPR005863   The bacterial cell wall provides strength and rigidity to counteract internal osmotic pressure, and protection against the environment. The peptidoglycan layer gives the cell wall its strength, and helps maintain the overall shape of the cell. The basic peptidoglycan structure of both Gram-positive and Gram-negative bacteria is comprised of a sheet of glycan chains connected by short cross-linking polypeptides. Biosynthesis of peptidoglycan is a multi-step (11-12 steps) process comprising three main stages:    (1) formation of UDP-N-acetylmuramic acid (UDPMurNAc) from N-acetylglucosamine (GlcNAc). (2) addition of a short polypeptide chain to the UDPMurNAc. (3) addition of a second GlcNAc to the disaccharide-pentapeptide building block and transport of this unit through the cytoplasmic membrane and incorporation into the growing peptidoglycan layer.    Stage two involves four key Mur ligase enzymes: MurC (6.3.2.8 from EC) , MurD (6.3.2.9 from EC) , MurE (6.3.2.13 from EC)  and MurF (6.3.2.10 from EC) . These four Mur ligases are responsible for the successive additions of L-alanine, D-glutamate, meso-diaminopimelate or L-lysine, and D-alanyl-D-alanine to UDP-N-acetylmuramic acid. All four Mur ligases are topologically similar to one another, even though they display low sequence identity. They are each composed of three domains: an N-terminal Rossmann-fold domain responsible for binding the UDPMurNAc substrate; a central domain (similar to ATP-binding domains of several ATPases and GTPases); and a C-terminal domain (similar to dihydrofolate reductase fold) that appears to be associated with binding the incoming amino acid. The conserved sequence motifs found in the four Mur enzymes also map to other members of the Mur ligase family, including folylpolyglutamate synthetase, cyanophycin synthetase and the capB enzyme from Bacillales .    This entry represents UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase (MurF, 6.3.2.15 from EC), which is required to catalyze the final step in the synthesis of the cytoplasmic precursor of the bacterial cell wall peptidoglycan.  ATP + UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminoheptanedioate + D-alanyl-D-alanine = ADP + phosphate + UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-6-carboxy-L-lysyl-D-alanyl-D-alanine.. The crystal structure of the MurF apo-enzyme has been determined and refined to 2.3 A resolution. It contains three consecutive open alpha/beta-sheet domains. The topology of the N-terminal domain of MurF is unique, while its central and C-terminal domains exhibit similar mononucleotide and dinucleotide-binding folds to MurD. The apo-enzyme of MurF crystal structure reveals an open conformation with the three domains juxtaposed in a crescent-like arrangement creating a wide-open space where substrates are expected to bind. As such, catalysis is not feasible and significant domain closure is expected upon substrate binding . ; GO: 0005524 ATP binding, 0008766 UDP-N-acetylmuramoylalanyl-D-glutamyl-26-diaminopimelate-D-alanyl-D-alanine ligase activity, 0008360 regulation of cell shape, 0009252 peptidoglycan biosynthetic process, 0009273 peptidoglycan-based cell wall biogenesis, 0051301 cell division, 0005737 cytoplasm.
Probab=85.72  E-value=0.79  Score=23.21  Aligned_cols=21  Identities=5%  Similarity=0.094  Sum_probs=9.5

Q ss_pred             HHHHHHHHCCCCC--EEE-ECCCC
Q ss_conf             8999876418997--699-67889
Q gi|254781225|r   80 TFKDTFEILHGTP--IVR-IGQKP  100 (789)
Q Consensus        80 ~~~~~~~~l~g~p--~~~-~g~~~  100 (789)
                      .+..+..+....+  ++= +|+.|
T Consensus        71 ~lA~~~~~~~~~~~~~igiTGS~G   94 (462)
T TIGR01143        71 ALASAKREKFSAKRRVIGITGSSG   94 (462)
T ss_pred             HHHHHHHHHCCCCEEEEEEECCCC
T ss_conf             999999974399758999856896


No 296
>cd03268 ABC_BcrA_bacitracin_resist The BcrA subfamily represents ABC transporters involved in peptide antibiotic resistance.  Bacitracin is a dodecapeptide antibiotic produced by B. licheniformis and B. subtilis.  The synthesis of bacitracin is non-ribosomally catalyzed by a multienzyme complex BcrABC.  Bacitracin has potent antibiotic activity against gram-positive bacteria.  The inhibition of peptidoglycan biosynthesis is the best characterized bacterial effect of bacitracin.  The bacitracin resistance of B. licheniformis is mediated by the ABC transporter Bcr which is composed of two identical BcrA ATP-binding subunits and one each of the integral membrane proteins, BcrB and BcrC.  B. subtilis cells carrying bcr genes on high-copy number plasmids develop collateral detergent sensitivity, a similar phenomenon in human cells with overexpressed multi-drug resistance P-glycoprotein.
Probab=85.67  E-value=0.68  Score=23.66  Aligned_cols=31  Identities=26%  Similarity=0.302  Sum_probs=24.4

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCCCC
Q ss_conf             4337999970788625789999999723300
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGNQY  529 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~  529 (789)
                      ..-.++-+.|+-++||||++++|..++-...
T Consensus        24 ~~Gei~gllG~NGaGKSTLl~~i~Gl~~p~~   54 (208)
T cd03268          24 KKGEIYGFLGPNGAGKTTTMKIILGLIKPDS   54 (208)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCCCC
T ss_conf             6981999999999999999999957837898


No 297
>CHL00131 ycf16 sulfate ABC transporter protein; Validated
Probab=85.66  E-value=0.75  Score=23.38  Aligned_cols=24  Identities=46%  Similarity=0.493  Sum_probs=17.1

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHH
Q ss_conf             337999970788625789999999
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKY  523 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~  523 (789)
                      .-.++-+.|+-|+|||||+++|..
T Consensus        31 ~Gei~aiiG~nGsGKSTL~~~i~G   54 (252)
T CHL00131         31 AGEIHAIMGPNGSGKSTLSKVIAG   54 (252)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHCC
T ss_conf             998999999999999999999727


No 298
>cd03284 ABC_MutS1 MutS1 homolog in eukaryotes.  The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch.  Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily.  MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined.  Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes.  The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis.  All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action.  MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clam
Probab=85.62  E-value=1.1  Score=22.16  Aligned_cols=25  Identities=24%  Similarity=0.393  Sum_probs=20.4

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             3379999707886257899999997
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYA  524 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~l  524 (789)
                      .+.+++++|+-..||||+++.+.-+
T Consensus        29 ~~~~~iiTGpN~sGKSt~Lk~igl~   53 (216)
T cd03284          29 ERQILLITGPNMAGKSTYLRQVALI   53 (216)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHH
T ss_conf             8459999899877459999999999


No 299
>cd03218 ABC_YhbG The ABC transporters belonging to the YhbG family are similar to members of the Mj1267_LivG family, which is involved in the transport of branched-chain amino acids.  The genes yhbG and yhbN are located in a single operon and may function together in cell envelope during biogenesis.  YhbG is the putative ATP-binding cassette component and YhbN is the putative periplasmic-binding protein.  Depletion of each gene product leads to growth arrest, irreversible cell damage and loss of viability in E. coli.  The YhbG homolog (NtrA) is essential in Rhizobium meliloti, a symbiotic nitrogen-fixing bacterium.
Probab=85.62  E-value=0.64  Score=23.84  Aligned_cols=26  Identities=23%  Similarity=0.351  Sum_probs=17.5

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             79999707886257899999997233
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      -++-+.|+-++||||++++|..++-.
T Consensus        27 ei~~llGpNGAGKSTll~~i~Gl~~p   52 (232)
T cd03218          27 EIVGLLGPNGAGKTTTFYMIVGLVKP   52 (232)
T ss_pred             CEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             59999999996199999999779999


No 300
>cd03281 ABC_MSH5_euk MutS5 homolog in eukaryotes.  The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch.  Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily.  MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined.  Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes.  The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis.  All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action.  MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c
Probab=85.61  E-value=1  Score=22.45  Aligned_cols=26  Identities=23%  Similarity=0.360  Sum_probs=21.7

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             43379999707886257899999997
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYA  524 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~l  524 (789)
                      ..+.+++++|+-..|||||+..+.-.
T Consensus        27 ~~~~~~iiTGpN~gGKSt~lkti~l~   52 (213)
T cd03281          27 GGPSIMVITGPNSSGKSVYLKQVALI   52 (213)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH
T ss_conf             98259999899987659999999999


No 301
>COG3910 Predicted ATPase [General function prediction only]
Probab=85.59  E-value=0.72  Score=23.49  Aligned_cols=24  Identities=46%  Similarity=0.682  Sum_probs=13.0

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             999970788625789999999723
Q gi|254781225|r  503 FIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       503 ~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      .-+++|.-++||||+++.|...+|
T Consensus        39 IT~i~GENGsGKSTLLEaiA~~~~   62 (233)
T COG3910          39 ITFITGENGSGKSTLLEAIAAGMG   62 (233)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHCC
T ss_conf             489976898657889999996565


No 302
>cd03265 ABC_DrrA DrrA is the ATP-binding protein component of a bacterial exporter complex that confers resistance to the antibiotics daunorubicin and doxorubicin.  In addition to DrrA, the complex includes an integral membrane protein called DrrB.  DrrA belongs to the ABC family of transporters and shares sequence and functional similarities with a protein found in cancer cells called  P-glycoprotein.  ABC transporters are a large family of proteins involved in the transport of a wide variety of different compounds, like sugars, ions, peptides, and more complex organic molecules.  The nucleotide binding domain shows the highest similarity between all members of the family.  ABC transporters are a subset of nucleotide hydrolases that contain a signature motif, Q-loop, and H-loop/switch region in addition to the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=85.57  E-value=0.69  Score=23.61  Aligned_cols=31  Identities=16%  Similarity=0.346  Sum_probs=23.7

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCCCC
Q ss_conf             4337999970788625789999999723300
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGNQY  529 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~  529 (789)
                      ...-++-+.|+-+.||||++++|..++-..+
T Consensus        24 ~~Gei~gllGpNGAGKSTll~~i~Gl~~p~~   54 (220)
T cd03265          24 RRGEIFGLLGPNGAGKTTTIKMLTTLLKPTS   54 (220)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHCCCCCCC
T ss_conf             8983999999998719999999976978896


No 303
>PRK00139 murE UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase; Provisional
Probab=85.51  E-value=1.8  Score=20.79  Aligned_cols=87  Identities=22%  Similarity=0.358  Sum_probs=38.5

Q ss_pred             CEEEEEEECCCC---CHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCCCCCHHHHHH-CC---CEEEEEECCCCCCCC
Q ss_conf             379999707886---25789999999723300034426764201245555689889973-89---809999346777601
Q gi|254781225|r  501 QRFIHIRGVGGS---GKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEAGKANPSLIRL-MG---SRIVIISETNENDEI  573 (789)
Q Consensus       501 ~~~~~~~G~G~n---GKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~~~~~~~~la~l-~g---~r~~~~~E~~~~~~~  573 (789)
                      .+...++|.||+   +|=-.+--+..-+-|+.+...     ..-|..+   +..-+..+ .|   +.+.+  .++....+
T Consensus       364 ~rli~VfG~gG~Rd~~KR~~mg~ia~~~ad~vi~T~-----DnPr~Ed---p~~I~~~i~~g~~~~~~~~--i~dR~~AI  433 (481)
T PRK00139        364 GRLICVFGCGGDRDKGKRPLMGAIAERLADVVIVTS-----DNPRSED---PAAIIADILAGITHANAVV--IEDRAEAI  433 (481)
T ss_pred             CCEEEEECCCCCCCCHHHHHHHHHHHHCCCEEEECC-----CCCCCCC---HHHHHHHHHHCCCCCCEEE--ECCHHHHH
T ss_conf             986999898677770141899999997199899939-----9989989---9999999982698799289--78999999


Q ss_pred             CCCEEEEEECCCEEEEEECCCCCCE
Q ss_conf             3100245415985873210478606
Q gi|254781225|r  574 NAAKIKQMTGGDCMTARLNYGNTYS  598 (789)
Q Consensus       574 ~~~~~K~ltggD~i~ar~~~~~~~~  598 (789)
                      ..+ |.....||.|-.-.|.-+.+.
T Consensus       434 ~~a-i~~a~~~d~vliaGKGhE~~q  457 (481)
T PRK00139        434 KYA-IALAKPGDVVLIAGKGHEDYQ  457 (481)
T ss_pred             HHH-HHHCCCCCEEEEEECCCCCCE
T ss_conf             999-985599999999735876668


No 304
>KOG2655 consensus
Probab=85.51  E-value=0.65  Score=23.78  Aligned_cols=30  Identities=17%  Similarity=0.231  Sum_probs=12.8

Q ss_pred             CCCCCEEEEEEECCCCCHHHH-HHHHHHHHC
Q ss_conf             874337999970788625789-999999723
Q gi|254781225|r  497 GNKAQRFIHIRGVGGSGKSTL-MNLIKYAFG  526 (789)
Q Consensus       497 ~~~~~~~~~~~G~G~nGKSt~-~~~l~~llG  526 (789)
                      +++-|+++.++-|-+.|=+.+ +.++..+-.
T Consensus       127 D~RVH~cLYFI~P~ghgL~p~Di~~Mk~l~~  157 (366)
T KOG2655         127 DNRVHCCLYFISPTGHGLKPLDIEFMKKLSK  157 (366)
T ss_pred             CCCEEEEEEEECCCCCCCCHHHHHHHHHHHC
T ss_conf             8844899998378888886866999997732


No 305
>COG3172 NadR Predicted ATPase/kinase involved in NAD metabolism [Coenzyme metabolism]
Probab=85.49  E-value=0.9  Score=22.86  Aligned_cols=28  Identities=36%  Similarity=0.427  Sum_probs=24.0

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             3379999707886257899999997233
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      +-+.+.+.|+-++||||+.+-+.+.|+.
T Consensus         7 F~K~VailG~ESsGKStLv~kLA~~fnt   34 (187)
T COG3172           7 FVKTVAILGGESSGKSTLVNKLANIFNT   34 (187)
T ss_pred             HHEEEEEECCCCCCHHHHHHHHHHHHCC
T ss_conf             3513556457665717999999999688


No 306
>TIGR02204 MsbA_rel ABC transporter, permease/ATP-binding protein; InterPro: IPR011918    This protein is related to a Proteobacterial ATP transporter that exports lipid A and to eukaryotic P-glycoproteins ..
Probab=85.41  E-value=0.61  Score=23.98  Aligned_cols=40  Identities=30%  Similarity=0.429  Sum_probs=27.0

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCCCC-CCCCCHHHH
Q ss_conf             4337999970788625789999999723300-034426764
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGNQY-VINAEASDI  538 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~-~~~~~~~~~  538 (789)
                      +.-.-+-+.||.|.||||+++||..-+-... ...++-..+
T Consensus       364 ~PGEtvAlVGPSGAGKSTlf~LLLRFYDP~~G~ilLDGvd~  404 (576)
T TIGR02204       364 RPGETVALVGPSGAGKSTLFQLLLRFYDPQSGRILLDGVDI  404 (576)
T ss_pred             CCCCEEEEECCCCCHHHHHHHHHHHCCCCCCCEEEECCCCH
T ss_conf             27765887668876279999999860488876577466414


No 307
>cd03266 ABC_NatA_sodium_exporter NatA is the ATPase component of a bacterial ABC-type Na+ transport system called NatAB, which catalyzes ATP-dependent electrogenic Na+ extrusion without mechanically coupled proton or K+ uptake.  NatB possess six putative membrane spanning regions at its C-terminus.  In B. subtilus, NatAB is inducible by agents such as ethanol and protonophores, which lower the protonmotive force across the membrane.  The closest sequence similarity to NatA is exhibited by DrrA of the two-component daunomycin- and doxorubicin-efflux system.  Hence, the functional NatAB is presumably assembled with two copies of a single ATP-binding protein and a single intergral membrane protein.
Probab=85.34  E-value=0.68  Score=23.66  Aligned_cols=30  Identities=20%  Similarity=0.349  Sum_probs=22.9

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             433799997078862578999999972330
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      ..--++-+.|+-++||||++++|..++-..
T Consensus        29 ~~Gei~gllG~NGaGKSTllk~i~Gl~~p~   58 (218)
T cd03266          29 KPGEVTGLLGPNGAGKTTTLRMLAGLLEPD   58 (218)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCCC
T ss_conf             598299999999984999999997797789


No 308
>PRK06620 hypothetical protein; Validated
Probab=85.33  E-value=1.3  Score=21.87  Aligned_cols=49  Identities=18%  Similarity=0.234  Sum_probs=34.5

Q ss_pred             CHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCC
Q ss_conf             999999999999999759874337999970788625789999999723300
Q gi|254781225|r  479 SEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQY  529 (789)
Q Consensus       479 d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~  529 (789)
                      +...+.++..|-..  .|.+.....++++|+.++|||-+.++.+..-+.+.
T Consensus        24 N~~A~~~i~~wp~~--~~~~~~~~~l~I~Gp~gSGKTHL~~i~~~~~~a~~   72 (214)
T PRK06620         24 NDQAYNIIKNWQCM--FGVNPYKFTLLIKGPSSSGKTYLTKIWQNLSNAYI   72 (214)
T ss_pred             HHHHHHHHHHCHHC--CCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCEE
T ss_conf             99999999836302--56686555599987999988999999999828588


No 309
>PRK03695 vitamin B12-transporter ATPase; Provisional
Probab=85.33  E-value=0.67  Score=23.69  Aligned_cols=29  Identities=31%  Similarity=0.505  Sum_probs=23.3

Q ss_pred             CCCCEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             74337999970788625789999999723
Q gi|254781225|r  498 NKAQRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       498 ~~~~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      ...-.++-+.|+-|+||||++++|..+..
T Consensus        20 v~~Ge~v~iiGpNGaGKSTLlk~i~Gl~p   48 (245)
T PRK03695         20 VRAGEILHLVGPNGAGKSTLLARMAGLLS   48 (245)
T ss_pred             ECCCCEEEEECCCCCHHHHHHHHHHCCCC
T ss_conf             95998999997899419999999846688


No 310
>COG0529 CysC Adenylylsulfate kinase and related kinases [Inorganic ion transport and metabolism]
Probab=85.31  E-value=1  Score=22.42  Aligned_cols=27  Identities=33%  Similarity=0.454  Sum_probs=23.3

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             379999707886257899999997233
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ...+.++|-.++||||+.+.+...|=.
T Consensus        23 ~~viW~TGLSGsGKSTiA~ale~~L~~   49 (197)
T COG0529          23 GAVIWFTGLSGSGKSTIANALEEKLFA   49 (197)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHH
T ss_conf             859996468888787999999999997


No 311
>COG0572 Udk Uridine kinase [Nucleotide transport and metabolism]
Probab=85.27  E-value=1.1  Score=22.19  Aligned_cols=35  Identities=26%  Similarity=0.292  Sum_probs=25.3

Q ss_pred             CCEEEEEE-ECCCCCHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             33799997-078862578999999972330003442
Q gi|254781225|r  500 AQRFIHIR-GVGGSGKSTLMNLIKYAFGNQYVINAE  534 (789)
Q Consensus       500 ~~~~~~~~-G~G~nGKSt~~~~l~~llG~~~~~~~~  534 (789)
                      .++++|-+ |..++||||+.+.|...||...++..+
T Consensus         6 ~~~iiIgIaG~SgSGKTTv~~~l~~~~~~~~~~~I~   41 (218)
T COG0572           6 EKVIIIGIAGGSGSGKTTVAKELSEQLGVEKVVVIS   41 (218)
T ss_pred             CCEEEEEEECCCCCCHHHHHHHHHHHHCCCCCEEEE
T ss_conf             766999986798778899999999982867524765


No 312
>TIGR03410 urea_trans_UrtE urea ABC transporter, ATP-binding protein UrtE. Members of this protein family are ABC transporter ATP-binding subunits 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.
Probab=85.23  E-value=0.67  Score=23.70  Aligned_cols=28  Identities=21%  Similarity=0.278  Sum_probs=19.9

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             3379999707886257899999997233
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ...++-+.|+-++||||++++|..++-.
T Consensus        25 ~Gei~~liGpNGaGKSTL~~~i~Gl~~p   52 (230)
T TIGR03410        25 KGEVTCVLGRNGVGKTTLLKTLMGLLPV   52 (230)
T ss_pred             CCCEEEEECCCCCHHHHHHHHHHCCCCC
T ss_conf             9979999999994099999999779999


No 313
>TIGR02857 CydD ABC transporter, CydDC cysteine exporter (CydDC-E) family, permease/ATP-binding protein CydD; InterPro: IPR014216   The gene pair cydCD encodes an ABC-family transporter in which each gene contains an N-terminal membrane-spanning domain and a C-terminal ATP-binding domain. In Escherichia coli these genes were discovered as mutants which caused the terminal heme-copper oxidase complex cytochrome bd to fail to assemble. Recent work has shown that the transporter is involved in the export of redox-active thiol compounds such as cysteine and glutathione , . The linkage to assembly of the cytochrome bd complex is further supported by the conserved operon structure found outside the gammaproteobacteria (cydABCD) containing both the transporter and oxidase genes components.    The genes used as the seed members for this entry are all either found in the gammaproteobacterial context, or the CydABCD context. All members of this entry scoring above the trusted cut off at the time of its creation were from genomes which encode a cytochrome bd complex. Unfortunately, the gene symbol nomenclature, based on this operon in Bacillus subtilis, assigns cydC to the third gene in the operon, where this gene is actually homologous to the E. coli cydD gene. We have chosen to name all homologues in this family in accordance with the precedence of publication of the E. coli name, CydD..
Probab=85.17  E-value=0.8  Score=23.19  Aligned_cols=31  Identities=29%  Similarity=0.355  Sum_probs=25.6

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCCCC
Q ss_conf             4337999970788625789999999723300
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGNQY  529 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~  529 (789)
                      +-...+-+.|+.|.||||+++++-..+..+.
T Consensus       376 ~pG~~vAl~G~SGaGKSTLL~lLLGf~~P~~  406 (570)
T TIGR02857       376 EPGERVALVGPSGAGKSTLLNLLLGFVEPTE  406 (570)
T ss_pred             CCCCEEEEEECCCCCHHHHHHHHHCCCCCCC
T ss_conf             3870488862799978899999971576446


No 314
>pfam00735 Septin Septin. Members of this family include CDC3, CDC10, CDC11 and CDC12/Septin. Members of this family bind GTP. As regards the septins, these are polypeptides of 30-65kDa with three characteristic GTPase motifs (G-1, G-3 and G-4) that are similar to those of the Ras family. The G-4 motif is strictly conserved with a unique septin consensus of AKAD. Most septins are thought to have at least one coiled-coil region, which in some cases is necessary for intermolecular interactions that allow septins to polymerize to form rod-shaped complexes. In turn, these are arranged into tandem arrays to form filaments. They are multifunctional proteins, with roles in cytokinesis, sporulation, germ cell development, exocytosis and apoptosis.
Probab=85.12  E-value=0.74  Score=23.42  Aligned_cols=31  Identities=13%  Similarity=0.052  Sum_probs=13.1

Q ss_pred             CCCCCCEEEEEEECCCC-CHHHHHHHHHHHHC
Q ss_conf             98743379999707886-25789999999723
Q gi|254781225|r  496 GGNKAQRFIHIRGVGGS-GKSTLMNLIKYAFG  526 (789)
Q Consensus       496 g~~~~~~~~~~~G~G~n-GKSt~~~~l~~llG  526 (789)
                      .+++-++++.+.-|.+. -|..=+.+|+.|-.
T Consensus       109 ~D~RVH~cLYFI~Ptgh~L~~lDi~~mk~Ls~  140 (280)
T pfam00735       109 VDNRVHCCLYFISPTGHGLKPLDVEFMKKLHE  140 (280)
T ss_pred             CCCCEEEEEEEECCCCCCCCHHHHHHHHHHHC
T ss_conf             88843799997568888886889999998714


No 315
>PRK00300 gmk guanylate kinase; Provisional
Probab=85.06  E-value=0.63  Score=23.90  Aligned_cols=67  Identities=22%  Similarity=0.320  Sum_probs=39.9

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCCCCCHHHHHHCCCEEEEEECCCCCCCCCCC
Q ss_conf             433799997078862578999999972330003442676420124555568988997389809999346777601310
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEAGKANPSLIRLMGSRIVIISETNENDEINAA  576 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~~~~~~~~la~l~g~r~~~~~E~~~~~~~~~~  576 (789)
                      +.-+++++.||.|.||+|+++.|..-..+....+.+.  ++  |.+..+       ...|.-..++++.+-...+..+
T Consensus         5 ~~g~livisGPSG~GK~tl~~~L~~~~p~~~~~~vs~--TT--R~pR~~-------E~dG~dY~Fvs~eeF~~~i~~g   71 (208)
T PRK00300          5 RRGLLIVLSAPSGAGKSTLVRALLERDPNDLQLSVSA--TT--RAPRPG-------EVDGVHYHFVSREEFEEMIENG   71 (208)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHCCCCEEEEEEE--EC--CCCCCC-------CCCCCEEEEECHHHHHHHHHHC
T ss_conf             1883899999998899999999997299868998974--68--898998-------7789657996199999998628


No 316
>COG1101 PhnK ABC-type uncharacterized transport system, ATPase component [General function prediction only]
Probab=85.06  E-value=0.76  Score=23.33  Aligned_cols=15  Identities=20%  Similarity=0.410  Sum_probs=7.3

Q ss_pred             EEEECCCCEEEECCCC
Q ss_conf             3485268438804776
Q gi|254781225|r  126 LDILGCGQYFVAYNIH  141 (789)
Q Consensus       126 iEi~~~G~q~V~~gsh  141 (789)
                      ++|- .|.++++-||.
T Consensus        27 L~I~-~g~FvtViGsN   41 (263)
T COG1101          27 LEIA-EGDFVTVIGSN   41 (263)
T ss_pred             EEEC-CCCEEEEECCC
T ss_conf             1224-78469997679


No 317
>PRK09580 sufC cysteine desulfurase ATPase component; Reviewed
Probab=85.03  E-value=0.87  Score=22.96  Aligned_cols=23  Identities=39%  Similarity=0.394  Sum_probs=11.7

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             79999707886257899999997
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYA  524 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~l  524 (789)
                      .++-+.|+-|+||||++++|..+
T Consensus        28 ei~~iiG~nGaGKSTLl~~i~G~   50 (248)
T PRK09580         28 EVHAIMGPNGSGKSTLSATLAGR   50 (248)
T ss_pred             CEEEEECCCCCCHHHHHHHHHCC
T ss_conf             79999999999999999998377


No 318
>TIGR00630 uvra excinuclease ABC, A subunit; InterPro: IPR004602   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).  During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products . The UvrC protein contain 4 conserved regions: a central region which interact with UvrB (Uvr domain), a Helix hairpin Helix (HhH) domain important for 5 prime incision of damage DNA and the homology regions 1 and 2 of unknown function. UvrC homology region 2 is specific for UvrC proteins, whereas UvrC homology region 1 is also shared by few other nucleases.; GO: 0009381 excinuclease ABC activity, 0006289 nucleotide-excision repair, 0009380 excinuclease repair complex.
Probab=85.02  E-value=0.69  Score=23.60  Aligned_cols=28  Identities=46%  Similarity=0.546  Sum_probs=21.2

Q ss_pred             CCCCEEEEEEECCCCCHHHHHH-HHHHHH
Q ss_conf             7433799997078862578999-999972
Q gi|254781225|r  498 NKAQRFIHIRGVGGSGKSTLMN-LIKYAF  525 (789)
Q Consensus       498 ~~~~~~~~~~G~G~nGKSt~~~-~l~~ll  525 (789)
                      .....|...+|..|+|||||++ +|-.++
T Consensus       662 iPLG~~t~iTGVSGSGKSTLind~L~~~~  690 (956)
T TIGR00630       662 IPLGLFTCITGVSGSGKSTLINDTLYPAL  690 (956)
T ss_pred             ECCCEEEEEECCCCCCHHHHHHHHHHHHH
T ss_conf             40771799974458745777999999999


No 319
>COG1122 CbiO ABC-type cobalt transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=85.02  E-value=0.56  Score=24.24  Aligned_cols=30  Identities=30%  Similarity=0.413  Sum_probs=19.6

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             433799997078862578999999972330
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      ....++.++|+-++||||++.++..++-..
T Consensus        28 ~~Ge~~~i~G~nGsGKSTL~~~l~GLl~p~   57 (235)
T COG1122          28 EKGERVLLIGPNGSGKSTLLKLLNGLLKPT   57 (235)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHCCCCCCC
T ss_conf             789899998899988999999953767688


No 320
>cd03282 ABC_MSH4_euk MutS4 homolog in eukaryotes.  The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch.  Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily.  MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined.  Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes.  The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis.  All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action.  MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c
Probab=85.02  E-value=1.3  Score=21.76  Aligned_cols=26  Identities=38%  Similarity=0.438  Sum_probs=20.6

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             43379999707886257899999997
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYA  524 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~l  524 (789)
                      ....+++++|+-..||||+++.+.-.
T Consensus        27 ~~~~~~iITGpN~gGKSt~Lktigl~   52 (204)
T cd03282          27 GSSRFHIITGPNMSGKSTYLKQIALL   52 (204)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHH
T ss_conf             97259999899988719999999999


No 321
>COG0194 Gmk Guanylate kinase [Nucleotide transport and metabolism]
Probab=85.00  E-value=0.95  Score=22.68  Aligned_cols=56  Identities=25%  Similarity=0.335  Sum_probs=35.2

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCCCCCHHHHHHCCCEEEEEECCC
Q ss_conf             337999970788625789999999723300034426764201245555689889973898099993467
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEAGKANPSLIRLMGSRIVIISETN  568 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~~~~~~~~la~l~g~r~~~~~E~~  568 (789)
                      .-.++++.||.+.||||++..|..-. +...+   .+.++  |.+..|       ...|+-..++++-+
T Consensus         3 ~G~l~vlsgPSG~GKsTl~k~L~~~~-~l~~S---VS~TT--R~pR~g-------Ev~G~dY~Fvs~~E   58 (191)
T COG0194           3 KGLLIVLSGPSGVGKSTLVKALLEDD-KLRFS---VSATT--RKPRPG-------EVDGVDYFFVTEEE   58 (191)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHC-CEEEE---EEECC--CCCCCC-------CCCCCEEEECCHHH
T ss_conf             86399998998888899999998634-93799---98526--799998-------75780247577999


No 322
>pfam03668 ATP_bind_2 P-loop ATPase protein family. This family contains an ATP-binding site and could be an ATPase (personal obs:C Yeats).
Probab=84.93  E-value=1.3  Score=21.80  Aligned_cols=60  Identities=18%  Similarity=0.202  Sum_probs=28.3

Q ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCE--EEEEEE-CCCCCHHHHH-HHHHHHHC
Q ss_conf             789999988879999999999999999759874337--999970-7886257899-99999723
Q gi|254781225|r  467 QEFLDLVSGYFESEEVMDYFTRCVGMALLGGNKAQR--FIHIRG-VGGSGKSTLM-NLIKYAFG  526 (789)
Q Consensus       467 p~~~~~l~~~~~d~e~~~~l~~~~g~~l~g~~~~~~--~~~~~G-~G~nGKSt~~-~~l~~llG  526 (789)
                      +...+|+.+.=.-.+..+.+..++.+.|-.-..+.+  +-|-+| +||-=-||++ +-+..-|.
T Consensus       205 ~~V~~yv~~~~~~~~f~~~i~~ll~~~lp~y~~egksyltIaiGCTGGqHRSV~iae~L~~~l~  268 (284)
T pfam03668       205 KPVADYVLHHTEVAEFIESTRRLLSLWLPMYEREGKSYLTIAIGCTGGKHRSVYIAEQLADYFR  268 (284)
T ss_pred             HHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCCCHHHHHHHHHHHHH
T ss_conf             5899999759109999999999999999989984998799997688986279999999999998


No 323
>TIGR02203 MsbA_lipidA lipid A export permease/ATP-binding protein MsbA; InterPro: IPR011917   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 consists of a single polypeptide chain transporter in the ATP-binding cassette (ABC) transporter family, MsbA, which exports lipid A. It may also act in multidrug resistance. Lipid A, a part of lipopolysaccharide, is found in the outer leaflet of the outer membrane of most Gram-negative bacteria. Members of this family are restricted to the Proteobacteria (although lipid A is more broadly distributed) and often are clustered with lipid A biosynthesis genes .; GO: 0005524 ATP binding, 0006869 lipid transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane.
Probab=84.93  E-value=0.64  Score=23.82  Aligned_cols=60  Identities=23%  Similarity=0.318  Sum_probs=36.0

Q ss_pred             CCCCEEEEEEECCCCCHHHHHHHHHHHHCCCC-CCCCCHHHHHHCCCCCCCCCCHHHHHHCCCEEEEEECC
Q ss_conf             74337999970788625789999999723300-03442676420124555568988997389809999346
Q gi|254781225|r  498 NKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQY-VINAEASDIMQNRPPEAGKANPSLIRLMGSRIVIISET  567 (789)
Q Consensus       498 ~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~-~~~~~~~~~~~~~~~~~~~~~~~la~l~g~r~~~~~E~  567 (789)
                      ...-..+-+.|..|+||||+.++|-.-+-... -+..+-..+.          .-.|+.|+.--..+.++.
T Consensus       385 ~~~G~~vALVGRSGSGKsTlv~LlPRFy~p~~G~IllDG~~l~----------d~~L~~LR~q~alVsQ~V  445 (603)
T TIGR02203       385 VEPGETVALVGRSGSGKSTLVNLLPRFYEPDSGQILLDGVDLQ----------DYTLADLRRQVALVSQDV  445 (603)
T ss_pred             ECCCCEEEEECCCCCHHHHHHHHCCCCCCCCCCCEEECCCHHH----------HCCHHHHHHHHHHHCCCE
T ss_conf             1587359987068853899985523660458885652784044----------302663562300021523


No 324
>PRK11144 modC molybdate transporter ATP-binding protein; Provisional
Probab=84.92  E-value=0.73  Score=23.45  Aligned_cols=21  Identities=24%  Similarity=0.135  Sum_probs=8.1

Q ss_pred             CCCEEECCCCCCC-CCCHHHHC
Q ss_conf             7937974388855-89865501
Q gi|254781225|r  432 QDGILDLETGQKV-KPTKELYI  452 (789)
Q Consensus       432 ~NGv~dl~t~~~~-~~~~~~~~  452 (789)
                      .+-|+=++.|++. .+.|++.+
T Consensus       196 aD~v~vm~~G~i~~~G~~~ev~  217 (352)
T PRK11144        196 ADHVVVLEQGKVKAFGPLEEVW  217 (352)
T ss_pred             CCEEEEEECCEEEEECCHHHHH
T ss_conf             9999999899999986999987


No 325
>TIGR01526 nadR_NMN_Atrans nicotinamide-nucleotide adenylyltransferase; InterPro: IPR006417   The NadR protein of Escherichia coli and closely related bacteria is both enzyme and regulatory protein. The first 60 or so amino acids, N-terminal region is a DNA-binding helix-turn-helix domain (IPR001387 from INTERPRO) responsible for repressing the nadAB genes of NAD de novo biosynthesis. The NadR homologs in Mycobacterium tuberculosis, Haemophilus influenzae, and others appear to lack the repressor domain. NadR has recently been shown to act as an enzyme of the salvage pathway of NAD biosynthesis, nicotinamide-nucleotide adenylyltransferase; members of this family are presumed to share this activity. E. coli NadR has also been found to regulate the import of its substrate, nicotinamide ribonucleotide, but it is not known if the other members of this family share that activity.  ; GO: 0003677 DNA binding, 0030528 transcription regulator activity, 0006810 transport, 0019363 pyridine nucleotide biosynthetic process, 0045449 regulation of transcription.
Probab=84.81  E-value=1.1  Score=22.23  Aligned_cols=27  Identities=30%  Similarity=0.310  Sum_probs=20.7

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             433799997078862578999999972
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~ll  525 (789)
                      .+-+.+-+.|+-++|||||.+-|...|
T Consensus       173 ~F~k~V~ilG~eStGKstLv~~lA~~~  199 (346)
T TIGR01526       173 FFVKTVAILGGESTGKSTLVNKLAEKL  199 (346)
T ss_pred             CEEEEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             204588885588863689999999984


No 326
>cd03286 ABC_MSH6_euk MutS6 homolog in eukaryotes.  The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch.  Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily.  MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined.  Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes.  The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis.  All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action.  MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c
Probab=84.77  E-value=1.3  Score=21.82  Aligned_cols=26  Identities=31%  Similarity=0.452  Sum_probs=20.9

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             43379999707886257899999997
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYA  524 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~l  524 (789)
                      ....+++++|+-..||||+++.+.-+
T Consensus        28 ~~~~~~iiTGpN~sGKSt~lk~i~l~   53 (218)
T cd03286          28 TSPRILVLTGPNMGGKSTLLRTVCLA   53 (218)
T ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHH
T ss_conf             97408999899988738999999999


No 327
>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.
Probab=84.72  E-value=1.2  Score=21.96  Aligned_cols=29  Identities=31%  Similarity=0.486  Sum_probs=23.7

Q ss_pred             CCCCEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             74337999970788625789999999723
Q gi|254781225|r  498 NKAQRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       498 ~~~~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      ...+-|.+++|.-|.||||++..+..-+.
T Consensus        40 ~~~~g~~lltGe~GtGKTtllr~l~~~l~   68 (269)
T TIGR03015        40 SQREGFILITGEVGAGKTTLIRNLLKRLD   68 (269)
T ss_pred             HCCCCEEEEECCCCCCHHHHHHHHHHHCC
T ss_conf             64896599972998988999999998459


No 328
>PRK09825 idnK D-gluconate kinase; Provisional
Probab=84.65  E-value=1.2  Score=22.11  Aligned_cols=25  Identities=36%  Similarity=0.420  Sum_probs=21.1

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             7999970788625789999999723
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      +.+++.|..|+||||+...|..-||
T Consensus         4 ~a~VVmGVsGsGKSTvg~~LA~~L~   28 (176)
T PRK09825          4 ESYILMGVSGSGKSLIGSKIAALFS   28 (176)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHHC
T ss_conf             5799982898998999999999959


No 329
>PRK13539 cytochrome c biogenesis protein CcmA; Provisional
Probab=84.62  E-value=0.74  Score=23.40  Aligned_cols=27  Identities=33%  Similarity=0.487  Sum_probs=19.6

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             337999970788625789999999723
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      ...++.+.|+-|.|||||+++|..++-
T Consensus        27 ~Gei~~l~G~NGaGKTTLlk~i~Gl~~   53 (206)
T PRK13539         27 AGEALVLTGPNGSGKTTLLRLLAGLLP   53 (206)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHCCCC
T ss_conf             994999989999989999999958878


No 330
>KOG0739 consensus
Probab=84.59  E-value=1.8  Score=20.84  Aligned_cols=130  Identities=19%  Similarity=0.176  Sum_probs=71.7

Q ss_pred             HHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCC---CCCCHHHHHHCCCEEEEEECCCC
Q ss_conf             975987433799997078862578999999972330003442676420124555---56898899738980999934677
Q gi|254781225|r  493 ALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEA---GKANPSLIRLMGSRIVIISETNE  569 (789)
Q Consensus       493 ~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~~---~~~~~~la~l~g~r~~~~~E~~~  569 (789)
                      .++|..+.=.-+.|||+.+.|||-+......--+...-+..+..+++.=-+ .|   -..-|++||-.---++++.|.+.
T Consensus       158 lFtGkR~PwrgiLLyGPPGTGKSYLAKAVATEAnSTFFSvSSSDLvSKWmG-ESEkLVknLFemARe~kPSIIFiDEiDs  236 (439)
T KOG0739         158 LFTGKRKPWRGILLYGPPGTGKSYLAKAVATEANSTFFSVSSSDLVSKWMG-ESEKLVKNLFEMARENKPSIIFIDEIDS  236 (439)
T ss_pred             HHCCCCCCCEEEEEECCCCCCHHHHHHHHHHHCCCCEEEEEHHHHHHHHHC-CHHHHHHHHHHHHHHCCCCEEEEEHHHH
T ss_conf             415887754257886799975779999987414770687301788998732-1799999999998734994798634444


Q ss_pred             CCCCCCCEEEEEECCCEEEEEEC-----CC-CCCEEEECCEEEEEECCCCCCCCCCCCCEEEEE---EEEECC
Q ss_conf             76013100245415985873210-----47-860687145289997388634267984166468---999658
Q gi|254781225|r  570 NDEINAAKIKQMTGGDCMTARLN-----YG-NTYSESPASFTPFIVPNKHLFVRNPDDAWWRRY---IVIPFD  633 (789)
Q Consensus       570 ~~~~~~~~~K~ltggD~i~ar~~-----~~-~~~~~~~p~~~~~~~~N~~P~~~~~d~~~~rR~---~iipF~  633 (789)
                      -   ..    +-.+|+.-.+|+.     -+ +. +.-.....|++.+-+.|-+  -|.||.||+   +-||.+
T Consensus       237 l---cg----~r~enEseasRRIKTEfLVQMqG-VG~d~~gvLVLgATNiPw~--LDsAIRRRFekRIYIPLP  299 (439)
T KOG0739         237 L---CG----SRSENESEASRRIKTEFLVQMQG-VGNDNDGVLVLGATNIPWV--LDSAIRRRFEKRIYIPLP  299 (439)
T ss_pred             H---CC----CCCCCCHHHHHHHHHHHHHHHHC-CCCCCCCEEEEECCCCCHH--HHHHHHHHHHCCEECCCC
T ss_conf             3---26----88777117777777788876406-6658886489723788436--779999876502301087


No 331
>cd03216 ABC_Carb_Monos_I This family represents the domain I of the carbohydrate uptake proteins that transport only monosaccharides (Monos).  The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis.  Pentoses include xylose, arabinose, and ribose.  Important hexoses include glucose, galactose, and fructose.  In members of the Carb_monos family, the single hydrophobic gene product forms a homodimer while the ABC protein represents a fusion of two nucleotide-binding domains.  However, it is assumed that two copies of the ABC domains are present in the assembled transporter.
Probab=84.57  E-value=0.78  Score=23.26  Aligned_cols=29  Identities=28%  Similarity=0.431  Sum_probs=23.3

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             33799997078862578999999972330
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      .-.++-+.|+-++||||++++|..++-..
T Consensus        25 ~Gei~~lvG~nGaGKSTl~~~i~Gl~~p~   53 (163)
T cd03216          25 RGEVHALLGENGAGKSTLMKILSGLYKPD   53 (163)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHCCCCCC
T ss_conf             99899999889989999999995776898


No 332
>TIGR00150 TIGR00150 conserved hypothetical protein TIGR00150; InterPro: IPR003442   This group consists of bacterial proteins, which contain a P-loop. They are probably essential to bacteria as members are found in all genomes so far sequenced and no equivalent genes have been found in the archaea and eukaryotes, suggesting the protein may be involved in cell wall biosynthesis. The sequence of YjeE, from Haemophilus influenzae, has been determined to 1.7-A resolution. The protein has a nucleotide-binding fold with a four-stranded parallel beta-sheet flanked by antiparallel beta-strands on each side. The topology of the beta-sheet is unique among P-loop proteins and has features of different families of enzymes. ADP has been shown to bind to the P-loop in the presence of Mg2+ and ATPase activity has been confirmed by kinetic measurements . .
Probab=84.53  E-value=2.4  Score=20.02  Aligned_cols=64  Identities=16%  Similarity=0.105  Sum_probs=44.2

Q ss_pred             CCCH-HH-HHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCC-CCCCCCHHHHHH
Q ss_conf             7999-99-9999999999975987433799997078862578999999972330-003442676420
Q gi|254781225|r  477 FESE-EV-MDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQ-YVINAEASDIMQ  540 (789)
Q Consensus       477 ~~d~-e~-~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~-~~~~~~~~~~~~  540 (789)
                      +||+ .. .++=++++--.|--+......+.|.|.=|+||+||..-+..-||-. ++.|++-+++..
T Consensus         2 ~pdEt~a~~~~~~~~a~~llklh~d~~~v~~L~GDlGaGKTtl~~G~~~~LG~~~~~~SPTftlv~~   68 (147)
T TIGR00150         2 LPDETKAMDKLGKAFAKPLLKLHLDLGTVVLLKGDLGAGKTTLVKGLLQGLGITGNVTSPTFTLVNE   68 (147)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHHCCCEEEEECCCCCEEEE
T ss_conf             7126789999999999999985199753899732346665899999998379226885793210100


No 333
>cd03279 ABC_sbcCD SbcCD and other Mre11/Rad50 (MR) complexes are implicated in the metabolism of DNA ends. They cleave ends sealed by hairpin structures and are thought to play a role in removing protein bound to DNA termini.
Probab=84.53  E-value=1.1  Score=22.16  Aligned_cols=25  Identities=40%  Similarity=0.686  Sum_probs=21.6

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             3799997078862578999999972
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~ll  525 (789)
                      .-++.+.|+-+.||||+++.|...|
T Consensus        28 ~~lflI~G~nGsGKSTIlDAI~~aL   52 (213)
T cd03279          28 NGLFLICGPTGAGKSTILDAITYAL   52 (213)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             8889998899997889999999998


No 334
>KOG0058 consensus
Probab=84.52  E-value=0.98  Score=22.59  Aligned_cols=31  Identities=26%  Similarity=0.432  Sum_probs=24.7

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCCCC
Q ss_conf             4337999970788625789999999723300
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGNQY  529 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~  529 (789)
                      +.-.-.-+.|+.++||||+.++|.++.-...
T Consensus       492 ~pGe~vALVGPSGsGKSTiasLL~rfY~Pts  522 (716)
T KOG0058         492 RPGEVVALVGPSGSGKSTIASLLLRFYDPTS  522 (716)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHCCCCC
T ss_conf             7997799988999888999999997368888


No 335
>PRK03839 putative kinase; Provisional
Probab=84.47  E-value=1.2  Score=22.08  Aligned_cols=25  Identities=36%  Similarity=0.602  Sum_probs=22.2

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             9999707886257899999997233
Q gi|254781225|r  503 FIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       503 ~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ++.++|+.|.||||+.++|+.-+|=
T Consensus         2 ~I~ITGTPGtGKTTva~~La~~lg~   26 (180)
T PRK03839          2 IIAITGTPGVGKTTISKLLAEKLGY   26 (180)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCC
T ss_conf             8999789999989999999997698


No 336
>cd01131 PilT Pilus retraction ATPase PilT. PilT is a nucleotide binding protein responsible for the retraction of type IV pili, likely by pili disassembly. This retraction provides the force required for travel of bacteria in low water environments by a mechanism known as twitching motility.
Probab=84.47  E-value=1.2  Score=22.09  Aligned_cols=26  Identities=27%  Similarity=0.382  Sum_probs=21.5

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             79999707886257899999997233
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      =++++.|+.++||||++..+-..+..
T Consensus         2 GliLitG~TGSGKTTtl~all~~i~~   27 (198)
T cd01131           2 GLVLVTGPTGSGKSTTLAAMIDYINK   27 (198)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHCC
T ss_conf             38999899999799999999985363


No 337
>PRK10938 putative molybdenum transport ATP-binding protein ModF; Provisional
Probab=84.36  E-value=0.77  Score=23.31  Aligned_cols=26  Identities=38%  Similarity=0.523  Sum_probs=19.2

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             43379999707886257899999997
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYA  524 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~l  524 (789)
                      +.--.+-+.|+-|+|||||+++|...
T Consensus       284 ~~GE~~~i~G~nGsGKSTLl~~l~G~  309 (490)
T PRK10938        284 NPGEHWQIVGPNGAGKSTLLSLITGD  309 (490)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCC
T ss_conf             38988999867888799999998088


No 338
>COG2256 MGS1 ATPase related to the helicase subunit of the Holliday junction resolvase [DNA replication, recombination, and repair]
Probab=84.32  E-value=1  Score=22.56  Aligned_cols=12  Identities=8%  Similarity=-0.272  Sum_probs=5.5

Q ss_pred             CCCCCCHHHHCC
Q ss_conf             855898655010
Q gi|254781225|r  442 QKVKPTKELYIT  453 (789)
Q Consensus       442 ~~~~~~~~~~~t  453 (789)
                      =..||+-.++..
T Consensus       383 YkY~HD~~~~~v  394 (436)
T COG2256         383 YKYPHDYPAGAV  394 (436)
T ss_pred             CCCCCCCCCCCC
T ss_conf             678988766630


No 339
>COG0606 Predicted ATPase with chaperone activity [Posttranslational modification, protein turnover, chaperones]
Probab=84.31  E-value=1.6  Score=21.10  Aligned_cols=147  Identities=20%  Similarity=0.199  Sum_probs=76.4

Q ss_pred             HHHHCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCC---------CCCCCHHHHH----
Q ss_conf             988879999999999999999759874337999970788625789999999723300---------0344267642----
Q gi|254781225|r  473 VSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQY---------VINAEASDIM----  539 (789)
Q Consensus       473 l~~~~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~---------~~~~~~~~~~----  539 (789)
                      |.++.|.+.-.+-    +=-+..|..    =++++|+-++|||.+..=+..+|..-.         +.+....+..    
T Consensus       178 ~~DV~GQ~~AKrA----leiAAAGgH----nLl~~GpPGtGKTmla~Rl~~lLPpls~~E~lE~s~I~s~~~~~~~~~~~  249 (490)
T COG0606         178 FKDVKGQEQAKRA----LEIAAAGGH----NLLLVGPPGTGKTMLASRLPGLLPPLSIPEALEVSAIHSLAGDLHEGCPL  249 (490)
T ss_pred             HHHHCCCHHHHHH----HHHHHHCCC----CEEEECCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf             6664384999999----999984388----67875699886567642310259998708889998887635432467864


Q ss_pred             -HCC---CC-----------CCCCCCHHHHHHCCCEEEEEECCCCCCC-CCCCEEEEEECCCEEEEEECCCCCCEEEECC
Q ss_conf             -012---45-----------5556898899738980999934677760-1310024541598587321047860687145
Q gi|254781225|r  540 -QNR---PP-----------EAGKANPSLIRLMGSRIVIISETNENDE-INAAKIKQMTGGDCMTARLNYGNTYSESPAS  603 (789)
Q Consensus       540 -~~~---~~-----------~~~~~~~~la~l~g~r~~~~~E~~~~~~-~~~~~~K~ltggD~i~ar~~~~~~~~~~~p~  603 (789)
                       ..|   .+           ..+.+.|.-..|.+--+.+.+|..+-++ +=+++.-=|-.|.-+-.|... +  ++|.-.
T Consensus       250 ~~~rPFr~PHHsaS~~aLvGGG~~p~PGeIsLAH~GVLFLDElpef~~~iLe~LR~PLE~g~i~IsRa~~-~--v~ypa~  326 (490)
T COG0606         250 KIHRPFRAPHHSASLAALVGGGGVPRPGEISLAHNGVLFLDELPEFKRSILEALREPLENGKIIISRAGS-K--VTYPAR  326 (490)
T ss_pred             CEECCCCCCCCCCHHHHHHCCCCCCCCCCEEEECCCEEEEECCCHHHHHHHHHHHCCCCCCCEEEEECCC-E--EEEEEE
T ss_conf             1107876887402288973789988987354303877886144210599999973741258179997587-1--687212


Q ss_pred             EEEEEECCCCCCCCCCCCCEEEEEEEEEC
Q ss_conf             28999738863426798416646899965
Q gi|254781225|r  604 FTPFIVPNKHLFVRNPDDAWWRRYIVIPF  632 (789)
Q Consensus       604 ~~~~~~~N~~P~~~~~d~~~~rR~~iipF  632 (789)
                      |.+++++|--|.  +++.+--+|...-|.
T Consensus       327 Fqlv~AmNpcpc--G~~~~~~~~C~c~~~  353 (490)
T COG0606         327 FQLVAAMNPCPC--GNLGAPLRRCPCSPR  353 (490)
T ss_pred             EEEHHHCCCCCC--CCCCCCCCCCCCCHH
T ss_conf             677522399976--478887777578878


No 340
>COG3842 PotA ABC-type spermidine/putrescine transport systems, ATPase components [Amino acid transport and metabolism]
Probab=84.25  E-value=1  Score=22.55  Aligned_cols=15  Identities=27%  Similarity=0.357  Sum_probs=6.8

Q ss_pred             EEECCCEEECCCCCC
Q ss_conf             660793797438885
Q gi|254781225|r  429 LGEQDGILDLETGQK  443 (789)
Q Consensus       429 l~~~NGv~dl~t~~~  443 (789)
                      +.+.+=|..++.|++
T Consensus       201 l~msDri~Vm~~G~I  215 (352)
T COG3842         201 LAMSDRIAVMNDGRI  215 (352)
T ss_pred             HHHCCCEEECCCCCE
T ss_conf             632362278217704


No 341
>cd03219 ABC_Mj1267_LivG_branched The Mj1267/LivG ABC transporter subfamily is involved in the transport of the hydrophobic amino acids leucine, isoleucine and valine.  MJ1267 is a branched-chain amino acid transporter with 29% similarity to both the LivF and LivG components of the E. coli  branched-chain amino acid transporter.  MJ1267 contains an insertion from residues 114 to 123 characteristic of LivG (Leucine-Isoleucine-Valine) homologs.  The branched-chain amino acid transporter from E. coli comprises a heterodimer of ABCs (LivF and LivG), a heterodimer of six-helix TM domains (LivM and LivH), and one of two alternative soluble periplasmic substrate binding proteins (LivK or LivJ).
Probab=84.24  E-value=0.81  Score=23.16  Aligned_cols=29  Identities=31%  Similarity=0.440  Sum_probs=22.0

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             43379999707886257899999997233
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ..--++-+.|+-++||||++++|..++-.
T Consensus        24 ~~Gei~gliG~nGaGKSTL~~~i~Gl~~p   52 (236)
T cd03219          24 RPGEIHGLIGPNGAGKTTLFNLISGFLRP   52 (236)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             89989999989997399999999679878


No 342
>PRK10762 D-ribose transporter ATP binding protein; Provisional
Probab=84.24  E-value=0.82  Score=23.11  Aligned_cols=30  Identities=20%  Similarity=0.456  Sum_probs=23.9

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             433799997078862578999999972330
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      +.--++-+.|.-++|||||+++|..++...
T Consensus       276 ~~GEi~gi~G~nGsGKsTL~~~l~Gl~~~~  305 (501)
T PRK10762        276 RKGEILGVSGLMGAGRTELMKVLYGALPRT  305 (501)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCCC
T ss_conf             688189966788876889999981876777


No 343
>PRK00064 recF recombination protein F; Reviewed
Probab=84.22  E-value=1.5  Score=21.30  Aligned_cols=21  Identities=29%  Similarity=0.528  Sum_probs=11.8

Q ss_pred             HHHHHHHCCCCCCCEEEEEEE
Q ss_conf             999999759874337999970
Q gi|254781225|r  488 RCVGMALLGGNKAQRFIHIRG  508 (789)
Q Consensus       488 ~~~g~~l~g~~~~~~~~~~~G  508 (789)
                      ...|+++.|-.+....+.+-|
T Consensus       247 ~~~g~T~~GPHRdD~~~~~~~  267 (355)
T PRK00064        247 RARGRTLVGPHRDDLRVRING  267 (355)
T ss_pred             HHHCCCCCCCCCCEEEEEECC
T ss_conf             982888889873438999898


No 344
>KOG0082 consensus
Probab=84.16  E-value=1.1  Score=22.34  Aligned_cols=45  Identities=7%  Similarity=0.041  Sum_probs=20.6

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCEEEEEEE--CCCCCHHHHHHHHHHHHC
Q ss_conf             9999999999999759874337999970--788625789999999723
Q gi|254781225|r  481 EVMDYFTRCVGMALLGGNKAQRFIHIRG--VGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       481 e~~~~l~~~~g~~l~g~~~~~~~~~~~G--~G~nGKSt~~~~l~~llG  526 (789)
                      +...|++.-+--...... ...+...+=  ...|=+.+|-.+...++.
T Consensus       299 ~a~~yI~~kF~~l~~~~~-k~iy~h~T~AtDT~nv~~vf~av~d~Ii~  345 (354)
T KOG0082         299 EAAKYIRKKFEELNKNKD-KKIYVHFTCATDTQNVQFVFDAVTDTIIQ  345 (354)
T ss_pred             HHHHHHHHHHHHHHCCCC-CCCEEEEEEECCHHHHHHHHHHHHHHHHH
T ss_conf             999999999999741557-76057787604588999999999999999


No 345
>cd03283 ABC_MutS-like MutS-like homolog in eukaryotes.  The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch.  Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily.  MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined.  Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes.  The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis.  All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action.  MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form slid
Probab=84.15  E-value=1.2  Score=22.00  Aligned_cols=24  Identities=38%  Similarity=0.376  Sum_probs=19.9

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             379999707886257899999997
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYA  524 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~l  524 (789)
                      +.+++++|+-..||||++..+.-.
T Consensus        25 ~~~~iiTGpN~~GKSt~Lk~i~l~   48 (199)
T cd03283          25 KNGILITGSNMSGKSTFLRTIGVN   48 (199)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHH
T ss_conf             858999899998659999999999


No 346
>cd03287 ABC_MSH3_euk MutS3 homolog in eukaryotes.  The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch.  Members of the MutS family possess C-terminal domain with a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily.  MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined.  Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes.  The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis.  All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action.  MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding c
Probab=83.92  E-value=1.5  Score=21.39  Aligned_cols=25  Identities=20%  Similarity=0.206  Sum_probs=20.3

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             3379999707886257899999997
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYA  524 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~l  524 (789)
                      .+.+++++|+-..||||+++.+.-+
T Consensus        30 ~~~~~iiTGpN~~GKSt~lk~i~l~   54 (222)
T cd03287          30 GGYCQIITGPNMGGKSSYIRQVALI   54 (222)
T ss_pred             CCEEEEEECCCCCCCHHHHHHHHHH
T ss_conf             8448999789988728999999999


No 347
>COG4604 CeuD ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=83.85  E-value=1.2  Score=21.96  Aligned_cols=22  Identities=36%  Similarity=0.603  Sum_probs=8.1

Q ss_pred             EEEECCCCCHHHHHHHHHHHHC
Q ss_conf             9970788625789999999723
Q gi|254781225|r  505 HIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       505 ~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      -++||-+.||||++.++..+++
T Consensus        31 s~IGPNGAGKSTLLS~~sRL~~   52 (252)
T COG4604          31 SIIGPNGAGKSTLLSMMSRLLK   52 (252)
T ss_pred             EEECCCCCCHHHHHHHHHHHCC
T ss_conf             8888998648889999998526


No 348
>cd02028 UMPK_like Uridine monophosphate kinase_like (UMPK_like) is a family of proteins highly similar to the uridine monophosphate kinase (UMPK, EC 2.7.1.48), also known as uridine kinase or uridine-cytidine kinase (UCK).
Probab=83.83  E-value=0.77  Score=23.28  Aligned_cols=26  Identities=27%  Similarity=0.382  Sum_probs=21.4

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHCCCC
Q ss_conf             99970788625789999999723300
Q gi|254781225|r  504 IHIRGVGGSGKSTLMNLIKYAFGNQY  529 (789)
Q Consensus       504 ~~~~G~G~nGKSt~~~~l~~llG~~~  529 (789)
                      +-+.|+.++|||||.+.|...|+...
T Consensus         2 IgIaG~SgSGKTT~a~~L~~~l~~~~   27 (179)
T cd02028           2 VGIAGPSGSGKTTFAKKLSNQLRVNG   27 (179)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCC
T ss_conf             89989897789999999999984648


No 349
>cd03243 ABC_MutS_homologs The MutS protein initiates DNA mismatch repair by recognizing mispaired and unpaired bases embedded in duplex DNA and activating endo- and exonucleases to remove the mismatch.  Members of the MutS family also possess a conserved ATPase activity that belongs to the ATP binding cassette (ABC) superfamily.  MutS homologs (MSH) have been identified in most prokaryotic and all eukaryotic organisms examined.  Prokaryotes have two homologs (MutS1 and MutS2), whereas seven MSH proteins (MSH1 to MSH7) have been identified in eukaryotes.  The homodimer MutS1 and heterodimers MSH2-MSH3 and MSH2-MSH6 are primarily involved in mitotic mismatch repair, whereas MSH4-MSH5 is involved in resolution of Holliday junctions during meiosis.  All members of the MutS family contain the highly conserved Walker A/B ATPase domain, and many share a common mechanism of action.  MutS1, MSH2-MSH3, MSH2-MSH6, and MSH4-MSH5 dimerize to form sliding clamps, and recognition of specific DNA stru
Probab=83.81  E-value=1.3  Score=21.82  Aligned_cols=24  Identities=38%  Similarity=0.463  Sum_probs=19.8

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             379999707886257899999997
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYA  524 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~l  524 (789)
                      ..+++++|+-..||||+++.+..+
T Consensus        29 ~~~~iiTGpN~sGKSt~lkti~l~   52 (202)
T cd03243          29 GRLLLITGPNMGGKSTYLRSIGLA   52 (202)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHH
T ss_conf             828999899887539999999999


No 350
>PRK13873 conjugal transfer ATPase TrbE; Provisional
Probab=83.78  E-value=1.2  Score=22.14  Aligned_cols=52  Identities=19%  Similarity=0.155  Sum_probs=33.5

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCCCCCHHHHHHCCCEEE
Q ss_conf             999970788625789999999723300034426764201245555689889973898099
Q gi|254781225|r  503 FIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEAGKANPSLIRLMGSRIV  562 (789)
Q Consensus       503 ~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~~~~~~~~la~l~g~r~~  562 (789)
                      -.+++|+.|.|||||+++|..-+..|...  ....+.++++      .....+..|.+.-
T Consensus       443 HtlI~GpTGsGKTvll~~l~~q~~ry~~~--~vf~FDkd~s------~~i~~~a~GG~y~  494 (815)
T PRK13873        443 HTLVVGPTGAGKSVLLALMALQFRRYPGS--QVFAFDFGGS------IRAAALAMGGDWH  494 (815)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHHCCCC--CEEEEECCCC------HHHHHHHHCCEEE
T ss_conf             43897889998999999999998644898--4899978987------8999998299876


No 351
>smart00382 AAA ATPases associated with a variety of cellular activities. AAA - ATPases associated with a variety of cellular activities. This profile/alignment only detects a fraction of this vast family. The poorly conserved N-terminal helix is missing from the alignment.
Probab=83.75  E-value=1.3  Score=21.89  Aligned_cols=27  Identities=37%  Similarity=0.506  Sum_probs=24.1

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             799997078862578999999972330
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      ..++++|+.|.||||++..+...++..
T Consensus         3 ~~ill~G~~GsGKTtl~~~la~~~~~~   29 (148)
T smart00382        3 EVILIVGPPGSGKTTLARALARELGPP   29 (148)
T ss_pred             CEEEEECCCCHHHHHHHHHHHHHHCCC
T ss_conf             789999999702999999999872668


No 352
>PRK13549 xylose transporter ATP-binding subunit; Provisional
Probab=83.75  E-value=0.88  Score=22.92  Aligned_cols=28  Identities=21%  Similarity=0.441  Sum_probs=22.1

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             4337999970788625789999999723
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      +.--++-+.|.-++|||||+++|..++.
T Consensus       286 ~~GEi~gi~G~nGsGKsTLl~~L~Gl~~  313 (513)
T PRK13549        286 RRGEILGIAGLVGAGRTELVQCLFGAYP  313 (513)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCC
T ss_conf             6884899747988658999999838988


No 353
>cd03215 ABC_Carb_Monos_II This family represents domain II of the carbohydrate uptake proteins that transport only monosaccharides (Monos).  The Carb_Monos family is involved in the uptake of monosaccharides, such as pentoses (such as xylose, arabinose, and ribose) and hexoses (such as xylose, arabinose, and ribose), that cannot be broken down to simple sugars by hydrolysis.  In members of Carb_Monos family the single hydrophobic gene product forms a homodimer, while the ABC protein represents a fusion of two nucleotide-binding domains.  However, it is assumed that two copies of the ABC domains are present in the assembled transporter.
Probab=83.69  E-value=0.54  Score=24.34  Aligned_cols=30  Identities=20%  Similarity=0.269  Sum_probs=24.7

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             433799997078862578999999972330
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      +.--++-+.|+-++||||++++|..++-..
T Consensus        24 ~~GEi~~liG~nGaGKSTll~~l~G~~~p~   53 (182)
T cd03215          24 RAGEIVGIAGLVGNGQTELAEALFGLRPPA   53 (182)
T ss_pred             CCCCEEEEECCCCCCCCHHHHHHCCCCCCC
T ss_conf             599699998889999263778766986788


No 354
>PRK11929 putative bifunctional UDP-N-acetylmuramoylalanyl-D-glutamate--2,6-diaminopimelate ligase/UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine ligase; Provisional
Probab=83.68  E-value=1.9  Score=20.70  Aligned_cols=39  Identities=15%  Similarity=0.186  Sum_probs=26.0

Q ss_pred             HHHHHHHHHHHHCCCCCCCEEEEEEE-CCCCCHHHHHHHHHHHHC
Q ss_conf             99999999999759874337999970-788625789999999723
Q gi|254781225|r  483 MDYFTRCVGMALLGGNKAQRFIHIRG-VGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       483 ~~~l~~~~g~~l~g~~~~~~~~~~~G-~G~nGKSt~~~~l~~llG  526 (789)
                      +..|+++..+..-. ..    .-++| +|.|||+|.-++|..+|.
T Consensus       575 ~~AL~~lA~~~r~~-~~----~~vIgITGSnGKTTTKeml~~iLs  614 (953)
T PRK11929        575 LAALGRMATAWRSS-FS----LPVIAITGSNGKTTTKEMIAAILA  614 (953)
T ss_pred             HHHHHHHHHHHHHH-CC----CCEEEEECCCCHHHHHHHHHHHHH
T ss_conf             99999999999975-79----978999678850789999999998


No 355
>cd01858 NGP_1 NGP-1.  Autoantigen NGP-1 (Nucleolar G-protein gene 1) has been shown to localize in the nucleolus and nucleolar organizers in all cell types analyzed, which is indicative of a function in ribosomal assembly. NGP-1 and its homologs show a circular permutation of the GTPase signature motifs so that the C-terminal strands 5, 6, and 7 (strand 6 contains the G4 box with NKXD motif) are relocated to the N terminus.
Probab=83.59  E-value=2.6  Score=19.76  Aligned_cols=25  Identities=28%  Similarity=0.440  Sum_probs=19.8

Q ss_pred             CCCCEEEEEEECCCCCHHHHHHHHH
Q ss_conf             7433799997078862578999999
Q gi|254781225|r  498 NKAQRFIHIRGVGGSGKSTLMNLIK  522 (789)
Q Consensus       498 ~~~~~~~~~~G~G~nGKSt~~~~l~  522 (789)
                      ...+.-+.+.|-.+-|||||+|.|.
T Consensus        99 ~~~~i~v~ivG~PNVGKSSlIN~L~  123 (157)
T cd01858          99 DKKQISVGFIGYPNVGKSSIINTLR  123 (157)
T ss_pred             CCCCEEEEEEECCCCCHHHHHHHHH
T ss_conf             5564699998258853368898872


No 356
>cd00071 GMPK Guanosine monophosphate kinase (GMPK, EC 2.7.4.8), also known as guanylate kinase (GKase), catalyzes the reversible phosphoryl transfer from adenosine triphosphate (ATP) to guanosine monophosphate (GMP) to yield adenosine diphosphate (ADP) and guanosine diphosphate (GDP). It plays an essential role in the biosynthesis of guanosine triphosphate (GTP). This enzyme is also important for the activation of some antiviral and anticancer agents, such as acyclovir, ganciclovir, carbovir, and thiopurines.
Probab=83.54  E-value=0.8  Score=23.18  Aligned_cols=27  Identities=33%  Similarity=0.584  Sum_probs=22.4

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHCCCC
Q ss_conf             999970788625789999999723300
Q gi|254781225|r  503 FIHIRGVGGSGKSTLMNLIKYAFGNQY  529 (789)
Q Consensus       503 ~~~~~G~G~nGKSt~~~~l~~llG~~~  529 (789)
                      ++++.|+.+.||+|+++.|...+..+.
T Consensus         1 livi~GPSG~GK~tl~~~L~~~~~~~~   27 (137)
T cd00071           1 LIVLSGPSGVGKSTLLKRLLEEFDPNF   27 (137)
T ss_pred             CEEEECCCCCCHHHHHHHHHHCCCCCE
T ss_conf             999999998899999999985198776


No 357
>PRK13830 conjugal transfer protein TrbE; Provisional
Probab=83.51  E-value=1.2  Score=22.11  Aligned_cols=54  Identities=30%  Similarity=0.234  Sum_probs=34.8

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCCCCCHHHHHHCCCEEEEE
Q ss_conf             99997078862578999999972330003442676420124555568988997389809999
Q gi|254781225|r  503 FIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEAGKANPSLIRLMGSRIVII  564 (789)
Q Consensus       503 ~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~~~~~~~~la~l~g~r~~~~  564 (789)
                      -.+++|+.|+|||||+++|...+-.|...  ....+.++++.      ..+.+..|-+..-+
T Consensus       458 HtlIiGpTGsGKTvll~fl~aq~~ky~~~--~vf~FDKd~s~------~i~~~a~GG~y~~l  511 (818)
T PRK13830        458 HTLIFGPTGSGKSTLLALIAAQFRRYAGA--QIFAFDKGRSM------LPLTLAAGGDHYEI  511 (818)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCC--EEEEECCCCCH------HHHHHHHCCEEEEE
T ss_conf             05898999998899999999998642798--38997488768------99999809925873


No 358
>TIGR03269 met_CoM_red_A2 methyl coenzyme M reductase system, component A2. The enzyme that catalyzes the final step in methanogenesis, methyl coenzyme M reductase, contains alpha, beta, and gamma chains. In older literature, the complex of alpha, beta, and gamma chains was termed component C, while this single chain protein was termed methyl coenzyme M reductase system component A2.
Probab=83.40  E-value=0.93  Score=22.74  Aligned_cols=32  Identities=28%  Similarity=0.374  Sum_probs=24.7

Q ss_pred             CCCCEEEEEEECCCCCHHHHHHHHHHHHCCCC
Q ss_conf             74337999970788625789999999723300
Q gi|254781225|r  498 NKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQY  529 (789)
Q Consensus       498 ~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~  529 (789)
                      .+.--++-+.|.-++||||++++|..++-...
T Consensus       307 v~~GEi~gi~G~nGsGKsTL~k~l~Gl~~p~~  338 (520)
T TIGR03269       307 VKEGEIFGIVGTSGAGKTTLSKIIAGVLEPTS  338 (520)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHHCCCCCCC
T ss_conf             72896899987888878999999948878987


No 359
>TIGR01978 sufC FeS assembly ATPase SufC; InterPro: IPR010230   Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems.   The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly .   The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets.   In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen .   This entry represents SufC, which acts as an ATPase in the SUF system. SufC belongs to the ATP-binding cassette transporter family (IPR003439 from INTERPRO) but is no longer thought to be part of a transporter. The complex is reported as cytosolic or associated with the membrane.; GO: 0005524 ATP binding, 0006810 transport.
Probab=83.28  E-value=1  Score=22.55  Aligned_cols=11  Identities=0%  Similarity=0.036  Sum_probs=4.8

Q ss_pred             HHHHHCCCCCC
Q ss_conf             99974035788
Q gi|254781225|r  250 ARRWSKQGSTY  260 (789)
Q Consensus       250 w~~wS~~~~~y  260 (789)
                      .++++.++-+.
T Consensus       136 ~d~~l~R~lNe  146 (248)
T TIGR01978       136 SDEFLNRSLNE  146 (248)
T ss_pred             HHHHHCCCCCC
T ss_conf             38871177874


No 360
>PRK10875 recD exonuclease V subunit alpha; Provisional
Probab=83.27  E-value=2.7  Score=19.67  Aligned_cols=19  Identities=26%  Similarity=0.228  Sum_probs=12.7

Q ss_pred             CCCCCHHHHHHHHHHHHCC
Q ss_conf             7886257899999997233
Q gi|254781225|r  509 VGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       509 ~G~nGKSt~~~~l~~llG~  527 (789)
                      .|--|=..+-..|+..+-.
T Consensus       444 ~G~~Gv~~LN~~i~~~l~~  462 (607)
T PRK10875        444 EGPFGVAGLNERIEQALHQ  462 (607)
T ss_pred             CCCHHHHHHHHHHHHHHCC
T ss_conf             6843099999999999560


No 361
>KOG0729 consensus
Probab=83.27  E-value=2  Score=20.54  Aligned_cols=155  Identities=15%  Similarity=0.183  Sum_probs=84.0

Q ss_pred             CCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHH
Q ss_conf             78888757947899999888799999999999999997598743379999707886257899999997233000344267
Q gi|254781225|r  457 GTPFVEGEPSQEFLDLVSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEAS  536 (789)
Q Consensus       457 ~~~y~~~a~~p~~~~~l~~~~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~  536 (789)
                      .+.|..---|..-.+-|.+++.-+     +..---++-.| ....+=+++||+.++||+.......+--+.-.+-..-..
T Consensus       173 DvTY~DvGGCKeqIEklREVVE~P-----lL~PErfv~LG-IdPPKGvllyGPPGtGKTL~ARAVANRTdAcFIRViGSE  246 (435)
T KOG0729         173 DVTYSDVGGCKEQIEKLREVVELP-----LLHPERFVNLG-IDPPKGVLLYGPPGTGKTLCARAVANRTDACFIRVIGSE  246 (435)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCC-----CCCHHHHHHCC-CCCCCCEEEECCCCCCHHHHHHHHHCCCCCEEEEEHHHH
T ss_conf             863034536699999999988432-----55888887527-899873378689998610899987456674587631189


Q ss_pred             HHHHCCCCC---CCCCCHHHHHHCCCEEEEEECCCCCCCCCCCEEEEEECCCEEEEEECC----C-CCCEEEECCEEEEE
Q ss_conf             642012455---556898899738980999934677760131002454159858732104----7-86068714528999
Q gi|254781225|r  537 DIMQNRPPE---AGKANPSLIRLMGSRIVIISETNENDEINAAKIKQMTGGDCMTARLNY----G-NTYSESPASFTPFI  608 (789)
Q Consensus       537 ~~~~~~~~~---~~~~~~~la~l~g~r~~~~~E~~~~~~~~~~~~K~ltggD~i~ar~~~----~-~~~~~~~p~~~~~~  608 (789)
                      +. ++.-..   --..-|++|+-+-+.++++.|.+.   +..++|-.=.|||.-.-|-+-    + +.| .-+-+.+++|
T Consensus       247 LV-QKYvGEGARMVRElFeMAr~KKACiiFFDEiDA---iGGaRFDDg~ggDNEVQRTMLEli~QLDGF-DpRGNIKVlm  321 (435)
T KOG0729         247 LV-QKYVGEGARMVRELFEMARTKKACIIFFDEIDA---IGGARFDDGAGGDNEVQRTMLELINQLDGF-DPRGNIKVLM  321 (435)
T ss_pred             HH-HHHHHHHHHHHHHHHHHHCCCCEEEEEEECCCC---CCCCCCCCCCCCCHHHHHHHHHHHHHCCCC-CCCCCEEEEE
T ss_conf             99-998624689999999985236527998410102---267203578887279999999999860377-8888758986


Q ss_pred             ECCCCCCCCCCCCCEEE
Q ss_conf             73886342679841664
Q gi|254781225|r  609 VPNKHLFVRNPDDAWWR  625 (789)
Q Consensus       609 ~~N~~P~~~~~d~~~~r  625 (789)
                      +||..-   .-|.|+.|
T Consensus       322 ATNRPd---tLDpALlR  335 (435)
T KOG0729         322 ATNRPD---TLDPALLR  335 (435)
T ss_pred             ECCCCC---CCCHHHCC
T ss_conf             348988---76876628


No 362
>pfam00488 MutS_V MutS domain V. This domain is found in proteins of the MutS family (DNA mismatch repair proteins) and is found associated with pfam01624, pfam05188, pfam05192 and pfam05190. The mutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair; other members of the family included the eukaryotic MSH 1,2,3, 4,5 and 6 proteins. These have various roles in DNA repair and recombination. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. The aligned region corresponds with domain V of Thermus aquaticus MutS, which contains a Walker A motif, and is structurally similar to the ATPase domain of ABC transporters.
Probab=83.26  E-value=1.6  Score=21.12  Aligned_cols=24  Identities=29%  Similarity=0.426  Sum_probs=19.4

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             379999707886257899999997
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYA  524 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~l  524 (789)
                      ..+++++|+-..||||++..+.-+
T Consensus        42 ~~~~iiTGpN~sGKSt~Lk~igl~   65 (234)
T pfam00488        42 SRILLITGPNMGGKSTYLRQVALI   65 (234)
T ss_pred             EEEEEEECCCCCCCHHHHHHHHHH
T ss_conf             169999788777619999999999


No 363
>cd02021 GntK Gluconate kinase (GntK) catalyzes the phosphoryl transfer from ATP to gluconate. The resulting product gluconate-6-phoshate is an important precursor of gluconate metabolism. GntK acts as a dimmer composed of two identical subunits.
Probab=83.20  E-value=1.1  Score=22.15  Aligned_cols=26  Identities=38%  Similarity=0.555  Sum_probs=22.2

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             99997078862578999999972330
Q gi|254781225|r  503 FIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       503 ~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      ++++.|.-|+||||+...|..-+|--
T Consensus         1 liiv~GvsGsGKSTia~~La~~lg~~   26 (150)
T cd02021           1 IIVVMGVSGSGKSTVGKALAERLGAP   26 (150)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHCCC
T ss_conf             98999189999999999999971995


No 364
>COG4962 CpaF Flp pilus assembly protein, ATPase CpaF [Intracellular trafficking and secretion]
Probab=83.17  E-value=2.7  Score=19.65  Aligned_cols=50  Identities=32%  Similarity=0.388  Sum_probs=34.1

Q ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             9999988879999999999999999759874337999970788625789999999723
Q gi|254781225|r  469 FLDLVSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       469 ~~~~l~~~~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      .++++.--.-+.+..+||+.+++.-        +=++.-|..++||+|++|.+.....
T Consensus       149 l~dli~~gt~~~~~a~~L~~av~~r--------~NILisGGTGSGKTTlLNal~~~i~  198 (355)
T COG4962         149 LLDLIIFGTMIRRAAKFLRRAVGIR--------CNILISGGTGSGKTTLLNALSGFID  198 (355)
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHC--------EEEEEECCCCCCHHHHHHHHHHCCC
T ss_conf             9999873895889999999998620--------1599967878879999999971579


No 365
>cd02024 NRK1 Nicotinamide riboside kinase (NRK) is an enzyme involved in the metabolism of nicotinamide adenine dinucleotide (NAD+). This enzyme catalyzes the phosphorylation of nicotinamide riboside (NR) to form nicotinamide mononucleotide (NMN). It defines the NR salvage pathway of NAD+ biosynthesis in addition to the pathways through nicotinic acid mononucleotide (NaMN). This enzyme can also phosphorylate the anticancer drug tiazofurin, which is an analog of nicotinamide riboside.
Probab=83.00  E-value=1.1  Score=22.18  Aligned_cols=24  Identities=42%  Similarity=0.546  Sum_probs=20.4

Q ss_pred             EEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             997078862578999999972330
Q gi|254781225|r  505 HIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       505 ~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      -+.|..++||||+.+.|...+++-
T Consensus         3 gIaG~S~SGKTTla~~L~~~l~~~   26 (187)
T cd02024           3 GISGVTNSGKTTLAKLLQRILPNC   26 (187)
T ss_pred             EEECCCCCCHHHHHHHHHHHCCCC
T ss_conf             996888875999999999987998


No 366
>COG1196 Smc Chromosome segregation ATPases [Cell division and chromosome partitioning]
Probab=82.98  E-value=1.3  Score=21.85  Aligned_cols=10  Identities=0%  Similarity=0.155  Sum_probs=4.0

Q ss_pred             HHHHHHHHHC
Q ss_conf             8999998887
Q gi|254781225|r  468 EFLDLVSGYF  477 (789)
Q Consensus       468 ~~~~~l~~~~  477 (789)
                      .|...|..++
T Consensus       530 ~y~~Aie~al  539 (1163)
T COG1196         530 KYETALEAAL  539 (1163)
T ss_pred             HHHHHHHHHH
T ss_conf             7999999995


No 367
>PRK07952 DNA replication protein DnaC; Validated
Probab=82.88  E-value=2.8  Score=19.57  Aligned_cols=118  Identities=15%  Similarity=0.137  Sum_probs=60.6

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHHCCC--CCCCCC-HHHHHHCCCC-CCCCCCHH--HHHHCCCEEEEEECCCCCC--CC
Q ss_conf             799997078862578999999972330--003442-6764201245-55568988--9973898099993467776--01
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYAFGNQ--YVINAE-ASDIMQNRPP-EAGKANPS--LIRLMGSRIVIISETNEND--EI  573 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~llG~~--~~~~~~-~~~~~~~~~~-~~~~~~~~--la~l~g~r~~~~~E~~~~~--~~  573 (789)
                      .-++++|+-|+|||.|...|.+-+=+.  .+.-.. ..++..-+.. ..+..+.+  +..+....|.|++|.....  ..
T Consensus        97 ~gLlF~G~~GTGKThLA~aIan~Li~~G~sVlf~t~~dLl~~lr~t~~~~~~~e~~~l~~l~~~dLLIiDdlG~e~~t~~  176 (242)
T PRK07952         97 ASFIFSGKPGTGKNHLAAAICNELLLRGKSVLIITVADIMSAMKDTFRNSETSEEQLLNDLSNVDLLVIDEIGVQTESRY  176 (242)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCEEEEECCCCCCCCHH
T ss_conf             71799789999789999999999998799499977999999999998068756999999863189898730146658888


Q ss_pred             CCCEEEEEECCCEEEEEECCCCCCEEEECCEEEEEECCCCCCC-CC-CCCCEEEEEE-----EEECC
Q ss_conf             3100245415985873210478606871452899973886342-67-9841664689-----99658
Q gi|254781225|r  574 NAAKIKQMTGGDCMTARLNYGNTYSESPASFTPFIVPNKHLFV-RN-PDDAWWRRYI-----VIPFD  633 (789)
Q Consensus       574 ~~~~~K~ltggD~i~ar~~~~~~~~~~~p~~~~~~~~N~~P~~-~~-~d~~~~rR~~-----iipF~  633 (789)
                      ....|=+     -|..|....+|.         ++.||..+.- .. -++.++.|+.     .|+|+
T Consensus       177 ~~~~lf~-----iId~Ry~~~kp~---------IitTNl~~~eL~~~lGeR~~dRl~~~~~~~l~f~  229 (242)
T PRK07952        177 EKVIINQ-----IVDRRSSSKRPT---------GMLTNSNMEEMTKLLGERVMDRMRLGNSLWVIFN  229 (242)
T ss_pred             HHHHHHH-----HHHHHHHCCCCE---------EEEECCCHHHHHHHHHHHHHHHHHHCCCEEEEEC
T ss_conf             9999999-----999999716988---------9981799999999970899999972798599606


No 368
>TIGR01166 cbiO cobalt ABC transporter, ATP-binding protein; InterPro: IPR005876   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 ATP binding subunit of the multisubunit cobalt transporter in bacteria and its equivalents in archaea. This superfamily includes two groups, one which catalyses the uptake of small molecules, including ions from the external milieu and the other group which is engaged in the efflux of small molecular weight compounds and ions from within the cell. Energy derived from the hydrolysis of ATP drives both the process of uptake and efflux.; GO: 0006824 cobalt ion transport, 0009276 1-2nm peptidoglycan-based cell wall.
Probab=82.87  E-value=1.4  Score=21.58  Aligned_cols=63  Identities=14%  Similarity=0.236  Sum_probs=44.2

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCCCCC-CCCCHHHHHHCCCCCCCCCCHHHHHHCCCEEEEEECCCC
Q ss_conf             43379999707886257899999997233000-344267642012455556898899738980999934677
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYV-INAEASDIMQNRPPEAGKANPSLIRLMGSRIVIISETNE  569 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~-~~~~~~~~~~~~~~~~~~~~~~la~l~g~r~~~~~E~~~  569 (789)
                      ..-..+-+.|+-+.|||||+..+.-+|=.... ....-.-+.-        .+-.|.+.+-+-..++++|+.
T Consensus        16 ~~G~~~aLlG~NGaGKsTLl~~LnG~LrP~~G~v~~dG~~l~Y--------srkgL~~~R~~V~~VfQdPDD   79 (190)
T TIGR01166        16 ERGEVLALLGANGAGKSTLLLHLNGLLRPQSGKVLLDGEPLDY--------SRKGLLEVRQRVGLVFQDPDD   79 (190)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHCCCCCCCCCEEEECCEECCC--------CCHHHHHHCCEEEEEEECHHH
T ss_conf             0571689872899857899887436777975558767854035--------724467525030037626344


No 369
>COG3451 VirB4 Type IV secretory pathway, VirB4 components [Intracellular trafficking and secretion]
Probab=82.79  E-value=1.2  Score=21.99  Aligned_cols=27  Identities=22%  Similarity=0.225  Sum_probs=23.7

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHCCCC
Q ss_conf             999970788625789999999723300
Q gi|254781225|r  503 FIHIRGVGGSGKSTLMNLIKYAFGNQY  529 (789)
Q Consensus       503 ~~~~~G~G~nGKSt~~~~l~~llG~~~  529 (789)
                      ..++.|+.|.|||||++++..-+..|.
T Consensus       438 hT~I~G~tGaGKTvLl~~lla~~~k~~  464 (796)
T COG3451         438 HTLIIGPTGAGKTVLLSFLLAQALKYG  464 (796)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHHHC
T ss_conf             749988988878999999999998745


No 370
>cd03271 ABC_UvrA_II The excision repair protein UvrA domain II; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion.  Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins.  Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins and UvrB having one ATP binding site that is structurally related to that of helicases.
Probab=82.71  E-value=1.2  Score=22.01  Aligned_cols=23  Identities=39%  Similarity=0.531  Sum_probs=18.1

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHH
Q ss_conf             43379999707886257899999
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLI  521 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l  521 (789)
                      ..-.+.-++|+-++|||||++.+
T Consensus        19 ~~G~~~aIiG~sGsGKSTLl~~~   41 (261)
T cd03271          19 PLGVLTCVTGVSGSGKSSLINDT   41 (261)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHH
T ss_conf             89999999879998699999999


No 371
>cd03242 ABC_RecF RecF is a recombinational DNA repair ATPase that maintains replication in the presence of DNA damage.  When replication is prematurely disrupted by DNA damage, several recF pathway gene products play critical roles processing the arrested replication fork, allowing it to resume and complete its task.  This CD represents the nucleotide binding domain of RecF.  RecF  belongs to a large superfamily of ABC transporters involved in the transport of a wide variety of different compounds including sugars, ions, peptides, and more complex organic molecules.  The nucleotide binding domain shows the highest similarity between all members of the family.  ABC transporters are a subset of nucleotide hydrolases with a signature motif, Q-loop, and H-loop/switch region, in addition to, the Walker A motif/P-loop and Walker B motif commonly found in a number of ATP- and GTP-binding and hydrolyzing proteins.
Probab=82.70  E-value=1.8  Score=20.79  Aligned_cols=26  Identities=19%  Similarity=0.267  Sum_probs=19.5

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             37999970788625789999999723
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      ....+++|+-|.||+.+++.|.-+..
T Consensus        21 ~~~n~i~G~NGsGKTnlLEAI~~ls~   46 (270)
T cd03242          21 PGVTVLVGENAQGKTNLLEAISLLAT   46 (270)
T ss_pred             CCCEEEECCCCCCHHHHHHHHHHHHC
T ss_conf             99489999998878999999999817


No 372
>COG2274 SunT ABC-type bacteriocin/lantibiotic exporters, contain an N-terminal double-glycine peptidase domain [Defense mechanisms]
Probab=82.64  E-value=1  Score=22.44  Aligned_cols=31  Identities=35%  Similarity=0.427  Sum_probs=24.6

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCCCC
Q ss_conf             4337999970788625789999999723300
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGNQY  529 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~  529 (789)
                      ....++-+.|..|+||||+++++..+.-.+.
T Consensus       497 ~~Ge~vaIvG~SGsGKSTL~KLL~gly~p~~  527 (709)
T COG2274         497 PPGEKVAIVGRSGSGKSTLLKLLLGLYKPQQ  527 (709)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHCCCCCCC
T ss_conf             7998899987999988999999836788888


No 373
>PRK09700 D-allose transporter ATP-binding protein; Provisional
Probab=82.61  E-value=1  Score=22.49  Aligned_cols=31  Identities=23%  Similarity=0.237  Sum_probs=24.6

Q ss_pred             CCCCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             7433799997078862578999999972330
Q gi|254781225|r  498 NKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       498 ~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      .+.--.+-+.|+-++|||||+++|..+....
T Consensus       286 v~~GEi~gl~G~nGsGKsTL~~~l~Gl~~~~  316 (510)
T PRK09700        286 VCRGEILGFAGLVGSGRTELMNCLFGVDKRA  316 (510)
T ss_pred             ECCCCEEEEECCCCCCHHHHHHHHHCCCCCC
T ss_conf             7488189997688862889999981988888


No 374
>PRK10636 putative ABC transporter ATP-binding protein; Provisional
Probab=82.55  E-value=0.89  Score=22.87  Aligned_cols=26  Identities=35%  Similarity=0.492  Sum_probs=21.1

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             79999707886257899999997233
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      -.+-+.|+-|.|||||+++|...+-.
T Consensus       339 eriaIvG~NGsGKSTLlk~L~G~l~p  364 (638)
T PRK10636        339 SRIGLLGRNGAGKSTLIKLLAGELAP  364 (638)
T ss_pred             CEEEEECCCCCCHHHHHHHHCCCCCC
T ss_conf             47999747871388999997288788


No 375
>PRK05541 adenylylsulfate kinase; Provisional
Probab=82.49  E-value=1.9  Score=20.63  Aligned_cols=30  Identities=27%  Similarity=0.372  Sum_probs=24.5

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             433799997078862578999999972330
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      .....++++|-.++||||+.+.+..-|-..
T Consensus         5 ~kg~viW~TGLsGSGKTTiA~~l~~~L~~~   34 (176)
T PRK05541          5 PNGYVIWITGLAGSGKTTIAKALYERLKLK   34 (176)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHHC
T ss_conf             886799978999998999999999999975


No 376
>PRK10982 galactose/methyl galaxtoside transporter ATP-binding protein; Provisional
Probab=82.41  E-value=1.1  Score=22.34  Aligned_cols=29  Identities=10%  Similarity=0.195  Sum_probs=22.9

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             43379999707886257899999997233
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      +.--++-+.|.-++||||++++|..+.-.
T Consensus       272 ~~GEivgl~G~nGsGKsTL~~~l~Gl~~~  300 (491)
T PRK10982        272 HKGEILGIAGLVGAKRTDIVETLFGIREK  300 (491)
T ss_pred             ECCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             68968997789999788999998198678


No 377
>TIGR01842 type_I_sec_PrtD type I secretion system ATPase; InterPro: IPR010128   Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N terminus, but rather carry signals located toward the extreme C terminus to direct type I secretion.; GO: 0005524 ATP binding, 0015031 protein transport, 0016021 integral to membrane.
Probab=82.38  E-value=1.1  Score=22.25  Aligned_cols=89  Identities=24%  Similarity=0.281  Sum_probs=50.8

Q ss_pred             CCCCCCEEEECCCEEECCCCCCCCCCHHHHCCEECCCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCC
Q ss_conf             05797176607937974388855898655010013788887579478999998887999999999999999975987433
Q gi|254781225|r  422 LDSSSRFLGEQDGILDLETGQKVKPTKELYITKSTGTPFVEGEPSQEFLDLVSGYFESEEVMDYFTRCVGMALLGGNKAQ  501 (789)
Q Consensus       422 ld~~~~ll~~~NGv~dl~t~~~~~~~~~~~~t~~~~~~y~~~a~~p~~~~~l~~~~~d~e~~~~l~~~~g~~l~g~~~~~  501 (789)
                      ....++-|+-++|.|+++.=.+.|+..+.+.   -          |        +.|-     ...+=++.++.    .-
T Consensus       307 ~~~~~m~LP~P~G~L~vE~v~~~PP~~~~Ws---q----------P--------ivPk-----~~l~gi~F~~~----aG  356 (556)
T TIGR01842       307 SRAEAMALPEPEGHLSVENVTIVPPGGKKWS---Q----------P--------IVPK-----PTLRGISFAIQ----AG  356 (556)
T ss_pred             CCCCCCCCCCCCCEEEEEEEEEECCCCCCCC---C----------C--------CCCH-----HHHCCCCEEEC----CC
T ss_conf             8875457889863688877651078631357---8----------9--------7761-----42278621563----77


Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHHCCCC-CCCCCHHHHHH
Q ss_conf             7999970788625789999999723300-03442676420
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYAFGNQY-VINAEASDIMQ  540 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~llG~~~-~~~~~~~~~~~  540 (789)
                      -++-++|+.++|||||.++|--+.-... ..-.+...+.+
T Consensus       357 e~laIIGPSgSGKStLaR~~vG~W~~~~G~VRLDGadl~q  396 (556)
T TIGR01842       357 EALAIIGPSGSGKSTLARILVGIWPPASGSVRLDGADLKQ  396 (556)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHCCCCCCCCEEEEHHHHHC
T ss_conf             4588874786525889878872101356533640334402


No 378
>COG1131 CcmA ABC-type multidrug transport system, ATPase component [Defense mechanisms]
Probab=82.35  E-value=1.1  Score=22.33  Aligned_cols=24  Identities=25%  Similarity=0.506  Sum_probs=11.7

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             999970788625789999999723
Q gi|254781225|r  503 FIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       503 ~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      ++-+.|+-|.||||++++|..++-
T Consensus        33 i~gllG~NGAGKTTllk~l~Gl~~   56 (293)
T COG1131          33 IFGLLGPNGAGKTTLLKILAGLLK   56 (293)
T ss_pred             EEEEECCCCCCHHHHHHHHHCCCC
T ss_conf             999989999989999999967977


No 379
>PRK02006 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=82.26  E-value=2.9  Score=19.42  Aligned_cols=10  Identities=10%  Similarity=-0.011  Sum_probs=4.0

Q ss_pred             CCCCCCHHHH
Q ss_conf             8558986550
Q gi|254781225|r  442 QKVKPTKELY  451 (789)
Q Consensus       442 ~~~~~~~~~~  451 (789)
                      +-.||+-+..
T Consensus       353 ~GlpHR~E~V  362 (501)
T PRK02006        353 RGEPHRVEVI  362 (501)
T ss_pred             CCCCCCEEEE
T ss_conf             7876525899


No 380
>KOG0979 consensus
Probab=82.23  E-value=1.3  Score=21.73  Aligned_cols=29  Identities=10%  Similarity=0.054  Sum_probs=16.9

Q ss_pred             CCCHHHHHHHHHHHHCCCCCEEEECCCCC
Q ss_conf             88125678999876418997699678896
Q gi|254781225|r   73 KDEKTANTFKDTFEILHGTPIVRIGQKPK  101 (789)
Q Consensus        73 ~d~~~~~~~~~~~~~l~g~p~~~~g~~~~  101 (789)
                      +++.+...+...++-.+|.+|-..|++-+
T Consensus        50 pNGSGKSSiVcAIcLglgG~Pk~lGRak~   78 (1072)
T KOG0979          50 PNGSGKSSIVCAICLGLGGKPKLLGRAKK   78 (1072)
T ss_pred             CCCCCCHHHHHHHHHHCCCCHHHCCCHHH
T ss_conf             89897048899999972797443143557


No 381
>COG3638 ABC-type phosphate/phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=82.22  E-value=1.2  Score=22.13  Aligned_cols=24  Identities=33%  Similarity=0.512  Sum_probs=12.6

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             799997078862578999999972
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~ll  525 (789)
                      -|+.++|+.+.||||++..|..+.
T Consensus        31 E~VaiIG~SGaGKSTLLR~lngl~   54 (258)
T COG3638          31 EMVAIIGPSGAGKSTLLRSLNGLV   54 (258)
T ss_pred             CEEEEECCCCCCHHHHHHHHHCCC
T ss_conf             689998788886899999986665


No 382
>KOG0738 consensus
Probab=82.21  E-value=3  Score=19.41  Aligned_cols=252  Identities=14%  Similarity=0.154  Sum_probs=114.1

Q ss_pred             HHCCEECCCCCCCCCCHHHHHHHHHHHC-CCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             5010013788887579478999998887-999999999999999975987433799997078862578999999972330
Q gi|254781225|r  450 LYITKSTGTPFVEGEPSQEFLDLVSGYF-ESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       450 ~~~t~~~~~~y~~~a~~p~~~~~l~~~~-~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      +.++...++.++.-+.-.+-.+.|.+.+ ---.+-+|        +-|-.+.=+-+.++|+.++||+.+...+..=-|..
T Consensus       201 dIl~~np~ikW~DIagl~~AK~lL~EAVvlPi~mPe~--------F~GirrPWkgvLm~GPPGTGKTlLAKAvATEc~tT  272 (491)
T KOG0738         201 DILQRNPNIKWDDIAGLHEAKKLLKEAVVLPIWMPEF--------FKGIRRPWKGVLMVGPPGTGKTLLAKAVATECGTT  272 (491)
T ss_pred             HHHCCCCCCCHHHHCCHHHHHHHHHHHHHHHHHHHHH--------HHHCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCE
T ss_conf             8860599867676316499999999887544424888--------74244653000556799974789999998861672


Q ss_pred             CCCCCCHHHHHHCCCCCCC---CCCHHHHHHCCCEEEEEECCCC--CCCCC----C--CEEEEEECCCEEEEEECCCCCC
Q ss_conf             0034426764201245555---6898899738980999934677--76013----1--0024541598587321047860
Q gi|254781225|r  529 YVINAEASDIMQNRPPEAG---KANPSLIRLMGSRIVIISETNE--NDEIN----A--AKIKQMTGGDCMTARLNYGNTY  597 (789)
Q Consensus       529 ~~~~~~~~~~~~~~~~~~~---~~~~~la~l~g~r~~~~~E~~~--~~~~~----~--~~~K~ltggD~i~ar~~~~~~~  597 (789)
                      .-...+..+.++=|+ .|.   .--|+||+.+---.++++|.+.  +++-+    +  -++|+=.   -|.-.++. ..+
T Consensus       273 FFNVSsstltSKwRG-eSEKlvRlLFemARfyAPStIFiDEIDslcs~RG~s~EHEaSRRvKsEL---LvQmDG~~-~t~  347 (491)
T KOG0738         273 FFNVSSSTLTSKWRG-ESEKLVRLLFEMARFYAPSTIFIDEIDSLCSQRGGSSEHEASRRVKSEL---LVQMDGVQ-GTL  347 (491)
T ss_pred             EEEECHHHHHHHHCC-CHHHHHHHHHHHHHHHCCCEEEHHHHHHHHHCCCCCCCHHHHHHHHHHH---HHHHHCCC-CCC
T ss_conf             787402456555325-2699999999999874885353356778872579865036788888899---99863344-444


Q ss_pred             EEEECCEEEEEECCCCCCCCCCCCCEEEEE---EEEECCCCCC--------------CCCCCHHHHHC-CCC---HHHHH
Q ss_conf             687145289997388634267984166468---9996588788--------------87878334220-120---44799
Q gi|254781225|r  598 SESPASFTPFIVPNKHLFVRNPDDAWWRRY---IVIPFDKPIA--------------NRDASFAQKLE-TKY---TLEAK  656 (789)
Q Consensus       598 ~~~~p~~~~~~~~N~~P~~~~~d~~~~rR~---~iipF~~~~~--------------~~d~~~~~~~~-~~e---~~~i~  656 (789)
                       +-.....+.-+||. |  -|-|+|+.||+   +.||.+..-.              +.+.++ +++. +-|   ...|-
T Consensus       348 -e~~k~VmVLAATN~-P--WdiDEAlrRRlEKRIyIPLP~~~~R~~Li~~~l~~~~~~~~~~~-~~lae~~eGySGaDI~  422 (491)
T KOG0738         348 -ENSKVVMVLAATNF-P--WDIDEALRRRLEKRIYIPLPDAEARSALIKILLRSVELDDPVNL-EDLAERSEGYSGADIT  422 (491)
T ss_pred             -CCCEEEEEEECCCC-C--CCHHHHHHHHHHHHEEEECCCHHHHHHHHHHHHCCCCCCCCCCH-HHHHHHHCCCCHHHHH
T ss_conf             -56516999843689-8--20579999987630331287878999999976235668887569-9999985688737799


Q ss_pred             HHHHHH----HHHHHHCCCCCCCCHHHHHHHHHHHHHCCHHHHHHHHHEEECCCCEECHHHHHHHHHHHHHHCC
Q ss_conf             999999----9999987889887889999999999842638888754326268841117999999999998504
Q gi|254781225|r  657 KWFLKG----VKAYISKGLDVDIPEVCLKAKEEERQGTDTYQAWIDDCCDIGENLWEESHSLAKSYSEYREQEL  726 (789)
Q Consensus       657 ~w~l~g----~~~~~~~g~~~~~p~~v~~a~~~y~~~~D~v~~fi~e~ce~~~~~~~~~~~l~~~y~~~~~~~~  726 (789)
                      +-|=+.    .++.+ .|+   .|..++....|--..-=....|=+-.-.+.+.  +.. .....|..|+.+.|
T Consensus       423 nvCreAsm~~mRR~i-~g~---~~~ei~~lakE~~~~pv~~~Dfe~Al~~v~pS--vs~-~d~~k~ekW~~efG  489 (491)
T KOG0738         423 NVCREASMMAMRRKI-AGL---TPREIRQLAKEEPKMPVTNEDFEEALRKVRPS--VSA-ADLEKYEKWMDEFG  489 (491)
T ss_pred             HHHHHHHHHHHHHHH-HCC---CCHHHHHHHHHCCCCCCCHHHHHHHHHHCCCC--CCH-HHHHHHHHHHHHHC
T ss_conf             999999999999997-247---91776443231434565156599999970867--788-89999999998705


No 383
>PRK11174 cysteine/glutathione ABC transporter membrane/ATP-binding component; Reviewed
Probab=82.19  E-value=1.4  Score=21.62  Aligned_cols=27  Identities=26%  Similarity=0.417  Sum_probs=21.0

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             433799997078862578999999972
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~ll  525 (789)
                      ..-..+-+.|+.|.||||++++|....
T Consensus       374 ~~Ge~vaIVG~SGsGKSTl~~LL~g~~  400 (588)
T PRK11174        374 PAGQRVALVGPSGAGKTSLLNALLGFL  400 (588)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHC
T ss_conf             499789998999864999999998728


No 384
>COG4172 ABC-type uncharacterized transport system, duplicated ATPase component [General function prediction only]
Probab=82.08  E-value=2.3  Score=20.12  Aligned_cols=59  Identities=25%  Similarity=0.240  Sum_probs=35.7

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCCCCCHHHHHHCCCEEEEEECCC
Q ss_conf             999970788625789999999723300034426764201245555689889973898099993467
Q gi|254781225|r  503 FIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEAGKANPSLIRLMGSRIVIISETN  568 (789)
Q Consensus       503 ~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~~~~~~~~la~l~g~r~~~~~E~~  568 (789)
                      -+=+.|..++||||+-..|..++.......-....+.       +..+-++-.++..-=+++.||-
T Consensus       315 TlGlVGESGSGKsTlG~allrL~~s~G~I~F~G~~i~-------~~~~~~mrplR~~mQvVFQDPy  373 (534)
T COG4172         315 TLGLVGESGSGKSTLGLALLRLIPSQGEIRFDGQDID-------GLSRKEMRPLRRRMQVVFQDPY  373 (534)
T ss_pred             EEEEEECCCCCCCHHHHHHHHHCCCCCEEEECCCCCC-------CCCHHHHHHHHHHCEEEEECCC
T ss_conf             6777705889811599999852476863897881166-------6485662035552269971787


No 385
>KOG0055 consensus
Probab=82.07  E-value=1.5  Score=21.36  Aligned_cols=27  Identities=33%  Similarity=0.576  Sum_probs=17.2

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             337999970788625789999999723
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      .-+-+-+.|+.|+||||.+.+|+...-
T Consensus      1015 ~GqTvALVG~SGsGKSTvI~LLeRfYd 1041 (1228)
T KOG0055        1015 AGQTVALVGPSGSGKSTVISLLERFYD 1041 (1228)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHCC
T ss_conf             998899988998879989999998438


No 386
>PRK11147 ABC transporter ATPase component; Reviewed
Probab=82.06  E-value=1  Score=22.45  Aligned_cols=27  Identities=30%  Similarity=0.434  Sum_probs=21.8

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             799997078862578999999972330
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      -.+-+.|+-|.|||||+++|..++-..
T Consensus       346 e~ialvG~NGsGKSTLlk~l~G~l~p~  372 (632)
T PRK11147        346 DKIALIGPNGCGKTTLLKLMLGQLQAD  372 (632)
T ss_pred             CEEEEECCCCCCHHHHHHHHHCCCCCC
T ss_conf             779998898842779999860666899


No 387
>PRK11819 putative ABC transporter ATP-binding protein; Reviewed
Probab=81.98  E-value=1.2  Score=22.12  Aligned_cols=26  Identities=35%  Similarity=0.437  Sum_probs=21.0

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             79999707886257899999997233
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      -.+-+.|+-|.|||||+++|..++-.
T Consensus       351 e~iaivG~NGsGKSTLlk~l~G~~~p  376 (556)
T PRK11819        351 GIVGIIGPNGAGKSTLFKMITGQEQP  376 (556)
T ss_pred             CEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             24789889877588999998386568


No 388
>CHL00181 cbbX CbbX; Provisional
Probab=81.92  E-value=3  Score=19.34  Aligned_cols=102  Identities=22%  Similarity=0.200  Sum_probs=53.1

Q ss_pred             CHHHHHHHHHH-HCCCHHHHHHHHHHHHHHH-------CCCCCC--CEEEEEEECCCCCHHHHHHHHHHHHCCCCC----
Q ss_conf             94789999988-8799999999999999997-------598743--379999707886257899999997233000----
Q gi|254781225|r  465 PSQEFLDLVSG-YFESEEVMDYFTRCVGMAL-------LGGNKA--QRFIHIRGVGGSGKSTLMNLIKYAFGNQYV----  530 (789)
Q Consensus       465 ~~p~~~~~l~~-~~~d~e~~~~l~~~~g~~l-------~g~~~~--~~~~~~~G~G~nGKSt~~~~l~~llG~~~~----  530 (789)
                      .-+..++-|++ ..|=+++.+.+.+++..+-       .|....  -.-+++.|+.|+||+|...++..++-.-.+    
T Consensus        13 ~lee~L~eLd~eliGL~~VK~~v~~l~~~~~~~~~R~~~Gl~~~~~s~h~vF~GnPGTGKTTVARl~a~il~~lG~L~~g   92 (287)
T CHL00181         13 QIQEVLDELDEELIGLVPVKTRIREIAALLLVDRLRKNLGLVSSSPGLHMSFTGSPGTGKTTVALKMADILYRLGYIKKG   92 (287)
T ss_pred             CHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCC
T ss_conf             49999999988646969999999999999999999998799988876538887899867999999999999986995589


Q ss_pred             --CCCC-HHHHHHCCCCCCCCCCHHHHHHCCCEEEEEECC
Q ss_conf             --3442-676420124555568988997389809999346
Q gi|254781225|r  531 --INAE-ASDIMQNRPPEAGKANPSLIRLMGSRIVIISET  567 (789)
Q Consensus       531 --~~~~-~~~~~~~~~~~~~~~~~~la~l~g~r~~~~~E~  567 (789)
                        ...+ ..+..+.-+.+....+..+.+..|. ..+++|.
T Consensus        93 ~vve~~r~dLvg~yvG~Ta~kt~~~i~~a~GG-VLfIDEA  131 (287)
T CHL00181         93 HLITVTRDDLVGQYIGHTAPKTKEVLKKAMGG-VLFIDEA  131 (287)
T ss_pred             EEEEECHHHHCCCCCCCCHHHHHHHHHHCCCC-EEEEECH
T ss_conf             58995358841635352169999999964598-7998244


No 389
>COG4778 PhnL ABC-type phosphonate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=81.78  E-value=1.3  Score=21.79  Aligned_cols=12  Identities=25%  Similarity=0.584  Sum_probs=4.9

Q ss_pred             HHCCCCCCCHHH
Q ss_conf             740357889789
Q gi|254781225|r  253 WSKQGSTYDEEN  264 (789)
Q Consensus       253 wS~~~~~y~~~~  264 (789)
                      |+....+|.-++
T Consensus       146 W~LaPaTFSGGE  157 (235)
T COG4778         146 WSLAPATFSGGE  157 (235)
T ss_pred             HCCCCCCCCCCH
T ss_conf             537986547730


No 390
>PRK13898 type IV secretion system ATPase VirB4; Provisional
Probab=81.78  E-value=2.1  Score=20.36  Aligned_cols=55  Identities=22%  Similarity=0.224  Sum_probs=37.7

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCCCCCHHHHHHCCCEEEEEEC
Q ss_conf             9999707886257899999997233000344267642012455556898899738980999934
Q gi|254781225|r  503 FIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEAGKANPSLIRLMGSRIVIISE  566 (789)
Q Consensus       503 ~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~~~~~~~~la~l~g~r~~~~~E  566 (789)
                      -.++.|+.++|||||++.|..-+-.|.   +....+..+++.      ....+..|.+...+.+
T Consensus       448 HtlI~G~TGsGKTtl~~fL~aq~~ky~---~~~f~fDkd~~~------~i~~~a~GG~Y~~l~~  502 (800)
T PRK13898        448 HTLIIGPTGAGKTVLMNFLCAQAMKFS---PRMFFFDKDRGA------EIFIRALNGVYTVIEP  502 (800)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHHHC---CEEEEEECCCCH------HHHHHHHCCEEEECCC
T ss_conf             569989999989999999999987548---879999799986------9999982988874379


No 391
>TIGR00635 ruvB Holliday junction DNA helicase RuvB; InterPro: IPR004605 All proteins in this family for which functions are known are 5'-3' DNA helicases that, as part of a complex with RuvA homologs serve as a 5'-3' Holliday junction helicase. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.; GO: 0003677 DNA binding, 0005524 ATP binding, 0009378 Holliday junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=81.72  E-value=3.1  Score=19.30  Aligned_cols=95  Identities=17%  Similarity=0.249  Sum_probs=62.4

Q ss_pred             HHHHCCCHHHHHHHHHHHHHHHCCCCC-CCEEEEEEECCCCCHHHHHHHHHHHHCCCC-CCCCCHHHHHHCCCCCCCCCC
Q ss_conf             988879999999999999999759874-337999970788625789999999723300-034426764201245555689
Q gi|254781225|r  473 VSGYFESEEVMDYFTRCVGMALLGGNK-AQRFIHIRGVGGSGKSTLMNLIKYAFGNQY-VINAEASDIMQNRPPEAGKAN  550 (789)
Q Consensus       473 l~~~~~d~e~~~~l~~~~g~~l~g~~~-~~~~~~~~G~G~nGKSt~~~~l~~llG~~~-~~~~~~~~~~~~~~~~~~~~~  550 (789)
                      |.++.|-+++++-||-++-.+=...-. .|  ++|+||.|=||+|+.++|.+=||..- +++.|...-.++-       -
T Consensus         3 L~eFiGQ~~vk~~L~l~I~AAk~R~e~LDH--~LL~GPPGLGKTTLA~IiA~Emg~~l~iTsGP~L~kPgDl-------a   73 (305)
T TIGR00635         3 LAEFIGQEKVKEQLQLFIEAAKMRQEALDH--LLLYGPPGLGKTTLAHIIANEMGVNLKITSGPALEKPGDL-------A   73 (305)
T ss_pred             CHHCCCCHHHHHHHHHHHHHHHHCCCCCCC--EEEECCCCCCHHHHHHHHHHHHCCCCEEEECCCCCCHHHH-------H
T ss_conf             011058288999999999999824897341--6631756874678999999983893267406755475789-------9


Q ss_pred             HHHHHHCCCEEEEEECCCCCCCCCCC
Q ss_conf             88997389809999346777601310
Q gi|254781225|r  551 PSLIRLMGSRIVIISETNENDEINAA  576 (789)
Q Consensus       551 ~~la~l~g~r~~~~~E~~~~~~~~~~  576 (789)
                      --|..|.-+=..+++|...=.+.-|.
T Consensus        74 aiLt~L~~gDVLFIDEIHRL~p~~EE   99 (305)
T TIGR00635        74 AILTNLEEGDVLFIDEIHRLSPAIEE   99 (305)
T ss_pred             HHHHHCCCCCEEECCHHHHCCHHHHH
T ss_conf             99970568963101256504833453


No 392
>TIGR02533 type_II_gspE general secretory pathway protein E; InterPro: IPR013369    GspE, the E protein of the type II secretion system, is also referred to as the main terminal branch of the general secretion pathway. ; GO: 0005524 ATP binding, 0008565 protein transporter activity, 0015628 protein secretion by the type II secretion system, 0015627 type II protein secretion system complex.
Probab=81.55  E-value=0.89  Score=22.87  Aligned_cols=86  Identities=21%  Similarity=0.256  Sum_probs=44.1

Q ss_pred             CCCCHHHCCCCCCE-EEECCCEEECCCCCCCCCCHHHHCCEECCCCCCCCCCHHHHHH-----HHHHHCCCHHHHHHHHH
Q ss_conf             12320220579717-6607937974388855898655010013788887579478999-----99888799999999999
Q gi|254781225|r  415 FSITSDLLDSSSRF-LGEQDGILDLETGQKVKPTKELYITKSTGTPFVEGEPSQEFLD-----LVSGYFESEEVMDYFTR  488 (789)
Q Consensus       415 ~~~~~~~ld~~~~l-l~~~NGv~dl~t~~~~~~~~~~~~t~~~~~~y~~~a~~p~~~~-----~l~~~~~d~e~~~~l~~  488 (789)
                      +.+.+.-|.||-.. |-+.-==+|++             -.++|+.|=+-.-.-..+|     -|..+=-.+++..-|.+
T Consensus       173 LnIAEKRLPQDGRI~Lrv~Gr~~DiR-------------VSt~Pt~fGERvVMRLLDK~~~~l~L~~LGm~~~~l~~~~~  239 (495)
T TIGR02533       173 LNIAEKRLPQDGRISLRVAGRDIDIR-------------VSTVPTSFGERVVMRLLDKDAVRLDLEALGMSPELLSSLER  239 (495)
T ss_pred             CCHHHCCCCCCCCEEEEECCEEEEEE-------------EEECCCCCCCEEEHHHHCHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf             77232178998726666737446678-------------85305899710000011204777758864888889999999


Q ss_pred             HHHHHHCCCCCCCEEEEEEECCCCCHHHHHHH
Q ss_conf             99999759874337999970788625789999
Q gi|254781225|r  489 CVGMALLGGNKAQRFIHIRGVGGSGKSTLMNL  520 (789)
Q Consensus       489 ~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~  520 (789)
                      ++.       +-+=.+..+||.|+||||.+-.
T Consensus       240 li~-------rpHGIiLVTGPTGSGKtTTLYa  264 (495)
T TIGR02533       240 LIK-------RPHGIILVTGPTGSGKTTTLYA  264 (495)
T ss_pred             HHH-------CCCCEEEECCCCCCCHHHHHHH
T ss_conf             971-------8896188417789852588999


No 393
>COG4088 Predicted nucleotide kinase [Nucleotide transport and metabolism]
Probab=81.55  E-value=1.3  Score=21.68  Aligned_cols=11  Identities=18%  Similarity=0.099  Sum_probs=4.2

Q ss_pred             HHHHHHHHHCC
Q ss_conf             99999999759
Q gi|254781225|r  486 FTRCVGMALLG  496 (789)
Q Consensus       486 l~~~~g~~l~g  496 (789)
                      +.+.+.-||.|
T Consensus       248 ~~e~f~e~Lng  258 (261)
T COG4088         248 AEEVFRECLNG  258 (261)
T ss_pred             HHHHHHHHHCC
T ss_conf             99999998565


No 394
>PRK13948 shikimate kinase; Provisional
Probab=81.52  E-value=1.8  Score=20.87  Aligned_cols=32  Identities=22%  Similarity=0.402  Sum_probs=27.4

Q ss_pred             CCCCEEEEEEECCCCCHHHHHHHHHHHHCCCC
Q ss_conf             74337999970788625789999999723300
Q gi|254781225|r  498 NKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQY  529 (789)
Q Consensus       498 ~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~  529 (789)
                      ++.+.+++|+|--++||||+-..|...||-..
T Consensus         7 p~~~~~IvLIG~mGsGKStiGk~LA~~l~~~f   38 (182)
T PRK13948          7 PRPATFVALAGFMGTGKSRIGWELSRALALHF   38 (182)
T ss_pred             CCCCCCEEEECCCCCCHHHHHHHHHHHHCCCE
T ss_conf             99998189889999988999999999969598


No 395
>COG0465 HflB ATP-dependent Zn proteases [Posttranslational modification, protein turnover, chaperones]
Probab=81.46  E-value=3.1  Score=19.23  Aligned_cols=17  Identities=35%  Similarity=0.487  Sum_probs=5.5

Q ss_pred             EEEECCCCCHHHHHHHH
Q ss_conf             99707886257899999
Q gi|254781225|r  505 HIRGVGGSGKSTLMNLI  521 (789)
Q Consensus       505 ~~~G~G~nGKSt~~~~l  521 (789)
                      +..++.+...-.+.|++
T Consensus       347 iAr~tpGfsGAdL~nl~  363 (596)
T COG0465         347 IARGTPGFSGADLANLL  363 (596)
T ss_pred             HHHHCCCCCCCHHHHHH
T ss_conf             86437785630676556


No 396
>PRK13853 type IV secretion system protein VirB4; Provisional
Probab=81.42  E-value=1.3  Score=21.79  Aligned_cols=55  Identities=25%  Similarity=0.283  Sum_probs=33.3

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHCCCCCC-CCCHHHHHHCCCCCCCCCCHHHHHHCCCEEEEE
Q ss_conf             9997078862578999999972330003-442676420124555568988997389809999
Q gi|254781225|r  504 IHIRGVGGSGKSTLMNLIKYAFGNQYVI-NAEASDIMQNRPPEAGKANPSLIRLMGSRIVII  564 (789)
Q Consensus       504 ~~~~G~G~nGKSt~~~~l~~llG~~~~~-~~~~~~~~~~~~~~~~~~~~~la~l~g~r~~~~  564 (789)
                      .+++|+.++|||||++.|...+..|... ......+.++++.      ..+.+..|.....+
T Consensus       429 t~I~G~TGsGKTtll~fL~aq~~ky~~~~~~~~~~fDkd~s~------~i~~~a~GG~y~~i  484 (789)
T PRK13853        429 TAIFGPIGRGKTTLMTFILAMLEQSMVDRAGAVVFFDKDRGG------ELLVRATGGTYLAL  484 (789)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCH------HHHHHHHCCEEEEC
T ss_conf             488789999889999999999997422357708999588638------99999829877612


No 397
>TIGR02397 dnaX_nterm DNA polymerase III, subunits gamma and tau; InterPro: IPR012763    This entry represents the well-conserved first N-terminal domain of DnaX, approx. 365 aa. The full-length product of the dnaX gene in Escherichia coli encodes the DNA polymerase III tau subunit. A translational frameshift leads to early termination and a truncated protein subunit gamma, about 1/3 shorter than tau and present in roughly equal amounts. This frameshift mechanism is not necessarily universal for species with DNA polymerase III but appears conserved in the extreme thermophile Thermus thermophilis.; GO: 0003887 DNA-directed DNA polymerase activity, 0005524 ATP binding, 0006260 DNA replication, 0009360 DNA polymerase III complex.
Probab=81.37  E-value=2.6  Score=19.80  Aligned_cols=144  Identities=13%  Similarity=0.179  Sum_probs=72.8

Q ss_pred             HHHHCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHH----HHCCCCCCCC
Q ss_conf             988879999999999999999759874337999970788625789999999723300034426764----2012455556
Q gi|254781225|r  473 VSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDI----MQNRPPEAGK  548 (789)
Q Consensus       473 l~~~~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~----~~~~~~~~~~  548 (789)
                      ++++.|-+-++..|+-.+-   .+  +-.-.+++.|+-|.||+|..+++.+.|   |+. .+...=    ..-..-+ .+
T Consensus        13 F~d~~GQ~~iv~tL~NAi~---~~--ri~HAYLF~GpRGtGKTS~ARIfAKaL---NC~-~~~~~PCn~C~~C~~i~-~g   82 (363)
T TIGR02397        13 FEDVIGQEHIVKTLKNAIK---NG--RIAHAYLFSGPRGTGKTSIARIFAKAL---NCQ-GPDGEPCNECESCKEIN-SG   82 (363)
T ss_pred             CCCCCCCHHHHHHHHHHHH---HC--CCCCEEEECCCCCCCHHHHHHHHHHHH---CCC-CCCCCCCCCCCHHHHHH-CC
T ss_conf             1102351799999999997---18--966234502859976355899999986---588-78778777750227765-28


Q ss_pred             CCHHHHHHCCCEEEEEECCCC---CCCC--CCCEEE--------EEECCCEEEEEECCCCCCEEEECCEEE-EEECCCCC
Q ss_conf             898899738980999934677---7601--310024--------541598587321047860687145289-99738863
Q gi|254781225|r  549 ANPSLIRLMGSRIVIISETNE---NDEI--NAAKIK--------QMTGGDCMTARLNYGNTYSESPASFTP-FIVPNKHL  614 (789)
Q Consensus       549 ~~~~la~l~g~r~~~~~E~~~---~~~~--~~~~~K--------~ltggD~i~ar~~~~~~~~~~~p~~~~-~~~~N~~P  614 (789)
                      .+.|+.++.++-=+-++|..+   .-..  ..++.|        .||. ....|  + =|. .|-+|.|.. ||+|-++=
T Consensus        83 ~~~DviEiDAASN~gVD~IR~l~e~v~y~P~~~kYKvYIIDEVHMLS~-~AFNA--L-LKT-LEEPP~hV~FIlATTE~~  157 (363)
T TIGR02397        83 SSLDVIEIDAASNNGVDDIRELRENVKYAPSKGKYKVYIIDEVHMLSK-SAFNA--L-LKT-LEEPPEHVVFILATTEPH  157 (363)
T ss_pred             CCCCEEEECCCCCCCHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCCH-HHHHH--H-HHH-HCCCCCCEEEEEECCCHH
T ss_conf             986668864865687889999987303687554433588732302865-68999--8-765-227987628887348711


Q ss_pred             CCCCCCCCEEEEEEEEECCC
Q ss_conf             42679841664689996588
Q gi|254781225|r  615 FVRNPDDAWWRRYIVIPFDK  634 (789)
Q Consensus       615 ~~~~~d~~~~rR~~iipF~~  634 (789)
                      +++.+   |--|---..|.+
T Consensus       158 KiP~T---IlSRCQrF~Fk~  174 (363)
T TIGR02397       158 KIPAT---ILSRCQRFDFKR  174 (363)
T ss_pred             HCCCC---CEEECEEECCCC
T ss_conf             20554---021000312678


No 398
>cd01428 ADK Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP). This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.
Probab=81.32  E-value=1.7  Score=21.04  Aligned_cols=24  Identities=33%  Similarity=0.451  Sum_probs=21.4

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             999707886257899999997233
Q gi|254781225|r  504 IHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       504 ~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      +++.|+.++||||....|..-+|=
T Consensus         2 i~l~G~PGsGKgTqa~~La~~~~~   25 (194)
T cd01428           2 ILLLGPPGSGKGTQAERLAKKYGL   25 (194)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCC
T ss_conf             899899999879999999999798


No 399
>PRK11153 metN DL-methionine transporter ATP-binding subunit; Provisional
Probab=81.24  E-value=1.2  Score=21.90  Aligned_cols=12  Identities=0%  Similarity=-0.003  Sum_probs=7.0

Q ss_pred             HHHHHHHHHHCC
Q ss_conf             789999988879
Q gi|254781225|r  467 QEFLDLVSGYFE  478 (789)
Q Consensus       467 p~~~~~l~~~~~  478 (789)
                      |.-.+|+...+.
T Consensus       235 ~~tk~li~~~~~  246 (343)
T PRK11153        235 PLAQKFIQSTLH  246 (343)
T ss_pred             HHHHHHCCCCCC
T ss_conf             799997088675


No 400
>COG1132 MdlB ABC-type multidrug transport system, ATPase and permease components [Defense mechanisms]
Probab=81.12  E-value=1.7  Score=20.97  Aligned_cols=30  Identities=33%  Similarity=0.452  Sum_probs=23.6

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHCCCC
Q ss_conf             337999970788625789999999723300
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFGNQY  529 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG~~~  529 (789)
                      ....+-+.|+.|+||||++++|..++-.+.
T Consensus       354 ~Ge~vaiVG~sGsGKSTl~~LL~r~~~~~~  383 (567)
T COG1132         354 PGEKVAIVGPSGSGKSTLIKLLLRLYDPTS  383 (567)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHHHCCCCC
T ss_conf             898788855888857899999986158888


No 401
>COG4913 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=80.98  E-value=1.4  Score=21.63  Aligned_cols=35  Identities=26%  Similarity=0.321  Sum_probs=17.2

Q ss_pred             EEEECCCCCCCC--CCCCCCCCCCCHHHHHHHHHC-CEEEEEC
Q ss_conf             977356778787--756545656898999742007-8899923
Q gi|254781225|r   20 LIPLRLGDKRPQ--RLGKWEEQLLSSEKIDKLPAC-GFGFVCG   59 (789)
Q Consensus        20 viPi~pg~KrP~--~~~~w~~~~~~~~~i~~~~~~-giGi~~G   59 (789)
                      +-||.||+=|-.  ..=+|.++.+     ..||.+ +=+++||
T Consensus         7 L~~i~~~~FRL~~iqliNWGTF~T-----~~~~~T~~G~LvTG   44 (1104)
T COG4913           7 LDPIHPGQFRLSRIQLINWGTFHT-----VDIPVTREGILVTG   44 (1104)
T ss_pred             CCCCCCCCEEEEEEEEEECCCCCE-----EEEEEECCCEEEEC
T ss_conf             777789861466778850244312-----46667516457746


No 402
>PRK06696 uridine kinase; Validated
Probab=80.81  E-value=3.3  Score=19.09  Aligned_cols=30  Identities=23%  Similarity=0.280  Sum_probs=23.8

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHCCCC
Q ss_conf             337999970788625789999999723300
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFGNQY  529 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG~~~  529 (789)
                      ....+=+-|..++|||||.+-|...|+...
T Consensus        25 rpl~VgIdG~~gSGKTTlA~~La~~L~~~G   54 (227)
T PRK06696         25 RPLRVAIDGITASGKTTFANELAEEIKKRG   54 (227)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHCC
T ss_conf             868999778998787999999999997469


No 403
>PRK13545 tagH teichoic acids export protein ATP-binding subunit; Provisional
Probab=80.80  E-value=0.93  Score=22.75  Aligned_cols=55  Identities=18%  Similarity=0.270  Sum_probs=27.0

Q ss_pred             CCCEEEEEECCCEEEEEECCCCCCEEEECCEEEEEECCCCCCCCCCCCCEEEEEEEEECC--CCCC
Q ss_conf             310024541598587321047860687145289997388634267984166468999658--8788
Q gi|254781225|r  574 NAAKIKQMTGGDCMTARLNYGNTYSESPASFTPFIVPNKHLFVRNPDDAWWRRYIVIPFD--KPIA  637 (789)
Q Consensus       574 ~~~~~K~ltggD~i~ar~~~~~~~~~~~p~~~~~~~~N~~P~~~~~d~~~~rR~~iipF~--~~~~  637 (789)
                      +...+--+-=|+.+++..+.++.-  -.   .-|+-.|    ..+...|+-.--+|.||+  ..+.
T Consensus       365 ~s~~~~~~~fg~~f~v~~~~k~~~--~~---~~w~~~~----~~~ge~gwis~~~v~~~~~~~~i~  421 (549)
T PRK13545        365 SSKRLAIANFGDIFTISDSNKNEK--KD---VEWIQIT----LSNGEIGWISTKFIEPFKSNNNII  421 (549)
T ss_pred             CCCEEEEECCCCEEEEECCCCCCC--CC---CEEEEEE----ECCCCCCEEEEEEEEEECCCCCHH
T ss_conf             755158862797799805664311--58---6059998----248863302101566414686101


No 404
>PRK07940 DNA polymerase III subunit delta'; Validated
Probab=80.79  E-value=3.3  Score=19.08  Aligned_cols=54  Identities=17%  Similarity=0.155  Sum_probs=36.9

Q ss_pred             HHHHCCCHHHHHHHHHHHHHHH-------CCCCCCCEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             9888799999999999999997-------59874337999970788625789999999723
Q gi|254781225|r  473 VSGYFESEEVMDYFTRCVGMAL-------LGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       473 l~~~~~d~e~~~~l~~~~g~~l-------~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      ++++.|-+.+++.|+..+...=       +...+---.+++.|+-|.||+++...+...|-
T Consensus         4 f~~ivGQe~v~~~L~~A~~~~R~~~~~~~~~~~~~~HAyLF~Gp~G~Gk~~~A~~~A~~l~   64 (395)
T PRK07940          4 WDRLVGQDAVVAELRAAARAARADSAHSAAAGSGMTHAWLFTGPPGSGRSNAARAFAAALQ   64 (395)
T ss_pred             CHHHCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHC
T ss_conf             0131592999999999998363434433334687660376368998788999999999966


No 405
>PRK09435 arginine/ornithine transport system ATPase; Provisional
Probab=80.70  E-value=3.3  Score=19.07  Aligned_cols=40  Identities=25%  Similarity=0.276  Sum_probs=24.0

Q ss_pred             HHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             99999999975987433799997078862578999999972
Q gi|254781225|r  485 YFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       485 ~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~ll  525 (789)
                      ...+++..++ +.+..-..+=++|+.+.|||||++-+...+
T Consensus        34 ~~~~ll~~l~-~~~g~a~~iGiTG~pG~GKStli~~l~~~~   73 (325)
T PRK09435         34 LAQELLDALL-PHTGNALRIGITGVPGVGKSTFIEALGMHL   73 (325)
T ss_pred             HHHHHHHHHH-HCCCCCEEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             9999999863-017982599742799986889999999999


No 406
>COG1100 GTPase SAR1 and related small G proteins [General function prediction only]
Probab=80.53  E-value=1.4  Score=21.55  Aligned_cols=22  Identities=41%  Similarity=0.480  Sum_probs=18.0

Q ss_pred             EEEEEEECCCCCHHHHHHHHHH
Q ss_conf             7999970788625789999999
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKY  523 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~  523 (789)
                      .-++++|+++.|||||++-+..
T Consensus         6 ~kivv~G~~g~GKTtl~~~l~~   27 (219)
T COG1100           6 FKIVVLGDGGVGKTTLLNRLVG   27 (219)
T ss_pred             EEEEEECCCCCCHHHHHHHHHC
T ss_conf             7999999999988999999964


No 407
>TIGR02633 xylG D-xylose ABC transporter, ATP-binding protein; InterPro: IPR013455   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).     Several bacterial species use the enzymes xylose isomerase and xylulokinase for xylose utilisation. This entry represents the ATP-binding cassette (ABC) subunit of the known, or predicted, high-affinity xylose ABC transporter used for xylose import. The genes encoding these proteins, which closely resemble other sugar transport ABC transporter genes, are typically found near xylose utilisation enzymes and regulatory proteins. .
Probab=80.52  E-value=1.2  Score=22.02  Aligned_cols=86  Identities=21%  Similarity=0.249  Sum_probs=38.2

Q ss_pred             CCCCCEEEEEEECCCC-CHHHHHHHHHHHHCCCCCCCCCHHHHHH-CCCCCCCCCCHHHHHHC------C-CEEEEEECC
Q ss_conf             8743379999707886-2578999999972330003442676420-12455556898899738------9-809999346
Q gi|254781225|r  497 GNKAQRFIHIRGVGGS-GKSTLMNLIKYAFGNQYVINAEASDIMQ-NRPPEAGKANPSLIRLM------G-SRIVIISET  567 (789)
Q Consensus       497 ~~~~~~~~~~~G~G~n-GKSt~~~~l~~llG~~~~~~~~~~~~~~-~~~~~~~~~~~~la~l~------g-~r~~~~~E~  567 (789)
                      .+....+-|--=+|+| =|.++...|.        ..+....++. .|+-+- +|..|+.+|.      | +-.++.||.
T Consensus       394 kt~~P~LpI~~LSGGNQQKA~Lak~Ll--------~~P~~LILDEPTRG~Dv-GAKyEIYkL~~~La~~G~a~iv~SSEL  464 (501)
T TIGR02633       394 KTASPFLPIGRLSGGNQQKAVLAKMLL--------LNPRVLILDEPTRGVDV-GAKYEIYKLINQLAQEGVAIIVVSSEL  464 (501)
T ss_pred             EECCCCCCCCCCCCCHHHHHHHHHHHH--------CCCCEEEEECCCCCCCC-CCHHHHHHHHHHHHHCCCEEEEECCCC
T ss_conf             322787542236773057999999874--------39948997478886103-640789999999984795899983431


Q ss_pred             CCCCCCCCCEEEEEECCCEEEEEECC
Q ss_conf             77760131002454159858732104
Q gi|254781225|r  568 NENDEINAAKIKQMTGGDCMTARLNY  593 (789)
Q Consensus       568 ~~~~~~~~~~~K~ltggD~i~ar~~~  593 (789)
                      .+---++. ++ -+.+...+.+.+.+
T Consensus       465 ~EVLG~sD-RV-LV~~eG~l~~~l~N  488 (501)
T TIGR02633       465 AEVLGLSD-RV-LVIGEGKLKADLVN  488 (501)
T ss_pred             HHHCCCCC-EE-EEEECCEEEEEEEC
T ss_conf             00305522-37-88736778854203


No 408
>TIGR01351 adk adenylate kinases; InterPro: IPR006259    Most members of this family are known or believed to be adenylate kinase.   Adenylate kinase (ADK) 2.7.4.3 from EC converts ATP + AMP to ADP + ADP, that is, it uses ATP as a phosphate donor for AMP. Two ADK isozymes have been identified in mammalian cells. These specifically bind AMP and favour binding to ATP over other nucleotide triphosphates (AK1 is cytosolic and AK2 is located in the mitochondria). However, some members accept other nucleotide triphosphates as donors, and may be unable to use ATP, and may fail to complement adenylate kinase mutants. An example of a nucleoside-triphosphate--adenylate kinase (2.7.4.10 from EC) is Q9UIJ7 from SWISSPROT, a GTP:AMP phosphotransferase that has been identified in bovine heart and human cells  and derived from mitrochondrail GTP AMP that is specific for the phosphorylation of AMP, but can only use GTP or ITP as a substrate .This family is designated subfamily rather than equivalog for this reason.   ADK has also been identified in different bacterial species and in yeast . Two further enzymes are known to be related to the ADK family, i.e. yeast uridine monophosphokinase and slime mold UMP-CMP kinase. Within the ADK family there are several conserved regions, including the ATP-binding domains. One of the most conserved areas includes an Arg residue, whose modification inactivates the enzyme, together with an Asp that resides in the catalytic cleft of the enzyme and participates in a salt bridge.  ; GO: 0005524 ATP binding, 0016776 phosphotransferase activity phosphate group as acceptor, 0019201 nucleotide kinase activity, 0006139 nucleobase nucleoside nucleotide and nucleic acid metabolic process.
Probab=80.46  E-value=1.9  Score=20.74  Aligned_cols=27  Identities=22%  Similarity=0.191  Sum_probs=24.5

Q ss_pred             CCCHHHHHHHHHHHHHCCHHHHHHHHH
Q ss_conf             878899999999998426388887543
Q gi|254781225|r  674 DIPEVCLKAKEEERQGTDTYQAWIDDC  700 (789)
Q Consensus       674 ~~p~~v~~a~~~y~~~~D~v~~fi~e~  700 (789)
                      +.|++|+.-.+.|++...||-.|-..+
T Consensus       175 D~~evv~~RL~~Y~~~t~Pli~yY~~~  201 (232)
T TIGR01351       175 DTEEVVKKRLEVYKEQTEPLIDYYRKK  201 (232)
T ss_pred             CCHHHHHHHHHHHHHHCCHHHHHHHHC
T ss_conf             988999999999888520089999846


No 409
>TIGR02142 modC_ABC molybdate ABC transporter, ATP-binding protein; InterPro: IPR011868   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 ATP-binding cassette (ABC) protein of the three subunit molybdate ABC transporter. The three proteins of this complex are homologous to proteins of the sulphate ABC transporter. Molybdenum may be used in nitrogenases of nitrogen-fixing bacteria and in molybdopterin cofactors. In some cases, molybdate may be transported by a sulphate transporter rather than by a specific molybdate transporter.; GO: 0005524 ATP binding, 0015098 molybdate ion transmembrane transporter activity, 0015689 molybdate ion transport, 0009276 1-2nm peptidoglycan-based cell wall.
Probab=80.33  E-value=1.1  Score=22.18  Aligned_cols=15  Identities=13%  Similarity=0.284  Sum_probs=8.7

Q ss_pred             CCCHHHHHHHHHHHH
Q ss_conf             488889999999986
Q gi|254781225|r  223 NGSHDEWIPVVMAVH  237 (789)
Q Consensus       223 ~~dyd~W~~vg~al~  237 (789)
                      .|+-...+.+|.||=
T Consensus       133 SGGEkQRVAIGRALL  147 (361)
T TIGR02142       133 SGGEKQRVAIGRALL  147 (361)
T ss_pred             CCCCHHHHHHHHHHH
T ss_conf             784047788998874


No 410
>TIGR02525 plasmid_TraJ plasmid transfer ATPase TraJ; InterPro: IPR013364    Proteins in this entry are predicted ATPases associated with plasmid transfer loci in bacteria. This family is most similar to the DotB ATPase (IPR013363 from INTERPRO) of a type-IV secretion-like system of the obligate intracellular pathogens Legionella pneumophila and Coxiella burnetii..
Probab=80.30  E-value=1.5  Score=21.39  Aligned_cols=56  Identities=11%  Similarity=0.194  Sum_probs=29.6

Q ss_pred             CCCHHHHHHHHH----C---CEEEEECCCCCCEEEEEEECCCC------HHHHHHHHHHHHCCCC---CEEEECCC
Q ss_conf             689899974200----7---88999234779879999646881------2567899987641899---76996788
Q gi|254781225|r   40 LLSSEKIDKLPA----C---GFGFVCGVGEQPLYAFDIDSKDE------KTANTFKDTFEILHGT---PIVRIGQK   99 (789)
Q Consensus        40 ~~~~~~i~~~~~----~---giGi~~G~~s~glv~iDiD~~d~------~~~~~~~~~~~~l~g~---p~~~~g~~   99 (789)
                      .+|.++++.|..    +   -|-+=.    +.=|+||.=++--      -....+..+++++.+.   |.+++|++
T Consensus         6 gltA~~Lr~FfvhC~r~~vSDI~LqG----G~~i~V~r~GR~~~~s~fpL~~~~l~~l~D~lFg~ei~~~v~sg~~   77 (374)
T TIGR02525         6 GLTADTLREFFVHCERHEVSDIHLQG----GSPIVVERHGRKVRASSFPLEDSELERLVDELFGPEIKPTVKSGRP   77 (374)
T ss_pred             CCCHHHHHHHHHHHCCCCCCCEEECC----CCEEEECCCCCEECCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCC
T ss_conf             88988999886611168634035217----6855774446610134477850579998766507320010247875


No 411
>cd03114 ArgK-like The function of this protein family is unkown. The protein sequences are similar to the ArgK protein in E. coli. ArgK protein is a membrane ATPase which is required for transporting arginine, ornithine and lysine into the cells by the arginine and ornithine (AO system) and lysine, arginine and ornithine (LAO) transport systems.
Probab=80.24  E-value=1.3  Score=21.78  Aligned_cols=21  Identities=48%  Similarity=0.700  Sum_probs=17.7

Q ss_pred             EEECCCCCHHHHHHHHHHHHC
Q ss_conf             970788625789999999723
Q gi|254781225|r  506 IRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       506 ~~G~G~nGKSt~~~~l~~llG  526 (789)
                      ++|+.+.|||||++-+...+-
T Consensus         4 itG~pGaGKStLi~~l~~~~~   24 (148)
T cd03114           4 ITGVPGAGKSTLIDALITALR   24 (148)
T ss_pred             ECCCCCCCHHHHHHHHHHHHH
T ss_conf             258997878999999999999


No 412
>TIGR00382 clpX ATP-dependent Clp protease, ATP-binding subunit ClpX; InterPro: IPR004487   ClpX is a member of the HSP (heat-shock protein) 100 family. Gel filtration and electron microscopy showed that ClpX subunits associate to form a six-membered ring that is stabilized by binding of ATP or nonhydrolyzable analogs of ATP . It functions as an ATP-depedent  molecular chaperone and is the regulatory subunit of the ClpXP protease .   ClpXP is involved in DNA damage repair, stationary-phase gene expression, and ssrA-mediated protein quality control. To date more than 50 proteins include transcription factors, metabolic enzymes, and proteins involved in the starvation and oxidative stress responses have been identified as substrates .    The N-terminal domain of ClpX is a C4-type zinc binding domain (ZBD) involved in substrate recognition. ZBD forms a very stable dimer that is essential for promoting the degradation of some typical ClpXP substrates such as lO and MuA .  ; GO: 0005515 protein binding, 0005524 ATP binding, 0016887 ATPase activity, 0015031 protein transport.
Probab=80.22  E-value=1.9  Score=20.72  Aligned_cols=129  Identities=16%  Similarity=0.159  Sum_probs=76.3

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCC-C--------CCCHHHHHHCCCEEEEEECCCCCCCCC
Q ss_conf             9997078862578999999972330003442676420124555-5--------689889973898099993467776013
Q gi|254781225|r  504 IHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEA-G--------KANPSLIRLMGSRIVIISETNENDEIN  574 (789)
Q Consensus       504 ~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~~-~--------~~~~~la~l~g~r~~~~~E~~~~~~~~  574 (789)
                      +.|+||.|+||+-+..+|.+.|-=-.+.+-.+++++...-.+. .        .+..+ .....|-.++++|.++=.+.+
T Consensus       155 ILLiGPTGSGKTLLAqTLA~~L~VPfAiADATtLTEAGYVGEDVENIL~~Llq~ad~D-V~kA~kGIiYIDEIDKIaRkS  233 (452)
T TIGR00382       155 ILLIGPTGSGKTLLAQTLARILNVPFAIADATTLTEAGYVGEDVENILLKLLQAADYD-VEKAQKGIIYIDEIDKIARKS  233 (452)
T ss_pred             EEEECCCCCCHHHHHHHHHHHCCCCEEECCHHHHHCCCCCCCCHHHHHHHHHHHCCCC-HHHHCCCEEEEECCCCHHHHC
T ss_conf             2454688852689999999873887421111102006642422889999998741455-245278508984223101215


Q ss_pred             CC---------------EEEEEECCCEEEE----EECC-CCCCEEEECCEEEEEECCCCCCCCCCCCCEEEEEE--E-EE
Q ss_conf             10---------------0245415985873----2104-78606871452899973886342679841664689--9-96
Q gi|254781225|r  575 AA---------------KIKQMTGGDCMTA----RLNY-GNTYSESPASFTPFIVPNKHLFVRNPDDAWWRRYI--V-IP  631 (789)
Q Consensus       575 ~~---------------~~K~ltggD~i~a----r~~~-~~~~~~~~p~~~~~~~~N~~P~~~~~d~~~~rR~~--i-ip  631 (789)
                      +.               +||-+=|. -..+    =+|| .+.|++..-+-.||+++=   .|.|-+.=+-+|+-  + |=
T Consensus       234 EN~SITRDVSGEGVQQALLKi~EGT-vA~vPPqGGRKHP~~~~iqiDTs~ILFICGG---AF~GL~~iI~~R~~~~~~iG  309 (452)
T TIGR00382       234 ENPSITRDVSGEGVQQALLKIIEGT-VANVPPQGGRKHPQQEFIQIDTSNILFICGG---AFVGLEKIIKKRTEKKSSIG  309 (452)
T ss_pred             CCCEEEEEECCCHHHHHHHHHHHCC-EEEECCCCCCCCCCCCEEEECCCCEEEEECC---HHHHHHHHHHHHHCCCCCCC
T ss_conf             7780112217554999999876032-3431754488688657688647640011054---34448999988745553335


Q ss_pred             CCCCCC
Q ss_conf             588788
Q gi|254781225|r  632 FDKPIA  637 (789)
Q Consensus       632 F~~~~~  637 (789)
                      |.+.-.
T Consensus       310 F~~~~~  315 (452)
T TIGR00382       310 FGAEVK  315 (452)
T ss_pred             CCCCHH
T ss_conf             455210


No 413
>cd01855 YqeH YqeH.  YqeH is an essential GTP-binding protein. Depletion of YqeH induces an excess initiation of DNA replication, suggesting that it negatively controls initiation of chromosome replication. The YqeH subfamily is common in eukaryotes and sporadically present in bacteria with probable acquisition by plants from chloroplasts.  Proteins of the YqeH family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases.
Probab=80.18  E-value=2.9  Score=19.50  Aligned_cols=38  Identities=24%  Similarity=0.289  Sum_probs=24.4

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9999999999999975987433799997078862578999999972
Q gi|254781225|r  480 EEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       480 ~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~ll  525 (789)
                      +++++++.+...      .+.  =+.+.|..+.|||||+|.|..-.
T Consensus       114 ~~L~~~i~~~~~------~~~--~vyvvG~~NvGKSTLiN~Ll~~~  151 (190)
T cd01855         114 EELINAIKKLAK------KGG--DVYVVGATNVGKSTLINALLKKD  151 (190)
T ss_pred             HHHHHHHHHHHC------CCC--CEEEECCCCCCHHHHHHHHHHHC
T ss_conf             999999999746------698--57998058754679999986302


No 414
>smart00534 MUTSac ATPase domain of DNA mismatch repair MUTS family.
Probab=80.06  E-value=1.7  Score=21.06  Aligned_cols=22  Identities=27%  Similarity=0.366  Sum_probs=18.1

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             9999707886257899999997
Q gi|254781225|r  503 FIHIRGVGGSGKSTLMNLIKYA  524 (789)
Q Consensus       503 ~~~~~G~G~nGKSt~~~~l~~l  524 (789)
                      .++++|+-..||||+++.+.-+
T Consensus         1 v~iiTGpN~sGKSt~lk~i~l~   22 (185)
T smart00534        1 VVIITGPNMGGKSTYLRQVGLI   22 (185)
T ss_pred             CEEEECCCCCCHHHHHHHHHHH
T ss_conf             9899799988489999999999


No 415
>pfam10236 DAP3 Mitochondrial ribosomal death-associated protein 3. This is a family of conserved proteins which were originally described as death-associated-protein-3 (DAP-3). The proteins carry a P-loop DNA-binding motif, and induce apoptosis. DAP3 has been shown to be a pro-apoptotic factor in the mitochondrial matrix and to be crucial for mitochondrial biogenesis and so has also been designated as MRP-S29 (mitochondrial ribosomal protein subunit 29).
Probab=80.04  E-value=3.5  Score=18.92  Aligned_cols=20  Identities=20%  Similarity=0.416  Sum_probs=9.2

Q ss_pred             CCCCCCHHHHHHHHHHHCCC
Q ss_conf             16468999999999762001
Q gi|254781225|r  161 DTPLLSEEDVEYLFKFFQEI  180 (789)
Q Consensus       161 ~~P~i~~~~~~~l~~~~~~~  180 (789)
                      +.|......++.+.+.....
T Consensus        81 dqP~~a~~~L~~~~~~N~~~  100 (274)
T pfam10236        81 DQPMYAAALLQRILKANEEV  100 (274)
T ss_pred             ECHHHHHHHHHHHHHHHHHH
T ss_conf             57899999999999986999


No 416
>PRK11288 araG L-arabinose transporter ATP-binding protein; Provisional
Probab=80.02  E-value=1.4  Score=21.58  Aligned_cols=31  Identities=26%  Similarity=0.359  Sum_probs=24.4

Q ss_pred             CCCCEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             7433799997078862578999999972330
Q gi|254781225|r  498 NKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       498 ~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      .+.--++-+.|.-++|||||+++|..++-..
T Consensus       276 v~~GEivgivG~nGsGKSTL~k~L~Gl~~p~  306 (501)
T PRK11288        276 VRRGEIVGFFGLVGAGRSELMKLLYGATRRT  306 (501)
T ss_pred             EECCEEEEEECCCCCCHHHHHHHHCCCCCCC
T ss_conf             7088399975688864879999843874887


No 417
>cd02029 PRK_like Phosphoribulokinase-like (PRK-like) is a family of proteins similar to phosphoribulokinase (PRK), the enzyme involved in the Benson-Calvin cycle in chloroplasts or photosynthetic prokaryotes. PRK catalyzes the phosphorylation of D-ribulose 5-phosphate to form D-ribulose 1, 5-biphosphate, using ATP and NADPH produced by the primary reactions of photosynthesis.
Probab=79.98  E-value=1.5  Score=21.28  Aligned_cols=27  Identities=19%  Similarity=0.391  Sum_probs=21.3

Q ss_pred             EEEECCCCCHHHHHHHHHHHHCCCCCC
Q ss_conf             997078862578999999972330003
Q gi|254781225|r  505 HIRGVGGSGKSTLMNLIKYAFGNQYVI  531 (789)
Q Consensus       505 ~~~G~G~nGKSt~~~~l~~llG~~~~~  531 (789)
                      -..|+.|.||||+.+.++.+||...+.
T Consensus         3 aVtGsSGAGtsTv~r~f~~IF~re~v~   29 (277)
T cd02029           3 AVTGSSGAGTTTVKRAFEHIFAREGIH   29 (277)
T ss_pred             EEECCCCCCHHHHHHHHHHHHHHCCCC
T ss_conf             993388884787999999987205885


No 418
>COG4559 ABC-type hemin transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=79.85  E-value=1.7  Score=21.08  Aligned_cols=11  Identities=64%  Similarity=1.035  Sum_probs=3.5

Q ss_pred             ECCCCCHHHHH
Q ss_conf             07886257899
Q gi|254781225|r  508 GVGGSGKSTLM  518 (789)
Q Consensus       508 G~G~nGKSt~~  518 (789)
                      |+-+.||||++
T Consensus        34 GPNGAGKSTlL   44 (259)
T COG4559          34 GPNGAGKSTLL   44 (259)
T ss_pred             CCCCCCHHHHH
T ss_conf             88986588899


No 419
>PRK02496 adk adenylate kinase; Provisional
Probab=79.81  E-value=2.4  Score=20.03  Aligned_cols=36  Identities=22%  Similarity=0.268  Sum_probs=27.6

Q ss_pred             HHHHHCCCCCCCCHHHHHHHHHHHHHCCHHHHHHHH
Q ss_conf             999987889887889999999999842638888754
Q gi|254781225|r  664 KAYISKGLDVDIPEVCLKAKEEERQGTDTYQAWIDD  699 (789)
Q Consensus       664 ~~~~~~g~~~~~p~~v~~a~~~y~~~~D~v~~fi~e  699 (789)
                      .|....|..-..++++..-.+.|.+...++-.|..+
T Consensus       123 ~Rl~~R~R~DD~~e~i~~Rl~~y~~~t~pvi~~y~~  158 (185)
T PRK02496        123 ERLLARGRKDDTEEVIRRRLEVYREQTAPLIDYYRD  158 (185)
T ss_pred             HHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             998746767898899999999999999999999984


No 420
>COG1149 MinD superfamily P-loop ATPase containing an inserted ferredoxin domain [Energy production and conversion]
Probab=79.81  E-value=2.1  Score=20.38  Aligned_cols=25  Identities=28%  Similarity=0.513  Sum_probs=14.0

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             9999707886257899999997233
Q gi|254781225|r  503 FIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       503 ~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ..+.-|.|+.||||+.--|..+||+
T Consensus         4 vAV~sGKGGtGKTTva~~la~~l~~   28 (284)
T COG1149           4 VAVASGKGGTGKTTVAANLAVLLGD   28 (284)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCC
T ss_conf             9996368877702289999998366


No 421
>TIGR03375 type_I_sec_LssB type I secretion system ATPase, LssB family. Type I protein secretion is a system in some Gram-negative bacteria to export proteins (often proteases) across both inner and outer membranes to the extracellular medium. This is one of three proteins of the type I secretion apparatus. Targeted proteins are not cleaved at the N-terminus, but rather carry signals located toward the extreme C-terminus to direct type I secretion. This model is related to models TIGR01842 and TIGR01846, and to bacteriocin ABC transporters that cleave their substrates during export.
Probab=79.79  E-value=1.3  Score=21.80  Aligned_cols=29  Identities=34%  Similarity=0.358  Sum_probs=22.8

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHCCCC
Q ss_conf             37999970788625789999999723300
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYAFGNQY  529 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~llG~~~  529 (789)
                      -..+-++|+.|+||||++++|..++-...
T Consensus       491 Ge~vaIvG~sGsGKSTL~kll~Gl~~p~~  519 (694)
T TIGR03375       491 GEKVAIIGRIGSGKSTLLKLLLGLYQPTE  519 (694)
T ss_pred             CCEEEEEECCCCCHHHHHHHHCCCCCCCC
T ss_conf             97899980589878899998556758998


No 422
>KOG1051 consensus
Probab=79.71  E-value=3.6  Score=18.86  Aligned_cols=140  Identities=13%  Similarity=0.163  Sum_probs=86.2

Q ss_pred             HHHHHHH-HCCCHHHHHHHHHHHHHHHCCCCC--CCEEEEEEECCCCCHHHHHHHHHHH-HCCCC-CCCCCHHHHHH---
Q ss_conf             9999988-879999999999999999759874--3379999707886257899999997-23300-03442676420---
Q gi|254781225|r  469 FLDLVSG-YFESEEVMDYFTRCVGMALLGGNK--AQRFIHIRGVGGSGKSTLMNLIKYA-FGNQY-VINAEASDIMQ---  540 (789)
Q Consensus       469 ~~~~l~~-~~~d~e~~~~l~~~~g~~l~g~~~--~~~~~~~~G~G~nGKSt~~~~l~~l-lG~~~-~~~~~~~~~~~---  540 (789)
                      ..+-|.+ |.+-.+.+.-+-+.+--|=.|..+  .-..|++.|+-+-||+-+...+... ||+.. ...++.+.+.+   
T Consensus       556 L~~~L~~~V~gQ~eAv~aIa~AI~~sr~gl~~~~~~awflflGpdgvGKt~lAkaLA~~~Fgse~~~IriDmse~~evsk  635 (898)
T KOG1051         556 LEERLHERVIGQDEAVAAIAAAIRRSRAGLKDPNPDAWFLFLGPDGVGKTELAKALAEYVFGSEENFIRLDMSEFQEVSK  635 (898)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEECCCCHHHHHHHHHHHHHHCCCCCCEEEECHHHHHHHHH
T ss_conf             99999754466377899999999843203578888858999788841389999999999728864268961455555653


Q ss_pred             -------CCCCCCCCCCHHHHHHCCCEEEEEECCCCCCCCCCCEEEEEECCCEEEEEECCCCCCEEEECCEEEEEECCC
Q ss_conf             -------124555568988997389809999346777601310024541598587321047860687145289997388
Q gi|254781225|r  541 -------NRPPEAGKANPSLIRLMGSRIVIISETNENDEINAAKIKQMTGGDCMTARLNYGNTYSESPASFTPFIVPNK  612 (789)
Q Consensus       541 -------~~~~~~~~~~~~la~l~g~r~~~~~E~~~~~~~~~~~~K~ltggD~i~ar~~~~~~~~~~~p~~~~~~~~N~  612 (789)
                             -++.+.++.-.+-.+-+--..+.+.|.++-....-..|+++.-...+  ..-++.. +.|+.. .+||.+|-
T Consensus       636 ligsp~gyvG~e~gg~LteavrrrP~sVvLfdeIEkAh~~v~n~llq~lD~Grl--tDs~Gr~-Vd~kN~-I~IMTsn~  710 (898)
T KOG1051         636 LIGSPPGYVGKEEGGQLTEAVKRRPYSVVLFEEIEKAHPDVLNILLQLLDRGRL--TDSHGRE-VDFKNA-IFIMTSNV  710 (898)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHCCCCEEEEEECHHHCCHHHHHHHHHHHHCCCC--CCCCCCE-EECCCE-EEEEECCC
T ss_conf             048995554630577888997169965999830222288899999999862740--0588867-504645-99994263


No 423
>PRK05563 DNA polymerase III subunits gamma and tau; Validated
Probab=79.64  E-value=3.6  Score=18.84  Aligned_cols=20  Identities=25%  Similarity=0.385  Sum_probs=11.5

Q ss_pred             CCCCCCHHHHHHHHHHHCCC
Q ss_conf             16468999999999762001
Q gi|254781225|r  161 DTPLLSEEDVEYLFKFFQEI  180 (789)
Q Consensus       161 ~~P~i~~~~~~~l~~~~~~~  180 (789)
                      +.-.++..-..+|++.++++
T Consensus       127 Evhmls~~a~nallKtlEeP  146 (541)
T PRK05563        127 EVHMLSQGAVNAFLKTLEEP  146 (541)
T ss_pred             CCCCCCHHHHHHHHHHHHCC
T ss_conf             72338999999999998548


No 424
>PRK03846 adenylylsulfate kinase; Provisional
Probab=79.61  E-value=2.6  Score=19.73  Aligned_cols=29  Identities=28%  Similarity=0.434  Sum_probs=24.4

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             43379999707886257899999997233
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      .....++++|-.++||||+.+.+...|-+
T Consensus        22 ~kg~viWlTGLSGSGKTTlA~~L~~~L~~   50 (198)
T PRK03846         22 HKGVVLWFTGLSGSGKSTVAGALEEALHE   50 (198)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHHHHHHHH
T ss_conf             99869998799999889999999999997


No 425
>COG1134 TagH ABC-type polysaccharide/polyol phosphate transport system, ATPase component [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]
Probab=79.57  E-value=1.1  Score=22.31  Aligned_cols=21  Identities=48%  Similarity=0.681  Sum_probs=10.3

Q ss_pred             EEEECCCCCHHHHHHHHHHHH
Q ss_conf             997078862578999999972
Q gi|254781225|r  505 HIRGVGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       505 ~~~G~G~nGKSt~~~~l~~ll  525 (789)
                      =++|.-++||||++++|..++
T Consensus        57 GiiG~NGaGKSTLlkliaGi~   77 (249)
T COG1134          57 GIIGHNGAGKSTLLKLIAGIY   77 (249)
T ss_pred             EEECCCCCCHHHHHHHHHCCC
T ss_conf             898789985899999995871


No 426
>KOG0061 consensus
Probab=79.49  E-value=1.5  Score=21.41  Aligned_cols=26  Identities=23%  Similarity=0.148  Sum_probs=13.7

Q ss_pred             HHHHHHHHHHHCCC-----------CCHHHHHHHHHH
Q ss_conf             99999999862167-----------815689999997
Q gi|254781225|r  228 EWIPVVMAVHHETR-----------GSSKGKEIARRW  253 (789)
Q Consensus       228 ~W~~vg~al~~~~~-----------~~~~~l~lw~~w  253 (789)
                      .-..+..+|++...           .+.+.+.++|+-
T Consensus       205 sA~~vv~~Lk~lA~~grtVi~tIHQPss~lf~lFD~l  241 (613)
T KOG0061         205 SALQVVQLLKRLARSGRTVICTIHQPSSELFELFDKL  241 (613)
T ss_pred             HHHHHHHHHHHHHHCCCEEEEEEECCCHHHHHHHHHH
T ss_conf             6899999999998679989999768728999999899


No 427
>COG0237 CoaE Dephospho-CoA kinase [Coenzyme metabolism]
Probab=79.43  E-value=2.2  Score=20.22  Aligned_cols=78  Identities=24%  Similarity=0.298  Sum_probs=45.3

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCCCCCHHHHHHCCCEEEEEECCCCCCCCCCCEEEEE
Q ss_conf             79999707886257899999997233000344267642012455556898899738980999934677760131002454
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEAGKANPSLIRLMGSRIVIISETNENDEINAAKIKQM  581 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~~~~~~~~la~l~g~r~~~~~E~~~~~~~~~~~~K~l  581 (789)
                      ..+-++|.-++||||+.++++. +|= .+...+...-  .--...+..-..++..+|.-+.-     ++..++-..|.+.
T Consensus         3 ~iIglTG~igsGKStva~~~~~-~G~-~vidaD~v~r--~~~~~~~~~~~~i~~~fG~~i~~-----~dg~~~r~~L~~~   73 (201)
T COG0237           3 LIIGLTGGIGSGKSTVAKILAE-LGF-PVIDADDVAR--EVVEPGGEALQEIAERFGLEILD-----EDGGLDRRKLREK   73 (201)
T ss_pred             EEEEEECCCCCCHHHHHHHHHH-CCC-EEEECCHHHH--HHHHCCCHHHHHHHHHCCCCCCC-----CCCHHHHHHHHHH
T ss_conf             4999957887788999999997-799-3998869999--98845635789999984997656-----6510589999999


Q ss_pred             ECCCEEE
Q ss_conf             1598587
Q gi|254781225|r  582 TGGDCMT  588 (789)
Q Consensus       582 tggD~i~  588 (789)
                      .+.|+..
T Consensus        74 vf~~~~~   80 (201)
T COG0237          74 VFNDPEA   80 (201)
T ss_pred             HCCCHHH
T ss_conf             7389999


No 428
>PRK04690 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=79.42  E-value=1.3  Score=21.86  Aligned_cols=14  Identities=21%  Similarity=0.221  Sum_probs=6.0

Q ss_pred             EEEEEECCCEEEEE
Q ss_conf             02454159858732
Q gi|254781225|r  577 KIKQMTGGDCMTAR  590 (789)
Q Consensus       577 ~~K~ltggD~i~ar  590 (789)
                      .||+|.|-|+-.+|
T Consensus       447 ~Fk~L~~~~~~~~~  460 (468)
T PRK04690        447 HFAQLAGFDPAAIS  460 (468)
T ss_pred             HHHHHHCCCHHHHH
T ss_conf             99998780877785


No 429
>COG5019 CDC3 Septin family protein [Cell division and chromosome partitioning / Cytoskeleton]
Probab=79.36  E-value=1.6  Score=21.16  Aligned_cols=32  Identities=13%  Similarity=0.163  Sum_probs=17.4

Q ss_pred             CCCCCCCEEEEEEECCCCCHHHH-HHHHHHHHC
Q ss_conf             59874337999970788625789-999999723
Q gi|254781225|r  495 LGGNKAQRFIHIRGVGGSGKSTL-MNLIKYAFG  526 (789)
Q Consensus       495 ~g~~~~~~~~~~~G~G~nGKSt~-~~~l~~llG  526 (789)
                      .-+++-++++++.-|.+.|=+.+ +.+|..+-.
T Consensus       129 ~~D~RVH~cLYFI~Ptgh~l~~~DIe~Mk~ls~  161 (373)
T COG5019         129 FKDTRVHACLYFIRPTGHGLKPLDIEAMKRLSK  161 (373)
T ss_pred             CCCCCEEEEEEEECCCCCCCCHHHHHHHHHHHC
T ss_conf             446824899998468988787888999999853


No 430
>COG1703 ArgK Putative periplasmic protein kinase ArgK and related GTPases of G3E family [Amino acid transport and metabolism]
Probab=79.35  E-value=2.6  Score=19.82  Aligned_cols=33  Identities=33%  Similarity=0.457  Sum_probs=22.2

Q ss_pred             HCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             759874337999970788625789999999723
Q gi|254781225|r  494 LLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       494 l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      +.+.+-.--.+=++|+++.|||||++.+-..|=
T Consensus        44 l~p~tG~a~viGITG~PGaGKSTli~~L~~~l~   76 (323)
T COG1703          44 LYPRTGNAHVIGITGVPGAGKSTLIEALGRELR   76 (323)
T ss_pred             HHHCCCCCCEEEECCCCCCCHHHHHHHHHHHHH
T ss_conf             731179983787317998866889999999999


No 431
>cd03275 ABC_SMC1_euk Eukaryotic SMC1 proteins; SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains.  Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins.  The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases.  The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences.  In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (for
Probab=79.22  E-value=2.1  Score=20.39  Aligned_cols=29  Identities=45%  Similarity=0.764  Sum_probs=25.7

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHCCCC
Q ss_conf             37999970788625789999999723300
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYAFGNQY  529 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~llG~~~  529 (789)
                      +.|-..+|+-++|||-+++.|+-+||..+
T Consensus        22 ~~~t~IvGpNGsGKSNi~DAi~~vlGe~s   50 (247)
T cd03275          22 DRFTCIIGPNGSGKSNLMDAISFVLGEKS   50 (247)
T ss_pred             CCCEEEECCCCCCHHHHHHHHHHHHCCCH
T ss_conf             98379989987765888999999965662


No 432
>KOG0018 consensus
Probab=79.20  E-value=1.8  Score=20.82  Aligned_cols=54  Identities=19%  Similarity=0.132  Sum_probs=26.2

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCCCCCHHHHHHCCCEEEEEE
Q ss_conf             99970788625789999999723300034426764201245555689889973898099993
Q gi|254781225|r  504 IHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEAGKANPSLIRLMGSRIVIIS  565 (789)
Q Consensus       504 ~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~~~~~~~~la~l~g~r~~~~~  565 (789)
                      .|.+-+-..+++...-+=..-+|..  +-+|+..+..+      ..+.-+-.+.|+|+++-.
T Consensus       533 aIiVdte~ta~~CI~ylKeqR~~~~--TFlPld~i~v~------~~~e~lr~~~g~rlv~Dv  586 (1141)
T KOG0018         533 AIIVDTEATARDCIQYLKEQRLEPM--TFLPLDSIRVK------PVNEKLRELGGVRLVIDV  586 (1141)
T ss_pred             EEEECCHHHHHHHHHHHHHHCCCCC--CCCCHHHHHCC------CCCCCCCCCCCEEEEEEE
T ss_conf             2786327679999999998445874--23420666357------600012576780799873


No 433
>KOG0730 consensus
Probab=79.18  E-value=1.7  Score=20.93  Aligned_cols=127  Identities=16%  Similarity=0.147  Sum_probs=66.3

Q ss_pred             CCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCC---CCCHHHHHHCCCEEEEEECCCC--CCC
Q ss_conf             74337999970788625789999999723300034426764201245555---6898899738980999934677--760
Q gi|254781225|r  498 NKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEAG---KANPSLIRLMGSRIVIISETNE--NDE  572 (789)
Q Consensus       498 ~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~~~---~~~~~la~l~g~r~~~~~E~~~--~~~  572 (789)
                      ....+=+++||+++-||+++...+.+--|-...+..-..+++.--+ .|.   ..-|..|+..---+++..|.+.  +.+
T Consensus       465 i~ppkGVLlyGPPGC~KT~lAkalAne~~~nFlsvkgpEL~sk~vG-eSEr~ir~iF~kAR~~aP~IiFfDEiDsi~~~R  543 (693)
T KOG0730         465 ISPPKGVLLYGPPGCGKTLLAKALANEAGMNFLSVKGPELFSKYVG-ESERAIREVFRKARQVAPCIIFFDEIDALAGSR  543 (693)
T ss_pred             CCCCCEEEEECCCCCCHHHHHHHHHHHHCCCEEECCCHHHHHHHCC-CHHHHHHHHHHHHHHCCCEEEEHHHHHHHHHCC
T ss_conf             7887547777899862478999986463587264157899877518-258999999999862698377446666666304


Q ss_pred             CCCCEEEEEECCCEEEEEECC-CCCCEEEECCEEEEEECCCCCCCCCCCCCEEE-----EEEEEECC
Q ss_conf             131002454159858732104-78606871452899973886342679841664-----68999658
Q gi|254781225|r  573 INAAKIKQMTGGDCMTARLNY-GNTYSESPASFTPFIVPNKHLFVRNPDDAWWR-----RYIVIPFD  633 (789)
Q Consensus       573 ~~~~~~K~ltggD~i~ar~~~-~~~~~~~~p~~~~~~~~N~~P~~~~~d~~~~r-----R~~iipF~  633 (789)
                      -..+.    .-.|.+-..-+. -+.+ +-.-+..++-+|| .|..  -|.|+-|     |++.||-+
T Consensus       544 ~g~~~----~v~~RVlsqLLtEmDG~-e~~k~V~ViAATN-Rpd~--ID~ALlRPGRlD~iiyVplP  602 (693)
T KOG0730         544 GGSSS----GVTDRVLSQLLTEMDGL-EALKNVLVIAATN-RPDM--IDPALLRPGRLDRIIYVPLP  602 (693)
T ss_pred             CCCCC----CHHHHHHHHHHHHCCCC-CCCCCEEEEECCC-CHHH--CCHHHCCCCCCCEEEEECCC
T ss_conf             78755----14899999999870041-0147089995058-8101--26977598653305751583


No 434
>PRK00889 adenylylsulfate kinase; Provisional
Probab=79.14  E-value=2.6  Score=19.77  Aligned_cols=28  Identities=18%  Similarity=0.372  Sum_probs=23.5

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             3799997078862578999999972330
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      -..++++|-.++||||+.+.+..-|-..
T Consensus         4 g~viWltGlsgSGKTTia~~l~~~L~~~   31 (175)
T PRK00889          4 GVTVWFTGLSGAGKTTISHALAEKLRAR   31 (175)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHHHHHC
T ss_conf             8899988989999999999999999986


No 435
>PRK08233 hypothetical protein; Provisional
Probab=79.11  E-value=2.8  Score=19.55  Aligned_cols=30  Identities=30%  Similarity=0.490  Sum_probs=22.0

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHHCCCCCC
Q ss_conf             799997078862578999999972330003
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYAFGNQYVI  531 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~llG~~~~~  531 (789)
                      ..+-.-|..++||||+.+.|..-++...+.
T Consensus         4 ~IIgIaGgSgSGKTtla~~l~~~l~~~~~~   33 (182)
T PRK08233          4 KIITIAAVSGGGKTTLTERLTHKLKNSKAL   33 (182)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHCCCCEEE
T ss_conf             899996888678999999999974677589


No 436
>cd03238 ABC_UvrA The excision repair protein UvrA; Nucleotide excision repair in eubacteria is a process that repairs DNA damage by the removal of a 12-13-mer oligonucleotide containing the lesion.  Recognition and cleavage of the damaged DNA is a multistep ATP-dependent reaction that requires the UvrA, UvrB, and UvrC proteins.  Both UvrA and UvrB are ATPases, with UvrA having two ATP binding sites, which have the characteristic signature of the family of ABC proteins, and UvrB having one ATP binding site that is structurally related to that of helicases.
Probab=78.90  E-value=2.4  Score=20.05  Aligned_cols=24  Identities=42%  Similarity=0.509  Sum_probs=18.9

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHH
Q ss_conf             433799997078862578999999
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIK  522 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~  522 (789)
                      ..-.++.+.|+-++|||||++.+.
T Consensus        19 ~~Ge~~~iiG~nGsGKSTLl~~~~   42 (176)
T cd03238          19 PLNVLVVVTGVSGSGKSTLVNEGL   42 (176)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHH
T ss_conf             899899999999998999999888


No 437
>PRK13409 putative ATPase RIL; Provisional
Probab=78.64  E-value=1.6  Score=21.26  Aligned_cols=28  Identities=29%  Similarity=0.411  Sum_probs=22.1

Q ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             3379999707886257899999997233
Q gi|254781225|r  500 AQRFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       500 ~~~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      .--.+-+.|+-|.|||||+++|..++-.
T Consensus       364 ~GEiigIvG~NGaGKTTLlKiLaG~lkP  391 (590)
T PRK13409        364 KGEVIGIVGPNGIGKTTFVKLLAGVLKP  391 (590)
T ss_pred             CCCEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             4748999888888789999998288778


No 438
>COG1119 ModF ABC-type molybdenum transport system, ATPase component/photorepair protein PhrA [Inorganic ion transport and metabolism]
Probab=78.62  E-value=2.2  Score=20.28  Aligned_cols=13  Identities=54%  Similarity=0.984  Sum_probs=4.4

Q ss_pred             ECCCCCHHHHHHH
Q ss_conf             0788625789999
Q gi|254781225|r  508 GVGGSGKSTLMNL  520 (789)
Q Consensus       508 G~G~nGKSt~~~~  520 (789)
                      |+-++||||++++
T Consensus        64 G~NGsGKTTLL~l   76 (257)
T COG1119          64 GPNGAGKTTLLSL   76 (257)
T ss_pred             CCCCCCHHHHHHH
T ss_conf             8898778999999


No 439
>cd01673 dNK Deoxyribonucleoside kinase (dNK) catalyzes the phosphorylation of deoxyribonucleosides to yield corresponding monophosphates (dNMPs). This family consists of various deoxynucleoside kinases including deoxyribo- cytidine (EC 2.7.1.74), guanosine (EC 2.7.1.113), adenosine (EC 2.7.1.76), and thymidine (EC 2.7.1.21) kinases. They are key enzymes in the salvage of deoxyribonucleosides originating from extra- or intracellular breakdown of DNA.
Probab=78.51  E-value=2  Score=20.49  Aligned_cols=24  Identities=38%  Similarity=0.487  Sum_probs=19.7

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             999707886257899999997233
Q gi|254781225|r  504 IHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       504 ~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      +.+-|.=|.||||+++.|...+|-
T Consensus         2 I~iEG~iGsGKSTl~~~L~~~~~~   25 (193)
T cd01673           2 IVVEGNIGAGKSTLAKELAEHLGY   25 (193)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCC
T ss_conf             899888888899999999996699


No 440
>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP).  It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.
Probab=78.44  E-value=3.9  Score=18.60  Aligned_cols=44  Identities=23%  Similarity=0.281  Sum_probs=28.4

Q ss_pred             HHHHCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHH
Q ss_conf             988879999999999999999759874337999970788625789999999
Q gi|254781225|r  473 VSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKY  523 (789)
Q Consensus       473 l~~~~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~  523 (789)
                      |++.--.++.++.+.+++.       ..+=++++.|+.++||||++..+-.
T Consensus        59 L~~LG~~~~~~~~l~~~~~-------~~~GlilitGptGSGKtTtl~a~l~  102 (264)
T cd01129          59 LEKLGLKPENLEIFRKLLE-------KPHGIILVTGPTGSGKTTTLYSALS  102 (264)
T ss_pred             HHHHCCCHHHHHHHHHHHH-------CCCCEEEEECCCCCCHHHHHHHHHH
T ss_conf             8795799999999999970-------8998899978999977999999998


No 441
>cd03276 ABC_SMC6_euk Eukaryotic SMC6 proteins; SMC proteins are large (approximately 110 to 170 kDa), and each is arranged into five recognizable domains.  Amino-acid sequence homology of SMC proteins between species is largely confined to the amino- and carboxy-terminal globular domains. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T, in the single-letter amino-acid code), which by mutational studies has been shown to be essential in several proteins.  The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif, and a motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases.  The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences.  In eukaryotic cells, the proteins are found as heterodimers of SMC1 paired with SMC3, SMC2 with SMC4, and SMC5 with SMC6 (for
Probab=78.42  E-value=3.2  Score=19.15  Aligned_cols=30  Identities=30%  Similarity=0.499  Sum_probs=25.4

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHCCCCC
Q ss_conf             379999707886257899999997233000
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYAFGNQYV  530 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~llG~~~~  530 (789)
                      ..+-+++|+-++|||+++..|.-.||..+.
T Consensus        21 p~lN~IiG~NGsGKSsIl~AI~lgLGgk~~   50 (198)
T cd03276          21 PRVNFIVGNNGSGKSAILTALTIGLGGKAS   50 (198)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHCCCCCC
T ss_conf             982899889999889999999986388813


No 442
>TIGR02237 recomb_radB DNA repair and recombination protein RadB; InterPro: IPR011939    This family consists exclusively of archaeal RadB protein, a homolog of bacterial RecA, eukaryotic RAD51 (IPR011941 from INTERPRO) and DMC1 (IPR011940 from INTERPRO), and archaeal RadA (IPR011938 from INTERPRO) ,, .; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0008094 DNA-dependent ATPase activity, 0006281 DNA repair, 0006310 DNA recombination.
Probab=78.38  E-value=1.9  Score=20.71  Aligned_cols=70  Identities=23%  Similarity=0.377  Sum_probs=45.0

Q ss_pred             HCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCCCCCHHHHHHCCCEEEEEECCCCCCCC
Q ss_conf             75987433799997078862578999999972330003442676420124555568988997389809999346777601
Q gi|254781225|r  494 LLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEAGKANPSLIRLMGSRIVIISETNENDEI  573 (789)
Q Consensus       494 l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~~~~~~~~la~l~g~r~~~~~E~~~~~~~  573 (789)
                      |-|+...-...-+||+|++||+++.=++. +           .                 |.-.||..++++ ++ |. +
T Consensus         5 LgGGvE~G~iTQiYGp~G~GKTn~c~~~a-~-----------~-----------------a~~~Gk~v~YiD-TE-GG-L   52 (223)
T TIGR02237         5 LGGGVERGIITQIYGPPGSGKTNICLILA-V-----------N-----------------AARQGKKVVYID-TE-GG-L   52 (223)
T ss_pred             CCCCCCCCEEEEEECCCCCCHHHHHHHHH-H-----------H-----------------HHHCCCCEEEEE-CC-CC-C
T ss_conf             05851203588987589986789999999-9-----------9-----------------986189589996-28-98-3


Q ss_pred             CCCEEEEEECCCEEEEEECCCC
Q ss_conf             3100245415985873210478
Q gi|254781225|r  574 NAAKIKQMTGGDCMTARLNYGN  595 (789)
Q Consensus       574 ~~~~~K~ltggD~i~ar~~~~~  595 (789)
                      +..+||+|.+.+.+.-+....+
T Consensus        53 S~ER~~q~~~~~~~D~e~~~~~   74 (223)
T TIGR02237        53 SPERFKQIAEDRALDPERVLSN   74 (223)
T ss_pred             HHHHHHHHHHCCCCCHHHHHCC
T ss_conf             2899999863058898888415


No 443
>TIGR01193 bacteriocin_ABC ABC-type bacteriocin transporter; InterPro: IPR005897   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).     This family contains ABC-type bacteriocin transporter. In general, bacteriocins are agents which are responsible for killing or inhibiting the closely related species or even different strains of the same species. Bacteriocins are encoded by bacterial plasmids. Bacteriocins are named after the species and hence in literature one encounters various names e.g., leucocin from Leuconostic geldium; pedicocin from Pedicoccus acidilactici; sakacin from Lactobacillus sake etc.    Peptide bacteriocins are exported across the cytoplasmic membrane by a dedicated ATP-binding cassette (ABC) transporter. These ABC-transporters have an N-terminal peptidase domain that belong to MEROPS peptidase family C39 (clan CA); a central multi-pass transmembrane region and a C-terminal ABC transporter domain. These transporters have dual function: (i) they remove the N-terminal leader peptide from its bacteriocin precursor by cleavage at a Gly-Gly bond and (ii) transport the mature bacteriocin across the cytoplasmic membrane. This represents a novel strategy for secretion of bacterial proteins . Many bacteria are known to regulate diverse physiological processes through this system, such as bioluminescence, regulation of sporulation, virulence factor expression, antibiotics production, competence for genetic transformation, and activation of biofilm formation .; GO: 0008234 cysteine-type peptidase activity, 0019534 toxin transporter activity, 0006810 transport, 0016020 membrane.
Probab=78.32  E-value=1.4  Score=21.57  Aligned_cols=54  Identities=11%  Similarity=0.061  Sum_probs=31.0

Q ss_pred             HHCCCCC-EEEECCCCCEEEEEEECCC---CC---C---CCCCCCCCCCCEEEECCCCEE-EECC
Q ss_conf             6418997-6996788965999950731---02---4---454444576753485268438-8047
Q gi|254781225|r   86 EILHGTP-IVRIGQKPKILIPFRMNKE---GI---K---KKKTTESTQGHLDILGCGQYF-VAYN  139 (789)
Q Consensus        86 ~~l~g~p-~~~~g~~~~~~~~yr~~~~---~~---~---~~~~~~~~~~~iEi~~~G~q~-V~~g  139 (789)
                      .+..+.| ++|+-|.++.-|+|-+..-   ..   +   .+..-+-.+..++-=|+|=.. .+|+
T Consensus        67 ~~~l~~PfIaHV~K~~K~pHYYVvy~~~kn~l~IaDPDpTvg~TK~sK~~F~~EWTGi~i~i~p~  131 (710)
T TIGR01193        67 DKNLPLPFIAHVIKEGKLPHYYVVYGVTKNSLLIADPDPTVGITKISKEDFEEEWTGIAIFIAPT  131 (710)
T ss_pred             HCCCCCCEEEEEEECCCCCCEEEEEEEECCEEEEECCCCCCCCEEECHHHHCCCCCEEEEEEECC
T ss_conf             10799976999980785212378973333667882688697621123788403264057776378


No 444
>TIGR02746 TraC-F-type type-IV secretion system protein TraC; InterPro: IPR014117   The proteins in this entry are found in the F, P and I-like type IV secretion systems. Gene symbols include TraC (F-type), TrbE/VirB4 (P-type) and TraU (I-type). The proteins contain the Walker A and B motifs and so are putative nucleotide triphosphatases..
Probab=78.31  E-value=4  Score=18.58  Aligned_cols=170  Identities=16%  Similarity=0.159  Sum_probs=81.9

Q ss_pred             EEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCCCCCHHHHHHCCCEEEEEECCCCCCCCCCCEEEEEECC
Q ss_conf             99707886257899999997233000344267642012455556898899738980999934677760131002454159
Q gi|254781225|r  505 HIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEAGKANPSLIRLMGSRIVIISETNENDEINAAKIKQMTGG  584 (789)
Q Consensus       505 ~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~~~~~~~~la~l~g~r~~~~~E~~~~~~~~~~~~K~ltgg  584 (789)
                      .++|..|.|||+|++.+....            +                 -.|. .|.+=|...+-    .+|..+.||
T Consensus       493 ~~~g~sG~GKSf~~Q~~~~~~------------L-----------------~~G~-kv~viDvG~Sy----~KLC~~lgG  538 (900)
T TIGR02746       493 AVVGGSGAGKSFFMQELIVSV------------L-----------------SRGG-KVWVIDVGRSY----KKLCEMLGG  538 (900)
T ss_pred             EEECCCCCCHHHHHHHHHHHH------------H-----------------HCCC-EEEEEEECCCH----HHHHHHHCC
T ss_conf             997288987168798999998------------5-----------------1798-48999607884----888765187


Q ss_pred             CEEEEEECCCCCCEEEECCEEEEEECCCCCCCCCCCCCEEEEEEEEECCCCCC-CCCCCHHHHHC-CCCHHHHHH----H
Q ss_conf             85873210478606871452899973886342679841664689996588788-87878334220-120447999----9
Q gi|254781225|r  585 DCMTARLNYGNTYSESPASFTPFIVPNKHLFVRNPDDAWWRRYIVIPFDKPIA-NRDASFAQKLE-TKYTLEAKK----W  658 (789)
Q Consensus       585 D~i~ar~~~~~~~~~~~p~~~~~~~~N~~P~~~~~d~~~~rR~~iipF~~~~~-~~d~~~~~~~~-~~e~~~i~~----w  658 (789)
                      +.|..+.-   ..+.+.|- +      |+- |...      |.-++.|+.... +-+-.-.+.+. .....|.++    =
T Consensus       539 ~Yie~~~e---~~i~LNPF-T------HL~-i~~A------~~~~~~~~~~~v~~i~Geqv~~~~~i~~~ia~MAGlDl~  601 (900)
T TIGR02746       539 TYIEFSPE---STICLNPF-T------HLD-IEEA------RFDIIDFDGNNVTEIDGEQVDEIDQITALIALMAGLDLS  601 (900)
T ss_pred             CEECCCCC---CCCCCCCC-C------CCC-CCCC------CCCEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             12104667---76323874-4------466-0003------332267363467756740288999999999988446668


Q ss_pred             HHHHHHHHHH------CCCCCCCCHHHHHHHHHHHH--HCCHHHHHHHHH-EEE-CCCCE---ECHHHHHHHHHHHHHHC
Q ss_conf             9999999998------78898878899999999998--426388887543-262-68841---11799999999999850
Q gi|254781225|r  659 FLKGVKAYIS------KGLDVDIPEVCLKAKEEERQ--GTDTYQAWIDDC-CDI-GENLW---EESHSLAKSYSEYREQE  725 (789)
Q Consensus       659 ~l~g~~~~~~------~g~~~~~p~~v~~a~~~y~~--~~D~v~~fi~e~-ce~-~~~~~---~~~~~l~~~y~~~~~~~  725 (789)
                      .-.++-..++      .-    .-++|+++-.+|..  ..|.|..++.+. +|. +.+..   ....+|...=.+||. .
T Consensus       602 P~~~l~~~q~lmaryCs~----l~~AI~~~W~~~g~~a~~tdV~~~L~~~~~e~~~~~~DGir~r~~~l~~~L~~Yt~-~  676 (900)
T TIGR02746       602 PEGGLSDEQELMARYCSL----LEEAILAAWKEKGNEATITDVADALEQLRLEEEDSENDGIRPRIKDLGKLLNPYTS-N  676 (900)
T ss_pred             CCCCCCHHHHHHHHHHHH----HHHHHHHHHHHHCCCCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHC-C
T ss_conf             455678888999999999----99999999997122488489999998521331345688601689999987326424-8


Q ss_pred             CCCCC
Q ss_conf             46675
Q gi|254781225|r  726 LNYDR  730 (789)
Q Consensus       726 ~~~~~  730 (789)
                      |.|++
T Consensus       677 G~YG~  681 (900)
T TIGR02746       677 GVYGR  681 (900)
T ss_pred             CCCEE
T ss_conf             71201


No 445
>pfam10662 PduV-EutP Ethanolamine utilisation - propanediol utilisation. Members of this family function in ethanolamine and propanediol degradation pathways, however the exact roles of these proteins is poorly understood.
Probab=78.31  E-value=1.8  Score=20.78  Aligned_cols=21  Identities=38%  Similarity=0.615  Sum_probs=17.6

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             999707886257899999997233
Q gi|254781225|r  504 IHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       504 ~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      +.+.|..+-|||||+|.|   +|.
T Consensus         4 VaivGrpNvGKSTLlN~L---~g~   24 (143)
T pfam10662         4 IMLIGRSGCGKTTLTQAL---NGE   24 (143)
T ss_pred             EEEECCCCCCHHHHHHHH---CCC
T ss_conf             999899999999999997---599


No 446
>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]
Probab=78.31  E-value=4  Score=18.58  Aligned_cols=202  Identities=18%  Similarity=0.218  Sum_probs=105.8

Q ss_pred             HHCCEECCCCCCCCCCHHHHHHHHHHHC-----CCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             5010013788887579478999998887-----99999999999999997598743379999707886257899999997
Q gi|254781225|r  450 LYITKSTGTPFVEGEPSQEFLDLVSGYF-----ESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYA  524 (789)
Q Consensus       450 ~~~t~~~~~~y~~~a~~p~~~~~l~~~~-----~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~l  524 (789)
                      .|+-+.+..+|........=++-..+++     |=+++.+-+.++++--..-.....-.+-|+||.|-||+.+.+-|...
T Consensus       294 nYlDwll~lPW~~~sk~~~Dl~~a~~iLd~dHYGLekVKeRIlEyLAV~~l~~~~kGpILcLVGPPGVGKTSLgkSIA~a  373 (782)
T COG0466         294 NYLDWLLDLPWGKRSKDKLDLKKAEKILDKDHYGLEKVKERILEYLAVQKLTKKLKGPILCLVGPPGVGKTSLGKSIAKA  373 (782)
T ss_pred             HHHHHHHHCCCCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHHH
T ss_conf             99999982887655421322999998744355671168999999999998614678857999789988701189999999


Q ss_pred             HCCCCCC-CCCHHHHHHCCCCCCCCCCHHHHHHCCCE-----------------------EEEEECCCCCCCCCCCEEEE
Q ss_conf             2330003-44267642012455556898899738980-----------------------99993467776013100245
Q gi|254781225|r  525 FGNQYVI-NAEASDIMQNRPPEAGKANPSLIRLMGSR-----------------------IVIISETNENDEINAAKIKQ  580 (789)
Q Consensus       525 lG~~~~~-~~~~~~~~~~~~~~~~~~~~~la~l~g~r-----------------------~~~~~E~~~~~~~~~~~~K~  580 (789)
                      +|..++- ++             |+.+ +-|.++|-|                       +...+|.++   ++.     
T Consensus       374 l~RkfvR~sL-------------GGvr-DEAEIRGHRRTYIGaMPGrIiQ~mkka~~~NPv~LLDEIDK---m~s-----  431 (782)
T COG0466         374 LGRKFVRISL-------------GGVR-DEAEIRGHRRTYIGAMPGKIIQGMKKAGVKNPVFLLDEIDK---MGS-----  431 (782)
T ss_pred             HCCCEEEEEC-------------CCCC-CHHHHCCCCCCCCCCCCHHHHHHHHHHCCCCCEEEEECHHH---CCC-----
T ss_conf             5897799954-------------7654-27775355312335687289999998677687478640333---167-----


Q ss_pred             EECCCEEEE---------EECCCCCCEE--EECCEEEEEE-CCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCHHHHHC
Q ss_conf             415985873---------2104786068--7145289997-388634267984166468999658878887878334220
Q gi|254781225|r  581 MTGGDCMTA---------RLNYGNTYSE--SPASFTPFIV-PNKHLFVRNPDDAWWRRYIVIPFDKPIANRDASFAQKLE  648 (789)
Q Consensus       581 ltggD~i~a---------r~~~~~~~~~--~~p~~~~~~~-~N~~P~~~~~d~~~~rR~~iipF~~~~~~~d~~~~~~~~  648 (789)
                      =--||+-+|         ...|.+.+.+  |...-.+|++ +|.+-.|+   ..+..||-+|....-..+          
T Consensus       432 s~rGDPaSALLEVLDPEQN~~F~DhYLev~yDLS~VmFiaTANsl~tIP---~PLlDRMEiI~lsgYt~~----------  498 (782)
T COG0466         432 SFRGDPASALLEVLDPEQNNTFSDHYLEVPYDLSKVMFIATANSLDTIP---APLLDRMEVIRLSGYTED----------  498 (782)
T ss_pred             CCCCCHHHHHHHHCCHHHCCCHHHCCCCCCCCHHHEEEEEECCCCCCCC---HHHHCCEEEEEECCCCHH----------
T ss_conf             7778868888862697656761222016766443258886037513298---678430305642688869----------


Q ss_pred             CCCHHHHH-HHHHHHHHHHHHCCCCC---C-CCHHHHHHHHHHHHHC
Q ss_conf             12044799-99999999999878898---8-7889999999999842
Q gi|254781225|r  649 TKYTLEAK-KWFLKGVKAYISKGLDV---D-IPEVCLKAKEEERQGT  690 (789)
Q Consensus       649 ~~e~~~i~-~w~l~g~~~~~~~g~~~---~-~p~~v~~a~~~y~~~~  690 (789)
                        |+..|. ++++  .+...++||+.   . ..+++....+.|-+|+
T Consensus       499 --EKl~IAk~~Li--Pk~~~~~gL~~~el~i~d~ai~~iI~~YTREA  541 (782)
T COG0466         499 --EKLEIAKRHLI--PKQLKEHGLKKGELTITDEAIKDIIRYYTREA  541 (782)
T ss_pred             --HHHHHHHHHCC--HHHHHHCCCCCCCEEECHHHHHHHHHHHHHHH
T ss_conf             --99999998445--68999759982335565899999999876762


No 447
>TIGR00634 recN DNA repair protein RecN; InterPro: IPR004604   DNA repair protein RecN is thought to be DNA damage inducible and involved in recombinational processes. The N-terminal region of most of the bacterial RecN proteins sequenced to date contains an ATP/GTP binding domain within an SMC-like motif. SMC-like domains are involved in chromosomal scaffolding and segregation. It is possible that the function of RecN in homologous recombination is either structural or enzymatic or both. RecN may be involved in the proper positioning of the recombining segments of DNA, ensuring normal recombination. The observation that inactivation of this gene leads to a decreased transformation efficiency, as well as increased sensitivity to DNA-damaging agents, may be due to some defect in chromosomal partitioning or positioning during these recombination-dependent processes . The protein may function presynaptically to process double-stranded breaks to produce 3 single-stranded DNA intermediates during recombination. ; GO: 0005524 ATP binding, 0006281 DNA repair, 0006310 DNA recombination.
Probab=78.26  E-value=1.6  Score=21.22  Aligned_cols=153  Identities=14%  Similarity=0.178  Sum_probs=69.8

Q ss_pred             CCCCCCCCCHHHC----CCCCCEEEECCCEEECCCCCCCCCCHHHHCCEECCCCCCCCCCHHHHHHHHHHHCCCHHHHHH
Q ss_conf             1000012320220----579717660793797438885589865501001378888757947899999888799999999
Q gi|254781225|r  410 EAGSIFSITSDLL----DSSSRFLGEQDGILDLETGQKVKPTKELYITKSTGTPFVEGEPSQEFLDLVSGYFESEEVMDY  485 (789)
Q Consensus       410 ~~~~~~~~~~~~l----d~~~~ll~~~NGv~dl~t~~~~~~~~~~~~t~~~~~~y~~~a~~p~~~~~l~~~~~d~e~~~~  485 (789)
                      .+.|.+.+..+.-    ..+|--+...||-.-=- +..=--.=+++|+-.++-+.-|-|          ++=---|+-++
T Consensus       406 ~a~F~v~~~~~~~~~~~~~~~~a~~L~~g~~~r~-~~~G~D~V~F~fs~n~G~~~~PLa----------k~ASGGELSRv  474 (605)
T TIGR00634       406 KAEFTVELKTSLPSRNDEAPSVALALVSGAKARA-GAYGADQVEFLFSANTGEPVKPLA----------KVASGGELSRV  474 (605)
T ss_pred             CEEEEEEEEECCCCCCCCCCCEEEEECCCCEEEC-CCCCCCEEEEEEECCCCCCCCCHH----------HHCCCCHHHHH
T ss_conf             1378998852353222357740566247850202-656743157864137878987535----------44366169999


Q ss_pred             HHHHHHHHHCCC--CCCCEEE---EEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCCCCCHHHHHHCCCE
Q ss_conf             999999997598--7433799---99707886257899999997233000344267642012455556898899738980
Q gi|254781225|r  486 FTRCVGMALLGG--NKAQRFI---HIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEAGKANPSLIRLMGSR  560 (789)
Q Consensus       486 l~~~~g~~l~g~--~~~~~~~---~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~~~~~~~~la~l~g~r  560 (789)
                      +. .+-.+|.-.  ..-+-++   |=.|.||--=....+.|..|=-..-+..     ++         |.|.+|..-.+.
T Consensus       475 ~L-AL~~~ls~~~~~~~~TliFDEvDvGvsG~~A~~ia~~L~~LS~~~QV~c-----vT---------Hlp~vAA~AD~h  539 (605)
T TIGR00634       475 ML-ALKVVLSSSDPAAVTTLIFDEVDVGVSGKTAQAIAKKLAQLSERKQVLC-----VT---------HLPQVAAHADAH  539 (605)
T ss_pred             HH-HHHHHCCCCCCCCCCCEEEEEEECCCCHHHHHHHHHHHHHHHHHCCEEE-----EC---------CCHHHHHHCCCC
T ss_conf             99-9998542346567871276316417646899999999999853095899-----81---------837989724881


Q ss_pred             EEEEECCC-------CCCCCC-----CCEEEEEECC-CEEE
Q ss_conf             99993467-------776013-----1002454159-8587
Q gi|254781225|r  561 IVIISETN-------ENDEIN-----AAKIKQMTGG-DCMT  588 (789)
Q Consensus       561 ~~~~~E~~-------~~~~~~-----~~~~K~ltgg-D~i~  588 (789)
                      |.+-.+..       .+-.++     ...++.|++. |.+.
T Consensus       540 ~~v~K~~~neniadPtnPqldeD~~T~~~v~~L~~~G~rV~  580 (605)
T TIGR00634       540 LKVEKELLNENIADPTNPQLDEDGRTATRVRPLSSEGERVA  580 (605)
T ss_pred             EEEEEEEECCCCCCCCCCCCCCCCCCCCEEECHHCCCCHHH
T ss_conf             46775420011467788766787886200220000263689


No 448
>PTZ00088 adenylate kinase 1; Provisional
Probab=78.22  E-value=2.4  Score=20.04  Aligned_cols=28  Identities=7%  Similarity=0.166  Sum_probs=24.2

Q ss_pred             CCCHHHHHHHHHHHHHCCHHHHHHH-HHE
Q ss_conf             8788999999999984263888875-432
Q gi|254781225|r  674 DIPEVCLKAKEEERQGTDTYQAWID-DCC  701 (789)
Q Consensus       674 ~~p~~v~~a~~~y~~~~D~v~~fi~-e~c  701 (789)
                      ..|++|+.-.+.|.+++-+|-.|.. +-|
T Consensus       172 D~~evI~~RL~~Y~~~T~PlidyYk~~k~  200 (225)
T PTZ00088        172 DEEDIIAHRLDSYESDNIHIINFFKNEKC  200 (225)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             99999999999999972189999981698


No 449
>KOG0652 consensus
Probab=78.19  E-value=4  Score=18.56  Aligned_cols=131  Identities=16%  Similarity=0.187  Sum_probs=65.6

Q ss_pred             CCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCC--CCCCHHHHHHCCCCCCCCCCHHHHHHCCCEEEEEECCCCCCCCCC
Q ss_conf             743379999707886257899999997233000--344267642012455556898899738980999934677760131
Q gi|254781225|r  498 NKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYV--INAEASDIMQNRPPEAGKANPSLIRLMGSRIVIISETNENDEINA  575 (789)
Q Consensus       498 ~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~--~~~~~~~~~~~~~~~~~~~~~~la~l~g~r~~~~~E~~~~~~~~~  575 (789)
                      .+..+=+.+||+.+.||+.+...+..--....-  +.+.+..+--..++..-.--|.||.-+--.++++.|.+.   +.+
T Consensus       202 i~pPKGvLmYGPPGTGKTlmARAcAaqT~aTFLKLAgPQLVQMfIGdGAkLVRDAFaLAKEkaP~IIFIDElDA---IGt  278 (424)
T KOG0652         202 IRPPKGVLMYGPPGTGKTLMARACAAQTNATFLKLAGPQLVQMFIGDGAKLVRDAFALAKEKAPTIIFIDELDA---IGT  278 (424)
T ss_pred             CCCCCCEEEECCCCCCHHHHHHHHHHHCCCHHHHHCCHHHHHHHHCCHHHHHHHHHHHHHCCCCEEEEEECHHH---HCC
T ss_conf             88997227657999757799999987401068873264777665334188999999875334983899730023---233


Q ss_pred             CEEEEEECCCEEEEEEC----C-CCCCEEEECCEEEEEECCCCCCCCCCCCCEEEEE---EEEECCCC
Q ss_conf             00245415985873210----4-7860687145289997388634267984166468---99965887
Q gi|254781225|r  576 AKIKQMTGGDCMTARLN----Y-GNTYSESPASFTPFIVPNKHLFVRNPDDAWWRRY---IVIPFDKP  635 (789)
Q Consensus       576 ~~~K~ltggD~i~ar~~----~-~~~~~~~~p~~~~~~~~N~~P~~~~~d~~~~rR~---~iipF~~~  635 (789)
                      .++-+=..||.-.-|-+    + -+.|+ -.-..+++-+||..-   --|.|+.|-=   +-|+|+++
T Consensus       279 KRfDSek~GDREVQRTMLELLNQLDGFs-s~~~vKviAATNRvD---iLDPALlRSGRLDRKIEfP~P  342 (424)
T KOG0652         279 KRFDSEKAGDREVQRTMLELLNQLDGFS-SDDRVKVIAATNRVD---ILDPALLRSGRLDRKIEFPHP  342 (424)
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHCCCCC-CCCCEEEEEECCCCC---CCCHHHHHCCCCCCCCCCCCC
T ss_conf             4365312343899999999998604899-756267885216434---348888644664444348899


No 450
>cd02019 NK Nucleoside/nucleotide kinase (NK) is a protein superfamily consisting of multiple families of enzymes that share structural similarity and are functionally related to the catalysis of the reversible phosphate group transfer from nucleoside triphosphates to nucleosides/nucleotides, nucleoside monophosphates, or sugars. Members of this family play a wide variety of essential roles in nucleotide metabolism, the biosynthesis of coenzymes and aromatic compounds, as well as the metabolism of sugar and sulfate.
Probab=78.19  E-value=2.2  Score=20.32  Aligned_cols=24  Identities=42%  Similarity=0.588  Sum_probs=20.6

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             999707886257899999997233
Q gi|254781225|r  504 IHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       504 ~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      +.+.|+-++||||+.+.++..|+.
T Consensus         2 I~I~G~~gsGKsT~a~~l~~~l~~   25 (69)
T cd02019           2 IAITGGSGSGKSTVAKKLAEQLGG   25 (69)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCC
T ss_conf             788368888725899999999589


No 451
>pfam03193 DUF258 Protein of unknown function, DUF258.
Probab=78.18  E-value=1.9  Score=20.74  Aligned_cols=16  Identities=50%  Similarity=0.733  Sum_probs=6.5

Q ss_pred             EEEECCCCCHHHHHHH
Q ss_conf             9970788625789999
Q gi|254781225|r  505 HIRGVGGSGKSTLMNL  520 (789)
Q Consensus       505 ~~~G~G~nGKSt~~~~  520 (789)
                      ++.|+.+-|||||+|.
T Consensus        39 v~~G~SGVGKSTLiN~   54 (161)
T pfam03193        39 VLAGQSGVGKSTLLNA   54 (161)
T ss_pred             EEECCCCCCHHHHHHH
T ss_conf             9988999889999988


No 452
>TIGR01313 therm_gnt_kin carbohydrate kinase, thermoresistant glucokinase family; InterPro: IPR006001    This family of proteins includes thermoresistant and thermosensitve isozymes of gluconate kinase (gluconokinase) in E. coli and other related proteins; members of this family are often named by similarity to the thermostable isozyme. These proteins show homology to shikimate kinases and adenylate kinases but not to gluconate kinases from the FGGY family of carbohydrate kinases (IPR000577 from INTERPRO).; GO: 0016301 kinase activity, 0005975 carbohydrate metabolic process.
Probab=78.17  E-value=1.7  Score=21.00  Aligned_cols=23  Identities=13%  Similarity=0.214  Sum_probs=11.8

Q ss_pred             HHHCCCCCCCCCHHHHHH-HHHHH
Q ss_conf             210122111488889999-99998
Q gi|254781225|r  214 LSCFGEEFYNGSHDEWIP-VVMAV  236 (789)
Q Consensus       214 l~~~~~~~~~~dyd~W~~-vg~al  236 (789)
                      ....+.++.++|+-.|+. ++-++
T Consensus        45 KMs~GiPL~DdDR~pWL~~l~~~~   68 (175)
T TIGR01313        45 KMSRGIPLNDDDRWPWLKNLADAL   68 (175)
T ss_pred             HHCCCCCCCCCCCHHHHHHHHHHH
T ss_conf             731788887012043799999999


No 453
>KOG2203 consensus
Probab=78.14  E-value=3  Score=19.37  Aligned_cols=12  Identities=17%  Similarity=0.454  Sum_probs=9.8

Q ss_pred             CEEEEEEECCCC
Q ss_conf             879999646881
Q gi|254781225|r   64 PLYAFDIDSKDE   75 (789)
Q Consensus        64 glv~iDiD~~d~   75 (789)
                      -+++.|+.+.|+
T Consensus        89 ~i~vmDvEGTDG  100 (772)
T KOG2203          89 CILVMDVEGTDG  100 (772)
T ss_pred             CEEEEECCCCCC
T ss_conf             169996456875


No 454
>COG4525 TauB ABC-type taurine transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=78.07  E-value=1.9  Score=20.71  Aligned_cols=18  Identities=50%  Similarity=0.756  Sum_probs=6.1

Q ss_pred             EEECCCCCHHHHHHHHHH
Q ss_conf             970788625789999999
Q gi|254781225|r  506 IRGVGGSGKSTLMNLIKY  523 (789)
Q Consensus       506 ~~G~G~nGKSt~~~~l~~  523 (789)
                      +.|+.+.||+|++|++..
T Consensus        36 ~lGpSGcGKTTLLnl~AG   53 (259)
T COG4525          36 VLGPSGCGKTTLLNLIAG   53 (259)
T ss_pred             EECCCCCCHHHHHHHHHC
T ss_conf             976888657889999862


No 455
>PRK09862 putative ATP-dependent protease; Provisional
Probab=77.83  E-value=3.7  Score=18.73  Aligned_cols=134  Identities=16%  Similarity=0.142  Sum_probs=76.0

Q ss_pred             HHHHCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCC-CCCCH-------------HHH
Q ss_conf             9888799999999999999997598743379999707886257899999997233000-34426-------------764
Q gi|254781225|r  473 VSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYV-INAEA-------------SDI  538 (789)
Q Consensus       473 l~~~~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~-~~~~~-------------~~~  538 (789)
                      +.++.|.+...    +.+-.+..|..    -++++|+-+.|||.+.+-+..+|.+-.. ..+..             ..+
T Consensus       190 ~~dv~Gq~~ak----raleIAAAGgH----nlLl~GpPG~GKTMlA~rlp~ILPpLt~~e~lEv~~I~Svag~~~~~~~~  261 (506)
T PRK09862        190 LSDVVGQEQGK----RGLEITAAGGH----NLLLIGPPGTGKTMLASRINGLLPDLSNEEALESAAILSLVNAESVQKQW  261 (506)
T ss_pred             HHHHCCCHHHH----HHHHHHHCCCC----CEEEECCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             56536979999----99999744688----65987699945989997751238998989999999999871898777754


Q ss_pred             HHCCCC-------------CCCCCCHHHHHHCCCEEEEEECCCCCCCCCCCEEEEEECCCEEEEEECCCCCCEEEECCEE
Q ss_conf             201245-------------5556898899738980999934677760131002454159858732104786068714528
Q gi|254781225|r  539 MQNRPP-------------EAGKANPSLIRLMGSRIVIISETNENDEINAAKIKQMTGGDCMTARLNYGNTYSESPASFT  605 (789)
Q Consensus       539 ~~~~~~-------------~~~~~~~~la~l~g~r~~~~~E~~~~~~~~~~~~K~ltggD~i~ar~~~~~~~~~~~p~~~  605 (789)
                      ...-+.             .+..++|.-..|.+.-+.+.+|..+-.+---..|.+=.-...|+.-+..+  .++|+-.|.
T Consensus       262 ~~rPfR~PHHs~S~~aliGGG~~~~PGEISLAH~GVLFLDElpEF~r~vLe~LRqPLE~g~I~IsRa~~--~~~~PA~F~  339 (506)
T PRK09862        262 RQRPFRSPHHSASLTAMVGGGAIPGPGEISLAHNGVLFLDELPEFERRTLDALREPIESGQIHLSRTRA--KITYPARFQ  339 (506)
T ss_pred             CCCCEECCCCCCCHHHHHCCCCCCCCCCEEECCCCEEEECCHHCCCHHHHHHHHHHHCCCEEEEEECCC--EEEECCHHH
T ss_conf             668503788765476663799999997222135757884550006888999877622477599996686--798615331


Q ss_pred             EEEECCCCCCC
Q ss_conf             99973886342
Q gi|254781225|r  606 PFIVPNKHLFV  616 (789)
Q Consensus       606 ~~~~~N~~P~~  616 (789)
                      |+.++|-=|-=
T Consensus       340 LVaAmNPCPCG  350 (506)
T PRK09862        340 LVAAMNPSPTG  350 (506)
T ss_pred             HEHHCCCCCCC
T ss_conf             11103788888


No 456
>KOG2028 consensus
Probab=77.76  E-value=4.1  Score=18.48  Aligned_cols=43  Identities=19%  Similarity=0.227  Sum_probs=20.1

Q ss_pred             CHHHHHHHHHHHHHH----CCCCCCCCCCHHH-HHHHHHHCCCCCCCC
Q ss_conf             179999999999985----0466755545256-899998635423331
Q gi|254781225|r  710 ESHSLAKSYSEYREQ----ELNYDRKRISTRT-VTLNLKQKGFIGGIK  752 (789)
Q Consensus       710 ~~~~l~~~y~~~~~~----~~~~~~~~~s~~~-~~~~l~~~g~~~~~~  752 (789)
                      ++-++|.+|..-...    .+....-|+--|+ =+.-++++||-.|.|
T Consensus       469 KSievYra~~~vka~ls~~~~~~~~vPlHlRNAPTkLMkeLGY~KgYk  516 (554)
T KOG2028         469 KSIEVYRAYNAVKACLSNHQGPLPEVPLHLRNAPTKLMKELGYGKGYK  516 (554)
T ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHCCCHHHHHHHCCCCCCC
T ss_conf             303999999999999743257888887303027378999837687755


No 457
>PRK00131 aroK shikimate kinase; Reviewed
Probab=77.74  E-value=2.5  Score=19.84  Aligned_cols=29  Identities=31%  Similarity=0.479  Sum_probs=24.4

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHCCCC
Q ss_conf             37999970788625789999999723300
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYAFGNQY  529 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~llG~~~  529 (789)
                      ..-+++.|.-++||||+...|...||-..
T Consensus         4 ~~nI~liG~~GsGKTtvgk~LA~~L~~~f   32 (175)
T PRK00131          4 GPNIVLIGMMGAGKSTIGRLLAKRLGYEF   32 (175)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHHCCCC
T ss_conf             98089888999998999999999959690


No 458
>COG0488 Uup ATPase components of ABC transporters with duplicated ATPase domains [General function prediction only]
Probab=77.67  E-value=2  Score=20.59  Aligned_cols=26  Identities=42%  Similarity=0.584  Sum_probs=21.4

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             99997078862578999999972330
Q gi|254781225|r  503 FIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       503 ~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      -+-++|+-+.|||||+++|...++..
T Consensus       350 rIaiiG~NG~GKSTLlk~l~g~~~~~  375 (530)
T COG0488         350 RIAIVGPNGAGKSTLLKLLAGELGPL  375 (530)
T ss_pred             EEEEECCCCCCHHHHHHHHHCCCCCC
T ss_conf             89998999877899999985213567


No 459
>pfam05970 DUF889 PIF1 helicase. The PIF1 helicase inhibits telomerase activity and is cell cycle regulated.
Probab=77.64  E-value=1.7  Score=21.07  Aligned_cols=11  Identities=9%  Similarity=0.486  Sum_probs=6.2

Q ss_pred             CCCEEEEEECC
Q ss_conf             89809999346
Q gi|254781225|r  557 MGSRIVIISET  567 (789)
Q Consensus       557 ~g~r~~~~~E~  567 (789)
                      .|++..+..-.
T Consensus       308 ~Ga~VMl~~Ni  318 (418)
T pfam05970       308 VGVPVMLLRNL  318 (418)
T ss_pred             CCCEEEEEEEC
T ss_conf             79859999722


No 460
>PRK11784 tRNA 2-selenouridine synthase; Provisional
Probab=77.48  E-value=4.2  Score=18.42  Aligned_cols=53  Identities=17%  Similarity=0.355  Sum_probs=37.5

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCC
Q ss_conf             999999999999997598743379999707886257899999997233000344267642012455
Q gi|254781225|r  480 EEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPE  545 (789)
Q Consensus       480 ~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~  545 (789)
                      ...+.++.+.+.         +.++++.|..|+||+-+++.|... |   ..++++.-++..||..
T Consensus       125 KayR~~v~~~l~---------~~~~vl~G~TG~GKT~lL~~L~~~-G---~~viDLEglA~HRGS~  177 (333)
T PRK11784        125 KAYRRFVIDTLE---------EPLVVLGGMTGSGKTRLLQALANA-G---AQVLDLEGLANHRGSS  177 (333)
T ss_pred             HHHHHHHHHHHC---------CCCEEEECCCCCCHHHHHHHHHHC-C---CCEECHHHHHHCCCCC
T ss_conf             999999999854---------685998678887789999999975-9---9743389886325642


No 461
>smart00072 GuKc Guanylate kinase homologues. Active enzymes catalyze ATP-dependent phosphorylation of GMP to GDP. Structure resembles that of adenylate kinase. So-called membrane-associated guanylate kinase homologues (MAGUKs) do not possess guanylate kinase activities; instead at least some possess protein-binding functions.
Probab=77.47  E-value=2.6  Score=19.81  Aligned_cols=57  Identities=25%  Similarity=0.404  Sum_probs=34.1

Q ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHHHHHCCCCCCCCCCHHHHHHCCCEEEEEECCC
Q ss_conf             37999970788625789999999723300034426764201245555689889973898099993467
Q gi|254781225|r  501 QRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASDIMQNRPPEAGKANPSLIRLMGSRIVIISETN  568 (789)
Q Consensus       501 ~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~~~~~~~~~~~~~~~~la~l~g~r~~~~~E~~  568 (789)
                      .+.+++.|+.+.||+|+.+.|..-..+....+.+-  ++  |.+..|       ...|+-..++++..
T Consensus         2 ~r~iil~Gpsg~GK~tl~~~l~~~~~~~~~~~v~~--TT--R~~r~g-------E~~G~dY~Fvs~~~   58 (184)
T smart00072        2 RRPIVLSGPSGVGKGTLLAELIQEIPDAFERVVSH--TT--RPPRPG-------EVNGVDYHFVSREE   58 (184)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHCCCCEEEEEEE--EC--CCCCCC-------CCCCCEEEEEEHHH
T ss_conf             97799999999999999999986396450577876--72--799889-------99996369971799


No 462
>PRK00279 adk adenylate kinase; Reviewed
Probab=77.45  E-value=2.6  Score=19.75  Aligned_cols=27  Identities=19%  Similarity=0.065  Sum_probs=22.7

Q ss_pred             CCCHHHHHHHHHHHHHCCHHHHHHHHH
Q ss_conf             878899999999998426388887543
Q gi|254781225|r  674 DIPEVCLKAKEEERQGTDTYQAWIDDC  700 (789)
Q Consensus       674 ~~p~~v~~a~~~y~~~~D~v~~fi~e~  700 (789)
                      ..++++..-.+.|+.+..+|-.|..+.
T Consensus       163 D~~e~i~~Rl~~y~~~t~pvi~~y~~~  189 (215)
T PRK00279        163 DNEETVRKRLEVYHKQTAPLIDYYKKK  189 (215)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             869999999999999888999999817


No 463
>PTZ00265 multidrug resistance protein (mdr1); Provisional
Probab=77.41  E-value=1.9  Score=20.64  Aligned_cols=28  Identities=39%  Similarity=0.560  Sum_probs=22.5

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             4337999970788625789999999723
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      .....+=+.|..|.||||++.+|..+.-
T Consensus      1193 ~~GqkVaiVGrSGsGKSTii~lL~Rfyd 1220 (1467)
T PTZ00265       1193 DSKKTTAIVGETGSGKSTFMNLLLRFYD 1220 (1467)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHHHHHHC
T ss_conf             7998899989999839999999997763


No 464
>pfam03266 DUF265 Protein of unknown function, DUF265.
Probab=77.35  E-value=2.5  Score=19.90  Aligned_cols=25  Identities=32%  Similarity=0.470  Sum_probs=20.2

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             9997078862578999999972330
Q gi|254781225|r  504 IHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       504 ~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      ++++|.-+.||||++.-+...|-+.
T Consensus         2 i~ITG~pGvGKTTli~kv~~~l~~~   26 (168)
T pfam03266         2 IFITGPPGVGKTTLVKKVIELLKSE   26 (168)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHC
T ss_conf             8997899988999999999999867


No 465
>pfam01583 APS_kinase Adenylylsulphate kinase. Enzyme that catalyses the phosphorylation of adenylylsulphate to 3'-phosphoadenylylsulfate. This domain contains an ATP binding P-loop motif.
Probab=77.24  E-value=3.2  Score=19.18  Aligned_cols=26  Identities=31%  Similarity=0.434  Sum_probs=22.0

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             79999707886257899999997233
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ..++++|-.++||||+.+.+..-|-.
T Consensus         3 ~viW~TGLsGsGKTTlA~~l~~~L~~   28 (157)
T pfam01583         3 CTVWFTGLSGSGKSTIANALERKLFA   28 (157)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHH
T ss_conf             89998898999999999999999997


No 466
>COG4175 ProV ABC-type proline/glycine betaine transport system, ATPase component [Amino acid transport and metabolism]
Probab=77.24  E-value=2.2  Score=20.26  Aligned_cols=19  Identities=32%  Similarity=0.539  Sum_probs=11.4

Q ss_pred             EEEECCCCEEEECCCCCCCCC
Q ss_conf             348526843880477688887
Q gi|254781225|r  126 LDILGCGQYFVAYNIHPKTKK  146 (789)
Q Consensus       126 iEi~~~G~q~V~~gshp~Tg~  146 (789)
                      ++|.. |.-||++|-. .+|+
T Consensus        49 l~v~~-GeIfViMGLS-GSGK   67 (386)
T COG4175          49 LDVEE-GEIFVIMGLS-GSGK   67 (386)
T ss_pred             EEECC-CEEEEEEECC-CCCH
T ss_conf             45458-7089999358-7878


No 467
>PRK03815 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=77.13  E-value=1.5  Score=21.31  Aligned_cols=18  Identities=22%  Similarity=0.399  Sum_probs=7.7

Q ss_pred             CCCCCHHHHHHHHHHHHC
Q ss_conf             788625789999999723
Q gi|254781225|r  509 VGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       509 ~G~nGKSt~~~~l~~llG  526 (789)
                      +|.|||||...++.++|.
T Consensus        95 TGTNGKsTtt~li~~iL~  112 (401)
T PRK03815         95 SGTNGKTTTTQMLTHLLE  112 (401)
T ss_pred             ECCCCHHHHHHHHHHHHH
T ss_conf             847777899999999998


No 468
>PRK08451 DNA polymerase III subunits gamma and tau; Validated
Probab=76.99  E-value=4.3  Score=18.33  Aligned_cols=22  Identities=23%  Similarity=0.365  Sum_probs=14.1

Q ss_pred             CCCCCCHHHHHHHHHHHCCCCC
Q ss_conf             1646899999999976200124
Q gi|254781225|r  161 DTPLLSEEDVEYLFKFFQEITV  182 (789)
Q Consensus       161 ~~P~i~~~~~~~l~~~~~~~~~  182 (789)
                      ++=.++..-..++++.++++-+
T Consensus       125 Eah~Lt~~A~NALLKTLEEPP~  146 (523)
T PRK08451        125 EVHMLTKEAFNALLKTLEEPPS  146 (523)
T ss_pred             CCCCCCHHHHHHHHHHCCCCCC
T ss_conf             6030489999999997038987


No 469
>COG1159 Era GTPase [General function prediction only]
Probab=76.86  E-value=2.4  Score=20.06  Aligned_cols=17  Identities=53%  Similarity=0.753  Sum_probs=6.9

Q ss_pred             EEEEEECCCCCHHHHHH
Q ss_conf             99997078862578999
Q gi|254781225|r  503 FIHIRGVGGSGKSTLMN  519 (789)
Q Consensus       503 ~~~~~G~G~nGKSt~~~  519 (789)
                      |+-+.|..+.|||||+|
T Consensus         8 fVaIiGrPNvGKSTLlN   24 (298)
T COG1159           8 FVAIIGRPNVGKSTLLN   24 (298)
T ss_pred             EEEEECCCCCCHHHHHH
T ss_conf             99998699876899998


No 470
>pfam03205 MobB Molybdopterin guanine dinucleotide synthesis protein B. This protein contains a P-loop.
Probab=76.74  E-value=2.8  Score=19.56  Aligned_cols=22  Identities=27%  Similarity=0.394  Sum_probs=0.0

Q ss_pred             EEEEECCCCCHHHHHHHHHHHH
Q ss_conf             9997078862578999999972
Q gi|254781225|r  504 IHIRGVGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       504 ~~~~G~G~nGKSt~~~~l~~ll  525 (789)
                      +++.|..+.|||||...|.+.+
T Consensus         3 v~i~G~~~sGKttl~~~L~~~~   24 (122)
T pfam03205         3 VLVVGPKDSGKTTLIRKLLNYL   24 (122)
T ss_pred             EEEECCCCCCHHHHHHHHHHHH
T ss_conf             9999489998999999999999


No 471
>KOG1969 consensus
Probab=76.57  E-value=2.8  Score=19.58  Aligned_cols=40  Identities=30%  Similarity=0.436  Sum_probs=0.0

Q ss_pred             CCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCHHH
Q ss_conf             87433799997078862578999999972330003442676
Q gi|254781225|r  497 GNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAEASD  537 (789)
Q Consensus       497 ~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~~~~  537 (789)
                      ....|++++|.|+.|-||+|+..+|.+=-| |.+.-...+.
T Consensus       322 ~RP~kKilLL~GppGlGKTTLAHViAkqaG-YsVvEINASD  361 (877)
T KOG1969         322 KRPPKKILLLCGPPGLGKTTLAHVIAKQAG-YSVVEINASD  361 (877)
T ss_pred             CCCCCCEEEEECCCCCCHHHHHHHHHHHCC-CEEEEECCCC
T ss_conf             798400687536887872479999998628-5488732555


No 472
>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I; InterPro: IPR011775    This entry represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll . This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria. It is also found in certain archaea not known to make chlorins.; GO: 0005524 ATP binding, 0016851 magnesium chelatase activity, 0006779 porphyrin biosynthetic process.
Probab=76.43  E-value=2.6  Score=19.78  Aligned_cols=24  Identities=25%  Similarity=0.394  Sum_probs=0.0

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHCC
Q ss_conf             999707886257899999997233
Q gi|254781225|r  504 IHIRGVGGSGKSTLMNLIKYAFGN  527 (789)
Q Consensus       504 ~~~~G~G~nGKSt~~~~l~~llG~  527 (789)
                      ++..|.-|+||||.+..|..||..
T Consensus        28 VmvmGdRGTgKSTavRALAalLP~   51 (340)
T TIGR02030        28 VMVMGDRGTGKSTAVRALAALLPE   51 (340)
T ss_pred             EEEECCCCCCHHHHHHHHHHHCCC
T ss_conf             888677898356899999974994


No 473
>COG0396 sufC Cysteine desulfurase activator ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=76.42  E-value=2.5  Score=19.88  Aligned_cols=20  Identities=50%  Similarity=0.519  Sum_probs=0.0

Q ss_pred             EEEEEECCCCCHHHHHHHHH
Q ss_conf             99997078862578999999
Q gi|254781225|r  503 FIHIRGVGGSGKSTLMNLIK  522 (789)
Q Consensus       503 ~~~~~G~G~nGKSt~~~~l~  522 (789)
                      ...+.||-++||||+..+|.
T Consensus        32 vhaiMGPNGsGKSTLa~~i~   51 (251)
T COG0396          32 VHAIMGPNGSGKSTLAYTIM   51 (251)
T ss_pred             EEEEECCCCCCHHHHHHHHH
T ss_conf             89998899878899999972


No 474
>pfam03308 ArgK ArgK protein. The ArgK protein acts as an ATPase enzyme and as a kinase, and phosphorylates periplasmic binding proteins involved in the LAO (lysine, arginine, ornithine)/AO transport systems.
Probab=76.41  E-value=3.7  Score=18.80  Aligned_cols=32  Identities=31%  Similarity=0.445  Sum_probs=0.0

Q ss_pred             HCCCCCCCEEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             75987433799997078862578999999972
Q gi|254781225|r  494 LLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       494 l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~ll  525 (789)
                      +...+..-.-+=++|+.+.|||||++.+...+
T Consensus        22 ~~~~~g~a~~iGiTG~PGaGKStli~~l~~~~   53 (267)
T pfam03308        22 LMPLTGRAHRVGITGVPGAGKSTLIEALGMEL   53 (267)
T ss_pred             HHHHCCCCEEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             87435995599876899887999999999999


No 475
>COG4988 CydD ABC-type transport system involved in cytochrome bd biosynthesis, ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones]
Probab=76.39  E-value=2.2  Score=20.25  Aligned_cols=27  Identities=33%  Similarity=0.529  Sum_probs=0.0

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHHCCC
Q ss_conf             799997078862578999999972330
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYAFGNQ  528 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~llG~~  528 (789)
                      ....+.|+.|.||||++++|...+-.+
T Consensus       348 ~~talvG~SGaGKSTLl~lL~G~~~~~  374 (559)
T COG4988         348 QLTALVGASGAGKSTLLNLLLGFLAPT  374 (559)
T ss_pred             CEEEEECCCCCCHHHHHHHHHCCCCCC
T ss_conf             679998899997899999984757777


No 476
>TIGR02729 Obg_CgtA GTP-binding protein Obg/CgtA; InterPro: IPR014100   This entry describes a universal, mostly one-gene-per-genome GTP-binding protein that associates with ribosomal subunits and appears to play a role in ribosomal RNA maturation. Mutations in this gene are pleiotropic, but it appears that effects on cellular functions such as chromosome partition may be secondary to the effect on ribosome structure..
Probab=76.37  E-value=1.5  Score=21.35  Aligned_cols=32  Identities=28%  Similarity=0.335  Sum_probs=0.0

Q ss_pred             EEECCCCCHHHHHHHHHHH---HCCCCCCCCCHHH
Q ss_conf             9707886257899999997---2330003442676
Q gi|254781225|r  506 IRGVGGSGKSTLMNLIKYA---FGNQYVINAEASD  537 (789)
Q Consensus       506 ~~G~G~nGKSt~~~~l~~l---lG~~~~~~~~~~~  537 (789)
                      |+|=.+.|||||++.|++.   +.+|-=+++.+.+
T Consensus       163 LvGfPNAGKSTLLs~~S~AkPKiAdYPFTTL~P~L  197 (296)
T TIGR02729       163 LVGFPNAGKSTLLSAISNAKPKIADYPFTTLEPNL  197 (296)
T ss_pred             EECCCCCCHHHHHHHHHCCCCEECCCCCCCCCCCE
T ss_conf             03578874688888876278822387874565311


No 477
>PRK04040 adenylate kinase; Provisional
Probab=76.36  E-value=3.9  Score=18.61  Aligned_cols=55  Identities=16%  Similarity=0.241  Sum_probs=0.0

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHHC-CCCCCCCCHHHHHHCCCCCCCCCCHHHHHH
Q ss_conf             7999970788625789999999723-300034426764201245555689889973
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYAFG-NQYVINAEASDIMQNRPPEAGKANPSLIRL  556 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~llG-~~~~~~~~~~~~~~~~~~~~~~~~~~la~l  556 (789)
                      +.++++|..|.||||+++.+...+. +|-+.+-...++..-.....-..+.+|-.|
T Consensus         3 k~VvvtGiPGvGKTTv~~~~~~~l~~~~~~vn~G~~M~e~A~~~glv~~RDemRkL   58 (189)
T PRK04040          3 KVVVVTGVPGVGKTTVLNKALEKLKEDYKIVNFGDVMLEVAKEEGLVEHRDEMRKL   58 (189)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHCCCCEEEEHHHHHHHHHHHCCCCCCHHHHCCC
T ss_conf             18999758988789999999997235875986779999999981773477887479


No 478
>PRK00089 era GTP-binding protein Era; Reviewed
Probab=76.34  E-value=3.3  Score=19.11  Aligned_cols=28  Identities=32%  Similarity=0.418  Sum_probs=0.0

Q ss_pred             HCCCCCCCEEEEEEECCCCCHHHHHHHH
Q ss_conf             7598743379999707886257899999
Q gi|254781225|r  494 LLGGNKAQRFIHIRGVGGSGKSTLMNLI  521 (789)
Q Consensus       494 l~g~~~~~~~~~~~G~G~nGKSt~~~~l  521 (789)
                      ++.....--|+-+.|..+.|||||+|.|
T Consensus         1 ~~~~~~ksG~VaivG~PNvGKSTL~N~l   28 (296)
T PRK00089          1 MSPEKFKSGFVAIVGRPNVGKSTLLNAL   28 (296)
T ss_pred             CCCCCCCEEEEEEECCCCCCHHHHHHHH
T ss_conf             9988983799999989998889999999


No 479
>PRK10418 nikD nickel transporter ATP-binding protein; Provisional
Probab=76.31  E-value=2  Score=20.54  Aligned_cols=23  Identities=26%  Similarity=0.244  Sum_probs=0.0

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             99997078862578999999972
Q gi|254781225|r  503 FIHIRGVGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       503 ~~~~~G~G~nGKSt~~~~l~~ll  525 (789)
                      ++-+.|+-|.||||++..+..++
T Consensus        31 ~~aiiG~SGsGKStl~k~llgll   53 (254)
T PRK10418         31 VLALVGGSGSGKSLTCAAALGIL   53 (254)
T ss_pred             EEEEECCCCCHHHHHHHHHHCCC
T ss_conf             99999999878999999995799


No 480
>KOG3347 consensus
Probab=76.30  E-value=2.6  Score=19.82  Aligned_cols=23  Identities=39%  Similarity=0.556  Sum_probs=0.0

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             99970788625789999999723
Q gi|254781225|r  504 IHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       504 ~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      ++++|+.|.|||||..-|...+|
T Consensus        10 ILvtGTPG~GKstl~~~lae~~~   32 (176)
T KOG3347          10 ILVTGTPGTGKSTLAERLAEKTG   32 (176)
T ss_pred             EEEECCCCCCCHHHHHHHHHHHC
T ss_conf             79867999880259999999739


No 481
>COG4598 HisP ABC-type histidine transport system, ATPase component [Amino acid transport and metabolism]
Probab=76.25  E-value=2.8  Score=19.56  Aligned_cols=22  Identities=45%  Similarity=0.714  Sum_probs=0.0

Q ss_pred             EEEEEECCCCCHHHHHHHHHHH
Q ss_conf             9999707886257899999997
Q gi|254781225|r  503 FIHIRGVGGSGKSTLMNLIKYA  524 (789)
Q Consensus       503 ~~~~~G~G~nGKSt~~~~l~~l  524 (789)
                      .+-++|+.++|||||+.-|.-+
T Consensus        34 VisIIGsSGSGKSTfLRCiN~L   55 (256)
T COG4598          34 VISIIGSSGSGKSTFLRCINFL   55 (256)
T ss_pred             EEEEECCCCCCHHHHHHHHHHH
T ss_conf             8999658998626899999863


No 482
>TIGR01187 potA polyamine ABC transporter, ATP-binding protein; InterPro: IPR005893   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).     This family comprises the spermidine/putrescine ABC transporter, ATP binding subunit in bacteria and its equivalents in archaea. This transport system belongs to the larger ATP-Binding Cassette (ABC) transporter superfamily. Polyamines like spermidine and putrescine play a vital role in cell proliferation, differentiation, and ion homeostasis. The concentration of polyamines within the cell are regulated by biosynthesis, degradation and transport (uptake and efflux included).; GO: 0015417 polyamine-transporting ATPase activity, 0015846 polyamine transport, 0016020 membrane.
Probab=76.22  E-value=1.3  Score=21.79  Aligned_cols=17  Identities=41%  Similarity=0.780  Sum_probs=0.0

Q ss_pred             EEECCCCCHHHHHHHHH
Q ss_conf             97078862578999999
Q gi|254781225|r  506 IRGVGGSGKSTLMNLIK  522 (789)
Q Consensus       506 ~~G~G~nGKSt~~~~l~  522 (789)
                      |.|+.|.||||++.+|.
T Consensus         1 LLGpSGcGKTTlLrlLA   17 (331)
T TIGR01187         1 LLGPSGCGKTTLLRLLA   17 (331)
T ss_pred             CCCCCCCCHHHHHHHHH
T ss_conf             97888874799999983


No 483
>PRK10773 murF UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase; Reviewed
Probab=76.18  E-value=3.4  Score=18.98  Aligned_cols=51  Identities=12%  Similarity=0.044  Sum_probs=0.0

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCEEEEEEE-CCCCCHHHHHHHHHHHHCCCCCCCCCH
Q ss_conf             99999999999999759874337999970-788625789999999723300034426
Q gi|254781225|r  480 EEVMDYFTRCVGMALLGGNKAQRFIHIRG-VGGSGKSTLMNLIKYAFGNQYVINAEA  535 (789)
Q Consensus       480 ~e~~~~l~~~~g~~l~g~~~~~~~~~~~G-~G~nGKSt~~~~l~~llG~~~~~~~~~  535 (789)
                      ++.+..++++..|..-.....     ++| +|.|||+|.-+++..+|..........
T Consensus        81 ~d~~~al~~la~~~~~~~~~~-----vIgITGSnGKTTtk~~i~~iL~~~g~~~~t~  132 (452)
T PRK10773         81 KDTRLAFGQLAAWVRQQVPAR-----VVALTGSSGKTSVKEMTAAILSQCGNTLYTA  132 (452)
T ss_pred             CCHHHHHHHHHHHHHHCCCCC-----EEEEEECCCCCHHHHHHHHHHHHHCCCCCCC
T ss_conf             999999999999875159975-----8999916996259999999999728841245


No 484
>PRK13946 shikimate kinase; Provisional
Probab=76.14  E-value=3  Score=19.35  Aligned_cols=23  Identities=30%  Similarity=0.491  Sum_probs=0.0

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             99970788625789999999723
Q gi|254781225|r  504 IHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       504 ~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      ++|+|--+.||||+-..|...||
T Consensus        23 IvLIG~mGsGKStvGk~LA~~L~   45 (195)
T PRK13946         23 VVLVGLMGAGKSTVGRRLATMLG   45 (195)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHC
T ss_conf             89989999988999999999979


No 485
>COG0497 RecN ATPase involved in DNA repair [DNA replication, recombination, and repair]
Probab=76.13  E-value=2.8  Score=19.55  Aligned_cols=31  Identities=19%  Similarity=0.386  Sum_probs=0.0

Q ss_pred             EEEEEECCCCCHHHHHHHHHHHHCCCCCCCC
Q ss_conf             9999707886257899999997233000344
Q gi|254781225|r  503 FIHIRGVGGSGKSTLMNLIKYAFGNQYVINA  533 (789)
Q Consensus       503 ~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~  533 (789)
                      |-+++|..|.|||.+++.|.-++|..+.++.
T Consensus        24 ltVlTGETGAGKSIiidAl~lllG~ra~~~~   54 (557)
T COG0497          24 LTVLTGETGAGKSIIIDALGLLLGGRADASL   54 (557)
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHCCCCCCCH
T ss_conf             5686568887566799899997278778112


No 486
>KOG0991 consensus
Probab=76.10  E-value=4.5  Score=18.18  Aligned_cols=65  Identities=17%  Similarity=0.266  Sum_probs=0.0

Q ss_pred             HHHHCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHH-HHHHHHHHCCCCCCCCCHHHHHHCCC
Q ss_conf             988879999999999999999759874337999970788625789-99999972330003442676420124
Q gi|254781225|r  473 VSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTL-MNLIKYAFGNQYVINAEASDIMQNRP  543 (789)
Q Consensus       473 l~~~~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~-~~~l~~llG~~~~~~~~~~~~~~~~~  543 (789)
                      |.+|+|+++.++.++-+.---=.++      +++.|+.+.||+|- +-+.+.+||+.+.-.+-...-+..|+
T Consensus        26 l~dIVGNe~tv~rl~via~~gnmP~------liisGpPG~GKTTsi~~LAr~LLG~~~ke~vLELNASdeRG   91 (333)
T KOG0991          26 LQDIVGNEDTVERLSVIAKEGNMPN------LIISGPPGTGKTTSILCLARELLGDSYKEAVLELNASDERG   91 (333)
T ss_pred             HHHHHCCHHHHHHHHHHHHCCCCCC------EEEECCCCCCHHHHHHHHHHHHHCHHHHHHHHHCCCCCCCC
T ss_conf             9882177989999999997289986------67527999861648999999983806665763205765546


No 487
>PRK00141 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=75.99  E-value=1.8  Score=20.84  Aligned_cols=17  Identities=24%  Similarity=0.431  Sum_probs=0.0

Q ss_pred             CCCCCHHHHHHHHHHHH
Q ss_conf             78862578999999972
Q gi|254781225|r  509 VGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       509 ~G~nGKSt~~~~l~~ll  525 (789)
                      +|.|||||...+|.++|
T Consensus       129 TGTnGKTTTtsli~~iL  145 (476)
T PRK00141        129 TGTNGKTTTTAMLAAMM  145 (476)
T ss_pred             ECCCCHHHHHHHHHHHH
T ss_conf             68996798999999999


No 488
>PRK05896 DNA polymerase III subunits gamma and tau; Validated
Probab=75.99  E-value=4.6  Score=18.16  Aligned_cols=48  Identities=17%  Similarity=0.239  Sum_probs=0.0

Q ss_pred             HHHHCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             98887999999999999999975987433799997078862578999999972
Q gi|254781225|r  473 VSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       473 l~~~~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~ll  525 (789)
                      +.++.|-+.++..|+..+.     ..+..-.++++|+-|.||.|+...+...|
T Consensus        15 F~eIIGQe~iv~~L~nAI~-----~~RiaHAYLFsGPrGvGKTTlArifAkaL   62 (613)
T PRK05896         15 FKQIIGQELIKKILVNAIL-----NNKLTHAYIFSGPRGIGKTSIAKIFAKAI   62 (613)
T ss_pred             HHHHCCCHHHHHHHHHHHH-----CCCCCCEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             6552382999999999998-----49976227755899848899999999996


No 489
>cd01854 YjeQ_engC YjeQ/EngC.  YjeQ (YloQ in Bacillus subtilis) represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. All YjeQ family proteins display a unique domain architecture, which includes an N-terminal OB-fold RNA-binding domain, the central permuted GTPase domain, and a zinc knuckle-like C-terminal cysteine domain. This domain architecture suggests a role for YjeQ as a regulator of translation.
Probab=75.90  E-value=2.3  Score=20.08  Aligned_cols=20  Identities=40%  Similarity=0.584  Sum_probs=0.0

Q ss_pred             EEEEEEECCCCCHHHHHHHH
Q ss_conf             79999707886257899999
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLI  521 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l  521 (789)
                      +..++.|+.|-|||||+|.|
T Consensus       162 k~~v~~G~SGvGKSSLiN~L  181 (287)
T cd01854         162 KTSVLVGQSGVGKSTLINAL  181 (287)
T ss_pred             CEEEEECCCCCCHHHHHHHH
T ss_conf             88999889988889999874


No 490
>PRK08727 hypothetical protein; Validated
Probab=75.87  E-value=4.6  Score=18.14  Aligned_cols=103  Identities=13%  Similarity=0.130  Sum_probs=0.0

Q ss_pred             HCCEECCCCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCCCCC
Q ss_conf             01001378888757947899999888799999999999999997598743379999707886257899999997233000
Q gi|254781225|r  451 YITKSTGTPFVEGEPSQEFLDLVSGYFESEEVMDYFTRCVGMALLGGNKAQRFIHIRGVGGSGKSTLMNLIKYAFGNQYV  530 (789)
Q Consensus       451 ~~t~~~~~~y~~~a~~p~~~~~l~~~~~d~e~~~~l~~~~g~~l~g~~~~~~~~~~~G~G~nGKSt~~~~l~~llG~~~~  530 (789)
                      +...+++.+...... +.|+.|+   .+.......++...-      ....-+++++|+.|+|||-++..+++.......
T Consensus         1 m~~~QLpL~l~~~~~-~tfdnFi---~~~n~~~a~l~~~~~------~~~~~~lyl~G~~GsGKTHLl~a~~~~~~~~~~   70 (233)
T PRK08727          1 MSVPQLPLALRAPSD-QRFDSYI---AAPDGLLAQLQALAA------GQSSDWLYLSGPAGTGKTHLALSLCAAAEQAGR   70 (233)
T ss_pred             CCCCCCCCCCCCCCC-CCHHHCC---CCCHHHHHHHHHHHC------CCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCC
T ss_conf             980104788999972-2421206---785599999998743------888898999899999889999999999982799


Q ss_pred             CCCCHHHHHHCCCCCCCCCCHHHHHHCCCEEEEEECCC
Q ss_conf             34426764201245555689889973898099993467
Q gi|254781225|r  531 INAEASDIMQNRPPEAGKANPSLIRLMGSRIVIISETN  568 (789)
Q Consensus       531 ~~~~~~~~~~~~~~~~~~~~~~la~l~g~r~~~~~E~~  568 (789)
                      ...-..+-....     .....+..+...-++++.+.+
T Consensus        71 ~~~yl~l~~~~~-----~~~~~l~~le~~~ll~iDDid  103 (233)
T PRK08727         71 SSAYLPLQAAAG-----RLRDALEALEGRSLVALDGVD  103 (233)
T ss_pred             CEEEEEHHHHHH-----HHHHHHHHHCCCCEEEEECCH
T ss_conf             728844788532-----025677531038978985501


No 491
>PRK05057 aroK shikimate kinase I; Reviewed
Probab=75.78  E-value=3.2  Score=19.17  Aligned_cols=28  Identities=29%  Similarity=0.380  Sum_probs=0.0

Q ss_pred             CCCEEEEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             4337999970788625789999999723
Q gi|254781225|r  499 KAQRFIHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       499 ~~~~~~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      ..++-++|+|.-+.||||+...|...||
T Consensus         2 ~~kknI~LiG~mGsGKstvgk~LA~~l~   29 (172)
T PRK05057          2 AEKRNIFLVGPMGAGKSTIGRQLAQQLN   29 (172)
T ss_pred             CCCCCEEEECCCCCCHHHHHHHHHHHHC
T ss_conf             9888289889999988999999999969


No 492
>cd00464 SK Shikimate kinase (SK) is the fifth enzyme in the shikimate pathway, a seven-step biosynthetic pathway which converts erythrose-4-phosphate to chorismic acid, found in bacteria, fungi and plants. Chorismic acid is a important intermediate in the synthesis of aromatic compounds, such as aromatic amino acids, p-aminobenzoic acid, folate and ubiquinone. Shikimate kinase catalyses the phosphorylation of the 3-hydroxyl group of shikimic acid using ATP.
Probab=75.64  E-value=3.2  Score=19.21  Aligned_cols=23  Identities=39%  Similarity=0.616  Sum_probs=0.0

Q ss_pred             EEEEECCCCCHHHHHHHHHHHHC
Q ss_conf             99970788625789999999723
Q gi|254781225|r  504 IHIRGVGGSGKSTLMNLIKYAFG  526 (789)
Q Consensus       504 ~~~~G~G~nGKSt~~~~l~~llG  526 (789)
                      ++|+|--+.||||+...+...+|
T Consensus         2 I~LiG~~G~GKstigk~la~~l~   24 (154)
T cd00464           2 IVLIGMMGAGKTTVGRLLAKALG   24 (154)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHC
T ss_conf             89988999988999999999979


No 493
>pfam00350 Dynamin_N Dynamin family.
Probab=75.58  E-value=2  Score=20.60  Aligned_cols=18  Identities=33%  Similarity=0.593  Sum_probs=0.0

Q ss_pred             EEEEECCCCCHHHHHHHH
Q ss_conf             999707886257899999
Q gi|254781225|r  504 IHIRGVGGSGKSTLMNLI  521 (789)
Q Consensus       504 ~~~~G~G~nGKSt~~~~l  521 (789)
                      +.+.|.-++|||+|+|.|
T Consensus         1 ivvvG~~ssGKSSliNAL   18 (168)
T pfam00350         1 IAVVGDQSAGKSSVLNAL   18 (168)
T ss_pred             CEEECCCCCCHHHHHHHH
T ss_conf             989917889899999999


No 494
>PRK05506 bifunctional sulfate adenylyltransferase subunit 1/adenylylsulfate kinase protein; Provisional
Probab=75.49  E-value=3.7  Score=18.78  Aligned_cols=24  Identities=38%  Similarity=0.642  Sum_probs=0.0

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHH
Q ss_conf             799997078862578999999972
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~ll  525 (789)
                      ++++++|..++||||+.+.|+..|
T Consensus       444 ~~iw~tGlsgsGKstiA~~le~~L  467 (613)
T PRK05506        444 ATVWFTGLSGSGKSTIANLVERRL  467 (613)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             699997789897479999999999


No 495
>cd04164 trmE TrmE (MnmE, ThdF, MSS1) is a 3-domain protein found in bacteria and eukaryotes.  It controls modification of the uridine at the wobble position (U34) of tRNAs that read codons ending with A or G in the mixed codon family boxes.  TrmE contains a GTPase domain that forms a canonical Ras-like fold.  It functions a molecular switch GTPase, and apparently uses a conformational change associated with GTP hydrolysis to promote the tRNA modification reaction, in which the conserved cysteine in the C-terminal domain is thought to function as a catalytic residue.  In bacteria that are able to survive in extremely low pH conditions, TrmE regulates glutamate-dependent acid resistance.
Probab=75.39  E-value=2.7  Score=19.72  Aligned_cols=19  Identities=37%  Similarity=0.546  Sum_probs=0.0

Q ss_pred             EEEEECCCCCHHHHHHHHH
Q ss_conf             9997078862578999999
Q gi|254781225|r  504 IHIRGVGGSGKSTLMNLIK  522 (789)
Q Consensus       504 ~~~~G~G~nGKSt~~~~l~  522 (789)
                      +.+.|..+.|||||+|.|.
T Consensus         4 ValvG~pN~GKStL~N~l~   22 (157)
T cd04164           4 VVIVGKPNVGKSSLLNALA   22 (157)
T ss_pred             EEEECCCCCCHHHHHHHHH
T ss_conf             9998899998999999996


No 496
>TIGR00750 lao LAO/AO transport system ATPase; InterPro: IPR005129   Bacterial periplasmic transport systems require the function of a specific substrate-binding protein, located in the periplasm, and several cytoplasmic membrane transport components. In Escherichia coli K-12, the arginine-ornithine transport system requires an arginine-ornithine-binding protein and the lysine-arginine-ornithine (LAO) transport system includes a LAO-binding protein. Both periplasmic proteins can be phosphorylated by a single kinase, ArgK  resulting in reduced levels of transport activity of the periplasmic transport systems that include each of the binding proteins. The ArgK protein acts as an ATPase enzyme and as a kinase..
Probab=75.34  E-value=2.4  Score=20.02  Aligned_cols=20  Identities=45%  Similarity=0.688  Sum_probs=0.0

Q ss_pred             EEECCCCCHHHHHHHHHHHH
Q ss_conf             97078862578999999972
Q gi|254781225|r  506 IRGVGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       506 ~~G~G~nGKSt~~~~l~~ll  525 (789)
                      ++|..|-|||||++-+...|
T Consensus        43 ~TG~PGaGKSTl~~~l~~~l   62 (333)
T TIGR00750        43 ITGVPGAGKSTLVEKLIMEL   62 (333)
T ss_pred             EECCCCCCHHHHHHHHHHHH
T ss_conf             64688885777999998999


No 497
>PRK02705 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=75.27  E-value=1.8  Score=20.77  Aligned_cols=17  Identities=29%  Similarity=0.550  Sum_probs=0.0

Q ss_pred             CCCCCHHHHHHHHHHHH
Q ss_conf             78862578999999972
Q gi|254781225|r  509 VGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       509 ~G~nGKSt~~~~l~~ll  525 (789)
                      +|.|||||...+|.++|
T Consensus       115 TGTnGKTTTt~ll~~iL  131 (459)
T PRK02705        115 TGTNGKTTVTHLLAHIL  131 (459)
T ss_pred             ECCCCCHHHHHHHHHHH
T ss_conf             17897278999999999


No 498
>PRK01889 ribosome-associated GTPase; Reviewed
Probab=75.21  E-value=2.5  Score=19.86  Aligned_cols=20  Identities=40%  Similarity=0.675  Sum_probs=0.0

Q ss_pred             EEEEEEECCCCCHHHHHHHH
Q ss_conf             79999707886257899999
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLI  521 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l  521 (789)
                      +-.++.|+.+-|||||+|.|
T Consensus       195 kT~vl~G~SGVGKSTLiN~L  214 (353)
T PRK01889        195 KTVALLGSSGVGKSTLVNAL  214 (353)
T ss_pred             CEEEEECCCCCCHHHHHHHH
T ss_conf             78999778886699999875


No 499
>PRK06547 hypothetical protein; Provisional
Probab=75.20  E-value=3.9  Score=18.60  Aligned_cols=33  Identities=24%  Similarity=0.393  Sum_probs=0.0

Q ss_pred             EEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             799997078862578999999972330003442
Q gi|254781225|r  502 RFIHIRGVGGSGKSTLMNLIKYAFGNQYVINAE  534 (789)
Q Consensus       502 ~~~~~~G~G~nGKSt~~~~l~~llG~~~~~~~~  534 (789)
                      .++-+=|++++|||||.+-|...+..-.+...+
T Consensus        16 ~iVaIDG~sGaGKTTLA~~La~~~~~~~vvHmD   48 (184)
T PRK06547         16 ITVLIDGRSGSGKTTLAGELAACWEGSQLVHLD   48 (184)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHCCCCCEEEEC
T ss_conf             999986899888899999999745798289705


No 500
>PRK01390 murD UDP-N-acetylmuramoyl-L-alanyl-D-glutamate synthetase; Provisional
Probab=75.20  E-value=2  Score=20.58  Aligned_cols=17  Identities=41%  Similarity=0.489  Sum_probs=0.0

Q ss_pred             CCCCCHHHHHHHHHHHH
Q ss_conf             78862578999999972
Q gi|254781225|r  509 VGGSGKSTLMNLIKYAF  525 (789)
Q Consensus       509 ~G~nGKSt~~~~l~~ll  525 (789)
                      +|.|||||...+|.++|
T Consensus       120 TGTnGKTTTtsli~~iL  136 (457)
T PRK01390        120 TGTNGKSTTTALIAHLL  136 (457)
T ss_pred             ECCCCHHHHHHHHHHHH
T ss_conf             28996498999999999


Done!