Query         gi|254780690|ref|YP_003065103.1| flagellar biosynthesis protein FlhB [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 354
No_of_seqs    156 out of 1618
Neff          7.0 
Searched_HMMs 39220
Date          Sun May 29 20:21:01 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780690.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR00328 flhB flagellar biosy 100.0       0       0  953.8  41.7  346    8-353     1-349 (352)
  2 PRK13109 flhB flagellar biosyn 100.0       0       0  890.6  45.5  353    1-353     1-353 (358)
  3 PRK05702 flhB flagellar biosyn 100.0       0       0  889.7  46.1  351    1-353     1-351 (352)
  4 PRK12772 bifunctional flagella 100.0       0       0  887.9  43.9  346    7-353   262-607 (609)
  5 PRK12468 flhB flagellar biosyn 100.0       0       0  874.1  44.1  351    1-353     1-351 (383)
  6 PRK06298 type III secretion sy 100.0       0       0  862.5  45.2  344    8-353     2-345 (360)
  7 PRK09108 type III secretion sy 100.0       0       0  857.3  44.0  343    8-353     3-346 (354)
  8 COG1377 FlhB Flagellar biosynt 100.0       0       0  856.3  44.2  350    3-353     2-351 (363)
  9 PRK12721 secretion system appa 100.0       0       0  857.7  43.0  342    9-353     3-344 (349)
 10 pfam01312 Bac_export_2 FlhB Hr 100.0       0       0  852.0  44.7  342    7-350     2-343 (343)
 11 PRK08156 surface presentation  100.0       0       0  853.0  43.3  337    9-353     3-339 (367)
 12 PRK12773 flhB flagellar biosyn 100.0       0       0  818.3  43.4  345    7-353   300-646 (649)
 13 TIGR01404 FlhB_rel_III type II 100.0       0       0  794.1  38.4  342    8-352     1-346 (346)
 14 COG4792 EscU Type III secretor 100.0       0       0  675.2  39.7  343    7-352     2-344 (349)
 15 TIGR00789 flhB_rel FlhB domain  99.8 3.8E-18 9.7E-23  164.1   8.2   80  272-352     1-80  (84)
 16 COG2257 Uncharacterized homolo  99.7 4.3E-17 1.1E-21  155.9   9.6   80  273-353     7-86  (92)
 17 COG1377 FlhB Flagellar biosynt  97.8  0.0066 1.7E-07   43.5  19.8  314    1-324     4-344 (363)
 18 PRK12468 flhB flagellar biosyn  97.6   0.014 3.6E-07   40.9  17.9  235   80-323    82-343 (383)
 19 PRK05702 flhB flagellar biosyn  97.5   0.017 4.4E-07   40.2  18.7  259   35-303    38-322 (352)
 20 PRK13109 flhB flagellar biosyn  97.3   0.031   8E-07   38.1  18.4  294    5-313     9-335 (358)
 21 PRK06298 type III secretion sy  97.1    0.04   1E-06   37.3  18.3  220   80-308    76-321 (360)
 22 PRK09108 type III secretion sy  97.0   0.049 1.3E-06   36.6  19.7  287    1-305     1-320 (354)
 23 PRK12721 secretion system appa  97.0   0.051 1.3E-06   36.4  17.7  185  111-304   109-316 (349)
 24 PRK12773 flhB flagellar biosyn  96.9   0.061 1.5E-06   35.9  17.7  285    2-294   298-611 (649)
 25 TIGR00328 flhB flagellar biosy  96.8   0.075 1.9E-06   35.1  20.1  221   34-260    31-260 (352)
 26 pfam01312 Bac_export_2 FlhB Hr  96.7   0.085 2.2E-06   34.7  18.1  286    1-304     1-318 (343)
 27 PRK12772 bifunctional flagella  95.3    0.35 8.9E-06   29.9  17.6  289    2-304   261-579 (609)
 28 PRK08156 surface presentation   95.1    0.39 9.9E-06   29.5  18.1  225   92-325    82-333 (367)
 29 COG1422 Predicted membrane pro  91.1     1.5 3.9E-05   24.8  11.1   56  201-256    56-113 (201)
 30 cd01423 MGS_CPS_I_III Methylgl  82.6     3.3 8.4E-05   22.1   5.1   59  235-324    56-114 (116)
 31 cd01821 Rhamnogalacturan_acety  81.7     4.2 0.00011   21.3   5.3   67  263-339   106-172 (198)
 32 PRK05294 carB carbamoyl phosph  80.4     3.7 9.4E-05   21.8   4.7   79  216-330   972-1050(1063)
 33 cd00532 MGS-like MGS-like doma  80.2     2.5 6.3E-05   23.1   3.7   75  217-323    36-111 (112)
 34 pfam09580 Spore_YhcN_YlaJ Spor  78.9     5.5 0.00014   20.4   6.9  108  234-350    51-168 (169)
 35 TIGR01402 fliQ flagellar biosy  76.5     6.4 0.00016   19.9   5.9   37   77-113     3-39  (88)
 36 TIGR02198 rfaE_dom_I rfaE bifu  75.9     6.6 0.00017   19.7   6.0   58  256-330   137-195 (321)
 37 PRK02201 putative inner membra  74.5     7.1 0.00018   19.5   7.5   58  199-256   164-226 (392)
 38 cd01424 MGS_CPS_II Methylglyox  72.2     5.9 0.00015   20.2   3.9   74  216-325    36-109 (110)
 39 PRK09804 putative cryptic C4-d  71.4     3.7 9.5E-05   21.7   2.7   90  131-221   105-223 (455)
 40 COG1167 ARO8 Transcriptional r  71.2     8.1 0.00021   19.0   4.4   48  264-324   226-273 (459)
 41 KOG2568 consensus               70.2     8.7 0.00022   18.8   5.0   27  142-168   377-403 (518)
 42 PRK13954 mscL large-conductanc  68.6     9.4 0.00024   18.5   8.3   21  134-154     3-23  (120)
 43 pfam01276 OKR_DC_1 Orn/Lys/Arg  67.5     8.9 0.00023   18.7   4.0   17  200-216   275-291 (417)
 44 COG2074 2-phosphoglycerate kin  66.3     4.6 0.00012   21.0   2.3   25  302-326   256-280 (299)
 45 KOG3171 consensus               63.9      11 0.00029   17.9   3.9   79  221-310    95-188 (273)
 46 TIGR01088 aroQ 3-dehydroquinat  63.9     1.1 2.7E-05   26.1  -1.4   32  260-291    63-98  (144)
 47 COG4209 LplB ABC-type polysacc  63.3      12  0.0003   17.8   9.1   68  167-234   194-265 (309)
 48 COG1149 MinD superfamily P-loo  63.2     6.5 0.00016   19.8   2.6   81  257-339   178-267 (284)
 49 cd07362 HPCD_like Class III ex  62.6      12  0.0003   17.7   7.0   78  236-316    15-111 (272)
 50 PRK05700 fliQ flagellar biosyn  62.3      12 0.00031   17.7   5.8   38   77-114     3-40  (89)
 51 PRK03881 hypothetical protein;  61.4      12 0.00032   17.6   6.2   45  215-260   277-321 (467)
 52 KOG3925 consensus               60.8     9.8 0.00025   18.4   3.1   15  122-136   155-172 (371)
 53 PRK06010 fliQ flagellar biosyn  60.7      13 0.00033   17.5   5.8   38   77-114     3-40  (88)
 54 cd02987 Phd_like_Phd Phosducin  60.5     6.2 0.00016   19.9   2.1   86  213-311    16-113 (175)
 55 PRK09983 pflD putative formate  59.9      11 0.00027   18.1   3.2   16  221-236   544-559 (765)
 56 pfam02142 MGS MGS-like domain.  59.2     9.6 0.00024   18.5   2.9   64  217-315    24-91  (92)
 57 COG4998 Predicted endonuclease  59.0       8  0.0002   19.1   2.5   25  288-315    75-99  (209)
 58 KOG2262 consensus               59.0      14 0.00035   17.3   6.2   40  135-174   612-651 (761)
 59 PRK12781 fliQ flagellar biosyn  58.2      14 0.00036   17.2   5.7   37   78-114     4-40  (88)
 60 pfam02179 BAG BAG domain. Doma  57.6      11 0.00029   17.9   3.0   22  234-255    46-67  (76)
 61 PRK01318 putative inner membra  57.5      14 0.00037   17.1   7.7   10  121-130   398-407 (565)
 62 PRK12339 2-phosphoglycerate ki  57.4      10 0.00026   18.3   2.8   30  298-327   162-191 (197)
 63 TIGR01838 PHA_synth_I poly(R)-  57.4     8.6 0.00022   18.8   2.4   40  229-273    73-113 (541)
 64 PRK10654 dcuC C4-dicarboxylate  56.9      10 0.00026   18.2   2.7   26  196-221   198-223 (452)
 65 COG2870 RfaE ADP-heptose synth  56.2      11 0.00027   18.1   2.7   17  288-304   417-433 (467)
 66 TIGR02898 spore_YhcN_YlaJ spor  56.0      11 0.00029   17.8   2.8  114  231-347    53-181 (185)
 67 PRK04220 2-phosphoglycerate ki  56.0      10 0.00026   18.3   2.5   28  299-326   256-283 (306)
 68 PRK13955 mscL large-conductanc  55.1      16  0.0004   16.8   7.2   19  135-153     4-22  (130)
 69 cd07371 2A5CPDO_AB The alpha a  54.5      16 0.00041   16.7   7.8   26  291-316    81-106 (268)
 70 pfam02603 Hpr_kinase_N HPr Ser  53.6      10 0.00025   18.3   2.2   34  290-324    85-118 (127)
 71 smart00264 BAG BAG domains, pr  53.6      14 0.00036   17.1   3.0   32  225-256    40-71  (79)
 72 TIGR00693 thiE thiamine-phosph  53.3      17 0.00042   16.6   3.5   36  297-332    52-90  (210)
 73 PRK00191 tatA twin arginine tr  53.2      17 0.00042   16.6   3.5   50  200-250    13-62  (107)
 74 COG0399 WecE Predicted pyridox  53.0      10 0.00026   18.2   2.2   93  221-323   229-322 (374)
 75 COG1987 FliQ Flagellar biosynt  52.9      17 0.00043   16.5   5.9   37   78-114     4-40  (89)
 76 TIGR03470 HpnH hopanoid biosyn  52.9      14 0.00037   17.1   2.9   96  213-315    48-166 (318)
 77 TIGR00514 accC acetyl-CoA carb  52.7      17 0.00043   16.5   3.5   57  291-347     5-68  (451)
 78 pfam02114 Phosducin Phosducin.  52.6      11 0.00029   17.8   2.4   33  224-256    85-117 (265)
 79 PRK09331 Sep-tRNA:Cys-tRNA syn  52.5      17 0.00043   16.5   5.1   19  296-314   367-385 (386)
 80 pfam03796 DnaB_C DnaB-like hel  52.4      12  0.0003   17.8   2.4   68  240-322   115-182 (186)
 81 pfam01767 Birna_VP3 Birnavirus  52.1      11 0.00027   18.1   2.2   96  235-348    95-205 (229)
 82 PRK12337 2-phosphoglycerate ki  51.6     9.7 0.00025   18.4   1.9   90  239-329   338-464 (492)
 83 cd05534 POLBc_zeta DNA polymer  51.5      18 0.00045   16.4   3.6   50  286-349   392-446 (451)
 84 COG1493 HprK Serine kinase of   51.4      18 0.00045   16.4   3.4   34  290-324    85-118 (308)
 85 PRK10364 sensor protein ZraS;   50.4      18 0.00046   16.3   6.4   12  209-220   211-222 (455)
 86 cd01990 Alpha_ANH_like_I This   50.1      14 0.00037   17.1   2.6   83  265-352    96-185 (202)
 87 pfam05134 GspL General secreti  50.0      18 0.00047   16.2   8.2  116  194-312   215-342 (357)
 88 PRK11706 TDP-4-oxo-6-deoxy-D-g  49.9      12 0.00029   17.8   2.1   14  302-315   304-317 (375)
 89 TIGR03588 PseC UDP-4-keto-6-de  49.6      12 0.00031   17.6   2.1   26  289-314   298-323 (380)
 90 pfam03552 Cellulose_synt Cellu  49.1      19 0.00048   16.1   4.3  112  102-224   448-565 (716)
 91 TIGR01369 CPSaseII_lrg carbamo  48.6      19 0.00049   16.0   3.9   52  263-326  1036-1087(1089)
 92 PRK11658 UDP-4-amino-4-deoxy-L  48.2      14 0.00035   17.2   2.2   32  319-350   343-377 (379)
 93 PRK00145 putative inner membra  47.3      20 0.00051   15.9   8.1   15  220-234   207-221 (225)
 94 pfam02571 CbiJ Precorrin-6x re  46.0      20 0.00051   16.0   2.8   54  287-352   190-246 (246)
 95 pfam01741 MscL Large-conductan  45.9      21 0.00054   15.8   9.2   20  134-153     3-22  (127)
 96 PRK01315 putative inner membra  44.8      22 0.00056   15.6  10.1   18  196-213   227-244 (325)
 97 pfam01313 Bac_export_3 Bacteri  44.7      22 0.00056   15.6   5.0   33   82-114     5-37  (76)
 98 PRK02944 OxaA-like protein pre  44.6      22 0.00056   15.6   8.3   12  120-131    88-99  (255)
 99 TIGR03600 phage_DnaB phage rep  44.5      19 0.00048   16.1   2.5  165  134-338   189-370 (421)
100 TIGR01403 fliQ_rel_III type II  43.7      23 0.00058   15.5   5.0   27   47-73     15-41  (81)
101 PRK10333 putative ligase; Prov  43.5      15 0.00038   16.9   1.8   17  220-236     5-21  (198)
102 cd00984 DnaB_C DnaB helicase C  43.5      19 0.00049   16.1   2.4   56  264-326   123-178 (242)
103 COG1139 Uncharacterized conser  43.1      23 0.00059   15.4   5.5  101  220-336   153-266 (459)
104 cd01122 GP4d_helicase GP4d_hel  43.0      21 0.00053   15.8   2.5  156  134-323    25-193 (271)
105 PRK10964 ADP-heptose:LPS hepto  41.8     9.2 0.00024   18.6   0.5   25  256-280   245-272 (322)
106 PRK02654 putative inner membra  41.6      24 0.00062   15.3   8.2   30  207-236   328-357 (376)
107 pfam01220 DHquinase_II Dehydro  41.3     5.6 0.00014   20.3  -0.7   43  262-328    64-112 (140)
108 pfam01041 DegT_DnrJ_EryC1 DegT  41.1      21 0.00052   15.8   2.2   34  289-322   281-316 (363)
109 pfam00846 Hanta_nucleocap Hant  40.8      25 0.00063   15.2   5.2   15   13-27     19-33  (428)
110 cd03063 TRX_Fd_FDH_beta TRX-li  40.0      18 0.00047   16.2   1.8   26  292-317    12-39  (92)
111 PRK08506 replicative DNA helic  39.8      25 0.00064   15.1   2.5  149  134-324   188-356 (473)
112 cd07320 Extradiol_Dioxygenase_  39.7      26 0.00066   15.1   4.3   27  292-318    78-104 (260)
113 cd07370 HPCD The Class III ext  39.1      26 0.00067   15.0   7.0   68  250-320    34-119 (280)
114 KOG3663 consensus               39.1      26 0.00067   15.0   5.3   28  216-245    38-70  (518)
115 PRK08760 replicative DNA helic  39.0      26 0.00066   15.0   2.5  154  134-326   224-394 (476)
116 COG3069 DcuC C4-dicarboxylate   38.7      27 0.00068   15.0   3.9   36  199-238   200-236 (451)
117 PRK05395 3-dehydroquinate dehy  38.5     4.7 0.00012   20.9  -1.4   43  262-328    65-113 (143)
118 TIGR00739 yajC preprotein tran  38.4      27 0.00068   14.9   3.0   30  246-275    22-51  (86)
119 PRK05595 replicative DNA helic  38.1      27 0.00069   14.9   2.5  140  148-326   212-366 (444)
120 PRK01001 putative inner membra  38.1      27 0.00069   14.9   5.8   21   13-33    517-539 (791)
121 TIGR01601 PYST-C1 Plasmodium y  38.0      16 0.00041   16.7   1.3   12  158-169     9-20  (86)
122 cd01993 Alpha_ANH_like_II This  37.6      27 0.00069   14.9   2.4   21  298-318   158-178 (185)
123 COG1179 Dinucleotide-utilizing  37.5      28  0.0007   14.8   3.6   37  270-317   159-201 (263)
124 cd00466 DHQase_II Dehydroquina  37.5     6.7 0.00017   19.7  -0.7   18  263-280    64-84  (140)
125 pfam07905 PucR Purine cataboli  37.3      28 0.00071   14.8   3.7   22  298-319    85-106 (122)
126 PRK06904 replicative DNA helic  37.3      28 0.00071   14.8   2.5  156  133-325   215-388 (472)
127 KOG4186 consensus               37.3      28 0.00071   14.8   7.1   61  209-275   139-199 (233)
128 COG1671 Uncharacterized protei  37.0      28 0.00072   14.8   3.0   57  266-327    28-84  (150)
129 PRK13015 3-dehydroquinate dehy  36.5       7 0.00018   19.5  -0.8   45  262-330    65-115 (148)
130 PRK08840 replicative DNA helic  36.5      29 0.00073   14.7   2.5  162  125-326   205-384 (464)
131 TIGR00018 panC pantoate--beta-  35.8      21 0.00053   15.8   1.5   73  240-327     8-104 (310)
132 COG4794 EscS Type III secretor  35.7      29 0.00075   14.6   5.3   34   80-113     6-39  (89)
133 PRK10902 FKBP-type peptidyl-pr  35.5      30 0.00075   14.6   8.2  114  150-271     2-145 (270)
134 pfam07085 DRTGG DRTGG domain.   35.3      17 0.00043   16.5   1.0   60  254-318    30-92  (105)
135 PRK10929 hypothetical protein;  35.2      30 0.00076   14.6  10.2   17  201-217   682-698 (1109)
136 cd07646 I-BAR_IMD_IRSp53 Inver  35.2      30 0.00076   14.5   6.2   44  127-178    17-60  (232)
137 pfam08423 Rad51 Rad51. Rad51 i  35.0      30 0.00076   14.5   3.9   38  236-273   155-192 (261)
138 pfam08664 YcbB YcbB domain. Yc  34.9      28 0.00072   14.8   2.1   63  183-245    61-123 (133)
139 cd01677 PFL2_DhaB_BssA Pyruvat  34.9      30 0.00077   14.5   3.7   44  295-347   348-391 (781)
140 COG0771 MurD UDP-N-acetylmuram  34.8      30 0.00077   14.5   2.9   21  221-241   290-310 (448)
141 pfam11803 UXS1_N UDP-glucurona  34.8      30 0.00077   14.5   3.8   60  195-255    16-75  (78)
142 PRK02463 OxaA-like protein pre  34.7      30 0.00077   14.5   7.5   12  226-237   256-267 (307)
143 PRK06321 replicative DNA helic  34.5      31 0.00078   14.5   2.5   30  296-325   364-393 (472)
144 PRK05748 replicative DNA helic  34.3      31 0.00078   14.5   2.5  143  147-326   213-370 (448)
145 PRK04531 acetylglutamate kinas  33.9      31 0.00079   14.4   2.2   71  221-296   203-274 (421)
146 PRK04654 sec-independent trans  33.9      31  0.0008   14.4   5.1   65  217-281    34-114 (214)
147 TIGR02644 Y_phosphoryl pyrimid  33.7      17 0.00044   16.4   0.9   91   55-151    51-144 (425)
148 PRK05428 HPr kinase/phosphoryl  33.5      32 0.00081   14.4   2.8   36  290-326    86-121 (308)
149 cd06325 PBP1_ABC_uncharacteriz  33.2      14 0.00036   17.2   0.3   19  299-317   199-217 (281)
150 PRK12311 rpsB 30S ribosomal pr  32.9      32 0.00082   14.3   4.0   62  229-316   119-187 (332)
151 cd06811 PLPDE_III_yhfX_like Ty  32.9      32 0.00082   14.3   4.2   45  267-316   185-230 (382)
152 PRK05636 replicative DNA helic  32.6      33 0.00083   14.3   2.5   56  264-326   377-432 (507)
153 PRK09165 replicative DNA helic  32.5      33 0.00083   14.2   2.5   29  296-324   356-384 (484)
154 PRK05771 V-type ATP synthase s  32.4      33 0.00083   14.2  17.0   57    8-64    311-375 (640)
155 pfam07817 GLE1 GLE1-like prote  32.2      26 0.00066   15.0   1.6   24   10-33     17-45  (249)
156 COG2082 CobH Precorrin isomera  32.2      27 0.00069   14.9   1.6   87  232-318    93-186 (210)
157 PRK08082 consensus              32.1      33 0.00084   14.2   2.5  142  147-326   213-369 (453)
158 PRK10062 hypothetical protein;  32.0      33 0.00085   14.2   8.0   76  134-210   209-293 (303)
159 TIGR00868 hCaCC calcium-activa  31.9      23 0.00059   15.4   1.3   13  261-273    98-110 (874)
160 cd01825 SGNH_hydrolase_peri1 S  31.6      34 0.00086   14.1   5.3   84  257-348    89-183 (189)
161 pfam10686 DUF2493 Protein of u  31.6      27 0.00069   14.9   1.6   24  293-319    42-65  (71)
162 pfam12174 RST RST domain of pl  31.5      34 0.00086   14.1   4.7   45  207-251    25-69  (70)
163 pfam02639 DUF188 Uncharacteriz  31.3      34 0.00087   14.1   2.9   58  265-327    12-69  (130)
164 PRK07449 2-succinyl-6-hydroxy-  31.3      34 0.00087   14.1   3.9   27  289-315   425-453 (548)
165 PRK07263 consensus              31.2      34 0.00087   14.1   2.5  140  148-326   214-369 (453)
166 COG0052 RpsB Ribosomal protein  30.9      35 0.00088   14.0   3.1   66  209-275    89-168 (252)
167 TIGR00853 pts-lac PTS system,   30.7      35 0.00089   14.0   2.3   20  296-315    59-78  (142)
168 cd00453 FTBP_aldolase_II Fruct  30.6      35 0.00089   14.0   2.7   18  120-137   122-139 (340)
169 cd07359 PCA_45_Doxase_B_like S  30.6      35 0.00089   14.0   8.0   30  287-316    84-113 (271)
170 cd00616 AHBA_syn 3-amino-5-hyd  30.1      36 0.00091   13.9   2.3   17  299-315   281-297 (352)
171 PRK02870 heat shock protein Ht  29.9      36 0.00091   13.9   7.6   18  235-252   263-281 (338)
172 PRK08694 consensus              29.6      36 0.00092   13.9   2.5  156  133-325   212-384 (468)
173 PRK06749 replicative DNA helic  29.4      36 0.00093   13.9   2.5   30  296-325   325-354 (428)
174 TIGR01478 STEVOR variant surfa  29.2      37 0.00094   13.8   6.6   71  138-222   234-305 (315)
175 PRK11172 dkgB 2,5-diketo-D-glu  28.9      12 0.00031   17.7  -0.6   51  302-352   163-214 (267)
176 TIGR01265 tyr_nico_aTase tyros  28.8      37 0.00095   13.8   2.2   48  257-319   178-225 (424)
177 PRK08006 replicative DNA helic  28.8      37 0.00095   13.8   2.5   67  241-326   322-391 (471)
178 pfam02404 SCF Stem cell factor  28.7     8.2 0.00021   19.0  -1.5   28  125-155   130-157 (273)
179 TIGR01740 pyrF orotidine 5'-ph  28.6      23 0.00059   15.4   0.8   36  286-321    31-66  (233)
180 PRK12737 gatY tagatose-bisphos  28.6      38 0.00096   13.8   2.9   61  288-349   203-270 (284)
181 TIGR02223 ftsN cell division p  28.3      38 0.00097   13.7   2.1   49    1-51      1-49  (354)
182 pfam07862 Nif11 Nitrogen fixat  28.3      38 0.00097   13.7   3.2   26  224-249     1-26  (49)
183 COG0757 AroQ 3-dehydroquinate   28.3     7.4 0.00019   19.3  -1.8   19  263-281    65-86  (146)
184 PRK06683 hypothetical protein;  28.2      38 0.00097   13.7   4.1   42  288-330    29-71  (82)
185 TIGR02024 FtcD glutamate formi  28.1      36 0.00091   13.9   1.7   17  301-317   254-270 (331)
186 TIGR02469 CbiT precorrin-6Y C5  28.0      26 0.00065   15.1   1.0   20  290-309   102-121 (135)
187 PRK07004 replicative DNA helic  27.7      39 0.00099   13.7   2.5  163  125-327   201-380 (460)
188 KOG2927 consensus               27.6      39 0.00099   13.6   6.3   90  130-219   156-279 (372)
189 cd00615 Orn_deC_like Ornithine  27.6      39 0.00099   13.6   3.9   76  199-318   111-190 (294)
190 pfam10881 DUF2726 Protein of u  27.5      39   0.001   13.6   6.7   61  251-318    47-109 (127)
191 PRK10916 ADP-heptose:LPS hepto  27.5      12 0.00031   17.7  -0.8   24  257-280   254-280 (348)
192 PRK13602 putative ribosomal pr  27.4      39   0.001   13.6   4.0   34  287-320    28-62  (82)
193 pfam04392 ABC_sub_bind ABC tra  27.4      18 0.00046   16.3   0.1   21  133-153   107-127 (292)
194 COG3384 Aromatic ring-opening   27.4      39   0.001   13.6   4.1   52  264-315    43-110 (268)
195 KOG0253 consensus               27.3      14 0.00037   17.1  -0.4   39  274-314   242-281 (528)
196 TIGR01461 greB transcription e  27.3      29 0.00073   14.7   1.1   47  277-334    91-137 (157)
197 pfam01171 ATP_bind_3 PP-loop f  27.3      39   0.001   13.6   2.5   23  297-319   146-168 (182)
198 PRK12338 hypothetical protein;  27.1      31  0.0008   14.4   1.3   74  238-314   159-234 (320)
199 COG2055 Malate/L-lactate dehyd  27.0      40   0.001   13.6   4.0   23  297-319   311-333 (349)
200 PRK09130 NADH dehydrogenase su  27.0      25 0.00064   15.1   0.8   15  301-315   588-602 (680)
201 TIGR01520 FruBisAldo_II_A fruc  26.8      36 0.00092   13.9   1.5   23  294-316    86-108 (365)
202 TIGR02617 tnaA_trp_ase tryptop  26.4      40   0.001   13.5   1.7   18  301-318   207-224 (468)
203 pfam03841 SelA L-seryl-tRNA se  26.2      41   0.001   13.5   2.3   27  126-152   142-169 (367)
204 pfam05661 DUF808 Protein of un  26.1      41   0.001   13.4   7.3   33  135-168   209-242 (293)
205 PRK12815 carB carbamoyl phosph  26.0      41  0.0011   13.4   3.6   30  299-328  1019-1048(1068)
206 cd00145 POLBc DNA polymerase t  25.9      42  0.0011   13.4   3.7   16  286-301   272-287 (323)
207 pfam12023 DUF3511 Domain of un  25.8      37 0.00094   13.8   1.4   13  237-249     3-15  (47)
208 pfam12226 Astro_capsid_p Turke  25.8      23  0.0006   15.4   0.4   17  226-242   113-129 (230)
209 PRK11091 aerobic respiration c  25.7      42  0.0011   13.4  10.9   16  144-159   402-417 (779)
210 pfam01956 DUF106 Integral memb  25.7      42  0.0011   13.4   5.6   23   11-33     48-70  (168)
211 TIGR02237 recomb_radB DNA repa  25.5      42  0.0011   13.4   4.6   64  235-304   119-183 (223)
212 PRK05575 cbiC precorrin-8X met  25.4      42  0.0011   13.4   2.8   82  237-318    98-184 (204)
213 pfam07964 Red1 Rec10 / Red1. R  25.1      39   0.001   13.6   1.5   21  236-256   342-362 (705)
214 TIGR03239 GarL 2-dehydro-3-deo  24.9      30 0.00077   14.5   0.9   63  257-325   155-220 (249)
215 PRK11316 bifunctional heptose   24.8      43  0.0011   13.3   2.4   11  289-299   426-436 (473)
216 COG1320 MnhG Multisubunit Na+/  24.8      43  0.0011   13.3   6.2   37  203-239    77-113 (113)
217 PRK00124 hypothetical protein;  24.8      43  0.0011   13.3   2.9   39  289-327    45-83  (149)
218 PRK12587 putative monovalent c  24.7      43  0.0011   13.3   6.9   32  208-239    84-115 (118)
219 cd01701 Pol_zeta Pol_zeta, a m  24.7      38 0.00097   13.7   1.3   33  236-268   303-335 (405)
220 TIGR01326 OAH_OAS_sulfhy O-ace  24.6      44  0.0011   13.2   2.2   16  302-317   164-181 (434)
221 COG5337 CotH Spore coat assemb  24.6      38 0.00096   13.7   1.3  111  209-340    47-174 (473)
222 cd07644 I-BAR_IMD_BAIAP2L2 Inv  24.5      44  0.0011   13.2   6.1   26  127-160    15-40  (215)
223 COG3977 Alanine-alpha-ketoisov  24.2      44  0.0011   13.2   2.5   19  216-234   342-360 (417)
224 pfam03342 Rhabdo_M1 Rhabdoviru  24.1      43  0.0011   13.3   1.5   14  102-115   127-140 (219)
225 PRK09195 gatY tagatose-bisphos  24.1      45  0.0011   13.2   3.0   61  287-348   202-269 (284)
226 pfam00606 Glycoprotein_B Herpe  24.0      45  0.0011   13.2   6.1   23  132-156   621-643 (711)
227 pfam06305 DUF1049 Protein of u  23.9      45  0.0011   13.1   4.9   33  205-237    45-77  (80)
228 cd01123 Rad51_DMC1_radA Rad51_  23.8      45  0.0012   13.1   4.0   37  236-272   132-168 (235)
229 cd06452 SepCysS Sep-tRNA:Cys-t  23.7      45  0.0012   13.1   2.6   57  288-349   302-359 (361)
230 PRK09554 feoB ferrous iron tra  23.7      45  0.0012   13.1   3.2   35  182-216   498-532 (772)
231 PRK10506 hypothetical protein;  23.6      45  0.0012   13.1   3.7   40  190-229     7-46  (155)
232 PRK13601 putative ribosomal pr  23.4      46  0.0012   13.1   4.2   43  286-329    25-68  (84)
233 TIGR02317 prpB methylisocitrat  23.4      46  0.0012   13.1   2.3   18   16-33      2-19  (287)
234 cd00946 FBP_aldolase_IIA Class  23.2      46  0.0012   13.1   2.5   29  286-315   244-272 (345)
235 cd05533 POLBc_delta DNA polyme  22.9      47  0.0012   13.0   4.0   54  286-349   339-392 (393)
236 pfam10785 NADH-u_ox-rdase NADH  22.8      28 0.00072   14.8   0.4   53  203-256    51-111 (148)
237 COG1929 Glycerate kinase [Carb  22.7      34 0.00086   14.1   0.7   44  258-316   278-321 (378)
238 COG5384 Mpp10 U3 small nucleol  22.6      47  0.0012   13.0   4.3   16  220-235   488-503 (569)
239 COG0410 LivF ABC-type branched  22.5      16 0.00041   16.7  -0.9  104  213-326    90-205 (237)
240 pfam02064 MAS20 MAS20 protein   22.5      48  0.0012   13.0   6.3   17  332-348   136-152 (184)
241 KOG0140 consensus               22.4      48  0.0012   12.9   4.0   84  261-347   243-348 (408)
242 PRK00404 tatB sec-independent   22.3      48  0.0012   12.9   4.9   31  217-247    34-64  (141)
243 PRK09440 avtA valine--pyruvate  22.3      48  0.0012   12.9   2.0   48  261-320   324-372 (416)
244 pfam01567 Hanta_G1 Hantavirus   21.8      49  0.0012   12.9   5.4   39  201-239   504-542 (542)
245 PRK10422 lipopolysaccharide co  21.7      18 0.00046   16.3  -0.8   24  257-280   255-281 (352)
246 PRK06988 putative formyltransf  21.6      49  0.0013   12.8   4.1   11  124-134   110-120 (313)
247 PRK05797 consensus              21.6      48  0.0012   12.9   1.3   62  261-325   514-575 (869)
248 TIGR00973 leuA_bact 2-isopropy  21.4      50  0.0013   12.8   1.6   11  220-230   111-121 (514)
249 KOG3637 consensus               21.3      44  0.0011   13.3   1.1   44  195-238   981-1024(1030)
250 pfam03839 Sec62 Translocation   21.2      50  0.0013   12.8   5.9   27  207-235   182-208 (217)
251 TIGR02432 lysidine_TilS_N tRNA  21.1      50  0.0013   12.7   2.2   17  302-318   170-186 (204)
252 pfam09659 Cas_Csm6 CRISPR-asso  21.0      51  0.0013   12.7   3.0   25    4-28    105-129 (382)
253 TIGR01957 nuoB_fam NADH-quinon  21.0      51  0.0013   12.7   2.5   32  264-295    57-92  (146)
254 cd00922 Cyt_c_Oxidase_IV Cytoc  20.8      51  0.0013   12.7   3.7   12  127-138   121-132 (136)
255 COG0859 RfaF ADP-heptose:LPS h  20.8      40   0.001   13.5   0.8   23  257-279   244-269 (334)
256 PRK07568 aspartate aminotransf  20.6      52  0.0013   12.7   1.7   25  131-155   170-194 (396)
257 KOG4403 consensus               20.5      52  0.0013   12.7   5.6   29  222-250   237-265 (575)
258 TIGR01122 ilvE_I branched-chai  20.5      52  0.0013   12.7   1.3   25  302-327   218-243 (302)
259 PRK05299 rpsB 30S ribosomal pr  20.5      52  0.0013   12.7   5.6   34  257-316   152-185 (255)
260 pfam03806 ABG_transport AbgT p  20.4      52  0.0013   12.6   8.0   16   24-41      8-23  (502)
261 pfam07230 Phage_T4_Gp20 Bacter  20.3      52  0.0013   12.6   2.8   29  210-238   471-499 (500)
262 pfam01075 Glyco_transf_9 Glyco  20.3      19 0.00048   16.1  -0.9   22  258-279   179-203 (249)
263 pfam11657 Activator-TraM Trans  20.3      52  0.0013   12.6   1.4   17   19-35      9-25  (144)
264 PRK10558 alpha-dehydro-beta-de  20.1      45  0.0011   13.2   0.9   64  257-326   162-228 (256)

No 1  
>TIGR00328 flhB flagellar biosynthetic protein FlhB; InterPro: IPR006136   The flhB and flhA genes constitute an operon called flhB operon on the Salmonella typhimurium chromosome. They, together with FliI and FliH, may constitute the export apparatus of flagellin, the component protein of flagellar filament. The flhB gene encodes a highly hydrophobic polypeptide with several potential membrane-spanning segments, suggesting that it may be an integral membrane protein .; GO: 0009306 protein secretion, 0016020 membrane.
Probab=100.00  E-value=0  Score=953.82  Aligned_cols=346  Identities=35%  Similarity=0.575  Sum_probs=337.5

Q ss_pred             CCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH
Q ss_conf             77686658787999998578751335999999999999999999999999999999997200012104979899999999
Q gi|254780690|r    8 DNKTEAPSSKKIEDALNEGNAPISREASLFSSILACLIYLLFFFSPGIYSVTSDLHVLLASATQRKLEDISHIVFLLTHL   87 (354)
Q Consensus         8 ~eKTE~PT~kRL~dARekGqV~kS~el~~~~~ll~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (354)
                      |||||+|||||++|||||||||+|+|++++++|++++..++++++.++.+....+...+.+....+..+...+...+...
T Consensus         1 ~eKTE~PT~kk~~~AReeG~V~~S~E~~~~~~ll~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (352)
T TIGR00328         1 EEKTEEPTPKKLRKAREEGNVPKSREVNTAAVLLAGVLVLLFFGSEGLADLLEALMSFFLSLETSDLLELESLVEIIIEL   80 (352)
T ss_pred             CCCCCCCCHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH
T ss_conf             99887776347888875089875311999999999999999988999999999999987532335531479999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCCCCH--HHHHHH-CCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999988776878532101371213779101693--430332-01266799999999999999999999
Q gi|254780690|r   88 SLSASRLVIPGLLLFMMFGIGSYLIQRIPVLNLNHVKPSFKRVSL--REGIKR-IYSINNLVNFMKSFVKIILVGTIITI  164 (354)
Q Consensus        88 ~~~~~~~~~p~~~~~~l~~i~~~l~q~G~~fs~k~l~pk~~rlNP--i~GlKr-iFS~k~lvel~KsllKv~li~~v~~~  164 (354)
                      ....+..++|+++.++++|++++++|+||+||+|+|+|||+||||  ++|+|| |||.+++||++||++|+.++|+++|+
T Consensus        81 ~~~~~~~llp~~~~~l~~g~~~~~~Q~G~~ft~k~l~Pk~~KiNP~~~~G~KRS~FS~~~lvEl~Ks~lKv~lv~~v~~~  160 (352)
T TIGR00328        81 IREVLLLLLPILVLLLVVGVLSNILQTGFLFTTKPLKPKLSKINPDVIKGLKRSLFSLQSLVELLKSILKVFLVSLVAYF  160 (352)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999998887302334354666767588768866768777788999999999999999999999


Q ss_pred             HHHHCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCHHHHH
Q ss_conf             99832156897840897999999999999999999999999999766799999998406998999999754489989999
Q gi|254780690|r  165 SLTENYFTMLDFISANPHSILYHAFFTVRKVLIMILLFIATLTVLDIGWSYHQWYSKLKMSKQEIKDEIKQSYGNPIIKN  244 (354)
Q Consensus       165 ~i~~~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD~~~qr~~~~k~lkMskqEvK~E~K~~EGdP~iK~  244 (354)
                      +++++++++..+...++.+.+..+.+...++++.++++++++|++||+||||+|.|+||||||||||||||+||||+|||
T Consensus       161 ~l~~~~~~~~~L~~~~~~~~~~~~~~~~~~~~~~v~~~l~~~a~~D~~~qr~~y~~~LkMtkQEvKdE~Kq~EGdP~vKg  240 (352)
T TIGR00328       161 VLKNSLGELLSLSLYSLQQALTNALDLALSLLLLVLLLLLVIAVFDYFFQRWQYIKSLKMTKQEVKDELKQSEGDPEVKG  240 (352)
T ss_pred             HHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCHHH
T ss_conf             99865889998861488899999999999999999999999999869999999987236776888777412694844368


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHHH
Q ss_conf             99999999999889860776869987355307888976888888889980765899999999997399788688999999
Q gi|254780690|r  245 RQKSIARSRIRHKMMEATSRATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSL  324 (354)
Q Consensus       245 ~~r~~~re~~~~~~~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~L  324 (354)
                      ||||+|||++++|||++||+||||||||||||||||||+|+|+||+|||||.|++|+||||+|+||||||+|||||||+|
T Consensus       241 RiRq~qr~~ar~rMm~~VPkAdVvITNPTHyAVALkY~~~~m~AP~VVAKG~D~~AlkI~eiA~en~v~~~e~PpLARaL  320 (352)
T TIGR00328       241 RIRQMQREAARRRMMQEVPKADVVITNPTHYAVALKYDPGKMKAPVVVAKGVDELALKIKEIAEENNVPIVENPPLARAL  320 (352)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEEECCCEEEEEEEECCCCCCCCEEEECCCCHHHHHHHHHHHHCCCCEECCCHHHHHH
T ss_conf             89999999999999874468978963760134556414888988877877885688999999988691144087358752


Q ss_pred             HHHCCCCCCCCHHHHHHHHHHHHHHHHHC
Q ss_conf             97288989489899999999999997302
Q gi|254780690|r  325 FKQVPINSAIPPVFYKAVAQLIYKIYHKK  353 (354)
Q Consensus       325 y~~~~ig~~Ip~~~y~aVA~il~~v~~lk  353 (354)
                      |++|||||+||+|||+||||||+|||++|
T Consensus       321 Y~~veig~~IP~~ly~AVAeVLa~Vy~l~  349 (352)
T TIGR00328       321 YRQVEIGQEIPVELYKAVAEVLAYVYKLK  349 (352)
T ss_pred             HHHCCCCCCCCHHHHHHHHHHHHHHHHHC
T ss_conf             11054766467679999999999999724


No 2  
>PRK13109 flhB flagellar biosynthesis protein FlhB; Reviewed
Probab=100.00  E-value=0  Score=890.61  Aligned_cols=353  Identities=37%  Similarity=0.655  Sum_probs=335.5

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH
Q ss_conf             99876787768665878799999857875133599999999999999999999999999999999720001210497989
Q gi|254780690|r    1 MSENDAPDNKTEAPSSKKIEDALNEGNAPISREASLFSSILACLIYLLFFFSPGIYSVTSDLHVLLASATQRKLEDISHI   80 (354)
Q Consensus         1 MAe~d~~~eKTE~PT~kRL~dARekGqV~kS~el~~~~~ll~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~   80 (354)
                      |||+||+|||||+||||||+|||||||||||+|+++++++++++++++++++.....+...+...+.+..+.......+.
T Consensus         1 Mae~~d~eeKTE~PT~kRL~~ARekGqVakS~El~~~~~ll~~l~~l~~~~~~~~~~l~~~~~~~l~~~~~~~~~~~~~~   80 (358)
T PRK13109          1 MSDDTDKESKTEEPTERKVRDAIEKGDIPVSREASIFASMLGLLIILAFFARGQVAQLTRDLAPLLDDPRGFTLETGADA   80 (358)
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHH
T ss_conf             99899999989999857899999679996578699999999999999999999999999999999827400242215659


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999887768785321013712137791016934303320126679999999999999999
Q gi|254780690|r   81 VFLLTHLSLSASRLVIPGLLLFMMFGIGSYLIQRIPVLNLNHVKPSFKRVSLREGIKRIYSINNLVNFMKSFVKIILVGT  160 (354)
Q Consensus        81 ~~~~~~~~~~~~~~~~p~~~~~~l~~i~~~l~q~G~~fs~k~l~pk~~rlNPi~GlKriFS~k~lvel~KsllKv~li~~  160 (354)
                      ...+..+......+++|+++++++++++++++|+||+||+|+++|||+||||++|+|||||.++++||+|+++|++++++
T Consensus        81 ~~~~~~~~~~~~~~l~P~~~~~~v~~i~~~~~Q~G~~fs~k~l~Pk~~kLNPi~GlKriFS~~~Lvel~KsllK~~~l~~  160 (358)
T PRK13109         81 ILLLSRVGLAAGRFLLPILLVLAVAGLAASLLQNLPRFVLDRIQPKWSRISPMKGWTRIFGTQGQVEFAKSLFKFLSVSV  160 (358)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEECCCCCCCCHHHCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999999999999986014030541268876765973505654258789999999999999999


Q ss_pred             HHHHHHHHCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCH
Q ss_conf             99999983215689784089799999999999999999999999999976679999999840699899999975448998
Q gi|254780690|r  161 IITISLTENYFTMLDFISANPHSILYHAFFTVRKVLIMILLFIATLTVLDIGWSYHQWYSKLKMSKQEIKDEIKQSYGNP  240 (354)
Q Consensus       161 v~~~~i~~~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD~~~qr~~~~k~lkMskqEvK~E~K~~EGdP  240 (354)
                      ++|++++++++.+..+..+++.+.+..+.+.+..+++.++++++++|++||+||||+|.|+||||||||||||||+||||
T Consensus       161 v~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~via~~D~~~Qr~~~~k~lkMskqEvK~E~K~~EGdP  240 (358)
T PRK13109        161 VVLLLLRSERAKAVNAMFVDPSALPELILTVAMRLVSAVSIATIVLVALDLVWARFHWRRSLRMTKQEIKDEHKQAEGDP  240 (358)
T ss_pred             HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCH
T ss_conf             99999998899999987448999999999999999999999999999999999999999864899999999988663999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHH
Q ss_conf             99999999999999988986077686998735530788897688888888998076589999999999739978868899
Q gi|254780690|r  241 IIKNRQKSIARSRIRHKMMEATSRATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSL  320 (354)
Q Consensus       241 ~iK~~~r~~~re~~~~~~~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~L  320 (354)
                      |||+||||+|||+++++|+++||+||||||||||||||||||+++++||+|||||+|++|++||++|+||||||+|||||
T Consensus       241 ~iK~r~R~~~re~a~~~m~~~V~~AdvVitNPTH~AVAL~Y~~~~~~aP~VvAKG~d~~A~~Ir~~A~~~~VPive~~pL  320 (358)
T PRK13109        241 SVKARLRSLAQDRARNRMLAAVPRATLVIANPTHFAIALRYERSENPAPLVVAKGQDLIALKIREIAERNGIPVIEDKPL  320 (358)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEECCHHH
T ss_conf             99999999999999877872589883899888715677666689999998888458699999999999879978707899


Q ss_pred             HHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHC
Q ss_conf             999997288989489899999999999997302
Q gi|254780690|r  321 ARSLFKQVPINSAIPPVFYKAVAQLIYKIYHKK  353 (354)
Q Consensus       321 AR~Ly~~~~ig~~Ip~~~y~aVA~il~~v~~lk  353 (354)
                      ||+||++||+||+||+|+|+|||+||+|||++|
T Consensus       321 ARaLy~~~~vg~~IP~~ly~aVA~iLa~vy~~~  353 (358)
T PRK13109        321 ARSLYDAVQVDQVIPAEFYRPVAEILYFLFSRA  353 (358)
T ss_pred             HHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             999997077899689999999999999999743


No 3  
>PRK05702 flhB flagellar biosynthesis protein FlhB; Reviewed
Probab=100.00  E-value=0  Score=889.68  Aligned_cols=351  Identities=36%  Similarity=0.557  Sum_probs=339.5

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH
Q ss_conf             99876787768665878799999857875133599999999999999999999999999999999720001210497989
Q gi|254780690|r    1 MSENDAPDNKTEAPSSKKIEDALNEGNAPISREASLFSSILACLIYLLFFFSPGIYSVTSDLHVLLASATQRKLEDISHI   80 (354)
Q Consensus         1 MAe~d~~~eKTE~PT~kRL~dARekGqV~kS~el~~~~~ll~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~   80 (354)
                      |||+| +|||||+||||||+|||||||||+|+|+++++++++++++++++++....++...+...+........ +...+
T Consensus         1 Mae~~-~~eKTE~PT~kKL~dARekGqV~kS~el~~a~~l~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~-~~~~~   78 (352)
T PRK05702          1 MAEDS-DQEKTEEPTPKKLEKAREKGQVPRSRELNTAAVLLAGLVGLWFFGGSLARRLAGMLRALFSFDREIAF-DPNDM   78 (352)
T ss_pred             CCCCC-CCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC-CHHHH
T ss_conf             99889-99989999857899999768987668699999999999999999999999999999999835441247-86899


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999887768785321013712137791016934303320126679999999999999999
Q gi|254780690|r   81 VFLLTHLSLSASRLVIPGLLLFMMFGIGSYLIQRIPVLNLNHVKPSFKRVSLREGIKRIYSINNLVNFMKSFVKIILVGT  160 (354)
Q Consensus        81 ~~~~~~~~~~~~~~~~p~~~~~~l~~i~~~l~q~G~~fs~k~l~pk~~rlNPi~GlKriFS~k~lvel~KsllKv~li~~  160 (354)
                      ...+...+...+..++|+++++++++++++++|+||+||+|+++|||+||||++|+|||||.++++|++||++|++++++
T Consensus        79 ~~~~~~~~~~~~~~~~p~~~~~~~~~i~~~~~Q~G~~fs~k~l~pk~~rlNPi~GlKriFS~k~LvEl~KsllKv~~i~~  158 (352)
T PRK05702         79 LSLFGLLILELLLALLPILLLLVLAALLAPILQGGWLFSGKALKPKFSKLNPLKGLKRMFSAQGLVELLKSLLKVLLVGG  158 (352)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHCCHHHCHHHHCCHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999999999999998527451642478884654972452312088899999999999999999


Q ss_pred             HHHHHHHHCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCH
Q ss_conf             99999983215689784089799999999999999999999999999976679999999840699899999975448998
Q gi|254780690|r  161 IITISLTENYFTMLDFISANPHSILYHAFFTVRKVLIMILLFIATLTVLDIGWSYHQWYSKLKMSKQEIKDEIKQSYGNP  240 (354)
Q Consensus       161 v~~~~i~~~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD~~~qr~~~~k~lkMskqEvK~E~K~~EGdP  240 (354)
                      ++|++++++++.+..+..+++.+.+..+.+++..+++.++++++++|++||+||||+|+|+||||||||||||||+||||
T Consensus       159 v~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~via~~D~~~qr~~~~k~lkMSkqEvKdE~K~~EGdP  238 (352)
T PRK05702        159 VAYFVLWSNLDELLSLAALPLEAALGHALDLVLKLLLLVVLALLVIAAIDVPFQRWQYLKKLKMTKQEVKDEYKQSEGDP  238 (352)
T ss_pred             HHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCH
T ss_conf             99999999999999885389999999999999999999999999999999999999999883899999999998652999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHH
Q ss_conf             99999999999999988986077686998735530788897688888888998076589999999999739978868899
Q gi|254780690|r  241 IIKNRQKSIARSRIRHKMMEATSRATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSL  320 (354)
Q Consensus       241 ~iK~~~r~~~re~~~~~~~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~L  320 (354)
                      |||+||||+|||+++++|+++||+||||||||||||||||||+++++||+|||||+|++|++||++|++|||||+|||||
T Consensus       239 ~iK~~~R~~~re~a~~~m~~~V~~A~vVItNPTH~AVAL~Y~~~~~~aP~VvAKG~d~~A~~Ir~~A~~~~VPive~~pL  318 (352)
T PRK05702        239 EVKGRIRQLQREMARRRMMAAVPKADVVITNPTHYAVALKYDRGKMAAPVVVAKGVDEVALRIREIAREHNVPIVENPPL  318 (352)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHH
T ss_conf             99999999999999867873388797899999862899887889999998877458699999999999869988747899


Q ss_pred             HHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHC
Q ss_conf             999997288989489899999999999997302
Q gi|254780690|r  321 ARSLFKQVPINSAIPPVFYKAVAQLIYKIYHKK  353 (354)
Q Consensus       321 AR~Ly~~~~ig~~Ip~~~y~aVA~il~~v~~lk  353 (354)
                      ||+||++||+||+||+|+|+|||+||+|||++|
T Consensus       319 ARaLy~~~~vg~~IP~~ly~aVA~il~~v~~lk  351 (352)
T PRK05702        319 ARALYATVEVGQEIPEELYKAVAEVLAYVYQLK  351 (352)
T ss_pred             HHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHC
T ss_conf             999997378999589999999999999999852


No 4  
>PRK12772 bifunctional flagellar biosynthesis protein FliR/FlhB; Provisional
Probab=100.00  E-value=0  Score=887.93  Aligned_cols=346  Identities=31%  Similarity=0.495  Sum_probs=334.4

Q ss_pred             CCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHH
Q ss_conf             87768665878799999857875133599999999999999999999999999999999720001210497989999999
Q gi|254780690|r    7 PDNKTEAPSSKKIEDALNEGNAPISREASLFSSILACLIYLLFFFSPGIYSVTSDLHVLLASATQRKLEDISHIVFLLTH   86 (354)
Q Consensus         7 ~~eKTE~PT~kRL~dARekGqV~kS~el~~~~~ll~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (354)
                      ||||||+||||||+|||||||||||||++++++++++++.+.++++....++.+.+...+....+... +...+...+..
T Consensus       262 sdEKTE~pTpKkl~dARkkGqVakS~el~~a~~ll~~~~~l~~~g~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~  340 (609)
T PRK12772        262 SDDKTEEATPKKKSDARKKGQVAKSKEVALAITLLACTLVLSALGEYVANTLKETMIYFLNNYLNMNL-NYLNLNSLIIF  340 (609)
T ss_pred             CCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CHHHHHHHHHH
T ss_conf             87778999815699898578987727499999999999999999999999999999999853300247-87889999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999887768785321013712137791016934303320126679999999999999999999999
Q gi|254780690|r   87 LSLSASRLVIPGLLLFMMFGIGSYLIQRIPVLNLNHVKPSFKRVSLREGIKRIYSINNLVNFMKSFVKIILVGTIITISL  166 (354)
Q Consensus        87 ~~~~~~~~~~p~~~~~~l~~i~~~l~q~G~~fs~k~l~pk~~rlNPi~GlKriFS~k~lvel~KsllKv~li~~v~~~~i  166 (354)
                      .......+++|+++++++++++++++|+||+||+|+++||++||||++|+|||||.|+++|++||++|++++|.++|+++
T Consensus       341 ~~~~~~~~~~P~~~~~~~~~i~a~~~Q~G~~fs~~~l~Pk~~klnPi~G~KriFS~~~l~El~KsllK~~~v~~v~y~~~  420 (609)
T PRK12772        341 TLLRVGKIFLPVALPIMVFGIAANLLQTGFLFTKEPLKPDLKKLNPINGFKRMFSMRTVMELLKDLVIITVVGIVGYKFL  420 (609)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEECCCCCCCCHHHCCHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999999986016341530158862644887789998178889999999999999999999999


Q ss_pred             HHCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCHHHHHHH
Q ss_conf             83215689784089799999999999999999999999999976679999999840699899999975448998999999
Q gi|254780690|r  167 TENYFTMLDFISANPHSILYHAFFTVRKVLIMILLFIATLTVLDIGWSYHQWYSKLKMSKQEIKDEIKQSYGNPIIKNRQ  246 (354)
Q Consensus       167 ~~~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD~~~qr~~~~k~lkMskqEvK~E~K~~EGdP~iK~~~  246 (354)
                      +++++.+..+..+++.+.+....+.+.+++..++++++++|++||.||||+|.|+||||||||||||||+|||||||+||
T Consensus       421 ~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~lvia~~D~~~Q~~~~~k~lkMskqEvK~E~K~~EGdP~iK~r~  500 (609)
T PRK12772        421 QDNYLDILNLGNLRLPYLITGLLSLVISIFFRITLIMIIIAVADYVYQKYQYNKDLKMTKQEVKEEYKQDEGDPQIKSKI  500 (609)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCHHHHHHH
T ss_conf             99999999874389999999999999999999999999999999999999999976898999998987553999999999


Q ss_pred             HHHHHHHHHHHHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHHHHH
Q ss_conf             99999999988986077686998735530788897688888888998076589999999999739978868899999997
Q gi|254780690|r  247 KSIARSRIRHKMMEATSRATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFK  326 (354)
Q Consensus       247 r~~~re~~~~~~~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~  326 (354)
                      ||+|||++++||+++||+||||||||||||||||||+++|+||+|||||+|++|+||||+|+||||||+|||||||+||+
T Consensus       501 Rq~~re~a~~rm~~~Vp~AdVVitNPTH~AVALkYd~~~~~AP~VvAKG~d~~A~~IreiA~e~~vPiven~pLARaLy~  580 (609)
T PRK12772        501 KQKQREMAMQRMMQEVPDATVVVTNPTHIAVALKYEKGKDTAPKVVAKGADYVALKIKEIAKENEVPIIENKPLARLIYK  580 (609)
T ss_pred             HHHHHHHHHHHHHHCCCCCCEEEECCCHHHEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEECCHHHHHHHHH
T ss_conf             99999999867873189899898873336404343689999998886178599999999999869987618298999997


Q ss_pred             HCCCCCCCCHHHHHHHHHHHHHHHHHC
Q ss_conf             288989489899999999999997302
Q gi|254780690|r  327 QVPINSAIPPVFYKAVAQLIYKIYHKK  353 (354)
Q Consensus       327 ~~~ig~~Ip~~~y~aVA~il~~v~~lk  353 (354)
                      +||+||+||+|+|+||||||+||||+|
T Consensus       581 ~~eig~~IP~~ly~AVAevLa~Vy~lk  607 (609)
T PRK12772        581 KVEIDSEIPQDMYQAVAEILAIVYKLK  607 (609)
T ss_pred             HCCCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             077899689999999999999999753


No 5  
>PRK12468 flhB flagellar biosynthesis protein FlhB; Reviewed
Probab=100.00  E-value=0  Score=874.12  Aligned_cols=351  Identities=28%  Similarity=0.442  Sum_probs=327.0

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH
Q ss_conf             99876787768665878799999857875133599999999999999999999999999999999720001210497989
Q gi|254780690|r    1 MSENDAPDNKTEAPSSKKIEDALNEGNAPISREASLFSSILACLIYLLFFFSPGIYSVTSDLHVLLASATQRKLEDISHI   80 (354)
Q Consensus         1 MAe~d~~~eKTE~PT~kRL~dARekGqV~kS~el~~~~~ll~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~   80 (354)
                      |||+| +|||||+||||||+|||||||||+|+|+++++++++++++++++++.....+...+...+. .+.....+....
T Consensus         1 MAed~-dqEKTE~PT~kKL~dARekGqV~kS~El~~~~~L~~~~~~l~~~~~~~~~~l~~~~~~~l~-~~~~~~~~~~~~   78 (383)
T PRK12468          1 MAEDS-DQEKSEEPTASKLEKAREKGQIPRSRELTSMLMLGAGLTILWMSGESMARQLSAMVAQGLH-FDHSMVSNDKQM   78 (383)
T ss_pred             CCCCC-CCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCHHHCCCHHHH
T ss_conf             99999-9999999986789999966999857759999999999999999999999999999998833-333420377999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999887768785321013712137791016934303320126679999999999999999
Q gi|254780690|r   81 VFLLTHLSLSASRLVIPGLLLFMMFGIGSYLIQRIPVLNLNHVKPSFKRVSLREGIKRIYSINNLVNFMKSFVKIILVGT  160 (354)
Q Consensus        81 ~~~~~~~~~~~~~~~~p~~~~~~l~~i~~~l~q~G~~fs~k~l~pk~~rlNPi~GlKriFS~k~lvel~KsllKv~li~~  160 (354)
                      ...+.......+..++|+++++++++++++++|+|++||+|+++|||+||||++|+|||||+++|+||+||++|++++++
T Consensus        79 ~~~~~~~l~~~~~~~lpi~~~~~i~~i~~~~~q~G~~fs~k~l~Pk~~rlNPi~GlKRiFS~k~LvEl~KsllK~~li~~  158 (383)
T PRK12468         79 LRQIGMLLRQTLLAMLPIFAGLVIVALAVPMLLGGVLFSGESIKFDLKRMSPVAGLKRMFSSQALAELLKAILKATLVGW  158 (383)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHCCHHHCCCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999999999999997104031443368655435864441111257789999999999999999


Q ss_pred             HHHHHHHHCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCH
Q ss_conf             99999983215689784089799999999999999999999999999976679999999840699899999975448998
Q gi|254780690|r  161 IITISLTENYFTMLDFISANPHSILYHAFFTVRKVLIMILLFIATLTVLDIGWSYHQWYSKLKMSKQEIKDEIKQSYGNP  240 (354)
Q Consensus       161 v~~~~i~~~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD~~~qr~~~~k~lkMskqEvK~E~K~~EGdP  240 (354)
                      ++|++++.+++.+..+...++.+.+......+..+++.+++++++++++||+||||+|.|+||||||||||||||+||||
T Consensus       159 v~~~~l~~~~~~~~~l~~~~~~~~l~~~~~~~~~~~~~~~l~l~~ia~iD~~~Qr~~~~k~LkMSKqEVKdE~Ke~EGdP  238 (383)
T PRK12468        159 VTGLFLWHNWPDMMRLIAAPPVAALGDALHLIIFCGLVVVLGLSPMVGFDVFYQITSHIKKLRMTKQDIRDEFKNQEGDP  238 (383)
T ss_pred             HHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCH
T ss_conf             99999999899999986248999999999999999999999999999999999999999874899999999988663999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHH
Q ss_conf             99999999999999988986077686998735530788897688888888998076589999999999739978868899
Q gi|254780690|r  241 IIKNRQKSIARSRIRHKMMEATSRATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSL  320 (354)
Q Consensus       241 ~iK~~~r~~~re~~~~~~~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~L  320 (354)
                      +||+||||+|||+++++|+++||+||||||||||||||||||+++|+||+|||||+|++|++||++|++|||||+|||||
T Consensus       239 ~iK~r~R~~~re~a~~~m~~~V~~AdvVItNPTH~AVAL~Y~~~~~~aP~VvAKG~d~~A~~Ir~~A~~~~VPiven~pL  318 (383)
T PRK12468        239 HVKGRIRQQQRAMARRRMMVDVPKADVIVTNPTHYAVALQYNESKMSAPKVLAKGAGAVALRIRELGAEHRIPLLEAPPL  318 (383)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCHHHHEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEECCHHH
T ss_conf             99999999999999878872689898899785538742353788899998988368499999999999869988637799


Q ss_pred             HHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHC
Q ss_conf             999997288989489899999999999997302
Q gi|254780690|r  321 ARSLFKQVPINSAIPPVFYKAVAQLIYKIYHKK  353 (354)
Q Consensus       321 AR~Ly~~~~ig~~Ip~~~y~aVA~il~~v~~lk  353 (354)
                      ||+||++||+||+||+|+|+|||+||+|||+||
T Consensus       319 AR~Ly~~~evg~~IP~ely~aVA~vLa~Vy~l~  351 (383)
T PRK12468        319 ARALFRHSEVGQHIPATLYAAVAEVLAWVYQLK  351 (383)
T ss_pred             HHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             999987177899789999999999999999999


No 6  
>PRK06298 type III secretion system protein; Validated
Probab=100.00  E-value=0  Score=862.53  Aligned_cols=344  Identities=23%  Similarity=0.316  Sum_probs=325.2

Q ss_pred             CCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH
Q ss_conf             77686658787999998578751335999999999999999999999999999999997200012104979899999999
Q gi|254780690|r    8 DNKTEAPSSKKIEDALNEGNAPISREASLFSSILACLIYLLFFFSPGIYSVTSDLHVLLASATQRKLEDISHIVFLLTHL   87 (354)
Q Consensus         8 ~eKTE~PT~kRL~dARekGqV~kS~el~~~~~ll~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (354)
                      +||||+||||||+|||||||||||+|+++++++++++++++++++.....+...+...+......  .++......+...
T Consensus         2 gEKTE~PT~kKL~dARekGqV~kS~El~~a~~ll~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~--~~~~~~~~~~~~~   79 (360)
T PRK06298          2 GEKTEKATPKRLRDARKKGQVAKSQDFPSAVTFIVSMFTTFSLASFFAKHLGSFLVSIFKQAPTN--HDPGVTLYYLKNC   79 (360)
T ss_pred             CCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC--CCHHHHHHHHHHH
T ss_conf             98899998578999996699985675999999999999999999999999999999999735554--5547899999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999998877687853210137121377910169343033201266799999999999999999999998
Q gi|254780690|r   88 SLSASRLVIPGLLLFMMFGIGSYLIQRIPVLNLNHVKPSFKRVSLREGIKRIYSINNLVNFMKSFVKIILVGTIITISLT  167 (354)
Q Consensus        88 ~~~~~~~~~p~~~~~~l~~i~~~l~q~G~~fs~k~l~pk~~rlNPi~GlKriFS~k~lvel~KsllKv~li~~v~~~~i~  167 (354)
                      ....+..++|+++++++++++++++|+||+||+|+++|||+||||++|+|||||.|+++||+||++|++++++++|++++
T Consensus        80 ~~~~~~~~lP~~~~~~~~~i~~~~~q~G~~fs~k~l~Pk~~rlNPi~GlKriFS~k~LvEl~KsllKv~~~~~v~~~~l~  159 (360)
T PRK06298         80 LMLILTASLPLLGAVAFVGVIIGFLIVGPTFSTEVFKPDIKKFNPIDNLKQKFKVKTLIELLKSILKISGAALILYIVLK  159 (360)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEECHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999999986455336101578742136878788860487899999999999999999999999


Q ss_pred             HCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf             32156897840897999999999999999999999999999766799999998406998999999754489989999999
Q gi|254780690|r  168 ENYFTMLDFISANPHSILYHAFFTVRKVLIMILLFIATLTVLDIGWSYHQWYSKLKMSKQEIKDEIKQSYGNPIIKNRQK  247 (354)
Q Consensus       168 ~~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD~~~qr~~~~k~lkMskqEvK~E~K~~EGdP~iK~~~r  247 (354)
                      ++++.+..+..+++.+.+.....++..+++.++++++++|++||+||||+|+|+||||||||||||||+|||||||+|||
T Consensus       160 ~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~via~~D~~~qr~~~~k~LkMSkqEvKdE~Ke~EGdP~vK~r~R  239 (360)
T PRK06298        160 NRVPLIIETAGVPPIVTAQIFKEILYKAVTSIGIFFLVVAVLDLVYQRHNFAKELKMEKFEVKQEFKDTEGNPEIKGRRR  239 (360)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCHHHHHHHH
T ss_conf             99999998825899999999999999999999999999999999999999998707999999989886639999999999


Q ss_pred             HHHHHHHHHHHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHHHHHH
Q ss_conf             99999999889860776869987355307888976888888889980765899999999997399788688999999972
Q gi|254780690|r  248 SIARSRIRHKMMEATSRATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFKQ  327 (354)
Q Consensus       248 ~~~re~~~~~~~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~~  327 (354)
                      |+|||+++++|+++||+||||||||||||||||||+++++||+|||||+|++|++||++|+||||||+|||||||+||++
T Consensus       240 ~~~re~a~~~m~~~V~~A~vVitNPTH~AVAL~Y~~~~~~aP~vvAKG~d~~A~~Ir~~A~~~~VPiven~pLARaLy~~  319 (360)
T PRK06298        240 QIAQEIAYEDTSSQVKHASAVVSNPKDIAVAIGYMPEKYKAPWIIAMGINLRAKRIIAEAEKYGIPIMRNVPLAHQLLDE  319 (360)
T ss_pred             HHHHHHHHHHHHHCCCCCCEEEECCCEEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEECCHHHHHHHHHH
T ss_conf             99999997178726999988998886178886666899999988885485999999999998799887176999999982


Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHC
Q ss_conf             88989489899999999999997302
Q gi|254780690|r  328 VPINSAIPPVFYKAVAQLIYKIYHKK  353 (354)
Q Consensus       328 ~~ig~~Ip~~~y~aVA~il~~v~~lk  353 (354)
                      +++||+||+|+|+|||+||+|||+||
T Consensus       320 ~~vg~~IP~~ly~aVA~iL~~v~~l~  345 (360)
T PRK06298        320 GKELKFIPESTYEAIGEILLYITSLN  345 (360)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             67888489999999999999999974


No 7  
>PRK09108 type III secretion system protein HrcU; Validated
Probab=100.00  E-value=0  Score=857.32  Aligned_cols=343  Identities=26%  Similarity=0.384  Sum_probs=325.9

Q ss_pred             CCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH
Q ss_conf             77686658787999998578751335999999999999999999999999999999997200012104979899999999
Q gi|254780690|r    8 DNKTEAPSSKKIEDALNEGNAPISREASLFSSILACLIYLLFFFSPGIYSVTSDLHVLLASATQRKLEDISHIVFLLTHL   87 (354)
Q Consensus         8 ~eKTE~PT~kRL~dARekGqV~kS~el~~~~~ll~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (354)
                      |||||+||||||+|||||||||+|+|+++++++++++++++++++....++...+...+..... . .++......+...
T Consensus         3 dEKTE~PT~kRl~dARekGqV~kS~El~~~~~L~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~-~-~~~~~~~~~~~~~   80 (354)
T PRK09108          3 DEKTEEPTEKKLKDARRDGEVAKSPDLTAAAVLLAALLVLTAAGSYLTDHLRALVRTALDFVSG-E-RSLQALLAALHHI   80 (354)
T ss_pred             CCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-C-CCHHHHHHHHHHH
T ss_conf             8889999857899999769997478699999999999999999999999999999999862245-4-6789999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999998877687853210137121377910169343033201266799999999999999999999998
Q gi|254780690|r   88 SLSASRLVIPGLLLFMMFGIGSYLIQRIPVLNLNHVKPSFKRVSLREGIKRIYSINNLVNFMKSFVKIILVGTIITISLT  167 (354)
Q Consensus        88 ~~~~~~~~~p~~~~~~l~~i~~~l~q~G~~fs~k~l~pk~~rlNPi~GlKriFS~k~lvel~KsllKv~li~~v~~~~i~  167 (354)
                      +...+.+++|+++++++++++++++|+||+||+|+++|||+||||++|+|||||.++++|++|+++|++++++++|++++
T Consensus        81 ~~~~~~~~lp~~~~~~~~~i~~~~~Q~G~~fs~k~l~pk~~rlNPi~GlKriFS~k~LvEl~KsllKv~~l~~v~~~~~~  160 (354)
T PRK09108         81 GAQALLLMLPFVAAALVAGILGQAPQTGLNISLKPVMPKFDSLNPAAGLKKIFSLRSLIELVKMIVKAVVIACVLWKTIT  160 (354)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHCCCCHHCCCHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999999840365405141367602058655442444688899999999999999999999999


Q ss_pred             HCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf             32156897840897999999999999999999999999999766799999998406998999999754489989999999
Q gi|254780690|r  168 ENYFTMLDFISANPHSILYHAFFTVRKVLIMILLFIATLTVLDIGWSYHQWYSKLKMSKQEIKDEIKQSYGNPIIKNRQK  247 (354)
Q Consensus       168 ~~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD~~~qr~~~~k~lkMskqEvK~E~K~~EGdP~iK~~~r  247 (354)
                      ++++.+..+..+++.+.+....+.+..+++.++++++++|++||+||||+|+|+||||||||||||||+|||||||+|||
T Consensus       161 ~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~via~~D~~~qr~~~~k~LkMSkqEvK~E~K~~EGdP~vK~r~R  240 (354)
T PRK09108        161 SLFPLIVGAAYESPPQLAQILWTVLMKLLAVAALVFLVVGAADWKIQRWLFIRDNRMSKDEVKREHKESEGDPHLKGERK  240 (354)
T ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCHHHHHHHH
T ss_conf             99999999850699999999999999999999999999999999999999999738998999999886649989999999


Q ss_pred             HHHHHHHHH-HHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHHHHH
Q ss_conf             999999998-8986077686998735530788897688888888998076589999999999739978868899999997
Q gi|254780690|r  248 SIARSRIRH-KMMEATSRATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFK  326 (354)
Q Consensus       248 ~~~re~~~~-~~~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~  326 (354)
                      |+|||++++ +|+++||+|||||||||||||||||||++|+||+|||||+|++|++||++|+||||||+|||||||+||+
T Consensus       241 ~~~re~a~~~~~~~~V~~A~vVitNPTH~AVAL~Y~~~~~~aP~VvAKG~d~~A~~Ir~~A~~~~VPiven~pLAR~Ly~  320 (354)
T PRK09108        241 RLARELATFAPPRQRVAKANVVVVNPTHYAVALRYAPDEHPLPRVVAKGVDDGALALRRHAHALGIPIVANPPVARALYR  320 (354)
T ss_pred             HHHHHHHHHHHHHHCCCCCCEEEECCCCEEEEEEECCCCCCCCEEHHHCCCHHHHHHHHHHHHCCCCEEECHHHHHHHHC
T ss_conf             99999997443653578784899876604678675788898898112168399999999999869978718899999970


Q ss_pred             HCCCCCCCCHHHHHHHHHHHHHHHHHC
Q ss_conf             288989489899999999999997302
Q gi|254780690|r  327 QVPINSAIPPVFYKAVAQLIYKIYHKK  353 (354)
Q Consensus       327 ~~~ig~~Ip~~~y~aVA~il~~v~~lk  353 (354)
                       +|+||+||+|+|+|||+||+|||+||
T Consensus       321 -v~vg~~IP~~~y~aVA~ila~v~~l~  346 (354)
T PRK09108        321 -VELDEPIPEELFETVAAILRWVDELG  346 (354)
T ss_pred             -CCCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             -76999689999999999999999985


No 8  
>COG1377 FlhB Flagellar biosynthesis pathway, component FlhB [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=100.00  E-value=0  Score=856.28  Aligned_cols=350  Identities=37%  Similarity=0.579  Sum_probs=335.6

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHH
Q ss_conf             87678776866587879999985787513359999999999999999999999999999999972000121049798999
Q gi|254780690|r    3 ENDAPDNKTEAPSSKKIEDALNEGNAPISREASLFSSILACLIYLLFFFSPGIYSVTSDLHVLLASATQRKLEDISHIVF   82 (354)
Q Consensus         3 e~d~~~eKTE~PT~kRL~dARekGqV~kS~el~~~~~ll~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~   82 (354)
                      ++++++||||+|||||++|||||||||||+|+++++++++++..++++++....++...+...+.......+ +......
T Consensus         2 ~~~~~~eKTE~pT~kKl~dArekG~v~kS~el~~a~~ll~g~~~l~~~~~~~~~~l~~~l~~~~~~~~~~~~-~~~~~~~   80 (363)
T COG1377           2 DDMADDEKTEKPTPKKLRDAREKGQVPKSRELTSAASLLVGFLLLFFFGSYFARRLSGFLRAFLEFPESMDL-DDESALE   80 (363)
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC-CCHHHHH
T ss_conf             654344567789856699999747886306689999999999999999999999999999999826242123-7225999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999988776878532101371213779101693430332012667999999999999999999
Q gi|254780690|r   83 LLTHLSLSASRLVIPGLLLFMMFGIGSYLIQRIPVLNLNHVKPSFKRVSLREGIKRIYSINNLVNFMKSFVKIILVGTII  162 (354)
Q Consensus        83 ~~~~~~~~~~~~~~p~~~~~~l~~i~~~l~q~G~~fs~k~l~pk~~rlNPi~GlKriFS~k~lvel~KsllKv~li~~v~  162 (354)
                      .+...+...+..++|+++++++++++++++|+||.||+|+++|||+||||++|+|||||.++++|++||++|+.++++++
T Consensus        81 ~~~~~~~~~~~~llp~~~~~~v~gi~~~~~q~g~~fs~e~ikP~~~kinP~~G~KRiFs~~~~vEllKsllKi~~v~~v~  160 (363)
T COG1377          81 LIKALLLEILKALLPFLLVLLVVGLLANILQVGFLFSTEALKPKFSKLNPIKGLKRIFSLQTLVELLKSLLKIVLVGLVA  160 (363)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999999999999984763146346777211493677899845889999999999999999999


Q ss_pred             HHHHHHCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCHHH
Q ss_conf             99998321568978408979999999999999999999999999997667999999984069989999997544899899
Q gi|254780690|r  163 TISLTENYFTMLDFISANPHSILYHAFFTVRKVLIMILLFIATLTVLDIGWSYHQWYSKLKMSKQEIKDEIKQSYGNPII  242 (354)
Q Consensus       163 ~~~i~~~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD~~~qr~~~~k~lkMskqEvK~E~K~~EGdP~i  242 (354)
                      |++++++++.++.+...++.+.+....+++.++++.++++++++|++||+||||+|.|+||||||||||||||+||||+|
T Consensus       161 ~~~l~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~liia~~D~~~qr~~~~k~lkMtKqEVKdE~K~sEGdPeV  240 (363)
T COG1377         161 YFVLKNHLSELLSLAGQSPVAALSIFMELLGKLLLAVLLLLLIVAAFDYFYQRFQYIKKLKMTKQEVKDEYKQSEGDPEV  240 (363)
T ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCHHH
T ss_conf             99999419999977048989999999999999999999999999999999999999996668689999998615698056


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHHHH
Q ss_conf             99999999999998898607768699873553078889768888888899807658999999999973997886889999
Q gi|254780690|r  243 KNRQKSIARSRIRHKMMEATSRATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLAR  322 (354)
Q Consensus       243 K~~~r~~~re~~~~~~~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR  322 (354)
                      ||||||+|||++++|||++||+|||||||||||||||||||++|+||+|||||+|++|++||++|+||||||+|||||||
T Consensus       241 Ksr~Rq~~re~a~~rm~~~Vp~AdvVItNPTH~AVAlkY~~~~~~AP~VvAKG~d~~AlkIreiA~e~~Ipi~enppLAR  320 (363)
T COG1377         241 KSRIRQMQREIARRRMMSDVPKADVVITNPTHYAVALKYDPEKMPAPVVVAKGVDLVALKIREIAKEHGIPIIENPPLAR  320 (363)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEECCHHHHH
T ss_conf             68999999999999998518998889727661134546655558999899817869999999999984995641807799


Q ss_pred             HHHHHCCCCCCCCHHHHHHHHHHHHHHHHHC
Q ss_conf             9997288989489899999999999997302
Q gi|254780690|r  323 SLFKQVPINSAIPPVFYKAVAQLIYKIYHKK  353 (354)
Q Consensus       323 ~Ly~~~~ig~~Ip~~~y~aVA~il~~v~~lk  353 (354)
                      +||+++++|++||+++|+||||||+|||++|
T Consensus       321 aLY~~~~v~~~IP~e~y~aVaevL~~V~~~~  351 (363)
T COG1377         321 ALYRQVEVGQQIPEELYKAVAEVLAYVYQLK  351 (363)
T ss_pred             HHHHHCCCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             9997257666489999999999999999865


No 9  
>PRK12721 secretion system apparatus protein SsaU; Reviewed
Probab=100.00  E-value=0  Score=857.69  Aligned_cols=342  Identities=23%  Similarity=0.305  Sum_probs=321.9

Q ss_pred             CCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH
Q ss_conf             76866587879999985787513359999999999999999999999999999999972000121049798999999999
Q gi|254780690|r    9 NKTEAPSSKKIEDALNEGNAPISREASLFSSILACLIYLLFFFSPGIYSVTSDLHVLLASATQRKLEDISHIVFLLTHLS   88 (354)
Q Consensus         9 eKTE~PT~kRL~dARekGqV~kS~el~~~~~ll~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   88 (354)
                      ||||+||||||+|||||||||+|+|+++++++++++++++++++.....+...+...+...++..   ......+.....
T Consensus         3 EKTE~PT~kKL~dARekGqV~kS~El~~a~~ll~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~---~~~~~~l~~~~~   79 (349)
T PRK12721          3 EKTEKPTPKKLRDARKKGQVVKSIEITSGVQLIALLLYFHLFGESLIEILIALINFTIQLLNQPF---SYALTQISGALL   79 (349)
T ss_pred             CCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCH---HHHHHHHHHHHH
T ss_conf             88999985789999977999766879999999999999999999999999999999998724705---679999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999988776878532101371213779101693430332012667999999999999999999999983
Q gi|254780690|r   89 LSASRLVIPGLLLFMMFGIGSYLIQRIPVLNLNHVKPSFKRVSLREGIKRIYSINNLVNFMKSFVKIILVGTIITISLTE  168 (354)
Q Consensus        89 ~~~~~~~~p~~~~~~l~~i~~~l~q~G~~fs~k~l~pk~~rlNPi~GlKriFS~k~lvel~KsllKv~li~~v~~~~i~~  168 (354)
                      ..+..+++|+++++++++++++++|+||+||+|+++|||+||||++|+|||||.++++||+||++|++++++++|+++++
T Consensus        80 ~~~~~~~~p~~~~~~~~~i~~~~~q~G~~fs~k~l~pk~~rlNPi~GlKriFS~k~lvEl~KsllKv~lv~~i~~~~l~~  159 (349)
T PRK12721         80 ESLMSILLFLGAGVIVATVGSVILQVGPVLATKAIGFKGEKINPVSNAKQIFSLHSVFELCKSLLKVIVLSLIFAFLLYY  159 (349)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCEECHHHCCCCHHHCCHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999999730635071414876654587453554337767999999999999999999999999


Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             21568978408979999999999999999999999999997667999999984069989999997544899899999999
Q gi|254780690|r  169 NYFTMLDFISANPHSILYHAFFTVRKVLIMILLFIATLTVLDIGWSYHQWYSKLKMSKQEIKDEIKQSYGNPIIKNRQKS  248 (354)
Q Consensus       169 ~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD~~~qr~~~~k~lkMskqEvK~E~K~~EGdP~iK~~~r~  248 (354)
                      +++.+..+..+++.+.+.....++..++..++++++++|++||+||||+|.|+||||||||||||||+|||||||+||||
T Consensus       160 ~~~~~~~l~~~~~~~~l~~~~~~~~~l~~~~~~~llviai~D~~~Qr~~~~k~LkMSKqEVKdE~K~~EGdP~iK~r~R~  239 (349)
T PRK12721        160 YAPTFRALPYCGSACALPVVSTLIKWLWGGVIAFYLVFGILDYAFQRYKIMKQLKMSKDDVKQEHKDSEGDPEIKQKRRE  239 (349)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf             99999987547999999999999999999999999999999999999999987389999999998866399999999999


Q ss_pred             HHHHHHHHHHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHHHHHHC
Q ss_conf             99999998898607768699873553078889768888888899807658999999999973997886889999999728
Q gi|254780690|r  249 IARSRIRHKMMEATSRATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFKQV  328 (354)
Q Consensus       249 ~~re~~~~~~~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~~~  328 (354)
                      +|||+++++|+++||+||||||||||||||||||+++++||+|||||+|++|++||++|++|||||+|||||||+||++|
T Consensus       240 ~~re~a~~~m~~~V~~AdvVitNPTH~AVAL~Y~~~~~~aP~vvAKG~d~~A~~Ir~~A~~~~vPiven~~LAR~Ly~~~  319 (349)
T PRK12721        240 LQSEIQSGSLAQNVKKSTAVVRNPTHIAVCLGYHPGETPLPRVLEKGSDAQALYIVNLAERNGIPVVENIPLARALFFEV  319 (349)
T ss_pred             HHHHHHHHHHHHCCCCCCEEEECCCHHHHHHHCCCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEECCHHHHHHHHHCC
T ss_conf             99999985787268999889988652764000268899999888853859999999999987997862879999999727


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHC
Q ss_conf             8989489899999999999997302
Q gi|254780690|r  329 PINSAIPPVFYKAVAQLIYKIYHKK  353 (354)
Q Consensus       329 ~ig~~Ip~~~y~aVA~il~~v~~lk  353 (354)
                      |+||+||+|+|+|||+||+|||+|+
T Consensus       320 ~vg~~IP~~ly~aVA~il~~v~~l~  344 (349)
T PRK12721        320 ECGDKIPETLFEPVAALLRMAMEID  344 (349)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHC
T ss_conf             7899589999999999999999625


No 10 
>pfam01312 Bac_export_2 FlhB HrpN YscU SpaS Family. This family includes the following members: FlhB, HrpN, YscU, SpaS, HrcU SsaU and YopU. All of these proteins export peptides using the type III secretion system. The peptides exported are quite diverse.
Probab=100.00  E-value=0  Score=852.03  Aligned_cols=342  Identities=33%  Similarity=0.517  Sum_probs=313.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHH
Q ss_conf             87768665878799999857875133599999999999999999999999999999999720001210497989999999
Q gi|254780690|r    7 PDNKTEAPSSKKIEDALNEGNAPISREASLFSSILACLIYLLFFFSPGIYSVTSDLHVLLASATQRKLEDISHIVFLLTH   86 (354)
Q Consensus         7 ~~eKTE~PT~kRL~dARekGqV~kS~el~~~~~ll~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (354)
                      ||||||+||||||+|||||||||+|+|+++++++++++++++++++.....+...+...+..... ...+ .........
T Consensus         2 S~EKTE~PT~kRL~dARekGqV~~S~el~~~~~l~~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~-~~~~-~~~~~~~~~   79 (343)
T pfam01312         2 SEEKTEKPTPKKLRDARKKGQVPKSQDLTSAASLLAGSAYLFLLGSVFARRLIALLLLTLILIPL-PFSL-SVTDLFSLV   79 (343)
T ss_pred             CCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-CCCH-HHHHHHHHH
T ss_conf             98889999857899999769997578799999999999999999999999999999999973654-4440-367999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999887768785321013712137791016934303320126679999999999999999999999
Q gi|254780690|r   87 LSLSASRLVIPGLLLFMMFGIGSYLIQRIPVLNLNHVKPSFKRVSLREGIKRIYSINNLVNFMKSFVKIILVGTIITISL  166 (354)
Q Consensus        87 ~~~~~~~~~~p~~~~~~l~~i~~~l~q~G~~fs~k~l~pk~~rlNPi~GlKriFS~k~lvel~KsllKv~li~~v~~~~i  166 (354)
                      ........+.|.++++++++++++++|+||+||+|+++|||+||||++|+|||||.++++||+||++|++++++++|+++
T Consensus        80 ~~~~~~~~~~~~~~~~~l~~i~~~~~q~G~~fs~k~l~Pk~~rlNPi~GlKriFS~~~LvEl~KsllKv~li~~v~~~~l  159 (343)
T pfam01312        80 VLLLLTVLLLLSLFVALLVGLASNLLQVGFLFSTEAIKPDFSKINPIKGLKRIFSARSLVELLKSILKVVAVGLIFYFFL  159 (343)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEECHHHCCCCHHHCCHHHCHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999999986036340603147773336874442200377789999999999999999999999


Q ss_pred             HHCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCHHHHHHH
Q ss_conf             83215689784089799999999999999999999999999976679999999840699899999975448998999999
Q gi|254780690|r  167 TENYFTMLDFISANPHSILYHAFFTVRKVLIMILLFIATLTVLDIGWSYHQWYSKLKMSKQEIKDEIKQSYGNPIIKNRQ  246 (354)
Q Consensus       167 ~~~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD~~~qr~~~~k~lkMskqEvK~E~K~~EGdP~iK~~~  246 (354)
                      +++++.+..+..+++.+.+..+.+.+..+++.++++++++|++||+||||+|.|+||||||||||||||+|||||||+||
T Consensus       160 ~~~~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~via~~D~~~Qr~~~~k~lkMSkqEvKdE~Ke~EGdP~iK~~~  239 (343)
T pfam01312       160 KNDLGTIVRLPGCSPMGIIVIVMTLLKKLLLVVLLFLLIVGLLDYLFQRYLFIKDLKMSKQEVKREYKESEGDPHVKGRR  239 (343)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCHHHHHHH
T ss_conf             99999999884499999999999999999999999999999999999999999980899999999988643998899999


Q ss_pred             HHHHHHHHHHHHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHHHHH
Q ss_conf             99999999988986077686998735530788897688888888998076589999999999739978868899999997
Q gi|254780690|r  247 KSIARSRIRHKMMEATSRATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFK  326 (354)
Q Consensus       247 r~~~re~~~~~~~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~  326 (354)
                      ||+|||+++++|+++||+||||||||||||||||||+++|+||+|||||+|++|++||++|++|||||+|||||||+||+
T Consensus       240 R~~~re~~~~~m~~~V~~A~vVItNPTH~AVAL~Y~~~~~~aP~vvAKG~d~~A~~Ir~~A~~~~VPiven~~LAR~Ly~  319 (343)
T pfam01312       240 RQIAREIASERMMQDVPKADVVVTNPTHYAVALYYDPEEMPAPRIVAKGEDEQALAIRAIAEENGIPVVENPPLARALYR  319 (343)
T ss_pred             HHHHHHHHHHHHHHCCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHHHHH
T ss_conf             99999999857872589898899999862789887889999998888548699999999999879978837799999998


Q ss_pred             HCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             288989489899999999999997
Q gi|254780690|r  327 QVPINSAIPPVFYKAVAQLIYKIY  350 (354)
Q Consensus       327 ~~~ig~~Ip~~~y~aVA~il~~v~  350 (354)
                      ++|+||+||+|+|+|||+||+|||
T Consensus       320 ~~~vg~~IP~~ly~aVA~iL~~vy  343 (343)
T pfam01312       320 TVEVGQEIPEELFEAVAEVLVWVY  343 (343)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHC
T ss_conf             077999589999999999998769


No 11 
>PRK08156 surface presentation of antigens protein SpaS; Validated
Probab=100.00  E-value=0  Score=852.96  Aligned_cols=337  Identities=23%  Similarity=0.319  Sum_probs=311.8

Q ss_pred             CCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH
Q ss_conf             76866587879999985787513359999999999999999999999999999999972000121049798999999999
Q gi|254780690|r    9 NKTEAPSSKKIEDALNEGNAPISREASLFSSILACLIYLLFFFSPGIYSVTSDLHVLLASATQRKLEDISHIVFLLTHLS   88 (354)
Q Consensus         9 eKTE~PT~kRL~dARekGqV~kS~el~~~~~ll~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   88 (354)
                      ||||+||||||+|||||||||||+|++++++++++++++.++++  +.++...+...+.+..+.   +.   ........
T Consensus         3 EKTE~PT~kKL~kARekGqVarSkEl~~a~~ll~g~l~l~~~~~--~~~~~~~~~~~~~~~~~~---~~---~~~~~~~~   74 (367)
T PRK08156          3 NKTEKPTKKKLRDAAKKGQSFKSKDLTTAVVILGGIAYLVSFGS--LNEFMGIYRRILADNFDI---SM---GDYFFAVA   74 (367)
T ss_pred             CCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHCCCCC---CH---HHHHHHHH
T ss_conf             88999985789999967999874879999999999999999999--999999999998174324---69---99999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999988776878532101371213779101693430332012667999999999999999999999983
Q gi|254780690|r   89 LSASRLVIPGLLLFMMFGIGSYLIQRIPVLNLNHVKPSFKRVSLREGIKRIYSINNLVNFMKSFVKIILVGTIITISLTE  168 (354)
Q Consensus        89 ~~~~~~~~p~~~~~~l~~i~~~l~q~G~~fs~k~l~pk~~rlNPi~GlKriFS~k~lvel~KsllKv~li~~v~~~~i~~  168 (354)
                      ..++..++|+++++++++++++++|+||+||+|+++|||+||||++|+|||||.++|+||+||++|++++++++|+++++
T Consensus        75 ~~~~~~~~P~~~~~~l~~i~a~l~Q~G~~fs~k~l~Pk~~kLNPi~GlKRiFS~k~LvEl~KsllK~~~l~~~~~~~~~~  154 (367)
T PRK08156         75 ILFLKILIPFLLLCLLAGALPSLLQTRFVLATEAIKLNFSALNPVKGLKKIFSLRTVKEFVKALLYLIVFALTAYVFWKK  154 (367)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCEECCHHCCCCHHHCCHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999999721764160203653643786441001135768999999999999999999999998


Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             21568978408979999999999999999999999999997667999999984069989999997544899899999999
Q gi|254780690|r  169 NYFTMLDFISANPHSILYHAFFTVRKVLIMILLFIATLTVLDIGWSYHQWYSKLKMSKQEIKDEIKQSYGNPIIKNRQKS  248 (354)
Q Consensus       169 ~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD~~~qr~~~~k~lkMskqEvK~E~K~~EGdP~iK~~~r~  248 (354)
                      +++.+..+..+++.+.+....+.+..+++.++++++++|++||+||||+|.|+||||||||||||||+|||||||+||||
T Consensus       155 ~~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~via~iD~~~Qr~~~~k~LrMSkqEVKdE~Ke~EGdP~vK~r~R~  234 (367)
T PRK08156        155 YKKEIFSQLNGNIVGLIVIWRELLVALVLTFLACALIVLILDAIAEYFLYMKDMKMDKQEVKREYKEQEGNPEIKSKRRE  234 (367)
T ss_pred             HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf             89999998507999999999999999999999999999999999999999997489989999998866399999999999


Q ss_pred             HHHHHHHHHHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHHHHHHC
Q ss_conf             99999998898607768699873553078889768888888899807658999999999973997886889999999728
Q gi|254780690|r  249 IARSRIRHKMMEATSRATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFKQV  328 (354)
Q Consensus       249 ~~re~~~~~~~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~~~  328 (354)
                      +|||++++||+++||+||||||||||||||||||+++++||+|||||+|++|++||++|++|||||+|||||||+||++|
T Consensus       235 ~~re~a~~~m~~~Vp~AdVVItNPTH~AVALkY~~~~~~AP~VvAKG~d~~A~~Ir~~A~e~~VPive~~pLARaLy~~~  314 (367)
T PRK08156        235 AHQEILSEQVKSDIENSRLIVANPTHIAIGIYFNPDLAPIPFISVRETNQRALAVRAYAEKVGVPVVRDIKLARSLYKTH  314 (367)
T ss_pred             HHHHHHHHHHHHCCCCCCEEEECCCHHHEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEECCHHHHHHHHHHC
T ss_conf             99999986797348999989988562204655468889999888746859999999999986998862769999999726


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHC
Q ss_conf             8989489899999999999997302
Q gi|254780690|r  329 PINSAIPPVFYKAVAQLIYKIYHKK  353 (354)
Q Consensus       329 ~ig~~Ip~~~y~aVA~il~~v~~lk  353 (354)
                      |+||+||+|+|+|||+||+|||++|
T Consensus       315 ~~~~~Ip~~ly~aVA~vl~~v~~l~  339 (367)
T PRK08156        315 RRYSFVSLEDIDEVLRLLIWLEEVE  339 (367)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             7888689999999999999999999


No 12 
>PRK12773 flhB flagellar biosynthesis protein FlhB; Reviewed
Probab=100.00  E-value=0  Score=818.29  Aligned_cols=345  Identities=23%  Similarity=0.346  Sum_probs=324.1

Q ss_pred             CCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHH
Q ss_conf             87768665878799999857875133599999999999999999999999999999999720001210497989999999
Q gi|254780690|r    7 PDNKTEAPSSKKIEDALNEGNAPISREASLFSSILACLIYLLFFFSPGIYSVTSDLHVLLASATQRKLEDISHIVFLLTH   86 (354)
Q Consensus         7 ~~eKTE~PT~kRL~dARekGqV~kS~el~~~~~ll~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (354)
                      +|+|||+|||||++|||||||||||+|++++++++++.+.+.++++....+....+..++.........+.......+..
T Consensus       300 DEGRTEpATpRRrRKAREEGqVpKS~EL~sAvVLLagvi~L~~mG~~~~~r~~~ll~~yl~~~~~~~~~~~~~~~~ll~~  379 (649)
T PRK12773        300 DEGRTEPGSERRRREEREKGNVPKSPELPAAVVLLAGVILVYLMGEYFFMRTYYILRKYIHGVGLRTDMSSESVTELLKN  379 (649)
T ss_pred             CCCCCCCCCHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHH
T ss_conf             67888999825689888557988761046899999999999999999999999999999874366632226789999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCCCCHHHHHHHCC-CHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999998877687853210137121377910169343033201-2667999999999999999999999
Q gi|254780690|r   87 LSLSASRLVIPGLLLFMMFGIGSYLIQRIPVLNLNHVKPSFKRVSLREGIKRIY-SINNLVNFMKSFVKIILVGTIITIS  165 (354)
Q Consensus        87 ~~~~~~~~~~p~~~~~~l~~i~~~l~q~G~~fs~k~l~pk~~rlNPi~GlKriF-S~k~lvel~KsllKv~li~~v~~~~  165 (354)
                      .....+.+++|+++++++++++++.+|+||+||+|+|+|||+|+||  |+||+| |.++|+||+||++|++++++++|.+
T Consensus       380 ~~~~~l~ll~PL~lv~~VaAllaNi~QVGFLFT~KpL~PKf~RINP--GFKriFsSr~sLfeL~KSL~KvvIIg~V~Ys~  457 (649)
T PRK12773        380 ASTDLFTLLWPLLGITLVGAIIGNVAQVGFIFTPRALSFNFSRIRP--NFKKVLPTRQTLFNLGKSLAKVGLIAWVSYII  457 (649)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHEEEEECCCCCCCCHHHCCC--CHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999999999888841346336777874442397--52220454789999999999999999999999


Q ss_pred             HHHCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCHHHHHH
Q ss_conf             98321568978408979999999999999999999999999997667999999984069989999997544899899999
Q gi|254780690|r  166 LTENYFTMLDFISANPHSILYHAFFTVRKVLIMILLFIATLTVLDIGWSYHQWYSKLKMSKQEIKDEIKQSYGNPIIKNR  245 (354)
Q Consensus       166 i~~~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD~~~qr~~~~k~lkMskqEvK~E~K~~EGdP~iK~~  245 (354)
                      ++.++..++.+...++...+.++..+...+++.+++++++||++||.||||+|+|+||||||||||||||+||||+||+|
T Consensus       458 Ir~~l~~il~l~dm~l~~~i~lv~~la~ki~l~~givLl~IAIiDy~yQR~e~~k~LKMSKQEVKdE~Ke~EGDP~IKar  537 (649)
T PRK12773        458 ISKDFFPILLSGEMGLEQAVALVMNSSFKIFLIVGIILLAISIVDYLYQRYEYEESLKMTPSEAKREAKESDGDRSLQAR  537 (649)
T ss_pred             HHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCHHHHHH
T ss_conf             99888877643158867899999999999999999999999999999999999996689889999886426799789999


Q ss_pred             HHHHHHHHHHH-HHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHHH
Q ss_conf             99999999998-89860776869987355307888976888888889980765899999999997399788688999999
Q gi|254780690|r  246 QKSIARSRIRH-KMMEATSRATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSL  324 (354)
Q Consensus       246 ~r~~~re~~~~-~~~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~L  324 (354)
                      |||+|||++++ +||++||+|||||||||||||||+||+++|+||+|||||+|++|++||++|+||||||+|||||||+|
T Consensus       538 iRq~qREma~~RrMm~~VPkADVVITNPTH~AVALkYd~~~m~AP~VVAKG~d~~A~rIreiArE~~VPIvEN~PLARAL  617 (649)
T PRK12773        538 RRQLARDMMNKRKMLAKVPEADVVITNPTHFAVALEYKPGIHKAPIVIAKGVDDFALLIIRIARENGVPTVEDRLQARGL  617 (649)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEEECCCEEEEEEEECCCCCCCCEEEECCCCHHHHHHHHHHHHCCCCEECCHHHHHHH
T ss_conf             99999999998889961999998982877156898855888889989863884799999999998599776187999999


Q ss_pred             HHHCCCCCCCCHHHHHHHHHHHHHHHHHC
Q ss_conf             97288989489899999999999997302
Q gi|254780690|r  325 FKQVPINSAIPPVFYKAVAQLIYKIYHKK  353 (354)
Q Consensus       325 y~~~~ig~~Ip~~~y~aVA~il~~v~~lk  353 (354)
                      |++||+|++||+|+|+||||||||+|++|
T Consensus       618 Y~~vEIG~eIP~elY~AVAEILA~vy~lr  646 (649)
T PRK12773        618 YEEVELGAEVPQQFYRAIATILSRLESFR  646 (649)
T ss_pred             HHCCCCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             85588888688999999999999999986


No 13 
>TIGR01404 FlhB_rel_III type III secretion protein, YscU/HrpY family; InterPro: IPR006307   This is one of several families of proteins related to bacterial flagellar biosynthesis proteins and involved in bacterial type III protein secretion systems. This family is homologous to, but distinguished from, the flagellar biosynthetic protein FlhB (IPR006136 from INTERPRO). This model may not identify all type III secretion system FlhB homologs. ; GO: 0006810 transport, 0016021 integral to membrane.
Probab=100.00  E-value=0  Score=794.11  Aligned_cols=342  Identities=25%  Similarity=0.373  Sum_probs=321.3

Q ss_pred             CCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHH
Q ss_conf             77686658787999998578751335999999999999999999999999999999997200012104979899999999
Q gi|254780690|r    8 DNKTEAPSSKKIEDALNEGNAPISREASLFSSILACLIYLLFFFSPGIYSVTSDLHVLLASATQRKLEDISHIVFLLTHL   87 (354)
Q Consensus         8 ~eKTE~PT~kRL~dARekGqV~kS~el~~~~~ll~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   87 (354)
                      +||||+|||||||||||||||+||+|+++++.+++++.+++++++.....+...+...+....+...   ..........
T Consensus         1 ~EKTEkPT~KKLrDarkKGQv~KS~Dl~~~~~~~~~~~~~~~~~~~~~~~l~~~~~l~~~~~~~~f~---~aL~~~~~~~   77 (346)
T TIGR01404         1 AEKTEKPTPKKLRDARKKGQVAKSKDLTSAVLLLAGFLYLLSLASVFLEHLIALLLLPLDFDDQPFA---YALKQVLSGF   77 (346)
T ss_pred             CCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHH---HHHHHHHHHH
T ss_conf             9999999701677667617853201799999999999999987678999999999878863044166---7799999999


Q ss_pred             -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             -9999999999999999887768785321013712137791016934303320126679999999999999999999999
Q gi|254780690|r   88 -SLSASRLVIPGLLLFMMFGIGSYLIQRIPVLNLNHVKPSFKRVSLREGIKRIYSINNLVNFMKSFVKIILVGTIITISL  166 (354)
Q Consensus        88 -~~~~~~~~~p~~~~~~l~~i~~~l~q~G~~fs~k~l~pk~~rlNPi~GlKriFS~k~lvel~KsllKv~li~~v~~~~i  166 (354)
                       +..++.+++|++++++++++++.++|+||+||+|+++||++||||++|+|||||.|+++||+||++|+++++.++|+++
T Consensus        78 ~l~~~~~~~l~~~~~v~~~~~~~~~~Q~Gf~lA~ea~Kpd~~klNP~~glK~IFS~rs~~El~Ks~lK~~~~a~~~~~~~  157 (346)
T TIGR01404        78 LLQLILTVLLPLLAIVLLATVLSGLLQVGFVLATEALKPDLSKLNPISGLKRIFSLRSLIELLKSILKVVALALIFYLFL  157 (346)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999999888733001101436681013835324677677649999999999999999999999


Q ss_pred             HHCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCHHHHHHH
Q ss_conf             83215689784089799999999999999999999999999976679999999840699899999975448998999999
Q gi|254780690|r  167 TENYFTMLDFISANPHSILYHAFFTVRKVLIMILLFIATLTVLDIGWSYHQWYSKLKMSKQEIKDEIKQSYGNPIIKNRQ  246 (354)
Q Consensus       167 ~~~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD~~~qr~~~~k~lkMskqEvK~E~K~~EGdP~iK~~~  246 (354)
                      .+++..+..++.+++.+.......++.+++..+++++++++++||+||||.|+|+||||||||||||||+||||||||+|
T Consensus       158 ~~~~~~l~~~~~~~~~~~~~~~~~ll~~l~~~~l~~~l~~~~~D~~~q~~~~~KdlkMsK~EVKrEyKe~EGdPeiK~~R  237 (346)
T TIGR01404       158 KNYLEELFALPYCGLDGLAPIVGELLKLLILVILGFFLVVGLADFAFQRYLFMKDLKMSKDEVKREYKEQEGDPEIKSKR  237 (346)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCHHHHH
T ss_conf             97499999851786678899999999999999999999999999999999998431899778864310278684134688


Q ss_pred             HHHHHHHHHHHHHHH---CCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHH
Q ss_conf             999999999889860---77686998735530788897688888888998076589999999999739978868899999
Q gi|254780690|r  247 KSIARSRIRHKMMEA---TSRATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARS  323 (354)
Q Consensus       247 r~~~re~~~~~~~~~---V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~  323 (354)
                      |++|+|++++++.++   |++||+||+|||||||||||.||++|+|.|+|||+|..|+++|++|++.|||||+|+||||+
T Consensus       238 R~lhqEi~se~~~~~sKPv~~s~~vv~NPTHiAi~iyY~p~etPlP~i~~~g~d~~A~~~~~~A~~~giPvv~~~~LAR~  317 (346)
T TIGR01404       238 RELHQEILSEQLKSDSKPVKRSTLVVANPTHIAIGIYYKPGETPLPLIIAKGTDAQALAVIAYAEEAGIPVVRDIPLARQ  317 (346)
T ss_pred             HHHHHHHHCCCCCCCCCCHHHCEEEEECCCCEEEEECCCCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEECCCHHHHH
T ss_conf             99998864154002688610286765566010112102567789877887356489999999999758985227479999


Q ss_pred             HHHHCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             99728898948989999999999999730
Q gi|254780690|r  324 LFKQVPINSAIPPVFYKAVAQLIYKIYHK  352 (354)
Q Consensus       324 Ly~~~~ig~~Ip~~~y~aVA~il~~v~~l  352 (354)
                      ||++++.|++||+++||+||+||+|+-++
T Consensus       318 Ly~~~~~~~~ip~~~~e~Va~~L~~l~~~  346 (346)
T TIGR01404       318 LYRTARVGQYIPEELLEAVAEVLRWLEQV  346 (346)
T ss_pred             HHHHCCCCCCCCHHHHHHHHHHHHHHHHC
T ss_conf             98405378888810078999999999609


No 14 
>COG4792 EscU Type III secretory pathway, component EscU [Intracellular trafficking and secretion]
Probab=100.00  E-value=0  Score=675.25  Aligned_cols=343  Identities=27%  Similarity=0.376  Sum_probs=318.5

Q ss_pred             CCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHH
Q ss_conf             87768665878799999857875133599999999999999999999999999999999720001210497989999999
Q gi|254780690|r    7 PDNKTEAPSSKKIEDALNEGNAPISREASLFSSILACLIYLLFFFSPGIYSVTSDLHVLLASATQRKLEDISHIVFLLTH   86 (354)
Q Consensus         7 ~~eKTE~PT~kRL~dARekGqV~kS~el~~~~~ll~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (354)
                      ++||||+||||||+||||||||+||+|+.+++.++++..+++.++......+...+.........+..   ..+...+..
T Consensus         2 s~EKTeqpTpKKLrDarkkGQV~kS~Eivs~v~~~al~~yf~l~g~~~~~~~~~ll~~~~~~~n~PF~---~Al~~il~~   78 (349)
T COG4792           2 SSEKTEQPTPKKLRDARKKGQVVKSKEIVSAVQLLALVAYFMLFGDSYFEHLVELLLFTIELLNLPFS---YALRQILGA   78 (349)
T ss_pred             CCCCCCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHH---HHHHHHHHH
T ss_conf             75446799815578788658864289999999999999999985289999999999428998368499---999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999887768785321013712137791016934303320126679999999999999999999999
Q gi|254780690|r   87 LSLSASRLVIPGLLLFMMFGIGSYLIQRIPVLNLNHVKPSFKRVSLREGIKRIYSINNLVNFMKSFVKIILVGTIITISL  166 (354)
Q Consensus        87 ~~~~~~~~~~p~~~~~~l~~i~~~l~q~G~~fs~k~l~pk~~rlNPi~GlKriFS~k~lvel~KsllKv~li~~v~~~~i  166 (354)
                      ....++..++|+.++.+++.+.+++.|.||+||.|+++||++||||++|+||+||.|++|||.||++|+++++.+.|+++
T Consensus        79 ll~~~l~~v~pl~~~~~v~tv~s~v~q~Gfl~a~eai~p~~~kINP~~~~K~ifS~rS~vEl~KS~lKV~vLslif~f~l  158 (349)
T COG4792          79 LLEELLYLVLPLLLVVIVATVLSGVLQVGFLFALEAIKPKAEKINPVQNAKRIFSLRSVVELLKSLLKVVVLSLIFWFML  158 (349)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999999886610257503568862206853417889739999999999999999999999999


Q ss_pred             HHCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCHHHHHHH
Q ss_conf             83215689784089799999999999999999999999999976679999999840699899999975448998999999
Q gi|254780690|r  167 TENYFTMLDFISANPHSILYHAFFTVRKVLIMILLFIATLTVLDIGWSYHQWYSKLKMSKQEIKDEIKQSYGNPIIKNRQ  246 (354)
Q Consensus       167 ~~~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD~~~qr~~~~k~lkMskqEvK~E~K~~EGdP~iK~~~  246 (354)
                      .+++.++.++..|+..|+.......+.++...+..++++++++||+||||++.|+|||||+|||+||||+|||||||++|
T Consensus       159 ~~~~~t~~~lp~CG~~C~~~Vv~~~~~~L~~g~~~~ylv~sv~Dy~fqr~~~~K~lkMSKdEVkRE~Kd~eG~PeiKskR  238 (349)
T COG4792         159 HGYANTFLYLPGCGLYCALPVVSFLLRLLWVGVAVGYLVFSVADYAFQRYQILKELKMSKDEVKREYKDMEGDPEIKSKR  238 (349)
T ss_pred             HHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHCCCCCCHHHHHH
T ss_conf             98899986046565006899999999999999999999999999999999999996167789989875036990366789


Q ss_pred             HHHHHHHHHHHHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHHHHH
Q ss_conf             99999999988986077686998735530788897688888888998076589999999999739978868899999997
Q gi|254780690|r  247 KSIARSRIRHKMMEATSRATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFK  326 (354)
Q Consensus       247 r~~~re~~~~~~~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~  326 (354)
                      ||+|.|++++++..+|+++|||+.||||+||+|+|.+|++|.|.|++||.|+.|.+|+.+|++++|||+||.||||+||+
T Consensus       239 Rq~~~Eiqsgsl~~nVkrStviv~nPThiaI~l~Y~~gETplPlVi~k~~daqA~~i~~iAe~~~ipVveni~LAraL~~  318 (349)
T COG4792         239 RQLHSEIQSGSLANNVKRSTVIVKNPTHIAICLRYKRGETPLPLVIEKGTDAQALQIVKIAEEEGIPVVENIPLARALYR  318 (349)
T ss_pred             HHHHHHHHCCCHHHCCCEEEEEEECCCEEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHHCCCEEECCHHHHHHHH
T ss_conf             99998873477432661104897268658999765268898877887267088999999999809970105398999986


Q ss_pred             HCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             28898948989999999999999730
Q gi|254780690|r  327 QVPINSAIPPVFYKAVAQLIYKIYHK  352 (354)
Q Consensus       327 ~~~ig~~Ip~~~y~aVA~il~~v~~l  352 (354)
                      .+++|++||+++||+||++|+|..++
T Consensus       319 d~~~g~~IP~~~fEpvA~lLr~a~~~  344 (349)
T COG4792         319 DVHVGQYIPEDFFEPVAALLRMAEDL  344 (349)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHC
T ss_conf             01048868389889999999999852


No 15 
>TIGR00789 flhB_rel FlhB domain protein; InterPro: IPR004683 This group describes a short protein (80-93 residues) homologous to the C-terminus of the flagellar biosynthetic protein FlhB. It is found so far only in species that also have FlhB. In a phylogenetic tree based on alignment of both this family and the homologous region of FlhB and its homologs, the members of this family form a monophyletic set..
Probab=99.75  E-value=3.8e-18  Score=164.15  Aligned_cols=80  Identities=33%  Similarity=0.550  Sum_probs=76.6

Q ss_pred             CCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             55307888976888888889980765899999999997399788688999999972889894898999999999999973
Q gi|254780690|r  272 PTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFKQVPINSAIPPVFYKAVAQLIYKIYH  351 (354)
Q Consensus       272 PTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~~~~ig~~Ip~~~y~aVA~il~~v~~  351 (354)
                      ++.=||||.|+.+.+.||+|||+|.|++|.||.+.|++||||+.||+.|.+.|-+ +++|..||+|+|++||+|.+|+|+
T Consensus         1 ~~~KAVAL~Y~~~~d~AP~V~AsG~GevA~~II~~AK~~gipi~ed~~L~~~L~~-l~l~~~IPee~Y~~Va~iFaFly~   79 (84)
T TIGR00789         1 KIKKAVALKYDKGKDKAPKVVASGVGEVAEKIIELAKKHGIPIKEDEDLVDVLLK-LDLDDEIPEELYEVVAEIFAFLYK   79 (84)
T ss_pred             CCCCCCCCCCCCCCCCCCEEEECCCCHHHHHHHHHHHHCCCCCCCCHHHHHHHHH-CCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             9742001365567886885774167657889999997638997658289998744-054576885788999999999998


Q ss_pred             H
Q ss_conf             0
Q gi|254780690|r  352 K  352 (354)
Q Consensus       352 l  352 (354)
                      +
T Consensus        80 ~   80 (84)
T TIGR00789        80 L   80 (84)
T ss_pred             H
T ss_conf             6


No 16 
>COG2257 Uncharacterized homolog of the cytoplasmic domain of flagellar protein FhlB [Function unknown]
Probab=99.72  E-value=4.3e-17  Score=155.86  Aligned_cols=80  Identities=36%  Similarity=0.567  Sum_probs=76.2

Q ss_pred             CCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             53078889768888888899807658999999999973997886889999999728898948989999999999999730
Q gi|254780690|r  273 THYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFKQVPINSAIPPVFYKAVAQLIYKIYHK  352 (354)
Q Consensus       273 TH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~~~~ig~~Ip~~~y~aVA~il~~v~~l  352 (354)
                      +.=||||+||.+++.||+|+|+|.|++|.+|.+.|++|+|||.|||.|++.|-+ .++|+.||+++|+.||||++|+|++
T Consensus         7 ~r~AvAl~Yd~~~~~AP~vvA~G~G~iAe~II~~Ake~~Vpi~edp~Lv~~L~~-lelg~~IPeelY~vVAEifafi~~~   85 (92)
T COG2257           7 IRKAVALAYDEGKDKAPKVVASGKGEIAEKIIEKAKEHGVPIQEDPLLVELLLK-LELGDEIPEELYEVVAEIFAFIYEV   85 (92)
T ss_pred             CCHHEEEEECCCCCCCCEEEEECCHHHHHHHHHHHHHCCCCCCCCHHHHHHHHH-CCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             441113322467888888776264289999999999849985118899999984-6456648999999999999999999


Q ss_pred             C
Q ss_conf             2
Q gi|254780690|r  353 K  353 (354)
Q Consensus       353 k  353 (354)
                      .
T Consensus        86 ~   86 (92)
T COG2257          86 D   86 (92)
T ss_pred             H
T ss_conf             7


No 17 
>COG1377 FlhB Flagellar biosynthesis pathway, component FlhB [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=97.81  E-value=0.0066  Score=43.48  Aligned_cols=314  Identities=16%  Similarity=0.169  Sum_probs=182.9

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHH--HHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHH
Q ss_conf             99876787768665878799999--8578751335999999999999999999999999999999997200012104979
Q gi|254780690|r    1 MSENDAPDNKTEAPSSKKIEDAL--NEGNAPISREASLFSSILACLIYLLFFFSPGIYSVTSDLHVLLASATQRKLEDIS   78 (354)
Q Consensus         1 MAe~d~~~eKTE~PT~kRL~dAR--ekGqV~kS~el~~~~~ll~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~   78 (354)
                      |++++-+|+=|++==++=++|-+  +--+++.+  ++..++++....+..++......-+...+........+.. ....
T Consensus         4 ~~~~eKTE~pT~kKl~dArekG~v~kS~el~~a--~~ll~g~~~l~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~-~~~~   80 (363)
T COG1377           4 MADDEKTEKPTPKKLRDAREKGQVPKSRELTSA--ASLLVGFLLLFFFGSYFARRLSGFLRAFLEFPESMDLDDE-SALE   80 (363)
T ss_pred             CCCCCCCCCCCHHHHHHHHHCCCCCCCHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCH-HHHH
T ss_conf             434456778985669999974788630668999--9999999999999999999999999999826242123722-5999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-H--HCCCHHHCCCCCCCCCHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             899999999999999999999999988776878532-1--0137121377910169343033201266799999999999
Q gi|254780690|r   79 HIVFLLTHLSLSASRLVIPGLLLFMMFGIGSYLIQR-I--PVLNLNHVKPSFKRVSLREGIKRIYSINNLVNFMKSFVKI  155 (354)
Q Consensus        79 ~~~~~~~~~~~~~~~~~~p~~~~~~l~~i~~~l~q~-G--~~fs~k~l~pk~~rlNPi~GlKriFS~k~lvel~KsllKv  155 (354)
                      .....+..++..++.++++++++.+++.++.+..+. +  .-.-++++.| ++.+.=+=+.+.++-.  +-.++|-++=.
T Consensus        81 ~~~~~~~~~~~~llp~~~~~~v~gi~~~~~q~g~~fs~e~ikP~~~kinP-~~G~KRiFs~~~~vEl--lKsllKi~~v~  157 (363)
T COG1377          81 LIKALLLEILKALLPFLLVLLVVGLLANILQVGFLFSTEALKPKFSKLNP-IKGLKRIFSLQTLVEL--LKSLLKIVLVG  157 (363)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCH-HHHHHHHHHHHHHHHH--HHHHHHHHHHH
T ss_conf             99999999999999999999999999999984763146346777211493-6778998458899999--99999999999


Q ss_pred             HHHHHHHHHHHHHCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCHHHHHHHHH
Q ss_conf             99999999999832156897840897999999999999999999999999999766799999998406-99899999975
Q gi|254780690|r  156 ILVGTIITISLTENYFTMLDFISANPHSILYHAFFTVRKVLIMILLFIATLTVLDIGWSYHQWYSKLK-MSKQEIKDEIK  234 (354)
Q Consensus       156 ~li~~v~~~~i~~~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD~~~qr~~~~k~lk-MskqEvK~E~K  234 (354)
                       ++++.++.--++.+..+..................+.-.+..+++.++++.++---||+.+-.|=-| =-|+|.||--=
T Consensus       158 -~v~~~~l~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~l~~~~~~liia~~D~~~qr~~~~k~lkMtKqEVKdE~K~sEG  236 (363)
T COG1377         158 -LVAYFVLKNHLSELLSLAGQSPVAALSIFMELLGKLLLAVLLLLLIVAAFDYFYQRFQYIKKLKMTKQEVKDEYKQSEG  236 (363)
T ss_pred             -HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCC
T ss_conf             -9999999941999997704898999999999999999999999999999999999999999666868999999861569


Q ss_pred             HCCCCHHHHHHHHHHHHHHHHHHHHHH-------------------CCCCCEEEEC-CCCEEEEEEECCCCCCCCEEEEE
Q ss_conf             448998999999999999999889860-------------------7768699873-55307888976888888889980
Q gi|254780690|r  235 QSYGNPIIKNRQKSIARSRIRHKMMEA-------------------TSRATIIITN-PTHYALALRYIQTENDAPVLVAK  294 (354)
Q Consensus       235 ~~EGdP~iK~~~r~~~re~~~~~~~~~-------------------V~~A~vvitN-PTH~AVAL~Y~~~~~~aP~vvaK  294 (354)
                      |-|=--.+|++.|+++|+..+...-.+                   -.+|-+||.- --|.|..+|=...+.+.|++-.+
T Consensus       237 dPeVKsr~Rq~~re~a~~rm~~~Vp~AdvVItNPTH~AVAlkY~~~~~~AP~VvAKG~d~~AlkIreiA~e~~Ipi~enp  316 (363)
T COG1377         237 DPEVKSRIRQMQREIARRRMMSDVPKADVVITNPTHYAVALKYDPEKMPAPVVVAKGVDLVALKIREIAKEHGIPIIENP  316 (363)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEECCH
T ss_conf             80566899999999999999851899888972766113454665555899989981786999999999998499564180


Q ss_pred             CCCHHHHHHHHHH-HHCCCCEEECHHHHHHH
Q ss_conf             7658999999999-97399788688999999
Q gi|254780690|r  295 GQNLIAKKMRKIA-YEHNIPIFEEPSLARSL  324 (354)
Q Consensus       295 G~~~~A~~Ir~~A-~~~~Vpive~~~LAR~L  324 (354)
                         .+|..+=... ...-||---=...|+-|
T Consensus       317 ---pLARaLY~~~~v~~~IP~e~y~aVaevL  344 (363)
T COG1377         317 ---PLARALYRQVEVGQQIPEELYKAVAEVL  344 (363)
T ss_pred             ---HHHHHHHHHCCCCCCCCHHHHHHHHHHH
T ss_conf             ---7799999725766648999999999999


No 18 
>PRK12468 flhB flagellar biosynthesis protein FlhB; Reviewed
Probab=97.58  E-value=0.014  Score=40.93  Aligned_cols=235  Identities=16%  Similarity=0.137  Sum_probs=127.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--H-HHHHCCCHHHCCC--CCCCCCHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999988776878--5-3210137121377--91016934303320126679999999999
Q gi|254780690|r   80 IVFLLTHLSLSASRLVIPGLLLFMMFGIGSYL--I-QRIPVLNLNHVKP--SFKRVSLREGIKRIYSINNLVNFMKSFVK  154 (354)
Q Consensus        80 ~~~~~~~~~~~~~~~~~p~~~~~~l~~i~~~l--~-q~G~~fs~k~l~p--k~~rlNPi~GlKriFS~k~lvel~KsllK  154 (354)
                      +...+......++.++++++++.+++.++.+.  . ---..+.+++|.|  .++|+=-.+++..+     +-.++|.++=
T Consensus        82 ~~~~l~~~~~~~lpi~~~~~i~~i~~~~~q~G~~fs~k~l~Pk~~rlNPi~GlKRiFS~k~LvEl-----~KsllK~~li  156 (383)
T PRK12468         82 IGMLLRQTLLAMLPIFAGLVIVALAVPMLLGGVLFSGESIKFDLKRMSPVAGLKRMFSSQALAEL-----LKAILKATLV  156 (383)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHCCHHHCCCCCCCHHHHHHH-----HHHHHHHHHH
T ss_conf             99999999999999999999999999997104031443368655435864441111257789999-----9999999999


Q ss_pred             HHHHHHHHHHHHHHCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHCCCHHHHHHHH
Q ss_conf             999999999999832156897840897999999999999999999999999999766799999998-4069989999997
Q gi|254780690|r  155 IILVGTIITISLTENYFTMLDFISANPHSILYHAFFTVRKVLIMILLFIATLTVLDIGWSYHQWYS-KLKMSKQEIKDEI  233 (354)
Q Consensus       155 v~li~~v~~~~i~~~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD~~~qr~~~~k-~lkMskqEvK~E~  233 (354)
                      ..+...++|..+...+........+.+...+....... ..+...+++++++..+--.|++.+-.| +-.==|+|-||--
T Consensus       157 ~~v~~~~l~~~~~~~~~l~~~~~~~~l~~~~~~~~~~~-~~~~l~l~~ia~iD~~~Qr~~~~k~LkMSKqEVKdE~Ke~E  235 (383)
T PRK12468        157 GWVTGLFLWHNWPDMMRLIAAPPVAALGDALHLIIFCG-LVVVLGLSPMVGFDVFYQITSHIKKLRMTKQDIRDEFKNQE  235 (383)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCC
T ss_conf             99999999998999999862489999999999999999-99999999999999999999999874899999999988663


Q ss_pred             HHCCCCHHHHHHHHHHHHHHHHHHHHHH-------------------CCCCCEEEEC-CCCEEEEEEECCCCCCCCEEEE
Q ss_conf             5448998999999999999999889860-------------------7768699873-5530788897688888888998
Q gi|254780690|r  234 KQSYGNPIIKNRQKSIARSRIRHKMMEA-------------------TSRATIIITN-PTHYALALRYIQTENDAPVLVA  293 (354)
Q Consensus       234 K~~EGdP~iK~~~r~~~re~~~~~~~~~-------------------V~~A~vvitN-PTH~AVAL~Y~~~~~~aP~vva  293 (354)
                      =|-|=--++|+++|+++++........+                   ...|-+|+.- --|.|-.+|=...+...|+|--
T Consensus       236 GdP~iK~r~R~~~re~a~~~m~~~V~~AdvVItNPTH~AVAL~Y~~~~~~aP~VvAKG~d~~A~~Ir~~A~~~~VPiven  315 (383)
T PRK12468        236 GDPHVKGRIRQQQRAMARRRMMVDVPKADVIVTNPTHYAVALQYNESKMSAPKVLAKGAGAVALRIRELGAEHRIPLLEA  315 (383)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCHHHHEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEECC
T ss_conf             99999999999999999878872689898899785538742353788899998988368499999999999869988637


Q ss_pred             ECCCHHHHHHHHHHH-HCCCCEEECHHHHHH
Q ss_conf             076589999999999-739978868899999
Q gi|254780690|r  294 KGQNLIAKKMRKIAY-EHNIPIFEEPSLARS  323 (354)
Q Consensus       294 KG~~~~A~~Ir~~A~-~~~Vpive~~~LAR~  323 (354)
                      +   .+|..+-...+ ...||---=.+.|+-
T Consensus       316 ~---pLAR~Ly~~~evg~~IP~ely~aVA~v  343 (383)
T PRK12468        316 P---PLARALFRHSEVGQHIPATLYAAVAEV  343 (383)
T ss_pred             H---HHHHHHHHCCCCCCCCCHHHHHHHHHH
T ss_conf             7---999999871778997899999999999


No 19 
>PRK05702 flhB flagellar biosynthesis protein FlhB; Reviewed
Probab=97.50  E-value=0.017  Score=40.22  Aligned_cols=259  Identities=15%  Similarity=0.174  Sum_probs=144.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--
Q ss_conf             999999999999999999999999999999972000121049798999999999999999999999999887768785--
Q gi|254780690|r   35 SLFSSILACLIYLLFFFSPGIYSVTSDLHVLLASATQRKLEDISHIVFLLTHLSLSASRLVIPGLLLFMMFGIGSYLI--  112 (354)
Q Consensus        35 ~~~~~ll~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~l~~i~~~l~--  112 (354)
                      ...+.+++...+..+++... .++.........................+..++...+.+++.++++.+++.++.+-.  
T Consensus        38 ~l~~~~~~l~~~~~~~~~~l-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~i~~~~~Q~G~~f  116 (352)
T PRK05702         38 VLLAGLVGLWFFGGSLARRL-AGMLRALFSFDREIAFDPNDMLSLFGLLILELLLALLPILLLLVLAALLAPILQGGWLF  116 (352)
T ss_pred             HHHHHHHHHHHHHHHHHHHH-HHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             99999999999999999999-99999998354412478689999999999999999999999999999999998527451


Q ss_pred             -HHHHCCCHHHCCC--CCCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             -3210137121377--9101693430332012667999999999999999999999983215689784089799999999
Q gi|254780690|r  113 -QRIPVLNLNHVKP--SFKRVSLREGIKRIYSINNLVNFMKSFVKIILVGTIITISLTENYFTMLDFISANPHSILYHAF  189 (354)
Q Consensus       113 -q~G~~fs~k~l~p--k~~rlNPi~GlKriFS~k~lvel~KsllKv~li~~v~~~~i~~~~~~l~~l~~~~~~~~l~~~~  189 (354)
                       -.-..+.+++|.|  .++|+=   +.|.++-.  +-.++|-++=..+...+.+..+ ..+..+...........+....
T Consensus       117 s~k~l~pk~~rlNPi~GlKriF---S~k~LvEl--~KsllKv~~i~~v~~~~~~~~~-~~~~~l~~~~~~~~~~~~~~~~  190 (352)
T PRK05702        117 SGKALKPKFSKLNPLKGLKRMF---SAQGLVEL--LKSLLKVLLVGGVAYFVLWSNL-DELLSLAALPLEAALGHALDLV  190 (352)
T ss_pred             CCCCCCCCHHHCCHHHCHHHHC---CHHHHHHH--HHHHHHHHHHHHHHHHHHHHHH-HHHHHHHCCCHHHHHHHHHHHH
T ss_conf             6424788846549724523120---88899999--9999999999999999999999-9999885389999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHH---C--C
Q ss_conf             9999999999999999999766799999998-40699899999975448998999999999999999889860---7--7
Q gi|254780690|r  190 FTVRKVLIMILLFIATLTVLDIGWSYHQWYS-KLKMSKQEIKDEIKQSYGNPIIKNRQKSIARSRIRHKMMEA---T--S  263 (354)
Q Consensus       190 ~~~~~l~~~~~~~~~via~iD~~~qr~~~~k-~lkMskqEvK~E~K~~EGdP~iK~~~r~~~re~~~~~~~~~---V--~  263 (354)
                      ..+...+..++++++++..+--.|++.+-.| +-.=-|+|-||--=|-|=--++|+++|++.|+..+.+...+   |  |
T Consensus       191 ~~l~~~~~~~~~via~~D~~~qr~~~~k~lkMSkqEvKdE~K~~EGdP~iK~~~R~~~re~a~~~m~~~V~~A~vVItNP  270 (352)
T PRK05702        191 LKLLLLVVLALLVIAAIDVPFQRWQYLKKLKMTKQEVKDEYKQSEGDPEVKGRIRQLQREMARRRMMAAVPKADVVITNP  270 (352)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEECC
T ss_conf             99999999999999999999999999988389999999999865299999999999999999867873388797899999


Q ss_pred             --------------CCCEEEEC-CCCEEEEEEECCCCCCCCEEEEECCCHHHHHH
Q ss_conf             --------------68699873-55307888976888888889980765899999
Q gi|254780690|r  264 --------------RATIIITN-PTHYALALRYIQTENDAPVLVAKGQNLIAKKM  303 (354)
Q Consensus       264 --------------~A~vvitN-PTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~I  303 (354)
                                    .|-+|+.- --|.|-.+|=...+.+.|+|--+   .+|+.+
T Consensus       271 TH~AVAL~Y~~~~~~aP~VvAKG~d~~A~~Ir~~A~~~~VPive~~---pLARaL  322 (352)
T PRK05702        271 THYAVALKYDRGKMAAPVVVAKGVDEVALRIREIAREHNVPIVENP---PLARAL  322 (352)
T ss_pred             CCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECH---HHHHHH
T ss_conf             8628998878899999988774586999999999998699887478---999999


No 20 
>PRK13109 flhB flagellar biosynthesis protein FlhB; Reviewed
Probab=97.26  E-value=0.031  Score=38.13  Aligned_cols=294  Identities=12%  Similarity=0.102  Sum_probs=145.4

Q ss_pred             CCCCCCCCCCCHHHHHH-----HHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHH
Q ss_conf             67877686658787999-----9985787513359999999999999999999999999999999972000121049798
Q gi|254780690|r    5 DAPDNKTEAPSSKKIED-----ALNEGNAPISREASLFSSILACLIYLLFFFSPGIYSVTSDLHVLLASATQRKLEDISH   79 (354)
Q Consensus         5 d~~~eKTE~PT~kRL~d-----ARekGqV~kS~el~~~~~ll~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~   79 (354)
                      |-+|+=|++==++=++|     +||   +  +.-....+.+++...+...........+...+.......... ..+...
T Consensus         9 eKTE~PT~kRL~~ARekGqVakS~E---l--~~~~~ll~~l~~l~~~~~~~~~~l~~~~~~~l~~~~~~~~~~-~~~~~~   82 (358)
T PRK13109          9 SKTEEPTERKVRDAIEKGDIPVSRE---A--SIFASMLGLLIILAFFARGQVAQLTRDLAPLLDDPRGFTLET-GADAIL   82 (358)
T ss_pred             CCCCCCCHHHHHHHHHCCCCCCHHH---H--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC-HHHHHH
T ss_conf             9899998578999996799965786---9--999999999999999999999999999999982740024221-565999


Q ss_pred             -HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHCCCHHHCCC--CCCCCCHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             -9999999999999999999999998877687---853210137121377--9101693430332012667999999999
Q gi|254780690|r   80 -IVFLLTHLSLSASRLVIPGLLLFMMFGIGSY---LIQRIPVLNLNHVKP--SFKRVSLREGIKRIYSINNLVNFMKSFV  153 (354)
Q Consensus        80 -~~~~~~~~~~~~~~~~~p~~~~~~l~~i~~~---l~q~G~~fs~k~l~p--k~~rlNPi~GlKriFS~k~lvel~Ksll  153 (354)
                       .......+....+.+++.++++.+++.++.+   +.-.-..+.+++|.|  .++|+=   +.+.++-.  +-.++|-++
T Consensus        83 ~~~~~~~~~~~~l~P~~~~~~v~~i~~~~~Q~G~~fs~k~l~Pk~~kLNPi~GlKriF---S~~~Lvel--~KsllK~~~  157 (358)
T PRK13109         83 LLSRVGLAAGRFLLPILLVLAVAGLAASLLQNLPRFVLDRIQPKWSRISPMKGWTRIF---GTQGQVEF--AKSLFKFLS  157 (358)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEECCCCCCCCHHHCCHHHHHHHHC---CHHHHHHH--HHHHHHHHH
T ss_conf             9999999999999999999999999999860140305412688767659735056542---58789999--999999999


Q ss_pred             HHHHHHHHHHHHHHHCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHCCCHHHHHHH
Q ss_conf             9999999999999832156897840897999999999999999999999999999766799999998-406998999999
Q gi|254780690|r  154 KIILVGTIITISLTENYFTMLDFISANPHSILYHAFFTVRKVLIMILLFIATLTVLDIGWSYHQWYS-KLKMSKQEIKDE  232 (354)
Q Consensus       154 Kv~li~~v~~~~i~~~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD~~~qr~~~~k-~lkMskqEvK~E  232 (354)
                      =.++...+.+..+.. +..+...........+......+...+..++++++++..+--.|++.+-.| +-.==|+|.||-
T Consensus       158 l~~v~~~~l~~~~~~-~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~via~~D~~~Qr~~~~k~lkMskqEvK~E~K~~  236 (358)
T PRK13109        158 VSVVVLLLLRSERAK-AVNAMFVDPSALPELILTVAMRLVSAVSIATIVLVALDLVWARFHWRRSLRMTKQEIKDEHKQA  236 (358)
T ss_pred             HHHHHHHHHHHHHHH-HHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHC
T ss_conf             999999999988999-9998744899999999999999999999999999999999999999986489999999998866


Q ss_pred             HHHCCCCHHHHHHHHHHHHHHHHHHHHHH-------------------CCCCCEEEE-CCCCEEEEEEECCCCCCCCEEE
Q ss_conf             75448998999999999999999889860-------------------776869987-3553078889768888888899
Q gi|254780690|r  233 IKQSYGNPIIKNRQKSIARSRIRHKMMEA-------------------TSRATIIIT-NPTHYALALRYIQTENDAPVLV  292 (354)
Q Consensus       233 ~K~~EGdP~iK~~~r~~~re~~~~~~~~~-------------------V~~A~vvit-NPTH~AVAL~Y~~~~~~aP~vv  292 (354)
                      -=|-|=--++|+++|+++++..+.....+                   ...|-+|+. .--|.|-.+|=...+...|+|-
T Consensus       237 EGdP~iK~r~R~~~re~a~~~m~~~V~~AdvVitNPTH~AVAL~Y~~~~~~aP~VvAKG~d~~A~~Ir~~A~~~~VPive  316 (358)
T PRK13109        237 EGDPSVKARLRSLAQDRARNRMLAAVPRATLVIANPTHFAIALRYERSENPAPLVVAKGQDLIALKIREIAERNGIPVIE  316 (358)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEC
T ss_conf             39999999999999999987787258988389988871567766668999999888845869999999999987997870


Q ss_pred             EECCCHHHHHHHHHHH-HCCCC
Q ss_conf             8076589999999999-73997
Q gi|254780690|r  293 AKGQNLIAKKMRKIAY-EHNIP  313 (354)
Q Consensus       293 aKG~~~~A~~Ir~~A~-~~~Vp  313 (354)
                      .+   .+|+.+-...+ ..-||
T Consensus       317 ~~---pLARaLy~~~~vg~~IP  335 (358)
T PRK13109        317 DK---PLARSLYDAVQVDQVIP  335 (358)
T ss_pred             CH---HHHHHHHHCCCCCCCCC
T ss_conf             78---99999997077899689


No 21 
>PRK06298 type III secretion system protein; Validated
Probab=97.15  E-value=0.04  Score=37.32  Aligned_cols=220  Identities=12%  Similarity=0.100  Sum_probs=125.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHCCCHHHCCC--CCCCCCHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             9999999999999999999999998877687---853210137121377--91016934303320126679999999999
Q gi|254780690|r   80 IVFLLTHLSLSASRLVIPGLLLFMMFGIGSY---LIQRIPVLNLNHVKP--SFKRVSLREGIKRIYSINNLVNFMKSFVK  154 (354)
Q Consensus        80 ~~~~~~~~~~~~~~~~~p~~~~~~l~~i~~~---l~q~G~~fs~k~l~p--k~~rlNPi~GlKriFS~k~lvel~KsllK  154 (354)
                      ....+..+....+.+++.++++.++++++..   +.-.-..+.+++|.|  .++|+=   +.|.++-.  +-.++|-++=
T Consensus        76 ~~~~~~~~~~~~lP~~~~~~~~~i~~~~~q~G~~fs~k~l~Pk~~rlNPi~GlKriF---S~k~LvEl--~KsllKv~~~  150 (360)
T PRK06298         76 LKNCLMLILTASLPLLGAVAFVGVIIGFLIVGPTFSTEVFKPDIKKFNPIDNLKQKF---KVKTLIEL--LKSILKISGA  150 (360)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCEECHHHHHHHHH---CHHHHHHH--HHHHHHHHHH
T ss_conf             999999999999999999999999999986455336101578742136878788860---48789999--9999999999


Q ss_pred             HHHHHHHHHHHHHHCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHCCCHHHHHHHH
Q ss_conf             999999999999832156897840897999999999999999999999999999766799999998-4069989999997
Q gi|254780690|r  155 IILVGTIITISLTENYFTMLDFISANPHSILYHAFFTVRKVLIMILLFIATLTVLDIGWSYHQWYS-KLKMSKQEIKDEI  233 (354)
Q Consensus       155 v~li~~v~~~~i~~~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD~~~qr~~~~k-~lkMskqEvK~E~  233 (354)
                      ..+...+++..+. .+..+..................+...+..+++++.++..+--.|++.+-.| +-.=-|+|-||--
T Consensus       151 ~~v~~~~l~~~~~-~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~via~~D~~~qr~~~~k~LkMSkqEvKdE~Ke~E  229 (360)
T PRK06298        151 ALILYIVLKNRVP-LIIETAGVPPIVTAQIFKEILYKAVTSIGIFFLVVAVLDLVYQRHNFAKELKMEKFEVKQEFKDTE  229 (360)
T ss_pred             HHHHHHHHHHHHH-HHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCC
T ss_conf             9999999999999-999882589999999999999999999999999999999999999999870799999998988663


Q ss_pred             HHCCCCHHHHHHHHHHHHHHHHHHHHHH-C----C--------------CCCEEEE-CCCCEEEEEEECCCCCCCCEEEE
Q ss_conf             5448998999999999999999889860-7----7--------------6869987-35530788897688888888998
Q gi|254780690|r  234 KQSYGNPIIKNRQKSIARSRIRHKMMEA-T----S--------------RATIIIT-NPTHYALALRYIQTENDAPVLVA  293 (354)
Q Consensus       234 K~~EGdP~iK~~~r~~~re~~~~~~~~~-V----~--------------~A~vvit-NPTH~AVAL~Y~~~~~~aP~vva  293 (354)
                      =|=|=--++|+.+|+++++..+.+...+ |    |              .|-+|+. .--|.|-.+|=-..+...|+|--
T Consensus       230 GdP~vK~r~R~~~re~a~~~m~~~V~~A~vVitNPTH~AVAL~Y~~~~~~aP~vvAKG~d~~A~~Ir~~A~~~~VPiven  309 (360)
T PRK06298        230 GNPEIKGRRRQIAQEIAYEDTSSQVKHASAVVSNPKDIAVAIGYMPEKYKAPWIIAMGINLRAKRIIAEAEKYGIPIMRN  309 (360)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCEEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEECC
T ss_conf             99999999999999999717872699998899888617888666689999998888548599999999999879988717


Q ss_pred             ECCCHHHHHHHHHHH
Q ss_conf             076589999999999
Q gi|254780690|r  294 KGQNLIAKKMRKIAY  308 (354)
Q Consensus       294 KG~~~~A~~Ir~~A~  308 (354)
                      +   .+|+.+-...+
T Consensus       310 ~---pLARaLy~~~~  321 (360)
T PRK06298        310 V---PLAHQLLDEGK  321 (360)
T ss_pred             H---HHHHHHHHHCC
T ss_conf             6---99999998267


No 22 
>PRK09108 type III secretion system protein HrcU; Validated
Probab=97.04  E-value=0.049  Score=36.60  Aligned_cols=287  Identities=13%  Similarity=0.123  Sum_probs=153.6

Q ss_pred             CCCCCCCCCCCCCCCHHHHHH-----HHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHH
Q ss_conf             998767877686658787999-----998578751335999999999999999999999999999999997200-01210
Q gi|254780690|r    1 MSENDAPDNKTEAPSSKKIED-----ALNEGNAPISREASLFSSILACLIYLLFFFSPGIYSVTSDLHVLLASA-TQRKL   74 (354)
Q Consensus         1 MAe~d~~~eKTE~PT~kRL~d-----ARekGqV~kS~el~~~~~ll~~~~~l~~~~~~~~~~l~~~~~~~~~~~-~~~~~   74 (354)
                      |||| -+|+=|++==++=++|     +||   +...-  ..+++++....+..+++... ..+........... +....
T Consensus         1 MSdE-KTE~PT~kRl~dARekGqV~kS~E---l~~~~--~L~~~~~~l~~~~~~~~~~l-~~~~~~~~~~~~~~~~~~~~   73 (354)
T PRK09108          1 MSDE-KTEEPTEKKLKDARRDGEVAKSPD---LTAAA--VLLAALLVLTAAGSYLTDHL-RALVRTALDFVSGERSLQAL   73 (354)
T ss_pred             CCCC-CCCCCCHHHHHHHHHCCCCCCHHH---HHHHH--HHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHCCCCCCHHHH
T ss_conf             9988-899998578999997699974786---99999--99999999999999999999-99999998622454678999


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHCCCHHHCCC--CCCCCCHHHHHHHCCCHHHHHHHH
Q ss_conf             497989999999999999999999999998877687---853210137121377--910169343033201266799999
Q gi|254780690|r   75 EDISHIVFLLTHLSLSASRLVIPGLLLFMMFGIGSY---LIQRIPVLNLNHVKP--SFKRVSLREGIKRIYSINNLVNFM  149 (354)
Q Consensus        75 ~~~~~~~~~~~~~~~~~~~~~~p~~~~~~l~~i~~~---l~q~G~~fs~k~l~p--k~~rlNPi~GlKriFS~k~lvel~  149 (354)
                        ...............+.+++..+++.+++.++..   +.--...+.+++|.|  .++|+=-.+++-.+     +-.++
T Consensus        74 --~~~~~~~~~~~~~~~lp~~~~~~~~~i~~~~~Q~G~~fs~k~l~pk~~rlNPi~GlKriFS~k~LvEl-----~Ksll  146 (354)
T PRK09108         74 --LAALHHIGAQALLLMLPFVAAALVAGILGQAPQTGLNISLKPVMPKFDSLNPAAGLKKIFSLRSLIEL-----VKMIV  146 (354)
T ss_pred             --HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHCCCCHHCCCHHHHHHCCCCHHHHHHH-----HHHHH
T ss_conf             --99999999999999999999999999999984036540514136760205865544244468889999-----99999


Q ss_pred             HHHHHHHHHHHHHHHHHHHCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHCCCHHH
Q ss_conf             99999999999999999832156897840897999999999999999999999999999766799999998-40699899
Q gi|254780690|r  150 KSFVKIILVGTIITISLTENYFTMLDFISANPHSILYHAFFTVRKVLIMILLFIATLTVLDIGWSYHQWYS-KLKMSKQE  228 (354)
Q Consensus       150 KsllKv~li~~v~~~~i~~~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD~~~qr~~~~k-~lkMskqE  228 (354)
                      |-++=.+++..+. .-....+..+...........+......+...+..+++++.++...--.|++.+-.| +-.==|+|
T Consensus       147 Kv~~l~~v~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~~~~~~~via~~D~~~qr~~~~k~LkMSkqEvK~E  225 (354)
T PRK09108        147 KAVVIACVLWKTI-TSLFPLIVGAAYESPPQLAQILWTVLMKLLAVAALVFLVVGAADWKIQRWLFIRDNRMSKDEVKRE  225 (354)
T ss_pred             HHHHHHHHHHHHH-HHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf             9999999999999-999999999850699999999999999999999999999999999999999999738998999999


Q ss_pred             HHHHHHHCCCCHHHHHHHHHHHHH-HHHHHHHHH---C----------------CCCCEEEEC-CCCEEEEEEECCCCCC
Q ss_conf             999975448998999999999999-999889860---7----------------768699873-5530788897688888
Q gi|254780690|r  229 IKDEIKQSYGNPIIKNRQKSIARS-RIRHKMMEA---T----------------SRATIIITN-PTHYALALRYIQTEND  287 (354)
Q Consensus       229 vK~E~K~~EGdP~iK~~~r~~~re-~~~~~~~~~---V----------------~~A~vvitN-PTH~AVAL~Y~~~~~~  287 (354)
                      .||--=|-|=--++|+++|+++++ +.+.+...+   |                ..|-+|+.- --|.|-.+|=...+..
T Consensus       226 ~K~~EGdP~vK~r~R~~~re~a~~~~~~~~V~~A~vVitNPTH~AVAL~Y~~~~~~aP~VvAKG~d~~A~~Ir~~A~~~~  305 (354)
T PRK09108        226 HKESEGDPHLKGERKRLARELATFAPPRQRVAKANVVVVNPTHYAVALRYAPDEHPLPRVVAKGVDDGALALRRHAHALG  305 (354)
T ss_pred             HHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCEEEEEEECCCCCCCCEEHHHCCCHHHHHHHHHHHHCC
T ss_conf             88664998999999999999997443653578784899876604678675788898898112168399999999999869


Q ss_pred             CCEEEEECCCHHHHHHHH
Q ss_conf             888998076589999999
Q gi|254780690|r  288 APVLVAKGQNLIAKKMRK  305 (354)
Q Consensus       288 aP~vvaKG~~~~A~~Ir~  305 (354)
                      .|+|--+   .+|..+-+
T Consensus       306 VPiven~---pLAR~Ly~  320 (354)
T PRK09108        306 IPIVANP---PVARALYR  320 (354)
T ss_pred             CCEEECH---HHHHHHHC
T ss_conf             9787188---99999970


No 23 
>PRK12721 secretion system apparatus protein SsaU; Reviewed
Probab=97.02  E-value=0.051  Score=36.45  Aligned_cols=185  Identities=12%  Similarity=0.097  Sum_probs=104.3

Q ss_pred             HHHHHHCCCHHHCCC--CCCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHCCCHHHHHHHH
Q ss_conf             853210137121377--910169343033201266799999999999999999999998321568978408979999999
Q gi|254780690|r  111 LIQRIPVLNLNHVKP--SFKRVSLREGIKRIYSINNLVNFMKSFVKIILVGTIITISLTENYFTMLDFISANPHSILYHA  188 (354)
Q Consensus       111 l~q~G~~fs~k~l~p--k~~rlNPi~GlKriFS~k~lvel~KsllKv~li~~v~~~~i~~~~~~l~~l~~~~~~~~l~~~  188 (354)
                      +.-.-..+.++.+.|  .++|+=-.+++-++     +-.++|.++=.++...+.+..+ ..+..+........-......
T Consensus       109 fs~k~l~pk~~rlNPi~GlKriFS~k~lvEl-----~KsllKv~lv~~i~~~~l~~~~-~~~~~l~~~~~~~~l~~~~~~  182 (349)
T PRK12721        109 LATKAIGFKGEKINPVSNAKQIFSLHSVFEL-----CKSLLKVIVLSLIFAFLLYYYA-PTFRALPYCGSACALPVVSTL  182 (349)
T ss_pred             ECHHHCCCCHHHCCHHHHHHHHCCHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHH-HHHHHHHCCCHHHHHHHHHHH
T ss_conf             0714148766545874535543377679999-----9999999999999999999999-999987547999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHH-H-----
Q ss_conf             99999999999999999999766799999998-4069989999997544899899999999999999988986-0-----
Q gi|254780690|r  189 FFTVRKVLIMILLFIATLTVLDIGWSYHQWYS-KLKMSKQEIKDEIKQSYGNPIIKNRQKSIARSRIRHKMME-A-----  261 (354)
Q Consensus       189 ~~~~~~l~~~~~~~~~via~iD~~~qr~~~~k-~lkMskqEvK~E~K~~EGdP~iK~~~r~~~re~~~~~~~~-~-----  261 (354)
                      ...+...++.+++++.++..+--.|++.+-.| +-.=-|+|-||--=|-|=--++|+.+|+++|+..+..... +     
T Consensus       183 ~~~l~~~~~~~llviai~D~~~Qr~~~~k~LkMSKqEVKdE~K~~EGdP~iK~r~R~~~re~a~~~m~~~V~~AdvVitN  262 (349)
T PRK12721        183 IKWLWGGVIAFYLVFGILDYAFQRYKIMKQLKMSKDDVKQEHKDSEGDPEIKQKRRELQSEIQSGSLAQNVKKSTAVVRN  262 (349)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEC
T ss_conf             99999999999999999999999999998738999999999886639999999999999999985787268999889988


Q ss_pred             -------------CCCCCEEEEC-CCCEEEEEEECCCCCCCCEEEEECCCHHHHHHH
Q ss_conf             -------------7768699873-553078889768888888899807658999999
Q gi|254780690|r  262 -------------TSRATIIITN-PTHYALALRYIQTENDAPVLVAKGQNLIAKKMR  304 (354)
Q Consensus       262 -------------V~~A~vvitN-PTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir  304 (354)
                                   ...|-+|+.- --|.|-.+|=...+...|+|-.+   .+|+.+-
T Consensus       263 PTH~AVAL~Y~~~~~~aP~vvAKG~d~~A~~Ir~~A~~~~vPiven~---~LAR~Ly  316 (349)
T PRK12721        263 PTHIAVCLGYHPGETPLPRVLEKGSDAQALYIVNLAERNGIPVVENI---PLARALF  316 (349)
T ss_pred             CCHHHHHHHCCCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEECCH---HHHHHHH
T ss_conf             65276400026889999988885385999999999998799786287---9999999


No 24 
>PRK12773 flhB flagellar biosynthesis protein FlhB; Reviewed
Probab=96.93  E-value=0.061  Score=35.87  Aligned_cols=285  Identities=14%  Similarity=0.165  Sum_probs=148.8

Q ss_pred             CCCCC-CCCCCCCCCHHHHHHHH-HHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHH
Q ss_conf             98767-87768665878799999-85787513359999999999999999999999999999999972000121049798
Q gi|254780690|r    2 SENDA-PDNKTEAPSSKKIEDAL-NEGNAPISREASLFSSILACLIYLLFFFSPGIYSVTSDLHVLLASATQRKLEDISH   79 (354)
Q Consensus         2 Ae~d~-~~eKTE~PT~kRL~dAR-ekGqV~kS~el~~~~~ll~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~   79 (354)
                      ||+|+ .|.=||.=-++=++|-+ -|-|=..| -+...+..++...+..++......-+...+...-.... ........
T Consensus       298 AEDEGRTEpATpRRrRKAREEGqVpKS~EL~s-AvVLLagvi~L~~mG~~~~~r~~~ll~~yl~~~~~~~~-~~~~~~~~  375 (649)
T PRK12773        298 AEDEGRTEPGSERRRREEREKGNVPKSPELPA-AVVLLAGVILVYLMGEYFFMRTYYILRKYIHGVGLRTD-MSSESVTE  375 (649)
T ss_pred             CCCCCCCCCCCHHHHHHHHHCCCCCCCCCHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC-CCHHHHHH
T ss_conf             45678889998256898885579887610468-99999999999999999999999999999874366632-22678999


Q ss_pred             HH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHH-HHCCCHHHCCCCCCCCCHHH-HHHHCCCHHHHHHHHHHHHH
Q ss_conf             99-99999999999999999999998877687--8532-10137121377910169343-03320126679999999999
Q gi|254780690|r   80 IV-FLLTHLSLSASRLVIPGLLLFMMFGIGSY--LIQR-IPVLNLNHVKPSFKRVSLRE-GIKRIYSINNLVNFMKSFVK  154 (354)
Q Consensus        80 ~~-~~~~~~~~~~~~~~~p~~~~~~l~~i~~~--l~q~-G~~fs~k~l~pk~~rlNPi~-GlKriFS~k~lvel~KsllK  154 (354)
                      .. ......+..+..+++..+++.+++.++..  +... -..+.++.+.|.|+|+.|.. ++=+++     -.++|..+=
T Consensus       376 ll~~~~~~~l~ll~PL~lv~~VaAllaNi~QVGFLFT~KpL~PKf~RINPGFKriFsSr~sLfeL~-----KSL~KvvII  450 (649)
T PRK12773        376 LLKNASTDLFTLLWPLLGITLVGAIIGNVAQVGFIFTPRALSFNFSRIRPNFKKVLPTRQTLFNLG-----KSLAKVGLI  450 (649)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEEECCCCCCCCHHHCCCCHHHCCCCHHHHHHHH-----HHHHHHHHH
T ss_conf             999999999999999999999999998888413463367778744423975222045478999999-----999999999


Q ss_pred             HHHHHHHHHHHHHHCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC-CCHHHHHHHH
Q ss_conf             999999999999832156897840897999999999999999999999999999766799999998406-9989999997
Q gi|254780690|r  155 IILVGTIITISLTENYFTMLDFISANPHSILYHAFFTVRKVLIMILLFIATLTVLDIGWSYHQWYSKLK-MSKQEIKDEI  233 (354)
Q Consensus       155 v~li~~v~~~~i~~~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD~~~qr~~~~k~lk-MskqEvK~E~  233 (354)
                      ..+.-.+..--+.. +..+...+..+....+......+.-.+..+++++.++..+--.|++.+-.|=-| =-|+|-||--
T Consensus       451 g~V~Ys~Ir~~l~~-il~l~dm~l~~~i~lv~~la~ki~l~~givLl~IAIiDy~yQR~e~~k~LKMSKQEVKdE~Ke~E  529 (649)
T PRK12773        451 AWVSYIIISKDFFP-ILLSGEMGLEQAVALVMNSSFKIFLIVGIILLAISIVDYLYQRYEYEESLKMTPSEAKREAKESD  529 (649)
T ss_pred             HHHHHHHHHHHHHH-HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCC
T ss_conf             99999999988887-76431588678999999999999999999999999999999999999966898899998864267


Q ss_pred             HHCCCCHHHHHHHHHHHHH--HHHHHHHHHC------------------CCCCEEEECC-CCEEEEEEECCCCCCCCEEE
Q ss_conf             5448998999999999999--9998898607------------------7686998735-53078889768888888899
Q gi|254780690|r  234 KQSYGNPIIKNRQKSIARS--RIRHKMMEAT------------------SRATIIITNP-THYALALRYIQTENDAPVLV  292 (354)
Q Consensus       234 K~~EGdP~iK~~~r~~~re--~~~~~~~~~V------------------~~A~vvitNP-TH~AVAL~Y~~~~~~aP~vv  292 (354)
                      -|-|=--.+|++.|++++.  |.++=..++|                  ..|-+|+.-- -+.|--+|=...+...|+|=
T Consensus       530 GDP~IKariRq~qREma~~RrMm~~VPkADVVITNPTH~AVALkYd~~~m~AP~VVAKG~d~~A~rIreiArE~~VPIvE  609 (649)
T PRK12773        530 GDRSLQARRRQLARDMMNKRKMLAKVPEADVVITNPTHFAVALEYKPGIHKAPIVIAKGVDDFALLIIRIARENGVPTVE  609 (649)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCEEEEEEEECCCCCCCCEEEECCCCHHHHHHHHHHHHCCCCEEC
T ss_conf             99789999999999999988899619999989828771568988558888899898638847999999999985997761


Q ss_pred             EE
Q ss_conf             80
Q gi|254780690|r  293 AK  294 (354)
Q Consensus       293 aK  294 (354)
                      .+
T Consensus       610 N~  611 (649)
T PRK12773        610 DR  611 (649)
T ss_pred             CH
T ss_conf             87


No 25 
>TIGR00328 flhB flagellar biosynthetic protein FlhB; InterPro: IPR006136   The flhB and flhA genes constitute an operon called flhB operon on the Salmonella typhimurium chromosome. They, together with FliI and FliH, may constitute the export apparatus of flagellin, the component protein of flagellar filament. The flhB gene encodes a highly hydrophobic polypeptide with several potential membrane-spanning segments, suggesting that it may be an integral membrane protein .; GO: 0009306 protein secretion, 0016020 membrane.
Probab=96.80  E-value=0.075  Score=35.12  Aligned_cols=221  Identities=17%  Similarity=0.170  Sum_probs=151.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999999999999720001210497989999999999999999999999998877687853
Q gi|254780690|r   34 ASLFSSILACLIYLLFFFSPGIYSVTSDLHVLLASATQRKLEDISHIVFLLTHLSLSASRLVIPGLLLFMMFGIGSYLIQ  113 (354)
Q Consensus        34 l~~~~~ll~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~l~~i~~~l~q  113 (354)
                      ++..++++..+.+...+.......+.......-.............+...+..++..++.++.+++++.++..++-+...
T Consensus        31 ~~ll~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~llp~~~~~l~~g~~~~~~Q~G~~  110 (352)
T TIGR00328        31 AVLLAGVLVLLFFGSEGLADLLEALMSFFLSLETSDLLELESLVEIIIELIREVLLLLLPILVLLLVVGVLSNILQTGFL  110 (352)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             99999999999988999999999999987532335531479999999999999999999999999999999988873023


Q ss_pred             -HH--HCCCHHHCCCCC----CC-CCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHCCCHHHHH
Q ss_conf             -21--013712137791----01-69343033201266799999999999999999999998321568978408979999
Q gi|254780690|r  114 -RI--PVLNLNHVKPSF----KR-VSLREGIKRIYSINNLVNFMKSFVKIILVGTIITISLTENYFTMLDFISANPHSIL  185 (354)
Q Consensus       114 -~G--~~fs~k~l~pk~----~r-lNPi~GlKriFS~k~lvel~KsllKv~li~~v~~~~i~~~~~~l~~l~~~~~~~~l  185 (354)
                       +.  .-+-+++|.||+    +| |   =|++-+|-.  +-.++|-++=.++...+++.-+..-..-........+...+
T Consensus       111 ft~k~l~Pk~~KiNP~~~~G~KRS~---FS~~~lvEl--~Ks~lKv~lv~~v~~~~l~~~~~~~~~L~~~~~~~~~~~~~  185 (352)
T TIGR00328       111 FTTKPLKPKLSKINPDVIKGLKRSL---FSLQSLVEL--LKSILKVFLVSLVAYFVLKNSLGELLSLSLYSLQQALTNAL  185 (352)
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHH---HHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHH
T ss_conf             3435466676758876886676877---778899999--99999999999999999986588999886148889999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999766799999998-4069989999997544899899999999999999988986
Q gi|254780690|r  186 YHAFFTVRKVLIMILLFIATLTVLDIGWSYHQWYS-KLKMSKQEIKDEIKQSYGNPIIKNRQKSIARSRIRHKMME  260 (354)
Q Consensus       186 ~~~~~~~~~l~~~~~~~~~via~iD~~~qr~~~~k-~lkMskqEvK~E~K~~EGdP~iK~~~r~~~re~~~~~~~~  260 (354)
                      . ....+...+..++++++++..+---||+.+-.| .-.==|+|.||--=|=|=-=.+|+++|++.|+.++...-+
T Consensus       186 ~-~~~~~~~~v~~~l~~~a~~D~~~qr~~y~~~LkMtkQEvKdE~Kq~EGdP~vKgRiRq~qr~~ar~rMm~~VPk  260 (352)
T TIGR00328       186 D-LALSLLLLVLLLLLVIAVFDYFFQRWQYIKSLKMTKQEVKDELKQSEGDPEVKGRIRQMQREAARRRMMQEVPK  260 (352)
T ss_pred             H-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             9-99999999999999999986999999998723677688877741269484436889999999999999874468


No 26 
>pfam01312 Bac_export_2 FlhB HrpN YscU SpaS Family. This family includes the following members: FlhB, HrpN, YscU, SpaS, HrcU SsaU and YopU. All of these proteins export peptides using the type III secretion system. The peptides exported are quite diverse.
Probab=96.72  E-value=0.085  Score=34.69  Aligned_cols=286  Identities=16%  Similarity=0.162  Sum_probs=151.1

Q ss_pred             CCCCCCCCCCCCCCCHHHHHH-----HHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             998767877686658787999-----998578751335999999999999999999999999999999997200012104
Q gi|254780690|r    1 MSENDAPDNKTEAPSSKKIED-----ALNEGNAPISREASLFSSILACLIYLLFFFSPGIYSVTSDLHVLLASATQRKLE   75 (354)
Q Consensus         1 MAe~d~~~eKTE~PT~kRL~d-----ARekGqV~kS~el~~~~~ll~~~~~l~~~~~~~~~~l~~~~~~~~~~~~~~~~~   75 (354)
                      |||| -+|+=|++==.+=++|     +||=+.   +  +...++++.......+++... .++.................
T Consensus         1 mS~E-KTE~PT~kRL~dARekGqV~~S~el~~---~--~~l~~~~~~l~~~~~~~~~~l-~~~~~~~~~~~~~~~~~~~~   73 (343)
T pfam01312         1 MSEE-KTEKPTPKKLRDARKKGQVPKSQDLTS---A--ASLLAGSAYLFLLGSVFARRL-IALLLLTLILIPLPFSLSVT   73 (343)
T ss_pred             CCCC-CCCCCCHHHHHHHHHCCCCCCHHHHHH---H--HHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHCCCCCCHHHH
T ss_conf             9988-899998578999997699975787999---9--999999999999999999999-99999999736544440367


Q ss_pred             CH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHCCCHHHCCC--CCCCCCHHHHHHHCCCHHHHHHHH
Q ss_conf             97-98999999999999999999999999887768---7853210137121377--910169343033201266799999
Q gi|254780690|r   76 DI-SHIVFLLTHLSLSASRLVIPGLLLFMMFGIGS---YLIQRIPVLNLNHVKP--SFKRVSLREGIKRIYSINNLVNFM  149 (354)
Q Consensus        76 ~~-~~~~~~~~~~~~~~~~~~~p~~~~~~l~~i~~---~l~q~G~~fs~k~l~p--k~~rlNPi~GlKriFS~k~lvel~  149 (354)
                      .. ............  ...++.++++.++..++.   .+.-.-..+.+++|.|  .++|+=-.+++-.+     +-.++
T Consensus        74 ~~~~~~~~~~~~~~~--~~~~~~~~l~~i~~~~~q~G~~fs~k~l~Pk~~rlNPi~GlKriFS~~~LvEl-----~Ksll  146 (343)
T pfam01312        74 DLFSLVVLLLLTVLL--LLSLFVALLVGLASNLLQVGFLFSTEAIKPDFSKINPIKGLKRIFSARSLVEL-----LKSIL  146 (343)
T ss_pred             HHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHCCCCEECHHHCCCCHHHCCHHHCHHCCCCHHHHHHH-----HHHHH
T ss_conf             999999999999999--99999999999999986036340603147773336874442200377789999-----99999


Q ss_pred             HHHHHHHHHHHHHHHHHHHCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHCCCHHH
Q ss_conf             99999999999999999832156897840897999999999999999999999999999766799999998-40699899
Q gi|254780690|r  150 KSFVKIILVGTIITISLTENYFTMLDFISANPHSILYHAFFTVRKVLIMILLFIATLTVLDIGWSYHQWYS-KLKMSKQE  228 (354)
Q Consensus       150 KsllKv~li~~v~~~~i~~~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD~~~qr~~~~k-~lkMskqE  228 (354)
                      |-++=..+...+.+.. ...+..+......+...........+...+..+++++.++...--.|++.+-.| +-.==|+|
T Consensus       147 Kv~li~~v~~~~l~~~-~~~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~via~~D~~~Qr~~~~k~lkMSkqEvKdE  225 (343)
T pfam01312       147 KVVAVGLIFYFFLKND-LGTIVRLPGCSPMGIIVIVMTLLKKLLLVVLLFLLIVGLLDYLFQRYLFIKDLKMSKQEVKRE  225 (343)
T ss_pred             HHHHHHHHHHHHHHHH-HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf             9999999999999999-999998844999999999999999999999999999999999999999999808999999999


Q ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH-HHC----C--------------CCCEEE-ECCCCEEEEEEECCCCCCC
Q ss_conf             9999754489989999999999999998898-607----7--------------686998-7355307888976888888
Q gi|254780690|r  229 IKDEIKQSYGNPIIKNRQKSIARSRIRHKMM-EAT----S--------------RATIII-TNPTHYALALRYIQTENDA  288 (354)
Q Consensus       229 vK~E~K~~EGdP~iK~~~r~~~re~~~~~~~-~~V----~--------------~A~vvi-tNPTH~AVAL~Y~~~~~~a  288 (354)
                      -||--=|-|=--++|+++|+++|+..+.+.. ++|    |              .|-+|+ -.--|.|-.+|=...+...
T Consensus       226 ~Ke~EGdP~iK~~~R~~~re~~~~~m~~~V~~A~vVItNPTH~AVAL~Y~~~~~~aP~vvAKG~d~~A~~Ir~~A~~~~V  305 (343)
T pfam01312       226 YKESEGDPHVKGRRRQIAREIASERMMQDVPKADVVVTNPTHYAVALYYDPEEMPAPRIVAKGEDEQALAIRAIAEENGI  305 (343)
T ss_pred             HHHCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCC
T ss_conf             88643998899999999999998578725898988999998627898878899999988885486999999999998799


Q ss_pred             CEEEEECCCHHHHHHH
Q ss_conf             8899807658999999
Q gi|254780690|r  289 PVLVAKGQNLIAKKMR  304 (354)
Q Consensus       289 P~vvaKG~~~~A~~Ir  304 (354)
                      |+|--+   .+|+.+-
T Consensus       306 Piven~---~LAR~Ly  318 (343)
T pfam01312       306 PVVENP---PLARALY  318 (343)
T ss_pred             CEEECH---HHHHHHH
T ss_conf             788377---9999999


No 27 
>PRK12772 bifunctional flagellar biosynthesis protein FliR/FlhB; Provisional
Probab=95.30  E-value=0.35  Score=29.87  Aligned_cols=289  Identities=16%  Similarity=0.167  Sum_probs=148.3

Q ss_pred             CCCCCCCCCCCCCCHHHHHH---HHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHCCH
Q ss_conf             98767877686658787999---998578751335999999999999999999999999999999997200-01210497
Q gi|254780690|r    2 SENDAPDNKTEAPSSKKIED---ALNEGNAPISREASLFSSILACLIYLLFFFSPGIYSVTSDLHVLLASA-TQRKLEDI   77 (354)
Q Consensus         2 Ae~d~~~eKTE~PT~kRL~d---ARekGqV~kS~el~~~~~ll~~~~~l~~~~~~~~~~l~~~~~~~~~~~-~~~~~~~~   77 (354)
                      |.+|-+||=|.+=-++=++|   ||.+- +..  -+...+.++....+..+++......+...+....... +....  .
T Consensus       261 asdEKTE~pTpKkl~dARkkGqVakS~e-l~~--a~~ll~~~~~l~~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~  335 (609)
T PRK12772        261 ASDDKTEEATPKKKSDARKKGQVAKSKE-VAL--AITLLACTLVLSALGEYVANTLKETMIYFLNNYLNMNLNYLNL--N  335 (609)
T ss_pred             CCCCCCCCCCHHHHHHHHHCCCCCCHHH-HHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHH--H
T ss_conf             4877789998156998985789877274-999--9999999999999999999999999999985330024787889--9


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHCCCHHHCCC--CCCCCCHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             98999999999999999999999999887768785---3210137121377--910169343033201266799999999
Q gi|254780690|r   78 SHIVFLLTHLSLSASRLVIPGLLLFMMFGIGSYLI---QRIPVLNLNHVKP--SFKRVSLREGIKRIYSINNLVNFMKSF  152 (354)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~p~~~~~~l~~i~~~l~---q~G~~fs~k~l~p--k~~rlNPi~GlKriFS~k~lvel~Ksl  152 (354)
                      ......+.......+.++++++++..++.++..-.   --.....++++.|  .++|+==.+++...     +-.++|-+
T Consensus       336 ~~~~~~~~~~~~~~~P~~~~~~~~~i~a~~~Q~G~~fs~~~l~Pk~~klnPi~G~KriFS~~~l~El-----~KsllK~~  410 (609)
T PRK12772        336 SLIIFTLLRVGKIFLPVALPIMVFGIAANLLQTGFLFTKEPLKPDLKKLNPINGFKRMFSMRTVMEL-----LKDLVIIT  410 (609)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEECCCCCCCCHHHCCHHHHHHHHHCHHHHHHH-----HHHHHHHH
T ss_conf             9999999999999999999999999999986016341530158862644887789998178889999-----99999999


Q ss_pred             HHHHHHHHHHHHHHHHCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHCCCHHHHHH
Q ss_conf             99999999999999832156897840897999999999999999999999999999766799999998-40699899999
Q gi|254780690|r  153 VKIILVGTIITISLTENYFTMLDFISANPHSILYHAFFTVRKVLIMILLFIATLTVLDIGWSYHQWYS-KLKMSKQEIKD  231 (354)
Q Consensus       153 lKv~li~~v~~~~i~~~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD~~~qr~~~~k-~lkMskqEvK~  231 (354)
                      +=..+...+.+ --+..+..+...........+......+...+....+.++++...--.|++.+-.| +-.=-|+|-||
T Consensus       411 ~v~~v~y~~~~-~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~lvia~~D~~~Q~~~~~k~lkMskqEvK~E~K~  489 (609)
T PRK12772        411 VVGIVGYKFLQ-DNYLDILNLGNLRLPYLITGLLSLVISIFFRITLIMIIIAVADYVYQKYQYNKDLKMTKQEVKEEYKQ  489 (609)
T ss_pred             HHHHHHHHHHH-HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf             99999999999-99999998743899999999999999999999999999999999999999999768989999989875


Q ss_pred             HHHHCCCCHHHHHHHHHHHHHHHHHHHHHH-------------------CCCCCEEEEC-CCCEEEEEEECCCCCCCCEE
Q ss_conf             975448998999999999999999889860-------------------7768699873-55307888976888888889
Q gi|254780690|r  232 EIKQSYGNPIIKNRQKSIARSRIRHKMMEA-------------------TSRATIIITN-PTHYALALRYIQTENDAPVL  291 (354)
Q Consensus       232 E~K~~EGdP~iK~~~r~~~re~~~~~~~~~-------------------V~~A~vvitN-PTH~AVAL~Y~~~~~~aP~v  291 (354)
                      --=|-|=--++|+++||++|+..+.+...+                   ...|-+|+.- --|.|-.+|=...+...|+|
T Consensus       490 ~EGdP~iK~r~Rq~~re~a~~rm~~~Vp~AdVVitNPTH~AVALkYd~~~~~AP~VvAKG~d~~A~~IreiA~e~~vPiv  569 (609)
T PRK12772        490 DEGDPQIKSKIKQKQREMAMQRMMQEVPDATVVVTNPTHIAVALKYEKGKDTAPKVVAKGADYVALKIKEIAKENEVPII  569 (609)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEECCCHHHEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEE
T ss_conf             53999999999999999998678731898998988733364043436899999988861785999999999998699876


Q ss_pred             EEECCCHHHHHHH
Q ss_conf             9807658999999
Q gi|254780690|r  292 VAKGQNLIAKKMR  304 (354)
Q Consensus       292 vaKG~~~~A~~Ir  304 (354)
                      -.+   .+|+.+-
T Consensus       570 en~---pLARaLy  579 (609)
T PRK12772        570 ENK---PLARLIY  579 (609)
T ss_pred             CCH---HHHHHHH
T ss_conf             182---9899999


No 28 
>PRK08156 surface presentation of antigens protein SpaS; Validated
Probab=95.13  E-value=0.39  Score=29.49  Aligned_cols=225  Identities=13%  Similarity=0.138  Sum_probs=134.6

Q ss_pred             HHHHHHHHHHHHHHHHHH---HHHHHHHCCCHHHCCC--CCCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999887768---7853210137121377--91016934303320126679999999999999999999999
Q gi|254780690|r   92 SRLVIPGLLLFMMFGIGS---YLIQRIPVLNLNHVKP--SFKRVSLREGIKRIYSINNLVNFMKSFVKIILVGTIITISL  166 (354)
Q Consensus        92 ~~~~~p~~~~~~l~~i~~---~l~q~G~~fs~k~l~p--k~~rlNPi~GlKriFS~k~lvel~KsllKv~li~~v~~~~i  166 (354)
                      +.+++.++++.+++.++.   .+.---..+.+++|.|  .++|+=-.+++-.+     +-.++|.++=.+ +++.++...
T Consensus        82 ~P~~~~~~l~~i~a~l~Q~G~~fs~k~l~Pk~~kLNPi~GlKRiFS~k~LvEl-----~KsllK~~~l~~-~~~~~~~~~  155 (367)
T PRK08156         82 IPFLLLCLLAGALPSLLQTRFVLATEAIKLNFSALNPVKGLKKIFSLRTVKEF-----VKALLYLIVFAL-TAYVFWKKY  155 (367)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCEECCHHCCCCHHHCCHHHHHCCCCCHHHHHHH-----HHHHHHHHHHHH-HHHHHHHHH
T ss_conf             99999999999999997217641602036536437864410011357689999-----999999999999-999999988


Q ss_pred             HHCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHCCCHHHHHHHHHHCCCCHHHHHH
Q ss_conf             832156897840897999999999999999999999999999766799999998-4069989999997544899899999
Q gi|254780690|r  167 TENYFTMLDFISANPHSILYHAFFTVRKVLIMILLFIATLTVLDIGWSYHQWYS-KLKMSKQEIKDEIKQSYGNPIIKNR  245 (354)
Q Consensus       167 ~~~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD~~~qr~~~~k-~lkMskqEvK~E~K~~EGdP~iK~~  245 (354)
                      ...+..+......+...........+...++.++++++++..+---|++.+-.| +-.=-|+|.||--=|=|=--++|++
T Consensus       156 ~~~l~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~via~iD~~~Qr~~~~k~LrMSkqEVKdE~Ke~EGdP~vK~r~R~~  235 (367)
T PRK08156        156 KKEIFSQLNGNIVGLIVIWRELLVALVLTFLACALIVLILDAIAEYFLYMKDMKMDKQEVKREYKEQEGNPEIKSKRREA  235 (367)
T ss_pred             HHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCHHHHHHHHHH
T ss_conf             99999985079999999999999999999999999999999999999999974899899999988663999999999999


Q ss_pred             HHHHHHHHHHHHHHH-H------------------CCCCCEEEE-CCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHH
Q ss_conf             999999999988986-0------------------776869987-35530788897688888888998076589999999
Q gi|254780690|r  246 QKSIARSRIRHKMME-A------------------TSRATIIIT-NPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRK  305 (354)
Q Consensus       246 ~r~~~re~~~~~~~~-~------------------V~~A~vvit-NPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~  305 (354)
                      +|+++|+..+...-. +                  ...|-+|+. .--|.|-.||=-..+...|+|-.+   .+|..+-.
T Consensus       236 ~re~a~~~m~~~Vp~AdVVItNPTH~AVALkY~~~~~~AP~VvAKG~d~~A~~Ir~~A~e~~VPive~~---pLARaLy~  312 (367)
T PRK08156        236 HQEILSEQVKSDIENSRLIVANPTHIAIGIYFNPDLAPIPFISVRETNQRALAVRAYAEKVGVPVVRDI---KLARSLYK  312 (367)
T ss_pred             HHHHHHHHHHHCCCCCCEEEECCCHHHEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEECCH---HHHHHHHH
T ss_conf             999998679734899998998856220465546888999988874685999999999998699886276---99999997


Q ss_pred             HHHHC-CCCEEECHHHHHHHH
Q ss_conf             99973-997886889999999
Q gi|254780690|r  306 IAYEH-NIPIFEEPSLARSLF  325 (354)
Q Consensus       306 ~A~~~-~Vpive~~~LAR~Ly  325 (354)
                      ..+.. -||---=...|+-|.
T Consensus       313 ~~~~~~~Ip~~ly~aVA~vl~  333 (367)
T PRK08156        313 THRRYSFVSLEDIDEVLRLLI  333 (367)
T ss_pred             HCCCCCCCCHHHHHHHHHHHH
T ss_conf             267888689999999999999


No 29 
>COG1422 Predicted membrane protein [Function unknown]
Probab=91.09  E-value=1.5  Score=24.80  Aligned_cols=56  Identities=11%  Similarity=0.082  Sum_probs=33.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHC--CCCHHHHHHHHHHHHHHHHH
Q ss_conf             999999997667999999984069989999997544--89989999999999999998
Q gi|254780690|r  201 LFIATLTVLDIGWSYHQWYSKLKMSKQEIKDEIKQS--YGNPIIKNRQKSIARSRIRH  256 (354)
Q Consensus       201 ~~~~via~iD~~~qr~~~~k~lkMskqEvK~E~K~~--EGdP~iK~~~r~~~re~~~~  256 (354)
                      +..+.+.++-+.+--|+-.++++=.-+|-++|+++.  +||+.-=-|.++.|+|+++-
T Consensus        56 i~gl~~~i~~~~liD~ekm~~~qk~m~efq~e~~eA~~~~d~~~lkkLq~~qmem~~~  113 (201)
T COG1422          56 ITGLYITILQKLLIDQEKMKELQKMMKEFQKEFREAQESGDMKKLKKLQEKQMEMMDD  113 (201)
T ss_pred             HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHH
T ss_conf             9999999999996029999999999999999999999808899999999999999999


No 30 
>cd01423 MGS_CPS_I_III Methylglyoxal synthase-like domain found in pyr1 and URA1-like carbamoyl phosphate synthetases (CPS), including ammonia-dependent CPS Type I, and glutamine-dependent CPS Type III. These are multidomain proteins, in which MGS is the C-terminal domain.
Probab=82.56  E-value=3.3  Score=22.12  Aligned_cols=59  Identities=17%  Similarity=0.298  Sum_probs=41.3

Q ss_pred             HCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCE
Q ss_conf             44899899999999999999988986077686998735530788897688888888998076589999999999739978
Q gi|254780690|r  235 QSYGNPIIKNRQKSIARSRIRHKMMEATSRATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPI  314 (354)
Q Consensus       235 ~~EGdP~iK~~~r~~~re~~~~~~~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpi  314 (354)
                      .++|.|.+..-+++              .+=|.||.=|+.-.                 +..+.-..+||+.|-+++||.
T Consensus        56 ~~~~~p~i~d~i~~--------------g~i~lVINtp~~~~-----------------~~~~~~g~~iRr~Av~~~Ip~  104 (116)
T cd01423          56 PQNDKPSLRELLAE--------------GKIDLVINLPSNRG-----------------KRVLDNDYVMRRAADDFAVPL  104 (116)
T ss_pred             CCCCCCCHHHHHHC--------------CCEEEEEECCCCCC-----------------CCCCCCCHHHHHHHHHCCCCE
T ss_conf             78999669999976--------------98689998889998-----------------643354589999999759998


Q ss_pred             EECHHHHHHH
Q ss_conf             8688999999
Q gi|254780690|r  315 FEEPSLARSL  324 (354)
Q Consensus       315 ve~~~LAR~L  324 (354)
                      +-|+..|+++
T Consensus       105 ~T~~~~A~~~  114 (116)
T cd01423         105 ITNPKCAKLF  114 (116)
T ss_pred             EECHHHHHHH
T ss_conf             9779999987


No 31 
>cd01821 Rhamnogalacturan_acetylesterase_like Rhamnogalacturan_acetylesterase_like subgroup of SGNH-hydrolases. Rhamnogalacturan acetylesterase removes acetyl esters from rhamnogalacturonan substrates, and renders them susceptible to degradation by rhamnogalacturonases. Rhamnogalacturonans are highly branched regions in pectic polysaccharides, consisting of repeating -(1,2)-L-Rha-(1,4)-D-GalUA disaccharide units, with many rhamnose residues substituted by neutral oligosaccharides such as arabinans, galactans and arabinogalactans. Extracellular enzymes participating in the degradation of plant cell wall polymers, such as Rhamnogalacturonan acetylesterase, would typically be found in saprophytic and plant pathogenic fungi and bacteria.
Probab=81.66  E-value=4.2  Score=21.30  Aligned_cols=67  Identities=19%  Similarity=0.333  Sum_probs=49.5

Q ss_pred             CCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHHHHHHCCCCCCCCHHHH
Q ss_conf             76869987355307888976888888889980765899999999997399788688999999972889894898999
Q gi|254780690|r  263 SRATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFKQVPINSAIPPVFY  339 (354)
Q Consensus       263 ~~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~~~~ig~~Ip~~~y  339 (354)
                      ..|++|+..|+.=   -.|+.+.     .+-..-+.-+..+|+.|++.+||.|.=-.+-+.+|.  .+|.+--..+|
T Consensus       106 ~ga~pIL~Tp~~R---r~~~~~~-----~~~~~~~~Y~~a~r~vA~e~~Vp~IDL~~~s~~~~~--~~G~~~s~~~~  172 (198)
T cd01821         106 KGATPILVTPVTR---RTFDEGG-----KVEDTLGDYPAAMRELAAEEGVPLIDLNAASRALYE--AIGPEKSKKYF  172 (198)
T ss_pred             CCCEEEEECCCCC---CCCCCCC-----EECCCCHHHHHHHHHHHHHCCCCEECHHHHHHHHHH--HHCHHHHHHHC
T ss_conf             5998999758877---6448998-----223772679999999999829989833899999999--87978899867


No 32 
>PRK05294 carB carbamoyl phosphate synthase large subunit; Reviewed
Probab=80.43  E-value=3.7  Score=21.75  Aligned_cols=79  Identities=16%  Similarity=0.202  Sum_probs=54.1

Q ss_pred             HHHHHHHCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEEC
Q ss_conf             99998406998999999754489989999999999999998898607768699873553078889768888888899807
Q gi|254780690|r  216 HQWYSKLKMSKQEIKDEIKQSYGNPIIKNRQKSIARSRIRHKMMEATSRATIIITNPTHYALALRYIQTENDAPVLVAKG  295 (354)
Q Consensus       216 ~~~~k~lkMskqEvK~E~K~~EGdP~iK~~~r~~~re~~~~~~~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG  295 (354)
                      ..|.++.--+-+.|   +|-.||.|.+...+|+              .+-|.||.-|++-      +             
T Consensus       972 a~~L~~~GI~~~~V---~Kv~e~~p~i~d~i~~--------------~~I~lVINt~~~~------~------------- 1015 (1063)
T PRK05294        972 AKFLEEAGIPVELV---NKVHEGRPHIVDLIKN--------------GEIDLVINTPEGR------Q------------- 1015 (1063)
T ss_pred             HHHHHHCCCCEEEE---CCCCCCCCCHHHHHHC--------------CCEEEEEECCCCC------C-------------
T ss_conf             99999769915996---4657899259999976--------------9826999799998------7-------------


Q ss_pred             CCHHHHHHHHHHHHCCCCEEECHHHHHHHHHHCCC
Q ss_conf             65899999999997399788688999999972889
Q gi|254780690|r  296 QNLIAKKMRKIAYEHNIPIFEEPSLARSLFKQVPI  330 (354)
Q Consensus       296 ~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~~~~i  330 (354)
                      ...-..+||+.|-+++||++-+...|+++-...+-
T Consensus      1016 ~~~dg~~IRR~Av~~~IP~~Tsl~~A~a~v~al~~ 1050 (1063)
T PRK05294       1016 AIRDGFSIRRAALEYKVPYITTLAGARAAAEAIEA 1050 (1063)
T ss_pred             CCCCCHHHHHHHHHHCCCEEECHHHHHHHHHHHHH
T ss_conf             77762999999997099989679999999999997


No 33 
>cd00532 MGS-like MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase, which catalyzes the enolization of dihydroxyacetone phosphate (DHAP) to produce methylglyoxal. The family also includes the C-terminal domain in carbamoyl phosphate synthetase (CPS) where it catalyzes the last phosphorylation of a coaboxyphosphate intermediate to form the product carbamoyl phosphate and may also play a regulatory role. This family also includes inosine monophosphate cyclohydrolase. The known structures in this family show a common phosphate binding site.
Probab=80.22  E-value=2.5  Score=23.10  Aligned_cols=75  Identities=11%  Similarity=0.140  Sum_probs=50.8

Q ss_pred             HHHHHHCCCHHHHHHHHHHCC-CCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEEC
Q ss_conf             999840699899999975448-9989999999999999998898607768699873553078889768888888899807
Q gi|254780690|r  217 QWYSKLKMSKQEIKDEIKQSY-GNPIIKNRQKSIARSRIRHKMMEATSRATIIITNPTHYALALRYIQTENDAPVLVAKG  295 (354)
Q Consensus       217 ~~~k~lkMskqEvK~E~K~~E-GdP~iK~~~r~~~re~~~~~~~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG  295 (354)
                      +|.++.-+.-+.|   +|-+| |+|++-..+++.             .+=|.||..|+.         +.       .++
T Consensus        36 ~~L~~~Gi~~~~V---~Ki~e~g~p~v~d~i~~~-------------g~I~lVINt~~~---------~~-------~~~   83 (112)
T cd00532          36 RVLADAGIPVRAV---SKRHEDGEPTVDAAIAEK-------------GKFDVVINLRDP---------RR-------DRC   83 (112)
T ss_pred             HHHHHCCCEEEEE---EECCCCCCCCHHHHHHCC-------------CCEEEEEECCCC---------CC-------CCC
T ss_conf             9999879834898---504878998899998668-------------967999988888---------87-------733


Q ss_pred             CCHHHHHHHHHHHHCCCCEEECHHHHHH
Q ss_conf             6589999999999739978868899999
Q gi|254780690|r  296 QNLIAKKMRKIAYEHNIPIFEEPSLARS  323 (354)
Q Consensus       296 ~~~~A~~Ir~~A~~~~Vpive~~~LAR~  323 (354)
                      .+.-...||+.|-+++||.+-+..-|++
T Consensus        84 ~~~Dg~~IRr~Av~~~IP~~Ttl~~A~a  111 (112)
T cd00532          84 TDEDGTALLRLARLYKIPVTTPNATAMF  111 (112)
T ss_pred             CCCCHHHHHHHHHHCCCCEECCHHHHHH
T ss_conf             2454899999999769998844898602


No 34 
>pfam09580 Spore_YhcN_YlaJ Sporulation lipoprotein YhcN/YlaJ (Spore_YhcN_YlaJ). This entry contains YhcN and YlaJ, which are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic, 40-residue C-terminal domain.
Probab=78.92  E-value=5.5  Score=20.36  Aligned_cols=108  Identities=14%  Similarity=0.227  Sum_probs=72.7

Q ss_pred             HHCCCCH-HHHHHHHHHHHHHHHHH-HHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHH--
Q ss_conf             5448998-99999999999999988-9860776869987355307888976888888889980765899999999997--
Q gi|254780690|r  234 KQSYGNP-IIKNRQKSIARSRIRHK-MMEATSRATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYE--  309 (354)
Q Consensus       234 K~~EGdP-~iK~~~r~~~re~~~~~-~~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~--  309 (354)
                      .+..|+| .-...+.+++..+++.- -+.+|.+|+||||+=+ .-||++-+.++       -.=.+.++.+|++.+++  
T Consensus        51 ~~~~~~~~~~~~~~~~~A~~i~~~~~~~~~V~dA~vvVt~~~-a~V~v~~~~~~-------~~~~~~ik~~V~~~v~~~~  122 (169)
T pfam09580        51 NNVTGENGYNNIERGEVADKIARRVAKLPEVEDAAVVVTGEE-ALVAVDLDNGE-------RSLTEEIKKQVKKAVKSVD  122 (169)
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCEEEEEEECCE-EEEEEECCCCC-------HHHHHHHHHHHHHHHHHCC
T ss_conf             765587678872099999999999961788644689998997-99999738864-------0358999999999998408


Q ss_pred             ---CCCCEEECHHHHHHH---HHHCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             ---399788688999999---97288989489899999999999997
Q gi|254780690|r  310 ---HNIPIFEEPSLARSL---FKQVPINSAIPPVFYKAVAQLIYKIY  350 (354)
Q Consensus       310 ---~~Vpive~~~LAR~L---y~~~~ig~~Ip~~~y~aVA~il~~v~  350 (354)
                         .+|-|..||-+=..+   -....-|.+| .++.+..++|+.-++
T Consensus       123 p~~~~VyVs~D~d~~~ri~~~~~~i~~g~p~-~~~~~e~~~ii~r~~  168 (169)
T pfam09580       123 PRIYNVYVSADPDLFTRIRNYGNDIRNGRPV-SGFFDEFEEIIRRMF  168 (169)
T ss_pred             CCCCEEEEECCHHHHHHHHHHHHHHHCCCCH-HHHHHHHHHHHHHHC
T ss_conf             8865699966989999999999887769977-899999999998528


No 35 
>TIGR01402 fliQ flagellar biosynthetic protein FliQ; InterPro: IPR006305   These sequences represent FliQ, a protein involved in biosynthesis of bacterial flagella. A related family of proteins, excluded from this model, participate in bacterial type III protein secretion systems. ; GO: 0016021 integral to membrane, 0019861 flagellum.
Probab=76.50  E-value=6.4  Score=19.86  Aligned_cols=37  Identities=19%  Similarity=0.137  Sum_probs=27.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             7989999999999999999999999998877687853
Q gi|254780690|r   77 ISHIVFLLTHLSLSASRLVIPGLLLFMMFGIGSYLIQ  113 (354)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~p~~~~~~l~~i~~~l~q  113 (354)
                      .+....+..++.+..+....|++++.+++|++.++.|
T Consensus         3 ~~~~l~l~~~a~~~~L~l~aP~L~~aL~VGLvIsIfQ   39 (88)
T TIGR01402         3 EETVLDLGREALWLTLLLSAPVLLVALVVGLVISIFQ   39 (88)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999999899999999999999999


No 36 
>TIGR02198 rfaE_dom_I rfaE bifunctional protein, domain I; InterPro: IPR011913    RfaE is a protein involved in the biosynthesis of ADP-L-glycero-D-manno-heptose, a precursor for LPS inner core biosynthesis. RfaE is a bifunctional protein in Escherichia coli, and separate proteins in some other genome. The longer, N-terminal domain I (this family) is suggested to act in D-glycero-D-manno-heptose 1-phosphate biosynthesis, while domain II (IPR011914 from INTERPRO) adds ADP to yield ADP-D-glycero-D-manno-heptose .; GO: 0016773 phosphotransferase activity alcohol group as acceptor, 0016779 nucleotidyltransferase activity, 0005975 carbohydrate metabolic process.
Probab=75.89  E-value=6.6  Score=19.75  Aligned_cols=58  Identities=14%  Similarity=0.221  Sum_probs=42.3

Q ss_pred             HHHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHHH-HHHHHHCCC
Q ss_conf             889860776869987355307888976888888889980765899999999997399788688999-999972889
Q gi|254780690|r  256 HKMMEATSRATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLA-RSLFKQVPI  330 (354)
Q Consensus       256 ~~~~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LA-R~Ly~~~~i  330 (354)
                      ......++++|+||-.        -|..|.=         ...+.+.++++||++++||+-||.-- .+.|+-+-+
T Consensus       137 ~~~~~~l~~~d~VvLS--------DYaKGvL---------t~~v~~~~I~~Ar~~~~pVlVDPKg~df~~Y~GAtl  195 (321)
T TIGR02198       137 AAIKEQLASADAVVLS--------DYAKGVL---------TPSVVQEVIAAAREAGKPVLVDPKGKDFSRYRGATL  195 (321)
T ss_pred             HHHHHHHCCCCEEEEE--------ECCCCCC---------CHHHHHHHHHHHHHCCCCEEEECCCCCHHHHCCCCC
T ss_conf             9999972328789998--------6687635---------857899999999966891998078762345146642


No 37 
>PRK02201 putative inner membrane protein translocase component YidC; Provisional
Probab=74.55  E-value=7.1  Score=19.50  Aligned_cols=58  Identities=16%  Similarity=0.305  Sum_probs=38.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCC-----CHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             99999999997667999999984069-----98999999754489989999999999999998
Q gi|254780690|r  199 ILLFIATLTVLDIGWSYHQWYSKLKM-----SKQEIKDEIKQSYGNPIIKNRQKSIARSRIRH  256 (354)
Q Consensus       199 ~~~~~~via~iD~~~qr~~~~k~lkM-----skqEvK~E~K~~EGdP~iK~~~r~~~re~~~~  256 (354)
                      +++..+++-++-+++........-||     -+.|+-.-||+-..||+.|+|..+-++++-++
T Consensus       164 i~~~~~ivrli~~~~t~kst~~q~KMqeiQpK~akIqaKYK~~kkD~qSkQKmQ~EMm~LYKK  226 (392)
T PRK02201        164 ILVLVLIIRLITFLITFKSTFNQEKMQELQGKKAKINAKYKDAKKDKQMKQRKQLEIQELYKK  226 (392)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             999999999999887699997699999862789999987356556999999999999999998


No 38 
>cd01424 MGS_CPS_II Methylglyoxal synthase-like domain from type II glutamine-dependent carbamoyl phosphate synthetase (CSP). CSP, a CarA and CarB heterodimer, catalyzes the production of carbamoyl phosphate which is subsequently employed in the metabolic pathways responsible for the synthesis of pyrimidine nucleotides or arginine. The MGS-like domain is the C-terminal domain of CarB and appears to play a regulatory role in CPS function by binding allosteric effector molecules, including UMP and ornithine.
Probab=72.20  E-value=5.9  Score=20.15  Aligned_cols=74  Identities=20%  Similarity=0.248  Sum_probs=50.8

Q ss_pred             HHHHHHHCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEEC
Q ss_conf             99998406998999999754489989999999999999998898607768699873553078889768888888899807
Q gi|254780690|r  216 HQWYSKLKMSKQEIKDEIKQSYGNPIIKNRQKSIARSRIRHKMMEATSRATIIITNPTHYALALRYIQTENDAPVLVAKG  295 (354)
Q Consensus       216 ~~~~k~lkMskqEvK~E~K~~EGdP~iK~~~r~~~re~~~~~~~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG  295 (354)
                      ++|.++.-..-+.|   +|..||.|++...+|+-              +=|.||.-|+.-      +.            
T Consensus        36 a~~L~~~Gi~~~~v---~k~~e~~p~i~d~i~~~--------------~i~lVINt~~~~------~~------------   80 (110)
T cd01424          36 AKYLQEAGIPVEVV---NKVSEGRPNIVDLIKNG--------------EIQLVINTPSGK------RA------------   80 (110)
T ss_pred             HHHHHHCCCCCEEE---ECCCCCCCCHHHHHHCC--------------CEEEEEECCCCC------CC------------
T ss_conf             99998649864033---00567997689999779--------------358999778898------65------------


Q ss_pred             CCHHHHHHHHHHHHCCCCEEECHHHHHHHH
Q ss_conf             658999999999973997886889999999
Q gi|254780690|r  296 QNLIAKKMRKIAYEHNIPIFEEPSLARSLF  325 (354)
Q Consensus       296 ~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly  325 (354)
                       ..-..+||+.|-+++||.+-|...|+++-
T Consensus        81 -~~dg~~IRr~Av~~~Ip~~Tsi~~A~a~v  109 (110)
T cd01424          81 -IRDGFSIRRAALEYKVPYFTTLDTARAAV  109 (110)
T ss_pred             -CCCHHHHHHHHHHCCCCEEECHHHHHHHH
T ss_conf             -74299999999976999996699999873


No 39 
>PRK09804 putative cryptic C4-dicarboxylate transporter DcuD; Provisional
Probab=71.43  E-value=3.7  Score=21.72  Aligned_cols=90  Identities=8%  Similarity=-0.025  Sum_probs=43.5

Q ss_pred             CHHHHHHHCCCHHHHHHHHHHHHHHHHHH--HHHHHHHHHCHHHHHHHHCCCHHHHHHHHH-------------------
Q ss_conf             93430332012667999999999999999--999999983215689784089799999999-------------------
Q gi|254780690|r  131 SLREGIKRIYSINNLVNFMKSFVKIILVG--TIITISLTENYFTMLDFISANPHSILYHAF-------------------  189 (354)
Q Consensus       131 NPi~GlKriFS~k~lvel~KsllKv~li~--~v~~~~i~~~~~~l~~l~~~~~~~~l~~~~-------------------  189 (354)
                      .|++.+|+-|=.=.+.=+.-.++.+++=+  .+.-.+.-..+|.+..+.- ++.++.....                   
T Consensus       105 kPL~~ikspYlll~~~~~ig~ll~i~IpSAaGLa~lLmaTl~PvLi~~Gv-s~~sAaAVia~t~~~~~gP~s~~~i~aA~  183 (455)
T PRK09804        105 RPLKLIRSPYIILSATYVIGQIMAQFITSASGLGMLLMVTLFPTLVSLGV-SRLSAVAVIATTMSIEWGILETNSIFAAQ  183 (455)
T ss_pred             HHHHHCCCCEEHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHCCCCCCCCCHHHHHH
T ss_conf             57877058601377999999999943376866999999999999998599-77888999998753267899754899999


Q ss_pred             --------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             --------99999999999999999997667999999984
Q gi|254780690|r  190 --------FTVRKVLIMILLFIATLTVLDIGWSYHQWYSK  221 (354)
Q Consensus       190 --------~~~~~l~~~~~~~~~via~iD~~~qr~~~~k~  221 (354)
                              ..+..-........+++++..|+||||.-+|+
T Consensus       184 ~~g~~v~~y~~~~ql~~~i~~ii~iai~h~f~qr~~Dkk~  223 (455)
T PRK09804        184 VAGMKIATYFFHYQLPVASCVIISVAISHFFVQRAFDKKD  223 (455)
T ss_pred             HHCCCHHHEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             8299667545651389999999999999999999987512


No 40 
>COG1167 ARO8 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]
Probab=71.24  E-value=8.1  Score=19.04  Aligned_cols=48  Identities=15%  Similarity=0.096  Sum_probs=31.7

Q ss_pred             CCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHHH
Q ss_conf             6869987355307888976888888889980765899999999997399788688999999
Q gi|254780690|r  264 RATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSL  324 (354)
Q Consensus       264 ~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~L  324 (354)
                      +..++.++|||=      +|....-       ..+...++.+.|++|+++||||-+..---
T Consensus       226 ~~k~~y~~P~~q------NPtG~tm-------s~~rR~~Ll~lA~~~~~~IIEDD~y~el~  273 (459)
T COG1167         226 KPKAVYVTPTFQ------NPTGVTM-------SLERRKALLALAEKYDVLIIEDDYYGELR  273 (459)
T ss_pred             CCCEEEECCCCC------CCCCCCC-------CHHHHHHHHHHHHHCCCEEEEECCCHHHC
T ss_conf             972899788963------8898745-------99999999999997598799867743321


No 41 
>KOG2568 consensus
Probab=70.21  E-value=8.7  Score=18.78  Aligned_cols=27  Identities=11%  Similarity=0.069  Sum_probs=11.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             667999999999999999999999983
Q gi|254780690|r  142 INNLVNFMKSFVKIILVGTIITISLTE  168 (354)
Q Consensus       142 ~k~lvel~KsllKv~li~~v~~~~i~~  168 (354)
                      +=++-.-+.+.+-+.++..++|.....
T Consensus       377 Kl~lYr~F~n~l~~~Vvas~~~i~~~~  403 (518)
T KOG2568         377 KLSLYRKFTNTLAFSVVASFAFILVET  403 (518)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999999999999999


No 42 
>PRK13954 mscL large-conductance mechanosensitive channel; Provisional
Probab=68.62  E-value=9.4  Score=18.54  Aligned_cols=21  Identities=14%  Similarity=0.192  Sum_probs=7.5

Q ss_pred             HHHHHCCCHHHHHHHHHHHHH
Q ss_conf             303320126679999999999
Q gi|254780690|r  134 EGIKRIYSINNLVNFMKSFVK  154 (354)
Q Consensus       134 ~GlKriFS~k~lvel~KsllK  154 (354)
                      +|||.-...-+++|++-++.=
T Consensus         3 keFK~Fi~rGNViDLAVaVIi   23 (120)
T PRK13954          3 KEFKEFALKGNVLDLAIAVVM   23 (120)
T ss_pred             HHHHHHHHHCCHHHHHHHHHH
T ss_conf             789999981578999999999


No 43 
>pfam01276 OKR_DC_1 Orn/Lys/Arg decarboxylase, major domain.
Probab=67.55  E-value=8.9  Score=18.70  Aligned_cols=17  Identities=18%  Similarity=0.223  Sum_probs=10.5

Q ss_pred             HHHHHHHHHHHHHHHHH
Q ss_conf             99999999976679999
Q gi|254780690|r  200 LLFIATLTVLDIGWSYH  216 (354)
Q Consensus       200 ~~~~~via~iD~~~qr~  216 (354)
                      .-.++++|-+|..-++.
T Consensus       275 SPsY~lmASLD~ar~~m  291 (417)
T pfam01276       275 SPFYPIVASLDVAAAMM  291 (417)
T ss_pred             CHHHHHHHHHHHHHHHH
T ss_conf             74899999999999997


No 44 
>COG2074 2-phosphoglycerate kinase [Carbohydrate transport and metabolism]
Probab=66.30  E-value=4.6  Score=21.01  Aligned_cols=25  Identities=20%  Similarity=0.422  Sum_probs=19.7

Q ss_pred             HHHHHHHHCCCCEEECHHHHHHHHH
Q ss_conf             9999999739978868899999997
Q gi|254780690|r  302 KMRKIAYEHNIPIFEEPSLARSLFK  326 (354)
Q Consensus       302 ~Ir~~A~~~~Vpive~~~LAR~Ly~  326 (354)
                      .+.+.|++||||+++|..+..+.-+
T Consensus       256 yl~~~Are~gVPvI~n~di~etv~~  280 (299)
T COG2074         256 YLVERAREHGVPVIENDDIDETVDR  280 (299)
T ss_pred             HHHHHHHHCCCCEECCCCHHHHHHH
T ss_conf             9999888659981125319999999


No 45 
>KOG3171 consensus
Probab=63.90  E-value=11  Score=17.88  Aligned_cols=79  Identities=16%  Similarity=0.101  Sum_probs=52.1

Q ss_pred             HHCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEC---------------CCCEEEEEEECCCC
Q ss_conf             406998999999754489989999999999999998898607768699873---------------55307888976888
Q gi|254780690|r  221 KLKMSKQEIKDEIKQSYGNPIIKNRQKSIARSRIRHKMMEATSRATIIITN---------------PTHYALALRYIQTE  285 (354)
Q Consensus       221 ~lkMskqEvK~E~K~~EGdP~iK~~~r~~~re~~~~~~~~~V~~A~vvitN---------------PTH~AVAL~Y~~~~  285 (354)
                      +-|||-||--.=+|+.|-.--+++-|||+++||.+.-  +.=|+--.|+-=               -|-+ |-+=|++|.
T Consensus        95 srkms~~E~~~m~~~~~de~~L~~yr~qrm~eMrq~l--~~gp~~~~V~El~~gkqfld~idke~ks~~i-~VhIYEdgi  171 (273)
T KOG3171          95 SRKMSIQEYELMHKEKEDENCLRKYRRQRMQEMRQKL--SFGPRYGFVYELETGKQFLDTIDKELKSTTI-VVHIYEDGI  171 (273)
T ss_pred             HCCCCHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHH--HCCCCCCEEEEECCCHHHHHHHHCCCCEEEE-EEEEECCCC
T ss_conf             2112177899875500328999999999999999986--2287642599951620478987403325899-999824898


Q ss_pred             CCCCEEEEECCCHHHHHHHHHHHHC
Q ss_conf             8888899807658999999999973
Q gi|254780690|r  286 NDAPVLVAKGQNLIAKKMRKIAYEH  310 (354)
Q Consensus       286 ~~aP~vvaKG~~~~A~~Ir~~A~~~  310 (354)
                              ||.+.+-.-+.-+|.+.
T Consensus       172 --------~gcealn~~~~cLAAey  188 (273)
T KOG3171         172 --------KGCEALNSSLTCLAAEY  188 (273)
T ss_pred             --------CHHHHHHHHHHHHHCCC
T ss_conf             --------42788865687865058


No 46 
>TIGR01088 aroQ 3-dehydroquinate dehydratase, type II; InterPro: IPR001874 3-dehydroquinate dehydratase (4.2.1.10 from EC), or dehydroquinase, catalyzes the conversion of 3-dehydroquinate into 3-dehydroshikimate. It is the third step in the shikimate pathway for the biosynthesis of aromatic amino acids from chorismate. Two classes of dehydroquinases exist, known as types I and II. Class-II enzymes are homododecameric enzymes of about 17 kDa. They are found in some bacteria such as actinomycetales ,  and some fungi where they act in a catabolic pathway that allows the use of quinic acid as a carbon source.; GO: 0003855 3-dehydroquinate dehydratase activity, 0009073 aromatic amino acid family biosynthetic process.
Probab=63.90  E-value=1.1  Score=26.06  Aligned_cols=32  Identities=38%  Similarity=0.456  Sum_probs=21.8

Q ss_pred             HHCCC-CCEEEECC---CCEEEEEEECCCCCCCCEE
Q ss_conf             60776-86998735---5307888976888888889
Q gi|254780690|r  260 EATSR-ATIIITNP---THYALALRYIQTENDAPVL  291 (354)
Q Consensus       260 ~~V~~-A~vvitNP---TH~AVAL~Y~~~~~~aP~v  291 (354)
                      +...+ .|-||-||   |||+||||=--..-..|.|
T Consensus        63 ~a~g~~~~GiviNpgA~THtSvAlRDA~~~v~~P~v   98 (144)
T TIGR01088        63 EALGQDYDGIVINPGAYTHTSVALRDALAAVSLPVV   98 (144)
T ss_pred             HHHCCCCCEEEECCCCCCHHHHHHHHHHHHHCCCEE
T ss_conf             872388653787873101367999999997039868


No 47 
>COG4209 LplB ABC-type polysaccharide transport system, permease component [Carbohydrate transport and metabolism]
Probab=63.32  E-value=12  Score=17.80  Aligned_cols=68  Identities=9%  Similarity=0.013  Sum_probs=31.8

Q ss_pred             HHCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHH-HHHHHHHCCCHHHHHHHHH
Q ss_conf             8321568978408979999999999999999999999999997667---999-9999840699899999975
Q gi|254780690|r  167 TENYFTMLDFISANPHSILYHAFFTVRKVLIMILLFIATLTVLDIG---WSY-HQWYSKLKMSKQEIKDEIK  234 (354)
Q Consensus       167 ~~~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD~~---~qr-~~~~k~lkMskqEvK~E~K  234 (354)
                      .+-=|++-..+..|-.+-...+-++..-.+.-+..+++++++.+..   |.. |.-.+++-++-.||=|-|=
T Consensus       194 ~~Idpt~YEAA~vDGA~rwqqiwhITlP~i~P~ivIllIL~iG~i~~~gFe~~yll~~~~~~~v~~vldtYV  265 (309)
T COG4209         194 AGIDPTLYEAAMVDGASRWQQIWHITLPAIRPLIVILLILNIGNIFNAGFELFYLLPNPSGYDVTEVLDTYV  265 (309)
T ss_pred             HCCCHHHHHHHHCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCHHHEEEECCCCCCCHHHHHHHHH
T ss_conf             727999999998054887788882110323149999999985237653725606605766874898999999


No 48 
>COG1149 MinD superfamily P-loop ATPase containing an inserted ferredoxin domain [Energy production and conversion]
Probab=63.24  E-value=6.5  Score=19.82  Aligned_cols=81  Identities=16%  Similarity=0.249  Sum_probs=52.5

Q ss_pred             HHHHHCCCCCE--EEECCCCEEE-----EEEECCCCCCCC--EEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHHHHHH
Q ss_conf             89860776869--9873553078-----889768888888--89980765899999999997399788688999999972
Q gi|254780690|r  257 KMMEATSRATI--IITNPTHYAL-----ALRYIQTENDAP--VLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFKQ  327 (354)
Q Consensus       257 ~~~~~V~~A~v--vitNPTH~AV-----AL~Y~~~~~~aP--~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~~  327 (354)
                      .+++.+..||.  +||-||-+++     +++-- +....|  +|+-|---..+ .|++.+++.++|++-..|--+.+-+.
T Consensus       178 pVi~sl~~aD~ai~VTEPTp~glhD~kr~~el~-~~f~ip~~iViNr~~~g~s-~ie~~~~e~gi~il~~IPyd~~i~~~  255 (284)
T COG1149         178 PVIASLKGADLAILVTEPTPFGLHDLKRALELV-EHFGIPTGIVINRYNLGDS-EIEEYCEEEGIPILGEIPYDKDIPEA  255 (284)
T ss_pred             HHHHHHCCCCEEEEEECCCCCCHHHHHHHHHHH-HHHCCCEEEEEECCCCCCH-HHHHHHHHCCCCEEEECCCCHHHHHH
T ss_conf             177764168779998168852366899999999-9839954999966777720-89998887399726878864258999


Q ss_pred             CCCCCCCCHHHH
Q ss_conf             889894898999
Q gi|254780690|r  328 VPINSAIPPVFY  339 (354)
Q Consensus       328 ~~ig~~Ip~~~y  339 (354)
                      .--|+++-...+
T Consensus       256 ~~~g~~~~~~~~  267 (284)
T COG1149         256 YVNGEPFVEPDS  267 (284)
T ss_pred             HHCCCCCCCCCC
T ss_conf             857885313552


No 49 
>cd07362 HPCD_like Class III extradiol dioxygenases with similarity to homoprotocatechuate 2,3-dioxygenase, which catalyzes the key ring cleavage step in the metabolism of homoprotocatechuate. This subfamily of class III extradiol dioxygenases consists of two types of  proteins with known enzymatic activities; 3,4-dihydroxyphenylacetate (homoprotocatechuate) 2,3-dioxygenase (HPCD) and 2-amino-5-chlorophenol 1,6-dioxygenase. HPCD catalyzes the key ring cleavage step in the metabolism of homoprotocatechuate (hpca), a central intermediate in the bacterial degradation of aromatic compounds. The enzyme incorporates both atoms of molecular oxygen into hpca, resulting in aromatic ring-opening to yield the product  alpha-hydroxy-delta-carboxymethyl cis-muconic semialdehyde. 2-amino-5-chlorophenol 1,6-dioxygenase catalyzes the oxidization and subsequent ring-opening of 2-amino-5-chlorophenol, which is an intermediate during p-chloronitrobenzene degradation. The enzyme is probably a heterotetrame
Probab=62.60  E-value=12  Score=17.71  Aligned_cols=78  Identities=12%  Similarity=0.181  Sum_probs=41.9

Q ss_pred             CCCCHHHHHHHH---HHHHHHHHHHHHHHCCCCCEEEECCCCEEE--EEEEC--------CCCCCCCEEEE------ECC
Q ss_conf             489989999999---999999998898607768699873553078--88976--------88888888998------076
Q gi|254780690|r  236 SYGNPIIKNRQK---SIARSRIRHKMMEATSRATIIITNPTHYAL--ALRYI--------QTENDAPVLVA------KGQ  296 (354)
Q Consensus       236 ~EGdP~iK~~~r---~~~re~~~~~~~~~V~~A~vvitNPTH~AV--AL~Y~--------~~~~~aP~vva------KG~  296 (354)
                      .||.++-++++.   .-+++++++ . .+..--||||.. ||+-+  +..+.        -....+|-...      +|-
T Consensus        15 ~~~~g~~~~~~~~ti~a~~~i~~~-i-~~~~pDtvVV~s-pHw~~~~~~~i~~~~~~~g~~~~~~~p~~~~~v~yd~~~d   91 (272)
T cd07362          15 EENPPENQGCLVGAIKGMKEIRKR-I-EELKPDVILVIS-CHWMSSSFHHFVDATPRHGGLTAVECPDLISDVPYDYPGD   91 (272)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHH-H-HHCCCCEEEEEC-CCCCCCCCEEEEECCCCCCCEECCCCCCCCCCCCCCCCCC
T ss_conf             878885206699999999999999-9-873989999986-9967504438740576646410346852004135677578


Q ss_pred             CHHHHHHHHHHHHCCCCEEE
Q ss_conf             58999999999973997886
Q gi|254780690|r  297 NLIAKKMRKIAYEHNIPIFE  316 (354)
Q Consensus       297 ~~~A~~Ir~~A~~~~Vpive  316 (354)
                      -++|..|.+.|+++|+|+..
T Consensus        92 ~eLa~~i~~~a~~~G~~~~~  111 (272)
T cd07362          92 PELGRLLVEEGQEAGLRVKA  111 (272)
T ss_pred             HHHHHHHHHHHHHCCCEEEE
T ss_conf             99999999999877980897


No 50 
>PRK05700 fliQ flagellar biosynthesis protein FliQ; Validated
Probab=62.29  E-value=12  Score=17.67  Aligned_cols=38  Identities=21%  Similarity=0.223  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             79899999999999999999999999988776878532
Q gi|254780690|r   77 ISHIVFLLTHLSLSASRLVIPGLLLFMMFGIGSYLIQR  114 (354)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~p~~~~~~l~~i~~~l~q~  114 (354)
                      .+.......+..+..+.+..|++++.+++|++.++.|.
T Consensus         3 ~~~~i~l~~~al~~~l~ls~P~L~~alvVGl~Isi~QA   40 (89)
T PRK05700          3 PESVMDLFREAMKVALMLAAPLLLVALIVGLVVSIFQA   40 (89)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             88999999999999999988899999999999999999


No 51 
>PRK03881 hypothetical protein; Provisional
Probab=61.40  E-value=12  Score=17.55  Aligned_cols=45  Identities=11%  Similarity=0.176  Sum_probs=34.1

Q ss_pred             HHHHHHHHCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999984069989999997544899899999999999999988986
Q gi|254780690|r  215 YHQWYSKLKMSKQEIKDEIKQSYGNPIIKNRQKSIARSRIRHKMME  260 (354)
Q Consensus       215 r~~~~k~lkMskqEvK~E~K~~EGdP~iK~~~r~~~re~~~~~~~~  260 (354)
                      ...+..++.+.++|--++.|+.| ||-+|=.|+.+..-...++.+.
T Consensus       277 ~~~~~~~~~~~~~~~~~~~r~~e-d~~v~lAr~~le~y~~~g~~~~  321 (467)
T PRK03881        277 DTSLLEKLEREREQRIEKRRAEE-SPYVRLARESLEYYLKTGKVLK  321 (467)
T ss_pred             CCCHHHHHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHHHCCCCCC
T ss_conf             51068899999999987654044-6799999999999982198688


No 52 
>KOG3925 consensus
Probab=60.78  E-value=9.8  Score=18.40  Aligned_cols=15  Identities=7%  Similarity=0.031  Sum_probs=6.9

Q ss_pred             HCCCCC---CCCCHHHHH
Q ss_conf             137791---016934303
Q gi|254780690|r  122 HVKPSF---KRVSLREGI  136 (354)
Q Consensus       122 ~l~pk~---~rlNPi~Gl  136 (354)
                      |+.|++   +.|||+.-.
T Consensus       155 p~~~~Lk~ag~lppLd~~  172 (371)
T KOG3925         155 PKHPDLKYAGLLPPLDTP  172 (371)
T ss_pred             CCCCCCCCCCCCCCCCCH
T ss_conf             578454101367998866


No 53 
>PRK06010 fliQ flagellar biosynthesis protein FliQ; Reviewed
Probab=60.70  E-value=13  Score=17.46  Aligned_cols=38  Identities=16%  Similarity=0.138  Sum_probs=28.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             79899999999999999999999999988776878532
Q gi|254780690|r   77 ISHIVFLLTHLSLSASRLVIPGLLLFMMFGIGSYLIQR  114 (354)
Q Consensus        77 ~~~~~~~~~~~~~~~~~~~~p~~~~~~l~~i~~~l~q~  114 (354)
                      .+.+.....+..+..+....|.+++.+++|++.++.|.
T Consensus         3 ~~~vi~l~~~al~~~l~ls~P~L~valvVGl~IslfQA   40 (88)
T PRK06010          3 EADALDVVRDAIWTVLIASGPAVLAAMVVGVAIALFQA   40 (88)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             88999999999999999987699999999999999999


No 54 
>cd02987 Phd_like_Phd Phosducin (Phd)-like family, Phd subfamily; Phd is a cytosolic regulator of G protein functions. It specifically binds G protein betagamma (Gbg)-subunits with high affinity, resulting in the solubilization of Gbg from the plasma membrane. This impedes the formation of a functional G protein trimer (G protein alphabetagamma), thereby inhibiting G protein-mediated signal transduction. Phd also inhibits the GTPase activity of G protein alpha. Phd can be phosphorylated by protein kinase A and G protein-coupled receptor kinase 2, leading to its inactivation. Phd was originally isolated from the retina, where it is highly expressed and has been implicated to play an important role in light adaptation. It is also found in the pineal gland, liver, spleen, striated muscle and the brain. The C-terminal domain of Phd adopts a thioredoxin fold, but it does not contain a CXXC motif. Phd interacts with G protein beta mostly through the N-terminal helical domain.
Probab=60.52  E-value=6.2  Score=19.93  Aligned_cols=86  Identities=15%  Similarity=0.166  Sum_probs=46.8

Q ss_pred             HHHHHHHHHHCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHH----HCCC----CCE--EE--ECCCCEEEEEE
Q ss_conf             999999984069989999997544899899999999999999988986----0776----869--98--73553078889
Q gi|254780690|r  213 WSYHQWYSKLKMSKQEIKDEIKQSYGNPIIKNRQKSIARSRIRHKMME----ATSR----ATI--II--TNPTHYALALR  280 (354)
Q Consensus       213 ~qr~~~~k~lkMskqEvK~E~K~~EGdP~iK~~~r~~~re~~~~~~~~----~V~~----A~v--vi--tNPTH~AVAL~  280 (354)
                      ||+|+   +++++.+|--++  +.|-|.-++.-|+++++||..+....    .|..    .+.  .|  .++..+.|..=
T Consensus        16 ~~~~k---~~~~~~~e~d~~--deede~fL~~yR~kRm~Em~~~~~~~~~fG~v~ei~s~~~fl~~V~~~~~~~~VVVhi   90 (175)
T cd02987          16 WRKFK---QLKESEQEDDDD--DEDKEEFLQQYREQRMQEMHAKLPFGRRFGKVYELDSGEQFLDAIDKEGKDTTVVVHI   90 (175)
T ss_pred             HHHHH---HHHHHHHCCCCC--CCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCHHHHHHHHHCCCCCCEEEEEE
T ss_conf             99999---988654003310--1068999999999999999987653655865897378889999985659983899999


Q ss_pred             ECCCCCCCCEEEEECCCHHHHHHHHHHHHCC
Q ss_conf             7688888888998076589999999999739
Q gi|254780690|r  281 YIQTENDAPVLVAKGQNLIAKKMRKIAYEHN  311 (354)
Q Consensus       281 Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~  311 (354)
                      |+++.   |     +-..+-...+.+|++|.
T Consensus        91 Y~~~~---~-----~C~~l~~~L~~LA~k~~  113 (175)
T cd02987          91 YEPGI---P-----GCAALNSSLLCLAAEYP  113 (175)
T ss_pred             EECCC---C-----HHHHHHHHHHHHHHHCC
T ss_conf             60999---6-----58999999999998689


No 55 
>PRK09983 pflD putative formate acetyltransferase 2; Provisional
Probab=59.90  E-value=11  Score=18.09  Aligned_cols=16  Identities=19%  Similarity=0.310  Sum_probs=7.1

Q ss_pred             HHCCCHHHHHHHHHHC
Q ss_conf             4069989999997544
Q gi|254780690|r  221 KLKMSKQEIKDEIKQS  236 (354)
Q Consensus       221 ~lkMskqEvK~E~K~~  236 (354)
                      +-+.|.+|+++=.+..
T Consensus       544 ~k~~t~~eL~~Al~~N  559 (765)
T PRK09983        544 QQRLSFDELLSVLKAN  559 (765)
T ss_pred             CCCCCHHHHHHHHHHC
T ss_conf             5666799999999853


No 56 
>pfam02142 MGS MGS-like domain. This domain composes the whole protein of methylglyoxal synthetase and the domain is also found in Carbamoyl phosphate synthetase (CPS) where it forms a regulatory domain that binds to the allosteric effector ornithine. This family also includes inosicase. The known structures in this family show a common phosphate binding site.
Probab=59.16  E-value=9.6  Score=18.47  Aligned_cols=64  Identities=16%  Similarity=0.224  Sum_probs=37.7

Q ss_pred             HHHHHHCCCHHHHHHHHHHCCCCHH----HHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEE
Q ss_conf             9998406998999999754489989----999999999999998898607768699873553078889768888888899
Q gi|254780690|r  217 QWYSKLKMSKQEIKDEIKQSYGNPI----IKNRQKSIARSRIRHKMMEATSRATIIITNPTHYALALRYIQTENDAPVLV  292 (354)
Q Consensus       217 ~~~k~lkMskqEvK~E~K~~EGdP~----iK~~~r~~~re~~~~~~~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vv  292 (354)
                      +|.++.-..   ++-.+|-.||.|.    +...+++              .+=|.||.||+.+.-..+            
T Consensus        24 ~~L~~~Gi~---~~~v~k~~~~~~~~~~~i~d~i~~--------------~~IdlVInt~~~~~~~~~------------   74 (92)
T pfam02142        24 KFLKEAGIP---TEVVNKTGEGRPGGRVQIGDLIKN--------------GEIDLVINTLYPFKATVH------------   74 (92)
T ss_pred             HHHHHCCCC---CEEEEECCCCCCCCCHHHHHHHHC--------------CCCCEEEECCCCCCEECC------------
T ss_conf             999955998---168634068999984769999982--------------995199983898851125------------


Q ss_pred             EECCCHHHHHHHHHHHHCCCCEE
Q ss_conf             80765899999999997399788
Q gi|254780690|r  293 AKGQNLIAKKMRKIAYEHNIPIF  315 (354)
Q Consensus       293 aKG~~~~A~~Ir~~A~~~~Vpiv  315 (354)
                            -...||+.|.+++||.+
T Consensus        75 ------dg~~iRr~a~~~~Ip~~   91 (92)
T pfam02142        75 ------DGYAIRRAAENIDIPLP   91 (92)
T ss_pred             ------CCHHHHHHHHHCCCCCC
T ss_conf             ------88789999992699854


No 57 
>COG4998 Predicted endonuclease (RecB family) [DNA replication, recombination, and repair]
Probab=59.00  E-value=8  Score=19.08  Aligned_cols=25  Identities=28%  Similarity=0.537  Sum_probs=13.9

Q ss_pred             CCEEEEECCCHHHHHHHHHHHHCCCCEE
Q ss_conf             8889980765899999999997399788
Q gi|254780690|r  288 APVLVAKGQNLIAKKMRKIAYEHNIPIF  315 (354)
Q Consensus       288 aP~vvaKG~~~~A~~Ir~~A~~~~Vpiv  315 (354)
                      -|+|+|+|.|+-|.   ..|++.||-++
T Consensus        75 rPmvvaR~ade~Ar---~LA~~LGVEvv   99 (209)
T COG4998          75 RPMVVARGADEAAR---KLAEKLGVEVV   99 (209)
T ss_pred             CCEEEECCCCHHHH---HHHHHHCCCHH
T ss_conf             73455504687899---99998295502


No 58 
>KOG2262 consensus
Probab=59.00  E-value=14  Score=17.25  Aligned_cols=40  Identities=18%  Similarity=0.206  Sum_probs=21.9

Q ss_pred             HHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHH
Q ss_conf             0332012667999999999999999999999983215689
Q gi|254780690|r  135 GIKRIYSINNLVNFMKSFVKIILVGTIITISLTENYFTML  174 (354)
Q Consensus       135 GlKriFS~k~lvel~KsllKv~li~~v~~~~i~~~~~~l~  174 (354)
                      |=|||||..+.-..++=.+-+.+++.+..+.++..+|..-
T Consensus       612 GP~riF~~~g~Y~~l~wFFLiGa~~pv~vw~~~k~fPk~~  651 (761)
T KOG2262         612 GPKRIFGSLGIYPGLNWFFLIGALAPVLVWLLQKKFPKKK  651 (761)
T ss_pred             CCHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHH
T ss_conf             6164438898667306888787775679999987534112


No 59 
>PRK12781 fliQ flagellar biosynthesis protein FliQ; Reviewed
Probab=58.17  E-value=14  Score=17.15  Aligned_cols=37  Identities=19%  Similarity=0.126  Sum_probs=27.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9899999999999999999999999988776878532
Q gi|254780690|r   78 SHIVFLLTHLSLSASRLVIPGLLLFMMFGIGSYLIQR  114 (354)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~p~~~~~~l~~i~~~l~q~  114 (354)
                      ..+..+..+..+..+.+..|++++.+++|++.++.|.
T Consensus         4 ~~vi~l~r~al~~~l~~s~PiL~~aL~VGl~IsifQA   40 (88)
T PRK12781          4 RDALELVRAAIWTIIVASGPAVGAAMLVGIAIALLQA   40 (88)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             8999999999999999977499999999999999999


No 60 
>pfam02179 BAG BAG domain. Domain present in Hsp70 regulators.
Probab=57.64  E-value=11  Score=17.91  Aligned_cols=22  Identities=23%  Similarity=0.324  Sum_probs=18.6

Q ss_pred             HHCCCCHHHHHHHHHHHHHHHH
Q ss_conf             5448998999999999999999
Q gi|254780690|r  234 KQSYGNPIIKNRQKSIARSRIR  255 (354)
Q Consensus       234 K~~EGdP~iK~~~r~~~re~~~  255 (354)
                      =+.+|||.+|.+||+.-+++..
T Consensus        46 I~~~g~~~~R~~RK~~v~~vq~   67 (76)
T pfam02179        46 IDTEGNPEIREARKRAVKRVQG   67 (76)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHH
T ss_conf             4658978999999999999999


No 61 
>PRK01318 putative inner membrane protein translocase component YidC; Provisional
Probab=57.49  E-value=14  Score=17.07  Aligned_cols=10  Identities=10%  Similarity=0.584  Sum_probs=4.4

Q ss_pred             HHCCCCCCCC
Q ss_conf             2137791016
Q gi|254780690|r  121 NHVKPSFKRV  130 (354)
Q Consensus       121 k~l~pk~~rl  130 (354)
                      +.|+|+.++|
T Consensus       398 ~~lqP~~~~~  407 (565)
T PRK01318        398 KELQPKMQEL  407 (565)
T ss_pred             HHHCHHHHHH
T ss_conf             7545679999


No 62 
>PRK12339 2-phosphoglycerate kinase; Provisional
Probab=57.41  E-value=10  Score=18.26  Aligned_cols=30  Identities=13%  Similarity=-0.025  Sum_probs=23.1

Q ss_pred             HHHHHHHHHHHHCCCCEEECHHHHHHHHHH
Q ss_conf             899999999997399788688999999972
Q gi|254780690|r  298 LIAKKMRKIAYEHNIPIFEEPSLARSLFKQ  327 (354)
Q Consensus       298 ~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~~  327 (354)
                      .+-..+.+.|++++||+++|..+-++.-.-
T Consensus       162 ~Iq~ylv~~A~~~~ipvI~n~~~d~s~~~i  191 (197)
T PRK12339        162 TIMDYSIADARGYNIKVIDTDNYREARNPL  191 (197)
T ss_pred             HHHHHHHHHHHHCCCCEECCCCHHHHHHHH
T ss_conf             999999998887399855377289999999


No 63 
>TIGR01838 PHA_synth_I poly(R)-hydroxyalkanoic acid synthase, class I; InterPro: IPR010963   This entry represents the class I subfamily of poly(R)-hydroxyalkanoate synthases, which polymerises hydroxyacyl-CoAs with three to five carbons in the hydroxyacyl backbone into aliphatic esters termed poly(R)-hydroxyalkanoic acids. These polymers accumulate as carbon and energy storage inclusions in many species and can amount to 90 percent of the dry weight of the cell.; GO: 0008415 acyltransferase activity, 0042619 poly-hydroxybutyrate biosynthetic process, 0005737 cytoplasm.
Probab=57.36  E-value=8.6  Score=18.84  Aligned_cols=40  Identities=23%  Similarity=0.351  Sum_probs=28.2

Q ss_pred             HHHHHHHCCCC-HHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCC
Q ss_conf             99997544899-8999999999999999889860776869987355
Q gi|254780690|r  229 IKDEIKQSYGN-PIIKNRQKSIARSRIRHKMMEATSRATIIITNPT  273 (354)
Q Consensus       229 vK~E~K~~EGd-P~iK~~~r~~~re~~~~~~~~~V~~A~vvitNPT  273 (354)
                      +.+=-++-||+ |+-|.|+|=.-||+..     ++.=+.+++|||.
T Consensus        73 ~~~~~~~~eG~d~k~r~R~~Ff~~Q~in-----A~aPSNFL~TNPe  113 (541)
T TIGR01838        73 LLELVDAVEGLDPKTRRRIEFFTRQLIN-----AMAPSNFLATNPE  113 (541)
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHHHH-----HCCCCCHHHCCHH
T ss_conf             9999998618882022799999999998-----5053141211579


No 64 
>PRK10654 dcuC C4-dicarboxylate transporter DcuC; Provisional
Probab=56.89  E-value=10  Score=18.21  Aligned_cols=26  Identities=12%  Similarity=0.102  Sum_probs=19.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999997667999999984
Q gi|254780690|r  196 LIMILLFIATLTVLDIGWSYHQWYSK  221 (354)
Q Consensus       196 ~~~~~~~~~via~iD~~~qr~~~~k~  221 (354)
                      ........+++++.-|+||||.-+|+
T Consensus       198 l~~~i~~~i~~ai~h~f~q~y~Dkk~  223 (452)
T PRK10654        198 LPISIAAIIGMAIAHFFWQRYLDKKE  223 (452)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             89999999999999999999820213


No 65 
>COG2870 RfaE ADP-heptose synthase, bifunctional sugar kinase/adenylyltransferase [Cell envelope biogenesis, outer membrane]
Probab=56.22  E-value=11  Score=18.06  Aligned_cols=17  Identities=24%  Similarity=0.432  Sum_probs=8.4

Q ss_pred             CCEEEEECCCHHHHHHH
Q ss_conf             88899807658999999
Q gi|254780690|r  288 APVLVAKGQNLIAKKMR  304 (354)
Q Consensus       288 aP~vvaKG~~~~A~~Ir  304 (354)
                      -|-++.||.|.-...|.
T Consensus       417 ~PdilVKGgDy~~~~i~  433 (467)
T COG2870         417 KPDILVKGGDYKIEKIV  433 (467)
T ss_pred             CCCEEECCCCCCHHHCC
T ss_conf             86658706888724403


No 66 
>TIGR02898 spore_YhcN_YlaJ sporulation lipoprotein,  YhcN/YlaJ family; InterPro: IPR014247   This entry contains YhcN and YlaJ, which are predicted lipoproteins that have been detected as spore proteins but not vegetative proteins in Bacillus subtilis. Both appear to be expressed under control of the RNA polymerase sigma-G factor. The YlaJ-like members of this family have a low-complexity, strongly acidic, 40-residue C-terminal domain. .
Probab=56.02  E-value=11  Score=17.85  Aligned_cols=114  Identities=12%  Similarity=0.185  Sum_probs=72.7

Q ss_pred             HHHHHCCCCHHH-HHHHHHHHHHHHHHHH--HHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHH
Q ss_conf             997544899899-9999999999999889--8607768699873553078889768888888899807658999999999
Q gi|254780690|r  231 DEIKQSYGNPII-KNRQKSIARSRIRHKM--MEATSRATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIA  307 (354)
Q Consensus       231 ~E~K~~EGdP~i-K~~~r~~~re~~~~~~--~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A  307 (354)
                      .-+++..+|+.- -+.+-+++.+++++-.  ..+|.+|+|||+.-+-| ||+--+-+...--- -...-|..-..||+..
T Consensus        53 ~~~~~~~~~~~~t~~~~~~~a~~~A~~~a~k~~gvk~A~vvi~g~~A~-VGv~~~~~~ennGn-nsqsG~~~~~~lK~~v  130 (185)
T TIGR02898        53 INGDNTTGDTNQTDGDLLKVADKIASEVAKKVKGVKDATVVITGNRAY-VGVDLTNGVENNGN-NSQSGGKVTDELKEKV  130 (185)
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEECCEEE-EEEEEECCCCCCCC-CCCCCCHHHHHHHHHH
T ss_conf             788666777433455078999999999986278862114887468158-98874147665655-3335750447889999


Q ss_pred             HH---------CCCCEEECHH---HHHHHHHHCCCCCCCCHHHHHHHHHHHH
Q ss_conf             97---------3997886889---9999997288989489899999999999
Q gi|254780690|r  308 YE---------HNIPIFEEPS---LARSLFKQVPINSAIPPVFYKAVAQLIY  347 (354)
Q Consensus       308 ~~---------~~Vpive~~~---LAR~Ly~~~~ig~~Ip~~~y~aVA~il~  347 (354)
                      .+         .+|-|.-||-   ..|..-....-|++|. +++...++++.
T Consensus       131 A~~vk~tD~~i~nVyV~adpD~veR~~~~~~~I~~G~P~~-gf~dE~~~~~~  181 (185)
T TIGR02898       131 AETVKSTDKRIKNVYVSADPDTVERIREYGKGIKEGRPVE-GFLDELAEIVR  181 (185)
T ss_pred             HHHHHHCCCCCCEEEEEECCCHHHHHHHHHHHHHCCCCCC-HHHHHHHHHHH
T ss_conf             9865300337872689728628899999875621796711-78889999863


No 67 
>PRK04220 2-phosphoglycerate kinase; Provisional
Probab=55.95  E-value=10  Score=18.31  Aligned_cols=28  Identities=29%  Similarity=0.441  Sum_probs=20.8

Q ss_pred             HHHHHHHHHHHCCCCEEECHHHHHHHHH
Q ss_conf             9999999999739978868899999997
Q gi|254780690|r  299 IAKKMRKIAYEHNIPIFEEPSLARSLFK  326 (354)
Q Consensus       299 ~A~~Ir~~A~~~~Vpive~~~LAR~Ly~  326 (354)
                      +-..+.+.|++|+||+++|..+-+++-.
T Consensus       256 IQ~yLv~~A~~~~vPiI~N~~id~tv~~  283 (306)
T PRK04220        256 IQDYIVEKAKEHGVPVIENVSIEETVDK  283 (306)
T ss_pred             HHHHHHHHHHHHCCCEECCCCHHHHHHH
T ss_conf             9999999988809981068668999999


No 68 
>PRK13955 mscL large-conductance mechanosensitive channel; Provisional
Probab=55.12  E-value=16  Score=16.79  Aligned_cols=19  Identities=16%  Similarity=0.261  Sum_probs=6.7

Q ss_pred             HHHHCCCHHHHHHHHHHHH
Q ss_conf             0332012667999999999
Q gi|254780690|r  135 GIKRIYSINNLVNFMKSFV  153 (354)
Q Consensus       135 GlKriFS~k~lvel~Ksll  153 (354)
                      +||.-...-++++++-+++
T Consensus         4 eFK~Fi~rGNVidLAVaVi   22 (130)
T PRK13955          4 EFKKFAFKGNVIDLAVGVV   22 (130)
T ss_pred             HHHHHHHHCCHHHHHHHHH
T ss_conf             8999998057999999999


No 69 
>cd07371 2A5CPDO_AB The alpha and beta subunits of the Class III extradiol dioxygenase, 2-amino-5-chlorophenol 1,6-dioxygenase, which catalyzes the oxidization and subsequent ring-opening of 2-amino-5-chlorophenol. This subfamily contains both alpha and beta subunits of 2-amino-5-chlorophenol 1,6-dioxygenase (2A5CPDO), which catalyzes the oxidization and subsequent ring-opening of 2-amino-5-chlorophenol, an intermediate during p-chloronitrobenzene degradation. 2A5CPDO is a member of the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. The active enzyme is probably a heterotetramer, composed of two alpha and two beta subunits. Alpha and beta subunits share significant sequence similarity and may have evolved by gene duplication.
Probab=54.45  E-value=16  Score=16.71  Aligned_cols=26  Identities=4%  Similarity=-0.152  Sum_probs=20.9

Q ss_pred             EEEECCCHHHHHHHHHHHHCCCCEEE
Q ss_conf             99807658999999999973997886
Q gi|254780690|r  291 LVAKGQNLIAKKMRKIAYEHNIPIFE  316 (354)
Q Consensus       291 vvaKG~~~~A~~Ir~~A~~~~Vpive  316 (354)
                      .-.+|--++|..|.+.|+++|+|+..
T Consensus        81 y~~~~D~eLa~~i~~~a~~~Gi~~~~  106 (268)
T cd07371          81 YSINVDVELAEACVEEGRKAGLVTRM  106 (268)
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCEEE
T ss_conf             45558899999999999977991577


No 70 
>pfam02603 Hpr_kinase_N HPr Serine kinase N terminus. This family represents the N-terminal region of Hpr Serine/threonine kinase PtsK. This kinase is the sensor in a multicomponent phospho-relay system in control of carbon catabolic repression in bacteria. This kinase in unusual in that it recognizes the tertiary structure of its target and is a member of a novel family unrelated to any previously described protein phosphorylating enzymes. X-ray analysis of the full-length crystalline enzyme from Staphylococcus xylosus at a resolution of 1.95 A shows the enzyme to consist of two clearly separated domains that are assembled in a hexameric structure resembling a three-bladed propeller. The blades are formed by two N-terminal domains each, and the compact central hub assembles the C-terminal kinase domains.
Probab=53.56  E-value=10  Score=18.31  Aligned_cols=34  Identities=18%  Similarity=0.302  Sum_probs=24.1

Q ss_pred             EEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHHH
Q ss_conf             89980765899999999997399788688999999
Q gi|254780690|r  290 VLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSL  324 (354)
Q Consensus       290 ~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~L  324 (354)
                      +|+++|. ..-..+.+.|++++||++..+--.-.+
T Consensus        85 iIvt~~~-~~p~~l~~~a~~~~vPll~t~~~ts~~  118 (127)
T pfam02603        85 LIVTRGL-EPPEELLEAAKKYGIPLLRSKLSTSRL  118 (127)
T ss_pred             EEEECCC-CCCHHHHHHHHHHCCCEEECCCCHHHH
T ss_conf             9997999-999999999999799579828858999


No 71 
>smart00264 BAG BAG domains, present in regulator of Hsp70 proteins. BAG domains, present in Bcl-2-associated athanogene 1 and silencer of death domains
Probab=53.56  E-value=14  Score=17.11  Aligned_cols=32  Identities=22%  Similarity=0.164  Sum_probs=24.4

Q ss_pred             CHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             98999999754489989999999999999998
Q gi|254780690|r  225 SKQEIKDEIKQSYGNPIIKNRQKSIARSRIRH  256 (354)
Q Consensus       225 skqEvK~E~K~~EGdP~iK~~~r~~~re~~~~  256 (354)
                      |++=.+=--.+.||+|.+|..||+..+++.+-
T Consensus        40 t~~ll~LD~v~~~g~~~~R~~RK~~v~~iq~~   71 (79)
T smart00264       40 MKLLLKLDSVDVEGCPDIREARKRLVRLIQNL   71 (79)
T ss_pred             HHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             99998743778789778999999999999999


No 72 
>TIGR00693 thiE thiamine-phosphate pyrophosphorylase; InterPro: IPR003733   Thiamine monophosphate synthase (TMP) (2.5.1.3 from EC) catalyzes the substitution of the pyrophosphate of 2-methyl-4-amino-5- hydroxymethylpyrimidine pyrophosphate by 4-methyl-5- (beta-hydroxyethyl)thiazole phosphate to yield thiamine phosphate in the thiamine biosynthesis pathway .   TENI, a protein from Bacillus subtilis that regulates the production of several extracellular enzymes by reducing alkaline protease production belongs to this group .; GO: 0004789 thiamin-phosphate diphosphorylase activity, 0009228 thiamin biosynthetic process.
Probab=53.29  E-value=17  Score=16.58  Aligned_cols=36  Identities=22%  Similarity=0.317  Sum_probs=29.2

Q ss_pred             CHHHHHHHHHHHHCCCCEEEC--HHHHHHHHHH-CCCCC
Q ss_conf             589999999999739978868--8999999972-88989
Q gi|254780690|r  297 NLIAKKMRKIAYEHNIPIFEE--PSLARSLFKQ-VPINS  332 (354)
Q Consensus       297 ~~~A~~Ir~~A~~~~Vpive~--~~LAR~Ly~~-~~ig~  332 (354)
                      =+.|.+.|+++++++||.+-|  ..||.++=.. +-+||
T Consensus        52 ~~~A~~l~~lc~~y~~~f~vND~vdlA~~~~ADGvHlGQ   90 (210)
T TIGR00693        52 LELAEKLRELCRKYGVPFIVNDRVDLALALGADGVHLGQ   90 (210)
T ss_pred             HHHHHHHHHHHHHCCCCEEECCHHHHHHHHCCCEEEECC
T ss_conf             999999999998708976882839999983798776678


No 73 
>PRK00191 tatA twin arginine translocase protein A; Provisional
Probab=53.20  E-value=17  Score=16.57  Aligned_cols=50  Identities=20%  Similarity=0.287  Sum_probs=22.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf             999999999766799999998406998999999754489989999999999
Q gi|254780690|r  200 LLFIATLTVLDIGWSYHQWYSKLKMSKQEIKDEIKQSYGNPIIKNRQKSIA  250 (354)
Q Consensus       200 ~~~~~via~iD~~~qr~~~~k~lkMskqEvK~E~K~~EGdP~iK~~~r~~~  250 (354)
                      ++++++++.--+.=--...-|+||-=|.|+|+ +|+..--|+=...+++.+
T Consensus        13 vvvllLFGaKKLPdlARslGks~RifKsE~k~-m~~d~~~~~~~q~~~~~a   62 (107)
T PRK00191         13 LLIIVLFGAKKLPDAARSIGRSMRIFKSEVKE-MNKDDDTPEQQQQQQQIA   62 (107)
T ss_pred             HHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHH-HHHCCCCCCCHHHCHHHH
T ss_conf             99999976530369999885899999999999-873457743322244676


No 74 
>COG0399 WecE Predicted pyridoxal phosphate-dependent enzyme apparently involved in regulation of cell wall biogenesis [Cell envelope biogenesis, outer membrane]
Probab=53.01  E-value=10  Score=18.21  Aligned_cols=93  Identities=12%  Similarity=0.063  Sum_probs=41.7

Q ss_pred             HHCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHH
Q ss_conf             40699899999975448998999999999999999889860776869987355307888976888888889980765899
Q gi|254780690|r  221 KLKMSKQEIKDEIKQSYGNPIIKNRQKSIARSRIRHKMMEATSRATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIA  300 (354)
Q Consensus       221 ~lkMskqEvK~E~K~~EGdP~iK~~~r~~~re~~~~~~~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A  300 (354)
                      +-|||-=.--==.-|.|-=++.-.+||++.....  +.+++.+...+-...+.+..+.=.|       |+.+-+. +.--
T Consensus       229 N~rm~~iqAAigl~QL~~l~~~~~~R~~~a~~Y~--~~l~~~~~~~~p~~~~~~~~~~~~~-------~i~~~~~-~~~R  298 (374)
T COG0399         229 NYRLTEIQAAIGLAQLERLDEINERRREIAQIYA--EALKGLPGITLPPEPDGAVHAWHLY-------TILVDEE-GISR  298 (374)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHCCCCCCCCCCCCCCEEEEEEE-------EEEECCC-CCCH
T ss_conf             0387799999999999888999999999999999--9861078743357898761230366-------8982677-7789


Q ss_pred             HHHHHHHHHCCCCE-EECHHHHHH
Q ss_conf             99999999739978-868899999
Q gi|254780690|r  301 KKMRKIAYEHNIPI-FEEPSLARS  323 (354)
Q Consensus       301 ~~Ir~~A~~~~Vpi-ve~~~LAR~  323 (354)
                      .++.+.=++.||+. +..+|+=..
T Consensus       299 ~~l~~~L~~~gi~~~~~~~P~~~~  322 (374)
T COG0399         299 DALMESLKEAGVGAVVYFRPLHLQ  322 (374)
T ss_pred             HHHHHHHHHCCCCCEEEEECCCCC
T ss_conf             999999986787751663134432


No 75 
>COG1987 FliQ Flagellar biosynthesis pathway, component FliQ [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=52.91  E-value=17  Score=16.54  Aligned_cols=37  Identities=16%  Similarity=0.156  Sum_probs=24.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9899999999999999999999999988776878532
Q gi|254780690|r   78 SHIVFLLTHLSLSASRLVIPGLLLFMMFGIGSYLIQR  114 (354)
Q Consensus        78 ~~~~~~~~~~~~~~~~~~~p~~~~~~l~~i~~~l~q~  114 (354)
                      +....+..+..+..+.+..|++++++++|++.++.|-
T Consensus         4 ~~~l~i~~~ai~~~L~l~~P~ll~alvvGLvIsifQA   40 (89)
T COG1987           4 EDVLDIGQEAIWLVLMLSAPVLLVALVVGLVISIFQA   40 (89)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             8999999999999999999899999999999999999


No 76 
>TIGR03470 HpnH hopanoid biosynthesis associated radical SAM protein HpnH. The sequences represented by this model are members of the radical SAM superfamily of enzymes (pfam04055). These enzymes utilize an iron-sulfur redox cluster and S-adenosylmethionine to carry out diverse radical mediated reactions. The members of this clade are frequently found in the same locus as squalene-hopene cyclase (SHC, TIGR01507) and other genes associated with the biosynthesis of hopanoid natural products. The linkage between SHC and this radical SAM enzyme is strong; one is nearly always observed in the same genome where the other is found. A hopanoid biosynthesis locus was described in Zymomonas mobilis consisting of the genes HpnA-E and SHC (HpnF). Continuing past SHC are found a phosphorylase enzyme (ZMO0873, i.e. HpnG, TIGR03468) and this radical SAM enzyme (ZMO0874) which we name here HpnH. Granted, in Z. mobilis, HpnH is in a convergent orientation with respect to HpnA-G, but one gene beyond HpnH
Probab=52.86  E-value=14  Score=17.06  Aligned_cols=96  Identities=19%  Similarity=0.221  Sum_probs=41.4

Q ss_pred             HHHHHHHHHHCCCHHHHHHHHHHC--------CCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCC-----------
Q ss_conf             999999984069989999997544--------8998999999999999999889860776869987355-----------
Q gi|254780690|r  213 WSYHQWYSKLKMSKQEIKDEIKQS--------YGNPIIKNRQKSIARSRIRHKMMEATSRATIIITNPT-----------  273 (354)
Q Consensus       213 ~qr~~~~k~lkMskqEvK~E~K~~--------EGdP~iK~~~r~~~re~~~~~~~~~V~~A~vvitNPT-----------  273 (354)
                      ||+.....+-+||-+|.-+--.+.        =|.|.++-.+-++-+....+.+      -..+.||.|           
T Consensus        48 i~~~~~~l~~~Ls~ee~~~~~~e~Gap~V~itGGEPLLr~dl~eIv~~a~~~g~------~v~l~TNG~Ll~k~i~~~~~  121 (318)
T TIGR03470        48 IQYPAEILKQRLSVEECLRAVDECGAPVVSIPGGEPLLHPEIDEIVRGLVARKK------FVYLCTNALLLEKKLDKFEP  121 (318)
T ss_pred             CCCCCHHHHCCCCHHHHHHHHHHCCCCEEEECCCCCCCCCCHHHHHHHHHHCCC------EEEEECCHHHHHHHHHHHHH
T ss_conf             136764654438999999999984997899518874556479999999997599------79997755200999999851


Q ss_pred             ----CEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEE
Q ss_conf             ----307888976888888889980765899999999997399788
Q gi|254780690|r  274 ----HYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIF  315 (354)
Q Consensus       274 ----H~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpiv  315 (354)
                          ++.|-|.-..++...-+- -+|.=+.|..-.+.|+++|+++-
T Consensus       122 ~~~~~~~VsLDG~~e~HD~~r~-~~G~Fd~av~aIr~ak~~G~~V~  166 (318)
T TIGR03470       122 SPYLTFSVHLDGLREHHDASVC-REGVFDRAVEAIREAKARGFRVT  166 (318)
T ss_pred             CCCCEEEEECCCCHHHHHHHHC-CCCHHHHHHHHHHHHHHCCCCEE
T ss_conf             8883699980178788668871-79779999999999998699467


No 77 
>TIGR00514 accC acetyl-CoA carboxylase, biotin carboxylase; InterPro: IPR004549   This family represents the biotin carboxylase subunit found usually as a component of acetyl-CoA carboxylase. Acetyl-CoA carboxylase (6.4.1.2 from EC) is a heterohexamer of biotin carboxyl carrier protein, biotin carboxylase (6.3.4.14 from EC), and two subunits of carboxyl transferase in a 2:2 complex. In the first step of long-chain fatty acid synthesis, biotin carboxylase catalyses the carboxylation of the carrier protein and then the transcarboxylase transfers the carboxyl group to form malonyl-coA. Homologous domains are found in eukaryotic forms of acetyl-CoA carboxylase and in a number of other carboxylases (e.g. pyruvate carboxylase). In some systems, the biotin carboxyl carrier protein and this protein (biotin carboxylase) may be shared by different carboxyltransferases. However, this model is not intended to identify the biotin carboxylase domain of propionyl-coA carboxylase. The model should hit the full length of proteins, except for chloroplast transit peptides in plants. If it hits a domain only of a longer protein, there may be a problem with the identification.; GO: 0016874 ligase activity.
Probab=52.73  E-value=17  Score=16.52  Aligned_cols=57  Identities=19%  Similarity=0.183  Sum_probs=37.5

Q ss_pred             EEEECCCHHHHHHHHHHHHCCCCEEECHHHHH-HHHH------HCCCCCCCCHHHHHHHHHHHH
Q ss_conf             99807658999999999973997886889999-9997------288989489899999999999
Q gi|254780690|r  291 LVAKGQNLIAKKMRKIAYEHNIPIFEEPSLAR-SLFK------QVPINSAIPPVFYKAVAQLIY  347 (354)
Q Consensus       291 vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR-~Ly~------~~~ig~~Ip~~~y~aVA~il~  347 (354)
                      ||-==+|++|.||.+-++|.||+.|---+-|= .+-|      ++=||+.=..+-|--|+.||+
T Consensus         5 ~lIANRGEIA~RIiRAC~ElGi~TVAVyS~aD~dalHV~LADEavCIGea~S~kSYL~IpnI~a   68 (451)
T TIGR00514         5 ILIANRGEIALRIIRACKELGIATVAVYSTADRDALHVLLADEAVCIGEAPSAKSYLNIPNIIA   68 (451)
T ss_pred             EEEECCHHHHHHHHHHHHHCCCCEEEECCHHHHHHHHHHHHCCCCCCCCCHHHCCCCHHHHHHH
T ss_conf             8995260678899998886498639860044133234343025300686221124411588999


No 78 
>pfam02114 Phosducin Phosducin.
Probab=52.56  E-value=11  Score=17.85  Aligned_cols=33  Identities=15%  Similarity=0.050  Sum_probs=21.1

Q ss_pred             CCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             998999999754489989999999999999998
Q gi|254780690|r  224 MSKQEIKDEIKQSYGNPIIKNRQKSIARSRIRH  256 (354)
Q Consensus       224 MskqEvK~E~K~~EGdP~iK~~~r~~~re~~~~  256 (354)
                      ||-||-.-++.+.|-|.-++.-|+++++||.++
T Consensus        85 ms~~E~~~~~~d~eDe~fL~~Yrkqrm~eM~~~  117 (265)
T pfam02114        85 MSLKECELIDKDKDDEECLQKYRKQCMDDMHQK  117 (265)
T ss_pred             HHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             456665301333015999999999999999986


No 79 
>PRK09331 Sep-tRNA:Cys-tRNA synthetase; Provisional
Probab=52.49  E-value=17  Score=16.49  Aligned_cols=19  Identities=16%  Similarity=0.321  Sum_probs=12.4

Q ss_pred             CCHHHHHHHHHHHHCCCCE
Q ss_conf             6589999999999739978
Q gi|254780690|r  296 QNLIAKKMRKIAYEHNIPI  314 (354)
Q Consensus       296 ~~~~A~~Ir~~A~~~~Vpi  314 (354)
                      .+.++..++|||++++.|+
T Consensus       367 v~~li~A~keIaeky~~~~  385 (386)
T PRK09331        367 VEYVADSFKEIAEKYGLVV  385 (386)
T ss_pred             HHHHHHHHHHHHHHHCCCC
T ss_conf             9999999999999828978


No 80 
>pfam03796 DnaB_C DnaB-like helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.
Probab=52.37  E-value=12  Score=17.76  Aligned_cols=68  Identities=15%  Similarity=0.294  Sum_probs=37.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHH
Q ss_conf             89999999999999998898607768699873553078889768888888899807658999999999973997886889
Q gi|254780690|r  240 PIIKNRQKSIARSRIRHKMMEATSRATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPS  319 (354)
Q Consensus       240 P~iK~~~r~~~re~~~~~~~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~  319 (354)
                      .+|++++|+..++          .+.|+||...-+. +  +.......-..  .--.+.++.++|.+|++++|||+----
T Consensus       115 ~~i~~~i~~~~~~----------~~~~~vvvDyl~l-~--~~~~~~~~~~r--~~~v~~i~~~Lk~lA~e~~i~ii~~sQ  179 (186)
T pfam03796       115 SELRAQARRLKRE----------HGLGLIVIDYLQL-M--QGSKASKSENR--QQEISEISRSLKALAKELNIPVIALSQ  179 (186)
T ss_pred             HHHHHHHHHHHHH----------CCCCEEEEEHHHH-C--CCCCCCCCCCH--HHHHHHHHHHHHHHHHHHCCCEEEEEC
T ss_conf             9999999999985----------5998899748986-3--67788877559--999999999999999997991899722


Q ss_pred             HHH
Q ss_conf             999
Q gi|254780690|r  320 LAR  322 (354)
Q Consensus       320 LAR  322 (354)
                      |=|
T Consensus       180 lNR  182 (186)
T pfam03796       180 LSR  182 (186)
T ss_pred             CCC
T ss_conf             575


No 81 
>pfam01767 Birna_VP3 Birnavirus VP3 protein. VP3 is a minor structural component of the virus. The large RNA segment of birnaviruses codes for a polyprotein (N-VP2-VP4-VP3-C).
Probab=52.11  E-value=11  Score=18.10  Aligned_cols=96  Identities=22%  Similarity=0.304  Sum_probs=47.7

Q ss_pred             HCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCC--EEEEC----CC--CEEEEEE----ECCC---CCCCCEEEEECCCHH
Q ss_conf             44899899999999999999988986077686--99873----55--3078889----7688---888888998076589
Q gi|254780690|r  235 QSYGNPIIKNRQKSIARSRIRHKMMEATSRAT--IIITN----PT--HYALALR----YIQT---ENDAPVLVAKGQNLI  299 (354)
Q Consensus       235 ~~EGdP~iK~~~r~~~re~~~~~~~~~V~~A~--vvitN----PT--H~AVAL~----Y~~~---~~~aP~vvaKG~~~~  299 (354)
                      ++.|+-+.-++ |.+.+.++.+.+..+..-|+  .|--|    ||  .|+-=+.    =|||   ++..|.-+-+-.|+ 
T Consensus        95 ~~kgpt~~~aq-~aKa~RIs~d~~~~g~~fat~eWVa~n~~RGPspgQ~kyy~~tg~~p~pgddy~dyi~~~i~rp~~~-  172 (229)
T pfam01767        95 RSKGPTQHAAQ-RAKATRISLDAVSAGAEFATPEWVAENGYRGPSPGQFKYYLITGRDPDPGDDYEDYIPPPITRPTDE-  172 (229)
T ss_pred             CCCCCCHHHHH-HHHHHHHHHHHHHCCCCCCCHHHHHHCCCCCCCHHHHHHHHHHCCCCCCCCHHHHCCCCCCCCCCHH-
T ss_conf             88998888999-9889898888886164106719998568889983677898871789998710543378634576528-


Q ss_pred             HHHHHHHHHHCCCCEEECHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             9999999997399788688999999972889894898999999999999
Q gi|254780690|r  300 AKKMRKIAYEHNIPIFEEPSLARSLFKQVPINSAIPPVFYKAVAQLIYK  348 (354)
Q Consensus       300 A~~Ir~~A~~~~Vpive~~~LAR~Ly~~~~ig~~Ip~~~y~aVA~il~~  348 (354)
                       .+|+              -||-++|. ..--++-|+++|++||.|++.
T Consensus       173 -~ki~--------------rla~Siyg-~P~Qepap~~f~d~Va~V~~e  205 (229)
T pfam01767       173 -NKIR--------------RLANSIYG-LPHQEPAPDAFYDEVAAVYAE  205 (229)
T ss_pred             -HHHH--------------HHCCCCCC-CCCCCCCCHHHHHHHHHHHHH
T ss_conf             -8999--------------87021248-987788868899999999998


No 82 
>PRK12337 2-phosphoglycerate kinase; Provisional
Probab=51.58  E-value=9.7  Score=18.41  Aligned_cols=90  Identities=17%  Similarity=0.250  Sum_probs=47.5

Q ss_pred             CHHHHHHHHHHHHHHHHHH-H-HHHCCCCCEEEECCCCEEEE----EEECCCCCCCCEEEEE---------------CC-
Q ss_conf             9899999999999999988-9-86077686998735530788----8976888888889980---------------76-
Q gi|254780690|r  239 NPIIKNRQKSIARSRIRHK-M-MEATSRATIIITNPTHYALA----LRYIQTENDAPVLVAK---------------GQ-  296 (354)
Q Consensus       239 dP~iK~~~r~~~re~~~~~-~-~~~V~~A~vvitNPTH~AVA----L~Y~~~~~~aP~vvaK---------------G~-  296 (354)
                      ++.+.|=+.|-+.=..--+ . -..+..-+-+|..-.|+-=.    ..++ +..-.|++|.-               +. 
T Consensus       338 ~~vi~GF~~Qv~~V~vGl~aVieRa~~EG~SvVIEGVHLvPg~i~~~~~e-~~~vIp~mV~i~dEe~Hr~RF~~R~r~t~  416 (492)
T PRK12337        338 VELLAGFRDQVQQVSVGLKAVVRRSILEGTSLVLEGVHLVPGYLQHAYQD-GALTVPMLVALPDEEEHRRHFELRDRETA  416 (492)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEECHHHHHHHHCC-CCEEEEEEEEECCHHHHHHHHHHHHHHHC
T ss_conf             68998999999999999999999999728867998333070666666415-87389999984767999999998751410


Q ss_pred             -C--------------HHHHHHHHHHHHCCCCEEECHHHHHHHHHHCC
Q ss_conf             -5--------------89999999999739978868899999997288
Q gi|254780690|r  297 -N--------------LIAKKMRKIAYEHNIPIFEEPSLARSLFKQVP  329 (354)
Q Consensus       297 -~--------------~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~~~~  329 (354)
                       +              .+-..+.+.|++|+|||++|-.|-.+.-+-+|
T Consensus       417 ~~Rp~ekYLk~F~eIR~IQdyLv~rAre~gVPVI~n~~ldesvd~~~e  464 (492)
T PRK12337        417 ASRPLHRYMRHFEEIRLMQDHLLRLAREEDVPVLDGETLDESADKAVE  464 (492)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHH
T ss_conf             368601799979999999999999998749982078766779999999


No 83 
>cd05534 POLBc_zeta DNA polymerase type-B zeta subfamily catalytic domain. DNA polymerase (Pol) zeta is a member of the eukaryotic B-family of DNA polymerases and distantly related to DNA Pol delta. Pol zeta plays a major role in translesion replication and the production of either spontaneous or induced mutations. Apart from its role in translesion replication, Pol zeta also appears to be involved in somatic hypermutability in B lymphocytes, an important element for the production of high affinity antibodies in response to an antigen.
Probab=51.47  E-value=18  Score=16.37  Aligned_cols=50  Identities=12%  Similarity=0.193  Sum_probs=26.5

Q ss_pred             CCCCEEEEECCCH--HHHH---HHHHHHHCCCCEEECHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             8888899807658--9999---99999973997886889999999728898948989999999999999
Q gi|254780690|r  286 NDAPVLVAKGQNL--IAKK---MRKIAYEHNIPIFEEPSLARSLFKQVPINSAIPPVFYKAVAQLIYKI  349 (354)
Q Consensus       286 ~~aP~vvaKG~~~--~A~~---Ir~~A~~~~Vpive~~~LAR~Ly~~~~ig~~Ip~~~y~aVA~il~~v  349 (354)
                      +..|.|++||.+.  +..+   .-+.+++++.+              .+.+=||-.++..+|.+||..+
T Consensus       392 drI~YVIvk~~~~~~~~dra~~p~~~~~~~~l~--------------iD~~YYi~~Qi~ppl~rile~i  446 (451)
T cd05534         392 ERVPYVVVRGEPGSRLIDLVVSPEEFLADPSLR--------------LDAEYYITKQIIPALDRLFNLV  446 (451)
T ss_pred             CEEEEEEEECCCCCCHHHHCCCHHHHHHCCCCC--------------CCHHHHHHHCCHHHHHHHHHHC
T ss_conf             999899998998763353125859887448999--------------8869999854576999999871


No 84 
>COG1493 HprK Serine kinase of the HPr protein, regulates carbohydrate metabolism [Signal transduction mechanisms]
Probab=51.41  E-value=18  Score=16.37  Aligned_cols=34  Identities=26%  Similarity=0.421  Sum_probs=20.8

Q ss_pred             EEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHHH
Q ss_conf             89980765899999999997399788688999999
Q gi|254780690|r  290 VLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSL  324 (354)
Q Consensus       290 ~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~L  324 (354)
                      +|++||.+. ...+.+.|+++++|++..+--.-.|
T Consensus        85 iI~sk~~~~-p~~l~~~a~~~~~pil~s~~~ts~l  118 (308)
T COG1493          85 LIVSKGLPI-PEELLDAAKKYNIPILTSKLSTSEL  118 (308)
T ss_pred             EEEECCCCC-CHHHHHHHHHCCCCEEEECCHHHHH
T ss_conf             999789999-7899999887099669853318999


No 85 
>PRK10364 sensor protein ZraS; Provisional
Probab=50.44  E-value=18  Score=16.26  Aligned_cols=12  Identities=0%  Similarity=-0.413  Sum_probs=6.0

Q ss_pred             HHHHHHHHHHHH
Q ss_conf             766799999998
Q gi|254780690|r  209 LDIGWSYHQWYS  220 (354)
Q Consensus       209 iD~~~qr~~~~k  220 (354)
                      ..|++|||.-.+
T Consensus       211 ~~~~~~~~~~~R  222 (455)
T PRK10364        211 SFFWYRRYLRSR  222 (455)
T ss_pred             HHHHHHHHHHHH
T ss_conf             999998778999


No 86 
>cd01990 Alpha_ANH_like_I This is a subfamily of Adenine nucleotide alpha hydrolases superfamily. Adenine nucleotide alpha hydrolases superfamily  includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which  binds to Adenosine group.  This subfamily   of proteins probably binds ATP. This domain is about 200 amino acids long with a strongly conserved motif SGGKD at the N terminus.
Probab=50.05  E-value=14  Score=17.06  Aligned_cols=83  Identities=19%  Similarity=0.247  Sum_probs=55.5

Q ss_pred             CCEEEECCCCEEEEEEECCCCCC-------CCEEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHHHHHHCCCCCCCCHH
Q ss_conf             86998735530788897688888-------88899807658999999999973997886889999999728898948989
Q gi|254780690|r  265 ATIIITNPTHYALALRYIQTEND-------APVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFKQVPINSAIPPV  337 (354)
Q Consensus       265 A~vvitNPTH~AVAL~Y~~~~~~-------aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~~~~ig~~Ip~~  337 (354)
                      .+. |.+-|++.=-..|.||...       -|.+-+   +.-=..||++|++.|+|+...|+-+ -|--..+-|++|.++
T Consensus        96 ~~~-v~dGtn~dDl~d~RPGl~A~~e~~v~sPL~e~---gl~K~eVR~la~~lgLp~~~kp~~~-CLasRip~g~~it~e  170 (202)
T cd01990          96 LDV-VLDGTNADDLGDYRPGLKALRELGVRSPLAEA---GLGKAEIRELARELGLPTWDKPAMA-CLASRIPYGTEITEE  170 (202)
T ss_pred             CCE-EEECCCCCCCCCCCCCHHHHHHCCCCCCHHHC---CCCHHHHHHHHHHCCCCCCCCCCCC-CEEEECCCCCCCCHH
T ss_conf             978-94157576323557868899876998852651---9788999999998399856689987-546665788848999


Q ss_pred             HHHHHHHHHHHHHHH
Q ss_conf             999999999999730
Q gi|254780690|r  338 FYKAVAQLIYKIYHK  352 (354)
Q Consensus       338 ~y~aVA~il~~v~~l  352 (354)
                      ..+-|-+.=.++.++
T Consensus       171 ~L~~v~~aE~~L~~~  185 (202)
T cd01990         171 RLKKVEAAEEFLRSL  185 (202)
T ss_pred             HHHHHHHHHHHHHHC
T ss_conf             999999999999981


No 87 
>pfam05134 GspL General secretion pathway protein L (GspL). This family consists of general secretion pathway protein L sequences from several gram-negative bacteria. The general secretion pathway of gram-negative bacteria is responsible for extracellular secretion of a number of different proteins, including proteases and toxins. This pathway supports secretion of proteins across the cell envelope in two distinct steps, in which the second step, involving translocation through the outer membrane, is assisted by at least 13 different gene products. GspL is predicted to contain a large cytoplasmic domain and has been shown to interact with the autophosphorylating cytoplasmic membrane protein GspE. It is thought that the tri-molecular complex of GspL, GspE and GspM might be involved in regulating the opening and closing of the secretion pore and/or transducing energy to the site of outer membrane translocation.
Probab=50.02  E-value=18  Score=16.21  Aligned_cols=116  Identities=15%  Similarity=0.182  Sum_probs=69.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCC-HHHHHHHHHHHHHHHHH----------HHHHHC
Q ss_conf             9999999999999997667999999984069989999997544899-89999999999999998----------898607
Q gi|254780690|r  194 KVLIMILLFIATLTVLDIGWSYHQWYSKLKMSKQEIKDEIKQSYGN-PIIKNRQKSIARSRIRH----------KMMEAT  262 (354)
Q Consensus       194 ~l~~~~~~~~~via~iD~~~qr~~~~k~lkMskqEvK~E~K~~EGd-P~iK~~~r~~~re~~~~----------~~~~~V  262 (354)
                      .....++++++++.++....|.|++.++..=.++++.+-|++.=.+ +.+-.-++|+.|++.+-          .++..+
T Consensus       215 r~~a~la~~~l~~~~~~~~~~~~~l~~q~~~l~~q~~~~y~~~FP~~~~v~d~~~Qm~~~l~~l~~~~~~~~fl~ll~~l  294 (357)
T pfam05134       215 RLVAILAALLLLLAVLNGGLQLYQLERQAQALRAQSEAVYRQLFPGAKRVVNLRAQMQQQLARLAGGGAGPGLLSLLAAL  294 (357)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHHHH
T ss_conf             99999999999999999999999999999999999999999867998766899999999999861789862499999999


Q ss_pred             CCCCEEEECCCCEEEEEEECCCCCCCCE-EEEECCCHHHHHHHHHHHHCCC
Q ss_conf             7686998735530788897688888888-9980765899999999997399
Q gi|254780690|r  263 SRATIIITNPTHYALALRYIQTENDAPV-LVAKGQNLIAKKMRKIAYEHNI  312 (354)
Q Consensus       263 ~~A~vvitNPTH~AVAL~Y~~~~~~aP~-vvaKG~~~~A~~Ir~~A~~~~V  312 (354)
                        +.++=-+|..=--.|+||.+....=. +.|+.-..+ .+.|....+.+.
T Consensus       295 --~~al~~~~~~~l~sL~y~~~~~eL~l~~~a~~f~~l-e~lr~~l~~~g~  342 (357)
T pfam05134       295 --QAALGSLPGVRLQSLDYDGARGELRLQLEAKDFADL-EQLRARLAEVGL  342 (357)
T ss_pred             --HHHHHCCCCCCEEEEEECCCCCEEEEEEECCCHHHH-HHHHHHHHHCCC
T ss_conf             --998713898733787873888759999836987999-999999986487


No 88 
>PRK11706 TDP-4-oxo-6-deoxy-D-glucose transaminase; Provisional
Probab=49.90  E-value=12  Score=17.81  Aligned_cols=14  Identities=14%  Similarity=0.064  Sum_probs=9.2

Q ss_pred             HHHHHHHHCCCCEE
Q ss_conf             99999997399788
Q gi|254780690|r  302 KMRKIAYEHNIPIF  315 (354)
Q Consensus       302 ~Ir~~A~~~~Vpiv  315 (354)
                      ++++.=+++||+..
T Consensus       304 ~l~~~L~~~gI~t~  317 (375)
T PRK11706        304 ALINFLKEAGIMAV  317 (375)
T ss_pred             HHHHHHHHCCCCEE
T ss_conf             99999998799832


No 89 
>TIGR03588 PseC UDP-4-keto-6-deoxy-N-acetylglucosamine 4-aminotransferase. This family of enzymes are aminotransferases of the pfam01041 family involved in the biosynthesis of pseudaminic acid. They convert UDP-4-keto-6-deoxy-N-acetylglucosamine into UDP-4-amino-4,6-dideoxy-N-acetylgalactose. Pseudaminic acid has a role in surface polysaccharide in Pseudomonas as well as in the modification of flagellin in Campylobacter and Helicobacter species.
Probab=49.63  E-value=12  Score=17.64  Aligned_cols=26  Identities=15%  Similarity=0.224  Sum_probs=13.8

Q ss_pred             CEEEEECCCHHHHHHHHHHHHCCCCE
Q ss_conf             88998076589999999999739978
Q gi|254780690|r  289 PVLVAKGQNLIAKKMRKIAYEHNIPI  314 (354)
Q Consensus       289 P~vvaKG~~~~A~~Ir~~A~~~~Vpi  314 (354)
                      |+.+-+....--.++.+.-+++||..
T Consensus       298 ~i~~~~~~~~~r~~l~~~L~~~gI~t  323 (380)
T TIGR03588       298 PILLDQEFGCTRKEVFEALRAAGIGV  323 (380)
T ss_pred             EEEECCCCCCCHHHHHHHHHHCCCCE
T ss_conf             99982667314999999999779985


No 90 
>pfam03552 Cellulose_synt Cellulose synthase. Cellulose, an aggregate of unbranched polymers of beta-1,4-linked glucose residues, is the major component of wood and thus paper, and is synthesized by plants, most algae, some bacteria and fungi, and even some animals. The genes that synthesize cellulose in higher plants differ greatly from the well-characterized genes found in Acetobacter and Agrobacterium sp. More correctly designated as 'cellulose synthase catalytic subunits', plant cellulose synthase (CesA) proteins are integral membrane proteins, approximately 1,000 amino acids in length. There are a number of highly conserved residues, including several motifs shown to be necessary for processive glycosyltransferase activity.
Probab=49.07  E-value=19  Score=16.10  Aligned_cols=112  Identities=15%  Similarity=0.130  Sum_probs=49.3

Q ss_pred             HHHHHHHHHHHHHHHCCCHHHCCCCCCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHH---HHHHHHHHCHHHHHHHHC
Q ss_conf             99887768785321013712137791016934303320126679999999999999999---999999832156897840
Q gi|254780690|r  102 FMMFGIGSYLIQRIPVLNLNHVKPSFKRVSLREGIKRIYSINNLVNFMKSFVKIILVGT---IITISLTENYFTMLDFIS  178 (354)
Q Consensus       102 ~~l~~i~~~l~q~G~~fs~k~l~pk~~rlNPi~GlKriFS~k~lvel~KsllKv~li~~---v~~~~i~~~~~~l~~l~~  178 (354)
                      .+-+.+.-.+.| .-.|+.-.+.-=|||-||+-.=+||       .+...+.-.-...+   ....+.+..+|.+.-+..
T Consensus       448 ~AP~nL~d~L~Q-~~RWa~G~lEI~fSr~~P~~~g~rl-------~~lq~laY~~~~~~p~~Sip~l~Y~~lPalcLl~g  519 (716)
T pfam03552       448 SAPINLSDRLHQ-VLRWALGSVEIFFSRHCPIWYGGRL-------KFLQRLAYINTIVYPFTSIPLIAYCFLPAICLLTG  519 (716)
T ss_pred             CCCCCHHHHHHH-HHHHHCCCEEEEEECCCCHHHCCCC-------CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             789987888777-7665416245663047813416755-------68787477744441434899999998679997459


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHCC
Q ss_conf             8979999999999999999999999999997667999---999984069
Q gi|254780690|r  179 ANPHSILYHAFFTVRKVLIMILLFIATLTVLDIGWSY---HQWYSKLKM  224 (354)
Q Consensus       179 ~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD~~~qr---~~~~k~lkM  224 (354)
                      ..+..-++   .....++..+.+.....+++++.|.-   ..|.++.||
T Consensus       520 ~~i~P~~s---~~~~~~~~~lf~~~~~~~llE~~wsG~si~~WWnnqr~  565 (716)
T pfam03552       520 KFIVPTLS---NYASIYFLSLFLSIIATGILELRWSGVSIEEWWRNEQF  565 (716)
T ss_pred             CEECCCCC---CHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHE
T ss_conf             71056676---03999999999999998877664248769998533235


No 91 
>TIGR01369 CPSaseII_lrg carbamoyl-phosphate synthase, large subunit; InterPro: IPR006275   Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates , . CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate . The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC).   Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain . CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites . The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain.   Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein . The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP . There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia . CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains .    This entry represents glutamine-dependent CPSase (6.3.5.5 from EC) from prokaryotes and eukaryotes (CPSase II). ; GO: 0004086 carbamoyl-phosphate synthase activity, 0006807 nitrogen compound metabolic process.
Probab=48.56  E-value=19  Score=16.05  Aligned_cols=52  Identities=12%  Similarity=0.226  Sum_probs=37.7

Q ss_pred             CCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHHHHH
Q ss_conf             7686998735530788897688888888998076589999999999739978868899999997
Q gi|254780690|r  263 SRATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFK  326 (354)
Q Consensus       263 ~~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~  326 (354)
                      .+.+.||.-|+         ++   .--+..+-.+.-..+||+.|-+++||++-|+.+|++.-.
T Consensus      1036 ~~~~~vIN~~~---------~~---~~~~~~~~~~~~gy~iRR~A~~~~vp~~t~~~~~~~~~~ 1087 (1089)
T TIGR01369      1036 GEIELVINLTS---------KG---KEGVLLRETATDGYKIRREAVDYGVPLITTLETAEAFLE 1087 (1089)
T ss_pred             CCCEEEEECCC---------CC---CCCEEECCCCCHHHHHHHHHHHCCCCEEECHHHHHHHHH
T ss_conf             88069996578---------88---663122024544589999999649977865689999998


No 92 
>PRK11658 UDP-4-amino-4-deoxy-L-arabinose--oxoglutarate aminotransferase; Provisional
Probab=48.20  E-value=14  Score=17.21  Aligned_cols=32  Identities=9%  Similarity=0.012  Sum_probs=18.1

Q ss_pred             HHHHHHHH---HCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             99999997---288989489899999999999997
Q gi|254780690|r  319 SLARSLFK---QVPINSAIPPVFYKAVAQLIYKIY  350 (354)
Q Consensus       319 ~LAR~Ly~---~~~ig~~Ip~~~y~aVA~il~~v~  350 (354)
                      |-|..++.   +.++......+--+-|.+.+..+.
T Consensus       343 pnae~~~~~~lsLP~~~~Lt~~di~~Ii~~ik~i~  377 (379)
T PRK11658        343 PNTEWNSERICSLPLFPDMTDSDVDRVITALQQIA  377 (379)
T ss_pred             HHHHHHHHCEEECCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             89999984889898998979999999999999997


No 93 
>PRK00145 putative inner membrane protein translocase component YidC; Provisional
Probab=47.35  E-value=20  Score=15.91  Aligned_cols=15  Identities=13%  Similarity=0.284  Sum_probs=5.1

Q ss_pred             HHHCCCHHHHHHHHH
Q ss_conf             840699899999975
Q gi|254780690|r  220 SKLKMSKQEIKDEIK  234 (354)
Q Consensus       220 k~lkMskqEvK~E~K  234 (354)
                      +.+=+.|.-.|++.|
T Consensus       207 Q~~~i~~~~~kk~~~  221 (225)
T PRK00145        207 QTYFIKKLPLKKKVE  221 (225)
T ss_pred             HHHHHHHHHHHHHHH
T ss_conf             999996210356787


No 94 
>pfam02571 CbiJ Precorrin-6x reductase CbiJ/CobK. This family consists of Precorrin-6x reductase EC:1.3.1.54. This enzyme catalyses the reaction: precorrin-6Y + NADP(+) <= precorrin-6X + NADPH. CbiJ and CobK both catalyse the reduction of macocycle in the colbalmin biosynthesis pathway.
Probab=46.04  E-value=20  Score=15.95  Aligned_cols=54  Identities=19%  Similarity=0.148  Sum_probs=35.7

Q ss_pred             CCCEEEEECCCHHH-HHHHHHHHHCCCCEE--ECHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             88889980765899-999999997399788--6889999999728898948989999999999999730
Q gi|254780690|r  287 DAPVLVAKGQNLIA-KKMRKIAYEHNIPIF--EEPSLARSLFKQVPINSAIPPVFYKAVAQLIYKIYHK  352 (354)
Q Consensus       287 ~aP~vvaKG~~~~A-~~Ir~~A~~~~Vpiv--e~~~LAR~Ly~~~~ig~~Ip~~~y~aVA~il~~v~~l  352 (354)
                      .+=.+|+|-.|..+ ..-.+.|++.|+|++  +.|++            +-|...+..+.+++.|+.++
T Consensus       190 ~i~~lVtK~SG~~g~~~Ki~AA~~lgi~vivI~RP~~------------~~~~~~~~~~~e~~~~l~~~  246 (246)
T pfam02571       190 GIDVLVTKNSGGAGTYAKLAAARELGLPVIMIKRPPL------------PYGVPTVEDVDEALAWLGNL  246 (246)
T ss_pred             CCCEEEEECCCCHHHHHHHHHHHHCCCEEEEEECCCC------------CCCCCCCCCHHHHHHHHHCC
T ss_conf             9999999288865069999999984992999958999------------98776069999999998529


No 95 
>pfam01741 MscL Large-conductance mechanosensitive channel, MscL.
Probab=45.94  E-value=21  Score=15.76  Aligned_cols=20  Identities=20%  Similarity=0.253  Sum_probs=7.7

Q ss_pred             HHHHHCCCHHHHHHHHHHHH
Q ss_conf             30332012667999999999
Q gi|254780690|r  134 EGIKRIYSINNLVNFMKSFV  153 (354)
Q Consensus       134 ~GlKriFS~k~lvel~Ksll  153 (354)
                      +|||.--..-+++|++-++.
T Consensus         3 keFK~Fi~rGNVidLAVgvI   22 (127)
T pfam01741         3 KEFKEFAMRGNVVDLAVGVV   22 (127)
T ss_pred             HHHHHHHHHCCHHHHHHHHH
T ss_conf             78999998157899999999


No 96 
>PRK01315 putative inner membrane protein translocase component YidC; Provisional
Probab=44.82  E-value=22  Score=15.63  Aligned_cols=18  Identities=11%  Similarity=-0.073  Sum_probs=6.7

Q ss_pred             HHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999976679
Q gi|254780690|r  196 LIMILLFIATLTVLDIGW  213 (354)
Q Consensus       196 ~~~~~~~~~via~iD~~~  213 (354)
                      ++.....-+..|+.=|+.
T Consensus       227 m~~~~~~~fPaGl~lYW~  244 (325)
T PRK01315        227 MFAVSGIAFPVGVLFYWL  244 (325)
T ss_pred             HHHHHHHHHHHHHHHHHH
T ss_conf             999999778999999999


No 97 
>pfam01313 Bac_export_3 Bacterial export proteins, family 3. This family includes the following members; FliQ, MopD, HrcS, Hrp, YopS and SpaQ All of these members export proteins, that do not possess signal peptides, through the membrane. Although the proteins that these exporters move may be different, the exporters are thought to function in similar ways.
Probab=44.67  E-value=22  Score=15.61  Aligned_cols=33  Identities=24%  Similarity=0.138  Sum_probs=18.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999988776878532
Q gi|254780690|r   82 FLLTHLSLSASRLVIPGLLLFMMFGIGSYLIQR  114 (354)
Q Consensus        82 ~~~~~~~~~~~~~~~p~~~~~~l~~i~~~l~q~  114 (354)
                      ....+..+..+....|.+++.+++|++.++.|.
T Consensus         5 ~l~~~al~~~l~~s~P~l~~alvVGlvIsi~QA   37 (76)
T pfam01313         5 DLGRQALWLVLLLSAPLLLVALVVGLVVSLFQA   37 (76)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999998899999999999999999


No 98 
>PRK02944 OxaA-like protein precursor; Validated
Probab=44.56  E-value=22  Score=15.60  Aligned_cols=12  Identities=8%  Similarity=0.509  Sum_probs=6.8

Q ss_pred             HHHCCCCCCCCC
Q ss_conf             121377910169
Q gi|254780690|r  120 LNHVKPSFKRVS  131 (354)
Q Consensus       120 ~k~l~pk~~rlN  131 (354)
                      ...++|+.++|+
T Consensus        88 Mq~lqPe~~~Iq   99 (255)
T PRK02944         88 MQALQPEMVKLK   99 (255)
T ss_pred             HHHHCHHHHHHH
T ss_conf             988486799999


No 99 
>TIGR03600 phage_DnaB phage replicative helicase, DnaB family, HK022 subfamily. Members of this family are phage (or prophage-region) homologs of the bacterial homohexameric replicative helicase DnaB. Some phage may rely on host DnaB, while others encode their own verions. This model describes the largest phage-specific clade among the close homologs of DnaB, but there are, or course, other DnaB homologs from phage that fall outside the scope of this model.
Probab=44.53  E-value=19  Score=16.11  Aligned_cols=165  Identities=12%  Similarity=0.170  Sum_probs=79.1

Q ss_pred             HHHHH--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             30332--0126679999999999999999999999832156897840897999999999999999999999999999766
Q gi|254780690|r  134 EGIKR--IYSINNLVNFMKSFVKIILVGTIITISLTENYFTMLDFISANPHSILYHAFFTVRKVLIMILLFIATLTVLDI  211 (354)
Q Consensus       134 ~GlKr--iFS~k~lvel~KsllKv~li~~v~~~~i~~~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD~  211 (354)
                      .||++  +.=.-+=--.+|+.+=+-+.   .-.......+.++....++..+...-+.....                ..
T Consensus       189 ~Gl~~g~LiIiaARPsmGKTafalnia---~n~A~~~g~~Vl~fSLEMs~eql~~R~la~~s----------------~i  249 (421)
T TIGR03600       189 NGLVKGDLIVIGARPSMGKTTLALNIA---ENVALREGKPVLFFSLEMSAEQLGERLLASKS----------------GI  249 (421)
T ss_pred             CCCCCCCEEEEEEECCCCHHHHHHHHH---HHHHHHCCCEEEEEECCCCHHHHHHHHHHHHC----------------CC
T ss_conf             699988689998546787459999999---99998669838999257999999999999854----------------89


Q ss_pred             HHHHHHHHHHHCCCHHHHHH------HHHHC------CCC---HHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCEE
Q ss_conf             79999999840699899999------97544------899---8999999999999999889860776869987355307
Q gi|254780690|r  212 GWSYHQWYSKLKMSKQEIKD------EIKQS------YGN---PIIKNRQKSIARSRIRHKMMEATSRATIIITNPTHYA  276 (354)
Q Consensus       212 ~~qr~~~~k~lkMskqEvK~------E~K~~------EGd---P~iK~~~r~~~re~~~~~~~~~V~~A~vvitNPTH~A  276 (354)
                      ..++.+   +-++|.+|...      +.++.      .++   .+|+++.|++.++         -.+-++||..=-+. 
T Consensus       250 ~~~~i~---~g~l~~~~~~~~~~a~~~l~~~~l~i~d~~~~ti~~ir~~~r~~~~~---------~~~l~livIDYLqL-  316 (421)
T TIGR03600       250 NTGNIR---TGRFNDSDFNRLLNAVDRLSEKDLYIDDTGGLTVAQIRSIARRIKRK---------KGGLDLIVVDYIQL-  316 (421)
T ss_pred             CHHHHH---CCCCCHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHHHHH---------CCCCCEEEECHHHH-
T ss_conf             776665---28999899999999999861687899669988767899999999986---------28986999757865-


Q ss_pred             EEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHHHHHHCCCCCCCCHHH
Q ss_conf             88897688888888998076589999999999739978868899999997288989489899
Q gi|254780690|r  277 LALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFKQVPINSAIPPVF  338 (354)
Q Consensus       277 VAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~~~~ig~~Ip~~~  338 (354)
                        ++-..+.+   +.  --.+++...+|.+|+|.+||||-=--|-|......+ -.|+-.+|
T Consensus       317 --i~~~~~~~---r~--~ei~~Isr~LK~lAkel~ipVi~lsQLnR~~e~R~d-krP~lsDL  370 (421)
T TIGR03600       317 --MAPTRGRD---RN--EELGGISRGLKALAKELDVPVVLLAQLNRGSEKRTD-KRPIMSDL  370 (421)
T ss_pred             --CCCCCCCC---HH--HHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCCCC-CCCCHHHH
T ss_conf             --37888888---89--999999999999999979978997057865233688-88654344


No 100
>TIGR01403 fliQ_rel_III type III secretion protein, HrpO family; InterPro: IPR006306   This is one of several families of proteins related to bacterial flagellar biosynthesis proteins and involved in bacterial type III protein secretion systems. This family is homologous to, but separate from, the flagellar biosynthetic protein FliQ.; GO: 0006810 transport, 0016021 integral to membrane.
Probab=43.73  E-value=23  Score=15.51  Aligned_cols=27  Identities=22%  Similarity=0.142  Sum_probs=14.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999972000121
Q gi|254780690|r   47 LLFFFSPGIYSVTSDLHVLLASATQRK   73 (354)
Q Consensus        47 l~~~~~~~~~~l~~~~~~~~~~~~~~~   73 (354)
                      +..+.|-.+....+.+..++...++-.
T Consensus        15 ~lSlPpv~vA~ivG~lvSLlQA~TQlQ   41 (81)
T TIGR01403        15 ILSLPPVLVAAIVGILVSLLQALTQLQ   41 (81)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999899999999999999999999988


No 101
>PRK10333 putative ligase; Provisional
Probab=43.52  E-value=15  Score=16.94  Aligned_cols=17  Identities=41%  Similarity=0.634  Sum_probs=14.4

Q ss_pred             HHHCCCHHHHHHHHHHC
Q ss_conf             84069989999997544
Q gi|254780690|r  220 SKLKMSKQEIKDEIKQS  236 (354)
Q Consensus       220 k~lkMskqEvK~E~K~~  236 (354)
                      ..|.|||+|+++++++.
T Consensus         5 ~~l~m~K~~LRk~~~~~   21 (198)
T PRK10333          5 PPLTLSRQEIRKMIRQR   21 (198)
T ss_pred             CCCCCCHHHHHHHHHHH
T ss_conf             98767999999999999


No 102
>cd00984 DnaB_C DnaB helicase C terminal domain. The hexameric helicase DnaB unwinds the DNA duplex at the  chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis.
Probab=43.49  E-value=19  Score=16.09  Aligned_cols=56  Identities=14%  Similarity=0.201  Sum_probs=34.5

Q ss_pred             CCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHHHHH
Q ss_conf             686998735530788897688888888998076589999999999739978868899999997
Q gi|254780690|r  264 RATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFK  326 (354)
Q Consensus       264 ~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~  326 (354)
                      +-|+||...-++-.   -+...  ...  -.-.+.++.++|.+|++++|||+----|-|..+.
T Consensus       123 ~~~~vvvDylql~~---~~~~~--~~~--~~~i~~i~~~Lk~lA~e~~v~Vi~~sQlnR~~~~  178 (242)
T cd00984         123 GLGLIVIDYLQLMS---GSKKK--GNR--QQEVAEISRSLKLLAKELNVPVIALSQLSRGVES  178 (242)
T ss_pred             CCCEEEEEHHHHCC---CCCCC--CCH--HHHHHHHHHHHHHHHHHHCCEEEEEECCCCCCCC
T ss_conf             99899982698546---77766--579--9999999999999999979939998467866122


No 103
>COG1139 Uncharacterized conserved protein containing a ferredoxin-like domain [Energy production and conversion]
Probab=43.09  E-value=23  Score=15.44  Aligned_cols=101  Identities=15%  Similarity=0.269  Sum_probs=54.2

Q ss_pred             HHHCCCHHHHHHHHHHCCC-----CHH--HHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCEEEEEEECCCCC----CC
Q ss_conf             8406998999999754489-----989--999999999999998898607768699873553078889768888----88
Q gi|254780690|r  220 SKLKMSKQEIKDEIKQSYG-----NPI--IKNRQKSIARSRIRHKMMEATSRATIIITNPTHYALALRYIQTEN----DA  288 (354)
Q Consensus       220 k~lkMskqEvK~E~K~~EG-----dP~--iK~~~r~~~re~~~~~~~~~V~~A~vvitNPTH~AVAL~Y~~~~~----~a  288 (354)
                      --+-|+|+||.+=+|+.-|     ||+  .+.-|+.++.....-  --++..|.+++.+-  =+|+|==+.|..    .+
T Consensus       153 PAlH~~reqIa~if~ekl~~~~~~~~eel~~~aR~~lR~kfl~A--dvGITGaNfa~Aet--Gsv~LVeNEGN~Rm~ttl  228 (459)
T COG1139         153 PALHKNREQIAEIFKEKLGYEGEDTPEELTAAAREFLREKFLKA--DVGITGANFAVAET--GSVCLVENEGNGRMSTTL  228 (459)
T ss_pred             CCCCCCHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHC--CCCCCCCCEEEECC--CCEEEEEECCCCEECCCC
T ss_conf             12036999999999986389889998999999999999987623--65665632256346--748999616874001347


Q ss_pred             C--EEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHHHHHHCCCCCCCCH
Q ss_conf             8--89980765899999999997399788688999999972889894898
Q gi|254780690|r  289 P--VLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFKQVPINSAIPP  336 (354)
Q Consensus       289 P--~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~~~~ig~~Ip~  336 (354)
                      |  -|.-.|.+.+            ||.+++-.+==.|-...-.||.||.
T Consensus       229 P~tHIav~GiEKi------------vps~eda~~~~~ll~rsa~G~~itt  266 (459)
T COG1139         229 PPTHIAVMGIEKI------------VPTLEDAAVLVSLLQRSATGQRITT  266 (459)
T ss_pred             CCEEEEEEEHHHH------------CCCHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             8745898307763------------4768888899998516650778873


No 104
>cd01122 GP4d_helicase GP4d_helicase is a homohexameric 5'-3' helicases. Helicases couple NTP hydrolysis to the unwinding of nucleic acid duplexes into their component strands.
Probab=42.96  E-value=21  Score=15.82  Aligned_cols=156  Identities=12%  Similarity=0.015  Sum_probs=73.4

Q ss_pred             HHHHH--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             30332--0126679999999999999999999999832156897840897999999999999999999999999999766
Q gi|254780690|r  134 EGIKR--IYSINNLVNFMKSFVKIILVGTIITISLTENYFTMLDFISANPHSILYHAFFTVRKVLIMILLFIATLTVLDI  211 (354)
Q Consensus       134 ~GlKr--iFS~k~lvel~KsllKv~li~~v~~~~i~~~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD~  211 (354)
                      .|+++  +.-.-+--..+||.+-.   -.+..++.....+.++....++....+.-+....              +-.+ 
T Consensus        25 ~Gl~~GeL~viaarpg~GKT~f~~---~~a~~~~~~~g~~vl~~SlEm~~~~~~~Rlls~~--------------~g~~-   86 (271)
T cd01122          25 KGLRKGELIILTAGTGVGKTTFLR---EYALDLITQHGVRVGTISLEEPVVRTARRLLGQY--------------AGKR-   86 (271)
T ss_pred             CCCCCCCEEEEEECCCCCHHHHHH---HHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHHH--------------HCCC-
T ss_conf             799998089999689986999999---9999999976990899970499999999999998--------------2997-


Q ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHCCCCH-----------HHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCEEEEEE
Q ss_conf             79999999840699899999975448998-----------9999999999999998898607768699873553078889
Q gi|254780690|r  212 GWSYHQWYSKLKMSKQEIKDEIKQSYGNP-----------IIKNRQKSIARSRIRHKMMEATSRATIIITNPTHYALALR  280 (354)
Q Consensus       212 ~~qr~~~~k~lkMskqEvK~E~K~~EGdP-----------~iK~~~r~~~re~~~~~~~~~V~~A~vvitNPTH~AVAL~  280 (354)
                       +.  .....-..+.++++.-.++.++.|           .+.. ++...|++      ....+.++||..+-++-..-.
T Consensus        87 -~~--~~~~~~~~~~e~~~~~~~~~~~~~~l~i~d~~~~~~~~~-i~~~ir~~------~~~~~~~~vvIDylqll~~~~  156 (271)
T cd01122          87 -LH--LPDTVFIYTLEEFDAAFDEFEGTGRLFMYDSFGEYSMDS-VLEKVRYM------AVSHGIQHIIIDNLSIMVSDE  156 (271)
T ss_pred             -HH--HCCCCCCCHHHHHHHHHHHHCCCCCEEEECCCCCCCHHH-HHHHHHHH------HHHCCCCEEEEEHHHHCCCCC
T ss_conf             -11--034467780999999999970799808878999988999-99999999------982899889983178503678


Q ss_pred             ECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHH
Q ss_conf             7688888888998076589999999999739978868899999
Q gi|254780690|r  281 YIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARS  323 (354)
Q Consensus       281 Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~  323 (354)
                      .    ...-..  .-.+.+..++|.+|++++|||+----|-|.
T Consensus       157 ~----~~~d~~--~~i~~i~~~Lk~lAke~~v~Vi~lsQlnR~  193 (271)
T cd01122         157 R----ASGDER--KALDEIMTKLRGFATEHGIHITLVSHLRRP  193 (271)
T ss_pred             C----CCCCHH--HHHHHHHHHHHHHHHHHCCCEEEEECCCCC
T ss_conf             6----773189--999999999999999979977999526765


No 105
>PRK10964 ADP-heptose:LPS heptosyl transferase I; Provisional
Probab=41.85  E-value=9.2  Score=18.59  Aligned_cols=25  Identities=16%  Similarity=0.264  Sum_probs=18.5

Q ss_pred             HHHHHHCCCCCEEEEC---CCCEEEEEE
Q ss_conf             8898607768699873---553078889
Q gi|254780690|r  256 HKMMEATSRATIIITN---PTHYALALR  280 (354)
Q Consensus       256 ~~~~~~V~~A~vvitN---PTH~AVAL~  280 (354)
                      ....+=+.+|+++|+|   |+|+|.|+.
T Consensus       245 ~elaall~~a~l~I~nDSG~mHlAaAlg  272 (322)
T PRK10964        245 EEVARVLAGAKAVVSVDTGLSHLTAALD  272 (322)
T ss_pred             HHHHHHHHHCCEEEECCCHHHHHHHHCC
T ss_conf             9999999709999966975999999839


No 106
>PRK02654 putative inner membrane protein translocase component YidC; Provisional
Probab=41.61  E-value=24  Score=15.28  Aligned_cols=30  Identities=20%  Similarity=0.210  Sum_probs=17.7

Q ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHHHHC
Q ss_conf             997667999999984069989999997544
Q gi|254780690|r  207 TVLDIGWSYHQWYSKLKMSKQEIKDEIKQS  236 (354)
Q Consensus       207 a~iD~~~qr~~~~k~lkMskqEvK~E~K~~  236 (354)
                      +++-..-|..-.+.=++.+-|++=||....
T Consensus       328 nIfq~vQq~iLnK~~~penlqkii~e~~~~  357 (376)
T PRK02654        328 NIFQTLQTFLLSREPLPENLQKILDELQKS  357 (376)
T ss_pred             HHHHHHHHHHHHCCCCHHHHHHHHHHHHHH
T ss_conf             999999999995568856599999999876


No 107
>pfam01220 DHquinase_II Dehydroquinase class II.
Probab=41.29  E-value=5.6  Score=20.33  Aligned_cols=43  Identities=35%  Similarity=0.424  Sum_probs=26.2

Q ss_pred             CCCCCEEEECC---CCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEE---CHHHHHHHHHHC
Q ss_conf             77686998735---53078889768888888899807658999999999973997886---889999999728
Q gi|254780690|r  262 TSRATIIITNP---THYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFE---EPSLARSLFKQV  328 (354)
Q Consensus       262 V~~A~vvitNP---TH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive---~~~LAR~Ly~~~  328 (354)
                      ..++|-+|-||   ||+++||+=                        --+.-++|+||   +.+-||.=|++.
T Consensus        64 ~~~~dgiIiNpga~THtS~ai~D------------------------Al~~~~~P~iEVHlSNi~~RE~fR~~  112 (140)
T pfam01220        64 RGDVDGIIINPAAYTHTSVALRD------------------------ALAAVGIPVIEVHLSNIHAREEFRHH  112 (140)
T ss_pred             HCCCCEEEECCCHHEEHHHHHHH------------------------HHHHCCCCEEEEECCCHHHCCCCCCC
T ss_conf             54476899856210110266799------------------------99864999899962781332542335


No 108
>pfam01041 DegT_DnrJ_EryC1 DegT/DnrJ/EryC1/StrS aminotransferase family. The members of this family are probably all pyridoxal-phosphate-dependent aminotransferase enzymes with a variety of molecular functions. The family includes StsA, StsC, and StsS. The aminotransferase activity was demonstrated for purified StsC protein as the L-glutamine:scyllo-inosose aminotransferase EC:2.6.1.50, which catalyses the first amino transfer in the biosynthesis of the streptidine subunit of streptomycin.
Probab=41.10  E-value=21  Score=15.84  Aligned_cols=34  Identities=21%  Similarity=0.105  Sum_probs=19.0

Q ss_pred             CEEEEECCCHHHHHHHHHHHHCCCCEEEC--HHHHH
Q ss_conf             88998076589999999999739978868--89999
Q gi|254780690|r  289 PVLVAKGQNLIAKKMRKIAYEHNIPIFEE--PSLAR  322 (354)
Q Consensus       289 P~vvaKG~~~~A~~Ir~~A~~~~Vpive~--~~LAR  322 (354)
                      |+++-.....--.++.+.-+++||++-..  .|+-+
T Consensus       281 ~i~~~~~~~~~R~~l~~~L~~~gI~t~~~y~~pl~~  316 (363)
T pfam01041       281 PVLVPEEAAGSRDELVEALKEAGIGTRVHYPIPLHL  316 (363)
T ss_pred             EEEECCCCHHHHHHHHHHHHHCCCCEEEECCCCHHH
T ss_conf             999764342339999999998799558658971342


No 109
>pfam00846 Hanta_nucleocap Hantavirus nucleocapsid protein.
Probab=40.77  E-value=25  Score=15.18  Aligned_cols=15  Identities=20%  Similarity=0.220  Sum_probs=8.4

Q ss_pred             CCCHHHHHHHHHHCC
Q ss_conf             658787999998578
Q gi|254780690|r   13 APSSKKIEDALNEGN   27 (354)
Q Consensus        13 ~PT~kRL~dARekGq   27 (354)
                      --..+||+||.+.=.
T Consensus        19 ~~ArQKlkda~~~~e   33 (428)
T pfam00846        19 VIARQKLKDAEKAVE   33 (428)
T ss_pred             HHHHHHHHHHHHHHC
T ss_conf             999999999999754


No 110
>cd03063 TRX_Fd_FDH_beta TRX-like [2Fe-2S] Ferredoxin (Fd) family, NAD-dependent formate dehydrogenase (FDH) beta subunit; composed of proteins similar to the beta subunit of NAD-linked FDH of Ralstonia eutropha, a soluble enzyme that catalyzes the irreversible oxidation of formate to carbon dioxide accompanied by the reduction of NAD to NADH. FDH is a heteromeric enzyme composed of four nonidentical subunits (alpha, beta, gamma and delta). The FDH beta subunit contains a NADH:ubiquinone oxidoreductase (Nuo) F domain C-terminal to a Fd-like domain without the active site cysteines. The absence of conserved metal-binding residues in the putative active site suggests that members of this subfamily have lost the ability to bind iron-sulfur clusters in the N-terminal Fd-like domain. The C-terminal NuoF domain is a component of Nuo, a multisubunit complex catalyzing the electron transfer of NADH to quinone coupled with the transfer of protons across the membrane. NuoF contains one [4Fe-4S] c
Probab=40.02  E-value=18  Score=16.20  Aligned_cols=26  Identities=15%  Similarity=0.244  Sum_probs=21.1

Q ss_pred             EEECCCHHHHHHHHHHHHCCCCE--EEC
Q ss_conf             98076589999999999739978--868
Q gi|254780690|r  292 VAKGQNLIAKKMRKIAYEHNIPI--FEE  317 (354)
Q Consensus       292 vaKG~~~~A~~Ir~~A~~~~Vpi--ve~  317 (354)
                      +|-|+|++|..|.+.|.+.++++  ++|
T Consensus        12 ~A~GAd~Va~ai~~~a~~r~l~i~ivRn   39 (92)
T cd03063          12 LALGADEVAEAIEAEAAARGLAATIVRN   39 (92)
T ss_pred             HHCCHHHHHHHHHHHHHHCCCCEEEEEC
T ss_conf             7448699999999999976995489976


No 111
>PRK08506 replicative DNA helicase; Provisional
Probab=39.75  E-value=25  Score=15.13  Aligned_cols=149  Identities=13%  Similarity=0.221  Sum_probs=72.6

Q ss_pred             HHHHH--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             30332--0126679999999999999999999999832156897840897999999999999999999999999999766
Q gi|254780690|r  134 EGIKR--IYSINNLVNFMKSFVKIILVGTIITISLTENYFTMLDFISANPHSILYHAFFTVRKVLIMILLFIATLTVLDI  211 (354)
Q Consensus       134 ~GlKr--iFS~k~lvel~KsllKv~li~~v~~~~i~~~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD~  211 (354)
                      .|+++  +.=+-+=--.+|+.+=+    -++.-+.....+.++.+..++-.+...-+.+.              .+-+| 
T Consensus       188 ~Gl~~gdLiIIAARPsmGKTAfAl----niA~~~a~~~~~V~~FSLEMs~~ql~~Rlls~--------------~s~V~-  248 (473)
T PRK08506        188 KGFNKGDLIIIAARPSMGKTTLVL----NMVLKALNQGKGVAFFSLEMPAEQLMLRMLSA--------------KTSIP-  248 (473)
T ss_pred             CCCCCCCEEEEECCCCCCHHHHHH----HHHHHHHHCCCCEEEEECCCCHHHHHHHHHHH--------------HCCCC-
T ss_conf             699856279995079986789999----99999996599658982247999999999997--------------28878-


Q ss_pred             HHHHHHHHHHHCCCHHHHHH------HHHHC----CCCH-----HHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCEE
Q ss_conf             79999999840699899999------97544----8998-----999999999999999889860776869987355307
Q gi|254780690|r  212 GWSYHQWYSKLKMSKQEIKD------EIKQS----YGNP-----IIKNRQKSIARSRIRHKMMEATSRATIIITNPTHYA  276 (354)
Q Consensus       212 ~~qr~~~~k~lkMskqEvK~------E~K~~----EGdP-----~iK~~~r~~~re~~~~~~~~~V~~A~vvitNPTH~A  276 (354)
                       .++.+   +=+||.+|.++      +..+.    +-.|     +|+++.|++.++         -++-++||..     
T Consensus       249 -~~~lr---~g~l~~~e~~~~~~a~~~l~~~~l~IdD~~~lti~~Ira~~Rr~k~~---------~~~l~livID-----  310 (473)
T PRK08506        249 -LQNLR---TGDLDDDEWENLSDACDELSQKKLFVYDSGYVNIHQVRAQLRKLKSQ---------HPEIGLAVID-----  310 (473)
T ss_pred             -CCCCC---CCCCCHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHHHHH---------CCCCCEEEEE-----
T ss_conf             -31000---68999999999999999986598899889999999999999999997---------6998789963-----


Q ss_pred             EEEEECCCCCCCCEEE---EECCCHHHHHHHHHHHHCCCCEEECHHHHHHH
Q ss_conf             8889768888888899---80765899999999997399788688999999
Q gi|254780690|r  277 LALRYIQTENDAPVLV---AKGQNLIAKKMRKIAYEHNIPIFEEPSLARSL  324 (354)
Q Consensus       277 VAL~Y~~~~~~aP~vv---aKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~L  324 (354)
                          |- .-+..+.=-   .--.+++...+|.+|+|.+||||-=--|=|..
T Consensus       311 ----YL-QLm~~~~~~~~R~~ev~~ISr~LK~lAkEl~vPViaLSQLnR~v  356 (473)
T PRK08506        311 ----YL-QLMSGSKNFKDRHLQISEISRGLKLLARELDIPIIALSQLNRSL  356 (473)
T ss_pred             ----HH-HHCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCEEEECCCCCCC
T ss_conf             ----67-55468887530889999999999999999699799970368765


No 112
>cd07320 Extradiol_Dioxygenase_3B_like Subunit B of Class III Extradiol ring-cleavage dioxygenases. Dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings. Two major groups of dioxygenases have been identified according to the cleavage site of the aromatic ring. Intradiol enzymes cleave the aromatic ring between two hydroxyl groups, whereas extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Extradiol dioxygenases can be further divided into three classes. Class I and II enzymes are evolutionary related and show sequence similarity, with the two-domain class II enzymes evolving from the class I enzyme through gene duplication. Class III enzymes are different in sequence and structure and usually have two subunits, designated A and B. This model represents the catalytic subunit B of extradiol dioxygenase class
Probab=39.68  E-value=26  Score=15.06  Aligned_cols=27  Identities=11%  Similarity=-0.026  Sum_probs=17.0

Q ss_pred             EEECCCHHHHHHHHHHHHCCCCEEECH
Q ss_conf             980765899999999997399788688
Q gi|254780690|r  292 VAKGQNLIAKKMRKIAYEHNIPIFEEP  318 (354)
Q Consensus       292 vaKG~~~~A~~Ir~~A~~~~Vpive~~  318 (354)
                      =++|.-++|..|.+.+++.+.....|.
T Consensus        78 ~~~gd~~la~~i~~~~~~~~~~~~~~~  104 (260)
T cd07320          78 DVKGDPDLAWEIAEELIKEIPVTIVNE  104 (260)
T ss_pred             CCCCCHHHHHHHHHHHHHCCCEEEECC
T ss_conf             886999999999999875498354145


No 113
>cd07370 HPCD The Class III extradiol dioxygenase, homoprotocatechuate 2,3-dioxygenase, catalyzes the key ring cleavage step in the metabolism of homoprotocatechuate. 3,4-dihydroxyphenylacetate (homoprotocatechuate) 2,3-dioxygenase (HPCD) catalyzes the key ring cleavage step in the metabolism of homoprotocatechuate (hpca), a central intermediate in the bacterial degradation of aromatic compounds. The enzyme incorporates both atoms of molecular oxygen into hpca, resulting in aromatic ring-opening to yield alpha-hydroxy-delta-carboxymethyl cis-muconic semialdehyde. HPCD is a member of the class III extradiol dioxygenase family, a group of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon.
Probab=39.12  E-value=26  Score=15.00  Aligned_cols=68  Identities=24%  Similarity=0.396  Sum_probs=37.4

Q ss_pred             HHHHHHHHHHHHCCCCCEEEECCCCEEEEEEE----------CCCCCCCCEEE------EECCCHHHHHHHHHHHHCCCC
Q ss_conf             99999988986077686998735530788897----------68888888899------807658999999999973997
Q gi|254780690|r  250 ARSRIRHKMMEATSRATIIITNPTHYALALRY----------IQTENDAPVLV------AKGQNLIAKKMRKIAYEHNIP  313 (354)
Q Consensus       250 ~re~~~~~~~~~V~~A~vvitNPTH~AVAL~Y----------~~~~~~aP~vv------aKG~~~~A~~Ir~~A~~~~Vp  313 (354)
                      .+|++++  ..+..--|+||..| |.-+-.-|          +-....+|...      .+|--++|..|.+.|+++|+|
T Consensus        34 ~~e~~rr--~~~~~pDtvVV~sp-Hw~~~~~~~i~~~~~~~G~~~~~~~P~~~~~~~y~~~gd~eLa~~Ia~~a~~~G~~  110 (280)
T cd07370          34 LKEIGRR--ARELGVDTIVVFDT-HWLVNAGYHINANARFSGLFTSNELPHFIADMPYDYAGDPELAHLIAEEATEHGVK  110 (280)
T ss_pred             HHHHHHH--HHHCCCCEEEEECC-CCCCCCCEEECCCCCEEEEECCCCCCCHHHCCCCCCCCCHHHHHHHHHHHHHCCCE
T ss_conf             9999999--98739998999858-86522566981577504432444588333345167899999999999999877974


Q ss_pred             EEE--CHHH
Q ss_conf             886--8899
Q gi|254780690|r  314 IFE--EPSL  320 (354)
Q Consensus       314 ive--~~~L  320 (354)
                      +..  |+.|
T Consensus       111 ~~~~~~~~~  119 (280)
T cd07370         111 TLAHEDPSL  119 (280)
T ss_pred             EEEECCCCC
T ss_conf             776227876


No 114
>KOG3663 consensus
Probab=39.06  E-value=26  Score=14.99  Aligned_cols=28  Identities=32%  Similarity=0.691  Sum_probs=18.6

Q ss_pred             HHHHH--HHCCCHHH---HHHHHHHCCCCHHHHHH
Q ss_conf             99998--40699899---99997544899899999
Q gi|254780690|r  216 HQWYS--KLKMSKQE---IKDEIKQSYGNPIIKNR  245 (354)
Q Consensus       216 ~~~~k--~lkMskqE---vK~E~K~~EGdP~iK~~  245 (354)
                      .+|.|  +-||||+|   +|||.-+  -.||||++
T Consensus        38 rkyfkkhekrMsk~EEravkdELl~--ekpEvKqK   70 (518)
T KOG3663          38 RKYFKKHEKRMSKDEERAVKDELLN--EKPEVKQK   70 (518)
T ss_pred             HHHHHHHHHHHCHHHHHHHHHHHHC--CCHHHHHH
T ss_conf             8888888765135578888888744--56488999


No 115
>PRK08760 replicative DNA helicase; Provisional
Probab=38.98  E-value=26  Score=15.02  Aligned_cols=154  Identities=10%  Similarity=0.158  Sum_probs=73.5

Q ss_pred             HHHHH--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             30332--0126679999999999999999999999832156897840897999999999999999999999999999766
Q gi|254780690|r  134 EGIKR--IYSINNLVNFMKSFVKIILVGTIITISLTENYFTMLDFISANPHSILYHAFFTVRKVLIMILLFIATLTVLDI  211 (354)
Q Consensus       134 ~GlKr--iFS~k~lvel~KsllKv~li~~v~~~~i~~~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD~  211 (354)
                      .|+++  +.=+-+=--.+|+.+=+-   .+....+....+.++....++..+...-+.+.              .+-+| 
T Consensus       224 ~Gl~~G~LiViaaRPsmGKTalaln---ia~~~A~~~~~~V~~fSLEMs~~ql~~Rlls~--------------~s~v~-  285 (476)
T PRK08760        224 AGLQPTDLIILAARPAMGKTTFALN---IAEYAAIKSKKGVAVFSMEMSASQLAMRLISS--------------NGRIN-  285 (476)
T ss_pred             CCCCCCCEEEEEECCCCCHHHHHHH---HHHHHHHHCCCCEEEEECCCCHHHHHHHHHHH--------------HCCCC-
T ss_conf             6998777799987788747899999---99999983799789970369999999999998--------------33897-


Q ss_pred             HHHHHHHHHHHCCCHHHHHH------HHH-------HCCC-CH-HHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCEE
Q ss_conf             79999999840699899999------975-------4489-98-999999999999999889860776869987355307
Q gi|254780690|r  212 GWSYHQWYSKLKMSKQEIKD------EIK-------QSYG-NP-IIKNRQKSIARSRIRHKMMEATSRATIIITNPTHYA  276 (354)
Q Consensus       212 ~~qr~~~~k~lkMskqEvK~------E~K-------~~EG-dP-~iK~~~r~~~re~~~~~~~~~V~~A~vvitNPTH~A  276 (354)
                       .+   ..++-++|.+|.++      +.+       ++-+ +| +|+++.|++.++          .+-++||..--+. 
T Consensus       286 -~~---~i~~g~l~~~e~~~~~~a~~~l~~~~l~idD~~~~t~~~ir~~~R~~k~~----------~~l~lvvIDYLqL-  350 (476)
T PRK08760        286 -AQ---RLRTGALEDEDWARVTGAIKMLKETKIFIDDTPGVSPEVLRSKCRRLKRE----------HDLGLIVIDYLQL-  350 (476)
T ss_pred             -HH---HHHCCCCCHHHHHHHHHHHHHHHHCCCEEECCCCCCHHHHHHHHHHHHHH----------CCCCEEEEEHHHH-
T ss_conf             -67---77648999999999999999986088168579999999999999999872----------7998799970764-


Q ss_pred             EEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHHHHH
Q ss_conf             88897688888888998076589999999999739978868899999997
Q gi|254780690|r  277 LALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFK  326 (354)
Q Consensus       277 VAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~  326 (354)
                        +.. ++. .-.+.  --.+++...+|.+|+|.+|||+-=--|-|..-.
T Consensus       351 --~~~-~~~-~~~r~--~~v~~isr~lK~lAkel~vpVi~LsQLnR~~e~  394 (476)
T PRK08760        351 --MSV-PGN-SENRA--TEISEISRSLKGLAKELNVPVIALSQLNRSLET  394 (476)
T ss_pred             --CCC-CCC-CCCHH--HHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCC
T ss_conf             --158-888-74488--999999999999999979978996315766344


No 116
>COG3069 DcuC C4-dicarboxylate transporter [Energy production and conversion]
Probab=38.69  E-value=27  Score=14.95  Aligned_cols=36  Identities=11%  Similarity=0.020  Sum_probs=21.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH-HHCCCHHHHHHHHHHCCC
Q ss_conf             9999999999766799999998-406998999999754489
Q gi|254780690|r  199 ILLFIATLTVLDIGWSYHQWYS-KLKMSKQEIKDEIKQSYG  238 (354)
Q Consensus       199 ~~~~~~via~iD~~~qr~~~~k-~lkMskqEvK~E~K~~EG  238 (354)
                      ..+..+.+++..|+||||.-.| ++.+.+    .|.|+.|+
T Consensus       200 ~i~~iI~~ai~hff~qr~~Dkk~~~~~e~----~eq~~~~~  236 (451)
T COG3069         200 SIAAIIGMAIAHFFWQRYLDKKENIEHEM----LEQKEIDT  236 (451)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCHHHH----HHHHHHCC
T ss_conf             99999999999999999961210430357----77765505


No 117
>PRK05395 3-dehydroquinate dehydratase; Provisional
Probab=38.51  E-value=4.7  Score=20.90  Aligned_cols=43  Identities=35%  Similarity=0.448  Sum_probs=25.8

Q ss_pred             CCCCCEEEECC---CCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEE---CHHHHHHHHHHC
Q ss_conf             77686998735---53078889768888888899807658999999999973997886---889999999728
Q gi|254780690|r  262 TSRATIIITNP---THYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFE---EPSLARSLFKQV  328 (354)
Q Consensus       262 V~~A~vvitNP---TH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive---~~~LAR~Ly~~~  328 (354)
                      ..++|-+|-||   ||+++||+                        +--+..++|+||   +.+-||.=|+..
T Consensus        65 ~~~~dgiIiNpga~THtS~al~------------------------DAl~~~~~P~iEVHlSNi~~RE~fR~~  113 (143)
T PRK05395         65 RDDVDGIIINPGAYTHTSVALR------------------------DALAAVSIPVVEVHLSNIHAREEFRHH  113 (143)
T ss_pred             HHCCCEEEECCCHHHHHHHHHH------------------------HHHHHCCCCEEEEECCCCHHCCCHHHC
T ss_conf             6337579973621332448899------------------------899874998899964891330530010


No 118
>TIGR00739 yajC preprotein translocase, YajC subunit; InterPro: IPR003849   This entry describes proteins of unknown function..
Probab=38.40  E-value=27  Score=14.92  Aligned_cols=30  Identities=13%  Similarity=0.213  Sum_probs=21.0

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCEEEECCCCE
Q ss_conf             999999999988986077686998735530
Q gi|254780690|r  246 QKSIARSRIRHKMMEATSRATIIITNPTHY  275 (354)
Q Consensus       246 ~r~~~re~~~~~~~~~V~~A~vvitNPTH~  275 (354)
                      |+|..|+-.++.|+.++.+=|=|+||--=+
T Consensus        22 RPQ~K~~k~~~kl~~~L~KGd~V~T~gGi~   51 (86)
T TIGR00739        22 RPQRKRRKAHKKLIESLKKGDKVLTIGGII   51 (86)
T ss_pred             CHHHHHHHHHHHHHHCCCCCCEEEECCCEE
T ss_conf             977988898888885279977899838838


No 119
>PRK05595 replicative DNA helicase; Provisional
Probab=38.12  E-value=27  Score=14.89  Aligned_cols=140  Identities=9%  Similarity=0.122  Sum_probs=66.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHH
Q ss_conf             99999999999999999998321568978408979999999999999999999999999997667999999984069989
Q gi|254780690|r  148 FMKSFVKIILVGTIITISLTENYFTMLDFISANPHSILYHAFFTVRKVLIMILLFIATLTVLDIGWSYHQWYSKLKMSKQ  227 (354)
Q Consensus       148 l~KsllKv~li~~v~~~~i~~~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD~~~qr~~~~k~lkMskq  227 (354)
                      .+|+.+=+-   .+....+....+.++....++..+...-+.....              -+|+  ++   .++=+++.+
T Consensus       212 mGKTa~aln---ia~~~a~~~g~~V~~fSlEMs~~ql~~R~ls~~s--------------~i~~--~~---i~~g~l~~~  269 (444)
T PRK05595        212 MGKTTFALN---IAEYAALREGKSVVIFSLEMSKEQLAYKLLCSEA--------------NVDM--LR---LRTGNLEDK  269 (444)
T ss_pred             CCCHHHHHH---HHHHHHHHCCCCEEEEECCCCHHHHHHHHHHHHC--------------CCCC--CC---CCCCCCCHH
T ss_conf             980799999---9999998669937999588999999999999646--------------9884--42---326897999


Q ss_pred             HHHH------HHHHC----CCCH-----HHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEE
Q ss_conf             9999------97544----8998-----9999999999999998898607768699873553078889768888888899
Q gi|254780690|r  228 EIKD------EIKQS----YGNP-----IIKNRQKSIARSRIRHKMMEATSRATIIITNPTHYALALRYIQTENDAPVLV  292 (354)
Q Consensus       228 EvK~------E~K~~----EGdP-----~iK~~~r~~~re~~~~~~~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vv  292 (354)
                      |.++      +.++.    +-.|     +|+++.|++.++          .+-++||..--|.-   +.+..  .-.+. 
T Consensus       270 ~~~~~~~a~~~l~~~~l~i~d~~~~ti~~i~~~~r~~~~~----------~~~~liiiDYlqLi---~~~~~--~~~r~-  333 (444)
T PRK05595        270 DWENIARASGPLAAAKIYIDDTAGVSVMEMRSKCRRLKIE----------HGIDLILIDYLQLM---SGGKS--SESRQ-  333 (444)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHH----------CCCCEEEEEHHHHC---CCCCC--CCCHH-
T ss_conf             9999999999985489705489996489999999999987----------39998998237635---78988--88899-


Q ss_pred             EECCCHHHHHHHHHHHHCCCCEEECHHHHHHHHH
Q ss_conf             8076589999999999739978868899999997
Q gi|254780690|r  293 AKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFK  326 (354)
Q Consensus       293 aKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~  326 (354)
                       --.+++...+|.+|+|.+|||+-=--|-|..-.
T Consensus       334 -~ev~~isr~LK~lAkel~ipvi~lsQLnR~~e~  366 (444)
T PRK05595        334 -QEVSEISRSIKALAKEMECPVIALSQLSRAPEQ  366 (444)
T ss_pred             -HHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCC
T ss_conf             -999999999999999969979997026854112


No 120
>PRK01001 putative inner membrane protein translocase component YidC; Provisional
Probab=38.09  E-value=27  Score=14.88  Aligned_cols=21  Identities=24%  Similarity=0.483  Sum_probs=12.5

Q ss_pred             CCCHHHHHHHH--HHCCCCCHHH
Q ss_conf             65878799999--8578751335
Q gi|254780690|r   13 APSSKKIEDAL--NEGNAPISRE   33 (354)
Q Consensus        13 ~PT~kRL~dAR--ekGqV~kS~e   33 (354)
                      +||=|-++++-  .||.-|.--|
T Consensus       517 ~~~lk~~d~~~~n~~g~~p~y~~  539 (791)
T PRK01001        517 DPTLKTLDRAYTNSKGENPEYLD  539 (791)
T ss_pred             CHHHHHHHHHHCCCCCCCCCHHE
T ss_conf             55888887763387888964001


No 121
>TIGR01601 PYST-C1 Plasmodium yoelii subtelomeric domain PYST-C1; InterPro: IPR006488    This group of sequences are defined by the N-terminal domain of a paralogous family of Plasmodium yoelii genes preferentially located in the subtelomeric regions of the chromosomes. There are no obvious homologs to these genes in any other organism. The C-terminal portions of the genes that contain this domain are divergent and some contain other yoelii-specific paralogous domains such as PYST-C2 (IPR006491 from INTERPRO). .
Probab=38.02  E-value=16  Score=16.66  Aligned_cols=12  Identities=25%  Similarity=0.288  Sum_probs=6.0

Q ss_pred             HHHHHHHHHHHC
Q ss_conf             999999999832
Q gi|254780690|r  158 VGTIITISLTEN  169 (354)
Q Consensus       158 i~~v~~~~i~~~  169 (354)
                      |.+++|.++--.
T Consensus         9 VcIvLY~llaVs   20 (86)
T TIGR01601         9 VCIVLYILLAVS   20 (86)
T ss_pred             HHHHHHHHHCCC
T ss_conf             899999987175


No 122
>cd01993 Alpha_ANH_like_II This is a subfamily of Adenine nucleotide alpha hydrolases superfamily.Adeninosine nucleotide alpha hydrolases superfamily  includes N type ATP PPases and ATP sulphurylases. It forms a apha/beta/apha fold which  binds to Adenosine group.  This subfamily   of proteins is predicted to  bind ATP. This domainhas  a strongly conserved motif SGGKD at the N terminus.
Probab=37.55  E-value=27  Score=14.90  Aligned_cols=21  Identities=24%  Similarity=0.290  Sum_probs=18.2

Q ss_pred             HHHHHHHHHHHHCCCCEEECH
Q ss_conf             899999999997399788688
Q gi|254780690|r  298 LIAKKMRKIAYEHNIPIFEEP  318 (354)
Q Consensus       298 ~~A~~Ir~~A~~~~Vpive~~  318 (354)
                      .--..|++.|+++++|.+|||
T Consensus       158 ~~k~ei~~y~~~~~l~~~eD~  178 (185)
T cd01993         158 VREKEIVLYAELNGLPFVEEE  178 (185)
T ss_pred             CCHHHHHHHHHHCCCCEEECC
T ss_conf             989999999998799878899


No 123
>COG1179 Dinucleotide-utilizing enzymes involved in molybdopterin and thiamine biosynthesis family 1 [Coenzyme metabolism]
Probab=37.52  E-value=28  Score=14.82  Aligned_cols=37  Identities=22%  Similarity=0.279  Sum_probs=22.2

Q ss_pred             ECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHC------CCCEEEC
Q ss_conf             73553078889768888888899807658999999999973------9978868
Q gi|254780690|r  270 TNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEH------NIPIFEE  317 (354)
Q Consensus       270 tNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~------~Vpive~  317 (354)
                      +|||++-|+==+.-.           .|.+|.++|+.=|+.      |||+|-+
T Consensus       159 ~DPTri~v~DiskT~-----------~DPLa~~vR~~LRk~~~~~~~gi~vVfS  201 (263)
T COG1179         159 LDPTRIQVADISKTI-----------QDPLAAKVRRKLRKRFPKIKFGVPVVFS  201 (263)
T ss_pred             CCCCEEEEEECHHHC-----------CCCHHHHHHHHHHHHCCCCCCCCCEEEC
T ss_conf             897357764102212-----------4808999999998743576568736855


No 124
>cd00466 DHQase_II Dehydroquinase (DHQase), type II. Dehydroquinase (or 3-dehydroquinate dehydratase) catalyzes the reversible dehydration of 3-dehydroquinate to form 3-dehydroshikimate. This reaction is part of two metabolic pathways: the biosynthetic shikimate pathway and the catabolic quinate pathway. There are two types of DHQases, which are distinct from each other in amino acid sequence and three-dimensional structure. Type I enzymes usually catalyze the biosynthetic reaction using a syn elimination mechanism. In contrast, type II enzymes, found in the quinate pathway of fungi and in the shikimate pathway of many bacteria, are dodecameric enzymes that employ an anti elimination reaction mechanism.
Probab=37.49  E-value=6.7  Score=19.69  Aligned_cols=18  Identities=56%  Similarity=0.700  Sum_probs=14.4

Q ss_pred             CCCCEEEECC---CCEEEEEE
Q ss_conf             7686998735---53078889
Q gi|254780690|r  263 SRATIIITNP---THYALALR  280 (354)
Q Consensus       263 ~~A~vvitNP---TH~AVAL~  280 (354)
                      .++|-+|-||   ||+++||+
T Consensus        64 ~~~dgiIiNpga~ThtSial~   84 (140)
T cd00466          64 DGADGIIINPGAYTHTSIALR   84 (140)
T ss_pred             CCCCEEEECCCHHHHHHHHHH
T ss_conf             757589975612200237779


No 125
>pfam07905 PucR Purine catabolism regulatory protein-like family. The bacterial proteins found in this family are similar to the purine catabolism regulatory protein expressed by Bacillus subtilis (PucR). PucR is thought to be a transcriptional activator involved in the induction of the purine degradation pathway, and may contain a LysR-like DNA-binding domain. It is similar to LysR-type regulators in that it represses its own expression. The other members of this family are also annotated as being putative regulatory proteins.
Probab=37.31  E-value=28  Score=14.80  Aligned_cols=22  Identities=23%  Similarity=0.386  Sum_probs=18.5

Q ss_pred             HHHHHHHHHHHHCCCCEEECHH
Q ss_conf             8999999999973997886889
Q gi|254780690|r  298 LIAKKMRKIAYEHNIPIFEEPS  319 (354)
Q Consensus       298 ~~A~~Ir~~A~~~~Vpive~~~  319 (354)
                      ++-..+++.|++++.|+++-|+
T Consensus        85 ~iP~~~i~~a~~~~~Pli~iP~  106 (122)
T pfam07905        85 EIPEELIAAANRLGLPLIELPR  106 (122)
T ss_pred             CCCHHHHHHHHHCCCCEEEECC
T ss_conf             6999999999974997799459


No 126
>PRK06904 replicative DNA helicase; Validated
Probab=37.29  E-value=28  Score=14.79  Aligned_cols=156  Identities=13%  Similarity=0.206  Sum_probs=74.2

Q ss_pred             HHHHHH--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             430332--012667999999999999999999999983215689784089799999999999999999999999999976
Q gi|254780690|r  133 REGIKR--IYSINNLVNFMKSFVKIILVGTIITISLTENYFTMLDFISANPHSILYHAFFTVRKVLIMILLFIATLTVLD  210 (354)
Q Consensus       133 i~GlKr--iFS~k~lvel~KsllKv~li~~v~~~~i~~~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD  210 (354)
                      ..||++  +.=+-+=--.+|+.+=+-+   +.-....+..+.++....++..+...-+.+....              ++
T Consensus       215 t~Gl~~g~LiViAaRPsmGKTa~alni---a~n~A~~~~~~V~~fSLEM~~~~l~~R~ls~~s~--------------v~  277 (472)
T PRK06904        215 TAGLQPSDLIIVAARPSMGKTTFAMNL---CENAAMASEKPVLVFSLEMPAEQIMMRMLASLSR--------------VD  277 (472)
T ss_pred             HCCCCCCCEEEEEECCCCCHHHHHHHH---HHHHHHHCCCCEEEECCCCCHHHHHHHHHHHHCC--------------CC
T ss_conf             158875757999737987568999999---9999995599579977879999999999998649--------------99


Q ss_pred             HHHHHHHHHHHHCCCHHHHHH------HHHH--------CCCC--HHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCC
Q ss_conf             679999999840699899999------9754--------4899--89999999999999998898607768699873553
Q gi|254780690|r  211 IGWSYHQWYSKLKMSKQEIKD------EIKQ--------SYGN--PIIKNRQKSIARSRIRHKMMEATSRATIIITNPTH  274 (354)
Q Consensus       211 ~~~qr~~~~k~lkMskqEvK~------E~K~--------~EGd--P~iK~~~r~~~re~~~~~~~~~V~~A~vvitNPTH  274 (354)
                      +  ++.+  ..-.++.+|.++      +.++        +-|-  .+|+++.|++.|+         -..-++||..--|
T Consensus       278 ~--~~i~--~g~~l~~~e~~~~~~~~~~l~~~~~l~idd~~~~t~~~i~~~~r~~~~~---------~~~l~~vvIDYLq  344 (472)
T PRK06904        278 Q--TKIR--TGQNLDQQDWAKISSTVGMFKQKPNLYIDDSSGLTPTELRSRARRVYRE---------NGGLSLIMVDYLQ  344 (472)
T ss_pred             H--HHHH--CCCCCHHHHHHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHHHH---------CCCCCEEEEEHHH
T ss_conf             8--8864--6885609999999999999846898168469999999999999999987---------3899789963886


Q ss_pred             EEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHHHH
Q ss_conf             078889768888888899807658999999999973997886889999999
Q gi|254780690|r  275 YALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLF  325 (354)
Q Consensus       275 ~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly  325 (354)
                      .-   +.+.  ..-.+..  -...+...+|.+|+|.+||||-=--|-|.+-
T Consensus       345 L~---~~~~--~~~~r~~--ei~~isr~LK~lAkel~ipvi~LsQLnR~~e  388 (472)
T PRK06904        345 LM---RAPG--FEDNRTL--EIAEISRSLKALAKELKVPVVALSQLNRTLE  388 (472)
T ss_pred             HC---CCCC--CCCCHHH--HHHHHHHHHHHHHHHHCCCEEEECCCCCCCC
T ss_conf             60---4888--7777889--9999999999999997998899732684311


No 127
>KOG4186 consensus
Probab=37.27  E-value=28  Score=14.79  Aligned_cols=61  Identities=10%  Similarity=0.034  Sum_probs=33.4

Q ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCE
Q ss_conf             7667999999984069989999997544899899999999999999988986077686998735530
Q gi|254780690|r  209 LDIGWSYHQWYSKLKMSKQEIKDEIKQSYGNPIIKNRQKSIARSRIRHKMMEATSRATIIITNPTHY  275 (354)
Q Consensus       209 iD~~~qr~~~~k~lkMskqEvK~E~K~~EGdP~iK~~~r~~~re~~~~~~~~~V~~A~vvitNPTH~  275 (354)
                      +|-.+|..+-..+.+      |.+.-..+||++..-..+..+.+..+..+.-..-.++.++++|--.
T Consensus       139 ~~~~~~~~r~~~~~k------~~~~~~~~~~e~~~~~l~~~~~~~~~~~l~l~~~~~~~~~~ipl~~  199 (233)
T KOG4186         139 MYEVFELQRLSSSIK------KKTKSISSGDEEDREKLQAQQLDQNHRLLLLSADFNAADSALPLGQ  199 (233)
T ss_pred             HHHHHHHHHHHCCCC------CCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHC
T ss_conf             999999876530212------3566778741778899999998714227999989988988613320


No 128
>COG1671 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.04  E-value=28  Score=14.76  Aligned_cols=57  Identities=16%  Similarity=0.153  Sum_probs=44.4

Q ss_pred             CEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHHHHHH
Q ss_conf             69987355307888976888888889980765899999999997399788688999999972
Q gi|254780690|r  266 TIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFKQ  327 (354)
Q Consensus       266 ~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~~  327 (354)
                      -.+|.|--|+-  . +.+.  ---++|..|.|..-..|.+.|+..+|=|-+|.|||-.|-..
T Consensus        28 v~~Van~~~~~--~-~~~~--i~~v~V~~g~DaaD~~Iv~~a~~gDlVVT~Di~LA~~ll~k   84 (150)
T COG1671          28 VTFVANFPHRV--P-PSPE--IRTVVVDAGFDAADDWIVNLAEKGDLVVTADIPLASLLLDK   84 (150)
T ss_pred             EEEEECCCCCC--C-CCCC--EEEEEECCCCCHHHHHHHHHCCCCCEEEECCHHHHHHHHHC
T ss_conf             99991787568--9-9985--36899557733288999983778998997764789999966


No 129
>PRK13015 3-dehydroquinate dehydratase; Reviewed
Probab=36.51  E-value=7  Score=19.54  Aligned_cols=45  Identities=27%  Similarity=0.430  Sum_probs=28.9

Q ss_pred             CCCCCEEEECC---CCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEE---CHHHHHHHHHHCCC
Q ss_conf             77686998735---53078889768888888899807658999999999973997886---88999999972889
Q gi|254780690|r  262 TSRATIIITNP---THYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFE---EPSLARSLFKQVPI  330 (354)
Q Consensus       262 V~~A~vvitNP---TH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive---~~~LAR~Ly~~~~i  330 (354)
                      ..++|-+|-||   ||+++||                        |+--...++|+||   +.+-+|.=|+..-+
T Consensus        65 ~~~~~giIiNpga~THtSiAl------------------------~DAl~~~~~P~iEVHlSNi~~RE~fR~~S~  115 (148)
T PRK13015         65 RGDVAGIVINPAAYTHTSVAI------------------------RDALAALELPVIEVHISNVHAREAFRHHSY  115 (148)
T ss_pred             HCCCCEEEECCCCCEEEHHHH------------------------HHHHHHCCCCEEEEECCCHHHCCCCCCCCC
T ss_conf             602808997373113310658------------------------999987499889996178243366444365


No 130
>PRK08840 replicative DNA helicase; Provisional
Probab=36.49  E-value=29  Score=14.70  Aligned_cols=162  Identities=11%  Similarity=0.193  Sum_probs=77.0

Q ss_pred             CCCCCCCHHHHHHH--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             79101693430332--0126679999999999999999999999832156897840897999999999999999999999
Q gi|254780690|r  125 PSFKRVSLREGIKR--IYSINNLVNFMKSFVKIILVGTIITISLTENYFTMLDFISANPHSILYHAFFTVRKVLIMILLF  202 (354)
Q Consensus       125 pk~~rlNPi~GlKr--iFS~k~lvel~KsllKv~li~~v~~~~i~~~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~  202 (354)
                      ++++++  ..||++  +.=+-+=--.+||.+=+-+.   ....+....+.++.+..++..+...-+.+..          
T Consensus       205 ~~LD~~--~~Gl~~G~LiviaaRPsmGKTalalnia---~n~a~~~~~~v~~fSlEMs~~ql~~Rlls~~----------  269 (464)
T PRK08840        205 TDLNKK--TAGLQGSDLIIVAARPSMGKTTFAMNLC---ENAAMDQDKPVLIFSLEMPAEQLMMRMLASL----------  269 (464)
T ss_pred             HHHHHH--CCCCCCCCEEEEEECCCCCHHHHHHHHH---HHHHHHCCCCEEEECCCCCHHHHHHHHHHHH----------
T ss_conf             999875--3698757679998379873689999999---9999965996799767799899999999985----------


Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHH---H---H-----CCCC-----HHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             9999997667999999984069989999997---5---4-----4899-----899999999999999988986077686
Q gi|254780690|r  203 IATLTVLDIGWSYHQWYSKLKMSKQEIKDEI---K---Q-----SYGN-----PIIKNRQKSIARSRIRHKMMEATSRAT  266 (354)
Q Consensus       203 ~~via~iD~~~qr~~~~k~lkMskqEvK~E~---K---~-----~EGd-----P~iK~~~r~~~re~~~~~~~~~V~~A~  266 (354)
                          +-+++  ++   ++.=++|.+|.++=.   +   +     -+-.     .+|+++.|++.|+    .     ..-+
T Consensus       270 ----s~i~~--~~---ir~g~l~~~e~~~i~~a~~~~~~~~~l~idd~~~~t~~~i~a~~r~~~~~----~-----~~l~  331 (464)
T PRK08840        270 ----SRVDQ--TK---IRTGQLDDEDWARISSTMGILMEKKNMYIDDSSGLTPTEVRSRARRVARE----H-----GGLS  331 (464)
T ss_pred             ----CCCCC--CH---HHCCCCCHHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHHHHH----C-----CCCC
T ss_conf             ----38982--01---11488899999999999999984799588569987579999999999986----4-----8987


Q ss_pred             EEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHHHHH
Q ss_conf             998735530788897688888888998076589999999999739978868899999997
Q gi|254780690|r  267 IIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFK  326 (354)
Q Consensus       267 vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~  326 (354)
                      +||..=-|.   ++.+ + ..-.+..  ..+++...+|.+|+|.+||||-=--|-|..-.
T Consensus       332 lvvIDYLqL---~~~~-~-~~~~r~~--~i~~isr~lK~lAkel~vpVv~lsQLnR~~e~  384 (464)
T PRK08840        332 MIMVDYLQL---MRVP-A-LQDNRTL--EIAEISRSLKALAKELNVPVVALSQLNRSLEQ  384 (464)
T ss_pred             EEEEEHHHH---CCCC-C-CCCHHHH--HHHHHHHHHHHHHHHHCCCEEEECCCCCCCCC
T ss_conf             899618866---0678-8-6403678--99999999999999969989996316853111


No 131
>TIGR00018 panC pantoate--beta-alanine ligase; InterPro: IPR003721 D-Pantothenate is synthesized via four enzymes from ketoisovalerate, which is an intermediate of branched-chain amino acid synthesis . Pantoate-beta-alanine ligase, also know as pantothenate synthase, (6.3.2.1 from EC) catalyzes the formation of pantothenate from pantoate and alanine in the pantothenate biosynthesis pathway .; GO: 0004592 pantoate-beta-alanine ligase activity, 0015940 pantothenate biosynthetic process.
Probab=35.79  E-value=21  Score=15.81  Aligned_cols=73  Identities=11%  Similarity=0.210  Sum_probs=46.1

Q ss_pred             HHHHHHHHHHHHHHHHH------------------HHHHHCCCCCEEE----ECCCCEEEEEEECCCCC--CCCEEEEEC
Q ss_conf             89999999999999998------------------8986077686998----73553078889768888--888899807
Q gi|254780690|r  240 PIIKNRQKSIARSRIRH------------------KMMEATSRATIII----TNPTHYALALRYIQTEN--DAPVLVAKG  295 (354)
Q Consensus       240 P~iK~~~r~~~re~~~~------------------~~~~~V~~A~vvi----tNPTH~AVAL~Y~~~~~--~aP~vvaKG  295 (354)
                      +++|..|||.++|-.-+                  =...++.++|+||    +||+-|      +|+|+  .=|+=+-  
T Consensus         8 ~~L~~~~~q~~~eGrfrk~vGfVPTMG~LH~GH~sL~~~a~~End~vvvSIFVNP~QF------gp~EDl~~YPR~l~--   79 (310)
T TIGR00018         8 EELREYIKQLEREGRFRKTVGFVPTMGALHEGHLSLIDRAVKENDLVVVSIFVNPLQF------GPNEDLEAYPRDLE--   79 (310)
T ss_pred             HHHHHHHHHHHHCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHCCEEEEEEEECCCCC------CCCCCHHHCCCCHH--
T ss_conf             8999999986516850123312267310156789999999866885899997578788------88754544579858--


Q ss_pred             CCHHHHHHHHHHHHCCCCEEECHHHHHHHHHH
Q ss_conf             65899999999997399788688999999972
Q gi|254780690|r  296 QNLIAKKMRKIAYEHNIPIFEEPSLARSLFKQ  327 (354)
Q Consensus       296 ~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~~  327 (354)
                            +=.+.+++.+|-++--|. ++.+|-.
T Consensus        80 ------~D~~l~E~lgVd~~FaP~-~~~mYP~  104 (310)
T TIGR00018        80 ------EDLALLEKLGVDVVFAPK-VHEMYPD  104 (310)
T ss_pred             ------HHHHHHHHCCCCEEECCC-CEEECCC
T ss_conf             ------999999838965885572-1440788


No 132
>COG4794 EscS Type III secretory pathway, component EscS [Intracellular trafficking and secretion]
Probab=35.71  E-value=29  Score=14.61  Aligned_cols=34  Identities=26%  Similarity=0.359  Sum_probs=15.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999999998877687853
Q gi|254780690|r   80 IVFLLTHLSLSASRLVIPGLLLFMMFGIGSYLIQ  113 (354)
Q Consensus        80 ~~~~~~~~~~~~~~~~~p~~~~~~l~~i~~~l~q  113 (354)
                      +.+...+..+..+...+|-.++..++|+..+++|
T Consensus         6 i~~~~~qaL~liLilSlPpvivAsvvGllVslvQ   39 (89)
T COG4794           6 IVFLTSQALWLILILSLPPVIVASVVGLLVSLVQ   39 (89)
T ss_pred             HHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHH
T ss_conf             9999999999999996119999999999999999


No 133
>PRK10902 FKBP-type peptidyl-prolyl cis-trans isomerase; Provisional
Probab=35.49  E-value=30  Score=14.59  Aligned_cols=114  Identities=15%  Similarity=0.130  Sum_probs=57.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHCHHHHHHHH------------CCCHHHHHHHHHHHHHHHHHHHH-----------HHHHHH
Q ss_conf             9999999999999999983215689784------------08979999999999999999999-----------999999
Q gi|254780690|r  150 KSFVKIILVGTIITISLTENYFTMLDFI------------SANPHSILYHAFFTVRKVLIMIL-----------LFIATL  206 (354)
Q Consensus       150 KsllKv~li~~v~~~~i~~~~~~l~~l~------------~~~~~~~l~~~~~~~~~l~~~~~-----------~~~~vi  206 (354)
                      ||++|+.++...+.+.+......-....            ..+-...-+.++..+..-+...+           .-.++-
T Consensus         2 k~~~k~~lla~t~a~~~~~~~~~~~~~~~~~~~~~~~~~l~t~~qk~sYaiGaslG~~~~~~l~~q~~lGi~lD~~~l~~   81 (270)
T PRK10902          2 KSLFKVTLLATTMAVALHAPITFAAEAAKPATTADSKAAFKNDDQKSAYALGASLGRYMENSLKEQEKLGIKLDKDQLIA   81 (270)
T ss_pred             CCHHHHHHHHHHHHHHHCCCHHHCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHH
T ss_conf             30568799999999994685132034676666666777767888889899999999999887766775186579999999


Q ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH-------HHHHCCCCCEEEEC
Q ss_conf             997667999999984069989999997544899899999999999999988-------98607768699873
Q gi|254780690|r  207 TVLDIGWSYHQWYSKLKMSKQEIKDEIKQSYGNPIIKNRQKSIARSRIRHK-------MMEATSRATIIITN  271 (354)
Q Consensus       207 a~iD~~~qr~~~~k~lkMskqEvK~E~K~~EGdP~iK~~~r~~~re~~~~~-------~~~~V~~A~vvitN  271 (354)
                      ++-|-      +..+.+||.+|+.....+-+  .+++..++..+.+.+..+       +-.+-.+..|+.|.
T Consensus        82 G~~Da------l~gk~~LtdeEi~~~l~~~~--~~~~~~~~~~~~~~a~~N~~~g~~fla~nakk~GV~~t~  145 (270)
T PRK10902         82 GVQDA------FADKSKLSDQEIEQTLQAFE--ARVKSSAQAKMEKDAADNEAKGKKYREKFAKEKGVKTSS  145 (270)
T ss_pred             HHHHH------HCCCCCCCHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEECC
T ss_conf             99999------67987789999999999999--999999999999999999999999999845799988988


No 134
>pfam07085 DRTGG DRTGG domain. This presumed domain is about 120 amino acids in length. It is found associated with CBS domains pfam00571, as well as the CbiA domain pfam01656. The function of this domain is unknown. It is named the DRTGG domain after some of the most conserved residues. This domain may be very distantly related to a pair of CBS domains. There are no significant sequence similarities, but its length and association with CBS domains supports this idea (Bateman A, pers. obs.).
Probab=35.33  E-value=17  Score=16.50  Aligned_cols=60  Identities=22%  Similarity=0.292  Sum_probs=38.9

Q ss_pred             HHHHHHHHCCCCCEEEE--CCCC-EEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECH
Q ss_conf             99889860776869987--3553-07888976888888889980765899999999997399788688
Q gi|254780690|r  254 IRHKMMEATSRATIIIT--NPTH-YALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEP  318 (354)
Q Consensus       254 ~~~~~~~~V~~A~vvit--NPTH-~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~  318 (354)
                      +...++.-+.+-+.|||  |=.. ...|+.     ..++-++--|--..-.++.+.|++.++||+..+
T Consensus        30 ~~~~~l~~~~~g~lvI~~gdR~di~~~a~~-----~~~~~iIlTgg~~p~~~v~~la~~~~ipii~t~   92 (105)
T pfam07085        30 SVENMLEYLRPGDLVITPGDREDIQLAALL-----AGIAGLILTGGFEPSEEVLKLAEEAGLPVLSTP   92 (105)
T ss_pred             CHHHHHHHHCCCCEEEEECCCHHHHHHHHH-----HCCCEEEEECCCCCCHHHHHHHHHCCCEEEEEC
T ss_conf             899999860689799992796899999998-----248789994898989999999987798399966


No 135
>PRK10929 hypothetical protein; Provisional
Probab=35.20  E-value=30  Score=14.55  Aligned_cols=17  Identities=6%  Similarity=-0.093  Sum_probs=6.2

Q ss_pred             HHHHHHHHHHHHHHHHH
Q ss_conf             99999999766799999
Q gi|254780690|r  201 LFIATLTVLDIGWSYHQ  217 (354)
Q Consensus       201 ~~~~via~iD~~~qr~~  217 (354)
                      +++++++++-|.|.-..
T Consensus       682 l~li~l~~~GY~yTA~~  698 (1109)
T PRK10929        682 LVAILASAVGYLATAQA  698 (1109)
T ss_pred             HHHHHHHHHHHHHHHHH
T ss_conf             99999999779999999


No 136
>cd07646 I-BAR_IMD_IRSp53 Inverse (I)-BAR, also known as the IRSp53/MIM homology Domain (IMD), of Insulin Receptor tyrosine kinase Substrate p53. The IMD domain, also called Inverse-Bin/Amphiphysin/Rvs (I-BAR) domain, is a dimerization and lipid-binding module that bends membranes and induces membrane protrusions. IRSp53 (Insulin Receptor tyrosine kinase Substrate p53) is also known as BAIAP2 (Brain-specific Angiogenesis Inhibitor 1-Associated Protein 2). It is a scaffolding protein that takes part in many signaling pathways including Cdc42-induced filopodia formation, Rac-mediated lamellipodia extension, and spine morphogenesis. IRSp53 exists as multiple splicing variants that differ mainly at the C-termini. One variant (T-form) is expressed exclusively in human breast cancer cells. The gene encoding IRSp53 is a putative susceptibility gene for Gilles de la Tourette syndrome. IRSp53 contains an N-terminal IMD, a CRIB (Cdc42 and Rac interactive binding motif), an SH3 domain, and a WASP 
Probab=35.16  E-value=30  Score=14.55  Aligned_cols=44  Identities=16%  Similarity=0.229  Sum_probs=28.1

Q ss_pred             CCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHC
Q ss_conf             1016934303320126679999999999999999999999832156897840
Q gi|254780690|r  127 FKRVSLREGIKRIYSINNLVNFMKSFVKIILVGTIITISLTENYFTMLDFIS  178 (354)
Q Consensus       127 ~~rlNPi~GlKriFS~k~lvel~KsllKv~li~~v~~~~i~~~~~~l~~l~~  178 (354)
                      ++++||        ++++|+.++|+..|-.--...+.-.+...+..+-..+.
T Consensus        17 meqFNP--------~lrnlv~~Gk~Y~kAl~~~~~Aa~~y~dAl~Kige~A~   60 (232)
T cd07646          17 MEQFNP--------SLRNFIAMGKNYEKALASVTFAAKGYFDALVKMGELAS   60 (232)
T ss_pred             HHHCCH--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             985397--------89999997799999999999989999999999999860


No 137
>pfam08423 Rad51 Rad51. Rad51 is a DNA repair and recombination protein and is a homologue of the bacterial ATPase RecA protein.
Probab=35.04  E-value=30  Score=14.54  Aligned_cols=38  Identities=18%  Similarity=0.210  Sum_probs=27.0

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCC
Q ss_conf             48998999999999999999889860776869987355
Q gi|254780690|r  236 SYGNPIIKNRQKSIARSRIRHKMMEATSRATIIITNPT  273 (354)
Q Consensus       236 ~EGdP~iK~~~r~~~re~~~~~~~~~V~~A~vvitNPT  273 (354)
                      -+|+.++..|.+.+++.+..=.-++.--+.-||+||-.
T Consensus       155 ~~g~~~l~~R~~~L~~~l~~L~~lA~~~~~aVvvTNQV  192 (261)
T pfam08423       155 FSGRGELAERQQHLAKFLRSLQRLADEFGVAVVITNQV  192 (261)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEE
T ss_conf             03675289999999999999999999809589996047


No 138
>pfam08664 YcbB YcbB domain. YcbB is a DNA-binding domain.
Probab=34.88  E-value=28  Score=14.76  Aligned_cols=63  Identities=16%  Similarity=0.141  Sum_probs=49.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCHHHHHH
Q ss_conf             999999999999999999999999997667999999984069989999997544899899999
Q gi|254780690|r  183 SILYHAFFTVRKVLIMILLFIATLTVLDIGWSYHQWYSKLKMSKQEIKDEIKQSYGNPIIKNR  245 (354)
Q Consensus       183 ~~l~~~~~~~~~l~~~~~~~~~via~iD~~~qr~~~~k~lkMskqEvK~E~K~~EGdP~iK~~  245 (354)
                      .-.-.+-.-+.+.+...+.-++-+++-||.=..+.+.-..=-.=+||++|+++.+|...-++|
T Consensus        61 ~e~Ka~EQRIRRai~~~l~nlAsLGl~Dy~N~~F~~YA~~lFdF~~Vr~eM~~i~~~~~~~g~  123 (133)
T pfam08664        61 HEAKAIEQRIRRAIKKALNNLASLGLEDYSNPKFEEYASKLFDFKEVRQEMKELRGKSSSGGK  123 (133)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCE
T ss_conf             788899999999999999999985766558747999989717899999999998587877870


No 139
>cd01677 PFL2_DhaB_BssA Pyruvate formate lyase 2 and related enzymes. This family includes pyruvate formate lyase 2 (PFL2), B12-independent glycerol dehydratase (DhaB) and the alpha subunit of benzylsuccinate synthase (BssA), all of which have a highly conserved ten-stranded alpha/beta barrel domain, which is similar to those of PFL1 (pyruvate formate lyase 1) and RNR (ribonucleotide reductase). Pyruvate formate lyase catalyzes a key step in anaerobic glycolysis, the conversion of pyruvate and CoenzymeA to formate and acetylCoA. DhaB catalyzes the first step in the conversion of glycerol to 1,3-propanediol while BssA catalyzes the first step in the anaerobic mineralization of both toluene and m-xylene.
Probab=34.86  E-value=30  Score=14.52  Aligned_cols=44  Identities=25%  Similarity=0.383  Sum_probs=28.2

Q ss_pred             CCCHHHHHHHHHHHHCCCCEEECHHHHHHHHHHCCCCCCCCHHHHHHHHHHHH
Q ss_conf             76589999999999739978868899999997288989489899999999999
Q gi|254780690|r  295 GQNLIAKKMRKIAYEHNIPIFEEPSLARSLFKQVPINSAIPPVFYKAVAQLIY  347 (354)
Q Consensus       295 G~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~~~~ig~~Ip~~~y~aVA~il~  347 (354)
                      +.+++-..+-+..++...|   .|-|      ++.+.+-.|++++..+++++.
T Consensus       348 a~N~ls~l~Lea~~~l~~~---qP~l------~vR~~~~~P~~f~~~a~e~i~  391 (781)
T cd01677         348 ATNELSYLILEATRRVRLP---QPSL------TVRYHAKSPDKFLKKAAEVIR  391 (781)
T ss_pred             CCCHHHHHHHHHHHHCCCC---CCCE------EEEECCCCCHHHHHHHHHHHH
T ss_conf             5588899999999864899---9987------999899999999999999973


No 140
>COG0771 MurD UDP-N-acetylmuramoylalanine-D-glutamate ligase [Cell envelope biogenesis, outer membrane]
Probab=34.83  E-value=30  Score=14.51  Aligned_cols=21  Identities=19%  Similarity=0.281  Sum_probs=14.4

Q ss_pred             HHCCCHHHHHHHHHHCCCCHH
Q ss_conf             406998999999754489989
Q gi|254780690|r  221 KLKMSKQEIKDEIKQSYGNPI  241 (354)
Q Consensus       221 ~lkMskqEvK~E~K~~EGdP~  241 (354)
                      .+-.+.+++.+=-+.-.|=||
T Consensus       290 ~~gv~~e~i~~~L~~F~gl~H  310 (448)
T COG0771         290 ALGVPPEAILEALSSFTGLPH  310 (448)
T ss_pred             HCCCCHHHHHHHHHHCCCCCC
T ss_conf             839998999999973899986


No 141
>pfam11803 UXS1_N UDP-glucuronate decarboxylase N-terminal. The N-terminus of the UDP-glucuronate decarboxylases may be involved in localisation to the perinuclear Golgi membrane.
Probab=34.81  E-value=30  Score=14.51  Aligned_cols=60  Identities=17%  Similarity=0.194  Sum_probs=37.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999976679999999840699899999975448998999999999999999
Q gi|254780690|r  195 VLIMILLFIATLTVLDIGWSYHQWYSKLKMSKQEIKDEIKQSYGNPIIKNRQKSIARSRIR  255 (354)
Q Consensus       195 l~~~~~~~~~via~iD~~~qr~~~~k~lkMskqEvK~E~K~~EGdP~iK~~~r~~~re~~~  255 (354)
                      -...+++.+..+|-+.-.|--|-.+++.+ ..-|+|=|.|.-|----.+-++|.++..-.+
T Consensus        16 r~mk~l~~~aliayiasvwg~y~nmrsIq-E~Ge~Kieqki~e~v~plrekir~le~s~~q   75 (78)
T pfam11803        16 RMMKILLGLALIAYIASVWGLYLNMRSIQ-EGGEVKIEQKIFETVAPLREKIRDLEYSFVQ   75 (78)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCHHHHH-HCCCEEHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             78999999999999999998522898897-5763224566666441187777788898763


No 142
>PRK02463 OxaA-like protein precursor; Provisional
Probab=34.66  E-value=30  Score=14.49  Aligned_cols=12  Identities=25%  Similarity=0.537  Sum_probs=8.5

Q ss_pred             HHHHHHHHHHCC
Q ss_conf             899999975448
Q gi|254780690|r  226 KQEIKDEIKQSY  237 (354)
Q Consensus       226 kqEvK~E~K~~E  237 (354)
                      |++|.+|+|+.-
T Consensus       256 ~~~i~~e~~~~p  267 (307)
T PRK02463        256 RKQIKEEFAKNP  267 (307)
T ss_pred             HHHHHHHHHHCC
T ss_conf             999999987289


No 143
>PRK06321 replicative DNA helicase; Provisional
Probab=34.50  E-value=31  Score=14.47  Aligned_cols=30  Identities=30%  Similarity=0.423  Sum_probs=24.0

Q ss_pred             CCHHHHHHHHHHHHCCCCEEECHHHHHHHH
Q ss_conf             658999999999973997886889999999
Q gi|254780690|r  296 QNLIAKKMRKIAYEHNIPIFEEPSLARSLF  325 (354)
Q Consensus       296 ~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly  325 (354)
                      ..++...+|.+|+|.+||||-=--|-|..-
T Consensus       364 i~~isr~lK~lAkel~vpvi~LsQLnR~~e  393 (472)
T PRK06321        364 ISEISRMLKNLARELNIPILCLSQLSRKVE  393 (472)
T ss_pred             HHHHHHHHHHHHHHHCCCEEEECCCCCCCC
T ss_conf             999999999999997997999722684312


No 144
>PRK05748 replicative DNA helicase; Provisional
Probab=34.34  E-value=31  Score=14.45  Aligned_cols=143  Identities=9%  Similarity=0.134  Sum_probs=68.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCH
Q ss_conf             99999999999999999999832156897840897999999999999999999999999999766799999998406998
Q gi|254780690|r  147 NFMKSFVKIILVGTIITISLTENYFTMLDFISANPHSILYHAFFTVRKVLIMILLFIATLTVLDIGWSYHQWYSKLKMSK  226 (354)
Q Consensus       147 el~KsllKv~li~~v~~~~i~~~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD~~~qr~~~~k~lkMsk  226 (354)
                      -.+|+.+=+-   .+.........+.++....++..+...-+...              .+-+++  +   .+++=++|.
T Consensus       213 ~mGKTa~aln---ia~~~a~~~~~~v~~fSlEM~~~~l~~R~la~--------------~s~v~~--~---~i~~g~l~~  270 (448)
T PRK05748        213 SVGKTAFALN---IAQNVATKTDKNVAIFSLEMGAESLVMRMLCA--------------EGRIDQ--Q---KLRTGQLTD  270 (448)
T ss_pred             CCCHHHHHHH---HHHHHHHHCCCEEEEEECCCCHHHHHHHHHHH--------------HHCCCH--H---HHHCCCCCH
T ss_conf             9876899999---99999985698089981778888999999999--------------746777--7---776289999


Q ss_pred             HHHHHH------HHH------CCCC---HHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEE
Q ss_conf             999999------754------4899---8999999999999999889860776869987355307888976888888889
Q gi|254780690|r  227 QEIKDE------IKQ------SYGN---PIIKNRQKSIARSRIRHKMMEATSRATIIITNPTHYALALRYIQTENDAPVL  291 (354)
Q Consensus       227 qEvK~E------~K~------~EGd---P~iK~~~r~~~re~~~~~~~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~v  291 (354)
                      +|.++=      .++      ...+   .+|+++.|++.    +     .-++-++||..--|.   ++.. +...-.+ 
T Consensus       271 ~~~~~~~~a~~~l~~~~l~i~d~~~~ti~~i~~~~r~~~----~-----~~~~~~~vviDYlql---i~~~-~~~~~~r-  336 (448)
T PRK05748        271 EDWPKLTIAVGSLSDAPIYIDDTPGIKVTEIRARCRRLA----Q-----EHGGLGLIVIDYLQL---IQGS-GRSGENR-  336 (448)
T ss_pred             HHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHHH----H-----HCCCCCEEEEEHHHH---CCCC-CCCCCCH-
T ss_conf             999999999999865983785589886899999999999----9-----759988999716864---4777-8776439-


Q ss_pred             EEECCCHHHHHHHHHHHHCCCCEEECHHHHHHHHH
Q ss_conf             98076589999999999739978868899999997
Q gi|254780690|r  292 VAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFK  326 (354)
Q Consensus       292 vaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~  326 (354)
                       .-..+++...+|.+|+|.+||||-=--|-|..-.
T Consensus       337 -~~ev~~isr~lK~lAkel~ipvi~lsQLnR~~e~  370 (448)
T PRK05748        337 -QQEVSEISRSLKALAKELKVPVIALSQLSRGVEQ  370 (448)
T ss_pred             -HHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCC
T ss_conf             -9999999999999999969988997026843222


No 145
>PRK04531 acetylglutamate kinase; Provisional
Probab=33.93  E-value=31  Score=14.41  Aligned_cols=71  Identities=20%  Similarity=0.251  Sum_probs=49.4

Q ss_pred             HHCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCC-CCEEEECCCCEEEEEEECCCCCCCCEEEEECC
Q ss_conf             40699899999975448998999999999999999889860776-86998735530788897688888888998076
Q gi|254780690|r  221 KLKMSKQEIKDEIKQSYGNPIIKNRQKSIARSRIRHKMMEATSR-ATIIITNPTHYALALRYIQTENDAPVLVAKGQ  296 (354)
Q Consensus       221 ~lkMskqEvK~E~K~~EGdP~iK~~~r~~~re~~~~~~~~~V~~-A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~  296 (354)
                      .-+.|-=-+.+||.+....|-++...|-.=+|+-.  .+...|+ ++|+||+|-+..=-|-=|.|   +.-.+-+|.
T Consensus       203 gk~Is~InL~~eyd~lm~~~w~~~g~klkl~~ik~--LLd~LP~~SSV~It~p~~L~kELFT~~G---sGTLirrg~  274 (421)
T PRK04531        203 GNKISSINLSTEFDQLMQQPSINGGMRLKLEQIKD--LLDRLPLESSVSITSPSDLAKELFTHKG---SGTLVRRGE  274 (421)
T ss_pred             CCEEEEEECCHHHHHHHHCCCCCHHHHHHHHHHHH--HHHCCCCCCEEEEECHHHHHHHHCCCCC---CCEEEECCC
T ss_conf             98863575440355452051035668998999999--9851998660787089998887626799---960486774


No 146
>PRK04654 sec-independent translocase; Provisional
Probab=33.88  E-value=31  Score=14.40  Aligned_cols=65  Identities=18%  Similarity=0.281  Sum_probs=30.0

Q ss_pred             HHHHHHCCCHHHHHHHHHHCCCCHHHHHH--------------HHHHHHHHHHH-H-HHHHCCCCCEEEECCCCEEEEEE
Q ss_conf             99984069989999997544899899999--------------99999999998-8-98607768699873553078889
Q gi|254780690|r  217 QWYSKLKMSKQEIKDEIKQSYGNPIIKNR--------------QKSIARSRIRH-K-MMEATSRATIIITNPTHYALALR  280 (354)
Q Consensus       217 ~~~k~lkMskqEvK~E~K~~EGdP~iK~~--------------~r~~~re~~~~-~-~~~~V~~A~vvitNPTH~AVAL~  280 (354)
                      .|++++|.+-..||+|.-.-.+--++|.-              .|.-+++.-+. | .-.+|.++-=+=+|-|..|-+++
T Consensus        34 lWi~r~R~~~~sVK~EleREl~~eELkr~Lq~~ea~~~~~~~~l~~t~Q~v~~~~Ra~~~dvs~~idi~~sa~~~A~~~e  113 (214)
T PRK04654         34 LWVRRARMQWDSVKQELERELEAEELKRSLQDVQASLREAEDQLRNTQQQVEQGARALHDDVSRDIDIRTSATPVATPLE  113 (214)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHH
T ss_conf             99999999999999999988549999999999999999999998888888887622002442356662002665457777


Q ss_pred             E
Q ss_conf             7
Q gi|254780690|r  281 Y  281 (354)
Q Consensus       281 Y  281 (354)
                      -
T Consensus       114 ~  114 (214)
T PRK04654        114 L  114 (214)
T ss_pred             H
T ss_conf             7


No 147
>TIGR02644 Y_phosphoryl pyrimidine-nucleoside phosphorylase; InterPro: IPR000053   Two highly similar activities are represented in this group: thymidine phosphorylase (TP, gene deoA, 2.4.2.4 from EC) and pyrimidine-nucleoside phosphorylase (PyNP, gene pdp, 2.4.2.2 from EC). Both are dimeric enzymes that function in the salvage pathway to catalyse the reversible phosphorolysis of pyrimidine nucleosides to the free base and sugar moieties. In the case of thymidine phosphorylase, thymidine (and to a lesser extent, 2'-deoxyuridine) is lysed to produce thymine (or uracil) and 2'-deoxyribose-1-phosphate. Pyrimidine-nucleoside phosphorylase performs the analogous reaction on thymidine (to produce the same products) and uridine (to produce uracil and ribose-1-phosphate). PyNP is typically the only pyrimidine nucleoside phosphorylase encoded by Gram positive bacteria, while eukaryotes and proteobacteria encode two: TP, and the unrelated uridine phosphorylase. In humans, TP was originally characterised as platelet-derived endothelial cell growth factor and gliostatin . Structurally, the enzymes are homodimers, each composed of a rigid all alpha-helix lobe and a mixed alpha-helix/beta-sheet lobe, which are connected by a flexible hinge , . Prior to substrate binding, the lobes are separated by a large cleft. A functional active site and subsequent catalysis occurs upon closing of the cleft. The active site, composed of a phosphate binding site and a (deoxy)ribonucleotide binding site within the cleft region, is highly conserved between the two enzymes of this group. Active site residues (Escherichia coli DeoA numbering) include the phosphate binding Lys84 and Ser86 (close to a glycine-rich loop), Ser113, and Thr123, and the pyrimidine nucleoside-binding Arg171, Ser186, and Lys190. Sequence comparison between the active site residues for both enzymes reveals only one difference , which has been proposed to partially mediate substrate specificity. In TP, position 111 is a methionine, while the analogous position in PyNP is lysine. It should be noted that the uncharacterised archaeal members of this family differ in a number of respects from either of the characterised activities. The residue at position 108 is lysine, indicating the activity might be PyNP-like (though the determinants of substrate specificity have not been fully elucidated). Position 171 is glutamate (negative charge side chain) rather than arginine (positive charge side chain). In addition, a large loop that may "lock in" the substrates within the active site is much smaller than in the characterised members. It is not clear what effect these and other differences have on activity and specificity.; GO: 0006206 pyrimidine base metabolic process.
Probab=33.72  E-value=17  Score=16.43  Aligned_cols=91  Identities=9%  Similarity=-0.029  Sum_probs=44.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHCCCCCCCCC
Q ss_conf             99999999999720001210497989---999999999999999999999998877687853210137121377910169
Q gi|254780690|r   55 IYSVTSDLHVLLASATQRKLEDISHI---VFLLTHLSLSASRLVIPGLLLFMMFGIGSYLIQRIPVLNLNHVKPSFKRVS  131 (354)
Q Consensus        55 ~~~l~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~p~~~~~~l~~i~~~l~q~G~~fs~k~l~pk~~rlN  131 (354)
                      -.+...+-.....+....++.+...+   -|.....+-..-+++.|++..+-+.  ++-+.-.|.-+|--    =++||-
T Consensus        51 ~~Et~~LT~AM~~SG~~~Dls~~~g~~vDKHSTGGVGDK~SL~L~P~vAa~G~~--Vak~SGRGLGhTGG----TlDKLE  124 (425)
T TIGR02644        51 DEETAYLTKAMIDSGEVLDLSSLKGPKVDKHSTGGVGDKVSLVLGPIVAALGVK--VAKMSGRGLGHTGG----TLDKLE  124 (425)
T ss_pred             HHHHHHHHHHHHHHCCEEECCCCCCCEECCCCCCCCCHHHHHHHHHHHHHCCCC--CCCCCCCCCCCCCC----CCHHHH
T ss_conf             889999999999738674002378851403557883402467779999974897--45514775676566----210542


Q ss_pred             HHHHHHHCCCHHHHHHHHHH
Q ss_conf             34303320126679999999
Q gi|254780690|r  132 LREGIKRIYSINNLVNFMKS  151 (354)
Q Consensus       132 Pi~GlKriFS~k~lvel~Ks  151 (354)
                      =+.|++==-|.+.+.|.+.-
T Consensus       125 SipG~~~~~s~~~f~~~~~~  144 (425)
T TIGR02644       125 SIPGFKTELSEAEFIEIVNK  144 (425)
T ss_pred             CCCCCCCCCCHHHHHHHHHH
T ss_conf             67983244896999999977


No 148
>PRK05428 HPr kinase/phosphorylase; Provisional
Probab=33.50  E-value=32  Score=14.36  Aligned_cols=36  Identities=19%  Similarity=0.340  Sum_probs=23.4

Q ss_pred             EEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHHHHH
Q ss_conf             8998076589999999999739978868899999997
Q gi|254780690|r  290 VLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFK  326 (354)
Q Consensus       290 ~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~  326 (354)
                      +|+++|. .....+.+.|+++++|++..+--...+..
T Consensus        86 iIvt~~~-~~~~~l~~~a~~~~ipll~t~~~ts~~i~  121 (308)
T PRK05428         86 IIVTRGL-EPPEELLEAAKEAGIPLLRTKLSTTRLIS  121 (308)
T ss_pred             EEEECCC-CCCHHHHHHHHHHCCCEEECCCCHHHHHH
T ss_conf             9997999-99999999999849958982875999999


No 149
>cd06325 PBP1_ABC_uncharacterized_transporter Type I periplasmic ligand-binding domain of uncharacterized ABC-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This group includes the type I periplasmic ligand-binding domain of uncharacterized ABC (ATPase Binding Cassette)-type transport systems that are predicted to be involved in the uptake of amino acids, peptides, or inorganic ions. This subgroup has high sequence similarity to members of the family of hydrophobic amino acid transporters (HAAT), such as leucine/isoleucine/valine binding protein (LIVBP); its ligand specificity has not been determined experimentally.
Probab=33.19  E-value=14  Score=17.15  Aligned_cols=19  Identities=26%  Similarity=0.452  Sum_probs=15.3

Q ss_pred             HHHHHHHHHHHCCCCEEEC
Q ss_conf             9999999999739978868
Q gi|254780690|r  299 IAKKMRKIAYEHNIPIFEE  317 (354)
Q Consensus       299 ~A~~Ir~~A~~~~Vpive~  317 (354)
                      ....|.+.|.+++||++-.
T Consensus       199 ~~~~i~~~a~~~~iPv~~~  217 (281)
T cd06325         199 AMEAVVKVANEAKIPVIAS  217 (281)
T ss_pred             HHHHHHHHHHHCCCCEEEC
T ss_conf             9999999998749988936


No 150
>PRK12311 rpsB 30S ribosomal protein S2; Provisional
Probab=32.95  E-value=32  Score=14.29  Aligned_cols=62  Identities=18%  Similarity=0.215  Sum_probs=30.7

Q ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHHH-------HHHHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHH
Q ss_conf             99997544899899999999999999-------98898607768699873553078889768888888899807658999
Q gi|254780690|r  229 IKDEIKQSYGNPIIKNRQKSIARSRI-------RHKMMEATSRATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAK  301 (354)
Q Consensus       229 vK~E~K~~EGdP~iK~~~r~~~re~~-------~~~~~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~  301 (354)
                      ..++.++-+.+-.-|-.+-.+.||..       -=+-|..+|++ ++|+||.+                      +..| 
T Consensus       119 le~~~~~g~~~~ltKKE~l~l~Re~~KL~k~lgGIk~M~~lPDl-vfViD~~k----------------------E~iA-  174 (332)
T PRK12311        119 LDEVLSSGDAGAYTKKERLTLQRERDKLDRSLGGIKDMGGLPDL-IFVIDTNK----------------------EDIA-  174 (332)
T ss_pred             HHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCE-EEEECCCC----------------------CHHH-
T ss_conf             99986126523358788999987999999854625420559998-99968973----------------------3899-


Q ss_pred             HHHHHHHHCCCCEEE
Q ss_conf             999999973997886
Q gi|254780690|r  302 KMRKIAYEHNIPIFE  316 (354)
Q Consensus       302 ~Ir~~A~~~~Vpive  316 (354)
                        ..+|++.+||||-
T Consensus       175 --V~EA~kLgIPvIa  187 (332)
T PRK12311        175 --IQEAQRLGIPVAA  187 (332)
T ss_pred             --HHHHHHCCCCEEE
T ss_conf             --9999980979899


No 151
>cd06811 PLPDE_III_yhfX_like Type III Pyridoxal 5-phosphate (PLP)-Dependent Enzyme yhfX. This subfamily is composed of the uncharacterized protein yhfX from Escherichia coli K-12 and similar bacterial proteins. These proteins are homologous to bacterial alanine racemases (AR), which are fold type III PLP-dependent enzymes containing an N-terminal PLP-binding TIM-barrel domain and a C-terminal beta-sandwich domain. AR exists as homodimers with active sites that lie at the interface between the TIM barrel domain of one subunit and the beta-sandwich domain of the other subunit. It catalyzes the interconversion between L- and D-alanine, which is an essential component of the peptidoglycan layer of bacterial cell walls. Members of this subfamily may act as PLP-dependent enzymes.
Probab=32.88  E-value=32  Score=14.28  Aligned_cols=45  Identities=20%  Similarity=0.273  Sum_probs=23.9

Q ss_pred             EEEECCCCEEEEEEECCCCC-CCCEEEEECCCHHHHHHHHHHHHCCCCEEE
Q ss_conf             99873553078889768888-888899807658999999999973997886
Q gi|254780690|r  267 IIITNPTHYALALRYIQTEN-DAPVLVAKGQNLIAKKMRKIAYEHNIPIFE  316 (354)
Q Consensus       267 vvitNPTH~AVAL~Y~~~~~-~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive  316 (354)
                      +=|..=||| =++-||++.. ..|    --.=.--.+-|++-+++|+-+.+
T Consensus       185 i~i~GvT~F-Pc~L~d~~~~~~~p----T~N~~Tl~~A~~~L~~~G~~~~q  230 (382)
T cd06811         185 IRIAGLTSF-PCFLYDEEQGDIAP----TPNLFTLLKAKELLEKRGIEILQ  230 (382)
T ss_pred             CEEEEEECE-EEEEECCCCCCCCC----CCCHHHHHHHHHHHHHCCCCEEE
T ss_conf             679664320-06877477795115----85299999999999975986279


No 152
>PRK05636 replicative DNA helicase; Provisional
Probab=32.59  E-value=33  Score=14.25  Aligned_cols=56  Identities=11%  Similarity=0.188  Sum_probs=33.5

Q ss_pred             CCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHHHHH
Q ss_conf             686998735530788897688888888998076589999999999739978868899999997
Q gi|254780690|r  264 RATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFK  326 (354)
Q Consensus       264 ~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~  326 (354)
                      +-++||+.--|.   +..  +.....+.  -...++...+|.+|+|.+||||-=--|-|..-.
T Consensus       377 ~l~livVDYLQL---m~~--~~~~~~R~--~ev~~ISr~LK~lAkel~vpVi~LsQLnR~~E~  432 (507)
T PRK05636        377 DLKMIVVDYLQL---MSS--GKRVESRQ--QEVSEFSRQLKLLAKELDVPLIAISQLNRGPES  432 (507)
T ss_pred             CCCEEEEEHHHH---CCC--CCCCCCHH--HHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCC
T ss_conf             999899845884---568--88876689--999999999999999979988997126844234


No 153
>PRK09165 replicative DNA helicase; Provisional
Probab=32.49  E-value=33  Score=14.24  Aligned_cols=29  Identities=28%  Similarity=0.463  Sum_probs=21.9

Q ss_pred             CCHHHHHHHHHHHHCCCCEEECHHHHHHH
Q ss_conf             65899999999997399788688999999
Q gi|254780690|r  296 QNLIAKKMRKIAYEHNIPIFEEPSLARSL  324 (354)
Q Consensus       296 ~~~~A~~Ir~~A~~~~Vpive~~~LAR~L  324 (354)
                      ..++...+|..|+|.+||||-=--|=|..
T Consensus       356 v~~Isr~LK~lAkel~ipVi~LsQLnR~~  384 (484)
T PRK09165        356 ISEITQGLKALAKELNIPVIALSQLSRQV  384 (484)
T ss_pred             HHHHHHHHHHHHHHHCCCEEEECCCCCCC
T ss_conf             99999999999999699699974578442


No 154
>PRK05771 V-type ATP synthase subunit I; Validated
Probab=32.45  E-value=33  Score=14.23  Aligned_cols=57  Identities=12%  Similarity=0.117  Sum_probs=28.9

Q ss_pred             CCCCCCCCHHHHHHHHHH-------CCCCCHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             776866587879999985-------787513359999999-999999999999999999999999
Q gi|254780690|r    8 DNKTEAPSSKKIEDALNE-------GNAPISREASLFSSI-LACLIYLLFFFSPGIYSVTSDLHV   64 (354)
Q Consensus         8 ~eKTE~PT~kRL~dARek-------GqV~kS~el~~~~~l-l~~~~~l~~~~~~~~~~l~~~~~~   64 (354)
                      +++..+||--|-.+-=+=       =.+|+.+|++-...+ ....+++.+++++..+.+.-.+..
T Consensus       311 ~~~e~pPt~l~n~~~~~pFe~iv~~Yg~P~Y~EiDPT~~~ai~Fp~fFG~m~gD~GyGlil~l~~  375 (640)
T PRK05771        311 EEEEEVPTKLKNPGFAKPFESLTEMYSLPKYNEIDPTPILAIFFPVFFGMMLGDAGYGLLLLLIS  375 (640)
T ss_pred             CCCCCCCEEEECCCHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             66799997752773666899999964899999878558999999999999986378899999999


No 155
>pfam07817 GLE1 GLE1-like protein. The members of this family are sequences that are similar to the human protein GLE1. This protein is localized at the nuclear pore complexes and functions in poly(A)+ RNA export to the cytoplasm.
Probab=32.22  E-value=26  Score=15.02  Aligned_cols=24  Identities=13%  Similarity=0.003  Sum_probs=16.3

Q ss_pred             CCCCCCHHHHHHHHHH-----CCCCCHHH
Q ss_conf             6866587879999985-----78751335
Q gi|254780690|r   10 KTEAPSSKKIEDALNE-----GNAPISRE   33 (354)
Q Consensus        10 KTE~PT~kRL~dARek-----GqV~kS~e   33 (354)
                      ||.+.+-|.+.+-|++     ||+..|..
T Consensus        17 ~~d~~lKk~~~~~kr~In~~vgQls~s~~   45 (249)
T pfam07817        17 NRDPELKKLRFTLKRKINPKFGQLSNSSS   45 (249)
T ss_pred             CCCHHHHHHHHHHHHHCCCCHHCCCCHHH
T ss_conf             26999999999977656651630036088


No 156
>COG2082 CobH Precorrin isomerase [Coenzyme metabolism]
Probab=32.20  E-value=27  Score=14.90  Aligned_cols=87  Identities=20%  Similarity=0.229  Sum_probs=57.9

Q ss_pred             HHHHCCCCHHHHHHHH--HHHHHHHHH-HHHHHCC-CCCEEEEC-CCCEEEEEEECCC-CCCCCEEEEECCCHH-HHHHH
Q ss_conf             9754489989999999--999999998-8986077-68699873-5530788897688-888888998076589-99999
Q gi|254780690|r  232 EIKQSYGNPIIKNRQK--SIARSRIRH-KMMEATS-RATIIITN-PTHYALALRYIQT-ENDAPVLVAKGQNLI-AKKMR  304 (354)
Q Consensus       232 E~K~~EGdP~iK~~~r--~~~re~~~~-~~~~~V~-~A~vvitN-PTH~AVAL~Y~~~-~~~aP~vvaKG~~~~-A~~Ir  304 (354)
                      +..-.=.||+++-..+  ..-|..+.- .-....+ ++=|||-| ||-.==.+++-.+ ....+.|++-=.|.. |..-|
T Consensus        93 ~v~c~i~d~~~~e~a~~~g~Trsaa~~~~~~~~~~~~~ivvIGNAPTAL~~l~elie~~~~~palvIg~PVGFv~AaesK  172 (210)
T COG2082          93 PVICYVDDPRVAELAKEEGITRSAAGMRLAAERGEGGAIVVIGNAPTALFELLELIEEGGIKPALVIGVPVGFVGAAESK  172 (210)
T ss_pred             CEEEEECCCCHHHHHHHHCCHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHHHCCCCCCCEEEECCCCCCCHHHHH
T ss_conf             37999358136778876283577999999987368964999928779999999999806999867997387655659999


Q ss_pred             HHHHHCCCCEEECH
Q ss_conf             99997399788688
Q gi|254780690|r  305 KIAYEHNIPIFEEP  318 (354)
Q Consensus       305 ~~A~~~~Vpive~~  318 (354)
                      +.-++.+||-+-+.
T Consensus       173 e~L~~~~iP~itv~  186 (210)
T COG2082         173 EALRESPIPYITVR  186 (210)
T ss_pred             HHHHHCCCCEEEEE
T ss_conf             99985899969996


No 157
>PRK08082 consensus
Probab=32.12  E-value=33  Score=14.19  Aligned_cols=142  Identities=7%  Similarity=0.094  Sum_probs=69.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCH
Q ss_conf             99999999999999999999832156897840897999999999999999999999999999766799999998406998
Q gi|254780690|r  147 NFMKSFVKIILVGTIITISLTENYFTMLDFISANPHSILYHAFFTVRKVLIMILLFIATLTVLDIGWSYHQWYSKLKMSK  226 (354)
Q Consensus       147 el~KsllKv~li~~v~~~~i~~~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD~~~qr~~~~k~lkMsk  226 (354)
                      -.+|+.+=+-   .+.........+.++....++..+...-+...              .+-++  .++   .++=++|.
T Consensus       213 smGKTa~aln---ia~~~a~~~~~~V~~fSlEM~~~~l~~R~la~--------------~s~i~--~~~---i~~g~l~~  270 (453)
T PRK08082        213 SVGKTAFALN---IAQNVATKTDENVAIFSLEMGADQLVMRMLCA--------------EGNID--AQR---LRTGSLTS  270 (453)
T ss_pred             CCCHHHHHHH---HHHHHHHHCCCCEEEEECCCCHHHHHHHHHHC--------------CCCCC--HHH---HHCCCCCH
T ss_conf             8757899999---99999985599489973138989999999971--------------55888--667---75189999


Q ss_pred             HHHHHHH------HHC------CCC---HHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEE
Q ss_conf             9999997------544------899---8999999999999999889860776869987355307888976888888889
Q gi|254780690|r  227 QEIKDEI------KQS------YGN---PIIKNRQKSIARSRIRHKMMEATSRATIIITNPTHYALALRYIQTENDAPVL  291 (354)
Q Consensus       227 qEvK~E~------K~~------EGd---P~iK~~~r~~~re~~~~~~~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~v  291 (354)
                      +|.++-.      ++.      ..+   .+|+++.|++.++          .+-++||..--+.   ++.+ +...-.+.
T Consensus       271 ~e~~~i~~a~~~l~~~~l~idd~~~~~i~~i~~~~r~~~~~----------~~~~livIDYlqL---i~~~-~~~~~~r~  336 (453)
T PRK08082        271 DDWGKLTMAMGSLSNAGIYIDDTPGIRVNEIRAKCRRLKQE----------QGLGMILIDYLQL---IQGS-GRSGENRQ  336 (453)
T ss_pred             HHHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHHHH----------CCCCEEEEECHHH---CCCC-CCCCCCHH
T ss_conf             99999999999850697389789999899999999999986----------6998899950773---3778-98887899


Q ss_pred             EEECCCHHHHHHHHHHHHCCCCEEECHHHHHHHHH
Q ss_conf             98076589999999999739978868899999997
Q gi|254780690|r  292 VAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFK  326 (354)
Q Consensus       292 vaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~  326 (354)
                        -..+++...+|.+|+|.+||||-=--|-|..-.
T Consensus       337 --~ev~~isr~LK~lAkel~ipvi~lsQLnR~~e~  369 (453)
T PRK08082        337 --QEVSEISRTLKALARELEVPVIALSQLSRGVES  369 (453)
T ss_pred             --HHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCC
T ss_conf             --999999999999999969979996447843123


No 158
>PRK10062 hypothetical protein; Provisional
Probab=32.01  E-value=33  Score=14.18  Aligned_cols=76  Identities=11%  Similarity=0.129  Sum_probs=33.0

Q ss_pred             HHHHHCCCHHHHHHHHHHHHHH-HHHHHHHHHHHHHC-----HHHHHHHHC---CCHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             3033201266799999999999-99999999999832-----156897840---89799999999999999999999999
Q gi|254780690|r  134 EGIKRIYSINNLVNFMKSFVKI-ILVGTIITISLTEN-----YFTMLDFIS---ANPHSILYHAFFTVRKVLIMILLFIA  204 (354)
Q Consensus       134 ~GlKriFS~k~lvel~KsllKv-~li~~v~~~~i~~~-----~~~l~~l~~---~~~~~~l~~~~~~~~~l~~~~~~~~~  204 (354)
                      +++.|-++ ++++...--++|. .++|.++-+..-+.     ++.+-....   .+....+......+...+..++...+
T Consensus       209 ~~~~~~~G-r~Lv~~mP~lmk~LsvvGT~AMl~VGG~Il~Hg~~~lhh~i~~~~~~~gg~~~~l~~~l~~~v~Glv~G~v  287 (303)
T PRK10062        209 SALAQALG-KGLLIIAPWLMKALSIVGTLAMFLVGGGIVVHGIAPLHHAIEHFAGQQSAVVAMILPTVLNLVLGFIIGGI  287 (303)
T ss_pred             CHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEECCHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             42899999-99999999999999999999999946535672658988789987540003999999999999999999999


Q ss_pred             HHHHHH
Q ss_conf             999976
Q gi|254780690|r  205 TLTVLD  210 (354)
Q Consensus       205 via~iD  210 (354)
                      ++++.-
T Consensus       288 vv~vv~  293 (303)
T PRK10062        288 VVLGVK  293 (303)
T ss_pred             HHHHHH
T ss_conf             999999


No 159
>TIGR00868 hCaCC calcium-activated chloride channel protein 1; InterPro: IPR004727   This entry represents a family of Ca(2+)-regulated chloride channels (CLCA) which includes bovine, murine and human proteins , . Each CLCA exhibits a distinct, often overlapping, tissue expression pattern. With the exception of the truncated, secreted protein hCLCA3 , they are synthesized as an approximately 125 kDa precursor transmembrane glycoprotein that is rapidly cleaved into 90 and 35 kDa subunits. The human proteins have been shown to affect a large number of cell functions including chloride conductance, epithelial secretion, cell-cell adhesion, apoptosis, cell cycle control, mucus production in asthma, and blood pressure. The CLCA proteins expressed on the luminal surface of lung vascular endothelia (bCLCA2; mCLCA1; hCLCA2) serve as adhesion molecules for lung metastatic cancer cells, mediating vascular arrest and lung colonization. Expression of hCLCA2 in normal mammary epithelium is consistently lost in human breast cancer and in all tumorigenic breast cancer cell lines. Re-expression of hCLCA2 in human breast cancer cells abrogates tumorigenicity in nude mice, implying that hCLCA2 acts as a tumour suppressor in breast cancer..
Probab=31.90  E-value=23  Score=15.41  Aligned_cols=13  Identities=31%  Similarity=0.672  Sum_probs=8.2

Q ss_pred             HCCCCCEEEECCC
Q ss_conf             0776869987355
Q gi|254780690|r  261 ATSRATIIITNPT  273 (354)
Q Consensus       261 ~V~~A~vvitNPT  273 (354)
                      .=.+|||||+||+
T Consensus        98 ~y~~AdViVa~P~  110 (874)
T TIGR00868        98 SYKKADVIVAEPT  110 (874)
T ss_pred             CCCCCCEEEECCC
T ss_conf             7666527880887


No 160
>cd01825 SGNH_hydrolase_peri1 SGNH_peri1; putative periplasmic member of the SGNH-family of hydrolases, a diverse family of lipases and esterases. The tertiary fold of the enzyme is substantially different from that of the alpha/beta hydrolase family and unique among all known hydrolases; its active site closely resembles the Ser-His-Asp(Glu) triad found in other serine hydrolases.
Probab=31.63  E-value=34  Score=14.14  Aligned_cols=84  Identities=18%  Similarity=0.289  Sum_probs=48.0

Q ss_pred             HHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECH-----------HHHHHHH
Q ss_conf             89860776869987355307888976888888889980765899999999997399788688-----------9999999
Q gi|254780690|r  257 KMMEATSRATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEP-----------SLARSLF  325 (354)
Q Consensus       257 ~~~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~-----------~LAR~Ly  325 (354)
                      +..+..|+|.++++-|.--     |.+. ...+.....+...+...++++|++++++++-=-           +....|.
T Consensus        89 ~ir~~~P~a~ill~~p~d~-----~~~~-~~~~~~~~~~l~~v~~~~~~vA~~~~~~f~D~~~~MGG~~s~~~w~~~~L~  162 (189)
T cd01825          89 RLRQILPNASILLVGPPDS-----LQKT-GAGRWRTPPGLDAVIAAQRRVAKEEGIAFWDLYAAMGGEGGIWQWAEPGLA  162 (189)
T ss_pred             HHHHHCCCCEEEEECCCCH-----HHCC-CCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEHHHHHCCCCHHHHHHHCCCC
T ss_conf             9997589980999828827-----6425-655442467799999999999998498598668964884157776312435


Q ss_pred             HHCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             72889894898999999999999
Q gi|254780690|r  326 KQVPINSAIPPVFYKAVAQLIYK  348 (354)
Q Consensus       326 ~~~~ig~~Ip~~~y~aVA~il~~  348 (354)
                      .  +-+=-..++=|+-+|+.|..
T Consensus       163 ~--~D~vH~t~~Gy~~~a~~l~~  183 (189)
T cd01825         163 R--KDYVHLTPRGYERLANLLYE  183 (189)
T ss_pred             C--CCCCCCCHHHHHHHHHHHHH
T ss_conf             7--99877286799999999999


No 161
>pfam10686 DUF2493 Protein of unknown function (DUF2493). Members of this family are all Proteobacteria. The function is not known.
Probab=31.57  E-value=27  Score=14.87  Aligned_cols=24  Identities=25%  Similarity=0.311  Sum_probs=19.2

Q ss_pred             EECCCHHHHHHHHHHHHCCCCEEECHH
Q ss_conf             807658999999999973997886889
Q gi|254780690|r  293 AKGQNLIAKKMRKIAYEHNIPIFEEPS  319 (354)
Q Consensus       293 aKG~~~~A~~Ir~~A~~~~Vpive~~~  319 (354)
                      +||.|.+|.   +-|++++||++.-+|
T Consensus        42 ~kGad~lA~---~WA~~~gv~~i~f~~   65 (71)
T pfam10686        42 PKGAERIAA---RWARRRGVPQVAFKP   65 (71)
T ss_pred             CCCHHHHHH---HHHHHCCCCEEEECC
T ss_conf             633799999---999986997697685


No 162
>pfam12174 RST RST domain of plant C-terminal. This domain is found in many plant proteins including SROs and RCD1s; it is required for interaction with multiple plant transcription factors.
Probab=31.46  E-value=34  Score=14.12  Aligned_cols=45  Identities=16%  Similarity=0.197  Sum_probs=35.6

Q ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCHHHHHHHHHHHH
Q ss_conf             997667999999984069989999997544899899999999999
Q gi|254780690|r  207 TVLDIGWSYHQWYSKLKMSKQEIKDEIKQSYGNPIIKNRQKSIAR  251 (354)
Q Consensus       207 a~iD~~~qr~~~~k~lkMskqEvK~E~K~~EGdP~iK~~~r~~~r  251 (354)
                      .-.+..-..|.-.|+-|.||+|.=+-.++-=||-.+++-++++|.
T Consensus        25 ~~~~ll~~~Y~~~k~~kIsr~~fvr~lR~IVGD~lL~~~I~~lq~   69 (70)
T pfam12174        25 DKMLLLNKHYAKLRKNKISREEFVRKLRDIVGDKLLKSAIKKLQQ   69 (70)
T ss_pred             HHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             899999999999983788899999999999989999999998646


No 163
>pfam02639 DUF188 Uncharacterized BCR, YaiI/YqxD family COG1671.
Probab=31.26  E-value=34  Score=14.09  Aligned_cols=58  Identities=16%  Similarity=0.189  Sum_probs=43.2

Q ss_pred             CCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHHHHHH
Q ss_conf             869987355307888976888888889980765899999999997399788688999999972
Q gi|254780690|r  265 ATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFKQ  327 (354)
Q Consensus       265 A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~~  327 (354)
                      -.++|.|--|.     -.+...---++|..|.|..=..|.+.+.+.++=|-+|.|||-.+-..
T Consensus        12 ~v~~Van~~~~-----~p~~~~i~~v~V~~g~D~AD~~I~~~~~~gDlVIT~Di~LAa~~l~K   69 (130)
T pfam02639        12 PVTLVANQPHR-----LPPSPLIESVVVDAGFDAADDYIVERAEPGDLVITQDIPLAARVLEK   69 (130)
T ss_pred             EEEEEECCCCC-----CCCCCCEEEEEECCCCCHHHHHHHHHCCCCCEEEECCHHHHHHHHHC
T ss_conf             79999589804-----89999858999899966299999983789999985888989999988


No 164
>PRK07449 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylic acid synthase/2-oxoglutarate decarboxylase; Validated
Probab=31.26  E-value=34  Score=14.09  Aligned_cols=27  Identities=11%  Similarity=0.220  Sum_probs=15.2

Q ss_pred             CEEEEECCCHHHHHHHHH--HHHCCCCEE
Q ss_conf             889980765899999999--997399788
Q gi|254780690|r  289 PVLVAKGQNLIAKKMRKI--AYEHNIPIF  315 (354)
Q Consensus       289 P~vvaKG~~~~A~~Ir~~--A~~~~Vpiv  315 (354)
                      |+|.--|-+-.-.-|-|+  |.++++|++
T Consensus       425 ~vv~i~GDGsf~~~~~eL~Ta~~~~lpv~  453 (548)
T PRK07449        425 PTVALIGDLSFLHDLNGLLLLKQESGPLT  453 (548)
T ss_pred             CEEEEECCHHHHHCHHHHHHHHHCCCCCE
T ss_conf             88999554587604579999986699958


No 165
>PRK07263 consensus
Probab=31.23  E-value=34  Score=14.09  Aligned_cols=140  Identities=10%  Similarity=0.139  Sum_probs=68.8

Q ss_pred             HHHHHHHHHHHHHHHH-HHHHHCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCH
Q ss_conf             9999999999999999-999832156897840897999999999999999999999999999766799999998406998
Q gi|254780690|r  148 FMKSFVKIILVGTIIT-ISLTENYFTMLDFISANPHSILYHAFFTVRKVLIMILLFIATLTVLDIGWSYHQWYSKLKMSK  226 (354)
Q Consensus       148 l~KsllKv~li~~v~~-~~i~~~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD~~~qr~~~~k~lkMsk  226 (354)
                      .+|+.+=+    -++. .......+.++....++..+...-+...              .+-+|+  +   ..++-++|.
T Consensus       214 mGKTa~al----nia~~iA~~~~~~V~~fSlEMs~~ql~~R~la~--------------~~~i~~--~---~i~~g~l~~  270 (453)
T PRK07263        214 VGKTAFVL----NIAQNVGTKQKKTVAIFSLEMGAESLVDRMLAA--------------EGMVDS--H---SLRTGQLTD  270 (453)
T ss_pred             CCHHHHHH----HHHHHHHHHCCCEEEEEECCCCHHHHHHHHHHH--------------HCCCCH--H---CCCCCCCCH
T ss_conf             84789999----999999985598289992469989999999998--------------617331--0---331365247


Q ss_pred             HHHHHHH---HHCCC---------C---HHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEE
Q ss_conf             9999997---54489---------9---8999999999999999889860776869987355307888976888888889
Q gi|254780690|r  227 QEIKDEI---KQSYG---------N---PIIKNRQKSIARSRIRHKMMEATSRATIIITNPTHYALALRYIQTENDAPVL  291 (354)
Q Consensus       227 qEvK~E~---K~~EG---------d---P~iK~~~r~~~re~~~~~~~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~v  291 (354)
                      +|.++=.   ++...         +   .+|+++.|++.++.        -.+-++||..=-|.-   .   +....-+ 
T Consensus       271 ~e~~~~~~a~~~l~~~~l~idd~~~~~i~~i~~~~r~~~~~~--------~~~l~livIDYlqLi---~---~~~~~~r-  335 (453)
T PRK07263        271 QDWNNVTIAQGALAEAPIYIDDTPGIKITEIRARSRKLSQEV--------DGGLGLIVIDYLQLI---T---GTKPENR-  335 (453)
T ss_pred             HHHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHHHHH--------CCCCCEEEEEHHHHC---C---CCCCCCH-
T ss_conf             999999999987406858997899999899999999999860--------589868997367644---6---8885359-


Q ss_pred             EEECCCHHHHHHHHHHHHCCCCEEECHHHHHHHHH
Q ss_conf             98076589999999999739978868899999997
Q gi|254780690|r  292 VAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFK  326 (354)
Q Consensus       292 vaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~  326 (354)
                       ....+++...+|..|+|.+||||-=--|-|..-.
T Consensus       336 -~~ev~~isr~lK~lAkel~ipvi~lsQLnR~~e~  369 (453)
T PRK07263        336 -QQEVSDISRQLKILAKELKVPVIALSQLSRGVEQ  369 (453)
T ss_pred             -HHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCC
T ss_conf             -9999999999999999879979997436843123


No 166
>COG0052 RpsB Ribosomal protein S2 [Translation, ribosomal structure and biogenesis]
Probab=30.88  E-value=35  Score=14.05  Aligned_cols=66  Identities=11%  Similarity=0.131  Sum_probs=33.0

Q ss_pred             HHHHHHHHH-----HHHHHCCCHHHHH--HHHHHCCCCHHHHHHHHHHHHHHHHH-------HHHHHCCCCCEEEECCCC
Q ss_conf             766799999-----9984069989999--99754489989999999999999998-------898607768699873553
Q gi|254780690|r  209 LDIGWSYHQ-----WYSKLKMSKQEIK--DEIKQSYGNPIIKNRQKSIARSRIRH-------KMMEATSRATIIITNPTH  274 (354)
Q Consensus       209 iD~~~qr~~-----~~k~lkMskqEvK--~E~K~~EGdP~iK~~~r~~~re~~~~-------~~~~~V~~A~vvitNPTH  274 (354)
                      .-|.-+||.     ..+-.+-|-+-.|  ++.-+.+-|-.-|.+.-++.||+.+-       +-|..+|++ ++|++|.|
T Consensus        89 ~~yV~~RwLgG~LTN~~ti~~si~rl~~lE~~~~~~~~~~tKkE~l~l~re~~kL~k~lgGIk~m~~~Pd~-l~ViDp~~  167 (252)
T COG0052          89 AYYVNGRWLGGMLTNFKTIRKSIKRLKELEKMEEDGFDGLTKKEALMLTRELEKLEKSLGGIKDMKGLPDV-LFVIDPRK  167 (252)
T ss_pred             CCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCHHHCCCCCCE-EEEECCCH
T ss_conf             95132764374244740588899999999987641432100788887777899998740141112679998-99968817


Q ss_pred             E
Q ss_conf             0
Q gi|254780690|r  275 Y  275 (354)
Q Consensus       275 ~  275 (354)
                      =
T Consensus       168 e  168 (252)
T COG0052         168 E  168 (252)
T ss_pred             H
T ss_conf             6


No 167
>TIGR00853 pts-lac PTS system, lactose/cellobiose family IIB component; InterPro: IPR014350   The phosphoenolpyruvate-dependent sugar phosphotransferase system (PTS) ,  is a major carbohydrate transport system in bacteria. The PTS catalyses the phosphorylation of incoming sugar substrates and coupled with translocation across the cell membrane, makes the PTS a link between the uptake and metabolism of sugars.   The general mechanism of the PTS is the following: a phosphoryl group from phosphoenolpyruvate (PEP) is transferred via a signal transduction pathway, to enzyme I (EI) which in turn transfers it to a phosphoryl carrier, the histidine protein (HPr). Phospho-HPr then transfers the phosphoryl group to a sugar-specific permease, a membrane-bound complex known as enzyme 2 (EII), which transports the sugar to the cell. EII consists of at least three structurally distinct domains IIA, IIB and IIC . These can either be fused together in a single polypeptide chain or exist as two or three interactive chains, formerly called enzymes II (EII) and III (EIII).    The first domain (IIA or EIIA) carries the first permease-specific phosphorylation site, a histidine which is phosphorylated by phospho-HPr. The second domain (IIB or EIIB) is phosphorylated by phospho-IIA on a cysteinyl or histidyl residue, depending on the sugar transported. Finally, the phosphoryl group is transferred from the IIB domain to the sugar substrate concomitantly with the sugar uptake processed by the IIC domain. This third domain (IIC or EIIC) forms the translocation channel and the specific substrate-binding site.    An additional transmembrane domain IID, homologous to IIC, can be found in some PTSs, e.g. for mannose , , , .    According to structural and sequence analyses, the PTS EIIB domain (2.7.1.69 from EC) can be divided in five groups , , :  The PTS EIIB type 1 domain, which is found in the Glucose class of PTS, has an average length of about 80 amino acids. It forms a split alpha/beta sandwich composed of an antiparallel sheet (beta 1 to beta 4) and three alpha helices superimposed onto one side of the sheet. The phosphorylation site (Cys) is located at the end of the first beta strand on a protrusion formed by the edge of beta 1 and the reverse turn between beta 1 and beta 2 . The PTS EIIB type 2 domain, which is found in the Mannitol class of PTS, has an average length of about 100 amino acids. It consists of a four stranded parallel beta sheet flanked by two alpha helices (alpha 1 and 3) on one face and helix alpha 2 on the opposite face, with a characteristic Rossmann fold comprising two right-handed beta-alpha-beta motifs. The phosphorylation site (Cys) is located at the N-terminus of the domain, in the first beta strand.  The PTS EIIB type 3 domain, which is found in the Lactose class of PTS, has an average length of about 100 amino acids. It is composed of a central four-stranded parallel open twisted beta sheet, which is flanked by three alpha helices on the concave side and two on the convex side of the beta sheet. The phosphorylation site (Cys) is located in the C-terminal end of the first beta strand . The PTS EIIB type 4 domain, which is found in the Mannose class of PTS, has an average length of about 160 amino acids. It has a central core of seven parallel beta strands surrounded by a total of six alpha-helices. Three helices cover the front face, one the back face with the remaining two capping the central beta sheet at the top and bottom. The phosphorylation site (His) is located at the suface exposed loop between strand 1 and helix 1 .  The PTS EIIB type 5 domain, which is found in the Sorbitol class of PTS, has an average length of about 190 amino acids. The phosphorylation site (Cys) is located in the N-terminus of the domain.      The EIIB type 3 protein is often found downstream of EIIC type 3. This entry hits fewer proteins than IPR013012 from INTERPRO. .
Probab=30.67  E-value=35  Score=14.02  Aligned_cols=20  Identities=30%  Similarity=0.499  Sum_probs=17.6

Q ss_pred             CCHHHHHHHHHHHHCCCCEE
Q ss_conf             65899999999997399788
Q gi|254780690|r  296 QNLIAKKMRKIAYEHNIPIF  315 (354)
Q Consensus       296 ~~~~A~~Ir~~A~~~~Vpiv  315 (354)
                      .+.+|.+|++.|++.|||+-
T Consensus        59 tsLLv~~l~k~A~~~~~~~~   78 (142)
T TIGR00853        59 TSLLVNKLNKAAKEYGVPVK   78 (142)
T ss_pred             HHHHHHHHHHHHHHCCCCEE
T ss_conf             47899999999984599758


No 168
>cd00453 FTBP_aldolase_II Fructose/tagarose-bisphosphate aldolase class II. This family includes fructose-1,6-bisphosphate (FBP) and tagarose 1,6-bisphosphate (TBP) aldolases. FBP-aldolase is homodimeric and used in gluconeogenesis and glycolysis; the enzyme controls the condensation of dihydroxyacetone phosphate with glyceraldehyde-3-phosphate to yield fructose-1,6-bisphosphate. TBP-aldolase is tetrameric and produces tagarose-1,6-bisphosphate. There is an absolute requirement for a divalent metal ion, usually zinc, and in addition the enzymes are activated by monovalent cations such as Na+. Although structurally similar, the class I aldolases use a different mechanism and are believed to have an independent evolutionary origin.
Probab=30.64  E-value=35  Score=14.02  Aligned_cols=18  Identities=22%  Similarity=0.274  Sum_probs=9.7

Q ss_pred             HHHCCCCCCCCCHHHHHH
Q ss_conf             121377910169343033
Q gi|254780690|r  120 LNHVKPSFKRVSLREGIK  137 (354)
Q Consensus       120 ~k~l~pk~~rlNPi~GlK  137 (354)
                      +..++.|.|.+.-=.|++
T Consensus       122 FsSvMiDgS~~p~eENi~  139 (340)
T cd00453         122 FSSHMIDLSEESLQENIE  139 (340)
T ss_pred             CCEEEEECCCCCHHHHHH
T ss_conf             845875389899999999


No 169
>cd07359 PCA_45_Doxase_B_like Subunit B of the Class III Extradiol dioxygenase, Protocatechuate 4,5-dioxygenase, and simlar enzymes. This subfamily of class III extradiol dioxygenases consists of a number of proteins with known enzymatic activities: Protocatechuate (PCA) 4,5-dioxygenase (LigAB), 2,3-dihydroxyphenylpropionate 1,2-dioxygenase (MhpB), 3-O-Methylgallate Dioxygenase, 2-aminophenol 1,6-dioxygenase, as well as proteins without any known enzymatic activity. These proteins play essential roles in the degradation of aromatic compounds by catalyzing the incorporation of both atoms of molecular oxygen into their preferred substrates. As members of the Class III extradiol dioxygenase family, the enzymes use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. LigAB-like class III enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model repres
Probab=30.59  E-value=35  Score=14.01  Aligned_cols=30  Identities=13%  Similarity=0.092  Sum_probs=21.6

Q ss_pred             CCCEEEEECCCHHHHHHHHHHHHCCCCEEE
Q ss_conf             888899807658999999999973997886
Q gi|254780690|r  287 DAPVLVAKGQNLIAKKMRKIAYEHNIPIFE  316 (354)
Q Consensus       287 ~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive  316 (354)
                      ..|..--+|-.++|..|.+.+.+.++++--
T Consensus        84 ~~~~~~~~~d~ela~~i~~~~~~~g~d~a~  113 (271)
T cd07359          84 GIPRAPVPGDADLARHLLAGLVEDGFDVAF  113 (271)
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHCCCCEEE
T ss_conf             787777669899999999999987996464


No 170
>cd00616 AHBA_syn 3-amino-5-hydroxybenzoic acid synthase family (AHBA_syn). AHBA_syn family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The members of this CD are involved in various biosynthetic pathways for secondary metabolites. Some well studied proteins in this CD are AHBA_synthase, protein product of pleiotropic regulatory gene degT,  Arnb aminotransferase and pilin glycosylation protein. The prototype of this family, the AHBA_synthase, is a dimeric PLP dependent enzyme. AHBA_syn is the terminal enzyme of 3-amino-5-hydroxybenzoic acid (AHBA) formation which is involved in the biosynthesis of ansamycin antibiotics, including rifamycin B. Some members of this CD are involved in 4-amino-6-deoxy-monosaccharide D-perosamine synthesis. Perosamine is an important element in the glycosylation of several cell products, such as antibiotics and lipopolysaccharides of gram-positive and gram-negative bacteria. The pilin glycosylation protein 
Probab=30.06  E-value=36  Score=13.95  Aligned_cols=17  Identities=12%  Similarity=-0.003  Sum_probs=11.0

Q ss_pred             HHHHHHHHHHHCCCCEE
Q ss_conf             99999999997399788
Q gi|254780690|r  299 IAKKMRKIAYEHNIPIF  315 (354)
Q Consensus       299 ~A~~Ir~~A~~~~Vpiv  315 (354)
                      .-..+.+.-+++||.+-
T Consensus       281 ~R~~l~~~L~~~gI~~~  297 (352)
T cd00616         281 SRDELIEALKEAGIETR  297 (352)
T ss_pred             CHHHHHHHHHHCCCCEE
T ss_conf             59999999998799858


No 171
>PRK02870 heat shock protein HtpX; Provisional
Probab=29.90  E-value=36  Score=13.93  Aligned_cols=18  Identities=6%  Similarity=0.089  Sum_probs=10.7

Q ss_pred             HCCCCHH-HHHHHHHHHHH
Q ss_conf             4489989-99999999999
Q gi|254780690|r  235 QSYGNPI-IKNRQKSIARS  252 (354)
Q Consensus       235 ~~EGdP~-iK~~~r~~~re  252 (354)
                      |--|||+ +-+..+++...
T Consensus       263 ~lt~~p~~LasAL~KI~~~  281 (338)
T PRK02870        263 ELMRDNEPMARALQKISND  281 (338)
T ss_pred             HHHCCCHHHHHHHHHHHHC
T ss_conf             9949919999999998603


No 172
>PRK08694 consensus
Probab=29.57  E-value=36  Score=13.89  Aligned_cols=156  Identities=12%  Similarity=0.176  Sum_probs=73.3

Q ss_pred             HHHHHH--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             430332--012667999999999999999999999983215689784089799999999999999999999999999976
Q gi|254780690|r  133 REGIKR--IYSINNLVNFMKSFVKIILVGTIITISLTENYFTMLDFISANPHSILYHAFFTVRKVLIMILLFIATLTVLD  210 (354)
Q Consensus       133 i~GlKr--iFS~k~lvel~KsllKv~li~~v~~~~i~~~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD  210 (354)
                      ..|+++  +.=+-+=--.+||.+=+-+   +......+..+.++....++..+...-+....              +-++
T Consensus       212 t~Gl~~G~LiVIaaRPsmGKTalalni---a~~~a~~~~~~V~~fSLEMs~~~l~~Rlla~~--------------s~v~  274 (468)
T PRK08694        212 TSGLQPGDLIIVAGRPSMGKTAFSINI---AEHVAVEGKLPVAVFSMEMGGAQLVMRMLGSV--------------GRLD  274 (468)
T ss_pred             HCCCCCCCEEEEEECCCCCHHHHHHHH---HHHHHHHCCCCEEEECCCCCHHHHHHHHHHHH--------------CCCC
T ss_conf             448887847999617865378999999---99999847984799778899999999999972--------------5986


Q ss_pred             HHHHHHHHHHHHCCCHHHHHH------HHHHC----CCCH-----HHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCE
Q ss_conf             679999999840699899999------97544----8998-----99999999999999988986077686998735530
Q gi|254780690|r  211 IGWSYHQWYSKLKMSKQEIKD------EIKQS----YGNP-----IIKNRQKSIARSRIRHKMMEATSRATIIITNPTHY  275 (354)
Q Consensus       211 ~~~qr~~~~k~lkMskqEvK~------E~K~~----EGdP-----~iK~~~r~~~re~~~~~~~~~V~~A~vvitNPTH~  275 (354)
                        .+   ..++-+||.+|.++      +.++.    +-+|     +++++.|++.++.       + .+-++||..=-|.
T Consensus       275 --~~---~i~~g~l~~~e~~~~~~a~~~l~~~pl~idd~~~~t~~~i~a~~r~~~~~~-------~-~kl~~vvIDYLqL  341 (468)
T PRK08694        275 --QS---VLKTGRLEDEHWGRLNEAVVKLSDAPVYIDETPGLTALELRARARRLARQF-------N-NKLGLIVIDYLQL  341 (468)
T ss_pred             --HH---HCCCCCCCHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHHHHHHHHH-------C-CCCCEEEEEHHHH
T ss_conf             --32---110489999999999999999862996897699998879999999999983-------8-9873899736754


Q ss_pred             EEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHHHH
Q ss_conf             78889768888888899807658999999999973997886889999999
Q gi|254780690|r  276 ALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLF  325 (354)
Q Consensus       276 AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly  325 (354)
                         ++.+ +. ...+.  -...++...+|.+|+|.+||||-=--|-|..-
T Consensus       342 ---i~~~-~~-~~~r~--~~i~~isr~LK~lAkel~ipvi~LsQLnR~~e  384 (468)
T PRK08694        342 ---MAGS-GR-SDNRA--SELGEISRSLKALAKELQVPIIALSQLSRTVE  384 (468)
T ss_pred             ---CCCC-CC-CCCHH--HHHHHHHHHHHHHHHHHCCCEEEECCCCCCCC
T ss_conf             ---1688-87-65599--99999999999999997998999632685423


No 173
>PRK06749 replicative DNA helicase; Provisional
Probab=29.43  E-value=36  Score=13.87  Aligned_cols=30  Identities=27%  Similarity=0.339  Sum_probs=24.2

Q ss_pred             CCHHHHHHHHHHHHCCCCEEECHHHHHHHH
Q ss_conf             658999999999973997886889999999
Q gi|254780690|r  296 QNLIAKKMRKIAYEHNIPIFEEPSLARSLF  325 (354)
Q Consensus       296 ~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly  325 (354)
                      .+++...+|..|+|.+|||+-=--|-|..-
T Consensus       325 v~~isr~lK~lAkel~vpvi~lsQLnR~~e  354 (428)
T PRK06749        325 ISEISRKLKLLARELNVCVVALSQLSRSVE  354 (428)
T ss_pred             HHHHHHHHHHHHHHHCCCEEEECCCCCCCC
T ss_conf             999999999999996998999713785523


No 174
>TIGR01478 STEVOR variant surface antigen, stevor family; InterPro: IPR006374   Malaria is still a major cause of mortality in many areas of the world. Plasmodium falciparum causes the most severe human form of the disease and is responsible for most fatalities. Severe cases of malaria can occur when the parasite invades and then proliferates within red blood cell erythrocytes. The parasite produces many variant antigenic proteins, encoded by multigene families, which are present on the surface of the infected erythrocyte and play important roles in virulence. A crucial survival mechanism for the malaria parasite is its ability to evade the immune response by switching these variant surface antigens. The high virulence of P. falciparum relative to other malarial parasites is in large part due to the fact that in this organism many of these surface antigens mediate the binding of infected erythrocytes to the vascular endothelium (cytoadherence) and non-infected erythrocytes (rosetting). This can lead to the accumulation of infected cells in the vasculature of a variety of organs, blocking the blood flow and reducing the oxygen supply. Clinical symptoms of severe infection can include fever, progressive anaemia, multi-organ dysfunction and coma. For more information see .   This entry represents the stevor (short for "subtelomeric variable open reading frame") family of predicted variant surface antigens. This is the third largest variant surface antigen family in P. falciparum, with 33 genes identified in the genome of this parasite . The function of these proteins is not known, but they are expressed during several stages of the parasite life-cycle and may play a variety of roles in parasite survival and infection ..
Probab=29.21  E-value=37  Score=13.84  Aligned_cols=71  Identities=14%  Similarity=0.219  Sum_probs=33.2

Q ss_pred             HCCCHHHHHHHHHHHHH-HHHHHHHHHHHHHHCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             20126679999999999-99999999999983215689784089799999999999999999999999999976679999
Q gi|254780690|r  138 RIYSINNLVNFMKSFVK-IILVGTIITISLTENYFTMLDFISANPHSILYHAFFTVRKVLIMILLFIATLTVLDIGWSYH  216 (354)
Q Consensus       138 riFS~k~lvel~KsllK-v~li~~v~~~~i~~~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~~~via~iD~~~qr~  216 (354)
                      ++|+..++..-.++-.- +..+-+..+..        ....+....      ...=..++..+++++.|+-++=|.|=|.
T Consensus       234 nff~~~SlEsa~~t~~~t~~~lmga~~~~--------~~~a~~~~S------tf~PyGIAAlVLi~L~V~LIiLYIWLYr  299 (315)
T TIGR01478       234 NFFFLSSLESALKTAVGTIVSLMGAADEA--------ESAASAATS------TFLPYGIAALVLIILTVVLIILYIWLYR  299 (315)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99978899999987345775365324666--------557888887------8613589999999999999999888856


Q ss_pred             HHHHHH
Q ss_conf             999840
Q gi|254780690|r  217 QWYSKL  222 (354)
Q Consensus       217 ~~~k~l  222 (354)
                      +-.++.
T Consensus       300 RRK~SW  305 (315)
T TIGR01478       300 RRKKSW  305 (315)
T ss_pred             HCCHHH
T ss_conf             403035


No 175
>PRK11172 dkgB 2,5-diketo-D-gluconate reductase B; Provisional
Probab=28.91  E-value=12  Score=17.68  Aligned_cols=51  Identities=22%  Similarity=0.158  Sum_probs=26.2

Q ss_pred             HHHHHHHHCCCCEEECHHHHHHHHHHCCCCCCCCHHHHHHHHHH-HHHHHHH
Q ss_conf             99999997399788688999999972889894898999999999-9999730
Q gi|254780690|r  302 KMRKIAYEHNIPIFEEPSLARSLFKQVPINSAIPPVFYKAVAQL-IYKIYHK  352 (354)
Q Consensus       302 ~Ir~~A~~~~Vpive~~~LAR~Ly~~~~ig~~Ip~~~y~aVA~i-l~~v~~l  352 (354)
                      .+++.++++||.++.--|||+.-.-.-++=+.|-.++=...|+| |+|+.+.
T Consensus       163 ~l~~~c~~~gI~~~ayspL~~g~~l~~~~l~~iA~k~g~s~aqvaLaW~lq~  214 (267)
T PRK11172        163 KVVAFAKEHGIHVTSYMTLAYGKVLKDPVIARIAAKHNATPAQVALAWAMQL  214 (267)
T ss_pred             HHHHHHHHCCCEEEEECCCCCCCCCCCHHHHHHHHHHCCCHHHHHHHHHHHC
T ss_conf             9999999759847995445568877761668999994999999999999808


No 176
>TIGR01265 tyr_nico_aTase tyrosine/nicotianamine aminotransferases; InterPro: IPR005958   This entry describes tyrosine aminotransferase (2.6.1.5 from EC) as found in animals and Trypanosoma cruzi (Euglenozoa). It is the first enzyme of a pathway of tyrosine degradation via homogentisate.  L-tyrosine + 2-oxoglutarate = 4-hydroxyphenylpyruvate + L-glutamate. Several plant enzyme designated as probable tyrosine aminotransferases are very closely related to an experimentally demonstrated nicotianamine aminotransferase, an enzyme in a siderophore (iron uptake chelator) biosynthesis pathway are included in this family. ; GO: 0008483 transaminase activity, 0030170 pyridoxal phosphate binding, 0006519 amino acid and derivative metabolic process.
Probab=28.79  E-value=37  Score=13.79  Aligned_cols=48  Identities=17%  Similarity=0.276  Sum_probs=27.9

Q ss_pred             HHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHH
Q ss_conf             898607768699873553078889768888888899807658999999999973997886889
Q gi|254780690|r  257 KMMEATSRATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPS  319 (354)
Q Consensus       257 ~~~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~  319 (354)
                      +.+.+=.++-.||+||-        +|-..    |   -.-..=++|-|.|++++|||+.|==
T Consensus       178 e~l~DekT~A~vv~NP~--------NPCGs----V---F~~~HL~k~~~~A~kl~i~iIADEi  225 (424)
T TIGR01265       178 ESLADEKTVAIVVINPS--------NPCGS----V---FSRDHLEKIAEVARKLGIPIIADEI  225 (424)
T ss_pred             HHHHCCCCEEEEEECCC--------CCCCC----C---CCHHHHHHHHHHHHHHCCCEEEEEE
T ss_conf             87632687699984756--------67888----8---7888899999999870982687763


No 177
>PRK08006 replicative DNA helicase; Provisional
Probab=28.78  E-value=37  Score=13.79  Aligned_cols=67  Identities=21%  Similarity=0.330  Sum_probs=39.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEEE---ECCCHHHHHHHHHHHHCCCCEEEC
Q ss_conf             99999999999999988986077686998735530788897688888888998---076589999999999739978868
Q gi|254780690|r  241 IIKNRQKSIARSRIRHKMMEATSRATIIITNPTHYALALRYIQTENDAPVLVA---KGQNLIAKKMRKIAYEHNIPIFEE  317 (354)
Q Consensus       241 ~iK~~~r~~~re~~~~~~~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vva---KG~~~~A~~Ir~~A~~~~Vpive~  317 (354)
                      +|+++.|++.++         -..-++||..=-|.          +..|.--.   --.+++...+|.+|+|.+||||-=
T Consensus       322 ~i~a~~r~~~~~---------~~gl~lvvIDYLqL----------~~~~~~~~~r~~ei~~isr~lK~lAkel~ipVi~L  382 (471)
T PRK08006        322 EVRSRARRIFRE---------HGGLSLIMIDYLQL----------MRVPSLSDNRTLEIAEISRSLKALAKELQVPVVAL  382 (471)
T ss_pred             HHHHHHHHHHHH---------CCCCCEEEEEHHHH----------CCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCEEEE
T ss_conf             999999999986---------48986899638866----------16787441066899999999999999969968997


Q ss_pred             HHHHHHHHH
Q ss_conf             899999997
Q gi|254780690|r  318 PSLARSLFK  326 (354)
Q Consensus       318 ~~LAR~Ly~  326 (354)
                      --|-|..-.
T Consensus       383 sQLnR~~e~  391 (471)
T PRK08006        383 SQLNRSLEQ  391 (471)
T ss_pred             CCCCCCCCC
T ss_conf             016831001


No 178
>pfam02404 SCF Stem cell factor. Stem cell factor (SCF) is a homodimer involved in hematopoiesis. SCF binds to and activates the SCF receptor (SCFR), a receptor tyrosine kinase. The crystal structure of human SCF has been resolved and a potential receptor-binding site identified.
Probab=28.72  E-value=8.2  Score=19.01  Aligned_cols=28  Identities=21%  Similarity=0.384  Sum_probs=12.5

Q ss_pred             CCCCCCCHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             7910169343033201266799999999999
Q gi|254780690|r  125 PSFKRVSLREGIKRIYSINNLVNFMKSFVKI  155 (354)
Q Consensus       125 pk~~rlNPi~GlKriFS~k~lvel~KsllKv  155 (354)
                      |+-+++.|- .|=|+|..  -+|.+|.+...
T Consensus       130 ye~~~F~Pe-~FF~~fn~--sId~FKd~~~~  157 (273)
T pfam02404       130 PEERRFTPE-NFFRIFNR--SIDAFKDFAVA  157 (273)
T ss_pred             CCCCCCCHH-HHHHHHHH--HHHHHHHHHCC
T ss_conf             676777889-99999988--99999998603


No 179
>TIGR01740 pyrF orotidine 5'-phosphate decarboxylase; InterPro: IPR014732   Orotidine 5'-phosphate decarboxylase (OMPdecase) (4.1.1.23 from EC) ,  catalyzes the last step in the de novo biosynthesis of pyrimidines, the decarboxylation of OMP into UMP. In higher eukaryotes OMPdecase is part, with orotate phosphoribosyltransferase, of a bifunctional enzyme, while the prokaryotic and fungal OMPdecases are monofunctional proteins.   Some parts of the sequence of OMPdecase are well conserved across species. The best conserved region is located in the N-terminal half of OMPdecases and is centred around a lysine residue which is essential for the catalytic function of the enzyme..
Probab=28.58  E-value=23  Score=15.44  Aligned_cols=36  Identities=25%  Similarity=0.389  Sum_probs=30.2

Q ss_pred             CCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHHH
Q ss_conf             888889980765899999999997399788688999
Q gi|254780690|r  286 NDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLA  321 (354)
Q Consensus       286 ~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LA  321 (354)
                      ..-|.+.+-|-.....++.+++.+||-+|++|-.+|
T Consensus        31 vg~~l~~~~~~~~~~~~L~~~~~KHNf~if~D~Kf~   66 (233)
T TIGR01740        31 VGIDLLLSGGYEKIIEELAKLNKKHNFLIFLDLKFA   66 (233)
T ss_pred             CCHHHHHCCCCHHHHHHHHHHHCCCCCEEEECCEEC
T ss_conf             142333327848899999997456882032120313


No 180
>PRK12737 gatY tagatose-bisphosphate aldolase; Reviewed
Probab=28.56  E-value=38  Score=13.76  Aligned_cols=61  Identities=10%  Similarity=0.163  Sum_probs=26.5

Q ss_pred             CCEEEEECCCHHHHHHHHHHHHCCCCEEE-----CHHHHHHHHHHC--CCCCCCCHHHHHHHHHHHHHH
Q ss_conf             88899807658999999999973997886-----889999999728--898948989999999999999
Q gi|254780690|r  288 APVLVAKGQNLIAKKMRKIAYEHNIPIFE-----EPSLARSLFKQV--PINSAIPPVFYKAVAQLIYKI  349 (354)
Q Consensus       288 aP~vvaKG~~~~A~~Ir~~A~~~~Vpive-----~~~LAR~Ly~~~--~ig~~Ip~~~y~aVA~il~~v  349 (354)
                      .|.|+-=|.|.--..||+ |-++||-=|-     .....+++-...  .-+.+=|..++...-+-+..+
T Consensus       203 iPLVLHGgSG~~~e~i~~-ai~~Gi~KiNi~T~l~~a~~~~~~~~l~~~p~~~d~~~~~~~~~~a~~e~  270 (284)
T PRK12737        203 IPLVLHGASGVPDEDVKK-AISLGICKVNVATELKIAFSDAVKKYFYENPKANDPRKYMTPGKEAMKEV  270 (284)
T ss_pred             CCEEEECCCCCCHHHHHH-HHHCCEEEEEECHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHH
T ss_conf             998966899999999999-99779589985858999999999999987878689699999999999999


No 181
>TIGR02223 ftsN cell division protein FtsN; InterPro: IPR011930    FtsN is a poorly conserved protein active in cell division in a number of Proteobacteria. The N-terminal 30 residue region tends to by Lys/Arg-rich, and is followed by a membrane-spanning region. This is followed by an acidic low-complexity region of variable length and a well-conserved C-terminal domain of two tandem regions (Sporulation related repeat), found in several cell division and sporulation proteins. The role of FtsN as a suppressor for other cell division mutations is poorly understood; it may involve cell wall hydrolysis ..
Probab=28.27  E-value=38  Score=13.72  Aligned_cols=49  Identities=22%  Similarity=0.268  Sum_probs=26.8

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             998767877686658787999998578751335999999999999999999
Q gi|254780690|r    1 MSENDAPDNKTEAPSSKKIEDALNEGNAPISREASLFSSILACLIYLLFFF   51 (354)
Q Consensus         1 MAe~d~~~eKTE~PT~kRL~dARekGqV~kS~el~~~~~ll~~~~~l~~~~   51 (354)
                      |+++|=..-=+=-|+-+|..+.|+|-.  ..+-+..+.+++++++++++.+
T Consensus         1 M~~rdy~~rg~g~~~~~~~~~srKK~~--~~~~l~~a~~~ia~~~i~l~~g   49 (354)
T TIGR02223         1 MAQRDYVRRGRGAPKKKKKKRSRKKKR--NLRRLVRATVLIAVILILLFIG   49 (354)
T ss_pred             CCCCCHHCCCCCCCCCCCCCCHHHHHH--HCCCCCHHHHHHHHHHHHHHHH
T ss_conf             963320003567553444551034564--2366624899999999999861


No 182
>pfam07862 Nif11 Nitrogen fixation protein of unknown function. This domain is found in the Cyanobacteria, and may be involved in nitrogen fixation, but no role has been assigned.
Probab=28.26  E-value=38  Score=13.72  Aligned_cols=26  Identities=19%  Similarity=0.427  Sum_probs=22.3

Q ss_pred             CCHHHHHHHHHHCCCCHHHHHHHHHH
Q ss_conf             99899999975448998999999999
Q gi|254780690|r  224 MSKQEIKDEIKQSYGNPIIKNRQKSI  249 (354)
Q Consensus       224 MskqEvK~E~K~~EGdP~iK~~~r~~  249 (354)
                      ||.+++|+=....+.||.++.+.++-
T Consensus         1 MS~e~l~~Fl~~~~~d~~l~~~l~~~   26 (49)
T pfam07862         1 MSEEQLKAFLEKVKSDPSLREQLKAC   26 (49)
T ss_pred             CCHHHHHHHHHHHHCCHHHHHHHHHC
T ss_conf             98999999999985399999999875


No 183
>COG0757 AroQ 3-dehydroquinate dehydratase II [Amino acid transport and metabolism]
Probab=28.25  E-value=7.4  Score=19.33  Aligned_cols=19  Identities=47%  Similarity=0.637  Sum_probs=12.5

Q ss_pred             CCCCEEEECC---CCEEEEEEE
Q ss_conf             7686998735---530788897
Q gi|254780690|r  263 SRATIIITNP---THYALALRY  281 (354)
Q Consensus       263 ~~A~vvitNP---TH~AVAL~Y  281 (354)
                      .+++.||-||   ||++||||=
T Consensus        65 ~~~~~IvINpga~THTSvAlrD   86 (146)
T COG0757          65 GKAGDIVINPGAYTHTSVALRD   86 (146)
T ss_pred             CCCCEEEECCCCCHHHHHHHHH
T ss_conf             2487299847631056899999


No 184
>PRK06683 hypothetical protein; Provisional
Probab=28.21  E-value=38  Score=13.72  Aligned_cols=42  Identities=31%  Similarity=0.464  Sum_probs=28.8

Q ss_pred             CCEEEEECCCH-HHHHHHHHHHHCCCCEEECHHHHHHHHHHCCC
Q ss_conf             88899807658-99999999997399788688999999972889
Q gi|254780690|r  288 APVLVAKGQNL-IAKKMRKIAYEHNIPIFEEPSLARSLFKQVPI  330 (354)
Q Consensus       288 aP~vvaKG~~~-~A~~Ir~~A~~~~Vpive~~~LAR~Ly~~~~i  330 (354)
                      --+++|+-.|. +-.++.+.|+++||||..-... +.|-+-|-|
T Consensus        29 ~~v~iA~DAD~~v~~~v~~~a~~~~ipV~~VdSm-k~LGkaCGI   71 (82)
T PRK06683         29 KEVVIAEDADMRLTHVIIRTALQHNIPITKVESV-RKLGKVAGI   71 (82)
T ss_pred             EEEEEEECCCHHHHHHHHHHHHHHCCCEEEEECH-HHHHHHCCC
T ss_conf             6999972586888999999999829987997129-887416080


No 185
>TIGR02024 FtcD glutamate formiminotransferase; InterPro: IPR004227   This entry represents the formiminotransferase (FT) domain of formiminotransferase-cyclodeaminase (FTCD), which forms a homodimer, with each protomer being comprised of two subdomains. Tetrahydrofolate (THF)-dependent glutamate formiminotransferase is involved in the histidine utilization pathway. This enzyme interconverts L-glutamate and N-formimino-L-glutamate. The enzyme is bifunctional as it also catalyzes the cyclodeaminase reaction on N-formimino-THF, converting it to 5,10-methenyl-THF and releasing ammonia; part of the process of regenerating THF. This model covers enzymes from metazoa as well as Gram-positive bacteria and archaea. In humans, deficiency of this enzyme results in a disease phenotype . The crystal structure of the enzyme has been studied in the context of the catalytic mechanism . ; GO: 0005542 folic acid binding, 0016740 transferase activity, 0008152 metabolic process.
Probab=28.05  E-value=36  Score=13.93  Aligned_cols=17  Identities=12%  Similarity=0.233  Sum_probs=11.0

Q ss_pred             HHHHHHHHHCCCCEEEC
Q ss_conf             99999999739978868
Q gi|254780690|r  301 KKMRKIAYEHNIPIFEE  317 (354)
Q Consensus       301 ~~Ir~~A~~~~Vpive~  317 (354)
                      .-||.+|++.|||||++
T Consensus       254 E~ik~EA~RYgVpvVgS  270 (331)
T TIGR02024       254 ELIKMEAERYGVPVVGS  270 (331)
T ss_pred             HHHHHHHHHCCCCCCCE
T ss_conf             57889998708980121


No 186
>TIGR02469 CbiT precorrin-6Y C5,15-methyltransferase (decarboxylating), CbiT subunit; InterPro: IPR014008   Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase . In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase .    There are at least two distinct cobalamin biosynthetic pathways in bacteria :  Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway ; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis ; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii shermanii.     Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) . There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans.   This entry represents CbiT subunit of precorrin-6Y C5,15-methyltransferase (2.1.1.132 from EC) from the anaerobic pathway, a bifunctional enzyme that catalyses two methylations (at C-5 and C-15) in precorrin-6Y, as well as the decarboxylation of the acetate side chain located in ring C, in order to generate precorrin-8X. In the anaerobic pathway, two enzymes are required to produce precorrin-8X: CbiE and CbiT, which can be fused as CbiET (sometimes called CobL) . In the aerobic pathway, the bifunctional enzyme is CobL .; GO: 0008276 protein methyltransferase activity, 0009236 cobalamin biosynthetic process.
Probab=28.04  E-value=26  Score=15.08  Aligned_cols=20  Identities=5%  Similarity=0.026  Sum_probs=7.7

Q ss_pred             EEEEECCCHHHHHHHHHHHH
Q ss_conf             89980765899999999997
Q gi|254780690|r  290 VLVAKGQNLIAKKMRKIAYE  309 (354)
Q Consensus       290 ~vvaKG~~~~A~~Ir~~A~~  309 (354)
                      .|.-=|-+..=..|.+...+
T Consensus       102 a~fvGGs~~~~~~il~~~~~  121 (135)
T TIGR02469       102 AVFVGGSGGKLEEILEAVER  121 (135)
T ss_pred             EEEECCCCHHHHHHHHHHHH
T ss_conf             88883897178999999985


No 187
>PRK07004 replicative DNA helicase; Provisional
Probab=27.73  E-value=39  Score=13.66  Aligned_cols=163  Identities=12%  Similarity=0.170  Sum_probs=78.6

Q ss_pred             CCCCCCCHHHHHHH--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             79101693430332--0126679999999999999999999999832156897840897999999999999999999999
Q gi|254780690|r  125 PSFKRVSLREGIKR--IYSINNLVNFMKSFVKIILVGTIITISLTENYFTMLDFISANPHSILYHAFFTVRKVLIMILLF  202 (354)
Q Consensus       125 pk~~rlNPi~GlKr--iFS~k~lvel~KsllKv~li~~v~~~~i~~~~~~l~~l~~~~~~~~l~~~~~~~~~l~~~~~~~  202 (354)
                      ++++++  ..||++  +.=+-+=--.+|+.+=+   -.+....+....+.++.+..++..+...-+....          
T Consensus       201 ~~LD~~--t~Gl~~gdLiIIAARPsmGKTafAl---niA~n~A~~~g~~V~~FSLEMs~eql~~Rlls~~----------  265 (460)
T PRK07004        201 VDLDRM--TSGMHGGELIIVAGRPSMGKTAFSM---NIGEYVAVEYGLPVAVFSMEMPGTQLAMRMLGSV----------  265 (460)
T ss_pred             HHHHHH--HCCCCCCCEEEEEECCCCCHHHHHH---HHHHHHHHHCCCCEEEECCCCCHHHHHHHHHHHC----------
T ss_conf             889865--2389877579997368764269999---9999998725886699847799999999999860----------


Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCHHHHHH------HHHH------CCCCH---HHHHHHHHHHHHHHHHHHHHHCCCCCE
Q ss_conf             99999976679999999840699899999------9754------48998---999999999999999889860776869
Q gi|254780690|r  203 IATLTVLDIGWSYHQWYSKLKMSKQEIKD------EIKQ------SYGNP---IIKNRQKSIARSRIRHKMMEATSRATI  267 (354)
Q Consensus       203 ~~via~iD~~~qr~~~~k~lkMskqEvK~------E~K~------~EGdP---~iK~~~r~~~re~~~~~~~~~V~~A~v  267 (354)
                          +-++  .++.   ++-++|.+|.++      +.++      ..++-   +|+++.|++.|+.         .+-++
T Consensus       266 ----s~I~--~~~i---r~g~l~~~e~~~i~~a~~~l~~~~l~IdD~~~lt~~~ira~~Rr~~~~~---------g~l~l  327 (460)
T PRK07004        266 ----GRLD--QHRM---RTGRLTDEDWPKLTHAVQKMSEAQLFIDETGGLNPMELRSRARRLARQC---------GKLGL  327 (460)
T ss_pred             ----CCCC--CCHH---HCCCCCHHHHHHHHHHHHHHHCCCEEEECCCCCHHHHHHHHHHHHHHHC---------CCCCE
T ss_conf             ----6988--2110---0788999999999999999855974896898730789999999999743---------58889


Q ss_pred             EEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHHHHHH
Q ss_conf             987355307888976888888889980765899999999997399788688999999972
Q gi|254780690|r  268 IITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFKQ  327 (354)
Q Consensus       268 vitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~~  327 (354)
                      ||..=-|.   +..+..  .-.+.  --..++...+|.+|+|.+|||+-=--|-|.....
T Consensus       328 vviDYlql---i~~~~~--~~~r~--~ei~~isr~lK~lAkel~ipvi~lsQLnR~~e~R  380 (460)
T PRK07004        328 IIIDYLQL---MSGSSQ--GENRA--TEISEISRSLKSLAKELDVPVIALSQLNRGLEQR  380 (460)
T ss_pred             EEEEHHHH---CCCCCC--CCCHH--HHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCC
T ss_conf             98507754---478888--88899--9999999999999999699789970468431227


No 188
>KOG2927 consensus
Probab=27.59  E-value=39  Score=13.64  Aligned_cols=90  Identities=11%  Similarity=0.180  Sum_probs=38.5

Q ss_pred             CCHHHHHH-HCCCHHHHHH-------------HHHHHHHHHHHHHHHHHHHHHCHHHHHH----HHCCCHHHHHHHHHHH
Q ss_conf             69343033-2012667999-------------9999999999999999999832156897----8408979999999999
Q gi|254780690|r  130 VSLREGIK-RIYSINNLVN-------------FMKSFVKIILVGTIITISLTENYFTMLD----FISANPHSILYHAFFT  191 (354)
Q Consensus       130 lNPi~GlK-riFS~k~lve-------------l~KsllKv~li~~v~~~~i~~~~~~l~~----l~~~~~~~~l~~~~~~  191 (354)
                      .++-+-++ .|++-|.+.|             +..-++-++++.+++.+++...||..+.    ....+..+++..++.+
T Consensus       156 ~kkkk~~~l~i~~dQ~F~d~de~YVW~yep~~~~~~vl~~~fvl~tlaivLFPLWP~~mR~gvyY~sig~~gfl~~IlvL  235 (372)
T KOG2927         156 KKKKKKFELEIHDDQAFQDGDEHYVWIYEPRPLMWQVLGVLFVLVTLAIVLFPLWPRRMRQGVYYLSIGAGGFLAFILVL  235 (372)
T ss_pred             HCCCCCCCEEECCCHHHCCCCCEEEEECCCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHCCEEEEECCHHHHHHHHHHH
T ss_conf             30367543030310320156725899616875269999999999999997313583887422113440315999999999


Q ss_pred             -HHHHHHHHHHHHHH---------------HHHHHHHHHHHHHH
Q ss_conf             -99999999999999---------------99976679999999
Q gi|254780690|r  192 -VRKVLIMILLFIAT---------------LTVLDIGWSYHQWY  219 (354)
Q Consensus       192 -~~~l~~~~~~~~~v---------------ia~iD~~~qr~~~~  219 (354)
                       +.++++.++..++.               .+++|-++-.|.|.
T Consensus       236 aIvRlILF~I~~il~~g~~g~W~FPNL~eDvGfleSF~PLy~~~  279 (372)
T KOG2927         236 AIVRLILFGITWILTGGKHGFWLFPNLTEDVGFLESFKPLYEYH  279 (372)
T ss_pred             HHHHHHHHHHHHHHHCCCCCEEECCCHHHHHHHHHHHCCCCCCC
T ss_conf             99999999999997378772575362565443787602131246


No 189
>cd00615 Orn_deC_like Ornithine decarboxylase family. This family belongs to pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). The major groups in this CD corresponds to ornithine decarboxylase (ODC), arginine decarboxylase (ADC) and lysine decarboxylase (LDC). ODC is a dodecamer composed of six homodimers and catalyzes the decarboxylation of tryptophan. ADC catalyzes the decarboxylation of arginine and LDC catalyzes the decarboxylation of lysine. Members of this family are widely found in all three forms of life.
Probab=27.58  E-value=39  Score=13.64  Aligned_cols=76  Identities=17%  Similarity=0.231  Sum_probs=43.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH----HHCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCC
Q ss_conf             9999999999766799999998----406998999999754489989999999999999998898607768699873553
Q gi|254780690|r  199 ILLFIATLTVLDIGWSYHQWYS----KLKMSKQEIKDEIKQSYGNPIIKNRQKSIARSRIRHKMMEATSRATIIITNPTH  274 (354)
Q Consensus       199 ~~~~~~via~iD~~~qr~~~~k----~lkMskqEvK~E~K~~EGdP~iK~~~r~~~re~~~~~~~~~V~~A~vvitNPTH  274 (354)
                      .+.-.++++-++-.|-.=.+..    -.-.|.+++++..++.   |                      .-.-|++||||=
T Consensus       111 Sv~~gl~l~g~~Pvyl~p~~~~~~gi~~~i~~~~~~~al~~~---p----------------------~~kav~lt~PtY  165 (294)
T cd00615         111 SVINGLVLSGAVPVYLKPERNPYYGIAGGIPPETFKKALIEH---P----------------------DAKAAVITNPTY  165 (294)
T ss_pred             HHHHHHHHCCCEEEEEECCCCCCCCCCCCCCHHHHHHHHHHC---C----------------------CCCEEEEECCCC
T ss_conf             999999986984899606435556953899999999999858---9----------------------965899977998


Q ss_pred             EEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECH
Q ss_conf             07888976888888889980765899999999997399788688
Q gi|254780690|r  275 YALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEP  318 (354)
Q Consensus       275 ~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~  318 (354)
                      |-+  -||                 -.+|.+++.++++|++-|-
T Consensus       166 ~G~--~~D-----------------l~~i~~~~h~~~~~llVDE  190 (294)
T cd00615         166 YGI--CYN-----------------LRKIVEEAHHRGLPVLVDE  190 (294)
T ss_pred             CEE--EEC-----------------HHHHHHHHHHCCCEEEEEC
T ss_conf             877--668-----------------9999999840499799977


No 190
>pfam10881 DUF2726 Protein of unknown function (DUF2726). This bacterial family of proteins has no known function.
Probab=27.50  E-value=39  Score=13.63  Aligned_cols=61  Identities=8%  Similarity=0.095  Sum_probs=37.0

Q ss_pred             HHHHHHHHHHHCCCCCEEEECCCC--EEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECH
Q ss_conf             999998898607768699873553--07888976888888889980765899999999997399788688
Q gi|254780690|r  251 RSRIRHKMMEATSRATIIITNPTH--YALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEP  318 (354)
Q Consensus       251 re~~~~~~~~~V~~A~vvitNPTH--~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~  318 (354)
                      .+.+.++..+  ...|+||.||..  .-.++-+|.....     -+++-..-....++-+.+|+|+++-+
T Consensus        47 ~~~~~~~i~~--k~~DFvi~d~~~~~~v~~IEld~~~h~-----~~~~~~rD~~k~~~~~~agipllR~~  109 (127)
T pfam10881        47 WQRAFNRISA--KHVDFVLCDKSDLRPVAAIELDDASHK-----QGKAAKRDAFKRAALESAGIPLLRVK  109 (127)
T ss_pred             HHHHHHHHHC--CEEEEEEEECCCCCEEEEEEECCCCCC-----CHHHHHHHHHHHHHHHHCCCCEEEEC
T ss_conf             9999998655--066699997799948999994686656-----55278889999999998799789854


No 191
>PRK10916 ADP-heptose:LPS heptosyltransferase II; Provisional
Probab=27.49  E-value=12  Score=17.66  Aligned_cols=24  Identities=29%  Similarity=0.300  Sum_probs=16.9

Q ss_pred             HHHHHCCCCCEEEEC---CCCEEEEEE
Q ss_conf             898607768699873---553078889
Q gi|254780690|r  257 KMMEATSRATIIITN---PTHYALALR  280 (354)
Q Consensus       257 ~~~~~V~~A~vvitN---PTH~AVAL~  280 (354)
                      ...+-+..|+++|+|   |+|+|.|+.
T Consensus       254 el~ali~~a~l~I~nDSGpmHlAaA~g  280 (348)
T PRK10916        254 QAVILIAACKAIVTNDSGLMHVAAALN  280 (348)
T ss_pred             HHHHHHHHCCEEEECCCHHHHHHHHCC
T ss_conf             999999855987844882899999809


No 192
>PRK13602 putative ribosomal protein L7Ae-like; Provisional
Probab=27.43  E-value=39  Score=13.62  Aligned_cols=34  Identities=24%  Similarity=0.327  Sum_probs=25.7

Q ss_pred             CCCEEEEECCCH-HHHHHHHHHHHCCCCEEECHHH
Q ss_conf             888899807658-9999999999739978868899
Q gi|254780690|r  287 DAPVLVAKGQNL-IAKKMRKIAYEHNIPIFEEPSL  320 (354)
Q Consensus       287 ~aP~vvaKG~~~-~A~~Ir~~A~~~~Vpive~~~L  320 (354)
                      .--+++|+-.|. +-..|.+.+++++||++.-..-
T Consensus        28 ~~~V~IA~Dad~~v~~~v~~l~~ek~Ipv~~V~Sm   62 (82)
T PRK13602         28 VKEVVVAKDADPCLTSGVINLANEQGVPVSMVESM   62 (82)
T ss_pred             EEEEEEEECCCHHHHHHHHHHHHHCCCCEEEECCH
T ss_conf             12999982598889999999999729987996289


No 193
>pfam04392 ABC_sub_bind ABC transporter substrate binding protein. This family contains many hypothetical proteins and some ABC transporter substrate binding proteins.
Probab=27.42  E-value=18  Score=16.27  Aligned_cols=21  Identities=10%  Similarity=0.455  Sum_probs=12.1

Q ss_pred             HHHHHHCCCHHHHHHHHHHHH
Q ss_conf             430332012667999999999
Q gi|254780690|r  133 REGIKRIYSINNLVNFMKSFV  153 (354)
Q Consensus       133 i~GlKriFS~k~lvel~Ksll  153 (354)
                      +.|.-.......-+|++|.++
T Consensus       107 vTGvs~~~~~~~~l~ll~~l~  127 (292)
T pfam04392       107 VTGVSDLVDVEQTIELIKKLL  127 (292)
T ss_pred             EEEEECCCCHHHHHHHHHHHC
T ss_conf             678527747999999999868


No 194
>COG3384 Aromatic ring-opening dioxygenase, catalytic LigB subunit related    enzyme [Amino acid transport and metabolism]
Probab=27.36  E-value=39  Score=13.61  Aligned_cols=52  Identities=21%  Similarity=0.328  Sum_probs=29.0

Q ss_pred             CCCEEEECCCCEEEEEEECCCCCCCCEEE----------------EECCCHHHHHHHHHHHHCCCCEE
Q ss_conf             68699873553078889768888888899----------------80765899999999997399788
Q gi|254780690|r  264 RATIIITNPTHYALALRYIQTENDAPVLV----------------AKGQNLIAKKMRKIAYEHNIPIF  315 (354)
Q Consensus       264 ~A~vvitNPTH~AVAL~Y~~~~~~aP~vv----------------aKG~~~~A~~Ir~~A~~~~Vpiv  315 (354)
                      +-|.||+=-|||-+-=-|.-.-++.|..+                |+|.-++|.+|++.+.+.+||--
T Consensus        43 rp~tIiV~SaHw~t~~~~~v~~~e~~~~i~DfygFP~~ly~~~Y~a~G~peLa~~i~~~l~~~~v~a~  110 (268)
T COG3384          43 RPDTIIVFSAHWETRGAYHVTASEHPETIHDFYGFPDELYDVKYPAPGSPELAQRIVELLAKLGVPAD  110 (268)
T ss_pred             CCCEEEEEECEEEECCCEEEECCCCCCEEECCCCCCHHHHHCCCCCCCCHHHHHHHHHHHCCCCCCCC
T ss_conf             89879998350786274368706676612215889889984337999998999999997412586666


No 195
>KOG0253 consensus
Probab=27.35  E-value=14  Score=17.05  Aligned_cols=39  Identities=23%  Similarity=0.265  Sum_probs=29.8

Q ss_pred             CEEEEEEECCCCCCCCEEEEECCCHHHHH-HHHHHHHCCCCE
Q ss_conf             30788897688888888998076589999-999999739978
Q gi|254780690|r  274 HYALALRYIQTENDAPVLVAKGQNLIAKK-MRKIAYEHNIPI  314 (354)
Q Consensus       274 H~AVAL~Y~~~~~~aP~vvaKG~~~~A~~-Ir~~A~~~~Vpi  314 (354)
                      -+|+.+.+.++  .+-.-++||.|+.|.. +.++||.|+.|.
T Consensus       242 ~~a~f~~w~~E--SpRf~~~~G~~~kAletL~kiArmNg~ql  281 (528)
T KOG0253         242 FAARFLVWVYE--SPRFYLAKGDDYKALETLHKIARMNGKQL  281 (528)
T ss_pred             HHHHHHHHCCC--CCCHHHHCCCHHHHHHHHHHHHHHCCCCC
T ss_conf             99999962565--74104543985779999999998448878


No 196
>TIGR01461 greB transcription elongation factor GreB; InterPro: IPR006358   Bacterial GreA IPR006359 from INTERPRO and GreB promote transcription elongation by stimulating an endogenous, endonucleolytic transcript cleavage activity of the RNA polymerase, allowing RNA transcription to continue past template-encoded arresting sites. GreA and GreB are sequence homologues and have homologues in every known bacterial genome. GreA and GreB stimulate transcript cleavage in different ways; GreA induces cleavage of 3'-RNA fragments 23 nt in length and can only prevent the formation of arrested complexes, whereas GreB induces cleavage of fragments up to 18 nt in length and can rescue preexisting arrested complexes .    A 15  resolution helical reconstruction of the Escherichia coli core RNA polymerase (RNAP)/GreB complex that allows fitting of high-resolution RNAP and GreB structures. The model of the complex reveals a remarkable binding mode for GreB; the globular C-terminal domain binds RNAP at the edge of the active site channel, while the N-terminal coiled-coil domain extends 45  into a channel directly to the RNAP active site. The results point to a key role for conserved acidic residues at the tip of the Gre factor coiled coil in modifying the RNAP active site to catalyse the transcript cleavage reaction, and mutational studies confirm that these positions are critical for Gre factor function. Functional differences between GreA and GreB correlate with the distribution of positively charged residues on one face of the N-terminal coiled coil.; GO: 0003677 DNA binding, 0003711 transcription elongation regulator activity, 0006355 regulation of transcription DNA-dependent.
Probab=27.35  E-value=29  Score=14.69  Aligned_cols=47  Identities=23%  Similarity=0.346  Sum_probs=30.1

Q ss_pred             EEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHHHHHHCCCCCCC
Q ss_conf             8889768888888899807658999999999973997886889999999728898948
Q gi|254780690|r  277 LALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFKQVPINSAI  334 (354)
Q Consensus       277 VAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~~~~ig~~I  334 (354)
                      |.|-=+-|...-=++|  |.|++-.      +++.|-+  +-||||+|-+ -++|+++
T Consensus        91 V~le~~DG~~~r~rIV--G~DEid~------r~n~ISi--dSPlARaL~k-ke~gdev  137 (157)
T TIGR01461        91 VELEDDDGREQRYRIV--GIDEIDT------RKNKISI--DSPLARALIK-KEVGDEV  137 (157)
T ss_pred             EEEECCCCCCCCEEEE--ECCCCCC------CCCCEEE--ECHHHHHHHC-CCCCCEE
T ss_conf             8865388832026886--0552123------5772014--2667888630-1258777


No 197
>pfam01171 ATP_bind_3 PP-loop family. This family of proteins belongs to the PP-loop superfamily.
Probab=27.28  E-value=39  Score=13.60  Aligned_cols=23  Identities=26%  Similarity=0.449  Sum_probs=19.0

Q ss_pred             CHHHHHHHHHHHHCCCCEEECHH
Q ss_conf             58999999999973997886889
Q gi|254780690|r  297 NLIAKKMRKIAYEHNIPIFEEPS  319 (354)
Q Consensus       297 ~~~A~~Ir~~A~~~~Vpive~~~  319 (354)
                      +.--..|++.|+++++|.++||.
T Consensus       146 ~~~k~ei~~~a~~~~l~~~~D~s  168 (182)
T pfam01171       146 KVTKSEIEEYLKEHGIPWVEDES  168 (182)
T ss_pred             CCCHHHHHHHHHHCCCCEEECCC
T ss_conf             48899999999986993689908


No 198
>PRK12338 hypothetical protein; Provisional
Probab=27.09  E-value=31  Score=14.39  Aligned_cols=74  Identities=14%  Similarity=0.044  Sum_probs=28.8

Q ss_pred             CCHHHH--HHHHHHHHHHHHHHHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCE
Q ss_conf             998999--99999999999988986077686998735530788897688888888998076589999999999739978
Q gi|254780690|r  238 GNPIIK--NRQKSIARSRIRHKMMEATSRATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPI  314 (354)
Q Consensus       238 GdP~iK--~~~r~~~re~~~~~~~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpi  314 (354)
                      |+-.+|  ..+|-+|.-+..+.-...||+-+-+=.+-| .+--+.|-.+. ..-+.+--+.|++ .+..++-++||--+
T Consensus       159 ~~Kyvkyf~niR~Iqd~L~~~Adeh~iP~I~N~nid~s-V~~i~~~I~~~-~~~~~~~hsVddl-~~e~eII~~~~~~i  234 (320)
T PRK12338        159 GGKHLEYFRENRIIHDFLVSQADEHGIPVIKNDDIDRT-VSKVLSVIREV-SVVVKLVHSVEDL-DVEDEIIKENNGRI  234 (320)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHH-HHHHHHHHHHH-HEEEECCCCHHHH-HHHHHHHHHCCCEE
T ss_conf             65089999988999999984167619973047635568-99999999987-3465226768888-88789999739758


No 199
>COG2055 Malate/L-lactate dehydrogenases [Energy production and conversion]
Probab=26.98  E-value=40  Score=13.56  Aligned_cols=23  Identities=22%  Similarity=0.098  Sum_probs=15.2

Q ss_pred             CHHHHHHHHHHHHCCCCEEECHH
Q ss_conf             58999999999973997886889
Q gi|254780690|r  297 NLIAKKMRKIAYEHNIPIFEEPS  319 (354)
Q Consensus       297 ~~~A~~Ir~~A~~~~Vpive~~~  319 (354)
                      |+.-.++++.++++||||-++..
T Consensus       311 G~~~~~~~~~~~~~GI~i~~~~~  333 (349)
T COG2055         311 GEREFAAREKRQKEGIPIDEDVW  333 (349)
T ss_pred             CCHHHHHHHHHHHCCCCCCHHHH
T ss_conf             82899999988734976689999


No 200
>PRK09130 NADH dehydrogenase subunit G; Validated
Probab=26.96  E-value=25  Score=15.13  Aligned_cols=15  Identities=7%  Similarity=-0.029  Sum_probs=9.1

Q ss_pred             HHHHHHHHHCCCCEE
Q ss_conf             999999997399788
Q gi|254780690|r  301 KKMRKIAYEHNIPIF  315 (354)
Q Consensus       301 ~~Ir~~A~~~~Vpiv  315 (354)
                      .=|+++|+..|.+.-
T Consensus       588 ~Il~~La~~lG~~~~  602 (680)
T PRK09130        588 AILRALSDVLGKKLP  602 (680)
T ss_pred             HHHHHHHHHHCCCCC
T ss_conf             999999998399999


No 201
>TIGR01520 FruBisAldo_II_A fructose-bisphosphate aldolase, class II; InterPro: IPR006411   Members of this family are class II examples of the glycolytic enzyme fructose-bisphosphate aldolase (FBA). They represent one of two deeply split, architecturally distinct clades of the family that includes class II fructose-bisphosphate aldolases, tagatose-bisphosphate aldolases, and related uncharacterised proteins. This family is well-conserved and includes characterised FBA from Saccharomyces cerevisiae, Escherichia coli, and Corynebacterium glutamicum.; GO: 0004332 fructose-bisphosphate aldolase activity, 0006096 glycolysis.
Probab=26.81  E-value=36  Score=13.91  Aligned_cols=23  Identities=22%  Similarity=0.313  Sum_probs=18.1

Q ss_pred             ECCCHHHHHHHHHHHHCCCCEEE
Q ss_conf             07658999999999973997886
Q gi|254780690|r  294 KGQNLIAKKMRKIAYEHNIPIFE  316 (354)
Q Consensus       294 KG~~~~A~~Ir~~A~~~~Vpive  316 (354)
                      +|+=-.|..||.+|...+||||+
T Consensus        86 ~GAIa~A~~~h~iA~~YGvPVvr  108 (365)
T TIGR01520        86 TGAIAAAHYVHSIAEHYGVPVVR  108 (365)
T ss_pred             HHHHHHHHHHHHHHHHCCCCEEE
T ss_conf             99888888999875327888277


No 202
>TIGR02617 tnaA_trp_ase tryptophanase; InterPro: IPR013440    Proteins in this entry belong to the beta-eliminating lyase family and are thought to act as tryptophanases (4.1.99.1 from EC) (also known as L-tryptophan indole-lyases). The genes encoding these proteins are, as a rule, found with a tryptophanase leader peptide TnaC (IPR013439 from INTERPRO) encoded upstream. ; GO: 0009034 tryptophanase activity, 0006568 tryptophan metabolic process.
Probab=26.42  E-value=40  Score=13.51  Aligned_cols=18  Identities=28%  Similarity=0.468  Sum_probs=13.1

Q ss_pred             HHHHHHHHHCCCCEEECH
Q ss_conf             999999997399788688
Q gi|254780690|r  301 KKMRKIAYEHNIPIFEEP  318 (354)
Q Consensus       301 ~~Ir~~A~~~~Vpive~~  318 (354)
                      ..+=+||++|+||||=|-
T Consensus       207 KAvY~IAk~yDIPVv~DS  224 (468)
T TIGR02617       207 KAVYEIAKKYDIPVVMDS  224 (468)
T ss_pred             HHHHHHHHHCCCCEEECC
T ss_conf             999999864599868623


No 203
>pfam03841 SelA L-seryl-tRNA selenium transferase.
Probab=26.18  E-value=41  Score=13.45  Aligned_cols=27  Identities=19%  Similarity=0.260  Sum_probs=18.2

Q ss_pred             CCCCCCH-HHHHHHCCCHHHHHHHHHHH
Q ss_conf             9101693-43033201266799999999
Q gi|254780690|r  126 SFKRVSL-REGIKRIYSINNLVNFMKSF  152 (354)
Q Consensus       126 k~~rlNP-i~GlKriFS~k~lvel~Ksl  152 (354)
                      |..+=|. +.||..--|.+-|++++|.-
T Consensus       142 kVH~SN~~i~GFt~~v~~~el~~la~~~  169 (367)
T pfam03841       142 KVHTSNYRIQGFTKEVSLAELVALGKEH  169 (367)
T ss_pred             EEECCCCEECCCCCCCCHHHHHHHHHHC
T ss_conf             9942651223746779999999999876


No 204
>pfam05661 DUF808 Protein of unknown function (DUF808). This family consists of several bacterial proteins of unknown function.
Probab=26.12  E-value=41  Score=13.45  Aligned_cols=33  Identities=18%  Similarity=0.197  Sum_probs=17.0

Q ss_pred             HHHHCCCHHHHHHHHHHHHHH-HHHHHHHHHHHHH
Q ss_conf             033201266799999999999-9999999999983
Q gi|254780690|r  135 GIKRIYSINNLVNFMKSFVKI-ILVGTIITISLTE  168 (354)
Q Consensus       135 GlKriFS~k~lvel~KsllKv-~li~~v~~~~i~~  168 (354)
                      ++.|-++ ++++...--++|. .++|.++-+..-+
T Consensus       209 ~~~~~~G-rgLV~~mP~lmk~LsvvGT~AMlwVGG  242 (293)
T pfam05661       209 ALARKLG-RGLLAAAPWLMKSLSVVGTAAMFLVGG  242 (293)
T ss_pred             HHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             3999999-899999999999999999999999454


No 205
>PRK12815 carB carbamoyl phosphate synthase large subunit; Reviewed
Probab=26.03  E-value=41  Score=13.44  Aligned_cols=30  Identities=27%  Similarity=0.402  Sum_probs=24.9

Q ss_pred             HHHHHHHHHHHCCCCEEECHHHHHHHHHHC
Q ss_conf             999999999973997886889999999728
Q gi|254780690|r  299 IAKKMRKIAYEHNIPIFEEPSLARSLFKQV  328 (354)
Q Consensus       299 ~A~~Ir~~A~~~~Vpive~~~LAR~Ly~~~  328 (354)
                      -..+||+.|-+++||.+-+...|+++-...
T Consensus      1019 D~~~IRr~Av~~~IP~~Ttl~~A~a~v~al 1048 (1068)
T PRK12815       1019 DAIKIRDEALTTHIPVFTSLETAQAFLDVL 1048 (1068)
T ss_pred             CHHHHHHHHHHHCCCEEECHHHHHHHHHHH
T ss_conf             439999999982998892799999999999


No 206
>cd00145 POLBc DNA polymerase type-B family catalytic domain. DNA-directed DNA polymerases elongate DNA by adding nucleotide triphosphate (dNTP) residues to the 5'-end of the growing chain of DNA. DNA-directed DNA polymerases are multifunctional with both synthetic (polymerase) and degradative modes (exonucleases) and play roles in the processes of DNA replication, repair, and recombination. DNA-dependent DNA polymerases can be classified in six main groups based upon their phylogenetic relationships with E. coli polymerase I (class A), E. coli polymerase II (class B), E. coli polymerase III (class C), euryarchaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB, and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y).  Family B DNA polymerases include E. coli DNA polymerase II, some eubacterial phage DNA polymerases, nuclear replicative DNA polymerases (alpha, delta, epsilon, and zeta), and eukaryotic viral and plasmid-borne enzymes. DNA polymerase is
Probab=25.86  E-value=42  Score=13.41  Aligned_cols=16  Identities=13%  Similarity=0.324  Sum_probs=10.7

Q ss_pred             CCCCEEEEECCCHHHH
Q ss_conf             8888899807658999
Q gi|254780690|r  286 NDAPVLVAKGQNLIAK  301 (354)
Q Consensus       286 ~~aP~vvaKG~~~~A~  301 (354)
                      +..|.|+.+|......
T Consensus       272 ~ri~yvi~~~~~~~~~  287 (323)
T cd00145         272 DKVKYVVTRGGKGVPD  287 (323)
T ss_pred             CEECEEEEECCCCCCH
T ss_conf             6307799928998565


No 207
>pfam12023 DUF3511 Domain of unknown function (DUF3511). This presumed domain is functionally uncharacterized. This domain is found in eukaryotes. This domain is about 50 amino acids in length. This domain has two completely conserved residues (Y and K) that may be functionally important.
Probab=25.83  E-value=37  Score=13.81  Aligned_cols=13  Identities=15%  Similarity=0.608  Sum_probs=9.0

Q ss_pred             CCCHHHHHHHHHH
Q ss_conf             8998999999999
Q gi|254780690|r  237 YGNPIIKNRQKSI  249 (354)
Q Consensus       237 EGdP~iK~~~r~~  249 (354)
                      -+|||+|.|+|-.
T Consensus         3 ~~DpE~kRkkRVA   15 (47)
T pfam12023         3 FSDPEMKRKKRVA   15 (47)
T ss_pred             CCCHHHHHHHHHH
T ss_conf             6778898898876


No 208
>pfam12226 Astro_capsid_p Turkey astrovirus capsid protein. This family of proteins is found in viruses. Proteins in this family are typically between 241 and 261 amino acids in length. These proteins are capsid proteins from various astrovirus strains.
Probab=25.78  E-value=23  Score=15.40  Aligned_cols=17  Identities=35%  Similarity=0.747  Sum_probs=12.1

Q ss_pred             HHHHHHHHHHCCCCHHH
Q ss_conf             89999997544899899
Q gi|254780690|r  226 KQEIKDEIKQSYGNPII  242 (354)
Q Consensus       226 kqEvK~E~K~~EGdP~i  242 (354)
                      -|++||-+|=.||||-|
T Consensus       113 d~~lK~RmnL~EgDPVi  129 (230)
T pfam12226       113 DQTLKDRLNLAEGDPVI  129 (230)
T ss_pred             HHHHHHHHCCCCCCCEE
T ss_conf             78999863333699656


No 209
>PRK11091 aerobic respiration control sensor protein ArcB; Provisional
Probab=25.73  E-value=42  Score=13.40  Aligned_cols=16  Identities=31%  Similarity=0.337  Sum_probs=8.6

Q ss_pred             HHHHHHHHHHHHHHHH
Q ss_conf             7999999999999999
Q gi|254780690|r  144 NLVNFMKSFVKIILVG  159 (354)
Q Consensus       144 ~lvel~KsllKv~li~  159 (354)
                      -+.+|+-+-+|+.==|
T Consensus       402 IL~NLlsNAIKFT~~G  417 (779)
T PRK11091        402 ILWNLISNAVKFTQQG  417 (779)
T ss_pred             HHHHHHHHHHHCCCCC
T ss_conf             9999999997738999


No 210
>pfam01956 DUF106 Integral membrane protein DUF106. This archaebacterial protein family has no known function. Members are predicted to be integral membrane proteins.
Probab=25.71  E-value=42  Score=13.39  Aligned_cols=23  Identities=9%  Similarity=0.153  Sum_probs=11.1

Q ss_pred             CCCCCHHHHHHHHHHCCCCCHHH
Q ss_conf             86658787999998578751335
Q gi|254780690|r   11 TEAPSSKKIEDALNEGNAPISRE   33 (354)
Q Consensus        11 TE~PT~kRL~dARekGqV~kS~e   33 (354)
                      .++-.++|-+++|+.|+..+.+.
T Consensus        48 ~~~~~~~~~~~l~~~~~~~~~~k   70 (168)
T pfam01956        48 RMKEIQKRARELRKNGDKLSPKK   70 (168)
T ss_pred             HHHHHHHHHHHHHHCCCCCCHHH
T ss_conf             99999999999987689557899


No 211
>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=25.49  E-value=42  Score=13.36  Aligned_cols=64  Identities=13%  Similarity=0.118  Sum_probs=42.1

Q ss_pred             HCCCCH-HHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHH
Q ss_conf             448998-9999999999999998898607768699873553078889768888888899807658999999
Q gi|254780690|r  235 QSYGNP-IIKNRQKSIARSRIRHKMMEATSRATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMR  304 (354)
Q Consensus       235 ~~EGdP-~iK~~~r~~~re~~~~~~~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir  304 (354)
                      |.++|- .--+..+++++|+.-=..|+.-.+=-|||||=      +++|-+.++.-.+.+-|--.+.-..|
T Consensus       119 e~~~d~nk~~~~~~~l~~Ql~~Ll~lArk~~~AVviTNQ------vy~d~~~gG~~~~~P~GG~~L~h~~K  183 (223)
T TIGR02237       119 ERSDDRNKQISLNRELARQLTLLLSLARKKDLAVVITNQ------VYTDVNNGGSETLRPLGGHLLEHWSK  183 (223)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEE------EEEEECCCCCCEEEECCCHHHHHHHC
T ss_conf             257860256799999999999999998764997899711------58863779732010033113431102


No 212
>PRK05575 cbiC precorrin-8X methylmutase; Validated
Probab=25.40  E-value=42  Score=13.35  Aligned_cols=82  Identities=15%  Similarity=0.155  Sum_probs=46.6

Q ss_pred             CCCHHHHHHHHHH--HHHHHHHHHHHHCCCCCEEEEC-CCCEEEEEEECCCCCCCC-EEEEECCCHH-HHHHHHHHHHCC
Q ss_conf             8998999999999--9999998898607768699873-553078889768888888-8998076589-999999999739
Q gi|254780690|r  237 YGNPIIKNRQKSI--ARSRIRHKMMEATSRATIIITN-PTHYALALRYIQTENDAP-VLVAKGQNLI-AKKMRKIAYEHN  311 (354)
Q Consensus       237 EGdP~iK~~~r~~--~re~~~~~~~~~V~~A~vvitN-PTH~AVAL~Y~~~~~~aP-~vvaKG~~~~-A~~Ir~~A~~~~  311 (354)
                      -+||.+...-|+.  -|.++.-+....-..+=|||-| ||-.-=-++.-.+...-| .|+.-=.|.+ |..=|+.-.+.+
T Consensus        98 i~d~~v~~~Ak~~g~TRs~aa~~~a~~~~~~IvvIGNAPTAL~~Lleli~~g~~~PalVIG~PVGFVgA~ESKe~L~~~~  177 (204)
T PRK05575         98 VSEEEVAKIAKEKGITRSMAAVEKAAEEGVEFFVFGNAPTALFKLKELIKEGKANPKFIIAVPVGFVGAAESKEELEKLD  177 (204)
T ss_pred             CCCCCHHHHHHHHCHHHHHHHHHHHHHCCCCEEEEECCHHHHHHHHHHHHCCCCCCCEEEECCCCCCCHHHHHHHHHHCC
T ss_conf             78964678877405359999999741318988999386899999999998589987579971886567399999998689


Q ss_pred             CCEEECH
Q ss_conf             9788688
Q gi|254780690|r  312 IPIFEEP  318 (354)
Q Consensus       312 Vpive~~  318 (354)
                      ||-+-+.
T Consensus       178 vP~It~~  184 (204)
T PRK05575        178 IPYITVR  184 (204)
T ss_pred             CCEEEEE
T ss_conf             9989982


No 213
>pfam07964 Red1 Rec10 / Red1. Rec10 / Red1 is involved in meiotic recombination and chromosome segregation during homologous chromosome formation. This protein localizes to the synaptonemal complex in S. cerevisiae and the analogous structures (linear elements) in S. pombe. This family is currently only found in fungi.
Probab=25.07  E-value=39  Score=13.62  Aligned_cols=21  Identities=19%  Similarity=0.460  Sum_probs=16.3

Q ss_pred             CCCCHHHHHHHHHHHHHHHHH
Q ss_conf             489989999999999999998
Q gi|254780690|r  236 SYGNPIIKNRQKSIARSRIRH  256 (354)
Q Consensus       236 ~EGdP~iK~~~r~~~re~~~~  256 (354)
                      -|-.|.+..+.|+++|+.++.
T Consensus       342 eeqSPlv~~QkrKl~R~~skt  362 (705)
T pfam07964       342 EEQSPLVRLQKRKLARSTSKT  362 (705)
T ss_pred             HHCCHHHHHHHHHHHHHHHHH
T ss_conf             104838999888888776666


No 214
>TIGR03239 GarL 2-dehydro-3-deoxyglucarate aldolase. In E. coli this enzyme (GarL, ) 2-dehydro-3-deoxyglucarate aldolase acts in the catabolism of several sugars including D-galactarate, D-glucarate and L-idarate. In fact, 5-dehydro-4-deoxy-D-glucarate aldolase is a synonym for this enzyme as it is unclear in the literature whether the enzyme acts on only one of these or, as seems likely, has no preference. (Despite the apparent large difference in substrate stucture indicated by their names, 2-DH-3DO- and 5-DH-4DO-glucarate differ only by the chirality of most central hydroxyl-bearing carbon and is alternately named 2-DH-3DO-galactarate.) The reported product of D-galactarate dehydratase (4.2.1.42) is the 5DH-4DO-glucarate isomer and this enzyme is found proximal to the aldolase in many genomes (GenProp0714) where no epimerase is known. Similarly, the product of D-glucarate dehydratase (4.2.1.40) is again the 5-DH-4DO isomer, so the provenance of the 2-DH-3DO-glucarate isomer for which
Probab=24.91  E-value=30  Score=14.51  Aligned_cols=63  Identities=19%  Similarity=0.162  Sum_probs=47.3

Q ss_pred             HHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCE---EECHHHHHHHH
Q ss_conf             8986077686998735530788897688888888998076589999999999739978---86889999999
Q gi|254780690|r  257 KMMEATSRATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPI---FEEPSLARSLF  325 (354)
Q Consensus       257 ~~~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpi---ve~~~LAR~Ly  325 (354)
                      .-..+||.=|+|...|..++..|-| ++....|.|.     ..-.++.+.+++||+|.   ..++.-|+.+-
T Consensus       155 deI~av~GvD~ifiGP~DLs~slG~-~g~~~~p~v~-----~ai~~v~~~~~~~gk~~Gi~~~~~~~~~~~~  220 (249)
T TIGR03239       155 DEIAAVDGVDGIFVGPSDLAAALGH-LGNPNHPDVQ-----KAIRHIFDRAAAHGKPCGILAPVEADARRYL  220 (249)
T ss_pred             HHHHCCCCCCEEEECHHHHHHHCCC-CCCCCCHHHH-----HHHHHHHHHHHHCCCCEEEECCCHHHHHHHH
T ss_conf             9996789988899884899987699-9999997999-----9999999999985996698279999999999


No 215
>PRK11316 bifunctional heptose 7-phosphate kinase/heptose 1-phosphate adenyltransferase; Provisional
Probab=24.84  E-value=43  Score=13.28  Aligned_cols=11  Identities=36%  Similarity=0.591  Sum_probs=4.6

Q ss_pred             CEEEEECCCHH
Q ss_conf             88998076589
Q gi|254780690|r  289 PVLVAKGQNLI  299 (354)
Q Consensus       289 P~vvaKG~~~~  299 (354)
                      |-|++||.|.-
T Consensus       426 pd~~~kg~dy~  436 (473)
T PRK11316        426 PDLLVKGGDYK  436 (473)
T ss_pred             CCEEEECCCCC
T ss_conf             98999888888


No 216
>COG1320 MnhG Multisubunit Na+/H+ antiporter, MnhG subunit [Inorganic ion transport and metabolism]
Probab=24.80  E-value=43  Score=13.27  Aligned_cols=37  Identities=19%  Similarity=0.232  Sum_probs=27.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCC
Q ss_conf             9999997667999999984069989999997544899
Q gi|254780690|r  203 IATLTVLDIGWSYHQWYSKLKMSKQEIKDEIKQSYGN  239 (354)
Q Consensus       203 ~~via~iD~~~qr~~~~k~lkMskqEvK~E~K~~EGd  239 (354)
                      ++.=-+.-...-|--|..+.++.++.+-|+|++.+|+
T Consensus        77 ~lt~Pv~ah~iarAay~~g~~~~~~~~~d~~~~~~~~  113 (113)
T COG1320          77 LLTAPVGAHAIARAAYLSGVPLWKRSVVDKYKEARGE  113 (113)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHCCC
T ss_conf             9980899999999998769983000107776542269


No 217
>PRK00124 hypothetical protein; Validated
Probab=24.76  E-value=43  Score=13.27  Aligned_cols=39  Identities=18%  Similarity=0.234  Sum_probs=35.7

Q ss_pred             CEEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHHHHHH
Q ss_conf             889980765899999999997399788688999999972
Q gi|254780690|r  289 PVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFKQ  327 (354)
Q Consensus       289 P~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~~  327 (354)
                      =++|..|.|..=..|-+.+++.++=|-+|.|||-.+-..
T Consensus        45 ~v~V~~g~DaAD~~I~~~~~~gDiVIT~DipLAa~~l~K   83 (149)
T PRK00124         45 TLYVDSGFDAADNEIVERAEKGDIVITQDYPLAAEALEK   83 (149)
T ss_pred             EEEECCCCCHHHHHHHHHCCCCCEEEECCHHHHHHHHHC
T ss_conf             999899976399999983889999996988999999987


No 218
>PRK12587 putative monovalent cation/H+ antiporter subunit G; Reviewed
Probab=24.73  E-value=43  Score=13.26  Aligned_cols=32  Identities=16%  Similarity=0.088  Sum_probs=23.6

Q ss_pred             HHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCC
Q ss_conf             97667999999984069989999997544899
Q gi|254780690|r  208 VLDIGWSYHQWYSKLKMSKQEIKDEIKQSYGN  239 (354)
Q Consensus       208 ~iD~~~qr~~~~k~lkMskqEvK~E~K~~EGd  239 (354)
                      +.--..-|--|..+.++.+.-+.||+||...|
T Consensus        84 vaaH~iaRAAy~~gv~~~~~t~~DeL~e~lk~  115 (118)
T PRK12587         84 LSSHMIMKAAYNIKTPYTKKTKVDEISEDLKD  115 (118)
T ss_pred             HHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHC
T ss_conf             99999999999809999777531678998852


No 219
>cd01701 Pol_zeta Pol_zeta, a member of the Y-family of DNA polymerases. Y-family polymerases can transverse normal replication-blocking DNA lesions, such as cyclobutane pyrimidine dimers resulting from UV damage, at higher error rate. The Y-family has no 3'-5' exonuclease activity. Pol zeta has also been named Rev1; this subfamily is mainly present in eukaryotes.
Probab=24.70  E-value=38  Score=13.73  Aligned_cols=33  Identities=6%  Similarity=-0.080  Sum_probs=20.9

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEE
Q ss_conf             489989999999999999998898607768699
Q gi|254780690|r  236 SYGNPIIKNRQKSIARSRIRHKMMEATSRATII  268 (354)
Q Consensus       236 ~EGdP~iK~~~r~~~re~~~~~~~~~V~~A~vv  268 (354)
                      .+...+++...+++..+.+.+--..++...+|.
T Consensus       303 ~~~~~ei~~~l~~la~~v~~rLr~~~~~~~tVt  335 (405)
T cd01701         303 FTTVEDVEQFLRRLSQEVCRRLEEIGVKGRQIT  335 (405)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHCCCEEEEEE
T ss_conf             899999999999999999999998498152899


No 220
>TIGR01326 OAH_OAS_sulfhy O-acetylhomoserine aminocarboxypropyltransferase/cysteine synthase; InterPro: IPR006235   This family of sequences is a distinct clade of the Cys/Met metabolism pyridoxal phosphate-dependent enzyme superfamily. Members include examples of OAH/OAS sulfhydrylase, an enzyme with activity both as O-acetylhomoserine sulfhydrylase (OAH, 2.5.1.49 from EC) and O-acetylserine sulfhydrylase (OAS, 2.5.1.47 from EC). An alternate name for OAH sulfhydrylase is homocysteine synthase.; GO: 0016765 transferase activity transferring alkyl or aryl (other than methyl) groups, 0006520 amino acid metabolic process.
Probab=24.63  E-value=44  Score=13.25  Aligned_cols=16  Identities=19%  Similarity=0.559  Sum_probs=7.2

Q ss_pred             HHHHHHHHC--CCCEEEC
Q ss_conf             999999973--9978868
Q gi|254780690|r  302 KMRKIAYEH--NIPIFEE  317 (354)
Q Consensus       302 ~Ir~~A~~~--~Vpive~  317 (354)
                      +|=++|++|  +||+|-|
T Consensus       164 ~~a~~Ah~~PhgvPliVD  181 (434)
T TIGR01326       164 AVAEVAHAHPHGVPLIVD  181 (434)
T ss_pred             HHHHHHHHCCCCCEEEEE
T ss_conf             999999867898348874


No 221
>COG5337 CotH Spore coat assembly protein [Cell envelope biogenesis, outer membrane]
Probab=24.63  E-value=38  Score=13.75  Aligned_cols=111  Identities=14%  Similarity=0.150  Sum_probs=61.4

Q ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCEEEEEEECC-----
Q ss_conf             766799999998406998999999754489989999999999999998898607768699873553078889768-----
Q gi|254780690|r  209 LDIGWSYHQWYSKLKMSKQEIKDEIKQSYGNPIIKNRQKSIARSRIRHKMMEATSRATIIITNPTHYALALRYIQ-----  283 (354)
Q Consensus       209 iD~~~qr~~~~k~lkMskqEvK~E~K~~EGdP~iK~~~r~~~re~~~~~~~~~V~~A~vvitNPTH~AVAL~Y~~-----  283 (354)
                      +|.+=|...|.-+|-|++++.++=-++-+-|                 . ..+--+|+++|-.-|---|.+||..     
T Consensus        47 vdifd~S~~h~~ql~v~~kdl~el~ady~ed-----------------g-~k~~vka~~~Idgvti~dVgIrlkGq~~~q  108 (473)
T COG5337          47 VDIFDQSNLHLYQLFVHPKDLRELKADYWED-----------------G-SKDPVKAVMKIDGVTILDVGIRLKGQSHIQ  108 (473)
T ss_pred             EEECCCCCCEEEEEECCHHHHHHHHHHHHHC-----------------C-CCCCEEEEEEECCEEEEEEEEEECCHHHHH
T ss_conf             1003566650157853888899999888750-----------------5-767502479985589865025761555677


Q ss_pred             ---------CCCCCCEEEE--ECC-CHHHHHHHHHHHHCCCCEEECHHHHHHHHHHCCCCCCCCHHHHH
Q ss_conf             ---------8888888998--076-58999999999973997886889999999728898948989999
Q gi|254780690|r  284 ---------TENDAPVLVA--KGQ-NLIAKKMRKIAYEHNIPIFEEPSLARSLFKQVPINSAIPPVFYK  340 (354)
Q Consensus       284 ---------~~~~aP~vva--KG~-~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~~~~ig~~Ip~~~y~  340 (354)
                               +.+.-|.++.  |-. +..++.|-+.|..-| |-+-+-+||  ||...+.|+-.|..-|.
T Consensus       109 ~~~k~ss~id~~~~p~lisFdky~dgr~yrgit~lA~r~g-~sl~~e~la--L~~~se~G~vsp~~sfa  174 (473)
T COG5337         109 DFKKKSSHIDVSTWPLLISFDKYKDGRGYRGITLLAERKG-PSLMREKLA--LDFFSELGTVSPKASFA  174 (473)
T ss_pred             HHHCCCCCCCCCCCCCEEEECCCCCCCCHHHHHHHHCCCC-CHHHHHHHH--HHHHHHHCCCCCCCEEE
T ss_conf             7644662001124410464134345641233667640578-267632577--89998745666653268


No 222
>cd07644 I-BAR_IMD_BAIAP2L2 Inverse (I)-BAR, also known as the IRSp53/MIM homology Domain (IMD), of Brain-specific Angiogenesis Inhibitor 1-Associated Protein 2-Like 2. The IMD domain, also called Inverse-Bin/Amphiphysin/Rvs (I-BAR) domain, is a dimerization and lipid-binding module that bends membranes and induces membrane protrusions. This group is composed of uncharacterized proteins known as BAIAP2L2 (Brain-specific Angiogenesis Inhibitor 1-Associated Protein 2-Like 2). They contain an N-terminal IMD, an SH3 domain, and a WASP homology 2 (WH2) actin-binding motif at the C-terminus. The related proteins, BAIAP2L1 and IRSp53, function as regulators of membrane dynamics and the actin cytoskeleton. The IMD domain binds and bundles actin filaments, binds membranes and produces membrane protrusions, and interacts with the small GTPase Rac.
Probab=24.46  E-value=44  Score=13.22  Aligned_cols=26  Identities=12%  Similarity=0.295  Sum_probs=19.6

Q ss_pred             CCCCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             1016934303320126679999999999999999
Q gi|254780690|r  127 FKRVSLREGIKRIYSINNLVNFMKSFVKIILVGT  160 (354)
Q Consensus       127 ~~rlNPi~GlKriFS~k~lvel~KsllKv~li~~  160 (354)
                      ++++||        ++++|+.++|+-.|..--..
T Consensus        15 meqFNP--------gLRnLV~lGk~YeKAl~a~s   40 (215)
T cd07644          15 MEQFNP--------ALENLVYLGNNYLRAFHALS   40 (215)
T ss_pred             HHHCCH--------HHHHHHHHHHHHHHHHHHHH
T ss_conf             986498--------89999998378999999999


No 223
>COG3977 Alanine-alpha-ketoisovalerate (or valine-pyruvate) aminotransferase [Amino acid transport and metabolism]
Probab=24.18  E-value=44  Score=13.19  Aligned_cols=19  Identities=21%  Similarity=0.672  Sum_probs=11.8

Q ss_pred             HHHHHHHCCCHHHHHHHHH
Q ss_conf             9999840699899999975
Q gi|254780690|r  216 HQWYSKLKMSKQEIKDEIK  234 (354)
Q Consensus       216 ~~~~k~lkMskqEvK~E~K  234 (354)
                      |.|.++|--|-+|.-++.|
T Consensus       342 WLWf~dLPItt~~LYq~LK  360 (417)
T COG3977         342 WLWFKDLPITTEELYQRLK  360 (417)
T ss_pred             HHHHCCCCCCHHHHHHHHH
T ss_conf             3355358766899999998


No 224
>pfam03342 Rhabdo_M1 Rhabdovirus M1 matrix protein (M1 polymerase-associated protein).
Probab=24.11  E-value=43  Score=13.31  Aligned_cols=14  Identities=21%  Similarity=0.081  Sum_probs=6.7

Q ss_pred             HHHHHHHHHHHHHH
Q ss_conf             99887768785321
Q gi|254780690|r  102 FMMFGIGSYLIQRI  115 (354)
Q Consensus       102 ~~l~~i~~~l~q~G  115 (354)
                      .+++++-+++.-.+
T Consensus       127 s~lIaiR~~~~En~  140 (219)
T pfam03342       127 SALIAIRSNLNENG  140 (219)
T ss_pred             HHHHHHHHHHCCCC
T ss_conf             99999986431037


No 225
>PRK09195 gatY tagatose-bisphosphate aldolase; Reviewed
Probab=24.07  E-value=45  Score=13.17  Aligned_cols=61  Identities=10%  Similarity=0.168  Sum_probs=25.0

Q ss_pred             CCCEEEEECCCHHHHHHHHHHHHCCCCEEE-CHHHHHHHHHH------CCCCCCCCHHHHHHHHHHHHH
Q ss_conf             888899807658999999999973997886-88999999972------889894898999999999999
Q gi|254780690|r  287 DAPVLVAKGQNLIAKKMRKIAYEHNIPIFE-EPSLARSLFKQ------VPINSAIPPVFYKAVAQLIYK  348 (354)
Q Consensus       287 ~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive-~~~LAR~Ly~~------~~ig~~Ip~~~y~aVA~il~~  348 (354)
                      +.|.|+==|.|.--..|++ |-++||-=|- +-.|-++-...      -.-+.+=|..+.+..-+-+..
T Consensus       202 ~vPLVLHGgSG~~~e~i~~-ai~~Gv~KiNi~T~l~~a~~~~~r~~l~~~p~~~dp~~~~~~~~~a~~~  269 (284)
T PRK09195        202 NIPLVLHGASGLPTKDIQQ-TIKLGICKVNVATELKIAFSQALKNYLTEHPEANDPRHYLQPAKAAMKD  269 (284)
T ss_pred             CCCEEEECCCCCCHHHHHH-HHHCCCEEEEECHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHH
T ss_conf             9998987899989999999-9984976998685899999999999998687968869999999999999


No 226
>pfam00606 Glycoprotein_B Herpesvirus Glycoprotein B. This family of proteins contains a transmembrane region.
Probab=23.96  E-value=45  Score=13.16  Aligned_cols=23  Identities=13%  Similarity=0.325  Sum_probs=16.4

Q ss_pred             HHHHHHHCCCHHHHHHHHHHHHHHH
Q ss_conf             3430332012667999999999999
Q gi|254780690|r  132 LREGIKRIYSINNLVNFMKSFVKII  156 (354)
Q Consensus       132 Pi~GlKriFS~k~lvel~KsllKv~  156 (354)
                      -+.|+..+|  ++|-..+|++.+++
T Consensus       621 ~~~gl~~~~--~~LG~vGk~vg~vv  643 (711)
T pfam00606       621 FVRGLDDFF--QGLGAVGKAVGNVV  643 (711)
T ss_pred             HHHHHHHHH--HHHHHHCHHHEEHH
T ss_conf             999899998--65424243010024


No 227
>pfam06305 DUF1049 Protein of unknown function (DUF1049). This family consists of several hypothetical bacterial proteins of unknown function.
Probab=23.89  E-value=45  Score=13.15  Aligned_cols=33  Identities=21%  Similarity=0.033  Sum_probs=15.2

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCC
Q ss_conf             999976679999999840699899999975448
Q gi|254780690|r  205 TLTVLDIGWSYHQWYSKLKMSKQEIKDEIKQSY  237 (354)
Q Consensus       205 via~iD~~~qr~~~~k~lkMskqEvK~E~K~~E  237 (354)
                      +++.+-....++++..+.|=-++++|+-.||.|
T Consensus        45 ~lg~L~~~~~~l~~r~~~r~l~k~lk~l~~e~~   77 (80)
T pfam06305        45 LLGWLISLPFYLRLRRRLRRLKKQLKKLEKELE   77 (80)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999999999999999999988


No 228
>cd01123 Rad51_DMC1_radA Rad51_DMC1_radA,B. This group of recombinases includes the eukaryotic proteins RAD51, RAD55/57 and the meiosis-specific protein DMC1, and the archaeal proteins radA and radB. They are closely related to the bacterial RecA group. Rad51 proteins catalyze a similiar recombination reaction as RecA, using ATP-dependent DNA binding activity and a DNA-dependent ATPase. However, this reaction is less efficient and requires accessory proteins such as RAD55/57 .
Probab=23.76  E-value=45  Score=13.13  Aligned_cols=37  Identities=22%  Similarity=0.240  Sum_probs=24.5

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECC
Q ss_conf             4899899999999999999988986077686998735
Q gi|254780690|r  236 SYGNPIIKNRQKSIARSRIRHKMMEATSRATIIITNP  272 (354)
Q Consensus       236 ~EGdP~iK~~~r~~~re~~~~~~~~~V~~A~vvitNP  272 (354)
                      ..|+.....|.+++.+.+..-+-.+.-.+..||+||=
T Consensus       132 ~~~~~~~~~r~~~l~~~~~~L~~lA~~~~~aVvvtNq  168 (235)
T cd01123         132 FDGRGELAERQQHLAKLLRTLKRLADEFNVAVVITNQ  168 (235)
T ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHHHCCCEEEEECE
T ss_conf             4488644789999999999999999980979999680


No 229
>cd06452 SepCysS Sep-tRNA:Cys-tRNA synthase. This family belongs to the pyridoxal phosphate (PLP)-dependent aspartate aminotransferase superfamily (fold I). Cys-tRNA(Cys) is produced by O-phosphoseryl-tRNA synthetase which ligates O-phosphoserine (Sep) to tRNA(Cys), and Sep-tRNA:Cys-tRNA synthase (SepCysS) converts Sep-tRNA(Cys) to Cys-tRNA(Cys), in methanogenic archaea. SepCysS forms a dimer, each monomer is composed of a large and small domain; the larger, a typical pyridoxal 5'-phosphate (PLP)-dependent-like enzyme fold.  In the active site of each monomer, PLP is covalently bound to a conserved Lys residue near the dimer interface.
Probab=23.67  E-value=45  Score=13.12  Aligned_cols=57  Identities=14%  Similarity=0.032  Sum_probs=25.0

Q ss_pred             CCEEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHHHHHHCCCCC-CCCHHHHHHHHHHHHHH
Q ss_conf             888998076589999999999739978868899999997288989-48989999999999999
Q gi|254780690|r  288 APVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFKQVPINS-AIPPVFYKAVAQLIYKI  349 (354)
Q Consensus       288 aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~~~~ig~-~Ip~~~y~aVA~il~~v  349 (354)
                      .--.+||..+......-++=++.||-+ +.+.+-+.    ..+.. -+..|-.+.|++.|..|
T Consensus       302 ~~~~~~~~~~~~G~~L~~~L~~rgI~~-~~~g~t~~----~~~~tyG~t~e~i~~l~~a~keI  359 (361)
T cd06452         302 SFDEIAKKHKRRGYFLYSELKKRGIHG-IKPGLTRY----FKLSTYGLTWEQVEYVVDAFKEI  359 (361)
T ss_pred             CCEEEEECCCCCCCHHHHHHHHCCCEE-ECCCCCCE----EEEEEECCCHHHHHHHHHHHHHH
T ss_conf             632441047865006999998769768-71685337----99999516888999999999997


No 230
>PRK09554 feoB ferrous iron transport protein B; Reviewed
Probab=23.65  E-value=45  Score=13.11  Aligned_cols=35  Identities=6%  Similarity=0.170  Sum_probs=14.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999999976679999
Q gi|254780690|r  182 HSILYHAFFTVRKVLIMILLFIATLTVLDIGWSYH  216 (354)
Q Consensus       182 ~~~l~~~~~~~~~l~~~~~~~~~via~iD~~~qr~  216 (354)
                      ...+..+..-....+....-+.+.++++=++.+.+
T Consensus       498 k~vl~~~w~r~k~Fl~kAGtiI~~~siviw~L~~f  532 (772)
T PRK09554        498 KSLIIQTWQRLKGFVLRAGKVIIIVSIFLSAFNSF  532 (772)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             99999999999999981004330399899887407


No 231
>PRK10506 hypothetical protein; Provisional
Probab=23.61  E-value=45  Score=13.11  Aligned_cols=40  Identities=23%  Similarity=0.374  Sum_probs=27.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHH
Q ss_conf             9999999999999999999766799999998406998999
Q gi|254780690|r  190 FTVRKVLIMILLFIATLTVLDIGWSYHQWYSKLKMSKQEI  229 (354)
Q Consensus       190 ~~~~~l~~~~~~~~~via~iD~~~qr~~~~k~lkMskqEv  229 (354)
                      +++..++..+.++.++.+..=+.||.|....+|.=+-+++
T Consensus         7 FTLiEllvvi~ii~il~~~a~p~~~~~~q~~~L~~~a~~l   46 (155)
T PRK10506          7 YTLIETLVAMTLVVILSAWGLYGWQYWQQQQRLWQTAQQL   46 (155)
T ss_pred             EEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             2799999999999999988777799999999999999999


No 232
>PRK13601 putative ribosomal protein L7Ae-like; Provisional
Probab=23.40  E-value=46  Score=13.08  Aligned_cols=43  Identities=23%  Similarity=0.254  Sum_probs=29.6

Q ss_pred             CCCCEEEEECCCH-HHHHHHHHHHHCCCCEEECHHHHHHHHHHCC
Q ss_conf             8888899807658-9999999999739978868899999997288
Q gi|254780690|r  286 NDAPVLVAKGQNL-IAKKMRKIAYEHNIPIFEEPSLARSLFKQVP  329 (354)
Q Consensus       286 ~~aP~vvaKG~~~-~A~~Ir~~A~~~~Vpive~~~LAR~Ly~~~~  329 (354)
                      ...-+.+||-.|. +-..|++.+++++|||+.-.... .|-+.|-
T Consensus        25 ~a~~V~vA~DAD~~v~~~v~~lc~e~~VpV~~VdsMk-eLGkaCG   68 (84)
T PRK13601         25 NVLQVYIAKDAEEHVTKKIKELCEEKSIKIVYVDTMK-ELGVMCG   68 (84)
T ss_pred             CCCEEEEEECCCHHHHHHHHHHHHHCCCCEEEECCHH-HHHHHCC
T ss_conf             8338999816868899999999997399869845599-8851609


No 233
>TIGR02317 prpB methylisocitrate lyase; InterPro: IPR012695   Propionate is the second most abundant low molecular mass carbon source found in soil, being generated by the degradation of several amino acids, fementation of crabohydrates and the oxidation of odd-chain fatty acids. Many different organisms are capable of metabolising propionate and several distinct pathways for utilising this compound exist, all of which begin with its activation to propionyl-CoA . Many bacteria metabolise propionate to pyruvate by the 2-methylcitric acid cycle. In the first step, catalysed by methycitrate synthase, oxaloacetate and propionyl-CoA are condensed to form 2-methylcitrate and CoA. The 2-methylcitrate is subsequently converted to 2-methylisocitrate by the combined actions of a dehydratase and an aconitase. In the final step, 2-methylisocitrate lyase cleaves a C-C bond within this compound to form succinate and pyruvate. The succinate is further oxidised to oxaloacetate which re-enters the cycle, while the pyruvate can be used further for either energy generation or biomass synthesis.   Proteins in this entry are mostly 2-methylisocitrate lyases. Some of them have been annotated (incorrectly it seems) as the related protein carboxyphosphoenolpyruvate phosphomutase, which is involved in synthesizing the antibiotic bialaphos in Streptomyces hygroscopicus. Structural studies indicate that these enzymes belong to the isocitrate lyase family, binding a Mg(2+) cofactor and forming a TIM barrel fold , . As with other enzymes in this family, substrate-binding induces a conformational change that prevents solvent access to the active site and which is important for catalysis.  .
Probab=23.39  E-value=46  Score=13.08  Aligned_cols=18  Identities=11%  Similarity=0.176  Sum_probs=9.7

Q ss_pred             HHHHHHHHHHCCCCCHHH
Q ss_conf             787999998578751335
Q gi|254780690|r   16 SKKIEDALNEGNAPISRE   33 (354)
Q Consensus        16 ~kRL~dARekGqV~kS~e   33 (354)
                      .+++|++=+++++.+-.=
T Consensus         2 g~~fR~a~~~~~ilq~pG   19 (287)
T TIGR02317         2 GKRFREAIAKEDILQIPG   19 (287)
T ss_pred             CHHHHHHHHCCCCEEECC
T ss_conf             310599985689748714


No 234
>cd00946 FBP_aldolase_IIA Class II Type A, Fructose-1,6-bisphosphate (FBP) aldolases. The enzyme catalyses the zinc-dependent, reversible aldol condensation of dihydroxyacetone phosphate with glyceraldehyde-3-phosphate to form fructose-1,6-bisphosphate. FBP aldolase is homodimeric and used in gluconeogenesis and glycolysis. The type A and type B Class II FBPA's differ in the presence and absence of distinct indels in the sequence that result in differing loop lengths in the structures.
Probab=23.23  E-value=46  Score=13.05  Aligned_cols=29  Identities=10%  Similarity=0.137  Sum_probs=15.7

Q ss_pred             CCCCEEEEECCCHHHHHHHHHHHHCCCCEE
Q ss_conf             888889980765899999999997399788
Q gi|254780690|r  286 NDAPVLVAKGQNLIAKKMRKIAYEHNIPIF  315 (354)
Q Consensus       286 ~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpiv  315 (354)
                      .|.|.|+-=|.|---..|++ |-++||-=|
T Consensus       244 ~pipLVLHGgSGvp~e~i~~-AI~~GV~KI  272 (345)
T cd00946         244 KPLYFVFHGGSGSTKEEIRE-AISYGVVKM  272 (345)
T ss_pred             CCCEEEECCCCCCCHHHHHH-HHHCCCEEC
T ss_conf             87307851899999999999-998395633


No 235
>cd05533 POLBc_delta DNA polymerase type-B delta subfamily catalytic domain. Three DNA-dependent DNA polymerases type B (alpha, delta, and epsilon) have been identified as essential for nuclear DNA replication in eukaryotes. Presently, no direct data is available regarding the strand specificity of DNA polymerase during DNA replication in vivo. However, mutation analysis supports the hypothesis that DNA polymerase delta is the enzyme responsible for both elongation and maturation of Okazaki fragments on the lagging strand.
Probab=22.91  E-value=47  Score=13.01  Aligned_cols=54  Identities=15%  Similarity=0.169  Sum_probs=24.3

Q ss_pred             CCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             8888899807658999999999973997886889999999728898948989999999999999
Q gi|254780690|r  286 NDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLFKQVPINSAIPPVFYKAVAQLIYKI  349 (354)
Q Consensus       286 ~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly~~~~ig~~Ip~~~y~aVA~il~~v  349 (354)
                      +..|.|++||.....+  .+.|        |+|.-+..=-...+..-||-.++..+|-+|+.-|
T Consensus       339 ~rI~YViv~~~~~~~~--~~ra--------e~p~~~~~~~~~iD~~YYi~kQi~~pv~ri~epI  392 (393)
T cd05533         339 DRVPYVIIKGAKGAKA--YEKA--------EDPIYVLENNIPIDTQYYLENQLSKPLLRIFEPI  392 (393)
T ss_pred             CEEEEEEEECCCCCCH--HHHC--------CCHHHHHHCCCCCCHHHHHHHCCHHHHHHHHHHH
T ss_conf             9878999979987630--5542--------6878897569998769999835687999998752


No 236
>pfam10785 NADH-u_ox-rdase NADH-ubiquinone oxidoreductase 21 kDa subunit. This family is conserved in the fungal Dikarya. The members are annotated as putative NADH-ubiquinone oxidoreductase 21 kDa subunits, but this could not be confirmed.
Probab=22.75  E-value=28  Score=14.75  Aligned_cols=53  Identities=8%  Similarity=0.083  Sum_probs=30.0

Q ss_pred             HHHHHHHHHHHHH--------HHHHHHHCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             9999997667999--------99998406998999999754489989999999999999998
Q gi|254780690|r  203 IATLTVLDIGWSY--------HQWYSKLKMSKQEIKDEIKQSYGNPIIKNRQKSIARSRIRH  256 (354)
Q Consensus       203 ~~via~iD~~~qr--------~~~~k~lkMskqEvK~E~K~~EGdP~iK~~~r~~~re~~~~  256 (354)
                      +.+++.+-+.|||        .+..++-+|...|++|--|+-|-... +|+.-..++.++.+
T Consensus        51 iG~~GGF~~~YqrS~~RF~G~~EN~REv~mD~~Em~~kvk~g~~lYg-~S~l~~~lQgvAaR  111 (148)
T pfam10785        51 LGLFGGFLLAYQRSSFRFYGWRENSREVEMDMREMVDKVKKGEPLYG-ESQLDPYLQGVAAR  111 (148)
T ss_pred             HHHHCHHEEEEECCCHHHCCCCCCHHHHHHHHHHHHHHHHCCCCCCC-CCCCCHHHHHHHHH
T ss_conf             51102200111201212137654769998679999987506999988-56599889888874


No 237
>COG1929 Glycerate kinase [Carbohydrate transport and metabolism]
Probab=22.69  E-value=34  Score=14.13  Aligned_cols=44  Identities=18%  Similarity=0.357  Sum_probs=29.0

Q ss_pred             HHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEE
Q ss_conf             98607768699873553078889768888888899807658999999999973997886
Q gi|254780690|r  258 MMEATSRATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFE  316 (354)
Q Consensus       258 ~~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive  316 (354)
                      .-..|++||.|||.--.+    .+..-...+|+           .+-+.|+++++|++-
T Consensus       278 le~~v~daDLVITGEGr~----D~Qs~~GK~pi-----------gVA~~Akk~~vPvIa  321 (378)
T COG1929         278 LEDAVKDADLVITGEGRI----DSQSLHGKTPI-----------GVAKLAKKYGVPVIA  321 (378)
T ss_pred             HHHHHCCCCEEEECCCCC----CCCCCCCCCCH-----------HHHHHHHHHCCCEEE
T ss_conf             997616698899678765----21013786116-----------999751661898899


No 238
>COG5384 Mpp10 U3 small nucleolar ribonucleoprotein component [Translation, ribosomal structure and biogenesis]
Probab=22.56  E-value=47  Score=12.96  Aligned_cols=16  Identities=38%  Similarity=0.470  Sum_probs=10.9

Q ss_pred             HHHCCCHHHHHHHHHH
Q ss_conf             8406998999999754
Q gi|254780690|r  220 SKLKMSKQEIKDEIKQ  235 (354)
Q Consensus       220 k~lkMskqEvK~E~K~  235 (354)
                      ...-||++|+-+|.|+
T Consensus       488 ~GvAmS~~El~~e~K~  503 (569)
T COG5384         488 NGVAMSKEELTREDKN  503 (569)
T ss_pred             CCCCCCHHHHHHHHHH
T ss_conf             4412046653478899


No 239
>COG0410 LivF ABC-type branched-chain amino acid transport systems, ATPase component [Amino acid transport and metabolism]
Probab=22.55  E-value=16  Score=16.67  Aligned_cols=104  Identities=19%  Similarity=0.240  Sum_probs=66.7

Q ss_pred             HHHHHHHHHHCCCHHHHHHHHHHCCCC--------HHHHHHHHHHHHHHHHH-HHHHHCCCCCEEEECCCCEEEEEEECC
Q ss_conf             999999984069989999997544899--------89999999999999998-898607768699873553078889768
Q gi|254780690|r  213 WSYHQWYSKLKMSKQEIKDEIKQSYGN--------PIIKNRQKSIARSRIRH-KMMEATSRATIIITNPTHYALALRYIQ  283 (354)
Q Consensus       213 ~qr~~~~k~lkMskqEvK~E~K~~EGd--------P~iK~~~r~~~re~~~~-~~~~~V~~A~vvitNPTH~AVAL~Y~~  283 (354)
                      |.+..-.++|.|--.-.++ .+..+.|        |.+|.|++|+.-.++-+ +-|-++  |-..+++|-   +=|==+|
T Consensus        90 F~~LTVeENL~~g~~~~~~-~~~~~~~~e~v~~lFP~Lker~~~~aG~LSGGEQQMLAi--aRALm~~Pk---lLLLDEP  163 (237)
T COG0410          90 FPRLTVEENLLLGAYARRD-KEAQERDLEEVYELFPRLKERRNQRAGTLSGGEQQMLAI--ARALMSRPK---LLLLDEP  163 (237)
T ss_pred             HHHCCHHHHHHHHHHCCCC-CCCCCCCHHHHHHHCHHHHHHHHCCCCCCCHHHHHHHHH--HHHHHCCCC---EEEECCC
T ss_conf             0007599987423102453-100011389999978638988408446778199999999--999961998---8996588


Q ss_pred             CCCCCCEEEEECCCHHHHHHHHHHHHCCCCEE---ECHHHHHHHHH
Q ss_conf             88888889980765899999999997399788---68899999997
Q gi|254780690|r  284 TENDAPVLVAKGQNLIAKKMRKIAYEHNIPIF---EEPSLARSLFK  326 (354)
Q Consensus       284 ~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpiv---e~~~LAR~Ly~  326 (354)
                      ...-+|.+|    .++-..|+++.++.++.|+   +|...|..+-.
T Consensus       164 s~GLaP~iv----~~I~~~i~~l~~~~g~tIlLVEQn~~~Al~iaD  205 (237)
T COG0410         164 SEGLAPKIV----EEIFEAIKELRKEGGMTILLVEQNARFALEIAD  205 (237)
T ss_pred             CCCCCHHHH----HHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHC
T ss_conf             667688999----999999999997489489999425889987408


No 240
>pfam02064 MAS20 MAS20 protein import receptor.
Probab=22.49  E-value=48  Score=12.95  Aligned_cols=17  Identities=18%  Similarity=0.305  Sum_probs=10.9

Q ss_pred             CCCCHHHHHHHHHHHHH
Q ss_conf             94898999999999999
Q gi|254780690|r  332 SAIPPVFYKAVAQLIYK  348 (354)
Q Consensus       332 ~~Ip~~~y~aVA~il~~  348 (354)
                      ..+|++-|+-+++-++.
T Consensus       136 ~TVP~~V~e~Lv~mIAi  152 (184)
T pfam02064       136 KSIAEAILDIIAEMIAI  152 (184)
T ss_pred             HCCCHHHHHHHHHHHCC
T ss_conf             11888999999999812


No 241
>KOG0140 consensus
Probab=22.44  E-value=48  Score=12.94  Aligned_cols=84  Identities=17%  Similarity=0.232  Sum_probs=64.9

Q ss_pred             HCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHC-------CCCEEEC-------------HHH
Q ss_conf             07768699873553078889768888888899807658999999999973-------9978868-------------899
Q gi|254780690|r  261 ATSRATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEH-------NIPIFEE-------------PSL  320 (354)
Q Consensus       261 ~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~-------~Vpive~-------------~~L  320 (354)
                      .||++.|+...-.-|-||.+==   +.--..||-|.=-+|.|-.++|.+|       |.|+..+             -.|
T Consensus       243 rVP~~Nvlg~~G~GFkvAm~~f---d~tRp~vAa~alG~A~r~ld~a~ky~~eRK~FG~~iA~hQ~vqF~LAdMA~~le~  319 (408)
T KOG0140         243 RVPKENVLGAPGAGFKVAMGGF---DKTRPNVAAGALGLAQRCLDEATKYALERKAFGTPIANHQAVQFMLADMAINLEL  319 (408)
T ss_pred             CCCHHCCCCCCCCCCEEHHHHC---CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             5530011268986401002122---5888751445467889999999999998987486702104578779999878999


Q ss_pred             HHHHHHH--CCCCCCCCHHHHHHHHHHHH
Q ss_conf             9999972--88989489899999999999
Q gi|254780690|r  321 ARSLFKQ--VPINSAIPPVFYKAVAQLIY  347 (354)
Q Consensus       321 AR~Ly~~--~~ig~~Ip~~~y~aVA~il~  347 (354)
                      ||..+++  .|+++.-|..+|.++|+..+
T Consensus       320 aRL~~~~aa~evd~~r~~sy~aSiAK~fA  348 (408)
T KOG0140         320 ARLMTRNAAWEVDNGRRNSYYASIAKLFA  348 (408)
T ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHHHHH
T ss_conf             99999988998626886127899999875


No 242
>PRK00404 tatB sec-independent translocase; Provisional
Probab=22.33  E-value=48  Score=12.93  Aligned_cols=31  Identities=29%  Similarity=0.512  Sum_probs=15.5

Q ss_pred             HHHHHHCCCHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf             9998406998999999754489989999999
Q gi|254780690|r  217 QWYSKLKMSKQEIKDEIKQSYGNPIIKNRQK  247 (354)
Q Consensus       217 ~~~k~lkMskqEvK~E~K~~EGdP~iK~~~r  247 (354)
                      +|..++|=+-+++|+|.-+-=|--++|.+.+
T Consensus        34 ~~~g~~rr~~~~~k~e~~~E~~~~elr~~l~   64 (141)
T PRK00404         34 LWIGRLKRSFNAIKQEVEREIGADEIRRQLH   64 (141)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999999876799999999


No 243
>PRK09440 avtA valine--pyruvate transaminase; Provisional
Probab=22.33  E-value=48  Score=12.93  Aligned_cols=48  Identities=13%  Similarity=0.087  Sum_probs=24.8

Q ss_pred             HCCCCCEEEECCCC-EEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHH
Q ss_conf             07768699873553-0788897688888888998076589999999999739978868899
Q gi|254780690|r  261 ATSRATIIITNPTH-YALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSL  320 (354)
Q Consensus       261 ~V~~A~vvitNPTH-~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~L  320 (354)
                      ..+...+-++.|.- |-+=++. |+   .      +.|..  ..-+.+++++|-++--...
T Consensus       324 ~l~~~~~~~~~P~Ggff~wv~~-p~---~------~~~~~--~l~~~l~e~gV~vvPG~~F  372 (416)
T PRK09440        324 ALPDLPCLIHKPEGAIFLWLWF-KD---L------PITTE--ELYQRLKARGVLIVPGHYF  372 (416)
T ss_pred             HCCCCCEEEECCCCCEEEEEEC-CC---C------CCCHH--HHHHHHHHCCEEEEECHHH
T ss_conf             5789814885798246999988-99---9------98999--9999999799799826431


No 244
>pfam01567 Hanta_G1 Hantavirus glycoprotein G1. The medium (M) genome segment of hantaviruses (family Bunyaviridae) encodes the two virion glycoproteins. G1 and G2, as a precursor protein in the complementary sense RNA.
Probab=21.82  E-value=49  Score=12.85  Aligned_cols=39  Identities=21%  Similarity=0.338  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCC
Q ss_conf             999999997667999999984069989999997544899
Q gi|254780690|r  201 LFIATLTVLDIGWSYHQWYSKLKMSKQEIKDEIKQSYGN  239 (354)
Q Consensus       201 ~~~~via~iD~~~qr~~~~k~lkMskqEvK~E~K~~EGd  239 (354)
                      +.+-++-++-|....+.-..+.|+--+-||+||..+-|+
T Consensus       504 ~il~~l~~~~~~~~~~~~~~kfk~il~kik~ey~kt~GS  542 (542)
T pfam01567       504 IILKILKFIAYSCSHYSQESKFKIILEKVKEEYQKTMGS  542 (542)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             999999999998603562567999999999998751389


No 245
>PRK10422 lipopolysaccharide core biosynthesis protein; Provisional
Probab=21.71  E-value=18  Score=16.29  Aligned_cols=24  Identities=25%  Similarity=0.361  Sum_probs=17.0

Q ss_pred             HHHHHCCCCCEEEEC---CCCEEEEEE
Q ss_conf             898607768699873---553078889
Q gi|254780690|r  257 KMMEATSRATIIITN---PTHYALALR  280 (354)
Q Consensus       257 ~~~~~V~~A~vvitN---PTH~AVAL~  280 (354)
                      ...+-+.+|+++|+|   |.|+|.|+.
T Consensus       255 el~ali~~a~l~I~nDSGpmHlAaAlg  281 (352)
T PRK10422        255 ELGALIDHAQLFIGVDSAPAHIAAAVN  281 (352)
T ss_pred             HHHHHHHHCCEEEECCCHHHHHHHHCC
T ss_conf             999999817875605981899999829


No 246
>PRK06988 putative formyltransferase; Provisional
Probab=21.58  E-value=49  Score=12.82  Aligned_cols=11  Identities=9%  Similarity=0.238  Sum_probs=5.5

Q ss_pred             CCCCCCCCHHH
Q ss_conf             77910169343
Q gi|254780690|r  124 KPSFKRVSLRE  134 (354)
Q Consensus       124 ~pk~~rlNPi~  134 (354)
                      -|++---+|++
T Consensus       110 LPkyRGaAPi~  120 (313)
T PRK06988        110 LPKYRGRVPTN  120 (313)
T ss_pred             CCCCCCCCHHH
T ss_conf             86767855899


No 247
>PRK05797 consensus
Probab=21.56  E-value=48  Score=12.94  Aligned_cols=62  Identities=19%  Similarity=0.150  Sum_probs=29.4

Q ss_pred             HCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEECHHHHHHHH
Q ss_conf             07768699873553078889768888888899807658999999999973997886889999999
Q gi|254780690|r  261 ATSRATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFEEPSLARSLF  325 (354)
Q Consensus       261 ~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive~~~LAR~Ly  325 (354)
                      ....-.+=|..|-..+.-|.-+-+ -+.+.=.-.|--.-+....+++.+|  |+++..-=-|.|.
T Consensus       514 ~~aG~eFNinSPKQL~~iLFe~Lg-Lp~~KKtKtG~STd~~vLe~L~~~h--pi~~~iLeyR~l~  575 (869)
T PRK05797        514 ELAGEEFNINSPKQLGKILFEKLD-LPVIKKTKTGYSTNAEVLEKLRDKH--PIIEKITEYRQLT  575 (869)
T ss_pred             HHCCCCCCCCCHHHHHHHHHHHCC-CCCCCCCCCCCCCCHHHHHHHHHCC--CCCHHHHHHHHHH
T ss_conf             862886678998999999898649-9988878899878599999765548--8519999987998


No 248
>TIGR00973 leuA_bact 2-isopropylmalate synthase; InterPro: IPR005671   The branched-chain amino acids are synthesised by a common pathway that leads from pyruvate and alpha-ketobutyrate to valine and isoleucine, and a branch that leads from the immediate precursor of valine, alpha-ketoisovalerate, to leucine . This pathway operates in archaea, bacteria, fungi and plants, but not mammals, making the enzymes suitable targets for the development of novel antibiotics and herbicides.   Isopropylmalate synthase is the enzyme responsible for the the first committed step in the leucine branch of this biosynthetic pathway, the conversion of alpha-ketoisovalerate to alpha-isopropylmalate. It is either dimeric or tetrameric, depending on the organism, with a monomer molecular mass of 60-70 kDa, a dependence on divalent metal ions for activity, and an alkaline pH optimum , , , . Like many other biosynthetic enzymes it is subject to feedback inhibition by the end product of the pathway, leucine.    This entry represents the isopropylmalate synthase most commonly found in bacteria. A related form of this enzyme is found mainly in eukaryotes and some other bacteria (IPR005668 from INTERPRO). A homologous family in archaea may represent isozymes and/or related enzymes (IPR005675 from INTERPRO). ; GO: 0003852 2-isopropylmalate synthase activity, 0009098 leucine biosynthetic process.
Probab=21.43  E-value=50  Score=12.80  Aligned_cols=11  Identities=45%  Similarity=0.733  Sum_probs=5.2

Q ss_pred             HHHCCCHHHHH
Q ss_conf             84069989999
Q gi|254780690|r  220 SKLKMSKQEIK  230 (354)
Q Consensus       220 k~lkMskqEvK  230 (354)
                      .|||||++||=
T Consensus       111 ~KLk~t~~~Vl  121 (514)
T TIGR00973       111 HKLKMTRDEVL  121 (514)
T ss_pred             HHCCCCHHHHH
T ss_conf             74168988999


No 249
>KOG3637 consensus
Probab=21.30  E-value=44  Score=13.25  Aligned_cols=44  Identities=14%  Similarity=0.137  Sum_probs=20.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCC
Q ss_conf             99999999999999766799999998406998999999754489
Q gi|254780690|r  195 VLIMILLFIATLTVLDIGWSYHQWYSKLKMSKQEIKDEIKQSYG  238 (354)
Q Consensus       195 l~~~~~~~~~via~iD~~~qr~~~~k~lkMskqEvK~E~K~~EG  238 (354)
                      +++.+++.+++++++=|..=+--|.|+-|=.+.|.++|-++.+.
T Consensus       981 Ii~svl~GLLlL~llv~~LwK~GFFKR~r~~~~~~~~~~~~~~~ 1024 (1030)
T KOG3637         981 IILSVLGGLLLLALLVLLLWKCGFFKRNRKHPKEQEEEDKSEEP 1024 (1030)
T ss_pred             EHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             54988999999999999998637222378871226411147875


No 250
>pfam03839 Sec62 Translocation protein Sec62.
Probab=21.24  E-value=50  Score=12.77  Aligned_cols=27  Identities=26%  Similarity=0.191  Sum_probs=12.9

Q ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             99766799999998406998999999754
Q gi|254780690|r  207 TVLDIGWSYHQWYSKLKMSKQEIKDEIKQ  235 (354)
Q Consensus       207 a~iD~~~qr~~~~k~lkMskqEvK~E~K~  235 (354)
                      +++|-+.-.|.|..+-.  |+|.|.+.|.
T Consensus       182 gf~eSF~Ply~~~~~~~--~~~~k~~~k~  208 (217)
T pfam03839       182 GFLDSFKPLYTWHYKGD--KSSAKKDKKS  208 (217)
T ss_pred             CCCEEECCCHHEEECCC--HHHHHHHHHH
T ss_conf             74023212201020476--5666665431


No 251
>TIGR02432 lysidine_TilS_N tRNA(Ile)-lysidine synthetase; InterPro: IPR012795   The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases .    The only examples in which the wobble position of a tRNA must discriminate between G and A of mRNA are AUA (Ile) vs. AUG (Met) and UGA (stop) vs. UGG (Trp). In all bacteria, the wobble position of the tRNA(Ile) recognizing AUA is lysidine, a lysine derivative of cytidine. This domain is found, apparently, in all bacteria in a single copy. Eukaryotic sequences appear to be organellar. The domain architecture of this protein is variable; some, including characterised proteins of Escherichia coli and Bacillus subtilis known to be tRNA(Ile)-lysidine synthetase, include a conserved 50-residue domain that many other members lack. This protein belongs to the ATP-binding PP-loop family. It appears in the literature and protein databases as TilS, YacA, and putative cell cycle protein MesJ (a misnomer).; GO: 0000166 nucleotide binding, 0005524 ATP binding, 0016879 ligase activity forming carbon-nitrogen bonds, 0008033 tRNA processing, 0005737 cytoplasm.
Probab=21.11  E-value=50  Score=12.75  Aligned_cols=17  Identities=24%  Similarity=0.569  Sum_probs=9.1

Q ss_pred             HHHHHHHHCCCCEEECH
Q ss_conf             99999997399788688
Q gi|254780690|r  302 KMRKIAYEHNIPIFEEP  318 (354)
Q Consensus       302 ~Ir~~A~~~~Vpive~~  318 (354)
                      .|.+.++++++|.+||+
T Consensus       170 ei~~y~~~~~l~~~eD~  186 (204)
T TIGR02432       170 EIEEYLKENGLPYFEDE  186 (204)
T ss_pred             HHHHHHHHCCCCEEECC
T ss_conf             99999996689656578


No 252
>pfam09659 Cas_Csm6 CRISPR-associated protein (Cas_Csm6). Clusters of short DNA repeats with nonhomologous spacers, which are found at regular intervals in the genomes of phylogenetically distinct prokaryotic species, comprise a family with recognisable features. This family is known as CRISPR (short for Clustered, Regularly Interspaced Short Palindromic Repeats). A number of protein families appear only in association with these repeats and are designated Cas (CRISPR-Associated) proteins.
Probab=21.03  E-value=51  Score=12.74  Aligned_cols=25  Identities=20%  Similarity=0.243  Sum_probs=18.3

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHCCC
Q ss_conf             7678776866587879999985787
Q gi|254780690|r    4 NDAPDNKTEAPSSKKIEDALNEGNA   28 (354)
Q Consensus         4 ~d~~~eKTE~PT~kRL~dARekGqV   28 (354)
                      +++++.++-+|+-.+++..-.|-++
T Consensus       105 ~~~~~nRc~e~~~~~~~~~l~k~~i  129 (382)
T pfam09659       105 KPGTNNRTQEVNSDNLRYLLLREAA  129 (382)
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf             7775566225338899999999999


No 253
>TIGR01957 nuoB_fam NADH-quinone oxidoreductase, B subunit; InterPro: IPR006138   Respiratory-chain NADH dehydrogenase (1.6.5.3 from EC) (also known as complex I or NADH-ubiquinone oxidoreductase) is an oligomeric enzymatic complex located in the inner mitochondrial membrane which also seems to exist in the chloroplast and in cyanobacteria (as a NADH-plastoquinone oxidoreductase).    Among the 25 to 30 polypeptide subunits of this bioenergetic enzyme complex there is one with a molecular weight of 20 kDa (in mammals) , which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 4Fe-4S iron-sulphur cluster. The 20 kDa subunit has been found to be nuclear encoded, as a precursor form with a transit peptide in mammals, and in Neurospora crassa. It is mitochondrial encoded in Paramecium (gene psbG) and chloroplast encoded in various higher plants (gene ndhK or psbG).; GO: 0008137 NADH dehydrogenase (ubiquinone) activity, 0006120 mitochondrial electron transport NADH to ubiquinone.
Probab=20.98  E-value=51  Score=12.73  Aligned_cols=32  Identities=25%  Similarity=0.394  Sum_probs=13.0

Q ss_pred             CCCEEEECCC---CEEEEEEECCCCCCCC-EEEEEC
Q ss_conf             6869987355---3078889768888888-899807
Q gi|254780690|r  264 RATIIITNPT---HYALALRYIQTENDAP-VLVAKG  295 (354)
Q Consensus       264 ~A~vvitNPT---H~AVAL~Y~~~~~~aP-~vvaKG  295 (354)
                      .|||+|+--|   =+|=+||=-=++|+-| .|++.|
T Consensus        57 QaDvMIvAGT~t~KmAP~lrrlYDQMPePKwVIsMG   92 (146)
T TIGR01957        57 QADVMIVAGTVTKKMAPVLRRLYDQMPEPKWVISMG   92 (146)
T ss_pred             CCCEEEECCCCCEEHHHHHHHHHHHCCCCCEEEECC
T ss_conf             133344548641004347766875378997798517


No 254
>cd00922 Cyt_c_Oxidase_IV Cytochrome c oxidase subunit IV. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit IV is the largest of the nuclear-encoded subunits. It binds ATP at the matrix side, leading to an allosteric inhibition of enzyme activity at high intramitochondrial ATP/ADP ratios. In mammals, subunit IV has a lung-specific isoform and a ubiquitously expressed isoform.
Probab=20.84  E-value=51  Score=12.71  Aligned_cols=12  Identities=17%  Similarity=0.047  Sum_probs=8.9

Q ss_pred             CCCCCHHHHHHH
Q ss_conf             101693430332
Q gi|254780690|r  127 FKRVSLREGIKR  138 (354)
Q Consensus       127 ~~rlNPi~GlKr  138 (354)
                      -.|.||+.|+-.
T Consensus       121 ~~~~nPitG~ss  132 (136)
T cd00922         121 DMKVNPITGYAS  132 (136)
T ss_pred             HCCCCCCCCCCC
T ss_conf             838999877445


No 255
>COG0859 RfaF ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]
Probab=20.82  E-value=40  Score=13.51  Aligned_cols=23  Identities=35%  Similarity=0.540  Sum_probs=15.1

Q ss_pred             HHHHHCCCCCEEEEC---CCCEEEEE
Q ss_conf             898607768699873---55307888
Q gi|254780690|r  257 KMMEATSRATIIITN---PTHYALAL  279 (354)
Q Consensus       257 ~~~~~V~~A~vvitN---PTH~AVAL  279 (354)
                      .+..-...||.+|+|   |+|.|-|+
T Consensus       244 e~~~li~~a~l~I~~DSg~~HlAaA~  269 (334)
T COG0859         244 ELAALIAGADLVIGNDSGPMHLAAAL  269 (334)
T ss_pred             HHHHHHHCCCEEECCCCHHHHHHHHC
T ss_conf             99999966989991488799999873


No 256
>PRK07568 aspartate aminotransferase; Provisional
Probab=20.59  E-value=52  Score=12.67  Aligned_cols=25  Identities=8%  Similarity=0.042  Sum_probs=15.7

Q ss_pred             CHHHHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             9343033201266799999999999
Q gi|254780690|r  131 SLREGIKRIYSINNLVNFMKSFVKI  155 (354)
Q Consensus       131 NPi~GlKriFS~k~lvel~KsllKv  155 (354)
                      ||-+=-.+.+|...+-+++.-.-|-
T Consensus       170 ~P~NPTG~v~s~~~~~~l~~la~~~  194 (396)
T PRK07568        170 NPGNPTGVVYTKEELRQLADIAKEH  194 (396)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             9929887540157899999999871


No 257
>KOG4403 consensus
Probab=20.53  E-value=52  Score=12.66  Aligned_cols=29  Identities=14%  Similarity=0.163  Sum_probs=11.6

Q ss_pred             HCCCHHHHHHHHHHCCCCHHHHHHHHHHH
Q ss_conf             06998999999754489989999999999
Q gi|254780690|r  222 LKMSKQEIKDEIKQSYGNPIIKNRQKSIA  250 (354)
Q Consensus       222 lkMskqEvK~E~K~~EGdP~iK~~~r~~~  250 (354)
                      .|-+|+-|++=+|+.||=-...+-...+|
T Consensus       237 nk~akehv~km~kdle~Lq~aEqsl~dlQ  265 (575)
T KOG4403         237 NKKAKEHVNKMMKDLEGLQRAEQSLEDLQ  265 (575)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             16789999999988888888998999999


No 258
>TIGR01122 ilvE_I branched-chain amino acid aminotransferase; InterPro: IPR005785   Aminotransferases share certain mechanistic features with other pyridoxal-phosphate dependent enzymes, such as the covalent binding of the pyridoxal-phosphate group to a lysine residue. On the basis of sequence similarity, these various enzymes can be grouped  into subfamilies.   One of these, called class-IV, currently consists of proteins of about 270 to 415 amino-acid residues that share a few regions of sequence similarity. Surprisingly, the best conserved region does not include the lysine residue to which the pyridoxal-phosphate group is known to be attached, in ilvE, but is located some 40 residues at the C-terminus side of the PlP-lysine.    Among the class IV aminotransferases are two phylogenetically separable groups of branched-chain amino acid aminotransferase (IlvE) (2.6.1.42 from EC). The last common ancestor of the two lineages appears also to have given rise to a family of D-amino acid aminotransferases (DAAT). This model represents the IlvE family more strongly similar to the DAAT family. ; GO: 0004084 branched-chain-amino-acid transaminase activity, 0009081 branched chain family amino acid metabolic process.
Probab=20.53  E-value=52  Score=12.66  Aligned_cols=25  Identities=20%  Similarity=0.294  Sum_probs=17.7

Q ss_pred             HHHHHHH-HCCCCEEECHHHHHHHHHH
Q ss_conf             9999999-7399788688999999972
Q gi|254780690|r  302 KMRKIAY-EHNIPIFEEPSLARSLFKQ  327 (354)
Q Consensus       302 ~Ir~~A~-~~~Vpive~~~LAR~Ly~~  327 (354)
                      .|..+|+ |+||+|.|.+ ++|.=-++
T Consensus       218 ~VitlA~ke~G~~V~E~~-I~R~eLYt  243 (302)
T TIGR01122       218 TVITLAKKELGIEVVEQR-ISRDELYT  243 (302)
T ss_pred             HHHHHHHHCCCEEEEECC-CCHHHHHH
T ss_conf             999998510862688233-57244322


No 259
>PRK05299 rpsB 30S ribosomal protein S2; Provisional
Probab=20.49  E-value=52  Score=12.65  Aligned_cols=34  Identities=29%  Similarity=0.415  Sum_probs=23.7

Q ss_pred             HHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCEEE
Q ss_conf             898607768699873553078889768888888899807658999999999973997886
Q gi|254780690|r  257 KMMEATSRATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPIFE  316 (354)
Q Consensus       257 ~~~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpive  316 (354)
                      +.|...|++ ++|+||.+                      +..|   ..+|...|||++-
T Consensus       152 ~~m~~lPd~-viv~d~~~----------------------e~~A---V~EA~kl~IPvI~  185 (255)
T PRK05299        152 KDMGGLPDA-LFVVDPNK----------------------EHIA---VKEARKLGIPVVA  185 (255)
T ss_pred             HHHCCCCCE-EEEECCCC----------------------CHHH---HHHHHHCCCCEEE
T ss_conf             324319987-99847853----------------------3799---9999975998887


No 260
>pfam03806 ABG_transport AbgT putative transporter family.
Probab=20.36  E-value=52  Score=12.63  Aligned_cols=16  Identities=25%  Similarity=0.187  Sum_probs=6.6

Q ss_pred             HHCCCCCHHHHHHHHHHH
Q ss_conf             857875133599999999
Q gi|254780690|r   24 NEGNAPISREASLFSSIL   41 (354)
Q Consensus        24 ekGqV~kS~el~~~~~ll   41 (354)
                      +-||  |=.|.......+
T Consensus         8 ~~GN--kLPhP~~LF~~l   23 (502)
T pfam03806         8 RLGN--KLPDPVTLFIIL   23 (502)
T ss_pred             HHCC--CCCCHHHHHHHH
T ss_conf             8748--798889999999


No 261
>pfam07230 Phage_T4_Gp20 Bacteriophage T4-like capsid assembly protein (Gp20). This family consists of several bacteriophage T4-like capsid assembly (or portal) proteins. The exact mechanism by which the double-stranded (ds) DNA bacteriophages incorporate the portal protein at a unique vertex of the icosahedral capsid is unknown. In phage T4, there is evidence that this vertex, constituted by 12 subunits of gp20, acts as an initiator for the assembly of the major capsid protein and the scaffolding proteins into a prolate icosahedron of precise dimensions. The regulation of portal protein gene expression is an important regulator of prohead assembly in bacteriophage T4.
Probab=20.34  E-value=52  Score=12.63  Aligned_cols=29  Identities=28%  Similarity=0.096  Sum_probs=21.3

Q ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHCCC
Q ss_conf             66799999998406998999999754489
Q gi|254780690|r  210 DIGWSYHQWYSKLKMSKQEIKDEIKQSYG  238 (354)
Q Consensus       210 D~~~qr~~~~k~lkMskqEvK~E~K~~EG  238 (354)
                      .|.=.+|-..+=|+||-+|++++.|+.+.
T Consensus       471 ky~S~~~v~kniL~~SdeEI~e~~~~i~~  499 (500)
T pfam07230       471 KYFSHEYVMKKILRMTDEEIKEEDKQIEE  499 (500)
T ss_pred             CCCCHHHHHHHHCCCCHHHHHHHHHHHHC
T ss_conf             73049999998638999999999998733


No 262
>pfam01075 Glyco_transf_9 Glycosyltransferase family 9 (heptosyltransferase). Members of this family belong to glycosyltransferase family 9. Lipopolysaccharide is a major component of the outer leaflet of the outer membrane in Gram-negative bacteria. It is composed of three domains; lipid A, Core oligosaccharide and the O-antigen. All of these enzymes transfer heptose to the lipopolysaccharide core.
Probab=20.27  E-value=19  Score=16.10  Aligned_cols=22  Identities=27%  Similarity=0.320  Sum_probs=15.6

Q ss_pred             HHHHCCCCCEEEEC---CCCEEEEE
Q ss_conf             98607768699873---55307888
Q gi|254780690|r  258 MMEATSRATIIITN---PTHYALAL  279 (354)
Q Consensus       258 ~~~~V~~A~vvitN---PTH~AVAL  279 (354)
                      ...=+.+|+++|+|   |.|+|.|+
T Consensus       179 l~ali~~a~l~I~nDSGp~HiAaA~  203 (249)
T pfam01075       179 AAALLAGADLVVGNDSGLMHLAAAL  203 (249)
T ss_pred             HHHHHHHCCEEEECCCHHHHHHHHC
T ss_conf             9999985066885798599999983


No 263
>pfam11657 Activator-TraM Transcriptional activator TraM. TraM is required for quorum dependence. It binds to and in-activates TraR which controls the replication of the tumour-inducing virulence plasmid. TraM interacts in a two-step process with DNA-TraR to form a large, stable anti-activation complex.
Probab=20.26  E-value=52  Score=12.62  Aligned_cols=17  Identities=12%  Similarity=0.321  Sum_probs=8.6

Q ss_pred             HHHHHHHCCCCCHHHHH
Q ss_conf             99999857875133599
Q gi|254780690|r   19 IEDALNEGNAPISREAS   35 (354)
Q Consensus        19 L~dARekGqV~kS~el~   35 (354)
                      +++=-.|--|+-|+|=+
T Consensus         9 I~~IA~KHGIal~rDDP   25 (144)
T pfam11657         9 IKEIAAKHGIAVGRDDP   25 (144)
T ss_pred             HHHHHHHCCCCCCCCCC
T ss_conf             99999981921489997


No 264
>PRK10558 alpha-dehydro-beta-deoxy-D-glucarate aldolase; Provisional
Probab=20.11  E-value=45  Score=13.18  Aligned_cols=64  Identities=20%  Similarity=0.187  Sum_probs=46.7

Q ss_pred             HHHHHCCCCCEEEECCCCEEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHCCCCE--E-ECHHHHHHHHH
Q ss_conf             8986077686998735530788897688888888998076589999999999739978--8-68899999997
Q gi|254780690|r  257 KMMEATSRATIIITNPTHYALALRYIQTENDAPVLVAKGQNLIAKKMRKIAYEHNIPI--F-EEPSLARSLFK  326 (354)
Q Consensus       257 ~~~~~V~~A~vvitNPTH~AVAL~Y~~~~~~aP~vvaKG~~~~A~~Ir~~A~~~~Vpi--v-e~~~LAR~Ly~  326 (354)
                      .-..+|+.=|++...|-.++..|-+ ++....|.|.     ..-.+|.+.|+++|+|.  + .++.-|+.+..
T Consensus       162 deI~av~GvD~ifiGp~DLs~slG~-~g~~~~pev~-----~ai~~v~~~~~~~gk~~G~~~~~~~~a~~~~~  228 (256)
T PRK10558        162 DAIAATEGVDGIFVGPSDLAAALGH-LGNASHPDVQ-----KAIQHIFARAKAHGKPSGILAPVEADARRYLE  228 (256)
T ss_pred             HHHHCCCCCCEEEECHHHHHHHCCC-CCCCCCHHHH-----HHHHHHHHHHHHCCCCEEEECCCHHHHHHHHH
T ss_conf             9996789988899885899986599-9999997999-----99999999999859987993699999999997


Done!